[1] "ofn"            "-oTCOADREAD-TP"
[1] "opt"       "-OPMUTSIG"
[1] "tl" ""  
[1] "dx" ""  
[1] "opt"    "MUTSIG"
[1] "dx" ""  
[1] "cfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/COADREAD-TP/19775152/COADREAD-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/COADREAD-TP/20217636/transformed.cor.cli.txt"

nPatients in clinical file=628, in cluster file=489, common to both=489
[1] "Reduce the number of clustering variables from 2225 to 2222."
[1] 2222  489
[1] "APC MUTATION ANALYSIS"
[1] 3
  APC MUTATED APC WILD-TYPE 
          403            86 
  APC MUTATED APC WILD-TYPE 
          403            86 
[1] "TP53 MUTATION ANALYSIS"
[1] 3
  TP53 MUTATED TP53 WILD-TYPE 
           323            166 
  TP53 MUTATED TP53 WILD-TYPE 
           323            166 
[1] "ARID1A MUTATION ANALYSIS"
[1] 3
  ARID1A MUTATED ARID1A WILD-TYPE 
              83              406 
  ARID1A MUTATED ARID1A WILD-TYPE 
              83              406 
[1] "RNF43 MUTATION ANALYSIS"
[1] 3
  RNF43 MUTATED RNF43 WILD-TYPE 
             47             442 
  RNF43 MUTATED RNF43 WILD-TYPE 
             47             442 
[1] "CRIPAK MUTATION ANALYSIS"
[1] 3
  CRIPAK MUTATED CRIPAK WILD-TYPE 
              29              460 
  CRIPAK MUTATED CRIPAK WILD-TYPE 
              29              460 
[1] "SOX9 MUTATION ANALYSIS"
[1] 3
  SOX9 MUTATED SOX9 WILD-TYPE 
            41            448 
  SOX9 MUTATED SOX9 WILD-TYPE 
            41            448 
[1] "FAM123B MUTATION ANALYSIS"
[1] 3
  FAM123B MUTATED FAM123B WILD-TYPE 
               60               429 
  FAM123B MUTATED FAM123B WILD-TYPE 
               60               429 
[1] "ZFP36L2 MUTATION ANALYSIS"
[1] 3
  ZFP36L2 MUTATED ZFP36L2 WILD-TYPE 
               17               472 
  ZFP36L2 MUTATED ZFP36L2 WILD-TYPE 
               17               472 
[1] "B2M MUTATION ANALYSIS"
[1] 3
  B2M MUTATED B2M WILD-TYPE 
           17           472 
  B2M MUTATED B2M WILD-TYPE 
           17           472 
[1] "TXNDC2 MUTATION ANALYSIS"
[1] 3
  TXNDC2 MUTATED TXNDC2 WILD-TYPE 
              24              465 
  TXNDC2 MUTATED TXNDC2 WILD-TYPE 
              24              465 
[1] "ACVR1B MUTATION ANALYSIS"
[1] 3
  ACVR1B MUTATED ACVR1B WILD-TYPE 
              28              461 
  ACVR1B MUTATED ACVR1B WILD-TYPE 
              28              461 
[1] "CDH1 MUTATION ANALYSIS"
[1] 3
  CDH1 MUTATED CDH1 WILD-TYPE 
            86            403 
  CDH1 MUTATED CDH1 WILD-TYPE 
            86            403 
[1] "MLH1 MUTATION ANALYSIS"
[1] 3
  MLH1 MUTATED MLH1 WILD-TYPE 
            59            430 
  MLH1 MUTATED MLH1 WILD-TYPE 
            59            430 
[1] "BCOR MUTATION ANALYSIS"
[1] 3
  BCOR MUTATED BCOR WILD-TYPE 
            30            459 
  BCOR MUTATED BCOR WILD-TYPE 
            30            459 
[1] "SMAD2 MUTATION ANALYSIS"
[1] 3
  SMAD2 MUTATED SMAD2 WILD-TYPE 
             22             467 
  SMAD2 MUTATED SMAD2 WILD-TYPE 
             22             467 
[1] "WNT1 MUTATION ANALYSIS"
[1] 3
  WNT1 MUTATED WNT1 WILD-TYPE 
             7            482 
  WNT1 MUTATED WNT1 WILD-TYPE 
             7            482 
[1] "FMN2 MUTATION ANALYSIS"
[1] 3
  FMN2 MUTATED FMN2 WILD-TYPE 
            63            426 
  FMN2 MUTATED FMN2 WILD-TYPE 
            63            426 
[1] "GGT1 MUTATION ANALYSIS"
[1] 3
  GGT1 MUTATED GGT1 WILD-TYPE 
            10            479 
  GGT1 MUTATED GGT1 WILD-TYPE 
            10            479 
[1] "STARD3NL MUTATION ANALYSIS"
[1] 3
  STARD3NL MUTATED STARD3NL WILD-TYPE 
                15                474 
  STARD3NL MUTATED STARD3NL WILD-TYPE 
                15                474 
[1] "SELPLG MUTATION ANALYSIS"
[1] 3
  SELPLG MUTATED SELPLG WILD-TYPE 
              19              470 
  SELPLG MUTATED SELPLG WILD-TYPE 
              19              470 
[1] "OR4D10 MUTATION ANALYSIS"
[1] 3
  OR4D10 MUTATED OR4D10 WILD-TYPE 
              16              473 
  OR4D10 MUTATED OR4D10 WILD-TYPE 
              16              473 
[1] "NF2 MUTATION ANALYSIS"
[1] 3
  NF2 MUTATED NF2 WILD-TYPE 
           67           422 
  NF2 MUTATED NF2 WILD-TYPE 
           67           422 
[1] "MAPK6 MUTATION ANALYSIS"
[1] 3
  MAPK6 MUTATED MAPK6 WILD-TYPE 
             19             470 
  MAPK6 MUTATED MAPK6 WILD-TYPE 
             19             470 
[1] "RHOA MUTATION ANALYSIS"
[1] 3
  RHOA MUTATED RHOA WILD-TYPE 
            13            476 
  RHOA MUTATED RHOA WILD-TYPE 
            13            476 
[1] "FAM9A MUTATION ANALYSIS"
[1] 3
  FAM9A MUTATED FAM9A WILD-TYPE 
             12             477 
  FAM9A MUTATED FAM9A WILD-TYPE 
             12             477 
[1] "EGR1 MUTATION ANALYSIS"
[1] 3
  EGR1 MUTATED EGR1 WILD-TYPE 
            12            477 
  EGR1 MUTATED EGR1 WILD-TYPE 
            12            477 
[1] "PRKDC MUTATION ANALYSIS"
[1] 3
  PRKDC MUTATED PRKDC WILD-TYPE 
             70             419 
  PRKDC MUTATED PRKDC WILD-TYPE 
             70             419 
[1] "RPTN MUTATION ANALYSIS"
[1] 3
  RPTN MUTATED RPTN WILD-TYPE 
            18            471 
  RPTN MUTATED RPTN WILD-TYPE 
            18            471 
[1] "THOC7 MUTATION ANALYSIS"
[1] 3
  THOC7 MUTATED THOC7 WILD-TYPE 
             11             478 
  THOC7 MUTATED THOC7 WILD-TYPE 
             11             478 
[1] "NF1 MUTATION ANALYSIS"
[1] 3
  NF1 MUTATED NF1 WILD-TYPE 
          107           382 
  NF1 MUTATED NF1 WILD-TYPE 
          107           382 
[1] "FBXW7 MUTATION ANALYSIS"
[1] 3
  FBXW7 MUTATED FBXW7 WILD-TYPE 
            131             358 
  FBXW7 MUTATED FBXW7 WILD-TYPE 
            131             358 
[1] "CHUK MUTATION ANALYSIS"
[1] 3
  CHUK MUTATED CHUK WILD-TYPE 
            24            465 
  CHUK MUTATED CHUK WILD-TYPE 
            24            465 
[1] "ATXN3L MUTATION ANALYSIS"
[1] 3
  ATXN3L MUTATED ATXN3L WILD-TYPE 
              20              469 
  ATXN3L MUTATED ATXN3L WILD-TYPE 
              20              469 
[1] "MGA MUTATION ANALYSIS"
[1] 3
  MGA MUTATED MGA WILD-TYPE 
           43           446 
  MGA MUTATED MGA WILD-TYPE 
           43           446 
[1] "TPRKB MUTATION ANALYSIS"
[1] 3
  TPRKB MUTATED TPRKB WILD-TYPE 
             10             479 
  TPRKB MUTATED TPRKB WILD-TYPE 
             10             479 
[1] "MVK MUTATION ANALYSIS"
[1] 3
  MVK MUTATED MVK WILD-TYPE 
           14           475 
  MVK MUTATED MVK WILD-TYPE 
           14           475 
[1] "ZBTB20 MUTATION ANALYSIS"
[1] 3
  ZBTB20 MUTATED ZBTB20 WILD-TYPE 
              22              467 
  ZBTB20 MUTATED ZBTB20 WILD-TYPE 
              22              467 
[1] "BCL9 MUTATION ANALYSIS"
[1] 3
  BCL9 MUTATED BCL9 WILD-TYPE 
            27            462 
  BCL9 MUTATED BCL9 WILD-TYPE 
            27            462 
[1] "ERBB2 MUTATION ANALYSIS"
[1] 3
  ERBB2 MUTATED ERBB2 WILD-TYPE 
             36             453 
  ERBB2 MUTATED ERBB2 WILD-TYPE 
             36             453 
[1] "P2RY13 MUTATION ANALYSIS"
[1] 3
  P2RY13 MUTATED P2RY13 WILD-TYPE 
              15              474 
  P2RY13 MUTATED P2RY13 WILD-TYPE 
              15              474 
[1] "ST3GAL6 MUTATION ANALYSIS"
[1] 3
  ST3GAL6 MUTATED ST3GAL6 WILD-TYPE 
               12               477 
  ST3GAL6 MUTATED ST3GAL6 WILD-TYPE 
               12               477 
[1] "IQCD MUTATION ANALYSIS"
[1] 3
  IQCD MUTATED IQCD WILD-TYPE 
            13            476 
  IQCD MUTATED IQCD WILD-TYPE 
            13            476 
[1] "PLEKHF2 MUTATION ANALYSIS"
[1] 3
  PLEKHF2 MUTATED PLEKHF2 WILD-TYPE 
               12               477 
  PLEKHF2 MUTATED PLEKHF2 WILD-TYPE 
               12               477 
[1] "NR1H3 MUTATION ANALYSIS"
[1] 3
  NR1H3 MUTATED NR1H3 WILD-TYPE 
             15             474 
  NR1H3 MUTATED NR1H3 WILD-TYPE 
             15             474 
[1] "ALPK2 MUTATION ANALYSIS"
[1] 3
  ALPK2 MUTATED ALPK2 WILD-TYPE 
             46             443 
  ALPK2 MUTATED ALPK2 WILD-TYPE 
             46             443 
[1] "ASXL1 MUTATION ANALYSIS"
[1] 3
  ASXL1 MUTATED ASXL1 WILD-TYPE 
             46             443 
  ASXL1 MUTATED ASXL1 WILD-TYPE 
             46             443 
[1] "ALG12 MUTATION ANALYSIS"
[1] 3
  ALG12 MUTATED ALG12 WILD-TYPE 
              7             482 
  ALG12 MUTATED ALG12 WILD-TYPE 
              7             482 
[1] "PTCH1 MUTATION ANALYSIS"
[1] 3
  PTCH1 MUTATED PTCH1 WILD-TYPE 
            103             386 
  PTCH1 MUTATED PTCH1 WILD-TYPE 
            103             386 
[1] "GRB2 MUTATION ANALYSIS"
[1] 3
  GRB2 MUTATED GRB2 WILD-TYPE 
            11            478 
  GRB2 MUTATED GRB2 WILD-TYPE 
            11            478 
[1] "NLRC4 MUTATION ANALYSIS"
[1] 3
  NLRC4 MUTATED NLRC4 WILD-TYPE 
             26             463 
  NLRC4 MUTATED NLRC4 WILD-TYPE 
             26             463 
[1] "PLAGL2 MUTATION ANALYSIS"
[1] 3
  PLAGL2 MUTATED PLAGL2 WILD-TYPE 
               6              483 
  PLAGL2 MUTATED PLAGL2 WILD-TYPE 
               6              483 
[1] "C11ORF30 MUTATION ANALYSIS"
[1] 3
  C11ORF30 MUTATED C11ORF30 WILD-TYPE 
                23                466 
  C11ORF30 MUTATED C11ORF30 WILD-TYPE 
                23                466 
[1] "DIP2B MUTATION ANALYSIS"
[1] 3
  DIP2B MUTATED DIP2B WILD-TYPE 
             30             459 
  DIP2B MUTATED DIP2B WILD-TYPE 
             30             459 
[1] "PRRG1 MUTATION ANALYSIS"
[1] 3
  PRRG1 MUTATED PRRG1 WILD-TYPE 
             14             475 
  PRRG1 MUTATED PRRG1 WILD-TYPE 
             14             475 
[1] "PIK3R1 MUTATION ANALYSIS"
[1] 3
  PIK3R1 MUTATED PIK3R1 WILD-TYPE 
              51              438 
  PIK3R1 MUTATED PIK3R1 WILD-TYPE 
              51              438 
[1] "PCBP1 MUTATION ANALYSIS"
[1] 3
  PCBP1 MUTATED PCBP1 WILD-TYPE 
             15             474 
  PCBP1 MUTATED PCBP1 WILD-TYPE 
             15             474 
[1] "IFT57 MUTATION ANALYSIS"
[1] 3
  IFT57 MUTATED IFT57 WILD-TYPE 
             13             476 
  IFT57 MUTATED IFT57 WILD-TYPE 
             13             476 
[1] "RSPH3 MUTATION ANALYSIS"
[1] 3
  RSPH3 MUTATED RSPH3 WILD-TYPE 
             11             478 
  RSPH3 MUTATED RSPH3 WILD-TYPE 
             11             478 
[1] "RLIM MUTATION ANALYSIS"
[1] 3
  RLIM MUTATED RLIM WILD-TYPE 
            18            471 
  RLIM MUTATED RLIM WILD-TYPE 
            18            471 
[1] "ROS1 MUTATION ANALYSIS"
[1] 3
  ROS1 MUTATED ROS1 WILD-TYPE 
            54            435 
  ROS1 MUTATED ROS1 WILD-TYPE 
            54            435 
[1] "MPHOSPH10 MUTATION ANALYSIS"
[1] 3
  MPHOSPH10 MUTATED MPHOSPH10 WILD-TYPE 
                 18                 471 
  MPHOSPH10 MUTATED MPHOSPH10 WILD-TYPE 
                 18                 471 
[1] "VCX2 MUTATION ANALYSIS"
[1] 3
  VCX2 MUTATED VCX2 WILD-TYPE 
            12            477 
  VCX2 MUTATED VCX2 WILD-TYPE 
            12            477 
[1] "C2ORF29 MUTATION ANALYSIS"
[1] 3
  C2ORF29 MUTATED C2ORF29 WILD-TYPE 
               19               470 
  C2ORF29 MUTATED C2ORF29 WILD-TYPE 
               19               470 
[1] "DDX26B MUTATION ANALYSIS"
[1] 3
  DDX26B MUTATED DDX26B WILD-TYPE 
              16              473 
  DDX26B MUTATED DDX26B WILD-TYPE 
              16              473 
[1] "RBPJ MUTATION ANALYSIS"
[1] 3
  RBPJ MUTATED RBPJ WILD-TYPE 
            18            471 
  RBPJ MUTATED RBPJ WILD-TYPE 
            18            471 
[1] "SMAD4 MUTATION ANALYSIS"
[1] 3
  SMAD4 MUTATED SMAD4 WILD-TYPE 
            144             345 
  SMAD4 MUTATED SMAD4 WILD-TYPE 
            144             345 
[1] "SLC26A8 MUTATION ANALYSIS"
[1] 3
  SLC26A8 MUTATED SLC26A8 WILD-TYPE 
               19               470 
  SLC26A8 MUTATED SLC26A8 WILD-TYPE 
               19               470 
[1] "RBBP7 MUTATION ANALYSIS"
[1] 3
  RBBP7 MUTATED RBBP7 WILD-TYPE 
             17             472 
  RBBP7 MUTATED RBBP7 WILD-TYPE 
             17             472 
[1] "RB1 MUTATION ANALYSIS"
[1] 3
  RB1 MUTATED RB1 WILD-TYPE 
          102           387 
  RB1 MUTATED RB1 WILD-TYPE 
          102           387 
[1] "L1TD1 MUTATION ANALYSIS"
[1] 3
  L1TD1 MUTATED L1TD1 WILD-TYPE 
             20             469 
  L1TD1 MUTATED L1TD1 WILD-TYPE 
             20             469 
[1] "TOP2B MUTATION ANALYSIS"
[1] 3
  TOP2B MUTATED TOP2B WILD-TYPE 
             25             464 
  TOP2B MUTATED TOP2B WILD-TYPE 
             25             464 
[1] "DCLK2 MUTATION ANALYSIS"
[1] 3
  DCLK2 MUTATED DCLK2 WILD-TYPE 
             16             473 
  DCLK2 MUTATED DCLK2 WILD-TYPE 
             16             473 
[1] "FKBP9 MUTATION ANALYSIS"
[1] 3
  FKBP9 MUTATED FKBP9 WILD-TYPE 
             19             470 
  FKBP9 MUTATED FKBP9 WILD-TYPE 
             19             470 
[1] "PTEN MUTATION ANALYSIS"
[1] 3
  PTEN MUTATED PTEN WILD-TYPE 
           186            303 
  PTEN MUTATED PTEN WILD-TYPE 
           186            303 
[1] "C14ORF184 MUTATION ANALYSIS"
[1] 3
  C14ORF184 MUTATED C14ORF184 WILD-TYPE 
                  7                 482 
  C14ORF184 MUTATED C14ORF184 WILD-TYPE 
                  7                 482 
[1] "HLA-A MUTATION ANALYSIS"
[1] 3
  HLA-A MUTATED HLA-A WILD-TYPE 
             19             470 
  HLA-A MUTATED HLA-A WILD-TYPE 
             19             470 
[1] "BMPR2 MUTATION ANALYSIS"
[1] 3
  BMPR2 MUTATED BMPR2 WILD-TYPE 
             36             453 
  BMPR2 MUTATED BMPR2 WILD-TYPE 
             36             453 
[1] "FYN MUTATION ANALYSIS"
[1] 3
  FYN MUTATED FYN WILD-TYPE 
           17           472 
  FYN MUTATED FYN WILD-TYPE 
           17           472 
[1] "ALDH1A3 MUTATION ANALYSIS"
[1] 3
  ALDH1A3 MUTATED ALDH1A3 WILD-TYPE 
               19               470 
  ALDH1A3 MUTATED ALDH1A3 WILD-TYPE 
               19               470 
[1] "LARP4B MUTATION ANALYSIS"
[1] 3
  LARP4B MUTATED LARP4B WILD-TYPE 
              31              458 
  LARP4B MUTATED LARP4B WILD-TYPE 
              31              458 
[1] "ZDHHC7 MUTATION ANALYSIS"
[1] 3
  ZDHHC7 MUTATED ZDHHC7 WILD-TYPE 
              12              477 
  ZDHHC7 MUTATED ZDHHC7 WILD-TYPE 
              12              477 
[1] "GPATCH8 MUTATION ANALYSIS"
[1] 3
  GPATCH8 MUTATED GPATCH8 WILD-TYPE 
               15               474 
  GPATCH8 MUTATED GPATCH8 WILD-TYPE 
               15               474 
[1] "BCORL1 MUTATION ANALYSIS"
[1] 3
  BCORL1 MUTATED BCORL1 WILD-TYPE 
              27              462 
  BCORL1 MUTATED BCORL1 WILD-TYPE 
              27              462 
[1] "SETD2 MUTATION ANALYSIS"
[1] 3
  SETD2 MUTATED SETD2 WILD-TYPE 
             46             443 
  SETD2 MUTATED SETD2 WILD-TYPE 
             46             443 
[1] "MAP4K3 MUTATION ANALYSIS"
[1] 3
  MAP4K3 MUTATED MAP4K3 WILD-TYPE 
              21              468 
  MAP4K3 MUTATED MAP4K3 WILD-TYPE 
              21              468 
[1] "SLC12A6 MUTATION ANALYSIS"
[1] 3
  SLC12A6 MUTATED SLC12A6 WILD-TYPE 
               26               463 
  SLC12A6 MUTATED SLC12A6 WILD-TYPE 
               26               463 
[1] "CDK12 MUTATION ANALYSIS"
[1] 3
  CDK12 MUTATED CDK12 WILD-TYPE 
             33             456 
  CDK12 MUTATED CDK12 WILD-TYPE 
             33             456 
[1] "NEXN MUTATION ANALYSIS"
[1] 3
  NEXN MUTATED NEXN WILD-TYPE 
            20            469 
  NEXN MUTATED NEXN WILD-TYPE 
            20            469 
[1] "GMPS MUTATION ANALYSIS"
[1] 3
  GMPS MUTATED GMPS WILD-TYPE 
            17            472 
  GMPS MUTATED GMPS WILD-TYPE 
            17            472 
[1] "PTGDR MUTATION ANALYSIS"
[1] 3
  PTGDR MUTATED PTGDR WILD-TYPE 
              9             480 
  PTGDR MUTATED PTGDR WILD-TYPE 
              9             480 
[1] "PRPS1 MUTATION ANALYSIS"
[1] 3
  PRPS1 MUTATED PRPS1 WILD-TYPE 
              9             480 
  PRPS1 MUTATED PRPS1 WILD-TYPE 
              9             480 
[1] "BIRC3 MUTATION ANALYSIS"
[1] 3
  BIRC3 MUTATED BIRC3 WILD-TYPE 
             15             474 
  BIRC3 MUTATED BIRC3 WILD-TYPE 
             15             474 
[1] "IDH1 MUTATION ANALYSIS"
[1] 3
  IDH1 MUTATED IDH1 WILD-TYPE 
            21            468 
  IDH1 MUTATED IDH1 WILD-TYPE 
            21            468 
[1] "ZNF486 MUTATION ANALYSIS"
[1] 3
  ZNF486 MUTATED ZNF486 WILD-TYPE 
              13              476 
  ZNF486 MUTATED ZNF486 WILD-TYPE 
              13              476 
[1] "ATM MUTATION ANALYSIS"
[1] 3
  ATM MUTATED ATM WILD-TYPE 
          156           333 
  ATM MUTATED ATM WILD-TYPE 
          156           333 
[1] "HIST1H1T MUTATION ANALYSIS"
[1] 3
  HIST1H1T MUTATED HIST1H1T WILD-TYPE 
                10                479 
  HIST1H1T MUTATED HIST1H1T WILD-TYPE 
                10                479 
[1] "CREBBP MUTATION ANALYSIS"
[1] 3
  CREBBP MUTATED CREBBP WILD-TYPE 
              70              419 
  CREBBP MUTATED CREBBP WILD-TYPE 
              70              419 
[1] "GMNN MUTATION ANALYSIS"
[1] 3
  GMNN MUTATED GMNN WILD-TYPE 
             5            484 
  GMNN MUTATED GMNN WILD-TYPE 
             5            484 
[1] "CTNNB1 MUTATION ANALYSIS"
[1] 3
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
              93              396 
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
              93              396 
[1] "KDM6A MUTATION ANALYSIS"
[1] 3
  KDM6A MUTATED KDM6A WILD-TYPE 
             28             461 
  KDM6A MUTATED KDM6A WILD-TYPE 
             28             461 
[1] "CLSPN MUTATION ANALYSIS"
[1] 3
  CLSPN MUTATED CLSPN WILD-TYPE 
             34             455 
  CLSPN MUTATED CLSPN WILD-TYPE 
             34             455 
[1] "FRMPD4 MUTATION ANALYSIS"
[1] 3
  FRMPD4 MUTATED FRMPD4 WILD-TYPE 
              36              453 
  FRMPD4 MUTATED FRMPD4 WILD-TYPE 
              36              453 
[1] "SAPS2 MUTATION ANALYSIS"
[1] 3
  SAPS2 MUTATED SAPS2 WILD-TYPE 
             13             476 
  SAPS2 MUTATED SAPS2 WILD-TYPE 
             13             476 
[1] "MYST4 MUTATION ANALYSIS"
[1] 3
  MYST4 MUTATED MYST4 WILD-TYPE 
             30             459 
  MYST4 MUTATED MYST4 WILD-TYPE 
             30             459 
[1] "PRPH2 MUTATION ANALYSIS"
[1] 3
  PRPH2 MUTATED PRPH2 WILD-TYPE 
             13             476 
  PRPH2 MUTATED PRPH2 WILD-TYPE 
             13             476 
[1] "RBMX MUTATION ANALYSIS"
[1] 3
  RBMX MUTATED RBMX WILD-TYPE 
            20            469 
  RBMX MUTATED RBMX WILD-TYPE 
            20            469 
[1] "LDHA MUTATION ANALYSIS"
[1] 3
  LDHA MUTATED LDHA WILD-TYPE 
            14            475 
  LDHA MUTATED LDHA WILD-TYPE 
            14            475 
[1] "GFI1 MUTATION ANALYSIS"
[1] 3
  GFI1 MUTATED GFI1 WILD-TYPE 
            11            478 
  GFI1 MUTATED GFI1 WILD-TYPE 
            11            478 
[1] "SLC9A10 MUTATION ANALYSIS"
[1] 3
  SLC9A10 MUTATED SLC9A10 WILD-TYPE 
               23               466 
  SLC9A10 MUTATED SLC9A10 WILD-TYPE 
               23               466 
[1] "OXSM MUTATION ANALYSIS"
[1] 3
  OXSM MUTATED OXSM WILD-TYPE 
            14            475 
  OXSM MUTATED OXSM WILD-TYPE 
            14            475 
[1] "NTAN1 MUTATION ANALYSIS"
[1] 3
  NTAN1 MUTATED NTAN1 WILD-TYPE 
             10             479 
  NTAN1 MUTATED NTAN1 WILD-TYPE 
             10             479 
[1] "ICAM5 MUTATION ANALYSIS"
[1] 3
  ICAM5 MUTATED ICAM5 WILD-TYPE 
             15             474 
  ICAM5 MUTATED ICAM5 WILD-TYPE 
             15             474 
[1] "KCTD3 MUTATION ANALYSIS"
[1] 3
  KCTD3 MUTATED KCTD3 WILD-TYPE 
             19             470 
  KCTD3 MUTATED KCTD3 WILD-TYPE 
             19             470 
[1] "RBM44 MUTATION ANALYSIS"
[1] 3
  RBM44 MUTATED RBM44 WILD-TYPE 
             15             474 
  RBM44 MUTATED RBM44 WILD-TYPE 
             15             474 
[1] "KIAA1586 MUTATION ANALYSIS"
[1] 3
  KIAA1586 MUTATED KIAA1586 WILD-TYPE 
                13                476 
  KIAA1586 MUTATED KIAA1586 WILD-TYPE 
                13                476 
[1] "CDX2 MUTATION ANALYSIS"
[1] 3
  CDX2 MUTATED CDX2 WILD-TYPE 
             6            483 
  CDX2 MUTATED CDX2 WILD-TYPE 
             6            483 
[1] "EXD2 MUTATION ANALYSIS"
[1] 3
  EXD2 MUTATED EXD2 WILD-TYPE 
            13            476 
  EXD2 MUTATED EXD2 WILD-TYPE 
            13            476 
[1] "CLEC4F MUTATION ANALYSIS"
[1] 3
  CLEC4F MUTATED CLEC4F WILD-TYPE 
              20              469 
  CLEC4F MUTATED CLEC4F WILD-TYPE 
              20              469 
[1] "GPR174 MUTATION ANALYSIS"
[1] 3
  GPR174 MUTATED GPR174 WILD-TYPE 
              10              479 
  GPR174 MUTATED GPR174 WILD-TYPE 
              10              479 
[1] "NAA25 MUTATION ANALYSIS"
[1] 3
  NAA25 MUTATED NAA25 WILD-TYPE 
             18             471 
  NAA25 MUTATED NAA25 WILD-TYPE 
             18             471 
[1] "FIGNL1 MUTATION ANALYSIS"
[1] 3
  FIGNL1 MUTATED FIGNL1 WILD-TYPE 
              19              470 
  FIGNL1 MUTATED FIGNL1 WILD-TYPE 
              19              470 
[1] "HMG20A MUTATION ANALYSIS"
[1] 3
  HMG20A MUTATED HMG20A WILD-TYPE 
              15              474 
  HMG20A MUTATED HMG20A WILD-TYPE 
              15              474 
[1] "SHROOM4 MUTATION ANALYSIS"
[1] 3
  SHROOM4 MUTATED SHROOM4 WILD-TYPE 
               28               461 
  SHROOM4 MUTATED SHROOM4 WILD-TYPE 
               28               461 
[1] "CASP8 MUTATION ANALYSIS"
[1] 3
  CASP8 MUTATED CASP8 WILD-TYPE 
             18             471 
  CASP8 MUTATED CASP8 WILD-TYPE 
             18             471 
[1] "HPS3 MUTATION ANALYSIS"
[1] 3
  HPS3 MUTATED HPS3 WILD-TYPE 
            23            466 
  HPS3 MUTATED HPS3 WILD-TYPE 
            23            466 
[1] "GLI1 MUTATION ANALYSIS"
[1] 3
  GLI1 MUTATED GLI1 WILD-TYPE 
            21            468 
  GLI1 MUTATED GLI1 WILD-TYPE 
            21            468 
[1] "PDCD5 MUTATION ANALYSIS"
[1] 3
  PDCD5 MUTATED PDCD5 WILD-TYPE 
             11             478 
  PDCD5 MUTATED PDCD5 WILD-TYPE 
             11             478 
[1] "BCL9L MUTATION ANALYSIS"
[1] 3
  BCL9L MUTATED BCL9L WILD-TYPE 
             25             464 
  BCL9L MUTATED BCL9L WILD-TYPE 
             25             464 
[1] "TPM4 MUTATION ANALYSIS"
[1] 3
  TPM4 MUTATED TPM4 WILD-TYPE 
             9            480 
  TPM4 MUTATED TPM4 WILD-TYPE 
             9            480 
[1] "CYLD MUTATION ANALYSIS"
[1] 3
  CYLD MUTATED CYLD WILD-TYPE 
            27            462 
  CYLD MUTATED CYLD WILD-TYPE 
            27            462 
[1] "AMOT MUTATION ANALYSIS"
[1] 3
  AMOT MUTATED AMOT WILD-TYPE 
            16            473 
  AMOT MUTATED AMOT WILD-TYPE 
            16            473 
[1] "GNPAT MUTATION ANALYSIS"
[1] 3
  GNPAT MUTATED GNPAT WILD-TYPE 
             19             470 
  GNPAT MUTATED GNPAT WILD-TYPE 
             19             470 
[1] "PRKAA2 MUTATION ANALYSIS"
[1] 3
  PRKAA2 MUTATED PRKAA2 WILD-TYPE 
              16              473 
  PRKAA2 MUTATED PRKAA2 WILD-TYPE 
              16              473 
[1] "TMEM126A MUTATION ANALYSIS"
[1] 3
  TMEM126A MUTATED TMEM126A WILD-TYPE 
                 7                482 
  TMEM126A MUTATED TMEM126A WILD-TYPE 
                 7                482 
[1] "OSBPL11 MUTATION ANALYSIS"
[1] 3
  OSBPL11 MUTATED OSBPL11 WILD-TYPE 
               19               470 
  OSBPL11 MUTATED OSBPL11 WILD-TYPE 
               19               470 
[1] "MLLT6 MUTATION ANALYSIS"
[1] 3
  MLLT6 MUTATED MLLT6 WILD-TYPE 
             17             472 
  MLLT6 MUTATED MLLT6 WILD-TYPE 
             17             472 
[1] "USP24 MUTATION ANALYSIS"
[1] 3
  USP24 MUTATED USP24 WILD-TYPE 
             34             455 
  USP24 MUTATED USP24 WILD-TYPE 
             34             455 
[1] "ARFGEF1 MUTATION ANALYSIS"
[1] 3
  ARFGEF1 MUTATED ARFGEF1 WILD-TYPE 
               37               452 
  ARFGEF1 MUTATED ARFGEF1 WILD-TYPE 
               37               452 
[1] "OR5V1 MUTATION ANALYSIS"
[1] 3
  OR5V1 MUTATED OR5V1 WILD-TYPE 
             18             471 
  OR5V1 MUTATED OR5V1 WILD-TYPE 
             18             471 
[1] "PRB4 MUTATION ANALYSIS"
[1] 3
  PRB4 MUTATED PRB4 WILD-TYPE 
            12            477 
  PRB4 MUTATED PRB4 WILD-TYPE 
            12            477 
[1] "TRIP11 MUTATION ANALYSIS"
[1] 3
  TRIP11 MUTATED TRIP11 WILD-TYPE 
              26              463 
  TRIP11 MUTATED TRIP11 WILD-TYPE 
              26              463 
[1] "SLK MUTATION ANALYSIS"
[1] 3
  SLK MUTATED SLK WILD-TYPE 
           25           464 
  SLK MUTATED SLK WILD-TYPE 
           25           464 
[1] "PON3 MUTATION ANALYSIS"
[1] 3
  PON3 MUTATED PON3 WILD-TYPE 
            14            475 
  PON3 MUTATED PON3 WILD-TYPE 
            14            475 
[1] "SLAMF7 MUTATION ANALYSIS"
[1] 3
  SLAMF7 MUTATED SLAMF7 WILD-TYPE 
              11              478 
  SLAMF7 MUTATED SLAMF7 WILD-TYPE 
              11              478 
[1] "ATG5 MUTATION ANALYSIS"
[1] 3
  ATG5 MUTATED ATG5 WILD-TYPE 
             9            480 
  ATG5 MUTATED ATG5 WILD-TYPE 
             9            480 
[1] "SCAI MUTATION ANALYSIS"
[1] 3
  SCAI MUTATED SCAI WILD-TYPE 
            15            474 
  SCAI MUTATED SCAI WILD-TYPE 
            15            474 
[1] "TAF7L MUTATION ANALYSIS"
[1] 3
  TAF7L MUTATED TAF7L WILD-TYPE 
             13             476 
  TAF7L MUTATED TAF7L WILD-TYPE 
             13             476 
[1] "ECT2 MUTATION ANALYSIS"
[1] 3
  ECT2 MUTATED ECT2 WILD-TYPE 
            19            470 
  ECT2 MUTATED ECT2 WILD-TYPE 
            19            470 
[1] "DUSP1 MUTATION ANALYSIS"
[1] 3
  DUSP1 MUTATED DUSP1 WILD-TYPE 
              7             482 
  DUSP1 MUTATED DUSP1 WILD-TYPE 
              7             482 
[1] "ZFX MUTATION ANALYSIS"
[1] 3
  ZFX MUTATED ZFX WILD-TYPE 
           14           475 
  ZFX MUTATED ZFX WILD-TYPE 
           14           475 
[1] "ATP11B MUTATION ANALYSIS"
[1] 3
  ATP11B MUTATED ATP11B WILD-TYPE 
              19              470 
  ATP11B MUTATED ATP11B WILD-TYPE 
              19              470 
[1] "NEFH MUTATION ANALYSIS"
[1] 3
  NEFH MUTATED NEFH WILD-TYPE 
            14            475 
  NEFH MUTATED NEFH WILD-TYPE 
            14            475 
[1] "ECM2 MUTATION ANALYSIS"
[1] 3
  ECM2 MUTATED ECM2 WILD-TYPE 
            20            469 
  ECM2 MUTATED ECM2 WILD-TYPE 
            20            469 
[1] "CHD3 MUTATION ANALYSIS"
[1] 3
  CHD3 MUTATED CHD3 WILD-TYPE 
            25            464 
  CHD3 MUTATED CHD3 WILD-TYPE 
            25            464 
[1] "KLK10 MUTATION ANALYSIS"
[1] 3
  KLK10 MUTATED KLK10 WILD-TYPE 
              8             481 
  KLK10 MUTATED KLK10 WILD-TYPE 
              8             481 
[1] "DST MUTATION ANALYSIS"
[1] 3
  DST MUTATED DST WILD-TYPE 
           77           412 
  DST MUTATED DST WILD-TYPE 
           77           412 
[1] "NEUROD1 MUTATION ANALYSIS"
[1] 3
  NEUROD1 MUTATED NEUROD1 WILD-TYPE 
               10               479 
  NEUROD1 MUTATED NEUROD1 WILD-TYPE 
               10               479 
[1] "KIAA1804 MUTATION ANALYSIS"
[1] 3
  KIAA1804 MUTATED KIAA1804 WILD-TYPE 
                26                463 
  KIAA1804 MUTATED KIAA1804 WILD-TYPE 
                26                463 
[1] "PIK3IP1 MUTATION ANALYSIS"
[1] 3
  PIK3IP1 MUTATED PIK3IP1 WILD-TYPE 
                9               480 
  PIK3IP1 MUTATED PIK3IP1 WILD-TYPE 
                9               480 
[1] "C10ORF79 MUTATION ANALYSIS"
[1] 3
  C10ORF79 MUTATED C10ORF79 WILD-TYPE 
                32                457 
  C10ORF79 MUTATED C10ORF79 WILD-TYPE 
                32                457 
[1] "KRT2 MUTATION ANALYSIS"
[1] 3
  KRT2 MUTATED KRT2 WILD-TYPE 
            15            474 
  KRT2 MUTATED KRT2 WILD-TYPE 
            15            474 
[1] "HTR2A MUTATION ANALYSIS"
[1] 3
  HTR2A MUTATED HTR2A WILD-TYPE 
             23             466 
  HTR2A MUTATED HTR2A WILD-TYPE 
             23             466 
[1] "PTK2 MUTATION ANALYSIS"
[1] 3
  PTK2 MUTATED PTK2 WILD-TYPE 
            21            468 
  PTK2 MUTATED PTK2 WILD-TYPE 
            21            468 
[1] "AXIN2 MUTATION ANALYSIS"
[1] 3
  AXIN2 MUTATED AXIN2 WILD-TYPE 
             24             465 
  AXIN2 MUTATED AXIN2 WILD-TYPE 
             24             465 
[1] "TM9SF2 MUTATION ANALYSIS"
[1] 3
  TM9SF2 MUTATED TM9SF2 WILD-TYPE 
              11              478 
  TM9SF2 MUTATED TM9SF2 WILD-TYPE 
              11              478 
[1] "FAHD2A MUTATION ANALYSIS"
[1] 3
  FAHD2A MUTATED FAHD2A WILD-TYPE 
               7              482 
  FAHD2A MUTATED FAHD2A WILD-TYPE 
               7              482 
[1] "KCNK1 MUTATION ANALYSIS"
[1] 3
  KCNK1 MUTATED KCNK1 WILD-TYPE 
             11             478 
  KCNK1 MUTATED KCNK1 WILD-TYPE 
             11             478 
[1] "C15ORF52 MUTATION ANALYSIS"
[1] 3
  C15ORF52 MUTATED C15ORF52 WILD-TYPE 
                12                477 
  C15ORF52 MUTATED C15ORF52 WILD-TYPE 
                12                477 
[1] "HAUS6 MUTATION ANALYSIS"
[1] 3
  HAUS6 MUTATED HAUS6 WILD-TYPE 
             17             472 
  HAUS6 MUTATED HAUS6 WILD-TYPE 
             17             472 
[1] "TUBA4A MUTATION ANALYSIS"
[1] 3
  TUBA4A MUTATED TUBA4A WILD-TYPE 
              12              477 
  TUBA4A MUTATED TUBA4A WILD-TYPE 
              12              477 
[1] "MBD6 MUTATION ANALYSIS"
[1] 3
  MBD6 MUTATED MBD6 WILD-TYPE 
            16            473 
  MBD6 MUTATED MBD6 WILD-TYPE 
            16            473 
[1] "TFE3 MUTATION ANALYSIS"
[1] 3
  TFE3 MUTATED TFE3 WILD-TYPE 
            11            478 
  TFE3 MUTATED TFE3 WILD-TYPE 
            11            478 
[1] "NCAPD2 MUTATION ANALYSIS"
[1] 3
  NCAPD2 MUTATED NCAPD2 WILD-TYPE 
              21              468 
  NCAPD2 MUTATED NCAPD2 WILD-TYPE 
              21              468 
[1] "NCOA6 MUTATION ANALYSIS"
[1] 3
  NCOA6 MUTATED NCOA6 WILD-TYPE 
             29             460 
  NCOA6 MUTATED NCOA6 WILD-TYPE 
             29             460 
[1] "SVIL MUTATION ANALYSIS"
[1] 3
  SVIL MUTATED SVIL WILD-TYPE 
            34            455 
  SVIL MUTATED SVIL WILD-TYPE 
            34            455 
[1] "XYLT2 MUTATION ANALYSIS"
[1] 3
  XYLT2 MUTATED XYLT2 WILD-TYPE 
             14             475 
  XYLT2 MUTATED XYLT2 WILD-TYPE 
             14             475 
[1] "ZNF789 MUTATION ANALYSIS"
[1] 3
  ZNF789 MUTATED ZNF789 WILD-TYPE 
               7              482 
  ZNF789 MUTATED ZNF789 WILD-TYPE 
               7              482 
[1] "DDX43 MUTATION ANALYSIS"
[1] 3
  DDX43 MUTATED DDX43 WILD-TYPE 
             14             475 
  DDX43 MUTATED DDX43 WILD-TYPE 
             14             475 
[1] "CEP135 MUTATION ANALYSIS"
[1] 3
  CEP135 MUTATED CEP135 WILD-TYPE 
              25              464 
  CEP135 MUTATED CEP135 WILD-TYPE 
              25              464 
[1] "IL12RB2 MUTATION ANALYSIS"
[1] 3
  IL12RB2 MUTATED IL12RB2 WILD-TYPE 
               19               470 
  IL12RB2 MUTATED IL12RB2 WILD-TYPE 
               19               470 
[1] "EHBP1 MUTATION ANALYSIS"
[1] 3
  EHBP1 MUTATED EHBP1 WILD-TYPE 
             25             464 
  EHBP1 MUTATED EHBP1 WILD-TYPE 
             25             464 
[1] "USP7 MUTATION ANALYSIS"
[1] 3
  USP7 MUTATED USP7 WILD-TYPE 
            26            463 
  USP7 MUTATED USP7 WILD-TYPE 
            26            463 
[1] "IVL MUTATION ANALYSIS"
[1] 3
  IVL MUTATED IVL WILD-TYPE 
           20           469 
  IVL MUTATED IVL WILD-TYPE 
           20           469 
[1] "IDH2 MUTATION ANALYSIS"
[1] 3
  IDH2 MUTATED IDH2 WILD-TYPE 
            18            471 
  IDH2 MUTATED IDH2 WILD-TYPE 
            18            471 
[1] "FGFR2 MUTATION ANALYSIS"
[1] 3
  FGFR2 MUTATED FGFR2 WILD-TYPE 
             53             436 
  FGFR2 MUTATED FGFR2 WILD-TYPE 
             53             436 
[1] "FAM134A MUTATION ANALYSIS"
[1] 3
  FAM134A MUTATED FAM134A WILD-TYPE 
                8               481 
  FAM134A MUTATED FAM134A WILD-TYPE 
                8               481 
[1] "MLL2 MUTATION ANALYSIS"
[1] 3
  MLL2 MUTATED MLL2 WILD-TYPE 
            59            430 
  MLL2 MUTATED MLL2 WILD-TYPE 
            59            430 
[1] "LRRC39 MUTATION ANALYSIS"
[1] 3
  LRRC39 MUTATED LRRC39 WILD-TYPE 
               9              480 
  LRRC39 MUTATED LRRC39 WILD-TYPE 
               9              480 
[1] "ST8SIA6 MUTATION ANALYSIS"
[1] 3
  ST8SIA6 MUTATED ST8SIA6 WILD-TYPE 
               14               475 
  ST8SIA6 MUTATED ST8SIA6 WILD-TYPE 
               14               475 
[1] "CAB39L MUTATION ANALYSIS"
[1] 3
  CAB39L MUTATED CAB39L WILD-TYPE 
              10              479 
  CAB39L MUTATED CAB39L WILD-TYPE 
              10              479 
[1] "ERBB4 MUTATION ANALYSIS"
[1] 3
  ERBB4 MUTATED ERBB4 WILD-TYPE 
             59             430 
  ERBB4 MUTATED ERBB4 WILD-TYPE 
             59             430 
[1] "UGT3A2 MUTATION ANALYSIS"
[1] 3
  UGT3A2 MUTATED UGT3A2 WILD-TYPE 
              22              467 
  UGT3A2 MUTATED UGT3A2 WILD-TYPE 
              22              467 
[1] "ARHGAP5 MUTATION ANALYSIS"
[1] 3
  ARHGAP5 MUTATED ARHGAP5 WILD-TYPE 
               23               466 
  ARHGAP5 MUTATED ARHGAP5 WILD-TYPE 
               23               466 
[1] "EP400 MUTATION ANALYSIS"
[1] 3
  EP400 MUTATED EP400 WILD-TYPE 
             40             449 
  EP400 MUTATED EP400 WILD-TYPE 
             40             449 
[1] "MEN1 MUTATION ANALYSIS"
[1] 3
  MEN1 MUTATED MEN1 WILD-TYPE 
            27            462 
  MEN1 MUTATED MEN1 WILD-TYPE 
            27            462 
[1] "SENP6 MUTATION ANALYSIS"
[1] 3
  SENP6 MUTATED SENP6 WILD-TYPE 
             18             471 
  SENP6 MUTATED SENP6 WILD-TYPE 
             18             471 
[1] "OR7C2 MUTATION ANALYSIS"
[1] 3
  OR7C2 MUTATED OR7C2 WILD-TYPE 
             12             477 
  OR7C2 MUTATED OR7C2 WILD-TYPE 
             12             477 
[1] "PDGFRA MUTATION ANALYSIS"
[1] 3
  PDGFRA MUTATED PDGFRA WILD-TYPE 
              54              435 
  PDGFRA MUTATED PDGFRA WILD-TYPE 
              54              435 
[1] "KLC4 MUTATION ANALYSIS"
[1] 3
  KLC4 MUTATED KLC4 WILD-TYPE 
            17            472 
  KLC4 MUTATED KLC4 WILD-TYPE 
            17            472 
[1] "INTS4 MUTATION ANALYSIS"
[1] 3
  INTS4 MUTATED INTS4 WILD-TYPE 
             22             467 
  INTS4 MUTATED INTS4 WILD-TYPE 
             22             467 
[1] "RBAK MUTATION ANALYSIS"
[1] 3
  RBAK MUTATED RBAK WILD-TYPE 
            18            471 
  RBAK MUTATED RBAK WILD-TYPE 
            18            471 
[1] "EIF4A2 MUTATION ANALYSIS"
[1] 3
  EIF4A2 MUTATED EIF4A2 WILD-TYPE 
              12              477 
  EIF4A2 MUTATED EIF4A2 WILD-TYPE 
              12              477 
[1] "FAM133B MUTATION ANALYSIS"
[1] 3
  FAM133B MUTATED FAM133B WILD-TYPE 
                5               484 
  FAM133B MUTATED FAM133B WILD-TYPE 
                5               484 
[1] "CATSPER1 MUTATION ANALYSIS"
[1] 3
  CATSPER1 MUTATED CATSPER1 WILD-TYPE 
                19                470 
  CATSPER1 MUTATED CATSPER1 WILD-TYPE 
                19                470 
[1] "GIGYF2 MUTATION ANALYSIS"
[1] 3
  GIGYF2 MUTATED GIGYF2 WILD-TYPE 
              30              459 
  GIGYF2 MUTATED GIGYF2 WILD-TYPE 
              30              459 
[1] "RBM12 MUTATION ANALYSIS"
[1] 3
  RBM12 MUTATED RBM12 WILD-TYPE 
             15             474 
  RBM12 MUTATED RBM12 WILD-TYPE 
             15             474 
[1] "EIF2AK4 MUTATION ANALYSIS"
[1] 3
  EIF2AK4 MUTATED EIF2AK4 WILD-TYPE 
               20               469 
  EIF2AK4 MUTATED EIF2AK4 WILD-TYPE 
               20               469 
[1] "PI4K2B MUTATION ANALYSIS"
[1] 3
  PI4K2B MUTATED PI4K2B WILD-TYPE 
              14              475 
  PI4K2B MUTATED PI4K2B WILD-TYPE 
              14              475 
[1] "HIPK2 MUTATION ANALYSIS"
[1] 3
  HIPK2 MUTATED HIPK2 WILD-TYPE 
             26             463 
  HIPK2 MUTATED HIPK2 WILD-TYPE 
             26             463 
[1] "SLC4A10 MUTATION ANALYSIS"
[1] 3
  SLC4A10 MUTATED SLC4A10 WILD-TYPE 
               29               460 
  SLC4A10 MUTATED SLC4A10 WILD-TYPE 
               29               460 
[1] "KLHL10 MUTATION ANALYSIS"
[1] 3
  KLHL10 MUTATED KLHL10 WILD-TYPE 
              21              468 
  KLHL10 MUTATED KLHL10 WILD-TYPE 
              21              468 
[1] "LINGO4 MUTATION ANALYSIS"
[1] 3
  LINGO4 MUTATED LINGO4 WILD-TYPE 
              10              479 
  LINGO4 MUTATED LINGO4 WILD-TYPE 
              10              479 
[1] "MMP13 MUTATION ANALYSIS"
[1] 3
  MMP13 MUTATED MMP13 WILD-TYPE 
             16             473 
  MMP13 MUTATED MMP13 WILD-TYPE 
             16             473 
[1] "DNAH12 MUTATION ANALYSIS"
[1] 3
  DNAH12 MUTATED DNAH12 WILD-TYPE 
              25              464 
  DNAH12 MUTATED DNAH12 WILD-TYPE 
              25              464 
[1] "UQCRC2 MUTATION ANALYSIS"
[1] 3
  UQCRC2 MUTATED UQCRC2 WILD-TYPE 
              10              479 
  UQCRC2 MUTATED UQCRC2 WILD-TYPE 
              10              479 
[1] "E2F7 MUTATION ANALYSIS"
[1] 3
  E2F7 MUTATED E2F7 WILD-TYPE 
            26            463 
  E2F7 MUTATED E2F7 WILD-TYPE 
            26            463 
[1] "FHOD3 MUTATION ANALYSIS"
[1] 3
  FHOD3 MUTATED FHOD3 WILD-TYPE 
             30             459 
  FHOD3 MUTATED FHOD3 WILD-TYPE 
             30             459 
[1] "MLL3 MUTATION ANALYSIS"
[1] 3
  MLL3 MUTATED MLL3 WILD-TYPE 
            66            423 
  MLL3 MUTATED MLL3 WILD-TYPE 
            66            423 
[1] "SCD5 MUTATION ANALYSIS"
[1] 3
  SCD5 MUTATED SCD5 WILD-TYPE 
             8            481 
  SCD5 MUTATED SCD5 WILD-TYPE 
             8            481 
[1] "DDX23 MUTATION ANALYSIS"
[1] 3
  DDX23 MUTATED DDX23 WILD-TYPE 
             21             468 
  DDX23 MUTATED DDX23 WILD-TYPE 
             21             468 
[1] "THOC5 MUTATION ANALYSIS"
[1] 3
  THOC5 MUTATED THOC5 WILD-TYPE 
             16             473 
  THOC5 MUTATED THOC5 WILD-TYPE 
             16             473 
[1] "ADAM28 MUTATION ANALYSIS"
[1] 3
  ADAM28 MUTATED ADAM28 WILD-TYPE 
              20              469 
  ADAM28 MUTATED ADAM28 WILD-TYPE 
              20              469 
[1] "SMAD3 MUTATION ANALYSIS"
[1] 3
  SMAD3 MUTATED SMAD3 WILD-TYPE 
             19             470 
  SMAD3 MUTATED SMAD3 WILD-TYPE 
             19             470 
[1] "SGK269 MUTATION ANALYSIS"
[1] 3
  SGK269 MUTATED SGK269 WILD-TYPE 
              23              466 
  SGK269 MUTATED SGK269 WILD-TYPE 
              23              466 
[1] "FLT3 MUTATION ANALYSIS"
[1] 3
  FLT3 MUTATED FLT3 WILD-TYPE 
            32            457 
  FLT3 MUTATED FLT3 WILD-TYPE 
            32            457 
[1] "RNF128 MUTATION ANALYSIS"
[1] 3
  RNF128 MUTATED RNF128 WILD-TYPE 
              15              474 
  RNF128 MUTATED RNF128 WILD-TYPE 
              15              474 
[1] "MOBKL2B MUTATION ANALYSIS"
[1] 3
  MOBKL2B MUTATED MOBKL2B WILD-TYPE 
                9               480 
  MOBKL2B MUTATED MOBKL2B WILD-TYPE 
                9               480 
[1] "NT5DC3 MUTATION ANALYSIS"
[1] 3
  NT5DC3 MUTATED NT5DC3 WILD-TYPE 
              14              475 
  NT5DC3 MUTATED NT5DC3 WILD-TYPE 
              14              475 
[1] "USP29 MUTATION ANALYSIS"
[1] 3
  USP29 MUTATED USP29 WILD-TYPE 
             22             467 
  USP29 MUTATED USP29 WILD-TYPE 
             22             467 
[1] "USP34 MUTATION ANALYSIS"
[1] 3
  USP34 MUTATED USP34 WILD-TYPE 
             47             442 
  USP34 MUTATED USP34 WILD-TYPE 
             47             442 
[1] "F8 MUTATION ANALYSIS"
[1] 3
  F8 MUTATED F8 WILD-TYPE 
          41          448 
  F8 MUTATED F8 WILD-TYPE 
          41          448 
[1] "SMTN MUTATION ANALYSIS"
[1] 3
  SMTN MUTATED SMTN WILD-TYPE 
            16            473 
  SMTN MUTATED SMTN WILD-TYPE 
            16            473 
[1] "CARD11 MUTATION ANALYSIS"
[1] 3
  CARD11 MUTATED CARD11 WILD-TYPE 
              49              440 
  CARD11 MUTATED CARD11 WILD-TYPE 
              49              440 
[1] "NUP188 MUTATION ANALYSIS"
[1] 3
  NUP188 MUTATED NUP188 WILD-TYPE 
              23              466 
  NUP188 MUTATED NUP188 WILD-TYPE 
              23              466 
[1] "PTPN3 MUTATION ANALYSIS"
[1] 3
  PTPN3 MUTATED PTPN3 WILD-TYPE 
             16             473 
  PTPN3 MUTATED PTPN3 WILD-TYPE 
             16             473 
[1] "NBEA MUTATION ANALYSIS"
[1] 3
  NBEA MUTATED NBEA WILD-TYPE 
            53            436 
  NBEA MUTATED NBEA WILD-TYPE 
            53            436 
[1] "CNIH4 MUTATION ANALYSIS"
[1] 3
  CNIH4 MUTATED CNIH4 WILD-TYPE 
              6             483 
  CNIH4 MUTATED CNIH4 WILD-TYPE 
              6             483 
[1] "CD58 MUTATION ANALYSIS"
[1] 3
  CD58 MUTATED CD58 WILD-TYPE 
            15            474 
  CD58 MUTATED CD58 WILD-TYPE 
            15            474 
[1] "GMCL1 MUTATION ANALYSIS"
[1] 3
  GMCL1 MUTATED GMCL1 WILD-TYPE 
             14             475 
  GMCL1 MUTATED GMCL1 WILD-TYPE 
             14             475 
[1] "AKAP3 MUTATION ANALYSIS"
[1] 3
  AKAP3 MUTATED AKAP3 WILD-TYPE 
             23             466 
  AKAP3 MUTATED AKAP3 WILD-TYPE 
             23             466 
[1] "RBMX2 MUTATION ANALYSIS"
[1] 3
  RBMX2 MUTATED RBMX2 WILD-TYPE 
             12             477 
  RBMX2 MUTATED RBMX2 WILD-TYPE 
             12             477 
[1] "DCBLD1 MUTATION ANALYSIS"
[1] 3
  DCBLD1 MUTATED DCBLD1 WILD-TYPE 
               7              482 
  DCBLD1 MUTATED DCBLD1 WILD-TYPE 
               7              482 
[1] "ZNF280B MUTATION ANALYSIS"
[1] 3
  ZNF280B MUTATED ZNF280B WILD-TYPE 
               13               476 
  ZNF280B MUTATED ZNF280B WILD-TYPE 
               13               476 
[1] "NCOA7 MUTATION ANALYSIS"
[1] 3
  NCOA7 MUTATED NCOA7 WILD-TYPE 
             17             472 
  NCOA7 MUTATED NCOA7 WILD-TYPE 
             17             472 
[1] "DENND4A MUTATION ANALYSIS"
[1] 3
  DENND4A MUTATED DENND4A WILD-TYPE 
               26               463 
  DENND4A MUTATED DENND4A WILD-TYPE 
               26               463 
[1] "ALDH2 MUTATION ANALYSIS"
[1] 3
  ALDH2 MUTATED ALDH2 WILD-TYPE 
             12             477 
  ALDH2 MUTATED ALDH2 WILD-TYPE 
             12             477 
[1] "CCDC160 MUTATION ANALYSIS"
[1] 3
  CCDC160 MUTATED CCDC160 WILD-TYPE 
               11               478 
  CCDC160 MUTATED CCDC160 WILD-TYPE 
               11               478 
[1] "EFTUD2 MUTATION ANALYSIS"
[1] 3
  EFTUD2 MUTATED EFTUD2 WILD-TYPE 
              17              472 
  EFTUD2 MUTATED EFTUD2 WILD-TYPE 
              17              472 
[1] "STBD1 MUTATION ANALYSIS"
[1] 3
  STBD1 MUTATED STBD1 WILD-TYPE 
              7             482 
  STBD1 MUTATED STBD1 WILD-TYPE 
              7             482 
[1] "TCF7L2 MUTATION ANALYSIS"
[1] 3
  TCF7L2 MUTATED TCF7L2 WILD-TYPE 
              35              454 
  TCF7L2 MUTATED TCF7L2 WILD-TYPE 
              35              454 
[1] "C17ORF47 MUTATION ANALYSIS"
[1] 3
  C17ORF47 MUTATED C17ORF47 WILD-TYPE 
                 7                482 
  C17ORF47 MUTATED C17ORF47 WILD-TYPE 
                 7                482 
[1] "TOP2A MUTATION ANALYSIS"
[1] 3
  TOP2A MUTATED TOP2A WILD-TYPE 
             20             469 
  TOP2A MUTATED TOP2A WILD-TYPE 
             20             469 
[1] "MIER3 MUTATION ANALYSIS"
[1] 3
  MIER3 MUTATED MIER3 WILD-TYPE 
             14             475 
  MIER3 MUTATED MIER3 WILD-TYPE 
             14             475 
[1] "FBXO21 MUTATION ANALYSIS"
[1] 3
  FBXO21 MUTATED FBXO21 WILD-TYPE 
               9              480 
  FBXO21 MUTATED FBXO21 WILD-TYPE 
               9              480 
[1] "CYP1B1 MUTATION ANALYSIS"
[1] 3
  CYP1B1 MUTATED CYP1B1 WILD-TYPE 
              12              477 
  CYP1B1 MUTATED CYP1B1 WILD-TYPE 
              12              477 
[1] "MSH6 MUTATION ANALYSIS"
[1] 3
  MSH6 MUTATED MSH6 WILD-TYPE 
            45            444 
  MSH6 MUTATED MSH6 WILD-TYPE 
            45            444 
[1] "MMP8 MUTATION ANALYSIS"
[1] 3
  MMP8 MUTATED MMP8 WILD-TYPE 
            13            476 
  MMP8 MUTATED MMP8 WILD-TYPE 
            13            476 
[1] "RAG1AP1 MUTATION ANALYSIS"
[1] 3
  RAG1AP1 MUTATED RAG1AP1 WILD-TYPE 
                6               483 
  RAG1AP1 MUTATED RAG1AP1 WILD-TYPE 
                6               483 
[1] "ALX4 MUTATION ANALYSIS"
[1] 3
  ALX4 MUTATED ALX4 WILD-TYPE 
            12            477 
  ALX4 MUTATED ALX4 WILD-TYPE 
            12            477 
[1] "OR51E1 MUTATION ANALYSIS"
[1] 3
  OR51E1 MUTATED OR51E1 WILD-TYPE 
              15              474 
  OR51E1 MUTATED OR51E1 WILD-TYPE 
              15              474 
[1] "CBL MUTATION ANALYSIS"
[1] 3
  CBL MUTATED CBL WILD-TYPE 
           39           450 
  CBL MUTATED CBL WILD-TYPE 
           39           450 
[1] "SLC28A2 MUTATION ANALYSIS"
[1] 3
  SLC28A2 MUTATED SLC28A2 WILD-TYPE 
               15               474 
  SLC28A2 MUTATED SLC28A2 WILD-TYPE 
               15               474 
[1] "ZNF222 MUTATION ANALYSIS"
[1] 3
  ZNF222 MUTATED ZNF222 WILD-TYPE 
              11              478 
  ZNF222 MUTATED ZNF222 WILD-TYPE 
              11              478 
[1] "UBQLN2 MUTATION ANALYSIS"
[1] 3
  UBQLN2 MUTATED UBQLN2 WILD-TYPE 
              12              477 
  UBQLN2 MUTATED UBQLN2 WILD-TYPE 
              12              477 
[1] "PPARGC1A MUTATION ANALYSIS"
[1] 3
  PPARGC1A MUTATED PPARGC1A WILD-TYPE 
                23                466 
  PPARGC1A MUTATED PPARGC1A WILD-TYPE 
                23                466 
[1] "ATP6V1B1 MUTATION ANALYSIS"
[1] 3
  ATP6V1B1 MUTATED ATP6V1B1 WILD-TYPE 
                16                473 
  ATP6V1B1 MUTATED ATP6V1B1 WILD-TYPE 
                16                473 
[1] "ZNF583 MUTATION ANALYSIS"
[1] 3
  ZNF583 MUTATED ZNF583 WILD-TYPE 
              18              471 
  ZNF583 MUTATED ZNF583 WILD-TYPE 
              18              471 
[1] "OSBPL2 MUTATION ANALYSIS"
[1] 3
  OSBPL2 MUTATED OSBPL2 WILD-TYPE 
              12              477 
  OSBPL2 MUTATED OSBPL2 WILD-TYPE 
              12              477 
[1] "CRY1 MUTATION ANALYSIS"
[1] 3
  CRY1 MUTATED CRY1 WILD-TYPE 
            16            473 
  CRY1 MUTATED CRY1 WILD-TYPE 
            16            473 
[1] "ZFYVE26 MUTATION ANALYSIS"
[1] 3
  ZFYVE26 MUTATED ZFYVE26 WILD-TYPE 
               32               457 
  ZFYVE26 MUTATED ZFYVE26 WILD-TYPE 
               32               457 
[1] "PALB2 MUTATION ANALYSIS"
[1] 3
  PALB2 MUTATED PALB2 WILD-TYPE 
             20             469 
  PALB2 MUTATED PALB2 WILD-TYPE 
             20             469 
[1] "PKD2L1 MUTATION ANALYSIS"
[1] 3
  PKD2L1 MUTATED PKD2L1 WILD-TYPE 
              24              465 
  PKD2L1 MUTATED PKD2L1 WILD-TYPE 
              24              465 
[1] "COLEC10 MUTATION ANALYSIS"
[1] 3
  COLEC10 MUTATED COLEC10 WILD-TYPE 
               10               479 
  COLEC10 MUTATED COLEC10 WILD-TYPE 
               10               479 
[1] "C2ORF77 MUTATION ANALYSIS"
[1] 3
  C2ORF77 MUTATED C2ORF77 WILD-TYPE 
                9               480 
  C2ORF77 MUTATED C2ORF77 WILD-TYPE 
                9               480 
[1] "DHRS7 MUTATION ANALYSIS"
[1] 3
  DHRS7 MUTATED DHRS7 WILD-TYPE 
             10             479 
  DHRS7 MUTATED DHRS7 WILD-TYPE 
             10             479 
[1] "PANK3 MUTATION ANALYSIS"
[1] 3
  PANK3 MUTATED PANK3 WILD-TYPE 
              7             482 
  PANK3 MUTATED PANK3 WILD-TYPE 
              7             482 
[1] "G3BP2 MUTATION ANALYSIS"
[1] 3
  G3BP2 MUTATED G3BP2 WILD-TYPE 
             10             479 
  G3BP2 MUTATED G3BP2 WILD-TYPE 
             10             479 
[1] "TET3 MUTATION ANALYSIS"
[1] 3
  TET3 MUTATED TET3 WILD-TYPE 
            24            465 
  TET3 MUTATED TET3 WILD-TYPE 
            24            465 
[1] "C12ORF5 MUTATION ANALYSIS"
[1] 3
  C12ORF5 MUTATED C12ORF5 WILD-TYPE 
                6               483 
  C12ORF5 MUTATED C12ORF5 WILD-TYPE 
                6               483 
[1] "GPR98 MUTATION ANALYSIS"
[1] 3
  GPR98 MUTATED GPR98 WILD-TYPE 
             69             420 
  GPR98 MUTATED GPR98 WILD-TYPE 
             69             420 
[1] "MAGEA1 MUTATION ANALYSIS"
[1] 3
  MAGEA1 MUTATED MAGEA1 WILD-TYPE 
              14              475 
  MAGEA1 MUTATED MAGEA1 WILD-TYPE 
              14              475 
[1] "HNF1B MUTATION ANALYSIS"
[1] 3
  HNF1B MUTATED HNF1B WILD-TYPE 
             10             479 
  HNF1B MUTATED HNF1B WILD-TYPE 
             10             479 
[1] "C19ORF66 MUTATION ANALYSIS"
[1] 3
  C19ORF66 MUTATED C19ORF66 WILD-TYPE 
                 4                485 
  C19ORF66 MUTATED C19ORF66 WILD-TYPE 
                 4                485 
[1] "INPP1 MUTATION ANALYSIS"
[1] 3
  INPP1 MUTATED INPP1 WILD-TYPE 
              8             481 
  INPP1 MUTATED INPP1 WILD-TYPE 
              8             481 
[1] "TRIM24 MUTATION ANALYSIS"
[1] 3
  TRIM24 MUTATED TRIM24 WILD-TYPE 
              20              469 
  TRIM24 MUTATED TRIM24 WILD-TYPE 
              20              469 
[1] "C12ORF40 MUTATION ANALYSIS"
[1] 3
  C12ORF40 MUTATED C12ORF40 WILD-TYPE 
                24                465 
  C12ORF40 MUTATED C12ORF40 WILD-TYPE 
                24                465 
[1] "SNAI2 MUTATION ANALYSIS"
[1] 3
  SNAI2 MUTATED SNAI2 WILD-TYPE 
             11             478 
  SNAI2 MUTATED SNAI2 WILD-TYPE 
             11             478 
[1] "DDX5 MUTATION ANALYSIS"
[1] 3
  DDX5 MUTATED DDX5 WILD-TYPE 
             9            480 
  DDX5 MUTATED DDX5 WILD-TYPE 
             9            480 
[1] "PTPDC1 MUTATION ANALYSIS"
[1] 3
  PTPDC1 MUTATED PTPDC1 WILD-TYPE 
              10              479 
  PTPDC1 MUTATED PTPDC1 WILD-TYPE 
              10              479 
[1] "BAG4 MUTATION ANALYSIS"
[1] 3
  BAG4 MUTATED BAG4 WILD-TYPE 
             8            481 
  BAG4 MUTATED BAG4 WILD-TYPE 
             8            481 
[1] "BAZ1B MUTATION ANALYSIS"
[1] 3
  BAZ1B MUTATED BAZ1B WILD-TYPE 
             27             462 
  BAZ1B MUTATED BAZ1B WILD-TYPE 
             27             462 
[1] "PAQR5 MUTATION ANALYSIS"
[1] 3
  PAQR5 MUTATED PAQR5 WILD-TYPE 
              8             481 
  PAQR5 MUTATED PAQR5 WILD-TYPE 
              8             481 
[1] "KDM3B MUTATION ANALYSIS"
[1] 3
  KDM3B MUTATED KDM3B WILD-TYPE 
             34             455 
  KDM3B MUTATED KDM3B WILD-TYPE 
             34             455 
[1] "FAHD2B MUTATION ANALYSIS"
[1] 3
  FAHD2B MUTATED FAHD2B WILD-TYPE 
               6              483 
  FAHD2B MUTATED FAHD2B WILD-TYPE 
               6              483 
[1] "ZCCHC6 MUTATION ANALYSIS"
[1] 3
  ZCCHC6 MUTATED ZCCHC6 WILD-TYPE 
              20              469 
  ZCCHC6 MUTATED ZCCHC6 WILD-TYPE 
              20              469 
[1] "TNMD MUTATION ANALYSIS"
[1] 3
  TNMD MUTATED TNMD WILD-TYPE 
            11            478 
  TNMD MUTATED TNMD WILD-TYPE 
            11            478 
[1] "RNF182 MUTATION ANALYSIS"
[1] 3
  RNF182 MUTATED RNF182 WILD-TYPE 
              16              473 
  RNF182 MUTATED RNF182 WILD-TYPE 
              16              473 
[1] "ERCC5 MUTATION ANALYSIS"
[1] 3
  ERCC5 MUTATED ERCC5 WILD-TYPE 
             23             466 
  ERCC5 MUTATED ERCC5 WILD-TYPE 
             23             466 
[1] "JAK3 MUTATION ANALYSIS"
[1] 3
  JAK3 MUTATED JAK3 WILD-TYPE 
            28            461 
  JAK3 MUTATED JAK3 WILD-TYPE 
            28            461 
[1] "HM13 MUTATION ANALYSIS"
[1] 3
  HM13 MUTATED HM13 WILD-TYPE 
             5            484 
  HM13 MUTATED HM13 WILD-TYPE 
             5            484 
[1] "RBM10 MUTATION ANALYSIS"
[1] 3
  RBM10 MUTATED RBM10 WILD-TYPE 
             18             471 
  RBM10 MUTATED RBM10 WILD-TYPE 
             18             471 
[1] "TRPM7 MUTATION ANALYSIS"
[1] 3
  TRPM7 MUTATED TRPM7 WILD-TYPE 
             30             459 
  TRPM7 MUTATED TRPM7 WILD-TYPE 
             30             459 
[1] "CAMSAP1L1 MUTATION ANALYSIS"
[1] 3
  CAMSAP1L1 MUTATED CAMSAP1L1 WILD-TYPE 
                 23                 466 
  CAMSAP1L1 MUTATED CAMSAP1L1 WILD-TYPE 
                 23                 466 
[1] "SLC33A1 MUTATION ANALYSIS"
[1] 3
  SLC33A1 MUTATED SLC33A1 WILD-TYPE 
               10               479 
  SLC33A1 MUTATED SLC33A1 WILD-TYPE 
               10               479 
[1] "F2RL1 MUTATION ANALYSIS"
[1] 3
  F2RL1 MUTATED F2RL1 WILD-TYPE 
              8             481 
  F2RL1 MUTATED F2RL1 WILD-TYPE 
              8             481 
[1] "USP26 MUTATION ANALYSIS"
[1] 3
  USP26 MUTATED USP26 WILD-TYPE 
             24             465 
  USP26 MUTATED USP26 WILD-TYPE 
             24             465 
[1] "WEE1 MUTATION ANALYSIS"
[1] 3
  WEE1 MUTATED WEE1 WILD-TYPE 
            12            477 
  WEE1 MUTATED WEE1 WILD-TYPE 
            12            477 
[1] "ERBB2IP MUTATION ANALYSIS"
[1] 3
  ERBB2IP MUTATED ERBB2IP WILD-TYPE 
               18               471 
  ERBB2IP MUTATED ERBB2IP WILD-TYPE 
               18               471 
[1] "B4GALNT4 MUTATION ANALYSIS"
[1] 3
  B4GALNT4 MUTATED B4GALNT4 WILD-TYPE 
                11                478 
  B4GALNT4 MUTATED B4GALNT4 WILD-TYPE 
                11                478 
[1] "NSUN6 MUTATION ANALYSIS"
[1] 3
  NSUN6 MUTATED NSUN6 WILD-TYPE 
             10             479 
  NSUN6 MUTATED NSUN6 WILD-TYPE 
             10             479 
[1] "KDM5B MUTATION ANALYSIS"
[1] 3
  KDM5B MUTATED KDM5B WILD-TYPE 
             28             461 
  KDM5B MUTATED KDM5B WILD-TYPE 
             28             461 
[1] "KRAS MUTATION ANALYSIS"
[1] 3
  KRAS MUTATED KRAS WILD-TYPE 
           231            258 
  KRAS MUTATED KRAS WILD-TYPE 
           231            258 
[1] "GATA3 MUTATION ANALYSIS"
[1] 3
  GATA3 MUTATED GATA3 WILD-TYPE 
             16             473 
  GATA3 MUTATED GATA3 WILD-TYPE 
             16             473 
[1] "OVCH1 MUTATION ANALYSIS"
[1] 3
  OVCH1 MUTATED OVCH1 WILD-TYPE 
             26             463 
  OVCH1 MUTATED OVCH1 WILD-TYPE 
             26             463 
[1] "MUC17 MUTATION ANALYSIS"
[1] 3
  MUC17 MUTATED MUC17 WILD-TYPE 
             55             434 
  MUC17 MUTATED MUC17 WILD-TYPE 
             55             434 
[1] "GTF2B MUTATION ANALYSIS"
[1] 3
  GTF2B MUTATED GTF2B WILD-TYPE 
             12             477 
  GTF2B MUTATED GTF2B WILD-TYPE 
             12             477 
[1] "RUNX1 MUTATION ANALYSIS"
[1] 3
  RUNX1 MUTATED RUNX1 WILD-TYPE 
             41             448 
  RUNX1 MUTATED RUNX1 WILD-TYPE 
             41             448 
[1] "C9ORF84 MUTATION ANALYSIS"
[1] 3
  C9ORF84 MUTATED C9ORF84 WILD-TYPE 
               21               468 
  C9ORF84 MUTATED C9ORF84 WILD-TYPE 
               21               468 
[1] "NR4A2 MUTATION ANALYSIS"
[1] 3
  NR4A2 MUTATED NR4A2 WILD-TYPE 
             13             476 
  NR4A2 MUTATED NR4A2 WILD-TYPE 
             13             476 
[1] "LATS1 MUTATION ANALYSIS"
[1] 3
  LATS1 MUTATED LATS1 WILD-TYPE 
             21             468 
  LATS1 MUTATED LATS1 WILD-TYPE 
             21             468 
[1] "THAP9 MUTATION ANALYSIS"
[1] 3
  THAP9 MUTATED THAP9 WILD-TYPE 
             16             473 
  THAP9 MUTATED THAP9 WILD-TYPE 
             16             473 
[1] "ZNF449 MUTATION ANALYSIS"
[1] 3
  ZNF449 MUTATED ZNF449 WILD-TYPE 
              14              475 
  ZNF449 MUTATED ZNF449 WILD-TYPE 
              14              475 
[1] "PRDM1 MUTATION ANALYSIS"
[1] 3
  PRDM1 MUTATED PRDM1 WILD-TYPE 
             22             467 
  PRDM1 MUTATED PRDM1 WILD-TYPE 
             22             467 
[1] "MBTD1 MUTATION ANALYSIS"
[1] 3
  MBTD1 MUTATED MBTD1 WILD-TYPE 
             11             478 
  MBTD1 MUTATED MBTD1 WILD-TYPE 
             11             478 
[1] "MKL2 MUTATION ANALYSIS"
[1] 3
  MKL2 MUTATED MKL2 WILD-TYPE 
            11            478 
  MKL2 MUTATED MKL2 WILD-TYPE 
            11            478 
[1] "LIG1 MUTATION ANALYSIS"
[1] 3
  LIG1 MUTATED LIG1 WILD-TYPE 
            20            469 
  LIG1 MUTATED LIG1 WILD-TYPE 
            20            469 
[1] "ZNF708 MUTATION ANALYSIS"
[1] 3
  ZNF708 MUTATED ZNF708 WILD-TYPE 
              13              476 
  ZNF708 MUTATED ZNF708 WILD-TYPE 
              13              476 
[1] "IL13RA2 MUTATION ANALYSIS"
[1] 3
  IL13RA2 MUTATED IL13RA2 WILD-TYPE 
               16               473 
  IL13RA2 MUTATED IL13RA2 WILD-TYPE 
               16               473 
[1] "FGFR3 MUTATION ANALYSIS"
[1] 3
  FGFR3 MUTATED FGFR3 WILD-TYPE 
             23             466 
  FGFR3 MUTATED FGFR3 WILD-TYPE 
             23             466 
[1] "PTPN12 MUTATION ANALYSIS"
[1] 3
  PTPN12 MUTATED PTPN12 WILD-TYPE 
              21              468 
  PTPN12 MUTATED PTPN12 WILD-TYPE 
              21              468 
[1] "TUBE1 MUTATION ANALYSIS"
[1] 3
  TUBE1 MUTATED TUBE1 WILD-TYPE 
             12             477 
  TUBE1 MUTATED TUBE1 WILD-TYPE 
             12             477 
[1] "TGFBR2 MUTATION ANALYSIS"
[1] 3
  TGFBR2 MUTATED TGFBR2 WILD-TYPE 
              23              466 
  TGFBR2 MUTATED TGFBR2 WILD-TYPE 
              23              466 
[1] "OR1J2 MUTATION ANALYSIS"
[1] 3
  OR1J2 MUTATED OR1J2 WILD-TYPE 
             13             476 
  OR1J2 MUTATED OR1J2 WILD-TYPE 
             13             476 
[1] "SPR MUTATION ANALYSIS"
[1] 3
  SPR MUTATED SPR WILD-TYPE 
            7           482 
  SPR MUTATED SPR WILD-TYPE 
            7           482 
[1] "TRIM32 MUTATION ANALYSIS"
[1] 3
  TRIM32 MUTATED TRIM32 WILD-TYPE 
              12              477 
  TRIM32 MUTATED TRIM32 WILD-TYPE 
              12              477 
[1] "TWISTNB MUTATION ANALYSIS"
[1] 3
  TWISTNB MUTATED TWISTNB WILD-TYPE 
                9               480 
  TWISTNB MUTATED TWISTNB WILD-TYPE 
                9               480 
[1] "PKDREJ MUTATION ANALYSIS"
[1] 3
  PKDREJ MUTATED PKDREJ WILD-TYPE 
              36              453 
  PKDREJ MUTATED PKDREJ WILD-TYPE 
              36              453 
[1] "SYNE1 MUTATION ANALYSIS"
[1] 3
  SYNE1 MUTATED SYNE1 WILD-TYPE 
            142             347 
  SYNE1 MUTATED SYNE1 WILD-TYPE 
            142             347 
[1] "WNT16 MUTATION ANALYSIS"
[1] 3
  WNT16 MUTATED WNT16 WILD-TYPE 
              8             481 
  WNT16 MUTATED WNT16 WILD-TYPE 
              8             481 
[1] "ZNF189 MUTATION ANALYSIS"
[1] 3
  ZNF189 MUTATED ZNF189 WILD-TYPE 
              19              470 
  ZNF189 MUTATED ZNF189 WILD-TYPE 
              19              470 
[1] "TRRAP MUTATION ANALYSIS"
[1] 3
  TRRAP MUTATED TRRAP WILD-TYPE 
             57             432 
  TRRAP MUTATED TRRAP WILD-TYPE 
             57             432 
[1] "C14ORF43 MUTATION ANALYSIS"
[1] 3
  C14ORF43 MUTATED C14ORF43 WILD-TYPE 
                20                469 
  C14ORF43 MUTATED C14ORF43 WILD-TYPE 
                20                469 
[1] "LHCGR MUTATION ANALYSIS"
[1] 3
  LHCGR MUTATED LHCGR WILD-TYPE 
             24             465 
  LHCGR MUTATED LHCGR WILD-TYPE 
             24             465 
[1] "ZC3H13 MUTATION ANALYSIS"
[1] 3
  ZC3H13 MUTATED ZC3H13 WILD-TYPE 
              40              449 
  ZC3H13 MUTATED ZC3H13 WILD-TYPE 
              40              449 
[1] "PRKCH MUTATION ANALYSIS"
[1] 3
  PRKCH MUTATED PRKCH WILD-TYPE 
             14             475 
  PRKCH MUTATED PRKCH WILD-TYPE 
             14             475 
[1] "FNDC7 MUTATION ANALYSIS"
[1] 3
  FNDC7 MUTATED FNDC7 WILD-TYPE 
              9             480 
  FNDC7 MUTATED FNDC7 WILD-TYPE 
              9             480 
[1] "ZNF438 MUTATION ANALYSIS"
[1] 3
  ZNF438 MUTATED ZNF438 WILD-TYPE 
              13              476 
  ZNF438 MUTATED ZNF438 WILD-TYPE 
              13              476 
[1] "NRAS MUTATION ANALYSIS"
[1] 3
  NRAS MUTATED NRAS WILD-TYPE 
            44            445 
  NRAS MUTATED NRAS WILD-TYPE 
            44            445 
[1] "HIST1H1E MUTATION ANALYSIS"
[1] 3
  HIST1H1E MUTATED HIST1H1E WILD-TYPE 
                 6                483 
  HIST1H1E MUTATED HIST1H1E WILD-TYPE 
                 6                483 
[1] "ZAK MUTATION ANALYSIS"
[1] 3
  ZAK MUTATED ZAK WILD-TYPE 
            9           480 
  ZAK MUTATED ZAK WILD-TYPE 
            9           480 
[1] "SLC24A2 MUTATION ANALYSIS"
[1] 3
  SLC24A2 MUTATED SLC24A2 WILD-TYPE 
               19               470 
  SLC24A2 MUTATED SLC24A2 WILD-TYPE 
               19               470 
[1] "HORMAD1 MUTATION ANALYSIS"
[1] 3
  HORMAD1 MUTATED HORMAD1 WILD-TYPE 
               13               476 
  HORMAD1 MUTATED HORMAD1 WILD-TYPE 
               13               476 
[1] "BRAF MUTATION ANALYSIS"
[1] 3
  BRAF MUTATED BRAF WILD-TYPE 
           109            380 
  BRAF MUTATED BRAF WILD-TYPE 
           109            380 
[1] "DDX59 MUTATION ANALYSIS"
[1] 3
  DDX59 MUTATED DDX59 WILD-TYPE 
             13             476 
  DDX59 MUTATED DDX59 WILD-TYPE 
             13             476 
[1] "NLRP13 MUTATION ANALYSIS"
[1] 3
  NLRP13 MUTATED NLRP13 WILD-TYPE 
              31              458 
  NLRP13 MUTATED NLRP13 WILD-TYPE 
              31              458 
[1] "MKI67 MUTATION ANALYSIS"
[1] 3
  MKI67 MUTATED MKI67 WILD-TYPE 
             44             445 
  MKI67 MUTATED MKI67 WILD-TYPE 
             44             445 
[1] "MET MUTATION ANALYSIS"
[1] 3
  MET MUTATED MET WILD-TYPE 
           49           440 
  MET MUTATED MET WILD-TYPE 
           49           440 
[1] "PIK3C2A MUTATION ANALYSIS"
[1] 3
  PIK3C2A MUTATED PIK3C2A WILD-TYPE 
               22               467 
  PIK3C2A MUTATED PIK3C2A WILD-TYPE 
               22               467 
[1] "ERBB3 MUTATION ANALYSIS"
[1] 3
  ERBB3 MUTATED ERBB3 WILD-TYPE 
             30             459 
  ERBB3 MUTATED ERBB3 WILD-TYPE 
             30             459 
[1] "CENPF MUTATION ANALYSIS"
[1] 3
  CENPF MUTATED CENPF WILD-TYPE 
             46             443 
  CENPF MUTATED CENPF WILD-TYPE 
             46             443 
[1] "TXNDC15 MUTATION ANALYSIS"
[1] 3
  TXNDC15 MUTATED TXNDC15 WILD-TYPE 
                7               482 
  TXNDC15 MUTATED TXNDC15 WILD-TYPE 
                7               482 
[1] "TSHR MUTATION ANALYSIS"
[1] 3
  TSHR MUTATED TSHR WILD-TYPE 
            48            441 
  TSHR MUTATED TSHR WILD-TYPE 
            48            441 
[1] "KIAA1012 MUTATION ANALYSIS"
[1] 3
  KIAA1012 MUTATED KIAA1012 WILD-TYPE 
                25                464 
  KIAA1012 MUTATED KIAA1012 WILD-TYPE 
                25                464 
[1] "CHML MUTATION ANALYSIS"
[1] 3
  CHML MUTATED CHML WILD-TYPE 
            24            465 
  CHML MUTATED CHML WILD-TYPE 
            24            465 
[1] "TGFBR1 MUTATION ANALYSIS"
[1] 3
  TGFBR1 MUTATED TGFBR1 WILD-TYPE 
              17              472 
  TGFBR1 MUTATED TGFBR1 WILD-TYPE 
              17              472 
[1] "ETAA1 MUTATION ANALYSIS"
[1] 3
  ETAA1 MUTATED ETAA1 WILD-TYPE 
             18             471 
  ETAA1 MUTATED ETAA1 WILD-TYPE 
             18             471 
[1] "DEPDC5 MUTATION ANALYSIS"
[1] 3
  DEPDC5 MUTATED DEPDC5 WILD-TYPE 
              24              465 
  DEPDC5 MUTATED DEPDC5 WILD-TYPE 
              24              465 
[1] "DPCR1 MUTATION ANALYSIS"
[1] 3
  DPCR1 MUTATED DPCR1 WILD-TYPE 
             15             474 
  DPCR1 MUTATED DPCR1 WILD-TYPE 
             15             474 
[1] "NOTCH2NL MUTATION ANALYSIS"
[1] 3
  NOTCH2NL MUTATED NOTCH2NL WILD-TYPE 
                 6                483 
  NOTCH2NL MUTATED NOTCH2NL WILD-TYPE 
                 6                483 
[1] "RNF160 MUTATION ANALYSIS"
[1] 3
  RNF160 MUTATED RNF160 WILD-TYPE 
              18              471 
  RNF160 MUTATED RNF160 WILD-TYPE 
              18              471 
[1] "MYO3B MUTATION ANALYSIS"
[1] 3
  MYO3B MUTATED MYO3B WILD-TYPE 
             34             455 
  MYO3B MUTATED MYO3B WILD-TYPE 
             34             455 
[1] "TRIM23 MUTATION ANALYSIS"
[1] 3
  TRIM23 MUTATED TRIM23 WILD-TYPE 
              13              476 
  TRIM23 MUTATED TRIM23 WILD-TYPE 
              13              476 
[1] "AGFG1 MUTATION ANALYSIS"
[1] 3
  AGFG1 MUTATED AGFG1 WILD-TYPE 
             16             473 
  AGFG1 MUTATED AGFG1 WILD-TYPE 
             16             473 
[1] "KCNS3 MUTATION ANALYSIS"
[1] 3
  KCNS3 MUTATED KCNS3 WILD-TYPE 
             21             468 
  KCNS3 MUTATED KCNS3 WILD-TYPE 
             21             468 
[1] "GPR112 MUTATION ANALYSIS"
[1] 3
  GPR112 MUTATED GPR112 WILD-TYPE 
              38              451 
  GPR112 MUTATED GPR112 WILD-TYPE 
              38              451 
[1] "PTPRK MUTATION ANALYSIS"
[1] 3
  PTPRK MUTATED PTPRK WILD-TYPE 
             38             451 
  PTPRK MUTATED PTPRK WILD-TYPE 
             38             451 
[1] "DCAF6 MUTATION ANALYSIS"
[1] 3
  DCAF6 MUTATED DCAF6 WILD-TYPE 
             18             471 
  DCAF6 MUTATED DCAF6 WILD-TYPE 
             18             471 
[1] "CCDC18 MUTATION ANALYSIS"
[1] 3
  CCDC18 MUTATED CCDC18 WILD-TYPE 
              13              476 
  CCDC18 MUTATED CCDC18 WILD-TYPE 
              13              476 
[1] "RAB28 MUTATION ANALYSIS"
[1] 3
  RAB28 MUTATED RAB28 WILD-TYPE 
              7             482 
  RAB28 MUTATED RAB28 WILD-TYPE 
              7             482 
[1] "ARHGEF10 MUTATION ANALYSIS"
[1] 3
  ARHGEF10 MUTATED ARHGEF10 WILD-TYPE 
                24                465 
  ARHGEF10 MUTATED ARHGEF10 WILD-TYPE 
                24                465 
[1] "HEPACAM2 MUTATION ANALYSIS"
[1] 3
  HEPACAM2 MUTATED HEPACAM2 WILD-TYPE 
                14                475 
  HEPACAM2 MUTATED HEPACAM2 WILD-TYPE 
                14                475 
[1] "KCNH7 MUTATION ANALYSIS"
[1] 3
  KCNH7 MUTATED KCNH7 WILD-TYPE 
             38             451 
  KCNH7 MUTATED KCNH7 WILD-TYPE 
             38             451 
[1] "AGBL2 MUTATION ANALYSIS"
[1] 3
  AGBL2 MUTATED AGBL2 WILD-TYPE 
             15             474 
  AGBL2 MUTATED AGBL2 WILD-TYPE 
             15             474 
[1] "ACP6 MUTATION ANALYSIS"
[1] 3
  ACP6 MUTATED ACP6 WILD-TYPE 
             6            483 
  ACP6 MUTATED ACP6 WILD-TYPE 
             6            483 
[1] "UBC MUTATION ANALYSIS"
[1] 3
  UBC MUTATED UBC WILD-TYPE 
            5           484 
  UBC MUTATED UBC WILD-TYPE 
            5           484 
[1] "BRCA2 MUTATION ANALYSIS"
[1] 3
  BRCA2 MUTATED BRCA2 WILD-TYPE 
             58             431 
  BRCA2 MUTATED BRCA2 WILD-TYPE 
             58             431 
[1] "EZH2 MUTATION ANALYSIS"
[1] 3
  EZH2 MUTATED EZH2 WILD-TYPE 
            46            443 
  EZH2 MUTATED EZH2 WILD-TYPE 
            46            443 
[1] "OR5B2 MUTATION ANALYSIS"
[1] 3
  OR5B2 MUTATED OR5B2 WILD-TYPE 
             15             474 
  OR5B2 MUTATED OR5B2 WILD-TYPE 
             15             474 
[1] "GABRA6 MUTATION ANALYSIS"
[1] 3
  GABRA6 MUTATED GABRA6 WILD-TYPE 
              21              468 
  GABRA6 MUTATED GABRA6 WILD-TYPE 
              21              468 
[1] "LYST MUTATION ANALYSIS"
[1] 3
  LYST MUTATED LYST WILD-TYPE 
            40            449 
  LYST MUTATED LYST WILD-TYPE 
            40            449 
[1] "PPP2R1A MUTATION ANALYSIS"
[1] 3
  PPP2R1A MUTATED PPP2R1A WILD-TYPE 
               14               475 
  PPP2R1A MUTATED PPP2R1A WILD-TYPE 
               14               475 
[1] "NUP54 MUTATION ANALYSIS"
[1] 3
  NUP54 MUTATED NUP54 WILD-TYPE 
             10             479 
  NUP54 MUTATED NUP54 WILD-TYPE 
             10             479 
[1] "OR11G2 MUTATION ANALYSIS"
[1] 3
  OR11G2 MUTATED OR11G2 WILD-TYPE 
               6              483 
  OR11G2 MUTATED OR11G2 WILD-TYPE 
               6              483 
[1] "FUBP3 MUTATION ANALYSIS"
[1] 3
  FUBP3 MUTATED FUBP3 WILD-TYPE 
              9             480 
  FUBP3 MUTATED FUBP3 WILD-TYPE 
              9             480 
[1] "TOB1 MUTATION ANALYSIS"
[1] 3
  TOB1 MUTATED TOB1 WILD-TYPE 
             8            481 
  TOB1 MUTATED TOB1 WILD-TYPE 
             8            481 
[1] "DAXX MUTATION ANALYSIS"
[1] 3
  DAXX MUTATED DAXX WILD-TYPE 
            16            473 
  DAXX MUTATED DAXX WILD-TYPE 
            16            473 
[1] "MARK1 MUTATION ANALYSIS"
[1] 3
  MARK1 MUTATED MARK1 WILD-TYPE 
             29             460 
  MARK1 MUTATED MARK1 WILD-TYPE 
             29             460 
[1] "USP25 MUTATION ANALYSIS"
[1] 3
  USP25 MUTATED USP25 WILD-TYPE 
             23             466 
  USP25 MUTATED USP25 WILD-TYPE 
             23             466 
[1] "TOPORS MUTATION ANALYSIS"
[1] 3
  TOPORS MUTATED TOPORS WILD-TYPE 
              22              467 
  TOPORS MUTATED TOPORS WILD-TYPE 
              22              467 
[1] "ENPEP MUTATION ANALYSIS"
[1] 3
  ENPEP MUTATED ENPEP WILD-TYPE 
             23             466 
  ENPEP MUTATED ENPEP WILD-TYPE 
             23             466 
[1] "RING1 MUTATION ANALYSIS"
[1] 3
  RING1 MUTATED RING1 WILD-TYPE 
             11             478 
  RING1 MUTATED RING1 WILD-TYPE 
             11             478 
[1] "NGEF MUTATION ANALYSIS"
[1] 3
  NGEF MUTATED NGEF WILD-TYPE 
            18            471 
  NGEF MUTATED NGEF WILD-TYPE 
            18            471 
[1] "MMAA MUTATION ANALYSIS"
[1] 3
  MMAA MUTATED MMAA WILD-TYPE 
            12            477 
  MMAA MUTATED MMAA WILD-TYPE 
            12            477 
[1] "ZNF630 MUTATION ANALYSIS"
[1] 3
  ZNF630 MUTATED ZNF630 WILD-TYPE 
               9              480 
  ZNF630 MUTATED ZNF630 WILD-TYPE 
               9              480 
[1] "KIR2DL3 MUTATION ANALYSIS"
[1] 3
  KIR2DL3 MUTATED KIR2DL3 WILD-TYPE 
               19               470 
  KIR2DL3 MUTATED KIR2DL3 WILD-TYPE 
               19               470 
[1] "SLC7A6 MUTATION ANALYSIS"
[1] 3
  SLC7A6 MUTATED SLC7A6 WILD-TYPE 
               7              482 
  SLC7A6 MUTATED SLC7A6 WILD-TYPE 
               7              482 
[1] "JMJD1C MUTATION ANALYSIS"
[1] 3
  JMJD1C MUTATED JMJD1C WILD-TYPE 
              27              462 
  JMJD1C MUTATED JMJD1C WILD-TYPE 
              27              462 
[1] "C6ORF170 MUTATION ANALYSIS"
[1] 3
  C6ORF170 MUTATED C6ORF170 WILD-TYPE 
                23                466 
  C6ORF170 MUTATED C6ORF170 WILD-TYPE 
                23                466 
[1] "MSH2 MUTATION ANALYSIS"
[1] 3
  MSH2 MUTATED MSH2 WILD-TYPE 
            37            452 
  MSH2 MUTATED MSH2 WILD-TYPE 
            37            452 
[1] "EP300 MUTATION ANALYSIS"
[1] 3
  EP300 MUTATED EP300 WILD-TYPE 
             46             443 
  EP300 MUTATED EP300 WILD-TYPE 
             46             443 
[1] "SKIL MUTATION ANALYSIS"
[1] 3
  SKIL MUTATED SKIL WILD-TYPE 
             9            480 
  SKIL MUTATED SKIL WILD-TYPE 
             9            480 
[1] "TIAL1 MUTATION ANALYSIS"
[1] 3
  TIAL1 MUTATED TIAL1 WILD-TYPE 
             13             476 
  TIAL1 MUTATED TIAL1 WILD-TYPE 
             13             476 
[1] "OR2T33 MUTATION ANALYSIS"
[1] 3
  OR2T33 MUTATED OR2T33 WILD-TYPE 
              18              471 
  OR2T33 MUTATED OR2T33 WILD-TYPE 
              18              471 
[1] "SMC2 MUTATION ANALYSIS"
[1] 3
  SMC2 MUTATED SMC2 WILD-TYPE 
            29            460 
  SMC2 MUTATED SMC2 WILD-TYPE 
            29            460 
[1] "C14ORF159 MUTATION ANALYSIS"
[1] 3
  C14ORF159 MUTATED C14ORF159 WILD-TYPE 
                 10                 479 
  C14ORF159 MUTATED C14ORF159 WILD-TYPE 
                 10                 479 
[1] "IQGAP2 MUTATION ANALYSIS"
[1] 3
  IQGAP2 MUTATED IQGAP2 WILD-TYPE 
              27              462 
  IQGAP2 MUTATED IQGAP2 WILD-TYPE 
              27              462 
[1] "DNAH11 MUTATION ANALYSIS"
[1] 3
  DNAH11 MUTATED DNAH11 WILD-TYPE 
              75              414 
  DNAH11 MUTATED DNAH11 WILD-TYPE 
              75              414 
[1] "EPHA7 MUTATION ANALYSIS"
[1] 3
  EPHA7 MUTATED EPHA7 WILD-TYPE 
             42             447 
  EPHA7 MUTATED EPHA7 WILD-TYPE 
             42             447 
[1] "DNAH8 MUTATION ANALYSIS"
[1] 3
  DNAH8 MUTATED DNAH8 WILD-TYPE 
             67             422 
  DNAH8 MUTATED DNAH8 WILD-TYPE 
             67             422 
[1] "MACF1 MUTATION ANALYSIS"
[1] 3
  MACF1 MUTATED MACF1 WILD-TYPE 
             66             423 
  MACF1 MUTATED MACF1 WILD-TYPE 
             66             423 
[1] "IL1RAPL1 MUTATION ANALYSIS"
[1] 3
  IL1RAPL1 MUTATED IL1RAPL1 WILD-TYPE 
                28                461 
  IL1RAPL1 MUTATED IL1RAPL1 WILD-TYPE 
                28                461 
[1] "WDR78 MUTATION ANALYSIS"
[1] 3
  WDR78 MUTATED WDR78 WILD-TYPE 
             16             473 
  WDR78 MUTATED WDR78 WILD-TYPE 
             16             473 
[1] "TRIM13 MUTATION ANALYSIS"
[1] 3
  TRIM13 MUTATED TRIM13 WILD-TYPE 
               8              481 
  TRIM13 MUTATED TRIM13 WILD-TYPE 
               8              481 
[1] "OR1I1 MUTATION ANALYSIS"
[1] 3
  OR1I1 MUTATED OR1I1 WILD-TYPE 
             11             478 
  OR1I1 MUTATED OR1I1 WILD-TYPE 
             11             478 
[1] "ACOT9 MUTATION ANALYSIS"
[1] 3
  ACOT9 MUTATED ACOT9 WILD-TYPE 
              5             484 
  ACOT9 MUTATED ACOT9 WILD-TYPE 
              5             484 
[1] "GPX6 MUTATION ANALYSIS"
[1] 3
  GPX6 MUTATED GPX6 WILD-TYPE 
            10            479 
  GPX6 MUTATED GPX6 WILD-TYPE 
            10            479 
[1] "KIAA1797 MUTATION ANALYSIS"
[1] 3
  KIAA1797 MUTATED KIAA1797 WILD-TYPE 
                24                465 
  KIAA1797 MUTATED KIAA1797 WILD-TYPE 
                24                465 
[1] "ODZ1 MUTATION ANALYSIS"
[1] 3
  ODZ1 MUTATED ODZ1 WILD-TYPE 
            77            412 
  ODZ1 MUTATED ODZ1 WILD-TYPE 
            77            412 
[1] "KPNA5 MUTATION ANALYSIS"
[1] 3
  KPNA5 MUTATED KPNA5 WILD-TYPE 
             11             478 
  KPNA5 MUTATED KPNA5 WILD-TYPE 
             11             478 
[1] "DMRTB1 MUTATION ANALYSIS"
[1] 3
  DMRTB1 MUTATED DMRTB1 WILD-TYPE 
               6              483 
  DMRTB1 MUTATED DMRTB1 WILD-TYPE 
               6              483 
[1] "NUP160 MUTATION ANALYSIS"
[1] 3
  NUP160 MUTATED NUP160 WILD-TYPE 
              11              478 
  NUP160 MUTATED NUP160 WILD-TYPE 
              11              478 
[1] "GRIA4 MUTATION ANALYSIS"
[1] 3
  GRIA4 MUTATED GRIA4 WILD-TYPE 
             37             452 
  GRIA4 MUTATED GRIA4 WILD-TYPE 
             37             452 
[1] "FBLN5 MUTATION ANALYSIS"
[1] 3
  FBLN5 MUTATED FBLN5 WILD-TYPE 
             10             479 
  FBLN5 MUTATED FBLN5 WILD-TYPE 
             10             479 
[1] "FBXO34 MUTATION ANALYSIS"
[1] 3
  FBXO34 MUTATED FBXO34 WILD-TYPE 
              12              477 
  FBXO34 MUTATED FBXO34 WILD-TYPE 
              12              477 
[1] "BRCA1 MUTATION ANALYSIS"
[1] 3
  BRCA1 MUTATED BRCA1 WILD-TYPE 
             29             460 
  BRCA1 MUTATED BRCA1 WILD-TYPE 
             29             460 
[1] "INSRR MUTATION ANALYSIS"
[1] 3
  INSRR MUTATED INSRR WILD-TYPE 
             32             457 
  INSRR MUTATED INSRR WILD-TYPE 
             32             457 
[1] "FBN2 MUTATION ANALYSIS"
[1] 3
  FBN2 MUTATED FBN2 WILD-TYPE 
            46            443 
  FBN2 MUTATED FBN2 WILD-TYPE 
            46            443 
[1] "STAB2 MUTATION ANALYSIS"
[1] 3
  STAB2 MUTATED STAB2 WILD-TYPE 
             36             453 
  STAB2 MUTATED STAB2 WILD-TYPE 
             36             453 
[1] "ATP6V1A MUTATION ANALYSIS"
[1] 3
  ATP6V1A MUTATED ATP6V1A WILD-TYPE 
               11               478 
  ATP6V1A MUTATED ATP6V1A WILD-TYPE 
               11               478 
[1] "DUSP19 MUTATION ANALYSIS"
[1] 3
  DUSP19 MUTATED DUSP19 WILD-TYPE 
              12              477 
  DUSP19 MUTATED DUSP19 WILD-TYPE 
              12              477 
[1] "MRPS5 MUTATION ANALYSIS"
[1] 3
  MRPS5 MUTATED MRPS5 WILD-TYPE 
             12             477 
  MRPS5 MUTATED MRPS5 WILD-TYPE 
             12             477 
[1] "UIMC1 MUTATION ANALYSIS"
[1] 3
  UIMC1 MUTATED UIMC1 WILD-TYPE 
              9             480 
  UIMC1 MUTATED UIMC1 WILD-TYPE 
              9             480 
[1] "LRP2 MUTATION ANALYSIS"
[1] 3
  LRP2 MUTATED LRP2 WILD-TYPE 
            87            402 
  LRP2 MUTATED LRP2 WILD-TYPE 
            87            402 
[1] "FUT10 MUTATION ANALYSIS"
[1] 3
  FUT10 MUTATED FUT10 WILD-TYPE 
              7             482 
  FUT10 MUTATED FUT10 WILD-TYPE 
              7             482 
[1] "GAB2 MUTATION ANALYSIS"
[1] 3
  GAB2 MUTATED GAB2 WILD-TYPE 
            10            479 
  GAB2 MUTATED GAB2 WILD-TYPE 
            10            479 
[1] "DSG1 MUTATION ANALYSIS"
[1] 3
  DSG1 MUTATED DSG1 WILD-TYPE 
            21            468 
  DSG1 MUTATED DSG1 WILD-TYPE 
            21            468 
[1] "DKK2 MUTATION ANALYSIS"
[1] 3
  DKK2 MUTATED DKK2 WILD-TYPE 
            26            463 
  DKK2 MUTATED DKK2 WILD-TYPE 
            26            463 
[1] "COX15 MUTATION ANALYSIS"
[1] 3
  COX15 MUTATED COX15 WILD-TYPE 
              7             482 
  COX15 MUTATED COX15 WILD-TYPE 
              7             482 
[1] "JAK2 MUTATION ANALYSIS"
[1] 3
  JAK2 MUTATED JAK2 WILD-TYPE 
            46            443 
  JAK2 MUTATED JAK2 WILD-TYPE 
            46            443 
[1] "HIVEP2 MUTATION ANALYSIS"
[1] 3
  HIVEP2 MUTATED HIVEP2 WILD-TYPE 
              24              465 
  HIVEP2 MUTATED HIVEP2 WILD-TYPE 
              24              465 
[1] "RELN MUTATION ANALYSIS"
[1] 3
  RELN MUTATED RELN WILD-TYPE 
            71            418 
  RELN MUTATED RELN WILD-TYPE 
            71            418 
[1] "FLG2 MUTATION ANALYSIS"
[1] 3
  FLG2 MUTATED FLG2 WILD-TYPE 
            33            456 
  FLG2 MUTATED FLG2 WILD-TYPE 
            33            456 
[1] "HMCN1 MUTATION ANALYSIS"
[1] 3
  HMCN1 MUTATED HMCN1 WILD-TYPE 
             82             407 
  HMCN1 MUTATED HMCN1 WILD-TYPE 
             82             407 
[1] "PIK3CA MUTATION ANALYSIS"
[1] 3
  PIK3CA MUTATED PIK3CA WILD-TYPE 
             211              278 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
             211              278 
[1] "PRKD1 MUTATION ANALYSIS"
[1] 3
  PRKD1 MUTATED PRKD1 WILD-TYPE 
             29             460 
  PRKD1 MUTATED PRKD1 WILD-TYPE 
             29             460 
[1] "ADAMTS19 MUTATION ANALYSIS"
[1] 3
  ADAMTS19 MUTATED ADAMTS19 WILD-TYPE 
                25                464 
  ADAMTS19 MUTATED ADAMTS19 WILD-TYPE 
                25                464 
[1] "CLVS2 MUTATION ANALYSIS"
[1] 3
  CLVS2 MUTATED CLVS2 WILD-TYPE 
             10             479 
  CLVS2 MUTATED CLVS2 WILD-TYPE 
             10             479 
[1] "GTF3C3 MUTATION ANALYSIS"
[1] 3
  GTF3C3 MUTATED GTF3C3 WILD-TYPE 
              18              471 
  GTF3C3 MUTATED GTF3C3 WILD-TYPE 
              18              471 
[1] "BAI3 MUTATION ANALYSIS"
[1] 3
  BAI3 MUTATED BAI3 WILD-TYPE 
            54            435 
  BAI3 MUTATED BAI3 WILD-TYPE 
            54            435 
[1] "AURKA MUTATION ANALYSIS"
[1] 3
  AURKA MUTATED AURKA WILD-TYPE 
              7             482 
  AURKA MUTATED AURKA WILD-TYPE 
              7             482 
[1] "RBM7 MUTATION ANALYSIS"
[1] 3
  RBM7 MUTATED RBM7 WILD-TYPE 
            11            478 
  RBM7 MUTATED RBM7 WILD-TYPE 
            11            478 
[1] "CNTNAP5 MUTATION ANALYSIS"
[1] 3
  CNTNAP5 MUTATED CNTNAP5 WILD-TYPE 
               47               442 
  CNTNAP5 MUTATED CNTNAP5 WILD-TYPE 
               47               442 
[1] "TMPRSS15 MUTATION ANALYSIS"
[1] 3
  TMPRSS15 MUTATED TMPRSS15 WILD-TYPE 
                26                463 
  TMPRSS15 MUTATED TMPRSS15 WILD-TYPE 
                26                463 
[1] "EGFR MUTATION ANALYSIS"
[1] 3
  EGFR MUTATED EGFR WILD-TYPE 
            84            405 
  EGFR MUTATED EGFR WILD-TYPE 
            84            405 
[1] "CTBP2 MUTATION ANALYSIS"
[1] 3
  CTBP2 MUTATED CTBP2 WILD-TYPE 
              7             482 
  CTBP2 MUTATED CTBP2 WILD-TYPE 
              7             482 
[1] "APOB MUTATION ANALYSIS"
[1] 3
  APOB MUTATED APOB WILD-TYPE 
            67            422 
  APOB MUTATED APOB WILD-TYPE 
            67            422 
[1] "EPHA3 MUTATION ANALYSIS"
[1] 3
  EPHA3 MUTATED EPHA3 WILD-TYPE 
             65             424 
  EPHA3 MUTATED EPHA3 WILD-TYPE 
             65             424 
[1] "PTPN11 MUTATION ANALYSIS"
[1] 3
  PTPN11 MUTATED PTPN11 WILD-TYPE 
              40              449 
  PTPN11 MUTATED PTPN11 WILD-TYPE 
              40              449 
[1] "KIAA1409 MUTATION ANALYSIS"
[1] 3
  KIAA1409 MUTATED KIAA1409 WILD-TYPE 
                43                446 
  KIAA1409 MUTATED KIAA1409 WILD-TYPE 
                43                446 
[1] "DOCK1 MUTATION ANALYSIS"
[1] 3
  DOCK1 MUTATED DOCK1 WILD-TYPE 
             27             462 
  DOCK1 MUTATED DOCK1 WILD-TYPE 
             27             462 
[1] "GRM8 MUTATION ANALYSIS"
[1] 3
  GRM8 MUTATED GRM8 WILD-TYPE 
            22            467 
  GRM8 MUTATED GRM8 WILD-TYPE 
            22            467 
[1] "NTRK3 MUTATION ANALYSIS"
[1] 3
  NTRK3 MUTATED NTRK3 WILD-TYPE 
             31             458 
  NTRK3 MUTATED NTRK3 WILD-TYPE 
             31             458 
[1] "ANKRD30A MUTATION ANALYSIS"
[1] 3
  ANKRD30A MUTATED ANKRD30A WILD-TYPE 
                33                456 
  ANKRD30A MUTATED ANKRD30A WILD-TYPE 
                33                456 
[1] "MYH1 MUTATION ANALYSIS"
[1] 3
  MYH1 MUTATED MYH1 WILD-TYPE 
            36            453 
  MYH1 MUTATED MYH1 WILD-TYPE 
            36            453 
[1] "PHF3 MUTATION ANALYSIS"
[1] 3
  PHF3 MUTATED PHF3 WILD-TYPE 
            26            463 
  PHF3 MUTATED PHF3 WILD-TYPE 
            26            463 
[1] "PLCB2 MUTATION ANALYSIS"
[1] 3
  PLCB2 MUTATED PLCB2 WILD-TYPE 
             10             479 
  PLCB2 MUTATED PLCB2 WILD-TYPE 
             10             479 
[1] "PTPRD MUTATION ANALYSIS"
[1] 3
  PTPRD MUTATED PTPRD WILD-TYPE 
             38             451 
  PTPRD MUTATED PTPRD WILD-TYPE 
             38             451 
[1] "CSMD3 MUTATION ANALYSIS"
[1] 3
  CSMD3 MUTATED CSMD3 WILD-TYPE 
            108             381 
  CSMD3 MUTATED CSMD3 WILD-TYPE 
            108             381 
[1] "USH2A MUTATION ANALYSIS"
[1] 3
  USH2A MUTATED USH2A WILD-TYPE 
             88             401 
  USH2A MUTATED USH2A WILD-TYPE 
             88             401 
[1] "MYEOV MUTATION ANALYSIS"
[1] 3
  MYEOV MUTATED MYEOV WILD-TYPE 
              7             482 
  MYEOV MUTATED MYEOV WILD-TYPE 
              7             482 
[1] "BRE MUTATION ANALYSIS"
[1] 3
  BRE MUTATED BRE WILD-TYPE 
           12           477 
  BRE MUTATED BRE WILD-TYPE 
           12           477 
[1] "SCN3A MUTATION ANALYSIS"
[1] 3
  SCN3A MUTATED SCN3A WILD-TYPE 
             49             440 
  SCN3A MUTATED SCN3A WILD-TYPE 
             49             440 
[1] "FKTN MUTATION ANALYSIS"
[1] 3
  FKTN MUTATED FKTN WILD-TYPE 
             9            480 
  FKTN MUTATED FKTN WILD-TYPE 
             9            480 
[1] "MIER1 MUTATION ANALYSIS"
[1] 3
  MIER1 MUTATED MIER1 WILD-TYPE 
              8             481 
  MIER1 MUTATED MIER1 WILD-TYPE 
              8             481 
[1] "KIRREL2 MUTATION ANALYSIS"
[1] 3
  KIRREL2 MUTATED KIRREL2 WILD-TYPE 
               15               474 
  KIRREL2 MUTATED KIRREL2 WILD-TYPE 
               15               474 
[1] "PAK3 MUTATION ANALYSIS"
[1] 3
  PAK3 MUTATED PAK3 WILD-TYPE 
            20            469 
  PAK3 MUTATED PAK3 WILD-TYPE 
            20            469 
[1] "RAF1 MUTATION ANALYSIS"
[1] 3
  RAF1 MUTATED RAF1 WILD-TYPE 
            15            474 
  RAF1 MUTATED RAF1 WILD-TYPE 
            15            474 
[1] "ASNSD1 MUTATION ANALYSIS"
[1] 3
  ASNSD1 MUTATED ASNSD1 WILD-TYPE 
              10              479 
  ASNSD1 MUTATED ASNSD1 WILD-TYPE 
              10              479 
[1] "ABCC4 MUTATION ANALYSIS"
[1] 3
  ABCC4 MUTATED ABCC4 WILD-TYPE 
             20             469 
  ABCC4 MUTATED ABCC4 WILD-TYPE 
             20             469 
[1] "CYLC1 MUTATION ANALYSIS"
[1] 3
  CYLC1 MUTATED CYLC1 WILD-TYPE 
             34             455 
  CYLC1 MUTATED CYLC1 WILD-TYPE 
             34             455 
[1] "RNF111 MUTATION ANALYSIS"
[1] 3
  RNF111 MUTATED RNF111 WILD-TYPE 
              16              473 
  RNF111 MUTATED RNF111 WILD-TYPE 
              16              473 
[1] "CLIP4 MUTATION ANALYSIS"
[1] 3
  CLIP4 MUTATED CLIP4 WILD-TYPE 
             14             475 
  CLIP4 MUTATED CLIP4 WILD-TYPE 
             14             475 
[1] "SULT6B1 MUTATION ANALYSIS"
[1] 3
  SULT6B1 MUTATED SULT6B1 WILD-TYPE 
               12               477 
  SULT6B1 MUTATED SULT6B1 WILD-TYPE 
               12               477 
[1] "PLA2G4E MUTATION ANALYSIS"
[1] 3
  PLA2G4E MUTATED PLA2G4E WILD-TYPE 
               11               478 
  PLA2G4E MUTATED PLA2G4E WILD-TYPE 
               11               478 
[1] "CLCNKA MUTATION ANALYSIS"
[1] 3
  CLCNKA MUTATED CLCNKA WILD-TYPE 
              10              479 
  CLCNKA MUTATED CLCNKA WILD-TYPE 
              10              479 
[1] "ERCC6 MUTATION ANALYSIS"
[1] 3
  ERCC6 MUTATED ERCC6 WILD-TYPE 
             33             456 
  ERCC6 MUTATED ERCC6 WILD-TYPE 
             33             456 
[1] "ALG2 MUTATION ANALYSIS"
[1] 3
  ALG2 MUTATED ALG2 WILD-TYPE 
             8            481 
  ALG2 MUTATED ALG2 WILD-TYPE 
             8            481 
[1] "C9ORF131 MUTATION ANALYSIS"
[1] 3
  C9ORF131 MUTATED C9ORF131 WILD-TYPE 
                13                476 
  C9ORF131 MUTATED C9ORF131 WILD-TYPE 
                13                476 
[1] "EXT1 MUTATION ANALYSIS"
[1] 3
  EXT1 MUTATED EXT1 WILD-TYPE 
            20            469 
  EXT1 MUTATED EXT1 WILD-TYPE 
            20            469 
[1] "IGFBP7 MUTATION ANALYSIS"
[1] 3
  IGFBP7 MUTATED IGFBP7 WILD-TYPE 
               5              484 
  IGFBP7 MUTATED IGFBP7 WILD-TYPE 
               5              484 
[1] "C6ORF89 MUTATION ANALYSIS"
[1] 3
  C6ORF89 MUTATED C6ORF89 WILD-TYPE 
                7               482 
  C6ORF89 MUTATED C6ORF89 WILD-TYPE 
                7               482 
[1] "ART5 MUTATION ANALYSIS"
[1] 3
  ART5 MUTATED ART5 WILD-TYPE 
            10            479 
  ART5 MUTATED ART5 WILD-TYPE 
            10            479 
[1] "CUL2 MUTATION ANALYSIS"
[1] 3
  CUL2 MUTATED CUL2 WILD-TYPE 
            15            474 
  CUL2 MUTATED CUL2 WILD-TYPE 
            15            474 
[1] "CDC6 MUTATION ANALYSIS"
[1] 3
  CDC6 MUTATED CDC6 WILD-TYPE 
            10            479 
  CDC6 MUTATED CDC6 WILD-TYPE 
            10            479 
[1] "SOX7 MUTATION ANALYSIS"
[1] 3
  SOX7 MUTATED SOX7 WILD-TYPE 
            12            477 
  SOX7 MUTATED SOX7 WILD-TYPE 
            12            477 
[1] "ZNF644 MUTATION ANALYSIS"
[1] 3
  ZNF644 MUTATED ZNF644 WILD-TYPE 
              21              468 
  ZNF644 MUTATED ZNF644 WILD-TYPE 
              21              468 
[1] "XPOT MUTATION ANALYSIS"
[1] 3
  XPOT MUTATED XPOT WILD-TYPE 
            11            478 
  XPOT MUTATED XPOT WILD-TYPE 
            11            478 
[1] "TIFA MUTATION ANALYSIS"
[1] 3
  TIFA MUTATED TIFA WILD-TYPE 
             6            483 
  TIFA MUTATED TIFA WILD-TYPE 
             6            483 
[1] "STK38L MUTATION ANALYSIS"
[1] 3
  STK38L MUTATED STK38L WILD-TYPE 
              10              479 
  STK38L MUTATED STK38L WILD-TYPE 
              10              479 
[1] "SMARCA4 MUTATION ANALYSIS"
[1] 3
  SMARCA4 MUTATED SMARCA4 WILD-TYPE 
               33               456 
  SMARCA4 MUTATED SMARCA4 WILD-TYPE 
               33               456 
[1] "ZNF691 MUTATION ANALYSIS"
[1] 3
  ZNF691 MUTATED ZNF691 WILD-TYPE 
               8              481 
  ZNF691 MUTATED ZNF691 WILD-TYPE 
               8              481 
[1] "UBR4 MUTATION ANALYSIS"
[1] 3
  UBR4 MUTATED UBR4 WILD-TYPE 
            47            442 
  UBR4 MUTATED UBR4 WILD-TYPE 
            47            442 
[1] "LPCAT3 MUTATION ANALYSIS"
[1] 3
  LPCAT3 MUTATED LPCAT3 WILD-TYPE 
               5              484 
  LPCAT3 MUTATED LPCAT3 WILD-TYPE 
               5              484 
[1] "STX7 MUTATION ANALYSIS"
[1] 3
  STX7 MUTATED STX7 WILD-TYPE 
             5            484 
  STX7 MUTATED STX7 WILD-TYPE 
             5            484 
[1] "SLC2A3 MUTATION ANALYSIS"
[1] 3
  SLC2A3 MUTATED SLC2A3 WILD-TYPE 
              12              477 
  SLC2A3 MUTATED SLC2A3 WILD-TYPE 
              12              477 
[1] "HDAC1 MUTATION ANALYSIS"
[1] 3
  HDAC1 MUTATED HDAC1 WILD-TYPE 
              5             484 
  HDAC1 MUTATED HDAC1 WILD-TYPE 
              5             484 
[1] "RUFY1 MUTATION ANALYSIS"
[1] 3
  RUFY1 MUTATED RUFY1 WILD-TYPE 
             14             475 
  RUFY1 MUTATED RUFY1 WILD-TYPE 
             14             475 
[1] "PSD MUTATION ANALYSIS"
[1] 3
  PSD MUTATED PSD WILD-TYPE 
           17           472 
  PSD MUTATED PSD WILD-TYPE 
           17           472 
[1] "CDC5L MUTATION ANALYSIS"
[1] 3
  CDC5L MUTATED CDC5L WILD-TYPE 
             13             476 
  CDC5L MUTATED CDC5L WILD-TYPE 
             13             476 
[1] "ARID2 MUTATION ANALYSIS"
[1] 3
  ARID2 MUTATED ARID2 WILD-TYPE 
             37             452 
  ARID2 MUTATED ARID2 WILD-TYPE 
             37             452 
[1] "SCLT1 MUTATION ANALYSIS"
[1] 3
  SCLT1 MUTATED SCLT1 WILD-TYPE 
             19             470 
  SCLT1 MUTATED SCLT1 WILD-TYPE 
             19             470 
[1] "ZFC3H1 MUTATION ANALYSIS"
[1] 3
  ZFC3H1 MUTATED ZFC3H1 WILD-TYPE 
              21              468 
  ZFC3H1 MUTATED ZFC3H1 WILD-TYPE 
              21              468 
[1] "OR2M3 MUTATION ANALYSIS"
[1] 3
  OR2M3 MUTATED OR2M3 WILD-TYPE 
             17             472 
  OR2M3 MUTATED OR2M3 WILD-TYPE 
             17             472 
[1] "RNF145 MUTATION ANALYSIS"
[1] 3
  RNF145 MUTATED RNF145 WILD-TYPE 
              17              472 
  RNF145 MUTATED RNF145 WILD-TYPE 
              17              472 
[1] "TMEM169 MUTATION ANALYSIS"
[1] 3
  TMEM169 MUTATED TMEM169 WILD-TYPE 
               14               475 
  TMEM169 MUTATED TMEM169 WILD-TYPE 
               14               475 
[1] "NOX5 MUTATION ANALYSIS"
[1] 3
  NOX5 MUTATED NOX5 WILD-TYPE 
             5            484 
  NOX5 MUTATED NOX5 WILD-TYPE 
             5            484 
[1] "HAS2 MUTATION ANALYSIS"
[1] 3
  HAS2 MUTATED HAS2 WILD-TYPE 
            10            479 
  HAS2 MUTATED HAS2 WILD-TYPE 
            10            479 
[1] "INSM2 MUTATION ANALYSIS"
[1] 3
  INSM2 MUTATED INSM2 WILD-TYPE 
             11             478 
  INSM2 MUTATED INSM2 WILD-TYPE 
             11             478 
[1] "SCLY MUTATION ANALYSIS"
[1] 3
  SCLY MUTATED SCLY WILD-TYPE 
            12            477 
  SCLY MUTATED SCLY WILD-TYPE 
            12            477 
[1] "CDK17 MUTATION ANALYSIS"
[1] 3
  CDK17 MUTATED CDK17 WILD-TYPE 
             11             478 
  CDK17 MUTATED CDK17 WILD-TYPE 
             11             478 
[1] "GOLPH3L MUTATION ANALYSIS"
[1] 3
  GOLPH3L MUTATED GOLPH3L WILD-TYPE 
                6               483 
  GOLPH3L MUTATED GOLPH3L WILD-TYPE 
                6               483 
[1] "GGTLC2 MUTATION ANALYSIS"
[1] 3
  GGTLC2 MUTATED GGTLC2 WILD-TYPE 
               7              482 
  GGTLC2 MUTATED GGTLC2 WILD-TYPE 
               7              482 
[1] "SYNCRIP MUTATION ANALYSIS"
[1] 3
  SYNCRIP MUTATED SYNCRIP WILD-TYPE 
               12               477 
  SYNCRIP MUTATED SYNCRIP WILD-TYPE 
               12               477 
[1] "IFITM3 MUTATION ANALYSIS"
[1] 3
  IFITM3 MUTATED IFITM3 WILD-TYPE 
               8              481 
  IFITM3 MUTATED IFITM3 WILD-TYPE 
               8              481 
[1] "SMG1 MUTATION ANALYSIS"
[1] 3
  SMG1 MUTATED SMG1 WILD-TYPE 
            27            462 
  SMG1 MUTATED SMG1 WILD-TYPE 
            27            462 
[1] "RBL2 MUTATION ANALYSIS"
[1] 3
  RBL2 MUTATED RBL2 WILD-TYPE 
            23            466 
  RBL2 MUTATED RBL2 WILD-TYPE 
            23            466 
[1] "CASC1 MUTATION ANALYSIS"
[1] 3
  CASC1 MUTATED CASC1 WILD-TYPE 
             14             475 
  CASC1 MUTATED CASC1 WILD-TYPE 
             14             475 
[1] "LNX2 MUTATION ANALYSIS"
[1] 3
  LNX2 MUTATED LNX2 WILD-TYPE 
            18            471 
  LNX2 MUTATED LNX2 WILD-TYPE 
            18            471 
[1] "N4BP2 MUTATION ANALYSIS"
[1] 3
  N4BP2 MUTATED N4BP2 WILD-TYPE 
             27             462 
  N4BP2 MUTATED N4BP2 WILD-TYPE 
             27             462 
[1] "KRT14 MUTATION ANALYSIS"
[1] 3
  KRT14 MUTATED KRT14 WILD-TYPE 
              9             480 
  KRT14 MUTATED KRT14 WILD-TYPE 
              9             480 
[1] "LNPEP MUTATION ANALYSIS"
[1] 3
  LNPEP MUTATED LNPEP WILD-TYPE 
             19             470 
  LNPEP MUTATED LNPEP WILD-TYPE 
             19             470 
[1] "SP110 MUTATION ANALYSIS"
[1] 3
  SP110 MUTATED SP110 WILD-TYPE 
             10             479 
  SP110 MUTATED SP110 WILD-TYPE 
             10             479 
[1] "C5ORF34 MUTATION ANALYSIS"
[1] 3
  C5ORF34 MUTATED C5ORF34 WILD-TYPE 
               12               477 
  C5ORF34 MUTATED C5ORF34 WILD-TYPE 
               12               477 
[1] "ADORA3 MUTATION ANALYSIS"
[1] 3
  ADORA3 MUTATED ADORA3 WILD-TYPE 
              15              474 
  ADORA3 MUTATED ADORA3 WILD-TYPE 
              15              474 
[1] "MAP2K4 MUTATION ANALYSIS"
[1] 3
  MAP2K4 MUTATED MAP2K4 WILD-TYPE 
              34              455 
  MAP2K4 MUTATED MAP2K4 WILD-TYPE 
              34              455 
[1] "OVGP1 MUTATION ANALYSIS"
[1] 3
  OVGP1 MUTATED OVGP1 WILD-TYPE 
             17             472 
  OVGP1 MUTATED OVGP1 WILD-TYPE 
             17             472 
[1] "GOLGB1 MUTATION ANALYSIS"
[1] 3
  GOLGB1 MUTATED GOLGB1 WILD-TYPE 
              42              447 
  GOLGB1 MUTATED GOLGB1 WILD-TYPE 
              42              447 
[1] "SYT1 MUTATION ANALYSIS"
[1] 3
  SYT1 MUTATED SYT1 WILD-TYPE 
            13            476 
  SYT1 MUTATED SYT1 WILD-TYPE 
            13            476 
[1] "UVRAG MUTATION ANALYSIS"
[1] 3
  UVRAG MUTATED UVRAG WILD-TYPE 
             11             478 
  UVRAG MUTATED UVRAG WILD-TYPE 
             11             478 
[1] "CLVS1 MUTATION ANALYSIS"
[1] 3
  CLVS1 MUTATED CLVS1 WILD-TYPE 
             12             477 
  CLVS1 MUTATED CLVS1 WILD-TYPE 
             12             477 
[1] "TTF1 MUTATION ANALYSIS"
[1] 3
  TTF1 MUTATED TTF1 WILD-TYPE 
            11            478 
  TTF1 MUTATED TTF1 WILD-TYPE 
            11            478 
[1] "FGFR1 MUTATION ANALYSIS"
[1] 3
  FGFR1 MUTATED FGFR1 WILD-TYPE 
             19             470 
  FGFR1 MUTATED FGFR1 WILD-TYPE 
             19             470 
[1] "OSMR MUTATION ANALYSIS"
[1] 3
  OSMR MUTATED OSMR WILD-TYPE 
            22            467 
  OSMR MUTATED OSMR WILD-TYPE 
            22            467 
[1] "LASS3 MUTATION ANALYSIS"
[1] 3
  LASS3 MUTATED LASS3 WILD-TYPE 
             17             472 
  LASS3 MUTATED LASS3 WILD-TYPE 
             17             472 
[1] "HGS MUTATION ANALYSIS"
[1] 3
  HGS MUTATED HGS WILD-TYPE 
           10           479 
  HGS MUTATED HGS WILD-TYPE 
           10           479 
[1] "PLEKHA6 MUTATION ANALYSIS"
[1] 3
  PLEKHA6 MUTATED PLEKHA6 WILD-TYPE 
               20               469 
  PLEKHA6 MUTATED PLEKHA6 WILD-TYPE 
               20               469 
[1] "MAP7D1 MUTATION ANALYSIS"
[1] 3
  MAP7D1 MUTATED MAP7D1 WILD-TYPE 
              15              474 
  MAP7D1 MUTATED MAP7D1 WILD-TYPE 
              15              474 
[1] "MPO MUTATION ANALYSIS"
[1] 3
  MPO MUTATED MPO WILD-TYPE 
           16           473 
  MPO MUTATED MPO WILD-TYPE 
           16           473 
[1] "WBP11 MUTATION ANALYSIS"
[1] 3
  WBP11 MUTATED WBP11 WILD-TYPE 
              8             481 
  WBP11 MUTATED WBP11 WILD-TYPE 
              8             481 
[1] "RASA2 MUTATION ANALYSIS"
[1] 3
  RASA2 MUTATED RASA2 WILD-TYPE 
             17             472 
  RASA2 MUTATED RASA2 WILD-TYPE 
             17             472 
[1] "PLCH2 MUTATION ANALYSIS"
[1] 3
  PLCH2 MUTATED PLCH2 WILD-TYPE 
             19             470 
  PLCH2 MUTATED PLCH2 WILD-TYPE 
             19             470 
[1] "C1ORF59 MUTATION ANALYSIS"
[1] 3
  C1ORF59 MUTATED C1ORF59 WILD-TYPE 
               10               479 
  C1ORF59 MUTATED C1ORF59 WILD-TYPE 
               10               479 
[1] "MEPE MUTATION ANALYSIS"
[1] 3
  MEPE MUTATED MEPE WILD-TYPE 
            18            471 
  MEPE MUTATED MEPE WILD-TYPE 
            18            471 
[1] "RNASEL MUTATION ANALYSIS"
[1] 3
  RNASEL MUTATED RNASEL WILD-TYPE 
              14              475 
  RNASEL MUTATED RNASEL WILD-TYPE 
              14              475 
[1] "ESCO2 MUTATION ANALYSIS"
[1] 3
  ESCO2 MUTATED ESCO2 WILD-TYPE 
             14             475 
  ESCO2 MUTATED ESCO2 WILD-TYPE 
             14             475 
[1] "CCDC88A MUTATION ANALYSIS"
[1] 3
  CCDC88A MUTATED CCDC88A WILD-TYPE 
               36               453 
  CCDC88A MUTATED CCDC88A WILD-TYPE 
               36               453 
[1] "ATP8B1 MUTATION ANALYSIS"
[1] 3
  ATP8B1 MUTATED ATP8B1 WILD-TYPE 
              28              461 
  ATP8B1 MUTATED ATP8B1 WILD-TYPE 
              28              461 
[1] "LAMC1 MUTATION ANALYSIS"
[1] 3
  LAMC1 MUTATED LAMC1 WILD-TYPE 
             23             466 
  LAMC1 MUTATED LAMC1 WILD-TYPE 
             23             466 
[1] "SLFN12L MUTATION ANALYSIS"
[1] 3
  SLFN12L MUTATED SLFN12L WILD-TYPE 
                8               481 
  SLFN12L MUTATED SLFN12L WILD-TYPE 
                8               481 
[1] "PLXNA3 MUTATION ANALYSIS"
[1] 3
  PLXNA3 MUTATED PLXNA3 WILD-TYPE 
              19              470 
  PLXNA3 MUTATED PLXNA3 WILD-TYPE 
              19              470 
[1] "ITGAV MUTATION ANALYSIS"
[1] 3
  ITGAV MUTATED ITGAV WILD-TYPE 
             17             472 
  ITGAV MUTATED ITGAV WILD-TYPE 
             17             472 
[1] "TAF12 MUTATION ANALYSIS"
[1] 3
  TAF12 MUTATED TAF12 WILD-TYPE 
              4             485 
  TAF12 MUTATED TAF12 WILD-TYPE 
              4             485 
[1] "ZNF473 MUTATION ANALYSIS"
[1] 3
  ZNF473 MUTATED ZNF473 WILD-TYPE 
              16              473 
  ZNF473 MUTATED ZNF473 WILD-TYPE 
              16              473 
[1] "ENPP3 MUTATION ANALYSIS"
[1] 3
  ENPP3 MUTATED ENPP3 WILD-TYPE 
             11             478 
  ENPP3 MUTATED ENPP3 WILD-TYPE 
             11             478 
[1] "OR4N4 MUTATION ANALYSIS"
[1] 3
  OR4N4 MUTATED OR4N4 WILD-TYPE 
             18             471 
  OR4N4 MUTATED OR4N4 WILD-TYPE 
             18             471 
[1] "CHEK2 MUTATION ANALYSIS"
[1] 3
  CHEK2 MUTATED CHEK2 WILD-TYPE 
             10             479 
  CHEK2 MUTATED CHEK2 WILD-TYPE 
             10             479 
[1] "GTF2IRD2 MUTATION ANALYSIS"
[1] 3
  GTF2IRD2 MUTATED GTF2IRD2 WILD-TYPE 
                 6                483 
  GTF2IRD2 MUTATED GTF2IRD2 WILD-TYPE 
                 6                483 
[1] "AKAP9 MUTATION ANALYSIS"
[1] 3
  AKAP9 MUTATED AKAP9 WILD-TYPE 
             50             439 
  AKAP9 MUTATED AKAP9 WILD-TYPE 
             50             439 
[1] "ABI3BP MUTATION ANALYSIS"
[1] 3
  ABI3BP MUTATED ABI3BP WILD-TYPE 
              23              466 
  ABI3BP MUTATED ABI3BP WILD-TYPE 
              23              466 
[1] "ENTPD4 MUTATION ANALYSIS"
[1] 3
  ENTPD4 MUTATED ENTPD4 WILD-TYPE 
              18              471 
  ENTPD4 MUTATED ENTPD4 WILD-TYPE 
              18              471 
[1] "HFE2 MUTATION ANALYSIS"
[1] 3
  HFE2 MUTATED HFE2 WILD-TYPE 
            10            479 
  HFE2 MUTATED HFE2 WILD-TYPE 
            10            479 
[1] "SPCS2 MUTATION ANALYSIS"
[1] 3
  SPCS2 MUTATED SPCS2 WILD-TYPE 
              5             484 
  SPCS2 MUTATED SPCS2 WILD-TYPE 
              5             484 
[1] "RAD51AP2 MUTATION ANALYSIS"
[1] 3
  RAD51AP2 MUTATED RAD51AP2 WILD-TYPE 
                19                470 
  RAD51AP2 MUTATED RAD51AP2 WILD-TYPE 
                19                470 
[1] "BMPR1A MUTATION ANALYSIS"
[1] 3
  BMPR1A MUTATED BMPR1A WILD-TYPE 
              18              471 
  BMPR1A MUTATED BMPR1A WILD-TYPE 
              18              471 
[1] "MLL4 MUTATION ANALYSIS"
[1] 3
  MLL4 MUTATED MLL4 WILD-TYPE 
            39            450 
  MLL4 MUTATED MLL4 WILD-TYPE 
            39            450 
[1] "KIF21A MUTATION ANALYSIS"
[1] 3
  KIF21A MUTATED KIF21A WILD-TYPE 
              29              460 
  KIF21A MUTATED KIF21A WILD-TYPE 
              29              460 
[1] "ZNF286A MUTATION ANALYSIS"
[1] 3
  ZNF286A MUTATED ZNF286A WILD-TYPE 
                9               480 
  ZNF286A MUTATED ZNF286A WILD-TYPE 
                9               480 
[1] "AK3L1 MUTATION ANALYSIS"
[1] 3
  AK3L1 MUTATED AK3L1 WILD-TYPE 
              4             485 
  AK3L1 MUTATED AK3L1 WILD-TYPE 
              4             485 
[1] "PIK3C3 MUTATION ANALYSIS"
[1] 3
  PIK3C3 MUTATED PIK3C3 WILD-TYPE 
              26              463 
  PIK3C3 MUTATED PIK3C3 WILD-TYPE 
              26              463 
[1] "POLE MUTATION ANALYSIS"
[1] 3
  POLE MUTATED POLE WILD-TYPE 
            34            455 
  POLE MUTATED POLE WILD-TYPE 
            34            455 
[1] "PNP MUTATION ANALYSIS"
[1] 3
  PNP MUTATED PNP WILD-TYPE 
            4           485 
  PNP MUTATED PNP WILD-TYPE 
            4           485 
[1] "ZNF570 MUTATION ANALYSIS"
[1] 3
  ZNF570 MUTATED ZNF570 WILD-TYPE 
              11              478 
  ZNF570 MUTATED ZNF570 WILD-TYPE 
              11              478 
[1] "TNPO1 MUTATION ANALYSIS"
[1] 3
  TNPO1 MUTATED TNPO1 WILD-TYPE 
             17             472 
  TNPO1 MUTATED TNPO1 WILD-TYPE 
             17             472 
[1] "MAP9 MUTATION ANALYSIS"
[1] 3
  MAP9 MUTATED MAP9 WILD-TYPE 
            18            471 
  MAP9 MUTATED MAP9 WILD-TYPE 
            18            471 
[1] "ITPR1 MUTATION ANALYSIS"
[1] 3
  ITPR1 MUTATED ITPR1 WILD-TYPE 
             41             448 
  ITPR1 MUTATED ITPR1 WILD-TYPE 
             41             448 
[1] "NME7 MUTATION ANALYSIS"
[1] 3
  NME7 MUTATED NME7 WILD-TYPE 
             9            480 
  NME7 MUTATED NME7 WILD-TYPE 
             9            480 
[1] "TNFAIP3 MUTATION ANALYSIS"
[1] 3
  TNFAIP3 MUTATED TNFAIP3 WILD-TYPE 
               37               452 
  TNFAIP3 MUTATED TNFAIP3 WILD-TYPE 
               37               452 
[1] "DDX3X MUTATION ANALYSIS"
[1] 3
  DDX3X MUTATED DDX3X WILD-TYPE 
             10             479 
  DDX3X MUTATED DDX3X WILD-TYPE 
             10             479 
[1] "ETV1 MUTATION ANALYSIS"
[1] 3
  ETV1 MUTATED ETV1 WILD-TYPE 
            15            474 
  ETV1 MUTATED ETV1 WILD-TYPE 
            15            474 
[1] "ACVR2A MUTATION ANALYSIS"
[1] 3
  ACVR2A MUTATED ACVR2A WILD-TYPE 
              18              471 
  ACVR2A MUTATED ACVR2A WILD-TYPE 
              18              471 
[1] "RNF20 MUTATION ANALYSIS"
[1] 3
  RNF20 MUTATED RNF20 WILD-TYPE 
             21             468 
  RNF20 MUTATED RNF20 WILD-TYPE 
             21             468 
[1] "ATG2B MUTATION ANALYSIS"
[1] 3
  ATG2B MUTATED ATG2B WILD-TYPE 
             18             471 
  ATG2B MUTATED ATG2B WILD-TYPE 
             18             471 
[1] "FRY MUTATION ANALYSIS"
[1] 3
  FRY MUTATED FRY WILD-TYPE 
           41           448 
  FRY MUTATED FRY WILD-TYPE 
           41           448 
[1] "SCN2A MUTATION ANALYSIS"
[1] 3
  SCN2A MUTATED SCN2A WILD-TYPE 
             50             439 
  SCN2A MUTATED SCN2A WILD-TYPE 
             50             439 
[1] "ALK MUTATION ANALYSIS"
[1] 3
  ALK MUTATED ALK WILD-TYPE 
           40           449 
  ALK MUTATED ALK WILD-TYPE 
           40           449 
[1] "SP4 MUTATION ANALYSIS"
[1] 3
  SP4 MUTATED SP4 WILD-TYPE 
           12           477 
  SP4 MUTATED SP4 WILD-TYPE 
           12           477 
[1] "IQSEC2 MUTATION ANALYSIS"
[1] 3
  IQSEC2 MUTATED IQSEC2 WILD-TYPE 
              17              472 
  IQSEC2 MUTATED IQSEC2 WILD-TYPE 
              17              472 
[1] "PPP1R12B MUTATION ANALYSIS"
[1] 3
  PPP1R12B MUTATED PPP1R12B WILD-TYPE 
                15                474 
  PPP1R12B MUTATED PPP1R12B WILD-TYPE 
                15                474 
[1] "WWTR1 MUTATION ANALYSIS"
[1] 3
  WWTR1 MUTATED WWTR1 WILD-TYPE 
              7             482 
  WWTR1 MUTATED WWTR1 WILD-TYPE 
              7             482 
[1] "ABLIM3 MUTATION ANALYSIS"
[1] 3
  ABLIM3 MUTATED ABLIM3 WILD-TYPE 
              18              471 
  ABLIM3 MUTATED ABLIM3 WILD-TYPE 
              18              471 
[1] "SNTN MUTATION ANALYSIS"
[1] 3
  SNTN MUTATED SNTN WILD-TYPE 
             7            482 
  SNTN MUTATED SNTN WILD-TYPE 
             7            482 
[1] "DSG4 MUTATION ANALYSIS"
[1] 3
  DSG4 MUTATED DSG4 WILD-TYPE 
            24            465 
  DSG4 MUTATED DSG4 WILD-TYPE 
            24            465 
[1] "PCDH12 MUTATION ANALYSIS"
[1] 3
  PCDH12 MUTATED PCDH12 WILD-TYPE 
              20              469 
  PCDH12 MUTATED PCDH12 WILD-TYPE 
              20              469 
[1] "EAPP MUTATION ANALYSIS"
[1] 3
  EAPP MUTATED EAPP WILD-TYPE 
             6            483 
  EAPP MUTATED EAPP WILD-TYPE 
             6            483 
[1] "SLC7A10 MUTATION ANALYSIS"
[1] 3
  SLC7A10 MUTATED SLC7A10 WILD-TYPE 
                8               481 
  SLC7A10 MUTATED SLC7A10 WILD-TYPE 
                8               481 
[1] "ZNF711 MUTATION ANALYSIS"
[1] 3
  ZNF711 MUTATED ZNF711 WILD-TYPE 
              11              478 
  ZNF711 MUTATED ZNF711 WILD-TYPE 
              11              478 
[1] "REXO4 MUTATION ANALYSIS"
[1] 3
  REXO4 MUTATED REXO4 WILD-TYPE 
              5             484 
  REXO4 MUTATED REXO4 WILD-TYPE 
              5             484 
[1] "ABCB4 MUTATION ANALYSIS"
[1] 3
  ABCB4 MUTATED ABCB4 WILD-TYPE 
             27             462 
  ABCB4 MUTATED ABCB4 WILD-TYPE 
             27             462 
[1] "FAAH2 MUTATION ANALYSIS"
[1] 3
  FAAH2 MUTATED FAAH2 WILD-TYPE 
             14             475 
  FAAH2 MUTATED FAAH2 WILD-TYPE 
             14             475 
[1] "RASAL2 MUTATION ANALYSIS"
[1] 3
  RASAL2 MUTATED RASAL2 WILD-TYPE 
              16              473 
  RASAL2 MUTATED RASAL2 WILD-TYPE 
              16              473 
[1] "ATAD5 MUTATION ANALYSIS"
[1] 3
  ATAD5 MUTATED ATAD5 WILD-TYPE 
             25             464 
  ATAD5 MUTATED ATAD5 WILD-TYPE 
             25             464 
[1] "ZNF14 MUTATION ANALYSIS"
[1] 3
  ZNF14 MUTATED ZNF14 WILD-TYPE 
             14             475 
  ZNF14 MUTATED ZNF14 WILD-TYPE 
             14             475 
[1] "NAP1L1 MUTATION ANALYSIS"
[1] 3
  NAP1L1 MUTATED NAP1L1 WILD-TYPE 
               9              480 
  NAP1L1 MUTATED NAP1L1 WILD-TYPE 
               9              480 
[1] "CHRM3 MUTATION ANALYSIS"
[1] 3
  CHRM3 MUTATED CHRM3 WILD-TYPE 
             15             474 
  CHRM3 MUTATED CHRM3 WILD-TYPE 
             15             474 
[1] "GPR87 MUTATION ANALYSIS"
[1] 3
  GPR87 MUTATED GPR87 WILD-TYPE 
             11             478 
  GPR87 MUTATED GPR87 WILD-TYPE 
             11             478 
[1] "AKR1C4 MUTATION ANALYSIS"
[1] 3
  AKR1C4 MUTATED AKR1C4 WILD-TYPE 
              11              478 
  AKR1C4 MUTATED AKR1C4 WILD-TYPE 
              11              478 
[1] "E2F6 MUTATION ANALYSIS"
[1] 3
  E2F6 MUTATED E2F6 WILD-TYPE 
             4            485 
  E2F6 MUTATED E2F6 WILD-TYPE 
             4            485 
[1] "PRKCI MUTATION ANALYSIS"
[1] 3
  PRKCI MUTATED PRKCI WILD-TYPE 
             20             469 
  PRKCI MUTATED PRKCI WILD-TYPE 
             20             469 
[1] "SEC31A MUTATION ANALYSIS"
[1] 3
  SEC31A MUTATED SEC31A WILD-TYPE 
              15              474 
  SEC31A MUTATED SEC31A WILD-TYPE 
              15              474 
[1] "KIAA0319L MUTATION ANALYSIS"
[1] 3
  KIAA0319L MUTATED KIAA0319L WILD-TYPE 
                 20                 469 
  KIAA0319L MUTATED KIAA0319L WILD-TYPE 
                 20                 469 
[1] "BACE2 MUTATION ANALYSIS"
[1] 3
  BACE2 MUTATED BACE2 WILD-TYPE 
             11             478 
  BACE2 MUTATED BACE2 WILD-TYPE 
             11             478 
[1] "VAV2 MUTATION ANALYSIS"
[1] 3
  VAV2 MUTATED VAV2 WILD-TYPE 
            19            470 
  VAV2 MUTATED VAV2 WILD-TYPE 
            19            470 
[1] "GAB1 MUTATION ANALYSIS"
[1] 3
  GAB1 MUTATED GAB1 WILD-TYPE 
            15            474 
  GAB1 MUTATED GAB1 WILD-TYPE 
            15            474 
[1] "RPA3 MUTATION ANALYSIS"
[1] 3
  RPA3 MUTATED RPA3 WILD-TYPE 
             4            485 
  RPA3 MUTATED RPA3 WILD-TYPE 
             4            485 
[1] "GPR61 MUTATION ANALYSIS"
[1] 3
  GPR61 MUTATED GPR61 WILD-TYPE 
             12             477 
  GPR61 MUTATED GPR61 WILD-TYPE 
             12             477 
[1] "OAS1 MUTATION ANALYSIS"
[1] 3
  OAS1 MUTATED OAS1 WILD-TYPE 
             9            480 
  OAS1 MUTATED OAS1 WILD-TYPE 
             9            480 
[1] "OLR1 MUTATION ANALYSIS"
[1] 3
  OLR1 MUTATED OLR1 WILD-TYPE 
            10            479 
  OLR1 MUTATED OLR1 WILD-TYPE 
            10            479 
[1] "ELFN2 MUTATION ANALYSIS"
[1] 3
  ELFN2 MUTATED ELFN2 WILD-TYPE 
              9             480 
  ELFN2 MUTATED ELFN2 WILD-TYPE 
              9             480 
[1] "ANAPC4 MUTATION ANALYSIS"
[1] 3
  ANAPC4 MUTATED ANAPC4 WILD-TYPE 
              12              477 
  ANAPC4 MUTATED ANAPC4 WILD-TYPE 
              12              477 
[1] "ITGB8 MUTATION ANALYSIS"
[1] 3
  ITGB8 MUTATED ITGB8 WILD-TYPE 
             12             477 
  ITGB8 MUTATED ITGB8 WILD-TYPE 
             12             477 
[1] "PAXIP1 MUTATION ANALYSIS"
[1] 3
  PAXIP1 MUTATED PAXIP1 WILD-TYPE 
              20              469 
  PAXIP1 MUTATED PAXIP1 WILD-TYPE 
              20              469 
[1] "HIST1H1C MUTATION ANALYSIS"
[1] 3
  HIST1H1C MUTATED HIST1H1C WILD-TYPE 
                 4                485 
  HIST1H1C MUTATED HIST1H1C WILD-TYPE 
                 4                485 
[1] "IL18R1 MUTATION ANALYSIS"
[1] 3
  IL18R1 MUTATED IL18R1 WILD-TYPE 
              16              473 
  IL18R1 MUTATED IL18R1 WILD-TYPE 
              16              473 
[1] "IBTK MUTATION ANALYSIS"
[1] 3
  IBTK MUTATED IBTK WILD-TYPE 
            23            466 
  IBTK MUTATED IBTK WILD-TYPE 
            23            466 
[1] "RTP3 MUTATION ANALYSIS"
[1] 3
  RTP3 MUTATED RTP3 WILD-TYPE 
             5            484 
  RTP3 MUTATED RTP3 WILD-TYPE 
             5            484 
[1] "TAOK3 MUTATION ANALYSIS"
[1] 3
  TAOK3 MUTATED TAOK3 WILD-TYPE 
             20             469 
  TAOK3 MUTATED TAOK3 WILD-TYPE 
             20             469 
[1] "RAE1 MUTATION ANALYSIS"
[1] 3
  RAE1 MUTATED RAE1 WILD-TYPE 
             8            481 
  RAE1 MUTATED RAE1 WILD-TYPE 
             8            481 
[1] "KIF2C MUTATION ANALYSIS"
[1] 3
  KIF2C MUTATED KIF2C WILD-TYPE 
             12             477 
  KIF2C MUTATED KIF2C WILD-TYPE 
             12             477 
[1] "C7ORF58 MUTATION ANALYSIS"
[1] 3
  C7ORF58 MUTATED C7ORF58 WILD-TYPE 
               26               463 
  C7ORF58 MUTATED C7ORF58 WILD-TYPE 
               26               463 
[1] "PVRL4 MUTATION ANALYSIS"
[1] 3
  PVRL4 MUTATED PVRL4 WILD-TYPE 
             10             479 
  PVRL4 MUTATED PVRL4 WILD-TYPE 
             10             479 
[1] "MTDH MUTATION ANALYSIS"
[1] 3
  MTDH MUTATED MTDH WILD-TYPE 
            13            476 
  MTDH MUTATED MTDH WILD-TYPE 
            13            476 
[1] "AIFM1 MUTATION ANALYSIS"
[1] 3
  AIFM1 MUTATED AIFM1 WILD-TYPE 
             13             476 
  AIFM1 MUTATED AIFM1 WILD-TYPE 
             13             476 
[1] "WNK4 MUTATION ANALYSIS"
[1] 3
  WNK4 MUTATED WNK4 WILD-TYPE 
            12            477 
  WNK4 MUTATED WNK4 WILD-TYPE 
            12            477 
[1] "POLM MUTATION ANALYSIS"
[1] 3
  POLM MUTATED POLM WILD-TYPE 
            12            477 
  POLM MUTATED POLM WILD-TYPE 
            12            477 
[1] "RCSD1 MUTATION ANALYSIS"
[1] 3
  RCSD1 MUTATED RCSD1 WILD-TYPE 
             16             473 
  RCSD1 MUTATED RCSD1 WILD-TYPE 
             16             473 
[1] "CSNK1D MUTATION ANALYSIS"
[1] 3
  CSNK1D MUTATED CSNK1D WILD-TYPE 
              15              474 
  CSNK1D MUTATED CSNK1D WILD-TYPE 
              15              474 
[1] "GPNMB MUTATION ANALYSIS"
[1] 3
  GPNMB MUTATED GPNMB WILD-TYPE 
             14             475 
  GPNMB MUTATED GPNMB WILD-TYPE 
             14             475 
[1] "ATP11C MUTATION ANALYSIS"
[1] 3
  ATP11C MUTATED ATP11C WILD-TYPE 
              29              460 
  ATP11C MUTATED ATP11C WILD-TYPE 
              29              460 
[1] "IQGAP1 MUTATION ANALYSIS"
[1] 3
  IQGAP1 MUTATED IQGAP1 WILD-TYPE 
              24              465 
  IQGAP1 MUTATED IQGAP1 WILD-TYPE 
              24              465 
[1] "TRMT5 MUTATION ANALYSIS"
[1] 3
  TRMT5 MUTATED TRMT5 WILD-TYPE 
              8             481 
  TRMT5 MUTATED TRMT5 WILD-TYPE 
              8             481 
[1] "MAP7D3 MUTATION ANALYSIS"
[1] 3
  MAP7D3 MUTATED MAP7D3 WILD-TYPE 
              23              466 
  MAP7D3 MUTATED MAP7D3 WILD-TYPE 
              23              466 
[1] "BFAR MUTATION ANALYSIS"
[1] 3
  BFAR MUTATED BFAR WILD-TYPE 
             9            480 
  BFAR MUTATED BFAR WILD-TYPE 
             9            480 
[1] "KCTD16 MUTATION ANALYSIS"
[1] 3
  KCTD16 MUTATED KCTD16 WILD-TYPE 
              14              475 
  KCTD16 MUTATED KCTD16 WILD-TYPE 
              14              475 
[1] "MFN1 MUTATION ANALYSIS"
[1] 3
  MFN1 MUTATED MFN1 WILD-TYPE 
            14            475 
  MFN1 MUTATED MFN1 WILD-TYPE 
            14            475 
[1] "ELF3 MUTATION ANALYSIS"
[1] 3
  ELF3 MUTATED ELF3 WILD-TYPE 
            10            479 
  ELF3 MUTATED ELF3 WILD-TYPE 
            10            479 
[1] "TAPBP MUTATION ANALYSIS"
[1] 3
  TAPBP MUTATED TAPBP WILD-TYPE 
              5             484 
  TAPBP MUTATED TAPBP WILD-TYPE 
              5             484 
[1] "RBM19 MUTATION ANALYSIS"
[1] 3
  RBM19 MUTATED RBM19 WILD-TYPE 
             21             468 
  RBM19 MUTATED RBM19 WILD-TYPE 
             21             468 
[1] "MSH4 MUTATION ANALYSIS"
[1] 3
  MSH4 MUTATED MSH4 WILD-TYPE 
            15            474 
  MSH4 MUTATED MSH4 WILD-TYPE 
            15            474 
[1] "ADAMTS4 MUTATION ANALYSIS"
[1] 3
  ADAMTS4 MUTATED ADAMTS4 WILD-TYPE 
               18               471 
  ADAMTS4 MUTATED ADAMTS4 WILD-TYPE 
               18               471 
[1] "ASPM MUTATION ANALYSIS"
[1] 3
  ASPM MUTATED ASPM WILD-TYPE 
            47            442 
  ASPM MUTATED ASPM WILD-TYPE 
            47            442 
[1] "ZNF180 MUTATION ANALYSIS"
[1] 3
  ZNF180 MUTATED ZNF180 WILD-TYPE 
              18              471 
  ZNF180 MUTATED ZNF180 WILD-TYPE 
              18              471 
[1] "HYDIN MUTATION ANALYSIS"
[1] 3
  HYDIN MUTATED HYDIN WILD-TYPE 
             93             396 
  HYDIN MUTATED HYDIN WILD-TYPE 
             93             396 
[1] "NCOA3 MUTATION ANALYSIS"
[1] 3
  NCOA3 MUTATED NCOA3 WILD-TYPE 
             17             472 
  NCOA3 MUTATED NCOA3 WILD-TYPE 
             17             472 
[1] "ARMCX5 MUTATION ANALYSIS"
[1] 3
  ARMCX5 MUTATED ARMCX5 WILD-TYPE 
               8              481 
  ARMCX5 MUTATED ARMCX5 WILD-TYPE 
               8              481 
[1] "YLPM1 MUTATION ANALYSIS"
[1] 3
  YLPM1 MUTATED YLPM1 WILD-TYPE 
             24             465 
  YLPM1 MUTATED YLPM1 WILD-TYPE 
             24             465 
[1] "PLEK MUTATION ANALYSIS"
[1] 3
  PLEK MUTATED PLEK WILD-TYPE 
            14            475 
  PLEK MUTATED PLEK WILD-TYPE 
            14            475 
[1] "MST4 MUTATION ANALYSIS"
[1] 3
  MST4 MUTATED MST4 WILD-TYPE 
             8            481 
  MST4 MUTATED MST4 WILD-TYPE 
             8            481 
[1] "MYL1 MUTATION ANALYSIS"
[1] 3
  MYL1 MUTATED MYL1 WILD-TYPE 
             8            481 
  MYL1 MUTATED MYL1 WILD-TYPE 
             8            481 
[1] "ANKHD1 MUTATION ANALYSIS"
[1] 3
  ANKHD1 MUTATED ANKHD1 WILD-TYPE 
              34              455 
  ANKHD1 MUTATED ANKHD1 WILD-TYPE 
              34              455 
[1] "CEPT1 MUTATION ANALYSIS"
[1] 3
  CEPT1 MUTATED CEPT1 WILD-TYPE 
              6             483 
  CEPT1 MUTATED CEPT1 WILD-TYPE 
              6             483 
[1] "TNFRSF9 MUTATION ANALYSIS"
[1] 3
  TNFRSF9 MUTATED TNFRSF9 WILD-TYPE 
               10               479 
  TNFRSF9 MUTATED TNFRSF9 WILD-TYPE 
               10               479 
[1] "KDM5C MUTATION ANALYSIS"
[1] 3
  KDM5C MUTATED KDM5C WILD-TYPE 
             23             466 
  KDM5C MUTATED KDM5C WILD-TYPE 
             23             466 
[1] "IFIT2 MUTATION ANALYSIS"
[1] 3
  IFIT2 MUTATED IFIT2 WILD-TYPE 
              8             481 
  IFIT2 MUTATED IFIT2 WILD-TYPE 
              8             481 
[1] "NUDCD1 MUTATION ANALYSIS"
[1] 3
  NUDCD1 MUTATED NUDCD1 WILD-TYPE 
              10              479 
  NUDCD1 MUTATED NUDCD1 WILD-TYPE 
              10              479 
[1] "RBPMS MUTATION ANALYSIS"
[1] 3
  RBPMS MUTATED RBPMS WILD-TYPE 
              4             485 
  RBPMS MUTATED RBPMS WILD-TYPE 
              4             485 
[1] "ZNF197 MUTATION ANALYSIS"
[1] 3
  ZNF197 MUTATED ZNF197 WILD-TYPE 
              12              477 
  ZNF197 MUTATED ZNF197 WILD-TYPE 
              12              477 
[1] "DOCK5 MUTATION ANALYSIS"
[1] 3
  DOCK5 MUTATED DOCK5 WILD-TYPE 
             29             460 
  DOCK5 MUTATED DOCK5 WILD-TYPE 
             29             460 
[1] "TNRC6C MUTATION ANALYSIS"
[1] 3
  TNRC6C MUTATED TNRC6C WILD-TYPE 
              20              469 
  TNRC6C MUTATED TNRC6C WILD-TYPE 
              20              469 
[1] "NIPA2 MUTATION ANALYSIS"
[1] 3
  NIPA2 MUTATED NIPA2 WILD-TYPE 
              8             481 
  NIPA2 MUTATED NIPA2 WILD-TYPE 
              8             481 
[1] "NSUN2 MUTATION ANALYSIS"
[1] 3
  NSUN2 MUTATED NSUN2 WILD-TYPE 
             12             477 
  NSUN2 MUTATED NSUN2 WILD-TYPE 
             12             477 
[1] "CYP4X1 MUTATION ANALYSIS"
[1] 3
  CYP4X1 MUTATED CYP4X1 WILD-TYPE 
               6              483 
  CYP4X1 MUTATED CYP4X1 WILD-TYPE 
               6              483 
[1] "C11ORF57 MUTATION ANALYSIS"
[1] 3
  C11ORF57 MUTATED C11ORF57 WILD-TYPE 
                11                478 
  C11ORF57 MUTATED C11ORF57 WILD-TYPE 
                11                478 
[1] "ZNF439 MUTATION ANALYSIS"
[1] 3
  ZNF439 MUTATED ZNF439 WILD-TYPE 
               5              484 
  ZNF439 MUTATED ZNF439 WILD-TYPE 
               5              484 
[1] "UBA3 MUTATION ANALYSIS"
[1] 3
  UBA3 MUTATED UBA3 WILD-TYPE 
             7            482 
  UBA3 MUTATED UBA3 WILD-TYPE 
             7            482 
[1] "KIAA0564 MUTATION ANALYSIS"
[1] 3
  KIAA0564 MUTATED KIAA0564 WILD-TYPE 
                25                464 
  KIAA0564 MUTATED KIAA0564 WILD-TYPE 
                25                464 
[1] "ATP8B2 MUTATION ANALYSIS"
[1] 3
  ATP8B2 MUTATED ATP8B2 WILD-TYPE 
              18              471 
  ATP8B2 MUTATED ATP8B2 WILD-TYPE 
              18              471 
[1] "PNPLA5 MUTATION ANALYSIS"
[1] 3
  PNPLA5 MUTATED PNPLA5 WILD-TYPE 
              12              477 
  PNPLA5 MUTATED PNPLA5 WILD-TYPE 
              12              477 
[1] "VPS13B MUTATION ANALYSIS"
[1] 3
  VPS13B MUTATED VPS13B WILD-TYPE 
              60              429 
  VPS13B MUTATED VPS13B WILD-TYPE 
              60              429 
[1] "GPR22 MUTATION ANALYSIS"
[1] 3
  GPR22 MUTATED GPR22 WILD-TYPE 
              9             480 
  GPR22 MUTATED GPR22 WILD-TYPE 
              9             480 
[1] "LRP6 MUTATION ANALYSIS"
[1] 3
  LRP6 MUTATED LRP6 WILD-TYPE 
            27            462 
  LRP6 MUTATED LRP6 WILD-TYPE 
            27            462 
[1] "EFHC1 MUTATION ANALYSIS"
[1] 3
  EFHC1 MUTATED EFHC1 WILD-TYPE 
             13             476 
  EFHC1 MUTATED EFHC1 WILD-TYPE 
             13             476 
[1] "CDC7 MUTATION ANALYSIS"
[1] 3
  CDC7 MUTATED CDC7 WILD-TYPE 
            12            477 
  CDC7 MUTATED CDC7 WILD-TYPE 
            12            477 
[1] "ATP5J2 MUTATION ANALYSIS"
[1] 3
  ATP5J2 MUTATED ATP5J2 WILD-TYPE 
               5              484 
  ATP5J2 MUTATED ATP5J2 WILD-TYPE 
               5              484 
[1] "ADH1B MUTATION ANALYSIS"
[1] 3
  ADH1B MUTATED ADH1B WILD-TYPE 
             10             479 
  ADH1B MUTATED ADH1B WILD-TYPE 
             10             479 
[1] "PARP12 MUTATION ANALYSIS"
[1] 3
  PARP12 MUTATED PARP12 WILD-TYPE 
              11              478 
  PARP12 MUTATED PARP12 WILD-TYPE 
              11              478 
[1] "CD101 MUTATION ANALYSIS"
[1] 3
  CD101 MUTATED CD101 WILD-TYPE 
             11             478 
  CD101 MUTATED CD101 WILD-TYPE 
             11             478 
[1] "PTPRC MUTATION ANALYSIS"
[1] 3
  PTPRC MUTATED PTPRC WILD-TYPE 
             29             460 
  PTPRC MUTATED PTPRC WILD-TYPE 
             29             460 
[1] "RIF1 MUTATION ANALYSIS"
[1] 3
  RIF1 MUTATED RIF1 WILD-TYPE 
            41            448 
  RIF1 MUTATED RIF1 WILD-TYPE 
            41            448 
[1] "LAS1L MUTATION ANALYSIS"
[1] 3
  LAS1L MUTATED LAS1L WILD-TYPE 
             11             478 
  LAS1L MUTATED LAS1L WILD-TYPE 
             11             478 
[1] "HSD17B11 MUTATION ANALYSIS"
[1] 3
  HSD17B11 MUTATED HSD17B11 WILD-TYPE 
                 5                484 
  HSD17B11 MUTATED HSD17B11 WILD-TYPE 
                 5                484 
[1] "RHEB MUTATION ANALYSIS"
[1] 3
  RHEB MUTATED RHEB WILD-TYPE 
             5            484 
  RHEB MUTATED RHEB WILD-TYPE 
             5            484 
[1] "KIAA0406 MUTATION ANALYSIS"
[1] 3
  KIAA0406 MUTATED KIAA0406 WILD-TYPE 
                15                474 
  KIAA0406 MUTATED KIAA0406 WILD-TYPE 
                15                474 
[1] "LRRC23 MUTATION ANALYSIS"
[1] 3
  LRRC23 MUTATED LRRC23 WILD-TYPE 
               9              480 
  LRRC23 MUTATED LRRC23 WILD-TYPE 
               9              480 
[1] "FAM179A MUTATION ANALYSIS"
[1] 3
  FAM179A MUTATED FAM179A WILD-TYPE 
               29               460 
  FAM179A MUTATED FAM179A WILD-TYPE 
               29               460 
[1] "OR2V2 MUTATION ANALYSIS"
[1] 3
  OR2V2 MUTATED OR2V2 WILD-TYPE 
              6             483 
  OR2V2 MUTATED OR2V2 WILD-TYPE 
              6             483 
[1] "WNK1 MUTATION ANALYSIS"
[1] 3
  WNK1 MUTATED WNK1 WILD-TYPE 
            22            467 
  WNK1 MUTATED WNK1 WILD-TYPE 
            22            467 
[1] "FRS3 MUTATION ANALYSIS"
[1] 3
  FRS3 MUTATED FRS3 WILD-TYPE 
            12            477 
  FRS3 MUTATED FRS3 WILD-TYPE 
            12            477 
[1] "EEF1D MUTATION ANALYSIS"
[1] 3
  EEF1D MUTATED EEF1D WILD-TYPE 
             12             477 
  EEF1D MUTATED EEF1D WILD-TYPE 
             12             477 
[1] "DOCK10 MUTATION ANALYSIS"
[1] 3
  DOCK10 MUTATED DOCK10 WILD-TYPE 
              28              461 
  DOCK10 MUTATED DOCK10 WILD-TYPE 
              28              461 
[1] "EXOC4 MUTATION ANALYSIS"
[1] 3
  EXOC4 MUTATED EXOC4 WILD-TYPE 
             20             469 
  EXOC4 MUTATED EXOC4 WILD-TYPE 
             20             469 
[1] "CEACAM1 MUTATION ANALYSIS"
[1] 3
  CEACAM1 MUTATED CEACAM1 WILD-TYPE 
                5               484 
  CEACAM1 MUTATED CEACAM1 WILD-TYPE 
                5               484 
[1] "EIF5B MUTATION ANALYSIS"
[1] 3
  EIF5B MUTATED EIF5B WILD-TYPE 
             16             473 
  EIF5B MUTATED EIF5B WILD-TYPE 
             16             473 
[1] "PRAMEF12 MUTATION ANALYSIS"
[1] 3
  PRAMEF12 MUTATED PRAMEF12 WILD-TYPE 
                 7                482 
  PRAMEF12 MUTATED PRAMEF12 WILD-TYPE 
                 7                482 
[1] "SF1 MUTATION ANALYSIS"
[1] 3
  SF1 MUTATED SF1 WILD-TYPE 
           16           473 
  SF1 MUTATED SF1 WILD-TYPE 
           16           473 
[1] "BTNL3 MUTATION ANALYSIS"
[1] 3
  BTNL3 MUTATED BTNL3 WILD-TYPE 
              8             481 
  BTNL3 MUTATED BTNL3 WILD-TYPE 
              8             481 
[1] "EFCAB1 MUTATION ANALYSIS"
[1] 3
  EFCAB1 MUTATED EFCAB1 WILD-TYPE 
               5              484 
  EFCAB1 MUTATED EFCAB1 WILD-TYPE 
               5              484 
[1] "IKZF4 MUTATION ANALYSIS"
[1] 3
  IKZF4 MUTATED IKZF4 WILD-TYPE 
             13             476 
  IKZF4 MUTATED IKZF4 WILD-TYPE 
             13             476 
[1] "ZNF564 MUTATION ANALYSIS"
[1] 3
  ZNF564 MUTATED ZNF564 WILD-TYPE 
              12              477 
  ZNF564 MUTATED ZNF564 WILD-TYPE 
              12              477 
[1] "SLC46A3 MUTATION ANALYSIS"
[1] 3
  SLC46A3 MUTATED SLC46A3 WILD-TYPE 
                9               480 
  SLC46A3 MUTATED SLC46A3 WILD-TYPE 
                9               480 
[1] "VAV3 MUTATION ANALYSIS"
[1] 3
  VAV3 MUTATED VAV3 WILD-TYPE 
            27            462 
  VAV3 MUTATED VAV3 WILD-TYPE 
            27            462 
[1] "RPGRIP1L MUTATION ANALYSIS"
[1] 3
  RPGRIP1L MUTATED RPGRIP1L WILD-TYPE 
                18                471 
  RPGRIP1L MUTATED RPGRIP1L WILD-TYPE 
                18                471 
[1] "GATA1 MUTATION ANALYSIS"
[1] 3
  GATA1 MUTATED GATA1 WILD-TYPE 
             17             472 
  GATA1 MUTATED GATA1 WILD-TYPE 
             17             472 
[1] "KIF21B MUTATION ANALYSIS"
[1] 3
  KIF21B MUTATED KIF21B WILD-TYPE 
              25              464 
  KIF21B MUTATED KIF21B WILD-TYPE 
              25              464 
[1] "HELQ MUTATION ANALYSIS"
[1] 3
  HELQ MUTATED HELQ WILD-TYPE 
            20            469 
  HELQ MUTATED HELQ WILD-TYPE 
            20            469 
[1] "ZNF799 MUTATION ANALYSIS"
[1] 3
  ZNF799 MUTATED ZNF799 WILD-TYPE 
               7              482 
  ZNF799 MUTATED ZNF799 WILD-TYPE 
               7              482 
[1] "CACHD1 MUTATION ANALYSIS"
[1] 3
  CACHD1 MUTATED CACHD1 WILD-TYPE 
              27              462 
  CACHD1 MUTATED CACHD1 WILD-TYPE 
              27              462 
[1] "CCDC93 MUTATION ANALYSIS"
[1] 3
  CCDC93 MUTATED CCDC93 WILD-TYPE 
              12              477 
  CCDC93 MUTATED CCDC93 WILD-TYPE 
              12              477 
[1] "SYNRG MUTATION ANALYSIS"
[1] 3
  SYNRG MUTATED SYNRG WILD-TYPE 
             18             471 
  SYNRG MUTATED SYNRG WILD-TYPE 
             18             471 
[1] "TRIM33 MUTATION ANALYSIS"
[1] 3
  TRIM33 MUTATED TRIM33 WILD-TYPE 
              20              469 
  TRIM33 MUTATED TRIM33 WILD-TYPE 
              20              469 
[1] "LPIN2 MUTATION ANALYSIS"
[1] 3
  LPIN2 MUTATED LPIN2 WILD-TYPE 
             10             479 
  LPIN2 MUTATED LPIN2 WILD-TYPE 
             10             479 
[1] "ING1 MUTATION ANALYSIS"
[1] 3
  ING1 MUTATED ING1 WILD-TYPE 
            12            477 
  ING1 MUTATED ING1 WILD-TYPE 
            12            477 
[1] "TAB3 MUTATION ANALYSIS"
[1] 3
  TAB3 MUTATED TAB3 WILD-TYPE 
            13            476 
  TAB3 MUTATED TAB3 WILD-TYPE 
            13            476 
[1] "ZFP3 MUTATION ANALYSIS"
[1] 3
  ZFP3 MUTATED ZFP3 WILD-TYPE 
            12            477 
  ZFP3 MUTATED ZFP3 WILD-TYPE 
            12            477 
[1] "ULK1 MUTATION ANALYSIS"
[1] 3
  ULK1 MUTATED ULK1 WILD-TYPE 
            11            478 
  ULK1 MUTATED ULK1 WILD-TYPE 
            11            478 
[1] "CLDN10 MUTATION ANALYSIS"
[1] 3
  CLDN10 MUTATED CLDN10 WILD-TYPE 
              13              476 
  CLDN10 MUTATED CLDN10 WILD-TYPE 
              13              476 
[1] "RHPN2 MUTATION ANALYSIS"
[1] 3
  RHPN2 MUTATED RHPN2 WILD-TYPE 
             18             471 
  RHPN2 MUTATED RHPN2 WILD-TYPE 
             18             471 
[1] "IL1RL1 MUTATION ANALYSIS"
[1] 3
  IL1RL1 MUTATED IL1RL1 WILD-TYPE 
              16              473 
  IL1RL1 MUTATED IL1RL1 WILD-TYPE 
              16              473 
[1] "TOX MUTATION ANALYSIS"
[1] 3
  TOX MUTATED TOX WILD-TYPE 
           18           471 
  TOX MUTATED TOX WILD-TYPE 
           18           471 
[1] "SNX2 MUTATION ANALYSIS"
[1] 3
  SNX2 MUTATED SNX2 WILD-TYPE 
            14            475 
  SNX2 MUTATED SNX2 WILD-TYPE 
            14            475 
[1] "HDAC5 MUTATION ANALYSIS"
[1] 3
  HDAC5 MUTATED HDAC5 WILD-TYPE 
             12             477 
  HDAC5 MUTATED HDAC5 WILD-TYPE 
             12             477 
[1] "IVNS1ABP MUTATION ANALYSIS"
[1] 3
  IVNS1ABP MUTATED IVNS1ABP WILD-TYPE 
                14                475 
  IVNS1ABP MUTATED IVNS1ABP WILD-TYPE 
                14                475 
[1] "SNRNP200 MUTATION ANALYSIS"
[1] 3
  SNRNP200 MUTATED SNRNP200 WILD-TYPE 
                23                466 
  SNRNP200 MUTATED SNRNP200 WILD-TYPE 
                23                466 
[1] "RFXAP MUTATION ANALYSIS"
[1] 3
  RFXAP MUTATED RFXAP WILD-TYPE 
              6             483 
  RFXAP MUTATED RFXAP WILD-TYPE 
              6             483 
[1] "ABCF3 MUTATION ANALYSIS"
[1] 3
  ABCF3 MUTATED ABCF3 WILD-TYPE 
             16             473 
  ABCF3 MUTATED ABCF3 WILD-TYPE 
             16             473 
[1] "ZMYM4 MUTATION ANALYSIS"
[1] 3
  ZMYM4 MUTATED ZMYM4 WILD-TYPE 
             19             470 
  ZMYM4 MUTATED ZMYM4 WILD-TYPE 
             19             470 
[1] "WWC3 MUTATION ANALYSIS"
[1] 3
  WWC3 MUTATED WWC3 WILD-TYPE 
            27            462 
  WWC3 MUTATED WWC3 WILD-TYPE 
            27            462 
[1] "OR7C1 MUTATION ANALYSIS"
[1] 3
  OR7C1 MUTATED OR7C1 WILD-TYPE 
             11             478 
  OR7C1 MUTATED OR7C1 WILD-TYPE 
             11             478 
[1] "GRM7 MUTATION ANALYSIS"
[1] 3
  GRM7 MUTATED GRM7 WILD-TYPE 
            30            459 
  GRM7 MUTATED GRM7 WILD-TYPE 
            30            459 
[1] "RANBP1 MUTATION ANALYSIS"
[1] 3
  RANBP1 MUTATED RANBP1 WILD-TYPE 
               6              483 
  RANBP1 MUTATED RANBP1 WILD-TYPE 
               6              483 
[1] "PAK7 MUTATION ANALYSIS"
[1] 3
  PAK7 MUTATED PAK7 WILD-TYPE 
            26            463 
  PAK7 MUTATED PAK7 WILD-TYPE 
            26            463 
[1] "LUM MUTATION ANALYSIS"
[1] 3
  LUM MUTATED LUM WILD-TYPE 
           14           475 
  LUM MUTATED LUM WILD-TYPE 
           14           475 
[1] "WDR66 MUTATION ANALYSIS"
[1] 3
  WDR66 MUTATED WDR66 WILD-TYPE 
             22             467 
  WDR66 MUTATED WDR66 WILD-TYPE 
             22             467 
[1] "IRAK3 MUTATION ANALYSIS"
[1] 3
  IRAK3 MUTATED IRAK3 WILD-TYPE 
              9             480 
  IRAK3 MUTATED IRAK3 WILD-TYPE 
              9             480 
[1] "SLC41A2 MUTATION ANALYSIS"
[1] 3
  SLC41A2 MUTATED SLC41A2 WILD-TYPE 
                9               480 
  SLC41A2 MUTATED SLC41A2 WILD-TYPE 
                9               480 
[1] "ING2 MUTATION ANALYSIS"
[1] 3
  ING2 MUTATED ING2 WILD-TYPE 
             7            482 
  ING2 MUTATED ING2 WILD-TYPE 
             7            482 
[1] "DNAJC11 MUTATION ANALYSIS"
[1] 3
  DNAJC11 MUTATED DNAJC11 WILD-TYPE 
               12               477 
  DNAJC11 MUTATED DNAJC11 WILD-TYPE 
               12               477 
[1] "CORO1C MUTATION ANALYSIS"
[1] 3
  CORO1C MUTATED CORO1C WILD-TYPE 
               8              481 
  CORO1C MUTATED CORO1C WILD-TYPE 
               8              481 
[1] "ATP6V1D MUTATION ANALYSIS"
[1] 3
  ATP6V1D MUTATED ATP6V1D WILD-TYPE 
                6               483 
  ATP6V1D MUTATED ATP6V1D WILD-TYPE 
                6               483 
[1] "WNK3 MUTATION ANALYSIS"
[1] 3
  WNK3 MUTATED WNK3 WILD-TYPE 
            32            457 
  WNK3 MUTATED WNK3 WILD-TYPE 
            32            457 
[1] "C1ORF168 MUTATION ANALYSIS"
[1] 3
  C1ORF168 MUTATED C1ORF168 WILD-TYPE 
                16                473 
  C1ORF168 MUTATED C1ORF168 WILD-TYPE 
                16                473 
[1] "VANGL1 MUTATION ANALYSIS"
[1] 3
  VANGL1 MUTATED VANGL1 WILD-TYPE 
              13              476 
  VANGL1 MUTATED VANGL1 WILD-TYPE 
              13              476 
[1] "SPANXC MUTATION ANALYSIS"
[1] 3
  SPANXC MUTATED SPANXC WILD-TYPE 
               4              485 
  SPANXC MUTATED SPANXC WILD-TYPE 
               4              485 
[1] "KLKB1 MUTATION ANALYSIS"
[1] 3
  KLKB1 MUTATED KLKB1 WILD-TYPE 
             15             474 
  KLKB1 MUTATED KLKB1 WILD-TYPE 
             15             474 
[1] "SV2A MUTATION ANALYSIS"
[1] 3
  SV2A MUTATED SV2A WILD-TYPE 
            23            466 
  SV2A MUTATED SV2A WILD-TYPE 
            23            466 
[1] "POLA1 MUTATION ANALYSIS"
[1] 3
  POLA1 MUTATED POLA1 WILD-TYPE 
             14             475 
  POLA1 MUTATED POLA1 WILD-TYPE 
             14             475 
[1] "RAB40C MUTATION ANALYSIS"
[1] 3
  RAB40C MUTATED RAB40C WILD-TYPE 
               8              481 
  RAB40C MUTATED RAB40C WILD-TYPE 
               8              481 
[1] "DHX35 MUTATION ANALYSIS"
[1] 3
  DHX35 MUTATED DHX35 WILD-TYPE 
             13             476 
  DHX35 MUTATED DHX35 WILD-TYPE 
             13             476 
[1] "SLC25A13 MUTATION ANALYSIS"
[1] 3
  SLC25A13 MUTATED SLC25A13 WILD-TYPE 
                17                472 
  SLC25A13 MUTATED SLC25A13 WILD-TYPE 
                17                472 
[1] "FAM26E MUTATION ANALYSIS"
[1] 3
  FAM26E MUTATED FAM26E WILD-TYPE 
               5              484 
  FAM26E MUTATED FAM26E WILD-TYPE 
               5              484 
[1] "SAFB MUTATION ANALYSIS"
[1] 3
  SAFB MUTATED SAFB WILD-TYPE 
            16            473 
  SAFB MUTATED SAFB WILD-TYPE 
            16            473 
[1] "YES1 MUTATION ANALYSIS"
[1] 3
  YES1 MUTATED YES1 WILD-TYPE 
            10            479 
  YES1 MUTATED YES1 WILD-TYPE 
            10            479 
[1] "ACTL8 MUTATION ANALYSIS"
[1] 3
  ACTL8 MUTATED ACTL8 WILD-TYPE 
              9             480 
  ACTL8 MUTATED ACTL8 WILD-TYPE 
              9             480 
[1] "CNTFR MUTATION ANALYSIS"
[1] 3
  CNTFR MUTATED CNTFR WILD-TYPE 
             10             479 
  CNTFR MUTATED CNTFR WILD-TYPE 
             10             479 
[1] "OR4E2 MUTATION ANALYSIS"
[1] 3
  OR4E2 MUTATED OR4E2 WILD-TYPE 
              5             484 
  OR4E2 MUTATED OR4E2 WILD-TYPE 
              5             484 
[1] "PPP1R12A MUTATION ANALYSIS"
[1] 3
  PPP1R12A MUTATED PPP1R12A WILD-TYPE 
                16                473 
  PPP1R12A MUTATED PPP1R12A WILD-TYPE 
                16                473 
[1] "ZNF721 MUTATION ANALYSIS"
[1] 3
  ZNF721 MUTATED ZNF721 WILD-TYPE 
              17              472 
  ZNF721 MUTATED ZNF721 WILD-TYPE 
              17              472 
[1] "KIFAP3 MUTATION ANALYSIS"
[1] 3
  KIFAP3 MUTATED KIFAP3 WILD-TYPE 
               9              480 
  KIFAP3 MUTATED KIFAP3 WILD-TYPE 
               9              480 
[1] "SLC22A9 MUTATION ANALYSIS"
[1] 3
  SLC22A9 MUTATED SLC22A9 WILD-TYPE 
               10               479 
  SLC22A9 MUTATED SLC22A9 WILD-TYPE 
               10               479 
[1] "C5ORF22 MUTATION ANALYSIS"
[1] 3
  C5ORF22 MUTATED C5ORF22 WILD-TYPE 
               11               478 
  C5ORF22 MUTATED C5ORF22 WILD-TYPE 
               11               478 
[1] "FOXN3 MUTATION ANALYSIS"
[1] 3
  FOXN3 MUTATED FOXN3 WILD-TYPE 
             11             478 
  FOXN3 MUTATED FOXN3 WILD-TYPE 
             11             478 
[1] "IL2RG MUTATION ANALYSIS"
[1] 3
  IL2RG MUTATED IL2RG WILD-TYPE 
              8             481 
  IL2RG MUTATED IL2RG WILD-TYPE 
              8             481 
[1] "CARD6 MUTATION ANALYSIS"
[1] 3
  CARD6 MUTATED CARD6 WILD-TYPE 
             18             471 
  CARD6 MUTATED CARD6 WILD-TYPE 
             18             471 
[1] "BAZ2B MUTATION ANALYSIS"
[1] 3
  BAZ2B MUTATED BAZ2B WILD-TYPE 
             19             470 
  BAZ2B MUTATED BAZ2B WILD-TYPE 
             19             470 
[1] "ZNF384 MUTATION ANALYSIS"
[1] 3
  ZNF384 MUTATED ZNF384 WILD-TYPE 
               9              480 
  ZNF384 MUTATED ZNF384 WILD-TYPE 
               9              480 
[1] "MORC2 MUTATION ANALYSIS"
[1] 3
  MORC2 MUTATED MORC2 WILD-TYPE 
             14             475 
  MORC2 MUTATED MORC2 WILD-TYPE 
             14             475 
[1] "OTX2 MUTATION ANALYSIS"
[1] 3
  OTX2 MUTATED OTX2 WILD-TYPE 
             8            481 
  OTX2 MUTATED OTX2 WILD-TYPE 
             8            481 
[1] "CYP4A22 MUTATION ANALYSIS"
[1] 3
  CYP4A22 MUTATED CYP4A22 WILD-TYPE 
               13               476 
  CYP4A22 MUTATED CYP4A22 WILD-TYPE 
               13               476 
[1] "C14ORF102 MUTATION ANALYSIS"
[1] 3
  C14ORF102 MUTATED C14ORF102 WILD-TYPE 
                 19                 470 
  C14ORF102 MUTATED C14ORF102 WILD-TYPE 
                 19                 470 
[1] "LPGAT1 MUTATION ANALYSIS"
[1] 3
  LPGAT1 MUTATED LPGAT1 WILD-TYPE 
               4              485 
  LPGAT1 MUTATED LPGAT1 WILD-TYPE 
               4              485 
[1] "MAGEC1 MUTATION ANALYSIS"
[1] 3
  MAGEC1 MUTATED MAGEC1 WILD-TYPE 
              33              456 
  MAGEC1 MUTATED MAGEC1 WILD-TYPE 
              33              456 
[1] "EEA1 MUTATION ANALYSIS"
[1] 3
  EEA1 MUTATED EEA1 WILD-TYPE 
            16            473 
  EEA1 MUTATED EEA1 WILD-TYPE 
            16            473 
[1] "ADAM22 MUTATION ANALYSIS"
[1] 3
  ADAM22 MUTATED ADAM22 WILD-TYPE 
              11              478 
  ADAM22 MUTATED ADAM22 WILD-TYPE 
              11              478 
[1] "DDB1 MUTATION ANALYSIS"
[1] 3
  DDB1 MUTATED DDB1 WILD-TYPE 
            15            474 
  DDB1 MUTATED DDB1 WILD-TYPE 
            15            474 
[1] "GLI2 MUTATION ANALYSIS"
[1] 3
  GLI2 MUTATED GLI2 WILD-TYPE 
            26            463 
  GLI2 MUTATED GLI2 WILD-TYPE 
            26            463 
[1] "ADAM30 MUTATION ANALYSIS"
[1] 3
  ADAM30 MUTATED ADAM30 WILD-TYPE 
              13              476 
  ADAM30 MUTATED ADAM30 WILD-TYPE 
              13              476 
[1] "RGS22 MUTATION ANALYSIS"
[1] 3
  RGS22 MUTATED RGS22 WILD-TYPE 
             27             462 
  RGS22 MUTATED RGS22 WILD-TYPE 
             27             462 
[1] "PPP1R3A MUTATION ANALYSIS"
[1] 3
  PPP1R3A MUTATED PPP1R3A WILD-TYPE 
               38               451 
  PPP1R3A MUTATED PPP1R3A WILD-TYPE 
               38               451 
[1] "CCR2 MUTATION ANALYSIS"
[1] 3
  CCR2 MUTATED CCR2 WILD-TYPE 
             7            482 
  CCR2 MUTATED CCR2 WILD-TYPE 
             7            482 
[1] "OR4D2 MUTATION ANALYSIS"
[1] 3
  OR4D2 MUTATED OR4D2 WILD-TYPE 
              4             485 
  OR4D2 MUTATED OR4D2 WILD-TYPE 
              4             485 
[1] "OR4M2 MUTATION ANALYSIS"
[1] 3
  OR4M2 MUTATED OR4M2 WILD-TYPE 
             16             473 
  OR4M2 MUTATED OR4M2 WILD-TYPE 
             16             473 
[1] "EYS MUTATION ANALYSIS"
[1] 3
  EYS MUTATED EYS WILD-TYPE 
           41           448 
  EYS MUTATED EYS WILD-TYPE 
           41           448 
[1] "ARNT2 MUTATION ANALYSIS"
[1] 3
  ARNT2 MUTATED ARNT2 WILD-TYPE 
             14             475 
  ARNT2 MUTATED ARNT2 WILD-TYPE 
             14             475 
[1] "NIPBL MUTATION ANALYSIS"
[1] 3
  NIPBL MUTATED NIPBL WILD-TYPE 
             37             452 
  NIPBL MUTATED NIPBL WILD-TYPE 
             37             452 
[1] "G2E3 MUTATION ANALYSIS"
[1] 3
  G2E3 MUTATED G2E3 WILD-TYPE 
            15            474 
  G2E3 MUTATED G2E3 WILD-TYPE 
            15            474 
[1] "NOS3 MUTATION ANALYSIS"
[1] 3
  NOS3 MUTATED NOS3 WILD-TYPE 
            20            469 
  NOS3 MUTATED NOS3 WILD-TYPE 
            20            469 
[1] "EFEMP1 MUTATION ANALYSIS"
[1] 3
  EFEMP1 MUTATED EFEMP1 WILD-TYPE 
              20              469 
  EFEMP1 MUTATED EFEMP1 WILD-TYPE 
              20              469 
[1] "SPANXN2 MUTATION ANALYSIS"
[1] 3
  SPANXN2 MUTATED SPANXN2 WILD-TYPE 
                8               481 
  SPANXN2 MUTATED SPANXN2 WILD-TYPE 
                8               481 
[1] "RPS6KA3 MUTATION ANALYSIS"
[1] 3
  RPS6KA3 MUTATED RPS6KA3 WILD-TYPE 
               16               473 
  RPS6KA3 MUTATED RPS6KA3 WILD-TYPE 
               16               473 
[1] "ICOSLG MUTATION ANALYSIS"
[1] 3
  ICOSLG MUTATED ICOSLG WILD-TYPE 
               5              484 
  ICOSLG MUTATED ICOSLG WILD-TYPE 
               5              484 
[1] "PPIG MUTATION ANALYSIS"
[1] 3
  PPIG MUTATED PPIG WILD-TYPE 
            15            474 
  PPIG MUTATED PPIG WILD-TYPE 
            15            474 
[1] "PTPRN MUTATION ANALYSIS"
[1] 3
  PTPRN MUTATED PTPRN WILD-TYPE 
             17             472 
  PTPRN MUTATED PTPRN WILD-TYPE 
             17             472 
[1] "THOC6 MUTATION ANALYSIS"
[1] 3
  THOC6 MUTATED THOC6 WILD-TYPE 
              8             481 
  THOC6 MUTATED THOC6 WILD-TYPE 
              8             481 
[1] "HNRNPH3 MUTATION ANALYSIS"
[1] 3
  HNRNPH3 MUTATED HNRNPH3 WILD-TYPE 
                4               485 
  HNRNPH3 MUTATED HNRNPH3 WILD-TYPE 
                4               485 
[1] "FSHR MUTATION ANALYSIS"
[1] 3
  FSHR MUTATED FSHR WILD-TYPE 
            19            470 
  FSHR MUTATED FSHR WILD-TYPE 
            19            470 
[1] "HUWE1 MUTATION ANALYSIS"
[1] 3
  HUWE1 MUTATED HUWE1 WILD-TYPE 
             47             442 
  HUWE1 MUTATED HUWE1 WILD-TYPE 
             47             442 
[1] "EIF2B5 MUTATION ANALYSIS"
[1] 3
  EIF2B5 MUTATED EIF2B5 WILD-TYPE 
              16              473 
  EIF2B5 MUTATED EIF2B5 WILD-TYPE 
              16              473 
[1] "C14ORF118 MUTATION ANALYSIS"
[1] 3
  C14ORF118 MUTATED C14ORF118 WILD-TYPE 
                 10                 479 
  C14ORF118 MUTATED C14ORF118 WILD-TYPE 
                 10                 479 
[1] "USP9X MUTATION ANALYSIS"
[1] 3
  USP9X MUTATED USP9X WILD-TYPE 
             33             456 
  USP9X MUTATED USP9X WILD-TYPE 
             33             456 
[1] "SLC35A5 MUTATION ANALYSIS"
[1] 3
  SLC35A5 MUTATED SLC35A5 WILD-TYPE 
                8               481 
  SLC35A5 MUTATED SLC35A5 WILD-TYPE 
                8               481 
[1] "FAS MUTATION ANALYSIS"
[1] 3
  FAS MUTATED FAS WILD-TYPE 
            9           480 
  FAS MUTATED FAS WILD-TYPE 
            9           480 
[1] "PGM2 MUTATION ANALYSIS"
[1] 3
  PGM2 MUTATED PGM2 WILD-TYPE 
             4            485 
  PGM2 MUTATED PGM2 WILD-TYPE 
             4            485 
[1] "STX16 MUTATION ANALYSIS"
[1] 3
  STX16 MUTATED STX16 WILD-TYPE 
              7             482 
  STX16 MUTATED STX16 WILD-TYPE 
              7             482 
[1] "TJP1 MUTATION ANALYSIS"
[1] 3
  TJP1 MUTATED TJP1 WILD-TYPE 
            22            467 
  TJP1 MUTATED TJP1 WILD-TYPE 
            22            467 
[1] "INTS3 MUTATION ANALYSIS"
[1] 3
  INTS3 MUTATED INTS3 WILD-TYPE 
              8             481 
  INTS3 MUTATED INTS3 WILD-TYPE 
              8             481 
[1] "DBN1 MUTATION ANALYSIS"
[1] 3
  DBN1 MUTATED DBN1 WILD-TYPE 
            13            476 
  DBN1 MUTATED DBN1 WILD-TYPE 
            13            476 
[1] "MCCC1 MUTATION ANALYSIS"
[1] 3
  MCCC1 MUTATED MCCC1 WILD-TYPE 
             19             470 
  MCCC1 MUTATED MCCC1 WILD-TYPE 
             19             470 
[1] "ETF1 MUTATION ANALYSIS"
[1] 3
  ETF1 MUTATED ETF1 WILD-TYPE 
            12            477 
  ETF1 MUTATED ETF1 WILD-TYPE 
            12            477 
[1] "ALDOB MUTATION ANALYSIS"
[1] 3
  ALDOB MUTATED ALDOB WILD-TYPE 
             15             474 
  ALDOB MUTATED ALDOB WILD-TYPE 
             15             474 
[1] "TFEC MUTATION ANALYSIS"
[1] 3
  TFEC MUTATED TFEC WILD-TYPE 
            12            477 
  TFEC MUTATED TFEC WILD-TYPE 
            12            477 
[1] "NFATC3 MUTATION ANALYSIS"
[1] 3
  NFATC3 MUTATED NFATC3 WILD-TYPE 
              14              475 
  NFATC3 MUTATED NFATC3 WILD-TYPE 
              14              475 
[1] "ZNF83 MUTATION ANALYSIS"
[1] 3
  ZNF83 MUTATED ZNF83 WILD-TYPE 
             20             469 
  ZNF83 MUTATED ZNF83 WILD-TYPE 
             20             469 
[1] "CDC27 MUTATION ANALYSIS"
[1] 3
  CDC27 MUTATED CDC27 WILD-TYPE 
             16             473 
  CDC27 MUTATED CDC27 WILD-TYPE 
             16             473 
[1] "PAAF1 MUTATION ANALYSIS"
[1] 3
  PAAF1 MUTATED PAAF1 WILD-TYPE 
              6             483 
  PAAF1 MUTATED PAAF1 WILD-TYPE 
              6             483 
[1] "CD244 MUTATION ANALYSIS"
[1] 3
  CD244 MUTATED CD244 WILD-TYPE 
              7             482 
  CD244 MUTATED CD244 WILD-TYPE 
              7             482 
[1] "UAP1L1 MUTATION ANALYSIS"
[1] 3
  UAP1L1 MUTATED UAP1L1 WILD-TYPE 
               7              482 
  UAP1L1 MUTATED UAP1L1 WILD-TYPE 
               7              482 
[1] "FAM189B MUTATION ANALYSIS"
[1] 3
  FAM189B MUTATED FAM189B WILD-TYPE 
               13               476 
  FAM189B MUTATED FAM189B WILD-TYPE 
               13               476 
[1] "MIA3 MUTATION ANALYSIS"
[1] 3
  MIA3 MUTATED MIA3 WILD-TYPE 
            21            468 
  MIA3 MUTATED MIA3 WILD-TYPE 
            21            468 
[1] "EFHC2 MUTATION ANALYSIS"
[1] 3
  EFHC2 MUTATED EFHC2 WILD-TYPE 
             17             472 
  EFHC2 MUTATED EFHC2 WILD-TYPE 
             17             472 
[1] "PALLD MUTATION ANALYSIS"
[1] 3
  PALLD MUTATED PALLD WILD-TYPE 
             12             477 
  PALLD MUTATED PALLD WILD-TYPE 
             12             477 
[1] "C1QL3 MUTATION ANALYSIS"
[1] 3
  C1QL3 MUTATED C1QL3 WILD-TYPE 
              4             485 
  C1QL3 MUTATED C1QL3 WILD-TYPE 
              4             485 
[1] "SFRS18 MUTATION ANALYSIS"
[1] 3
  SFRS18 MUTATED SFRS18 WILD-TYPE 
              13              476 
  SFRS18 MUTATED SFRS18 WILD-TYPE 
              13              476 
[1] "TAT MUTATION ANALYSIS"
[1] 3
  TAT MUTATED TAT WILD-TYPE 
           15           474 
  TAT MUTATED TAT WILD-TYPE 
           15           474 
[1] "LRRC6 MUTATION ANALYSIS"
[1] 3
  LRRC6 MUTATED LRRC6 WILD-TYPE 
              4             485 
  LRRC6 MUTATED LRRC6 WILD-TYPE 
              4             485 
[1] "ADAM18 MUTATION ANALYSIS"
[1] 3
  ADAM18 MUTATED ADAM18 WILD-TYPE 
              23              466 
  ADAM18 MUTATED ADAM18 WILD-TYPE 
              23              466 
[1] "MRAS MUTATION ANALYSIS"
[1] 3
  MRAS MUTATED MRAS WILD-TYPE 
             4            485 
  MRAS MUTATED MRAS WILD-TYPE 
             4            485 
[1] "ADNP2 MUTATION ANALYSIS"
[1] 3
  ADNP2 MUTATED ADNP2 WILD-TYPE 
             17             472 
  ADNP2 MUTATED ADNP2 WILD-TYPE 
             17             472 
[1] "SLC22A16 MUTATION ANALYSIS"
[1] 3
  SLC22A16 MUTATED SLC22A16 WILD-TYPE 
                15                474 
  SLC22A16 MUTATED SLC22A16 WILD-TYPE 
                15                474 
[1] "GSS MUTATION ANALYSIS"
[1] 3
  GSS MUTATED GSS WILD-TYPE 
            9           480 
  GSS MUTATED GSS WILD-TYPE 
            9           480 
[1] "IGF2R MUTATION ANALYSIS"
[1] 3
  IGF2R MUTATED IGF2R WILD-TYPE 
             41             448 
  IGF2R MUTATED IGF2R WILD-TYPE 
             41             448 
[1] "OR51A4 MUTATION ANALYSIS"
[1] 3
  OR51A4 MUTATED OR51A4 WILD-TYPE 
               8              481 
  OR51A4 MUTATED OR51A4 WILD-TYPE 
               8              481 
[1] "CRYGA MUTATION ANALYSIS"
[1] 3
  CRYGA MUTATED CRYGA WILD-TYPE 
              5             484 
  CRYGA MUTATED CRYGA WILD-TYPE 
              5             484 
[1] "RNF10 MUTATION ANALYSIS"
[1] 3
  RNF10 MUTATED RNF10 WILD-TYPE 
             15             474 
  RNF10 MUTATED RNF10 WILD-TYPE 
             15             474 
[1] "NCAPD3 MUTATION ANALYSIS"
[1] 3
  NCAPD3 MUTATED NCAPD3 WILD-TYPE 
              26              463 
  NCAPD3 MUTATED NCAPD3 WILD-TYPE 
              26              463 
[1] "MTTP MUTATION ANALYSIS"
[1] 3
  MTTP MUTATED MTTP WILD-TYPE 
            28            461 
  MTTP MUTATED MTTP WILD-TYPE 
            28            461 
[1] "HEPH MUTATION ANALYSIS"
[1] 3
  HEPH MUTATED HEPH WILD-TYPE 
            19            470 
  HEPH MUTATED HEPH WILD-TYPE 
            19            470 
[1] "MAP2 MUTATION ANALYSIS"
[1] 3
  MAP2 MUTATED MAP2 WILD-TYPE 
            43            446 
  MAP2 MUTATED MAP2 WILD-TYPE 
            43            446 
[1] "NOD2 MUTATION ANALYSIS"
[1] 3
  NOD2 MUTATED NOD2 WILD-TYPE 
            20            469 
  NOD2 MUTATED NOD2 WILD-TYPE 
            20            469 
[1] "RSPO2 MUTATION ANALYSIS"
[1] 3
  RSPO2 MUTATED RSPO2 WILD-TYPE 
             21             468 
  RSPO2 MUTATED RSPO2 WILD-TYPE 
             21             468 
[1] "PCDH20 MUTATION ANALYSIS"
[1] 3
  PCDH20 MUTATED PCDH20 WILD-TYPE 
              24              465 
  PCDH20 MUTATED PCDH20 WILD-TYPE 
              24              465 
[1] "OR5H15 MUTATION ANALYSIS"
[1] 3
  OR5H15 MUTATED OR5H15 WILD-TYPE 
               7              482 
  OR5H15 MUTATED OR5H15 WILD-TYPE 
               7              482 
[1] "ACTL6B MUTATION ANALYSIS"
[1] 3
  ACTL6B MUTATED ACTL6B WILD-TYPE 
               9              480 
  ACTL6B MUTATED ACTL6B WILD-TYPE 
               9              480 
[1] "ZNF167 MUTATION ANALYSIS"
[1] 3
  ZNF167 MUTATED ZNF167 WILD-TYPE 
              18              471 
  ZNF167 MUTATED ZNF167 WILD-TYPE 
              18              471 
[1] "LPAR6 MUTATION ANALYSIS"
[1] 3
  LPAR6 MUTATED LPAR6 WILD-TYPE 
              8             481 
  LPAR6 MUTATED LPAR6 WILD-TYPE 
              8             481 
[1] "EIF4G2 MUTATION ANALYSIS"
[1] 3
  EIF4G2 MUTATED EIF4G2 WILD-TYPE 
              15              474 
  EIF4G2 MUTATED EIF4G2 WILD-TYPE 
              15              474 
[1] "PDP2 MUTATION ANALYSIS"
[1] 3
  PDP2 MUTATED PDP2 WILD-TYPE 
             6            483 
  PDP2 MUTATED PDP2 WILD-TYPE 
             6            483 
[1] "C4ORF49 MUTATION ANALYSIS"
[1] 3
  C4ORF49 MUTATED C4ORF49 WILD-TYPE 
                5               484 
  C4ORF49 MUTATED C4ORF49 WILD-TYPE 
                5               484 
[1] "KLRC3 MUTATION ANALYSIS"
[1] 3
  KLRC3 MUTATED KLRC3 WILD-TYPE 
              6             483 
  KLRC3 MUTATED KLRC3 WILD-TYPE 
              6             483 
[1] "RARS2 MUTATION ANALYSIS"
[1] 3
  RARS2 MUTATED RARS2 WILD-TYPE 
             10             479 
  RARS2 MUTATED RARS2 WILD-TYPE 
             10             479 
[1] "OR5K2 MUTATION ANALYSIS"
[1] 3
  OR5K2 MUTATED OR5K2 WILD-TYPE 
             11             478 
  OR5K2 MUTATED OR5K2 WILD-TYPE 
             11             478 
[1] "GABRP MUTATION ANALYSIS"
[1] 3
  GABRP MUTATED GABRP WILD-TYPE 
             13             476 
  GABRP MUTATED GABRP WILD-TYPE 
             13             476 
[1] "CCT5 MUTATION ANALYSIS"
[1] 3
  CCT5 MUTATED CCT5 WILD-TYPE 
             8            481 
  CCT5 MUTATED CCT5 WILD-TYPE 
             8            481 
[1] "MRPS18B MUTATION ANALYSIS"
[1] 3
  MRPS18B MUTATED MRPS18B WILD-TYPE 
                5               484 
  MRPS18B MUTATED MRPS18B WILD-TYPE 
                5               484 
[1] "LEF1 MUTATION ANALYSIS"
[1] 3
  LEF1 MUTATED LEF1 WILD-TYPE 
             9            480 
  LEF1 MUTATED LEF1 WILD-TYPE 
             9            480 
[1] "CD55 MUTATION ANALYSIS"
[1] 3
  CD55 MUTATED CD55 WILD-TYPE 
             8            481 
  CD55 MUTATED CD55 WILD-TYPE 
             8            481 
[1] "CIC MUTATION ANALYSIS"
[1] 3
  CIC MUTATED CIC WILD-TYPE 
           23           466 
  CIC MUTATED CIC WILD-TYPE 
           23           466 
[1] "TXNDC6 MUTATION ANALYSIS"
[1] 3
  TXNDC6 MUTATED TXNDC6 WILD-TYPE 
               9              480 
  TXNDC6 MUTATED TXNDC6 WILD-TYPE 
               9              480 
[1] "HERC5 MUTATION ANALYSIS"
[1] 3
  HERC5 MUTATED HERC5 WILD-TYPE 
             21             468 
  HERC5 MUTATED HERC5 WILD-TYPE 
             21             468 
[1] "ENSA MUTATION ANALYSIS"
[1] 3
  ENSA MUTATED ENSA WILD-TYPE 
             6            483 
  ENSA MUTATED ENSA WILD-TYPE 
             6            483 
[1] "TMEM45A MUTATION ANALYSIS"
[1] 3
  TMEM45A MUTATED TMEM45A WILD-TYPE 
                4               485 
  TMEM45A MUTATED TMEM45A WILD-TYPE 
                4               485 
[1] "TNNI3K MUTATION ANALYSIS"
[1] 3
  TNNI3K MUTATED TNNI3K WILD-TYPE 
              26              463 
  TNNI3K MUTATED TNNI3K WILD-TYPE 
              26              463 
[1] "PFN4 MUTATION ANALYSIS"
[1] 3
  PFN4 MUTATED PFN4 WILD-TYPE 
             6            483 
  PFN4 MUTATED PFN4 WILD-TYPE 
             6            483 
[1] "GPR75 MUTATION ANALYSIS"
[1] 3
  GPR75 MUTATED GPR75 WILD-TYPE 
              9             480 
  GPR75 MUTATED GPR75 WILD-TYPE 
              9             480 
[1] "LAX1 MUTATION ANALYSIS"
[1] 3
  LAX1 MUTATED LAX1 WILD-TYPE 
             5            484 
  LAX1 MUTATED LAX1 WILD-TYPE 
             5            484 
[1] "DHX36 MUTATION ANALYSIS"
[1] 3
  DHX36 MUTATED DHX36 WILD-TYPE 
             17             472 
  DHX36 MUTATED DHX36 WILD-TYPE 
             17             472 
[1] "C13ORF23 MUTATION ANALYSIS"
[1] 3
  C13ORF23 MUTATED C13ORF23 WILD-TYPE 
                13                476 
  C13ORF23 MUTATED C13ORF23 WILD-TYPE 
                13                476 
[1] "BAG5 MUTATION ANALYSIS"
[1] 3
  BAG5 MUTATED BAG5 WILD-TYPE 
             3            486 
  BAG5 MUTATED BAG5 WILD-TYPE 
             3            486 
[1] "MIPOL1 MUTATION ANALYSIS"
[1] 3
  MIPOL1 MUTATED MIPOL1 WILD-TYPE 
               5              484 
  MIPOL1 MUTATED MIPOL1 WILD-TYPE 
               5              484 
[1] "CDH22 MUTATION ANALYSIS"
[1] 3
  CDH22 MUTATED CDH22 WILD-TYPE 
             20             469 
  CDH22 MUTATED CDH22 WILD-TYPE 
             20             469 
[1] "MAPK9 MUTATION ANALYSIS"
[1] 3
  MAPK9 MUTATED MAPK9 WILD-TYPE 
             12             477 
  MAPK9 MUTATED MAPK9 WILD-TYPE 
             12             477 
[1] "NRK MUTATION ANALYSIS"
[1] 3
  NRK MUTATED NRK WILD-TYPE 
           29           460 
  NRK MUTATED NRK WILD-TYPE 
           29           460 
[1] "TMEM131 MUTATION ANALYSIS"
[1] 3
  TMEM131 MUTATED TMEM131 WILD-TYPE 
               22               467 
  TMEM131 MUTATED TMEM131 WILD-TYPE 
               22               467 
[1] "DOCK8 MUTATION ANALYSIS"
[1] 3
  DOCK8 MUTATED DOCK8 WILD-TYPE 
             22             467 
  DOCK8 MUTATED DOCK8 WILD-TYPE 
             22             467 
[1] "FLNB MUTATION ANALYSIS"
[1] 3
  FLNB MUTATED FLNB WILD-TYPE 
            31            458 
  FLNB MUTATED FLNB WILD-TYPE 
            31            458 
[1] "PTTG1IP MUTATION ANALYSIS"
[1] 3
  PTTG1IP MUTATED PTTG1IP WILD-TYPE 
                7               482 
  PTTG1IP MUTATED PTTG1IP WILD-TYPE 
                7               482 
[1] "FUCA2 MUTATION ANALYSIS"
[1] 3
  FUCA2 MUTATED FUCA2 WILD-TYPE 
              5             484 
  FUCA2 MUTATED FUCA2 WILD-TYPE 
              5             484 
[1] "VN1R4 MUTATION ANALYSIS"
[1] 3
  VN1R4 MUTATED VN1R4 WILD-TYPE 
              8             481 
  VN1R4 MUTATED VN1R4 WILD-TYPE 
              8             481 
[1] "ARFIP1 MUTATION ANALYSIS"
[1] 3
  ARFIP1 MUTATED ARFIP1 WILD-TYPE 
              12              477 
  ARFIP1 MUTATED ARFIP1 WILD-TYPE 
              12              477 
[1] "UPF2 MUTATION ANALYSIS"
[1] 3
  UPF2 MUTATED UPF2 WILD-TYPE 
            19            470 
  UPF2 MUTATED UPF2 WILD-TYPE 
            19            470 
[1] "DCUN1D3 MUTATION ANALYSIS"
[1] 3
  DCUN1D3 MUTATED DCUN1D3 WILD-TYPE 
                7               482 
  DCUN1D3 MUTATED DCUN1D3 WILD-TYPE 
                7               482 
[1] "GPR115 MUTATION ANALYSIS"
[1] 3
  GPR115 MUTATED GPR115 WILD-TYPE 
              22              467 
  GPR115 MUTATED GPR115 WILD-TYPE 
              22              467 
[1] "NLK MUTATION ANALYSIS"
[1] 3
  NLK MUTATED NLK WILD-TYPE 
           11           478 
  NLK MUTATED NLK WILD-TYPE 
           11           478 
[1] "ARHGAP32 MUTATION ANALYSIS"
[1] 3
  ARHGAP32 MUTATED ARHGAP32 WILD-TYPE 
                26                463 
  ARHGAP32 MUTATED ARHGAP32 WILD-TYPE 
                26                463 
[1] "PIK3R4 MUTATION ANALYSIS"
[1] 3
  PIK3R4 MUTATED PIK3R4 WILD-TYPE 
              17              472 
  PIK3R4 MUTATED PIK3R4 WILD-TYPE 
              17              472 
[1] "GNAS MUTATION ANALYSIS"
[1] 3
  GNAS MUTATED GNAS WILD-TYPE 
            36            453 
  GNAS MUTATED GNAS WILD-TYPE 
            36            453 
[1] "TRIB1 MUTATION ANALYSIS"
[1] 3
  TRIB1 MUTATED TRIB1 WILD-TYPE 
              9             480 
  TRIB1 MUTATED TRIB1 WILD-TYPE 
              9             480 
[1] "VWCE MUTATION ANALYSIS"
[1] 3
  VWCE MUTATED VWCE WILD-TYPE 
            15            474 
  VWCE MUTATED VWCE WILD-TYPE 
            15            474 
[1] "JMJD6 MUTATION ANALYSIS"
[1] 3
  JMJD6 MUTATED JMJD6 WILD-TYPE 
              9             480 
  JMJD6 MUTATED JMJD6 WILD-TYPE 
              9             480 
[1] "AGFG2 MUTATION ANALYSIS"
[1] 3
  AGFG2 MUTATED AGFG2 WILD-TYPE 
             12             477 
  AGFG2 MUTATED AGFG2 WILD-TYPE 
             12             477 
[1] "VWA5A MUTATION ANALYSIS"
[1] 3
  VWA5A MUTATED VWA5A WILD-TYPE 
             15             474 
  VWA5A MUTATED VWA5A WILD-TYPE 
             15             474 
[1] "BAIAP2L1 MUTATION ANALYSIS"
[1] 3
  BAIAP2L1 MUTATED BAIAP2L1 WILD-TYPE 
                13                476 
  BAIAP2L1 MUTATED BAIAP2L1 WILD-TYPE 
                13                476 
[1] "BRD4 MUTATION ANALYSIS"
[1] 3
  BRD4 MUTATED BRD4 WILD-TYPE 
            21            468 
  BRD4 MUTATED BRD4 WILD-TYPE 
            21            468 
[1] "GUCY1A3 MUTATION ANALYSIS"
[1] 3
  GUCY1A3 MUTATED GUCY1A3 WILD-TYPE 
               26               463 
  GUCY1A3 MUTATED GUCY1A3 WILD-TYPE 
               26               463 
[1] "MCF2L2 MUTATION ANALYSIS"
[1] 3
  MCF2L2 MUTATED MCF2L2 WILD-TYPE 
              23              466 
  MCF2L2 MUTATED MCF2L2 WILD-TYPE 
              23              466 
[1] "DNAH17 MUTATION ANALYSIS"
[1] 3
  DNAH17 MUTATED DNAH17 WILD-TYPE 
              32              457 
  DNAH17 MUTATED DNAH17 WILD-TYPE 
              32              457 
[1] "ANKRD17 MUTATION ANALYSIS"
[1] 3
  ANKRD17 MUTATED ANKRD17 WILD-TYPE 
               30               459 
  ANKRD17 MUTATED ANKRD17 WILD-TYPE 
               30               459 
[1] "RAB42 MUTATION ANALYSIS"
[1] 3
  RAB42 MUTATED RAB42 WILD-TYPE 
              4             485 
  RAB42 MUTATED RAB42 WILD-TYPE 
              4             485 
[1] "PSMA2 MUTATION ANALYSIS"
[1] 3
  PSMA2 MUTATED PSMA2 WILD-TYPE 
              6             483 
  PSMA2 MUTATED PSMA2 WILD-TYPE 
              6             483 
[1] "ZKSCAN1 MUTATION ANALYSIS"
[1] 3
  ZKSCAN1 MUTATED ZKSCAN1 WILD-TYPE 
                8               481 
  ZKSCAN1 MUTATED ZKSCAN1 WILD-TYPE 
                8               481 
[1] "SLC27A2 MUTATION ANALYSIS"
[1] 3
  SLC27A2 MUTATED SLC27A2 WILD-TYPE 
                7               482 
  SLC27A2 MUTATED SLC27A2 WILD-TYPE 
                7               482 
[1] "OR6C75 MUTATION ANALYSIS"
[1] 3
  OR6C75 MUTATED OR6C75 WILD-TYPE 
               8              481 
  OR6C75 MUTATED OR6C75 WILD-TYPE 
               8              481 
[1] "TRIM54 MUTATION ANALYSIS"
[1] 3
  TRIM54 MUTATED TRIM54 WILD-TYPE 
               9              480 
  TRIM54 MUTATED TRIM54 WILD-TYPE 
               9              480 
[1] "ERCC6L MUTATION ANALYSIS"
[1] 3
  ERCC6L MUTATED ERCC6L WILD-TYPE 
              16              473 
  ERCC6L MUTATED ERCC6L WILD-TYPE 
              16              473 
[1] "CXORF38 MUTATION ANALYSIS"
[1] 3
  CXORF38 MUTATED CXORF38 WILD-TYPE 
                6               483 
  CXORF38 MUTATED CXORF38 WILD-TYPE 
                6               483 
[1] "C12ORF49 MUTATION ANALYSIS"
[1] 3
  C12ORF49 MUTATED C12ORF49 WILD-TYPE 
                 4                485 
  C12ORF49 MUTATED C12ORF49 WILD-TYPE 
                 4                485 
[1] "VEZF1 MUTATION ANALYSIS"
[1] 3
  VEZF1 MUTATED VEZF1 WILD-TYPE 
              7             482 
  VEZF1 MUTATED VEZF1 WILD-TYPE 
              7             482 
[1] "DNAH6 MUTATION ANALYSIS"
[1] 3
  DNAH6 MUTATED DNAH6 WILD-TYPE 
             24             465 
  DNAH6 MUTATED DNAH6 WILD-TYPE 
             24             465 
[1] "ATP12A MUTATION ANALYSIS"
[1] 3
  ATP12A MUTATED ATP12A WILD-TYPE 
              30              459 
  ATP12A MUTATED ATP12A WILD-TYPE 
              30              459 
[1] "SGK3 MUTATION ANALYSIS"
[1] 3
  SGK3 MUTATED SGK3 WILD-TYPE 
            10            479 
  SGK3 MUTATED SGK3 WILD-TYPE 
            10            479 
[1] "ODAM MUTATION ANALYSIS"
[1] 3
  ODAM MUTATED ODAM WILD-TYPE 
             6            483 
  ODAM MUTATED ODAM WILD-TYPE 
             6            483 
[1] "CYSLTR2 MUTATION ANALYSIS"
[1] 3
  CYSLTR2 MUTATED CYSLTR2 WILD-TYPE 
               17               472 
  CYSLTR2 MUTATED CYSLTR2 WILD-TYPE 
               17               472 
[1] "RAB6C MUTATION ANALYSIS"
[1] 3
  RAB6C MUTATED RAB6C WILD-TYPE 
              5             484 
  RAB6C MUTATED RAB6C WILD-TYPE 
              5             484 
[1] "ZC3H6 MUTATION ANALYSIS"
[1] 3
  ZC3H6 MUTATED ZC3H6 WILD-TYPE 
             18             471 
  ZC3H6 MUTATED ZC3H6 WILD-TYPE 
             18             471 
[1] "TMEM48 MUTATION ANALYSIS"
[1] 3
  TMEM48 MUTATED TMEM48 WILD-TYPE 
              11              478 
  TMEM48 MUTATED TMEM48 WILD-TYPE 
              11              478 
[1] "C12ORF10 MUTATION ANALYSIS"
[1] 3
  C12ORF10 MUTATED C12ORF10 WILD-TYPE 
                 4                485 
  C12ORF10 MUTATED C12ORF10 WILD-TYPE 
                 4                485 
[1] "OSTM1 MUTATION ANALYSIS"
[1] 3
  OSTM1 MUTATED OSTM1 WILD-TYPE 
              5             484 
  OSTM1 MUTATED OSTM1 WILD-TYPE 
              5             484 
[1] "PLEKHB2 MUTATION ANALYSIS"
[1] 3
  PLEKHB2 MUTATED PLEKHB2 WILD-TYPE 
                6               483 
  PLEKHB2 MUTATED PLEKHB2 WILD-TYPE 
                6               483 
[1] "RALA MUTATION ANALYSIS"
[1] 3
  RALA MUTATED RALA WILD-TYPE 
             8            481 
  RALA MUTATED RALA WILD-TYPE 
             8            481 
[1] "BRD8 MUTATION ANALYSIS"
[1] 3
  BRD8 MUTATED BRD8 WILD-TYPE 
            18            471 
  BRD8 MUTATED BRD8 WILD-TYPE 
            18            471 
[1] "PER3 MUTATION ANALYSIS"
[1] 3
  PER3 MUTATED PER3 WILD-TYPE 
            18            471 
  PER3 MUTATED PER3 WILD-TYPE 
            18            471 
[1] "WT1 MUTATION ANALYSIS"
[1] 3
  WT1 MUTATED WT1 WILD-TYPE 
           30           459 
  WT1 MUTATED WT1 WILD-TYPE 
           30           459 
[1] "METTL9 MUTATION ANALYSIS"
[1] 3
  METTL9 MUTATED METTL9 WILD-TYPE 
               4              485 
  METTL9 MUTATED METTL9 WILD-TYPE 
               4              485 
[1] "FH MUTATION ANALYSIS"
[1] 3
  FH MUTATED FH WILD-TYPE 
          10          479 
  FH MUTATED FH WILD-TYPE 
          10          479 
[1] "H2AFJ MUTATION ANALYSIS"
[1] 3
  H2AFJ MUTATED H2AFJ WILD-TYPE 
              3             486 
  H2AFJ MUTATED H2AFJ WILD-TYPE 
              3             486 
[1] "CDH10 MUTATION ANALYSIS"
[1] 3
  CDH10 MUTATED CDH10 WILD-TYPE 
             42             447 
  CDH10 MUTATED CDH10 WILD-TYPE 
             42             447 
[1] "HCRTR2 MUTATION ANALYSIS"
[1] 3
  HCRTR2 MUTATED HCRTR2 WILD-TYPE 
               7              482 
  HCRTR2 MUTATED HCRTR2 WILD-TYPE 
               7              482 
[1] "MTF1 MUTATION ANALYSIS"
[1] 3
  MTF1 MUTATED MTF1 WILD-TYPE 
            10            479 
  MTF1 MUTATED MTF1 WILD-TYPE 
            10            479 
[1] "ZNF518B MUTATION ANALYSIS"
[1] 3
  ZNF518B MUTATED ZNF518B WILD-TYPE 
               14               475 
  ZNF518B MUTATED ZNF518B WILD-TYPE 
               14               475 
[1] "KIAA0195 MUTATION ANALYSIS"
[1] 3
  KIAA0195 MUTATED KIAA0195 WILD-TYPE 
                18                471 
  KIAA0195 MUTATED KIAA0195 WILD-TYPE 
                18                471 
[1] "FAM20B MUTATION ANALYSIS"
[1] 3
  FAM20B MUTATED FAM20B WILD-TYPE 
              10              479 
  FAM20B MUTATED FAM20B WILD-TYPE 
              10              479 
[1] "EPHB1 MUTATION ANALYSIS"
[1] 3
  EPHB1 MUTATED EPHB1 WILD-TYPE 
             43             446 
  EPHB1 MUTATED EPHB1 WILD-TYPE 
             43             446 
[1] "APBB1IP MUTATION ANALYSIS"
[1] 3
  APBB1IP MUTATED APBB1IP WILD-TYPE 
               19               470 
  APBB1IP MUTATED APBB1IP WILD-TYPE 
               19               470 
[1] "TXNDC17 MUTATION ANALYSIS"
[1] 3
  TXNDC17 MUTATED TXNDC17 WILD-TYPE 
                5               484 
  TXNDC17 MUTATED TXNDC17 WILD-TYPE 
                5               484 
[1] "HPSE MUTATION ANALYSIS"
[1] 3
  HPSE MUTATED HPSE WILD-TYPE 
            11            478 
  HPSE MUTATED HPSE WILD-TYPE 
            11            478 
[1] "SLC39A2 MUTATION ANALYSIS"
[1] 3
  SLC39A2 MUTATED SLC39A2 WILD-TYPE 
               10               479 
  SLC39A2 MUTATED SLC39A2 WILD-TYPE 
               10               479 
[1] "C9ORF71 MUTATION ANALYSIS"
[1] 3
  C9ORF71 MUTATED C9ORF71 WILD-TYPE 
                4               485 
  C9ORF71 MUTATED C9ORF71 WILD-TYPE 
                4               485 
[1] "STYK1 MUTATION ANALYSIS"
[1] 3
  STYK1 MUTATED STYK1 WILD-TYPE 
              7             482 
  STYK1 MUTATED STYK1 WILD-TYPE 
              7             482 
[1] "LGR4 MUTATION ANALYSIS"
[1] 3
  LGR4 MUTATED LGR4 WILD-TYPE 
            17            472 
  LGR4 MUTATED LGR4 WILD-TYPE 
            17            472 
[1] "C14ORF28 MUTATION ANALYSIS"
[1] 3
  C14ORF28 MUTATED C14ORF28 WILD-TYPE 
                 5                484 
  C14ORF28 MUTATED C14ORF28 WILD-TYPE 
                 5                484 
[1] "ACTL6A MUTATION ANALYSIS"
[1] 3
  ACTL6A MUTATED ACTL6A WILD-TYPE 
               7              482 
  ACTL6A MUTATED ACTL6A WILD-TYPE 
               7              482 
[1] "UPF3A MUTATION ANALYSIS"
[1] 3
  UPF3A MUTATED UPF3A WILD-TYPE 
              9             480 
  UPF3A MUTATED UPF3A WILD-TYPE 
              9             480 
[1] "MDH1 MUTATION ANALYSIS"
[1] 3
  MDH1 MUTATED MDH1 WILD-TYPE 
             8            481 
  MDH1 MUTATED MDH1 WILD-TYPE 
             8            481 
[1] "MYH11 MUTATION ANALYSIS"
[1] 3
  MYH11 MUTATED MYH11 WILD-TYPE 
             35             454 
  MYH11 MUTATED MYH11 WILD-TYPE 
             35             454 
[1] "KLF11 MUTATION ANALYSIS"
[1] 3
  KLF11 MUTATED KLF11 WILD-TYPE 
              8             481 
  KLF11 MUTATED KLF11 WILD-TYPE 
              8             481 
[1] "MED12L MUTATION ANALYSIS"
[1] 3
  MED12L MUTATED MED12L WILD-TYPE 
              31              458 
  MED12L MUTATED MED12L WILD-TYPE 
              31              458 
[1] "ZNF620 MUTATION ANALYSIS"
[1] 3
  ZNF620 MUTATED ZNF620 WILD-TYPE 
               9              480 
  ZNF620 MUTATED ZNF620 WILD-TYPE 
               9              480 
[1] "UGT1A7 MUTATION ANALYSIS"
[1] 3
  UGT1A7 MUTATED UGT1A7 WILD-TYPE 
               8              481 
  UGT1A7 MUTATED UGT1A7 WILD-TYPE 
               8              481 
[1] "UST MUTATION ANALYSIS"
[1] 3
  UST MUTATED UST WILD-TYPE 
           11           478 
  UST MUTATED UST WILD-TYPE 
           11           478 
[1] "NDUFAF1 MUTATION ANALYSIS"
[1] 3
  NDUFAF1 MUTATED NDUFAF1 WILD-TYPE 
                7               482 
  NDUFAF1 MUTATED NDUFAF1 WILD-TYPE 
                7               482 
[1] "ENPP1 MUTATION ANALYSIS"
[1] 3
  ENPP1 MUTATED ENPP1 WILD-TYPE 
             15             474 
  ENPP1 MUTATED ENPP1 WILD-TYPE 
             15             474 
[1] "CASP4 MUTATION ANALYSIS"
[1] 3
  CASP4 MUTATED CASP4 WILD-TYPE 
             10             479 
  CASP4 MUTATED CASP4 WILD-TYPE 
             10             479 
[1] "STK36 MUTATION ANALYSIS"
[1] 3
  STK36 MUTATED STK36 WILD-TYPE 
             18             471 
  STK36 MUTATED STK36 WILD-TYPE 
             18             471 
[1] "KRT19 MUTATION ANALYSIS"
[1] 3
  KRT19 MUTATED KRT19 WILD-TYPE 
              4             485 
  KRT19 MUTATED KRT19 WILD-TYPE 
              4             485 
[1] "KIF16B MUTATION ANALYSIS"
[1] 3
  KIF16B MUTATED KIF16B WILD-TYPE 
              31              458 
  KIF16B MUTATED KIF16B WILD-TYPE 
              31              458 
[1] "ZHX1 MUTATION ANALYSIS"
[1] 3
  ZHX1 MUTATED ZHX1 WILD-TYPE 
            11            478 
  ZHX1 MUTATED ZHX1 WILD-TYPE 
            11            478 
[1] "ZNF658 MUTATION ANALYSIS"
[1] 3
  ZNF658 MUTATED ZNF658 WILD-TYPE 
              14              475 
  ZNF658 MUTATED ZNF658 WILD-TYPE 
              14              475 
[1] "GPR141 MUTATION ANALYSIS"
[1] 3
  GPR141 MUTATED GPR141 WILD-TYPE 
              11              478 
  GPR141 MUTATED GPR141 WILD-TYPE 
              11              478 
[1] "ZNF585A MUTATION ANALYSIS"
[1] 3
  ZNF585A MUTATED ZNF585A WILD-TYPE 
               19               470 
  ZNF585A MUTATED ZNF585A WILD-TYPE 
               19               470 
[1] "DIAPH2 MUTATION ANALYSIS"
[1] 3
  DIAPH2 MUTATED DIAPH2 WILD-TYPE 
              25              464 
  DIAPH2 MUTATED DIAPH2 WILD-TYPE 
              25              464 
[1] "ANKRD10 MUTATION ANALYSIS"
[1] 3
  ANKRD10 MUTATED ANKRD10 WILD-TYPE 
                9               480 
  ANKRD10 MUTATED ANKRD10 WILD-TYPE 
                9               480 
[1] "ASPG MUTATION ANALYSIS"
[1] 3
  ASPG MUTATED ASPG WILD-TYPE 
             7            482 
  ASPG MUTATED ASPG WILD-TYPE 
             7            482 
[1] "CDK14 MUTATION ANALYSIS"
[1] 3
  CDK14 MUTATED CDK14 WILD-TYPE 
             17             472 
  CDK14 MUTATED CDK14 WILD-TYPE 
             17             472 
[1] "OR8A1 MUTATION ANALYSIS"
[1] 3
  OR8A1 MUTATED OR8A1 WILD-TYPE 
              5             484 
  OR8A1 MUTATED OR8A1 WILD-TYPE 
              5             484 
[1] "SPINT4 MUTATION ANALYSIS"
[1] 3
  SPINT4 MUTATED SPINT4 WILD-TYPE 
               4              485 
  SPINT4 MUTATED SPINT4 WILD-TYPE 
               4              485 
[1] "E2F5 MUTATION ANALYSIS"
[1] 3
  E2F5 MUTATED E2F5 WILD-TYPE 
             7            482 
  E2F5 MUTATED E2F5 WILD-TYPE 
             7            482 
[1] "STRADB MUTATION ANALYSIS"
[1] 3
  STRADB MUTATED STRADB WILD-TYPE 
               7              482 
  STRADB MUTATED STRADB WILD-TYPE 
               7              482 
[1] "RANBP17 MUTATION ANALYSIS"
[1] 3
  RANBP17 MUTATED RANBP17 WILD-TYPE 
               12               477 
  RANBP17 MUTATED RANBP17 WILD-TYPE 
               12               477 
[1] "AHCTF1 MUTATION ANALYSIS"
[1] 3
  AHCTF1 MUTATED AHCTF1 WILD-TYPE 
              23              466 
  AHCTF1 MUTATED AHCTF1 WILD-TYPE 
              23              466 
[1] "OR10J1 MUTATION ANALYSIS"
[1] 3
  OR10J1 MUTATED OR10J1 WILD-TYPE 
              13              476 
  OR10J1 MUTATED OR10J1 WILD-TYPE 
              13              476 
[1] "MATN3 MUTATION ANALYSIS"
[1] 3
  MATN3 MUTATED MATN3 WILD-TYPE 
              6             483 
  MATN3 MUTATED MATN3 WILD-TYPE 
              6             483 
[1] "HNMT MUTATION ANALYSIS"
[1] 3
  HNMT MUTATED HNMT WILD-TYPE 
             8            481 
  HNMT MUTATED HNMT WILD-TYPE 
             8            481 
[1] "PAGE2 MUTATION ANALYSIS"
[1] 3
  PAGE2 MUTATED PAGE2 WILD-TYPE 
              9             480 
  PAGE2 MUTATED PAGE2 WILD-TYPE 
              9             480 
[1] "MYH3 MUTATION ANALYSIS"
[1] 3
  MYH3 MUTATED MYH3 WILD-TYPE 
            37            452 
  MYH3 MUTATED MYH3 WILD-TYPE 
            37            452 
[1] "OR6C1 MUTATION ANALYSIS"
[1] 3
  OR6C1 MUTATED OR6C1 WILD-TYPE 
              8             481 
  OR6C1 MUTATED OR6C1 WILD-TYPE 
              8             481 
[1] "GDE1 MUTATION ANALYSIS"
[1] 3
  GDE1 MUTATED GDE1 WILD-TYPE 
             6            483 
  GDE1 MUTATED GDE1 WILD-TYPE 
             6            483 
[1] "GRINA MUTATION ANALYSIS"
[1] 3
  GRINA MUTATED GRINA WILD-TYPE 
              4             485 
  GRINA MUTATED GRINA WILD-TYPE 
              4             485 
[1] "FRMD4B MUTATION ANALYSIS"
[1] 3
  FRMD4B MUTATED FRMD4B WILD-TYPE 
               8              481 
  FRMD4B MUTATED FRMD4B WILD-TYPE 
               8              481 
[1] "ARHGAP11A MUTATION ANALYSIS"
[1] 3
  ARHGAP11A MUTATED ARHGAP11A WILD-TYPE 
                 16                 473 
  ARHGAP11A MUTATED ARHGAP11A WILD-TYPE 
                 16                 473 
[1] "CHRM2 MUTATION ANALYSIS"
[1] 3
  CHRM2 MUTATED CHRM2 WILD-TYPE 
             26             463 
  CHRM2 MUTATED CHRM2 WILD-TYPE 
             26             463 
[1] "CEP290 MUTATION ANALYSIS"
[1] 3
  CEP290 MUTATED CEP290 WILD-TYPE 
              31              458 
  CEP290 MUTATED CEP290 WILD-TYPE 
              31              458 
[1] "MYBPH MUTATION ANALYSIS"
[1] 3
  MYBPH MUTATED MYBPH WILD-TYPE 
              7             482 
  MYBPH MUTATED MYBPH WILD-TYPE 
              7             482 
[1] "A2M MUTATION ANALYSIS"
[1] 3
  A2M MUTATED A2M WILD-TYPE 
           28           461 
  A2M MUTATED A2M WILD-TYPE 
           28           461 
[1] "ADM MUTATION ANALYSIS"
[1] 3
  ADM MUTATED ADM WILD-TYPE 
            6           483 
  ADM MUTATED ADM WILD-TYPE 
            6           483 
[1] "COL3A1 MUTATION ANALYSIS"
[1] 3
  COL3A1 MUTATED COL3A1 WILD-TYPE 
              32              457 
  COL3A1 MUTATED COL3A1 WILD-TYPE 
              32              457 
[1] "CCAR1 MUTATION ANALYSIS"
[1] 3
  CCAR1 MUTATED CCAR1 WILD-TYPE 
             20             469 
  CCAR1 MUTATED CCAR1 WILD-TYPE 
             20             469 
[1] "ZNF182 MUTATION ANALYSIS"
[1] 3
  ZNF182 MUTATED ZNF182 WILD-TYPE 
              16              473 
  ZNF182 MUTATED ZNF182 WILD-TYPE 
              16              473 
[1] "CXXC5 MUTATION ANALYSIS"
[1] 3
  CXXC5 MUTATED CXXC5 WILD-TYPE 
              6             483 
  CXXC5 MUTATED CXXC5 WILD-TYPE 
              6             483 
[1] "SPAG1 MUTATION ANALYSIS"
[1] 3
  SPAG1 MUTATED SPAG1 WILD-TYPE 
             12             477 
  SPAG1 MUTATED SPAG1 WILD-TYPE 
             12             477 
[1] "KIAA0649 MUTATION ANALYSIS"
[1] 3
  KIAA0649 MUTATED KIAA0649 WILD-TYPE 
                10                479 
  KIAA0649 MUTATED KIAA0649 WILD-TYPE 
                10                479 
[1] "SPZ1 MUTATION ANALYSIS"
[1] 3
  SPZ1 MUTATED SPZ1 WILD-TYPE 
            11            478 
  SPZ1 MUTATED SPZ1 WILD-TYPE 
            11            478 
[1] "MLLT1 MUTATION ANALYSIS"
[1] 3
  MLLT1 MUTATED MLLT1 WILD-TYPE 
              6             483 
  MLLT1 MUTATED MLLT1 WILD-TYPE 
              6             483 
[1] "DLL3 MUTATION ANALYSIS"
[1] 3
  DLL3 MUTATED DLL3 WILD-TYPE 
             7            482 
  DLL3 MUTATED DLL3 WILD-TYPE 
             7            482 
[1] "PHF1 MUTATION ANALYSIS"
[1] 3
  PHF1 MUTATED PHF1 WILD-TYPE 
             7            482 
  PHF1 MUTATED PHF1 WILD-TYPE 
             7            482 
[1] "IFNAR1 MUTATION ANALYSIS"
[1] 3
  IFNAR1 MUTATED IFNAR1 WILD-TYPE 
               7              482 
  IFNAR1 MUTATED IFNAR1 WILD-TYPE 
               7              482 
[1] "MAP4K4 MUTATION ANALYSIS"
[1] 3
  MAP4K4 MUTATED MAP4K4 WILD-TYPE 
              21              468 
  MAP4K4 MUTATED MAP4K4 WILD-TYPE 
              21              468 
[1] "CSNK2A2 MUTATION ANALYSIS"
[1] 3
  CSNK2A2 MUTATED CSNK2A2 WILD-TYPE 
                7               482 
  CSNK2A2 MUTATED CSNK2A2 WILD-TYPE 
                7               482 
[1] "CBX3 MUTATION ANALYSIS"
[1] 3
  CBX3 MUTATED CBX3 WILD-TYPE 
             7            482 
  CBX3 MUTATED CBX3 WILD-TYPE 
             7            482 
[1] "MCART1 MUTATION ANALYSIS"
[1] 3
  MCART1 MUTATED MCART1 WILD-TYPE 
              13              476 
  MCART1 MUTATED MCART1 WILD-TYPE 
              13              476 
[1] "USP28 MUTATION ANALYSIS"
[1] 3
  USP28 MUTATED USP28 WILD-TYPE 
             28             461 
  USP28 MUTATED USP28 WILD-TYPE 
             28             461 
[1] "ZBP1 MUTATION ANALYSIS"
[1] 3
  ZBP1 MUTATED ZBP1 WILD-TYPE 
            13            476 
  ZBP1 MUTATED ZBP1 WILD-TYPE 
            13            476 
[1] "MYLK4 MUTATION ANALYSIS"
[1] 3
  MYLK4 MUTATED MYLK4 WILD-TYPE 
             14             475 
  MYLK4 MUTATED MYLK4 WILD-TYPE 
             14             475 
[1] "FER MUTATION ANALYSIS"
[1] 3
  FER MUTATED FER WILD-TYPE 
           17           472 
  FER MUTATED FER WILD-TYPE 
           17           472 
[1] "GNA11 MUTATION ANALYSIS"
[1] 3
  GNA11 MUTATED GNA11 WILD-TYPE 
              7             482 
  GNA11 MUTATED GNA11 WILD-TYPE 
              7             482 
[1] "CHRNA1 MUTATION ANALYSIS"
[1] 3
  CHRNA1 MUTATED CHRNA1 WILD-TYPE 
              12              477 
  CHRNA1 MUTATED CHRNA1 WILD-TYPE 
              12              477 
[1] "SLC16A1 MUTATION ANALYSIS"
[1] 3
  SLC16A1 MUTATED SLC16A1 WILD-TYPE 
               10               479 
  SLC16A1 MUTATED SLC16A1 WILD-TYPE 
               10               479 
[1] "TRAM1L1 MUTATION ANALYSIS"
[1] 3
  TRAM1L1 MUTATED TRAM1L1 WILD-TYPE 
               14               475 
  TRAM1L1 MUTATED TRAM1L1 WILD-TYPE 
               14               475 
[1] "MRPL13 MUTATION ANALYSIS"
[1] 3
  MRPL13 MUTATED MRPL13 WILD-TYPE 
               8              481 
  MRPL13 MUTATED MRPL13 WILD-TYPE 
               8              481 
[1] "MARVELD2 MUTATION ANALYSIS"
[1] 3
  MARVELD2 MUTATED MARVELD2 WILD-TYPE 
                11                478 
  MARVELD2 MUTATED MARVELD2 WILD-TYPE 
                11                478 
[1] "PAX6 MUTATION ANALYSIS"
[1] 3
  PAX6 MUTATED PAX6 WILD-TYPE 
            16            473 
  PAX6 MUTATED PAX6 WILD-TYPE 
            16            473 
[1] "ZNF547 MUTATION ANALYSIS"
[1] 3
  ZNF547 MUTATED ZNF547 WILD-TYPE 
              10              479 
  ZNF547 MUTATED ZNF547 WILD-TYPE 
              10              479 
[1] "ADCY9 MUTATION ANALYSIS"
[1] 3
  ADCY9 MUTATED ADCY9 WILD-TYPE 
             20             469 
  ADCY9 MUTATED ADCY9 WILD-TYPE 
             20             469 
[1] "AGAP4 MUTATION ANALYSIS"
[1] 3
  AGAP4 MUTATED AGAP4 WILD-TYPE 
              4             485 
  AGAP4 MUTATED AGAP4 WILD-TYPE 
              4             485 
[1] "OR11H12 MUTATION ANALYSIS"
[1] 3
  OR11H12 MUTATED OR11H12 WILD-TYPE 
                5               484 
  OR11H12 MUTATED OR11H12 WILD-TYPE 
                5               484 
[1] "SLC22A3 MUTATION ANALYSIS"
[1] 3
  SLC22A3 MUTATED SLC22A3 WILD-TYPE 
               13               476 
  SLC22A3 MUTATED SLC22A3 WILD-TYPE 
               13               476 
[1] "ATAD2B MUTATION ANALYSIS"
[1] 3
  ATAD2B MUTATED ATAD2B WILD-TYPE 
              18              471 
  ATAD2B MUTATED ATAD2B WILD-TYPE 
              18              471 
[1] "GPR126 MUTATION ANALYSIS"
[1] 3
  GPR126 MUTATED GPR126 WILD-TYPE 
              19              470 
  GPR126 MUTATED GPR126 WILD-TYPE 
              19              470 
[1] "CHMP4C MUTATION ANALYSIS"
[1] 3
  CHMP4C MUTATED CHMP4C WILD-TYPE 
               4              485 
  CHMP4C MUTATED CHMP4C WILD-TYPE 
               4              485 
[1] "POLQ MUTATION ANALYSIS"
[1] 3
  POLQ MUTATED POLQ WILD-TYPE 
            33            456 
  POLQ MUTATED POLQ WILD-TYPE 
            33            456 
[1] "CLGN MUTATION ANALYSIS"
[1] 3
  CLGN MUTATED CLGN WILD-TYPE 
            13            476 
  CLGN MUTATED CLGN WILD-TYPE 
            13            476 
[1] "EML4 MUTATION ANALYSIS"
[1] 3
  EML4 MUTATED EML4 WILD-TYPE 
            10            479 
  EML4 MUTATED EML4 WILD-TYPE 
            10            479 
[1] "AP1G2 MUTATION ANALYSIS"
[1] 3
  AP1G2 MUTATED AP1G2 WILD-TYPE 
             15             474 
  AP1G2 MUTATED AP1G2 WILD-TYPE 
             15             474 
[1] "CD3D MUTATION ANALYSIS"
[1] 3
  CD3D MUTATED CD3D WILD-TYPE 
             5            484 
  CD3D MUTATED CD3D WILD-TYPE 
             5            484 
[1] "CCDC69 MUTATION ANALYSIS"
[1] 3
  CCDC69 MUTATED CCDC69 WILD-TYPE 
               5              484 
  CCDC69 MUTATED CCDC69 WILD-TYPE 
               5              484 
[1] "NOL9 MUTATION ANALYSIS"
[1] 3
  NOL9 MUTATED NOL9 WILD-TYPE 
             7            482 
  NOL9 MUTATED NOL9 WILD-TYPE 
             7            482 
[1] "DSC2 MUTATION ANALYSIS"
[1] 3
  DSC2 MUTATED DSC2 WILD-TYPE 
            15            474 
  DSC2 MUTATED DSC2 WILD-TYPE 
            15            474 
[1] "AGTPBP1 MUTATION ANALYSIS"
[1] 3
  AGTPBP1 MUTATED AGTPBP1 WILD-TYPE 
               21               468 
  AGTPBP1 MUTATED AGTPBP1 WILD-TYPE 
               21               468 
[1] "C18ORF19 MUTATION ANALYSIS"
[1] 3
  C18ORF19 MUTATED C18ORF19 WILD-TYPE 
                 9                480 
  C18ORF19 MUTATED C18ORF19 WILD-TYPE 
                 9                480 
[1] "AWAT1 MUTATION ANALYSIS"
[1] 3
  AWAT1 MUTATED AWAT1 WILD-TYPE 
              9             480 
  AWAT1 MUTATED AWAT1 WILD-TYPE 
              9             480 
[1] "YSK4 MUTATION ANALYSIS"
[1] 3
  YSK4 MUTATED YSK4 WILD-TYPE 
            30            459 
  YSK4 MUTATED YSK4 WILD-TYPE 
            30            459 
[1] "GSTA5 MUTATION ANALYSIS"
[1] 3
  GSTA5 MUTATED GSTA5 WILD-TYPE 
              8             481 
  GSTA5 MUTATED GSTA5 WILD-TYPE 
              8             481 
[1] "PCOLCE2 MUTATION ANALYSIS"
[1] 3
  PCOLCE2 MUTATED PCOLCE2 WILD-TYPE 
               15               474 
  PCOLCE2 MUTATED PCOLCE2 WILD-TYPE 
               15               474 
[1] "BUB1B MUTATION ANALYSIS"
[1] 3
  BUB1B MUTATED BUB1B WILD-TYPE 
             11             478 
  BUB1B MUTATED BUB1B WILD-TYPE 
             11             478 
[1] "MC3R MUTATION ANALYSIS"
[1] 3
  MC3R MUTATED MC3R WILD-TYPE 
            14            475 
  MC3R MUTATED MC3R WILD-TYPE 
            14            475 
[1] "DNASE1L3 MUTATION ANALYSIS"
[1] 3
  DNASE1L3 MUTATED DNASE1L3 WILD-TYPE 
                 8                481 
  DNASE1L3 MUTATED DNASE1L3 WILD-TYPE 
                 8                481 
[1] "FAM98B MUTATION ANALYSIS"
[1] 3
  FAM98B MUTATED FAM98B WILD-TYPE 
               5              484 
  FAM98B MUTATED FAM98B WILD-TYPE 
               5              484 
[1] "DCTN5 MUTATION ANALYSIS"
[1] 3
  DCTN5 MUTATED DCTN5 WILD-TYPE 
              6             483 
  DCTN5 MUTATED DCTN5 WILD-TYPE 
              6             483 
[1] "SLC11A2 MUTATION ANALYSIS"
[1] 3
  SLC11A2 MUTATED SLC11A2 WILD-TYPE 
                9               480 
  SLC11A2 MUTATED SLC11A2 WILD-TYPE 
                9               480 
[1] "SERPINB7 MUTATION ANALYSIS"
[1] 3
  SERPINB7 MUTATED SERPINB7 WILD-TYPE 
                 8                481 
  SERPINB7 MUTATED SERPINB7 WILD-TYPE 
                 8                481 
[1] "PTPRJ MUTATION ANALYSIS"
[1] 3
  PTPRJ MUTATED PTPRJ WILD-TYPE 
             18             471 
  PTPRJ MUTATED PTPRJ WILD-TYPE 
             18             471 
[1] "WDR5 MUTATION ANALYSIS"
[1] 3
  WDR5 MUTATED WDR5 WILD-TYPE 
             6            483 
  WDR5 MUTATED WDR5 WILD-TYPE 
             6            483 
[1] "MAP3K4 MUTATION ANALYSIS"
[1] 3
  MAP3K4 MUTATED MAP3K4 WILD-TYPE 
              39              450 
  MAP3K4 MUTATED MAP3K4 WILD-TYPE 
              39              450 
[1] "KRTAP5-3 MUTATION ANALYSIS"
[1] 3
  KRTAP5-3 MUTATED KRTAP5-3 WILD-TYPE 
                 4                485 
  KRTAP5-3 MUTATED KRTAP5-3 WILD-TYPE 
                 4                485 
[1] "CPS1 MUTATION ANALYSIS"
[1] 3
  CPS1 MUTATED CPS1 WILD-TYPE 
            34            455 
  CPS1 MUTATED CPS1 WILD-TYPE 
            34            455 
[1] "MDN1 MUTATION ANALYSIS"
[1] 3
  MDN1 MUTATED MDN1 WILD-TYPE 
            57            432 
  MDN1 MUTATED MDN1 WILD-TYPE 
            57            432 
[1] "COCH MUTATION ANALYSIS"
[1] 3
  COCH MUTATED COCH WILD-TYPE 
             7            482 
  COCH MUTATED COCH WILD-TYPE 
             7            482 
[1] "MFSD9 MUTATION ANALYSIS"
[1] 3
  MFSD9 MUTATED MFSD9 WILD-TYPE 
             12             477 
  MFSD9 MUTATED MFSD9 WILD-TYPE 
             12             477 
[1] "HSPA4L MUTATION ANALYSIS"
[1] 3
  HSPA4L MUTATED HSPA4L WILD-TYPE 
              12              477 
  HSPA4L MUTATED HSPA4L WILD-TYPE 
              12              477 
[1] "TMTC4 MUTATION ANALYSIS"
[1] 3
  TMTC4 MUTATED TMTC4 WILD-TYPE 
             15             474 
  TMTC4 MUTATED TMTC4 WILD-TYPE 
             15             474 
[1] "TGIF1 MUTATION ANALYSIS"
[1] 3
  TGIF1 MUTATED TGIF1 WILD-TYPE 
             11             478 
  TGIF1 MUTATED TGIF1 WILD-TYPE 
             11             478 
[1] "TBL1XR1 MUTATION ANALYSIS"
[1] 3
  TBL1XR1 MUTATED TBL1XR1 WILD-TYPE 
               13               476 
  TBL1XR1 MUTATED TBL1XR1 WILD-TYPE 
               13               476 
[1] "NXF3 MUTATION ANALYSIS"
[1] 3
  NXF3 MUTATED NXF3 WILD-TYPE 
            12            477 
  NXF3 MUTATED NXF3 WILD-TYPE 
            12            477 
[1] "SBNO1 MUTATION ANALYSIS"
[1] 3
  SBNO1 MUTATED SBNO1 WILD-TYPE 
             18             471 
  SBNO1 MUTATED SBNO1 WILD-TYPE 
             18             471 
[1] "FLT1 MUTATION ANALYSIS"
[1] 3
  FLT1 MUTATED FLT1 WILD-TYPE 
            35            454 
  FLT1 MUTATED FLT1 WILD-TYPE 
            35            454 
[1] "NCL MUTATION ANALYSIS"
[1] 3
  NCL MUTATED NCL WILD-TYPE 
           12           477 
  NCL MUTATED NCL WILD-TYPE 
           12           477 
[1] "SMC1B MUTATION ANALYSIS"
[1] 3
  SMC1B MUTATED SMC1B WILD-TYPE 
             22             467 
  SMC1B MUTATED SMC1B WILD-TYPE 
             22             467 
[1] "HRSP12 MUTATION ANALYSIS"
[1] 3
  HRSP12 MUTATED HRSP12 WILD-TYPE 
               7              482 
  HRSP12 MUTATED HRSP12 WILD-TYPE 
               7              482 
[1] "RRS1 MUTATION ANALYSIS"
[1] 3
  RRS1 MUTATED RRS1 WILD-TYPE 
             4            485 
  RRS1 MUTATED RRS1 WILD-TYPE 
             4            485 
[1] "CTCF MUTATION ANALYSIS"
[1] 3
  CTCF MUTATED CTCF WILD-TYPE 
            19            470 
  CTCF MUTATED CTCF WILD-TYPE 
            19            470 
[1] "RNF38 MUTATION ANALYSIS"
[1] 3
  RNF38 MUTATED RNF38 WILD-TYPE 
              6             483 
  RNF38 MUTATED RNF38 WILD-TYPE 
              6             483 
[1] "ANKRD50 MUTATION ANALYSIS"
[1] 3
  ANKRD50 MUTATED ANKRD50 WILD-TYPE 
               21               468 
  ANKRD50 MUTATED ANKRD50 WILD-TYPE 
               21               468 
[1] "DNAJC16 MUTATION ANALYSIS"
[1] 3
  DNAJC16 MUTATED DNAJC16 WILD-TYPE 
               11               478 
  DNAJC16 MUTATED DNAJC16 WILD-TYPE 
               11               478 
[1] "PIGK MUTATION ANALYSIS"
[1] 3
  PIGK MUTATED PIGK WILD-TYPE 
            12            477 
  PIGK MUTATED PIGK WILD-TYPE 
            12            477 
[1] "COPB2 MUTATION ANALYSIS"
[1] 3
  COPB2 MUTATED COPB2 WILD-TYPE 
             16             473 
  COPB2 MUTATED COPB2 WILD-TYPE 
             16             473 
[1] "CIZ1 MUTATION ANALYSIS"
[1] 3
  CIZ1 MUTATED CIZ1 WILD-TYPE 
            16            473 
  CIZ1 MUTATED CIZ1 WILD-TYPE 
            16            473 
[1] "TMEM92 MUTATION ANALYSIS"
[1] 3
  TMEM92 MUTATED TMEM92 WILD-TYPE 
               3              486 
  TMEM92 MUTATED TMEM92 WILD-TYPE 
               3              486 
[1] "TAS2R1 MUTATION ANALYSIS"
[1] 3
  TAS2R1 MUTATED TAS2R1 WILD-TYPE 
               5              484 
  TAS2R1 MUTATED TAS2R1 WILD-TYPE 
               5              484 
[1] "EHHADH MUTATION ANALYSIS"
[1] 3
  EHHADH MUTATED EHHADH WILD-TYPE 
              15              474 
  EHHADH MUTATED EHHADH WILD-TYPE 
              15              474 
[1] "KDM2B MUTATION ANALYSIS"
[1] 3
  KDM2B MUTATED KDM2B WILD-TYPE 
             22             467 
  KDM2B MUTATED KDM2B WILD-TYPE 
             22             467 
[1] "ITGB6 MUTATION ANALYSIS"
[1] 3
  ITGB6 MUTATED ITGB6 WILD-TYPE 
             18             471 
  ITGB6 MUTATED ITGB6 WILD-TYPE 
             18             471 
[1] "ESCO1 MUTATION ANALYSIS"
[1] 3
  ESCO1 MUTATED ESCO1 WILD-TYPE 
             17             472 
  ESCO1 MUTATED ESCO1 WILD-TYPE 
             17             472 
[1] "SERPINB10 MUTATION ANALYSIS"
[1] 3
  SERPINB10 MUTATED SERPINB10 WILD-TYPE 
                 12                 477 
  SERPINB10 MUTATED SERPINB10 WILD-TYPE 
                 12                 477 
[1] "GRB14 MUTATION ANALYSIS"
[1] 3
  GRB14 MUTATED GRB14 WILD-TYPE 
             11             478 
  GRB14 MUTATED GRB14 WILD-TYPE 
             11             478 
[1] "OR6K2 MUTATION ANALYSIS"
[1] 3
  OR6K2 MUTATED OR6K2 WILD-TYPE 
             16             473 
  OR6K2 MUTATED OR6K2 WILD-TYPE 
             16             473 
[1] "ARAP3 MUTATION ANALYSIS"
[1] 3
  ARAP3 MUTATED ARAP3 WILD-TYPE 
             24             465 
  ARAP3 MUTATED ARAP3 WILD-TYPE 
             24             465 
[1] "ZNF334 MUTATION ANALYSIS"
[1] 3
  ZNF334 MUTATED ZNF334 WILD-TYPE 
              21              468 
  ZNF334 MUTATED ZNF334 WILD-TYPE 
              21              468 
[1] "SIRT4 MUTATION ANALYSIS"
[1] 3
  SIRT4 MUTATED SIRT4 WILD-TYPE 
              7             482 
  SIRT4 MUTATED SIRT4 WILD-TYPE 
              7             482 
[1] "C1ORF35 MUTATION ANALYSIS"
[1] 3
  C1ORF35 MUTATED C1ORF35 WILD-TYPE 
                5               484 
  C1ORF35 MUTATED C1ORF35 WILD-TYPE 
                5               484 
[1] "PLK2 MUTATION ANALYSIS"
[1] 3
  PLK2 MUTATED PLK2 WILD-TYPE 
             7            482 
  PLK2 MUTATED PLK2 WILD-TYPE 
             7            482 
[1] "CCT4 MUTATION ANALYSIS"
[1] 3
  CCT4 MUTATED CCT4 WILD-TYPE 
            14            475 
  CCT4 MUTATED CCT4 WILD-TYPE 
            14            475 
[1] "MAP3K12 MUTATION ANALYSIS"
[1] 3
  MAP3K12 MUTATED MAP3K12 WILD-TYPE 
               14               475 
  MAP3K12 MUTATED MAP3K12 WILD-TYPE 
               14               475 
[1] "FGD3 MUTATION ANALYSIS"
[1] 3
  FGD3 MUTATED FGD3 WILD-TYPE 
            14            475 
  FGD3 MUTATED FGD3 WILD-TYPE 
            14            475 
[1] "ACAT2 MUTATION ANALYSIS"
[1] 3
  ACAT2 MUTATED ACAT2 WILD-TYPE 
              9             480 
  ACAT2 MUTATED ACAT2 WILD-TYPE 
              9             480 
[1] "PRRT2 MUTATION ANALYSIS"
[1] 3
  PRRT2 MUTATED PRRT2 WILD-TYPE 
              6             483 
  PRRT2 MUTATED PRRT2 WILD-TYPE 
              6             483 
[1] "C14ORF50 MUTATION ANALYSIS"
[1] 3
  C14ORF50 MUTATED C14ORF50 WILD-TYPE 
                 8                481 
  C14ORF50 MUTATED C14ORF50 WILD-TYPE 
                 8                481 
[1] "KCNG4 MUTATION ANALYSIS"
[1] 3
  KCNG4 MUTATED KCNG4 WILD-TYPE 
             10             479 
  KCNG4 MUTATED KCNG4 WILD-TYPE 
             10             479 
[1] "ANKRD23 MUTATION ANALYSIS"
[1] 3
  ANKRD23 MUTATED ANKRD23 WILD-TYPE 
                5               484 
  ANKRD23 MUTATED ANKRD23 WILD-TYPE 
                5               484 
[1] "KIAA0556 MUTATION ANALYSIS"
[1] 3
  KIAA0556 MUTATED KIAA0556 WILD-TYPE 
                24                465 
  KIAA0556 MUTATED KIAA0556 WILD-TYPE 
                24                465 
[1] "SLC25A44 MUTATION ANALYSIS"
[1] 3
  SLC25A44 MUTATED SLC25A44 WILD-TYPE 
                 5                484 
  SLC25A44 MUTATED SLC25A44 WILD-TYPE 
                 5                484 
[1] "VPS13C MUTATION ANALYSIS"
[1] 3
  VPS13C MUTATED VPS13C WILD-TYPE 
              28              461 
  VPS13C MUTATED VPS13C WILD-TYPE 
              28              461 
[1] "PGAP3 MUTATION ANALYSIS"
[1] 3
  PGAP3 MUTATED PGAP3 WILD-TYPE 
              8             481 
  PGAP3 MUTATED PGAP3 WILD-TYPE 
              8             481 
[1] "PARP1 MUTATION ANALYSIS"
[1] 3
  PARP1 MUTATED PARP1 WILD-TYPE 
             15             474 
  PARP1 MUTATED PARP1 WILD-TYPE 
             15             474 
[1] "EPC1 MUTATION ANALYSIS"
[1] 3
  EPC1 MUTATED EPC1 WILD-TYPE 
            13            476 
  EPC1 MUTATED EPC1 WILD-TYPE 
            13            476 
[1] "ST6GALNAC3 MUTATION ANALYSIS"
[1] 3
  ST6GALNAC3 MUTATED ST6GALNAC3 WILD-TYPE 
                  13                  476 
  ST6GALNAC3 MUTATED ST6GALNAC3 WILD-TYPE 
                  13                  476 
[1] "BRSK1 MUTATION ANALYSIS"
[1] 3
  BRSK1 MUTATED BRSK1 WILD-TYPE 
             18             471 
  BRSK1 MUTATED BRSK1 WILD-TYPE 
             18             471 
[1] "FAM91A1 MUTATION ANALYSIS"
[1] 3
  FAM91A1 MUTATED FAM91A1 WILD-TYPE 
               12               477 
  FAM91A1 MUTATED FAM91A1 WILD-TYPE 
               12               477 
[1] "FAM119A MUTATION ANALYSIS"
[1] 3
  FAM119A MUTATED FAM119A WILD-TYPE 
                6               483 
  FAM119A MUTATED FAM119A WILD-TYPE 
                6               483 
[1] "ZKSCAN2 MUTATION ANALYSIS"
[1] 3
  ZKSCAN2 MUTATED ZKSCAN2 WILD-TYPE 
               17               472 
  ZKSCAN2 MUTATED ZKSCAN2 WILD-TYPE 
               17               472 
[1] "HLA-B MUTATION ANALYSIS"
[1] 3
  HLA-B MUTATED HLA-B WILD-TYPE 
             12             477 
  HLA-B MUTATED HLA-B WILD-TYPE 
             12             477 
[1] "NHLRC2 MUTATION ANALYSIS"
[1] 3
  NHLRC2 MUTATED NHLRC2 WILD-TYPE 
               9              480 
  NHLRC2 MUTATED NHLRC2 WILD-TYPE 
               9              480 
[1] "BST2 MUTATION ANALYSIS"
[1] 3
  BST2 MUTATED BST2 WILD-TYPE 
             6            483 
  BST2 MUTATED BST2 WILD-TYPE 
             6            483 
[1] "VASH1 MUTATION ANALYSIS"
[1] 3
  VASH1 MUTATED VASH1 WILD-TYPE 
              5             484 
  VASH1 MUTATED VASH1 WILD-TYPE 
              5             484 
[1] "CT47B1 MUTATION ANALYSIS"
[1] 3
  CT47B1 MUTATED CT47B1 WILD-TYPE 
               8              481 
  CT47B1 MUTATED CT47B1 WILD-TYPE 
               8              481 
[1] "ZNF619 MUTATION ANALYSIS"
[1] 3
  ZNF619 MUTATED ZNF619 WILD-TYPE 
              11              478 
  ZNF619 MUTATED ZNF619 WILD-TYPE 
              11              478 
[1] "LIX1 MUTATION ANALYSIS"
[1] 3
  LIX1 MUTATED LIX1 WILD-TYPE 
            11            478 
  LIX1 MUTATED LIX1 WILD-TYPE 
            11            478 
[1] "BCLAF1 MUTATION ANALYSIS"
[1] 3
  BCLAF1 MUTATED BCLAF1 WILD-TYPE 
              22              467 
  BCLAF1 MUTATED BCLAF1 WILD-TYPE 
              22              467 
[1] "OR2Y1 MUTATION ANALYSIS"
[1] 3
  OR2Y1 MUTATED OR2Y1 WILD-TYPE 
              8             481 
  OR2Y1 MUTATED OR2Y1 WILD-TYPE 
              8             481 
[1] "KTN1 MUTATION ANALYSIS"
[1] 3
  KTN1 MUTATED KTN1 WILD-TYPE 
            20            469 
  KTN1 MUTATED KTN1 WILD-TYPE 
            20            469 
[1] "CBLL1 MUTATION ANALYSIS"
[1] 3
  CBLL1 MUTATED CBLL1 WILD-TYPE 
              6             483 
  CBLL1 MUTATED CBLL1 WILD-TYPE 
              6             483 
[1] "CTSZ MUTATION ANALYSIS"
[1] 3
  CTSZ MUTATED CTSZ WILD-TYPE 
             6            483 
  CTSZ MUTATED CTSZ WILD-TYPE 
             6            483 
[1] "GLDN MUTATION ANALYSIS"
[1] 3
  GLDN MUTATED GLDN WILD-TYPE 
             9            480 
  GLDN MUTATED GLDN WILD-TYPE 
             9            480 
[1] "RARRES3 MUTATION ANALYSIS"
[1] 3
  RARRES3 MUTATED RARRES3 WILD-TYPE 
                5               484 
  RARRES3 MUTATED RARRES3 WILD-TYPE 
                5               484 
[1] "CBLN3 MUTATION ANALYSIS"
[1] 3
  CBLN3 MUTATED CBLN3 WILD-TYPE 
              6             483 
  CBLN3 MUTATED CBLN3 WILD-TYPE 
              6             483 
[1] "LRRN3 MUTATION ANALYSIS"
[1] 3
  LRRN3 MUTATED LRRN3 WILD-TYPE 
             23             466 
  LRRN3 MUTATED LRRN3 WILD-TYPE 
             23             466 
[1] "WDR5B MUTATION ANALYSIS"
[1] 3
  WDR5B MUTATED WDR5B WILD-TYPE 
             13             476 
  WDR5B MUTATED WDR5B WILD-TYPE 
             13             476 
[1] "CLDND1 MUTATION ANALYSIS"
[1] 3
  CLDND1 MUTATED CLDND1 WILD-TYPE 
              10              479 
  CLDND1 MUTATED CLDND1 WILD-TYPE 
              10              479 
[1] "MERTK MUTATION ANALYSIS"
[1] 3
  MERTK MUTATED MERTK WILD-TYPE 
             20             469 
  MERTK MUTATED MERTK WILD-TYPE 
             20             469 
[1] "PRMT8 MUTATION ANALYSIS"
[1] 3
  PRMT8 MUTATED PRMT8 WILD-TYPE 
             14             475 
  PRMT8 MUTATED PRMT8 WILD-TYPE 
             14             475 
[1] "TCEAL5 MUTATION ANALYSIS"
[1] 3
  TCEAL5 MUTATED TCEAL5 WILD-TYPE 
               5              484 
  TCEAL5 MUTATED TCEAL5 WILD-TYPE 
               5              484 
[1] "OR9Q2 MUTATION ANALYSIS"
[1] 3
  OR9Q2 MUTATED OR9Q2 WILD-TYPE 
             14             475 
  OR9Q2 MUTATED OR9Q2 WILD-TYPE 
             14             475 
[1] "CTNNA3 MUTATION ANALYSIS"
[1] 3
  CTNNA3 MUTATED CTNNA3 WILD-TYPE 
              26              463 
  CTNNA3 MUTATED CTNNA3 WILD-TYPE 
              26              463 
[1] "C14ORF39 MUTATION ANALYSIS"
[1] 3
  C14ORF39 MUTATED C14ORF39 WILD-TYPE 
                17                472 
  C14ORF39 MUTATED C14ORF39 WILD-TYPE 
                17                472 
[1] "SAPS3 MUTATION ANALYSIS"
[1] 3
  SAPS3 MUTATED SAPS3 WILD-TYPE 
             15             474 
  SAPS3 MUTATED SAPS3 WILD-TYPE 
             15             474 
[1] "TRIM31 MUTATION ANALYSIS"
[1] 3
  TRIM31 MUTATED TRIM31 WILD-TYPE 
               5              484 
  TRIM31 MUTATED TRIM31 WILD-TYPE 
               5              484 
[1] "PHF14 MUTATION ANALYSIS"
[1] 3
  PHF14 MUTATED PHF14 WILD-TYPE 
             16             473 
  PHF14 MUTATED PHF14 WILD-TYPE 
             16             473 
[1] "MOV10 MUTATION ANALYSIS"
[1] 3
  MOV10 MUTATED MOV10 WILD-TYPE 
             14             475 
  MOV10 MUTATED MOV10 WILD-TYPE 
             14             475 
[1] "PTCH2 MUTATION ANALYSIS"
[1] 3
  PTCH2 MUTATED PTCH2 WILD-TYPE 
             19             470 
  PTCH2 MUTATED PTCH2 WILD-TYPE 
             19             470 
[1] "POMGNT1 MUTATION ANALYSIS"
[1] 3
  POMGNT1 MUTATED POMGNT1 WILD-TYPE 
                8               481 
  POMGNT1 MUTATED POMGNT1 WILD-TYPE 
                8               481 
[1] "NAA10 MUTATION ANALYSIS"
[1] 3
  NAA10 MUTATED NAA10 WILD-TYPE 
              3             486 
  NAA10 MUTATED NAA10 WILD-TYPE 
              3             486 
[1] "OR2A5 MUTATION ANALYSIS"
[1] 3
  OR2A5 MUTATED OR2A5 WILD-TYPE 
             13             476 
  OR2A5 MUTATED OR2A5 WILD-TYPE 
             13             476 
[1] "HAUS3 MUTATION ANALYSIS"
[1] 3
  HAUS3 MUTATED HAUS3 WILD-TYPE 
             10             479 
  HAUS3 MUTATED HAUS3 WILD-TYPE 
             10             479 
[1] "IFIH1 MUTATION ANALYSIS"
[1] 3
  IFIH1 MUTATED IFIH1 WILD-TYPE 
             16             473 
  IFIH1 MUTATED IFIH1 WILD-TYPE 
             16             473 
[1] "AKAP11 MUTATION ANALYSIS"
[1] 3
  AKAP11 MUTATED AKAP11 WILD-TYPE 
              25              464 
  AKAP11 MUTATED AKAP11 WILD-TYPE 
              25              464 
[1] "CRTC1 MUTATION ANALYSIS"
[1] 3
  CRTC1 MUTATED CRTC1 WILD-TYPE 
             13             476 
  CRTC1 MUTATED CRTC1 WILD-TYPE 
             13             476 
[1] "PKHD1L1 MUTATION ANALYSIS"
[1] 3
  PKHD1L1 MUTATED PKHD1L1 WILD-TYPE 
               46               443 
  PKHD1L1 MUTATED PKHD1L1 WILD-TYPE 
               46               443 
[1] "UFSP2 MUTATION ANALYSIS"
[1] 3
  UFSP2 MUTATED UFSP2 WILD-TYPE 
              5             484 
  UFSP2 MUTATED UFSP2 WILD-TYPE 
              5             484 
[1] "MUC7 MUTATION ANALYSIS"
[1] 3
  MUC7 MUTATED MUC7 WILD-TYPE 
            11            478 
  MUC7 MUTATED MUC7 WILD-TYPE 
            11            478 
[1] "RIMBP3 MUTATION ANALYSIS"
[1] 3
  RIMBP3 MUTATED RIMBP3 WILD-TYPE 
               6              483 
  RIMBP3 MUTATED RIMBP3 WILD-TYPE 
               6              483 
[1] "S100A2 MUTATION ANALYSIS"
[1] 3
  S100A2 MUTATED S100A2 WILD-TYPE 
               8              481 
  S100A2 MUTATED S100A2 WILD-TYPE 
               8              481 
[1] "PCSK1 MUTATION ANALYSIS"
[1] 3
  PCSK1 MUTATED PCSK1 WILD-TYPE 
             19             470 
  PCSK1 MUTATED PCSK1 WILD-TYPE 
             19             470 
[1] "RTN4 MUTATION ANALYSIS"
[1] 3
  RTN4 MUTATED RTN4 WILD-TYPE 
            21            468 
  RTN4 MUTATED RTN4 WILD-TYPE 
            21            468 
[1] "C14ORF104 MUTATION ANALYSIS"
[1] 3
  C14ORF104 MUTATED C14ORF104 WILD-TYPE 
                  5                 484 
  C14ORF104 MUTATED C14ORF104 WILD-TYPE 
                  5                 484 
[1] "USF1 MUTATION ANALYSIS"
[1] 3
  USF1 MUTATED USF1 WILD-TYPE 
             5            484 
  USF1 MUTATED USF1 WILD-TYPE 
             5            484 
[1] "KLF12 MUTATION ANALYSIS"
[1] 3
  KLF12 MUTATED KLF12 WILD-TYPE 
              5             484 
  KLF12 MUTATED KLF12 WILD-TYPE 
              5             484 
[1] "VIM MUTATION ANALYSIS"
[1] 3
  VIM MUTATED VIM WILD-TYPE 
            9           480 
  VIM MUTATED VIM WILD-TYPE 
            9           480 
[1] "GLG1 MUTATION ANALYSIS"
[1] 3
  GLG1 MUTATED GLG1 WILD-TYPE 
            14            475 
  GLG1 MUTATED GLG1 WILD-TYPE 
            14            475 
[1] "CETN3 MUTATION ANALYSIS"
[1] 3
  CETN3 MUTATED CETN3 WILD-TYPE 
              6             483 
  CETN3 MUTATED CETN3 WILD-TYPE 
              6             483 
[1] "SFRS15 MUTATION ANALYSIS"
[1] 3
  SFRS15 MUTATED SFRS15 WILD-TYPE 
              20              469 
  SFRS15 MUTATED SFRS15 WILD-TYPE 
              20              469 
[1] "ADAMTSL3 MUTATION ANALYSIS"
[1] 3
  ADAMTSL3 MUTATED ADAMTSL3 WILD-TYPE 
                46                443 
  ADAMTSL3 MUTATED ADAMTSL3 WILD-TYPE 
                46                443 
[1] "CASP1 MUTATION ANALYSIS"
[1] 3
  CASP1 MUTATED CASP1 WILD-TYPE 
              6             483 
  CASP1 MUTATED CASP1 WILD-TYPE 
              6             483 
[1] "B4GALT6 MUTATION ANALYSIS"
[1] 3
  B4GALT6 MUTATED B4GALT6 WILD-TYPE 
               10               479 
  B4GALT6 MUTATED B4GALT6 WILD-TYPE 
               10               479 
[1] "RAD21 MUTATION ANALYSIS"
[1] 3
  RAD21 MUTATED RAD21 WILD-TYPE 
             17             472 
  RAD21 MUTATED RAD21 WILD-TYPE 
             17             472 
[1] "HUS1 MUTATION ANALYSIS"
[1] 3
  HUS1 MUTATED HUS1 WILD-TYPE 
             8            481 
  HUS1 MUTATED HUS1 WILD-TYPE 
             8            481 
[1] "PTPN14 MUTATION ANALYSIS"
[1] 3
  PTPN14 MUTATED PTPN14 WILD-TYPE 
              21              468 
  PTPN14 MUTATED PTPN14 WILD-TYPE 
              21              468 
[1] "FZD6 MUTATION ANALYSIS"
[1] 3
  FZD6 MUTATED FZD6 WILD-TYPE 
            15            474 
  FZD6 MUTATED FZD6 WILD-TYPE 
            15            474 
[1] "C6ORF222 MUTATION ANALYSIS"
[1] 3
  C6ORF222 MUTATED C6ORF222 WILD-TYPE 
                 6                483 
  C6ORF222 MUTATED C6ORF222 WILD-TYPE 
                 6                483 
[1] "ANKRD26 MUTATION ANALYSIS"
[1] 3
  ANKRD26 MUTATED ANKRD26 WILD-TYPE 
               23               466 
  ANKRD26 MUTATED ANKRD26 WILD-TYPE 
               23               466 
[1] "TDRD7 MUTATION ANALYSIS"
[1] 3
  TDRD7 MUTATED TDRD7 WILD-TYPE 
             16             473 
  TDRD7 MUTATED TDRD7 WILD-TYPE 
             16             473 
[1] "MFSD6 MUTATION ANALYSIS"
[1] 3
  MFSD6 MUTATED MFSD6 WILD-TYPE 
              8             481 
  MFSD6 MUTATED MFSD6 WILD-TYPE 
              8             481 
[1] "KIAA1632 MUTATION ANALYSIS"
[1] 3
  KIAA1632 MUTATED KIAA1632 WILD-TYPE 
                31                458 
  KIAA1632 MUTATED KIAA1632 WILD-TYPE 
                31                458 
[1] "ADK MUTATION ANALYSIS"
[1] 3
  ADK MUTATED ADK WILD-TYPE 
            7           482 
  ADK MUTATED ADK WILD-TYPE 
            7           482 
[1] "PTPRB MUTATION ANALYSIS"
[1] 3
  PTPRB MUTATED PTPRB WILD-TYPE 
             18             471 
  PTPRB MUTATED PTPRB WILD-TYPE 
             18             471 
[1] "ZNF280C MUTATION ANALYSIS"
[1] 3
  ZNF280C MUTATED ZNF280C WILD-TYPE 
               14               475 
  ZNF280C MUTATED ZNF280C WILD-TYPE 
               14               475 
[1] "ATIC MUTATION ANALYSIS"
[1] 3
  ATIC MUTATED ATIC WILD-TYPE 
            14            475 
  ATIC MUTATED ATIC WILD-TYPE 
            14            475 
[1] "USP16 MUTATION ANALYSIS"
[1] 3
  USP16 MUTATED USP16 WILD-TYPE 
              8             481 
  USP16 MUTATED USP16 WILD-TYPE 
              8             481 
[1] "CIR1 MUTATION ANALYSIS"
[1] 3
  CIR1 MUTATED CIR1 WILD-TYPE 
            10            479 
  CIR1 MUTATED CIR1 WILD-TYPE 
            10            479 
[1] "OR4C15 MUTATION ANALYSIS"
[1] 3
  OR4C15 MUTATED OR4C15 WILD-TYPE 
              16              473 
  OR4C15 MUTATED OR4C15 WILD-TYPE 
              16              473 
[1] "ANK3 MUTATION ANALYSIS"
[1] 3
  ANK3 MUTATED ANK3 WILD-TYPE 
            54            435 
  ANK3 MUTATED ANK3 WILD-TYPE 
            54            435 
[1] "PPFIBP1 MUTATION ANALYSIS"
[1] 3
  PPFIBP1 MUTATED PPFIBP1 WILD-TYPE 
               14               475 
  PPFIBP1 MUTATED PPFIBP1 WILD-TYPE 
               14               475 
[1] "NTNG1 MUTATION ANALYSIS"
[1] 3
  NTNG1 MUTATED NTNG1 WILD-TYPE 
             17             472 
  NTNG1 MUTATED NTNG1 WILD-TYPE 
             17             472 
[1] "TRPA1 MUTATION ANALYSIS"
[1] 3
  TRPA1 MUTATED TRPA1 WILD-TYPE 
             32             457 
  TRPA1 MUTATED TRPA1 WILD-TYPE 
             32             457 
[1] "CWF19L2 MUTATION ANALYSIS"
[1] 3
  CWF19L2 MUTATED CWF19L2 WILD-TYPE 
               19               470 
  CWF19L2 MUTATED CWF19L2 WILD-TYPE 
               19               470 
[1] "SERPINA9 MUTATION ANALYSIS"
[1] 3
  SERPINA9 MUTATED SERPINA9 WILD-TYPE 
                11                478 
  SERPINA9 MUTATED SERPINA9 WILD-TYPE 
                11                478 
[1] "HSP90AA1 MUTATION ANALYSIS"
[1] 3
  HSP90AA1 MUTATED HSP90AA1 WILD-TYPE 
                 9                480 
  HSP90AA1 MUTATED HSP90AA1 WILD-TYPE 
                 9                480 
[1] "SATB1 MUTATION ANALYSIS"
[1] 3
  SATB1 MUTATED SATB1 WILD-TYPE 
             17             472 
  SATB1 MUTATED SATB1 WILD-TYPE 
             17             472 
[1] "FBXO45 MUTATION ANALYSIS"
[1] 3
  FBXO45 MUTATED FBXO45 WILD-TYPE 
               6              483 
  FBXO45 MUTATED FBXO45 WILD-TYPE 
               6              483 
[1] "MMP7 MUTATION ANALYSIS"
[1] 3
  MMP7 MUTATED MMP7 WILD-TYPE 
            10            479 
  MMP7 MUTATED MMP7 WILD-TYPE 
            10            479 
[1] "TMCO6 MUTATION ANALYSIS"
[1] 3
  TMCO6 MUTATED TMCO6 WILD-TYPE 
              7             482 
  TMCO6 MUTATED TMCO6 WILD-TYPE 
              7             482 
[1] "APAF1 MUTATION ANALYSIS"
[1] 3
  APAF1 MUTATED APAF1 WILD-TYPE 
             20             469 
  APAF1 MUTATED APAF1 WILD-TYPE 
             20             469 
[1] "FGB MUTATION ANALYSIS"
[1] 3
  FGB MUTATED FGB WILD-TYPE 
            6           483 
  FGB MUTATED FGB WILD-TYPE 
            6           483 
[1] "POLD3 MUTATION ANALYSIS"
[1] 3
  POLD3 MUTATED POLD3 WILD-TYPE 
             11             478 
  POLD3 MUTATED POLD3 WILD-TYPE 
             11             478 
[1] "CYP7B1 MUTATION ANALYSIS"
[1] 3
  CYP7B1 MUTATED CYP7B1 WILD-TYPE 
              21              468 
  CYP7B1 MUTATED CYP7B1 WILD-TYPE 
              21              468 
[1] "ZNF605 MUTATION ANALYSIS"
[1] 3
  ZNF605 MUTATED ZNF605 WILD-TYPE 
               8              481 
  ZNF605 MUTATED ZNF605 WILD-TYPE 
               8              481 
[1] "ITPR2 MUTATION ANALYSIS"
[1] 3
  ITPR2 MUTATED ITPR2 WILD-TYPE 
             28             461 
  ITPR2 MUTATED ITPR2 WILD-TYPE 
             28             461 
[1] "ZBTB33 MUTATION ANALYSIS"
[1] 3
  ZBTB33 MUTATED ZBTB33 WILD-TYPE 
              16              473 
  ZBTB33 MUTATED ZBTB33 WILD-TYPE 
              16              473 
[1] "PHF21A MUTATION ANALYSIS"
[1] 3
  PHF21A MUTATED PHF21A WILD-TYPE 
              12              477 
  PHF21A MUTATED PHF21A WILD-TYPE 
              12              477 
[1] "INADL MUTATION ANALYSIS"
[1] 3
  INADL MUTATED INADL WILD-TYPE 
             16             473 
  INADL MUTATED INADL WILD-TYPE 
             16             473 
[1] "DDX17 MUTATION ANALYSIS"
[1] 3
  DDX17 MUTATED DDX17 WILD-TYPE 
              8             481 
  DDX17 MUTATED DDX17 WILD-TYPE 
              8             481 
[1] "DMXL2 MUTATION ANALYSIS"
[1] 3
  DMXL2 MUTATED DMXL2 WILD-TYPE 
             37             452 
  DMXL2 MUTATED DMXL2 WILD-TYPE 
             37             452 
[1] "DPAGT1 MUTATION ANALYSIS"
[1] 3
  DPAGT1 MUTATED DPAGT1 WILD-TYPE 
               8              481 
  DPAGT1 MUTATED DPAGT1 WILD-TYPE 
               8              481 
[1] "SLC38A9 MUTATION ANALYSIS"
[1] 3
  SLC38A9 MUTATED SLC38A9 WILD-TYPE 
               12               477 
  SLC38A9 MUTATED SLC38A9 WILD-TYPE 
               12               477 
[1] "HIST2H2AC MUTATION ANALYSIS"
[1] 3
  HIST2H2AC MUTATED HIST2H2AC WILD-TYPE 
                  6                 483 
  HIST2H2AC MUTATED HIST2H2AC WILD-TYPE 
                  6                 483 
[1] "SLCO1B1 MUTATION ANALYSIS"
[1] 3
  SLCO1B1 MUTATED SLCO1B1 WILD-TYPE 
               23               466 
  SLCO1B1 MUTATED SLCO1B1 WILD-TYPE 
               23               466 
[1] "LBP MUTATION ANALYSIS"
[1] 3
  LBP MUTATED LBP WILD-TYPE 
            8           481 
  LBP MUTATED LBP WILD-TYPE 
            8           481 
[1] "THUMPD3 MUTATION ANALYSIS"
[1] 3
  THUMPD3 MUTATED THUMPD3 WILD-TYPE 
               12               477 
  THUMPD3 MUTATED THUMPD3 WILD-TYPE 
               12               477 
[1] "GPSM2 MUTATION ANALYSIS"
[1] 3
  GPSM2 MUTATED GPSM2 WILD-TYPE 
             13             476 
  GPSM2 MUTATED GPSM2 WILD-TYPE 
             13             476 
[1] "OR4B1 MUTATION ANALYSIS"
[1] 3
  OR4B1 MUTATED OR4B1 WILD-TYPE 
              6             483 
  OR4B1 MUTATED OR4B1 WILD-TYPE 
              6             483 
[1] "LEO1 MUTATION ANALYSIS"
[1] 3
  LEO1 MUTATED LEO1 WILD-TYPE 
            12            477 
  LEO1 MUTATED LEO1 WILD-TYPE 
            12            477 
[1] "SETX MUTATION ANALYSIS"
[1] 3
  SETX MUTATED SETX WILD-TYPE 
            34            455 
  SETX MUTATED SETX WILD-TYPE 
            34            455 
[1] "ZBTB5 MUTATION ANALYSIS"
[1] 3
  ZBTB5 MUTATED ZBTB5 WILD-TYPE 
              7             482 
  ZBTB5 MUTATED ZBTB5 WILD-TYPE 
              7             482 
[1] "C16ORF45 MUTATION ANALYSIS"
[1] 3
  C16ORF45 MUTATED C16ORF45 WILD-TYPE 
                 6                483 
  C16ORF45 MUTATED C16ORF45 WILD-TYPE 
                 6                483 
[1] "HCLS1 MUTATION ANALYSIS"
[1] 3
  HCLS1 MUTATED HCLS1 WILD-TYPE 
             16             473 
  HCLS1 MUTATED HCLS1 WILD-TYPE 
             16             473 
[1] "DNAJB9 MUTATION ANALYSIS"
[1] 3
  DNAJB9 MUTATED DNAJB9 WILD-TYPE 
               6              483 
  DNAJB9 MUTATED DNAJB9 WILD-TYPE 
               6              483 
[1] "ICA1 MUTATION ANALYSIS"
[1] 3
  ICA1 MUTATED ICA1 WILD-TYPE 
             7            482 
  ICA1 MUTATED ICA1 WILD-TYPE 
             7            482 
[1] "SMARCB1 MUTATION ANALYSIS"
[1] 3
  SMARCB1 MUTATED SMARCB1 WILD-TYPE 
               24               465 
  SMARCB1 MUTATED SMARCB1 WILD-TYPE 
               24               465 
[1] "MTOR MUTATION ANALYSIS"
[1] 3
  MTOR MUTATED MTOR WILD-TYPE 
            38            451 
  MTOR MUTATED MTOR WILD-TYPE 
            38            451 
[1] "RNF219 MUTATION ANALYSIS"
[1] 3
  RNF219 MUTATED RNF219 WILD-TYPE 
              19              470 
  RNF219 MUTATED RNF219 WILD-TYPE 
              19              470 
[1] "KIAA0528 MUTATION ANALYSIS"
[1] 3
  KIAA0528 MUTATED KIAA0528 WILD-TYPE 
                17                472 
  KIAA0528 MUTATED KIAA0528 WILD-TYPE 
                17                472 
[1] "GABPA MUTATION ANALYSIS"
[1] 3
  GABPA MUTATED GABPA WILD-TYPE 
             12             477 
  GABPA MUTATED GABPA WILD-TYPE 
             12             477 
[1] "PPP2R2B MUTATION ANALYSIS"
[1] 3
  PPP2R2B MUTATED PPP2R2B WILD-TYPE 
               11               478 
  PPP2R2B MUTATED PPP2R2B WILD-TYPE 
               11               478 
[1] "NEK1 MUTATION ANALYSIS"
[1] 3
  NEK1 MUTATED NEK1 WILD-TYPE 
            14            475 
  NEK1 MUTATED NEK1 WILD-TYPE 
            14            475 
[1] "CEACAM6 MUTATION ANALYSIS"
[1] 3
  CEACAM6 MUTATED CEACAM6 WILD-TYPE 
                4               485 
  CEACAM6 MUTATED CEACAM6 WILD-TYPE 
                4               485 
[1] "MED14 MUTATION ANALYSIS"
[1] 3
  MED14 MUTATED MED14 WILD-TYPE 
             19             470 
  MED14 MUTATED MED14 WILD-TYPE 
             19             470 
[1] "AGTR2 MUTATION ANALYSIS"
[1] 3
  AGTR2 MUTATED AGTR2 WILD-TYPE 
             17             472 
  AGTR2 MUTATED AGTR2 WILD-TYPE 
             17             472 
[1] "COL4A6 MUTATION ANALYSIS"
[1] 3
  COL4A6 MUTATED COL4A6 WILD-TYPE 
              22              467 
  COL4A6 MUTATED COL4A6 WILD-TYPE 
              22              467 
[1] "KRTAP12-3 MUTATION ANALYSIS"
[1] 3
  KRTAP12-3 MUTATED KRTAP12-3 WILD-TYPE 
                  3                 486 
  KRTAP12-3 MUTATED KRTAP12-3 WILD-TYPE 
                  3                 486 
[1] "EMR3 MUTATION ANALYSIS"
[1] 3
  EMR3 MUTATED EMR3 WILD-TYPE 
            17            472 
  EMR3 MUTATED EMR3 WILD-TYPE 
            17            472 
[1] "STAU2 MUTATION ANALYSIS"
[1] 3
  STAU2 MUTATED STAU2 WILD-TYPE 
             10             479 
  STAU2 MUTATED STAU2 WILD-TYPE 
             10             479 
[1] "GGA2 MUTATION ANALYSIS"
[1] 3
  GGA2 MUTATED GGA2 WILD-TYPE 
            13            476 
  GGA2 MUTATED GGA2 WILD-TYPE 
            13            476 
[1] "ATRNL1 MUTATION ANALYSIS"
[1] 3
  ATRNL1 MUTATED ATRNL1 WILD-TYPE 
              27              462 
  ATRNL1 MUTATED ATRNL1 WILD-TYPE 
              27              462 
[1] "OSR1 MUTATION ANALYSIS"
[1] 3
  OSR1 MUTATED OSR1 WILD-TYPE 
             4            485 
  OSR1 MUTATED OSR1 WILD-TYPE 
             4            485 
[1] "IRS4 MUTATION ANALYSIS"
[1] 3
  IRS4 MUTATED IRS4 WILD-TYPE 
            31            458 
  IRS4 MUTATED IRS4 WILD-TYPE 
            31            458 
[1] "CEL MUTATION ANALYSIS"
[1] 3
  CEL MUTATED CEL WILD-TYPE 
            9           480 
  CEL MUTATED CEL WILD-TYPE 
            9           480 
[1] "ZHX2 MUTATION ANALYSIS"
[1] 3
  ZHX2 MUTATED ZHX2 WILD-TYPE 
            20            469 
  ZHX2 MUTATED ZHX2 WILD-TYPE 
            20            469 
[1] "HEATR3 MUTATION ANALYSIS"
[1] 3
  HEATR3 MUTATED HEATR3 WILD-TYPE 
              10              479 
  HEATR3 MUTATED HEATR3 WILD-TYPE 
              10              479 
[1] "STAT3 MUTATION ANALYSIS"
[1] 3
  STAT3 MUTATED STAT3 WILD-TYPE 
              9             480 
  STAT3 MUTATED STAT3 WILD-TYPE 
              9             480 
[1] "STK35 MUTATION ANALYSIS"
[1] 3
  STK35 MUTATED STK35 WILD-TYPE 
              6             483 
  STK35 MUTATED STK35 WILD-TYPE 
              6             483 
[1] "ASB11 MUTATION ANALYSIS"
[1] 3
  ASB11 MUTATED ASB11 WILD-TYPE 
              8             481 
  ASB11 MUTATED ASB11 WILD-TYPE 
              8             481 
[1] "C7ORF50 MUTATION ANALYSIS"
[1] 3
  C7ORF50 MUTATED C7ORF50 WILD-TYPE 
                5               484 
  C7ORF50 MUTATED C7ORF50 WILD-TYPE 
                5               484 
[1] "ATP13A5 MUTATION ANALYSIS"
[1] 3
  ATP13A5 MUTATED ATP13A5 WILD-TYPE 
               27               462 
  ATP13A5 MUTATED ATP13A5 WILD-TYPE 
               27               462 
[1] "ZNF43 MUTATION ANALYSIS"
[1] 3
  ZNF43 MUTATED ZNF43 WILD-TYPE 
             22             467 
  ZNF43 MUTATED ZNF43 WILD-TYPE 
             22             467 
[1] "INPPL1 MUTATION ANALYSIS"
[1] 3
  INPPL1 MUTATED INPPL1 WILD-TYPE 
              14              475 
  INPPL1 MUTATED INPPL1 WILD-TYPE 
              14              475 
[1] "TFAP2C MUTATION ANALYSIS"
[1] 3
  TFAP2C MUTATED TFAP2C WILD-TYPE 
              11              478 
  TFAP2C MUTATED TFAP2C WILD-TYPE 
              11              478 
[1] "GAD2 MUTATION ANALYSIS"
[1] 3
  GAD2 MUTATED GAD2 WILD-TYPE 
            16            473 
  GAD2 MUTATED GAD2 WILD-TYPE 
            16            473 
[1] "CCDC66 MUTATION ANALYSIS"
[1] 3
  CCDC66 MUTATED CCDC66 WILD-TYPE 
              13              476 
  CCDC66 MUTATED CCDC66 WILD-TYPE 
              13              476 
[1] "C10ORF119 MUTATION ANALYSIS"
[1] 3
  C10ORF119 MUTATED C10ORF119 WILD-TYPE 
                  9                 480 
  C10ORF119 MUTATED C10ORF119 WILD-TYPE 
                  9                 480 
[1] "ZMYND8 MUTATION ANALYSIS"
[1] 3
  ZMYND8 MUTATED ZMYND8 WILD-TYPE 
              29              460 
  ZMYND8 MUTATED ZMYND8 WILD-TYPE 
              29              460 
[1] "NFASC MUTATION ANALYSIS"
[1] 3
  NFASC MUTATED NFASC WILD-TYPE 
             35             454 
  NFASC MUTATED NFASC WILD-TYPE 
             35             454 
[1] "ACTA1 MUTATION ANALYSIS"
[1] 3
  ACTA1 MUTATED ACTA1 WILD-TYPE 
             14             475 
  ACTA1 MUTATED ACTA1 WILD-TYPE 
             14             475 
[1] "LYG1 MUTATION ANALYSIS"
[1] 3
  LYG1 MUTATED LYG1 WILD-TYPE 
             6            483 
  LYG1 MUTATED LYG1 WILD-TYPE 
             6            483 
[1] "EXPH5 MUTATION ANALYSIS"
[1] 3
  EXPH5 MUTATED EXPH5 WILD-TYPE 
             24             465 
  EXPH5 MUTATED EXPH5 WILD-TYPE 
             24             465 
[1] "LEPRE1 MUTATION ANALYSIS"
[1] 3
  LEPRE1 MUTATED LEPRE1 WILD-TYPE 
               9              480 
  LEPRE1 MUTATED LEPRE1 WILD-TYPE 
               9              480 
[1] "COL6A5 MUTATION ANALYSIS"
[1] 3
  COL6A5 MUTATED COL6A5 WILD-TYPE 
              36              453 
  COL6A5 MUTATED COL6A5 WILD-TYPE 
              36              453 
[1] "RAB3C MUTATION ANALYSIS"
[1] 3
  RAB3C MUTATED RAB3C WILD-TYPE 
             15             474 
  RAB3C MUTATED RAB3C WILD-TYPE 
             15             474 
[1] "MAP2K1 MUTATION ANALYSIS"
[1] 3
  MAP2K1 MUTATED MAP2K1 WILD-TYPE 
              12              477 
  MAP2K1 MUTATED MAP2K1 WILD-TYPE 
              12              477 
[1] "RRAS2 MUTATION ANALYSIS"
[1] 3
  RRAS2 MUTATED RRAS2 WILD-TYPE 
              7             482 
  RRAS2 MUTATED RRAS2 WILD-TYPE 
              7             482 
[1] "TMLHE MUTATION ANALYSIS"
[1] 3
  TMLHE MUTATED TMLHE WILD-TYPE 
              5             484 
  TMLHE MUTATED TMLHE WILD-TYPE 
              5             484 
[1] "UGT1A1 MUTATION ANALYSIS"
[1] 3
  UGT1A1 MUTATED UGT1A1 WILD-TYPE 
              11              478 
  UGT1A1 MUTATED UGT1A1 WILD-TYPE 
              11              478 
[1] "NCR3 MUTATION ANALYSIS"
[1] 3
  NCR3 MUTATED NCR3 WILD-TYPE 
             5            484 
  NCR3 MUTATED NCR3 WILD-TYPE 
             5            484 
[1] "AP1M1 MUTATION ANALYSIS"
[1] 3
  AP1M1 MUTATED AP1M1 WILD-TYPE 
              9             480 
  AP1M1 MUTATED AP1M1 WILD-TYPE 
              9             480 
[1] "FBXL4 MUTATION ANALYSIS"
[1] 3
  FBXL4 MUTATED FBXL4 WILD-TYPE 
              8             481 
  FBXL4 MUTATED FBXL4 WILD-TYPE 
              8             481 
[1] "KRT222 MUTATION ANALYSIS"
[1] 3
  KRT222 MUTATED KRT222 WILD-TYPE 
               8              481 
  KRT222 MUTATED KRT222 WILD-TYPE 
               8              481 
[1] "CDC42BPA MUTATION ANALYSIS"
[1] 3
  CDC42BPA MUTATED CDC42BPA WILD-TYPE 
                30                459 
  CDC42BPA MUTATED CDC42BPA WILD-TYPE 
                30                459 
[1] "USP44 MUTATION ANALYSIS"
[1] 3
  USP44 MUTATED USP44 WILD-TYPE 
             17             472 
  USP44 MUTATED USP44 WILD-TYPE 
             17             472 
[1] "PLCG2 MUTATION ANALYSIS"
[1] 3
  PLCG2 MUTATED PLCG2 WILD-TYPE 
             21             468 
  PLCG2 MUTATED PLCG2 WILD-TYPE 
             21             468 
[1] "RDBP MUTATION ANALYSIS"
[1] 3
  RDBP MUTATED RDBP WILD-TYPE 
             7            482 
  RDBP MUTATED RDBP WILD-TYPE 
             7            482 
[1] "RAPGEF2 MUTATION ANALYSIS"
[1] 3
  RAPGEF2 MUTATED RAPGEF2 WILD-TYPE 
               24               465 
  RAPGEF2 MUTATED RAPGEF2 WILD-TYPE 
               24               465 
[1] "GDA MUTATION ANALYSIS"
[1] 3
  GDA MUTATED GDA WILD-TYPE 
            7           482 
  GDA MUTATED GDA WILD-TYPE 
            7           482 
[1] "PEBP4 MUTATION ANALYSIS"
[1] 3
  PEBP4 MUTATED PEBP4 WILD-TYPE 
              7             482 
  PEBP4 MUTATED PEBP4 WILD-TYPE 
              7             482 
[1] "CYP2A6 MUTATION ANALYSIS"
[1] 3
  CYP2A6 MUTATED CYP2A6 WILD-TYPE 
              12              477 
  CYP2A6 MUTATED CYP2A6 WILD-TYPE 
              12              477 
[1] "DEK MUTATION ANALYSIS"
[1] 3
  DEK MUTATED DEK WILD-TYPE 
            6           483 
  DEK MUTATED DEK WILD-TYPE 
            6           483 
[1] "HAUS1 MUTATION ANALYSIS"
[1] 3
  HAUS1 MUTATED HAUS1 WILD-TYPE 
              6             483 
  HAUS1 MUTATED HAUS1 WILD-TYPE 
              6             483 
[1] "DBF4B MUTATION ANALYSIS"
[1] 3
  DBF4B MUTATED DBF4B WILD-TYPE 
              7             482 
  DBF4B MUTATED DBF4B WILD-TYPE 
              7             482 
[1] "PLA2G15 MUTATION ANALYSIS"
[1] 3
  PLA2G15 MUTATED PLA2G15 WILD-TYPE 
                6               483 
  PLA2G15 MUTATED PLA2G15 WILD-TYPE 
                6               483 
[1] "STAT5B MUTATION ANALYSIS"
[1] 3
  STAT5B MUTATED STAT5B WILD-TYPE 
              13              476 
  STAT5B MUTATED STAT5B WILD-TYPE 
              13              476 
[1] "NCOA5 MUTATION ANALYSIS"
[1] 3
  NCOA5 MUTATED NCOA5 WILD-TYPE 
             13             476 
  NCOA5 MUTATED NCOA5 WILD-TYPE 
             13             476 
[1] "MR1 MUTATION ANALYSIS"
[1] 3
  MR1 MUTATED MR1 WILD-TYPE 
            7           482 
  MR1 MUTATED MR1 WILD-TYPE 
            7           482 
[1] "FAM155B MUTATION ANALYSIS"
[1] 3
  FAM155B MUTATED FAM155B WILD-TYPE 
                8               481 
  FAM155B MUTATED FAM155B WILD-TYPE 
                8               481 
[1] "MCF2 MUTATION ANALYSIS"
[1] 3
  MCF2 MUTATED MCF2 WILD-TYPE 
            32            457 
  MCF2 MUTATED MCF2 WILD-TYPE 
            32            457 
[1] "PSD3 MUTATION ANALYSIS"
[1] 3
  PSD3 MUTATED PSD3 WILD-TYPE 
            11            478 
  PSD3 MUTATED PSD3 WILD-TYPE 
            11            478 
[1] "ARHGAP27 MUTATION ANALYSIS"
[1] 3
  ARHGAP27 MUTATED ARHGAP27 WILD-TYPE 
                12                477 
  ARHGAP27 MUTATED ARHGAP27 WILD-TYPE 
                12                477 
[1] "C20ORF117 MUTATION ANALYSIS"
[1] 3
  C20ORF117 MUTATED C20ORF117 WILD-TYPE 
                 18                 471 
  C20ORF117 MUTATED C20ORF117 WILD-TYPE 
                 18                 471 
[1] "NKTR MUTATION ANALYSIS"
[1] 3
  NKTR MUTATED NKTR WILD-TYPE 
            14            475 
  NKTR MUTATED NKTR WILD-TYPE 
            14            475 
[1] "KLF5 MUTATION ANALYSIS"
[1] 3
  KLF5 MUTATED KLF5 WILD-TYPE 
            12            477 
  KLF5 MUTATED KLF5 WILD-TYPE 
            12            477 
[1] "PARG MUTATION ANALYSIS"
[1] 3
  PARG MUTATED PARG WILD-TYPE 
            12            477 
  PARG MUTATED PARG WILD-TYPE 
            12            477 
[1] "OR6A2 MUTATION ANALYSIS"
[1] 3
  OR6A2 MUTATED OR6A2 WILD-TYPE 
              8             481 
  OR6A2 MUTATED OR6A2 WILD-TYPE 
              8             481 
[1] "MAGI1 MUTATION ANALYSIS"
[1] 3
  MAGI1 MUTATED MAGI1 WILD-TYPE 
             26             463 
  MAGI1 MUTATED MAGI1 WILD-TYPE 
             26             463 
[1] "CALCOCO2 MUTATION ANALYSIS"
[1] 3
  CALCOCO2 MUTATED CALCOCO2 WILD-TYPE 
                 8                481 
  CALCOCO2 MUTATED CALCOCO2 WILD-TYPE 
                 8                481 
[1] "IKBKE MUTATION ANALYSIS"
[1] 3
  IKBKE MUTATED IKBKE WILD-TYPE 
              8             481 
  IKBKE MUTATED IKBKE WILD-TYPE 
              8             481 
[1] "SLC44A4 MUTATION ANALYSIS"
[1] 3
  SLC44A4 MUTATED SLC44A4 WILD-TYPE 
               12               477 
  SLC44A4 MUTATED SLC44A4 WILD-TYPE 
               12               477 
[1] "GANAB MUTATION ANALYSIS"
[1] 3
  GANAB MUTATED GANAB WILD-TYPE 
             14             475 
  GANAB MUTATED GANAB WILD-TYPE 
             14             475 
[1] "SAMD9L MUTATION ANALYSIS"
[1] 3
  SAMD9L MUTATED SAMD9L WILD-TYPE 
              30              459 
  SAMD9L MUTATED SAMD9L WILD-TYPE 
              30              459 
[1] "CLPTM1 MUTATION ANALYSIS"
[1] 3
  CLPTM1 MUTATED CLPTM1 WILD-TYPE 
              12              477 
  CLPTM1 MUTATED CLPTM1 WILD-TYPE 
              12              477 
[1] "SCARA5 MUTATION ANALYSIS"
[1] 3
  SCARA5 MUTATED SCARA5 WILD-TYPE 
              15              474 
  SCARA5 MUTATED SCARA5 WILD-TYPE 
              15              474 
[1] "RAPGEF6 MUTATION ANALYSIS"
[1] 3
  RAPGEF6 MUTATED RAPGEF6 WILD-TYPE 
               20               469 
  RAPGEF6 MUTATED RAPGEF6 WILD-TYPE 
               20               469 
[1] "CEP164 MUTATION ANALYSIS"
[1] 3
  CEP164 MUTATED CEP164 WILD-TYPE 
              25              464 
  CEP164 MUTATED CEP164 WILD-TYPE 
              25              464 
[1] "PAK4 MUTATION ANALYSIS"
[1] 3
  PAK4 MUTATED PAK4 WILD-TYPE 
             6            483 
  PAK4 MUTATED PAK4 WILD-TYPE 
             6            483 
[1] "DIMT1L MUTATION ANALYSIS"
[1] 3
  DIMT1L MUTATED DIMT1L WILD-TYPE 
               6              483 
  DIMT1L MUTATED DIMT1L WILD-TYPE 
               6              483 
[1] "TAF2 MUTATION ANALYSIS"
[1] 3
  TAF2 MUTATED TAF2 WILD-TYPE 
            20            469 
  TAF2 MUTATED TAF2 WILD-TYPE 
            20            469 
[1] "NR3C1 MUTATION ANALYSIS"
[1] 3
  NR3C1 MUTATED NR3C1 WILD-TYPE 
             10             479 
  NR3C1 MUTATED NR3C1 WILD-TYPE 
             10             479 
[1] "HEATR4 MUTATION ANALYSIS"
[1] 3
  HEATR4 MUTATED HEATR4 WILD-TYPE 
              17              472 
  HEATR4 MUTATED HEATR4 WILD-TYPE 
              17              472 
[1] "BCAR3 MUTATION ANALYSIS"
[1] 3
  BCAR3 MUTATED BCAR3 WILD-TYPE 
             13             476 
  BCAR3 MUTATED BCAR3 WILD-TYPE 
             13             476 
[1] "OR2T34 MUTATION ANALYSIS"
[1] 3
  OR2T34 MUTATED OR2T34 WILD-TYPE 
               6              483 
  OR2T34 MUTATED OR2T34 WILD-TYPE 
               6              483 
[1] "POLDIP3 MUTATION ANALYSIS"
[1] 3
  POLDIP3 MUTATED POLDIP3 WILD-TYPE 
                7               482 
  POLDIP3 MUTATED POLDIP3 WILD-TYPE 
                7               482 
[1] "PNPLA8 MUTATION ANALYSIS"
[1] 3
  PNPLA8 MUTATED PNPLA8 WILD-TYPE 
              19              470 
  PNPLA8 MUTATED PNPLA8 WILD-TYPE 
              19              470 
[1] "C7ORF60 MUTATION ANALYSIS"
[1] 3
  C7ORF60 MUTATED C7ORF60 WILD-TYPE 
                6               483 
  C7ORF60 MUTATED C7ORF60 WILD-TYPE 
                6               483 
[1] "SLC25A17 MUTATION ANALYSIS"
[1] 3
  SLC25A17 MUTATED SLC25A17 WILD-TYPE 
                 8                481 
  SLC25A17 MUTATED SLC25A17 WILD-TYPE 
                 8                481 
[1] "KRTAP10-11 MUTATION ANALYSIS"
[1] 3
  KRTAP10-11 MUTATED KRTAP10-11 WILD-TYPE 
                   6                  483 
  KRTAP10-11 MUTATED KRTAP10-11 WILD-TYPE 
                   6                  483 
[1] "GTF3C1 MUTATION ANALYSIS"
[1] 3
  GTF3C1 MUTATED GTF3C1 WILD-TYPE 
              30              459 
  GTF3C1 MUTATED GTF3C1 WILD-TYPE 
              30              459 
[1] "WAC MUTATION ANALYSIS"
[1] 3
  WAC MUTATED WAC WILD-TYPE 
           15           474 
  WAC MUTATED WAC WILD-TYPE 
           15           474 
[1] "NFKBIE MUTATION ANALYSIS"
[1] 3
  NFKBIE MUTATED NFKBIE WILD-TYPE 
               4              485 
  NFKBIE MUTATED NFKBIE WILD-TYPE 
               4              485 
[1] "RRM2B MUTATION ANALYSIS"
[1] 3
  RRM2B MUTATED RRM2B WILD-TYPE 
              5             484 
  RRM2B MUTATED RRM2B WILD-TYPE 
              5             484 
[1] "KRTAP20-1 MUTATION ANALYSIS"
[1] 3
  KRTAP20-1 MUTATED KRTAP20-1 WILD-TYPE 
                  3                 486 
  KRTAP20-1 MUTATED KRTAP20-1 WILD-TYPE 
                  3                 486 
[1] "TAF6 MUTATION ANALYSIS"
[1] 3
  TAF6 MUTATED TAF6 WILD-TYPE 
            10            479 
  TAF6 MUTATED TAF6 WILD-TYPE 
            10            479 
[1] "URGCP MUTATION ANALYSIS"
[1] 3
  URGCP MUTATED URGCP WILD-TYPE 
             18             471 
  URGCP MUTATED URGCP WILD-TYPE 
             18             471 
[1] "CHRNA3 MUTATION ANALYSIS"
[1] 3
  CHRNA3 MUTATED CHRNA3 WILD-TYPE 
              11              478 
  CHRNA3 MUTATED CHRNA3 WILD-TYPE 
              11              478 
[1] "RUNX2 MUTATION ANALYSIS"
[1] 3
  RUNX2 MUTATED RUNX2 WILD-TYPE 
              9             480 
  RUNX2 MUTATED RUNX2 WILD-TYPE 
              9             480 
[1] "ZNF354C MUTATION ANALYSIS"
[1] 3
  ZNF354C MUTATED ZNF354C WILD-TYPE 
               18               471 
  ZNF354C MUTATED ZNF354C WILD-TYPE 
               18               471 
[1] "PACS2 MUTATION ANALYSIS"
[1] 3
  PACS2 MUTATED PACS2 WILD-TYPE 
              5             484 
  PACS2 MUTATED PACS2 WILD-TYPE 
              5             484 
[1] "HIF3A MUTATION ANALYSIS"
[1] 3
  HIF3A MUTATED HIF3A WILD-TYPE 
             15             474 
  HIF3A MUTATED HIF3A WILD-TYPE 
             15             474 
[1] "ADH7 MUTATION ANALYSIS"
[1] 3
  ADH7 MUTATED ADH7 WILD-TYPE 
             7            482 
  ADH7 MUTATED ADH7 WILD-TYPE 
             7            482 
[1] "RYR2 MUTATION ANALYSIS"
[1] 3
  RYR2 MUTATED RYR2 WILD-TYPE 
           104            385 
  RYR2 MUTATED RYR2 WILD-TYPE 
           104            385 
[1] "DACT1 MUTATION ANALYSIS"
[1] 3
  DACT1 MUTATED DACT1 WILD-TYPE 
             16             473 
  DACT1 MUTATED DACT1 WILD-TYPE 
             16             473 
[1] "TMC8 MUTATION ANALYSIS"
[1] 3
  TMC8 MUTATED TMC8 WILD-TYPE 
             7            482 
  TMC8 MUTATED TMC8 WILD-TYPE 
             7            482 
[1] "SULF2 MUTATION ANALYSIS"
[1] 3
  SULF2 MUTATED SULF2 WILD-TYPE 
             25             464 
  SULF2 MUTATED SULF2 WILD-TYPE 
             25             464 
[1] "AIM2 MUTATION ANALYSIS"
[1] 3
  AIM2 MUTATED AIM2 WILD-TYPE 
             9            480 
  AIM2 MUTATED AIM2 WILD-TYPE 
             9            480 
[1] "SPAG7 MUTATION ANALYSIS"
[1] 3
  SPAG7 MUTATED SPAG7 WILD-TYPE 
              3             486 
  SPAG7 MUTATED SPAG7 WILD-TYPE 
              3             486 
[1] "WDR75 MUTATION ANALYSIS"
[1] 3
  WDR75 MUTATED WDR75 WILD-TYPE 
              8             481 
  WDR75 MUTATED WDR75 WILD-TYPE 
              8             481 
[1] "CPN2 MUTATION ANALYSIS"
[1] 3
  CPN2 MUTATED CPN2 WILD-TYPE 
            10            479 
  CPN2 MUTATED CPN2 WILD-TYPE 
            10            479 
[1] "NFKBIB MUTATION ANALYSIS"
[1] 3
  NFKBIB MUTATED NFKBIB WILD-TYPE 
               5              484 
  NFKBIB MUTATED NFKBIB WILD-TYPE 
               5              484 
[1] "ATRX MUTATION ANALYSIS"
[1] 3
  ATRX MUTATED ATRX WILD-TYPE 
            33            456 
  ATRX MUTATED ATRX WILD-TYPE 
            33            456 
[1] "TTC24 MUTATION ANALYSIS"
[1] 3
  TTC24 MUTATED TTC24 WILD-TYPE 
              7             482 
  TTC24 MUTATED TTC24 WILD-TYPE 
              7             482 
[1] "ARMC9 MUTATION ANALYSIS"
[1] 3
  ARMC9 MUTATED ARMC9 WILD-TYPE 
              8             481 
  ARMC9 MUTATED ARMC9 WILD-TYPE 
              8             481 
[1] "SNAPC1 MUTATION ANALYSIS"
[1] 3
  SNAPC1 MUTATED SNAPC1 WILD-TYPE 
               7              482 
  SNAPC1 MUTATED SNAPC1 WILD-TYPE 
               7              482 
[1] "C20ORF151 MUTATION ANALYSIS"
[1] 3
  C20ORF151 MUTATED C20ORF151 WILD-TYPE 
                 11                 478 
  C20ORF151 MUTATED C20ORF151 WILD-TYPE 
                 11                 478 
[1] "DNAJC7 MUTATION ANALYSIS"
[1] 3
  DNAJC7 MUTATED DNAJC7 WILD-TYPE 
               8              481 
  DNAJC7 MUTATED DNAJC7 WILD-TYPE 
               8              481 
[1] "NUP205 MUTATION ANALYSIS"
[1] 3
  NUP205 MUTATED NUP205 WILD-TYPE 
              26              463 
  NUP205 MUTATED NUP205 WILD-TYPE 
              26              463 
[1] "TF MUTATION ANALYSIS"
[1] 3
  TF MUTATED TF WILD-TYPE 
          14          475 
  TF MUTATED TF WILD-TYPE 
          14          475 
[1] "LRRC37B MUTATION ANALYSIS"
[1] 3
  LRRC37B MUTATED LRRC37B WILD-TYPE 
                9               480 
  LRRC37B MUTATED LRRC37B WILD-TYPE 
                9               480 
[1] "BCHE MUTATION ANALYSIS"
[1] 3
  BCHE MUTATED BCHE WILD-TYPE 
            29            460 
  BCHE MUTATED BCHE WILD-TYPE 
            29            460 
[1] "TRYX3 MUTATION ANALYSIS"
[1] 3
  TRYX3 MUTATED TRYX3 WILD-TYPE 
              7             482 
  TRYX3 MUTATED TRYX3 WILD-TYPE 
              7             482 
[1] "ZNF436 MUTATION ANALYSIS"
[1] 3
  ZNF436 MUTATED ZNF436 WILD-TYPE 
               7              482 
  ZNF436 MUTATED ZNF436 WILD-TYPE 
               7              482 
[1] "A1CF MUTATION ANALYSIS"
[1] 3
  A1CF MUTATED A1CF WILD-TYPE 
             8            481 
  A1CF MUTATED A1CF WILD-TYPE 
             8            481 
[1] "TXLNG MUTATION ANALYSIS"
[1] 3
  TXLNG MUTATED TXLNG WILD-TYPE 
             10             479 
  TXLNG MUTATED TXLNG WILD-TYPE 
             10             479 
[1] "P2RX7 MUTATION ANALYSIS"
[1] 3
  P2RX7 MUTATED P2RX7 WILD-TYPE 
             13             476 
  P2RX7 MUTATED P2RX7 WILD-TYPE 
             13             476 
[1] "RCOR3 MUTATION ANALYSIS"
[1] 3
  RCOR3 MUTATED RCOR3 WILD-TYPE 
             13             476 
  RCOR3 MUTATED RCOR3 WILD-TYPE 
             13             476 
[1] "HMOX1 MUTATION ANALYSIS"
[1] 3
  HMOX1 MUTATED HMOX1 WILD-TYPE 
              6             483 
  HMOX1 MUTATED HMOX1 WILD-TYPE 
              6             483 
[1] "UCHL5 MUTATION ANALYSIS"
[1] 3
  UCHL5 MUTATED UCHL5 WILD-TYPE 
              5             484 
  UCHL5 MUTATED UCHL5 WILD-TYPE 
              5             484 
[1] "NTRK2 MUTATION ANALYSIS"
[1] 3
  NTRK2 MUTATED NTRK2 WILD-TYPE 
             25             464 
  NTRK2 MUTATED NTRK2 WILD-TYPE 
             25             464 
[1] "MFAP1 MUTATION ANALYSIS"
[1] 3
  MFAP1 MUTATED MFAP1 WILD-TYPE 
              5             484 
  MFAP1 MUTATED MFAP1 WILD-TYPE 
              5             484 
[1] "RNF215 MUTATION ANALYSIS"
[1] 3
  RNF215 MUTATED RNF215 WILD-TYPE 
               3              486 
  RNF215 MUTATED RNF215 WILD-TYPE 
               3              486 
[1] "FANCD2 MUTATION ANALYSIS"
[1] 3
  FANCD2 MUTATED FANCD2 WILD-TYPE 
              18              471 
  FANCD2 MUTATED FANCD2 WILD-TYPE 
              18              471 
[1] "CD34 MUTATION ANALYSIS"
[1] 3
  CD34 MUTATED CD34 WILD-TYPE 
             6            483 
  CD34 MUTATED CD34 WILD-TYPE 
             6            483 
[1] "ZSWIM3 MUTATION ANALYSIS"
[1] 3
  ZSWIM3 MUTATED ZSWIM3 WILD-TYPE 
              13              476 
  ZSWIM3 MUTATED ZSWIM3 WILD-TYPE 
              13              476 
[1] "SLC16A2 MUTATION ANALYSIS"
[1] 3
  SLC16A2 MUTATED SLC16A2 WILD-TYPE 
                8               481 
  SLC16A2 MUTATED SLC16A2 WILD-TYPE 
                8               481 
[1] "DDHD2 MUTATION ANALYSIS"
[1] 3
  DDHD2 MUTATED DDHD2 WILD-TYPE 
             11             478 
  DDHD2 MUTATED DDHD2 WILD-TYPE 
             11             478 
[1] "GKN1 MUTATION ANALYSIS"
[1] 3
  GKN1 MUTATED GKN1 WILD-TYPE 
             6            483 
  GKN1 MUTATED GKN1 WILD-TYPE 
             6            483 
[1] "F2R MUTATION ANALYSIS"
[1] 3
  F2R MUTATED F2R WILD-TYPE 
           11           478 
  F2R MUTATED F2R WILD-TYPE 
           11           478 
[1] "CYP20A1 MUTATION ANALYSIS"
[1] 3
  CYP20A1 MUTATED CYP20A1 WILD-TYPE 
                8               481 
  CYP20A1 MUTATED CYP20A1 WILD-TYPE 
                8               481 
[1] "ZP2 MUTATION ANALYSIS"
[1] 3
  ZP2 MUTATED ZP2 WILD-TYPE 
           14           475 
  ZP2 MUTATED ZP2 WILD-TYPE 
           14           475 
[1] "RAB38 MUTATION ANALYSIS"
[1] 3
  RAB38 MUTATED RAB38 WILD-TYPE 
              5             484 
  RAB38 MUTATED RAB38 WILD-TYPE 
              5             484 
[1] "TCF7 MUTATION ANALYSIS"
[1] 3
  TCF7 MUTATED TCF7 WILD-TYPE 
            12            477 
  TCF7 MUTATED TCF7 WILD-TYPE 
            12            477 
[1] "NUFIP1 MUTATION ANALYSIS"
[1] 3
  NUFIP1 MUTATED NUFIP1 WILD-TYPE 
               8              481 
  NUFIP1 MUTATED NUFIP1 WILD-TYPE 
               8              481 
[1] "OR7D4 MUTATION ANALYSIS"
[1] 3
  OR7D4 MUTATED OR7D4 WILD-TYPE 
             10             479 
  OR7D4 MUTATED OR7D4 WILD-TYPE 
             10             479 
[1] "NUPL2 MUTATION ANALYSIS"
[1] 3
  NUPL2 MUTATED NUPL2 WILD-TYPE 
             11             478 
  NUPL2 MUTATED NUPL2 WILD-TYPE 
             11             478 
[1] "GNA14 MUTATION ANALYSIS"
[1] 3
  GNA14 MUTATED GNA14 WILD-TYPE 
             13             476 
  GNA14 MUTATED GNA14 WILD-TYPE 
             13             476 
[1] "PREX2 MUTATION ANALYSIS"
[1] 3
  PREX2 MUTATED PREX2 WILD-TYPE 
             35             454 
  PREX2 MUTATED PREX2 WILD-TYPE 
             35             454 
[1] "NEB MUTATION ANALYSIS"
[1] 3
  NEB MUTATED NEB WILD-TYPE 
           66           423 
  NEB MUTATED NEB WILD-TYPE 
           66           423 
[1] "DTX3L MUTATION ANALYSIS"
[1] 3
  DTX3L MUTATED DTX3L WILD-TYPE 
             11             478 
  DTX3L MUTATED DTX3L WILD-TYPE 
             11             478 
[1] "ARHGEF1 MUTATION ANALYSIS"
[1] 3
  ARHGEF1 MUTATED ARHGEF1 WILD-TYPE 
               15               474 
  ARHGEF1 MUTATED ARHGEF1 WILD-TYPE 
               15               474 
[1] "VPS33A MUTATION ANALYSIS"
[1] 3
  VPS33A MUTATED VPS33A WILD-TYPE 
               8              481 
  VPS33A MUTATED VPS33A WILD-TYPE 
               8              481 
[1] "FSTL4 MUTATION ANALYSIS"
[1] 3
  FSTL4 MUTATED FSTL4 WILD-TYPE 
             17             472 
  FSTL4 MUTATED FSTL4 WILD-TYPE 
             17             472 
[1] "PTPRG MUTATION ANALYSIS"
[1] 3
  PTPRG MUTATED PTPRG WILD-TYPE 
             25             464 
  PTPRG MUTATED PTPRG WILD-TYPE 
             25             464 
[1] "ATF2 MUTATION ANALYSIS"
[1] 3
  ATF2 MUTATED ATF2 WILD-TYPE 
             7            482 
  ATF2 MUTATED ATF2 WILD-TYPE 
             7            482 
[1] "CREG2 MUTATION ANALYSIS"
[1] 3
  CREG2 MUTATED CREG2 WILD-TYPE 
              5             484 
  CREG2 MUTATED CREG2 WILD-TYPE 
              5             484 
[1] "GTF2A1L MUTATION ANALYSIS"
[1] 3
  GTF2A1L MUTATED GTF2A1L WILD-TYPE 
               21               468 
  GTF2A1L MUTATED GTF2A1L WILD-TYPE 
               21               468 
[1] "MALT1 MUTATION ANALYSIS"
[1] 3
  MALT1 MUTATED MALT1 WILD-TYPE 
             12             477 
  MALT1 MUTATED MALT1 WILD-TYPE 
             12             477 
[1] "PSMD6 MUTATION ANALYSIS"
[1] 3
  PSMD6 MUTATED PSMD6 WILD-TYPE 
              8             481 
  PSMD6 MUTATED PSMD6 WILD-TYPE 
              8             481 
[1] "DLEC1 MUTATION ANALYSIS"
[1] 3
  DLEC1 MUTATED DLEC1 WILD-TYPE 
             19             470 
  DLEC1 MUTATED DLEC1 WILD-TYPE 
             19             470 
[1] "DPP8 MUTATION ANALYSIS"
[1] 3
  DPP8 MUTATED DPP8 WILD-TYPE 
            14            475 
  DPP8 MUTATED DPP8 WILD-TYPE 
            14            475 
[1] "CAPRIN1 MUTATION ANALYSIS"
[1] 3
  CAPRIN1 MUTATED CAPRIN1 WILD-TYPE 
               12               477 
  CAPRIN1 MUTATED CAPRIN1 WILD-TYPE 
               12               477 
[1] "MTA2 MUTATION ANALYSIS"
[1] 3
  MTA2 MUTATED MTA2 WILD-TYPE 
            12            477 
  MTA2 MUTATED MTA2 WILD-TYPE 
            12            477 
[1] "GFRA4 MUTATION ANALYSIS"
[1] 3
  GFRA4 MUTATED GFRA4 WILD-TYPE 
              3             486 
  GFRA4 MUTATED GFRA4 WILD-TYPE 
              3             486 
[1] "FGD4 MUTATION ANALYSIS"
[1] 3
  FGD4 MUTATED FGD4 WILD-TYPE 
            10            479 
  FGD4 MUTATED FGD4 WILD-TYPE 
            10            479 
[1] "HPS6 MUTATION ANALYSIS"
[1] 3
  HPS6 MUTATED HPS6 WILD-TYPE 
             7            482 
  HPS6 MUTATED HPS6 WILD-TYPE 
             7            482 
[1] "AP4B1 MUTATION ANALYSIS"
[1] 3
  AP4B1 MUTATED AP4B1 WILD-TYPE 
             12             477 
  AP4B1 MUTATED AP4B1 WILD-TYPE 
             12             477 
[1] "STK38 MUTATION ANALYSIS"
[1] 3
  STK38 MUTATED STK38 WILD-TYPE 
             11             478 
  STK38 MUTATED STK38 WILD-TYPE 
             11             478 
[1] "PRKCD MUTATION ANALYSIS"
[1] 3
  PRKCD MUTATED PRKCD WILD-TYPE 
             13             476 
  PRKCD MUTATED PRKCD WILD-TYPE 
             13             476 
[1] "HIST1H2BC MUTATION ANALYSIS"
[1] 3
  HIST1H2BC MUTATED HIST1H2BC WILD-TYPE 
                  4                 485 
  HIST1H2BC MUTATED HIST1H2BC WILD-TYPE 
                  4                 485 
[1] "RIMS2 MUTATION ANALYSIS"
[1] 3
  RIMS2 MUTATED RIMS2 WILD-TYPE 
             40             449 
  RIMS2 MUTATED RIMS2 WILD-TYPE 
             40             449 
[1] "LEMD1 MUTATION ANALYSIS"
[1] 3
  LEMD1 MUTATED LEMD1 WILD-TYPE 
              3             486 
  LEMD1 MUTATED LEMD1 WILD-TYPE 
              3             486 
[1] "RC3H2 MUTATION ANALYSIS"
[1] 3
  RC3H2 MUTATED RC3H2 WILD-TYPE 
             10             479 
  RC3H2 MUTATED RC3H2 WILD-TYPE 
             10             479 
[1] "ZFYVE16 MUTATION ANALYSIS"
[1] 3
  ZFYVE16 MUTATED ZFYVE16 WILD-TYPE 
               19               470 
  ZFYVE16 MUTATED ZFYVE16 WILD-TYPE 
               19               470 
[1] "APOBEC4 MUTATION ANALYSIS"
[1] 3
  APOBEC4 MUTATED APOBEC4 WILD-TYPE 
                9               480 
  APOBEC4 MUTATED APOBEC4 WILD-TYPE 
                9               480 
[1] "ARID5A MUTATION ANALYSIS"
[1] 3
  ARID5A MUTATED ARID5A WILD-TYPE 
               8              481 
  ARID5A MUTATED ARID5A WILD-TYPE 
               8              481 
[1] "CYP2C18 MUTATION ANALYSIS"
[1] 3
  CYP2C18 MUTATED CYP2C18 WILD-TYPE 
                7               482 
  CYP2C18 MUTATED CYP2C18 WILD-TYPE 
                7               482 
[1] "BEND2 MUTATION ANALYSIS"
[1] 3
  BEND2 MUTATED BEND2 WILD-TYPE 
             23             466 
  BEND2 MUTATED BEND2 WILD-TYPE 
             23             466 
[1] "KCTD9 MUTATION ANALYSIS"
[1] 3
  KCTD9 MUTATED KCTD9 WILD-TYPE 
              5             484 
  KCTD9 MUTATED KCTD9 WILD-TYPE 
              5             484 
[1] "SBDS MUTATION ANALYSIS"
[1] 3
  SBDS MUTATED SBDS WILD-TYPE 
             3            486 
  SBDS MUTATED SBDS WILD-TYPE 
             3            486 
[1] "KIFC2 MUTATION ANALYSIS"
[1] 3
  KIFC2 MUTATED KIFC2 WILD-TYPE 
              6             483 
  KIFC2 MUTATED KIFC2 WILD-TYPE 
              6             483 
[1] "PSMD11 MUTATION ANALYSIS"
[1] 3
  PSMD11 MUTATED PSMD11 WILD-TYPE 
               8              481 
  PSMD11 MUTATED PSMD11 WILD-TYPE 
               8              481 
[1] "PPYR1 MUTATION ANALYSIS"
[1] 3
  PPYR1 MUTATED PPYR1 WILD-TYPE 
              7             482 
  PPYR1 MUTATED PPYR1 WILD-TYPE 
              7             482 
[1] "MCM4 MUTATION ANALYSIS"
[1] 3
  MCM4 MUTATED MCM4 WILD-TYPE 
            14            475 
  MCM4 MUTATED MCM4 WILD-TYPE 
            14            475 
[1] "ARHGEF3 MUTATION ANALYSIS"
[1] 3
  ARHGEF3 MUTATED ARHGEF3 WILD-TYPE 
               11               478 
  ARHGEF3 MUTATED ARHGEF3 WILD-TYPE 
               11               478 
[1] "KLF3 MUTATION ANALYSIS"
[1] 3
  KLF3 MUTATED KLF3 WILD-TYPE 
             7            482 
  KLF3 MUTATED KLF3 WILD-TYPE 
             7            482 
[1] "SENP8 MUTATION ANALYSIS"
[1] 3
  SENP8 MUTATED SENP8 WILD-TYPE 
              4             485 
  SENP8 MUTATED SENP8 WILD-TYPE 
              4             485 
[1] "GCM2 MUTATION ANALYSIS"
[1] 3
  GCM2 MUTATED GCM2 WILD-TYPE 
            14            475 
  GCM2 MUTATED GCM2 WILD-TYPE 
            14            475 
[1] "KRT9 MUTATION ANALYSIS"
[1] 3
  KRT9 MUTATED KRT9 WILD-TYPE 
            13            476 
  KRT9 MUTATED KRT9 WILD-TYPE 
            13            476 
[1] "CHD7 MUTATION ANALYSIS"
[1] 3
  CHD7 MUTATED CHD7 WILD-TYPE 
            39            450 
  CHD7 MUTATED CHD7 WILD-TYPE 
            39            450 
[1] "CHD1 MUTATION ANALYSIS"
[1] 3
  CHD1 MUTATED CHD1 WILD-TYPE 
            25            464 
  CHD1 MUTATED CHD1 WILD-TYPE 
            25            464 
[1] "LRIG2 MUTATION ANALYSIS"
[1] 3
  LRIG2 MUTATED LRIG2 WILD-TYPE 
              9             480 
  LRIG2 MUTATED LRIG2 WILD-TYPE 
              9             480 
[1] "SAMD9 MUTATION ANALYSIS"
[1] 3
  SAMD9 MUTATED SAMD9 WILD-TYPE 
             29             460 
  SAMD9 MUTATED SAMD9 WILD-TYPE 
             29             460 
[1] "CROT MUTATION ANALYSIS"
[1] 3
  CROT MUTATED CROT WILD-TYPE 
            11            478 
  CROT MUTATED CROT WILD-TYPE 
            11            478 
[1] "BUB1 MUTATION ANALYSIS"
[1] 3
  BUB1 MUTATED BUB1 WILD-TYPE 
            16            473 
  BUB1 MUTATED BUB1 WILD-TYPE 
            16            473 
[1] "SULT1E1 MUTATION ANALYSIS"
[1] 3
  SULT1E1 MUTATED SULT1E1 WILD-TYPE 
                5               484 
  SULT1E1 MUTATED SULT1E1 WILD-TYPE 
                5               484 
[1] "TTBK2 MUTATION ANALYSIS"
[1] 3
  TTBK2 MUTATED TTBK2 WILD-TYPE 
             18             471 
  TTBK2 MUTATED TTBK2 WILD-TYPE 
             18             471 
[1] "SMO MUTATION ANALYSIS"
[1] 3
  SMO MUTATED SMO WILD-TYPE 
           13           476 
  SMO MUTATED SMO WILD-TYPE 
           13           476 
[1] "FBXO40 MUTATION ANALYSIS"
[1] 3
  FBXO40 MUTATED FBXO40 WILD-TYPE 
              21              468 
  FBXO40 MUTATED FBXO40 WILD-TYPE 
              21              468 
[1] "ARHGAP29 MUTATION ANALYSIS"
[1] 3
  ARHGAP29 MUTATED ARHGAP29 WILD-TYPE 
                19                470 
  ARHGAP29 MUTATED ARHGAP29 WILD-TYPE 
                19                470 
[1] "PAK2 MUTATION ANALYSIS"
[1] 3
  PAK2 MUTATED PAK2 WILD-TYPE 
            11            478 
  PAK2 MUTATED PAK2 WILD-TYPE 
            11            478 
[1] "MAOA MUTATION ANALYSIS"
[1] 3
  MAOA MUTATED MAOA WILD-TYPE 
             7            482 
  MAOA MUTATED MAOA WILD-TYPE 
             7            482 
[1] "FAM120C MUTATION ANALYSIS"
[1] 3
  FAM120C MUTATED FAM120C WILD-TYPE 
                8               481 
  FAM120C MUTATED FAM120C WILD-TYPE 
                8               481 
[1] "MED13 MUTATION ANALYSIS"
[1] 3
  MED13 MUTATED MED13 WILD-TYPE 
             22             467 
  MED13 MUTATED MED13 WILD-TYPE 
             22             467 
[1] "ALCAM MUTATION ANALYSIS"
[1] 3
  ALCAM MUTATED ALCAM WILD-TYPE 
             12             477 
  ALCAM MUTATED ALCAM WILD-TYPE 
             12             477 
[1] "MEGF8 MUTATION ANALYSIS"
[1] 3
  MEGF8 MUTATED MEGF8 WILD-TYPE 
             27             462 
  MEGF8 MUTATED MEGF8 WILD-TYPE 
             27             462 
[1] "SLIT3 MUTATION ANALYSIS"
[1] 3
  SLIT3 MUTATED SLIT3 WILD-TYPE 
             27             462 
  SLIT3 MUTATED SLIT3 WILD-TYPE 
             27             462 
[1] "KIF14 MUTATION ANALYSIS"
[1] 3
  KIF14 MUTATED KIF14 WILD-TYPE 
             13             476 
  KIF14 MUTATED KIF14 WILD-TYPE 
             13             476 
[1] "CDKL2 MUTATION ANALYSIS"
[1] 3
  CDKL2 MUTATED CDKL2 WILD-TYPE 
             11             478 
  CDKL2 MUTATED CDKL2 WILD-TYPE 
             11             478 
[1] "ITGA5 MUTATION ANALYSIS"
[1] 3
  ITGA5 MUTATED ITGA5 WILD-TYPE 
             17             472 
  ITGA5 MUTATED ITGA5 WILD-TYPE 
             17             472 
[1] "SULT1C4 MUTATION ANALYSIS"
[1] 3
  SULT1C4 MUTATED SULT1C4 WILD-TYPE 
                3               486 
  SULT1C4 MUTATED SULT1C4 WILD-TYPE 
                3               486 
[1] "C6ORF146 MUTATION ANALYSIS"
[1] 3
  C6ORF146 MUTATED C6ORF146 WILD-TYPE 
                 8                481 
  C6ORF146 MUTATED C6ORF146 WILD-TYPE 
                 8                481 
[1] "DYM MUTATION ANALYSIS"
[1] 3
  DYM MUTATED DYM WILD-TYPE 
           10           479 
  DYM MUTATED DYM WILD-TYPE 
           10           479 
[1] "PCDH9 MUTATION ANALYSIS"
[1] 3
  PCDH9 MUTATED PCDH9 WILD-TYPE 
             45             444 
  PCDH9 MUTATED PCDH9 WILD-TYPE 
             45             444 
[1] "MRE11A MUTATION ANALYSIS"
[1] 3
  MRE11A MUTATED MRE11A WILD-TYPE 
              14              475 
  MRE11A MUTATED MRE11A WILD-TYPE 
              14              475 
[1] "CASP10 MUTATION ANALYSIS"
[1] 3
  CASP10 MUTATED CASP10 WILD-TYPE 
               7              482 
  CASP10 MUTATED CASP10 WILD-TYPE 
               7              482 
[1] "TSHZ1 MUTATION ANALYSIS"
[1] 3
  TSHZ1 MUTATED TSHZ1 WILD-TYPE 
             13             476 
  TSHZ1 MUTATED TSHZ1 WILD-TYPE 
             13             476 
[1] "CCDC158 MUTATION ANALYSIS"
[1] 3
  CCDC158 MUTATED CCDC158 WILD-TYPE 
               19               470 
  CCDC158 MUTATED CCDC158 WILD-TYPE 
               19               470 
[1] "BRD2 MUTATION ANALYSIS"
[1] 3
  BRD2 MUTATED BRD2 WILD-TYPE 
            12            477 
  BRD2 MUTATED BRD2 WILD-TYPE 
            12            477 
[1] "KIAA2022 MUTATION ANALYSIS"
[1] 3
  KIAA2022 MUTATED KIAA2022 WILD-TYPE 
                39                450 
  KIAA2022 MUTATED KIAA2022 WILD-TYPE 
                39                450 
[1] "GRM1 MUTATION ANALYSIS"
[1] 3
  GRM1 MUTATED GRM1 WILD-TYPE 
            32            457 
  GRM1 MUTATED GRM1 WILD-TYPE 
            32            457 
[1] "WFDC10B MUTATION ANALYSIS"
[1] 3
  WFDC10B MUTATED WFDC10B WILD-TYPE 
                5               484 
  WFDC10B MUTATED WFDC10B WILD-TYPE 
                5               484 
[1] "KIAA0240 MUTATION ANALYSIS"
[1] 3
  KIAA0240 MUTATED KIAA0240 WILD-TYPE 
                11                478 
  KIAA0240 MUTATED KIAA0240 WILD-TYPE 
                11                478 
[1] "PSMB8 MUTATION ANALYSIS"
[1] 3
  PSMB8 MUTATED PSMB8 WILD-TYPE 
              7             482 
  PSMB8 MUTATED PSMB8 WILD-TYPE 
              7             482 
[1] "BTF3L4 MUTATION ANALYSIS"
[1] 3
  BTF3L4 MUTATED BTF3L4 WILD-TYPE 
               5              484 
  BTF3L4 MUTATED BTF3L4 WILD-TYPE 
               5              484 
[1] "SYNGR4 MUTATION ANALYSIS"
[1] 3
  SYNGR4 MUTATED SYNGR4 WILD-TYPE 
               6              483 
  SYNGR4 MUTATED SYNGR4 WILD-TYPE 
               6              483 
[1] "OR2AE1 MUTATION ANALYSIS"
[1] 3
  OR2AE1 MUTATED OR2AE1 WILD-TYPE 
               3              486 
  OR2AE1 MUTATED OR2AE1 WILD-TYPE 
               3              486 
[1] "SMAP1 MUTATION ANALYSIS"
[1] 3
  SMAP1 MUTATED SMAP1 WILD-TYPE 
              3             486 
  SMAP1 MUTATED SMAP1 WILD-TYPE 
              3             486 
[1] "GON4L MUTATION ANALYSIS"
[1] 3
  GON4L MUTATED GON4L WILD-TYPE 
             23             466 
  GON4L MUTATED GON4L WILD-TYPE 
             23             466 
[1] "NDST3 MUTATION ANALYSIS"
[1] 3
  NDST3 MUTATED NDST3 WILD-TYPE 
             18             471 
  NDST3 MUTATED NDST3 WILD-TYPE 
             18             471 
[1] "MAGEA4 MUTATION ANALYSIS"
[1] 3
  MAGEA4 MUTATED MAGEA4 WILD-TYPE 
               7              482 
  MAGEA4 MUTATED MAGEA4 WILD-TYPE 
               7              482 
[1] "RPS6KA5 MUTATION ANALYSIS"
[1] 3
  RPS6KA5 MUTATED RPS6KA5 WILD-TYPE 
               11               478 
  RPS6KA5 MUTATED RPS6KA5 WILD-TYPE 
               11               478 
[1] "KLHL34 MUTATION ANALYSIS"
[1] 3
  KLHL34 MUTATED KLHL34 WILD-TYPE 
              13              476 
  KLHL34 MUTATED KLHL34 WILD-TYPE 
              13              476 
[1] "EIF2AK3 MUTATION ANALYSIS"
[1] 3
  EIF2AK3 MUTATED EIF2AK3 WILD-TYPE 
               12               477 
  EIF2AK3 MUTATED EIF2AK3 WILD-TYPE 
               12               477 
[1] "CDC73 MUTATION ANALYSIS"
[1] 3
  CDC73 MUTATED CDC73 WILD-TYPE 
             22             467 
  CDC73 MUTATED CDC73 WILD-TYPE 
             22             467 
[1] "MYH15 MUTATION ANALYSIS"
[1] 3
  MYH15 MUTATED MYH15 WILD-TYPE 
             29             460 
  MYH15 MUTATED MYH15 WILD-TYPE 
             29             460 
[1] "SPEN MUTATION ANALYSIS"
[1] 3
  SPEN MUTATED SPEN WILD-TYPE 
            34            455 
  SPEN MUTATED SPEN WILD-TYPE 
            34            455 
[1] "IL1F8 MUTATION ANALYSIS"
[1] 3
  IL1F8 MUTATED IL1F8 WILD-TYPE 
              3             486 
  IL1F8 MUTATED IL1F8 WILD-TYPE 
              3             486 
[1] "CCR8 MUTATION ANALYSIS"
[1] 3
  CCR8 MUTATED CCR8 WILD-TYPE 
             7            482 
  CCR8 MUTATED CCR8 WILD-TYPE 
             7            482 
[1] "HSPBAP1 MUTATION ANALYSIS"
[1] 3
  HSPBAP1 MUTATED HSPBAP1 WILD-TYPE 
                8               481 
  HSPBAP1 MUTATED HSPBAP1 WILD-TYPE 
                8               481 
[1] "XG MUTATION ANALYSIS"
[1] 3
  XG MUTATED XG WILD-TYPE 
           7          482 
  XG MUTATED XG WILD-TYPE 
           7          482 
[1] "UHRF1BP1L MUTATION ANALYSIS"
[1] 3
  UHRF1BP1L MUTATED UHRF1BP1L WILD-TYPE 
                 21                 468 
  UHRF1BP1L MUTATED UHRF1BP1L WILD-TYPE 
                 21                 468 
[1] "CATSPER2 MUTATION ANALYSIS"
[1] 3
  CATSPER2 MUTATED CATSPER2 WILD-TYPE 
                 7                482 
  CATSPER2 MUTATED CATSPER2 WILD-TYPE 
                 7                482 
[1] "PPP2R5E MUTATION ANALYSIS"
[1] 3
  PPP2R5E MUTATED PPP2R5E WILD-TYPE 
                8               481 
  PPP2R5E MUTATED PPP2R5E WILD-TYPE 
                8               481 
[1] "SPOPL MUTATION ANALYSIS"
[1] 3
  SPOPL MUTATED SPOPL WILD-TYPE 
             10             479 
  SPOPL MUTATED SPOPL WILD-TYPE 
             10             479 
[1] "FCRL4 MUTATION ANALYSIS"
[1] 3
  FCRL4 MUTATED FCRL4 WILD-TYPE 
             13             476 
  FCRL4 MUTATED FCRL4 WILD-TYPE 
             13             476 
[1] "THRAP3 MUTATION ANALYSIS"
[1] 3
  THRAP3 MUTATED THRAP3 WILD-TYPE 
              12              477 
  THRAP3 MUTATED THRAP3 WILD-TYPE 
              12              477 
[1] "ATP2B4 MUTATION ANALYSIS"
[1] 3
  ATP2B4 MUTATED ATP2B4 WILD-TYPE 
              21              468 
  ATP2B4 MUTATED ATP2B4 WILD-TYPE 
              21              468 
[1] "PCDHGA8 MUTATION ANALYSIS"
[1] 3
  PCDHGA8 MUTATED PCDHGA8 WILD-TYPE 
               18               471 
  PCDHGA8 MUTATED PCDHGA8 WILD-TYPE 
               18               471 
[1] "TRIM46 MUTATION ANALYSIS"
[1] 3
  TRIM46 MUTATED TRIM46 WILD-TYPE 
              15              474 
  TRIM46 MUTATED TRIM46 WILD-TYPE 
              15              474 
[1] "TNKS MUTATION ANALYSIS"
[1] 3
  TNKS MUTATED TNKS WILD-TYPE 
            10            479 
  TNKS MUTATED TNKS WILD-TYPE 
            10            479 
[1] "ADAM20 MUTATION ANALYSIS"
[1] 3
  ADAM20 MUTATED ADAM20 WILD-TYPE 
               6              483 
  ADAM20 MUTATED ADAM20 WILD-TYPE 
               6              483 
[1] "CDK5RAP2 MUTATION ANALYSIS"
[1] 3
  CDK5RAP2 MUTATED CDK5RAP2 WILD-TYPE 
                25                464 
  CDK5RAP2 MUTATED CDK5RAP2 WILD-TYPE 
                25                464 
[1] "NXPH1 MUTATION ANALYSIS"
[1] 3
  NXPH1 MUTATED NXPH1 WILD-TYPE 
              9             480 
  NXPH1 MUTATED NXPH1 WILD-TYPE 
              9             480 
[1] "ATP10B MUTATION ANALYSIS"
[1] 3
  ATP10B MUTATED ATP10B WILD-TYPE 
              17              472 
  ATP10B MUTATED ATP10B WILD-TYPE 
              17              472 
[1] "ERGIC1 MUTATION ANALYSIS"
[1] 3
  ERGIC1 MUTATED ERGIC1 WILD-TYPE 
               5              484 
  ERGIC1 MUTATED ERGIC1 WILD-TYPE 
               5              484 
[1] "IVD MUTATION ANALYSIS"
[1] 3
  IVD MUTATED IVD WILD-TYPE 
            6           483 
  IVD MUTATED IVD WILD-TYPE 
            6           483 
[1] "YTHDF2 MUTATION ANALYSIS"
[1] 3
  YTHDF2 MUTATED YTHDF2 WILD-TYPE 
              12              477 
  YTHDF2 MUTATED YTHDF2 WILD-TYPE 
              12              477 
[1] "KCNN4 MUTATION ANALYSIS"
[1] 3
  KCNN4 MUTATED KCNN4 WILD-TYPE 
              7             482 
  KCNN4 MUTATED KCNN4 WILD-TYPE 
              7             482 
[1] "C20ORF177 MUTATION ANALYSIS"
[1] 3
  C20ORF177 MUTATED C20ORF177 WILD-TYPE 
                 13                 476 
  C20ORF177 MUTATED C20ORF177 WILD-TYPE 
                 13                 476 
[1] "RBL1 MUTATION ANALYSIS"
[1] 3
  RBL1 MUTATED RBL1 WILD-TYPE 
            19            470 
  RBL1 MUTATED RBL1 WILD-TYPE 
            19            470 
[1] "RBM15B MUTATION ANALYSIS"
[1] 3
  RBM15B MUTATED RBM15B WILD-TYPE 
               9              480 
  RBM15B MUTATED RBM15B WILD-TYPE 
               9              480 
[1] "PCDH19 MUTATION ANALYSIS"
[1] 3
  PCDH19 MUTATED PCDH19 WILD-TYPE 
              22              467 
  PCDH19 MUTATED PCDH19 WILD-TYPE 
              22              467 
[1] "MOV10L1 MUTATION ANALYSIS"
[1] 3
  MOV10L1 MUTATED MOV10L1 WILD-TYPE 
               17               472 
  MOV10L1 MUTATED MOV10L1 WILD-TYPE 
               17               472 
[1] "FAF2 MUTATION ANALYSIS"
[1] 3
  FAF2 MUTATED FAF2 WILD-TYPE 
             8            481 
  FAF2 MUTATED FAF2 WILD-TYPE 
             8            481 
[1] "RBM15 MUTATION ANALYSIS"
[1] 3
  RBM15 MUTATED RBM15 WILD-TYPE 
             20             469 
  RBM15 MUTATED RBM15 WILD-TYPE 
             20             469 
[1] "C5ORF42 MUTATION ANALYSIS"
[1] 3
  C5ORF42 MUTATED C5ORF42 WILD-TYPE 
               41               448 
  C5ORF42 MUTATED C5ORF42 WILD-TYPE 
               41               448 
[1] "BTBD3 MUTATION ANALYSIS"
[1] 3
  BTBD3 MUTATED BTBD3 WILD-TYPE 
             13             476 
  BTBD3 MUTATED BTBD3 WILD-TYPE 
             13             476 
[1] "NOVA1 MUTATION ANALYSIS"
[1] 3
  NOVA1 MUTATED NOVA1 WILD-TYPE 
             19             470 
  NOVA1 MUTATED NOVA1 WILD-TYPE 
             19             470 
[1] "SBSN MUTATION ANALYSIS"
[1] 3
  SBSN MUTATED SBSN WILD-TYPE 
            10            479 
  SBSN MUTATED SBSN WILD-TYPE 
            10            479 
[1] "OR8B12 MUTATION ANALYSIS"
[1] 3
  OR8B12 MUTATED OR8B12 WILD-TYPE 
               4              485 
  OR8B12 MUTATED OR8B12 WILD-TYPE 
               4              485 
[1] "AGXT2L1 MUTATION ANALYSIS"
[1] 3
  AGXT2L1 MUTATED AGXT2L1 WILD-TYPE 
               13               476 
  AGXT2L1 MUTATED AGXT2L1 WILD-TYPE 
               13               476 
[1] "JAK1 MUTATION ANALYSIS"
[1] 3
  JAK1 MUTATED JAK1 WILD-TYPE 
            20            469 
  JAK1 MUTATED JAK1 WILD-TYPE 
            20            469 
[1] "CCDC110 MUTATION ANALYSIS"
[1] 3
  CCDC110 MUTATED CCDC110 WILD-TYPE 
               14               475 
  CCDC110 MUTATED CCDC110 WILD-TYPE 
               14               475 
[1] "LMOD1 MUTATION ANALYSIS"
[1] 3
  LMOD1 MUTATED LMOD1 WILD-TYPE 
             13             476 
  LMOD1 MUTATED LMOD1 WILD-TYPE 
             13             476 
[1] "C2CD3 MUTATION ANALYSIS"
[1] 3
  C2CD3 MUTATED C2CD3 WILD-TYPE 
             17             472 
  C2CD3 MUTATED C2CD3 WILD-TYPE 
             17             472 
[1] "AFF1 MUTATION ANALYSIS"
[1] 3
  AFF1 MUTATED AFF1 WILD-TYPE 
            14            475 
  AFF1 MUTATED AFF1 WILD-TYPE 
            14            475 
[1] "MANBA MUTATION ANALYSIS"
[1] 3
  MANBA MUTATED MANBA WILD-TYPE 
             13             476 
  MANBA MUTATED MANBA WILD-TYPE 
             13             476 
[1] "PROM1 MUTATION ANALYSIS"
[1] 3
  PROM1 MUTATED PROM1 WILD-TYPE 
             16             473 
  PROM1 MUTATED PROM1 WILD-TYPE 
             16             473 
[1] "AMBRA1 MUTATION ANALYSIS"
[1] 3
  AMBRA1 MUTATED AMBRA1 WILD-TYPE 
              19              470 
  AMBRA1 MUTATED AMBRA1 WILD-TYPE 
              19              470 
[1] "TBC1D10C MUTATION ANALYSIS"
[1] 3
  TBC1D10C MUTATED TBC1D10C WILD-TYPE 
                 9                480 
  TBC1D10C MUTATED TBC1D10C WILD-TYPE 
                 9                480 
[1] "CD84 MUTATION ANALYSIS"
[1] 3
  CD84 MUTATED CD84 WILD-TYPE 
            12            477 
  CD84 MUTATED CD84 WILD-TYPE 
            12            477 
[1] "DNMT1 MUTATION ANALYSIS"
[1] 3
  DNMT1 MUTATED DNMT1 WILD-TYPE 
             24             465 
  DNMT1 MUTATED DNMT1 WILD-TYPE 
             24             465 
[1] "TUT1 MUTATION ANALYSIS"
[1] 3
  TUT1 MUTATED TUT1 WILD-TYPE 
            10            479 
  TUT1 MUTATED TUT1 WILD-TYPE 
            10            479 
[1] "OR9G4 MUTATION ANALYSIS"
[1] 3
  OR9G4 MUTATED OR9G4 WILD-TYPE 
              8             481 
  OR9G4 MUTATED OR9G4 WILD-TYPE 
              8             481 
[1] "SLC45A2 MUTATION ANALYSIS"
[1] 3
  SLC45A2 MUTATED SLC45A2 WILD-TYPE 
               11               478 
  SLC45A2 MUTATED SLC45A2 WILD-TYPE 
               11               478 
[1] "SPARCL1 MUTATION ANALYSIS"
[1] 3
  SPARCL1 MUTATED SPARCL1 WILD-TYPE 
               15               474 
  SPARCL1 MUTATED SPARCL1 WILD-TYPE 
               15               474 
[1] "NBPF14 MUTATION ANALYSIS"
[1] 3
  NBPF14 MUTATED NBPF14 WILD-TYPE 
               3              486 
  NBPF14 MUTATED NBPF14 WILD-TYPE 
               3              486 
[1] "SLC44A1 MUTATION ANALYSIS"
[1] 3
  SLC44A1 MUTATED SLC44A1 WILD-TYPE 
               10               479 
  SLC44A1 MUTATED SLC44A1 WILD-TYPE 
               10               479 
[1] "C14ORF105 MUTATION ANALYSIS"
[1] 3
  C14ORF105 MUTATED C14ORF105 WILD-TYPE 
                  3                 486 
  C14ORF105 MUTATED C14ORF105 WILD-TYPE 
                  3                 486 
[1] "CCDC141 MUTATION ANALYSIS"
[1] 3
  CCDC141 MUTATED CCDC141 WILD-TYPE 
               23               466 
  CCDC141 MUTATED CCDC141 WILD-TYPE 
               23               466 
[1] "SSX2IP MUTATION ANALYSIS"
[1] 3
  SSX2IP MUTATED SSX2IP WILD-TYPE 
               9              480 
  SSX2IP MUTATED SSX2IP WILD-TYPE 
               9              480 
[1] "CSPP1 MUTATION ANALYSIS"
[1] 3
  CSPP1 MUTATED CSPP1 WILD-TYPE 
             18             471 
  CSPP1 MUTATED CSPP1 WILD-TYPE 
             18             471 
[1] "CDS2 MUTATION ANALYSIS"
[1] 3
  CDS2 MUTATED CDS2 WILD-TYPE 
            10            479 
  CDS2 MUTATED CDS2 WILD-TYPE 
            10            479 
[1] "EPHA4 MUTATION ANALYSIS"
[1] 3
  EPHA4 MUTATED EPHA4 WILD-TYPE 
             25             464 
  EPHA4 MUTATED EPHA4 WILD-TYPE 
             25             464 
[1] "TMEM195 MUTATION ANALYSIS"
[1] 3
  TMEM195 MUTATED TMEM195 WILD-TYPE 
                9               480 
  TMEM195 MUTATED TMEM195 WILD-TYPE 
                9               480 
[1] "AGT MUTATION ANALYSIS"
[1] 3
  AGT MUTATED AGT WILD-TYPE 
           10           479 
  AGT MUTATED AGT WILD-TYPE 
           10           479 
[1] "ARHGEF11 MUTATION ANALYSIS"
[1] 3
  ARHGEF11 MUTATED ARHGEF11 WILD-TYPE 
                23                466 
  ARHGEF11 MUTATED ARHGEF11 WILD-TYPE 
                23                466 
[1] "MRPS22 MUTATION ANALYSIS"
[1] 3
  MRPS22 MUTATED MRPS22 WILD-TYPE 
              10              479 
  MRPS22 MUTATED MRPS22 WILD-TYPE 
              10              479 
[1] "TMEM229B MUTATION ANALYSIS"
[1] 3
  TMEM229B MUTATED TMEM229B WILD-TYPE 
                 4                485 
  TMEM229B MUTATED TMEM229B WILD-TYPE 
                 4                485 
[1] "ABCG2 MUTATION ANALYSIS"
[1] 3
  ABCG2 MUTATED ABCG2 WILD-TYPE 
             15             474 
  ABCG2 MUTATED ABCG2 WILD-TYPE 
             15             474 
[1] "TMEM168 MUTATION ANALYSIS"
[1] 3
  TMEM168 MUTATED TMEM168 WILD-TYPE 
               16               473 
  TMEM168 MUTATED TMEM168 WILD-TYPE 
               16               473 
[1] "NUDT15 MUTATION ANALYSIS"
[1] 3
  NUDT15 MUTATED NUDT15 WILD-TYPE 
               4              485 
  NUDT15 MUTATED NUDT15 WILD-TYPE 
               4              485 
[1] "PANK1 MUTATION ANALYSIS"
[1] 3
  PANK1 MUTATED PANK1 WILD-TYPE 
              7             482 
  PANK1 MUTATED PANK1 WILD-TYPE 
              7             482 
[1] "SYT14 MUTATION ANALYSIS"
[1] 3
  SYT14 MUTATED SYT14 WILD-TYPE 
             15             474 
  SYT14 MUTATED SYT14 WILD-TYPE 
             15             474 
[1] "ARHGAP25 MUTATION ANALYSIS"
[1] 3
  ARHGAP25 MUTATED ARHGAP25 WILD-TYPE 
                12                477 
  ARHGAP25 MUTATED ARHGAP25 WILD-TYPE 
                12                477 
[1] "HCFC1R1 MUTATION ANALYSIS"
[1] 3
  HCFC1R1 MUTATED HCFC1R1 WILD-TYPE 
                5               484 
  HCFC1R1 MUTATED HCFC1R1 WILD-TYPE 
                5               484 
[1] "C7ORF66 MUTATION ANALYSIS"
[1] 3
  C7ORF66 MUTATED C7ORF66 WILD-TYPE 
                8               481 
  C7ORF66 MUTATED C7ORF66 WILD-TYPE 
                8               481 
[1] "CD47 MUTATION ANALYSIS"
[1] 3
  CD47 MUTATED CD47 WILD-TYPE 
             8            481 
  CD47 MUTATED CD47 WILD-TYPE 
             8            481 
[1] "RWDD4A MUTATION ANALYSIS"
[1] 3
  RWDD4A MUTATED RWDD4A WILD-TYPE 
               5              484 
  RWDD4A MUTATED RWDD4A WILD-TYPE 
               5              484 
[1] "EPRS MUTATION ANALYSIS"
[1] 3
  EPRS MUTATED EPRS WILD-TYPE 
            23            466 
  EPRS MUTATED EPRS WILD-TYPE 
            23            466 
[1] "DUSP9 MUTATION ANALYSIS"
[1] 3
  DUSP9 MUTATED DUSP9 WILD-TYPE 
              9             480 
  DUSP9 MUTATED DUSP9 WILD-TYPE 
              9             480 
[1] "HIST1H1A MUTATION ANALYSIS"
[1] 3
  HIST1H1A MUTATED HIST1H1A WILD-TYPE 
                 9                480 
  HIST1H1A MUTATED HIST1H1A WILD-TYPE 
                 9                480 
[1] "ZSCAN20 MUTATION ANALYSIS"
[1] 3
  ZSCAN20 MUTATED ZSCAN20 WILD-TYPE 
               17               472 
  ZSCAN20 MUTATED ZSCAN20 WILD-TYPE 
               17               472 
[1] "ERCC3 MUTATION ANALYSIS"
[1] 3
  ERCC3 MUTATED ERCC3 WILD-TYPE 
             20             469 
  ERCC3 MUTATED ERCC3 WILD-TYPE 
             20             469 
[1] "XKR3 MUTATION ANALYSIS"
[1] 3
  XKR3 MUTATED XKR3 WILD-TYPE 
            15            474 
  XKR3 MUTATED XKR3 WILD-TYPE 
            15            474 
[1] "PIGS MUTATION ANALYSIS"
[1] 3
  PIGS MUTATED PIGS WILD-TYPE 
             8            481 
  PIGS MUTATED PIGS WILD-TYPE 
             8            481 
[1] "AAMP MUTATION ANALYSIS"
[1] 3
  AAMP MUTATED AAMP WILD-TYPE 
             3            486 
  AAMP MUTATED AAMP WILD-TYPE 
             3            486 
[1] "IL21R MUTATION ANALYSIS"
[1] 3
  IL21R MUTATED IL21R WILD-TYPE 
             14             475 
  IL21R MUTATED IL21R WILD-TYPE 
             14             475 
[1] "MBP MUTATION ANALYSIS"
[1] 3
  MBP MUTATED MBP WILD-TYPE 
            6           483 
  MBP MUTATED MBP WILD-TYPE 
            6           483 
[1] "DLGAP5 MUTATION ANALYSIS"
[1] 3
  DLGAP5 MUTATED DLGAP5 WILD-TYPE 
              10              479 
  DLGAP5 MUTATED DLGAP5 WILD-TYPE 
              10              479 
[1] "MAP7 MUTATION ANALYSIS"
[1] 3
  MAP7 MUTATED MAP7 WILD-TYPE 
            14            475 
  MAP7 MUTATED MAP7 WILD-TYPE 
            14            475 
[1] "OR4A16 MUTATION ANALYSIS"
[1] 3
  OR4A16 MUTATED OR4A16 WILD-TYPE 
              15              474 
  OR4A16 MUTATED OR4A16 WILD-TYPE 
              15              474 
[1] "IRF6 MUTATION ANALYSIS"
[1] 3
  IRF6 MUTATED IRF6 WILD-TYPE 
             6            483 
  IRF6 MUTATED IRF6 WILD-TYPE 
             6            483 
[1] "LGALS9C MUTATION ANALYSIS"
[1] 3
  LGALS9C MUTATED LGALS9C WILD-TYPE 
                6               483 
  LGALS9C MUTATED LGALS9C WILD-TYPE 
                6               483 
[1] "ZNF512 MUTATION ANALYSIS"
[1] 3
  ZNF512 MUTATED ZNF512 WILD-TYPE 
               3              486 
  ZNF512 MUTATED ZNF512 WILD-TYPE 
               3              486 
[1] "HIF1A MUTATION ANALYSIS"
[1] 3
  HIF1A MUTATED HIF1A WILD-TYPE 
             12             477 
  HIF1A MUTATED HIF1A WILD-TYPE 
             12             477 
[1] "CD79A MUTATION ANALYSIS"
[1] 3
  CD79A MUTATED CD79A WILD-TYPE 
              6             483 
  CD79A MUTATED CD79A WILD-TYPE 
              6             483 
[1] "HIVEP1 MUTATION ANALYSIS"
[1] 3
  HIVEP1 MUTATED HIVEP1 WILD-TYPE 
              20              469 
  HIVEP1 MUTATED HIVEP1 WILD-TYPE 
              20              469 
[1] "C1S MUTATION ANALYSIS"
[1] 3
  C1S MUTATED C1S WILD-TYPE 
           13           476 
  C1S MUTATED C1S WILD-TYPE 
           13           476 
[1] "OR8K3 MUTATION ANALYSIS"
[1] 3
  OR8K3 MUTATED OR8K3 WILD-TYPE 
             12             477 
  OR8K3 MUTATED OR8K3 WILD-TYPE 
             12             477 
[1] "NUP210L MUTATION ANALYSIS"
[1] 3
  NUP210L MUTATED NUP210L WILD-TYPE 
               24               465 
  NUP210L MUTATED NUP210L WILD-TYPE 
               24               465 
[1] "RRAGD MUTATION ANALYSIS"
[1] 3
  RRAGD MUTATED RRAGD WILD-TYPE 
              7             482 
  RRAGD MUTATED RRAGD WILD-TYPE 
              7             482 
[1] "BLM MUTATION ANALYSIS"
[1] 3
  BLM MUTATED BLM WILD-TYPE 
           19           470 
  BLM MUTATED BLM WILD-TYPE 
           19           470 
[1] "CLCN3 MUTATION ANALYSIS"
[1] 3
  CLCN3 MUTATED CLCN3 WILD-TYPE 
             13             476 
  CLCN3 MUTATED CLCN3 WILD-TYPE 
             13             476 
[1] "ANKRD40 MUTATION ANALYSIS"
[1] 3
  ANKRD40 MUTATED ANKRD40 WILD-TYPE 
                9               480 
  ANKRD40 MUTATED ANKRD40 WILD-TYPE 
                9               480 
[1] "SNAPC2 MUTATION ANALYSIS"
[1] 3
  SNAPC2 MUTATED SNAPC2 WILD-TYPE 
               6              483 
  SNAPC2 MUTATED SNAPC2 WILD-TYPE 
               6              483 
[1] "UPF3B MUTATION ANALYSIS"
[1] 3
  UPF3B MUTATED UPF3B WILD-TYPE 
             11             478 
  UPF3B MUTATED UPF3B WILD-TYPE 
             11             478 
[1] "LMTK3 MUTATION ANALYSIS"
[1] 3
  LMTK3 MUTATED LMTK3 WILD-TYPE 
             16             473 
  LMTK3 MUTATED LMTK3 WILD-TYPE 
             16             473 
[1] "FCAMR MUTATION ANALYSIS"
[1] 3
  FCAMR MUTATED FCAMR WILD-TYPE 
             12             477 
  FCAMR MUTATED FCAMR WILD-TYPE 
             12             477 
[1] "XCL2 MUTATION ANALYSIS"
[1] 3
  XCL2 MUTATED XCL2 WILD-TYPE 
             4            485 
  XCL2 MUTATED XCL2 WILD-TYPE 
             4            485 
[1] "AASS MUTATION ANALYSIS"
[1] 3
  AASS MUTATED AASS WILD-TYPE 
            13            476 
  AASS MUTATED AASS WILD-TYPE 
            13            476 
[1] "CCNH MUTATION ANALYSIS"
[1] 3
  CCNH MUTATED CCNH WILD-TYPE 
             7            482 
  CCNH MUTATED CCNH WILD-TYPE 
             7            482 
[1] "ITGA4 MUTATION ANALYSIS"
[1] 3
  ITGA4 MUTATED ITGA4 WILD-TYPE 
             17             472 
  ITGA4 MUTATED ITGA4 WILD-TYPE 
             17             472 
[1] "ST18 MUTATION ANALYSIS"
[1] 3
  ST18 MUTATED ST18 WILD-TYPE 
            27            462 
  ST18 MUTATED ST18 WILD-TYPE 
            27            462 
[1] "SECISBP2 MUTATION ANALYSIS"
[1] 3
  SECISBP2 MUTATED SECISBP2 WILD-TYPE 
                 8                481 
  SECISBP2 MUTATED SECISBP2 WILD-TYPE 
                 8                481 
[1] "GPX8 MUTATION ANALYSIS"
[1] 3
  GPX8 MUTATED GPX8 WILD-TYPE 
             3            486 
  GPX8 MUTATED GPX8 WILD-TYPE 
             3            486 
[1] "C6ORF150 MUTATION ANALYSIS"
[1] 3
  C6ORF150 MUTATED C6ORF150 WILD-TYPE 
                10                479 
  C6ORF150 MUTATED C6ORF150 WILD-TYPE 
                10                479 
[1] "NAP1L4 MUTATION ANALYSIS"
[1] 3
  NAP1L4 MUTATED NAP1L4 WILD-TYPE 
               6              483 
  NAP1L4 MUTATED NAP1L4 WILD-TYPE 
               6              483 
[1] "MANF MUTATION ANALYSIS"
[1] 3
  MANF MUTATED MANF WILD-TYPE 
             4            485 
  MANF MUTATED MANF WILD-TYPE 
             4            485 
[1] "CUX1 MUTATION ANALYSIS"
[1] 3
  CUX1 MUTATED CUX1 WILD-TYPE 
            17            472 
  CUX1 MUTATED CUX1 WILD-TYPE 
            17            472 
[1] "SLC16A5 MUTATION ANALYSIS"
[1] 3
  SLC16A5 MUTATED SLC16A5 WILD-TYPE 
               10               479 
  SLC16A5 MUTATED SLC16A5 WILD-TYPE 
               10               479 
[1] "TUBB4 MUTATION ANALYSIS"
[1] 3
  TUBB4 MUTATED TUBB4 WILD-TYPE 
              7             482 
  TUBB4 MUTATED TUBB4 WILD-TYPE 
              7             482 
[1] "SUPT3H MUTATION ANALYSIS"
[1] 3
  SUPT3H MUTATED SUPT3H WILD-TYPE 
              11              478 
  SUPT3H MUTATED SUPT3H WILD-TYPE 
              11              478 
[1] "FAM151A MUTATION ANALYSIS"
[1] 3
  FAM151A MUTATED FAM151A WILD-TYPE 
                6               483 
  FAM151A MUTATED FAM151A WILD-TYPE 
                6               483 
[1] "HERC1 MUTATION ANALYSIS"
[1] 3
  HERC1 MUTATED HERC1 WILD-TYPE 
             33             456 
  HERC1 MUTATED HERC1 WILD-TYPE 
             33             456 
[1] "TBX4 MUTATION ANALYSIS"
[1] 3
  TBX4 MUTATED TBX4 WILD-TYPE 
            11            478 
  TBX4 MUTATED TBX4 WILD-TYPE 
            11            478 
[1] "TRIP6 MUTATION ANALYSIS"
[1] 3
  TRIP6 MUTATED TRIP6 WILD-TYPE 
             11             478 
  TRIP6 MUTATED TRIP6 WILD-TYPE 
             11             478 
[1] "SERPINB5 MUTATION ANALYSIS"
[1] 3
  SERPINB5 MUTATED SERPINB5 WILD-TYPE 
                 6                483 
  SERPINB5 MUTATED SERPINB5 WILD-TYPE 
                 6                483 
[1] "HIPK3 MUTATION ANALYSIS"
[1] 3
  HIPK3 MUTATED HIPK3 WILD-TYPE 
              8             481 
  HIPK3 MUTATED HIPK3 WILD-TYPE 
              8             481 
[1] "NLRP11 MUTATION ANALYSIS"
[1] 3
  NLRP11 MUTATED NLRP11 WILD-TYPE 
              20              469 
  NLRP11 MUTATED NLRP11 WILD-TYPE 
              20              469 
[1] "DZIP1L MUTATION ANALYSIS"
[1] 3
  DZIP1L MUTATED DZIP1L WILD-TYPE 
              16              473 
  DZIP1L MUTATED DZIP1L WILD-TYPE 
              16              473 
[1] "GSG2 MUTATION ANALYSIS"
[1] 3
  GSG2 MUTATED GSG2 WILD-TYPE 
             6            483 
  GSG2 MUTATED GSG2 WILD-TYPE 
             6            483 
[1] "FAM193A MUTATION ANALYSIS"
[1] 3
  FAM193A MUTATED FAM193A WILD-TYPE 
               17               472 
  FAM193A MUTATED FAM193A WILD-TYPE 
               17               472 
[1] "ENC1 MUTATION ANALYSIS"
[1] 3
  ENC1 MUTATED ENC1 WILD-TYPE 
            13            476 
  ENC1 MUTATED ENC1 WILD-TYPE 
            13            476 
[1] "RUSC2 MUTATION ANALYSIS"
[1] 3
  RUSC2 MUTATED RUSC2 WILD-TYPE 
             13             476 
  RUSC2 MUTATED RUSC2 WILD-TYPE 
             13             476 
[1] "WHAMM MUTATION ANALYSIS"
[1] 3
  WHAMM MUTATED WHAMM WILD-TYPE 
              6             483 
  WHAMM MUTATED WHAMM WILD-TYPE 
              6             483 
[1] "TAF1 MUTATION ANALYSIS"
[1] 3
  TAF1 MUTATED TAF1 WILD-TYPE 
            26            463 
  TAF1 MUTATED TAF1 WILD-TYPE 
            26            463 
[1] "METTL5 MUTATION ANALYSIS"
[1] 3
  METTL5 MUTATED METTL5 WILD-TYPE 
               6              483 
  METTL5 MUTATED METTL5 WILD-TYPE 
               6              483 
[1] "ITPRIPL1 MUTATION ANALYSIS"
[1] 3
  ITPRIPL1 MUTATED ITPRIPL1 WILD-TYPE 
                 8                481 
  ITPRIPL1 MUTATED ITPRIPL1 WILD-TYPE 
                 8                481 
[1] "WFS1 MUTATION ANALYSIS"
[1] 3
  WFS1 MUTATED WFS1 WILD-TYPE 
            12            477 
  WFS1 MUTATED WFS1 WILD-TYPE 
            12            477 
[1] "GOT1 MUTATION ANALYSIS"
[1] 3
  GOT1 MUTATED GOT1 WILD-TYPE 
             6            483 
  GOT1 MUTATED GOT1 WILD-TYPE 
             6            483 
[1] "SRGAP3 MUTATION ANALYSIS"
[1] 3
  SRGAP3 MUTATED SRGAP3 WILD-TYPE 
              19              470 
  SRGAP3 MUTATED SRGAP3 WILD-TYPE 
              19              470 
[1] "MTMR8 MUTATION ANALYSIS"
[1] 3
  MTMR8 MUTATED MTMR8 WILD-TYPE 
             15             474 
  MTMR8 MUTATED MTMR8 WILD-TYPE 
             15             474 
[1] "GAB3 MUTATION ANALYSIS"
[1] 3
  GAB3 MUTATED GAB3 WILD-TYPE 
            12            477 
  GAB3 MUTATED GAB3 WILD-TYPE 
            12            477 
[1] "GIMAP5 MUTATION ANALYSIS"
[1] 3
  GIMAP5 MUTATED GIMAP5 WILD-TYPE 
               8              481 
  GIMAP5 MUTATED GIMAP5 WILD-TYPE 
               8              481 
[1] "ZEB1 MUTATION ANALYSIS"
[1] 3
  ZEB1 MUTATED ZEB1 WILD-TYPE 
            23            466 
  ZEB1 MUTATED ZEB1 WILD-TYPE 
            23            466 
[1] "CATSPER4 MUTATION ANALYSIS"
[1] 3
  CATSPER4 MUTATED CATSPER4 WILD-TYPE 
                13                476 
  CATSPER4 MUTATED CATSPER4 WILD-TYPE 
                13                476 
[1] "ERN1 MUTATION ANALYSIS"
[1] 3
  ERN1 MUTATED ERN1 WILD-TYPE 
             3            486 
  ERN1 MUTATED ERN1 WILD-TYPE 
             3            486 
[1] "HECW2 MUTATION ANALYSIS"
[1] 3
  HECW2 MUTATED HECW2 WILD-TYPE 
             32             457 
  HECW2 MUTATED HECW2 WILD-TYPE 
             32             457 
[1] "CASP6 MUTATION ANALYSIS"
[1] 3
  CASP6 MUTATED CASP6 WILD-TYPE 
              3             486 
  CASP6 MUTATED CASP6 WILD-TYPE 
              3             486 
[1] "CSGALNACT1 MUTATION ANALYSIS"
[1] 3
  CSGALNACT1 MUTATED CSGALNACT1 WILD-TYPE 
                   9                  480 
  CSGALNACT1 MUTATED CSGALNACT1 WILD-TYPE 
                   9                  480 
[1] "SF3B2 MUTATION ANALYSIS"
[1] 3
  SF3B2 MUTATED SF3B2 WILD-TYPE 
             10             479 
  SF3B2 MUTATED SF3B2 WILD-TYPE 
             10             479 
[1] "ZNF232 MUTATION ANALYSIS"
[1] 3
  ZNF232 MUTATED ZNF232 WILD-TYPE 
               4              485 
  ZNF232 MUTATED ZNF232 WILD-TYPE 
               4              485 
[1] "TRIM55 MUTATION ANALYSIS"
[1] 3
  TRIM55 MUTATED TRIM55 WILD-TYPE 
              19              470 
  TRIM55 MUTATED TRIM55 WILD-TYPE 
              19              470 
[1] "IFITM5 MUTATION ANALYSIS"
[1] 3
  IFITM5 MUTATED IFITM5 WILD-TYPE 
               4              485 
  IFITM5 MUTATED IFITM5 WILD-TYPE 
               4              485 
[1] "C9ORF125 MUTATION ANALYSIS"
[1] 3
  C9ORF125 MUTATED C9ORF125 WILD-TYPE 
                12                477 
  C9ORF125 MUTATED C9ORF125 WILD-TYPE 
                12                477 
[1] "IPPK MUTATION ANALYSIS"
[1] 3
  IPPK MUTATED IPPK WILD-TYPE 
             9            480 
  IPPK MUTATED IPPK WILD-TYPE 
             9            480 
[1] "ARHGEF7 MUTATION ANALYSIS"
[1] 3
  ARHGEF7 MUTATED ARHGEF7 WILD-TYPE 
               21               468 
  ARHGEF7 MUTATED ARHGEF7 WILD-TYPE 
               21               468 
[1] "WDR65 MUTATION ANALYSIS"
[1] 3
  WDR65 MUTATED WDR65 WILD-TYPE 
              6             483 
  WDR65 MUTATED WDR65 WILD-TYPE 
              6             483 
[1] "APLP1 MUTATION ANALYSIS"
[1] 3
  APLP1 MUTATED APLP1 WILD-TYPE 
             17             472 
  APLP1 MUTATED APLP1 WILD-TYPE 
             17             472 
[1] "KIAA0319 MUTATION ANALYSIS"
[1] 3
  KIAA0319 MUTATED KIAA0319 WILD-TYPE 
                17                472 
  KIAA0319 MUTATED KIAA0319 WILD-TYPE 
                17                472 
[1] "MECOM MUTATION ANALYSIS"
[1] 3
  MECOM MUTATED MECOM WILD-TYPE 
             21             468 
  MECOM MUTATED MECOM WILD-TYPE 
             21             468 
[1] "MYO3A MUTATION ANALYSIS"
[1] 3
  MYO3A MUTATED MYO3A WILD-TYPE 
             43             446 
  MYO3A MUTATED MYO3A WILD-TYPE 
             43             446 
[1] "PIK3C2G MUTATION ANALYSIS"
[1] 3
  PIK3C2G MUTATED PIK3C2G WILD-TYPE 
               23               466 
  PIK3C2G MUTATED PIK3C2G WILD-TYPE 
               23               466 
[1] "WFDC5 MUTATION ANALYSIS"
[1] 3
  WFDC5 MUTATED WFDC5 WILD-TYPE 
              5             484 
  WFDC5 MUTATED WFDC5 WILD-TYPE 
              5             484 
[1] "ABCD4 MUTATION ANALYSIS"
[1] 3
  ABCD4 MUTATED ABCD4 WILD-TYPE 
             10             479 
  ABCD4 MUTATED ABCD4 WILD-TYPE 
             10             479 
[1] "PCSK5 MUTATION ANALYSIS"
[1] 3
  PCSK5 MUTATED PCSK5 WILD-TYPE 
             15             474 
  PCSK5 MUTATED PCSK5 WILD-TYPE 
             15             474 
[1] "DLGAP3 MUTATION ANALYSIS"
[1] 3
  DLGAP3 MUTATED DLGAP3 WILD-TYPE 
              17              472 
  DLGAP3 MUTATED DLGAP3 WILD-TYPE 
              17              472 
[1] "MFSD4 MUTATION ANALYSIS"
[1] 3
  MFSD4 MUTATED MFSD4 WILD-TYPE 
              6             483 
  MFSD4 MUTATED MFSD4 WILD-TYPE 
              6             483 
[1] "HECTD2 MUTATION ANALYSIS"
[1] 3
  HECTD2 MUTATED HECTD2 WILD-TYPE 
              12              477 
  HECTD2 MUTATED HECTD2 WILD-TYPE 
              12              477 
[1] "CDH18 MUTATION ANALYSIS"
[1] 3
  CDH18 MUTATED CDH18 WILD-TYPE 
             37             452 
  CDH18 MUTATED CDH18 WILD-TYPE 
             37             452 
[1] "SIX5 MUTATION ANALYSIS"
[1] 3
  SIX5 MUTATED SIX5 WILD-TYPE 
             5            484 
  SIX5 MUTATED SIX5 WILD-TYPE 
             5            484 
[1] "C1ORF85 MUTATION ANALYSIS"
[1] 3
  C1ORF85 MUTATED C1ORF85 WILD-TYPE 
                8               481 
  C1ORF85 MUTATED C1ORF85 WILD-TYPE 
                8               481 
[1] "NAE1 MUTATION ANALYSIS"
[1] 3
  NAE1 MUTATED NAE1 WILD-TYPE 
             9            480 
  NAE1 MUTATED NAE1 WILD-TYPE 
             9            480 
[1] "CYP3A7 MUTATION ANALYSIS"
[1] 3
  CYP3A7 MUTATED CYP3A7 WILD-TYPE 
              12              477 
  CYP3A7 MUTATED CYP3A7 WILD-TYPE 
              12              477 
[1] "DEFB129 MUTATION ANALYSIS"
[1] 3
  DEFB129 MUTATED DEFB129 WILD-TYPE 
                5               484 
  DEFB129 MUTATED DEFB129 WILD-TYPE 
                5               484 
[1] "EFNB3 MUTATION ANALYSIS"
[1] 3
  EFNB3 MUTATED EFNB3 WILD-TYPE 
              9             480 
  EFNB3 MUTATED EFNB3 WILD-TYPE 
              9             480 
[1] "DYRK3 MUTATION ANALYSIS"
[1] 3
  DYRK3 MUTATED DYRK3 WILD-TYPE 
             16             473 
  DYRK3 MUTATED DYRK3 WILD-TYPE 
             16             473 
[1] "ZBTB24 MUTATION ANALYSIS"
[1] 3
  ZBTB24 MUTATED ZBTB24 WILD-TYPE 
              11              478 
  ZBTB24 MUTATED ZBTB24 WILD-TYPE 
              11              478 
[1] "TNRC6B MUTATION ANALYSIS"
[1] 3
  TNRC6B MUTATED TNRC6B WILD-TYPE 
              23              466 
  TNRC6B MUTATED TNRC6B WILD-TYPE 
              23              466 
[1] "PAK1 MUTATION ANALYSIS"
[1] 3
  PAK1 MUTATED PAK1 WILD-TYPE 
            11            478 
  PAK1 MUTATED PAK1 WILD-TYPE 
            11            478 
[1] "PODXL MUTATION ANALYSIS"
[1] 3
  PODXL MUTATED PODXL WILD-TYPE 
             10             479 
  PODXL MUTATED PODXL WILD-TYPE 
             10             479 
[1] "OR5AK2 MUTATION ANALYSIS"
[1] 3
  OR5AK2 MUTATED OR5AK2 WILD-TYPE 
               9              480 
  OR5AK2 MUTATED OR5AK2 WILD-TYPE 
               9              480 
[1] "LGALS9 MUTATION ANALYSIS"
[1] 3
  LGALS9 MUTATED LGALS9 WILD-TYPE 
               5              484 
  LGALS9 MUTATED LGALS9 WILD-TYPE 
               5              484 
[1] "IRGQ MUTATION ANALYSIS"
[1] 3
  IRGQ MUTATED IRGQ WILD-TYPE 
             5            484 
  IRGQ MUTATED IRGQ WILD-TYPE 
             5            484 
[1] "NLRP1 MUTATION ANALYSIS"
[1] 3
  NLRP1 MUTATED NLRP1 WILD-TYPE 
             28             461 
  NLRP1 MUTATED NLRP1 WILD-TYPE 
             28             461 
[1] "TPR MUTATION ANALYSIS"
[1] 3
  TPR MUTATED TPR WILD-TYPE 
           25           464 
  TPR MUTATED TPR WILD-TYPE 
           25           464 
[1] "METT5D1 MUTATION ANALYSIS"
[1] 3
  METT5D1 MUTATED METT5D1 WILD-TYPE 
                7               482 
  METT5D1 MUTATED METT5D1 WILD-TYPE 
                7               482 
[1] "BCAP29 MUTATION ANALYSIS"
[1] 3
  BCAP29 MUTATED BCAP29 WILD-TYPE 
               8              481 
  BCAP29 MUTATED BCAP29 WILD-TYPE 
               8              481 
[1] "MSH5 MUTATION ANALYSIS"
[1] 3
  MSH5 MUTATED MSH5 WILD-TYPE 
             8            481 
  MSH5 MUTATED MSH5 WILD-TYPE 
             8            481 
[1] "BTBD11 MUTATION ANALYSIS"
[1] 3
  BTBD11 MUTATED BTBD11 WILD-TYPE 
              23              466 
  BTBD11 MUTATED BTBD11 WILD-TYPE 
              23              466 
[1] "ATAD1 MUTATION ANALYSIS"
[1] 3
  ATAD1 MUTATED ATAD1 WILD-TYPE 
              9             480 
  ATAD1 MUTATED ATAD1 WILD-TYPE 
              9             480 
[1] "PRPF4B MUTATION ANALYSIS"
[1] 3
  PRPF4B MUTATED PRPF4B WILD-TYPE 
              16              473 
  PRPF4B MUTATED PRPF4B WILD-TYPE 
              16              473 
[1] "ARHGEF6 MUTATION ANALYSIS"
[1] 3
  ARHGEF6 MUTATED ARHGEF6 WILD-TYPE 
               15               474 
  ARHGEF6 MUTATED ARHGEF6 WILD-TYPE 
               15               474 
[1] "HK3 MUTATION ANALYSIS"
[1] 3
  HK3 MUTATED HK3 WILD-TYPE 
           22           467 
  HK3 MUTATED HK3 WILD-TYPE 
           22           467 
[1] "OR5R1 MUTATION ANALYSIS"
[1] 3
  OR5R1 MUTATED OR5R1 WILD-TYPE 
             14             475 
  OR5R1 MUTATED OR5R1 WILD-TYPE 
             14             475 
[1] "TCEANC MUTATION ANALYSIS"
[1] 3
  TCEANC MUTATED TCEANC WILD-TYPE 
               9              480 
  TCEANC MUTATED TCEANC WILD-TYPE 
               9              480 
[1] "GJA10 MUTATION ANALYSIS"
[1] 3
  GJA10 MUTATED GJA10 WILD-TYPE 
             14             475 
  GJA10 MUTATED GJA10 WILD-TYPE 
             14             475 
[1] "AP1G1 MUTATION ANALYSIS"
[1] 3
  AP1G1 MUTATED AP1G1 WILD-TYPE 
             13             476 
  AP1G1 MUTATED AP1G1 WILD-TYPE 
             13             476 
[1] "PLEKHA3 MUTATION ANALYSIS"
[1] 3
  PLEKHA3 MUTATED PLEKHA3 WILD-TYPE 
                8               481 
  PLEKHA3 MUTATED PLEKHA3 WILD-TYPE 
                8               481 
[1] "PCNA MUTATION ANALYSIS"
[1] 3
  PCNA MUTATED PCNA WILD-TYPE 
             5            484 
  PCNA MUTATED PCNA WILD-TYPE 
             5            484 
[1] "ABCB6 MUTATION ANALYSIS"
[1] 3
  ABCB6 MUTATED ABCB6 WILD-TYPE 
              8             481 
  ABCB6 MUTATED ABCB6 WILD-TYPE 
              8             481 
[1] "GGNBP2 MUTATION ANALYSIS"
[1] 3
  GGNBP2 MUTATED GGNBP2 WILD-TYPE 
              13              476 
  GGNBP2 MUTATED GGNBP2 WILD-TYPE 
              13              476 
[1] "CCDC3 MUTATION ANALYSIS"
[1] 3
  CCDC3 MUTATED CCDC3 WILD-TYPE 
              5             484 
  CCDC3 MUTATED CCDC3 WILD-TYPE 
              5             484 
[1] "TATDN2 MUTATION ANALYSIS"
[1] 3
  TATDN2 MUTATED TATDN2 WILD-TYPE 
              12              477 
  TATDN2 MUTATED TATDN2 WILD-TYPE 
              12              477 
[1] "USP1 MUTATION ANALYSIS"
[1] 3
  USP1 MUTATED USP1 WILD-TYPE 
             9            480 
  USP1 MUTATED USP1 WILD-TYPE 
             9            480 
[1] "IFLTD1 MUTATION ANALYSIS"
[1] 3
  IFLTD1 MUTATED IFLTD1 WILD-TYPE 
              13              476 
  IFLTD1 MUTATED IFLTD1 WILD-TYPE 
              13              476 
[1] "TLX1NB MUTATION ANALYSIS"
[1] 3
  TLX1NB MUTATED TLX1NB WILD-TYPE 
               3              486 
  TLX1NB MUTATED TLX1NB WILD-TYPE 
               3              486 
[1] "ZNF323 MUTATION ANALYSIS"
[1] 3
  ZNF323 MUTATED ZNF323 WILD-TYPE 
              11              478 
  ZNF323 MUTATED ZNF323 WILD-TYPE 
              11              478 
[1] "ANAPC16 MUTATION ANALYSIS"
[1] 3
  ANAPC16 MUTATED ANAPC16 WILD-TYPE 
                3               486 
  ANAPC16 MUTATED ANAPC16 WILD-TYPE 
                3               486 
[1] "AKAP7 MUTATION ANALYSIS"
[1] 3
  AKAP7 MUTATED AKAP7 WILD-TYPE 
              6             483 
  AKAP7 MUTATED AKAP7 WILD-TYPE 
              6             483 
[1] "MUM1L1 MUTATION ANALYSIS"
[1] 3
  MUM1L1 MUTATED MUM1L1 WILD-TYPE 
              16              473 
  MUM1L1 MUTATED MUM1L1 WILD-TYPE 
              16              473 
[1] "ISOC2 MUTATION ANALYSIS"
[1] 3
  ISOC2 MUTATED ISOC2 WILD-TYPE 
              5             484 
  ISOC2 MUTATED ISOC2 WILD-TYPE 
              5             484 
[1] "GLTSCR1 MUTATION ANALYSIS"
[1] 3
  GLTSCR1 MUTATED GLTSCR1 WILD-TYPE 
               12               477 
  GLTSCR1 MUTATED GLTSCR1 WILD-TYPE 
               12               477 
[1] "DNAJB11 MUTATION ANALYSIS"
[1] 3
  DNAJB11 MUTATED DNAJB11 WILD-TYPE 
                9               480 
  DNAJB11 MUTATED DNAJB11 WILD-TYPE 
                9               480 
[1] "LEPROTL1 MUTATION ANALYSIS"
[1] 3
  LEPROTL1 MUTATED LEPROTL1 WILD-TYPE 
                 5                484 
  LEPROTL1 MUTATED LEPROTL1 WILD-TYPE 
                 5                484 
[1] "OR9Q1 MUTATION ANALYSIS"
[1] 3
  OR9Q1 MUTATED OR9Q1 WILD-TYPE 
              6             483 
  OR9Q1 MUTATED OR9Q1 WILD-TYPE 
              6             483 
[1] "ARID4B MUTATION ANALYSIS"
[1] 3
  ARID4B MUTATED ARID4B WILD-TYPE 
              13              476 
  ARID4B MUTATED ARID4B WILD-TYPE 
              13              476 
[1] "ABHD2 MUTATION ANALYSIS"
[1] 3
  ABHD2 MUTATED ABHD2 WILD-TYPE 
             12             477 
  ABHD2 MUTATED ABHD2 WILD-TYPE 
             12             477 
[1] "HIST1H1B MUTATION ANALYSIS"
[1] 3
  HIST1H1B MUTATED HIST1H1B WILD-TYPE 
                 8                481 
  HIST1H1B MUTATED HIST1H1B WILD-TYPE 
                 8                481 
[1] "MAGOHB MUTATION ANALYSIS"
[1] 3
  MAGOHB MUTATED MAGOHB WILD-TYPE 
               4              485 
  MAGOHB MUTATED MAGOHB WILD-TYPE 
               4              485 
[1] "ATL1 MUTATION ANALYSIS"
[1] 3
  ATL1 MUTATED ATL1 WILD-TYPE 
            12            477 
  ATL1 MUTATED ATL1 WILD-TYPE 
            12            477 
[1] "ACRC MUTATION ANALYSIS"
[1] 3
  ACRC MUTATED ACRC WILD-TYPE 
            15            474 
  ACRC MUTATED ACRC WILD-TYPE 
            15            474 
[1] "ZNF577 MUTATION ANALYSIS"
[1] 3
  ZNF577 MUTATED ZNF577 WILD-TYPE 
              13              476 
  ZNF577 MUTATED ZNF577 WILD-TYPE 
              13              476 
[1] "POPDC3 MUTATION ANALYSIS"
[1] 3
  POPDC3 MUTATED POPDC3 WILD-TYPE 
               8              481 
  POPDC3 MUTATED POPDC3 WILD-TYPE 
               8              481 
[1] "ESR1 MUTATION ANALYSIS"
[1] 3
  ESR1 MUTATED ESR1 WILD-TYPE 
            20            469 
  ESR1 MUTATED ESR1 WILD-TYPE 
            20            469 
[1] "SLC25A40 MUTATION ANALYSIS"
[1] 3
  SLC25A40 MUTATED SLC25A40 WILD-TYPE 
                 5                484 
  SLC25A40 MUTATED SLC25A40 WILD-TYPE 
                 5                484 
[1] "DHX32 MUTATION ANALYSIS"
[1] 3
  DHX32 MUTATED DHX32 WILD-TYPE 
             12             477 
  DHX32 MUTATED DHX32 WILD-TYPE 
             12             477 
[1] "BFSP1 MUTATION ANALYSIS"
[1] 3
  BFSP1 MUTATED BFSP1 WILD-TYPE 
              9             480 
  BFSP1 MUTATED BFSP1 WILD-TYPE 
              9             480 
[1] "CLEC1A MUTATION ANALYSIS"
[1] 3
  CLEC1A MUTATED CLEC1A WILD-TYPE 
              10              479 
  CLEC1A MUTATED CLEC1A WILD-TYPE 
              10              479 
[1] "BIRC6 MUTATION ANALYSIS"
[1] 3
  BIRC6 MUTATED BIRC6 WILD-TYPE 
             39             450 
  BIRC6 MUTATED BIRC6 WILD-TYPE 
             39             450 
[1] "MTIF2 MUTATION ANALYSIS"
[1] 3
  MTIF2 MUTATED MTIF2 WILD-TYPE 
             11             478 
  MTIF2 MUTATED MTIF2 WILD-TYPE 
             11             478 
[1] "IGDCC3 MUTATION ANALYSIS"
[1] 3
  IGDCC3 MUTATED IGDCC3 WILD-TYPE 
              12              477 
  IGDCC3 MUTATED IGDCC3 WILD-TYPE 
              12              477 
[1] "ZNF124 MUTATION ANALYSIS"
[1] 3
  ZNF124 MUTATED ZNF124 WILD-TYPE 
               8              481 
  ZNF124 MUTATED ZNF124 WILD-TYPE 
               8              481 
[1] "SLC38A5 MUTATION ANALYSIS"
[1] 3
  SLC38A5 MUTATED SLC38A5 WILD-TYPE 
                6               483 
  SLC38A5 MUTATED SLC38A5 WILD-TYPE 
                6               483 
[1] "C15ORF33 MUTATION ANALYSIS"
[1] 3
  C15ORF33 MUTATED C15ORF33 WILD-TYPE 
                12                477 
  C15ORF33 MUTATED C15ORF33 WILD-TYPE 
                12                477 
[1] "WEE2 MUTATION ANALYSIS"
[1] 3
  WEE2 MUTATED WEE2 WILD-TYPE 
            10            479 
  WEE2 MUTATED WEE2 WILD-TYPE 
            10            479 
[1] "MAOB MUTATION ANALYSIS"
[1] 3
  MAOB MUTATED MAOB WILD-TYPE 
             9            480 
  MAOB MUTATED MAOB WILD-TYPE 
             9            480 
[1] "REL MUTATION ANALYSIS"
[1] 3
  REL MUTATED REL WILD-TYPE 
           11           478 
  REL MUTATED REL WILD-TYPE 
           11           478 
[1] "MMP27 MUTATION ANALYSIS"
[1] 3
  MMP27 MUTATED MMP27 WILD-TYPE 
              9             480 
  MMP27 MUTATED MMP27 WILD-TYPE 
              9             480 
[1] "ZNF7 MUTATION ANALYSIS"
[1] 3
  ZNF7 MUTATED ZNF7 WILD-TYPE 
            14            475 
  ZNF7 MUTATED ZNF7 WILD-TYPE 
            14            475 
[1] "LDLRAD3 MUTATION ANALYSIS"
[1] 3
  LDLRAD3 MUTATED LDLRAD3 WILD-TYPE 
                6               483 
  LDLRAD3 MUTATED LDLRAD3 WILD-TYPE 
                6               483 
[1] "HOOK3 MUTATION ANALYSIS"
[1] 3
  HOOK3 MUTATED HOOK3 WILD-TYPE 
             11             478 
  HOOK3 MUTATED HOOK3 WILD-TYPE 
             11             478 
[1] "NAPA MUTATION ANALYSIS"
[1] 3
  NAPA MUTATED NAPA WILD-TYPE 
             7            482 
  NAPA MUTATED NAPA WILD-TYPE 
             7            482 
[1] "METT10D MUTATION ANALYSIS"
[1] 3
  METT10D MUTATED METT10D WILD-TYPE 
               11               478 
  METT10D MUTATED METT10D WILD-TYPE 
               11               478 
[1] "PLD5 MUTATION ANALYSIS"
[1] 3
  PLD5 MUTATED PLD5 WILD-TYPE 
            15            474 
  PLD5 MUTATED PLD5 WILD-TYPE 
            15            474 
[1] "SON MUTATION ANALYSIS"
[1] 3
  SON MUTATED SON WILD-TYPE 
           24           465 
  SON MUTATED SON WILD-TYPE 
           24           465 
[1] "ATP6V0A4 MUTATION ANALYSIS"
[1] 3
  ATP6V0A4 MUTATED ATP6V0A4 WILD-TYPE 
                13                476 
  ATP6V0A4 MUTATED ATP6V0A4 WILD-TYPE 
                13                476 
[1] "CACNA1D MUTATION ANALYSIS"
[1] 3
  CACNA1D MUTATED CACNA1D WILD-TYPE 
               23               466 
  CACNA1D MUTATED CACNA1D WILD-TYPE 
               23               466 
[1] "RCOR1 MUTATION ANALYSIS"
[1] 3
  RCOR1 MUTATED RCOR1 WILD-TYPE 
              4             485 
  RCOR1 MUTATED RCOR1 WILD-TYPE 
              4             485 
[1] "ZNF286B MUTATION ANALYSIS"
[1] 3
  ZNF286B MUTATED ZNF286B WILD-TYPE 
                5               484 
  ZNF286B MUTATED ZNF286B WILD-TYPE 
                5               484 
[1] "SPATA16 MUTATION ANALYSIS"
[1] 3
  SPATA16 MUTATED SPATA16 WILD-TYPE 
               12               477 
  SPATA16 MUTATED SPATA16 WILD-TYPE 
               12               477 
[1] "OR1L1 MUTATION ANALYSIS"
[1] 3
  OR1L1 MUTATED OR1L1 WILD-TYPE 
              8             481 
  OR1L1 MUTATED OR1L1 WILD-TYPE 
              8             481 
[1] "CCDC55 MUTATION ANALYSIS"
[1] 3
  CCDC55 MUTATED CCDC55 WILD-TYPE 
              13              476 
  CCDC55 MUTATED CCDC55 WILD-TYPE 
              13              476 
[1] "AASDH MUTATION ANALYSIS"
[1] 3
  AASDH MUTATED AASDH WILD-TYPE 
             21             468 
  AASDH MUTATED AASDH WILD-TYPE 
             21             468 
[1] "CTSA MUTATION ANALYSIS"
[1] 3
  CTSA MUTATED CTSA WILD-TYPE 
             6            483 
  CTSA MUTATED CTSA WILD-TYPE 
             6            483 
[1] "ALAS1 MUTATION ANALYSIS"
[1] 3
  ALAS1 MUTATED ALAS1 WILD-TYPE 
             10             479 
  ALAS1 MUTATED ALAS1 WILD-TYPE 
             10             479 
[1] "DDX55 MUTATION ANALYSIS"
[1] 3
  DDX55 MUTATED DDX55 WILD-TYPE 
             11             478 
  DDX55 MUTATED DDX55 WILD-TYPE 
             11             478 
[1] "SFRP2 MUTATION ANALYSIS"
[1] 3
  SFRP2 MUTATED SFRP2 WILD-TYPE 
             10             479 
  SFRP2 MUTATED SFRP2 WILD-TYPE 
             10             479 
[1] "IGSF5 MUTATION ANALYSIS"
[1] 3
  IGSF5 MUTATED IGSF5 WILD-TYPE 
             15             474 
  IGSF5 MUTATED IGSF5 WILD-TYPE 
             15             474 
[1] "MFRP MUTATION ANALYSIS"
[1] 3
  MFRP MUTATED MFRP WILD-TYPE 
            12            477 
  MFRP MUTATED MFRP WILD-TYPE 
            12            477 
[1] "PIGN MUTATION ANALYSIS"
[1] 3
  PIGN MUTATED PIGN WILD-TYPE 
             9            480 
  PIGN MUTATED PIGN WILD-TYPE 
             9            480 
[1] "TPK1 MUTATION ANALYSIS"
[1] 3
  TPK1 MUTATED TPK1 WILD-TYPE 
             8            481 
  TPK1 MUTATED TPK1 WILD-TYPE 
             8            481 
[1] "IGFN1 MUTATION ANALYSIS"
[1] 3
  IGFN1 MUTATED IGFN1 WILD-TYPE 
             17             472 
  IGFN1 MUTATED IGFN1 WILD-TYPE 
             17             472 
[1] "GRK5 MUTATION ANALYSIS"
[1] 3
  GRK5 MUTATED GRK5 WILD-TYPE 
            12            477 
  GRK5 MUTATED GRK5 WILD-TYPE 
            12            477 
[1] "ZNF555 MUTATION ANALYSIS"
[1] 3
  ZNF555 MUTATED ZNF555 WILD-TYPE 
               9              480 
  ZNF555 MUTATED ZNF555 WILD-TYPE 
               9              480 
[1] "NRAP MUTATION ANALYSIS"
[1] 3
  NRAP MUTATED NRAP WILD-TYPE 
            27            462 
  NRAP MUTATED NRAP WILD-TYPE 
            27            462 
[1] "STAU1 MUTATION ANALYSIS"
[1] 3
  STAU1 MUTATED STAU1 WILD-TYPE 
             11             478 
  STAU1 MUTATED STAU1 WILD-TYPE 
             11             478 
[1] "KIAA1919 MUTATION ANALYSIS"
[1] 3
  KIAA1919 MUTATED KIAA1919 WILD-TYPE 
                 9                480 
  KIAA1919 MUTATED KIAA1919 WILD-TYPE 
                 9                480 
[1] "CTCFL MUTATION ANALYSIS"
[1] 3
  CTCFL MUTATED CTCFL WILD-TYPE 
             16             473 
  CTCFL MUTATED CTCFL WILD-TYPE 
             16             473 
[1] "LRRC31 MUTATION ANALYSIS"
[1] 3
  LRRC31 MUTATED LRRC31 WILD-TYPE 
              16              473 
  LRRC31 MUTATED LRRC31 WILD-TYPE 
              16              473 
[1] "RARG MUTATION ANALYSIS"
[1] 3
  RARG MUTATED RARG WILD-TYPE 
            10            479 
  RARG MUTATED RARG WILD-TYPE 
            10            479 
[1] "SFRS2IP MUTATION ANALYSIS"
[1] 3
  SFRS2IP MUTATED SFRS2IP WILD-TYPE 
               27               462 
  SFRS2IP MUTATED SFRS2IP WILD-TYPE 
               27               462 
[1] "TCTEX1D2 MUTATION ANALYSIS"
[1] 3
  TCTEX1D2 MUTATED TCTEX1D2 WILD-TYPE 
                 7                482 
  TCTEX1D2 MUTATED TCTEX1D2 WILD-TYPE 
                 7                482 
[1] "IKBKB MUTATION ANALYSIS"
[1] 3
  IKBKB MUTATED IKBKB WILD-TYPE 
              9             480 
  IKBKB MUTATED IKBKB WILD-TYPE 
              9             480 
[1] "PPIL5 MUTATION ANALYSIS"
[1] 3
  PPIL5 MUTATED PPIL5 WILD-TYPE 
              4             485 
  PPIL5 MUTATED PPIL5 WILD-TYPE 
              4             485 
[1] "RNF8 MUTATION ANALYSIS"
[1] 3
  RNF8 MUTATED RNF8 WILD-TYPE 
             7            482 
  RNF8 MUTATED RNF8 WILD-TYPE 
             7            482 
[1] "EPHA6 MUTATION ANALYSIS"
[1] 3
  EPHA6 MUTATED EPHA6 WILD-TYPE 
             24             465 
  EPHA6 MUTATED EPHA6 WILD-TYPE 
             24             465 
[1] "KIAA1407 MUTATION ANALYSIS"
[1] 3
  KIAA1407 MUTATED KIAA1407 WILD-TYPE 
                13                476 
  KIAA1407 MUTATED KIAA1407 WILD-TYPE 
                13                476 
[1] "LIMCH1 MUTATION ANALYSIS"
[1] 3
  LIMCH1 MUTATED LIMCH1 WILD-TYPE 
              15              474 
  LIMCH1 MUTATED LIMCH1 WILD-TYPE 
              15              474 
[1] "ATAD2 MUTATION ANALYSIS"
[1] 3
  ATAD2 MUTATED ATAD2 WILD-TYPE 
             22             467 
  ATAD2 MUTATED ATAD2 WILD-TYPE 
             22             467 
[1] "ZNF594 MUTATION ANALYSIS"
[1] 3
  ZNF594 MUTATED ZNF594 WILD-TYPE 
              16              473 
  ZNF594 MUTATED ZNF594 WILD-TYPE 
              16              473 
[1] "ACTRT1 MUTATION ANALYSIS"
[1] 3
  ACTRT1 MUTATED ACTRT1 WILD-TYPE 
              13              476 
  ACTRT1 MUTATED ACTRT1 WILD-TYPE 
              13              476 
[1] "CNTNAP3 MUTATION ANALYSIS"
[1] 3
  CNTNAP3 MUTATED CNTNAP3 WILD-TYPE 
               14               475 
  CNTNAP3 MUTATED CNTNAP3 WILD-TYPE 
               14               475 
[1] "GRIN2B MUTATION ANALYSIS"
[1] 3
  GRIN2B MUTATED GRIN2B WILD-TYPE 
              28              461 
  GRIN2B MUTATED GRIN2B WILD-TYPE 
              28              461 
[1] "CXORF23 MUTATION ANALYSIS"
[1] 3
  CXORF23 MUTATED CXORF23 WILD-TYPE 
                7               482 
  CXORF23 MUTATED CXORF23 WILD-TYPE 
                7               482 
[1] "EFCAB4B MUTATION ANALYSIS"
[1] 3
  EFCAB4B MUTATED EFCAB4B WILD-TYPE 
                7               482 
  EFCAB4B MUTATED EFCAB4B WILD-TYPE 
                7               482 
[1] "EPSTI1 MUTATION ANALYSIS"
[1] 3
  EPSTI1 MUTATED EPSTI1 WILD-TYPE 
               7              482 
  EPSTI1 MUTATED EPSTI1 WILD-TYPE 
               7              482 
[1] "GPR160 MUTATION ANALYSIS"
[1] 3
  GPR160 MUTATED GPR160 WILD-TYPE 
               5              484 
  GPR160 MUTATED GPR160 WILD-TYPE 
               5              484 
[1] "EPHA2 MUTATION ANALYSIS"
[1] 3
  EPHA2 MUTATED EPHA2 WILD-TYPE 
             11             478 
  EPHA2 MUTATED EPHA2 WILD-TYPE 
             11             478 
[1] "ZBTB7C MUTATION ANALYSIS"
[1] 3
  ZBTB7C MUTATED ZBTB7C WILD-TYPE 
              15              474 
  ZBTB7C MUTATED ZBTB7C WILD-TYPE 
              15              474 
[1] "CHM MUTATION ANALYSIS"
[1] 3
  CHM MUTATED CHM WILD-TYPE 
            5           484 
  CHM MUTATED CHM WILD-TYPE 
            5           484 
[1] "MAPK14 MUTATION ANALYSIS"
[1] 3
  MAPK14 MUTATED MAPK14 WILD-TYPE 
               8              481 
  MAPK14 MUTATED MAPK14 WILD-TYPE 
               8              481 
[1] "C12ORF11 MUTATION ANALYSIS"
[1] 3
  C12ORF11 MUTATED C12ORF11 WILD-TYPE 
                14                475 
  C12ORF11 MUTATED C12ORF11 WILD-TYPE 
                14                475 
[1] "AOX1 MUTATION ANALYSIS"
[1] 3
  AOX1 MUTATED AOX1 WILD-TYPE 
            13            476 
  AOX1 MUTATED AOX1 WILD-TYPE 
            13            476 
[1] "SLC12A2 MUTATION ANALYSIS"
[1] 3
  SLC12A2 MUTATED SLC12A2 WILD-TYPE 
               18               471 
  SLC12A2 MUTATED SLC12A2 WILD-TYPE 
               18               471 
[1] "UGT2A1 MUTATION ANALYSIS"
[1] 3
  UGT2A1 MUTATED UGT2A1 WILD-TYPE 
              10              479 
  UGT2A1 MUTATED UGT2A1 WILD-TYPE 
              10              479 
[1] "CXCR7 MUTATION ANALYSIS"
[1] 3
  CXCR7 MUTATED CXCR7 WILD-TYPE 
             21             468 
  CXCR7 MUTATED CXCR7 WILD-TYPE 
             21             468 
[1] "SSRP1 MUTATION ANALYSIS"
[1] 3
  SSRP1 MUTATED SSRP1 WILD-TYPE 
             15             474 
  SSRP1 MUTATED SSRP1 WILD-TYPE 
             15             474 
[1] "IGFBP3 MUTATION ANALYSIS"
[1] 3
  IGFBP3 MUTATED IGFBP3 WILD-TYPE 
               8              481 
  IGFBP3 MUTATED IGFBP3 WILD-TYPE 
               8              481 
[1] "RELA MUTATION ANALYSIS"
[1] 3
  RELA MUTATED RELA WILD-TYPE 
            10            479 
  RELA MUTATED RELA WILD-TYPE 
            10            479 
[1] "KCNA3 MUTATION ANALYSIS"
[1] 3
  KCNA3 MUTATED KCNA3 WILD-TYPE 
             20             469 
  KCNA3 MUTATED KCNA3 WILD-TYPE 
             20             469 
[1] "CPT1B MUTATION ANALYSIS"
[1] 3
  CPT1B MUTATED CPT1B WILD-TYPE 
             11             478 
  CPT1B MUTATED CPT1B WILD-TYPE 
             11             478 
[1] "SLC14A1 MUTATION ANALYSIS"
[1] 3
  SLC14A1 MUTATED SLC14A1 WILD-TYPE 
                7               482 
  SLC14A1 MUTATED SLC14A1 WILD-TYPE 
                7               482 
[1] "PLEKHH2 MUTATION ANALYSIS"
[1] 3
  PLEKHH2 MUTATED PLEKHH2 WILD-TYPE 
               23               466 
  PLEKHH2 MUTATED PLEKHH2 WILD-TYPE 
               23               466 
[1] "ESRP2 MUTATION ANALYSIS"
[1] 3
  ESRP2 MUTATED ESRP2 WILD-TYPE 
             10             479 
  ESRP2 MUTATED ESRP2 WILD-TYPE 
             10             479 
[1] "MMP21 MUTATION ANALYSIS"
[1] 3
  MMP21 MUTATED MMP21 WILD-TYPE 
             12             477 
  MMP21 MUTATED MMP21 WILD-TYPE 
             12             477 
[1] "IL6R MUTATION ANALYSIS"
[1] 3
  IL6R MUTATED IL6R WILD-TYPE 
             8            481 
  IL6R MUTATED IL6R WILD-TYPE 
             8            481 
[1] "KSR2 MUTATION ANALYSIS"
[1] 3
  KSR2 MUTATED KSR2 WILD-TYPE 
            21            468 
  KSR2 MUTATED KSR2 WILD-TYPE 
            21            468 
[1] "ZNF443 MUTATION ANALYSIS"
[1] 3
  ZNF443 MUTATED ZNF443 WILD-TYPE 
               9              480 
  ZNF443 MUTATED ZNF443 WILD-TYPE 
               9              480 
[1] "PDSS2 MUTATION ANALYSIS"
[1] 3
  PDSS2 MUTATED PDSS2 WILD-TYPE 
              6             483 
  PDSS2 MUTATED PDSS2 WILD-TYPE 
              6             483 
[1] "ACTN1 MUTATION ANALYSIS"
[1] 3
  ACTN1 MUTATED ACTN1 WILD-TYPE 
             13             476 
  ACTN1 MUTATED ACTN1 WILD-TYPE 
             13             476 
[1] "CCPG1 MUTATION ANALYSIS"
[1] 3
  CCPG1 MUTATED CCPG1 WILD-TYPE 
             12             477 
  CCPG1 MUTATED CCPG1 WILD-TYPE 
             12             477 
[1] "PIGC MUTATION ANALYSIS"
[1] 3
  PIGC MUTATED PIGC WILD-TYPE 
             4            485 
  PIGC MUTATED PIGC WILD-TYPE 
             4            485 
[1] "CNOT3 MUTATION ANALYSIS"
[1] 3
  CNOT3 MUTATED CNOT3 WILD-TYPE 
              8             481 
  CNOT3 MUTATED CNOT3 WILD-TYPE 
              8             481 
[1] "TYW3 MUTATION ANALYSIS"
[1] 3
  TYW3 MUTATED TYW3 WILD-TYPE 
             7            482 
  TYW3 MUTATED TYW3 WILD-TYPE 
             7            482 
[1] "LPPR4 MUTATION ANALYSIS"
[1] 3
  LPPR4 MUTATED LPPR4 WILD-TYPE 
             27             462 
  LPPR4 MUTATED LPPR4 WILD-TYPE 
             27             462 
[1] "UBR2 MUTATION ANALYSIS"
[1] 3
  UBR2 MUTATED UBR2 WILD-TYPE 
            19            470 
  UBR2 MUTATED UBR2 WILD-TYPE 
            19            470 
[1] "GPBP1 MUTATION ANALYSIS"
[1] 3
  GPBP1 MUTATED GPBP1 WILD-TYPE 
             13             476 
  GPBP1 MUTATED GPBP1 WILD-TYPE 
             13             476 
[1] "SPAM1 MUTATION ANALYSIS"
[1] 3
  SPAM1 MUTATED SPAM1 WILD-TYPE 
             13             476 
  SPAM1 MUTATED SPAM1 WILD-TYPE 
             13             476 
[1] "ZFP91 MUTATION ANALYSIS"
[1] 3
  ZFP91 MUTATED ZFP91 WILD-TYPE 
              8             481 
  ZFP91 MUTATED ZFP91 WILD-TYPE 
              8             481 
[1] "OR13C5 MUTATION ANALYSIS"
[1] 3
  OR13C5 MUTATED OR13C5 WILD-TYPE 
              13              476 
  OR13C5 MUTATED OR13C5 WILD-TYPE 
              13              476 
[1] "SLC43A3 MUTATION ANALYSIS"
[1] 3
  SLC43A3 MUTATED SLC43A3 WILD-TYPE 
               13               476 
  SLC43A3 MUTATED SLC43A3 WILD-TYPE 
               13               476 
[1] "GOLGA1 MUTATION ANALYSIS"
[1] 3
  GOLGA1 MUTATED GOLGA1 WILD-TYPE 
               8              481 
  GOLGA1 MUTATED GOLGA1 WILD-TYPE 
               8              481 
[1] "C5ORF36 MUTATION ANALYSIS"
[1] 3
  C5ORF36 MUTATED C5ORF36 WILD-TYPE 
               20               469 
  C5ORF36 MUTATED C5ORF36 WILD-TYPE 
               20               469 
[1] "CPLX4 MUTATION ANALYSIS"
[1] 3
  CPLX4 MUTATED CPLX4 WILD-TYPE 
              5             484 
  CPLX4 MUTATED CPLX4 WILD-TYPE 
              5             484 
[1] "TEX2 MUTATION ANALYSIS"
[1] 3
  TEX2 MUTATED TEX2 WILD-TYPE 
            12            477 
  TEX2 MUTATED TEX2 WILD-TYPE 
            12            477 
[1] "ARHGAP28 MUTATION ANALYSIS"
[1] 3
  ARHGAP28 MUTATED ARHGAP28 WILD-TYPE 
                14                475 
  ARHGAP28 MUTATED ARHGAP28 WILD-TYPE 
                14                475 
[1] "STK33 MUTATION ANALYSIS"
[1] 3
  STK33 MUTATED STK33 WILD-TYPE 
             16             473 
  STK33 MUTATED STK33 WILD-TYPE 
             16             473 
[1] "GNG12 MUTATION ANALYSIS"
[1] 3
  GNG12 MUTATED GNG12 WILD-TYPE 
              8             481 
  GNG12 MUTATED GNG12 WILD-TYPE 
              8             481 
[1] "FAM70A MUTATION ANALYSIS"
[1] 3
  FAM70A MUTATED FAM70A WILD-TYPE 
               8              481 
  FAM70A MUTATED FAM70A WILD-TYPE 
               8              481 
[1] "ACPP MUTATION ANALYSIS"
[1] 3
  ACPP MUTATED ACPP WILD-TYPE 
             4            485 
  ACPP MUTATED ACPP WILD-TYPE 
             4            485 
[1] "RUNDC2A MUTATION ANALYSIS"
[1] 3
  RUNDC2A MUTATED RUNDC2A WILD-TYPE 
                7               482 
  RUNDC2A MUTATED RUNDC2A WILD-TYPE 
                7               482 
[1] "IMMT MUTATION ANALYSIS"
[1] 3
  IMMT MUTATED IMMT WILD-TYPE 
             8            481 
  IMMT MUTATED IMMT WILD-TYPE 
             8            481 
[1] "COLEC12 MUTATION ANALYSIS"
[1] 3
  COLEC12 MUTATED COLEC12 WILD-TYPE 
               19               470 
  COLEC12 MUTATED COLEC12 WILD-TYPE 
               19               470 
[1] "SCYL2 MUTATION ANALYSIS"
[1] 3
  SCYL2 MUTATED SCYL2 WILD-TYPE 
             21             468 
  SCYL2 MUTATED SCYL2 WILD-TYPE 
             21             468 
[1] "CAPRIN2 MUTATION ANALYSIS"
[1] 3
  CAPRIN2 MUTATED CAPRIN2 WILD-TYPE 
               17               472 
  CAPRIN2 MUTATED CAPRIN2 WILD-TYPE 
               17               472 
[1] "CNOT10 MUTATION ANALYSIS"
[1] 3
  CNOT10 MUTATED CNOT10 WILD-TYPE 
              10              479 
  CNOT10 MUTATED CNOT10 WILD-TYPE 
              10              479 
[1] "LUZP1 MUTATION ANALYSIS"
[1] 3
  LUZP1 MUTATED LUZP1 WILD-TYPE 
             16             473 
  LUZP1 MUTATED LUZP1 WILD-TYPE 
             16             473 
[1] "VCX3A MUTATION ANALYSIS"
[1] 3
  VCX3A MUTATED VCX3A WILD-TYPE 
              5             484 
  VCX3A MUTATED VCX3A WILD-TYPE 
              5             484 
[1] "BAP1 MUTATION ANALYSIS"
[1] 3
  BAP1 MUTATED BAP1 WILD-TYPE 
            14            475 
  BAP1 MUTATED BAP1 WILD-TYPE 
            14            475 
[1] "CDHR5 MUTATION ANALYSIS"
[1] 3
  CDHR5 MUTATED CDHR5 WILD-TYPE 
             12             477 
  CDHR5 MUTATED CDHR5 WILD-TYPE 
             12             477 
[1] "SLCO1B3 MUTATION ANALYSIS"
[1] 3
  SLCO1B3 MUTATED SLCO1B3 WILD-TYPE 
               19               470 
  SLCO1B3 MUTATED SLCO1B3 WILD-TYPE 
               19               470 
[1] "TRAF3IP3 MUTATION ANALYSIS"
[1] 3
  TRAF3IP3 MUTATED TRAF3IP3 WILD-TYPE 
                13                476 
  TRAF3IP3 MUTATED TRAF3IP3 WILD-TYPE 
                13                476 
[1] "RXRA MUTATION ANALYSIS"
[1] 3
  RXRA MUTATED RXRA WILD-TYPE 
             8            481 
  RXRA MUTATED RXRA WILD-TYPE 
             8            481 
[1] "DOPEY2 MUTATION ANALYSIS"
[1] 3
  DOPEY2 MUTATED DOPEY2 WILD-TYPE 
              16              473 
  DOPEY2 MUTATED DOPEY2 WILD-TYPE 
              16              473 
[1] "LCN9 MUTATION ANALYSIS"
[1] 3
  LCN9 MUTATED LCN9 WILD-TYPE 
             4            485 
  LCN9 MUTATED LCN9 WILD-TYPE 
             4            485 
[1] "LAMB4 MUTATION ANALYSIS"
[1] 3
  LAMB4 MUTATED LAMB4 WILD-TYPE 
             30             459 
  LAMB4 MUTATED LAMB4 WILD-TYPE 
             30             459 
[1] "MED24 MUTATION ANALYSIS"
[1] 3
  MED24 MUTATED MED24 WILD-TYPE 
             11             478 
  MED24 MUTATED MED24 WILD-TYPE 
             11             478 
[1] "CUBN MUTATION ANALYSIS"
[1] 3
  CUBN MUTATED CUBN WILD-TYPE 
            58            431 
  CUBN MUTATED CUBN WILD-TYPE 
            58            431 
[1] "ACVR1C MUTATION ANALYSIS"
[1] 3
  ACVR1C MUTATED ACVR1C WILD-TYPE 
              11              478 
  ACVR1C MUTATED ACVR1C WILD-TYPE 
              11              478 
[1] "MKLN1 MUTATION ANALYSIS"
[1] 3
  MKLN1 MUTATED MKLN1 WILD-TYPE 
             11             478 
  MKLN1 MUTATED MKLN1 WILD-TYPE 
             11             478 
[1] "IFNA2 MUTATION ANALYSIS"
[1] 3
  IFNA2 MUTATED IFNA2 WILD-TYPE 
             10             479 
  IFNA2 MUTATED IFNA2 WILD-TYPE 
             10             479 
[1] "MPHOSPH9 MUTATION ANALYSIS"
[1] 3
  MPHOSPH9 MUTATED MPHOSPH9 WILD-TYPE 
                10                479 
  MPHOSPH9 MUTATED MPHOSPH9 WILD-TYPE 
                10                479 
[1] "TM7SF4 MUTATION ANALYSIS"
[1] 3
  TM7SF4 MUTATED TM7SF4 WILD-TYPE 
               9              480 
  TM7SF4 MUTATED TM7SF4 WILD-TYPE 
               9              480 
[1] "ZNF585B MUTATION ANALYSIS"
[1] 3
  ZNF585B MUTATED ZNF585B WILD-TYPE 
                8               481 
  ZNF585B MUTATED ZNF585B WILD-TYPE 
                8               481 
[1] "ATP1A4 MUTATION ANALYSIS"
[1] 3
  ATP1A4 MUTATED ATP1A4 WILD-TYPE 
              19              470 
  ATP1A4 MUTATED ATP1A4 WILD-TYPE 
              19              470 
[1] "GUCY2F MUTATION ANALYSIS"
[1] 3
  GUCY2F MUTATED GUCY2F WILD-TYPE 
              23              466 
  GUCY2F MUTATED GUCY2F WILD-TYPE 
              23              466 
[1] "DRD3 MUTATION ANALYSIS"
[1] 3
  DRD3 MUTATED DRD3 WILD-TYPE 
             6            483 
  DRD3 MUTATED DRD3 WILD-TYPE 
             6            483 
[1] "SMG7 MUTATION ANALYSIS"
[1] 3
  SMG7 MUTATED SMG7 WILD-TYPE 
            12            477 
  SMG7 MUTATED SMG7 WILD-TYPE 
            12            477 
[1] "OR51T1 MUTATION ANALYSIS"
[1] 3
  OR51T1 MUTATED OR51T1 WILD-TYPE 
              13              476 
  OR51T1 MUTATED OR51T1 WILD-TYPE 
              13              476 
[1] "NPPB MUTATION ANALYSIS"
[1] 3
  NPPB MUTATED NPPB WILD-TYPE 
             5            484 
  NPPB MUTATED NPPB WILD-TYPE 
             5            484 
[1] "ZNF643 MUTATION ANALYSIS"
[1] 3
  ZNF643 MUTATED ZNF643 WILD-TYPE 
              10              479 
  ZNF643 MUTATED ZNF643 WILD-TYPE 
              10              479 
[1] "DUSP7 MUTATION ANALYSIS"
[1] 3
  DUSP7 MUTATED DUSP7 WILD-TYPE 
              8             481 
  DUSP7 MUTATED DUSP7 WILD-TYPE 
              8             481 
[1] "ZDHHC21 MUTATION ANALYSIS"
[1] 3
  ZDHHC21 MUTATED ZDHHC21 WILD-TYPE 
                5               484 
  ZDHHC21 MUTATED ZDHHC21 WILD-TYPE 
                5               484 
[1] "SOX6 MUTATION ANALYSIS"
[1] 3
  SOX6 MUTATED SOX6 WILD-TYPE 
            16            473 
  SOX6 MUTATED SOX6 WILD-TYPE 
            16            473 
[1] "APBA1 MUTATION ANALYSIS"
[1] 3
  APBA1 MUTATED APBA1 WILD-TYPE 
             14             475 
  APBA1 MUTATED APBA1 WILD-TYPE 
             14             475 
[1] "RREB1 MUTATION ANALYSIS"
[1] 3
  RREB1 MUTATED RREB1 WILD-TYPE 
             13             476 
  RREB1 MUTATED RREB1 WILD-TYPE 
             13             476 
[1] "KIAA0355 MUTATION ANALYSIS"
[1] 3
  KIAA0355 MUTATED KIAA0355 WILD-TYPE 
                 7                482 
  KIAA0355 MUTATED KIAA0355 WILD-TYPE 
                 7                482 
[1] "PTPN13 MUTATION ANALYSIS"
[1] 3
  PTPN13 MUTATED PTPN13 WILD-TYPE 
              25              464 
  PTPN13 MUTATED PTPN13 WILD-TYPE 
              25              464 
[1] "TNKS2 MUTATION ANALYSIS"
[1] 3
  TNKS2 MUTATED TNKS2 WILD-TYPE 
             22             467 
  TNKS2 MUTATED TNKS2 WILD-TYPE 
             22             467 
[1] "XPO4 MUTATION ANALYSIS"
[1] 3
  XPO4 MUTATED XPO4 WILD-TYPE 
            20            469 
  XPO4 MUTATED XPO4 WILD-TYPE 
            20            469 
[1] "AKNA MUTATION ANALYSIS"
[1] 3
  AKNA MUTATED AKNA WILD-TYPE 
            12            477 
  AKNA MUTATED AKNA WILD-TYPE 
            12            477 
[1] "TRIM36 MUTATION ANALYSIS"
[1] 3
  TRIM36 MUTATED TRIM36 WILD-TYPE 
              15              474 
  TRIM36 MUTATED TRIM36 WILD-TYPE 
              15              474 
[1] "DIAPH3 MUTATION ANALYSIS"
[1] 3
  DIAPH3 MUTATED DIAPH3 WILD-TYPE 
              18              471 
  DIAPH3 MUTATED DIAPH3 WILD-TYPE 
              18              471 
[1] "KDR MUTATION ANALYSIS"
[1] 3
  KDR MUTATED KDR WILD-TYPE 
           32           457 
  KDR MUTATED KDR WILD-TYPE 
           32           457 
[1] "STK40 MUTATION ANALYSIS"
[1] 3
  STK40 MUTATED STK40 WILD-TYPE 
              9             480 
  STK40 MUTATED STK40 WILD-TYPE 
              9             480 
[1] "XRCC6 MUTATION ANALYSIS"
[1] 3
  XRCC6 MUTATED XRCC6 WILD-TYPE 
              8             481 
  XRCC6 MUTATED XRCC6 WILD-TYPE 
              8             481 
[1] "PHLDB2 MUTATION ANALYSIS"
[1] 3
  PHLDB2 MUTATED PHLDB2 WILD-TYPE 
              20              469 
  PHLDB2 MUTATED PHLDB2 WILD-TYPE 
              20              469 
[1] "MRPL44 MUTATION ANALYSIS"
[1] 3
  MRPL44 MUTATED MRPL44 WILD-TYPE 
              10              479 
  MRPL44 MUTATED MRPL44 WILD-TYPE 
              10              479 
[1] "IDI1 MUTATION ANALYSIS"
[1] 3
  IDI1 MUTATED IDI1 WILD-TYPE 
             4            485 
  IDI1 MUTATED IDI1 WILD-TYPE 
             4            485 
[1] "SMOX MUTATION ANALYSIS"
[1] 3
  SMOX MUTATED SMOX WILD-TYPE 
             8            481 
  SMOX MUTATED SMOX WILD-TYPE 
             8            481 
[1] "CENPJ MUTATION ANALYSIS"
[1] 3
  CENPJ MUTATED CENPJ WILD-TYPE 
             22             467 
  CENPJ MUTATED CENPJ WILD-TYPE 
             22             467 
[1] "DUSP16 MUTATION ANALYSIS"
[1] 3
  DUSP16 MUTATED DUSP16 WILD-TYPE 
              11              478 
  DUSP16 MUTATED DUSP16 WILD-TYPE 
              11              478 
[1] "ZHX3 MUTATION ANALYSIS"
[1] 3
  ZHX3 MUTATED ZHX3 WILD-TYPE 
            14            475 
  ZHX3 MUTATED ZHX3 WILD-TYPE 
            14            475 
[1] "PDK1 MUTATION ANALYSIS"
[1] 3
  PDK1 MUTATED PDK1 WILD-TYPE 
             7            482 
  PDK1 MUTATED PDK1 WILD-TYPE 
             7            482 
[1] "EPHA5 MUTATION ANALYSIS"
[1] 3
  EPHA5 MUTATED EPHA5 WILD-TYPE 
             39             450 
  EPHA5 MUTATED EPHA5 WILD-TYPE 
             39             450 
[1] "SPAST MUTATION ANALYSIS"
[1] 3
  SPAST MUTATED SPAST WILD-TYPE 
             10             479 
  SPAST MUTATED SPAST WILD-TYPE 
             10             479 
[1] "SIN3A MUTATION ANALYSIS"
[1] 3
  SIN3A MUTATED SIN3A WILD-TYPE 
             20             469 
  SIN3A MUTATED SIN3A WILD-TYPE 
             20             469 
[1] "C1ORF88 MUTATION ANALYSIS"
[1] 3
  C1ORF88 MUTATED C1ORF88 WILD-TYPE 
                6               483 
  C1ORF88 MUTATED C1ORF88 WILD-TYPE 
                6               483 
[1] "GLB1L2 MUTATION ANALYSIS"
[1] 3
  GLB1L2 MUTATED GLB1L2 WILD-TYPE 
              14              475 
  GLB1L2 MUTATED GLB1L2 WILD-TYPE 
              14              475 
[1] "OSBPL1A MUTATION ANALYSIS"
[1] 3
  OSBPL1A MUTATED OSBPL1A WILD-TYPE 
               11               478 
  OSBPL1A MUTATED OSBPL1A WILD-TYPE 
               11               478 
[1] "AFM MUTATION ANALYSIS"
[1] 3
  AFM MUTATED AFM WILD-TYPE 
           17           472 
  AFM MUTATED AFM WILD-TYPE 
           17           472 
[1] "YIPF1 MUTATION ANALYSIS"
[1] 3
  YIPF1 MUTATED YIPF1 WILD-TYPE 
              6             483 
  YIPF1 MUTATED YIPF1 WILD-TYPE 
              6             483 
[1] "TSPAN7 MUTATION ANALYSIS"
[1] 3
  TSPAN7 MUTATED TSPAN7 WILD-TYPE 
               9              480 
  TSPAN7 MUTATED TSPAN7 WILD-TYPE 
               9              480 
[1] "MLLT10 MUTATION ANALYSIS"
[1] 3
  MLLT10 MUTATED MLLT10 WILD-TYPE 
              11              478 
  MLLT10 MUTATED MLLT10 WILD-TYPE 
              11              478 
[1] "CCDC6 MUTATION ANALYSIS"
[1] 3
  CCDC6 MUTATED CCDC6 WILD-TYPE 
             11             478 
  CCDC6 MUTATED CCDC6 WILD-TYPE 
             11             478 
[1] "SGOL2 MUTATION ANALYSIS"
[1] 3
  SGOL2 MUTATED SGOL2 WILD-TYPE 
             16             473 
  SGOL2 MUTATED SGOL2 WILD-TYPE 
             16             473 
[1] "HECW1 MUTATION ANALYSIS"
[1] 3
  HECW1 MUTATED HECW1 WILD-TYPE 
             39             450 
  HECW1 MUTATED HECW1 WILD-TYPE 
             39             450 
[1] "C14ORF180 MUTATION ANALYSIS"
[1] 3
  C14ORF180 MUTATED C14ORF180 WILD-TYPE 
                  4                 485 
  C14ORF180 MUTATED C14ORF180 WILD-TYPE 
                  4                 485 
[1] "USP14 MUTATION ANALYSIS"
[1] 3
  USP14 MUTATED USP14 WILD-TYPE 
              7             482 
  USP14 MUTATED USP14 WILD-TYPE 
              7             482 
[1] "TMEM144 MUTATION ANALYSIS"
[1] 3
  TMEM144 MUTATED TMEM144 WILD-TYPE 
                8               481 
  TMEM144 MUTATED TMEM144 WILD-TYPE 
                8               481 
[1] "PIAS2 MUTATION ANALYSIS"
[1] 3
  PIAS2 MUTATED PIAS2 WILD-TYPE 
              5             484 
  PIAS2 MUTATED PIAS2 WILD-TYPE 
              5             484 
[1] "HIST4H4 MUTATION ANALYSIS"
[1] 3
  HIST4H4 MUTATED HIST4H4 WILD-TYPE 
                3               486 
  HIST4H4 MUTATED HIST4H4 WILD-TYPE 
                3               486 
[1] "ASTE1 MUTATION ANALYSIS"
[1] 3
  ASTE1 MUTATED ASTE1 WILD-TYPE 
             10             479 
  ASTE1 MUTATED ASTE1 WILD-TYPE 
             10             479 
[1] "FBXO38 MUTATION ANALYSIS"
[1] 3
  FBXO38 MUTATED FBXO38 WILD-TYPE 
              18              471 
  FBXO38 MUTATED FBXO38 WILD-TYPE 
              18              471 
[1] "HAP1 MUTATION ANALYSIS"
[1] 3
  HAP1 MUTATED HAP1 WILD-TYPE 
             8            481 
  HAP1 MUTATED HAP1 WILD-TYPE 
             8            481 
[1] "TRAF3IP1 MUTATION ANALYSIS"
[1] 3
  TRAF3IP1 MUTATED TRAF3IP1 WILD-TYPE 
                 7                482 
  TRAF3IP1 MUTATED TRAF3IP1 WILD-TYPE 
                 7                482 
[1] "ZNF318 MUTATION ANALYSIS"
[1] 3
  ZNF318 MUTATED ZNF318 WILD-TYPE 
              30              459 
  ZNF318 MUTATED ZNF318 WILD-TYPE 
              30              459 
[1] "NUP133 MUTATION ANALYSIS"
[1] 3
  NUP133 MUTATED NUP133 WILD-TYPE 
              19              470 
  NUP133 MUTATED NUP133 WILD-TYPE 
              19              470 
[1] "ARAF MUTATION ANALYSIS"
[1] 3
  ARAF MUTATED ARAF WILD-TYPE 
            10            479 
  ARAF MUTATED ARAF WILD-TYPE 
            10            479 
[1] "MXRA5 MUTATION ANALYSIS"
[1] 3
  MXRA5 MUTATED MXRA5 WILD-TYPE 
             46             443 
  MXRA5 MUTATED MXRA5 WILD-TYPE 
             46             443 
[1] "PAX2 MUTATION ANALYSIS"
[1] 3
  PAX2 MUTATED PAX2 WILD-TYPE 
             7            482 
  PAX2 MUTATED PAX2 WILD-TYPE 
             7            482 
[1] "FZD3 MUTATION ANALYSIS"
[1] 3
  FZD3 MUTATED FZD3 WILD-TYPE 
            14            475 
  FZD3 MUTATED FZD3 WILD-TYPE 
            14            475 
[1] "LRRFIP2 MUTATION ANALYSIS"
[1] 3
  LRRFIP2 MUTATED LRRFIP2 WILD-TYPE 
               16               473 
  LRRFIP2 MUTATED LRRFIP2 WILD-TYPE 
               16               473 
[1] "SEZ6L MUTATION ANALYSIS"
[1] 3
  SEZ6L MUTATED SEZ6L WILD-TYPE 
             20             469 
  SEZ6L MUTATED SEZ6L WILD-TYPE 
             20             469 
[1] "ENTHD1 MUTATION ANALYSIS"
[1] 3
  ENTHD1 MUTATED ENTHD1 WILD-TYPE 
              11              478 
  ENTHD1 MUTATED ENTHD1 WILD-TYPE 
              11              478 
[1] "NEDD9 MUTATION ANALYSIS"
[1] 3
  NEDD9 MUTATED NEDD9 WILD-TYPE 
             13             476 
  NEDD9 MUTATED NEDD9 WILD-TYPE 
             13             476 
[1] "GDF6 MUTATION ANALYSIS"
[1] 3
  GDF6 MUTATED GDF6 WILD-TYPE 
             7            482 
  GDF6 MUTATED GDF6 WILD-TYPE 
             7            482 
[1] "ZNF259 MUTATION ANALYSIS"
[1] 3
  ZNF259 MUTATED ZNF259 WILD-TYPE 
               3              486 
  ZNF259 MUTATED ZNF259 WILD-TYPE 
               3              486 
[1] "SRL MUTATION ANALYSIS"
[1] 3
  SRL MUTATED SRL WILD-TYPE 
           12           477 
  SRL MUTATED SRL WILD-TYPE 
           12           477 
[1] "G3BP1 MUTATION ANALYSIS"
[1] 3
  G3BP1 MUTATED G3BP1 WILD-TYPE 
             12             477 
  G3BP1 MUTATED G3BP1 WILD-TYPE 
             12             477 
[1] "CYP4F11 MUTATION ANALYSIS"
[1] 3
  CYP4F11 MUTATED CYP4F11 WILD-TYPE 
                7               482 
  CYP4F11 MUTATED CYP4F11 WILD-TYPE 
                7               482 
[1] "UBE3C MUTATION ANALYSIS"
[1] 3
  UBE3C MUTATED UBE3C WILD-TYPE 
             19             470 
  UBE3C MUTATED UBE3C WILD-TYPE 
             19             470 
[1] "LIPH MUTATION ANALYSIS"
[1] 3
  LIPH MUTATED LIPH WILD-TYPE 
            10            479 
  LIPH MUTATED LIPH WILD-TYPE 
            10            479 
[1] "GLT8D1 MUTATION ANALYSIS"
[1] 3
  GLT8D1 MUTATED GLT8D1 WILD-TYPE 
               9              480 
  GLT8D1 MUTATED GLT8D1 WILD-TYPE 
               9              480 
[1] "C20ORF43 MUTATION ANALYSIS"
[1] 3
  C20ORF43 MUTATED C20ORF43 WILD-TYPE 
                 4                485 
  C20ORF43 MUTATED C20ORF43 WILD-TYPE 
                 4                485 
[1] "GOLIM4 MUTATION ANALYSIS"
[1] 3
  GOLIM4 MUTATED GOLIM4 WILD-TYPE 
              11              478 
  GOLIM4 MUTATED GOLIM4 WILD-TYPE 
              11              478 
[1] "MTMR1 MUTATION ANALYSIS"
[1] 3
  MTMR1 MUTATED MTMR1 WILD-TYPE 
             13             476 
  MTMR1 MUTATED MTMR1 WILD-TYPE 
             13             476 
[1] "TRPM6 MUTATION ANALYSIS"
[1] 3
  TRPM6 MUTATED TRPM6 WILD-TYPE 
             30             459 
  TRPM6 MUTATED TRPM6 WILD-TYPE 
             30             459 
[1] "GABRA4 MUTATION ANALYSIS"
[1] 3
  GABRA4 MUTATED GABRA4 WILD-TYPE 
              13              476 
  GABRA4 MUTATED GABRA4 WILD-TYPE 
              13              476 
[1] "C17ORF71 MUTATION ANALYSIS"
[1] 3
  C17ORF71 MUTATED C17ORF71 WILD-TYPE 
                11                478 
  C17ORF71 MUTATED C17ORF71 WILD-TYPE 
                11                478 
[1] "VCAN MUTATION ANALYSIS"
[1] 3
  VCAN MUTATED VCAN WILD-TYPE 
            43            446 
  VCAN MUTATED VCAN WILD-TYPE 
            43            446 
[1] "CDH24 MUTATION ANALYSIS"
[1] 3
  CDH24 MUTATED CDH24 WILD-TYPE 
             12             477 
  CDH24 MUTATED CDH24 WILD-TYPE 
             12             477 
[1] "SMARCA1 MUTATION ANALYSIS"
[1] 3
  SMARCA1 MUTATED SMARCA1 WILD-TYPE 
               26               463 
  SMARCA1 MUTATED SMARCA1 WILD-TYPE 
               26               463 
[1] "MORC1 MUTATION ANALYSIS"
[1] 3
  MORC1 MUTATED MORC1 WILD-TYPE 
             18             471 
  MORC1 MUTATED MORC1 WILD-TYPE 
             18             471 
[1] "ABL1 MUTATION ANALYSIS"
[1] 3
  ABL1 MUTATED ABL1 WILD-TYPE 
            30            459 
  ABL1 MUTATED ABL1 WILD-TYPE 
            30            459 
[1] "TTC13 MUTATION ANALYSIS"
[1] 3
  TTC13 MUTATED TTC13 WILD-TYPE 
             10             479 
  TTC13 MUTATED TTC13 WILD-TYPE 
             10             479 
[1] "PTPMT1 MUTATION ANALYSIS"
[1] 3
  PTPMT1 MUTATED PTPMT1 WILD-TYPE 
               7              482 
  PTPMT1 MUTATED PTPMT1 WILD-TYPE 
               7              482 
[1] "HEXIM2 MUTATION ANALYSIS"
[1] 3
  HEXIM2 MUTATED HEXIM2 WILD-TYPE 
               7              482 
  HEXIM2 MUTATED HEXIM2 WILD-TYPE 
               7              482 
[1] "ST14 MUTATION ANALYSIS"
[1] 3
  ST14 MUTATED ST14 WILD-TYPE 
            12            477 
  ST14 MUTATED ST14 WILD-TYPE 
            12            477 
[1] "DPPA2 MUTATION ANALYSIS"
[1] 3
  DPPA2 MUTATED DPPA2 WILD-TYPE 
              8             481 
  DPPA2 MUTATED DPPA2 WILD-TYPE 
              8             481 
[1] "MUC2 MUTATION ANALYSIS"
[1] 3
  MUC2 MUTATED MUC2 WILD-TYPE 
            25            464 
  MUC2 MUTATED MUC2 WILD-TYPE 
            25            464 
[1] "CTTN MUTATION ANALYSIS"
[1] 3
  CTTN MUTATED CTTN WILD-TYPE 
             5            484 
  CTTN MUTATED CTTN WILD-TYPE 
             5            484 
[1] "NFIB MUTATION ANALYSIS"
[1] 3
  NFIB MUTATED NFIB WILD-TYPE 
            14            475 
  NFIB MUTATED NFIB WILD-TYPE 
            14            475 
[1] "IFNA1 MUTATION ANALYSIS"
[1] 3
  IFNA1 MUTATED IFNA1 WILD-TYPE 
              7             482 
  IFNA1 MUTATED IFNA1 WILD-TYPE 
              7             482 
[1] "RGS3 MUTATION ANALYSIS"
[1] 3
  RGS3 MUTATED RGS3 WILD-TYPE 
            18            471 
  RGS3 MUTATED RGS3 WILD-TYPE 
            18            471 
[1] "CCDC89 MUTATION ANALYSIS"
[1] 3
  CCDC89 MUTATED CCDC89 WILD-TYPE 
               4              485 
  CCDC89 MUTATED CCDC89 WILD-TYPE 
               4              485 
[1] "MIA2 MUTATION ANALYSIS"
[1] 3
  MIA2 MUTATED MIA2 WILD-TYPE 
            12            477 
  MIA2 MUTATED MIA2 WILD-TYPE 
            12            477 
[1] "DDR2 MUTATION ANALYSIS"
[1] 3
  DDR2 MUTATED DDR2 WILD-TYPE 
            15            474 
  DDR2 MUTATED DDR2 WILD-TYPE 
            15            474 
[1] "IL3 MUTATION ANALYSIS"
[1] 3
  IL3 MUTATED IL3 WILD-TYPE 
            6           483 
  IL3 MUTATED IL3 WILD-TYPE 
            6           483 
[1] "NCF2 MUTATION ANALYSIS"
[1] 3
  NCF2 MUTATED NCF2 WILD-TYPE 
            10            479 
  NCF2 MUTATED NCF2 WILD-TYPE 
            10            479 
[1] "DCLRE1A MUTATION ANALYSIS"
[1] 3
  DCLRE1A MUTATED DCLRE1A WILD-TYPE 
               13               476 
  DCLRE1A MUTATED DCLRE1A WILD-TYPE 
               13               476 
[1] "ORC4L MUTATION ANALYSIS"
[1] 3
  ORC4L MUTATED ORC4L WILD-TYPE 
              7             482 
  ORC4L MUTATED ORC4L WILD-TYPE 
              7             482 
[1] "LRRN1 MUTATION ANALYSIS"
[1] 3
  LRRN1 MUTATED LRRN1 WILD-TYPE 
             19             470 
  LRRN1 MUTATED LRRN1 WILD-TYPE 
             19             470 
[1] "KIAA1267 MUTATION ANALYSIS"
[1] 3
  KIAA1267 MUTATED KIAA1267 WILD-TYPE 
                19                470 
  KIAA1267 MUTATED KIAA1267 WILD-TYPE 
                19                470 
[1] "RPS6KA6 MUTATION ANALYSIS"
[1] 3
  RPS6KA6 MUTATED RPS6KA6 WILD-TYPE 
               18               471 
  RPS6KA6 MUTATED RPS6KA6 WILD-TYPE 
               18               471 
[1] "GPRIN3 MUTATION ANALYSIS"
[1] 3
  GPRIN3 MUTATED GPRIN3 WILD-TYPE 
              10              479 
  GPRIN3 MUTATED GPRIN3 WILD-TYPE 
              10              479 
[1] "DHDDS MUTATION ANALYSIS"
[1] 3
  DHDDS MUTATED DHDDS WILD-TYPE 
              6             483 
  DHDDS MUTATED DHDDS WILD-TYPE 
              6             483 
[1] "ARL11 MUTATION ANALYSIS"
[1] 3
  ARL11 MUTATED ARL11 WILD-TYPE 
              7             482 
  ARL11 MUTATED ARL11 WILD-TYPE 
              7             482 
[1] "ATP2A2 MUTATION ANALYSIS"
[1] 3
  ATP2A2 MUTATED ATP2A2 WILD-TYPE 
              16              473 
  ATP2A2 MUTATED ATP2A2 WILD-TYPE 
              16              473 
[1] "HSF5 MUTATION ANALYSIS"
[1] 3
  HSF5 MUTATED HSF5 WILD-TYPE 
             8            481 
  HSF5 MUTATED HSF5 WILD-TYPE 
             8            481 
[1] "ACCN5 MUTATION ANALYSIS"
[1] 3
  ACCN5 MUTATED ACCN5 WILD-TYPE 
             14             475 
  ACCN5 MUTATED ACCN5 WILD-TYPE 
             14             475 
[1] "LRRTM2 MUTATION ANALYSIS"
[1] 3
  LRRTM2 MUTATED LRRTM2 WILD-TYPE 
               9              480 
  LRRTM2 MUTATED LRRTM2 WILD-TYPE 
               9              480 
[1] "ATR MUTATION ANALYSIS"
[1] 3
  ATR MUTATED ATR WILD-TYPE 
           33           456 
  ATR MUTATED ATR WILD-TYPE 
           33           456 
[1] "FBLIM1 MUTATION ANALYSIS"
[1] 3
  FBLIM1 MUTATED FBLIM1 WILD-TYPE 
               6              483 
  FBLIM1 MUTATED FBLIM1 WILD-TYPE 
               6              483 
[1] "CCDC14 MUTATION ANALYSIS"
[1] 3
  CCDC14 MUTATED CCDC14 WILD-TYPE 
              11              478 
  CCDC14 MUTATED CCDC14 WILD-TYPE 
              11              478 
[1] "SKAP2 MUTATION ANALYSIS"
[1] 3
  SKAP2 MUTATED SKAP2 WILD-TYPE 
              5             484 
  SKAP2 MUTATED SKAP2 WILD-TYPE 
              5             484 
[1] "MYO1D MUTATION ANALYSIS"
[1] 3
  MYO1D MUTATED MYO1D WILD-TYPE 
             11             478 
  MYO1D MUTATED MYO1D WILD-TYPE 
             11             478 
[1] "ZNF608 MUTATION ANALYSIS"
[1] 3
  ZNF608 MUTATED ZNF608 WILD-TYPE 
              13              476 
  ZNF608 MUTATED ZNF608 WILD-TYPE 
              13              476 
[1] "IDE MUTATION ANALYSIS"
[1] 3
  IDE MUTATED IDE WILD-TYPE 
           13           476 
  IDE MUTATED IDE WILD-TYPE 
           13           476 
[1] "BEX5 MUTATION ANALYSIS"
[1] 3
  BEX5 MUTATED BEX5 WILD-TYPE 
             7            482 
  BEX5 MUTATED BEX5 WILD-TYPE 
             7            482 
[1] "AGBL5 MUTATION ANALYSIS"
[1] 3
  AGBL5 MUTATED AGBL5 WILD-TYPE 
             13             476 
  AGBL5 MUTATED AGBL5 WILD-TYPE 
             13             476 
[1] "LDLR MUTATION ANALYSIS"
[1] 3
  LDLR MUTATED LDLR WILD-TYPE 
            12            477 
  LDLR MUTATED LDLR WILD-TYPE 
            12            477 
[1] "NUF2 MUTATION ANALYSIS"
[1] 3
  NUF2 MUTATED NUF2 WILD-TYPE 
            16            473 
  NUF2 MUTATED NUF2 WILD-TYPE 
            16            473 
[1] "ZNF521 MUTATION ANALYSIS"
[1] 3
  ZNF521 MUTATED ZNF521 WILD-TYPE 
              34              455 
  ZNF521 MUTATED ZNF521 WILD-TYPE 
              34              455 
[1] "OR4N2 MUTATION ANALYSIS"
[1] 3
  OR4N2 MUTATED OR4N2 WILD-TYPE 
             10             479 
  OR4N2 MUTATED OR4N2 WILD-TYPE 
             10             479 
[1] "CELSR1 MUTATION ANALYSIS"
[1] 3
  CELSR1 MUTATED CELSR1 WILD-TYPE 
              23              466 
  CELSR1 MUTATED CELSR1 WILD-TYPE 
              23              466 
[1] "SDAD1 MUTATION ANALYSIS"
[1] 3
  SDAD1 MUTATED SDAD1 WILD-TYPE 
              8             481 
  SDAD1 MUTATED SDAD1 WILD-TYPE 
              8             481 
[1] "GTDC1 MUTATION ANALYSIS"
[1] 3
  GTDC1 MUTATED GTDC1 WILD-TYPE 
             10             479 
  GTDC1 MUTATED GTDC1 WILD-TYPE 
             10             479 
[1] "PLCG1 MUTATION ANALYSIS"
[1] 3
  PLCG1 MUTATED PLCG1 WILD-TYPE 
             19             470 
  PLCG1 MUTATED PLCG1 WILD-TYPE 
             19             470 
[1] "SMC4 MUTATION ANALYSIS"
[1] 3
  SMC4 MUTATED SMC4 WILD-TYPE 
            20            469 
  SMC4 MUTATED SMC4 WILD-TYPE 
            20            469 
[1] "NDUFV2 MUTATION ANALYSIS"
[1] 3
  NDUFV2 MUTATED NDUFV2 WILD-TYPE 
               3              486 
  NDUFV2 MUTATED NDUFV2 WILD-TYPE 
               3              486 
[1] "SYT2 MUTATION ANALYSIS"
[1] 3
  SYT2 MUTATED SYT2 WILD-TYPE 
             9            480 
  SYT2 MUTATED SYT2 WILD-TYPE 
             9            480 
[1] "KIT MUTATION ANALYSIS"
[1] 3
  KIT MUTATED KIT WILD-TYPE 
          112           377 
  KIT MUTATED KIT WILD-TYPE 
          112           377 
[1] "ERMP1 MUTATION ANALYSIS"
[1] 3
  ERMP1 MUTATED ERMP1 WILD-TYPE 
             11             478 
  ERMP1 MUTATED ERMP1 WILD-TYPE 
             11             478 
[1] "NOV MUTATION ANALYSIS"
[1] 3
  NOV MUTATED NOV WILD-TYPE 
           10           479 
  NOV MUTATED NOV WILD-TYPE 
           10           479 
[1] "MYOG MUTATION ANALYSIS"
[1] 3
  MYOG MUTATED MYOG WILD-TYPE 
             6            483 
  MYOG MUTATED MYOG WILD-TYPE 
             6            483 
[1] "NTN4 MUTATION ANALYSIS"
[1] 3
  NTN4 MUTATED NTN4 WILD-TYPE 
             9            480 
  NTN4 MUTATED NTN4 WILD-TYPE 
             9            480 
[1] "XRN1 MUTATION ANALYSIS"
[1] 3
  XRN1 MUTATED XRN1 WILD-TYPE 
            24            465 
  XRN1 MUTATED XRN1 WILD-TYPE 
            24            465 
[1] "FAM175A MUTATION ANALYSIS"
[1] 3
  FAM175A MUTATED FAM175A WILD-TYPE 
                8               481 
  FAM175A MUTATED FAM175A WILD-TYPE 
                8               481 
[1] "CSF3R MUTATION ANALYSIS"
[1] 3
  CSF3R MUTATED CSF3R WILD-TYPE 
             15             474 
  CSF3R MUTATED CSF3R WILD-TYPE 
             15             474 
[1] "RAB22A MUTATION ANALYSIS"
[1] 3
  RAB22A MUTATED RAB22A WILD-TYPE 
               3              486 
  RAB22A MUTATED RAB22A WILD-TYPE 
               3              486 
[1] "SAMD4A MUTATION ANALYSIS"
[1] 3
  SAMD4A MUTATED SAMD4A WILD-TYPE 
              11              478 
  SAMD4A MUTATED SAMD4A WILD-TYPE 
              11              478 
[1] "CCDC11 MUTATION ANALYSIS"
[1] 3
  CCDC11 MUTATED CCDC11 WILD-TYPE 
              10              479 
  CCDC11 MUTATED CCDC11 WILD-TYPE 
              10              479 
[1] "TRPM2 MUTATION ANALYSIS"
[1] 3
  TRPM2 MUTATED TRPM2 WILD-TYPE 
             26             463 
  TRPM2 MUTATED TRPM2 WILD-TYPE 
             26             463 
[1] "TRIP12 MUTATION ANALYSIS"
[1] 3
  TRIP12 MUTATED TRIP12 WILD-TYPE 
              31              458 
  TRIP12 MUTATED TRIP12 WILD-TYPE 
              31              458 
[1] "BBS2 MUTATION ANALYSIS"
[1] 3
  BBS2 MUTATED BBS2 WILD-TYPE 
            14            475 
  BBS2 MUTATED BBS2 WILD-TYPE 
            14            475 
[1] "PDGFC MUTATION ANALYSIS"
[1] 3
  PDGFC MUTATED PDGFC WILD-TYPE 
             10             479 
  PDGFC MUTATED PDGFC WILD-TYPE 
             10             479 
[1] "KIF13A MUTATION ANALYSIS"
[1] 3
  KIF13A MUTATED KIF13A WILD-TYPE 
              22              467 
  KIF13A MUTATED KIF13A WILD-TYPE 
              22              467 
[1] "KNTC1 MUTATION ANALYSIS"
[1] 3
  KNTC1 MUTATED KNTC1 WILD-TYPE 
             25             464 
  KNTC1 MUTATED KNTC1 WILD-TYPE 
             25             464 
[1] "TRIM45 MUTATION ANALYSIS"
[1] 3
  TRIM45 MUTATED TRIM45 WILD-TYPE 
              14              475 
  TRIM45 MUTATED TRIM45 WILD-TYPE 
              14              475 
[1] "UEVLD MUTATION ANALYSIS"
[1] 3
  UEVLD MUTATED UEVLD WILD-TYPE 
              4             485 
  UEVLD MUTATED UEVLD WILD-TYPE 
              4             485 
[1] "PEX2 MUTATION ANALYSIS"
[1] 3
  PEX2 MUTATED PEX2 WILD-TYPE 
            10            479 
  PEX2 MUTATED PEX2 WILD-TYPE 
            10            479 
[1] "C16ORF71 MUTATION ANALYSIS"
[1] 3
  C16ORF71 MUTATED C16ORF71 WILD-TYPE 
                 7                482 
  C16ORF71 MUTATED C16ORF71 WILD-TYPE 
                 7                482 
[1] "SLC6A3 MUTATION ANALYSIS"
[1] 3
  SLC6A3 MUTATED SLC6A3 WILD-TYPE 
               8              481 
  SLC6A3 MUTATED SLC6A3 WILD-TYPE 
               8              481 
[1] "MLNR MUTATION ANALYSIS"
[1] 3
  MLNR MUTATED MLNR WILD-TYPE 
             4            485 
  MLNR MUTATED MLNR WILD-TYPE 
             4            485 
[1] "GSK3B MUTATION ANALYSIS"
[1] 3
  GSK3B MUTATED GSK3B WILD-TYPE 
             15             474 
  GSK3B MUTATED GSK3B WILD-TYPE 
             15             474 
[1] "ZNF462 MUTATION ANALYSIS"
[1] 3
  ZNF462 MUTATED ZNF462 WILD-TYPE 
              28              461 
  ZNF462 MUTATED ZNF462 WILD-TYPE 
              28              461 
[1] "HOXD9 MUTATION ANALYSIS"
[1] 3
  HOXD9 MUTATED HOXD9 WILD-TYPE 
              5             484 
  HOXD9 MUTATED HOXD9 WILD-TYPE 
              5             484 
[1] "MGEA5 MUTATION ANALYSIS"
[1] 3
  MGEA5 MUTATED MGEA5 WILD-TYPE 
              8             481 
  MGEA5 MUTATED MGEA5 WILD-TYPE 
              8             481 
[1] "C7ORF33 MUTATION ANALYSIS"
[1] 3
  C7ORF33 MUTATED C7ORF33 WILD-TYPE 
                6               483 
  C7ORF33 MUTATED C7ORF33 WILD-TYPE 
                6               483 
[1] "ATP2C2 MUTATION ANALYSIS"
[1] 3
  ATP2C2 MUTATED ATP2C2 WILD-TYPE 
              11              478 
  ATP2C2 MUTATED ATP2C2 WILD-TYPE 
              11              478 
[1] "DCAF8L1 MUTATION ANALYSIS"
[1] 3
  DCAF8L1 MUTATED DCAF8L1 WILD-TYPE 
               18               471 
  DCAF8L1 MUTATED DCAF8L1 WILD-TYPE 
               18               471 
[1] "CENPA MUTATION ANALYSIS"
[1] 3
  CENPA MUTATED CENPA WILD-TYPE 
              5             484 
  CENPA MUTATED CENPA WILD-TYPE 
              5             484 
[1] "MST1R MUTATION ANALYSIS"
[1] 3
  MST1R MUTATED MST1R WILD-TYPE 
             14             475 
  MST1R MUTATED MST1R WILD-TYPE 
             14             475 
[1] "NONO MUTATION ANALYSIS"
[1] 3
  NONO MUTATED NONO WILD-TYPE 
            12            477 
  NONO MUTATED NONO WILD-TYPE 
            12            477 
[1] "CYP2C9 MUTATION ANALYSIS"
[1] 3
  CYP2C9 MUTATED CYP2C9 WILD-TYPE 
               9              480 
  CYP2C9 MUTATED CYP2C9 WILD-TYPE 
               9              480 
[1] "ADAM33 MUTATION ANALYSIS"
[1] 3
  ADAM33 MUTATED ADAM33 WILD-TYPE 
               7              482 
  ADAM33 MUTATED ADAM33 WILD-TYPE 
               7              482 
[1] "DYRK4 MUTATION ANALYSIS"
[1] 3
  DYRK4 MUTATED DYRK4 WILD-TYPE 
             14             475 
  DYRK4 MUTATED DYRK4 WILD-TYPE 
             14             475 
[1] "ZMIZ1 MUTATION ANALYSIS"
[1] 3
  ZMIZ1 MUTATED ZMIZ1 WILD-TYPE 
             11             478 
  ZMIZ1 MUTATED ZMIZ1 WILD-TYPE 
             11             478 
[1] "NLRP8 MUTATION ANALYSIS"
[1] 3
  NLRP8 MUTATED NLRP8 WILD-TYPE 
             28             461 
  NLRP8 MUTATED NLRP8 WILD-TYPE 
             28             461 
[1] "RALGAPB MUTATION ANALYSIS"
[1] 3
  RALGAPB MUTATED RALGAPB WILD-TYPE 
               15               474 
  RALGAPB MUTATED RALGAPB WILD-TYPE 
               15               474 
[1] "DCLRE1C MUTATION ANALYSIS"
[1] 3
  DCLRE1C MUTATED DCLRE1C WILD-TYPE 
               12               477 
  DCLRE1C MUTATED DCLRE1C WILD-TYPE 
               12               477 
[1] "SLC9A9 MUTATION ANALYSIS"
[1] 3
  SLC9A9 MUTATED SLC9A9 WILD-TYPE 
              23              466 
  SLC9A9 MUTATED SLC9A9 WILD-TYPE 
              23              466 
[1] "C17ORF58 MUTATION ANALYSIS"
[1] 3
  C17ORF58 MUTATED C17ORF58 WILD-TYPE 
                 3                486 
  C17ORF58 MUTATED C17ORF58 WILD-TYPE 
                 3                486 
[1] "GORASP1 MUTATION ANALYSIS"
[1] 3
  GORASP1 MUTATED GORASP1 WILD-TYPE 
               11               478 
  GORASP1 MUTATED GORASP1 WILD-TYPE 
               11               478 
[1] "RAD18 MUTATION ANALYSIS"
[1] 3
  RAD18 MUTATED RAD18 WILD-TYPE 
             15             474 
  RAD18 MUTATED RAD18 WILD-TYPE 
             15             474 
[1] "ZCWPW2 MUTATION ANALYSIS"
[1] 3
  ZCWPW2 MUTATED ZCWPW2 WILD-TYPE 
              14              475 
  ZCWPW2 MUTATED ZCWPW2 WILD-TYPE 
              14              475 
[1] "OR5H1 MUTATION ANALYSIS"
[1] 3
  OR5H1 MUTATED OR5H1 WILD-TYPE 
             10             479 
  OR5H1 MUTATED OR5H1 WILD-TYPE 
             10             479 
[1] "MDM2 MUTATION ANALYSIS"
[1] 3
  MDM2 MUTATED MDM2 WILD-TYPE 
             9            480 
  MDM2 MUTATED MDM2 WILD-TYPE 
             9            480 
[1] "ROR1 MUTATION ANALYSIS"
[1] 3
  ROR1 MUTATED ROR1 WILD-TYPE 
            23            466 
  ROR1 MUTATED ROR1 WILD-TYPE 
            23            466 
[1] "BATF MUTATION ANALYSIS"
[1] 3
  BATF MUTATED BATF WILD-TYPE 
             3            486 
  BATF MUTATED BATF WILD-TYPE 
             3            486 
[1] "RNASE2 MUTATION ANALYSIS"
[1] 3
  RNASE2 MUTATED RNASE2 WILD-TYPE 
               5              484 
  RNASE2 MUTATED RNASE2 WILD-TYPE 
               5              484 
[1] "TRIO MUTATION ANALYSIS"
[1] 3
  TRIO MUTATED TRIO WILD-TYPE 
            32            457 
  TRIO MUTATED TRIO WILD-TYPE 
            32            457 
[1] "CTSL1 MUTATION ANALYSIS"
[1] 3
  CTSL1 MUTATED CTSL1 WILD-TYPE 
              8             481 
  CTSL1 MUTATED CTSL1 WILD-TYPE 
              8             481 
[1] "KIF5B MUTATION ANALYSIS"
[1] 3
  KIF5B MUTATED KIF5B WILD-TYPE 
             17             472 
  KIF5B MUTATED KIF5B WILD-TYPE 
             17             472 
[1] "TMEM41B MUTATION ANALYSIS"
[1] 3
  TMEM41B MUTATED TMEM41B WILD-TYPE 
                5               484 
  TMEM41B MUTATED TMEM41B WILD-TYPE 
                5               484 
[1] "NUDT16L1 MUTATION ANALYSIS"
[1] 3
  NUDT16L1 MUTATED NUDT16L1 WILD-TYPE 
                 3                486 
  NUDT16L1 MUTATED NUDT16L1 WILD-TYPE 
                 3                486 
[1] "SEMA3A MUTATION ANALYSIS"
[1] 3
  SEMA3A MUTATED SEMA3A WILD-TYPE 
              16              473 
  SEMA3A MUTATED SEMA3A WILD-TYPE 
              16              473 
[1] "PCDHGA4 MUTATION ANALYSIS"
[1] 3
  PCDHGA4 MUTATED PCDHGA4 WILD-TYPE 
               19               470 
  PCDHGA4 MUTATED PCDHGA4 WILD-TYPE 
               19               470 
[1] "SNX33 MUTATION ANALYSIS"
[1] 3
  SNX33 MUTATED SNX33 WILD-TYPE 
             11             478 
  SNX33 MUTATED SNX33 WILD-TYPE 
             11             478 
[1] "BATF3 MUTATION ANALYSIS"
[1] 3
  BATF3 MUTATED BATF3 WILD-TYPE 
              4             485 
  BATF3 MUTATED BATF3 WILD-TYPE 
              4             485 
[1] "KBTBD8 MUTATION ANALYSIS"
[1] 3
  KBTBD8 MUTATED KBTBD8 WILD-TYPE 
               8              481 
  KBTBD8 MUTATED KBTBD8 WILD-TYPE 
               8              481 
[1] "RHBDD1 MUTATION ANALYSIS"
[1] 3
  RHBDD1 MUTATED RHBDD1 WILD-TYPE 
               8              481 
  RHBDD1 MUTATED RHBDD1 WILD-TYPE 
               8              481 
[1] "CPEB1 MUTATION ANALYSIS"
[1] 3
  CPEB1 MUTATED CPEB1 WILD-TYPE 
              7             482 
  CPEB1 MUTATED CPEB1 WILD-TYPE 
              7             482 
[1] "SKIV2L2 MUTATION ANALYSIS"
[1] 3
  SKIV2L2 MUTATED SKIV2L2 WILD-TYPE 
               13               476 
  SKIV2L2 MUTATED SKIV2L2 WILD-TYPE 
               13               476 
[1] "AMPD1 MUTATION ANALYSIS"
[1] 3
  AMPD1 MUTATED AMPD1 WILD-TYPE 
             18             471 
  AMPD1 MUTATED AMPD1 WILD-TYPE 
             18             471 
[1] "MIPEP MUTATION ANALYSIS"
[1] 3
  MIPEP MUTATED MIPEP WILD-TYPE 
              9             480 
  MIPEP MUTATED MIPEP WILD-TYPE 
              9             480 
[1] "KRT39 MUTATION ANALYSIS"
[1] 3
  KRT39 MUTATED KRT39 WILD-TYPE 
              7             482 
  KRT39 MUTATED KRT39 WILD-TYPE 
              7             482 
[1] "DDX11 MUTATION ANALYSIS"
[1] 3
  DDX11 MUTATED DDX11 WILD-TYPE 
              8             481 
  DDX11 MUTATED DDX11 WILD-TYPE 
              8             481 
[1] "VEPH1 MUTATION ANALYSIS"
[1] 3
  VEPH1 MUTATED VEPH1 WILD-TYPE 
             20             469 
  VEPH1 MUTATED VEPH1 WILD-TYPE 
             20             469 
[1] "OR2M5 MUTATION ANALYSIS"
[1] 3
  OR2M5 MUTATED OR2M5 WILD-TYPE 
             12             477 
  OR2M5 MUTATED OR2M5 WILD-TYPE 
             12             477 
[1] "RBP3 MUTATION ANALYSIS"
[1] 3
  RBP3 MUTATED RBP3 WILD-TYPE 
            14            475 
  RBP3 MUTATED RBP3 WILD-TYPE 
            14            475 
[1] "SGCE MUTATION ANALYSIS"
[1] 3
  SGCE MUTATED SGCE WILD-TYPE 
             8            481 
  SGCE MUTATED SGCE WILD-TYPE 
             8            481 
[1] "ZNF622 MUTATION ANALYSIS"
[1] 3
  ZNF622 MUTATED ZNF622 WILD-TYPE 
               9              480 
  ZNF622 MUTATED ZNF622 WILD-TYPE 
               9              480 
[1] "FAM160B1 MUTATION ANALYSIS"
[1] 3
  FAM160B1 MUTATED FAM160B1 WILD-TYPE 
                 9                480 
  FAM160B1 MUTATED FAM160B1 WILD-TYPE 
                 9                480 
[1] "UBD MUTATION ANALYSIS"
[1] 3
  UBD MUTATED UBD WILD-TYPE 
            4           485 
  UBD MUTATED UBD WILD-TYPE 
            4           485 
[1] "OR8K1 MUTATION ANALYSIS"
[1] 3
  OR8K1 MUTATED OR8K1 WILD-TYPE 
             13             476 
  OR8K1 MUTATED OR8K1 WILD-TYPE 
             13             476 
[1] "TAB1 MUTATION ANALYSIS"
[1] 3
  TAB1 MUTATED TAB1 WILD-TYPE 
             3            486 
  TAB1 MUTATED TAB1 WILD-TYPE 
             3            486 
[1] "SLC30A8 MUTATION ANALYSIS"
[1] 3
  SLC30A8 MUTATED SLC30A8 WILD-TYPE 
               17               472 
  SLC30A8 MUTATED SLC30A8 WILD-TYPE 
               17               472 
[1] "MPZL1 MUTATION ANALYSIS"
[1] 3
  MPZL1 MUTATED MPZL1 WILD-TYPE 
              7             482 
  MPZL1 MUTATED MPZL1 WILD-TYPE 
              7             482 
[1] "CCDC112 MUTATION ANALYSIS"
[1] 3
  CCDC112 MUTATED CCDC112 WILD-TYPE 
                9               480 
  CCDC112 MUTATED CCDC112 WILD-TYPE 
                9               480 
[1] "TOMM70A MUTATION ANALYSIS"
[1] 3
  TOMM70A MUTATED TOMM70A WILD-TYPE 
               10               479 
  TOMM70A MUTATED TOMM70A WILD-TYPE 
               10               479 
[1] "CDHR3 MUTATION ANALYSIS"
[1] 3
  CDHR3 MUTATED CDHR3 WILD-TYPE 
             15             474 
  CDHR3 MUTATED CDHR3 WILD-TYPE 
             15             474 
[1] "ZNF559 MUTATION ANALYSIS"
[1] 3
  ZNF559 MUTATED ZNF559 WILD-TYPE 
              16              473 
  ZNF559 MUTATED ZNF559 WILD-TYPE 
              16              473 
[1] "MAK MUTATION ANALYSIS"
[1] 3
  MAK MUTATED MAK WILD-TYPE 
           12           477 
  MAK MUTATED MAK WILD-TYPE 
           12           477 
[1] "GPR156 MUTATION ANALYSIS"
[1] 3
  GPR156 MUTATED GPR156 WILD-TYPE 
              14              475 
  GPR156 MUTATED GPR156 WILD-TYPE 
              14              475 
[1] "NIT2 MUTATION ANALYSIS"
[1] 3
  NIT2 MUTATED NIT2 WILD-TYPE 
             5            484 
  NIT2 MUTATED NIT2 WILD-TYPE 
             5            484 
[1] "KIAA2018 MUTATION ANALYSIS"
[1] 3
  KIAA2018 MUTATED KIAA2018 WILD-TYPE 
                22                467 
  KIAA2018 MUTATED KIAA2018 WILD-TYPE 
                22                467 
[1] "DCAF12L2 MUTATION ANALYSIS"
[1] 3
  DCAF12L2 MUTATED DCAF12L2 WILD-TYPE 
                20                469 
  DCAF12L2 MUTATED DCAF12L2 WILD-TYPE 
                20                469 
[1] "BMP10 MUTATION ANALYSIS"
[1] 3
  BMP10 MUTATED BMP10 WILD-TYPE 
             14             475 
  BMP10 MUTATED BMP10 WILD-TYPE 
             14             475 
[1] "FOXO4 MUTATION ANALYSIS"
[1] 3
  FOXO4 MUTATED FOXO4 WILD-TYPE 
             13             476 
  FOXO4 MUTATED FOXO4 WILD-TYPE 
             13             476 
[1] "SLITRK2 MUTATION ANALYSIS"
[1] 3
  SLITRK2 MUTATED SLITRK2 WILD-TYPE 
               26               463 
  SLITRK2 MUTATED SLITRK2 WILD-TYPE 
               26               463 
[1] "MTF2 MUTATION ANALYSIS"
[1] 3
  MTF2 MUTATED MTF2 WILD-TYPE 
             9            480 
  MTF2 MUTATED MTF2 WILD-TYPE 
             9            480 
[1] "UBA7 MUTATION ANALYSIS"
[1] 3
  UBA7 MUTATED UBA7 WILD-TYPE 
            12            477 
  UBA7 MUTATED UBA7 WILD-TYPE 
            12            477 
[1] "MICAL1 MUTATION ANALYSIS"
[1] 3
  MICAL1 MUTATED MICAL1 WILD-TYPE 
               9              480 
  MICAL1 MUTATED MICAL1 WILD-TYPE 
               9              480 
[1] "TSPYL4 MUTATION ANALYSIS"
[1] 3
  TSPYL4 MUTATED TSPYL4 WILD-TYPE 
               4              485 
  TSPYL4 MUTATED TSPYL4 WILD-TYPE 
               4              485 
[1] "ZNF41 MUTATION ANALYSIS"
[1] 3
  ZNF41 MUTATED ZNF41 WILD-TYPE 
             11             478 
  ZNF41 MUTATED ZNF41 WILD-TYPE 
             11             478 
[1] "SLC26A7 MUTATION ANALYSIS"
[1] 3
  SLC26A7 MUTATED SLC26A7 WILD-TYPE 
               18               471 
  SLC26A7 MUTATED SLC26A7 WILD-TYPE 
               18               471 
[1] "ARMC2 MUTATION ANALYSIS"
[1] 3
  ARMC2 MUTATED ARMC2 WILD-TYPE 
              8             481 
  ARMC2 MUTATED ARMC2 WILD-TYPE 
              8             481 
[1] "RAGE MUTATION ANALYSIS"
[1] 3
  RAGE MUTATED RAGE WILD-TYPE 
             9            480 
  RAGE MUTATED RAGE WILD-TYPE 
             9            480 
[1] "TNNT2 MUTATION ANALYSIS"
[1] 3
  TNNT2 MUTATED TNNT2 WILD-TYPE 
              8             481 
  TNNT2 MUTATED TNNT2 WILD-TYPE 
              8             481 
[1] "CDH8 MUTATION ANALYSIS"
[1] 3
  CDH8 MUTATED CDH8 WILD-TYPE 
            40            449 
  CDH8 MUTATED CDH8 WILD-TYPE 
            40            449 
[1] "ADAM17 MUTATION ANALYSIS"
[1] 3
  ADAM17 MUTATED ADAM17 WILD-TYPE 
              13              476 
  ADAM17 MUTATED ADAM17 WILD-TYPE 
              13              476 
[1] "CHMP4B MUTATION ANALYSIS"
[1] 3
  CHMP4B MUTATED CHMP4B WILD-TYPE 
               3              486 
  CHMP4B MUTATED CHMP4B WILD-TYPE 
               3              486 
[1] "TMPRSS5 MUTATION ANALYSIS"
[1] 3
  TMPRSS5 MUTATED TMPRSS5 WILD-TYPE 
                7               482 
  TMPRSS5 MUTATED TMPRSS5 WILD-TYPE 
                7               482 
[1] "TTR MUTATION ANALYSIS"
[1] 3
  TTR MUTATED TTR WILD-TYPE 
            4           485 
  TTR MUTATED TTR WILD-TYPE 
            4           485 
[1] "TBC1D25 MUTATION ANALYSIS"
[1] 3
  TBC1D25 MUTATED TBC1D25 WILD-TYPE 
               11               478 
  TBC1D25 MUTATED TBC1D25 WILD-TYPE 
               11               478 
[1] "ZNF418 MUTATION ANALYSIS"
[1] 3
  ZNF418 MUTATED ZNF418 WILD-TYPE 
              14              475 
  ZNF418 MUTATED ZNF418 WILD-TYPE 
              14              475 
[1] "FOXA2 MUTATION ANALYSIS"
[1] 3
  FOXA2 MUTATED FOXA2 WILD-TYPE 
              7             482 
  FOXA2 MUTATED FOXA2 WILD-TYPE 
              7             482 
[1] "GSTM4 MUTATION ANALYSIS"
[1] 3
  GSTM4 MUTATED GSTM4 WILD-TYPE 
              6             483 
  GSTM4 MUTATED GSTM4 WILD-TYPE 
              6             483 
[1] "PCDHGC4 MUTATION ANALYSIS"
[1] 3
  PCDHGC4 MUTATED PCDHGC4 WILD-TYPE 
               15               474 
  PCDHGC4 MUTATED PCDHGC4 WILD-TYPE 
               15               474 
[1] "KIAA1967 MUTATION ANALYSIS"
[1] 3
  KIAA1967 MUTATED KIAA1967 WILD-TYPE 
                12                477 
  KIAA1967 MUTATED KIAA1967 WILD-TYPE 
                12                477 
[1] "CPB1 MUTATION ANALYSIS"
[1] 3
  CPB1 MUTATED CPB1 WILD-TYPE 
             9            480 
  CPB1 MUTATED CPB1 WILD-TYPE 
             9            480 
[1] "PTPN1 MUTATION ANALYSIS"
[1] 3
  PTPN1 MUTATED PTPN1 WILD-TYPE 
             10             479 
  PTPN1 MUTATED PTPN1 WILD-TYPE 
             10             479 
[1] "ZNF266 MUTATION ANALYSIS"
[1] 3
  ZNF266 MUTATED ZNF266 WILD-TYPE 
               9              480 
  ZNF266 MUTATED ZNF266 WILD-TYPE 
               9              480 
[1] "BHLHE41 MUTATION ANALYSIS"
[1] 3
  BHLHE41 MUTATED BHLHE41 WILD-TYPE 
                5               484 
  BHLHE41 MUTATED BHLHE41 WILD-TYPE 
                5               484 
[1] "ADAMTS16 MUTATION ANALYSIS"
[1] 3
  ADAMTS16 MUTATED ADAMTS16 WILD-TYPE 
                33                456 
  ADAMTS16 MUTATED ADAMTS16 WILD-TYPE 
                33                456 
[1] "MCM9 MUTATION ANALYSIS"
[1] 3
  MCM9 MUTATED MCM9 WILD-TYPE 
             9            480 
  MCM9 MUTATED MCM9 WILD-TYPE 
             9            480 
[1] "NSF MUTATION ANALYSIS"
[1] 3
  NSF MUTATED NSF WILD-TYPE 
            4           485 
  NSF MUTATED NSF WILD-TYPE 
            4           485 
[1] "SAMD11 MUTATION ANALYSIS"
[1] 3
  SAMD11 MUTATED SAMD11 WILD-TYPE 
               6              483 
  SAMD11 MUTATED SAMD11 WILD-TYPE 
               6              483 
[1] "MMP19 MUTATION ANALYSIS"
[1] 3
  MMP19 MUTATED MMP19 WILD-TYPE 
             12             477 
  MMP19 MUTATED MMP19 WILD-TYPE 
             12             477 
[1] "ATG10 MUTATION ANALYSIS"
[1] 3
  ATG10 MUTATED ATG10 WILD-TYPE 
              5             484 
  ATG10 MUTATED ATG10 WILD-TYPE 
              5             484 
[1] "TMSB15B MUTATION ANALYSIS"
[1] 3
  TMSB15B MUTATED TMSB15B WILD-TYPE 
                4               485 
  TMSB15B MUTATED TMSB15B WILD-TYPE 
                4               485 
[1] "GIMAP8 MUTATION ANALYSIS"
[1] 3
  GIMAP8 MUTATED GIMAP8 WILD-TYPE 
              21              468 
  GIMAP8 MUTATED GIMAP8 WILD-TYPE 
              21              468 
[1] "TNXB MUTATION ANALYSIS"
[1] 3
  TNXB MUTATED TNXB WILD-TYPE 
            43            446 
  TNXB MUTATED TNXB WILD-TYPE 
            43            446 
[1] "FBXL19 MUTATION ANALYSIS"
[1] 3
  FBXL19 MUTATED FBXL19 WILD-TYPE 
               7              482 
  FBXL19 MUTATED FBXL19 WILD-TYPE 
               7              482 
[1] "ANKRD6 MUTATION ANALYSIS"
[1] 3
  ANKRD6 MUTATED ANKRD6 WILD-TYPE 
              13              476 
  ANKRD6 MUTATED ANKRD6 WILD-TYPE 
              13              476 
[1] "WDR17 MUTATION ANALYSIS"
[1] 3
  WDR17 MUTATED WDR17 WILD-TYPE 
             26             463 
  WDR17 MUTATED WDR17 WILD-TYPE 
             26             463 
[1] "MRPL47 MUTATION ANALYSIS"
[1] 3
  MRPL47 MUTATED MRPL47 WILD-TYPE 
               6              483 
  MRPL47 MUTATED MRPL47 WILD-TYPE 
               6              483 
[1] "TRPV2 MUTATION ANALYSIS"
[1] 3
  TRPV2 MUTATED TRPV2 WILD-TYPE 
             12             477 
  TRPV2 MUTATED TRPV2 WILD-TYPE 
             12             477 
[1] "RAG1 MUTATION ANALYSIS"
[1] 3
  RAG1 MUTATED RAG1 WILD-TYPE 
            17            472 
  RAG1 MUTATED RAG1 WILD-TYPE 
            17            472 
[1] "IL8 MUTATION ANALYSIS"
[1] 3
  IL8 MUTATED IL8 WILD-TYPE 
            6           483 
  IL8 MUTATED IL8 WILD-TYPE 
            6           483 
[1] "CLTCL1 MUTATION ANALYSIS"
[1] 3
  CLTCL1 MUTATED CLTCL1 WILD-TYPE 
              20              469 
  CLTCL1 MUTATED CLTCL1 WILD-TYPE 
              20              469 
[1] "DCTN4 MUTATION ANALYSIS"
[1] 3
  DCTN4 MUTATED DCTN4 WILD-TYPE 
              6             483 
  DCTN4 MUTATED DCTN4 WILD-TYPE 
              6             483 
[1] "KLRK1 MUTATION ANALYSIS"
[1] 3
  KLRK1 MUTATED KLRK1 WILD-TYPE 
              8             481 
  KLRK1 MUTATED KLRK1 WILD-TYPE 
              8             481 
[1] "MGAT5 MUTATION ANALYSIS"
[1] 3
  MGAT5 MUTATED MGAT5 WILD-TYPE 
             13             476 
  MGAT5 MUTATED MGAT5 WILD-TYPE 
             13             476 
[1] "SPANXN3 MUTATION ANALYSIS"
[1] 3
  SPANXN3 MUTATED SPANXN3 WILD-TYPE 
                9               480 
  SPANXN3 MUTATED SPANXN3 WILD-TYPE 
                9               480 
[1] "CYP27B1 MUTATION ANALYSIS"
[1] 3
  CYP27B1 MUTATED CYP27B1 WILD-TYPE 
                8               481 
  CYP27B1 MUTATED CYP27B1 WILD-TYPE 
                8               481 
[1] "CASC5 MUTATION ANALYSIS"
[1] 3
  CASC5 MUTATED CASC5 WILD-TYPE 
             22             467 
  CASC5 MUTATED CASC5 WILD-TYPE 
             22             467 
[1] "PRKCG MUTATION ANALYSIS"
[1] 3
  PRKCG MUTATED PRKCG WILD-TYPE 
             24             465 
  PRKCG MUTATED PRKCG WILD-TYPE 
             24             465 
[1] "COL11A1 MUTATION ANALYSIS"
[1] 3
  COL11A1 MUTATED COL11A1 WILD-TYPE 
               52               437 
  COL11A1 MUTATED COL11A1 WILD-TYPE 
               52               437 
[1] "OR5L2 MUTATION ANALYSIS"
[1] 3
  OR5L2 MUTATED OR5L2 WILD-TYPE 
             15             474 
  OR5L2 MUTATED OR5L2 WILD-TYPE 
             15             474 
[1] "EHBP1L1 MUTATION ANALYSIS"
[1] 3
  EHBP1L1 MUTATED EHBP1L1 WILD-TYPE 
                8               481 
  EHBP1L1 MUTATED EHBP1L1 WILD-TYPE 
                8               481 
[1] "CNOT6L MUTATION ANALYSIS"
[1] 3
  CNOT6L MUTATED CNOT6L WILD-TYPE 
               7              482 
  CNOT6L MUTATED CNOT6L WILD-TYPE 
               7              482 
[1] "C3ORF27 MUTATION ANALYSIS"
[1] 3
  C3ORF27 MUTATED C3ORF27 WILD-TYPE 
                3               486 
  C3ORF27 MUTATED C3ORF27 WILD-TYPE 
                3               486 
[1] "TNFRSF13B MUTATION ANALYSIS"
[1] 3
  TNFRSF13B MUTATED TNFRSF13B WILD-TYPE 
                  7                 482 
  TNFRSF13B MUTATED TNFRSF13B WILD-TYPE 
                  7                 482 
[1] "OTUD4 MUTATION ANALYSIS"
[1] 3
  OTUD4 MUTATED OTUD4 WILD-TYPE 
             20             469 
  OTUD4 MUTATED OTUD4 WILD-TYPE 
             20             469 
[1] "MYO5A MUTATION ANALYSIS"
[1] 3
  MYO5A MUTATED MYO5A WILD-TYPE 
             23             466 
  MYO5A MUTATED MYO5A WILD-TYPE 
             23             466 
[1] "MNT MUTATION ANALYSIS"
[1] 3
  MNT MUTATED MNT WILD-TYPE 
            8           481 
  MNT MUTATED MNT WILD-TYPE 
            8           481 
[1] "CAMK1 MUTATION ANALYSIS"
[1] 3
  CAMK1 MUTATED CAMK1 WILD-TYPE 
              8             481 
  CAMK1 MUTATED CAMK1 WILD-TYPE 
              8             481 
[1] "SRRM3 MUTATION ANALYSIS"
[1] 3
  SRRM3 MUTATED SRRM3 WILD-TYPE 
              3             486 
  SRRM3 MUTATED SRRM3 WILD-TYPE 
              3             486 
[1] "SFRS12IP1 MUTATION ANALYSIS"
[1] 3
  SFRS12IP1 MUTATED SFRS12IP1 WILD-TYPE 
                  5                 484 
  SFRS12IP1 MUTATED SFRS12IP1 WILD-TYPE 
                  5                 484 
[1] "SBF1 MUTATION ANALYSIS"
[1] 3
  SBF1 MUTATED SBF1 WILD-TYPE 
            16            473 
  SBF1 MUTATED SBF1 WILD-TYPE 
            16            473 
[1] "MYST3 MUTATION ANALYSIS"
[1] 3
  MYST3 MUTATED MYST3 WILD-TYPE 
             27             462 
  MYST3 MUTATED MYST3 WILD-TYPE 
             27             462 
[1] "ZNF846 MUTATION ANALYSIS"
[1] 3
  ZNF846 MUTATED ZNF846 WILD-TYPE 
              10              479 
  ZNF846 MUTATED ZNF846 WILD-TYPE 
              10              479 
[1] "TEX11 MUTATION ANALYSIS"
[1] 3
  TEX11 MUTATED TEX11 WILD-TYPE 
             21             468 
  TEX11 MUTATED TEX11 WILD-TYPE 
             21             468 
[1] "ZP3 MUTATION ANALYSIS"
[1] 3
  ZP3 MUTATED ZP3 WILD-TYPE 
            7           482 
  ZP3 MUTATED ZP3 WILD-TYPE 
            7           482 
[1] "GLI4 MUTATION ANALYSIS"
[1] 3
  GLI4 MUTATED GLI4 WILD-TYPE 
             5            484 
  GLI4 MUTATED GLI4 WILD-TYPE 
             5            484 
[1] "SORBS1 MUTATION ANALYSIS"
[1] 3
  SORBS1 MUTATED SORBS1 WILD-TYPE 
              12              477 
  SORBS1 MUTATED SORBS1 WILD-TYPE 
              12              477 
[1] "ITGA2 MUTATION ANALYSIS"
[1] 3
  ITGA2 MUTATED ITGA2 WILD-TYPE 
              9             480 
  ITGA2 MUTATED ITGA2 WILD-TYPE 
              9             480 
[1] "PRSS27 MUTATION ANALYSIS"
[1] 3
  PRSS27 MUTATED PRSS27 WILD-TYPE 
               4              485 
  PRSS27 MUTATED PRSS27 WILD-TYPE 
               4              485 
[1] "GLT25D1 MUTATION ANALYSIS"
[1] 3
  GLT25D1 MUTATED GLT25D1 WILD-TYPE 
                9               480 
  GLT25D1 MUTATED GLT25D1 WILD-TYPE 
                9               480 
[1] "FAM167B MUTATION ANALYSIS"
[1] 3
  FAM167B MUTATED FAM167B WILD-TYPE 
                4               485 
  FAM167B MUTATED FAM167B WILD-TYPE 
                4               485 
[1] "OR5AN1 MUTATION ANALYSIS"
[1] 3
  OR5AN1 MUTATED OR5AN1 WILD-TYPE 
               6              483 
  OR5AN1 MUTATED OR5AN1 WILD-TYPE 
               6              483 
[1] "SETD7 MUTATION ANALYSIS"
[1] 3
  SETD7 MUTATED SETD7 WILD-TYPE 
              9             480 
  SETD7 MUTATED SETD7 WILD-TYPE 
              9             480 
[1] "ARHGAP10 MUTATION ANALYSIS"
[1] 3
  ARHGAP10 MUTATED ARHGAP10 WILD-TYPE 
                 9                480 
  ARHGAP10 MUTATED ARHGAP10 WILD-TYPE 
                 9                480 
[1] "C9ORF102 MUTATION ANALYSIS"
[1] 3
  C9ORF102 MUTATED C9ORF102 WILD-TYPE 
                10                479 
  C9ORF102 MUTATED C9ORF102 WILD-TYPE 
                10                479 
[1] "LRMP MUTATION ANALYSIS"
[1] 3
  LRMP MUTATED LRMP WILD-TYPE 
             7            482 
  LRMP MUTATED LRMP WILD-TYPE 
             7            482 
[1] "LSM14A MUTATION ANALYSIS"
[1] 3
  LSM14A MUTATED LSM14A WILD-TYPE 
              11              478 
  LSM14A MUTATED LSM14A WILD-TYPE 
              11              478 
[1] "SMPDL3B MUTATION ANALYSIS"
[1] 3
  SMPDL3B MUTATED SMPDL3B WILD-TYPE 
                9               480 
  SMPDL3B MUTATED SMPDL3B WILD-TYPE 
                9               480 
[1] "KIF26A MUTATION ANALYSIS"
[1] 3
  KIF26A MUTATED KIF26A WILD-TYPE 
              10              479 
  KIF26A MUTATED KIF26A WILD-TYPE 
              10              479 
[1] "KDELR2 MUTATION ANALYSIS"
[1] 3
  KDELR2 MUTATED KDELR2 WILD-TYPE 
               6              483 
  KDELR2 MUTATED KDELR2 WILD-TYPE 
               6              483 
[1] "SIAH2 MUTATION ANALYSIS"
[1] 3
  SIAH2 MUTATED SIAH2 WILD-TYPE 
              9             480 
  SIAH2 MUTATED SIAH2 WILD-TYPE 
              9             480 
[1] "C6ORF203 MUTATION ANALYSIS"
[1] 3
  C6ORF203 MUTATED C6ORF203 WILD-TYPE 
                 5                484 
  C6ORF203 MUTATED C6ORF203 WILD-TYPE 
                 5                484 
[1] "GPR158 MUTATION ANALYSIS"
[1] 3
  GPR158 MUTATED GPR158 WILD-TYPE 
              29              460 
  GPR158 MUTATED GPR158 WILD-TYPE 
              29              460 
[1] "CSNK1E MUTATION ANALYSIS"
[1] 3
  CSNK1E MUTATED CSNK1E WILD-TYPE 
               9              480 
  CSNK1E MUTATED CSNK1E WILD-TYPE 
               9              480 
[1] "RNF103 MUTATION ANALYSIS"
[1] 3
  RNF103 MUTATED RNF103 WILD-TYPE 
               9              480 
  RNF103 MUTATED RNF103 WILD-TYPE 
               9              480 
[1] "CEBPA MUTATION ANALYSIS"
[1] 3
  CEBPA MUTATED CEBPA WILD-TYPE 
             17             472 
  CEBPA MUTATED CEBPA WILD-TYPE 
             17             472 
[1] "YWHAH MUTATION ANALYSIS"
[1] 3
  YWHAH MUTATED YWHAH WILD-TYPE 
              5             484 
  YWHAH MUTATED YWHAH WILD-TYPE 
              5             484 
[1] "OR5A1 MUTATION ANALYSIS"
[1] 3
  OR5A1 MUTATED OR5A1 WILD-TYPE 
              5             484 
  OR5A1 MUTATED OR5A1 WILD-TYPE 
              5             484 
[1] "IP6K3 MUTATION ANALYSIS"
[1] 3
  IP6K3 MUTATED IP6K3 WILD-TYPE 
              9             480 
  IP6K3 MUTATED IP6K3 WILD-TYPE 
              9             480 
[1] "CLSTN1 MUTATION ANALYSIS"
[1] 3
  CLSTN1 MUTATED CLSTN1 WILD-TYPE 
              16              473 
  CLSTN1 MUTATED CLSTN1 WILD-TYPE 
              16              473 
[1] "EPC2 MUTATION ANALYSIS"
[1] 3
  EPC2 MUTATED EPC2 WILD-TYPE 
            10            479 
  EPC2 MUTATED EPC2 WILD-TYPE 
            10            479 
[1] "SKIV2L MUTATION ANALYSIS"
[1] 3
  SKIV2L MUTATED SKIV2L WILD-TYPE 
              13              476 
  SKIV2L MUTATED SKIV2L WILD-TYPE 
              13              476 
[1] "COL5A2 MUTATION ANALYSIS"
[1] 3
  COL5A2 MUTATED COL5A2 WILD-TYPE 
              22              467 
  COL5A2 MUTATED COL5A2 WILD-TYPE 
              22              467 
[1] "CPO MUTATION ANALYSIS"
[1] 3
  CPO MUTATED CPO WILD-TYPE 
            9           480 
  CPO MUTATED CPO WILD-TYPE 
            9           480 
[1] "CLK4 MUTATION ANALYSIS"
[1] 3
  CLK4 MUTATED CLK4 WILD-TYPE 
             9            480 
  CLK4 MUTATED CLK4 WILD-TYPE 
             9            480 
[1] "SLC9A2 MUTATION ANALYSIS"
[1] 3
  SLC9A2 MUTATED SLC9A2 WILD-TYPE 
              12              477 
  SLC9A2 MUTATED SLC9A2 WILD-TYPE 
              12              477 
[1] "KIAA0196 MUTATION ANALYSIS"
[1] 3
  KIAA0196 MUTATED KIAA0196 WILD-TYPE 
                11                478 
  KIAA0196 MUTATED KIAA0196 WILD-TYPE 
                11                478 
[1] "ANGPTL2 MUTATION ANALYSIS"
[1] 3
  ANGPTL2 MUTATED ANGPTL2 WILD-TYPE 
               13               476 
  ANGPTL2 MUTATED ANGPTL2 WILD-TYPE 
               13               476 
[1] "C2ORF49 MUTATION ANALYSIS"
[1] 3
  C2ORF49 MUTATED C2ORF49 WILD-TYPE 
                5               484 
  C2ORF49 MUTATED C2ORF49 WILD-TYPE 
                5               484 
[1] "ATG4D MUTATION ANALYSIS"
[1] 3
  ATG4D MUTATED ATG4D WILD-TYPE 
             12             477 
  ATG4D MUTATED ATG4D WILD-TYPE 
             12             477 
[1] "MUS81 MUTATION ANALYSIS"
[1] 3
  MUS81 MUTATED MUS81 WILD-TYPE 
              7             482 
  MUS81 MUTATED MUS81 WILD-TYPE 
              7             482 
[1] "AKT1 MUTATION ANALYSIS"
[1] 3
  AKT1 MUTATED AKT1 WILD-TYPE 
            11            478 
  AKT1 MUTATED AKT1 WILD-TYPE 
            11            478 
[1] "OGFRL1 MUTATION ANALYSIS"
[1] 3
  OGFRL1 MUTATED OGFRL1 WILD-TYPE 
              10              479 
  OGFRL1 MUTATED OGFRL1 WILD-TYPE 
              10              479 
[1] "VPS72 MUTATION ANALYSIS"
[1] 3
  VPS72 MUTATED VPS72 WILD-TYPE 
              8             481 
  VPS72 MUTATED VPS72 WILD-TYPE 
              8             481 
[1] "ALG9 MUTATION ANALYSIS"
[1] 3
  ALG9 MUTATED ALG9 WILD-TYPE 
             4            485 
  ALG9 MUTATED ALG9 WILD-TYPE 
             4            485 
[1] "TAX1BP1 MUTATION ANALYSIS"
[1] 3
  TAX1BP1 MUTATED TAX1BP1 WILD-TYPE 
               14               475 
  TAX1BP1 MUTATED TAX1BP1 WILD-TYPE 
               14               475 
[1] "MAGEB2 MUTATION ANALYSIS"
[1] 3
  MAGEB2 MUTATED MAGEB2 WILD-TYPE 
              14              475 
  MAGEB2 MUTATED MAGEB2 WILD-TYPE 
              14              475 
[1] "SLCO6A1 MUTATION ANALYSIS"
[1] 3
  SLCO6A1 MUTATED SLCO6A1 WILD-TYPE 
               28               461 
  SLCO6A1 MUTATED SLCO6A1 WILD-TYPE 
               28               461 
[1] "HIST1H3B MUTATION ANALYSIS"
[1] 3
  HIST1H3B MUTATED HIST1H3B WILD-TYPE 
                 4                485 
  HIST1H3B MUTATED HIST1H3B WILD-TYPE 
                 4                485 
[1] "TBCE MUTATION ANALYSIS"
[1] 3
  TBCE MUTATED TBCE WILD-TYPE 
             3            486 
  TBCE MUTATED TBCE WILD-TYPE 
             3            486 
[1] "GLTPD2 MUTATION ANALYSIS"
[1] 3
  GLTPD2 MUTATED GLTPD2 WILD-TYPE 
               4              485 
  GLTPD2 MUTATED GLTPD2 WILD-TYPE 
               4              485 
[1] "KIAA0922 MUTATION ANALYSIS"
[1] 3
  KIAA0922 MUTATED KIAA0922 WILD-TYPE 
                21                468 
  KIAA0922 MUTATED KIAA0922 WILD-TYPE 
                21                468 
[1] "STK3 MUTATION ANALYSIS"
[1] 3
  STK3 MUTATED STK3 WILD-TYPE 
             9            480 
  STK3 MUTATED STK3 WILD-TYPE 
             9            480 
[1] "SLC35A1 MUTATION ANALYSIS"
[1] 3
  SLC35A1 MUTATED SLC35A1 WILD-TYPE 
                3               486 
  SLC35A1 MUTATED SLC35A1 WILD-TYPE 
                3               486 
[1] "GLRA3 MUTATION ANALYSIS"
[1] 3
  GLRA3 MUTATED GLRA3 WILD-TYPE 
             10             479 
  GLRA3 MUTATED GLRA3 WILD-TYPE 
             10             479 
[1] "FKBP5 MUTATION ANALYSIS"
[1] 3
  FKBP5 MUTATED FKBP5 WILD-TYPE 
              7             482 
  FKBP5 MUTATED FKBP5 WILD-TYPE 
              7             482 
[1] "C6ORF15 MUTATION ANALYSIS"
[1] 3
  C6ORF15 MUTATED C6ORF15 WILD-TYPE 
                6               483 
  C6ORF15 MUTATED C6ORF15 WILD-TYPE 
                6               483 
[1] "ZC3H12C MUTATION ANALYSIS"
[1] 3
  ZC3H12C MUTATED ZC3H12C WILD-TYPE 
               15               474 
  ZC3H12C MUTATED ZC3H12C WILD-TYPE 
               15               474 
[1] "IFI35 MUTATION ANALYSIS"
[1] 3
  IFI35 MUTATED IFI35 WILD-TYPE 
              8             481 
  IFI35 MUTATED IFI35 WILD-TYPE 
              8             481 
[1] "OR2F2 MUTATION ANALYSIS"
[1] 3
  OR2F2 MUTATED OR2F2 WILD-TYPE 
              8             481 
  OR2F2 MUTATED OR2F2 WILD-TYPE 
              8             481 
[1] "SLC27A3 MUTATION ANALYSIS"
[1] 3
  SLC27A3 MUTATED SLC27A3 WILD-TYPE 
                7               482 
  SLC27A3 MUTATED SLC27A3 WILD-TYPE 
                7               482 
[1] "C6ORF70 MUTATION ANALYSIS"
[1] 3
  C6ORF70 MUTATED C6ORF70 WILD-TYPE 
               14               475 
  C6ORF70 MUTATED C6ORF70 WILD-TYPE 
               14               475 
[1] "SFI1 MUTATION ANALYSIS"
[1] 3
  SFI1 MUTATED SFI1 WILD-TYPE 
            12            477 
  SFI1 MUTATED SFI1 WILD-TYPE 
            12            477 
[1] "ELANE MUTATION ANALYSIS"
[1] 3
  ELANE MUTATED ELANE WILD-TYPE 
              7             482 
  ELANE MUTATED ELANE WILD-TYPE 
              7             482 
[1] "QSER1 MUTATION ANALYSIS"
[1] 3
  QSER1 MUTATED QSER1 WILD-TYPE 
             17             472 
  QSER1 MUTATED QSER1 WILD-TYPE 
             17             472 
[1] "DAGLB MUTATION ANALYSIS"
[1] 3
  DAGLB MUTATED DAGLB WILD-TYPE 
              6             483 
  DAGLB MUTATED DAGLB WILD-TYPE 
              6             483 
[1] "CXCL9 MUTATION ANALYSIS"
[1] 3
  CXCL9 MUTATED CXCL9 WILD-TYPE 
              7             482 
  CXCL9 MUTATED CXCL9 WILD-TYPE 
              7             482 
[1] "CCDC111 MUTATION ANALYSIS"
[1] 3
  CCDC111 MUTATED CCDC111 WILD-TYPE 
                9               480 
  CCDC111 MUTATED CCDC111 WILD-TYPE 
                9               480 
[1] "FER1L6 MUTATION ANALYSIS"
[1] 3
  FER1L6 MUTATED FER1L6 WILD-TYPE 
              33              456 
  FER1L6 MUTATED FER1L6 WILD-TYPE 
              33              456 
[1] "NUP107 MUTATION ANALYSIS"
[1] 3
  NUP107 MUTATED NUP107 WILD-TYPE 
              13              476 
  NUP107 MUTATED NUP107 WILD-TYPE 
              13              476 
[1] "HIP1 MUTATION ANALYSIS"
[1] 3
  HIP1 MUTATED HIP1 WILD-TYPE 
            14            475 
  HIP1 MUTATED HIP1 WILD-TYPE 
            14            475 
[1] "AP3B1 MUTATION ANALYSIS"
[1] 3
  AP3B1 MUTATED AP3B1 WILD-TYPE 
             12             477 
  AP3B1 MUTATED AP3B1 WILD-TYPE 
             12             477 
[1] "C10ORF81 MUTATION ANALYSIS"
[1] 3
  C10ORF81 MUTATED C10ORF81 WILD-TYPE 
                 4                485 
  C10ORF81 MUTATED C10ORF81 WILD-TYPE 
                 4                485 
[1] "LY75 MUTATION ANALYSIS"
[1] 3
  LY75 MUTATED LY75 WILD-TYPE 
            11            478 
  LY75 MUTATED LY75 WILD-TYPE 
            11            478 
[1] "RRP9 MUTATION ANALYSIS"
[1] 3
  RRP9 MUTATED RRP9 WILD-TYPE 
            14            475 
  RRP9 MUTATED RRP9 WILD-TYPE 
            14            475 
[1] "CUTC MUTATION ANALYSIS"
[1] 3
  CUTC MUTATED CUTC WILD-TYPE 
             5            484 
  CUTC MUTATED CUTC WILD-TYPE 
             5            484 
[1] "CAPS2 MUTATION ANALYSIS"
[1] 3
  CAPS2 MUTATED CAPS2 WILD-TYPE 
             12             477 
  CAPS2 MUTATED CAPS2 WILD-TYPE 
             12             477 
[1] "ESYT1 MUTATION ANALYSIS"
[1] 3
  ESYT1 MUTATED ESYT1 WILD-TYPE 
             10             479 
  ESYT1 MUTATED ESYT1 WILD-TYPE 
             10             479 
[1] "KRT1 MUTATION ANALYSIS"
[1] 3
  KRT1 MUTATED KRT1 WILD-TYPE 
            15            474 
  KRT1 MUTATED KRT1 WILD-TYPE 
            15            474 
[1] "SUPT6H MUTATION ANALYSIS"
[1] 3
  SUPT6H MUTATED SUPT6H WILD-TYPE 
              23              466 
  SUPT6H MUTATED SUPT6H WILD-TYPE 
              23              466 
[1] "IGJ MUTATION ANALYSIS"
[1] 3
  IGJ MUTATED IGJ WILD-TYPE 
            4           485 
  IGJ MUTATED IGJ WILD-TYPE 
            4           485 
[1] "TRAF3 MUTATION ANALYSIS"
[1] 3
  TRAF3 MUTATED TRAF3 WILD-TYPE 
             12             477 
  TRAF3 MUTATED TRAF3 WILD-TYPE 
             12             477 
[1] "IPO11 MUTATION ANALYSIS"
[1] 3
  IPO11 MUTATED IPO11 WILD-TYPE 
             15             474 
  IPO11 MUTATED IPO11 WILD-TYPE 
             15             474 
[1] "AFF3 MUTATION ANALYSIS"
[1] 3
  AFF3 MUTATED AFF3 WILD-TYPE 
            25            464 
  AFF3 MUTATED AFF3 WILD-TYPE 
            25            464 
[1] "BTBD7 MUTATION ANALYSIS"
[1] 3
  BTBD7 MUTATED BTBD7 WILD-TYPE 
             12             477 
  BTBD7 MUTATED BTBD7 WILD-TYPE 
             12             477 
[1] "SUSD5 MUTATION ANALYSIS"
[1] 3
  SUSD5 MUTATED SUSD5 WILD-TYPE 
              9             480 
  SUSD5 MUTATED SUSD5 WILD-TYPE 
              9             480 
[1] "CDKL4 MUTATION ANALYSIS"
[1] 3
  CDKL4 MUTATED CDKL4 WILD-TYPE 
              5             484 
  CDKL4 MUTATED CDKL4 WILD-TYPE 
              5             484 
[1] "B3GALNT2 MUTATION ANALYSIS"
[1] 3
  B3GALNT2 MUTATED B3GALNT2 WILD-TYPE 
                 3                486 
  B3GALNT2 MUTATED B3GALNT2 WILD-TYPE 
                 3                486 
[1] "OR4N5 MUTATION ANALYSIS"
[1] 3
  OR4N5 MUTATED OR4N5 WILD-TYPE 
              3             486 
  OR4N5 MUTATED OR4N5 WILD-TYPE 
              3             486 
[1] "GADD45GIP1 MUTATION ANALYSIS"
[1] 3
  GADD45GIP1 MUTATED GADD45GIP1 WILD-TYPE 
                   4                  485 
  GADD45GIP1 MUTATED GADD45GIP1 WILD-TYPE 
                   4                  485 
[1] "RASGRP3 MUTATION ANALYSIS"
[1] 3
  RASGRP3 MUTATED RASGRP3 WILD-TYPE 
               13               476 
  RASGRP3 MUTATED RASGRP3 WILD-TYPE 
               13               476 
[1] "STOX2 MUTATION ANALYSIS"
[1] 3
  STOX2 MUTATED STOX2 WILD-TYPE 
             10             479 
  STOX2 MUTATED STOX2 WILD-TYPE 
             10             479 
[1] "SIGLEC14 MUTATION ANALYSIS"
[1] 3
  SIGLEC14 MUTATED SIGLEC14 WILD-TYPE 
                 8                481 
  SIGLEC14 MUTATED SIGLEC14 WILD-TYPE 
                 8                481 
[1] "CALCR MUTATION ANALYSIS"
[1] 3
  CALCR MUTATED CALCR WILD-TYPE 
             12             477 
  CALCR MUTATED CALCR WILD-TYPE 
             12             477 
[1] "TXNRD1 MUTATION ANALYSIS"
[1] 3
  TXNRD1 MUTATED TXNRD1 WILD-TYPE 
               9              480 
  TXNRD1 MUTATED TXNRD1 WILD-TYPE 
               9              480 
[1] "ZFP1 MUTATION ANALYSIS"
[1] 3
  ZFP1 MUTATED ZFP1 WILD-TYPE 
             4            485 
  ZFP1 MUTATED ZFP1 WILD-TYPE 
             4            485 
[1] "FAM199X MUTATION ANALYSIS"
[1] 3
  FAM199X MUTATED FAM199X WILD-TYPE 
               10               479 
  FAM199X MUTATED FAM199X WILD-TYPE 
               10               479 
[1] "GABRB2 MUTATION ANALYSIS"
[1] 3
  GABRB2 MUTATED GABRB2 WILD-TYPE 
              10              479 
  GABRB2 MUTATED GABRB2 WILD-TYPE 
              10              479 
[1] "NAA15 MUTATION ANALYSIS"
[1] 3
  NAA15 MUTATED NAA15 WILD-TYPE 
             15             474 
  NAA15 MUTATED NAA15 WILD-TYPE 
             15             474 
[1] "GNA15 MUTATION ANALYSIS"
[1] 3
  GNA15 MUTATED GNA15 WILD-TYPE 
              6             483 
  GNA15 MUTATED GNA15 WILD-TYPE 
              6             483 
[1] "ZNF274 MUTATION ANALYSIS"
[1] 3
  ZNF274 MUTATED ZNF274 WILD-TYPE 
               7              482 
  ZNF274 MUTATED ZNF274 WILD-TYPE 
               7              482 
[1] "ZNF763 MUTATION ANALYSIS"
[1] 3
  ZNF763 MUTATED ZNF763 WILD-TYPE 
              11              478 
  ZNF763 MUTATED ZNF763 WILD-TYPE 
              11              478 
[1] "PRKRIR MUTATION ANALYSIS"
[1] 3
  PRKRIR MUTATED PRKRIR WILD-TYPE 
              12              477 
  PRKRIR MUTATED PRKRIR WILD-TYPE 
              12              477 
[1] "PKIA MUTATION ANALYSIS"
[1] 3
  PKIA MUTATED PKIA WILD-TYPE 
            10            479 
  PKIA MUTATED PKIA WILD-TYPE 
            10            479 
[1] "SYNJ1 MUTATION ANALYSIS"
[1] 3
  SYNJ1 MUTATED SYNJ1 WILD-TYPE 
             19             470 
  SYNJ1 MUTATED SYNJ1 WILD-TYPE 
             19             470 
[1] "TEX14 MUTATION ANALYSIS"
[1] 3
  TEX14 MUTATED TEX14 WILD-TYPE 
             25             464 
  TEX14 MUTATED TEX14 WILD-TYPE 
             25             464 
[1] "F9 MUTATION ANALYSIS"
[1] 3
  F9 MUTATED F9 WILD-TYPE 
          20          469 
  F9 MUTATED F9 WILD-TYPE 
          20          469 
[1] "SMEK1 MUTATION ANALYSIS"
[1] 3
  SMEK1 MUTATED SMEK1 WILD-TYPE 
              9             480 
  SMEK1 MUTATED SMEK1 WILD-TYPE 
              9             480 
[1] "TSC1 MUTATION ANALYSIS"
[1] 3
  TSC1 MUTATED TSC1 WILD-TYPE 
            14            475 
  TSC1 MUTATED TSC1 WILD-TYPE 
            14            475 
[1] "HPCA MUTATION ANALYSIS"
[1] 3
  HPCA MUTATED HPCA WILD-TYPE 
             6            483 
  HPCA MUTATED HPCA WILD-TYPE 
             6            483 
[1] "EIF2B3 MUTATION ANALYSIS"
[1] 3
  EIF2B3 MUTATED EIF2B3 WILD-TYPE 
               6              483 
  EIF2B3 MUTATED EIF2B3 WILD-TYPE 
               6              483 
[1] "LRIG1 MUTATION ANALYSIS"
[1] 3
  LRIG1 MUTATED LRIG1 WILD-TYPE 
             15             474 
  LRIG1 MUTATED LRIG1 WILD-TYPE 
             15             474 
[1] "SEC14L1 MUTATION ANALYSIS"
[1] 3
  SEC14L1 MUTATED SEC14L1 WILD-TYPE 
               11               478 
  SEC14L1 MUTATED SEC14L1 WILD-TYPE 
               11               478 
[1] "ZNF142 MUTATION ANALYSIS"
[1] 3
  ZNF142 MUTATED ZNF142 WILD-TYPE 
              15              474 
  ZNF142 MUTATED ZNF142 WILD-TYPE 
              15              474 
[1] "SLC22A4 MUTATION ANALYSIS"
[1] 3
  SLC22A4 MUTATED SLC22A4 WILD-TYPE 
                5               484 
  SLC22A4 MUTATED SLC22A4 WILD-TYPE 
                5               484 
[1] "KLHDC9 MUTATION ANALYSIS"
[1] 3
  KLHDC9 MUTATED KLHDC9 WILD-TYPE 
               5              484 
  KLHDC9 MUTATED KLHDC9 WILD-TYPE 
               5              484 
[1] "ANKRD12 MUTATION ANALYSIS"
[1] 3
  ANKRD12 MUTATED ANKRD12 WILD-TYPE 
               26               463 
  ANKRD12 MUTATED ANKRD12 WILD-TYPE 
               26               463 
[1] "CTNND1 MUTATION ANALYSIS"
[1] 3
  CTNND1 MUTATED CTNND1 WILD-TYPE 
              20              469 
  CTNND1 MUTATED CTNND1 WILD-TYPE 
              20              469 
[1] "RBM16 MUTATION ANALYSIS"
[1] 3
  RBM16 MUTATED RBM16 WILD-TYPE 
             16             473 
  RBM16 MUTATED RBM16 WILD-TYPE 
             16             473 
[1] "RASA1 MUTATION ANALYSIS"
[1] 3
  RASA1 MUTATED RASA1 WILD-TYPE 
             19             470 
  RASA1 MUTATED RASA1 WILD-TYPE 
             19             470 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                      
 [2] "VITAL_STATUS"                        
 [3] "DAYS_TO_DEATH"                       
 [4] "DAYS_TO_LAST_FOLLOWUP"               
 [5] "TUMOR_TISSUE_SITE"                   
 [6] "PATHOLOGIC_STAGE"                    
 [7] "PATHOLOGY_T_STAGE"                   
 [8] "PATHOLOGY_N_STAGE"                   
 [9] "PATHOLOGY_M_STAGE"                   
[10] "GENDER"                              
[11] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"
[12] "DAYS_TO_LAST_KNOWN_ALIVE"            
[13] "RADIATION_THERAPY"                   
[14] "HISTOLOGICAL_TYPE"                   
[15] "RESIDUAL_TUMOR"                      
[16] "NUMBER_OF_LYMPH_NODES"               
[17] "RACE"                                
[18] "ETHNICITY"                           

Input Data has 18 rows and 489 columns.

[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=58,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=80,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 4:'DAYS_TO_LAST_FOLLOWUP':	nDistinctValues=289,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'TUMOR_TISSUE_SITE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'PATHOLOGIC_STAGE':	nDistinctValues=13,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY_T_STAGE':	nDistinctValues=7,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY_N_STAGE':	nDistinctValues=9,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY_M_STAGE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=13,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 12:'DAYS_TO_LAST_KNOWN_ALIVE':	nDistinctValues=23,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 13:'RADIATION_THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'HISTOLOGICAL_TYPE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'RESIDUAL_TUMOR':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'NUMBER_OF_LYMPH_NODES':	nDistinctValues=23,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 17:'RACE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 18:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "ETHNICITY excluded in the analysis because there is no case of (both >= 3) in the table below"
              HISPANIC OR LATINO NOT HISPANIC OR LATINO
freq.values   "1"                "247"                 
freq.contrast "247"              "1"                   
both >= 3     "FALSE"            "FALSE"               
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "PATHOLOGY_T_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_N_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_M_STAGE is converted to rank data using modified categoies"
[1] "****** SUMMARY ***** "
Output Data has 489 columns, 1 survival variables, and 12 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
 [1] "YEARS_TO_BIRTH"        "TUMOR_TISSUE_SITE"     "PATHOLOGIC_STAGE"     
 [4] "PATHOLOGY_T_STAGE"     "PATHOLOGY_N_STAGE"     "PATHOLOGY_M_STAGE"    
 [7] "GENDER"                "RADIATION_THERAPY"     "HISTOLOGICAL_TYPE"    
[10] "RESIDUAL_TUMOR"        "NUMBER_OF_LYMPH_NODES" "RACE"                 
YEARS_TO_BIRTH, nv=58, binary=FALSE, numeric=TRUE
TUMOR_TISSUE_SITE, nv=2, binary=FALSE, numeric=FALSE
PATHOLOGIC_STAGE, nv=13, binary=FALSE, numeric=FALSE
PATHOLOGY_T_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T1  T2  T3  T4 
 17  92 329  50 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
 17  92 329  50 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T1  T2  T3  T4 
 17  92 329  50 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
 17  92 329  50 
PATHOLOGY_N_STAGE, nv=3, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2 
287 113  87 
[1] "table(vv)"
vv
 N0  N1  N2 
287 113  87 
$ClinVariableName
[1] "PATHOLOGY_N_STAGE"

$Table
vv
 N0  N1  N2 
287 113  87 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


 N0  N1  N2 
287 113  87 
PATHOLOGY_M_STAGE, nv=2, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
RADIATION_THERAPY, nv=2, binary=FALSE, numeric=FALSE
HISTOLOGICAL_TYPE, nv=4, binary=FALSE, numeric=FALSE
RESIDUAL_TUMOR, nv=4, binary=FALSE, numeric=FALSE
NUMBER_OF_LYMPH_NODES, nv=23, binary=FALSE, numeric=TRUE
RACE, nv=4, binary=FALSE, numeric=FALSE

Clustering(1) Variable = APC MUTATION ANALYSIS
D1V1, survival
               sevent
clus2             0   1
  APC MUTATED   314  73
  APC WILD-TYPE  64  20
  APC MUTATED APC WILD-TYPE 
          387            84 
  APC MUTATED APC WILD-TYPE 
           73            20 
$`APC MUTATED`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 
       43.76        43.76        24.33        34.65        33.34        32.75 
TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 
       36.53        32.91        31.63        30.44        29.19        33.53 
TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 
       23.61        22.09        22.06        32.71        27.09        22.52 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 
       23.87        19.66        20.28         7.04         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3519 TCGA-AA-3522 TCGA-AA-3530 TCGA-AA-3531 
       63.98         6.97         9.07        37.05        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       29.00        26.01        12.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
        2.01        14.01        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3710 
        5.98        37.05        19.00        36.00        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3837 
       19.04        19.04        35.05        33.04         0.99        38.99 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       17.03        10.06        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3870 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3950 
       29.98         2.01        12.99        24.00        33.01        24.00 
TCGA-AA-3952 TCGA-AA-3968 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
        2.01        21.99        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       25.02        24.00        27.02        27.02         7.96        27.02 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       38.04        19.00        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
       27.02        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01F TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       32.02        31.00        31.00         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       33.04        35.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A03F 
        2.01         5.03        14.01         0.92        41.00        18.05 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
        0.07        21.37        15.52         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4616 
        0.95        33.01        21.44        17.82        58.39         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
      106.75        22.36        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.69         3.29         0.07        12.20        12.76        10.06 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       20.02        37.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 
       21.99        14.99        12.99        13.02        15.02        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       20.19        18.25         1.32        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        4.80        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6806 
       98.24         8.61        31.96        35.74        47.87        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       16.24        33.67        13.25        47.41        35.31       133.18 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       61.91        36.00        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       46.75        24.13        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        8.02         7.07        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3609 
       34.03         2.01        50.04        12.03         0.99        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A011 TCGA-AG-A014 
        1.02        20.98        13.94         6.02        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
       36.03        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        4.01         5.03       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6510 
       51.48        32.61         0.49        20.55        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

$`APC WILD-TYPE`
TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-4105 TCGA-A6-6648 
       46.65        42.90        42.28        16.57        14.53        25.18 
TCGA-A6-6780 TCGA-AA-3492 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       20.12         3.02         1.02        13.02        38.99         1.02 
TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3534 
       24.03        36.03         8.05        19.07         0.00        29.00 
TCGA-AA-3543 TCGA-AA-3560 TCGA-AA-3664 TCGA-AA-3672 TCGA-AA-3696 TCGA-AA-3811 
        0.99        19.99        54.02         0.92         5.03        10.06 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3842 TCGA-AA-3844 
       25.02         1.02        17.98        15.95        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3850 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
        0.00         0.00        24.03        27.02        18.05        31.00 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3986 
       26.01        20.98        34.03         2.01        16.08        19.07 
TCGA-AA-A004 TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A01D 
       13.94        30.02        34.03        42.02         0.99        10.98 
TCGA-AA-A01G TCGA-AA-A01P TCGA-AA-A01X TCGA-AA-A02Y TCGA-AA-A03J TCGA-AD-6889 
       12.00        38.07        26.01        39.98        40.96        56.55 
TCGA-AY-4070 TCGA-AZ-4323 TCGA-AZ-5403 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-6719 
       16.31         1.41        62.79         3.06         3.25        14.30 
TCGA-CM-4747 TCGA-CM-6171 TCGA-D5-6534 TCGA-D5-6930 TCGA-F4-6570 TCGA-F4-6704 
       25.02        14.04        43.27         1.51         6.18         1.55 
TCGA-F4-6805 TCGA-F4-6854 TCGA-G4-6299 TCGA-G4-6321 TCGA-G4-6628 TCGA-AF-2689 
       34.42         0.53        74.56        22.09        79.69        39.48 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3582 TCGA-AG-3600 TCGA-AG-3608 
       36.03        12.00        32.02        36.03         6.05        15.95 
TCGA-AG-4008 TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A016 TCGA-DT-5265 TCGA-EI-6507 
       17.03        25.97        23.01         9.07         5.29        19.96 

  APC MUTATED APC WILD-TYPE 
            0             0 
  APC MUTATED APC WILD-TYPE 
       148.01         79.69 
  APC MUTATED APC WILD-TYPE 
        20.98         19.07 
[1] "0.0 - 148.0 (21.0)" "0.0 - 79.7 (19.1)" 
[1] "hr=" "1.6"
D1V2, continuous
D1V3, binary
               cls
clus              0   1
  APC MUTATED   294 105
  APC WILD-TYPE  72  14
[1] "tbl2"
               cls
clus            [,1] [,2]
  APC MUTATED    294  105
  APC WILD-TYPE   72   14
        clus
vv       APC MUTATED APC WILD-TYPE
  COLON          294            72
  RECTUM         105            14
[1] 2 2
[1] FALSE
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  APC MUTATED        78        1       23       109         9         1
  APC WILD-TYPE      13        0        9        29         1         0
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  APC MUTATED          17         10         52         33       40        16
  APC WILD-TYPE         7          1          7          9        8         2
               vv
clus            STAGE IVB
  APC MUTATED           1
  APC WILD-TYPE         0
D1V4, multiclass
            clus
vv           APC MUTATED APC WILD-TYPE
  STAGE I             78            13
  STAGE IA             1             0
  STAGE II            23             9
  STAGE IIA          109            29
  STAGE IIB            9             1
  STAGE IIC            1             0
  STAGE III           17             7
  STAGE IIIA          10             1
  STAGE IIIB          52             7
  STAGE IIIC          33             9
  STAGE IV            40             8
  STAGE IVA           16             2
  STAGE IVB            1             0
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  APC MUTATED    15  77 267  43
  APC WILD-TYPE   2  15  62   7
D1V5, multiclass
    clus
vv   APC MUTATED APC WILD-TYPE
  T1          15             2
  T2          77            15
  T3         267            62
  T4          43             7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2
  APC MUTATED   233  98  70
  APC WILD-TYPE  54  15  17
D1V6, multiclass
    clus
vv   APC MUTATED APC WILD-TYPE
  N0         233            54
  N1          98            15
  N2          70            17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V7, binary
               cls
clus              0   1
  APC MUTATED   303  55
  APC WILD-TYPE  72  10
[1] "tbl2"
               cls
clus            [,1] [,2]
  APC MUTATED    303   55
  APC WILD-TYPE   72   10
   clus
vv  APC MUTATED APC WILD-TYPE
  0         303            72
  1          55            10
[1] 2 2
[1] FALSE
D1V8, binary
               cls
clus              0   1
  APC MUTATED   180 223
  APC WILD-TYPE  45  41
[1] "tbl2"
               cls
clus            [,1] [,2]
  APC MUTATED    180  223
  APC WILD-TYPE   45   41
        clus
vv       APC MUTATED APC WILD-TYPE
  FEMALE         180            45
  MALE           223            41
[1] 2 2
[1] FALSE
D1V9, binary
               cls
clus              0   1
  APC MUTATED   279  18
  APC WILD-TYPE  71   4
[1] "tbl2"
               cls
clus            [,1] [,2]
  APC MUTATED    279   18
  APC WILD-TYPE   71    4
     clus
vv    APC MUTATED APC WILD-TYPE
  NO          279            71
  YES          18             4
[1] 2 2
[1] FALSE
               vv
clus            COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  APC MUTATED                    256                            34
  APC WILD-TYPE                   59                            13
               vv
clus            RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  APC MUTATED                      95                              7
  APC WILD-TYPE                    11                              3
D1V10, multiclass
                                clus
vv                               APC MUTATED APC WILD-TYPE
  COLON ADENOCARCINOMA                   256            59
  COLON MUCINOUS ADENOCARCINOMA           34            13
  RECTAL ADENOCARCINOMA                   95            11
  RECTAL MUCINOUS ADENOCARCINOMA           7             3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             R0  R1  R2  RX
  APC MUTATED   277   3  26  21
  APC WILD-TYPE  68   1   5   4
D1V11, multiclass
    clus
vv   APC MUTATED APC WILD-TYPE
  R0         277            68
  R1           3             1
  R2          26             5
  RX          21             4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V12, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  APC MUTATED                                  0     6
  APC WILD-TYPE                                1     5
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  APC MUTATED                          21   205
  APC WILD-TYPE                         1    21
D1V13, multiclass
                                  clus
vv                                 APC MUTATED APC WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      6             5
  BLACK OR AFRICAN AMERICAN                 21             1
  WHITE                                    205            21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2) Variable = TP53 MUTATION ANALYSIS
D2V1, survival
                sevent
clus2              0   1
  TP53 MUTATED   256  59
  TP53 WILD-TYPE 122  34
  TP53 MUTATED TP53 WILD-TYPE 
           315            156 
  TP53 MUTATED TP53 WILD-TYPE 
            59             34 
$`TP53 MUTATED`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       43.76        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 
       36.53        14.53        32.91        30.44        29.19        23.61 
TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6649 TCGA-A6-6651 
       22.06        27.09        22.52        25.08        24.16        21.76 
TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6782 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3510 
       24.69        23.87        20.28         3.02         1.02        63.98 
TCGA-AA-3511 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3526 
        6.97        38.99         9.07        24.03        36.03        19.07 
TCGA-AA-3531 TCGA-AA-3542 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3556 
       34.03        12.99        21.01        13.02        24.00        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       20.98        19.99        13.94        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3679 TCGA-AA-3681 
        6.97         2.01        14.01        50.04        15.02         5.98 
TCGA-AA-3685 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3815 TCGA-AA-3842 
       37.05        85.05        19.04        10.06        33.04        37.02 
TCGA-AA-3844 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
       14.93        10.06        33.07         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3930 
       30.05        17.03        24.03        27.02        18.05         2.01 
TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3972 
       24.00        26.01        20.98        34.03        21.99        50.99 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00L TCGA-AA-A00O 
       13.94        19.00        30.02        34.03        38.04        27.02 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01K 
       14.99        34.98        10.98        32.02        12.00        31.00 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01Z TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
        1.02        33.04        37.02        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02W TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       14.01        41.00        40.96         0.07        21.37        15.52 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AZ-4323 TCGA-AZ-4616 
       16.31         0.95        33.01        21.44         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
      106.75        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5797 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5914 TCGA-CM-4743 TCGA-CM-4744 
      148.01        85.45        15.62         9.99        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       37.02        13.02        29.06        22.98        30.08        32.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       13.02        14.04        11.01        13.05        11.08        11.08 
TCGA-CM-6679 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6532 TCGA-D5-6533 
       10.06        12.26        56.09        55.92        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       43.27        15.12        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-DM-A0XD 
        9.44         4.80         1.51        12.00        11.38        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A285 
      140.38         7.50        44.32       131.51       135.65         6.12 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
      119.93        35.97       117.07        98.24         8.61        31.96 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
       13.25         0.53        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       53.62        44.68        55.04        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       22.09        13.78        35.80        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       24.13        39.48        43.04        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3575 TCGA-AG-3578 
       14.50        15.39        20.02        10.39        12.00        32.02 
TCGA-AG-3581 TCGA-AG-3587 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3605 TCGA-AG-3608 
        7.07        46.03         2.01        50.04         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3731 TCGA-AG-3732 
       19.99        13.94        19.99         7.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3882 TCGA-AG-3885 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3896 
        0.99        19.99        17.95        17.03        35.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
        1.02        17.03         6.02        23.01        37.02        15.95 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A026 
        9.07        12.00        70.03        64.01        10.98         1.94 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6549 
       61.97        41.00        38.04       117.11        38.56        17.49 
TCGA-AH-6643 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.69         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
       19.99         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       57.24        24.13        51.48         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       20.91        18.28         9.96        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
        0.66         0.69        55.76 

$`TP53 WILD-TYPE`
TCGA-A6-2672 TCGA-A6-2677 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-5657 TCGA-A6-5661 
       46.65        24.33        33.34        32.75        31.63        33.53 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6653 TCGA-A6-6780 
       22.09        32.71         8.38        25.18        24.39        20.12 
TCGA-A6-6781 TCGA-AA-3489 TCGA-AA-3502 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3518 
       19.66         7.04        35.01         1.02        13.02         1.02 
TCGA-AA-3522 TCGA-AA-3525 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3532 TCGA-AA-3534 
       37.05         8.05         0.00        19.07        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3554 TCGA-AA-3555 
       26.01         0.99        14.01        33.99        17.95        29.95 
TCGA-AA-3562 TCGA-AA-3664 TCGA-AA-3672 TCGA-AA-3678 TCGA-AA-3680 TCGA-AA-3688 
       19.99        54.02         0.92        47.01        11.01        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3818 
       36.00         5.03        26.99        19.04        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3845 
       25.02         1.02        17.98        15.95        38.99         0.00 
TCGA-AA-3846 TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3864 
       17.03         0.00         0.00        36.03        32.05        53.00 
TCGA-AA-3870 TCGA-AA-3877 TCGA-AA-3939 TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-3952 
       29.98        31.00        12.99        33.01        24.00         2.01 
TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
        2.01        16.08        13.05        19.07         7.96        27.02 
TCGA-AA-A00A TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00Q TCGA-AA-A00R 
       38.04        18.05        18.05         4.01        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q 
       17.03        21.99         1.02        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02O 
       35.01        35.01        26.01        39.06        51.98         0.92 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6964 
       39.98        18.05        56.55         0.79         0.72        10.88 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4682 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       17.82        58.39        22.36        12.69         3.06         3.25 
TCGA-CA-6715 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
        0.07        49.08        51.32        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4747 TCGA-CM-5344 TCGA-CM-5861 TCGA-CM-6170 TCGA-CM-6674 
      124.27        25.02        22.03        15.02        15.02        12.95 
TCGA-CM-6678 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5539 TCGA-D5-6529 TCGA-D5-6536 
       11.01        12.03        45.40        19.59        20.19        17.85 
TCGA-D5-6537 TCGA-D5-6928 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A282 TCGA-DM-A28C 
        4.80        11.64        10.26       119.70       139.17        81.37 
TCGA-DM-A28G TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6855 TCGA-G4-6309 TCGA-G4-6588 
       60.79        35.74         6.18        47.41        85.48        26.17 
TCGA-AF-2692 TCGA-AF-5654 TCGA-AG-3574 TCGA-AG-3580 TCGA-AG-3582 TCGA-AG-3583 
       13.55        16.83        36.03         8.02        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3593 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3727 
       24.00         1.02        34.03        12.03         6.05         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3894 
        0.99        19.04         1.02        36.95        13.02        14.01 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00H TCGA-AG-A015 TCGA-AG-A025 TCGA-AG-A02G 
       20.98        13.94        25.97        36.03        49.97        38.96 
TCGA-AH-6547 TCGA-AH-6644 TCGA-DC-6681 TCGA-DY-A1H8 TCGA-F5-6465 TCGA-G5-6641 
        1.45         0.72         5.95        32.61        49.51        26.43 

  TP53 MUTATED TP53 WILD-TYPE 
          0.07           0.00 
  TP53 MUTATED TP53 WILD-TYPE 
        148.01         139.17 
  TP53 MUTATED TP53 WILD-TYPE 
         20.91          20.02 
[1] "0.1 - 148.0 (20.9)" "0.0 - 139.2 (20.0)"
[1] "hr=" "1.3"
D2V2, continuous
D2V3, binary
                cls
clus               0   1
  TP53 MUTATED   231  89
  TP53 WILD-TYPE 135  30
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED    231   89
  TP53 WILD-TYPE  135   30
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  COLON           231            135
  RECTUM           89             30
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TP53 MUTATED        57        1       21        82         6         0
  TP53 WILD-TYPE      34        0       11        56         4         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TP53 MUTATED          14          8         45         34       33        13
  TP53 WILD-TYPE        10          3         14          8       15         5
                vv
clus             STAGE IVB
  TP53 MUTATED           1
  TP53 WILD-TYPE         0
D2V4, multiclass
            clus
vv           TP53 MUTATED TP53 WILD-TYPE
  STAGE I              57             34
  STAGE IA              1              0
  STAGE II             21             11
  STAGE IIA            82             56
  STAGE IIB             6              4
  STAGE IIC             0              1
  STAGE III            14             10
  STAGE IIIA            8              3
  STAGE IIIB           45             14
  STAGE IIIC           34              8
  STAGE IV             33             15
  STAGE IVA            13              5
  STAGE IVB             1              0
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  TP53 MUTATED     9  60 220  33
  TP53 WILD-TYPE   8  32 109  17
D2V5, multiclass
    clus
vv   TP53 MUTATED TP53 WILD-TYPE
  T1            9              8
  T2           60             32
  T3          220            109
  T4           33             17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  TP53 MUTATED   178  81  63
  TP53 WILD-TYPE 109  32  24
D2V6, multiclass
    clus
vv   TP53 MUTATED TP53 WILD-TYPE
  N0          178            109
  N1           81             32
  N2           63             24
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V7, binary
                cls
clus               0   1
  TP53 MUTATED   246  45
  TP53 WILD-TYPE 129  20
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED    246   45
  TP53 WILD-TYPE  129   20
   clus
vv  TP53 MUTATED TP53 WILD-TYPE
  0          246            129
  1           45             20
[1] 2 2
[1] FALSE
D2V8, binary
                cls
clus               0   1
  TP53 MUTATED   143 180
  TP53 WILD-TYPE  82  84
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED    143  180
  TP53 WILD-TYPE   82   84
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  FEMALE          143             82
  MALE            180             84
[1] 2 2
[1] FALSE
D2V9, binary
                cls
clus               0   1
  TP53 MUTATED   236  14
  TP53 WILD-TYPE 114   8
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED    236   14
  TP53 WILD-TYPE  114    8
     clus
vv    TP53 MUTATED TP53 WILD-TYPE
  NO           236            114
  YES           14              8
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  TP53 MUTATED                    208                            19
  TP53 WILD-TYPE                  107                            28
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  TP53 MUTATED                      84                              5
  TP53 WILD-TYPE                    22                              5
D2V10, multiclass
                                clus
vv                               TP53 MUTATED TP53 WILD-TYPE
  COLON ADENOCARCINOMA                    208            107
  COLON MUCINOUS ADENOCARCINOMA            19             28
  RECTAL ADENOCARCINOMA                    84             22
  RECTAL MUCINOUS ADENOCARCINOMA            5              5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  TP53 MUTATED   225   4  18  12
  TP53 WILD-TYPE 120   0  13  13
D2V11, multiclass
    clus
vv   TP53 MUTATED TP53 WILD-TYPE
  R0          225            120
  R1            4              0
  R2           18             13
  RX           12             13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TP53 MUTATED                                  1     6
  TP53 WILD-TYPE                                0     5
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  TP53 MUTATED                          16   174
  TP53 WILD-TYPE                         6    52
D2V13, multiclass
                                  clus
vv                                 TP53 MUTATED TP53 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            1              0
  ASIAN                                       6              5
  BLACK OR AFRICAN AMERICAN                  16              6
  WHITE                                     174             52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(3) Variable = ARID1A MUTATION ANALYSIS
D3V1, survival
                  sevent
clus2                0   1
  ARID1A MUTATED    63  16
  ARID1A WILD-TYPE 315  77
  ARID1A MUTATED ARID1A WILD-TYPE 
              79              392 
  ARID1A MUTATED ARID1A WILD-TYPE 
              16               77 
$`ARID1A MUTATED`
TCGA-A6-2676 TCGA-A6-4105 TCGA-A6-5665 TCGA-A6-6141 TCGA-A6-6780 TCGA-A6-6781 
       42.90        14.53        22.06         8.38        20.12        19.66 
TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3554 TCGA-AA-3555 
        3.02         1.02         1.02        13.02        17.95        29.95 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3713 TCGA-AA-3831 TCGA-AA-3867 
       78.08         6.05         6.97        19.04        17.98        24.03 
TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00L TCGA-AA-A010 
       33.01        24.00        38.04        30.02        38.04        34.98 
TCGA-AA-A017 TCGA-AA-A01R TCGA-AD-6895 TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-4616 
        1.02        35.01         0.72        21.44        58.39         5.13 
TCGA-AZ-4681 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-CA-5254 
      106.75        49.41         6.77       100.01        29.56        12.69 
TCGA-CA-5797 TCGA-CA-6716 TCGA-CA-6717 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-6747 
        3.29        12.20        12.76        15.62        51.32        82.95 
TCGA-CM-5864 TCGA-CM-6162 TCGA-CM-6166 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       15.02        12.00        21.99        14.04        11.01        12.95 
TCGA-CM-6677 TCGA-CM-6679 TCGA-D5-5538 TCGA-D5-5541 TCGA-D5-6540 TCGA-D5-6898 
       11.08        10.06        12.26        55.92        16.14         1.48 
TCGA-D5-6930 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1HB TCGA-F4-6460 TCGA-F4-6570 
        1.51        24.43        38.20       135.65        31.96         6.18 
TCGA-F4-6854 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6310 TCGA-G4-6317 TCGA-G4-6586 
        0.53        35.31       133.18        63.62        36.00        35.80 
TCGA-G4-6588 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2693 TCGA-AG-3574 TCGA-AG-3878 
       26.17        79.69        24.13        19.10        36.03         0.99 
TCGA-AG-3892 TCGA-AG-A00H TCGA-AG-A025 TCGA-CI-6620 TCGA-CI-6624 TCGA-DY-A1DF 
       13.02        25.97        49.97        33.17         4.73        24.13 
TCGA-DY-A1DG 
       51.48 

$`ARID1A WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 
       34.65        33.34        32.75        36.53        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 
       30.44        29.19        33.53        23.61        22.09        32.71 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 
       27.09        22.52        25.08        25.18        24.16        21.76 
TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3502 
       24.69        24.39        23.87        20.28         7.04        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
       63.98         6.97        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3556 
       14.01        33.99        21.01        13.02        24.00        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3664 
       20.98        19.99        13.94        19.99        61.02        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       85.05        26.99        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
        0.99        25.02         1.02        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       30.05        53.00        17.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3952 
       31.00         2.01        12.99        24.00        26.01         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00D 
       27.02        19.07         7.96        27.02        13.94        19.00 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A01D TCGA-AA-A01F 
        0.99        17.03        14.99        21.99        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S 
       12.00        31.00        31.00        38.07         1.02         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
       56.55         0.79         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6600 
       17.82         1.41        22.36        62.79        88.21        12.10 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19         1.61         3.06         3.25 
TCGA-CA-6715 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.07        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       49.08         9.99        21.14         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6167 
       17.03        15.02         2.96        29.03        16.04        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6678 
       12.99        13.02        15.02        13.05        11.08        11.01 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-6529 TCGA-D5-6532 
       12.03        45.40        19.59        56.09        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       12.49        15.58         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 
        9.04         9.44        11.64         4.80        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       10.26       119.70       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 
       12.59       140.38         7.50        44.32       131.51       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       98.24         8.61        35.74        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6855 TCGA-G4-6299 
       41.42        16.24        33.67        13.25        47.41        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6315 
       65.85        53.62        44.68        55.04        85.48        61.91 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2689 TCGA-AF-2691 
       22.09        13.78        91.79        46.75        39.48        43.04 
TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       13.55        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       20.02        10.39        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
       32.98         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       36.95        17.03        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 
       17.03        20.98        13.94         6.02        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       10.98         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6622 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.05         6.97        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1H8 
        5.03         5.29       126.44        41.36        57.24        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  ARID1A MUTATED ARID1A WILD-TYPE 
            0.53             0.00 
  ARID1A MUTATED ARID1A WILD-TYPE 
          135.65           148.01 
  ARID1A MUTATED ARID1A WILD-TYPE 
           21.44            20.12 
[1] "0.5 - 135.7 (21.4)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1"  
D3V2, continuous
D3V3, binary
                  cls
clus                 0   1
  ARID1A MUTATED    72  10
  ARID1A WILD-TYPE 294 109
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED     72   10
  ARID1A WILD-TYPE  294  109
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  COLON              72              294
  RECTUM             10              109
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ARID1A MUTATED        15        0        7        32         3         0
  ARID1A WILD-TYPE      76        1       25       106         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ARID1A MUTATED           4          0          7          7        4
  ARID1A WILD-TYPE        20         11         52         35       44
                  vv
clus               STAGE IVA STAGE IVB
  ARID1A MUTATED           2         0
  ARID1A WILD-TYPE        16         1
D3V4, multiclass
            clus
vv           ARID1A MUTATED ARID1A WILD-TYPE
  STAGE I                15               76
  STAGE IA                0                1
  STAGE II                7               25
  STAGE IIA              32              106
  STAGE IIB               3                7
  STAGE IIC               0                1
  STAGE III               4               20
  STAGE IIIA              0               11
  STAGE IIIB              7               52
  STAGE IIIC              7               35
  STAGE IV                4               44
  STAGE IVA               2               16
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ARID1A MUTATED     2  14  61   6
  ARID1A WILD-TYPE  15  78 268  44
D3V5, multiclass
    clus
vv   ARID1A MUTATED ARID1A WILD-TYPE
  T1              2               15
  T2             14               78
  T3             61              268
  T4              6               44
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  ARID1A MUTATED    58  13  12
  ARID1A WILD-TYPE 229 100  75
D3V6, multiclass
    clus
vv   ARID1A MUTATED ARID1A WILD-TYPE
  N0             58              229
  N1             13              100
  N2             12               75
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V7, binary
                  cls
clus                 0   1
  ARID1A MUTATED    64   6
  ARID1A WILD-TYPE 311  59
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED     64    6
  ARID1A WILD-TYPE  311   59
   clus
vv  ARID1A MUTATED ARID1A WILD-TYPE
  0             64              311
  1              6               59
[1] 2 2
[1] FALSE
D3V8, binary
                  cls
clus                 0   1
  ARID1A MUTATED    44  39
  ARID1A WILD-TYPE 181 225
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED     44   39
  ARID1A WILD-TYPE  181  225
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  FEMALE             44              181
  MALE               39              225
[1] 2 2
[1] FALSE
D3V9, binary
                  cls
clus                 0   1
  ARID1A MUTATED    60   5
  ARID1A WILD-TYPE 290  17
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED     60    5
  ARID1A WILD-TYPE  290   17
     clus
vv    ARID1A MUTATED ARID1A WILD-TYPE
  NO              60              290
  YES              5               17
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ARID1A MUTATED                     56                            14
  ARID1A WILD-TYPE                  259                            33
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ARID1A MUTATED                      10                              0
  ARID1A WILD-TYPE                    96                             10
D3V10, multiclass
                                clus
vv                               ARID1A MUTATED ARID1A WILD-TYPE
  COLON ADENOCARCINOMA                       56              259
  COLON MUCINOUS ADENOCARCINOMA              14               33
  RECTAL ADENOCARCINOMA                      10               96
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ARID1A MUTATED    55   0   3   7
  ARID1A WILD-TYPE 290   4  28  18
D3V11, multiclass
    clus
vv   ARID1A MUTATED ARID1A WILD-TYPE
  R0             55              290
  R1              0                4
  R2              3               28
  RX              7               18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ARID1A MUTATED                                  0     4
  ARID1A WILD-TYPE                                1     7
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ARID1A MUTATED                           1    51
  ARID1A WILD-TYPE                        21   175
D3V13, multiclass
                                  clus
vv                                 ARID1A MUTATED ARID1A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         4                7
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                        51              175
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(4) Variable = RNF43 MUTATION ANALYSIS
D4V1, survival
                 sevent
clus2               0   1
  RNF43 MUTATED    38   8
  RNF43 WILD-TYPE 340  85
  RNF43 MUTATED RNF43 WILD-TYPE 
             46             425 
  RNF43 MUTATED RNF43 WILD-TYPE 
              8              85 
$`RNF43 MUTATED`
TCGA-A6-2671 TCGA-A6-5661 TCGA-A6-5665 TCGA-A6-6649 TCGA-A6-6653 TCGA-A6-6781 
       43.76        33.53        22.06        24.16        24.39        19.66 
TCGA-AA-3492 TCGA-AA-3518 TCGA-AA-3555 TCGA-AA-3663 TCGA-AA-3672 TCGA-AA-3710 
        3.02         1.02        29.95         6.97         0.92        26.99 
TCGA-AA-3715 TCGA-AA-3947 TCGA-AA-A00K TCGA-AA-A010 TCGA-AA-A01I TCGA-AA-A01P 
       19.04        33.01        18.05        34.98        31.00        38.07 
TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6895 TCGA-AD-6964 TCGA-AU-6004 TCGA-AZ-6598 
        0.07        56.55         0.72        10.88        27.09        49.41 
TCGA-CA-5796 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CM-4743 TCGA-CM-4746 
        3.25        51.32        21.14        82.95        23.05        37.02 
TCGA-CM-5861 TCGA-CM-6162 TCGA-CM-6171 TCGA-CM-6674 TCGA-D5-6540 TCGA-D5-6928 
       15.02        12.00        14.04        12.95        16.14        11.64 
TCGA-D5-6930 TCGA-F4-6570 TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6309 TCGA-G4-6315 
        1.51         6.18        35.31        74.56        85.48        61.91 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 TCGA-AG-A002 
       35.80        26.17        79.69        20.98 

$`RNF43 WILD-TYPE`
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       46.65        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 
       31.63        30.44        29.19        23.61        22.09        32.71 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 
       27.09        22.52         8.38        25.08        25.18        21.76 
TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       24.69        23.87        20.12        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       24.00        17.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02        78.08         6.05        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
       14.01        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 
       37.05        19.00        36.00         5.03        85.05        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
        2.01        12.99        24.00        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00L TCGA-AA-A00N 
       19.00        30.02        34.03        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01K TCGA-AA-A01Q 
        1.02        10.98        32.02        12.00        31.00         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 
        0.92        41.00        39.98        18.05        40.96        21.37 
TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       15.52         0.79         5.79        22.42        27.42         0.20 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       14.50        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       88.21         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5797 
       11.74         3.19         1.61        12.69         3.06         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-6748 
      148.01        85.45        15.62        49.08         9.99         1.91 
TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
      124.27        20.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       22.98        30.08        32.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       17.03        15.02         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6675 
       14.99        12.99        13.02        15.02        11.01        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       12.49        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 
       14.30         9.04         9.44         4.80        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       35.74        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6303 
       33.67        13.25         0.53        47.41       133.18        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6317 TCGA-G4-6321 
       53.62        44.68        55.04        63.62        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       13.78        91.79        46.75        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  RNF43 MUTATED RNF43 WILD-TYPE 
           0.07            0.00 
  RNF43 MUTATED RNF43 WILD-TYPE 
          85.48          148.01 
  RNF43 MUTATED RNF43 WILD-TYPE 
         23.605          20.020 
[1] "0.1 - 85.5 (23.6)"  "0.0 - 148.0 (20.0)"
[1] "hr=" "1.2"
D4V2, continuous
D4V3, binary
                 cls
clus                0   1
  RNF43 MUTATED    46   1
  RNF43 WILD-TYPE 320 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RNF43 MUTATED     46    1
  RNF43 WILD-TYPE  320  118
        clus
vv       RNF43 MUTATED RNF43 WILD-TYPE
  COLON             46             320
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RNF43 MUTATED        11        0        4        18         3         0
  RNF43 WILD-TYPE      80        1       28       120         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RNF43 MUTATED           2          0          3          2        2         0
  RNF43 WILD-TYPE        22         11         56         40       46        18
                 vv
clus              STAGE IVB
  RNF43 MUTATED           0
  RNF43 WILD-TYPE         1
D4V4, multiclass
            clus
vv           RNF43 MUTATED RNF43 WILD-TYPE
  STAGE I               11              80
  STAGE IA               0               1
  STAGE II               4              28
  STAGE IIA             18             120
  STAGE IIB              3               7
  STAGE IIC              0               1
  STAGE III              2              22
  STAGE IIIA             0              11
  STAGE IIIB             3              56
  STAGE IIIC             2              40
  STAGE IV               2              46
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  RNF43 MUTATED     1  10  31   5
  RNF43 WILD-TYPE  16  82 298  45
D4V5, multiclass
    clus
vv   RNF43 MUTATED RNF43 WILD-TYPE
  T1             1              16
  T2            10              82
  T3            31             298
  T4             5              45
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  RNF43 MUTATED    36   8   3
  RNF43 WILD-TYPE 251 105  84
D4V6, multiclass
    clus
vv   RNF43 MUTATED RNF43 WILD-TYPE
  N0            36             251
  N1             8             105
  N2             3              84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V7, binary
                 cls
clus                0   1
  RNF43 MUTATED    37   2
  RNF43 WILD-TYPE 338  63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RNF43 MUTATED     37    2
  RNF43 WILD-TYPE  338   63
   clus
vv  RNF43 MUTATED RNF43 WILD-TYPE
  0            37             338
  1             2              63
[1] 2 2
[1] FALSE
D4V8, binary
                 cls
clus                0   1
  RNF43 MUTATED    24  23
  RNF43 WILD-TYPE 201 241
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RNF43 MUTATED     24   23
  RNF43 WILD-TYPE  201  241
        clus
vv       RNF43 MUTATED RNF43 WILD-TYPE
  FEMALE            24             201
  MALE              23             241
[1] 2 2
[1] FALSE
D4V9, binary
                 cls
clus                0   1
  RNF43 MUTATED    39   0
  RNF43 WILD-TYPE 311  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RNF43 MUTATED     39    0
  RNF43 WILD-TYPE  311   22
     clus
vv    RNF43 MUTATED RNF43 WILD-TYPE
  NO             39             311
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  RNF43 MUTATED                     36                            10
  RNF43 WILD-TYPE                  279                            37
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  RNF43 MUTATED                       1                              0
  RNF43 WILD-TYPE                   105                             10
D4V10, multiclass
                                clus
vv                               RNF43 MUTATED RNF43 WILD-TYPE
  COLON ADENOCARCINOMA                      36             279
  COLON MUCINOUS ADENOCARCINOMA             10              37
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  RNF43 MUTATED    37   0   0   4
  RNF43 WILD-TYPE 308   4  31  21
D4V11, multiclass
    clus
vv   RNF43 MUTATED RNF43 WILD-TYPE
  R0            37             308
  R1             0               4
  R2             0              31
  RX             4              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RNF43 MUTATED                                  0     2
  RNF43 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  RNF43 MUTATED                           3    29
  RNF43 WILD-TYPE                        19   197
D4V13, multiclass
                                  clus
vv                                 RNF43 MUTATED RNF43 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               9
  BLACK OR AFRICAN AMERICAN                    3              19
  WHITE                                       29             197
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(5) Variable = CRIPAK MUTATION ANALYSIS
D5V1, survival
                  sevent
clus2                0   1
  CRIPAK MUTATED    20   8
  CRIPAK WILD-TYPE 358  85
  CRIPAK MUTATED CRIPAK WILD-TYPE 
              28              443 
  CRIPAK MUTATED CRIPAK WILD-TYPE 
               8               85 
$`CRIPAK MUTATED`
TCGA-A6-6142 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3662 TCGA-AY-6386 TCGA-AZ-6598 
       25.08         7.04         3.02         6.05        17.82        49.41 
TCGA-AZ-6606 TCGA-CM-4747 TCGA-CM-6168 TCGA-CM-6172 TCGA-D5-6927 TCGA-D5-6928 
       11.74        25.02        12.99        11.01         9.44        11.64 
TCGA-D5-6930 TCGA-DM-A1D4 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-F4-6570 TCGA-AF-2687 
        1.51        92.75        12.59       140.38         6.18        24.13 
TCGA-AF-2693 TCGA-CI-6620 TCGA-DC-5869 TCGA-DC-6155 TCGA-DY-A1DD TCGA-EI-6506 
       19.10        33.17         5.03        13.97        57.24        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-F5-6465 TCGA-G5-6641 
       19.96        20.91        49.51        26.43 

$`CRIPAK WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.12        19.66        20.28         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02        78.08         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       88.21         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       37.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 
       14.99        13.02        15.02        14.04        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 
       12.43        14.30         9.04         4.80        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D6 
       10.26       119.70        24.43        38.20       130.65        49.91 
TCGA-DM-A1D7 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
       13.32         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 
       98.24         8.61        31.96        35.74        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3913 
       79.69        39.48        43.04        13.55        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.69         0.72         6.05         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        7.17        15.02        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DF 
        4.01         5.03         5.29       126.44        41.36        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6571 
       51.48        32.61         0.49        18.28         9.96        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       28.57        32.19         0.66         0.69        55.76 

  CRIPAK MUTATED CRIPAK WILD-TYPE 
            1.51             0.00 
  CRIPAK MUTATED CRIPAK WILD-TYPE 
          140.38           148.01 
  CRIPAK MUTATED CRIPAK WILD-TYPE 
           18.46            20.98 
[1] "1.5 - 140.4 (18.5)" "0.0 - 148.0 (21.0)"
[1] "hr=" "1.5"
D5V2, continuous
D5V3, binary
                  cls
clus                 0   1
  CRIPAK MUTATED    18  10
  CRIPAK WILD-TYPE 348 109
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CRIPAK MUTATED     18   10
  CRIPAK WILD-TYPE  348  109
        clus
vv       CRIPAK MUTATED CRIPAK WILD-TYPE
  COLON              18              348
  RECTUM             10              109
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CRIPAK MUTATED         1        0        3        10         0         0
  CRIPAK WILD-TYPE      90        1       29       128        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CRIPAK MUTATED           0          2          5          2        2
  CRIPAK WILD-TYPE        24          9         54         40       46
                  vv
clus               STAGE IVA STAGE IVB
  CRIPAK MUTATED           3         0
  CRIPAK WILD-TYPE        15         1
D5V4, multiclass
            clus
vv           CRIPAK MUTATED CRIPAK WILD-TYPE
  STAGE I                 1               90
  STAGE IA                0                1
  STAGE II                3               29
  STAGE IIA              10              128
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              2                9
  STAGE IIIB              5               54
  STAGE IIIC              2               40
  STAGE IV                2               46
  STAGE IVA               3               15
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  CRIPAK MUTATED     1   2  23   3
  CRIPAK WILD-TYPE  16  90 306  47
D5V5, multiclass
    clus
vv   CRIPAK MUTATED CRIPAK WILD-TYPE
  T1              1               16
  T2              2               90
  T3             23              306
  T4              3               47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  CRIPAK MUTATED    14  11   4
  CRIPAK WILD-TYPE 273 102  83
D5V6, multiclass
    clus
vv   CRIPAK MUTATED CRIPAK WILD-TYPE
  N0             14              273
  N1             11              102
  N2              4               83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V7, binary
                  cls
clus                 0   1
  CRIPAK MUTATED    19   5
  CRIPAK WILD-TYPE 356  60
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CRIPAK MUTATED     19    5
  CRIPAK WILD-TYPE  356   60
   clus
vv  CRIPAK MUTATED CRIPAK WILD-TYPE
  0             19              356
  1              5               60
[1] 2 2
[1] FALSE
D5V8, binary
                  cls
clus                 0   1
  CRIPAK MUTATED    17  12
  CRIPAK WILD-TYPE 208 252
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CRIPAK MUTATED     17   12
  CRIPAK WILD-TYPE  208  252
        clus
vv       CRIPAK MUTATED CRIPAK WILD-TYPE
  FEMALE             17              208
  MALE               12              252
[1] 2 2
[1] FALSE
D5V9, binary
                  cls
clus                 0   1
  CRIPAK MUTATED    21   1
  CRIPAK WILD-TYPE 329  21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CRIPAK MUTATED     21    1
  CRIPAK WILD-TYPE  329   21
     clus
vv    CRIPAK MUTATED CRIPAK WILD-TYPE
  NO              21              329
  YES              1               21
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CRIPAK MUTATED                     15                             3
  CRIPAK WILD-TYPE                  300                            44
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CRIPAK MUTATED                       9                              1
  CRIPAK WILD-TYPE                    97                              9
D5V10, multiclass
                                clus
vv                               CRIPAK MUTATED CRIPAK WILD-TYPE
  COLON ADENOCARCINOMA                       15              300
  COLON MUCINOUS ADENOCARCINOMA               3               44
  RECTAL ADENOCARCINOMA                       9               97
  RECTAL MUCINOUS ADENOCARCINOMA              1                9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  CRIPAK MUTATED    19   0   1   0
  CRIPAK WILD-TYPE 326   4  30  25
D5V11, multiclass
    clus
vv   CRIPAK MUTATED CRIPAK WILD-TYPE
  R0             19              326
  R1              0                4
  R2              1               30
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CRIPAK MUTATED                                  0     0
  CRIPAK WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  CRIPAK MUTATED                           3    23
  CRIPAK WILD-TYPE                        19   203
D5V13, multiclass
                                  clus
vv                                 CRIPAK MUTATED CRIPAK WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     3               19
  WHITE                                        23              203
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(6) Variable = SOX9 MUTATION ANALYSIS
D6V1, survival
                sevent
clus2              0   1
  SOX9 MUTATED    32   7
  SOX9 WILD-TYPE 346  86
  SOX9 MUTATED SOX9 WILD-TYPE 
            39            432 
  SOX9 MUTATED SOX9 WILD-TYPE 
             7             86 
$`SOX9 MUTATED`
TCGA-A6-4105 TCGA-A6-6141 TCGA-A6-6652 TCGA-AA-3492 TCGA-AA-3672 TCGA-AA-3713 
       14.53         8.38        24.69         3.02         0.92        19.04 
TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3939 TCGA-AA-3979 TCGA-AA-3989 TCGA-AA-A03F 
       25.02        17.98        12.99        24.00         7.96        18.05 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AY-6386 TCGA-AZ-4681 TCGA-AZ-6601 
       56.55         0.79         0.72        17.82       106.75       100.01 
TCGA-CA-5255 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4744 
        3.06        17.56        85.45        82.95       124.27        20.02 
TCGA-CM-4746 TCGA-CM-6674 TCGA-CM-6677 TCGA-D5-5537 TCGA-D5-6920 TCGA-D5-6929 
       37.02        12.95        11.08        45.40         3.68         4.80 
TCGA-D5-6931 TCGA-DM-A0XD TCGA-G4-6293 TCGA-G4-6306 TCGA-AG-A025 TCGA-CI-6622 
       12.00        24.43       133.18        44.68        49.97         6.97 
TCGA-DC-5337 TCGA-DC-6681 TCGA-F5-6465 
       15.02         5.95        49.51 

$`SOX9 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 
       16.57        34.65        33.34        32.75        36.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 
       22.06        32.71        27.09        22.52        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       24.16        21.76        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
       20.28         7.04         1.02        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
       14.01        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3821 
       19.04        10.06        35.05        33.04         0.99         1.02 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        25.02        27.02        27.02        19.07 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03J TCGA-AD-5900 
       14.01         0.92        41.00        39.98        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
       21.37        15.52         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5403 
       21.44        58.39         1.41         5.13        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 
       88.21        49.41         6.77        12.10        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5796 TCGA-CA-5797 
       11.74         3.19         1.61        12.69         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4948 
        0.07        12.20        12.76        10.06        14.30       148.01 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6748 
       15.62        49.08        51.32         9.99        21.14         1.91 
TCGA-CM-4743 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       23.05        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       11.01        13.05        11.08        11.01        10.06        12.03 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6923 
       12.49        16.14        15.58         1.48         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6932 
       14.30         9.04         9.44        11.64         1.51        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
       10.26       119.70        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6299 
       33.67        13.25         0.53        47.41        35.31        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       65.85        53.62        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A026 
        9.07        12.00        70.03        64.01        10.98         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
        4.73        78.12         7.17         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       10.98        19.99         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6571 
       20.55        19.96        20.91        18.28         9.96        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  SOX9 MUTATED SOX9 WILD-TYPE 
          0.72           0.00 
  SOX9 MUTATED SOX9 WILD-TYPE 
        133.18         148.01 
  SOX9 MUTATED SOX9 WILD-TYPE 
        17.980         20.945 
[1] "0.7 - 133.2 (18.0)" "0.0 - 148.0 (20.9)"
[1] "hr=" "1.4"
D6V2, continuous
D6V3, binary
                cls
clus               0   1
  SOX9 MUTATED    36   5
  SOX9 WILD-TYPE 330 114
[1] "tbl2"
                cls
clus             [,1] [,2]
  SOX9 MUTATED     36    5
  SOX9 WILD-TYPE  330  114
        clus
vv       SOX9 MUTATED SOX9 WILD-TYPE
  COLON            36            330
  RECTUM            5            114
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SOX9 MUTATED         5        0        2        19         1         0
  SOX9 WILD-TYPE      86        1       30       119         9         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SOX9 MUTATED           3          0          3          1        3         2
  SOX9 WILD-TYPE        21         11         56         41       45        16
                vv
clus             STAGE IVB
  SOX9 MUTATED           0
  SOX9 WILD-TYPE         1
D6V4, multiclass
            clus
vv           SOX9 MUTATED SOX9 WILD-TYPE
  STAGE I               5             86
  STAGE IA              0              1
  STAGE II              2             30
  STAGE IIA            19            119
  STAGE IIB             1              9
  STAGE IIC             0              1
  STAGE III             3             21
  STAGE IIIA            0             11
  STAGE IIIB            3             56
  STAGE IIIC            1             41
  STAGE IV              3             45
  STAGE IVA             2             16
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  SOX9 MUTATED     3   4  31   3
  SOX9 WILD-TYPE  14  88 298  47
D6V5, multiclass
    clus
vv   SOX9 MUTATED SOX9 WILD-TYPE
  T1            3             14
  T2            4             88
  T3           31            298
  T4            3             47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  SOX9 MUTATED    29   7   5
  SOX9 WILD-TYPE 258 106  82
D6V6, multiclass
    clus
vv   SOX9 MUTATED SOX9 WILD-TYPE
  N0           29            258
  N1            7            106
  N2            5             82
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V7, binary
                cls
clus               0   1
  SOX9 MUTATED    31   5
  SOX9 WILD-TYPE 344  60
[1] "tbl2"
                cls
clus             [,1] [,2]
  SOX9 MUTATED     31    5
  SOX9 WILD-TYPE  344   60
   clus
vv  SOX9 MUTATED SOX9 WILD-TYPE
  0           31            344
  1            5             60
[1] 2 2
[1] FALSE
D6V8, binary
                cls
clus               0   1
  SOX9 MUTATED    19  22
  SOX9 WILD-TYPE 206 242
[1] "tbl2"
                cls
clus             [,1] [,2]
  SOX9 MUTATED     19   22
  SOX9 WILD-TYPE  206  242
        clus
vv       SOX9 MUTATED SOX9 WILD-TYPE
  FEMALE           19            206
  MALE             22            242
[1] 2 2
[1] FALSE
D6V9, binary
                cls
clus               0   1
  SOX9 MUTATED    27   2
  SOX9 WILD-TYPE 323  20
[1] "tbl2"
                cls
clus             [,1] [,2]
  SOX9 MUTATED     27    2
  SOX9 WILD-TYPE  323   20
     clus
vv    SOX9 MUTATED SOX9 WILD-TYPE
  NO            27            323
  YES            2             20
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SOX9 MUTATED                     34                             2
  SOX9 WILD-TYPE                  281                            45
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SOX9 MUTATED                       5                              0
  SOX9 WILD-TYPE                   101                             10
D6V10, multiclass
                                clus
vv                               SOX9 MUTATED SOX9 WILD-TYPE
  COLON ADENOCARCINOMA                     34            281
  COLON MUCINOUS ADENOCARCINOMA             2             45
  RECTAL ADENOCARCINOMA                     5            101
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  SOX9 MUTATED    24   1   2   5
  SOX9 WILD-TYPE 321   3  29  20
D6V11, multiclass
    clus
vv   SOX9 MUTATED SOX9 WILD-TYPE
  R0           24            321
  R1            1              3
  R2            2             29
  RX            5             20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SOX9 MUTATED                                  0     2
  SOX9 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  SOX9 MUTATED                           5    22
  SOX9 WILD-TYPE                        17   204
D6V13, multiclass
                                  clus
vv                                 SOX9 MUTATED SOX9 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              9
  BLACK OR AFRICAN AMERICAN                   5             17
  WHITE                                      22            204
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(7) Variable = FAM123B MUTATION ANALYSIS
D7V1, survival
                   sevent
clus2                 0   1
  FAM123B MUTATED    40  17
  FAM123B WILD-TYPE 338  76
  FAM123B MUTATED FAM123B WILD-TYPE 
               57               414 
  FAM123B MUTATED FAM123B WILD-TYPE 
               17                76 
$`FAM123B MUTATED`
TCGA-A6-3808 TCGA-A6-4105 TCGA-A6-6137 TCGA-AA-3492 TCGA-AA-3511 TCGA-AA-3516 
       33.34        14.53        27.09         3.02         6.97        13.02 
TCGA-AA-3530 TCGA-AA-3548 TCGA-AA-3554 TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3666 
       19.07        33.99        17.95        61.02         6.97         2.01 
TCGA-AA-3680 TCGA-AA-3821 TCGA-AA-3845 TCGA-AA-3864 TCGA-AA-3869 TCGA-AA-3939 
       11.01         1.02         0.00        53.00        27.02        12.99 
TCGA-AA-3977 TCGA-AA-A00A TCGA-AA-A010 TCGA-AA-A01D TCGA-AD-6890 TCGA-AD-6895 
       25.02        38.04        34.98        10.98         0.79         0.72 
TCGA-AU-6004 TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-5407 TCGA-CA-6717 TCGA-CK-4947 
       27.09        21.44        58.39        88.21        12.76        17.56 
TCGA-CK-6747 TCGA-CM-4744 TCGA-CM-5860 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6171 
       82.95        20.02        32.02        14.99        12.99        14.04 
TCGA-CM-6677 TCGA-D5-5537 TCGA-D5-6922 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A28H 
       11.08        45.40         4.41        12.59       140.38       117.07 
TCGA-DM-A28K TCGA-F4-6570 TCGA-F4-6809 TCGA-G4-6315 TCGA-G4-6626 TCGA-AG-3584 
       98.24         6.18        13.25        61.91        46.75        24.00 
TCGA-AG-3892 TCGA-AG-3896 TCGA-AG-A002 TCGA-AG-A02G TCGA-AG-A02N TCGA-AH-6544 
       13.02         1.02        20.98        38.96        61.97        38.56 
TCGA-AH-6644 TCGA-DY-A1DD TCGA-DY-A1DF 
        0.72        57.24        24.13 

$`FAM123B WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 
       16.57        34.65        32.75        36.53        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       30.44        29.19        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       32.71        22.52         8.38        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3514 
       20.28         7.04         1.02        35.01        63.98         1.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
        8.05        19.07         0.00        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3549 TCGA-AA-3552 
       26.01        12.99         0.99        14.01        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       24.00        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3672 
       19.99        78.08         6.05        54.02        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       50.04        47.01        15.02         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 
       10.06        35.05        33.04         0.99        25.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 
       15.95        38.99        37.02        14.93        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3870 
       31.07        31.07        30.05        17.03        24.03        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       18.05        31.00         2.01        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       21.99         1.02        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6899 
       40.96         0.07        21.37        15.52        56.55         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 
       22.42        27.42        10.88         0.20        14.50        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
        0.95        33.01        17.82         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07        12.20        10.06 
TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       14.30       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4746 
        9.99        21.14         1.91       124.27        23.05        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6169 
       12.00         2.96        29.03        16.04        21.99        13.02 
TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6678 
       15.02        11.01        12.95        13.05        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       10.06        12.03        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        3.68        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-F4-6459 TCGA-F4-6460 
       81.37       119.93        35.97        60.79         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       35.74        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       33.67         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       36.03        20.05         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3902 
       36.95        17.03        35.01        14.01        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6547 
       49.97         1.94        41.00        38.04       117.11         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
       17.49         0.69         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
      126.44        41.36        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  FAM123B MUTATED FAM123B WILD-TYPE 
                0                 0 
  FAM123B MUTATED FAM123B WILD-TYPE 
           140.38            148.01 
  FAM123B MUTATED FAM123B WILD-TYPE 
           20.020            20.235 
[1] "0.0 - 140.4 (20.0)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.4"
D7V2, continuous
D7V3, binary
                   cls
clus                  0   1
  FAM123B MUTATED    50  10
  FAM123B WILD-TYPE 316 109
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM123B MUTATED     50   10
  FAM123B WILD-TYPE  316  109
        clus
vv       FAM123B MUTATED FAM123B WILD-TYPE
  COLON               50               316
  RECTUM              10               109
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FAM123B MUTATED         9        0        7        20         1         0
  FAM123B WILD-TYPE      82        1       25       118         9         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FAM123B MUTATED           2          1          3          5        5
  FAM123B WILD-TYPE        22         10         56         37       43
                   vv
clus                STAGE IVA STAGE IVB
  FAM123B MUTATED           1         0
  FAM123B WILD-TYPE        17         1
D7V4, multiclass
            clus
vv           FAM123B MUTATED FAM123B WILD-TYPE
  STAGE I                  9                82
  STAGE IA                 0                 1
  STAGE II                 7                25
  STAGE IIA               20               118
  STAGE IIB                1                 9
  STAGE IIC                0                 1
  STAGE III                2                22
  STAGE IIIA               1                10
  STAGE IIIB               3                56
  STAGE IIIC               5                37
  STAGE IV                 5                43
  STAGE IVA                1                17
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  FAM123B MUTATED     3   9  43   5
  FAM123B WILD-TYPE  14  83 286  45
D7V5, multiclass
    clus
vv   FAM123B MUTATED FAM123B WILD-TYPE
  T1               3                14
  T2               9                83
  T3              43               286
  T4               5                45
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  FAM123B MUTATED    38  11  10
  FAM123B WILD-TYPE 249 102  77
D7V6, multiclass
    clus
vv   FAM123B MUTATED FAM123B WILD-TYPE
  N0              38               249
  N1              11               102
  N2              10                77
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V7, binary
                   cls
clus                  0   1
  FAM123B MUTATED    45   7
  FAM123B WILD-TYPE 330  58
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM123B MUTATED     45    7
  FAM123B WILD-TYPE  330   58
   clus
vv  FAM123B MUTATED FAM123B WILD-TYPE
  0              45               330
  1               7                58
[1] 2 2
[1] FALSE
D7V8, binary
                   cls
clus                  0   1
  FAM123B MUTATED    27  33
  FAM123B WILD-TYPE 198 231
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM123B MUTATED     27   33
  FAM123B WILD-TYPE  198  231
        clus
vv       FAM123B MUTATED FAM123B WILD-TYPE
  FEMALE              27               198
  MALE                33               231
[1] 2 2
[1] FALSE
D7V9, binary
                   cls
clus                  0   1
  FAM123B MUTATED    42   0
  FAM123B WILD-TYPE 308  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM123B MUTATED     42    0
  FAM123B WILD-TYPE  308   22
     clus
vv    FAM123B MUTATED FAM123B WILD-TYPE
  NO               42               308
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  FAM123B MUTATED                     45                             5
  FAM123B WILD-TYPE                  270                            42
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  FAM123B MUTATED                      10                              0
  FAM123B WILD-TYPE                    96                             10
D7V10, multiclass
                                clus
vv                               FAM123B MUTATED FAM123B WILD-TYPE
  COLON ADENOCARCINOMA                        45               270
  COLON MUCINOUS ADENOCARCINOMA                5                42
  RECTAL ADENOCARCINOMA                       10                96
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  FAM123B MUTATED    37   0   4   4
  FAM123B WILD-TYPE 308   4  27  21
D7V11, multiclass
    clus
vv   FAM123B MUTATED FAM123B WILD-TYPE
  R0              37               308
  R1               0                 4
  R2               4                27
  RX               4                21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FAM123B MUTATED                                  0     1
  FAM123B WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  FAM123B MUTATED                           2    29
  FAM123B WILD-TYPE                        20   197
D7V13, multiclass
                                  clus
vv                                 FAM123B MUTATED FAM123B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                10
  BLACK OR AFRICAN AMERICAN                      2                20
  WHITE                                         29               197
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(8) Variable = ZFP36L2 MUTATION ANALYSIS
D8V1, survival
                   sevent
clus2                 0   1
  ZFP36L2 MUTATED    12   4
  ZFP36L2 WILD-TYPE 366  89
  ZFP36L2 MUTATED ZFP36L2 WILD-TYPE 
               16               455 
  ZFP36L2 MUTATED ZFP36L2 WILD-TYPE 
                4                89 
$`ZFP36L2 MUTATED`
TCGA-A6-5666 TCGA-AA-3989 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6598 TCGA-CA-5797 
       32.71         7.96        10.88       106.75        49.41         3.29 
TCGA-CM-6171 TCGA-D5-6536 TCGA-D5-6540 TCGA-D5-6928 TCGA-DM-A1D9 TCGA-DM-A1HA 
       14.04        17.85        16.14        11.64       140.38       131.51 
TCGA-G4-6588 TCGA-AF-5654 TCGA-AG-3742 TCGA-EI-6507 
       26.17        16.83         0.99        19.96 

$`ZFP36L2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        22.06        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        27.02        19.07        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 
       21.44        17.82        58.39         1.41         5.13        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        88.21         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.25         0.07        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
        4.80        17.13        12.49        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 
        4.41        12.43        14.30         9.04         9.44         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
        7.50        44.32       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       13.78        35.80        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       14.50        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3878 TCGA-AG-3881 
        7.99         0.99        37.02        32.98         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  ZFP36L2 MUTATED ZFP36L2 WILD-TYPE 
             0.99              0.00 
  ZFP36L2 MUTATED ZFP36L2 WILD-TYPE 
           140.38            148.01 
  ZFP36L2 MUTATED ZFP36L2 WILD-TYPE 
            17.34             20.55 
[1] "1.0 - 140.4 (17.3)" "0.0 - 148.0 (20.6)"
[1] "hr=" "1"  
D8V2, continuous
D8V3, binary
                   cls
clus                  0   1
  ZFP36L2 MUTATED    14   3
  ZFP36L2 WILD-TYPE 352 116
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZFP36L2 MUTATED     14    3
  ZFP36L2 WILD-TYPE  352  116
        clus
vv       ZFP36L2 MUTATED ZFP36L2 WILD-TYPE
  COLON               14               352
  RECTUM               3               116
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZFP36L2 MUTATED         4        0        1         7         1         1
  ZFP36L2 WILD-TYPE      87        1       31       131         9         0
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZFP36L2 MUTATED           0          0          0          1        1
  ZFP36L2 WILD-TYPE        24         11         59         41       47
                   vv
clus                STAGE IVA STAGE IVB
  ZFP36L2 MUTATED           0         0
  ZFP36L2 WILD-TYPE        18         1
D8V4, multiclass
            clus
vv           ZFP36L2 MUTATED ZFP36L2 WILD-TYPE
  STAGE I                  4                87
  STAGE IA                 0                 1
  STAGE II                 1                31
  STAGE IIA                7               131
  STAGE IIB                1                 9
  STAGE IIC                1                 0
  STAGE III                0                24
  STAGE IIIA               0                11
  STAGE IIIB               0                59
  STAGE IIIC               1                41
  STAGE IV                 1                47
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  ZFP36L2 MUTATED     1   3  10   3
  ZFP36L2 WILD-TYPE  16  89 319  47
D8V5, multiclass
    clus
vv   ZFP36L2 MUTATED ZFP36L2 WILD-TYPE
  T1               1                16
  T2               3                89
  T3              10               319
  T4               3                47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  ZFP36L2 MUTATED    14   0   3
  ZFP36L2 WILD-TYPE 273 113  84
D8V6, multiclass
    clus
vv   ZFP36L2 MUTATED ZFP36L2 WILD-TYPE
  N0              14               273
  N1               0               113
  N2               3                84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V7, binary
                   cls
clus                  0   1
  ZFP36L2 MUTATED    13   1
  ZFP36L2 WILD-TYPE 362  64
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZFP36L2 MUTATED     13    1
  ZFP36L2 WILD-TYPE  362   64
   clus
vv  ZFP36L2 MUTATED ZFP36L2 WILD-TYPE
  0              13               362
  1               1                64
[1] 2 2
[1] FALSE
D8V8, binary
                   cls
clus                  0   1
  ZFP36L2 MUTATED     8   9
  ZFP36L2 WILD-TYPE 217 255
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZFP36L2 MUTATED      8    9
  ZFP36L2 WILD-TYPE  217  255
        clus
vv       ZFP36L2 MUTATED ZFP36L2 WILD-TYPE
  FEMALE               8               217
  MALE                 9               255
[1] 2 2
[1] FALSE
D8V9, binary
                   cls
clus                  0   1
  ZFP36L2 MUTATED    13   0
  ZFP36L2 WILD-TYPE 337  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZFP36L2 MUTATED     13    0
  ZFP36L2 WILD-TYPE  337   22
     clus
vv    ZFP36L2 MUTATED ZFP36L2 WILD-TYPE
  NO               13               337
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ZFP36L2 MUTATED                     12                             2
  ZFP36L2 WILD-TYPE                  303                            45
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ZFP36L2 MUTATED                       3                              0
  ZFP36L2 WILD-TYPE                   103                             10
D8V10, multiclass
                                clus
vv                               ZFP36L2 MUTATED ZFP36L2 WILD-TYPE
  COLON ADENOCARCINOMA                        12               303
  COLON MUCINOUS ADENOCARCINOMA                2                45
  RECTAL ADENOCARCINOMA                        3               103
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  ZFP36L2 MUTATED    10   0   1   1
  ZFP36L2 WILD-TYPE 335   4  30  24
D8V11, multiclass
    clus
vv   ZFP36L2 MUTATED ZFP36L2 WILD-TYPE
  R0              10               335
  R1               0                 4
  R2               1                30
  RX               1                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZFP36L2 MUTATED                                  0     1
  ZFP36L2 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  ZFP36L2 MUTATED                           0    14
  ZFP36L2 WILD-TYPE                        22   212
D8V13, multiclass
                                  clus
vv                                 ZFP36L2 MUTATED ZFP36L2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                10
  BLACK OR AFRICAN AMERICAN                      0                22
  WHITE                                         14               212
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(9) Variable = B2M MUTATION ANALYSIS
D9V1, survival
               sevent
clus2             0   1
  B2M MUTATED    12   4
  B2M WILD-TYPE 366  89
  B2M MUTATED B2M WILD-TYPE 
           16           455 
  B2M MUTATED B2M WILD-TYPE 
            4            89 
$`B2M MUTATED`
TCGA-A6-3809 TCGA-A6-6653 TCGA-A6-6780 TCGA-AA-3510 TCGA-AA-3845 TCGA-AA-A010 
       32.75        24.39        20.12        63.98         0.00        34.98 
TCGA-AZ-6601 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-5913 TCGA-D5-5538 TCGA-DM-A28F 
      100.01        12.76        10.06        51.32        12.26        35.97 
TCGA-F4-6703 TCGA-G4-6628 TCGA-AG-3892 TCGA-AG-A02N 
       47.87        79.69        13.02        61.97 

$`B2M WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6781 
       25.18        24.16        21.76        24.69        23.87        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 
       20.28         7.04         3.02         1.02        35.01         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02        14.93        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       49.41         6.77        12.10        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.07        12.20        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        49.08         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
       81.37       119.93        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       31.96        35.74         6.18         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 
       35.80        26.17        91.79        46.75        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
       49.97         1.94        38.96        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  B2M MUTATED B2M WILD-TYPE 
            0             0 
  B2M MUTATED B2M WILD-TYPE 
       100.01        148.01 
  B2M MUTATED B2M WILD-TYPE 
       33.865        20.020 
[1] "0.0 - 100.0 (33.9)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.2"
D9V2, continuous
D9V3, binary
               cls
clus              0   1
  B2M MUTATED    15   2
  B2M WILD-TYPE 351 117
[1] "tbl2"
               cls
clus            [,1] [,2]
  B2M MUTATED     15    2
  B2M WILD-TYPE  351  117
        clus
vv       B2M MUTATED B2M WILD-TYPE
  COLON           15           351
  RECTUM           2           117
[1] 2 2
[1] FALSE
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  B2M MUTATED         3        0        3         6         3         0
  B2M WILD-TYPE      88        1       29       132         7         1
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  B2M MUTATED           0          0          2          0        0         0
  B2M WILD-TYPE        24         11         57         42       48        18
               vv
clus            STAGE IVB
  B2M MUTATED           0
  B2M WILD-TYPE         1
D9V4, multiclass
            clus
vv           B2M MUTATED B2M WILD-TYPE
  STAGE I              3            88
  STAGE IA             0             1
  STAGE II             3            29
  STAGE IIA            6           132
  STAGE IIB            3             7
  STAGE IIC            0             1
  STAGE III            0            24
  STAGE IIIA           0            11
  STAGE IIIB           2            57
  STAGE IIIC           0            42
  STAGE IV             0            48
  STAGE IVA            0            18
  STAGE IVB            0             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  B2M MUTATED     1   2  11   3
  B2M WILD-TYPE  16  90 318  47
D9V5, multiclass
    clus
vv   B2M MUTATED B2M WILD-TYPE
  T1           1            16
  T2           2            90
  T3          11           318
  T4           3            47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2
  B2M MUTATED    15   2   0
  B2M WILD-TYPE 272 111  87
D9V6, multiclass
    clus
vv   B2M MUTATED B2M WILD-TYPE
  N0          15           272
  N1           2           111
  N2           0            87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V7, binary
               cls
clus              0   1
  B2M MUTATED    14   0
  B2M WILD-TYPE 361  65
[1] "tbl2"
               cls
clus            [,1] [,2]
  B2M MUTATED     14    0
  B2M WILD-TYPE  361   65
   clus
vv  B2M MUTATED B2M WILD-TYPE
  0          14           361
  1           0            65
[1] 2 2
[1] FALSE
D9V8, binary
               cls
clus              0   1
  B2M MUTATED     7  10
  B2M WILD-TYPE 218 254
[1] "tbl2"
               cls
clus            [,1] [,2]
  B2M MUTATED      7   10
  B2M WILD-TYPE  218  254
        clus
vv       B2M MUTATED B2M WILD-TYPE
  FEMALE           7           218
  MALE            10           254
[1] 2 2
[1] FALSE
D9V9, binary
               cls
clus              0   1
  B2M MUTATED    13   0
  B2M WILD-TYPE 337  22
[1] "tbl2"
               cls
clus            [,1] [,2]
  B2M MUTATED     13    0
  B2M WILD-TYPE  337   22
     clus
vv    B2M MUTATED B2M WILD-TYPE
  NO           13           337
  YES           0            22
[1] 2 2
[1] FALSE
               vv
clus            COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  B2M MUTATED                     12                             3
  B2M WILD-TYPE                  303                            44
               vv
clus            RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  B2M MUTATED                       2                              0
  B2M WILD-TYPE                   104                             10
D9V10, multiclass
                                clus
vv                               B2M MUTATED B2M WILD-TYPE
  COLON ADENOCARCINOMA                    12           303
  COLON MUCINOUS ADENOCARCINOMA            3            44
  RECTAL ADENOCARCINOMA                    2           104
  RECTAL MUCINOUS ADENOCARCINOMA           0            10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             R0  R1  R2  RX
  B2M MUTATED     9   0   0   4
  B2M WILD-TYPE 336   4  31  21
D9V11, multiclass
    clus
vv   B2M MUTATED B2M WILD-TYPE
  R0           9           336
  R1           0             4
  R2           0            31
  RX           4            21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V12, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  B2M MUTATED                                  0     2
  B2M WILD-TYPE                                1     9
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  B2M MUTATED                           0    10
  B2M WILD-TYPE                        22   216
D9V13, multiclass
                                  clus
vv                                 B2M MUTATED B2M WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      2             9
  BLACK OR AFRICAN AMERICAN                  0            22
  WHITE                                     10           216
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(10) Variable = TXNDC2 MUTATION ANALYSIS
D10V1, survival
                  sevent
clus2                0   1
  TXNDC2 MUTATED    20   4
  TXNDC2 WILD-TYPE 358  89
  TXNDC2 MUTATED TXNDC2 WILD-TYPE 
              24              447 
  TXNDC2 MUTATED TXNDC2 WILD-TYPE 
               4               89 
$`TXNDC2 MUTATED`
TCGA-A6-5659 TCGA-A6-6142 TCGA-A6-6780 TCGA-AA-3660 TCGA-AA-3672 TCGA-AA-3713 
       30.44        25.08        20.12        78.08         0.92        19.04 
TCGA-AA-3977 TCGA-AD-6888 TCGA-AD-6901 TCGA-CA-6717 TCGA-CK-6747 TCGA-CK-6748 
       25.02        15.52        22.42        12.76        82.95         1.91 
TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6167 TCGA-CM-6170 TCGA-CM-6172 TCGA-D5-6533 
       15.02         2.96        14.99        15.02        11.01         1.32 
TCGA-D5-6538 TCGA-DM-A28C TCGA-G4-6321 TCGA-G4-6628 TCGA-CL-5917 TCGA-DC-6158 
       17.13        81.37        22.09        79.69        78.12        10.98 

$`TXNDC2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6648 
       22.06        32.71        27.09        22.52         8.38        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6781 
       24.16        21.76        24.69        24.39        23.87        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
       14.01        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6964 
       56.55         0.79         0.72         5.79        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6751 TCGA-CM-4743 
       49.08        51.32         9.99        21.14       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6162 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        17.03        12.00        29.03        16.04        21.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       12.99        13.02        14.04        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6534 
       19.59        56.09        55.92        20.19        18.25        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       15.12        17.85         4.80        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28E TCGA-DM-A28F 
      131.51       135.65       139.17         6.12       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       63.62        61.91        36.00        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       91.79        46.75        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
       33.17         6.97         4.73         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       13.97        27.95        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  TXNDC2 MUTATED TXNDC2 WILD-TYPE 
            0.92             0.00 
  TXNDC2 MUTATED TXNDC2 WILD-TYPE 
           82.95           148.01 
  TXNDC2 MUTATED TXNDC2 WILD-TYPE 
          18.085           20.550 
[1] "0.9 - 83.0 (18.1)"  "0.0 - 148.0 (20.6)"
[1] "hr=" "1.3"
D10V2, continuous
D10V3, binary
                  cls
clus                 0   1
  TXNDC2 MUTATED    22   2
  TXNDC2 WILD-TYPE 344 117
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TXNDC2 MUTATED     22    2
  TXNDC2 WILD-TYPE  344  117
        clus
vv       TXNDC2 MUTATED TXNDC2 WILD-TYPE
  COLON              22              344
  RECTUM              2              117
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TXNDC2 MUTATED         6        0        1         4         0         0
  TXNDC2 WILD-TYPE      85        1       31       134        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TXNDC2 MUTATED           2          0          4          2        2
  TXNDC2 WILD-TYPE        22         11         55         40       46
                  vv
clus               STAGE IVA STAGE IVB
  TXNDC2 MUTATED           1         0
  TXNDC2 WILD-TYPE        17         1
D10V4, multiclass
            clus
vv           TXNDC2 MUTATED TXNDC2 WILD-TYPE
  STAGE I                 6               85
  STAGE IA                0                1
  STAGE II                1               31
  STAGE IIA               4              134
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               2               22
  STAGE IIIA              0               11
  STAGE IIIB              4               55
  STAGE IIIC              2               40
  STAGE IV                2               46
  STAGE IVA               1               17
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  TXNDC2 MUTATED     1   7  15   1
  TXNDC2 WILD-TYPE  16  85 314  49
D10V5, multiclass
    clus
vv   TXNDC2 MUTATED TXNDC2 WILD-TYPE
  T1              1               16
  T2              7               85
  T3             15              314
  T4              1               49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  TXNDC2 MUTATED    15   6   3
  TXNDC2 WILD-TYPE 272 107  84
D10V6, multiclass
    clus
vv   TXNDC2 MUTATED TXNDC2 WILD-TYPE
  N0             15              272
  N1              6              107
  N2              3               84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V7, binary
                  cls
clus                 0   1
  TXNDC2 MUTATED    15   3
  TXNDC2 WILD-TYPE 360  62
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TXNDC2 MUTATED     15    3
  TXNDC2 WILD-TYPE  360   62
   clus
vv  TXNDC2 MUTATED TXNDC2 WILD-TYPE
  0             15              360
  1              3               62
[1] 2 2
[1] FALSE
D10V8, binary
                  cls
clus                 0   1
  TXNDC2 MUTATED    13  11
  TXNDC2 WILD-TYPE 212 253
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TXNDC2 MUTATED     13   11
  TXNDC2 WILD-TYPE  212  253
        clus
vv       TXNDC2 MUTATED TXNDC2 WILD-TYPE
  FEMALE             13              212
  MALE               11              253
[1] 2 2
[1] FALSE
D10V9, binary
                  cls
clus                 0   1
  TXNDC2 MUTATED    21   1
  TXNDC2 WILD-TYPE 329  21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TXNDC2 MUTATED     21    1
  TXNDC2 WILD-TYPE  329   21
     clus
vv    TXNDC2 MUTATED TXNDC2 WILD-TYPE
  NO              21              329
  YES              1               21
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  TXNDC2 MUTATED                     19                             3
  TXNDC2 WILD-TYPE                  296                            44
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  TXNDC2 MUTATED                       2                              0
  TXNDC2 WILD-TYPE                   104                             10
D10V10, multiclass
                                clus
vv                               TXNDC2 MUTATED TXNDC2 WILD-TYPE
  COLON ADENOCARCINOMA                       19              296
  COLON MUCINOUS ADENOCARCINOMA               3               44
  RECTAL ADENOCARCINOMA                       2              104
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  TXNDC2 MUTATED    14   0   1   4
  TXNDC2 WILD-TYPE 331   4  30  21
D10V11, multiclass
    clus
vv   TXNDC2 MUTATED TXNDC2 WILD-TYPE
  R0             14              331
  R1              0                4
  R2              1               30
  RX              4               21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TXNDC2 MUTATED                                  0     1
  TXNDC2 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  TXNDC2 MUTATED                           1    18
  TXNDC2 WILD-TYPE                        21   208
D10V13, multiclass
                                  clus
vv                                 TXNDC2 MUTATED TXNDC2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                        18              208
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(11) Variable = ACVR1B MUTATION ANALYSIS
D11V1, survival
                  sevent
clus2                0   1
  ACVR1B MUTATED    20   6
  ACVR1B WILD-TYPE 358  87
  ACVR1B MUTATED ACVR1B WILD-TYPE 
              26              445 
  ACVR1B MUTATED ACVR1B WILD-TYPE 
               6               87 
$`ACVR1B MUTATED`
TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-6652 TCGA-AA-3715 TCGA-AA-3831 TCGA-AA-3833 
       34.65        32.75        24.69        19.04        17.98        15.95 
TCGA-AA-3877 TCGA-AA-3994 TCGA-AA-A00J TCGA-AA-A010 TCGA-AA-A01R TCGA-AA-A029 
       31.00        27.02        18.05        34.98        35.01        51.98 
TCGA-AA-A02J TCGA-AA-A03F TCGA-AZ-6601 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 
        5.03        18.05       100.01         0.07        12.76        10.06 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-6674 TCGA-D5-6536 TCGA-D5-6928 TCGA-F4-6806 
      124.27        23.05        12.95        17.85        11.64        41.42 
TCGA-AG-A01L TCGA-DC-6158 
       12.00        10.98 

$`ACVR1B WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5657 
       16.57        33.34        36.53        14.53        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       30.44        29.19        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       24.16        21.76        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       85.05        26.99        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        0.99        25.02         1.02        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        27.02        19.07         7.96        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       19.00        30.02        34.03        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
       38.07         1.02         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02K TCGA-AA-A02O 
       37.02        39.06        39.98         2.01        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       41.00        39.98        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
       12.10        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6716 TCGA-CA-6719 
       12.69         3.06         3.25         3.29        12.20        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CM-4744 TCGA-CM-4746 
        9.99        21.14        82.95         1.91        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 
       18.25         1.32        43.27        15.12         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6930 
       12.43        14.30         9.04         9.44         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       34.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01W 
       23.01        37.02        15.95        36.03         9.07        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  ACVR1B MUTATED ACVR1B WILD-TYPE 
            0.07             0.00 
  ACVR1B MUTATED ACVR1B WILD-TYPE 
          124.27           148.01 
  ACVR1B MUTATED ACVR1B WILD-TYPE 
          18.545           20.280 
[1] "0.1 - 124.3 (18.5)" "0.0 - 148.0 (20.3)"
[1] "hr=" "1.1"
D11V2, continuous
D11V3, binary
                  cls
clus                 0   1
  ACVR1B MUTATED    26   2
  ACVR1B WILD-TYPE 340 117
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ACVR1B MUTATED     26    2
  ACVR1B WILD-TYPE  340  117
        clus
vv       ACVR1B MUTATED ACVR1B WILD-TYPE
  COLON              26              340
  RECTUM              2              117
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ACVR1B MUTATED         5        0        4         8         2         0
  ACVR1B WILD-TYPE      86        1       28       130         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ACVR1B MUTATED           2          0          4          1        1
  ACVR1B WILD-TYPE        22         11         55         41       47
                  vv
clus               STAGE IVA STAGE IVB
  ACVR1B MUTATED           1         0
  ACVR1B WILD-TYPE        17         1
D11V4, multiclass
            clus
vv           ACVR1B MUTATED ACVR1B WILD-TYPE
  STAGE I                 5               86
  STAGE IA                0                1
  STAGE II                4               28
  STAGE IIA               8              130
  STAGE IIB               2                8
  STAGE IIC               0                1
  STAGE III               2               22
  STAGE IIIA              0               11
  STAGE IIIB              4               55
  STAGE IIIC              1               41
  STAGE IV                1               47
  STAGE IVA               1               17
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ACVR1B MUTATED     1   4  19   4
  ACVR1B WILD-TYPE  16  88 310  46
D11V5, multiclass
    clus
vv   ACVR1B MUTATED ACVR1B WILD-TYPE
  T1              1               16
  T2              4               88
  T3             19              310
  T4              4               46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  ACVR1B MUTATED    21   4   3
  ACVR1B WILD-TYPE 266 109  84
D11V6, multiclass
    clus
vv   ACVR1B MUTATED ACVR1B WILD-TYPE
  N0             21              266
  N1              4              109
  N2              3               84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V7, binary
                  cls
clus                 0   1
  ACVR1B MUTATED    24   2
  ACVR1B WILD-TYPE 351  63
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ACVR1B MUTATED     24    2
  ACVR1B WILD-TYPE  351   63
   clus
vv  ACVR1B MUTATED ACVR1B WILD-TYPE
  0             24              351
  1              2               63
[1] 2 2
[1] FALSE
D11V8, binary
                  cls
clus                 0   1
  ACVR1B MUTATED    10  18
  ACVR1B WILD-TYPE 215 246
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ACVR1B MUTATED     10   18
  ACVR1B WILD-TYPE  215  246
        clus
vv       ACVR1B MUTATED ACVR1B WILD-TYPE
  FEMALE             10              215
  MALE               18              246
[1] 2 2
[1] FALSE
D11V9, binary
                  cls
clus                 0   1
  ACVR1B MUTATED    21   1
  ACVR1B WILD-TYPE 329  21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ACVR1B MUTATED     21    1
  ACVR1B WILD-TYPE  329   21
     clus
vv    ACVR1B MUTATED ACVR1B WILD-TYPE
  NO              21              329
  YES              1               21
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ACVR1B MUTATED                     17                             9
  ACVR1B WILD-TYPE                  298                            38
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ACVR1B MUTATED                       2                              0
  ACVR1B WILD-TYPE                   104                             10
D11V10, multiclass
                                clus
vv                               ACVR1B MUTATED ACVR1B WILD-TYPE
  COLON ADENOCARCINOMA                       17              298
  COLON MUCINOUS ADENOCARCINOMA               9               38
  RECTAL ADENOCARCINOMA                       2              104
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ACVR1B MUTATED    20   0   1   5
  ACVR1B WILD-TYPE 325   4  30  20
D11V11, multiclass
    clus
vv   ACVR1B MUTATED ACVR1B WILD-TYPE
  R0             20              325
  R1              0                4
  R2              1               30
  RX              5               20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ACVR1B MUTATED                                  0     3
  ACVR1B WILD-TYPE                                1     8
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ACVR1B MUTATED                           1    11
  ACVR1B WILD-TYPE                        21   215
D11V13, multiclass
                                  clus
vv                                 ACVR1B MUTATED ACVR1B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         3                8
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                        11              215
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(12) Variable = CDH1 MUTATION ANALYSIS
D12V1, survival
                sevent
clus2              0   1
  CDH1 MUTATED    71  14
  CDH1 WILD-TYPE 307  79
  CDH1 MUTATED CDH1 WILD-TYPE 
            85            386 
  CDH1 MUTATED CDH1 WILD-TYPE 
            14             79 
$`CDH1 MUTATED`
TCGA-A6-3809 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-6141 
       32.75        31.63        30.44        33.53        23.61         8.38 
TCGA-A6-6648 TCGA-A6-6780 TCGA-AA-3502 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3697 
       25.18        20.12        35.01         6.05         6.97        85.05 
TCGA-AA-3713 TCGA-AA-3821 TCGA-AA-A00N TCGA-AA-A00U TCGA-AA-A01R TCGA-AA-A02K 
       19.04         1.02         4.01        17.03        35.01        14.01 
TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6964 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-6197 
        0.07        56.55        10.88        14.50        27.09        21.44 
TCGA-AY-6386 TCGA-AZ-4616 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-CA-5797 
       17.82         5.13        49.41         6.77        12.10         3.29 
TCGA-CA-6715 TCGA-CA-6717 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 
        0.07        12.76        85.45        15.62        49.08         9.99 
TCGA-CK-6747 TCGA-CM-4743 TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       82.95        23.05        13.02        22.03        22.98        30.08 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6678 
       17.03        15.02        15.02        14.04        11.01        11.01 
TCGA-CM-6679 TCGA-D5-6529 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6539 
       10.06        20.19        15.12        17.85         4.80        12.49 
TCGA-D5-6540 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6932 TCGA-DM-A1D4 TCGA-DM-A1HA 
       16.14        11.64         1.51        11.38        92.75       131.51 
TCGA-DM-A282 TCGA-DM-A28E TCGA-DM-A28F TCGA-F4-6460 TCGA-F4-6570 TCGA-F4-6856 
      139.17       119.93        35.97        31.96         6.18        35.31 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6310 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       53.62        44.68        63.62        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-AF-2687 TCGA-AF-6136 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3892 
       35.80        24.13        15.39        37.02        32.98        13.02 
TCGA-AH-6544 TCGA-AH-6643 TCGA-DC-5337 TCGA-DY-A1DG TCGA-EF-5830 TCGA-F5-6465 
       38.56         0.69        15.02        51.48         0.49        49.51 
TCGA-G5-6235 
       55.76 

$`CDH1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5660 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 
       29.19        22.09        22.06        32.71        27.09        22.52 
TCGA-A6-6142 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.08        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3510 
       19.66        20.28         7.04         3.02         1.02        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       19.99        61.02        78.08        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3715 
       37.05        19.00        36.00         5.03        26.99        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 
       10.06        35.05        33.04         0.99        25.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       27.02        42.02         0.99        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
       38.07         1.02         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 
        0.92        41.00        39.98        18.05        40.96        21.37 
TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       15.52         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AZ-4315 TCGA-AZ-4323 
        0.20        16.31         0.95        33.01        58.39         1.41 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6601 TCGA-AZ-6603 
      106.75        22.36        62.79        88.21       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        3.25        12.20        10.06        14.30        17.56       148.01 
TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 
       51.32        21.14         1.91       124.27        20.02        37.02 
TCGA-CM-4747 TCGA-CM-5341 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       25.02        29.06        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       14.99        12.99        13.02        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       11.08        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6538 TCGA-D5-6541 
       55.92        18.25         1.32        43.27        17.13        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        9.44         4.80        12.00        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
       38.20       130.65        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28G 
        7.50        44.32       135.65         6.12        81.37        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 
      117.07        98.24         8.61        35.74        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6307 TCGA-G4-6309 
       47.41       133.18        74.56        65.85        55.04        85.48 
TCGA-G4-6315 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2689 
       61.91        26.17        91.79        46.75        79.69        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       16.83        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
        0.99         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       17.95        36.95        17.03        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6547 TCGA-AH-6549 
       61.97        41.00        38.04       117.11         1.45        17.49 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
        7.17         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       57.24        24.13        32.61        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
       18.28         9.96        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6641 
        0.69        26.43 

  CDH1 MUTATED CDH1 WILD-TYPE 
          0.07           0.00 
  CDH1 MUTATED CDH1 WILD-TYPE 
        139.17         148.01 
  CDH1 MUTATED CDH1 WILD-TYPE 
         19.04          20.73 
[1] "0.1 - 139.2 (19.0)" "0.0 - 148.0 (20.7)"
[1] "hr=" "1.3"
D12V2, continuous
D12V3, binary
                cls
clus               0   1
  CDH1 MUTATED    74  12
  CDH1 WILD-TYPE 292 107
[1] "tbl2"
                cls
clus             [,1] [,2]
  CDH1 MUTATED     74   12
  CDH1 WILD-TYPE  292  107
        clus
vv       CDH1 MUTATED CDH1 WILD-TYPE
  COLON            74            292
  RECTUM           12            107
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CDH1 MUTATED        16        1        2        25         4         0
  CDH1 WILD-TYPE      75        0       30       113         6         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CDH1 MUTATED           3          1         16          5        6         5
  CDH1 WILD-TYPE        21         10         43         37       42        13
                vv
clus             STAGE IVB
  CDH1 MUTATED           0
  CDH1 WILD-TYPE         1
D12V4, multiclass
            clus
vv           CDH1 MUTATED CDH1 WILD-TYPE
  STAGE I              16             75
  STAGE IA              1              0
  STAGE II              2             30
  STAGE IIA            25            113
  STAGE IIB             4              6
  STAGE IIC             0              1
  STAGE III             3             21
  STAGE IIIA            1             10
  STAGE IIIB           16             43
  STAGE IIIC            5             37
  STAGE IV              6             42
  STAGE IVA             5             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  CDH1 MUTATED     2  16  56  11
  CDH1 WILD-TYPE  15  76 273  39
D12V5, multiclass
    clus
vv   CDH1 MUTATED CDH1 WILD-TYPE
  T1            2             15
  T2           16             76
  T3           56            273
  T4           11             39
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  CDH1 MUTATED    52  23  11
  CDH1 WILD-TYPE 235  90  76
D12V6, multiclass
    clus
vv   CDH1 MUTATED CDH1 WILD-TYPE
  N0           52            235
  N1           23             90
  N2           11             76
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V7, binary
                cls
clus               0   1
  CDH1 MUTATED    57  12
  CDH1 WILD-TYPE 318  53
[1] "tbl2"
                cls
clus             [,1] [,2]
  CDH1 MUTATED     57   12
  CDH1 WILD-TYPE  318   53
   clus
vv  CDH1 MUTATED CDH1 WILD-TYPE
  0           57            318
  1           12             53
[1] 2 2
[1] FALSE
D12V8, binary
                cls
clus               0   1
  CDH1 MUTATED    34  52
  CDH1 WILD-TYPE 191 212
[1] "tbl2"
                cls
clus             [,1] [,2]
  CDH1 MUTATED     34   52
  CDH1 WILD-TYPE  191  212
        clus
vv       CDH1 MUTATED CDH1 WILD-TYPE
  FEMALE           34            191
  MALE             52            212
[1] 2 2
[1] FALSE
D12V9, binary
                cls
clus               0   1
  CDH1 MUTATED    63   5
  CDH1 WILD-TYPE 287  17
[1] "tbl2"
                cls
clus             [,1] [,2]
  CDH1 MUTATED     63    5
  CDH1 WILD-TYPE  287   17
     clus
vv    CDH1 MUTATED CDH1 WILD-TYPE
  NO            63            287
  YES            5             17
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CDH1 MUTATED                     62                            12
  CDH1 WILD-TYPE                  253                            35
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CDH1 MUTATED                      12                              0
  CDH1 WILD-TYPE                    94                             10
D12V10, multiclass
                                clus
vv                               CDH1 MUTATED CDH1 WILD-TYPE
  COLON ADENOCARCINOMA                     62            253
  COLON MUCINOUS ADENOCARCINOMA            12             35
  RECTAL ADENOCARCINOMA                    12             94
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  CDH1 MUTATED    54   2   4   8
  CDH1 WILD-TYPE 291   2  27  17
D12V11, multiclass
    clus
vv   CDH1 MUTATED CDH1 WILD-TYPE
  R0           54            291
  R1            2              2
  R2            4             27
  RX            8             17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CDH1 MUTATED                                  0     4
  CDH1 WILD-TYPE                                1     7
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  CDH1 MUTATED                           8    61
  CDH1 WILD-TYPE                        14   165
D12V13, multiclass
                                  clus
vv                                 CDH1 MUTATED CDH1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       4              7
  BLACK OR AFRICAN AMERICAN                   8             14
  WHITE                                      61            165
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(13) Variable = MLH1 MUTATION ANALYSIS
D13V1, survival
                sevent
clus2              0   1
  MLH1 MUTATED    44  11
  MLH1 WILD-TYPE 334  82
  MLH1 MUTATED MLH1 WILD-TYPE 
            55            416 
  MLH1 MUTATED MLH1 WILD-TYPE 
            11             82 
$`MLH1 MUTATED`
TCGA-A6-2671 TCGA-A6-3809 TCGA-A6-4105 TCGA-A6-6138 TCGA-A6-6780 TCGA-A6-6781 
       43.76        32.75        14.53        22.52        20.12        19.66 
TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3864 TCGA-AA-A01P TCGA-AA-A02J 
       85.05        19.04        19.04        53.00        38.07         5.03 
TCGA-AD-6889 TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-5403 TCGA-AZ-6599 TCGA-AZ-6601 
       56.55        33.01        17.82        62.79         6.77       100.01 
TCGA-CA-6719 TCGA-CK-4950 TCGA-CK-5916 TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-4752 
       14.30        85.45        21.14        23.05        37.02        13.02 
TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5868 TCGA-CM-6167 TCGA-CM-6171 
       22.03        30.08        32.02        17.03        14.99        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6678 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.01        12.95        11.01         1.32        43.27        15.12 
TCGA-D5-6537 TCGA-D5-6540 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6809 TCGA-F4-6856 
        4.80        16.14        34.42        41.42        13.25        35.31 
TCGA-G4-6293 TCGA-G4-6306 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 
      133.18        44.68        63.62        61.91        36.00        13.78 
TCGA-G4-6586 TCGA-AG-A002 TCGA-AG-A02N TCGA-DC-6157 TCGA-EF-5830 TCGA-EI-6510 
       35.80        20.98        61.97        27.95         0.49        18.28 
TCGA-F5-6813 
        0.69 

$`MLH1 WILD-TYPE`
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       46.65        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       34.65        33.34        36.53        32.91        31.63        30.44 
TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 
       29.19        33.53        23.61        22.09        22.06        32.71 
TCGA-A6-6137 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 
       27.09         8.38        25.08        25.18        24.16        21.76 
TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       24.69        24.39        23.87        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
       19.00        36.00         5.03        26.99        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        31.07        30.05        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02K 
       37.02        39.06        51.98        39.98         2.01        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       21.37        15.52         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
        0.95        21.44        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 
       22.36        88.21        49.41        12.10        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 
        3.29         0.07        12.20        12.76        10.06        17.56 
TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 
      148.01        15.62        49.08        51.32         9.99        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-5341 TCGA-CM-5348 
        1.91       124.27        20.02        25.02        29.06        22.98 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6162 
       15.02         5.03        15.02        15.02        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6168 TCGA-CM-6169 
        2.96        29.03        16.04        21.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6679 TCGA-CM-6680 
       15.02        13.05        11.08        11.08        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 
       18.25        17.85        17.13        12.49        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6854 
        6.18        47.87         1.55        16.24        33.67         0.53 
TCGA-F4-6855 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 
       47.41        74.56        65.85        53.62        55.04        85.48 
TCGA-G4-6321 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       22.09        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 
       10.98        49.97         1.94        38.96        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
       15.02         5.03        13.97        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       24.13        51.48        32.61        20.55        19.96        20.91 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  MLH1 MUTATED MLH1 WILD-TYPE 
          0.49           0.00 
  MLH1 MUTATED MLH1 WILD-TYPE 
        133.18         148.01 
  MLH1 MUTATED MLH1 WILD-TYPE 
         22.03          20.02 
[1] "0.5 - 133.2 (22.0)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.2"
D13V2, continuous
D13V3, binary
                cls
clus               0   1
  MLH1 MUTATED    53   6
  MLH1 WILD-TYPE 313 113
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLH1 MUTATED     53    6
  MLH1 WILD-TYPE  313  113
        clus
vv       MLH1 MUTATED MLH1 WILD-TYPE
  COLON            53            313
  RECTUM            6            113
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MLH1 MUTATED        11        1        5        13         3         0
  MLH1 WILD-TYPE      80        0       27       125         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MLH1 MUTATED           4          0          8          5        4         5
  MLH1 WILD-TYPE        20         11         51         37       44        13
                vv
clus             STAGE IVB
  MLH1 MUTATED           0
  MLH1 WILD-TYPE         1
D13V4, multiclass
            clus
vv           MLH1 MUTATED MLH1 WILD-TYPE
  STAGE I              11             80
  STAGE IA              1              0
  STAGE II              5             27
  STAGE IIA            13            125
  STAGE IIB             3              7
  STAGE IIC             0              1
  STAGE III             4             20
  STAGE IIIA            0             11
  STAGE IIIB            8             51
  STAGE IIIC            5             37
  STAGE IV              4             44
  STAGE IVA             5             13
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  MLH1 MUTATED     1  12  37   8
  MLH1 WILD-TYPE  16  80 292  42
D13V5, multiclass
    clus
vv   MLH1 MUTATED MLH1 WILD-TYPE
  T1            1             16
  T2           12             80
  T3           37            292
  T4            8             42
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  MLH1 MUTATED    38  15   6
  MLH1 WILD-TYPE 249  98  81
D13V6, multiclass
    clus
vv   MLH1 MUTATED MLH1 WILD-TYPE
  N0           38            249
  N1           15             98
  N2            6             81
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V7, binary
                cls
clus               0   1
  MLH1 MUTATED    39   8
  MLH1 WILD-TYPE 336  57
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLH1 MUTATED     39    8
  MLH1 WILD-TYPE  336   57
   clus
vv  MLH1 MUTATED MLH1 WILD-TYPE
  0           39            336
  1            8             57
[1] 2 2
[1] FALSE
D13V8, binary
                cls
clus               0   1
  MLH1 MUTATED    25  34
  MLH1 WILD-TYPE 200 230
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLH1 MUTATED     25   34
  MLH1 WILD-TYPE  200  230
        clus
vv       MLH1 MUTATED MLH1 WILD-TYPE
  FEMALE           25            200
  MALE             34            230
[1] 2 2
[1] FALSE
D13V9, binary
                cls
clus               0   1
  MLH1 MUTATED    46   2
  MLH1 WILD-TYPE 304  20
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLH1 MUTATED     46    2
  MLH1 WILD-TYPE  304   20
     clus
vv    MLH1 MUTATED MLH1 WILD-TYPE
  NO            46            304
  YES            2             20
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MLH1 MUTATED                     46                             7
  MLH1 WILD-TYPE                  269                            40
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MLH1 MUTATED                       6                              0
  MLH1 WILD-TYPE                   100                             10
D13V10, multiclass
                                clus
vv                               MLH1 MUTATED MLH1 WILD-TYPE
  COLON ADENOCARCINOMA                     46            269
  COLON MUCINOUS ADENOCARCINOMA             7             40
  RECTAL ADENOCARCINOMA                     6            100
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  MLH1 MUTATED    44   1   2   5
  MLH1 WILD-TYPE 301   3  29  20
D13V11, multiclass
    clus
vv   MLH1 MUTATED MLH1 WILD-TYPE
  R0           44            301
  R1            1              3
  R2            2             29
  RX            5             20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MLH1 MUTATED                                  0     2
  MLH1 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  MLH1 MUTATED                           8    40
  MLH1 WILD-TYPE                        14   186
D13V13, multiclass
                                  clus
vv                                 MLH1 MUTATED MLH1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              9
  BLACK OR AFRICAN AMERICAN                   8             14
  WHITE                                      40            186
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(14) Variable = BCOR MUTATION ANALYSIS
D14V1, survival
                sevent
clus2              0   1
  BCOR MUTATED    23   4
  BCOR WILD-TYPE 355  89
  BCOR MUTATED BCOR WILD-TYPE 
            27            444 
  BCOR MUTATED BCOR WILD-TYPE 
             4             89 
$`BCOR MUTATED`
TCGA-A6-3809 TCGA-A6-5661 TCGA-A6-6780 TCGA-AA-3555 TCGA-AA-3672 TCGA-AA-3930 
       32.75        33.53        20.12        29.95         0.92         2.01 
TCGA-AA-A010 TCGA-AD-6895 TCGA-AY-5543 TCGA-AZ-4323 TCGA-AZ-6598 TCGA-CM-5348 
       34.98         0.72        33.01         1.41        49.41        22.98 
TCGA-CM-6162 TCGA-CM-6169 TCGA-CM-6171 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-7000 
       12.00        13.02        14.04        11.64         1.51        10.26 
TCGA-DM-A1HA TCGA-F4-6570 TCGA-F4-6805 TCGA-G4-6304 TCGA-G4-6317 TCGA-G4-6588 
      131.51         6.18        34.42        53.62        36.00        26.17 
TCGA-AG-3605 TCGA-AG-3878 TCGA-AG-3892 
        0.99         0.99        13.02 

$`BCOR WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       31.63        30.44        29.19        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6781 
       24.16        21.76        24.69        24.39        23.87        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       17.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
       14.01        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       18.05        31.00        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       15.52        56.55         0.79         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82        58.39         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        88.21         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.03        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       15.02        17.03        15.02         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 
       21.99        14.99        12.99        15.02        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 
        4.41        12.43        14.30         9.04         9.44         4.80 
TCGA-D5-6931 TCGA-D5-6932 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       12.00        11.38       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
       44.32       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.74        47.87         1.55        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       65.85        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       22.09        13.78        35.80        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       50.04        12.03         6.05        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  BCOR MUTATED BCOR WILD-TYPE 
          0.72           0.00 
  BCOR MUTATED BCOR WILD-TYPE 
        131.51         148.01 
  BCOR MUTATED BCOR WILD-TYPE 
        14.040         20.415 
[1] "0.7 - 131.5 (14.0)" "0.0 - 148.0 (20.4)"
[1] "hr=" "1.1"
D14V2, continuous
D14V3, binary
                cls
clus               0   1
  BCOR MUTATED    27   3
  BCOR WILD-TYPE 339 116
[1] "tbl2"
                cls
clus             [,1] [,2]
  BCOR MUTATED     27    3
  BCOR WILD-TYPE  339  116
        clus
vv       BCOR MUTATED BCOR WILD-TYPE
  COLON            27            339
  RECTUM            3            116
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  BCOR MUTATED         5        0        2         9         3         0
  BCOR WILD-TYPE      86        1       30       129         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  BCOR MUTATED           1          0          2          3        3         1
  BCOR WILD-TYPE        23         11         57         39       45        17
                vv
clus             STAGE IVB
  BCOR MUTATED           0
  BCOR WILD-TYPE         1
D14V4, multiclass
            clus
vv           BCOR MUTATED BCOR WILD-TYPE
  STAGE I               5             86
  STAGE IA              0              1
  STAGE II              2             30
  STAGE IIA             9            129
  STAGE IIB             3              7
  STAGE IIC             0              1
  STAGE III             1             23
  STAGE IIIA            0             11
  STAGE IIIB            2             57
  STAGE IIIC            3             39
  STAGE IV              3             45
  STAGE IVA             1             17
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  BCOR MUTATED     1   4  20   5
  BCOR WILD-TYPE  16  88 309  45
D14V5, multiclass
    clus
vv   BCOR MUTATED BCOR WILD-TYPE
  T1            1             16
  T2            4             88
  T3           20            309
  T4            5             45
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  BCOR MUTATED    19   6   5
  BCOR WILD-TYPE 268 107  82
D14V6, multiclass
    clus
vv   BCOR MUTATED BCOR WILD-TYPE
  N0           19            268
  N1            6            107
  N2            5             82
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V7, binary
                cls
clus               0   1
  BCOR MUTATED    20   4
  BCOR WILD-TYPE 355  61
[1] "tbl2"
                cls
clus             [,1] [,2]
  BCOR MUTATED     20    4
  BCOR WILD-TYPE  355   61
   clus
vv  BCOR MUTATED BCOR WILD-TYPE
  0           20            355
  1            4             61
[1] 2 2
[1] FALSE
D14V8, binary
                cls
clus               0   1
  BCOR MUTATED    18  12
  BCOR WILD-TYPE 207 252
[1] "tbl2"
                cls
clus             [,1] [,2]
  BCOR MUTATED     18   12
  BCOR WILD-TYPE  207  252
        clus
vv       BCOR MUTATED BCOR WILD-TYPE
  FEMALE           18            207
  MALE             12            252
[1] 2 2
[1] FALSE
D14V9, binary
                cls
clus               0   1
  BCOR MUTATED    22   0
  BCOR WILD-TYPE 328  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  BCOR MUTATED     22    0
  BCOR WILD-TYPE  328   22
     clus
vv    BCOR MUTATED BCOR WILD-TYPE
  NO            22            328
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  BCOR MUTATED                     19                             8
  BCOR WILD-TYPE                  296                            39
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  BCOR MUTATED                       3                              0
  BCOR WILD-TYPE                   103                             10
D14V10, multiclass
                                clus
vv                               BCOR MUTATED BCOR WILD-TYPE
  COLON ADENOCARCINOMA                     19            296
  COLON MUCINOUS ADENOCARCINOMA             8             39
  RECTAL ADENOCARCINOMA                     3            103
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  BCOR MUTATED    22   0   2   1
  BCOR WILD-TYPE 323   4  29  24
D14V11, multiclass
    clus
vv   BCOR MUTATED BCOR WILD-TYPE
  R0           22            323
  R1            0              4
  R2            2             29
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  BCOR MUTATED                                  0     0
  BCOR WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  BCOR MUTATED                           3    19
  BCOR WILD-TYPE                        19   207
D14V13, multiclass
                                  clus
vv                                 BCOR MUTATED BCOR WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   3             19
  WHITE                                      19            207
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(15) Variable = SMAD2 MUTATION ANALYSIS
D15V1, survival
                 sevent
clus2               0   1
  SMAD2 MUTATED    17   4
  SMAD2 WILD-TYPE 361  89
  SMAD2 MUTATED SMAD2 WILD-TYPE 
             21             450 
  SMAD2 MUTATED SMAD2 WILD-TYPE 
              4              89 
$`SMAD2 MUTATED`
TCGA-A6-6780 TCGA-AA-3510 TCGA-AA-3520 TCGA-AA-3663 TCGA-AA-3696 TCGA-AA-3842 
       20.12        63.98        24.03         6.97         5.03        37.02 
TCGA-AA-3864 TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A01V TCGA-AA-A024 TCGA-AA-A029 
       53.00        25.02         4.01        35.01        39.06        51.98 
TCGA-AZ-6600 TCGA-CM-6168 TCGA-CM-6169 TCGA-AG-3608 TCGA-AG-3890 TCGA-AG-A002 
       12.10        12.99        13.02        15.95        17.03        20.98 
TCGA-AG-A01W TCGA-F5-6465 TCGA-G5-6235 
       70.03        49.51        55.76 

$`SMAD2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
        9.07        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02        78.08         6.05        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3710 
        5.98        37.05        19.00        36.00        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3844 
       25.02         1.02        17.98        15.95        38.99        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       26.01        37.02        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       49.41         6.77       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       21.99        14.99        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
        0.99        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
        1.02        17.95        36.95        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6641 
       31.30        28.57        32.19         0.66         0.69        26.43 

  SMAD2 MUTATED SMAD2 WILD-TYPE 
           4.01            0.00 
  SMAD2 MUTATED SMAD2 WILD-TYPE 
          70.03          148.01 
  SMAD2 MUTATED SMAD2 WILD-TYPE 
         24.030          20.035 
[1] "4.0 - 70.0 (24.0)"  "0.0 - 148.0 (20.0)"
[1] "hr=" "1.3"
D15V2, continuous
D15V3, binary
                 cls
clus                0   1
  SMAD2 MUTATED    16   6
  SMAD2 WILD-TYPE 350 113
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAD2 MUTATED     16    6
  SMAD2 WILD-TYPE  350  113
        clus
vv       SMAD2 MUTATED SMAD2 WILD-TYPE
  COLON             16             350
  RECTUM             6             113
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SMAD2 MUTATED         3        0        7         5         1         0
  SMAD2 WILD-TYPE      88        1       25       133         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SMAD2 MUTATED           0          1          1          0        3         0
  SMAD2 WILD-TYPE        24         10         58         42       45        18
                 vv
clus              STAGE IVB
  SMAD2 MUTATED           0
  SMAD2 WILD-TYPE         1
D15V4, multiclass
            clus
vv           SMAD2 MUTATED SMAD2 WILD-TYPE
  STAGE I                3              88
  STAGE IA               0               1
  STAGE II               7              25
  STAGE IIA              5             133
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             1              10
  STAGE IIIB             1              58
  STAGE IIIC             0              42
  STAGE IV               3              45
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  SMAD2 MUTATED     0   5  14   3
  SMAD2 WILD-TYPE  17  87 315  47
D15V5, multiclass
    clus
vv   SMAD2 MUTATED SMAD2 WILD-TYPE
  T1             0              17
  T2             5              87
  T3            14             315
  T4             3              47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  SMAD2 MUTATED    17   4   1
  SMAD2 WILD-TYPE 270 109  86
D15V6, multiclass
    clus
vv   SMAD2 MUTATED SMAD2 WILD-TYPE
  N0            17             270
  N1             4             109
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V7, binary
                 cls
clus                0   1
  SMAD2 MUTATED    16   3
  SMAD2 WILD-TYPE 359  62
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAD2 MUTATED     16    3
  SMAD2 WILD-TYPE  359   62
   clus
vv  SMAD2 MUTATED SMAD2 WILD-TYPE
  0            16             359
  1             3              62
[1] 2 2
[1] FALSE
D15V8, binary
                 cls
clus                0   1
  SMAD2 MUTATED     7  15
  SMAD2 WILD-TYPE 218 249
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAD2 MUTATED      7   15
  SMAD2 WILD-TYPE  218  249
        clus
vv       SMAD2 MUTATED SMAD2 WILD-TYPE
  FEMALE             7             218
  MALE              15             249
[1] 2 2
[1] FALSE
D15V9, binary
                 cls
clus                0   1
  SMAD2 MUTATED    17   0
  SMAD2 WILD-TYPE 333  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAD2 MUTATED     17    0
  SMAD2 WILD-TYPE  333   22
     clus
vv    SMAD2 MUTATED SMAD2 WILD-TYPE
  NO             17             333
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SMAD2 MUTATED                     12                             4
  SMAD2 WILD-TYPE                  303                            43
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SMAD2 MUTATED                       6                              0
  SMAD2 WILD-TYPE                   100                             10
D15V10, multiclass
                                clus
vv                               SMAD2 MUTATED SMAD2 WILD-TYPE
  COLON ADENOCARCINOMA                      12             303
  COLON MUCINOUS ADENOCARCINOMA              4              43
  RECTAL ADENOCARCINOMA                      6             100
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  SMAD2 MUTATED    16   1   2   0
  SMAD2 WILD-TYPE 329   3  29  25
D15V11, multiclass
    clus
vv   SMAD2 MUTATED SMAD2 WILD-TYPE
  R0            16             329
  R1             1               3
  R2             2              29
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SMAD2 MUTATED                                  0     0
  SMAD2 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  SMAD2 MUTATED                           3     3
  SMAD2 WILD-TYPE                        19   223
D15V13, multiclass
                                  clus
vv                                 SMAD2 MUTATED SMAD2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    3              19
  WHITE                                        3             223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(16) Variable = WNT1 MUTATION ANALYSIS
D16V1, survival
                sevent
clus2              0   1
  WNT1 MUTATED     4   2
  WNT1 WILD-TYPE 374  91
  WNT1 MUTATED WNT1 WILD-TYPE 
             6            465 
  WNT1 MUTATED WNT1 WILD-TYPE 
             2             91 
$`WNT1 MUTATED`
TCGA-AD-6889 TCGA-AZ-6598 TCGA-CK-5916 TCGA-CM-4743 TCGA-DM-A1HB TCGA-G4-6586 
       56.55        49.41        21.14        23.05       135.65        35.80 

$`WNT1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       21.37        15.52         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 
        5.13       106.75        22.36        62.79        88.21         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 
       85.45        15.62        49.08        51.32         9.99        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
        1.91       124.27        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 
      140.38         7.50        44.32       131.51       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       22.09        13.78        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  WNT1 MUTATED WNT1 WILD-TYPE 
         21.14           0.00 
  WNT1 MUTATED WNT1 WILD-TYPE 
        135.65         148.01 
  WNT1 MUTATED WNT1 WILD-TYPE 
        42.605         20.020 
[1] "21.1 - 135.7 (42.6)" "0.0 - 148.0 (20.0)" 
[1] "hr=" "1.1"
D16V2, continuous
D16V3, binary
                cls
clus               0   1
  WNT1 MUTATED     7   0
  WNT1 WILD-TYPE 359 119
[1] "tbl2"
                cls
clus             [,1] [,2]
  WNT1 MUTATED      7    0
  WNT1 WILD-TYPE  359  119
        clus
vv       WNT1 MUTATED WNT1 WILD-TYPE
  COLON             7            359
  RECTUM            0            119
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  WNT1 MUTATED         1        0        2         3         0         0
  WNT1 WILD-TYPE      90        1       30       135        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  WNT1 MUTATED           0          0          1          0        0         0
  WNT1 WILD-TYPE        24         11         58         42       48        18
                vv
clus             STAGE IVB
  WNT1 MUTATED           0
  WNT1 WILD-TYPE         1
D16V4, multiclass
            clus
vv           WNT1 MUTATED WNT1 WILD-TYPE
  STAGE I               1             90
  STAGE IA              0              1
  STAGE II              2             30
  STAGE IIA             3            135
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            1             58
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  WNT1 MUTATED     1   0   5   1
  WNT1 WILD-TYPE  16  92 324  49
D16V5, multiclass
    clus
vv   WNT1 MUTATED WNT1 WILD-TYPE
  T1            1             16
  T2            0             92
  T3            5            324
  T4            1             49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  WNT1 MUTATED     6   1   0
  WNT1 WILD-TYPE 281 112  87
D16V6, multiclass
    clus
vv   WNT1 MUTATED WNT1 WILD-TYPE
  N0            6            281
  N1            1            112
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V7, binary
                cls
clus               0   1
  WNT1 MUTATED     6   0
  WNT1 WILD-TYPE 369  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  WNT1 MUTATED      6    0
  WNT1 WILD-TYPE  369   65
   clus
vv  WNT1 MUTATED WNT1 WILD-TYPE
  0            6            369
  1            0             65
[1] 2 2
[1] FALSE
D16V8, binary
                cls
clus               0   1
  WNT1 MUTATED     4   3
  WNT1 WILD-TYPE 221 261
[1] "tbl2"
                cls
clus             [,1] [,2]
  WNT1 MUTATED      4    3
  WNT1 WILD-TYPE  221  261
        clus
vv       WNT1 MUTATED WNT1 WILD-TYPE
  FEMALE            4            221
  MALE              3            261
[1] 2 2
[1] FALSE
D16V9, binary
                cls
clus               0   1
  WNT1 MUTATED     4   0
  WNT1 WILD-TYPE 346  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  WNT1 MUTATED      4    0
  WNT1 WILD-TYPE  346   22
     clus
vv    WNT1 MUTATED WNT1 WILD-TYPE
  NO             4            346
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  WNT1 MUTATED                      6                             0
  WNT1 WILD-TYPE                  309                            47
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  WNT1 MUTATED                       0                              0
  WNT1 WILD-TYPE                   106                             10
D16V10, multiclass
                                clus
vv                               WNT1 MUTATED WNT1 WILD-TYPE
  COLON ADENOCARCINOMA                      6            309
  COLON MUCINOUS ADENOCARCINOMA             0             47
  RECTAL ADENOCARCINOMA                     0            106
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  WNT1 MUTATED     3   0   0   1
  WNT1 WILD-TYPE 342   4  31  24
D16V11, multiclass
    clus
vv   WNT1 MUTATED WNT1 WILD-TYPE
  R0            3            342
  R1            0              4
  R2            0             31
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  WNT1 MUTATED                                  0     1
  WNT1 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  WNT1 MUTATED                           0     5
  WNT1 WILD-TYPE                        22   221
D16V13, multiclass
                                  clus
vv                                 WNT1 MUTATED WNT1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       5            221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(17) Variable = FMN2 MUTATION ANALYSIS
D17V1, survival
                sevent
clus2              0   1
  FMN2 MUTATED    48  15
  FMN2 WILD-TYPE 330  78
  FMN2 MUTATED FMN2 WILD-TYPE 
            63            408 
  FMN2 MUTATED FMN2 WILD-TYPE 
            15             78 
$`FMN2 MUTATED`
TCGA-A6-5657 TCGA-A6-5661 TCGA-A6-5665 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       31.63        33.53        22.06        24.69        24.39        23.87 
TCGA-AA-3713 TCGA-AA-3861 TCGA-AA-3956 TCGA-AA-3973 TCGA-AA-A00N TCGA-AA-A010 
       19.04        30.05        34.03        13.05         4.01        34.98 
TCGA-AD-6889 TCGA-AZ-6599 TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-6717 TCGA-CA-6718 
       56.55         6.77        11.74         1.61        12.76        10.06 
TCGA-CK-4947 TCGA-CK-5916 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-5861 
       17.56        21.14       124.27        23.05        37.02        15.02 
TCGA-CM-5862 TCGA-CM-6161 TCGA-CM-6169 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6679 
        5.03        15.02        13.02        14.04        11.01        10.06 
TCGA-CM-6680 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6540 
       12.03        20.19        18.25         1.32        43.27        16.14 
TCGA-D5-6927 TCGA-D5-7000 TCGA-DM-A1D4 TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        9.44        10.26        92.75       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-G4-6586 TCGA-G4-6588 
       81.37        31.96        35.74         6.18        35.80        26.17 
TCGA-G4-6628 TCGA-AG-3732 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-A026 TCGA-AH-6547 
       79.69        32.98        19.04        19.99         1.94         1.45 
TCGA-CI-6619 TCGA-CI-6622 TCGA-CL-5917 TCGA-DC-5869 TCGA-DC-6682 TCGA-DT-5265 
        6.05         6.97        78.12         5.03         4.01         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DG 
      126.44        41.36        51.48 

$`FMN2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 
       32.91        30.44        29.19        23.61        22.09        32.71 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       27.09        22.52         8.38        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       21.76        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 
       32.05         0.99        31.07        31.07        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3975 
       20.98         2.01        21.99        16.08        50.99        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       21.37        15.52         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-CA-5254 
       12.10       100.01        29.56         5.23         3.19        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 
        3.06         3.25         3.29         0.07        12.20        14.30 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       82.95         1.91        20.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5863 TCGA-CM-5864 
       22.03        22.98        30.08        32.02        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       17.03        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6170 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       14.99        12.99        15.02        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       11.08        11.01        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       55.92        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.04        11.64         4.80         1.51        12.00        11.38 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-DM-A1D7 
      119.70        24.43        38.20       130.65        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A28E 
       12.59       140.38         7.50        44.32       131.51       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6703 
       35.97        60.79       117.07        98.24         8.61        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 
       36.00        22.09        13.78        91.79        46.75        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 
       19.99         7.99         0.99        37.02         0.99         0.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6620 TCGA-CI-6624 TCGA-CL-5918 
       17.49         0.69         0.72        33.17         4.73         7.17 
TCGA-DC-5337 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
       15.02        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6683 TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
        5.03        57.24        24.13        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  FMN2 MUTATED FMN2 WILD-TYPE 
          1.32           0.00 
  FMN2 MUTATED FMN2 WILD-TYPE 
        139.17         148.01 
  FMN2 MUTATED FMN2 WILD-TYPE 
         19.04          20.73 
[1] "1.3 - 139.2 (19.0)" "0.0 - 148.0 (20.7)"
[1] "hr=" "1.2"
D17V2, continuous
D17V3, binary
                cls
clus               0   1
  FMN2 MUTATED    49  14
  FMN2 WILD-TYPE 317 105
[1] "tbl2"
                cls
clus             [,1] [,2]
  FMN2 MUTATED     49   14
  FMN2 WILD-TYPE  317  105
        clus
vv       FMN2 MUTATED FMN2 WILD-TYPE
  COLON            49            317
  RECTUM           14            105
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FMN2 MUTATED        13        0        2        25         3         0
  FMN2 WILD-TYPE      78        1       30       113         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  FMN2 MUTATED           0          1          9          1        5         3
  FMN2 WILD-TYPE        24         10         50         41       43        15
                vv
clus             STAGE IVB
  FMN2 MUTATED           0
  FMN2 WILD-TYPE         1
D17V4, multiclass
            clus
vv           FMN2 MUTATED FMN2 WILD-TYPE
  STAGE I              13             78
  STAGE IA              0              1
  STAGE II              2             30
  STAGE IIA            25            113
  STAGE IIB             3              7
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            1             10
  STAGE IIIB            9             50
  STAGE IIIC            1             41
  STAGE IV              5             43
  STAGE IVA             3             15
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  FMN2 MUTATED     1  13  41   8
  FMN2 WILD-TYPE  16  79 288  42
D17V5, multiclass
    clus
vv   FMN2 MUTATED FMN2 WILD-TYPE
  T1            1             16
  T2           13             79
  T3           41            288
  T4            8             42
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  FMN2 MUTATED    47  12   4
  FMN2 WILD-TYPE 240 101  83
D17V6, multiclass
    clus
vv   FMN2 MUTATED FMN2 WILD-TYPE
  N0           47            240
  N1           12            101
  N2            4             83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V7, binary
                cls
clus               0   1
  FMN2 MUTATED    51   8
  FMN2 WILD-TYPE 324  57
[1] "tbl2"
                cls
clus             [,1] [,2]
  FMN2 MUTATED     51    8
  FMN2 WILD-TYPE  324   57
   clus
vv  FMN2 MUTATED FMN2 WILD-TYPE
  0           51            324
  1            8             57
[1] 2 2
[1] FALSE
D17V8, binary
                cls
clus               0   1
  FMN2 MUTATED    30  33
  FMN2 WILD-TYPE 195 231
[1] "tbl2"
                cls
clus             [,1] [,2]
  FMN2 MUTATED     30   33
  FMN2 WILD-TYPE  195  231
        clus
vv       FMN2 MUTATED FMN2 WILD-TYPE
  FEMALE           30            195
  MALE             33            231
[1] 2 2
[1] FALSE
D17V9, binary
                cls
clus               0   1
  FMN2 MUTATED    45   1
  FMN2 WILD-TYPE 305  21
[1] "tbl2"
                cls
clus             [,1] [,2]
  FMN2 MUTATED     45    1
  FMN2 WILD-TYPE  305   21
     clus
vv    FMN2 MUTATED FMN2 WILD-TYPE
  NO            45            305
  YES            1             21
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  FMN2 MUTATED                     41                             7
  FMN2 WILD-TYPE                  274                            40
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  FMN2 MUTATED                      12                              1
  FMN2 WILD-TYPE                    94                              9
D17V10, multiclass
                                clus
vv                               FMN2 MUTATED FMN2 WILD-TYPE
  COLON ADENOCARCINOMA                     41            274
  COLON MUCINOUS ADENOCARCINOMA             7             40
  RECTAL ADENOCARCINOMA                    12             94
  RECTAL MUCINOUS ADENOCARCINOMA            1              9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  FMN2 MUTATED    34   1   2   7
  FMN2 WILD-TYPE 311   3  29  18
D17V11, multiclass
    clus
vv   FMN2 MUTATED FMN2 WILD-TYPE
  R0           34            311
  R1            1              3
  R2            2             29
  RX            7             18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FMN2 MUTATED                                  0     4
  FMN2 WILD-TYPE                                1     7
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  FMN2 MUTATED                           6    43
  FMN2 WILD-TYPE                        16   183
D17V13, multiclass
                                  clus
vv                                 FMN2 MUTATED FMN2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       4              7
  BLACK OR AFRICAN AMERICAN                   6             16
  WHITE                                      43            183
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(18) Variable = GGT1 MUTATION ANALYSIS
D18V1, survival
                sevent
clus2              0   1
  GGT1 MUTATED     7   3
  GGT1 WILD-TYPE 371  90
  GGT1 MUTATED GGT1 WILD-TYPE 
            10            461 
  GGT1 MUTATED GGT1 WILD-TYPE 
             3             90 
$`GGT1 MUTATED`
TCGA-A6-5662 TCGA-CK-6748 TCGA-CM-5862 TCGA-CM-6170 TCGA-D5-6537 TCGA-D5-6538 
       23.61         1.91         5.03        15.02         4.80        17.13 
TCGA-DM-A1D0 TCGA-G4-6306 TCGA-DY-A1DD TCGA-F5-6571 
      130.65        44.68        57.24        31.30 

$`GGT1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        33.53        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       21.14        82.95       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       32.02        15.02        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       12.99        13.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6539 TCGA-D5-6540 
        1.32        43.27        15.12        17.85        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D4 
       11.38        10.26       119.70        24.43        38.20        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 
      133.18        74.56        65.85        53.62        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       41.36        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6702 
       19.96        20.91        18.28         9.96        49.51        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  GGT1 MUTATED GGT1 WILD-TYPE 
          1.91           0.00 
  GGT1 MUTATED GGT1 WILD-TYPE 
        130.65         148.01 
  GGT1 MUTATED GGT1 WILD-TYPE 
         20.37          20.19 
[1] "1.9 - 130.7 (20.4)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.3"
D18V2, continuous
D18V3, binary
                cls
clus               0   1
  GGT1 MUTATED     8   2
  GGT1 WILD-TYPE 358 117
[1] "tbl2"
                cls
clus             [,1] [,2]
  GGT1 MUTATED      8    2
  GGT1 WILD-TYPE  358  117
        clus
vv       GGT1 MUTATED GGT1 WILD-TYPE
  COLON             8            358
  RECTUM            2            117
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GGT1 MUTATED         1        0        0         3         0         0
  GGT1 WILD-TYPE      90        1       32       135        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  GGT1 MUTATED           0          0          3          0        1         2
  GGT1 WILD-TYPE        24         11         56         42       47        16
                vv
clus             STAGE IVB
  GGT1 MUTATED           0
  GGT1 WILD-TYPE         1
D18V4, multiclass
            clus
vv           GGT1 MUTATED GGT1 WILD-TYPE
  STAGE I               1             90
  STAGE IA              0              1
  STAGE II              0             32
  STAGE IIA             3            135
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            3             56
  STAGE IIIC            0             42
  STAGE IV              1             47
  STAGE IVA             2             16
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  GGT1 MUTATED     0   2   8   0
  GGT1 WILD-TYPE  17  90 321  50
D18V5, multiclass
    clus
vv   GGT1 MUTATED GGT1 WILD-TYPE
  T1            0             17
  T2            2             90
  T3            8            321
  T4            0             50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  GGT1 MUTATED     4   4   2
  GGT1 WILD-TYPE 283 109  85
D18V6, multiclass
    clus
vv   GGT1 MUTATED GGT1 WILD-TYPE
  N0            4            283
  N1            4            109
  N2            2             85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V7, binary
                cls
clus               0   1
  GGT1 MUTATED     6   3
  GGT1 WILD-TYPE 369  62
[1] "tbl2"
                cls
clus             [,1] [,2]
  GGT1 MUTATED      6    3
  GGT1 WILD-TYPE  369   62
   clus
vv  GGT1 MUTATED GGT1 WILD-TYPE
  0            6            369
  1            3             62
[1] 2 2
[1] FALSE
D18V8, binary
                cls
clus               0   1
  GGT1 MUTATED     6   4
  GGT1 WILD-TYPE 219 260
[1] "tbl2"
                cls
clus             [,1] [,2]
  GGT1 MUTATED      6    4
  GGT1 WILD-TYPE  219  260
        clus
vv       GGT1 MUTATED GGT1 WILD-TYPE
  FEMALE            6            219
  MALE              4            260
[1] 2 2
[1] FALSE
D18V9, binary
                cls
clus               0   1
  GGT1 MUTATED     8   0
  GGT1 WILD-TYPE 342  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  GGT1 MUTATED      8    0
  GGT1 WILD-TYPE  342   22
     clus
vv    GGT1 MUTATED GGT1 WILD-TYPE
  NO             8            342
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  GGT1 MUTATED                      7                             1
  GGT1 WILD-TYPE                  308                            46
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  GGT1 MUTATED                       2                              0
  GGT1 WILD-TYPE                   104                             10
D18V10, multiclass
                                clus
vv                               GGT1 MUTATED GGT1 WILD-TYPE
  COLON ADENOCARCINOMA                      7            308
  COLON MUCINOUS ADENOCARCINOMA             1             46
  RECTAL ADENOCARCINOMA                     2            104
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  GGT1 MUTATED     6   0   0   1
  GGT1 WILD-TYPE 339   4  31  24
D18V11, multiclass
    clus
vv   GGT1 MUTATED GGT1 WILD-TYPE
  R0            6            339
  R1            0              4
  R2            0             31
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GGT1 MUTATED                                  0     0
  GGT1 WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  GGT1 MUTATED                           0    10
  GGT1 WILD-TYPE                        22   216
D18V13, multiclass
                                  clus
vv                                 GGT1 MUTATED GGT1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                      10            216
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(19) Variable = STARD3NL MUTATION ANALYSIS
D19V1, survival
                    sevent
clus2                  0   1
  STARD3NL MUTATED    14   1
  STARD3NL WILD-TYPE 364  92
  STARD3NL MUTATED STARD3NL WILD-TYPE 
                15                456 
  STARD3NL MUTATED STARD3NL WILD-TYPE 
                 1                 92 
$`STARD3NL MUTATED`
TCGA-A6-6781 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-A010 TCGA-AA-A01R TCGA-AY-6197 
       19.66         6.05         6.97        34.98        35.01        21.44 
TCGA-AZ-6599 TCGA-CK-4950 TCGA-CM-6167 TCGA-D5-5540 TCGA-D5-6536 TCGA-G4-6323 
        6.77        85.45        14.99        56.09        17.85        13.78 
TCGA-G4-6588 TCGA-EI-6506 TCGA-F5-6811 
       26.17        20.55        32.19 

$`STARD3NL WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 
       19.99        13.94        19.99        61.02        78.08        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
       38.07         1.02         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4315 
       27.09        16.31         0.95        33.01        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       49.41        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
      148.01        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       45.40        12.26        19.59        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
        1.32        43.27        15.12         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       22.09        35.80        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
        0.49        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       31.30        28.57         0.66         0.69        55.76        26.43 

  STARD3NL MUTATED STARD3NL WILD-TYPE 
              6.05               0.00 
  STARD3NL MUTATED STARD3NL WILD-TYPE 
             85.45             148.01 
  STARD3NL MUTATED STARD3NL WILD-TYPE 
            20.550             20.155 
[1] "6.0 - 85.5 (20.6)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "3"  
D19V2, continuous
D19V3, binary
                    cls
clus                   0   1
  STARD3NL MUTATED    13   2
  STARD3NL WILD-TYPE 353 117
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  STARD3NL MUTATED     13    2
  STARD3NL WILD-TYPE  353  117
        clus
vv       STARD3NL MUTATED STARD3NL WILD-TYPE
  COLON                13                353
  RECTUM                2                117
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  STARD3NL MUTATED         1        1        1         6         1         0
  STARD3NL WILD-TYPE      90        0       31       132         9         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  STARD3NL MUTATED           1          0          1          2        1
  STARD3NL WILD-TYPE        23         11         58         40       47
                    vv
clus                 STAGE IVA STAGE IVB
  STARD3NL MUTATED           0         0
  STARD3NL WILD-TYPE        18         1
D19V4, multiclass
            clus
vv           STARD3NL MUTATED STARD3NL WILD-TYPE
  STAGE I                   1                 90
  STAGE IA                  1                  0
  STAGE II                  1                 31
  STAGE IIA                 6                132
  STAGE IIB                 1                  9
  STAGE IIC                 0                  1
  STAGE III                 1                 23
  STAGE IIIA                0                 11
  STAGE IIIB                1                 58
  STAGE IIIC                2                 40
  STAGE IV                  1                 47
  STAGE IVA                 0                 18
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  STARD3NL MUTATED     0   1  10   3
  STARD3NL WILD-TYPE  17  91 319  47
D19V5, multiclass
    clus
vv   STARD3NL MUTATED STARD3NL WILD-TYPE
  T1                0                 17
  T2                1                 91
  T3               10                319
  T4                3                 47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  STARD3NL MUTATED    10   2   3
  STARD3NL WILD-TYPE 277 111  84
D19V6, multiclass
    clus
vv   STARD3NL MUTATED STARD3NL WILD-TYPE
  N0               10                277
  N1                2                111
  N2                3                 84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V7, binary
                    cls
clus                   0   1
  STARD3NL MUTATED    10   1
  STARD3NL WILD-TYPE 365  64
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  STARD3NL MUTATED     10    1
  STARD3NL WILD-TYPE  365   64
   clus
vv  STARD3NL MUTATED STARD3NL WILD-TYPE
  0               10                365
  1                1                 64
[1] 2 2
[1] FALSE
D19V8, binary
                    cls
clus                   0   1
  STARD3NL MUTATED     7   8
  STARD3NL WILD-TYPE 218 256
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  STARD3NL MUTATED      7    8
  STARD3NL WILD-TYPE  218  256
        clus
vv       STARD3NL MUTATED STARD3NL WILD-TYPE
  FEMALE                7                218
  MALE                  8                256
[1] 2 2
[1] FALSE
D19V9, binary
                    cls
clus                   0   1
  STARD3NL MUTATED    14   1
  STARD3NL WILD-TYPE 336  21
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  STARD3NL MUTATED     14    1
  STARD3NL WILD-TYPE  336   21
     clus
vv    STARD3NL MUTATED STARD3NL WILD-TYPE
  NO                14                336
  YES                1                 21
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  STARD3NL MUTATED                     11                             2
  STARD3NL WILD-TYPE                  304                            45
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  STARD3NL MUTATED                       2                              0
  STARD3NL WILD-TYPE                   104                             10
D19V10, multiclass
                                clus
vv                               STARD3NL MUTATED STARD3NL WILD-TYPE
  COLON ADENOCARCINOMA                         11                304
  COLON MUCINOUS ADENOCARCINOMA                 2                 45
  RECTAL ADENOCARCINOMA                         2                104
  RECTAL MUCINOUS ADENOCARCINOMA                0                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  STARD3NL MUTATED    11   1   1   0
  STARD3NL WILD-TYPE 334   3  30  25
D19V11, multiclass
    clus
vv   STARD3NL MUTATED STARD3NL WILD-TYPE
  R0               11                334
  R1                1                  3
  R2                1                 30
  RX                0                 25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  STARD3NL MUTATED                                  0     0
  STARD3NL WILD-TYPE                                1    11
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  STARD3NL MUTATED                           3     8
  STARD3NL WILD-TYPE                        19   218
D19V13, multiclass
                                  clus
vv                                 STARD3NL MUTATED STARD3NL WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 11
  BLACK OR AFRICAN AMERICAN                       3                 19
  WHITE                                           8                218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(20) Variable = SELPLG MUTATION ANALYSIS
D20V1, survival
                  sevent
clus2                0   1
  SELPLG MUTATED    18   1
  SELPLG WILD-TYPE 360  92
  SELPLG MUTATED SELPLG WILD-TYPE 
              19              452 
  SELPLG MUTATED SELPLG WILD-TYPE 
               1               92 
$`SELPLG MUTATED`
TCGA-A6-5660 TCGA-A6-5664 TCGA-AA-3864 TCGA-AZ-4315 TCGA-CA-5255 TCGA-CM-4752 
       29.19        22.09        53.00        58.39         3.06        13.02 
TCGA-CM-5864 TCGA-CM-6679 TCGA-D5-6533 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       15.02        10.06         1.32        17.85         4.80        17.13 
TCGA-F4-6855 TCGA-G4-6307 TCGA-G4-6317 TCGA-G4-6625 TCGA-AF-6655 TCGA-AG-A002 
       47.41        55.04        36.00        91.79        20.02        20.98 
TCGA-EI-6507 
       19.96 

$`SELPLG WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5665 
       32.91        31.63        30.44        33.53        23.61        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 
        0.99        31.07        31.07        30.05        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-5341 TCGA-CM-5344 
       23.05        20.02        37.02        25.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6539 TCGA-D5-6540 
       20.19        18.25        43.27        15.12        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6856 
       41.42        16.24        33.67        13.25         0.53        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 
      133.18        74.56        65.85        53.62        44.68        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       63.62        61.91        22.09        13.78        35.80        26.17 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
       32.61         0.49        20.55        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  SELPLG MUTATED SELPLG WILD-TYPE 
            1.32             0.00 
  SELPLG MUTATED SELPLG WILD-TYPE 
           91.79           148.01 
  SELPLG MUTATED SELPLG WILD-TYPE 
          20.020           20.235 
[1] "1.3 - 91.8 (20.0)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "4.3"
D20V2, continuous
D20V3, binary
                  cls
clus                 0   1
  SELPLG MUTATED    16   3
  SELPLG WILD-TYPE 350 116
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SELPLG MUTATED     16    3
  SELPLG WILD-TYPE  350  116
        clus
vv       SELPLG MUTATED SELPLG WILD-TYPE
  COLON              16              350
  RECTUM              3              116
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SELPLG MUTATED         2        0        1         8         0         0
  SELPLG WILD-TYPE      89        1       31       130        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SELPLG MUTATED           0          1          4          3        0
  SELPLG WILD-TYPE        24         10         55         39       48
                  vv
clus               STAGE IVA STAGE IVB
  SELPLG MUTATED           0         0
  SELPLG WILD-TYPE        18         1
D20V4, multiclass
            clus
vv           SELPLG MUTATED SELPLG WILD-TYPE
  STAGE I                 2               89
  STAGE IA                0                1
  STAGE II                1               31
  STAGE IIA               8              130
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              1               10
  STAGE IIIB              4               55
  STAGE IIIC              3               39
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  SELPLG MUTATED     0   3  14   2
  SELPLG WILD-TYPE  17  89 315  48
D20V5, multiclass
    clus
vv   SELPLG MUTATED SELPLG WILD-TYPE
  T1              0               17
  T2              3               89
  T3             14              315
  T4              2               48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  SELPLG MUTATED    12   3   4
  SELPLG WILD-TYPE 275 110  83
D20V6, multiclass
    clus
vv   SELPLG MUTATED SELPLG WILD-TYPE
  N0             12              275
  N1              3              110
  N2              4               83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V7, binary
                  cls
clus                 0   1
  SELPLG MUTATED    16   0
  SELPLG WILD-TYPE 359  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SELPLG MUTATED     16    0
  SELPLG WILD-TYPE  359   65
   clus
vv  SELPLG MUTATED SELPLG WILD-TYPE
  0             16              359
  1              0               65
[1] 2 2
[1] FALSE
D20V8, binary
                  cls
clus                 0   1
  SELPLG MUTATED     6  13
  SELPLG WILD-TYPE 219 251
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SELPLG MUTATED      6   13
  SELPLG WILD-TYPE  219  251
        clus
vv       SELPLG MUTATED SELPLG WILD-TYPE
  FEMALE              6              219
  MALE               13              251
[1] 2 2
[1] FALSE
D20V9, binary
                  cls
clus                 0   1
  SELPLG MUTATED    17   1
  SELPLG WILD-TYPE 333  21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SELPLG MUTATED     17    1
  SELPLG WILD-TYPE  333   21
     clus
vv    SELPLG MUTATED SELPLG WILD-TYPE
  NO              17              333
  YES              1               21
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SELPLG MUTATED                     16                             0
  SELPLG WILD-TYPE                  299                            47
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SELPLG MUTATED                       3                              0
  SELPLG WILD-TYPE                   103                             10
D20V10, multiclass
                                clus
vv                               SELPLG MUTATED SELPLG WILD-TYPE
  COLON ADENOCARCINOMA                       16              299
  COLON MUCINOUS ADENOCARCINOMA               0               47
  RECTAL ADENOCARCINOMA                       3              103
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  SELPLG MUTATED    16   0   0   1
  SELPLG WILD-TYPE 329   4  31  24
D20V11, multiclass
    clus
vv   SELPLG MUTATED SELPLG WILD-TYPE
  R0             16              329
  R1              0                4
  R2              0               31
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SELPLG MUTATED                                  0     1
  SELPLG WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  SELPLG MUTATED                           3    13
  SELPLG WILD-TYPE                        19   213
D20V13, multiclass
                                  clus
vv                                 SELPLG MUTATED SELPLG WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     3               19
  WHITE                                        13              213
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(21) Variable = OR4D10 MUTATION ANALYSIS
D21V1, survival
                  sevent
clus2                0   1
  OR4D10 MUTATED    11   5
  OR4D10 WILD-TYPE 367  88
  OR4D10 MUTATED OR4D10 WILD-TYPE 
              16              455 
  OR4D10 MUTATED OR4D10 WILD-TYPE 
               5               88 
$`OR4D10 MUTATED`
TCGA-A6-5657 TCGA-AA-3864 TCGA-AA-A00N TCGA-AD-6899 TCGA-AY-5543 TCGA-AZ-4315 
       31.63        53.00         4.01         5.79        33.01        58.39 
TCGA-AZ-6601 TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-4752 TCGA-CM-5860 TCGA-CM-6161 
      100.01        12.76        10.06        13.02        32.02        15.02 
TCGA-D5-5537 TCGA-D5-6541 TCGA-AG-A002 TCGA-DY-A0XA 
       45.40        15.58        20.98       126.44 

$`OR4D10 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 
       32.05         0.99        31.07        31.07        30.05        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.79         0.72        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6197 TCGA-AY-6386 
       14.50        27.09        16.31         0.95        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       49.41         6.77        12.10        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.07        12.20        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-5862 
       29.06        22.03        22.98        30.08        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        15.02        17.03        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       11.01        10.06        12.03        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6898 
       17.85         4.80        17.13        12.49        16.14         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD 
        5.95         4.01         5.03         5.29        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  OR4D10 MUTATED OR4D10 WILD-TYPE 
            4.01             0.00 
  OR4D10 MUTATED OR4D10 WILD-TYPE 
          126.44           148.01 
  OR4D10 MUTATED OR4D10 WILD-TYPE 
          26.305           20.120 
[1] "4.0 - 126.4 (26.3)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.2"
D21V2, continuous
D21V3, binary
                  cls
clus                 0   1
  OR4D10 MUTATED    14   2
  OR4D10 WILD-TYPE 352 117
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR4D10 MUTATED     14    2
  OR4D10 WILD-TYPE  352  117
        clus
vv       OR4D10 MUTATED OR4D10 WILD-TYPE
  COLON              14              352
  RECTUM              2              117
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  OR4D10 MUTATED         2        0        2         8         1         0
  OR4D10 WILD-TYPE      89        1       30       130         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  OR4D10 MUTATED           0          0          1          1        0
  OR4D10 WILD-TYPE        24         11         58         41       48
                  vv
clus               STAGE IVA STAGE IVB
  OR4D10 MUTATED           1         0
  OR4D10 WILD-TYPE        17         1
D21V4, multiclass
            clus
vv           OR4D10 MUTATED OR4D10 WILD-TYPE
  STAGE I                 2               89
  STAGE IA                0                1
  STAGE II                2               30
  STAGE IIA               8              130
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              1               58
  STAGE IIIC              1               41
  STAGE IV                0               48
  STAGE IVA               1               17
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  OR4D10 MUTATED     0   2  12   2
  OR4D10 WILD-TYPE  17  90 317  48
D21V5, multiclass
    clus
vv   OR4D10 MUTATED OR4D10 WILD-TYPE
  T1              0               17
  T2              2               90
  T3             12              317
  T4              2               48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  OR4D10 MUTATED    12   2   2
  OR4D10 WILD-TYPE 275 111  85
D21V6, multiclass
    clus
vv   OR4D10 MUTATED OR4D10 WILD-TYPE
  N0             12              275
  N1              2              111
  N2              2               85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V7, binary
                  cls
clus                 0   1
  OR4D10 MUTATED    13   1
  OR4D10 WILD-TYPE 362  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR4D10 MUTATED     13    1
  OR4D10 WILD-TYPE  362   64
   clus
vv  OR4D10 MUTATED OR4D10 WILD-TYPE
  0             13              362
  1              1               64
[1] 2 2
[1] FALSE
D21V8, binary
                  cls
clus                 0   1
  OR4D10 MUTATED     3  13
  OR4D10 WILD-TYPE 222 251
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR4D10 MUTATED      3   13
  OR4D10 WILD-TYPE  222  251
        clus
vv       OR4D10 MUTATED OR4D10 WILD-TYPE
  FEMALE              3              222
  MALE               13              251
[1] 2 2
[1] FALSE
D21V9, binary
                  cls
clus                 0   1
  OR4D10 MUTATED    14   0
  OR4D10 WILD-TYPE 336  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR4D10 MUTATED     14    0
  OR4D10 WILD-TYPE  336   22
     clus
vv    OR4D10 MUTATED OR4D10 WILD-TYPE
  NO              14              336
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  OR4D10 MUTATED                     11                             3
  OR4D10 WILD-TYPE                  304                            44
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  OR4D10 MUTATED                       2                              0
  OR4D10 WILD-TYPE                   104                             10
D21V10, multiclass
                                clus
vv                               OR4D10 MUTATED OR4D10 WILD-TYPE
  COLON ADENOCARCINOMA                       11              304
  COLON MUCINOUS ADENOCARCINOMA               3               44
  RECTAL ADENOCARCINOMA                       2              104
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  OR4D10 MUTATED    10   0   0   3
  OR4D10 WILD-TYPE 335   4  31  22
D21V11, multiclass
    clus
vv   OR4D10 MUTATED OR4D10 WILD-TYPE
  R0             10              335
  R1              0                4
  R2              0               31
  RX              3               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OR4D10 MUTATED                                  0     2
  OR4D10 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  OR4D10 MUTATED                           3     8
  OR4D10 WILD-TYPE                        19   218
D21V13, multiclass
                                  clus
vv                                 OR4D10 MUTATED OR4D10 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                9
  BLACK OR AFRICAN AMERICAN                     3               19
  WHITE                                         8              218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(22) Variable = NF2 MUTATION ANALYSIS
D22V1, survival
               sevent
clus2             0   1
  NF2 MUTATED    58   8
  NF2 WILD-TYPE 320  85
  NF2 MUTATED NF2 WILD-TYPE 
           66           405 
  NF2 MUTATED NF2 WILD-TYPE 
            8            85 
$`NF2 MUTATED`
TCGA-A6-5657 TCGA-A6-5661 TCGA-A6-5666 TCGA-A6-6141 TCGA-A6-6142 TCGA-AA-3516 
       31.63        33.53        32.71         8.38        25.08        13.02 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3713 TCGA-AA-3950 TCGA-AA-3968 TCGA-AA-A01R 
        6.05         6.97        19.04        24.00        21.99        35.01 
TCGA-AD-6963 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-6598 
       27.42        14.50        27.09        17.82        58.39        49.41 
TCGA-AZ-6599 TCGA-AZ-6603 TCGA-CA-6716 TCGA-CA-6717 TCGA-CK-4947 TCGA-CK-4952 
        6.77        29.56        12.20        12.76        17.56        15.62 
TCGA-CK-5912 TCGA-CM-4743 TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5864 
       49.08        23.05        13.02        22.03        30.08        15.02 
TCGA-CM-6161 TCGA-CM-6164 TCGA-CM-6167 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       15.02        29.03        14.99        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-D5-5538 TCGA-D5-5541 TCGA-D5-6532 TCGA-D5-6535 
       12.95        13.05        12.26        55.92        18.25        15.12 
TCGA-D5-6536 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6922 TCGA-D5-6926 TCGA-D5-6927 
       17.85        12.49        15.58         4.41         9.04         9.44 
TCGA-DM-A1DB TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6807 TCGA-F4-6856 TCGA-G4-6299 
       44.32         6.18        47.87        16.24        35.31        74.56 
TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       55.04        63.62        22.09        13.78        35.80        26.17 
TCGA-G4-6626 TCGA-AG-3732 TCGA-AG-A002 TCGA-AH-6643 TCGA-DC-5337 TCGA-EI-6507 
       46.75        32.98        20.98         0.69        15.02        19.96 

$`NF2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       32.91        30.44        29.19        23.61        22.09        22.06 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 
       27.09        22.52        25.18        24.16        21.76        24.69 
TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 
       24.39        23.87        20.12        19.66        20.28         7.04 
TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
        3.02         1.02        35.01        63.98         6.97         1.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        33.01        26.01         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
        2.01        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
        1.02         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6964 TCGA-AD-6965 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       22.42        10.88         0.20        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       21.44         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       88.21        12.10       100.01         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5913 TCGA-CK-5914 
       10.06        14.30       148.01        85.45        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 
       21.14        82.95         1.91       124.27        20.02        37.02 
TCGA-CM-4747 TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       25.02        29.06        22.98        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5868 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6165 TCGA-CM-6166 
       15.02        17.03        12.00         2.96        16.04        21.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.99        13.02        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-6529 TCGA-D5-6533 
       12.03        45.40        19.59        56.09        20.19         1.32 
TCGA-D5-6534 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6898 TCGA-D5-6920 
       43.27         4.80        17.13        16.14         1.48         3.68 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
       12.43        14.30        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6808 TCGA-F4-6809 
       35.74         1.55        34.42        41.42        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
        0.53        47.41       133.18        65.85        53.62        44.68 
TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6625 TCGA-G4-6628 TCGA-AF-2687 
       85.48        61.91        36.00        91.79        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 
       19.99         7.99         0.99        37.02         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6644 TCGA-CI-6619 
      117.11        38.56         1.45        17.49         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5869 
       33.17         6.97         4.73        78.12         7.17         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6510 
       51.48        32.61         0.49        20.55        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  NF2 MUTATED NF2 WILD-TYPE 
         0.69          0.00 
  NF2 MUTATED NF2 WILD-TYPE 
        74.56        148.01 
  NF2 MUTATED NF2 WILD-TYPE 
        18.05         20.91 
[1] "0.7 - 74.6 (18.1)"  "0.0 - 148.0 (20.9)"
[1] "hr=" "1.6"
D22V2, continuous
D22V3, binary
               cls
clus              0   1
  NF2 MUTATED    62   5
  NF2 WILD-TYPE 304 114
[1] "tbl2"
               cls
clus            [,1] [,2]
  NF2 MUTATED     62    5
  NF2 WILD-TYPE  304  114
        clus
vv       NF2 MUTATED NF2 WILD-TYPE
  COLON           62           304
  RECTUM           5           114
[1] 2 2
[1] FALSE
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NF2 MUTATED        12        1        2        23         1         1
  NF2 WILD-TYPE      79        0       30       115         9         0
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NF2 MUTATED           3          2         11          5        2         1
  NF2 WILD-TYPE        21          9         48         37       46        17
               vv
clus            STAGE IVB
  NF2 MUTATED           1
  NF2 WILD-TYPE         0
D22V4, multiclass
            clus
vv           NF2 MUTATED NF2 WILD-TYPE
  STAGE I             12            79
  STAGE IA             1             0
  STAGE II             2            30
  STAGE IIA           23           115
  STAGE IIB            1             9
  STAGE IIC            1             0
  STAGE III            3            21
  STAGE IIIA           2             9
  STAGE IIIB          11            48
  STAGE IIIC           5            37
  STAGE IV             2            46
  STAGE IVA            1            17
  STAGE IVB            1             0
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  NF2 MUTATED     1  13  46   6
  NF2 WILD-TYPE  16  79 283  44
D22V5, multiclass
    clus
vv   NF2 MUTATED NF2 WILD-TYPE
  T1           1            16
  T2          13            79
  T3          46           283
  T4           6            44
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2
  NF2 MUTATED    43  15   9
  NF2 WILD-TYPE 244  98  78
D22V6, multiclass
    clus
vv   NF2 MUTATED NF2 WILD-TYPE
  N0          43           244
  N1          15            98
  N2           9            78
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V7, binary
               cls
clus              0   1
  NF2 MUTATED    54   4
  NF2 WILD-TYPE 321  61
[1] "tbl2"
               cls
clus            [,1] [,2]
  NF2 MUTATED     54    4
  NF2 WILD-TYPE  321   61
   clus
vv  NF2 MUTATED NF2 WILD-TYPE
  0          54           321
  1           4            61
[1] 2 2
[1] FALSE
D22V8, binary
               cls
clus              0   1
  NF2 MUTATED    32  35
  NF2 WILD-TYPE 193 229
[1] "tbl2"
               cls
clus            [,1] [,2]
  NF2 MUTATED     32   35
  NF2 WILD-TYPE  193  229
        clus
vv       NF2 MUTATED NF2 WILD-TYPE
  FEMALE          32           193
  MALE            35           229
[1] 2 2
[1] FALSE
D22V9, binary
               cls
clus              0   1
  NF2 MUTATED    57   4
  NF2 WILD-TYPE 293  18
[1] "tbl2"
               cls
clus            [,1] [,2]
  NF2 MUTATED     57    4
  NF2 WILD-TYPE  293   18
     clus
vv    NF2 MUTATED NF2 WILD-TYPE
  NO           57           293
  YES           4            18
[1] 2 2
[1] FALSE
               vv
clus            COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  NF2 MUTATED                     56                             6
  NF2 WILD-TYPE                  259                            41
               vv
clus            RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  NF2 MUTATED                       5                              0
  NF2 WILD-TYPE                   101                             10
D22V10, multiclass
                                clus
vv                               NF2 MUTATED NF2 WILD-TYPE
  COLON ADENOCARCINOMA                    56           259
  COLON MUCINOUS ADENOCARCINOMA            6            41
  RECTAL ADENOCARCINOMA                    5           101
  RECTAL MUCINOUS ADENOCARCINOMA           0            10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             R0  R1  R2  RX
  NF2 MUTATED    49   0   2   7
  NF2 WILD-TYPE 296   4  29  18
D22V11, multiclass
    clus
vv   NF2 MUTATED NF2 WILD-TYPE
  R0          49           296
  R1           0             4
  R2           2            29
  RX           7            18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V12, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NF2 MUTATED                                  0     2
  NF2 WILD-TYPE                                1     9
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  NF2 MUTATED                           8    48
  NF2 WILD-TYPE                        14   178
D22V13, multiclass
                                  clus
vv                                 NF2 MUTATED NF2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      2             9
  BLACK OR AFRICAN AMERICAN                  8            14
  WHITE                                     48           178
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(23) Variable = MAPK6 MUTATION ANALYSIS
D23V1, survival
                 sevent
clus2               0   1
  MAPK6 MUTATED    15   4
  MAPK6 WILD-TYPE 363  89
  MAPK6 MUTATED MAPK6 WILD-TYPE 
             19             452 
  MAPK6 MUTATED MAPK6 WILD-TYPE 
              4              89 
$`MAPK6 MUTATED`
TCGA-A6-5661 TCGA-A6-5665 TCGA-A6-6648 TCGA-AA-3510 TCGA-AA-3672 TCGA-AA-3977 
       33.53        22.06        25.18        63.98         0.92        25.02 
TCGA-AZ-6598 TCGA-AZ-6601 TCGA-CA-6717 TCGA-CK-4950 TCGA-CK-4952 TCGA-CM-4752 
       49.41       100.01        12.76        85.45        15.62        13.02 
TCGA-CM-5344 TCGA-D5-5537 TCGA-F4-6704 TCGA-G4-6303 TCGA-G4-6321 TCGA-G4-6625 
       22.03        45.40         1.55        65.85        22.09        91.79 
TCGA-AG-A002 
       20.98 

$`MAPK6 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6649 
       32.71        27.09        22.52         8.38        25.08        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 
       20.28         7.04         3.02         1.02        35.01         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
       14.01        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77        12.10        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-5912 
       12.20        10.06        14.30        17.56       148.01        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-5341 TCGA-CM-5348 
       23.05        20.02        37.02        25.02        29.06        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       10.06        12.03        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
        6.18        47.87        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6626 TCGA-G4-6628 
       36.00        13.78        35.80        26.17        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  MAPK6 MUTATED MAPK6 WILD-TYPE 
           0.92            0.00 
  MAPK6 MUTATED MAPK6 WILD-TYPE 
         100.01          148.01 
  MAPK6 MUTATED MAPK6 WILD-TYPE 
         25.020          20.005 
[1] "0.9 - 100.0 (25.0)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.4"
D23V2, continuous
D23V3, binary
                 cls
clus                0   1
  MAPK6 MUTATED    18   1
  MAPK6 WILD-TYPE 348 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MAPK6 MUTATED     18    1
  MAPK6 WILD-TYPE  348  118
        clus
vv       MAPK6 MUTATED MAPK6 WILD-TYPE
  COLON             18             348
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MAPK6 MUTATED         1        0        3         6         0         0
  MAPK6 WILD-TYPE      90        1       29       132        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MAPK6 MUTATED           2          0          2          2        1         1
  MAPK6 WILD-TYPE        22         11         57         40       47        17
                 vv
clus              STAGE IVB
  MAPK6 MUTATED           0
  MAPK6 WILD-TYPE         1
D23V4, multiclass
            clus
vv           MAPK6 MUTATED MAPK6 WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               3              29
  STAGE IIA              6             132
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              2              22
  STAGE IIIA             0              11
  STAGE IIIB             2              57
  STAGE IIIC             2              40
  STAGE IV               1              47
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  MAPK6 MUTATED     0   3  15   1
  MAPK6 WILD-TYPE  17  89 314  49
D23V5, multiclass
    clus
vv   MAPK6 MUTATED MAPK6 WILD-TYPE
  T1             0              17
  T2             3              89
  T3            15             314
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  MAPK6 MUTATED    11   5   3
  MAPK6 WILD-TYPE 276 108  84
D23V6, multiclass
    clus
vv   MAPK6 MUTATED MAPK6 WILD-TYPE
  N0            11             276
  N1             5             108
  N2             3              84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V7, binary
                 cls
clus                0   1
  MAPK6 MUTATED    12   2
  MAPK6 WILD-TYPE 363  63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MAPK6 MUTATED     12    2
  MAPK6 WILD-TYPE  363   63
   clus
vv  MAPK6 MUTATED MAPK6 WILD-TYPE
  0            12             363
  1             2              63
[1] 2 2
[1] FALSE
D23V8, binary
                 cls
clus                0   1
  MAPK6 MUTATED    10   9
  MAPK6 WILD-TYPE 215 255
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MAPK6 MUTATED     10    9
  MAPK6 WILD-TYPE  215  255
        clus
vv       MAPK6 MUTATED MAPK6 WILD-TYPE
  FEMALE            10             215
  MALE               9             255
[1] 2 2
[1] FALSE
D23V9, binary
                 cls
clus                0   1
  MAPK6 MUTATED    17   0
  MAPK6 WILD-TYPE 333  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MAPK6 MUTATED     17    0
  MAPK6 WILD-TYPE  333   22
     clus
vv    MAPK6 MUTATED MAPK6 WILD-TYPE
  NO             17             333
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MAPK6 MUTATED                     15                             3
  MAPK6 WILD-TYPE                  300                            44
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MAPK6 MUTATED                       1                              0
  MAPK6 WILD-TYPE                   105                             10
D23V10, multiclass
                                clus
vv                               MAPK6 MUTATED MAPK6 WILD-TYPE
  COLON ADENOCARCINOMA                      15             300
  COLON MUCINOUS ADENOCARCINOMA              3              44
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  MAPK6 MUTATED    11   1   0   3
  MAPK6 WILD-TYPE 334   3  31  22
D23V11, multiclass
    clus
vv   MAPK6 MUTATED MAPK6 WILD-TYPE
  R0            11             334
  R1             1               3
  R2             0              31
  RX             3              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MAPK6 MUTATED                                  1     1
  MAPK6 WILD-TYPE                                0    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  MAPK6 MUTATED                           3    10
  MAPK6 WILD-TYPE                        19   216
D23V13, multiclass
                                  clus
vv                                 MAPK6 MUTATED MAPK6 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             1               0
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    3              19
  WHITE                                       10             216
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(24) Variable = RHOA MUTATION ANALYSIS
D24V1, survival
                sevent
clus2              0   1
  RHOA MUTATED    10   3
  RHOA WILD-TYPE 368  90
  RHOA MUTATED RHOA WILD-TYPE 
            13            458 
  RHOA MUTATED RHOA WILD-TYPE 
             3             90 
$`RHOA MUTATED`
TCGA-AA-3845 TCGA-AA-3972 TCGA-AA-A01P TCGA-AA-A01R TCGA-AD-6895 TCGA-AD-6965 
        0.00        50.99        38.07        35.01         0.72         0.20 
TCGA-AZ-6598 TCGA-CK-4948 TCGA-CK-4950 TCGA-CM-6678 TCGA-D5-6536 TCGA-G4-6310 
       49.41       148.01        85.45        11.01        17.85        63.62 
TCGA-AG-3892 
       13.02 

$`RHOA WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       31.00        31.00         1.02         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        10.88        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       13.05        11.08        11.08        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
        1.32        43.27        15.12         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       44.68        55.04        85.48        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       36.95        17.03        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  RHOA MUTATED RHOA WILD-TYPE 
             0              0 
  RHOA MUTATED RHOA WILD-TYPE 
        148.01         140.38 
  RHOA MUTATED RHOA WILD-TYPE 
        35.010         20.155 
[1] "0.0 - 148.0 (35.0)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.2"
D24V2, continuous
D24V3, binary
                cls
clus               0   1
  RHOA MUTATED    12   1
  RHOA WILD-TYPE 354 118
[1] "tbl2"
                cls
clus             [,1] [,2]
  RHOA MUTATED     12    1
  RHOA WILD-TYPE  354  118
        clus
vv       RHOA MUTATED RHOA WILD-TYPE
  COLON            12            354
  RECTUM            1            118
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RHOA MUTATED         1        0        1         2         0         0
  RHOA WILD-TYPE      90        1       31       136        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RHOA MUTATED           3          0          2          0        1         1
  RHOA WILD-TYPE        21         11         57         42       47        17
                vv
clus             STAGE IVB
  RHOA MUTATED           0
  RHOA WILD-TYPE         1
D24V4, multiclass
            clus
vv           RHOA MUTATED RHOA WILD-TYPE
  STAGE I               1             90
  STAGE IA              0              1
  STAGE II              1             31
  STAGE IIA             2            136
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             3             21
  STAGE IIIA            0             11
  STAGE IIIB            2             57
  STAGE IIIC            0             42
  STAGE IV              1             47
  STAGE IVA             1             17
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  RHOA MUTATED     1   0  10   2
  RHOA WILD-TYPE  16  92 319  48
D24V5, multiclass
    clus
vv   RHOA MUTATED RHOA WILD-TYPE
  T1            1             16
  T2            0             92
  T3           10            319
  T4            2             48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  RHOA MUTATED     4   7   2
  RHOA WILD-TYPE 283 106  85
D24V6, multiclass
    clus
vv   RHOA MUTATED RHOA WILD-TYPE
  N0            4            283
  N1            7            106
  N2            2             85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V7, binary
                cls
clus               0   1
  RHOA MUTATED     8   2
  RHOA WILD-TYPE 367  63
[1] "tbl2"
                cls
clus             [,1] [,2]
  RHOA MUTATED      8    2
  RHOA WILD-TYPE  367   63
   clus
vv  RHOA MUTATED RHOA WILD-TYPE
  0            8            367
  1            2             63
[1] 2 2
[1] FALSE
D24V8, binary
                cls
clus               0   1
  RHOA MUTATED     7   6
  RHOA WILD-TYPE 218 258
[1] "tbl2"
                cls
clus             [,1] [,2]
  RHOA MUTATED      7    6
  RHOA WILD-TYPE  218  258
        clus
vv       RHOA MUTATED RHOA WILD-TYPE
  FEMALE            7            218
  MALE              6            258
[1] 2 2
[1] FALSE
D24V9, binary
                cls
clus               0   1
  RHOA MUTATED     8   2
  RHOA WILD-TYPE 342  20
[1] "tbl2"
                cls
clus             [,1] [,2]
  RHOA MUTATED      8    2
  RHOA WILD-TYPE  342   20
     clus
vv    RHOA MUTATED RHOA WILD-TYPE
  NO             8            342
  YES            2             20
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  RHOA MUTATED                     11                             1
  RHOA WILD-TYPE                  304                            46
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  RHOA MUTATED                       1                              0
  RHOA WILD-TYPE                   105                             10
D24V10, multiclass
                                clus
vv                               RHOA MUTATED RHOA WILD-TYPE
  COLON ADENOCARCINOMA                     11            304
  COLON MUCINOUS ADENOCARCINOMA             1             46
  RECTAL ADENOCARCINOMA                     1            105
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  RHOA MUTATED     8   1   1   0
  RHOA WILD-TYPE 337   3  30  25
D24V11, multiclass
    clus
vv   RHOA MUTATED RHOA WILD-TYPE
  R0            8            337
  R1            1              3
  R2            1             30
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RHOA MUTATED                                  0     0
  RHOA WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  RHOA MUTATED                           1     7
  RHOA WILD-TYPE                        21   219
D24V13, multiclass
                                  clus
vv                                 RHOA MUTATED RHOA WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                       7            219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(25) Variable = FAM9A MUTATION ANALYSIS
D25V1, survival
                 sevent
clus2               0   1
  FAM9A MUTATED     5   6
  FAM9A WILD-TYPE 373  87
  FAM9A MUTATED FAM9A WILD-TYPE 
             11             460 
  FAM9A MUTATED FAM9A WILD-TYPE 
              6              87 
$`FAM9A MUTATED`
TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3815 TCGA-AD-6964 TCGA-AZ-6598 TCGA-AZ-6601 
       20.12        19.66        33.04        10.88        49.41       100.01 
TCGA-AZ-6603 TCGA-CK-5913 TCGA-F4-6570 TCGA-G4-6588 TCGA-AF-5654 
       29.56        51.32         6.18        26.17        16.83 

$`FAM9A WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       23.87        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       35.05         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
        0.79         0.72         5.79        22.42        27.42         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6605 TCGA-AZ-6606 
       62.79        88.21         6.77        12.10         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 
      148.01        85.45        15.62        49.08         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 
       61.91        36.00        22.09        13.78        35.80        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6655 
       19.10        34.49        10.39        14.50        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  FAM9A MUTATED FAM9A WILD-TYPE 
           6.18            0.00 
  FAM9A MUTATED FAM9A WILD-TYPE 
         100.01          148.01 
  FAM9A MUTATED FAM9A WILD-TYPE 
          26.17           20.12 
[1] "6.2 - 100.0 (26.2)" "0.0 - 148.0 (20.1)"
[1] "hr=" "2.2"
D25V2, continuous
D25V3, binary
                 cls
clus                0   1
  FAM9A MUTATED    11   1
  FAM9A WILD-TYPE 355 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FAM9A MUTATED     11    1
  FAM9A WILD-TYPE  355  118
        clus
vv       FAM9A MUTATED FAM9A WILD-TYPE
  COLON             11             355
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FAM9A MUTATED         1        0        2         6         0         0
  FAM9A WILD-TYPE      90        1       30       132        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  FAM9A MUTATED           0          0          0          1        0         0
  FAM9A WILD-TYPE        24         11         59         41       48        18
                 vv
clus              STAGE IVB
  FAM9A MUTATED           0
  FAM9A WILD-TYPE         1
D25V4, multiclass
            clus
vv           FAM9A MUTATED FAM9A WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA              6             132
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             1              41
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  FAM9A MUTATED     0   2   8   2
  FAM9A WILD-TYPE  17  90 321  48
D25V5, multiclass
    clus
vv   FAM9A MUTATED FAM9A WILD-TYPE
  T1             0              17
  T2             2              90
  T3             8             321
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  FAM9A MUTATED     9   2   1
  FAM9A WILD-TYPE 278 111  86
D25V6, multiclass
    clus
vv   FAM9A MUTATED FAM9A WILD-TYPE
  N0             9             278
  N1             2             111
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V7, binary
                 cls
clus                0   1
  FAM9A MUTATED     6   0
  FAM9A WILD-TYPE 369  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FAM9A MUTATED      6    0
  FAM9A WILD-TYPE  369   65
   clus
vv  FAM9A MUTATED FAM9A WILD-TYPE
  0             6             369
  1             0              65
[1] 2 2
[1] FALSE
D25V8, binary
                 cls
clus                0   1
  FAM9A MUTATED     8   4
  FAM9A WILD-TYPE 217 260
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FAM9A MUTATED      8    4
  FAM9A WILD-TYPE  217  260
        clus
vv       FAM9A MUTATED FAM9A WILD-TYPE
  FEMALE             8             217
  MALE               4             260
[1] 2 2
[1] FALSE
D25V9, binary
                 cls
clus                0   1
  FAM9A MUTATED    11   0
  FAM9A WILD-TYPE 339  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FAM9A MUTATED     11    0
  FAM9A WILD-TYPE  339   22
     clus
vv    FAM9A MUTATED FAM9A WILD-TYPE
  NO             11             339
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  FAM9A MUTATED                      9                             2
  FAM9A WILD-TYPE                  306                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  FAM9A MUTATED                       1                              0
  FAM9A WILD-TYPE                   105                             10
D25V10, multiclass
                                clus
vv                               FAM9A MUTATED FAM9A WILD-TYPE
  COLON ADENOCARCINOMA                       9             306
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  FAM9A MUTATED     6   0   0   1
  FAM9A WILD-TYPE 339   4  31  24
D25V11, multiclass
    clus
vv   FAM9A MUTATED FAM9A WILD-TYPE
  R0             6             339
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FAM9A MUTATED                                  0     0
  FAM9A WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  FAM9A MUTATED                           0    10
  FAM9A WILD-TYPE                        22   216
D25V13, multiclass
                                  clus
vv                                 FAM9A MUTATED FAM9A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                       10             216
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(26) Variable = EGR1 MUTATION ANALYSIS
D26V1, survival
                sevent
clus2              0   1
  EGR1 MUTATED    11   1
  EGR1 WILD-TYPE 367  92
  EGR1 MUTATED EGR1 WILD-TYPE 
            12            459 
  EGR1 MUTATED EGR1 WILD-TYPE 
             1             92 
$`EGR1 MUTATED`
TCGA-A6-5665 TCGA-A6-6780 TCGA-AA-3663 TCGA-AA-3877 TCGA-AA-3994 TCGA-AZ-6598 
       22.06        20.12         6.97        31.00        27.02        49.41 
TCGA-CM-4743 TCGA-G4-6588 TCGA-G4-6628 TCGA-AG-A02N TCGA-CI-6622 TCGA-G5-6641 
       23.05        26.17        79.69        61.97         6.97        26.43 

$`EGR1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       27.02        29.98        18.05         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
        7.96        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       88.21         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 
        9.99        21.14        82.95         1.91       124.27        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       35.80        91.79        46.75        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
       49.97         1.94        38.96        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
       33.17         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
        0.66         0.69        55.76 

  EGR1 MUTATED EGR1 WILD-TYPE 
          6.97           0.00 
  EGR1 MUTATED EGR1 WILD-TYPE 
         79.69         148.01 
  EGR1 MUTATED EGR1 WILD-TYPE 
         26.30          20.02 
[1] "7.0 - 79.7 (26.3)"  "0.0 - 148.0 (20.0)"
[1] "hr=" "2.9"
D26V2, continuous
D26V3, binary
                cls
clus               0   1
  EGR1 MUTATED     9   3
  EGR1 WILD-TYPE 357 116
[1] "tbl2"
                cls
clus             [,1] [,2]
  EGR1 MUTATED      9    3
  EGR1 WILD-TYPE  357  116
        clus
vv       EGR1 MUTATED EGR1 WILD-TYPE
  COLON             9            357
  RECTUM            3            116
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  EGR1 MUTATED         2        0        3         4         1         0
  EGR1 WILD-TYPE      89        1       29       134         9         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  EGR1 MUTATED           0          1          1          0        0         0
  EGR1 WILD-TYPE        24         10         58         42       48        18
                vv
clus             STAGE IVB
  EGR1 MUTATED           0
  EGR1 WILD-TYPE         1
D26V4, multiclass
            clus
vv           EGR1 MUTATED EGR1 WILD-TYPE
  STAGE I               2             89
  STAGE IA              0              1
  STAGE II              3             29
  STAGE IIA             4            134
  STAGE IIB             1              9
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            1             10
  STAGE IIIB            1             58
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  EGR1 MUTATED     2   1   8   1
  EGR1 WILD-TYPE  15  91 321  49
D26V5, multiclass
    clus
vv   EGR1 MUTATED EGR1 WILD-TYPE
  T1            2             15
  T2            1             91
  T3            8            321
  T4            1             49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  EGR1 MUTATED    10   2   0
  EGR1 WILD-TYPE 277 111  87
D26V6, multiclass
    clus
vv   EGR1 MUTATED EGR1 WILD-TYPE
  N0           10            277
  N1            2            111
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V7, binary
                cls
clus               0   1
  EGR1 MUTATED     9   0
  EGR1 WILD-TYPE 366  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  EGR1 MUTATED      9    0
  EGR1 WILD-TYPE  366   65
   clus
vv  EGR1 MUTATED EGR1 WILD-TYPE
  0            9            366
  1            0             65
[1] 2 2
[1] FALSE
D26V8, binary
                cls
clus               0   1
  EGR1 MUTATED     4   8
  EGR1 WILD-TYPE 221 256
[1] "tbl2"
                cls
clus             [,1] [,2]
  EGR1 MUTATED      4    8
  EGR1 WILD-TYPE  221  256
        clus
vv       EGR1 MUTATED EGR1 WILD-TYPE
  FEMALE            4            221
  MALE              8            256
[1] 2 2
[1] FALSE
D26V9, binary
                cls
clus               0   1
  EGR1 MUTATED    10   0
  EGR1 WILD-TYPE 340  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  EGR1 MUTATED     10    0
  EGR1 WILD-TYPE  340   22
     clus
vv    EGR1 MUTATED EGR1 WILD-TYPE
  NO            10            340
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  EGR1 MUTATED                      6                             3
  EGR1 WILD-TYPE                  309                            44
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  EGR1 MUTATED                       2                              1
  EGR1 WILD-TYPE                   104                              9
D26V10, multiclass
                                clus
vv                               EGR1 MUTATED EGR1 WILD-TYPE
  COLON ADENOCARCINOMA                      6            309
  COLON MUCINOUS ADENOCARCINOMA             3             44
  RECTAL ADENOCARCINOMA                     2            104
  RECTAL MUCINOUS ADENOCARCINOMA            1              9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  EGR1 MUTATED     9   0   0   0
  EGR1 WILD-TYPE 336   4  31  25
D26V11, multiclass
    clus
vv   EGR1 MUTATED EGR1 WILD-TYPE
  R0            9            336
  R1            0              4
  R2            0             31
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  EGR1 MUTATED                                  0     0
  EGR1 WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  EGR1 MUTATED                           0     8
  EGR1 WILD-TYPE                        22   218
D26V13, multiclass
                                  clus
vv                                 EGR1 MUTATED EGR1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       8            218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(27) Variable = PRKDC MUTATION ANALYSIS
D27V1, survival
                 sevent
clus2               0   1
  PRKDC MUTATED    56  13
  PRKDC WILD-TYPE 322  80
  PRKDC MUTATED PRKDC WILD-TYPE 
             69             402 
  PRKDC MUTATED PRKDC WILD-TYPE 
             13              80 
$`PRKDC MUTATED`
TCGA-A6-3809 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6141 
       32.75        31.63        30.44        22.06        32.71         8.38 
TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3510 TCGA-AA-3655 TCGA-AA-3663 
       24.39        20.12        19.66        63.98        61.02         6.97 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3864 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-A00N 
       19.04        10.06        53.00        31.00         2.01         4.01 
TCGA-AA-A010 TCGA-AA-A01P TCGA-AD-6889 TCGA-AD-6964 TCGA-AU-3779 TCGA-AU-6004 
       34.98        38.07        56.55        10.88        14.50        27.09 
TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-6601 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-6717 
       21.44        58.39       100.01         3.19         1.61        12.76 
TCGA-CA-6718 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5913 TCGA-CM-5349 TCGA-CM-5860 
       10.06       148.01        15.62        51.32        30.08        32.02 
TCGA-CM-6161 TCGA-CM-6166 TCGA-CM-6676 TCGA-CM-6680 TCGA-D5-5540 TCGA-D5-6532 
       15.02        21.99        11.08        12.03        56.09        18.25 
TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6927 TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6570 
       15.12         4.80         9.44       117.07        98.24         6.18 
TCGA-F4-6703 TCGA-F4-6854 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6303 TCGA-G4-6304 
       47.87         0.53        35.31       133.18        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6586 TCGA-G4-6588 
       44.68        55.04        61.91        36.00        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-AF-4110 TCGA-AG-A002 TCGA-AG-A011 TCGA-AG-A014 
       91.79        79.69        14.50        20.98        37.02        15.95 
TCGA-AG-A02N TCGA-CL-5918 TCGA-G5-6235 
       61.97         7.17        55.76 

$`PRKDC WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-6137 TCGA-A6-6138 
       29.19        33.53        23.61        22.09        27.09        22.52 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
       25.08        25.18        24.16        21.76        24.69        23.87 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 
       20.28         7.04         3.02         1.02        35.01         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
       78.08         6.05        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 
        0.99        31.07        31.07        30.05        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       27.02        29.98        18.05        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       12.00        31.00        31.00         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
        0.79         0.72         5.79        22.42        27.42         0.20 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
       16.31         0.95        33.01        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-CA-5254 TCGA-CA-5255 
       12.10        29.56         5.23        11.74        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 
        3.25         3.29         0.07        12.20        14.30        17.56 
TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       85.45        49.08         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       29.06        22.03        22.98        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       15.02        17.03        12.00         2.96        29.03        16.04 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-D5-5537 
       12.95        13.05        11.08        11.01        10.06        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6534 
       12.26        19.59        55.92        20.19         1.32        43.27 
TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
       17.85        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6928 
        3.68         4.41        12.43        14.30         9.04        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
        8.61        31.96        35.74         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6855 TCGA-G4-6299 TCGA-G4-6309 
       16.24        33.67        13.25        47.41        74.56        85.48 
TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 
       63.62        22.09        13.78        46.75        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-5654 
       43.04        13.55        19.10        34.49        10.39        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
        6.02        25.97        23.01        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
       78.12        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6641 
       31.30        28.57        32.19         0.66         0.69        26.43 

  PRKDC MUTATED PRKDC WILD-TYPE 
           0.53            0.00 
  PRKDC MUTATED PRKDC WILD-TYPE 
         148.01          140.38 
  PRKDC MUTATED PRKDC WILD-TYPE 
          30.08           19.99 
[1] "0.5 - 148.0 (30.1)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1.5"
D27V2, continuous
D27V3, binary
                 cls
clus                0   1
  PRKDC MUTATED    63   6
  PRKDC WILD-TYPE 303 113
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRKDC MUTATED     63    6
  PRKDC WILD-TYPE  303  113
        clus
vv       PRKDC MUTATED PRKDC WILD-TYPE
  COLON             63             303
  RECTUM             6             113
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PRKDC MUTATED        11        0        7        26         4         1
  PRKDC WILD-TYPE      80        1       25       112         6         0
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PRKDC MUTATED           4          1          6          4        4         1
  PRKDC WILD-TYPE        20         10         53         38       44        17
                 vv
clus              STAGE IVB
  PRKDC MUTATED           0
  PRKDC WILD-TYPE         1
D27V4, multiclass
            clus
vv           PRKDC MUTATED PRKDC WILD-TYPE
  STAGE I               11              80
  STAGE IA               0               1
  STAGE II               7              25
  STAGE IIA             26             112
  STAGE IIB              4               6
  STAGE IIC              1               0
  STAGE III              4              20
  STAGE IIIA             1              10
  STAGE IIIB             6              53
  STAGE IIIC             4              38
  STAGE IV               4              44
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PRKDC MUTATED     1  12  47  10
  PRKDC WILD-TYPE  16  80 282  40
D27V5, multiclass
    clus
vv   PRKDC MUTATED PRKDC WILD-TYPE
  T1             1              16
  T2            12              80
  T3            47             282
  T4            10              40
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  PRKDC MUTATED    49  12   9
  PRKDC WILD-TYPE 238 101  78
D27V6, multiclass
    clus
vv   PRKDC MUTATED PRKDC WILD-TYPE
  N0            49             238
  N1            12             101
  N2             9              78
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V7, binary
                 cls
clus                0   1
  PRKDC MUTATED    55   4
  PRKDC WILD-TYPE 320  61
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRKDC MUTATED     55    4
  PRKDC WILD-TYPE  320   61
   clus
vv  PRKDC MUTATED PRKDC WILD-TYPE
  0            55             320
  1             4              61
[1] 2 2
[1] FALSE
D27V8, binary
                 cls
clus                0   1
  PRKDC MUTATED    29  41
  PRKDC WILD-TYPE 196 223
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRKDC MUTATED     29   41
  PRKDC WILD-TYPE  196  223
        clus
vv       PRKDC MUTATED PRKDC WILD-TYPE
  FEMALE            29             196
  MALE              41             223
[1] 2 2
[1] FALSE
D27V9, binary
                 cls
clus                0   1
  PRKDC MUTATED    61   0
  PRKDC WILD-TYPE 289  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRKDC MUTATED     61    0
  PRKDC WILD-TYPE  289   22
     clus
vv    PRKDC MUTATED PRKDC WILD-TYPE
  NO             61             289
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PRKDC MUTATED                     54                             9
  PRKDC WILD-TYPE                  261                            38
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PRKDC MUTATED                       6                              0
  PRKDC WILD-TYPE                   100                             10
D27V10, multiclass
                                clus
vv                               PRKDC MUTATED PRKDC WILD-TYPE
  COLON ADENOCARCINOMA                      54             261
  COLON MUCINOUS ADENOCARCINOMA              9              38
  RECTAL ADENOCARCINOMA                      6             100
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  PRKDC MUTATED    51   1   1   6
  PRKDC WILD-TYPE 294   3  30  19
D27V11, multiclass
    clus
vv   PRKDC MUTATED PRKDC WILD-TYPE
  R0            51             294
  R1             1               3
  R2             1              30
  RX             6              19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PRKDC MUTATED                                  0     3
  PRKDC WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PRKDC MUTATED                           2    49
  PRKDC WILD-TYPE                        20   177
D27V13, multiclass
                                  clus
vv                                 PRKDC MUTATED PRKDC WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        3               8
  BLACK OR AFRICAN AMERICAN                    2              20
  WHITE                                       49             177
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(28) Variable = RPTN MUTATION ANALYSIS
D28V1, survival
                sevent
clus2              0   1
  RPTN MUTATED    15   3
  RPTN WILD-TYPE 363  90
  RPTN MUTATED RPTN WILD-TYPE 
            18            453 
  RPTN MUTATED RPTN WILD-TYPE 
             3             90 
$`RPTN MUTATED`
TCGA-AA-3663 TCGA-AA-3713 TCGA-AZ-6601 TCGA-CA-6716 TCGA-CA-6717 TCGA-CM-5344 
        6.97        19.04       100.01        12.20        12.76        22.03 
TCGA-CM-6166 TCGA-CM-6171 TCGA-CM-6679 TCGA-D5-6932 TCGA-F4-6704 TCGA-G4-6323 
       21.99        14.04        10.06        11.38         1.55        13.78 
TCGA-G4-6628 TCGA-AG-3732 TCGA-AH-6549 TCGA-DC-5869 TCGA-DY-A1DF TCGA-F5-6464 
       79.69        32.98        17.49         5.03        24.13         9.96 

$`RPTN WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.05        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
       12.10        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6718 
       12.69         3.06         3.25         3.29         0.07        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 
       16.04        14.99        12.99        13.02        15.02        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6680 
       12.95        13.05        11.08        11.08        11.01        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        4.80         1.51        12.00        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 
       22.09        35.80        26.17        91.79        46.75        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 
       19.99         7.99         0.99        37.02         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 
       38.04       117.11        38.56         1.45         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
       15.02        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
       18.28        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  RPTN MUTATED RPTN WILD-TYPE 
          1.55           0.00 
  RPTN MUTATED RPTN WILD-TYPE 
        100.01         148.01 
  RPTN MUTATED RPTN WILD-TYPE 
         13.91          20.91 
[1] "1.6 - 100.0 (13.9)" "0.0 - 148.0 (20.9)"
[1] "hr=" "1.1"
D28V2, continuous
D28V3, binary
                cls
clus               0   1
  RPTN MUTATED    13   5
  RPTN WILD-TYPE 353 114
[1] "tbl2"
                cls
clus             [,1] [,2]
  RPTN MUTATED     13    5
  RPTN WILD-TYPE  353  114
        clus
vv       RPTN MUTATED RPTN WILD-TYPE
  COLON            13            353
  RECTUM            5            114
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RPTN MUTATED         4        1        2         4         0         0
  RPTN WILD-TYPE      87        0       30       134        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RPTN MUTATED           0          0          2          3        1         0
  RPTN WILD-TYPE        24         11         57         39       47        18
                vv
clus             STAGE IVB
  RPTN MUTATED           0
  RPTN WILD-TYPE         1
D28V4, multiclass
            clus
vv           RPTN MUTATED RPTN WILD-TYPE
  STAGE I               4             87
  STAGE IA              1              0
  STAGE II              2             30
  STAGE IIA             4            134
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            2             57
  STAGE IIIC            3             39
  STAGE IV              1             47
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  RPTN MUTATED     0   4  12   1
  RPTN WILD-TYPE  17  88 317  49
D28V5, multiclass
    clus
vv   RPTN MUTATED RPTN WILD-TYPE
  T1            0             17
  T2            4             88
  T3           12            317
  T4            1             49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  RPTN MUTATED    12   2   3
  RPTN WILD-TYPE 275 111  84
D28V6, multiclass
    clus
vv   RPTN MUTATED RPTN WILD-TYPE
  N0           12            275
  N1            2            111
  N2            3             84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V7, binary
                cls
clus               0   1
  RPTN MUTATED    14   1
  RPTN WILD-TYPE 361  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  RPTN MUTATED     14    1
  RPTN WILD-TYPE  361   64
   clus
vv  RPTN MUTATED RPTN WILD-TYPE
  0           14            361
  1            1             64
[1] 2 2
[1] FALSE
D28V8, binary
                cls
clus               0   1
  RPTN MUTATED     7  11
  RPTN WILD-TYPE 218 253
[1] "tbl2"
                cls
clus             [,1] [,2]
  RPTN MUTATED      7   11
  RPTN WILD-TYPE  218  253
        clus
vv       RPTN MUTATED RPTN WILD-TYPE
  FEMALE            7            218
  MALE             11            253
[1] 2 2
[1] FALSE
D28V9, binary
                cls
clus               0   1
  RPTN MUTATED    14   1
  RPTN WILD-TYPE 336  21
[1] "tbl2"
                cls
clus             [,1] [,2]
  RPTN MUTATED     14    1
  RPTN WILD-TYPE  336   21
     clus
vv    RPTN MUTATED RPTN WILD-TYPE
  NO            14            336
  YES            1             21
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  RPTN MUTATED                     11                             2
  RPTN WILD-TYPE                  304                            45
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  RPTN MUTATED                       5                              0
  RPTN WILD-TYPE                   101                             10
D28V10, multiclass
                                clus
vv                               RPTN MUTATED RPTN WILD-TYPE
  COLON ADENOCARCINOMA                     11            304
  COLON MUCINOUS ADENOCARCINOMA             2             45
  RECTAL ADENOCARCINOMA                     5            101
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  RPTN MUTATED    12   0   1   3
  RPTN WILD-TYPE 333   4  30  22
D28V11, multiclass
    clus
vv   RPTN MUTATED RPTN WILD-TYPE
  R0           12            333
  R1            0              4
  R2            1             30
  RX            3             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RPTN MUTATED                                  1     2
  RPTN WILD-TYPE                                0     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  RPTN MUTATED                           2    10
  RPTN WILD-TYPE                        20   216
D28V13, multiclass
                                  clus
vv                                 RPTN MUTATED RPTN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            1              0
  ASIAN                                       2              9
  BLACK OR AFRICAN AMERICAN                   2             20
  WHITE                                      10            216
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(29) Variable = THOC7 MUTATION ANALYSIS
D29V1, survival
                 sevent
clus2               0   1
  THOC7 MUTATED     8   3
  THOC7 WILD-TYPE 370  90
  THOC7 MUTATED THOC7 WILD-TYPE 
             11             460 
  THOC7 MUTATED THOC7 WILD-TYPE 
              3              90 
$`THOC7 MUTATED`
TCGA-A6-6654 TCGA-AA-A01Q TCGA-AY-5543 TCGA-AZ-6605 TCGA-CM-4746 TCGA-CM-5864 
       23.87         1.02        33.01         5.23        37.02        15.02 
TCGA-D5-6534 TCGA-D5-6538 TCGA-F4-6808 TCGA-F4-6809 TCGA-F5-6464 
       43.27        17.13        33.67        13.25         9.96 

$`THOC7 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01R TCGA-AA-A01S 
       12.00        31.00        31.00        38.07        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
      100.01        29.56        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
      124.27        23.05        20.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6535 
       56.09        55.92        20.19        18.25         1.32        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
       17.85         4.80        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       20.91        18.28        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  THOC7 MUTATED THOC7 WILD-TYPE 
           1.02            0.00 
  THOC7 MUTATED THOC7 WILD-TYPE 
          43.27          148.01 
  THOC7 MUTATED THOC7 WILD-TYPE 
         17.130          20.235 
[1] "1.0 - 43.3 (17.1)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.8"
D29V2, continuous
D29V3, binary
                 cls
clus                0   1
  THOC7 MUTATED    10   1
  THOC7 WILD-TYPE 356 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  THOC7 MUTATED     10    1
  THOC7 WILD-TYPE  356  118
        clus
vv       THOC7 MUTATED THOC7 WILD-TYPE
  COLON             10             356
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  THOC7 MUTATED         3        0        1         1         0         0
  THOC7 WILD-TYPE      88        1       31       137        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  THOC7 MUTATED           0          0          3          1        0         2
  THOC7 WILD-TYPE        24         11         56         41       48        16
                 vv
clus              STAGE IVB
  THOC7 MUTATED           0
  THOC7 WILD-TYPE         1
D29V4, multiclass
            clus
vv           THOC7 MUTATED THOC7 WILD-TYPE
  STAGE I                3              88
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              1             137
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             3              56
  STAGE IIIC             1              41
  STAGE IV               0              48
  STAGE IVA              2              16
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  THOC7 MUTATED     1   2   6   2
  THOC7 WILD-TYPE  16  90 323  48
D29V5, multiclass
    clus
vv   THOC7 MUTATED THOC7 WILD-TYPE
  T1             1              16
  T2             2              90
  T3             6             323
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  THOC7 MUTATED     5   4   2
  THOC7 WILD-TYPE 282 109  85
D29V6, multiclass
    clus
vv   THOC7 MUTATED THOC7 WILD-TYPE
  N0             5             282
  N1             4             109
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V7, binary
                 cls
clus                0   1
  THOC7 MUTATED     9   2
  THOC7 WILD-TYPE 366  63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  THOC7 MUTATED      9    2
  THOC7 WILD-TYPE  366   63
   clus
vv  THOC7 MUTATED THOC7 WILD-TYPE
  0             9             366
  1             2              63
[1] 2 2
[1] FALSE
D29V8, binary
                 cls
clus                0   1
  THOC7 MUTATED     8   3
  THOC7 WILD-TYPE 217 261
[1] "tbl2"
                 cls
clus              [,1] [,2]
  THOC7 MUTATED      8    3
  THOC7 WILD-TYPE  217  261
        clus
vv       THOC7 MUTATED THOC7 WILD-TYPE
  FEMALE             8             217
  MALE               3             261
[1] 2 2
[1] FALSE
D29V9, binary
                 cls
clus                0   1
  THOC7 MUTATED    10   0
  THOC7 WILD-TYPE 340  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  THOC7 MUTATED     10    0
  THOC7 WILD-TYPE  340   22
     clus
vv    THOC7 MUTATED THOC7 WILD-TYPE
  NO             10             340
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  THOC7 MUTATED                      9                             1
  THOC7 WILD-TYPE                  306                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  THOC7 MUTATED                       1                              0
  THOC7 WILD-TYPE                   105                             10
D29V10, multiclass
                                clus
vv                               THOC7 MUTATED THOC7 WILD-TYPE
  COLON ADENOCARCINOMA                       9             306
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  THOC7 MUTATED     9   0   0   0
  THOC7 WILD-TYPE 336   4  31  25
D29V11, multiclass
    clus
vv   THOC7 MUTATED THOC7 WILD-TYPE
  R0             9             336
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  THOC7 MUTATED                                  0     0
  THOC7 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  THOC7 MUTATED                           2     8
  THOC7 WILD-TYPE                        20   218
D29V13, multiclass
                                  clus
vv                                 THOC7 MUTATED THOC7 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    2              20
  WHITE                                        8             218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(30) Variable = NF1 MUTATION ANALYSIS
D30V1, survival
               sevent
clus2             0   1
  NF1 MUTATED    85  21
  NF1 WILD-TYPE 293  72
  NF1 MUTATED NF1 WILD-TYPE 
          106           365 
  NF1 MUTATED NF1 WILD-TYPE 
           21            72 
$`NF1 MUTATED`
TCGA-A6-2671 TCGA-A6-3809 TCGA-A6-5657 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5665 
       43.76        32.75        31.63        33.53        23.61        22.06 
TCGA-A6-5666 TCGA-A6-6142 TCGA-A6-6652 TCGA-A6-6781 TCGA-AA-3496 TCGA-AA-3555 
       32.71        25.08        24.69        19.66         1.02        29.95 
TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3950 TCGA-AA-3956 
       61.02         6.05        85.05        19.04        24.00        34.03 
TCGA-AA-A00N TCGA-AA-A010 TCGA-AD-6890 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        4.01        34.98         0.79         0.20        14.50        27.09 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4616 TCGA-AZ-5407 
       33.01        21.44        17.82        58.39         5.13        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6607 
       49.41         6.77        12.10       100.01         5.23         3.19 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4952 
        3.06         3.25         0.07        12.76        14.30        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-5348 TCGA-CM-5349 
       49.08        51.32       124.27        23.05        22.98        30.08 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6167 TCGA-CM-6171 
       15.02         5.03         2.96        29.03        14.99        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-D5-5539 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       11.01        12.95        19.59        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A0XD 
       17.13        12.49        16.14         4.80        11.38        24.43 
TCGA-DM-A1D0 TCGA-DM-A1D7 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A285 
      130.65        13.32         7.50        44.32       135.65         6.12 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6570 TCGA-F4-6704 
      117.07        98.24         8.61        31.96         6.18         1.55 
TCGA-F4-6807 TCGA-G4-6293 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6317 TCGA-G4-6321 
       16.24       133.18        44.68        55.04        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-AF-2693 TCGA-AF-6655 
       13.78        35.80        91.79        79.69        19.10        20.02 
TCGA-AG-3892 TCGA-AG-A002 TCGA-AG-A015 TCGA-AH-6643 TCGA-CI-6622 TCGA-CI-6624 
       13.02        20.98        36.03         0.69         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-6155 TCGA-DC-6683 TCGA-DY-A1DG TCGA-EF-5830 
       78.12         7.17        13.97         5.03        51.48         0.49 
TCGA-EI-6506 TCGA-EI-6510 TCGA-F5-6813 TCGA-G5-6235 
       20.55        18.28         0.69        55.76 

$`NF1 WILD-TYPE`
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       46.65        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5659 
       34.65        33.34        36.53        14.53        32.91        30.44 
TCGA-A6-5660 TCGA-A6-5664 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6648 
       29.19        22.09        27.09        22.52         8.38        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 
       24.16        21.76        24.39        23.87        20.12        20.28 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
        7.04         3.02        35.01        63.98         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
       13.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       36.03         8.05        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 
       33.99        21.01        13.02        24.00        17.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3663 
       20.98        19.99        13.94        19.99        78.08         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
        5.03        26.99        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01         2.01        20.98         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
       56.55         0.72         5.79        22.42        27.42        10.88 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AZ-4323 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       16.31         0.95         1.41       106.75        22.36        62.79 
TCGA-AZ-6603 TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5797 TCGA-CA-6716 
       29.56        11.74         1.61        12.69         3.29        12.20 
TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5914 TCGA-CK-5916 
       10.06        17.56       148.01        85.45         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
       82.95         1.91        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5860 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       29.06        22.03        32.02        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6168 TCGA-CM-6169 
       15.02        12.00        16.04        21.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       15.02        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       12.03        45.40        12.26        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       18.25         1.32        43.27        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XF TCGA-DM-A1D4 
        1.51        12.00        10.26       119.70        38.20        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A28C 
       49.91        12.59       140.38       131.51       139.17        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6805 
      119.93        35.97        60.79        35.74        47.87        34.42 
TCGA-F4-6806 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       41.42        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       74.56        65.85        53.62        85.48        63.62        61.91 
TCGA-G4-6588 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       26.17        46.75        24.13        39.48        43.04        13.55 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6672 
       34.49        10.39        14.50        16.83        15.39        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       36.95        17.03        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       15.95         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6644 TCGA-CI-6619 
      117.11        38.56         1.45        17.49         0.72         6.05 
TCGA-CI-6620 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       33.17        15.02         5.03        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        5.95         4.01         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EI-6507 TCGA-EI-6508 TCGA-F5-6464 TCGA-F5-6465 
       24.13        32.61        19.96        20.91         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-G5-6641 
       31.30        28.57        32.19         0.66        26.43 

  NF1 MUTATED NF1 WILD-TYPE 
         0.07          0.00 
  NF1 MUTATED NF1 WILD-TYPE 
       135.65        148.01 
  NF1 MUTATED NF1 WILD-TYPE 
       19.345        20.980 
[1] "0.1 - 135.7 (19.3)" "0.0 - 148.0 (21.0)"
[1] "hr=" "1.1"
D30V2, continuous
D30V3, binary
               cls
clus              0   1
  NF1 MUTATED    89  17
  NF1 WILD-TYPE 277 102
[1] "tbl2"
               cls
clus            [,1] [,2]
  NF1 MUTATED     89   17
  NF1 WILD-TYPE  277  102
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  COLON           89           277
  RECTUM          17           102
[1] 2 2
[1] FALSE
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NF1 MUTATED        14        1        4        32         5         1
  NF1 WILD-TYPE      77        0       28       106         5         0
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NF1 MUTATED           3          4         15         11        8         7
  NF1 WILD-TYPE        21          7         44         31       40        11
               vv
clus            STAGE IVB
  NF1 MUTATED           0
  NF1 WILD-TYPE         1
D30V4, multiclass
            clus
vv           NF1 MUTATED NF1 WILD-TYPE
  STAGE I             14            77
  STAGE IA             1             0
  STAGE II             4            28
  STAGE IIA           32           106
  STAGE IIB            5             5
  STAGE IIC            1             0
  STAGE III            3            21
  STAGE IIIA           4             7
  STAGE IIIB          15            44
  STAGE IIIC          11            31
  STAGE IV             8            40
  STAGE IVA            7            11
  STAGE IVB            0             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  NF1 MUTATED     5  15  72  14
  NF1 WILD-TYPE  12  77 257  36
D30V5, multiclass
    clus
vv   NF1 MUTATED NF1 WILD-TYPE
  T1           5            12
  T2          15            77
  T3          72           257
  T4          14            36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2
  NF1 MUTATED    63  25  19
  NF1 WILD-TYPE 224  88  68
D30V6, multiclass
    clus
vv   NF1 MUTATED NF1 WILD-TYPE
  N0          63           224
  N1          25            88
  N2          19            68
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V7, binary
               cls
clus              0   1
  NF1 MUTATED    73  14
  NF1 WILD-TYPE 302  51
[1] "tbl2"
               cls
clus            [,1] [,2]
  NF1 MUTATED     73   14
  NF1 WILD-TYPE  302   51
   clus
vv  NF1 MUTATED NF1 WILD-TYPE
  0          73           302
  1          14            51
[1] 2 2
[1] FALSE
D30V8, binary
               cls
clus              0   1
  NF1 MUTATED    52  55
  NF1 WILD-TYPE 173 209
[1] "tbl2"
               cls
clus            [,1] [,2]
  NF1 MUTATED     52   55
  NF1 WILD-TYPE  173  209
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  FEMALE          52           173
  MALE            55           209
[1] 2 2
[1] FALSE
D30V9, binary
               cls
clus              0   1
  NF1 MUTATED    78   2
  NF1 WILD-TYPE 272  20
[1] "tbl2"
               cls
clus            [,1] [,2]
  NF1 MUTATED     78    2
  NF1 WILD-TYPE  272   20
     clus
vv    NF1 MUTATED NF1 WILD-TYPE
  NO           78           272
  YES           2            20
[1] 2 2
[1] FALSE
               vv
clus            COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  NF1 MUTATED                     73                            14
  NF1 WILD-TYPE                  242                            33
               vv
clus            RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  NF1 MUTATED                      17                              0
  NF1 WILD-TYPE                    89                             10
D30V10, multiclass
                                clus
vv                               NF1 MUTATED NF1 WILD-TYPE
  COLON ADENOCARCINOMA                    73           242
  COLON MUCINOUS ADENOCARCINOMA           14            33
  RECTAL ADENOCARCINOMA                   17            89
  RECTAL MUCINOUS ADENOCARCINOMA           0            10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             R0  R1  R2  RX
  NF1 MUTATED    66   1   2  11
  NF1 WILD-TYPE 279   3  29  14
D30V11, multiclass
    clus
vv   NF1 MUTATED NF1 WILD-TYPE
  R0          66           279
  R1           1             3
  R2           2            29
  RX          11            14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V12, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NF1 MUTATED                                  1     5
  NF1 WILD-TYPE                                0     6
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  NF1 MUTATED                           8    79
  NF1 WILD-TYPE                        14   147
D30V13, multiclass
                                  clus
vv                                 NF1 MUTATED NF1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           1             0
  ASIAN                                      5             6
  BLACK OR AFRICAN AMERICAN                  8            14
  WHITE                                     79           147
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(31) Variable = FBXW7 MUTATION ANALYSIS
D31V1, survival
                 sevent
clus2               0   1
  FBXW7 MUTATED   101  27
  FBXW7 WILD-TYPE 277  66
  FBXW7 MUTATED FBXW7 WILD-TYPE 
            128             343 
  FBXW7 MUTATED FBXW7 WILD-TYPE 
             27              66 
$`FBXW7 MUTATED`
TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-5656 
       46.65        42.90        24.33        34.65        32.75        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-6137 TCGA-A6-6142 TCGA-A6-6651 
       31.63        30.44        33.53        27.09        25.08        21.76 
TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3524 TCGA-AA-3543 TCGA-AA-3560 TCGA-AA-3655 
       13.02         1.02        36.03         0.99        19.99        61.02 
TCGA-AA-3672 TCGA-AA-3681 TCGA-AA-3713 TCGA-AA-3815 TCGA-AA-3831 TCGA-AA-3833 
        0.92         5.98        19.04        33.04        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3845 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3949 
       38.99         0.00        10.06         0.00         0.00        26.01 
TCGA-AA-3982 TCGA-AA-A01K TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01Z TCGA-AA-A024 
       27.02        31.00         1.02        35.01        37.02        39.06 
TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6889 TCGA-AD-6899 TCGA-AD-6964 
       18.05         0.07        21.37        56.55         5.79        10.88 
TCGA-AU-6004 TCGA-AY-6386 TCGA-AZ-4681 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
       27.09        17.82       106.75        62.79        88.21        49.41 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4948 TCGA-CK-4950 
      100.01         1.61        12.76        10.06       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-6747 TCGA-CK-6748 TCGA-CM-4744 
       15.62        49.08        51.32        82.95         1.91        20.02 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5864 
       22.03        22.98        30.08        15.02         5.03        15.02 
TCGA-CM-6171 TCGA-CM-6676 TCGA-CM-6677 TCGA-D5-6532 TCGA-D5-6541 TCGA-D5-6898 
       14.04        11.08        11.08        18.25        15.58         1.48 
TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
       14.30         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-7000 TCGA-DM-A0XD TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-DM-A1DA TCGA-DM-A1DB 
       10.26        24.43       130.65        49.91         7.50        44.32 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A28G TCGA-DM-A28H TCGA-F4-6703 TCGA-F4-6704 
      135.65       139.17        60.79       117.07        47.87         1.55 
TCGA-G4-6293 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
      133.18        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6588 TCGA-AF-2687 TCGA-AF-5654 
       61.91        36.00        22.09        26.17        24.13        16.83 
TCGA-AF-6655 TCGA-AG-3594 TCGA-AG-3600 TCGA-AG-3608 TCGA-AG-3731 TCGA-AG-3742 
       20.02         2.01         6.05        15.95        37.02         0.99 
TCGA-AG-3881 TCGA-AG-3885 TCGA-AG-3892 TCGA-AG-3898 TCGA-AG-A002 TCGA-AG-A011 
       19.04        17.95        13.02        48.03        20.98        37.02 
TCGA-AG-A02N TCGA-CI-6619 TCGA-CI-6620 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
       61.97         6.05        33.17         7.17        15.02         5.03 
TCGA-DC-6158 TCGA-DC-6682 TCGA-DY-A0XA TCGA-EF-5830 TCGA-EI-6507 TCGA-F5-6465 
       10.98         4.01       126.44         0.49        19.96        49.51 
TCGA-F5-6813 TCGA-G5-6235 
        0.69        55.76 

$`FBXW7 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3808 TCGA-A6-3810 
       43.76        43.76        42.28        16.57        33.34        36.53 
TCGA-A6-4105 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 
       14.53        29.19        23.61        22.09        22.06        32.71 
TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6652 TCGA-A6-6653 
       22.52         8.38        25.18        24.16        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        1.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
        9.07        24.03        37.05         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3660 
       29.95        23.01        20.98        13.94        19.99        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
        6.05         6.97        54.02         2.01        14.01        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       47.01        15.02        11.01        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 
        0.99        25.02         1.02        37.02        14.93        17.03 
TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
       33.07        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       24.00        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       12.00        31.00        38.07         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       26.01        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03J TCGA-AD-6888 TCGA-AD-6890 
        0.92        41.00        39.98        40.96        15.52         0.79 
TCGA-AD-6895 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 
        0.72        22.42        27.42         0.20        14.50        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        33.01        21.44        58.39         1.41         5.13 
TCGA-AZ-4682 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       22.36         6.77        12.10        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        3.19        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6751 
       12.20        14.30        17.56         9.99        21.14       124.27 
TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5860 
       23.05        37.02        25.02        13.02        29.06        32.02 
TCGA-CM-5863 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       11.01        12.95        13.05        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 
       12.49        16.14         3.68         4.41        12.43         9.04 
TCGA-D5-6932 TCGA-DM-A0X9 TCGA-DM-A0XF TCGA-DM-A1D4 TCGA-DM-A1D7 TCGA-DM-A1D8 
       11.38       119.70        38.20        92.75        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1HA TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      140.38       131.51         6.12        81.37       119.93        35.97 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6805 
       98.24         8.61        31.96        35.74         6.18        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6310 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 
       35.31        74.56        63.62        13.78        35.80        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       46.75        79.69        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6672 TCGA-AG-3574 
       34.49        10.39        14.50        15.39        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3598 TCGA-AG-3599 
       24.00         1.02        46.03        34.03        50.04        12.03 
TCGA-AG-3605 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
        0.99        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3732 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 
       32.98         0.99        19.99         1.02        36.95        17.03 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       35.01        14.01         1.02        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       25.97        23.01        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-DC-6155 
        0.69         0.72         6.97         4.73        78.12        13.97 
TCGA-DC-6157 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC 
       27.95        19.99         5.95         5.03         5.29        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EI-6506 TCGA-EI-6508 
       57.24        24.13        51.48        32.61        20.55        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
       18.28         9.96        31.30        28.57        32.19         0.66 
TCGA-G5-6641 
       26.43 

  FBXW7 MUTATED FBXW7 WILD-TYPE 
              0               0 
  FBXW7 MUTATED FBXW7 WILD-TYPE 
         148.01          140.38 
  FBXW7 MUTATED FBXW7 WILD-TYPE 
         21.895          19.990 
[1] "0.0 - 148.0 (21.9)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1.2"
D31V2, continuous
D31V3, binary
                 cls
clus                0   1
  FBXW7 MUTATED   103  28
  FBXW7 WILD-TYPE 263  91
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FBXW7 MUTATED    103   28
  FBXW7 WILD-TYPE  263   91
        clus
vv       FBXW7 MUTATED FBXW7 WILD-TYPE
  COLON            103             263
  RECTUM            28              91
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FBXW7 MUTATED        21        0       10        43         5         0
  FBXW7 WILD-TYPE      70        1       22        95         5         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  FBXW7 MUTATED           8          2         16         15        7         3
  FBXW7 WILD-TYPE        16          9         43         27       41        15
                 vv
clus              STAGE IVB
  FBXW7 MUTATED           0
  FBXW7 WILD-TYPE         1
D31V4, multiclass
            clus
vv           FBXW7 MUTATED FBXW7 WILD-TYPE
  STAGE I               21              70
  STAGE IA               0               1
  STAGE II              10              22
  STAGE IIA             43              95
  STAGE IIB              5               5
  STAGE IIC              0               1
  STAGE III              8              16
  STAGE IIIA             2               9
  STAGE IIIB            16              43
  STAGE IIIC            15              27
  STAGE IV               7              41
  STAGE IVA              3              15
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  FBXW7 MUTATED     4  21  95  11
  FBXW7 WILD-TYPE  13  71 234  39
D31V5, multiclass
    clus
vv   FBXW7 MUTATED FBXW7 WILD-TYPE
  T1             4              13
  T2            21              71
  T3            95             234
  T4            11              39
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  FBXW7 MUTATED    80  32  19
  FBXW7 WILD-TYPE 207  81  68
D31V6, multiclass
    clus
vv   FBXW7 MUTATED FBXW7 WILD-TYPE
  N0            80             207
  N1            32              81
  N2            19              68
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V7, binary
                 cls
clus                0   1
  FBXW7 MUTATED   106  10
  FBXW7 WILD-TYPE 269  55
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FBXW7 MUTATED    106   10
  FBXW7 WILD-TYPE  269   55
   clus
vv  FBXW7 MUTATED FBXW7 WILD-TYPE
  0           106             269
  1            10              55
[1] 2 2
[1] FALSE
D31V8, binary
                 cls
clus                0   1
  FBXW7 MUTATED    67  64
  FBXW7 WILD-TYPE 158 200
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FBXW7 MUTATED     67   64
  FBXW7 WILD-TYPE  158  200
        clus
vv       FBXW7 MUTATED FBXW7 WILD-TYPE
  FEMALE            67             158
  MALE              64             200
[1] 2 2
[1] FALSE
D31V9, binary
                 cls
clus                0   1
  FBXW7 MUTATED    92   5
  FBXW7 WILD-TYPE 258  17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FBXW7 MUTATED     92    5
  FBXW7 WILD-TYPE  258   17
     clus
vv    FBXW7 MUTATED FBXW7 WILD-TYPE
  NO             92             258
  YES             5              17
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  FBXW7 MUTATED                     83                            19
  FBXW7 WILD-TYPE                  232                            28
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  FBXW7 MUTATED                      26                              1
  FBXW7 WILD-TYPE                    80                              9
D31V10, multiclass
                                clus
vv                               FBXW7 MUTATED FBXW7 WILD-TYPE
  COLON ADENOCARCINOMA                      83             232
  COLON MUCINOUS ADENOCARCINOMA             19              28
  RECTAL ADENOCARCINOMA                     26              80
  RECTAL MUCINOUS ADENOCARCINOMA             1               9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  FBXW7 MUTATED    91   2   2   9
  FBXW7 WILD-TYPE 254   2  29  16
D31V11, multiclass
    clus
vv   FBXW7 MUTATED FBXW7 WILD-TYPE
  R0            91             254
  R1             2               2
  R2             2              29
  RX             9              16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FBXW7 MUTATED                                  1     3
  FBXW7 WILD-TYPE                                0     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  FBXW7 MUTATED                           6    82
  FBXW7 WILD-TYPE                        16   144
D31V13, multiclass
                                  clus
vv                                 FBXW7 MUTATED FBXW7 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             1               0
  ASIAN                                        3               8
  BLACK OR AFRICAN AMERICAN                    6              16
  WHITE                                       82             144
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(32) Variable = CHUK MUTATION ANALYSIS
D32V1, survival
                sevent
clus2              0   1
  CHUK MUTATED    18   6
  CHUK WILD-TYPE 360  87
  CHUK MUTATED CHUK WILD-TYPE 
            24            447 
  CHUK MUTATED CHUK WILD-TYPE 
             6             87 
$`CHUK MUTATED`
TCGA-A6-5659 TCGA-AA-3510 TCGA-AA-3555 TCGA-AA-3662 TCGA-AA-A00A TCGA-AA-A010 
       30.44        63.98        29.95         6.05        38.04        34.98 
TCGA-AA-A02K TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6607 TCGA-CA-6718 
       14.01        88.21        49.41         6.77         3.19        10.06 
TCGA-CA-6719 TCGA-CM-4743 TCGA-CM-5349 TCGA-CM-6161 TCGA-CM-6677 TCGA-D5-6534 
       14.30        23.05        30.08        15.02        11.08        43.27 
TCGA-DM-A1D8 TCGA-F4-6856 TCGA-G4-6304 TCGA-AG-A002 TCGA-CI-6624 TCGA-DC-6681 
       12.59        35.31        53.62        20.98         4.73         5.95 

$`CHUK WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       24.00        17.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02        78.08         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
        7.96        27.02        13.94        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O 
       39.06        51.98        39.98         2.01         5.03         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6600 TCGA-AZ-6601 
        5.13       106.75        22.36        62.79        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CK-4947 
        3.25         3.29         0.07        12.20        12.76        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 
       21.14        82.95         1.91       124.27        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5860 
       25.02        13.02        29.06        22.03        22.98        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6162 
       15.02         5.03        15.02        15.02        17.03        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       92.75        49.91        13.32       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 
       16.24        33.67        13.25         0.53        47.41       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       74.56        65.85        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
       33.17         6.97        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6682 TCGA-DC-6683 
       13.97        27.95        10.98        19.99         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  CHUK MUTATED CHUK WILD-TYPE 
          3.19           0.00 
  CHUK MUTATED CHUK WILD-TYPE 
         88.21         148.01 
  CHUK MUTATED CHUK WILD-TYPE 
        22.015         20.120 
[1] "3.2 - 88.2 (22.0)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.2"
D32V2, continuous
D32V3, binary
                cls
clus               0   1
  CHUK MUTATED    21   3
  CHUK WILD-TYPE 345 116
[1] "tbl2"
                cls
clus             [,1] [,2]
  CHUK MUTATED     21    3
  CHUK WILD-TYPE  345  116
        clus
vv       CHUK MUTATED CHUK WILD-TYPE
  COLON            21            345
  RECTUM            3            116
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CHUK MUTATED         7        0        2         8         2         0
  CHUK WILD-TYPE      84        1       30       130         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CHUK MUTATED           0          0          0          0        3         1
  CHUK WILD-TYPE        24         11         59         42       45        17
                vv
clus             STAGE IVB
  CHUK MUTATED           0
  CHUK WILD-TYPE         1
D32V4, multiclass
            clus
vv           CHUK MUTATED CHUK WILD-TYPE
  STAGE I               7             84
  STAGE IA              0              1
  STAGE II              2             30
  STAGE IIA             8            130
  STAGE IIB             2              8
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            0             59
  STAGE IIIC            0             42
  STAGE IV              3             45
  STAGE IVA             1             17
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  CHUK MUTATED     1   6  12   5
  CHUK WILD-TYPE  16  86 317  45
D32V5, multiclass
    clus
vv   CHUK MUTATED CHUK WILD-TYPE
  T1            1             16
  T2            6             86
  T3           12            317
  T4            5             45
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  CHUK MUTATED    19   1   4
  CHUK WILD-TYPE 268 112  83
D32V6, multiclass
    clus
vv   CHUK MUTATED CHUK WILD-TYPE
  N0           19            268
  N1            1            112
  N2            4             83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V7, binary
                cls
clus               0   1
  CHUK MUTATED    17   4
  CHUK WILD-TYPE 358  61
[1] "tbl2"
                cls
clus             [,1] [,2]
  CHUK MUTATED     17    4
  CHUK WILD-TYPE  358   61
   clus
vv  CHUK MUTATED CHUK WILD-TYPE
  0           17            358
  1            4             61
[1] 2 2
[1] FALSE
D32V8, binary
                cls
clus               0   1
  CHUK MUTATED    13  11
  CHUK WILD-TYPE 212 253
[1] "tbl2"
                cls
clus             [,1] [,2]
  CHUK MUTATED     13   11
  CHUK WILD-TYPE  212  253
        clus
vv       CHUK MUTATED CHUK WILD-TYPE
  FEMALE           13            212
  MALE             11            253
[1] 2 2
[1] FALSE
D32V9, binary
                cls
clus               0   1
  CHUK MUTATED    21   0
  CHUK WILD-TYPE 329  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  CHUK MUTATED     21    0
  CHUK WILD-TYPE  329   22
     clus
vv    CHUK MUTATED CHUK WILD-TYPE
  NO            21            329
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CHUK MUTATED                     18                             3
  CHUK WILD-TYPE                  297                            44
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CHUK MUTATED                       3                              0
  CHUK WILD-TYPE                   103                             10
D32V10, multiclass
                                clus
vv                               CHUK MUTATED CHUK WILD-TYPE
  COLON ADENOCARCINOMA                     18            297
  COLON MUCINOUS ADENOCARCINOMA             3             44
  RECTAL ADENOCARCINOMA                     3            103
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  CHUK MUTATED    14   0   2   2
  CHUK WILD-TYPE 331   4  29  23
D32V11, multiclass
    clus
vv   CHUK MUTATED CHUK WILD-TYPE
  R0           14            331
  R1            0              4
  R2            2             29
  RX            2             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CHUK MUTATED                                  0     2
  CHUK WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  CHUK MUTATED                           0    15
  CHUK WILD-TYPE                        22   211
D32V13, multiclass
                                  clus
vv                                 CHUK MUTATED CHUK WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              9
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                      15            211
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(33) Variable = ATXN3L MUTATION ANALYSIS
D33V1, survival
                  sevent
clus2                0   1
  ATXN3L MUTATED    14   4
  ATXN3L WILD-TYPE 364  89
  ATXN3L MUTATED ATXN3L WILD-TYPE 
              18              453 
  ATXN3L MUTATED ATXN3L WILD-TYPE 
               4               89 
$`ATXN3L MUTATED`
TCGA-A6-2671 TCGA-A6-5661 TCGA-A6-5662 TCGA-AA-3713 TCGA-AA-3818 TCGA-AA-3947 
       43.76        33.53        23.61        19.04         0.99        33.01 
TCGA-AA-A00N TCGA-CM-5348 TCGA-CM-5861 TCGA-CM-6166 TCGA-D5-6536 TCGA-D5-6930 
        4.01        22.98        15.02        21.99        17.85         1.51 
TCGA-DM-A1HA TCGA-F4-6809 TCGA-G4-6293 TCGA-G4-6310 TCGA-AG-A002 TCGA-F5-6465 
      131.51        13.25       133.18        63.62        20.98        49.51 

$`ATXN3L WILD-TYPE`
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       46.65        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 
       31.63        30.44        29.19        22.09        22.06        32.71 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       27.09        22.52         8.38        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       85.05        26.99        19.04        10.06        35.05        33.04 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 
       18.05        31.00         2.01        12.99        24.00        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5349 
       37.02        25.02        13.02        29.06        22.03        30.08 
TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       32.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6168 
       12.00         2.96        29.03        16.04        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
        1.32        43.27        15.12         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6931 
       14.30         9.04         9.44        11.64         4.80        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
       44.32       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6299 
       16.24        33.67         0.53        47.41        35.31        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6315 
       65.85        53.62        44.68        55.04        85.48        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
       18.28         9.96        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  ATXN3L MUTATED ATXN3L WILD-TYPE 
            0.99             0.00 
  ATXN3L MUTATED ATXN3L WILD-TYPE 
          133.18           148.01 
  ATXN3L MUTATED ATXN3L WILD-TYPE 
          22.485           20.050 
[1] "1.0 - 133.2 (22.5)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.1"
D33V2, continuous
D33V3, binary
                  cls
clus                 0   1
  ATXN3L MUTATED    17   3
  ATXN3L WILD-TYPE 349 116
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATXN3L MUTATED     17    3
  ATXN3L WILD-TYPE  349  116
        clus
vv       ATXN3L MUTATED ATXN3L WILD-TYPE
  COLON              17              349
  RECTUM              3              116
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ATXN3L MUTATED         2        0        0         7         2         0
  ATXN3L WILD-TYPE      89        1       32       131         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ATXN3L MUTATED           1          0          2          2        2
  ATXN3L WILD-TYPE        23         11         57         40       46
                  vv
clus               STAGE IVA STAGE IVB
  ATXN3L MUTATED           2         0
  ATXN3L WILD-TYPE        16         1
D33V4, multiclass
            clus
vv           ATXN3L MUTATED ATXN3L WILD-TYPE
  STAGE I                 2               89
  STAGE IA                0                1
  STAGE II                0               32
  STAGE IIA               7              131
  STAGE IIB               2                8
  STAGE IIC               0                1
  STAGE III               1               23
  STAGE IIIA              0               11
  STAGE IIIB              2               57
  STAGE IIIC              2               40
  STAGE IV                2               46
  STAGE IVA               2               16
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ATXN3L MUTATED     0   2  16   2
  ATXN3L WILD-TYPE  17  90 313  48
D33V5, multiclass
    clus
vv   ATXN3L MUTATED ATXN3L WILD-TYPE
  T1              0               17
  T2              2               90
  T3             16              313
  T4              2               48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  ATXN3L MUTATED    12   4   4
  ATXN3L WILD-TYPE 275 109  83
D33V6, multiclass
    clus
vv   ATXN3L MUTATED ATXN3L WILD-TYPE
  N0             12              275
  N1              4              109
  N2              4               83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V7, binary
                  cls
clus                 0   1
  ATXN3L MUTATED    15   4
  ATXN3L WILD-TYPE 360  61
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATXN3L MUTATED     15    4
  ATXN3L WILD-TYPE  360   61
   clus
vv  ATXN3L MUTATED ATXN3L WILD-TYPE
  0             15              360
  1              4               61
[1] 2 2
[1] FALSE
D33V8, binary
                  cls
clus                 0   1
  ATXN3L MUTATED     9  11
  ATXN3L WILD-TYPE 216 253
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATXN3L MUTATED      9   11
  ATXN3L WILD-TYPE  216  253
        clus
vv       ATXN3L MUTATED ATXN3L WILD-TYPE
  FEMALE              9              216
  MALE               11              253
[1] 2 2
[1] FALSE
D33V9, binary
                  cls
clus                 0   1
  ATXN3L MUTATED    12   2
  ATXN3L WILD-TYPE 338  20
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATXN3L MUTATED     12    2
  ATXN3L WILD-TYPE  338   20
     clus
vv    ATXN3L MUTATED ATXN3L WILD-TYPE
  NO              12              338
  YES              2               20
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ATXN3L MUTATED                     13                             4
  ATXN3L WILD-TYPE                  302                            43
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ATXN3L MUTATED                       3                              0
  ATXN3L WILD-TYPE                   103                             10
D33V10, multiclass
                                clus
vv                               ATXN3L MUTATED ATXN3L WILD-TYPE
  COLON ADENOCARCINOMA                       13              302
  COLON MUCINOUS ADENOCARCINOMA               4               43
  RECTAL ADENOCARCINOMA                       3              103
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ATXN3L MUTATED    17   0   1   0
  ATXN3L WILD-TYPE 328   4  30  25
D33V11, multiclass
    clus
vv   ATXN3L MUTATED ATXN3L WILD-TYPE
  R0             17              328
  R1              0                4
  R2              1               30
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ATXN3L MUTATED                                  0     0
  ATXN3L WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ATXN3L MUTATED                           1    13
  ATXN3L WILD-TYPE                        21   213
D33V13, multiclass
                                  clus
vv                                 ATXN3L MUTATED ATXN3L WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                        13              213
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(34) Variable = MGA MUTATION ANALYSIS
D34V1, survival
               sevent
clus2             0   1
  MGA MUTATED    34   6
  MGA WILD-TYPE 344  87
  MGA MUTATED MGA WILD-TYPE 
           40           431 
  MGA MUTATED MGA WILD-TYPE 
            6            87 
$`MGA MUTATED`
TCGA-A6-5661 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6141 TCGA-A6-6781 TCGA-AA-3492 
       33.53        22.06        32.71         8.38        19.66         3.02 
TCGA-AA-3510 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3672 TCGA-AA-3715 TCGA-AA-3811 
       63.98        78.08         6.97         0.92        19.04        10.06 
TCGA-AA-3812 TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01R TCGA-AA-A024 TCGA-AD-6895 
       35.05         4.01        34.98        35.01        39.06         0.72 
TCGA-AU-6004 TCGA-AY-6197 TCGA-AZ-5407 TCGA-CA-6717 TCGA-CK-5913 TCGA-CM-5348 
       27.09        21.44        88.21        12.76        51.32        22.98 
TCGA-CM-5861 TCGA-CM-5863 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6920 TCGA-D5-6927 
       15.02        15.02        17.13        16.14         3.68         9.44 
TCGA-D5-6928 TCGA-D5-6930 TCGA-DM-A1DB TCGA-G4-6306 TCGA-AG-3999 TCGA-AG-A002 
       11.64         1.51        44.32        44.68        28.04        20.98 
TCGA-AH-6643 TCGA-DC-6160 TCGA-EI-6507 TCGA-F5-6811 
        0.69        19.99        19.96        32.19 

$`MGA WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 
       27.09        22.52        25.08        25.18        24.16        21.76 
TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 
       24.69        24.39        23.87        20.12        20.28         7.04 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3664 
       19.99        13.94        19.99        61.02         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
        2.01        14.01        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       26.99        19.04        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       31.00        38.07         1.02         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       26.01        37.02        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 
        0.07        21.37        15.52        56.55         0.79         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 
       22.42        27.42        10.88         0.20        14.50        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        33.01        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
      106.75        22.36        62.79        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       49.08         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-5868 
       22.03        30.08        32.02         5.03        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6923 
        4.80        12.49        15.58         1.48         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       14.30         9.04         4.80        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A1HB 
       13.32        12.59       140.38         7.50       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       65.85        53.62        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-4001 
       14.01         1.02        48.03        32.02        19.99        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
       17.49         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       10.98         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       20.55        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57         0.66         0.69        55.76        26.43 

  MGA MUTATED MGA WILD-TYPE 
         0.69          0.00 
  MGA MUTATED MGA WILD-TYPE 
        88.21        148.01 
  MGA MUTATED MGA WILD-TYPE 
       19.975        20.280 
[1] "0.7 - 88.2 (20.0)"  "0.0 - 148.0 (20.3)"
[1] "hr=" "1.2"
D34V2, continuous
D34V3, binary
               cls
clus              0   1
  MGA MUTATED    37   6
  MGA WILD-TYPE 329 113
[1] "tbl2"
               cls
clus            [,1] [,2]
  MGA MUTATED     37    6
  MGA WILD-TYPE  329  113
        clus
vv       MGA MUTATED MGA WILD-TYPE
  COLON           37           329
  RECTUM           6           113
[1] 2 2
[1] FALSE
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MGA MUTATED         5        0        7        17         2         1
  MGA WILD-TYPE      86        1       25       121         8         0
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MGA MUTATED           3          0          3          4        0         0
  MGA WILD-TYPE        21         11         56         38       48        18
               vv
clus            STAGE IVB
  MGA MUTATED           0
  MGA WILD-TYPE         1
D34V4, multiclass
            clus
vv           MGA MUTATED MGA WILD-TYPE
  STAGE I              5            86
  STAGE IA             0             1
  STAGE II             7            25
  STAGE IIA           17           121
  STAGE IIB            2             8
  STAGE IIC            1             0
  STAGE III            3            21
  STAGE IIIA           0            11
  STAGE IIIB           3            56
  STAGE IIIC           4            38
  STAGE IV             0            48
  STAGE IVA            0            18
  STAGE IVB            0             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  MGA MUTATED     1   5  32   5
  MGA WILD-TYPE  16  87 297  45
D34V5, multiclass
    clus
vv   MGA MUTATED MGA WILD-TYPE
  T1           1            16
  T2           5            87
  T3          32           297
  T4           5            45
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2
  MGA MUTATED    32   5   6
  MGA WILD-TYPE 255 108  81
D34V6, multiclass
    clus
vv   MGA MUTATED MGA WILD-TYPE
  N0          32           255
  N1           5           108
  N2           6            81
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V7, binary
               cls
clus              0   1
  MGA MUTATED    38   0
  MGA WILD-TYPE 337  65
[1] "tbl2"
               cls
clus            [,1] [,2]
  MGA MUTATED     38    0
  MGA WILD-TYPE  337   65
   clus
vv  MGA MUTATED MGA WILD-TYPE
  0          38           337
  1           0            65
[1] 2 2
[1] FALSE
D34V8, binary
               cls
clus              0   1
  MGA MUTATED    19  24
  MGA WILD-TYPE 206 240
[1] "tbl2"
               cls
clus            [,1] [,2]
  MGA MUTATED     19   24
  MGA WILD-TYPE  206  240
        clus
vv       MGA MUTATED MGA WILD-TYPE
  FEMALE          19           206
  MALE            24           240
[1] 2 2
[1] FALSE
D34V9, binary
               cls
clus              0   1
  MGA MUTATED    31   1
  MGA WILD-TYPE 319  21
[1] "tbl2"
               cls
clus            [,1] [,2]
  MGA MUTATED     31    1
  MGA WILD-TYPE  319   21
     clus
vv    MGA MUTATED MGA WILD-TYPE
  NO           31           319
  YES           1            21
[1] 2 2
[1] FALSE
               vv
clus            COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MGA MUTATED                     27                            10
  MGA WILD-TYPE                  288                            37
               vv
clus            RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MGA MUTATED                       6                              0
  MGA WILD-TYPE                   100                             10
D34V10, multiclass
                                clus
vv                               MGA MUTATED MGA WILD-TYPE
  COLON ADENOCARCINOMA                    27           288
  COLON MUCINOUS ADENOCARCINOMA           10            37
  RECTAL ADENOCARCINOMA                    6           100
  RECTAL MUCINOUS ADENOCARCINOMA           0            10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             R0  R1  R2  RX
  MGA MUTATED    35   0   0   2
  MGA WILD-TYPE 310   4  31  23
D34V11, multiclass
    clus
vv   MGA MUTATED MGA WILD-TYPE
  R0          35           310
  R1           0             4
  R2           0            31
  RX           2            23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V12, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MGA MUTATED                                  0     1
  MGA WILD-TYPE                                1    10
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  MGA MUTATED                           2    24
  MGA WILD-TYPE                        20   202
D34V13, multiclass
                                  clus
vv                                 MGA MUTATED MGA WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      1            10
  BLACK OR AFRICAN AMERICAN                  2            20
  WHITE                                     24           202
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(35) Variable = TPRKB MUTATION ANALYSIS
D35V1, survival
                 sevent
clus2               0   1
  TPRKB MUTATED     8   2
  TPRKB WILD-TYPE 370  91
  TPRKB MUTATED TPRKB WILD-TYPE 
             10             461 
  TPRKB MUTATED TPRKB WILD-TYPE 
              2              91 
$`TPRKB MUTATED`
TCGA-AZ-6601 TCGA-CA-6717 TCGA-CK-4952 TCGA-CM-5348 TCGA-CM-5861 TCGA-D5-5539 
      100.01        12.76        15.62        22.98        15.02        19.59 
TCGA-D5-6538 TCGA-D5-6928 TCGA-D5-7000 TCGA-DM-A28C 
       17.13        11.64        10.26        81.37 

$`TPRKB WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       49.41         6.77        12.10        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07        12.20        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       85.45        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 
       13.02        29.06        22.03        30.08        32.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       15.12        17.85         4.80        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-DM-A0X9 
        9.44         4.80         1.51        12.00        11.38       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
      139.17         6.12       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  TPRKB MUTATED TPRKB WILD-TYPE 
          10.26            0.00 
  TPRKB MUTATED TPRKB WILD-TYPE 
         100.01          148.01 
  TPRKB MUTATED TPRKB WILD-TYPE 
         16.375          20.550 
[1] "10.3 - 100.0 (16.4)" "0.0 - 148.0 (20.6)" 
[1] "hr=" "1.2"
D35V2, continuous
D35V3, binary
                 cls
clus                0   1
  TPRKB MUTATED    10   0
  TPRKB WILD-TYPE 356 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TPRKB MUTATED     10    0
  TPRKB WILD-TYPE  356  119
        clus
vv       TPRKB MUTATED TPRKB WILD-TYPE
  COLON             10             356
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TPRKB MUTATED         1        0        1         4         0         0
  TPRKB WILD-TYPE      90        1       31       134        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TPRKB MUTATED           0          1          2          1        0         0
  TPRKB WILD-TYPE        24         10         57         41       48        18
                 vv
clus              STAGE IVB
  TPRKB MUTATED           0
  TPRKB WILD-TYPE         1
D35V4, multiclass
            clus
vv           TPRKB MUTATED TPRKB WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              4             134
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             1              10
  STAGE IIIB             2              57
  STAGE IIIC             1              41
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  TPRKB MUTATED     0   1   8   1
  TPRKB WILD-TYPE  17  91 321  49
D35V5, multiclass
    clus
vv   TPRKB MUTATED TPRKB WILD-TYPE
  T1             0              17
  T2             1              91
  T3             8             321
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  TPRKB MUTATED     6   2   2
  TPRKB WILD-TYPE 281 111  85
D35V6, multiclass
    clus
vv   TPRKB MUTATED TPRKB WILD-TYPE
  N0             6             281
  N1             2             111
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V7, binary
                 cls
clus                0   1
  TPRKB MUTATED    10   0
  TPRKB WILD-TYPE 365  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TPRKB MUTATED     10    0
  TPRKB WILD-TYPE  365   65
   clus
vv  TPRKB MUTATED TPRKB WILD-TYPE
  0            10             365
  1             0              65
[1] 2 2
[1] FALSE
D35V8, binary
                 cls
clus                0   1
  TPRKB MUTATED     4   6
  TPRKB WILD-TYPE 221 258
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TPRKB MUTATED      4    6
  TPRKB WILD-TYPE  221  258
        clus
vv       TPRKB MUTATED TPRKB WILD-TYPE
  FEMALE             4             221
  MALE               6             258
[1] 2 2
[1] FALSE
D35V9, binary
                 cls
clus                0   1
  TPRKB MUTATED     8   0
  TPRKB WILD-TYPE 342  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TPRKB MUTATED      8    0
  TPRKB WILD-TYPE  342   22
     clus
vv    TPRKB MUTATED TPRKB WILD-TYPE
  NO              8             342
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  TPRKB MUTATED                      5                             5
  TPRKB WILD-TYPE                  310                            42
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  TPRKB MUTATED                       0                              0
  TPRKB WILD-TYPE                   106                             10
D35V10, multiclass
                                clus
vv                               TPRKB MUTATED TPRKB WILD-TYPE
  COLON ADENOCARCINOMA                       5             310
  COLON MUCINOUS ADENOCARCINOMA              5              42
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  TPRKB MUTATED     6   0   0   2
  TPRKB WILD-TYPE 339   4  31  23
D35V11, multiclass
    clus
vv   TPRKB MUTATED TPRKB WILD-TYPE
  R0             6             339
  R1             0               4
  R2             0              31
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TPRKB MUTATED                                  0     1
  TPRKB WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  TPRKB MUTATED                           0     9
  TPRKB WILD-TYPE                        22   217
D35V13, multiclass
                                  clus
vv                                 TPRKB MUTATED TPRKB WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        9             217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(36) Variable = MVK MUTATION ANALYSIS
D36V1, survival
               sevent
clus2             0   1
  MVK MUTATED    11   1
  MVK WILD-TYPE 367  92
  MVK MUTATED MVK WILD-TYPE 
           12           459 
  MVK MUTATED MVK WILD-TYPE 
            1            92 
$`MVK MUTATED`
TCGA-A6-5665 TCGA-A6-6781 TCGA-AA-3950 TCGA-AD-5900 TCGA-AD-6889 TCGA-CA-6717 
       22.06        19.66        24.00         0.07        56.55        12.76 
TCGA-CK-5916 TCGA-CM-4746 TCGA-CM-6162 TCGA-CM-6674 TCGA-D5-6540 TCGA-G4-6588 
       21.14        37.02        12.00        12.95        16.14        26.17 

$`MVK WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 
       12.99        24.00        33.01        26.01         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 
       18.05        40.96        21.37        15.52         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07        12.20        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
        9.99        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       15.02         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6675 
       12.99        13.02        15.02        14.04        11.01        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       12.49        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       22.09        13.78        35.80        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  MVK MUTATED MVK WILD-TYPE 
         0.07          0.00 
  MVK MUTATED MVK WILD-TYPE 
        56.55        148.01 
  MVK MUTATED MVK WILD-TYPE 
        20.40         20.19 
[1] "0.1 - 56.5 (20.4)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "2"  
D36V2, continuous
D36V3, binary
               cls
clus              0   1
  MVK MUTATED    14   0
  MVK WILD-TYPE 352 119
[1] "tbl2"
               cls
clus            [,1] [,2]
  MVK MUTATED     14    0
  MVK WILD-TYPE  352  119
        clus
vv       MVK MUTATED MVK WILD-TYPE
  COLON           14           352
  RECTUM           0           119
[1] 2 2
[1] FALSE
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MVK MUTATED         4        0        1         6         1         0
  MVK WILD-TYPE      87        1       31       132         9         1
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MVK MUTATED           0          0          1          1        0         0
  MVK WILD-TYPE        24         11         58         41       48        18
               vv
clus            STAGE IVB
  MVK MUTATED           0
  MVK WILD-TYPE         1
D36V4, multiclass
            clus
vv           MVK MUTATED MVK WILD-TYPE
  STAGE I              4            87
  STAGE IA             0             1
  STAGE II             1            31
  STAGE IIA            6           132
  STAGE IIB            1             9
  STAGE IIC            0             1
  STAGE III            0            24
  STAGE IIIA           0            11
  STAGE IIIB           1            58
  STAGE IIIC           1            41
  STAGE IV             0            48
  STAGE IVA            0            18
  STAGE IVB            0             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  MVK MUTATED     1   3   7   3
  MVK WILD-TYPE  16  89 322  47
D36V5, multiclass
    clus
vv   MVK MUTATED MVK WILD-TYPE
  T1           1            16
  T2           3            89
  T3           7           322
  T4           3            47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2
  MVK MUTATED    12   2   0
  MVK WILD-TYPE 275 111  87
D36V6, multiclass
    clus
vv   MVK MUTATED MVK WILD-TYPE
  N0          12           275
  N1           2           111
  N2           0            87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V7, binary
               cls
clus              0   1
  MVK MUTATED    11   0
  MVK WILD-TYPE 364  65
[1] "tbl2"
               cls
clus            [,1] [,2]
  MVK MUTATED     11    0
  MVK WILD-TYPE  364   65
   clus
vv  MVK MUTATED MVK WILD-TYPE
  0          11           364
  1           0            65
[1] 2 2
[1] FALSE
D36V8, binary
               cls
clus              0   1
  MVK MUTATED     7   7
  MVK WILD-TYPE 218 257
[1] "tbl2"
               cls
clus            [,1] [,2]
  MVK MUTATED      7    7
  MVK WILD-TYPE  218  257
        clus
vv       MVK MUTATED MVK WILD-TYPE
  FEMALE           7           218
  MALE             7           257
[1] 2 2
[1] FALSE
D36V9, binary
               cls
clus              0   1
  MVK MUTATED    10   0
  MVK WILD-TYPE 340  22
[1] "tbl2"
               cls
clus            [,1] [,2]
  MVK MUTATED     10    0
  MVK WILD-TYPE  340   22
     clus
vv    MVK MUTATED MVK WILD-TYPE
  NO           10           340
  YES           0            22
[1] 2 2
[1] FALSE
               vv
clus            COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MVK MUTATED                      8                             6
  MVK WILD-TYPE                  307                            41
               vv
clus            RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MVK MUTATED                       0                              0
  MVK WILD-TYPE                   106                             10
D36V10, multiclass
                                clus
vv                               MVK MUTATED MVK WILD-TYPE
  COLON ADENOCARCINOMA                     8           307
  COLON MUCINOUS ADENOCARCINOMA            6            41
  RECTAL ADENOCARCINOMA                    0           106
  RECTAL MUCINOUS ADENOCARCINOMA           0            10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             R0  R1  R2  RX
  MVK MUTATED    10   0   0   3
  MVK WILD-TYPE 335   4  31  22
D36V11, multiclass
    clus
vv   MVK MUTATED MVK WILD-TYPE
  R0          10           335
  R1           0             4
  R2           0            31
  RX           3            22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V12, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MVK MUTATED                                  0     2
  MVK WILD-TYPE                                1     9
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  MVK MUTATED                           1     9
  MVK WILD-TYPE                        21   217
D36V13, multiclass
                                  clus
vv                                 MVK MUTATED MVK WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      2             9
  BLACK OR AFRICAN AMERICAN                  1            21
  WHITE                                      9           217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(37) Variable = ZBTB20 MUTATION ANALYSIS
D37V1, survival
                  sevent
clus2                0   1
  ZBTB20 MUTATED    17   4
  ZBTB20 WILD-TYPE 361  89
  ZBTB20 MUTATED ZBTB20 WILD-TYPE 
              21              450 
  ZBTB20 MUTATED ZBTB20 WILD-TYPE 
               4               89 
$`ZBTB20 MUTATED`
TCGA-A6-5661 TCGA-A6-6653 TCGA-A6-6780 TCGA-AA-3663 TCGA-AA-3672 TCGA-AA-3815 
       33.53        24.39        20.12         6.97         0.92        33.04 
TCGA-AA-3845 TCGA-AA-3950 TCGA-AA-3966 TCGA-AD-6964 TCGA-AY-6197 TCGA-CK-5913 
        0.00        24.00         2.01        10.88        21.44        51.32 
TCGA-CK-5916 TCGA-CM-6171 TCGA-D5-6538 TCGA-D5-6922 TCGA-F4-6570 TCGA-F4-6856 
       21.14        14.04        17.13         4.41         6.18        35.31 
TCGA-G4-6588 TCGA-AG-3892 TCGA-AG-A002 
       26.17        13.02        20.98 

$`ZBTB20 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6781 
       25.18        24.16        21.76        24.69        23.87        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02        78.08         6.05        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
       14.01        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
       19.04        19.04        10.06        35.05         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 
        2.01        12.99        24.00        33.01        26.01         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       20.98        34.03        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
        0.79         0.72         5.79        22.42        27.42         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 
       14.50        27.09        16.31         0.95        33.01        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
        9.99        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 
       21.99        14.99        12.99        13.02        15.02        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
        4.80        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 
       98.24         8.61        31.96        35.74        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       47.41       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       13.78        35.80        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       17.03        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  ZBTB20 MUTATED ZBTB20 WILD-TYPE 
               0                0 
  ZBTB20 MUTATED ZBTB20 WILD-TYPE 
           51.32           148.01 
  ZBTB20 MUTATED ZBTB20 WILD-TYPE 
          20.120           20.235 
[1] "0.0 - 51.3 (20.1)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.4"
D37V2, continuous
D37V3, binary
                  cls
clus                 0   1
  ZBTB20 MUTATED    20   2
  ZBTB20 WILD-TYPE 346 117
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZBTB20 MUTATED     20    2
  ZBTB20 WILD-TYPE  346  117
        clus
vv       ZBTB20 MUTATED ZBTB20 WILD-TYPE
  COLON              20              346
  RECTUM              2              117
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZBTB20 MUTATED         6        0        1        10         1         0
  ZBTB20 WILD-TYPE      85        1       31       128         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZBTB20 MUTATED           1          1          1          0        0
  ZBTB20 WILD-TYPE        23         10         58         42       48
                  vv
clus               STAGE IVA STAGE IVB
  ZBTB20 MUTATED           0         0
  ZBTB20 WILD-TYPE        18         1
D37V4, multiclass
            clus
vv           ZBTB20 MUTATED ZBTB20 WILD-TYPE
  STAGE I                 6               85
  STAGE IA                0                1
  STAGE II                1               31
  STAGE IIA              10              128
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               1               23
  STAGE IIIA              1               10
  STAGE IIIB              1               58
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZBTB20 MUTATED     2   4  14   2
  ZBTB20 WILD-TYPE  15  88 315  48
D37V5, multiclass
    clus
vv   ZBTB20 MUTATED ZBTB20 WILD-TYPE
  T1              2               15
  T2              4               88
  T3             14              315
  T4              2               48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  ZBTB20 MUTATED    18   2   2
  ZBTB20 WILD-TYPE 269 111  85
D37V6, multiclass
    clus
vv   ZBTB20 MUTATED ZBTB20 WILD-TYPE
  N0             18              269
  N1              2              111
  N2              2               85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V7, binary
                  cls
clus                 0   1
  ZBTB20 MUTATED    17   0
  ZBTB20 WILD-TYPE 358  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZBTB20 MUTATED     17    0
  ZBTB20 WILD-TYPE  358   65
   clus
vv  ZBTB20 MUTATED ZBTB20 WILD-TYPE
  0             17              358
  1              0               65
[1] 2 2
[1] FALSE
D37V8, binary
                  cls
clus                 0   1
  ZBTB20 MUTATED    14   8
  ZBTB20 WILD-TYPE 211 256
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZBTB20 MUTATED     14    8
  ZBTB20 WILD-TYPE  211  256
        clus
vv       ZBTB20 MUTATED ZBTB20 WILD-TYPE
  FEMALE             14              211
  MALE                8              256
[1] 2 2
[1] FALSE
D37V9, binary
                  cls
clus                 0   1
  ZBTB20 MUTATED    18   0
  ZBTB20 WILD-TYPE 332  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZBTB20 MUTATED     18    0
  ZBTB20 WILD-TYPE  332   22
     clus
vv    ZBTB20 MUTATED ZBTB20 WILD-TYPE
  NO              18              332
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ZBTB20 MUTATED                     16                             4
  ZBTB20 WILD-TYPE                  299                            43
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ZBTB20 MUTATED                       2                              0
  ZBTB20 WILD-TYPE                   104                             10
D37V10, multiclass
                                clus
vv                               ZBTB20 MUTATED ZBTB20 WILD-TYPE
  COLON ADENOCARCINOMA                       16              299
  COLON MUCINOUS ADENOCARCINOMA               4               43
  RECTAL ADENOCARCINOMA                       2              104
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ZBTB20 MUTATED    15   0   0   3
  ZBTB20 WILD-TYPE 330   4  31  22
D37V11, multiclass
    clus
vv   ZBTB20 MUTATED ZBTB20 WILD-TYPE
  R0             15              330
  R1              0                4
  R2              0               31
  RX              3               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZBTB20 MUTATED                                  0     0
  ZBTB20 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZBTB20 MUTATED                           1    13
  ZBTB20 WILD-TYPE                        21   213
D37V13, multiclass
                                  clus
vv                                 ZBTB20 MUTATED ZBTB20 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                        13              213
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(38) Variable = BCL9 MUTATION ANALYSIS
D38V1, survival
                sevent
clus2              0   1
  BCL9 MUTATED    18   9
  BCL9 WILD-TYPE 360  84
  BCL9 MUTATED BCL9 WILD-TYPE 
            27            444 
  BCL9 MUTATED BCL9 WILD-TYPE 
             9             84 
$`BCL9 MUTATED`
TCGA-A6-5661 TCGA-A6-6781 TCGA-AA-3555 TCGA-AA-3663 TCGA-AA-3715 TCGA-AA-3815 
       33.53        19.66        29.95         6.97        19.04        33.04 
TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01R 
       33.01        24.00        25.02         4.01        34.98        35.01 
TCGA-AD-6964 TCGA-AZ-6601 TCGA-CA-6718 TCGA-CM-6678 TCGA-DM-A0X9 TCGA-DM-A282 
       10.88       100.01        10.06        11.01       119.70       139.17 
TCGA-DM-A285 TCGA-F4-6570 TCGA-F4-6854 TCGA-G4-6586 TCGA-AF-4110 TCGA-AG-3583 
        6.12         6.18         0.53        35.80        14.50        20.05 
TCGA-AG-4001 TCGA-AG-A002 TCGA-DY-A1DG 
       36.03        20.98        51.48 

$`BCL9 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       24.00        17.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02        78.08         6.05        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
       26.99        19.04        10.06        35.05         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3952 
       31.00         2.01        12.99        24.00        26.01         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
        1.02         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77        12.10        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.20        12.76        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       13.05        11.08        11.08        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0XD TCGA-DM-A0XF 
        1.51        12.00        11.38        10.26        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A28C TCGA-DM-A28E 
        7.50        44.32       131.51       135.65        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       35.74        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       33.67        13.25        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 
       61.91        36.00        22.09        13.78        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       19.10        34.49        10.39        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       36.03        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4007 
       48.03        32.02        19.99        28.04        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       41.36        57.24        24.13        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  BCL9 MUTATED BCL9 WILD-TYPE 
          0.53           0.00 
  BCL9 MUTATED BCL9 WILD-TYPE 
        139.17         148.01 
  BCL9 MUTATED BCL9 WILD-TYPE 
         24.00          20.07 
[1] "0.5 - 139.2 (24.0)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.6"
D38V2, continuous
D38V3, binary
                cls
clus               0   1
  BCL9 MUTATED    22   4
  BCL9 WILD-TYPE 344 115
[1] "tbl2"
                cls
clus             [,1] [,2]
  BCL9 MUTATED     22    4
  BCL9 WILD-TYPE  344  115
        clus
vv       BCL9 MUTATED BCL9 WILD-TYPE
  COLON            22            344
  RECTUM            4            115
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  BCL9 MUTATED         1        0        3        11         3         0
  BCL9 WILD-TYPE      90        1       29       127         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  BCL9 MUTATED           1          0          0          1        2         3
  BCL9 WILD-TYPE        23         11         59         41       46        15
                vv
clus             STAGE IVB
  BCL9 MUTATED           0
  BCL9 WILD-TYPE         1
D38V4, multiclass
            clus
vv           BCL9 MUTATED BCL9 WILD-TYPE
  STAGE I               1             90
  STAGE IA              0              1
  STAGE II              3             29
  STAGE IIA            11            127
  STAGE IIB             3              7
  STAGE IIC             0              1
  STAGE III             1             23
  STAGE IIIA            0             11
  STAGE IIIB            0             59
  STAGE IIIC            1             41
  STAGE IV              2             46
  STAGE IVA             3             15
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  BCL9 MUTATED     0   2  18   7
  BCL9 WILD-TYPE  17  90 311  43
D38V5, multiclass
    clus
vv   BCL9 MUTATED BCL9 WILD-TYPE
  T1            0             17
  T2            2             90
  T3           18            311
  T4            7             43
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  BCL9 MUTATED    19   3   5
  BCL9 WILD-TYPE 268 110  82
D38V6, multiclass
    clus
vv   BCL9 MUTATED BCL9 WILD-TYPE
  N0           19            268
  N1            3            110
  N2            5             82
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V7, binary
                cls
clus               0   1
  BCL9 MUTATED    19   4
  BCL9 WILD-TYPE 356  61
[1] "tbl2"
                cls
clus             [,1] [,2]
  BCL9 MUTATED     19    4
  BCL9 WILD-TYPE  356   61
   clus
vv  BCL9 MUTATED BCL9 WILD-TYPE
  0           19            356
  1            4             61
[1] 2 2
[1] FALSE
D38V8, binary
                cls
clus               0   1
  BCL9 MUTATED    14  13
  BCL9 WILD-TYPE 211 251
[1] "tbl2"
                cls
clus             [,1] [,2]
  BCL9 MUTATED     14   13
  BCL9 WILD-TYPE  211  251
        clus
vv       BCL9 MUTATED BCL9 WILD-TYPE
  FEMALE           14            211
  MALE             13            251
[1] 2 2
[1] FALSE
D38V9, binary
                cls
clus               0   1
  BCL9 MUTATED    21   1
  BCL9 WILD-TYPE 329  21
[1] "tbl2"
                cls
clus             [,1] [,2]
  BCL9 MUTATED     21    1
  BCL9 WILD-TYPE  329   21
     clus
vv    BCL9 MUTATED BCL9 WILD-TYPE
  NO            21            329
  YES            1             21
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  BCL9 MUTATED                     15                             7
  BCL9 WILD-TYPE                  300                            40
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  BCL9 MUTATED                       3                              1
  BCL9 WILD-TYPE                   103                              9
D38V10, multiclass
                                clus
vv                               BCL9 MUTATED BCL9 WILD-TYPE
  COLON ADENOCARCINOMA                     15            300
  COLON MUCINOUS ADENOCARCINOMA             7             40
  RECTAL ADENOCARCINOMA                     3            103
  RECTAL MUCINOUS ADENOCARCINOMA            1              9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  BCL9 MUTATED    18   0   1   1
  BCL9 WILD-TYPE 327   4  30  24
D38V11, multiclass
    clus
vv   BCL9 MUTATED BCL9 WILD-TYPE
  R0           18            327
  R1            0              4
  R2            1             30
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  BCL9 MUTATED                                  0     1
  BCL9 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  BCL9 MUTATED                           1    12
  BCL9 WILD-TYPE                        21   214
D38V13, multiclass
                                  clus
vv                                 BCL9 MUTATED BCL9 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                      12            214
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(39) Variable = ERBB2 MUTATION ANALYSIS
D39V1, survival
                 sevent
clus2               0   1
  ERBB2 MUTATED    27   9
  ERBB2 WILD-TYPE 351  84
  ERBB2 MUTATED ERBB2 WILD-TYPE 
             36             435 
  ERBB2 MUTATED ERBB2 WILD-TYPE 
              9              84 
$`ERBB2 MUTATED`
TCGA-A6-4105 TCGA-A6-6138 TCGA-AA-3502 TCGA-AA-3660 TCGA-AA-3864 TCGA-AA-3869 
       14.53        22.52        35.01        78.08        53.00        27.02 
TCGA-AA-3947 TCGA-AA-3977 TCGA-AA-3994 TCGA-AD-6888 TCGA-AY-5543 TCGA-AZ-6599 
       33.01        25.02        27.02        15.52        33.01         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-CK-4947 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-6162 
       12.10       100.01        17.56        30.08        32.02        12.00 
TCGA-CM-6171 TCGA-CM-6675 TCGA-D5-6532 TCGA-D5-6539 TCGA-D5-6927 TCGA-DM-A0XF 
       14.04        13.05        18.25        12.49         9.44        38.20 
TCGA-F4-6855 TCGA-G4-6303 TCGA-G4-6307 TCGA-AF-2693 TCGA-AG-3599 TCGA-AG-3732 
       47.41        65.85        55.04        19.10        12.03        32.98 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-A002 TCGA-AH-6544 TCGA-AH-6644 TCGA-F5-6464 
       48.03        32.02        20.98        38.56         0.72         9.96 

$`ERBB2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 
       16.57        34.65        33.34        32.75        36.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       22.06        32.71        27.09         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3510 
       19.66        20.28         7.04         3.02         1.02        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3875 
       31.07        30.05        17.03        24.03        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 
       31.00         2.01        12.99        24.00        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       27.02        19.07         7.96        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6889 TCGA-AD-6890 
       18.05        40.96         0.07        21.37        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6197 TCGA-AY-6386 
       14.50        27.09        16.31         0.95        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       88.21        49.41        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-4950 
       12.20        12.76        10.06        14.30       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5861 TCGA-CM-5862 
       13.02        29.06        22.03        22.98        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 
       15.02        15.02        17.03        15.02         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       11.01        12.95        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       20.19         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       17.13        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       12.43        14.30         9.04        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A1D0 
       12.00        11.38        10.26       119.70        24.43       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6856 
       41.42        16.24        33.67        13.25         0.53        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6310 
      133.18        74.56        53.62        44.68        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       13.55        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
       34.03         2.01        50.04         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-CI-6619 TCGA-CI-6620 
      117.11         1.45        17.49         0.69         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
       18.28        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  ERBB2 MUTATED ERBB2 WILD-TYPE 
           0.72            0.00 
  ERBB2 MUTATED ERBB2 WILD-TYPE 
         100.01          148.01 
  ERBB2 MUTATED ERBB2 WILD-TYPE 
          26.02           20.02 
[1] "0.7 - 100.0 (26.0)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.1"
D39V2, continuous
D39V3, binary
                 cls
clus                0   1
  ERBB2 MUTATED    27   8
  ERBB2 WILD-TYPE 339 111
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERBB2 MUTATED     27    8
  ERBB2 WILD-TYPE  339  111
        clus
vv       ERBB2 MUTATED ERBB2 WILD-TYPE
  COLON             27             339
  RECTUM             8             111
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ERBB2 MUTATED         8        0        3         8         1         0
  ERBB2 WILD-TYPE      83        1       29       130         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ERBB2 MUTATED           0          1          5          2        3         1
  ERBB2 WILD-TYPE        24         10         54         40       45        17
                 vv
clus              STAGE IVB
  ERBB2 MUTATED           1
  ERBB2 WILD-TYPE         0
D39V4, multiclass
            clus
vv           ERBB2 MUTATED ERBB2 WILD-TYPE
  STAGE I                8              83
  STAGE IA               0               1
  STAGE II               3              29
  STAGE IIA              8             130
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             1              10
  STAGE IIIB             5              54
  STAGE IIIC             2              40
  STAGE IV               3              45
  STAGE IVA              1              17
  STAGE IVB              1               0
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ERBB2 MUTATED     0   9  22   5
  ERBB2 WILD-TYPE  17  83 307  45
D39V5, multiclass
    clus
vv   ERBB2 MUTATED ERBB2 WILD-TYPE
  T1             0              17
  T2             9              83
  T3            22             307
  T4             5              45
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  ERBB2 MUTATED    22   9   4
  ERBB2 WILD-TYPE 265 104  83
D39V6, multiclass
    clus
vv   ERBB2 MUTATED ERBB2 WILD-TYPE
  N0            22             265
  N1             9             104
  N2             4              83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V7, binary
                 cls
clus                0   1
  ERBB2 MUTATED    26   6
  ERBB2 WILD-TYPE 349  59
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERBB2 MUTATED     26    6
  ERBB2 WILD-TYPE  349   59
   clus
vv  ERBB2 MUTATED ERBB2 WILD-TYPE
  0            26             349
  1             6              59
[1] 2 2
[1] FALSE
D39V8, binary
                 cls
clus                0   1
  ERBB2 MUTATED    14  22
  ERBB2 WILD-TYPE 211 242
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERBB2 MUTATED     14   22
  ERBB2 WILD-TYPE  211  242
        clus
vv       ERBB2 MUTATED ERBB2 WILD-TYPE
  FEMALE            14             211
  MALE              22             242
[1] 2 2
[1] FALSE
D39V9, binary
                 cls
clus                0   1
  ERBB2 MUTATED    33   0
  ERBB2 WILD-TYPE 317  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERBB2 MUTATED     33    0
  ERBB2 WILD-TYPE  317   22
     clus
vv    ERBB2 MUTATED ERBB2 WILD-TYPE
  NO             33             317
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ERBB2 MUTATED                     23                             3
  ERBB2 WILD-TYPE                  292                            44
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ERBB2 MUTATED                       7                              0
  ERBB2 WILD-TYPE                    99                             10
D39V10, multiclass
                                clus
vv                               ERBB2 MUTATED ERBB2 WILD-TYPE
  COLON ADENOCARCINOMA                      23             292
  COLON MUCINOUS ADENOCARCINOMA              3              44
  RECTAL ADENOCARCINOMA                      7              99
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  ERBB2 MUTATED    24   0   1   1
  ERBB2 WILD-TYPE 321   4  30  24
D39V11, multiclass
    clus
vv   ERBB2 MUTATED ERBB2 WILD-TYPE
  R0            24             321
  R1             0               4
  R2             1              30
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ERBB2 MUTATED                                  0     0
  ERBB2 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ERBB2 MUTATED                           3    21
  ERBB2 WILD-TYPE                        19   205
D39V13, multiclass
                                  clus
vv                                 ERBB2 MUTATED ERBB2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    3              19
  WHITE                                       21             205
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(40) Variable = P2RY13 MUTATION ANALYSIS
D40V1, survival
                  sevent
clus2                0   1
  P2RY13 MUTATED    12   1
  P2RY13 WILD-TYPE 366  92
  P2RY13 MUTATED P2RY13 WILD-TYPE 
              13              458 
  P2RY13 MUTATED P2RY13 WILD-TYPE 
               1               92 
$`P2RY13 MUTATED`
TCGA-A6-6780 TCGA-AA-3496 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3713 TCGA-AA-3977 
       20.12         1.02         6.05         6.97        19.04        25.02 
TCGA-AD-6889 TCGA-CA-6717 TCGA-CM-6678 TCGA-D5-6539 TCGA-DM-A28G TCGA-DM-A28H 
       56.55        12.76        11.01        12.49        60.79       117.07 
TCGA-F4-6569 
       35.74 

$`P2RY13 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 
       23.87        19.66        20.28         7.04         3.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 
       13.94        19.99        61.02        78.08        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       26.99        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       21.37        15.52         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07        12.20        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6679 TCGA-CM-6680 
       12.95        13.05        11.08        11.08        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       17.13        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28K TCGA-F4-6459 
        6.12        81.37       119.93        35.97        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       31.96         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  P2RY13 MUTATED P2RY13 WILD-TYPE 
            1.02             0.00 
  P2RY13 MUTATED P2RY13 WILD-TYPE 
          117.07           148.01 
  P2RY13 MUTATED P2RY13 WILD-TYPE 
          19.040           20.415 
[1] "1.0 - 117.1 (19.0)" "0.0 - 148.0 (20.4)"
[1] "hr=" "2.9"
D40V2, continuous
D40V3, binary
                  cls
clus                 0   1
  P2RY13 MUTATED    15   0
  P2RY13 WILD-TYPE 351 119
[1] "tbl2"
                  cls
clus               [,1] [,2]
  P2RY13 MUTATED     15    0
  P2RY13 WILD-TYPE  351  119
        clus
vv       P2RY13 MUTATED P2RY13 WILD-TYPE
  COLON              15              351
  RECTUM              0              119
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  P2RY13 MUTATED         1        0        2         5         1         0
  P2RY13 WILD-TYPE      90        1       30       133         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  P2RY13 MUTATED           0          1          0          1        2
  P2RY13 WILD-TYPE        24         10         59         41       46
                  vv
clus               STAGE IVA STAGE IVB
  P2RY13 MUTATED           1         0
  P2RY13 WILD-TYPE        17         1
D40V4, multiclass
            clus
vv           P2RY13 MUTATED P2RY13 WILD-TYPE
  STAGE I                 1               90
  STAGE IA                0                1
  STAGE II                2               30
  STAGE IIA               5              133
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              1               10
  STAGE IIIB              0               59
  STAGE IIIC              1               41
  STAGE IV                2               46
  STAGE IVA               1               17
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  P2RY13 MUTATED     0   2  10   3
  P2RY13 WILD-TYPE  17  90 319  47
D40V5, multiclass
    clus
vv   P2RY13 MUTATED P2RY13 WILD-TYPE
  T1              0               17
  T2              2               90
  T3             10              319
  T4              3               47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  P2RY13 MUTATED    12   1   2
  P2RY13 WILD-TYPE 275 112  85
D40V6, multiclass
    clus
vv   P2RY13 MUTATED P2RY13 WILD-TYPE
  N0             12              275
  N1              1              112
  N2              2               85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V7, binary
                  cls
clus                 0   1
  P2RY13 MUTATED     9   3
  P2RY13 WILD-TYPE 366  62
[1] "tbl2"
                  cls
clus               [,1] [,2]
  P2RY13 MUTATED      9    3
  P2RY13 WILD-TYPE  366   62
   clus
vv  P2RY13 MUTATED P2RY13 WILD-TYPE
  0              9              366
  1              3               62
[1] 2 2
[1] FALSE
D40V8, binary
                  cls
clus                 0   1
  P2RY13 MUTATED     6   9
  P2RY13 WILD-TYPE 219 255
[1] "tbl2"
                  cls
clus               [,1] [,2]
  P2RY13 MUTATED      6    9
  P2RY13 WILD-TYPE  219  255
        clus
vv       P2RY13 MUTATED P2RY13 WILD-TYPE
  FEMALE              6              219
  MALE                9              255
[1] 2 2
[1] FALSE
D40V9, binary
                  cls
clus                 0   1
  P2RY13 MUTATED     8   1
  P2RY13 WILD-TYPE 342  21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  P2RY13 MUTATED      8    1
  P2RY13 WILD-TYPE  342   21
     clus
vv    P2RY13 MUTATED P2RY13 WILD-TYPE
  NO               8              342
  YES              1               21
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  P2RY13 MUTATED                     13                             2
  P2RY13 WILD-TYPE                  302                            45
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  P2RY13 MUTATED                       0                              0
  P2RY13 WILD-TYPE                   106                             10
D40V10, multiclass
                                clus
vv                               P2RY13 MUTATED P2RY13 WILD-TYPE
  COLON ADENOCARCINOMA                       13              302
  COLON MUCINOUS ADENOCARCINOMA               2               45
  RECTAL ADENOCARCINOMA                       0              106
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  P2RY13 MUTATED     6   0   2   2
  P2RY13 WILD-TYPE 339   4  29  23
D40V11, multiclass
    clus
vv   P2RY13 MUTATED P2RY13 WILD-TYPE
  R0              6              339
  R1              0                4
  R2              2               29
  RX              2               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  P2RY13 MUTATED                                  0     2
  P2RY13 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  P2RY13 MUTATED                           0     7
  P2RY13 WILD-TYPE                        22   219
D40V13, multiclass
                                  clus
vv                                 P2RY13 MUTATED P2RY13 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                9
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         7              219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(41) Variable = ST3GAL6 MUTATION ANALYSIS
D41V1, survival
                   sevent
clus2                 0   1
  ST3GAL6 MUTATED     8   4
  ST3GAL6 WILD-TYPE 370  89
  ST3GAL6 MUTATED ST3GAL6 WILD-TYPE 
               12               459 
  ST3GAL6 MUTATED ST3GAL6 WILD-TYPE 
                4                89 
$`ST3GAL6 MUTATED`
TCGA-AA-3663 TCGA-AA-3715 TCGA-AA-3947 TCGA-AA-A00N TCGA-AA-A00R TCGA-AD-6895 
        6.97        19.04        33.01         4.01         0.99         0.72 
TCGA-AZ-6598 TCGA-CA-6717 TCGA-CK-5916 TCGA-CM-5864 TCGA-AF-2687 TCGA-AG-A002 
       49.41        12.76        21.14        15.02        24.13        20.98 

$`ST3GAL6 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.05        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 
       36.00         5.03        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       12.99        24.00        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
       42.02        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 
        0.07        21.37        15.52        56.55         0.79         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07        12.20        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 
       85.45        15.62        49.08        51.32         9.99        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
       15.02         5.03        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       46.75        79.69        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  ST3GAL6 MUTATED ST3GAL6 WILD-TYPE 
             0.72              0.00 
  ST3GAL6 MUTATED ST3GAL6 WILD-TYPE 
            49.41            148.01 
  ST3GAL6 MUTATED ST3GAL6 WILD-TYPE 
            17.03             20.28 
[1] "0.7 - 49.4 (17.0)"  "0.0 - 148.0 (20.3)"
[1] "hr=" "2.5"
D41V2, continuous
D41V3, binary
                   cls
clus                  0   1
  ST3GAL6 MUTATED    10   2
  ST3GAL6 WILD-TYPE 356 117
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ST3GAL6 MUTATED     10    2
  ST3GAL6 WILD-TYPE  356  117
        clus
vv       ST3GAL6 MUTATED ST3GAL6 WILD-TYPE
  COLON               10               356
  RECTUM               2               117
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ST3GAL6 MUTATED         4        0        3         1         2         0
  ST3GAL6 WILD-TYPE      87        1       29       137         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ST3GAL6 MUTATED           0          0          0          1        0
  ST3GAL6 WILD-TYPE        24         11         59         41       48
                   vv
clus                STAGE IVA STAGE IVB
  ST3GAL6 MUTATED           0         0
  ST3GAL6 WILD-TYPE        18         1
D41V4, multiclass
            clus
vv           ST3GAL6 MUTATED ST3GAL6 WILD-TYPE
  STAGE I                  4                87
  STAGE IA                 0                 1
  STAGE II                 3                29
  STAGE IIA                1               137
  STAGE IIB                2                 8
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               0                11
  STAGE IIIB               0                59
  STAGE IIIC               1                41
  STAGE IV                 0                48
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  ST3GAL6 MUTATED     1   3   6   2
  ST3GAL6 WILD-TYPE  16  89 323  48
D41V5, multiclass
    clus
vv   ST3GAL6 MUTATED ST3GAL6 WILD-TYPE
  T1               1                16
  T2               3                89
  T3               6               323
  T4               2                48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  ST3GAL6 MUTATED    10   1   1
  ST3GAL6 WILD-TYPE 277 112  86
D41V6, multiclass
    clus
vv   ST3GAL6 MUTATED ST3GAL6 WILD-TYPE
  N0              10               277
  N1               1               112
  N2               1                86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V7, binary
                   cls
clus                  0   1
  ST3GAL6 MUTATED    10   0
  ST3GAL6 WILD-TYPE 365  65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ST3GAL6 MUTATED     10    0
  ST3GAL6 WILD-TYPE  365   65
   clus
vv  ST3GAL6 MUTATED ST3GAL6 WILD-TYPE
  0              10               365
  1               0                65
[1] 2 2
[1] FALSE
D41V8, binary
                   cls
clus                  0   1
  ST3GAL6 MUTATED     4   8
  ST3GAL6 WILD-TYPE 221 256
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ST3GAL6 MUTATED      4    8
  ST3GAL6 WILD-TYPE  221  256
        clus
vv       ST3GAL6 MUTATED ST3GAL6 WILD-TYPE
  FEMALE               4               221
  MALE                 8               256
[1] 2 2
[1] FALSE
D41V9, binary
                   cls
clus                  0   1
  ST3GAL6 MUTATED     8   1
  ST3GAL6 WILD-TYPE 342  21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ST3GAL6 MUTATED      8    1
  ST3GAL6 WILD-TYPE  342   21
     clus
vv    ST3GAL6 MUTATED ST3GAL6 WILD-TYPE
  NO                8               342
  YES               1                21
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ST3GAL6 MUTATED                      7                             3
  ST3GAL6 WILD-TYPE                  308                            44
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ST3GAL6 MUTATED                       2                              0
  ST3GAL6 WILD-TYPE                   104                             10
D41V10, multiclass
                                clus
vv                               ST3GAL6 MUTATED ST3GAL6 WILD-TYPE
  COLON ADENOCARCINOMA                         7               308
  COLON MUCINOUS ADENOCARCINOMA                3                44
  RECTAL ADENOCARCINOMA                        2               104
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  ST3GAL6 MUTATED     8   0   0   2
  ST3GAL6 WILD-TYPE 337   4  31  23
D41V11, multiclass
    clus
vv   ST3GAL6 MUTATED ST3GAL6 WILD-TYPE
  R0               8               337
  R1               0                 4
  R2               0                31
  RX               2                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ST3GAL6 MUTATED                                  0     1
  ST3GAL6 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  ST3GAL6 MUTATED                           0     5
  ST3GAL6 WILD-TYPE                        22   221
D41V13, multiclass
                                  clus
vv                                 ST3GAL6 MUTATED ST3GAL6 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                10
  BLACK OR AFRICAN AMERICAN                      0                22
  WHITE                                          5               221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(42) Variable = IQCD MUTATION ANALYSIS
D42V1, survival
                sevent
clus2              0   1
  IQCD MUTATED    11   1
  IQCD WILD-TYPE 367  92
  IQCD MUTATED IQCD WILD-TYPE 
            12            459 
  IQCD MUTATED IQCD WILD-TYPE 
             1             92 
$`IQCD MUTATED`
TCGA-A6-6141 TCGA-A6-6654 TCGA-AA-3538 TCGA-AA-3672 TCGA-AZ-6599 TCGA-CM-4744 
        8.38        23.87        26.01         0.92         6.77        20.02 
TCGA-CM-5861 TCGA-CM-6171 TCGA-G4-6317 TCGA-AF-4110 TCGA-AG-A002 TCGA-AH-6643 
       15.02        14.04        36.00        14.50        20.98         0.69 

$`IQCD WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 
       22.09        22.06        32.71        27.09        22.52        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 
       25.18        24.16        21.76        24.69        24.39        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3542 
        0.00        19.07        34.03        29.00        29.00        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
        2.01        14.01        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        88.21        49.41        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       23.05        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       22.98        30.08        32.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 
       21.99        14.99        12.99        13.02        15.02        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       63.62        61.91        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6136 
       13.55        19.10        34.49        10.39        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
        1.45        17.49         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  IQCD MUTATED IQCD WILD-TYPE 
          0.69           0.00 
  IQCD MUTATED IQCD WILD-TYPE 
         36.00         148.01 
  IQCD MUTATED IQCD WILD-TYPE 
         14.76          20.55 
[1] "0.7 - 36.0 (14.8)"  "0.0 - 148.0 (20.6)"
[1] "hr=" "1.4"
D42V2, continuous
D42V3, binary
                cls
clus               0   1
  IQCD MUTATED    10   2
  IQCD WILD-TYPE 356 117
[1] "tbl2"
                cls
clus             [,1] [,2]
  IQCD MUTATED     10    2
  IQCD WILD-TYPE  356  117
        clus
vv       IQCD MUTATED IQCD WILD-TYPE
  COLON            10            356
  RECTUM            2            117
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  IQCD MUTATED         5        0        0         2         0         0
  IQCD WILD-TYPE      86        1       32       136        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  IQCD MUTATED           1          0          1          3        0         1
  IQCD WILD-TYPE        23         11         58         39       48        17
                vv
clus             STAGE IVB
  IQCD MUTATED           0
  IQCD WILD-TYPE         1
D42V4, multiclass
            clus
vv           IQCD MUTATED IQCD WILD-TYPE
  STAGE I               5             86
  STAGE IA              0              1
  STAGE II              0             32
  STAGE IIA             2            136
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             1             23
  STAGE IIIA            0             11
  STAGE IIIB            1             58
  STAGE IIIC            3             39
  STAGE IV              0             48
  STAGE IVA             1             17
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  IQCD MUTATED     0   5   7   1
  IQCD WILD-TYPE  17  87 322  49
D42V5, multiclass
    clus
vv   IQCD MUTATED IQCD WILD-TYPE
  T1            0             17
  T2            5             87
  T3            7            322
  T4            1             49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  IQCD MUTATED     7   2   4
  IQCD WILD-TYPE 280 111  83
D42V6, multiclass
    clus
vv   IQCD MUTATED IQCD WILD-TYPE
  N0            7            280
  N1            2            111
  N2            4             83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V7, binary
                cls
clus               0   1
  IQCD MUTATED     9   0
  IQCD WILD-TYPE 366  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  IQCD MUTATED      9    0
  IQCD WILD-TYPE  366   65
   clus
vv  IQCD MUTATED IQCD WILD-TYPE
  0            9            366
  1            0             65
[1] 2 2
[1] FALSE
D42V8, binary
                cls
clus               0   1
  IQCD MUTATED     6   7
  IQCD WILD-TYPE 219 257
[1] "tbl2"
                cls
clus             [,1] [,2]
  IQCD MUTATED      6    7
  IQCD WILD-TYPE  219  257
        clus
vv       IQCD MUTATED IQCD WILD-TYPE
  FEMALE            6            219
  MALE              7            257
[1] 2 2
[1] FALSE
D42V9, binary
                cls
clus               0   1
  IQCD MUTATED    11   0
  IQCD WILD-TYPE 339  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  IQCD MUTATED     11    0
  IQCD WILD-TYPE  339   22
     clus
vv    IQCD MUTATED IQCD WILD-TYPE
  NO            11            339
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  IQCD MUTATED                      9                             1
  IQCD WILD-TYPE                  306                            46
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  IQCD MUTATED                       2                              0
  IQCD WILD-TYPE                   104                             10
D42V10, multiclass
                                clus
vv                               IQCD MUTATED IQCD WILD-TYPE
  COLON ADENOCARCINOMA                      9            306
  COLON MUCINOUS ADENOCARCINOMA             1             46
  RECTAL ADENOCARCINOMA                     2            104
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  IQCD MUTATED    10   0   0   0
  IQCD WILD-TYPE 335   4  31  25
D42V11, multiclass
    clus
vv   IQCD MUTATED IQCD WILD-TYPE
  R0           10            335
  R1            0              4
  R2            0             31
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  IQCD MUTATED                                  0     0
  IQCD WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  IQCD MUTATED                           1     9
  IQCD WILD-TYPE                        21   217
D42V13, multiclass
                                  clus
vv                                 IQCD MUTATED IQCD WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                       9            217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(43) Variable = PLEKHF2 MUTATION ANALYSIS
D43V1, survival
                   sevent
clus2                 0   1
  PLEKHF2 MUTATED     9   2
  PLEKHF2 WILD-TYPE 369  91
  PLEKHF2 MUTATED PLEKHF2 WILD-TYPE 
               11               460 
  PLEKHF2 MUTATED PLEKHF2 WILD-TYPE 
                2                91 
$`PLEKHF2 MUTATED`
TCGA-A6-5665 TCGA-AA-3713 TCGA-AA-3977 TCGA-D5-6533 TCGA-D5-6541 TCGA-G4-6303 
       22.06        19.04        25.02         1.32        15.58        65.85 
TCGA-G4-6309 TCGA-G4-6323 TCGA-G4-6626 TCGA-AG-3731 TCGA-AH-6547 
       85.48        13.78        46.75        37.02         1.45 

$`PLEKHF2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       18.25        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       12.49        16.14         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6304 TCGA-G4-6306 
       47.41        35.31       133.18        74.56        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6586 
       55.04        63.62        61.91        36.00        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       26.17        91.79        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
        0.99        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
       38.56        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  PLEKHF2 MUTATED PLEKHF2 WILD-TYPE 
             1.32              0.00 
  PLEKHF2 MUTATED PLEKHF2 WILD-TYPE 
            85.48            148.01 
  PLEKHF2 MUTATED PLEKHF2 WILD-TYPE 
           22.060            20.155 
[1] "1.3 - 85.5 (22.1)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.3"
D43V2, continuous
D43V3, binary
                   cls
clus                  0   1
  PLEKHF2 MUTATED    10   2
  PLEKHF2 WILD-TYPE 356 117
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLEKHF2 MUTATED     10    2
  PLEKHF2 WILD-TYPE  356  117
        clus
vv       PLEKHF2 MUTATED PLEKHF2 WILD-TYPE
  COLON               10               356
  RECTUM               2               117
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PLEKHF2 MUTATED         1        1        0         3         0         0
  PLEKHF2 WILD-TYPE      90        0       32       135        10         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PLEKHF2 MUTATED           0          0          2          0        3
  PLEKHF2 WILD-TYPE        24         11         57         42       45
                   vv
clus                STAGE IVA STAGE IVB
  PLEKHF2 MUTATED           0         0
  PLEKHF2 WILD-TYPE        18         1
D43V4, multiclass
            clus
vv           PLEKHF2 MUTATED PLEKHF2 WILD-TYPE
  STAGE I                  1                90
  STAGE IA                 1                 0
  STAGE II                 0                32
  STAGE IIA                3               135
  STAGE IIB                0                10
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               0                11
  STAGE IIIB               2                57
  STAGE IIIC               0                42
  STAGE IV                 3                45
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  PLEKHF2 MUTATED     0   2   8   1
  PLEKHF2 WILD-TYPE  17  90 321  49
D43V5, multiclass
    clus
vv   PLEKHF2 MUTATED PLEKHF2 WILD-TYPE
  T1               0                17
  T2               2                90
  T3               8               321
  T4               1                49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  PLEKHF2 MUTATED     9   3   0
  PLEKHF2 WILD-TYPE 278 110  87
D43V6, multiclass
    clus
vv   PLEKHF2 MUTATED PLEKHF2 WILD-TYPE
  N0               9               278
  N1               3               110
  N2               0                87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V7, binary
                   cls
clus                  0   1
  PLEKHF2 MUTATED     5   3
  PLEKHF2 WILD-TYPE 370  62
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLEKHF2 MUTATED      5    3
  PLEKHF2 WILD-TYPE  370   62
   clus
vv  PLEKHF2 MUTATED PLEKHF2 WILD-TYPE
  0               5               370
  1               3                62
[1] 2 2
[1] FALSE
D43V8, binary
                   cls
clus                  0   1
  PLEKHF2 MUTATED     5   7
  PLEKHF2 WILD-TYPE 220 257
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLEKHF2 MUTATED      5    7
  PLEKHF2 WILD-TYPE  220  257
        clus
vv       PLEKHF2 MUTATED PLEKHF2 WILD-TYPE
  FEMALE               5               220
  MALE                 7               257
[1] 2 2
[1] FALSE
D43V9, binary
                   cls
clus                  0   1
  PLEKHF2 MUTATED     8   1
  PLEKHF2 WILD-TYPE 342  21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLEKHF2 MUTATED      8    1
  PLEKHF2 WILD-TYPE  342   21
     clus
vv    PLEKHF2 MUTATED PLEKHF2 WILD-TYPE
  NO                8               342
  YES               1                21
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PLEKHF2 MUTATED                     10                             0
  PLEKHF2 WILD-TYPE                  305                            47
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PLEKHF2 MUTATED                       2                              0
  PLEKHF2 WILD-TYPE                   104                             10
D43V10, multiclass
                                clus
vv                               PLEKHF2 MUTATED PLEKHF2 WILD-TYPE
  COLON ADENOCARCINOMA                        10               305
  COLON MUCINOUS ADENOCARCINOMA                0                47
  RECTAL ADENOCARCINOMA                        2               104
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  PLEKHF2 MUTATED     7   0   2   1
  PLEKHF2 WILD-TYPE 338   4  29  24
D43V11, multiclass
    clus
vv   PLEKHF2 MUTATED PLEKHF2 WILD-TYPE
  R0               7               338
  R1               0                 4
  R2               2                29
  RX               1                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PLEKHF2 MUTATED                                  0     0
  PLEKHF2 WILD-TYPE                                1    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  PLEKHF2 MUTATED                           2     7
  PLEKHF2 WILD-TYPE                        20   219
D43V13, multiclass
                                  clus
vv                                 PLEKHF2 MUTATED PLEKHF2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                      2                20
  WHITE                                          7               219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(44) Variable = NR1H3 MUTATION ANALYSIS
D44V1, survival
                 sevent
clus2               0   1
  NR1H3 MUTATED    12   2
  NR1H3 WILD-TYPE 366  91
  NR1H3 MUTATED NR1H3 WILD-TYPE 
             14             457 
  NR1H3 MUTATED NR1H3 WILD-TYPE 
              2              91 
$`NR1H3 MUTATED`
TCGA-A6-6648 TCGA-AA-3660 TCGA-AA-3864 TCGA-AA-A00J TCGA-AA-A00R TCGA-AA-A02J 
       25.18        78.08        53.00        18.05         0.99         5.03 
TCGA-CK-5913 TCGA-CK-5916 TCGA-CM-6163 TCGA-CM-6171 TCGA-CM-6674 TCGA-D5-6536 
       51.32        21.14         2.96        14.04        12.95        17.85 
TCGA-G4-6309 TCGA-G4-6628 
       85.48        79.69 

$`NR1H3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.08        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 
       19.99        13.94        19.99        61.02         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 
        0.99        31.07        31.07        30.05        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
       42.02        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02K 
       37.02        39.06        51.98        39.98         2.01        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 
       17.56       148.01        85.45        15.62        49.08         9.99 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       15.02        12.00        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6676 
       12.99        13.02        15.02        11.01        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       43.27        15.12         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       55.04        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 
       35.80        26.17        91.79        46.75        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  NR1H3 MUTATED NR1H3 WILD-TYPE 
           0.99            0.00 
  NR1H3 MUTATED NR1H3 WILD-TYPE 
          85.48          148.01 
  NR1H3 MUTATED NR1H3 WILD-TYPE 
         19.595          20.190 
[1] "1.0 - 85.5 (19.6)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.9"
D44V2, continuous
D44V3, binary
                 cls
clus                0   1
  NR1H3 MUTATED    15   0
  NR1H3 WILD-TYPE 351 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NR1H3 MUTATED     15    0
  NR1H3 WILD-TYPE  351  119
        clus
vv       NR1H3 MUTATED NR1H3 WILD-TYPE
  COLON             15             351
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NR1H3 MUTATED         6        0        2         3         0         0
  NR1H3 WILD-TYPE      85        1       30       135        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NR1H3 MUTATED           0          0          2          0        1         1
  NR1H3 WILD-TYPE        24         11         57         42       47        17
                 vv
clus              STAGE IVB
  NR1H3 MUTATED           0
  NR1H3 WILD-TYPE         1
D44V4, multiclass
            clus
vv           NR1H3 MUTATED NR1H3 WILD-TYPE
  STAGE I                6              85
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA              3             135
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             2              57
  STAGE IIIC             0              42
  STAGE IV               1              47
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  NR1H3 MUTATED     2   4   8   1
  NR1H3 WILD-TYPE  15  88 321  49
D44V5, multiclass
    clus
vv   NR1H3 MUTATED NR1H3 WILD-TYPE
  T1             2              15
  T2             4              88
  T3             8             321
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  NR1H3 MUTATED    13   2   0
  NR1H3 WILD-TYPE 274 111  87
D44V6, multiclass
    clus
vv   NR1H3 MUTATED NR1H3 WILD-TYPE
  N0            13             274
  N1             2             111
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V7, binary
                 cls
clus                0   1
  NR1H3 MUTATED    11   2
  NR1H3 WILD-TYPE 364  63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NR1H3 MUTATED     11    2
  NR1H3 WILD-TYPE  364   63
   clus
vv  NR1H3 MUTATED NR1H3 WILD-TYPE
  0            11             364
  1             2              63
[1] 2 2
[1] FALSE
D44V8, binary
                 cls
clus                0   1
  NR1H3 MUTATED     7   8
  NR1H3 WILD-TYPE 218 256
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NR1H3 MUTATED      7    8
  NR1H3 WILD-TYPE  218  256
        clus
vv       NR1H3 MUTATED NR1H3 WILD-TYPE
  FEMALE             7             218
  MALE               8             256
[1] 2 2
[1] FALSE
D44V9, binary
                 cls
clus                0   1
  NR1H3 MUTATED    12   0
  NR1H3 WILD-TYPE 338  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NR1H3 MUTATED     12    0
  NR1H3 WILD-TYPE  338   22
     clus
vv    NR1H3 MUTATED NR1H3 WILD-TYPE
  NO             12             338
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  NR1H3 MUTATED                     14                             1
  NR1H3 WILD-TYPE                  301                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  NR1H3 MUTATED                       0                              0
  NR1H3 WILD-TYPE                   106                             10
D44V10, multiclass
                                clus
vv                               NR1H3 MUTATED NR1H3 WILD-TYPE
  COLON ADENOCARCINOMA                      14             301
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  NR1H3 MUTATED    10   0   1   3
  NR1H3 WILD-TYPE 335   4  30  22
D44V11, multiclass
    clus
vv   NR1H3 MUTATED NR1H3 WILD-TYPE
  R0            10             335
  R1             0               4
  R2             1              30
  RX             3              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NR1H3 MUTATED                                  0     0
  NR1H3 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  NR1H3 MUTATED                           1     9
  NR1H3 WILD-TYPE                        21   217
D44V13, multiclass
                                  clus
vv                                 NR1H3 MUTATED NR1H3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        9             217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(45) Variable = ALPK2 MUTATION ANALYSIS
D45V1, survival
                 sevent
clus2               0   1
  ALPK2 MUTATED    37   8
  ALPK2 WILD-TYPE 341  85
  ALPK2 MUTATED ALPK2 WILD-TYPE 
             45             426 
  ALPK2 MUTATED ALPK2 WILD-TYPE 
              8              85 
$`ALPK2 MUTATED`
TCGA-A6-5661 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6780 
       33.53        32.71        27.09         8.38        25.18        20.12 
TCGA-A6-6781 TCGA-AA-3492 TCGA-AA-3525 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3697 
       19.66         3.02         8.05        78.08         6.97        85.05 
TCGA-AA-3821 TCGA-AA-3844 TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A010 TCGA-AD-5900 
        1.02        14.93        25.02         4.01        34.98         0.07 
TCGA-AU-6004 TCGA-AY-6197 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-CA-5255 TCGA-CA-6717 
       27.09        21.44        49.41         6.77         3.06        12.76 
TCGA-CA-6718 TCGA-CK-4952 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4752 TCGA-CM-5861 
       10.06        15.62        23.05        20.02        13.02        15.02 
TCGA-CM-6162 TCGA-CM-6168 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-D5-5540 
       12.00        12.99        15.02        14.04        11.01        56.09 
TCGA-D5-6540 TCGA-DM-A28G TCGA-F4-6809 TCGA-G4-6309 TCGA-G4-6588 TCGA-AG-3731 
       16.14        60.79        13.25        85.48        26.17        37.02 
TCGA-AG-A002 TCGA-DY-A1H8 TCGA-EI-6507 
       20.98        32.61        19.96 

$`ALPK2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 
       22.06        22.52        25.08        24.16        21.76        24.69 
TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 
       24.39        23.87        20.28         7.04         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3529 
        9.07        24.03        37.05        36.03        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       19.99        61.02         6.05        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 
       37.05        19.00        36.00         5.03        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3846 
       17.98        15.95        38.99        37.02         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 
       22.42        27.42        10.88         0.20        14.50        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        33.01        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6600 TCGA-AZ-6601 
      106.75        22.36        62.79        88.21        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 
        3.25         3.29         0.07        12.20        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
      148.01        85.45        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-5341 
       82.95         1.91       124.27        37.02        25.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 
       22.03        22.98        30.08        32.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       15.02        17.03        15.02         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6169 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       21.99        14.99        13.02        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       19.59        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 
       15.12        17.85         4.80        17.13        12.49        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       35.97       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       33.67         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 
       65.85        53.62        44.68        55.04        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        35.80        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3732 
       19.99        13.94        19.99         7.99         0.99        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EF-5830 
      126.44        41.36        57.24        24.13        51.48         0.49 
TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       20.55        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  ALPK2 MUTATED ALPK2 WILD-TYPE 
           0.07            0.00 
  ALPK2 MUTATED ALPK2 WILD-TYPE 
          85.48          148.01 
  ALPK2 MUTATED ALPK2 WILD-TYPE 
         19.660          20.945 
[1] "0.1 - 85.5 (19.7)"  "0.0 - 148.0 (20.9)"
[1] "hr=" "1"  
D45V2, continuous
D45V3, binary
                 cls
clus                0   1
  ALPK2 MUTATED    42   4
  ALPK2 WILD-TYPE 324 115
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ALPK2 MUTATED     42    4
  ALPK2 WILD-TYPE  324  115
        clus
vv       ALPK2 MUTATED ALPK2 WILD-TYPE
  COLON             42             324
  RECTUM             4             115
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ALPK2 MUTATED         9        0        4        16         2         1
  ALPK2 WILD-TYPE      82        1       28       122         8         0
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ALPK2 MUTATED           1          1          5          3        1         2
  ALPK2 WILD-TYPE        23         10         54         39       47        16
                 vv
clus              STAGE IVB
  ALPK2 MUTATED           0
  ALPK2 WILD-TYPE         1
D45V4, multiclass
            clus
vv           ALPK2 MUTATED ALPK2 WILD-TYPE
  STAGE I                9              82
  STAGE IA               0               1
  STAGE II               4              28
  STAGE IIA             16             122
  STAGE IIB              2               8
  STAGE IIC              1               0
  STAGE III              1              23
  STAGE IIIA             1              10
  STAGE IIIB             5              54
  STAGE IIIC             3              39
  STAGE IV               1              47
  STAGE IVA              2              16
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ALPK2 MUTATED     0  11  30   5
  ALPK2 WILD-TYPE  17  81 299  45
D45V5, multiclass
    clus
vv   ALPK2 MUTATED ALPK2 WILD-TYPE
  T1             0              17
  T2            11              81
  T3            30             299
  T4             5              45
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  ALPK2 MUTATED    35   9   2
  ALPK2 WILD-TYPE 252 104  85
D45V6, multiclass
    clus
vv   ALPK2 MUTATED ALPK2 WILD-TYPE
  N0            35             252
  N1             9             104
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V7, binary
                 cls
clus                0   1
  ALPK2 MUTATED    36   3
  ALPK2 WILD-TYPE 339  62
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ALPK2 MUTATED     36    3
  ALPK2 WILD-TYPE  339   62
   clus
vv  ALPK2 MUTATED ALPK2 WILD-TYPE
  0            36             339
  1             3              62
[1] 2 2
[1] FALSE
D45V8, binary
                 cls
clus                0   1
  ALPK2 MUTATED    20  26
  ALPK2 WILD-TYPE 205 238
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ALPK2 MUTATED     20   26
  ALPK2 WILD-TYPE  205  238
        clus
vv       ALPK2 MUTATED ALPK2 WILD-TYPE
  FEMALE            20             205
  MALE              26             238
[1] 2 2
[1] FALSE
D45V9, binary
                 cls
clus                0   1
  ALPK2 MUTATED    37   2
  ALPK2 WILD-TYPE 313  20
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ALPK2 MUTATED     37    2
  ALPK2 WILD-TYPE  313   20
     clus
vv    ALPK2 MUTATED ALPK2 WILD-TYPE
  NO             37             313
  YES             2              20
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ALPK2 MUTATED                     33                             9
  ALPK2 WILD-TYPE                  282                            38
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ALPK2 MUTATED                       4                              0
  ALPK2 WILD-TYPE                   102                             10
D45V10, multiclass
                                clus
vv                               ALPK2 MUTATED ALPK2 WILD-TYPE
  COLON ADENOCARCINOMA                      33             282
  COLON MUCINOUS ADENOCARCINOMA              9              38
  RECTAL ADENOCARCINOMA                      4             102
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  ALPK2 MUTATED    31   0   1   4
  ALPK2 WILD-TYPE 314   4  30  21
D45V11, multiclass
    clus
vv   ALPK2 MUTATED ALPK2 WILD-TYPE
  R0            31             314
  R1             0               4
  R2             1              30
  RX             4              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ALPK2 MUTATED                                  0     3
  ALPK2 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ALPK2 MUTATED                           5    25
  ALPK2 WILD-TYPE                        17   201
D45V13, multiclass
                                  clus
vv                                 ALPK2 MUTATED ALPK2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        3               8
  BLACK OR AFRICAN AMERICAN                    5              17
  WHITE                                       25             201
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(46) Variable = ASXL1 MUTATION ANALYSIS
D46V1, survival
                 sevent
clus2               0   1
  ASXL1 MUTATED    32  13
  ASXL1 WILD-TYPE 346  80
  ASXL1 MUTATED ASXL1 WILD-TYPE 
             45             426 
  ASXL1 MUTATED ASXL1 WILD-TYPE 
             13              80 
$`ASXL1 MUTATED`
TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5665 TCGA-AA-3510 TCGA-AA-3542 TCGA-AA-3561 
       31.63        29.19        22.06        63.98        12.99        13.94 
TCGA-AA-3672 TCGA-AA-3680 TCGA-AA-3715 TCGA-AA-3864 TCGA-AA-A00E TCGA-AA-A010 
        0.92        11.01        19.04        53.00        30.02        34.98 
TCGA-AD-5900 TCGA-AD-6901 TCGA-AD-6964 TCGA-AU-6004 TCGA-AZ-4315 TCGA-AZ-4323 
        0.07        22.42        10.88        27.09        58.39         1.41 
TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-CA-6718 TCGA-CA-6719 TCGA-CM-5860 
       88.21         6.77       100.01        10.06        14.30        32.02 
TCGA-CM-5861 TCGA-CM-6164 TCGA-CM-6170 TCGA-CM-6172 TCGA-D5-5540 TCGA-D5-6535 
       15.02        29.03        15.02        11.01        56.09        15.12 
TCGA-DM-A282 TCGA-DM-A28F TCGA-F4-6570 TCGA-F4-6806 TCGA-F4-6809 TCGA-G4-6304 
      139.17        35.97         6.18        41.42        13.25        53.62 
TCGA-G4-6323 TCGA-G4-6626 TCGA-G4-6628 TCGA-AG-3892 TCGA-CI-6619 TCGA-DC-5337 
       13.78        46.75        79.69        13.02         6.05        15.02 
TCGA-DC-6681 TCGA-DY-A1DD TCGA-F5-6571 
        5.95        57.24        31.30 

$`ASXL1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 
       32.91        30.44        33.53        23.61        22.09        32.71 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       27.09        22.52         8.38        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 
       20.28         7.04         3.02         1.02        35.01         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3543 TCGA-AA-3544 
       34.03        29.00        29.00        26.01         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       23.01        20.98        19.99        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
        6.05         6.97        54.02         2.01        14.01        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       47.01        15.02         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        31.07        30.05        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00F 
        7.96        27.02        13.94        38.04        19.00        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 
        0.92        41.00        39.98        18.05        40.96        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6963 
       15.52        56.55         0.79         0.72         5.79        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
        0.20        14.50        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6598 
       17.82         5.13       106.75        22.36        62.79        49.41 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
       12.10        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       12.76        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       22.03        22.98        30.08         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6165 TCGA-CM-6166 
       17.03        15.02        12.00         2.96        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 
       14.99        12.99        13.02        14.04        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       12.26        19.59        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       43.27        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
       44.32       131.51       135.65         6.12        81.37       119.93 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6854 
       47.87         1.55        34.42        16.24        33.67         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 
       47.41        35.31       133.18        74.56        65.85        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       35.80        26.17        91.79        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 
       19.99         1.02        17.95        36.95        17.03        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6620 
       38.56         1.45        17.49         0.69         0.72        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5869 TCGA-DC-6155 
        6.97         4.73        78.12         7.17         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       27.95        10.98        19.99         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
      126.44        41.36        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  ASXL1 MUTATED ASXL1 WILD-TYPE 
           0.07            0.00 
  ASXL1 MUTATED ASXL1 WILD-TYPE 
         139.17          148.01 
  ASXL1 MUTATED ASXL1 WILD-TYPE 
         22.060          20.155 
[1] "0.1 - 139.2 (22.1)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.3"
D46V2, continuous
D46V3, binary
                 cls
clus                0   1
  ASXL1 MUTATED    40   6
  ASXL1 WILD-TYPE 326 113
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASXL1 MUTATED     40    6
  ASXL1 WILD-TYPE  326  113
        clus
vv       ASXL1 MUTATED ASXL1 WILD-TYPE
  COLON             40             326
  RECTUM             6             113
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ASXL1 MUTATED        10        1        4        14         2         0
  ASXL1 WILD-TYPE      81        0       28       124         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ASXL1 MUTATED           1          0          5          2        3         2
  ASXL1 WILD-TYPE        23         11         54         40       45        16
                 vv
clus              STAGE IVB
  ASXL1 MUTATED           0
  ASXL1 WILD-TYPE         1
D46V4, multiclass
            clus
vv           ASXL1 MUTATED ASXL1 WILD-TYPE
  STAGE I               10              81
  STAGE IA               1               0
  STAGE II               4              28
  STAGE IIA             14             124
  STAGE IIB              2               8
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             5              54
  STAGE IIIC             2              40
  STAGE IV               3              45
  STAGE IVA              2              16
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ASXL1 MUTATED     3   7  30   5
  ASXL1 WILD-TYPE  14  85 299  45
D46V5, multiclass
    clus
vv   ASXL1 MUTATED ASXL1 WILD-TYPE
  T1             3              14
  T2             7              85
  T3            30             299
  T4             5              45
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  ASXL1 MUTATED    32   8   6
  ASXL1 WILD-TYPE 255 105  81
D46V6, multiclass
    clus
vv   ASXL1 MUTATED ASXL1 WILD-TYPE
  N0            32             255
  N1             8             105
  N2             6              81
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V7, binary
                 cls
clus                0   1
  ASXL1 MUTATED    34   5
  ASXL1 WILD-TYPE 341  60
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASXL1 MUTATED     34    5
  ASXL1 WILD-TYPE  341   60
   clus
vv  ASXL1 MUTATED ASXL1 WILD-TYPE
  0            34             341
  1             5              60
[1] 2 2
[1] FALSE
D46V8, binary
                 cls
clus                0   1
  ASXL1 MUTATED    20  26
  ASXL1 WILD-TYPE 205 238
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASXL1 MUTATED     20   26
  ASXL1 WILD-TYPE  205  238
        clus
vv       ASXL1 MUTATED ASXL1 WILD-TYPE
  FEMALE            20             205
  MALE              26             238
[1] 2 2
[1] FALSE
D46V9, binary
                 cls
clus                0   1
  ASXL1 MUTATED    38   0
  ASXL1 WILD-TYPE 312  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASXL1 MUTATED     38    0
  ASXL1 WILD-TYPE  312   22
     clus
vv    ASXL1 MUTATED ASXL1 WILD-TYPE
  NO             38             312
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ASXL1 MUTATED                     39                             1
  ASXL1 WILD-TYPE                  276                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ASXL1 MUTATED                       6                              0
  ASXL1 WILD-TYPE                   100                             10
D46V10, multiclass
                                clus
vv                               ASXL1 MUTATED ASXL1 WILD-TYPE
  COLON ADENOCARCINOMA                      39             276
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      6             100
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  ASXL1 MUTATED    30   0   1   4
  ASXL1 WILD-TYPE 315   4  30  21
D46V11, multiclass
    clus
vv   ASXL1 MUTATED ASXL1 WILD-TYPE
  R0            30             315
  R1             0               4
  R2             1              30
  RX             4              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ASXL1 MUTATED                                  0     2
  ASXL1 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ASXL1 MUTATED                           3    31
  ASXL1 WILD-TYPE                        19   195
D46V13, multiclass
                                  clus
vv                                 ASXL1 MUTATED ASXL1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               9
  BLACK OR AFRICAN AMERICAN                    3              19
  WHITE                                       31             195
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(47) Variable = ALG12 MUTATION ANALYSIS
D47V1, survival
                 sevent
clus2               0   1
  ALG12 MUTATED     5   2
  ALG12 WILD-TYPE 373  91
  ALG12 MUTATED ALG12 WILD-TYPE 
              7             464 
  ALG12 MUTATED ALG12 WILD-TYPE 
              2              91 
$`ALG12 MUTATED`
TCGA-AA-3713 TCGA-AA-3989 TCGA-AA-A00J TCGA-AZ-6598 TCGA-CM-4746 TCGA-CM-5861 
       19.04         7.96        18.05        49.41        37.02        15.02 
TCGA-DM-A1HB 
      135.65 

$`ALG12 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        27.02        19.07        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       19.00        30.02        34.03        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        88.21         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
      124.27        23.05        20.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 
       22.03        22.98        30.08        32.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
       44.32       131.51       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  ALG12 MUTATED ALG12 WILD-TYPE 
           7.96            0.00 
  ALG12 MUTATED ALG12 WILD-TYPE 
         135.65          148.01 
  ALG12 MUTATED ALG12 WILD-TYPE 
         19.040          20.235 
[1] "8.0 - 135.7 (19.0)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1"  
D47V2, continuous
D47V3, binary
                 cls
clus                0   1
  ALG12 MUTATED     7   0
  ALG12 WILD-TYPE 359 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ALG12 MUTATED      7    0
  ALG12 WILD-TYPE  359  119
        clus
vv       ALG12 MUTATED ALG12 WILD-TYPE
  COLON              7             359
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ALG12 MUTATED         1        0        1         1         0         0
  ALG12 WILD-TYPE      90        1       31       137        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ALG12 MUTATED           0          0          2          0        2         0
  ALG12 WILD-TYPE        24         11         57         42       46        18
                 vv
clus              STAGE IVB
  ALG12 MUTATED           0
  ALG12 WILD-TYPE         1
D47V4, multiclass
            clus
vv           ALG12 MUTATED ALG12 WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              1             137
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             2              57
  STAGE IIIC             0              42
  STAGE IV               2              46
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ALG12 MUTATED     0   1   5   1
  ALG12 WILD-TYPE  17  91 324  49
D47V5, multiclass
    clus
vv   ALG12 MUTATED ALG12 WILD-TYPE
  T1             0              17
  T2             1              91
  T3             5             324
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  ALG12 MUTATED     4   2   1
  ALG12 WILD-TYPE 283 111  86
D47V6, multiclass
    clus
vv   ALG12 MUTATED ALG12 WILD-TYPE
  N0             4             283
  N1             2             111
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V7, binary
                 cls
clus                0   1
  ALG12 MUTATED     4   2
  ALG12 WILD-TYPE 371  63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ALG12 MUTATED      4    2
  ALG12 WILD-TYPE  371   63
   clus
vv  ALG12 MUTATED ALG12 WILD-TYPE
  0             4             371
  1             2              63
[1] 2 2
[1] FALSE
D47V8, binary
                 cls
clus                0   1
  ALG12 MUTATED     2   5
  ALG12 WILD-TYPE 223 259
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ALG12 MUTATED      2    5
  ALG12 WILD-TYPE  223  259
        clus
vv       ALG12 MUTATED ALG12 WILD-TYPE
  FEMALE             2             223
  MALE               5             259
[1] 2 2
[1] FALSE
D47V9, binary
                 cls
clus                0   1
  ALG12 MUTATED     5   1
  ALG12 WILD-TYPE 345  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ALG12 MUTATED      5    1
  ALG12 WILD-TYPE  345   21
     clus
vv    ALG12 MUTATED ALG12 WILD-TYPE
  NO              5             345
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ALG12 MUTATED                      5                             1
  ALG12 WILD-TYPE                  310                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ALG12 MUTATED                       0                              0
  ALG12 WILD-TYPE                   106                             10
D47V10, multiclass
                                clus
vv                               ALG12 MUTATED ALG12 WILD-TYPE
  COLON ADENOCARCINOMA                       5             310
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  ALG12 MUTATED     3   0   2   0
  ALG12 WILD-TYPE 342   4  29  25
D47V11, multiclass
    clus
vv   ALG12 MUTATED ALG12 WILD-TYPE
  R0             3             342
  R1             0               4
  R2             2              29
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ALG12 MUTATED                                  0     0
  ALG12 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ALG12 MUTATED                           1     3
  ALG12 WILD-TYPE                        21   223
D47V13, multiclass
                                  clus
vv                                 ALG12 MUTATED ALG12 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        3             223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(48) Variable = PTCH1 MUTATION ANALYSIS
D48V1, survival
                 sevent
clus2               0   1
  PTCH1 MUTATED    80  21
  PTCH1 WILD-TYPE 298  72
  PTCH1 MUTATED PTCH1 WILD-TYPE 
            101             370 
  PTCH1 MUTATED PTCH1 WILD-TYPE 
             21              72 
$`PTCH1 MUTATED`
TCGA-A6-3809 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6649 
       32.75        29.19        23.61        22.09        22.06        24.16 
TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6781 TCGA-AA-3543 TCGA-AA-3554 TCGA-AA-3660 
       24.69        23.87        19.66         0.99        17.95        78.08 
TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3950 
       85.05        19.04        19.04        30.05        53.00        24.00 
TCGA-AA-A00R TCGA-AA-A010 TCGA-AA-A01P TCGA-AA-A01R TCGA-AA-A02K TCGA-AD-5900 
        0.99        34.98        38.07        35.01        14.01         0.07 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6901 TCGA-AD-6964 TCGA-AU-3779 TCGA-AU-6004 
       56.55         0.79        22.42        10.88        14.50        27.09 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6601 
       33.01        21.44        58.39        88.21         6.77       100.01 
TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 TCGA-CM-4743 TCGA-CM-4752 
      148.01        15.62        49.08         9.99        23.05        13.02 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-6164 
       22.03        22.98        30.08        32.02        15.02        29.03 
TCGA-CM-6168 TCGA-CM-6172 TCGA-CM-6676 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       12.99        11.01        11.08        45.40        12.26        19.59 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       18.25         1.32        43.27        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6929 
       12.49        16.14        15.58        14.30         9.44         4.80 
TCGA-D5-6930 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A1D4 TCGA-DM-A1D8 TCGA-DM-A1DA 
        1.51       119.70        24.43        92.75        12.59         7.50 
TCGA-DM-A1DB TCGA-DM-A285 TCGA-DM-A28F TCGA-DM-A28K TCGA-F4-6570 TCGA-G4-6304 
       44.32         6.12        35.97        98.24         6.18        53.62 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       55.04        85.48        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-6672 TCGA-AG-3732 
       35.80        26.17        46.75        24.13        10.39        32.98 
TCGA-AG-3742 TCGA-AG-A002 TCGA-DC-5337 TCGA-DC-6155 TCGA-DC-6160 TCGA-DC-6682 
        0.99        20.98        15.02        13.97        19.99         4.01 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-F5-6465 
       51.48        32.61         0.49        20.55        49.51 

$`PTCH1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 
       31.63        30.44        33.53        32.71        27.09        22.52 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6780 
        8.38        25.08        25.18        21.76        24.39        20.12 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3555 
       14.01        33.99        21.01        13.02        24.00        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
       19.00        36.00         5.03        26.99        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       31.07        31.07        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       26.01         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00U 
       18.05        38.04         4.01        27.02        42.02        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       31.00        31.00         1.02         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
        5.03         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6965 
       21.37        15.52         0.72         5.79        27.42         0.20 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       16.31         0.95        17.82         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 
       22.36        62.79        49.41        12.10        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       17.56        85.45        51.32        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-5341 TCGA-CM-5862 
      124.27        20.02        37.02        25.02        29.06         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       16.04        21.99        14.99        13.02        15.02        14.04 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       12.95        13.05        11.08        11.01        10.06        12.03 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6535 TCGA-D5-6898 TCGA-D5-6920 
       56.09        55.92        20.19        15.12         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6931 TCGA-D5-6932 
        4.41        12.43         9.04        11.64        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D9 
       10.26        38.20       130.65        49.91        13.32       140.38 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G 
      131.51       135.65       139.17        81.37       119.93        60.79 
TCGA-DM-A28H TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 
      117.07         8.61        31.96        35.74        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 
       47.41        35.31       133.18        74.56        65.85        44.68 
TCGA-G4-6310 TCGA-G4-6625 TCGA-G4-6628 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       63.62        91.79        79.69        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       20.02        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5869 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6681 TCGA-DC-6683 
        7.17         5.03        27.95        10.98         5.95         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-EI-6507 
        5.29       126.44        41.36        57.24        24.13        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       20.91        18.28         9.96        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  PTCH1 MUTATED PTCH1 WILD-TYPE 
           0.07            0.00 
  PTCH1 MUTATED PTCH1 WILD-TYPE 
         148.01          140.38 
  PTCH1 MUTATED PTCH1 WILD-TYPE 
          22.09           19.99 
[1] "0.1 - 148.0 (22.1)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1.1"
D48V2, continuous
D48V3, binary
                 cls
clus                0   1
  PTCH1 MUTATED    89  14
  PTCH1 WILD-TYPE 277 105
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTCH1 MUTATED     89   14
  PTCH1 WILD-TYPE  277  105
        clus
vv       PTCH1 MUTATED PTCH1 WILD-TYPE
  COLON             89             277
  RECTUM            14             105
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PTCH1 MUTATED        14        1        4        35         5         0
  PTCH1 WILD-TYPE      77        0       28       103         5         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PTCH1 MUTATED           5          4         13          8        6         4
  PTCH1 WILD-TYPE        19          7         46         34       42        14
                 vv
clus              STAGE IVB
  PTCH1 MUTATED           0
  PTCH1 WILD-TYPE         1
D48V4, multiclass
            clus
vv           PTCH1 MUTATED PTCH1 WILD-TYPE
  STAGE I               14              77
  STAGE IA               1               0
  STAGE II               4              28
  STAGE IIA             35             103
  STAGE IIB              5               5
  STAGE IIC              0               1
  STAGE III              5              19
  STAGE IIIA             4               7
  STAGE IIIB            13              46
  STAGE IIIC             8              34
  STAGE IV               6              42
  STAGE IVA              4              14
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PTCH1 MUTATED     4  14  72  12
  PTCH1 WILD-TYPE  13  78 257  38
D48V5, multiclass
    clus
vv   PTCH1 MUTATED PTCH1 WILD-TYPE
  T1             4              13
  T2            14              78
  T3            72             257
  T4            12              38
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  PTCH1 MUTATED    65  23  15
  PTCH1 WILD-TYPE 222  90  72
D48V6, multiclass
    clus
vv   PTCH1 MUTATED PTCH1 WILD-TYPE
  N0            65             222
  N1            23              90
  N2            15              72
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V7, binary
                 cls
clus                0   1
  PTCH1 MUTATED    75   9
  PTCH1 WILD-TYPE 300  56
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTCH1 MUTATED     75    9
  PTCH1 WILD-TYPE  300   56
   clus
vv  PTCH1 MUTATED PTCH1 WILD-TYPE
  0            75             300
  1             9              56
[1] 2 2
[1] FALSE
D48V8, binary
                 cls
clus                0   1
  PTCH1 MUTATED    46  57
  PTCH1 WILD-TYPE 179 207
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTCH1 MUTATED     46   57
  PTCH1 WILD-TYPE  179  207
        clus
vv       PTCH1 MUTATED PTCH1 WILD-TYPE
  FEMALE            46             179
  MALE              57             207
[1] 2 2
[1] FALSE
D48V9, binary
                 cls
clus                0   1
  PTCH1 MUTATED    72   4
  PTCH1 WILD-TYPE 278  18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTCH1 MUTATED     72    4
  PTCH1 WILD-TYPE  278   18
     clus
vv    PTCH1 MUTATED PTCH1 WILD-TYPE
  NO             72             278
  YES             4              18
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PTCH1 MUTATED                     75                            14
  PTCH1 WILD-TYPE                  240                            33
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PTCH1 MUTATED                      14                              0
  PTCH1 WILD-TYPE                    92                             10
D48V10, multiclass
                                clus
vv                               PTCH1 MUTATED PTCH1 WILD-TYPE
  COLON ADENOCARCINOMA                      75             240
  COLON MUCINOUS ADENOCARCINOMA             14              33
  RECTAL ADENOCARCINOMA                     14              92
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  PTCH1 MUTATED    71   0   2   5
  PTCH1 WILD-TYPE 274   4  29  20
D48V11, multiclass
    clus
vv   PTCH1 MUTATED PTCH1 WILD-TYPE
  R0            71             274
  R1             0               4
  R2             2              29
  RX             5              20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PTCH1 MUTATED                                  0     1
  PTCH1 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PTCH1 MUTATED                           8    77
  PTCH1 WILD-TYPE                        14   149
D48V13, multiclass
                                  clus
vv                                 PTCH1 MUTATED PTCH1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    8              14
  WHITE                                       77             149
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(49) Variable = GRB2 MUTATION ANALYSIS
D49V1, survival
                sevent
clus2              0   1
  GRB2 MUTATED     7   3
  GRB2 WILD-TYPE 371  90
  GRB2 MUTATED GRB2 WILD-TYPE 
            10            461 
  GRB2 MUTATED GRB2 WILD-TYPE 
             3             90 
$`GRB2 MUTATED`
TCGA-A6-5661 TCGA-AA-3543 TCGA-AA-A00N TCGA-AD-6964 TCGA-AY-6197 TCGA-D5-6538 
       33.53         0.99         4.01        10.88        21.44        17.13 
TCGA-DM-A1DA TCGA-G4-6625 TCGA-AF-6136 TCGA-AG-A002 
        7.50        91.79        15.39        20.98 

$`GRB2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       26.01        12.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
        0.79         0.72         5.79        22.42        27.42         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 
       14.50        27.09        16.31         0.95        33.01        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6539 TCGA-D5-6540 
       43.27        15.12        17.85         4.80        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB 
       92.75        49.91        13.32        12.59       140.38        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       35.80        26.17        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       16.83        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  GRB2 MUTATED GRB2 WILD-TYPE 
          0.99           0.00 
  GRB2 MUTATED GRB2 WILD-TYPE 
         91.79         148.01 
  GRB2 MUTATED GRB2 WILD-TYPE 
         16.26          20.28 
[1] "1.0 - 91.8 (16.3)"  "0.0 - 148.0 (20.3)"
[1] "hr=" "1.9"
D49V2, continuous
D49V3, binary
                cls
clus               0   1
  GRB2 MUTATED     9   2
  GRB2 WILD-TYPE 357 117
[1] "tbl2"
                cls
clus             [,1] [,2]
  GRB2 MUTATED      9    2
  GRB2 WILD-TYPE  357  117
        clus
vv       GRB2 MUTATED GRB2 WILD-TYPE
  COLON             9            357
  RECTUM            2            117
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GRB2 MUTATED         2        0        0         3         1         0
  GRB2 WILD-TYPE      89        1       32       135         9         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  GRB2 MUTATED           1          0          2          1        0         0
  GRB2 WILD-TYPE        23         11         57         41       48        18
                vv
clus             STAGE IVB
  GRB2 MUTATED           0
  GRB2 WILD-TYPE         1
D49V4, multiclass
            clus
vv           GRB2 MUTATED GRB2 WILD-TYPE
  STAGE I               2             89
  STAGE IA              0              1
  STAGE II              0             32
  STAGE IIA             3            135
  STAGE IIB             1              9
  STAGE IIC             0              1
  STAGE III             1             23
  STAGE IIIA            0             11
  STAGE IIIB            2             57
  STAGE IIIC            1             41
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  GRB2 MUTATED     0   2   7   2
  GRB2 WILD-TYPE  17  90 322  48
D49V5, multiclass
    clus
vv   GRB2 MUTATED GRB2 WILD-TYPE
  T1            0             17
  T2            2             90
  T3            7            322
  T4            2             48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  GRB2 MUTATED     6   1   4
  GRB2 WILD-TYPE 281 112  83
D49V6, multiclass
    clus
vv   GRB2 MUTATED GRB2 WILD-TYPE
  N0            6            281
  N1            1            112
  N2            4             83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V7, binary
                cls
clus               0   1
  GRB2 MUTATED     8   0
  GRB2 WILD-TYPE 367  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  GRB2 MUTATED      8    0
  GRB2 WILD-TYPE  367   65
   clus
vv  GRB2 MUTATED GRB2 WILD-TYPE
  0            8            367
  1            0             65
[1] 2 2
[1] FALSE
D49V8, binary
                cls
clus               0   1
  GRB2 MUTATED     5   6
  GRB2 WILD-TYPE 220 258
[1] "tbl2"
                cls
clus             [,1] [,2]
  GRB2 MUTATED      5    6
  GRB2 WILD-TYPE  220  258
        clus
vv       GRB2 MUTATED GRB2 WILD-TYPE
  FEMALE            5            220
  MALE              6            258
[1] 2 2
[1] FALSE
D49V9, binary
                cls
clus               0   1
  GRB2 MUTATED     7   1
  GRB2 WILD-TYPE 343  21
[1] "tbl2"
                cls
clus             [,1] [,2]
  GRB2 MUTATED      7    1
  GRB2 WILD-TYPE  343   21
     clus
vv    GRB2 MUTATED GRB2 WILD-TYPE
  NO             7            343
  YES            1             21
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  GRB2 MUTATED                      7                             2
  GRB2 WILD-TYPE                  308                            45
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  GRB2 MUTATED                       2                              0
  GRB2 WILD-TYPE                   104                             10
D49V10, multiclass
                                clus
vv                               GRB2 MUTATED GRB2 WILD-TYPE
  COLON ADENOCARCINOMA                      7            308
  COLON MUCINOUS ADENOCARCINOMA             2             45
  RECTAL ADENOCARCINOMA                     2            104
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  GRB2 MUTATED     8   0   0   0
  GRB2 WILD-TYPE 337   4  31  25
D49V11, multiclass
    clus
vv   GRB2 MUTATED GRB2 WILD-TYPE
  R0            8            337
  R1            0              4
  R2            0             31
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GRB2 MUTATED                                  0     0
  GRB2 WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  GRB2 MUTATED                           1     6
  GRB2 WILD-TYPE                        21   220
D49V13, multiclass
                                  clus
vv                                 GRB2 MUTATED GRB2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                       6            220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(50) Variable = NLRC4 MUTATION ANALYSIS
D50V1, survival
                 sevent
clus2               0   1
  NLRC4 MUTATED    21   4
  NLRC4 WILD-TYPE 357  89
  NLRC4 MUTATED NLRC4 WILD-TYPE 
             25             446 
  NLRC4 MUTATED NLRC4 WILD-TYPE 
              4              89 
$`NLRC4 MUTATED`
TCGA-A6-6141 TCGA-A6-6781 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3966 
        8.38        19.66        85.05        19.04        19.04         2.01 
TCGA-AA-3977 TCGA-AA-A010 TCGA-AD-6895 TCGA-AD-6901 TCGA-AU-3779 TCGA-CA-5796 
       25.02        34.98         0.72        22.42        14.50         3.25 
TCGA-CA-6717 TCGA-CK-5916 TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-5349 TCGA-D5-6536 
       12.76        21.14        13.02        22.03        30.08        17.85 
TCGA-D5-6928 TCGA-DM-A1DA TCGA-G4-6293 TCGA-G4-6317 TCGA-G4-6588 TCGA-AG-3892 
       11.64         7.50       133.18        36.00        26.17        13.02 
TCGA-AG-A002 
       20.98 

$`NLRC4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 
       22.09        22.06        32.71        27.09        22.52        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
        5.03        26.99        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 
       26.01        24.00         2.01        20.98        34.03        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
       56.55         0.79         5.79        27.42        10.88         0.20 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07        12.20        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       25.02        29.06        22.98        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       43.27        15.12         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.04         9.44         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA 
       49.91        13.32        12.59       140.38        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6299 
       33.67        13.25         0.53        47.41        35.31        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 
       61.91        22.09        13.78        35.80        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       17.95        36.95        17.03        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  NLRC4 MUTATED NLRC4 WILD-TYPE 
           0.72            0.00 
  NLRC4 MUTATED NLRC4 WILD-TYPE 
         133.18          148.01 
  NLRC4 MUTATED NLRC4 WILD-TYPE 
         19.040          20.415 
[1] "0.7 - 133.2 (19.0)" "0.0 - 148.0 (20.4)"
[1] "hr=" "1.1"
D50V2, continuous
D50V3, binary
                 cls
clus                0   1
  NLRC4 MUTATED    24   2
  NLRC4 WILD-TYPE 342 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NLRC4 MUTATED     24    2
  NLRC4 WILD-TYPE  342  117
        clus
vv       NLRC4 MUTATED NLRC4 WILD-TYPE
  COLON             24             342
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NLRC4 MUTATED         3        0        1        10         1         0
  NLRC4 WILD-TYPE      88        1       31       128         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NLRC4 MUTATED           2          0          1          4        1         0
  NLRC4 WILD-TYPE        22         11         58         38       47        18
                 vv
clus              STAGE IVB
  NLRC4 MUTATED           0
  NLRC4 WILD-TYPE         1
D50V4, multiclass
            clus
vv           NLRC4 MUTATED NLRC4 WILD-TYPE
  STAGE I                3              88
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA             10             128
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              2              22
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             4              38
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  NLRC4 MUTATED     2   2  20   2
  NLRC4 WILD-TYPE  15  90 309  48
D50V5, multiclass
    clus
vv   NLRC4 MUTATED NLRC4 WILD-TYPE
  T1             2              15
  T2             2              90
  T3            20             309
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  NLRC4 MUTATED    19   4   3
  NLRC4 WILD-TYPE 268 109  84
D50V6, multiclass
    clus
vv   NLRC4 MUTATED NLRC4 WILD-TYPE
  N0            19             268
  N1             4             109
  N2             3              84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V7, binary
                 cls
clus                0   1
  NLRC4 MUTATED    19   1
  NLRC4 WILD-TYPE 356  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NLRC4 MUTATED     19    1
  NLRC4 WILD-TYPE  356   64
   clus
vv  NLRC4 MUTATED NLRC4 WILD-TYPE
  0            19             356
  1             1              64
[1] 2 2
[1] FALSE
D50V8, binary
                 cls
clus                0   1
  NLRC4 MUTATED    12  14
  NLRC4 WILD-TYPE 213 250
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NLRC4 MUTATED     12   14
  NLRC4 WILD-TYPE  213  250
        clus
vv       NLRC4 MUTATED NLRC4 WILD-TYPE
  FEMALE            12             213
  MALE              14             250
[1] 2 2
[1] FALSE
D50V9, binary
                 cls
clus                0   1
  NLRC4 MUTATED    21   1
  NLRC4 WILD-TYPE 329  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NLRC4 MUTATED     21    1
  NLRC4 WILD-TYPE  329   21
     clus
vv    NLRC4 MUTATED NLRC4 WILD-TYPE
  NO             21             329
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  NLRC4 MUTATED                     18                             6
  NLRC4 WILD-TYPE                  297                            41
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  NLRC4 MUTATED                       2                              0
  NLRC4 WILD-TYPE                   104                             10
D50V10, multiclass
                                clus
vv                               NLRC4 MUTATED NLRC4 WILD-TYPE
  COLON ADENOCARCINOMA                      18             297
  COLON MUCINOUS ADENOCARCINOMA              6              41
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  NLRC4 MUTATED    17   0   1   2
  NLRC4 WILD-TYPE 328   4  30  23
D50V11, multiclass
    clus
vv   NLRC4 MUTATED NLRC4 WILD-TYPE
  R0            17             328
  R1             0               4
  R2             1              30
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NLRC4 MUTATED                                  0     2
  NLRC4 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  NLRC4 MUTATED                           2    14
  NLRC4 WILD-TYPE                        20   212
D50V13, multiclass
                                  clus
vv                                 NLRC4 MUTATED NLRC4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               9
  BLACK OR AFRICAN AMERICAN                    2              20
  WHITE                                       14             212
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(51) Variable = PLAGL2 MUTATION ANALYSIS
D51V1, survival
                  sevent
clus2                0   1
  PLAGL2 MUTATED     5   1
  PLAGL2 WILD-TYPE 373  92
  PLAGL2 MUTATED PLAGL2 WILD-TYPE 
               6              465 
  PLAGL2 MUTATED PLAGL2 WILD-TYPE 
               1               92 
$`PLAGL2 MUTATED`
TCGA-A6-5665 TCGA-AA-3713 TCGA-AY-6197 TCGA-AZ-6598 TCGA-CM-4743 TCGA-G4-6586 
       22.06        19.04        21.44        49.41        23.05        35.80 

$`PLAGL2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       33.01        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        88.21         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
      124.27        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       22.09        13.78        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  PLAGL2 MUTATED PLAGL2 WILD-TYPE 
           19.04             0.00 
  PLAGL2 MUTATED PLAGL2 WILD-TYPE 
           49.41           148.01 
  PLAGL2 MUTATED PLAGL2 WILD-TYPE 
          22.555           20.050 
[1] "19.0 - 49.4 (22.6)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.3"
D51V2, continuous
D51V3, binary
                  cls
clus                 0   1
  PLAGL2 MUTATED     6   0
  PLAGL2 WILD-TYPE 360 119
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PLAGL2 MUTATED      6    0
  PLAGL2 WILD-TYPE  360  119
        clus
vv       PLAGL2 MUTATED PLAGL2 WILD-TYPE
  COLON               6              360
  RECTUM              0              119
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PLAGL2 MUTATED         0        0        1         4         0         0
  PLAGL2 WILD-TYPE      91        1       31       134        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PLAGL2 MUTATED           0          0          0          0        1
  PLAGL2 WILD-TYPE        24         11         59         42       47
                  vv
clus               STAGE IVA STAGE IVB
  PLAGL2 MUTATED           0         0
  PLAGL2 WILD-TYPE        18         1
D51V4, multiclass
            clus
vv           PLAGL2 MUTATED PLAGL2 WILD-TYPE
  STAGE I                 0               91
  STAGE IA                0                1
  STAGE II                1               31
  STAGE IIA               4              134
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              0               59
  STAGE IIIC              0               42
  STAGE IV                1               47
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  PLAGL2 MUTATED     0   0   6   0
  PLAGL2 WILD-TYPE  17  92 323  50
D51V5, multiclass
    clus
vv   PLAGL2 MUTATED PLAGL2 WILD-TYPE
  T1              0               17
  T2              0               92
  T3              6              323
  T4              0               50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  PLAGL2 MUTATED     6   0   0
  PLAGL2 WILD-TYPE 281 113  87
D51V6, multiclass
    clus
vv   PLAGL2 MUTATED PLAGL2 WILD-TYPE
  N0              6              281
  N1              0              113
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V7, binary
                  cls
clus                 0   1
  PLAGL2 MUTATED     3   1
  PLAGL2 WILD-TYPE 372  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PLAGL2 MUTATED      3    1
  PLAGL2 WILD-TYPE  372   64
   clus
vv  PLAGL2 MUTATED PLAGL2 WILD-TYPE
  0              3              372
  1              1               64
[1] 2 2
[1] FALSE
D51V8, binary
                  cls
clus                 0   1
  PLAGL2 MUTATED     3   3
  PLAGL2 WILD-TYPE 222 261
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PLAGL2 MUTATED      3    3
  PLAGL2 WILD-TYPE  222  261
        clus
vv       PLAGL2 MUTATED PLAGL2 WILD-TYPE
  FEMALE              3              222
  MALE                3              261
[1] 2 2
[1] FALSE
D51V9, binary
                  cls
clus                 0   1
  PLAGL2 MUTATED     5   1
  PLAGL2 WILD-TYPE 345  21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PLAGL2 MUTATED      5    1
  PLAGL2 WILD-TYPE  345   21
     clus
vv    PLAGL2 MUTATED PLAGL2 WILD-TYPE
  NO               5              345
  YES              1               21
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PLAGL2 MUTATED                      6                             0
  PLAGL2 WILD-TYPE                  309                            47
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PLAGL2 MUTATED                       0                              0
  PLAGL2 WILD-TYPE                   106                             10
D51V10, multiclass
                                clus
vv                               PLAGL2 MUTATED PLAGL2 WILD-TYPE
  COLON ADENOCARCINOMA                        6              309
  COLON MUCINOUS ADENOCARCINOMA               0               47
  RECTAL ADENOCARCINOMA                       0              106
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  PLAGL2 MUTATED     4   0   1   0
  PLAGL2 WILD-TYPE 341   4  30  25
D51V11, multiclass
    clus
vv   PLAGL2 MUTATED PLAGL2 WILD-TYPE
  R0              4              341
  R1              0                4
  R2              1               30
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PLAGL2 MUTATED                                  0     0
  PLAGL2 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  PLAGL2 MUTATED                           0     5
  PLAGL2 WILD-TYPE                        22   221
D51V13, multiclass
                                  clus
vv                                 PLAGL2 MUTATED PLAGL2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         5              221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(52) Variable = C11ORF30 MUTATION ANALYSIS
D52V1, survival
                    sevent
clus2                  0   1
  C11ORF30 MUTATED    19   3
  C11ORF30 WILD-TYPE 359  90
  C11ORF30 MUTATED C11ORF30 WILD-TYPE 
                22                449 
  C11ORF30 MUTATED C11ORF30 WILD-TYPE 
                 3                 90 
$`C11ORF30 MUTATED`
TCGA-A6-5665 TCGA-A6-6780 TCGA-AA-3554 TCGA-AA-3672 TCGA-AA-3947 TCGA-AA-3949 
       22.06        20.12        17.95         0.92        33.01        26.01 
TCGA-AA-3977 TCGA-AA-A00N TCGA-AD-6889 TCGA-AD-6895 TCGA-AZ-4315 TCGA-AZ-6599 
       25.02         4.01        56.55         0.72        58.39         6.77 
TCGA-CA-6715 TCGA-CA-6717 TCGA-CM-6161 TCGA-D5-6541 TCGA-D5-6927 TCGA-DM-A0XD 
        0.07        12.76        15.02        15.58         9.44        24.43 
TCGA-F4-6807 TCGA-G4-6586 TCGA-AG-A002 TCGA-F5-6702 
       16.24        35.80        20.98        28.57 

$`C11ORF30 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       24.00        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
        2.01        14.01        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.79         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       88.21        49.41        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        3.29        12.20        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       17.13        12.49        16.14         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       12.43        14.30         9.04        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XF TCGA-DM-A1D0 
       12.00        11.38        10.26       119.70        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       41.42        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  C11ORF30 MUTATED C11ORF30 WILD-TYPE 
              0.07               0.00 
  C11ORF30 MUTATED C11ORF30 WILD-TYPE 
             58.39             148.01 
  C11ORF30 MUTATED C11ORF30 WILD-TYPE 
            19.035             20.280 
[1] "0.1 - 58.4 (19.0)"  "0.0 - 148.0 (20.3)"
[1] "hr=" "1.1"
D52V2, continuous
D52V3, binary
                    cls
clus                   0   1
  C11ORF30 MUTATED    21   2
  C11ORF30 WILD-TYPE 345 117
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C11ORF30 MUTATED     21    2
  C11ORF30 WILD-TYPE  345  117
        clus
vv       C11ORF30 MUTATED C11ORF30 WILD-TYPE
  COLON                21                345
  RECTUM                2                117
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  C11ORF30 MUTATED         3        0        0        11         2         0
  C11ORF30 WILD-TYPE      88        1       32       127         8         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C11ORF30 MUTATED           1          0          2          1        0
  C11ORF30 WILD-TYPE        23         11         57         41       48
                    vv
clus                 STAGE IVA STAGE IVB
  C11ORF30 MUTATED           1         0
  C11ORF30 WILD-TYPE        17         1
D52V4, multiclass
            clus
vv           C11ORF30 MUTATED C11ORF30 WILD-TYPE
  STAGE I                   3                 88
  STAGE IA                  0                  1
  STAGE II                  0                 32
  STAGE IIA                11                127
  STAGE IIB                 2                  8
  STAGE IIC                 0                  1
  STAGE III                 1                 23
  STAGE IIIA                0                 11
  STAGE IIIB                2                 57
  STAGE IIIC                1                 41
  STAGE IV                  0                 48
  STAGE IVA                 1                 17
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  C11ORF30 MUTATED     0   4  17   2
  C11ORF30 WILD-TYPE  17  88 312  48
D52V5, multiclass
    clus
vv   C11ORF30 MUTATED C11ORF30 WILD-TYPE
  T1                0                 17
  T2                4                 88
  T3               17                312
  T4                2                 48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  C11ORF30 MUTATED    17   5   1
  C11ORF30 WILD-TYPE 270 108  86
D52V6, multiclass
    clus
vv   C11ORF30 MUTATED C11ORF30 WILD-TYPE
  N0               17                270
  N1                5                108
  N2                1                 86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V7, binary
                    cls
clus                   0   1
  C11ORF30 MUTATED    18   1
  C11ORF30 WILD-TYPE 357  64
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C11ORF30 MUTATED     18    1
  C11ORF30 WILD-TYPE  357   64
   clus
vv  C11ORF30 MUTATED C11ORF30 WILD-TYPE
  0               18                357
  1                1                 64
[1] 2 2
[1] FALSE
D52V8, binary
                    cls
clus                   0   1
  C11ORF30 MUTATED     9  14
  C11ORF30 WILD-TYPE 216 250
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C11ORF30 MUTATED      9   14
  C11ORF30 WILD-TYPE  216  250
        clus
vv       C11ORF30 MUTATED C11ORF30 WILD-TYPE
  FEMALE                9                216
  MALE                 14                250
[1] 2 2
[1] FALSE
D52V9, binary
                    cls
clus                   0   1
  C11ORF30 MUTATED    17   0
  C11ORF30 WILD-TYPE 333  22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C11ORF30 MUTATED     17    0
  C11ORF30 WILD-TYPE  333   22
     clus
vv    C11ORF30 MUTATED C11ORF30 WILD-TYPE
  NO                17                333
  YES                0                 22
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  C11ORF30 MUTATED                     16                             5
  C11ORF30 WILD-TYPE                  299                            42
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  C11ORF30 MUTATED                       2                              0
  C11ORF30 WILD-TYPE                   104                             10
D52V10, multiclass
                                clus
vv                               C11ORF30 MUTATED C11ORF30 WILD-TYPE
  COLON ADENOCARCINOMA                         16                299
  COLON MUCINOUS ADENOCARCINOMA                 5                 42
  RECTAL ADENOCARCINOMA                         2                104
  RECTAL MUCINOUS ADENOCARCINOMA                0                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  C11ORF30 MUTATED    15   0   0   2
  C11ORF30 WILD-TYPE 330   4  31  23
D52V11, multiclass
    clus
vv   C11ORF30 MUTATED C11ORF30 WILD-TYPE
  R0               15                330
  R1                0                  4
  R2                0                 31
  RX                2                 23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C11ORF30 MUTATED                                  0     3
  C11ORF30 WILD-TYPE                                1     8
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  C11ORF30 MUTATED                           0    12
  C11ORF30 WILD-TYPE                        22   214
D52V13, multiclass
                                  clus
vv                                 C11ORF30 MUTATED C11ORF30 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           3                  8
  BLACK OR AFRICAN AMERICAN                       0                 22
  WHITE                                          12                214
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(53) Variable = DIP2B MUTATION ANALYSIS
D53V1, survival
                 sevent
clus2               0   1
  DIP2B MUTATED    25   3
  DIP2B WILD-TYPE 353  90
  DIP2B MUTATED DIP2B WILD-TYPE 
             28             443 
  DIP2B MUTATED DIP2B WILD-TYPE 
              3              90 
$`DIP2B MUTATED`
TCGA-A6-2672 TCGA-A6-5661 TCGA-A6-5665 TCGA-A6-6780 TCGA-AA-3496 TCGA-AA-3517 
       46.65        33.53        22.06        20.12         1.02        38.99 
TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3973 TCGA-AA-A00J TCGA-AA-A00N TCGA-AA-A010 
        6.05         0.92        13.05        18.05         4.01        34.98 
TCGA-AY-5543 TCGA-AZ-4315 TCGA-AZ-5407 TCGA-CA-5254 TCGA-CK-4952 TCGA-D5-6926 
       33.01        58.39        88.21        12.69        15.62         9.04 
TCGA-F4-6570 TCGA-F4-6808 TCGA-G4-6307 TCGA-G4-6315 TCGA-G4-6323 TCGA-G4-6588 
        6.18        33.67        55.04        61.91        13.78        26.17 
TCGA-G4-6626 TCGA-AG-A002 TCGA-F5-6812 TCGA-G5-6235 
       46.75        20.98         0.66        55.76 

$`DIP2B WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 
       31.63        30.44        29.19        23.61        22.09        32.71 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       27.09        22.52         8.38        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 
       21.76        24.69        24.39        23.87        19.66        20.28 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
        7.04         3.02        35.01        63.98         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       13.02         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 
        6.97        54.02         2.01        14.01        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       30.02        34.03        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
       16.31         0.95        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
      106.75        22.36        62.79        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 
       10.06        14.30        17.56       148.01        85.45        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
       14.30         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       31.96        35.74        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       16.24        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6310 
       74.56        65.85        53.62        44.68        85.48        63.62 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-AF-2687 
       36.00        22.09        35.80        91.79        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6813 TCGA-G5-6641 
       31.30        28.57        32.19         0.69        26.43 

  DIP2B MUTATED DIP2B WILD-TYPE 
           0.66            0.00 
  DIP2B MUTATED DIP2B WILD-TYPE 
          88.21          148.01 
  DIP2B MUTATED DIP2B WILD-TYPE 
          21.52           20.05 
[1] "0.7 - 88.2 (21.5)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "2.1"
D53V2, continuous
D53V3, binary
                 cls
clus                0   1
  DIP2B MUTATED    27   3
  DIP2B WILD-TYPE 339 116
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DIP2B MUTATED     27    3
  DIP2B WILD-TYPE  339  116
        clus
vv       DIP2B MUTATED DIP2B WILD-TYPE
  COLON             27             339
  RECTUM             3             116
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DIP2B MUTATED         3        1        1        11         2         0
  DIP2B WILD-TYPE      88        0       31       127         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DIP2B MUTATED           1          0          5          1        4         1
  DIP2B WILD-TYPE        23         11         54         41       44        17
                 vv
clus              STAGE IVB
  DIP2B MUTATED           0
  DIP2B WILD-TYPE         1
D53V4, multiclass
            clus
vv           DIP2B MUTATED DIP2B WILD-TYPE
  STAGE I                3              88
  STAGE IA               1               0
  STAGE II               1              31
  STAGE IIA             11             127
  STAGE IIB              2               8
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             5              54
  STAGE IIIC             1              41
  STAGE IV               4              44
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  DIP2B MUTATED     2   1  18   8
  DIP2B WILD-TYPE  15  91 311  42
D53V5, multiclass
    clus
vv   DIP2B MUTATED DIP2B WILD-TYPE
  T1             2              15
  T2             1              91
  T3            18             311
  T4             8              42
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  DIP2B MUTATED    18   9   3
  DIP2B WILD-TYPE 269 104  84
D53V6, multiclass
    clus
vv   DIP2B MUTATED DIP2B WILD-TYPE
  N0            18             269
  N1             9             104
  N2             3              84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V7, binary
                 cls
clus                0   1
  DIP2B MUTATED    22   5
  DIP2B WILD-TYPE 353  60
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DIP2B MUTATED     22    5
  DIP2B WILD-TYPE  353   60
   clus
vv  DIP2B MUTATED DIP2B WILD-TYPE
  0            22             353
  1             5              60
[1] 2 2
[1] FALSE
D53V8, binary
                 cls
clus                0   1
  DIP2B MUTATED    17  13
  DIP2B WILD-TYPE 208 251
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DIP2B MUTATED     17   13
  DIP2B WILD-TYPE  208  251
        clus
vv       DIP2B MUTATED DIP2B WILD-TYPE
  FEMALE            17             208
  MALE              13             251
[1] 2 2
[1] FALSE
D53V9, binary
                 cls
clus                0   1
  DIP2B MUTATED    23   1
  DIP2B WILD-TYPE 327  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DIP2B MUTATED     23    1
  DIP2B WILD-TYPE  327   21
     clus
vv    DIP2B MUTATED DIP2B WILD-TYPE
  NO             23             327
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  DIP2B MUTATED                     22                             5
  DIP2B WILD-TYPE                  293                            42
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  DIP2B MUTATED                       3                              0
  DIP2B WILD-TYPE                   103                             10
D53V10, multiclass
                                clus
vv                               DIP2B MUTATED DIP2B WILD-TYPE
  COLON ADENOCARCINOMA                      22             293
  COLON MUCINOUS ADENOCARCINOMA              5              42
  RECTAL ADENOCARCINOMA                      3             103
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  DIP2B MUTATED    22   1   3   2
  DIP2B WILD-TYPE 323   3  28  23
D53V11, multiclass
    clus
vv   DIP2B MUTATED DIP2B WILD-TYPE
  R0            22             323
  R1             1               3
  R2             3              28
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DIP2B MUTATED                                  0     1
  DIP2B WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  DIP2B MUTATED                           3    15
  DIP2B WILD-TYPE                        19   211
D53V13, multiclass
                                  clus
vv                                 DIP2B MUTATED DIP2B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    3              19
  WHITE                                       15             211
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(54) Variable = PRRG1 MUTATION ANALYSIS
D54V1, survival
                 sevent
clus2               0   1
  PRRG1 MUTATED    12   2
  PRRG1 WILD-TYPE 366  91
  PRRG1 MUTATED PRRG1 WILD-TYPE 
             14             457 
  PRRG1 MUTATED PRRG1 WILD-TYPE 
              2              91 
$`PRRG1 MUTATED`
TCGA-A6-5661 TCGA-AD-5900 TCGA-AZ-6598 TCGA-CA-6717 TCGA-CK-5913 TCGA-CM-6162 
       33.53         0.07        49.41        12.76        51.32        12.00 
TCGA-CM-6171 TCGA-D5-5538 TCGA-DM-A28K TCGA-G4-6303 TCGA-G4-6586 TCGA-AF-6672 
       14.04        12.26        98.24        65.85        35.80        10.39 
TCGA-AG-A002 TCGA-F5-6813 
       20.98         0.69 

$`PRRG1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 
       41.00        39.98        18.05        40.96        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 
      106.75        22.36        62.79        88.21         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       49.08         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 
       15.02        15.02        17.03        15.02         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       10.06        12.03        45.40        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
       60.79       117.07         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-G5-6235 
       49.51        31.30        28.57        32.19         0.66        55.76 
TCGA-G5-6641 
       26.43 

  PRRG1 MUTATED PRRG1 WILD-TYPE 
           0.07            0.00 
  PRRG1 MUTATED PRRG1 WILD-TYPE 
          98.24          148.01 
  PRRG1 MUTATED PRRG1 WILD-TYPE 
          17.51           20.19 
[1] "0.1 - 98.2 (17.5)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.6"
D54V2, continuous
D54V3, binary
                 cls
clus                0   1
  PRRG1 MUTATED    11   3
  PRRG1 WILD-TYPE 355 116
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRRG1 MUTATED     11    3
  PRRG1 WILD-TYPE  355  116
        clus
vv       PRRG1 MUTATED PRRG1 WILD-TYPE
  COLON             11             355
  RECTUM             3             116
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PRRG1 MUTATED         3        0        1         5         0         0
  PRRG1 WILD-TYPE      88        1       31       133        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PRRG1 MUTATED           0          0          2          1        2         0
  PRRG1 WILD-TYPE        24         11         57         41       46        18
                 vv
clus              STAGE IVB
  PRRG1 MUTATED           0
  PRRG1 WILD-TYPE         1
D54V4, multiclass
            clus
vv           PRRG1 MUTATED PRRG1 WILD-TYPE
  STAGE I                3              88
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              5             133
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             2              57
  STAGE IIIC             1              41
  STAGE IV               2              46
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PRRG1 MUTATED     0   3   9   2
  PRRG1 WILD-TYPE  17  89 320  48
D54V5, multiclass
    clus
vv   PRRG1 MUTATED PRRG1 WILD-TYPE
  T1             0              17
  T2             3              89
  T3             9             320
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  PRRG1 MUTATED     9   3   2
  PRRG1 WILD-TYPE 278 110  85
D54V6, multiclass
    clus
vv   PRRG1 MUTATED PRRG1 WILD-TYPE
  N0             9             278
  N1             3             110
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V7, binary
                 cls
clus                0   1
  PRRG1 MUTATED     9   1
  PRRG1 WILD-TYPE 366  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRRG1 MUTATED      9    1
  PRRG1 WILD-TYPE  366   64
   clus
vv  PRRG1 MUTATED PRRG1 WILD-TYPE
  0             9             366
  1             1              64
[1] 2 2
[1] FALSE
D54V8, binary
                 cls
clus                0   1
  PRRG1 MUTATED     8   6
  PRRG1 WILD-TYPE 217 258
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRRG1 MUTATED      8    6
  PRRG1 WILD-TYPE  217  258
        clus
vv       PRRG1 MUTATED PRRG1 WILD-TYPE
  FEMALE             8             217
  MALE               6             258
[1] 2 2
[1] FALSE
D54V9, binary
                 cls
clus                0   1
  PRRG1 MUTATED    10   1
  PRRG1 WILD-TYPE 340  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRRG1 MUTATED     10    1
  PRRG1 WILD-TYPE  340   21
     clus
vv    PRRG1 MUTATED PRRG1 WILD-TYPE
  NO             10             340
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PRRG1 MUTATED                      7                             4
  PRRG1 WILD-TYPE                  308                            43
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PRRG1 MUTATED                       3                              0
  PRRG1 WILD-TYPE                   103                             10
D54V10, multiclass
                                clus
vv                               PRRG1 MUTATED PRRG1 WILD-TYPE
  COLON ADENOCARCINOMA                       7             308
  COLON MUCINOUS ADENOCARCINOMA              4              43
  RECTAL ADENOCARCINOMA                      3             103
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  PRRG1 MUTATED     9   0   0   2
  PRRG1 WILD-TYPE 336   4  31  23
D54V11, multiclass
    clus
vv   PRRG1 MUTATED PRRG1 WILD-TYPE
  R0             9             336
  R1             0               4
  R2             0              31
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PRRG1 MUTATED                                  0     1
  PRRG1 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PRRG1 MUTATED                           1    11
  PRRG1 WILD-TYPE                        21   215
D54V13, multiclass
                                  clus
vv                                 PRRG1 MUTATED PRRG1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                       11             215
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(55) Variable = PIK3R1 MUTATION ANALYSIS
D55V1, survival
                  sevent
clus2                0   1
  PIK3R1 MUTATED    41   9
  PIK3R1 WILD-TYPE 337  84
  PIK3R1 MUTATED PIK3R1 WILD-TYPE 
              50              421 
  PIK3R1 MUTATED PIK3R1 WILD-TYPE 
               9               84 
$`PIK3R1 MUTATED`
TCGA-A6-5660 TCGA-A6-5665 TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3511 TCGA-AA-3552 
       29.19        22.06        20.12        19.66         6.97        13.02 
TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3697 TCGA-AA-3833 TCGA-AA-A010 TCGA-AD-6895 
        6.05        54.02        85.05        15.95        34.98         0.72 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-5543 TCGA-AZ-4315 TCGA-AZ-6608 TCGA-CA-5255 
       14.50        27.09        33.01        58.39         1.61         3.06 
TCGA-CA-6717 TCGA-CK-4950 TCGA-CK-5914 TCGA-CK-5916 TCGA-CM-4752 TCGA-CM-5862 
       12.76        85.45         9.99        21.14        13.02         5.03 
TCGA-CM-6161 TCGA-CM-6164 TCGA-CM-6167 TCGA-CM-6171 TCGA-CM-6674 TCGA-D5-5541 
       15.02        29.03        14.99        14.04        12.95        55.92 
TCGA-D5-6532 TCGA-D5-6922 TCGA-D5-6927 TCGA-DM-A0XD TCGA-DM-A1D9 TCGA-DM-A1DB 
       18.25         4.41         9.44        24.43       140.38        44.32 
TCGA-DM-A1HB TCGA-F4-6460 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6626 
      135.65        31.96        55.04        85.48        61.91        46.75 
TCGA-AG-3726 TCGA-AG-3892 TCGA-AG-A002 TCGA-AG-A025 TCGA-AH-6549 TCGA-DY-A1DG 
        7.99        13.02        20.98        49.97        17.49        51.48 
TCGA-EI-6507 TCGA-EI-6508 
       19.96        20.91 

$`PIK3R1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        33.53        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6782 
       24.16        21.76        24.69        24.39        23.87        20.28 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3514 
        7.04         3.02         1.02        35.01        63.98         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
       13.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       36.03         8.05        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       33.99        21.01        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3663 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
        6.97         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3837 
       33.04         0.99        25.02         1.02        17.98        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 
        0.07        21.37        15.52        56.55         0.79         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AY-4070 TCGA-AY-4071 
       22.42        27.42        10.88         0.20        16.31         0.95 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5796 
       29.56         5.23        11.74         3.19        12.69         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07        12.20        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-6747 TCGA-CK-6748 
      148.01        15.62        49.08        51.32        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-5341 
      124.27        23.05        20.02        37.02        25.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 
       22.03        22.98        30.08        32.02        15.02        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6165 TCGA-CM-6166 
       15.02        17.03        12.00         2.96        16.04        21.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6676 
       12.99        13.02        15.02        11.01        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       19.59        56.09        20.19         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6928 
        1.48         3.68        12.43        14.30         9.04        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
        7.50       131.51       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6569 
       35.97        60.79       117.07        98.24         8.61        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6310 TCGA-G4-6317 
       74.56        65.85        53.62        44.68        63.62        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 
       22.09        13.78        35.80        26.17        91.79        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       13.94        19.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       17.03        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
       38.56         1.45         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       32.61         0.49        20.55        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  PIK3R1 MUTATED PIK3R1 WILD-TYPE 
            0.72             0.00 
  PIK3R1 MUTATED PIK3R1 WILD-TYPE 
          140.38           148.01 
  PIK3R1 MUTATED PIK3R1 WILD-TYPE 
          20.515           20.190 
[1] "0.7 - 140.4 (20.5)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.4"
D55V2, continuous
D55V3, binary
                  cls
clus                 0   1
  PIK3R1 MUTATED    43   8
  PIK3R1 WILD-TYPE 323 111
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3R1 MUTATED     43    8
  PIK3R1 WILD-TYPE  323  111
        clus
vv       PIK3R1 MUTATED PIK3R1 WILD-TYPE
  COLON              43              323
  RECTUM              8              111
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PIK3R1 MUTATED         8        0        2        18         1         0
  PIK3R1 WILD-TYPE      83        1       30       120         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PIK3R1 MUTATED           1          2          8          4        2
  PIK3R1 WILD-TYPE        23          9         51         38       46
                  vv
clus               STAGE IVA STAGE IVB
  PIK3R1 MUTATED           3         0
  PIK3R1 WILD-TYPE        15         1
D55V4, multiclass
            clus
vv           PIK3R1 MUTATED PIK3R1 WILD-TYPE
  STAGE I                 8               83
  STAGE IA                0                1
  STAGE II                2               30
  STAGE IIA              18              120
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               1               23
  STAGE IIIA              2                9
  STAGE IIIB              8               51
  STAGE IIIC              4               38
  STAGE IV                2               46
  STAGE IVA               3               15
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  PIK3R1 MUTATED     3   6  38   4
  PIK3R1 WILD-TYPE  14  86 291  46
D55V5, multiclass
    clus
vv   PIK3R1 MUTATED PIK3R1 WILD-TYPE
  T1              3               14
  T2              6               86
  T3             38              291
  T4              4               46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  PIK3R1 MUTATED    30  16   4
  PIK3R1 WILD-TYPE 257  97  83
D55V6, multiclass
    clus
vv   PIK3R1 MUTATED PIK3R1 WILD-TYPE
  N0             30              257
  N1             16               97
  N2              4               83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V7, binary
                  cls
clus                 0   1
  PIK3R1 MUTATED    41   5
  PIK3R1 WILD-TYPE 334  60
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3R1 MUTATED     41    5
  PIK3R1 WILD-TYPE  334   60
   clus
vv  PIK3R1 MUTATED PIK3R1 WILD-TYPE
  0             41              334
  1              5               60
[1] 2 2
[1] FALSE
D55V8, binary
                  cls
clus                 0   1
  PIK3R1 MUTATED    24  27
  PIK3R1 WILD-TYPE 201 237
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3R1 MUTATED     24   27
  PIK3R1 WILD-TYPE  201  237
        clus
vv       PIK3R1 MUTATED PIK3R1 WILD-TYPE
  FEMALE             24              201
  MALE               27              237
[1] 2 2
[1] FALSE
D55V9, binary
                  cls
clus                 0   1
  PIK3R1 MUTATED    39   1
  PIK3R1 WILD-TYPE 311  21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3R1 MUTATED     39    1
  PIK3R1 WILD-TYPE  311   21
     clus
vv    PIK3R1 MUTATED PIK3R1 WILD-TYPE
  NO              39              311
  YES              1               21
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PIK3R1 MUTATED                     39                             3
  PIK3R1 WILD-TYPE                  276                            44
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PIK3R1 MUTATED                       8                              0
  PIK3R1 WILD-TYPE                    98                             10
D55V10, multiclass
                                clus
vv                               PIK3R1 MUTATED PIK3R1 WILD-TYPE
  COLON ADENOCARCINOMA                       39              276
  COLON MUCINOUS ADENOCARCINOMA               3               44
  RECTAL ADENOCARCINOMA                       8               98
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  PIK3R1 MUTATED    35   1   1   5
  PIK3R1 WILD-TYPE 310   3  30  20
D55V11, multiclass
    clus
vv   PIK3R1 MUTATED PIK3R1 WILD-TYPE
  R0             35              310
  R1              1                3
  R2              1               30
  RX              5               20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PIK3R1 MUTATED                                  0     2
  PIK3R1 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  PIK3R1 MUTATED                           6    31
  PIK3R1 WILD-TYPE                        16   195
D55V13, multiclass
                                  clus
vv                                 PIK3R1 MUTATED PIK3R1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                9
  BLACK OR AFRICAN AMERICAN                     6               16
  WHITE                                        31              195
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(56) Variable = PCBP1 MUTATION ANALYSIS
D56V1, survival
                 sevent
clus2               0   1
  PCBP1 MUTATED    13   1
  PCBP1 WILD-TYPE 365  92
  PCBP1 MUTATED PCBP1 WILD-TYPE 
             14             457 
  PCBP1 MUTATED PCBP1 WILD-TYPE 
              1              92 
$`PCBP1 MUTATED`
TCGA-AA-3941 TCGA-AA-3979 TCGA-AA-A01I TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4950 
       24.00        24.00        31.00        10.06        17.56        85.45 
TCGA-CK-6751 TCGA-CM-6680 TCGA-D5-6529 TCGA-AG-3894 TCGA-AG-A002 TCGA-AH-6544 
      124.27        12.03        20.19        14.01        20.98        38.56 
TCGA-CI-6622 TCGA-F5-6465 
        6.97        49.51 

$`PCBP1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
       31.00         2.01        12.99        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        25.02        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       12.76        14.30       148.01        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CM-4743 TCGA-CM-4744 
        9.99        21.14        82.95         1.91        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       10.06        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       35.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6547 
       38.96        61.97        41.00        38.04       117.11         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6624 
       17.49         0.69         0.72         6.05        33.17         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  PCBP1 MUTATED PCBP1 WILD-TYPE 
           6.97            0.00 
  PCBP1 MUTATED PCBP1 WILD-TYPE 
         124.27          148.01 
  PCBP1 MUTATED PCBP1 WILD-TYPE 
          22.49           20.05 
[1] "7.0 - 124.3 (22.5)" "0.0 - 148.0 (20.1)"
[1] "hr=" "3.5"
D56V2, continuous
D56V3, binary
                 cls
clus                0   1
  PCBP1 MUTATED    10   5
  PCBP1 WILD-TYPE 356 114
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PCBP1 MUTATED     10    5
  PCBP1 WILD-TYPE  356  114
        clus
vv       PCBP1 MUTATED PCBP1 WILD-TYPE
  COLON             10             356
  RECTUM             5             114
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PCBP1 MUTATED         3        0        0         6         1         0
  PCBP1 WILD-TYPE      88        1       32       132         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PCBP1 MUTATED           0          0          3          0        0         1
  PCBP1 WILD-TYPE        24         11         56         42       48        17
                 vv
clus              STAGE IVB
  PCBP1 MUTATED           0
  PCBP1 WILD-TYPE         1
D56V4, multiclass
            clus
vv           PCBP1 MUTATED PCBP1 WILD-TYPE
  STAGE I                3              88
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              6             132
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             3              56
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PCBP1 MUTATED     0   3   9   3
  PCBP1 WILD-TYPE  17  89 320  47
D56V5, multiclass
    clus
vv   PCBP1 MUTATED PCBP1 WILD-TYPE
  T1             0              17
  T2             3              89
  T3             9             320
  T4             3              47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  PCBP1 MUTATED    10   4   1
  PCBP1 WILD-TYPE 277 109  86
D56V6, multiclass
    clus
vv   PCBP1 MUTATED PCBP1 WILD-TYPE
  N0            10             277
  N1             4             109
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V7, binary
                 cls
clus                0   1
  PCBP1 MUTATED    12   2
  PCBP1 WILD-TYPE 363  63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PCBP1 MUTATED     12    2
  PCBP1 WILD-TYPE  363   63
   clus
vv  PCBP1 MUTATED PCBP1 WILD-TYPE
  0            12             363
  1             2              63
[1] 2 2
[1] FALSE
D56V8, binary
                 cls
clus                0   1
  PCBP1 MUTATED     7   8
  PCBP1 WILD-TYPE 218 256
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PCBP1 MUTATED      7    8
  PCBP1 WILD-TYPE  218  256
        clus
vv       PCBP1 MUTATED PCBP1 WILD-TYPE
  FEMALE             7             218
  MALE               8             256
[1] 2 2
[1] FALSE
D56V9, binary
                 cls
clus                0   1
  PCBP1 MUTATED    12   1
  PCBP1 WILD-TYPE 338  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PCBP1 MUTATED     12    1
  PCBP1 WILD-TYPE  338   21
     clus
vv    PCBP1 MUTATED PCBP1 WILD-TYPE
  NO             12             338
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PCBP1 MUTATED                      9                             1
  PCBP1 WILD-TYPE                  306                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PCBP1 MUTATED                       5                              0
  PCBP1 WILD-TYPE                   101                             10
D56V10, multiclass
                                clus
vv                               PCBP1 MUTATED PCBP1 WILD-TYPE
  COLON ADENOCARCINOMA                       9             306
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      5             101
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  PCBP1 MUTATED     9   1   0   3
  PCBP1 WILD-TYPE 336   3  31  22
D56V11, multiclass
    clus
vv   PCBP1 MUTATED PCBP1 WILD-TYPE
  R0             9             336
  R1             1               3
  R2             0              31
  RX             3              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PCBP1 MUTATED                                  0     1
  PCBP1 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PCBP1 MUTATED                           1     7
  PCBP1 WILD-TYPE                        21   219
D56V13, multiclass
                                  clus
vv                                 PCBP1 MUTATED PCBP1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        7             219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(57) Variable = IFT57 MUTATION ANALYSIS
D57V1, survival
                 sevent
clus2               0   1
  IFT57 MUTATED    11   2
  IFT57 WILD-TYPE 367  91
  IFT57 MUTATED IFT57 WILD-TYPE 
             13             458 
  IFT57 MUTATED IFT57 WILD-TYPE 
              2              91 
$`IFT57 MUTATED`
TCGA-A6-5665 TCGA-A6-5666 TCGA-AA-A00N TCGA-AZ-4315 TCGA-CM-4743 TCGA-CM-5868 
       22.06        32.71         4.01        58.39        23.05        17.03 
TCGA-CM-6162 TCGA-DM-A1DA TCGA-G4-6323 TCGA-G4-6588 TCGA-AF-6136 TCGA-AG-3726 
       12.00         7.50        13.78        26.17        15.39         7.99 
TCGA-EI-6507 
       19.96 

$`IFT57 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       22.09        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
      124.27        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       15.02        15.02        15.02         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA 
       49.91        13.32        12.59       140.38        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 
       63.62        61.91        36.00        22.09        35.80        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6655 
       19.10        34.49        10.39        14.50        16.83        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       19.99        13.94        19.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
       32.61         0.49        20.55        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  IFT57 MUTATED IFT57 WILD-TYPE 
           4.01            0.00 
  IFT57 MUTATED IFT57 WILD-TYPE 
          58.39          148.01 
  IFT57 MUTATED IFT57 WILD-TYPE 
         17.030          20.415 
[1] "4.0 - 58.4 (17.0)"  "0.0 - 148.0 (20.4)"
[1] "hr=" "1"  
D57V2, continuous
D57V3, binary
                 cls
clus                0   1
  IFT57 MUTATED    10   3
  IFT57 WILD-TYPE 356 116
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IFT57 MUTATED     10    3
  IFT57 WILD-TYPE  356  116
        clus
vv       IFT57 MUTATED IFT57 WILD-TYPE
  COLON             10             356
  RECTUM             3             116
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  IFT57 MUTATED         1        1        0         5         1         1
  IFT57 WILD-TYPE      90        0       32       133         9         0
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  IFT57 MUTATED           0          0          2          1        0         1
  IFT57 WILD-TYPE        24         11         57         41       48        17
                 vv
clus              STAGE IVB
  IFT57 MUTATED           0
  IFT57 WILD-TYPE         1
D57V4, multiclass
            clus
vv           IFT57 MUTATED IFT57 WILD-TYPE
  STAGE I                1              90
  STAGE IA               1               0
  STAGE II               0              32
  STAGE IIA              5             133
  STAGE IIB              1               9
  STAGE IIC              1               0
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             2              57
  STAGE IIIC             1              41
  STAGE IV               0              48
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  IFT57 MUTATED     0   1   8   3
  IFT57 WILD-TYPE  17  91 321  47
D57V5, multiclass
    clus
vv   IFT57 MUTATED IFT57 WILD-TYPE
  T1             0              17
  T2             1              91
  T3             8             321
  T4             3              47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  IFT57 MUTATED     9   3   1
  IFT57 WILD-TYPE 278 110  86
D57V6, multiclass
    clus
vv   IFT57 MUTATED IFT57 WILD-TYPE
  N0             9             278
  N1             3             110
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V7, binary
                 cls
clus                0   1
  IFT57 MUTATED    10   1
  IFT57 WILD-TYPE 365  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IFT57 MUTATED     10    1
  IFT57 WILD-TYPE  365   64
   clus
vv  IFT57 MUTATED IFT57 WILD-TYPE
  0            10             365
  1             1              64
[1] 2 2
[1] FALSE
D57V8, binary
                 cls
clus                0   1
  IFT57 MUTATED     7   6
  IFT57 WILD-TYPE 218 258
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IFT57 MUTATED      7    6
  IFT57 WILD-TYPE  218  258
        clus
vv       IFT57 MUTATED IFT57 WILD-TYPE
  FEMALE             7             218
  MALE               6             258
[1] 2 2
[1] FALSE
D57V9, binary
                 cls
clus                0   1
  IFT57 MUTATED    10   1
  IFT57 WILD-TYPE 340  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IFT57 MUTATED     10    1
  IFT57 WILD-TYPE  340   21
     clus
vv    IFT57 MUTATED IFT57 WILD-TYPE
  NO             10             340
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  IFT57 MUTATED                      8                             2
  IFT57 WILD-TYPE                  307                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  IFT57 MUTATED                       3                              0
  IFT57 WILD-TYPE                   103                             10
D57V10, multiclass
                                clus
vv                               IFT57 MUTATED IFT57 WILD-TYPE
  COLON ADENOCARCINOMA                       8             307
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      3             103
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  IFT57 MUTATED    10   0   0   0
  IFT57 WILD-TYPE 335   4  31  25
D57V11, multiclass
    clus
vv   IFT57 MUTATED IFT57 WILD-TYPE
  R0            10             335
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  IFT57 MUTATED                                  0     0
  IFT57 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  IFT57 MUTATED                           1    10
  IFT57 WILD-TYPE                        21   216
D57V13, multiclass
                                  clus
vv                                 IFT57 MUTATED IFT57 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                       10             216
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(58) Variable = RSPH3 MUTATION ANALYSIS
D58V1, survival
                 sevent
clus2               0   1
  RSPH3 MUTATED     8   3
  RSPH3 WILD-TYPE 370  90
  RSPH3 MUTATED RSPH3 WILD-TYPE 
             11             460 
  RSPH3 MUTATED RSPH3 WILD-TYPE 
              3              90 
$`RSPH3 MUTATED`
TCGA-A6-6652 TCGA-A6-6653 TCGA-AA-A010 TCGA-AD-6895 TCGA-AD-6965 TCGA-AZ-6599 
       24.69        24.39        34.98         0.72         0.20         6.77 
TCGA-AZ-6601 TCGA-DM-A1DA TCGA-DM-A28H TCGA-G4-6309 TCGA-AH-6643 
      100.01         7.50       117.07        85.48         0.69 

$`RSPH3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6654 TCGA-A6-6780 
       25.08        25.18        24.16        21.76        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AU-3779 
        0.79         5.79        22.42        27.42        10.88        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       88.21        49.41        12.10        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA 
       49.91        13.32        12.59       140.38        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
       60.79        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 
       65.85        53.62        44.68        55.04        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
       38.56         1.45        17.49         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  RSPH3 MUTATED RSPH3 WILD-TYPE 
            0.2             0.0 
  RSPH3 MUTATED RSPH3 WILD-TYPE 
         117.07          148.01 
  RSPH3 MUTATED RSPH3 WILD-TYPE 
         24.390          20.155 
[1] "0.2 - 117.1 (24.4)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.1"
D58V2, continuous
D58V3, binary
                 cls
clus                0   1
  RSPH3 MUTATED    10   1
  RSPH3 WILD-TYPE 356 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RSPH3 MUTATED     10    1
  RSPH3 WILD-TYPE  356  118
        clus
vv       RSPH3 MUTATED RSPH3 WILD-TYPE
  COLON             10             356
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RSPH3 MUTATED         2        0        1         0         1         0
  RSPH3 WILD-TYPE      89        1       31       138         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RSPH3 MUTATED           0          0          1          3        0         1
  RSPH3 WILD-TYPE        24         11         58         39       48        17
                 vv
clus              STAGE IVB
  RSPH3 MUTATED           0
  RSPH3 WILD-TYPE         1
D58V4, multiclass
            clus
vv           RSPH3 MUTATED RSPH3 WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              0             138
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             3              39
  STAGE IV               0              48
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  RSPH3 MUTATED     0   2   7   2
  RSPH3 WILD-TYPE  17  90 322  48
D58V5, multiclass
    clus
vv   RSPH3 MUTATED RSPH3 WILD-TYPE
  T1             0              17
  T2             2              90
  T3             7             322
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  RSPH3 MUTATED     5   2   4
  RSPH3 WILD-TYPE 282 111  83
D58V6, multiclass
    clus
vv   RSPH3 MUTATED RSPH3 WILD-TYPE
  N0             5             282
  N1             2             111
  N2             4              83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V7, binary
                 cls
clus                0   1
  RSPH3 MUTATED     7   1
  RSPH3 WILD-TYPE 368  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RSPH3 MUTATED      7    1
  RSPH3 WILD-TYPE  368   64
   clus
vv  RSPH3 MUTATED RSPH3 WILD-TYPE
  0             7             368
  1             1              64
[1] 2 2
[1] FALSE
D58V8, binary
                 cls
clus                0   1
  RSPH3 MUTATED     3   8
  RSPH3 WILD-TYPE 222 256
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RSPH3 MUTATED      3    8
  RSPH3 WILD-TYPE  222  256
        clus
vv       RSPH3 MUTATED RSPH3 WILD-TYPE
  FEMALE             3             222
  MALE               8             256
[1] 2 2
[1] FALSE
D58V9, binary
                 cls
clus                0   1
  RSPH3 MUTATED     6   0
  RSPH3 WILD-TYPE 344  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RSPH3 MUTATED      6    0
  RSPH3 WILD-TYPE  344   22
     clus
vv    RSPH3 MUTATED RSPH3 WILD-TYPE
  NO              6             344
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  RSPH3 MUTATED                     10                             0
  RSPH3 WILD-TYPE                  305                            47
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  RSPH3 MUTATED                       1                              0
  RSPH3 WILD-TYPE                   105                             10
D58V10, multiclass
                                clus
vv                               RSPH3 MUTATED RSPH3 WILD-TYPE
  COLON ADENOCARCINOMA                      10             305
  COLON MUCINOUS ADENOCARCINOMA              0              47
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  RSPH3 MUTATED     3   0   0   0
  RSPH3 WILD-TYPE 342   4  31  25
D58V11, multiclass
    clus
vv   RSPH3 MUTATED RSPH3 WILD-TYPE
  R0             3             342
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RSPH3 MUTATED                                  0     0
  RSPH3 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  RSPH3 MUTATED                           2     8
  RSPH3 WILD-TYPE                        20   218
D58V13, multiclass
                                  clus
vv                                 RSPH3 MUTATED RSPH3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    2              20
  WHITE                                        8             218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(59) Variable = RLIM MUTATION ANALYSIS
D59V1, survival
                sevent
clus2              0   1
  RLIM MUTATED    15   3
  RLIM WILD-TYPE 363  90
  RLIM MUTATED RLIM WILD-TYPE 
            18            453 
  RLIM MUTATED RLIM WILD-TYPE 
             3             90 
$`RLIM MUTATED`
TCGA-A6-6651 TCGA-AA-3678 TCGA-AA-3947 TCGA-AZ-5407 TCGA-CK-4952 TCGA-CM-4752 
       21.76        47.01        33.01        88.21        15.62        13.02 
TCGA-D5-5540 TCGA-F4-6570 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6303 TCGA-G4-6321 
       56.09         6.18        47.41       133.18        65.85        22.09 
TCGA-G4-6586 TCGA-G4-6625 TCGA-AF-2687 TCGA-AG-A002 TCGA-DY-A0XA TCGA-DY-A1DG 
       35.80        91.79        24.13        20.98       126.44        51.48 

$`RLIM WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.08        25.18        24.16        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       12.99        24.00        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 
       10.06        14.30        17.56       148.01        85.45        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-5341 TCGA-CM-5344 
       23.05        20.02        37.02        25.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       35.74        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6304 
       33.67        13.25         0.53        35.31        74.56        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2689 TCGA-AF-2691 
       13.78        26.17        46.75        79.69        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        4.01         5.03         5.29        41.36        57.24        24.13 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  RLIM MUTATED RLIM WILD-TYPE 
          6.18           0.00 
  RLIM MUTATED RLIM WILD-TYPE 
        133.18         148.01 
  RLIM MUTATED RLIM WILD-TYPE 
        41.405         19.990 
[1] "6.2 - 133.2 (41.4)" "0.0 - 148.0 (20.0)"
[1] "hr=" "2.2"
D59V2, continuous
D59V3, binary
                cls
clus               0   1
  RLIM MUTATED    14   4
  RLIM WILD-TYPE 352 115
[1] "tbl2"
                cls
clus             [,1] [,2]
  RLIM MUTATED     14    4
  RLIM WILD-TYPE  352  115
        clus
vv       RLIM MUTATED RLIM WILD-TYPE
  COLON            14            352
  RECTUM            4            115
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RLIM MUTATED         2        0        0         7         1         0
  RLIM WILD-TYPE      89        1       32       131         9         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RLIM MUTATED           3          0          1          2        1         1
  RLIM WILD-TYPE        21         11         58         40       47        17
                vv
clus             STAGE IVB
  RLIM MUTATED           0
  RLIM WILD-TYPE         1
D59V4, multiclass
            clus
vv           RLIM MUTATED RLIM WILD-TYPE
  STAGE I               2             89
  STAGE IA              0              1
  STAGE II              0             32
  STAGE IIA             7            131
  STAGE IIB             1              9
  STAGE IIC             0              1
  STAGE III             3             21
  STAGE IIIA            0             11
  STAGE IIIB            1             58
  STAGE IIIC            2             40
  STAGE IV              1             47
  STAGE IVA             1             17
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  RLIM MUTATED     1   3  12   2
  RLIM WILD-TYPE  16  89 317  48
D59V5, multiclass
    clus
vv   RLIM MUTATED RLIM WILD-TYPE
  T1            1             16
  T2            3             89
  T3           12            317
  T4            2             48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  RLIM MUTATED    10   6   2
  RLIM WILD-TYPE 277 107  85
D59V6, multiclass
    clus
vv   RLIM MUTATED RLIM WILD-TYPE
  N0           10            277
  N1            6            107
  N2            2             85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V7, binary
                cls
clus               0   1
  RLIM MUTATED    14   2
  RLIM WILD-TYPE 361  63
[1] "tbl2"
                cls
clus             [,1] [,2]
  RLIM MUTATED     14    2
  RLIM WILD-TYPE  361   63
   clus
vv  RLIM MUTATED RLIM WILD-TYPE
  0           14            361
  1            2             63
[1] 2 2
[1] FALSE
D59V8, binary
                cls
clus               0   1
  RLIM MUTATED    13   5
  RLIM WILD-TYPE 212 259
[1] "tbl2"
                cls
clus             [,1] [,2]
  RLIM MUTATED     13    5
  RLIM WILD-TYPE  212  259
        clus
vv       RLIM MUTATED RLIM WILD-TYPE
  FEMALE           13            212
  MALE              5            259
[1] 2 2
[1] FALSE
D59V9, binary
                cls
clus               0   1
  RLIM MUTATED    14   1
  RLIM WILD-TYPE 336  21
[1] "tbl2"
                cls
clus             [,1] [,2]
  RLIM MUTATED     14    1
  RLIM WILD-TYPE  336   21
     clus
vv    RLIM MUTATED RLIM WILD-TYPE
  NO            14            336
  YES            1             21
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  RLIM MUTATED                     12                             2
  RLIM WILD-TYPE                  303                            45
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  RLIM MUTATED                       4                              0
  RLIM WILD-TYPE                   102                             10
D59V10, multiclass
                                clus
vv                               RLIM MUTATED RLIM WILD-TYPE
  COLON ADENOCARCINOMA                     12            303
  COLON MUCINOUS ADENOCARCINOMA             2             45
  RECTAL ADENOCARCINOMA                     4            102
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  RLIM MUTATED    13   0   0   1
  RLIM WILD-TYPE 332   4  31  24
D59V11, multiclass
    clus
vv   RLIM MUTATED RLIM WILD-TYPE
  R0           13            332
  R1            0              4
  R2            0             31
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RLIM MUTATED                                  0     0
  RLIM WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  RLIM MUTATED                           1    14
  RLIM WILD-TYPE                        21   212
D59V13, multiclass
                                  clus
vv                                 RLIM MUTATED RLIM WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                      14            212
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(60) Variable = ROS1 MUTATION ANALYSIS
D60V1, survival
                sevent
clus2              0   1
  ROS1 MUTATED    39  11
  ROS1 WILD-TYPE 339  82
  ROS1 MUTATED ROS1 WILD-TYPE 
            50            421 
  ROS1 MUTATED ROS1 WILD-TYPE 
            11             82 
$`ROS1 MUTATED`
TCGA-A6-5657 TCGA-A6-6781 TCGA-AA-3496 TCGA-AA-3510 TCGA-AA-3555 TCGA-AA-3662 
       31.63        19.66         1.02        63.98        29.95         6.05 
TCGA-AA-3663 TCGA-AA-3672 TCGA-AA-3821 TCGA-AA-3864 TCGA-AA-3875 TCGA-AA-3950 
        6.97         0.92         1.02        53.00        18.05        24.00 
TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A010 TCGA-AD-6895 TCGA-AD-6964 TCGA-AD-6965 
       25.02         4.01        34.98         0.72        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AZ-4315 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 
       14.50        27.09        58.39        88.21        49.41        12.10 
TCGA-AZ-6607 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4952 TCGA-CK-5916 TCGA-CM-4743 
        3.19        12.76        10.06        15.62        21.14        23.05 
TCGA-CM-5344 TCGA-CM-6165 TCGA-CM-6171 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6538 
       22.03        16.04        14.04         1.32        15.12        17.13 
TCGA-D5-6541 TCGA-F4-6570 TCGA-F4-6856 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6586 
       15.58         6.18        35.31        36.00        22.09        35.80 
TCGA-G4-6588 TCGA-AF-5654 TCGA-AG-3612 TCGA-AG-A002 TCGA-CI-6622 TCGA-DY-A1DC 
       26.17        16.83        19.99        20.98         6.97        41.36 
TCGA-DY-A1DD TCGA-F5-6812 
       57.24         0.66 

$`ROS1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3511 
       20.12        20.28         7.04         3.02        35.01         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 
       78.08        54.02         2.01        14.01        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 
       35.05        33.04         0.99        25.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        31.07        30.05        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       29.98        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       26.01         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AY-4070 TCGA-AY-4071 
        0.79         5.79        22.42        27.42        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       33.01        21.44        17.82         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       22.36        62.79         6.77       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
       11.74         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.07        12.20        14.30        17.56       148.01        85.45 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       49.08        51.32         9.99        82.95         1.91       124.27 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5348 
       20.02        37.02        25.02        13.02        29.06        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6166 
       17.03        15.02        12.00         2.96        29.03        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 
       14.99        12.99        13.02        15.02        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6539 TCGA-D5-6540 
       18.25        43.27        17.85         4.80        12.49        16.14 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       35.74        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 
       33.67        13.25         0.53        47.41       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6323 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       61.91        13.78        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       14.50        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3726 
        6.05         0.99        15.95        19.99        13.94         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
       33.17         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
        5.03         5.29       126.44        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6813 TCGA-G5-6235 
       49.51        31.30        28.57        32.19         0.69        55.76 
TCGA-G5-6641 
       26.43 

  ROS1 MUTATED ROS1 WILD-TYPE 
           0.2            0.0 
  ROS1 MUTATED ROS1 WILD-TYPE 
         88.21         148.01 
  ROS1 MUTATED ROS1 WILD-TYPE 
         17.59          20.91 
[1] "0.2 - 88.2 (17.6)"  "0.0 - 148.0 (20.9)"
[1] "hr=" "1.4"
D60V2, continuous
D60V3, binary
                cls
clus               0   1
  ROS1 MUTATED    47   7
  ROS1 WILD-TYPE 319 112
[1] "tbl2"
                cls
clus             [,1] [,2]
  ROS1 MUTATED     47    7
  ROS1 WILD-TYPE  319  112
        clus
vv       ROS1 MUTATED ROS1 WILD-TYPE
  COLON            47            319
  RECTUM            7            112
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ROS1 MUTATED         9        0        6        15         3         0
  ROS1 WILD-TYPE      82        1       26       123         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ROS1 MUTATED           3          0          7          4        3         0
  ROS1 WILD-TYPE        21         11         52         38       45        18
                vv
clus             STAGE IVB
  ROS1 MUTATED           0
  ROS1 WILD-TYPE         1
D60V4, multiclass
            clus
vv           ROS1 MUTATED ROS1 WILD-TYPE
  STAGE I               9             82
  STAGE IA              0              1
  STAGE II              6             26
  STAGE IIA            15            123
  STAGE IIB             3              7
  STAGE IIC             0              1
  STAGE III             3             21
  STAGE IIIA            0             11
  STAGE IIIB            7             52
  STAGE IIIC            4             38
  STAGE IV              3             45
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  ROS1 MUTATED     3   8  31  12
  ROS1 WILD-TYPE  14  84 298  38
D60V5, multiclass
    clus
vv   ROS1 MUTATED ROS1 WILD-TYPE
  T1            3             14
  T2            8             84
  T3           31            298
  T4           12             38
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  ROS1 MUTATED    35  10   9
  ROS1 WILD-TYPE 252 103  78
D60V6, multiclass
    clus
vv   ROS1 MUTATED ROS1 WILD-TYPE
  N0           35            252
  N1           10            103
  N2            9             78
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V7, binary
                cls
clus               0   1
  ROS1 MUTATED    41   3
  ROS1 WILD-TYPE 334  62
[1] "tbl2"
                cls
clus             [,1] [,2]
  ROS1 MUTATED     41    3
  ROS1 WILD-TYPE  334   62
   clus
vv  ROS1 MUTATED ROS1 WILD-TYPE
  0           41            334
  1            3             62
[1] 2 2
[1] FALSE
D60V8, binary
                cls
clus               0   1
  ROS1 MUTATED    30  24
  ROS1 WILD-TYPE 195 240
[1] "tbl2"
                cls
clus             [,1] [,2]
  ROS1 MUTATED     30   24
  ROS1 WILD-TYPE  195  240
        clus
vv       ROS1 MUTATED ROS1 WILD-TYPE
  FEMALE           30            195
  MALE             24            240
[1] 2 2
[1] FALSE
D60V9, binary
                cls
clus               0   1
  ROS1 MUTATED    38   0
  ROS1 WILD-TYPE 312  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  ROS1 MUTATED     38    0
  ROS1 WILD-TYPE  312   22
     clus
vv    ROS1 MUTATED ROS1 WILD-TYPE
  NO            38            312
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ROS1 MUTATED                     38                             9
  ROS1 WILD-TYPE                  277                            38
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ROS1 MUTATED                       7                              0
  ROS1 WILD-TYPE                    99                             10
D60V10, multiclass
                                clus
vv                               ROS1 MUTATED ROS1 WILD-TYPE
  COLON ADENOCARCINOMA                     38            277
  COLON MUCINOUS ADENOCARCINOMA             9             38
  RECTAL ADENOCARCINOMA                     7             99
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  ROS1 MUTATED    37   0   1   5
  ROS1 WILD-TYPE 308   4  30  20
D60V11, multiclass
    clus
vv   ROS1 MUTATED ROS1 WILD-TYPE
  R0           37            308
  R1            0              4
  R2            1             30
  RX            5             20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ROS1 MUTATED                                  0     2
  ROS1 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  ROS1 MUTATED                           2    32
  ROS1 WILD-TYPE                        20   194
D60V13, multiclass
                                  clus
vv                                 ROS1 MUTATED ROS1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              9
  BLACK OR AFRICAN AMERICAN                   2             20
  WHITE                                      32            194
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(61) Variable = MPHOSPH10 MUTATION ANALYSIS
D61V1, survival
                     sevent
clus2                   0   1
  MPHOSPH10 MUTATED    12   5
  MPHOSPH10 WILD-TYPE 366  88
  MPHOSPH10 MUTATED MPHOSPH10 WILD-TYPE 
                 17                 454 
  MPHOSPH10 MUTATED MPHOSPH10 WILD-TYPE 
                  5                  88 
$`MPHOSPH10 MUTATED`
TCGA-A6-6651 TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-A00K TCGA-AD-6895 TCGA-AD-6901 
       21.76        20.12        19.66        18.05         0.72        22.42 
TCGA-AD-6964 TCGA-AU-6004 TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-CA-6718 
       10.88        27.09        21.44        58.39        49.41        10.06 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-5344 TCGA-D5-6927 TCGA-DM-A285 
      124.27        23.05        22.03         9.44         6.12 

$`MPHOSPH10 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.08        25.18        24.16        24.69        24.39        23.87 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 
        5.79        27.42         0.20        14.50        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       33.01        17.82         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        88.21         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 
        3.25         3.29         0.07        12.20        12.76        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CM-4744 TCGA-CM-4746 
        9.99        21.14        82.95         1.91        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       25.02        13.02        29.06        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6929 
        4.41        12.43        14.30         9.04        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  MPHOSPH10 MUTATED MPHOSPH10 WILD-TYPE 
               0.72                0.00 
  MPHOSPH10 MUTATED MPHOSPH10 WILD-TYPE 
             124.27              148.01 
  MPHOSPH10 MUTATED MPHOSPH10 WILD-TYPE 
              21.44               20.12 
[1] "0.7 - 124.3 (21.4)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.5"
D61V2, continuous
D61V3, binary
                     cls
clus                    0   1
  MPHOSPH10 MUTATED    18   0
  MPHOSPH10 WILD-TYPE 348 119
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  MPHOSPH10 MUTATED     18    0
  MPHOSPH10 WILD-TYPE  348  119
        clus
vv       MPHOSPH10 MUTATED MPHOSPH10 WILD-TYPE
  COLON                 18                 348
  RECTUM                 0                 119
[1] 2 2
[1] FALSE
                     vv
clus                  STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MPHOSPH10 MUTATED         2        0        1         8         0         0
  MPHOSPH10 WILD-TYPE      89        1       31       130        10         1
                     vv
clus                  STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MPHOSPH10 MUTATED           0          0          2          1        1
  MPHOSPH10 WILD-TYPE        24         11         57         41       47
                     vv
clus                  STAGE IVA STAGE IVB
  MPHOSPH10 MUTATED           0         0
  MPHOSPH10 WILD-TYPE        18         1
D61V4, multiclass
            clus
vv           MPHOSPH10 MUTATED MPHOSPH10 WILD-TYPE
  STAGE I                    2                  89
  STAGE IA                   0                   1
  STAGE II                   1                  31
  STAGE IIA                  8                 130
  STAGE IIB                  0                  10
  STAGE IIC                  0                   1
  STAGE III                  0                  24
  STAGE IIIA                 0                  11
  STAGE IIIB                 2                  57
  STAGE IIIC                 1                  41
  STAGE IV                   1                  47
  STAGE IVA                  0                  18
  STAGE IVB                  0                   1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                   T1  T2  T3  T4
  MPHOSPH10 MUTATED     0   2  14   2
  MPHOSPH10 WILD-TYPE  17  90 315  48
D61V5, multiclass
    clus
vv   MPHOSPH10 MUTATED MPHOSPH10 WILD-TYPE
  T1                 0                  17
  T2                 2                  90
  T3                14                 315
  T4                 2                  48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                   N0  N1  N2
  MPHOSPH10 MUTATED    12   4   2
  MPHOSPH10 WILD-TYPE 275 109  85
D61V6, multiclass
    clus
vv   MPHOSPH10 MUTATED MPHOSPH10 WILD-TYPE
  N0                12                 275
  N1                 4                 109
  N2                 2                  85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V7, binary
                     cls
clus                    0   1
  MPHOSPH10 MUTATED     8   1
  MPHOSPH10 WILD-TYPE 367  64
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  MPHOSPH10 MUTATED      8    1
  MPHOSPH10 WILD-TYPE  367   64
   clus
vv  MPHOSPH10 MUTATED MPHOSPH10 WILD-TYPE
  0                 8                 367
  1                 1                  64
[1] 2 2
[1] FALSE
D61V8, binary
                     cls
clus                    0   1
  MPHOSPH10 MUTATED     7  11
  MPHOSPH10 WILD-TYPE 218 253
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  MPHOSPH10 MUTATED      7   11
  MPHOSPH10 WILD-TYPE  218  253
        clus
vv       MPHOSPH10 MUTATED MPHOSPH10 WILD-TYPE
  FEMALE                 7                 218
  MALE                  11                 253
[1] 2 2
[1] FALSE
D61V9, binary
                     cls
clus                    0   1
  MPHOSPH10 MUTATED    13   0
  MPHOSPH10 WILD-TYPE 337  22
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  MPHOSPH10 MUTATED     13    0
  MPHOSPH10 WILD-TYPE  337   22
     clus
vv    MPHOSPH10 MUTATED MPHOSPH10 WILD-TYPE
  NO                 13                 337
  YES                 0                  22
[1] 2 2
[1] FALSE
                     vv
clus                  COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MPHOSPH10 MUTATED                     14                             4
  MPHOSPH10 WILD-TYPE                  301                            43
                     vv
clus                  RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MPHOSPH10 MUTATED                       0                              0
  MPHOSPH10 WILD-TYPE                   106                             10
D61V10, multiclass
                                clus
vv                               MPHOSPH10 MUTATED MPHOSPH10 WILD-TYPE
  COLON ADENOCARCINOMA                          14                 301
  COLON MUCINOUS ADENOCARCINOMA                  4                  43
  RECTAL ADENOCARCINOMA                          0                 106
  RECTAL MUCINOUS ADENOCARCINOMA                 0                  10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                   R0  R1  R2  RX
  MPHOSPH10 MUTATED     9   0   0   2
  MPHOSPH10 WILD-TYPE 336   4  31  23
D61V11, multiclass
    clus
vv   MPHOSPH10 MUTATED MPHOSPH10 WILD-TYPE
  R0                 9                 336
  R1                 0                   4
  R2                 0                  31
  RX                 2                  23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V12, continuous
                     vv
clus                  AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MPHOSPH10 MUTATED                                  0     1
  MPHOSPH10 WILD-TYPE                                1    10
                     vv
clus                  BLACK OR AFRICAN AMERICAN WHITE
  MPHOSPH10 MUTATED                           0    15
  MPHOSPH10 WILD-TYPE                        22   211
D61V13, multiclass
                                  clus
vv                                 MPHOSPH10 MUTATED MPHOSPH10 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                 0                   1
  ASIAN                                            1                  10
  BLACK OR AFRICAN AMERICAN                        0                  22
  WHITE                                           15                 211
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(62) Variable = VCX2 MUTATION ANALYSIS
D62V1, survival
                sevent
clus2              0   1
  VCX2 MUTATED     8   3
  VCX2 WILD-TYPE 370  90
  VCX2 MUTATED VCX2 WILD-TYPE 
            11            460 
  VCX2 MUTATED VCX2 WILD-TYPE 
             3             90 
$`VCX2 MUTATED`
TCGA-A6-5656 TCGA-A6-5657 TCGA-D5-6932 TCGA-DM-A1D7 TCGA-F4-6460 TCGA-G4-6586 
       32.91        31.63        11.38        13.32        31.96        35.80 
TCGA-AH-6547 TCGA-CI-6619 TCGA-CL-5918 TCGA-DY-A1DD TCGA-F5-6702 
        1.45         6.05         7.17        57.24        28.57 

$`VCX2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       30.44        29.19        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 
       11.64         4.80         1.51        12.00        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D8 
       24.43        38.20       130.65        92.75        49.91        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
       98.24         8.61        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       22.09        13.78        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6549 
       61.97        41.00        38.04       117.11        38.56        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.69         0.72        33.17         6.97         4.73        78.12 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6811 
       20.91        18.28         9.96        49.51        31.30        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  VCX2 MUTATED VCX2 WILD-TYPE 
          1.45           0.00 
  VCX2 MUTATED VCX2 WILD-TYPE 
         57.24         148.01 
  VCX2 MUTATED VCX2 WILD-TYPE 
        28.570         20.155 
[1] "1.4 - 57.2 (28.6)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.6"
D62V2, continuous
D62V3, binary
                cls
clus               0   1
  VCX2 MUTATED     7   5
  VCX2 WILD-TYPE 359 114
[1] "tbl2"
                cls
clus             [,1] [,2]
  VCX2 MUTATED      7    5
  VCX2 WILD-TYPE  359  114
        clus
vv       VCX2 MUTATED VCX2 WILD-TYPE
  COLON             7            359
  RECTUM            5            114
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  VCX2 MUTATED         1        0        0         4         0         0
  VCX2 WILD-TYPE      90        1       32       134        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  VCX2 MUTATED           1          0          3          0        1         1
  VCX2 WILD-TYPE        23         11         56         42       47        17
                vv
clus             STAGE IVB
  VCX2 MUTATED           0
  VCX2 WILD-TYPE         1
D62V4, multiclass
            clus
vv           VCX2 MUTATED VCX2 WILD-TYPE
  STAGE I               1             90
  STAGE IA              0              1
  STAGE II              0             32
  STAGE IIA             4            134
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             1             23
  STAGE IIIA            0             11
  STAGE IIIB            3             56
  STAGE IIIC            0             42
  STAGE IV              1             47
  STAGE IVA             1             17
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  VCX2 MUTATED     0   1  11   0
  VCX2 WILD-TYPE  17  91 318  50
D62V5, multiclass
    clus
vv   VCX2 MUTATED VCX2 WILD-TYPE
  T1            0             17
  T2            1             91
  T3           11            318
  T4            0             50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  VCX2 MUTATED     6   5   1
  VCX2 WILD-TYPE 281 108  86
D62V6, multiclass
    clus
vv   VCX2 MUTATED VCX2 WILD-TYPE
  N0            6            281
  N1            5            108
  N2            1             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V7, binary
                cls
clus               0   1
  VCX2 MUTATED     8   2
  VCX2 WILD-TYPE 367  63
[1] "tbl2"
                cls
clus             [,1] [,2]
  VCX2 MUTATED      8    2
  VCX2 WILD-TYPE  367   63
   clus
vv  VCX2 MUTATED VCX2 WILD-TYPE
  0            8            367
  1            2             63
[1] 2 2
[1] FALSE
D62V8, binary
                cls
clus               0   1
  VCX2 MUTATED     5   7
  VCX2 WILD-TYPE 220 257
[1] "tbl2"
                cls
clus             [,1] [,2]
  VCX2 MUTATED      5    7
  VCX2 WILD-TYPE  220  257
        clus
vv       VCX2 MUTATED VCX2 WILD-TYPE
  FEMALE            5            220
  MALE              7            257
[1] 2 2
[1] FALSE
D62V9, binary
                cls
clus               0   1
  VCX2 MUTATED     7   0
  VCX2 WILD-TYPE 343  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  VCX2 MUTATED      7    0
  VCX2 WILD-TYPE  343   22
     clus
vv    VCX2 MUTATED VCX2 WILD-TYPE
  NO             7            343
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  VCX2 MUTATED                      6                             0
  VCX2 WILD-TYPE                  309                            47
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  VCX2 MUTATED                       5                              0
  VCX2 WILD-TYPE                   101                             10
D62V10, multiclass
                                clus
vv                               VCX2 MUTATED VCX2 WILD-TYPE
  COLON ADENOCARCINOMA                      6            309
  COLON MUCINOUS ADENOCARCINOMA             0             47
  RECTAL ADENOCARCINOMA                     5            101
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  VCX2 MUTATED     6   0   0   1
  VCX2 WILD-TYPE 339   4  31  24
D62V11, multiclass
    clus
vv   VCX2 MUTATED VCX2 WILD-TYPE
  R0            6            339
  R1            0              4
  R2            0             31
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  VCX2 MUTATED                                  0     0
  VCX2 WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  VCX2 MUTATED                           1    10
  VCX2 WILD-TYPE                        21   216
D62V13, multiclass
                                  clus
vv                                 VCX2 MUTATED VCX2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                      10            216
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(63) Variable = C2ORF29 MUTATION ANALYSIS
D63V1, survival
                   sevent
clus2                 0   1
  C2ORF29 MUTATED    16   3
  C2ORF29 WILD-TYPE 362  90
  C2ORF29 MUTATED C2ORF29 WILD-TYPE 
               19               452 
  C2ORF29 MUTATED C2ORF29 WILD-TYPE 
                3                90 
$`C2ORF29 MUTATED`
TCGA-A6-4105 TCGA-AA-A010 TCGA-AZ-6599 TCGA-CA-5255 TCGA-CK-4952 TCGA-CM-5348 
       14.53        34.98         6.77         3.06        15.62        22.98 
TCGA-CM-6163 TCGA-CM-6168 TCGA-CM-6171 TCGA-CM-6677 TCGA-D5-6529 TCGA-D5-6540 
        2.96        12.99        14.04        11.08        20.19        16.14 
TCGA-D5-6929 TCGA-DM-A1HA TCGA-F4-6460 TCGA-G4-6293 TCGA-G4-6309 TCGA-DY-A0XA 
        4.80       131.51        31.96       133.18        85.48       126.44 
TCGA-EF-5830 
        0.49 

$`C2ORF29 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 
       16.57        34.65        33.34        32.75        36.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 
      106.75        22.36        62.79        88.21        49.41        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
       12.69         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 
       10.06        14.30        17.56       148.01        85.45        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.03        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6164 TCGA-CM-6165 
       15.02        17.03        15.02        12.00        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 
       21.99        14.99        13.02        15.02        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       13.05        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6532 TCGA-D5-6533 
       12.26        19.59        56.09        55.92        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.04         9.44        11.64         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6569 TCGA-F4-6570 
       60.79       117.07        98.24         8.61        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6303 
       13.25         0.53        47.41        35.31        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       53.62        44.68        55.04        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.03         5.29        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
       32.61        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  C2ORF29 MUTATED C2ORF29 WILD-TYPE 
             0.49              0.00 
  C2ORF29 MUTATED C2ORF29 WILD-TYPE 
           133.18            148.01 
  C2ORF29 MUTATED C2ORF29 WILD-TYPE 
            15.62             20.73 
[1] "0.5 - 133.2 (15.6)" "0.0 - 148.0 (20.7)"
[1] "hr=" "1.5"
D63V2, continuous
D63V3, binary
                   cls
clus                  0   1
  C2ORF29 MUTATED    17   2
  C2ORF29 WILD-TYPE 349 117
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C2ORF29 MUTATED     17    2
  C2ORF29 WILD-TYPE  349  117
        clus
vv       C2ORF29 MUTATED C2ORF29 WILD-TYPE
  COLON               17               349
  RECTUM               2               117
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  C2ORF29 MUTATED         4        0        0         6         2         0
  C2ORF29 WILD-TYPE      87        1       32       132         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C2ORF29 MUTATED           1          0          3          2        1
  C2ORF29 WILD-TYPE        23         11         56         40       47
                   vv
clus                STAGE IVA STAGE IVB
  C2ORF29 MUTATED           0         0
  C2ORF29 WILD-TYPE        18         1
D63V4, multiclass
            clus
vv           C2ORF29 MUTATED C2ORF29 WILD-TYPE
  STAGE I                  4                87
  STAGE IA                 0                 1
  STAGE II                 0                32
  STAGE IIA                6               132
  STAGE IIB                2                 8
  STAGE IIC                0                 1
  STAGE III                1                23
  STAGE IIIA               0                11
  STAGE IIIB               3                56
  STAGE IIIC               2                40
  STAGE IV                 1                47
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  C2ORF29 MUTATED     1   3  12   3
  C2ORF29 WILD-TYPE  16  89 317  47
D63V5, multiclass
    clus
vv   C2ORF29 MUTATED C2ORF29 WILD-TYPE
  T1               1                16
  T2               3                89
  T3              12               317
  T4               3                47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  C2ORF29 MUTATED    12   5   2
  C2ORF29 WILD-TYPE 275 108  85
D63V6, multiclass
    clus
vv   C2ORF29 MUTATED C2ORF29 WILD-TYPE
  N0              12               275
  N1               5               108
  N2               2                85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V7, binary
                   cls
clus                  0   1
  C2ORF29 MUTATED    17   1
  C2ORF29 WILD-TYPE 358  64
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C2ORF29 MUTATED     17    1
  C2ORF29 WILD-TYPE  358   64
   clus
vv  C2ORF29 MUTATED C2ORF29 WILD-TYPE
  0              17               358
  1               1                64
[1] 2 2
[1] FALSE
D63V8, binary
                   cls
clus                  0   1
  C2ORF29 MUTATED    10   9
  C2ORF29 WILD-TYPE 215 255
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C2ORF29 MUTATED     10    9
  C2ORF29 WILD-TYPE  215  255
        clus
vv       C2ORF29 MUTATED C2ORF29 WILD-TYPE
  FEMALE              10               215
  MALE                 9               255
[1] 2 2
[1] FALSE
D63V9, binary
                   cls
clus                  0   1
  C2ORF29 MUTATED    13   1
  C2ORF29 WILD-TYPE 337  21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C2ORF29 MUTATED     13    1
  C2ORF29 WILD-TYPE  337   21
     clus
vv    C2ORF29 MUTATED C2ORF29 WILD-TYPE
  NO               13               337
  YES               1                21
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  C2ORF29 MUTATED                     15                             2
  C2ORF29 WILD-TYPE                  300                            45
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  C2ORF29 MUTATED                       2                              0
  C2ORF29 WILD-TYPE                   104                             10
D63V10, multiclass
                                clus
vv                               C2ORF29 MUTATED C2ORF29 WILD-TYPE
  COLON ADENOCARCINOMA                        15               300
  COLON MUCINOUS ADENOCARCINOMA                2                45
  RECTAL ADENOCARCINOMA                        2               104
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  C2ORF29 MUTATED    13   0   0   2
  C2ORF29 WILD-TYPE 332   4  31  23
D63V11, multiclass
    clus
vv   C2ORF29 MUTATED C2ORF29 WILD-TYPE
  R0              13               332
  R1               0                 4
  R2               0                31
  RX               2                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C2ORF29 MUTATED                                  0     1
  C2ORF29 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  C2ORF29 MUTATED                           2    15
  C2ORF29 WILD-TYPE                        20   211
D63V13, multiclass
                                  clus
vv                                 C2ORF29 MUTATED C2ORF29 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                10
  BLACK OR AFRICAN AMERICAN                      2                20
  WHITE                                         15               211
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(64) Variable = DDX26B MUTATION ANALYSIS
D64V1, survival
                  sevent
clus2                0   1
  DDX26B MUTATED    13   2
  DDX26B WILD-TYPE 365  91
  DDX26B MUTATED DDX26B WILD-TYPE 
              15              456 
  DDX26B MUTATED DDX26B WILD-TYPE 
               2               91 
$`DDX26B MUTATED`
TCGA-A6-5661 TCGA-A6-5665 TCGA-A6-6780 TCGA-AA-3713 TCGA-AA-3950 TCGA-AU-6004 
       33.53        22.06        20.12        19.04        24.00        27.09 
TCGA-CA-6717 TCGA-CK-5913 TCGA-CK-5916 TCGA-CM-6162 TCGA-CM-6674 TCGA-D5-6536 
       12.76        51.32        21.14        12.00        12.95        17.85 
TCGA-F4-6570 TCGA-G4-6586 TCGA-AG-3890 
        6.18        35.80        17.03 

$`DDX26B WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6781 
       24.16        21.76        24.69        24.39        23.87        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       85.05        26.99        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       33.01        26.01         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07        12.20        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-6747 
      148.01        85.45        15.62        49.08         9.99        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6676 
       13.02        15.02        14.04        11.01        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       43.27        15.12         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       31.96        35.74        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3892 
       19.04        19.99         1.02        17.95        36.95        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  DDX26B MUTATED DDX26B WILD-TYPE 
            6.18             0.00 
  DDX26B MUTATED DDX26B WILD-TYPE 
           51.32           148.01 
  DDX26B MUTATED DDX26B WILD-TYPE 
          20.120           20.235 
[1] "6.2 - 51.3 (20.1)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.3"
D64V2, continuous
D64V3, binary
                  cls
clus                 0   1
  DDX26B MUTATED    15   1
  DDX26B WILD-TYPE 351 118
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DDX26B MUTATED     15    1
  DDX26B WILD-TYPE  351  118
        clus
vv       DDX26B MUTATED DDX26B WILD-TYPE
  COLON              15              351
  RECTUM              1              118
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DDX26B MUTATED         3        0        0        10         1         0
  DDX26B WILD-TYPE      88        1       32       128         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DDX26B MUTATED           0          0          1          0        1
  DDX26B WILD-TYPE        24         11         58         42       47
                  vv
clus               STAGE IVA STAGE IVB
  DDX26B MUTATED           0         0
  DDX26B WILD-TYPE        18         1
D64V4, multiclass
            clus
vv           DDX26B MUTATED DDX26B WILD-TYPE
  STAGE I                 3               88
  STAGE IA                0                1
  STAGE II                0               32
  STAGE IIA              10              128
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              1               58
  STAGE IIIC              0               42
  STAGE IV                1               47
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  DDX26B MUTATED     1   2  12   1
  DDX26B WILD-TYPE  16  90 317  49
D64V5, multiclass
    clus
vv   DDX26B MUTATED DDX26B WILD-TYPE
  T1              1               16
  T2              2               90
  T3             12              317
  T4              1               49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  DDX26B MUTATED    15   1   0
  DDX26B WILD-TYPE 272 112  87
D64V6, multiclass
    clus
vv   DDX26B MUTATED DDX26B WILD-TYPE
  N0             15              272
  N1              1              112
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V7, binary
                  cls
clus                 0   1
  DDX26B MUTATED    12   1
  DDX26B WILD-TYPE 363  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DDX26B MUTATED     12    1
  DDX26B WILD-TYPE  363   64
   clus
vv  DDX26B MUTATED DDX26B WILD-TYPE
  0             12              363
  1              1               64
[1] 2 2
[1] FALSE
D64V8, binary
                  cls
clus                 0   1
  DDX26B MUTATED    10   6
  DDX26B WILD-TYPE 215 258
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DDX26B MUTATED     10    6
  DDX26B WILD-TYPE  215  258
        clus
vv       DDX26B MUTATED DDX26B WILD-TYPE
  FEMALE             10              215
  MALE                6              258
[1] 2 2
[1] FALSE
D64V9, binary
                  cls
clus                 0   1
  DDX26B MUTATED    13   1
  DDX26B WILD-TYPE 337  21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DDX26B MUTATED     13    1
  DDX26B WILD-TYPE  337   21
     clus
vv    DDX26B MUTATED DDX26B WILD-TYPE
  NO              13              337
  YES              1               21
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  DDX26B MUTATED                     11                             4
  DDX26B WILD-TYPE                  304                            43
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  DDX26B MUTATED                       1                              0
  DDX26B WILD-TYPE                   105                             10
D64V10, multiclass
                                clus
vv                               DDX26B MUTATED DDX26B WILD-TYPE
  COLON ADENOCARCINOMA                       11              304
  COLON MUCINOUS ADENOCARCINOMA               4               43
  RECTAL ADENOCARCINOMA                       1              105
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  DDX26B MUTATED    10   0   1   4
  DDX26B WILD-TYPE 335   4  30  21
D64V11, multiclass
    clus
vv   DDX26B MUTATED DDX26B WILD-TYPE
  R0             10              335
  R1              0                4
  R2              1               30
  RX              4               21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DDX26B MUTATED                                  0     1
  DDX26B WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  DDX26B MUTATED                           1    11
  DDX26B WILD-TYPE                        21   215
D64V13, multiclass
                                  clus
vv                                 DDX26B MUTATED DDX26B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                        11              215
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(65) Variable = RBPJ MUTATION ANALYSIS
D65V1, survival
                sevent
clus2              0   1
  RBPJ MUTATED    14   4
  RBPJ WILD-TYPE 364  89
  RBPJ MUTATED RBPJ WILD-TYPE 
            18            453 
  RBPJ MUTATED RBPJ WILD-TYPE 
             4             89 
$`RBPJ MUTATED`
TCGA-A6-3809 TCGA-A6-6141 TCGA-A6-6782 TCGA-AA-3815 TCGA-AA-A00Q TCGA-AD-5900 
       32.75         8.38        20.28        33.04        42.02         0.07 
TCGA-AD-6889 TCGA-AY-6197 TCGA-CA-6716 TCGA-CA-6717 TCGA-CM-5860 TCGA-CM-6674 
       56.55        21.44        12.20        12.76        32.02        12.95 
TCGA-D5-6537 TCGA-G4-6303 TCGA-G4-6626 TCGA-AG-3892 TCGA-AG-A002 TCGA-DY-A1H8 
        4.80        65.85        46.75        13.02        20.98        32.61 

$`RBPJ WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 
       22.06        32.71        27.09        22.52        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       19.66         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       21.37        15.52         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        33.01        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-5862 
       29.06        22.03        22.98        30.08        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       15.02        14.04        11.01        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       15.12        17.85        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
      133.18        74.56        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       26.17        91.79        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 
       19.99         1.02        17.95        36.95        17.03        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       51.48         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  RBPJ MUTATED RBPJ WILD-TYPE 
          0.07           0.00 
  RBPJ MUTATED RBPJ WILD-TYPE 
         65.85         148.01 
  RBPJ MUTATED RBPJ WILD-TYPE 
         21.21          20.05 
[1] "0.1 - 65.8 (21.2)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.1"
D65V2, continuous
D65V3, binary
                cls
clus               0   1
  RBPJ MUTATED    15   3
  RBPJ WILD-TYPE 351 116
[1] "tbl2"
                cls
clus             [,1] [,2]
  RBPJ MUTATED     15    3
  RBPJ WILD-TYPE  351  116
        clus
vv       RBPJ MUTATED RBPJ WILD-TYPE
  COLON            15            351
  RECTUM            3            116
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RBPJ MUTATED         3        0        0         9         2         0
  RBPJ WILD-TYPE      88        1       32       129         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RBPJ MUTATED           0          1          2          0        1         0
  RBPJ WILD-TYPE        24         10         57         42       47        18
                vv
clus             STAGE IVB
  RBPJ MUTATED           0
  RBPJ WILD-TYPE         1
D65V4, multiclass
            clus
vv           RBPJ MUTATED RBPJ WILD-TYPE
  STAGE I               3             88
  STAGE IA              0              1
  STAGE II              0             32
  STAGE IIA             9            129
  STAGE IIB             2              8
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            1             10
  STAGE IIIB            2             57
  STAGE IIIC            0             42
  STAGE IV              1             47
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  RBPJ MUTATED     1   3  11   3
  RBPJ WILD-TYPE  16  89 318  47
D65V5, multiclass
    clus
vv   RBPJ MUTATED RBPJ WILD-TYPE
  T1            1             16
  T2            3             89
  T3           11            318
  T4            3             47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  RBPJ MUTATED    14   4   0
  RBPJ WILD-TYPE 273 109  87
D65V6, multiclass
    clus
vv   RBPJ MUTATED RBPJ WILD-TYPE
  N0           14            273
  N1            4            109
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V7, binary
                cls
clus               0   1
  RBPJ MUTATED    13   1
  RBPJ WILD-TYPE 362  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  RBPJ MUTATED     13    1
  RBPJ WILD-TYPE  362   64
   clus
vv  RBPJ MUTATED RBPJ WILD-TYPE
  0           13            362
  1            1             64
[1] 2 2
[1] FALSE
D65V8, binary
                cls
clus               0   1
  RBPJ MUTATED     6  12
  RBPJ WILD-TYPE 219 252
[1] "tbl2"
                cls
clus             [,1] [,2]
  RBPJ MUTATED      6   12
  RBPJ WILD-TYPE  219  252
        clus
vv       RBPJ MUTATED RBPJ WILD-TYPE
  FEMALE            6            219
  MALE             12            252
[1] 2 2
[1] FALSE
D65V9, binary
                cls
clus               0   1
  RBPJ MUTATED    15   0
  RBPJ WILD-TYPE 335  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  RBPJ MUTATED     15    0
  RBPJ WILD-TYPE  335   22
     clus
vv    RBPJ MUTATED RBPJ WILD-TYPE
  NO            15            335
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  RBPJ MUTATED                     12                             3
  RBPJ WILD-TYPE                  303                            44
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  RBPJ MUTATED                       3                              0
  RBPJ WILD-TYPE                   103                             10
D65V10, multiclass
                                clus
vv                               RBPJ MUTATED RBPJ WILD-TYPE
  COLON ADENOCARCINOMA                     12            303
  COLON MUCINOUS ADENOCARCINOMA             3             44
  RECTAL ADENOCARCINOMA                     3            103
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  RBPJ MUTATED    12   0   0   2
  RBPJ WILD-TYPE 333   4  31  23
D65V11, multiclass
    clus
vv   RBPJ MUTATED RBPJ WILD-TYPE
  R0           12            333
  R1            0              4
  R2            0             31
  RX            2             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RBPJ MUTATED                                  0     3
  RBPJ WILD-TYPE                                1     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  RBPJ MUTATED                           1    10
  RBPJ WILD-TYPE                        21   216
D65V13, multiclass
                                  clus
vv                                 RBPJ MUTATED RBPJ WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       3              8
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                      10            216
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(66) Variable = SMAD4 MUTATION ANALYSIS
D66V1, survival
                 sevent
clus2               0   1
  SMAD4 MUTATED   107  32
  SMAD4 WILD-TYPE 271  61
  SMAD4 MUTATED SMAD4 WILD-TYPE 
            139             332 
  SMAD4 MUTATED SMAD4 WILD-TYPE 
             32              61 
$`SMAD4 MUTATED`
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-3809 TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 
       42.90        42.28        32.75        32.91        30.44        29.19 
TCGA-A6-5664 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
       22.09        27.09        22.52        21.76        24.69        23.87 
TCGA-AA-3496 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3530 TCGA-AA-3555 TCGA-AA-3558 
        1.02        24.03        37.05        19.07        29.95        20.98 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3666 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 
       78.08         6.05         2.01        36.00        85.05        19.04 
TCGA-AA-3811 TCGA-AA-3821 TCGA-AA-3845 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3950 
       10.06         1.02         0.00        30.05        53.00        24.00 
TCGA-AA-3968 TCGA-AA-3973 TCGA-AA-A00K TCGA-AA-A01D TCGA-AA-A02O TCGA-AD-6888 
       21.99        13.05        18.05        10.98         0.92        15.52 
TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6964 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-6197 
        5.79        27.42        10.88        14.50        27.09        21.44 
TCGA-AY-6386 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 
       17.82         5.13       106.75        62.79        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-CA-5796 
       12.10       100.01        29.56         5.23         3.19         3.25 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4950 TCGA-CK-5914 
       12.20        12.76        10.06        14.30        85.45         9.99 
TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       13.02        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6170 
       17.03        15.02         2.96        16.04        21.99        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6680 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       14.04        11.01        12.03        12.26        19.59        56.09 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6541 TCGA-D5-6898 
       18.25         1.32        43.27        17.85        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-7000 
        3.68        14.30         9.44        11.64         1.51        10.26 
TCGA-DM-A0XF TCGA-DM-A1D4 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A285 
       38.20        92.75        12.59       140.38        44.32         6.12 
TCGA-DM-A28H TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6805 TCGA-F4-6807 
      117.07        31.96        35.74         6.18        34.42        16.24 
TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6309 
       47.41       133.18        74.56        65.85        53.62        85.48 
TCGA-G4-6310 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 
       63.62        36.00        13.78        35.80        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2693 TCGA-AF-6672 TCGA-AG-3732 TCGA-AG-3885 TCGA-AG-3887 
       79.69        19.10        10.39        32.98        17.95        36.95 
TCGA-AG-4005 TCGA-AG-A008 TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A020 TCGA-AG-A02X 
       14.04        13.94        37.02         9.07        10.98        41.00 
TCGA-AH-6547 TCGA-DC-5337 TCGA-DC-6155 TCGA-DC-6681 TCGA-DY-A0XA TCGA-DY-A1DD 
        1.45        15.02        13.97         5.95       126.44        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EI-6506 TCGA-EI-6508 TCGA-F5-6464 TCGA-F5-6465 
       24.13        51.48        20.55        20.91         9.96        49.51 
TCGA-F5-6812 
        0.66 

$`SMAD4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2683 TCGA-A6-3807 
       43.76        46.65        43.76        24.33        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5657 TCGA-A6-5661 TCGA-A6-5662 
       33.34        36.53        14.53        31.63        33.53        23.61 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       22.06        32.71         8.38        25.08        25.18        24.16 
TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       24.39        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
        1.02         9.07        36.03         8.05        19.07         0.00 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3663 
       23.01        19.99        13.94        19.99        61.02         6.97 
TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
       54.02        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3696 TCGA-AA-3710 
       11.01         5.98        37.05        19.00         5.03        26.99 
TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 
       19.04        35.05        33.04         0.99        25.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 
       15.95        38.99        37.02        14.93        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       31.07        31.07        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3971 
       26.01         2.01        20.98        34.03         2.01        16.08 
TCGA-AA-3972 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       50.99        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00L TCGA-AA-A00N 
       19.00        30.02        34.03        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       34.98         1.02        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
        5.03        14.01        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6901 
        0.07        21.37        56.55         0.79         0.72        22.42 
TCGA-AD-6965 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AZ-4315 TCGA-AZ-4323 
        0.20        16.31         0.95        33.01        58.39         1.41 
TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
       22.36        88.21        11.74         1.61        12.69         3.06 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5912 
        3.29         0.07        17.56       148.01        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       51.32        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-5341 TCGA-CM-5862 TCGA-CM-5863 
       20.02        37.02        25.02        29.06         5.03        15.02 
TCGA-CM-5864 TCGA-CM-6162 TCGA-CM-6164 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       15.02        12.00        29.03        14.99        12.99        13.02 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-D5-5537 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 
       45.40        55.92        20.19        15.12         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 TCGA-D5-6929 
       12.49        16.14         4.41        12.43         9.04         4.80 
TCGA-D5-6931 TCGA-D5-6932 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A1D0 TCGA-DM-A1D6 
       12.00        11.38       119.70        24.43       130.65        49.91 
TCGA-DM-A1D7 TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A28C 
       13.32         7.50       131.51       135.65       139.17        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6703 
      119.93        35.97        60.79        98.24         8.61        47.87 
TCGA-F4-6704 TCGA-F4-6806 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6856 
        1.55        41.42        33.67        13.25         0.53        35.31 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6315 TCGA-G4-6321 TCGA-G4-6588 TCGA-AF-2687 
       44.68        55.04        61.91        22.09        26.17        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       39.48        43.04        13.55        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       16.83        15.39        20.02        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
        0.99        37.02         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
        1.02        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4007 
       48.03        32.02        19.99        28.04        36.03         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A014 
       17.03        20.98         6.02        25.97        23.01        15.95 
TCGA-AG-A015 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A025 TCGA-AG-A026 
       36.03        12.00        70.03        64.01        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6549 
       38.96        61.97        38.04       117.11        38.56        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5869 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       78.12         7.17         5.03        27.95        10.98        19.99 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1H8 TCGA-EF-5830 
        4.01         5.03         5.29        41.36        32.61         0.49 
TCGA-EI-6507 TCGA-EI-6510 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6813 
       19.96        18.28        31.30        28.57        32.19         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  SMAD4 MUTATED SMAD4 WILD-TYPE 
              0               0 
  SMAD4 MUTATED SMAD4 WILD-TYPE 
         140.38          148.01 
  SMAD4 MUTATED SMAD4 WILD-TYPE 
         20.550          20.155 
[1] "0.0 - 140.4 (20.6)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.1"
D66V2, continuous
D66V3, binary
                 cls
clus                0   1
  SMAD4 MUTATED   119  24
  SMAD4 WILD-TYPE 247  95
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAD4 MUTATED    119   24
  SMAD4 WILD-TYPE  247   95
        clus
vv       SMAD4 MUTATED SMAD4 WILD-TYPE
  COLON            119             247
  RECTUM            24              95
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SMAD4 MUTATED        24        1        8        45         4         0
  SMAD4 WILD-TYPE      67        0       24        93         6         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SMAD4 MUTATED           5          2         22         12       12         4
  SMAD4 WILD-TYPE        19          9         37         30       36        14
                 vv
clus              STAGE IVB
  SMAD4 MUTATED           0
  SMAD4 WILD-TYPE         1
D66V4, multiclass
            clus
vv           SMAD4 MUTATED SMAD4 WILD-TYPE
  STAGE I               24              67
  STAGE IA               1               0
  STAGE II               8              24
  STAGE IIA             45              93
  STAGE IIB              4               6
  STAGE IIC              0               1
  STAGE III              5              19
  STAGE IIIA             2               9
  STAGE IIIB            22              37
  STAGE IIIC            12              30
  STAGE IV              12              36
  STAGE IVA              4              14
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  SMAD4 MUTATED     2  24 101  16
  SMAD4 WILD-TYPE  15  68 228  34
D66V5, multiclass
    clus
vv   SMAD4 MUTATED SMAD4 WILD-TYPE
  T1             2              15
  T2            24              68
  T3           101             228
  T4            16              34
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  SMAD4 MUTATED    88  32  24
  SMAD4 WILD-TYPE 199  81  63
D66V6, multiclass
    clus
vv   SMAD4 MUTATED SMAD4 WILD-TYPE
  N0            88             199
  N1            32              81
  N2            24              63
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V7, binary
                 cls
clus                0   1
  SMAD4 MUTATED   109  15
  SMAD4 WILD-TYPE 266  50
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAD4 MUTATED    109   15
  SMAD4 WILD-TYPE  266   50
   clus
vv  SMAD4 MUTATED SMAD4 WILD-TYPE
  0           109             266
  1            15              50
[1] 2 2
[1] FALSE
D66V8, binary
                 cls
clus                0   1
  SMAD4 MUTATED    75  69
  SMAD4 WILD-TYPE 150 195
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAD4 MUTATED     75   69
  SMAD4 WILD-TYPE  150  195
        clus
vv       SMAD4 MUTATED SMAD4 WILD-TYPE
  FEMALE            75             150
  MALE              69             195
[1] 2 2
[1] FALSE
D66V9, binary
                 cls
clus                0   1
  SMAD4 MUTATED   105   6
  SMAD4 WILD-TYPE 245  16
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAD4 MUTATED    105    6
  SMAD4 WILD-TYPE  245   16
     clus
vv    SMAD4 MUTATED SMAD4 WILD-TYPE
  NO            105             245
  YES             6              16
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SMAD4 MUTATED                    102                            16
  SMAD4 WILD-TYPE                  213                            31
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SMAD4 MUTATED                      20                              4
  SMAD4 WILD-TYPE                    86                              6
D66V10, multiclass
                                clus
vv                               SMAD4 MUTATED SMAD4 WILD-TYPE
  COLON ADENOCARCINOMA                     102             213
  COLON MUCINOUS ADENOCARCINOMA             16              31
  RECTAL ADENOCARCINOMA                     20              86
  RECTAL MUCINOUS ADENOCARCINOMA             4               6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  SMAD4 MUTATED    96   1   6   7
  SMAD4 WILD-TYPE 249   3  25  18
D66V11, multiclass
    clus
vv   SMAD4 MUTATED SMAD4 WILD-TYPE
  R0            96             249
  R1             1               3
  R2             6              25
  RX             7              18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SMAD4 MUTATED                                  0     5
  SMAD4 WILD-TYPE                                1     6
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  SMAD4 MUTATED                           9    96
  SMAD4 WILD-TYPE                        13   130
D66V13, multiclass
                                  clus
vv                                 SMAD4 MUTATED SMAD4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        5               6
  BLACK OR AFRICAN AMERICAN                    9              13
  WHITE                                       96             130
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(67) Variable = SLC26A8 MUTATION ANALYSIS
D67V1, survival
                   sevent
clus2                 0   1
  SLC26A8 MUTATED    14   4
  SLC26A8 WILD-TYPE 364  89
  SLC26A8 MUTATED SLC26A8 WILD-TYPE 
               18               453 
  SLC26A8 MUTATED SLC26A8 WILD-TYPE 
                4                89 
$`SLC26A8 MUTATED`
TCGA-A6-5665 TCGA-A6-6781 TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-A00E TCGA-AA-A010 
       22.06        19.66         3.02        63.98        30.02        34.98 
TCGA-AA-A01D TCGA-CA-6717 TCGA-CM-4743 TCGA-D5-6537 TCGA-D5-6924 TCGA-DM-A1HB 
       10.98        12.76        23.05         4.80        14.30       135.65 
TCGA-DM-A28F TCGA-G4-6588 TCGA-G4-6628 TCGA-AG-A002 TCGA-DC-6681 TCGA-G5-6641 
       35.97        26.17        79.69        20.98         5.95        26.43 

$`SLC26A8 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 
       20.12        20.28         7.04         1.02        35.01         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00F 
        7.96        27.02        13.94        38.04        19.00        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01F 
        0.99        17.03        14.99        21.99         1.02        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07        12.20        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
       82.95         1.91       124.27        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6538 
       18.25         1.32        43.27        15.12        17.85        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       12.43         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
        7.50        44.32       131.51       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
      119.93        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       35.80        91.79        46.75        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6682 
        5.03        13.97        27.95        10.98        19.99         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
        0.66         0.69        55.76 

  SLC26A8 MUTATED SLC26A8 WILD-TYPE 
             3.02              0.00 
  SLC26A8 MUTATED SLC26A8 WILD-TYPE 
           135.65            148.01 
  SLC26A8 MUTATED SLC26A8 WILD-TYPE 
           22.555            20.050 
[1] "3.0 - 135.7 (22.6)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1"  
D67V2, continuous
D67V3, binary
                   cls
clus                  0   1
  SLC26A8 MUTATED    16   3
  SLC26A8 WILD-TYPE 350 116
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC26A8 MUTATED     16    3
  SLC26A8 WILD-TYPE  350  116
        clus
vv       SLC26A8 MUTATED SLC26A8 WILD-TYPE
  COLON               16               350
  RECTUM               3               116
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SLC26A8 MUTATED         2        0        2         7         1         0
  SLC26A8 WILD-TYPE      89        1       30       131         9         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC26A8 MUTATED           0          1          3          2        0
  SLC26A8 WILD-TYPE        24         10         56         40       48
                   vv
clus                STAGE IVA STAGE IVB
  SLC26A8 MUTATED           1         0
  SLC26A8 WILD-TYPE        17         1
D67V4, multiclass
            clus
vv           SLC26A8 MUTATED SLC26A8 WILD-TYPE
  STAGE I                  2                89
  STAGE IA                 0                 1
  STAGE II                 2                30
  STAGE IIA                7               131
  STAGE IIB                1                 9
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               1                10
  STAGE IIIB               3                56
  STAGE IIIC               2                40
  STAGE IV                 0                48
  STAGE IVA                1                17
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  SLC26A8 MUTATED     1   2  14   2
  SLC26A8 WILD-TYPE  16  90 315  48
D67V5, multiclass
    clus
vv   SLC26A8 MUTATED SLC26A8 WILD-TYPE
  T1               1                16
  T2               2                90
  T3              14               315
  T4               2                48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  SLC26A8 MUTATED    12   5   2
  SLC26A8 WILD-TYPE 275 108  85
D67V6, multiclass
    clus
vv   SLC26A8 MUTATED SLC26A8 WILD-TYPE
  N0              12               275
  N1               5               108
  N2               2                85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V7, binary
                   cls
clus                  0   1
  SLC26A8 MUTATED    15   1
  SLC26A8 WILD-TYPE 360  64
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC26A8 MUTATED     15    1
  SLC26A8 WILD-TYPE  360   64
   clus
vv  SLC26A8 MUTATED SLC26A8 WILD-TYPE
  0              15               360
  1               1                64
[1] 2 2
[1] FALSE
D67V8, binary
                   cls
clus                  0   1
  SLC26A8 MUTATED     7  12
  SLC26A8 WILD-TYPE 218 252
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC26A8 MUTATED      7   12
  SLC26A8 WILD-TYPE  218  252
        clus
vv       SLC26A8 MUTATED SLC26A8 WILD-TYPE
  FEMALE               7               218
  MALE                12               252
[1] 2 2
[1] FALSE
D67V9, binary
                   cls
clus                  0   1
  SLC26A8 MUTATED    15   0
  SLC26A8 WILD-TYPE 335  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC26A8 MUTATED     15    0
  SLC26A8 WILD-TYPE  335   22
     clus
vv    SLC26A8 MUTATED SLC26A8 WILD-TYPE
  NO               15               335
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SLC26A8 MUTATED                     12                             3
  SLC26A8 WILD-TYPE                  303                            44
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SLC26A8 MUTATED                       2                              1
  SLC26A8 WILD-TYPE                   104                              9
D67V10, multiclass
                                clus
vv                               SLC26A8 MUTATED SLC26A8 WILD-TYPE
  COLON ADENOCARCINOMA                        12               303
  COLON MUCINOUS ADENOCARCINOMA                3                44
  RECTAL ADENOCARCINOMA                        2               104
  RECTAL MUCINOUS ADENOCARCINOMA               1                 9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  SLC26A8 MUTATED    16   0   0   1
  SLC26A8 WILD-TYPE 329   4  31  24
D67V11, multiclass
    clus
vv   SLC26A8 MUTATED SLC26A8 WILD-TYPE
  R0              16               329
  R1               0                 4
  R2               0                31
  RX               1                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SLC26A8 MUTATED                                  0     1
  SLC26A8 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  SLC26A8 MUTATED                           0    11
  SLC26A8 WILD-TYPE                        22   215
D67V13, multiclass
                                  clus
vv                                 SLC26A8 MUTATED SLC26A8 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                10
  BLACK OR AFRICAN AMERICAN                      0                22
  WHITE                                         11               215
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(68) Variable = RBBP7 MUTATION ANALYSIS
D68V1, survival
                 sevent
clus2               0   1
  RBBP7 MUTATED    14   3
  RBBP7 WILD-TYPE 364  90
  RBBP7 MUTATED RBBP7 WILD-TYPE 
             17             454 
  RBBP7 MUTATED RBBP7 WILD-TYPE 
              3              90 
$`RBBP7 MUTATED`
TCGA-A6-2671 TCGA-AA-3662 TCGA-AA-3864 TCGA-AA-3941 TCGA-AA-A00N TCGA-AA-A010 
       43.76         6.05        53.00        24.00         4.01        34.98 
TCGA-AA-A01Q TCGA-AD-5900 TCGA-AZ-4315 TCGA-CA-6717 TCGA-CK-5916 TCGA-CM-5344 
        1.02         0.07        58.39        12.76        21.14        22.03 
TCGA-CM-5861 TCGA-CM-6171 TCGA-D5-5538 TCGA-AG-A002 TCGA-DC-5337 
       15.02        14.04        12.26        20.98        15.02 

$`RBBP7 WILD-TYPE`
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       46.65        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       19.99        13.94        19.99        61.02        78.08         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 
        0.99        31.07        31.07        30.05        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01R 
       32.02        12.00        31.00        31.00        38.07        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 
       41.00        39.98        18.05        40.96        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       33.01        21.44        17.82         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       49.08        51.32         9.99        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       22.98        30.08        32.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 
       21.99        14.99        12.99        13.02        15.02        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       12.03        45.40        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5869 
       33.17         6.97         4.73        78.12         7.17         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  RBBP7 MUTATED RBBP7 WILD-TYPE 
           0.07            0.00 
  RBBP7 MUTATED RBBP7 WILD-TYPE 
          58.39          148.01 
  RBBP7 MUTATED RBBP7 WILD-TYPE 
         15.020          20.235 
[1] "0.1 - 58.4 (15.0)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.1"
D68V2, continuous
D68V3, binary
                 cls
clus                0   1
  RBBP7 MUTATED    15   2
  RBBP7 WILD-TYPE 351 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBBP7 MUTATED     15    2
  RBBP7 WILD-TYPE  351  117
        clus
vv       RBBP7 MUTATED RBBP7 WILD-TYPE
  COLON             15             351
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RBBP7 MUTATED         5        0        2         3         2         0
  RBBP7 WILD-TYPE      86        1       30       135         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RBBP7 MUTATED           0          0          2          0        2         1
  RBBP7 WILD-TYPE        24         11         57         42       46        17
                 vv
clus              STAGE IVB
  RBBP7 MUTATED           0
  RBBP7 WILD-TYPE         1
D68V4, multiclass
            clus
vv           RBBP7 MUTATED RBBP7 WILD-TYPE
  STAGE I                5              86
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA              3             135
  STAGE IIB              2               8
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             2              57
  STAGE IIIC             0              42
  STAGE IV               2              46
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  RBBP7 MUTATED     2   3   8   4
  RBBP7 WILD-TYPE  15  89 321  46
D68V5, multiclass
    clus
vv   RBBP7 MUTATED RBBP7 WILD-TYPE
  T1             2              15
  T2             3              89
  T3             8             321
  T4             4              46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  RBBP7 MUTATED    12   3   2
  RBBP7 WILD-TYPE 275 110  85
D68V6, multiclass
    clus
vv   RBBP7 MUTATED RBBP7 WILD-TYPE
  N0            12             275
  N1             3             110
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V7, binary
                 cls
clus                0   1
  RBBP7 MUTATED    13   3
  RBBP7 WILD-TYPE 362  62
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBBP7 MUTATED     13    3
  RBBP7 WILD-TYPE  362   62
   clus
vv  RBBP7 MUTATED RBBP7 WILD-TYPE
  0            13             362
  1             3              62
[1] 2 2
[1] FALSE
D68V8, binary
                 cls
clus                0   1
  RBBP7 MUTATED     9   8
  RBBP7 WILD-TYPE 216 256
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBBP7 MUTATED      9    8
  RBBP7 WILD-TYPE  216  256
        clus
vv       RBBP7 MUTATED RBBP7 WILD-TYPE
  FEMALE             9             216
  MALE               8             256
[1] 2 2
[1] FALSE
D68V9, binary
                 cls
clus                0   1
  RBBP7 MUTATED    14   0
  RBBP7 WILD-TYPE 336  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBBP7 MUTATED     14    0
  RBBP7 WILD-TYPE  336   22
     clus
vv    RBBP7 MUTATED RBBP7 WILD-TYPE
  NO             14             336
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  RBBP7 MUTATED                     12                             3
  RBBP7 WILD-TYPE                  303                            44
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  RBBP7 MUTATED                       2                              0
  RBBP7 WILD-TYPE                   104                             10
D68V10, multiclass
                                clus
vv                               RBBP7 MUTATED RBBP7 WILD-TYPE
  COLON ADENOCARCINOMA                      12             303
  COLON MUCINOUS ADENOCARCINOMA              3              44
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  RBBP7 MUTATED    14   0   1   2
  RBBP7 WILD-TYPE 331   4  30  23
D68V11, multiclass
    clus
vv   RBBP7 MUTATED RBBP7 WILD-TYPE
  R0            14             331
  R1             0               4
  R2             1              30
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RBBP7 MUTATED                                  0     1
  RBBP7 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  RBBP7 MUTATED                           0     9
  RBBP7 WILD-TYPE                        22   217
D68V13, multiclass
                                  clus
vv                                 RBBP7 MUTATED RBBP7 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        9             217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(69) Variable = RB1 MUTATION ANALYSIS
D69V1, survival
               sevent
clus2             0   1
  RB1 MUTATED    84  18
  RB1 WILD-TYPE 294  75
  RB1 MUTATED RB1 WILD-TYPE 
          102           369 
  RB1 MUTATED RB1 WILD-TYPE 
           18            75 
$`RB1 MUTATED`
TCGA-A6-4105 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6141 
       14.53        33.53        23.61        22.06        32.71         8.38 
TCGA-A6-6142 TCGA-A6-6649 TCGA-A6-6652 TCGA-A6-6780 TCGA-AA-3496 TCGA-AA-3502 
       25.08        24.16        24.69        20.12         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
       63.98        61.02         6.05        85.05        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3968 TCGA-AA-A010 TCGA-AD-6889 TCGA-AD-6895 TCGA-AD-6901 
       10.06        21.99        34.98        56.55         0.72        22.42 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-6197 TCGA-AZ-4323 TCGA-AZ-6598 TCGA-AZ-6599 
       14.50        27.09        21.44         1.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-CA-5797 TCGA-CA-6717 TCGA-CA-6719 
       12.10       100.01        29.56         3.29        12.76        14.30 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CM-4743 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       85.45        15.62        23.05        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-6161 TCGA-CM-6162 
       22.03        22.98        30.08        32.02        15.02        12.00 
TCGA-CM-6165 TCGA-CM-6169 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6678 
       16.04        13.02        14.04        11.01        12.95        11.01 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       12.26        19.59        18.25         1.32        43.27        15.12 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6923 TCGA-D5-6927 
       12.49        16.14         1.48         3.68        12.43         9.44 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0XD TCGA-DM-A1D4 TCGA-DM-A1HB TCGA-DM-A28C 
       11.38        10.26        24.43        92.75       135.65        81.37 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-F4-6570 TCGA-F4-6806 TCGA-G4-6293 
       35.97        60.79       117.07         6.18        41.42       133.18 
TCGA-G4-6299 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       74.56        53.62        44.68        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-AF-2693 TCGA-AF-4110 
       13.78        35.80        26.17        91.79        19.10        14.50 
TCGA-AF-6672 TCGA-AG-3742 TCGA-AG-3881 TCGA-AG-A002 TCGA-AH-6549 TCGA-CI-6619 
       10.39         0.99        19.04        20.98        17.49         6.05 
TCGA-CI-6620 TCGA-DY-A0XA TCGA-DY-A1H8 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6812 
       33.17       126.44        32.61        18.28         9.96         0.66 

$`RB1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 
       16.57        34.65        33.34        32.75        36.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5664 TCGA-A6-6137 TCGA-A6-6138 
       31.63        30.44        29.19        22.09        27.09        22.52 
TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 
       25.18        21.76        24.39        23.87        19.66        20.28 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        7.04         3.02         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       19.99        13.94        19.99        78.08         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3710 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       26.99        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3972 
        2.01        20.98        34.03         2.01        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 
       18.05        40.96         0.07        21.37        15.52         0.79 
TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AY-4070 TCGA-AY-4071 
        5.79        27.42        10.88         0.20        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       33.01        17.82        58.39         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
       62.79        88.21         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
       12.69         3.06         3.25         0.07        12.20        10.06 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       17.56       148.01        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-5861 
       82.95         1.91       124.27        20.02        37.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6163 TCGA-CM-6164 
        5.03        15.02        15.02        17.03         2.96        29.03 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6170 TCGA-CM-6675 TCGA-CM-6676 
       21.99        14.99        12.99        15.02        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5540 TCGA-D5-5541 
       11.08        10.06        12.03        45.40        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6541 TCGA-D5-6922 
       20.19        17.85         4.80        17.13        15.58         4.41 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
       14.30         9.04        11.64         4.80         1.51        12.00 
TCGA-DM-A0X9 TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
      119.70        38.20       130.65        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 
      140.38         7.50        44.32       131.51       139.17         6.12 
TCGA-DM-A28E TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 
      119.93        98.24         8.61        31.96        35.74        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
        1.55        34.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6303 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       47.41        35.31        65.85        55.04        85.48        63.62 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AG-3574 
       34.49        10.39        16.83        15.39        20.02        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3878 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6622 TCGA-CI-6624 
       38.56         1.45         0.69         0.72         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EF-5830 TCGA-EI-6506 
       41.36        57.24        24.13        51.48         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       19.96        20.91        49.51        31.30        28.57        32.19 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  RB1 MUTATED RB1 WILD-TYPE 
         0.66          0.00 
  RB1 MUTATED RB1 WILD-TYPE 
       135.65        148.01 
  RB1 MUTATED RB1 WILD-TYPE 
        20.55         20.19 
[1] "0.7 - 135.7 (20.6)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.3"
D69V2, continuous
D69V3, binary
               cls
clus              0   1
  RB1 MUTATED    88  12
  RB1 WILD-TYPE 278 107
[1] "tbl2"
               cls
clus            [,1] [,2]
  RB1 MUTATED     88   12
  RB1 WILD-TYPE  278  107
        clus
vv       RB1 MUTATED RB1 WILD-TYPE
  COLON           88           278
  RECTUM          12           107
[1] 2 2
[1] FALSE
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RB1 MUTATED        14        1        6        35         2         1
  RB1 WILD-TYPE      77        0       26       103         8         0
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RB1 MUTATED           4          4         11          5        7         8
  RB1 WILD-TYPE        20          7         48         37       41        10
               vv
clus            STAGE IVB
  RB1 MUTATED           0
  RB1 WILD-TYPE         1
D69V4, multiclass
            clus
vv           RB1 MUTATED RB1 WILD-TYPE
  STAGE I             14            77
  STAGE IA             1             0
  STAGE II             6            26
  STAGE IIA           35           103
  STAGE IIB            2             8
  STAGE IIC            1             0
  STAGE III            4            20
  STAGE IIIA           4             7
  STAGE IIIB          11            48
  STAGE IIIC           5            37
  STAGE IV             7            41
  STAGE IVA            8            10
  STAGE IVB            0             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  RB1 MUTATED     1  19  68  13
  RB1 WILD-TYPE  16  73 261  37
D69V5, multiclass
    clus
vv   RB1 MUTATED RB1 WILD-TYPE
  T1           1            16
  T2          19            73
  T3          68           261
  T4          13            37
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2
  RB1 MUTATED    66  24  11
  RB1 WILD-TYPE 221  89  76
D69V6, multiclass
    clus
vv   RB1 MUTATED RB1 WILD-TYPE
  N0          66           221
  N1          24            89
  N2          11            76
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V7, binary
               cls
clus              0   1
  RB1 MUTATED    74  12
  RB1 WILD-TYPE 301  53
[1] "tbl2"
               cls
clus            [,1] [,2]
  RB1 MUTATED     74   12
  RB1 WILD-TYPE  301   53
   clus
vv  RB1 MUTATED RB1 WILD-TYPE
  0          74           301
  1          12            53
[1] 2 2
[1] FALSE
D69V8, binary
               cls
clus              0   1
  RB1 MUTATED    46  56
  RB1 WILD-TYPE 179 208
[1] "tbl2"
               cls
clus            [,1] [,2]
  RB1 MUTATED     46   56
  RB1 WILD-TYPE  179  208
        clus
vv       RB1 MUTATED RB1 WILD-TYPE
  FEMALE          46           179
  MALE            56           208
[1] 2 2
[1] FALSE
D69V9, binary
               cls
clus              0   1
  RB1 MUTATED    79   2
  RB1 WILD-TYPE 271  20
[1] "tbl2"
               cls
clus            [,1] [,2]
  RB1 MUTATED     79    2
  RB1 WILD-TYPE  271   20
     clus
vv    RB1 MUTATED RB1 WILD-TYPE
  NO           79           271
  YES           2            20
[1] 2 2
[1] FALSE
               vv
clus            COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  RB1 MUTATED                     79                             8
  RB1 WILD-TYPE                  236                            39
               vv
clus            RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  RB1 MUTATED                      11                              0
  RB1 WILD-TYPE                    95                             10
D69V10, multiclass
                                clus
vv                               RB1 MUTATED RB1 WILD-TYPE
  COLON ADENOCARCINOMA                    79           236
  COLON MUCINOUS ADENOCARCINOMA            8            39
  RECTAL ADENOCARCINOMA                   11            95
  RECTAL MUCINOUS ADENOCARCINOMA           0            10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             R0  R1  R2  RX
  RB1 MUTATED    63   1   2   5
  RB1 WILD-TYPE 282   3  29  20
D69V11, multiclass
    clus
vv   RB1 MUTATED RB1 WILD-TYPE
  R0          63           282
  R1           1             3
  R2           2            29
  RX           5            20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V12, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RB1 MUTATED                                  0     4
  RB1 WILD-TYPE                                1     7
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  RB1 MUTATED                           8    76
  RB1 WILD-TYPE                        14   150
D69V13, multiclass
                                  clus
vv                                 RB1 MUTATED RB1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      4             7
  BLACK OR AFRICAN AMERICAN                  8            14
  WHITE                                     76           150
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(70) Variable = L1TD1 MUTATION ANALYSIS
D70V1, survival
                 sevent
clus2               0   1
  L1TD1 MUTATED    17   2
  L1TD1 WILD-TYPE 361  91
  L1TD1 MUTATED L1TD1 WILD-TYPE 
             19             452 
  L1TD1 MUTATED L1TD1 WILD-TYPE 
              2              91 
$`L1TD1 MUTATED`
TCGA-A6-3809 TCGA-A6-6654 TCGA-A6-6781 TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3525 
       32.75        23.87        19.66         3.02        63.98         8.05 
TCGA-AA-3663 TCGA-AA-A00J TCGA-AA-A00N TCGA-AA-A010 TCGA-CA-5254 TCGA-CA-6717 
        6.97        18.05         4.01        34.98        12.69        12.76 
TCGA-CM-6166 TCGA-D5-6929 TCGA-G4-6309 TCGA-G4-6588 TCGA-AF-4110 TCGA-AG-A002 
       21.99         4.80        85.48        26.17        14.50        20.98 
TCGA-CI-6624 
        4.73 

$`L1TD1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 
       25.18        24.16        21.76        24.69        24.39        20.12 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 
       20.28         7.04         1.02        35.01         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
       13.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
       36.03        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.05        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L 
       38.04        19.00        30.02        34.03        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5255 
       29.56         5.23        11.74         3.19         1.61         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07        12.20        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       16.04        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
        9.44        11.64         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 
       74.56        65.85        53.62        44.68        55.04        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 
       61.91        36.00        22.09        13.78        35.80        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       19.10        34.49        10.39        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  L1TD1 MUTATED L1TD1 WILD-TYPE 
           3.02            0.00 
  L1TD1 MUTATED L1TD1 WILD-TYPE 
          85.48          148.01 
  L1TD1 MUTATED L1TD1 WILD-TYPE 
         18.050          20.415 
[1] "3.0 - 85.5 (18.1)"  "0.0 - 148.0 (20.4)"
[1] "hr=" "1.6"
D70V2, continuous
D70V3, binary
                 cls
clus                0   1
  L1TD1 MUTATED    17   2
  L1TD1 WILD-TYPE 349 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  L1TD1 MUTATED     17    2
  L1TD1 WILD-TYPE  349  117
        clus
vv       L1TD1 MUTATED L1TD1 WILD-TYPE
  COLON             17             349
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  L1TD1 MUTATED         3        0        3         4         3         0
  L1TD1 WILD-TYPE      88        1       29       134         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  L1TD1 MUTATED           0          0          4          1        1         1
  L1TD1 WILD-TYPE        24         11         55         41       47        17
                 vv
clus              STAGE IVB
  L1TD1 MUTATED           0
  L1TD1 WILD-TYPE         1
D70V4, multiclass
            clus
vv           L1TD1 MUTATED L1TD1 WILD-TYPE
  STAGE I                3              88
  STAGE IA               0               1
  STAGE II               3              29
  STAGE IIA              4             134
  STAGE IIB              3               7
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             4              55
  STAGE IIIC             1              41
  STAGE IV               1              47
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  L1TD1 MUTATED     0   3  11   6
  L1TD1 WILD-TYPE  17  89 318  44
D70V5, multiclass
    clus
vv   L1TD1 MUTATED L1TD1 WILD-TYPE
  T1             0              17
  T2             3              89
  T3            11             318
  T4             6              44
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  L1TD1 MUTATED    13   6   1
  L1TD1 WILD-TYPE 274 107  86
D70V6, multiclass
    clus
vv   L1TD1 MUTATED L1TD1 WILD-TYPE
  N0            13             274
  N1             6             107
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V7, binary
                 cls
clus                0   1
  L1TD1 MUTATED    17   1
  L1TD1 WILD-TYPE 358  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  L1TD1 MUTATED     17    1
  L1TD1 WILD-TYPE  358   64
   clus
vv  L1TD1 MUTATED L1TD1 WILD-TYPE
  0            17             358
  1             1              64
[1] 2 2
[1] FALSE
D70V8, binary
                 cls
clus                0   1
  L1TD1 MUTATED    11   9
  L1TD1 WILD-TYPE 214 255
[1] "tbl2"
                 cls
clus              [,1] [,2]
  L1TD1 MUTATED     11    9
  L1TD1 WILD-TYPE  214  255
        clus
vv       L1TD1 MUTATED L1TD1 WILD-TYPE
  FEMALE            11             214
  MALE               9             255
[1] 2 2
[1] FALSE
D70V9, binary
                 cls
clus                0   1
  L1TD1 MUTATED    16   0
  L1TD1 WILD-TYPE 334  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  L1TD1 MUTATED     16    0
  L1TD1 WILD-TYPE  334   22
     clus
vv    L1TD1 MUTATED L1TD1 WILD-TYPE
  NO             16             334
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  L1TD1 MUTATED                     12                             5
  L1TD1 WILD-TYPE                  303                            42
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  L1TD1 MUTATED                       2                              0
  L1TD1 WILD-TYPE                   104                             10
D70V10, multiclass
                                clus
vv                               L1TD1 MUTATED L1TD1 WILD-TYPE
  COLON ADENOCARCINOMA                      12             303
  COLON MUCINOUS ADENOCARCINOMA              5              42
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  L1TD1 MUTATED    16   0   0   2
  L1TD1 WILD-TYPE 329   4  31  23
D70V11, multiclass
    clus
vv   L1TD1 MUTATED L1TD1 WILD-TYPE
  R0            16             329
  R1             0               4
  R2             0              31
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  L1TD1 MUTATED                                  0     2
  L1TD1 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  L1TD1 MUTATED                           1     8
  L1TD1 WILD-TYPE                        21   218
D70V13, multiclass
                                  clus
vv                                 L1TD1 MUTATED L1TD1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               9
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        8             218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(71) Variable = TOP2B MUTATION ANALYSIS
D71V1, survival
                 sevent
clus2               0   1
  TOP2B MUTATED    21   3
  TOP2B WILD-TYPE 357  90
  TOP2B MUTATED TOP2B WILD-TYPE 
             24             447 
  TOP2B MUTATED TOP2B WILD-TYPE 
              3              90 
$`TOP2B MUTATED`
TCGA-A6-5661 TCGA-A6-5665 TCGA-AA-3510 TCGA-AA-3815 TCGA-AA-3855 TCGA-AA-3864 
       33.53        22.06        63.98        33.04        32.05        53.00 
TCGA-AA-A010 TCGA-AA-A01R TCGA-AD-6889 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-CK-5912 
       34.98        35.01        56.55        58.39        49.41        49.08 
TCGA-CM-4743 TCGA-CM-5861 TCGA-CM-6161 TCGA-CM-6165 TCGA-D5-6536 TCGA-DM-A0XD 
       23.05        15.02        15.02        16.04        17.85        24.43 
TCGA-F4-6856 TCGA-G4-6315 TCGA-G4-6586 TCGA-G4-6628 TCGA-AG-A002 TCGA-EI-6510 
       35.31        61.91        35.80        79.69        20.98        18.28 

$`TOP2B WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
       33.07         0.00        36.03         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       30.05        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S 
       12.00        31.00        31.00        38.07         1.02         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        88.21         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5913 
       14.30        17.56       148.01        85.45        15.62        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 
        9.99        21.14        82.95         1.91       124.27        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       30.08        32.02         5.03        15.02        15.02        17.03 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
       12.00         2.96        29.03        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
        1.32        43.27        15.12         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XF TCGA-DM-A1D0 
       12.00        11.38        10.26       119.70        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 
       85.48        63.62        36.00        22.09        13.78        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       91.79        46.75        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  TOP2B MUTATED TOP2B WILD-TYPE 
          15.02            0.00 
  TOP2B MUTATED TOP2B WILD-TYPE 
          79.69          148.01 
  TOP2B MUTATED TOP2B WILD-TYPE 
         34.255          19.990 
[1] "15.0 - 79.7 (34.3)" "0.0 - 148.0 (20.0)"
[1] "hr=" "2.3"
D71V2, continuous
D71V3, binary
                 cls
clus                0   1
  TOP2B MUTATED    23   2
  TOP2B WILD-TYPE 343 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TOP2B MUTATED     23    2
  TOP2B WILD-TYPE  343  117
        clus
vv       TOP2B MUTATED TOP2B WILD-TYPE
  COLON             23             343
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TOP2B MUTATED         6        0        4        11         1         0
  TOP2B WILD-TYPE      85        1       28       127         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TOP2B MUTATED           1          0          0          0        1         1
  TOP2B WILD-TYPE        23         11         59         42       47        17
                 vv
clus              STAGE IVB
  TOP2B MUTATED           0
  TOP2B WILD-TYPE         1
D71V4, multiclass
            clus
vv           TOP2B MUTATED TOP2B WILD-TYPE
  STAGE I                6              85
  STAGE IA               0               1
  STAGE II               4              28
  STAGE IIA             11             127
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             0              42
  STAGE IV               1              47
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  TOP2B MUTATED     0   7  16   2
  TOP2B WILD-TYPE  17  85 313  48
D71V5, multiclass
    clus
vv   TOP2B MUTATED TOP2B WILD-TYPE
  T1             0              17
  T2             7              85
  T3            16             313
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  TOP2B MUTATED    23   1   1
  TOP2B WILD-TYPE 264 112  86
D71V6, multiclass
    clus
vv   TOP2B MUTATED TOP2B WILD-TYPE
  N0            23             264
  N1             1             112
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V7, binary
                 cls
clus                0   1
  TOP2B MUTATED    21   1
  TOP2B WILD-TYPE 354  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TOP2B MUTATED     21    1
  TOP2B WILD-TYPE  354   64
   clus
vv  TOP2B MUTATED TOP2B WILD-TYPE
  0            21             354
  1             1              64
[1] 2 2
[1] FALSE
D71V8, binary
                 cls
clus                0   1
  TOP2B MUTATED    10  15
  TOP2B WILD-TYPE 215 249
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TOP2B MUTATED     10   15
  TOP2B WILD-TYPE  215  249
        clus
vv       TOP2B MUTATED TOP2B WILD-TYPE
  FEMALE            10             215
  MALE              15             249
[1] 2 2
[1] FALSE
D71V9, binary
                 cls
clus                0   1
  TOP2B MUTATED    21   1
  TOP2B WILD-TYPE 329  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TOP2B MUTATED     21    1
  TOP2B WILD-TYPE  329   21
     clus
vv    TOP2B MUTATED TOP2B WILD-TYPE
  NO             21             329
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  TOP2B MUTATED                     21                             2
  TOP2B WILD-TYPE                  294                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  TOP2B MUTATED                       2                              0
  TOP2B WILD-TYPE                   104                             10
D71V10, multiclass
                                clus
vv                               TOP2B MUTATED TOP2B WILD-TYPE
  COLON ADENOCARCINOMA                      21             294
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  TOP2B MUTATED    21   0   0   1
  TOP2B WILD-TYPE 324   4  31  24
D71V11, multiclass
    clus
vv   TOP2B MUTATED TOP2B WILD-TYPE
  R0            21             324
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TOP2B MUTATED                                  0     1
  TOP2B WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  TOP2B MUTATED                           1    15
  TOP2B WILD-TYPE                        21   211
D71V13, multiclass
                                  clus
vv                                 TOP2B MUTATED TOP2B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                       15             211
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(72) Variable = DCLK2 MUTATION ANALYSIS
D72V1, survival
                 sevent
clus2               0   1
  DCLK2 MUTATED    15   0
  DCLK2 WILD-TYPE 363  93
  DCLK2 MUTATED DCLK2 WILD-TYPE 
             15             456 
  DCLK2 MUTATED DCLK2 WILD-TYPE 
              0              93 
$`DCLK2 MUTATED`
TCGA-AA-3663 TCGA-AA-3815 TCGA-AA-3821 TCGA-AA-3947 TCGA-AZ-4315 TCGA-AZ-5407 
        6.97        33.04         1.02        33.01        58.39        88.21 
TCGA-CM-5868 TCGA-CM-6679 TCGA-D5-6533 TCGA-D5-6539 TCGA-D5-6928 TCGA-F4-6703 
       17.03        10.06         1.32        12.49        11.64        47.87 
TCGA-G4-6306 TCGA-AG-3883 TCGA-AG-A002 
       44.68         1.02        20.98 

$`DCLK2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.05        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 
       10.06        35.05         0.99        25.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       15.02        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       20.19        18.25        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       17.13        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6930 
       12.43        14.30         9.04         9.44         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6704 TCGA-F4-6805 
        8.61        31.96        35.74         6.18         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6307 
       35.31       133.18        74.56        65.85        53.62        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
        0.99        19.04        19.99        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  DCLK2 MUTATED DCLK2 WILD-TYPE 
           1.02            0.00 
  DCLK2 MUTATED DCLK2 WILD-TYPE 
          88.21          148.01 
  DCLK2 MUTATED DCLK2 WILD-TYPE 
         17.030          20.235 
[1] "1.0 - 88.2 (17.0)"  "0.0 - 148.0 (20.2)"
[1] "hr="     "2.6e+07"
D72V2, continuous
D72V3, binary
                 cls
clus                0   1
  DCLK2 MUTATED    14   2
  DCLK2 WILD-TYPE 352 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DCLK2 MUTATED     14    2
  DCLK2 WILD-TYPE  352  117
        clus
vv       DCLK2 MUTATED DCLK2 WILD-TYPE
  COLON             14             352
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DCLK2 MUTATED         4        0        1         7         1         0
  DCLK2 WILD-TYPE      87        1       31       131         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DCLK2 MUTATED           0          1          1          0        0         1
  DCLK2 WILD-TYPE        24         10         58         42       48        17
                 vv
clus              STAGE IVB
  DCLK2 MUTATED           0
  DCLK2 WILD-TYPE         1
D72V4, multiclass
            clus
vv           DCLK2 MUTATED DCLK2 WILD-TYPE
  STAGE I                4              87
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              7             131
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             1              10
  STAGE IIIB             1              58
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  DCLK2 MUTATED     1   4   8   3
  DCLK2 WILD-TYPE  16  88 321  47
D72V5, multiclass
    clus
vv   DCLK2 MUTATED DCLK2 WILD-TYPE
  T1             1              16
  T2             4              88
  T3             8             321
  T4             3              47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  DCLK2 MUTATED    15   1   0
  DCLK2 WILD-TYPE 272 112  87
D72V6, multiclass
    clus
vv   DCLK2 MUTATED DCLK2 WILD-TYPE
  N0            15             272
  N1             1             112
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V7, binary
                 cls
clus                0   1
  DCLK2 MUTATED    15   1
  DCLK2 WILD-TYPE 360  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DCLK2 MUTATED     15    1
  DCLK2 WILD-TYPE  360   64
   clus
vv  DCLK2 MUTATED DCLK2 WILD-TYPE
  0            15             360
  1             1              64
[1] 2 2
[1] FALSE
D72V8, binary
                 cls
clus                0   1
  DCLK2 MUTATED     8   8
  DCLK2 WILD-TYPE 217 256
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DCLK2 MUTATED      8    8
  DCLK2 WILD-TYPE  217  256
        clus
vv       DCLK2 MUTATED DCLK2 WILD-TYPE
  FEMALE             8             217
  MALE               8             256
[1] 2 2
[1] FALSE
D72V9, binary
                 cls
clus                0   1
  DCLK2 MUTATED    13   0
  DCLK2 WILD-TYPE 337  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DCLK2 MUTATED     13    0
  DCLK2 WILD-TYPE  337   22
     clus
vv    DCLK2 MUTATED DCLK2 WILD-TYPE
  NO             13             337
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  DCLK2 MUTATED                     11                             3
  DCLK2 WILD-TYPE                  304                            44
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  DCLK2 MUTATED                       2                              0
  DCLK2 WILD-TYPE                   104                             10
D72V10, multiclass
                                clus
vv                               DCLK2 MUTATED DCLK2 WILD-TYPE
  COLON ADENOCARCINOMA                      11             304
  COLON MUCINOUS ADENOCARCINOMA              3              44
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  DCLK2 MUTATED    15   0   0   0
  DCLK2 WILD-TYPE 330   4  31  25
D72V11, multiclass
    clus
vv   DCLK2 MUTATED DCLK2 WILD-TYPE
  R0            15             330
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DCLK2 MUTATED                                  0     0
  DCLK2 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  DCLK2 MUTATED                           0     9
  DCLK2 WILD-TYPE                        22   217
D72V13, multiclass
                                  clus
vv                                 DCLK2 MUTATED DCLK2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        9             217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(73) Variable = FKBP9 MUTATION ANALYSIS
D73V1, survival
                 sevent
clus2               0   1
  FKBP9 MUTATED    17   2
  FKBP9 WILD-TYPE 361  91
  FKBP9 MUTATED FKBP9 WILD-TYPE 
             19             452 
  FKBP9 MUTATED FKBP9 WILD-TYPE 
              2              91 
$`FKBP9 MUTATED`
TCGA-A6-6780 TCGA-AA-3697 TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01Q 
       20.12        85.05        25.02         4.01        34.98         1.02 
TCGA-AD-6889 TCGA-AZ-4315 TCGA-AZ-6601 TCGA-CK-5913 TCGA-CM-5348 TCGA-CM-5861 
       56.55        58.39       100.01        51.32        22.98        15.02 
TCGA-CM-6678 TCGA-D5-6930 TCGA-DM-A28H TCGA-G4-6588 TCGA-G4-6628 TCGA-AG-A002 
       11.01         1.51       117.07        26.17        79.69        20.98 
TCGA-CI-6619 
        6.05 

$`FKBP9 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       21.37        15.52         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        33.01        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
       12.10        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        49.08         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 
       29.06        22.03        30.08        32.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
        9.44        11.64         4.80        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
       60.79        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 
       61.91        36.00        22.09        13.78        35.80        91.79 
TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       46.75        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
       17.49         0.69         0.72        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  FKBP9 MUTATED FKBP9 WILD-TYPE 
           1.02            0.00 
  FKBP9 MUTATED FKBP9 WILD-TYPE 
         117.07          148.01 
  FKBP9 MUTATED FKBP9 WILD-TYPE 
          25.02           20.02 
[1] "1.0 - 117.1 (25.0)" "0.0 - 148.0 (20.0)"
[1] "hr=" "2.9"
D73V2, continuous
D73V3, binary
                 cls
clus                0   1
  FKBP9 MUTATED    17   2
  FKBP9 WILD-TYPE 349 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FKBP9 MUTATED     17    2
  FKBP9 WILD-TYPE  349  117
        clus
vv       FKBP9 MUTATED FKBP9 WILD-TYPE
  COLON             17             349
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FKBP9 MUTATED         2        0        2         7         2         0
  FKBP9 WILD-TYPE      89        1       30       131         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  FKBP9 MUTATED           1          0          1          1        1         1
  FKBP9 WILD-TYPE        23         11         58         41       47        17
                 vv
clus              STAGE IVB
  FKBP9 MUTATED           0
  FKBP9 WILD-TYPE         1
D73V4, multiclass
            clus
vv           FKBP9 MUTATED FKBP9 WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA              7             131
  STAGE IIB              2               8
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             1              41
  STAGE IV               1              47
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  FKBP9 MUTATED     0   3  13   3
  FKBP9 WILD-TYPE  17  89 316  47
D73V5, multiclass
    clus
vv   FKBP9 MUTATED FKBP9 WILD-TYPE
  T1             0              17
  T2             3              89
  T3            13             316
  T4             3              47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  FKBP9 MUTATED    15   3   1
  FKBP9 WILD-TYPE 272 110  86
D73V6, multiclass
    clus
vv   FKBP9 MUTATED FKBP9 WILD-TYPE
  N0            15             272
  N1             3             110
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V7, binary
                 cls
clus                0   1
  FKBP9 MUTATED    14   2
  FKBP9 WILD-TYPE 361  63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FKBP9 MUTATED     14    2
  FKBP9 WILD-TYPE  361   63
   clus
vv  FKBP9 MUTATED FKBP9 WILD-TYPE
  0            14             361
  1             2              63
[1] 2 2
[1] FALSE
D73V8, binary
                 cls
clus                0   1
  FKBP9 MUTATED     6  13
  FKBP9 WILD-TYPE 219 251
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FKBP9 MUTATED      6   13
  FKBP9 WILD-TYPE  219  251
        clus
vv       FKBP9 MUTATED FKBP9 WILD-TYPE
  FEMALE             6             219
  MALE              13             251
[1] 2 2
[1] FALSE
D73V9, binary
                 cls
clus                0   1
  FKBP9 MUTATED    13   0
  FKBP9 WILD-TYPE 337  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FKBP9 MUTATED     13    0
  FKBP9 WILD-TYPE  337   22
     clus
vv    FKBP9 MUTATED FKBP9 WILD-TYPE
  NO             13             337
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  FKBP9 MUTATED                     14                             3
  FKBP9 WILD-TYPE                  301                            44
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  FKBP9 MUTATED                       2                              0
  FKBP9 WILD-TYPE                   104                             10
D73V10, multiclass
                                clus
vv                               FKBP9 MUTATED FKBP9 WILD-TYPE
  COLON ADENOCARCINOMA                      14             301
  COLON MUCINOUS ADENOCARCINOMA              3              44
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  FKBP9 MUTATED    12   0   0   1
  FKBP9 WILD-TYPE 333   4  31  24
D73V11, multiclass
    clus
vv   FKBP9 MUTATED FKBP9 WILD-TYPE
  R0            12             333
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FKBP9 MUTATED                                  0     1
  FKBP9 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  FKBP9 MUTATED                           0    12
  FKBP9 WILD-TYPE                        22   214
D73V13, multiclass
                                  clus
vv                                 FKBP9 MUTATED FKBP9 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                       12             214
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(74) Variable = PTEN MUTATION ANALYSIS
D74V1, survival
                sevent
clus2              0   1
  PTEN MUTATED   148  34
  PTEN WILD-TYPE 230  59
  PTEN MUTATED PTEN WILD-TYPE 
           182            289 
  PTEN MUTATED PTEN WILD-TYPE 
            34             59 
$`PTEN MUTATED`
TCGA-A6-2671 TCGA-A6-3809 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       43.76        32.75        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6648 TCGA-A6-6649 
       33.53        23.61        22.09        32.71        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6781 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3655 
       21.76        24.69        19.66         1.02        35.01        61.02 
TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3692 TCGA-AA-3713 TCGA-AA-3815 TCGA-AA-3864 
       78.08         6.97        36.00        19.04        33.04        53.00 
TCGA-AA-3950 TCGA-AA-3968 TCGA-AA-3977 TCGA-AA-A010 TCGA-AD-5900 TCGA-AD-6888 
       24.00        21.99        25.02        34.98         0.07        15.52 
TCGA-AD-6889 TCGA-AD-6895 TCGA-AD-6901 TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-5543 
       56.55         0.72        22.42         0.20        27.09        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
       21.44        17.82        58.39        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       49.41         6.77       100.01        29.56         5.23        11.74 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-6716 TCGA-CA-6718 
        1.61        12.69         3.06         3.25        12.20        10.06 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-4747 
        9.99        82.95         1.91        23.05        37.02        25.02 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6162 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        17.03        12.00        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6680 TCGA-D5-5539 
       13.05        11.08        11.08        11.01        12.03        19.59 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6898 
       17.85         4.80        17.13        12.49        16.14         1.48 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
        4.41        12.43        14.30         9.44        11.64         4.80 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D6 
       11.38        10.26       119.70        24.43        38.20        49.91 
TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
       12.59         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28K TCGA-F4-6569 
       81.37       119.93        35.97        60.79        98.24        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
        6.18        47.87        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6317 
       65.85        44.68        55.04        85.48        61.91        36.00 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2693 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6672 TCGA-AG-3732 
       24.13        19.10        16.83        15.39        10.39        32.98 
TCGA-AG-3885 TCGA-AG-3892 TCGA-AG-A002 TCGA-AH-6547 TCGA-AH-6549 TCGA-CI-6619 
       17.95        13.02        20.98         1.45        17.49         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CL-5917 TCGA-DC-5337 TCGA-DC-6157 TCGA-DC-6160 
       33.17         6.97        78.12        15.02        27.95        19.99 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
        5.03         5.29       126.44        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6510 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6811 
        0.49        20.55        18.28        49.51        31.30        32.19 
TCGA-F5-6813 TCGA-G5-6235 
        0.69        55.76 

$`PTEN WILD-TYPE`
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       46.65        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5665 TCGA-A6-6137 
       34.65        33.34        36.53        14.53        22.06        27.09 
TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       22.52         8.38        25.08        24.39        23.87        20.12 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
       20.28         7.04         3.02        63.98         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
       13.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       36.03         8.05        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3662 
       23.01        20.98        19.99        13.94        19.99         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3696 
       15.02        11.01         5.98        37.05        19.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
       85.05        26.99        19.04        10.06        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       30.05        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3972 
        2.01        20.98        34.03         2.01        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6964 
       40.96        21.37         0.79         5.79        27.42        10.88 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       14.50        16.31         0.95         1.41         5.13       106.75 
TCGA-AZ-6600 TCGA-AZ-6607 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6719 
       12.10         3.19         3.29         0.07        12.76        14.30 
TCGA-CK-5916 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5863 
       21.14       124.27        20.02        13.02        29.06        15.02 
TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6674 TCGA-CM-6679 TCGA-D5-5537 TCGA-D5-5538 
       15.02         2.96        12.95        10.06        45.40        12.26 
TCGA-D5-5540 TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6926 TCGA-D5-6930 TCGA-D5-6931 
       56.09        15.58         3.68         9.04         1.51        12.00 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A285 TCGA-DM-A28H 
      130.65        92.75        13.32       140.38         6.12       117.07 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6704 TCGA-G4-6304 TCGA-G4-6310 TCGA-G4-6321 
        8.61        31.96         1.55        53.62        63.62        22.09 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       39.48        43.04        13.55        34.49        10.39        14.50 
TCGA-AF-6655 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       20.02        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 
        0.99         0.99        19.04        19.99         1.02        36.95 
TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       17.03        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6624 TCGA-CL-5918 
      117.11        38.56         0.69         0.72         4.73         7.17 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6158 TCGA-DC-6681 TCGA-DC-6682 TCGA-DY-A1DC 
        5.03        13.97        10.98         5.95         4.01        41.36 
TCGA-DY-A1DD TCGA-EI-6507 TCGA-EI-6508 TCGA-F5-6464 TCGA-F5-6702 TCGA-F5-6812 
       57.24        19.96        20.91         9.96        28.57         0.66 
TCGA-G5-6641 
       26.43 

  PTEN MUTATED PTEN WILD-TYPE 
          0.07           0.00 
  PTEN MUTATED PTEN WILD-TYPE 
        148.01         140.38 
  PTEN MUTATED PTEN WILD-TYPE 
         22.39          19.99 
[1] "0.1 - 148.0 (22.4)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1.5"
D74V2, continuous
D74V3, binary
                cls
clus               0   1
  PTEN MUTATED   153  32
  PTEN WILD-TYPE 213  87
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED    153   32
  PTEN WILD-TYPE  213   87
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  COLON           153            213
  RECTUM           32             87
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PTEN MUTATED        33        1        9        54         5         1
  PTEN WILD-TYPE      58        0       23        84         5         0
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PTEN MUTATED           3          5         28         15       10        13
  PTEN WILD-TYPE        21          6         31         27       38         5
                vv
clus             STAGE IVB
  PTEN MUTATED           1
  PTEN WILD-TYPE         0
D74V4, multiclass
            clus
vv           PTEN MUTATED PTEN WILD-TYPE
  STAGE I              33             58
  STAGE IA              1              0
  STAGE II              9             23
  STAGE IIA            54             84
  STAGE IIB             5              5
  STAGE IIC             1              0
  STAGE III             3             21
  STAGE IIIA            5              6
  STAGE IIIB           28             31
  STAGE IIIC           15             27
  STAGE IV             10             38
  STAGE IVA            13              5
  STAGE IVB             1              0
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  PTEN MUTATED     4  35 127  19
  PTEN WILD-TYPE  13  57 202  31
D74V5, multiclass
    clus
vv   PTEN MUTATED PTEN WILD-TYPE
  T1            4             13
  T2           35             57
  T3          127            202
  T4           19             31
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  PTEN MUTATED   113  48  24
  PTEN WILD-TYPE 174  65  63
D74V6, multiclass
    clus
vv   PTEN MUTATED PTEN WILD-TYPE
  N0          113            174
  N1           48             65
  N2           24             63
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V7, binary
                cls
clus               0   1
  PTEN MUTATED   132  22
  PTEN WILD-TYPE 243  43
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED    132   22
  PTEN WILD-TYPE  243   43
   clus
vv  PTEN MUTATED PTEN WILD-TYPE
  0          132            243
  1           22             43
[1] 2 2
[1] FALSE
D74V8, binary
                cls
clus               0   1
  PTEN MUTATED    89  97
  PTEN WILD-TYPE 136 167
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED     89   97
  PTEN WILD-TYPE  136  167
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  FEMALE           89            136
  MALE             97            167
[1] 2 2
[1] FALSE
D74V9, binary
                cls
clus               0   1
  PTEN MUTATED   136   7
  PTEN WILD-TYPE 214  15
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED    136    7
  PTEN WILD-TYPE  214   15
     clus
vv    PTEN MUTATED PTEN WILD-TYPE
  NO           136            214
  YES            7             15
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PTEN MUTATED                    134                            17
  PTEN WILD-TYPE                  181                            30
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PTEN MUTATED                      30                              2
  PTEN WILD-TYPE                    76                              8
D74V10, multiclass
                                clus
vv                               PTEN MUTATED PTEN WILD-TYPE
  COLON ADENOCARCINOMA                    134            181
  COLON MUCINOUS ADENOCARCINOMA            17             30
  RECTAL ADENOCARCINOMA                    30             76
  RECTAL MUCINOUS ADENOCARCINOMA            2              8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  PTEN MUTATED   115   2   2  17
  PTEN WILD-TYPE 230   2  29   8
D74V11, multiclass
    clus
vv   PTEN MUTATED PTEN WILD-TYPE
  R0          115            230
  R1            2              2
  R2            2             29
  RX           17              8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PTEN MUTATED                                  0     7
  PTEN WILD-TYPE                                1     4
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  PTEN MUTATED                          16   144
  PTEN WILD-TYPE                         6    82
D74V13, multiclass
                                  clus
vv                                 PTEN MUTATED PTEN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       7              4
  BLACK OR AFRICAN AMERICAN                  16              6
  WHITE                                     144             82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(75) Variable = C14ORF184 MUTATION ANALYSIS
D75V1, survival
                     sevent
clus2                   0   1
  C14ORF184 MUTATED     5   2
  C14ORF184 WILD-TYPE 373  91
  C14ORF184 MUTATED C14ORF184 WILD-TYPE 
                  7                 464 
  C14ORF184 MUTATED C14ORF184 WILD-TYPE 
                  2                  91 
$`C14ORF184 MUTATED`
TCGA-AA-3655 TCGA-AZ-6600 TCGA-CM-5349 TCGA-D5-6540 TCGA-DM-A1DA TCGA-G4-6307 
       61.02        12.10        30.08        16.14         7.50        55.04 
TCGA-CL-5917 
       78.12 

$`C14ORF184 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 
       20.98        19.99        13.94        19.99        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5860 
       25.02        13.02        29.06        22.03        22.98        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       17.13        12.49        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
      140.38        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       44.68        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
        4.73         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  C14ORF184 MUTATED C14ORF184 WILD-TYPE 
                7.5                 0.0 
  C14ORF184 MUTATED C14ORF184 WILD-TYPE 
              78.12              148.01 
  C14ORF184 MUTATED C14ORF184 WILD-TYPE 
             30.080              20.155 
[1] "7.5 - 78.1 (30.1)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1"  
D75V2, continuous
D75V3, binary
                     cls
clus                    0   1
  C14ORF184 MUTATED     6   1
  C14ORF184 WILD-TYPE 360 118
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  C14ORF184 MUTATED      6    1
  C14ORF184 WILD-TYPE  360  118
        clus
vv       C14ORF184 MUTATED C14ORF184 WILD-TYPE
  COLON                  6                 360
  RECTUM                 1                 118
[1] 2 2
[1] FALSE
                     vv
clus                  STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  C14ORF184 MUTATED         1        0        1         1         0         0
  C14ORF184 WILD-TYPE      90        1       31       137        10         1
                     vv
clus                  STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C14ORF184 MUTATED           0          0          1          2        1
  C14ORF184 WILD-TYPE        24         11         58         40       47
                     vv
clus                  STAGE IVA STAGE IVB
  C14ORF184 MUTATED           0         0
  C14ORF184 WILD-TYPE        18         1
D75V4, multiclass
            clus
vv           C14ORF184 MUTATED C14ORF184 WILD-TYPE
  STAGE I                    1                  90
  STAGE IA                   0                   1
  STAGE II                   1                  31
  STAGE IIA                  1                 137
  STAGE IIB                  0                  10
  STAGE IIC                  0                   1
  STAGE III                  0                  24
  STAGE IIIA                 0                  11
  STAGE IIIB                 1                  58
  STAGE IIIC                 2                  40
  STAGE IV                   1                  47
  STAGE IVA                  0                  18
  STAGE IVB                  0                   1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                   T1  T2  T3  T4
  C14ORF184 MUTATED     0   1   5   1
  C14ORF184 WILD-TYPE  17  91 324  49
D75V5, multiclass
    clus
vv   C14ORF184 MUTATED C14ORF184 WILD-TYPE
  T1                 0                  17
  T2                 1                  91
  T3                 5                 324
  T4                 1                  49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                   N0  N1  N2
  C14ORF184 MUTATED     3   2   2
  C14ORF184 WILD-TYPE 284 111  85
D75V6, multiclass
    clus
vv   C14ORF184 MUTATED C14ORF184 WILD-TYPE
  N0                 3                 284
  N1                 2                 111
  N2                 2                  85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V7, binary
                     cls
clus                    0   1
  C14ORF184 MUTATED     5   1
  C14ORF184 WILD-TYPE 370  64
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  C14ORF184 MUTATED      5    1
  C14ORF184 WILD-TYPE  370   64
   clus
vv  C14ORF184 MUTATED C14ORF184 WILD-TYPE
  0                 5                 370
  1                 1                  64
[1] 2 2
[1] FALSE
D75V8, binary
                     cls
clus                    0   1
  C14ORF184 MUTATED     4   3
  C14ORF184 WILD-TYPE 221 261
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  C14ORF184 MUTATED      4    3
  C14ORF184 WILD-TYPE  221  261
        clus
vv       C14ORF184 MUTATED C14ORF184 WILD-TYPE
  FEMALE                 4                 221
  MALE                   3                 261
[1] 2 2
[1] FALSE
D75V9, binary
                     cls
clus                    0   1
  C14ORF184 MUTATED     5   0
  C14ORF184 WILD-TYPE 345  22
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  C14ORF184 MUTATED      5    0
  C14ORF184 WILD-TYPE  345   22
     clus
vv    C14ORF184 MUTATED C14ORF184 WILD-TYPE
  NO                  5                 345
  YES                 0                  22
[1] 2 2
[1] FALSE
                     vv
clus                  COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  C14ORF184 MUTATED                      5                             1
  C14ORF184 WILD-TYPE                  310                            46
                     vv
clus                  RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  C14ORF184 MUTATED                       1                              0
  C14ORF184 WILD-TYPE                   105                             10
D75V10, multiclass
                                clus
vv                               C14ORF184 MUTATED C14ORF184 WILD-TYPE
  COLON ADENOCARCINOMA                           5                 310
  COLON MUCINOUS ADENOCARCINOMA                  1                  46
  RECTAL ADENOCARCINOMA                          1                 105
  RECTAL MUCINOUS ADENOCARCINOMA                 0                  10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                   R0  R1  R2  RX
  C14ORF184 MUTATED     4   0   0   1
  C14ORF184 WILD-TYPE 341   4  31  24
D75V11, multiclass
    clus
vv   C14ORF184 MUTATED C14ORF184 WILD-TYPE
  R0                 4                 341
  R1                 0                   4
  R2                 0                  31
  RX                 1                  24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V12, continuous
                     vv
clus                  AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C14ORF184 MUTATED                                  0     0
  C14ORF184 WILD-TYPE                                1    11
                     vv
clus                  BLACK OR AFRICAN AMERICAN WHITE
  C14ORF184 MUTATED                           1     5
  C14ORF184 WILD-TYPE                        21   221
D75V13, multiclass
                                  clus
vv                                 C14ORF184 MUTATED C14ORF184 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                 0                   1
  ASIAN                                            0                  11
  BLACK OR AFRICAN AMERICAN                        1                  21
  WHITE                                            5                 221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(76) Variable = HLA-A MUTATION ANALYSIS
D76V1, survival
                 sevent
clus2               0   1
  HLA-A MUTATED    17   2
  HLA-A WILD-TYPE 361  91
  HLA-A MUTATED HLA-A WILD-TYPE 
             19             452 
  HLA-A MUTATED HLA-A WILD-TYPE 
              2              91 
$`HLA-A MUTATED`
TCGA-A6-5665 TCGA-A6-6781 TCGA-AA-3492 TCGA-AA-3662 TCGA-AA-3713 TCGA-AA-3815 
       22.06        19.66         3.02         6.05        19.04        33.04 
TCGA-AA-3861 TCGA-AA-3977 TCGA-AD-6889 TCGA-AZ-4315 TCGA-CA-6718 TCGA-CK-5913 
       30.05        25.02        56.55        58.39        10.06        51.32 
TCGA-CM-4743 TCGA-D5-6541 TCGA-D5-6931 TCGA-G4-6304 TCGA-G4-6586 TCGA-AG-3885 
       23.05        15.58        12.00        53.62        35.80        17.95 
TCGA-AG-A002 
       20.98 

$`HLA-A WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.12        20.28         7.04         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02        78.08         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
       26.99        19.04        10.06        35.05         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        31.07        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 
        9.99        21.14        82.95         1.91       124.27        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6898 
       17.85         4.80        17.13        12.49        16.14         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       11.64         4.80         1.51        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       65.85        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  HLA-A MUTATED HLA-A WILD-TYPE 
           3.02            0.00 
  HLA-A MUTATED HLA-A WILD-TYPE 
          58.39          148.01 
  HLA-A MUTATED HLA-A WILD-TYPE 
         22.060          20.085 
[1] "3.0 - 58.4 (22.1)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "2"  
D76V2, continuous
D76V3, binary
                 cls
clus                0   1
  HLA-A MUTATED    17   2
  HLA-A WILD-TYPE 349 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-A MUTATED     17    2
  HLA-A WILD-TYPE  349  117
        clus
vv       HLA-A MUTATED HLA-A WILD-TYPE
  COLON             17             349
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  HLA-A MUTATED         1        0        1        10         1         0
  HLA-A WILD-TYPE      90        1       31       128         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  HLA-A MUTATED           0          0          1          2        2         0
  HLA-A WILD-TYPE        24         11         58         40       46        18
                 vv
clus              STAGE IVB
  HLA-A MUTATED           0
  HLA-A WILD-TYPE         1
D76V4, multiclass
            clus
vv           HLA-A MUTATED HLA-A WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA             10             128
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             2              40
  STAGE IV               2              46
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  HLA-A MUTATED     0   2  13   4
  HLA-A WILD-TYPE  17  90 316  46
D76V5, multiclass
    clus
vv   HLA-A MUTATED HLA-A WILD-TYPE
  T1             0              17
  T2             2              90
  T3            13             316
  T4             4              46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  HLA-A MUTATED    15   2   2
  HLA-A WILD-TYPE 272 111  85
D76V6, multiclass
    clus
vv   HLA-A MUTATED HLA-A WILD-TYPE
  N0            15             272
  N1             2             111
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V7, binary
                 cls
clus                0   1
  HLA-A MUTATED    14   2
  HLA-A WILD-TYPE 361  63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-A MUTATED     14    2
  HLA-A WILD-TYPE  361   63
   clus
vv  HLA-A MUTATED HLA-A WILD-TYPE
  0            14             361
  1             2              63
[1] 2 2
[1] FALSE
D76V8, binary
                 cls
clus                0   1
  HLA-A MUTATED     8  11
  HLA-A WILD-TYPE 217 253
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-A MUTATED      8   11
  HLA-A WILD-TYPE  217  253
        clus
vv       HLA-A MUTATED HLA-A WILD-TYPE
  FEMALE             8             217
  MALE              11             253
[1] 2 2
[1] FALSE
D76V9, binary
                 cls
clus                0   1
  HLA-A MUTATED    16   2
  HLA-A WILD-TYPE 334  20
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-A MUTATED     16    2
  HLA-A WILD-TYPE  334   20
     clus
vv    HLA-A MUTATED HLA-A WILD-TYPE
  NO             16             334
  YES             2              20
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  HLA-A MUTATED                     16                             1
  HLA-A WILD-TYPE                  299                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  HLA-A MUTATED                       2                              0
  HLA-A WILD-TYPE                   104                             10
D76V10, multiclass
                                clus
vv                               HLA-A MUTATED HLA-A WILD-TYPE
  COLON ADENOCARCINOMA                      16             299
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  HLA-A MUTATED    13   0   2   2
  HLA-A WILD-TYPE 332   4  29  23
D76V11, multiclass
    clus
vv   HLA-A MUTATED HLA-A WILD-TYPE
  R0            13             332
  R1             0               4
  R2             2              29
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HLA-A MUTATED                                  0     2
  HLA-A WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  HLA-A MUTATED                           0     9
  HLA-A WILD-TYPE                        22   217
D76V13, multiclass
                                  clus
vv                                 HLA-A MUTATED HLA-A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               9
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        9             217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(77) Variable = BMPR2 MUTATION ANALYSIS
D77V1, survival
                 sevent
clus2               0   1
  BMPR2 MUTATED    28   6
  BMPR2 WILD-TYPE 350  87
  BMPR2 MUTATED BMPR2 WILD-TYPE 
             34             437 
  BMPR2 MUTATED BMPR2 WILD-TYPE 
              6              87 
$`BMPR2 MUTATED`
TCGA-A6-3809 TCGA-A6-5661 TCGA-A6-5665 TCGA-AA-3492 TCGA-AA-3516 TCGA-AA-3525 
       32.75        33.53        22.06         3.02        13.02         8.05 
TCGA-AA-3554 TCGA-AA-3672 TCGA-AA-3815 TCGA-AA-3950 TCGA-AA-A00E TCGA-AA-A00N 
       17.95         0.92        33.04        24.00        30.02         4.01 
TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6895 TCGA-AU-6004 TCGA-AY-6197 TCGA-AZ-4315 
        0.07        56.55         0.72        27.09        21.44        58.39 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-CA-6717 TCGA-CK-4952 TCGA-CK-6747 TCGA-CM-6676 
       88.21        49.41        12.76        15.62        82.95        11.08 
TCGA-D5-6540 TCGA-D5-6930 TCGA-DM-A1D6 TCGA-F4-6570 TCGA-F4-6808 TCGA-G4-6309 
       16.14         1.51        49.91         6.18        33.67        85.48 
TCGA-G4-6315 TCGA-G4-6586 TCGA-G4-6588 TCGA-AG-A002 
       61.91        35.80        26.17        20.98 

$`BMPR2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 
       31.63        30.44        29.19        23.61        22.09        32.71 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       27.09        22.52         8.38        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
       20.28         7.04         1.02        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
        1.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
       36.03        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       21.01        13.02        24.00        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 
        6.97        54.02         2.01        14.01        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       35.05         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        33.01        26.01         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00F 
        7.96        27.02        13.94        38.04        19.00        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 
        0.92        41.00        39.98        18.05        40.96        21.37 
TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
       15.52         0.79         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 
        0.20        14.50        16.31         0.95        33.01        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6599 
        1.41         5.13       106.75        22.36        62.79         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.20        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6748 TCGA-CK-6751 
       49.08        51.32         9.99        21.14         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6677 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 
       15.12        17.85         4.80        17.13        12.49        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
        9.44        11.64         4.80        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D7 
      119.70        24.43        38.20       130.65        92.75        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 
      117.07        98.24         8.61        31.96        35.74        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6854 
        1.55        34.42        41.42        16.24        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       44.68        55.04        63.62        36.00        22.09        13.78 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  BMPR2 MUTATED BMPR2 WILD-TYPE 
           0.07            0.00 
  BMPR2 MUTATED BMPR2 WILD-TYPE 
          88.21          148.01 
  BMPR2 MUTATED BMPR2 WILD-TYPE 
          23.03           20.02 
[1] "0.1 - 88.2 (23.0)"  "0.0 - 148.0 (20.0)"
[1] "hr=" "1.3"
D77V2, continuous
D77V3, binary
                 cls
clus                0   1
  BMPR2 MUTATED    35   1
  BMPR2 WILD-TYPE 331 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BMPR2 MUTATED     35    1
  BMPR2 WILD-TYPE  331  118
        clus
vv       BMPR2 MUTATED BMPR2 WILD-TYPE
  COLON             35             331
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  BMPR2 MUTATED         7        0        2        16         3         0
  BMPR2 WILD-TYPE      84        1       30       122         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  BMPR2 MUTATED           2          0          2          2        1         0
  BMPR2 WILD-TYPE        22         11         57         40       47        18
                 vv
clus              STAGE IVB
  BMPR2 MUTATED           0
  BMPR2 WILD-TYPE         1
D77V4, multiclass
            clus
vv           BMPR2 MUTATED BMPR2 WILD-TYPE
  STAGE I                7              84
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA             16             122
  STAGE IIB              3               7
  STAGE IIC              0               1
  STAGE III              2              22
  STAGE IIIA             0              11
  STAGE IIIB             2              57
  STAGE IIIC             2              40
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  BMPR2 MUTATED     2   5  25   4
  BMPR2 WILD-TYPE  15  87 304  46
D77V5, multiclass
    clus
vv   BMPR2 MUTATED BMPR2 WILD-TYPE
  T1             2              15
  T2             5              87
  T3            25             304
  T4             4              46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  BMPR2 MUTATED    28   5   3
  BMPR2 WILD-TYPE 259 108  84
D77V6, multiclass
    clus
vv   BMPR2 MUTATED BMPR2 WILD-TYPE
  N0            28             259
  N1             5             108
  N2             3              84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V7, binary
                 cls
clus                0   1
  BMPR2 MUTATED    28   1
  BMPR2 WILD-TYPE 347  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BMPR2 MUTATED     28    1
  BMPR2 WILD-TYPE  347   64
   clus
vv  BMPR2 MUTATED BMPR2 WILD-TYPE
  0            28             347
  1             1              64
[1] 2 2
[1] FALSE
D77V8, binary
                 cls
clus                0   1
  BMPR2 MUTATED    20  16
  BMPR2 WILD-TYPE 205 248
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BMPR2 MUTATED     20   16
  BMPR2 WILD-TYPE  205  248
        clus
vv       BMPR2 MUTATED BMPR2 WILD-TYPE
  FEMALE            20             205
  MALE              16             248
[1] 2 2
[1] FALSE
D77V9, binary
                 cls
clus                0   1
  BMPR2 MUTATED    26   0
  BMPR2 WILD-TYPE 324  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BMPR2 MUTATED     26    0
  BMPR2 WILD-TYPE  324   22
     clus
vv    BMPR2 MUTATED BMPR2 WILD-TYPE
  NO             26             324
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  BMPR2 MUTATED                     24                            11
  BMPR2 WILD-TYPE                  291                            36
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  BMPR2 MUTATED                       1                              0
  BMPR2 WILD-TYPE                   105                             10
D77V10, multiclass
                                clus
vv                               BMPR2 MUTATED BMPR2 WILD-TYPE
  COLON ADENOCARCINOMA                      24             291
  COLON MUCINOUS ADENOCARCINOMA             11              36
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  BMPR2 MUTATED    26   0   0   4
  BMPR2 WILD-TYPE 319   4  31  21
D77V11, multiclass
    clus
vv   BMPR2 MUTATED BMPR2 WILD-TYPE
  R0            26             319
  R1             0               4
  R2             0              31
  RX             4              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  BMPR2 MUTATED                                  0     2
  BMPR2 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  BMPR2 MUTATED                           2    22
  BMPR2 WILD-TYPE                        20   204
D77V13, multiclass
                                  clus
vv                                 BMPR2 MUTATED BMPR2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               9
  BLACK OR AFRICAN AMERICAN                    2              20
  WHITE                                       22             204
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(78) Variable = FYN MUTATION ANALYSIS
D78V1, survival
               sevent
clus2             0   1
  FYN MUTATED    14   2
  FYN WILD-TYPE 364  91
  FYN MUTATED FYN WILD-TYPE 
           16           455 
  FYN MUTATED FYN WILD-TYPE 
            2            91 
$`FYN MUTATED`
TCGA-A6-2671 TCGA-A6-5666 TCGA-A6-6141 TCGA-A6-6653 TCGA-AA-3713 TCGA-AA-3815 
       43.76        32.71         8.38        24.39        19.04        33.04 
TCGA-AA-3994 TCGA-AA-A010 TCGA-AA-A01P TCGA-AZ-4315 TCGA-CM-5341 TCGA-CM-6162 
       27.02        34.98        38.07        58.39        29.06        12.00 
TCGA-G4-6293 TCGA-G4-6323 TCGA-AF-4110 TCGA-AG-A002 
      133.18        13.78        14.50        20.98 

$`FYN WILD-TYPE`
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       46.65        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       22.06        27.09        22.52        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       21.76        24.69        23.87        20.12        19.66        20.28 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
        7.04         3.02         1.02        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
       26.99        19.04        10.06        35.05         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-A004 
       24.00        27.02        27.02        19.07         7.96        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        31.00         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 
       15.02        15.02        17.03        15.02         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
       35.31        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6586 
       85.48        63.62        61.91        36.00        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-5654 
       43.04        13.55        19.10        34.49        10.39        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  FYN MUTATED FYN WILD-TYPE 
         8.38          0.00 
  FYN MUTATED FYN WILD-TYPE 
       133.18        148.01 
  FYN MUTATED FYN WILD-TYPE 
        28.04         20.02 
[1] "8.4 - 133.2 (28.0)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.9"
D78V2, continuous
D78V3, binary
               cls
clus              0   1
  FYN MUTATED    15   1
  FYN WILD-TYPE 351 118
[1] "tbl2"
               cls
clus            [,1] [,2]
  FYN MUTATED     15    1
  FYN WILD-TYPE  351  118
        clus
vv       FYN MUTATED FYN WILD-TYPE
  COLON           15           351
  RECTUM           1           118
[1] 2 2
[1] FALSE
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FYN MUTATED         2        1        0         4         1         1
  FYN WILD-TYPE      89        0       32       134         9         0
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  FYN MUTATED           2          1          2          0        2         1
  FYN WILD-TYPE        22         10         57         42       46        17
               vv
clus            STAGE IVB
  FYN MUTATED           0
  FYN WILD-TYPE         1
D78V4, multiclass
            clus
vv           FYN MUTATED FYN WILD-TYPE
  STAGE I              2            89
  STAGE IA             1             0
  STAGE II             0            32
  STAGE IIA            4           134
  STAGE IIB            1             9
  STAGE IIC            1             0
  STAGE III            2            22
  STAGE IIIA           1            10
  STAGE IIIB           2            57
  STAGE IIIC           0            42
  STAGE IV             2            46
  STAGE IVA            1            17
  STAGE IVB            0             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  FYN MUTATED     0   3  10   3
  FYN WILD-TYPE  17  89 319  47
D78V5, multiclass
    clus
vv   FYN MUTATED FYN WILD-TYPE
  T1           0            17
  T2           3            89
  T3          10           319
  T4           3            47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2
  FYN MUTATED    10   5   2
  FYN WILD-TYPE 277 108  85
D78V6, multiclass
    clus
vv   FYN MUTATED FYN WILD-TYPE
  N0          10           277
  N1           5           108
  N2           2            85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V7, binary
               cls
clus              0   1
  FYN MUTATED    13   2
  FYN WILD-TYPE 362  63
[1] "tbl2"
               cls
clus            [,1] [,2]
  FYN MUTATED     13    2
  FYN WILD-TYPE  362   63
   clus
vv  FYN MUTATED FYN WILD-TYPE
  0          13           362
  1           2            63
[1] 2 2
[1] FALSE
D78V8, binary
               cls
clus              0   1
  FYN MUTATED     7  10
  FYN WILD-TYPE 218 254
[1] "tbl2"
               cls
clus            [,1] [,2]
  FYN MUTATED      7   10
  FYN WILD-TYPE  218  254
        clus
vv       FYN MUTATED FYN WILD-TYPE
  FEMALE           7           218
  MALE            10           254
[1] 2 2
[1] FALSE
D78V9, binary
               cls
clus              0   1
  FYN MUTATED    15   1
  FYN WILD-TYPE 335  21
[1] "tbl2"
               cls
clus            [,1] [,2]
  FYN MUTATED     15    1
  FYN WILD-TYPE  335   21
     clus
vv    FYN MUTATED FYN WILD-TYPE
  NO           15           335
  YES           1            21
[1] 2 2
[1] FALSE
               vv
clus            COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  FYN MUTATED                     13                             2
  FYN WILD-TYPE                  302                            45
               vv
clus            RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  FYN MUTATED                       1                              0
  FYN WILD-TYPE                   105                             10
D78V10, multiclass
                                clus
vv                               FYN MUTATED FYN WILD-TYPE
  COLON ADENOCARCINOMA                    13           302
  COLON MUCINOUS ADENOCARCINOMA            2            45
  RECTAL ADENOCARCINOMA                    1           105
  RECTAL MUCINOUS ADENOCARCINOMA           0            10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             R0  R1  R2  RX
  FYN MUTATED    13   0   1   0
  FYN WILD-TYPE 332   4  30  25
D78V11, multiclass
    clus
vv   FYN MUTATED FYN WILD-TYPE
  R0          13           332
  R1           0             4
  R2           1            30
  RX           0            25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V12, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FYN MUTATED                                  0     0
  FYN WILD-TYPE                                1    11
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  FYN MUTATED                           2     8
  FYN WILD-TYPE                        20   218
D78V13, multiclass
                                  clus
vv                                 FYN MUTATED FYN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      0            11
  BLACK OR AFRICAN AMERICAN                  2            20
  WHITE                                      8           218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(79) Variable = ALDH1A3 MUTATION ANALYSIS
D79V1, survival
                   sevent
clus2                 0   1
  ALDH1A3 MUTATED    13   4
  ALDH1A3 WILD-TYPE 365  89
  ALDH1A3 MUTATED ALDH1A3 WILD-TYPE 
               17               454 
  ALDH1A3 MUTATED ALDH1A3 WILD-TYPE 
                4                89 
$`ALDH1A3 MUTATED`
TCGA-A6-6654 TCGA-AA-3510 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3655 TCGA-AA-3950 
       23.87        63.98        29.95        20.98        61.02        24.00 
TCGA-AA-3977 TCGA-AD-6964 TCGA-AZ-6598 TCGA-CK-4952 TCGA-CK-5916 TCGA-D5-6539 
       25.02        10.88        49.41        15.62        21.14        12.49 
TCGA-D5-6930 TCGA-DM-A1D6 TCGA-G4-6304 TCGA-G4-6309 TCGA-AG-A002 
        1.51        49.91        53.62        85.48        20.98 

$`ALDH1A3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       24.00        17.95        23.01        19.99        13.94        19.99 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       78.08         6.05         6.97        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       26.01         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 
      106.75        22.36        62.79        88.21         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       49.08        51.32         9.99        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 
       43.27        15.12        17.85         4.80        17.13        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 
        9.04         9.44        11.64         4.80        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 
       74.56        65.85        44.68        55.04        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  ALDH1A3 MUTATED ALDH1A3 WILD-TYPE 
             1.51              0.00 
  ALDH1A3 MUTATED ALDH1A3 WILD-TYPE 
            85.48            148.01 
  ALDH1A3 MUTATED ALDH1A3 WILD-TYPE 
           24.000            20.005 
[1] "1.5 - 85.5 (24.0)"  "0.0 - 148.0 (20.0)"
[1] "hr=" "1.1"
D79V2, continuous
D79V3, binary
                   cls
clus                  0   1
  ALDH1A3 MUTATED    18   1
  ALDH1A3 WILD-TYPE 348 118
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ALDH1A3 MUTATED     18    1
  ALDH1A3 WILD-TYPE  348  118
        clus
vv       ALDH1A3 MUTATED ALDH1A3 WILD-TYPE
  COLON               18               348
  RECTUM               1               118
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ALDH1A3 MUTATED         3        0        3         5         2         0
  ALDH1A3 WILD-TYPE      88        1       29       133         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ALDH1A3 MUTATED           0          1          2          1        0
  ALDH1A3 WILD-TYPE        24         10         57         41       48
                   vv
clus                STAGE IVA STAGE IVB
  ALDH1A3 MUTATED           0         0
  ALDH1A3 WILD-TYPE        18         1
D79V4, multiclass
            clus
vv           ALDH1A3 MUTATED ALDH1A3 WILD-TYPE
  STAGE I                  3                88
  STAGE IA                 0                 1
  STAGE II                 3                29
  STAGE IIA                5               133
  STAGE IIB                2                 8
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               1                10
  STAGE IIIB               2                57
  STAGE IIIC               1                41
  STAGE IV                 0                48
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  ALDH1A3 MUTATED     1   3  11   4
  ALDH1A3 WILD-TYPE  16  89 318  46
D79V5, multiclass
    clus
vv   ALDH1A3 MUTATED ALDH1A3 WILD-TYPE
  T1               1                16
  T2               3                89
  T3              11               318
  T4               4                46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  ALDH1A3 MUTATED    15   2   2
  ALDH1A3 WILD-TYPE 272 111  85
D79V6, multiclass
    clus
vv   ALDH1A3 MUTATED ALDH1A3 WILD-TYPE
  N0              15               272
  N1               2               111
  N2               2                85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V7, binary
                   cls
clus                  0   1
  ALDH1A3 MUTATED    15   0
  ALDH1A3 WILD-TYPE 360  65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ALDH1A3 MUTATED     15    0
  ALDH1A3 WILD-TYPE  360   65
   clus
vv  ALDH1A3 MUTATED ALDH1A3 WILD-TYPE
  0              15               360
  1               0                65
[1] 2 2
[1] FALSE
D79V8, binary
                   cls
clus                  0   1
  ALDH1A3 MUTATED    11   8
  ALDH1A3 WILD-TYPE 214 256
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ALDH1A3 MUTATED     11    8
  ALDH1A3 WILD-TYPE  214  256
        clus
vv       ALDH1A3 MUTATED ALDH1A3 WILD-TYPE
  FEMALE              11               214
  MALE                 8               256
[1] 2 2
[1] FALSE
D79V9, binary
                   cls
clus                  0   1
  ALDH1A3 MUTATED    14   0
  ALDH1A3 WILD-TYPE 336  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ALDH1A3 MUTATED     14    0
  ALDH1A3 WILD-TYPE  336   22
     clus
vv    ALDH1A3 MUTATED ALDH1A3 WILD-TYPE
  NO               14               336
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ALDH1A3 MUTATED                     13                             5
  ALDH1A3 WILD-TYPE                  302                            42
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ALDH1A3 MUTATED                       1                              0
  ALDH1A3 WILD-TYPE                   105                             10
D79V10, multiclass
                                clus
vv                               ALDH1A3 MUTATED ALDH1A3 WILD-TYPE
  COLON ADENOCARCINOMA                        13               302
  COLON MUCINOUS ADENOCARCINOMA                5                42
  RECTAL ADENOCARCINOMA                        1               105
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  ALDH1A3 MUTATED    10   0   1   3
  ALDH1A3 WILD-TYPE 335   4  30  22
D79V11, multiclass
    clus
vv   ALDH1A3 MUTATED ALDH1A3 WILD-TYPE
  R0              10               335
  R1               0                 4
  R2               1                30
  RX               3                22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ALDH1A3 MUTATED                                  0     0
  ALDH1A3 WILD-TYPE                                1    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  ALDH1A3 MUTATED                           1    10
  ALDH1A3 WILD-TYPE                        21   216
D79V13, multiclass
                                  clus
vv                                 ALDH1A3 MUTATED ALDH1A3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                      1                21
  WHITE                                         10               216
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(80) Variable = LARP4B MUTATION ANALYSIS
D80V1, survival
                  sevent
clus2                0   1
  LARP4B MUTATED    27   3
  LARP4B WILD-TYPE 351  90
  LARP4B MUTATED LARP4B WILD-TYPE 
              30              441 
  LARP4B MUTATED LARP4B WILD-TYPE 
               3               90 
$`LARP4B MUTATED`
TCGA-A6-5666 TCGA-AA-3663 TCGA-AA-3672 TCGA-AA-3713 TCGA-AA-3815 TCGA-AA-3821 
       32.71         6.97         0.92        19.04        33.04         1.02 
TCGA-AA-3845 TCGA-AA-3877 TCGA-AA-3949 TCGA-AA-3977 TCGA-AA-A01Q TCGA-AA-A02O 
        0.00        31.00        26.01        25.02         1.02         0.92 
TCGA-AY-5543 TCGA-AZ-6598 TCGA-AZ-6601 TCGA-CA-6717 TCGA-CK-4950 TCGA-CM-4743 
       33.01        49.41       100.01        12.76        85.45        23.05 
TCGA-CM-4752 TCGA-CM-5861 TCGA-CM-6162 TCGA-D5-6540 TCGA-D5-6930 TCGA-DM-A1HB 
       13.02        15.02        12.00        16.14         1.51       135.65 
TCGA-F4-6856 TCGA-G4-6309 TCGA-G4-6586 TCGA-G4-6588 TCGA-AG-A002 TCGA-AG-A011 
       35.31        85.48        35.80        26.17        20.98        37.02 

$`LARP4B WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        22.06        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
       54.02         2.01        14.01        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
       85.05        26.99        19.04        10.06        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
       25.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 
       17.03        24.03        27.02        29.98        18.05         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       12.99        24.00        33.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
       38.07        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
       14.01        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       16.31         0.95        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 
        5.13       106.75        22.36        62.79        88.21         6.77 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
       12.10        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5912 
       10.06        14.30        17.56       148.01        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       20.02        37.02        25.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       30.08        32.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       15.02         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       17.13        12.49        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
        7.50        44.32       131.51       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6625 
       63.62        61.91        36.00        22.09        13.78        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       25.97        23.01        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  LARP4B MUTATED LARP4B WILD-TYPE 
               0                0 
  LARP4B MUTATED LARP4B WILD-TYPE 
          135.65           148.01 
  LARP4B MUTATED LARP4B WILD-TYPE 
          24.035           20.050 
[1] "0.0 - 135.7 (24.0)" "0.0 - 148.0 (20.1)"
[1] "hr=" "2.2"
D80V2, continuous
D80V3, binary
                  cls
clus                 0   1
  LARP4B MUTATED    29   2
  LARP4B WILD-TYPE 337 117
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LARP4B MUTATED     29    2
  LARP4B WILD-TYPE  337  117
        clus
vv       LARP4B MUTATED LARP4B WILD-TYPE
  COLON              29              337
  RECTUM              2              117
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  LARP4B MUTATED         5        0        5        11         0         1
  LARP4B WILD-TYPE      86        1       27       127        10         0
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  LARP4B MUTATED           1          0          5          0        1
  LARP4B WILD-TYPE        23         11         54         42       47
                  vv
clus               STAGE IVA STAGE IVB
  LARP4B MUTATED           1         0
  LARP4B WILD-TYPE        17         1
D80V4, multiclass
            clus
vv           LARP4B MUTATED LARP4B WILD-TYPE
  STAGE I                 5               86
  STAGE IA                0                1
  STAGE II                5               27
  STAGE IIA              11              127
  STAGE IIB               0               10
  STAGE IIC               1                0
  STAGE III               1               23
  STAGE IIIA              0               11
  STAGE IIIB              5               54
  STAGE IIIC              0               42
  STAGE IV                1               47
  STAGE IVA               1               17
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  LARP4B MUTATED     1   5  24   1
  LARP4B WILD-TYPE  16  87 305  49
D80V5, multiclass
    clus
vv   LARP4B MUTATED LARP4B WILD-TYPE
  T1              1               16
  T2              5               87
  T3             24              305
  T4              1               49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  LARP4B MUTATED    24   7   0
  LARP4B WILD-TYPE 263 106  87
D80V6, multiclass
    clus
vv   LARP4B MUTATED LARP4B WILD-TYPE
  N0             24              263
  N1              7              106
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V7, binary
                  cls
clus                 0   1
  LARP4B MUTATED    27   2
  LARP4B WILD-TYPE 348  63
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LARP4B MUTATED     27    2
  LARP4B WILD-TYPE  348   63
   clus
vv  LARP4B MUTATED LARP4B WILD-TYPE
  0             27              348
  1              2               63
[1] 2 2
[1] FALSE
D80V8, binary
                  cls
clus                 0   1
  LARP4B MUTATED    16  15
  LARP4B WILD-TYPE 209 249
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LARP4B MUTATED     16   15
  LARP4B WILD-TYPE  209  249
        clus
vv       LARP4B MUTATED LARP4B WILD-TYPE
  FEMALE             16              209
  MALE               15              249
[1] 2 2
[1] FALSE
D80V9, binary
                  cls
clus                 0   1
  LARP4B MUTATED    24   1
  LARP4B WILD-TYPE 326  21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LARP4B MUTATED     24    1
  LARP4B WILD-TYPE  326   21
     clus
vv    LARP4B MUTATED LARP4B WILD-TYPE
  NO              24              326
  YES              1               21
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  LARP4B MUTATED                     20                             8
  LARP4B WILD-TYPE                  295                            39
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  LARP4B MUTATED                       2                              0
  LARP4B WILD-TYPE                   104                             10
D80V10, multiclass
                                clus
vv                               LARP4B MUTATED LARP4B WILD-TYPE
  COLON ADENOCARCINOMA                       20              295
  COLON MUCINOUS ADENOCARCINOMA               8               39
  RECTAL ADENOCARCINOMA                       2              104
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  LARP4B MUTATED    23   1   1   1
  LARP4B WILD-TYPE 322   3  30  24
D80V11, multiclass
    clus
vv   LARP4B MUTATED LARP4B WILD-TYPE
  R0             23              322
  R1              1                3
  R2              1               30
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  LARP4B MUTATED                                  0     1
  LARP4B WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  LARP4B MUTATED                           4    12
  LARP4B WILD-TYPE                        18   214
D80V13, multiclass
                                  clus
vv                                 LARP4B MUTATED LARP4B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     4               18
  WHITE                                        12              214
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(81) Variable = ZDHHC7 MUTATION ANALYSIS
D81V1, survival
                  sevent
clus2                0   1
  ZDHHC7 MUTATED     9   2
  ZDHHC7 WILD-TYPE 369  91
  ZDHHC7 MUTATED ZDHHC7 WILD-TYPE 
              11              460 
  ZDHHC7 MUTATED ZDHHC7 WILD-TYPE 
               2               91 
$`ZDHHC7 MUTATED`
TCGA-A6-6653 TCGA-AA-3662 TCGA-AA-3811 TCGA-AA-3947 TCGA-AA-3949 TCGA-AU-6004 
       24.39         6.05        10.06        33.01        26.01        27.09 
TCGA-AZ-4315 TCGA-D5-6930 TCGA-DM-A28F TCGA-G4-6304 TCGA-G4-6628 
       58.39         1.51        35.97        53.62        79.69 

$`ZDHHC7 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
       25.08        25.18        24.16        21.76        24.69        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       19.99        13.94        19.99        61.02        78.08         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        19.04        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
       16.31         0.95        33.01        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
        9.44        11.64         4.80        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G 
      135.65       139.17         6.12        81.37       119.93        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       65.85        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       46.75        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  ZDHHC7 MUTATED ZDHHC7 WILD-TYPE 
            1.51             0.00 
  ZDHHC7 MUTATED ZDHHC7 WILD-TYPE 
           79.69           148.01 
  ZDHHC7 MUTATED ZDHHC7 WILD-TYPE 
          27.090           20.035 
[1] "1.5 - 79.7 (27.1)"  "0.0 - 148.0 (20.0)"
[1] "hr=" "1.3"
D81V2, continuous
D81V3, binary
                  cls
clus                 0   1
  ZDHHC7 MUTATED    12   0
  ZDHHC7 WILD-TYPE 354 119
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZDHHC7 MUTATED     12    0
  ZDHHC7 WILD-TYPE  354  119
        clus
vv       ZDHHC7 MUTATED ZDHHC7 WILD-TYPE
  COLON              12              354
  RECTUM              0              119
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZDHHC7 MUTATED         3        0        0         3         2         0
  ZDHHC7 WILD-TYPE      88        1       32       135         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZDHHC7 MUTATED           1          0          2          0        1
  ZDHHC7 WILD-TYPE        23         11         57         42       47
                  vv
clus               STAGE IVA STAGE IVB
  ZDHHC7 MUTATED           0         0
  ZDHHC7 WILD-TYPE        18         1
D81V4, multiclass
            clus
vv           ZDHHC7 MUTATED ZDHHC7 WILD-TYPE
  STAGE I                 3               88
  STAGE IA                0                1
  STAGE II                0               32
  STAGE IIA               3              135
  STAGE IIB               2                8
  STAGE IIC               0                1
  STAGE III               1               23
  STAGE IIIA              0               11
  STAGE IIIB              2               57
  STAGE IIIC              0               42
  STAGE IV                1               47
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZDHHC7 MUTATED     0   3   6   3
  ZDHHC7 WILD-TYPE  17  89 323  47
D81V5, multiclass
    clus
vv   ZDHHC7 MUTATED ZDHHC7 WILD-TYPE
  T1              0               17
  T2              3               89
  T3              6              323
  T4              3               47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  ZDHHC7 MUTATED     8   2   2
  ZDHHC7 WILD-TYPE 279 111  85
D81V6, multiclass
    clus
vv   ZDHHC7 MUTATED ZDHHC7 WILD-TYPE
  N0              8              279
  N1              2              111
  N2              2               85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D81V7, binary
                  cls
clus                 0   1
  ZDHHC7 MUTATED    11   1
  ZDHHC7 WILD-TYPE 364  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZDHHC7 MUTATED     11    1
  ZDHHC7 WILD-TYPE  364   64
   clus
vv  ZDHHC7 MUTATED ZDHHC7 WILD-TYPE
  0             11              364
  1              1               64
[1] 2 2
[1] FALSE
D81V8, binary
                  cls
clus                 0   1
  ZDHHC7 MUTATED     7   5
  ZDHHC7 WILD-TYPE 218 259
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZDHHC7 MUTATED      7    5
  ZDHHC7 WILD-TYPE  218  259
        clus
vv       ZDHHC7 MUTATED ZDHHC7 WILD-TYPE
  FEMALE              7              218
  MALE                5              259
[1] 2 2
[1] FALSE
D81V9, binary
                  cls
clus                 0   1
  ZDHHC7 MUTATED     8   0
  ZDHHC7 WILD-TYPE 342  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZDHHC7 MUTATED      8    0
  ZDHHC7 WILD-TYPE  342   22
     clus
vv    ZDHHC7 MUTATED ZDHHC7 WILD-TYPE
  NO               8              342
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ZDHHC7 MUTATED                      9                             3
  ZDHHC7 WILD-TYPE                  306                            44
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ZDHHC7 MUTATED                       0                              0
  ZDHHC7 WILD-TYPE                   106                             10
D81V10, multiclass
                                clus
vv                               ZDHHC7 MUTATED ZDHHC7 WILD-TYPE
  COLON ADENOCARCINOMA                        9              306
  COLON MUCINOUS ADENOCARCINOMA               3               44
  RECTAL ADENOCARCINOMA                       0              106
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ZDHHC7 MUTATED     9   0   1   0
  ZDHHC7 WILD-TYPE 336   4  30  25
D81V11, multiclass
    clus
vv   ZDHHC7 MUTATED ZDHHC7 WILD-TYPE
  R0              9              336
  R1              0                4
  R2              1               30
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D81V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZDHHC7 MUTATED                                  0     0
  ZDHHC7 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZDHHC7 MUTATED                           0     7
  ZDHHC7 WILD-TYPE                        22   219
D81V13, multiclass
                                  clus
vv                                 ZDHHC7 MUTATED ZDHHC7 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         7              219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(82) Variable = GPATCH8 MUTATION ANALYSIS
D82V1, survival
                   sevent
clus2                 0   1
  GPATCH8 MUTATED    13   2
  GPATCH8 WILD-TYPE 365  91
  GPATCH8 MUTATED GPATCH8 WILD-TYPE 
               15               456 
  GPATCH8 MUTATED GPATCH8 WILD-TYPE 
                2                91 
$`GPATCH8 MUTATED`
TCGA-A6-6653 TCGA-A6-6781 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3947 TCGA-AA-3977 
       24.39        19.66        19.04        10.06        33.01        25.02 
TCGA-AD-5900 TCGA-AU-6004 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-CA-6717 TCGA-CM-5860 
        0.07        27.09        58.39        49.41        12.76        32.02 
TCGA-G4-6321 TCGA-G4-6586 TCGA-EI-6507 
       22.09        35.80        19.96 

$`GPATCH8 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
       25.08        25.18        24.16        21.76        24.69        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3815 
        5.03        85.05        26.99        19.04        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 
        0.92        41.00        39.98        18.05        40.96        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 
       27.42        10.88         0.20        14.50        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       33.01        21.44        17.82         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        88.21         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07        12.20        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.03        22.98        30.08        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 
       55.04        85.48        63.62        61.91        36.00        13.78 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       20.55        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  GPATCH8 MUTATED GPATCH8 WILD-TYPE 
             0.07              0.00 
  GPATCH8 MUTATED GPATCH8 WILD-TYPE 
            58.39            148.01 
  GPATCH8 MUTATED GPATCH8 WILD-TYPE 
           24.390            20.085 
[1] "0.1 - 58.4 (24.4)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.5"
D82V2, continuous
D82V3, binary
                   cls
clus                  0   1
  GPATCH8 MUTATED    14   1
  GPATCH8 WILD-TYPE 352 118
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GPATCH8 MUTATED     14    1
  GPATCH8 WILD-TYPE  352  118
        clus
vv       GPATCH8 MUTATED GPATCH8 WILD-TYPE
  COLON               14               352
  RECTUM               1               118
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GPATCH8 MUTATED         3        0        1         5         1         0
  GPATCH8 WILD-TYPE      88        1       31       133         9         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GPATCH8 MUTATED           2          0          0          1        1
  GPATCH8 WILD-TYPE        22         11         59         41       47
                   vv
clus                STAGE IVA STAGE IVB
  GPATCH8 MUTATED           0         0
  GPATCH8 WILD-TYPE        18         1
D82V4, multiclass
            clus
vv           GPATCH8 MUTATED GPATCH8 WILD-TYPE
  STAGE I                  3                88
  STAGE IA                 0                 1
  STAGE II                 1                31
  STAGE IIA                5               133
  STAGE IIB                1                 9
  STAGE IIC                0                 1
  STAGE III                2                22
  STAGE IIIA               0                11
  STAGE IIIB               0                59
  STAGE IIIC               1                41
  STAGE IV                 1                47
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  GPATCH8 MUTATED     0   5   8   2
  GPATCH8 WILD-TYPE  17  87 321  48
D82V5, multiclass
    clus
vv   GPATCH8 MUTATED GPATCH8 WILD-TYPE
  T1               0                17
  T2               5                87
  T3               8               321
  T4               2                48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  GPATCH8 MUTATED    12   2   1
  GPATCH8 WILD-TYPE 275 111  86
D82V6, multiclass
    clus
vv   GPATCH8 MUTATED GPATCH8 WILD-TYPE
  N0              12               275
  N1               2               111
  N2               1                86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D82V7, binary
                   cls
clus                  0   1
  GPATCH8 MUTATED     9   1
  GPATCH8 WILD-TYPE 366  64
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GPATCH8 MUTATED      9    1
  GPATCH8 WILD-TYPE  366   64
   clus
vv  GPATCH8 MUTATED GPATCH8 WILD-TYPE
  0               9               366
  1               1                64
[1] 2 2
[1] FALSE
D82V8, binary
                   cls
clus                  0   1
  GPATCH8 MUTATED     6   9
  GPATCH8 WILD-TYPE 219 255
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GPATCH8 MUTATED      6    9
  GPATCH8 WILD-TYPE  219  255
        clus
vv       GPATCH8 MUTATED GPATCH8 WILD-TYPE
  FEMALE               6               219
  MALE                 9               255
[1] 2 2
[1] FALSE
D82V9, binary
                   cls
clus                  0   1
  GPATCH8 MUTATED    12   1
  GPATCH8 WILD-TYPE 338  21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GPATCH8 MUTATED     12    1
  GPATCH8 WILD-TYPE  338   21
     clus
vv    GPATCH8 MUTATED GPATCH8 WILD-TYPE
  NO               12               338
  YES               1                21
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  GPATCH8 MUTATED                     10                             4
  GPATCH8 WILD-TYPE                  305                            43
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  GPATCH8 MUTATED                       1                              0
  GPATCH8 WILD-TYPE                   105                             10
D82V10, multiclass
                                clus
vv                               GPATCH8 MUTATED GPATCH8 WILD-TYPE
  COLON ADENOCARCINOMA                        10               305
  COLON MUCINOUS ADENOCARCINOMA                4                43
  RECTAL ADENOCARCINOMA                        1               105
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  GPATCH8 MUTATED    10   0   1   1
  GPATCH8 WILD-TYPE 335   4  30  24
D82V11, multiclass
    clus
vv   GPATCH8 MUTATED GPATCH8 WILD-TYPE
  R0              10               335
  R1               0                 4
  R2               1                30
  RX               1                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D82V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GPATCH8 MUTATED                                  0     1
  GPATCH8 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  GPATCH8 MUTATED                           0    10
  GPATCH8 WILD-TYPE                        22   216
D82V13, multiclass
                                  clus
vv                                 GPATCH8 MUTATED GPATCH8 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                10
  BLACK OR AFRICAN AMERICAN                      0                22
  WHITE                                         10               216
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(83) Variable = BCORL1 MUTATION ANALYSIS
D83V1, survival
                  sevent
clus2                0   1
  BCORL1 MUTATED    19   6
  BCORL1 WILD-TYPE 359  87
  BCORL1 MUTATED BCORL1 WILD-TYPE 
              25              446 
  BCORL1 MUTATED BCORL1 WILD-TYPE 
               6               87 
$`BCORL1 MUTATED`
TCGA-A6-2676 TCGA-A6-5665 TCGA-A6-6781 TCGA-AA-3510 TCGA-AA-3713 TCGA-AA-3811 
       42.90        22.06        19.66        63.98        19.04        10.06 
TCGA-AA-3861 TCGA-AA-A010 TCGA-AD-6889 TCGA-AD-6895 TCGA-AU-6004 TCGA-AY-6197 
       30.05        34.98        56.55         0.72        27.09        21.44 
TCGA-AZ-4323 TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5916 TCGA-CM-5861 TCGA-CM-6162 
        1.41       106.75         1.61        21.14        15.02        12.00 
TCGA-CM-6674 TCGA-D5-6533 TCGA-D5-6538 TCGA-DM-A1DA TCGA-DM-A28H TCGA-G4-6588 
       12.95         1.32        17.13         7.50       117.07        26.17 
TCGA-EI-6507 
       19.96 

$`BCORL1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 
       20.28         7.04         3.02         1.02        35.01         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       26.99        19.04        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        31.07        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.79         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4315 
       14.50        16.31         0.95        33.01        17.82        58.39 
TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
        5.13        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 
       15.62        49.08        51.32         9.99        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 
       29.06        22.03        22.98        30.08        32.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 
       15.02        15.02        17.03        15.02         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       14.04        11.01        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       55.92        20.19        18.25        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
        4.80        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
       12.59       140.38        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28K 
        6.12        81.37       119.93        35.97        60.79        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       22.09        13.78        35.80        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
       32.61         0.49        20.55        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  BCORL1 MUTATED BCORL1 WILD-TYPE 
            0.72             0.00 
  BCORL1 MUTATED BCORL1 WILD-TYPE 
          117.07           148.01 
  BCORL1 MUTATED BCORL1 WILD-TYPE 
          19.960           20.235 
[1] "0.7 - 117.1 (20.0)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.2"
D83V2, continuous
D83V3, binary
                  cls
clus                 0   1
  BCORL1 MUTATED    25   2
  BCORL1 WILD-TYPE 341 117
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BCORL1 MUTATED     25    2
  BCORL1 WILD-TYPE  341  117
        clus
vv       BCORL1 MUTATED BCORL1 WILD-TYPE
  COLON              25              341
  RECTUM              2              117
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  BCORL1 MUTATED         2        0        1         9         3         0
  BCORL1 WILD-TYPE      89        1       31       129         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  BCORL1 MUTATED           1          1          4          3        2
  BCORL1 WILD-TYPE        23         10         55         39       46
                  vv
clus               STAGE IVA STAGE IVB
  BCORL1 MUTATED           0         0
  BCORL1 WILD-TYPE        18         1
D83V4, multiclass
            clus
vv           BCORL1 MUTATED BCORL1 WILD-TYPE
  STAGE I                 2               89
  STAGE IA                0                1
  STAGE II                1               31
  STAGE IIA               9              129
  STAGE IIB               3                7
  STAGE IIC               0                1
  STAGE III               1               23
  STAGE IIIA              1               10
  STAGE IIIB              4               55
  STAGE IIIC              3               39
  STAGE IV                2               46
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  BCORL1 MUTATED     1   2  18   6
  BCORL1 WILD-TYPE  16  90 311  44
D83V5, multiclass
    clus
vv   BCORL1 MUTATED BCORL1 WILD-TYPE
  T1              1               16
  T2              2               90
  T3             18              311
  T4              6               44
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  BCORL1 MUTATED    17   5   5
  BCORL1 WILD-TYPE 270 108  82
D83V6, multiclass
    clus
vv   BCORL1 MUTATED BCORL1 WILD-TYPE
  N0             17              270
  N1              5              108
  N2              5               82
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D83V7, binary
                  cls
clus                 0   1
  BCORL1 MUTATED    21   2
  BCORL1 WILD-TYPE 354  63
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BCORL1 MUTATED     21    2
  BCORL1 WILD-TYPE  354   63
   clus
vv  BCORL1 MUTATED BCORL1 WILD-TYPE
  0             21              354
  1              2               63
[1] 2 2
[1] FALSE
D83V8, binary
                  cls
clus                 0   1
  BCORL1 MUTATED    16  11
  BCORL1 WILD-TYPE 209 253
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BCORL1 MUTATED     16   11
  BCORL1 WILD-TYPE  209  253
        clus
vv       BCORL1 MUTATED BCORL1 WILD-TYPE
  FEMALE             16              209
  MALE               11              253
[1] 2 2
[1] FALSE
D83V9, binary
                  cls
clus                 0   1
  BCORL1 MUTATED    18   1
  BCORL1 WILD-TYPE 332  21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BCORL1 MUTATED     18    1
  BCORL1 WILD-TYPE  332   21
     clus
vv    BCORL1 MUTATED BCORL1 WILD-TYPE
  NO              18              332
  YES              1               21
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  BCORL1 MUTATED                     23                             2
  BCORL1 WILD-TYPE                  292                            45
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  BCORL1 MUTATED                       1                              1
  BCORL1 WILD-TYPE                   105                              9
D83V10, multiclass
                                clus
vv                               BCORL1 MUTATED BCORL1 WILD-TYPE
  COLON ADENOCARCINOMA                       23              292
  COLON MUCINOUS ADENOCARCINOMA               2               45
  RECTAL ADENOCARCINOMA                       1              105
  RECTAL MUCINOUS ADENOCARCINOMA              1                9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  BCORL1 MUTATED    18   0   1   2
  BCORL1 WILD-TYPE 327   4  30  23
D83V11, multiclass
    clus
vv   BCORL1 MUTATED BCORL1 WILD-TYPE
  R0             18              327
  R1              0                4
  R2              1               30
  RX              2               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D83V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  BCORL1 MUTATED                                  0     1
  BCORL1 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  BCORL1 MUTATED                           0    20
  BCORL1 WILD-TYPE                        22   206
D83V13, multiclass
                                  clus
vv                                 BCORL1 MUTATED BCORL1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                        20              206
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(84) Variable = SETD2 MUTATION ANALYSIS
D84V1, survival
                 sevent
clus2               0   1
  SETD2 MUTATED    39   6
  SETD2 WILD-TYPE 339  87
  SETD2 MUTATED SETD2 WILD-TYPE 
             45             426 
  SETD2 MUTATED SETD2 WILD-TYPE 
              6              87 
$`SETD2 MUTATED`
TCGA-A6-2672 TCGA-A6-5659 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6141 TCGA-AA-3525 
       46.65        30.44        22.09        22.06         8.38         8.05 
TCGA-AA-3543 TCGA-AA-3663 TCGA-AA-3680 TCGA-AA-3710 TCGA-AA-3851 TCGA-AA-A00E 
        0.99         6.97        11.01        26.99        33.07        30.02 
TCGA-AA-A00N TCGA-AD-6548 TCGA-AD-6889 TCGA-AU-6004 TCGA-AY-6197 TCGA-AY-6386 
        4.01        21.37        56.55        27.09        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-6599 TCGA-CA-6717 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5913 
       58.39         6.77        12.76        85.45        15.62        51.32 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-5344 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-6163 
      124.27        23.05        22.03        32.02        15.02         2.96 
TCGA-CM-6171 TCGA-CM-6680 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-6532 TCGA-D5-6540 
       14.04        12.03        12.26        56.09        18.25        16.14 
TCGA-DM-A28F TCGA-F4-6570 TCGA-F4-6805 TCGA-F4-6809 TCGA-AF-2691 TCGA-AG-3892 
       35.97         6.18        34.42        13.25        43.04        13.02 
TCGA-AG-A002 TCGA-AH-6549 TCGA-DC-6681 
       20.98        17.49         5.95 

$`SETD2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5666 TCGA-A6-6137 
       31.63        29.19        33.53        23.61        32.71        27.09 
TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 
       22.52        25.08        25.18        24.16        21.76        24.69 
TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 
       24.39        23.87        20.12        19.66        20.28         7.04 
TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
        3.02         1.02        35.01        63.98         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
       13.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
       36.03        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       29.00        26.01        12.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       15.02         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       85.05        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00J 
       27.02        13.94        38.04        19.00        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6888 
       41.00        39.98        18.05        40.96         0.07        15.52 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AZ-4323 
        0.20        14.50        16.31         0.95        33.01         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-5912 
       12.20        10.06        14.30        17.56       148.01        49.08 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CM-4744 TCGA-CM-4746 
        9.99        21.14        82.95         1.91        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5862 
       25.02        13.02        29.06        22.98        30.08         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6164 
       15.02        15.02        17.03        15.02        12.00        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-D5-5537 TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6533 
       10.06        45.40        19.59        55.92        20.19         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
      119.93        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.74        47.87         1.55        41.42        16.24        33.67 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2692 TCGA-AF-2693 
       46.75        79.69        24.13        39.48        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       17.95        36.95        17.03        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 
       41.00        38.04       117.11        38.56         1.45         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
       19.99         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  SETD2 MUTATED SETD2 WILD-TYPE 
           0.99            0.00 
  SETD2 MUTATED SETD2 WILD-TYPE 
         124.27          148.01 
  SETD2 MUTATED SETD2 WILD-TYPE 
         20.980          20.155 
[1] "1.0 - 124.3 (21.0)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.5"
D84V2, continuous
D84V3, binary
                 cls
clus                0   1
  SETD2 MUTATED    41   5
  SETD2 WILD-TYPE 325 114
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SETD2 MUTATED     41    5
  SETD2 WILD-TYPE  325  114
        clus
vv       SETD2 MUTATED SETD2 WILD-TYPE
  COLON             41             325
  RECTUM             5             114
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SETD2 MUTATED        12        0        1        18         1         0
  SETD2 WILD-TYPE      79        1       31       120         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SETD2 MUTATED           0          0          8          2        1         2
  SETD2 WILD-TYPE        24         11         51         40       47        16
                 vv
clus              STAGE IVB
  SETD2 MUTATED           0
  SETD2 WILD-TYPE         1
D84V4, multiclass
            clus
vv           SETD2 MUTATED SETD2 WILD-TYPE
  STAGE I               12              79
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA             18             120
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             8              51
  STAGE IIIC             2              40
  STAGE IV               1              47
  STAGE IVA              2              16
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  SETD2 MUTATED     3   9  30   4
  SETD2 WILD-TYPE  14  83 299  46
D84V5, multiclass
    clus
vv   SETD2 MUTATED SETD2 WILD-TYPE
  T1             3              14
  T2             9              83
  T3            30             299
  T4             4              46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  SETD2 MUTATED    32   8   5
  SETD2 WILD-TYPE 255 105  82
D84V6, multiclass
    clus
vv   SETD2 MUTATED SETD2 WILD-TYPE
  N0            32             255
  N1             8             105
  N2             5              82
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D84V7, binary
                 cls
clus                0   1
  SETD2 MUTATED    37   3
  SETD2 WILD-TYPE 338  62
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SETD2 MUTATED     37    3
  SETD2 WILD-TYPE  338   62
   clus
vv  SETD2 MUTATED SETD2 WILD-TYPE
  0            37             338
  1             3              62
[1] 2 2
[1] FALSE
D84V8, binary
                 cls
clus                0   1
  SETD2 MUTATED    23  23
  SETD2 WILD-TYPE 202 241
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SETD2 MUTATED     23   23
  SETD2 WILD-TYPE  202  241
        clus
vv       SETD2 MUTATED SETD2 WILD-TYPE
  FEMALE            23             202
  MALE              23             241
[1] 2 2
[1] FALSE
D84V9, binary
                 cls
clus                0   1
  SETD2 MUTATED    39   0
  SETD2 WILD-TYPE 311  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SETD2 MUTATED     39    0
  SETD2 WILD-TYPE  311   22
     clus
vv    SETD2 MUTATED SETD2 WILD-TYPE
  NO             39             311
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SETD2 MUTATED                     35                             6
  SETD2 WILD-TYPE                  280                            41
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SETD2 MUTATED                       5                              0
  SETD2 WILD-TYPE                   101                             10
D84V10, multiclass
                                clus
vv                               SETD2 MUTATED SETD2 WILD-TYPE
  COLON ADENOCARCINOMA                      35             280
  COLON MUCINOUS ADENOCARCINOMA              6              41
  RECTAL ADENOCARCINOMA                      5             101
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  SETD2 MUTATED    34   1   1   5
  SETD2 WILD-TYPE 311   3  30  20
D84V11, multiclass
    clus
vv   SETD2 MUTATED SETD2 WILD-TYPE
  R0            34             311
  R1             1               3
  R2             1              30
  RX             5              20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D84V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SETD2 MUTATED                                  0     2
  SETD2 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  SETD2 MUTATED                           4    29
  SETD2 WILD-TYPE                        18   197
D84V13, multiclass
                                  clus
vv                                 SETD2 MUTATED SETD2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               9
  BLACK OR AFRICAN AMERICAN                    4              18
  WHITE                                       29             197
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(85) Variable = MAP4K3 MUTATION ANALYSIS
D85V1, survival
                  sevent
clus2                0   1
  MAP4K3 MUTATED    14   6
  MAP4K3 WILD-TYPE 364  87
  MAP4K3 MUTATED MAP4K3 WILD-TYPE 
              20              451 
  MAP4K3 MUTATED MAP4K3 WILD-TYPE 
               6               87 
$`MAP4K3 MUTATED`
TCGA-A6-5661 TCGA-AA-3489 TCGA-AA-3663 TCGA-AA-3947 TCGA-AA-A00N TCGA-AA-A010 
       33.53         7.04         6.97        33.01         4.01        34.98 
TCGA-AD-6889 TCGA-AZ-6605 TCGA-CA-6717 TCGA-CM-6169 TCGA-CM-6679 TCGA-DM-A28G 
       56.55         5.23        12.76        13.02        10.06        60.79 
TCGA-DM-A28H TCGA-F4-6569 TCGA-G4-6588 TCGA-G4-6628 TCGA-AG-3583 TCGA-AG-3892 
      117.07        35.74        26.17        79.69        20.05        13.02 
TCGA-DC-6158 TCGA-EI-6508 
       10.98        20.91 

$`MAP4K3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        19.66        20.28         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       21.37        15.52         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77        12.10       100.01        29.56        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.20        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       12.99        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.08        11.01        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       81.37       119.93        35.97        98.24         8.61        31.96 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       91.79        46.75        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
        7.07        36.03        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       17.95        36.95        17.03        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       27.95        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
        0.49        20.55        19.96        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  MAP4K3 MUTATED MAP4K3 WILD-TYPE 
            4.01             0.00 
  MAP4K3 MUTATED MAP4K3 WILD-TYPE 
          117.07           148.01 
  MAP4K3 MUTATED MAP4K3 WILD-TYPE 
           20.48            20.19 
[1] "4.0 - 117.1 (20.5)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.4"
D85V2, continuous
D85V3, binary
                  cls
clus                 0   1
  MAP4K3 MUTATED    17   4
  MAP4K3 WILD-TYPE 349 115
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP4K3 MUTATED     17    4
  MAP4K3 WILD-TYPE  349  115
        clus
vv       MAP4K3 MUTATED MAP4K3 WILD-TYPE
  COLON              17              349
  RECTUM              4              115
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MAP4K3 MUTATED         4        0        2         7         4         0
  MAP4K3 WILD-TYPE      87        1       30       131         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MAP4K3 MUTATED           0          0          2          1        1
  MAP4K3 WILD-TYPE        24         11         57         41       47
                  vv
clus               STAGE IVA STAGE IVB
  MAP4K3 MUTATED           0         0
  MAP4K3 WILD-TYPE        18         1
D85V4, multiclass
            clus
vv           MAP4K3 MUTATED MAP4K3 WILD-TYPE
  STAGE I                 4               87
  STAGE IA                0                1
  STAGE II                2               30
  STAGE IIA               7              131
  STAGE IIB               4                6
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              2               57
  STAGE IIIC              1               41
  STAGE IV                1               47
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  MAP4K3 MUTATED     1   3  12   5
  MAP4K3 WILD-TYPE  16  89 317  45
D85V5, multiclass
    clus
vv   MAP4K3 MUTATED MAP4K3 WILD-TYPE
  T1              1               16
  T2              3               89
  T3             12              317
  T4              5               45
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  MAP4K3 MUTATED    17   2   2
  MAP4K3 WILD-TYPE 270 111  85
D85V6, multiclass
    clus
vv   MAP4K3 MUTATED MAP4K3 WILD-TYPE
  N0             17              270
  N1              2              111
  N2              2               85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D85V7, binary
                  cls
clus                 0   1
  MAP4K3 MUTATED    19   1
  MAP4K3 WILD-TYPE 356  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP4K3 MUTATED     19    1
  MAP4K3 WILD-TYPE  356   64
   clus
vv  MAP4K3 MUTATED MAP4K3 WILD-TYPE
  0             19              356
  1              1               64
[1] 2 2
[1] FALSE
D85V8, binary
                  cls
clus                 0   1
  MAP4K3 MUTATED     7  14
  MAP4K3 WILD-TYPE 218 250
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP4K3 MUTATED      7   14
  MAP4K3 WILD-TYPE  218  250
        clus
vv       MAP4K3 MUTATED MAP4K3 WILD-TYPE
  FEMALE              7              218
  MALE               14              250
[1] 2 2
[1] FALSE
D85V9, binary
                  cls
clus                 0   1
  MAP4K3 MUTATED    16   0
  MAP4K3 WILD-TYPE 334  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP4K3 MUTATED     16    0
  MAP4K3 WILD-TYPE  334   22
     clus
vv    MAP4K3 MUTATED MAP4K3 WILD-TYPE
  NO              16              334
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MAP4K3 MUTATED                     14                             3
  MAP4K3 WILD-TYPE                  301                            44
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MAP4K3 MUTATED                       3                              1
  MAP4K3 WILD-TYPE                   103                              9
D85V10, multiclass
                                clus
vv                               MAP4K3 MUTATED MAP4K3 WILD-TYPE
  COLON ADENOCARCINOMA                       14              301
  COLON MUCINOUS ADENOCARCINOMA               3               44
  RECTAL ADENOCARCINOMA                       3              103
  RECTAL MUCINOUS ADENOCARCINOMA              1                9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  MAP4K3 MUTATED    14   0   1   2
  MAP4K3 WILD-TYPE 331   4  30  23
D85V11, multiclass
    clus
vv   MAP4K3 MUTATED MAP4K3 WILD-TYPE
  R0             14              331
  R1              0                4
  R2              1               30
  RX              2               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D85V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MAP4K3 MUTATED                                  0     2
  MAP4K3 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  MAP4K3 MUTATED                           2    10
  MAP4K3 WILD-TYPE                        20   216
D85V13, multiclass
                                  clus
vv                                 MAP4K3 MUTATED MAP4K3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                9
  BLACK OR AFRICAN AMERICAN                     2               20
  WHITE                                        10              216
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(86) Variable = SLC12A6 MUTATION ANALYSIS
D86V1, survival
                   sevent
clus2                 0   1
  SLC12A6 MUTATED    22   4
  SLC12A6 WILD-TYPE 356  89
  SLC12A6 MUTATED SLC12A6 WILD-TYPE 
               26               445 
  SLC12A6 MUTATED SLC12A6 WILD-TYPE 
                4                89 
$`SLC12A6 MUTATED`
TCGA-A6-5665 TCGA-AA-3518 TCGA-AA-3662 TCGA-AA-3715 TCGA-AA-A010 TCGA-AA-A01I 
       22.06         1.02         6.05        19.04        34.98        31.00 
TCGA-AD-5900 TCGA-AU-6004 TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-AZ-6601 
        0.07        27.09        21.44        58.39        49.41       100.01 
TCGA-CM-4744 TCGA-CM-6162 TCGA-CM-6680 TCGA-D5-6536 TCGA-DM-A28H TCGA-F4-6570 
       20.02        12.00        12.03        17.85       117.07         6.18 
TCGA-G4-6323 TCGA-G4-6588 TCGA-AF-2693 TCGA-AG-3892 TCGA-AG-A002 TCGA-AH-6547 
       13.78        26.17        19.10        13.02        20.98         1.45 
TCGA-CI-6622 TCGA-F5-6811 
        6.97        32.19 

$`SLC12A6 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       85.05        26.99        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       10.98        32.02        12.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 
        0.92        41.00        39.98        18.05        40.96        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 
       27.42        10.88         0.20        14.50        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       33.01        17.82         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 
       62.79        88.21         6.77        12.10        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       17.03        15.02         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 
       18.25         1.32        43.27        15.12         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28K 
        6.12        81.37       119.93        35.97        60.79        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
        8.61        31.96        35.74        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       35.80        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       43.04        13.55        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 
       19.99         1.02        17.95        36.95        17.03        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6624 
       17.49         0.69         0.72         6.05        33.17         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       49.51        31.30        28.57         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  SLC12A6 MUTATED SLC12A6 WILD-TYPE 
             0.07              0.00 
  SLC12A6 MUTATED SLC12A6 WILD-TYPE 
           117.07            148.01 
  SLC12A6 MUTATED SLC12A6 WILD-TYPE 
            19.56             20.28 
[1] "0.1 - 117.1 (19.6)" "0.0 - 148.0 (20.3)"
[1] "hr=" "1.3"
D86V2, continuous
D86V3, binary
                   cls
clus                  0   1
  SLC12A6 MUTATED    20   5
  SLC12A6 WILD-TYPE 346 114
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC12A6 MUTATED     20    5
  SLC12A6 WILD-TYPE  346  114
        clus
vv       SLC12A6 MUTATED SLC12A6 WILD-TYPE
  COLON               20               346
  RECTUM               5               114
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SLC12A6 MUTATED         7        1        3         8         2         0
  SLC12A6 WILD-TYPE      84        0       29       130         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC12A6 MUTATED           0          0          2          1        1
  SLC12A6 WILD-TYPE        24         11         57         41       47
                   vv
clus                STAGE IVA STAGE IVB
  SLC12A6 MUTATED           0         0
  SLC12A6 WILD-TYPE        18         1
D86V4, multiclass
            clus
vv           SLC12A6 MUTATED SLC12A6 WILD-TYPE
  STAGE I                  7                84
  STAGE IA                 1                 0
  STAGE II                 3                29
  STAGE IIA                8               130
  STAGE IIB                2                 8
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               0                11
  STAGE IIIB               2                57
  STAGE IIIC               1                41
  STAGE IV                 1                47
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  SLC12A6 MUTATED     1   6  15   3
  SLC12A6 WILD-TYPE  16  86 314  47
D86V5, multiclass
    clus
vv   SLC12A6 MUTATED SLC12A6 WILD-TYPE
  T1               1                16
  T2               6                86
  T3              15               314
  T4               3                47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  SLC12A6 MUTATED    22   1   3
  SLC12A6 WILD-TYPE 265 112  84
D86V6, multiclass
    clus
vv   SLC12A6 MUTATED SLC12A6 WILD-TYPE
  N0              22               265
  N1               1               112
  N2               3                84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D86V7, binary
                   cls
clus                  0   1
  SLC12A6 MUTATED    19   1
  SLC12A6 WILD-TYPE 356  64
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC12A6 MUTATED     19    1
  SLC12A6 WILD-TYPE  356   64
   clus
vv  SLC12A6 MUTATED SLC12A6 WILD-TYPE
  0              19               356
  1               1                64
[1] 2 2
[1] FALSE
D86V8, binary
                   cls
clus                  0   1
  SLC12A6 MUTATED    13  13
  SLC12A6 WILD-TYPE 212 251
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC12A6 MUTATED     13   13
  SLC12A6 WILD-TYPE  212  251
        clus
vv       SLC12A6 MUTATED SLC12A6 WILD-TYPE
  FEMALE              13               212
  MALE                13               251
[1] 2 2
[1] FALSE
D86V9, binary
                   cls
clus                  0   1
  SLC12A6 MUTATED    20   0
  SLC12A6 WILD-TYPE 330  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC12A6 MUTATED     20    0
  SLC12A6 WILD-TYPE  330   22
     clus
vv    SLC12A6 MUTATED SLC12A6 WILD-TYPE
  NO               20               330
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SLC12A6 MUTATED                     18                             2
  SLC12A6 WILD-TYPE                  297                            45
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SLC12A6 MUTATED                       5                              0
  SLC12A6 WILD-TYPE                   101                             10
D86V10, multiclass
                                clus
vv                               SLC12A6 MUTATED SLC12A6 WILD-TYPE
  COLON ADENOCARCINOMA                        18               297
  COLON MUCINOUS ADENOCARCINOMA                2                45
  RECTAL ADENOCARCINOMA                        5               101
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  SLC12A6 MUTATED    18   0   1   0
  SLC12A6 WILD-TYPE 327   4  30  25
D86V11, multiclass
    clus
vv   SLC12A6 MUTATED SLC12A6 WILD-TYPE
  R0              18               327
  R1               0                 4
  R2               1                30
  RX               0                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D86V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SLC12A6 MUTATED                                  0     0
  SLC12A6 WILD-TYPE                                1    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  SLC12A6 MUTATED                           1    18
  SLC12A6 WILD-TYPE                        21   208
D86V13, multiclass
                                  clus
vv                                 SLC12A6 MUTATED SLC12A6 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                      1                21
  WHITE                                         18               208
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(87) Variable = CDK12 MUTATION ANALYSIS
D87V1, survival
                 sevent
clus2               0   1
  CDK12 MUTATED    26   5
  CDK12 WILD-TYPE 352  88
  CDK12 MUTATED CDK12 WILD-TYPE 
             31             440 
  CDK12 MUTATED CDK12 WILD-TYPE 
              5              88 
$`CDK12 MUTATED`
TCGA-A6-5659 TCGA-A6-5665 TCGA-A6-6780 TCGA-AA-3492 TCGA-AA-3660 TCGA-AA-3663 
       30.44        22.06        20.12         3.02        78.08         6.97 
TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3815 TCGA-AA-3864 TCGA-AA-3989 TCGA-AA-A00R 
       85.05        19.04        33.04        53.00         7.96         0.99 
TCGA-AA-A010 TCGA-AA-A01P TCGA-AY-5543 TCGA-AZ-4315 TCGA-CK-4948 TCGA-CK-4950 
       34.98        38.07        33.01        58.39       148.01        85.45 
TCGA-CM-4746 TCGA-CM-5861 TCGA-D5-6928 TCGA-F4-6459 TCGA-F4-6570 TCGA-G4-6309 
       37.02        15.02        11.64         8.61         6.18        85.48 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 TCGA-AG-3892 TCGA-AG-A02N TCGA-F5-6571 
       35.80        26.17        79.69        13.02        61.97        31.30 
TCGA-G5-6235 
       55.76 

$`CDK12 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        29.19        33.53        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6781 
       24.16        21.76        24.69        24.39        23.87        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
       20.28         7.04         1.02        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
       61.02         6.05        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 
       19.00        36.00         5.03        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       35.05         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        31.07        30.05        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       12.00        31.00        31.00         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       10.06        14.30        17.56        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       20.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       30.08        32.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 
      117.07        98.24        31.96        35.74        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       44.68        55.04        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       13.78        91.79        46.75        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 
       19.99         1.02        17.95        36.95        17.03        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
        1.94        38.96        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
       18.28         9.96        49.51        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6641 
        0.69        26.43 

  CDK12 MUTATED CDK12 WILD-TYPE 
           0.99            0.00 
  CDK12 MUTATED CDK12 WILD-TYPE 
         148.01          140.38 
  CDK12 MUTATED CDK12 WILD-TYPE 
          33.01           19.99 
[1] "1.0 - 148.0 (33.0)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1.8"
D87V2, continuous
D87V3, binary
                 cls
clus                0   1
  CDK12 MUTATED    29   4
  CDK12 WILD-TYPE 337 115
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDK12 MUTATED     29    4
  CDK12 WILD-TYPE  337  115
        clus
vv       CDK12 MUTATED CDK12 WILD-TYPE
  COLON             29             337
  RECTUM             4             115
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CDK12 MUTATED         5        0        5        11         1         0
  CDK12 WILD-TYPE      86        1       27       127         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CDK12 MUTATED           3          0          4          0        3         1
  CDK12 WILD-TYPE        21         11         55         42       45        17
                 vv
clus              STAGE IVB
  CDK12 MUTATED           0
  CDK12 WILD-TYPE         1
D87V4, multiclass
            clus
vv           CDK12 MUTATED CDK12 WILD-TYPE
  STAGE I                5              86
  STAGE IA               0               1
  STAGE II               5              27
  STAGE IIA             11             127
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              3              21
  STAGE IIIA             0              11
  STAGE IIIB             4              55
  STAGE IIIC             0              42
  STAGE IV               3              45
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CDK12 MUTATED     1   4  26   2
  CDK12 WILD-TYPE  16  88 303  48
D87V5, multiclass
    clus
vv   CDK12 MUTATED CDK12 WILD-TYPE
  T1             1              16
  T2             4              88
  T3            26             303
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  CDK12 MUTATED    24   7   2
  CDK12 WILD-TYPE 263 106  85
D87V6, multiclass
    clus
vv   CDK12 MUTATED CDK12 WILD-TYPE
  N0            24             263
  N1             7             106
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D87V7, binary
                 cls
clus                0   1
  CDK12 MUTATED    27   4
  CDK12 WILD-TYPE 348  61
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDK12 MUTATED     27    4
  CDK12 WILD-TYPE  348   61
   clus
vv  CDK12 MUTATED CDK12 WILD-TYPE
  0            27             348
  1             4              61
[1] 2 2
[1] FALSE
D87V8, binary
                 cls
clus                0   1
  CDK12 MUTATED    20  13
  CDK12 WILD-TYPE 205 251
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDK12 MUTATED     20   13
  CDK12 WILD-TYPE  205  251
        clus
vv       CDK12 MUTATED CDK12 WILD-TYPE
  FEMALE            20             205
  MALE              13             251
[1] 2 2
[1] FALSE
D87V9, binary
                 cls
clus                0   1
  CDK12 MUTATED    28   1
  CDK12 WILD-TYPE 322  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDK12 MUTATED     28    1
  CDK12 WILD-TYPE  322   21
     clus
vv    CDK12 MUTATED CDK12 WILD-TYPE
  NO             28             322
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CDK12 MUTATED                     27                             2
  CDK12 WILD-TYPE                  288                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CDK12 MUTATED                       4                              0
  CDK12 WILD-TYPE                   102                             10
D87V10, multiclass
                                clus
vv                               CDK12 MUTATED CDK12 WILD-TYPE
  COLON ADENOCARCINOMA                      27             288
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      4             102
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  CDK12 MUTATED    27   2   3   0
  CDK12 WILD-TYPE 318   2  28  25
D87V11, multiclass
    clus
vv   CDK12 MUTATED CDK12 WILD-TYPE
  R0            27             318
  R1             2               2
  R2             3              28
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D87V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CDK12 MUTATED                                  0     0
  CDK12 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CDK12 MUTATED                           4    14
  CDK12 WILD-TYPE                        18   212
D87V13, multiclass
                                  clus
vv                                 CDK12 MUTATED CDK12 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    4              18
  WHITE                                       14             212
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(88) Variable = NEXN MUTATION ANALYSIS
D88V1, survival
                sevent
clus2              0   1
  NEXN MUTATED    15   5
  NEXN WILD-TYPE 363  88
  NEXN MUTATED NEXN WILD-TYPE 
            20            451 
  NEXN MUTATED NEXN WILD-TYPE 
             5             88 
$`NEXN MUTATED`
TCGA-A6-5661 TCGA-AA-3510 TCGA-AA-3976 TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01I 
       33.53        63.98        26.01         4.01        34.98        31.00 
TCGA-AZ-6603 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-6747 TCGA-CM-6171 TCGA-CM-6679 
       29.56        12.76        14.30        82.95        14.04        10.06 
TCGA-D5-6920 TCGA-DM-A285 TCGA-F4-6805 TCGA-G4-6293 TCGA-G4-6303 TCGA-AG-A002 
        3.68         6.12        34.42       133.18        65.85        20.98 
TCGA-AH-6643 TCGA-DY-A1DG 
        0.69        51.48 

$`NEXN WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       10.98        32.02        12.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6606 
       49.41         6.77        12.10       100.01         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.07        12.20        10.06        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6748 
       15.62        49.08        51.32         9.99        21.14         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       13.02        15.02        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.08        11.01        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
       15.58         1.48         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      131.51       135.65       139.17        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
        6.18        47.87         1.55        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6304 
       13.25         0.53        47.41        35.31        74.56        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
       17.49         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 
      126.44        41.36        57.24        24.13        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  NEXN MUTATED NEXN WILD-TYPE 
          0.69           0.00 
  NEXN MUTATED NEXN WILD-TYPE 
        133.18         148.01 
  NEXN MUTATED NEXN WILD-TYPE 
        27.785         20.050 
[1] "0.7 - 133.2 (27.8)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1"  
D88V2, continuous
D88V3, binary
                cls
clus               0   1
  NEXN MUTATED    17   3
  NEXN WILD-TYPE 349 116
[1] "tbl2"
                cls
clus             [,1] [,2]
  NEXN MUTATED     17    3
  NEXN WILD-TYPE  349  116
        clus
vv       NEXN MUTATED NEXN WILD-TYPE
  COLON            17            349
  RECTUM            3            116
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NEXN MUTATED         3        0        1         7         2         0
  NEXN WILD-TYPE      88        1       31       131         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NEXN MUTATED           1          1          0          1        2         1
  NEXN WILD-TYPE        23         10         59         41       46        17
                vv
clus             STAGE IVB
  NEXN MUTATED           0
  NEXN WILD-TYPE         1
D88V4, multiclass
            clus
vv           NEXN MUTATED NEXN WILD-TYPE
  STAGE I               3             88
  STAGE IA              0              1
  STAGE II              1             31
  STAGE IIA             7            131
  STAGE IIB             2              8
  STAGE IIC             0              1
  STAGE III             1             23
  STAGE IIIA            1             10
  STAGE IIIB            0             59
  STAGE IIIC            1             41
  STAGE IV              2             46
  STAGE IVA             1             17
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  NEXN MUTATED     0   5  13   2
  NEXN WILD-TYPE  17  87 316  48
D88V5, multiclass
    clus
vv   NEXN MUTATED NEXN WILD-TYPE
  T1            0             17
  T2            5             87
  T3           13            316
  T4            2             48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  NEXN MUTATED    13   5   2
  NEXN WILD-TYPE 274 108  85
D88V6, multiclass
    clus
vv   NEXN MUTATED NEXN WILD-TYPE
  N0           13            274
  N1            5            108
  N2            2             85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D88V7, binary
                cls
clus               0   1
  NEXN MUTATED    15   3
  NEXN WILD-TYPE 360  62
[1] "tbl2"
                cls
clus             [,1] [,2]
  NEXN MUTATED     15    3
  NEXN WILD-TYPE  360   62
   clus
vv  NEXN MUTATED NEXN WILD-TYPE
  0           15            360
  1            3             62
[1] 2 2
[1] FALSE
D88V8, binary
                cls
clus               0   1
  NEXN MUTATED    10  10
  NEXN WILD-TYPE 215 254
[1] "tbl2"
                cls
clus             [,1] [,2]
  NEXN MUTATED     10   10
  NEXN WILD-TYPE  215  254
        clus
vv       NEXN MUTATED NEXN WILD-TYPE
  FEMALE           10            215
  MALE             10            254
[1] 2 2
[1] FALSE
D88V9, binary
                cls
clus               0   1
  NEXN MUTATED    15   0
  NEXN WILD-TYPE 335  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  NEXN MUTATED     15    0
  NEXN WILD-TYPE  335   22
     clus
vv    NEXN MUTATED NEXN WILD-TYPE
  NO            15            335
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  NEXN MUTATED                     14                             3
  NEXN WILD-TYPE                  301                            44
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  NEXN MUTATED                       3                              0
  NEXN WILD-TYPE                   103                             10
D88V10, multiclass
                                clus
vv                               NEXN MUTATED NEXN WILD-TYPE
  COLON ADENOCARCINOMA                     14            301
  COLON MUCINOUS ADENOCARCINOMA             3             44
  RECTAL ADENOCARCINOMA                     3            103
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  NEXN MUTATED    14   0   0   3
  NEXN WILD-TYPE 331   4  31  22
D88V11, multiclass
    clus
vv   NEXN MUTATED NEXN WILD-TYPE
  R0           14            331
  R1            0              4
  R2            0             31
  RX            3             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D88V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NEXN MUTATED                                  0     2
  NEXN WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  NEXN MUTATED                           1    11
  NEXN WILD-TYPE                        21   215
D88V13, multiclass
                                  clus
vv                                 NEXN MUTATED NEXN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              9
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                      11            215
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(89) Variable = GMPS MUTATION ANALYSIS
D89V1, survival
                sevent
clus2              0   1
  GMPS MUTATED    15   1
  GMPS WILD-TYPE 363  92
  GMPS MUTATED GMPS WILD-TYPE 
            16            455 
  GMPS MUTATED GMPS WILD-TYPE 
             1             92 
$`GMPS MUTATED`
TCGA-A6-3809 TCGA-AA-3710 TCGA-AA-3977 TCGA-AA-A010 TCGA-AA-A01I TCGA-AD-6890 
       32.75        26.99        25.02        34.98        31.00         0.79 
TCGA-AZ-4315 TCGA-AZ-6600 TCGA-CA-6717 TCGA-CM-4752 TCGA-CM-5864 TCGA-D5-6540 
       58.39        12.10        12.76        13.02        15.02        16.14 
TCGA-D5-6922 TCGA-D5-6930 TCGA-F4-6569 TCGA-G4-6588 
        4.41         1.51        35.74        26.17 

$`GMPS WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        85.05        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01K TCGA-AA-A01P 
        1.02        10.98        32.02        12.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6895 TCGA-AD-6899 
        0.07        21.37        15.52        56.55         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
       16.31         0.95        33.01        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.20        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
        5.03        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
       15.58         1.48         3.68        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
        9.44        11.64         4.80        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6570 
       60.79       117.07        98.24         8.61        31.96         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 
       61.91        36.00        22.09        13.78        35.80        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  GMPS MUTATED GMPS WILD-TYPE 
          0.79           0.00 
  GMPS MUTATED GMPS WILD-TYPE 
         58.39         148.01 
  GMPS MUTATED GMPS WILD-TYPE 
         20.58          20.19 
[1] "0.8 - 58.4 (20.6)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "2.6"
D89V2, continuous
D89V3, binary
                cls
clus               0   1
  GMPS MUTATED    17   0
  GMPS WILD-TYPE 349 119
[1] "tbl2"
                cls
clus             [,1] [,2]
  GMPS MUTATED     17    0
  GMPS WILD-TYPE  349  119
        clus
vv       GMPS MUTATED GMPS WILD-TYPE
  COLON            17            349
  RECTUM            0            119
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GMPS MUTATED         4        0        0         7         2         0
  GMPS WILD-TYPE      87        1       32       131         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  GMPS MUTATED           0          1          0          0        1         0
  GMPS WILD-TYPE        24         10         59         42       47        18
                vv
clus             STAGE IVB
  GMPS MUTATED           0
  GMPS WILD-TYPE         1
D89V4, multiclass
            clus
vv           GMPS MUTATED GMPS WILD-TYPE
  STAGE I               4             87
  STAGE IA              0              1
  STAGE II              0             32
  STAGE IIA             7            131
  STAGE IIB             2              8
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            1             10
  STAGE IIIB            0             59
  STAGE IIIC            0             42
  STAGE IV              1             47
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  GMPS MUTATED     1   5   8   3
  GMPS WILD-TYPE  16  87 321  47
D89V5, multiclass
    clus
vv   GMPS MUTATED GMPS WILD-TYPE
  T1            1             16
  T2            5             87
  T3            8            321
  T4            3             47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  GMPS MUTATED    15   2   0
  GMPS WILD-TYPE 272 111  87
D89V6, multiclass
    clus
vv   GMPS MUTATED GMPS WILD-TYPE
  N0           15            272
  N1            2            111
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D89V7, binary
                cls
clus               0   1
  GMPS MUTATED    14   1
  GMPS WILD-TYPE 361  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  GMPS MUTATED     14    1
  GMPS WILD-TYPE  361   64
   clus
vv  GMPS MUTATED GMPS WILD-TYPE
  0           14            361
  1            1             64
[1] 2 2
[1] FALSE
D89V8, binary
                cls
clus               0   1
  GMPS MUTATED     5  12
  GMPS WILD-TYPE 220 252
[1] "tbl2"
                cls
clus             [,1] [,2]
  GMPS MUTATED      5   12
  GMPS WILD-TYPE  220  252
        clus
vv       GMPS MUTATED GMPS WILD-TYPE
  FEMALE            5            220
  MALE             12            252
[1] 2 2
[1] FALSE
D89V9, binary
                cls
clus               0   1
  GMPS MUTATED    12   0
  GMPS WILD-TYPE 338  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  GMPS MUTATED     12    0
  GMPS WILD-TYPE  338   22
     clus
vv    GMPS MUTATED GMPS WILD-TYPE
  NO            12            338
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  GMPS MUTATED                     13                             4
  GMPS WILD-TYPE                  302                            43
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  GMPS MUTATED                       0                              0
  GMPS WILD-TYPE                   106                             10
D89V10, multiclass
                                clus
vv                               GMPS MUTATED GMPS WILD-TYPE
  COLON ADENOCARCINOMA                     13            302
  COLON MUCINOUS ADENOCARCINOMA             4             43
  RECTAL ADENOCARCINOMA                     0            106
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  GMPS MUTATED    13   0   0   1
  GMPS WILD-TYPE 332   4  31  24
D89V11, multiclass
    clus
vv   GMPS MUTATED GMPS WILD-TYPE
  R0           13            332
  R1            0              4
  R2            0             31
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D89V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GMPS MUTATED                                  0     1
  GMPS WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  GMPS MUTATED                           2     9
  GMPS WILD-TYPE                        20   217
D89V13, multiclass
                                  clus
vv                                 GMPS MUTATED GMPS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   2             20
  WHITE                                       9            217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(90) Variable = PTGDR MUTATION ANALYSIS
D90V1, survival
                 sevent
clus2               0   1
  PTGDR MUTATED     8   0
  PTGDR WILD-TYPE 370  93
  PTGDR MUTATED PTGDR WILD-TYPE 
              8             463 
  PTGDR MUTATED PTGDR WILD-TYPE 
              0              93 
$`PTGDR MUTATED`
TCGA-AA-3510 TCGA-AY-6197 TCGA-CM-4752 TCGA-D5-6535 TCGA-D5-6538 TCGA-D5-6930 
       63.98        21.44        13.02        15.12        17.13         1.51 
TCGA-AG-A002 TCGA-F5-6812 
       20.98         0.66 

$`PTGDR WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        33.01        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       25.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6539 
       18.25         1.32        43.27        17.85         4.80        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6931 
       14.30         9.04         9.44        11.64         4.80        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6813 TCGA-G5-6235 
       49.51        31.30        28.57        32.19         0.69        55.76 
TCGA-G5-6641 
       26.43 

  PTGDR MUTATED PTGDR WILD-TYPE 
           0.66            0.00 
  PTGDR MUTATED PTGDR WILD-TYPE 
          63.98          148.01 
  PTGDR MUTATED PTGDR WILD-TYPE 
         16.125          20.280 
[1] "0.7 - 64.0 (16.1)"  "0.0 - 148.0 (20.3)"
[1] "hr="     "9100000"
D90V2, continuous
D90V3, binary
                 cls
clus                0   1
  PTGDR MUTATED     7   2
  PTGDR WILD-TYPE 359 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTGDR MUTATED      7    2
  PTGDR WILD-TYPE  359  117
        clus
vv       PTGDR MUTATED PTGDR WILD-TYPE
  COLON              7             359
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PTGDR MUTATED         1        0        1         4         0         0
  PTGDR WILD-TYPE      90        1       31       134        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PTGDR MUTATED           1          0          2          0        0         0
  PTGDR WILD-TYPE        23         11         57         42       48        18
                 vv
clus              STAGE IVB
  PTGDR MUTATED           0
  PTGDR WILD-TYPE         1
D90V4, multiclass
            clus
vv           PTGDR MUTATED PTGDR WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              4             134
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             2              57
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PTGDR MUTATED     0   1   8   0
  PTGDR WILD-TYPE  17  91 321  50
D90V5, multiclass
    clus
vv   PTGDR MUTATED PTGDR WILD-TYPE
  T1             0              17
  T2             1              91
  T3             8             321
  T4             0              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  PTGDR MUTATED     6   1   2
  PTGDR WILD-TYPE 281 112  85
D90V6, multiclass
    clus
vv   PTGDR MUTATED PTGDR WILD-TYPE
  N0             6             281
  N1             1             112
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D90V7, binary
                 cls
clus                0   1
  PTGDR MUTATED     7   0
  PTGDR WILD-TYPE 368  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTGDR MUTATED      7    0
  PTGDR WILD-TYPE  368   65
   clus
vv  PTGDR MUTATED PTGDR WILD-TYPE
  0             7             368
  1             0              65
[1] 2 2
[1] FALSE
D90V8, binary
                 cls
clus                0   1
  PTGDR MUTATED     2   7
  PTGDR WILD-TYPE 223 257
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTGDR MUTATED      2    7
  PTGDR WILD-TYPE  223  257
        clus
vv       PTGDR MUTATED PTGDR WILD-TYPE
  FEMALE             2             223
  MALE               7             257
[1] 2 2
[1] FALSE
D90V9, binary
                 cls
clus                0   1
  PTGDR MUTATED     6   0
  PTGDR WILD-TYPE 344  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTGDR MUTATED      6    0
  PTGDR WILD-TYPE  344   22
     clus
vv    PTGDR MUTATED PTGDR WILD-TYPE
  NO              6             344
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PTGDR MUTATED                      6                             1
  PTGDR WILD-TYPE                  309                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PTGDR MUTATED                       2                              0
  PTGDR WILD-TYPE                   104                             10
D90V10, multiclass
                                clus
vv                               PTGDR MUTATED PTGDR WILD-TYPE
  COLON ADENOCARCINOMA                       6             309
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  PTGDR MUTATED     8   0   0   1
  PTGDR WILD-TYPE 337   4  31  24
D90V11, multiclass
    clus
vv   PTGDR MUTATED PTGDR WILD-TYPE
  R0             8             337
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D90V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PTGDR MUTATED                                  0     0
  PTGDR WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PTGDR MUTATED                           1     5
  PTGDR WILD-TYPE                        21   221
D90V13, multiclass
                                  clus
vv                                 PTGDR MUTATED PTGDR WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        5             221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(91) Variable = PRPS1 MUTATION ANALYSIS
D91V1, survival
                 sevent
clus2               0   1
  PRPS1 MUTATED     8   1
  PRPS1 WILD-TYPE 370  92
  PRPS1 MUTATED PRPS1 WILD-TYPE 
              9             462 
  PRPS1 MUTATED PRPS1 WILD-TYPE 
              1              92 
$`PRPS1 MUTATED`
TCGA-A6-5660 TCGA-A6-6781 TCGA-AA-3713 TCGA-AZ-6598 TCGA-CM-4752 TCGA-CM-5348 
       29.19        19.66        19.04        49.41        13.02        22.98 
TCGA-D5-6539 TCGA-DM-A1HB TCGA-AG-3587 
       12.49       135.65        46.03 

$`PRPS1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        88.21         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-5341 
      124.27        23.05        20.02        37.02        25.02        29.06 
TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.03        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 
       15.12        17.85         4.80        17.13        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      131.51       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
        1.02        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  PRPS1 MUTATED PRPS1 WILD-TYPE 
          12.49            0.00 
  PRPS1 MUTATED PRPS1 WILD-TYPE 
         135.65          148.01 
  PRPS1 MUTATED PRPS1 WILD-TYPE 
         22.980          20.155 
[1] "12.5 - 135.7 (23.0)" "0.0 - 148.0 (20.2)" 
[1] "hr=" "2.5"
D91V2, continuous
D91V3, binary
                 cls
clus                0   1
  PRPS1 MUTATED     8   1
  PRPS1 WILD-TYPE 358 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRPS1 MUTATED      8    1
  PRPS1 WILD-TYPE  358  118
        clus
vv       PRPS1 MUTATED PRPS1 WILD-TYPE
  COLON              8             358
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PRPS1 MUTATED         1        0        1         1         0         0
  PRPS1 WILD-TYPE      90        1       31       137        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PRPS1 MUTATED           0          1          2          2        1         0
  PRPS1 WILD-TYPE        24         10         57         40       47        18
                 vv
clus              STAGE IVB
  PRPS1 MUTATED           0
  PRPS1 WILD-TYPE         1
D91V4, multiclass
            clus
vv           PRPS1 MUTATED PRPS1 WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              1             137
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             1              10
  STAGE IIIB             2              57
  STAGE IIIC             2              40
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PRPS1 MUTATED     0   1   7   1
  PRPS1 WILD-TYPE  17  91 322  49
D91V5, multiclass
    clus
vv   PRPS1 MUTATED PRPS1 WILD-TYPE
  T1             0              17
  T2             1              91
  T3             7             322
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  PRPS1 MUTATED     5   3   1
  PRPS1 WILD-TYPE 282 110  86
D91V6, multiclass
    clus
vv   PRPS1 MUTATED PRPS1 WILD-TYPE
  N0             5             282
  N1             3             110
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D91V7, binary
                 cls
clus                0   1
  PRPS1 MUTATED     6   1
  PRPS1 WILD-TYPE 369  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRPS1 MUTATED      6    1
  PRPS1 WILD-TYPE  369   64
   clus
vv  PRPS1 MUTATED PRPS1 WILD-TYPE
  0             6             369
  1             1              64
[1] 2 2
[1] FALSE
D91V8, binary
                 cls
clus                0   1
  PRPS1 MUTATED     2   7
  PRPS1 WILD-TYPE 223 257
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRPS1 MUTATED      2    7
  PRPS1 WILD-TYPE  223  257
        clus
vv       PRPS1 MUTATED PRPS1 WILD-TYPE
  FEMALE             2             223
  MALE               7             257
[1] 2 2
[1] FALSE
D91V9, binary
                 cls
clus                0   1
  PRPS1 MUTATED     6   2
  PRPS1 WILD-TYPE 344  20
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRPS1 MUTATED      6    2
  PRPS1 WILD-TYPE  344   20
     clus
vv    PRPS1 MUTATED PRPS1 WILD-TYPE
  NO              6             344
  YES             2              20
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PRPS1 MUTATED                      6                             1
  PRPS1 WILD-TYPE                  309                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PRPS1 MUTATED                       1                              0
  PRPS1 WILD-TYPE                   105                             10
D91V10, multiclass
                                clus
vv                               PRPS1 MUTATED PRPS1 WILD-TYPE
  COLON ADENOCARCINOMA                       6             309
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  PRPS1 MUTATED     5   0   1   0
  PRPS1 WILD-TYPE 340   4  30  25
D91V11, multiclass
    clus
vv   PRPS1 MUTATED PRPS1 WILD-TYPE
  R0             5             340
  R1             0               4
  R2             1              30
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D91V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PRPS1 MUTATED                                  0     0
  PRPS1 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PRPS1 MUTATED                           2     5
  PRPS1 WILD-TYPE                        20   221
D91V13, multiclass
                                  clus
vv                                 PRPS1 MUTATED PRPS1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    2              20
  WHITE                                        5             221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(92) Variable = BIRC3 MUTATION ANALYSIS
D92V1, survival
                 sevent
clus2               0   1
  BIRC3 MUTATED    13   1
  BIRC3 WILD-TYPE 365  92
  BIRC3 MUTATED BIRC3 WILD-TYPE 
             14             457 
  BIRC3 MUTATED BIRC3 WILD-TYPE 
              1              92 
$`BIRC3 MUTATED`
TCGA-A6-3809 TCGA-A6-5665 TCGA-AA-3663 TCGA-AA-3821 TCGA-AA-A010 TCGA-AY-5543 
       32.75        22.06         6.97         1.02        34.98        33.01 
TCGA-CA-6718 TCGA-CM-5868 TCGA-D5-6929 TCGA-F4-6808 TCGA-AG-A002 TCGA-AG-A02N 
       10.06        17.03         4.80        33.67        20.98        61.97 
TCGA-EI-6508 TCGA-G5-6235 
       20.91        55.76 

$`BIRC3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
       33.04         0.99        25.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       27.09        16.31         0.95        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07        12.20        12.76        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       11.64         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6809 
       47.87         1.55        34.42        41.42        16.24        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       38.96        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6510 TCGA-F5-6464 
       32.61         0.49        20.55        19.96        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6641 
       26.43 

  BIRC3 MUTATED BIRC3 WILD-TYPE 
           1.02            0.00 
  BIRC3 MUTATED BIRC3 WILD-TYPE 
          61.97          148.01 
  BIRC3 MUTATED BIRC3 WILD-TYPE 
          21.52           20.05 
[1] "1.0 - 62.0 (21.5)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "2.7"
D92V2, continuous
D92V3, binary
                 cls
clus                0   1
  BIRC3 MUTATED    11   4
  BIRC3 WILD-TYPE 355 115
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BIRC3 MUTATED     11    4
  BIRC3 WILD-TYPE  355  115
        clus
vv       BIRC3 MUTATED BIRC3 WILD-TYPE
  COLON             11             355
  RECTUM             4             115
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  BIRC3 MUTATED         3        0        2         2         2         0
  BIRC3 WILD-TYPE      88        1       30       136         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  BIRC3 MUTATED           0          0          2          1        1         2
  BIRC3 WILD-TYPE        24         11         57         41       47        16
                 vv
clus              STAGE IVB
  BIRC3 MUTATED           0
  BIRC3 WILD-TYPE         1
D92V4, multiclass
            clus
vv           BIRC3 MUTATED BIRC3 WILD-TYPE
  STAGE I                3              88
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA              2             136
  STAGE IIB              2               8
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             2              57
  STAGE IIIC             1              41
  STAGE IV               1              47
  STAGE IVA              2              16
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  BIRC3 MUTATED     1   2   9   3
  BIRC3 WILD-TYPE  16  90 320  47
D92V5, multiclass
    clus
vv   BIRC3 MUTATED BIRC3 WILD-TYPE
  T1             1              16
  T2             2              90
  T3             9             320
  T4             3              47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  BIRC3 MUTATED     9   5   1
  BIRC3 WILD-TYPE 278 108  86
D92V6, multiclass
    clus
vv   BIRC3 MUTATED BIRC3 WILD-TYPE
  N0             9             278
  N1             5             108
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D92V7, binary
                 cls
clus                0   1
  BIRC3 MUTATED    10   3
  BIRC3 WILD-TYPE 365  62
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BIRC3 MUTATED     10    3
  BIRC3 WILD-TYPE  365   62
   clus
vv  BIRC3 MUTATED BIRC3 WILD-TYPE
  0            10             365
  1             3              62
[1] 2 2
[1] FALSE
D92V8, binary
                 cls
clus                0   1
  BIRC3 MUTATED     9   6
  BIRC3 WILD-TYPE 216 258
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BIRC3 MUTATED      9    6
  BIRC3 WILD-TYPE  216  258
        clus
vv       BIRC3 MUTATED BIRC3 WILD-TYPE
  FEMALE             9             216
  MALE               6             258
[1] 2 2
[1] FALSE
D92V9, binary
                 cls
clus                0   1
  BIRC3 MUTATED    12   0
  BIRC3 WILD-TYPE 338  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BIRC3 MUTATED     12    0
  BIRC3 WILD-TYPE  338   22
     clus
vv    BIRC3 MUTATED BIRC3 WILD-TYPE
  NO             12             338
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  BIRC3 MUTATED                      8                             3
  BIRC3 WILD-TYPE                  307                            44
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  BIRC3 MUTATED                       4                              0
  BIRC3 WILD-TYPE                   102                             10
D92V10, multiclass
                                clus
vv                               BIRC3 MUTATED BIRC3 WILD-TYPE
  COLON ADENOCARCINOMA                       8             307
  COLON MUCINOUS ADENOCARCINOMA              3              44
  RECTAL ADENOCARCINOMA                      4             102
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  BIRC3 MUTATED    13   1   0   1
  BIRC3 WILD-TYPE 332   3  31  24
D92V11, multiclass
    clus
vv   BIRC3 MUTATED BIRC3 WILD-TYPE
  R0            13             332
  R1             1               3
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D92V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  BIRC3 MUTATED                                  0     1
  BIRC3 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  BIRC3 MUTATED                           1     8
  BIRC3 WILD-TYPE                        21   218
D92V13, multiclass
                                  clus
vv                                 BIRC3 MUTATED BIRC3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        8             218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(93) Variable = IDH1 MUTATION ANALYSIS
D93V1, survival
                sevent
clus2              0   1
  IDH1 MUTATED    17   4
  IDH1 WILD-TYPE 361  89
  IDH1 MUTATED IDH1 WILD-TYPE 
            21            450 
  IDH1 MUTATED IDH1 WILD-TYPE 
             4             89 
$`IDH1 MUTATED`
TCGA-AA-3555 TCGA-AA-3947 TCGA-AA-3949 TCGA-AD-5900 TCGA-AD-6889 TCGA-AY-6386 
       29.95        33.01        26.01         0.07        56.55        17.82 
TCGA-AZ-6598 TCGA-AZ-6600 TCGA-CA-5796 TCGA-CK-6748 TCGA-CM-4743 TCGA-CM-6168 
       49.41        12.10         3.25         1.91        23.05        12.99 
TCGA-CM-6677 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6922 TCGA-DM-A282 TCGA-F4-6460 
       11.08        55.92        20.19         4.41       139.17        31.96 
TCGA-F5-6464 TCGA-F5-6702 TCGA-F5-6813 
        9.96        28.57         0.69 

$`IDH1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 
       21.01        13.02        24.00        17.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
        2.01        12.99        24.00        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 
       18.05        40.96        21.37        15.52         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AZ-4315 
       27.09        16.31         0.95        33.01        21.44        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        1.61        12.69         3.06         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
      124.27        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6169 TCGA-CM-6170 
       29.03        16.04        21.99        14.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6678 
       14.04        11.01        12.95        13.05        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A285 
      140.38         7.50        44.32       131.51       135.65         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
        8.61        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6811 TCGA-F5-6812 TCGA-G5-6235 TCGA-G5-6641 
       49.51        31.30        32.19         0.66        55.76        26.43 

  IDH1 MUTATED IDH1 WILD-TYPE 
          0.07           0.00 
  IDH1 MUTATED IDH1 WILD-TYPE 
        139.17         148.01 
  IDH1 MUTATED IDH1 WILD-TYPE 
         20.19          20.20 
[1] "0.1 - 139.2 (20.2)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1"  
D93V2, continuous
D93V3, binary
                cls
clus               0   1
  IDH1 MUTATED    18   3
  IDH1 WILD-TYPE 348 116
[1] "tbl2"
                cls
clus             [,1] [,2]
  IDH1 MUTATED     18    3
  IDH1 WILD-TYPE  348  116
        clus
vv       IDH1 MUTATED IDH1 WILD-TYPE
  COLON            18            348
  RECTUM            3            116
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  IDH1 MUTATED         1        0        1         8         1         0
  IDH1 WILD-TYPE      90        1       31       130         9         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  IDH1 MUTATED           0          1          4          2        2         1
  IDH1 WILD-TYPE        24         10         55         40       46        17
                vv
clus             STAGE IVB
  IDH1 MUTATED           0
  IDH1 WILD-TYPE         1
D93V4, multiclass
            clus
vv           IDH1 MUTATED IDH1 WILD-TYPE
  STAGE I               1             90
  STAGE IA              0              1
  STAGE II              1             31
  STAGE IIA             8            130
  STAGE IIB             1              9
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            1             10
  STAGE IIIB            4             55
  STAGE IIIC            2             40
  STAGE IV              2             46
  STAGE IVA             1             17
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  IDH1 MUTATED     0   1  16   4
  IDH1 WILD-TYPE  17  91 313  46
D93V5, multiclass
    clus
vv   IDH1 MUTATED IDH1 WILD-TYPE
  T1            0             17
  T2            1             91
  T3           16            313
  T4            4             46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  IDH1 MUTATED    11   8   2
  IDH1 WILD-TYPE 276 105  85
D93V6, multiclass
    clus
vv   IDH1 MUTATED IDH1 WILD-TYPE
  N0           11            276
  N1            8            105
  N2            2             85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D93V7, binary
                cls
clus               0   1
  IDH1 MUTATED    16   3
  IDH1 WILD-TYPE 359  62
[1] "tbl2"
                cls
clus             [,1] [,2]
  IDH1 MUTATED     16    3
  IDH1 WILD-TYPE  359   62
   clus
vv  IDH1 MUTATED IDH1 WILD-TYPE
  0           16            359
  1            3             62
[1] 2 2
[1] FALSE
D93V8, binary
                cls
clus               0   1
  IDH1 MUTATED    12   9
  IDH1 WILD-TYPE 213 255
[1] "tbl2"
                cls
clus             [,1] [,2]
  IDH1 MUTATED     12    9
  IDH1 WILD-TYPE  213  255
        clus
vv       IDH1 MUTATED IDH1 WILD-TYPE
  FEMALE           12            213
  MALE              9            255
[1] 2 2
[1] FALSE
D93V9, binary
                cls
clus               0   1
  IDH1 MUTATED    15   0
  IDH1 WILD-TYPE 335  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  IDH1 MUTATED     15    0
  IDH1 WILD-TYPE  335   22
     clus
vv    IDH1 MUTATED IDH1 WILD-TYPE
  NO            15            335
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  IDH1 MUTATED                     12                             6
  IDH1 WILD-TYPE                  303                            41
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  IDH1 MUTATED                       3                              0
  IDH1 WILD-TYPE                   103                             10
D93V10, multiclass
                                clus
vv                               IDH1 MUTATED IDH1 WILD-TYPE
  COLON ADENOCARCINOMA                     12            303
  COLON MUCINOUS ADENOCARCINOMA             6             41
  RECTAL ADENOCARCINOMA                     3            103
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  IDH1 MUTATED    16   0   0   1
  IDH1 WILD-TYPE 329   4  31  24
D93V11, multiclass
    clus
vv   IDH1 MUTATED IDH1 WILD-TYPE
  R0           16            329
  R1            0              4
  R2            0             31
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D93V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  IDH1 MUTATED                                  0     2
  IDH1 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  IDH1 MUTATED                           3    13
  IDH1 WILD-TYPE                        19   213
D93V13, multiclass
                                  clus
vv                                 IDH1 MUTATED IDH1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              9
  BLACK OR AFRICAN AMERICAN                   3             19
  WHITE                                      13            213
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(94) Variable = ZNF486 MUTATION ANALYSIS
D94V1, survival
                  sevent
clus2                0   1
  ZNF486 MUTATED     7   5
  ZNF486 WILD-TYPE 371  88
  ZNF486 MUTATED ZNF486 WILD-TYPE 
              12              459 
  ZNF486 MUTATED ZNF486 WILD-TYPE 
               5               88 
$`ZNF486 MUTATED`
TCGA-A6-4105 TCGA-A6-5661 TCGA-AA-3864 TCGA-AA-3949 TCGA-AA-A01P TCGA-AD-6895 
       14.53        33.53        53.00        26.01        38.07         0.72 
TCGA-CK-5912 TCGA-CM-5861 TCGA-DM-A0XD TCGA-DM-A285 TCGA-G4-6588 TCGA-AG-A002 
       49.08        15.02        24.43         6.12        26.17        20.98 

$`ZNF486 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 
       16.57        34.65        33.34        32.75        36.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       31.63        30.44        29.19        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 
        0.99        31.07        31.07        30.05        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        33.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 
        0.07        21.37        15.52        56.55         0.79         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 
       17.56       148.01        85.45        15.62        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       30.08        32.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
      119.70        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
      139.17        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        35.80        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  ZNF486 MUTATED ZNF486 WILD-TYPE 
            0.72             0.00 
  ZNF486 MUTATED ZNF486 WILD-TYPE 
           53.00           148.01 
  ZNF486 MUTATED ZNF486 WILD-TYPE 
           25.22            20.05 
[1] "0.7 - 53.0 (25.2)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "2.2"
D94V2, continuous
D94V3, binary
                  cls
clus                 0   1
  ZNF486 MUTATED    12   1
  ZNF486 WILD-TYPE 354 118
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF486 MUTATED     12    1
  ZNF486 WILD-TYPE  354  118
        clus
vv       ZNF486 MUTATED ZNF486 WILD-TYPE
  COLON              12              354
  RECTUM              1              118
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZNF486 MUTATED         2        0        1         5         1         0
  ZNF486 WILD-TYPE      89        1       31       133         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF486 MUTATED           1          0          1          0        1
  ZNF486 WILD-TYPE        23         11         58         42       47
                  vv
clus               STAGE IVA STAGE IVB
  ZNF486 MUTATED           0         0
  ZNF486 WILD-TYPE        18         1
D94V4, multiclass
            clus
vv           ZNF486 MUTATED ZNF486 WILD-TYPE
  STAGE I                 2               89
  STAGE IA                0                1
  STAGE II                1               31
  STAGE IIA               5              133
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               1               23
  STAGE IIIA              0               11
  STAGE IIIB              1               58
  STAGE IIIC              0               42
  STAGE IV                1               47
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZNF486 MUTATED     0   2  10   1
  ZNF486 WILD-TYPE  17  90 319  49
D94V5, multiclass
    clus
vv   ZNF486 MUTATED ZNF486 WILD-TYPE
  T1              0               17
  T2              2               90
  T3             10              319
  T4              1               49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  ZNF486 MUTATED     9   3   1
  ZNF486 WILD-TYPE 278 110  86
D94V6, multiclass
    clus
vv   ZNF486 MUTATED ZNF486 WILD-TYPE
  N0              9              278
  N1              3              110
  N2              1               86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D94V7, binary
                  cls
clus                 0   1
  ZNF486 MUTATED     9   1
  ZNF486 WILD-TYPE 366  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF486 MUTATED      9    1
  ZNF486 WILD-TYPE  366   64
   clus
vv  ZNF486 MUTATED ZNF486 WILD-TYPE
  0              9              366
  1              1               64
[1] 2 2
[1] FALSE
D94V8, binary
                  cls
clus                 0   1
  ZNF486 MUTATED     7   6
  ZNF486 WILD-TYPE 218 258
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF486 MUTATED      7    6
  ZNF486 WILD-TYPE  218  258
        clus
vv       ZNF486 MUTATED ZNF486 WILD-TYPE
  FEMALE              7              218
  MALE                6              258
[1] 2 2
[1] FALSE
D94V9, binary
                  cls
clus                 0   1
  ZNF486 MUTATED     9   0
  ZNF486 WILD-TYPE 341  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF486 MUTATED      9    0
  ZNF486 WILD-TYPE  341   22
     clus
vv    ZNF486 MUTATED ZNF486 WILD-TYPE
  NO               9              341
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ZNF486 MUTATED                     10                             2
  ZNF486 WILD-TYPE                  305                            45
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ZNF486 MUTATED                       1                              0
  ZNF486 WILD-TYPE                   105                             10
D94V10, multiclass
                                clus
vv                               ZNF486 MUTATED ZNF486 WILD-TYPE
  COLON ADENOCARCINOMA                       10              305
  COLON MUCINOUS ADENOCARCINOMA               2               45
  RECTAL ADENOCARCINOMA                       1              105
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ZNF486 MUTATED     7   0   0   2
  ZNF486 WILD-TYPE 338   4  31  23
D94V11, multiclass
    clus
vv   ZNF486 MUTATED ZNF486 WILD-TYPE
  R0              7              338
  R1              0                4
  R2              0               31
  RX              2               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D94V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF486 MUTATED                                  0     0
  ZNF486 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZNF486 MUTATED                           1     8
  ZNF486 WILD-TYPE                        21   218
D94V13, multiclass
                                  clus
vv                                 ZNF486 MUTATED ZNF486 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                         8              218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(95) Variable = ATM MUTATION ANALYSIS
D95V1, survival
               sevent
clus2             0   1
  ATM MUTATED   123  28
  ATM WILD-TYPE 255  65
  ATM MUTATED ATM WILD-TYPE 
          151           320 
  ATM MUTATED ATM WILD-TYPE 
           28            65 
$`ATM MUTATED`
TCGA-A6-4105 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6141 
       14.53        29.19        33.53        22.09        22.06         8.38 
TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       24.39        20.12        19.66         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3522 TCGA-AA-3530 TCGA-AA-3555 
       63.98        13.02         1.02        37.05        19.07        29.95 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3678 
       61.02        78.08         6.05         6.97        54.02        47.01 
TCGA-AA-3679 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3819 
       15.02        85.05        26.99        19.04        10.06        25.02 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3950 TCGA-AA-3966 TCGA-AA-3977 TCGA-AA-A00N 
       31.07        30.05        24.00         2.01        25.02         4.01 
TCGA-AA-A010 TCGA-AA-A01R TCGA-AA-A02Y TCGA-AD-6548 TCGA-AD-6889 TCGA-AD-6890 
       34.98        35.01        39.98        21.37        56.55         0.79 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-6197 
        5.79        22.42        27.42        14.50        27.09        21.44 
TCGA-AZ-4315 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       58.39        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6608 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 
      100.01        29.56         1.61         0.07        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
       14.30        17.56        15.62        49.08        51.32         9.99 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4752 TCGA-CM-5348 TCGA-CM-5349 
        1.91       124.27        23.05        13.02        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6164 
       32.02        15.02         5.03        15.02        17.03        29.03 
TCGA-CM-6171 TCGA-CM-6677 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5538 TCGA-D5-5539 
       14.04        11.08        10.06        12.03        12.26        19.59 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       20.19        18.25         1.32        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-7000 TCGA-DM-A0XF 
       12.43        14.30        11.64         4.80        10.26        38.20 
TCGA-DM-A1D4 TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
       92.75        44.32       135.65        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6570 TCGA-F4-6807 TCGA-F4-6808 
       60.79       117.07        98.24         6.18        16.24        33.67 
TCGA-F4-6854 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
        0.53        35.31       133.18        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
       85.48        61.91        36.00        22.09        35.80        26.17 
TCGA-G4-6628 TCGA-AF-2693 TCGA-AF-6655 TCGA-AG-3600 TCGA-AG-3727 TCGA-AG-3731 
       79.69        19.10        20.02         6.05         0.99        37.02 
TCGA-AG-3742 TCGA-AG-3885 TCGA-AG-3892 TCGA-AG-A002 TCGA-AH-6544 TCGA-CL-5917 
        0.99        17.95        13.02        20.98        38.56        78.12 
TCGA-DC-5337 TCGA-DC-6155 TCGA-DC-6683 TCGA-DY-A1DC TCGA-DY-A1DF TCGA-DY-A1H8 
       15.02        13.97         5.03        41.36        24.13        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-F5-6813 TCGA-G5-6235 
        0.49        20.55        19.96        20.91         0.69        55.76 
TCGA-G5-6641 
       26.43 

$`ATM WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 
       16.57        34.65        33.34        32.75        36.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5662 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 
       31.63        30.44        23.61        32.71        27.09        22.52 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
       25.08        25.18        24.16        21.76        24.69        23.87 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3519 
       20.28         7.04         6.97         1.02        38.99         9.07 
TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3531 
       24.03        36.03         8.05        19.07         0.00        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 
       33.99        21.01        13.02        24.00        17.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3666 TCGA-AA-3667 
       20.98        19.99        13.94        19.99         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
        0.92        50.04        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       36.00         5.03        19.04        35.05        33.04         0.99 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3866 
       36.03        32.05         0.99        31.07        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 
       12.99        24.00        33.01        26.01         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
       34.03        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S 
       12.00        31.00        31.00        38.07         1.02         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       18.05        40.96         0.07        15.52         0.72        10.88 
TCGA-AD-6965 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4323 
        0.20        16.31         0.95        33.01        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-6600 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
        5.13       106.75        12.10         5.23        11.74         3.19 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6716 TCGA-CK-4948 
       12.69         3.06         3.25         3.29        12.20       148.01 
TCGA-CK-4950 TCGA-CK-5916 TCGA-CK-6747 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
       85.45        21.14        82.95        20.02        37.02        25.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5863 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       29.06        22.03        15.02        15.02        12.00         2.96 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6678 TCGA-D5-5537 
       11.01        12.95        13.05        11.08        11.01        45.40 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6534 TCGA-D5-6922 TCGA-D5-6926 TCGA-D5-6927 
       56.09        55.92        43.27         4.41         9.04         9.44 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A1D0 
        1.51        12.00        11.38       119.70        24.43       130.65 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HA 
       49.91        13.32        12.59       140.38         7.50       131.51 
TCGA-DM-A282 TCGA-DM-A285 TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 
      139.17         6.12         8.61        31.96        35.74        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6809 TCGA-F4-6855 TCGA-G4-6299 
        1.55        34.42        41.42        13.25        47.41        74.56 
TCGA-G4-6303 TCGA-G4-6310 TCGA-G4-6323 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 
       65.85        63.62        13.78        91.79        46.75        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       39.48        43.04        13.55        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       16.83        15.39        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 
       46.03        34.03         2.01        50.04        12.03         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3732 
       15.95        19.99        13.94        19.99         7.99        32.98 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 
        0.99        19.04        19.99         1.02        36.95        17.03 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5918 TCGA-DC-5869 TCGA-DC-6157 TCGA-DC-6158 
        6.97         4.73         7.17         5.03        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DD 
       19.99         5.95         4.01         5.29       126.44        57.24 
TCGA-DY-A1DG TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       51.48        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 
       32.19         0.66 

  ATM MUTATED ATM WILD-TYPE 
         0.07          0.00 
  ATM MUTATED ATM WILD-TYPE 
       135.65        148.01 
  ATM MUTATED ATM WILD-TYPE 
        20.98         19.99 
[1] "0.1 - 135.7 (21.0)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.3"
D95V2, continuous
D95V3, binary
               cls
clus              0   1
  ATM MUTATED   132  23
  ATM WILD-TYPE 234  96
[1] "tbl2"
               cls
clus            [,1] [,2]
  ATM MUTATED    132   23
  ATM WILD-TYPE  234   96
        clus
vv       ATM MUTATED ATM WILD-TYPE
  COLON          132           234
  RECTUM          23            96
[1] 2 2
[1] FALSE
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ATM MUTATED        24        0       11        52         5         0
  ATM WILD-TYPE      67        1       21        86         5         1
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ATM MUTATED           8          7         19         14        7         3
  ATM WILD-TYPE        16          4         40         28       41        15
               vv
clus            STAGE IVB
  ATM MUTATED           0
  ATM WILD-TYPE         1
D95V4, multiclass
            clus
vv           ATM MUTATED ATM WILD-TYPE
  STAGE I             24            67
  STAGE IA             0             1
  STAGE II            11            21
  STAGE IIA           52            86
  STAGE IIB            5             5
  STAGE IIC            0             1
  STAGE III            8            16
  STAGE IIIA           7             4
  STAGE IIIB          19            40
  STAGE IIIC          14            28
  STAGE IV             7            41
  STAGE IVA            3            15
  STAGE IVB            0             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  ATM MUTATED     7  28 106  15
  ATM WILD-TYPE  10  64 223  35
D95V5, multiclass
    clus
vv   ATM MUTATED ATM WILD-TYPE
  T1           7            10
  T2          28            64
  T3         106           223
  T4          15            35
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2
  ATM MUTATED   101  35  20
  ATM WILD-TYPE 186  78  67
D95V6, multiclass
    clus
vv   ATM MUTATED ATM WILD-TYPE
  N0         101           186
  N1          35            78
  N2          20            67
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D95V7, binary
               cls
clus              0   1
  ATM MUTATED   118  11
  ATM WILD-TYPE 257  54
[1] "tbl2"
               cls
clus            [,1] [,2]
  ATM MUTATED    118   11
  ATM WILD-TYPE  257   54
   clus
vv  ATM MUTATED ATM WILD-TYPE
  0         118           257
  1          11            54
[1] 2 2
[1] FALSE
D95V8, binary
               cls
clus              0   1
  ATM MUTATED    75  81
  ATM WILD-TYPE 150 183
[1] "tbl2"
               cls
clus            [,1] [,2]
  ATM MUTATED     75   81
  ATM WILD-TYPE  150  183
        clus
vv       ATM MUTATED ATM WILD-TYPE
  FEMALE          75           150
  MALE            81           183
[1] 2 2
[1] FALSE
D95V9, binary
               cls
clus              0   1
  ATM MUTATED   115   4
  ATM WILD-TYPE 235  18
[1] "tbl2"
               cls
clus            [,1] [,2]
  ATM MUTATED    115    4
  ATM WILD-TYPE  235   18
     clus
vv    ATM MUTATED ATM WILD-TYPE
  NO          115           235
  YES           4            18
[1] 2 2
[1] FALSE
               vv
clus            COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ATM MUTATED                    110                            20
  ATM WILD-TYPE                  205                            27
               vv
clus            RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ATM MUTATED                      22                              1
  ATM WILD-TYPE                    84                              9
D95V10, multiclass
                                clus
vv                               ATM MUTATED ATM WILD-TYPE
  COLON ADENOCARCINOMA                   110           205
  COLON MUCINOUS ADENOCARCINOMA           20            27
  RECTAL ADENOCARCINOMA                   22            84
  RECTAL MUCINOUS ADENOCARCINOMA           1             9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             R0  R1  R2  RX
  ATM MUTATED   101   1   4  14
  ATM WILD-TYPE 244   3  27  11
D95V11, multiclass
    clus
vv   ATM MUTATED ATM WILD-TYPE
  R0         101           244
  R1           1             3
  R2           4            27
  RX          14            11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D95V12, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ATM MUTATED                                  0     5
  ATM WILD-TYPE                                1     6
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  ATM MUTATED                           6   105
  ATM WILD-TYPE                        16   121
D95V13, multiclass
                                  clus
vv                                 ATM MUTATED ATM WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      5             6
  BLACK OR AFRICAN AMERICAN                  6            16
  WHITE                                    105           121
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(96) Variable = HIST1H1T MUTATION ANALYSIS
D96V1, survival
                    sevent
clus2                  0   1
  HIST1H1T MUTATED     8   2
  HIST1H1T WILD-TYPE 370  91
  HIST1H1T MUTATED HIST1H1T WILD-TYPE 
                10                461 
  HIST1H1T MUTATED HIST1H1T WILD-TYPE 
                 2                 91 
$`HIST1H1T MUTATED`
TCGA-A6-5661 TCGA-A6-6141 TCGA-AA-3663 TCGA-D5-5538 TCGA-D5-6533 TCGA-D5-6922 
       33.53         8.38         6.97        12.26         1.32         4.41 
TCGA-D5-6930 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-EI-6506 
        1.51        92.75        49.91        20.55 

$`HIST1H1T WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 
       22.06        32.71        27.09        22.52        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       45.40        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6923 TCGA-D5-6924 
       16.14        15.58         1.48         3.68        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 
        9.04         9.44        11.64         4.80        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D7 
       10.26       119.70        24.43        38.20       130.65        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6507 
       57.24        24.13        51.48        32.61         0.49        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  HIST1H1T MUTATED HIST1H1T WILD-TYPE 
              1.32               0.00 
  HIST1H1T MUTATED HIST1H1T WILD-TYPE 
             92.75             148.01 
  HIST1H1T MUTATED HIST1H1T WILD-TYPE 
             10.32              20.28 
[1] "1.3 - 92.8 (10.3)"  "0.0 - 148.0 (20.3)"
[1] "hr=" "1.1"
D96V2, continuous
D96V3, binary
                    cls
clus                   0   1
  HIST1H1T MUTATED     9   1
  HIST1H1T WILD-TYPE 357 118
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HIST1H1T MUTATED      9    1
  HIST1H1T WILD-TYPE  357  118
        clus
vv       HIST1H1T MUTATED HIST1H1T WILD-TYPE
  COLON                 9                357
  RECTUM                1                118
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  HIST1H1T MUTATED         0        0        1         6         0         0
  HIST1H1T WILD-TYPE      91        1       31       132        10         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HIST1H1T MUTATED           0          1          2          0        0
  HIST1H1T WILD-TYPE        24         10         57         42       48
                    vv
clus                 STAGE IVA STAGE IVB
  HIST1H1T MUTATED           0         0
  HIST1H1T WILD-TYPE        18         1
D96V4, multiclass
            clus
vv           HIST1H1T MUTATED HIST1H1T WILD-TYPE
  STAGE I                   0                 91
  STAGE IA                  0                  1
  STAGE II                  1                 31
  STAGE IIA                 6                132
  STAGE IIB                 0                 10
  STAGE IIC                 0                  1
  STAGE III                 0                 24
  STAGE IIIA                1                 10
  STAGE IIIB                2                 57
  STAGE IIIC                0                 42
  STAGE IV                  0                 48
  STAGE IVA                 0                 18
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  HIST1H1T MUTATED     0   0   9   1
  HIST1H1T WILD-TYPE  17  92 320  49
D96V5, multiclass
    clus
vv   HIST1H1T MUTATED HIST1H1T WILD-TYPE
  T1                0                 17
  T2                0                 92
  T3                9                320
  T4                1                 49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  HIST1H1T MUTATED     8   2   0
  HIST1H1T WILD-TYPE 279 111  87
D96V6, multiclass
    clus
vv   HIST1H1T MUTATED HIST1H1T WILD-TYPE
  N0                8                279
  N1                2                111
  N2                0                 87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D96V7, binary
                    cls
clus                   0   1
  HIST1H1T MUTATED    10   0
  HIST1H1T WILD-TYPE 365  65
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HIST1H1T MUTATED     10    0
  HIST1H1T WILD-TYPE  365   65
   clus
vv  HIST1H1T MUTATED HIST1H1T WILD-TYPE
  0               10                365
  1                0                 65
[1] 2 2
[1] FALSE
D96V8, binary
                    cls
clus                   0   1
  HIST1H1T MUTATED     4   6
  HIST1H1T WILD-TYPE 221 258
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HIST1H1T MUTATED      4    6
  HIST1H1T WILD-TYPE  221  258
        clus
vv       HIST1H1T MUTATED HIST1H1T WILD-TYPE
  FEMALE                4                221
  MALE                  6                258
[1] 2 2
[1] FALSE
D96V9, binary
                    cls
clus                   0   1
  HIST1H1T MUTATED     5   0
  HIST1H1T WILD-TYPE 345  22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HIST1H1T MUTATED      5    0
  HIST1H1T WILD-TYPE  345   22
     clus
vv    HIST1H1T MUTATED HIST1H1T WILD-TYPE
  NO                 5                345
  YES                0                 22
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  HIST1H1T MUTATED                      7                             2
  HIST1H1T WILD-TYPE                  308                            45
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  HIST1H1T MUTATED                       1                              0
  HIST1H1T WILD-TYPE                   105                             10
D96V10, multiclass
                                clus
vv                               HIST1H1T MUTATED HIST1H1T WILD-TYPE
  COLON ADENOCARCINOMA                          7                308
  COLON MUCINOUS ADENOCARCINOMA                 2                 45
  RECTAL ADENOCARCINOMA                         1                105
  RECTAL MUCINOUS ADENOCARCINOMA                0                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  HIST1H1T MUTATED     7   0   0   0
  HIST1H1T WILD-TYPE 338   4  31  25
D96V11, multiclass
    clus
vv   HIST1H1T MUTATED HIST1H1T WILD-TYPE
  R0                7                338
  R1                0                  4
  R2                0                 31
  RX                0                 25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D96V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HIST1H1T MUTATED                                  0     0
  HIST1H1T WILD-TYPE                                1    11
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  HIST1H1T MUTATED                           2     7
  HIST1H1T WILD-TYPE                        20   219
D96V13, multiclass
                                  clus
vv                                 HIST1H1T MUTATED HIST1H1T WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 11
  BLACK OR AFRICAN AMERICAN                       2                 20
  WHITE                                           7                219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(97) Variable = CREBBP MUTATION ANALYSIS
D97V1, survival
                  sevent
clus2                0   1
  CREBBP MUTATED    56  11
  CREBBP WILD-TYPE 322  82
  CREBBP MUTATED CREBBP WILD-TYPE 
              67              404 
  CREBBP MUTATED CREBBP WILD-TYPE 
              11               82 
$`CREBBP MUTATED`
TCGA-A6-5665 TCGA-AA-3510 TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3525 TCGA-AA-3662 
       22.06        63.98        13.02         1.02         8.05         6.05 
TCGA-AA-3672 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3815 TCGA-AA-3818 
        0.92        19.04        19.04        10.06        33.04         0.99 
TCGA-AA-3864 TCGA-AA-3877 TCGA-AA-3947 TCGA-AA-3966 TCGA-AA-3973 TCGA-AA-A00E 
       53.00        31.00        33.01         2.01        13.05        30.02 
TCGA-AA-A010 TCGA-AA-A029 TCGA-AD-5900 TCGA-AD-6963 TCGA-AU-3779 TCGA-AU-6004 
       34.98        51.98         0.07        27.42        14.50        27.09 
TCGA-AY-5543 TCGA-AZ-4315 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-CA-6717 TCGA-CK-4948 
       33.01        58.39         6.77       100.01        12.76       148.01 
TCGA-CM-4743 TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-6164 TCGA-CM-6168 
       23.05        22.03        30.08        15.02        29.03        12.99 
TCGA-CM-6171 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-6535 TCGA-D5-6540 
       14.04        12.03        45.40        12.26        15.12        16.14 
TCGA-D5-6923 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A28H 
       12.43        13.32        12.59         7.50       131.51       117.07 
TCGA-F4-6460 TCGA-F4-6808 TCGA-G4-6293 TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6586 
       31.96        33.67       133.18        53.62        55.04        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-AG-3731 TCGA-AG-A002 TCGA-AG-A02N 
       26.17        91.79        79.69        37.02        20.98        61.97 
TCGA-AH-6544 TCGA-AH-6549 TCGA-AH-6643 TCGA-CI-6620 TCGA-EI-6507 TCGA-EI-6510 
       38.56        17.49         0.69        33.17        19.96        18.28 
TCGA-F5-6812 
        0.66 

$`CREBBP WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3520 
       35.01         6.97         1.02        38.99         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       37.05        36.03        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
       78.08         6.97        54.02         2.01        14.01        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3812 TCGA-AA-3819 
       36.00         5.03        85.05        26.99        35.05        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 
       17.03        24.03        27.02        29.98        18.05         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       12.99        24.00        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3975 TCGA-AA-3976 
       34.03        21.99        16.08        50.99        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00J 
       27.02        13.94        38.04        19.00        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       39.98        18.05        40.96        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6964 TCGA-AD-6965 
        0.79         0.72         5.79        22.42        10.88         0.20 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
       16.31         0.95        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 
      106.75        22.36        62.79        88.21        49.41        12.10 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07        12.20        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       14.30        17.56        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 
        9.99        21.14        82.95         1.91       124.27        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5860 
       37.02        25.02        13.02        29.06        22.98        32.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6169 TCGA-CM-6170 
        2.96        16.04        21.99        14.99        13.02        15.02 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       10.06        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
        1.32        43.27        17.85         4.80        17.13        12.49 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6924 TCGA-D5-6926 
       15.58         1.48         3.68         4.41        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
       49.91       140.38        44.32       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28K TCGA-F4-6459 
       81.37       119.93        35.97        60.79        98.24         8.61 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6299 
       16.24        13.25         0.53        47.41        35.31        74.56 
TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       65.85        44.68        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       22.09        13.78        46.75        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
        0.99        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6547 TCGA-AH-6644 
       38.96        41.00        38.04       117.11         1.45         0.72 
TCGA-CI-6619 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
        6.05         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6508 
       24.13        51.48        32.61         0.49        20.55        20.91 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6813 
        9.96        49.51        31.30        28.57        32.19         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  CREBBP MUTATED CREBBP WILD-TYPE 
            0.07             0.00 
  CREBBP MUTATED CREBBP WILD-TYPE 
          148.01           140.38 
  CREBBP MUTATED CREBBP WILD-TYPE 
          22.060           20.035 
[1] "0.1 - 148.0 (22.1)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1.5"
D97V2, continuous
D97V3, binary
                  cls
clus                 0   1
  CREBBP MUTATED    60  10
  CREBBP WILD-TYPE 306 109
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CREBBP MUTATED     60   10
  CREBBP WILD-TYPE  306  109
        clus
vv       CREBBP MUTATED CREBBP WILD-TYPE
  COLON              60              306
  RECTUM             10              109
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CREBBP MUTATED        10        0        7        22         4         0
  CREBBP WILD-TYPE      81        1       25       116         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CREBBP MUTATED           5          0          7          4        4
  CREBBP WILD-TYPE        19         11         52         38       44
                  vv
clus               STAGE IVA STAGE IVB
  CREBBP MUTATED           3         0
  CREBBP WILD-TYPE        15         1
D97V4, multiclass
            clus
vv           CREBBP MUTATED CREBBP WILD-TYPE
  STAGE I                10               81
  STAGE IA                0                1
  STAGE II                7               25
  STAGE IIA              22              116
  STAGE IIB               4                6
  STAGE IIC               0                1
  STAGE III               5               19
  STAGE IIIA              0               11
  STAGE IIIB              7               52
  STAGE IIIC              4               38
  STAGE IV                4               44
  STAGE IVA               3               15
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  CREBBP MUTATED     2   9  52   7
  CREBBP WILD-TYPE  15  83 277  43
D97V5, multiclass
    clus
vv   CREBBP MUTATED CREBBP WILD-TYPE
  T1              2               15
  T2              9               83
  T3             52              277
  T4              7               43
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  CREBBP MUTATED    45  15   9
  CREBBP WILD-TYPE 242  98  78
D97V6, multiclass
    clus
vv   CREBBP MUTATED CREBBP WILD-TYPE
  N0             45              242
  N1             15               98
  N2              9               78
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D97V7, binary
                  cls
clus                 0   1
  CREBBP MUTATED    54   7
  CREBBP WILD-TYPE 321  58
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CREBBP MUTATED     54    7
  CREBBP WILD-TYPE  321   58
   clus
vv  CREBBP MUTATED CREBBP WILD-TYPE
  0             54              321
  1              7               58
[1] 2 2
[1] FALSE
D97V8, binary
                  cls
clus                 0   1
  CREBBP MUTATED    40  30
  CREBBP WILD-TYPE 185 234
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CREBBP MUTATED     40   30
  CREBBP WILD-TYPE  185  234
        clus
vv       CREBBP MUTATED CREBBP WILD-TYPE
  FEMALE             40              185
  MALE               30              234
[1] 2 2
[1] FALSE
D97V9, binary
                  cls
clus                 0   1
  CREBBP MUTATED    53   1
  CREBBP WILD-TYPE 297  21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CREBBP MUTATED     53    1
  CREBBP WILD-TYPE  297   21
     clus
vv    CREBBP MUTATED CREBBP WILD-TYPE
  NO              53              297
  YES              1               21
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CREBBP MUTATED                     52                             7
  CREBBP WILD-TYPE                  263                            40
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CREBBP MUTATED                      10                              0
  CREBBP WILD-TYPE                    96                             10
D97V10, multiclass
                                clus
vv                               CREBBP MUTATED CREBBP WILD-TYPE
  COLON ADENOCARCINOMA                       52              263
  COLON MUCINOUS ADENOCARCINOMA               7               40
  RECTAL ADENOCARCINOMA                      10               96
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  CREBBP MUTATED    49   0   4   5
  CREBBP WILD-TYPE 296   4  27  20
D97V11, multiclass
    clus
vv   CREBBP MUTATED CREBBP WILD-TYPE
  R0             49              296
  R1              0                4
  R2              4               27
  RX              5               20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D97V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CREBBP MUTATED                                  0     1
  CREBBP WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  CREBBP MUTATED                           2    43
  CREBBP WILD-TYPE                        20   183
D97V13, multiclass
                                  clus
vv                                 CREBBP MUTATED CREBBP WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     2               20
  WHITE                                        43              183
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(98) Variable = GMNN MUTATION ANALYSIS
D98V1, survival
                sevent
clus2              0   1
  GMNN MUTATED     4   0
  GMNN WILD-TYPE 374  93
  GMNN MUTATED GMNN WILD-TYPE 
             4            467 
  GMNN MUTATED GMNN WILD-TYPE 
             0             93 
$`GMNN MUTATED`
TCGA-AA-A010 TCGA-D5-5538 TCGA-D5-6538 TCGA-AF-6655 
       34.98        12.26        17.13        20.02 

$`GMNN WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       10.06        12.03        45.40        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
        4.80        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       15.39        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  GMNN MUTATED GMNN WILD-TYPE 
         12.26           0.00 
  GMNN MUTATED GMNN WILD-TYPE 
         34.98         148.01 
  GMNN MUTATED GMNN WILD-TYPE 
        18.575         20.280 
[1] "12.3 - 35.0 (18.6)" "0.0 - 148.0 (20.3)"
[1] "hr="     "3300000"
D98V2, continuous
D98V3, binary
                cls
clus               0   1
  GMNN MUTATED     3   2
  GMNN WILD-TYPE 363 117
[1] "tbl2"
                cls
clus             [,1] [,2]
  GMNN MUTATED      3    2
  GMNN WILD-TYPE  363  117
        clus
vv       GMNN MUTATED GMNN WILD-TYPE
  COLON             3            363
  RECTUM            2            117
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GMNN MUTATED         0        0        0         0         1         0
  GMNN WILD-TYPE      91        1       32       138         9         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  GMNN MUTATED           1          1          2          0        0         0
  GMNN WILD-TYPE        23         10         57         42       48        18
                vv
clus             STAGE IVB
  GMNN MUTATED           0
  GMNN WILD-TYPE         1
D98V4, multiclass
            clus
vv           GMNN MUTATED GMNN WILD-TYPE
  STAGE I               0             91
  STAGE IA              0              1
  STAGE II              0             32
  STAGE IIA             0            138
  STAGE IIB             1              9
  STAGE IIC             0              1
  STAGE III             1             23
  STAGE IIIA            1             10
  STAGE IIIB            2             57
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  GMNN MUTATED     0   1   3   1
  GMNN WILD-TYPE  17  91 326  49
D98V5, multiclass
    clus
vv   GMNN MUTATED GMNN WILD-TYPE
  T1            0             17
  T2            1             91
  T3            3            326
  T4            1             49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  GMNN MUTATED     1   3   1
  GMNN WILD-TYPE 286 110  86
D98V6, multiclass
    clus
vv   GMNN MUTATED GMNN WILD-TYPE
  N0            1            286
  N1            3            110
  N2            1             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D98V7, binary
                cls
clus               0   1
  GMNN MUTATED     4   0
  GMNN WILD-TYPE 371  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  GMNN MUTATED      4    0
  GMNN WILD-TYPE  371   65
   clus
vv  GMNN MUTATED GMNN WILD-TYPE
  0            4            371
  1            0             65
[1] 2 2
[1] FALSE
D98V8, binary
                cls
clus               0   1
  GMNN MUTATED     3   2
  GMNN WILD-TYPE 222 262
[1] "tbl2"
                cls
clus             [,1] [,2]
  GMNN MUTATED      3    2
  GMNN WILD-TYPE  222  262
        clus
vv       GMNN MUTATED GMNN WILD-TYPE
  FEMALE            3            222
  MALE              2            262
[1] 2 2
[1] FALSE
D98V9, binary
                cls
clus               0   1
  GMNN MUTATED     4   0
  GMNN WILD-TYPE 346  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  GMNN MUTATED      4    0
  GMNN WILD-TYPE  346   22
     clus
vv    GMNN MUTATED GMNN WILD-TYPE
  NO             4            346
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  GMNN MUTATED                      3                             0
  GMNN WILD-TYPE                  312                            47
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  GMNN MUTATED                       2                              0
  GMNN WILD-TYPE                   104                             10
D98V10, multiclass
                                clus
vv                               GMNN MUTATED GMNN WILD-TYPE
  COLON ADENOCARCINOMA                      3            312
  COLON MUCINOUS ADENOCARCINOMA             0             47
  RECTAL ADENOCARCINOMA                     2            104
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  GMNN MUTATED     4   0   0   0
  GMNN WILD-TYPE 341   4  31  25
D98V11, multiclass
    clus
vv   GMNN MUTATED GMNN WILD-TYPE
  R0            4            341
  R1            0              4
  R2            0             31
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D98V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GMNN MUTATED                                  0     0
  GMNN WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  GMNN MUTATED                           0     4
  GMNN WILD-TYPE                        22   222
D98V13, multiclass
                                  clus
vv                                 GMNN MUTATED GMNN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       4            222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(99) Variable = CTNNB1 MUTATION ANALYSIS
D99V1, survival
                  sevent
clus2                0   1
  CTNNB1 MUTATED    69  21
  CTNNB1 WILD-TYPE 309  72
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
              90              381 
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
              21               72 
$`CTNNB1 MUTATED`
TCGA-A6-2678 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5665 TCGA-A6-6780 TCGA-AA-3496 
       42.28        29.19        33.53        22.06        20.12         1.02 
TCGA-AA-3510 TCGA-AA-3534 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       63.98        29.00        61.02        78.08         6.05         6.97 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3831 TCGA-AA-A00N TCGA-AA-A00U TCGA-AA-A01K 
        5.03        85.05        17.98         4.01        17.03        31.00 
TCGA-AD-6901 TCGA-AD-6964 TCGA-AU-3779 TCGA-AZ-4315 TCGA-AZ-5407 TCGA-AZ-6598 
       22.42        10.88        14.50        58.39        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6608 TCGA-CA-6717 TCGA-CA-6718 
        6.77       100.01         5.23         1.61        12.76        10.06 
TCGA-CK-4952 TCGA-CK-5916 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4752 
       15.62        21.14        23.05        20.02        25.02        13.02 
TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6167 
       22.03        30.08        32.02         2.96        29.03        14.99 
TCGA-CM-6168 TCGA-CM-6171 TCGA-CM-6675 TCGA-D5-5540 TCGA-D5-6533 TCGA-D5-6535 
       12.99        14.04        13.05        56.09         1.32        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 TCGA-DM-A0XF 
       17.85         4.80        17.13        16.14        15.58        38.20 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1DB TCGA-F4-6569 TCGA-F4-6703 
       92.75        49.91        13.32        44.32        35.74        47.87 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6303 TCGA-G4-6315 TCGA-G4-6323 
        0.53        47.41        35.31        65.85        61.91        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2693 
       35.80        26.17        91.79        46.75        79.69        19.10 
TCGA-AF-6655 TCGA-AG-3575 TCGA-AG-3732 TCGA-AG-3881 TCGA-AG-3892 TCGA-AG-A020 
       20.02        12.00        32.98        19.04        13.02        10.98 
TCGA-AH-6547 TCGA-CL-5917 TCGA-DC-5337 TCGA-DC-6682 TCGA-DY-A0XA TCGA-DY-A1DF 
        1.45        78.12        15.02         4.01       126.44        24.13 
TCGA-DY-A1DG TCGA-EI-6510 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6811 TCGA-F5-6813 
       51.48        18.28        49.51        31.30        32.19         0.69 

$`CTNNB1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2683 
       43.76        46.65        43.76        42.90        24.33        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 
       31.63        30.44        23.61        22.09        32.71        27.09 
TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 
       22.52         8.38        25.08        25.18        24.16        21.76 
TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 
       24.69        24.39        23.87        19.66        20.28         7.04 
TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        3.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3538 
       19.07         0.00        19.07        34.03        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
       13.94        19.99        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
       19.00        36.00        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3833 
       35.05        33.04         0.99        25.02         1.02        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q 
       10.98        32.02        12.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       27.42         0.20        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 
       62.79        12.10        29.56        11.74         3.19        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 
        3.06         3.25         3.29         0.07        12.20        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
       17.56       148.01        85.45        49.08        51.32         9.99 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4746 TCGA-CM-5341 TCGA-CM-5348 
       82.95         1.91       124.27        37.02        29.06        22.98 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 
       12.00        16.04        21.99        13.02        15.02        11.01 
TCGA-CM-6674 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       12.95        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       45.40        12.26        19.59        55.92        20.19        18.25 
TCGA-D5-6534 TCGA-D5-6539 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       43.27        12.49         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A1D0 
       12.00        11.38        10.26       119.70        24.43       130.65 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
       12.59       140.38         7.50       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6570 TCGA-F4-6704 TCGA-F4-6805 
       98.24         8.61        31.96         6.18         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-G4-6293 TCGA-G4-6299 
       41.42        16.24        33.67        13.25       133.18        74.56 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6317 
       53.62        44.68        55.04        85.48        63.62        36.00 
TCGA-G4-6321 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 
       22.09        24.13        39.48        43.04        13.55        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6672 TCGA-AG-3574 
       10.39        14.50        16.83        15.39        10.39        36.03 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 
        7.99         0.99        37.02         0.99         0.99        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 
        1.02        17.95        36.95        17.03        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       12.00        70.03        64.01        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6549 
       61.97        41.00        38.04       117.11        38.56        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5918 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
        7.17         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1H8 
        5.95         5.03         5.29        41.36        57.24        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-F5-6464 TCGA-F5-6702 
        0.49        20.55        19.96        20.91         9.96        28.57 
TCGA-F5-6812 TCGA-G5-6235 TCGA-G5-6641 
        0.66        55.76        26.43 

  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
            0.53             0.00 
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
          126.44           148.01 
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
          21.585           20.050 
[1] "0.5 - 126.4 (21.6)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1"  
D99V2, continuous
D99V3, binary
                  cls
clus                 0   1
  CTNNB1 MUTATED    74  18
  CTNNB1 WILD-TYPE 292 101
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CTNNB1 MUTATED     74   18
  CTNNB1 WILD-TYPE  292  101
        clus
vv       CTNNB1 MUTATED CTNNB1 WILD-TYPE
  COLON              74              292
  RECTUM             18              101
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CTNNB1 MUTATED        15        1        8        35         2         0
  CTNNB1 WILD-TYPE      76        0       24       103         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CTNNB1 MUTATED           3          2          8          8        4
  CTNNB1 WILD-TYPE        21          9         51         34       44
                  vv
clus               STAGE IVA STAGE IVB
  CTNNB1 MUTATED           3         1
  CTNNB1 WILD-TYPE        15         0
D99V4, multiclass
            clus
vv           CTNNB1 MUTATED CTNNB1 WILD-TYPE
  STAGE I                15               76
  STAGE IA                1                0
  STAGE II                8               24
  STAGE IIA              35              103
  STAGE IIB               2                8
  STAGE IIC               0                1
  STAGE III               3               21
  STAGE IIIA              2                9
  STAGE IIIB              8               51
  STAGE IIIC              8               34
  STAGE IV                4               44
  STAGE IVA               3               15
  STAGE IVB               1                0
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  CTNNB1 MUTATED     5  13  65   9
  CTNNB1 WILD-TYPE  12  79 264  41
D99V5, multiclass
    clus
vv   CTNNB1 MUTATED CTNNB1 WILD-TYPE
  T1              5               12
  T2             13               79
  T3             65              264
  T4              9               41
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  CTNNB1 MUTATED    66  14  13
  CTNNB1 WILD-TYPE 221  99  74
D99V6, multiclass
    clus
vv   CTNNB1 MUTATED CTNNB1 WILD-TYPE
  N0             66              221
  N1             14               99
  N2             13               74
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D99V7, binary
                  cls
clus                 0   1
  CTNNB1 MUTATED    72   7
  CTNNB1 WILD-TYPE 303  58
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CTNNB1 MUTATED     72    7
  CTNNB1 WILD-TYPE  303   58
   clus
vv  CTNNB1 MUTATED CTNNB1 WILD-TYPE
  0             72              303
  1              7               58
[1] 2 2
[1] FALSE
D99V8, binary
                  cls
clus                 0   1
  CTNNB1 MUTATED    44  49
  CTNNB1 WILD-TYPE 181 215
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CTNNB1 MUTATED     44   49
  CTNNB1 WILD-TYPE  181  215
        clus
vv       CTNNB1 MUTATED CTNNB1 WILD-TYPE
  FEMALE             44              181
  MALE               49              215
[1] 2 2
[1] FALSE
D99V9, binary
                  cls
clus                 0   1
  CTNNB1 MUTATED    74   0
  CTNNB1 WILD-TYPE 276  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CTNNB1 MUTATED     74    0
  CTNNB1 WILD-TYPE  276   22
     clus
vv    CTNNB1 MUTATED CTNNB1 WILD-TYPE
  NO              74              276
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CTNNB1 MUTATED                     65                             7
  CTNNB1 WILD-TYPE                  250                            40
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CTNNB1 MUTATED                      16                              1
  CTNNB1 WILD-TYPE                    90                              9
D99V10, multiclass
                                clus
vv                               CTNNB1 MUTATED CTNNB1 WILD-TYPE
  COLON ADENOCARCINOMA                       65              250
  COLON MUCINOUS ADENOCARCINOMA               7               40
  RECTAL ADENOCARCINOMA                      16               90
  RECTAL MUCINOUS ADENOCARCINOMA              1                9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  CTNNB1 MUTATED    61   0   2   8
  CTNNB1 WILD-TYPE 284   4  29  17
D99V11, multiclass
    clus
vv   CTNNB1 MUTATED CTNNB1 WILD-TYPE
  R0             61              284
  R1              0                4
  R2              2               29
  RX              8               17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D99V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CTNNB1 MUTATED                                  0     2
  CTNNB1 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  CTNNB1 MUTATED                           7    65
  CTNNB1 WILD-TYPE                        15   161
D99V13, multiclass
                                  clus
vv                                 CTNNB1 MUTATED CTNNB1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                9
  BLACK OR AFRICAN AMERICAN                     7               15
  WHITE                                        65              161
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(100) Variable = KDM6A MUTATION ANALYSIS
D100V1, survival
                 sevent
clus2               0   1
  KDM6A MUTATED    23   5
  KDM6A WILD-TYPE 355  88
  KDM6A MUTATED KDM6A WILD-TYPE 
             28             443 
  KDM6A MUTATED KDM6A WILD-TYPE 
              5              88 
$`KDM6A MUTATED`
TCGA-A6-3809 TCGA-A6-5666 TCGA-AA-3713 TCGA-AA-A010 TCGA-AD-6964 TCGA-AZ-4315 
       32.75        32.71        19.04        34.98        10.88        58.39 
TCGA-CA-6717 TCGA-CK-5914 TCGA-CM-4747 TCGA-CM-5348 TCGA-CM-6164 TCGA-CM-6168 
       12.76         9.99        25.02        22.98        29.03        12.99 
TCGA-CM-6169 TCGA-CM-6676 TCGA-D5-6529 TCGA-D5-6535 TCGA-D5-6540 TCGA-D5-6926 
       13.02        11.08        20.19        15.12        16.14         9.04 
TCGA-D5-6929 TCGA-D5-7000 TCGA-DM-A0XF TCGA-DM-A1HB TCGA-DM-A28C TCGA-DM-A28F 
        4.80        10.26        38.20       135.65        81.37        35.97 
TCGA-F4-6805 TCGA-G4-6303 TCGA-G4-6586 TCGA-DC-6681 
       34.42        65.85        35.80         5.95 

$`KDM6A WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       22.06        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
        0.72         5.79        22.42        27.42         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07        12.20        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5916 
      148.01        85.45        15.62        49.08        51.32        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       13.02        29.06        22.03        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6170 TCGA-CM-6171 
        2.96        16.04        21.99        14.99        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       11.01        12.95        13.05        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       18.25         1.32        43.27        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       12.49        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
       14.30         9.44        11.64         1.51        12.00        11.38 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
      119.70        24.43       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 
       12.59       140.38         7.50        44.32       131.51       139.17 
TCGA-DM-A285 TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
        6.12       119.93        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6806 
       31.96        35.74         6.18        47.87         1.55        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
      133.18        74.56        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 
       63.62        61.91        36.00        22.09        13.78        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  KDM6A MUTATED KDM6A WILD-TYPE 
            4.8             0.0 
  KDM6A MUTATED KDM6A WILD-TYPE 
         135.65          148.01 
  KDM6A MUTATED KDM6A WILD-TYPE 
         21.585          20.120 
[1] "4.8 - 135.7 (21.6)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.2"
D100V2, continuous
D100V3, binary
                 cls
clus                0   1
  KDM6A MUTATED    27   1
  KDM6A WILD-TYPE 339 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM6A MUTATED     27    1
  KDM6A WILD-TYPE  339  118
        clus
vv       KDM6A MUTATED KDM6A WILD-TYPE
  COLON             27             339
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KDM6A MUTATED         3        0        0         9         2         1
  KDM6A WILD-TYPE      88        1       32       129         8         0
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  KDM6A MUTATED           0          0          6          1        3         2
  KDM6A WILD-TYPE        24         11         53         41       45        16
                 vv
clus              STAGE IVB
  KDM6A MUTATED           0
  KDM6A WILD-TYPE         1
D100V4, multiclass
            clus
vv           KDM6A MUTATED KDM6A WILD-TYPE
  STAGE I                3              88
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              9             129
  STAGE IIB              2               8
  STAGE IIC              1               0
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             6              53
  STAGE IIIC             1              41
  STAGE IV               3              45
  STAGE IVA              2              16
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  KDM6A MUTATED     0   3  19   6
  KDM6A WILD-TYPE  17  89 310  44
D100V5, multiclass
    clus
vv   KDM6A MUTATED KDM6A WILD-TYPE
  T1             0              17
  T2             3              89
  T3            19             310
  T4             6              44
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  KDM6A MUTATED    16   9   3
  KDM6A WILD-TYPE 271 104  84
D100V6, multiclass
    clus
vv   KDM6A MUTATED KDM6A WILD-TYPE
  N0            16             271
  N1             9             104
  N2             3              84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D100V7, binary
                 cls
clus                0   1
  KDM6A MUTATED    20   5
  KDM6A WILD-TYPE 355  60
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM6A MUTATED     20    5
  KDM6A WILD-TYPE  355   60
   clus
vv  KDM6A MUTATED KDM6A WILD-TYPE
  0            20             355
  1             5              60
[1] 2 2
[1] FALSE
D100V8, binary
                 cls
clus                0   1
  KDM6A MUTATED    12  16
  KDM6A WILD-TYPE 213 248
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM6A MUTATED     12   16
  KDM6A WILD-TYPE  213  248
        clus
vv       KDM6A MUTATED KDM6A WILD-TYPE
  FEMALE            12             213
  MALE              16             248
[1] 2 2
[1] FALSE
D100V9, binary
                 cls
clus                0   1
  KDM6A MUTATED    19   2
  KDM6A WILD-TYPE 331  20
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM6A MUTATED     19    2
  KDM6A WILD-TYPE  331   20
     clus
vv    KDM6A MUTATED KDM6A WILD-TYPE
  NO             19             331
  YES             2              20
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  KDM6A MUTATED                     21                             4
  KDM6A WILD-TYPE                  294                            43
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  KDM6A MUTATED                       1                              0
  KDM6A WILD-TYPE                   105                             10
D100V10, multiclass
                                clus
vv                               KDM6A MUTATED KDM6A WILD-TYPE
  COLON ADENOCARCINOMA                      21             294
  COLON MUCINOUS ADENOCARCINOMA              4              43
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  KDM6A MUTATED    18   0   1   3
  KDM6A WILD-TYPE 327   4  30  22
D100V11, multiclass
    clus
vv   KDM6A MUTATED KDM6A WILD-TYPE
  R0            18             327
  R1             0               4
  R2             1              30
  RX             3              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D100V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KDM6A MUTATED                                  0     1
  KDM6A WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  KDM6A MUTATED                           2    23
  KDM6A WILD-TYPE                        20   203
D100V13, multiclass
                                  clus
vv                                 KDM6A MUTATED KDM6A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    2              20
  WHITE                                       23             203
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(101) Variable = CLSPN MUTATION ANALYSIS
D101V1, survival
                 sevent
clus2               0   1
  CLSPN MUTATED    27   6
  CLSPN WILD-TYPE 351  87
  CLSPN MUTATED CLSPN WILD-TYPE 
             33             438 
  CLSPN MUTATED CLSPN WILD-TYPE 
              6              87 
$`CLSPN MUTATED`
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6651 TCGA-A6-6782 TCGA-AA-3496 TCGA-AA-3664 
        8.38        25.08        21.76        20.28         1.02        54.02 
TCGA-AA-A00A TCGA-AA-A02J TCGA-AZ-4315 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-CA-5797 
       38.04         5.03        58.39        49.41        12.10         3.29 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CK-4948 TCGA-CM-5348 TCGA-CM-6166 TCGA-CM-6678 
       12.20        12.76       148.01        22.98        21.99        11.01 
TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6931 TCGA-DM-A0X9 TCGA-DM-A282 TCGA-F4-6460 
       17.13        16.14        12.00       119.70       139.17        31.96 
TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6809 TCGA-G4-6586 TCGA-G4-6626 TCGA-AG-3885 
       35.74        47.87        13.25        35.80        46.75        17.95 
TCGA-AG-A002 TCGA-CI-6619 TCGA-DC-5869 
       20.98         6.05         5.03 

$`CLSPN WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6648 
       22.09        22.06        32.71        27.09        22.52        25.18 
TCGA-A6-6649 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       24.16        24.69        24.39        23.87        20.12        19.66 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
        7.04         3.02        35.01        63.98         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
       13.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       36.03         8.05        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
       78.08         6.05         6.97         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       13.94        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       51.98        39.98         2.01        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       33.01        21.44        17.82         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6603 
       22.36        62.79        88.21         6.77       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 
        3.25         0.07        10.06        14.30        17.56        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       13.02        29.06        22.03        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
        2.96        29.03        16.04        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.08        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 
       15.12        17.85         4.80        12.49        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0XD 
       11.64         4.80         1.51        11.38        10.26        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A285 
      140.38         7.50        44.32       131.51       135.65         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6570 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        8.61         6.18         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       33.67         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 
       61.91        36.00        22.09        13.78        26.17        91.79 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.69         0.72        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
        7.17        15.02        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  CLSPN MUTATED CLSPN WILD-TYPE 
           1.02            0.00 
  CLSPN MUTATED CLSPN WILD-TYPE 
         148.01          140.38 
  CLSPN MUTATED CLSPN WILD-TYPE 
         20.980          20.085 
[1] "1.0 - 148.0 (21.0)" "0.0 - 140.4 (20.1)"
[1] "hr=" "1.3"
D101V2, continuous
D101V3, binary
                 cls
clus                0   1
  CLSPN MUTATED    30   4
  CLSPN WILD-TYPE 336 115
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CLSPN MUTATED     30    4
  CLSPN WILD-TYPE  336  115
        clus
vv       CLSPN MUTATED CLSPN WILD-TYPE
  COLON             30             336
  RECTUM             4             115
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CLSPN MUTATED         4        0        3        12         1         0
  CLSPN WILD-TYPE      87        1       29       126         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CLSPN MUTATED           1          0          6          1        3         3
  CLSPN WILD-TYPE        23         11         53         41       45        15
                 vv
clus              STAGE IVB
  CLSPN MUTATED           0
  CLSPN WILD-TYPE         1
D101V4, multiclass
            clus
vv           CLSPN MUTATED CLSPN WILD-TYPE
  STAGE I                4              87
  STAGE IA               0               1
  STAGE II               3              29
  STAGE IIA             12             126
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             6              53
  STAGE IIIC             1              41
  STAGE IV               3              45
  STAGE IVA              3              15
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CLSPN MUTATED     0   4  26   4
  CLSPN WILD-TYPE  17  88 303  46
D101V5, multiclass
    clus
vv   CLSPN MUTATED CLSPN WILD-TYPE
  T1             0              17
  T2             4              88
  T3            26             303
  T4             4              46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  CLSPN MUTATED    21  11   2
  CLSPN WILD-TYPE 266 102  85
D101V6, multiclass
    clus
vv   CLSPN MUTATED CLSPN WILD-TYPE
  N0            21             266
  N1            11             102
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D101V7, binary
                 cls
clus                0   1
  CLSPN MUTATED    25   6
  CLSPN WILD-TYPE 350  59
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CLSPN MUTATED     25    6
  CLSPN WILD-TYPE  350   59
   clus
vv  CLSPN MUTATED CLSPN WILD-TYPE
  0            25             350
  1             6              59
[1] 2 2
[1] FALSE
D101V8, binary
                 cls
clus                0   1
  CLSPN MUTATED    18  16
  CLSPN WILD-TYPE 207 248
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CLSPN MUTATED     18   16
  CLSPN WILD-TYPE  207  248
        clus
vv       CLSPN MUTATED CLSPN WILD-TYPE
  FEMALE            18             207
  MALE              16             248
[1] 2 2
[1] FALSE
D101V9, binary
                 cls
clus                0   1
  CLSPN MUTATED    25   1
  CLSPN WILD-TYPE 325  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CLSPN MUTATED     25    1
  CLSPN WILD-TYPE  325   21
     clus
vv    CLSPN MUTATED CLSPN WILD-TYPE
  NO             25             325
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CLSPN MUTATED                     28                             2
  CLSPN WILD-TYPE                  287                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CLSPN MUTATED                       4                              0
  CLSPN WILD-TYPE                   102                             10
D101V10, multiclass
                                clus
vv                               CLSPN MUTATED CLSPN WILD-TYPE
  COLON ADENOCARCINOMA                      28             287
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      4             102
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  CLSPN MUTATED    22   0   1   2
  CLSPN WILD-TYPE 323   4  30  23
D101V11, multiclass
    clus
vv   CLSPN MUTATED CLSPN WILD-TYPE
  R0            22             323
  R1             0               4
  R2             1              30
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D101V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CLSPN MUTATED                                  0     3
  CLSPN WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CLSPN MUTATED                           3    21
  CLSPN WILD-TYPE                        19   205
D101V13, multiclass
                                  clus
vv                                 CLSPN MUTATED CLSPN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        3               8
  BLACK OR AFRICAN AMERICAN                    3              19
  WHITE                                       21             205
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(102) Variable = FRMPD4 MUTATION ANALYSIS
D102V1, survival
                  sevent
clus2                0   1
  FRMPD4 MUTATED    29   6
  FRMPD4 WILD-TYPE 349  87
  FRMPD4 MUTATED FRMPD4 WILD-TYPE 
              35              436 
  FRMPD4 MUTATED FRMPD4 WILD-TYPE 
               6               87 
$`FRMPD4 MUTATED`
TCGA-A6-2672 TCGA-A6-5662 TCGA-A6-5665 TCGA-A6-6780 TCGA-AA-A00N TCGA-AA-A01P 
       46.65        23.61        22.06        20.12         4.01        38.07 
TCGA-AD-6899 TCGA-AU-3779 TCGA-AU-6004 TCGA-AZ-4315 TCGA-AZ-5403 TCGA-CA-6717 
        5.79        14.50        27.09        58.39        62.79        12.76 
TCGA-CM-4752 TCGA-CM-5348 TCGA-CM-5861 TCGA-CM-5868 TCGA-CM-6163 TCGA-D5-5540 
       13.02        22.98        15.02        17.03         2.96        56.09 
TCGA-D5-5541 TCGA-D5-6532 TCGA-D5-6539 TCGA-DM-A0X9 TCGA-DM-A1DA TCGA-DM-A1DB 
       55.92        18.25        12.49       119.70         7.50        44.32 
TCGA-DM-A282 TCGA-DM-A28H TCGA-F4-6856 TCGA-G4-6310 TCGA-G4-6586 TCGA-AF-2693 
      139.17       117.07        35.31        63.62        35.80        19.10 
TCGA-AG-3731 TCGA-AG-3887 TCGA-AG-A002 TCGA-AG-A02N TCGA-F5-6465 
       37.02        36.95        20.98        61.97        49.51 

$`FRMPD4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5664 TCGA-A6-5666 
       31.63        30.44        29.19        33.53        22.09        32.71 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       27.09        22.52         8.38        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 
       21.76        24.69        24.39        23.87        19.66        20.28 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
        7.04         3.02         1.02        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01Q 
       10.98        32.02        12.00        31.00        31.00         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6901 
       21.37        15.52        56.55         0.79         0.72        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       27.42        10.88         0.20        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13       106.75        22.36 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07        12.20        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5349 
       20.02        37.02        25.02        29.06        22.03        30.08 
TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6162 
       32.02         5.03        15.02        15.02        15.02        12.00 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       19.59        20.19         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
        4.80        17.13        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0XD 
        4.80         1.51        12.00        11.38        10.26        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      140.38       131.51       135.65         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       35.97        60.79        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 
       33.67        13.25         0.53        47.41       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6315 
       65.85        53.62        44.68        55.04        85.48        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 
       79.69        24.13        39.48        43.04        13.55        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3732 TCGA-AG-3742 
       13.94        19.99         7.99         0.99        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3890 
        0.99        19.04        19.99         1.02        17.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
       49.97         1.94        38.96        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       20.91        18.28         9.96        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  FRMPD4 MUTATED FRMPD4 WILD-TYPE 
            2.96             0.00 
  FRMPD4 MUTATED FRMPD4 WILD-TYPE 
          139.17           148.01 
  FRMPD4 MUTATED FRMPD4 WILD-TYPE 
           27.09            19.99 
[1] "3.0 - 139.2 (27.1)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.7"
D102V2, continuous
D102V3, binary
                  cls
clus                 0   1
  FRMPD4 MUTATED    30   5
  FRMPD4 WILD-TYPE 336 114
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FRMPD4 MUTATED     30    5
  FRMPD4 WILD-TYPE  336  114
        clus
vv       FRMPD4 MUTATED FRMPD4 WILD-TYPE
  COLON              30              336
  RECTUM              5              114
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FRMPD4 MUTATED         5        0        2        15         1         0
  FRMPD4 WILD-TYPE      86        1       30       123         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FRMPD4 MUTATED           1          1          4          3        2
  FRMPD4 WILD-TYPE        23         10         55         39       46
                  vv
clus               STAGE IVA STAGE IVB
  FRMPD4 MUTATED           2         0
  FRMPD4 WILD-TYPE        16         1
D102V4, multiclass
            clus
vv           FRMPD4 MUTATED FRMPD4 WILD-TYPE
  STAGE I                 5               86
  STAGE IA                0                1
  STAGE II                2               30
  STAGE IIA              15              123
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               1               23
  STAGE IIIA              1               10
  STAGE IIIB              4               55
  STAGE IIIC              3               39
  STAGE IV                2               46
  STAGE IVA               2               16
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  FRMPD4 MUTATED     1   4  28   3
  FRMPD4 WILD-TYPE  16  88 301  47
D102V5, multiclass
    clus
vv   FRMPD4 MUTATED FRMPD4 WILD-TYPE
  T1              1               16
  T2              4               88
  T3             28              301
  T4              3               47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  FRMPD4 MUTATED    24   7   5
  FRMPD4 WILD-TYPE 263 106  82
D102V6, multiclass
    clus
vv   FRMPD4 MUTATED FRMPD4 WILD-TYPE
  N0             24              263
  N1              7              106
  N2              5               82
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D102V7, binary
                  cls
clus                 0   1
  FRMPD4 MUTATED    28   4
  FRMPD4 WILD-TYPE 347  61
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FRMPD4 MUTATED     28    4
  FRMPD4 WILD-TYPE  347   61
   clus
vv  FRMPD4 MUTATED FRMPD4 WILD-TYPE
  0             28              347
  1              4               61
[1] 2 2
[1] FALSE
D102V8, binary
                  cls
clus                 0   1
  FRMPD4 MUTATED    14  22
  FRMPD4 WILD-TYPE 211 242
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FRMPD4 MUTATED     14   22
  FRMPD4 WILD-TYPE  211  242
        clus
vv       FRMPD4 MUTATED FRMPD4 WILD-TYPE
  FEMALE             14              211
  MALE               22              242
[1] 2 2
[1] FALSE
D102V9, binary
                  cls
clus                 0   1
  FRMPD4 MUTATED    25   2
  FRMPD4 WILD-TYPE 325  20
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FRMPD4 MUTATED     25    2
  FRMPD4 WILD-TYPE  325   20
     clus
vv    FRMPD4 MUTATED FRMPD4 WILD-TYPE
  NO              25              325
  YES              2               20
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  FRMPD4 MUTATED                     25                             5
  FRMPD4 WILD-TYPE                  290                            42
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  FRMPD4 MUTATED                       4                              1
  FRMPD4 WILD-TYPE                   102                              9
D102V10, multiclass
                                clus
vv                               FRMPD4 MUTATED FRMPD4 WILD-TYPE
  COLON ADENOCARCINOMA                       25              290
  COLON MUCINOUS ADENOCARCINOMA               5               42
  RECTAL ADENOCARCINOMA                       4              102
  RECTAL MUCINOUS ADENOCARCINOMA              1                9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  FRMPD4 MUTATED    23   0   2   1
  FRMPD4 WILD-TYPE 322   4  29  24
D102V11, multiclass
    clus
vv   FRMPD4 MUTATED FRMPD4 WILD-TYPE
  R0             23              322
  R1              0                4
  R2              2               29
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D102V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FRMPD4 MUTATED                                  0     1
  FRMPD4 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  FRMPD4 MUTATED                           1    27
  FRMPD4 WILD-TYPE                        21   199
D102V13, multiclass
                                  clus
vv                                 FRMPD4 MUTATED FRMPD4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                        27              199
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(103) Variable = SAPS2 MUTATION ANALYSIS
D103V1, survival
                 sevent
clus2               0   1
  SAPS2 MUTATED    11   2
  SAPS2 WILD-TYPE 367  91
  SAPS2 MUTATED SAPS2 WILD-TYPE 
             13             458 
  SAPS2 MUTATED SAPS2 WILD-TYPE 
              2              91 
$`SAPS2 MUTATED`
TCGA-AA-3518 TCGA-AA-3663 TCGA-AA-3713 TCGA-AA-3966 TCGA-AD-6889 TCGA-AZ-6598 
        1.02         6.97        19.04         2.01        56.55        49.41 
TCGA-CM-4746 TCGA-CM-6171 TCGA-CM-6674 TCGA-D5-6930 TCGA-F4-6570 TCGA-EI-6507 
       37.02        14.04        12.95         1.51         6.18        19.96 
TCGA-G5-6235 
       55.76 

$`SAPS2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
       38.99         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
       34.03        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 
       40.96         0.07        21.37        15.52         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       88.21         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       20.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 
       21.99        14.99        12.99        13.02        15.02        11.01 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        4.80        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 
       98.24         8.61        31.96        35.74        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6510 
       51.48        32.61         0.49        20.55        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6641 
        0.69        26.43 

  SAPS2 MUTATED SAPS2 WILD-TYPE 
           1.02            0.00 
  SAPS2 MUTATED SAPS2 WILD-TYPE 
          56.55          148.01 
  SAPS2 MUTATED SAPS2 WILD-TYPE 
          14.04           20.73 
[1] "1.0 - 56.5 (14.0)"  "0.0 - 148.0 (20.7)"
[1] "hr=" "1.2"
D103V2, continuous
D103V3, binary
                 cls
clus                0   1
  SAPS2 MUTATED    11   2
  SAPS2 WILD-TYPE 355 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SAPS2 MUTATED     11    2
  SAPS2 WILD-TYPE  355  117
        clus
vv       SAPS2 MUTATED SAPS2 WILD-TYPE
  COLON             11             355
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SAPS2 MUTATED         2        0        2         7         0         0
  SAPS2 WILD-TYPE      89        1       30       131        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SAPS2 MUTATED           0          0          1          0        1         0
  SAPS2 WILD-TYPE        24         11         58         42       47        18
                 vv
clus              STAGE IVB
  SAPS2 MUTATED           0
  SAPS2 WILD-TYPE         1
D103V4, multiclass
            clus
vv           SAPS2 MUTATED SAPS2 WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA              7             131
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             0              42
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  SAPS2 MUTATED     0   2  11   0
  SAPS2 WILD-TYPE  17  90 318  50
D103V5, multiclass
    clus
vv   SAPS2 MUTATED SAPS2 WILD-TYPE
  T1             0              17
  T2             2              90
  T3            11             318
  T4             0              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  SAPS2 MUTATED    12   1   0
  SAPS2 WILD-TYPE 275 112  87
D103V6, multiclass
    clus
vv   SAPS2 MUTATED SAPS2 WILD-TYPE
  N0            12             275
  N1             1             112
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D103V7, binary
                 cls
clus                0   1
  SAPS2 MUTATED    10   1
  SAPS2 WILD-TYPE 365  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SAPS2 MUTATED     10    1
  SAPS2 WILD-TYPE  365   64
   clus
vv  SAPS2 MUTATED SAPS2 WILD-TYPE
  0            10             365
  1             1              64
[1] 2 2
[1] FALSE
D103V8, binary
                 cls
clus                0   1
  SAPS2 MUTATED     5   8
  SAPS2 WILD-TYPE 220 256
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SAPS2 MUTATED      5    8
  SAPS2 WILD-TYPE  220  256
        clus
vv       SAPS2 MUTATED SAPS2 WILD-TYPE
  FEMALE             5             220
  MALE               8             256
[1] 2 2
[1] FALSE
D103V9, binary
                 cls
clus                0   1
  SAPS2 MUTATED     8   1
  SAPS2 WILD-TYPE 342  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SAPS2 MUTATED      8    1
  SAPS2 WILD-TYPE  342   21
     clus
vv    SAPS2 MUTATED SAPS2 WILD-TYPE
  NO              8             342
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SAPS2 MUTATED                      9                             2
  SAPS2 WILD-TYPE                  306                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SAPS2 MUTATED                       2                              0
  SAPS2 WILD-TYPE                   104                             10
D103V10, multiclass
                                clus
vv                               SAPS2 MUTATED SAPS2 WILD-TYPE
  COLON ADENOCARCINOMA                       9             306
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  SAPS2 MUTATED     8   1   1   0
  SAPS2 WILD-TYPE 337   3  30  25
D103V11, multiclass
    clus
vv   SAPS2 MUTATED SAPS2 WILD-TYPE
  R0             8             337
  R1             1               3
  R2             1              30
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D103V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SAPS2 MUTATED                                  0     1
  SAPS2 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  SAPS2 MUTATED                           1     7
  SAPS2 WILD-TYPE                        21   219
D103V13, multiclass
                                  clus
vv                                 SAPS2 MUTATED SAPS2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        7             219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(104) Variable = MYST4 MUTATION ANALYSIS
D104V1, survival
                 sevent
clus2               0   1
  MYST4 MUTATED    24   6
  MYST4 WILD-TYPE 354  87
  MYST4 MUTATED MYST4 WILD-TYPE 
             30             441 
  MYST4 MUTATED MYST4 WILD-TYPE 
              6              87 
$`MYST4 MUTATED`
TCGA-A6-4105 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3710 
       14.53         3.02        35.01        17.95        29.95        26.99 
TCGA-AA-3864 TCGA-AA-3950 TCGA-AA-3966 TCGA-AD-6895 TCGA-AU-6004 TCGA-AY-6197 
       53.00        24.00         2.01         0.72        27.09        21.44 
TCGA-AZ-4315 TCGA-AZ-5407 TCGA-AZ-6601 TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-4744 
       58.39        88.21       100.01        12.76        10.06        20.02 
TCGA-CM-5344 TCGA-CM-5348 TCGA-D5-6532 TCGA-F4-6856 TCGA-G4-6309 TCGA-AF-6672 
       22.03        22.98        18.25        35.31        85.48        10.39 
TCGA-AG-3587 TCGA-AG-3892 TCGA-AG-A002 TCGA-AG-A02X TCGA-DY-A1DC TCGA-DY-A1H8 
       46.03        13.02        20.98        41.00        41.36        32.61 

$`MYST4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 
       16.57        34.65        33.34        32.75        36.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3510 
       20.12        19.66        20.28         7.04         1.02        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       78.08         6.05         6.97        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 
       37.05        19.00        36.00         5.03        85.05        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 
        2.01        12.99        24.00        33.01        26.01         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       20.98        34.03        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.79         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4323 
       14.50        16.31         0.95        33.01        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 
        5.13       106.75        22.36        62.79        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
       12.10        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5349 
       23.05        37.02        25.02        13.02        29.06        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       20.19         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
       13.25         0.53        47.41       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       53.62        44.68        55.04        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       20.05        24.00         1.02        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       17.03        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A032 TCGA-AG-A036 
       49.97         1.94        38.96        61.97        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DD TCGA-DY-A1DF 
        4.01         5.03         5.29       126.44        57.24        24.13 
TCGA-DY-A1DG TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       51.48         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  MYST4 MUTATED MYST4 WILD-TYPE 
           0.72            0.00 
  MYST4 MUTATED MYST4 WILD-TYPE 
         100.01          148.01 
  MYST4 MUTATED MYST4 WILD-TYPE 
          23.49           19.99 
[1] "0.7 - 100.0 (23.5)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.2"
D104V2, continuous
D104V3, binary
                 cls
clus                0   1
  MYST4 MUTATED    23   7
  MYST4 WILD-TYPE 343 112
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYST4 MUTATED     23    7
  MYST4 WILD-TYPE  343  112
        clus
vv       MYST4 MUTATED MYST4 WILD-TYPE
  COLON             23             343
  RECTUM             7             112
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MYST4 MUTATED         9        0        3        12         0         0
  MYST4 WILD-TYPE      82        1       29       126        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MYST4 MUTATED           0          1          3          0        1         0
  MYST4 WILD-TYPE        24         10         56         42       47        18
                 vv
clus              STAGE IVB
  MYST4 MUTATED           0
  MYST4 WILD-TYPE         1
D104V4, multiclass
            clus
vv           MYST4 MUTATED MYST4 WILD-TYPE
  STAGE I                9              82
  STAGE IA               0               1
  STAGE II               3              29
  STAGE IIA             12             126
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             1              10
  STAGE IIIB             3              56
  STAGE IIIC             0              42
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  MYST4 MUTATED     2   8  19   1
  MYST4 WILD-TYPE  15  84 310  49
D104V5, multiclass
    clus
vv   MYST4 MUTATED MYST4 WILD-TYPE
  T1             2              15
  T2             8              84
  T3            19             310
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  MYST4 MUTATED    24   5   1
  MYST4 WILD-TYPE 263 108  86
D104V6, multiclass
    clus
vv   MYST4 MUTATED MYST4 WILD-TYPE
  N0            24             263
  N1             5             108
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D104V7, binary
                 cls
clus                0   1
  MYST4 MUTATED    27   0
  MYST4 WILD-TYPE 348  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYST4 MUTATED     27    0
  MYST4 WILD-TYPE  348   65
   clus
vv  MYST4 MUTATED MYST4 WILD-TYPE
  0            27             348
  1             0              65
[1] 2 2
[1] FALSE
D104V8, binary
                 cls
clus                0   1
  MYST4 MUTATED    13  17
  MYST4 WILD-TYPE 212 247
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYST4 MUTATED     13   17
  MYST4 WILD-TYPE  212  247
        clus
vv       MYST4 MUTATED MYST4 WILD-TYPE
  FEMALE            13             212
  MALE              17             247
[1] 2 2
[1] FALSE
D104V9, binary
                 cls
clus                0   1
  MYST4 MUTATED    22   2
  MYST4 WILD-TYPE 328  20
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYST4 MUTATED     22    2
  MYST4 WILD-TYPE  328   20
     clus
vv    MYST4 MUTATED MYST4 WILD-TYPE
  NO             22             328
  YES             2              20
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MYST4 MUTATED                     18                             5
  MYST4 WILD-TYPE                  297                            42
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MYST4 MUTATED                       7                              0
  MYST4 WILD-TYPE                    99                             10
D104V10, multiclass
                                clus
vv                               MYST4 MUTATED MYST4 WILD-TYPE
  COLON ADENOCARCINOMA                      18             297
  COLON MUCINOUS ADENOCARCINOMA              5              42
  RECTAL ADENOCARCINOMA                      7              99
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  MYST4 MUTATED    20   0   0   2
  MYST4 WILD-TYPE 325   4  31  23
D104V11, multiclass
    clus
vv   MYST4 MUTATED MYST4 WILD-TYPE
  R0            20             325
  R1             0               4
  R2             0              31
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D104V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MYST4 MUTATED                                  0     2
  MYST4 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  MYST4 MUTATED                           1    15
  MYST4 WILD-TYPE                        21   211
D104V13, multiclass
                                  clus
vv                                 MYST4 MUTATED MYST4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               9
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                       15             211
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(105) Variable = PRPH2 MUTATION ANALYSIS
D105V1, survival
                 sevent
clus2               0   1
  PRPH2 MUTATED     8   4
  PRPH2 WILD-TYPE 370  89
  PRPH2 MUTATED PRPH2 WILD-TYPE 
             12             459 
  PRPH2 MUTATED PRPH2 WILD-TYPE 
              4              89 
$`PRPH2 MUTATED`
TCGA-AA-3516 TCGA-AA-3947 TCGA-AA-3977 TCGA-AA-A02O TCGA-CA-6718 TCGA-D5-6926 
       13.02        33.01        25.02         0.92        10.06         9.04 
TCGA-DM-A1DB TCGA-G4-6306 TCGA-G4-6307 TCGA-CI-6624 TCGA-DY-A1DF TCGA-EI-6510 
       44.32        44.68        55.04         4.73        24.13        18.28 

$`PRPH2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        1.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
        2.01        12.99        24.00        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        2.01         5.03        14.01        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
       14.30         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6309 TCGA-G4-6310 
      133.18        74.56        65.85        53.62        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
        6.05        33.17         6.97        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  PRPH2 MUTATED PRPH2 WILD-TYPE 
           0.92            0.00 
  PRPH2 MUTATED PRPH2 WILD-TYPE 
          55.04          148.01 
  PRPH2 MUTATED PRPH2 WILD-TYPE 
         21.205          20.190 
[1] "0.9 - 55.0 (21.2)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.8"
D105V2, continuous
D105V3, binary
                 cls
clus                0   1
  PRPH2 MUTATED    10   3
  PRPH2 WILD-TYPE 356 116
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRPH2 MUTATED     10    3
  PRPH2 WILD-TYPE  356  116
        clus
vv       PRPH2 MUTATED PRPH2 WILD-TYPE
  COLON             10             356
  RECTUM             3             116
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PRPH2 MUTATED         1        0        1         3         1         0
  PRPH2 WILD-TYPE      90        1       31       135         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PRPH2 MUTATED           2          0          2          1        0         1
  PRPH2 WILD-TYPE        22         11         57         41       48        17
                 vv
clus              STAGE IVB
  PRPH2 MUTATED           0
  PRPH2 WILD-TYPE         1
D105V4, multiclass
            clus
vv           PRPH2 MUTATED PRPH2 WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              3             135
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              2              22
  STAGE IIIA             0              11
  STAGE IIIB             2              57
  STAGE IIIC             1              41
  STAGE IV               0              48
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PRPH2 MUTATED     0   4   7   2
  PRPH2 WILD-TYPE  17  88 322  48
D105V5, multiclass
    clus
vv   PRPH2 MUTATED PRPH2 WILD-TYPE
  T1             0              17
  T2             4              88
  T3             7             322
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  PRPH2 MUTATED     8   2   3
  PRPH2 WILD-TYPE 279 111  84
D105V6, multiclass
    clus
vv   PRPH2 MUTATED PRPH2 WILD-TYPE
  N0             8             279
  N1             2             111
  N2             3              84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D105V7, binary
                 cls
clus                0   1
  PRPH2 MUTATED    11   0
  PRPH2 WILD-TYPE 364  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRPH2 MUTATED     11    0
  PRPH2 WILD-TYPE  364   65
   clus
vv  PRPH2 MUTATED PRPH2 WILD-TYPE
  0            11             364
  1             0              65
[1] 2 2
[1] FALSE
D105V8, binary
                 cls
clus                0   1
  PRPH2 MUTATED     6   7
  PRPH2 WILD-TYPE 219 257
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRPH2 MUTATED      6    7
  PRPH2 WILD-TYPE  219  257
        clus
vv       PRPH2 MUTATED PRPH2 WILD-TYPE
  FEMALE             6             219
  MALE               7             257
[1] 2 2
[1] FALSE
D105V9, binary
                 cls
clus                0   1
  PRPH2 MUTATED     7   1
  PRPH2 WILD-TYPE 343  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRPH2 MUTATED      7    1
  PRPH2 WILD-TYPE  343   21
     clus
vv    PRPH2 MUTATED PRPH2 WILD-TYPE
  NO              7             343
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PRPH2 MUTATED                      8                             2
  PRPH2 WILD-TYPE                  307                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PRPH2 MUTATED                       3                              0
  PRPH2 WILD-TYPE                   103                             10
D105V10, multiclass
                                clus
vv                               PRPH2 MUTATED PRPH2 WILD-TYPE
  COLON ADENOCARCINOMA                       8             307
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      3             103
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  PRPH2 MUTATED     7   0   0   1
  PRPH2 WILD-TYPE 338   4  31  24
D105V11, multiclass
    clus
vv   PRPH2 MUTATED PRPH2 WILD-TYPE
  R0             7             338
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D105V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PRPH2 MUTATED                                  0     1
  PRPH2 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PRPH2 MUTATED                           0     7
  PRPH2 WILD-TYPE                        22   219
D105V13, multiclass
                                  clus
vv                                 PRPH2 MUTATED PRPH2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        7             219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(106) Variable = RBMX MUTATION ANALYSIS
D106V1, survival
                sevent
clus2              0   1
  RBMX MUTATED    19   0
  RBMX WILD-TYPE 359  93
  RBMX MUTATED RBMX WILD-TYPE 
            19            452 
  RBMX MUTATED RBMX WILD-TYPE 
             0             93 
$`RBMX MUTATED`
TCGA-A6-5656 TCGA-A6-5664 TCGA-A6-6142 TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3549 
       32.91        22.09        25.08        20.12        19.66        21.01 
TCGA-AD-5900 TCGA-CA-6717 TCGA-D5-6898 TCGA-D5-7000 TCGA-DM-A1HB TCGA-DM-A28H 
        0.07        12.76         1.48        10.26       135.65       117.07 
TCGA-DM-A28K TCGA-F4-6703 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6628 TCGA-CI-6620 
       98.24        47.87        47.41        35.31        79.69        33.17 
TCGA-CI-6624 
        4.73 

$`RBMX WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5665 
       31.63        30.44        29.19        33.53        23.61        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6649 
       32.71        27.09        22.52         8.38        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6782 TCGA-AA-3489 
       21.76        24.69        24.39        23.87        20.28         7.04 
TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
        3.02         1.02        35.01        63.98         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
       13.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       36.03         8.05        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       33.99        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 
        0.92        41.00        39.98        18.05        40.96        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07        12.20        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 
        4.80        17.13        12.49        16.14        15.58         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-DM-A0X9 TCGA-DM-A0XD 
        4.80         1.51        12.00        11.38       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 
      140.38         7.50        44.32       131.51       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-F4-6459 TCGA-F4-6460 
       81.37       119.93        35.97        60.79         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       35.74         6.18         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
       33.67        13.25         0.53       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       46.75        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6622 
        1.45        17.49         0.69         0.72         6.05         6.97 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  RBMX MUTATED RBMX WILD-TYPE 
          0.07           0.00 
  RBMX MUTATED RBMX WILD-TYPE 
        135.65         148.01 
  RBMX MUTATED RBMX WILD-TYPE 
         25.08          20.02 
[1] "0.1 - 135.7 (25.1)" "0.0 - 148.0 (20.0)"
[1] "hr="     "2.7e+07"
D106V2, continuous
D106V3, binary
                cls
clus               0   1
  RBMX MUTATED    18   2
  RBMX WILD-TYPE 348 117
[1] "tbl2"
                cls
clus             [,1] [,2]
  RBMX MUTATED     18    2
  RBMX WILD-TYPE  348  117
        clus
vv       RBMX MUTATED RBMX WILD-TYPE
  COLON            18            348
  RECTUM            2            117
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RBMX MUTATED         8        0        0         5         1         0
  RBMX WILD-TYPE      83        1       32       133         9         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RBMX MUTATED           0          0          1          3        0         2
  RBMX WILD-TYPE        24         11         58         39       48        16
                vv
clus             STAGE IVB
  RBMX MUTATED           0
  RBMX WILD-TYPE         1
D106V4, multiclass
            clus
vv           RBMX MUTATED RBMX WILD-TYPE
  STAGE I               8             83
  STAGE IA              0              1
  STAGE II              0             32
  STAGE IIA             5            133
  STAGE IIB             1              9
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            1             58
  STAGE IIIC            3             39
  STAGE IV              0             48
  STAGE IVA             2             16
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  RBMX MUTATED     0   8   9   3
  RBMX WILD-TYPE  17  84 320  47
D106V5, multiclass
    clus
vv   RBMX MUTATED RBMX WILD-TYPE
  T1            0             17
  T2            8             84
  T3            9            320
  T4            3             47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  RBMX MUTATED    14   4   2
  RBMX WILD-TYPE 273 109  85
D106V6, multiclass
    clus
vv   RBMX MUTATED RBMX WILD-TYPE
  N0           14            273
  N1            4            109
  N2            2             85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D106V7, binary
                cls
clus               0   1
  RBMX MUTATED    13   2
  RBMX WILD-TYPE 362  63
[1] "tbl2"
                cls
clus             [,1] [,2]
  RBMX MUTATED     13    2
  RBMX WILD-TYPE  362   63
   clus
vv  RBMX MUTATED RBMX WILD-TYPE
  0           13            362
  1            2             63
[1] 2 2
[1] FALSE
D106V8, binary
                cls
clus               0   1
  RBMX MUTATED     7  13
  RBMX WILD-TYPE 218 251
[1] "tbl2"
                cls
clus             [,1] [,2]
  RBMX MUTATED      7   13
  RBMX WILD-TYPE  218  251
        clus
vv       RBMX MUTATED RBMX WILD-TYPE
  FEMALE            7            218
  MALE             13            251
[1] 2 2
[1] FALSE
D106V9, binary
                cls
clus               0   1
  RBMX MUTATED    12   1
  RBMX WILD-TYPE 338  21
[1] "tbl2"
                cls
clus             [,1] [,2]
  RBMX MUTATED     12    1
  RBMX WILD-TYPE  338   21
     clus
vv    RBMX MUTATED RBMX WILD-TYPE
  NO            12            338
  YES            1             21
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  RBMX MUTATED                     10                             7
  RBMX WILD-TYPE                  305                            40
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  RBMX MUTATED                       2                              0
  RBMX WILD-TYPE                   104                             10
D106V10, multiclass
                                clus
vv                               RBMX MUTATED RBMX WILD-TYPE
  COLON ADENOCARCINOMA                     10            305
  COLON MUCINOUS ADENOCARCINOMA             7             40
  RECTAL ADENOCARCINOMA                     2            104
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  RBMX MUTATED     9   0   0   2
  RBMX WILD-TYPE 336   4  31  23
D106V11, multiclass
    clus
vv   RBMX MUTATED RBMX WILD-TYPE
  R0            9            336
  R1            0              4
  R2            0             31
  RX            2             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D106V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RBMX MUTATED                                  0     1
  RBMX WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  RBMX MUTATED                           1    17
  RBMX WILD-TYPE                        21   209
D106V13, multiclass
                                  clus
vv                                 RBMX MUTATED RBMX WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                      17            209
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(107) Variable = LDHA MUTATION ANALYSIS
D107V1, survival
                sevent
clus2              0   1
  LDHA MUTATED    10   3
  LDHA WILD-TYPE 368  90
  LDHA MUTATED LDHA WILD-TYPE 
            13            458 
  LDHA MUTATED LDHA WILD-TYPE 
             3             90 
$`LDHA MUTATED`
TCGA-A6-2671 TCGA-AA-3815 TCGA-AA-A01Q TCGA-CK-5916 TCGA-CK-6748 TCGA-D5-6536 
       43.76        33.04         1.02        21.14         1.91        17.85 
TCGA-D5-6540 TCGA-DM-A28K TCGA-G4-6293 TCGA-AG-3892 TCGA-CL-5917 TCGA-CL-5918 
       16.14        98.24       133.18        13.02        78.12         7.17 
TCGA-DC-6158 
       10.98 

$`LDHA WILD-TYPE`
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       46.65        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       10.06        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        31.00        38.07        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6751 
       15.62        49.08        51.32         9.99        82.95       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 
       43.27        15.12         4.80        17.13        12.49        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       35.97        60.79       117.07         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6299 
       33.67        13.25         0.53        47.41        35.31        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 
       19.99         1.02        17.95        36.95        17.03        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
       33.17         6.97         4.73        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       27.95        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  LDHA MUTATED LDHA WILD-TYPE 
          1.02           0.00 
  LDHA MUTATED LDHA WILD-TYPE 
        133.18         148.01 
  LDHA MUTATED LDHA WILD-TYPE 
        17.850         20.235 
[1] "1.0 - 133.2 (17.9)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.1"
D107V2, continuous
D107V3, binary
                cls
clus               0   1
  LDHA MUTATED    10   4
  LDHA WILD-TYPE 356 115
[1] "tbl2"
                cls
clus             [,1] [,2]
  LDHA MUTATED     10    4
  LDHA WILD-TYPE  356  115
        clus
vv       LDHA MUTATED LDHA WILD-TYPE
  COLON            10            356
  RECTUM            4            115
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  LDHA MUTATED         5        0        1         4         0         0
  LDHA WILD-TYPE      86        1       31       134        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  LDHA MUTATED           1          0          0          1        2         0
  LDHA WILD-TYPE        23         11         59         41       46        18
                vv
clus             STAGE IVB
  LDHA MUTATED           0
  LDHA WILD-TYPE         1
D107V4, multiclass
            clus
vv           LDHA MUTATED LDHA WILD-TYPE
  STAGE I               5             86
  STAGE IA              0              1
  STAGE II              1             31
  STAGE IIA             4            134
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             1             23
  STAGE IIIA            0             11
  STAGE IIIB            0             59
  STAGE IIIC            1             41
  STAGE IV              2             46
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  LDHA MUTATED     2   3   9   0
  LDHA WILD-TYPE  15  89 320  50
D107V5, multiclass
    clus
vv   LDHA MUTATED LDHA WILD-TYPE
  T1            2             15
  T2            3             89
  T3            9            320
  T4            0             50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  LDHA MUTATED    10   2   2
  LDHA WILD-TYPE 277 111  85
D107V6, multiclass
    clus
vv   LDHA MUTATED LDHA WILD-TYPE
  N0           10            277
  N1            2            111
  N2            2             85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D107V7, binary
                cls
clus               0   1
  LDHA MUTATED     9   2
  LDHA WILD-TYPE 366  63
[1] "tbl2"
                cls
clus             [,1] [,2]
  LDHA MUTATED      9    2
  LDHA WILD-TYPE  366   63
   clus
vv  LDHA MUTATED LDHA WILD-TYPE
  0            9            366
  1            2             63
[1] 2 2
[1] FALSE
D107V8, binary
                cls
clus               0   1
  LDHA MUTATED     8   6
  LDHA WILD-TYPE 217 258
[1] "tbl2"
                cls
clus             [,1] [,2]
  LDHA MUTATED      8    6
  LDHA WILD-TYPE  217  258
        clus
vv       LDHA MUTATED LDHA WILD-TYPE
  FEMALE            8            217
  MALE              6            258
[1] 2 2
[1] FALSE
D107V9, binary
                cls
clus               0   1
  LDHA MUTATED    11   0
  LDHA WILD-TYPE 339  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  LDHA MUTATED     11    0
  LDHA WILD-TYPE  339   22
     clus
vv    LDHA MUTATED LDHA WILD-TYPE
  NO            11            339
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  LDHA MUTATED                      7                             3
  LDHA WILD-TYPE                  308                            44
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  LDHA MUTATED                       4                              0
  LDHA WILD-TYPE                   102                             10
D107V10, multiclass
                                clus
vv                               LDHA MUTATED LDHA WILD-TYPE
  COLON ADENOCARCINOMA                      7            308
  COLON MUCINOUS ADENOCARCINOMA             3             44
  RECTAL ADENOCARCINOMA                     4            102
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  LDHA MUTATED     8   0   0   5
  LDHA WILD-TYPE 337   4  31  20
D107V11, multiclass
    clus
vv   LDHA MUTATED LDHA WILD-TYPE
  R0            8            337
  R1            0              4
  R2            0             31
  RX            5             20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D107V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  LDHA MUTATED                                  0     0
  LDHA WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  LDHA MUTATED                           0    11
  LDHA WILD-TYPE                        22   215
D107V13, multiclass
                                  clus
vv                                 LDHA MUTATED LDHA WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                      11            215
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(108) Variable = GFI1 MUTATION ANALYSIS
D108V1, survival
                sevent
clus2              0   1
  GFI1 MUTATED     7   4
  GFI1 WILD-TYPE 371  89
  GFI1 MUTATED GFI1 WILD-TYPE 
            11            460 
  GFI1 MUTATED GFI1 WILD-TYPE 
             4             89 
$`GFI1 MUTATED`
TCGA-A6-4105 TCGA-AA-3516 TCGA-AA-3947 TCGA-AA-3950 TCGA-AZ-4682 TCGA-AZ-6608 
       14.53        13.02        33.01        24.00        22.36         1.61 
TCGA-CM-5860 TCGA-D5-6539 TCGA-D5-6541 TCGA-F4-6703 TCGA-AG-3731 
       32.02        12.49        15.58        47.87        37.02 

$`GFI1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 
       16.57        34.65        33.34        32.75        36.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       12.99        24.00        26.01         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-5403 
       17.82        58.39         1.41         5.13       106.75        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       22.98        30.08        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6898 TCGA-D5-6920 
       17.85         4.80        17.13        16.14         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  GFI1 MUTATED GFI1 WILD-TYPE 
          1.61           0.00 
  GFI1 MUTATED GFI1 WILD-TYPE 
         47.87         148.01 
  GFI1 MUTATED GFI1 WILD-TYPE 
        22.360         20.155 
[1] "1.6 - 47.9 (22.4)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "2.2"
D108V2, continuous
D108V3, binary
                cls
clus               0   1
  GFI1 MUTATED    10   1
  GFI1 WILD-TYPE 356 118
[1] "tbl2"
                cls
clus             [,1] [,2]
  GFI1 MUTATED     10    1
  GFI1 WILD-TYPE  356  118
        clus
vv       GFI1 MUTATED GFI1 WILD-TYPE
  COLON            10            356
  RECTUM            1            118
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GFI1 MUTATED         0        0        0         5         1         0
  GFI1 WILD-TYPE      91        1       32       133         9         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  GFI1 MUTATED           1          2          0          0        1         1
  GFI1 WILD-TYPE        23          9         59         42       47        17
                vv
clus             STAGE IVB
  GFI1 MUTATED           0
  GFI1 WILD-TYPE         1
D108V4, multiclass
            clus
vv           GFI1 MUTATED GFI1 WILD-TYPE
  STAGE I               0             91
  STAGE IA              0              1
  STAGE II              0             32
  STAGE IIA             5            133
  STAGE IIB             1              9
  STAGE IIC             0              1
  STAGE III             1             23
  STAGE IIIA            2              9
  STAGE IIIB            0             59
  STAGE IIIC            0             42
  STAGE IV              1             47
  STAGE IVA             1             17
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  GFI1 MUTATED     0   1   9   1
  GFI1 WILD-TYPE  17  91 320  49
D108V5, multiclass
    clus
vv   GFI1 MUTATED GFI1 WILD-TYPE
  T1            0             17
  T2            1             91
  T3            9            320
  T4            1             49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  GFI1 MUTATED     8   2   1
  GFI1 WILD-TYPE 279 111  86
D108V6, multiclass
    clus
vv   GFI1 MUTATED GFI1 WILD-TYPE
  N0            8            279
  N1            2            111
  N2            1             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D108V7, binary
                cls
clus               0   1
  GFI1 MUTATED     9   2
  GFI1 WILD-TYPE 366  63
[1] "tbl2"
                cls
clus             [,1] [,2]
  GFI1 MUTATED      9    2
  GFI1 WILD-TYPE  366   63
   clus
vv  GFI1 MUTATED GFI1 WILD-TYPE
  0            9            366
  1            2             63
[1] 2 2
[1] FALSE
D108V8, binary
                cls
clus               0   1
  GFI1 MUTATED     5   6
  GFI1 WILD-TYPE 220 258
[1] "tbl2"
                cls
clus             [,1] [,2]
  GFI1 MUTATED      5    6
  GFI1 WILD-TYPE  220  258
        clus
vv       GFI1 MUTATED GFI1 WILD-TYPE
  FEMALE            5            220
  MALE              6            258
[1] 2 2
[1] FALSE
D108V9, binary
                cls
clus               0   1
  GFI1 MUTATED    11   0
  GFI1 WILD-TYPE 339  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  GFI1 MUTATED     11    0
  GFI1 WILD-TYPE  339   22
     clus
vv    GFI1 MUTATED GFI1 WILD-TYPE
  NO            11            339
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  GFI1 MUTATED                      7                             3
  GFI1 WILD-TYPE                  308                            44
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  GFI1 MUTATED                       1                              0
  GFI1 WILD-TYPE                   105                             10
D108V10, multiclass
                                clus
vv                               GFI1 MUTATED GFI1 WILD-TYPE
  COLON ADENOCARCINOMA                      7            308
  COLON MUCINOUS ADENOCARCINOMA             3             44
  RECTAL ADENOCARCINOMA                     1            105
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  GFI1 MUTATED     7   0   1   0
  GFI1 WILD-TYPE 338   4  30  25
D108V11, multiclass
    clus
vv   GFI1 MUTATED GFI1 WILD-TYPE
  R0            7            338
  R1            0              4
  R2            1             30
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D108V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GFI1 MUTATED                                  0     0
  GFI1 WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  GFI1 MUTATED                           0     7
  GFI1 WILD-TYPE                        22   219
D108V13, multiclass
                                  clus
vv                                 GFI1 MUTATED GFI1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       7            219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(109) Variable = SLC9A10 MUTATION ANALYSIS
D109V1, survival
                   sevent
clus2                 0   1
  SLC9A10 MUTATED    19   4
  SLC9A10 WILD-TYPE 359  89
  SLC9A10 MUTATED SLC9A10 WILD-TYPE 
               23               448 
  SLC9A10 MUTATED SLC9A10 WILD-TYPE 
                4                89 
$`SLC9A10 MUTATED`
TCGA-A6-6780 TCGA-AA-3534 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-A010 TCGA-AA-A01Q 
       20.12        29.00        26.99        19.04        34.98         1.02 
TCGA-AZ-4315 TCGA-CA-6717 TCGA-CK-5916 TCGA-CM-4743 TCGA-CM-6161 TCGA-CM-6164 
       58.39        12.76        21.14        23.05        15.02        29.03 
TCGA-CM-6168 TCGA-CM-6674 TCGA-D5-6540 TCGA-DM-A1D9 TCGA-DM-A28F TCGA-F4-6703 
       12.99        12.95        16.14       140.38        35.97        47.87 
TCGA-AF-2689 TCGA-AF-6655 TCGA-AG-A002 TCGA-DC-6682 TCGA-DY-A1DG 
       39.48        20.02        20.98         4.01        51.48 

$`SLC9A10 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3538 
       19.07         0.00        19.07        34.03        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
        5.03        85.05        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
       16.31         0.95        33.01        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07        12.20        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 
       85.45        15.62        49.08        51.32         9.99        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
        1.91       124.27        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6162 TCGA-CM-6163 
        5.03        15.02        15.02        17.03        12.00         2.96 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       16.04        21.99        14.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       11.01        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
        4.80        17.13        12.49        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
       12.59         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
        6.12        81.37       119.93        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6704 TCGA-F4-6805 
        8.61        31.96        35.74         6.18         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       24.13        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       14.50        16.83        15.39        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        5.95         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       24.13        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  SLC9A10 MUTATED SLC9A10 WILD-TYPE 
             1.02              0.00 
  SLC9A10 MUTATED SLC9A10 WILD-TYPE 
           140.38            148.01 
  SLC9A10 MUTATED SLC9A10 WILD-TYPE 
           21.140            20.035 
[1] "1.0 - 140.4 (21.1)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.3"
D109V2, continuous
D109V3, binary
                   cls
clus                  0   1
  SLC9A10 MUTATED    18   5
  SLC9A10 WILD-TYPE 348 114
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC9A10 MUTATED     18    5
  SLC9A10 WILD-TYPE  348  114
        clus
vv       SLC9A10 MUTATED SLC9A10 WILD-TYPE
  COLON               18               348
  RECTUM               5               114
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SLC9A10 MUTATED         4        0        1        12         1         0
  SLC9A10 WILD-TYPE      87        1       31       126         9         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC9A10 MUTATED           0          1          1          0        2
  SLC9A10 WILD-TYPE        24         10         58         42       46
                   vv
clus                STAGE IVA STAGE IVB
  SLC9A10 MUTATED           1         0
  SLC9A10 WILD-TYPE        17         1
D109V4, multiclass
            clus
vv           SLC9A10 MUTATED SLC9A10 WILD-TYPE
  STAGE I                  4                87
  STAGE IA                 0                 1
  STAGE II                 1                31
  STAGE IIA               12               126
  STAGE IIB                1                 9
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               1                10
  STAGE IIIB               1                58
  STAGE IIIC               0                42
  STAGE IV                 2                46
  STAGE IVA                1                17
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  SLC9A10 MUTATED     1   4  17   1
  SLC9A10 WILD-TYPE  16  88 312  49
D109V5, multiclass
    clus
vv   SLC9A10 MUTATED SLC9A10 WILD-TYPE
  T1               1                16
  T2               4                88
  T3              17               312
  T4               1                49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  SLC9A10 MUTATED    19   3   1
  SLC9A10 WILD-TYPE 268 110  86
D109V6, multiclass
    clus
vv   SLC9A10 MUTATED SLC9A10 WILD-TYPE
  N0              19               268
  N1               3               110
  N2               1                86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D109V7, binary
                   cls
clus                  0   1
  SLC9A10 MUTATED    19   3
  SLC9A10 WILD-TYPE 356  62
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC9A10 MUTATED     19    3
  SLC9A10 WILD-TYPE  356   62
   clus
vv  SLC9A10 MUTATED SLC9A10 WILD-TYPE
  0              19               356
  1               3                62
[1] 2 2
[1] FALSE
D109V8, binary
                   cls
clus                  0   1
  SLC9A10 MUTATED    10  13
  SLC9A10 WILD-TYPE 215 251
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC9A10 MUTATED     10   13
  SLC9A10 WILD-TYPE  215  251
        clus
vv       SLC9A10 MUTATED SLC9A10 WILD-TYPE
  FEMALE              10               215
  MALE                13               251
[1] 2 2
[1] FALSE
D109V9, binary
                   cls
clus                  0   1
  SLC9A10 MUTATED    17   1
  SLC9A10 WILD-TYPE 333  21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC9A10 MUTATED     17    1
  SLC9A10 WILD-TYPE  333   21
     clus
vv    SLC9A10 MUTATED SLC9A10 WILD-TYPE
  NO               17               333
  YES               1                21
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SLC9A10 MUTATED                     15                             3
  SLC9A10 WILD-TYPE                  300                            44
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SLC9A10 MUTATED                       5                              0
  SLC9A10 WILD-TYPE                   101                             10
D109V10, multiclass
                                clus
vv                               SLC9A10 MUTATED SLC9A10 WILD-TYPE
  COLON ADENOCARCINOMA                        15               300
  COLON MUCINOUS ADENOCARCINOMA                3                44
  RECTAL ADENOCARCINOMA                        5               101
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  SLC9A10 MUTATED    16   0   1   2
  SLC9A10 WILD-TYPE 329   4  30  23
D109V11, multiclass
    clus
vv   SLC9A10 MUTATED SLC9A10 WILD-TYPE
  R0              16               329
  R1               0                 4
  R2               1                30
  RX               2                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D109V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SLC9A10 MUTATED                                  0     1
  SLC9A10 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  SLC9A10 MUTATED                           1    15
  SLC9A10 WILD-TYPE                        21   211
D109V13, multiclass
                                  clus
vv                                 SLC9A10 MUTATED SLC9A10 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                10
  BLACK OR AFRICAN AMERICAN                      1                21
  WHITE                                         15               211
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(110) Variable = OXSM MUTATION ANALYSIS
D110V1, survival
                sevent
clus2              0   1
  OXSM MUTATED    13   1
  OXSM WILD-TYPE 365  92
  OXSM MUTATED OXSM WILD-TYPE 
            14            457 
  OXSM MUTATED OXSM WILD-TYPE 
             1             92 
$`OXSM MUTATED`
TCGA-AA-3710 TCGA-AA-3977 TCGA-AA-A00E TCGA-AA-A00N TCGA-AD-5900 TCGA-CM-4744 
       26.99        25.02        30.02         4.01         0.07        20.02 
TCGA-CM-4746 TCGA-D5-6923 TCGA-DM-A1D9 TCGA-G4-6304 TCGA-AG-3892 TCGA-CL-5918 
       37.02        12.43       140.38        53.62        13.02         7.17 
TCGA-DC-6682 TCGA-DT-5265 
        4.01         5.29 

$`OXSM WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
       19.00        36.00         5.03        85.05        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       19.00        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
       40.96        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       23.05        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        1.48         3.68         4.41        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       13.32        12.59         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       65.85        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 
        1.02        17.95        36.95        17.03        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        6.97         4.73        78.12        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 TCGA-DY-A0XA 
       27.95        10.98        19.99         5.95         5.03       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  OXSM MUTATED OXSM WILD-TYPE 
          0.07           0.00 
  OXSM MUTATED OXSM WILD-TYPE 
        140.38         148.01 
  OXSM MUTATED OXSM WILD-TYPE 
         16.52          20.28 
[1] "0.1 - 140.4 (16.5)" "0.0 - 148.0 (20.3)"
[1] "hr=" "2.6"
D110V2, continuous
D110V3, binary
                cls
clus               0   1
  OXSM MUTATED    10   4
  OXSM WILD-TYPE 356 115
[1] "tbl2"
                cls
clus             [,1] [,2]
  OXSM MUTATED     10    4
  OXSM WILD-TYPE  356  115
        clus
vv       OXSM MUTATED OXSM WILD-TYPE
  COLON            10            356
  RECTUM            4            115
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  OXSM MUTATED         5        0        1         5         2         0
  OXSM WILD-TYPE      86        1       31       133         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  OXSM MUTATED           0          0          0          0        0         0
  OXSM WILD-TYPE        24         11         59         42       48        18
                vv
clus             STAGE IVB
  OXSM MUTATED           0
  OXSM WILD-TYPE         1
D110V4, multiclass
            clus
vv           OXSM MUTATED OXSM WILD-TYPE
  STAGE I               5             86
  STAGE IA              0              1
  STAGE II              1             31
  STAGE IIA             5            133
  STAGE IIB             2              8
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            0             59
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  OXSM MUTATED     1   5   6   2
  OXSM WILD-TYPE  16  87 323  48
D110V5, multiclass
    clus
vv   OXSM MUTATED OXSM WILD-TYPE
  T1            1             16
  T2            5             87
  T3            6            323
  T4            2             48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  OXSM MUTATED    14   0   0
  OXSM WILD-TYPE 273 113  87
D110V6, multiclass
    clus
vv   OXSM MUTATED OXSM WILD-TYPE
  N0           14            273
  N1            0            113
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D110V7, binary
                cls
clus               0   1
  OXSM MUTATED    11   0
  OXSM WILD-TYPE 364  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  OXSM MUTATED     11    0
  OXSM WILD-TYPE  364   65
   clus
vv  OXSM MUTATED OXSM WILD-TYPE
  0           11            364
  1            0             65
[1] 2 2
[1] FALSE
D110V8, binary
                cls
clus               0   1
  OXSM MUTATED     5   9
  OXSM WILD-TYPE 220 255
[1] "tbl2"
                cls
clus             [,1] [,2]
  OXSM MUTATED      5    9
  OXSM WILD-TYPE  220  255
        clus
vv       OXSM MUTATED OXSM WILD-TYPE
  FEMALE            5            220
  MALE              9            255
[1] 2 2
[1] FALSE
D110V9, binary
                cls
clus               0   1
  OXSM MUTATED    10   0
  OXSM WILD-TYPE 340  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  OXSM MUTATED     10    0
  OXSM WILD-TYPE  340   22
     clus
vv    OXSM MUTATED OXSM WILD-TYPE
  NO            10            340
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  OXSM MUTATED                      8                             2
  OXSM WILD-TYPE                  307                            45
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  OXSM MUTATED                       3                              1
  OXSM WILD-TYPE                   103                              9
D110V10, multiclass
                                clus
vv                               OXSM MUTATED OXSM WILD-TYPE
  COLON ADENOCARCINOMA                      8            307
  COLON MUCINOUS ADENOCARCINOMA             2             45
  RECTAL ADENOCARCINOMA                     3            103
  RECTAL MUCINOUS ADENOCARCINOMA            1              9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  OXSM MUTATED    10   0   0   2
  OXSM WILD-TYPE 335   4  31  23
D110V11, multiclass
    clus
vv   OXSM MUTATED OXSM WILD-TYPE
  R0           10            335
  R1            0              4
  R2            0             31
  RX            2             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D110V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OXSM MUTATED                                  0     1
  OXSM WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  OXSM MUTATED                           1     7
  OXSM WILD-TYPE                        21   219
D110V13, multiclass
                                  clus
vv                                 OXSM MUTATED OXSM WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                       7            219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(111) Variable = NTAN1 MUTATION ANALYSIS
D111V1, survival
                 sevent
clus2               0   1
  NTAN1 MUTATED     8   2
  NTAN1 WILD-TYPE 370  91
  NTAN1 MUTATED NTAN1 WILD-TYPE 
             10             461 
  NTAN1 MUTATED NTAN1 WILD-TYPE 
              2              91 
$`NTAN1 MUTATED`
TCGA-A6-5665 TCGA-AA-3555 TCGA-AA-3663 TCGA-AA-3715 TCGA-AA-A00N TCGA-AD-5900 
       22.06        29.95         6.97        19.04         4.01         0.07 
TCGA-CM-4743 TCGA-D5-6540 TCGA-G4-6586 TCGA-G4-6628 
       23.05        16.14        35.80        79.69 

$`NTAN1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       13.02        24.00        17.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       85.05        26.99        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 
        9.99        21.14        82.95         1.91       124.27        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 
       17.85         4.80        17.13        12.49        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 
       63.62        61.91        36.00        22.09        13.78        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       91.79        46.75        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  NTAN1 MUTATED NTAN1 WILD-TYPE 
           0.07            0.00 
  NTAN1 MUTATED NTAN1 WILD-TYPE 
          79.69          148.01 
  NTAN1 MUTATED NTAN1 WILD-TYPE 
          20.55           20.19 
[1] "0.1 - 79.7 (20.5)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.2"
D111V2, continuous
D111V3, binary
                 cls
clus                0   1
  NTAN1 MUTATED    10   0
  NTAN1 WILD-TYPE 356 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NTAN1 MUTATED     10    0
  NTAN1 WILD-TYPE  356  119
        clus
vv       NTAN1 MUTATED NTAN1 WILD-TYPE
  COLON             10             356
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NTAN1 MUTATED         3        0        2         4         1         0
  NTAN1 WILD-TYPE      88        1       30       134         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NTAN1 MUTATED           0          0          0          0        0         0
  NTAN1 WILD-TYPE        24         11         59         42       48        18
                 vv
clus              STAGE IVB
  NTAN1 MUTATED           0
  NTAN1 WILD-TYPE         1
D111V4, multiclass
            clus
vv           NTAN1 MUTATED NTAN1 WILD-TYPE
  STAGE I                3              88
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA              4             134
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  NTAN1 MUTATED     0   3   6   1
  NTAN1 WILD-TYPE  17  89 323  49
D111V5, multiclass
    clus
vv   NTAN1 MUTATED NTAN1 WILD-TYPE
  T1             0              17
  T2             3              89
  T3             6             323
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  NTAN1 MUTATED    10   0   0
  NTAN1 WILD-TYPE 277 113  87
D111V6, multiclass
    clus
vv   NTAN1 MUTATED NTAN1 WILD-TYPE
  N0            10             277
  N1             0             113
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D111V7, binary
                 cls
clus                0   1
  NTAN1 MUTATED     9   0
  NTAN1 WILD-TYPE 366  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NTAN1 MUTATED      9    0
  NTAN1 WILD-TYPE  366   65
   clus
vv  NTAN1 MUTATED NTAN1 WILD-TYPE
  0             9             366
  1             0              65
[1] 2 2
[1] FALSE
D111V8, binary
                 cls
clus                0   1
  NTAN1 MUTATED     3   7
  NTAN1 WILD-TYPE 222 257
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NTAN1 MUTATED      3    7
  NTAN1 WILD-TYPE  222  257
        clus
vv       NTAN1 MUTATED NTAN1 WILD-TYPE
  FEMALE             3             222
  MALE               7             257
[1] 2 2
[1] FALSE
D111V9, binary
                 cls
clus                0   1
  NTAN1 MUTATED     8   0
  NTAN1 WILD-TYPE 342  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NTAN1 MUTATED      8    0
  NTAN1 WILD-TYPE  342   22
     clus
vv    NTAN1 MUTATED NTAN1 WILD-TYPE
  NO              8             342
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  NTAN1 MUTATED                      6                             4
  NTAN1 WILD-TYPE                  309                            43
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  NTAN1 MUTATED                       0                              0
  NTAN1 WILD-TYPE                   106                             10
D111V10, multiclass
                                clus
vv                               NTAN1 MUTATED NTAN1 WILD-TYPE
  COLON ADENOCARCINOMA                       6             309
  COLON MUCINOUS ADENOCARCINOMA              4              43
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  NTAN1 MUTATED    10   0   0   0
  NTAN1 WILD-TYPE 335   4  31  25
D111V11, multiclass
    clus
vv   NTAN1 MUTATED NTAN1 WILD-TYPE
  R0            10             335
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D111V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NTAN1 MUTATED                                  0     0
  NTAN1 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  NTAN1 MUTATED                           0     6
  NTAN1 WILD-TYPE                        22   220
D111V13, multiclass
                                  clus
vv                                 NTAN1 MUTATED NTAN1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        6             220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(112) Variable = ICAM5 MUTATION ANALYSIS
D112V1, survival
                 sevent
clus2               0   1
  ICAM5 MUTATED    12   2
  ICAM5 WILD-TYPE 366  91
  ICAM5 MUTATED ICAM5 WILD-TYPE 
             14             457 
  ICAM5 MUTATED ICAM5 WILD-TYPE 
              2              91 
$`ICAM5 MUTATED`
TCGA-A6-5665 TCGA-AA-3492 TCGA-AA-3713 TCGA-AZ-6600 TCGA-CM-4746 TCGA-D5-6540 
       22.06         3.02        19.04        12.10        37.02        16.14 
TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6588 TCGA-AG-A002 TCGA-AG-A02N TCGA-EF-5830 
       63.62        22.09        26.17        20.98        61.97         0.49 
TCGA-EI-6507 TCGA-F5-6571 
       19.96        31.30 

$`ICAM5 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 
       20.12        19.66        20.28         7.04         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 
       22.36        62.79        88.21        49.41         6.77       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
      124.27        23.05        20.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6586 
       55.04        85.48        61.91        36.00        13.78        35.80 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
        1.94        38.96        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
       51.48        32.61        20.55        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       49.51        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  ICAM5 MUTATED ICAM5 WILD-TYPE 
           0.49            0.00 
  ICAM5 MUTATED ICAM5 WILD-TYPE 
          63.62          148.01 
  ICAM5 MUTATED ICAM5 WILD-TYPE 
          21.52           20.12 
[1] "0.5 - 63.6 (21.5)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.4"
D112V2, continuous
D112V3, binary
                 cls
clus                0   1
  ICAM5 MUTATED    10   5
  ICAM5 WILD-TYPE 356 114
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ICAM5 MUTATED     10    5
  ICAM5 WILD-TYPE  356  114
        clus
vv       ICAM5 MUTATED ICAM5 WILD-TYPE
  COLON             10             356
  RECTUM             5             114
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ICAM5 MUTATED         3        0        2         5         1         0
  ICAM5 WILD-TYPE      88        1       30       133         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ICAM5 MUTATED           1          0          1          0        2         0
  ICAM5 WILD-TYPE        23         11         58         42       46        18
                 vv
clus              STAGE IVB
  ICAM5 MUTATED           0
  ICAM5 WILD-TYPE         1
D112V4, multiclass
            clus
vv           ICAM5 MUTATED ICAM5 WILD-TYPE
  STAGE I                3              88
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA              5             133
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             0              42
  STAGE IV               2              46
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ICAM5 MUTATED     0   4   9   2
  ICAM5 WILD-TYPE  17  88 320  48
D112V5, multiclass
    clus
vv   ICAM5 MUTATED ICAM5 WILD-TYPE
  T1             0              17
  T2             4              88
  T3             9             320
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  ICAM5 MUTATED    12   3   0
  ICAM5 WILD-TYPE 275 110  87
D112V6, multiclass
    clus
vv   ICAM5 MUTATED ICAM5 WILD-TYPE
  N0            12             275
  N1             3             110
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D112V7, binary
                 cls
clus                0   1
  ICAM5 MUTATED    12   2
  ICAM5 WILD-TYPE 363  63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ICAM5 MUTATED     12    2
  ICAM5 WILD-TYPE  363   63
   clus
vv  ICAM5 MUTATED ICAM5 WILD-TYPE
  0            12             363
  1             2              63
[1] 2 2
[1] FALSE
D112V8, binary
                 cls
clus                0   1
  ICAM5 MUTATED     6   9
  ICAM5 WILD-TYPE 219 255
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ICAM5 MUTATED      6    9
  ICAM5 WILD-TYPE  219  255
        clus
vv       ICAM5 MUTATED ICAM5 WILD-TYPE
  FEMALE             6             219
  MALE               9             255
[1] 2 2
[1] FALSE
D112V9, binary
                 cls
clus                0   1
  ICAM5 MUTATED     9   2
  ICAM5 WILD-TYPE 341  20
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ICAM5 MUTATED      9    2
  ICAM5 WILD-TYPE  341   20
     clus
vv    ICAM5 MUTATED ICAM5 WILD-TYPE
  NO              9             341
  YES             2              20
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ICAM5 MUTATED                      9                             1
  ICAM5 WILD-TYPE                  306                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ICAM5 MUTATED                       5                              0
  ICAM5 WILD-TYPE                   101                             10
D112V10, multiclass
                                clus
vv                               ICAM5 MUTATED ICAM5 WILD-TYPE
  COLON ADENOCARCINOMA                       9             306
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      5             101
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  ICAM5 MUTATED    13   0   1   0
  ICAM5 WILD-TYPE 332   4  30  25
D112V11, multiclass
    clus
vv   ICAM5 MUTATED ICAM5 WILD-TYPE
  R0            13             332
  R1             0               4
  R2             1              30
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D112V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ICAM5 MUTATED                                  0     0
  ICAM5 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ICAM5 MUTATED                           2     8
  ICAM5 WILD-TYPE                        20   218
D112V13, multiclass
                                  clus
vv                                 ICAM5 MUTATED ICAM5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    2              20
  WHITE                                        8             218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(113) Variable = KCTD3 MUTATION ANALYSIS
D113V1, survival
                 sevent
clus2               0   1
  KCTD3 MUTATED    13   5
  KCTD3 WILD-TYPE 365  88
  KCTD3 MUTATED KCTD3 WILD-TYPE 
             18             453 
  KCTD3 MUTATED KCTD3 WILD-TYPE 
              5              88 
$`KCTD3 MUTATED`
TCGA-A6-5664 TCGA-A6-6649 TCGA-A6-6653 TCGA-AA-A00N TCGA-AA-A010 TCGA-AD-5900 
       22.09        24.16        24.39         4.01        34.98         0.07 
TCGA-AD-6964 TCGA-AZ-4682 TCGA-CA-6718 TCGA-CM-4743 TCGA-CM-6171 TCGA-F4-6570 
       10.88        22.36        10.06        23.05        14.04         6.18 
TCGA-G4-6309 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 TCGA-AG-3892 TCGA-AG-A002 
       85.48        35.80        26.17        79.69        13.02        20.98 

$`KCTD3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       25.18        21.76        24.69        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
        5.13       106.75        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.20        12.76        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
        1.91       124.27        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       13.02        15.02        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
        8.61        31.96        35.74        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       55.04        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       91.79        46.75        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 
        1.02        17.95        36.95        17.03        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  KCTD3 MUTATED KCTD3 WILD-TYPE 
           0.07            0.00 
  KCTD3 MUTATED KCTD3 WILD-TYPE 
          85.48          148.01 
  KCTD3 MUTATED KCTD3 WILD-TYPE 
         22.225          20.050 
[1] "0.1 - 85.5 (22.2)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.5"
D113V2, continuous
D113V3, binary
                 cls
clus                0   1
  KCTD3 MUTATED    17   2
  KCTD3 WILD-TYPE 349 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCTD3 MUTATED     17    2
  KCTD3 WILD-TYPE  349  117
        clus
vv       KCTD3 MUTATED KCTD3 WILD-TYPE
  COLON             17             349
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KCTD3 MUTATED         6        0        1         5         2         0
  KCTD3 WILD-TYPE      85        1       31       133         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  KCTD3 MUTATED           0          0          2          1        0         1
  KCTD3 WILD-TYPE        24         11         57         41       48        17
                 vv
clus              STAGE IVB
  KCTD3 MUTATED           0
  KCTD3 WILD-TYPE         1
D113V4, multiclass
            clus
vv           KCTD3 MUTATED KCTD3 WILD-TYPE
  STAGE I                6              85
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              5             133
  STAGE IIB              2               8
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             2              57
  STAGE IIIC             1              41
  STAGE IV               0              48
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  KCTD3 MUTATED     1   5   8   5
  KCTD3 WILD-TYPE  16  87 321  45
D113V5, multiclass
    clus
vv   KCTD3 MUTATED KCTD3 WILD-TYPE
  T1             1              16
  T2             5              87
  T3             8             321
  T4             5              45
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  KCTD3 MUTATED    15   2   2
  KCTD3 WILD-TYPE 272 111  85
D113V6, multiclass
    clus
vv   KCTD3 MUTATED KCTD3 WILD-TYPE
  N0            15             272
  N1             2             111
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D113V7, binary
                 cls
clus                0   1
  KCTD3 MUTATED    15   1
  KCTD3 WILD-TYPE 360  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCTD3 MUTATED     15    1
  KCTD3 WILD-TYPE  360   64
   clus
vv  KCTD3 MUTATED KCTD3 WILD-TYPE
  0            15             360
  1             1              64
[1] 2 2
[1] FALSE
D113V8, binary
                 cls
clus                0   1
  KCTD3 MUTATED     8  11
  KCTD3 WILD-TYPE 217 253
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCTD3 MUTATED      8   11
  KCTD3 WILD-TYPE  217  253
        clus
vv       KCTD3 MUTATED KCTD3 WILD-TYPE
  FEMALE             8             217
  MALE              11             253
[1] 2 2
[1] FALSE
D113V9, binary
                 cls
clus                0   1
  KCTD3 MUTATED    16   0
  KCTD3 WILD-TYPE 334  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCTD3 MUTATED     16    0
  KCTD3 WILD-TYPE  334   22
     clus
vv    KCTD3 MUTATED KCTD3 WILD-TYPE
  NO             16             334
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  KCTD3 MUTATED                     15                             2
  KCTD3 WILD-TYPE                  300                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  KCTD3 MUTATED                       2                              0
  KCTD3 WILD-TYPE                   104                             10
D113V10, multiclass
                                clus
vv                               KCTD3 MUTATED KCTD3 WILD-TYPE
  COLON ADENOCARCINOMA                      15             300
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  KCTD3 MUTATED    14   0   0   1
  KCTD3 WILD-TYPE 331   4  31  24
D113V11, multiclass
    clus
vv   KCTD3 MUTATED KCTD3 WILD-TYPE
  R0            14             331
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D113V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KCTD3 MUTATED                                  0     1
  KCTD3 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  KCTD3 MUTATED                           2    11
  KCTD3 WILD-TYPE                        20   215
D113V13, multiclass
                                  clus
vv                                 KCTD3 MUTATED KCTD3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    2              20
  WHITE                                       11             215
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(114) Variable = RBM44 MUTATION ANALYSIS
D114V1, survival
                 sevent
clus2               0   1
  RBM44 MUTATED    12   2
  RBM44 WILD-TYPE 366  91
  RBM44 MUTATED RBM44 WILD-TYPE 
             14             457 
  RBM44 MUTATED RBM44 WILD-TYPE 
              2              91 
$`RBM44 MUTATED`
TCGA-A6-6141 TCGA-A6-6653 TCGA-A6-6781 TCGA-AA-3510 TCGA-AA-3672 TCGA-AA-3811 
        8.38        24.39        19.66        63.98         0.92        10.06 
TCGA-AA-A00N TCGA-AA-A010 TCGA-CA-6717 TCGA-CM-4746 TCGA-F4-6703 TCGA-G4-6588 
        4.01        34.98        12.76        37.02        47.87        26.17 
TCGA-AG-3892 TCGA-AG-A002 
       13.02        20.98 

$`RBM44 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 
       22.09        22.06        32.71        27.09        22.52        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 
       25.18        24.16        21.76        24.69        23.87        20.12 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 
       20.28         7.04         3.02         1.02        35.01         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
       14.01        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        19.04        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.20        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4752 
        1.91       124.27        23.05        20.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6704 
       98.24         8.61        31.96        35.74         6.18         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       22.09        13.78        35.80        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       36.95        17.03        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  RBM44 MUTATED RBM44 WILD-TYPE 
           0.92            0.00 
  RBM44 MUTATED RBM44 WILD-TYPE 
          63.98          148.01 
  RBM44 MUTATED RBM44 WILD-TYPE 
          20.32           20.19 
[1] "0.9 - 64.0 (20.3)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.2"
D114V2, continuous
D114V3, binary
                 cls
clus                0   1
  RBM44 MUTATED    13   2
  RBM44 WILD-TYPE 353 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM44 MUTATED     13    2
  RBM44 WILD-TYPE  353  117
        clus
vv       RBM44 MUTATED RBM44 WILD-TYPE
  COLON             13             353
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RBM44 MUTATED         4        0        1         5         2         0
  RBM44 WILD-TYPE      87        1       31       133         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RBM44 MUTATED           2          0          0          1        0         0
  RBM44 WILD-TYPE        22         11         59         41       48        18
                 vv
clus              STAGE IVB
  RBM44 MUTATED           0
  RBM44 WILD-TYPE         1
D114V4, multiclass
            clus
vv           RBM44 MUTATED RBM44 WILD-TYPE
  STAGE I                4              87
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              5             133
  STAGE IIB              2               8
  STAGE IIC              0               1
  STAGE III              2              22
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             1              41
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  RBM44 MUTATED     1   3   8   3
  RBM44 WILD-TYPE  16  89 321  47
D114V5, multiclass
    clus
vv   RBM44 MUTATED RBM44 WILD-TYPE
  T1             1              16
  T2             3              89
  T3             8             321
  T4             3              47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  RBM44 MUTATED    12   2   1
  RBM44 WILD-TYPE 275 111  86
D114V6, multiclass
    clus
vv   RBM44 MUTATED RBM44 WILD-TYPE
  N0            12             275
  N1             2             111
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D114V7, binary
                 cls
clus                0   1
  RBM44 MUTATED    14   0
  RBM44 WILD-TYPE 361  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM44 MUTATED     14    0
  RBM44 WILD-TYPE  361   65
   clus
vv  RBM44 MUTATED RBM44 WILD-TYPE
  0            14             361
  1             0              65
[1] 2 2
[1] FALSE
D114V8, binary
                 cls
clus                0   1
  RBM44 MUTATED     6   9
  RBM44 WILD-TYPE 219 255
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM44 MUTATED      6    9
  RBM44 WILD-TYPE  219  255
        clus
vv       RBM44 MUTATED RBM44 WILD-TYPE
  FEMALE             6             219
  MALE               9             255
[1] 2 2
[1] FALSE
D114V9, binary
                 cls
clus                0   1
  RBM44 MUTATED    13   0
  RBM44 WILD-TYPE 337  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM44 MUTATED     13    0
  RBM44 WILD-TYPE  337   22
     clus
vv    RBM44 MUTATED RBM44 WILD-TYPE
  NO             13             337
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  RBM44 MUTATED                     10                             3
  RBM44 WILD-TYPE                  305                            44
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  RBM44 MUTATED                       2                              0
  RBM44 WILD-TYPE                   104                             10
D114V10, multiclass
                                clus
vv                               RBM44 MUTATED RBM44 WILD-TYPE
  COLON ADENOCARCINOMA                      10             305
  COLON MUCINOUS ADENOCARCINOMA              3              44
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  RBM44 MUTATED    12   0   0   1
  RBM44 WILD-TYPE 333   4  31  24
D114V11, multiclass
    clus
vv   RBM44 MUTATED RBM44 WILD-TYPE
  R0            12             333
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D114V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RBM44 MUTATED                                  0     1
  RBM44 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  RBM44 MUTATED                           2     4
  RBM44 WILD-TYPE                        20   222
D114V13, multiclass
                                  clus
vv                                 RBM44 MUTATED RBM44 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    2              20
  WHITE                                        4             222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(115) Variable = KIAA1586 MUTATION ANALYSIS
D115V1, survival
                    sevent
clus2                  0   1
  KIAA1586 MUTATED     8   3
  KIAA1586 WILD-TYPE 370  90
  KIAA1586 MUTATED KIAA1586 WILD-TYPE 
                11                460 
  KIAA1586 MUTATED KIAA1586 WILD-TYPE 
                 3                 90 
$`KIAA1586 MUTATED`
TCGA-AA-3510 TCGA-AA-3815 TCGA-AA-3977 TCGA-AZ-4315 TCGA-CA-6717 TCGA-CA-6718 
       63.98        33.04        25.02        58.39        12.76        10.06 
TCGA-CK-6748 TCGA-DM-A1D7 TCGA-F4-6570 TCGA-AG-A002 TCGA-AG-A015 
        1.91        13.32         6.18        20.98        36.03 

$`KIAA1586 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       10.06        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 
        3.06         3.25         3.29         0.07        12.20        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
        9.99        21.14        82.95       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       49.91        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A016 
        6.02        25.97        23.01        37.02        15.95         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  KIAA1586 MUTATED KIAA1586 WILD-TYPE 
              1.91               0.00 
  KIAA1586 MUTATED KIAA1586 WILD-TYPE 
             63.98             148.01 
  KIAA1586 MUTATED KIAA1586 WILD-TYPE 
            20.980             20.155 
[1] "1.9 - 64.0 (21.0)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.4"
D115V2, continuous
D115V3, binary
                    cls
clus                   0   1
  KIAA1586 MUTATED    11   2
  KIAA1586 WILD-TYPE 355 117
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1586 MUTATED     11    2
  KIAA1586 WILD-TYPE  355  117
        clus
vv       KIAA1586 MUTATED KIAA1586 WILD-TYPE
  COLON                11                355
  RECTUM                2                117
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KIAA1586 MUTATED         2        0        1         7         1         0
  KIAA1586 WILD-TYPE      89        1       31       131         9         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIAA1586 MUTATED           0          0          0          0        1
  KIAA1586 WILD-TYPE        24         11         59         42       47
                    vv
clus                 STAGE IVA STAGE IVB
  KIAA1586 MUTATED           0         0
  KIAA1586 WILD-TYPE        18         1
D115V4, multiclass
            clus
vv           KIAA1586 MUTATED KIAA1586 WILD-TYPE
  STAGE I                   2                 89
  STAGE IA                  0                  1
  STAGE II                  1                 31
  STAGE IIA                 7                131
  STAGE IIB                 1                  9
  STAGE IIC                 0                  1
  STAGE III                 0                 24
  STAGE IIIA                0                 11
  STAGE IIIB                0                 59
  STAGE IIIC                0                 42
  STAGE IV                  1                 47
  STAGE IVA                 0                 18
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  KIAA1586 MUTATED     1   2   9   1
  KIAA1586 WILD-TYPE  16  90 320  49
D115V5, multiclass
    clus
vv   KIAA1586 MUTATED KIAA1586 WILD-TYPE
  T1                1                 16
  T2                2                 90
  T3                9                320
  T4                1                 49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  KIAA1586 MUTATED    12   1   0
  KIAA1586 WILD-TYPE 275 112  87
D115V6, multiclass
    clus
vv   KIAA1586 MUTATED KIAA1586 WILD-TYPE
  N0               12                275
  N1                1                112
  N2                0                 87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D115V7, binary
                    cls
clus                   0   1
  KIAA1586 MUTATED    10   1
  KIAA1586 WILD-TYPE 365  64
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1586 MUTATED     10    1
  KIAA1586 WILD-TYPE  365   64
   clus
vv  KIAA1586 MUTATED KIAA1586 WILD-TYPE
  0               10                365
  1                1                 64
[1] 2 2
[1] FALSE
D115V8, binary
                    cls
clus                   0   1
  KIAA1586 MUTATED     6   7
  KIAA1586 WILD-TYPE 219 257
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1586 MUTATED      6    7
  KIAA1586 WILD-TYPE  219  257
        clus
vv       KIAA1586 MUTATED KIAA1586 WILD-TYPE
  FEMALE                6                219
  MALE                  7                257
[1] 2 2
[1] FALSE
D115V9, binary
                    cls
clus                   0   1
  KIAA1586 MUTATED    10   0
  KIAA1586 WILD-TYPE 340  22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1586 MUTATED     10    0
  KIAA1586 WILD-TYPE  340   22
     clus
vv    KIAA1586 MUTATED KIAA1586 WILD-TYPE
  NO                10                340
  YES                0                 22
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  KIAA1586 MUTATED                      8                             2
  KIAA1586 WILD-TYPE                  307                            45
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  KIAA1586 MUTATED                       2                              0
  KIAA1586 WILD-TYPE                   104                             10
D115V10, multiclass
                                clus
vv                               KIAA1586 MUTATED KIAA1586 WILD-TYPE
  COLON ADENOCARCINOMA                          8                307
  COLON MUCINOUS ADENOCARCINOMA                 2                 45
  RECTAL ADENOCARCINOMA                         2                104
  RECTAL MUCINOUS ADENOCARCINOMA                0                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  KIAA1586 MUTATED     7   0   0   4
  KIAA1586 WILD-TYPE 338   4  31  21
D115V11, multiclass
    clus
vv   KIAA1586 MUTATED KIAA1586 WILD-TYPE
  R0                7                338
  R1                0                  4
  R2                0                 31
  RX                4                 21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D115V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KIAA1586 MUTATED                                  0     2
  KIAA1586 WILD-TYPE                                1     9
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  KIAA1586 MUTATED                           0     5
  KIAA1586 WILD-TYPE                        22   221
D115V13, multiclass
                                  clus
vv                                 KIAA1586 MUTATED KIAA1586 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           2                  9
  BLACK OR AFRICAN AMERICAN                       0                 22
  WHITE                                           5                221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(116) Variable = CDX2 MUTATION ANALYSIS
D116V1, survival
                sevent
clus2              0   1
  CDX2 MUTATED     5   1
  CDX2 WILD-TYPE 373  92
  CDX2 MUTATED CDX2 WILD-TYPE 
             6            465 
  CDX2 MUTATED CDX2 WILD-TYPE 
             1             92 
$`CDX2 MUTATED`
TCGA-A6-2672 TCGA-AA-3713 TCGA-AD-6889 TCGA-AZ-6598 TCGA-D5-6927 TCGA-G4-6586 
       46.65        19.04        56.55        49.41         9.44        35.80 

$`CDX2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        88.21         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       12.43        14.30         9.04        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       22.09        13.78        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  CDX2 MUTATED CDX2 WILD-TYPE 
          9.44           0.00 
  CDX2 MUTATED CDX2 WILD-TYPE 
         56.55         148.01 
  CDX2 MUTATED CDX2 WILD-TYPE 
        41.225         20.120 
[1] "9.4 - 56.5 (41.2)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.7"
D116V2, continuous
D116V3, binary
                cls
clus               0   1
  CDX2 MUTATED     6   0
  CDX2 WILD-TYPE 360 119
[1] "tbl2"
                cls
clus             [,1] [,2]
  CDX2 MUTATED      6    0
  CDX2 WILD-TYPE  360  119
        clus
vv       CDX2 MUTATED CDX2 WILD-TYPE
  COLON             6            360
  RECTUM            0            119
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CDX2 MUTATED         0        0        1         3         0         0
  CDX2 WILD-TYPE      91        1       31       135        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CDX2 MUTATED           0          0          1          0        1         0
  CDX2 WILD-TYPE        24         11         58         42       47        18
                vv
clus             STAGE IVB
  CDX2 MUTATED           0
  CDX2 WILD-TYPE         1
D116V4, multiclass
            clus
vv           CDX2 MUTATED CDX2 WILD-TYPE
  STAGE I               0             91
  STAGE IA              0              1
  STAGE II              1             31
  STAGE IIA             3            135
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            1             58
  STAGE IIIC            0             42
  STAGE IV              1             47
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  CDX2 MUTATED     0   0   6   0
  CDX2 WILD-TYPE  17  92 323  50
D116V5, multiclass
    clus
vv   CDX2 MUTATED CDX2 WILD-TYPE
  T1            0             17
  T2            0             92
  T3            6            323
  T4            0             50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  CDX2 MUTATED     5   1   0
  CDX2 WILD-TYPE 282 112  87
D116V6, multiclass
    clus
vv   CDX2 MUTATED CDX2 WILD-TYPE
  N0            5            282
  N1            1            112
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D116V7, binary
                cls
clus               0   1
  CDX2 MUTATED     4   1
  CDX2 WILD-TYPE 371  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  CDX2 MUTATED      4    1
  CDX2 WILD-TYPE  371   64
   clus
vv  CDX2 MUTATED CDX2 WILD-TYPE
  0            4            371
  1            1             64
[1] 2 2
[1] FALSE
D116V8, binary
                cls
clus               0   1
  CDX2 MUTATED     3   3
  CDX2 WILD-TYPE 222 261
[1] "tbl2"
                cls
clus             [,1] [,2]
  CDX2 MUTATED      3    3
  CDX2 WILD-TYPE  222  261
        clus
vv       CDX2 MUTATED CDX2 WILD-TYPE
  FEMALE            3            222
  MALE              3            261
[1] 2 2
[1] FALSE
D116V9, binary
                cls
clus               0   1
  CDX2 MUTATED     4   1
  CDX2 WILD-TYPE 346  21
[1] "tbl2"
                cls
clus             [,1] [,2]
  CDX2 MUTATED      4    1
  CDX2 WILD-TYPE  346   21
     clus
vv    CDX2 MUTATED CDX2 WILD-TYPE
  NO             4            346
  YES            1             21
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CDX2 MUTATED                      6                             0
  CDX2 WILD-TYPE                  309                            47
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CDX2 MUTATED                       0                              0
  CDX2 WILD-TYPE                   106                             10
D116V10, multiclass
                                clus
vv                               CDX2 MUTATED CDX2 WILD-TYPE
  COLON ADENOCARCINOMA                      6            309
  COLON MUCINOUS ADENOCARCINOMA             0             47
  RECTAL ADENOCARCINOMA                     0            106
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  CDX2 MUTATED     3   0   1   0
  CDX2 WILD-TYPE 342   4  30  25
D116V11, multiclass
    clus
vv   CDX2 MUTATED CDX2 WILD-TYPE
  R0            3            342
  R1            0              4
  R2            1             30
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D116V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CDX2 MUTATED                                  0     1
  CDX2 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  CDX2 MUTATED                           0     4
  CDX2 WILD-TYPE                        22   222
D116V13, multiclass
                                  clus
vv                                 CDX2 MUTATED CDX2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       4            222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(117) Variable = EXD2 MUTATION ANALYSIS
D117V1, survival
                sevent
clus2              0   1
  EXD2 MUTATED    10   3
  EXD2 WILD-TYPE 368  90
  EXD2 MUTATED EXD2 WILD-TYPE 
            13            458 
  EXD2 MUTATED EXD2 WILD-TYPE 
             3             90 
$`EXD2 MUTATED`
TCGA-AA-3713 TCGA-AA-3950 TCGA-AA-A00N TCGA-AD-6964 TCGA-CA-6717 TCGA-CM-5864 
       19.04        24.00         4.01        10.88        12.76        15.02 
TCGA-D5-6534 TCGA-D5-6539 TCGA-F4-6459 TCGA-G4-6323 TCGA-AF-6672 TCGA-DT-5265 
       43.27        12.49         8.61        13.78        10.39         5.29 
TCGA-EI-6507 
       19.96 

$`EXD2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 
        2.01        12.99        24.00        33.01        26.01         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
        0.79         0.72         5.79        22.42        27.42         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07        12.20        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6535 
       56.09        55.92        20.19        18.25         1.32        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
       17.85         4.80        17.13        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
       60.79       117.07        98.24        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       61.91        36.00        22.09        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       20.02        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.03       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
       32.61         0.49        20.55        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  EXD2 MUTATED EXD2 WILD-TYPE 
          4.01           0.00 
  EXD2 MUTATED EXD2 WILD-TYPE 
         43.27         148.01 
  EXD2 MUTATED EXD2 WILD-TYPE 
         12.76          20.98 
[1] "4.0 - 43.3 (12.8)"  "0.0 - 148.0 (21.0)"
[1] "hr=" "1.9"
D117V2, continuous
D117V3, binary
                cls
clus               0   1
  EXD2 MUTATED    10   3
  EXD2 WILD-TYPE 356 116
[1] "tbl2"
                cls
clus             [,1] [,2]
  EXD2 MUTATED     10    3
  EXD2 WILD-TYPE  356  116
        clus
vv       EXD2 MUTATED EXD2 WILD-TYPE
  COLON            10            356
  RECTUM            3            116
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  EXD2 MUTATED         1        1        1         4         1         0
  EXD2 WILD-TYPE      90        0       31       134         9         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  EXD2 MUTATED           0          1          1          0        2         0
  EXD2 WILD-TYPE        24         10         58         42       46        18
                vv
clus             STAGE IVB
  EXD2 MUTATED           0
  EXD2 WILD-TYPE         1
D117V4, multiclass
            clus
vv           EXD2 MUTATED EXD2 WILD-TYPE
  STAGE I               1             90
  STAGE IA              1              0
  STAGE II              1             31
  STAGE IIA             4            134
  STAGE IIB             1              9
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            1             10
  STAGE IIIB            1             58
  STAGE IIIC            0             42
  STAGE IV              2             46
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  EXD2 MUTATED     0   1   8   3
  EXD2 WILD-TYPE  17  91 321  47
D117V5, multiclass
    clus
vv   EXD2 MUTATED EXD2 WILD-TYPE
  T1            0             17
  T2            1             91
  T3            8            321
  T4            3             47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  EXD2 MUTATED    10   0   3
  EXD2 WILD-TYPE 277 113  84
D117V6, multiclass
    clus
vv   EXD2 MUTATED EXD2 WILD-TYPE
  N0           10            277
  N1            0            113
  N2            3             84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D117V7, binary
                cls
clus               0   1
  EXD2 MUTATED     9   1
  EXD2 WILD-TYPE 366  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  EXD2 MUTATED      9    1
  EXD2 WILD-TYPE  366   64
   clus
vv  EXD2 MUTATED EXD2 WILD-TYPE
  0            9            366
  1            1             64
[1] 2 2
[1] FALSE
D117V8, binary
                cls
clus               0   1
  EXD2 MUTATED     4   9
  EXD2 WILD-TYPE 221 255
[1] "tbl2"
                cls
clus             [,1] [,2]
  EXD2 MUTATED      4    9
  EXD2 WILD-TYPE  221  255
        clus
vv       EXD2 MUTATED EXD2 WILD-TYPE
  FEMALE            4            221
  MALE              9            255
[1] 2 2
[1] FALSE
D117V9, binary
                cls
clus               0   1
  EXD2 MUTATED    10   2
  EXD2 WILD-TYPE 340  20
[1] "tbl2"
                cls
clus             [,1] [,2]
  EXD2 MUTATED     10    2
  EXD2 WILD-TYPE  340   20
     clus
vv    EXD2 MUTATED EXD2 WILD-TYPE
  NO            10            340
  YES            2             20
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  EXD2 MUTATED                      6                             4
  EXD2 WILD-TYPE                  309                            43
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  EXD2 MUTATED                       2                              1
  EXD2 WILD-TYPE                   104                              9
D117V10, multiclass
                                clus
vv                               EXD2 MUTATED EXD2 WILD-TYPE
  COLON ADENOCARCINOMA                      6            309
  COLON MUCINOUS ADENOCARCINOMA             4             43
  RECTAL ADENOCARCINOMA                     2            104
  RECTAL MUCINOUS ADENOCARCINOMA            1              9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  EXD2 MUTATED     8   0   1   2
  EXD2 WILD-TYPE 337   4  30  23
D117V11, multiclass
    clus
vv   EXD2 MUTATED EXD2 WILD-TYPE
  R0            8            337
  R1            0              4
  R2            1             30
  RX            2             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D117V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  EXD2 MUTATED                                  0     2
  EXD2 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  EXD2 MUTATED                           1     7
  EXD2 WILD-TYPE                        21   219
D117V13, multiclass
                                  clus
vv                                 EXD2 MUTATED EXD2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              9
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                       7            219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(118) Variable = CLEC4F MUTATION ANALYSIS
D118V1, survival
                  sevent
clus2                0   1
  CLEC4F MUTATED    16   4
  CLEC4F WILD-TYPE 362  89
  CLEC4F MUTATED CLEC4F WILD-TYPE 
              20              451 
  CLEC4F MUTATED CLEC4F WILD-TYPE 
               4               89 
$`CLEC4F MUTATED`
TCGA-A6-6653 TCGA-AA-3510 TCGA-AA-3534 TCGA-AA-3713 TCGA-AA-3864 TCGA-AA-A00N 
       24.39        63.98        29.00        19.04        53.00         4.01 
TCGA-AD-5900 TCGA-AD-6964 TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4315 TCGA-CA-6717 
        0.07        10.88        33.01        17.82        58.39        12.76 
TCGA-CA-6718 TCGA-CM-4743 TCGA-CM-4752 TCGA-D5-6529 TCGA-D5-6532 TCGA-DM-A28C 
       10.06        23.05        13.02        20.19        18.25        81.37 
TCGA-G4-6588 TCGA-AG-A02N 
       26.17        61.97 

$`CLEC4F WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
       25.08        25.18        24.16        21.76        24.69        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3538 TCGA-AA-3542 
        0.00        19.07        34.03        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       85.05        26.99        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       31.07        30.05        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 
        0.92        41.00        39.98        18.05        40.96        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-6197 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       21.44         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 
        3.25         3.29         0.07        12.20        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 
       21.14        82.95         1.91       124.27        20.02        37.02 
TCGA-CM-4747 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       25.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6533 
       45.40        12.26        19.59        56.09        55.92         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       13.78        35.80        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X 
       64.01        10.98        49.97         1.94        38.96        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  CLEC4F MUTATED CLEC4F WILD-TYPE 
            0.07             0.00 
  CLEC4F MUTATED CLEC4F WILD-TYPE 
           81.37           148.01 
  CLEC4F MUTATED CLEC4F WILD-TYPE 
           21.62            20.12 
[1] "0.1 - 81.4 (21.6)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.2"
D118V2, continuous
D118V3, binary
                  cls
clus                 0   1
  CLEC4F MUTATED    19   1
  CLEC4F WILD-TYPE 347 118
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CLEC4F MUTATED     19    1
  CLEC4F WILD-TYPE  347  118
        clus
vv       CLEC4F MUTATED CLEC4F WILD-TYPE
  COLON              19              347
  RECTUM              1              118
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CLEC4F MUTATED         2        0        3        10         1         0
  CLEC4F WILD-TYPE      89        1       29       128         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CLEC4F MUTATED           0          0          1          0        1
  CLEC4F WILD-TYPE        24         11         58         42       47
                  vv
clus               STAGE IVA STAGE IVB
  CLEC4F MUTATED           1         0
  CLEC4F WILD-TYPE        17         1
D118V4, multiclass
            clus
vv           CLEC4F MUTATED CLEC4F WILD-TYPE
  STAGE I                 2               89
  STAGE IA                0                1
  STAGE II                3               29
  STAGE IIA              10              128
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              1               58
  STAGE IIIC              0               42
  STAGE IV                1               47
  STAGE IVA               1               17
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  CLEC4F MUTATED     0   2  16   2
  CLEC4F WILD-TYPE  17  90 313  48
D118V5, multiclass
    clus
vv   CLEC4F MUTATED CLEC4F WILD-TYPE
  T1              0               17
  T2              2               90
  T3             16              313
  T4              2               48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  CLEC4F MUTATED    17   2   1
  CLEC4F WILD-TYPE 270 111  86
D118V6, multiclass
    clus
vv   CLEC4F MUTATED CLEC4F WILD-TYPE
  N0             17              270
  N1              2              111
  N2              1               86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D118V7, binary
                  cls
clus                 0   1
  CLEC4F MUTATED    16   2
  CLEC4F WILD-TYPE 359  63
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CLEC4F MUTATED     16    2
  CLEC4F WILD-TYPE  359   63
   clus
vv  CLEC4F MUTATED CLEC4F WILD-TYPE
  0             16              359
  1              2               63
[1] 2 2
[1] FALSE
D118V8, binary
                  cls
clus                 0   1
  CLEC4F MUTATED     4  16
  CLEC4F WILD-TYPE 221 248
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CLEC4F MUTATED      4   16
  CLEC4F WILD-TYPE  221  248
        clus
vv       CLEC4F MUTATED CLEC4F WILD-TYPE
  FEMALE              4              221
  MALE               16              248
[1] 2 2
[1] FALSE
D118V9, binary
                  cls
clus                 0   1
  CLEC4F MUTATED    15   1
  CLEC4F WILD-TYPE 335  21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CLEC4F MUTATED     15    1
  CLEC4F WILD-TYPE  335   21
     clus
vv    CLEC4F MUTATED CLEC4F WILD-TYPE
  NO              15              335
  YES              1               21
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CLEC4F MUTATED                     16                             3
  CLEC4F WILD-TYPE                  299                            44
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CLEC4F MUTATED                       1                              0
  CLEC4F WILD-TYPE                   105                             10
D118V10, multiclass
                                clus
vv                               CLEC4F MUTATED CLEC4F WILD-TYPE
  COLON ADENOCARCINOMA                       16              299
  COLON MUCINOUS ADENOCARCINOMA               3               44
  RECTAL ADENOCARCINOMA                       1              105
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  CLEC4F MUTATED    14   0   1   2
  CLEC4F WILD-TYPE 331   4  30  23
D118V11, multiclass
    clus
vv   CLEC4F MUTATED CLEC4F WILD-TYPE
  R0             14              331
  R1              0                4
  R2              1               30
  RX              2               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D118V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CLEC4F MUTATED                                  0     2
  CLEC4F WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  CLEC4F MUTATED                           3     9
  CLEC4F WILD-TYPE                        19   217
D118V13, multiclass
                                  clus
vv                                 CLEC4F MUTATED CLEC4F WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                9
  BLACK OR AFRICAN AMERICAN                     3               19
  WHITE                                         9              217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(119) Variable = GPR174 MUTATION ANALYSIS
D119V1, survival
                  sevent
clus2                0   1
  GPR174 MUTATED     9   1
  GPR174 WILD-TYPE 369  92
  GPR174 MUTATED GPR174 WILD-TYPE 
              10              461 
  GPR174 MUTATED GPR174 WILD-TYPE 
               1               92 
$`GPR174 MUTATED`
TCGA-A6-5659 TCGA-AA-3543 TCGA-AA-3955 TCGA-CA-6718 TCGA-CM-6679 TCGA-D5-5538 
       30.44         0.99        20.98        10.06        10.06        12.26 
TCGA-D5-6539 TCGA-G4-6625 TCGA-AF-6136 TCGA-AG-3881 
       12.49        91.79        15.39        19.04 

$`GPR174 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       26.01        12.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       12.76        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5539 
       11.08        11.08        11.01        12.03        45.40        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 
       15.12        17.85         4.80        17.13        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       35.80        26.17        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       16.83        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 
        0.99        37.02        32.98         0.99         0.99        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  GPR174 MUTATED GPR174 WILD-TYPE 
            0.99             0.00 
  GPR174 MUTATED GPR174 WILD-TYPE 
           91.79           148.01 
  GPR174 MUTATED GPR174 WILD-TYPE 
           13.94            20.55 
[1] "1.0 - 91.8 (13.9)"  "0.0 - 148.0 (20.6)"
[1] "hr=" "1.6"
D119V2, continuous
D119V3, binary
                  cls
clus                 0   1
  GPR174 MUTATED     8   2
  GPR174 WILD-TYPE 358 117
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR174 MUTATED      8    2
  GPR174 WILD-TYPE  358  117
        clus
vv       GPR174 MUTATED GPR174 WILD-TYPE
  COLON               8              358
  RECTUM              2              117
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GPR174 MUTATED         2        0        0         4         0         0
  GPR174 WILD-TYPE      89        1       32       134        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GPR174 MUTATED           0          1          3          0        0
  GPR174 WILD-TYPE        24         10         56         42       48
                  vv
clus               STAGE IVA STAGE IVB
  GPR174 MUTATED           0         0
  GPR174 WILD-TYPE        18         1
D119V4, multiclass
            clus
vv           GPR174 MUTATED GPR174 WILD-TYPE
  STAGE I                 2               89
  STAGE IA                0                1
  STAGE II                0               32
  STAGE IIA               4              134
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              1               10
  STAGE IIIB              3               56
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  GPR174 MUTATED     0   3   7   0
  GPR174 WILD-TYPE  17  89 322  50
D119V5, multiclass
    clus
vv   GPR174 MUTATED GPR174 WILD-TYPE
  T1              0               17
  T2              3               89
  T3              7              322
  T4              0               50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  GPR174 MUTATED     7   2   1
  GPR174 WILD-TYPE 280 111  86
D119V6, multiclass
    clus
vv   GPR174 MUTATED GPR174 WILD-TYPE
  N0              7              280
  N1              2              111
  N2              1               86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D119V7, binary
                  cls
clus                 0   1
  GPR174 MUTATED     9   0
  GPR174 WILD-TYPE 366  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR174 MUTATED      9    0
  GPR174 WILD-TYPE  366   65
   clus
vv  GPR174 MUTATED GPR174 WILD-TYPE
  0              9              366
  1              0               65
[1] 2 2
[1] FALSE
D119V8, binary
                  cls
clus                 0   1
  GPR174 MUTATED     5   5
  GPR174 WILD-TYPE 220 259
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR174 MUTATED      5    5
  GPR174 WILD-TYPE  220  259
        clus
vv       GPR174 MUTATED GPR174 WILD-TYPE
  FEMALE              5              220
  MALE                5              259
[1] 2 2
[1] FALSE
D119V9, binary
                  cls
clus                 0   1
  GPR174 MUTATED     9   1
  GPR174 WILD-TYPE 341  21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR174 MUTATED      9    1
  GPR174 WILD-TYPE  341   21
     clus
vv    GPR174 MUTATED GPR174 WILD-TYPE
  NO               9              341
  YES              1               21
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  GPR174 MUTATED                      7                             1
  GPR174 WILD-TYPE                  308                            46
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  GPR174 MUTATED                       1                              0
  GPR174 WILD-TYPE                   105                             10
D119V10, multiclass
                                clus
vv                               GPR174 MUTATED GPR174 WILD-TYPE
  COLON ADENOCARCINOMA                        7              308
  COLON MUCINOUS ADENOCARCINOMA               1               46
  RECTAL ADENOCARCINOMA                       1              105
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  GPR174 MUTATED     7   0   0   1
  GPR174 WILD-TYPE 338   4  31  24
D119V11, multiclass
    clus
vv   GPR174 MUTATED GPR174 WILD-TYPE
  R0              7              338
  R1              0                4
  R2              0               31
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D119V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GPR174 MUTATED                                  0     1
  GPR174 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  GPR174 MUTATED                           0     6
  GPR174 WILD-TYPE                        22   220
D119V13, multiclass
                                  clus
vv                                 GPR174 MUTATED GPR174 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         6              220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(120) Variable = NAA25 MUTATION ANALYSIS
D120V1, survival
                 sevent
clus2               0   1
  NAA25 MUTATED    15   2
  NAA25 WILD-TYPE 363  91
  NAA25 MUTATED NAA25 WILD-TYPE 
             17             454 
  NAA25 MUTATED NAA25 WILD-TYPE 
              2              91 
$`NAA25 MUTATED`
TCGA-A6-3809 TCGA-A6-5661 TCGA-A6-5664 TCGA-A6-6780 TCGA-AA-3555 TCGA-AA-3710 
       32.75        33.53        22.09        20.12        29.95        26.99 
TCGA-AA-3715 TCGA-AA-3864 TCGA-AA-3950 TCGA-AA-A00N TCGA-AA-A010 TCGA-CM-6678 
       19.04        53.00        24.00         4.01        34.98        11.01 
TCGA-F4-6808 TCGA-AG-3896 TCGA-AG-A002 TCGA-CI-6624 TCGA-F5-6812 
       33.67         1.02        20.98         4.73         0.66 

$`NAA25 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5665 TCGA-A6-5666 
       31.63        30.44        29.19        23.61        22.06        32.71 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       27.09        22.52         8.38        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 
       21.76        24.69        24.39        23.87        19.66        20.28 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
        7.04         3.02         1.02        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       78.08         6.05         6.97        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 
       37.05        19.00        36.00         5.03        85.05        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 
       32.05         0.99        31.07        31.07        30.05        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 
       12.99        24.00        33.01        26.01         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.08        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       41.42        16.24        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3902 
       17.03        13.02        35.01        14.01        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
        6.05        33.17         6.97        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.69        55.76        26.43 

  NAA25 MUTATED NAA25 WILD-TYPE 
           0.66            0.00 
  NAA25 MUTATED NAA25 WILD-TYPE 
          53.00          148.01 
  NAA25 MUTATED NAA25 WILD-TYPE 
         22.090          20.035 
[1] "0.7 - 53.0 (22.1)"  "0.0 - 148.0 (20.0)"
[1] "hr=" "1.3"
D120V2, continuous
D120V3, binary
                 cls
clus                0   1
  NAA25 MUTATED    14   4
  NAA25 WILD-TYPE 352 115
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NAA25 MUTATED     14    4
  NAA25 WILD-TYPE  352  115
        clus
vv       NAA25 MUTATED NAA25 WILD-TYPE
  COLON             14             352
  RECTUM             4             115
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NAA25 MUTATED         4        0        2         7         3         0
  NAA25 WILD-TYPE      87        1       30       131         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NAA25 MUTATED           0          0          0          1        0         1
  NAA25 WILD-TYPE        24         11         59         41       48        17
                 vv
clus              STAGE IVB
  NAA25 MUTATED           0
  NAA25 WILD-TYPE         1
D120V4, multiclass
            clus
vv           NAA25 MUTATED NAA25 WILD-TYPE
  STAGE I                4              87
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA              7             131
  STAGE IIB              3               7
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             1              41
  STAGE IV               0              48
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  NAA25 MUTATED     1   3   9   5
  NAA25 WILD-TYPE  16  89 320  45
D120V5, multiclass
    clus
vv   NAA25 MUTATED NAA25 WILD-TYPE
  T1             1              16
  T2             3              89
  T3             9             320
  T4             5              45
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  NAA25 MUTATED    16   1   1
  NAA25 WILD-TYPE 271 112  86
D120V6, multiclass
    clus
vv   NAA25 MUTATED NAA25 WILD-TYPE
  N0            16             271
  N1             1             112
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D120V7, binary
                 cls
clus                0   1
  NAA25 MUTATED    15   1
  NAA25 WILD-TYPE 360  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NAA25 MUTATED     15    1
  NAA25 WILD-TYPE  360   64
   clus
vv  NAA25 MUTATED NAA25 WILD-TYPE
  0            15             360
  1             1              64
[1] 2 2
[1] FALSE
D120V8, binary
                 cls
clus                0   1
  NAA25 MUTATED    11   7
  NAA25 WILD-TYPE 214 257
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NAA25 MUTATED     11    7
  NAA25 WILD-TYPE  214  257
        clus
vv       NAA25 MUTATED NAA25 WILD-TYPE
  FEMALE            11             214
  MALE               7             257
[1] 2 2
[1] FALSE
D120V9, binary
                 cls
clus                0   1
  NAA25 MUTATED    13   0
  NAA25 WILD-TYPE 337  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NAA25 MUTATED     13    0
  NAA25 WILD-TYPE  337   22
     clus
vv    NAA25 MUTATED NAA25 WILD-TYPE
  NO             13             337
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  NAA25 MUTATED                      9                             5
  NAA25 WILD-TYPE                  306                            42
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  NAA25 MUTATED                       4                              0
  NAA25 WILD-TYPE                   102                             10
D120V10, multiclass
                                clus
vv                               NAA25 MUTATED NAA25 WILD-TYPE
  COLON ADENOCARCINOMA                       9             306
  COLON MUCINOUS ADENOCARCINOMA              5              42
  RECTAL ADENOCARCINOMA                      4             102
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  NAA25 MUTATED    15   0   0   0
  NAA25 WILD-TYPE 330   4  31  25
D120V11, multiclass
    clus
vv   NAA25 MUTATED NAA25 WILD-TYPE
  R0            15             330
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D120V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NAA25 MUTATED                                  0     0
  NAA25 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  NAA25 MUTATED                           2     6
  NAA25 WILD-TYPE                        20   220
D120V13, multiclass
                                  clus
vv                                 NAA25 MUTATED NAA25 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    2              20
  WHITE                                        6             220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(121) Variable = FIGNL1 MUTATION ANALYSIS
D121V1, survival
                  sevent
clus2                0   1
  FIGNL1 MUTATED    17   1
  FIGNL1 WILD-TYPE 361  92
  FIGNL1 MUTATED FIGNL1 WILD-TYPE 
              18              453 
  FIGNL1 MUTATED FIGNL1 WILD-TYPE 
               1               92 
$`FIGNL1 MUTATED`
TCGA-A6-5661 TCGA-A6-5662 TCGA-AA-3510 TCGA-AA-3518 TCGA-AA-A00J TCGA-AA-A010 
       33.53        23.61        63.98         1.02        18.05        34.98 
TCGA-AZ-4315 TCGA-CA-6717 TCGA-CK-4952 TCGA-CM-5349 TCGA-DM-A0X9 TCGA-DM-A1HB 
       58.39        12.76        15.62        30.08       119.70       135.65 
TCGA-F4-6703 TCGA-G4-6293 TCGA-G4-6303 TCGA-AG-3892 TCGA-CI-6622 TCGA-F5-6813 
       47.87       133.18        65.85        13.02         6.97         0.69 

$`FIGNL1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5664 TCGA-A6-5665 
       32.91        31.63        30.44        29.19        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3520 
        6.97         1.02        13.02        38.99         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
       16.31         0.95        33.01        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07        12.20        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       85.45        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5861 
       13.02        29.06        22.03        22.98        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0XD TCGA-DM-A0XF 
        1.51        12.00        11.38        10.26        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
        7.50        44.32       131.51       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       31.96        35.74         6.18         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6299 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       74.56        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 
       19.99         1.02        17.95        36.95        17.03        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
       33.17         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-G5-6235 TCGA-G5-6641 
        0.66        55.76        26.43 

  FIGNL1 MUTATED FIGNL1 WILD-TYPE 
            0.69             0.00 
  FIGNL1 MUTATED FIGNL1 WILD-TYPE 
          135.65           148.01 
  FIGNL1 MUTATED FIGNL1 WILD-TYPE 
          31.805           20.050 
[1] "0.7 - 135.7 (31.8)" "0.0 - 148.0 (20.1)"
[1] "hr=" "6"  
D121V2, continuous
D121V3, binary
                  cls
clus                 0   1
  FIGNL1 MUTATED    16   3
  FIGNL1 WILD-TYPE 350 116
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FIGNL1 MUTATED     16    3
  FIGNL1 WILD-TYPE  350  116
        clus
vv       FIGNL1 MUTATED FIGNL1 WILD-TYPE
  COLON              16              350
  RECTUM              3              116
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FIGNL1 MUTATED         1        0        1         8         2         0
  FIGNL1 WILD-TYPE      90        1       31       130         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FIGNL1 MUTATED           1          0          2          2        1
  FIGNL1 WILD-TYPE        23         11         57         40       47
                  vv
clus               STAGE IVA STAGE IVB
  FIGNL1 MUTATED           1         0
  FIGNL1 WILD-TYPE        17         1
D121V4, multiclass
            clus
vv           FIGNL1 MUTATED FIGNL1 WILD-TYPE
  STAGE I                 1               90
  STAGE IA                0                1
  STAGE II                1               31
  STAGE IIA               8              130
  STAGE IIB               2                8
  STAGE IIC               0                1
  STAGE III               1               23
  STAGE IIIA              0               11
  STAGE IIIB              2               57
  STAGE IIIC              2               40
  STAGE IV                1               47
  STAGE IVA               1               17
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  FIGNL1 MUTATED     1   0  13   5
  FIGNL1 WILD-TYPE  16  92 316  45
D121V5, multiclass
    clus
vv   FIGNL1 MUTATED FIGNL1 WILD-TYPE
  T1              1               16
  T2              0               92
  T3             13              316
  T4              5               45
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  FIGNL1 MUTATED    12   4   3
  FIGNL1 WILD-TYPE 275 109  84
D121V6, multiclass
    clus
vv   FIGNL1 MUTATED FIGNL1 WILD-TYPE
  N0             12              275
  N1              4              109
  N2              3               84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D121V7, binary
                  cls
clus                 0   1
  FIGNL1 MUTATED    17   2
  FIGNL1 WILD-TYPE 358  63
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FIGNL1 MUTATED     17    2
  FIGNL1 WILD-TYPE  358   63
   clus
vv  FIGNL1 MUTATED FIGNL1 WILD-TYPE
  0             17              358
  1              2               63
[1] 2 2
[1] FALSE
D121V8, binary
                  cls
clus                 0   1
  FIGNL1 MUTATED    10   9
  FIGNL1 WILD-TYPE 215 255
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FIGNL1 MUTATED     10    9
  FIGNL1 WILD-TYPE  215  255
        clus
vv       FIGNL1 MUTATED FIGNL1 WILD-TYPE
  FEMALE             10              215
  MALE                9              255
[1] 2 2
[1] FALSE
D121V9, binary
                  cls
clus                 0   1
  FIGNL1 MUTATED    12   0
  FIGNL1 WILD-TYPE 338  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FIGNL1 MUTATED     12    0
  FIGNL1 WILD-TYPE  338   22
     clus
vv    FIGNL1 MUTATED FIGNL1 WILD-TYPE
  NO              12              338
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  FIGNL1 MUTATED                     12                             3
  FIGNL1 WILD-TYPE                  303                            44
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  FIGNL1 MUTATED                       3                              0
  FIGNL1 WILD-TYPE                   103                             10
D121V10, multiclass
                                clus
vv                               FIGNL1 MUTATED FIGNL1 WILD-TYPE
  COLON ADENOCARCINOMA                       12              303
  COLON MUCINOUS ADENOCARCINOMA               3               44
  RECTAL ADENOCARCINOMA                       3              103
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  FIGNL1 MUTATED    13   0   0   2
  FIGNL1 WILD-TYPE 332   4  31  23
D121V11, multiclass
    clus
vv   FIGNL1 MUTATED FIGNL1 WILD-TYPE
  R0             13              332
  R1              0                4
  R2              0               31
  RX              2               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D121V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FIGNL1 MUTATED                                  0     1
  FIGNL1 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  FIGNL1 MUTATED                           1    11
  FIGNL1 WILD-TYPE                        21   215
D121V13, multiclass
                                  clus
vv                                 FIGNL1 MUTATED FIGNL1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                        11              215
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(122) Variable = HMG20A MUTATION ANALYSIS
D122V1, survival
                  sevent
clus2                0   1
  HMG20A MUTATED    11   3
  HMG20A WILD-TYPE 367  90
  HMG20A MUTATED HMG20A WILD-TYPE 
              14              457 
  HMG20A MUTATED HMG20A WILD-TYPE 
               3               90 
$`HMG20A MUTATED`
TCGA-A6-6141 TCGA-AA-3553 TCGA-AA-3845 TCGA-AA-3968 TCGA-AA-A010 TCGA-AZ-4315 
        8.38        24.00         0.00        21.99        34.98        58.39 
TCGA-CA-6717 TCGA-CK-4950 TCGA-CK-5916 TCGA-CM-4752 TCGA-CM-6172 TCGA-DM-A1D8 
       12.76        85.45        21.14        13.02        11.01        12.59 
TCGA-DM-A1HB TCGA-AG-A015 
      135.65        36.03 

$`HMG20A WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 
       22.09        22.06        32.71        27.09        22.52        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       13.02        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 
       15.95        38.99        37.02        14.93        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07        12.20        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 
      148.01        15.62        49.08        51.32         9.99        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       13.02        15.02        14.04        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A1DA 
      130.65        92.75        49.91        13.32       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
       44.32       131.51       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       37.02        15.95         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  HMG20A MUTATED HMG20A WILD-TYPE 
               0                0 
  HMG20A MUTATED HMG20A WILD-TYPE 
          135.65           148.01 
  HMG20A MUTATED HMG20A WILD-TYPE 
          21.565           20.120 
[1] "0.0 - 135.7 (21.6)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.1"
D122V2, continuous
D122V3, binary
                  cls
clus                 0   1
  HMG20A MUTATED    13   2
  HMG20A WILD-TYPE 353 117
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HMG20A MUTATED     13    2
  HMG20A WILD-TYPE  353  117
        clus
vv       HMG20A MUTATED HMG20A WILD-TYPE
  COLON              13              353
  RECTUM              2              117
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  HMG20A MUTATED         4        0        0         6         1         0
  HMG20A WILD-TYPE      87        1       32       132         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HMG20A MUTATED           0          0          3          0        0
  HMG20A WILD-TYPE        24         11         56         42       48
                  vv
clus               STAGE IVA STAGE IVB
  HMG20A MUTATED           0         0
  HMG20A WILD-TYPE        18         1
D122V4, multiclass
            clus
vv           HMG20A MUTATED HMG20A WILD-TYPE
  STAGE I                 4               87
  STAGE IA                0                1
  STAGE II                0               32
  STAGE IIA               6              132
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              3               56
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  HMG20A MUTATED     2   2  10   1
  HMG20A WILD-TYPE  15  90 319  49
D122V5, multiclass
    clus
vv   HMG20A MUTATED HMG20A WILD-TYPE
  T1              2               15
  T2              2               90
  T3             10              319
  T4              1               49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  HMG20A MUTATED    11   4   0
  HMG20A WILD-TYPE 276 109  87
D122V6, multiclass
    clus
vv   HMG20A MUTATED HMG20A WILD-TYPE
  N0             11              276
  N1              4              109
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D122V7, binary
                  cls
clus                 0   1
  HMG20A MUTATED    14   0
  HMG20A WILD-TYPE 361  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HMG20A MUTATED     14    0
  HMG20A WILD-TYPE  361   65
   clus
vv  HMG20A MUTATED HMG20A WILD-TYPE
  0             14              361
  1              0               65
[1] 2 2
[1] FALSE
D122V8, binary
                  cls
clus                 0   1
  HMG20A MUTATED    10   5
  HMG20A WILD-TYPE 215 259
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HMG20A MUTATED     10    5
  HMG20A WILD-TYPE  215  259
        clus
vv       HMG20A MUTATED HMG20A WILD-TYPE
  FEMALE             10              215
  MALE                5              259
[1] 2 2
[1] FALSE
D122V9, binary
                  cls
clus                 0   1
  HMG20A MUTATED    11   0
  HMG20A WILD-TYPE 339  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HMG20A MUTATED     11    0
  HMG20A WILD-TYPE  339   22
     clus
vv    HMG20A MUTATED HMG20A WILD-TYPE
  NO              11              339
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  HMG20A MUTATED                     11                             1
  HMG20A WILD-TYPE                  304                            46
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  HMG20A MUTATED                       2                              0
  HMG20A WILD-TYPE                   104                             10
D122V10, multiclass
                                clus
vv                               HMG20A MUTATED HMG20A WILD-TYPE
  COLON ADENOCARCINOMA                       11              304
  COLON MUCINOUS ADENOCARCINOMA               1               46
  RECTAL ADENOCARCINOMA                       2              104
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  HMG20A MUTATED     9   1   0   2
  HMG20A WILD-TYPE 336   3  31  23
D122V11, multiclass
    clus
vv   HMG20A MUTATED HMG20A WILD-TYPE
  R0              9              336
  R1              1                3
  R2              0               31
  RX              2               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D122V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HMG20A MUTATED                                  0     1
  HMG20A WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  HMG20A MUTATED                           3     5
  HMG20A WILD-TYPE                        19   221
D122V13, multiclass
                                  clus
vv                                 HMG20A MUTATED HMG20A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     3               19
  WHITE                                         5              221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(123) Variable = SHROOM4 MUTATION ANALYSIS
D123V1, survival
                   sevent
clus2                 0   1
  SHROOM4 MUTATED    20   5
  SHROOM4 WILD-TYPE 358  88
  SHROOM4 MUTATED SHROOM4 WILD-TYPE 
               25               446 
  SHROOM4 MUTATED SHROOM4 WILD-TYPE 
                5                88 
$`SHROOM4 MUTATED`
TCGA-A6-5661 TCGA-AA-3811 TCGA-AA-3815 TCGA-AA-3947 TCGA-AA-A00N TCGA-AD-6889 
       33.53        10.06        33.04        33.01         4.01        56.55 
TCGA-CA-5796 TCGA-CK-5913 TCGA-CM-6164 TCGA-CM-6678 TCGA-D5-6537 TCGA-D5-6540 
        3.25        51.32        29.03        11.01         4.80        16.14 
TCGA-D5-6922 TCGA-D5-7000 TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A28E TCGA-F4-6570 
        4.41        10.26       135.65       139.17       119.93         6.18 
TCGA-AF-5654 TCGA-CL-5918 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6160 TCGA-EI-6506 
       16.83         7.17         5.03        13.97        19.99        20.55 
TCGA-F5-6813 
        0.69 

$`SHROOM4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       35.05         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
        0.07        21.37        15.52         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5797 
       11.74         3.19         1.61        12.69         3.06         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 
      148.01        85.45        15.62        49.08         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       15.02        12.00         2.96        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       13.05        11.08        11.08        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6539 
        1.32        43.27        15.12        17.85        17.13        12.49 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
       15.58         1.48         3.68        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
        6.12        81.37        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
        8.61        31.96        35.74        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       10.39        14.50        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-DC-5337 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6681 TCGA-DC-6682 
       78.12        15.02        27.95        10.98         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       51.48        32.61         0.49        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  SHROOM4 MUTATED SHROOM4 WILD-TYPE 
             0.69              0.00 
  SHROOM4 MUTATED SHROOM4 WILD-TYPE 
           139.17            148.01 
  SHROOM4 MUTATED SHROOM4 WILD-TYPE 
           16.140            20.945 
[1] "0.7 - 139.2 (16.1)" "0.0 - 148.0 (20.9)"
[1] "hr=" "1.1"
D123V2, continuous
D123V3, binary
                   cls
clus                  0   1
  SHROOM4 MUTATED    21   7
  SHROOM4 WILD-TYPE 345 112
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SHROOM4 MUTATED     21    7
  SHROOM4 WILD-TYPE  345  112
        clus
vv       SHROOM4 MUTATED SHROOM4 WILD-TYPE
  COLON               21               345
  RECTUM               7               112
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SHROOM4 MUTATED         5        0        0        12         3         0
  SHROOM4 WILD-TYPE      86        1       32       126         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SHROOM4 MUTATED           1          2          3          1        0
  SHROOM4 WILD-TYPE        23          9         56         41       48
                   vv
clus                STAGE IVA STAGE IVB
  SHROOM4 MUTATED           1         0
  SHROOM4 WILD-TYPE        17         1
D123V4, multiclass
            clus
vv           SHROOM4 MUTATED SHROOM4 WILD-TYPE
  STAGE I                  5                86
  STAGE IA                 0                 1
  STAGE II                 0                32
  STAGE IIA               12               126
  STAGE IIB                3                 7
  STAGE IIC                0                 1
  STAGE III                1                23
  STAGE IIIA               2                 9
  STAGE IIIB               3                56
  STAGE IIIC               1                41
  STAGE IV                 0                48
  STAGE IVA                1                17
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  SHROOM4 MUTATED     0   6  17   5
  SHROOM4 WILD-TYPE  17  86 312  45
D123V5, multiclass
    clus
vv   SHROOM4 MUTATED SHROOM4 WILD-TYPE
  T1               0                17
  T2               6                86
  T3              17               312
  T4               5                45
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  SHROOM4 MUTATED    20   6   2
  SHROOM4 WILD-TYPE 267 107  85
D123V6, multiclass
    clus
vv   SHROOM4 MUTATED SHROOM4 WILD-TYPE
  N0              20               267
  N1               6               107
  N2               2                85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D123V7, binary
                   cls
clus                  0   1
  SHROOM4 MUTATED    22   1
  SHROOM4 WILD-TYPE 353  64
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SHROOM4 MUTATED     22    1
  SHROOM4 WILD-TYPE  353   64
   clus
vv  SHROOM4 MUTATED SHROOM4 WILD-TYPE
  0              22               353
  1               1                64
[1] 2 2
[1] FALSE
D123V8, binary
                   cls
clus                  0   1
  SHROOM4 MUTATED    19   9
  SHROOM4 WILD-TYPE 206 255
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SHROOM4 MUTATED     19    9
  SHROOM4 WILD-TYPE  206  255
        clus
vv       SHROOM4 MUTATED SHROOM4 WILD-TYPE
  FEMALE              19               206
  MALE                 9               255
[1] 2 2
[1] FALSE
D123V9, binary
                   cls
clus                  0   1
  SHROOM4 MUTATED    16   0
  SHROOM4 WILD-TYPE 334  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SHROOM4 MUTATED     16    0
  SHROOM4 WILD-TYPE  334   22
     clus
vv    SHROOM4 MUTATED SHROOM4 WILD-TYPE
  NO               16               334
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SHROOM4 MUTATED                     15                             5
  SHROOM4 WILD-TYPE                  300                            42
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SHROOM4 MUTATED                       7                              0
  SHROOM4 WILD-TYPE                    99                             10
D123V10, multiclass
                                clus
vv                               SHROOM4 MUTATED SHROOM4 WILD-TYPE
  COLON ADENOCARCINOMA                        15               300
  COLON MUCINOUS ADENOCARCINOMA                5                42
  RECTAL ADENOCARCINOMA                        7                99
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  SHROOM4 MUTATED    20   0   0   4
  SHROOM4 WILD-TYPE 325   4  31  21
D123V11, multiclass
    clus
vv   SHROOM4 MUTATED SHROOM4 WILD-TYPE
  R0              20               325
  R1               0                 4
  R2               0                31
  RX               4                21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D123V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SHROOM4 MUTATED                                  0     2
  SHROOM4 WILD-TYPE                                1     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  SHROOM4 MUTATED                           2    19
  SHROOM4 WILD-TYPE                        20   207
D123V13, multiclass
                                  clus
vv                                 SHROOM4 MUTATED SHROOM4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          2                 9
  BLACK OR AFRICAN AMERICAN                      2                20
  WHITE                                         19               207
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(124) Variable = CASP8 MUTATION ANALYSIS
D124V1, survival
                 sevent
clus2               0   1
  CASP8 MUTATED    13   4
  CASP8 WILD-TYPE 365  89
  CASP8 MUTATED CASP8 WILD-TYPE 
             17             454 
  CASP8 MUTATED CASP8 WILD-TYPE 
              4              89 
$`CASP8 MUTATED`
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3518 TCGA-AA-3543 TCGA-AA-3710 TCGA-AA-3715 
        7.04         3.02         1.02         0.99        26.99        19.04 
TCGA-AA-3864 TCGA-AA-3947 TCGA-AA-A00A TCGA-AA-A00J TCGA-AA-A00R TCGA-AD-6895 
       53.00        33.01        38.04        18.05         0.99         0.72 
TCGA-AY-6197 TCGA-CA-6717 TCGA-CM-4746 TCGA-DM-A28F TCGA-EI-6507 
       21.44        12.76        37.02        35.97        19.96 

$`CASP8 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3496 TCGA-AA-3502 
       23.87        20.12        19.66        20.28         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3519 
       63.98         6.97         1.02        13.02        38.99         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
        2.01        12.99        24.00        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00D 
       27.02        19.07         7.96        27.02        13.94        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
       42.02        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 
        0.07        21.37        15.52        56.55         0.79         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       16.31         0.95        33.01        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07        12.20        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4747 
       82.95         1.91       124.27        23.05        20.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H 
      139.17         6.12        81.37       119.93        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6508 
       24.13        51.48        32.61         0.49        20.55        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  CASP8 MUTATED CASP8 WILD-TYPE 
           0.72            0.00 
  CASP8 MUTATED CASP8 WILD-TYPE 
          53.00          148.01 
  CASP8 MUTATED CASP8 WILD-TYPE 
         19.040          20.415 
[1] "0.7 - 53.0 (19.0)"  "0.0 - 148.0 (20.4)"
[1] "hr=" "1.7"
D124V2, continuous
D124V3, binary
                 cls
clus                0   1
  CASP8 MUTATED    17   1
  CASP8 WILD-TYPE 349 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASP8 MUTATED     17    1
  CASP8 WILD-TYPE  349  118
        clus
vv       CASP8 MUTATED CASP8 WILD-TYPE
  COLON             17             349
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CASP8 MUTATED         3        0        5         6         1         0
  CASP8 WILD-TYPE      88        1       27       132         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CASP8 MUTATED           0          0          2          0        0         0
  CASP8 WILD-TYPE        24         11         57         42       48        18
                 vv
clus              STAGE IVB
  CASP8 MUTATED           0
  CASP8 WILD-TYPE         1
D124V4, multiclass
            clus
vv           CASP8 MUTATED CASP8 WILD-TYPE
  STAGE I                3              88
  STAGE IA               0               1
  STAGE II               5              27
  STAGE IIA              6             132
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             2              57
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CASP8 MUTATED     0   3  12   3
  CASP8 WILD-TYPE  17  89 317  47
D124V5, multiclass
    clus
vv   CASP8 MUTATED CASP8 WILD-TYPE
  T1             0              17
  T2             3              89
  T3            12             317
  T4             3              47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  CASP8 MUTATED    15   3   0
  CASP8 WILD-TYPE 272 110  87
D124V6, multiclass
    clus
vv   CASP8 MUTATED CASP8 WILD-TYPE
  N0            15             272
  N1             3             110
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D124V7, binary
                 cls
clus                0   1
  CASP8 MUTATED    16   0
  CASP8 WILD-TYPE 359  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASP8 MUTATED     16    0
  CASP8 WILD-TYPE  359   65
   clus
vv  CASP8 MUTATED CASP8 WILD-TYPE
  0            16             359
  1             0              65
[1] 2 2
[1] FALSE
D124V8, binary
                 cls
clus                0   1
  CASP8 MUTATED     6  12
  CASP8 WILD-TYPE 219 252
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASP8 MUTATED      6   12
  CASP8 WILD-TYPE  219  252
        clus
vv       CASP8 MUTATED CASP8 WILD-TYPE
  FEMALE             6             219
  MALE              12             252
[1] 2 2
[1] FALSE
D124V9, binary
                 cls
clus                0   1
  CASP8 MUTATED    13   0
  CASP8 WILD-TYPE 337  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASP8 MUTATED     13    0
  CASP8 WILD-TYPE  337   22
     clus
vv    CASP8 MUTATED CASP8 WILD-TYPE
  NO             13             337
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CASP8 MUTATED                     13                             4
  CASP8 WILD-TYPE                  302                            43
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CASP8 MUTATED                       1                              0
  CASP8 WILD-TYPE                   105                             10
D124V10, multiclass
                                clus
vv                               CASP8 MUTATED CASP8 WILD-TYPE
  COLON ADENOCARCINOMA                      13             302
  COLON MUCINOUS ADENOCARCINOMA              4              43
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  CASP8 MUTATED    15   0   0   1
  CASP8 WILD-TYPE 330   4  31  24
D124V11, multiclass
    clus
vv   CASP8 MUTATED CASP8 WILD-TYPE
  R0            15             330
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D124V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CASP8 MUTATED                                  0     1
  CASP8 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CASP8 MUTATED                           1     4
  CASP8 WILD-TYPE                        21   222
D124V13, multiclass
                                  clus
vv                                 CASP8 MUTATED CASP8 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        4             222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(125) Variable = HPS3 MUTATION ANALYSIS
D125V1, survival
                sevent
clus2              0   1
  HPS3 MUTATED    19   4
  HPS3 WILD-TYPE 359  89
  HPS3 MUTATED HPS3 WILD-TYPE 
            23            448 
  HPS3 MUTATED HPS3 WILD-TYPE 
             4             89 
$`HPS3 MUTATED`
TCGA-A6-5659 TCGA-AA-3510 TCGA-AA-3660 TCGA-AA-3697 TCGA-AA-3950 TCGA-AA-3977 
       30.44        63.98        78.08        85.05        24.00        25.02 
TCGA-AA-A00N TCGA-AA-A01Q TCGA-AD-6548 TCGA-AD-6895 TCGA-AZ-4315 TCGA-AZ-4682 
        4.01         1.02        21.37         0.72        58.39        22.36 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-CA-5797 TCGA-CK-4950 TCGA-CM-6172 TCGA-G4-6307 
       49.41         6.77         3.29        85.45        11.01        55.04 
TCGA-G4-6321 TCGA-G4-6588 TCGA-AG-3892 TCGA-AG-A002 TCGA-AH-6643 
       22.09        26.17        13.02        20.98         0.69 

$`HPS3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       13.94        19.99        61.02         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       33.01        26.01         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01R TCGA-AA-A01S 
       12.00        31.00        31.00        38.07        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6888 TCGA-AD-6889 
       39.98        18.05        40.96         0.07        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.79         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-5403 TCGA-AZ-5407 
       17.82         1.41         5.13       106.75        62.79        88.21 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6716 
        1.61        12.69         3.06         3.25         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 
       12.76        10.06        14.30        17.56       148.01        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       13.02        15.02        14.04        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 
       44.68        85.48        63.62        61.91        36.00        13.78 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       35.80        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
       38.56         1.45        17.49         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  HPS3 MUTATED HPS3 WILD-TYPE 
          0.69           0.00 
  HPS3 MUTATED HPS3 WILD-TYPE 
         85.45         148.01 
  HPS3 MUTATED HPS3 WILD-TYPE 
         22.36          20.02 
[1] "0.7 - 85.5 (22.4)"  "0.0 - 148.0 (20.0)"
[1] "hr=" "1.4"
D125V2, continuous
D125V3, binary
                cls
clus               0   1
  HPS3 MUTATED    20   3
  HPS3 WILD-TYPE 346 116
[1] "tbl2"
                cls
clus             [,1] [,2]
  HPS3 MUTATED     20    3
  HPS3 WILD-TYPE  346  116
        clus
vv       HPS3 MUTATED HPS3 WILD-TYPE
  COLON            20            346
  RECTUM            3            116
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  HPS3 MUTATED         5        0        4         4         1         0
  HPS3 WILD-TYPE      86        1       28       134         9         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  HPS3 MUTATED           2          0          3          1        0         1
  HPS3 WILD-TYPE        22         11         56         41       48        17
                vv
clus             STAGE IVB
  HPS3 MUTATED           0
  HPS3 WILD-TYPE         1
D125V4, multiclass
            clus
vv           HPS3 MUTATED HPS3 WILD-TYPE
  STAGE I               5             86
  STAGE IA              0              1
  STAGE II              4             28
  STAGE IIA             4            134
  STAGE IIB             1              9
  STAGE IIC             0              1
  STAGE III             2             22
  STAGE IIIA            0             11
  STAGE IIIB            3             56
  STAGE IIIC            1             41
  STAGE IV              0             48
  STAGE IVA             1             17
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  HPS3 MUTATED     1   6  15   1
  HPS3 WILD-TYPE  16  86 314  49
D125V5, multiclass
    clus
vv   HPS3 MUTATED HPS3 WILD-TYPE
  T1            1             16
  T2            6             86
  T3           15            314
  T4            1             49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  HPS3 MUTATED    17   5   1
  HPS3 WILD-TYPE 270 108  86
D125V6, multiclass
    clus
vv   HPS3 MUTATED HPS3 WILD-TYPE
  N0           17            270
  N1            5            108
  N2            1             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D125V7, binary
                cls
clus               0   1
  HPS3 MUTATED    17   1
  HPS3 WILD-TYPE 358  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  HPS3 MUTATED     17    1
  HPS3 WILD-TYPE  358   64
   clus
vv  HPS3 MUTATED HPS3 WILD-TYPE
  0           17            358
  1            1             64
[1] 2 2
[1] FALSE
D125V8, binary
                cls
clus               0   1
  HPS3 MUTATED    11  12
  HPS3 WILD-TYPE 214 252
[1] "tbl2"
                cls
clus             [,1] [,2]
  HPS3 MUTATED     11   12
  HPS3 WILD-TYPE  214  252
        clus
vv       HPS3 MUTATED HPS3 WILD-TYPE
  FEMALE           11            214
  MALE             12            252
[1] 2 2
[1] FALSE
D125V9, binary
                cls
clus               0   1
  HPS3 MUTATED    19   0
  HPS3 WILD-TYPE 331  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  HPS3 MUTATED     19    0
  HPS3 WILD-TYPE  331   22
     clus
vv    HPS3 MUTATED HPS3 WILD-TYPE
  NO            19            331
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  HPS3 MUTATED                     18                             2
  HPS3 WILD-TYPE                  297                            45
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  HPS3 MUTATED                       3                              0
  HPS3 WILD-TYPE                   103                             10
D125V10, multiclass
                                clus
vv                               HPS3 MUTATED HPS3 WILD-TYPE
  COLON ADENOCARCINOMA                     18            297
  COLON MUCINOUS ADENOCARCINOMA             2             45
  RECTAL ADENOCARCINOMA                     3            103
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  HPS3 MUTATED    18   1   0   0
  HPS3 WILD-TYPE 327   3  31  25
D125V11, multiclass
    clus
vv   HPS3 MUTATED HPS3 WILD-TYPE
  R0           18            327
  R1            1              3
  R2            0             31
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D125V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HPS3 MUTATED                                  0     1
  HPS3 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  HPS3 MUTATED                           1    12
  HPS3 WILD-TYPE                        21   214
D125V13, multiclass
                                  clus
vv                                 HPS3 MUTATED HPS3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                      12            214
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(126) Variable = GLI1 MUTATION ANALYSIS
D126V1, survival
                sevent
clus2              0   1
  GLI1 MUTATED    16   5
  GLI1 WILD-TYPE 362  88
  GLI1 MUTATED GLI1 WILD-TYPE 
            21            450 
  GLI1 MUTATED GLI1 WILD-TYPE 
             5             88 
$`GLI1 MUTATED`
TCGA-A6-4105 TCGA-AA-3555 TCGA-AA-A00N TCGA-AA-A010 TCGA-AU-6004 TCGA-AZ-4315 
       14.53        29.95         4.01        34.98        27.09        58.39 
TCGA-AZ-6600 TCGA-CA-6718 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5916 TCGA-CM-5341 
       12.10        10.06        15.62        51.32        21.14        29.06 
TCGA-CM-5860 TCGA-CM-6161 TCGA-CM-6171 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6628 
       32.02        15.02        14.04        35.31       133.18        79.69 
TCGA-AG-A011 TCGA-DC-5337 TCGA-EI-6507 
       37.02        15.02        19.96 

$`GLI1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 
       16.57        34.65        33.34        32.75        36.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       13.02        24.00        17.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       14.50        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       49.41         6.77       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07        12.20        12.76        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       85.45        49.08         9.99        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5344 
       23.05        20.02        37.02        25.02        13.02        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       22.98        30.08        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       17.03        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 
       14.99        12.99        13.02        15.02        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       13.25         0.53        47.41        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       23.01        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
       78.12         7.17         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       20.55        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  GLI1 MUTATED GLI1 WILD-TYPE 
          4.01           0.00 
  GLI1 MUTATED GLI1 WILD-TYPE 
        133.18         148.01 
  GLI1 MUTATED GLI1 WILD-TYPE 
        27.090         20.085 
[1] "4.0 - 133.2 (27.1)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1"  
D126V2, continuous
D126V3, binary
                cls
clus               0   1
  GLI1 MUTATED    18   3
  GLI1 WILD-TYPE 348 116
[1] "tbl2"
                cls
clus             [,1] [,2]
  GLI1 MUTATED     18    3
  GLI1 WILD-TYPE  348  116
        clus
vv       GLI1 MUTATED GLI1 WILD-TYPE
  COLON            18            348
  RECTUM            3            116
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GLI1 MUTATED         7        0        0         8         2         0
  GLI1 WILD-TYPE      84        1       32       130         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  GLI1 MUTATED           1          1          0          1        1         0
  GLI1 WILD-TYPE        23         10         59         41       47        18
                vv
clus             STAGE IVB
  GLI1 MUTATED           0
  GLI1 WILD-TYPE         1
D126V4, multiclass
            clus
vv           GLI1 MUTATED GLI1 WILD-TYPE
  STAGE I               7             84
  STAGE IA              0              1
  STAGE II              0             32
  STAGE IIA             8            130
  STAGE IIB             2              8
  STAGE IIC             0              1
  STAGE III             1             23
  STAGE IIIA            1             10
  STAGE IIIB            0             59
  STAGE IIIC            1             41
  STAGE IV              1             47
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  GLI1 MUTATED     2   6   9   4
  GLI1 WILD-TYPE  15  86 320  46
D126V5, multiclass
    clus
vv   GLI1 MUTATED GLI1 WILD-TYPE
  T1            2             15
  T2            6             86
  T3            9            320
  T4            4             46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  GLI1 MUTATED    17   3   1
  GLI1 WILD-TYPE 270 110  86
D126V6, multiclass
    clus
vv   GLI1 MUTATED GLI1 WILD-TYPE
  N0           17            270
  N1            3            110
  N2            1             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D126V7, binary
                cls
clus               0   1
  GLI1 MUTATED    19   1
  GLI1 WILD-TYPE 356  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  GLI1 MUTATED     19    1
  GLI1 WILD-TYPE  356   64
   clus
vv  GLI1 MUTATED GLI1 WILD-TYPE
  0           19            356
  1            1             64
[1] 2 2
[1] FALSE
D126V8, binary
                cls
clus               0   1
  GLI1 MUTATED    10  11
  GLI1 WILD-TYPE 215 253
[1] "tbl2"
                cls
clus             [,1] [,2]
  GLI1 MUTATED     10   11
  GLI1 WILD-TYPE  215  253
        clus
vv       GLI1 MUTATED GLI1 WILD-TYPE
  FEMALE           10            215
  MALE             11            253
[1] 2 2
[1] FALSE
D126V9, binary
                cls
clus               0   1
  GLI1 MUTATED    17   0
  GLI1 WILD-TYPE 333  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  GLI1 MUTATED     17    0
  GLI1 WILD-TYPE  333   22
     clus
vv    GLI1 MUTATED GLI1 WILD-TYPE
  NO            17            333
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  GLI1 MUTATED                     14                             4
  GLI1 WILD-TYPE                  301                            43
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  GLI1 MUTATED                       3                              0
  GLI1 WILD-TYPE                   103                             10
D126V10, multiclass
                                clus
vv                               GLI1 MUTATED GLI1 WILD-TYPE
  COLON ADENOCARCINOMA                     14            301
  COLON MUCINOUS ADENOCARCINOMA             4             43
  RECTAL ADENOCARCINOMA                     3            103
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  GLI1 MUTATED    15   0   0   4
  GLI1 WILD-TYPE 330   4  31  21
D126V11, multiclass
    clus
vv   GLI1 MUTATED GLI1 WILD-TYPE
  R0           15            330
  R1            0              4
  R2            0             31
  RX            4             21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D126V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GLI1 MUTATED                                  0     1
  GLI1 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  GLI1 MUTATED                           1    15
  GLI1 WILD-TYPE                        21   211
D126V13, multiclass
                                  clus
vv                                 GLI1 MUTATED GLI1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                      15            211
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(127) Variable = PDCD5 MUTATION ANALYSIS
D127V1, survival
                 sevent
clus2               0   1
  PDCD5 MUTATED    10   1
  PDCD5 WILD-TYPE 368  92
  PDCD5 MUTATED PDCD5 WILD-TYPE 
             11             460 
  PDCD5 MUTATED PDCD5 WILD-TYPE 
              1              92 
$`PDCD5 MUTATED`
TCGA-A6-6651 TCGA-AA-3502 TCGA-AA-3672 TCGA-AD-6895 TCGA-AZ-4315 TCGA-CK-5914 
       21.76        35.01         0.92         0.72        58.39         9.99 
TCGA-D5-6920 TCGA-F4-6855 TCGA-AG-A002 TCGA-DC-6682 TCGA-F5-6464 
        3.68        47.41        20.98         4.01         9.96 

$`PDCD5 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.08        25.18        24.16        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
       54.02         2.01        14.01        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.79         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       51.32        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
       15.58         1.48         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6856 TCGA-G4-6293 
       16.24        33.67        13.25         0.53        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        5.95         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       20.91        18.28        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  PDCD5 MUTATED PDCD5 WILD-TYPE 
           0.72            0.00 
  PDCD5 MUTATED PDCD5 WILD-TYPE 
          58.39          148.01 
  PDCD5 MUTATED PDCD5 WILD-TYPE 
          9.990          20.235 
[1] "0.7 - 58.4 (10.0)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.7"
D127V2, continuous
D127V3, binary
                 cls
clus                0   1
  PDCD5 MUTATED     8   3
  PDCD5 WILD-TYPE 358 116
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PDCD5 MUTATED      8    3
  PDCD5 WILD-TYPE  358  116
        clus
vv       PDCD5 MUTATED PDCD5 WILD-TYPE
  COLON              8             358
  RECTUM             3             116
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PDCD5 MUTATED         2        0        0         4         0         0
  PDCD5 WILD-TYPE      89        1       32       134        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PDCD5 MUTATED           1          0          2          1        0         0
  PDCD5 WILD-TYPE        23         11         57         41       48        18
                 vv
clus              STAGE IVB
  PDCD5 MUTATED           0
  PDCD5 WILD-TYPE         1
D127V4, multiclass
            clus
vv           PDCD5 MUTATED PDCD5 WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              4             134
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             2              57
  STAGE IIIC             1              41
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PDCD5 MUTATED     0   2   8   1
  PDCD5 WILD-TYPE  17  90 321  49
D127V5, multiclass
    clus
vv   PDCD5 MUTATED PDCD5 WILD-TYPE
  T1             0              17
  T2             2              90
  T3             8             321
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  PDCD5 MUTATED     6   4   1
  PDCD5 WILD-TYPE 281 109  86
D127V6, multiclass
    clus
vv   PDCD5 MUTATED PDCD5 WILD-TYPE
  N0             6             281
  N1             4             109
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D127V7, binary
                 cls
clus                0   1
  PDCD5 MUTATED     8   0
  PDCD5 WILD-TYPE 367  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PDCD5 MUTATED      8    0
  PDCD5 WILD-TYPE  367   65
   clus
vv  PDCD5 MUTATED PDCD5 WILD-TYPE
  0             8             367
  1             0              65
[1] 2 2
[1] FALSE
D127V8, binary
                 cls
clus                0   1
  PDCD5 MUTATED     5   6
  PDCD5 WILD-TYPE 220 258
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PDCD5 MUTATED      5    6
  PDCD5 WILD-TYPE  220  258
        clus
vv       PDCD5 MUTATED PDCD5 WILD-TYPE
  FEMALE             5             220
  MALE               6             258
[1] 2 2
[1] FALSE
D127V9, binary
                 cls
clus                0   1
  PDCD5 MUTATED     7   0
  PDCD5 WILD-TYPE 343  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PDCD5 MUTATED      7    0
  PDCD5 WILD-TYPE  343   22
     clus
vv    PDCD5 MUTATED PDCD5 WILD-TYPE
  NO              7             343
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PDCD5 MUTATED                      8                             0
  PDCD5 WILD-TYPE                  307                            47
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PDCD5 MUTATED                       3                              0
  PDCD5 WILD-TYPE                   103                             10
D127V10, multiclass
                                clus
vv                               PDCD5 MUTATED PDCD5 WILD-TYPE
  COLON ADENOCARCINOMA                       8             307
  COLON MUCINOUS ADENOCARCINOMA              0              47
  RECTAL ADENOCARCINOMA                      3             103
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  PDCD5 MUTATED     8   0   0   1
  PDCD5 WILD-TYPE 337   4  31  24
D127V11, multiclass
    clus
vv   PDCD5 MUTATED PDCD5 WILD-TYPE
  R0             8             337
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D127V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PDCD5 MUTATED                                  0     0
  PDCD5 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PDCD5 MUTATED                           0     8
  PDCD5 WILD-TYPE                        22   218
D127V13, multiclass
                                  clus
vv                                 PDCD5 MUTATED PDCD5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        8             218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(128) Variable = BCL9L MUTATION ANALYSIS
D128V1, survival
                 sevent
clus2               0   1
  BCL9L MUTATED    22   3
  BCL9L WILD-TYPE 356  90
  BCL9L MUTATED BCL9L WILD-TYPE 
             25             446 
  BCL9L MUTATED BCL9L WILD-TYPE 
              3              90 
$`BCL9L MUTATED`
TCGA-A6-6781 TCGA-AA-3663 TCGA-AA-3713 TCGA-AA-3833 TCGA-AA-3866 TCGA-AA-3870 
       19.66         6.97        19.04        15.95        17.03        29.98 
TCGA-AA-3972 TCGA-AA-A01R TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6964 TCGA-AU-6004 
       50.99        35.01         0.79         0.72        10.88        27.09 
TCGA-AZ-4315 TCGA-AZ-6601 TCGA-CM-6161 TCGA-D5-6536 TCGA-DM-A1HB TCGA-F4-6856 
       58.39       100.01        15.02        17.85       135.65        35.31 
TCGA-G4-6304 TCGA-AF-2689 TCGA-AF-2693 TCGA-AG-3999 TCGA-AG-A002 TCGA-AG-A02N 
       53.62        39.48        19.10        28.04        20.98        61.97 
TCGA-EI-6507 
       19.96 

$`BCL9L WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3837 
       33.04         0.99        25.02         1.02        17.98        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3875 
       31.07        30.05        53.00        24.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       16.08        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S 
       12.00        31.00        31.00        38.07         1.02         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
       56.55         5.79        22.42        27.42         0.20        14.50 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
       16.31         0.95        33.01        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77        12.10        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 
       18.25         1.32        43.27        15.12         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 
      140.38         7.50        44.32       131.51       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 
       47.41       133.18        74.56        65.85        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       43.04        13.55        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       38.96        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
       32.61         0.49        20.55        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  BCL9L MUTATED BCL9L WILD-TYPE 
           0.72            0.00 
  BCL9L MUTATED BCL9L WILD-TYPE 
         135.65          148.01 
  BCL9L MUTATED BCL9L WILD-TYPE 
         20.980          20.155 
[1] "0.7 - 135.7 (21.0)" "0.0 - 148.0 (20.2)"
[1] "hr=" "2.1"
D128V2, continuous
D128V3, binary
                 cls
clus                0   1
  BCL9L MUTATED    19   5
  BCL9L WILD-TYPE 347 114
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BCL9L MUTATED     19    5
  BCL9L WILD-TYPE  347  114
        clus
vv       BCL9L MUTATED BCL9L WILD-TYPE
  COLON             19             347
  RECTUM             5             114
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  BCL9L MUTATED         6        0        3         4         1         0
  BCL9L WILD-TYPE      85        1       29       134         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  BCL9L MUTATED           1          0          1          2        4         0
  BCL9L WILD-TYPE        23         11         58         40       44        18
                 vv
clus              STAGE IVB
  BCL9L MUTATED           0
  BCL9L WILD-TYPE         1
D128V4, multiclass
            clus
vv           BCL9L MUTATED BCL9L WILD-TYPE
  STAGE I                6              85
  STAGE IA               0               1
  STAGE II               3              29
  STAGE IIA              4             134
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             2              40
  STAGE IV               4              44
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  BCL9L MUTATED     1   6  15   3
  BCL9L WILD-TYPE  16  86 314  47
D128V5, multiclass
    clus
vv   BCL9L MUTATED BCL9L WILD-TYPE
  T1             1              16
  T2             6              86
  T3            15             314
  T4             3              47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  BCL9L MUTATED    16   4   5
  BCL9L WILD-TYPE 271 109  82
D128V6, multiclass
    clus
vv   BCL9L MUTATED BCL9L WILD-TYPE
  N0            16             271
  N1             4             109
  N2             5              82
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D128V7, binary
                 cls
clus                0   1
  BCL9L MUTATED    16   4
  BCL9L WILD-TYPE 359  61
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BCL9L MUTATED     16    4
  BCL9L WILD-TYPE  359   61
   clus
vv  BCL9L MUTATED BCL9L WILD-TYPE
  0            16             359
  1             4              61
[1] 2 2
[1] FALSE
D128V8, binary
                 cls
clus                0   1
  BCL9L MUTATED     8  17
  BCL9L WILD-TYPE 217 247
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BCL9L MUTATED      8   17
  BCL9L WILD-TYPE  217  247
        clus
vv       BCL9L MUTATED BCL9L WILD-TYPE
  FEMALE             8             217
  MALE              17             247
[1] 2 2
[1] FALSE
D128V9, binary
                 cls
clus                0   1
  BCL9L MUTATED    17   2
  BCL9L WILD-TYPE 333  20
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BCL9L MUTATED     17    2
  BCL9L WILD-TYPE  333   20
     clus
vv    BCL9L MUTATED BCL9L WILD-TYPE
  NO             17             333
  YES             2              20
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  BCL9L MUTATED                     15                             3
  BCL9L WILD-TYPE                  300                            44
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  BCL9L MUTATED                       5                              0
  BCL9L WILD-TYPE                   101                             10
D128V10, multiclass
                                clus
vv                               BCL9L MUTATED BCL9L WILD-TYPE
  COLON ADENOCARCINOMA                      15             300
  COLON MUCINOUS ADENOCARCINOMA              3              44
  RECTAL ADENOCARCINOMA                      5             101
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  BCL9L MUTATED    17   0   2   0
  BCL9L WILD-TYPE 328   4  29  25
D128V11, multiclass
    clus
vv   BCL9L MUTATED BCL9L WILD-TYPE
  R0            17             328
  R1             0               4
  R2             2              29
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D128V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  BCL9L MUTATED                                  0     0
  BCL9L WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  BCL9L MUTATED                           0    15
  BCL9L WILD-TYPE                        22   211
D128V13, multiclass
                                  clus
vv                                 BCL9L MUTATED BCL9L WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                       15             211
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(129) Variable = TPM4 MUTATION ANALYSIS
D129V1, survival
                sevent
clus2              0   1
  TPM4 MUTATED     9   0
  TPM4 WILD-TYPE 369  93
  TPM4 MUTATED TPM4 WILD-TYPE 
             9            462 
  TPM4 MUTATED TPM4 WILD-TYPE 
             0             93 
$`TPM4 MUTATED`
TCGA-A6-6653 TCGA-AA-3510 TCGA-AA-3821 TCGA-AA-3864 TCGA-AA-3977 TCGA-AU-6004 
       24.39        63.98         1.02        53.00        25.02        27.09 
TCGA-CA-6715 TCGA-CK-4952 TCGA-AG-A002 
        0.07        15.62        20.98 

$`TPM4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
       25.08        25.18        24.16        21.76        24.69        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 
       35.05        33.04         0.99        25.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        31.07        30.05        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
      148.01        85.45        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  TPM4 MUTATED TPM4 WILD-TYPE 
          0.07           0.00 
  TPM4 MUTATED TPM4 WILD-TYPE 
         63.98         148.01 
  TPM4 MUTATED TPM4 WILD-TYPE 
        24.390         20.085 
[1] "0.1 - 64.0 (24.4)"  "0.0 - 148.0 (20.1)"
[1] "hr="     "9200000"
D129V2, continuous
D129V3, binary
                cls
clus               0   1
  TPM4 MUTATED     8   1
  TPM4 WILD-TYPE 358 118
[1] "tbl2"
                cls
clus             [,1] [,2]
  TPM4 MUTATED      8    1
  TPM4 WILD-TYPE  358  118
        clus
vv       TPM4 MUTATED TPM4 WILD-TYPE
  COLON             8            358
  RECTUM            1            118
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TPM4 MUTATED         4        0        2         0         0         0
  TPM4 WILD-TYPE      87        1       30       138        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TPM4 MUTATED           0          0          1          1        0         0
  TPM4 WILD-TYPE        24         11         58         41       48        18
                vv
clus             STAGE IVB
  TPM4 MUTATED           0
  TPM4 WILD-TYPE         1
D129V4, multiclass
            clus
vv           TPM4 MUTATED TPM4 WILD-TYPE
  STAGE I               4             87
  STAGE IA              0              1
  STAGE II              2             30
  STAGE IIA             0            138
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            1             58
  STAGE IIIC            1             41
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  TPM4 MUTATED     0   5   3   1
  TPM4 WILD-TYPE  17  87 326  49
D129V5, multiclass
    clus
vv   TPM4 MUTATED TPM4 WILD-TYPE
  T1            0             17
  T2            5             87
  T3            3            326
  T4            1             49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  TPM4 MUTATED     7   1   1
  TPM4 WILD-TYPE 280 112  86
D129V6, multiclass
    clus
vv   TPM4 MUTATED TPM4 WILD-TYPE
  N0            7            280
  N1            1            112
  N2            1             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D129V7, binary
                cls
clus               0   1
  TPM4 MUTATED     8   0
  TPM4 WILD-TYPE 367  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  TPM4 MUTATED      8    0
  TPM4 WILD-TYPE  367   65
   clus
vv  TPM4 MUTATED TPM4 WILD-TYPE
  0            8            367
  1            0             65
[1] 2 2
[1] FALSE
D129V8, binary
                cls
clus               0   1
  TPM4 MUTATED     3   6
  TPM4 WILD-TYPE 222 258
[1] "tbl2"
                cls
clus             [,1] [,2]
  TPM4 MUTATED      3    6
  TPM4 WILD-TYPE  222  258
        clus
vv       TPM4 MUTATED TPM4 WILD-TYPE
  FEMALE            3            222
  MALE              6            258
[1] 2 2
[1] FALSE
D129V9, binary
                cls
clus               0   1
  TPM4 MUTATED     6   0
  TPM4 WILD-TYPE 344  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  TPM4 MUTATED      6    0
  TPM4 WILD-TYPE  344   22
     clus
vv    TPM4 MUTATED TPM4 WILD-TYPE
  NO             6            344
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  TPM4 MUTATED                      6                             2
  TPM4 WILD-TYPE                  309                            45
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  TPM4 MUTATED                       1                              0
  TPM4 WILD-TYPE                   105                             10
D129V10, multiclass
                                clus
vv                               TPM4 MUTATED TPM4 WILD-TYPE
  COLON ADENOCARCINOMA                      6            309
  COLON MUCINOUS ADENOCARCINOMA             2             45
  RECTAL ADENOCARCINOMA                     1            105
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  TPM4 MUTATED     5   0   0   2
  TPM4 WILD-TYPE 340   4  31  23
D129V11, multiclass
    clus
vv   TPM4 MUTATED TPM4 WILD-TYPE
  R0            5            340
  R1            0              4
  R2            0             31
  RX            2             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D129V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TPM4 MUTATED                                  0     1
  TPM4 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  TPM4 MUTATED                           0     3
  TPM4 WILD-TYPE                        22   223
D129V13, multiclass
                                  clus
vv                                 TPM4 MUTATED TPM4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       3            223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(130) Variable = CYLD MUTATION ANALYSIS
D130V1, survival
                sevent
clus2              0   1
  CYLD MUTATED    23   4
  CYLD WILD-TYPE 355  89
  CYLD MUTATED CYLD WILD-TYPE 
            27            444 
  CYLD MUTATED CYLD WILD-TYPE 
             4             89 
$`CYLD MUTATED`
TCGA-A6-5657 TCGA-AA-3496 TCGA-AA-3510 TCGA-AA-3660 TCGA-AA-3715 TCGA-AA-3815 
       31.63         1.02        63.98        78.08        19.04        33.04 
TCGA-AA-3973 TCGA-AA-A010 TCGA-AD-6889 TCGA-AZ-4315 TCGA-AZ-5407 TCGA-CA-6717 
       13.05        34.98        56.55        58.39        88.21        12.76 
TCGA-CK-4952 TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-6171 TCGA-CM-6677 TCGA-D5-5539 
       15.62        22.98        32.02        14.04        11.08        19.59 
TCGA-D5-6539 TCGA-F4-6808 TCGA-G4-6303 TCGA-G4-6626 TCGA-AF-2693 TCGA-AG-A002 
       12.49        33.67        65.85        46.75        19.10        20.98 
TCGA-DY-A1DC TCGA-F5-6571 TCGA-G5-6235 
       41.36        31.30        55.76 

$`CYLD WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 
       20.12        19.66        20.28         7.04         3.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
       26.99        19.04        10.06        35.05         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       16.08        50.99        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07        12.20        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
       17.56       148.01        85.45        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5349 
       37.02        25.02        13.02        29.06        22.03        30.08 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       12.99        13.02        15.02        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 
       15.12        17.85         4.80        17.13        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       16.24        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       74.56        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       91.79        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
        5.29       126.44        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6641 
       49.51        28.57        32.19         0.66         0.69        26.43 

  CYLD MUTATED CYLD WILD-TYPE 
          1.02           0.00 
  CYLD MUTATED CYLD WILD-TYPE 
         88.21         148.01 
  CYLD MUTATED CYLD WILD-TYPE 
         31.63          20.02 
[1] "1.0 - 88.2 (31.6)"  "0.0 - 148.0 (20.0)"
[1] "hr=" "1.9"
D130V2, continuous
D130V3, binary
                cls
clus               0   1
  CYLD MUTATED    22   4
  CYLD WILD-TYPE 344 115
[1] "tbl2"
                cls
clus             [,1] [,2]
  CYLD MUTATED     22    4
  CYLD WILD-TYPE  344  115
        clus
vv       CYLD MUTATED CYLD WILD-TYPE
  COLON            22            344
  RECTUM            4            115
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CYLD MUTATED         5        0        4         9         1         0
  CYLD WILD-TYPE      86        1       28       129         9         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CYLD MUTATED           0          2          3          1        2         0
  CYLD WILD-TYPE        24          9         56         41       46        18
                vv
clus             STAGE IVB
  CYLD MUTATED           0
  CYLD WILD-TYPE         1
D130V4, multiclass
            clus
vv           CYLD MUTATED CYLD WILD-TYPE
  STAGE I               5             86
  STAGE IA              0              1
  STAGE II              4             28
  STAGE IIA             9            129
  STAGE IIB             1              9
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            2              9
  STAGE IIIB            3             56
  STAGE IIIC            1             41
  STAGE IV              2             46
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  CYLD MUTATED     2   3  19   3
  CYLD WILD-TYPE  15  89 310  47
D130V5, multiclass
    clus
vv   CYLD MUTATED CYLD WILD-TYPE
  T1            2             15
  T2            3             89
  T3           19            310
  T4            3             47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  CYLD MUTATED    20   6   1
  CYLD WILD-TYPE 267 107  86
D130V6, multiclass
    clus
vv   CYLD MUTATED CYLD WILD-TYPE
  N0           20            267
  N1            6            107
  N2            1             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D130V7, binary
                cls
clus               0   1
  CYLD MUTATED    23   2
  CYLD WILD-TYPE 352  63
[1] "tbl2"
                cls
clus             [,1] [,2]
  CYLD MUTATED     23    2
  CYLD WILD-TYPE  352   63
   clus
vv  CYLD MUTATED CYLD WILD-TYPE
  0           23            352
  1            2             63
[1] 2 2
[1] FALSE
D130V8, binary
                cls
clus               0   1
  CYLD MUTATED    13  14
  CYLD WILD-TYPE 212 250
[1] "tbl2"
                cls
clus             [,1] [,2]
  CYLD MUTATED     13   14
  CYLD WILD-TYPE  212  250
        clus
vv       CYLD MUTATED CYLD WILD-TYPE
  FEMALE           13            212
  MALE             14            250
[1] 2 2
[1] FALSE
D130V9, binary
                cls
clus               0   1
  CYLD MUTATED    23   0
  CYLD WILD-TYPE 327  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  CYLD MUTATED     23    0
  CYLD WILD-TYPE  327   22
     clus
vv    CYLD MUTATED CYLD WILD-TYPE
  NO            23            327
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CYLD MUTATED                     19                             3
  CYLD WILD-TYPE                  296                            44
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CYLD MUTATED                       4                              0
  CYLD WILD-TYPE                   102                             10
D130V10, multiclass
                                clus
vv                               CYLD MUTATED CYLD WILD-TYPE
  COLON ADENOCARCINOMA                     19            296
  COLON MUCINOUS ADENOCARCINOMA             3             44
  RECTAL ADENOCARCINOMA                     4            102
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  CYLD MUTATED    19   1   1   2
  CYLD WILD-TYPE 326   3  30  23
D130V11, multiclass
    clus
vv   CYLD MUTATED CYLD WILD-TYPE
  R0           19            326
  R1            1              3
  R2            1             30
  RX            2             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D130V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CYLD MUTATED                                  0     2
  CYLD WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  CYLD MUTATED                           1    16
  CYLD WILD-TYPE                        21   210
D130V13, multiclass
                                  clus
vv                                 CYLD MUTATED CYLD WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              9
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                      16            210
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(131) Variable = AMOT MUTATION ANALYSIS
D131V1, survival
                sevent
clus2              0   1
  AMOT MUTATED    10   4
  AMOT WILD-TYPE 368  89
  AMOT MUTATED AMOT WILD-TYPE 
            14            457 
  AMOT MUTATED AMOT WILD-TYPE 
             4             89 
$`AMOT MUTATED`
TCGA-A6-2676 TCGA-A6-6781 TCGA-AA-3492 TCGA-AA-3713 TCGA-AA-A00R TCGA-AA-A01P 
       42.90        19.66         3.02        19.04         0.99        38.07 
TCGA-AY-6197 TCGA-AZ-4315 TCGA-CA-6717 TCGA-CM-6162 TCGA-DM-A1D8 TCGA-AG-3611 
       21.44        58.39        12.76        12.00        12.59        13.94 
TCGA-AG-A02N TCGA-DC-6682 
       61.97         4.01 

$`AMOT WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.12        20.28         7.04         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       85.05        26.99        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
       42.02        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01Q 
       10.98        32.02        12.00        31.00        31.00         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
       16.31         0.95        33.01        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.20        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D9 
       38.20       130.65        92.75        49.91        13.32       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       19.99        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       10.98        19.99         5.95         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  AMOT MUTATED AMOT WILD-TYPE 
          0.99           0.00 
  AMOT MUTATED AMOT WILD-TYPE 
         61.97         148.01 
  AMOT MUTATED AMOT WILD-TYPE 
         16.49          20.55 
[1] "1.0 - 62.0 (16.5)"  "0.0 - 148.0 (20.6)"
[1] "hr=" "1.6"
D131V2, continuous
D131V3, binary
                cls
clus               0   1
  AMOT MUTATED    13   3
  AMOT WILD-TYPE 353 116
[1] "tbl2"
                cls
clus             [,1] [,2]
  AMOT MUTATED     13    3
  AMOT WILD-TYPE  353  116
        clus
vv       AMOT MUTATED AMOT WILD-TYPE
  COLON            13            353
  RECTUM            3            116
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  AMOT MUTATED         2        0        2         5         2         0
  AMOT WILD-TYPE      89        1       30       133         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AMOT MUTATED           1          0          1          1        1         0
  AMOT WILD-TYPE        23         11         58         41       47        18
                vv
clus             STAGE IVB
  AMOT MUTATED           0
  AMOT WILD-TYPE         1
D131V4, multiclass
            clus
vv           AMOT MUTATED AMOT WILD-TYPE
  STAGE I               2             89
  STAGE IA              0              1
  STAGE II              2             30
  STAGE IIA             5            133
  STAGE IIB             2              8
  STAGE IIC             0              1
  STAGE III             1             23
  STAGE IIIA            0             11
  STAGE IIIB            1             58
  STAGE IIIC            1             41
  STAGE IV              1             47
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  AMOT MUTATED     0   2  11   3
  AMOT WILD-TYPE  17  90 318  47
D131V5, multiclass
    clus
vv   AMOT MUTATED AMOT WILD-TYPE
  T1            0             17
  T2            2             90
  T3           11            318
  T4            3             47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  AMOT MUTATED    12   4   0
  AMOT WILD-TYPE 275 109  87
D131V6, multiclass
    clus
vv   AMOT MUTATED AMOT WILD-TYPE
  N0           12            275
  N1            4            109
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D131V7, binary
                cls
clus               0   1
  AMOT MUTATED    10   1
  AMOT WILD-TYPE 365  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  AMOT MUTATED     10    1
  AMOT WILD-TYPE  365   64
   clus
vv  AMOT MUTATED AMOT WILD-TYPE
  0           10            365
  1            1             64
[1] 2 2
[1] FALSE
D131V8, binary
                cls
clus               0   1
  AMOT MUTATED     7   9
  AMOT WILD-TYPE 218 255
[1] "tbl2"
                cls
clus             [,1] [,2]
  AMOT MUTATED      7    9
  AMOT WILD-TYPE  218  255
        clus
vv       AMOT MUTATED AMOT WILD-TYPE
  FEMALE            7            218
  MALE              9            255
[1] 2 2
[1] FALSE
D131V9, binary
                cls
clus               0   1
  AMOT MUTATED     9   1
  AMOT WILD-TYPE 341  21
[1] "tbl2"
                cls
clus             [,1] [,2]
  AMOT MUTATED      9    1
  AMOT WILD-TYPE  341   21
     clus
vv    AMOT MUTATED AMOT WILD-TYPE
  NO             9            341
  YES            1             21
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  AMOT MUTATED                     10                             3
  AMOT WILD-TYPE                  305                            44
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  AMOT MUTATED                       3                              0
  AMOT WILD-TYPE                   103                             10
D131V10, multiclass
                                clus
vv                               AMOT MUTATED AMOT WILD-TYPE
  COLON ADENOCARCINOMA                     10            305
  COLON MUCINOUS ADENOCARCINOMA             3             44
  RECTAL ADENOCARCINOMA                     3            103
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  AMOT MUTATED    11   0   1   3
  AMOT WILD-TYPE 334   4  30  22
D131V11, multiclass
    clus
vv   AMOT MUTATED AMOT WILD-TYPE
  R0           11            334
  R1            0              4
  R2            1             30
  RX            3             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D131V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMOT MUTATED                                  0     1
  AMOT WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  AMOT MUTATED                           0     9
  AMOT WILD-TYPE                        22   217
D131V13, multiclass
                                  clus
vv                                 AMOT MUTATED AMOT WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       9            217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(132) Variable = GNPAT MUTATION ANALYSIS
D132V1, survival
                 sevent
clus2               0   1
  GNPAT MUTATED    13   6
  GNPAT WILD-TYPE 365  87
  GNPAT MUTATED GNPAT WILD-TYPE 
             19             452 
  GNPAT MUTATED GNPAT WILD-TYPE 
              6              87 
$`GNPAT MUTATED`
TCGA-A6-5665 TCGA-A6-6781 TCGA-AA-3710 TCGA-AY-6197 TCGA-AZ-6598 TCGA-CA-5797 
       22.06        19.66        26.99        21.44        49.41         3.29 
TCGA-CA-6717 TCGA-CK-5914 TCGA-CK-5916 TCGA-CM-6163 TCGA-CM-6675 TCGA-D5-5541 
       12.76         9.99        21.14         2.96        13.05        55.92 
TCGA-DM-A1D4 TCGA-F4-6460 TCGA-F4-6570 TCGA-G4-6315 TCGA-G4-6321 TCGA-AG-A02N 
       92.75        31.96         6.18        61.91        22.09        61.97 
TCGA-DY-A1DD 
       57.24 

$`GNPAT WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        88.21         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.25         0.07        12.20        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-6747 
      148.01        85.45        15.62        49.08        51.32        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
       12.00        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6676 
       13.02        15.02        14.04        11.01        12.95        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       19.59        56.09        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6569 
       35.97        60.79       117.07        98.24         8.61        35.74 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       36.00        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       38.96        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
        5.29       126.44        41.36        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  GNPAT MUTATED GNPAT WILD-TYPE 
           2.96            0.00 
  GNPAT MUTATED GNPAT WILD-TYPE 
          92.75          148.01 
  GNPAT MUTATED GNPAT WILD-TYPE 
         22.060          20.035 
[1] "3.0 - 92.8 (22.1)"  "0.0 - 148.0 (20.0)"
[1] "hr=" "1.3"
D132V2, continuous
D132V3, binary
                 cls
clus                0   1
  GNPAT MUTATED    17   2
  GNPAT WILD-TYPE 349 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GNPAT MUTATED     17    2
  GNPAT WILD-TYPE  349  117
        clus
vv       GNPAT MUTATED GNPAT WILD-TYPE
  COLON             17             349
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GNPAT MUTATED         2        0        2         7         0         0
  GNPAT WILD-TYPE      89        1       30       131        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  GNPAT MUTATED           1          0          4          1        1         0
  GNPAT WILD-TYPE        23         11         55         41       47        18
                 vv
clus              STAGE IVB
  GNPAT MUTATED           1
  GNPAT WILD-TYPE         0
D132V4, multiclass
            clus
vv           GNPAT MUTATED GNPAT WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA              7             131
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             4              55
  STAGE IIIC             1              41
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              1               0
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  GNPAT MUTATED     2   1  15   1
  GNPAT WILD-TYPE  15  91 314  49
D132V5, multiclass
    clus
vv   GNPAT MUTATED GNPAT WILD-TYPE
  T1             2              15
  T2             1              91
  T3            15             314
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  GNPAT MUTATED    11   7   1
  GNPAT WILD-TYPE 276 106  86
D132V6, multiclass
    clus
vv   GNPAT MUTATED GNPAT WILD-TYPE
  N0            11             276
  N1             7             106
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D132V7, binary
                 cls
clus                0   1
  GNPAT MUTATED    12   2
  GNPAT WILD-TYPE 363  63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GNPAT MUTATED     12    2
  GNPAT WILD-TYPE  363   63
   clus
vv  GNPAT MUTATED GNPAT WILD-TYPE
  0            12             363
  1             2              63
[1] 2 2
[1] FALSE
D132V8, binary
                 cls
clus                0   1
  GNPAT MUTATED     8  11
  GNPAT WILD-TYPE 217 253
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GNPAT MUTATED      8   11
  GNPAT WILD-TYPE  217  253
        clus
vv       GNPAT MUTATED GNPAT WILD-TYPE
  FEMALE             8             217
  MALE              11             253
[1] 2 2
[1] FALSE
D132V9, binary
                 cls
clus                0   1
  GNPAT MUTATED    15   0
  GNPAT WILD-TYPE 335  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GNPAT MUTATED     15    0
  GNPAT WILD-TYPE  335   22
     clus
vv    GNPAT MUTATED GNPAT WILD-TYPE
  NO             15             335
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  GNPAT MUTATED                     15                             2
  GNPAT WILD-TYPE                  300                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  GNPAT MUTATED                       2                              0
  GNPAT WILD-TYPE                   104                             10
D132V10, multiclass
                                clus
vv                               GNPAT MUTATED GNPAT WILD-TYPE
  COLON ADENOCARCINOMA                      15             300
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  GNPAT MUTATED    13   0   0   3
  GNPAT WILD-TYPE 332   4  31  22
D132V11, multiclass
    clus
vv   GNPAT MUTATED GNPAT WILD-TYPE
  R0            13             332
  R1             0               4
  R2             0              31
  RX             3              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D132V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GNPAT MUTATED                                  0     2
  GNPAT WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  GNPAT MUTATED                           1    14
  GNPAT WILD-TYPE                        21   212
D132V13, multiclass
                                  clus
vv                                 GNPAT MUTATED GNPAT WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               9
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                       14             212
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(133) Variable = PRKAA2 MUTATION ANALYSIS
D133V1, survival
                  sevent
clus2                0   1
  PRKAA2 MUTATED    10   5
  PRKAA2 WILD-TYPE 368  88
  PRKAA2 MUTATED PRKAA2 WILD-TYPE 
              15              456 
  PRKAA2 MUTATED PRKAA2 WILD-TYPE 
               5               88 
$`PRKAA2 MUTATED`
TCGA-A6-6780 TCGA-AA-3492 TCGA-AA-3837 TCGA-AA-3858 TCGA-AA-A00A TCGA-AA-A00N 
       20.12         3.02        38.99        31.07        38.04         4.01 
TCGA-AZ-4315 TCGA-AZ-6598 TCGA-CA-6717 TCGA-CM-6674 TCGA-F4-6570 TCGA-AG-A002 
       58.39        49.41        12.76        12.95         6.18        20.98 
TCGA-AG-A025 TCGA-DY-A1DF TCGA-F5-6465 
       49.97        24.13        49.51 

$`PRKAA2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 
       23.87        19.66        20.28         7.04         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       15.95        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
        7.96        27.02        13.94        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
       16.31         0.95        33.01        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 
        5.13       106.75        22.36        62.79        88.21         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.20        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6675 
       12.99        13.02        15.02        14.04        11.01        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 
       98.24         8.61        31.96        35.74        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       70.03        64.01        10.98         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
      126.44        41.36        57.24        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6571 
       20.55        19.96        20.91        18.28         9.96        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  PRKAA2 MUTATED PRKAA2 WILD-TYPE 
            3.02             0.00 
  PRKAA2 MUTATED PRKAA2 WILD-TYPE 
           58.39           148.01 
  PRKAA2 MUTATED PRKAA2 WILD-TYPE 
          24.130           20.035 
[1] "3.0 - 58.4 (24.1)"  "0.0 - 148.0 (20.0)"
[1] "hr=" "1.5"
D133V2, continuous
D133V3, binary
                  cls
clus                 0   1
  PRKAA2 MUTATED    12   4
  PRKAA2 WILD-TYPE 354 115
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PRKAA2 MUTATED     12    4
  PRKAA2 WILD-TYPE  354  115
        clus
vv       PRKAA2 MUTATED PRKAA2 WILD-TYPE
  COLON              12              354
  RECTUM              4              115
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PRKAA2 MUTATED         3        0        2         9         1         0
  PRKAA2 WILD-TYPE      88        1       30       129         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PRKAA2 MUTATED           0          0          0          1        0
  PRKAA2 WILD-TYPE        24         11         59         41       48
                  vv
clus               STAGE IVA STAGE IVB
  PRKAA2 MUTATED           0         0
  PRKAA2 WILD-TYPE        18         1
D133V4, multiclass
            clus
vv           PRKAA2 MUTATED PRKAA2 WILD-TYPE
  STAGE I                 3               88
  STAGE IA                0                1
  STAGE II                2               30
  STAGE IIA               9              129
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              0               59
  STAGE IIIC              1               41
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  PRKAA2 MUTATED     1   2  12   1
  PRKAA2 WILD-TYPE  16  90 317  49
D133V5, multiclass
    clus
vv   PRKAA2 MUTATED PRKAA2 WILD-TYPE
  T1              1               16
  T2              2               90
  T3             12              317
  T4              1               49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  PRKAA2 MUTATED    15   0   1
  PRKAA2 WILD-TYPE 272 113  86
D133V6, multiclass
    clus
vv   PRKAA2 MUTATED PRKAA2 WILD-TYPE
  N0             15              272
  N1              0              113
  N2              1               86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D133V7, binary
                  cls
clus                 0   1
  PRKAA2 MUTATED    14   0
  PRKAA2 WILD-TYPE 361  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PRKAA2 MUTATED     14    0
  PRKAA2 WILD-TYPE  361   65
   clus
vv  PRKAA2 MUTATED PRKAA2 WILD-TYPE
  0             14              361
  1              0               65
[1] 2 2
[1] FALSE
D133V8, binary
                  cls
clus                 0   1
  PRKAA2 MUTATED     7   9
  PRKAA2 WILD-TYPE 218 255
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PRKAA2 MUTATED      7    9
  PRKAA2 WILD-TYPE  218  255
        clus
vv       PRKAA2 MUTATED PRKAA2 WILD-TYPE
  FEMALE              7              218
  MALE                9              255
[1] 2 2
[1] FALSE
D133V9, binary
                  cls
clus                 0   1
  PRKAA2 MUTATED    12   0
  PRKAA2 WILD-TYPE 338  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PRKAA2 MUTATED     12    0
  PRKAA2 WILD-TYPE  338   22
     clus
vv    PRKAA2 MUTATED PRKAA2 WILD-TYPE
  NO              12              338
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PRKAA2 MUTATED                      8                             4
  PRKAA2 WILD-TYPE                  307                            43
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PRKAA2 MUTATED                       4                              0
  PRKAA2 WILD-TYPE                   102                             10
D133V10, multiclass
                                clus
vv                               PRKAA2 MUTATED PRKAA2 WILD-TYPE
  COLON ADENOCARCINOMA                        8              307
  COLON MUCINOUS ADENOCARCINOMA               4               43
  RECTAL ADENOCARCINOMA                       4              102
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  PRKAA2 MUTATED    12   0   0   1
  PRKAA2 WILD-TYPE 333   4  31  24
D133V11, multiclass
    clus
vv   PRKAA2 MUTATED PRKAA2 WILD-TYPE
  R0             12              333
  R1              0                4
  R2              0               31
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D133V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PRKAA2 MUTATED                                  0     1
  PRKAA2 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  PRKAA2 MUTATED                           0     7
  PRKAA2 WILD-TYPE                        22   219
D133V13, multiclass
                                  clus
vv                                 PRKAA2 MUTATED PRKAA2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         7              219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(134) Variable = TMEM126A MUTATION ANALYSIS
D134V1, survival
                    sevent
clus2                  0   1
  TMEM126A MUTATED     4   3
  TMEM126A WILD-TYPE 374  90
  TMEM126A MUTATED TMEM126A WILD-TYPE 
                 7                464 
  TMEM126A MUTATED TMEM126A WILD-TYPE 
                 3                 90 
$`TMEM126A MUTATED`
TCGA-AA-3662 TCGA-AD-6895 TCGA-AZ-6603 TCGA-AZ-6608 TCGA-DM-A1HA TCGA-DM-A28G 
        6.05         0.72        29.56         1.61       131.51        60.79 
TCGA-DM-A28K 
       98.24 

$`TMEM126A WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       15.52        56.55         0.79         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 
       12.10       100.01         5.23        11.74         3.19        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
      140.38         7.50        44.32       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28H TCGA-F4-6459 TCGA-F4-6460 
       81.37       119.93        35.97       117.07         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  TMEM126A MUTATED TMEM126A WILD-TYPE 
              0.72               0.00 
  TMEM126A MUTATED TMEM126A WILD-TYPE 
            131.51             148.01 
  TMEM126A MUTATED TMEM126A WILD-TYPE 
            29.560             20.155 
[1] "0.7 - 131.5 (29.6)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.4"
D134V2, continuous
D134V3, binary
                    cls
clus                   0   1
  TMEM126A MUTATED     7   0
  TMEM126A WILD-TYPE 359 119
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  TMEM126A MUTATED      7    0
  TMEM126A WILD-TYPE  359  119
        clus
vv       TMEM126A MUTATED TMEM126A WILD-TYPE
  COLON                 7                359
  RECTUM                0                119
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TMEM126A MUTATED         0        0        0         2         0         0
  TMEM126A WILD-TYPE      91        1       32       136        10         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TMEM126A MUTATED           0          1          0          1        1
  TMEM126A WILD-TYPE        24         10         59         41       47
                    vv
clus                 STAGE IVA STAGE IVB
  TMEM126A MUTATED           0         0
  TMEM126A WILD-TYPE        18         1
D134V4, multiclass
            clus
vv           TMEM126A MUTATED TMEM126A WILD-TYPE
  STAGE I                   0                 91
  STAGE IA                  0                  1
  STAGE II                  0                 32
  STAGE IIA                 2                136
  STAGE IIB                 0                 10
  STAGE IIC                 0                  1
  STAGE III                 0                 24
  STAGE IIIA                1                 10
  STAGE IIIB                0                 59
  STAGE IIIC                1                 41
  STAGE IV                  1                 47
  STAGE IVA                 0                 18
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  TMEM126A MUTATED     0   2   4   1
  TMEM126A WILD-TYPE  17  90 325  49
D134V5, multiclass
    clus
vv   TMEM126A MUTATED TMEM126A WILD-TYPE
  T1                0                 17
  T2                2                 90
  T3                4                325
  T4                1                 49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  TMEM126A MUTATED     2   3   2
  TMEM126A WILD-TYPE 285 110  85
D134V6, multiclass
    clus
vv   TMEM126A MUTATED TMEM126A WILD-TYPE
  N0                2                285
  N1                3                110
  N2                2                 85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D134V7, binary
                    cls
clus                   0   1
  TMEM126A MUTATED     4   1
  TMEM126A WILD-TYPE 371  64
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  TMEM126A MUTATED      4    1
  TMEM126A WILD-TYPE  371   64
   clus
vv  TMEM126A MUTATED TMEM126A WILD-TYPE
  0                4                371
  1                1                 64
[1] 2 2
[1] FALSE
D134V8, binary
                    cls
clus                   0   1
  TMEM126A MUTATED     3   4
  TMEM126A WILD-TYPE 222 260
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  TMEM126A MUTATED      3    4
  TMEM126A WILD-TYPE  222  260
        clus
vv       TMEM126A MUTATED TMEM126A WILD-TYPE
  FEMALE                3                222
  MALE                  4                260
[1] 2 2
[1] FALSE
D134V9, binary
                    cls
clus                   0   1
  TMEM126A MUTATED     3   0
  TMEM126A WILD-TYPE 347  22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  TMEM126A MUTATED      3    0
  TMEM126A WILD-TYPE  347   22
     clus
vv    TMEM126A MUTATED TMEM126A WILD-TYPE
  NO                 3                347
  YES                0                 22
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  TMEM126A MUTATED                      6                             1
  TMEM126A WILD-TYPE                  309                            46
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  TMEM126A MUTATED                       0                              0
  TMEM126A WILD-TYPE                   106                             10
D134V10, multiclass
                                clus
vv                               TMEM126A MUTATED TMEM126A WILD-TYPE
  COLON ADENOCARCINOMA                          6                309
  COLON MUCINOUS ADENOCARCINOMA                 1                 46
  RECTAL ADENOCARCINOMA                         0                106
  RECTAL MUCINOUS ADENOCARCINOMA                0                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  TMEM126A MUTATED     0   0   1   0
  TMEM126A WILD-TYPE 345   4  30  25
D134V11, multiclass
[1] "Remove cluster labels:" "TMEM126A MUTATED"      
clus
  TMEM126A MUTATED TMEM126A WILD-TYPE 
                 1                404 
        TCGA-A6-2671         TCGA-A6-2672         TCGA-A6-2674 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-A6-2676         TCGA-A6-2677         TCGA-A6-2678 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-A6-2683         TCGA-A6-3807         TCGA-A6-3808 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-A6-3809         TCGA-A6-3810         TCGA-A6-5657 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-A6-5659         TCGA-A6-5661         TCGA-A6-5665 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-A6-6781         TCGA-AA-3489         TCGA-AA-3492 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AA-3496         TCGA-AA-3502         TCGA-AA-3510 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AA-3511         TCGA-AA-3514         TCGA-AA-3517 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AA-3518         TCGA-AA-3519         TCGA-AA-3520 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AA-3521         TCGA-AA-3522         TCGA-AA-3524 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AA-3525         TCGA-AA-3526         TCGA-AA-3527 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AA-3529         TCGA-AA-3530         TCGA-AA-3531 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AA-3532         TCGA-AA-3534         TCGA-AA-3538 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AA-3542         TCGA-AA-3543         TCGA-AA-3544 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AA-3548         TCGA-AA-3549         TCGA-AA-3552 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AA-3553         TCGA-AA-3554         TCGA-AA-3555 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AA-3556         TCGA-AA-3558         TCGA-AA-3560 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AA-3561         TCGA-AA-3562         TCGA-AA-3655 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AA-3660         TCGA-AA-3663         TCGA-AA-3664 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AA-3666         TCGA-AA-3667         TCGA-AA-3672 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AA-3673         TCGA-AA-3678         TCGA-AA-3679 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AA-3680         TCGA-AA-3681         TCGA-AA-3684 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AA-3685         TCGA-AA-3688         TCGA-AA-3692 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AA-3693         TCGA-AA-3695         TCGA-AA-3696 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AA-3697         TCGA-AA-3710         TCGA-AA-3712 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AA-3713         TCGA-AA-3715         TCGA-AA-3811 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AA-3812         TCGA-AA-3814         TCGA-AA-3815 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AA-3818         TCGA-AA-3819         TCGA-AA-3821 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AA-3831         TCGA-AA-3833         TCGA-AA-3837 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AA-3842         TCGA-AA-3844         TCGA-AA-3845 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AA-3846         TCGA-AA-3848         TCGA-AA-3850 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AA-3851         TCGA-AA-3852         TCGA-AA-3854 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AA-3855         TCGA-AA-3856         TCGA-AA-3858 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AA-3860         TCGA-AA-3861         TCGA-AA-3864 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AA-3866         TCGA-AA-3867         TCGA-AA-3869 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AA-3870         TCGA-AA-3872         TCGA-AA-3875 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AA-3877         TCGA-AA-3930         TCGA-AA-3939 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AA-3941         TCGA-AA-3947         TCGA-AA-3949 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AA-3950         TCGA-AA-3952         TCGA-AA-3955 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AA-3956         TCGA-AA-3968         TCGA-AA-3971 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AA-3972         TCGA-AA-3973         TCGA-AA-3975 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AA-3976         TCGA-AA-3979         TCGA-AA-3984 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AA-3986         TCGA-AA-3989         TCGA-AA-3994 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AA-A004         TCGA-AA-A00A         TCGA-AA-A00D 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AA-A00E         TCGA-AA-A00F         TCGA-AA-A00J 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AA-A00K         TCGA-AA-A00L         TCGA-AA-A00N 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AA-A00O         TCGA-AA-A00Q         TCGA-AA-A00R 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AA-A00U         TCGA-AA-A00W         TCGA-AA-A00Z 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AA-A010         TCGA-AA-A017         TCGA-AA-A01D 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AA-A01F         TCGA-AA-A01G         TCGA-AA-A01I 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AA-A01K         TCGA-AA-A01P         TCGA-AA-A01Q 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AA-A01R         TCGA-AA-A01S         TCGA-AA-A01T 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AA-A01V         TCGA-AA-A01X         TCGA-AA-A01Z 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AA-A022         TCGA-AA-A024         TCGA-AA-A029 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AA-A02F         TCGA-AA-A02H         TCGA-AA-A02J 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AA-A02K         TCGA-AA-A02O         TCGA-AA-A02W 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AA-A02Y         TCGA-AA-A03F         TCGA-AA-A03J 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AD-5900         TCGA-AD-6548         TCGA-AD-6888 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AU-3779         TCGA-AU-6004         TCGA-AY-4070 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AY-4071         TCGA-AY-5543         TCGA-AY-6196 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AY-6197         TCGA-AY-6386         TCGA-AZ-4315 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AZ-4681         TCGA-AZ-4682         TCGA-CA-5254 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-CA-5255         TCGA-CA-5796         TCGA-CA-5797 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-CA-6715         TCGA-CA-6716         TCGA-CA-6717 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-CA-6718         TCGA-CA-6719         TCGA-CK-4947 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-CK-4948         TCGA-CK-4950         TCGA-CK-4952 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-CK-5912         TCGA-CK-5913         TCGA-CK-5914 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-CK-5915         TCGA-CK-5916         TCGA-CK-6746 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-CK-6747         TCGA-CK-6748         TCGA-CK-6751 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-CM-4743         TCGA-CM-4744         TCGA-CM-4746 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-CM-4747         TCGA-CM-4752         TCGA-CM-5341 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-CM-5344         TCGA-CM-5348         TCGA-CM-5349 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-CM-5860         TCGA-CM-5861         TCGA-CM-5862 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-CM-5863         TCGA-CM-5864         TCGA-CM-5868 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-CM-6161         TCGA-CM-6162         TCGA-CM-6163 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-CM-6164         TCGA-CM-6165         TCGA-CM-6166 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-CM-6167         TCGA-CM-6168         TCGA-CM-6169 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-CM-6170         TCGA-CM-6171         TCGA-CM-6172 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-CM-6674         TCGA-CM-6675         TCGA-CM-6676 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-CM-6677         TCGA-CM-6678         TCGA-CM-6679 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-CM-6680         TCGA-D5-5537         TCGA-D5-5538 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-D5-5539         TCGA-D5-5540         TCGA-D5-5541 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-D5-6529         TCGA-D5-6532         TCGA-D5-6533 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-D5-6534         TCGA-D5-6535         TCGA-D5-6536 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-D5-6537         TCGA-D5-6538         TCGA-D5-6539 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-D5-6540         TCGA-D5-6541         TCGA-D5-6898 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-D5-6920         TCGA-D5-6922         TCGA-D5-6923 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-D5-6924         TCGA-D5-6926         TCGA-D5-6927 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-D5-6928         TCGA-D5-6929         TCGA-D5-6930 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-D5-6931         TCGA-D5-6932         TCGA-D5-7000 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-F4-6459         TCGA-F4-6460         TCGA-F4-6569 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-F4-6570         TCGA-F4-6703         TCGA-F4-6704 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-F4-6805         TCGA-F4-6806         TCGA-F4-6807 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-F4-6808         TCGA-F4-6809         TCGA-F4-6854 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-F4-6855         TCGA-F4-6856         TCGA-G4-6293 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-G4-6299         TCGA-G4-6303         TCGA-G4-6304 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-G4-6306         TCGA-G4-6307         TCGA-G4-6309 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-G4-6310         TCGA-G4-6315         TCGA-G4-6317 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-G4-6321         TCGA-G4-6323         TCGA-G4-6586 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-G4-6588         TCGA-G4-6625         TCGA-G4-6626 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-G4-6628         TCGA-AF-2687         TCGA-AF-2689 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-3400 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AF-3913         TCGA-AF-4110         TCGA-AF-5654 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AF-6655         TCGA-AG-3574         TCGA-AG-3575 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AG-3578         TCGA-AG-3580         TCGA-AG-3581 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3584 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3593 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AG-3594         TCGA-AG-3598         TCGA-AG-3599 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AG-3600         TCGA-AG-3601         TCGA-AG-3602 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3608         TCGA-AG-3609 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AG-3611         TCGA-AG-3612         TCGA-AG-3726 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AG-3727         TCGA-AG-3731         TCGA-AG-3732 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AG-3742         TCGA-AG-3878         TCGA-AG-3882 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AG-3883         TCGA-AG-3885         TCGA-AG-3887 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AG-3890         TCGA-AG-3892         TCGA-AG-3893 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AG-3894         TCGA-AG-3896         TCGA-AG-3898 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AG-3901         TCGA-AG-3902         TCGA-AG-3909 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AG-3999         TCGA-AG-4001         TCGA-AG-4005 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AG-4007         TCGA-AG-4008         TCGA-AG-4015 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AG-A002         TCGA-AG-A008         TCGA-AG-A00C 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AG-A00H         TCGA-AG-A00Y         TCGA-AG-A011 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AG-A014         TCGA-AG-A015         TCGA-AG-A016 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01W         TCGA-AG-A01Y 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AG-A020         TCGA-AG-A025         TCGA-AG-A026 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AG-A02G         TCGA-AG-A02N         TCGA-AG-A02X 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AG-A032         TCGA-AG-A036         TCGA-AH-6549 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-AH-6643         TCGA-CL-5917         TCGA-CL-5918 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-DC-5337         TCGA-DC-5869         TCGA-DC-6155 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-DC-6157         TCGA-DC-6158         TCGA-DC-6160 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-DC-6681         TCGA-DC-6682         TCGA-DC-6683 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-DT-5265         TCGA-EF-5830         TCGA-EI-6506 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6510 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-F5-6464         TCGA-F5-6465         TCGA-F5-6571 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6812         TCGA-F5-6813 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
        TCGA-G5-6235         TCGA-G5-6641 
"TMEM126A WILD-TYPE" "TMEM126A WILD-TYPE" 
D134V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TMEM126A MUTATED                                  0     0
  TMEM126A WILD-TYPE                                1    11
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  TMEM126A MUTATED                           0     6
  TMEM126A WILD-TYPE                        22   220
D134V13, multiclass
                                  clus
vv                                 TMEM126A MUTATED TMEM126A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 11
  BLACK OR AFRICAN AMERICAN                       0                 22
  WHITE                                           6                220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(135) Variable = OSBPL11 MUTATION ANALYSIS
D135V1, survival
                   sevent
clus2                 0   1
  OSBPL11 MUTATED    10   8
  OSBPL11 WILD-TYPE 368  85
  OSBPL11 MUTATED OSBPL11 WILD-TYPE 
               18               453 
  OSBPL11 MUTATED OSBPL11 WILD-TYPE 
                8                85 
$`OSBPL11 MUTATED`
TCGA-AA-3554 TCGA-AA-3662 TCGA-AA-3715 TCGA-AA-3966 TCGA-AA-A00A TCGA-AA-A00N 
       17.95         6.05        19.04         2.01        38.04         4.01 
TCGA-AD-6964 TCGA-CA-6717 TCGA-D5-5537 TCGA-DM-A0XD TCGA-F4-6570 TCGA-G4-6293 
       10.88        12.76        45.40        24.43         6.18       133.18 
TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6626 TCGA-AG-A002 TCGA-EI-6508 TCGA-F5-6813 
       65.85        44.68        46.75        20.98        20.91         0.69 

$`OSBPL11 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       21.01        13.02        24.00        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       19.99        13.94        19.99        61.02        78.08         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
       34.03        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
        7.96        27.02        13.94        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07        12.20        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       12.03        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 
       98.24         8.61        31.96        35.74        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 
       47.41        35.31        74.56        53.62        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       26.17        91.79        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-G5-6235 TCGA-G5-6641 
        0.66        55.76        26.43 

  OSBPL11 MUTATED OSBPL11 WILD-TYPE 
             0.69              0.00 
  OSBPL11 MUTATED OSBPL11 WILD-TYPE 
           133.18            148.01 
  OSBPL11 MUTATED OSBPL11 WILD-TYPE 
           19.975            20.190 
[1] "0.7 - 133.2 (20.0)" "0.0 - 148.0 (20.2)"
[1] "hr=" "2.2"
D135V2, continuous
D135V3, binary
                   cls
clus                  0   1
  OSBPL11 MUTATED    16   3
  OSBPL11 WILD-TYPE 350 116
[1] "tbl2"
                   cls
clus                [,1] [,2]
  OSBPL11 MUTATED     16    3
  OSBPL11 WILD-TYPE  350  116
        clus
vv       OSBPL11 MUTATED OSBPL11 WILD-TYPE
  COLON               16               350
  RECTUM               3               116
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  OSBPL11 MUTATED         1        0        1         9         1         0
  OSBPL11 WILD-TYPE      90        1       31       129         9         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  OSBPL11 MUTATED           1          0          1          2        2
  OSBPL11 WILD-TYPE        23         11         58         40       46
                   vv
clus                STAGE IVA STAGE IVB
  OSBPL11 MUTATED           0         0
  OSBPL11 WILD-TYPE        18         1
D135V4, multiclass
            clus
vv           OSBPL11 MUTATED OSBPL11 WILD-TYPE
  STAGE I                  1                90
  STAGE IA                 0                 1
  STAGE II                 1                31
  STAGE IIA                9               129
  STAGE IIB                1                 9
  STAGE IIC                0                 1
  STAGE III                1                23
  STAGE IIIA               0                11
  STAGE IIIB               1                58
  STAGE IIIC               2                40
  STAGE IV                 2                46
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  OSBPL11 MUTATED     0   2  13   4
  OSBPL11 WILD-TYPE  17  90 316  46
D135V5, multiclass
    clus
vv   OSBPL11 MUTATED OSBPL11 WILD-TYPE
  T1               0                17
  T2               2                90
  T3              13               316
  T4               4                46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  OSBPL11 MUTATED    11   3   5
  OSBPL11 WILD-TYPE 276 110  82
D135V6, multiclass
    clus
vv   OSBPL11 MUTATED OSBPL11 WILD-TYPE
  N0              11               276
  N1               3               110
  N2               5                82
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D135V7, binary
                   cls
clus                  0   1
  OSBPL11 MUTATED    14   2
  OSBPL11 WILD-TYPE 361  63
[1] "tbl2"
                   cls
clus                [,1] [,2]
  OSBPL11 MUTATED     14    2
  OSBPL11 WILD-TYPE  361   63
   clus
vv  OSBPL11 MUTATED OSBPL11 WILD-TYPE
  0              14               361
  1               2                63
[1] 2 2
[1] FALSE
D135V8, binary
                   cls
clus                  0   1
  OSBPL11 MUTATED     7  12
  OSBPL11 WILD-TYPE 218 252
[1] "tbl2"
                   cls
clus                [,1] [,2]
  OSBPL11 MUTATED      7   12
  OSBPL11 WILD-TYPE  218  252
        clus
vv       OSBPL11 MUTATED OSBPL11 WILD-TYPE
  FEMALE               7               218
  MALE                12               252
[1] 2 2
[1] FALSE
D135V9, binary
                   cls
clus                  0   1
  OSBPL11 MUTATED    14   0
  OSBPL11 WILD-TYPE 336  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  OSBPL11 MUTATED     14    0
  OSBPL11 WILD-TYPE  336   22
     clus
vv    OSBPL11 MUTATED OSBPL11 WILD-TYPE
  NO               14               336
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  OSBPL11 MUTATED                     12                             4
  OSBPL11 WILD-TYPE                  303                            43
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  OSBPL11 MUTATED                       3                              0
  OSBPL11 WILD-TYPE                   103                             10
D135V10, multiclass
                                clus
vv                               OSBPL11 MUTATED OSBPL11 WILD-TYPE
  COLON ADENOCARCINOMA                        12               303
  COLON MUCINOUS ADENOCARCINOMA                4                43
  RECTAL ADENOCARCINOMA                        3               103
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  OSBPL11 MUTATED    13   0   1   2
  OSBPL11 WILD-TYPE 332   4  30  23
D135V11, multiclass
    clus
vv   OSBPL11 MUTATED OSBPL11 WILD-TYPE
  R0              13               332
  R1               0                 4
  R2               1                30
  RX               2                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D135V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OSBPL11 MUTATED                                  0     1
  OSBPL11 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  OSBPL11 MUTATED                           0    11
  OSBPL11 WILD-TYPE                        22   215
D135V13, multiclass
                                  clus
vv                                 OSBPL11 MUTATED OSBPL11 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                10
  BLACK OR AFRICAN AMERICAN                      0                22
  WHITE                                         11               215
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(136) Variable = MLLT6 MUTATION ANALYSIS
D136V1, survival
                 sevent
clus2               0   1
  MLLT6 MUTATED    12   5
  MLLT6 WILD-TYPE 366  88
  MLLT6 MUTATED MLLT6 WILD-TYPE 
             17             454 
  MLLT6 MUTATED MLLT6 WILD-TYPE 
              5              88 
$`MLLT6 MUTATED`
TCGA-A6-5665 TCGA-A6-6652 TCGA-A6-6781 TCGA-AA-3492 TCGA-AA-3672 TCGA-AA-3715 
       22.06        24.69        19.66         3.02         0.92        19.04 
TCGA-AA-A01K TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-CM-6162 TCGA-CM-6170 
       31.00         6.77       100.01        29.56        12.00        15.02 
TCGA-CM-6674 TCGA-D5-6927 TCGA-DM-A28H TCGA-G4-6588 TCGA-F5-6702 
       12.95         9.44       117.07        26.17        28.57 

$`MLLT6 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       25.18        24.16        21.76        24.39        23.87        20.12 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
       20.28         7.04         1.02        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
       14.01        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       32.02        12.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6600 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       12.10         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 
        5.03        15.02        15.02        17.03        15.02         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       14.04        11.01        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
       60.79        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 
       61.91        36.00        22.09        13.78        35.80        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6811 
       20.91        18.28         9.96        49.51        31.30        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  MLLT6 MUTATED MLLT6 WILD-TYPE 
           0.92            0.00 
  MLLT6 MUTATED MLLT6 WILD-TYPE 
         117.07          148.01 
  MLLT6 MUTATED MLLT6 WILD-TYPE 
         19.660          20.235 
[1] "0.9 - 117.1 (19.7)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.5"
D136V2, continuous
D136V3, binary
                 cls
clus                0   1
  MLLT6 MUTATED    16   1
  MLLT6 WILD-TYPE 350 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MLLT6 MUTATED     16    1
  MLLT6 WILD-TYPE  350  118
        clus
vv       MLLT6 MUTATED MLLT6 WILD-TYPE
  COLON             16             350
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MLLT6 MUTATED         2        0        3         4         0         0
  MLLT6 WILD-TYPE      89        1       29       134        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MLLT6 MUTATED           1          0          1          3        0         2
  MLLT6 WILD-TYPE        23         11         58         39       48        16
                 vv
clus              STAGE IVB
  MLLT6 MUTATED           0
  MLLT6 WILD-TYPE         1
D136V4, multiclass
            clus
vv           MLLT6 MUTATED MLLT6 WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               3              29
  STAGE IIA              4             134
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             3              39
  STAGE IV               0              48
  STAGE IVA              2              16
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  MLLT6 MUTATED     0   3  13   1
  MLLT6 WILD-TYPE  17  89 316  49
D136V5, multiclass
    clus
vv   MLLT6 MUTATED MLLT6 WILD-TYPE
  T1             0              17
  T2             3              89
  T3            13             316
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  MLLT6 MUTATED    10   5   2
  MLLT6 WILD-TYPE 277 108  85
D136V6, multiclass
    clus
vv   MLLT6 MUTATED MLLT6 WILD-TYPE
  N0            10             277
  N1             5             108
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D136V7, binary
                 cls
clus                0   1
  MLLT6 MUTATED    12   2
  MLLT6 WILD-TYPE 363  63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MLLT6 MUTATED     12    2
  MLLT6 WILD-TYPE  363   63
   clus
vv  MLLT6 MUTATED MLLT6 WILD-TYPE
  0            12             363
  1             2              63
[1] 2 2
[1] FALSE
D136V8, binary
                 cls
clus                0   1
  MLLT6 MUTATED     8   9
  MLLT6 WILD-TYPE 217 255
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MLLT6 MUTATED      8    9
  MLLT6 WILD-TYPE  217  255
        clus
vv       MLLT6 MUTATED MLLT6 WILD-TYPE
  FEMALE             8             217
  MALE               9             255
[1] 2 2
[1] FALSE
D136V9, binary
                 cls
clus                0   1
  MLLT6 MUTATED    16   0
  MLLT6 WILD-TYPE 334  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MLLT6 MUTATED     16    0
  MLLT6 WILD-TYPE  334   22
     clus
vv    MLLT6 MUTATED MLLT6 WILD-TYPE
  NO             16             334
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MLLT6 MUTATED                     14                             2
  MLLT6 WILD-TYPE                  301                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MLLT6 MUTATED                       1                              0
  MLLT6 WILD-TYPE                   105                             10
D136V10, multiclass
                                clus
vv                               MLLT6 MUTATED MLLT6 WILD-TYPE
  COLON ADENOCARCINOMA                      14             301
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  MLLT6 MUTATED    12   0   0   0
  MLLT6 WILD-TYPE 333   4  31  25
D136V11, multiclass
    clus
vv   MLLT6 MUTATED MLLT6 WILD-TYPE
  R0            12             333
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D136V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MLLT6 MUTATED                                  0     0
  MLLT6 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  MLLT6 MUTATED                           1    12
  MLLT6 WILD-TYPE                        21   214
D136V13, multiclass
                                  clus
vv                                 MLLT6 MUTATED MLLT6 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                       12             214
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(137) Variable = USP24 MUTATION ANALYSIS
D137V1, survival
                 sevent
clus2               0   1
  USP24 MUTATED    26   7
  USP24 WILD-TYPE 352  86
  USP24 MUTATED USP24 WILD-TYPE 
             33             438 
  USP24 MUTATED USP24 WILD-TYPE 
              7              86 
$`USP24 MUTATED`
TCGA-A6-5661 TCGA-A6-6653 TCGA-A6-6781 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3663 
       33.53        24.39        19.66        63.98         6.97         6.97 
TCGA-AA-3815 TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-A00N TCGA-AA-A010 TCGA-AD-6964 
       33.04        37.02         0.00         4.01        34.98        10.88 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6606 TCGA-CA-5797 TCGA-CK-4950 TCGA-CM-6167 
       88.21        49.41        11.74         3.29        85.45        14.99 
TCGA-CM-6680 TCGA-D5-5540 TCGA-D5-6535 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       12.03        56.09        15.12        17.13        12.49        16.14 
TCGA-DM-A1D6 TCGA-DM-A1D8 TCGA-DM-A282 TCGA-G4-6323 TCGA-G4-6586 TCGA-AG-3731 
       49.91        12.59       139.17        13.78        35.80        37.02 
TCGA-AG-A002 TCGA-AH-6643 TCGA-DY-A0XA 
       20.98         0.69       126.44 

$`USP24 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 
       25.18        24.16        21.76        24.69        23.87        20.12 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3514 
       20.28         7.04         3.02         1.02        35.01         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
       13.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       36.03         8.05        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
       78.08         6.05        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       19.04        10.06        35.05         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 
       17.98        15.95        38.99        14.93        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6599 
        1.41         5.13       106.75        22.36        62.79         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-AZ-6608 
       12.10       100.01        29.56         5.23         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
       12.69         3.06         3.25         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5912 
       10.06        14.30        17.56       148.01        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       29.03        16.04        21.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5541 
       11.01        10.06        45.40        12.26        19.59        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 
       20.19        18.25         1.32        43.27        17.85         4.80 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       92.75        13.32       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      135.65         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       61.91        36.00        22.09        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3732 
       19.99        13.94        19.99         7.99         0.99        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC 
       19.99         5.95         4.01         5.03         5.29        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  USP24 MUTATED USP24 WILD-TYPE 
              0               0 
  USP24 MUTATED USP24 WILD-TYPE 
         139.17          148.01 
  USP24 MUTATED USP24 WILD-TYPE 
         19.660          20.235 
[1] "0.0 - 139.2 (19.7)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.1"
D137V2, continuous
D137V3, binary
                 cls
clus                0   1
  USP24 MUTATED    30   4
  USP24 WILD-TYPE 336 115
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP24 MUTATED     30    4
  USP24 WILD-TYPE  336  115
        clus
vv       USP24 MUTATED USP24 WILD-TYPE
  COLON             30             336
  RECTUM             4             115
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  USP24 MUTATED         4        1        4         9         3         0
  USP24 WILD-TYPE      87        0       28       129         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  USP24 MUTATED           0          2          4          3        2         0
  USP24 WILD-TYPE        24          9         55         39       46        18
                 vv
clus              STAGE IVB
  USP24 MUTATED           0
  USP24 WILD-TYPE         1
D137V4, multiclass
            clus
vv           USP24 MUTATED USP24 WILD-TYPE
  STAGE I                4              87
  STAGE IA               1               0
  STAGE II               4              28
  STAGE IIA              9             129
  STAGE IIB              3               7
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             2               9
  STAGE IIIB             4              55
  STAGE IIIC             3              39
  STAGE IV               2              46
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  USP24 MUTATED     1   4  21   7
  USP24 WILD-TYPE  16  88 308  43
D137V5, multiclass
    clus
vv   USP24 MUTATED USP24 WILD-TYPE
  T1             1              16
  T2             4              88
  T3            21             308
  T4             7              43
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  USP24 MUTATED    22   6   6
  USP24 WILD-TYPE 265 107  81
D137V6, multiclass
    clus
vv   USP24 MUTATED USP24 WILD-TYPE
  N0            22             265
  N1             6             107
  N2             6              81
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D137V7, binary
                 cls
clus                0   1
  USP24 MUTATED    25   2
  USP24 WILD-TYPE 350  63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP24 MUTATED     25    2
  USP24 WILD-TYPE  350   63
   clus
vv  USP24 MUTATED USP24 WILD-TYPE
  0            25             350
  1             2              63
[1] 2 2
[1] FALSE
D137V8, binary
                 cls
clus                0   1
  USP24 MUTATED    17  17
  USP24 WILD-TYPE 208 247
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP24 MUTATED     17   17
  USP24 WILD-TYPE  208  247
        clus
vv       USP24 MUTATED USP24 WILD-TYPE
  FEMALE            17             208
  MALE              17             247
[1] 2 2
[1] FALSE
D137V9, binary
                 cls
clus                0   1
  USP24 MUTATED    26   0
  USP24 WILD-TYPE 324  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP24 MUTATED     26    0
  USP24 WILD-TYPE  324   22
     clus
vv    USP24 MUTATED USP24 WILD-TYPE
  NO             26             324
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  USP24 MUTATED                     26                             4
  USP24 WILD-TYPE                  289                            43
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  USP24 MUTATED                       4                              0
  USP24 WILD-TYPE                   102                             10
D137V10, multiclass
                                clus
vv                               USP24 MUTATED USP24 WILD-TYPE
  COLON ADENOCARCINOMA                      26             289
  COLON MUCINOUS ADENOCARCINOMA              4              43
  RECTAL ADENOCARCINOMA                      4             102
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  USP24 MUTATED    21   1   1   2
  USP24 WILD-TYPE 324   3  30  23
D137V11, multiclass
    clus
vv   USP24 MUTATED USP24 WILD-TYPE
  R0            21             324
  R1             1               3
  R2             1              30
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D137V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  USP24 MUTATED                                  0     1
  USP24 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  USP24 MUTATED                           4    19
  USP24 WILD-TYPE                        18   207
D137V13, multiclass
                                  clus
vv                                 USP24 MUTATED USP24 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    4              18
  WHITE                                       19             207
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(138) Variable = ARFGEF1 MUTATION ANALYSIS
D138V1, survival
                   sevent
clus2                 0   1
  ARFGEF1 MUTATED    26   9
  ARFGEF1 WILD-TYPE 352  84
  ARFGEF1 MUTATED ARFGEF1 WILD-TYPE 
               35               436 
  ARFGEF1 MUTATED ARFGEF1 WILD-TYPE 
                9                84 
$`ARFGEF1 MUTATED`
TCGA-A6-5665 TCGA-AA-3492 TCGA-AA-3526 TCGA-AA-3555 TCGA-AA-3660 TCGA-AA-3662 
       22.06         3.02        19.07        29.95        78.08         6.05 
TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3852 TCGA-AA-3864 TCGA-AA-3977 TCGA-AA-A00N 
       85.05        19.04         0.00        53.00        25.02         4.01 
TCGA-AA-A010 TCGA-AZ-4681 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-CA-5797 TCGA-CA-6717 
       34.98       106.75        62.79        49.41         3.29        12.76 
TCGA-CA-6718 TCGA-CK-5912 TCGA-CK-6747 TCGA-CM-4743 TCGA-CM-5344 TCGA-CM-6171 
       10.06        49.08        82.95        23.05        22.03        14.04 
TCGA-D5-6930 TCGA-DM-A0X9 TCGA-DM-A282 TCGA-DM-A28C TCGA-DM-A28K TCGA-F4-6460 
        1.51       119.70       139.17        81.37        98.24        31.96 
TCGA-F4-6704 TCGA-G4-6586 TCGA-AG-3892 TCGA-AG-A002 TCGA-EI-6507 
        1.55        35.80        13.02        20.98        19.96 

$`ARFGEF1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 
       20.12        19.66        20.28         7.04         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3529 
        9.07        24.03        37.05        36.03         8.05         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       17.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
       61.02         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 
       19.00        36.00         5.03        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
       10.06         0.00        33.07        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        31.07        30.05        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
        5.13        22.36        88.21         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 
        3.06         3.25         0.07        12.20        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
      148.01        85.45        15.62        51.32         9.99        21.14 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
        1.91       124.27        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       29.06        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       15.02        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 
        9.04         9.44        11.64         4.80        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
       10.26        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A285 TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
      135.65         6.12       119.93        35.97        60.79       117.07 
TCGA-F4-6459 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 
        8.61        35.74         6.18        47.87        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6508 
       24.13        51.48        32.61         0.49        20.55        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  ARFGEF1 MUTATED ARFGEF1 WILD-TYPE 
                0                 0 
  ARFGEF1 MUTATED ARFGEF1 WILD-TYPE 
           139.17            148.01 
  ARFGEF1 MUTATED ARFGEF1 WILD-TYPE 
            23.05             20.02 
[1] "0.0 - 139.2 (23.1)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.1"
D138V2, continuous
D138V3, binary
                   cls
clus                  0   1
  ARFGEF1 MUTATED    34   3
  ARFGEF1 WILD-TYPE 332 116
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ARFGEF1 MUTATED     34    3
  ARFGEF1 WILD-TYPE  332  116
        clus
vv       ARFGEF1 MUTATED ARFGEF1 WILD-TYPE
  COLON               34               332
  RECTUM               3               116
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ARFGEF1 MUTATED         5        0        5        17         2         0
  ARFGEF1 WILD-TYPE      86        1       27       121         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ARFGEF1 MUTATED           2          0          2          1        2
  ARFGEF1 WILD-TYPE        22         11         57         41       46
                   vv
clus                STAGE IVA STAGE IVB
  ARFGEF1 MUTATED           0         0
  ARFGEF1 WILD-TYPE        18         1
D138V4, multiclass
            clus
vv           ARFGEF1 MUTATED ARFGEF1 WILD-TYPE
  STAGE I                  5                86
  STAGE IA                 0                 1
  STAGE II                 5                27
  STAGE IIA               17               121
  STAGE IIB                2                 8
  STAGE IIC                0                 1
  STAGE III                2                22
  STAGE IIIA               0                11
  STAGE IIIB               2                57
  STAGE IIIC               1                41
  STAGE IV                 2                46
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  ARFGEF1 MUTATED     1   5  28   3
  ARFGEF1 WILD-TYPE  16  87 301  47
D138V5, multiclass
    clus
vv   ARFGEF1 MUTATED ARFGEF1 WILD-TYPE
  T1               1                16
  T2               5                87
  T3              28               301
  T4               3                47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  ARFGEF1 MUTATED    32   2   3
  ARFGEF1 WILD-TYPE 255 111  84
D138V6, multiclass
    clus
vv   ARFGEF1 MUTATED ARFGEF1 WILD-TYPE
  N0              32               255
  N1               2               111
  N2               3                84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D138V7, binary
                   cls
clus                  0   1
  ARFGEF1 MUTATED    29   2
  ARFGEF1 WILD-TYPE 346  63
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ARFGEF1 MUTATED     29    2
  ARFGEF1 WILD-TYPE  346   63
   clus
vv  ARFGEF1 MUTATED ARFGEF1 WILD-TYPE
  0              29               346
  1               2                63
[1] 2 2
[1] FALSE
D138V8, binary
                   cls
clus                  0   1
  ARFGEF1 MUTATED    17  20
  ARFGEF1 WILD-TYPE 208 244
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ARFGEF1 MUTATED     17   20
  ARFGEF1 WILD-TYPE  208  244
        clus
vv       ARFGEF1 MUTATED ARFGEF1 WILD-TYPE
  FEMALE              17               208
  MALE                20               244
[1] 2 2
[1] FALSE
D138V9, binary
                   cls
clus                  0   1
  ARFGEF1 MUTATED    26   1
  ARFGEF1 WILD-TYPE 324  21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ARFGEF1 MUTATED     26    1
  ARFGEF1 WILD-TYPE  324   21
     clus
vv    ARFGEF1 MUTATED ARFGEF1 WILD-TYPE
  NO               26               324
  YES               1                21
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ARFGEF1 MUTATED                     27                             7
  ARFGEF1 WILD-TYPE                  288                            40
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ARFGEF1 MUTATED                       3                              0
  ARFGEF1 WILD-TYPE                   103                             10
D138V10, multiclass
                                clus
vv                               ARFGEF1 MUTATED ARFGEF1 WILD-TYPE
  COLON ADENOCARCINOMA                        27               288
  COLON MUCINOUS ADENOCARCINOMA                7                40
  RECTAL ADENOCARCINOMA                        3               103
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  ARFGEF1 MUTATED    24   0   2   4
  ARFGEF1 WILD-TYPE 321   4  29  21
D138V11, multiclass
    clus
vv   ARFGEF1 MUTATED ARFGEF1 WILD-TYPE
  R0              24               321
  R1               0                 4
  R2               2                29
  RX               4                21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D138V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ARFGEF1 MUTATED                                  1     3
  ARFGEF1 WILD-TYPE                                0     8
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  ARFGEF1 MUTATED                           0    17
  ARFGEF1 WILD-TYPE                        22   209
D138V13, multiclass
                                  clus
vv                                 ARFGEF1 MUTATED ARFGEF1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                          3                 8
  BLACK OR AFRICAN AMERICAN                      0                22
  WHITE                                         17               209
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(139) Variable = OR5V1 MUTATION ANALYSIS
D139V1, survival
                 sevent
clus2               0   1
  OR5V1 MUTATED    17   1
  OR5V1 WILD-TYPE 361  92
  OR5V1 MUTATED OR5V1 WILD-TYPE 
             18             453 
  OR5V1 MUTATED OR5V1 WILD-TYPE 
              1              92 
$`OR5V1 MUTATED`
TCGA-AA-3866 TCGA-AA-3977 TCGA-AU-3779 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4950 
       17.03        25.02        14.50        12.76        14.30        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CM-6164 TCGA-CM-6676 TCGA-D5-6535 TCGA-D5-6928 
       15.62        49.08        29.03        11.08        15.12        11.64 
TCGA-DM-A1HB TCGA-G4-6321 TCGA-AG-A002 TCGA-DC-6682 TCGA-EI-6506 TCGA-F5-6465 
      135.65        22.09        20.98         4.01        20.55        49.51 

$`OR5V1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       53.00        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       10.88         0.20        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       10.06        17.56       148.01        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       15.02        12.00         2.96        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       13.05        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
        1.32        43.27        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
       14.30         9.04         9.44         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
       44.32       131.51       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6586 
       85.48        63.62        61.91        36.00        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        5.95         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6507 TCGA-EI-6508 
       24.13        51.48        32.61         0.49        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
       18.28         9.96        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  OR5V1 MUTATED OR5V1 WILD-TYPE 
           4.01            0.00 
  OR5V1 MUTATED OR5V1 WILD-TYPE 
         135.65          148.01 
  OR5V1 MUTATED OR5V1 WILD-TYPE 
          18.79           20.19 
[1] "4.0 - 135.7 (18.8)" "0.0 - 148.0 (20.2)"
[1] "hr=" "4.2"
D139V2, continuous
D139V3, binary
                 cls
clus                0   1
  OR5V1 MUTATED    14   4
  OR5V1 WILD-TYPE 352 115
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR5V1 MUTATED     14    4
  OR5V1 WILD-TYPE  352  115
        clus
vv       OR5V1 MUTATED OR5V1 WILD-TYPE
  COLON             14             352
  RECTUM             4             115
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  OR5V1 MUTATED         4        0        0         8         0         0
  OR5V1 WILD-TYPE      87        1       32       130        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  OR5V1 MUTATED           1          0          3          1        0         0
  OR5V1 WILD-TYPE        23         11         56         41       48        18
                 vv
clus              STAGE IVB
  OR5V1 MUTATED           0
  OR5V1 WILD-TYPE         1
D139V4, multiclass
            clus
vv           OR5V1 MUTATED OR5V1 WILD-TYPE
  STAGE I                4              87
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              8             130
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             3              56
  STAGE IIIC             1              41
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  OR5V1 MUTATED     0   6  11   1
  OR5V1 WILD-TYPE  17  86 318  49
D139V5, multiclass
    clus
vv   OR5V1 MUTATED OR5V1 WILD-TYPE
  T1             0              17
  T2             6              86
  T3            11             318
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  OR5V1 MUTATED    13   4   1
  OR5V1 WILD-TYPE 274 109  86
D139V6, multiclass
    clus
vv   OR5V1 MUTATED OR5V1 WILD-TYPE
  N0            13             274
  N1             4             109
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D139V7, binary
                 cls
clus                0   1
  OR5V1 MUTATED    14   0
  OR5V1 WILD-TYPE 361  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR5V1 MUTATED     14    0
  OR5V1 WILD-TYPE  361   65
   clus
vv  OR5V1 MUTATED OR5V1 WILD-TYPE
  0            14             361
  1             0              65
[1] 2 2
[1] FALSE
D139V8, binary
                 cls
clus                0   1
  OR5V1 MUTATED     9   9
  OR5V1 WILD-TYPE 216 255
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR5V1 MUTATED      9    9
  OR5V1 WILD-TYPE  216  255
        clus
vv       OR5V1 MUTATED OR5V1 WILD-TYPE
  FEMALE             9             216
  MALE               9             255
[1] 2 2
[1] FALSE
D139V9, binary
                 cls
clus                0   1
  OR5V1 MUTATED    15   0
  OR5V1 WILD-TYPE 335  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR5V1 MUTATED     15    0
  OR5V1 WILD-TYPE  335   22
     clus
vv    OR5V1 MUTATED OR5V1 WILD-TYPE
  NO             15             335
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  OR5V1 MUTATED                     10                             3
  OR5V1 WILD-TYPE                  305                            44
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  OR5V1 MUTATED                       4                              0
  OR5V1 WILD-TYPE                   102                             10
D139V10, multiclass
                                clus
vv                               OR5V1 MUTATED OR5V1 WILD-TYPE
  COLON ADENOCARCINOMA                      10             305
  COLON MUCINOUS ADENOCARCINOMA              3              44
  RECTAL ADENOCARCINOMA                      4             102
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  OR5V1 MUTATED    10   1   0   5
  OR5V1 WILD-TYPE 335   3  31  20
D139V11, multiclass
    clus
vv   OR5V1 MUTATED OR5V1 WILD-TYPE
  R0            10             335
  R1             1               3
  R2             0              31
  RX             5              20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D139V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OR5V1 MUTATED                                  0     2
  OR5V1 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  OR5V1 MUTATED                           1    12
  OR5V1 WILD-TYPE                        21   214
D139V13, multiclass
                                  clus
vv                                 OR5V1 MUTATED OR5V1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               9
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                       12             214
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(140) Variable = PRB4 MUTATION ANALYSIS
D140V1, survival
                sevent
clus2              0   1
  PRB4 MUTATED    12   0
  PRB4 WILD-TYPE 366  93
  PRB4 MUTATED PRB4 WILD-TYPE 
            12            459 
  PRB4 MUTATED PRB4 WILD-TYPE 
             0             93 
$`PRB4 MUTATED`
TCGA-A6-6651 TCGA-AA-3812 TCGA-AA-3855 TCGA-AA-A010 TCGA-CA-6717 TCGA-CM-6169 
       21.76        35.05        32.05        34.98        12.76        13.02 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6898 TCGA-G4-6625 TCGA-CI-6619 TCGA-CI-6622 
       18.25         1.32         1.48        91.79         6.05         6.97 

$`PRB4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.08        25.18        24.16        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       10.06        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3856 
       10.06         0.00        33.07         0.00        36.03         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07        12.20        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6170 
       29.03        16.04        21.99        14.99        12.99        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       56.09        55.92        20.19        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 
        4.80        17.13        12.49        16.14        15.58         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6620 
       38.56         1.45        17.49         0.69         0.72        33.17 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  PRB4 MUTATED PRB4 WILD-TYPE 
          1.32           0.00 
  PRB4 MUTATED PRB4 WILD-TYPE 
         91.79         148.01 
  PRB4 MUTATED PRB4 WILD-TYPE 
        15.635         20.280 
[1] "1.3 - 91.8 (15.6)"  "0.0 - 148.0 (20.3)"
[1] "hr="     "9200000"
D140V2, continuous
D140V3, binary
                cls
clus               0   1
  PRB4 MUTATED    10   2
  PRB4 WILD-TYPE 356 117
[1] "tbl2"
                cls
clus             [,1] [,2]
  PRB4 MUTATED     10    2
  PRB4 WILD-TYPE  356  117
        clus
vv       PRB4 MUTATED PRB4 WILD-TYPE
  COLON            10            356
  RECTUM            2            117
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PRB4 MUTATED         2        0        0         5         2         0
  PRB4 WILD-TYPE      89        1       32       133         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PRB4 MUTATED           0          0          2          0        1         0
  PRB4 WILD-TYPE        24         11         57         42       47        18
                vv
clus             STAGE IVB
  PRB4 MUTATED           0
  PRB4 WILD-TYPE         1
D140V4, multiclass
            clus
vv           PRB4 MUTATED PRB4 WILD-TYPE
  STAGE I               2             89
  STAGE IA              0              1
  STAGE II              0             32
  STAGE IIA             5            133
  STAGE IIB             2              8
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            2             57
  STAGE IIIC            0             42
  STAGE IV              1             47
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  PRB4 MUTATED     0   2   7   3
  PRB4 WILD-TYPE  17  90 322  47
D140V5, multiclass
    clus
vv   PRB4 MUTATED PRB4 WILD-TYPE
  T1            0             17
  T2            2             90
  T3            7            322
  T4            3             47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  PRB4 MUTATED    10   2   0
  PRB4 WILD-TYPE 277 111  87
D140V6, multiclass
    clus
vv   PRB4 MUTATED PRB4 WILD-TYPE
  N0           10            277
  N1            2            111
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D140V7, binary
                cls
clus               0   1
  PRB4 MUTATED    10   1
  PRB4 WILD-TYPE 365  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  PRB4 MUTATED     10    1
  PRB4 WILD-TYPE  365   64
   clus
vv  PRB4 MUTATED PRB4 WILD-TYPE
  0           10            365
  1            1             64
[1] 2 2
[1] FALSE
D140V8, binary
                cls
clus               0   1
  PRB4 MUTATED     6   6
  PRB4 WILD-TYPE 219 258
[1] "tbl2"
                cls
clus             [,1] [,2]
  PRB4 MUTATED      6    6
  PRB4 WILD-TYPE  219  258
        clus
vv       PRB4 MUTATED PRB4 WILD-TYPE
  FEMALE            6            219
  MALE              6            258
[1] 2 2
[1] FALSE
D140V9, binary
                cls
clus               0   1
  PRB4 MUTATED     8   0
  PRB4 WILD-TYPE 342  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  PRB4 MUTATED      8    0
  PRB4 WILD-TYPE  342   22
     clus
vv    PRB4 MUTATED PRB4 WILD-TYPE
  NO             8            342
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PRB4 MUTATED                      9                             1
  PRB4 WILD-TYPE                  306                            46
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PRB4 MUTATED                       2                              0
  PRB4 WILD-TYPE                   104                             10
D140V10, multiclass
                                clus
vv                               PRB4 MUTATED PRB4 WILD-TYPE
  COLON ADENOCARCINOMA                      9            306
  COLON MUCINOUS ADENOCARCINOMA             1             46
  RECTAL ADENOCARCINOMA                     2            104
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  PRB4 MUTATED     8   0   0   1
  PRB4 WILD-TYPE 337   4  31  24
D140V11, multiclass
    clus
vv   PRB4 MUTATED PRB4 WILD-TYPE
  R0            8            337
  R1            0              4
  R2            0             31
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D140V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PRB4 MUTATED                                  0     1
  PRB4 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  PRB4 MUTATED                           1     7
  PRB4 WILD-TYPE                        21   219
D140V13, multiclass
                                  clus
vv                                 PRB4 MUTATED PRB4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                       7            219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(141) Variable = TRIP11 MUTATION ANALYSIS
D141V1, survival
                  sevent
clus2                0   1
  TRIP11 MUTATED    21   4
  TRIP11 WILD-TYPE 357  89
  TRIP11 MUTATED TRIP11 WILD-TYPE 
              25              446 
  TRIP11 MUTATED TRIP11 WILD-TYPE 
               4               89 
$`TRIP11 MUTATED`
TCGA-A6-5661 TCGA-A6-5665 TCGA-AA-3663 TCGA-AA-3966 TCGA-AA-3977 TCGA-AA-A00N 
       33.53        22.06         6.97         2.01        25.02         4.01 
TCGA-AA-A010 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-6603 TCGA-CA-6717 
       34.98        21.44        17.82        58.39        29.56        12.76 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CM-6168 TCGA-D5-6532 TCGA-D5-6540 TCGA-G4-6628 
       51.32         9.99        12.99        18.25        16.14        79.69 
TCGA-AG-3892 TCGA-AG-A002 TCGA-AG-A014 TCGA-DC-6157 TCGA-DY-A1DC TCGA-DY-A1DD 
       13.02        20.98        15.95        27.95        41.36        57.24 
TCGA-EI-6507 
       19.96 

$`TRIP11 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
       34.03        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
        0.95        33.01         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07        12.20        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5916 
       17.56       148.01        85.45        15.62        49.08        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       14.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       12.49        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       36.95        17.03        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
       15.02         5.03        13.97        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DF TCGA-DY-A1DG 
        4.01         5.03         5.29       126.44        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
       32.61         0.49        20.55        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  TRIP11 MUTATED TRIP11 WILD-TYPE 
            2.01             0.00 
  TRIP11 MUTATED TRIP11 WILD-TYPE 
           79.69           148.01 
  TRIP11 MUTATED TRIP11 WILD-TYPE 
          20.980           20.155 
[1] "2.0 - 79.7 (21.0)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.3"
D141V2, continuous
D141V3, binary
                  cls
clus                 0   1
  TRIP11 MUTATED    19   7
  TRIP11 WILD-TYPE 347 112
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIP11 MUTATED     19    7
  TRIP11 WILD-TYPE  347  112
        clus
vv       TRIP11 MUTATED TRIP11 WILD-TYPE
  COLON              19              347
  RECTUM              7              112
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TRIP11 MUTATED         6        0        1        12         2         0
  TRIP11 WILD-TYPE      85        1       31       126         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TRIP11 MUTATED           0          0          3          0        0
  TRIP11 WILD-TYPE        24         11         56         42       48
                  vv
clus               STAGE IVA STAGE IVB
  TRIP11 MUTATED           0         0
  TRIP11 WILD-TYPE        18         1
D141V4, multiclass
            clus
vv           TRIP11 MUTATED TRIP11 WILD-TYPE
  STAGE I                 6               85
  STAGE IA                0                1
  STAGE II                1               31
  STAGE IIA              12              126
  STAGE IIB               2                8
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              3               56
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  TRIP11 MUTATED     1   7  16   2
  TRIP11 WILD-TYPE  16  85 313  48
D141V5, multiclass
    clus
vv   TRIP11 MUTATED TRIP11 WILD-TYPE
  T1              1               16
  T2              7               85
  T3             16              313
  T4              2               48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  TRIP11 MUTATED    22   4   0
  TRIP11 WILD-TYPE 265 109  87
D141V6, multiclass
    clus
vv   TRIP11 MUTATED TRIP11 WILD-TYPE
  N0             22              265
  N1              4              109
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D141V7, binary
                  cls
clus                 0   1
  TRIP11 MUTATED    21   0
  TRIP11 WILD-TYPE 354  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIP11 MUTATED     21    0
  TRIP11 WILD-TYPE  354   65
   clus
vv  TRIP11 MUTATED TRIP11 WILD-TYPE
  0             21              354
  1              0               65
[1] 2 2
[1] FALSE
D141V8, binary
                  cls
clus                 0   1
  TRIP11 MUTATED    12  14
  TRIP11 WILD-TYPE 213 250
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIP11 MUTATED     12   14
  TRIP11 WILD-TYPE  213  250
        clus
vv       TRIP11 MUTATED TRIP11 WILD-TYPE
  FEMALE             12              213
  MALE               14              250
[1] 2 2
[1] FALSE
D141V9, binary
                  cls
clus                 0   1
  TRIP11 MUTATED    18   0
  TRIP11 WILD-TYPE 332  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIP11 MUTATED     18    0
  TRIP11 WILD-TYPE  332   22
     clus
vv    TRIP11 MUTATED TRIP11 WILD-TYPE
  NO              18              332
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  TRIP11 MUTATED                     15                             4
  TRIP11 WILD-TYPE                  300                            43
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  TRIP11 MUTATED                       7                              0
  TRIP11 WILD-TYPE                    99                             10
D141V10, multiclass
                                clus
vv                               TRIP11 MUTATED TRIP11 WILD-TYPE
  COLON ADENOCARCINOMA                       15              300
  COLON MUCINOUS ADENOCARCINOMA               4               43
  RECTAL ADENOCARCINOMA                       7               99
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  TRIP11 MUTATED    18   0   0   3
  TRIP11 WILD-TYPE 327   4  31  22
D141V11, multiclass
    clus
vv   TRIP11 MUTATED TRIP11 WILD-TYPE
  R0             18              327
  R1              0                4
  R2              0               31
  RX              3               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D141V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TRIP11 MUTATED                                  0     1
  TRIP11 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  TRIP11 MUTATED                           4    12
  TRIP11 WILD-TYPE                        18   214
D141V13, multiclass
                                  clus
vv                                 TRIP11 MUTATED TRIP11 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     4               18
  WHITE                                        12              214
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(142) Variable = SLK MUTATION ANALYSIS
D142V1, survival
               sevent
clus2             0   1
  SLK MUTATED    21   2
  SLK WILD-TYPE 357  91
  SLK MUTATED SLK WILD-TYPE 
           23           448 
  SLK MUTATED SLK WILD-TYPE 
            2            91 
$`SLK MUTATED`
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6651 TCGA-A6-6782 TCGA-AA-3510 TCGA-AA-3663 
       22.06        32.71        21.76        20.28        63.98         6.97 
TCGA-AA-3710 TCGA-AA-3877 TCGA-AA-A010 TCGA-AA-A01I TCGA-AD-6889 TCGA-AU-6004 
       26.99        31.00        34.98        31.00        56.55        27.09 
TCGA-AZ-4315 TCGA-AZ-6603 TCGA-CA-6717 TCGA-CM-6172 TCGA-D5-6533 TCGA-D5-6924 
       58.39        29.56        12.76        11.01         1.32        14.30 
TCGA-D5-7000 TCGA-G4-6303 TCGA-G4-6321 TCGA-AG-A002 TCGA-CI-6622 
       10.26        65.85        22.09        20.98         6.97 

$`SLK WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       22.09        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       24.16        24.69        24.39        23.87        20.12        19.66 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 
        7.04         3.02         1.02        35.01         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
       13.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       36.03         8.05        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
       78.08         6.05        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
       19.00        36.00         5.03        85.05        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 
       17.03        24.03        27.02        29.98        18.05         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01K 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 
       40.96         0.07        21.37        15.52         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
       16.31         0.95        33.01        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77        12.10       100.01         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.20        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 
       12.99        13.02        15.02        14.04        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       11.38       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
      133.18        74.56        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       63.62        61.91        36.00        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
       33.17         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  SLK MUTATED SLK WILD-TYPE 
         1.32          0.00 
  SLK MUTATED SLK WILD-TYPE 
        65.85        148.01 
  SLK MUTATED SLK WILD-TYPE 
       22.090        20.005 
[1] "1.3 - 65.8 (22.1)"  "0.0 - 148.0 (20.0)"
[1] "hr=" "2.5"
D142V2, continuous
D142V3, binary
               cls
clus              0   1
  SLK MUTATED    23   2
  SLK WILD-TYPE 343 117
[1] "tbl2"
               cls
clus            [,1] [,2]
  SLK MUTATED     23    2
  SLK WILD-TYPE  343  117
        clus
vv       SLK MUTATED SLK WILD-TYPE
  COLON           23           343
  RECTUM           2           117
[1] 2 2
[1] FALSE
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SLK MUTATED         6        0        3         6         3         1
  SLK WILD-TYPE      85        1       29       132         7         0
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SLK MUTATED           1          0          3          0        1         0
  SLK WILD-TYPE        23         11         56         42       47        18
               vv
clus            STAGE IVB
  SLK MUTATED           0
  SLK WILD-TYPE         1
D142V4, multiclass
            clus
vv           SLK MUTATED SLK WILD-TYPE
  STAGE I              6            85
  STAGE IA             0             1
  STAGE II             3            29
  STAGE IIA            6           132
  STAGE IIB            3             7
  STAGE IIC            1             0
  STAGE III            1            23
  STAGE IIIA           0            11
  STAGE IIIB           3            56
  STAGE IIIC           0            42
  STAGE IV             1            47
  STAGE IVA            0            18
  STAGE IVB            0             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  SLK MUTATED     1   7  11   6
  SLK WILD-TYPE  16  85 318  44
D142V5, multiclass
    clus
vv   SLK MUTATED SLK WILD-TYPE
  T1           1            16
  T2           7            85
  T3          11           318
  T4           6            44
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2
  SLK MUTATED    20   5   0
  SLK WILD-TYPE 267 108  87
D142V6, multiclass
    clus
vv   SLK MUTATED SLK WILD-TYPE
  N0          20           267
  N1           5           108
  N2           0            87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D142V7, binary
               cls
clus              0   1
  SLK MUTATED    19   1
  SLK WILD-TYPE 356  64
[1] "tbl2"
               cls
clus            [,1] [,2]
  SLK MUTATED     19    1
  SLK WILD-TYPE  356   64
   clus
vv  SLK MUTATED SLK WILD-TYPE
  0          19           356
  1           1            64
[1] 2 2
[1] FALSE
D142V8, binary
               cls
clus              0   1
  SLK MUTATED    13  12
  SLK WILD-TYPE 212 252
[1] "tbl2"
               cls
clus            [,1] [,2]
  SLK MUTATED     13   12
  SLK WILD-TYPE  212  252
        clus
vv       SLK MUTATED SLK WILD-TYPE
  FEMALE          13           212
  MALE            12           252
[1] 2 2
[1] FALSE
D142V9, binary
               cls
clus              0   1
  SLK MUTATED    19   0
  SLK WILD-TYPE 331  22
[1] "tbl2"
               cls
clus            [,1] [,2]
  SLK MUTATED     19    0
  SLK WILD-TYPE  331   22
     clus
vv    SLK MUTATED SLK WILD-TYPE
  NO           19           331
  YES           0            22
[1] 2 2
[1] FALSE
               vv
clus            COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SLK MUTATED                     20                             3
  SLK WILD-TYPE                  295                            44
               vv
clus            RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SLK MUTATED                       2                              0
  SLK WILD-TYPE                   104                             10
D142V10, multiclass
                                clus
vv                               SLK MUTATED SLK WILD-TYPE
  COLON ADENOCARCINOMA                    20           295
  COLON MUCINOUS ADENOCARCINOMA            3            44
  RECTAL ADENOCARCINOMA                    2           104
  RECTAL MUCINOUS ADENOCARCINOMA           0            10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             R0  R1  R2  RX
  SLK MUTATED    17   0   0   2
  SLK WILD-TYPE 328   4  31  23
D142V11, multiclass
    clus
vv   SLK MUTATED SLK WILD-TYPE
  R0          17           328
  R1           0             4
  R2           0            31
  RX           2            23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D142V12, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SLK MUTATED                                  0     2
  SLK WILD-TYPE                                1     9
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  SLK MUTATED                           0    15
  SLK WILD-TYPE                        22   211
D142V13, multiclass
                                  clus
vv                                 SLK MUTATED SLK WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      2             9
  BLACK OR AFRICAN AMERICAN                  0            22
  WHITE                                     15           211
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(143) Variable = PON3 MUTATION ANALYSIS
D143V1, survival
                sevent
clus2              0   1
  PON3 MUTATED    10   4
  PON3 WILD-TYPE 368  89
  PON3 MUTATED PON3 WILD-TYPE 
            14            457 
  PON3 MUTATED PON3 WILD-TYPE 
             4             89 
$`PON3 MUTATED`
TCGA-A6-5659 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3715 TCGA-AA-3971 TCGA-CA-6717 
       30.44        63.98         6.97        19.04        16.08        12.76 
TCGA-CA-6718 TCGA-CK-5916 TCGA-G4-6588 TCGA-G4-6628 TCGA-AF-2693 TCGA-CI-6620 
       10.06        21.14        26.17        79.69        19.10        33.17 
TCGA-CL-5918 TCGA-DY-A1DG 
        7.17        51.48 

$`PON3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
       35.01         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       85.05        26.99        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
        2.01        21.99        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 
        3.25         3.29         0.07        12.20        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       91.79        46.75        24.13        39.48        43.04        13.55 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6622 
        1.45        17.49         0.69         0.72         6.05         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
        4.73        78.12        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 
      126.44        41.36        57.24        24.13        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  PON3 MUTATED PON3 WILD-TYPE 
          6.97           0.00 
  PON3 MUTATED PON3 WILD-TYPE 
         79.69         148.01 
  PON3 MUTATED PON3 WILD-TYPE 
         20.12          20.19 
[1] "7.0 - 79.7 (20.1)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.3"
D143V2, continuous
D143V3, binary
                cls
clus               0   1
  PON3 MUTATED    10   3
  PON3 WILD-TYPE 356 116
[1] "tbl2"
                cls
clus             [,1] [,2]
  PON3 MUTATED     10    3
  PON3 WILD-TYPE  356  116
        clus
vv       PON3 MUTATED PON3 WILD-TYPE
  COLON            10            356
  RECTUM            3            116
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PON3 MUTATED         4        0        3         4         0         0
  PON3 WILD-TYPE      87        1       29       134        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PON3 MUTATED           1          0          0          0        0         2
  PON3 WILD-TYPE        23         11         59         42       48        16
                vv
clus             STAGE IVB
  PON3 MUTATED           0
  PON3 WILD-TYPE         1
D143V4, multiclass
            clus
vv           PON3 MUTATED PON3 WILD-TYPE
  STAGE I               4             87
  STAGE IA              0              1
  STAGE II              3             29
  STAGE IIA             4            134
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             1             23
  STAGE IIIA            0             11
  STAGE IIIB            0             59
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             2             16
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  PON3 MUTATED     1   3   9   1
  PON3 WILD-TYPE  16  89 320  49
D143V5, multiclass
    clus
vv   PON3 MUTATED PON3 WILD-TYPE
  T1            1             16
  T2            3             89
  T3            9            320
  T4            1             49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  PON3 MUTATED    11   3   0
  PON3 WILD-TYPE 276 110  87
D143V6, multiclass
    clus
vv   PON3 MUTATED PON3 WILD-TYPE
  N0           11            276
  N1            3            110
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D143V7, binary
                cls
clus               0   1
  PON3 MUTATED    10   2
  PON3 WILD-TYPE 365  63
[1] "tbl2"
                cls
clus             [,1] [,2]
  PON3 MUTATED     10    2
  PON3 WILD-TYPE  365   63
   clus
vv  PON3 MUTATED PON3 WILD-TYPE
  0           10            365
  1            2             63
[1] 2 2
[1] FALSE
D143V8, binary
                cls
clus               0   1
  PON3 MUTATED     4  10
  PON3 WILD-TYPE 221 254
[1] "tbl2"
                cls
clus             [,1] [,2]
  PON3 MUTATED      4   10
  PON3 WILD-TYPE  221  254
        clus
vv       PON3 MUTATED PON3 WILD-TYPE
  FEMALE            4            221
  MALE             10            254
[1] 2 2
[1] FALSE
D143V9, binary
                cls
clus               0   1
  PON3 MUTATED    13   0
  PON3 WILD-TYPE 337  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  PON3 MUTATED     13    0
  PON3 WILD-TYPE  337   22
     clus
vv    PON3 MUTATED PON3 WILD-TYPE
  NO            13            337
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PON3 MUTATED                      9                             1
  PON3 WILD-TYPE                  306                            46
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PON3 MUTATED                       3                              0
  PON3 WILD-TYPE                   103                             10
D143V10, multiclass
                                clus
vv                               PON3 MUTATED PON3 WILD-TYPE
  COLON ADENOCARCINOMA                      9            306
  COLON MUCINOUS ADENOCARCINOMA             1             46
  RECTAL ADENOCARCINOMA                     3            103
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  PON3 MUTATED     7   0   0   4
  PON3 WILD-TYPE 338   4  31  21
D143V11, multiclass
    clus
vv   PON3 MUTATED PON3 WILD-TYPE
  R0            7            338
  R1            0              4
  R2            0             31
  RX            4             21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D143V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PON3 MUTATED                                  0     2
  PON3 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  PON3 MUTATED                           0     8
  PON3 WILD-TYPE                        22   218
D143V13, multiclass
                                  clus
vv                                 PON3 MUTATED PON3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              9
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       8            218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(144) Variable = SLAMF7 MUTATION ANALYSIS
D144V1, survival
                  sevent
clus2                0   1
  SLAMF7 MUTATED     9   2
  SLAMF7 WILD-TYPE 369  91
  SLAMF7 MUTATED SLAMF7 WILD-TYPE 
              11              460 
  SLAMF7 MUTATED SLAMF7 WILD-TYPE 
               2               91 
$`SLAMF7 MUTATED`
TCGA-A6-5665 TCGA-AA-3510 TCGA-AA-3662 TCGA-AA-A00N TCGA-AA-A010 TCGA-CK-6748 
       22.06        63.98         6.05         4.01        34.98         1.91 
TCGA-CM-5348 TCGA-CM-6168 TCGA-D5-6541 TCGA-F4-6809 TCGA-G4-6588 
       22.98        12.99        15.58        13.25        26.17 

$`SLAMF7 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 
       51.32         9.99        21.14        82.95       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       21.99        14.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6898 TCGA-D5-6920 
        4.80        17.13        12.49        16.14         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        35.80        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  SLAMF7 MUTATED SLAMF7 WILD-TYPE 
            1.91             0.00 
  SLAMF7 MUTATED SLAMF7 WILD-TYPE 
           63.98           148.01 
  SLAMF7 MUTATED SLAMF7 WILD-TYPE 
          15.580           20.235 
[1] "1.9 - 64.0 (15.6)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.2"
D144V2, continuous
D144V3, binary
                  cls
clus                 0   1
  SLAMF7 MUTATED    11   0
  SLAMF7 WILD-TYPE 355 119
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLAMF7 MUTATED     11    0
  SLAMF7 WILD-TYPE  355  119
        clus
vv       SLAMF7 MUTATED SLAMF7 WILD-TYPE
  COLON              11              355
  RECTUM              0              119
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SLAMF7 MUTATED         0        0        1         4         2         0
  SLAMF7 WILD-TYPE      91        1       31       134         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLAMF7 MUTATED           0          0          1          0        2
  SLAMF7 WILD-TYPE        24         11         58         42       46
                  vv
clus               STAGE IVA STAGE IVB
  SLAMF7 MUTATED           1         0
  SLAMF7 WILD-TYPE        17         1
D144V4, multiclass
            clus
vv           SLAMF7 MUTATED SLAMF7 WILD-TYPE
  STAGE I                 0               91
  STAGE IA                0                1
  STAGE II                1               31
  STAGE IIA               4              134
  STAGE IIB               2                8
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              1               58
  STAGE IIIC              0               42
  STAGE IV                2               46
  STAGE IVA               1               17
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  SLAMF7 MUTATED     0   0   8   3
  SLAMF7 WILD-TYPE  17  92 321  47
D144V5, multiclass
    clus
vv   SLAMF7 MUTATED SLAMF7 WILD-TYPE
  T1              0               17
  T2              0               92
  T3              8              321
  T4              3               47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  SLAMF7 MUTATED     7   3   1
  SLAMF7 WILD-TYPE 280 110  86
D144V6, multiclass
    clus
vv   SLAMF7 MUTATED SLAMF7 WILD-TYPE
  N0              7              280
  N1              3              110
  N2              1               86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D144V7, binary
                  cls
clus                 0   1
  SLAMF7 MUTATED     8   3
  SLAMF7 WILD-TYPE 367  62
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLAMF7 MUTATED      8    3
  SLAMF7 WILD-TYPE  367   62
   clus
vv  SLAMF7 MUTATED SLAMF7 WILD-TYPE
  0              8              367
  1              3               62
[1] 2 2
[1] FALSE
D144V8, binary
                  cls
clus                 0   1
  SLAMF7 MUTATED     7   4
  SLAMF7 WILD-TYPE 218 260
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLAMF7 MUTATED      7    4
  SLAMF7 WILD-TYPE  218  260
        clus
vv       SLAMF7 MUTATED SLAMF7 WILD-TYPE
  FEMALE              7              218
  MALE                4              260
[1] 2 2
[1] FALSE
D144V9, binary
                  cls
clus                 0   1
  SLAMF7 MUTATED    10   0
  SLAMF7 WILD-TYPE 340  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLAMF7 MUTATED     10    0
  SLAMF7 WILD-TYPE  340   22
     clus
vv    SLAMF7 MUTATED SLAMF7 WILD-TYPE
  NO              10              340
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SLAMF7 MUTATED                      9                             2
  SLAMF7 WILD-TYPE                  306                            45
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SLAMF7 MUTATED                       0                              0
  SLAMF7 WILD-TYPE                   106                             10
D144V10, multiclass
                                clus
vv                               SLAMF7 MUTATED SLAMF7 WILD-TYPE
  COLON ADENOCARCINOMA                        9              306
  COLON MUCINOUS ADENOCARCINOMA               2               45
  RECTAL ADENOCARCINOMA                       0              106
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  SLAMF7 MUTATED     9   0   1   1
  SLAMF7 WILD-TYPE 336   4  30  24
D144V11, multiclass
    clus
vv   SLAMF7 MUTATED SLAMF7 WILD-TYPE
  R0              9              336
  R1              0                4
  R2              1               30
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D144V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SLAMF7 MUTATED                                  0     0
  SLAMF7 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  SLAMF7 MUTATED                           1     6
  SLAMF7 WILD-TYPE                        21   220
D144V13, multiclass
                                  clus
vv                                 SLAMF7 MUTATED SLAMF7 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                         6              220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(145) Variable = ATG5 MUTATION ANALYSIS
D145V1, survival
                sevent
clus2              0   1
  ATG5 MUTATED     8   0
  ATG5 WILD-TYPE 370  93
  ATG5 MUTATED ATG5 WILD-TYPE 
             8            463 
  ATG5 MUTATED ATG5 WILD-TYPE 
             0             93 
$`ATG5 MUTATED`
TCGA-AA-3977 TCGA-AA-A017 TCGA-AY-6197 TCGA-CM-4744 TCGA-D5-6532 TCGA-D5-6540 
       25.02         1.02        21.44        20.02        18.25        16.14 
TCGA-D5-6929 TCGA-AG-A002 
        4.80        20.98 

$`ATG5 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        34.98        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       33.01        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
        1.91       124.27        23.05        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6533 
       12.26        19.59        56.09        55.92        20.19         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.04         9.44        11.64         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  ATG5 MUTATED ATG5 WILD-TYPE 
          1.02           0.00 
  ATG5 MUTATED ATG5 WILD-TYPE 
         25.02         148.01 
  ATG5 MUTATED ATG5 WILD-TYPE 
        19.135         20.280 
[1] "1.0 - 25.0 (19.1)"  "0.0 - 148.0 (20.3)"
[1] "hr="     "9100000"
D145V2, continuous
D145V3, binary
                cls
clus               0   1
  ATG5 MUTATED     8   1
  ATG5 WILD-TYPE 358 118
[1] "tbl2"
                cls
clus             [,1] [,2]
  ATG5 MUTATED      8    1
  ATG5 WILD-TYPE  358  118
        clus
vv       ATG5 MUTATED ATG5 WILD-TYPE
  COLON             8            358
  RECTUM            1            118
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ATG5 MUTATED         3        0        0         3         1         0
  ATG5 WILD-TYPE      88        1       32       135         9         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ATG5 MUTATED           0          0          0          0        1         0
  ATG5 WILD-TYPE        24         11         59         42       47        18
                vv
clus             STAGE IVB
  ATG5 MUTATED           0
  ATG5 WILD-TYPE         1
D145V4, multiclass
            clus
vv           ATG5 MUTATED ATG5 WILD-TYPE
  STAGE I               3             88
  STAGE IA              0              1
  STAGE II              0             32
  STAGE IIA             3            135
  STAGE IIB             1              9
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            0             59
  STAGE IIIC            0             42
  STAGE IV              1             47
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  ATG5 MUTATED     0   4   4   1
  ATG5 WILD-TYPE  17  88 325  49
D145V5, multiclass
    clus
vv   ATG5 MUTATED ATG5 WILD-TYPE
  T1            0             17
  T2            4             88
  T3            4            325
  T4            1             49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  ATG5 MUTATED     8   1   0
  ATG5 WILD-TYPE 279 112  87
D145V6, multiclass
    clus
vv   ATG5 MUTATED ATG5 WILD-TYPE
  N0            8            279
  N1            1            112
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D145V7, binary
                cls
clus               0   1
  ATG5 MUTATED     5   1
  ATG5 WILD-TYPE 370  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  ATG5 MUTATED      5    1
  ATG5 WILD-TYPE  370   64
   clus
vv  ATG5 MUTATED ATG5 WILD-TYPE
  0            5            370
  1            1             64
[1] 2 2
[1] FALSE
D145V8, binary
                cls
clus               0   1
  ATG5 MUTATED     3   6
  ATG5 WILD-TYPE 222 258
[1] "tbl2"
                cls
clus             [,1] [,2]
  ATG5 MUTATED      3    6
  ATG5 WILD-TYPE  222  258
        clus
vv       ATG5 MUTATED ATG5 WILD-TYPE
  FEMALE            3            222
  MALE              6            258
[1] 2 2
[1] FALSE
D145V9, binary
                cls
clus               0   1
  ATG5 MUTATED     6   0
  ATG5 WILD-TYPE 344  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  ATG5 MUTATED      6    0
  ATG5 WILD-TYPE  344   22
     clus
vv    ATG5 MUTATED ATG5 WILD-TYPE
  NO             6            344
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ATG5 MUTATED                      7                             1
  ATG5 WILD-TYPE                  308                            46
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ATG5 MUTATED                       1                              0
  ATG5 WILD-TYPE                   105                             10
D145V10, multiclass
                                clus
vv                               ATG5 MUTATED ATG5 WILD-TYPE
  COLON ADENOCARCINOMA                      7            308
  COLON MUCINOUS ADENOCARCINOMA             1             46
  RECTAL ADENOCARCINOMA                     1            105
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  ATG5 MUTATED     7   0   0   1
  ATG5 WILD-TYPE 338   4  31  24
D145V11, multiclass
    clus
vv   ATG5 MUTATED ATG5 WILD-TYPE
  R0            7            338
  R1            0              4
  R2            0             31
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D145V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ATG5 MUTATED                                  0     0
  ATG5 WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  ATG5 MUTATED                           0     6
  ATG5 WILD-TYPE                        22   220
D145V13, multiclass
                                  clus
vv                                 ATG5 MUTATED ATG5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       6            220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(146) Variable = SCAI MUTATION ANALYSIS
D146V1, survival
                sevent
clus2              0   1
  SCAI MUTATED    11   3
  SCAI WILD-TYPE 367  90
  SCAI MUTATED SCAI WILD-TYPE 
            14            457 
  SCAI MUTATED SCAI WILD-TYPE 
             3             90 
$`SCAI MUTATED`
TCGA-AA-3950 TCGA-AA-A01R TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-5403 TCGA-CA-6717 
       24.00        35.01        15.52         0.72        62.79        12.76 
TCGA-CK-5913 TCGA-D5-6541 TCGA-D5-6927 TCGA-DM-A1HB TCGA-DM-A285 TCGA-DM-A28H 
       51.32        15.58         9.44       135.65         6.12       117.07 
TCGA-DM-A28K TCGA-AG-A002 
       98.24        20.98 

$`SCAI WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S 
       12.00        31.00        31.00        38.07         1.02         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6889 
       39.98        18.05        40.96         0.07        21.37        56.55 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.79         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07        12.20        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 
       17.56       148.01        85.45        15.62        49.08         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6898 
       17.85         4.80        17.13        12.49        16.14         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6928 
        3.68         4.41        12.43        14.30         9.04        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 
       12.59       140.38         7.50        44.32       131.51       139.17 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-F4-6459 TCGA-F4-6460 
       81.37       119.93        35.97        60.79         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  SCAI MUTATED SCAI WILD-TYPE 
          0.72           0.00 
  SCAI MUTATED SCAI WILD-TYPE 
        135.65         148.01 
  SCAI MUTATED SCAI WILD-TYPE 
         22.49          20.12 
[1] "0.7 - 135.7 (22.5)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.4"
D146V2, continuous
D146V3, binary
                cls
clus               0   1
  SCAI MUTATED    14   1
  SCAI WILD-TYPE 352 118
[1] "tbl2"
                cls
clus             [,1] [,2]
  SCAI MUTATED     14    1
  SCAI WILD-TYPE  352  118
        clus
vv       SCAI MUTATED SCAI WILD-TYPE
  COLON            14            352
  RECTUM            1            118
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SCAI MUTATED         1        0        1         7         0         0
  SCAI WILD-TYPE      90        1       31       131        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SCAI MUTATED           1          0          2          1        1         0
  SCAI WILD-TYPE        23         11         57         41       47        18
                vv
clus             STAGE IVB
  SCAI MUTATED           0
  SCAI WILD-TYPE         1
D146V4, multiclass
            clus
vv           SCAI MUTATED SCAI WILD-TYPE
  STAGE I               1             90
  STAGE IA              0              1
  STAGE II              1             31
  STAGE IIA             7            131
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             1             23
  STAGE IIIA            0             11
  STAGE IIIB            2             57
  STAGE IIIC            1             41
  STAGE IV              1             47
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  SCAI MUTATED     0   1  14   0
  SCAI WILD-TYPE  17  91 315  50
D146V5, multiclass
    clus
vv   SCAI MUTATED SCAI WILD-TYPE
  T1            0             17
  T2            1             91
  T3           14            315
  T4            0             50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  SCAI MUTATED     9   3   3
  SCAI WILD-TYPE 278 110  84
D146V6, multiclass
    clus
vv   SCAI MUTATED SCAI WILD-TYPE
  N0            9            278
  N1            3            110
  N2            3             84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D146V7, binary
                cls
clus               0   1
  SCAI MUTATED    11   1
  SCAI WILD-TYPE 364  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  SCAI MUTATED     11    1
  SCAI WILD-TYPE  364   64
   clus
vv  SCAI MUTATED SCAI WILD-TYPE
  0           11            364
  1            1             64
[1] 2 2
[1] FALSE
D146V8, binary
                cls
clus               0   1
  SCAI MUTATED     4  11
  SCAI WILD-TYPE 221 253
[1] "tbl2"
                cls
clus             [,1] [,2]
  SCAI MUTATED      4   11
  SCAI WILD-TYPE  221  253
        clus
vv       SCAI MUTATED SCAI WILD-TYPE
  FEMALE            4            221
  MALE             11            253
[1] 2 2
[1] FALSE
D146V9, binary
                cls
clus               0   1
  SCAI MUTATED     8   1
  SCAI WILD-TYPE 342  21
[1] "tbl2"
                cls
clus             [,1] [,2]
  SCAI MUTATED      8    1
  SCAI WILD-TYPE  342   21
     clus
vv    SCAI MUTATED SCAI WILD-TYPE
  NO             8            342
  YES            1             21
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SCAI MUTATED                      8                             5
  SCAI WILD-TYPE                  307                            42
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SCAI MUTATED                       1                              0
  SCAI WILD-TYPE                   105                             10
D146V10, multiclass
                                clus
vv                               SCAI MUTATED SCAI WILD-TYPE
  COLON ADENOCARCINOMA                      8            307
  COLON MUCINOUS ADENOCARCINOMA             5             42
  RECTAL ADENOCARCINOMA                     1            105
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  SCAI MUTATED     7   0   0   2
  SCAI WILD-TYPE 338   4  31  23
D146V11, multiclass
    clus
vv   SCAI MUTATED SCAI WILD-TYPE
  R0            7            338
  R1            0              4
  R2            0             31
  RX            2             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D146V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SCAI MUTATED                                  0     1
  SCAI WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  SCAI MUTATED                           0    10
  SCAI WILD-TYPE                        22   216
D146V13, multiclass
                                  clus
vv                                 SCAI MUTATED SCAI WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                      10            216
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(147) Variable = TAF7L MUTATION ANALYSIS
D147V1, survival
                 sevent
clus2               0   1
  TAF7L MUTATED     9   4
  TAF7L WILD-TYPE 369  89
  TAF7L MUTATED TAF7L WILD-TYPE 
             13             458 
  TAF7L MUTATED TAF7L WILD-TYPE 
              4              89 
$`TAF7L MUTATED`
TCGA-A6-4105 TCGA-A6-5665 TCGA-AA-3875 TCGA-AA-A010 TCGA-CM-4743 TCGA-D5-6929 
       14.53        22.06        18.05        34.98        23.05         4.80 
TCGA-F4-6570 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6321 TCGA-AG-3892 
        6.18        65.85        44.68        85.48        22.09        13.02 
TCGA-F5-6464 
        9.96 

$`TAF7L WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 
       16.57        34.65        33.34        32.75        36.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       24.03        27.02        29.98        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
      124.27        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 
       14.30         9.04         9.44        11.64         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       31.96        35.74        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 
      133.18        74.56        53.62        55.04        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       36.00        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       17.95        36.95        17.03        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  TAF7L MUTATED TAF7L WILD-TYPE 
            4.8             0.0 
  TAF7L MUTATED TAF7L WILD-TYPE 
          85.48          148.01 
  TAF7L MUTATED TAF7L WILD-TYPE 
         22.060          20.155 
[1] "4.8 - 85.5 (22.1)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.4"
D147V2, continuous
D147V3, binary
                 cls
clus                0   1
  TAF7L MUTATED    11   2
  TAF7L WILD-TYPE 355 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TAF7L MUTATED     11    2
  TAF7L WILD-TYPE  355  117
        clus
vv       TAF7L MUTATED TAF7L WILD-TYPE
  COLON             11             355
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TAF7L MUTATED         2        0        0         5         1         0
  TAF7L WILD-TYPE      89        1       32       133         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TAF7L MUTATED           1          0          1          1        2         0
  TAF7L WILD-TYPE        23         11         58         41       46        18
                 vv
clus              STAGE IVB
  TAF7L MUTATED           0
  TAF7L WILD-TYPE         1
D147V4, multiclass
            clus
vv           TAF7L MUTATED TAF7L WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              5             133
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             1              41
  STAGE IV               2              46
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  TAF7L MUTATED     2   2   7   2
  TAF7L WILD-TYPE  15  90 322  48
D147V5, multiclass
    clus
vv   TAF7L MUTATED TAF7L WILD-TYPE
  T1             2              15
  T2             2              90
  T3             7             322
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  TAF7L MUTATED     8   4   1
  TAF7L WILD-TYPE 279 109  86
D147V6, multiclass
    clus
vv   TAF7L MUTATED TAF7L WILD-TYPE
  N0             8             279
  N1             4             109
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D147V7, binary
                 cls
clus                0   1
  TAF7L MUTATED    10   2
  TAF7L WILD-TYPE 365  63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TAF7L MUTATED     10    2
  TAF7L WILD-TYPE  365   63
   clus
vv  TAF7L MUTATED TAF7L WILD-TYPE
  0            10             365
  1             2              63
[1] 2 2
[1] FALSE
D147V8, binary
                 cls
clus                0   1
  TAF7L MUTATED    10   3
  TAF7L WILD-TYPE 215 261
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TAF7L MUTATED     10    3
  TAF7L WILD-TYPE  215  261
        clus
vv       TAF7L MUTATED TAF7L WILD-TYPE
  FEMALE            10             215
  MALE               3             261
[1] 2 2
[1] FALSE
D147V9, binary
                 cls
clus                0   1
  TAF7L MUTATED    12   0
  TAF7L WILD-TYPE 338  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TAF7L MUTATED     12    0
  TAF7L WILD-TYPE  338   22
     clus
vv    TAF7L MUTATED TAF7L WILD-TYPE
  NO             12             338
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  TAF7L MUTATED                     11                             0
  TAF7L WILD-TYPE                  304                            47
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  TAF7L MUTATED                       2                              0
  TAF7L WILD-TYPE                   104                             10
D147V10, multiclass
                                clus
vv                               TAF7L MUTATED TAF7L WILD-TYPE
  COLON ADENOCARCINOMA                      11             304
  COLON MUCINOUS ADENOCARCINOMA              0              47
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  TAF7L MUTATED    12   0   0   0
  TAF7L WILD-TYPE 333   4  31  25
D147V11, multiclass
    clus
vv   TAF7L MUTATED TAF7L WILD-TYPE
  R0            12             333
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D147V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TAF7L MUTATED                                  0     0
  TAF7L WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  TAF7L MUTATED                           1     9
  TAF7L WILD-TYPE                        21   217
D147V13, multiclass
                                  clus
vv                                 TAF7L MUTATED TAF7L WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        9             217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(148) Variable = ECT2 MUTATION ANALYSIS
D148V1, survival
                sevent
clus2              0   1
  ECT2 MUTATED    14   5
  ECT2 WILD-TYPE 364  88
  ECT2 MUTATED ECT2 WILD-TYPE 
            19            452 
  ECT2 MUTATED ECT2 WILD-TYPE 
             5             88 
$`ECT2 MUTATED`
TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-6781 TCGA-AA-3713 TCGA-AA-3950 TCGA-AA-A00D 
       46.65        42.90        19.66        19.04        24.00        19.00 
TCGA-AA-A00N TCGA-AZ-5403 TCGA-AZ-6608 TCGA-CK-5913 TCGA-CM-5861 TCGA-CM-6170 
        4.01        62.79         1.61        51.32        15.02        15.02 
TCGA-D5-6926 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6309 TCGA-G4-6586 TCGA-G4-6628 
        9.04        65.85        53.62        85.48        35.80        79.69 
TCGA-AG-A002 
       20.98 

$`ECT2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       43.76        43.76        24.33        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5657 
       33.34        32.75        36.53        14.53        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       30.44        29.19        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       85.05        26.99        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       33.01        26.01         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       27.02        13.94        38.04        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
        5.13       106.75        22.36        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        49.08         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 
       29.06        22.03        22.98        30.08        32.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 
      133.18        74.56        44.68        55.04        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        26.17        91.79        46.75 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  ECT2 MUTATED ECT2 WILD-TYPE 
          1.61           0.00 
  ECT2 MUTATED ECT2 WILD-TYPE 
         85.48         148.01 
  ECT2 MUTATED ECT2 WILD-TYPE 
        24.000         20.085 
[1] "1.6 - 85.5 (24.0)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.1"
D148V2, continuous
D148V3, binary
                cls
clus               0   1
  ECT2 MUTATED    18   1
  ECT2 WILD-TYPE 348 118
[1] "tbl2"
                cls
clus             [,1] [,2]
  ECT2 MUTATED     18    1
  ECT2 WILD-TYPE  348  118
        clus
vv       ECT2 MUTATED ECT2 WILD-TYPE
  COLON            18            348
  RECTUM            1            118
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ECT2 MUTATED         4        0        1         4         3         0
  ECT2 WILD-TYPE      87        1       31       134         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ECT2 MUTATED           0          1          3          1        2         0
  ECT2 WILD-TYPE        24         10         56         41       46        18
                vv
clus             STAGE IVB
  ECT2 MUTATED           0
  ECT2 WILD-TYPE         1
D148V4, multiclass
            clus
vv           ECT2 MUTATED ECT2 WILD-TYPE
  STAGE I               4             87
  STAGE IA              0              1
  STAGE II              1             31
  STAGE IIA             4            134
  STAGE IIB             3              7
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            1             10
  STAGE IIIB            3             56
  STAGE IIIC            1             41
  STAGE IV              2             46
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  ECT2 MUTATED     0   5   9   5
  ECT2 WILD-TYPE  17  87 320  45
D148V5, multiclass
    clus
vv   ECT2 MUTATED ECT2 WILD-TYPE
  T1            0             17
  T2            5             87
  T3            9            320
  T4            5             45
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  ECT2 MUTATED    13   6   0
  ECT2 WILD-TYPE 274 107  87
D148V6, multiclass
    clus
vv   ECT2 MUTATED ECT2 WILD-TYPE
  N0           13            274
  N1            6            107
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D148V7, binary
                cls
clus               0   1
  ECT2 MUTATED    14   2
  ECT2 WILD-TYPE 361  63
[1] "tbl2"
                cls
clus             [,1] [,2]
  ECT2 MUTATED     14    2
  ECT2 WILD-TYPE  361   63
   clus
vv  ECT2 MUTATED ECT2 WILD-TYPE
  0           14            361
  1            2             63
[1] 2 2
[1] FALSE
D148V8, binary
                cls
clus               0   1
  ECT2 MUTATED    11   8
  ECT2 WILD-TYPE 214 256
[1] "tbl2"
                cls
clus             [,1] [,2]
  ECT2 MUTATED     11    8
  ECT2 WILD-TYPE  214  256
        clus
vv       ECT2 MUTATED ECT2 WILD-TYPE
  FEMALE           11            214
  MALE              8            256
[1] 2 2
[1] FALSE
D148V9, binary
                cls
clus               0   1
  ECT2 MUTATED    16   2
  ECT2 WILD-TYPE 334  20
[1] "tbl2"
                cls
clus             [,1] [,2]
  ECT2 MUTATED     16    2
  ECT2 WILD-TYPE  334   20
     clus
vv    ECT2 MUTATED ECT2 WILD-TYPE
  NO            16            334
  YES            2             20
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ECT2 MUTATED                     15                             3
  ECT2 WILD-TYPE                  300                            44
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ECT2 MUTATED                       1                              0
  ECT2 WILD-TYPE                   105                             10
D148V10, multiclass
                                clus
vv                               ECT2 MUTATED ECT2 WILD-TYPE
  COLON ADENOCARCINOMA                     15            300
  COLON MUCINOUS ADENOCARCINOMA             3             44
  RECTAL ADENOCARCINOMA                     1            105
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  ECT2 MUTATED    15   0   1   1
  ECT2 WILD-TYPE 330   4  30  24
D148V11, multiclass
    clus
vv   ECT2 MUTATED ECT2 WILD-TYPE
  R0           15            330
  R1            0              4
  R2            1             30
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D148V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ECT2 MUTATED                                  0     0
  ECT2 WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  ECT2 MUTATED                           1    13
  ECT2 WILD-TYPE                        21   213
D148V13, multiclass
                                  clus
vv                                 ECT2 MUTATED ECT2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                      13            213
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(149) Variable = DUSP1 MUTATION ANALYSIS
D149V1, survival
                 sevent
clus2               0   1
  DUSP1 MUTATED     7   0
  DUSP1 WILD-TYPE 371  93
  DUSP1 MUTATED DUSP1 WILD-TYPE 
              7             464 
  DUSP1 MUTATED DUSP1 WILD-TYPE 
              0              93 
$`DUSP1 MUTATED`
TCGA-A6-5657 TCGA-AA-3514 TCGA-AA-3655 TCGA-AA-3660 TCGA-CA-5796 TCGA-G4-6628 
       31.63         1.02        61.02        78.08         3.25        79.69 
TCGA-F5-6811 
       32.19 

$`DUSP1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01        63.98         6.97        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        19.99         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.06         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6812 TCGA-F5-6813 
        9.96        49.51        31.30        28.57         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  DUSP1 MUTATED DUSP1 WILD-TYPE 
           1.02            0.00 
  DUSP1 MUTATED DUSP1 WILD-TYPE 
          79.69          148.01 
  DUSP1 MUTATED DUSP1 WILD-TYPE 
         32.190          20.085 
[1] "1.0 - 79.7 (32.2)"  "0.0 - 148.0 (20.1)"
[1] "hr="     "9400000"
D149V2, continuous
D149V3, binary
                 cls
clus                0   1
  DUSP1 MUTATED     6   1
  DUSP1 WILD-TYPE 360 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DUSP1 MUTATED      6    1
  DUSP1 WILD-TYPE  360  118
        clus
vv       DUSP1 MUTATED DUSP1 WILD-TYPE
  COLON              6             360
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DUSP1 MUTATED         2        0        2         2         0         0
  DUSP1 WILD-TYPE      89        1       30       136        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DUSP1 MUTATED           0          0          1          0        0         0
  DUSP1 WILD-TYPE        24         11         58         42       48        18
                 vv
clus              STAGE IVB
  DUSP1 MUTATED           0
  DUSP1 WILD-TYPE         1
D149V4, multiclass
            clus
vv           DUSP1 MUTATED DUSP1 WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA              2             136
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  DUSP1 MUTATED     0   2   5   0
  DUSP1 WILD-TYPE  17  90 324  50
D149V5, multiclass
    clus
vv   DUSP1 MUTATED DUSP1 WILD-TYPE
  T1             0              17
  T2             2              90
  T3             5             324
  T4             0              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  DUSP1 MUTATED     6   1   0
  DUSP1 WILD-TYPE 281 112  87
D149V6, multiclass
    clus
vv   DUSP1 MUTATED DUSP1 WILD-TYPE
  N0             6             281
  N1             1             112
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D149V7, binary
                 cls
clus                0   1
  DUSP1 MUTATED     7   0
  DUSP1 WILD-TYPE 368  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DUSP1 MUTATED      7    0
  DUSP1 WILD-TYPE  368   65
   clus
vv  DUSP1 MUTATED DUSP1 WILD-TYPE
  0             7             368
  1             0              65
[1] 2 2
[1] FALSE
D149V8, binary
                 cls
clus                0   1
  DUSP1 MUTATED     4   3
  DUSP1 WILD-TYPE 221 261
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DUSP1 MUTATED      4    3
  DUSP1 WILD-TYPE  221  261
        clus
vv       DUSP1 MUTATED DUSP1 WILD-TYPE
  FEMALE             4             221
  MALE               3             261
[1] 2 2
[1] FALSE
D149V9, binary
                 cls
clus                0   1
  DUSP1 MUTATED     7   0
  DUSP1 WILD-TYPE 343  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DUSP1 MUTATED      7    0
  DUSP1 WILD-TYPE  343   22
     clus
vv    DUSP1 MUTATED DUSP1 WILD-TYPE
  NO              7             343
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  DUSP1 MUTATED                      5                             1
  DUSP1 WILD-TYPE                  310                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  DUSP1 MUTATED                       1                              0
  DUSP1 WILD-TYPE                   105                             10
D149V10, multiclass
                                clus
vv                               DUSP1 MUTATED DUSP1 WILD-TYPE
  COLON ADENOCARCINOMA                       5             310
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  DUSP1 MUTATED     6   0   0   0
  DUSP1 WILD-TYPE 339   4  31  25
D149V11, multiclass
    clus
vv   DUSP1 MUTATED DUSP1 WILD-TYPE
  R0             6             339
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D149V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DUSP1 MUTATED                                  0     1
  DUSP1 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  DUSP1 MUTATED                           1     2
  DUSP1 WILD-TYPE                        21   224
D149V13, multiclass
                                  clus
vv                                 DUSP1 MUTATED DUSP1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        2             224
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(150) Variable = ZFX MUTATION ANALYSIS
D150V1, survival
               sevent
clus2             0   1
  ZFX MUTATED     9   4
  ZFX WILD-TYPE 369  89
  ZFX MUTATED ZFX WILD-TYPE 
           13           458 
  ZFX MUTATED ZFX WILD-TYPE 
            4            89 
$`ZFX MUTATED`
TCGA-A6-2676 TCGA-A6-5656 TCGA-A6-5662 TCGA-AA-3492 TCGA-AA-3516 TCGA-AA-3949 
       42.90        32.91        23.61         3.02        13.02        26.01 
TCGA-AA-3966 TCGA-AA-A010 TCGA-AD-6889 TCGA-AZ-6599 TCGA-CM-5860 TCGA-G4-6588 
        2.01        34.98        56.55         6.77        32.02        26.17 
TCGA-AF-2693 
       19.10 

$`ZFX WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5657 
       34.65        33.34        32.75        36.53        14.53        31.63 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 
       30.44        29.19        33.53        22.09        22.06        32.71 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       27.09        22.52         8.38        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
       20.28         7.04         1.02        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
        1.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       36.03         8.05        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       78.08         6.05         6.97        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 
       24.00         2.01        20.98        34.03        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        88.21        49.41        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-5862 
       29.06        22.03        22.98        30.08        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       22.09        13.78        35.80        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3913 
       24.13        39.48        43.04        13.55        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  ZFX MUTATED ZFX WILD-TYPE 
         2.01          0.00 
  ZFX MUTATED ZFX WILD-TYPE 
        56.55        148.01 
  ZFX MUTATED ZFX WILD-TYPE 
       26.010        20.085 
[1] "2.0 - 56.5 (26.0)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.7"
D150V2, continuous
D150V3, binary
               cls
clus              0   1
  ZFX MUTATED    13   0
  ZFX WILD-TYPE 353 119
[1] "tbl2"
               cls
clus            [,1] [,2]
  ZFX MUTATED     13    0
  ZFX WILD-TYPE  353  119
        clus
vv       ZFX MUTATED ZFX WILD-TYPE
  COLON           13           353
  RECTUM           0           119
[1] 2 2
[1] FALSE
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZFX MUTATED         3        0        1         4         2         0
  ZFX WILD-TYPE      88        1       31       134         8         1
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ZFX MUTATED           1          0          1          1        0         1
  ZFX WILD-TYPE        23         11         58         41       48        17
               vv
clus            STAGE IVB
  ZFX MUTATED           0
  ZFX WILD-TYPE         1
D150V4, multiclass
            clus
vv           ZFX MUTATED ZFX WILD-TYPE
  STAGE I              3            88
  STAGE IA             0             1
  STAGE II             1            31
  STAGE IIA            4           134
  STAGE IIB            2             8
  STAGE IIC            0             1
  STAGE III            1            23
  STAGE IIIA           0            11
  STAGE IIIB           1            58
  STAGE IIIC           1            41
  STAGE IV             0            48
  STAGE IVA            1            17
  STAGE IVB            0             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  ZFX MUTATED     0   3   9   2
  ZFX WILD-TYPE  17  89 320  48
D150V5, multiclass
    clus
vv   ZFX MUTATED ZFX WILD-TYPE
  T1           0            17
  T2           3            89
  T3           9           320
  T4           2            48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2
  ZFX MUTATED    10   1   3
  ZFX WILD-TYPE 277 112  84
D150V6, multiclass
    clus
vv   ZFX MUTATED ZFX WILD-TYPE
  N0          10           277
  N1           1           112
  N2           3            84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D150V7, binary
               cls
clus              0   1
  ZFX MUTATED    10   1
  ZFX WILD-TYPE 365  64
[1] "tbl2"
               cls
clus            [,1] [,2]
  ZFX MUTATED     10    1
  ZFX WILD-TYPE  365   64
   clus
vv  ZFX MUTATED ZFX WILD-TYPE
  0          10           365
  1           1            64
[1] 2 2
[1] FALSE
D150V8, binary
               cls
clus              0   1
  ZFX MUTATED     7   7
  ZFX WILD-TYPE 218 257
[1] "tbl2"
               cls
clus            [,1] [,2]
  ZFX MUTATED      7    7
  ZFX WILD-TYPE  218  257
        clus
vv       ZFX MUTATED ZFX WILD-TYPE
  FEMALE           7           218
  MALE             7           257
[1] 2 2
[1] FALSE
D150V9, binary
               cls
clus              0   1
  ZFX MUTATED    11   0
  ZFX WILD-TYPE 339  22
[1] "tbl2"
               cls
clus            [,1] [,2]
  ZFX MUTATED     11    0
  ZFX WILD-TYPE  339   22
     clus
vv    ZFX MUTATED ZFX WILD-TYPE
  NO           11           339
  YES           0            22
[1] 2 2
[1] FALSE
               vv
clus            COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ZFX MUTATED                      9                             4
  ZFX WILD-TYPE                  306                            43
               vv
clus            RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ZFX MUTATED                       0                              0
  ZFX WILD-TYPE                   106                             10
D150V10, multiclass
                                clus
vv                               ZFX MUTATED ZFX WILD-TYPE
  COLON ADENOCARCINOMA                     9           306
  COLON MUCINOUS ADENOCARCINOMA            4            43
  RECTAL ADENOCARCINOMA                    0           106
  RECTAL MUCINOUS ADENOCARCINOMA           0            10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             R0  R1  R2  RX
  ZFX MUTATED     7   0   0   0
  ZFX WILD-TYPE 338   4  31  25
D150V11, multiclass
    clus
vv   ZFX MUTATED ZFX WILD-TYPE
  R0           7           338
  R1           0             4
  R2           0            31
  RX           0            25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D150V12, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZFX MUTATED                                  0     1
  ZFX WILD-TYPE                                1    10
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  ZFX MUTATED                           0     8
  ZFX WILD-TYPE                        22   218
D150V13, multiclass
                                  clus
vv                                 ZFX MUTATED ZFX WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      1            10
  BLACK OR AFRICAN AMERICAN                  0            22
  WHITE                                      8           218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(151) Variable = ATP11B MUTATION ANALYSIS
D151V1, survival
                  sevent
clus2                0   1
  ATP11B MUTATED    15   3
  ATP11B WILD-TYPE 363  90
  ATP11B MUTATED ATP11B WILD-TYPE 
              18              453 
  ATP11B MUTATED ATP11B WILD-TYPE 
               3               90 
$`ATP11B MUTATED`
TCGA-AA-3516 TCGA-AA-3672 TCGA-AA-3713 TCGA-AZ-4315 TCGA-CA-6717 TCGA-CA-6718 
       13.02         0.92        19.04        58.39        12.76        10.06 
TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-5861 TCGA-CM-6170 TCGA-D5-6533 TCGA-DM-A0XD 
       23.05        37.02        15.02        15.02         1.32        24.43 
TCGA-F4-6569 TCGA-F4-6808 TCGA-G4-6304 TCGA-G4-6315 TCGA-AG-A002 TCGA-CI-6624 
       35.74        33.67        53.62        61.91        20.98         4.73 

$`ATP11B WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        1.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 
        6.97        54.02         2.01        14.01        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 
        3.06         3.25         3.29         0.07        12.20        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 
        9.99        21.14        82.95         1.91       124.27        20.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       32.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       12.99        13.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XF TCGA-DM-A1D0 
       12.00        11.38        10.26       119.70        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       31.96         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       16.24        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       74.56        65.85        44.68        55.04        85.48        63.62 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        6.97        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  ATP11B MUTATED ATP11B WILD-TYPE 
            0.92             0.00 
  ATP11B MUTATED ATP11B WILD-TYPE 
           61.91           148.01 
  ATP11B MUTATED ATP11B WILD-TYPE 
           20.01            20.19 
[1] "0.9 - 61.9 (20.0)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.1"
D151V2, continuous
D151V3, binary
                  cls
clus                 0   1
  ATP11B MUTATED    17   2
  ATP11B WILD-TYPE 349 117
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP11B MUTATED     17    2
  ATP11B WILD-TYPE  349  117
        clus
vv       ATP11B MUTATED ATP11B WILD-TYPE
  COLON              17              349
  RECTUM              2              117
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ATP11B MUTATED         6        0        0         7         1         0
  ATP11B WILD-TYPE      85        1       32       131         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ATP11B MUTATED           2          0          1          0        2
  ATP11B WILD-TYPE        22         11         58         42       46
                  vv
clus               STAGE IVA STAGE IVB
  ATP11B MUTATED           0         0
  ATP11B WILD-TYPE        18         1
D151V4, multiclass
            clus
vv           ATP11B MUTATED ATP11B WILD-TYPE
  STAGE I                 6               85
  STAGE IA                0                1
  STAGE II                0               32
  STAGE IIA               7              131
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               2               22
  STAGE IIIA              0               11
  STAGE IIIB              1               58
  STAGE IIIC              0               42
  STAGE IV                2               46
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ATP11B MUTATED     1   5  11   2
  ATP11B WILD-TYPE  16  87 318  48
D151V5, multiclass
    clus
vv   ATP11B MUTATED ATP11B WILD-TYPE
  T1              1               16
  T2              5               87
  T3             11              318
  T4              2               48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  ATP11B MUTATED    16   2   1
  ATP11B WILD-TYPE 271 111  86
D151V6, multiclass
    clus
vv   ATP11B MUTATED ATP11B WILD-TYPE
  N0             16              271
  N1              2              111
  N2              1               86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D151V7, binary
                  cls
clus                 0   1
  ATP11B MUTATED    17   2
  ATP11B WILD-TYPE 358  63
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP11B MUTATED     17    2
  ATP11B WILD-TYPE  358   63
   clus
vv  ATP11B MUTATED ATP11B WILD-TYPE
  0             17              358
  1              2               63
[1] 2 2
[1] FALSE
D151V8, binary
                  cls
clus                 0   1
  ATP11B MUTATED     9  10
  ATP11B WILD-TYPE 216 254
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP11B MUTATED      9   10
  ATP11B WILD-TYPE  216  254
        clus
vv       ATP11B MUTATED ATP11B WILD-TYPE
  FEMALE              9              216
  MALE               10              254
[1] 2 2
[1] FALSE
D151V9, binary
                  cls
clus                 0   1
  ATP11B MUTATED    14   1
  ATP11B WILD-TYPE 336  21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP11B MUTATED     14    1
  ATP11B WILD-TYPE  336   21
     clus
vv    ATP11B MUTATED ATP11B WILD-TYPE
  NO              14              336
  YES              1               21
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ATP11B MUTATED                     15                             2
  ATP11B WILD-TYPE                  300                            45
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ATP11B MUTATED                       2                              0
  ATP11B WILD-TYPE                   104                             10
D151V10, multiclass
                                clus
vv                               ATP11B MUTATED ATP11B WILD-TYPE
  COLON ADENOCARCINOMA                       15              300
  COLON MUCINOUS ADENOCARCINOMA               2               45
  RECTAL ADENOCARCINOMA                       2              104
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ATP11B MUTATED    13   0   1   2
  ATP11B WILD-TYPE 332   4  30  23
D151V11, multiclass
    clus
vv   ATP11B MUTATED ATP11B WILD-TYPE
  R0             13              332
  R1              0                4
  R2              1               30
  RX              2               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D151V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ATP11B MUTATED                                  0     2
  ATP11B WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ATP11B MUTATED                           1    11
  ATP11B WILD-TYPE                        21   215
D151V13, multiclass
                                  clus
vv                                 ATP11B MUTATED ATP11B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                9
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                        11              215
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(152) Variable = NEFH MUTATION ANALYSIS
D152V1, survival
                sevent
clus2              0   1
  NEFH MUTATED    13   1
  NEFH WILD-TYPE 365  92
  NEFH MUTATED NEFH WILD-TYPE 
            14            457 
  NEFH MUTATED NEFH WILD-TYPE 
             1             92 
$`NEFH MUTATED`
TCGA-A6-6142 TCGA-AA-3947 TCGA-AA-A010 TCGA-AA-A02K TCGA-AD-6965 TCGA-AY-6197 
       25.08        33.01        34.98        14.01         0.20        21.44 
TCGA-AZ-4315 TCGA-CK-4948 TCGA-CM-6161 TCGA-D5-6920 TCGA-DM-A28K TCGA-F4-6856 
       58.39       148.01        15.02         3.68        98.24        35.31 
TCGA-G4-6588 TCGA-AG-A002 
       26.17        20.98 

$`NEFH WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
        2.01        12.99        24.00        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        2.01         5.03         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AU-3779 
        0.72         5.79        22.42        27.42        10.88        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4323 
       27.09        16.31         0.95        33.01        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6922 
       17.13        12.49        16.14        15.58         1.48         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       47.41       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       13.78        35.80        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  NEFH MUTATED NEFH WILD-TYPE 
           0.2            0.0 
  NEFH MUTATED NEFH WILD-TYPE 
        148.01         140.38 
  NEFH MUTATED NEFH WILD-TYPE 
        25.625         20.020 
[1] "0.2 - 148.0 (25.6)" "0.0 - 140.4 (20.0)"
[1] "hr=" "3.6"
D152V2, continuous
D152V3, binary
                cls
clus               0   1
  NEFH MUTATED    13   1
  NEFH WILD-TYPE 353 118
[1] "tbl2"
                cls
clus             [,1] [,2]
  NEFH MUTATED     13    1
  NEFH WILD-TYPE  353  118
        clus
vv       NEFH MUTATED NEFH WILD-TYPE
  COLON            13            353
  RECTUM            1            118
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NEFH MUTATED         3        0        0         5         2         0
  NEFH WILD-TYPE      88        1       32       133         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NEFH MUTATED           1          0          0          0        1         1
  NEFH WILD-TYPE        23         11         59         42       47        17
                vv
clus             STAGE IVB
  NEFH MUTATED           0
  NEFH WILD-TYPE         1
D152V4, multiclass
            clus
vv           NEFH MUTATED NEFH WILD-TYPE
  STAGE I               3             88
  STAGE IA              0              1
  STAGE II              0             32
  STAGE IIA             5            133
  STAGE IIB             2              8
  STAGE IIC             0              1
  STAGE III             1             23
  STAGE IIIA            0             11
  STAGE IIIB            0             59
  STAGE IIIC            0             42
  STAGE IV              1             47
  STAGE IVA             1             17
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  NEFH MUTATED     0   3   7   4
  NEFH WILD-TYPE  17  89 322  46
D152V5, multiclass
    clus
vv   NEFH MUTATED NEFH WILD-TYPE
  T1            0             17
  T2            3             89
  T3            7            322
  T4            4             46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  NEFH MUTATED    10   2   2
  NEFH WILD-TYPE 277 111  85
D152V6, multiclass
    clus
vv   NEFH MUTATED NEFH WILD-TYPE
  N0           10            277
  N1            2            111
  N2            2             85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D152V7, binary
                cls
clus               0   1
  NEFH MUTATED    10   2
  NEFH WILD-TYPE 365  63
[1] "tbl2"
                cls
clus             [,1] [,2]
  NEFH MUTATED     10    2
  NEFH WILD-TYPE  365   63
   clus
vv  NEFH MUTATED NEFH WILD-TYPE
  0           10            365
  1            2             63
[1] 2 2
[1] FALSE
D152V8, binary
                cls
clus               0   1
  NEFH MUTATED     7   7
  NEFH WILD-TYPE 218 257
[1] "tbl2"
                cls
clus             [,1] [,2]
  NEFH MUTATED      7    7
  NEFH WILD-TYPE  218  257
        clus
vv       NEFH MUTATED NEFH WILD-TYPE
  FEMALE            7            218
  MALE              7            257
[1] 2 2
[1] FALSE
D152V9, binary
                cls
clus               0   1
  NEFH MUTATED    11   0
  NEFH WILD-TYPE 339  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  NEFH MUTATED     11    0
  NEFH WILD-TYPE  339   22
     clus
vv    NEFH MUTATED NEFH WILD-TYPE
  NO            11            339
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  NEFH MUTATED                     10                             3
  NEFH WILD-TYPE                  305                            44
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  NEFH MUTATED                       1                              0
  NEFH WILD-TYPE                   105                             10
D152V10, multiclass
                                clus
vv                               NEFH MUTATED NEFH WILD-TYPE
  COLON ADENOCARCINOMA                     10            305
  COLON MUCINOUS ADENOCARCINOMA             3             44
  RECTAL ADENOCARCINOMA                     1            105
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  NEFH MUTATED    10   0   1   0
  NEFH WILD-TYPE 335   4  30  25
D152V11, multiclass
    clus
vv   NEFH MUTATED NEFH WILD-TYPE
  R0           10            335
  R1            0              4
  R2            1             30
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D152V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NEFH MUTATED                                  0     0
  NEFH WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  NEFH MUTATED                           0    10
  NEFH WILD-TYPE                        22   216
D152V13, multiclass
                                  clus
vv                                 NEFH MUTATED NEFH WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                      10            216
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(153) Variable = ECM2 MUTATION ANALYSIS
D153V1, survival
                sevent
clus2              0   1
  ECM2 MUTATED    15   3
  ECM2 WILD-TYPE 363  90
  ECM2 MUTATED ECM2 WILD-TYPE 
            18            453 
  ECM2 MUTATED ECM2 WILD-TYPE 
             3             90 
$`ECM2 MUTATED`
TCGA-A6-3808 TCGA-A6-6653 TCGA-AA-3510 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3815 
       33.34        24.39        63.98        19.04        10.06        33.04 
TCGA-AA-A00N TCGA-AU-3779 TCGA-AU-6004 TCGA-AZ-4315 TCGA-AZ-5407 TCGA-AZ-6599 
        4.01        14.50        27.09        58.39        88.21         6.77 
TCGA-CA-6717 TCGA-CM-4752 TCGA-CM-6164 TCGA-AF-2687 TCGA-AG-A015 TCGA-EF-5830 
       12.76        13.02        29.03        24.13        36.03         0.49 

$`ECM2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 
       25.18        24.16        21.76        24.69        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
       85.05        26.99        19.04        35.05         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       27.42        10.88         0.20        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       62.79        49.41        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07        12.20        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       37.02        25.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       15.02        12.00         2.96        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       91.79        46.75        79.69        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A016 
        6.02        25.97        23.01        37.02        15.95         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       51.48        32.61        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  ECM2 MUTATED ECM2 WILD-TYPE 
          0.49           0.00 
  ECM2 MUTATED ECM2 WILD-TYPE 
         88.21         148.01 
  ECM2 MUTATED ECM2 WILD-TYPE 
         24.26          20.12 
[1] "0.5 - 88.2 (24.3)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.3"
D153V2, continuous
D153V3, binary
                cls
clus               0   1
  ECM2 MUTATED    17   3
  ECM2 WILD-TYPE 349 116
[1] "tbl2"
                cls
clus             [,1] [,2]
  ECM2 MUTATED     17    3
  ECM2 WILD-TYPE  349  116
        clus
vv       ECM2 MUTATED ECM2 WILD-TYPE
  COLON            17            349
  RECTUM            3            116
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ECM2 MUTATED         5        0        1         7         3         0
  ECM2 WILD-TYPE      86        1       31       131         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ECM2 MUTATED           1          0          0          2        1         0
  ECM2 WILD-TYPE        23         11         59         40       47        18
                vv
clus             STAGE IVB
  ECM2 MUTATED           0
  ECM2 WILD-TYPE         1
D153V4, multiclass
            clus
vv           ECM2 MUTATED ECM2 WILD-TYPE
  STAGE I               5             86
  STAGE IA              0              1
  STAGE II              1             31
  STAGE IIA             7            131
  STAGE IIB             3              7
  STAGE IIC             0              1
  STAGE III             1             23
  STAGE IIIA            0             11
  STAGE IIIB            0             59
  STAGE IIIC            2             40
  STAGE IV              1             47
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  ECM2 MUTATED     2   3  12   3
  ECM2 WILD-TYPE  15  89 317  47
D153V5, multiclass
    clus
vv   ECM2 MUTATED ECM2 WILD-TYPE
  T1            2             15
  T2            3             89
  T3           12            317
  T4            3             47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  ECM2 MUTATED    17   0   3
  ECM2 WILD-TYPE 270 113  84
D153V6, multiclass
    clus
vv   ECM2 MUTATED ECM2 WILD-TYPE
  N0           17            270
  N1            0            113
  N2            3             84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D153V7, binary
                cls
clus               0   1
  ECM2 MUTATED    16   1
  ECM2 WILD-TYPE 359  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  ECM2 MUTATED     16    1
  ECM2 WILD-TYPE  359   64
   clus
vv  ECM2 MUTATED ECM2 WILD-TYPE
  0           16            359
  1            1             64
[1] 2 2
[1] FALSE
D153V8, binary
                cls
clus               0   1
  ECM2 MUTATED     8  12
  ECM2 WILD-TYPE 217 252
[1] "tbl2"
                cls
clus             [,1] [,2]
  ECM2 MUTATED      8   12
  ECM2 WILD-TYPE  217  252
        clus
vv       ECM2 MUTATED ECM2 WILD-TYPE
  FEMALE            8            217
  MALE             12            252
[1] 2 2
[1] FALSE
D153V9, binary
                cls
clus               0   1
  ECM2 MUTATED    13   2
  ECM2 WILD-TYPE 337  20
[1] "tbl2"
                cls
clus             [,1] [,2]
  ECM2 MUTATED     13    2
  ECM2 WILD-TYPE  337   20
     clus
vv    ECM2 MUTATED ECM2 WILD-TYPE
  NO            13            337
  YES            2             20
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ECM2 MUTATED                     14                             3
  ECM2 WILD-TYPE                  301                            44
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ECM2 MUTATED                       3                              0
  ECM2 WILD-TYPE                   103                             10
D153V10, multiclass
                                clus
vv                               ECM2 MUTATED ECM2 WILD-TYPE
  COLON ADENOCARCINOMA                     14            301
  COLON MUCINOUS ADENOCARCINOMA             3             44
  RECTAL ADENOCARCINOMA                     3            103
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  ECM2 MUTATED    14   0   1   2
  ECM2 WILD-TYPE 331   4  30  23
D153V11, multiclass
    clus
vv   ECM2 MUTATED ECM2 WILD-TYPE
  R0           14            331
  R1            0              4
  R2            1             30
  RX            2             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D153V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ECM2 MUTATED                                  0     1
  ECM2 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  ECM2 MUTATED                           1    12
  ECM2 WILD-TYPE                        21   214
D153V13, multiclass
                                  clus
vv                                 ECM2 MUTATED ECM2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                      12            214
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(154) Variable = CHD3 MUTATION ANALYSIS
D154V1, survival
                sevent
clus2              0   1
  CHD3 MUTATED    18   6
  CHD3 WILD-TYPE 360  87
  CHD3 MUTATED CHD3 WILD-TYPE 
            24            447 
  CHD3 MUTATED CHD3 WILD-TYPE 
             6             87 
$`CHD3 MUTATED`
TCGA-A6-2676 TCGA-A6-5661 TCGA-A6-6653 TCGA-A6-6781 TCGA-AA-3492 TCGA-AA-3710 
       42.90        33.53        24.39        19.66         3.02        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3845 TCGA-AA-3864 TCGA-AA-A00J TCGA-AA-A00N 
       19.04        19.04         0.00        53.00        18.05         4.01 
TCGA-AA-A010 TCGA-AA-A01Q TCGA-AD-6895 TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-6601 
       34.98         1.02         0.72        21.44        58.39       100.01 
TCGA-D5-6927 TCGA-DM-A1HB TCGA-F4-6854 TCGA-G4-6309 TCGA-G4-6588 TCGA-AG-A002 
        9.44       135.65         0.53        85.48        26.17        20.98 

$`CHD3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       31.63        30.44        29.19        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 
       24.16        21.76        24.69        23.87        20.12        20.28 
TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
        7.04         1.02        35.01        63.98         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
       13.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       36.03         8.05        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       78.08         6.05         6.97        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3811 
       37.05        19.00        36.00         5.03        85.05        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 
       15.95        38.99        37.02        14.93        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        31.07        30.05        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       34.03        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01R TCGA-AA-A01S 
       12.00        31.00        31.00        38.07        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
       56.55         0.79         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 
       88.21        49.41         6.77        12.10        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.04        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      131.51       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       33.67        13.25        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 
       65.85        53.62        44.68        55.04        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        35.80        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  CHD3 MUTATED CHD3 WILD-TYPE 
             0              0 
  CHD3 MUTATED CHD3 WILD-TYPE 
        135.65         148.01 
  CHD3 MUTATED CHD3 WILD-TYPE 
         21.21          20.12 
[1] "0.0 - 135.7 (21.2)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.1"
D154V2, continuous
D154V3, binary
                cls
clus               0   1
  CHD3 MUTATED    24   1
  CHD3 WILD-TYPE 342 118
[1] "tbl2"
                cls
clus             [,1] [,2]
  CHD3 MUTATED     24    1
  CHD3 WILD-TYPE  342  118
        clus
vv       CHD3 MUTATED CHD3 WILD-TYPE
  COLON            24            342
  RECTUM            1            118
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CHD3 MUTATED         2        0        5         8         4         0
  CHD3 WILD-TYPE      89        1       27       130         6         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CHD3 MUTATED           0          0          3          1        1         0
  CHD3 WILD-TYPE        24         11         56         41       47        18
                vv
clus             STAGE IVB
  CHD3 MUTATED           0
  CHD3 WILD-TYPE         1
D154V4, multiclass
            clus
vv           CHD3 MUTATED CHD3 WILD-TYPE
  STAGE I               2             89
  STAGE IA              0              1
  STAGE II              5             27
  STAGE IIA             8            130
  STAGE IIB             4              6
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            3             56
  STAGE IIIC            1             41
  STAGE IV              1             47
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  CHD3 MUTATED     0   2  17   6
  CHD3 WILD-TYPE  17  90 312  44
D154V5, multiclass
    clus
vv   CHD3 MUTATED CHD3 WILD-TYPE
  T1            0             17
  T2            2             90
  T3           17            312
  T4            6             44
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  CHD3 MUTATED    20   5   0
  CHD3 WILD-TYPE 267 108  87
D154V6, multiclass
    clus
vv   CHD3 MUTATED CHD3 WILD-TYPE
  N0           20            267
  N1            5            108
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D154V7, binary
                cls
clus               0   1
  CHD3 MUTATED    20   1
  CHD3 WILD-TYPE 355  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  CHD3 MUTATED     20    1
  CHD3 WILD-TYPE  355   64
   clus
vv  CHD3 MUTATED CHD3 WILD-TYPE
  0           20            355
  1            1             64
[1] 2 2
[1] FALSE
D154V8, binary
                cls
clus               0   1
  CHD3 MUTATED    11  14
  CHD3 WILD-TYPE 214 250
[1] "tbl2"
                cls
clus             [,1] [,2]
  CHD3 MUTATED     11   14
  CHD3 WILD-TYPE  214  250
        clus
vv       CHD3 MUTATED CHD3 WILD-TYPE
  FEMALE           11            214
  MALE             14            250
[1] 2 2
[1] FALSE
D154V9, binary
                cls
clus               0   1
  CHD3 MUTATED    18   1
  CHD3 WILD-TYPE 332  21
[1] "tbl2"
                cls
clus             [,1] [,2]
  CHD3 MUTATED     18    1
  CHD3 WILD-TYPE  332   21
     clus
vv    CHD3 MUTATED CHD3 WILD-TYPE
  NO            18            332
  YES            1             21
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CHD3 MUTATED                     20                             3
  CHD3 WILD-TYPE                  295                            44
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CHD3 MUTATED                       1                              0
  CHD3 WILD-TYPE                   105                             10
D154V10, multiclass
                                clus
vv                               CHD3 MUTATED CHD3 WILD-TYPE
  COLON ADENOCARCINOMA                     20            295
  COLON MUCINOUS ADENOCARCINOMA             3             44
  RECTAL ADENOCARCINOMA                     1            105
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  CHD3 MUTATED    19   0   1   1
  CHD3 WILD-TYPE 326   4  30  24
D154V11, multiclass
    clus
vv   CHD3 MUTATED CHD3 WILD-TYPE
  R0           19            326
  R1            0              4
  R2            1             30
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D154V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CHD3 MUTATED                                  0     0
  CHD3 WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  CHD3 MUTATED                           2    12
  CHD3 WILD-TYPE                        20   214
D154V13, multiclass
                                  clus
vv                                 CHD3 MUTATED CHD3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   2             20
  WHITE                                      12            214
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(155) Variable = KLK10 MUTATION ANALYSIS
D155V1, survival
                 sevent
clus2               0   1
  KLK10 MUTATED     5   2
  KLK10 WILD-TYPE 373  91
  KLK10 MUTATED KLK10 WILD-TYPE 
              7             464 
  KLK10 MUTATED KLK10 WILD-TYPE 
              2              91 
$`KLK10 MUTATED`
TCGA-A6-6651 TCGA-AA-3815 TCGA-AZ-6601 TCGA-D5-6540 TCGA-DM-A1DA TCGA-DM-A1HB 
       21.76        33.04       100.01        16.14         7.50       135.65 
TCGA-AF-2693 
       19.10 

$`KLK10 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.08        25.18        24.16        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       10.06        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
       12.10        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       17.13        12.49        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
      140.38        44.32       131.51       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3913 
       24.13        39.48        43.04        13.55        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  KLK10 MUTATED KLK10 WILD-TYPE 
            7.5             0.0 
  KLK10 MUTATED KLK10 WILD-TYPE 
         135.65          148.01 
  KLK10 MUTATED KLK10 WILD-TYPE 
         21.760          20.155 
[1] "7.5 - 135.7 (21.8)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.1"
D155V2, continuous
D155V3, binary
                 cls
clus                0   1
  KLK10 MUTATED     7   0
  KLK10 WILD-TYPE 359 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLK10 MUTATED      7    0
  KLK10 WILD-TYPE  359  119
        clus
vv       KLK10 MUTATED KLK10 WILD-TYPE
  COLON              7             359
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KLK10 MUTATED         3        0        1         1         0         0
  KLK10 WILD-TYPE      88        1       31       137        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  KLK10 MUTATED           0          0          2          1        0         0
  KLK10 WILD-TYPE        24         11         57         41       48        18
                 vv
clus              STAGE IVB
  KLK10 MUTATED           0
  KLK10 WILD-TYPE         1
D155V4, multiclass
            clus
vv           KLK10 MUTATED KLK10 WILD-TYPE
  STAGE I                3              88
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              1             137
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             2              57
  STAGE IIIC             1              41
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  KLK10 MUTATED     0   3   5   0
  KLK10 WILD-TYPE  17  89 324  50
D155V5, multiclass
    clus
vv   KLK10 MUTATED KLK10 WILD-TYPE
  T1             0              17
  T2             3              89
  T3             5             324
  T4             0              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  KLK10 MUTATED     5   2   1
  KLK10 WILD-TYPE 282 111  86
D155V6, multiclass
    clus
vv   KLK10 MUTATED KLK10 WILD-TYPE
  N0             5             282
  N1             2             111
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D155V7, binary
                 cls
clus                0   1
  KLK10 MUTATED     5   0
  KLK10 WILD-TYPE 370  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLK10 MUTATED      5    0
  KLK10 WILD-TYPE  370   65
   clus
vv  KLK10 MUTATED KLK10 WILD-TYPE
  0             5             370
  1             0              65
[1] 2 2
[1] FALSE
D155V8, binary
                 cls
clus                0   1
  KLK10 MUTATED     3   5
  KLK10 WILD-TYPE 222 259
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLK10 MUTATED      3    5
  KLK10 WILD-TYPE  222  259
        clus
vv       KLK10 MUTATED KLK10 WILD-TYPE
  FEMALE             3             222
  MALE               5             259
[1] 2 2
[1] FALSE
D155V9, binary
                 cls
clus                0   1
  KLK10 MUTATED     5   0
  KLK10 WILD-TYPE 345  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLK10 MUTATED      5    0
  KLK10 WILD-TYPE  345   22
     clus
vv    KLK10 MUTATED KLK10 WILD-TYPE
  NO              5             345
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  KLK10 MUTATED                      5                             1
  KLK10 WILD-TYPE                  310                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  KLK10 MUTATED                       0                              0
  KLK10 WILD-TYPE                   106                             10
D155V10, multiclass
                                clus
vv                               KLK10 MUTATED KLK10 WILD-TYPE
  COLON ADENOCARCINOMA                       5             310
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  KLK10 MUTATED     2   0   0   1
  KLK10 WILD-TYPE 343   4  31  24
D155V11, multiclass
    clus
vv   KLK10 MUTATED KLK10 WILD-TYPE
  R0             2             343
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D155V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KLK10 MUTATED                                  0     0
  KLK10 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  KLK10 MUTATED                           0     7
  KLK10 WILD-TYPE                        22   219
D155V13, multiclass
                                  clus
vv                                 KLK10 MUTATED KLK10 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        7             219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(156) Variable = DST MUTATION ANALYSIS
D156V1, survival
               sevent
clus2             0   1
  DST MUTATED    60  13
  DST WILD-TYPE 318  80
  DST MUTATED DST WILD-TYPE 
           73           398 
  DST MUTATED DST WILD-TYPE 
           13            80 
$`DST MUTATED`
TCGA-A6-2676 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5661 TCGA-A6-6649 
       42.90        33.34        36.53        32.91        33.53        24.16 
TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3492 TCGA-AA-3496 
       21.76        24.39        20.12        19.66         3.02         1.02 
TCGA-AA-3510 TCGA-AA-3660 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3821 TCGA-AA-3845 
       63.98        78.08        14.01         0.92         1.02         0.00 
TCGA-AA-3941 TCGA-AA-3966 TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01R 
       24.00         2.01        25.02         4.01        34.98        35.01 
TCGA-AD-5900 TCGA-AD-6964 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-6197 TCGA-AZ-4315 
        0.07        10.88        14.50        27.09        21.44        58.39 
TCGA-AZ-5407 TCGA-AZ-6599 TCGA-CA-5254 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-5914 
       88.21         6.77        12.69        12.76        10.06         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CM-4746 TCGA-CM-5341 TCGA-CM-5860 TCGA-CM-5861 
       21.14        82.95        37.02        29.06        32.02        15.02 
TCGA-CM-6162 TCGA-CM-6166 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-6540 TCGA-D5-6928 
       12.00        21.99        45.40        12.26        16.14        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6932 TCGA-DM-A1D6 TCGA-DM-A1HA TCGA-DM-A1HB 
        4.80         1.51        11.38        49.91       131.51       135.65 
TCGA-DM-A28F TCGA-F4-6460 TCGA-F4-6703 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6309 
       35.97        31.96        47.87        65.85        53.62        85.48 
TCGA-G4-6310 TCGA-G4-6588 TCGA-G4-6628 TCGA-AF-2693 TCGA-AF-6136 TCGA-AG-3892 
       63.62        26.17        79.69        19.10        15.39        13.02 
TCGA-AG-A002 TCGA-AG-A014 TCGA-AH-6644 TCGA-EI-6506 TCGA-F5-6465 TCGA-F5-6811 
       20.98        15.95         0.72        20.55        49.51        32.19 
TCGA-F5-6812 
        0.66 

$`DST WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-4105 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       34.65        32.75        14.53        31.63        30.44        29.19 
TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 
       23.61        22.09        22.06        32.71        27.09        22.52 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6782 
        8.38        25.08        25.18        24.69        23.87        20.28 
TCGA-AA-3489 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        7.04        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 
       19.99        13.94        19.99        61.02         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       54.02         2.01        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
        0.99        25.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
       14.93        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
       31.00         2.01        12.99        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
        2.01        20.98        34.03        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
        1.02         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 
        0.92        41.00        39.98        18.05        40.96        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 
       27.42         0.20        16.31         0.95        33.01        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6598 
        1.41         5.13       106.75        22.36        62.79        49.41 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        1.61         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4747 
       51.32         1.91       124.27        23.05        20.02        25.02 
TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5862 TCGA-CM-5863 
       13.02        22.03        22.98        30.08         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       15.02        17.03        15.02         2.96        29.03        16.04 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.03        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       12.49        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 
       14.30         9.04         9.44        12.00        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D7 TCGA-DM-A1D8 
       24.43        38.20       130.65        92.75        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
      140.38         7.50        44.32       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6569 
      119.93        60.79       117.07        98.24         8.61        35.74 
TCGA-F4-6570 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
        6.18         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       44.68        55.04        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       35.80        91.79        46.75        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6655 
       13.55        34.49        10.39        14.50        16.83        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       17.95        36.95        17.03        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       37.02        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6507 
       57.24        24.13        51.48        32.61         0.49        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6813 
       20.91        18.28         9.96        31.30        28.57         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  DST MUTATED DST WILD-TYPE 
            0             0 
  DST MUTATED DST WILD-TYPE 
       135.65        148.01 
  DST MUTATED DST WILD-TYPE 
        21.76         19.99 
[1] "0.0 - 135.7 (21.8)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.3"
D156V2, continuous
D156V3, binary
               cls
clus              0   1
  DST MUTATED    66  10
  DST WILD-TYPE 300 109
[1] "tbl2"
               cls
clus            [,1] [,2]
  DST MUTATED     66   10
  DST WILD-TYPE  300  109
        clus
vv       DST MUTATED DST WILD-TYPE
  COLON           66           300
  RECTUM          10           109
[1] 2 2
[1] FALSE
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DST MUTATED        17        0        5        27         4         0
  DST WILD-TYPE      74        1       27       111         6         1
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DST MUTATED           3          1         11          3        2         1
  DST WILD-TYPE        21         10         48         39       46        17
               vv
clus            STAGE IVB
  DST MUTATED           0
  DST WILD-TYPE         1
D156V4, multiclass
            clus
vv           DST MUTATED DST WILD-TYPE
  STAGE I             17            74
  STAGE IA             0             1
  STAGE II             5            27
  STAGE IIA           27           111
  STAGE IIB            4             6
  STAGE IIC            0             1
  STAGE III            3            21
  STAGE IIIA           1            10
  STAGE IIIB          11            48
  STAGE IIIC           3            39
  STAGE IV             2            46
  STAGE IVA            1            17
  STAGE IVB            0             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  DST MUTATED     3  16  50   8
  DST WILD-TYPE  14  76 279  42
D156V5, multiclass
    clus
vv   DST MUTATED DST WILD-TYPE
  T1           3            14
  T2          16            76
  T3          50           279
  T4           8            42
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2
  DST MUTATED    53  18   5
  DST WILD-TYPE 234  95  82
D156V6, multiclass
    clus
vv   DST MUTATED DST WILD-TYPE
  N0          53           234
  N1          18            95
  N2           5            82
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D156V7, binary
               cls
clus              0   1
  DST MUTATED    58   3
  DST WILD-TYPE 317  62
[1] "tbl2"
               cls
clus            [,1] [,2]
  DST MUTATED     58    3
  DST WILD-TYPE  317   62
   clus
vv  DST MUTATED DST WILD-TYPE
  0          58           317
  1           3            62
[1] 2 2
[1] FALSE
D156V8, binary
               cls
clus              0   1
  DST MUTATED    37  40
  DST WILD-TYPE 188 224
[1] "tbl2"
               cls
clus            [,1] [,2]
  DST MUTATED     37   40
  DST WILD-TYPE  188  224
        clus
vv       DST MUTATED DST WILD-TYPE
  FEMALE          37           188
  MALE            40           224
[1] 2 2
[1] FALSE
D156V9, binary
               cls
clus              0   1
  DST MUTATED    54   3
  DST WILD-TYPE 296  19
[1] "tbl2"
               cls
clus            [,1] [,2]
  DST MUTATED     54    3
  DST WILD-TYPE  296   19
     clus
vv    DST MUTATED DST WILD-TYPE
  NO           54           296
  YES           3            19
[1] 2 2
[1] FALSE
               vv
clus            COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  DST MUTATED                     51                            14
  DST WILD-TYPE                  264                            33
               vv
clus            RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  DST MUTATED                      10                              0
  DST WILD-TYPE                    96                             10
D156V10, multiclass
                                clus
vv                               DST MUTATED DST WILD-TYPE
  COLON ADENOCARCINOMA                    51           264
  COLON MUCINOUS ADENOCARCINOMA           14            33
  RECTAL ADENOCARCINOMA                   10            96
  RECTAL MUCINOUS ADENOCARCINOMA           0            10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             R0  R1  R2  RX
  DST MUTATED    51   0   0   7
  DST WILD-TYPE 294   4  31  18
D156V11, multiclass
    clus
vv   DST MUTATED DST WILD-TYPE
  R0          51           294
  R1           0             4
  R2           0            31
  RX           7            18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D156V12, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DST MUTATED                                  0     3
  DST WILD-TYPE                                1     8
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  DST MUTATED                           3    52
  DST WILD-TYPE                        19   174
D156V13, multiclass
                                  clus
vv                                 DST MUTATED DST WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      3             8
  BLACK OR AFRICAN AMERICAN                  3            19
  WHITE                                     52           174
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(157) Variable = NEUROD1 MUTATION ANALYSIS
D157V1, survival
                   sevent
clus2                 0   1
  NEUROD1 MUTATED    10   0
  NEUROD1 WILD-TYPE 368  93
  NEUROD1 MUTATED NEUROD1 WILD-TYPE 
               10               461 
  NEUROD1 MUTATED NEUROD1 WILD-TYPE 
                0                93 
$`NEUROD1 MUTATED`
TCGA-AA-3510 TCGA-AA-3713 TCGA-AA-3950 TCGA-AA-A00J TCGA-AZ-4315 TCGA-CM-4752 
       63.98        19.04        24.00        18.05        58.39        13.02 
TCGA-CM-6164 TCGA-CM-6172 TCGA-AG-A002 TCGA-AG-A02N 
       29.03        11.01        20.98        61.97 

$`NEUROD1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 
       12.99        24.00        33.01        26.01         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-5341 TCGA-CM-5344 
       23.05        20.02        37.02        25.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6165 
       15.02        17.03        15.02        12.00         2.96        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
       49.97         1.94        38.96        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  NEUROD1 MUTATED NEUROD1 WILD-TYPE 
            11.01              0.00 
  NEUROD1 MUTATED NEUROD1 WILD-TYPE 
            63.98            148.01 
  NEUROD1 MUTATED NEUROD1 WILD-TYPE 
            22.49             20.12 
[1] "11.0 - 64.0 (22.5)" "0.0 - 148.0 (20.1)"
[1] "hr="     "9400000"
D157V2, continuous
D157V3, binary
                   cls
clus                  0   1
  NEUROD1 MUTATED     8   2
  NEUROD1 WILD-TYPE 358 117
[1] "tbl2"
                   cls
clus                [,1] [,2]
  NEUROD1 MUTATED      8    2
  NEUROD1 WILD-TYPE  358  117
        clus
vv       NEUROD1 MUTATED NEUROD1 WILD-TYPE
  COLON                8               358
  RECTUM               2               117
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NEUROD1 MUTATED         1        0        2         4         0         0
  NEUROD1 WILD-TYPE      90        1       30       134        10         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NEUROD1 MUTATED           0          0          2          0        1
  NEUROD1 WILD-TYPE        24         11         57         42       47
                   vv
clus                STAGE IVA STAGE IVB
  NEUROD1 MUTATED           0         0
  NEUROD1 WILD-TYPE        18         1
D157V4, multiclass
            clus
vv           NEUROD1 MUTATED NEUROD1 WILD-TYPE
  STAGE I                  1                90
  STAGE IA                 0                 1
  STAGE II                 2                30
  STAGE IIA                4               134
  STAGE IIB                0                10
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               0                11
  STAGE IIIB               2                57
  STAGE IIIC               0                42
  STAGE IV                 1                47
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  NEUROD1 MUTATED     0   1   8   1
  NEUROD1 WILD-TYPE  17  91 321  49
D157V5, multiclass
    clus
vv   NEUROD1 MUTATED NEUROD1 WILD-TYPE
  T1               0                17
  T2               1                91
  T3               8               321
  T4               1                49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  NEUROD1 MUTATED     8   2   0
  NEUROD1 WILD-TYPE 279 111  87
D157V6, multiclass
    clus
vv   NEUROD1 MUTATED NEUROD1 WILD-TYPE
  N0               8               279
  N1               2               111
  N2               0                87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D157V7, binary
                   cls
clus                  0   1
  NEUROD1 MUTATED     9   1
  NEUROD1 WILD-TYPE 366  64
[1] "tbl2"
                   cls
clus                [,1] [,2]
  NEUROD1 MUTATED      9    1
  NEUROD1 WILD-TYPE  366   64
   clus
vv  NEUROD1 MUTATED NEUROD1 WILD-TYPE
  0               9               366
  1               1                64
[1] 2 2
[1] FALSE
D157V8, binary
                   cls
clus                  0   1
  NEUROD1 MUTATED     3   7
  NEUROD1 WILD-TYPE 222 257
[1] "tbl2"
                   cls
clus                [,1] [,2]
  NEUROD1 MUTATED      3    7
  NEUROD1 WILD-TYPE  222  257
        clus
vv       NEUROD1 MUTATED NEUROD1 WILD-TYPE
  FEMALE               3               222
  MALE                 7               257
[1] 2 2
[1] FALSE
D157V9, binary
                   cls
clus                  0   1
  NEUROD1 MUTATED     8   1
  NEUROD1 WILD-TYPE 342  21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  NEUROD1 MUTATED      8    1
  NEUROD1 WILD-TYPE  342   21
     clus
vv    NEUROD1 MUTATED NEUROD1 WILD-TYPE
  NO                8               342
  YES               1                21
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  NEUROD1 MUTATED                      6                             2
  NEUROD1 WILD-TYPE                  309                            45
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  NEUROD1 MUTATED                       2                              0
  NEUROD1 WILD-TYPE                   104                             10
D157V10, multiclass
                                clus
vv                               NEUROD1 MUTATED NEUROD1 WILD-TYPE
  COLON ADENOCARCINOMA                         6               309
  COLON MUCINOUS ADENOCARCINOMA                2                45
  RECTAL ADENOCARCINOMA                        2               104
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  NEUROD1 MUTATED     9   0   1   0
  NEUROD1 WILD-TYPE 336   4  30  25
D157V11, multiclass
    clus
vv   NEUROD1 MUTATED NEUROD1 WILD-TYPE
  R0               9               336
  R1               0                 4
  R2               1                30
  RX               0                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D157V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NEUROD1 MUTATED                                  0     0
  NEUROD1 WILD-TYPE                                1    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  NEUROD1 MUTATED                           1     3
  NEUROD1 WILD-TYPE                        21   223
D157V13, multiclass
                                  clus
vv                                 NEUROD1 MUTATED NEUROD1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                      1                21
  WHITE                                          3               223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(158) Variable = KIAA1804 MUTATION ANALYSIS
D158V1, survival
                    sevent
clus2                  0   1
  KIAA1804 MUTATED    21   4
  KIAA1804 WILD-TYPE 357  89
  KIAA1804 MUTATED KIAA1804 WILD-TYPE 
                25                446 
  KIAA1804 MUTATED KIAA1804 WILD-TYPE 
                 4                 89 
$`KIAA1804 MUTATED`
TCGA-A6-5665 TCGA-AA-3510 TCGA-AA-3555 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3845 
       22.06        63.98        29.95         0.92        19.00         0.00 
TCGA-AA-3966 TCGA-AA-A010 TCGA-AD-6964 TCGA-AZ-6598 TCGA-CA-6717 TCGA-CM-4744 
        2.01        34.98        10.88        49.41        12.76        20.02 
TCGA-CM-5861 TCGA-D5-6538 TCGA-G4-6317 TCGA-G4-6628 TCGA-AF-2691 TCGA-AG-3582 
       15.02        17.13        36.00        79.69        43.04        36.03 
TCGA-AG-3598 TCGA-AG-3727 TCGA-AG-3898 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A02N 
       50.04         0.99        48.03        20.98        13.94        61.97 
TCGA-EI-6508 
       20.91 

$`KIAA1804 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       24.00        17.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
        2.01        14.01        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
        5.98        37.05        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
       14.93        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 
       24.00         2.01        20.98        34.03        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        88.21         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07        12.20        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       23.05        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       22.98        30.08        32.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
       17.85         4.80        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       63.62        61.91        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2692 TCGA-AF-2693 
       91.79        46.75        24.13        39.48        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
       19.99         7.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3902 TCGA-AG-3909 
       13.02        35.01        14.01         1.02        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A00C 
       28.04        36.03        14.04         1.02        17.03         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       38.96        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6510 TCGA-F5-6464 
       32.61         0.49        20.55        19.96        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  KIAA1804 MUTATED KIAA1804 WILD-TYPE 
                 0                  0 
  KIAA1804 MUTATED KIAA1804 WILD-TYPE 
             79.69             148.01 
  KIAA1804 MUTATED KIAA1804 WILD-TYPE 
            20.980             20.085 
[1] "0.0 - 79.7 (21.0)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.4"
D158V2, continuous
D158V3, binary
                    cls
clus                   0   1
  KIAA1804 MUTATED    16  10
  KIAA1804 WILD-TYPE 350 109
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1804 MUTATED     16   10
  KIAA1804 WILD-TYPE  350  109
        clus
vv       KIAA1804 MUTATED KIAA1804 WILD-TYPE
  COLON                16                350
  RECTUM               10                109
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KIAA1804 MUTATED         5        0        3         8         1         0
  KIAA1804 WILD-TYPE      86        1       29       130         9         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIAA1804 MUTATED           2          0          2          2        2
  KIAA1804 WILD-TYPE        22         11         57         40       46
                    vv
clus                 STAGE IVA STAGE IVB
  KIAA1804 MUTATED           0         0
  KIAA1804 WILD-TYPE        18         1
D158V4, multiclass
            clus
vv           KIAA1804 MUTATED KIAA1804 WILD-TYPE
  STAGE I                   5                 86
  STAGE IA                  0                  1
  STAGE II                  3                 29
  STAGE IIA                 8                130
  STAGE IIB                 1                  9
  STAGE IIC                 0                  1
  STAGE III                 2                 22
  STAGE IIIA                0                 11
  STAGE IIIB                2                 57
  STAGE IIIC                2                 40
  STAGE IV                  2                 46
  STAGE IVA                 0                 18
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  KIAA1804 MUTATED     1   4  19   2
  KIAA1804 WILD-TYPE  16  88 310  48
D158V5, multiclass
    clus
vv   KIAA1804 MUTATED KIAA1804 WILD-TYPE
  T1                1                 16
  T2                4                 88
  T3               19                310
  T4                2                 48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  KIAA1804 MUTATED    17   5   4
  KIAA1804 WILD-TYPE 270 108  83
D158V6, multiclass
    clus
vv   KIAA1804 MUTATED KIAA1804 WILD-TYPE
  N0               17                270
  N1                5                108
  N2                4                 83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D158V7, binary
                    cls
clus                   0   1
  KIAA1804 MUTATED    21   2
  KIAA1804 WILD-TYPE 354  63
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1804 MUTATED     21    2
  KIAA1804 WILD-TYPE  354   63
   clus
vv  KIAA1804 MUTATED KIAA1804 WILD-TYPE
  0               21                354
  1                2                 63
[1] 2 2
[1] FALSE
D158V8, binary
                    cls
clus                   0   1
  KIAA1804 MUTATED    15  11
  KIAA1804 WILD-TYPE 210 253
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1804 MUTATED     15   11
  KIAA1804 WILD-TYPE  210  253
        clus
vv       KIAA1804 MUTATED KIAA1804 WILD-TYPE
  FEMALE               15                210
  MALE                 11                253
[1] 2 2
[1] FALSE
D158V9, binary
                    cls
clus                   0   1
  KIAA1804 MUTATED    21   0
  KIAA1804 WILD-TYPE 329  22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1804 MUTATED     21    0
  KIAA1804 WILD-TYPE  329   22
     clus
vv    KIAA1804 MUTATED KIAA1804 WILD-TYPE
  NO                21                329
  YES                0                 22
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  KIAA1804 MUTATED                     13                             3
  KIAA1804 WILD-TYPE                  302                            44
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  KIAA1804 MUTATED                       9                              1
  KIAA1804 WILD-TYPE                    97                              9
D158V10, multiclass
                                clus
vv                               KIAA1804 MUTATED KIAA1804 WILD-TYPE
  COLON ADENOCARCINOMA                         13                302
  COLON MUCINOUS ADENOCARCINOMA                 3                 44
  RECTAL ADENOCARCINOMA                         9                 97
  RECTAL MUCINOUS ADENOCARCINOMA                1                  9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  KIAA1804 MUTATED    20   0   2   1
  KIAA1804 WILD-TYPE 325   4  29  24
D158V11, multiclass
    clus
vv   KIAA1804 MUTATED KIAA1804 WILD-TYPE
  R0               20                325
  R1                0                  4
  R2                2                 29
  RX                1                 24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D158V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KIAA1804 MUTATED                                  0     1
  KIAA1804 WILD-TYPE                                1    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  KIAA1804 MUTATED                           0    10
  KIAA1804 WILD-TYPE                        22   216
D158V13, multiclass
                                  clus
vv                                 KIAA1804 MUTATED KIAA1804 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                 10
  BLACK OR AFRICAN AMERICAN                       0                 22
  WHITE                                          10                216
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(159) Variable = PIK3IP1 MUTATION ANALYSIS
D159V1, survival
                   sevent
clus2                 0   1
  PIK3IP1 MUTATED     7   1
  PIK3IP1 WILD-TYPE 371  92
  PIK3IP1 MUTATED PIK3IP1 WILD-TYPE 
                8               463 
  PIK3IP1 MUTATED PIK3IP1 WILD-TYPE 
                1                92 
$`PIK3IP1 MUTATED`
TCGA-A6-3807 TCGA-AA-3663 TCGA-CM-6171 TCGA-D5-6536 TCGA-D5-6540 TCGA-DM-A1D6 
       34.65         6.97        14.04        17.85        16.14        49.91 
TCGA-G4-6293 TCGA-EI-6506 
      133.18        20.55 

$`PIK3IP1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 
       14.99        12.99        13.02        15.02        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 
       18.25         1.32        43.27        15.12         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       12.49        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
      130.65        92.75        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
       35.31        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
        0.49        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  PIK3IP1 MUTATED PIK3IP1 WILD-TYPE 
             6.97              0.00 
  PIK3IP1 MUTATED PIK3IP1 WILD-TYPE 
           133.18            148.01 
  PIK3IP1 MUTATED PIK3IP1 WILD-TYPE 
            19.20             20.19 
[1] "7.0 - 133.2 (19.2)" "0.0 - 148.0 (20.2)"
[1] "hr=" "2"  
D159V2, continuous
D159V3, binary
                   cls
clus                  0   1
  PIK3IP1 MUTATED     8   1
  PIK3IP1 WILD-TYPE 358 118
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PIK3IP1 MUTATED      8    1
  PIK3IP1 WILD-TYPE  358  118
        clus
vv       PIK3IP1 MUTATED PIK3IP1 WILD-TYPE
  COLON                8               358
  RECTUM               1               118
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PIK3IP1 MUTATED         2        0        1         3         0         0
  PIK3IP1 WILD-TYPE      89        1       31       135        10         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PIK3IP1 MUTATED           1          0          0          2        0
  PIK3IP1 WILD-TYPE        23         11         59         40       48
                   vv
clus                STAGE IVA STAGE IVB
  PIK3IP1 MUTATED           0         0
  PIK3IP1 WILD-TYPE        18         1
D159V4, multiclass
            clus
vv           PIK3IP1 MUTATED PIK3IP1 WILD-TYPE
  STAGE I                  2                89
  STAGE IA                 0                 1
  STAGE II                 1                31
  STAGE IIA                3               135
  STAGE IIB                0                10
  STAGE IIC                0                 1
  STAGE III                1                23
  STAGE IIIA               0                11
  STAGE IIIB               0                59
  STAGE IIIC               2                40
  STAGE IV                 0                48
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  PIK3IP1 MUTATED     0   2   7   0
  PIK3IP1 WILD-TYPE  17  90 322  50
D159V5, multiclass
    clus
vv   PIK3IP1 MUTATED PIK3IP1 WILD-TYPE
  T1               0                17
  T2               2                90
  T3               7               322
  T4               0                50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  PIK3IP1 MUTATED     6   1   2
  PIK3IP1 WILD-TYPE 281 112  85
D159V6, multiclass
    clus
vv   PIK3IP1 MUTATED PIK3IP1 WILD-TYPE
  N0               6               281
  N1               1               112
  N2               2                85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D159V7, binary
                   cls
clus                  0   1
  PIK3IP1 MUTATED     8   0
  PIK3IP1 WILD-TYPE 367  65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PIK3IP1 MUTATED      8    0
  PIK3IP1 WILD-TYPE  367   65
   clus
vv  PIK3IP1 MUTATED PIK3IP1 WILD-TYPE
  0               8               367
  1               0                65
[1] 2 2
[1] FALSE
D159V8, binary
                   cls
clus                  0   1
  PIK3IP1 MUTATED     4   5
  PIK3IP1 WILD-TYPE 221 259
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PIK3IP1 MUTATED      4    5
  PIK3IP1 WILD-TYPE  221  259
        clus
vv       PIK3IP1 MUTATED PIK3IP1 WILD-TYPE
  FEMALE               4               221
  MALE                 5               259
[1] 2 2
[1] FALSE
D159V9, binary
                   cls
clus                  0   1
  PIK3IP1 MUTATED     7   0
  PIK3IP1 WILD-TYPE 343  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PIK3IP1 MUTATED      7    0
  PIK3IP1 WILD-TYPE  343   22
     clus
vv    PIK3IP1 MUTATED PIK3IP1 WILD-TYPE
  NO                7               343
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PIK3IP1 MUTATED                      5                             3
  PIK3IP1 WILD-TYPE                  310                            44
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PIK3IP1 MUTATED                       1                              0
  PIK3IP1 WILD-TYPE                   105                             10
D159V10, multiclass
                                clus
vv                               PIK3IP1 MUTATED PIK3IP1 WILD-TYPE
  COLON ADENOCARCINOMA                         5               310
  COLON MUCINOUS ADENOCARCINOMA                3                44
  RECTAL ADENOCARCINOMA                        1               105
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  PIK3IP1 MUTATED     8   0   0   0
  PIK3IP1 WILD-TYPE 337   4  31  25
D159V11, multiclass
    clus
vv   PIK3IP1 MUTATED PIK3IP1 WILD-TYPE
  R0               8               337
  R1               0                 4
  R2               0                31
  RX               0                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D159V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PIK3IP1 MUTATED                                  0     0
  PIK3IP1 WILD-TYPE                                1    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  PIK3IP1 MUTATED                           0     8
  PIK3IP1 WILD-TYPE                        22   218
D159V13, multiclass
                                  clus
vv                                 PIK3IP1 MUTATED PIK3IP1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                      0                22
  WHITE                                          8               218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(160) Variable = C10ORF79 MUTATION ANALYSIS
D160V1, survival
                    sevent
clus2                  0   1
  C10ORF79 MUTATED    27   4
  C10ORF79 WILD-TYPE 351  89
  C10ORF79 MUTATED C10ORF79 WILD-TYPE 
                31                440 
  C10ORF79 MUTATED C10ORF79 WILD-TYPE 
                 4                 89 
$`C10ORF79 MUTATED`
TCGA-A6-5656 TCGA-A6-6141 TCGA-AA-3555 TCGA-AA-3660 TCGA-AA-3672 TCGA-AA-3864 
       32.91         8.38        29.95        78.08         0.92        53.00 
TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01K TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6964 
        4.01        34.98        31.00         0.07        56.55        10.88 
TCGA-AZ-4315 TCGA-AZ-4681 TCGA-AZ-6599 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4948 
       58.39       106.75         6.77        12.76        10.06       148.01 
TCGA-CM-5861 TCGA-CM-6163 TCGA-CM-6674 TCGA-D5-6532 TCGA-D5-6923 TCGA-DM-A28E 
       15.02         2.96        12.95        18.25        12.43       119.93 
TCGA-F4-6805 TCGA-G4-6306 TCGA-AF-6672 TCGA-AG-3892 TCGA-AG-A002 TCGA-AG-A02N 
       34.42        44.68        10.39        13.02        20.98        61.97 
TCGA-F5-6813 
        0.69 

$`C10ORF79 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 
       22.06        32.71        27.09        22.52        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       24.00        17.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
       14.01        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       30.05        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 
       18.05        40.96        21.37        15.52         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
       16.31         0.95        33.01        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 
        5.13        22.36        62.79        88.21        49.41        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       14.30        17.56        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       22.98        30.08        32.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       17.03        15.02        12.00        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
       81.37        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6806 
       31.96        35.74         6.18        47.87         1.55        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 
      133.18        74.56        65.85        53.62        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       16.83        15.39        20.02        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 
       19.99         1.02        17.95        36.95        17.03        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       38.96        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  C10ORF79 MUTATED C10ORF79 WILD-TYPE 
              0.07               0.00 
  C10ORF79 MUTATED C10ORF79 WILD-TYPE 
            148.01             140.38 
  C10ORF79 MUTATED C10ORF79 WILD-TYPE 
            18.250             20.235 
[1] "0.1 - 148.0 (18.2)" "0.0 - 140.4 (20.2)"
[1] "hr=" "2"  
D160V2, continuous
D160V3, binary
                    cls
clus                   0   1
  C10ORF79 MUTATED    27   5
  C10ORF79 WILD-TYPE 339 114
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C10ORF79 MUTATED     27    5
  C10ORF79 WILD-TYPE  339  114
        clus
vv       C10ORF79 MUTATED C10ORF79 WILD-TYPE
  COLON                27                339
  RECTUM                5                114
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  C10ORF79 MUTATED         7        0        4        13         2         0
  C10ORF79 WILD-TYPE      84        1       28       125         8         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C10ORF79 MUTATED           2          0          0          2        1
  C10ORF79 WILD-TYPE        22         11         59         40       47
                    vv
clus                 STAGE IVA STAGE IVB
  C10ORF79 MUTATED           0         0
  C10ORF79 WILD-TYPE        18         1
D160V4, multiclass
            clus
vv           C10ORF79 MUTATED C10ORF79 WILD-TYPE
  STAGE I                   7                 84
  STAGE IA                  0                  1
  STAGE II                  4                 28
  STAGE IIA                13                125
  STAGE IIB                 2                  8
  STAGE IIC                 0                  1
  STAGE III                 2                 22
  STAGE IIIA                0                 11
  STAGE IIIB                0                 59
  STAGE IIIC                2                 40
  STAGE IV                  1                 47
  STAGE IVA                 0                 18
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  C10ORF79 MUTATED     2   6  18   6
  C10ORF79 WILD-TYPE  15  86 311  44
D160V5, multiclass
    clus
vv   C10ORF79 MUTATED C10ORF79 WILD-TYPE
  T1                2                 15
  T2                6                 86
  T3               18                311
  T4                6                 44
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  C10ORF79 MUTATED    26   2   4
  C10ORF79 WILD-TYPE 261 111  83
D160V6, multiclass
    clus
vv   C10ORF79 MUTATED C10ORF79 WILD-TYPE
  N0               26                261
  N1                2                111
  N2                4                 83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D160V7, binary
                    cls
clus                   0   1
  C10ORF79 MUTATED    28   0
  C10ORF79 WILD-TYPE 347  65
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C10ORF79 MUTATED     28    0
  C10ORF79 WILD-TYPE  347   65
   clus
vv  C10ORF79 MUTATED C10ORF79 WILD-TYPE
  0               28                347
  1                0                 65
[1] 2 2
[1] FALSE
D160V8, binary
                    cls
clus                   0   1
  C10ORF79 MUTATED    12  20
  C10ORF79 WILD-TYPE 213 244
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C10ORF79 MUTATED     12   20
  C10ORF79 WILD-TYPE  213  244
        clus
vv       C10ORF79 MUTATED C10ORF79 WILD-TYPE
  FEMALE               12                213
  MALE                 20                244
[1] 2 2
[1] FALSE
D160V9, binary
                    cls
clus                   0   1
  C10ORF79 MUTATED    24   1
  C10ORF79 WILD-TYPE 326  21
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C10ORF79 MUTATED     24    1
  C10ORF79 WILD-TYPE  326   21
     clus
vv    C10ORF79 MUTATED C10ORF79 WILD-TYPE
  NO                24                326
  YES                1                 21
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  C10ORF79 MUTATED                     23                             4
  C10ORF79 WILD-TYPE                  292                            43
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  C10ORF79 MUTATED                       5                              0
  C10ORF79 WILD-TYPE                   101                             10
D160V10, multiclass
                                clus
vv                               C10ORF79 MUTATED C10ORF79 WILD-TYPE
  COLON ADENOCARCINOMA                         23                292
  COLON MUCINOUS ADENOCARCINOMA                 4                 43
  RECTAL ADENOCARCINOMA                         5                101
  RECTAL MUCINOUS ADENOCARCINOMA                0                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  C10ORF79 MUTATED    23   0   0   2
  C10ORF79 WILD-TYPE 322   4  31  23
D160V11, multiclass
    clus
vv   C10ORF79 MUTATED C10ORF79 WILD-TYPE
  R0               23                322
  R1                0                  4
  R2                0                 31
  RX                2                 23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D160V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C10ORF79 MUTATED                                  0     3
  C10ORF79 WILD-TYPE                                1     8
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  C10ORF79 MUTATED                           1    17
  C10ORF79 WILD-TYPE                        21   209
D160V13, multiclass
                                  clus
vv                                 C10ORF79 MUTATED C10ORF79 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           3                  8
  BLACK OR AFRICAN AMERICAN                       1                 21
  WHITE                                          17                209
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(161) Variable = KRT2 MUTATION ANALYSIS
D161V1, survival
                sevent
clus2              0   1
  KRT2 MUTATED    14   0
  KRT2 WILD-TYPE 364  93
  KRT2 MUTATED KRT2 WILD-TYPE 
            14            457 
  KRT2 MUTATED KRT2 WILD-TYPE 
             0             93 
$`KRT2 MUTATED`
TCGA-A6-5665 TCGA-A6-6138 TCGA-A6-6781 TCGA-AA-3511 TCGA-CA-6717 TCGA-CA-6719 
       22.06        22.52        19.66         6.97        12.76        14.30 
TCGA-CM-5868 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6926 TCGA-DM-A0X9 
       17.03        16.14        15.58         3.68         9.04       119.70 
TCGA-DM-A28K TCGA-CL-5917 
       98.24        78.12 

$`KRT2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       22.09        32.71        27.09         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07        12.20        10.06 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       15.02        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6898 TCGA-D5-6922 
       17.85         4.80        17.13        12.49         1.48         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       12.43        14.30         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       12.00        11.38        10.26        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-F4-6459 TCGA-F4-6460 
      119.93        35.97        60.79       117.07         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  KRT2 MUTATED KRT2 WILD-TYPE 
          3.68           0.00 
  KRT2 MUTATED KRT2 WILD-TYPE 
        119.70         148.01 
  KRT2 MUTATED KRT2 WILD-TYPE 
        16.585         20.550 
[1] "3.7 - 119.7 (16.6)" "0.0 - 148.0 (20.6)"
[1] "hr="     "2.6e+07"
D161V2, continuous
D161V3, binary
                cls
clus               0   1
  KRT2 MUTATED    14   1
  KRT2 WILD-TYPE 352 118
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRT2 MUTATED     14    1
  KRT2 WILD-TYPE  352  118
        clus
vv       KRT2 MUTATED KRT2 WILD-TYPE
  COLON            14            352
  RECTUM            1            118
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KRT2 MUTATED         2        0        1         8         0         0
  KRT2 WILD-TYPE      89        1       31       130        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  KRT2 MUTATED           0          0          1          2        0         1
  KRT2 WILD-TYPE        24         11         58         40       48        17
                vv
clus             STAGE IVB
  KRT2 MUTATED           0
  KRT2 WILD-TYPE         1
D161V4, multiclass
            clus
vv           KRT2 MUTATED KRT2 WILD-TYPE
  STAGE I               2             89
  STAGE IA              0              1
  STAGE II              1             31
  STAGE IIA             8            130
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            1             58
  STAGE IIIC            2             40
  STAGE IV              0             48
  STAGE IVA             1             17
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  KRT2 MUTATED     0   2   9   4
  KRT2 WILD-TYPE  17  90 320  46
D161V5, multiclass
    clus
vv   KRT2 MUTATED KRT2 WILD-TYPE
  T1            0             17
  T2            2             90
  T3            9            320
  T4            4             46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  KRT2 MUTATED    11   3   1
  KRT2 WILD-TYPE 276 110  86
D161V6, multiclass
    clus
vv   KRT2 MUTATED KRT2 WILD-TYPE
  N0           11            276
  N1            3            110
  N2            1             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D161V7, binary
                cls
clus               0   1
  KRT2 MUTATED    12   1
  KRT2 WILD-TYPE 363  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRT2 MUTATED     12    1
  KRT2 WILD-TYPE  363   64
   clus
vv  KRT2 MUTATED KRT2 WILD-TYPE
  0           12            363
  1            1             64
[1] 2 2
[1] FALSE
D161V8, binary
                cls
clus               0   1
  KRT2 MUTATED     6   9
  KRT2 WILD-TYPE 219 255
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRT2 MUTATED      6    9
  KRT2 WILD-TYPE  219  255
        clus
vv       KRT2 MUTATED KRT2 WILD-TYPE
  FEMALE            6            219
  MALE              9            255
[1] 2 2
[1] FALSE
D161V9, binary
                cls
clus               0   1
  KRT2 MUTATED    10   1
  KRT2 WILD-TYPE 340  21
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRT2 MUTATED     10    1
  KRT2 WILD-TYPE  340   21
     clus
vv    KRT2 MUTATED KRT2 WILD-TYPE
  NO            10            340
  YES            1             21
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  KRT2 MUTATED                     10                             4
  KRT2 WILD-TYPE                  305                            43
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  KRT2 MUTATED                       1                              0
  KRT2 WILD-TYPE                   105                             10
D161V10, multiclass
                                clus
vv                               KRT2 MUTATED KRT2 WILD-TYPE
  COLON ADENOCARCINOMA                     10            305
  COLON MUCINOUS ADENOCARCINOMA             4             43
  RECTAL ADENOCARCINOMA                     1            105
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  KRT2 MUTATED     9   0   0   3
  KRT2 WILD-TYPE 336   4  31  22
D161V11, multiclass
    clus
vv   KRT2 MUTATED KRT2 WILD-TYPE
  R0            9            336
  R1            0              4
  R2            0             31
  RX            3             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D161V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KRT2 MUTATED                                  0     2
  KRT2 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  KRT2 MUTATED                           0    11
  KRT2 WILD-TYPE                        22   215
D161V13, multiclass
                                  clus
vv                                 KRT2 MUTATED KRT2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              9
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                      11            215
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(162) Variable = HTR2A MUTATION ANALYSIS
D162V1, survival
                 sevent
clus2               0   1
  HTR2A MUTATED    17   6
  HTR2A WILD-TYPE 361  87
  HTR2A MUTATED HTR2A WILD-TYPE 
             23             448 
  HTR2A MUTATED HTR2A WILD-TYPE 
              6              87 
$`HTR2A MUTATED`
TCGA-A6-5660 TCGA-A6-5665 TCGA-A6-6651 TCGA-AA-A00N TCGA-AA-A010 TCGA-CA-5255 
       29.19        22.06        21.76         4.01        34.98         3.06 
TCGA-CA-6717 TCGA-CK-4952 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-6161 TCGA-D5-5539 
       12.76        15.62        32.02         5.03        15.02        19.59 
TCGA-D5-6535 TCGA-D5-6539 TCGA-DM-A1D7 TCGA-DM-A1HA TCGA-DM-A28C TCGA-DM-A28F 
       15.12        12.49        13.32       131.51        81.37        35.97 
TCGA-G4-6299 TCGA-AG-3731 TCGA-AG-A002 TCGA-DY-A1DG TCGA-EI-6507 
       74.56        37.02        20.98        51.48        19.96 

$`HTR2A WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        33.53        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       24.16        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5796 
        5.23        11.74         3.19         1.61        12.69         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07        12.20        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
      148.01        85.45        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        15.02        17.03        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
       17.85         4.80        17.13        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A282 
       12.59       140.38         7.50        44.32       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
        6.12       119.93        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
       35.31       133.18        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
       19.99         7.99         0.99        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6508 
       57.24        24.13        32.61         0.49        20.55        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  HTR2A MUTATED HTR2A WILD-TYPE 
           3.06            0.00 
  HTR2A MUTATED HTR2A WILD-TYPE 
         131.51          148.01 
  HTR2A MUTATED HTR2A WILD-TYPE 
         20.980          20.155 
[1] "3.1 - 131.5 (21.0)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.2"
D162V2, continuous
D162V3, binary
                 cls
clus                0   1
  HTR2A MUTATED    19   4
  HTR2A WILD-TYPE 347 115
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HTR2A MUTATED     19    4
  HTR2A WILD-TYPE  347  115
        clus
vv       HTR2A MUTATED HTR2A WILD-TYPE
  COLON             19             347
  RECTUM             4             115
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  HTR2A MUTATED         2        0        0         7         2         0
  HTR2A WILD-TYPE      89        1       32       131         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  HTR2A MUTATED           0          2          3          4        1         2
  HTR2A WILD-TYPE        24          9         56         38       47        16
                 vv
clus              STAGE IVB
  HTR2A MUTATED           0
  HTR2A WILD-TYPE         1
D162V4, multiclass
            clus
vv           HTR2A MUTATED HTR2A WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              7             131
  STAGE IIB              2               8
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             2               9
  STAGE IIIB             3              56
  STAGE IIIC             4              38
  STAGE IV               1              47
  STAGE IVA              2              16
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  HTR2A MUTATED     0   2  18   3
  HTR2A WILD-TYPE  17  90 311  47
D162V5, multiclass
    clus
vv   HTR2A MUTATED HTR2A WILD-TYPE
  T1             0              17
  T2             2              90
  T3            18             311
  T4             3              47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  HTR2A MUTATED    12   7   4
  HTR2A WILD-TYPE 275 106  83
D162V6, multiclass
    clus
vv   HTR2A MUTATED HTR2A WILD-TYPE
  N0            12             275
  N1             7             106
  N2             4              83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D162V7, binary
                 cls
clus                0   1
  HTR2A MUTATED    18   3
  HTR2A WILD-TYPE 357  62
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HTR2A MUTATED     18    3
  HTR2A WILD-TYPE  357   62
   clus
vv  HTR2A MUTATED HTR2A WILD-TYPE
  0            18             357
  1             3              62
[1] 2 2
[1] FALSE
D162V8, binary
                 cls
clus                0   1
  HTR2A MUTATED     7  16
  HTR2A WILD-TYPE 218 248
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HTR2A MUTATED      7   16
  HTR2A WILD-TYPE  218  248
        clus
vv       HTR2A MUTATED HTR2A WILD-TYPE
  FEMALE             7             218
  MALE              16             248
[1] 2 2
[1] FALSE
D162V9, binary
                 cls
clus                0   1
  HTR2A MUTATED    15   1
  HTR2A WILD-TYPE 335  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HTR2A MUTATED     15    1
  HTR2A WILD-TYPE  335   21
     clus
vv    HTR2A MUTATED HTR2A WILD-TYPE
  NO             15             335
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  HTR2A MUTATED                     14                             4
  HTR2A WILD-TYPE                  301                            43
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  HTR2A MUTATED                       4                              0
  HTR2A WILD-TYPE                   102                             10
D162V10, multiclass
                                clus
vv                               HTR2A MUTATED HTR2A WILD-TYPE
  COLON ADENOCARCINOMA                      14             301
  COLON MUCINOUS ADENOCARCINOMA              4              43
  RECTAL ADENOCARCINOMA                      4             102
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  HTR2A MUTATED    11   0   1   4
  HTR2A WILD-TYPE 334   4  30  21
D162V11, multiclass
    clus
vv   HTR2A MUTATED HTR2A WILD-TYPE
  R0            11             334
  R1             0               4
  R2             1              30
  RX             4              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D162V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HTR2A MUTATED                                  0     2
  HTR2A WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  HTR2A MUTATED                           1    16
  HTR2A WILD-TYPE                        21   210
D162V13, multiclass
                                  clus
vv                                 HTR2A MUTATED HTR2A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               9
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                       16             210
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(163) Variable = PTK2 MUTATION ANALYSIS
D163V1, survival
                sevent
clus2              0   1
  PTK2 MUTATED    16   5
  PTK2 WILD-TYPE 362  88
  PTK2 MUTATED PTK2 WILD-TYPE 
            21            450 
  PTK2 MUTATED PTK2 WILD-TYPE 
             5             88 
$`PTK2 MUTATED`
TCGA-A6-5665 TCGA-A6-6780 TCGA-AA-3510 TCGA-AA-3526 TCGA-AA-3821 TCGA-AA-3877 
       22.06        20.12        63.98        19.07         1.02        31.00 
TCGA-AA-A010 TCGA-AY-5543 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-CA-6718 
       34.98        33.01        88.21         6.77       100.01        10.06 
TCGA-CK-6747 TCGA-CM-5861 TCGA-CM-6171 TCGA-D5-5538 TCGA-D5-6920 TCGA-D5-6931 
       82.95        15.02        14.04        12.26         3.68        12.00 
TCGA-DM-A0XF TCGA-G4-6299 TCGA-G4-6303 
       38.20        74.56        65.85 

$`PTK2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3529 TCGA-AA-3530 
       24.03        37.05        36.03         8.05         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
        0.99        25.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       18.05         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6603 
      106.75        22.36        62.79        49.41        12.10        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 
        3.25         3.29         0.07        12.20        12.76        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
        9.99        21.14         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       30.08        32.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 
       14.99        12.99        13.02        15.02        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       45.40        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6923 
       12.49        16.14        15.58         1.48         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A1D0 TCGA-DM-A1D4 
       11.38        10.26       119.70        24.43       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
      133.18        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  PTK2 MUTATED PTK2 WILD-TYPE 
          1.02           0.00 
  PTK2 MUTATED PTK2 WILD-TYPE 
        100.01         148.01 
  PTK2 MUTATED PTK2 WILD-TYPE 
         22.06          20.12 
[1] "1.0 - 100.0 (22.1)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.1"
D163V2, continuous
D163V3, binary
                cls
clus               0   1
  PTK2 MUTATED    21   0
  PTK2 WILD-TYPE 345 119
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTK2 MUTATED     21    0
  PTK2 WILD-TYPE  345  119
        clus
vv       PTK2 MUTATED PTK2 WILD-TYPE
  COLON            21            345
  RECTUM            0            119
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PTK2 MUTATED         6        0        2         6         1         0
  PTK2 WILD-TYPE      85        1       30       132         9         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PTK2 MUTATED           0          0          1          3        1         1
  PTK2 WILD-TYPE        24         11         58         39       47        17
                vv
clus             STAGE IVB
  PTK2 MUTATED           0
  PTK2 WILD-TYPE         1
D163V4, multiclass
            clus
vv           PTK2 MUTATED PTK2 WILD-TYPE
  STAGE I               6             85
  STAGE IA              0              1
  STAGE II              2             30
  STAGE IIA             6            132
  STAGE IIB             1              9
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            1             58
  STAGE IIIC            3             39
  STAGE IV              1             47
  STAGE IVA             1             17
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  PTK2 MUTATED     2   4  13   2
  PTK2 WILD-TYPE  15  88 316  48
D163V5, multiclass
    clus
vv   PTK2 MUTATED PTK2 WILD-TYPE
  T1            2             15
  T2            4             88
  T3           13            316
  T4            2             48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  PTK2 MUTATED    15   3   3
  PTK2 WILD-TYPE 272 110  84
D163V6, multiclass
    clus
vv   PTK2 MUTATED PTK2 WILD-TYPE
  N0           15            272
  N1            3            110
  N2            3             84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D163V7, binary
                cls
clus               0   1
  PTK2 MUTATED    16   2
  PTK2 WILD-TYPE 359  63
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTK2 MUTATED     16    2
  PTK2 WILD-TYPE  359   63
   clus
vv  PTK2 MUTATED PTK2 WILD-TYPE
  0           16            359
  1            2             63
[1] 2 2
[1] FALSE
D163V8, binary
                cls
clus               0   1
  PTK2 MUTATED    13   8
  PTK2 WILD-TYPE 212 256
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTK2 MUTATED     13    8
  PTK2 WILD-TYPE  212  256
        clus
vv       PTK2 MUTATED PTK2 WILD-TYPE
  FEMALE           13            212
  MALE              8            256
[1] 2 2
[1] FALSE
D163V9, binary
                cls
clus               0   1
  PTK2 MUTATED    19   0
  PTK2 WILD-TYPE 331  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTK2 MUTATED     19    0
  PTK2 WILD-TYPE  331   22
     clus
vv    PTK2 MUTATED PTK2 WILD-TYPE
  NO            19            331
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PTK2 MUTATED                     17                             3
  PTK2 WILD-TYPE                  298                            44
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PTK2 MUTATED                       0                              0
  PTK2 WILD-TYPE                   106                             10
D163V10, multiclass
                                clus
vv                               PTK2 MUTATED PTK2 WILD-TYPE
  COLON ADENOCARCINOMA                     17            298
  COLON MUCINOUS ADENOCARCINOMA             3             44
  RECTAL ADENOCARCINOMA                     0            106
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  PTK2 MUTATED    14   0   0   2
  PTK2 WILD-TYPE 331   4  31  23
D163V11, multiclass
    clus
vv   PTK2 MUTATED PTK2 WILD-TYPE
  R0           14            331
  R1            0              4
  R2            0             31
  RX            2             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D163V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PTK2 MUTATED                                  0     1
  PTK2 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  PTK2 MUTATED                           1    14
  PTK2 WILD-TYPE                        21   212
D163V13, multiclass
                                  clus
vv                                 PTK2 MUTATED PTK2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                      14            212
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(164) Variable = AXIN2 MUTATION ANALYSIS
D164V1, survival
                 sevent
clus2               0   1
  AXIN2 MUTATED    16   7
  AXIN2 WILD-TYPE 362  86
  AXIN2 MUTATED AXIN2 WILD-TYPE 
             23             448 
  AXIN2 MUTATED AXIN2 WILD-TYPE 
              7              86 
$`AXIN2 MUTATED`
TCGA-A6-2676 TCGA-A6-5661 TCGA-AA-3492 TCGA-AA-3542 TCGA-AA-3672 TCGA-AA-3972 
       42.90        33.53         3.02        12.99         0.92        50.99 
TCGA-AA-A00E TCGA-AA-A010 TCGA-AD-5900 TCGA-AD-6964 TCGA-CA-5255 TCGA-CK-5916 
       30.02        34.98         0.07        10.88         3.06        21.14 
TCGA-CM-5349 TCGA-CM-6162 TCGA-D5-6537 TCGA-D5-6930 TCGA-DM-A1D6 TCGA-DM-A1DB 
       30.08        12.00         4.80         1.51        49.91        44.32 
TCGA-G4-6304 TCGA-G4-6628 TCGA-AF-6136 TCGA-AG-4005 TCGA-AG-A002 
       53.62        79.69        15.39        14.04        20.98 

$`AXIN2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       31.63        30.44        29.19        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       19.66        20.28         7.04         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3543 
       19.07        34.03        29.00        29.00        26.01         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
       14.01        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       21.99        16.08        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       13.94        38.04        19.00        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       39.98        18.05        40.96        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
        0.79         0.72         5.79        22.42        27.42         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       51.32         9.99        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       22.98        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       17.03        15.02         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        4.80        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
       38.20       130.65        92.75        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
        7.50       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 
       35.31       133.18        74.56        65.85        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 
       35.80        26.17        91.79        46.75        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       16.83        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       28.04        36.03         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  AXIN2 MUTATED AXIN2 WILD-TYPE 
           0.07            0.00 
  AXIN2 MUTATED AXIN2 WILD-TYPE 
          79.69          148.01 
  AXIN2 MUTATED AXIN2 WILD-TYPE 
         20.980          20.155 
[1] "0.1 - 79.7 (21.0)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.6"
D164V2, continuous
D164V3, binary
                 cls
clus                0   1
  AXIN2 MUTATED    21   3
  AXIN2 WILD-TYPE 345 116
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AXIN2 MUTATED     21    3
  AXIN2 WILD-TYPE  345  116
        clus
vv       AXIN2 MUTATED AXIN2 WILD-TYPE
  COLON             21             345
  RECTUM             3             116
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  AXIN2 MUTATED         4        0        2         7         3         0
  AXIN2 WILD-TYPE      87        1       30       131         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AXIN2 MUTATED           1          0          3          1        2         0
  AXIN2 WILD-TYPE        23         11         56         41       46        18
                 vv
clus              STAGE IVB
  AXIN2 MUTATED           0
  AXIN2 WILD-TYPE         1
D164V4, multiclass
            clus
vv           AXIN2 MUTATED AXIN2 WILD-TYPE
  STAGE I                4              87
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA              7             131
  STAGE IIB              3               7
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             3              56
  STAGE IIIC             1              41
  STAGE IV               2              46
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  AXIN2 MUTATED     1   3  15   5
  AXIN2 WILD-TYPE  16  89 314  45
D164V5, multiclass
    clus
vv   AXIN2 MUTATED AXIN2 WILD-TYPE
  T1             1              16
  T2             3              89
  T3            15             314
  T4             5              45
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  AXIN2 MUTATED    16   5   3
  AXIN2 WILD-TYPE 271 108  84
D164V6, multiclass
    clus
vv   AXIN2 MUTATED AXIN2 WILD-TYPE
  N0            16             271
  N1             5             108
  N2             3              84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D164V7, binary
                 cls
clus                0   1
  AXIN2 MUTATED    18   2
  AXIN2 WILD-TYPE 357  63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AXIN2 MUTATED     18    2
  AXIN2 WILD-TYPE  357   63
   clus
vv  AXIN2 MUTATED AXIN2 WILD-TYPE
  0            18             357
  1             2              63
[1] 2 2
[1] FALSE
D164V8, binary
                 cls
clus                0   1
  AXIN2 MUTATED    11  13
  AXIN2 WILD-TYPE 214 251
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AXIN2 MUTATED     11   13
  AXIN2 WILD-TYPE  214  251
        clus
vv       AXIN2 MUTATED AXIN2 WILD-TYPE
  FEMALE            11             214
  MALE              13             251
[1] 2 2
[1] FALSE
D164V9, binary
                 cls
clus                0   1
  AXIN2 MUTATED    17   2
  AXIN2 WILD-TYPE 333  20
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AXIN2 MUTATED     17    2
  AXIN2 WILD-TYPE  333   20
     clus
vv    AXIN2 MUTATED AXIN2 WILD-TYPE
  NO             17             333
  YES             2              20
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  AXIN2 MUTATED                     17                             4
  AXIN2 WILD-TYPE                  298                            43
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  AXIN2 MUTATED                       3                              0
  AXIN2 WILD-TYPE                   103                             10
D164V10, multiclass
                                clus
vv                               AXIN2 MUTATED AXIN2 WILD-TYPE
  COLON ADENOCARCINOMA                      17             298
  COLON MUCINOUS ADENOCARCINOMA              4              43
  RECTAL ADENOCARCINOMA                      3             103
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  AXIN2 MUTATED    17   0   1   2
  AXIN2 WILD-TYPE 328   4  30  23
D164V11, multiclass
    clus
vv   AXIN2 MUTATED AXIN2 WILD-TYPE
  R0            17             328
  R1             0               4
  R2             1              30
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D164V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AXIN2 MUTATED                                  0     1
  AXIN2 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  AXIN2 MUTATED                           1    13
  AXIN2 WILD-TYPE                        21   213
D164V13, multiclass
                                  clus
vv                                 AXIN2 MUTATED AXIN2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                       13             213
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(165) Variable = TM9SF2 MUTATION ANALYSIS
D165V1, survival
                  sevent
clus2                0   1
  TM9SF2 MUTATED     9   2
  TM9SF2 WILD-TYPE 369  91
  TM9SF2 MUTATED TM9SF2 WILD-TYPE 
              11              460 
  TM9SF2 MUTATED TM9SF2 WILD-TYPE 
               2               91 
$`TM9SF2 MUTATED`
TCGA-A6-5665 TCGA-AA-3510 TCGA-AA-A00R TCGA-AA-A01R TCGA-AD-6548 TCGA-AD-6964 
       22.06        63.98         0.99        35.01        21.37        10.88 
TCGA-AU-3779 TCGA-AY-6197 TCGA-AZ-6598 TCGA-CM-6680 TCGA-AG-3892 
       14.50        21.44        49.41        12.03        13.02 

$`TM9SF2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
        4.01        27.02        42.02        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       31.00        38.07         1.02         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
       40.96         0.07        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 
        5.79        22.42        27.42         0.20        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        33.01        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 
      106.75        22.36        62.79        88.21         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-D5-5537 
       13.05        11.08        11.08        11.01        10.06        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 
        1.02        17.95        36.95        17.03        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  TM9SF2 MUTATED TM9SF2 WILD-TYPE 
            0.99             0.00 
  TM9SF2 MUTATED TM9SF2 WILD-TYPE 
           63.98           148.01 
  TM9SF2 MUTATED TM9SF2 WILD-TYPE 
          21.370           20.155 
[1] "1.0 - 64.0 (21.4)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1"  
D165V2, continuous
D165V3, binary
                  cls
clus                 0   1
  TM9SF2 MUTATED    10   1
  TM9SF2 WILD-TYPE 356 118
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TM9SF2 MUTATED     10    1
  TM9SF2 WILD-TYPE  356  118
        clus
vv       TM9SF2 MUTATED TM9SF2 WILD-TYPE
  COLON              10              356
  RECTUM              1              118
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TM9SF2 MUTATED         3        0        2         3         0         0
  TM9SF2 WILD-TYPE      88        1       30       135        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TM9SF2 MUTATED           1          0          1          0        0
  TM9SF2 WILD-TYPE        23         11         58         42       48
                  vv
clus               STAGE IVA STAGE IVB
  TM9SF2 MUTATED           0         0
  TM9SF2 WILD-TYPE        18         1
D165V4, multiclass
            clus
vv           TM9SF2 MUTATED TM9SF2 WILD-TYPE
  STAGE I                 3               88
  STAGE IA                0                1
  STAGE II                2               30
  STAGE IIA               3              135
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               1               23
  STAGE IIIA              0               11
  STAGE IIIB              1               58
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  TM9SF2 MUTATED     1   2   7   1
  TM9SF2 WILD-TYPE  16  90 322  49
D165V5, multiclass
    clus
vv   TM9SF2 MUTATED TM9SF2 WILD-TYPE
  T1              1               16
  T2              2               90
  T3              7              322
  T4              1               49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  TM9SF2 MUTATED     8   0   3
  TM9SF2 WILD-TYPE 279 113  84
D165V6, multiclass
    clus
vv   TM9SF2 MUTATED TM9SF2 WILD-TYPE
  N0              8              279
  N1              0              113
  N2              3               84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D165V7, binary
                  cls
clus                 0   1
  TM9SF2 MUTATED     8   0
  TM9SF2 WILD-TYPE 367  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TM9SF2 MUTATED      8    0
  TM9SF2 WILD-TYPE  367   65
   clus
vv  TM9SF2 MUTATED TM9SF2 WILD-TYPE
  0              8              367
  1              0               65
[1] 2 2
[1] FALSE
D165V8, binary
                  cls
clus                 0   1
  TM9SF2 MUTATED     7   4
  TM9SF2 WILD-TYPE 218 260
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TM9SF2 MUTATED      7    4
  TM9SF2 WILD-TYPE  218  260
        clus
vv       TM9SF2 MUTATED TM9SF2 WILD-TYPE
  FEMALE              7              218
  MALE                4              260
[1] 2 2
[1] FALSE
D165V9, binary
                  cls
clus                 0   1
  TM9SF2 MUTATED     9   1
  TM9SF2 WILD-TYPE 341  21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TM9SF2 MUTATED      9    1
  TM9SF2 WILD-TYPE  341   21
     clus
vv    TM9SF2 MUTATED TM9SF2 WILD-TYPE
  NO               9              341
  YES              1               21
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  TM9SF2 MUTATED                      9                             1
  TM9SF2 WILD-TYPE                  306                            46
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  TM9SF2 MUTATED                       1                              0
  TM9SF2 WILD-TYPE                   105                             10
D165V10, multiclass
                                clus
vv                               TM9SF2 MUTATED TM9SF2 WILD-TYPE
  COLON ADENOCARCINOMA                        9              306
  COLON MUCINOUS ADENOCARCINOMA               1               46
  RECTAL ADENOCARCINOMA                       1              105
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  TM9SF2 MUTATED     9   0   0   0
  TM9SF2 WILD-TYPE 336   4  31  25
D165V11, multiclass
    clus
vv   TM9SF2 MUTATED TM9SF2 WILD-TYPE
  R0              9              336
  R1              0                4
  R2              0               31
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D165V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TM9SF2 MUTATED                                  0     0
  TM9SF2 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  TM9SF2 MUTATED                           0     7
  TM9SF2 WILD-TYPE                        22   219
D165V13, multiclass
                                  clus
vv                                 TM9SF2 MUTATED TM9SF2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         7              219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(166) Variable = FAHD2A MUTATION ANALYSIS
D166V1, survival
                  sevent
clus2                0   1
  FAHD2A MUTATED     6   1
  FAHD2A WILD-TYPE 372  92
  FAHD2A MUTATED FAHD2A WILD-TYPE 
               7              464 
  FAHD2A MUTATED FAHD2A WILD-TYPE 
               1               92 
$`FAHD2A MUTATED`
TCGA-A6-5665 TCGA-A6-6653 TCGA-AA-3950 TCGA-CK-5916 TCGA-D5-6533 TCGA-G4-6586 
       22.06        24.39        24.00        21.14         1.32        35.80 
TCGA-EI-6507 
       19.96 

$`FAHD2A WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 
       25.18        24.16        21.76        24.69        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 
       12.99        24.00        33.01        26.01         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 
       15.62        49.08        51.32         9.99        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       22.09        13.78        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
       32.61         0.49        20.55        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  FAHD2A MUTATED FAHD2A WILD-TYPE 
            1.32             0.00 
  FAHD2A MUTATED FAHD2A WILD-TYPE 
           35.80           148.01 
  FAHD2A MUTATED FAHD2A WILD-TYPE 
          22.060           20.085 
[1] "1.3 - 35.8 (22.1)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1"  
D166V2, continuous
D166V3, binary
                  cls
clus                 0   1
  FAHD2A MUTATED     6   1
  FAHD2A WILD-TYPE 360 118
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAHD2A MUTATED      6    1
  FAHD2A WILD-TYPE  360  118
        clus
vv       FAHD2A MUTATED FAHD2A WILD-TYPE
  COLON               6              360
  RECTUM              1              118
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FAHD2A MUTATED         2        0        0         4         0         0
  FAHD2A WILD-TYPE      89        1       32       134        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FAHD2A MUTATED           0          0          1          0        0
  FAHD2A WILD-TYPE        24         11         58         42       48
                  vv
clus               STAGE IVA STAGE IVB
  FAHD2A MUTATED           0         0
  FAHD2A WILD-TYPE        18         1
D166V4, multiclass
            clus
vv           FAHD2A MUTATED FAHD2A WILD-TYPE
  STAGE I                 2               89
  STAGE IA                0                1
  STAGE II                0               32
  STAGE IIA               4              134
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              1               58
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  FAHD2A MUTATED     1   1   4   1
  FAHD2A WILD-TYPE  16  91 325  49
D166V5, multiclass
    clus
vv   FAHD2A MUTATED FAHD2A WILD-TYPE
  T1              1               16
  T2              1               91
  T3              4              325
  T4              1               49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  FAHD2A MUTATED     7   0   0
  FAHD2A WILD-TYPE 280 113  87
D166V6, multiclass
    clus
vv   FAHD2A MUTATED FAHD2A WILD-TYPE
  N0              7              280
  N1              0              113
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D166V7, binary
                  cls
clus                 0   1
  FAHD2A MUTATED     7   0
  FAHD2A WILD-TYPE 368  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAHD2A MUTATED      7    0
  FAHD2A WILD-TYPE  368   65
   clus
vv  FAHD2A MUTATED FAHD2A WILD-TYPE
  0              7              368
  1              0               65
[1] 2 2
[1] FALSE
D166V8, binary
                  cls
clus                 0   1
  FAHD2A MUTATED     5   2
  FAHD2A WILD-TYPE 220 262
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAHD2A MUTATED      5    2
  FAHD2A WILD-TYPE  220  262
        clus
vv       FAHD2A MUTATED FAHD2A WILD-TYPE
  FEMALE              5              220
  MALE                2              262
[1] 2 2
[1] FALSE
D166V9, binary
                  cls
clus                 0   1
  FAHD2A MUTATED     6   0
  FAHD2A WILD-TYPE 344  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAHD2A MUTATED      6    0
  FAHD2A WILD-TYPE  344   22
     clus
vv    FAHD2A MUTATED FAHD2A WILD-TYPE
  NO               6              344
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  FAHD2A MUTATED                      5                             1
  FAHD2A WILD-TYPE                  310                            46
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  FAHD2A MUTATED                       1                              0
  FAHD2A WILD-TYPE                   105                             10
D166V10, multiclass
                                clus
vv                               FAHD2A MUTATED FAHD2A WILD-TYPE
  COLON ADENOCARCINOMA                        5              310
  COLON MUCINOUS ADENOCARCINOMA               1               46
  RECTAL ADENOCARCINOMA                       1              105
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  FAHD2A MUTATED     5   0   0   1
  FAHD2A WILD-TYPE 340   4  31  24
D166V11, multiclass
    clus
vv   FAHD2A MUTATED FAHD2A WILD-TYPE
  R0              5              340
  R1              0                4
  R2              0               31
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D166V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FAHD2A MUTATED                                  0     0
  FAHD2A WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  FAHD2A MUTATED                           0     6
  FAHD2A WILD-TYPE                        22   220
D166V13, multiclass
                                  clus
vv                                 FAHD2A MUTATED FAHD2A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         6              220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(167) Variable = KCNK1 MUTATION ANALYSIS
D167V1, survival
                 sevent
clus2               0   1
  KCNK1 MUTATED     9   2
  KCNK1 WILD-TYPE 369  91
  KCNK1 MUTATED KCNK1 WILD-TYPE 
             11             460 
  KCNK1 MUTATED KCNK1 WILD-TYPE 
              2              91 
$`KCNK1 MUTATED`
TCGA-A6-5661 TCGA-AA-3845 TCGA-AD-6964 TCGA-CM-4747 TCGA-CM-5344 TCGA-CM-5864 
       33.53         0.00        10.88        25.02        22.03        15.02 
TCGA-CM-6163 TCGA-CM-6679 TCGA-G4-6315 TCGA-G4-6588 TCGA-AG-3909 
        2.96        10.06        61.91        26.17        19.99 

$`KCNK1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 
       17.98        15.95        38.99        37.02        14.93        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4752 
        1.91       124.27        23.05        20.02        37.02        13.02 
TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       29.06        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6164 TCGA-CM-6165 
       15.02        17.03        15.02        12.00        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 
       63.62        36.00        22.09        13.78        35.80        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3999 TCGA-AG-4001 
       14.01         1.02        48.03        32.02        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  KCNK1 MUTATED KCNK1 WILD-TYPE 
              0               0 
  KCNK1 MUTATED KCNK1 WILD-TYPE 
          61.91          148.01 
  KCNK1 MUTATED KCNK1 WILD-TYPE 
         19.990          20.235 
[1] "0.0 - 61.9 (20.0)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.2"
D167V2, continuous
D167V3, binary
                 cls
clus                0   1
  KCNK1 MUTATED    10   1
  KCNK1 WILD-TYPE 356 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNK1 MUTATED     10    1
  KCNK1 WILD-TYPE  356  118
        clus
vv       KCNK1 MUTATED KCNK1 WILD-TYPE
  COLON             10             356
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KCNK1 MUTATED         2        0        0         4         0         0
  KCNK1 WILD-TYPE      89        1       32       134        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  KCNK1 MUTATED           0          0          2          0        1         1
  KCNK1 WILD-TYPE        24         11         57         42       47        17
                 vv
clus              STAGE IVB
  KCNK1 MUTATED           0
  KCNK1 WILD-TYPE         1
D167V4, multiclass
            clus
vv           KCNK1 MUTATED KCNK1 WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              4             134
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             2              57
  STAGE IIIC             0              42
  STAGE IV               1              47
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  KCNK1 MUTATED     1   1   7   2
  KCNK1 WILD-TYPE  16  91 322  48
D167V5, multiclass
    clus
vv   KCNK1 MUTATED KCNK1 WILD-TYPE
  T1             1              16
  T2             1              91
  T3             7             322
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  KCNK1 MUTATED     6   4   1
  KCNK1 WILD-TYPE 281 109  86
D167V6, multiclass
    clus
vv   KCNK1 MUTATED KCNK1 WILD-TYPE
  N0             6             281
  N1             4             109
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D167V7, binary
                 cls
clus                0   1
  KCNK1 MUTATED     8   2
  KCNK1 WILD-TYPE 367  63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNK1 MUTATED      8    2
  KCNK1 WILD-TYPE  367   63
   clus
vv  KCNK1 MUTATED KCNK1 WILD-TYPE
  0             8             367
  1             2              63
[1] 2 2
[1] FALSE
D167V8, binary
                 cls
clus                0   1
  KCNK1 MUTATED     5   6
  KCNK1 WILD-TYPE 220 258
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNK1 MUTATED      5    6
  KCNK1 WILD-TYPE  220  258
        clus
vv       KCNK1 MUTATED KCNK1 WILD-TYPE
  FEMALE             5             220
  MALE               6             258
[1] 2 2
[1] FALSE
D167V9, binary
                 cls
clus                0   1
  KCNK1 MUTATED    10   0
  KCNK1 WILD-TYPE 340  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNK1 MUTATED     10    0
  KCNK1 WILD-TYPE  340   22
     clus
vv    KCNK1 MUTATED KCNK1 WILD-TYPE
  NO             10             340
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  KCNK1 MUTATED                     10                             0
  KCNK1 WILD-TYPE                  305                            47
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  KCNK1 MUTATED                       1                              0
  KCNK1 WILD-TYPE                   105                             10
D167V10, multiclass
                                clus
vv                               KCNK1 MUTATED KCNK1 WILD-TYPE
  COLON ADENOCARCINOMA                      10             305
  COLON MUCINOUS ADENOCARCINOMA              0              47
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  KCNK1 MUTATED    10   0   0   0
  KCNK1 WILD-TYPE 335   4  31  25
D167V11, multiclass
    clus
vv   KCNK1 MUTATED KCNK1 WILD-TYPE
  R0            10             335
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D167V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KCNK1 MUTATED                                  0     0
  KCNK1 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  KCNK1 MUTATED                           1     8
  KCNK1 WILD-TYPE                        21   218
D167V13, multiclass
                                  clus
vv                                 KCNK1 MUTATED KCNK1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        8             218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(168) Variable = C15ORF52 MUTATION ANALYSIS
D168V1, survival
                    sevent
clus2                  0   1
  C15ORF52 MUTATED     8   4
  C15ORF52 WILD-TYPE 370  89
  C15ORF52 MUTATED C15ORF52 WILD-TYPE 
                12                459 
  C15ORF52 MUTATED C15ORF52 WILD-TYPE 
                 4                 89 
$`C15ORF52 MUTATED`
TCGA-A6-5665 TCGA-A6-6141 TCGA-A6-6653 TCGA-AA-3492 TCGA-AA-3663 TCGA-AA-3672 
       22.06         8.38        24.39         3.02         6.97         0.92 
TCGA-AA-3845 TCGA-AA-3950 TCGA-AD-6889 TCGA-AD-6964 TCGA-CK-5913 TCGA-DM-A28G 
        0.00        24.00        56.55        10.88        51.32        60.79 

$`C15ORF52 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 
       22.09        32.71        27.09        22.52        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       24.16        21.76        24.69        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
       20.28         7.04         1.02        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       61.02        78.08         6.05        54.02         2.01        14.01 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 
        2.01        12.99        24.00        33.01        26.01         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
        0.79         0.72         5.79        22.42        27.42         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       49.08         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
       81.37       119.93        35.97       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  C15ORF52 MUTATED C15ORF52 WILD-TYPE 
                 0                  0 
  C15ORF52 MUTATED C15ORF52 WILD-TYPE 
             60.79             148.01 
  C15ORF52 MUTATED C15ORF52 WILD-TYPE 
             16.47              20.19 
[1] "0.0 - 60.8 (16.5)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.9"
D168V2, continuous
D168V3, binary
                    cls
clus                   0   1
  C15ORF52 MUTATED    12   0
  C15ORF52 WILD-TYPE 354 119
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C15ORF52 MUTATED     12    0
  C15ORF52 WILD-TYPE  354  119
        clus
vv       C15ORF52 MUTATED C15ORF52 WILD-TYPE
  COLON                12                354
  RECTUM                0                119
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  C15ORF52 MUTATED         1        0        2         7         0         0
  C15ORF52 WILD-TYPE      90        1       30       131        10         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C15ORF52 MUTATED           1          0          0          0        0
  C15ORF52 WILD-TYPE        23         11         59         42       48
                    vv
clus                 STAGE IVA STAGE IVB
  C15ORF52 MUTATED           0         0
  C15ORF52 WILD-TYPE        18         1
D168V4, multiclass
            clus
vv           C15ORF52 MUTATED C15ORF52 WILD-TYPE
  STAGE I                   1                 90
  STAGE IA                  0                  1
  STAGE II                  2                 30
  STAGE IIA                 7                131
  STAGE IIB                 0                 10
  STAGE IIC                 0                  1
  STAGE III                 1                 23
  STAGE IIIA                0                 11
  STAGE IIIB                0                 59
  STAGE IIIC                0                 42
  STAGE IV                  0                 48
  STAGE IVA                 0                 18
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  C15ORF52 MUTATED     0   1  10   1
  C15ORF52 WILD-TYPE  17  91 319  49
D168V5, multiclass
    clus
vv   C15ORF52 MUTATED C15ORF52 WILD-TYPE
  T1                0                 17
  T2                1                 91
  T3               10                319
  T4                1                 49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  C15ORF52 MUTATED    10   1   1
  C15ORF52 WILD-TYPE 277 112  86
D168V6, multiclass
    clus
vv   C15ORF52 MUTATED C15ORF52 WILD-TYPE
  N0               10                277
  N1                1                112
  N2                1                 86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D168V7, binary
                    cls
clus                   0   1
  C15ORF52 MUTATED    10   0
  C15ORF52 WILD-TYPE 365  65
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C15ORF52 MUTATED     10    0
  C15ORF52 WILD-TYPE  365   65
   clus
vv  C15ORF52 MUTATED C15ORF52 WILD-TYPE
  0               10                365
  1                0                 65
[1] 2 2
[1] FALSE
D168V8, binary
                    cls
clus                   0   1
  C15ORF52 MUTATED     6   6
  C15ORF52 WILD-TYPE 219 258
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C15ORF52 MUTATED      6    6
  C15ORF52 WILD-TYPE  219  258
        clus
vv       C15ORF52 MUTATED C15ORF52 WILD-TYPE
  FEMALE                6                219
  MALE                  6                258
[1] 2 2
[1] FALSE
D168V9, binary
                    cls
clus                   0   1
  C15ORF52 MUTATED     9   0
  C15ORF52 WILD-TYPE 341  22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C15ORF52 MUTATED      9    0
  C15ORF52 WILD-TYPE  341   22
     clus
vv    C15ORF52 MUTATED C15ORF52 WILD-TYPE
  NO                 9                341
  YES                0                 22
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  C15ORF52 MUTATED                     11                             1
  C15ORF52 WILD-TYPE                  304                            46
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  C15ORF52 MUTATED                       0                              0
  C15ORF52 WILD-TYPE                   106                             10
D168V10, multiclass
                                clus
vv                               C15ORF52 MUTATED C15ORF52 WILD-TYPE
  COLON ADENOCARCINOMA                         11                304
  COLON MUCINOUS ADENOCARCINOMA                 1                 46
  RECTAL ADENOCARCINOMA                         0                106
  RECTAL MUCINOUS ADENOCARCINOMA                0                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  C15ORF52 MUTATED     6   0   0   1
  C15ORF52 WILD-TYPE 339   4  31  24
D168V11, multiclass
    clus
vv   C15ORF52 MUTATED C15ORF52 WILD-TYPE
  R0                6                339
  R1                0                  4
  R2                0                 31
  RX                1                 24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D168V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C15ORF52 MUTATED                                  0     1
  C15ORF52 WILD-TYPE                                1    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  C15ORF52 MUTATED                           1     5
  C15ORF52 WILD-TYPE                        21   221
D168V13, multiclass
                                  clus
vv                                 C15ORF52 MUTATED C15ORF52 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                 10
  BLACK OR AFRICAN AMERICAN                       1                 21
  WHITE                                           5                221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(169) Variable = HAUS6 MUTATION ANALYSIS
D169V1, survival
                 sevent
clus2               0   1
  HAUS6 MUTATED    10   3
  HAUS6 WILD-TYPE 368  90
  HAUS6 MUTATED HAUS6 WILD-TYPE 
             13             458 
  HAUS6 MUTATED HAUS6 WILD-TYPE 
              3              90 
$`HAUS6 MUTATED`
TCGA-AA-3864 TCGA-AA-3977 TCGA-AZ-4315 TCGA-CK-5916 TCGA-CM-5341 TCGA-D5-6532 
       53.00        25.02        58.39        21.14        29.06        18.25 
TCGA-DM-A0XF TCGA-DM-A1D4 TCGA-DM-A1HB TCGA-AG-3742 TCGA-AG-3892 TCGA-EI-6506 
       38.20        92.75       135.65         0.99        13.02        20.55 
TCGA-F5-6465 
       49.51 

$`HAUS6 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       33.01        21.44        17.82         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 
       15.62        49.08        51.32         9.99        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6534 
       19.59        56.09        55.92        20.19         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A1D0 TCGA-DM-A1D6 
       11.38        10.26       119.70        24.43       130.65        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
        0.99        37.02        32.98         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 
        1.02        17.95        36.95        17.03        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       51.48        32.61         0.49        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
        9.96        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  HAUS6 MUTATED HAUS6 WILD-TYPE 
           0.99            0.00 
  HAUS6 MUTATED HAUS6 WILD-TYPE 
         135.65          148.01 
  HAUS6 MUTATED HAUS6 WILD-TYPE 
          29.06           20.02 
[1] "1.0 - 135.7 (29.1)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.4"
D169V2, continuous
D169V3, binary
                 cls
clus                0   1
  HAUS6 MUTATED    12   5
  HAUS6 WILD-TYPE 354 114
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HAUS6 MUTATED     12    5
  HAUS6 WILD-TYPE  354  114
        clus
vv       HAUS6 MUTATED HAUS6 WILD-TYPE
  COLON             12             354
  RECTUM             5             114
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  HAUS6 MUTATED         3        0        1         6         1         0
  HAUS6 WILD-TYPE      88        1       31       132         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  HAUS6 MUTATED           1          1          1          1        1         0
  HAUS6 WILD-TYPE        23         10         58         41       47        18
                 vv
clus              STAGE IVB
  HAUS6 MUTATED           0
  HAUS6 WILD-TYPE         1
D169V4, multiclass
            clus
vv           HAUS6 MUTATED HAUS6 WILD-TYPE
  STAGE I                3              88
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              6             132
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             1              10
  STAGE IIIB             1              58
  STAGE IIIC             1              41
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  HAUS6 MUTATED     3   2  10   2
  HAUS6 WILD-TYPE  14  90 319  48
D169V5, multiclass
    clus
vv   HAUS6 MUTATED HAUS6 WILD-TYPE
  T1             3              14
  T2             2              90
  T3            10             319
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  HAUS6 MUTATED    12   3   2
  HAUS6 WILD-TYPE 275 110  85
D169V6, multiclass
    clus
vv   HAUS6 MUTATED HAUS6 WILD-TYPE
  N0            12             275
  N1             3             110
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D169V7, binary
                 cls
clus                0   1
  HAUS6 MUTATED    13   1
  HAUS6 WILD-TYPE 362  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HAUS6 MUTATED     13    1
  HAUS6 WILD-TYPE  362   64
   clus
vv  HAUS6 MUTATED HAUS6 WILD-TYPE
  0            13             362
  1             1              64
[1] 2 2
[1] FALSE
D169V8, binary
                 cls
clus                0   1
  HAUS6 MUTATED    10   7
  HAUS6 WILD-TYPE 215 257
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HAUS6 MUTATED     10    7
  HAUS6 WILD-TYPE  215  257
        clus
vv       HAUS6 MUTATED HAUS6 WILD-TYPE
  FEMALE            10             215
  MALE               7             257
[1] 2 2
[1] FALSE
D169V9, binary
                 cls
clus                0   1
  HAUS6 MUTATED     9   0
  HAUS6 WILD-TYPE 341  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HAUS6 MUTATED      9    0
  HAUS6 WILD-TYPE  341   22
     clus
vv    HAUS6 MUTATED HAUS6 WILD-TYPE
  NO              9             341
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  HAUS6 MUTATED                      9                             1
  HAUS6 WILD-TYPE                  306                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  HAUS6 MUTATED                       5                              0
  HAUS6 WILD-TYPE                   101                             10
D169V10, multiclass
                                clus
vv                               HAUS6 MUTATED HAUS6 WILD-TYPE
  COLON ADENOCARCINOMA                       9             306
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      5             101
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  HAUS6 MUTATED     9   0   1   2
  HAUS6 WILD-TYPE 336   4  30  23
D169V11, multiclass
    clus
vv   HAUS6 MUTATED HAUS6 WILD-TYPE
  R0             9             336
  R1             0               4
  R2             1              30
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D169V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HAUS6 MUTATED                                  0     0
  HAUS6 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  HAUS6 MUTATED                           0    11
  HAUS6 WILD-TYPE                        22   215
D169V13, multiclass
                                  clus
vv                                 HAUS6 MUTATED HAUS6 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                       11             215
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(170) Variable = TUBA4A MUTATION ANALYSIS
D170V1, survival
                  sevent
clus2                0   1
  TUBA4A MUTATED    10   2
  TUBA4A WILD-TYPE 368  91
  TUBA4A MUTATED TUBA4A WILD-TYPE 
              12              459 
  TUBA4A MUTATED TUBA4A WILD-TYPE 
               2               91 
$`TUBA4A MUTATED`
TCGA-A6-5665 TCGA-AA-3662 TCGA-AA-3977 TCGA-AZ-6601 TCGA-CK-4950 TCGA-CK-4952 
       22.06         6.05        25.02       100.01        85.45        15.62 
TCGA-CK-5916 TCGA-DM-A282 TCGA-F4-6856 TCGA-AG-3898 TCGA-AG-A002 TCGA-F5-6465 
       21.14       139.17        35.31        48.03        20.98        49.51 

$`TUBA4A WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       19.99        13.94        19.99        61.02        78.08         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-5912 TCGA-CK-5913 
       10.06        14.30        17.56       148.01        49.08        51.32 
TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
        9.99        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      131.51       135.65         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 
       33.67        13.25         0.53        47.41       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       35.01        14.01         1.02        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
       18.28         9.96        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  TUBA4A MUTATED TUBA4A WILD-TYPE 
            6.05             0.00 
  TUBA4A MUTATED TUBA4A WILD-TYPE 
          139.17           148.01 
  TUBA4A MUTATED TUBA4A WILD-TYPE 
          30.165           20.020 
[1] "6.0 - 139.2 (30.2)" "0.0 - 148.0 (20.0)"
[1] "hr=" "2"  
D170V2, continuous
D170V3, binary
                  cls
clus                 0   1
  TUBA4A MUTATED     9   3
  TUBA4A WILD-TYPE 357 116
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TUBA4A MUTATED      9    3
  TUBA4A WILD-TYPE  357  116
        clus
vv       TUBA4A MUTATED TUBA4A WILD-TYPE
  COLON               9              357
  RECTUM              3              116
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TUBA4A MUTATED         3        0        1         4         0         0
  TUBA4A WILD-TYPE      88        1       31       134        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TUBA4A MUTATED           0          0          1          1        1
  TUBA4A WILD-TYPE        24         11         58         41       47
                  vv
clus               STAGE IVA STAGE IVB
  TUBA4A MUTATED           0         0
  TUBA4A WILD-TYPE        18         1
D170V4, multiclass
            clus
vv           TUBA4A MUTATED TUBA4A WILD-TYPE
  STAGE I                 3               88
  STAGE IA                0                1
  STAGE II                1               31
  STAGE IIA               4              134
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              1               58
  STAGE IIIC              1               41
  STAGE IV                1               47
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  TUBA4A MUTATED     1   3   6   2
  TUBA4A WILD-TYPE  16  89 323  48
D170V5, multiclass
    clus
vv   TUBA4A MUTATED TUBA4A WILD-TYPE
  T1              1               16
  T2              3               89
  T3              6              323
  T4              2               48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  TUBA4A MUTATED     9   1   2
  TUBA4A WILD-TYPE 278 112  85
D170V6, multiclass
    clus
vv   TUBA4A MUTATED TUBA4A WILD-TYPE
  N0              9              278
  N1              1              112
  N2              2               85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D170V7, binary
                  cls
clus                 0   1
  TUBA4A MUTATED    10   1
  TUBA4A WILD-TYPE 365  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TUBA4A MUTATED     10    1
  TUBA4A WILD-TYPE  365   64
   clus
vv  TUBA4A MUTATED TUBA4A WILD-TYPE
  0             10              365
  1              1               64
[1] 2 2
[1] FALSE
D170V8, binary
                  cls
clus                 0   1
  TUBA4A MUTATED     7   5
  TUBA4A WILD-TYPE 218 259
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TUBA4A MUTATED      7    5
  TUBA4A WILD-TYPE  218  259
        clus
vv       TUBA4A MUTATED TUBA4A WILD-TYPE
  FEMALE              7              218
  MALE                5              259
[1] 2 2
[1] FALSE
D170V9, binary
                  cls
clus                 0   1
  TUBA4A MUTATED    10   0
  TUBA4A WILD-TYPE 340  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TUBA4A MUTATED     10    0
  TUBA4A WILD-TYPE  340   22
     clus
vv    TUBA4A MUTATED TUBA4A WILD-TYPE
  NO              10              340
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  TUBA4A MUTATED                      7                             2
  TUBA4A WILD-TYPE                  308                            45
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  TUBA4A MUTATED                       3                              0
  TUBA4A WILD-TYPE                   103                             10
D170V10, multiclass
                                clus
vv                               TUBA4A MUTATED TUBA4A WILD-TYPE
  COLON ADENOCARCINOMA                        7              308
  COLON MUCINOUS ADENOCARCINOMA               2               45
  RECTAL ADENOCARCINOMA                       3              103
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  TUBA4A MUTATED     5   1   1   2
  TUBA4A WILD-TYPE 340   3  30  23
D170V11, multiclass
    clus
vv   TUBA4A MUTATED TUBA4A WILD-TYPE
  R0              5              340
  R1              1                3
  R2              1               30
  RX              2               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D170V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TUBA4A MUTATED                                  0     0
  TUBA4A WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  TUBA4A MUTATED                           1     7
  TUBA4A WILD-TYPE                        21   219
D170V13, multiclass
                                  clus
vv                                 TUBA4A MUTATED TUBA4A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                         7              219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(171) Variable = MBD6 MUTATION ANALYSIS
D171V1, survival
                sevent
clus2              0   1
  MBD6 MUTATED    10   5
  MBD6 WILD-TYPE 368  88
  MBD6 MUTATED MBD6 WILD-TYPE 
            15            456 
  MBD6 MUTATED MBD6 WILD-TYPE 
             5             88 
$`MBD6 MUTATED`
TCGA-AA-3492 TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01R TCGA-AD-6895 TCGA-AU-6004 
        3.02         4.01        34.98        35.01         0.72        27.09 
TCGA-AZ-6598 TCGA-AZ-6608 TCGA-CK-5913 TCGA-CM-6171 TCGA-D5-6928 TCGA-D5-6930 
       49.41         1.61        51.32        14.04        11.64         1.51 
TCGA-F4-6570 TCGA-G4-6304 TCGA-AG-3893 
        6.18        53.62        35.01 

$`MBD6 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       31.00        38.07         1.02         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        3.19        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       85.45        15.62        49.08         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       12.99        13.02        15.02        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6931 
       12.43        14.30         9.04         9.44         4.80        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       31.96        35.74        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
      133.18        74.56        65.85        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       13.02        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  MBD6 MUTATED MBD6 WILD-TYPE 
          0.72           0.00 
  MBD6 MUTATED MBD6 WILD-TYPE 
         53.62         148.01 
  MBD6 MUTATED MBD6 WILD-TYPE 
        14.040         20.235 
[1] "0.7 - 53.6 (14.0)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "2"  
D171V2, continuous
D171V3, binary
                cls
clus               0   1
  MBD6 MUTATED    15   1
  MBD6 WILD-TYPE 351 118
[1] "tbl2"
                cls
clus             [,1] [,2]
  MBD6 MUTATED     15    1
  MBD6 WILD-TYPE  351  118
        clus
vv       MBD6 MUTATED MBD6 WILD-TYPE
  COLON            15            351
  RECTUM            1            118
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MBD6 MUTATED         2        0        2         4         3         0
  MBD6 WILD-TYPE      89        1       30       134         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MBD6 MUTATED           2          1          1          0        0         0
  MBD6 WILD-TYPE        22         10         58         42       48        18
                vv
clus             STAGE IVB
  MBD6 MUTATED           0
  MBD6 WILD-TYPE         1
D171V4, multiclass
            clus
vv           MBD6 MUTATED MBD6 WILD-TYPE
  STAGE I               2             89
  STAGE IA              0              1
  STAGE II              2             30
  STAGE IIA             4            134
  STAGE IIB             3              7
  STAGE IIC             0              1
  STAGE III             2             22
  STAGE IIIA            1             10
  STAGE IIIB            1             58
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  MBD6 MUTATED     0   3  10   3
  MBD6 WILD-TYPE  17  89 319  47
D171V5, multiclass
    clus
vv   MBD6 MUTATED MBD6 WILD-TYPE
  T1            0             17
  T2            3             89
  T3           10            319
  T4            3             47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  MBD6 MUTATED    11   3   2
  MBD6 WILD-TYPE 276 110  85
D171V6, multiclass
    clus
vv   MBD6 MUTATED MBD6 WILD-TYPE
  N0           11            276
  N1            3            110
  N2            2             85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D171V7, binary
                cls
clus               0   1
  MBD6 MUTATED    13   0
  MBD6 WILD-TYPE 362  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  MBD6 MUTATED     13    0
  MBD6 WILD-TYPE  362   65
   clus
vv  MBD6 MUTATED MBD6 WILD-TYPE
  0           13            362
  1            0             65
[1] 2 2
[1] FALSE
D171V8, binary
                cls
clus               0   1
  MBD6 MUTATED     9   7
  MBD6 WILD-TYPE 216 257
[1] "tbl2"
                cls
clus             [,1] [,2]
  MBD6 MUTATED      9    7
  MBD6 WILD-TYPE  216  257
        clus
vv       MBD6 MUTATED MBD6 WILD-TYPE
  FEMALE            9            216
  MALE              7            257
[1] 2 2
[1] FALSE
D171V9, binary
                cls
clus               0   1
  MBD6 MUTATED    10   1
  MBD6 WILD-TYPE 340  21
[1] "tbl2"
                cls
clus             [,1] [,2]
  MBD6 MUTATED     10    1
  MBD6 WILD-TYPE  340   21
     clus
vv    MBD6 MUTATED MBD6 WILD-TYPE
  NO            10            340
  YES            1             21
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MBD6 MUTATED                     11                             4
  MBD6 WILD-TYPE                  304                            43
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MBD6 MUTATED                       1                              0
  MBD6 WILD-TYPE                   105                             10
D171V10, multiclass
                                clus
vv                               MBD6 MUTATED MBD6 WILD-TYPE
  COLON ADENOCARCINOMA                     11            304
  COLON MUCINOUS ADENOCARCINOMA             4             43
  RECTAL ADENOCARCINOMA                     1            105
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  MBD6 MUTATED    12   0   0   1
  MBD6 WILD-TYPE 333   4  31  24
D171V11, multiclass
    clus
vv   MBD6 MUTATED MBD6 WILD-TYPE
  R0           12            333
  R1            0              4
  R2            0             31
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D171V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MBD6 MUTATED                                  0     0
  MBD6 WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  MBD6 MUTATED                           0    10
  MBD6 WILD-TYPE                        22   216
D171V13, multiclass
                                  clus
vv                                 MBD6 MUTATED MBD6 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                      10            216
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(172) Variable = TFE3 MUTATION ANALYSIS
D172V1, survival
                sevent
clus2              0   1
  TFE3 MUTATED    11   0
  TFE3 WILD-TYPE 367  93
  TFE3 MUTATED TFE3 WILD-TYPE 
            11            460 
  TFE3 MUTATED TFE3 WILD-TYPE 
             0             93 
$`TFE3 MUTATED`
TCGA-AA-3532 TCGA-AA-3710 TCGA-AA-3947 TCGA-AD-6889 TCGA-AY-6197 TCGA-CK-5913 
       29.00        26.99        33.01        56.55        21.44        51.32 
TCGA-CM-6171 TCGA-D5-6920 TCGA-D5-6928 TCGA-F4-6703 TCGA-G4-6588 
       14.04         3.68        11.64        47.87        26.17 

$`TFE3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3534 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        85.05        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       12.99        24.00        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 
       18.05        40.96         0.07        21.37        15.52         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 
       14.50        27.09        16.31         0.95        33.01        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        1.48         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        35.80        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  TFE3 MUTATED TFE3 WILD-TYPE 
          3.68           0.00 
  TFE3 MUTATED TFE3 WILD-TYPE 
         56.55         148.01 
  TFE3 MUTATED TFE3 WILD-TYPE 
        26.990         20.035 
[1] "3.7 - 56.5 (27.0)"  "0.0 - 148.0 (20.0)"
[1] "hr="     "9300000"
D172V2, continuous
D172V3, binary
                cls
clus               0   1
  TFE3 MUTATED    11   0
  TFE3 WILD-TYPE 355 119
[1] "tbl2"
                cls
clus             [,1] [,2]
  TFE3 MUTATED     11    0
  TFE3 WILD-TYPE  355  119
        clus
vv       TFE3 MUTATED TFE3 WILD-TYPE
  COLON            11            355
  RECTUM            0            119
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TFE3 MUTATED         1        0        0         9         1         0
  TFE3 WILD-TYPE      90        1       32       129         9         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TFE3 MUTATED           0          0          0          0        0         0
  TFE3 WILD-TYPE        24         11         59         42       48        18
                vv
clus             STAGE IVB
  TFE3 MUTATED           0
  TFE3 WILD-TYPE         1
D172V4, multiclass
            clus
vv           TFE3 MUTATED TFE3 WILD-TYPE
  STAGE I               1             90
  STAGE IA              0              1
  STAGE II              0             32
  STAGE IIA             9            129
  STAGE IIB             1              9
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            0             59
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  TFE3 MUTATED     0   1   9   1
  TFE3 WILD-TYPE  17  91 320  49
D172V5, multiclass
    clus
vv   TFE3 MUTATED TFE3 WILD-TYPE
  T1            0             17
  T2            1             91
  T3            9            320
  T4            1             49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  TFE3 MUTATED    11   0   0
  TFE3 WILD-TYPE 276 113  87
D172V6, multiclass
    clus
vv   TFE3 MUTATED TFE3 WILD-TYPE
  N0           11            276
  N1            0            113
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D172V7, binary
                cls
clus               0   1
  TFE3 MUTATED     9   0
  TFE3 WILD-TYPE 366  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  TFE3 MUTATED      9    0
  TFE3 WILD-TYPE  366   65
   clus
vv  TFE3 MUTATED TFE3 WILD-TYPE
  0            9            366
  1            0             65
[1] 2 2
[1] FALSE
D172V8, binary
                cls
clus               0   1
  TFE3 MUTATED     6   5
  TFE3 WILD-TYPE 219 259
[1] "tbl2"
                cls
clus             [,1] [,2]
  TFE3 MUTATED      6    5
  TFE3 WILD-TYPE  219  259
        clus
vv       TFE3 MUTATED TFE3 WILD-TYPE
  FEMALE            6            219
  MALE              5            259
[1] 2 2
[1] FALSE
D172V9, binary
                cls
clus               0   1
  TFE3 MUTATED     9   0
  TFE3 WILD-TYPE 341  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  TFE3 MUTATED      9    0
  TFE3 WILD-TYPE  341   22
     clus
vv    TFE3 MUTATED TFE3 WILD-TYPE
  NO             9            341
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  TFE3 MUTATED                      9                             2
  TFE3 WILD-TYPE                  306                            45
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  TFE3 MUTATED                       0                              0
  TFE3 WILD-TYPE                   106                             10
D172V10, multiclass
                                clus
vv                               TFE3 MUTATED TFE3 WILD-TYPE
  COLON ADENOCARCINOMA                      9            306
  COLON MUCINOUS ADENOCARCINOMA             2             45
  RECTAL ADENOCARCINOMA                     0            106
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  TFE3 MUTATED     9   0   0   1
  TFE3 WILD-TYPE 336   4  31  24
D172V11, multiclass
    clus
vv   TFE3 MUTATED TFE3 WILD-TYPE
  R0            9            336
  R1            0              4
  R2            0             31
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D172V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TFE3 MUTATED                                  0     1
  TFE3 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  TFE3 MUTATED                           0     7
  TFE3 WILD-TYPE                        22   219
D172V13, multiclass
                                  clus
vv                                 TFE3 MUTATED TFE3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       7            219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(173) Variable = NCAPD2 MUTATION ANALYSIS
D173V1, survival
                  sevent
clus2                0   1
  NCAPD2 MUTATED    18   1
  NCAPD2 WILD-TYPE 360  92
  NCAPD2 MUTATED NCAPD2 WILD-TYPE 
              19              452 
  NCAPD2 MUTATED NCAPD2 WILD-TYPE 
               1               92 
$`NCAPD2 MUTATED`
TCGA-A6-6653 TCGA-A6-6781 TCGA-AA-3510 TCGA-AA-3663 TCGA-AA-3950 TCGA-AA-A00K 
       24.39        19.66        63.98         6.97        24.00        18.05 
TCGA-AA-A010 TCGA-AA-A01Q TCGA-AZ-4315 TCGA-AZ-6601 TCGA-CM-4743 TCGA-CM-6162 
       34.98         1.02        58.39       100.01        23.05        12.00 
TCGA-D5-6930 TCGA-DM-A28K TCGA-G4-6293 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6628 
        1.51        98.24       133.18        53.62        44.68        79.69 
TCGA-AG-3892 
       13.02 

$`NCAPD2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
       25.08        25.18        24.16        21.76        24.69        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02        78.08         6.05        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       33.01        26.01         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01R TCGA-AA-A01S 
       12.00        31.00        31.00        38.07        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       33.01        21.44        17.82         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
      124.27        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 
       15.02        15.02        17.03        15.02         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 
        9.04         9.44        11.64         4.80        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       35.97        60.79       117.07         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6299 
       33.67        13.25         0.53        47.41        35.31        74.56 
TCGA-G4-6303 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       65.85        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       36.95        17.03        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  NCAPD2 MUTATED NCAPD2 WILD-TYPE 
            1.02             0.00 
  NCAPD2 MUTATED NCAPD2 WILD-TYPE 
          133.18           148.01 
  NCAPD2 MUTATED NCAPD2 WILD-TYPE 
          24.390           20.035 
[1] "1.0 - 133.2 (24.4)" "0.0 - 148.0 (20.0)"
[1] "hr=" "6.4"
D173V2, continuous
D173V3, binary
                  cls
clus                 0   1
  NCAPD2 MUTATED    20   1
  NCAPD2 WILD-TYPE 346 118
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NCAPD2 MUTATED     20    1
  NCAPD2 WILD-TYPE  346  118
        clus
vv       NCAPD2 MUTATED NCAPD2 WILD-TYPE
  COLON              20              346
  RECTUM              1              118
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NCAPD2 MUTATED         3        0        4         8         3         0
  NCAPD2 WILD-TYPE      88        1       28       130         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NCAPD2 MUTATED           1          0          1          1        0
  NCAPD2 WILD-TYPE        23         11         58         41       48
                  vv
clus               STAGE IVA STAGE IVB
  NCAPD2 MUTATED           0         0
  NCAPD2 WILD-TYPE        18         1
D173V4, multiclass
            clus
vv           NCAPD2 MUTATED NCAPD2 WILD-TYPE
  STAGE I                 3               88
  STAGE IA                0                1
  STAGE II                4               28
  STAGE IIA               8              130
  STAGE IIB               3                7
  STAGE IIC               0                1
  STAGE III               1               23
  STAGE IIIA              0               11
  STAGE IIIB              1               58
  STAGE IIIC              1               41
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  NCAPD2 MUTATED     1   3  13   4
  NCAPD2 WILD-TYPE  16  89 316  46
D173V5, multiclass
    clus
vv   NCAPD2 MUTATED NCAPD2 WILD-TYPE
  T1              1               16
  T2              3               89
  T3             13              316
  T4              4               46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  NCAPD2 MUTATED    18   3   0
  NCAPD2 WILD-TYPE 269 110  87
D173V6, multiclass
    clus
vv   NCAPD2 MUTATED NCAPD2 WILD-TYPE
  N0             18              269
  N1              3              110
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D173V7, binary
                  cls
clus                 0   1
  NCAPD2 MUTATED    19   0
  NCAPD2 WILD-TYPE 356  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NCAPD2 MUTATED     19    0
  NCAPD2 WILD-TYPE  356   65
   clus
vv  NCAPD2 MUTATED NCAPD2 WILD-TYPE
  0             19              356
  1              0               65
[1] 2 2
[1] FALSE
D173V8, binary
                  cls
clus                 0   1
  NCAPD2 MUTATED     9  12
  NCAPD2 WILD-TYPE 216 252
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NCAPD2 MUTATED      9   12
  NCAPD2 WILD-TYPE  216  252
        clus
vv       NCAPD2 MUTATED NCAPD2 WILD-TYPE
  FEMALE              9              216
  MALE               12              252
[1] 2 2
[1] FALSE
D173V9, binary
                  cls
clus                 0   1
  NCAPD2 MUTATED    15   0
  NCAPD2 WILD-TYPE 335  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NCAPD2 MUTATED     15    0
  NCAPD2 WILD-TYPE  335   22
     clus
vv    NCAPD2 MUTATED NCAPD2 WILD-TYPE
  NO              15              335
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  NCAPD2 MUTATED                     15                             5
  NCAPD2 WILD-TYPE                  300                            42
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  NCAPD2 MUTATED                       1                              0
  NCAPD2 WILD-TYPE                   105                             10
D173V10, multiclass
                                clus
vv                               NCAPD2 MUTATED NCAPD2 WILD-TYPE
  COLON ADENOCARCINOMA                       15              300
  COLON MUCINOUS ADENOCARCINOMA               5               42
  RECTAL ADENOCARCINOMA                       1              105
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  NCAPD2 MUTATED    17   0   0   1
  NCAPD2 WILD-TYPE 328   4  31  24
D173V11, multiclass
    clus
vv   NCAPD2 MUTATED NCAPD2 WILD-TYPE
  R0             17              328
  R1              0                4
  R2              0               31
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D173V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NCAPD2 MUTATED                                  0     0
  NCAPD2 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  NCAPD2 MUTATED                           0    13
  NCAPD2 WILD-TYPE                        22   213
D173V13, multiclass
                                  clus
vv                                 NCAPD2 MUTATED NCAPD2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                        13              213
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(174) Variable = NCOA6 MUTATION ANALYSIS
D174V1, survival
                 sevent
clus2               0   1
  NCOA6 MUTATED    23   6
  NCOA6 WILD-TYPE 355  87
  NCOA6 MUTATED NCOA6 WILD-TYPE 
             29             442 
  NCOA6 MUTATED NCOA6 WILD-TYPE 
              6              87 
$`NCOA6 MUTATED`
TCGA-A6-6781 TCGA-AA-3510 TCGA-AA-3525 TCGA-AA-3663 TCGA-AA-3715 TCGA-AA-3966 
       19.66        63.98         8.05         6.97        19.04         2.01 
TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A010 TCGA-AZ-6607 TCGA-CA-6716 TCGA-CA-6717 
       25.02         4.01        34.98         3.19        12.20        12.76 
TCGA-CA-6718 TCGA-CK-5913 TCGA-CM-5344 TCGA-CM-6679 TCGA-D5-5538 TCGA-D5-6927 
       10.06        51.32        22.03        10.06        12.26         9.44 
TCGA-DM-A1DB TCGA-F4-6570 TCGA-G4-6299 TCGA-G4-6307 TCGA-G4-6588 TCGA-G4-6628 
       44.32         6.18        74.56        55.04        26.17        79.69 
TCGA-AF-6672 TCGA-AG-3893 TCGA-AG-A002 TCGA-CI-6620 TCGA-EI-6508 
       10.39        35.01        20.98        33.17        20.91 

$`NCOA6 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3529 
        9.07        24.03        37.05        36.03        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02        78.08         6.05        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       26.99        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 
       26.01        24.00         2.01        20.98        34.03        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5254 
      100.01        29.56         5.23        11.74         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6719 TCGA-CK-4947 
        3.06         3.25         3.29         0.07        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 
      148.01        85.45        15.62        49.08         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       25.02        13.02        29.06        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6680 TCGA-D5-5537 
       13.05        11.08        11.08        11.01        12.03        45.40 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
       14.30         9.04        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       35.74        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       65.85        53.62        44.68        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        35.80        91.79        46.75 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AG-3574 
       10.39        14.50        16.83        15.39        20.02        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       17.03        13.02        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
        6.05         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  NCOA6 MUTATED NCOA6 WILD-TYPE 
           2.01            0.00 
  NCOA6 MUTATED NCOA6 WILD-TYPE 
          79.69          148.01 
  NCOA6 MUTATED NCOA6 WILD-TYPE 
         19.660          20.235 
[1] "2.0 - 79.7 (19.7)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.1"
D174V2, continuous
D174V3, binary
                 cls
clus                0   1
  NCOA6 MUTATED    24   5
  NCOA6 WILD-TYPE 342 114
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NCOA6 MUTATED     24    5
  NCOA6 WILD-TYPE  342  114
        clus
vv       NCOA6 MUTATED NCOA6 WILD-TYPE
  COLON             24             342
  RECTUM             5             114
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NCOA6 MUTATED         2        0        3        10         2         0
  NCOA6 WILD-TYPE      89        1       29       128         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NCOA6 MUTATED           0          0          6          2        2         1
  NCOA6 WILD-TYPE        24         11         53         40       46        17
                 vv
clus              STAGE IVB
  NCOA6 MUTATED           0
  NCOA6 WILD-TYPE         1
D174V4, multiclass
            clus
vv           NCOA6 MUTATED NCOA6 WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               3              29
  STAGE IIA             10             128
  STAGE IIB              2               8
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             6              53
  STAGE IIIC             2              40
  STAGE IV               2              46
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  NCOA6 MUTATED     0   3  21   5
  NCOA6 WILD-TYPE  17  89 308  45
D174V5, multiclass
    clus
vv   NCOA6 MUTATED NCOA6 WILD-TYPE
  T1             0              17
  T2             3              89
  T3            21             308
  T4             5              45
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  NCOA6 MUTATED    18   8   3
  NCOA6 WILD-TYPE 269 105  84
D174V6, multiclass
    clus
vv   NCOA6 MUTATED NCOA6 WILD-TYPE
  N0            18             269
  N1             8             105
  N2             3              84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D174V7, binary
                 cls
clus                0   1
  NCOA6 MUTATED    23   2
  NCOA6 WILD-TYPE 352  63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NCOA6 MUTATED     23    2
  NCOA6 WILD-TYPE  352   63
   clus
vv  NCOA6 MUTATED NCOA6 WILD-TYPE
  0            23             352
  1             2              63
[1] 2 2
[1] FALSE
D174V8, binary
                 cls
clus                0   1
  NCOA6 MUTATED    10  19
  NCOA6 WILD-TYPE 215 245
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NCOA6 MUTATED     10   19
  NCOA6 WILD-TYPE  215  245
        clus
vv       NCOA6 MUTATED NCOA6 WILD-TYPE
  FEMALE            10             215
  MALE              19             245
[1] 2 2
[1] FALSE
D174V9, binary
                 cls
clus                0   1
  NCOA6 MUTATED    25   1
  NCOA6 WILD-TYPE 325  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NCOA6 MUTATED     25    1
  NCOA6 WILD-TYPE  325   21
     clus
vv    NCOA6 MUTATED NCOA6 WILD-TYPE
  NO             25             325
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  NCOA6 MUTATED                     20                             4
  NCOA6 WILD-TYPE                  295                            43
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  NCOA6 MUTATED                       5                              0
  NCOA6 WILD-TYPE                   101                             10
D174V10, multiclass
                                clus
vv                               NCOA6 MUTATED NCOA6 WILD-TYPE
  COLON ADENOCARCINOMA                      20             295
  COLON MUCINOUS ADENOCARCINOMA              4              43
  RECTAL ADENOCARCINOMA                      5             101
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  NCOA6 MUTATED    19   0   0   4
  NCOA6 WILD-TYPE 326   4  31  21
D174V11, multiclass
    clus
vv   NCOA6 MUTATED NCOA6 WILD-TYPE
  R0            19             326
  R1             0               4
  R2             0              31
  RX             4              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D174V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NCOA6 MUTATED                                  0     3
  NCOA6 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  NCOA6 MUTATED                           0    16
  NCOA6 WILD-TYPE                        22   210
D174V13, multiclass
                                  clus
vv                                 NCOA6 MUTATED NCOA6 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        3               8
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                       16             210
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(175) Variable = SVIL MUTATION ANALYSIS
D175V1, survival
                sevent
clus2              0   1
  SVIL MUTATED    23   9
  SVIL WILD-TYPE 355  84
  SVIL MUTATED SVIL WILD-TYPE 
            32            439 
  SVIL MUTATED SVIL WILD-TYPE 
             9             84 
$`SVIL MUTATED`
TCGA-A6-3809 TCGA-A6-5665 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3518 
       32.75        22.06        24.39        20.12        19.66         1.02 
TCGA-AA-3696 TCGA-AA-3713 TCGA-AA-3845 TCGA-AA-3864 TCGA-AD-5900 TCGA-AD-6889 
        5.03        19.04         0.00        53.00         0.07        56.55 
TCGA-AD-6964 TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-AZ-6601 TCGA-CK-5916 
       10.88        21.44        58.39        49.41       100.01        21.14 
TCGA-CM-5861 TCGA-CM-6162 TCGA-CM-6171 TCGA-D5-6537 TCGA-D5-6540 TCGA-D5-6541 
       15.02        12.00        14.04         4.80        16.14        15.58 
TCGA-DM-A1HB TCGA-F4-6459 TCGA-F4-6570 TCGA-G4-6307 TCGA-G4-6588 TCGA-G4-6628 
      135.65         8.61         6.18        55.04        26.17        79.69 
TCGA-AG-A002 TCGA-EI-6507 
       20.98        19.96 

$`SVIL WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6782 TCGA-AA-3489 
       24.16        21.76        24.69        23.87        20.28         7.04 
TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
        3.02         1.02        35.01        63.98         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       13.02        38.99         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 
       19.00        36.00        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 
       15.95        38.99        37.02        14.93        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        31.07        30.05        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       40.96        21.37        15.52         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
        0.95        33.01        17.82         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 
       22.36        62.79        88.21         6.77        12.10        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       51.32         9.99        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       22.98        30.08        32.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       17.03        15.02         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 
       14.99        12.99        13.02        15.02        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6538 
       18.25         1.32        43.27        15.12        17.85        17.13 
TCGA-D5-6539 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       12.49         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
       44.32       131.51       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6460 TCGA-F4-6569 
       35.97        60.79       117.07        98.24        31.96        35.74 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       65.85        53.62        44.68        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        35.80        91.79        46.75 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
        0.49        20.55        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  SVIL MUTATED SVIL WILD-TYPE 
             0              0 
  SVIL MUTATED SVIL WILD-TYPE 
        135.65         148.01 
  SVIL MUTATED SVIL WILD-TYPE 
         20.04          20.28 
[1] "0.0 - 135.7 (20.0)" "0.0 - 148.0 (20.3)"
[1] "hr=" "1.3"
D175V2, continuous
D175V3, binary
                cls
clus               0   1
  SVIL MUTATED    32   2
  SVIL WILD-TYPE 334 117
[1] "tbl2"
                cls
clus             [,1] [,2]
  SVIL MUTATED     32    2
  SVIL WILD-TYPE  334  117
        clus
vv       SVIL MUTATED SVIL WILD-TYPE
  COLON            32            334
  RECTUM            2            117
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SVIL MUTATED         7        0        4        13         1         0
  SVIL WILD-TYPE      84        1       28       125         9         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SVIL MUTATED           0          0          5          1        2         0
  SVIL WILD-TYPE        24         11         54         41       46        18
                vv
clus             STAGE IVB
  SVIL MUTATED           0
  SVIL WILD-TYPE         1
D175V4, multiclass
            clus
vv           SVIL MUTATED SVIL WILD-TYPE
  STAGE I               7             84
  STAGE IA              0              1
  STAGE II              4             28
  STAGE IIA            13            125
  STAGE IIB             1              9
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            5             54
  STAGE IIIC            1             41
  STAGE IV              2             46
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  SVIL MUTATED     1   6  23   4
  SVIL WILD-TYPE  16  86 306  46
D175V5, multiclass
    clus
vv   SVIL MUTATED SVIL WILD-TYPE
  T1            1             16
  T2            6             86
  T3           23            306
  T4            4             46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  SVIL MUTATED    26   6   2
  SVIL WILD-TYPE 261 107  85
D175V6, multiclass
    clus
vv   SVIL MUTATED SVIL WILD-TYPE
  N0           26            261
  N1            6            107
  N2            2             85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D175V7, binary
                cls
clus               0   1
  SVIL MUTATED    25   2
  SVIL WILD-TYPE 350  63
[1] "tbl2"
                cls
clus             [,1] [,2]
  SVIL MUTATED     25    2
  SVIL WILD-TYPE  350   63
   clus
vv  SVIL MUTATED SVIL WILD-TYPE
  0           25            350
  1            2             63
[1] 2 2
[1] FALSE
D175V8, binary
                cls
clus               0   1
  SVIL MUTATED    16  18
  SVIL WILD-TYPE 209 246
[1] "tbl2"
                cls
clus             [,1] [,2]
  SVIL MUTATED     16   18
  SVIL WILD-TYPE  209  246
        clus
vv       SVIL MUTATED SVIL WILD-TYPE
  FEMALE           16            209
  MALE             18            246
[1] 2 2
[1] FALSE
D175V9, binary
                cls
clus               0   1
  SVIL MUTATED    26   1
  SVIL WILD-TYPE 324  21
[1] "tbl2"
                cls
clus             [,1] [,2]
  SVIL MUTATED     26    1
  SVIL WILD-TYPE  324   21
     clus
vv    SVIL MUTATED SVIL WILD-TYPE
  NO            26            324
  YES            1             21
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SVIL MUTATED                     25                             6
  SVIL WILD-TYPE                  290                            41
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SVIL MUTATED                       2                              0
  SVIL WILD-TYPE                   104                             10
D175V10, multiclass
                                clus
vv                               SVIL MUTATED SVIL WILD-TYPE
  COLON ADENOCARCINOMA                     25            290
  COLON MUCINOUS ADENOCARCINOMA             6             41
  RECTAL ADENOCARCINOMA                     2            104
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  SVIL MUTATED    24   0   2   1
  SVIL WILD-TYPE 321   4  29  24
D175V11, multiclass
    clus
vv   SVIL MUTATED SVIL WILD-TYPE
  R0           24            321
  R1            0              4
  R2            2             29
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D175V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SVIL MUTATED                                  0     1
  SVIL WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  SVIL MUTATED                           0    25
  SVIL WILD-TYPE                        22   201
D175V13, multiclass
                                  clus
vv                                 SVIL MUTATED SVIL WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                      25            201
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(176) Variable = XYLT2 MUTATION ANALYSIS
D176V1, survival
                 sevent
clus2               0   1
  XYLT2 MUTATED    12   2
  XYLT2 WILD-TYPE 366  91
  XYLT2 MUTATED XYLT2 WILD-TYPE 
             14             457 
  XYLT2 MUTATED XYLT2 WILD-TYPE 
              2              91 
$`XYLT2 MUTATED`
TCGA-A6-5661 TCGA-A6-5665 TCGA-A6-6781 TCGA-AA-3663 TCGA-AA-3672 TCGA-AD-5900 
       33.53        22.06        19.66         6.97         0.92         0.07 
TCGA-AZ-4315 TCGA-AZ-6598 TCGA-CM-4746 TCGA-CM-5861 TCGA-D5-6923 TCGA-F4-6570 
       58.39        49.41        37.02        15.02        12.43         6.18 
TCGA-G4-6586 TCGA-G4-6588 
       35.80        26.17 

$`XYLT2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02        78.08         6.05        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
       14.01        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
       16.31         0.95        33.01        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 
        5.13       106.75        22.36        62.79        88.21         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4747 
       82.95         1.91       124.27        23.05        20.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
        8.61        31.96        35.74        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       13.78        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  XYLT2 MUTATED XYLT2 WILD-TYPE 
           0.07            0.00 
  XYLT2 MUTATED XYLT2 WILD-TYPE 
          58.39          148.01 
  XYLT2 MUTATED XYLT2 WILD-TYPE 
          20.86           20.19 
[1] "0.1 - 58.4 (20.9)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.2"
D176V2, continuous
D176V3, binary
                 cls
clus                0   1
  XYLT2 MUTATED    14   0
  XYLT2 WILD-TYPE 352 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  XYLT2 MUTATED     14    0
  XYLT2 WILD-TYPE  352  119
        clus
vv       XYLT2 MUTATED XYLT2 WILD-TYPE
  COLON             14             352
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  XYLT2 MUTATED         3        0        2         7         0         0
  XYLT2 WILD-TYPE      88        1       30       131        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  XYLT2 MUTATED           1          0          0          1        0         0
  XYLT2 WILD-TYPE        23         11         59         41       48        18
                 vv
clus              STAGE IVB
  XYLT2 MUTATED           0
  XYLT2 WILD-TYPE         1
D176V4, multiclass
            clus
vv           XYLT2 MUTATED XYLT2 WILD-TYPE
  STAGE I                3              88
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA              7             131
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             1              41
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  XYLT2 MUTATED     0   3  10   1
  XYLT2 WILD-TYPE  17  89 319  49
D176V5, multiclass
    clus
vv   XYLT2 MUTATED XYLT2 WILD-TYPE
  T1             0              17
  T2             3              89
  T3            10             319
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  XYLT2 MUTATED    12   2   0
  XYLT2 WILD-TYPE 275 111  87
D176V6, multiclass
    clus
vv   XYLT2 MUTATED XYLT2 WILD-TYPE
  N0            12             275
  N1             2             111
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D176V7, binary
                 cls
clus                0   1
  XYLT2 MUTATED    11   0
  XYLT2 WILD-TYPE 364  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  XYLT2 MUTATED     11    0
  XYLT2 WILD-TYPE  364   65
   clus
vv  XYLT2 MUTATED XYLT2 WILD-TYPE
  0            11             364
  1             0              65
[1] 2 2
[1] FALSE
D176V8, binary
                 cls
clus                0   1
  XYLT2 MUTATED     8   6
  XYLT2 WILD-TYPE 217 258
[1] "tbl2"
                 cls
clus              [,1] [,2]
  XYLT2 MUTATED      8    6
  XYLT2 WILD-TYPE  217  258
        clus
vv       XYLT2 MUTATED XYLT2 WILD-TYPE
  FEMALE             8             217
  MALE               6             258
[1] 2 2
[1] FALSE
D176V9, binary
                 cls
clus                0   1
  XYLT2 MUTATED    13   0
  XYLT2 WILD-TYPE 337  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  XYLT2 MUTATED     13    0
  XYLT2 WILD-TYPE  337   22
     clus
vv    XYLT2 MUTATED XYLT2 WILD-TYPE
  NO             13             337
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  XYLT2 MUTATED                     12                             2
  XYLT2 WILD-TYPE                  303                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  XYLT2 MUTATED                       0                              0
  XYLT2 WILD-TYPE                   106                             10
D176V10, multiclass
                                clus
vv                               XYLT2 MUTATED XYLT2 WILD-TYPE
  COLON ADENOCARCINOMA                      12             303
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  XYLT2 MUTATED    13   0   0   0
  XYLT2 WILD-TYPE 332   4  31  25
D176V11, multiclass
    clus
vv   XYLT2 MUTATED XYLT2 WILD-TYPE
  R0            13             332
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D176V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  XYLT2 MUTATED                                  0     0
  XYLT2 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  XYLT2 MUTATED                           2    10
  XYLT2 WILD-TYPE                        20   216
D176V13, multiclass
                                  clus
vv                                 XYLT2 MUTATED XYLT2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    2              20
  WHITE                                       10             216
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(177) Variable = ZNF789 MUTATION ANALYSIS
D177V1, survival
                  sevent
clus2                0   1
  ZNF789 MUTATED     5   2
  ZNF789 WILD-TYPE 373  91
  ZNF789 MUTATED ZNF789 WILD-TYPE 
               7              464 
  ZNF789 MUTATED ZNF789 WILD-TYPE 
               2               91 
$`ZNF789 MUTATED`
TCGA-AA-3977 TCGA-AA-A00N TCGA-AZ-4315 TCGA-CA-6717 TCGA-CM-5349 TCGA-CM-6171 
       25.02         4.01        58.39        12.76        30.08        14.04 
TCGA-G4-6626 
       46.75 

$`ZNF789 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       33.01        21.44        17.82         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       29.06        22.03        22.98        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       15.02        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-AF-2687 
       13.78        35.80        26.17        91.79        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  ZNF789 MUTATED ZNF789 WILD-TYPE 
            4.01             0.00 
  ZNF789 MUTATED ZNF789 WILD-TYPE 
           58.39           148.01 
  ZNF789 MUTATED ZNF789 WILD-TYPE 
          25.020           20.155 
[1] "4.0 - 58.4 (25.0)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.3"
D177V2, continuous
D177V3, binary
                  cls
clus                 0   1
  ZNF789 MUTATED     7   0
  ZNF789 WILD-TYPE 359 119
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF789 MUTATED      7    0
  ZNF789 WILD-TYPE  359  119
        clus
vv       ZNF789 MUTATED ZNF789 WILD-TYPE
  COLON               7              359
  RECTUM              0              119
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZNF789 MUTATED         1        0        0         4         1         0
  ZNF789 WILD-TYPE      90        1       32       134         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF789 MUTATED           0          0          0          0        0
  ZNF789 WILD-TYPE        24         11         59         42       48
                  vv
clus               STAGE IVA STAGE IVB
  ZNF789 MUTATED           0         0
  ZNF789 WILD-TYPE        18         1
D177V4, multiclass
            clus
vv           ZNF789 MUTATED ZNF789 WILD-TYPE
  STAGE I                 1               90
  STAGE IA                0                1
  STAGE II                0               32
  STAGE IIA               4              134
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              0               59
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZNF789 MUTATED     0   2   4   1
  ZNF789 WILD-TYPE  17  90 325  49
D177V5, multiclass
    clus
vv   ZNF789 MUTATED ZNF789 WILD-TYPE
  T1              0               17
  T2              2               90
  T3              4              325
  T4              1               49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  ZNF789 MUTATED     7   0   0
  ZNF789 WILD-TYPE 280 113  87
D177V6, multiclass
    clus
vv   ZNF789 MUTATED ZNF789 WILD-TYPE
  N0              7              280
  N1              0              113
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D177V7, binary
                  cls
clus                 0   1
  ZNF789 MUTATED     6   0
  ZNF789 WILD-TYPE 369  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF789 MUTATED      6    0
  ZNF789 WILD-TYPE  369   65
   clus
vv  ZNF789 MUTATED ZNF789 WILD-TYPE
  0              6              369
  1              0               65
[1] 2 2
[1] FALSE
D177V8, binary
                  cls
clus                 0   1
  ZNF789 MUTATED     2   5
  ZNF789 WILD-TYPE 223 259
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF789 MUTATED      2    5
  ZNF789 WILD-TYPE  223  259
        clus
vv       ZNF789 MUTATED ZNF789 WILD-TYPE
  FEMALE              2              223
  MALE                5              259
[1] 2 2
[1] FALSE
D177V9, binary
                  cls
clus                 0   1
  ZNF789 MUTATED     6   0
  ZNF789 WILD-TYPE 344  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF789 MUTATED      6    0
  ZNF789 WILD-TYPE  344   22
     clus
vv    ZNF789 MUTATED ZNF789 WILD-TYPE
  NO               6              344
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ZNF789 MUTATED                      5                             2
  ZNF789 WILD-TYPE                  310                            45
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ZNF789 MUTATED                       0                              0
  ZNF789 WILD-TYPE                   106                             10
D177V10, multiclass
                                clus
vv                               ZNF789 MUTATED ZNF789 WILD-TYPE
  COLON ADENOCARCINOMA                        5              310
  COLON MUCINOUS ADENOCARCINOMA               2               45
  RECTAL ADENOCARCINOMA                       0              106
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ZNF789 MUTATED     5   0   0   1
  ZNF789 WILD-TYPE 340   4  31  24
D177V11, multiclass
    clus
vv   ZNF789 MUTATED ZNF789 WILD-TYPE
  R0              5              340
  R1              0                4
  R2              0               31
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D177V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF789 MUTATED                                  0     1
  ZNF789 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZNF789 MUTATED                           0     4
  ZNF789 WILD-TYPE                        22   222
D177V13, multiclass
                                  clus
vv                                 ZNF789 MUTATED ZNF789 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         4              222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(178) Variable = DDX43 MUTATION ANALYSIS
D178V1, survival
                 sevent
clus2               0   1
  DDX43 MUTATED    11   3
  DDX43 WILD-TYPE 367  90
  DDX43 MUTATED DDX43 WILD-TYPE 
             14             457 
  DDX43 MUTATED DDX43 WILD-TYPE 
              3              90 
$`DDX43 MUTATED`
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6653 TCGA-AA-3510 TCGA-AA-3815 TCGA-AZ-4315 
        8.38        25.08        24.39        63.98        33.04        58.39 
TCGA-CK-5916 TCGA-CM-6171 TCGA-D5-6534 TCGA-G4-6309 TCGA-G4-6626 TCGA-AG-3605 
       21.14        14.04        43.27        85.48        46.75         0.99 
TCGA-AG-3883 TCGA-DC-6158 
        1.02        10.98 

$`DDX43 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6648 
       22.09        22.06        32.71        27.09        22.52        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       24.16        21.76        24.69        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 
       20.28         7.04         3.02         1.02        35.01         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
       26.99        19.04        19.04        10.06        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
        9.99        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 
       21.99        14.99        12.99        13.02        15.02        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       20.19        18.25         1.32        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 
       65.85        53.62        44.68        55.04        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3608 TCGA-AG-3609 
        2.01        50.04        12.03         6.05        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3885 TCGA-AG-3887 
        0.99         0.99        19.04        19.99        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  DDX43 MUTATED DDX43 WILD-TYPE 
           0.99            0.00 
  DDX43 MUTATED DDX43 WILD-TYPE 
          85.48          148.01 
  DDX43 MUTATED DDX43 WILD-TYPE 
         24.735          20.050 
[1] "1.0 - 85.5 (24.7)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.1"
D178V2, continuous
D178V3, binary
                 cls
clus                0   1
  DDX43 MUTATED    11   3
  DDX43 WILD-TYPE 355 116
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX43 MUTATED     11    3
  DDX43 WILD-TYPE  355  116
        clus
vv       DDX43 MUTATED DDX43 WILD-TYPE
  COLON             11             355
  RECTUM             3             116
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DDX43 MUTATED         5        0        1         5         0         0
  DDX43 WILD-TYPE      86        1       31       133        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DDX43 MUTATED           0          0          1          0        1         1
  DDX43 WILD-TYPE        24         11         58         42       47        17
                 vv
clus              STAGE IVB
  DDX43 MUTATED           0
  DDX43 WILD-TYPE         1
D178V4, multiclass
            clus
vv           DDX43 MUTATED DDX43 WILD-TYPE
  STAGE I                5              86
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              5             133
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             0              42
  STAGE IV               1              47
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  DDX43 MUTATED     1   4   9   0
  DDX43 WILD-TYPE  16  88 320  50
D178V5, multiclass
    clus
vv   DDX43 MUTATED DDX43 WILD-TYPE
  T1             1              16
  T2             4              88
  T3             9             320
  T4             0              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  DDX43 MUTATED    11   3   0
  DDX43 WILD-TYPE 276 110  87
D178V6, multiclass
    clus
vv   DDX43 MUTATED DDX43 WILD-TYPE
  N0            11             276
  N1             3             110
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D178V7, binary
                 cls
clus                0   1
  DDX43 MUTATED    12   2
  DDX43 WILD-TYPE 363  63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX43 MUTATED     12    2
  DDX43 WILD-TYPE  363   63
   clus
vv  DDX43 MUTATED DDX43 WILD-TYPE
  0            12             363
  1             2              63
[1] 2 2
[1] FALSE
D178V8, binary
                 cls
clus                0   1
  DDX43 MUTATED     7   7
  DDX43 WILD-TYPE 218 257
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX43 MUTATED      7    7
  DDX43 WILD-TYPE  218  257
        clus
vv       DDX43 MUTATED DDX43 WILD-TYPE
  FEMALE             7             218
  MALE               7             257
[1] 2 2
[1] FALSE
D178V9, binary
                 cls
clus                0   1
  DDX43 MUTATED    12   0
  DDX43 WILD-TYPE 338  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX43 MUTATED     12    0
  DDX43 WILD-TYPE  338   22
     clus
vv    DDX43 MUTATED DDX43 WILD-TYPE
  NO             12             338
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  DDX43 MUTATED                     10                             1
  DDX43 WILD-TYPE                  305                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  DDX43 MUTATED                       3                              0
  DDX43 WILD-TYPE                   103                             10
D178V10, multiclass
                                clus
vv                               DDX43 MUTATED DDX43 WILD-TYPE
  COLON ADENOCARCINOMA                      10             305
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      3             103
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  DDX43 MUTATED     9   0   1   1
  DDX43 WILD-TYPE 336   4  30  24
D178V11, multiclass
    clus
vv   DDX43 MUTATED DDX43 WILD-TYPE
  R0             9             336
  R1             0               4
  R2             1              30
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D178V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DDX43 MUTATED                                  0     0
  DDX43 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  DDX43 MUTATED                           2     8
  DDX43 WILD-TYPE                        20   218
D178V13, multiclass
                                  clus
vv                                 DDX43 MUTATED DDX43 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    2              20
  WHITE                                        8             218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(179) Variable = CEP135 MUTATION ANALYSIS
D179V1, survival
                  sevent
clus2                0   1
  CEP135 MUTATED    17   6
  CEP135 WILD-TYPE 361  87
  CEP135 MUTATED CEP135 WILD-TYPE 
              23              448 
  CEP135 MUTATED CEP135 WILD-TYPE 
               6               87 
$`CEP135 MUTATED`
TCGA-A6-6782 TCGA-AA-3554 TCGA-AA-3811 TCGA-AA-3977 TCGA-AA-A00E TCGA-AA-A00N 
       20.28        17.95        10.06        25.02        30.02         4.01 
TCGA-AZ-4315 TCGA-AZ-6601 TCGA-CA-6715 TCGA-CA-6717 TCGA-CM-6676 TCGA-CM-6679 
       58.39       100.01         0.07        12.76        11.08        10.06 
TCGA-D5-6538 TCGA-DM-A1D8 TCGA-DM-A1DB TCGA-DM-A1HB TCGA-F4-6570 TCGA-G4-6586 
       17.13        12.59        44.32       135.65         6.18        35.80 
TCGA-G4-6628 TCGA-AG-3878 TCGA-AG-A002 TCGA-CI-6622 TCGA-DC-6682 
       79.69         0.99        20.98         6.97         4.01 

$`CEP135 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        19.66         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       13.02        24.00        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        19.04        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00F 
        7.96        27.02        13.94        38.04        19.00        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
       16.31         0.95        33.01        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77        12.10        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6716 
        1.61        12.69         3.06         3.25         3.29        12.20 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.08        11.01        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       15.12        17.85         4.80        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A282 
       49.91        13.32       140.38         7.50       131.51       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 
       98.24         8.61        31.96        35.74        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 
       22.09        13.78        26.17        91.79        46.75        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
        6.05        33.17         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  CEP135 MUTATED CEP135 WILD-TYPE 
            0.07             0.00 
  CEP135 MUTATED CEP135 WILD-TYPE 
          135.65           148.01 
  CEP135 MUTATED CEP135 WILD-TYPE 
           17.13            20.73 
[1] "0.1 - 135.7 (17.1)" "0.0 - 148.0 (20.7)"
[1] "hr=" "1.3"
D179V2, continuous
D179V3, binary
                  cls
clus                 0   1
  CEP135 MUTATED    21   4
  CEP135 WILD-TYPE 345 115
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CEP135 MUTATED     21    4
  CEP135 WILD-TYPE  345  115
        clus
vv       CEP135 MUTATED CEP135 WILD-TYPE
  COLON              21              345
  RECTUM              4              115
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CEP135 MUTATED         4        0        1        10         4         0
  CEP135 WILD-TYPE      87        1       31       128         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CEP135 MUTATED           1          0          3          0        0
  CEP135 WILD-TYPE        23         11         56         42       48
                  vv
clus               STAGE IVA STAGE IVB
  CEP135 MUTATED           0         0
  CEP135 WILD-TYPE        18         1
D179V4, multiclass
            clus
vv           CEP135 MUTATED CEP135 WILD-TYPE
  STAGE I                 4               87
  STAGE IA                0                1
  STAGE II                1               31
  STAGE IIA              10              128
  STAGE IIB               4                6
  STAGE IIC               0                1
  STAGE III               1               23
  STAGE IIIA              0               11
  STAGE IIIB              3               56
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  CEP135 MUTATED     0   5  16   4
  CEP135 WILD-TYPE  17  87 313  46
D179V5, multiclass
    clus
vv   CEP135 MUTATED CEP135 WILD-TYPE
  T1              0               17
  T2              5               87
  T3             16              313
  T4              4               46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  CEP135 MUTATED    20   3   2
  CEP135 WILD-TYPE 267 110  85
D179V6, multiclass
    clus
vv   CEP135 MUTATED CEP135 WILD-TYPE
  N0             20              267
  N1              3              110
  N2              2               85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D179V7, binary
                  cls
clus                 0   1
  CEP135 MUTATED    21   0
  CEP135 WILD-TYPE 354  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CEP135 MUTATED     21    0
  CEP135 WILD-TYPE  354   65
   clus
vv  CEP135 MUTATED CEP135 WILD-TYPE
  0             21              354
  1              0               65
[1] 2 2
[1] FALSE
D179V8, binary
                  cls
clus                 0   1
  CEP135 MUTATED     8  17
  CEP135 WILD-TYPE 217 247
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CEP135 MUTATED      8   17
  CEP135 WILD-TYPE  217  247
        clus
vv       CEP135 MUTATED CEP135 WILD-TYPE
  FEMALE              8              217
  MALE               17              247
[1] 2 2
[1] FALSE
D179V9, binary
                  cls
clus                 0   1
  CEP135 MUTATED    15   0
  CEP135 WILD-TYPE 335  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CEP135 MUTATED     15    0
  CEP135 WILD-TYPE  335   22
     clus
vv    CEP135 MUTATED CEP135 WILD-TYPE
  NO              15              335
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CEP135 MUTATED                     18                             2
  CEP135 WILD-TYPE                  297                            45
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CEP135 MUTATED                       4                              0
  CEP135 WILD-TYPE                   102                             10
D179V10, multiclass
                                clus
vv                               CEP135 MUTATED CEP135 WILD-TYPE
  COLON ADENOCARCINOMA                       18              297
  COLON MUCINOUS ADENOCARCINOMA               2               45
  RECTAL ADENOCARCINOMA                       4              102
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  CEP135 MUTATED    15   0   0   3
  CEP135 WILD-TYPE 330   4  31  22
D179V11, multiclass
    clus
vv   CEP135 MUTATED CEP135 WILD-TYPE
  R0             15              330
  R1              0                4
  R2              0               31
  RX              3               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D179V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CEP135 MUTATED                                  0     2
  CEP135 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  CEP135 MUTATED                           0    15
  CEP135 WILD-TYPE                        22   211
D179V13, multiclass
                                  clus
vv                                 CEP135 MUTATED CEP135 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                9
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                        15              211
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(180) Variable = IL12RB2 MUTATION ANALYSIS
D180V1, survival
                   sevent
clus2                 0   1
  IL12RB2 MUTATED    13   5
  IL12RB2 WILD-TYPE 365  88
  IL12RB2 MUTATED IL12RB2 WILD-TYPE 
               18               453 
  IL12RB2 MUTATED IL12RB2 WILD-TYPE 
                5                88 
$`IL12RB2 MUTATED`
TCGA-AA-3525 TCGA-AA-3811 TCGA-AA-A010 TCGA-AA-A01I TCGA-AD-6889 TCGA-AU-6004 
        8.05        10.06        34.98        31.00        56.55        27.09 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4950 TCGA-CK-5916 TCGA-D5-5538 TCGA-DM-A28C 
       12.76        10.06        85.45        21.14        12.26        81.37 
TCGA-G4-6588 TCGA-AG-3732 TCGA-AG-3892 TCGA-DC-6160 TCGA-DY-A1DC TCGA-EI-6507 
       26.17        32.98        13.02        19.99        41.36        19.96 

$`IL12RB2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01K 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 
       40.96         0.07        21.37        15.52         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        3.29         0.07        12.20        14.30        17.56       148.01 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 
       15.62        49.08        51.32         9.99        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       13.78        35.80        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 
       19.99         7.99         0.99        37.02         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6681 
       15.02         5.03        13.97        27.95        10.98         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DD TCGA-DY-A1DF 
        4.01         5.03         5.29       126.44        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6510 
       51.48        32.61         0.49        20.55        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  IL12RB2 MUTATED IL12RB2 WILD-TYPE 
             8.05              0.00 
  IL12RB2 MUTATED IL12RB2 WILD-TYPE 
            85.45            148.01 
  IL12RB2 MUTATED IL12RB2 WILD-TYPE 
           23.655            20.120 
[1] "8.1 - 85.5 (23.7)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.3"
D180V2, continuous
D180V3, binary
                   cls
clus                  0   1
  IL12RB2 MUTATED    14   5
  IL12RB2 WILD-TYPE 352 114
[1] "tbl2"
                   cls
clus                [,1] [,2]
  IL12RB2 MUTATED     14    5
  IL12RB2 WILD-TYPE  352  114
        clus
vv       IL12RB2 MUTATED IL12RB2 WILD-TYPE
  COLON               14               352
  RECTUM               5               114
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  IL12RB2 MUTATED         6        0        0         8         1         0
  IL12RB2 WILD-TYPE      85        1       32       130         9         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  IL12RB2 MUTATED           1          0          3          0        0
  IL12RB2 WILD-TYPE        23         11         56         42       48
                   vv
clus                STAGE IVA STAGE IVB
  IL12RB2 MUTATED           0         0
  IL12RB2 WILD-TYPE        18         1
D180V4, multiclass
            clus
vv           IL12RB2 MUTATED IL12RB2 WILD-TYPE
  STAGE I                  6                85
  STAGE IA                 0                 1
  STAGE II                 0                32
  STAGE IIA                8               130
  STAGE IIB                1                 9
  STAGE IIC                0                 1
  STAGE III                1                23
  STAGE IIIA               0                11
  STAGE IIIB               3                56
  STAGE IIIC               0                42
  STAGE IV                 0                48
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  IL12RB2 MUTATED     2   4  12   1
  IL12RB2 WILD-TYPE  15  88 317  49
D180V5, multiclass
    clus
vv   IL12RB2 MUTATED IL12RB2 WILD-TYPE
  T1               2                15
  T2               4                88
  T3              12               317
  T4               1                49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  IL12RB2 MUTATED    15   3   1
  IL12RB2 WILD-TYPE 272 110  86
D180V6, multiclass
    clus
vv   IL12RB2 MUTATED IL12RB2 WILD-TYPE
  N0              15               272
  N1               3               110
  N2               1                86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D180V7, binary
                   cls
clus                  0   1
  IL12RB2 MUTATED    19   0
  IL12RB2 WILD-TYPE 356  65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  IL12RB2 MUTATED     19    0
  IL12RB2 WILD-TYPE  356   65
   clus
vv  IL12RB2 MUTATED IL12RB2 WILD-TYPE
  0              19               356
  1               0                65
[1] 2 2
[1] FALSE
D180V8, binary
                   cls
clus                  0   1
  IL12RB2 MUTATED    11   8
  IL12RB2 WILD-TYPE 214 256
[1] "tbl2"
                   cls
clus                [,1] [,2]
  IL12RB2 MUTATED     11    8
  IL12RB2 WILD-TYPE  214  256
        clus
vv       IL12RB2 MUTATED IL12RB2 WILD-TYPE
  FEMALE              11               214
  MALE                 8               256
[1] 2 2
[1] FALSE
D180V9, binary
                   cls
clus                  0   1
  IL12RB2 MUTATED    13   0
  IL12RB2 WILD-TYPE 337  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  IL12RB2 MUTATED     13    0
  IL12RB2 WILD-TYPE  337   22
     clus
vv    IL12RB2 MUTATED IL12RB2 WILD-TYPE
  NO               13               337
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  IL12RB2 MUTATED                     13                             1
  IL12RB2 WILD-TYPE                  302                            46
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  IL12RB2 MUTATED                       5                              0
  IL12RB2 WILD-TYPE                   101                             10
D180V10, multiclass
                                clus
vv                               IL12RB2 MUTATED IL12RB2 WILD-TYPE
  COLON ADENOCARCINOMA                        13               302
  COLON MUCINOUS ADENOCARCINOMA                1                46
  RECTAL ADENOCARCINOMA                        5               101
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  IL12RB2 MUTATED    12   1   0   3
  IL12RB2 WILD-TYPE 333   3  31  22
D180V11, multiclass
    clus
vv   IL12RB2 MUTATED IL12RB2 WILD-TYPE
  R0              12               333
  R1               1                 3
  R2               0                31
  RX               3                22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D180V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  IL12RB2 MUTATED                                  0     3
  IL12RB2 WILD-TYPE                                1     8
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  IL12RB2 MUTATED                           1     8
  IL12RB2 WILD-TYPE                        21   218
D180V13, multiclass
                                  clus
vv                                 IL12RB2 MUTATED IL12RB2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          3                 8
  BLACK OR AFRICAN AMERICAN                      1                21
  WHITE                                          8               218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(181) Variable = EHBP1 MUTATION ANALYSIS
D181V1, survival
                 sevent
clus2               0   1
  EHBP1 MUTATED    21   3
  EHBP1 WILD-TYPE 357  90
  EHBP1 MUTATED EHBP1 WILD-TYPE 
             24             447 
  EHBP1 MUTATED EHBP1 WILD-TYPE 
              3              90 
$`EHBP1 MUTATED`
TCGA-A6-5666 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3845 TCGA-AA-3864 TCGA-AA-3977 
       32.71         1.02        35.01         0.00        53.00        25.02 
TCGA-AD-6889 TCGA-AU-6004 TCGA-CK-5913 TCGA-CK-5914 TCGA-CM-6167 TCGA-D5-5538 
       56.55        27.09        51.32         9.99        14.99        12.26 
TCGA-D5-6532 TCGA-D5-6535 TCGA-D5-6540 TCGA-DM-A1D7 TCGA-DM-A28H TCGA-F4-6570 
       18.25        15.12        16.14        13.32       117.07         6.18 
TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6588 TCGA-AG-4008 TCGA-AG-A002 TCGA-AH-6547 
       55.04        63.62        26.17        17.03        20.98         1.45 

$`EHBP1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        22.06        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3510 
       20.12        19.66        20.28         7.04         3.02        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       38.99        37.02        14.93        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       31.07        30.05        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       21.37        15.52         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 
       27.42        10.88         0.20        14.50        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       85.45        15.62        49.08        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6168 TCGA-CM-6169 
        2.96        29.03        16.04        21.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5539 
       11.08        11.01        10.06        12.03        45.40        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 
       56.09        55.92        20.19         1.32        43.27        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
        4.80        17.13        12.49        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D8 
       24.43        38.20       130.65        92.75        49.91        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28K 
        6.12        81.37       119.93        35.97        60.79        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
        8.61        31.96        35.74        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       85.48        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-A008 TCGA-AG-A00C 
       28.04        36.03        14.04         1.02        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  EHBP1 MUTATED EHBP1 WILD-TYPE 
              0               0 
  EHBP1 MUTATED EHBP1 WILD-TYPE 
         117.07          148.01 
  EHBP1 MUTATED EHBP1 WILD-TYPE 
         19.615          20.190 
[1] "0.0 - 117.1 (19.6)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.8"
D181V2, continuous
D181V3, binary
                 cls
clus                0   1
  EHBP1 MUTATED    22   3
  EHBP1 WILD-TYPE 344 116
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EHBP1 MUTATED     22    3
  EHBP1 WILD-TYPE  344  116
        clus
vv       EHBP1 MUTATED EHBP1 WILD-TYPE
  COLON             22             344
  RECTUM             3             116
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  EHBP1 MUTATED         4        0        2         9         0         1
  EHBP1 WILD-TYPE      87        1       30       129        10         0
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  EHBP1 MUTATED           0          0          5          2        0         0
  EHBP1 WILD-TYPE        24         11         54         40       48        18
                 vv
clus              STAGE IVB
  EHBP1 MUTATED           0
  EHBP1 WILD-TYPE         1
D181V4, multiclass
            clus
vv           EHBP1 MUTATED EHBP1 WILD-TYPE
  STAGE I                4              87
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA              9             129
  STAGE IIB              0              10
  STAGE IIC              1               0
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             5              54
  STAGE IIIC             2              40
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  EHBP1 MUTATED     0   5  19   1
  EHBP1 WILD-TYPE  17  87 310  49
D181V5, multiclass
    clus
vv   EHBP1 MUTATED EHBP1 WILD-TYPE
  T1             0              17
  T2             5              87
  T3            19             310
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  EHBP1 MUTATED    18   5   2
  EHBP1 WILD-TYPE 269 108  85
D181V6, multiclass
    clus
vv   EHBP1 MUTATED EHBP1 WILD-TYPE
  N0            18             269
  N1             5             108
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D181V7, binary
                 cls
clus                0   1
  EHBP1 MUTATED    20   0
  EHBP1 WILD-TYPE 355  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EHBP1 MUTATED     20    0
  EHBP1 WILD-TYPE  355   65
   clus
vv  EHBP1 MUTATED EHBP1 WILD-TYPE
  0            20             355
  1             0              65
[1] 2 2
[1] FALSE
D181V8, binary
                 cls
clus                0   1
  EHBP1 MUTATED    12  13
  EHBP1 WILD-TYPE 213 251
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EHBP1 MUTATED     12   13
  EHBP1 WILD-TYPE  213  251
        clus
vv       EHBP1 MUTATED EHBP1 WILD-TYPE
  FEMALE            12             213
  MALE              13             251
[1] 2 2
[1] FALSE
D181V9, binary
                 cls
clus                0   1
  EHBP1 MUTATED    15   1
  EHBP1 WILD-TYPE 335  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EHBP1 MUTATED     15    1
  EHBP1 WILD-TYPE  335   21
     clus
vv    EHBP1 MUTATED EHBP1 WILD-TYPE
  NO             15             335
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  EHBP1 MUTATED                     20                             1
  EHBP1 WILD-TYPE                  295                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  EHBP1 MUTATED                       3                              0
  EHBP1 WILD-TYPE                   103                             10
D181V10, multiclass
                                clus
vv                               EHBP1 MUTATED EHBP1 WILD-TYPE
  COLON ADENOCARCINOMA                      20             295
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      3             103
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  EHBP1 MUTATED    16   0   0   3
  EHBP1 WILD-TYPE 329   4  31  22
D181V11, multiclass
    clus
vv   EHBP1 MUTATED EHBP1 WILD-TYPE
  R0            16             329
  R1             0               4
  R2             0              31
  RX             3              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D181V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  EHBP1 MUTATED                                  0     1
  EHBP1 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  EHBP1 MUTATED                           1    15
  EHBP1 WILD-TYPE                        21   211
D181V13, multiclass
                                  clus
vv                                 EHBP1 MUTATED EHBP1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                       15             211
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(182) Variable = USP7 MUTATION ANALYSIS
D182V1, survival
                sevent
clus2              0   1
  USP7 MUTATED    18   6
  USP7 WILD-TYPE 360  87
  USP7 MUTATED USP7 WILD-TYPE 
            24            447 
  USP7 MUTATED USP7 WILD-TYPE 
             6             87 
$`USP7 MUTATED`
TCGA-AA-3510 TCGA-AA-3518 TCGA-AA-3663 TCGA-AA-3715 TCGA-AA-A00N TCGA-AA-A010 
       63.98         1.02         6.97        19.04         4.01        34.98 
TCGA-AA-A01P TCGA-AA-A01R TCGA-AD-6889 TCGA-AU-6004 TCGA-AY-5543 TCGA-AZ-4315 
       38.07        35.01        56.55        27.09        33.01        58.39 
TCGA-AZ-6598 TCGA-AZ-6606 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-D5-6540 
       49.41        11.74        12.76        10.06        17.56        16.14 
TCGA-D5-6541 TCGA-F4-6856 TCGA-G4-6317 TCGA-G4-6588 TCGA-AG-A002 TCGA-G5-6235 
       15.58        35.31        36.00        26.17        20.98        55.76 

$`USP7 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       85.05        26.99        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01Q TCGA-AA-A01S 
       32.02        12.00        31.00        31.00         1.02         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6197 TCGA-AY-6386 
        0.20        14.50        16.31         0.95        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 
        6.77        12.10       100.01        29.56         5.23         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       12.20        14.30       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 
       16.24        33.67        13.25         0.53        47.41       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 
       63.62        61.91        22.09        13.78        35.80        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6641 
        0.66         0.69        26.43 

  USP7 MUTATED USP7 WILD-TYPE 
          1.02           0.00 
  USP7 MUTATED USP7 WILD-TYPE 
         63.98         148.01 
  USP7 MUTATED USP7 WILD-TYPE 
         26.63          20.05 
[1] "1.0 - 64.0 (26.6)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.2"
D182V2, continuous
D182V3, binary
                cls
clus               0   1
  USP7 MUTATED    24   2
  USP7 WILD-TYPE 342 117
[1] "tbl2"
                cls
clus             [,1] [,2]
  USP7 MUTATED     24    2
  USP7 WILD-TYPE  342  117
        clus
vv       USP7 MUTATED USP7 WILD-TYPE
  COLON            24            342
  RECTUM            2            117
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  USP7 MUTATED         4        0        4         8         2         0
  USP7 WILD-TYPE      87        1       28       130         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  USP7 MUTATED           3          0          2          1        1         1
  USP7 WILD-TYPE        21         11         57         41       47        17
                vv
clus             STAGE IVB
  USP7 MUTATED           0
  USP7 WILD-TYPE         1
D182V4, multiclass
            clus
vv           USP7 MUTATED USP7 WILD-TYPE
  STAGE I               4             87
  STAGE IA              0              1
  STAGE II              4             28
  STAGE IIA             8            130
  STAGE IIB             2              8
  STAGE IIC             0              1
  STAGE III             3             21
  STAGE IIIA            0             11
  STAGE IIIB            2             57
  STAGE IIIC            1             41
  STAGE IV              1             47
  STAGE IVA             1             17
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  USP7 MUTATED     0   4  18   4
  USP7 WILD-TYPE  17  88 311  46
D182V5, multiclass
    clus
vv   USP7 MUTATED USP7 WILD-TYPE
  T1            0             17
  T2            4             88
  T3           18            311
  T4            4             46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  USP7 MUTATED    18   4   4
  USP7 WILD-TYPE 269 109  83
D182V6, multiclass
    clus
vv   USP7 MUTATED USP7 WILD-TYPE
  N0           18            269
  N1            4            109
  N2            4             83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D182V7, binary
                cls
clus               0   1
  USP7 MUTATED    21   2
  USP7 WILD-TYPE 354  63
[1] "tbl2"
                cls
clus             [,1] [,2]
  USP7 MUTATED     21    2
  USP7 WILD-TYPE  354   63
   clus
vv  USP7 MUTATED USP7 WILD-TYPE
  0           21            354
  1            2             63
[1] 2 2
[1] FALSE
D182V8, binary
                cls
clus               0   1
  USP7 MUTATED    10  16
  USP7 WILD-TYPE 215 248
[1] "tbl2"
                cls
clus             [,1] [,2]
  USP7 MUTATED     10   16
  USP7 WILD-TYPE  215  248
        clus
vv       USP7 MUTATED USP7 WILD-TYPE
  FEMALE           10            215
  MALE             16            248
[1] 2 2
[1] FALSE
D182V9, binary
                cls
clus               0   1
  USP7 MUTATED    19   1
  USP7 WILD-TYPE 331  21
[1] "tbl2"
                cls
clus             [,1] [,2]
  USP7 MUTATED     19    1
  USP7 WILD-TYPE  331   21
     clus
vv    USP7 MUTATED USP7 WILD-TYPE
  NO            19            331
  YES            1             21
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  USP7 MUTATED                     19                             5
  USP7 WILD-TYPE                  296                            42
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  USP7 MUTATED                       2                              0
  USP7 WILD-TYPE                   104                             10
D182V10, multiclass
                                clus
vv                               USP7 MUTATED USP7 WILD-TYPE
  COLON ADENOCARCINOMA                     19            296
  COLON MUCINOUS ADENOCARCINOMA             5             42
  RECTAL ADENOCARCINOMA                     2            104
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  USP7 MUTATED    19   1   0   3
  USP7 WILD-TYPE 326   3  31  22
D182V11, multiclass
    clus
vv   USP7 MUTATED USP7 WILD-TYPE
  R0           19            326
  R1            1              3
  R2            0             31
  RX            3             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D182V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  USP7 MUTATED                                  0     3
  USP7 WILD-TYPE                                1     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  USP7 MUTATED                           1    11
  USP7 WILD-TYPE                        21   215
D182V13, multiclass
                                  clus
vv                                 USP7 MUTATED USP7 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       3              8
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                      11            215
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(183) Variable = IVL MUTATION ANALYSIS
D183V1, survival
               sevent
clus2             0   1
  IVL MUTATED    14   5
  IVL WILD-TYPE 364  88
  IVL MUTATED IVL WILD-TYPE 
           19           452 
  IVL MUTATED IVL WILD-TYPE 
            5            88 
$`IVL MUTATED`
TCGA-A6-5659 TCGA-A6-6138 TCGA-A6-6781 TCGA-AA-3663 TCGA-AA-3673 TCGA-AA-3977 
       30.44        22.52        19.66         6.97        50.04        25.02 
TCGA-AD-6901 TCGA-AZ-4682 TCGA-CK-4947 TCGA-CM-4752 TCGA-CM-6168 TCGA-D5-6540 
       22.42        22.36        17.56        13.02        12.99        16.14 
TCGA-D5-6922 TCGA-DM-A28C TCGA-DM-A28E TCGA-G4-6303 TCGA-AG-3574 TCGA-EF-5830 
        4.41        81.37       119.93        65.85        36.03         0.49 
TCGA-EI-6508 
       20.91 

$`IVL WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       22.06        32.71        27.09         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02        78.08         6.05        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
       14.01         0.92        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
        5.13       106.75        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-4950 
       12.20        12.76        10.06        14.30       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6169 
        2.96        29.03        16.04        21.99        14.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
       15.58         1.48         3.68        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28F TCGA-DM-A28G 
      131.51       135.65       139.17         6.12        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       20.02        10.39        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6510 TCGA-F5-6464 
       51.48        32.61        20.55        19.96        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  IVL MUTATED IVL WILD-TYPE 
         0.49          0.00 
  IVL MUTATED IVL WILD-TYPE 
       119.93        148.01 
  IVL MUTATED IVL WILD-TYPE 
       22.360        20.085 
[1] "0.5 - 119.9 (22.4)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.1"
D183V2, continuous
D183V3, binary
               cls
clus              0   1
  IVL MUTATED    17   3
  IVL WILD-TYPE 349 116
[1] "tbl2"
               cls
clus            [,1] [,2]
  IVL MUTATED     17    3
  IVL WILD-TYPE  349  116
        clus
vv       IVL MUTATED IVL WILD-TYPE
  COLON           17           349
  RECTUM           3           116
[1] 2 2
[1] FALSE
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  IVL MUTATED         3        0        3         4         1         0
  IVL WILD-TYPE      88        1       29       134         9         1
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  IVL MUTATED           1          1          2          1        1         1
  IVL WILD-TYPE        23         10         57         41       47        17
               vv
clus            STAGE IVB
  IVL MUTATED           0
  IVL WILD-TYPE         1
D183V4, multiclass
            clus
vv           IVL MUTATED IVL WILD-TYPE
  STAGE I              3            88
  STAGE IA             0             1
  STAGE II             3            29
  STAGE IIA            4           134
  STAGE IIB            1             9
  STAGE IIC            0             1
  STAGE III            1            23
  STAGE IIIA           1            10
  STAGE IIIB           2            57
  STAGE IIIC           1            41
  STAGE IV             1            47
  STAGE IVA            1            17
  STAGE IVB            0             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  IVL MUTATED     0   4  13   3
  IVL WILD-TYPE  17  88 316  47
D183V5, multiclass
    clus
vv   IVL MUTATED IVL WILD-TYPE
  T1           0            17
  T2           4            88
  T3          13           316
  T4           3            47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2
  IVL MUTATED    14   5   1
  IVL WILD-TYPE 273 108  86
D183V6, multiclass
    clus
vv   IVL MUTATED IVL WILD-TYPE
  N0          14           273
  N1           5           108
  N2           1            86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D183V7, binary
               cls
clus              0   1
  IVL MUTATED    15   2
  IVL WILD-TYPE 360  63
[1] "tbl2"
               cls
clus            [,1] [,2]
  IVL MUTATED     15    2
  IVL WILD-TYPE  360   63
   clus
vv  IVL MUTATED IVL WILD-TYPE
  0          15           360
  1           2            63
[1] 2 2
[1] FALSE
D183V8, binary
               cls
clus              0   1
  IVL MUTATED     7  13
  IVL WILD-TYPE 218 251
[1] "tbl2"
               cls
clus            [,1] [,2]
  IVL MUTATED      7   13
  IVL WILD-TYPE  218  251
        clus
vv       IVL MUTATED IVL WILD-TYPE
  FEMALE           7           218
  MALE            13           251
[1] 2 2
[1] FALSE
D183V9, binary
               cls
clus              0   1
  IVL MUTATED    15   0
  IVL WILD-TYPE 335  22
[1] "tbl2"
               cls
clus            [,1] [,2]
  IVL MUTATED     15    0
  IVL WILD-TYPE  335   22
     clus
vv    IVL MUTATED IVL WILD-TYPE
  NO           15           335
  YES           0            22
[1] 2 2
[1] FALSE
               vv
clus            COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  IVL MUTATED                     15                             2
  IVL WILD-TYPE                  300                            45
               vv
clus            RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  IVL MUTATED                       3                              0
  IVL WILD-TYPE                   103                             10
D183V10, multiclass
                                clus
vv                               IVL MUTATED IVL WILD-TYPE
  COLON ADENOCARCINOMA                    15           300
  COLON MUCINOUS ADENOCARCINOMA            2            45
  RECTAL ADENOCARCINOMA                    3           103
  RECTAL MUCINOUS ADENOCARCINOMA           0            10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             R0  R1  R2  RX
  IVL MUTATED    14   0   0   1
  IVL WILD-TYPE 331   4  31  24
D183V11, multiclass
    clus
vv   IVL MUTATED IVL WILD-TYPE
  R0          14           331
  R1           0             4
  R2           0            31
  RX           1            24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D183V12, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  IVL MUTATED                                  0     0
  IVL WILD-TYPE                                1    11
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  IVL MUTATED                           2    13
  IVL WILD-TYPE                        20   213
D183V13, multiclass
                                  clus
vv                                 IVL MUTATED IVL WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      0            11
  BLACK OR AFRICAN AMERICAN                  2            20
  WHITE                                     13           213
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(184) Variable = IDH2 MUTATION ANALYSIS
D184V1, survival
                sevent
clus2              0   1
  IDH2 MUTATED    13   1
  IDH2 WILD-TYPE 365  92
  IDH2 MUTATED IDH2 WILD-TYPE 
            14            457 
  IDH2 MUTATED IDH2 WILD-TYPE 
             1             92 
$`IDH2 MUTATED`
TCGA-A6-5661 TCGA-AA-3556 TCGA-AA-3672 TCGA-AA-3715 TCGA-AA-3833 TCGA-AA-3864 
       33.53        23.01         0.92        19.04        15.95        53.00 
TCGA-AA-A01Z TCGA-AD-6889 TCGA-CK-4948 TCGA-CM-6164 TCGA-CM-6170 TCGA-D5-6535 
       37.02        56.55       148.01        29.03        15.02        15.12 
TCGA-G4-6307 TCGA-EI-6510 
       55.04        18.28 

$`IDH2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3560 
       13.02        24.00        17.95        29.95        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
       54.02         2.01        14.01        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       85.05        26.99        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3837 TCGA-AA-3842 
        0.99        25.02         1.02        17.98        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       30.05        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A024 
       35.01         1.02        33.04        35.01        26.01        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       15.52         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 
       12.20        12.76        10.06        14.30        17.56        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
       12.00         2.96        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       13.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       43.27        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-F5-6464 TCGA-F5-6465 
        0.49        20.55        19.96        20.91         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  IDH2 MUTATED IDH2 WILD-TYPE 
          0.92           0.00 
  IDH2 MUTATED IDH2 WILD-TYPE 
        148.01         140.38 
  IDH2 MUTATED IDH2 WILD-TYPE 
         26.02          20.12 
[1] "0.9 - 148.0 (26.0)" "0.0 - 140.4 (20.1)"
[1] "hr=" "3.7"
D184V2, continuous
D184V3, binary
                cls
clus               0   1
  IDH2 MUTATED    17   1
  IDH2 WILD-TYPE 349 118
[1] "tbl2"
                cls
clus             [,1] [,2]
  IDH2 MUTATED     17    1
  IDH2 WILD-TYPE  349  118
        clus
vv       IDH2 MUTATED IDH2 WILD-TYPE
  COLON            17            349
  RECTUM            1            118
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  IDH2 MUTATED         2        0        4         4         1         0
  IDH2 WILD-TYPE      89        1       28       134         9         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  IDH2 MUTATED           2          0          2          1        1         1
  IDH2 WILD-TYPE        22         11         57         41       47        17
                vv
clus             STAGE IVB
  IDH2 MUTATED           0
  IDH2 WILD-TYPE         1
D184V4, multiclass
            clus
vv           IDH2 MUTATED IDH2 WILD-TYPE
  STAGE I               2             89
  STAGE IA              0              1
  STAGE II              4             28
  STAGE IIA             4            134
  STAGE IIB             1              9
  STAGE IIC             0              1
  STAGE III             2             22
  STAGE IIIA            0             11
  STAGE IIIB            2             57
  STAGE IIIC            1             41
  STAGE IV              1             47
  STAGE IVA             1             17
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  IDH2 MUTATED     0   3  12   3
  IDH2 WILD-TYPE  17  89 317  47
D184V5, multiclass
    clus
vv   IDH2 MUTATED IDH2 WILD-TYPE
  T1            0             17
  T2            3             89
  T3           12            317
  T4            3             47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  IDH2 MUTATED    12   5   1
  IDH2 WILD-TYPE 275 108  86
D184V6, multiclass
    clus
vv   IDH2 MUTATED IDH2 WILD-TYPE
  N0           12            275
  N1            5            108
  N2            1             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D184V7, binary
                cls
clus               0   1
  IDH2 MUTATED    13   1
  IDH2 WILD-TYPE 362  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  IDH2 MUTATED     13    1
  IDH2 WILD-TYPE  362   64
   clus
vv  IDH2 MUTATED IDH2 WILD-TYPE
  0           13            362
  1            1             64
[1] 2 2
[1] FALSE
D184V8, binary
                cls
clus               0   1
  IDH2 MUTATED    12   6
  IDH2 WILD-TYPE 213 258
[1] "tbl2"
                cls
clus             [,1] [,2]
  IDH2 MUTATED     12    6
  IDH2 WILD-TYPE  213  258
        clus
vv       IDH2 MUTATED IDH2 WILD-TYPE
  FEMALE           12            213
  MALE              6            258
[1] 2 2
[1] FALSE
D184V9, binary
                cls
clus               0   1
  IDH2 MUTATED    13   0
  IDH2 WILD-TYPE 337  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  IDH2 MUTATED     13    0
  IDH2 WILD-TYPE  337   22
     clus
vv    IDH2 MUTATED IDH2 WILD-TYPE
  NO            13            337
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  IDH2 MUTATED                     15                             1
  IDH2 WILD-TYPE                  300                            46
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  IDH2 MUTATED                       1                              0
  IDH2 WILD-TYPE                   105                             10
D184V10, multiclass
                                clus
vv                               IDH2 MUTATED IDH2 WILD-TYPE
  COLON ADENOCARCINOMA                     15            300
  COLON MUCINOUS ADENOCARCINOMA             1             46
  RECTAL ADENOCARCINOMA                     1            105
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  IDH2 MUTATED    14   0   1   2
  IDH2 WILD-TYPE 331   4  30  23
D184V11, multiclass
    clus
vv   IDH2 MUTATED IDH2 WILD-TYPE
  R0           14            331
  R1            0              4
  R2            1             30
  RX            2             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D184V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  IDH2 MUTATED                                  0     1
  IDH2 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  IDH2 MUTATED                           1     8
  IDH2 WILD-TYPE                        21   218
D184V13, multiclass
                                  clus
vv                                 IDH2 MUTATED IDH2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                       8            218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(185) Variable = FGFR2 MUTATION ANALYSIS
D185V1, survival
                 sevent
clus2               0   1
  FGFR2 MUTATED    38  14
  FGFR2 WILD-TYPE 340  79
  FGFR2 MUTATED FGFR2 WILD-TYPE 
             52             419 
  FGFR2 MUTATED FGFR2 WILD-TYPE 
             14              79 
$`FGFR2 MUTATED`
TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5666 TCGA-A6-6138 TCGA-A6-6142 TCGA-AA-3489 
       29.19        23.61        32.71        22.52        25.08         7.04 
TCGA-AA-3510 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3710 TCGA-AA-3713 TCGA-AD-6889 
       63.98        78.08         6.97        26.99        19.04        56.55 
TCGA-AD-6901 TCGA-AY-6386 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       22.42        17.82        49.41         6.77        12.10       100.01 
TCGA-CA-6717 TCGA-CK-4950 TCGA-CK-4952 TCGA-CM-4743 TCGA-CM-4752 TCGA-CM-5348 
       12.76        85.45        15.62        23.05        13.02        22.98 
TCGA-CM-5862 TCGA-CM-6168 TCGA-D5-6529 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6539 
        5.03        12.99        20.19        15.12         4.80        12.49 
TCGA-D5-6540 TCGA-D5-6898 TCGA-DM-A0XF TCGA-DM-A1D6 TCGA-DM-A1DB TCGA-DM-A28F 
       16.14         1.48        38.20        49.91        44.32        35.97 
TCGA-DM-A28G TCGA-F4-6570 TCGA-G4-6304 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6588 
       60.79         6.18        53.62        36.00        13.78        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-AF-2693 TCGA-AF-6655 TCGA-AG-3892 TCGA-AG-A002 
       91.79        79.69        19.10        20.02        13.02        20.98 
TCGA-DY-A0XA TCGA-EI-6506 TCGA-F5-6811 TCGA-G5-6235 
      126.44        20.55        32.19        55.76 

$`FGFR2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5664 TCGA-A6-5665 
       32.91        31.63        30.44        33.53        22.09        22.06 
TCGA-A6-6137 TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 
       27.09         8.38        25.18        24.16        21.76        24.69 
TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3492 
       24.39        23.87        20.12        19.66        20.28         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3664 
       19.99        13.94        19.99        61.02         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       85.05        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
        0.07        21.37        15.52         0.79         0.72         5.79 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        33.01        21.44        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6603 TCGA-AZ-6605 
      106.75        22.36        62.79        88.21        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07        12.20        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
      148.01        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-5341 
        1.91       124.27        20.02        37.02        25.02        29.06 
TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5864 
       22.03        30.08        32.02        15.02        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       21.99        14.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6541 
       18.25         1.32        43.27        17.85        17.13        15.58 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D7 TCGA-DM-A1D8 
      119.70        24.43       130.65        92.75        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
      140.38         7.50       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       81.37       119.93       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       35.74        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       74.56        65.85        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 
       61.91        22.09        35.80        46.75        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       43.04        13.55        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       15.39        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 
        1.02        17.95        36.95        17.03        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
        5.29        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
        0.49        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6641 
       31.30        28.57         0.66         0.69        26.43 

  FGFR2 MUTATED FGFR2 WILD-TYPE 
           1.48            0.00 
  FGFR2 MUTATED FGFR2 WILD-TYPE 
         126.44          148.01 
  FGFR2 MUTATED FGFR2 WILD-TYPE 
          22.75           19.99 
[1] "1.5 - 126.4 (22.8)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.1"
D185V2, continuous
D185V3, binary
                 cls
clus                0   1
  FGFR2 MUTATED    45   7
  FGFR2 WILD-TYPE 321 112
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FGFR2 MUTATED     45    7
  FGFR2 WILD-TYPE  321  112
        clus
vv       FGFR2 MUTATED FGFR2 WILD-TYPE
  COLON             45             321
  RECTUM             7             112
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FGFR2 MUTATED         8        1        6        16         1         1
  FGFR2 WILD-TYPE      83        0       26       122         9         0
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  FGFR2 MUTATED           0          2          7          5        2         3
  FGFR2 WILD-TYPE        24          9         52         37       46        15
                 vv
clus              STAGE IVB
  FGFR2 MUTATED           0
  FGFR2 WILD-TYPE         1
D185V4, multiclass
            clus
vv           FGFR2 MUTATED FGFR2 WILD-TYPE
  STAGE I                8              83
  STAGE IA               1               0
  STAGE II               6              26
  STAGE IIA             16             122
  STAGE IIB              1               9
  STAGE IIC              1               0
  STAGE III              0              24
  STAGE IIIA             2               9
  STAGE IIIB             7              52
  STAGE IIIC             5              37
  STAGE IV               2              46
  STAGE IVA              3              15
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  FGFR2 MUTATED     1   8  39   4
  FGFR2 WILD-TYPE  16  84 290  46
D185V5, multiclass
    clus
vv   FGFR2 MUTATED FGFR2 WILD-TYPE
  T1             1              16
  T2             8              84
  T3            39             290
  T4             4              46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  FGFR2 MUTATED    36  11   6
  FGFR2 WILD-TYPE 251 102  81
D185V6, multiclass
    clus
vv   FGFR2 MUTATED FGFR2 WILD-TYPE
  N0            36             251
  N1            11             102
  N2             6              81
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D185V7, binary
                 cls
clus                0   1
  FGFR2 MUTATED    38   5
  FGFR2 WILD-TYPE 337  60
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FGFR2 MUTATED     38    5
  FGFR2 WILD-TYPE  337   60
   clus
vv  FGFR2 MUTATED FGFR2 WILD-TYPE
  0            38             337
  1             5              60
[1] 2 2
[1] FALSE
D185V8, binary
                 cls
clus                0   1
  FGFR2 MUTATED    21  32
  FGFR2 WILD-TYPE 204 232
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FGFR2 MUTATED     21   32
  FGFR2 WILD-TYPE  204  232
        clus
vv       FGFR2 MUTATED FGFR2 WILD-TYPE
  FEMALE            21             204
  MALE              32             232
[1] 2 2
[1] FALSE
D185V9, binary
                 cls
clus                0   1
  FGFR2 MUTATED    41   1
  FGFR2 WILD-TYPE 309  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FGFR2 MUTATED     41    1
  FGFR2 WILD-TYPE  309   21
     clus
vv    FGFR2 MUTATED FGFR2 WILD-TYPE
  NO             41             309
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  FGFR2 MUTATED                     39                             5
  FGFR2 WILD-TYPE                  276                            42
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  FGFR2 MUTATED                       7                              0
  FGFR2 WILD-TYPE                    99                             10
D185V10, multiclass
                                clus
vv                               FGFR2 MUTATED FGFR2 WILD-TYPE
  COLON ADENOCARCINOMA                      39             276
  COLON MUCINOUS ADENOCARCINOMA              5              42
  RECTAL ADENOCARCINOMA                      7              99
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  FGFR2 MUTATED    28   2   1   3
  FGFR2 WILD-TYPE 317   2  30  22
D185V11, multiclass
    clus
vv   FGFR2 MUTATED FGFR2 WILD-TYPE
  R0            28             317
  R1             2               2
  R2             1              30
  RX             3              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D185V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FGFR2 MUTATED                                  0     2
  FGFR2 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  FGFR2 MUTATED                           7    36
  FGFR2 WILD-TYPE                        15   190
D185V13, multiclass
                                  clus
vv                                 FGFR2 MUTATED FGFR2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               9
  BLACK OR AFRICAN AMERICAN                    7              15
  WHITE                                       36             190
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(186) Variable = FAM134A MUTATION ANALYSIS
D186V1, survival
                   sevent
clus2                 0   1
  FAM134A MUTATED     5   3
  FAM134A WILD-TYPE 373  90
  FAM134A MUTATED FAM134A WILD-TYPE 
                8               463 
  FAM134A MUTATED FAM134A WILD-TYPE 
                3                90 
$`FAM134A MUTATED`
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-A00N TCGA-AY-5543 TCGA-AZ-6598 TCGA-CK-4950 
       17.98        15.95         4.01        33.01        49.41        85.45 
TCGA-CM-5861 TCGA-DM-A1D7 
       15.02        13.32 

$`FAM134A WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
        1.02        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6197 
        0.20        14.50        27.09        16.31         0.95        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        88.21         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       14.30        17.56       148.01        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       22.98        30.08        32.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       49.91        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  FAM134A MUTATED FAM134A WILD-TYPE 
             4.01              0.00 
  FAM134A MUTATED FAM134A WILD-TYPE 
            85.45            148.01 
  FAM134A MUTATED FAM134A WILD-TYPE 
           16.965            20.280 
[1] "4.0 - 85.5 (17.0)"  "0.0 - 148.0 (20.3)"
[1] "hr=" "1.7"
D186V2, continuous
D186V3, binary
                   cls
clus                  0   1
  FAM134A MUTATED     8   0
  FAM134A WILD-TYPE 358 119
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM134A MUTATED      8    0
  FAM134A WILD-TYPE  358  119
        clus
vv       FAM134A MUTATED FAM134A WILD-TYPE
  COLON                8               358
  RECTUM               0               119
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FAM134A MUTATED         0        0        1         4         1         0
  FAM134A WILD-TYPE      91        1       31       134         9         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FAM134A MUTATED           0          0          1          0        0
  FAM134A WILD-TYPE        24         11         58         42       48
                   vv
clus                STAGE IVA STAGE IVB
  FAM134A MUTATED           1         0
  FAM134A WILD-TYPE        17         1
D186V4, multiclass
            clus
vv           FAM134A MUTATED FAM134A WILD-TYPE
  STAGE I                  0                91
  STAGE IA                 0                 1
  STAGE II                 1                31
  STAGE IIA                4               134
  STAGE IIB                1                 9
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               0                11
  STAGE IIIB               1                58
  STAGE IIIC               0                42
  STAGE IV                 0                48
  STAGE IVA                1                17
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  FAM134A MUTATED     0   0   7   1
  FAM134A WILD-TYPE  17  92 322  49
D186V5, multiclass
    clus
vv   FAM134A MUTATED FAM134A WILD-TYPE
  T1               0                17
  T2               0                92
  T3               7               322
  T4               1                49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  FAM134A MUTATED     6   2   0
  FAM134A WILD-TYPE 281 111  87
D186V6, multiclass
    clus
vv   FAM134A MUTATED FAM134A WILD-TYPE
  N0               6               281
  N1               2               111
  N2               0                87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D186V7, binary
                   cls
clus                  0   1
  FAM134A MUTATED     6   1
  FAM134A WILD-TYPE 369  64
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM134A MUTATED      6    1
  FAM134A WILD-TYPE  369   64
   clus
vv  FAM134A MUTATED FAM134A WILD-TYPE
  0               6               369
  1               1                64
[1] 2 2
[1] FALSE
D186V8, binary
                   cls
clus                  0   1
  FAM134A MUTATED     5   3
  FAM134A WILD-TYPE 220 261
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM134A MUTATED      5    3
  FAM134A WILD-TYPE  220  261
        clus
vv       FAM134A MUTATED FAM134A WILD-TYPE
  FEMALE               5               220
  MALE                 3               261
[1] 2 2
[1] FALSE
D186V9, binary
                   cls
clus                  0   1
  FAM134A MUTATED     6   0
  FAM134A WILD-TYPE 344  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM134A MUTATED      6    0
  FAM134A WILD-TYPE  344   22
     clus
vv    FAM134A MUTATED FAM134A WILD-TYPE
  NO                6               344
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  FAM134A MUTATED                      6                             1
  FAM134A WILD-TYPE                  309                            46
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  FAM134A MUTATED                       0                              0
  FAM134A WILD-TYPE                   106                             10
D186V10, multiclass
                                clus
vv                               FAM134A MUTATED FAM134A WILD-TYPE
  COLON ADENOCARCINOMA                         6               309
  COLON MUCINOUS ADENOCARCINOMA                1                46
  RECTAL ADENOCARCINOMA                        0               106
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  FAM134A MUTATED     5   1   0   0
  FAM134A WILD-TYPE 340   3  31  25
D186V11, multiclass
    clus
vv   FAM134A MUTATED FAM134A WILD-TYPE
  R0               5               340
  R1               1                 3
  R2               0                31
  RX               0                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D186V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FAM134A MUTATED                                  0     0
  FAM134A WILD-TYPE                                1    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  FAM134A MUTATED                           2     3
  FAM134A WILD-TYPE                        20   223
D186V13, multiclass
                                  clus
vv                                 FAM134A MUTATED FAM134A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                      2                20
  WHITE                                          3               223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(187) Variable = MLL2 MUTATION ANALYSIS
D187V1, survival
                sevent
clus2              0   1
  MLL2 MUTATED    46  12
  MLL2 WILD-TYPE 332  81
  MLL2 MUTATED MLL2 WILD-TYPE 
            58            413 
  MLL2 MUTATED MLL2 WILD-TYPE 
            12             81 
$`MLL2 MUTATED`
TCGA-A6-3808 TCGA-A6-5661 TCGA-A6-5665 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6652 
       33.34        33.53        22.06        25.18        24.16        24.69 
TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3510 TCGA-AA-3663 TCGA-AA-3672 
       24.39        20.12        19.66        63.98         6.97         0.92 
TCGA-AA-3681 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3833 
        5.98        85.05        26.99        19.04        10.06        15.95 
TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01R TCGA-AD-5900 TCGA-AD-6964 TCGA-AY-6197 
        4.01        34.98        35.01         0.07        10.88        21.44 
TCGA-AZ-4315 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-CA-6715 TCGA-CA-6717 
       58.39        49.41        12.10       100.01         0.07        12.76 
TCGA-CA-6718 TCGA-CK-5916 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4747 TCGA-CM-4752 
       10.06        21.14       124.27        23.05        25.02        13.02 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6171 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6535 
       14.99        12.99        14.04        18.25         1.32        15.12 
TCGA-D5-6538 TCGA-D5-6540 TCGA-DM-A1D6 TCGA-DM-A285 TCGA-F4-6570 TCGA-F4-6703 
       17.13        16.14        49.91         6.12         6.18        47.87 
TCGA-G4-6315 TCGA-G4-6586 TCGA-G4-6628 TCGA-AF-6136 TCGA-AG-A025 TCGA-AG-A02N 
       61.91        35.80        79.69        15.39        49.97        61.97 
TCGA-CL-5917 TCGA-DC-6682 TCGA-EI-6507 TCGA-G5-6235 
       78.12         4.01        19.96        55.76 

$`MLL2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 
       31.63        30.44        29.19        23.61        22.09        32.71 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6651 TCGA-A6-6654 
       27.09        22.52         8.38        25.08        21.76        23.87 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 
       20.28         7.04         3.02         1.02        35.01         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       61.02        78.08         6.05        54.02         2.01        14.01 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3685 TCGA-AA-3688 
       50.04        47.01        15.02        11.01        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3713 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       36.00         5.03        19.04        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
       25.02         1.02        17.98        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T 
       31.00        31.00        38.07         1.02         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       18.05        40.96        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
        0.72         5.79        22.42        27.42         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4323 
       27.09        16.31         0.95        33.01        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 
        5.13       106.75        22.36        62.79        88.21         6.77 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 
        3.06         3.25         3.29        12.20        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-5341 TCGA-CM-5344 
       82.95         1.91        20.02        37.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 
       16.04        21.99        13.02        15.02        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 
       43.27        17.85         4.80        12.49        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D7 
      119.70        24.43        38.20       130.65        92.75        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
      139.17        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6704 TCGA-F4-6805 
       98.24         8.61        31.96        35.74         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       55.04        85.48        63.62        36.00        22.09        13.78 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       26.17        91.79        46.75        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A026 
        9.07        12.00        70.03        64.01        10.98         1.94 
TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       38.96        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
        4.73         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       10.98        19.99         5.95         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       20.55        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        26.43 

  MLL2 MUTATED MLL2 WILD-TYPE 
          0.07           0.00 
  MLL2 MUTATED MLL2 WILD-TYPE 
        124.27         148.01 
  MLL2 MUTATED MLL2 WILD-TYPE 
         20.63          20.19 
[1] "0.1 - 124.3 (20.6)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.1"
D187V2, continuous
D187V3, binary
                cls
clus               0   1
  MLL2 MUTATED    52   7
  MLL2 WILD-TYPE 314 112
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL2 MUTATED     52    7
  MLL2 WILD-TYPE  314  112
        clus
vv       MLL2 MUTATED MLL2 WILD-TYPE
  COLON            52            314
  RECTUM            7            112
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MLL2 MUTATED         8        0        6        20         3         0
  MLL2 WILD-TYPE      83        1       26       118         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MLL2 MUTATED           5          0          7          3        3         3
  MLL2 WILD-TYPE        19         11         52         39       45        15
                vv
clus             STAGE IVB
  MLL2 MUTATED           0
  MLL2 WILD-TYPE         1
D187V4, multiclass
            clus
vv           MLL2 MUTATED MLL2 WILD-TYPE
  STAGE I               8             83
  STAGE IA              0              1
  STAGE II              6             26
  STAGE IIA            20            118
  STAGE IIB             3              7
  STAGE IIC             0              1
  STAGE III             5             19
  STAGE IIIA            0             11
  STAGE IIIB            7             52
  STAGE IIIC            3             39
  STAGE IV              3             45
  STAGE IVA             3             15
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  MLL2 MUTATED     2   6  43   8
  MLL2 WILD-TYPE  15  86 286  42
D187V5, multiclass
    clus
vv   MLL2 MUTATED MLL2 WILD-TYPE
  T1            2             15
  T2            6             86
  T3           43            286
  T4            8             42
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  MLL2 MUTATED    41  11   7
  MLL2 WILD-TYPE 246 102  80
D187V6, multiclass
    clus
vv   MLL2 MUTATED MLL2 WILD-TYPE
  N0           41            246
  N1           11            102
  N2            7             80
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D187V7, binary
                cls
clus               0   1
  MLL2 MUTATED    41   6
  MLL2 WILD-TYPE 334  59
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL2 MUTATED     41    6
  MLL2 WILD-TYPE  334   59
   clus
vv  MLL2 MUTATED MLL2 WILD-TYPE
  0           41            334
  1            6             59
[1] 2 2
[1] FALSE
D187V8, binary
                cls
clus               0   1
  MLL2 MUTATED    24  35
  MLL2 WILD-TYPE 201 229
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL2 MUTATED     24   35
  MLL2 WILD-TYPE  201  229
        clus
vv       MLL2 MUTATED MLL2 WILD-TYPE
  FEMALE           24            201
  MALE             35            229
[1] 2 2
[1] FALSE
D187V9, binary
                cls
clus               0   1
  MLL2 MUTATED    46   2
  MLL2 WILD-TYPE 304  20
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL2 MUTATED     46    2
  MLL2 WILD-TYPE  304   20
     clus
vv    MLL2 MUTATED MLL2 WILD-TYPE
  NO            46            304
  YES            2             20
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MLL2 MUTATED                     42                            10
  MLL2 WILD-TYPE                  273                            37
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MLL2 MUTATED                       7                              0
  MLL2 WILD-TYPE                    99                             10
D187V10, multiclass
                                clus
vv                               MLL2 MUTATED MLL2 WILD-TYPE
  COLON ADENOCARCINOMA                     42            273
  COLON MUCINOUS ADENOCARCINOMA            10             37
  RECTAL ADENOCARCINOMA                     7             99
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  MLL2 MUTATED    38   1   0   8
  MLL2 WILD-TYPE 307   3  31  17
D187V11, multiclass
    clus
vv   MLL2 MUTATED MLL2 WILD-TYPE
  R0           38            307
  R1            1              3
  R2            0             31
  RX            8             17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D187V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MLL2 MUTATED                                  0     3
  MLL2 WILD-TYPE                                1     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  MLL2 MUTATED                           6    36
  MLL2 WILD-TYPE                        16   190
D187V13, multiclass
                                  clus
vv                                 MLL2 MUTATED MLL2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       3              8
  BLACK OR AFRICAN AMERICAN                   6             16
  WHITE                                      36            190
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(188) Variable = LRRC39 MUTATION ANALYSIS
D188V1, survival
                  sevent
clus2                0   1
  LRRC39 MUTATED     8   1
  LRRC39 WILD-TYPE 370  92
  LRRC39 MUTATED LRRC39 WILD-TYPE 
               9              462 
  LRRC39 MUTATED LRRC39 WILD-TYPE 
               1               92 
$`LRRC39 MUTATED`
TCGA-A6-5662 TCGA-AA-3811 TCGA-AA-3977 TCGA-AU-6004 TCGA-CA-6717 TCGA-CM-4743 
       23.61        10.06        25.02        27.09        12.76        23.05 
TCGA-D5-6540 TCGA-G4-6628 TCGA-AF-6655 
       16.14        79.69        20.02 

$`LRRC39 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        33.53        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
        0.20        14.50        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07        12.20        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 
       15.12        17.85         4.80        17.13        12.49        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 
       35.80        26.17        91.79        46.75        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       16.83        15.39        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  LRRC39 MUTATED LRRC39 WILD-TYPE 
           10.06             0.00 
  LRRC39 MUTATED LRRC39 WILD-TYPE 
           79.69           148.01 
  LRRC39 MUTATED LRRC39 WILD-TYPE 
          23.050           20.155 
[1] "10.1 - 79.7 (23.1)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.8"
D188V2, continuous
D188V3, binary
                  cls
clus                 0   1
  LRRC39 MUTATED     8   1
  LRRC39 WILD-TYPE 358 118
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LRRC39 MUTATED      8    1
  LRRC39 WILD-TYPE  358  118
        clus
vv       LRRC39 MUTATED LRRC39 WILD-TYPE
  COLON               8              358
  RECTUM              1              118
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  LRRC39 MUTATED         3        0        0         2         0         0
  LRRC39 WILD-TYPE      88        1       32       136        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  LRRC39 MUTATED           1          1          0          0        0
  LRRC39 WILD-TYPE        23         10         59         42       48
                  vv
clus               STAGE IVA STAGE IVB
  LRRC39 MUTATED           1         0
  LRRC39 WILD-TYPE        17         1
D188V4, multiclass
            clus
vv           LRRC39 MUTATED LRRC39 WILD-TYPE
  STAGE I                 3               88
  STAGE IA                0                1
  STAGE II                0               32
  STAGE IIA               2              136
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               1               23
  STAGE IIIA              1               10
  STAGE IIIB              0               59
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               1               17
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  LRRC39 MUTATED     0   5   4   0
  LRRC39 WILD-TYPE  17  87 325  50
D188V5, multiclass
    clus
vv   LRRC39 MUTATED LRRC39 WILD-TYPE
  T1              0               17
  T2              5               87
  T3              4              325
  T4              0               50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  LRRC39 MUTATED     6   1   2
  LRRC39 WILD-TYPE 281 112  85
D188V6, multiclass
    clus
vv   LRRC39 MUTATED LRRC39 WILD-TYPE
  N0              6              281
  N1              1              112
  N2              2               85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D188V7, binary
                  cls
clus                 0   1
  LRRC39 MUTATED     7   1
  LRRC39 WILD-TYPE 368  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LRRC39 MUTATED      7    1
  LRRC39 WILD-TYPE  368   64
   clus
vv  LRRC39 MUTATED LRRC39 WILD-TYPE
  0              7              368
  1              1               64
[1] 2 2
[1] FALSE
D188V8, binary
                  cls
clus                 0   1
  LRRC39 MUTATED     2   7
  LRRC39 WILD-TYPE 223 257
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LRRC39 MUTATED      2    7
  LRRC39 WILD-TYPE  223  257
        clus
vv       LRRC39 MUTATED LRRC39 WILD-TYPE
  FEMALE              2              223
  MALE                7              257
[1] 2 2
[1] FALSE
D188V9, binary
                  cls
clus                 0   1
  LRRC39 MUTATED     8   0
  LRRC39 WILD-TYPE 342  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LRRC39 MUTATED      8    0
  LRRC39 WILD-TYPE  342   22
     clus
vv    LRRC39 MUTATED LRRC39 WILD-TYPE
  NO               8              342
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  LRRC39 MUTATED                      6                             2
  LRRC39 WILD-TYPE                  309                            45
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  LRRC39 MUTATED                       1                              0
  LRRC39 WILD-TYPE                   105                             10
D188V10, multiclass
                                clus
vv                               LRRC39 MUTATED LRRC39 WILD-TYPE
  COLON ADENOCARCINOMA                        6              309
  COLON MUCINOUS ADENOCARCINOMA               2               45
  RECTAL ADENOCARCINOMA                       1              105
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  LRRC39 MUTATED     6   0   0   1
  LRRC39 WILD-TYPE 339   4  31  24
D188V11, multiclass
    clus
vv   LRRC39 MUTATED LRRC39 WILD-TYPE
  R0              6              339
  R1              0                4
  R2              0               31
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D188V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  LRRC39 MUTATED                                  0     1
  LRRC39 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  LRRC39 MUTATED                           0     6
  LRRC39 WILD-TYPE                        22   220
D188V13, multiclass
                                  clus
vv                                 LRRC39 MUTATED LRRC39 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         6              220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(189) Variable = ST8SIA6 MUTATION ANALYSIS
D189V1, survival
                   sevent
clus2                 0   1
  ST8SIA6 MUTATED    10   3
  ST8SIA6 WILD-TYPE 368  90
  ST8SIA6 MUTATED ST8SIA6 WILD-TYPE 
               13               458 
  ST8SIA6 MUTATED ST8SIA6 WILD-TYPE 
                3                90 
$`ST8SIA6 MUTATED`
TCGA-AA-3492 TCGA-AA-A00E TCGA-AA-A010 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4315 
        3.02        30.02        34.98         0.72        10.88        58.39 
TCGA-CA-6717 TCGA-CK-5913 TCGA-CK-6751 TCGA-AF-6136 TCGA-AG-A002 TCGA-DC-5869 
       12.76        51.32       124.27        15.39        20.98         5.03 
TCGA-DY-A1DC 
       41.36 

$`ST8SIA6 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       38.04        19.00        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
        0.79         5.79        22.42        27.42         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07        12.20        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 
      148.01        85.45        15.62        49.08         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
       82.95         1.91        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-6155 
        6.97         4.73        78.12         7.17        15.02        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
        5.29       126.44        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  ST8SIA6 MUTATED ST8SIA6 WILD-TYPE 
             0.72              0.00 
  ST8SIA6 MUTATED ST8SIA6 WILD-TYPE 
           124.27            148.01 
  ST8SIA6 MUTATED ST8SIA6 WILD-TYPE 
           20.980            20.155 
[1] "0.7 - 124.3 (21.0)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1"  
D189V2, continuous
D189V3, binary
                   cls
clus                  0   1
  ST8SIA6 MUTATED    10   4
  ST8SIA6 WILD-TYPE 356 115
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ST8SIA6 MUTATED     10    4
  ST8SIA6 WILD-TYPE  356  115
        clus
vv       ST8SIA6 MUTATED ST8SIA6 WILD-TYPE
  COLON               10               356
  RECTUM               4               115
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ST8SIA6 MUTATED         2        0        1         5         2         0
  ST8SIA6 WILD-TYPE      89        1       31       133         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ST8SIA6 MUTATED           0          0          2          0        0
  ST8SIA6 WILD-TYPE        24         11         57         42       48
                   vv
clus                STAGE IVA STAGE IVB
  ST8SIA6 MUTATED           0         0
  ST8SIA6 WILD-TYPE        18         1
D189V4, multiclass
            clus
vv           ST8SIA6 MUTATED ST8SIA6 WILD-TYPE
  STAGE I                  2                89
  STAGE IA                 0                 1
  STAGE II                 1                31
  STAGE IIA                5               133
  STAGE IIB                2                 8
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               0                11
  STAGE IIIB               2                57
  STAGE IIIC               0                42
  STAGE IV                 0                48
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  ST8SIA6 MUTATED     0   2   9   3
  ST8SIA6 WILD-TYPE  17  90 320  47
D189V5, multiclass
    clus
vv   ST8SIA6 MUTATED ST8SIA6 WILD-TYPE
  T1               0                17
  T2               2                90
  T3               9               320
  T4               3                47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  ST8SIA6 MUTATED    10   3   1
  ST8SIA6 WILD-TYPE 277 110  86
D189V6, multiclass
    clus
vv   ST8SIA6 MUTATED ST8SIA6 WILD-TYPE
  N0              10               277
  N1               3               110
  N2               1                86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D189V7, binary
                   cls
clus                  0   1
  ST8SIA6 MUTATED     8   0
  ST8SIA6 WILD-TYPE 367  65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ST8SIA6 MUTATED      8    0
  ST8SIA6 WILD-TYPE  367   65
   clus
vv  ST8SIA6 MUTATED ST8SIA6 WILD-TYPE
  0               8               367
  1               0                65
[1] 2 2
[1] FALSE
D189V8, binary
                   cls
clus                  0   1
  ST8SIA6 MUTATED     8   6
  ST8SIA6 WILD-TYPE 217 258
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ST8SIA6 MUTATED      8    6
  ST8SIA6 WILD-TYPE  217  258
        clus
vv       ST8SIA6 MUTATED ST8SIA6 WILD-TYPE
  FEMALE               8               217
  MALE                 6               258
[1] 2 2
[1] FALSE
D189V9, binary
                   cls
clus                  0   1
  ST8SIA6 MUTATED     9   1
  ST8SIA6 WILD-TYPE 341  21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ST8SIA6 MUTATED      9    1
  ST8SIA6 WILD-TYPE  341   21
     clus
vv    ST8SIA6 MUTATED ST8SIA6 WILD-TYPE
  NO                9               341
  YES               1                21
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ST8SIA6 MUTATED                      8                             2
  ST8SIA6 WILD-TYPE                  307                            45
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ST8SIA6 MUTATED                       4                              0
  ST8SIA6 WILD-TYPE                   102                             10
D189V10, multiclass
                                clus
vv                               ST8SIA6 MUTATED ST8SIA6 WILD-TYPE
  COLON ADENOCARCINOMA                         8               307
  COLON MUCINOUS ADENOCARCINOMA                2                45
  RECTAL ADENOCARCINOMA                        4               102
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  ST8SIA6 MUTATED     6   0   0   4
  ST8SIA6 WILD-TYPE 339   4  31  21
D189V11, multiclass
    clus
vv   ST8SIA6 MUTATED ST8SIA6 WILD-TYPE
  R0               6               339
  R1               0                 4
  R2               0                31
  RX               4                21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D189V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ST8SIA6 MUTATED                                  0     1
  ST8SIA6 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  ST8SIA6 MUTATED                           1     8
  ST8SIA6 WILD-TYPE                        21   218
D189V13, multiclass
                                  clus
vv                                 ST8SIA6 MUTATED ST8SIA6 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                10
  BLACK OR AFRICAN AMERICAN                      1                21
  WHITE                                          8               218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(190) Variable = CAB39L MUTATION ANALYSIS
D190V1, survival
                  sevent
clus2                0   1
  CAB39L MUTATED     9   1
  CAB39L WILD-TYPE 369  92
  CAB39L MUTATED CAB39L WILD-TYPE 
              10              461 
  CAB39L MUTATED CAB39L WILD-TYPE 
               1               92 
$`CAB39L MUTATED`
TCGA-A6-5661 TCGA-A6-6653 TCGA-A6-6780 TCGA-AA-A010 TCGA-AD-5900 TCGA-AY-6197 
       33.53        24.39        20.12        34.98         0.07        21.44 
TCGA-CK-5916 TCGA-F4-6856 TCGA-G4-6588 TCGA-AG-A002 
       21.14        35.31        26.17        20.98 

$`CAB39L WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6781 
       25.18        24.16        21.76        24.69        23.87        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
       40.96        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4315 
       27.09        16.31         0.95        33.01        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
        9.99        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 
       16.24        33.67        13.25         0.53        47.41       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  CAB39L MUTATED CAB39L WILD-TYPE 
            0.07             0.00 
  CAB39L MUTATED CAB39L WILD-TYPE 
           35.31           148.01 
  CAB39L MUTATED CAB39L WILD-TYPE 
          22.915           20.020 
[1] "0.1 - 35.3 (22.9)"  "0.0 - 148.0 (20.0)"
[1] "hr=" "1.6"
D190V2, continuous
D190V3, binary
                  cls
clus                 0   1
  CAB39L MUTATED     9   1
  CAB39L WILD-TYPE 357 118
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CAB39L MUTATED      9    1
  CAB39L WILD-TYPE  357  118
        clus
vv       CAB39L MUTATED CAB39L WILD-TYPE
  COLON               9              357
  RECTUM              1              118
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CAB39L MUTATED         5        0        0         4         1         0
  CAB39L WILD-TYPE      86        1       32       134         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CAB39L MUTATED           0          0          0          0        0
  CAB39L WILD-TYPE        24         11         59         42       48
                  vv
clus               STAGE IVA STAGE IVB
  CAB39L MUTATED           0         0
  CAB39L WILD-TYPE        18         1
D190V4, multiclass
            clus
vv           CAB39L MUTATED CAB39L WILD-TYPE
  STAGE I                 5               86
  STAGE IA                0                1
  STAGE II                0               32
  STAGE IIA               4              134
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              0               59
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  CAB39L MUTATED     1   4   4   1
  CAB39L WILD-TYPE  16  88 325  49
D190V5, multiclass
    clus
vv   CAB39L MUTATED CAB39L WILD-TYPE
  T1              1               16
  T2              4               88
  T3              4              325
  T4              1               49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  CAB39L MUTATED    10   0   0
  CAB39L WILD-TYPE 277 113  87
D190V6, multiclass
    clus
vv   CAB39L MUTATED CAB39L WILD-TYPE
  N0             10              277
  N1              0              113
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D190V7, binary
                  cls
clus                 0   1
  CAB39L MUTATED     7   0
  CAB39L WILD-TYPE 368  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CAB39L MUTATED      7    0
  CAB39L WILD-TYPE  368   65
   clus
vv  CAB39L MUTATED CAB39L WILD-TYPE
  0              7              368
  1              0               65
[1] 2 2
[1] FALSE
D190V8, binary
                  cls
clus                 0   1
  CAB39L MUTATED     4   6
  CAB39L WILD-TYPE 221 258
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CAB39L MUTATED      4    6
  CAB39L WILD-TYPE  221  258
        clus
vv       CAB39L MUTATED CAB39L WILD-TYPE
  FEMALE              4              221
  MALE                6              258
[1] 2 2
[1] FALSE
D190V9, binary
                  cls
clus                 0   1
  CAB39L MUTATED     9   0
  CAB39L WILD-TYPE 341  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CAB39L MUTATED      9    0
  CAB39L WILD-TYPE  341   22
     clus
vv    CAB39L MUTATED CAB39L WILD-TYPE
  NO               9              341
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CAB39L MUTATED                      6                             3
  CAB39L WILD-TYPE                  309                            44
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CAB39L MUTATED                       1                              0
  CAB39L WILD-TYPE                   105                             10
D190V10, multiclass
                                clus
vv                               CAB39L MUTATED CAB39L WILD-TYPE
  COLON ADENOCARCINOMA                        6              309
  COLON MUCINOUS ADENOCARCINOMA               3               44
  RECTAL ADENOCARCINOMA                       1              105
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  CAB39L MUTATED     7   0   0   1
  CAB39L WILD-TYPE 338   4  31  24
D190V11, multiclass
    clus
vv   CAB39L MUTATED CAB39L WILD-TYPE
  R0              7              338
  R1              0                4
  R2              0               31
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D190V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CAB39L MUTATED                                  0     0
  CAB39L WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  CAB39L MUTATED                           1     7
  CAB39L WILD-TYPE                        21   219
D190V13, multiclass
                                  clus
vv                                 CAB39L MUTATED CAB39L WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                         7              219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(191) Variable = ERBB4 MUTATION ANALYSIS
D191V1, survival
                 sevent
clus2               0   1
  ERBB4 MUTATED    43  13
  ERBB4 WILD-TYPE 335  80
  ERBB4 MUTATED ERBB4 WILD-TYPE 
             56             415 
  ERBB4 MUTATED ERBB4 WILD-TYPE 
             13              80 
$`ERBB4 MUTATED`
TCGA-A6-2672 TCGA-A6-5659 TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6649 TCGA-AA-3510 
       46.65        30.44        22.06        27.09        24.16        63.98 
TCGA-AA-3713 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3850 TCGA-AA-3861 TCGA-AA-3864 
       19.04        33.04         0.99         0.00        30.05        53.00 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3947 TCGA-AA-3966 TCGA-AA-3982 TCGA-AA-A00N 
       29.98        18.05        33.01         2.01        27.02         4.01 
TCGA-AA-A010 TCGA-AA-A01Q TCGA-AD-6895 TCGA-AD-6899 TCGA-AY-4071 TCGA-AZ-4616 
       34.98         1.02         0.72         5.79         0.95         5.13 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CA-6717 TCGA-CK-4948 TCGA-CM-4743 TCGA-CM-5861 
      100.01         1.61        12.76       148.01        23.05        15.02 
TCGA-CM-6163 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6170 TCGA-CM-6172 TCGA-D5-5538 
        2.96        14.99        12.99        15.02        11.01        12.26 
TCGA-D5-5540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6928 TCGA-D5-6932 TCGA-DM-A1DA 
       56.09        15.58         1.48        11.64        11.38         7.50 
TCGA-DM-A1DB TCGA-DM-A285 TCGA-DM-A28H TCGA-F4-6459 TCGA-F4-6703 TCGA-G4-6588 
       44.32         6.12       117.07         8.61        47.87        26.17 
TCGA-AF-4110 TCGA-AG-3581 TCGA-AG-3599 TCGA-AG-A002 TCGA-AG-A02N TCGA-AH-6544 
       14.50         7.07        12.03        20.98        61.97        38.56 
TCGA-DY-A1DG TCGA-EI-6510 
       51.48        18.28 

$`ERBB4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 
       31.63        29.19        33.53        23.61        22.09        32.71 
TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 
       22.52         8.38        25.08        25.18        21.76        24.69 
TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 
       24.39        23.87        20.12        19.66        20.28         7.04 
TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        3.02         1.02        35.01         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       10.06        35.05        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3877 TCGA-AA-3930 
       31.07        17.03        24.03        27.02        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       12.99        24.00        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
       34.03        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3986 TCGA-AA-3989 
       26.01        25.02        24.00        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01R TCGA-AA-A01S 
       12.00        31.00        31.00        38.07        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
       56.55         0.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       14.50        27.09        16.31        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
       58.39         1.41       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       49.41         6.77        12.10        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        3.19        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4952 
       12.20        10.06        14.30        17.56        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
      124.27        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 
       22.03        22.98        30.08        32.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6164 TCGA-CM-6165 
       15.02        17.03        15.02        12.00        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6169 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       21.99        13.02        14.04        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5539 
       11.08        11.01        10.06        12.03        45.40        19.59 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6920 
       17.85         4.80        17.13        12.49        16.14         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 
        4.41        12.43        14.30         9.04         9.44         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
        1.51        12.00        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      131.51       135.65       139.17        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28K TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6704 
       60.79        98.24        31.96        35.74         6.18         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       22.09        13.78        35.80        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       10.39        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       12.00        32.02         8.02        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3600 
        1.02        46.03        34.03         2.01        50.04         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6547 
        1.94        38.96        41.00        38.04       117.11         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1H8 
        5.29       126.44        41.36        57.24        24.13        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-F5-6464 TCGA-F5-6465 
        0.49        20.55        19.96        20.91         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  ERBB4 MUTATED ERBB4 WILD-TYPE 
              0               0 
  ERBB4 MUTATED ERBB4 WILD-TYPE 
         148.01          140.38 
  ERBB4 MUTATED ERBB4 WILD-TYPE 
         16.815          20.910 
[1] "0.0 - 148.0 (16.8)" "0.0 - 140.4 (20.9)"
[1] "hr=" "1.2"
D191V2, continuous
D191V3, binary
                 cls
clus                0   1
  ERBB4 MUTATED    50   7
  ERBB4 WILD-TYPE 316 112
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERBB4 MUTATED     50    7
  ERBB4 WILD-TYPE  316  112
        clus
vv       ERBB4 MUTATED ERBB4 WILD-TYPE
  COLON             50             316
  RECTUM             7             112
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ERBB4 MUTATED        10        0        5        18         4         0
  ERBB4 WILD-TYPE      81        1       27       120         6         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ERBB4 MUTATED           1          1          7          4        4         3
  ERBB4 WILD-TYPE        23         10         52         38       44        15
                 vv
clus              STAGE IVB
  ERBB4 MUTATED           0
  ERBB4 WILD-TYPE         1
D191V4, multiclass
            clus
vv           ERBB4 MUTATED ERBB4 WILD-TYPE
  STAGE I               10              81
  STAGE IA               0               1
  STAGE II               5              27
  STAGE IIA             18             120
  STAGE IIB              4               6
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             1              10
  STAGE IIIB             7              52
  STAGE IIIC             4              38
  STAGE IV               4              44
  STAGE IVA              3              15
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ERBB4 MUTATED     3   9  41   6
  ERBB4 WILD-TYPE  14  83 288  44
D191V5, multiclass
    clus
vv   ERBB4 MUTATED ERBB4 WILD-TYPE
  T1             3              14
  T2             9              83
  T3            41             288
  T4             6              44
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  ERBB4 MUTATED    39  11   9
  ERBB4 WILD-TYPE 248 102  78
D191V6, multiclass
    clus
vv   ERBB4 MUTATED ERBB4 WILD-TYPE
  N0            39             248
  N1            11             102
  N2             9              78
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D191V7, binary
                 cls
clus                0   1
  ERBB4 MUTATED    47   6
  ERBB4 WILD-TYPE 328  59
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERBB4 MUTATED     47    6
  ERBB4 WILD-TYPE  328   59
   clus
vv  ERBB4 MUTATED ERBB4 WILD-TYPE
  0            47             328
  1             6              59
[1] 2 2
[1] FALSE
D191V8, binary
                 cls
clus                0   1
  ERBB4 MUTATED    29  30
  ERBB4 WILD-TYPE 196 234
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERBB4 MUTATED     29   30
  ERBB4 WILD-TYPE  196  234
        clus
vv       ERBB4 MUTATED ERBB4 WILD-TYPE
  FEMALE            29             196
  MALE              30             234
[1] 2 2
[1] FALSE
D191V9, binary
                 cls
clus                0   1
  ERBB4 MUTATED    41   1
  ERBB4 WILD-TYPE 309  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERBB4 MUTATED     41    1
  ERBB4 WILD-TYPE  309   21
     clus
vv    ERBB4 MUTATED ERBB4 WILD-TYPE
  NO             41             309
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ERBB4 MUTATED                     43                             7
  ERBB4 WILD-TYPE                  272                            40
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ERBB4 MUTATED                       6                              0
  ERBB4 WILD-TYPE                   100                             10
D191V10, multiclass
                                clus
vv                               ERBB4 MUTATED ERBB4 WILD-TYPE
  COLON ADENOCARCINOMA                      43             272
  COLON MUCINOUS ADENOCARCINOMA              7              40
  RECTAL ADENOCARCINOMA                      6             100
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  ERBB4 MUTATED    41   0   1   2
  ERBB4 WILD-TYPE 304   4  30  23
D191V11, multiclass
    clus
vv   ERBB4 MUTATED ERBB4 WILD-TYPE
  R0            41             304
  R1             0               4
  R2             1              30
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D191V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ERBB4 MUTATED                                  0     1
  ERBB4 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ERBB4 MUTATED                           2    35
  ERBB4 WILD-TYPE                        20   191
D191V13, multiclass
                                  clus
vv                                 ERBB4 MUTATED ERBB4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    2              20
  WHITE                                       35             191
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(192) Variable = UGT3A2 MUTATION ANALYSIS
D192V1, survival
                  sevent
clus2                0   1
  UGT3A2 MUTATED    19   3
  UGT3A2 WILD-TYPE 359  90
  UGT3A2 MUTATED UGT3A2 WILD-TYPE 
              22              449 
  UGT3A2 MUTATED UGT3A2 WILD-TYPE 
               3               90 
$`UGT3A2 MUTATED`
TCGA-A6-5661 TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3555 TCGA-AA-3977 TCGA-AA-3982 
       33.53         3.02        63.98        29.95        25.02        27.02 
TCGA-AA-A010 TCGA-AZ-6601 TCGA-CA-6717 TCGA-CK-5913 TCGA-CK-5916 TCGA-CM-4743 
       34.98       100.01        12.76        51.32        21.14        23.05 
TCGA-CM-6674 TCGA-D5-6533 TCGA-D5-6536 TCGA-D5-6920 TCGA-G4-6307 TCGA-G4-6586 
       12.95         1.32        17.85         3.68        55.04        35.80 
TCGA-AG-3732 TCGA-AG-3885 TCGA-AG-A002 TCGA-DT-5265 
       32.98        17.95        20.98         5.29 

$`UGT3A2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 
       20.12        19.66        20.28         7.04         1.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       17.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       26.01        24.00        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77        12.10        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.20        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       15.62        49.08         9.99        82.95         1.91       124.27 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       14.04        11.01        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 
       55.92        20.19        18.25        43.27        15.12         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6922 
       17.13        12.49        16.14        15.58         1.48         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       53.62        44.68        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       22.09        13.78        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 
       13.94        19.99         7.99         0.99        37.02         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 
        0.99        19.04        19.99         1.02        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        5.95         4.01         5.03       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  UGT3A2 MUTATED UGT3A2 WILD-TYPE 
            1.32             0.00 
  UGT3A2 MUTATED UGT3A2 WILD-TYPE 
          100.01           148.01 
  UGT3A2 MUTATED UGT3A2 WILD-TYPE 
          24.035           20.020 
[1] "1.3 - 100.0 (24.0)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.6"
D192V2, continuous
D192V3, binary
                  cls
clus                 0   1
  UGT3A2 MUTATED    18   4
  UGT3A2 WILD-TYPE 348 115
[1] "tbl2"
                  cls
clus               [,1] [,2]
  UGT3A2 MUTATED     18    4
  UGT3A2 WILD-TYPE  348  115
        clus
vv       UGT3A2 MUTATED UGT3A2 WILD-TYPE
  COLON              18              348
  RECTUM              4              115
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  UGT3A2 MUTATED         3        0        4         9         1         0
  UGT3A2 WILD-TYPE      88        1       28       129         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  UGT3A2 MUTATED           0          0          4          0        0
  UGT3A2 WILD-TYPE        24         11         55         42       48
                  vv
clus               STAGE IVA STAGE IVB
  UGT3A2 MUTATED           0         0
  UGT3A2 WILD-TYPE        18         1
D192V4, multiclass
            clus
vv           UGT3A2 MUTATED UGT3A2 WILD-TYPE
  STAGE I                 3               88
  STAGE IA                0                1
  STAGE II                4               28
  STAGE IIA               9              129
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              4               55
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  UGT3A2 MUTATED     1   3  16   2
  UGT3A2 WILD-TYPE  16  89 313  48
D192V5, multiclass
    clus
vv   UGT3A2 MUTATED UGT3A2 WILD-TYPE
  T1              1               16
  T2              3               89
  T3             16              313
  T4              2               48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  UGT3A2 MUTATED    19   3   0
  UGT3A2 WILD-TYPE 268 110  87
D192V6, multiclass
    clus
vv   UGT3A2 MUTATED UGT3A2 WILD-TYPE
  N0             19              268
  N1              3              110
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D192V7, binary
                  cls
clus                 0   1
  UGT3A2 MUTATED    20   0
  UGT3A2 WILD-TYPE 355  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  UGT3A2 MUTATED     20    0
  UGT3A2 WILD-TYPE  355   65
   clus
vv  UGT3A2 MUTATED UGT3A2 WILD-TYPE
  0             20              355
  1              0               65
[1] 2 2
[1] FALSE
D192V8, binary
                  cls
clus                 0   1
  UGT3A2 MUTATED    12  10
  UGT3A2 WILD-TYPE 213 254
[1] "tbl2"
                  cls
clus               [,1] [,2]
  UGT3A2 MUTATED     12   10
  UGT3A2 WILD-TYPE  213  254
        clus
vv       UGT3A2 MUTATED UGT3A2 WILD-TYPE
  FEMALE             12              213
  MALE               10              254
[1] 2 2
[1] FALSE
D192V9, binary
                  cls
clus                 0   1
  UGT3A2 MUTATED    19   1
  UGT3A2 WILD-TYPE 331  21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  UGT3A2 MUTATED     19    1
  UGT3A2 WILD-TYPE  331   21
     clus
vv    UGT3A2 MUTATED UGT3A2 WILD-TYPE
  NO              19              331
  YES              1               21
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  UGT3A2 MUTATED                     16                             2
  UGT3A2 WILD-TYPE                  299                            45
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  UGT3A2 MUTATED                       3                              1
  UGT3A2 WILD-TYPE                   103                              9
D192V10, multiclass
                                clus
vv                               UGT3A2 MUTATED UGT3A2 WILD-TYPE
  COLON ADENOCARCINOMA                       16              299
  COLON MUCINOUS ADENOCARCINOMA               2               45
  RECTAL ADENOCARCINOMA                       3              103
  RECTAL MUCINOUS ADENOCARCINOMA              1                9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  UGT3A2 MUTATED    15   0   0   4
  UGT3A2 WILD-TYPE 330   4  31  21
D192V11, multiclass
    clus
vv   UGT3A2 MUTATED UGT3A2 WILD-TYPE
  R0             15              330
  R1              0                4
  R2              0               31
  RX              4               21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D192V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  UGT3A2 MUTATED                                  0     2
  UGT3A2 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  UGT3A2 MUTATED                           1    10
  UGT3A2 WILD-TYPE                        21   216
D192V13, multiclass
                                  clus
vv                                 UGT3A2 MUTATED UGT3A2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                9
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                        10              216
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(193) Variable = ARHGAP5 MUTATION ANALYSIS
D193V1, survival
                   sevent
clus2                 0   1
  ARHGAP5 MUTATED    17   6
  ARHGAP5 WILD-TYPE 361  87
  ARHGAP5 MUTATED ARHGAP5 WILD-TYPE 
               23               448 
  ARHGAP5 MUTATED ARHGAP5 WILD-TYPE 
                6                87 
$`ARHGAP5 MUTATED`
TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3555 TCGA-AA-3821 TCGA-AA-3845 TCGA-AA-3973 
        3.02        63.98        29.95         1.02         0.00        13.05 
TCGA-AA-A01R TCGA-AD-6889 TCGA-AD-6899 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-5913 
       35.01        56.55         5.79        12.76        10.06        51.32 
TCGA-CM-5860 TCGA-CM-6678 TCGA-D5-6540 TCGA-D5-6930 TCGA-DM-A1HB TCGA-F4-6570 
       32.02        11.01        16.14         1.51       135.65         6.18 
TCGA-G4-6628 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-A002 TCGA-DY-A1DG 
       79.69        36.95        13.02        20.98        51.48 

$`ARHGAP5 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       24.00        17.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
       33.04         0.99        25.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02        14.93        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       21.99        16.08        50.99        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
       15.52         0.79         0.72        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       22.98        30.08        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6679 
       11.01        12.95        13.05        11.08        11.08        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
        4.80        17.13        12.49        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        4.80        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 
      140.38         7.50        44.32       131.51       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
        8.61        31.96        35.74        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 
       13.78        35.80        26.17        91.79        46.75        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3890 
        0.99        19.04        19.99         1.02        17.95        17.03 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       24.13        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  ARHGAP5 MUTATED ARHGAP5 WILD-TYPE 
                0                 0 
  ARHGAP5 MUTATED ARHGAP5 WILD-TYPE 
           135.65            148.01 
  ARHGAP5 MUTATED ARHGAP5 WILD-TYPE 
           16.140            20.235 
[1] "0.0 - 135.7 (16.1)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.2"
D193V2, continuous
D193V3, binary
                   cls
clus                  0   1
  ARHGAP5 MUTATED    19   4
  ARHGAP5 WILD-TYPE 347 115
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ARHGAP5 MUTATED     19    4
  ARHGAP5 WILD-TYPE  347  115
        clus
vv       ARHGAP5 MUTATED ARHGAP5 WILD-TYPE
  COLON               19               347
  RECTUM               4               115
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ARHGAP5 MUTATED         5        0        2        10         0         0
  ARHGAP5 WILD-TYPE      86        1       30       128        10         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ARHGAP5 MUTATED           1          0          1          1        1
  ARHGAP5 WILD-TYPE        23         11         58         41       47
                   vv
clus                STAGE IVA STAGE IVB
  ARHGAP5 MUTATED           2         0
  ARHGAP5 WILD-TYPE        16         1
D193V4, multiclass
            clus
vv           ARHGAP5 MUTATED ARHGAP5 WILD-TYPE
  STAGE I                  5                86
  STAGE IA                 0                 1
  STAGE II                 2                30
  STAGE IIA               10               128
  STAGE IIB                0                10
  STAGE IIC                0                 1
  STAGE III                1                23
  STAGE IIIA               0                11
  STAGE IIIB               1                58
  STAGE IIIC               1                41
  STAGE IV                 1                47
  STAGE IVA                2                16
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  ARHGAP5 MUTATED     1   4  15   3
  ARHGAP5 WILD-TYPE  16  88 314  47
D193V5, multiclass
    clus
vv   ARHGAP5 MUTATED ARHGAP5 WILD-TYPE
  T1               1                16
  T2               4                88
  T3              15               314
  T4               3                47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  ARHGAP5 MUTATED    17   4   2
  ARHGAP5 WILD-TYPE 270 109  85
D193V6, multiclass
    clus
vv   ARHGAP5 MUTATED ARHGAP5 WILD-TYPE
  N0              17               270
  N1               4               109
  N2               2                85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D193V7, binary
                   cls
clus                  0   1
  ARHGAP5 MUTATED    18   3
  ARHGAP5 WILD-TYPE 357  62
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ARHGAP5 MUTATED     18    3
  ARHGAP5 WILD-TYPE  357   62
   clus
vv  ARHGAP5 MUTATED ARHGAP5 WILD-TYPE
  0              18               357
  1               3                62
[1] 2 2
[1] FALSE
D193V8, binary
                   cls
clus                  0   1
  ARHGAP5 MUTATED     8  15
  ARHGAP5 WILD-TYPE 217 249
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ARHGAP5 MUTATED      8   15
  ARHGAP5 WILD-TYPE  217  249
        clus
vv       ARHGAP5 MUTATED ARHGAP5 WILD-TYPE
  FEMALE               8               217
  MALE                15               249
[1] 2 2
[1] FALSE
D193V9, binary
                   cls
clus                  0   1
  ARHGAP5 MUTATED    16   2
  ARHGAP5 WILD-TYPE 334  20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ARHGAP5 MUTATED     16    2
  ARHGAP5 WILD-TYPE  334   20
     clus
vv    ARHGAP5 MUTATED ARHGAP5 WILD-TYPE
  NO               16               334
  YES               2                20
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ARHGAP5 MUTATED                     11                             7
  ARHGAP5 WILD-TYPE                  304                            40
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ARHGAP5 MUTATED                       3                              1
  ARHGAP5 WILD-TYPE                   103                              9
D193V10, multiclass
                                clus
vv                               ARHGAP5 MUTATED ARHGAP5 WILD-TYPE
  COLON ADENOCARCINOMA                        11               304
  COLON MUCINOUS ADENOCARCINOMA                7                40
  RECTAL ADENOCARCINOMA                        3               103
  RECTAL MUCINOUS ADENOCARCINOMA               1                 9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  ARHGAP5 MUTATED    15   0   1   3
  ARHGAP5 WILD-TYPE 330   4  30  22
D193V11, multiclass
    clus
vv   ARHGAP5 MUTATED ARHGAP5 WILD-TYPE
  R0              15               330
  R1               0                 4
  R2               1                30
  RX               3                22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D193V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ARHGAP5 MUTATED                                  0     3
  ARHGAP5 WILD-TYPE                                1     8
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  ARHGAP5 MUTATED                           0    10
  ARHGAP5 WILD-TYPE                        22   216
D193V13, multiclass
                                  clus
vv                                 ARHGAP5 MUTATED ARHGAP5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          3                 8
  BLACK OR AFRICAN AMERICAN                      0                22
  WHITE                                         10               216
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(194) Variable = EP400 MUTATION ANALYSIS
D194V1, survival
                 sevent
clus2               0   1
  EP400 MUTATED    30   8
  EP400 WILD-TYPE 348  85
  EP400 MUTATED EP400 WILD-TYPE 
             38             433 
  EP400 MUTATED EP400 WILD-TYPE 
              8              85 
$`EP400 MUTATED`
TCGA-A6-2672 TCGA-A6-5661 TCGA-AA-3492 TCGA-AA-3511 TCGA-AA-3555 TCGA-AA-3663 
       46.65        33.53         3.02         6.97        29.95         6.97 
TCGA-AA-3672 TCGA-AA-3713 TCGA-AA-3850 TCGA-AA-3864 TCGA-AA-3977 TCGA-AA-A00E 
        0.92        19.04         0.00        53.00        25.02        30.02 
TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01Q TCGA-AA-A01R TCGA-AD-6888 TCGA-AY-6386 
        4.01        34.98         1.02        35.01        15.52        17.82 
TCGA-AZ-6598 TCGA-CK-4952 TCGA-CK-5913 TCGA-CM-4744 TCGA-CM-4752 TCGA-CM-5341 
       49.41        15.62        51.32        20.02        13.02        29.06 
TCGA-CM-5348 TCGA-CM-5349 TCGA-D5-6532 TCGA-D5-6540 TCGA-D5-6898 TCGA-D5-7000 
       22.98        30.08        18.25        16.14         1.48        10.26 
TCGA-DM-A1D8 TCGA-DM-A1DB TCGA-F4-6809 TCGA-G4-6588 TCGA-AF-4110 TCGA-AG-3599 
       12.59        44.32        13.25        26.17        14.50        12.03 
TCGA-AG-A015 TCGA-F5-6465 
       36.03        49.51 

$`EP400 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       31.63        30.44        29.19        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       19.66        20.28         7.04         1.02        35.01        63.98 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
       78.08         6.05        54.02         2.01        14.01        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
       10.06        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        31.07        30.05        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00J 
       27.02        13.94        38.04        19.00        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       31.00        31.00        38.07         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
       40.96         0.07        21.37        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AZ-4315 
       27.09        16.31         0.95        33.01        21.44        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
      148.01        85.45        49.08         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-5344 
        1.91       124.27        23.05        37.02        25.02        22.03 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       20.19         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       17.13        12.49        15.58         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       12.00        11.38       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HA 
       92.75        49.91        13.32       140.38         7.50       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       33.67         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 
       61.91        36.00        22.09        13.78        35.80        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       19.10        34.49        10.39        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
        2.01        50.04         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       23.01        37.02        15.95         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  EP400 MUTATED EP400 WILD-TYPE 
              0               0 
  EP400 MUTATED EP400 WILD-TYPE 
          53.00          148.01 
  EP400 MUTATED EP400 WILD-TYPE 
         18.645          20.550 
[1] "0.0 - 53.0 (18.6)"  "0.0 - 148.0 (20.6)"
[1] "hr=" "1.2"
D194V2, continuous
D194V3, binary
                 cls
clus                0   1
  EP400 MUTATED    36   3
  EP400 WILD-TYPE 330 116
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EP400 MUTATED     36    3
  EP400 WILD-TYPE  330  116
        clus
vv       EP400 MUTATED EP400 WILD-TYPE
  COLON             36             330
  RECTUM             3             116
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  EP400 MUTATED         7        0        6        11         3         0
  EP400 WILD-TYPE      84        1       26       127         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  EP400 MUTATED           2          1          4          1        1         2
  EP400 WILD-TYPE        22         10         55         41       47        16
                 vv
clus              STAGE IVB
  EP400 MUTATED           0
  EP400 WILD-TYPE         1
D194V4, multiclass
            clus
vv           EP400 MUTATED EP400 WILD-TYPE
  STAGE I                7              84
  STAGE IA               0               1
  STAGE II               6              26
  STAGE IIA             11             127
  STAGE IIB              3               7
  STAGE IIC              0               1
  STAGE III              2              22
  STAGE IIIA             1              10
  STAGE IIIB             4              55
  STAGE IIIC             1              41
  STAGE IV               1              47
  STAGE IVA              2              16
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  EP400 MUTATED     1   8  25   6
  EP400 WILD-TYPE  16  84 304  44
D194V5, multiclass
    clus
vv   EP400 MUTATED EP400 WILD-TYPE
  T1             1              16
  T2             8              84
  T3            25             304
  T4             6              44
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  EP400 MUTATED    29   8   3
  EP400 WILD-TYPE 258 105  84
D194V6, multiclass
    clus
vv   EP400 MUTATED EP400 WILD-TYPE
  N0            29             258
  N1             8             105
  N2             3              84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D194V7, binary
                 cls
clus                0   1
  EP400 MUTATED    32   2
  EP400 WILD-TYPE 343  63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EP400 MUTATED     32    2
  EP400 WILD-TYPE  343   63
   clus
vv  EP400 MUTATED EP400 WILD-TYPE
  0            32             343
  1             2              63
[1] 2 2
[1] FALSE
D194V8, binary
                 cls
clus                0   1
  EP400 MUTATED    22  18
  EP400 WILD-TYPE 203 246
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EP400 MUTATED     22   18
  EP400 WILD-TYPE  203  246
        clus
vv       EP400 MUTATED EP400 WILD-TYPE
  FEMALE            22             203
  MALE              18             246
[1] 2 2
[1] FALSE
D194V9, binary
                 cls
clus                0   1
  EP400 MUTATED    29   2
  EP400 WILD-TYPE 321  20
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EP400 MUTATED     29    2
  EP400 WILD-TYPE  321   20
     clus
vv    EP400 MUTATED EP400 WILD-TYPE
  NO             29             321
  YES             2              20
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  EP400 MUTATED                     30                             6
  EP400 WILD-TYPE                  285                            41
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  EP400 MUTATED                       2                              0
  EP400 WILD-TYPE                   104                             10
D194V10, multiclass
                                clus
vv                               EP400 MUTATED EP400 WILD-TYPE
  COLON ADENOCARCINOMA                      30             285
  COLON MUCINOUS ADENOCARCINOMA              6              41
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  EP400 MUTATED    32   0   1   3
  EP400 WILD-TYPE 313   4  30  22
D194V11, multiclass
    clus
vv   EP400 MUTATED EP400 WILD-TYPE
  R0            32             313
  R1             0               4
  R2             1              30
  RX             3              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D194V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  EP400 MUTATED                                  0     0
  EP400 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  EP400 MUTATED                           3    20
  EP400 WILD-TYPE                        19   206
D194V13, multiclass
                                  clus
vv                                 EP400 MUTATED EP400 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    3              19
  WHITE                                       20             206
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(195) Variable = MEN1 MUTATION ANALYSIS
D195V1, survival
                sevent
clus2              0   1
  MEN1 MUTATED    17   9
  MEN1 WILD-TYPE 361  84
  MEN1 MUTATED MEN1 WILD-TYPE 
            26            445 
  MEN1 MUTATED MEN1 WILD-TYPE 
             9             84 
$`MEN1 MUTATED`
TCGA-A6-2676 TCGA-A6-4105 TCGA-A6-6137 TCGA-AA-3492 TCGA-AA-3662 TCGA-AY-5543 
       42.90        14.53        27.09         3.02         6.05        33.01 
TCGA-AZ-6598 TCGA-AZ-6601 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CM-6168 
       49.41       100.01       148.01        85.45        15.62        12.99 
TCGA-D5-5537 TCGA-D5-6533 TCGA-D5-6540 TCGA-D5-6922 TCGA-DM-A1D6 TCGA-F4-6460 
       45.40         1.32        16.14         4.41        49.91        31.96 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-AG-3731 
       35.31       133.18        22.09        35.80        26.17        37.02 
TCGA-DC-5337 TCGA-DY-A1DD 
       15.02        57.24 

$`MEN1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 
       34.65        33.34        32.75        36.53        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       30.44        29.19        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       32.71        22.52         8.38        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
       20.28         7.04         1.02        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       61.02        78.08         6.97        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       27.09        16.31         0.95        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77        12.10        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-5912 
       12.20        12.76        10.06        14.30        17.56        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6169 TCGA-CM-6170 
       29.03        16.04        21.99        14.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       11.01        10.06        12.03        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       55.92        20.19        18.25        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
        4.80        17.13        12.49        15.58         1.48         3.68 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
       38.20       130.65        92.75        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
        8.61        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6625 TCGA-G4-6626 
       63.62        61.91        36.00        13.78        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3732 
       19.99        13.94        19.99         7.99         0.99        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
        4.73        78.12         7.17         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
      126.44        41.36        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  MEN1 MUTATED MEN1 WILD-TYPE 
          1.32           0.00 
  MEN1 MUTATED MEN1 WILD-TYPE 
        148.01         140.38 
  MEN1 MUTATED MEN1 WILD-TYPE 
        32.485         20.020 
[1] "1.3 - 148.0 (32.5)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1.3"
D195V2, continuous
D195V3, binary
                cls
clus               0   1
  MEN1 MUTATED    24   3
  MEN1 WILD-TYPE 342 116
[1] "tbl2"
                cls
clus             [,1] [,2]
  MEN1 MUTATED     24    3
  MEN1 WILD-TYPE  342  116
        clus
vv       MEN1 MUTATED MEN1 WILD-TYPE
  COLON            24            342
  RECTUM            3            116
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MEN1 MUTATED         3        0        3         6         1         0
  MEN1 WILD-TYPE      88        1       29       132         9         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MEN1 MUTATED           4          1          5          1        2         1
  MEN1 WILD-TYPE        20         10         54         41       46        17
                vv
clus             STAGE IVB
  MEN1 MUTATED           0
  MEN1 WILD-TYPE         1
D195V4, multiclass
            clus
vv           MEN1 MUTATED MEN1 WILD-TYPE
  STAGE I               3             88
  STAGE IA              0              1
  STAGE II              3             29
  STAGE IIA             6            132
  STAGE IIB             1              9
  STAGE IIC             0              1
  STAGE III             4             20
  STAGE IIIA            1             10
  STAGE IIIB            5             54
  STAGE IIIC            1             41
  STAGE IV              2             46
  STAGE IVA             1             17
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  MEN1 MUTATED     1   3  19   4
  MEN1 WILD-TYPE  16  89 310  46
D195V5, multiclass
    clus
vv   MEN1 MUTATED MEN1 WILD-TYPE
  T1            1             16
  T2            3             89
  T3           19            310
  T4            4             46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  MEN1 MUTATED    13  10   4
  MEN1 WILD-TYPE 274 103  83
D195V6, multiclass
    clus
vv   MEN1 MUTATED MEN1 WILD-TYPE
  N0           13            274
  N1           10            103
  N2            4             83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D195V7, binary
                cls
clus               0   1
  MEN1 MUTATED    21   3
  MEN1 WILD-TYPE 354  62
[1] "tbl2"
                cls
clus             [,1] [,2]
  MEN1 MUTATED     21    3
  MEN1 WILD-TYPE  354   62
   clus
vv  MEN1 MUTATED MEN1 WILD-TYPE
  0           21            354
  1            3             62
[1] 2 2
[1] FALSE
D195V8, binary
                cls
clus               0   1
  MEN1 MUTATED    16  11
  MEN1 WILD-TYPE 209 253
[1] "tbl2"
                cls
clus             [,1] [,2]
  MEN1 MUTATED     16   11
  MEN1 WILD-TYPE  209  253
        clus
vv       MEN1 MUTATED MEN1 WILD-TYPE
  FEMALE           16            209
  MALE             11            253
[1] 2 2
[1] FALSE
D195V9, binary
                cls
clus               0   1
  MEN1 MUTATED    21   0
  MEN1 WILD-TYPE 329  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  MEN1 MUTATED     21    0
  MEN1 WILD-TYPE  329   22
     clus
vv    MEN1 MUTATED MEN1 WILD-TYPE
  NO            21            329
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MEN1 MUTATED                     20                             4
  MEN1 WILD-TYPE                  295                            43
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MEN1 MUTATED                       3                              0
  MEN1 WILD-TYPE                   103                             10
D195V10, multiclass
                                clus
vv                               MEN1 MUTATED MEN1 WILD-TYPE
  COLON ADENOCARCINOMA                     20            295
  COLON MUCINOUS ADENOCARCINOMA             4             43
  RECTAL ADENOCARCINOMA                     3            103
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  MEN1 MUTATED    16   1   2   2
  MEN1 WILD-TYPE 329   3  29  23
D195V11, multiclass
    clus
vv   MEN1 MUTATED MEN1 WILD-TYPE
  R0           16            329
  R1            1              3
  R2            2             29
  RX            2             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D195V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MEN1 MUTATED                                  0     0
  MEN1 WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  MEN1 MUTATED                           3    20
  MEN1 WILD-TYPE                        19   206
D195V13, multiclass
                                  clus
vv                                 MEN1 MUTATED MEN1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   3             19
  WHITE                                      20            206
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(196) Variable = SENP6 MUTATION ANALYSIS
D196V1, survival
                 sevent
clus2               0   1
  SENP6 MUTATED    13   4
  SENP6 WILD-TYPE 365  89
  SENP6 MUTATED SENP6 WILD-TYPE 
             17             454 
  SENP6 MUTATED SENP6 WILD-TYPE 
              4              89 
$`SENP6 MUTATED`
TCGA-A6-5665 TCGA-A6-6781 TCGA-AA-3663 TCGA-AA-A00N TCGA-AU-6004 TCGA-AY-6197 
       22.06        19.66         6.97         4.01        27.09        21.44 
TCGA-AZ-6598 TCGA-CA-6717 TCGA-CK-5912 TCGA-CM-5348 TCGA-D5-5539 TCGA-D5-5540 
       49.41        12.76        49.08        22.98        19.59        56.09 
TCGA-DM-A1HB TCGA-G4-6588 TCGA-AG-A002 TCGA-DC-6682 TCGA-DY-A1DF 
      135.65        26.17        20.98         4.01        24.13 

$`SENP6 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4315 
       14.50        16.31         0.95        33.01        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07        12.20        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       85.45        15.62        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       13.02        29.06        22.03        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       12.26        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
       44.32       131.51       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       35.80        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        5.95         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  SENP6 MUTATED SENP6 WILD-TYPE 
           4.01            0.00 
  SENP6 MUTATED SENP6 WILD-TYPE 
         135.65          148.01 
  SENP6 MUTATED SENP6 WILD-TYPE 
         22.060          20.035 
[1] "4.0 - 135.7 (22.1)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.1"
D196V2, continuous
D196V3, binary
                 cls
clus                0   1
  SENP6 MUTATED    15   3
  SENP6 WILD-TYPE 351 116
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SENP6 MUTATED     15    3
  SENP6 WILD-TYPE  351  116
        clus
vv       SENP6 MUTATED SENP6 WILD-TYPE
  COLON             15             351
  RECTUM             3             116
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SENP6 MUTATED         3        0        2         6         2         0
  SENP6 WILD-TYPE      88        1       30       132         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SENP6 MUTATED           0          1          2          2        0         0
  SENP6 WILD-TYPE        24         10         57         40       48        18
                 vv
clus              STAGE IVB
  SENP6 MUTATED           0
  SENP6 WILD-TYPE         1
D196V4, multiclass
            clus
vv           SENP6 MUTATED SENP6 WILD-TYPE
  STAGE I                3              88
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA              6             132
  STAGE IIB              2               8
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             1              10
  STAGE IIIB             2              57
  STAGE IIIC             2              40
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  SENP6 MUTATED     0   3  12   3
  SENP6 WILD-TYPE  17  89 317  47
D196V5, multiclass
    clus
vv   SENP6 MUTATED SENP6 WILD-TYPE
  T1             0              17
  T2             3              89
  T3            12             317
  T4             3              47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  SENP6 MUTATED    13   4   1
  SENP6 WILD-TYPE 274 109  86
D196V6, multiclass
    clus
vv   SENP6 MUTATED SENP6 WILD-TYPE
  N0            13             274
  N1             4             109
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D196V7, binary
                 cls
clus                0   1
  SENP6 MUTATED    13   0
  SENP6 WILD-TYPE 362  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SENP6 MUTATED     13    0
  SENP6 WILD-TYPE  362   65
   clus
vv  SENP6 MUTATED SENP6 WILD-TYPE
  0            13             362
  1             0              65
[1] 2 2
[1] FALSE
D196V8, binary
                 cls
clus                0   1
  SENP6 MUTATED     6  12
  SENP6 WILD-TYPE 219 252
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SENP6 MUTATED      6   12
  SENP6 WILD-TYPE  219  252
        clus
vv       SENP6 MUTATED SENP6 WILD-TYPE
  FEMALE             6             219
  MALE              12             252
[1] 2 2
[1] FALSE
D196V9, binary
                 cls
clus                0   1
  SENP6 MUTATED    12   0
  SENP6 WILD-TYPE 338  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SENP6 MUTATED     12    0
  SENP6 WILD-TYPE  338   22
     clus
vv    SENP6 MUTATED SENP6 WILD-TYPE
  NO             12             338
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SENP6 MUTATED                     10                             4
  SENP6 WILD-TYPE                  305                            43
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SENP6 MUTATED                       3                              0
  SENP6 WILD-TYPE                   103                             10
D196V10, multiclass
                                clus
vv                               SENP6 MUTATED SENP6 WILD-TYPE
  COLON ADENOCARCINOMA                      10             305
  COLON MUCINOUS ADENOCARCINOMA              4              43
  RECTAL ADENOCARCINOMA                      3             103
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  SENP6 MUTATED    12   0   0   3
  SENP6 WILD-TYPE 333   4  31  22
D196V11, multiclass
    clus
vv   SENP6 MUTATED SENP6 WILD-TYPE
  R0            12             333
  R1             0               4
  R2             0              31
  RX             3              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D196V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SENP6 MUTATED                                  0     1
  SENP6 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  SENP6 MUTATED                           0    14
  SENP6 WILD-TYPE                        22   212
D196V13, multiclass
                                  clus
vv                                 SENP6 MUTATED SENP6 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                       14             212
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(197) Variable = OR7C2 MUTATION ANALYSIS
D197V1, survival
                 sevent
clus2               0   1
  OR7C2 MUTATED    10   2
  OR7C2 WILD-TYPE 368  91
  OR7C2 MUTATED OR7C2 WILD-TYPE 
             12             459 
  OR7C2 MUTATED OR7C2 WILD-TYPE 
              2              91 
$`OR7C2 MUTATED`
TCGA-A6-6781 TCGA-AA-3950 TCGA-AA-A010 TCGA-AU-3779 TCGA-AZ-5407 TCGA-AZ-6601 
       19.66        24.00        34.98        14.50        88.21       100.01 
TCGA-CA-6717 TCGA-D5-5540 TCGA-D5-6926 TCGA-G4-6588 TCGA-AH-6644 TCGA-DY-A1DC 
       12.76        56.09         9.04        26.17         0.72        41.36 

$`OR7C2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 
        2.01        12.99        24.00        33.01        26.01         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
        0.20        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 
       62.79        49.41         6.77        12.10        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07        12.20        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5541 
       10.06        12.03        45.40        12.26        19.59        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6928 
        3.68         4.41        12.43        14.30         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 
       61.91        36.00        22.09        13.78        35.80        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-CI-6619 TCGA-CI-6620 
       38.56         1.45        17.49         0.69         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.03         5.29       126.44        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  OR7C2 MUTATED OR7C2 WILD-TYPE 
           0.72            0.00 
  OR7C2 MUTATED OR7C2 WILD-TYPE 
         100.01          148.01 
  OR7C2 MUTATED OR7C2 WILD-TYPE 
         25.085          20.120 
[1] "0.7 - 100.0 (25.1)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.6"
D197V2, continuous
D197V3, binary
                 cls
clus                0   1
  OR7C2 MUTATED    10   2
  OR7C2 WILD-TYPE 356 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR7C2 MUTATED     10    2
  OR7C2 WILD-TYPE  356  117
        clus
vv       OR7C2 MUTATED OR7C2 WILD-TYPE
  COLON             10             356
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  OR7C2 MUTATED         1        0        1         6         1         0
  OR7C2 WILD-TYPE      90        1       31       132         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  OR7C2 MUTATED           0          0          1          1        0         0
  OR7C2 WILD-TYPE        24         11         58         41       48        18
                 vv
clus              STAGE IVB
  OR7C2 MUTATED           0
  OR7C2 WILD-TYPE         1
D197V4, multiclass
            clus
vv           OR7C2 MUTATED OR7C2 WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              6             132
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             1              41
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  OR7C2 MUTATED     1   0   8   3
  OR7C2 WILD-TYPE  16  92 321  47
D197V5, multiclass
    clus
vv   OR7C2 MUTATED OR7C2 WILD-TYPE
  T1             1              16
  T2             0              92
  T3             8             321
  T4             3              47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  OR7C2 MUTATED     9   2   0
  OR7C2 WILD-TYPE 278 111  87
D197V6, multiclass
    clus
vv   OR7C2 MUTATED OR7C2 WILD-TYPE
  N0             9             278
  N1             2             111
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D197V7, binary
                 cls
clus                0   1
  OR7C2 MUTATED    10   0
  OR7C2 WILD-TYPE 365  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR7C2 MUTATED     10    0
  OR7C2 WILD-TYPE  365   65
   clus
vv  OR7C2 MUTATED OR7C2 WILD-TYPE
  0            10             365
  1             0              65
[1] 2 2
[1] FALSE
D197V8, binary
                 cls
clus                0   1
  OR7C2 MUTATED     6   6
  OR7C2 WILD-TYPE 219 258
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR7C2 MUTATED      6    6
  OR7C2 WILD-TYPE  219  258
        clus
vv       OR7C2 MUTATED OR7C2 WILD-TYPE
  FEMALE             6             219
  MALE               6             258
[1] 2 2
[1] FALSE
D197V9, binary
                 cls
clus                0   1
  OR7C2 MUTATED     9   1
  OR7C2 WILD-TYPE 341  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR7C2 MUTATED      9    1
  OR7C2 WILD-TYPE  341   21
     clus
vv    OR7C2 MUTATED OR7C2 WILD-TYPE
  NO              9             341
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  OR7C2 MUTATED                      7                             3
  OR7C2 WILD-TYPE                  308                            44
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  OR7C2 MUTATED                       2                              0
  OR7C2 WILD-TYPE                   104                             10
D197V10, multiclass
                                clus
vv                               OR7C2 MUTATED OR7C2 WILD-TYPE
  COLON ADENOCARCINOMA                       7             308
  COLON MUCINOUS ADENOCARCINOMA              3              44
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  OR7C2 MUTATED     7   0   0   1
  OR7C2 WILD-TYPE 338   4  31  24
D197V11, multiclass
    clus
vv   OR7C2 MUTATED OR7C2 WILD-TYPE
  R0             7             338
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D197V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OR7C2 MUTATED                                  0     1
  OR7C2 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  OR7C2 MUTATED                           0     9
  OR7C2 WILD-TYPE                        22   217
D197V13, multiclass
                                  clus
vv                                 OR7C2 MUTATED OR7C2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        9             217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(198) Variable = PDGFRA MUTATION ANALYSIS
D198V1, survival
                  sevent
clus2                0   1
  PDGFRA MUTATED    41  11
  PDGFRA WILD-TYPE 337  82
  PDGFRA MUTATED PDGFRA WILD-TYPE 
              52              419 
  PDGFRA MUTATED PDGFRA WILD-TYPE 
              11               82 
$`PDGFRA MUTATED`
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5665 TCGA-A6-5666 TCGA-AA-3510 TCGA-AA-3660 
       30.44        29.19        22.06        32.71        63.98        78.08 
TCGA-AA-3662 TCGA-AA-3666 TCGA-AA-3672 TCGA-AA-3864 TCGA-AA-3947 TCGA-AA-3952 
        6.05         2.01         0.92        53.00        33.01         2.01 
TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01R TCGA-AD-6895 TCGA-AY-6197 TCGA-AY-6386 
        4.01        34.98        35.01         0.72        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-5407 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
       58.39         1.41        88.21         0.07        12.20        12.76 
TCGA-CK-4950 TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5868 TCGA-CM-6172 TCGA-CM-6675 
       85.45        22.03        30.08        17.03        11.01        13.05 
TCGA-D5-6539 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6928 TCGA-D5-7000 TCGA-DM-A0XF 
       12.49         4.41        12.43        11.64        10.26        38.20 
TCGA-DM-A1D4 TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HB TCGA-DM-A282 
       92.75        13.32       140.38         7.50       135.65       139.17 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6570 TCGA-G4-6310 TCGA-G4-6586 TCGA-AG-3892 
        8.61        31.96         6.18        63.62        35.80        13.02 
TCGA-AG-A002 TCGA-EI-6510 TCGA-F5-6465 TCGA-G5-6235 
       20.98        18.28        49.51        55.76 

$`PDGFRA WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-6137 
       32.91        31.63        33.53        23.61        22.09        27.09 
TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 
       22.52         8.38        25.08        25.18        24.16        21.76 
TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       24.69        24.39        23.87        20.12        19.66        20.28 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 
        7.04         3.02         1.02        35.01         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
       13.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       36.03         8.05        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        6.97        54.02        14.01        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        31.07        30.05        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       26.01        24.00        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T 
       31.00        31.00        38.07         1.02         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.79         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AZ-4616 
       14.50        27.09        16.31         0.95        33.01         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
      106.75        22.36        62.79        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6718 TCGA-CA-6719 
       12.69         3.06         3.25         3.29        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
       17.56       148.01        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5860 
       37.02        25.02        13.02        29.06        22.98        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6162 
       15.02         5.03        15.02        15.02        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6676 TCGA-CM-6677 
       13.02        15.02        14.04        12.95        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 
       15.12        17.85         4.80        17.13        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 
        1.48         3.68        14.30         9.04         9.44         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A1D0 
        1.51        12.00        11.38       119.70        24.43       130.65 
TCGA-DM-A1D6 TCGA-DM-A1D8 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A285 TCGA-DM-A28C 
       49.91        12.59        44.32       131.51         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6569 
      119.93        35.97        60.79       117.07        98.24        35.74 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6315 
       65.85        53.62        44.68        55.04        85.48        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       17.95        36.95        17.03        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-F5-6464 TCGA-F5-6571 
        0.49        20.55        19.96        20.91         9.96        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        26.43 

  PDGFRA MUTATED PDGFRA WILD-TYPE 
            0.07             0.00 
  PDGFRA MUTATED PDGFRA WILD-TYPE 
          140.38           148.01 
  PDGFRA MUTATED PDGFRA WILD-TYPE 
           21.21            20.12 
[1] "0.1 - 140.4 (21.2)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.1"
D198V2, continuous
D198V3, binary
                  cls
clus                 0   1
  PDGFRA MUTATED    49   5
  PDGFRA WILD-TYPE 317 114
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PDGFRA MUTATED     49    5
  PDGFRA WILD-TYPE  317  114
        clus
vv       PDGFRA MUTATED PDGFRA WILD-TYPE
  COLON              49              317
  RECTUM              5              114
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PDGFRA MUTATED         6        0        3        15         3         1
  PDGFRA WILD-TYPE      85        1       29       123         7         0
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PDGFRA MUTATED           3          2         10          5        2
  PDGFRA WILD-TYPE        21          9         49         37       46
                  vv
clus               STAGE IVA STAGE IVB
  PDGFRA MUTATED           2         1
  PDGFRA WILD-TYPE        16         0
D198V4, multiclass
            clus
vv           PDGFRA MUTATED PDGFRA WILD-TYPE
  STAGE I                 6               85
  STAGE IA                0                1
  STAGE II                3               29
  STAGE IIA              15              123
  STAGE IIB               3                7
  STAGE IIC               1                0
  STAGE III               3               21
  STAGE IIIA              2                9
  STAGE IIIB             10               49
  STAGE IIIC              5               37
  STAGE IV                2               46
  STAGE IVA               2               16
  STAGE IVB               1                0
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  PDGFRA MUTATED     2   5  40   7
  PDGFRA WILD-TYPE  15  87 289  43
D198V5, multiclass
    clus
vv   PDGFRA MUTATED PDGFRA WILD-TYPE
  T1              2               15
  T2              5               87
  T3             40              289
  T4              7               43
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  PDGFRA MUTATED    30  14  10
  PDGFRA WILD-TYPE 257  99  77
D198V6, multiclass
    clus
vv   PDGFRA MUTATED PDGFRA WILD-TYPE
  N0             30              257
  N1             14               99
  N2             10               77
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D198V7, binary
                  cls
clus                 0   1
  PDGFRA MUTATED    45   4
  PDGFRA WILD-TYPE 330  61
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PDGFRA MUTATED     45    4
  PDGFRA WILD-TYPE  330   61
   clus
vv  PDGFRA MUTATED PDGFRA WILD-TYPE
  0             45              330
  1              4               61
[1] 2 2
[1] FALSE
D198V8, binary
                  cls
clus                 0   1
  PDGFRA MUTATED    27  27
  PDGFRA WILD-TYPE 198 237
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PDGFRA MUTATED     27   27
  PDGFRA WILD-TYPE  198  237
        clus
vv       PDGFRA MUTATED PDGFRA WILD-TYPE
  FEMALE             27              198
  MALE               27              237
[1] 2 2
[1] FALSE
D198V9, binary
                  cls
clus                 0   1
  PDGFRA MUTATED    37   2
  PDGFRA WILD-TYPE 313  20
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PDGFRA MUTATED     37    2
  PDGFRA WILD-TYPE  313   20
     clus
vv    PDGFRA MUTATED PDGFRA WILD-TYPE
  NO              37              313
  YES              2               20
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PDGFRA MUTATED                     39                             7
  PDGFRA WILD-TYPE                  276                            40
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PDGFRA MUTATED                       5                              0
  PDGFRA WILD-TYPE                   101                             10
D198V10, multiclass
                                clus
vv                               PDGFRA MUTATED PDGFRA WILD-TYPE
  COLON ADENOCARCINOMA                       39              276
  COLON MUCINOUS ADENOCARCINOMA               7               40
  RECTAL ADENOCARCINOMA                       5              101
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  PDGFRA MUTATED    36   2   1   3
  PDGFRA WILD-TYPE 309   2  30  22
D198V11, multiclass
    clus
vv   PDGFRA MUTATED PDGFRA WILD-TYPE
  R0             36              309
  R1              2                2
  R2              1               30
  RX              3               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D198V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PDGFRA MUTATED                                  0     3
  PDGFRA WILD-TYPE                                1     8
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  PDGFRA MUTATED                           4    33
  PDGFRA WILD-TYPE                        18   193
D198V13, multiclass
                                  clus
vv                                 PDGFRA MUTATED PDGFRA WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         3                8
  BLACK OR AFRICAN AMERICAN                     4               18
  WHITE                                        33              193
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(199) Variable = KLC4 MUTATION ANALYSIS
D199V1, survival
                sevent
clus2              0   1
  KLC4 MUTATED    11   4
  KLC4 WILD-TYPE 367  89
  KLC4 MUTATED KLC4 WILD-TYPE 
            15            456 
  KLC4 MUTATED KLC4 WILD-TYPE 
             4             89 
$`KLC4 MUTATED`
TCGA-A6-2676 TCGA-AA-3518 TCGA-AA-3713 TCGA-AA-3845 TCGA-AA-3860 TCGA-AA-3864 
       42.90         1.02        19.04         0.00        31.07        53.00 
TCGA-CA-6718 TCGA-CK-5913 TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-6166 TCGA-CM-6677 
       10.06        51.32        23.05        37.02        21.99        11.08 
TCGA-D5-5539 TCGA-F4-6460 TCGA-AG-3727 
       19.59        31.96         0.99 

$`KLC4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       38.99        37.02        14.93        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       30.05        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07        12.20        12.76        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 
      148.01        85.45        15.62        49.08         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4752 
       82.95         1.91       124.27        20.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
        2.96        29.03        16.04        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 
       11.01        10.06        12.03        45.40        12.26        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6569 
       35.97        60.79       117.07        98.24         8.61        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        7.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  KLC4 MUTATED KLC4 WILD-TYPE 
             0              0 
  KLC4 MUTATED KLC4 WILD-TYPE 
         53.00         148.01 
  KLC4 MUTATED KLC4 WILD-TYPE 
        21.990         20.155 
[1] "0.0 - 53.0 (22.0)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.5"
D199V2, continuous
D199V3, binary
                cls
clus               0   1
  KLC4 MUTATED    16   1
  KLC4 WILD-TYPE 350 118
[1] "tbl2"
                cls
clus             [,1] [,2]
  KLC4 MUTATED     16    1
  KLC4 WILD-TYPE  350  118
        clus
vv       KLC4 MUTATED KLC4 WILD-TYPE
  COLON            16            350
  RECTUM            1            118
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KLC4 MUTATED         3        0        1         6         1         0
  KLC4 WILD-TYPE      88        1       31       132         9         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  KLC4 MUTATED           1          1          2          0        2         0
  KLC4 WILD-TYPE        23         10         57         42       46        18
                vv
clus             STAGE IVB
  KLC4 MUTATED           0
  KLC4 WILD-TYPE         1
D199V4, multiclass
            clus
vv           KLC4 MUTATED KLC4 WILD-TYPE
  STAGE I               3             88
  STAGE IA              0              1
  STAGE II              1             31
  STAGE IIA             6            132
  STAGE IIB             1              9
  STAGE IIC             0              1
  STAGE III             1             23
  STAGE IIIA            1             10
  STAGE IIIB            2             57
  STAGE IIIC            0             42
  STAGE IV              2             46
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  KLC4 MUTATED     0   3  13   1
  KLC4 WILD-TYPE  17  89 316  49
D199V5, multiclass
    clus
vv   KLC4 MUTATED KLC4 WILD-TYPE
  T1            0             17
  T2            3             89
  T3           13            316
  T4            1             49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  KLC4 MUTATED    12   4   1
  KLC4 WILD-TYPE 275 109  86
D199V6, multiclass
    clus
vv   KLC4 MUTATED KLC4 WILD-TYPE
  N0           12            275
  N1            4            109
  N2            1             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D199V7, binary
                cls
clus               0   1
  KLC4 MUTATED    13   2
  KLC4 WILD-TYPE 362  63
[1] "tbl2"
                cls
clus             [,1] [,2]
  KLC4 MUTATED     13    2
  KLC4 WILD-TYPE  362   63
   clus
vv  KLC4 MUTATED KLC4 WILD-TYPE
  0           13            362
  1            2             63
[1] 2 2
[1] FALSE
D199V8, binary
                cls
clus               0   1
  KLC4 MUTATED    10   7
  KLC4 WILD-TYPE 215 257
[1] "tbl2"
                cls
clus             [,1] [,2]
  KLC4 MUTATED     10    7
  KLC4 WILD-TYPE  215  257
        clus
vv       KLC4 MUTATED KLC4 WILD-TYPE
  FEMALE           10            215
  MALE              7            257
[1] 2 2
[1] FALSE
D199V9, binary
                cls
clus               0   1
  KLC4 MUTATED    11   1
  KLC4 WILD-TYPE 339  21
[1] "tbl2"
                cls
clus             [,1] [,2]
  KLC4 MUTATED     11    1
  KLC4 WILD-TYPE  339   21
     clus
vv    KLC4 MUTATED KLC4 WILD-TYPE
  NO            11            339
  YES            1             21
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  KLC4 MUTATED                     15                             1
  KLC4 WILD-TYPE                  300                            46
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  KLC4 MUTATED                       1                              0
  KLC4 WILD-TYPE                   105                             10
D199V10, multiclass
                                clus
vv                               KLC4 MUTATED KLC4 WILD-TYPE
  COLON ADENOCARCINOMA                     15            300
  COLON MUCINOUS ADENOCARCINOMA             1             46
  RECTAL ADENOCARCINOMA                     1            105
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  KLC4 MUTATED    12   0   2   3
  KLC4 WILD-TYPE 333   4  29  22
D199V11, multiclass
    clus
vv   KLC4 MUTATED KLC4 WILD-TYPE
  R0           12            333
  R1            0              4
  R2            2             29
  RX            3             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D199V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KLC4 MUTATED                                  0     1
  KLC4 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  KLC4 MUTATED                           1     8
  KLC4 WILD-TYPE                        21   218
D199V13, multiclass
                                  clus
vv                                 KLC4 MUTATED KLC4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                       8            218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(200) Variable = INTS4 MUTATION ANALYSIS
D200V1, survival
                 sevent
clus2               0   1
  INTS4 MUTATED    14   7
  INTS4 WILD-TYPE 364  86
  INTS4 MUTATED INTS4 WILD-TYPE 
             21             450 
  INTS4 MUTATED INTS4 WILD-TYPE 
              7              86 
$`INTS4 MUTATED`
TCGA-A6-5660 TCGA-A6-5664 TCGA-AA-3525 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3672 
       29.19        22.09         8.05         6.05         6.97         0.92 
TCGA-AZ-4315 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6601 TCGA-CA-6718 TCGA-CM-5868 
       58.39        62.79        49.41       100.01        10.06        17.03 
TCGA-CM-6171 TCGA-D5-6537 TCGA-D5-6930 TCGA-F4-6459 TCGA-G4-6306 TCGA-AG-3883 
       14.04         4.80         1.51         8.61        44.68         1.02 
TCGA-AG-A002 TCGA-AH-6549 TCGA-DY-A1DG 
       20.98        17.49        51.48 

$`INTS4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5665 
       32.91        31.63        30.44        33.53        23.61        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3529 
        9.07        24.03        37.05        36.03        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       19.99        61.02        78.08        54.02         2.01        14.01 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
       16.31         0.95        33.01        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 
        5.13       106.75        22.36        88.21         6.77        12.10 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        15.02        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
       17.85        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       11.64         4.80        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
      117.07        98.24        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       53.62        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3885 
       32.98         0.99         0.99        19.04        19.99        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 
       41.00        38.04       117.11        38.56         1.45         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       41.36        57.24        24.13        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  INTS4 MUTATED INTS4 WILD-TYPE 
           0.92            0.00 
  INTS4 MUTATED INTS4 WILD-TYPE 
         100.01          148.01 
  INTS4 MUTATED INTS4 WILD-TYPE 
         17.030          20.415 
[1] "0.9 - 100.0 (17.0)" "0.0 - 148.0 (20.4)"
[1] "hr=" "1.7"
D200V2, continuous
D200V3, binary
                 cls
clus                0   1
  INTS4 MUTATED    18   4
  INTS4 WILD-TYPE 348 115
[1] "tbl2"
                 cls
clus              [,1] [,2]
  INTS4 MUTATED     18    4
  INTS4 WILD-TYPE  348  115
        clus
vv       INTS4 MUTATED INTS4 WILD-TYPE
  COLON             18             348
  RECTUM             4             115
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  INTS4 MUTATED         4        0        4         4         0         0
  INTS4 WILD-TYPE      87        1       28       134        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  INTS4 MUTATED           1          0          3          2        1         2
  INTS4 WILD-TYPE        23         11         56         40       47        16
                 vv
clus              STAGE IVB
  INTS4 MUTATED           0
  INTS4 WILD-TYPE         1
D200V4, multiclass
            clus
vv           INTS4 MUTATED INTS4 WILD-TYPE
  STAGE I                4              87
  STAGE IA               0               1
  STAGE II               4              28
  STAGE IIA              4             134
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             3              56
  STAGE IIIC             2              40
  STAGE IV               1              47
  STAGE IVA              2              16
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  INTS4 MUTATED     0   5  14   3
  INTS4 WILD-TYPE  17  87 315  47
D200V5, multiclass
    clus
vv   INTS4 MUTATED INTS4 WILD-TYPE
  T1             0              17
  T2             5              87
  T3            14             315
  T4             3              47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  INTS4 MUTATED    12   5   4
  INTS4 WILD-TYPE 275 108  83
D200V6, multiclass
    clus
vv   INTS4 MUTATED INTS4 WILD-TYPE
  N0            12             275
  N1             5             108
  N2             4              83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D200V7, binary
                 cls
clus                0   1
  INTS4 MUTATED    13   3
  INTS4 WILD-TYPE 362  62
[1] "tbl2"
                 cls
clus              [,1] [,2]
  INTS4 MUTATED     13    3
  INTS4 WILD-TYPE  362   62
   clus
vv  INTS4 MUTATED INTS4 WILD-TYPE
  0            13             362
  1             3              62
[1] 2 2
[1] FALSE
D200V8, binary
                 cls
clus                0   1
  INTS4 MUTATED     6  16
  INTS4 WILD-TYPE 219 248
[1] "tbl2"
                 cls
clus              [,1] [,2]
  INTS4 MUTATED      6   16
  INTS4 WILD-TYPE  219  248
        clus
vv       INTS4 MUTATED INTS4 WILD-TYPE
  FEMALE             6             219
  MALE              16             248
[1] 2 2
[1] FALSE
D200V9, binary
                 cls
clus                0   1
  INTS4 MUTATED    18   0
  INTS4 WILD-TYPE 332  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  INTS4 MUTATED     18    0
  INTS4 WILD-TYPE  332   22
     clus
vv    INTS4 MUTATED INTS4 WILD-TYPE
  NO             18             332
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  INTS4 MUTATED                     17                             1
  INTS4 WILD-TYPE                  298                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  INTS4 MUTATED                       4                              0
  INTS4 WILD-TYPE                   102                             10
D200V10, multiclass
                                clus
vv                               INTS4 MUTATED INTS4 WILD-TYPE
  COLON ADENOCARCINOMA                      17             298
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      4             102
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  INTS4 MUTATED    12   0   1   3
  INTS4 WILD-TYPE 333   4  30  22
D200V11, multiclass
    clus
vv   INTS4 MUTATED INTS4 WILD-TYPE
  R0            12             333
  R1             0               4
  R2             1              30
  RX             3              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D200V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  INTS4 MUTATED                                  0     1
  INTS4 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  INTS4 MUTATED                           2    13
  INTS4 WILD-TYPE                        20   213
D200V13, multiclass
                                  clus
vv                                 INTS4 MUTATED INTS4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    2              20
  WHITE                                       13             213
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(201) Variable = RBAK MUTATION ANALYSIS
D201V1, survival
                sevent
clus2              0   1
  RBAK MUTATED    16   2
  RBAK WILD-TYPE 362  91
  RBAK MUTATED RBAK WILD-TYPE 
            18            453 
  RBAK MUTATED RBAK WILD-TYPE 
             2             91 
$`RBAK MUTATED`
TCGA-AA-3525 TCGA-AA-3660 TCGA-AA-3939 TCGA-AA-A010 TCGA-AZ-4315 TCGA-CA-6717 
        8.05        78.08        12.99        34.98        58.39        12.76 
TCGA-CK-4952 TCGA-CK-5916 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-6164 
       15.62        21.14       124.27        23.05        37.02        29.03 
TCGA-D5-6924 TCGA-DM-A1HA TCGA-F4-6809 TCGA-G4-6293 TCGA-G4-6304 TCGA-F5-6465 
       14.30       131.51        13.25       133.18        53.62        49.51 

$`RBAK WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 
       19.99        13.94        19.99        61.02         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07        12.20        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
       17.56       148.01        85.45        49.08        51.32         9.99 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       82.95         1.91        20.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 
       15.58         1.48         3.68         4.41        12.43         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6303 
       33.67         0.53        47.41        35.31        74.56        65.85 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
       18.28         9.96        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  RBAK MUTATED RBAK WILD-TYPE 
          8.05           0.00 
  RBAK MUTATED RBAK WILD-TYPE 
        133.18         148.01 
  RBAK MUTATED RBAK WILD-TYPE 
        32.005         20.020 
[1] "8.1 - 133.2 (32.0)" "0.0 - 148.0 (20.0)"
[1] "hr=" "3.1"
D201V2, continuous
D201V3, binary
                cls
clus               0   1
  RBAK MUTATED    17   1
  RBAK WILD-TYPE 349 118
[1] "tbl2"
                cls
clus             [,1] [,2]
  RBAK MUTATED     17    1
  RBAK WILD-TYPE  349  118
        clus
vv       RBAK MUTATED RBAK WILD-TYPE
  COLON            17            349
  RECTUM            1            118
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RBAK MUTATED         3        0        1         7         2         0
  RBAK WILD-TYPE      88        1       31       131         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RBAK MUTATED           1          0          1          2        0         1
  RBAK WILD-TYPE        23         11         58         40       48        17
                vv
clus             STAGE IVB
  RBAK MUTATED           0
  RBAK WILD-TYPE         1
D201V4, multiclass
            clus
vv           RBAK MUTATED RBAK WILD-TYPE
  STAGE I               3             88
  STAGE IA              0              1
  STAGE II              1             31
  STAGE IIA             7            131
  STAGE IIB             2              8
  STAGE IIC             0              1
  STAGE III             1             23
  STAGE IIIA            0             11
  STAGE IIIB            1             58
  STAGE IIIC            2             40
  STAGE IV              0             48
  STAGE IVA             1             17
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  RBAK MUTATED     1   2  12   3
  RBAK WILD-TYPE  16  90 317  47
D201V5, multiclass
    clus
vv   RBAK MUTATED RBAK WILD-TYPE
  T1            1             16
  T2            2             90
  T3           12            317
  T4            3             47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  RBAK MUTATED    13   3   2
  RBAK WILD-TYPE 274 110  85
D201V6, multiclass
    clus
vv   RBAK MUTATED RBAK WILD-TYPE
  N0           13            274
  N1            3            110
  N2            2             85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D201V7, binary
                cls
clus               0   1
  RBAK MUTATED    16   1
  RBAK WILD-TYPE 359  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  RBAK MUTATED     16    1
  RBAK WILD-TYPE  359   64
   clus
vv  RBAK MUTATED RBAK WILD-TYPE
  0           16            359
  1            1             64
[1] 2 2
[1] FALSE
D201V8, binary
                cls
clus               0   1
  RBAK MUTATED    10   8
  RBAK WILD-TYPE 215 256
[1] "tbl2"
                cls
clus             [,1] [,2]
  RBAK MUTATED     10    8
  RBAK WILD-TYPE  215  256
        clus
vv       RBAK MUTATED RBAK WILD-TYPE
  FEMALE           10            215
  MALE              8            256
[1] 2 2
[1] FALSE
D201V9, binary
                cls
clus               0   1
  RBAK MUTATED    16   0
  RBAK WILD-TYPE 334  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  RBAK MUTATED     16    0
  RBAK WILD-TYPE  334   22
     clus
vv    RBAK MUTATED RBAK WILD-TYPE
  NO            16            334
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  RBAK MUTATED                     14                             3
  RBAK WILD-TYPE                  301                            44
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  RBAK MUTATED                       1                              0
  RBAK WILD-TYPE                   105                             10
D201V10, multiclass
                                clus
vv                               RBAK MUTATED RBAK WILD-TYPE
  COLON ADENOCARCINOMA                     14            301
  COLON MUCINOUS ADENOCARCINOMA             3             44
  RECTAL ADENOCARCINOMA                     1            105
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  RBAK MUTATED    13   0   0   4
  RBAK WILD-TYPE 332   4  31  21
D201V11, multiclass
    clus
vv   RBAK MUTATED RBAK WILD-TYPE
  R0           13            332
  R1            0              4
  R2            0             31
  RX            4             21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D201V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RBAK MUTATED                                  0     1
  RBAK WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  RBAK MUTATED                           1    12
  RBAK WILD-TYPE                        21   214
D201V13, multiclass
                                  clus
vv                                 RBAK MUTATED RBAK WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                      12            214
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(202) Variable = EIF4A2 MUTATION ANALYSIS
D202V1, survival
                  sevent
clus2                0   1
  EIF4A2 MUTATED    11   0
  EIF4A2 WILD-TYPE 367  93
  EIF4A2 MUTATED EIF4A2 WILD-TYPE 
              11              460 
  EIF4A2 MUTATED EIF4A2 WILD-TYPE 
               0               93 
$`EIF4A2 MUTATED`
TCGA-A6-6654 TCGA-AA-3667 TCGA-AA-3831 TCGA-AA-3973 TCGA-AA-A017 TCGA-CM-4746 
       23.87        14.01        17.98        13.05         1.02        37.02 
TCGA-CM-6168 TCGA-DM-A1HB TCGA-F4-6704 TCGA-AG-A01Y TCGA-AH-6643 
       12.99       135.65         1.55        64.01         0.69 

$`EIF4A2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
        6.97        54.02         2.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3833 
       35.05        33.04         0.99        25.02         1.02        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        50.99        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       23.05        20.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       16.04        21.99        14.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      131.51       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
        6.18        47.87        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A020 TCGA-AG-A025 
       36.03         9.07        12.00        70.03        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
       38.56         1.45        17.49         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  EIF4A2 MUTATED EIF4A2 WILD-TYPE 
            0.69             0.00 
  EIF4A2 MUTATED EIF4A2 WILD-TYPE 
          135.65           148.01 
  EIF4A2 MUTATED EIF4A2 WILD-TYPE 
          14.010           20.415 
[1] "0.7 - 135.7 (14.0)" "0.0 - 148.0 (20.4)"
[1] "hr="     "9300000"
D202V2, continuous
D202V3, binary
                  cls
clus                 0   1
  EIF4A2 MUTATED    10   2
  EIF4A2 WILD-TYPE 356 117
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EIF4A2 MUTATED     10    2
  EIF4A2 WILD-TYPE  356  117
        clus
vv       EIF4A2 MUTATED EIF4A2 WILD-TYPE
  COLON              10              356
  RECTUM              2              117
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  EIF4A2 MUTATED         2        0        1         3         1         0
  EIF4A2 WILD-TYPE      89        1       31       135         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  EIF4A2 MUTATED           0          0          2          2        1
  EIF4A2 WILD-TYPE        24         11         57         40       47
                  vv
clus               STAGE IVA STAGE IVB
  EIF4A2 MUTATED           0         0
  EIF4A2 WILD-TYPE        18         1
D202V4, multiclass
            clus
vv           EIF4A2 MUTATED EIF4A2 WILD-TYPE
  STAGE I                 2               89
  STAGE IA                0                1
  STAGE II                1               31
  STAGE IIA               3              135
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              2               57
  STAGE IIIC              2               40
  STAGE IV                1               47
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  EIF4A2 MUTATED     0   2   8   2
  EIF4A2 WILD-TYPE  17  90 321  48
D202V5, multiclass
    clus
vv   EIF4A2 MUTATED EIF4A2 WILD-TYPE
  T1              0               17
  T2              2               90
  T3              8              321
  T4              2               48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  EIF4A2 MUTATED     7   3   2
  EIF4A2 WILD-TYPE 280 110  85
D202V6, multiclass
    clus
vv   EIF4A2 MUTATED EIF4A2 WILD-TYPE
  N0              7              280
  N1              3              110
  N2              2               85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D202V7, binary
                  cls
clus                 0   1
  EIF4A2 MUTATED     9   1
  EIF4A2 WILD-TYPE 366  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EIF4A2 MUTATED      9    1
  EIF4A2 WILD-TYPE  366   64
   clus
vv  EIF4A2 MUTATED EIF4A2 WILD-TYPE
  0              9              366
  1              1               64
[1] 2 2
[1] FALSE
D202V8, binary
                  cls
clus                 0   1
  EIF4A2 MUTATED     6   6
  EIF4A2 WILD-TYPE 219 258
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EIF4A2 MUTATED      6    6
  EIF4A2 WILD-TYPE  219  258
        clus
vv       EIF4A2 MUTATED EIF4A2 WILD-TYPE
  FEMALE              6              219
  MALE                6              258
[1] 2 2
[1] FALSE
D202V9, binary
                  cls
clus                 0   1
  EIF4A2 MUTATED     6   0
  EIF4A2 WILD-TYPE 344  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EIF4A2 MUTATED      6    0
  EIF4A2 WILD-TYPE  344   22
     clus
vv    EIF4A2 MUTATED EIF4A2 WILD-TYPE
  NO               6              344
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  EIF4A2 MUTATED                      8                             1
  EIF4A2 WILD-TYPE                  307                            46
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  EIF4A2 MUTATED                       2                              0
  EIF4A2 WILD-TYPE                   104                             10
D202V10, multiclass
                                clus
vv                               EIF4A2 MUTATED EIF4A2 WILD-TYPE
  COLON ADENOCARCINOMA                        8              307
  COLON MUCINOUS ADENOCARCINOMA               1               46
  RECTAL ADENOCARCINOMA                       2              104
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  EIF4A2 MUTATED     8   0   1   1
  EIF4A2 WILD-TYPE 337   4  30  24
D202V11, multiclass
    clus
vv   EIF4A2 MUTATED EIF4A2 WILD-TYPE
  R0              8              337
  R1              0                4
  R2              1               30
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D202V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  EIF4A2 MUTATED                                  1     0
  EIF4A2 WILD-TYPE                                0    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  EIF4A2 MUTATED                           2     4
  EIF4A2 WILD-TYPE                        20   222
D202V13, multiclass
                                  clus
vv                                 EIF4A2 MUTATED EIF4A2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              1                0
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     2               20
  WHITE                                         4              222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(203) Variable = FAM133B MUTATION ANALYSIS
D203V1, survival
                   sevent
clus2                 0   1
  FAM133B MUTATED     4   1
  FAM133B WILD-TYPE 374  92
  FAM133B MUTATED FAM133B WILD-TYPE 
                5               466 
  FAM133B MUTATED FAM133B WILD-TYPE 
                1                92 
$`FAM133B MUTATED`
TCGA-A6-3809 TCGA-CK-5916 TCGA-CM-6167 TCGA-G4-6309 TCGA-G4-6628 
       32.75        21.14        14.99        85.48        79.69 

$`FAM133B WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 
       65.85        53.62        44.68        55.04        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       46.75        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  FAM133B MUTATED FAM133B WILD-TYPE 
            14.99              0.00 
  FAM133B MUTATED FAM133B WILD-TYPE 
            85.48            148.01 
  FAM133B MUTATED FAM133B WILD-TYPE 
           32.750            20.085 
[1] "15.0 - 85.5 (32.8)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.7"
D203V2, continuous
D203V3, binary
                   cls
clus                  0   1
  FAM133B MUTATED     5   0
  FAM133B WILD-TYPE 361 119
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM133B MUTATED      5    0
  FAM133B WILD-TYPE  361  119
        clus
vv       FAM133B MUTATED FAM133B WILD-TYPE
  COLON                5               361
  RECTUM               0               119
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FAM133B MUTATED         2        0        0         0         1         0
  FAM133B WILD-TYPE      89        1       32       138         9         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FAM133B MUTATED           0          0          1          1        0
  FAM133B WILD-TYPE        24         11         58         41       48
                   vv
clus                STAGE IVA STAGE IVB
  FAM133B MUTATED           0         0
  FAM133B WILD-TYPE        18         1
D203V4, multiclass
            clus
vv           FAM133B MUTATED FAM133B WILD-TYPE
  STAGE I                  2                89
  STAGE IA                 0                 1
  STAGE II                 0                32
  STAGE IIA                0               138
  STAGE IIB                1                 9
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               0                11
  STAGE IIIB               1                58
  STAGE IIIC               1                41
  STAGE IV                 0                48
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  FAM133B MUTATED     1   1   2   1
  FAM133B WILD-TYPE  16  91 327  49
D203V5, multiclass
    clus
vv   FAM133B MUTATED FAM133B WILD-TYPE
  T1               1                16
  T2               1                91
  T3               2               327
  T4               1                49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  FAM133B MUTATED     3   1   1
  FAM133B WILD-TYPE 284 112  86
D203V6, multiclass
    clus
vv   FAM133B MUTATED FAM133B WILD-TYPE
  N0               3               284
  N1               1               112
  N2               1                86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D203V7, binary
                   cls
clus                  0   1
  FAM133B MUTATED     5   0
  FAM133B WILD-TYPE 370  65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM133B MUTATED      5    0
  FAM133B WILD-TYPE  370   65
   clus
vv  FAM133B MUTATED FAM133B WILD-TYPE
  0               5               370
  1               0                65
[1] 2 2
[1] FALSE
D203V8, binary
                   cls
clus                  0   1
  FAM133B MUTATED     4   1
  FAM133B WILD-TYPE 221 263
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM133B MUTATED      4    1
  FAM133B WILD-TYPE  221  263
        clus
vv       FAM133B MUTATED FAM133B WILD-TYPE
  FEMALE               4               221
  MALE                 1               263
[1] 2 2
[1] FALSE
D203V9, binary
                   cls
clus                  0   1
  FAM133B MUTATED     5   0
  FAM133B WILD-TYPE 345  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM133B MUTATED      5    0
  FAM133B WILD-TYPE  345   22
     clus
vv    FAM133B MUTATED FAM133B WILD-TYPE
  NO                5               345
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  FAM133B MUTATED                      4                             1
  FAM133B WILD-TYPE                  311                            46
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  FAM133B MUTATED                       0                              0
  FAM133B WILD-TYPE                   106                             10
D203V10, multiclass
                                clus
vv                               FAM133B MUTATED FAM133B WILD-TYPE
  COLON ADENOCARCINOMA                         4               311
  COLON MUCINOUS ADENOCARCINOMA                1                46
  RECTAL ADENOCARCINOMA                        0               106
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  FAM133B MUTATED     4   0   0   1
  FAM133B WILD-TYPE 341   4  31  24
D203V11, multiclass
    clus
vv   FAM133B MUTATED FAM133B WILD-TYPE
  R0               4               341
  R1               0                 4
  R2               0                31
  RX               1                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D203V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FAM133B MUTATED                                  0     0
  FAM133B WILD-TYPE                                1    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  FAM133B MUTATED                           2     3
  FAM133B WILD-TYPE                        20   223
D203V13, multiclass
                                  clus
vv                                 FAM133B MUTATED FAM133B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                      2                20
  WHITE                                          3               223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(204) Variable = CATSPER1 MUTATION ANALYSIS
D204V1, survival
                    sevent
clus2                  0   1
  CATSPER1 MUTATED    14   4
  CATSPER1 WILD-TYPE 364  89
  CATSPER1 MUTATED CATSPER1 WILD-TYPE 
                18                453 
  CATSPER1 MUTATED CATSPER1 WILD-TYPE 
                 4                 89 
$`CATSPER1 MUTATED`
TCGA-A6-5666 TCGA-A6-6780 TCGA-AA-3530 TCGA-AA-3555 TCGA-AA-3710 TCGA-AA-3713 
       32.71        20.12        19.07        29.95        26.99        19.04 
TCGA-AA-3815 TCGA-AZ-5403 TCGA-AZ-6608 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6171 
       33.04        62.79         1.61        15.02        17.03        14.04 
TCGA-DM-A0XD TCGA-DM-A28F TCGA-F4-6854 TCGA-AG-A002 TCGA-AH-6549 TCGA-AH-6644 
       24.43        35.97         0.53        20.98        17.49         0.72 

$`CATSPER1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        22.06        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
        0.00        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       17.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       19.04        10.06        35.05         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
        5.13       106.75        22.36        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02         5.03        15.02        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       15.02        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       11.38        10.26       119.70        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       33.67        13.25        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       38.56         1.45         0.69         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  CATSPER1 MUTATED CATSPER1 WILD-TYPE 
              0.53               0.00 
  CATSPER1 MUTATED CATSPER1 WILD-TYPE 
             62.79             148.01 
  CATSPER1 MUTATED CATSPER1 WILD-TYPE 
            19.595             20.280 
[1] "0.5 - 62.8 (19.6)"  "0.0 - 148.0 (20.3)"
[1] "hr=" "1.4"
D204V2, continuous
D204V3, binary
                    cls
clus                   0   1
  CATSPER1 MUTATED    16   3
  CATSPER1 WILD-TYPE 350 116
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  CATSPER1 MUTATED     16    3
  CATSPER1 WILD-TYPE  350  116
        clus
vv       CATSPER1 MUTATED CATSPER1 WILD-TYPE
  COLON                16                350
  RECTUM                3                116
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CATSPER1 MUTATED         4        0        1         7         0         1
  CATSPER1 WILD-TYPE      87        1       31       131        10         0
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CATSPER1 MUTATED           0          1          1          0        1
  CATSPER1 WILD-TYPE        24         10         58         42       47
                    vv
clus                 STAGE IVA STAGE IVB
  CATSPER1 MUTATED           1         0
  CATSPER1 WILD-TYPE        17         1
D204V4, multiclass
            clus
vv           CATSPER1 MUTATED CATSPER1 WILD-TYPE
  STAGE I                   4                 87
  STAGE IA                  0                  1
  STAGE II                  1                 31
  STAGE IIA                 7                131
  STAGE IIB                 0                 10
  STAGE IIC                 1                  0
  STAGE III                 0                 24
  STAGE IIIA                1                 10
  STAGE IIIB                1                 58
  STAGE IIIC                0                 42
  STAGE IV                  1                 47
  STAGE IVA                 1                 17
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  CATSPER1 MUTATED     0   5  12   2
  CATSPER1 WILD-TYPE  17  87 317  48
D204V5, multiclass
    clus
vv   CATSPER1 MUTATED CATSPER1 WILD-TYPE
  T1                0                 17
  T2                5                 87
  T3               12                317
  T4                2                 48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  CATSPER1 MUTATED    14   3   0
  CATSPER1 WILD-TYPE 273 110  87
D204V6, multiclass
    clus
vv   CATSPER1 MUTATED CATSPER1 WILD-TYPE
  N0               14                273
  N1                3                110
  N2                0                 87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D204V7, binary
                    cls
clus                   0   1
  CATSPER1 MUTATED    13   2
  CATSPER1 WILD-TYPE 362  63
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  CATSPER1 MUTATED     13    2
  CATSPER1 WILD-TYPE  362   63
   clus
vv  CATSPER1 MUTATED CATSPER1 WILD-TYPE
  0               13                362
  1                2                 63
[1] 2 2
[1] FALSE
D204V8, binary
                    cls
clus                   0   1
  CATSPER1 MUTATED     8  11
  CATSPER1 WILD-TYPE 217 253
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  CATSPER1 MUTATED      8   11
  CATSPER1 WILD-TYPE  217  253
        clus
vv       CATSPER1 MUTATED CATSPER1 WILD-TYPE
  FEMALE                8                217
  MALE                 11                253
[1] 2 2
[1] FALSE
D204V9, binary
                    cls
clus                   0   1
  CATSPER1 MUTATED    14   1
  CATSPER1 WILD-TYPE 336  21
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  CATSPER1 MUTATED     14    1
  CATSPER1 WILD-TYPE  336   21
     clus
vv    CATSPER1 MUTATED CATSPER1 WILD-TYPE
  NO                14                336
  YES                1                 21
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CATSPER1 MUTATED                     14                             2
  CATSPER1 WILD-TYPE                  301                            45
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CATSPER1 MUTATED                       3                              0
  CATSPER1 WILD-TYPE                   103                             10
D204V10, multiclass
                                clus
vv                               CATSPER1 MUTATED CATSPER1 WILD-TYPE
  COLON ADENOCARCINOMA                         14                301
  COLON MUCINOUS ADENOCARCINOMA                 2                 45
  RECTAL ADENOCARCINOMA                         3                103
  RECTAL MUCINOUS ADENOCARCINOMA                0                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  CATSPER1 MUTATED    10   0   1   1
  CATSPER1 WILD-TYPE 335   4  30  24
D204V11, multiclass
    clus
vv   CATSPER1 MUTATED CATSPER1 WILD-TYPE
  R0               10                335
  R1                0                  4
  R2                1                 30
  RX                1                 24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D204V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CATSPER1 MUTATED                                  0     0
  CATSPER1 WILD-TYPE                                1    11
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  CATSPER1 MUTATED                           0    12
  CATSPER1 WILD-TYPE                        22   214
D204V13, multiclass
                                  clus
vv                                 CATSPER1 MUTATED CATSPER1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 11
  BLACK OR AFRICAN AMERICAN                       0                 22
  WHITE                                          12                214
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(205) Variable = GIGYF2 MUTATION ANALYSIS
D205V1, survival
                  sevent
clus2                0   1
  GIGYF2 MUTATED    24   4
  GIGYF2 WILD-TYPE 354  89
  GIGYF2 MUTATED GIGYF2 WILD-TYPE 
              28              443 
  GIGYF2 MUTATED GIGYF2 WILD-TYPE 
               4               89 
$`GIGYF2 MUTATED`
TCGA-A6-5661 TCGA-A6-5665 TCGA-AA-3492 TCGA-AA-3672 TCGA-AA-3877 TCGA-AA-3949 
       33.53        22.06         3.02         0.92        31.00        26.01 
TCGA-AA-A00J TCGA-AA-A010 TCGA-AD-6895 TCGA-AY-6197 TCGA-AZ-5403 TCGA-AZ-6598 
       18.05        34.98         0.72        21.44        62.79        49.41 
TCGA-AZ-6601 TCGA-CM-4743 TCGA-CM-5863 TCGA-CM-6163 TCGA-CM-6172 TCGA-D5-6536 
      100.01        23.05        15.02         2.96        11.01        17.85 
TCGA-D5-6920 TCGA-D5-6928 TCGA-D5-6929 TCGA-DM-A28H TCGA-F4-6856 TCGA-G4-6628 
        3.68        11.64         4.80       117.07        35.31        79.69 
TCGA-AG-3883 TCGA-AG-3892 TCGA-AG-3896 TCGA-AG-A002 
        1.02        13.02         1.02        20.98 

$`GIGYF2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       19.66        20.28         7.04         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
        2.01        14.01        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       29.98        18.05         2.01        12.99        24.00        33.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
       56.55         0.79         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       88.21         6.77        12.10        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 
       21.14        82.95         1.91       124.27        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       32.02        15.02         5.03        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
       12.00        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       13.02        15.02        14.04        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       43.27        15.12         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
       15.58         1.48         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        9.44         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
        0.53        47.41       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3885 TCGA-AG-3887 
        0.99         0.99        19.04        19.99        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       17.03        35.01        14.01        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  GIGYF2 MUTATED GIGYF2 WILD-TYPE 
            0.72             0.00 
  GIGYF2 MUTATED GIGYF2 WILD-TYPE 
          117.07           148.01 
  GIGYF2 MUTATED GIGYF2 WILD-TYPE 
          19.515           20.190 
[1] "0.7 - 117.1 (19.5)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.4"
D205V2, continuous
D205V3, binary
                  cls
clus                 0   1
  GIGYF2 MUTATED    26   4
  GIGYF2 WILD-TYPE 340 115
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GIGYF2 MUTATED     26    4
  GIGYF2 WILD-TYPE  340  115
        clus
vv       GIGYF2 MUTATED GIGYF2 WILD-TYPE
  COLON              26              340
  RECTUM              4              115
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GIGYF2 MUTATED         8        0        4         8         1         0
  GIGYF2 WILD-TYPE      83        1       28       130         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GIGYF2 MUTATED           1          0          4          2        1
  GIGYF2 WILD-TYPE        23         11         55         40       47
                  vv
clus               STAGE IVA STAGE IVB
  GIGYF2 MUTATED           0         0
  GIGYF2 WILD-TYPE        18         1
D205V4, multiclass
            clus
vv           GIGYF2 MUTATED GIGYF2 WILD-TYPE
  STAGE I                 8               83
  STAGE IA                0                1
  STAGE II                4               28
  STAGE IIA               8              130
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               1               23
  STAGE IIIA              0               11
  STAGE IIIB              4               55
  STAGE IIIC              2               40
  STAGE IV                1               47
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  GIGYF2 MUTATED     3   5  20   2
  GIGYF2 WILD-TYPE  14  87 309  48
D205V5, multiclass
    clus
vv   GIGYF2 MUTATED GIGYF2 WILD-TYPE
  T1              3               14
  T2              5               87
  T3             20              309
  T4              2               48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  GIGYF2 MUTATED    21   7   2
  GIGYF2 WILD-TYPE 266 106  85
D205V6, multiclass
    clus
vv   GIGYF2 MUTATED GIGYF2 WILD-TYPE
  N0             21              266
  N1              7              106
  N2              2               85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D205V7, binary
                  cls
clus                 0   1
  GIGYF2 MUTATED    24   1
  GIGYF2 WILD-TYPE 351  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GIGYF2 MUTATED     24    1
  GIGYF2 WILD-TYPE  351   64
   clus
vv  GIGYF2 MUTATED GIGYF2 WILD-TYPE
  0             24              351
  1              1               64
[1] 2 2
[1] FALSE
D205V8, binary
                  cls
clus                 0   1
  GIGYF2 MUTATED    15  15
  GIGYF2 WILD-TYPE 210 249
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GIGYF2 MUTATED     15   15
  GIGYF2 WILD-TYPE  210  249
        clus
vv       GIGYF2 MUTATED GIGYF2 WILD-TYPE
  FEMALE             15              210
  MALE               15              249
[1] 2 2
[1] FALSE
D205V9, binary
                  cls
clus                 0   1
  GIGYF2 MUTATED    22   0
  GIGYF2 WILD-TYPE 328  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GIGYF2 MUTATED     22    0
  GIGYF2 WILD-TYPE  328   22
     clus
vv    GIGYF2 MUTATED GIGYF2 WILD-TYPE
  NO              22              328
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  GIGYF2 MUTATED                     19                             7
  GIGYF2 WILD-TYPE                  296                            40
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  GIGYF2 MUTATED                       4                              0
  GIGYF2 WILD-TYPE                   102                             10
D205V10, multiclass
                                clus
vv                               GIGYF2 MUTATED GIGYF2 WILD-TYPE
  COLON ADENOCARCINOMA                       19              296
  COLON MUCINOUS ADENOCARCINOMA               7               40
  RECTAL ADENOCARCINOMA                       4              102
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  GIGYF2 MUTATED    25   0   0   0
  GIGYF2 WILD-TYPE 320   4  31  25
D205V11, multiclass
    clus
vv   GIGYF2 MUTATED GIGYF2 WILD-TYPE
  R0             25              320
  R1              0                4
  R2              0               31
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D205V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GIGYF2 MUTATED                                  0     0
  GIGYF2 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  GIGYF2 MUTATED                           1    18
  GIGYF2 WILD-TYPE                        21   208
D205V13, multiclass
                                  clus
vv                                 GIGYF2 MUTATED GIGYF2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                        18              208
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(206) Variable = RBM12 MUTATION ANALYSIS
D206V1, survival
                 sevent
clus2               0   1
  RBM12 MUTATED    13   2
  RBM12 WILD-TYPE 365  91
  RBM12 MUTATED RBM12 WILD-TYPE 
             15             456 
  RBM12 MUTATED RBM12 WILD-TYPE 
              2              91 
$`RBM12 MUTATED`
TCGA-A6-6651 TCGA-AA-3529 TCGA-AA-3663 TCGA-AA-3713 TCGA-AA-3949 TCGA-AD-5900 
       21.76         0.00         6.97        19.04        26.01         0.07 
TCGA-AZ-4315 TCGA-AZ-6599 TCGA-CM-6171 TCGA-DM-A28K TCGA-G4-6315 TCGA-G4-6625 
       58.39         6.77        14.04        98.24        61.91        91.79 
TCGA-AG-A002 TCGA-CI-6620 TCGA-EI-6508 
       20.98        33.17        20.91 

$`RBM12 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.08        25.18        24.16        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
       19.07        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       85.05        26.99        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       33.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
       16.31         0.95        33.01        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 
       14.99        12.99        13.02        15.02        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
      117.07         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6317 
       53.62        44.68        55.04        85.48        63.62        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6626 TCGA-G4-6628 
       22.09        13.78        35.80        26.17        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.69         0.72         6.05         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       20.55        19.96        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  RBM12 MUTATED RBM12 WILD-TYPE 
              0               0 
  RBM12 MUTATED RBM12 WILD-TYPE 
          98.24          148.01 
  RBM12 MUTATED RBM12 WILD-TYPE 
         20.980          20.085 
[1] "0.0 - 98.2 (21.0)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.8"
D206V2, continuous
D206V3, binary
                 cls
clus                0   1
  RBM12 MUTATED    12   3
  RBM12 WILD-TYPE 354 116
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM12 MUTATED     12    3
  RBM12 WILD-TYPE  354  116
        clus
vv       RBM12 MUTATED RBM12 WILD-TYPE
  COLON             12             354
  RECTUM             3             116
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RBM12 MUTATED         4        0        1         3         0         0
  RBM12 WILD-TYPE      87        1       31       135        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RBM12 MUTATED           0          0          3          1        2         1
  RBM12 WILD-TYPE        24         11         56         41       46        17
                 vv
clus              STAGE IVB
  RBM12 MUTATED           0
  RBM12 WILD-TYPE         1
D206V4, multiclass
            clus
vv           RBM12 MUTATED RBM12 WILD-TYPE
  STAGE I                4              87
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              3             135
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             3              56
  STAGE IIIC             1              41
  STAGE IV               2              46
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  RBM12 MUTATED     0   4  11   0
  RBM12 WILD-TYPE  17  88 318  50
D206V5, multiclass
    clus
vv   RBM12 MUTATED RBM12 WILD-TYPE
  T1             0              17
  T2             4              88
  T3            11             318
  T4             0              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  RBM12 MUTATED     9   5   1
  RBM12 WILD-TYPE 278 108  86
D206V6, multiclass
    clus
vv   RBM12 MUTATED RBM12 WILD-TYPE
  N0             9             278
  N1             5             108
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D206V7, binary
                 cls
clus                0   1
  RBM12 MUTATED     9   3
  RBM12 WILD-TYPE 366  62
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM12 MUTATED      9    3
  RBM12 WILD-TYPE  366   62
   clus
vv  RBM12 MUTATED RBM12 WILD-TYPE
  0             9             366
  1             3              62
[1] 2 2
[1] FALSE
D206V8, binary
                 cls
clus                0   1
  RBM12 MUTATED     7   8
  RBM12 WILD-TYPE 218 256
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM12 MUTATED      7    8
  RBM12 WILD-TYPE  218  256
        clus
vv       RBM12 MUTATED RBM12 WILD-TYPE
  FEMALE             7             218
  MALE               8             256
[1] 2 2
[1] FALSE
D206V9, binary
                 cls
clus                0   1
  RBM12 MUTATED    11   1
  RBM12 WILD-TYPE 339  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM12 MUTATED     11    1
  RBM12 WILD-TYPE  339   21
     clus
vv    RBM12 MUTATED RBM12 WILD-TYPE
  NO             11             339
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  RBM12 MUTATED                      9                             3
  RBM12 WILD-TYPE                  306                            44
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  RBM12 MUTATED                       3                              0
  RBM12 WILD-TYPE                   103                             10
D206V10, multiclass
                                clus
vv                               RBM12 MUTATED RBM12 WILD-TYPE
  COLON ADENOCARCINOMA                       9             306
  COLON MUCINOUS ADENOCARCINOMA              3              44
  RECTAL ADENOCARCINOMA                      3             103
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  RBM12 MUTATED    10   0   1   0
  RBM12 WILD-TYPE 335   4  30  25
D206V11, multiclass
    clus
vv   RBM12 MUTATED RBM12 WILD-TYPE
  R0            10             335
  R1             0               4
  R2             1              30
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D206V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RBM12 MUTATED                                  0     0
  RBM12 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  RBM12 MUTATED                           0    10
  RBM12 WILD-TYPE                        22   216
D206V13, multiclass
                                  clus
vv                                 RBM12 MUTATED RBM12 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                       10             216
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(207) Variable = EIF2AK4 MUTATION ANALYSIS
D207V1, survival
                   sevent
clus2                 0   1
  EIF2AK4 MUTATED    18   2
  EIF2AK4 WILD-TYPE 360  91
  EIF2AK4 MUTATED EIF2AK4 WILD-TYPE 
               20               451 
  EIF2AK4 MUTATED EIF2AK4 WILD-TYPE 
                2                91 
$`EIF2AK4 MUTATED`
TCGA-A6-3809 TCGA-A6-5661 TCGA-A6-6780 TCGA-AA-3681 TCGA-AA-3815 TCGA-AA-3864 
       32.75        33.53        20.12         5.98        33.04        53.00 
TCGA-AA-3977 TCGA-AA-A024 TCGA-AD-6895 TCGA-AZ-6601 TCGA-CA-6717 TCGA-CM-5349 
       25.02        39.06         0.72       100.01        12.76        30.08 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6169 TCGA-CM-6171 TCGA-D5-6534 TCGA-F4-6856 
       12.00         2.96        13.02        14.04        43.27        35.31 
TCGA-AG-A002 TCGA-DC-5869 
       20.98         5.03 

$`EIF2AK4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       31.63        30.44        29.19        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6781 
       24.16        21.76        24.69        24.39        23.87        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
       11.01        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
       26.99        19.04        19.04        10.06        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       30.05        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 
        1.02        33.04        35.01        26.01        37.02        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
       56.55         0.79         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07        12.20        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.03        22.98        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        17.03        15.02        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       14.99        12.99        15.02        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
        1.32        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       47.41       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
       78.12         7.17        15.02        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  EIF2AK4 MUTATED EIF2AK4 WILD-TYPE 
             0.72              0.00 
  EIF2AK4 MUTATED EIF2AK4 WILD-TYPE 
           100.01            148.01 
  EIF2AK4 MUTATED EIF2AK4 WILD-TYPE 
            23.00             20.05 
[1] "0.7 - 100.0 (23.0)" "0.0 - 148.0 (20.1)"
[1] "hr=" "2"  
D207V2, continuous
D207V3, binary
                   cls
clus                  0   1
  EIF2AK4 MUTATED    18   2
  EIF2AK4 WILD-TYPE 348 117
[1] "tbl2"
                   cls
clus                [,1] [,2]
  EIF2AK4 MUTATED     18    2
  EIF2AK4 WILD-TYPE  348  117
        clus
vv       EIF2AK4 MUTATED EIF2AK4 WILD-TYPE
  COLON               18               348
  RECTUM               2               117
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  EIF2AK4 MUTATED         4        0        3         7         1         0
  EIF2AK4 WILD-TYPE      87        1       29       131         9         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  EIF2AK4 MUTATED           1          0          2          0        0
  EIF2AK4 WILD-TYPE        23         11         57         42       48
                   vv
clus                STAGE IVA STAGE IVB
  EIF2AK4 MUTATED           0         0
  EIF2AK4 WILD-TYPE        18         1
D207V4, multiclass
            clus
vv           EIF2AK4 MUTATED EIF2AK4 WILD-TYPE
  STAGE I                  4                87
  STAGE IA                 0                 1
  STAGE II                 3                29
  STAGE IIA                7               131
  STAGE IIB                1                 9
  STAGE IIC                0                 1
  STAGE III                1                23
  STAGE IIIA               0                11
  STAGE IIIB               2                57
  STAGE IIIC               0                42
  STAGE IV                 0                48
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  EIF2AK4 MUTATED     1   4  14   1
  EIF2AK4 WILD-TYPE  16  88 315  49
D207V5, multiclass
    clus
vv   EIF2AK4 MUTATED EIF2AK4 WILD-TYPE
  T1               1                16
  T2               4                88
  T3              14               315
  T4               1                49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  EIF2AK4 MUTATED    16   4   0
  EIF2AK4 WILD-TYPE 271 109  87
D207V6, multiclass
    clus
vv   EIF2AK4 MUTATED EIF2AK4 WILD-TYPE
  N0              16               271
  N1               4               109
  N2               0                87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D207V7, binary
                   cls
clus                  0   1
  EIF2AK4 MUTATED    17   0
  EIF2AK4 WILD-TYPE 358  65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  EIF2AK4 MUTATED     17    0
  EIF2AK4 WILD-TYPE  358   65
   clus
vv  EIF2AK4 MUTATED EIF2AK4 WILD-TYPE
  0              17               358
  1               0                65
[1] 2 2
[1] FALSE
D207V8, binary
                   cls
clus                  0   1
  EIF2AK4 MUTATED     9  11
  EIF2AK4 WILD-TYPE 216 253
[1] "tbl2"
                   cls
clus                [,1] [,2]
  EIF2AK4 MUTATED      9   11
  EIF2AK4 WILD-TYPE  216  253
        clus
vv       EIF2AK4 MUTATED EIF2AK4 WILD-TYPE
  FEMALE               9               216
  MALE                11               253
[1] 2 2
[1] FALSE
D207V9, binary
                   cls
clus                  0   1
  EIF2AK4 MUTATED    18   0
  EIF2AK4 WILD-TYPE 332  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  EIF2AK4 MUTATED     18    0
  EIF2AK4 WILD-TYPE  332   22
     clus
vv    EIF2AK4 MUTATED EIF2AK4 WILD-TYPE
  NO               18               332
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  EIF2AK4 MUTATED                     11                             7
  EIF2AK4 WILD-TYPE                  304                            40
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  EIF2AK4 MUTATED                       2                              0
  EIF2AK4 WILD-TYPE                   104                             10
D207V10, multiclass
                                clus
vv                               EIF2AK4 MUTATED EIF2AK4 WILD-TYPE
  COLON ADENOCARCINOMA                        11               304
  COLON MUCINOUS ADENOCARCINOMA                7                40
  RECTAL ADENOCARCINOMA                        2               104
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  EIF2AK4 MUTATED    15   0   0   1
  EIF2AK4 WILD-TYPE 330   4  31  24
D207V11, multiclass
    clus
vv   EIF2AK4 MUTATED EIF2AK4 WILD-TYPE
  R0              15               330
  R1               0                 4
  R2               0                31
  RX               1                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D207V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  EIF2AK4 MUTATED                                  0     1
  EIF2AK4 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  EIF2AK4 MUTATED                           3    10
  EIF2AK4 WILD-TYPE                        19   216
D207V13, multiclass
                                  clus
vv                                 EIF2AK4 MUTATED EIF2AK4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                10
  BLACK OR AFRICAN AMERICAN                      3                19
  WHITE                                         10               216
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(208) Variable = PI4K2B MUTATION ANALYSIS
D208V1, survival
                  sevent
clus2                0   1
  PI4K2B MUTATED    10   2
  PI4K2B WILD-TYPE 368  91
  PI4K2B MUTATED PI4K2B WILD-TYPE 
              12              459 
  PI4K2B MUTATED PI4K2B WILD-TYPE 
               2               91 
$`PI4K2B MUTATED`
TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-6648 TCGA-AA-A00J TCGA-AZ-6608 TCGA-CA-6717 
       32.91        30.44        25.18        18.05         1.61        12.76 
TCGA-CK-5913 TCGA-DM-A1HA TCGA-AG-3742 TCGA-AG-3892 TCGA-CI-6622 TCGA-DY-A1DG 
       51.32       131.51         0.99        13.02         6.97        51.48 

$`PI4K2B WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       31.63        29.19        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6649 
       32.71        27.09        22.52         8.38        25.08        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07        12.20        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 
       17.56       148.01        85.45        15.62        49.08         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3878 TCGA-AG-3881 
        7.99         0.99        37.02        32.98         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 
       19.99         1.02        17.95        36.95        17.03        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
       33.17         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  PI4K2B MUTATED PI4K2B WILD-TYPE 
            0.99             0.00 
  PI4K2B MUTATED PI4K2B WILD-TYPE 
          131.51           148.01 
  PI4K2B MUTATED PI4K2B WILD-TYPE 
          21.615           20.190 
[1] "1.0 - 131.5 (21.6)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.4"
D208V2, continuous
D208V3, binary
                  cls
clus                 0   1
  PI4K2B MUTATED    10   4
  PI4K2B WILD-TYPE 356 115
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PI4K2B MUTATED     10    4
  PI4K2B WILD-TYPE  356  115
        clus
vv       PI4K2B MUTATED PI4K2B WILD-TYPE
  COLON              10              356
  RECTUM              4              115
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PI4K2B MUTATED         4        0        0         2         1         0
  PI4K2B WILD-TYPE      87        1       32       136         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PI4K2B MUTATED           1          1          1          2        0
  PI4K2B WILD-TYPE        23         10         58         40       48
                  vv
clus               STAGE IVA STAGE IVB
  PI4K2B MUTATED           2         0
  PI4K2B WILD-TYPE        16         1
D208V4, multiclass
            clus
vv           PI4K2B MUTATED PI4K2B WILD-TYPE
  STAGE I                 4               87
  STAGE IA                0                1
  STAGE II                0               32
  STAGE IIA               2              136
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               1               23
  STAGE IIIA              1               10
  STAGE IIIB              1               58
  STAGE IIIC              2               40
  STAGE IV                0               48
  STAGE IVA               2               16
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  PI4K2B MUTATED     2   3   7   2
  PI4K2B WILD-TYPE  15  89 322  48
D208V5, multiclass
    clus
vv   PI4K2B MUTATED PI4K2B WILD-TYPE
  T1              2               15
  T2              3               89
  T3              7              322
  T4              2               48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  PI4K2B MUTATED     8   3   3
  PI4K2B WILD-TYPE 279 110  84
D208V6, multiclass
    clus
vv   PI4K2B MUTATED PI4K2B WILD-TYPE
  N0              8              279
  N1              3              110
  N2              3               84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D208V7, binary
                  cls
clus                 0   1
  PI4K2B MUTATED    10   2
  PI4K2B WILD-TYPE 365  63
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PI4K2B MUTATED     10    2
  PI4K2B WILD-TYPE  365   63
   clus
vv  PI4K2B MUTATED PI4K2B WILD-TYPE
  0             10              365
  1              2               63
[1] 2 2
[1] FALSE
D208V8, binary
                  cls
clus                 0   1
  PI4K2B MUTATED     4  10
  PI4K2B WILD-TYPE 221 254
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PI4K2B MUTATED      4   10
  PI4K2B WILD-TYPE  221  254
        clus
vv       PI4K2B MUTATED PI4K2B WILD-TYPE
  FEMALE              4              221
  MALE               10              254
[1] 2 2
[1] FALSE
D208V9, binary
                  cls
clus                 0   1
  PI4K2B MUTATED     8   0
  PI4K2B WILD-TYPE 342  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PI4K2B MUTATED      8    0
  PI4K2B WILD-TYPE  342   22
     clus
vv    PI4K2B MUTATED PI4K2B WILD-TYPE
  NO               8              342
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PI4K2B MUTATED                      7                             3
  PI4K2B WILD-TYPE                  308                            44
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PI4K2B MUTATED                       4                              0
  PI4K2B WILD-TYPE                   102                             10
D208V10, multiclass
                                clus
vv                               PI4K2B MUTATED PI4K2B WILD-TYPE
  COLON ADENOCARCINOMA                        7              308
  COLON MUCINOUS ADENOCARCINOMA               3               44
  RECTAL ADENOCARCINOMA                       4              102
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  PI4K2B MUTATED     6   0   0   2
  PI4K2B WILD-TYPE 339   4  31  23
D208V11, multiclass
    clus
vv   PI4K2B MUTATED PI4K2B WILD-TYPE
  R0              6              339
  R1              0                4
  R2              0               31
  RX              2               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D208V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PI4K2B MUTATED                                  0     1
  PI4K2B WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  PI4K2B MUTATED                           0     9
  PI4K2B WILD-TYPE                        22   217
D208V13, multiclass
                                  clus
vv                                 PI4K2B MUTATED PI4K2B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         9              217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(209) Variable = HIPK2 MUTATION ANALYSIS
D209V1, survival
                 sevent
clus2               0   1
  HIPK2 MUTATED    20   6
  HIPK2 WILD-TYPE 358  87
  HIPK2 MUTATED HIPK2 WILD-TYPE 
             26             445 
  HIPK2 MUTATED HIPK2 WILD-TYPE 
              6              87 
$`HIPK2 MUTATED`
TCGA-A6-6654 TCGA-AA-3492 TCGA-AA-3811 TCGA-AA-3947 TCGA-AA-A02O TCGA-AD-6901 
       23.87         3.02        10.06        33.01         0.92        22.42 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-6197 TCGA-CK-4950 TCGA-CM-5861 TCGA-CM-6163 
       14.50        27.09        21.44        85.45        15.02         2.96 
TCGA-CM-6171 TCGA-D5-6533 TCGA-D5-6539 TCGA-D5-6541 TCGA-DM-A1D6 TCGA-DM-A1DB 
       14.04         1.32        12.49        15.58        49.91        44.32 
TCGA-F4-6856 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 
       35.31        65.85        53.62        35.80        26.17        79.69 
TCGA-AG-A02X TCGA-CL-5917 
       41.00        78.12 

$`HIPK2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 
       20.12        19.66        20.28         7.04         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        19.04        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
        5.03        14.01        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AY-4070 TCGA-AY-4071 
        5.79        27.42        10.88         0.20        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       33.01        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 
       12.76        10.06        14.30        17.56       148.01        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 
       29.06        22.03        22.98        30.08        32.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6164 
       15.02        15.02        17.03        15.02        12.00        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       55.92        20.19        18.25        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
        4.80        17.13        16.14         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
       38.20       130.65        92.75        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
        7.50       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
      133.18        74.56        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6625 TCGA-G4-6626 
       61.91        36.00        22.09        13.78        91.79        46.75 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       61.97        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  HIPK2 MUTATED HIPK2 WILD-TYPE 
           0.92            0.00 
  HIPK2 MUTATED HIPK2 WILD-TYPE 
          85.45          148.01 
  HIPK2 MUTATED HIPK2 WILD-TYPE 
          25.02           20.02 
[1] "0.9 - 85.5 (25.0)"  "0.0 - 148.0 (20.0)"
[1] "hr=" "1"  
D209V2, continuous
D209V3, binary
                 cls
clus                0   1
  HIPK2 MUTATED    24   2
  HIPK2 WILD-TYPE 342 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HIPK2 MUTATED     24    2
  HIPK2 WILD-TYPE  342  117
        clus
vv       HIPK2 MUTATED HIPK2 WILD-TYPE
  COLON             24             342
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  HIPK2 MUTATED         6        0        2         8         2         0
  HIPK2 WILD-TYPE      85        1       30       130         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  HIPK2 MUTATED           1          1          3          1        1         0
  HIPK2 WILD-TYPE        23         10         56         41       47        18
                 vv
clus              STAGE IVB
  HIPK2 MUTATED           0
  HIPK2 WILD-TYPE         1
D209V4, multiclass
            clus
vv           HIPK2 MUTATED HIPK2 WILD-TYPE
  STAGE I                6              85
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA              8             130
  STAGE IIB              2               8
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             1              10
  STAGE IIIB             3              56
  STAGE IIIC             1              41
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  HIPK2 MUTATED     1   5  17   3
  HIPK2 WILD-TYPE  16  87 312  47
D209V5, multiclass
    clus
vv   HIPK2 MUTATED HIPK2 WILD-TYPE
  T1             1              16
  T2             5              87
  T3            17             312
  T4             3              47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  HIPK2 MUTATED    21   3   2
  HIPK2 WILD-TYPE 266 110  85
D209V6, multiclass
    clus
vv   HIPK2 MUTATED HIPK2 WILD-TYPE
  N0            21             266
  N1             3             110
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D209V7, binary
                 cls
clus                0   1
  HIPK2 MUTATED    22   1
  HIPK2 WILD-TYPE 353  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HIPK2 MUTATED     22    1
  HIPK2 WILD-TYPE  353   64
   clus
vv  HIPK2 MUTATED HIPK2 WILD-TYPE
  0            22             353
  1             1              64
[1] 2 2
[1] FALSE
D209V8, binary
                 cls
clus                0   1
  HIPK2 MUTATED    16  10
  HIPK2 WILD-TYPE 209 254
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HIPK2 MUTATED     16   10
  HIPK2 WILD-TYPE  209  254
        clus
vv       HIPK2 MUTATED HIPK2 WILD-TYPE
  FEMALE            16             209
  MALE              10             254
[1] 2 2
[1] FALSE
D209V9, binary
                 cls
clus                0   1
  HIPK2 MUTATED    20   0
  HIPK2 WILD-TYPE 330  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HIPK2 MUTATED     20    0
  HIPK2 WILD-TYPE  330   22
     clus
vv    HIPK2 MUTATED HIPK2 WILD-TYPE
  NO             20             330
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  HIPK2 MUTATED                     21                             3
  HIPK2 WILD-TYPE                  294                            44
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  HIPK2 MUTATED                       2                              0
  HIPK2 WILD-TYPE                   104                             10
D209V10, multiclass
                                clus
vv                               HIPK2 MUTATED HIPK2 WILD-TYPE
  COLON ADENOCARCINOMA                      21             294
  COLON MUCINOUS ADENOCARCINOMA              3              44
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  HIPK2 MUTATED    20   1   0   1
  HIPK2 WILD-TYPE 325   3  31  24
D209V11, multiclass
    clus
vv   HIPK2 MUTATED HIPK2 WILD-TYPE
  R0            20             325
  R1             1               3
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D209V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HIPK2 MUTATED                                  0     0
  HIPK2 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  HIPK2 MUTATED                           1    20
  HIPK2 WILD-TYPE                        21   206
D209V13, multiclass
                                  clus
vv                                 HIPK2 MUTATED HIPK2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                       20             206
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(210) Variable = SLC4A10 MUTATION ANALYSIS
D210V1, survival
                   sevent
clus2                 0   1
  SLC4A10 MUTATED    22   6
  SLC4A10 WILD-TYPE 356  87
  SLC4A10 MUTATED SLC4A10 WILD-TYPE 
               28               443 
  SLC4A10 MUTATED SLC4A10 WILD-TYPE 
                6                87 
$`SLC4A10 MUTATED`
TCGA-A6-3809 TCGA-A6-5659 TCGA-A6-6141 TCGA-AA-A010 TCGA-AA-A01R TCGA-AD-6901 
       32.75        30.44         8.38        34.98        35.01        22.42 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4681 TCGA-AZ-6606 TCGA-CK-6747 TCGA-CM-5860 
       17.82        58.39       106.75        11.74        82.95        32.02 
TCGA-CM-5864 TCGA-CM-6162 TCGA-D5-6536 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.02        12.00        17.85         4.41        12.43        14.30 
TCGA-D5-6930 TCGA-DM-A1D6 TCGA-DM-A285 TCGA-DM-A28G TCGA-DM-A28K TCGA-F4-6570 
        1.51        49.91         6.12        60.79        98.24         6.18 
TCGA-F4-6856 TCGA-G4-6293 TCGA-AG-A002 TCGA-DC-6682 
       35.31       133.18        20.98         4.01 

$`SLC4A10 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       31.63        29.19        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       32.71        27.09        22.52        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
       38.07         1.02         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AZ-4323 TCGA-AZ-4616 
       16.31         0.95        33.01        21.44         1.41         5.13 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
      100.01        29.56         5.23         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6748 TCGA-CK-6751 
       49.08        51.32         9.99        21.14         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.03        22.98        30.08        15.02         5.03        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       17.03        15.02         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 
       20.19        18.25         1.32        43.27        15.12         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 
        9.04         9.44        11.64         4.80        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28H 
      135.65       139.17        81.37       119.93        35.97       117.07 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
        8.61        31.96        35.74        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        5.95         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  SLC4A10 MUTATED SLC4A10 WILD-TYPE 
             1.51              0.00 
  SLC4A10 MUTATED SLC4A10 WILD-TYPE 
           133.18            148.01 
  SLC4A10 MUTATED SLC4A10 WILD-TYPE 
            21.70             20.12 
[1] "1.5 - 133.2 (21.7)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.2"
D210V2, continuous
D210V3, binary
                   cls
clus                  0   1
  SLC4A10 MUTATED    27   2
  SLC4A10 WILD-TYPE 339 117
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC4A10 MUTATED     27    2
  SLC4A10 WILD-TYPE  339  117
        clus
vv       SLC4A10 MUTATED SLC4A10 WILD-TYPE
  COLON               27               339
  RECTUM               2               117
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SLC4A10 MUTATED         5        0        0        13         2         0
  SLC4A10 WILD-TYPE      86        1       32       125         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC4A10 MUTATED           2          1          2          0        3
  SLC4A10 WILD-TYPE        22         10         57         42       45
                   vv
clus                STAGE IVA STAGE IVB
  SLC4A10 MUTATED           0         0
  SLC4A10 WILD-TYPE        18         1
D210V4, multiclass
            clus
vv           SLC4A10 MUTATED SLC4A10 WILD-TYPE
  STAGE I                  5                86
  STAGE IA                 0                 1
  STAGE II                 0                32
  STAGE IIA               13               125
  STAGE IIB                2                 8
  STAGE IIC                0                 1
  STAGE III                2                22
  STAGE IIIA               1                10
  STAGE IIIB               2                57
  STAGE IIIC               0                42
  STAGE IV                 3                45
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  SLC4A10 MUTATED     0   5  21   3
  SLC4A10 WILD-TYPE  17  87 308  47
D210V5, multiclass
    clus
vv   SLC4A10 MUTATED SLC4A10 WILD-TYPE
  T1               0                17
  T2               5                87
  T3              21               308
  T4               3                47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  SLC4A10 MUTATED    21   4   4
  SLC4A10 WILD-TYPE 266 109  83
D210V6, multiclass
    clus
vv   SLC4A10 MUTATED SLC4A10 WILD-TYPE
  N0              21               266
  N1               4               109
  N2               4                83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D210V7, binary
                   cls
clus                  0   1
  SLC4A10 MUTATED    24   3
  SLC4A10 WILD-TYPE 351  62
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC4A10 MUTATED     24    3
  SLC4A10 WILD-TYPE  351   62
   clus
vv  SLC4A10 MUTATED SLC4A10 WILD-TYPE
  0              24               351
  1               3                62
[1] 2 2
[1] FALSE
D210V8, binary
                   cls
clus                  0   1
  SLC4A10 MUTATED    10  19
  SLC4A10 WILD-TYPE 215 245
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC4A10 MUTATED     10   19
  SLC4A10 WILD-TYPE  215  245
        clus
vv       SLC4A10 MUTATED SLC4A10 WILD-TYPE
  FEMALE              10               215
  MALE                19               245
[1] 2 2
[1] FALSE
D210V9, binary
                   cls
clus                  0   1
  SLC4A10 MUTATED    20   1
  SLC4A10 WILD-TYPE 330  21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC4A10 MUTATED     20    1
  SLC4A10 WILD-TYPE  330   21
     clus
vv    SLC4A10 MUTATED SLC4A10 WILD-TYPE
  NO               20               330
  YES               1                21
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SLC4A10 MUTATED                     19                             8
  SLC4A10 WILD-TYPE                  296                            39
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SLC4A10 MUTATED                       2                              0
  SLC4A10 WILD-TYPE                   104                             10
D210V10, multiclass
                                clus
vv                               SLC4A10 MUTATED SLC4A10 WILD-TYPE
  COLON ADENOCARCINOMA                        19               296
  COLON MUCINOUS ADENOCARCINOMA                8                39
  RECTAL ADENOCARCINOMA                        2               104
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  SLC4A10 MUTATED    20   0   1   1
  SLC4A10 WILD-TYPE 325   4  30  24
D210V11, multiclass
    clus
vv   SLC4A10 MUTATED SLC4A10 WILD-TYPE
  R0              20               325
  R1               0                 4
  R2               1                30
  RX               1                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D210V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SLC4A10 MUTATED                                  0     0
  SLC4A10 WILD-TYPE                                1    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  SLC4A10 MUTATED                           2    23
  SLC4A10 WILD-TYPE                        20   203
D210V13, multiclass
                                  clus
vv                                 SLC4A10 MUTATED SLC4A10 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                      2                20
  WHITE                                         23               203
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(211) Variable = KLHL10 MUTATION ANALYSIS
D211V1, survival
                  sevent
clus2                0   1
  KLHL10 MUTATED    13   6
  KLHL10 WILD-TYPE 365  87
  KLHL10 MUTATED KLHL10 WILD-TYPE 
              19              452 
  KLHL10 MUTATED KLHL10 WILD-TYPE 
               6               87 
$`KLHL10 MUTATED`
TCGA-A6-5659 TCGA-A6-5660 TCGA-AA-3663 TCGA-AD-6964 TCGA-AU-6004 TCGA-AY-6197 
       30.44        29.19         6.97        10.88        27.09        21.44 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CA-6718 TCGA-CM-4743 TCGA-CM-5868 TCGA-D5-6533 
      100.01         1.61        10.06        23.05        17.03         1.32 
TCGA-D5-6535 TCGA-D5-6928 TCGA-DM-A1D4 TCGA-G4-6588 TCGA-G4-6626 TCGA-AG-A002 
       15.12        11.64        92.75        26.17        46.75        20.98 
TCGA-F5-6812 
        0.66 

$`KLHL10 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       32.91        31.63        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
        0.79         0.72         5.79        22.42        27.42         0.20 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4315 
       14.50        16.31         0.95        33.01        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       49.41         6.77        12.10        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        3.19        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.20        12.76        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
        1.91       124.27        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
        5.03        15.02        15.02        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6534 
       19.59        56.09        55.92        20.19        18.25        43.27 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
        9.44         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-DM-A1D7 
      119.70        24.43        38.20       130.65        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 
       61.91        36.00        22.09        13.78        35.80        91.79 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6813 
        9.96        49.51        31.30        28.57        32.19         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  KLHL10 MUTATED KLHL10 WILD-TYPE 
            0.66             0.00 
  KLHL10 MUTATED KLHL10 WILD-TYPE 
          100.01           148.01 
  KLHL10 MUTATED KLHL10 WILD-TYPE 
          20.980           20.155 
[1] "0.7 - 100.0 (21.0)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.7"
D211V2, continuous
D211V3, binary
                  cls
clus                 0   1
  KLHL10 MUTATED    19   2
  KLHL10 WILD-TYPE 347 117
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KLHL10 MUTATED     19    2
  KLHL10 WILD-TYPE  347  117
        clus
vv       KLHL10 MUTATED KLHL10 WILD-TYPE
  COLON              19              347
  RECTUM              2              117
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KLHL10 MUTATED         3        0        2         8         0         0
  KLHL10 WILD-TYPE      88        1       30       130        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KLHL10 MUTATED           0          1          2          2        1
  KLHL10 WILD-TYPE        24         10         57         40       47
                  vv
clus               STAGE IVA STAGE IVB
  KLHL10 MUTATED           1         0
  KLHL10 WILD-TYPE        17         1
D211V4, multiclass
            clus
vv           KLHL10 MUTATED KLHL10 WILD-TYPE
  STAGE I                 3               88
  STAGE IA                0                1
  STAGE II                2               30
  STAGE IIA               8              130
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              1               10
  STAGE IIIB              2               57
  STAGE IIIC              2               40
  STAGE IV                1               47
  STAGE IVA               1               17
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  KLHL10 MUTATED     0   4  14   3
  KLHL10 WILD-TYPE  17  88 315  47
D211V5, multiclass
    clus
vv   KLHL10 MUTATED KLHL10 WILD-TYPE
  T1              0               17
  T2              4               88
  T3             14              315
  T4              3               47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  KLHL10 MUTATED    14   3   4
  KLHL10 WILD-TYPE 273 110  83
D211V6, multiclass
    clus
vv   KLHL10 MUTATED KLHL10 WILD-TYPE
  N0             14              273
  N1              3              110
  N2              4               83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D211V7, binary
                  cls
clus                 0   1
  KLHL10 MUTATED    15   2
  KLHL10 WILD-TYPE 360  63
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KLHL10 MUTATED     15    2
  KLHL10 WILD-TYPE  360   63
   clus
vv  KLHL10 MUTATED KLHL10 WILD-TYPE
  0             15              360
  1              2               63
[1] 2 2
[1] FALSE
D211V8, binary
                  cls
clus                 0   1
  KLHL10 MUTATED     7  14
  KLHL10 WILD-TYPE 218 250
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KLHL10 MUTATED      7   14
  KLHL10 WILD-TYPE  218  250
        clus
vv       KLHL10 MUTATED KLHL10 WILD-TYPE
  FEMALE              7              218
  MALE               14              250
[1] 2 2
[1] FALSE
D211V9, binary
                  cls
clus                 0   1
  KLHL10 MUTATED    15   0
  KLHL10 WILD-TYPE 335  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KLHL10 MUTATED     15    0
  KLHL10 WILD-TYPE  335   22
     clus
vv    KLHL10 MUTATED KLHL10 WILD-TYPE
  NO              15              335
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  KLHL10 MUTATED                     17                             2
  KLHL10 WILD-TYPE                  298                            45
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  KLHL10 MUTATED                       2                              0
  KLHL10 WILD-TYPE                   104                             10
D211V10, multiclass
                                clus
vv                               KLHL10 MUTATED KLHL10 WILD-TYPE
  COLON ADENOCARCINOMA                       17              298
  COLON MUCINOUS ADENOCARCINOMA               2               45
  RECTAL ADENOCARCINOMA                       2              104
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  KLHL10 MUTATED    13   0   1   2
  KLHL10 WILD-TYPE 332   4  30  23
D211V11, multiclass
    clus
vv   KLHL10 MUTATED KLHL10 WILD-TYPE
  R0             13              332
  R1              0                4
  R2              1               30
  RX              2               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D211V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KLHL10 MUTATED                                  0     1
  KLHL10 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  KLHL10 MUTATED                           1    16
  KLHL10 WILD-TYPE                        21   210
D211V13, multiclass
                                  clus
vv                                 KLHL10 MUTATED KLHL10 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                        16              210
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(212) Variable = LINGO4 MUTATION ANALYSIS
D212V1, survival
                  sevent
clus2                0   1
  LINGO4 MUTATED     5   4
  LINGO4 WILD-TYPE 373  89
  LINGO4 MUTATED LINGO4 WILD-TYPE 
               9              462 
  LINGO4 MUTATED LINGO4 WILD-TYPE 
               4               89 
$`LINGO4 MUTATED`
TCGA-A6-2671 TCGA-AA-3672 TCGA-AA-3864 TCGA-AA-3950 TCGA-AA-A00N TCGA-AZ-6598 
       43.76         0.92        53.00        24.00         4.01        49.41 
TCGA-CM-6171 TCGA-D5-6537 TCGA-D5-6930 
       14.04         4.80         1.51 

$`LINGO4 WILD-TYPE`
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       46.65        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 
        6.97        54.02         2.01        14.01        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 
        0.99        31.07        31.07        30.05        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        33.01        26.01         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       88.21         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
       17.85        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       11.64         4.80        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  LINGO4 MUTATED LINGO4 WILD-TYPE 
            0.92             0.00 
  LINGO4 MUTATED LINGO4 WILD-TYPE 
           53.00           148.01 
  LINGO4 MUTATED LINGO4 WILD-TYPE 
          14.040           20.235 
[1] "0.9 - 53.0 (14.0)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "2.5"
D212V2, continuous
D212V3, binary
                  cls
clus                 0   1
  LINGO4 MUTATED    10   0
  LINGO4 WILD-TYPE 356 119
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LINGO4 MUTATED     10    0
  LINGO4 WILD-TYPE  356  119
        clus
vv       LINGO4 MUTATED LINGO4 WILD-TYPE
  COLON              10              356
  RECTUM              0              119
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  LINGO4 MUTATED         1        0        3         2         1         0
  LINGO4 WILD-TYPE      90        1       29       136         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  LINGO4 MUTATED           1          0          1          0        1
  LINGO4 WILD-TYPE        23         11         58         42       47
                  vv
clus               STAGE IVA STAGE IVB
  LINGO4 MUTATED           0         0
  LINGO4 WILD-TYPE        18         1
D212V4, multiclass
            clus
vv           LINGO4 MUTATED LINGO4 WILD-TYPE
  STAGE I                 1               90
  STAGE IA                0                1
  STAGE II                3               29
  STAGE IIA               2              136
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               1               23
  STAGE IIIA              0               11
  STAGE IIIB              1               58
  STAGE IIIC              0               42
  STAGE IV                1               47
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  LINGO4 MUTATED     0   1   7   2
  LINGO4 WILD-TYPE  17  91 322  48
D212V5, multiclass
    clus
vv   LINGO4 MUTATED LINGO4 WILD-TYPE
  T1              0               17
  T2              1               91
  T3              7              322
  T4              2               48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  LINGO4 MUTATED     7   2   1
  LINGO4 WILD-TYPE 280 111  86
D212V6, multiclass
    clus
vv   LINGO4 MUTATED LINGO4 WILD-TYPE
  N0              7              280
  N1              2              111
  N2              1               86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D212V7, binary
                  cls
clus                 0   1
  LINGO4 MUTATED     7   1
  LINGO4 WILD-TYPE 368  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LINGO4 MUTATED      7    1
  LINGO4 WILD-TYPE  368   64
   clus
vv  LINGO4 MUTATED LINGO4 WILD-TYPE
  0              7              368
  1              1               64
[1] 2 2
[1] FALSE
D212V8, binary
                  cls
clus                 0   1
  LINGO4 MUTATED     5   5
  LINGO4 WILD-TYPE 220 259
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LINGO4 MUTATED      5    5
  LINGO4 WILD-TYPE  220  259
        clus
vv       LINGO4 MUTATED LINGO4 WILD-TYPE
  FEMALE              5              220
  MALE                5              259
[1] 2 2
[1] FALSE
D212V9, binary
                  cls
clus                 0   1
  LINGO4 MUTATED     7   0
  LINGO4 WILD-TYPE 343  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LINGO4 MUTATED      7    0
  LINGO4 WILD-TYPE  343   22
     clus
vv    LINGO4 MUTATED LINGO4 WILD-TYPE
  NO               7              343
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  LINGO4 MUTATED                      7                             3
  LINGO4 WILD-TYPE                  308                            44
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  LINGO4 MUTATED                       0                              0
  LINGO4 WILD-TYPE                   106                             10
D212V10, multiclass
                                clus
vv                               LINGO4 MUTATED LINGO4 WILD-TYPE
  COLON ADENOCARCINOMA                        7              308
  COLON MUCINOUS ADENOCARCINOMA               3               44
  RECTAL ADENOCARCINOMA                       0              106
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  LINGO4 MUTATED     9   0   0   0
  LINGO4 WILD-TYPE 336   4  31  25
D212V11, multiclass
    clus
vv   LINGO4 MUTATED LINGO4 WILD-TYPE
  R0              9              336
  R1              0                4
  R2              0               31
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D212V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  LINGO4 MUTATED                                  0     0
  LINGO4 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  LINGO4 MUTATED                           0     5
  LINGO4 WILD-TYPE                        22   221
D212V13, multiclass
                                  clus
vv                                 LINGO4 MUTATED LINGO4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         5              221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(213) Variable = MMP13 MUTATION ANALYSIS
D213V1, survival
                 sevent
clus2               0   1
  MMP13 MUTATED    12   4
  MMP13 WILD-TYPE 366  89
  MMP13 MUTATED MMP13 WILD-TYPE 
             16             455 
  MMP13 MUTATED MMP13 WILD-TYPE 
              4              89 
$`MMP13 MUTATED`
TCGA-A6-6654 TCGA-AA-3861 TCGA-AA-A010 TCGA-AZ-6598 TCGA-CA-5254 TCGA-CA-6717 
       23.87        30.05        34.98        49.41        12.69        12.76 
TCGA-CK-5916 TCGA-CM-4743 TCGA-CM-6162 TCGA-CM-6680 TCGA-D5-5539 TCGA-DM-A28F 
       21.14        23.05        12.00        12.03        19.59        35.97 
TCGA-F4-6570 TCGA-AG-3892 TCGA-DY-A0XA TCGA-EI-6506 
        6.18        13.02       126.44        20.55 

$`MMP13 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 
       32.05         0.99        31.07        31.07        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        88.21         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5255 
       29.56         5.23        11.74         3.19         1.61         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07        12.20        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 
        9.99        82.95         1.91       124.27        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       15.02         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-D5-5537 
       13.05        11.08        11.08        11.01        10.06        45.40 
TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       12.26        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
       81.37       119.93        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       31.96        35.74        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       17.03        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC 
       19.99         5.95         4.01         5.03         5.29        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6507 
       57.24        24.13        51.48        32.61         0.49        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  MMP13 MUTATED MMP13 WILD-TYPE 
           6.18            0.00 
  MMP13 MUTATED MMP13 WILD-TYPE 
         126.44          148.01 
  MMP13 MUTATED MMP13 WILD-TYPE 
         20.845          20.120 
[1] "6.2 - 126.4 (20.8)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.3"
D213V2, continuous
D213V3, binary
                 cls
clus                0   1
  MMP13 MUTATED    13   3
  MMP13 WILD-TYPE 353 116
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MMP13 MUTATED     13    3
  MMP13 WILD-TYPE  353  116
        clus
vv       MMP13 MUTATED MMP13 WILD-TYPE
  COLON             13             353
  RECTUM             3             116
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MMP13 MUTATED         2        0        1         7         1         0
  MMP13 WILD-TYPE      89        1       31       131         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MMP13 MUTATED           0          1          4          0        0         0
  MMP13 WILD-TYPE        24         10         55         42       48        18
                 vv
clus              STAGE IVB
  MMP13 MUTATED           0
  MMP13 WILD-TYPE         1
D213V4, multiclass
            clus
vv           MMP13 MUTATED MMP13 WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              7             131
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             1              10
  STAGE IIIB             4              55
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  MMP13 MUTATED     2   0  13   1
  MMP13 WILD-TYPE  15  92 316  49
D213V5, multiclass
    clus
vv   MMP13 MUTATED MMP13 WILD-TYPE
  T1             2              15
  T2             0              92
  T3            13             316
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  MMP13 MUTATED    11   4   1
  MMP13 WILD-TYPE 276 109  86
D213V6, multiclass
    clus
vv   MMP13 MUTATED MMP13 WILD-TYPE
  N0            11             276
  N1             4             109
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D213V7, binary
                 cls
clus                0   1
  MMP13 MUTATED    15   0
  MMP13 WILD-TYPE 360  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MMP13 MUTATED     15    0
  MMP13 WILD-TYPE  360   65
   clus
vv  MMP13 MUTATED MMP13 WILD-TYPE
  0            15             360
  1             0              65
[1] 2 2
[1] FALSE
D213V8, binary
                 cls
clus                0   1
  MMP13 MUTATED    11   5
  MMP13 WILD-TYPE 214 259
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MMP13 MUTATED     11    5
  MMP13 WILD-TYPE  214  259
        clus
vv       MMP13 MUTATED MMP13 WILD-TYPE
  FEMALE            11             214
  MALE               5             259
[1] 2 2
[1] FALSE
D213V9, binary
                 cls
clus                0   1
  MMP13 MUTATED    14   0
  MMP13 WILD-TYPE 336  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MMP13 MUTATED     14    0
  MMP13 WILD-TYPE  336   22
     clus
vv    MMP13 MUTATED MMP13 WILD-TYPE
  NO             14             336
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MMP13 MUTATED                     10                             3
  MMP13 WILD-TYPE                  305                            44
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MMP13 MUTATED                       3                              0
  MMP13 WILD-TYPE                   103                             10
D213V10, multiclass
                                clus
vv                               MMP13 MUTATED MMP13 WILD-TYPE
  COLON ADENOCARCINOMA                      10             305
  COLON MUCINOUS ADENOCARCINOMA              3              44
  RECTAL ADENOCARCINOMA                      3             103
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  MMP13 MUTATED     9   0   0   3
  MMP13 WILD-TYPE 336   4  31  22
D213V11, multiclass
    clus
vv   MMP13 MUTATED MMP13 WILD-TYPE
  R0             9             336
  R1             0               4
  R2             0              31
  RX             3              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D213V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MMP13 MUTATED                                  0     2
  MMP13 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  MMP13 MUTATED                           0    11
  MMP13 WILD-TYPE                        22   215
D213V13, multiclass
                                  clus
vv                                 MMP13 MUTATED MMP13 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               9
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                       11             215
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(214) Variable = DNAH12 MUTATION ANALYSIS
D214V1, survival
                  sevent
clus2                0   1
  DNAH12 MUTATED    21   4
  DNAH12 WILD-TYPE 357  89
  DNAH12 MUTATED DNAH12 WILD-TYPE 
              25              446 
  DNAH12 MUTATED DNAH12 WILD-TYPE 
               4               89 
$`DNAH12 MUTATED`
TCGA-A6-3809 TCGA-A6-5665 TCGA-A6-6141 TCGA-A6-6780 TCGA-AA-3489 TCGA-AA-3502 
       32.75        22.06         8.38        20.12         7.04        35.01 
TCGA-AA-3510 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3815 TCGA-AA-3877 TCGA-AA-3950 
       63.98        19.04        10.06        33.04        31.00        24.00 
TCGA-AA-A010 TCGA-AD-6895 TCGA-AY-6197 TCGA-AZ-4315 TCGA-CA-6717 TCGA-CA-6718 
       34.98         0.72        21.44        58.39        12.76        10.06 
TCGA-CM-5341 TCGA-D5-6923 TCGA-D5-6927 TCGA-DM-A1HB TCGA-F4-6570 TCGA-AG-A002 
       29.06        12.43         9.44       135.65         6.18        20.98 
TCGA-CI-6620 
       33.17 

$`DNAH12 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       32.71        27.09        22.52        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 
       21.76        24.69        24.39        23.87        19.66        20.28 
TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        3.02         1.02         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3812 
       36.00         5.03        85.05        26.99        19.04        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       29.98        18.05         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       26.01         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       15.52        56.55         0.79         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       33.01        17.82         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 
        3.06         3.25         3.29         0.07        12.20        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-5348 
       20.02        37.02        25.02        13.02        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6928 
        1.48         3.68         4.41        14.30         9.04        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 
       12.59       140.38         7.50        44.32       131.51       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 
       98.24         8.61        31.96        35.74        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6622 TCGA-CI-6624 
       17.49         0.69         0.72         6.05         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  DNAH12 MUTATED DNAH12 WILD-TYPE 
            0.72             0.00 
  DNAH12 MUTATED DNAH12 WILD-TYPE 
          135.65           148.01 
  DNAH12 MUTATED DNAH12 WILD-TYPE 
          21.440           20.035 
[1] "0.7 - 135.7 (21.4)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.2"
D214V2, continuous
D214V3, binary
                  cls
clus                 0   1
  DNAH12 MUTATED    23   2
  DNAH12 WILD-TYPE 343 117
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DNAH12 MUTATED     23    2
  DNAH12 WILD-TYPE  343  117
        clus
vv       DNAH12 MUTATED DNAH12 WILD-TYPE
  COLON              23              343
  RECTUM              2              117
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DNAH12 MUTATED         4        0        2        11         2         0
  DNAH12 WILD-TYPE      87        1       30       127         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DNAH12 MUTATED           1          1          1          0        1
  DNAH12 WILD-TYPE        23         10         58         42       47
                  vv
clus               STAGE IVA STAGE IVB
  DNAH12 MUTATED           1         0
  DNAH12 WILD-TYPE        17         1
D214V4, multiclass
            clus
vv           DNAH12 MUTATED DNAH12 WILD-TYPE
  STAGE I                 4               87
  STAGE IA                0                1
  STAGE II                2               30
  STAGE IIA              11              127
  STAGE IIB               2                8
  STAGE IIC               0                1
  STAGE III               1               23
  STAGE IIIA              1               10
  STAGE IIIB              1               58
  STAGE IIIC              0               42
  STAGE IV                1               47
  STAGE IVA               1               17
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  DNAH12 MUTATED     1   4  18   2
  DNAH12 WILD-TYPE  16  88 311  48
D214V5, multiclass
    clus
vv   DNAH12 MUTATED DNAH12 WILD-TYPE
  T1              1               16
  T2              4               88
  T3             18              311
  T4              2               48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  DNAH12 MUTATED    20   4   1
  DNAH12 WILD-TYPE 267 109  86
D214V6, multiclass
    clus
vv   DNAH12 MUTATED DNAH12 WILD-TYPE
  N0             20              267
  N1              4              109
  N2              1               86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D214V7, binary
                  cls
clus                 0   1
  DNAH12 MUTATED    20   2
  DNAH12 WILD-TYPE 355  63
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DNAH12 MUTATED     20    2
  DNAH12 WILD-TYPE  355   63
   clus
vv  DNAH12 MUTATED DNAH12 WILD-TYPE
  0             20              355
  1              2               63
[1] 2 2
[1] FALSE
D214V8, binary
                  cls
clus                 0   1
  DNAH12 MUTATED    10  15
  DNAH12 WILD-TYPE 215 249
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DNAH12 MUTATED     10   15
  DNAH12 WILD-TYPE  215  249
        clus
vv       DNAH12 MUTATED DNAH12 WILD-TYPE
  FEMALE             10              215
  MALE               15              249
[1] 2 2
[1] FALSE
D214V9, binary
                  cls
clus                 0   1
  DNAH12 MUTATED    22   1
  DNAH12 WILD-TYPE 328  21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DNAH12 MUTATED     22    1
  DNAH12 WILD-TYPE  328   21
     clus
vv    DNAH12 MUTATED DNAH12 WILD-TYPE
  NO              22              328
  YES              1               21
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  DNAH12 MUTATED                     17                             5
  DNAH12 WILD-TYPE                  298                            42
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  DNAH12 MUTATED                       2                              0
  DNAH12 WILD-TYPE                   104                             10
D214V10, multiclass
                                clus
vv                               DNAH12 MUTATED DNAH12 WILD-TYPE
  COLON ADENOCARCINOMA                       17              298
  COLON MUCINOUS ADENOCARCINOMA               5               42
  RECTAL ADENOCARCINOMA                       2              104
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  DNAH12 MUTATED    17   0   1   2
  DNAH12 WILD-TYPE 328   4  30  23
D214V11, multiclass
    clus
vv   DNAH12 MUTATED DNAH12 WILD-TYPE
  R0             17              328
  R1              0                4
  R2              1               30
  RX              2               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D214V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DNAH12 MUTATED                                  0     2
  DNAH12 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  DNAH12 MUTATED                           1    12
  DNAH12 WILD-TYPE                        21   214
D214V13, multiclass
                                  clus
vv                                 DNAH12 MUTATED DNAH12 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                9
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                        12              214
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(215) Variable = UQCRC2 MUTATION ANALYSIS
D215V1, survival
                  sevent
clus2                0   1
  UQCRC2 MUTATED     7   3
  UQCRC2 WILD-TYPE 371  90
  UQCRC2 MUTATED UQCRC2 WILD-TYPE 
              10              461 
  UQCRC2 MUTATED UQCRC2 WILD-TYPE 
               3               90 
$`UQCRC2 MUTATED`
TCGA-A6-2671 TCGA-A6-6653 TCGA-AA-A010 TCGA-CK-4947 TCGA-CM-5862 TCGA-D5-6535 
       43.76        24.39        34.98        17.56         5.03        15.12 
TCGA-DM-A28K TCGA-G4-6303 TCGA-AG-3611 TCGA-DC-6683 
       98.24        65.85        13.94         5.03 

$`UQCRC2 WILD-TYPE`
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       46.65        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 
       25.18        24.16        21.76        24.69        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       12.76        10.06        14.30       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       43.27        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-F4-6459 TCGA-F4-6460 
      119.93        35.97        60.79       117.07         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
      133.18        74.56        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 
        6.05         0.99        15.95        19.99        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        5.95         4.01         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  UQCRC2 MUTATED UQCRC2 WILD-TYPE 
            5.03             0.00 
  UQCRC2 MUTATED UQCRC2 WILD-TYPE 
           98.24           148.01 
  UQCRC2 MUTATED UQCRC2 WILD-TYPE 
          20.975           20.190 
[1] "5.0 - 98.2 (21.0)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.2"
D215V2, continuous
D215V3, binary
                  cls
clus                 0   1
  UQCRC2 MUTATED     8   2
  UQCRC2 WILD-TYPE 358 117
[1] "tbl2"
                  cls
clus               [,1] [,2]
  UQCRC2 MUTATED      8    2
  UQCRC2 WILD-TYPE  358  117
        clus
vv       UQCRC2 MUTATED UQCRC2 WILD-TYPE
  COLON               8              358
  RECTUM              2              117
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  UQCRC2 MUTATED         1        0        0         2         1         0
  UQCRC2 WILD-TYPE      90        1       32       136         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  UQCRC2 MUTATED           0          0          3          0        2
  UQCRC2 WILD-TYPE        24         11         56         42       46
                  vv
clus               STAGE IVA STAGE IVB
  UQCRC2 MUTATED           1         0
  UQCRC2 WILD-TYPE        17         1
D215V4, multiclass
            clus
vv           UQCRC2 MUTATED UQCRC2 WILD-TYPE
  STAGE I                 1               90
  STAGE IA                0                1
  STAGE II                0               32
  STAGE IIA               2              136
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              3               56
  STAGE IIIC              0               42
  STAGE IV                2               46
  STAGE IVA               1               17
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  UQCRC2 MUTATED     0   1   7   2
  UQCRC2 WILD-TYPE  17  91 322  48
D215V5, multiclass
    clus
vv   UQCRC2 MUTATED UQCRC2 WILD-TYPE
  T1              0               17
  T2              1               91
  T3              7              322
  T4              2               48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  UQCRC2 MUTATED     4   5   1
  UQCRC2 WILD-TYPE 283 108  86
D215V6, multiclass
    clus
vv   UQCRC2 MUTATED UQCRC2 WILD-TYPE
  N0              4              283
  N1              5              108
  N2              1               86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D215V7, binary
                  cls
clus                 0   1
  UQCRC2 MUTATED     6   3
  UQCRC2 WILD-TYPE 369  62
[1] "tbl2"
                  cls
clus               [,1] [,2]
  UQCRC2 MUTATED      6    3
  UQCRC2 WILD-TYPE  369   62
   clus
vv  UQCRC2 MUTATED UQCRC2 WILD-TYPE
  0              6              369
  1              3               62
[1] 2 2
[1] FALSE
D215V8, binary
                  cls
clus                 0   1
  UQCRC2 MUTATED     4   6
  UQCRC2 WILD-TYPE 221 258
[1] "tbl2"
                  cls
clus               [,1] [,2]
  UQCRC2 MUTATED      4    6
  UQCRC2 WILD-TYPE  221  258
        clus
vv       UQCRC2 MUTATED UQCRC2 WILD-TYPE
  FEMALE              4              221
  MALE                6              258
[1] 2 2
[1] FALSE
D215V9, binary
                  cls
clus                 0   1
  UQCRC2 MUTATED     8   0
  UQCRC2 WILD-TYPE 342  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  UQCRC2 MUTATED      8    0
  UQCRC2 WILD-TYPE  342   22
     clus
vv    UQCRC2 MUTATED UQCRC2 WILD-TYPE
  NO               8              342
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  UQCRC2 MUTATED                      7                             1
  UQCRC2 WILD-TYPE                  308                            46
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  UQCRC2 MUTATED                       2                              0
  UQCRC2 WILD-TYPE                   104                             10
D215V10, multiclass
                                clus
vv                               UQCRC2 MUTATED UQCRC2 WILD-TYPE
  COLON ADENOCARCINOMA                        7              308
  COLON MUCINOUS ADENOCARCINOMA               1               46
  RECTAL ADENOCARCINOMA                       2              104
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  UQCRC2 MUTATED     6   0   0   2
  UQCRC2 WILD-TYPE 339   4  31  23
D215V11, multiclass
    clus
vv   UQCRC2 MUTATED UQCRC2 WILD-TYPE
  R0              6              339
  R1              0                4
  R2              0               31
  RX              2               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D215V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  UQCRC2 MUTATED                                  0     0
  UQCRC2 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  UQCRC2 MUTATED                           0     8
  UQCRC2 WILD-TYPE                        22   218
D215V13, multiclass
                                  clus
vv                                 UQCRC2 MUTATED UQCRC2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         8              218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(216) Variable = E2F7 MUTATION ANALYSIS
D216V1, survival
                sevent
clus2              0   1
  E2F7 MUTATED    18   6
  E2F7 WILD-TYPE 360  87
  E2F7 MUTATED E2F7 WILD-TYPE 
            24            447 
  E2F7 MUTATED E2F7 WILD-TYPE 
             6             87 
$`E2F7 MUTATED`
TCGA-A6-5659 TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3663 TCGA-AA-3672 TCGA-AA-3697 
       30.44        13.02         1.02         6.97         0.92        85.05 
TCGA-AA-3715 TCGA-AA-3821 TCGA-AA-A00N TCGA-AA-A010 TCGA-AD-5900 TCGA-AD-6964 
       19.04         1.02         4.01        34.98         0.07        10.88 
TCGA-CK-4952 TCGA-CK-5916 TCGA-CM-5862 TCGA-D5-5541 TCGA-D5-6930 TCGA-G4-6310 
       15.62        21.14         5.03        55.92         1.51        63.62 
TCGA-G4-6586 TCGA-AG-3580 TCGA-AG-A002 TCGA-CL-5917 TCGA-EI-6507 TCGA-G5-6641 
       35.80         8.02        20.98        78.12        19.96        26.43 

$`E2F7 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3519 
       35.01        63.98         6.97         1.02        38.99         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02        78.08         6.05        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
       14.01        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 
       37.05        19.00        36.00         5.03        26.99        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 
       10.06        35.05        33.04         0.99        25.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
       40.96        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
       17.56       148.01        85.45        49.08        51.32         9.99 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       32.02        15.02        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-6529 TCGA-D5-6532 
       45.40        12.26        19.59        56.09        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       44.68        55.04        85.48        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       13.78        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       12.00        32.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5918 TCGA-DC-5337 
        6.05        33.17         6.97         4.73         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6508 
       24.13        51.48        32.61         0.49        20.55        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
        0.66         0.69        55.76 

  E2F7 MUTATED E2F7 WILD-TYPE 
          0.07           0.00 
  E2F7 MUTATED E2F7 WILD-TYPE 
         85.05         148.01 
  E2F7 MUTATED E2F7 WILD-TYPE 
         17.33          20.55 
[1] "0.1 - 85.0 (17.3)"  "0.0 - 148.0 (20.6)"
[1] "hr=" "1.5"
D216V2, continuous
D216V3, binary
                cls
clus               0   1
  E2F7 MUTATED    21   5
  E2F7 WILD-TYPE 345 114
[1] "tbl2"
                cls
clus             [,1] [,2]
  E2F7 MUTATED     21    5
  E2F7 WILD-TYPE  345  114
        clus
vv       E2F7 MUTATED E2F7 WILD-TYPE
  COLON            21            345
  RECTUM            5            114
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  E2F7 MUTATED         6        0        2         5         3         0
  E2F7 WILD-TYPE      85        1       30       133         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  E2F7 MUTATED           3          1          2          2        0         1
  E2F7 WILD-TYPE        21         10         57         40       48        17
                vv
clus             STAGE IVB
  E2F7 MUTATED           0
  E2F7 WILD-TYPE         1
D216V4, multiclass
            clus
vv           E2F7 MUTATED E2F7 WILD-TYPE
  STAGE I               6             85
  STAGE IA              0              1
  STAGE II              2             30
  STAGE IIA             5            133
  STAGE IIB             3              7
  STAGE IIC             0              1
  STAGE III             3             21
  STAGE IIIA            1             10
  STAGE IIIB            2             57
  STAGE IIIC            2             40
  STAGE IV              0             48
  STAGE IVA             1             17
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  E2F7 MUTATED     3   4  14   5
  E2F7 WILD-TYPE  14  88 315  45
D216V5, multiclass
    clus
vv   E2F7 MUTATED E2F7 WILD-TYPE
  T1            3             14
  T2            4             88
  T3           14            315
  T4            5             45
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  E2F7 MUTATED    17   5   4
  E2F7 WILD-TYPE 270 108  83
D216V6, multiclass
    clus
vv   E2F7 MUTATED E2F7 WILD-TYPE
  N0           17            270
  N1            5            108
  N2            4             83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D216V7, binary
                cls
clus               0   1
  E2F7 MUTATED    20   1
  E2F7 WILD-TYPE 355  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  E2F7 MUTATED     20    1
  E2F7 WILD-TYPE  355   64
   clus
vv  E2F7 MUTATED E2F7 WILD-TYPE
  0           20            355
  1            1             64
[1] 2 2
[1] FALSE
D216V8, binary
                cls
clus               0   1
  E2F7 MUTATED    11  15
  E2F7 WILD-TYPE 214 249
[1] "tbl2"
                cls
clus             [,1] [,2]
  E2F7 MUTATED     11   15
  E2F7 WILD-TYPE  214  249
        clus
vv       E2F7 MUTATED E2F7 WILD-TYPE
  FEMALE           11            214
  MALE             15            249
[1] 2 2
[1] FALSE
D216V9, binary
                cls
clus               0   1
  E2F7 MUTATED    18   1
  E2F7 WILD-TYPE 332  21
[1] "tbl2"
                cls
clus             [,1] [,2]
  E2F7 MUTATED     18    1
  E2F7 WILD-TYPE  332   21
     clus
vv    E2F7 MUTATED E2F7 WILD-TYPE
  NO            18            332
  YES            1             21
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  E2F7 MUTATED                     15                             6
  E2F7 WILD-TYPE                  300                            41
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  E2F7 MUTATED                       4                              1
  E2F7 WILD-TYPE                   102                              9
D216V10, multiclass
                                clus
vv                               E2F7 MUTATED E2F7 WILD-TYPE
  COLON ADENOCARCINOMA                     15            300
  COLON MUCINOUS ADENOCARCINOMA             6             41
  RECTAL ADENOCARCINOMA                     4            102
  RECTAL MUCINOUS ADENOCARCINOMA            1              9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  E2F7 MUTATED    20   0   0   4
  E2F7 WILD-TYPE 325   4  31  21
D216V11, multiclass
    clus
vv   E2F7 MUTATED E2F7 WILD-TYPE
  R0           20            325
  R1            0              4
  R2            0             31
  RX            4             21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D216V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  E2F7 MUTATED                                  0     0
  E2F7 WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  E2F7 MUTATED                           0    14
  E2F7 WILD-TYPE                        22   212
D216V13, multiclass
                                  clus
vv                                 E2F7 MUTATED E2F7 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                      14            212
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(217) Variable = FHOD3 MUTATION ANALYSIS
D217V1, survival
                 sevent
clus2               0   1
  FHOD3 MUTATED    21   7
  FHOD3 WILD-TYPE 357  86
  FHOD3 MUTATED FHOD3 WILD-TYPE 
             28             443 
  FHOD3 MUTATED FHOD3 WILD-TYPE 
              7              86 
$`FHOD3 MUTATED`
TCGA-A6-5661 TCGA-A6-6781 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3525 TCGA-AA-3930 
       33.53        19.66         3.02        35.01         8.05         2.01 
TCGA-AA-3947 TCGA-AA-3966 TCGA-AA-A00A TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01Q 
       33.01         2.01        38.04         4.01        34.98         1.02 
TCGA-AY-6197 TCGA-AZ-6598 TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-4743 TCGA-CM-6162 
       21.44        49.41        12.76        10.06        23.05        12.00 
TCGA-D5-6536 TCGA-D5-6927 TCGA-DM-A28C TCGA-F4-6570 TCGA-G4-6309 TCGA-G4-6588 
       17.85         9.44        81.37         6.18        85.48        26.17 
TCGA-G4-6628 TCGA-AG-A002 TCGA-AG-A00C TCGA-AG-A02N 
       79.69        20.98         6.02        61.97 

$`FHOD3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3510 TCGA-AA-3511 
       20.12        20.28         7.04         1.02        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       37.05        36.03        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       78.08         6.05         6.97        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 
       18.05        31.00        12.99        24.00        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
        2.01        20.98        34.03        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00D 
       27.02        19.07         7.96        27.02        13.94        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       16.31         0.95        33.01        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 
        5.13       106.75        22.36        62.79        88.21         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       12.20        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
      124.27        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 
       15.02        15.02        17.03        15.02         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       15.12         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      135.65       139.17         6.12       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 
      117.07        98.24         8.61        31.96        35.74        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       53.62        44.68        55.04        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 
       22.09        13.78        35.80        91.79        46.75        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       17.03        13.94        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
       49.97         1.94        38.96        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  FHOD3 MUTATED FHOD3 WILD-TYPE 
           1.02            0.00 
  FHOD3 MUTATED FHOD3 WILD-TYPE 
          85.48          148.01 
  FHOD3 MUTATED FHOD3 WILD-TYPE 
          20.32           20.19 
[1] "1.0 - 85.5 (20.3)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.3"
D217V2, continuous
D217V3, binary
                 cls
clus                0   1
  FHOD3 MUTATED    27   3
  FHOD3 WILD-TYPE 339 116
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FHOD3 MUTATED     27    3
  FHOD3 WILD-TYPE  339  116
        clus
vv       FHOD3 MUTATED FHOD3 WILD-TYPE
  COLON             27             339
  RECTUM             3             116
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FHOD3 MUTATED         4        0        4        13         3         0
  FHOD3 WILD-TYPE      87        1       28       125         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  FHOD3 MUTATED           0          0          4          1        1         0
  FHOD3 WILD-TYPE        24         11         55         41       47        18
                 vv
clus              STAGE IVB
  FHOD3 MUTATED           0
  FHOD3 WILD-TYPE         1
D217V4, multiclass
            clus
vv           FHOD3 MUTATED FHOD3 WILD-TYPE
  STAGE I                4              87
  STAGE IA               0               1
  STAGE II               4              28
  STAGE IIA             13             125
  STAGE IIB              3               7
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             4              55
  STAGE IIIC             1              41
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  FHOD3 MUTATED     0   4  22   4
  FHOD3 WILD-TYPE  17  88 307  46
D217V5, multiclass
    clus
vv   FHOD3 MUTATED FHOD3 WILD-TYPE
  T1             0              17
  T2             4              88
  T3            22             307
  T4             4              46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  FHOD3 MUTATED    24   5   1
  FHOD3 WILD-TYPE 263 108  86
D217V6, multiclass
    clus
vv   FHOD3 MUTATED FHOD3 WILD-TYPE
  N0            24             263
  N1             5             108
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D217V7, binary
                 cls
clus                0   1
  FHOD3 MUTATED    25   1
  FHOD3 WILD-TYPE 350  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FHOD3 MUTATED     25    1
  FHOD3 WILD-TYPE  350   64
   clus
vv  FHOD3 MUTATED FHOD3 WILD-TYPE
  0            25             350
  1             1              64
[1] 2 2
[1] FALSE
D217V8, binary
                 cls
clus                0   1
  FHOD3 MUTATED    13  17
  FHOD3 WILD-TYPE 212 247
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FHOD3 MUTATED     13   17
  FHOD3 WILD-TYPE  212  247
        clus
vv       FHOD3 MUTATED FHOD3 WILD-TYPE
  FEMALE            13             212
  MALE              17             247
[1] 2 2
[1] FALSE
D217V9, binary
                 cls
clus                0   1
  FHOD3 MUTATED    22   1
  FHOD3 WILD-TYPE 328  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FHOD3 MUTATED     22    1
  FHOD3 WILD-TYPE  328   21
     clus
vv    FHOD3 MUTATED FHOD3 WILD-TYPE
  NO             22             328
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  FHOD3 MUTATED                     21                             6
  FHOD3 WILD-TYPE                  294                            41
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  FHOD3 MUTATED                       3                              0
  FHOD3 WILD-TYPE                   103                             10
D217V10, multiclass
                                clus
vv                               FHOD3 MUTATED FHOD3 WILD-TYPE
  COLON ADENOCARCINOMA                      21             294
  COLON MUCINOUS ADENOCARCINOMA              6              41
  RECTAL ADENOCARCINOMA                      3             103
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  FHOD3 MUTATED    23   0   1   3
  FHOD3 WILD-TYPE 322   4  30  22
D217V11, multiclass
    clus
vv   FHOD3 MUTATED FHOD3 WILD-TYPE
  R0            23             322
  R1             0               4
  R2             1              30
  RX             3              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D217V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FHOD3 MUTATED                                  0     2
  FHOD3 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  FHOD3 MUTATED                           2    12
  FHOD3 WILD-TYPE                        20   214
D217V13, multiclass
                                  clus
vv                                 FHOD3 MUTATED FHOD3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               9
  BLACK OR AFRICAN AMERICAN                    2              20
  WHITE                                       12             214
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(218) Variable = MLL3 MUTATION ANALYSIS
D218V1, survival
                sevent
clus2              0   1
  MLL3 MUTATED    51  13
  MLL3 WILD-TYPE 327  80
  MLL3 MUTATED MLL3 WILD-TYPE 
            64            407 
  MLL3 MUTATED MLL3 WILD-TYPE 
            13             80 
$`MLL3 MUTATED`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6138 TCGA-A6-6141 
       43.76        46.65        22.06        32.71        22.52         8.38 
TCGA-A6-6654 TCGA-A6-6781 TCGA-AA-3496 TCGA-AA-3510 TCGA-AA-3525 TCGA-AA-3660 
       23.87        19.66         1.02        63.98         8.05        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3710 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3869 
        6.05         6.97        26.99         0.00        17.03        27.02 
TCGA-AA-3950 TCGA-AA-3977 TCGA-AA-A00N TCGA-AD-6899 TCGA-AD-6964 TCGA-AU-3779 
       24.00        25.02         4.01         5.79        10.88        14.50 
TCGA-AZ-4315 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6603 TCGA-AZ-6608 TCGA-CA-6717 
       58.39        88.21        49.41        29.56         1.61        12.76 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5913 TCGA-CM-5344 TCGA-CM-5861 TCGA-CM-5862 
       85.45        15.62        51.32        22.03        15.02         5.03 
TCGA-CM-5868 TCGA-CM-6162 TCGA-CM-6167 TCGA-CM-6674 TCGA-D5-5539 TCGA-D5-6532 
       17.03        12.00        14.99        12.95        19.59        18.25 
TCGA-D5-6540 TCGA-D5-6920 TCGA-D5-6923 TCGA-D5-6928 TCGA-D5-6929 TCGA-DM-A1D0 
       16.14         3.68        12.43        11.64         4.80       130.65 
TCGA-DM-A1D7 TCGA-DM-A28C TCGA-G4-6293 TCGA-G4-6310 TCGA-G4-6586 TCGA-G4-6588 
       13.32        81.37       133.18        63.62        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-AG-3732 TCGA-AG-A002 TCGA-AG-A036 TCGA-AH-6549 
       91.79        79.69        32.98        20.98       117.11        17.49 
TCGA-AH-6644 TCGA-DC-6681 TCGA-DY-A1DF TCGA-EF-5830 
        0.72         5.95        24.13         0.49 

$`MLL3 WILD-TYPE`
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       43.76        42.90        24.33        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5657 
       33.34        32.75        36.53        14.53        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-6137 
       30.44        29.19        33.53        23.61        22.09        27.09 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3511 
       20.12        20.28         7.04         3.02        35.01         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       37.05        36.03        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       38.99        37.02        14.93        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3875 
       30.05        53.00        17.03        24.03        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-6004 
        0.79         0.72        22.42        27.42         0.20        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
       16.31         0.95        33.01        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6599 TCGA-AZ-6600 
        5.13       106.75        22.36        62.79         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 
      100.01         5.23        11.74         3.19        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07        12.20        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       17.56       148.01        49.08         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5863 
       13.02        29.06        22.98        30.08        32.02        15.02 
TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        15.02         2.96        29.03        16.04        21.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6675 
       12.99        13.02        15.02        14.04        11.01        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6534 
       12.26        56.09        55.92        20.19         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 
       15.12        17.85         4.80        17.13        12.49        15.58 
TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6930 
        1.48         4.41        14.30         9.04         9.44         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       92.75        49.91        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28E TCGA-DM-A28F 
      131.51       135.65       139.17         6.12       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6299 
       33.67        13.25         0.53        47.41        35.31        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6315 
       65.85        53.62        44.68        55.04        85.48        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 
       36.00        22.09        13.78        46.75        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        7.99         0.99        37.02         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 
        1.94        38.96        61.97        41.00        38.04        38.56 
TCGA-AH-6547 TCGA-AH-6643 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        1.45         0.69         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       10.98        19.99         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EI-6506 TCGA-EI-6507 
       41.36        57.24        51.48        32.61        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  MLL3 MUTATED MLL3 WILD-TYPE 
             0              0 
  MLL3 MUTATED MLL3 WILD-TYPE 
        133.18         148.01 
  MLL3 MUTATED MLL3 WILD-TYPE 
        19.625         20.280 
[1] "0.0 - 133.2 (19.6)" "0.0 - 148.0 (20.3)"
[1] "hr=" "1.1"
D218V2, continuous
D218V3, binary
                cls
clus               0   1
  MLL3 MUTATED    58   8
  MLL3 WILD-TYPE 308 111
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL3 MUTATED     58    8
  MLL3 WILD-TYPE  308  111
        clus
vv       MLL3 MUTATED MLL3 WILD-TYPE
  COLON            58            308
  RECTUM            8            111
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MLL3 MUTATED         7        0        5        22         3         1
  MLL3 WILD-TYPE      84        1       27       116         7         0
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MLL3 MUTATED           2          2          7          5        4         3
  MLL3 WILD-TYPE        22          9         52         37       44        15
                vv
clus             STAGE IVB
  MLL3 MUTATED           0
  MLL3 WILD-TYPE         1
D218V4, multiclass
            clus
vv           MLL3 MUTATED MLL3 WILD-TYPE
  STAGE I               7             84
  STAGE IA              0              1
  STAGE II              5             27
  STAGE IIA            22            116
  STAGE IIB             3              7
  STAGE IIC             1              0
  STAGE III             2             22
  STAGE IIIA            2              9
  STAGE IIIB            7             52
  STAGE IIIC            5             37
  STAGE IV              4             44
  STAGE IVA             3             15
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  MLL3 MUTATED     1   9  45  11
  MLL3 WILD-TYPE  16  83 284  39
D218V5, multiclass
    clus
vv   MLL3 MUTATED MLL3 WILD-TYPE
  T1            1             16
  T2            9             83
  T3           45            284
  T4           11             39
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  MLL3 MUTATED    39  15  10
  MLL3 WILD-TYPE 248  98  77
D218V6, multiclass
    clus
vv   MLL3 MUTATED MLL3 WILD-TYPE
  N0           39            248
  N1           15             98
  N2           10             77
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D218V7, binary
                cls
clus               0   1
  MLL3 MUTATED    49   7
  MLL3 WILD-TYPE 326  58
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL3 MUTATED     49    7
  MLL3 WILD-TYPE  326   58
   clus
vv  MLL3 MUTATED MLL3 WILD-TYPE
  0           49            326
  1            7             58
[1] 2 2
[1] FALSE
D218V8, binary
                cls
clus               0   1
  MLL3 MUTATED    35  31
  MLL3 WILD-TYPE 190 233
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL3 MUTATED     35   31
  MLL3 WILD-TYPE  190  233
        clus
vv       MLL3 MUTATED MLL3 WILD-TYPE
  FEMALE           35            190
  MALE             31            233
[1] 2 2
[1] FALSE
D218V9, binary
                cls
clus               0   1
  MLL3 MUTATED    49   2
  MLL3 WILD-TYPE 301  20
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL3 MUTATED     49    2
  MLL3 WILD-TYPE  301   20
     clus
vv    MLL3 MUTATED MLL3 WILD-TYPE
  NO            49            301
  YES            2             20
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MLL3 MUTATED                     47                            10
  MLL3 WILD-TYPE                  268                            37
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MLL3 MUTATED                       8                              0
  MLL3 WILD-TYPE                    98                             10
D218V10, multiclass
                                clus
vv                               MLL3 MUTATED MLL3 WILD-TYPE
  COLON ADENOCARCINOMA                     47            268
  COLON MUCINOUS ADENOCARCINOMA            10             37
  RECTAL ADENOCARCINOMA                     8             98
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  MLL3 MUTATED    42   1   2   5
  MLL3 WILD-TYPE 303   3  29  20
D218V11, multiclass
    clus
vv   MLL3 MUTATED MLL3 WILD-TYPE
  R0           42            303
  R1            1              3
  R2            2             29
  RX            5             20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D218V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MLL3 MUTATED                                  0     1
  MLL3 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  MLL3 MUTATED                           3    45
  MLL3 WILD-TYPE                        19   181
D218V13, multiclass
                                  clus
vv                                 MLL3 MUTATED MLL3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   3             19
  WHITE                                      45            181
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(219) Variable = SCD5 MUTATION ANALYSIS
D219V1, survival
                sevent
clus2              0   1
  SCD5 MUTATED     5   3
  SCD5 WILD-TYPE 373  90
  SCD5 MUTATED SCD5 WILD-TYPE 
             8            463 
  SCD5 MUTATED SCD5 WILD-TYPE 
             3             90 
$`SCD5 MUTATED`
TCGA-AA-3696 TCGA-AA-3710 TCGA-AD-6964 TCGA-CM-6162 TCGA-DM-A28K TCGA-G4-6586 
        5.03        26.99        10.88        12.00        98.24        35.80 
TCGA-G4-6626 TCGA-AF-6136 
       46.75        15.39 

$`SCD5 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
       19.00        36.00        85.05        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-AF-2687 
       22.09        13.78        26.17        91.79        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       14.50        16.83        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  SCD5 MUTATED SCD5 WILD-TYPE 
          5.03           0.00 
  SCD5 MUTATED SCD5 WILD-TYPE 
         98.24         148.01 
  SCD5 MUTATED SCD5 WILD-TYPE 
         21.19          20.19 
[1] "5.0 - 98.2 (21.2)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.7"
D219V2, continuous
D219V3, binary
                cls
clus               0   1
  SCD5 MUTATED     7   1
  SCD5 WILD-TYPE 359 118
[1] "tbl2"
                cls
clus             [,1] [,2]
  SCD5 MUTATED      7    1
  SCD5 WILD-TYPE  359  118
        clus
vv       SCD5 MUTATED SCD5 WILD-TYPE
  COLON             7            359
  RECTUM            1            118
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SCD5 MUTATED         0        0        0         4         0         0
  SCD5 WILD-TYPE      91        1       32       134        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SCD5 MUTATED           0          0          2          0        1         0
  SCD5 WILD-TYPE        24         11         57         42       47        18
                vv
clus             STAGE IVB
  SCD5 MUTATED           0
  SCD5 WILD-TYPE         1
D219V4, multiclass
            clus
vv           SCD5 MUTATED SCD5 WILD-TYPE
  STAGE I               0             91
  STAGE IA              0              1
  STAGE II              0             32
  STAGE IIA             4            134
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            2             57
  STAGE IIIC            0             42
  STAGE IV              1             47
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  SCD5 MUTATED     0   0   7   1
  SCD5 WILD-TYPE  17  92 322  49
D219V5, multiclass
    clus
vv   SCD5 MUTATED SCD5 WILD-TYPE
  T1            0             17
  T2            0             92
  T3            7            322
  T4            1             49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  SCD5 MUTATED     4   3   1
  SCD5 WILD-TYPE 283 110  86
D219V6, multiclass
    clus
vv   SCD5 MUTATED SCD5 WILD-TYPE
  N0            4            283
  N1            3            110
  N2            1             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D219V7, binary
                cls
clus               0   1
  SCD5 MUTATED     5   1
  SCD5 WILD-TYPE 370  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  SCD5 MUTATED      5    1
  SCD5 WILD-TYPE  370   64
   clus
vv  SCD5 MUTATED SCD5 WILD-TYPE
  0            5            370
  1            1             64
[1] 2 2
[1] FALSE
D219V8, binary
                cls
clus               0   1
  SCD5 MUTATED     5   3
  SCD5 WILD-TYPE 220 261
[1] "tbl2"
                cls
clus             [,1] [,2]
  SCD5 MUTATED      5    3
  SCD5 WILD-TYPE  220  261
        clus
vv       SCD5 MUTATED SCD5 WILD-TYPE
  FEMALE            5            220
  MALE              3            261
[1] 2 2
[1] FALSE
D219V9, binary
                cls
clus               0   1
  SCD5 MUTATED     6   1
  SCD5 WILD-TYPE 344  21
[1] "tbl2"
                cls
clus             [,1] [,2]
  SCD5 MUTATED      6    1
  SCD5 WILD-TYPE  344   21
     clus
vv    SCD5 MUTATED SCD5 WILD-TYPE
  NO             6            344
  YES            1             21
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SCD5 MUTATED                      5                             2
  SCD5 WILD-TYPE                  310                            45
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SCD5 MUTATED                       1                              0
  SCD5 WILD-TYPE                   105                             10
D219V10, multiclass
                                clus
vv                               SCD5 MUTATED SCD5 WILD-TYPE
  COLON ADENOCARCINOMA                      5            310
  COLON MUCINOUS ADENOCARCINOMA             2             45
  RECTAL ADENOCARCINOMA                     1            105
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  SCD5 MUTATED     4   0   1   0
  SCD5 WILD-TYPE 341   4  30  25
D219V11, multiclass
    clus
vv   SCD5 MUTATED SCD5 WILD-TYPE
  R0            4            341
  R1            0              4
  R2            1             30
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D219V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SCD5 MUTATED                                  0     0
  SCD5 WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  SCD5 MUTATED                           0     6
  SCD5 WILD-TYPE                        22   220
D219V13, multiclass
                                  clus
vv                                 SCD5 MUTATED SCD5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       6            220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(220) Variable = DDX23 MUTATION ANALYSIS
D220V1, survival
                 sevent
clus2               0   1
  DDX23 MUTATED    16   4
  DDX23 WILD-TYPE 362  89
  DDX23 MUTATED DDX23 WILD-TYPE 
             20             451 
  DDX23 MUTATED DDX23 WILD-TYPE 
              4              89 
$`DDX23 MUTATED`
TCGA-A6-6781 TCGA-AA-3660 TCGA-AA-3713 TCGA-AA-3815 TCGA-AA-A004 TCGA-AA-A00N 
       19.66        78.08        19.04        33.04        13.94         4.01 
TCGA-AA-A00R TCGA-AD-6548 TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-CA-6717 
        0.99        21.37        21.44        58.39        49.41        12.76 
TCGA-CK-4952 TCGA-CM-5349 TCGA-DM-A1D4 TCGA-F4-6854 TCGA-G4-6315 TCGA-AF-6655 
       15.62        30.08        92.75         0.53        61.91        20.02 
TCGA-DC-5337 TCGA-DY-A1DC 
       15.02        41.36 

$`DDX23 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 
       19.99        13.94        19.99        61.02         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
        7.96        27.02        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00U 
       18.05        18.05        38.04        27.02        42.02        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6888 
       41.00        39.98        18.05        40.96         0.07        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       33.01        17.82         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        88.21         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07        12.20        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
       17.56       148.01        85.45        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-DM-A1D7 
      119.70        24.43        38.20       130.65        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
       13.25        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6317 
       53.62        44.68        55.04        85.48        63.62        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6672 
       34.49        10.39        14.50        16.83        15.39        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
        4.73        78.12         7.17         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
      126.44        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  DDX23 MUTATED DDX23 WILD-TYPE 
           0.53            0.00 
  DDX23 MUTATED DDX23 WILD-TYPE 
          92.75          148.01 
  DDX23 MUTATED DDX23 WILD-TYPE 
         20.695          20.190 
[1] "0.5 - 92.8 (20.7)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.2"
D220V2, continuous
D220V3, binary
                 cls
clus                0   1
  DDX23 MUTATED    18   3
  DDX23 WILD-TYPE 348 116
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX23 MUTATED     18    3
  DDX23 WILD-TYPE  348  116
        clus
vv       DDX23 MUTATED DDX23 WILD-TYPE
  COLON             18             348
  RECTUM             3             116
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DDX23 MUTATED         3        0        2        10         1         0
  DDX23 WILD-TYPE      88        1       30       128         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DDX23 MUTATED           0          1          0          2        2         0
  DDX23 WILD-TYPE        24         10         59         40       46        18
                 vv
clus              STAGE IVB
  DDX23 MUTATED           0
  DDX23 WILD-TYPE         1
D220V4, multiclass
            clus
vv           DDX23 MUTATED DDX23 WILD-TYPE
  STAGE I                3              88
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA             10             128
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             1              10
  STAGE IIIB             0              59
  STAGE IIIC             2              40
  STAGE IV               2              46
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  DDX23 MUTATED     1   3  14   3
  DDX23 WILD-TYPE  16  89 315  47
D220V5, multiclass
    clus
vv   DDX23 MUTATED DDX23 WILD-TYPE
  T1             1              16
  T2             3              89
  T3            14             315
  T4             3              47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  DDX23 MUTATED    17   3   1
  DDX23 WILD-TYPE 270 110  86
D220V6, multiclass
    clus
vv   DDX23 MUTATED DDX23 WILD-TYPE
  N0            17             270
  N1             3             110
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D220V7, binary
                 cls
clus                0   1
  DDX23 MUTATED    16   2
  DDX23 WILD-TYPE 359  63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX23 MUTATED     16    2
  DDX23 WILD-TYPE  359   63
   clus
vv  DDX23 MUTATED DDX23 WILD-TYPE
  0            16             359
  1             2              63
[1] 2 2
[1] FALSE
D220V8, binary
                 cls
clus                0   1
  DDX23 MUTATED    10  11
  DDX23 WILD-TYPE 215 253
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX23 MUTATED     10   11
  DDX23 WILD-TYPE  215  253
        clus
vv       DDX23 MUTATED DDX23 WILD-TYPE
  FEMALE            10             215
  MALE              11             253
[1] 2 2
[1] FALSE
D220V9, binary
                 cls
clus                0   1
  DDX23 MUTATED    14   1
  DDX23 WILD-TYPE 336  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX23 MUTATED     14    1
  DDX23 WILD-TYPE  336   21
     clus
vv    DDX23 MUTATED DDX23 WILD-TYPE
  NO             14             336
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  DDX23 MUTATED                     14                             4
  DDX23 WILD-TYPE                  301                            43
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  DDX23 MUTATED                       3                              0
  DDX23 WILD-TYPE                   103                             10
D220V10, multiclass
                                clus
vv                               DDX23 MUTATED DDX23 WILD-TYPE
  COLON ADENOCARCINOMA                      14             301
  COLON MUCINOUS ADENOCARCINOMA              4              43
  RECTAL ADENOCARCINOMA                      3             103
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  DDX23 MUTATED    15   0   1   2
  DDX23 WILD-TYPE 330   4  30  23
D220V11, multiclass
    clus
vv   DDX23 MUTATED DDX23 WILD-TYPE
  R0            15             330
  R1             0               4
  R2             1              30
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D220V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DDX23 MUTATED                                  0     1
  DDX23 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  DDX23 MUTATED                           0    13
  DDX23 WILD-TYPE                        22   213
D220V13, multiclass
                                  clus
vv                                 DDX23 MUTATED DDX23 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                       13             213
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(221) Variable = THOC5 MUTATION ANALYSIS
D221V1, survival
                 sevent
clus2               0   1
  THOC5 MUTATED    11   5
  THOC5 WILD-TYPE 367  88
  THOC5 MUTATED THOC5 WILD-TYPE 
             16             455 
  THOC5 MUTATED THOC5 WILD-TYPE 
              5              88 
$`THOC5 MUTATED`
TCGA-AA-3492 TCGA-AA-3518 TCGA-AA-3663 TCGA-AA-A00N TCGA-AA-A010 TCGA-AY-6197 
        3.02         1.02         6.97         4.01        34.98        21.44 
TCGA-AZ-4681 TCGA-AZ-6600 TCGA-CA-6718 TCGA-CK-4950 TCGA-CK-6747 TCGA-CM-6171 
      106.75        12.10        10.06        85.45        82.95        14.04 
TCGA-DM-A285 TCGA-G4-6309 TCGA-AG-3575 TCGA-AG-3731 
        6.12        85.48        12.00        37.02 

$`THOC5 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4315 
       27.09        16.31         0.95        33.01        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        1.41         5.13        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 
       12.20        12.76        14.30        17.56       148.01        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6748 TCGA-CK-6751 
       49.08        51.32         9.99        21.14         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       15.02        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A28C TCGA-DM-A28E 
       44.32       131.51       135.65       139.17        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3578 
       16.83        15.39        20.02        10.39        36.03        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
        0.99        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  THOC5 MUTATED THOC5 WILD-TYPE 
           1.02            0.00 
  THOC5 MUTATED THOC5 WILD-TYPE 
         106.75          148.01 
  THOC5 MUTATED THOC5 WILD-TYPE 
          13.07           20.28 
[1] "1.0 - 106.8 (13.1)" "0.0 - 148.0 (20.3)"
[1] "hr=" "1.3"
D221V2, continuous
D221V3, binary
                 cls
clus                0   1
  THOC5 MUTATED    14   2
  THOC5 WILD-TYPE 352 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  THOC5 MUTATED     14    2
  THOC5 WILD-TYPE  352  117
        clus
vv       THOC5 MUTATED THOC5 WILD-TYPE
  COLON             14             352
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  THOC5 MUTATED         1        0        3         5         2         0
  THOC5 WILD-TYPE      90        1       29       133         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  THOC5 MUTATED           0          0          2          0        3         0
  THOC5 WILD-TYPE        24         11         57         42       45        18
                 vv
clus              STAGE IVB
  THOC5 MUTATED           0
  THOC5 WILD-TYPE         1
D221V4, multiclass
            clus
vv           THOC5 MUTATED THOC5 WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               3              29
  STAGE IIA              5             133
  STAGE IIB              2               8
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             2              57
  STAGE IIIC             0              42
  STAGE IV               3              45
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  THOC5 MUTATED     0   1  12   3
  THOC5 WILD-TYPE  17  91 317  47
D221V5, multiclass
    clus
vv   THOC5 MUTATED THOC5 WILD-TYPE
  T1             0              17
  T2             1              91
  T3            12             317
  T4             3              47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  THOC5 MUTATED    11   4   1
  THOC5 WILD-TYPE 276 109  86
D221V6, multiclass
    clus
vv   THOC5 MUTATED THOC5 WILD-TYPE
  N0            11             276
  N1             4             109
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D221V7, binary
                 cls
clus                0   1
  THOC5 MUTATED    11   3
  THOC5 WILD-TYPE 364  62
[1] "tbl2"
                 cls
clus              [,1] [,2]
  THOC5 MUTATED     11    3
  THOC5 WILD-TYPE  364   62
   clus
vv  THOC5 MUTATED THOC5 WILD-TYPE
  0            11             364
  1             3              62
[1] 2 2
[1] FALSE
D221V8, binary
                 cls
clus                0   1
  THOC5 MUTATED     9   7
  THOC5 WILD-TYPE 216 257
[1] "tbl2"
                 cls
clus              [,1] [,2]
  THOC5 MUTATED      9    7
  THOC5 WILD-TYPE  216  257
        clus
vv       THOC5 MUTATED THOC5 WILD-TYPE
  FEMALE             9             216
  MALE               7             257
[1] 2 2
[1] FALSE
D221V9, binary
                 cls
clus                0   1
  THOC5 MUTATED    12   0
  THOC5 WILD-TYPE 338  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  THOC5 MUTATED     12    0
  THOC5 WILD-TYPE  338   22
     clus
vv    THOC5 MUTATED THOC5 WILD-TYPE
  NO             12             338
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  THOC5 MUTATED                     12                             2
  THOC5 WILD-TYPE                  303                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  THOC5 MUTATED                       2                              0
  THOC5 WILD-TYPE                   104                             10
D221V10, multiclass
                                clus
vv                               THOC5 MUTATED THOC5 WILD-TYPE
  COLON ADENOCARCINOMA                      12             303
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  THOC5 MUTATED    10   1   1   2
  THOC5 WILD-TYPE 335   3  30  23
D221V11, multiclass
    clus
vv   THOC5 MUTATED THOC5 WILD-TYPE
  R0            10             335
  R1             1               3
  R2             1              30
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D221V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  THOC5 MUTATED                                  0     1
  THOC5 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  THOC5 MUTATED                           3     5
  THOC5 WILD-TYPE                        19   221
D221V13, multiclass
                                  clus
vv                                 THOC5 MUTATED THOC5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    3              19
  WHITE                                        5             221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(222) Variable = ADAM28 MUTATION ANALYSIS
D222V1, survival
                  sevent
clus2                0   1
  ADAM28 MUTATED    12   6
  ADAM28 WILD-TYPE 366  87
  ADAM28 MUTATED ADAM28 WILD-TYPE 
              18              453 
  ADAM28 MUTATED ADAM28 WILD-TYPE 
               6               87 
$`ADAM28 MUTATED`
TCGA-A6-5660 TCGA-A6-6652 TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3543 TCGA-AA-A00N 
       29.19        24.69         3.02        63.98         0.99         4.01 
TCGA-AZ-6599 TCGA-AZ-6605 TCGA-CK-5913 TCGA-CM-5344 TCGA-CM-5863 TCGA-D5-6928 
        6.77         5.23        51.32        22.03        15.02        11.64 
TCGA-DM-A28F TCGA-F4-6569 TCGA-G4-6626 TCGA-AG-A002 TCGA-AH-6643 TCGA-EI-6508 
       35.97        35.74        46.75        20.98         0.69        20.91 

$`ADAM28 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       25.18        24.16        21.76        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 
       19.66        20.28         7.04         1.02        35.01         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
       34.03        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       78.08         6.05         6.97        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6606 TCGA-AZ-6607 
       49.41        12.10       100.01        29.56        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       85.45        15.62        49.08         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       13.02        29.06        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
        5.03        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
       14.30         9.04         9.44         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
      119.93        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       26.17        91.79        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
       38.56         1.45        17.49         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6510 
       51.48        32.61         0.49        20.55        19.96        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  ADAM28 MUTATED ADAM28 WILD-TYPE 
            0.69             0.00 
  ADAM28 MUTATED ADAM28 WILD-TYPE 
           63.98           148.01 
  ADAM28 MUTATED ADAM28 WILD-TYPE 
          20.945           20.120 
[1] "0.7 - 64.0 (20.9)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "2"  
D222V2, continuous
D222V3, binary
                  cls
clus                 0   1
  ADAM28 MUTATED    17   3
  ADAM28 WILD-TYPE 349 116
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ADAM28 MUTATED     17    3
  ADAM28 WILD-TYPE  349  116
        clus
vv       ADAM28 MUTATED ADAM28 WILD-TYPE
  COLON              17              349
  RECTUM              3              116
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ADAM28 MUTATED         4        0        2         4         2         0
  ADAM28 WILD-TYPE      87        1       30       134         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ADAM28 MUTATED           0          0          5          2        0
  ADAM28 WILD-TYPE        24         11         54         40       48
                  vv
clus               STAGE IVA STAGE IVB
  ADAM28 MUTATED           1         0
  ADAM28 WILD-TYPE        17         1
D222V4, multiclass
            clus
vv           ADAM28 MUTATED ADAM28 WILD-TYPE
  STAGE I                 4               87
  STAGE IA                0                1
  STAGE II                2               30
  STAGE IIA               4              134
  STAGE IIB               2                8
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              5               54
  STAGE IIIC              2               40
  STAGE IV                0               48
  STAGE IVA               1               17
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ADAM28 MUTATED     0   4  13   3
  ADAM28 WILD-TYPE  17  88 316  47
D222V5, multiclass
    clus
vv   ADAM28 MUTATED ADAM28 WILD-TYPE
  T1              0               17
  T2              4               88
  T3             13              316
  T4              3               47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  ADAM28 MUTATED    13   5   2
  ADAM28 WILD-TYPE 274 108  85
D222V6, multiclass
    clus
vv   ADAM28 MUTATED ADAM28 WILD-TYPE
  N0             13              274
  N1              5              108
  N2              2               85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D222V7, binary
                  cls
clus                 0   1
  ADAM28 MUTATED    16   1
  ADAM28 WILD-TYPE 359  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ADAM28 MUTATED     16    1
  ADAM28 WILD-TYPE  359   64
   clus
vv  ADAM28 MUTATED ADAM28 WILD-TYPE
  0             16              359
  1              1               64
[1] 2 2
[1] FALSE
D222V8, binary
                  cls
clus                 0   1
  ADAM28 MUTATED     7  13
  ADAM28 WILD-TYPE 218 251
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ADAM28 MUTATED      7   13
  ADAM28 WILD-TYPE  218  251
        clus
vv       ADAM28 MUTATED ADAM28 WILD-TYPE
  FEMALE              7              218
  MALE               13              251
[1] 2 2
[1] FALSE
D222V9, binary
                  cls
clus                 0   1
  ADAM28 MUTATED    15   0
  ADAM28 WILD-TYPE 335  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ADAM28 MUTATED     15    0
  ADAM28 WILD-TYPE  335   22
     clus
vv    ADAM28 MUTATED ADAM28 WILD-TYPE
  NO              15              335
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ADAM28 MUTATED                     13                             4
  ADAM28 WILD-TYPE                  302                            43
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ADAM28 MUTATED                       3                              0
  ADAM28 WILD-TYPE                   103                             10
D222V10, multiclass
                                clus
vv                               ADAM28 MUTATED ADAM28 WILD-TYPE
  COLON ADENOCARCINOMA                       13              302
  COLON MUCINOUS ADENOCARCINOMA               4               43
  RECTAL ADENOCARCINOMA                       3              103
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ADAM28 MUTATED    13   0   0   2
  ADAM28 WILD-TYPE 332   4  31  23
D222V11, multiclass
    clus
vv   ADAM28 MUTATED ADAM28 WILD-TYPE
  R0             13              332
  R1              0                4
  R2              0               31
  RX              2               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D222V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ADAM28 MUTATED                                  0     0
  ADAM28 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ADAM28 MUTATED                           2    12
  ADAM28 WILD-TYPE                        20   214
D222V13, multiclass
                                  clus
vv                                 ADAM28 MUTATED ADAM28 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     2               20
  WHITE                                        12              214
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(223) Variable = SMAD3 MUTATION ANALYSIS
D223V1, survival
                 sevent
clus2               0   1
  SMAD3 MUTATED    16   2
  SMAD3 WILD-TYPE 362  91
  SMAD3 MUTATED SMAD3 WILD-TYPE 
             18             453 
  SMAD3 MUTATED SMAD3 WILD-TYPE 
              2              91 
$`SMAD3 MUTATED`
TCGA-AA-3510 TCGA-AA-3710 TCGA-AA-3815 TCGA-AA-3831 TCGA-AA-3864 TCGA-AA-A010 
       63.98        26.99        33.04        17.98        53.00        34.98 
TCGA-AZ-4315 TCGA-CK-4948 TCGA-CK-4952 TCGA-CM-5348 TCGA-CM-6171 TCGA-DM-A1DA 
       58.39       148.01        15.62        22.98        14.04         7.50 
TCGA-G4-6310 TCGA-AG-3896 TCGA-AG-A002 TCGA-AG-A036 TCGA-DY-A0XA TCGA-DY-A1DC 
       63.62         1.02        20.98       117.11       126.44        41.36 

$`SMAD3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        85.05        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3833 TCGA-AA-3837 
       35.05         0.99        25.02         1.02        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       31.07        30.05        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
       16.31         0.95        33.01        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       85.45        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       13.02        29.06        22.03        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       13.02        15.02        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       55.04        85.48        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3902 
       17.03        13.02        35.01        14.01        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        4.01         5.03         5.29        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  SMAD3 MUTATED SMAD3 WILD-TYPE 
           1.02            0.00 
  SMAD3 MUTATED SMAD3 WILD-TYPE 
         148.01          140.38 
  SMAD3 MUTATED SMAD3 WILD-TYPE 
          34.01           20.02 
[1] "1.0 - 148.0 (34.0)" "0.0 - 140.4 (20.0)"
[1] "hr=" "3.2"
D223V2, continuous
D223V3, binary
                 cls
clus                0   1
  SMAD3 MUTATED    14   5
  SMAD3 WILD-TYPE 352 114
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAD3 MUTATED     14    5
  SMAD3 WILD-TYPE  352  114
        clus
vv       SMAD3 MUTATED SMAD3 WILD-TYPE
  COLON             14             352
  RECTUM             5             114
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SMAD3 MUTATED         3        0        2         7         1         0
  SMAD3 WILD-TYPE      88        1       30       131         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SMAD3 MUTATED           2          0          2          2        0         0
  SMAD3 WILD-TYPE        22         11         57         40       48        18
                 vv
clus              STAGE IVB
  SMAD3 MUTATED           0
  SMAD3 WILD-TYPE         1
D223V4, multiclass
            clus
vv           SMAD3 MUTATED SMAD3 WILD-TYPE
  STAGE I                3              88
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA              7             131
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              2              22
  STAGE IIIA             0              11
  STAGE IIIB             2              57
  STAGE IIIC             2              40
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  SMAD3 MUTATED     0   3  14   2
  SMAD3 WILD-TYPE  17  89 315  48
D223V5, multiclass
    clus
vv   SMAD3 MUTATED SMAD3 WILD-TYPE
  T1             0              17
  T2             3              89
  T3            14             315
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  SMAD3 MUTATED    13   3   3
  SMAD3 WILD-TYPE 274 110  84
D223V6, multiclass
    clus
vv   SMAD3 MUTATED SMAD3 WILD-TYPE
  N0            13             274
  N1             3             110
  N2             3              84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D223V7, binary
                 cls
clus                0   1
  SMAD3 MUTATED    19   0
  SMAD3 WILD-TYPE 356  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAD3 MUTATED     19    0
  SMAD3 WILD-TYPE  356   65
   clus
vv  SMAD3 MUTATED SMAD3 WILD-TYPE
  0            19             356
  1             0              65
[1] 2 2
[1] FALSE
D223V8, binary
                 cls
clus                0   1
  SMAD3 MUTATED    11   8
  SMAD3 WILD-TYPE 214 256
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAD3 MUTATED     11    8
  SMAD3 WILD-TYPE  214  256
        clus
vv       SMAD3 MUTATED SMAD3 WILD-TYPE
  FEMALE            11             214
  MALE               8             256
[1] 2 2
[1] FALSE
D223V9, binary
                 cls
clus                0   1
  SMAD3 MUTATED    11   2
  SMAD3 WILD-TYPE 339  20
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAD3 MUTATED     11    2
  SMAD3 WILD-TYPE  339   20
     clus
vv    SMAD3 MUTATED SMAD3 WILD-TYPE
  NO             11             339
  YES             2              20
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SMAD3 MUTATED                     13                             1
  SMAD3 WILD-TYPE                  302                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SMAD3 MUTATED                       5                              0
  SMAD3 WILD-TYPE                   101                             10
D223V10, multiclass
                                clus
vv                               SMAD3 MUTATED SMAD3 WILD-TYPE
  COLON ADENOCARCINOMA                      13             302
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      5             101
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  SMAD3 MUTATED    15   0   0   1
  SMAD3 WILD-TYPE 330   4  31  24
D223V11, multiclass
    clus
vv   SMAD3 MUTATED SMAD3 WILD-TYPE
  R0            15             330
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D223V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SMAD3 MUTATED                                  0     0
  SMAD3 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  SMAD3 MUTATED                           0     9
  SMAD3 WILD-TYPE                        22   217
D223V13, multiclass
                                  clus
vv                                 SMAD3 MUTATED SMAD3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        9             217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(224) Variable = SGK269 MUTATION ANALYSIS
D224V1, survival
                  sevent
clus2                0   1
  SGK269 MUTATED    19   4
  SGK269 WILD-TYPE 359  89
  SGK269 MUTATED SGK269 WILD-TYPE 
              23              448 
  SGK269 MUTATED SGK269 WILD-TYPE 
               4               89 
$`SGK269 MUTATED`
TCGA-A6-4105 TCGA-A6-5661 TCGA-A6-5665 TCGA-A6-6141 TCGA-A6-6780 TCGA-AA-3663 
       14.53        33.53        22.06         8.38        20.12         6.97 
TCGA-AA-3864 TCGA-AD-6889 TCGA-AU-6004 TCGA-AY-6386 TCGA-CA-6716 TCGA-CA-6717 
       53.00        56.55        27.09        17.82        12.20        12.76 
TCGA-CM-6171 TCGA-D5-6533 TCGA-D5-6927 TCGA-D5-6930 TCGA-F4-6570 TCGA-G4-6303 
       14.04         1.32         9.44         1.51         6.18        65.85 
TCGA-G4-6586 TCGA-G4-6628 TCGA-AG-3892 TCGA-AG-A002 TCGA-DY-A1DG 
       35.80        79.69        13.02        20.98        51.48 

$`SGK269 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 
       16.57        34.65        33.34        32.75        36.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 
       31.63        30.44        29.19        23.61        22.09        32.71 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 
       27.09        22.52        25.08        25.18        24.16        21.76 
TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 
       24.69        24.39        23.87        19.66        20.28         7.04 
TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
        3.02         1.02        35.01        63.98         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
       13.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       36.03         8.05        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
       78.08         6.05        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       15.52         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       10.88         0.20        14.50        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6718 TCGA-CA-6719 
        3.06         3.25         3.29         0.07        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       55.92        20.19        18.25        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6928 
        3.68         4.41        12.43        14.30         9.04        11.64 
TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        4.80        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 
       98.24         8.61        31.96        35.74        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6304 TCGA-G4-6306 
       47.41        35.31       133.18        74.56        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 
       13.78        26.17        91.79        46.75        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       24.13        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  SGK269 MUTATED SGK269 WILD-TYPE 
            1.32             0.00 
  SGK269 MUTATED SGK269 WILD-TYPE 
           79.69           148.01 
  SGK269 MUTATED SGK269 WILD-TYPE 
          17.820           20.415 
[1] "1.3 - 79.7 (17.8)"  "0.0 - 148.0 (20.4)"
[1] "hr=" "1.2"
D224V2, continuous
D224V3, binary
                  cls
clus                 0   1
  SGK269 MUTATED    20   3
  SGK269 WILD-TYPE 346 116
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SGK269 MUTATED     20    3
  SGK269 WILD-TYPE  346  116
        clus
vv       SGK269 MUTATED SGK269 WILD-TYPE
  COLON              20              346
  RECTUM              3              116
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SGK269 MUTATED         5        0        2        12         0         0
  SGK269 WILD-TYPE      86        1       30       126        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SGK269 MUTATED           0          0          2          0        1
  SGK269 WILD-TYPE        24         11         57         42       47
                  vv
clus               STAGE IVA STAGE IVB
  SGK269 MUTATED           1         0
  SGK269 WILD-TYPE        17         1
D224V4, multiclass
            clus
vv           SGK269 MUTATED SGK269 WILD-TYPE
  STAGE I                 5               86
  STAGE IA                0                1
  STAGE II                2               30
  STAGE IIA              12              126
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              2               57
  STAGE IIIC              0               42
  STAGE IV                1               47
  STAGE IVA               1               17
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  SGK269 MUTATED     1   4  17   1
  SGK269 WILD-TYPE  16  88 312  49
D224V5, multiclass
    clus
vv   SGK269 MUTATED SGK269 WILD-TYPE
  T1              1               16
  T2              4               88
  T3             17              312
  T4              1               49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  SGK269 MUTATED    20   3   0
  SGK269 WILD-TYPE 267 110  87
D224V6, multiclass
    clus
vv   SGK269 MUTATED SGK269 WILD-TYPE
  N0             20              267
  N1              3              110
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D224V7, binary
                  cls
clus                 0   1
  SGK269 MUTATED    20   2
  SGK269 WILD-TYPE 355  63
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SGK269 MUTATED     20    2
  SGK269 WILD-TYPE  355   63
   clus
vv  SGK269 MUTATED SGK269 WILD-TYPE
  0             20              355
  1              2               63
[1] 2 2
[1] FALSE
D224V8, binary
                  cls
clus                 0   1
  SGK269 MUTATED    10  13
  SGK269 WILD-TYPE 215 251
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SGK269 MUTATED     10   13
  SGK269 WILD-TYPE  215  251
        clus
vv       SGK269 MUTATED SGK269 WILD-TYPE
  FEMALE             10              215
  MALE               13              251
[1] 2 2
[1] FALSE
D224V9, binary
                  cls
clus                 0   1
  SGK269 MUTATED    18   0
  SGK269 WILD-TYPE 332  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SGK269 MUTATED     18    0
  SGK269 WILD-TYPE  332   22
     clus
vv    SGK269 MUTATED SGK269 WILD-TYPE
  NO              18              332
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SGK269 MUTATED                     17                             3
  SGK269 WILD-TYPE                  298                            44
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SGK269 MUTATED                       3                              0
  SGK269 WILD-TYPE                   103                             10
D224V10, multiclass
                                clus
vv                               SGK269 MUTATED SGK269 WILD-TYPE
  COLON ADENOCARCINOMA                       17              298
  COLON MUCINOUS ADENOCARCINOMA               3               44
  RECTAL ADENOCARCINOMA                       3              103
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  SGK269 MUTATED    16   0   0   2
  SGK269 WILD-TYPE 329   4  31  23
D224V11, multiclass
    clus
vv   SGK269 MUTATED SGK269 WILD-TYPE
  R0             16              329
  R1              0                4
  R2              0               31
  RX              2               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D224V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SGK269 MUTATED                                  0     3
  SGK269 WILD-TYPE                                1     8
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  SGK269 MUTATED                           3    13
  SGK269 WILD-TYPE                        19   213
D224V13, multiclass
                                  clus
vv                                 SGK269 MUTATED SGK269 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         3                8
  BLACK OR AFRICAN AMERICAN                     3               19
  WHITE                                        13              213
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(225) Variable = FLT3 MUTATION ANALYSIS
D225V1, survival
                sevent
clus2              0   1
  FLT3 MUTATED    25   6
  FLT3 WILD-TYPE 353  87
  FLT3 MUTATED FLT3 WILD-TYPE 
            31            440 
  FLT3 MUTATED FLT3 WILD-TYPE 
             6             87 
$`FLT3 MUTATED`
TCGA-A6-5656 TCGA-A6-5666 TCGA-A6-6141 TCGA-AA-3864 TCGA-AA-3950 TCGA-AA-A010 
       32.91        32.71         8.38        53.00        24.00        34.98 
TCGA-AA-A02K TCGA-AD-6899 TCGA-AU-6004 TCGA-AY-5543 TCGA-AZ-6608 TCGA-CA-6717 
       14.01         5.79        27.09        33.01         1.61        12.76 
TCGA-CM-5860 TCGA-CM-5864 TCGA-CM-6171 TCGA-D5-6537 TCGA-D5-6922 TCGA-D5-6923 
       32.02        15.02        14.04         4.80         4.41        12.43 
TCGA-D5-6927 TCGA-DM-A1D7 TCGA-G4-6293 TCGA-G4-6315 TCGA-G4-6323 TCGA-AG-A002 
        9.44        13.32       133.18        61.91        13.78        20.98 
TCGA-AH-6643 TCGA-CI-6624 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DG TCGA-F5-6571 
        0.69         4.73         5.03       126.44        51.48        31.30 
TCGA-F5-6811 
       32.19 

$`FLT3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       22.06        27.09        22.52        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        31.07        30.05        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       33.01        26.01         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O 
       39.06        51.98        39.98         2.01         5.03         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6901 TCGA-AD-6963 
       15.52        56.55         0.79         0.72        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6197 
       10.88         0.20        14.50        16.31         0.95        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07        12.20        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5868 
       22.98        30.08        15.02         5.03        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 
       14.99        12.99        13.02        15.02        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6538 
       18.25         1.32        43.27        15.12        17.85        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6924 
       12.49        16.14        15.58         1.48         3.68        14.30 
TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.04        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       49.91        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6299 
       33.67        13.25         0.53        47.41        35.31        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CL-5917 
       17.49         0.72         6.05        33.17         6.97        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD 
       19.99         5.95         4.01         5.29        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       24.13        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6702 TCGA-F5-6812 TCGA-F5-6813 
       18.28         9.96        49.51        28.57         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  FLT3 MUTATED FLT3 WILD-TYPE 
          0.69           0.00 
  FLT3 MUTATED FLT3 WILD-TYPE 
        133.18         148.01 
  FLT3 MUTATED FLT3 WILD-TYPE 
        15.020         20.235 
[1] "0.7 - 133.2 (15.0)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1"  
D225V2, continuous
D225V3, binary
                cls
clus               0   1
  FLT3 MUTATED    24   8
  FLT3 WILD-TYPE 342 111
[1] "tbl2"
                cls
clus             [,1] [,2]
  FLT3 MUTATED     24    8
  FLT3 WILD-TYPE  342  111
        clus
vv       FLT3 MUTATED FLT3 WILD-TYPE
  COLON            24            342
  RECTUM            8            111
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FLT3 MUTATED         7        1        1        10         1         1
  FLT3 WILD-TYPE      84        0       31       128         9         0
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  FLT3 MUTATED           1          2          2          2        2         2
  FLT3 WILD-TYPE        23          9         57         40       46        16
                vv
clus             STAGE IVB
  FLT3 MUTATED           0
  FLT3 WILD-TYPE         1
D225V4, multiclass
            clus
vv           FLT3 MUTATED FLT3 WILD-TYPE
  STAGE I               7             84
  STAGE IA              1              0
  STAGE II              1             31
  STAGE IIA            10            128
  STAGE IIB             1              9
  STAGE IIC             1              0
  STAGE III             1             23
  STAGE IIIA            2              9
  STAGE IIIB            2             57
  STAGE IIIC            2             40
  STAGE IV              2             46
  STAGE IVA             2             16
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  FLT3 MUTATED     0   8  19   4
  FLT3 WILD-TYPE  17  84 310  46
D225V5, multiclass
    clus
vv   FLT3 MUTATED FLT3 WILD-TYPE
  T1            0             17
  T2            8             84
  T3           19            310
  T4            4             46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  FLT3 MUTATED    21   8   3
  FLT3 WILD-TYPE 266 105  84
D225V6, multiclass
    clus
vv   FLT3 MUTATED FLT3 WILD-TYPE
  N0           21            266
  N1            8            105
  N2            3             84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D225V7, binary
                cls
clus               0   1
  FLT3 MUTATED    25   4
  FLT3 WILD-TYPE 350  61
[1] "tbl2"
                cls
clus             [,1] [,2]
  FLT3 MUTATED     25    4
  FLT3 WILD-TYPE  350   61
   clus
vv  FLT3 MUTATED FLT3 WILD-TYPE
  0           25            350
  1            4             61
[1] 2 2
[1] FALSE
D225V8, binary
                cls
clus               0   1
  FLT3 MUTATED    12  20
  FLT3 WILD-TYPE 213 244
[1] "tbl2"
                cls
clus             [,1] [,2]
  FLT3 MUTATED     12   20
  FLT3 WILD-TYPE  213  244
        clus
vv       FLT3 MUTATED FLT3 WILD-TYPE
  FEMALE           12            213
  MALE             20            244
[1] 2 2
[1] FALSE
D225V9, binary
                cls
clus               0   1
  FLT3 MUTATED    23   0
  FLT3 WILD-TYPE 327  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  FLT3 MUTATED     23    0
  FLT3 WILD-TYPE  327   22
     clus
vv    FLT3 MUTATED FLT3 WILD-TYPE
  NO            23            327
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  FLT3 MUTATED                     20                             3
  FLT3 WILD-TYPE                  295                            44
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  FLT3 MUTATED                       8                              0
  FLT3 WILD-TYPE                    98                             10
D225V10, multiclass
                                clus
vv                               FLT3 MUTATED FLT3 WILD-TYPE
  COLON ADENOCARCINOMA                     20            295
  COLON MUCINOUS ADENOCARCINOMA             3             44
  RECTAL ADENOCARCINOMA                     8             98
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  FLT3 MUTATED    20   0   1   1
  FLT3 WILD-TYPE 325   4  30  24
D225V11, multiclass
    clus
vv   FLT3 MUTATED FLT3 WILD-TYPE
  R0           20            325
  R1            0              4
  R2            1             30
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D225V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FLT3 MUTATED                                  0     1
  FLT3 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  FLT3 MUTATED                           3    22
  FLT3 WILD-TYPE                        19   204
D225V13, multiclass
                                  clus
vv                                 FLT3 MUTATED FLT3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   3             19
  WHITE                                      22            204
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(226) Variable = RNF128 MUTATION ANALYSIS
D226V1, survival
                  sevent
clus2                0   1
  RNF128 MUTATED    11   3
  RNF128 WILD-TYPE 367  90
  RNF128 MUTATED RNF128 WILD-TYPE 
              14              457 
  RNF128 MUTATED RNF128 WILD-TYPE 
               3               90 
$`RNF128 MUTATED`
TCGA-A6-5665 TCGA-AA-3492 TCGA-AA-3697 TCGA-AD-6548 TCGA-AD-6895 TCGA-AD-6964 
       22.06         3.02        85.05        21.37         0.72        10.88 
TCGA-AZ-4315 TCGA-CM-4746 TCGA-D5-6928 TCGA-DM-A0X9 TCGA-G4-6586 TCGA-G4-6588 
       58.39        37.02        11.64       119.70        35.80        26.17 
TCGA-G4-6628 TCGA-AF-5654 
       79.69        16.83 

$`RNF128 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 
       20.12        19.66        20.28         7.04         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       18.05        40.96         0.07        15.52        56.55         0.79 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
       16.31         0.95        33.01        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0XD 
        4.80         1.51        12.00        11.38        10.26        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 
       36.00        22.09        13.78        91.79        46.75        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       14.50        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  RNF128 MUTATED RNF128 WILD-TYPE 
            0.72             0.00 
  RNF128 MUTATED RNF128 WILD-TYPE 
          119.70           148.01 
  RNF128 MUTATED RNF128 WILD-TYPE 
          24.115           20.050 
[1] "0.7 - 119.7 (24.1)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.3"
D226V2, continuous
D226V3, binary
                  cls
clus                 0   1
  RNF128 MUTATED    14   1
  RNF128 WILD-TYPE 352 118
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF128 MUTATED     14    1
  RNF128 WILD-TYPE  352  118
        clus
vv       RNF128 MUTATED RNF128 WILD-TYPE
  COLON              14              352
  RECTUM              1              118
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RNF128 MUTATED         4        0        1         6         1         0
  RNF128 WILD-TYPE      87        1       31       132         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RNF128 MUTATED           1          0          0          0        0
  RNF128 WILD-TYPE        23         11         59         42       48
                  vv
clus               STAGE IVA STAGE IVB
  RNF128 MUTATED           0         0
  RNF128 WILD-TYPE        18         1
D226V4, multiclass
            clus
vv           RNF128 MUTATED RNF128 WILD-TYPE
  STAGE I                 4               87
  STAGE IA                0                1
  STAGE II                1               31
  STAGE IIA               6              132
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               1               23
  STAGE IIIA              0               11
  STAGE IIIB              0               59
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  RNF128 MUTATED     0   4   9   2
  RNF128 WILD-TYPE  17  88 320  48
D226V5, multiclass
    clus
vv   RNF128 MUTATED RNF128 WILD-TYPE
  T1              0               17
  T2              4               88
  T3              9              320
  T4              2               48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  RNF128 MUTATED    13   1   1
  RNF128 WILD-TYPE 274 112  86
D226V6, multiclass
    clus
vv   RNF128 MUTATED RNF128 WILD-TYPE
  N0             13              274
  N1              1              112
  N2              1               86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D226V7, binary
                  cls
clus                 0   1
  RNF128 MUTATED    12   0
  RNF128 WILD-TYPE 363  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF128 MUTATED     12    0
  RNF128 WILD-TYPE  363   65
   clus
vv  RNF128 MUTATED RNF128 WILD-TYPE
  0             12              363
  1              0               65
[1] 2 2
[1] FALSE
D226V8, binary
                  cls
clus                 0   1
  RNF128 MUTATED     8   7
  RNF128 WILD-TYPE 217 257
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF128 MUTATED      8    7
  RNF128 WILD-TYPE  217  257
        clus
vv       RNF128 MUTATED RNF128 WILD-TYPE
  FEMALE              8              217
  MALE                7              257
[1] 2 2
[1] FALSE
D226V9, binary
                  cls
clus                 0   1
  RNF128 MUTATED    12   0
  RNF128 WILD-TYPE 338  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF128 MUTATED     12    0
  RNF128 WILD-TYPE  338   22
     clus
vv    RNF128 MUTATED RNF128 WILD-TYPE
  NO              12              338
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  RNF128 MUTATED                     13                             1
  RNF128 WILD-TYPE                  302                            46
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  RNF128 MUTATED                       1                              0
  RNF128 WILD-TYPE                   105                             10
D226V10, multiclass
                                clus
vv                               RNF128 MUTATED RNF128 WILD-TYPE
  COLON ADENOCARCINOMA                       13              302
  COLON MUCINOUS ADENOCARCINOMA               1               46
  RECTAL ADENOCARCINOMA                       1              105
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  RNF128 MUTATED    11   0   0   1
  RNF128 WILD-TYPE 334   4  31  24
D226V11, multiclass
    clus
vv   RNF128 MUTATED RNF128 WILD-TYPE
  R0             11              334
  R1              0                4
  R2              0               31
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D226V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RNF128 MUTATED                                  0     0
  RNF128 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  RNF128 MUTATED                           1    12
  RNF128 WILD-TYPE                        21   214
D226V13, multiclass
                                  clus
vv                                 RNF128 MUTATED RNF128 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                        12              214
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(227) Variable = MOBKL2B MUTATION ANALYSIS
D227V1, survival
                   sevent
clus2                 0   1
  MOBKL2B MUTATED     8   1
  MOBKL2B WILD-TYPE 370  92
  MOBKL2B MUTATED MOBKL2B WILD-TYPE 
                9               462 
  MOBKL2B MUTATED MOBKL2B WILD-TYPE 
                1                92 
$`MOBKL2B MUTATED`
TCGA-A6-6781 TCGA-AA-A02K TCGA-AD-6963 TCGA-AY-6386 TCGA-CK-5914 TCGA-CK-6747 
       19.66        14.01        27.42        17.82         9.99        82.95 
TCGA-DM-A1HA TCGA-EI-6510 TCGA-F5-6465 
      131.51        18.28        49.51 

$`MOBKL2B WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02W 
       51.98        39.98         2.01         5.03         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6964 
       56.55         0.79         0.72         5.79        22.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       49.08        51.32        21.14         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
       44.32       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-F5-6464 TCGA-F5-6571 
        0.49        20.55        19.96        20.91         9.96        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  MOBKL2B MUTATED MOBKL2B WILD-TYPE 
             9.99              0.00 
  MOBKL2B MUTATED MOBKL2B WILD-TYPE 
           131.51            148.01 
  MOBKL2B MUTATED MOBKL2B WILD-TYPE 
           19.660            20.235 
[1] "10.0 - 131.5 (19.7)" "0.0 - 148.0 (20.2)" 
[1] "hr=" "2.7"
D227V2, continuous
D227V3, binary
                   cls
clus                  0   1
  MOBKL2B MUTATED     7   2
  MOBKL2B WILD-TYPE 359 117
[1] "tbl2"
                   cls
clus                [,1] [,2]
  MOBKL2B MUTATED      7    2
  MOBKL2B WILD-TYPE  359  117
        clus
vv       MOBKL2B MUTATED MOBKL2B WILD-TYPE
  COLON                7               359
  RECTUM               2               117
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MOBKL2B MUTATED         0        0        0         2         0         0
  MOBKL2B WILD-TYPE      91        1       32       136        10         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MOBKL2B MUTATED           0          0          2          2        1
  MOBKL2B WILD-TYPE        24         11         57         40       47
                   vv
clus                STAGE IVA STAGE IVB
  MOBKL2B MUTATED           1         0
  MOBKL2B WILD-TYPE        17         1
D227V4, multiclass
            clus
vv           MOBKL2B MUTATED MOBKL2B WILD-TYPE
  STAGE I                  0                91
  STAGE IA                 0                 1
  STAGE II                 0                32
  STAGE IIA                2               136
  STAGE IIB                0                10
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               0                11
  STAGE IIIB               2                57
  STAGE IIIC               2                40
  STAGE IV                 1                47
  STAGE IVA                1                17
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  MOBKL2B MUTATED     0   1   6   2
  MOBKL2B WILD-TYPE  17  91 323  48
D227V5, multiclass
    clus
vv   MOBKL2B MUTATED MOBKL2B WILD-TYPE
  T1               0                17
  T2               1                91
  T3               6               323
  T4               2                48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  MOBKL2B MUTATED     4   3   2
  MOBKL2B WILD-TYPE 283 110  85
D227V6, multiclass
    clus
vv   MOBKL2B MUTATED MOBKL2B WILD-TYPE
  N0               4               283
  N1               3               110
  N2               2                85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D227V7, binary
                   cls
clus                  0   1
  MOBKL2B MUTATED     3   1
  MOBKL2B WILD-TYPE 372  64
[1] "tbl2"
                   cls
clus                [,1] [,2]
  MOBKL2B MUTATED      3    1
  MOBKL2B WILD-TYPE  372   64
   clus
vv  MOBKL2B MUTATED MOBKL2B WILD-TYPE
  0               3               372
  1               1                64
[1] 2 2
[1] FALSE
D227V8, binary
                   cls
clus                  0   1
  MOBKL2B MUTATED     4   5
  MOBKL2B WILD-TYPE 221 259
[1] "tbl2"
                   cls
clus                [,1] [,2]
  MOBKL2B MUTATED      4    5
  MOBKL2B WILD-TYPE  221  259
        clus
vv       MOBKL2B MUTATED MOBKL2B WILD-TYPE
  FEMALE               4               221
  MALE                 5               259
[1] 2 2
[1] FALSE
D227V9, binary
                   cls
clus                  0   1
  MOBKL2B MUTATED     7   0
  MOBKL2B WILD-TYPE 343  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  MOBKL2B MUTATED      7    0
  MOBKL2B WILD-TYPE  343   22
     clus
vv    MOBKL2B MUTATED MOBKL2B WILD-TYPE
  NO                7               343
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MOBKL2B MUTATED                      6                             1
  MOBKL2B WILD-TYPE                  309                            46
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MOBKL2B MUTATED                       2                              0
  MOBKL2B WILD-TYPE                   104                             10
D227V10, multiclass
                                clus
vv                               MOBKL2B MUTATED MOBKL2B WILD-TYPE
  COLON ADENOCARCINOMA                         6               309
  COLON MUCINOUS ADENOCARCINOMA                1                46
  RECTAL ADENOCARCINOMA                        2               104
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  MOBKL2B MUTATED     4   0   1   2
  MOBKL2B WILD-TYPE 341   4  30  23
D227V11, multiclass
    clus
vv   MOBKL2B MUTATED MOBKL2B WILD-TYPE
  R0               4               341
  R1               0                 4
  R2               1                30
  RX               2                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D227V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MOBKL2B MUTATED                                  0     0
  MOBKL2B WILD-TYPE                                1    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  MOBKL2B MUTATED                           1     7
  MOBKL2B WILD-TYPE                        21   219
D227V13, multiclass
                                  clus
vv                                 MOBKL2B MUTATED MOBKL2B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                      1                21
  WHITE                                          7               219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(228) Variable = NT5DC3 MUTATION ANALYSIS
D228V1, survival
                  sevent
clus2                0   1
  NT5DC3 MUTATED    11   3
  NT5DC3 WILD-TYPE 367  90
  NT5DC3 MUTATED NT5DC3 WILD-TYPE 
              14              457 
  NT5DC3 MUTATED NT5DC3 WILD-TYPE 
               3               90 
$`NT5DC3 MUTATED`
TCGA-A6-2672 TCGA-A6-6780 TCGA-AA-3502 TCGA-AA-3697 TCGA-AZ-6598 TCGA-AZ-6601 
       46.65        20.12        35.01        85.05        49.41       100.01 
TCGA-CM-6171 TCGA-D5-5539 TCGA-D5-6541 TCGA-D5-6929 TCGA-F4-6570 TCGA-G4-6310 
       14.04        19.59        15.58         4.80         6.18        63.62 
TCGA-EI-6506 TCGA-EI-6507 
       20.55        19.96 

$`NT5DC3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3510 
       19.66        20.28         7.04         3.02         1.02        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 
       62.79        88.21         6.77        12.10        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-5541 
       10.06        12.03        45.40        12.26        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6898 TCGA-D5-6920 
        4.80        17.13        12.49        16.14         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 
       98.24         8.61        31.96        35.74        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       44.68        55.04        85.48        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       32.61         0.49        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  NT5DC3 MUTATED NT5DC3 WILD-TYPE 
             4.8              0.0 
  NT5DC3 MUTATED NT5DC3 WILD-TYPE 
          100.01           148.01 
  NT5DC3 MUTATED NT5DC3 WILD-TYPE 
          20.335           20.190 
[1] "4.8 - 100.0 (20.3)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.3"
D228V2, continuous
D228V3, binary
                  cls
clus                 0   1
  NT5DC3 MUTATED    12   2
  NT5DC3 WILD-TYPE 354 117
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NT5DC3 MUTATED     12    2
  NT5DC3 WILD-TYPE  354  117
        clus
vv       NT5DC3 MUTATED NT5DC3 WILD-TYPE
  COLON              12              354
  RECTUM              2              117
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NT5DC3 MUTATED         2        0        2         5         0         0
  NT5DC3 WILD-TYPE      89        1       30       133        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NT5DC3 MUTATED           1          1          2          0        1
  NT5DC3 WILD-TYPE        23         10         57         42       47
                  vv
clus               STAGE IVA STAGE IVB
  NT5DC3 MUTATED           0         0
  NT5DC3 WILD-TYPE        18         1
D228V4, multiclass
            clus
vv           NT5DC3 MUTATED NT5DC3 WILD-TYPE
  STAGE I                 2               89
  STAGE IA                0                1
  STAGE II                2               30
  STAGE IIA               5              133
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               1               23
  STAGE IIIA              1               10
  STAGE IIIB              2               57
  STAGE IIIC              0               42
  STAGE IV                1               47
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  NT5DC3 MUTATED     0   2  12   0
  NT5DC3 WILD-TYPE  17  90 317  50
D228V5, multiclass
    clus
vv   NT5DC3 MUTATED NT5DC3 WILD-TYPE
  T1              0               17
  T2              2               90
  T3             12              317
  T4              0               50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  NT5DC3 MUTATED    10   4   0
  NT5DC3 WILD-TYPE 277 109  87
D228V6, multiclass
    clus
vv   NT5DC3 MUTATED NT5DC3 WILD-TYPE
  N0             10              277
  N1              4              109
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D228V7, binary
                  cls
clus                 0   1
  NT5DC3 MUTATED    11   1
  NT5DC3 WILD-TYPE 364  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NT5DC3 MUTATED     11    1
  NT5DC3 WILD-TYPE  364   64
   clus
vv  NT5DC3 MUTATED NT5DC3 WILD-TYPE
  0             11              364
  1              1               64
[1] 2 2
[1] FALSE
D228V8, binary
                  cls
clus                 0   1
  NT5DC3 MUTATED     6   8
  NT5DC3 WILD-TYPE 219 256
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NT5DC3 MUTATED      6    8
  NT5DC3 WILD-TYPE  219  256
        clus
vv       NT5DC3 MUTATED NT5DC3 WILD-TYPE
  FEMALE              6              219
  MALE                8              256
[1] 2 2
[1] FALSE
D228V9, binary
                  cls
clus                 0   1
  NT5DC3 MUTATED    12   1
  NT5DC3 WILD-TYPE 338  21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NT5DC3 MUTATED     12    1
  NT5DC3 WILD-TYPE  338   21
     clus
vv    NT5DC3 MUTATED NT5DC3 WILD-TYPE
  NO              12              338
  YES              1               21
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  NT5DC3 MUTATED                     10                             2
  NT5DC3 WILD-TYPE                  305                            45
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  NT5DC3 MUTATED                       2                              0
  NT5DC3 WILD-TYPE                   104                             10
D228V10, multiclass
                                clus
vv                               NT5DC3 MUTATED NT5DC3 WILD-TYPE
  COLON ADENOCARCINOMA                       10              305
  COLON MUCINOUS ADENOCARCINOMA               2               45
  RECTAL ADENOCARCINOMA                       2              104
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  NT5DC3 MUTATED    11   0   0   0
  NT5DC3 WILD-TYPE 334   4  31  25
D228V11, multiclass
    clus
vv   NT5DC3 MUTATED NT5DC3 WILD-TYPE
  R0             11              334
  R1              0                4
  R2              0               31
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D228V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NT5DC3 MUTATED                                  0     0
  NT5DC3 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  NT5DC3 MUTATED                           0    12
  NT5DC3 WILD-TYPE                        22   214
D228V13, multiclass
                                  clus
vv                                 NT5DC3 MUTATED NT5DC3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                        12              214
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(229) Variable = USP29 MUTATION ANALYSIS
D229V1, survival
                 sevent
clus2               0   1
  USP29 MUTATED    16   4
  USP29 WILD-TYPE 362  89
  USP29 MUTATED USP29 WILD-TYPE 
             20             451 
  USP29 MUTATED USP29 WILD-TYPE 
              4              89 
$`USP29 MUTATED`
TCGA-AA-3492 TCGA-AA-3543 TCGA-AA-3672 TCGA-AA-3710 TCGA-AA-3950 TCGA-AA-A00N 
        3.02         0.99         0.92        26.99        24.00         4.01 
TCGA-AA-A010 TCGA-AD-5900 TCGA-AZ-4315 TCGA-CA-6718 TCGA-CK-4950 TCGA-D5-6535 
       34.98         0.07        58.39        10.06        85.45        15.12 
TCGA-D5-6928 TCGA-D5-6931 TCGA-DM-A28H TCGA-F4-6570 TCGA-AG-3892 TCGA-AG-A002 
       11.64        12.00       117.07         6.18        13.02        20.98 
TCGA-AH-6544 TCGA-DT-5265 
       38.56         5.29 

$`USP29 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       26.01        12.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
       54.02         2.01        14.01        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       85.05        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       33.01        26.01         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 
       41.00        39.98        18.05        40.96        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       33.01        21.44        17.82         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5912 
       12.76        14.30        17.56       148.01        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       43.27        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6932 TCGA-D5-7000 
        9.04         9.44         4.80         1.51        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 
       60.79        98.24         8.61        31.96        35.74        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 
        1.02        17.95        36.95        17.03        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6547 TCGA-AH-6549 
       61.97        41.00        38.04       117.11         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A0XA 
       10.98        19.99         5.95         4.01         5.03       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  USP29 MUTATED USP29 WILD-TYPE 
           0.07            0.00 
  USP29 MUTATED USP29 WILD-TYPE 
         117.07          148.01 
  USP29 MUTATED USP29 WILD-TYPE 
          12.51           20.55 
[1] "0.1 - 117.1 (12.5)" "0.0 - 148.0 (20.6)"
[1] "hr=" "1.1"
D229V2, continuous
D229V3, binary
                 cls
clus                0   1
  USP29 MUTATED    18   4
  USP29 WILD-TYPE 348 115
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP29 MUTATED     18    4
  USP29 WILD-TYPE  348  115
        clus
vv       USP29 MUTATED USP29 WILD-TYPE
  COLON             18             348
  RECTUM             4             115
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  USP29 MUTATED         5        0        2         7         2         0
  USP29 WILD-TYPE      86        1       30       131         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  USP29 MUTATED           1          0          2          2        0         0
  USP29 WILD-TYPE        23         11         57         40       48        18
                 vv
clus              STAGE IVB
  USP29 MUTATED           0
  USP29 WILD-TYPE         1
D229V4, multiclass
            clus
vv           USP29 MUTATED USP29 WILD-TYPE
  STAGE I                5              86
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA              7             131
  STAGE IIB              2               8
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             2              57
  STAGE IIIC             2              40
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  USP29 MUTATED     1   4  14   3
  USP29 WILD-TYPE  16  88 315  47
D229V5, multiclass
    clus
vv   USP29 MUTATED USP29 WILD-TYPE
  T1             1              16
  T2             4              88
  T3            14             315
  T4             3              47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  USP29 MUTATED    16   4   2
  USP29 WILD-TYPE 271 109  85
D229V6, multiclass
    clus
vv   USP29 MUTATED USP29 WILD-TYPE
  N0            16             271
  N1             4             109
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D229V7, binary
                 cls
clus                0   1
  USP29 MUTATED    18   1
  USP29 WILD-TYPE 357  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP29 MUTATED     18    1
  USP29 WILD-TYPE  357   64
   clus
vv  USP29 MUTATED USP29 WILD-TYPE
  0            18             357
  1             1              64
[1] 2 2
[1] FALSE
D229V8, binary
                 cls
clus                0   1
  USP29 MUTATED    10  12
  USP29 WILD-TYPE 215 252
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP29 MUTATED     10   12
  USP29 WILD-TYPE  215  252
        clus
vv       USP29 MUTATED USP29 WILD-TYPE
  FEMALE            10             215
  MALE              12             252
[1] 2 2
[1] FALSE
D229V9, binary
                 cls
clus                0   1
  USP29 MUTATED    17   0
  USP29 WILD-TYPE 333  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP29 MUTATED     17    0
  USP29 WILD-TYPE  333   22
     clus
vv    USP29 MUTATED USP29 WILD-TYPE
  NO             17             333
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  USP29 MUTATED                     13                             5
  USP29 WILD-TYPE                  302                            42
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  USP29 MUTATED                       3                              1
  USP29 WILD-TYPE                   103                              9
D229V10, multiclass
                                clus
vv                               USP29 MUTATED USP29 WILD-TYPE
  COLON ADENOCARCINOMA                      13             302
  COLON MUCINOUS ADENOCARCINOMA              5              42
  RECTAL ADENOCARCINOMA                      3             103
  RECTAL MUCINOUS ADENOCARCINOMA             1               9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  USP29 MUTATED    15   1   0   4
  USP29 WILD-TYPE 330   3  31  21
D229V11, multiclass
    clus
vv   USP29 MUTATED USP29 WILD-TYPE
  R0            15             330
  R1             1               3
  R2             0              31
  RX             4              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D229V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  USP29 MUTATED                                  0     2
  USP29 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  USP29 MUTATED                           1     9
  USP29 WILD-TYPE                        21   217
D229V13, multiclass
                                  clus
vv                                 USP29 MUTATED USP29 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               9
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        9             217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(230) Variable = USP34 MUTATION ANALYSIS
D230V1, survival
                 sevent
clus2               0   1
  USP34 MUTATED    34  12
  USP34 WILD-TYPE 344  81
  USP34 MUTATED USP34 WILD-TYPE 
             46             425 
  USP34 MUTATED USP34 WILD-TYPE 
             12              81 
$`USP34 MUTATED`
TCGA-A6-6781 TCGA-AA-3663 TCGA-AA-3673 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3815 
       19.66         6.97        50.04        19.04        19.04        33.04 
TCGA-AA-3867 TCGA-AA-3947 TCGA-AA-3955 TCGA-AA-3977 TCGA-AA-A00N TCGA-AD-5900 
       24.03        33.01        20.98        25.02         4.01         0.07 
TCGA-AD-6889 TCGA-AD-6895 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-AZ-6601 TCGA-AZ-6606 
       56.55         0.72        58.39        49.41       100.01        11.74 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4950 TCGA-CK-6748 TCGA-CM-4743 TCGA-CM-4752 
       12.76        10.06        85.45         1.91        23.05        13.02 
TCGA-CM-6167 TCGA-CM-6171 TCGA-D5-6535 TCGA-D5-6540 TCGA-D5-6927 TCGA-D5-6932 
       14.99        14.04        15.12        16.14         9.44        11.38 
TCGA-DM-A1D7 TCGA-DM-A1DA TCGA-DM-A1HB TCGA-F4-6570 TCGA-G4-6303 TCGA-G4-6309 
       13.32         7.50       135.65         6.18        65.85        85.48 
TCGA-G4-6315 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-6655 
       61.91        22.09        35.80        46.75        79.69        20.02 
TCGA-AG-A002 TCGA-AG-A026 TCGA-EI-6510 TCGA-G5-6641 
       20.98         1.94        18.28        26.43 

$`USP34 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3678 TCGA-AA-3679 
       54.02         2.01        14.01         0.92        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
       85.05        26.99        10.06        35.05         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       53.00        17.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
        2.01        12.99        24.00        26.01        24.00         2.01 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       21.37        15.52         0.79         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       33.01        21.44        17.82         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 
       22.36        62.79        88.21         6.77        12.10        29.56 
TCGA-AZ-6605 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        3.29         0.07        12.20        14.30        17.56       148.01 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-5341 TCGA-CM-5344 
      124.27        20.02        37.02        25.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 
       16.04        21.99        12.99        13.02        15.02        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 
       20.19        18.25         1.32        43.27        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       17.13        12.49        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       12.43        14.30         9.04        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       12.00        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA 
       92.75        49.91        12.59       140.38        44.32       131.51 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 
      117.07        98.24         8.61        31.96        35.74        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6304 
        0.53        47.41        35.31       133.18        74.56        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6588 
       44.68        55.04        63.62        36.00        13.78        26.17 
TCGA-G4-6625 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       91.79        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6672 
       34.49        10.39        14.50        16.83        15.39        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       64.01        10.98        49.97        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       20.55        19.96        20.91         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       28.57        32.19         0.66         0.69        55.76 

  USP34 MUTATED USP34 WILD-TYPE 
           0.07            0.00 
  USP34 MUTATED USP34 WILD-TYPE 
         135.65          148.01 
  USP34 MUTATED USP34 WILD-TYPE 
          19.84           20.28 
[1] "0.1 - 135.7 (19.8)" "0.0 - 148.0 (20.3)"
[1] "hr=" "1.1"
D230V2, continuous
D230V3, binary
                 cls
clus                0   1
  USP34 MUTATED    42   5
  USP34 WILD-TYPE 324 114
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP34 MUTATED     42    5
  USP34 WILD-TYPE  324  114
        clus
vv       USP34 MUTATED USP34 WILD-TYPE
  COLON             42             324
  RECTUM             5             114
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  USP34 MUTATED         5        0        6        13         3         0
  USP34 WILD-TYPE      86        1       26       125         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  USP34 MUTATED           1          2          5          3        6         1
  USP34 WILD-TYPE        23          9         54         39       42        17
                 vv
clus              STAGE IVB
  USP34 MUTATED           0
  USP34 WILD-TYPE         1
D230V4, multiclass
            clus
vv           USP34 MUTATED USP34 WILD-TYPE
  STAGE I                5              86
  STAGE IA               0               1
  STAGE II               6              26
  STAGE IIA             13             125
  STAGE IIB              3               7
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             2               9
  STAGE IIIB             5              54
  STAGE IIIC             3              39
  STAGE IV               6              42
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  USP34 MUTATED     1  10  30   6
  USP34 WILD-TYPE  16  82 299  44
D230V5, multiclass
    clus
vv   USP34 MUTATED USP34 WILD-TYPE
  T1             1              16
  T2            10              82
  T3            30             299
  T4             6              44
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  USP34 MUTATED    30  12   5
  USP34 WILD-TYPE 257 101  82
D230V6, multiclass
    clus
vv   USP34 MUTATED USP34 WILD-TYPE
  N0            30             257
  N1            12             101
  N2             5              82
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D230V7, binary
                 cls
clus                0   1
  USP34 MUTATED    31   6
  USP34 WILD-TYPE 344  59
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP34 MUTATED     31    6
  USP34 WILD-TYPE  344   59
   clus
vv  USP34 MUTATED USP34 WILD-TYPE
  0            31             344
  1             6              59
[1] 2 2
[1] FALSE
D230V8, binary
                 cls
clus                0   1
  USP34 MUTATED    17  30
  USP34 WILD-TYPE 208 234
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP34 MUTATED     17   30
  USP34 WILD-TYPE  208  234
        clus
vv       USP34 MUTATED USP34 WILD-TYPE
  FEMALE            17             208
  MALE              30             234
[1] 2 2
[1] FALSE
D230V9, binary
                 cls
clus                0   1
  USP34 MUTATED    37   1
  USP34 WILD-TYPE 313  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP34 MUTATED     37    1
  USP34 WILD-TYPE  313   21
     clus
vv    USP34 MUTATED USP34 WILD-TYPE
  NO             37             313
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  USP34 MUTATED                     33                             7
  USP34 WILD-TYPE                  282                            40
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  USP34 MUTATED                       4                              1
  USP34 WILD-TYPE                   102                              9
D230V10, multiclass
                                clus
vv                               USP34 MUTATED USP34 WILD-TYPE
  COLON ADENOCARCINOMA                      33             282
  COLON MUCINOUS ADENOCARCINOMA              7              40
  RECTAL ADENOCARCINOMA                      4             102
  RECTAL MUCINOUS ADENOCARCINOMA             1               9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  USP34 MUTATED    29   2   2   5
  USP34 WILD-TYPE 316   2  29  20
D230V11, multiclass
    clus
vv   USP34 MUTATED USP34 WILD-TYPE
  R0            29             316
  R1             2               2
  R2             2              29
  RX             5              20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D230V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  USP34 MUTATED                                  0     3
  USP34 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  USP34 MUTATED                           4    28
  USP34 WILD-TYPE                        18   198
D230V13, multiclass
                                  clus
vv                                 USP34 MUTATED USP34 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        3               8
  BLACK OR AFRICAN AMERICAN                    4              18
  WHITE                                       28             198
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(231) Variable = F8 MUTATION ANALYSIS
D231V1, survival
              sevent
clus2            0   1
  F8 MUTATED    29  10
  F8 WILD-TYPE 349  83
  F8 MUTATED F8 WILD-TYPE 
          39          432 
  F8 MUTATED F8 WILD-TYPE 
          10           83 
$`F8 MUTATED`
TCGA-A6-5656 TCGA-A6-5660 TCGA-A6-6142 TCGA-A6-6781 TCGA-AA-3492 TCGA-AA-3502 
       32.91        29.19        25.08        19.66         3.02        35.01 
TCGA-AA-3510 TCGA-AA-3555 TCGA-AA-3710 TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-3952 
       63.98        29.95        26.99        33.01        24.00         2.01 
TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A010 TCGA-AD-6889 TCGA-AD-6895 TCGA-AD-6964 
       25.02         4.01        34.98        56.55         0.72        10.88 
TCGA-AY-6197 TCGA-AZ-6598 TCGA-AZ-6601 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
       21.44        49.41       100.01         3.25         3.29         0.07 
TCGA-CA-6717 TCGA-CM-4743 TCGA-CM-5344 TCGA-CM-6172 TCGA-D5-6930 TCGA-DM-A1D6 
       12.76        23.05        22.03        11.01         1.51        49.91 
TCGA-G4-6309 TCGA-G4-6586 TCGA-G4-6588 TCGA-AF-5654 TCGA-AG-3732 TCGA-AG-3892 
       85.48        35.80        26.17        16.83        32.98        13.02 
TCGA-AG-A002 TCGA-DY-A1DF TCGA-F5-6464 
       20.98        24.13         9.96 

$`F8 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       31.63        30.44        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6649 
       32.71        27.09        22.52         8.38        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 
       21.76        24.69        24.39        23.87        20.12        20.28 
TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        7.04         1.02         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       13.02        24.00        17.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 
       18.05        40.96         0.07        21.37        15.52         0.79 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       16.31         0.95        33.01        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 
        5.13       106.75        22.36        62.79        88.21         6.77 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
       12.10        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.69         3.06        12.20        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 
       21.14        82.95         1.91       124.27        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       25.02        13.02        29.06        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 
       12.99        13.02        15.02        14.04        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
      130.65        92.75        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       55.04        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-6136 
       13.55        19.10        34.49        10.39        14.50        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       37.02         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       17.95        36.95        17.03        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
      126.44        41.36        57.24        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6465 TCGA-F5-6571 
       20.55        19.96        20.91        18.28        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  F8 MUTATED F8 WILD-TYPE 
        0.07         0.00 
  F8 MUTATED F8 WILD-TYPE 
      100.01       148.01 
  F8 MUTATED F8 WILD-TYPE 
      24.000       20.005 
[1] "0.1 - 100.0 (24.0)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.4"
D231V2, continuous
D231V3, binary
              cls
clus             0   1
  F8 MUTATED    35   6
  F8 WILD-TYPE 331 113
[1] "tbl2"
              cls
clus           [,1] [,2]
  F8 MUTATED     35    6
  F8 WILD-TYPE  331  113
        clus
vv       F8 MUTATED F8 WILD-TYPE
  COLON          35          331
  RECTUM          6          113
[1] 2 2
[1] FALSE
              vv
clus           STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  F8 MUTATED         6        0        4        14         4         0
  F8 WILD-TYPE      85        1       28       124         6         1
              vv
clus           STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  F8 MUTATED           0          0          4          5        0         1
  F8 WILD-TYPE        24         11         55         37       48        17
              vv
clus           STAGE IVB
  F8 MUTATED           0
  F8 WILD-TYPE         1
D231V4, multiclass
            clus
vv           F8 MUTATED F8 WILD-TYPE
  STAGE I             6           85
  STAGE IA            0            1
  STAGE II            4           28
  STAGE IIA          14          124
  STAGE IIB           4            6
  STAGE IIC           0            1
  STAGE III           0           24
  STAGE IIIA          0           11
  STAGE IIIB          4           55
  STAGE IIIC          5           37
  STAGE IV            0           48
  STAGE IVA           1           17
  STAGE IVB           0            1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
              vv
clus            T1  T2  T3  T4
  F8 MUTATED     1   6  27   7
  F8 WILD-TYPE  16  86 302  43
D231V5, multiclass
    clus
vv   F8 MUTATED F8 WILD-TYPE
  T1          1           16
  T2          6           86
  T3         27          302
  T4          7           43
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
              vv
clus            N0  N1  N2
  F8 MUTATED    29   7   5
  F8 WILD-TYPE 258 106  82
D231V6, multiclass
    clus
vv   F8 MUTATED F8 WILD-TYPE
  N0         29          258
  N1          7          106
  N2          5           82
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D231V7, binary
              cls
clus             0   1
  F8 MUTATED    33   1
  F8 WILD-TYPE 342  64
[1] "tbl2"
              cls
clus           [,1] [,2]
  F8 MUTATED     33    1
  F8 WILD-TYPE  342   64
   clus
vv  F8 MUTATED F8 WILD-TYPE
  0         33          342
  1          1           64
[1] 2 2
[1] FALSE
D231V8, binary
              cls
clus             0   1
  F8 MUTATED    21  20
  F8 WILD-TYPE 204 244
[1] "tbl2"
              cls
clus           [,1] [,2]
  F8 MUTATED     21   20
  F8 WILD-TYPE  204  244
        clus
vv       F8 MUTATED F8 WILD-TYPE
  FEMALE         21          204
  MALE           20          244
[1] 2 2
[1] FALSE
D231V9, binary
              cls
clus             0   1
  F8 MUTATED    31   0
  F8 WILD-TYPE 319  22
[1] "tbl2"
              cls
clus           [,1] [,2]
  F8 MUTATED     31    0
  F8 WILD-TYPE  319   22
     clus
vv    F8 MUTATED F8 WILD-TYPE
  NO          31          319
  YES          0           22
[1] 2 2
[1] FALSE
              vv
clus           COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  F8 MUTATED                     26                             9
  F8 WILD-TYPE                  289                            38
              vv
clus           RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  F8 MUTATED                       6                              0
  F8 WILD-TYPE                   100                             10
D231V10, multiclass
                                clus
vv                               F8 MUTATED F8 WILD-TYPE
  COLON ADENOCARCINOMA                   26          289
  COLON MUCINOUS ADENOCARCINOMA           9           38
  RECTAL ADENOCARCINOMA                   6          100
  RECTAL MUCINOUS ADENOCARCINOMA          0           10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
              vv
clus            R0  R1  R2  RX
  F8 MUTATED    27   0   0   3
  F8 WILD-TYPE 318   4  31  22
D231V11, multiclass
    clus
vv   F8 MUTATED F8 WILD-TYPE
  R0         27          318
  R1          0            4
  R2          0           31
  RX          3           22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D231V12, continuous
              vv
clus           AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  F8 MUTATED                                  0     5                         2
  F8 WILD-TYPE                                1     6                        20
              vv
clus           WHITE
  F8 MUTATED      19
  F8 WILD-TYPE   207
D231V13, multiclass
                                  clus
vv                                 F8 MUTATED F8 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE          0            1
  ASIAN                                     5            6
  BLACK OR AFRICAN AMERICAN                 2           20
  WHITE                                    19          207
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(232) Variable = SMTN MUTATION ANALYSIS
D232V1, survival
                sevent
clus2              0   1
  SMTN MUTATED    11   4
  SMTN WILD-TYPE 367  89
  SMTN MUTATED SMTN WILD-TYPE 
            15            456 
  SMTN MUTATED SMTN WILD-TYPE 
             4             89 
$`SMTN MUTATED`
TCGA-A6-5665 TCGA-AA-3492 TCGA-AA-3845 TCGA-AA-A00A TCGA-AD-6964 TCGA-AU-6004 
       22.06         3.02         0.00        38.04        10.88        27.09 
TCGA-CM-6674 TCGA-D5-6920 TCGA-D5-6928 TCGA-D5-6930 TCGA-G4-6304 TCGA-G4-6588 
       12.95         3.68        11.64         1.51        53.62        26.17 
TCGA-G4-6628 TCGA-DY-A1DF TCGA-EI-6507 
       79.69        24.13        19.96 

$`SMTN WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 
       20.12        19.66        20.28         7.04         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 
       15.95        38.99        37.02        14.93        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00E 
       19.07         7.96        27.02        13.94        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
        0.72         5.79        22.42        27.42         0.20        14.50 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       14.04        11.01        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        1.48         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        4.80        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 
       22.09        13.78        35.80        91.79        46.75        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
      126.44        41.36        57.24        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       20.55        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  SMTN MUTATED SMTN WILD-TYPE 
             0              0 
  SMTN MUTATED SMTN WILD-TYPE 
         79.69         148.01 
  SMTN MUTATED SMTN WILD-TYPE 
        19.960         20.235 
[1] "0.0 - 79.7 (20.0)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.6"
D232V2, continuous
D232V3, binary
                cls
clus               0   1
  SMTN MUTATED    14   2
  SMTN WILD-TYPE 352 117
[1] "tbl2"
                cls
clus             [,1] [,2]
  SMTN MUTATED     14    2
  SMTN WILD-TYPE  352  117
        clus
vv       SMTN MUTATED SMTN WILD-TYPE
  COLON            14            352
  RECTUM            2            117
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SMTN MUTATED         2        0        2         9         1         0
  SMTN WILD-TYPE      89        1       30       129         9         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SMTN MUTATED           0          0          0          1        0         0
  SMTN WILD-TYPE        24         11         59         41       48        18
                vv
clus             STAGE IVB
  SMTN MUTATED           0
  SMTN WILD-TYPE         1
D232V4, multiclass
            clus
vv           SMTN MUTATED SMTN WILD-TYPE
  STAGE I               2             89
  STAGE IA              0              1
  STAGE II              2             30
  STAGE IIA             9            129
  STAGE IIB             1              9
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            0             59
  STAGE IIIC            1             41
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  SMTN MUTATED     0   2  11   3
  SMTN WILD-TYPE  17  90 318  47
D232V5, multiclass
    clus
vv   SMTN MUTATED SMTN WILD-TYPE
  T1            0             17
  T2            2             90
  T3           11            318
  T4            3             47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  SMTN MUTATED    14   0   2
  SMTN WILD-TYPE 273 113  85
D232V6, multiclass
    clus
vv   SMTN MUTATED SMTN WILD-TYPE
  N0           14            273
  N1            0            113
  N2            2             85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D232V7, binary
                cls
clus               0   1
  SMTN MUTATED    15   0
  SMTN WILD-TYPE 360  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  SMTN MUTATED     15    0
  SMTN WILD-TYPE  360   65
   clus
vv  SMTN MUTATED SMTN WILD-TYPE
  0           15            360
  1            0             65
[1] 2 2
[1] FALSE
D232V8, binary
                cls
clus               0   1
  SMTN MUTATED     9   7
  SMTN WILD-TYPE 216 257
[1] "tbl2"
                cls
clus             [,1] [,2]
  SMTN MUTATED      9    7
  SMTN WILD-TYPE  216  257
        clus
vv       SMTN MUTATED SMTN WILD-TYPE
  FEMALE            9            216
  MALE              7            257
[1] 2 2
[1] FALSE
D232V9, binary
                cls
clus               0   1
  SMTN MUTATED    10   0
  SMTN WILD-TYPE 340  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  SMTN MUTATED     10    0
  SMTN WILD-TYPE  340   22
     clus
vv    SMTN MUTATED SMTN WILD-TYPE
  NO            10            340
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SMTN MUTATED                     12                             2
  SMTN WILD-TYPE                  303                            45
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SMTN MUTATED                       2                              0
  SMTN WILD-TYPE                   104                             10
D232V10, multiclass
                                clus
vv                               SMTN MUTATED SMTN WILD-TYPE
  COLON ADENOCARCINOMA                     12            303
  COLON MUCINOUS ADENOCARCINOMA             2             45
  RECTAL ADENOCARCINOMA                     2            104
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  SMTN MUTATED    14   0   0   0
  SMTN WILD-TYPE 331   4  31  25
D232V11, multiclass
    clus
vv   SMTN MUTATED SMTN WILD-TYPE
  R0           14            331
  R1            0              4
  R2            0             31
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D232V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SMTN MUTATED                                  0     0
  SMTN WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  SMTN MUTATED                           0    12
  SMTN WILD-TYPE                        22   214
D232V13, multiclass
                                  clus
vv                                 SMTN MUTATED SMTN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                      12            214
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(233) Variable = CARD11 MUTATION ANALYSIS
D233V1, survival
                  sevent
clus2                0   1
  CARD11 MUTATED    39   8
  CARD11 WILD-TYPE 339  85
  CARD11 MUTATED CARD11 WILD-TYPE 
              47              424 
  CARD11 MUTATED CARD11 WILD-TYPE 
               8               85 
$`CARD11 MUTATED`
TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-6651 TCGA-A6-6652 TCGA-AA-3663 TCGA-AA-3715 
       32.91        30.44        21.76        24.69         6.97        19.04 
TCGA-AA-3864 TCGA-AA-3950 TCGA-AA-3980 TCGA-AA-A00R TCGA-AD-6964 TCGA-AY-4071 
       53.00        24.00        27.02         0.99        10.88         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-CA-5796 TCGA-CA-5797 
       33.01        21.44        58.39         1.41         3.25         3.29 
TCGA-CA-6716 TCGA-CK-4948 TCGA-CK-4950 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-5344 
       12.20       148.01        85.45        20.02        37.02        22.03 
TCGA-CM-5863 TCGA-CM-5868 TCGA-CM-6162 TCGA-CM-6166 TCGA-D5-6532 TCGA-D5-6537 
       15.02        17.03        12.00        21.99        18.25         4.80 
TCGA-D5-6539 TCGA-D5-6926 TCGA-D5-6928 TCGA-DM-A1D4 TCGA-DM-A1D9 TCGA-DM-A1DB 
       12.49         9.04        11.64        92.75       140.38        44.32 
TCGA-DM-A1HA TCGA-F4-6704 TCGA-G4-6323 TCGA-AF-5654 TCGA-AF-6136 TCGA-AG-3727 
      131.51         1.55        13.78        16.83        15.39         0.99 
TCGA-AG-A015 TCGA-AG-A02N TCGA-AH-6643 TCGA-EF-5830 TCGA-F5-6811 
       36.03        61.97         0.69         0.49        32.19 

$`CARD11 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       31.63        29.19        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       24.16        24.39        23.87        20.12        19.66        20.28 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
        7.04         3.02         1.02        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       61.02        78.08         6.05        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 
        2.01        12.99        24.00        33.01        26.01         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       27.02        42.02        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
        0.72         5.79        22.42        27.42         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-6386 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       27.09        16.31        17.82         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.06         0.07        12.76        10.06        14.30        17.56 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
        1.91       124.27        23.05        25.02        13.02        29.06 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5864 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6168 
       15.02         2.96        29.03        16.04        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6533 
       12.26        19.59        56.09        55.92        20.19         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 
       43.27        15.12        17.85        17.13        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6927 
        1.48         3.68         4.41        12.43        14.30         9.44 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       24.43        38.20       130.65        49.91        13.32        12.59 
TCGA-DM-A1DA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
        7.50       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       35.74         6.18        47.87        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
       63.62        61.91        36.00        22.09        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-6655 
       13.55        19.10        34.49        10.39        14.50        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3731 TCGA-AG-3732 
       19.99        13.94        19.99         7.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       23.01        37.02        15.95         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X 
       64.01        10.98        49.97         1.94        38.96        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6644 
       38.04       117.11        38.56         1.45        17.49         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EI-6506 TCGA-EI-6507 
       57.24        24.13        51.48        32.61        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  CARD11 MUTATED CARD11 WILD-TYPE 
            0.49             0.00 
  CARD11 MUTATED CARD11 WILD-TYPE 
          148.01           139.17 
  CARD11 MUTATED CARD11 WILD-TYPE 
          19.040           20.415 
[1] "0.5 - 148.0 (19.0)" "0.0 - 139.2 (20.4)"
[1] "hr=" "1.3"
D233V2, continuous
D233V3, binary
                  cls
clus                 0   1
  CARD11 MUTATED    40   8
  CARD11 WILD-TYPE 326 111
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CARD11 MUTATED     40    8
  CARD11 WILD-TYPE  326  111
        clus
vv       CARD11 MUTATED CARD11 WILD-TYPE
  COLON              40              326
  RECTUM              8              111
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CARD11 MUTATED        10        1        4        13         1         0
  CARD11 WILD-TYPE      81        0       28       125         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CARD11 MUTATED           3          1          8          3        1
  CARD11 WILD-TYPE        21         10         51         39       47
                  vv
clus               STAGE IVA STAGE IVB
  CARD11 MUTATED           3         0
  CARD11 WILD-TYPE        15         1
D233V4, multiclass
            clus
vv           CARD11 MUTATED CARD11 WILD-TYPE
  STAGE I                10               81
  STAGE IA                1                0
  STAGE II                4               28
  STAGE IIA              13              125
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               3               21
  STAGE IIIA              1               10
  STAGE IIIB              8               51
  STAGE IIIC              3               39
  STAGE IV                1               47
  STAGE IVA               3               15
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  CARD11 MUTATED     2   8  33   5
  CARD11 WILD-TYPE  15  84 296  45
D233V5, multiclass
    clus
vv   CARD11 MUTATED CARD11 WILD-TYPE
  T1              2               15
  T2              8               84
  T3             33              296
  T4              5               45
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  CARD11 MUTATED    31  12   6
  CARD11 WILD-TYPE 256 101  81
D233V6, multiclass
    clus
vv   CARD11 MUTATED CARD11 WILD-TYPE
  N0             31              256
  N1             12              101
  N2              6               81
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D233V7, binary
                  cls
clus                 0   1
  CARD11 MUTATED    37   4
  CARD11 WILD-TYPE 338  61
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CARD11 MUTATED     37    4
  CARD11 WILD-TYPE  338   61
   clus
vv  CARD11 MUTATED CARD11 WILD-TYPE
  0             37              338
  1              4               61
[1] 2 2
[1] FALSE
D233V8, binary
                  cls
clus                 0   1
  CARD11 MUTATED    22  27
  CARD11 WILD-TYPE 203 237
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CARD11 MUTATED     22   27
  CARD11 WILD-TYPE  203  237
        clus
vv       CARD11 MUTATED CARD11 WILD-TYPE
  FEMALE             22              203
  MALE               27              237
[1] 2 2
[1] FALSE
D233V9, binary
                  cls
clus                 0   1
  CARD11 MUTATED    35   2
  CARD11 WILD-TYPE 315  20
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CARD11 MUTATED     35    2
  CARD11 WILD-TYPE  315   20
     clus
vv    CARD11 MUTATED CARD11 WILD-TYPE
  NO              35              315
  YES              2               20
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CARD11 MUTATED                     34                             6
  CARD11 WILD-TYPE                  281                            41
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CARD11 MUTATED                       8                              0
  CARD11 WILD-TYPE                    98                             10
D233V10, multiclass
                                clus
vv                               CARD11 MUTATED CARD11 WILD-TYPE
  COLON ADENOCARCINOMA                       34              281
  COLON MUCINOUS ADENOCARCINOMA               6               41
  RECTAL ADENOCARCINOMA                       8               98
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  CARD11 MUTATED    35   1   0   1
  CARD11 WILD-TYPE 310   3  31  24
D233V11, multiclass
    clus
vv   CARD11 MUTATED CARD11 WILD-TYPE
  R0             35              310
  R1              1                3
  R2              0               31
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D233V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CARD11 MUTATED                                  1     3
  CARD11 WILD-TYPE                                0     8
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  CARD11 MUTATED                           5    29
  CARD11 WILD-TYPE                        17   197
D233V13, multiclass
                                  clus
vv                                 CARD11 MUTATED CARD11 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              1                0
  ASIAN                                         3                8
  BLACK OR AFRICAN AMERICAN                     5               17
  WHITE                                        29              197
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(234) Variable = NUP188 MUTATION ANALYSIS
D234V1, survival
                  sevent
clus2                0   1
  NUP188 MUTATED    17   5
  NUP188 WILD-TYPE 361  88
  NUP188 MUTATED NUP188 WILD-TYPE 
              22              449 
  NUP188 MUTATED NUP188 WILD-TYPE 
               5               88 
$`NUP188 MUTATED`
TCGA-A6-5657 TCGA-A6-6653 TCGA-AA-3510 TCGA-AA-3713 TCGA-AA-3955 TCGA-AA-A00R 
       31.63        24.39        63.98        19.04        20.98         0.99 
TCGA-AA-A010 TCGA-AA-A01Q TCGA-AD-6895 TCGA-AZ-4315 TCGA-AZ-5403 TCGA-AZ-6601 
       34.98         1.02         0.72        58.39        62.79       100.01 
TCGA-CM-6171 TCGA-D5-6923 TCGA-DM-A1DA TCGA-F4-6459 TCGA-F4-6570 TCGA-F4-6856 
       14.04        12.43         7.50         8.61         6.18        35.31 
TCGA-AG-3892 TCGA-AG-A002 TCGA-DC-6155 TCGA-F5-6811 
       13.02        20.98        13.97        32.19 

$`NUP188 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 
       25.18        24.16        21.76        24.69        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       85.05        26.99        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3956 TCGA-AA-3966 
       33.01        26.01        24.00         2.01        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01R TCGA-AA-A01S 
       12.00        31.00        31.00        38.07        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
       56.55         0.79         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13       106.75        22.36 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 
       88.21        49.41         6.77        12.10        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        1.48         3.68         4.41        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       13.32        12.59       140.38        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 
      117.07        98.24        31.96        35.74        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       47.41       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       36.95        17.03        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
        7.17        15.02         5.03        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57         0.66         0.69        55.76        26.43 

  NUP188 MUTATED NUP188 WILD-TYPE 
            0.72             0.00 
  NUP188 MUTATED NUP188 WILD-TYPE 
          100.01           148.01 
  NUP188 MUTATED NUP188 WILD-TYPE 
           20.01            20.19 
[1] "0.7 - 100.0 (20.0)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.1"
D234V2, continuous
D234V3, binary
                  cls
clus                 0   1
  NUP188 MUTATED    19   4
  NUP188 WILD-TYPE 347 115
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NUP188 MUTATED     19    4
  NUP188 WILD-TYPE  347  115
        clus
vv       NUP188 MUTATED NUP188 WILD-TYPE
  COLON              19              347
  RECTUM              4              115
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NUP188 MUTATED         7        0        4         4         1         0
  NUP188 WILD-TYPE      84        1       28       134         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NUP188 MUTATED           0          1          3          1        1
  NUP188 WILD-TYPE        24         10         56         41       47
                  vv
clus               STAGE IVA STAGE IVB
  NUP188 MUTATED           0         0
  NUP188 WILD-TYPE        18         1
D234V4, multiclass
            clus
vv           NUP188 MUTATED NUP188 WILD-TYPE
  STAGE I                 7               84
  STAGE IA                0                1
  STAGE II                4               28
  STAGE IIA               4              134
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              1               10
  STAGE IIIB              3               56
  STAGE IIIC              1               41
  STAGE IV                1               47
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  NUP188 MUTATED     1   8  13   1
  NUP188 WILD-TYPE  16  84 316  49
D234V5, multiclass
    clus
vv   NUP188 MUTATED NUP188 WILD-TYPE
  T1              1               16
  T2              8               84
  T3             13              316
  T4              1               49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  NUP188 MUTATED    17   3   3
  NUP188 WILD-TYPE 270 110  84
D234V6, multiclass
    clus
vv   NUP188 MUTATED NUP188 WILD-TYPE
  N0             17              270
  N1              3              110
  N2              3               84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D234V7, binary
                  cls
clus                 0   1
  NUP188 MUTATED    20   1
  NUP188 WILD-TYPE 355  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NUP188 MUTATED     20    1
  NUP188 WILD-TYPE  355   64
   clus
vv  NUP188 MUTATED NUP188 WILD-TYPE
  0             20              355
  1              1               64
[1] 2 2
[1] FALSE
D234V8, binary
                  cls
clus                 0   1
  NUP188 MUTATED    11  12
  NUP188 WILD-TYPE 214 252
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NUP188 MUTATED     11   12
  NUP188 WILD-TYPE  214  252
        clus
vv       NUP188 MUTATED NUP188 WILD-TYPE
  FEMALE             11              214
  MALE               12              252
[1] 2 2
[1] FALSE
D234V9, binary
                  cls
clus                 0   1
  NUP188 MUTATED    17   1
  NUP188 WILD-TYPE 333  21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NUP188 MUTATED     17    1
  NUP188 WILD-TYPE  333   21
     clus
vv    NUP188 MUTATED NUP188 WILD-TYPE
  NO              17              333
  YES              1               21
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  NUP188 MUTATED                     18                             1
  NUP188 WILD-TYPE                  297                            46
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  NUP188 MUTATED                       4                              0
  NUP188 WILD-TYPE                   102                             10
D234V10, multiclass
                                clus
vv                               NUP188 MUTATED NUP188 WILD-TYPE
  COLON ADENOCARCINOMA                       18              297
  COLON MUCINOUS ADENOCARCINOMA               1               46
  RECTAL ADENOCARCINOMA                       4              102
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  NUP188 MUTATED    16   0   1   0
  NUP188 WILD-TYPE 329   4  30  25
D234V11, multiclass
    clus
vv   NUP188 MUTATED NUP188 WILD-TYPE
  R0             16              329
  R1              0                4
  R2              1               30
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D234V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NUP188 MUTATED                                  0     0
  NUP188 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  NUP188 MUTATED                           1    13
  NUP188 WILD-TYPE                        21   213
D234V13, multiclass
                                  clus
vv                                 NUP188 MUTATED NUP188 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                        13              213
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(235) Variable = PTPN3 MUTATION ANALYSIS
D235V1, survival
                 sevent
clus2               0   1
  PTPN3 MUTATED    13   2
  PTPN3 WILD-TYPE 365  91
  PTPN3 MUTATED PTPN3 WILD-TYPE 
             15             456 
  PTPN3 MUTATED PTPN3 WILD-TYPE 
              2              91 
$`PTPN3 MUTATED`
TCGA-AA-3542 TCGA-AA-A00J TCGA-AA-A00N TCGA-AA-A010 TCGA-AD-5900 TCGA-AU-3779 
       12.99        18.05         4.01        34.98         0.07        14.50 
TCGA-AY-6197 TCGA-AZ-6598 TCGA-CK-5914 TCGA-CM-6162 TCGA-CM-6166 TCGA-CM-6171 
       21.44        49.41         9.99        12.00        21.99        14.04 
TCGA-D5-6539 TCGA-G4-6315 TCGA-CI-6620 
       12.49        61.91        33.17 

$`PTPN3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       29.00        26.01         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L 
       38.04        19.00        30.02        34.03        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
       40.96        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-6004 
        5.79        22.42        27.42        10.88         0.20        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       16.31         0.95        33.01        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 
        5.13       106.75        22.36        62.79        88.21         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 
       85.45        15.62        49.08        51.32        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
        2.96        29.03        16.04        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       15.02        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 
       15.12        17.85         4.80        17.13        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       85.48        63.62        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        0.72         6.05         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  PTPN3 MUTATED PTPN3 WILD-TYPE 
           0.07            0.00 
  PTPN3 MUTATED PTPN3 WILD-TYPE 
          61.91          148.01 
  PTPN3 MUTATED PTPN3 WILD-TYPE 
         14.500          20.415 
[1] "0.1 - 61.9 (14.5)"  "0.0 - 148.0 (20.4)"
[1] "hr=" "1.3"
D235V2, continuous
D235V3, binary
                 cls
clus                0   1
  PTPN3 MUTATED    15   1
  PTPN3 WILD-TYPE 351 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPN3 MUTATED     15    1
  PTPN3 WILD-TYPE  351  118
        clus
vv       PTPN3 MUTATED PTPN3 WILD-TYPE
  COLON             15             351
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PTPN3 MUTATED         3        0        1         3         2         0
  PTPN3 WILD-TYPE      88        1       31       135         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PTPN3 MUTATED           0          1          3          1        1         1
  PTPN3 WILD-TYPE        24         10         56         41       47        17
                 vv
clus              STAGE IVB
  PTPN3 MUTATED           0
  PTPN3 WILD-TYPE         1
D235V4, multiclass
            clus
vv           PTPN3 MUTATED PTPN3 WILD-TYPE
  STAGE I                3              88
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              3             135
  STAGE IIB              2               8
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             1              10
  STAGE IIIB             3              56
  STAGE IIIC             1              41
  STAGE IV               1              47
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PTPN3 MUTATED     0   3  10   3
  PTPN3 WILD-TYPE  17  89 319  47
D235V5, multiclass
    clus
vv   PTPN3 MUTATED PTPN3 WILD-TYPE
  T1             0              17
  T2             3              89
  T3            10             319
  T4             3              47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  PTPN3 MUTATED    10   5   1
  PTPN3 WILD-TYPE 277 108  86
D235V6, multiclass
    clus
vv   PTPN3 MUTATED PTPN3 WILD-TYPE
  N0            10             277
  N1             5             108
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D235V7, binary
                 cls
clus                0   1
  PTPN3 MUTATED    10   2
  PTPN3 WILD-TYPE 365  63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPN3 MUTATED     10    2
  PTPN3 WILD-TYPE  365   63
   clus
vv  PTPN3 MUTATED PTPN3 WILD-TYPE
  0            10             365
  1             2              63
[1] 2 2
[1] FALSE
D235V8, binary
                 cls
clus                0   1
  PTPN3 MUTATED     9   7
  PTPN3 WILD-TYPE 216 257
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPN3 MUTATED      9    7
  PTPN3 WILD-TYPE  216  257
        clus
vv       PTPN3 MUTATED PTPN3 WILD-TYPE
  FEMALE             9             216
  MALE               7             257
[1] 2 2
[1] FALSE
D235V9, binary
                 cls
clus                0   1
  PTPN3 MUTATED    12   0
  PTPN3 WILD-TYPE 338  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPN3 MUTATED     12    0
  PTPN3 WILD-TYPE  338   22
     clus
vv    PTPN3 MUTATED PTPN3 WILD-TYPE
  NO             12             338
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PTPN3 MUTATED                     11                             4
  PTPN3 WILD-TYPE                  304                            43
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PTPN3 MUTATED                       1                              0
  PTPN3 WILD-TYPE                   105                             10
D235V10, multiclass
                                clus
vv                               PTPN3 MUTATED PTPN3 WILD-TYPE
  COLON ADENOCARCINOMA                      11             304
  COLON MUCINOUS ADENOCARCINOMA              4              43
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  PTPN3 MUTATED    13   0   0   1
  PTPN3 WILD-TYPE 332   4  31  24
D235V11, multiclass
    clus
vv   PTPN3 MUTATED PTPN3 WILD-TYPE
  R0            13             332
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D235V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PTPN3 MUTATED                                  0     0
  PTPN3 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PTPN3 MUTATED                           0    11
  PTPN3 WILD-TYPE                        22   215
D235V13, multiclass
                                  clus
vv                                 PTPN3 MUTATED PTPN3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                       11             215
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(236) Variable = NBEA MUTATION ANALYSIS
D236V1, survival
                sevent
clus2              0   1
  NBEA MUTATED    44   7
  NBEA WILD-TYPE 334  86
  NBEA MUTATED NBEA WILD-TYPE 
            51            420 
  NBEA MUTATED NBEA WILD-TYPE 
             7             86 
$`NBEA MUTATED`
TCGA-A6-5665 TCGA-A6-6653 TCGA-A6-6780 TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3688 
       22.06        24.39        20.12         3.02        63.98        19.00 
TCGA-AA-3713 TCGA-AA-3949 TCGA-AA-3971 TCGA-AA-3977 TCGA-AA-3994 TCGA-AA-A00N 
       19.04        26.01        16.08        25.02        27.02         4.01 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AD-5900 TCGA-AD-6899 TCGA-AU-3779 TCGA-AU-6004 
       34.98         1.02         0.07         5.79        14.50        27.09 
TCGA-AY-4070 TCGA-AZ-4315 TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-6716 TCGA-CA-6717 
       16.31        58.39        11.74         1.61        12.20        12.76 
TCGA-CA-6718 TCGA-CK-6747 TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5864 TCGA-CM-6162 
       10.06        82.95        22.98        32.02        15.02        12.00 
TCGA-CM-6166 TCGA-CM-6170 TCGA-CM-6172 TCGA-D5-6529 TCGA-D5-6922 TCGA-D5-6927 
       21.99        15.02        11.01        20.19         4.41         9.44 
TCGA-D5-6932 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6806 TCGA-G4-6293 TCGA-G4-6299 
       11.38        35.74        47.87        41.42       133.18        74.56 
TCGA-G4-6586 TCGA-G4-6625 TCGA-AG-3878 TCGA-AG-3892 TCGA-AG-A002 TCGA-AG-A00H 
       35.80        91.79         0.99        13.02        20.98        25.97 
TCGA-AH-6549 TCGA-CL-5918 TCGA-DC-5337 
       17.49         7.17        15.02 

$`NBEA WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6781 
       25.18        24.16        21.76        24.69        23.87        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 
       20.28         7.04         1.02        35.01         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
       13.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       36.03         8.05        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       78.08         6.05         6.97        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 
       37.05        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-3952 
        2.01        12.99        24.00        33.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3972 TCGA-AA-3973 
       20.98        34.03         2.01        21.99        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
        7.96        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       17.03        14.99        21.99        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       39.98        18.05        40.96        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.79         0.72        22.42        27.42        10.88         0.20 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        33.01        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-CA-5254 
       12.10       100.01        29.56         5.23         3.19        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6719 TCGA-CK-4947 
        3.06         3.25         3.29         0.07        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       21.14         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5861 
       25.02        13.02        29.06        22.03        30.08        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 
        5.03        15.02        17.03        15.02         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6171 TCGA-CM-6674 
       16.04        14.99        12.99        13.02        14.04        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6532 
       45.40        12.26        19.59        56.09        55.92        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6923 
       12.49        16.14        15.58         1.48         3.68        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
       14.30         9.04        11.64         4.80         1.51        12.00 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6570 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        6.18         1.55        34.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
        0.53        47.41        35.31        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       13.78        26.17        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3881 
        7.99         0.99        37.02        32.98         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 
       19.99         1.02        17.95        36.95        17.03        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       78.12         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  NBEA MUTATED NBEA WILD-TYPE 
          0.07           0.00 
  NBEA MUTATED NBEA WILD-TYPE 
        133.18         148.01 
  NBEA MUTATED NBEA WILD-TYPE 
        19.000         20.945 
[1] "0.1 - 133.2 (19.0)" "0.0 - 148.0 (20.9)"
[1] "hr=" "1.4"
D236V2, continuous
D236V3, binary
                cls
clus               0   1
  NBEA MUTATED    46   7
  NBEA WILD-TYPE 320 112
[1] "tbl2"
                cls
clus             [,1] [,2]
  NBEA MUTATED     46    7
  NBEA WILD-TYPE  320  112
        clus
vv       NBEA MUTATED NBEA WILD-TYPE
  COLON            46            320
  RECTUM            7            112
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NBEA MUTATED        12        0        2        19         3         0
  NBEA WILD-TYPE      79        1       30       119         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NBEA MUTATED           2          2          5          3        3         0
  NBEA WILD-TYPE        22          9         54         39       45        18
                vv
clus             STAGE IVB
  NBEA MUTATED           0
  NBEA WILD-TYPE         1
D236V4, multiclass
            clus
vv           NBEA MUTATED NBEA WILD-TYPE
  STAGE I              12             79
  STAGE IA              0              1
  STAGE II              2             30
  STAGE IIA            19            119
  STAGE IIB             3              7
  STAGE IIC             0              1
  STAGE III             2             22
  STAGE IIIA            2              9
  STAGE IIIB            5             54
  STAGE IIIC            3             39
  STAGE IV              3             45
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  NBEA MUTATED     2  12  34   5
  NBEA WILD-TYPE  15  80 295  45
D236V5, multiclass
    clus
vv   NBEA MUTATED NBEA WILD-TYPE
  T1            2             15
  T2           12             80
  T3           34            295
  T4            5             45
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  NBEA MUTATED    38  10   4
  NBEA WILD-TYPE 249 103  83
D236V6, multiclass
    clus
vv   NBEA MUTATED NBEA WILD-TYPE
  N0           38            249
  N1           10            103
  N2            4             83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D236V7, binary
                cls
clus               0   1
  NBEA MUTATED    42   3
  NBEA WILD-TYPE 333  62
[1] "tbl2"
                cls
clus             [,1] [,2]
  NBEA MUTATED     42    3
  NBEA WILD-TYPE  333   62
   clus
vv  NBEA MUTATED NBEA WILD-TYPE
  0           42            333
  1            3             62
[1] 2 2
[1] FALSE
D236V8, binary
                cls
clus               0   1
  NBEA MUTATED    22  31
  NBEA WILD-TYPE 203 233
[1] "tbl2"
                cls
clus             [,1] [,2]
  NBEA MUTATED     22   31
  NBEA WILD-TYPE  203  233
        clus
vv       NBEA MUTATED NBEA WILD-TYPE
  FEMALE           22            203
  MALE             31            233
[1] 2 2
[1] FALSE
D236V9, binary
                cls
clus               0   1
  NBEA MUTATED    43   2
  NBEA WILD-TYPE 307  20
[1] "tbl2"
                cls
clus             [,1] [,2]
  NBEA MUTATED     43    2
  NBEA WILD-TYPE  307   20
     clus
vv    NBEA MUTATED NBEA WILD-TYPE
  NO            43            307
  YES            2             20
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  NBEA MUTATED                     38                             8
  NBEA WILD-TYPE                  277                            39
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  NBEA MUTATED                       7                              0
  NBEA WILD-TYPE                    99                             10
D236V10, multiclass
                                clus
vv                               NBEA MUTATED NBEA WILD-TYPE
  COLON ADENOCARCINOMA                     38            277
  COLON MUCINOUS ADENOCARCINOMA             8             39
  RECTAL ADENOCARCINOMA                     7             99
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  NBEA MUTATED    37   1   2   7
  NBEA WILD-TYPE 308   3  29  18
D236V11, multiclass
    clus
vv   NBEA MUTATED NBEA WILD-TYPE
  R0           37            308
  R1            1              3
  R2            2             29
  RX            7             18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D236V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NBEA MUTATED                                  0     3
  NBEA WILD-TYPE                                1     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  NBEA MUTATED                           1    33
  NBEA WILD-TYPE                        21   193
D236V13, multiclass
                                  clus
vv                                 NBEA MUTATED NBEA WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       3              8
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                      33            193
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(237) Variable = CNIH4 MUTATION ANALYSIS
D237V1, survival
                 sevent
clus2               0   1
  CNIH4 MUTATED     6   0
  CNIH4 WILD-TYPE 372  93
  CNIH4 MUTATED CNIH4 WILD-TYPE 
              6             465 
  CNIH4 MUTATED CNIH4 WILD-TYPE 
              0              93 
$`CNIH4 MUTATED`
TCGA-A6-6142 TCGA-CM-5344 TCGA-D5-7000 TCGA-F4-6807 TCGA-F4-6808 TCGA-G4-6299 
       25.08        22.03        10.26        16.24        33.67        74.56 

$`CNIH4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5349 
       37.02        25.02        13.02        29.06        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-DM-A0X9 
       11.64         4.80         1.51        12.00        11.38       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6809 TCGA-F4-6854 
       47.87         1.55        34.42        41.42        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       47.41        35.31       133.18        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  CNIH4 MUTATED CNIH4 WILD-TYPE 
          10.26            0.00 
  CNIH4 MUTATED CNIH4 WILD-TYPE 
          74.56          148.01 
  CNIH4 MUTATED CNIH4 WILD-TYPE 
         23.555          20.120 
[1] "10.3 - 74.6 (23.6)" "0.0 - 148.0 (20.1)"
[1] "hr="     "9100000"
D237V2, continuous
D237V3, binary
                 cls
clus                0   1
  CNIH4 MUTATED     6   0
  CNIH4 WILD-TYPE 360 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CNIH4 MUTATED      6    0
  CNIH4 WILD-TYPE  360  119
        clus
vv       CNIH4 MUTATED CNIH4 WILD-TYPE
  COLON              6             360
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CNIH4 MUTATED         2        0        0         0         0         0
  CNIH4 WILD-TYPE      89        1       32       138        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CNIH4 MUTATED           0          0          1          2        0         1
  CNIH4 WILD-TYPE        24         11         58         40       48        17
                 vv
clus              STAGE IVB
  CNIH4 MUTATED           0
  CNIH4 WILD-TYPE         1
D237V4, multiclass
            clus
vv           CNIH4 MUTATED CNIH4 WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              0             138
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             2              40
  STAGE IV               0              48
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CNIH4 MUTATED     1   1   4   0
  CNIH4 WILD-TYPE  16  91 325  50
D237V5, multiclass
    clus
vv   CNIH4 MUTATED CNIH4 WILD-TYPE
  T1             1              16
  T2             1              91
  T3             4             325
  T4             0              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  CNIH4 MUTATED     2   2   2
  CNIH4 WILD-TYPE 285 111  85
D237V6, multiclass
    clus
vv   CNIH4 MUTATED CNIH4 WILD-TYPE
  N0             2             285
  N1             2             111
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D237V7, binary
                 cls
clus                0   1
  CNIH4 MUTATED     5   1
  CNIH4 WILD-TYPE 370  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CNIH4 MUTATED      5    1
  CNIH4 WILD-TYPE  370   64
   clus
vv  CNIH4 MUTATED CNIH4 WILD-TYPE
  0             5             370
  1             1              64
[1] 2 2
[1] FALSE
D237V8, binary
                 cls
clus                0   1
  CNIH4 MUTATED     5   1
  CNIH4 WILD-TYPE 220 263
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CNIH4 MUTATED      5    1
  CNIH4 WILD-TYPE  220  263
        clus
vv       CNIH4 MUTATED CNIH4 WILD-TYPE
  FEMALE             5             220
  MALE               1             263
[1] 2 2
[1] FALSE
D237V9, binary
                 cls
clus                0   1
  CNIH4 MUTATED     6   0
  CNIH4 WILD-TYPE 344  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CNIH4 MUTATED      6    0
  CNIH4 WILD-TYPE  344   22
     clus
vv    CNIH4 MUTATED CNIH4 WILD-TYPE
  NO              6             344
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CNIH4 MUTATED                      5                             1
  CNIH4 WILD-TYPE                  310                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CNIH4 MUTATED                       0                              0
  CNIH4 WILD-TYPE                   106                             10
D237V10, multiclass
                                clus
vv                               CNIH4 MUTATED CNIH4 WILD-TYPE
  COLON ADENOCARCINOMA                       5             310
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  CNIH4 MUTATED     5   0   0   0
  CNIH4 WILD-TYPE 340   4  31  25
D237V11, multiclass
    clus
vv   CNIH4 MUTATED CNIH4 WILD-TYPE
  R0             5             340
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D237V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CNIH4 MUTATED                                  0     0
  CNIH4 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CNIH4 MUTATED                           0     6
  CNIH4 WILD-TYPE                        22   220
D237V13, multiclass
                                  clus
vv                                 CNIH4 MUTATED CNIH4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        6             220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(238) Variable = CD58 MUTATION ANALYSIS
D238V1, survival
                sevent
clus2              0   1
  CD58 MUTATED    12   3
  CD58 WILD-TYPE 366  90
  CD58 MUTATED CD58 WILD-TYPE 
            15            456 
  CD58 MUTATED CD58 WILD-TYPE 
             3             90 
$`CD58 MUTATED`
TCGA-A6-5665 TCGA-AA-3663 TCGA-AA-A010 TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6895 
       22.06         6.97        34.98         0.07        56.55         0.72 
TCGA-AZ-4315 TCGA-AZ-6598 TCGA-CA-6717 TCGA-CK-5916 TCGA-CM-5861 TCGA-F4-6570 
       58.39        49.41        12.76        21.14        15.02         6.18 
TCGA-G4-6625 TCGA-G4-6628 TCGA-AG-A002 
       91.79        79.69        20.98 

$`CD58 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        21.37        15.52         0.79         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
       16.31         0.95        33.01        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 
        5.13       106.75        22.36        62.79        88.21         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.20        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 
       15.62        49.08        51.32         9.99        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 
       29.06        22.03        22.98        30.08        32.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
        8.61        31.96        35.74        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 
       13.78        35.80        26.17        46.75        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  CD58 MUTATED CD58 WILD-TYPE 
          0.07           0.00 
  CD58 MUTATED CD58 WILD-TYPE 
         91.79         148.01 
  CD58 MUTATED CD58 WILD-TYPE 
        21.140         20.085 
[1] "0.1 - 91.8 (21.1)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.2"
D238V2, continuous
D238V3, binary
                cls
clus               0   1
  CD58 MUTATED    14   1
  CD58 WILD-TYPE 352 118
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD58 MUTATED     14    1
  CD58 WILD-TYPE  352  118
        clus
vv       CD58 MUTATED CD58 WILD-TYPE
  COLON            14            352
  RECTUM            1            118
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CD58 MUTATED         4        0        2         7         1         0
  CD58 WILD-TYPE      87        1       30       131         9         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CD58 MUTATED           0          0          0          0        0         0
  CD58 WILD-TYPE        24         11         59         42       48        18
                vv
clus             STAGE IVB
  CD58 MUTATED           0
  CD58 WILD-TYPE         1
D238V4, multiclass
            clus
vv           CD58 MUTATED CD58 WILD-TYPE
  STAGE I               4             87
  STAGE IA              0              1
  STAGE II              2             30
  STAGE IIA             7            131
  STAGE IIB             1              9
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            0             59
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  CD58 MUTATED     1   3  10   1
  CD58 WILD-TYPE  16  89 319  49
D238V5, multiclass
    clus
vv   CD58 MUTATED CD58 WILD-TYPE
  T1            1             16
  T2            3             89
  T3           10            319
  T4            1             49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  CD58 MUTATED    14   1   0
  CD58 WILD-TYPE 273 112  87
D238V6, multiclass
    clus
vv   CD58 MUTATED CD58 WILD-TYPE
  N0           14            273
  N1            1            112
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D238V7, binary
                cls
clus               0   1
  CD58 MUTATED    12   0
  CD58 WILD-TYPE 363  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD58 MUTATED     12    0
  CD58 WILD-TYPE  363   65
   clus
vv  CD58 MUTATED CD58 WILD-TYPE
  0           12            363
  1            0             65
[1] 2 2
[1] FALSE
D238V8, binary
                cls
clus               0   1
  CD58 MUTATED     7   8
  CD58 WILD-TYPE 218 256
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD58 MUTATED      7    8
  CD58 WILD-TYPE  218  256
        clus
vv       CD58 MUTATED CD58 WILD-TYPE
  FEMALE            7            218
  MALE              8            256
[1] 2 2
[1] FALSE
D238V9, binary
                cls
clus               0   1
  CD58 MUTATED    12   0
  CD58 WILD-TYPE 338  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD58 MUTATED     12    0
  CD58 WILD-TYPE  338   22
     clus
vv    CD58 MUTATED CD58 WILD-TYPE
  NO            12            338
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CD58 MUTATED                     12                             2
  CD58 WILD-TYPE                  303                            45
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CD58 MUTATED                       1                              0
  CD58 WILD-TYPE                   105                             10
D238V10, multiclass
                                clus
vv                               CD58 MUTATED CD58 WILD-TYPE
  COLON ADENOCARCINOMA                     12            303
  COLON MUCINOUS ADENOCARCINOMA             2             45
  RECTAL ADENOCARCINOMA                     1            105
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  CD58 MUTATED    10   0   0   2
  CD58 WILD-TYPE 335   4  31  23
D238V11, multiclass
    clus
vv   CD58 MUTATED CD58 WILD-TYPE
  R0           10            335
  R1            0              4
  R2            0             31
  RX            2             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D238V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CD58 MUTATED                                  0     2
  CD58 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  CD58 MUTATED                           0    10
  CD58 WILD-TYPE                        22   216
D238V13, multiclass
                                  clus
vv                                 CD58 MUTATED CD58 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              9
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                      10            216
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(239) Variable = GMCL1 MUTATION ANALYSIS
D239V1, survival
                 sevent
clus2               0   1
  GMCL1 MUTATED    11   2
  GMCL1 WILD-TYPE 367  91
  GMCL1 MUTATED GMCL1 WILD-TYPE 
             13             458 
  GMCL1 MUTATED GMCL1 WILD-TYPE 
              2              91 
$`GMCL1 MUTATED`
TCGA-AD-6548 TCGA-AZ-4315 TCGA-AZ-6601 TCGA-AZ-6605 TCGA-CM-5863 TCGA-CM-6161 
       21.37        58.39       100.01         5.23        15.02        15.02 
TCGA-DM-A1D9 TCGA-G4-6307 TCGA-G4-6625 TCGA-AG-A002 TCGA-AH-6643 TCGA-DC-6683 
      140.38        55.04        91.79        20.98         0.69         5.03 
TCGA-F5-6465 
       49.51 

$`GMCL1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        33.01        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       12.10        29.56        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
        5.03        15.02        17.03        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A1DB 
       92.75        49.91        13.32        12.59         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 
      133.18        74.56        65.85        53.62        44.68        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       26.17        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
       38.56         1.45        17.49         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
        9.96        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  GMCL1 MUTATED GMCL1 WILD-TYPE 
           0.69            0.00 
  GMCL1 MUTATED GMCL1 WILD-TYPE 
         140.38          148.01 
  GMCL1 MUTATED GMCL1 WILD-TYPE 
         21.370          20.085 
[1] "0.7 - 140.4 (21.4)" "0.0 - 148.0 (20.1)"
[1] "hr=" "2.1"
D239V2, continuous
D239V3, binary
                 cls
clus                0   1
  GMCL1 MUTATED    10   4
  GMCL1 WILD-TYPE 356 115
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GMCL1 MUTATED     10    4
  GMCL1 WILD-TYPE  356  115
        clus
vv       GMCL1 MUTATED GMCL1 WILD-TYPE
  COLON             10             356
  RECTUM             4             115
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GMCL1 MUTATED         3        0        1         4         1         0
  GMCL1 WILD-TYPE      88        1       31       134         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  GMCL1 MUTATED           0          0          4          1        0         0
  GMCL1 WILD-TYPE        24         11         55         41       48        18
                 vv
clus              STAGE IVB
  GMCL1 MUTATED           0
  GMCL1 WILD-TYPE         1
D239V4, multiclass
            clus
vv           GMCL1 MUTATED GMCL1 WILD-TYPE
  STAGE I                3              88
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              4             134
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             4              55
  STAGE IIIC             1              41
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  GMCL1 MUTATED     0   3   9   2
  GMCL1 WILD-TYPE  17  89 320  48
D239V5, multiclass
    clus
vv   GMCL1 MUTATED GMCL1 WILD-TYPE
  T1             0              17
  T2             3              89
  T3             9             320
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  GMCL1 MUTATED     9   4   1
  GMCL1 WILD-TYPE 278 109  86
D239V6, multiclass
    clus
vv   GMCL1 MUTATED GMCL1 WILD-TYPE
  N0             9             278
  N1             4             109
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D239V7, binary
                 cls
clus                0   1
  GMCL1 MUTATED    13   0
  GMCL1 WILD-TYPE 362  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GMCL1 MUTATED     13    0
  GMCL1 WILD-TYPE  362   65
   clus
vv  GMCL1 MUTATED GMCL1 WILD-TYPE
  0            13             362
  1             0              65
[1] 2 2
[1] FALSE
D239V8, binary
                 cls
clus                0   1
  GMCL1 MUTATED     8   6
  GMCL1 WILD-TYPE 217 258
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GMCL1 MUTATED      8    6
  GMCL1 WILD-TYPE  217  258
        clus
vv       GMCL1 MUTATED GMCL1 WILD-TYPE
  FEMALE             8             217
  MALE               6             258
[1] 2 2
[1] FALSE
D239V9, binary
                 cls
clus                0   1
  GMCL1 MUTATED    10   0
  GMCL1 WILD-TYPE 340  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GMCL1 MUTATED     10    0
  GMCL1 WILD-TYPE  340   22
     clus
vv    GMCL1 MUTATED GMCL1 WILD-TYPE
  NO             10             340
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  GMCL1 MUTATED                      9                             1
  GMCL1 WILD-TYPE                  306                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  GMCL1 MUTATED                       4                              0
  GMCL1 WILD-TYPE                   102                             10
D239V10, multiclass
                                clus
vv                               GMCL1 MUTATED GMCL1 WILD-TYPE
  COLON ADENOCARCINOMA                       9             306
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      4             102
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  GMCL1 MUTATED    10   0   0   1
  GMCL1 WILD-TYPE 335   4  31  24
D239V11, multiclass
    clus
vv   GMCL1 MUTATED GMCL1 WILD-TYPE
  R0            10             335
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D239V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GMCL1 MUTATED                                  0     0
  GMCL1 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  GMCL1 MUTATED                           0    13
  GMCL1 WILD-TYPE                        22   213
D239V13, multiclass
                                  clus
vv                                 GMCL1 MUTATED GMCL1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                       13             213
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(240) Variable = AKAP3 MUTATION ANALYSIS
D240V1, survival
                 sevent
clus2               0   1
  AKAP3 MUTATED    21   2
  AKAP3 WILD-TYPE 357  91
  AKAP3 MUTATED AKAP3 WILD-TYPE 
             23             448 
  AKAP3 MUTATED AKAP3 WILD-TYPE 
              2              91 
$`AKAP3 MUTATED`
TCGA-A6-6141 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3655 TCGA-AA-3713 TCGA-AA-3968 
        8.38         3.02        35.01        61.02        19.04        21.99 
TCGA-AA-3977 TCGA-AA-A010 TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A02F TCGA-AD-6963 
       25.02        34.98         1.02        35.01        39.98        27.42 
TCGA-AZ-4315 TCGA-AZ-6600 TCGA-CA-6717 TCGA-CK-4952 TCGA-CM-5348 TCGA-CM-5860 
       58.39        12.10        12.76        15.62        22.98        32.02 
TCGA-CM-5861 TCGA-D5-6931 TCGA-G4-6588 TCGA-AG-3892 TCGA-AG-A002 
       15.02        12.00        26.17        13.02        20.98 

$`AKAP3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 
       22.09        22.06        32.71        27.09        22.52        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3510 
       20.12        19.66        20.28         7.04         1.02        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       19.99        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       26.99        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       31.00        31.00        38.07         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02H TCGA-AA-A02J 
       26.01        37.02        39.06        51.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
       16.31         0.95        33.01        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.20        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       29.06        22.03        30.08         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6932 TCGA-D5-7000 
        9.44        11.64         4.80         1.51        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 
       19.99         1.02        17.95        36.95        17.03        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  AKAP3 MUTATED AKAP3 WILD-TYPE 
           1.02            0.00 
  AKAP3 MUTATED AKAP3 WILD-TYPE 
          61.02          148.01 
  AKAP3 MUTATED AKAP3 WILD-TYPE 
         21.990          20.085 
[1] "1.0 - 61.0 (22.0)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "2.1"
D240V2, continuous
D240V3, binary
                 cls
clus                0   1
  AKAP3 MUTATED    21   2
  AKAP3 WILD-TYPE 345 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AKAP3 MUTATED     21    2
  AKAP3 WILD-TYPE  345  117
        clus
vv       AKAP3 MUTATED AKAP3 WILD-TYPE
  COLON             21             345
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  AKAP3 MUTATED         4        0        3         6         1         0
  AKAP3 WILD-TYPE      87        1       29       132         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AKAP3 MUTATED           1          0          1          2        3         0
  AKAP3 WILD-TYPE        23         11         58         40       45        18
                 vv
clus              STAGE IVB
  AKAP3 MUTATED           0
  AKAP3 WILD-TYPE         1
D240V4, multiclass
            clus
vv           AKAP3 MUTATED AKAP3 WILD-TYPE
  STAGE I                4              87
  STAGE IA               0               1
  STAGE II               3              29
  STAGE IIA              6             132
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             2              40
  STAGE IV               3              45
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  AKAP3 MUTATED     1   4  14   4
  AKAP3 WILD-TYPE  16  88 315  46
D240V5, multiclass
    clus
vv   AKAP3 MUTATED AKAP3 WILD-TYPE
  T1             1              16
  T2             4              88
  T3            14             315
  T4             4              46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  AKAP3 MUTATED    17   3   3
  AKAP3 WILD-TYPE 270 110  84
D240V6, multiclass
    clus
vv   AKAP3 MUTATED AKAP3 WILD-TYPE
  N0            17             270
  N1             3             110
  N2             3              84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D240V7, binary
                 cls
clus                0   1
  AKAP3 MUTATED    18   3
  AKAP3 WILD-TYPE 357  62
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AKAP3 MUTATED     18    3
  AKAP3 WILD-TYPE  357   62
   clus
vv  AKAP3 MUTATED AKAP3 WILD-TYPE
  0            18             357
  1             3              62
[1] 2 2
[1] FALSE
D240V8, binary
                 cls
clus                0   1
  AKAP3 MUTATED     9  14
  AKAP3 WILD-TYPE 216 250
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AKAP3 MUTATED      9   14
  AKAP3 WILD-TYPE  216  250
        clus
vv       AKAP3 MUTATED AKAP3 WILD-TYPE
  FEMALE             9             216
  MALE              14             250
[1] 2 2
[1] FALSE
D240V9, binary
                 cls
clus                0   1
  AKAP3 MUTATED    18   2
  AKAP3 WILD-TYPE 332  20
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AKAP3 MUTATED     18    2
  AKAP3 WILD-TYPE  332   20
     clus
vv    AKAP3 MUTATED AKAP3 WILD-TYPE
  NO             18             332
  YES             2              20
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  AKAP3 MUTATED                     18                             3
  AKAP3 WILD-TYPE                  297                            44
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  AKAP3 MUTATED                       2                              0
  AKAP3 WILD-TYPE                   104                             10
D240V10, multiclass
                                clus
vv                               AKAP3 MUTATED AKAP3 WILD-TYPE
  COLON ADENOCARCINOMA                      18             297
  COLON MUCINOUS ADENOCARCINOMA              3              44
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  AKAP3 MUTATED    15   0   2   2
  AKAP3 WILD-TYPE 330   4  29  23
D240V11, multiclass
    clus
vv   AKAP3 MUTATED AKAP3 WILD-TYPE
  R0            15             330
  R1             0               4
  R2             2              29
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D240V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AKAP3 MUTATED                                  0     1
  AKAP3 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  AKAP3 MUTATED                           2     8
  AKAP3 WILD-TYPE                        20   218
D240V13, multiclass
                                  clus
vv                                 AKAP3 MUTATED AKAP3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    2              20
  WHITE                                        8             218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(241) Variable = RBMX2 MUTATION ANALYSIS
D241V1, survival
                 sevent
clus2               0   1
  RBMX2 MUTATED    11   1
  RBMX2 WILD-TYPE 367  92
  RBMX2 MUTATED RBMX2 WILD-TYPE 
             12             459 
  RBMX2 MUTATED RBMX2 WILD-TYPE 
              1              92 
$`RBMX2 MUTATED`
TCGA-AA-3492 TCGA-AA-3710 TCGA-AY-6197 TCGA-AZ-4315 TCGA-CM-6171 TCGA-D5-6930 
        3.02        26.99        21.44        58.39        14.04         1.51 
TCGA-F4-6806 TCGA-G4-6299 TCGA-G4-6310 TCGA-G4-6588 TCGA-G4-6625 TCGA-DY-A0XA 
       41.42        74.56        63.62        26.17        91.79       126.44 

$`RBMX2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        85.05        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       33.01        17.82         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       13.02        15.02        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6931 
       14.30         9.04         9.44        11.64         4.80        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
      133.18        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6626 
       61.91        36.00        22.09        13.78        35.80        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.03         5.29        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  RBMX2 MUTATED RBMX2 WILD-TYPE 
           1.51            0.00 
  RBMX2 MUTATED RBMX2 WILD-TYPE 
         126.44          148.01 
  RBMX2 MUTATED RBMX2 WILD-TYPE 
         34.205          20.020 
[1] "1.5 - 126.4 (34.2)" "0.0 - 148.0 (20.0)"
[1] "hr=" "4.2"
D241V2, continuous
D241V3, binary
                 cls
clus                0   1
  RBMX2 MUTATED    11   1
  RBMX2 WILD-TYPE 355 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBMX2 MUTATED     11    1
  RBMX2 WILD-TYPE  355  118
        clus
vv       RBMX2 MUTATED RBMX2 WILD-TYPE
  COLON             11             355
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RBMX2 MUTATED         2        0        1         7         0         0
  RBMX2 WILD-TYPE      89        1       31       131        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RBMX2 MUTATED           0          0          1          1        0         0
  RBMX2 WILD-TYPE        24         11         58         41       48        18
                 vv
clus              STAGE IVB
  RBMX2 MUTATED           0
  RBMX2 WILD-TYPE         1
D241V4, multiclass
            clus
vv           RBMX2 MUTATED RBMX2 WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              7             131
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             1              41
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  RBMX2 MUTATED     0   2  10   0
  RBMX2 WILD-TYPE  17  90 319  50
D241V5, multiclass
    clus
vv   RBMX2 MUTATED RBMX2 WILD-TYPE
  T1             0              17
  T2             2              90
  T3            10             319
  T4             0              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  RBMX2 MUTATED    10   1   1
  RBMX2 WILD-TYPE 277 112  86
D241V6, multiclass
    clus
vv   RBMX2 MUTATED RBMX2 WILD-TYPE
  N0            10             277
  N1             1             112
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D241V7, binary
                 cls
clus                0   1
  RBMX2 MUTATED    11   0
  RBMX2 WILD-TYPE 364  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBMX2 MUTATED     11    0
  RBMX2 WILD-TYPE  364   65
   clus
vv  RBMX2 MUTATED RBMX2 WILD-TYPE
  0            11             364
  1             0              65
[1] 2 2
[1] FALSE
D241V8, binary
                 cls
clus                0   1
  RBMX2 MUTATED     7   5
  RBMX2 WILD-TYPE 218 259
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBMX2 MUTATED      7    5
  RBMX2 WILD-TYPE  218  259
        clus
vv       RBMX2 MUTATED RBMX2 WILD-TYPE
  FEMALE             7             218
  MALE               5             259
[1] 2 2
[1] FALSE
D241V9, binary
                 cls
clus                0   1
  RBMX2 MUTATED     9   1
  RBMX2 WILD-TYPE 341  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBMX2 MUTATED      9    1
  RBMX2 WILD-TYPE  341   21
     clus
vv    RBMX2 MUTATED RBMX2 WILD-TYPE
  NO              9             341
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  RBMX2 MUTATED                     10                             1
  RBMX2 WILD-TYPE                  305                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  RBMX2 MUTATED                       1                              0
  RBMX2 WILD-TYPE                   105                             10
D241V10, multiclass
                                clus
vv                               RBMX2 MUTATED RBMX2 WILD-TYPE
  COLON ADENOCARCINOMA                      10             305
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  RBMX2 MUTATED    11   0   0   0
  RBMX2 WILD-TYPE 334   4  31  25
D241V11, multiclass
    clus
vv   RBMX2 MUTATED RBMX2 WILD-TYPE
  R0            11             334
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D241V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RBMX2 MUTATED                                  0     0
  RBMX2 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  RBMX2 MUTATED                           0    10
  RBMX2 WILD-TYPE                        22   216
D241V13, multiclass
                                  clus
vv                                 RBMX2 MUTATED RBMX2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                       10             216
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(242) Variable = DCBLD1 MUTATION ANALYSIS
D242V1, survival
                  sevent
clus2                0   1
  DCBLD1 MUTATED     5   2
  DCBLD1 WILD-TYPE 373  91
  DCBLD1 MUTATED DCBLD1 WILD-TYPE 
               7              464 
  DCBLD1 MUTATED DCBLD1 WILD-TYPE 
               2               91 
$`DCBLD1 MUTATED`
TCGA-A6-6781 TCGA-AA-3697 TCGA-AA-3977 TCGA-D5-6922 TCGA-DM-A28G TCGA-DC-5337 
       19.66        85.05        25.02         4.41        60.79        15.02 
TCGA-F5-6464 
        9.96 

$`DCBLD1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28H TCGA-DM-A28K 
        6.12        81.37       119.93        35.97       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5869 TCGA-DC-6155 
        6.97         4.73        78.12         7.17         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  DCBLD1 MUTATED DCBLD1 WILD-TYPE 
            4.41             0.00 
  DCBLD1 MUTATED DCBLD1 WILD-TYPE 
           85.05           148.01 
  DCBLD1 MUTATED DCBLD1 WILD-TYPE 
          19.660           20.235 
[1] "4.4 - 85.0 (19.7)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.2"
D242V2, continuous
D242V3, binary
                  cls
clus                 0   1
  DCBLD1 MUTATED     5   2
  DCBLD1 WILD-TYPE 361 117
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DCBLD1 MUTATED      5    2
  DCBLD1 WILD-TYPE  361  117
        clus
vv       DCBLD1 MUTATED DCBLD1 WILD-TYPE
  COLON               5              361
  RECTUM              2              117
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DCBLD1 MUTATED         1        0        0         1         0         0
  DCBLD1 WILD-TYPE      90        1       32       137        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DCBLD1 MUTATED           1          1          0          2        0
  DCBLD1 WILD-TYPE        23         10         59         40       48
                  vv
clus               STAGE IVA STAGE IVB
  DCBLD1 MUTATED           0         0
  DCBLD1 WILD-TYPE        18         1
D242V4, multiclass
            clus
vv           DCBLD1 MUTATED DCBLD1 WILD-TYPE
  STAGE I                 1               90
  STAGE IA                0                1
  STAGE II                0               32
  STAGE IIA               1              137
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               1               23
  STAGE IIIA              1               10
  STAGE IIIB              0               59
  STAGE IIIC              2               40
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  DCBLD1 MUTATED     1   1   3   2
  DCBLD1 WILD-TYPE  16  91 326  48
D242V5, multiclass
    clus
vv   DCBLD1 MUTATED DCBLD1 WILD-TYPE
  T1              1               16
  T2              1               91
  T3              3              326
  T4              2               48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  DCBLD1 MUTATED     4   2   1
  DCBLD1 WILD-TYPE 283 111  86
D242V6, multiclass
    clus
vv   DCBLD1 MUTATED DCBLD1 WILD-TYPE
  N0              4              283
  N1              2              111
  N2              1               86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D242V7, binary
                  cls
clus                 0   1
  DCBLD1 MUTATED     5   0
  DCBLD1 WILD-TYPE 370  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DCBLD1 MUTATED      5    0
  DCBLD1 WILD-TYPE  370   65
   clus
vv  DCBLD1 MUTATED DCBLD1 WILD-TYPE
  0              5              370
  1              0               65
[1] 2 2
[1] FALSE
D242V8, binary
                  cls
clus                 0   1
  DCBLD1 MUTATED     1   6
  DCBLD1 WILD-TYPE 224 258
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DCBLD1 MUTATED      1    6
  DCBLD1 WILD-TYPE  224  258
        clus
vv       DCBLD1 MUTATED DCBLD1 WILD-TYPE
  FEMALE              1              224
  MALE                6              258
[1] 2 2
[1] FALSE
D242V9, binary
                  cls
clus                 0   1
  DCBLD1 MUTATED     5   0
  DCBLD1 WILD-TYPE 345  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DCBLD1 MUTATED      5    0
  DCBLD1 WILD-TYPE  345   22
     clus
vv    DCBLD1 MUTATED DCBLD1 WILD-TYPE
  NO               5              345
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  DCBLD1 MUTATED                      4                             1
  DCBLD1 WILD-TYPE                  311                            46
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  DCBLD1 MUTATED                       2                              0
  DCBLD1 WILD-TYPE                   104                             10
D242V10, multiclass
                                clus
vv                               DCBLD1 MUTATED DCBLD1 WILD-TYPE
  COLON ADENOCARCINOMA                        4              311
  COLON MUCINOUS ADENOCARCINOMA               1               46
  RECTAL ADENOCARCINOMA                       2              104
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  DCBLD1 MUTATED     5   0   0   0
  DCBLD1 WILD-TYPE 340   4  31  25
D242V11, multiclass
    clus
vv   DCBLD1 MUTATED DCBLD1 WILD-TYPE
  R0              5              340
  R1              0                4
  R2              0               31
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D242V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DCBLD1 MUTATED                                  0     0
  DCBLD1 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  DCBLD1 MUTATED                           0     5
  DCBLD1 WILD-TYPE                        22   221
D242V13, multiclass
                                  clus
vv                                 DCBLD1 MUTATED DCBLD1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         5              221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(243) Variable = ZNF280B MUTATION ANALYSIS
D243V1, survival
                   sevent
clus2                 0   1
  ZNF280B MUTATED    11   1
  ZNF280B WILD-TYPE 367  92
  ZNF280B MUTATED ZNF280B WILD-TYPE 
               12               459 
  ZNF280B MUTATED ZNF280B WILD-TYPE 
                1                92 
$`ZNF280B MUTATED`
TCGA-A6-6142 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-A010 TCGA-CA-6716 TCGA-CA-6717 
       25.08        33.01        26.01        34.98        12.20        12.76 
TCGA-CK-5913 TCGA-CM-6161 TCGA-D5-6930 TCGA-G4-6293 TCGA-G4-6299 TCGA-DC-6158 
       51.32        15.02         1.51       133.18        74.56        10.98 

$`ZNF280B WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
        2.01        12.99        24.00        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6718 TCGA-CA-6719 
        3.06         3.25         3.29         0.07        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 
       17.56       148.01        85.45        15.62        49.08         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       17.03        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       11.64         4.80        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6303 TCGA-G4-6304 
       13.25         0.53        47.41        35.31        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       13.97        27.95        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  ZNF280B MUTATED ZNF280B WILD-TYPE 
             1.51              0.00 
  ZNF280B MUTATED ZNF280B WILD-TYPE 
           133.18            148.01 
  ZNF280B MUTATED ZNF280B WILD-TYPE 
           25.545            20.120 
[1] "1.5 - 133.2 (25.5)" "0.0 - 148.0 (20.1)"
[1] "hr=" "3.1"
D243V2, continuous
D243V3, binary
                   cls
clus                  0   1
  ZNF280B MUTATED    12   1
  ZNF280B WILD-TYPE 354 118
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZNF280B MUTATED     12    1
  ZNF280B WILD-TYPE  354  118
        clus
vv       ZNF280B MUTATED ZNF280B WILD-TYPE
  COLON               12               354
  RECTUM               1               118
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZNF280B MUTATED         2        0        0         5         2         0
  ZNF280B WILD-TYPE      89        1       32       133         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF280B MUTATED           1          0          1          1        0
  ZNF280B WILD-TYPE        23         11         58         41       48
                   vv
clus                STAGE IVA STAGE IVB
  ZNF280B MUTATED           1         0
  ZNF280B WILD-TYPE        17         1
D243V4, multiclass
            clus
vv           ZNF280B MUTATED ZNF280B WILD-TYPE
  STAGE I                  2                89
  STAGE IA                 0                 1
  STAGE II                 0                32
  STAGE IIA                5               133
  STAGE IIB                2                 8
  STAGE IIC                0                 1
  STAGE III                1                23
  STAGE IIIA               0                11
  STAGE IIIB               1                58
  STAGE IIIC               1                41
  STAGE IV                 0                48
  STAGE IVA                1                17
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  ZNF280B MUTATED     0   2   9   2
  ZNF280B WILD-TYPE  17  90 320  48
D243V5, multiclass
    clus
vv   ZNF280B MUTATED ZNF280B WILD-TYPE
  T1               0                17
  T2               2                90
  T3               9               320
  T4               2                48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  ZNF280B MUTATED     9   3   1
  ZNF280B WILD-TYPE 278 110  86
D243V6, multiclass
    clus
vv   ZNF280B MUTATED ZNF280B WILD-TYPE
  N0               9               278
  N1               3               110
  N2               1                86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D243V7, binary
                   cls
clus                  0   1
  ZNF280B MUTATED    11   1
  ZNF280B WILD-TYPE 364  64
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZNF280B MUTATED     11    1
  ZNF280B WILD-TYPE  364   64
   clus
vv  ZNF280B MUTATED ZNF280B WILD-TYPE
  0              11               364
  1               1                64
[1] 2 2
[1] FALSE
D243V8, binary
                   cls
clus                  0   1
  ZNF280B MUTATED     8   5
  ZNF280B WILD-TYPE 217 259
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZNF280B MUTATED      8    5
  ZNF280B WILD-TYPE  217  259
        clus
vv       ZNF280B MUTATED ZNF280B WILD-TYPE
  FEMALE               8               217
  MALE                 5               259
[1] 2 2
[1] FALSE
D243V9, binary
                   cls
clus                  0   1
  ZNF280B MUTATED    11   0
  ZNF280B WILD-TYPE 339  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZNF280B MUTATED     11    0
  ZNF280B WILD-TYPE  339   22
     clus
vv    ZNF280B MUTATED ZNF280B WILD-TYPE
  NO               11               339
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ZNF280B MUTATED                      8                             4
  ZNF280B WILD-TYPE                  307                            43
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ZNF280B MUTATED                       1                              0
  ZNF280B WILD-TYPE                   105                             10
D243V10, multiclass
                                clus
vv                               ZNF280B MUTATED ZNF280B WILD-TYPE
  COLON ADENOCARCINOMA                         8               307
  COLON MUCINOUS ADENOCARCINOMA                4                43
  RECTAL ADENOCARCINOMA                        1               105
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  ZNF280B MUTATED     9   0   0   3
  ZNF280B WILD-TYPE 336   4  31  22
D243V11, multiclass
    clus
vv   ZNF280B MUTATED ZNF280B WILD-TYPE
  R0               9               336
  R1               0                 4
  R2               0                31
  RX               3                22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D243V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF280B MUTATED                                  0     2
  ZNF280B WILD-TYPE                                1     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  ZNF280B MUTATED                           0     7
  ZNF280B WILD-TYPE                        22   219
D243V13, multiclass
                                  clus
vv                                 ZNF280B MUTATED ZNF280B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          2                 9
  BLACK OR AFRICAN AMERICAN                      0                22
  WHITE                                          7               219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(244) Variable = NCOA7 MUTATION ANALYSIS
D244V1, survival
                 sevent
clus2               0   1
  NCOA7 MUTATED    16   1
  NCOA7 WILD-TYPE 362  92
  NCOA7 MUTATED NCOA7 WILD-TYPE 
             17             454 
  NCOA7 MUTATED NCOA7 WILD-TYPE 
              1              92 
$`NCOA7 MUTATED`
TCGA-A6-6653 TCGA-A6-6654 TCGA-AA-3496 TCGA-AA-3518 TCGA-AA-3655 TCGA-AA-3966 
       24.39        23.87         1.02         1.02        61.02         2.01 
TCGA-AA-A00J TCGA-AD-5900 TCGA-AU-6004 TCGA-AZ-4616 TCGA-CM-5861 TCGA-CM-6170 
       18.05         0.07        27.09         5.13        15.02        15.02 
TCGA-CM-6171 TCGA-D5-6928 TCGA-G4-6317 TCGA-AF-6672 TCGA-AG-A002 
       14.04        11.64        36.00        10.39        20.98 

$`NCOA7 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6780 
       25.08        25.18        24.16        21.76        24.69        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3510 
       19.66        20.28         7.04         3.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3520 
        6.97         1.02        13.02        38.99         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       78.08         6.05         6.97        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 
       26.01        24.00         2.01        20.98        34.03        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 
       41.00        39.98        18.05        40.96        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       10.88         0.20        14.50        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82        58.39         1.41       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 
       29.06        22.03        22.98        30.08        32.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
        9.44         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       63.62        61.91        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       15.39        20.02        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  NCOA7 MUTATED NCOA7 WILD-TYPE 
           0.07            0.00 
  NCOA7 MUTATED NCOA7 WILD-TYPE 
          61.02          148.01 
  NCOA7 MUTATED NCOA7 WILD-TYPE 
          15.02           20.73 
[1] "0.1 - 61.0 (15.0)"  "0.0 - 148.0 (20.7)"
[1] "hr=" "2.3"
D244V2, continuous
D244V3, binary
                 cls
clus                0   1
  NCOA7 MUTATED    15   2
  NCOA7 WILD-TYPE 351 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NCOA7 MUTATED     15    2
  NCOA7 WILD-TYPE  351  117
        clus
vv       NCOA7 MUTATED NCOA7 WILD-TYPE
  COLON             15             351
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NCOA7 MUTATED         6        0        2         4         0         0
  NCOA7 WILD-TYPE      85        1       30       134        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NCOA7 MUTATED           0          0          2          1        2         0
  NCOA7 WILD-TYPE        24         11         57         41       46        18
                 vv
clus              STAGE IVB
  NCOA7 MUTATED           0
  NCOA7 WILD-TYPE         1
D244V4, multiclass
            clus
vv           NCOA7 MUTATED NCOA7 WILD-TYPE
  STAGE I                6              85
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA              4             134
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             2              57
  STAGE IIIC             1              41
  STAGE IV               2              46
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  NCOA7 MUTATED     0   6   9   2
  NCOA7 WILD-TYPE  17  86 320  48
D244V5, multiclass
    clus
vv   NCOA7 MUTATED NCOA7 WILD-TYPE
  T1             0              17
  T2             6              86
  T3             9             320
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  NCOA7 MUTATED    12   2   3
  NCOA7 WILD-TYPE 275 111  84
D244V6, multiclass
    clus
vv   NCOA7 MUTATED NCOA7 WILD-TYPE
  N0            12             275
  N1             2             111
  N2             3              84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D244V7, binary
                 cls
clus                0   1
  NCOA7 MUTATED    13   1
  NCOA7 WILD-TYPE 362  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NCOA7 MUTATED     13    1
  NCOA7 WILD-TYPE  362   64
   clus
vv  NCOA7 MUTATED NCOA7 WILD-TYPE
  0            13             362
  1             1              64
[1] 2 2
[1] FALSE
D244V8, binary
                 cls
clus                0   1
  NCOA7 MUTATED    10   7
  NCOA7 WILD-TYPE 215 257
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NCOA7 MUTATED     10    7
  NCOA7 WILD-TYPE  215  257
        clus
vv       NCOA7 MUTATED NCOA7 WILD-TYPE
  FEMALE            10             215
  MALE               7             257
[1] 2 2
[1] FALSE
D244V9, binary
                 cls
clus                0   1
  NCOA7 MUTATED    11   1
  NCOA7 WILD-TYPE 339  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NCOA7 MUTATED     11    1
  NCOA7 WILD-TYPE  339   21
     clus
vv    NCOA7 MUTATED NCOA7 WILD-TYPE
  NO             11             339
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  NCOA7 MUTATED                     11                             4
  NCOA7 WILD-TYPE                  304                            43
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  NCOA7 MUTATED                       2                              0
  NCOA7 WILD-TYPE                   104                             10
D244V10, multiclass
                                clus
vv                               NCOA7 MUTATED NCOA7 WILD-TYPE
  COLON ADENOCARCINOMA                      11             304
  COLON MUCINOUS ADENOCARCINOMA              4              43
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  NCOA7 MUTATED    12   0   0   0
  NCOA7 WILD-TYPE 333   4  31  25
D244V11, multiclass
    clus
vv   NCOA7 MUTATED NCOA7 WILD-TYPE
  R0            12             333
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D244V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NCOA7 MUTATED                                  0     0
  NCOA7 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  NCOA7 MUTATED                           0    11
  NCOA7 WILD-TYPE                        22   215
D244V13, multiclass
                                  clus
vv                                 NCOA7 MUTATED NCOA7 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                       11             215
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(245) Variable = DENND4A MUTATION ANALYSIS
D245V1, survival
                   sevent
clus2                 0   1
  DENND4A MUTATED    20   4
  DENND4A WILD-TYPE 358  89
  DENND4A MUTATED DENND4A WILD-TYPE 
               24               447 
  DENND4A MUTATED DENND4A WILD-TYPE 
                4                89 
$`DENND4A MUTATED`
TCGA-A6-5657 TCGA-A6-5665 TCGA-AA-3663 TCGA-AA-3672 TCGA-AA-3715 TCGA-AA-3864 
       31.63        22.06         6.97         0.92        19.04        53.00 
TCGA-AA-3947 TCGA-AA-3966 TCGA-AA-A00N TCGA-AA-A010 TCGA-AD-6889 TCGA-AZ-4315 
       33.01         2.01         4.01        34.98        56.55        58.39 
TCGA-AZ-6605 TCGA-CK-5914 TCGA-CK-6747 TCGA-CM-5864 TCGA-CM-6171 TCGA-DM-A1HB 
        5.23         9.99        82.95        15.02        14.04       135.65 
TCGA-G4-6303 TCGA-G4-6586 TCGA-AG-3892 TCGA-AG-4001 TCGA-AG-A002 TCGA-DC-6160 
       65.85        35.80        13.02        36.03        20.98        19.99 

$`DENND4A WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
        2.01        14.01        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       26.99        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       30.05        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 
       31.00         2.01        12.99        24.00        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
        2.01        20.98        34.03        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 
       40.96         0.07        21.37        15.52         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6606 
       49.41         6.77        12.10       100.01        29.56        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5916 
      148.01        85.45        15.62        49.08        51.32        21.14 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
       15.02         5.03        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       13.02        15.02        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
        7.50        44.32       131.51       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
       35.31       133.18        74.56        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       28.04        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       13.97        27.95        10.98         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  DENND4A MUTATED DENND4A WILD-TYPE 
             0.92              0.00 
  DENND4A MUTATED DENND4A WILD-TYPE 
           135.65            148.01 
  DENND4A MUTATED DENND4A WILD-TYPE 
            21.52             20.12 
[1] "0.9 - 135.7 (21.5)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.4"
D245V2, continuous
D245V3, binary
                   cls
clus                  0   1
  DENND4A MUTATED    22   4
  DENND4A WILD-TYPE 344 115
[1] "tbl2"
                   cls
clus                [,1] [,2]
  DENND4A MUTATED     22    4
  DENND4A WILD-TYPE  344  115
        clus
vv       DENND4A MUTATED DENND4A WILD-TYPE
  COLON               22               344
  RECTUM               4               115
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DENND4A MUTATED         5        0        3         8         3         0
  DENND4A WILD-TYPE      86        1       29       130         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DENND4A MUTATED           1          0          4          1        1
  DENND4A WILD-TYPE        23         11         55         41       47
                   vv
clus                STAGE IVA STAGE IVB
  DENND4A MUTATED           0         0
  DENND4A WILD-TYPE        18         1
D245V4, multiclass
            clus
vv           DENND4A MUTATED DENND4A WILD-TYPE
  STAGE I                  5                86
  STAGE IA                 0                 1
  STAGE II                 3                29
  STAGE IIA                8               130
  STAGE IIB                3                 7
  STAGE IIC                0                 1
  STAGE III                1                23
  STAGE IIIA               0                11
  STAGE IIIB               4                55
  STAGE IIIC               1                41
  STAGE IV                 1                47
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  DENND4A MUTATED     1   4  17   4
  DENND4A WILD-TYPE  16  88 312  46
D245V5, multiclass
    clus
vv   DENND4A MUTATED DENND4A WILD-TYPE
  T1               1                16
  T2               4                88
  T3              17               312
  T4               4                46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  DENND4A MUTATED    19   6   1
  DENND4A WILD-TYPE 268 107  86
D245V6, multiclass
    clus
vv   DENND4A MUTATED DENND4A WILD-TYPE
  N0              19               268
  N1               6               107
  N2               1                86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D245V7, binary
                   cls
clus                  0   1
  DENND4A MUTATED    22   1
  DENND4A WILD-TYPE 353  64
[1] "tbl2"
                   cls
clus                [,1] [,2]
  DENND4A MUTATED     22    1
  DENND4A WILD-TYPE  353   64
   clus
vv  DENND4A MUTATED DENND4A WILD-TYPE
  0              22               353
  1               1                64
[1] 2 2
[1] FALSE
D245V8, binary
                   cls
clus                  0   1
  DENND4A MUTATED    12  14
  DENND4A WILD-TYPE 213 250
[1] "tbl2"
                   cls
clus                [,1] [,2]
  DENND4A MUTATED     12   14
  DENND4A WILD-TYPE  213  250
        clus
vv       DENND4A MUTATED DENND4A WILD-TYPE
  FEMALE              12               213
  MALE                14               250
[1] 2 2
[1] FALSE
D245V9, binary
                   cls
clus                  0   1
  DENND4A MUTATED    18   0
  DENND4A WILD-TYPE 332  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  DENND4A MUTATED     18    0
  DENND4A WILD-TYPE  332   22
     clus
vv    DENND4A MUTATED DENND4A WILD-TYPE
  NO               18               332
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  DENND4A MUTATED                     17                             4
  DENND4A WILD-TYPE                  298                            43
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  DENND4A MUTATED                       4                              0
  DENND4A WILD-TYPE                   102                             10
D245V10, multiclass
                                clus
vv                               DENND4A MUTATED DENND4A WILD-TYPE
  COLON ADENOCARCINOMA                        17               298
  COLON MUCINOUS ADENOCARCINOMA                4                43
  RECTAL ADENOCARCINOMA                        4               102
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  DENND4A MUTATED    20   0   0   2
  DENND4A WILD-TYPE 325   4  31  23
D245V11, multiclass
    clus
vv   DENND4A MUTATED DENND4A WILD-TYPE
  R0              20               325
  R1               0                 4
  R2               0                31
  RX               2                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D245V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DENND4A MUTATED                                  0     1
  DENND4A WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  DENND4A MUTATED                           1    12
  DENND4A WILD-TYPE                        21   214
D245V13, multiclass
                                  clus
vv                                 DENND4A MUTATED DENND4A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                10
  BLACK OR AFRICAN AMERICAN                      1                21
  WHITE                                         12               214
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(246) Variable = ALDH2 MUTATION ANALYSIS
D246V1, survival
                 sevent
clus2               0   1
  ALDH2 MUTATED     8   3
  ALDH2 WILD-TYPE 370  90
  ALDH2 MUTATED ALDH2 WILD-TYPE 
             11             460 
  ALDH2 MUTATED ALDH2 WILD-TYPE 
              3              90 
$`ALDH2 MUTATED`
TCGA-AA-3502 TCGA-AA-3518 TCGA-AA-3663 TCGA-AA-A00J TCGA-AD-6901 TCGA-AY-5543 
       35.01         1.02         6.97        18.05        22.42        33.01 
TCGA-AZ-6598 TCGA-CA-5797 TCGA-D5-6928 TCGA-G4-6304 TCGA-DY-A1DG 
       49.41         3.29        11.64        53.62        51.48 

$`ALDH2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        0.72         5.79        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       27.09        16.31         0.95        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-6715 
        3.19         1.61        12.69         3.06         3.25         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       65.85        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       24.13        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  ALDH2 MUTATED ALDH2 WILD-TYPE 
           1.02            0.00 
  ALDH2 MUTATED ALDH2 WILD-TYPE 
          53.62          148.01 
  ALDH2 MUTATED ALDH2 WILD-TYPE 
         22.420          20.155 
[1] "1.0 - 53.6 (22.4)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.3"
D246V2, continuous
D246V3, binary
                 cls
clus                0   1
  ALDH2 MUTATED    11   1
  ALDH2 WILD-TYPE 355 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ALDH2 MUTATED     11    1
  ALDH2 WILD-TYPE  355  118
        clus
vv       ALDH2 MUTATED ALDH2 WILD-TYPE
  COLON             11             355
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ALDH2 MUTATED         1        0        3         3         1         0
  ALDH2 WILD-TYPE      90        1       29       135         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ALDH2 MUTATED           0          0          1          0        0         2
  ALDH2 WILD-TYPE        24         11         58         42       48        16
                 vv
clus              STAGE IVB
  ALDH2 MUTATED           0
  ALDH2 WILD-TYPE         1
D246V4, multiclass
            clus
vv           ALDH2 MUTATED ALDH2 WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               3              29
  STAGE IIA              3             135
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              2              16
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ALDH2 MUTATED     0   1   8   3
  ALDH2 WILD-TYPE  17  91 321  47
D246V5, multiclass
    clus
vv   ALDH2 MUTATED ALDH2 WILD-TYPE
  T1             0              17
  T2             1              91
  T3             8             321
  T4             3              47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  ALDH2 MUTATED     9   3   0
  ALDH2 WILD-TYPE 278 110  87
D246V6, multiclass
    clus
vv   ALDH2 MUTATED ALDH2 WILD-TYPE
  N0             9             278
  N1             3             110
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D246V7, binary
                 cls
clus                0   1
  ALDH2 MUTATED     8   2
  ALDH2 WILD-TYPE 367  63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ALDH2 MUTATED      8    2
  ALDH2 WILD-TYPE  367   63
   clus
vv  ALDH2 MUTATED ALDH2 WILD-TYPE
  0             8             367
  1             2              63
[1] 2 2
[1] FALSE
D246V8, binary
                 cls
clus                0   1
  ALDH2 MUTATED     5   7
  ALDH2 WILD-TYPE 220 257
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ALDH2 MUTATED      5    7
  ALDH2 WILD-TYPE  220  257
        clus
vv       ALDH2 MUTATED ALDH2 WILD-TYPE
  FEMALE             5             220
  MALE               7             257
[1] 2 2
[1] FALSE
D246V9, binary
                 cls
clus                0   1
  ALDH2 MUTATED     9   0
  ALDH2 WILD-TYPE 341  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ALDH2 MUTATED      9    0
  ALDH2 WILD-TYPE  341   22
     clus
vv    ALDH2 MUTATED ALDH2 WILD-TYPE
  NO              9             341
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ALDH2 MUTATED                      9                             2
  ALDH2 WILD-TYPE                  306                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ALDH2 MUTATED                       1                              0
  ALDH2 WILD-TYPE                   105                             10
D246V10, multiclass
                                clus
vv                               ALDH2 MUTATED ALDH2 WILD-TYPE
  COLON ADENOCARCINOMA                       9             306
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  ALDH2 MUTATED     9   0   0   0
  ALDH2 WILD-TYPE 336   4  31  25
D246V11, multiclass
    clus
vv   ALDH2 MUTATED ALDH2 WILD-TYPE
  R0             9             336
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D246V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ALDH2 MUTATED                                  0     1
  ALDH2 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ALDH2 MUTATED                           1     5
  ALDH2 WILD-TYPE                        21   221
D246V13, multiclass
                                  clus
vv                                 ALDH2 MUTATED ALDH2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        5             221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(247) Variable = CCDC160 MUTATION ANALYSIS
D247V1, survival
                   sevent
clus2                 0   1
  CCDC160 MUTATED     9   0
  CCDC160 WILD-TYPE 369  93
  CCDC160 MUTATED CCDC160 WILD-TYPE 
                9               462 
  CCDC160 MUTATED CCDC160 WILD-TYPE 
                0                93 
$`CCDC160 MUTATED`
TCGA-A6-6653 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-A010 TCGA-CK-6751 TCGA-G4-6586 
       24.39         0.92        19.00        34.98       124.27        35.80 
TCGA-G4-6588 TCGA-G4-6628 TCGA-AG-A002 
       26.17        79.69        20.98 

$`CCDC160 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
       25.08        25.18        24.16        21.76        24.69        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 
        6.97        54.02         2.01        14.01        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3692 TCGA-AA-3696 
       15.02        11.01         5.98        37.05        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 
       22.09        13.78        91.79        46.75        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  CCDC160 MUTATED CCDC160 WILD-TYPE 
             0.92              0.00 
  CCDC160 MUTATED CCDC160 WILD-TYPE 
           124.27            148.01 
  CCDC160 MUTATED CCDC160 WILD-TYPE 
           26.170            20.035 
[1] "0.9 - 124.3 (26.2)" "0.0 - 148.0 (20.0)"
[1] "hr="     "9300000"
D247V2, continuous
D247V3, binary
                   cls
clus                  0   1
  CCDC160 MUTATED    10   1
  CCDC160 WILD-TYPE 356 118
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC160 MUTATED     10    1
  CCDC160 WILD-TYPE  356  118
        clus
vv       CCDC160 MUTATED CCDC160 WILD-TYPE
  COLON               10               356
  RECTUM               1               118
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CCDC160 MUTATED         4        0        1         3         1         0
  CCDC160 WILD-TYPE      87        1       31       135         9         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CCDC160 MUTATED           1          0          0          0        1
  CCDC160 WILD-TYPE        23         11         59         42       47
                   vv
clus                STAGE IVA STAGE IVB
  CCDC160 MUTATED           0         0
  CCDC160 WILD-TYPE        18         1
D247V4, multiclass
            clus
vv           CCDC160 MUTATED CCDC160 WILD-TYPE
  STAGE I                  4                87
  STAGE IA                 0                 1
  STAGE II                 1                31
  STAGE IIA                3               135
  STAGE IIB                1                 9
  STAGE IIC                0                 1
  STAGE III                1                23
  STAGE IIIA               0                11
  STAGE IIIB               0                59
  STAGE IIIC               0                42
  STAGE IV                 1                47
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  CCDC160 MUTATED     0   4   5   2
  CCDC160 WILD-TYPE  17  88 324  48
D247V5, multiclass
    clus
vv   CCDC160 MUTATED CCDC160 WILD-TYPE
  T1               0                17
  T2               4                88
  T3               5               324
  T4               2                48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  CCDC160 MUTATED     9   2   0
  CCDC160 WILD-TYPE 278 111  87
D247V6, multiclass
    clus
vv   CCDC160 MUTATED CCDC160 WILD-TYPE
  N0               9               278
  N1               2               111
  N2               0                87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D247V7, binary
                   cls
clus                  0   1
  CCDC160 MUTATED     9   1
  CCDC160 WILD-TYPE 366  64
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC160 MUTATED      9    1
  CCDC160 WILD-TYPE  366   64
   clus
vv  CCDC160 MUTATED CCDC160 WILD-TYPE
  0               9               366
  1               1                64
[1] 2 2
[1] FALSE
D247V8, binary
                   cls
clus                  0   1
  CCDC160 MUTATED     7   4
  CCDC160 WILD-TYPE 218 260
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC160 MUTATED      7    4
  CCDC160 WILD-TYPE  218  260
        clus
vv       CCDC160 MUTATED CCDC160 WILD-TYPE
  FEMALE               7               218
  MALE                 4               260
[1] 2 2
[1] FALSE
D247V9, binary
                   cls
clus                  0   1
  CCDC160 MUTATED     9   0
  CCDC160 WILD-TYPE 341  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC160 MUTATED      9    0
  CCDC160 WILD-TYPE  341   22
     clus
vv    CCDC160 MUTATED CCDC160 WILD-TYPE
  NO                9               341
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CCDC160 MUTATED                      9                             1
  CCDC160 WILD-TYPE                  306                            46
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CCDC160 MUTATED                       1                              0
  CCDC160 WILD-TYPE                   105                             10
D247V10, multiclass
                                clus
vv                               CCDC160 MUTATED CCDC160 WILD-TYPE
  COLON ADENOCARCINOMA                         9               306
  COLON MUCINOUS ADENOCARCINOMA                1                46
  RECTAL ADENOCARCINOMA                        1               105
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  CCDC160 MUTATED     8   0   1   1
  CCDC160 WILD-TYPE 337   4  30  24
D247V11, multiclass
    clus
vv   CCDC160 MUTATED CCDC160 WILD-TYPE
  R0               8               337
  R1               0                 4
  R2               1                30
  RX               1                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D247V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CCDC160 MUTATED                                  0     0
  CCDC160 WILD-TYPE                                1    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  CCDC160 MUTATED                           0     5
  CCDC160 WILD-TYPE                        22   221
D247V13, multiclass
                                  clus
vv                                 CCDC160 MUTATED CCDC160 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                      0                22
  WHITE                                          5               221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(248) Variable = EFTUD2 MUTATION ANALYSIS
D248V1, survival
                  sevent
clus2                0   1
  EFTUD2 MUTATED    10   7
  EFTUD2 WILD-TYPE 368  86
  EFTUD2 MUTATED EFTUD2 WILD-TYPE 
              17              454 
  EFTUD2 MUTATED EFTUD2 WILD-TYPE 
               7               86 
$`EFTUD2 MUTATED`
TCGA-A6-3809 TCGA-AA-3510 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3543 TCGA-AA-3662 
       32.75        63.98        13.02        38.99         0.99         6.05 
TCGA-AA-A01R TCGA-AD-6964 TCGA-AZ-6601 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6676 
       35.01        10.88       100.01        14.04        12.95        11.08 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-AG-3582 TCGA-AG-A002 TCGA-DY-A1DG 
       24.43        38.20        36.03        20.98        51.48 

$`EFTUD2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
       35.01         6.97         1.02         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
       34.03        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
       78.08         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
       12.10        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6677 
       12.99        13.02        15.02        11.01        13.05        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
       11.38        10.26       119.70       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
       32.02         8.02         7.07        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       24.13        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  EFTUD2 MUTATED EFTUD2 WILD-TYPE 
            0.99             0.00 
  EFTUD2 MUTATED EFTUD2 WILD-TYPE 
          100.01           148.01 
  EFTUD2 MUTATED EFTUD2 WILD-TYPE 
          24.430           20.085 
[1] "1.0 - 100.0 (24.4)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.9"
D248V2, continuous
D248V3, binary
                  cls
clus                 0   1
  EFTUD2 MUTATED    14   3
  EFTUD2 WILD-TYPE 352 116
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EFTUD2 MUTATED     14    3
  EFTUD2 WILD-TYPE  352  116
        clus
vv       EFTUD2 MUTATED EFTUD2 WILD-TYPE
  COLON              14              352
  RECTUM              3              116
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  EFTUD2 MUTATED         4        0        2         3         1         0
  EFTUD2 WILD-TYPE      87        1       30       135         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  EFTUD2 MUTATED           2          0          0          1        2
  EFTUD2 WILD-TYPE        22         11         59         41       46
                  vv
clus               STAGE IVA STAGE IVB
  EFTUD2 MUTATED           1         0
  EFTUD2 WILD-TYPE        17         1
D248V4, multiclass
            clus
vv           EFTUD2 MUTATED EFTUD2 WILD-TYPE
  STAGE I                 4               87
  STAGE IA                0                1
  STAGE II                2               30
  STAGE IIA               3              135
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               2               22
  STAGE IIIA              0               11
  STAGE IIIB              0               59
  STAGE IIIC              1               41
  STAGE IV                2               46
  STAGE IVA               1               17
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  EFTUD2 MUTATED     0   4  10   3
  EFTUD2 WILD-TYPE  17  88 319  47
D248V5, multiclass
    clus
vv   EFTUD2 MUTATED EFTUD2 WILD-TYPE
  T1              0               17
  T2              4               88
  T3             10              319
  T4              3               47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  EFTUD2 MUTATED    10   2   5
  EFTUD2 WILD-TYPE 277 111  82
D248V6, multiclass
    clus
vv   EFTUD2 MUTATED EFTUD2 WILD-TYPE
  N0             10              277
  N1              2              111
  N2              5               82
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D248V7, binary
                  cls
clus                 0   1
  EFTUD2 MUTATED    13   3
  EFTUD2 WILD-TYPE 362  62
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EFTUD2 MUTATED     13    3
  EFTUD2 WILD-TYPE  362   62
   clus
vv  EFTUD2 MUTATED EFTUD2 WILD-TYPE
  0             13              362
  1              3               62
[1] 2 2
[1] FALSE
D248V8, binary
                  cls
clus                 0   1
  EFTUD2 MUTATED     5  12
  EFTUD2 WILD-TYPE 220 252
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EFTUD2 MUTATED      5   12
  EFTUD2 WILD-TYPE  220  252
        clus
vv       EFTUD2 MUTATED EFTUD2 WILD-TYPE
  FEMALE              5              220
  MALE               12              252
[1] 2 2
[1] FALSE
D248V9, binary
                  cls
clus                 0   1
  EFTUD2 MUTATED    13   1
  EFTUD2 WILD-TYPE 337  21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EFTUD2 MUTATED     13    1
  EFTUD2 WILD-TYPE  337   21
     clus
vv    EFTUD2 MUTATED EFTUD2 WILD-TYPE
  NO              13              337
  YES              1               21
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  EFTUD2 MUTATED                      9                             4
  EFTUD2 WILD-TYPE                  306                            43
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  EFTUD2 MUTATED                       3                              0
  EFTUD2 WILD-TYPE                   103                             10
D248V10, multiclass
                                clus
vv                               EFTUD2 MUTATED EFTUD2 WILD-TYPE
  COLON ADENOCARCINOMA                        9              306
  COLON MUCINOUS ADENOCARCINOMA               4               43
  RECTAL ADENOCARCINOMA                       3              103
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  EFTUD2 MUTATED     9   0   2   0
  EFTUD2 WILD-TYPE 336   4  29  25
D248V11, multiclass
    clus
vv   EFTUD2 MUTATED EFTUD2 WILD-TYPE
  R0              9              336
  R1              0                4
  R2              2               29
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D248V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  EFTUD2 MUTATED                                  0     0
  EFTUD2 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  EFTUD2 MUTATED                           0     9
  EFTUD2 WILD-TYPE                        22   217
D248V13, multiclass
                                  clus
vv                                 EFTUD2 MUTATED EFTUD2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         9              217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(249) Variable = STBD1 MUTATION ANALYSIS
D249V1, survival
                 sevent
clus2               0   1
  STBD1 MUTATED     6   1
  STBD1 WILD-TYPE 372  92
  STBD1 MUTATED STBD1 WILD-TYPE 
              7             464 
  STBD1 MUTATED STBD1 WILD-TYPE 
              1              92 
$`STBD1 MUTATED`
TCGA-A6-5666 TCGA-AA-3678 TCGA-CK-4948 TCGA-D5-6541 TCGA-DM-A1DB TCGA-F4-6856 
       32.71        47.01       148.01        15.58        44.32        35.31 
TCGA-AG-3593 
       34.03 

$`STBD1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        22.06        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 
       12.20        12.76        10.06        14.30        17.56        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       17.13        12.49        16.14         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
      140.38         7.50       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       47.41       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3594 TCGA-AG-3598 
       20.05        24.00         1.02        46.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  STBD1 MUTATED STBD1 WILD-TYPE 
          15.58            0.00 
  STBD1 MUTATED STBD1 WILD-TYPE 
         148.01          140.38 
  STBD1 MUTATED STBD1 WILD-TYPE 
         35.310          20.035 
[1] "15.6 - 148.0 (35.3)" "0.0 - 140.4 (20.0)" 
[1] "hr=" "2.3"
D249V2, continuous
D249V3, binary
                 cls
clus                0   1
  STBD1 MUTATED     6   1
  STBD1 WILD-TYPE 360 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STBD1 MUTATED      6    1
  STBD1 WILD-TYPE  360  118
        clus
vv       STBD1 MUTATED STBD1 WILD-TYPE
  COLON              6             360
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  STBD1 MUTATED         1        0        0         3         0         1
  STBD1 WILD-TYPE      90        1       32       135        10         0
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  STBD1 MUTATED           2          0          0          0        0         0
  STBD1 WILD-TYPE        22         11         59         42       48        18
                 vv
clus              STAGE IVB
  STBD1 MUTATED           0
  STBD1 WILD-TYPE         1
D249V4, multiclass
            clus
vv           STBD1 MUTATED STBD1 WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              3             135
  STAGE IIB              0              10
  STAGE IIC              1               0
  STAGE III              2              22
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  STBD1 MUTATED     0   2   4   1
  STBD1 WILD-TYPE  17  90 325  49
D249V5, multiclass
    clus
vv   STBD1 MUTATED STBD1 WILD-TYPE
  T1             0              17
  T2             2              90
  T3             4             325
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  STBD1 MUTATED     5   2   0
  STBD1 WILD-TYPE 282 111  87
D249V6, multiclass
    clus
vv   STBD1 MUTATED STBD1 WILD-TYPE
  N0             5             282
  N1             2             111
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D249V7, binary
                 cls
clus                0   1
  STBD1 MUTATED     7   0
  STBD1 WILD-TYPE 368  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STBD1 MUTATED      7    0
  STBD1 WILD-TYPE  368   65
   clus
vv  STBD1 MUTATED STBD1 WILD-TYPE
  0             7             368
  1             0              65
[1] 2 2
[1] FALSE
D249V8, binary
                 cls
clus                0   1
  STBD1 MUTATED     3   4
  STBD1 WILD-TYPE 222 260
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STBD1 MUTATED      3    4
  STBD1 WILD-TYPE  222  260
        clus
vv       STBD1 MUTATED STBD1 WILD-TYPE
  FEMALE             3             222
  MALE               4             260
[1] 2 2
[1] FALSE
D249V9, binary
                 cls
clus                0   1
  STBD1 MUTATED     5   1
  STBD1 WILD-TYPE 345  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STBD1 MUTATED      5    1
  STBD1 WILD-TYPE  345   21
     clus
vv    STBD1 MUTATED STBD1 WILD-TYPE
  NO              5             345
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  STBD1 MUTATED                      5                             1
  STBD1 WILD-TYPE                  310                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  STBD1 MUTATED                       1                              0
  STBD1 WILD-TYPE                   105                             10
D249V10, multiclass
                                clus
vv                               STBD1 MUTATED STBD1 WILD-TYPE
  COLON ADENOCARCINOMA                       5             310
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  STBD1 MUTATED     5   0   0   0
  STBD1 WILD-TYPE 340   4  31  25
D249V11, multiclass
    clus
vv   STBD1 MUTATED STBD1 WILD-TYPE
  R0             5             340
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D249V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  STBD1 MUTATED                                  0     0
  STBD1 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  STBD1 MUTATED                           0     5
  STBD1 WILD-TYPE                        22   221
D249V13, multiclass
                                  clus
vv                                 STBD1 MUTATED STBD1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        5             221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(250) Variable = TCF7L2 MUTATION ANALYSIS
D250V1, survival
                  sevent
clus2                0   1
  TCF7L2 MUTATED    29   3
  TCF7L2 WILD-TYPE 349  90
  TCF7L2 MUTATED TCF7L2 WILD-TYPE 
              32              439 
  TCF7L2 MUTATED TCF7L2 WILD-TYPE 
               3               90 
$`TCF7L2 MUTATED`
TCGA-A6-6781 TCGA-AA-3663 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3955 TCGA-AA-3977 
       19.66         6.97         0.92        50.04        20.98        25.02 
TCGA-AA-A00K TCGA-AA-A010 TCGA-AA-A01I TCGA-AU-6004 TCGA-AY-6197 TCGA-AZ-4315 
       18.05        34.98        31.00        27.09        21.44        58.39 
TCGA-AZ-6601 TCGA-CK-4947 TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-6165 TCGA-CM-6171 
      100.01        17.56        30.08        15.02        16.04        14.04 
TCGA-D5-6922 TCGA-DM-A282 TCGA-AF-2692 TCGA-AF-4110 TCGA-AF-6655 TCGA-AG-3582 
        4.41       139.17        13.55        14.50        20.02        36.03 
TCGA-AG-3726 TCGA-AG-3882 TCGA-AG-3898 TCGA-AG-A032 TCGA-AH-6544 TCGA-CI-6619 
        7.99        19.99        48.03        38.04        38.56         6.05 
TCGA-DC-6683 TCGA-DY-A1DG 
        5.03        51.48 

$`TCF7L2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       54.02         2.01        14.01        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3956 TCGA-AA-3966 
       33.01        26.01        24.00         2.01        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 
        0.20        14.50        16.31         0.95        33.01        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       49.41         6.77        12.10        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4948 
        0.07        12.20        12.76        10.06        14.30       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5860 
       25.02        13.02        29.06        22.03        22.98        32.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
        2.96        29.03        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       15.02        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
       15.58         1.48         3.68        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      131.51       135.65         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6136 
       43.04        19.10        34.49        10.39        16.83        15.39 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       13.94        19.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
        0.99        19.04         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3902 TCGA-AG-3909 
       13.02        35.01        14.01         1.02        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A036 
       49.97         1.94        38.96        61.97        41.00       117.11 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6620 TCGA-CI-6622 
        1.45        17.49         0.69         0.72        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DT-5265 
       27.95        10.98        19.99         5.95         4.01         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 
      126.44        41.36        57.24        24.13        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  TCF7L2 MUTATED TCF7L2 WILD-TYPE 
            0.92             0.00 
  TCF7L2 MUTATED TCF7L2 WILD-TYPE 
          139.17           148.01 
  TCF7L2 MUTATED TCF7L2 WILD-TYPE 
           20.50            20.19 
[1] "0.9 - 139.2 (20.5)" "0.0 - 148.0 (20.2)"
[1] "hr=" "2.4"
D250V2, continuous
D250V3, binary
                  cls
clus                 0   1
  TCF7L2 MUTATED    23  10
  TCF7L2 WILD-TYPE 343 109
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TCF7L2 MUTATED     23   10
  TCF7L2 WILD-TYPE  343  109
        clus
vv       TCF7L2 MUTATED TCF7L2 WILD-TYPE
  COLON              23              343
  RECTUM             10              109
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TCF7L2 MUTATED         5        0        4        10         1         0
  TCF7L2 WILD-TYPE      86        1       28       128         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TCF7L2 MUTATED           1          2          4          1        3
  TCF7L2 WILD-TYPE        23          9         55         41       45
                  vv
clus               STAGE IVA STAGE IVB
  TCF7L2 MUTATED           2         0
  TCF7L2 WILD-TYPE        16         1
D250V4, multiclass
            clus
vv           TCF7L2 MUTATED TCF7L2 WILD-TYPE
  STAGE I                 5               86
  STAGE IA                0                1
  STAGE II                4               28
  STAGE IIA              10              128
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               1               23
  STAGE IIIA              2                9
  STAGE IIIB              4               55
  STAGE IIIC              1               41
  STAGE IV                3               45
  STAGE IVA               2               16
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  TCF7L2 MUTATED     0   8  22   5
  TCF7L2 WILD-TYPE  17  84 307  45
D250V5, multiclass
    clus
vv   TCF7L2 MUTATED TCF7L2 WILD-TYPE
  T1              0               17
  T2              8               84
  T3             22              307
  T4              5               45
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  TCF7L2 MUTATED    21  11   3
  TCF7L2 WILD-TYPE 266 102  84
D250V6, multiclass
    clus
vv   TCF7L2 MUTATED TCF7L2 WILD-TYPE
  N0             21              266
  N1             11              102
  N2              3               84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D250V7, binary
                  cls
clus                 0   1
  TCF7L2 MUTATED    26   5
  TCF7L2 WILD-TYPE 349  60
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TCF7L2 MUTATED     26    5
  TCF7L2 WILD-TYPE  349   60
   clus
vv  TCF7L2 MUTATED TCF7L2 WILD-TYPE
  0             26              349
  1              5               60
[1] 2 2
[1] FALSE
D250V8, binary
                  cls
clus                 0   1
  TCF7L2 MUTATED    15  20
  TCF7L2 WILD-TYPE 210 244
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TCF7L2 MUTATED     15   20
  TCF7L2 WILD-TYPE  210  244
        clus
vv       TCF7L2 MUTATED TCF7L2 WILD-TYPE
  FEMALE             15              210
  MALE               20              244
[1] 2 2
[1] FALSE
D250V9, binary
                  cls
clus                 0   1
  TCF7L2 MUTATED    24   1
  TCF7L2 WILD-TYPE 326  21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TCF7L2 MUTATED     24    1
  TCF7L2 WILD-TYPE  326   21
     clus
vv    TCF7L2 MUTATED TCF7L2 WILD-TYPE
  NO              24              326
  YES              1               21
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  TCF7L2 MUTATED                     22                             1
  TCF7L2 WILD-TYPE                  293                            46
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  TCF7L2 MUTATED                      10                              0
  TCF7L2 WILD-TYPE                    96                             10
D250V10, multiclass
                                clus
vv                               TCF7L2 MUTATED TCF7L2 WILD-TYPE
  COLON ADENOCARCINOMA                       22              293
  COLON MUCINOUS ADENOCARCINOMA               1               46
  RECTAL ADENOCARCINOMA                      10               96
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  TCF7L2 MUTATED    26   0   2   1
  TCF7L2 WILD-TYPE 319   4  29  24
D250V11, multiclass
    clus
vv   TCF7L2 MUTATED TCF7L2 WILD-TYPE
  R0             26              319
  R1              0                4
  R2              2               29
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D250V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TCF7L2 MUTATED                                  0     0
  TCF7L2 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  TCF7L2 MUTATED                           0    19
  TCF7L2 WILD-TYPE                        22   207
D250V13, multiclass
                                  clus
vv                                 TCF7L2 MUTATED TCF7L2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                        19              207
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(251) Variable = C17ORF47 MUTATION ANALYSIS
D251V1, survival
                    sevent
clus2                  0   1
  C17ORF47 MUTATED     6   1
  C17ORF47 WILD-TYPE 372  92
  C17ORF47 MUTATED C17ORF47 WILD-TYPE 
                 7                464 
  C17ORF47 MUTATED C17ORF47 WILD-TYPE 
                 1                 92 
$`C17ORF47 MUTATED`
TCGA-A6-5666 TCGA-A6-6649 TCGA-AA-A010 TCGA-CA-6717 TCGA-CM-5862 TCGA-AG-3881 
       32.71        24.16        34.98        12.76         5.03        19.04 
TCGA-AG-A002 
       20.98 

$`C17ORF47 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        22.06        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       25.18        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
       32.98         0.99         0.99        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  C17ORF47 MUTATED C17ORF47 WILD-TYPE 
              5.03               0.00 
  C17ORF47 MUTATED C17ORF47 WILD-TYPE 
             34.98             148.01 
  C17ORF47 MUTATED C17ORF47 WILD-TYPE 
            20.980             20.155 
[1] "5.0 - 35.0 (21.0)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.1"
D251V2, continuous
D251V3, binary
                    cls
clus                   0   1
  C17ORF47 MUTATED     5   2
  C17ORF47 WILD-TYPE 361 117
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C17ORF47 MUTATED      5    2
  C17ORF47 WILD-TYPE  361  117
        clus
vv       C17ORF47 MUTATED C17ORF47 WILD-TYPE
  COLON                 5                361
  RECTUM                2                117
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  C17ORF47 MUTATED         1        0        0         2         1         1
  C17ORF47 WILD-TYPE      90        1       32       136         9         0
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C17ORF47 MUTATED           0          0          1          0        0
  C17ORF47 WILD-TYPE        24         11         58         42       48
                    vv
clus                 STAGE IVA STAGE IVB
  C17ORF47 MUTATED           1         0
  C17ORF47 WILD-TYPE        17         1
D251V4, multiclass
            clus
vv           C17ORF47 MUTATED C17ORF47 WILD-TYPE
  STAGE I                   1                 90
  STAGE IA                  0                  1
  STAGE II                  0                 32
  STAGE IIA                 2                136
  STAGE IIB                 1                  9
  STAGE IIC                 1                  0
  STAGE III                 0                 24
  STAGE IIIA                0                 11
  STAGE IIIB                1                 58
  STAGE IIIC                0                 42
  STAGE IV                  0                 48
  STAGE IVA                 1                 17
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  C17ORF47 MUTATED     0   1   4   2
  C17ORF47 WILD-TYPE  17  91 325  48
D251V5, multiclass
    clus
vv   C17ORF47 MUTATED C17ORF47 WILD-TYPE
  T1                0                 17
  T2                1                 91
  T3                4                325
  T4                2                 48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  C17ORF47 MUTATED     5   2   0
  C17ORF47 WILD-TYPE 282 111  87
D251V6, multiclass
    clus
vv   C17ORF47 MUTATED C17ORF47 WILD-TYPE
  N0                5                282
  N1                2                111
  N2                0                 87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D251V7, binary
                    cls
clus                   0   1
  C17ORF47 MUTATED     6   1
  C17ORF47 WILD-TYPE 369  64
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C17ORF47 MUTATED      6    1
  C17ORF47 WILD-TYPE  369   64
   clus
vv  C17ORF47 MUTATED C17ORF47 WILD-TYPE
  0                6                369
  1                1                 64
[1] 2 2
[1] FALSE
D251V8, binary
                    cls
clus                   0   1
  C17ORF47 MUTATED     2   5
  C17ORF47 WILD-TYPE 223 259
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C17ORF47 MUTATED      2    5
  C17ORF47 WILD-TYPE  223  259
        clus
vv       C17ORF47 MUTATED C17ORF47 WILD-TYPE
  FEMALE                2                223
  MALE                  5                259
[1] 2 2
[1] FALSE
D251V9, binary
                    cls
clus                   0   1
  C17ORF47 MUTATED     7   0
  C17ORF47 WILD-TYPE 343  22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C17ORF47 MUTATED      7    0
  C17ORF47 WILD-TYPE  343   22
     clus
vv    C17ORF47 MUTATED C17ORF47 WILD-TYPE
  NO                 7                343
  YES                0                 22
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  C17ORF47 MUTATED                      4                             1
  C17ORF47 WILD-TYPE                  311                            46
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  C17ORF47 MUTATED                       1                              0
  C17ORF47 WILD-TYPE                   105                             10
D251V10, multiclass
                                clus
vv                               C17ORF47 MUTATED C17ORF47 WILD-TYPE
  COLON ADENOCARCINOMA                          4                311
  COLON MUCINOUS ADENOCARCINOMA                 1                 46
  RECTAL ADENOCARCINOMA                         1                105
  RECTAL MUCINOUS ADENOCARCINOMA                0                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  C17ORF47 MUTATED     3   0   0   1
  C17ORF47 WILD-TYPE 342   4  31  24
D251V11, multiclass
    clus
vv   C17ORF47 MUTATED C17ORF47 WILD-TYPE
  R0                3                342
  R1                0                  4
  R2                0                 31
  RX                1                 24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D251V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C17ORF47 MUTATED                                  0     1
  C17ORF47 WILD-TYPE                                1    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  C17ORF47 MUTATED                           0     3
  C17ORF47 WILD-TYPE                        22   223
D251V13, multiclass
                                  clus
vv                                 C17ORF47 MUTATED C17ORF47 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                 10
  BLACK OR AFRICAN AMERICAN                       0                 22
  WHITE                                           3                223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(252) Variable = TOP2A MUTATION ANALYSIS
D252V1, survival
                 sevent
clus2               0   1
  TOP2A MUTATED    17   2
  TOP2A WILD-TYPE 361  91
  TOP2A MUTATED TOP2A WILD-TYPE 
             19             452 
  TOP2A MUTATED TOP2A WILD-TYPE 
              2              91 
$`TOP2A MUTATED`
TCGA-A6-5665 TCGA-AA-3496 TCGA-AA-3510 TCGA-AA-3663 TCGA-AA-3672 TCGA-AA-3697 
       22.06         1.02        63.98         6.97         0.92        85.05 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AU-6004 TCGA-AY-6386 TCGA-CA-6718 TCGA-CK-5913 
        0.79         0.72        27.09        17.82        10.06        51.32 
TCGA-CM-6171 TCGA-CM-6675 TCGA-D5-6539 TCGA-F4-6570 TCGA-AG-3892 TCGA-AG-A002 
       14.04        13.05        12.49         6.18        13.02        20.98 
TCGA-G5-6235 
       55.76 

$`TOP2A WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 
       20.12        19.66        20.28         7.04         3.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02        78.08         6.05        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
       14.01        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 
       37.05        19.00        36.00         5.03        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       21.37        15.52        56.55         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       10.88         0.20        14.50        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       11.01        12.95        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
        4.80        17.13        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 
      117.07        98.24         8.61        31.96        35.74        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 
        1.02        17.95        36.95        17.03        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6641 
        0.69        26.43 

  TOP2A MUTATED TOP2A WILD-TYPE 
           0.72            0.00 
  TOP2A MUTATED TOP2A WILD-TYPE 
          85.05          148.01 
  TOP2A MUTATED TOP2A WILD-TYPE 
          13.05           20.73 
[1] "0.7 - 85.0 (13.1)"  "0.0 - 148.0 (20.7)"
[1] "hr=" "1.7"
D252V2, continuous
D252V3, binary
                 cls
clus                0   1
  TOP2A MUTATED    17   3
  TOP2A WILD-TYPE 349 116
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TOP2A MUTATED     17    3
  TOP2A WILD-TYPE  349  116
        clus
vv       TOP2A MUTATED TOP2A WILD-TYPE
  COLON             17             349
  RECTUM             3             116
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TOP2A MUTATED         4        0        3         5         0         0
  TOP2A WILD-TYPE      87        1       29       133        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TOP2A MUTATED           2          1          2          0        0         0
  TOP2A WILD-TYPE        22         10         57         42       48        18
                 vv
clus              STAGE IVB
  TOP2A MUTATED           1
  TOP2A WILD-TYPE         0
D252V4, multiclass
            clus
vv           TOP2A MUTATED TOP2A WILD-TYPE
  STAGE I                4              87
  STAGE IA               0               1
  STAGE II               3              29
  STAGE IIA              5             133
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              2              22
  STAGE IIIA             1              10
  STAGE IIIB             2              57
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              1               0
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  TOP2A MUTATED     2   3  15   0
  TOP2A WILD-TYPE  15  89 314  50
D252V5, multiclass
    clus
vv   TOP2A MUTATED TOP2A WILD-TYPE
  T1             2              15
  T2             3              89
  T3            15             314
  T4             0              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  TOP2A MUTATED    15   4   1
  TOP2A WILD-TYPE 272 109  86
D252V6, multiclass
    clus
vv   TOP2A MUTATED TOP2A WILD-TYPE
  N0            15             272
  N1             4             109
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D252V7, binary
                 cls
clus                0   1
  TOP2A MUTATED    15   1
  TOP2A WILD-TYPE 360  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TOP2A MUTATED     15    1
  TOP2A WILD-TYPE  360   64
   clus
vv  TOP2A MUTATED TOP2A WILD-TYPE
  0            15             360
  1             1              64
[1] 2 2
[1] FALSE
D252V8, binary
                 cls
clus                0   1
  TOP2A MUTATED    11   9
  TOP2A WILD-TYPE 214 255
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TOP2A MUTATED     11    9
  TOP2A WILD-TYPE  214  255
        clus
vv       TOP2A MUTATED TOP2A WILD-TYPE
  FEMALE            11             214
  MALE               9             255
[1] 2 2
[1] FALSE
D252V9, binary
                 cls
clus                0   1
  TOP2A MUTATED    15   0
  TOP2A WILD-TYPE 335  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TOP2A MUTATED     15    0
  TOP2A WILD-TYPE  335   22
     clus
vv    TOP2A MUTATED TOP2A WILD-TYPE
  NO             15             335
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  TOP2A MUTATED                     17                             0
  TOP2A WILD-TYPE                  298                            47
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  TOP2A MUTATED                       3                              0
  TOP2A WILD-TYPE                   103                             10
D252V10, multiclass
                                clus
vv                               TOP2A MUTATED TOP2A WILD-TYPE
  COLON ADENOCARCINOMA                      17             298
  COLON MUCINOUS ADENOCARCINOMA              0              47
  RECTAL ADENOCARCINOMA                      3             103
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  TOP2A MUTATED    15   1   0   2
  TOP2A WILD-TYPE 330   3  31  23
D252V11, multiclass
    clus
vv   TOP2A MUTATED TOP2A WILD-TYPE
  R0            15             330
  R1             1               3
  R2             0              31
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D252V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TOP2A MUTATED                                  0     1
  TOP2A WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  TOP2A MUTATED                           2     9
  TOP2A WILD-TYPE                        20   217
D252V13, multiclass
                                  clus
vv                                 TOP2A MUTATED TOP2A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    2              20
  WHITE                                        9             217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(253) Variable = MIER3 MUTATION ANALYSIS
D253V1, survival
                 sevent
clus2               0   1
  MIER3 MUTATED    11   1
  MIER3 WILD-TYPE 367  92
  MIER3 MUTATED MIER3 WILD-TYPE 
             12             459 
  MIER3 MUTATED MIER3 WILD-TYPE 
              1              92 
$`MIER3 MUTATED`
TCGA-A6-2672 TCGA-A6-5665 TCGA-AA-3526 TCGA-AA-3555 TCGA-AA-3672 TCGA-AA-3715 
       46.65        22.06        19.07        29.95         0.92        19.04 
TCGA-AA-3864 TCGA-AA-3977 TCGA-AA-A010 TCGA-AU-6004 TCGA-CM-5861 TCGA-AG-A002 
       53.00        25.02        34.98        27.09        15.02        20.98 

$`MIER3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3529 
        9.07        24.03        37.05        36.03         8.05         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       17.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
       14.01        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
        0.20        14.50        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 
       29.06        22.03        22.98        30.08        32.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  MIER3 MUTATED MIER3 WILD-TYPE 
           0.92            0.00 
  MIER3 MUTATED MIER3 WILD-TYPE 
          53.00          148.01 
  MIER3 MUTATED MIER3 WILD-TYPE 
          23.54           20.05 
[1] "0.9 - 53.0 (23.5)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "2.4"
D253V2, continuous
D253V3, binary
                 cls
clus                0   1
  MIER3 MUTATED    13   1
  MIER3 WILD-TYPE 353 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MIER3 MUTATED     13    1
  MIER3 WILD-TYPE  353  118
        clus
vv       MIER3 MUTATED MIER3 WILD-TYPE
  COLON             13             353
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MIER3 MUTATED         3        0        3         4         1         0
  MIER3 WILD-TYPE      88        1       29       134         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MIER3 MUTATED           1          0          1          0        0         0
  MIER3 WILD-TYPE        23         11         58         42       48        18
                 vv
clus              STAGE IVB
  MIER3 MUTATED           0
  MIER3 WILD-TYPE         1
D253V4, multiclass
            clus
vv           MIER3 MUTATED MIER3 WILD-TYPE
  STAGE I                3              88
  STAGE IA               0               1
  STAGE II               3              29
  STAGE IIA              4             134
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  MIER3 MUTATED     0   4   8   2
  MIER3 WILD-TYPE  17  88 321  48
D253V5, multiclass
    clus
vv   MIER3 MUTATED MIER3 WILD-TYPE
  T1             0              17
  T2             4              88
  T3             8             321
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  MIER3 MUTATED    12   2   0
  MIER3 WILD-TYPE 275 111  87
D253V6, multiclass
    clus
vv   MIER3 MUTATED MIER3 WILD-TYPE
  N0            12             275
  N1             2             111
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D253V7, binary
                 cls
clus                0   1
  MIER3 MUTATED    13   0
  MIER3 WILD-TYPE 362  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MIER3 MUTATED     13    0
  MIER3 WILD-TYPE  362   65
   clus
vv  MIER3 MUTATED MIER3 WILD-TYPE
  0            13             362
  1             0              65
[1] 2 2
[1] FALSE
D253V8, binary
                 cls
clus                0   1
  MIER3 MUTATED     9   5
  MIER3 WILD-TYPE 216 259
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MIER3 MUTATED      9    5
  MIER3 WILD-TYPE  216  259
        clus
vv       MIER3 MUTATED MIER3 WILD-TYPE
  FEMALE             9             216
  MALE               5             259
[1] 2 2
[1] FALSE
D253V9, binary
                 cls
clus                0   1
  MIER3 MUTATED    11   0
  MIER3 WILD-TYPE 339  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MIER3 MUTATED     11    0
  MIER3 WILD-TYPE  339   22
     clus
vv    MIER3 MUTATED MIER3 WILD-TYPE
  NO             11             339
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MIER3 MUTATED                     12                             1
  MIER3 WILD-TYPE                  303                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MIER3 MUTATED                       1                              0
  MIER3 WILD-TYPE                   105                             10
D253V10, multiclass
                                clus
vv                               MIER3 MUTATED MIER3 WILD-TYPE
  COLON ADENOCARCINOMA                      12             303
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  MIER3 MUTATED    13   0   0   0
  MIER3 WILD-TYPE 332   4  31  25
D253V11, multiclass
    clus
vv   MIER3 MUTATED MIER3 WILD-TYPE
  R0            13             332
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D253V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MIER3 MUTATED                                  0     0
  MIER3 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  MIER3 MUTATED                           0     4
  MIER3 WILD-TYPE                        22   222
D253V13, multiclass
                                  clus
vv                                 MIER3 MUTATED MIER3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        4             222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(254) Variable = FBXO21 MUTATION ANALYSIS
D254V1, survival
                  sevent
clus2                0   1
  FBXO21 MUTATED     7   2
  FBXO21 WILD-TYPE 371  91
  FBXO21 MUTATED FBXO21 WILD-TYPE 
               9              462 
  FBXO21 MUTATED FBXO21 WILD-TYPE 
               2               91 
$`FBXO21 MUTATED`
TCGA-A6-5661 TCGA-AA-3672 TCGA-AA-3950 TCGA-AZ-6598 TCGA-CK-4952 TCGA-D5-6928 
       33.53         0.92        24.00        49.41        15.62        11.64 
TCGA-AG-3583 TCGA-AG-3892 TCGA-AG-A002 
       20.05        13.02        20.98 

$`FBXO21 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 
        6.97        54.02         2.01        14.01        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 
       12.99        24.00        33.01        26.01         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        88.21         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 
       10.06        14.30        17.56       148.01        85.45        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
       14.30         9.04         9.44         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       17.03        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  FBXO21 MUTATED FBXO21 WILD-TYPE 
            0.92             0.00 
  FBXO21 MUTATED FBXO21 WILD-TYPE 
           49.41           148.01 
  FBXO21 MUTATED FBXO21 WILD-TYPE 
          20.050           20.235 
[1] "0.9 - 49.4 (20.1)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.4"
D254V2, continuous
D254V3, binary
                  cls
clus                 0   1
  FBXO21 MUTATED     6   3
  FBXO21 WILD-TYPE 360 116
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FBXO21 MUTATED      6    3
  FBXO21 WILD-TYPE  360  116
        clus
vv       FBXO21 MUTATED FBXO21 WILD-TYPE
  COLON               6              360
  RECTUM              3              116
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FBXO21 MUTATED         2        0        1         3         0         0
  FBXO21 WILD-TYPE      89        1       31       135        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FBXO21 MUTATED           1          0          0          1        1
  FBXO21 WILD-TYPE        23         11         59         41       47
                  vv
clus               STAGE IVA STAGE IVB
  FBXO21 MUTATED           0         0
  FBXO21 WILD-TYPE        18         1
D254V4, multiclass
            clus
vv           FBXO21 MUTATED FBXO21 WILD-TYPE
  STAGE I                 2               89
  STAGE IA                0                1
  STAGE II                1               31
  STAGE IIA               3              135
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               1               23
  STAGE IIIA              0               11
  STAGE IIIB              0               59
  STAGE IIIC              1               41
  STAGE IV                1               47
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  FBXO21 MUTATED     1   1   6   1
  FBXO21 WILD-TYPE  16  91 323  49
D254V5, multiclass
    clus
vv   FBXO21 MUTATED FBXO21 WILD-TYPE
  T1              1               16
  T2              1               91
  T3              6              323
  T4              1               49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  FBXO21 MUTATED     6   1   2
  FBXO21 WILD-TYPE 281 112  85
D254V6, multiclass
    clus
vv   FBXO21 MUTATED FBXO21 WILD-TYPE
  N0              6              281
  N1              1              112
  N2              2               85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D254V7, binary
                  cls
clus                 0   1
  FBXO21 MUTATED     7   1
  FBXO21 WILD-TYPE 368  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FBXO21 MUTATED      7    1
  FBXO21 WILD-TYPE  368   64
   clus
vv  FBXO21 MUTATED FBXO21 WILD-TYPE
  0              7              368
  1              1               64
[1] 2 2
[1] FALSE
D254V8, binary
                  cls
clus                 0   1
  FBXO21 MUTATED     6   3
  FBXO21 WILD-TYPE 219 261
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FBXO21 MUTATED      6    3
  FBXO21 WILD-TYPE  219  261
        clus
vv       FBXO21 MUTATED FBXO21 WILD-TYPE
  FEMALE              6              219
  MALE                3              261
[1] 2 2
[1] FALSE
D254V9, binary
                  cls
clus                 0   1
  FBXO21 MUTATED     8   0
  FBXO21 WILD-TYPE 342  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FBXO21 MUTATED      8    0
  FBXO21 WILD-TYPE  342   22
     clus
vv    FBXO21 MUTATED FBXO21 WILD-TYPE
  NO               8              342
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  FBXO21 MUTATED                      3                             3
  FBXO21 WILD-TYPE                  312                            44
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  FBXO21 MUTATED                       2                              1
  FBXO21 WILD-TYPE                   104                              9
D254V10, multiclass
                                clus
vv                               FBXO21 MUTATED FBXO21 WILD-TYPE
  COLON ADENOCARCINOMA                        3              312
  COLON MUCINOUS ADENOCARCINOMA               3               44
  RECTAL ADENOCARCINOMA                       2              104
  RECTAL MUCINOUS ADENOCARCINOMA              1                9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  FBXO21 MUTATED     6   0   1   1
  FBXO21 WILD-TYPE 339   4  30  24
D254V11, multiclass
    clus
vv   FBXO21 MUTATED FBXO21 WILD-TYPE
  R0              6              339
  R1              0                4
  R2              1               30
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D254V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FBXO21 MUTATED                                  0     0
  FBXO21 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  FBXO21 MUTATED                           1     3
  FBXO21 WILD-TYPE                        21   223
D254V13, multiclass
                                  clus
vv                                 FBXO21 MUTATED FBXO21 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                         3              223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(255) Variable = CYP1B1 MUTATION ANALYSIS
D255V1, survival
                  sevent
clus2                0   1
  CYP1B1 MUTATED     9   2
  CYP1B1 WILD-TYPE 369  91
  CYP1B1 MUTATED CYP1B1 WILD-TYPE 
              11              460 
  CYP1B1 MUTATED CYP1B1 WILD-TYPE 
               2               91 
$`CYP1B1 MUTATED`
TCGA-A6-5665 TCGA-A6-6654 TCGA-AA-3715 TCGA-AA-3861 TCGA-CA-6717 TCGA-CM-5348 
       22.06        23.87        19.04        30.05        12.76        22.98 
TCGA-D5-6533 TCGA-G4-6303 TCGA-G4-6586 TCGA-G4-6588 TCGA-AG-A002 
        1.32        65.85        35.80        26.17        20.98 

$`CYP1B1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 
       25.18        24.16        21.76        24.69        24.39        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        31.07        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07        12.20        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.03        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 
       56.09        55.92        20.19        18.25        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
      133.18        74.56        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6625 
       63.62        61.91        36.00        22.09        13.78        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  CYP1B1 MUTATED CYP1B1 WILD-TYPE 
            1.32             0.00 
  CYP1B1 MUTATED CYP1B1 WILD-TYPE 
           65.85           148.01 
  CYP1B1 MUTATED CYP1B1 WILD-TYPE 
          22.980           20.035 
[1] "1.3 - 65.8 (23.0)"  "0.0 - 148.0 (20.0)"
[1] "hr=" "1"  
D255V2, continuous
D255V3, binary
                  cls
clus                 0   1
  CYP1B1 MUTATED    11   1
  CYP1B1 WILD-TYPE 355 118
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CYP1B1 MUTATED     11    1
  CYP1B1 WILD-TYPE  355  118
        clus
vv       CYP1B1 MUTATED CYP1B1 WILD-TYPE
  COLON              11              355
  RECTUM              1              118
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CYP1B1 MUTATED         1        0        1         6         0         0
  CYP1B1 WILD-TYPE      90        1       31       132        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CYP1B1 MUTATED           0          0          3          0        1
  CYP1B1 WILD-TYPE        24         11         56         42       47
                  vv
clus               STAGE IVA STAGE IVB
  CYP1B1 MUTATED           0         0
  CYP1B1 WILD-TYPE        18         1
D255V4, multiclass
            clus
vv           CYP1B1 MUTATED CYP1B1 WILD-TYPE
  STAGE I                 1               90
  STAGE IA                0                1
  STAGE II                1               31
  STAGE IIA               6              132
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              3               56
  STAGE IIIC              0               42
  STAGE IV                1               47
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  CYP1B1 MUTATED     0   1  10   1
  CYP1B1 WILD-TYPE  17  91 319  49
D255V5, multiclass
    clus
vv   CYP1B1 MUTATED CYP1B1 WILD-TYPE
  T1              0               17
  T2              1               91
  T3             10              319
  T4              1               49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  CYP1B1 MUTATED     9   3   0
  CYP1B1 WILD-TYPE 278 110  87
D255V6, multiclass
    clus
vv   CYP1B1 MUTATED CYP1B1 WILD-TYPE
  N0              9              278
  N1              3              110
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D255V7, binary
                  cls
clus                 0   1
  CYP1B1 MUTATED    11   1
  CYP1B1 WILD-TYPE 364  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CYP1B1 MUTATED     11    1
  CYP1B1 WILD-TYPE  364   64
   clus
vv  CYP1B1 MUTATED CYP1B1 WILD-TYPE
  0             11              364
  1              1               64
[1] 2 2
[1] FALSE
D255V8, binary
                  cls
clus                 0   1
  CYP1B1 MUTATED     7   5
  CYP1B1 WILD-TYPE 218 259
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CYP1B1 MUTATED      7    5
  CYP1B1 WILD-TYPE  218  259
        clus
vv       CYP1B1 MUTATED CYP1B1 WILD-TYPE
  FEMALE              7              218
  MALE                5              259
[1] 2 2
[1] FALSE
D255V9, binary
                  cls
clus                 0   1
  CYP1B1 MUTATED    10   0
  CYP1B1 WILD-TYPE 340  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CYP1B1 MUTATED     10    0
  CYP1B1 WILD-TYPE  340   22
     clus
vv    CYP1B1 MUTATED CYP1B1 WILD-TYPE
  NO              10              340
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CYP1B1 MUTATED                     10                             1
  CYP1B1 WILD-TYPE                  305                            46
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CYP1B1 MUTATED                       1                              0
  CYP1B1 WILD-TYPE                   105                             10
D255V10, multiclass
                                clus
vv                               CYP1B1 MUTATED CYP1B1 WILD-TYPE
  COLON ADENOCARCINOMA                       10              305
  COLON MUCINOUS ADENOCARCINOMA               1               46
  RECTAL ADENOCARCINOMA                       1              105
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  CYP1B1 MUTATED    10   0   0   1
  CYP1B1 WILD-TYPE 335   4  31  24
D255V11, multiclass
    clus
vv   CYP1B1 MUTATED CYP1B1 WILD-TYPE
  R0             10              335
  R1              0                4
  R2              0               31
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D255V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CYP1B1 MUTATED                                  0     1
  CYP1B1 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  CYP1B1 MUTATED                           0     7
  CYP1B1 WILD-TYPE                        22   219
D255V13, multiclass
                                  clus
vv                                 CYP1B1 MUTATED CYP1B1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         7              219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(256) Variable = MSH6 MUTATION ANALYSIS
D256V1, survival
                sevent
clus2              0   1
  MSH6 MUTATED    38   6
  MSH6 WILD-TYPE 340  87
  MSH6 MUTATED MSH6 WILD-TYPE 
            44            427 
  MSH6 MUTATED MSH6 WILD-TYPE 
             6             87 
$`MSH6 MUTATED`
TCGA-A6-3809 TCGA-A6-5662 TCGA-AA-3525 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3710 
       32.75        23.61         8.05        61.02        78.08        26.99 
TCGA-AA-3715 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3968 TCGA-AA-3977 TCGA-AA-A00N 
       19.04        26.01        24.00        21.99        25.02         4.01 
TCGA-AA-A010 TCGA-AD-6890 TCGA-AD-6963 TCGA-AU-3779 TCGA-AZ-4315 TCGA-AZ-5403 
       34.98         0.79        27.42        14.50        58.39        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-CA-5255 TCGA-CA-6717 
       88.21        49.41        12.10       100.01         3.06        12.76 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-6751 TCGA-CM-5344 TCGA-CM-6164 
      148.01        85.45        15.62       124.27        22.03        29.03 
TCGA-CM-6169 TCGA-D5-6533 TCGA-D5-6541 TCGA-D5-6929 TCGA-D5-6930 TCGA-DM-A1HB 
       13.02         1.32        15.58         4.80         1.51       135.65 
TCGA-DM-A28H TCGA-G4-6307 TCGA-G4-6321 TCGA-AG-3892 TCGA-AG-4001 TCGA-AG-A002 
      117.07        55.04        22.09        13.02        36.03        20.98 
TCGA-CL-5917 TCGA-DC-6157 
       78.12        27.95 

$`MSH6 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5664 TCGA-A6-5665 
       31.63        30.44        29.19        33.53        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3529 
        9.07        24.03        37.05        36.03        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       19.99         6.05         6.97        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 
       37.05        19.00        36.00         5.03        85.05        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3952 TCGA-AA-3955 
        2.01        12.99        24.00        33.01         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6964 
       15.52        56.55         0.72         5.79        22.42        10.88 
TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
        0.20        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-6599 
       17.82         1.41         5.13       106.75        22.36         6.77 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07        12.20        10.06        14.30 
TCGA-CK-4947 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       17.56        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
        1.91        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       29.06        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6170 TCGA-CM-6171 
       16.04        21.99        14.99        12.99        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       55.92        20.19        18.25        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6898 TCGA-D5-6920 
        4.80        17.13        12.49        16.14         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
        7.50        44.32       131.51       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
      119.93        35.97        60.79        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 
      133.18        74.56        65.85        53.62        44.68        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       63.62        61.91        36.00        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 
       19.99         1.02        17.95        36.95        17.03        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6158 
        4.73         7.17        15.02         5.03        13.97        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  MSH6 MUTATED MSH6 WILD-TYPE 
          0.79           0.00 
  MSH6 MUTATED MSH6 WILD-TYPE 
        148.01         140.38 
  MSH6 MUTATED MSH6 WILD-TYPE 
        25.515         19.990 
[1] "0.8 - 148.0 (25.5)" "0.0 - 140.4 (20.0)"
[1] "hr=" "2.3"
D256V2, continuous
D256V3, binary
                cls
clus               0   1
  MSH6 MUTATED    39   6
  MSH6 WILD-TYPE 327 113
[1] "tbl2"
                cls
clus             [,1] [,2]
  MSH6 MUTATED     39    6
  MSH6 WILD-TYPE  327  113
        clus
vv       MSH6 MUTATED MSH6 WILD-TYPE
  COLON            39            327
  RECTUM            6            113
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MSH6 MUTATED         6        0        6        11         3         0
  MSH6 WILD-TYPE      85        1       26       127         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MSH6 MUTATED           3          0          7          3        2         1
  MSH6 WILD-TYPE        21         11         52         39       46        17
                vv
clus             STAGE IVB
  MSH6 MUTATED           0
  MSH6 WILD-TYPE         1
D256V4, multiclass
            clus
vv           MSH6 MUTATED MSH6 WILD-TYPE
  STAGE I               6             85
  STAGE IA              0              1
  STAGE II              6             26
  STAGE IIA            11            127
  STAGE IIB             3              7
  STAGE IIC             0              1
  STAGE III             3             21
  STAGE IIIA            0             11
  STAGE IIIB            7             52
  STAGE IIIC            3             39
  STAGE IV              2             46
  STAGE IVA             1             17
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  MSH6 MUTATED     3   6  30   6
  MSH6 WILD-TYPE  14  86 299  44
D256V5, multiclass
    clus
vv   MSH6 MUTATED MSH6 WILD-TYPE
  T1            3             14
  T2            6             86
  T3           30            299
  T4            6             44
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  MSH6 MUTATED    30  11   4
  MSH6 WILD-TYPE 257 102  83
D256V6, multiclass
    clus
vv   MSH6 MUTATED MSH6 WILD-TYPE
  N0           30            257
  N1           11            102
  N2            4             83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D256V7, binary
                cls
clus               0   1
  MSH6 MUTATED    33   3
  MSH6 WILD-TYPE 342  62
[1] "tbl2"
                cls
clus             [,1] [,2]
  MSH6 MUTATED     33    3
  MSH6 WILD-TYPE  342   62
   clus
vv  MSH6 MUTATED MSH6 WILD-TYPE
  0           33            342
  1            3             62
[1] 2 2
[1] FALSE
D256V8, binary
                cls
clus               0   1
  MSH6 MUTATED    23  22
  MSH6 WILD-TYPE 202 242
[1] "tbl2"
                cls
clus             [,1] [,2]
  MSH6 MUTATED     23   22
  MSH6 WILD-TYPE  202  242
        clus
vv       MSH6 MUTATED MSH6 WILD-TYPE
  FEMALE           23            202
  MALE             22            242
[1] 2 2
[1] FALSE
D256V9, binary
                cls
clus               0   1
  MSH6 MUTATED    33   1
  MSH6 WILD-TYPE 317  21
[1] "tbl2"
                cls
clus             [,1] [,2]
  MSH6 MUTATED     33    1
  MSH6 WILD-TYPE  317   21
     clus
vv    MSH6 MUTATED MSH6 WILD-TYPE
  NO            33            317
  YES            1             21
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MSH6 MUTATED                     30                             8
  MSH6 WILD-TYPE                  285                            39
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MSH6 MUTATED                       6                              0
  MSH6 WILD-TYPE                   100                             10
D256V10, multiclass
                                clus
vv                               MSH6 MUTATED MSH6 WILD-TYPE
  COLON ADENOCARCINOMA                     30            285
  COLON MUCINOUS ADENOCARCINOMA             8             39
  RECTAL ADENOCARCINOMA                     6            100
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  MSH6 MUTATED    27   1   0   5
  MSH6 WILD-TYPE 318   3  31  20
D256V11, multiclass
    clus
vv   MSH6 MUTATED MSH6 WILD-TYPE
  R0           27            318
  R1            1              3
  R2            0             31
  RX            5             20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D256V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MSH6 MUTATED                                  0     2
  MSH6 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  MSH6 MUTATED                           4    25
  MSH6 WILD-TYPE                        18   201
D256V13, multiclass
                                  clus
vv                                 MSH6 MUTATED MSH6 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              9
  BLACK OR AFRICAN AMERICAN                   4             18
  WHITE                                      25            201
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(257) Variable = MMP8 MUTATION ANALYSIS
D257V1, survival
                sevent
clus2              0   1
  MMP8 MUTATED    10   3
  MMP8 WILD-TYPE 368  90
  MMP8 MUTATED MMP8 WILD-TYPE 
            13            458 
  MMP8 MUTATED MMP8 WILD-TYPE 
             3             90 
$`MMP8 MUTATED`
TCGA-A6-5664 TCGA-A6-6780 TCGA-AA-3510 TCGA-AA-A010 TCGA-AZ-5403 TCGA-AZ-6598 
       22.09        20.12        63.98        34.98        62.79        49.41 
TCGA-CA-5254 TCGA-CK-5913 TCGA-CK-5914 TCGA-CM-4746 TCGA-CM-6168 TCGA-F4-6570 
       12.69        51.32         9.99        37.02        12.99         6.18 
TCGA-DY-A0XA 
      126.44 

$`MMP8 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       88.21         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
       11.74         3.19         1.61         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5916 TCGA-CK-6747 
      148.01        85.45        15.62        49.08        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4752 
        1.91       124.27        23.05        20.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6169 
        2.96        29.03        16.04        21.99        14.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
        8.61        31.96        35.74        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
        5.29        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  MMP8 MUTATED MMP8 WILD-TYPE 
          6.18           0.00 
  MMP8 MUTATED MMP8 WILD-TYPE 
        126.44         148.01 
  MMP8 MUTATED MMP8 WILD-TYPE 
        34.980         20.035 
[1] "6.2 - 126.4 (35.0)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.3"
D257V2, continuous
D257V3, binary
                cls
clus               0   1
  MMP8 MUTATED    12   1
  MMP8 WILD-TYPE 354 118
[1] "tbl2"
                cls
clus             [,1] [,2]
  MMP8 MUTATED     12    1
  MMP8 WILD-TYPE  354  118
        clus
vv       MMP8 MUTATED MMP8 WILD-TYPE
  COLON            12            354
  RECTUM            1            118
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MMP8 MUTATED         1        0        3         6         1         0
  MMP8 WILD-TYPE      90        1       29       132         9         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MMP8 MUTATED           0          0          1          1        0         0
  MMP8 WILD-TYPE        24         11         58         41       48        18
                vv
clus             STAGE IVB
  MMP8 MUTATED           0
  MMP8 WILD-TYPE         1
D257V4, multiclass
            clus
vv           MMP8 MUTATED MMP8 WILD-TYPE
  STAGE I               1             90
  STAGE IA              0              1
  STAGE II              3             29
  STAGE IIA             6            132
  STAGE IIB             1              9
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            1             58
  STAGE IIIC            1             41
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  MMP8 MUTATED     0   1  10   2
  MMP8 WILD-TYPE  17  91 319  48
D257V5, multiclass
    clus
vv   MMP8 MUTATED MMP8 WILD-TYPE
  T1            0             17
  T2            1             91
  T3           10            319
  T4            2             48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  MMP8 MUTATED    11   1   1
  MMP8 WILD-TYPE 276 112  86
D257V6, multiclass
    clus
vv   MMP8 MUTATED MMP8 WILD-TYPE
  N0           11            276
  N1            1            112
  N2            1             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D257V7, binary
                cls
clus               0   1
  MMP8 MUTATED     7   0
  MMP8 WILD-TYPE 368  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  MMP8 MUTATED      7    0
  MMP8 WILD-TYPE  368   65
   clus
vv  MMP8 MUTATED MMP8 WILD-TYPE
  0            7            368
  1            0             65
[1] 2 2
[1] FALSE
D257V8, binary
                cls
clus               0   1
  MMP8 MUTATED     7   6
  MMP8 WILD-TYPE 218 258
[1] "tbl2"
                cls
clus             [,1] [,2]
  MMP8 MUTATED      7    6
  MMP8 WILD-TYPE  218  258
        clus
vv       MMP8 MUTATED MMP8 WILD-TYPE
  FEMALE            7            218
  MALE              6            258
[1] 2 2
[1] FALSE
D257V9, binary
                cls
clus               0   1
  MMP8 MUTATED    11   0
  MMP8 WILD-TYPE 339  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  MMP8 MUTATED     11    0
  MMP8 WILD-TYPE  339   22
     clus
vv    MMP8 MUTATED MMP8 WILD-TYPE
  NO            11            339
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MMP8 MUTATED                     11                             1
  MMP8 WILD-TYPE                  304                            46
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MMP8 MUTATED                       1                              0
  MMP8 WILD-TYPE                   105                             10
D257V10, multiclass
                                clus
vv                               MMP8 MUTATED MMP8 WILD-TYPE
  COLON ADENOCARCINOMA                     11            304
  COLON MUCINOUS ADENOCARCINOMA             1             46
  RECTAL ADENOCARCINOMA                     1            105
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  MMP8 MUTATED     5   0   0   3
  MMP8 WILD-TYPE 340   4  31  22
D257V11, multiclass
    clus
vv   MMP8 MUTATED MMP8 WILD-TYPE
  R0            5            340
  R1            0              4
  R2            0             31
  RX            3             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D257V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MMP8 MUTATED                                  0     1
  MMP8 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  MMP8 MUTATED                           3     7
  MMP8 WILD-TYPE                        19   219
D257V13, multiclass
                                  clus
vv                                 MMP8 MUTATED MMP8 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   3             19
  WHITE                                       7            219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(258) Variable = RAG1AP1 MUTATION ANALYSIS
D258V1, survival
                   sevent
clus2                 0   1
  RAG1AP1 MUTATED     5   1
  RAG1AP1 WILD-TYPE 373  92
  RAG1AP1 MUTATED RAG1AP1 WILD-TYPE 
                6               465 
  RAG1AP1 MUTATED RAG1AP1 WILD-TYPE 
                1                92 
$`RAG1AP1 MUTATED`
TCGA-A6-5661 TCGA-A6-6653 TCGA-AA-3660 TCGA-AA-3815 TCGA-AU-6004 TCGA-G4-6303 
       33.53        24.39        78.08        33.04        27.09        65.85 

$`RAG1AP1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 
       25.18        24.16        21.76        24.69        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       13.94        19.99        61.02         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       14.50        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6304 TCGA-G4-6306 
       47.41        35.31       133.18        74.56        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  RAG1AP1 MUTATED RAG1AP1 WILD-TYPE 
            24.39              0.00 
  RAG1AP1 MUTATED RAG1AP1 WILD-TYPE 
            78.08            148.01 
  RAG1AP1 MUTATED RAG1AP1 WILD-TYPE 
           33.285            20.020 
[1] "24.4 - 78.1 (33.3)" "0.0 - 148.0 (20.0)"
[1] "hr=" "2"  
D258V2, continuous
D258V3, binary
                   cls
clus                  0   1
  RAG1AP1 MUTATED     6   0
  RAG1AP1 WILD-TYPE 360 119
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RAG1AP1 MUTATED      6    0
  RAG1AP1 WILD-TYPE  360  119
        clus
vv       RAG1AP1 MUTATED RAG1AP1 WILD-TYPE
  COLON                6               360
  RECTUM               0               119
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RAG1AP1 MUTATED         2        0        1         2         0         0
  RAG1AP1 WILD-TYPE      89        1       31       136        10         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RAG1AP1 MUTATED           0          0          0          0        1
  RAG1AP1 WILD-TYPE        24         11         59         42       47
                   vv
clus                STAGE IVA STAGE IVB
  RAG1AP1 MUTATED           0         0
  RAG1AP1 WILD-TYPE        18         1
D258V4, multiclass
            clus
vv           RAG1AP1 MUTATED RAG1AP1 WILD-TYPE
  STAGE I                  2                89
  STAGE IA                 0                 1
  STAGE II                 1                31
  STAGE IIA                2               136
  STAGE IIB                0                10
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               0                11
  STAGE IIIB               0                59
  STAGE IIIC               0                42
  STAGE IV                 1                47
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  RAG1AP1 MUTATED     0   2   4   0
  RAG1AP1 WILD-TYPE  17  90 325  50
D258V5, multiclass
    clus
vv   RAG1AP1 MUTATED RAG1AP1 WILD-TYPE
  T1               0                17
  T2               2                90
  T3               4               325
  T4               0                50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  RAG1AP1 MUTATED     5   1   0
  RAG1AP1 WILD-TYPE 282 112  87
D258V6, multiclass
    clus
vv   RAG1AP1 MUTATED RAG1AP1 WILD-TYPE
  N0               5               282
  N1               1               112
  N2               0                87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D258V7, binary
                   cls
clus                  0   1
  RAG1AP1 MUTATED     5   1
  RAG1AP1 WILD-TYPE 370  64
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RAG1AP1 MUTATED      5    1
  RAG1AP1 WILD-TYPE  370   64
   clus
vv  RAG1AP1 MUTATED RAG1AP1 WILD-TYPE
  0               5               370
  1               1                64
[1] 2 2
[1] FALSE
D258V8, binary
                   cls
clus                  0   1
  RAG1AP1 MUTATED     5   1
  RAG1AP1 WILD-TYPE 220 263
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RAG1AP1 MUTATED      5    1
  RAG1AP1 WILD-TYPE  220  263
        clus
vv       RAG1AP1 MUTATED RAG1AP1 WILD-TYPE
  FEMALE               5               220
  MALE                 1               263
[1] 2 2
[1] FALSE
D258V9, binary
                   cls
clus                  0   1
  RAG1AP1 MUTATED     5   0
  RAG1AP1 WILD-TYPE 345  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RAG1AP1 MUTATED      5    0
  RAG1AP1 WILD-TYPE  345   22
     clus
vv    RAG1AP1 MUTATED RAG1AP1 WILD-TYPE
  NO                5               345
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  RAG1AP1 MUTATED                      6                             0
  RAG1AP1 WILD-TYPE                  309                            47
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  RAG1AP1 MUTATED                       0                              0
  RAG1AP1 WILD-TYPE                   106                             10
D258V10, multiclass
                                clus
vv                               RAG1AP1 MUTATED RAG1AP1 WILD-TYPE
  COLON ADENOCARCINOMA                         6               309
  COLON MUCINOUS ADENOCARCINOMA                0                47
  RECTAL ADENOCARCINOMA                        0               106
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  RAG1AP1 MUTATED     5   0   0   0
  RAG1AP1 WILD-TYPE 340   4  31  25
D258V11, multiclass
    clus
vv   RAG1AP1 MUTATED RAG1AP1 WILD-TYPE
  R0               5               340
  R1               0                 4
  R2               0                31
  RX               0                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D258V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RAG1AP1 MUTATED                                  0     0
  RAG1AP1 WILD-TYPE                                1    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  RAG1AP1 MUTATED                           1     3
  RAG1AP1 WILD-TYPE                        21   223
D258V13, multiclass
                                  clus
vv                                 RAG1AP1 MUTATED RAG1AP1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                      1                21
  WHITE                                          3               223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(259) Variable = ALX4 MUTATION ANALYSIS
D259V1, survival
                sevent
clus2              0   1
  ALX4 MUTATED    10   2
  ALX4 WILD-TYPE 368  91
  ALX4 MUTATED ALX4 WILD-TYPE 
            12            459 
  ALX4 MUTATED ALX4 WILD-TYPE 
             2             91 
$`ALX4 MUTATED`
TCGA-A6-6653 TCGA-AA-3713 TCGA-AA-3949 TCGA-AY-6197 TCGA-AZ-6598 TCGA-AZ-6601 
       24.39        19.04        26.01        21.44        49.41       100.01 
TCGA-CM-5861 TCGA-CM-6170 TCGA-D5-6540 TCGA-D5-6927 TCGA-G4-6588 TCGA-CI-6624 
       15.02        15.02        16.14         9.44        26.17         4.73 

$`ALX4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
       25.08        25.18        24.16        21.76        24.69        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       12.99        24.00        33.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 
       62.79        88.21         6.77        12.10        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       22.98        30.08        32.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6171 TCGA-CM-6172 
       21.99        14.99        12.99        13.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
        4.80        17.13        12.49        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6929 
        4.41        12.43        14.30         9.04        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        35.80        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        6.97        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  ALX4 MUTATED ALX4 WILD-TYPE 
          4.73           0.00 
  ALX4 MUTATED ALX4 WILD-TYPE 
        100.01         148.01 
  ALX4 MUTATED ALX4 WILD-TYPE 
         20.24          20.19 
[1] "4.7 - 100.0 (20.2)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.3"
D259V2, continuous
D259V3, binary
                cls
clus               0   1
  ALX4 MUTATED    11   1
  ALX4 WILD-TYPE 355 118
[1] "tbl2"
                cls
clus             [,1] [,2]
  ALX4 MUTATED     11    1
  ALX4 WILD-TYPE  355  118
        clus
vv       ALX4 MUTATED ALX4 WILD-TYPE
  COLON            11            355
  RECTUM            1            118
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ALX4 MUTATED         4        0        2         4         0         0
  ALX4 WILD-TYPE      87        1       30       134        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ALX4 MUTATED           0          0          1          0        1         0
  ALX4 WILD-TYPE        24         11         58         42       47        18
                vv
clus             STAGE IVB
  ALX4 MUTATED           0
  ALX4 WILD-TYPE         1
D259V4, multiclass
            clus
vv           ALX4 MUTATED ALX4 WILD-TYPE
  STAGE I               4             87
  STAGE IA              0              1
  STAGE II              2             30
  STAGE IIA             4            134
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            1             58
  STAGE IIIC            0             42
  STAGE IV              1             47
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  ALX4 MUTATED     0   4   8   0
  ALX4 WILD-TYPE  17  88 321  50
D259V5, multiclass
    clus
vv   ALX4 MUTATED ALX4 WILD-TYPE
  T1            0             17
  T2            4             88
  T3            8            321
  T4            0             50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  ALX4 MUTATED    11   1   0
  ALX4 WILD-TYPE 276 112  87
D259V6, multiclass
    clus
vv   ALX4 MUTATED ALX4 WILD-TYPE
  N0           11            276
  N1            1            112
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D259V7, binary
                cls
clus               0   1
  ALX4 MUTATED     9   1
  ALX4 WILD-TYPE 366  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  ALX4 MUTATED      9    1
  ALX4 WILD-TYPE  366   64
   clus
vv  ALX4 MUTATED ALX4 WILD-TYPE
  0            9            366
  1            1             64
[1] 2 2
[1] FALSE
D259V8, binary
                cls
clus               0   1
  ALX4 MUTATED     6   6
  ALX4 WILD-TYPE 219 258
[1] "tbl2"
                cls
clus             [,1] [,2]
  ALX4 MUTATED      6    6
  ALX4 WILD-TYPE  219  258
        clus
vv       ALX4 MUTATED ALX4 WILD-TYPE
  FEMALE            6            219
  MALE              6            258
[1] 2 2
[1] FALSE
D259V9, binary
                cls
clus               0   1
  ALX4 MUTATED    10   1
  ALX4 WILD-TYPE 340  21
[1] "tbl2"
                cls
clus             [,1] [,2]
  ALX4 MUTATED     10    1
  ALX4 WILD-TYPE  340   21
     clus
vv    ALX4 MUTATED ALX4 WILD-TYPE
  NO            10            340
  YES            1             21
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ALX4 MUTATED                      9                             2
  ALX4 WILD-TYPE                  306                            45
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ALX4 MUTATED                       1                              0
  ALX4 WILD-TYPE                   105                             10
D259V10, multiclass
                                clus
vv                               ALX4 MUTATED ALX4 WILD-TYPE
  COLON ADENOCARCINOMA                      9            306
  COLON MUCINOUS ADENOCARCINOMA             2             45
  RECTAL ADENOCARCINOMA                     1            105
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  ALX4 MUTATED     7   0   1   0
  ALX4 WILD-TYPE 338   4  30  25
D259V11, multiclass
    clus
vv   ALX4 MUTATED ALX4 WILD-TYPE
  R0            7            338
  R1            0              4
  R2            1             30
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D259V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ALX4 MUTATED                                  0     0
  ALX4 WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  ALX4 MUTATED                           0    10
  ALX4 WILD-TYPE                        22   216
D259V13, multiclass
                                  clus
vv                                 ALX4 MUTATED ALX4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                      10            216
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(260) Variable = OR51E1 MUTATION ANALYSIS
D260V1, survival
                  sevent
clus2                0   1
  OR51E1 MUTATED    11   4
  OR51E1 WILD-TYPE 367  89
  OR51E1 MUTATED OR51E1 WILD-TYPE 
              15              456 
  OR51E1 MUTATED OR51E1 WILD-TYPE 
               4               89 
$`OR51E1 MUTATED`
TCGA-A6-5665 TCGA-AA-3492 TCGA-AA-3866 TCGA-AA-3950 TCGA-AY-6197 TCGA-CK-5913 
       22.06         3.02        17.03        24.00        21.44        51.32 
TCGA-CM-5348 TCGA-CM-5862 TCGA-CM-6164 TCGA-DM-A1D7 TCGA-DM-A1HB TCGA-DM-A28F 
       22.98         5.03        29.03        13.32       135.65        35.97 
TCGA-G4-6299 TCGA-AG-A002 TCGA-G5-6235 
       74.56        20.98        55.76 

$`OR51E1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 
       20.12        19.66        20.28         7.04         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3867 
        0.99        31.07        31.07        30.05        53.00        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        33.01        26.01         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 
       14.50        27.09        16.31         0.95        33.01        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       30.08        32.02        15.02        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       15.02        12.00         2.96        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D8 
       24.43        38.20       130.65        92.75        49.91        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 
      140.38         7.50        44.32       131.51       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
       81.37       119.93        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
       35.31       133.18        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6641 
       31.30        28.57        32.19         0.66         0.69        26.43 

  OR51E1 MUTATED OR51E1 WILD-TYPE 
            3.02             0.00 
  OR51E1 MUTATED OR51E1 WILD-TYPE 
          135.65           148.01 
  OR51E1 MUTATED OR51E1 WILD-TYPE 
           22.98            20.02 
[1] "3.0 - 135.7 (23.0)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.1"
D260V2, continuous
D260V3, binary
                  cls
clus                 0   1
  OR51E1 MUTATED    13   2
  OR51E1 WILD-TYPE 353 117
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR51E1 MUTATED     13    2
  OR51E1 WILD-TYPE  353  117
        clus
vv       OR51E1 MUTATED OR51E1 WILD-TYPE
  COLON              13              353
  RECTUM              2              117
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  OR51E1 MUTATED         2        0        1         6         0         0
  OR51E1 WILD-TYPE      89        1       31       132        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  OR51E1 MUTATED           0          0          4          1        0
  OR51E1 WILD-TYPE        24         11         55         41       48
                  vv
clus               STAGE IVA STAGE IVB
  OR51E1 MUTATED           1         0
  OR51E1 WILD-TYPE        17         1
D260V4, multiclass
            clus
vv           OR51E1 MUTATED OR51E1 WILD-TYPE
  STAGE I                 2               89
  STAGE IA                0                1
  STAGE II                1               31
  STAGE IIA               6              132
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              4               55
  STAGE IIIC              1               41
  STAGE IV                0               48
  STAGE IVA               1               17
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  OR51E1 MUTATED     0   2  13   0
  OR51E1 WILD-TYPE  17  90 316  50
D260V5, multiclass
    clus
vv   OR51E1 MUTATED OR51E1 WILD-TYPE
  T1              0               17
  T2              2               90
  T3             13              316
  T4              0               50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  OR51E1 MUTATED     9   5   1
  OR51E1 WILD-TYPE 278 108  86
D260V6, multiclass
    clus
vv   OR51E1 MUTATED OR51E1 WILD-TYPE
  N0              9              278
  N1              5              108
  N2              1               86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D260V7, binary
                  cls
clus                 0   1
  OR51E1 MUTATED    11   1
  OR51E1 WILD-TYPE 364  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR51E1 MUTATED     11    1
  OR51E1 WILD-TYPE  364   64
   clus
vv  OR51E1 MUTATED OR51E1 WILD-TYPE
  0             11              364
  1              1               64
[1] 2 2
[1] FALSE
D260V8, binary
                  cls
clus                 0   1
  OR51E1 MUTATED     6   9
  OR51E1 WILD-TYPE 219 255
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR51E1 MUTATED      6    9
  OR51E1 WILD-TYPE  219  255
        clus
vv       OR51E1 MUTATED OR51E1 WILD-TYPE
  FEMALE              6              219
  MALE                9              255
[1] 2 2
[1] FALSE
D260V9, binary
                  cls
clus                 0   1
  OR51E1 MUTATED    12   0
  OR51E1 WILD-TYPE 338  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR51E1 MUTATED     12    0
  OR51E1 WILD-TYPE  338   22
     clus
vv    OR51E1 MUTATED OR51E1 WILD-TYPE
  NO              12              338
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  OR51E1 MUTATED                     10                             1
  OR51E1 WILD-TYPE                  305                            46
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  OR51E1 MUTATED                       2                              0
  OR51E1 WILD-TYPE                   104                             10
D260V10, multiclass
                                clus
vv                               OR51E1 MUTATED OR51E1 WILD-TYPE
  COLON ADENOCARCINOMA                       10              305
  COLON MUCINOUS ADENOCARCINOMA               1               46
  RECTAL ADENOCARCINOMA                       2              104
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  OR51E1 MUTATED    10   1   0   1
  OR51E1 WILD-TYPE 335   3  31  24
D260V11, multiclass
    clus
vv   OR51E1 MUTATED OR51E1 WILD-TYPE
  R0             10              335
  R1              1                3
  R2              0               31
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D260V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OR51E1 MUTATED                                  0     0
  OR51E1 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  OR51E1 MUTATED                           0    11
  OR51E1 WILD-TYPE                        22   215
D260V13, multiclass
                                  clus
vv                                 OR51E1 MUTATED OR51E1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                        11              215
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(261) Variable = CBL MUTATION ANALYSIS
D261V1, survival
               sevent
clus2             0   1
  CBL MUTATED    32   7
  CBL WILD-TYPE 346  86
  CBL MUTATED CBL WILD-TYPE 
           39           432 
  CBL MUTATED CBL WILD-TYPE 
            7            86 
$`CBL MUTATED`
TCGA-A6-5657 TCGA-A6-5662 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3518 TCGA-AA-3662 
       31.63        23.61        63.98         6.97         1.02         6.05 
TCGA-AA-3968 TCGA-AA-A010 TCGA-AD-5900 TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4315 
       21.99        34.98         0.07        33.01        17.82        58.39 
TCGA-AZ-5407 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6608 TCGA-CA-6718 
       88.21        12.10       100.01        29.56         1.61        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CM-4743 TCGA-CM-4752 TCGA-CM-5862 TCGA-CM-6164 
       14.30        17.56        23.05        13.02         5.03        29.03 
TCGA-CM-6172 TCGA-CM-6676 TCGA-D5-6533 TCGA-D5-6923 TCGA-DM-A1DB TCGA-DM-A28E 
       11.01        11.08         1.32        12.43        44.32       119.93 
TCGA-DM-A28K TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6628 TCGA-AF-2687 TCGA-AG-3742 
       98.24        85.48        63.62        79.69        24.13         0.99 
TCGA-AG-A002 TCGA-DY-A0XA TCGA-EF-5830 
       20.98       126.44         0.49 

$`CBL WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5664 TCGA-A6-5665 
       32.91        30.44        29.19        33.53        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
        1.02        13.02        38.99         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       36.03         8.05        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
       78.08         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3971 
       24.00         2.01        20.98        34.03         2.01        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       39.98        18.05        40.96        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6197 
        0.20        14.50        27.09        16.31         0.95        21.44 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6598 
        1.41         5.13       106.75        22.36        62.79        49.41 
TCGA-AZ-6599 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 
        6.77         5.23        11.74         3.19        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CK-4948 
        3.25         3.29         0.07        12.20        12.76       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
       82.95         1.91       124.27        20.02        37.02        25.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       14.04        12.95        13.05        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       20.19        18.25        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
        4.41        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
      140.38         7.50       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-F4-6459 TCGA-F4-6460 
       81.37        35.97        60.79       117.07         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       91.79        46.75        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
       32.98         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EI-6506 
       41.36        57.24        24.13        51.48        32.61        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  CBL MUTATED CBL WILD-TYPE 
         0.07          0.00 
  CBL MUTATED CBL WILD-TYPE 
       126.44        148.01 
  CBL MUTATED CBL WILD-TYPE 
       21.990        20.085 
[1] "0.1 - 126.4 (22.0)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.4"
D261V2, continuous
D261V3, binary
               cls
clus              0   1
  CBL MUTATED    34   5
  CBL WILD-TYPE 332 114
[1] "tbl2"
               cls
clus            [,1] [,2]
  CBL MUTATED     34    5
  CBL WILD-TYPE  332  114
        clus
vv       CBL MUTATED CBL WILD-TYPE
  COLON           34           332
  RECTUM           5           114
[1] 2 2
[1] FALSE
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CBL MUTATED         8        0        3        11         2         0
  CBL WILD-TYPE      83        1       29       127         8         1
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CBL MUTATED           0          1          7          1        2         3
  CBL WILD-TYPE        24         10         52         41       46        15
               vv
clus            STAGE IVB
  CBL MUTATED           0
  CBL WILD-TYPE         1
D261V4, multiclass
            clus
vv           CBL MUTATED CBL WILD-TYPE
  STAGE I              8            83
  STAGE IA             0             1
  STAGE II             3            29
  STAGE IIA           11           127
  STAGE IIB            2             8
  STAGE IIC            0             1
  STAGE III            0            24
  STAGE IIIA           1            10
  STAGE IIIB           7            52
  STAGE IIIC           1            41
  STAGE IV             2            46
  STAGE IVA            3            15
  STAGE IVB            0             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  CBL MUTATED     2   8  22   7
  CBL WILD-TYPE  15  84 307  43
D261V5, multiclass
    clus
vv   CBL MUTATED CBL WILD-TYPE
  T1           2            15
  T2           8            84
  T3          22           307
  T4           7            43
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2
  CBL MUTATED    25  11   3
  CBL WILD-TYPE 262 102  84
D261V6, multiclass
    clus
vv   CBL MUTATED CBL WILD-TYPE
  N0          25           262
  N1          11           102
  N2           3            84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D261V7, binary
               cls
clus              0   1
  CBL MUTATED    32   5
  CBL WILD-TYPE 343  60
[1] "tbl2"
               cls
clus            [,1] [,2]
  CBL MUTATED     32    5
  CBL WILD-TYPE  343   60
   clus
vv  CBL MUTATED CBL WILD-TYPE
  0          32           343
  1           5            60
[1] 2 2
[1] FALSE
D261V8, binary
               cls
clus              0   1
  CBL MUTATED    17  22
  CBL WILD-TYPE 208 242
[1] "tbl2"
               cls
clus            [,1] [,2]
  CBL MUTATED     17   22
  CBL WILD-TYPE  208  242
        clus
vv       CBL MUTATED CBL WILD-TYPE
  FEMALE          17           208
  MALE            22           242
[1] 2 2
[1] FALSE
D261V9, binary
               cls
clus              0   1
  CBL MUTATED    27   2
  CBL WILD-TYPE 323  20
[1] "tbl2"
               cls
clus            [,1] [,2]
  CBL MUTATED     27    2
  CBL WILD-TYPE  323   20
     clus
vv    CBL MUTATED CBL WILD-TYPE
  NO           27           323
  YES           2            20
[1] 2 2
[1] FALSE
               vv
clus            COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CBL MUTATED                     32                             2
  CBL WILD-TYPE                  283                            45
               vv
clus            RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CBL MUTATED                       5                              0
  CBL WILD-TYPE                   101                             10
D261V10, multiclass
                                clus
vv                               CBL MUTATED CBL WILD-TYPE
  COLON ADENOCARCINOMA                    32           283
  COLON MUCINOUS ADENOCARCINOMA            2            45
  RECTAL ADENOCARCINOMA                    5           101
  RECTAL MUCINOUS ADENOCARCINOMA           0            10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             R0  R1  R2  RX
  CBL MUTATED    25   0   1   3
  CBL WILD-TYPE 320   4  30  22
D261V11, multiclass
    clus
vv   CBL MUTATED CBL WILD-TYPE
  R0          25           320
  R1           0             4
  R2           1            30
  RX           3            22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D261V12, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CBL MUTATED                                  0     2
  CBL WILD-TYPE                                1     9
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  CBL MUTATED                           6    23
  CBL WILD-TYPE                        16   203
D261V13, multiclass
                                  clus
vv                                 CBL MUTATED CBL WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      2             9
  BLACK OR AFRICAN AMERICAN                  6            16
  WHITE                                     23           203
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(262) Variable = SLC28A2 MUTATION ANALYSIS
D262V1, survival
                   sevent
clus2                 0   1
  SLC28A2 MUTATED    12   1
  SLC28A2 WILD-TYPE 366  92
  SLC28A2 MUTATED SLC28A2 WILD-TYPE 
               13               458 
  SLC28A2 MUTATED SLC28A2 WILD-TYPE 
                1                92 
$`SLC28A2 MUTATED`
TCGA-AA-3655 TCGA-AA-3672 TCGA-AA-A02F TCGA-AZ-6601 TCGA-CA-6717 TCGA-CK-4950 
       61.02         0.92        39.98       100.01        12.76        85.45 
TCGA-CM-6168 TCGA-CM-6674 TCGA-D5-5538 TCGA-G4-6293 TCGA-G4-6588 TCGA-DC-6681 
       12.99        12.95        12.26       133.18        26.17         5.95 
TCGA-DY-A0XA 
      126.44 

$`SLC28A2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 
       20.98        19.99        13.94        19.99        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 
        6.97        54.02         2.01        14.01        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07        12.20        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       14.30        17.56       148.01        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       16.04        21.99        14.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       11.01        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       12.03        45.40        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6303 
       13.25         0.53        47.41        35.31        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        35.80        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6682 TCGA-DC-6683 
       13.97        27.95        10.98        19.99         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
        5.29        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  SLC28A2 MUTATED SLC28A2 WILD-TYPE 
             0.92              0.00 
  SLC28A2 MUTATED SLC28A2 WILD-TYPE 
           133.18            148.01 
  SLC28A2 MUTATED SLC28A2 WILD-TYPE 
           26.170            20.155 
[1] "0.9 - 133.2 (26.2)" "0.0 - 148.0 (20.2)"
[1] "hr=" "4.6"
D262V2, continuous
D262V3, binary
                   cls
clus                  0   1
  SLC28A2 MUTATED    13   2
  SLC28A2 WILD-TYPE 353 117
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC28A2 MUTATED     13    2
  SLC28A2 WILD-TYPE  353  117
        clus
vv       SLC28A2 MUTATED SLC28A2 WILD-TYPE
  COLON               13               353
  RECTUM               2               117
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SLC28A2 MUTATED         0        0        2         5         1         0
  SLC28A2 WILD-TYPE      91        1       30       133         9         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC28A2 MUTATED           3          0          2          0        1
  SLC28A2 WILD-TYPE        21         11         57         42       47
                   vv
clus                STAGE IVA STAGE IVB
  SLC28A2 MUTATED           1         0
  SLC28A2 WILD-TYPE        17         1
D262V4, multiclass
            clus
vv           SLC28A2 MUTATED SLC28A2 WILD-TYPE
  STAGE I                  0                91
  STAGE IA                 0                 1
  STAGE II                 2                30
  STAGE IIA                5               133
  STAGE IIB                1                 9
  STAGE IIC                0                 1
  STAGE III                3                21
  STAGE IIIA               0                11
  STAGE IIIB               2                57
  STAGE IIIC               0                42
  STAGE IV                 1                47
  STAGE IVA                1                17
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  SLC28A2 MUTATED     0   0  14   1
  SLC28A2 WILD-TYPE  17  92 315  49
D262V5, multiclass
    clus
vv   SLC28A2 MUTATED SLC28A2 WILD-TYPE
  T1               0                17
  T2               0                92
  T3              14               315
  T4               1                49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  SLC28A2 MUTATED     8   5   2
  SLC28A2 WILD-TYPE 279 108  85
D262V6, multiclass
    clus
vv   SLC28A2 MUTATED SLC28A2 WILD-TYPE
  N0               8               279
  N1               5               108
  N2               2                85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D262V7, binary
                   cls
clus                  0   1
  SLC28A2 MUTATED    12   2
  SLC28A2 WILD-TYPE 363  63
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC28A2 MUTATED     12    2
  SLC28A2 WILD-TYPE  363   63
   clus
vv  SLC28A2 MUTATED SLC28A2 WILD-TYPE
  0              12               363
  1               2                63
[1] 2 2
[1] FALSE
D262V8, binary
                   cls
clus                  0   1
  SLC28A2 MUTATED    10   5
  SLC28A2 WILD-TYPE 215 259
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC28A2 MUTATED     10    5
  SLC28A2 WILD-TYPE  215  259
        clus
vv       SLC28A2 MUTATED SLC28A2 WILD-TYPE
  FEMALE              10               215
  MALE                 5               259
[1] 2 2
[1] FALSE
D262V9, binary
                   cls
clus                  0   1
  SLC28A2 MUTATED    11   0
  SLC28A2 WILD-TYPE 339  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC28A2 MUTATED     11    0
  SLC28A2 WILD-TYPE  339   22
     clus
vv    SLC28A2 MUTATED SLC28A2 WILD-TYPE
  NO               11               339
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SLC28A2 MUTATED                     12                             1
  SLC28A2 WILD-TYPE                  303                            46
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SLC28A2 MUTATED                       2                              0
  SLC28A2 WILD-TYPE                   104                             10
D262V10, multiclass
                                clus
vv                               SLC28A2 MUTATED SLC28A2 WILD-TYPE
  COLON ADENOCARCINOMA                        12               303
  COLON MUCINOUS ADENOCARCINOMA                1                46
  RECTAL ADENOCARCINOMA                        2               104
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  SLC28A2 MUTATED     9   1   1   2
  SLC28A2 WILD-TYPE 336   3  30  23
D262V11, multiclass
    clus
vv   SLC28A2 MUTATED SLC28A2 WILD-TYPE
  R0               9               336
  R1               1                 3
  R2               1                30
  RX               2                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D262V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SLC28A2 MUTATED                                  0     1
  SLC28A2 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  SLC28A2 MUTATED                           2     8
  SLC28A2 WILD-TYPE                        20   218
D262V13, multiclass
                                  clus
vv                                 SLC28A2 MUTATED SLC28A2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                10
  BLACK OR AFRICAN AMERICAN                      2                20
  WHITE                                          8               218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(263) Variable = ZNF222 MUTATION ANALYSIS
D263V1, survival
                  sevent
clus2                0   1
  ZNF222 MUTATED     7   2
  ZNF222 WILD-TYPE 371  91
  ZNF222 MUTATED ZNF222 WILD-TYPE 
               9              462 
  ZNF222 MUTATED ZNF222 WILD-TYPE 
               2               91 
$`ZNF222 MUTATED`
TCGA-A6-4105 TCGA-A6-5657 TCGA-AA-A010 TCGA-CM-4743 TCGA-G4-6321 TCGA-G4-6588 
       14.53        31.63        34.98        23.05        22.09        26.17 
TCGA-AG-A002 TCGA-AG-A00Y TCGA-DY-A1DD 
       20.98        23.01        57.24 

$`ZNF222 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 
       16.57        34.65        33.34        32.75        36.53        32.91 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       30.44        29.19        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
        1.91       124.27        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       36.00        13.78        35.80        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A011 
        1.02        17.03        13.94         6.02        25.97        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       41.36        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  ZNF222 MUTATED ZNF222 WILD-TYPE 
           14.53             0.00 
  ZNF222 MUTATED ZNF222 WILD-TYPE 
           57.24           148.01 
  ZNF222 MUTATED ZNF222 WILD-TYPE 
           23.05            20.02 
[1] "14.5 - 57.2 (23.1)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.1"
D263V2, continuous
D263V3, binary
                  cls
clus                 0   1
  ZNF222 MUTATED     8   3
  ZNF222 WILD-TYPE 358 116
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF222 MUTATED      8    3
  ZNF222 WILD-TYPE  358  116
        clus
vv       ZNF222 MUTATED ZNF222 WILD-TYPE
  COLON               8              358
  RECTUM              3              116
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZNF222 MUTATED         1        0        0         5         2         0
  ZNF222 WILD-TYPE      90        1       32       133         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF222 MUTATED           1          0          2          0        0
  ZNF222 WILD-TYPE        23         11         57         42       48
                  vv
clus               STAGE IVA STAGE IVB
  ZNF222 MUTATED           0         0
  ZNF222 WILD-TYPE        18         1
D263V4, multiclass
            clus
vv           ZNF222 MUTATED ZNF222 WILD-TYPE
  STAGE I                 1               90
  STAGE IA                0                1
  STAGE II                0               32
  STAGE IIA               5              133
  STAGE IIB               2                8
  STAGE IIC               0                1
  STAGE III               1               23
  STAGE IIIA              0               11
  STAGE IIIB              2               57
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZNF222 MUTATED     0   2   7   2
  ZNF222 WILD-TYPE  17  90 322  48
D263V5, multiclass
    clus
vv   ZNF222 MUTATED ZNF222 WILD-TYPE
  T1              0               17
  T2              2               90
  T3              7              322
  T4              2               48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  ZNF222 MUTATED     8   3   0
  ZNF222 WILD-TYPE 279 110  87
D263V6, multiclass
    clus
vv   ZNF222 MUTATED ZNF222 WILD-TYPE
  N0              8              279
  N1              3              110
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D263V7, binary
                  cls
clus                 0   1
  ZNF222 MUTATED     9   0
  ZNF222 WILD-TYPE 366  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF222 MUTATED      9    0
  ZNF222 WILD-TYPE  366   65
   clus
vv  ZNF222 MUTATED ZNF222 WILD-TYPE
  0              9              366
  1              0               65
[1] 2 2
[1] FALSE
D263V8, binary
                  cls
clus                 0   1
  ZNF222 MUTATED     6   5
  ZNF222 WILD-TYPE 219 259
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF222 MUTATED      6    5
  ZNF222 WILD-TYPE  219  259
        clus
vv       ZNF222 MUTATED ZNF222 WILD-TYPE
  FEMALE              6              219
  MALE                5              259
[1] 2 2
[1] FALSE
D263V9, binary
                  cls
clus                 0   1
  ZNF222 MUTATED     8   0
  ZNF222 WILD-TYPE 342  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF222 MUTATED      8    0
  ZNF222 WILD-TYPE  342   22
     clus
vv    ZNF222 MUTATED ZNF222 WILD-TYPE
  NO               8              342
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ZNF222 MUTATED                      8                             0
  ZNF222 WILD-TYPE                  307                            47
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ZNF222 MUTATED                       3                              0
  ZNF222 WILD-TYPE                   103                             10
D263V10, multiclass
                                clus
vv                               ZNF222 MUTATED ZNF222 WILD-TYPE
  COLON ADENOCARCINOMA                        8              307
  COLON MUCINOUS ADENOCARCINOMA               0               47
  RECTAL ADENOCARCINOMA                       3              103
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ZNF222 MUTATED     8   0   0   1
  ZNF222 WILD-TYPE 337   4  31  24
D263V11, multiclass
    clus
vv   ZNF222 MUTATED ZNF222 WILD-TYPE
  R0              8              337
  R1              0                4
  R2              0               31
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D263V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF222 MUTATED                                  0     0
  ZNF222 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZNF222 MUTATED                           1     6
  ZNF222 WILD-TYPE                        21   220
D263V13, multiclass
                                  clus
vv                                 ZNF222 MUTATED ZNF222 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                         6              220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(264) Variable = UBQLN2 MUTATION ANALYSIS
D264V1, survival
                  sevent
clus2                0   1
  UBQLN2 MUTATED     9   2
  UBQLN2 WILD-TYPE 369  91
  UBQLN2 MUTATED UBQLN2 WILD-TYPE 
              11              460 
  UBQLN2 MUTATED UBQLN2 WILD-TYPE 
               2               91 
$`UBQLN2 MUTATED`
TCGA-A6-6653 TCGA-A6-6781 TCGA-AA-3672 TCGA-AA-A01Q TCGA-CM-5861 TCGA-CM-6168 
       24.39        19.66         0.92         1.02        15.02        12.99 
TCGA-D5-6920 TCGA-G4-6586 TCGA-G4-6588 TCGA-DY-A1DD TCGA-F5-6464 
        3.68        35.80        26.17        57.24         9.96 

$`UBQLN2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
       25.08        25.18        24.16        21.76        24.69        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
       54.02         2.01        14.01        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       31.00        38.07        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 
       29.06        22.03        22.98        30.08        32.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6169 TCGA-CM-6170 
       29.03        16.04        21.99        14.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
       15.58         1.48         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       20.91        18.28        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  UBQLN2 MUTATED UBQLN2 WILD-TYPE 
            0.92             0.00 
  UBQLN2 MUTATED UBQLN2 WILD-TYPE 
           57.24           148.01 
  UBQLN2 MUTATED UBQLN2 WILD-TYPE 
          15.020           20.415 
[1] "0.9 - 57.2 (15.0)"  "0.0 - 148.0 (20.4)"
[1] "hr=" "1.3"
D264V2, continuous
D264V3, binary
                  cls
clus                 0   1
  UBQLN2 MUTATED    10   2
  UBQLN2 WILD-TYPE 356 117
[1] "tbl2"
                  cls
clus               [,1] [,2]
  UBQLN2 MUTATED     10    2
  UBQLN2 WILD-TYPE  356  117
        clus
vv       UBQLN2 MUTATED UBQLN2 WILD-TYPE
  COLON              10              356
  RECTUM              2              117
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  UBQLN2 MUTATED         1        0        1         5         1         0
  UBQLN2 WILD-TYPE      90        1       31       133         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  UBQLN2 MUTATED           1          0          1          2        0
  UBQLN2 WILD-TYPE        23         11         58         40       48
                  vv
clus               STAGE IVA STAGE IVB
  UBQLN2 MUTATED           0         0
  UBQLN2 WILD-TYPE        18         1
D264V4, multiclass
            clus
vv           UBQLN2 MUTATED UBQLN2 WILD-TYPE
  STAGE I                 1               90
  STAGE IA                0                1
  STAGE II                1               31
  STAGE IIA               5              133
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               1               23
  STAGE IIIA              0               11
  STAGE IIIB              1               58
  STAGE IIIC              2               40
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  UBQLN2 MUTATED     0   1   8   3
  UBQLN2 WILD-TYPE  17  91 321  47
D264V5, multiclass
    clus
vv   UBQLN2 MUTATED UBQLN2 WILD-TYPE
  T1              0               17
  T2              1               91
  T3              8              321
  T4              3               47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  UBQLN2 MUTATED     8   3   1
  UBQLN2 WILD-TYPE 279 110  86
D264V6, multiclass
    clus
vv   UBQLN2 MUTATED UBQLN2 WILD-TYPE
  N0              8              279
  N1              3              110
  N2              1               86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D264V7, binary
                  cls
clus                 0   1
  UBQLN2 MUTATED    10   0
  UBQLN2 WILD-TYPE 365  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  UBQLN2 MUTATED     10    0
  UBQLN2 WILD-TYPE  365   65
   clus
vv  UBQLN2 MUTATED UBQLN2 WILD-TYPE
  0             10              365
  1              0               65
[1] 2 2
[1] FALSE
D264V8, binary
                  cls
clus                 0   1
  UBQLN2 MUTATED    10   2
  UBQLN2 WILD-TYPE 215 262
[1] "tbl2"
                  cls
clus               [,1] [,2]
  UBQLN2 MUTATED     10    2
  UBQLN2 WILD-TYPE  215  262
        clus
vv       UBQLN2 MUTATED UBQLN2 WILD-TYPE
  FEMALE             10              215
  MALE                2              262
[1] 2 2
[1] FALSE
D264V9, binary
                  cls
clus                 0   1
  UBQLN2 MUTATED     8   0
  UBQLN2 WILD-TYPE 342  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  UBQLN2 MUTATED      8    0
  UBQLN2 WILD-TYPE  342   22
     clus
vv    UBQLN2 MUTATED UBQLN2 WILD-TYPE
  NO               8              342
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  UBQLN2 MUTATED                      9                             1
  UBQLN2 WILD-TYPE                  306                            46
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  UBQLN2 MUTATED                       2                              0
  UBQLN2 WILD-TYPE                   104                             10
D264V10, multiclass
                                clus
vv                               UBQLN2 MUTATED UBQLN2 WILD-TYPE
  COLON ADENOCARCINOMA                        9              306
  COLON MUCINOUS ADENOCARCINOMA               1               46
  RECTAL ADENOCARCINOMA                       2              104
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  UBQLN2 MUTATED     9   0   0   1
  UBQLN2 WILD-TYPE 336   4  31  24
D264V11, multiclass
    clus
vv   UBQLN2 MUTATED UBQLN2 WILD-TYPE
  R0              9              336
  R1              0                4
  R2              0               31
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D264V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  UBQLN2 MUTATED                                  0     0
  UBQLN2 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  UBQLN2 MUTATED                           1     9
  UBQLN2 WILD-TYPE                        21   217
D264V13, multiclass
                                  clus
vv                                 UBQLN2 MUTATED UBQLN2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                         9              217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(265) Variable = PPARGC1A MUTATION ANALYSIS
D265V1, survival
                    sevent
clus2                  0   1
  PPARGC1A MUTATED    16   6
  PPARGC1A WILD-TYPE 362  87
  PPARGC1A MUTATED PPARGC1A WILD-TYPE 
                22                449 
  PPARGC1A MUTATED PPARGC1A WILD-TYPE 
                 6                 87 
$`PPARGC1A MUTATED`
TCGA-A6-3809 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6648 TCGA-A6-6780 TCGA-A6-6782 
       32.75        22.06        32.71        25.18        20.12        20.28 
TCGA-AA-3662 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3864 TCGA-AA-3947 
        6.05        26.99        19.04        19.04        53.00        33.01 
TCGA-AD-6889 TCGA-AY-6386 TCGA-AZ-6598 TCGA-AZ-6606 TCGA-CA-6717 TCGA-CA-6718 
       56.55        17.82        49.41        11.74        12.76        10.06 
TCGA-CM-6162 TCGA-D5-6537 TCGA-D5-6923 TCGA-G4-6626 
       12.00         4.80        12.43        46.75 

$`PPARGC1A WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6649 TCGA-A6-6651 
       27.09        22.52         8.38        25.08        24.16        21.76 
TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6781 TCGA-AA-3489 TCGA-AA-3492 
       24.69        24.39        23.87        19.66         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       36.00         5.03        85.05        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       31.07        30.05        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 
       18.05        31.00         2.01        12.99        24.00        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       21.37        15.52         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        33.01        21.44        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 
      106.75        22.36        62.79        88.21         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
      100.01        29.56         5.23         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 
        3.06         3.25         3.29         0.07        12.20        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       15.02        17.03        15.02         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
       17.85        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        3.68         4.41        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       91.79        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  PPARGC1A MUTATED PPARGC1A WILD-TYPE 
               4.8                0.0 
  PPARGC1A MUTATED PPARGC1A WILD-TYPE 
             56.55             148.01 
  PPARGC1A MUTATED PPARGC1A WILD-TYPE 
             20.20              20.19 
[1] "4.8 - 56.5 (20.2)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.4"
D265V2, continuous
D265V3, binary
                    cls
clus                   0   1
  PPARGC1A MUTATED    23   0
  PPARGC1A WILD-TYPE 343 119
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  PPARGC1A MUTATED     23    0
  PPARGC1A WILD-TYPE  343  119
        clus
vv       PPARGC1A MUTATED PPARGC1A WILD-TYPE
  COLON                23                343
  RECTUM                0                119
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PPARGC1A MUTATED         1        0        4         7         3         1
  PPARGC1A WILD-TYPE      90        1       28       131         7         0
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PPARGC1A MUTATED           0          0          3          0        3
  PPARGC1A WILD-TYPE        24         11         56         42       45
                    vv
clus                 STAGE IVA STAGE IVB
  PPARGC1A MUTATED           1         0
  PPARGC1A WILD-TYPE        17         1
D265V4, multiclass
            clus
vv           PPARGC1A MUTATED PPARGC1A WILD-TYPE
  STAGE I                   1                 90
  STAGE IA                  0                  1
  STAGE II                  4                 28
  STAGE IIA                 7                131
  STAGE IIB                 3                  7
  STAGE IIC                 1                  0
  STAGE III                 0                 24
  STAGE IIIA                0                 11
  STAGE IIIB                3                 56
  STAGE IIIC                0                 42
  STAGE IV                  3                 45
  STAGE IVA                 1                 17
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  PPARGC1A MUTATED     0   1  15   7
  PPARGC1A WILD-TYPE  17  91 314  43
D265V5, multiclass
    clus
vv   PPARGC1A MUTATED PPARGC1A WILD-TYPE
  T1                0                 17
  T2                1                 91
  T3               15                314
  T4                7                 43
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  PPARGC1A MUTATED    18   3   2
  PPARGC1A WILD-TYPE 269 110  85
D265V6, multiclass
    clus
vv   PPARGC1A MUTATED PPARGC1A WILD-TYPE
  N0               18                269
  N1                3                110
  N2                2                 85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D265V7, binary
                    cls
clus                   0   1
  PPARGC1A MUTATED    15   4
  PPARGC1A WILD-TYPE 360  61
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  PPARGC1A MUTATED     15    4
  PPARGC1A WILD-TYPE  360   61
   clus
vv  PPARGC1A MUTATED PPARGC1A WILD-TYPE
  0               15                360
  1                4                 61
[1] 2 2
[1] FALSE
D265V8, binary
                    cls
clus                   0   1
  PPARGC1A MUTATED     9  14
  PPARGC1A WILD-TYPE 216 250
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  PPARGC1A MUTATED      9   14
  PPARGC1A WILD-TYPE  216  250
        clus
vv       PPARGC1A MUTATED PPARGC1A WILD-TYPE
  FEMALE                9                216
  MALE                 14                250
[1] 2 2
[1] FALSE
D265V9, binary
                    cls
clus                   0   1
  PPARGC1A MUTATED    20   1
  PPARGC1A WILD-TYPE 330  21
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  PPARGC1A MUTATED     20    1
  PPARGC1A WILD-TYPE  330   21
     clus
vv    PPARGC1A MUTATED PPARGC1A WILD-TYPE
  NO                20                330
  YES                1                 21
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PPARGC1A MUTATED                     18                             5
  PPARGC1A WILD-TYPE                  297                            42
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PPARGC1A MUTATED                       0                              0
  PPARGC1A WILD-TYPE                   106                             10
D265V10, multiclass
                                clus
vv                               PPARGC1A MUTATED PPARGC1A WILD-TYPE
  COLON ADENOCARCINOMA                         18                297
  COLON MUCINOUS ADENOCARCINOMA                 5                 42
  RECTAL ADENOCARCINOMA                         0                106
  RECTAL MUCINOUS ADENOCARCINOMA                0                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  PPARGC1A MUTATED    12   0   2   2
  PPARGC1A WILD-TYPE 333   4  29  23
D265V11, multiclass
    clus
vv   PPARGC1A MUTATED PPARGC1A WILD-TYPE
  R0               12                333
  R1                0                  4
  R2                2                 29
  RX                2                 23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D265V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PPARGC1A MUTATED                                  0     3
  PPARGC1A WILD-TYPE                                1     8
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  PPARGC1A MUTATED                           1    12
  PPARGC1A WILD-TYPE                        21   214
D265V13, multiclass
                                  clus
vv                                 PPARGC1A MUTATED PPARGC1A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           3                  8
  BLACK OR AFRICAN AMERICAN                       1                 21
  WHITE                                          12                214
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(266) Variable = ATP6V1B1 MUTATION ANALYSIS
D266V1, survival
                    sevent
clus2                  0   1
  ATP6V1B1 MUTATED    13   2
  ATP6V1B1 WILD-TYPE 365  91
  ATP6V1B1 MUTATED ATP6V1B1 WILD-TYPE 
                15                456 
  ATP6V1B1 MUTATED ATP6V1B1 WILD-TYPE 
                 2                 91 
$`ATP6V1B1 MUTATED`
TCGA-A6-3809 TCGA-A6-6781 TCGA-AA-3664 TCGA-AA-3713 TCGA-AA-3877 TCGA-AA-3950 
       32.75        19.66        54.02        19.04        31.00        24.00 
TCGA-AA-3966 TCGA-AD-5900 TCGA-AD-6548 TCGA-CA-6716 TCGA-CK-5916 TCGA-CM-5861 
        2.01         0.07        21.37        12.20        21.14        15.02 
TCGA-G4-6309 TCGA-AG-3583 TCGA-DC-6681 
       85.48        20.05         5.95 

$`ATP6V1B1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       85.05        26.99        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       29.98        18.05         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 
       26.01         2.01        20.98        34.03        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6888 TCGA-AD-6889 
       41.00        39.98        18.05        40.96        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6717 
       12.69         3.06         3.25         3.29         0.07        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       49.08        51.32         9.99        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 
       22.03        22.98        30.08        32.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       55.04        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3584 
       12.00        32.02         8.02         7.07        36.03        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
       19.99         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  ATP6V1B1 MUTATED ATP6V1B1 WILD-TYPE 
              0.07               0.00 
  ATP6V1B1 MUTATED ATP6V1B1 WILD-TYPE 
             85.48             148.01 
  ATP6V1B1 MUTATED ATP6V1B1 WILD-TYPE 
            20.050             20.235 
[1] "0.1 - 85.5 (20.1)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.4"
D266V2, continuous
D266V3, binary
                    cls
clus                   0   1
  ATP6V1B1 MUTATED    14   2
  ATP6V1B1 WILD-TYPE 352 117
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ATP6V1B1 MUTATED     14    2
  ATP6V1B1 WILD-TYPE  352  117
        clus
vv       ATP6V1B1 MUTATED ATP6V1B1 WILD-TYPE
  COLON                14                352
  RECTUM                2                117
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ATP6V1B1 MUTATED         4        0        1         5         1         0
  ATP6V1B1 WILD-TYPE      87        1       31       133         9         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ATP6V1B1 MUTATED           0          0          1          1        2
  ATP6V1B1 WILD-TYPE        24         11         58         41       46
                    vv
clus                 STAGE IVA STAGE IVB
  ATP6V1B1 MUTATED           1         0
  ATP6V1B1 WILD-TYPE        17         1
D266V4, multiclass
            clus
vv           ATP6V1B1 MUTATED ATP6V1B1 WILD-TYPE
  STAGE I                   4                 87
  STAGE IA                  0                  1
  STAGE II                  1                 31
  STAGE IIA                 5                133
  STAGE IIB                 1                  9
  STAGE IIC                 0                  1
  STAGE III                 0                 24
  STAGE IIIA                0                 11
  STAGE IIIB                1                 58
  STAGE IIIC                1                 41
  STAGE IV                  2                 46
  STAGE IVA                 1                 17
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  ATP6V1B1 MUTATED     2   2  10   2
  ATP6V1B1 WILD-TYPE  15  90 319  48
D266V5, multiclass
    clus
vv   ATP6V1B1 MUTATED ATP6V1B1 WILD-TYPE
  T1                2                 15
  T2                2                 90
  T3               10                319
  T4                2                 48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  ATP6V1B1 MUTATED    12   2   2
  ATP6V1B1 WILD-TYPE 275 111  85
D266V6, multiclass
    clus
vv   ATP6V1B1 MUTATED ATP6V1B1 WILD-TYPE
  N0               12                275
  N1                2                111
  N2                2                 85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D266V7, binary
                    cls
clus                   0   1
  ATP6V1B1 MUTATED    11   3
  ATP6V1B1 WILD-TYPE 364  62
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ATP6V1B1 MUTATED     11    3
  ATP6V1B1 WILD-TYPE  364   62
   clus
vv  ATP6V1B1 MUTATED ATP6V1B1 WILD-TYPE
  0               11                364
  1                3                 62
[1] 2 2
[1] FALSE
D266V8, binary
                    cls
clus                   0   1
  ATP6V1B1 MUTATED    11   5
  ATP6V1B1 WILD-TYPE 214 259
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ATP6V1B1 MUTATED     11    5
  ATP6V1B1 WILD-TYPE  214  259
        clus
vv       ATP6V1B1 MUTATED ATP6V1B1 WILD-TYPE
  FEMALE               11                214
  MALE                  5                259
[1] 2 2
[1] FALSE
D266V9, binary
                    cls
clus                   0   1
  ATP6V1B1 MUTATED    11   1
  ATP6V1B1 WILD-TYPE 339  21
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ATP6V1B1 MUTATED     11    1
  ATP6V1B1 WILD-TYPE  339   21
     clus
vv    ATP6V1B1 MUTATED ATP6V1B1 WILD-TYPE
  NO                11                339
  YES                1                 21
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ATP6V1B1 MUTATED                      8                             6
  ATP6V1B1 WILD-TYPE                  307                            41
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ATP6V1B1 MUTATED                       1                              1
  ATP6V1B1 WILD-TYPE                   105                              9
D266V10, multiclass
                                clus
vv                               ATP6V1B1 MUTATED ATP6V1B1 WILD-TYPE
  COLON ADENOCARCINOMA                          8                307
  COLON MUCINOUS ADENOCARCINOMA                 6                 41
  RECTAL ADENOCARCINOMA                         1                105
  RECTAL MUCINOUS ADENOCARCINOMA                1                  9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  ATP6V1B1 MUTATED    11   0   2   2
  ATP6V1B1 WILD-TYPE 334   4  29  23
D266V11, multiclass
    clus
vv   ATP6V1B1 MUTATED ATP6V1B1 WILD-TYPE
  R0               11                334
  R1                0                  4
  R2                2                 29
  RX                2                 23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D266V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ATP6V1B1 MUTATED                                  0     1
  ATP6V1B1 WILD-TYPE                                1    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  ATP6V1B1 MUTATED                           1     7
  ATP6V1B1 WILD-TYPE                        21   219
D266V13, multiclass
                                  clus
vv                                 ATP6V1B1 MUTATED ATP6V1B1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                 10
  BLACK OR AFRICAN AMERICAN                       1                 21
  WHITE                                           7                219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(267) Variable = ZNF583 MUTATION ANALYSIS
D267V1, survival
                  sevent
clus2                0   1
  ZNF583 MUTATED    16   2
  ZNF583 WILD-TYPE 362  91
  ZNF583 MUTATED ZNF583 WILD-TYPE 
              18              453 
  ZNF583 MUTATED ZNF583 WILD-TYPE 
               2               91 
$`ZNF583 MUTATED`
TCGA-A6-6138 TCGA-AA-3939 TCGA-AA-3977 TCGA-AA-A00O TCGA-AA-A010 TCGA-AD-5900 
       22.52        12.99        25.02        27.02        34.98         0.07 
TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4315 TCGA-CA-6717 TCGA-CK-4952 TCGA-CK-5913 
        0.72        10.88        58.39        12.76        15.62        51.32 
TCGA-CM-5862 TCGA-CM-5868 TCGA-DM-A1HB TCGA-AG-3892 TCGA-AG-A002 TCGA-AG-A036 
        5.03        17.03       135.65        13.02        20.98       117.11 

$`ZNF583 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6141 TCGA-A6-6142 
       22.09        22.06        32.71        27.09         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
        2.01        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       21.37        15.52        56.55         0.79         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       33.01        21.44        17.82         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 
       10.06        14.30        17.56       148.01        85.45        49.08 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5864 
       22.98        30.08        32.02        15.02        15.02        15.02 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 
       19.99         1.02        17.95        36.95        17.03        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 
       38.96        61.97        41.00        38.04        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  ZNF583 MUTATED ZNF583 WILD-TYPE 
            0.07             0.00 
  ZNF583 MUTATED ZNF583 WILD-TYPE 
          135.65           148.01 
  ZNF583 MUTATED ZNF583 WILD-TYPE 
          19.005           20.190 
[1] "0.1 - 135.7 (19.0)" "0.0 - 148.0 (20.2)"
[1] "hr=" "2.1"
D267V2, continuous
D267V3, binary
                  cls
clus                 0   1
  ZNF583 MUTATED    15   3
  ZNF583 WILD-TYPE 351 116
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF583 MUTATED     15    3
  ZNF583 WILD-TYPE  351  116
        clus
vv       ZNF583 MUTATED ZNF583 WILD-TYPE
  COLON              15              351
  RECTUM              3              116
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZNF583 MUTATED         4        0        0         4         1         0
  ZNF583 WILD-TYPE      87        1       32       134         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF583 MUTATED           1          0          1          2        0
  ZNF583 WILD-TYPE        23         11         58         40       48
                  vv
clus               STAGE IVA STAGE IVB
  ZNF583 MUTATED           2         0
  ZNF583 WILD-TYPE        16         1
D267V4, multiclass
            clus
vv           ZNF583 MUTATED ZNF583 WILD-TYPE
  STAGE I                 4               87
  STAGE IA                0                1
  STAGE II                0               32
  STAGE IIA               4              134
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               1               23
  STAGE IIIA              0               11
  STAGE IIIB              1               58
  STAGE IIIC              2               40
  STAGE IV                0               48
  STAGE IVA               2               16
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZNF583 MUTATED     1   4   9   4
  ZNF583 WILD-TYPE  16  88 320  46
D267V5, multiclass
    clus
vv   ZNF583 MUTATED ZNF583 WILD-TYPE
  T1              1               16
  T2              4               88
  T3              9              320
  T4              4               46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  ZNF583 MUTATED    10   4   4
  ZNF583 WILD-TYPE 277 109  83
D267V6, multiclass
    clus
vv   ZNF583 MUTATED ZNF583 WILD-TYPE
  N0             10              277
  N1              4              109
  N2              4               83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D267V7, binary
                  cls
clus                 0   1
  ZNF583 MUTATED    11   2
  ZNF583 WILD-TYPE 364  63
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF583 MUTATED     11    2
  ZNF583 WILD-TYPE  364   63
   clus
vv  ZNF583 MUTATED ZNF583 WILD-TYPE
  0             11              364
  1              2               63
[1] 2 2
[1] FALSE
D267V8, binary
                  cls
clus                 0   1
  ZNF583 MUTATED     6  12
  ZNF583 WILD-TYPE 219 252
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF583 MUTATED      6   12
  ZNF583 WILD-TYPE  219  252
        clus
vv       ZNF583 MUTATED ZNF583 WILD-TYPE
  FEMALE              6              219
  MALE               12              252
[1] 2 2
[1] FALSE
D267V9, binary
                  cls
clus                 0   1
  ZNF583 MUTATED    13   1
  ZNF583 WILD-TYPE 337  21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF583 MUTATED     13    1
  ZNF583 WILD-TYPE  337   21
     clus
vv    ZNF583 MUTATED ZNF583 WILD-TYPE
  NO              13              337
  YES              1               21
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ZNF583 MUTATED                     11                             3
  ZNF583 WILD-TYPE                  304                            44
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ZNF583 MUTATED                       3                              0
  ZNF583 WILD-TYPE                   103                             10
D267V10, multiclass
                                clus
vv                               ZNF583 MUTATED ZNF583 WILD-TYPE
  COLON ADENOCARCINOMA                       11              304
  COLON MUCINOUS ADENOCARCINOMA               3               44
  RECTAL ADENOCARCINOMA                       3              103
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ZNF583 MUTATED    10   0   0   3
  ZNF583 WILD-TYPE 335   4  31  22
D267V11, multiclass
    clus
vv   ZNF583 MUTATED ZNF583 WILD-TYPE
  R0             10              335
  R1              0                4
  R2              0               31
  RX              3               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D267V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF583 MUTATED                                  0     1
  ZNF583 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZNF583 MUTATED                           0    10
  ZNF583 WILD-TYPE                        22   216
D267V13, multiclass
                                  clus
vv                                 ZNF583 MUTATED ZNF583 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                        10              216
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(268) Variable = OSBPL2 MUTATION ANALYSIS
D268V1, survival
                  sevent
clus2                0   1
  OSBPL2 MUTATED    11   1
  OSBPL2 WILD-TYPE 367  92
  OSBPL2 MUTATED OSBPL2 WILD-TYPE 
              12              459 
  OSBPL2 MUTATED OSBPL2 WILD-TYPE 
               1               92 
$`OSBPL2 MUTATED`
TCGA-A6-5661 TCGA-A6-6654 TCGA-AU-6004 TCGA-AZ-4315 TCGA-CA-6715 TCGA-CK-5913 
       33.53        23.87        27.09        58.39         0.07        51.32 
TCGA-CM-5349 TCGA-CM-5862 TCGA-D5-7000 TCGA-DM-A28K TCGA-G4-6293 TCGA-AG-A002 
       30.08         5.03        10.26        98.24       133.18        20.98 

$`OSBPL2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 
       25.18        24.16        21.76        24.69        24.39        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       10.88         0.20        14.50        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.06         3.25         3.29        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       22.98        32.02        15.02        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-DM-A0X9 
       11.64         4.80         1.51        12.00        11.38       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
      117.07         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
        0.53        47.41        35.31        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  OSBPL2 MUTATED OSBPL2 WILD-TYPE 
            0.07             0.00 
  OSBPL2 MUTATED OSBPL2 WILD-TYPE 
          133.18           148.01 
  OSBPL2 MUTATED OSBPL2 WILD-TYPE 
          28.585           20.020 
[1] "0.1 - 133.2 (28.6)" "0.0 - 148.0 (20.0)"
[1] "hr=" "3.5"
D268V2, continuous
D268V3, binary
                  cls
clus                 0   1
  OSBPL2 MUTATED    11   1
  OSBPL2 WILD-TYPE 355 118
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OSBPL2 MUTATED     11    1
  OSBPL2 WILD-TYPE  355  118
        clus
vv       OSBPL2 MUTATED OSBPL2 WILD-TYPE
  COLON              11              355
  RECTUM              1              118
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  OSBPL2 MUTATED         3        0        0         5         0         0
  OSBPL2 WILD-TYPE      88        1       32       133        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  OSBPL2 MUTATED           1          0          2          0        0
  OSBPL2 WILD-TYPE        23         11         57         42       48
                  vv
clus               STAGE IVA STAGE IVB
  OSBPL2 MUTATED           1         0
  OSBPL2 WILD-TYPE        17         1
D268V4, multiclass
            clus
vv           OSBPL2 MUTATED OSBPL2 WILD-TYPE
  STAGE I                 3               88
  STAGE IA                0                1
  STAGE II                0               32
  STAGE IIA               5              133
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               1               23
  STAGE IIIA              0               11
  STAGE IIIB              2               57
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               1               17
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  OSBPL2 MUTATED     0   3   9   0
  OSBPL2 WILD-TYPE  17  89 320  50
D268V5, multiclass
    clus
vv   OSBPL2 MUTATED OSBPL2 WILD-TYPE
  T1              0               17
  T2              3               89
  T3              9              320
  T4              0               50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  OSBPL2 MUTATED     8   4   0
  OSBPL2 WILD-TYPE 279 109  87
D268V6, multiclass
    clus
vv   OSBPL2 MUTATED OSBPL2 WILD-TYPE
  N0              8              279
  N1              4              109
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D268V7, binary
                  cls
clus                 0   1
  OSBPL2 MUTATED    10   1
  OSBPL2 WILD-TYPE 365  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OSBPL2 MUTATED     10    1
  OSBPL2 WILD-TYPE  365   64
   clus
vv  OSBPL2 MUTATED OSBPL2 WILD-TYPE
  0             10              365
  1              1               64
[1] 2 2
[1] FALSE
D268V8, binary
                  cls
clus                 0   1
  OSBPL2 MUTATED     7   5
  OSBPL2 WILD-TYPE 218 259
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OSBPL2 MUTATED      7    5
  OSBPL2 WILD-TYPE  218  259
        clus
vv       OSBPL2 MUTATED OSBPL2 WILD-TYPE
  FEMALE              7              218
  MALE                5              259
[1] 2 2
[1] FALSE
D268V9, binary
                  cls
clus                 0   1
  OSBPL2 MUTATED     9   0
  OSBPL2 WILD-TYPE 341  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OSBPL2 MUTATED      9    0
  OSBPL2 WILD-TYPE  341   22
     clus
vv    OSBPL2 MUTATED OSBPL2 WILD-TYPE
  NO               9              341
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  OSBPL2 MUTATED                      9                             2
  OSBPL2 WILD-TYPE                  306                            45
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  OSBPL2 MUTATED                       1                              0
  OSBPL2 WILD-TYPE                   105                             10
D268V10, multiclass
                                clus
vv                               OSBPL2 MUTATED OSBPL2 WILD-TYPE
  COLON ADENOCARCINOMA                        9              306
  COLON MUCINOUS ADENOCARCINOMA               2               45
  RECTAL ADENOCARCINOMA                       1              105
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  OSBPL2 MUTATED     8   0   0   2
  OSBPL2 WILD-TYPE 337   4  31  23
D268V11, multiclass
    clus
vv   OSBPL2 MUTATED OSBPL2 WILD-TYPE
  R0              8              337
  R1              0                4
  R2              0               31
  RX              2               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D268V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OSBPL2 MUTATED                                  0     1
  OSBPL2 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  OSBPL2 MUTATED                           1     9
  OSBPL2 WILD-TYPE                        21   217
D268V13, multiclass
                                  clus
vv                                 OSBPL2 MUTATED OSBPL2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                         9              217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(269) Variable = CRY1 MUTATION ANALYSIS
D269V1, survival
                sevent
clus2              0   1
  CRY1 MUTATED    12   4
  CRY1 WILD-TYPE 366  89
  CRY1 MUTATED CRY1 WILD-TYPE 
            16            455 
  CRY1 MUTATED CRY1 WILD-TYPE 
             4             89 
$`CRY1 MUTATED`
TCGA-A6-6651 TCGA-AA-3492 TCGA-AA-3511 TCGA-AA-3672 TCGA-AA-3713 TCGA-AD-6895 
       21.76         3.02         6.97         0.92        19.04         0.72 
TCGA-CA-6717 TCGA-CM-6168 TCGA-D5-5537 TCGA-DM-A1HB TCGA-F4-6570 TCGA-G4-6317 
       12.76        12.99        45.40       135.65         6.18        36.00 
TCGA-G4-6626 TCGA-AG-A002 TCGA-AG-A02N TCGA-DC-6682 
       46.75        20.98        61.97         4.01 

$`CRY1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.08        25.18        24.16        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 
       20.12        19.66        20.28         7.04         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
       63.98         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
        2.01        14.01        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       26.99        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 
        0.07        21.37        15.52        56.55         0.79         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07        12.20        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       21.99        14.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       12.03        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 
       12.59       140.38         7.50        44.32       131.51       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 
       98.24         8.61        31.96        35.74        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6321 
       44.68        55.04        85.48        63.62        61.91        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-AF-2687 
       13.78        35.80        26.17        91.79        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 
       10.98        49.97         1.94        38.96        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        5.95         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  CRY1 MUTATED CRY1 WILD-TYPE 
          0.72           0.00 
  CRY1 MUTATED CRY1 WILD-TYPE 
        135.65         148.01 
  CRY1 MUTATED CRY1 WILD-TYPE 
        16.015         20.280 
[1] "0.7 - 135.7 (16.0)" "0.0 - 148.0 (20.3)"
[1] "hr=" "1.3"
D269V2, continuous
D269V3, binary
                cls
clus               0   1
  CRY1 MUTATED    13   3
  CRY1 WILD-TYPE 353 116
[1] "tbl2"
                cls
clus             [,1] [,2]
  CRY1 MUTATED     13    3
  CRY1 WILD-TYPE  353  116
        clus
vv       CRY1 MUTATED CRY1 WILD-TYPE
  COLON            13            353
  RECTUM            3            116
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CRY1 MUTATED         1        0        3         6         0         0
  CRY1 WILD-TYPE      90        1       29       132        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CRY1 MUTATED           1          0          2          1        1         0
  CRY1 WILD-TYPE        23         11         57         41       47        18
                vv
clus             STAGE IVB
  CRY1 MUTATED           0
  CRY1 WILD-TYPE         1
D269V4, multiclass
            clus
vv           CRY1 MUTATED CRY1 WILD-TYPE
  STAGE I               1             90
  STAGE IA              0              1
  STAGE II              3             29
  STAGE IIA             6            132
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             1             23
  STAGE IIIA            0             11
  STAGE IIIB            2             57
  STAGE IIIC            1             41
  STAGE IV              1             47
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  CRY1 MUTATED     0   1  14   1
  CRY1 WILD-TYPE  17  91 315  49
D269V5, multiclass
    clus
vv   CRY1 MUTATED CRY1 WILD-TYPE
  T1            0             17
  T2            1             91
  T3           14            315
  T4            1             49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  CRY1 MUTATED    10   4   2
  CRY1 WILD-TYPE 277 109  85
D269V6, multiclass
    clus
vv   CRY1 MUTATED CRY1 WILD-TYPE
  N0           10            277
  N1            4            109
  N2            2             85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D269V7, binary
                cls
clus               0   1
  CRY1 MUTATED    11   1
  CRY1 WILD-TYPE 364  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  CRY1 MUTATED     11    1
  CRY1 WILD-TYPE  364   64
   clus
vv  CRY1 MUTATED CRY1 WILD-TYPE
  0           11            364
  1            1             64
[1] 2 2
[1] FALSE
D269V8, binary
                cls
clus               0   1
  CRY1 MUTATED     6  10
  CRY1 WILD-TYPE 219 254
[1] "tbl2"
                cls
clus             [,1] [,2]
  CRY1 MUTATED      6   10
  CRY1 WILD-TYPE  219  254
        clus
vv       CRY1 MUTATED CRY1 WILD-TYPE
  FEMALE            6            219
  MALE             10            254
[1] 2 2
[1] FALSE
D269V9, binary
                cls
clus               0   1
  CRY1 MUTATED    11   1
  CRY1 WILD-TYPE 339  21
[1] "tbl2"
                cls
clus             [,1] [,2]
  CRY1 MUTATED     11    1
  CRY1 WILD-TYPE  339   21
     clus
vv    CRY1 MUTATED CRY1 WILD-TYPE
  NO            11            339
  YES            1             21
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CRY1 MUTATED                     11                             1
  CRY1 WILD-TYPE                  304                            46
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CRY1 MUTATED                       3                              0
  CRY1 WILD-TYPE                   103                             10
D269V10, multiclass
                                clus
vv                               CRY1 MUTATED CRY1 WILD-TYPE
  COLON ADENOCARCINOMA                     11            304
  COLON MUCINOUS ADENOCARCINOMA             1             46
  RECTAL ADENOCARCINOMA                     3            103
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  CRY1 MUTATED    10   0   1   2
  CRY1 WILD-TYPE 335   4  30  23
D269V11, multiclass
    clus
vv   CRY1 MUTATED CRY1 WILD-TYPE
  R0           10            335
  R1            0              4
  R2            1             30
  RX            2             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D269V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CRY1 MUTATED                                  0     1
  CRY1 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  CRY1 MUTATED                           1     8
  CRY1 WILD-TYPE                        21   218
D269V13, multiclass
                                  clus
vv                                 CRY1 MUTATED CRY1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                       8            218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(270) Variable = ZFYVE26 MUTATION ANALYSIS
D270V1, survival
                   sevent
clus2                 0   1
  ZFYVE26 MUTATED    25   6
  ZFYVE26 WILD-TYPE 353  87
  ZFYVE26 MUTATED ZFYVE26 WILD-TYPE 
               31               440 
  ZFYVE26 MUTATED ZFYVE26 WILD-TYPE 
                6                87 
$`ZFYVE26 MUTATED`
TCGA-A6-3809 TCGA-A6-6137 TCGA-A6-6651 TCGA-A6-6653 TCGA-AA-3555 TCGA-AA-3864 
       32.75        27.09        21.76        24.39        29.95        53.00 
TCGA-AA-3947 TCGA-AA-3977 TCGA-AA-A00N TCGA-AD-6889 TCGA-AU-3779 TCGA-AY-6197 
       33.01        25.02         4.01        56.55        14.50        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6605 TCGA-AZ-6608 
       17.82        58.39        49.41        12.10         5.23         1.61 
TCGA-CK-4952 TCGA-CM-5861 TCGA-CM-6171 TCGA-D5-6538 TCGA-D5-6928 TCGA-DM-A28H 
       15.62        15.02        14.04        17.13        11.64       117.07 
TCGA-F4-6570 TCGA-G4-6588 TCGA-G4-6628 TCGA-AG-3731 TCGA-AG-A002 TCGA-EI-6506 
        6.18        26.17        79.69        37.02        20.98        20.55 
TCGA-EI-6507 
       19.96 

$`ZFYVE26 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       22.06        32.71        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       24.16        24.69        23.87        20.12        19.66        20.28 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
        7.04         3.02         1.02        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       78.08         6.05         6.97        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       30.05        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 
       31.00         2.01        12.99        24.00        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 
       18.05        40.96         0.07        21.37        15.52         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AZ-4323 TCGA-AZ-4616 
       27.09        16.31         0.95        33.01         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6601 
      106.75        22.36        62.79        88.21         6.77       100.01 
TCGA-AZ-6603 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       29.56        11.74         3.19        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
       17.56       148.01        85.45        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       30.08        32.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 
       14.99        12.99        13.02        15.02        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6930 
       12.43        14.30         9.04         9.44         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28K TCGA-F4-6459 
       81.37       119.93        35.97        60.79        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       31.96        35.74        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       35.80        91.79        46.75        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
        0.99        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
       51.48        32.61         0.49        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  ZFYVE26 MUTATED ZFYVE26 WILD-TYPE 
             1.61              0.00 
  ZFYVE26 MUTATED ZFYVE26 WILD-TYPE 
           117.07            148.01 
  ZFYVE26 MUTATED ZFYVE26 WILD-TYPE 
           21.440            20.035 
[1] "1.6 - 117.1 (21.4)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.1"
D270V2, continuous
D270V3, binary
                   cls
clus                  0   1
  ZFYVE26 MUTATED    28   4
  ZFYVE26 WILD-TYPE 338 115
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZFYVE26 MUTATED     28    4
  ZFYVE26 WILD-TYPE  338  115
        clus
vv       ZFYVE26 MUTATED ZFYVE26 WILD-TYPE
  COLON               28               338
  RECTUM               4               115
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZFYVE26 MUTATED         4        0        2        12         3         0
  ZFYVE26 WILD-TYPE      87        1       30       126         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZFYVE26 MUTATED           0          1          5          2        2
  ZFYVE26 WILD-TYPE        24         10         54         40       46
                   vv
clus                STAGE IVA STAGE IVB
  ZFYVE26 MUTATED           0         0
  ZFYVE26 WILD-TYPE        18         1
D270V4, multiclass
            clus
vv           ZFYVE26 MUTATED ZFYVE26 WILD-TYPE
  STAGE I                  4                87
  STAGE IA                 0                 1
  STAGE II                 2                30
  STAGE IIA               12               126
  STAGE IIB                3                 7
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               1                10
  STAGE IIIB               5                54
  STAGE IIIC               2                40
  STAGE IV                 2                46
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  ZFYVE26 MUTATED     0   6  20   6
  ZFYVE26 WILD-TYPE  17  86 309  44
D270V5, multiclass
    clus
vv   ZFYVE26 MUTATED ZFYVE26 WILD-TYPE
  T1               0                17
  T2               6                86
  T3              20               309
  T4               6                44
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  ZFYVE26 MUTATED    22   7   3
  ZFYVE26 WILD-TYPE 265 106  84
D270V6, multiclass
    clus
vv   ZFYVE26 MUTATED ZFYVE26 WILD-TYPE
  N0              22               265
  N1               7               106
  N2               3                84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D270V7, binary
                   cls
clus                  0   1
  ZFYVE26 MUTATED    26   2
  ZFYVE26 WILD-TYPE 349  63
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZFYVE26 MUTATED     26    2
  ZFYVE26 WILD-TYPE  349   63
   clus
vv  ZFYVE26 MUTATED ZFYVE26 WILD-TYPE
  0              26               349
  1               2                63
[1] 2 2
[1] FALSE
D270V8, binary
                   cls
clus                  0   1
  ZFYVE26 MUTATED    16  16
  ZFYVE26 WILD-TYPE 209 248
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZFYVE26 MUTATED     16   16
  ZFYVE26 WILD-TYPE  209  248
        clus
vv       ZFYVE26 MUTATED ZFYVE26 WILD-TYPE
  FEMALE              16               209
  MALE                16               248
[1] 2 2
[1] FALSE
D270V9, binary
                   cls
clus                  0   1
  ZFYVE26 MUTATED    26   0
  ZFYVE26 WILD-TYPE 324  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZFYVE26 MUTATED     26    0
  ZFYVE26 WILD-TYPE  324   22
     clus
vv    ZFYVE26 MUTATED ZFYVE26 WILD-TYPE
  NO               26               324
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ZFYVE26 MUTATED                     22                             6
  ZFYVE26 WILD-TYPE                  293                            41
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ZFYVE26 MUTATED                       4                              0
  ZFYVE26 WILD-TYPE                   102                             10
D270V10, multiclass
                                clus
vv                               ZFYVE26 MUTATED ZFYVE26 WILD-TYPE
  COLON ADENOCARCINOMA                        22               293
  COLON MUCINOUS ADENOCARCINOMA                6                41
  RECTAL ADENOCARCINOMA                        4               102
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  ZFYVE26 MUTATED    20   0   1   1
  ZFYVE26 WILD-TYPE 325   4  30  24
D270V11, multiclass
    clus
vv   ZFYVE26 MUTATED ZFYVE26 WILD-TYPE
  R0              20               325
  R1               0                 4
  R2               1                30
  RX               1                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D270V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZFYVE26 MUTATED                                  0     1
  ZFYVE26 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  ZFYVE26 MUTATED                           2    21
  ZFYVE26 WILD-TYPE                        20   205
D270V13, multiclass
                                  clus
vv                                 ZFYVE26 MUTATED ZFYVE26 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                10
  BLACK OR AFRICAN AMERICAN                      2                20
  WHITE                                         21               205
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(271) Variable = PALB2 MUTATION ANALYSIS
D271V1, survival
                 sevent
clus2               0   1
  PALB2 MUTATED    18   2
  PALB2 WILD-TYPE 360  91
  PALB2 MUTATED PALB2 WILD-TYPE 
             20             451 
  PALB2 MUTATED PALB2 WILD-TYPE 
              2              91 
$`PALB2 MUTATED`
TCGA-A6-4105 TCGA-A6-5661 TCGA-A6-6653 TCGA-AA-3510 TCGA-AA-3543 TCGA-AA-3660 
       14.53        33.53        24.39        63.98         0.99        78.08 
TCGA-AA-3819 TCGA-AA-3854 TCGA-AA-3864 TCGA-AA-3947 TCGA-AZ-6599 TCGA-CA-6716 
       25.02        36.03        53.00        33.01         6.77        12.20 
TCGA-CK-6751 TCGA-CM-4752 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6166 TCGA-CM-6171 
      124.27        13.02        15.02        12.00        21.99        14.04 
TCGA-F4-6856 TCGA-AG-A002 
       35.31        20.98 

$`PALB2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 
       16.57        34.65        33.34        32.75        36.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       31.63        30.44        29.19        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       24.16        21.76        24.69        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 
       20.28         7.04         3.02         1.02        35.01         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
       34.03        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3821 
       19.04        10.06        35.05        33.04         0.99         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3855 
       17.03        10.06         0.00        33.07         0.00        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 
        0.99        31.07        31.07        30.05        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        88.21        49.41        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CM-4743 TCGA-CM-4744 
        9.99        21.14        82.95         1.91        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       37.02        25.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
        2.96        29.03        16.04        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       15.02        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  PALB2 MUTATED PALB2 WILD-TYPE 
           0.99            0.00 
  PALB2 MUTATED PALB2 WILD-TYPE 
         124.27          148.01 
  PALB2 MUTATED PALB2 WILD-TYPE 
          23.19           20.05 
[1] "1.0 - 124.3 (23.2)" "0.0 - 148.0 (20.1)"
[1] "hr=" "2.4"
D271V2, continuous
D271V3, binary
                 cls
clus                0   1
  PALB2 MUTATED    19   1
  PALB2 WILD-TYPE 347 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PALB2 MUTATED     19    1
  PALB2 WILD-TYPE  347  118
        clus
vv       PALB2 MUTATED PALB2 WILD-TYPE
  COLON             19             347
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PALB2 MUTATED        10        0        3         5         1         0
  PALB2 WILD-TYPE      81        1       29       133         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PALB2 MUTATED           0          0          1          0        0         0
  PALB2 WILD-TYPE        24         11         58         42       48        18
                 vv
clus              STAGE IVB
  PALB2 MUTATED           0
  PALB2 WILD-TYPE         1
D271V4, multiclass
            clus
vv           PALB2 MUTATED PALB2 WILD-TYPE
  STAGE I               10              81
  STAGE IA               0               1
  STAGE II               3              29
  STAGE IIA              5             133
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PALB2 MUTATED     0  10   9   1
  PALB2 WILD-TYPE  17  82 320  49
D271V5, multiclass
    clus
vv   PALB2 MUTATED PALB2 WILD-TYPE
  T1             0              17
  T2            10              82
  T3             9             320
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  PALB2 MUTATED    19   1   0
  PALB2 WILD-TYPE 268 112  87
D271V6, multiclass
    clus
vv   PALB2 MUTATED PALB2 WILD-TYPE
  N0            19             268
  N1             1             112
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D271V7, binary
                 cls
clus                0   1
  PALB2 MUTATED    18   0
  PALB2 WILD-TYPE 357  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PALB2 MUTATED     18    0
  PALB2 WILD-TYPE  357   65
   clus
vv  PALB2 MUTATED PALB2 WILD-TYPE
  0            18             357
  1             0              65
[1] 2 2
[1] FALSE
D271V8, binary
                 cls
clus                0   1
  PALB2 MUTATED    10  10
  PALB2 WILD-TYPE 215 254
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PALB2 MUTATED     10   10
  PALB2 WILD-TYPE  215  254
        clus
vv       PALB2 MUTATED PALB2 WILD-TYPE
  FEMALE            10             215
  MALE              10             254
[1] 2 2
[1] FALSE
D271V9, binary
                 cls
clus                0   1
  PALB2 MUTATED    20   0
  PALB2 WILD-TYPE 330  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PALB2 MUTATED     20    0
  PALB2 WILD-TYPE  330   22
     clus
vv    PALB2 MUTATED PALB2 WILD-TYPE
  NO             20             330
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PALB2 MUTATED                     13                             6
  PALB2 WILD-TYPE                  302                            41
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PALB2 MUTATED                       1                              0
  PALB2 WILD-TYPE                   105                             10
D271V10, multiclass
                                clus
vv                               PALB2 MUTATED PALB2 WILD-TYPE
  COLON ADENOCARCINOMA                      13             302
  COLON MUCINOUS ADENOCARCINOMA              6              41
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  PALB2 MUTATED    15   0   0   2
  PALB2 WILD-TYPE 330   4  31  23
D271V11, multiclass
    clus
vv   PALB2 MUTATED PALB2 WILD-TYPE
  R0            15             330
  R1             0               4
  R2             0              31
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D271V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PALB2 MUTATED                                  0     1
  PALB2 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PALB2 MUTATED                           2     9
  PALB2 WILD-TYPE                        20   217
D271V13, multiclass
                                  clus
vv                                 PALB2 MUTATED PALB2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    2              20
  WHITE                                        9             217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(272) Variable = PKD2L1 MUTATION ANALYSIS
D272V1, survival
                  sevent
clus2                0   1
  PKD2L1 MUTATED    20   3
  PKD2L1 WILD-TYPE 358  90
  PKD2L1 MUTATED PKD2L1 WILD-TYPE 
              23              448 
  PKD2L1 MUTATED PKD2L1 WILD-TYPE 
               3               90 
$`PKD2L1 MUTATED`
TCGA-A6-5659 TCGA-A6-6141 TCGA-A6-6781 TCGA-AA-3548 TCGA-AA-3552 TCGA-AA-3555 
       30.44         8.38        19.66        33.99        13.02        29.95 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-A010 TCGA-AA-A01R TCGA-AD-5900 TCGA-AD-6889 
       19.04        19.04        34.98        35.01         0.07        56.55 
TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-CA-6716 TCGA-CK-4952 TCGA-CM-4743 
       21.44        58.39        49.41        12.20        15.62        23.05 
TCGA-CM-6171 TCGA-D5-6535 TCGA-D5-6540 TCGA-G4-6293 TCGA-DC-6157 
       14.04        15.12        16.14       133.18        27.95 

$`PKD2L1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 
       22.06        32.71        27.09        22.52        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 
        0.99        14.01        21.01        24.00        17.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3811 
       19.00        36.00         5.03        85.05        26.99        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       31.00        38.07         1.02         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       40.96        21.37        15.52         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
       16.31         0.95        33.01        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 
      106.75        22.36        62.79        88.21         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6717 
       12.69         3.06         3.25         3.29         0.07        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 
       10.06        14.30        17.56       148.01        85.45        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 
       55.92        20.19        18.25         1.32        43.27        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
        4.80        17.13        12.49        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6303 
       13.25         0.53        47.41        35.31        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
        5.03        13.97        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  PKD2L1 MUTATED PKD2L1 WILD-TYPE 
            0.07             0.00 
  PKD2L1 MUTATED PKD2L1 WILD-TYPE 
          133.18           148.01 
  PKD2L1 MUTATED PKD2L1 WILD-TYPE 
          21.440           20.155 
[1] "0.1 - 133.2 (21.4)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.7"
D272V2, continuous
D272V3, binary
                  cls
clus                 0   1
  PKD2L1 MUTATED    23   1
  PKD2L1 WILD-TYPE 343 118
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PKD2L1 MUTATED     23    1
  PKD2L1 WILD-TYPE  343  118
        clus
vv       PKD2L1 MUTATED PKD2L1 WILD-TYPE
  COLON              23              343
  RECTUM              1              118
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PKD2L1 MUTATED         5        0        2         8         1         0
  PKD2L1 WILD-TYPE      86        1       30       130         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PKD2L1 MUTATED           2          0          1          4        1
  PKD2L1 WILD-TYPE        22         11         58         38       47
                  vv
clus               STAGE IVA STAGE IVB
  PKD2L1 MUTATED           0         0
  PKD2L1 WILD-TYPE        18         1
D272V4, multiclass
            clus
vv           PKD2L1 MUTATED PKD2L1 WILD-TYPE
  STAGE I                 5               86
  STAGE IA                0                1
  STAGE II                2               30
  STAGE IIA               8              130
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               2               22
  STAGE IIIA              0               11
  STAGE IIIB              1               58
  STAGE IIIC              4               38
  STAGE IV                1               47
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  PKD2L1 MUTATED     0   5  16   3
  PKD2L1 WILD-TYPE  17  87 313  47
D272V5, multiclass
    clus
vv   PKD2L1 MUTATED PKD2L1 WILD-TYPE
  T1              0               17
  T2              5               87
  T3             16              313
  T4              3               47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  PKD2L1 MUTATED    17   3   4
  PKD2L1 WILD-TYPE 270 110  83
D272V6, multiclass
    clus
vv   PKD2L1 MUTATED PKD2L1 WILD-TYPE
  N0             17              270
  N1              3              110
  N2              4               83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D272V7, binary
                  cls
clus                 0   1
  PKD2L1 MUTATED    18   1
  PKD2L1 WILD-TYPE 357  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PKD2L1 MUTATED     18    1
  PKD2L1 WILD-TYPE  357   64
   clus
vv  PKD2L1 MUTATED PKD2L1 WILD-TYPE
  0             18              357
  1              1               64
[1] 2 2
[1] FALSE
D272V8, binary
                  cls
clus                 0   1
  PKD2L1 MUTATED     9  15
  PKD2L1 WILD-TYPE 216 249
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PKD2L1 MUTATED      9   15
  PKD2L1 WILD-TYPE  216  249
        clus
vv       PKD2L1 MUTATED PKD2L1 WILD-TYPE
  FEMALE              9              216
  MALE               15              249
[1] 2 2
[1] FALSE
D272V9, binary
                  cls
clus                 0   1
  PKD2L1 MUTATED    17   2
  PKD2L1 WILD-TYPE 333  20
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PKD2L1 MUTATED     17    2
  PKD2L1 WILD-TYPE  333   20
     clus
vv    PKD2L1 MUTATED PKD2L1 WILD-TYPE
  NO              17              333
  YES              2               20
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PKD2L1 MUTATED                     17                             6
  PKD2L1 WILD-TYPE                  298                            41
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PKD2L1 MUTATED                       1                              0
  PKD2L1 WILD-TYPE                   105                             10
D272V10, multiclass
                                clus
vv                               PKD2L1 MUTATED PKD2L1 WILD-TYPE
  COLON ADENOCARCINOMA                       17              298
  COLON MUCINOUS ADENOCARCINOMA               6               41
  RECTAL ADENOCARCINOMA                       1              105
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  PKD2L1 MUTATED    17   0   1   3
  PKD2L1 WILD-TYPE 328   4  30  22
D272V11, multiclass
    clus
vv   PKD2L1 MUTATED PKD2L1 WILD-TYPE
  R0             17              328
  R1              0                4
  R2              1               30
  RX              3               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D272V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PKD2L1 MUTATED                                  0     2
  PKD2L1 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  PKD2L1 MUTATED                           2    12
  PKD2L1 WILD-TYPE                        20   214
D272V13, multiclass
                                  clus
vv                                 PKD2L1 MUTATED PKD2L1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                9
  BLACK OR AFRICAN AMERICAN                     2               20
  WHITE                                        12              214
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(273) Variable = COLEC10 MUTATION ANALYSIS
D273V1, survival
                   sevent
clus2                 0   1
  COLEC10 MUTATED     8   2
  COLEC10 WILD-TYPE 370  91
  COLEC10 MUTATED COLEC10 WILD-TYPE 
               10               461 
  COLEC10 MUTATED COLEC10 WILD-TYPE 
                2                91 
$`COLEC10 MUTATED`
TCGA-A6-5660 TCGA-AA-3715 TCGA-AA-3821 TCGA-AZ-4681 TCGA-CM-5348 TCGA-CM-5862 
       29.19        19.04         1.02       106.75        22.98         5.03 
TCGA-D5-5541 TCGA-DM-A1HA TCGA-AG-A002 TCGA-DC-6157 
       55.92       131.51        20.98        27.95 

$`COLEC10 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 
       36.00         5.03        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 
       35.05        33.04         0.99        25.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 
       21.44        17.82        58.39         1.41         5.13        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 
       29.06        22.03        30.08        32.02        15.02        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       56.09        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
       15.02         5.03        13.97        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  COLEC10 MUTATED COLEC10 WILD-TYPE 
             1.02              0.00 
  COLEC10 MUTATED COLEC10 WILD-TYPE 
           131.51            148.01 
  COLEC10 MUTATED COLEC10 WILD-TYPE 
           25.465            20.050 
[1] "1.0 - 131.5 (25.5)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.4"
D273V2, continuous
D273V3, binary
                   cls
clus                  0   1
  COLEC10 MUTATED     8   2
  COLEC10 WILD-TYPE 358 117
[1] "tbl2"
                   cls
clus                [,1] [,2]
  COLEC10 MUTATED      8    2
  COLEC10 WILD-TYPE  358  117
        clus
vv       COLEC10 MUTATED COLEC10 WILD-TYPE
  COLON                8               358
  RECTUM               2               117
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  COLEC10 MUTATED         3        0        1         1         0         0
  COLEC10 WILD-TYPE      88        1       31       137        10         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  COLEC10 MUTATED           0          0          2          2        0
  COLEC10 WILD-TYPE        24         11         57         40       48
                   vv
clus                STAGE IVA STAGE IVB
  COLEC10 MUTATED           1         0
  COLEC10 WILD-TYPE        17         1
D273V4, multiclass
            clus
vv           COLEC10 MUTATED COLEC10 WILD-TYPE
  STAGE I                  3                88
  STAGE IA                 0                 1
  STAGE II                 1                31
  STAGE IIA                1               137
  STAGE IIB                0                10
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               0                11
  STAGE IIIB               2                57
  STAGE IIIC               2                40
  STAGE IV                 0                48
  STAGE IVA                1                17
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  COLEC10 MUTATED     0   3   7   0
  COLEC10 WILD-TYPE  17  89 322  50
D273V5, multiclass
    clus
vv   COLEC10 MUTATED COLEC10 WILD-TYPE
  T1               0                17
  T2               3                89
  T3               7               322
  T4               0                50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  COLEC10 MUTATED     5   3   2
  COLEC10 WILD-TYPE 282 110  85
D273V6, multiclass
    clus
vv   COLEC10 MUTATED COLEC10 WILD-TYPE
  N0               5               282
  N1               3               110
  N2               2                85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D273V7, binary
                   cls
clus                  0   1
  COLEC10 MUTATED     9   1
  COLEC10 WILD-TYPE 366  64
[1] "tbl2"
                   cls
clus                [,1] [,2]
  COLEC10 MUTATED      9    1
  COLEC10 WILD-TYPE  366   64
   clus
vv  COLEC10 MUTATED COLEC10 WILD-TYPE
  0               9               366
  1               1                64
[1] 2 2
[1] FALSE
D273V8, binary
                   cls
clus                  0   1
  COLEC10 MUTATED     2   8
  COLEC10 WILD-TYPE 223 256
[1] "tbl2"
                   cls
clus                [,1] [,2]
  COLEC10 MUTATED      2    8
  COLEC10 WILD-TYPE  223  256
        clus
vv       COLEC10 MUTATED COLEC10 WILD-TYPE
  FEMALE               2               223
  MALE                 8               256
[1] 2 2
[1] FALSE
D273V9, binary
                   cls
clus                  0   1
  COLEC10 MUTATED     8   0
  COLEC10 WILD-TYPE 342  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  COLEC10 MUTATED      8    0
  COLEC10 WILD-TYPE  342   22
     clus
vv    COLEC10 MUTATED COLEC10 WILD-TYPE
  NO                8               342
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  COLEC10 MUTATED                      7                             1
  COLEC10 WILD-TYPE                  308                            46
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  COLEC10 MUTATED                       2                              0
  COLEC10 WILD-TYPE                   104                             10
D273V10, multiclass
                                clus
vv                               COLEC10 MUTATED COLEC10 WILD-TYPE
  COLON ADENOCARCINOMA                         7               308
  COLON MUCINOUS ADENOCARCINOMA                1                46
  RECTAL ADENOCARCINOMA                        2               104
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  COLEC10 MUTATED     8   0   0   0
  COLEC10 WILD-TYPE 337   4  31  25
D273V11, multiclass
    clus
vv   COLEC10 MUTATED COLEC10 WILD-TYPE
  R0               8               337
  R1               0                 4
  R2               0                31
  RX               0                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D273V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  COLEC10 MUTATED                                  0     0
  COLEC10 WILD-TYPE                                1    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  COLEC10 MUTATED                           2     5
  COLEC10 WILD-TYPE                        20   221
D273V13, multiclass
                                  clus
vv                                 COLEC10 MUTATED COLEC10 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                      2                20
  WHITE                                          5               221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(274) Variable = C2ORF77 MUTATION ANALYSIS
D274V1, survival
                   sevent
clus2                 0   1
  C2ORF77 MUTATED     9   0
  C2ORF77 WILD-TYPE 369  93
  C2ORF77 MUTATED C2ORF77 WILD-TYPE 
                9               462 
  C2ORF77 MUTATED C2ORF77 WILD-TYPE 
                0                93 
$`C2ORF77 MUTATED`
TCGA-AA-3713 TCGA-AA-3866 TCGA-AA-3950 TCGA-AA-A010 TCGA-AD-5900 TCGA-CA-6717 
       19.04        17.03        24.00        34.98         0.07        12.76 
TCGA-D5-6928 TCGA-G4-6586 TCGA-AG-A002 
       11.64        35.80        20.98 

$`C2ORF77 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 
       12.99        24.00        33.01        26.01         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
       40.96        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07        12.20        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.04         9.44         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  C2ORF77 MUTATED C2ORF77 WILD-TYPE 
             0.07              0.00 
  C2ORF77 MUTATED C2ORF77 WILD-TYPE 
            35.80            148.01 
  C2ORF77 MUTATED C2ORF77 WILD-TYPE 
           19.040            20.235 
[1] "0.1 - 35.8 (19.0)"  "0.0 - 148.0 (20.2)"
[1] "hr="     "9200000"
D274V2, continuous
D274V3, binary
                   cls
clus                  0   1
  C2ORF77 MUTATED     8   1
  C2ORF77 WILD-TYPE 358 118
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C2ORF77 MUTATED      8    1
  C2ORF77 WILD-TYPE  358  118
        clus
vv       C2ORF77 MUTATED C2ORF77 WILD-TYPE
  COLON                8               358
  RECTUM               1               118
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  C2ORF77 MUTATED         3        0        0         4         1         0
  C2ORF77 WILD-TYPE      88        1       32       134         9         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C2ORF77 MUTATED           0          0          0          0        1
  C2ORF77 WILD-TYPE        24         11         59         42       47
                   vv
clus                STAGE IVA STAGE IVB
  C2ORF77 MUTATED           0         0
  C2ORF77 WILD-TYPE        18         1
D274V4, multiclass
            clus
vv           C2ORF77 MUTATED C2ORF77 WILD-TYPE
  STAGE I                  3                88
  STAGE IA                 0                 1
  STAGE II                 0                32
  STAGE IIA                4               134
  STAGE IIB                1                 9
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               0                11
  STAGE IIIB               0                59
  STAGE IIIC               0                42
  STAGE IV                 1                47
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  C2ORF77 MUTATED     0   3   5   1
  C2ORF77 WILD-TYPE  17  89 324  49
D274V5, multiclass
    clus
vv   C2ORF77 MUTATED C2ORF77 WILD-TYPE
  T1               0                17
  T2               3                89
  T3               5               324
  T4               1                49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  C2ORF77 MUTATED     9   0   0
  C2ORF77 WILD-TYPE 278 113  87
D274V6, multiclass
    clus
vv   C2ORF77 MUTATED C2ORF77 WILD-TYPE
  N0               9               278
  N1               0               113
  N2               0                87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D274V7, binary
                   cls
clus                  0   1
  C2ORF77 MUTATED     7   1
  C2ORF77 WILD-TYPE 368  64
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C2ORF77 MUTATED      7    1
  C2ORF77 WILD-TYPE  368   64
   clus
vv  C2ORF77 MUTATED C2ORF77 WILD-TYPE
  0               7               368
  1               1                64
[1] 2 2
[1] FALSE
D274V8, binary
                   cls
clus                  0   1
  C2ORF77 MUTATED     4   5
  C2ORF77 WILD-TYPE 221 259
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C2ORF77 MUTATED      4    5
  C2ORF77 WILD-TYPE  221  259
        clus
vv       C2ORF77 MUTATED C2ORF77 WILD-TYPE
  FEMALE               4               221
  MALE                 5               259
[1] 2 2
[1] FALSE
D274V9, binary
                   cls
clus                  0   1
  C2ORF77 MUTATED     7   1
  C2ORF77 WILD-TYPE 343  21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C2ORF77 MUTATED      7    1
  C2ORF77 WILD-TYPE  343   21
     clus
vv    C2ORF77 MUTATED C2ORF77 WILD-TYPE
  NO                7               343
  YES               1                21
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  C2ORF77 MUTATED                      4                             4
  C2ORF77 WILD-TYPE                  311                            43
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  C2ORF77 MUTATED                       1                              0
  C2ORF77 WILD-TYPE                   105                             10
D274V10, multiclass
                                clus
vv                               C2ORF77 MUTATED C2ORF77 WILD-TYPE
  COLON ADENOCARCINOMA                         4               311
  COLON MUCINOUS ADENOCARCINOMA                4                43
  RECTAL ADENOCARCINOMA                        1               105
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  C2ORF77 MUTATED     7   0   1   1
  C2ORF77 WILD-TYPE 338   4  30  24
D274V11, multiclass
    clus
vv   C2ORF77 MUTATED C2ORF77 WILD-TYPE
  R0               7               338
  R1               0                 4
  R2               1                30
  RX               1                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D274V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C2ORF77 MUTATED                                  0     1
  C2ORF77 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  C2ORF77 MUTATED                           0     3
  C2ORF77 WILD-TYPE                        22   223
D274V13, multiclass
                                  clus
vv                                 C2ORF77 MUTATED C2ORF77 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                10
  BLACK OR AFRICAN AMERICAN                      0                22
  WHITE                                          3               223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(275) Variable = DHRS7 MUTATION ANALYSIS
D275V1, survival
                 sevent
clus2               0   1
  DHRS7 MUTATED     9   1
  DHRS7 WILD-TYPE 369  92
  DHRS7 MUTATED DHRS7 WILD-TYPE 
             10             461 
  DHRS7 MUTATED DHRS7 WILD-TYPE 
              1              92 
$`DHRS7 MUTATED`
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-6781 TCGA-AA-3510 TCGA-AA-3950 TCGA-AU-6004 
       33.53        23.61        19.66        63.98        24.00        27.09 
TCGA-AY-6197 TCGA-AZ-6601 TCGA-CK-4950 TCGA-CM-6172 
       21.44       100.01        85.45        11.01 

$`DHRS7 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5664 TCGA-A6-5665 
       32.91        31.63        30.44        29.19        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 
       20.28         7.04         3.02         1.02        35.01         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       33.01        26.01         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       16.31         0.95        33.01        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77        12.10        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 
       12.99        13.02        15.02        14.04        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  DHRS7 MUTATED DHRS7 WILD-TYPE 
          11.01            0.00 
  DHRS7 MUTATED DHRS7 WILD-TYPE 
         100.01          148.01 
  DHRS7 MUTATED DHRS7 WILD-TYPE 
         25.545          20.020 
[1] "11.0 - 100.0 (25.5)" "0.0 - 148.0 (20.0)" 
[1] "hr=" "3.1"
D275V2, continuous
D275V3, binary
                 cls
clus                0   1
  DHRS7 MUTATED    10   0
  DHRS7 WILD-TYPE 356 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DHRS7 MUTATED     10    0
  DHRS7 WILD-TYPE  356  119
        clus
vv       DHRS7 MUTATED DHRS7 WILD-TYPE
  COLON             10             356
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DHRS7 MUTATED         1        0        2         3         0         0
  DHRS7 WILD-TYPE      90        1       30       135        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DHRS7 MUTATED           0          0          2          1        0         1
  DHRS7 WILD-TYPE        24         11         57         41       48        17
                 vv
clus              STAGE IVB
  DHRS7 MUTATED           0
  DHRS7 WILD-TYPE         1
D275V4, multiclass
            clus
vv           DHRS7 MUTATED DHRS7 WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA              3             135
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             2              57
  STAGE IIIC             1              41
  STAGE IV               0              48
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  DHRS7 MUTATED     0   1   8   1
  DHRS7 WILD-TYPE  17  91 321  49
D275V5, multiclass
    clus
vv   DHRS7 MUTATED DHRS7 WILD-TYPE
  T1             0              17
  T2             1              91
  T3             8             321
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  DHRS7 MUTATED     6   3   1
  DHRS7 WILD-TYPE 281 110  86
D275V6, multiclass
    clus
vv   DHRS7 MUTATED DHRS7 WILD-TYPE
  N0             6             281
  N1             3             110
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D275V7, binary
                 cls
clus                0   1
  DHRS7 MUTATED     7   1
  DHRS7 WILD-TYPE 368  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DHRS7 MUTATED      7    1
  DHRS7 WILD-TYPE  368   64
   clus
vv  DHRS7 MUTATED DHRS7 WILD-TYPE
  0             7             368
  1             1              64
[1] 2 2
[1] FALSE
D275V8, binary
                 cls
clus                0   1
  DHRS7 MUTATED     5   5
  DHRS7 WILD-TYPE 220 259
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DHRS7 MUTATED      5    5
  DHRS7 WILD-TYPE  220  259
        clus
vv       DHRS7 MUTATED DHRS7 WILD-TYPE
  FEMALE             5             220
  MALE               5             259
[1] 2 2
[1] FALSE
D275V9, binary
                 cls
clus                0   1
  DHRS7 MUTATED     9   0
  DHRS7 WILD-TYPE 341  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DHRS7 MUTATED      9    0
  DHRS7 WILD-TYPE  341   22
     clus
vv    DHRS7 MUTATED DHRS7 WILD-TYPE
  NO              9             341
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  DHRS7 MUTATED                      8                             2
  DHRS7 WILD-TYPE                  307                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  DHRS7 MUTATED                       0                              0
  DHRS7 WILD-TYPE                   106                             10
D275V10, multiclass
                                clus
vv                               DHRS7 MUTATED DHRS7 WILD-TYPE
  COLON ADENOCARCINOMA                       8             307
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  DHRS7 MUTATED     7   1   0   0
  DHRS7 WILD-TYPE 338   3  31  25
D275V11, multiclass
    clus
vv   DHRS7 MUTATED DHRS7 WILD-TYPE
  R0             7             338
  R1             1               3
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D275V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DHRS7 MUTATED                                  0     0
  DHRS7 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  DHRS7 MUTATED                           2     6
  DHRS7 WILD-TYPE                        20   220
D275V13, multiclass
                                  clus
vv                                 DHRS7 MUTATED DHRS7 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    2              20
  WHITE                                        6             220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(276) Variable = PANK3 MUTATION ANALYSIS
D276V1, survival
                 sevent
clus2               0   1
  PANK3 MUTATED     6   1
  PANK3 WILD-TYPE 372  92
  PANK3 MUTATED PANK3 WILD-TYPE 
              7             464 
  PANK3 MUTATED PANK3 WILD-TYPE 
              1              92 
$`PANK3 MUTATED`
TCGA-A6-2672 TCGA-AA-3815 TCGA-AA-A010 TCGA-CM-5349 TCGA-CM-6163 TCGA-DM-A1DA 
       46.65        33.04        34.98        30.08         2.96         7.50 
TCGA-AG-A002 
       20.98 

$`PANK3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       10.06        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5861 
       13.02        29.06        22.03        22.98        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  PANK3 MUTATED PANK3 WILD-TYPE 
           2.96            0.00 
  PANK3 MUTATED PANK3 WILD-TYPE 
          46.65          148.01 
  PANK3 MUTATED PANK3 WILD-TYPE 
         30.080          20.085 
[1] "3.0 - 46.6 (30.1)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.3"
D276V2, continuous
D276V3, binary
                 cls
clus                0   1
  PANK3 MUTATED     6   1
  PANK3 WILD-TYPE 360 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PANK3 MUTATED      6    1
  PANK3 WILD-TYPE  360  118
        clus
vv       PANK3 MUTATED PANK3 WILD-TYPE
  COLON              6             360
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PANK3 MUTATED         2        0        0         2         1         0
  PANK3 WILD-TYPE      89        1       32       136         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PANK3 MUTATED           0          0          1          1        0         0
  PANK3 WILD-TYPE        24         11         58         41       48        18
                 vv
clus              STAGE IVB
  PANK3 MUTATED           0
  PANK3 WILD-TYPE         1
D276V4, multiclass
            clus
vv           PANK3 MUTATED PANK3 WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              2             136
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             1              41
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PANK3 MUTATED     1   1   4   1
  PANK3 WILD-TYPE  16  91 325  49
D276V5, multiclass
    clus
vv   PANK3 MUTATED PANK3 WILD-TYPE
  T1             1              16
  T2             1              91
  T3             4             325
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  PANK3 MUTATED     5   1   1
  PANK3 WILD-TYPE 282 112  86
D276V6, multiclass
    clus
vv   PANK3 MUTATED PANK3 WILD-TYPE
  N0             5             282
  N1             1             112
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D276V7, binary
                 cls
clus                0   1
  PANK3 MUTATED     7   0
  PANK3 WILD-TYPE 368  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PANK3 MUTATED      7    0
  PANK3 WILD-TYPE  368   65
   clus
vv  PANK3 MUTATED PANK3 WILD-TYPE
  0             7             368
  1             0              65
[1] 2 2
[1] FALSE
D276V8, binary
                 cls
clus                0   1
  PANK3 MUTATED     5   2
  PANK3 WILD-TYPE 220 262
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PANK3 MUTATED      5    2
  PANK3 WILD-TYPE  220  262
        clus
vv       PANK3 MUTATED PANK3 WILD-TYPE
  FEMALE             5             220
  MALE               2             262
[1] 2 2
[1] FALSE
D276V9, binary
                 cls
clus                0   1
  PANK3 MUTATED     6   0
  PANK3 WILD-TYPE 344  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PANK3 MUTATED      6    0
  PANK3 WILD-TYPE  344   22
     clus
vv    PANK3 MUTATED PANK3 WILD-TYPE
  NO              6             344
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PANK3 MUTATED                      6                             0
  PANK3 WILD-TYPE                  309                            47
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PANK3 MUTATED                       1                              0
  PANK3 WILD-TYPE                   105                             10
D276V10, multiclass
                                clus
vv                               PANK3 MUTATED PANK3 WILD-TYPE
  COLON ADENOCARCINOMA                       6             309
  COLON MUCINOUS ADENOCARCINOMA              0              47
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  PANK3 MUTATED     6   0   0   0
  PANK3 WILD-TYPE 339   4  31  25
D276V11, multiclass
    clus
vv   PANK3 MUTATED PANK3 WILD-TYPE
  R0             6             339
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D276V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PANK3 MUTATED                                  0     0
  PANK3 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PANK3 MUTATED                           0     4
  PANK3 WILD-TYPE                        22   222
D276V13, multiclass
                                  clus
vv                                 PANK3 MUTATED PANK3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        4             222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(277) Variable = G3BP2 MUTATION ANALYSIS
D277V1, survival
                 sevent
clus2               0   1
  G3BP2 MUTATED     8   2
  G3BP2 WILD-TYPE 370  91
  G3BP2 MUTATED G3BP2 WILD-TYPE 
             10             461 
  G3BP2 MUTATED G3BP2 WILD-TYPE 
              2              91 
$`G3BP2 MUTATED`
TCGA-A6-5661 TCGA-AA-A00N TCGA-AA-A010 TCGA-AD-6548 TCGA-CA-6717 TCGA-D5-6536 
       33.53         4.01        34.98        21.37        12.76        17.85 
TCGA-D5-6540 TCGA-DM-A0XD TCGA-G4-6628 TCGA-AG-A002 
       16.14        24.43        79.69        20.98 

$`G3BP2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       18.05        40.96         0.07        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07        12.20        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 
       43.27        15.12         4.80        17.13        12.49        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
       10.26       119.70        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       26.17        91.79        46.75        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  G3BP2 MUTATED G3BP2 WILD-TYPE 
           4.01            0.00 
  G3BP2 MUTATED G3BP2 WILD-TYPE 
          79.69          148.01 
  G3BP2 MUTATED G3BP2 WILD-TYPE 
         21.175          20.120 
[1] "4.0 - 79.7 (21.2)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1"  
D277V2, continuous
D277V3, binary
                 cls
clus                0   1
  G3BP2 MUTATED     9   1
  G3BP2 WILD-TYPE 357 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  G3BP2 MUTATED      9    1
  G3BP2 WILD-TYPE  357  118
        clus
vv       G3BP2 MUTATED G3BP2 WILD-TYPE
  COLON              9             357
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  G3BP2 MUTATED         4        0        0         4         2         0
  G3BP2 WILD-TYPE      87        1       32       134         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  G3BP2 MUTATED           0          0          0          0        0         0
  G3BP2 WILD-TYPE        24         11         59         42       48        18
                 vv
clus              STAGE IVB
  G3BP2 MUTATED           0
  G3BP2 WILD-TYPE         1
D277V4, multiclass
            clus
vv           G3BP2 MUTATED G3BP2 WILD-TYPE
  STAGE I                4              87
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              4             134
  STAGE IIB              2               8
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  G3BP2 MUTATED     0   4   4   2
  G3BP2 WILD-TYPE  17  88 325  48
D277V5, multiclass
    clus
vv   G3BP2 MUTATED G3BP2 WILD-TYPE
  T1             0              17
  T2             4              88
  T3             4             325
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  G3BP2 MUTATED    10   0   0
  G3BP2 WILD-TYPE 277 113  87
D277V6, multiclass
    clus
vv   G3BP2 MUTATED G3BP2 WILD-TYPE
  N0            10             277
  N1             0             113
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D277V7, binary
                 cls
clus                0   1
  G3BP2 MUTATED    10   0
  G3BP2 WILD-TYPE 365  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  G3BP2 MUTATED     10    0
  G3BP2 WILD-TYPE  365   65
   clus
vv  G3BP2 MUTATED G3BP2 WILD-TYPE
  0            10             365
  1             0              65
[1] 2 2
[1] FALSE
D277V8, binary
                 cls
clus                0   1
  G3BP2 MUTATED     3   7
  G3BP2 WILD-TYPE 222 257
[1] "tbl2"
                 cls
clus              [,1] [,2]
  G3BP2 MUTATED      3    7
  G3BP2 WILD-TYPE  222  257
        clus
vv       G3BP2 MUTATED G3BP2 WILD-TYPE
  FEMALE             3             222
  MALE               7             257
[1] 2 2
[1] FALSE
D277V9, binary
                 cls
clus                0   1
  G3BP2 MUTATED     8   0
  G3BP2 WILD-TYPE 342  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  G3BP2 MUTATED      8    0
  G3BP2 WILD-TYPE  342   22
     clus
vv    G3BP2 MUTATED G3BP2 WILD-TYPE
  NO              8             342
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  G3BP2 MUTATED                      6                             3
  G3BP2 WILD-TYPE                  309                            44
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  G3BP2 MUTATED                       1                              0
  G3BP2 WILD-TYPE                   105                             10
D277V10, multiclass
                                clus
vv                               G3BP2 MUTATED G3BP2 WILD-TYPE
  COLON ADENOCARCINOMA                       6             309
  COLON MUCINOUS ADENOCARCINOMA              3              44
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  G3BP2 MUTATED     8   0   0   1
  G3BP2 WILD-TYPE 337   4  31  24
D277V11, multiclass
    clus
vv   G3BP2 MUTATED G3BP2 WILD-TYPE
  R0             8             337
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D277V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  G3BP2 MUTATED                                  0     1
  G3BP2 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  G3BP2 MUTATED                           1     5
  G3BP2 WILD-TYPE                        21   221
D277V13, multiclass
                                  clus
vv                                 G3BP2 MUTATED G3BP2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        5             221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(278) Variable = TET3 MUTATION ANALYSIS
D278V1, survival
                sevent
clus2              0   1
  TET3 MUTATED    17   5
  TET3 WILD-TYPE 361  88
  TET3 MUTATED TET3 WILD-TYPE 
            22            449 
  TET3 MUTATED TET3 WILD-TYPE 
             5             88 
$`TET3 MUTATED`
TCGA-A6-6653 TCGA-AA-3663 TCGA-AA-3673 TCGA-AA-3713 TCGA-AA-3846 TCGA-AA-3864 
       24.39         6.97        50.04        19.04        17.03        53.00 
TCGA-AA-3950 TCGA-AD-6889 TCGA-CA-6715 TCGA-CA-6718 TCGA-CK-5913 TCGA-CM-4743 
       24.00        56.55         0.07        10.06        51.32        23.05 
TCGA-CM-4746 TCGA-CM-6171 TCGA-D5-6533 TCGA-DM-A1D4 TCGA-F4-6570 TCGA-G4-6321 
       37.02        14.04         1.32        92.75         6.18        22.09 
TCGA-AF-5654 TCGA-AG-3883 TCGA-AG-3893 TCGA-DY-A1DD 
       16.83         1.02        35.01        57.24 

$`TET3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
       25.08        25.18        24.16        21.76        24.69        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3678 TCGA-AA-3679 
       54.02         2.01        14.01         0.92        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       85.05        26.99        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02        14.93         0.00        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       30.05        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       15.52         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6716 
        1.61        12.69         3.06         3.25         3.29        12.20 
TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       12.76        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       49.08         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       20.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 
       21.99        14.99        12.99        13.02        15.02        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       20.19        18.25        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       24.43        38.20       130.65        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 
       98.24         8.61        31.96        35.74        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       10.39        14.50        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
        0.99        19.04        19.99        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       13.02        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  TET3 MUTATED TET3 WILD-TYPE 
          0.07           0.00 
  TET3 MUTATED TET3 WILD-TYPE 
         92.75         148.01 
  TET3 MUTATED TET3 WILD-TYPE 
         22.57          20.12 
[1] "0.1 - 92.8 (22.6)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1"  
D278V2, continuous
D278V3, binary
                cls
clus               0   1
  TET3 MUTATED    20   4
  TET3 WILD-TYPE 346 115
[1] "tbl2"
                cls
clus             [,1] [,2]
  TET3 MUTATED     20    4
  TET3 WILD-TYPE  346  115
        clus
vv       TET3 MUTATED TET3 WILD-TYPE
  COLON            20            346
  RECTUM            4            115
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TET3 MUTATED         5        0        4         8         1         0
  TET3 WILD-TYPE      86        1       28       130         9         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TET3 MUTATED           1          0          4          0        1         0
  TET3 WILD-TYPE        23         11         55         42       47        18
                vv
clus             STAGE IVB
  TET3 MUTATED           0
  TET3 WILD-TYPE         1
D278V4, multiclass
            clus
vv           TET3 MUTATED TET3 WILD-TYPE
  STAGE I               5             86
  STAGE IA              0              1
  STAGE II              4             28
  STAGE IIA             8            130
  STAGE IIB             1              9
  STAGE IIC             0              1
  STAGE III             1             23
  STAGE IIIA            0             11
  STAGE IIIB            4             55
  STAGE IIIC            0             42
  STAGE IV              1             47
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  TET3 MUTATED     0   6  15   3
  TET3 WILD-TYPE  17  86 314  47
D278V5, multiclass
    clus
vv   TET3 MUTATED TET3 WILD-TYPE
  T1            0             17
  T2            6             86
  T3           15            314
  T4            3             47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  TET3 MUTATED    20   4   0
  TET3 WILD-TYPE 267 109  87
D278V6, multiclass
    clus
vv   TET3 MUTATED TET3 WILD-TYPE
  N0           20            267
  N1            4            109
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D278V7, binary
                cls
clus               0   1
  TET3 MUTATED    20   1
  TET3 WILD-TYPE 355  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  TET3 MUTATED     20    1
  TET3 WILD-TYPE  355   64
   clus
vv  TET3 MUTATED TET3 WILD-TYPE
  0           20            355
  1            1             64
[1] 2 2
[1] FALSE
D278V8, binary
                cls
clus               0   1
  TET3 MUTATED    12  12
  TET3 WILD-TYPE 213 252
[1] "tbl2"
                cls
clus             [,1] [,2]
  TET3 MUTATED     12   12
  TET3 WILD-TYPE  213  252
        clus
vv       TET3 MUTATED TET3 WILD-TYPE
  FEMALE           12            213
  MALE             12            252
[1] 2 2
[1] FALSE
D278V9, binary
                cls
clus               0   1
  TET3 MUTATED    15   1
  TET3 WILD-TYPE 335  21
[1] "tbl2"
                cls
clus             [,1] [,2]
  TET3 MUTATED     15    1
  TET3 WILD-TYPE  335   21
     clus
vv    TET3 MUTATED TET3 WILD-TYPE
  NO            15            335
  YES            1             21
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  TET3 MUTATED                     19                             1
  TET3 WILD-TYPE                  296                            46
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  TET3 MUTATED                       4                              0
  TET3 WILD-TYPE                   102                             10
D278V10, multiclass
                                clus
vv                               TET3 MUTATED TET3 WILD-TYPE
  COLON ADENOCARCINOMA                     19            296
  COLON MUCINOUS ADENOCARCINOMA             1             46
  RECTAL ADENOCARCINOMA                     4            102
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  TET3 MUTATED    15   0   1   4
  TET3 WILD-TYPE 330   4  30  21
D278V11, multiclass
    clus
vv   TET3 MUTATED TET3 WILD-TYPE
  R0           15            330
  R1            0              4
  R2            1             30
  RX            4             21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D278V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TET3 MUTATED                                  0     3
  TET3 WILD-TYPE                                1     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  TET3 MUTATED                           1    11
  TET3 WILD-TYPE                        21   215
D278V13, multiclass
                                  clus
vv                                 TET3 MUTATED TET3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       3              8
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                      11            215
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(279) Variable = C12ORF5 MUTATION ANALYSIS
D279V1, survival
                   sevent
clus2                 0   1
  C12ORF5 MUTATED     6   0
  C12ORF5 WILD-TYPE 372  93
  C12ORF5 MUTATED C12ORF5 WILD-TYPE 
                6               465 
  C12ORF5 MUTATED C12ORF5 WILD-TYPE 
                0                93 
$`C12ORF5 MUTATED`
TCGA-A6-5660 TCGA-AZ-4315 TCGA-CM-6164 TCGA-D5-5538 TCGA-G4-6293 TCGA-G4-6306 
       29.19        58.39        29.03        12.26       133.18        44.68 

$`C12ORF5 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        33.01        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       15.02        12.00         2.96        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       45.40        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
        0.53        47.41        35.31        74.56        65.85        53.62 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  C12ORF5 MUTATED C12ORF5 WILD-TYPE 
            12.26              0.00 
  C12ORF5 MUTATED C12ORF5 WILD-TYPE 
           133.18            148.01 
  C12ORF5 MUTATED C12ORF5 WILD-TYPE 
           36.935            20.050 
[1] "12.3 - 133.2 (36.9)" "0.0 - 148.0 (20.1)" 
[1] "hr="     "9300000"
D279V2, continuous
D279V3, binary
                   cls
clus                  0   1
  C12ORF5 MUTATED     6   0
  C12ORF5 WILD-TYPE 360 119
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C12ORF5 MUTATED      6    0
  C12ORF5 WILD-TYPE  360  119
        clus
vv       C12ORF5 MUTATED C12ORF5 WILD-TYPE
  COLON                6               360
  RECTUM               0               119
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  C12ORF5 MUTATED         0        0        0         3         0         0
  C12ORF5 WILD-TYPE      91        1       32       135        10         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C12ORF5 MUTATED           1          0          1          1        0
  C12ORF5 WILD-TYPE        23         11         58         41       48
                   vv
clus                STAGE IVA STAGE IVB
  C12ORF5 MUTATED           0         0
  C12ORF5 WILD-TYPE        18         1
D279V4, multiclass
            clus
vv           C12ORF5 MUTATED C12ORF5 WILD-TYPE
  STAGE I                  0                91
  STAGE IA                 0                 1
  STAGE II                 0                32
  STAGE IIA                3               135
  STAGE IIB                0                10
  STAGE IIC                0                 1
  STAGE III                1                23
  STAGE IIIA               0                11
  STAGE IIIB               1                58
  STAGE IIIC               1                41
  STAGE IV                 0                48
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  C12ORF5 MUTATED     0   1   5   0
  C12ORF5 WILD-TYPE  17  91 324  50
D279V5, multiclass
    clus
vv   C12ORF5 MUTATED C12ORF5 WILD-TYPE
  T1               0                17
  T2               1                91
  T3               5               324
  T4               0                50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  C12ORF5 MUTATED     3   2   1
  C12ORF5 WILD-TYPE 284 111  86
D279V6, multiclass
    clus
vv   C12ORF5 MUTATED C12ORF5 WILD-TYPE
  N0               3               284
  N1               2               111
  N2               1                86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D279V7, binary
                   cls
clus                  0   1
  C12ORF5 MUTATED     6   0
  C12ORF5 WILD-TYPE 369  65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C12ORF5 MUTATED      6    0
  C12ORF5 WILD-TYPE  369   65
   clus
vv  C12ORF5 MUTATED C12ORF5 WILD-TYPE
  0               6               369
  1               0                65
[1] 2 2
[1] FALSE
D279V8, binary
                   cls
clus                  0   1
  C12ORF5 MUTATED     3   3
  C12ORF5 WILD-TYPE 222 261
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C12ORF5 MUTATED      3    3
  C12ORF5 WILD-TYPE  222  261
        clus
vv       C12ORF5 MUTATED C12ORF5 WILD-TYPE
  FEMALE               3               222
  MALE                 3               261
[1] 2 2
[1] FALSE
D279V9, binary
                   cls
clus                  0   1
  C12ORF5 MUTATED     6   0
  C12ORF5 WILD-TYPE 344  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C12ORF5 MUTATED      6    0
  C12ORF5 WILD-TYPE  344   22
     clus
vv    C12ORF5 MUTATED C12ORF5 WILD-TYPE
  NO                6               344
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  C12ORF5 MUTATED                      6                             0
  C12ORF5 WILD-TYPE                  309                            47
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  C12ORF5 MUTATED                       0                              0
  C12ORF5 WILD-TYPE                   106                             10
D279V10, multiclass
                                clus
vv                               C12ORF5 MUTATED C12ORF5 WILD-TYPE
  COLON ADENOCARCINOMA                         6               309
  COLON MUCINOUS ADENOCARCINOMA                0                47
  RECTAL ADENOCARCINOMA                        0               106
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  C12ORF5 MUTATED     5   0   0   0
  C12ORF5 WILD-TYPE 340   4  31  25
D279V11, multiclass
    clus
vv   C12ORF5 MUTATED C12ORF5 WILD-TYPE
  R0               5               340
  R1               0                 4
  R2               0                31
  RX               0                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D279V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C12ORF5 MUTATED                                  0     0
  C12ORF5 WILD-TYPE                                1    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  C12ORF5 MUTATED                           1     5
  C12ORF5 WILD-TYPE                        21   221
D279V13, multiclass
                                  clus
vv                                 C12ORF5 MUTATED C12ORF5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                      1                21
  WHITE                                          5               221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(280) Variable = GPR98 MUTATION ANALYSIS
D280V1, survival
                 sevent
clus2               0   1
  GPR98 MUTATED    56  12
  GPR98 WILD-TYPE 322  81
  GPR98 MUTATED GPR98 WILD-TYPE 
             68             403 
  GPR98 MUTATED GPR98 WILD-TYPE 
             12              81 
$`GPR98 MUTATED`
TCGA-A6-3809 TCGA-A6-5660 TCGA-A6-5665 TCGA-A6-6651 TCGA-A6-6654 TCGA-AA-3489 
       32.75        29.19        22.06        21.76        23.87         7.04 
TCGA-AA-3492 TCGA-AA-3663 TCGA-AA-3672 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3819 
        3.02         6.97         0.92        85.05        19.04        25.02 
TCGA-AA-3833 TCGA-AA-3852 TCGA-AA-3864 TCGA-AA-3877 TCGA-AA-3941 TCGA-AA-3950 
       15.95         0.00        53.00        31.00        24.00        24.00 
TCGA-AA-3955 TCGA-AA-3966 TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01R 
       20.98         2.01        25.02         4.01        34.98        35.01 
TCGA-AD-6889 TCGA-AD-6895 TCGA-AU-3779 TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-4616 
       56.55         0.72        14.50        21.44        58.39         5.13 
TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-5912 
       62.79        49.41         6.77        12.76        10.06        49.08 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-6171 
      124.27        23.05        37.02        30.08        15.02        14.04 
TCGA-CM-6674 TCGA-CM-6678 TCGA-D5-5541 TCGA-D5-6535 TCGA-D5-6927 TCGA-D5-6928 
       12.95        11.01        55.92        15.12         9.44        11.64 
TCGA-D5-6930 TCGA-D5-6932 TCGA-DM-A1HB TCGA-DM-A28H TCGA-F4-6570 TCGA-F4-6856 
        1.51        11.38       135.65       117.07         6.18        35.31 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6586 TCGA-G4-6588 
       44.68        55.04        85.48        61.91        35.80        26.17 
TCGA-AG-3881 TCGA-AG-3892 TCGA-AG-A002 TCGA-CI-6622 TCGA-DY-A0XA TCGA-DY-A1DC 
       19.04        13.02        20.98         6.97       126.44        41.36 
TCGA-EI-6507 TCGA-G5-6235 
       19.96        55.76 

$`GPR98 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 
       31.63        30.44        33.53        23.61        22.09        32.71 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       27.09        22.52         8.38        25.08        25.18        24.16 
TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3496 
       24.69        24.39        20.12        19.66        20.28         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
       54.02         2.01        14.01        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       26.99        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
        1.02        17.98        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 
       17.03        10.06         0.00        33.07        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 
        0.99        31.07        31.07        30.05        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3947 
       27.02        29.98        18.05         2.01        12.99        33.01 
TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       26.01         2.01        34.03        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
        1.02         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       21.37        15.52         0.79         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       10.88         0.20        27.09        16.31         0.95        33.01 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6600 
       17.82         1.41       106.75        22.36        88.21        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5913 
       14.30        17.56       148.01        85.45        15.62        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CM-4744 TCGA-CM-4747 
        9.99        21.14        82.95         1.91        20.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5862 
       13.02        29.06        22.03        22.98        32.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6679 
       15.02        11.01        13.05        11.08        11.08        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-6529 
       12.03        45.40        12.26        19.59        56.09        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       18.25         1.32        43.27        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-7000 
       12.43        14.30         9.04         4.80        12.00        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 
       98.24         8.61        31.96        35.74        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6310 
       47.41       133.18        74.56        65.85        53.62        63.62 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       36.00        22.09        13.78        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99         0.99        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       17.03        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
        6.05        33.17         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        4.01         5.03         5.29        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
       32.61         0.49        20.55        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6641 
       26.43 

  GPR98 MUTATED GPR98 WILD-TYPE 
              0               0 
  GPR98 MUTATED GPR98 WILD-TYPE 
         135.65          148.01 
  GPR98 MUTATED GPR98 WILD-TYPE 
         22.555          19.990 
[1] "0.0 - 135.7 (22.6)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.4"
D280V2, continuous
D280V3, binary
                 cls
clus                0   1
  GPR98 MUTATED    61   8
  GPR98 WILD-TYPE 305 111
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPR98 MUTATED     61    8
  GPR98 WILD-TYPE  305  111
        clus
vv       GPR98 MUTATED GPR98 WILD-TYPE
  COLON             61             305
  RECTUM             8             111
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GPR98 MUTATED         9        0        6        29         4         0
  GPR98 WILD-TYPE      82        1       26       109         6         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  GPR98 MUTATED           3          0          9          2        3         2
  GPR98 WILD-TYPE        21         11         50         40       45        16
                 vv
clus              STAGE IVB
  GPR98 MUTATED           0
  GPR98 WILD-TYPE         1
D280V4, multiclass
            clus
vv           GPR98 MUTATED GPR98 WILD-TYPE
  STAGE I                9              82
  STAGE IA               0               1
  STAGE II               6              26
  STAGE IIA             29             109
  STAGE IIB              4               6
  STAGE IIC              0               1
  STAGE III              3              21
  STAGE IIIA             0              11
  STAGE IIIB             9              50
  STAGE IIIC             2              40
  STAGE IV               3              45
  STAGE IVA              2              16
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  GPR98 MUTATED     2  10  51   6
  GPR98 WILD-TYPE  15  82 278  44
D280V5, multiclass
    clus
vv   GPR98 MUTATED GPR98 WILD-TYPE
  T1             2              15
  T2            10              82
  T3            51             278
  T4             6              44
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  GPR98 MUTATED    51  13   5
  GPR98 WILD-TYPE 236 100  82
D280V6, multiclass
    clus
vv   GPR98 MUTATED GPR98 WILD-TYPE
  N0            51             236
  N1            13             100
  N2             5              82
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D280V7, binary
                 cls
clus                0   1
  GPR98 MUTATED    53   5
  GPR98 WILD-TYPE 322  60
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPR98 MUTATED     53    5
  GPR98 WILD-TYPE  322   60
   clus
vv  GPR98 MUTATED GPR98 WILD-TYPE
  0            53             322
  1             5              60
[1] 2 2
[1] FALSE
D280V8, binary
                 cls
clus                0   1
  GPR98 MUTATED    32  37
  GPR98 WILD-TYPE 193 227
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPR98 MUTATED     32   37
  GPR98 WILD-TYPE  193  227
        clus
vv       GPR98 MUTATED GPR98 WILD-TYPE
  FEMALE            32             193
  MALE              37             227
[1] 2 2
[1] FALSE
D280V9, binary
                 cls
clus                0   1
  GPR98 MUTATED    55   2
  GPR98 WILD-TYPE 295  20
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPR98 MUTATED     55    2
  GPR98 WILD-TYPE  295   20
     clus
vv    GPR98 MUTATED GPR98 WILD-TYPE
  NO             55             295
  YES             2              20
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  GPR98 MUTATED                     48                            12
  GPR98 WILD-TYPE                  267                            35
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  GPR98 MUTATED                       7                              0
  GPR98 WILD-TYPE                    99                             10
D280V10, multiclass
                                clus
vv                               GPR98 MUTATED GPR98 WILD-TYPE
  COLON ADENOCARCINOMA                      48             267
  COLON MUCINOUS ADENOCARCINOMA             12              35
  RECTAL ADENOCARCINOMA                      7              99
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  GPR98 MUTATED    45   1   1   5
  GPR98 WILD-TYPE 300   3  30  20
D280V11, multiclass
    clus
vv   GPR98 MUTATED GPR98 WILD-TYPE
  R0            45             300
  R1             1               3
  R2             1              30
  RX             5              20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D280V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GPR98 MUTATED                                  0     3
  GPR98 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  GPR98 MUTATED                           3    40
  GPR98 WILD-TYPE                        19   186
D280V13, multiclass
                                  clus
vv                                 GPR98 MUTATED GPR98 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        3               8
  BLACK OR AFRICAN AMERICAN                    3              19
  WHITE                                       40             186
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(281) Variable = MAGEA1 MUTATION ANALYSIS
D281V1, survival
                  sevent
clus2                0   1
  MAGEA1 MUTATED    11   3
  MAGEA1 WILD-TYPE 367  90
  MAGEA1 MUTATED MAGEA1 WILD-TYPE 
              14              457 
  MAGEA1 MUTATED MAGEA1 WILD-TYPE 
               3               90 
$`MAGEA1 MUTATED`
TCGA-AA-3510 TCGA-AY-5543 TCGA-AY-6197 TCGA-AZ-4616 TCGA-AZ-5403 TCGA-CK-4948 
       63.98        33.01        21.44         5.13        62.79       148.01 
TCGA-CK-5914 TCGA-CK-6748 TCGA-D5-6539 TCGA-F4-6805 TCGA-G4-6303 TCGA-G4-6588 
        9.99         1.91        12.49        34.42        65.85        26.17 
TCGA-G4-6628 TCGA-EI-6507 
       79.69        19.96 

$`MAGEA1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4681 TCGA-AZ-4682 
        0.95        17.82        58.39         1.41       106.75        22.36 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       14.30        17.56        85.45        15.62        49.08        51.32 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       21.14        82.95       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
        4.80        17.13        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
       47.87         1.55        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6304 
        0.53        47.41        35.31       133.18        74.56        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 
       22.09        13.78        35.80        91.79        46.75        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
        0.49        20.55        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  MAGEA1 MUTATED MAGEA1 WILD-TYPE 
            1.91             0.00 
  MAGEA1 MUTATED MAGEA1 WILD-TYPE 
          148.01           140.38 
  MAGEA1 MUTATED MAGEA1 WILD-TYPE 
           29.59            20.05 
[1] "1.9 - 148.0 (29.6)" "0.0 - 140.4 (20.1)"
[1] "hr=" "1.4"
D281V2, continuous
D281V3, binary
                  cls
clus                 0   1
  MAGEA1 MUTATED    13   1
  MAGEA1 WILD-TYPE 353 118
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAGEA1 MUTATED     13    1
  MAGEA1 WILD-TYPE  353  118
        clus
vv       MAGEA1 MUTATED MAGEA1 WILD-TYPE
  COLON              13              353
  RECTUM              1              118
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MAGEA1 MUTATED         1        0        2         4         0         0
  MAGEA1 WILD-TYPE      90        1       30       134        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MAGEA1 MUTATED           1          1          1          0        3
  MAGEA1 WILD-TYPE        23         10         58         42       45
                  vv
clus               STAGE IVA STAGE IVB
  MAGEA1 MUTATED           1         0
  MAGEA1 WILD-TYPE        17         1
D281V4, multiclass
            clus
vv           MAGEA1 MUTATED MAGEA1 WILD-TYPE
  STAGE I                 1               90
  STAGE IA                0                1
  STAGE II                2               30
  STAGE IIA               4              134
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               1               23
  STAGE IIIA              1               10
  STAGE IIIB              1               58
  STAGE IIIC              0               42
  STAGE IV                3               45
  STAGE IVA               1               17
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  MAGEA1 MUTATED     0   1  13   0
  MAGEA1 WILD-TYPE  17  91 316  50
D281V5, multiclass
    clus
vv   MAGEA1 MUTATED MAGEA1 WILD-TYPE
  T1              0               17
  T2              1               91
  T3             13              316
  T4              0               50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  MAGEA1 MUTATED     8   5   1
  MAGEA1 WILD-TYPE 279 108  86
D281V6, multiclass
    clus
vv   MAGEA1 MUTATED MAGEA1 WILD-TYPE
  N0              8              279
  N1              5              108
  N2              1               86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D281V7, binary
                  cls
clus                 0   1
  MAGEA1 MUTATED     7   4
  MAGEA1 WILD-TYPE 368  61
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAGEA1 MUTATED      7    4
  MAGEA1 WILD-TYPE  368   61
   clus
vv  MAGEA1 MUTATED MAGEA1 WILD-TYPE
  0              7              368
  1              4               61
[1] 2 2
[1] FALSE
D281V8, binary
                  cls
clus                 0   1
  MAGEA1 MUTATED     8   6
  MAGEA1 WILD-TYPE 217 258
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAGEA1 MUTATED      8    6
  MAGEA1 WILD-TYPE  217  258
        clus
vv       MAGEA1 MUTATED MAGEA1 WILD-TYPE
  FEMALE              8              217
  MALE                6              258
[1] 2 2
[1] FALSE
D281V9, binary
                  cls
clus                 0   1
  MAGEA1 MUTATED    13   0
  MAGEA1 WILD-TYPE 337  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAGEA1 MUTATED     13    0
  MAGEA1 WILD-TYPE  337   22
     clus
vv    MAGEA1 MUTATED MAGEA1 WILD-TYPE
  NO              13              337
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MAGEA1 MUTATED                     12                             1
  MAGEA1 WILD-TYPE                  303                            46
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MAGEA1 MUTATED                       1                              0
  MAGEA1 WILD-TYPE                   105                             10
D281V10, multiclass
                                clus
vv                               MAGEA1 MUTATED MAGEA1 WILD-TYPE
  COLON ADENOCARCINOMA                       12              303
  COLON MUCINOUS ADENOCARCINOMA               1               46
  RECTAL ADENOCARCINOMA                       1              105
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  MAGEA1 MUTATED    10   0   0   2
  MAGEA1 WILD-TYPE 335   4  31  23
D281V11, multiclass
    clus
vv   MAGEA1 MUTATED MAGEA1 WILD-TYPE
  R0             10              335
  R1              0                4
  R2              0               31
  RX              2               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D281V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MAGEA1 MUTATED                                  0     0
  MAGEA1 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  MAGEA1 MUTATED                           1    12
  MAGEA1 WILD-TYPE                        21   214
D281V13, multiclass
                                  clus
vv                                 MAGEA1 MUTATED MAGEA1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                        12              214
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(282) Variable = HNF1B MUTATION ANALYSIS
D282V1, survival
                 sevent
clus2               0   1
  HNF1B MUTATED     8   2
  HNF1B WILD-TYPE 370  91
  HNF1B MUTATED HNF1B WILD-TYPE 
             10             461 
  HNF1B MUTATED HNF1B WILD-TYPE 
              2              91 
$`HNF1B MUTATED`
TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-6141 TCGA-AA-3819 TCGA-AD-6889 TCGA-AD-6899 
       14.53        32.91         8.38        25.02        56.55         5.79 
TCGA-AD-6965 TCGA-D5-6540 TCGA-G4-6586 TCGA-AG-A002 
        0.20        16.14        35.80        20.98 

$`HNF1B WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5657 
       16.57        34.65        33.34        32.75        36.53        31.63 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       30.44        29.19        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       32.71        27.09        22.52        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
       33.04         0.99         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 
       40.96         0.07        21.37        15.52         0.79         0.72 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        10.88        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 
       17.85         4.80        17.13        12.49        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 
       63.62        61.91        36.00        22.09        13.78        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  HNF1B MUTATED HNF1B WILD-TYPE 
            0.2             0.0 
  HNF1B MUTATED HNF1B WILD-TYPE 
          56.55          148.01 
  HNF1B MUTATED HNF1B WILD-TYPE 
          18.56           20.19 
[1] "0.2 - 56.5 (18.6)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.2"
D282V2, continuous
D282V3, binary
                 cls
clus                0   1
  HNF1B MUTATED     9   1
  HNF1B WILD-TYPE 357 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HNF1B MUTATED      9    1
  HNF1B WILD-TYPE  357  118
        clus
vv       HNF1B MUTATED HNF1B WILD-TYPE
  COLON              9             357
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  HNF1B MUTATED         3        0        0         5         0         0
  HNF1B WILD-TYPE      88        1       32       133        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  HNF1B MUTATED           0          0          0          1        0         0
  HNF1B WILD-TYPE        24         11         59         41       48        18
                 vv
clus              STAGE IVB
  HNF1B MUTATED           0
  HNF1B WILD-TYPE         1
D282V4, multiclass
            clus
vv           HNF1B MUTATED HNF1B WILD-TYPE
  STAGE I                3              88
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              5             133
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             1              41
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  HNF1B MUTATED     0   3   5   2
  HNF1B WILD-TYPE  17  89 324  48
D282V5, multiclass
    clus
vv   HNF1B MUTATED HNF1B WILD-TYPE
  T1             0              17
  T2             3              89
  T3             5             324
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  HNF1B MUTATED     8   0   2
  HNF1B WILD-TYPE 279 113  85
D282V6, multiclass
    clus
vv   HNF1B MUTATED HNF1B WILD-TYPE
  N0             8             279
  N1             0             113
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D282V7, binary
                 cls
clus                0   1
  HNF1B MUTATED     8   0
  HNF1B WILD-TYPE 367  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HNF1B MUTATED      8    0
  HNF1B WILD-TYPE  367   65
   clus
vv  HNF1B MUTATED HNF1B WILD-TYPE
  0             8             367
  1             0              65
[1] 2 2
[1] FALSE
D282V8, binary
                 cls
clus                0   1
  HNF1B MUTATED     2   8
  HNF1B WILD-TYPE 223 256
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HNF1B MUTATED      2    8
  HNF1B WILD-TYPE  223  256
        clus
vv       HNF1B MUTATED HNF1B WILD-TYPE
  FEMALE             2             223
  MALE               8             256
[1] 2 2
[1] FALSE
D282V9, binary
                 cls
clus                0   1
  HNF1B MUTATED     8   0
  HNF1B WILD-TYPE 342  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HNF1B MUTATED      8    0
  HNF1B WILD-TYPE  342   22
     clus
vv    HNF1B MUTATED HNF1B WILD-TYPE
  NO              8             342
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  HNF1B MUTATED                      7                             2
  HNF1B WILD-TYPE                  308                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  HNF1B MUTATED                       1                              0
  HNF1B WILD-TYPE                   105                             10
D282V10, multiclass
                                clus
vv                               HNF1B MUTATED HNF1B WILD-TYPE
  COLON ADENOCARCINOMA                       7             308
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  HNF1B MUTATED     4   0   0   0
  HNF1B WILD-TYPE 341   4  31  25
D282V11, multiclass
    clus
vv   HNF1B MUTATED HNF1B WILD-TYPE
  R0             4             341
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D282V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HNF1B MUTATED                                  0     1
  HNF1B WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  HNF1B MUTATED                           1     6
  HNF1B WILD-TYPE                        21   220
D282V13, multiclass
                                  clus
vv                                 HNF1B MUTATED HNF1B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        6             220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(283) Variable = C19ORF66 MUTATION ANALYSIS
D283V1, survival
                    sevent
clus2                  0   1
  C19ORF66 MUTATED     4   0
  C19ORF66 WILD-TYPE 374  93
  C19ORF66 MUTATED C19ORF66 WILD-TYPE 
                 4                467 
  C19ORF66 MUTATED C19ORF66 WILD-TYPE 
                 0                 93 
$`C19ORF66 MUTATED`
TCGA-AA-3663 TCGA-AA-3713 TCGA-AA-3949 TCGA-D5-6540 
        6.97        19.04        26.01        16.14 

$`C19ORF66 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.05        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       12.99        24.00        33.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       17.13        12.49        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  C19ORF66 MUTATED C19ORF66 WILD-TYPE 
              6.97               0.00 
  C19ORF66 MUTATED C19ORF66 WILD-TYPE 
             26.01             148.01 
  C19ORF66 MUTATED C19ORF66 WILD-TYPE 
             17.59              20.28 
[1] "7.0 - 26.0 (17.6)"  "0.0 - 148.0 (20.3)"
[1] "hr="     "3300000"
D283V2, continuous
D283V3, binary
                    cls
clus                   0   1
  C19ORF66 MUTATED     4   0
  C19ORF66 WILD-TYPE 362 119
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C19ORF66 MUTATED      4    0
  C19ORF66 WILD-TYPE  362  119
        clus
vv       C19ORF66 MUTATED C19ORF66 WILD-TYPE
  COLON                 4                362
  RECTUM                0                119
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  C19ORF66 MUTATED         1        0        1         0         0         0
  C19ORF66 WILD-TYPE      90        1       31       138        10         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C19ORF66 MUTATED           0          0          1          0        1
  C19ORF66 WILD-TYPE        24         11         58         42       47
                    vv
clus                 STAGE IVA STAGE IVB
  C19ORF66 MUTATED           0         0
  C19ORF66 WILD-TYPE        18         1
D283V4, multiclass
            clus
vv           C19ORF66 MUTATED C19ORF66 WILD-TYPE
  STAGE I                   1                 90
  STAGE IA                  0                  1
  STAGE II                  1                 31
  STAGE IIA                 0                138
  STAGE IIB                 0                 10
  STAGE IIC                 0                  1
  STAGE III                 0                 24
  STAGE IIIA                0                 11
  STAGE IIIB                1                 58
  STAGE IIIC                0                 42
  STAGE IV                  1                 47
  STAGE IVA                 0                 18
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  C19ORF66 MUTATED     0   1   3   0
  C19ORF66 WILD-TYPE  17  91 326  50
D283V5, multiclass
    clus
vv   C19ORF66 MUTATED C19ORF66 WILD-TYPE
  T1                0                 17
  T2                1                 91
  T3                3                326
  T4                0                 50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  C19ORF66 MUTATED     3   1   0
  C19ORF66 WILD-TYPE 284 112  87
D283V6, multiclass
    clus
vv   C19ORF66 MUTATED C19ORF66 WILD-TYPE
  N0                3                284
  N1                1                112
  N2                0                 87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D283V7, binary
                    cls
clus                   0   1
  C19ORF66 MUTATED     3   1
  C19ORF66 WILD-TYPE 372  64
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C19ORF66 MUTATED      3    1
  C19ORF66 WILD-TYPE  372   64
   clus
vv  C19ORF66 MUTATED C19ORF66 WILD-TYPE
  0                3                372
  1                1                 64
[1] 2 2
[1] FALSE
D283V8, binary
                    cls
clus                   0   1
  C19ORF66 MUTATED     1   3
  C19ORF66 WILD-TYPE 224 261
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C19ORF66 MUTATED      1    3
  C19ORF66 WILD-TYPE  224  261
        clus
vv       C19ORF66 MUTATED C19ORF66 WILD-TYPE
  FEMALE                1                224
  MALE                  3                261
[1] 2 2
[1] FALSE
D283V9, binary
                    cls
clus                   0   1
  C19ORF66 MUTATED     3   1
  C19ORF66 WILD-TYPE 347  21
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C19ORF66 MUTATED      3    1
  C19ORF66 WILD-TYPE  347   21
     clus
vv    C19ORF66 MUTATED C19ORF66 WILD-TYPE
  NO                 3                347
  YES                1                 21
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  C19ORF66 MUTATED                      2                             2
  C19ORF66 WILD-TYPE                  313                            45
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  C19ORF66 MUTATED                       0                              0
  C19ORF66 WILD-TYPE                   106                             10
D283V10, multiclass
                                clus
vv                               C19ORF66 MUTATED C19ORF66 WILD-TYPE
  COLON ADENOCARCINOMA                          2                313
  COLON MUCINOUS ADENOCARCINOMA                 2                 45
  RECTAL ADENOCARCINOMA                         0                106
  RECTAL MUCINOUS ADENOCARCINOMA                0                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  C19ORF66 MUTATED     3   0   1   0
  C19ORF66 WILD-TYPE 342   4  30  25
D283V11, multiclass
    clus
vv   C19ORF66 MUTATED C19ORF66 WILD-TYPE
  R0                3                342
  R1                0                  4
  R2                1                 30
  RX                0                 25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D283V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C19ORF66 MUTATED                                  0     0
  C19ORF66 WILD-TYPE                                1    11
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  C19ORF66 MUTATED                           0     1
  C19ORF66 WILD-TYPE                        22   225
D283V13, multiclass
[1] "Remove cluster labels:" "C19ORF66 MUTATED"      
clus
  C19ORF66 MUTATED C19ORF66 WILD-TYPE 
                 1                259 
        TCGA-A6-2671         TCGA-A6-2672         TCGA-A6-2674 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-A6-2676         TCGA-A6-2677         TCGA-A6-2678 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-A6-2683         TCGA-A6-3807         TCGA-A6-3808 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-A6-3809         TCGA-A6-3810         TCGA-A6-4105 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-A6-5656         TCGA-A6-5657         TCGA-A6-5659 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-A6-5660         TCGA-A6-5661         TCGA-A6-5662 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-A6-5664         TCGA-A6-5665         TCGA-A6-5666 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-A6-6137         TCGA-A6-6138         TCGA-A6-6141 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-A6-6142         TCGA-A6-6648         TCGA-A6-6649 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-A6-6651         TCGA-A6-6652         TCGA-A6-6653 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-A6-6654         TCGA-A6-6780         TCGA-A6-6781 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-A6-6782         TCGA-AD-5900         TCGA-AD-6548 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-AD-6888         TCGA-AD-6889         TCGA-AD-6890 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-AD-6895         TCGA-AD-6899         TCGA-AD-6901 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-AD-6963         TCGA-AD-6964         TCGA-AD-6965 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-AU-3779         TCGA-AU-6004         TCGA-AY-4070 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-AY-4071         TCGA-AY-5543         TCGA-AY-6196 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-AY-6197         TCGA-AY-6386         TCGA-AZ-4315 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-AZ-4323         TCGA-AZ-4616         TCGA-AZ-4681 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-AZ-4682         TCGA-AZ-5403         TCGA-AZ-5407 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-AZ-6598         TCGA-AZ-6599         TCGA-AZ-6600 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-AZ-6601         TCGA-AZ-6603         TCGA-AZ-6605 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-AZ-6606         TCGA-AZ-6607         TCGA-AZ-6608 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-CA-5254         TCGA-CA-5255         TCGA-CA-5796 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-CA-5797         TCGA-CA-6715         TCGA-CA-6716 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-CA-6717         TCGA-CA-6718         TCGA-CA-6719 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-CK-4947         TCGA-CK-4948         TCGA-CK-4950 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-CK-4952         TCGA-CK-5912         TCGA-CK-5913 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-CK-5914         TCGA-CK-5915         TCGA-CK-5916 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-CK-6746         TCGA-CK-6747         TCGA-CK-6748 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-CK-6751         TCGA-CM-4743         TCGA-CM-4744 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-CM-4746         TCGA-CM-4747         TCGA-CM-4752 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-CM-5341         TCGA-CM-5344         TCGA-CM-5348 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-CM-5349         TCGA-CM-5860         TCGA-CM-5861 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-CM-5862         TCGA-CM-5863         TCGA-CM-5864 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-CM-5868         TCGA-CM-6161         TCGA-CM-6162 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-CM-6163         TCGA-CM-6164         TCGA-CM-6165 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-CM-6166         TCGA-CM-6167         TCGA-CM-6168 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-CM-6169         TCGA-CM-6170         TCGA-CM-6171 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-CM-6172         TCGA-CM-6674         TCGA-CM-6675 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-CM-6676         TCGA-CM-6677         TCGA-CM-6678 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-CM-6679         TCGA-CM-6680         TCGA-D5-5537 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-D5-5538         TCGA-D5-5539         TCGA-D5-5540 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-D5-5541         TCGA-D5-6529         TCGA-D5-6532 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-D5-6533         TCGA-D5-6534         TCGA-D5-6535 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-D5-6536         TCGA-D5-6537         TCGA-D5-6538 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-D5-6539         TCGA-D5-6541         TCGA-D5-6898 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-D5-6920         TCGA-D5-6922         TCGA-D5-6923 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-D5-6924         TCGA-D5-6926         TCGA-D5-6927 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-D5-6928         TCGA-D5-6929         TCGA-D5-6930 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-D5-6931         TCGA-D5-6932         TCGA-D5-7000 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-DM-A0X9         TCGA-DM-A0XD         TCGA-DM-A0XF 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-DM-A1D0         TCGA-DM-A1D4         TCGA-DM-A1D6 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-DM-A1D7         TCGA-DM-A1D8         TCGA-DM-A1D9 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-DM-A1DA         TCGA-DM-A1DB         TCGA-DM-A1HA 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-DM-A1HB         TCGA-DM-A282         TCGA-DM-A285 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-DM-A28C         TCGA-DM-A28E         TCGA-DM-A28F 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-DM-A28G         TCGA-DM-A28H         TCGA-DM-A28K 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-F4-6459         TCGA-F4-6460         TCGA-F4-6569 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-F4-6570         TCGA-F4-6703         TCGA-F4-6704 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-F4-6805         TCGA-F4-6806         TCGA-F4-6807 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-F4-6808         TCGA-F4-6809         TCGA-F4-6854 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-F4-6855         TCGA-F4-6856         TCGA-G4-6293 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-G4-6299         TCGA-G4-6303         TCGA-G4-6304 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-G4-6306         TCGA-G4-6307         TCGA-G4-6309 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-G4-6310         TCGA-G4-6315         TCGA-G4-6317 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-G4-6321         TCGA-G4-6323         TCGA-G4-6586 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-G4-6588         TCGA-G4-6625         TCGA-G4-6626 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-G4-6628         TCGA-AF-2687         TCGA-AF-2689 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3913         TCGA-AF-4110 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-AF-5654         TCGA-AF-6136         TCGA-AF-6655 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-AF-6672         TCGA-AH-6544         TCGA-AH-6547 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-AH-6549         TCGA-AH-6643         TCGA-AH-6644 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-CI-6619         TCGA-CI-6620         TCGA-CI-6621 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6624         TCGA-CL-5917 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-CL-5918         TCGA-DC-5337         TCGA-DC-5869 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-DC-6155         TCGA-DC-6157         TCGA-DC-6158 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DF 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-DY-A1DG         TCGA-DY-A1H8         TCGA-EF-5830 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-EI-6506         TCGA-EI-6507         TCGA-EI-6508 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-EI-6510         TCGA-F5-6464         TCGA-F5-6465 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-F5-6571         TCGA-F5-6702         TCGA-F5-6811 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-G5-6235 
"C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" "C19ORF66 WILD-TYPE" 
        TCGA-G5-6641 
"C19ORF66 WILD-TYPE" 

Clustering(284) Variable = INPP1 MUTATION ANALYSIS
D284V1, survival
                 sevent
clus2               0   1
  INPP1 MUTATED     5   2
  INPP1 WILD-TYPE 373  91
  INPP1 MUTATED INPP1 WILD-TYPE 
              7             464 
  INPP1 MUTATED INPP1 WILD-TYPE 
              2              91 
$`INPP1 MUTATED`
TCGA-AA-3697 TCGA-AA-3866 TCGA-AA-A010 TCGA-CK-5916 TCGA-CM-6163 TCGA-F4-6570 
       85.05        17.03        34.98        21.14         2.96         6.18 
TCGA-DY-A0XA 
      126.44 

$`INPP1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       19.00        36.00         5.03        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 
       15.62        49.08        51.32         9.99        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
        8.61        31.96        35.74        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
        5.29        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  INPP1 MUTATED INPP1 WILD-TYPE 
           2.96            0.00 
  INPP1 MUTATED INPP1 WILD-TYPE 
         126.44          148.01 
  INPP1 MUTATED INPP1 WILD-TYPE 
         21.140          20.155 
[1] "3.0 - 126.4 (21.1)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1"  
D284V2, continuous
D284V3, binary
                 cls
clus                0   1
  INPP1 MUTATED     7   1
  INPP1 WILD-TYPE 359 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  INPP1 MUTATED      7    1
  INPP1 WILD-TYPE  359  118
        clus
vv       INPP1 MUTATED INPP1 WILD-TYPE
  COLON              7             359
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  INPP1 MUTATED         4        0        0         2         1         0
  INPP1 WILD-TYPE      87        1       32       136         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  INPP1 MUTATED           1          0          0          0        0         0
  INPP1 WILD-TYPE        23         11         59         42       48        18
                 vv
clus              STAGE IVB
  INPP1 MUTATED           0
  INPP1 WILD-TYPE         1
D284V4, multiclass
            clus
vv           INPP1 MUTATED INPP1 WILD-TYPE
  STAGE I                4              87
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              2             136
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  INPP1 MUTATED     2   2   3   1
  INPP1 WILD-TYPE  15  90 326  49
D284V5, multiclass
    clus
vv   INPP1 MUTATED INPP1 WILD-TYPE
  T1             2              15
  T2             2              90
  T3             3             326
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  INPP1 MUTATED     8   0   0
  INPP1 WILD-TYPE 279 113  87
D284V6, multiclass
    clus
vv   INPP1 MUTATED INPP1 WILD-TYPE
  N0             8             279
  N1             0             113
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D284V7, binary
                 cls
clus                0   1
  INPP1 MUTATED     7   0
  INPP1 WILD-TYPE 368  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  INPP1 MUTATED      7    0
  INPP1 WILD-TYPE  368   65
   clus
vv  INPP1 MUTATED INPP1 WILD-TYPE
  0             7             368
  1             0              65
[1] 2 2
[1] FALSE
D284V8, binary
                 cls
clus                0   1
  INPP1 MUTATED     5   3
  INPP1 WILD-TYPE 220 261
[1] "tbl2"
                 cls
clus              [,1] [,2]
  INPP1 MUTATED      5    3
  INPP1 WILD-TYPE  220  261
        clus
vv       INPP1 MUTATED INPP1 WILD-TYPE
  FEMALE             5             220
  MALE               3             261
[1] 2 2
[1] FALSE
D284V9, binary
                 cls
clus                0   1
  INPP1 MUTATED     6   0
  INPP1 WILD-TYPE 344  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  INPP1 MUTATED      6    0
  INPP1 WILD-TYPE  344   22
     clus
vv    INPP1 MUTATED INPP1 WILD-TYPE
  NO              6             344
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  INPP1 MUTATED                      7                             0
  INPP1 WILD-TYPE                  308                            47
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  INPP1 MUTATED                       1                              0
  INPP1 WILD-TYPE                   105                             10
D284V10, multiclass
                                clus
vv                               INPP1 MUTATED INPP1 WILD-TYPE
  COLON ADENOCARCINOMA                       7             308
  COLON MUCINOUS ADENOCARCINOMA              0              47
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  INPP1 MUTATED     5   0   0   2
  INPP1 WILD-TYPE 340   4  31  23
D284V11, multiclass
    clus
vv   INPP1 MUTATED INPP1 WILD-TYPE
  R0             5             340
  R1             0               4
  R2             0              31
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D284V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  INPP1 MUTATED                                  0     0
  INPP1 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  INPP1 MUTATED                           0     5
  INPP1 WILD-TYPE                        22   221
D284V13, multiclass
                                  clus
vv                                 INPP1 MUTATED INPP1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        5             221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(285) Variable = TRIM24 MUTATION ANALYSIS
D285V1, survival
                  sevent
clus2                0   1
  TRIM24 MUTATED     9  10
  TRIM24 WILD-TYPE 369  83
  TRIM24 MUTATED TRIM24 WILD-TYPE 
              19              452 
  TRIM24 MUTATED TRIM24 WILD-TYPE 
              10               83 
$`TRIM24 MUTATED`
TCGA-A6-6782 TCGA-AA-3811 TCGA-AA-3833 TCGA-AA-A00N TCGA-AA-A02W TCGA-AD-5900 
       20.28        10.06        15.95         4.01        41.00         0.07 
TCGA-AZ-5403 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-CA-6718 TCGA-D5-6535 
       62.79         6.77        12.10        29.56        10.06        15.12 
TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-G4-6293 TCGA-G4-6628 TCGA-AG-A002 TCGA-DY-A1DC 
       12.59         7.50       133.18        79.69        20.98        41.36 
TCGA-F5-6813 
        0.69 

$`TRIM24 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        19.66         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
        5.03        14.01         0.92        39.98        18.05        40.96 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6598 
        1.41         5.13       106.75        22.36        88.21        49.41 
TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
      100.01         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       43.27        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA 
       92.75        49.91        13.32       140.38        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6299 
       33.67        13.25         0.53        47.41        35.31        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       91.79        46.75        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.03         5.29       126.44        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  TRIM24 MUTATED TRIM24 WILD-TYPE 
            0.07             0.00 
  TRIM24 MUTATED TRIM24 WILD-TYPE 
          133.18           148.01 
  TRIM24 MUTATED TRIM24 WILD-TYPE 
           15.12            20.73 
[1] "0.1 - 133.2 (15.1)" "0.0 - 148.0 (20.7)"
[1] "hr=" "2.8"
D285V2, continuous
D285V3, binary
                  cls
clus                 0   1
  TRIM24 MUTATED    17   3
  TRIM24 WILD-TYPE 349 116
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIM24 MUTATED     17    3
  TRIM24 WILD-TYPE  349  116
        clus
vv       TRIM24 MUTATED TRIM24 WILD-TYPE
  COLON              17              349
  RECTUM              3              116
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TRIM24 MUTATED         5        0        1         4         2         0
  TRIM24 WILD-TYPE      86        1       31       134         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TRIM24 MUTATED           2          0          1          2        1
  TRIM24 WILD-TYPE        22         11         58         40       47
                  vv
clus               STAGE IVA STAGE IVB
  TRIM24 MUTATED           0         0
  TRIM24 WILD-TYPE        18         1
D285V4, multiclass
            clus
vv           TRIM24 MUTATED TRIM24 WILD-TYPE
  STAGE I                 5               86
  STAGE IA                0                1
  STAGE II                1               31
  STAGE IIA               4              134
  STAGE IIB               2                8
  STAGE IIC               0                1
  STAGE III               2               22
  STAGE IIIA              0               11
  STAGE IIIB              1               58
  STAGE IIIC              2               40
  STAGE IV                1               47
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  TRIM24 MUTATED     0   6  10   4
  TRIM24 WILD-TYPE  17  86 319  46
D285V5, multiclass
    clus
vv   TRIM24 MUTATED TRIM24 WILD-TYPE
  T1              0               17
  T2              6               86
  T3             10              319
  T4              4               46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  TRIM24 MUTATED    12   5   3
  TRIM24 WILD-TYPE 275 108  84
D285V6, multiclass
    clus
vv   TRIM24 MUTATED TRIM24 WILD-TYPE
  N0             12              275
  N1              5              108
  N2              3               84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D285V7, binary
                  cls
clus                 0   1
  TRIM24 MUTATED    12   1
  TRIM24 WILD-TYPE 363  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIM24 MUTATED     12    1
  TRIM24 WILD-TYPE  363   64
   clus
vv  TRIM24 MUTATED TRIM24 WILD-TYPE
  0             12              363
  1              1               64
[1] 2 2
[1] FALSE
D285V8, binary
                  cls
clus                 0   1
  TRIM24 MUTATED    10  10
  TRIM24 WILD-TYPE 215 254
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIM24 MUTATED     10   10
  TRIM24 WILD-TYPE  215  254
        clus
vv       TRIM24 MUTATED TRIM24 WILD-TYPE
  FEMALE             10              215
  MALE               10              254
[1] 2 2
[1] FALSE
D285V9, binary
                  cls
clus                 0   1
  TRIM24 MUTATED    12   0
  TRIM24 WILD-TYPE 338  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIM24 MUTATED     12    0
  TRIM24 WILD-TYPE  338   22
     clus
vv    TRIM24 MUTATED TRIM24 WILD-TYPE
  NO              12              338
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  TRIM24 MUTATED                     15                             2
  TRIM24 WILD-TYPE                  300                            45
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  TRIM24 MUTATED                       3                              0
  TRIM24 WILD-TYPE                   103                             10
D285V10, multiclass
                                clus
vv                               TRIM24 MUTATED TRIM24 WILD-TYPE
  COLON ADENOCARCINOMA                       15              300
  COLON MUCINOUS ADENOCARCINOMA               2               45
  RECTAL ADENOCARCINOMA                       3              103
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  TRIM24 MUTATED    10   0   0   2
  TRIM24 WILD-TYPE 335   4  31  23
D285V11, multiclass
    clus
vv   TRIM24 MUTATED TRIM24 WILD-TYPE
  R0             10              335
  R1              0                4
  R2              0               31
  RX              2               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D285V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TRIM24 MUTATED                                  0     1
  TRIM24 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  TRIM24 MUTATED                           1    12
  TRIM24 WILD-TYPE                        21   214
D285V13, multiclass
                                  clus
vv                                 TRIM24 MUTATED TRIM24 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                        12              214
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(286) Variable = C12ORF40 MUTATION ANALYSIS
D286V1, survival
                    sevent
clus2                  0   1
  C12ORF40 MUTATED    18   4
  C12ORF40 WILD-TYPE 360  89
  C12ORF40 MUTATED C12ORF40 WILD-TYPE 
                22                449 
  C12ORF40 MUTATED C12ORF40 WILD-TYPE 
                 4                 89 
$`C12ORF40 MUTATED`
TCGA-A6-5661 TCGA-A6-6648 TCGA-AA-3713 TCGA-AA-A00N TCGA-AD-6889 TCGA-AU-3779 
       33.53        25.18        19.04         4.01        56.55        14.50 
TCGA-AU-6004 TCGA-AZ-6598 TCGA-CA-6717 TCGA-CK-4947 TCGA-CK-5912 TCGA-CK-6748 
       27.09        49.41        12.76        17.56        49.08         1.91 
TCGA-CM-5344 TCGA-CM-6171 TCGA-CM-6676 TCGA-D5-6931 TCGA-DM-A1D6 TCGA-DM-A1HB 
       22.03        14.04        11.08        12.00        49.91       135.65 
TCGA-G4-6588 TCGA-AF-2693 TCGA-AG-A002 TCGA-EI-6506 
       26.17        19.10        20.98        20.55 

$`C12ORF40 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 
       40.96         0.07        21.37        15.52         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AY-4070 
        5.79        22.42        27.42        10.88         0.20        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 
        5.13       106.75        22.36        62.79        88.21         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       12.20        10.06        14.30       148.01        85.45        15.62 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 
       51.32         9.99        21.14        82.95       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5348 
       20.02        37.02        25.02        13.02        29.06        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 
       21.99        14.99        12.99        13.02        15.02        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       12.95        13.05        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        4.80         1.51        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
       38.20       130.65        92.75        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
        7.50        44.32       131.51       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       13.78        35.80        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       39.48        43.04        13.55        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6507 
       57.24        24.13        51.48        32.61         0.49        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  C12ORF40 MUTATED C12ORF40 WILD-TYPE 
              1.91               0.00 
  C12ORF40 MUTATED C12ORF40 WILD-TYPE 
            135.65             148.01 
  C12ORF40 MUTATED C12ORF40 WILD-TYPE 
            20.765             20.120 
[1] "1.9 - 135.7 (20.8)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.2"
D286V2, continuous
D286V3, binary
                    cls
clus                   0   1
  C12ORF40 MUTATED    21   2
  C12ORF40 WILD-TYPE 345 117
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C12ORF40 MUTATED     21    2
  C12ORF40 WILD-TYPE  345  117
        clus
vv       C12ORF40 MUTATED C12ORF40 WILD-TYPE
  COLON                21                345
  RECTUM                2                117
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  C12ORF40 MUTATED         6        0        1         7         1         0
  C12ORF40 WILD-TYPE      85        1       31       131         9         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C12ORF40 MUTATED           0          0          3          2        3
  C12ORF40 WILD-TYPE        24         11         56         40       45
                    vv
clus                 STAGE IVA STAGE IVB
  C12ORF40 MUTATED           1         0
  C12ORF40 WILD-TYPE        17         1
D286V4, multiclass
            clus
vv           C12ORF40 MUTATED C12ORF40 WILD-TYPE
  STAGE I                   6                 85
  STAGE IA                  0                  1
  STAGE II                  1                 31
  STAGE IIA                 7                131
  STAGE IIB                 1                  9
  STAGE IIC                 0                  1
  STAGE III                 0                 24
  STAGE IIIA                0                 11
  STAGE IIIB                3                 56
  STAGE IIIC                2                 40
  STAGE IV                  3                 45
  STAGE IVA                 1                 17
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  C12ORF40 MUTATED     0   6  14   4
  C12ORF40 WILD-TYPE  17  86 315  46
D286V5, multiclass
    clus
vv   C12ORF40 MUTATED C12ORF40 WILD-TYPE
  T1                0                 17
  T2                6                 86
  T3               14                315
  T4                4                 46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  C12ORF40 MUTATED    17   4   3
  C12ORF40 WILD-TYPE 270 109  84
D286V6, multiclass
    clus
vv   C12ORF40 MUTATED C12ORF40 WILD-TYPE
  N0               17                270
  N1                4                109
  N2                3                 84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D286V7, binary
                    cls
clus                   0   1
  C12ORF40 MUTATED    16   4
  C12ORF40 WILD-TYPE 359  61
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C12ORF40 MUTATED     16    4
  C12ORF40 WILD-TYPE  359   61
   clus
vv  C12ORF40 MUTATED C12ORF40 WILD-TYPE
  0               16                359
  1                4                 61
[1] 2 2
[1] FALSE
D286V8, binary
                    cls
clus                   0   1
  C12ORF40 MUTATED    10  14
  C12ORF40 WILD-TYPE 215 250
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C12ORF40 MUTATED     10   14
  C12ORF40 WILD-TYPE  215  250
        clus
vv       C12ORF40 MUTATED C12ORF40 WILD-TYPE
  FEMALE               10                215
  MALE                 14                250
[1] 2 2
[1] FALSE
D286V9, binary
                    cls
clus                   0   1
  C12ORF40 MUTATED    16   1
  C12ORF40 WILD-TYPE 334  21
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C12ORF40 MUTATED     16    1
  C12ORF40 WILD-TYPE  334   21
     clus
vv    C12ORF40 MUTATED C12ORF40 WILD-TYPE
  NO                16                334
  YES                1                 21
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  C12ORF40 MUTATED                     15                             5
  C12ORF40 WILD-TYPE                  300                            42
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  C12ORF40 MUTATED                       2                              0
  C12ORF40 WILD-TYPE                   104                             10
D286V10, multiclass
                                clus
vv                               C12ORF40 MUTATED C12ORF40 WILD-TYPE
  COLON ADENOCARCINOMA                         15                300
  COLON MUCINOUS ADENOCARCINOMA                 5                 42
  RECTAL ADENOCARCINOMA                         2                104
  RECTAL MUCINOUS ADENOCARCINOMA                0                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  C12ORF40 MUTATED    12   0   2   4
  C12ORF40 WILD-TYPE 333   4  29  21
D286V11, multiclass
    clus
vv   C12ORF40 MUTATED C12ORF40 WILD-TYPE
  R0               12                333
  R1                0                  4
  R2                2                 29
  RX                4                 21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D286V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C12ORF40 MUTATED                                  0     2
  C12ORF40 WILD-TYPE                                1     9
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  C12ORF40 MUTATED                           1    17
  C12ORF40 WILD-TYPE                        21   209
D286V13, multiclass
                                  clus
vv                                 C12ORF40 MUTATED C12ORF40 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           2                  9
  BLACK OR AFRICAN AMERICAN                       1                 21
  WHITE                                          17                209
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(287) Variable = SNAI2 MUTATION ANALYSIS
D287V1, survival
                 sevent
clus2               0   1
  SNAI2 MUTATED    10   1
  SNAI2 WILD-TYPE 368  92
  SNAI2 MUTATED SNAI2 WILD-TYPE 
             11             460 
  SNAI2 MUTATED SNAI2 WILD-TYPE 
              1              92 
$`SNAI2 MUTATED`
TCGA-AA-3655 TCGA-AA-A00N TCGA-CA-6717 TCGA-CK-4952 TCGA-CK-6748 TCGA-CM-4743 
       61.02         4.01        12.76        15.62         1.91        23.05 
TCGA-CM-4752 TCGA-G4-6306 TCGA-G4-6321 TCGA-G4-6323 TCGA-AG-3892 
       13.02        44.68        22.09        13.78        13.02 

$`SNAI2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 
       20.98        19.99        13.94        19.99        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.20        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 
       49.08        51.32         9.99        21.14        82.95       124.27 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       20.02        37.02        25.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 
      133.18        74.56        65.85        53.62        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       63.62        61.91        36.00        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 
        1.02        17.95        36.95        17.03        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  SNAI2 MUTATED SNAI2 WILD-TYPE 
           1.91            0.00 
  SNAI2 MUTATED SNAI2 WILD-TYPE 
          61.02          148.01 
  SNAI2 MUTATED SNAI2 WILD-TYPE 
         13.780          20.415 
[1] "1.9 - 61.0 (13.8)"  "0.0 - 148.0 (20.4)"
[1] "hr=" "1.9"
D287V2, continuous
D287V3, binary
                 cls
clus                0   1
  SNAI2 MUTATED    10   1
  SNAI2 WILD-TYPE 356 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SNAI2 MUTATED     10    1
  SNAI2 WILD-TYPE  356  118
        clus
vv       SNAI2 MUTATED SNAI2 WILD-TYPE
  COLON             10             356
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SNAI2 MUTATED         1        1        1         4         1         0
  SNAI2 WILD-TYPE      90        0       31       134         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SNAI2 MUTATED           1          0          0          1        1         0
  SNAI2 WILD-TYPE        23         11         59         41       47        18
                 vv
clus              STAGE IVB
  SNAI2 MUTATED           0
  SNAI2 WILD-TYPE         1
D287V4, multiclass
            clus
vv           SNAI2 MUTATED SNAI2 WILD-TYPE
  STAGE I                1              90
  STAGE IA               1               0
  STAGE II               1              31
  STAGE IIA              4             134
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             1              41
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  SNAI2 MUTATED     1   2   5   2
  SNAI2 WILD-TYPE  16  90 324  48
D287V5, multiclass
    clus
vv   SNAI2 MUTATED SNAI2 WILD-TYPE
  T1             1              16
  T2             2              90
  T3             5             324
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  SNAI2 MUTATED     8   2   1
  SNAI2 WILD-TYPE 279 111  86
D287V6, multiclass
    clus
vv   SNAI2 MUTATED SNAI2 WILD-TYPE
  N0             8             279
  N1             2             111
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D287V7, binary
                 cls
clus                0   1
  SNAI2 MUTATED     8   1
  SNAI2 WILD-TYPE 367  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SNAI2 MUTATED      8    1
  SNAI2 WILD-TYPE  367   64
   clus
vv  SNAI2 MUTATED SNAI2 WILD-TYPE
  0             8             367
  1             1              64
[1] 2 2
[1] FALSE
D287V8, binary
                 cls
clus                0   1
  SNAI2 MUTATED     4   7
  SNAI2 WILD-TYPE 221 257
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SNAI2 MUTATED      4    7
  SNAI2 WILD-TYPE  221  257
        clus
vv       SNAI2 MUTATED SNAI2 WILD-TYPE
  FEMALE             4             221
  MALE               7             257
[1] 2 2
[1] FALSE
D287V9, binary
                 cls
clus                0   1
  SNAI2 MUTATED     9   0
  SNAI2 WILD-TYPE 341  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SNAI2 MUTATED      9    0
  SNAI2 WILD-TYPE  341   22
     clus
vv    SNAI2 MUTATED SNAI2 WILD-TYPE
  NO              9             341
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SNAI2 MUTATED                      6                             4
  SNAI2 WILD-TYPE                  309                            43
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SNAI2 MUTATED                       1                              0
  SNAI2 WILD-TYPE                   105                             10
D287V10, multiclass
                                clus
vv                               SNAI2 MUTATED SNAI2 WILD-TYPE
  COLON ADENOCARCINOMA                       6             309
  COLON MUCINOUS ADENOCARCINOMA              4              43
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  SNAI2 MUTATED     8   0   0   3
  SNAI2 WILD-TYPE 337   4  31  22
D287V11, multiclass
    clus
vv   SNAI2 MUTATED SNAI2 WILD-TYPE
  R0             8             337
  R1             0               4
  R2             0              31
  RX             3              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D287V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SNAI2 MUTATED                                  0     1
  SNAI2 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  SNAI2 MUTATED                           2     5
  SNAI2 WILD-TYPE                        20   221
D287V13, multiclass
                                  clus
vv                                 SNAI2 MUTATED SNAI2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    2              20
  WHITE                                        5             221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(288) Variable = DDX5 MUTATION ANALYSIS
D288V1, survival
                sevent
clus2              0   1
  DDX5 MUTATED     8   1
  DDX5 WILD-TYPE 370  92
  DDX5 MUTATED DDX5 WILD-TYPE 
             9            462 
  DDX5 MUTATED DDX5 WILD-TYPE 
             1             92 
$`DDX5 MUTATED`
TCGA-AA-3662 TCGA-AA-3713 TCGA-AA-3966 TCGA-AA-A00N TCGA-CA-6717 TCGA-CM-4744 
        6.05        19.04         2.01         4.01        12.76        20.02 
TCGA-D5-6533 TCGA-G4-6304 TCGA-G4-6323 
        1.32        53.62        13.78 

$`DDX5 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       20.98        34.03        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07        12.20        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       23.05        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 
       56.09        55.92        20.19        18.25        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
      133.18        74.56        65.85        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
       63.62        61.91        36.00        22.09        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  DDX5 MUTATED DDX5 WILD-TYPE 
          1.32           0.00 
  DDX5 MUTATED DDX5 WILD-TYPE 
         53.62         148.01 
  DDX5 MUTATED DDX5 WILD-TYPE 
        12.760         20.945 
[1] "1.3 - 53.6 (12.8)"  "0.0 - 148.0 (20.9)"
[1] "hr=" "1.1"
D288V2, continuous
D288V3, binary
                cls
clus               0   1
  DDX5 MUTATED     9   0
  DDX5 WILD-TYPE 357 119
[1] "tbl2"
                cls
clus             [,1] [,2]
  DDX5 MUTATED      9    0
  DDX5 WILD-TYPE  357  119
        clus
vv       DDX5 MUTATED DDX5 WILD-TYPE
  COLON             9            357
  RECTUM            0            119
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DDX5 MUTATED         1        1        0         2         2         0
  DDX5 WILD-TYPE      90        0       32       136         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DDX5 MUTATED           0          0          1          0        2         0
  DDX5 WILD-TYPE        24         11         58         42       46        18
                vv
clus             STAGE IVB
  DDX5 MUTATED           0
  DDX5 WILD-TYPE         1
D288V4, multiclass
            clus
vv           DDX5 MUTATED DDX5 WILD-TYPE
  STAGE I               1             90
  STAGE IA              1              0
  STAGE II              0             32
  STAGE IIA             2            136
  STAGE IIB             2              8
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            1             58
  STAGE IIIC            0             42
  STAGE IV              2             46
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  DDX5 MUTATED     0   1   3   4
  DDX5 WILD-TYPE  17  91 326  46
D288V5, multiclass
    clus
vv   DDX5 MUTATED DDX5 WILD-TYPE
  T1            0             17
  T2            1             91
  T3            3            326
  T4            4             46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  DDX5 MUTATED     8   0   1
  DDX5 WILD-TYPE 279 113  86
D288V6, multiclass
    clus
vv   DDX5 MUTATED DDX5 WILD-TYPE
  N0            8            279
  N1            0            113
  N2            1             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D288V7, binary
                cls
clus               0   1
  DDX5 MUTATED     6   2
  DDX5 WILD-TYPE 369  63
[1] "tbl2"
                cls
clus             [,1] [,2]
  DDX5 MUTATED      6    2
  DDX5 WILD-TYPE  369   63
   clus
vv  DDX5 MUTATED DDX5 WILD-TYPE
  0            6            369
  1            2             63
[1] 2 2
[1] FALSE
D288V8, binary
                cls
clus               0   1
  DDX5 MUTATED     4   5
  DDX5 WILD-TYPE 221 259
[1] "tbl2"
                cls
clus             [,1] [,2]
  DDX5 MUTATED      4    5
  DDX5 WILD-TYPE  221  259
        clus
vv       DDX5 MUTATED DDX5 WILD-TYPE
  FEMALE            4            221
  MALE              5            259
[1] 2 2
[1] FALSE
D288V9, binary
                cls
clus               0   1
  DDX5 MUTATED     5   1
  DDX5 WILD-TYPE 345  21
[1] "tbl2"
                cls
clus             [,1] [,2]
  DDX5 MUTATED      5    1
  DDX5 WILD-TYPE  345   21
     clus
vv    DDX5 MUTATED DDX5 WILD-TYPE
  NO             5            345
  YES            1             21
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  DDX5 MUTATED                      6                             3
  DDX5 WILD-TYPE                  309                            44
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  DDX5 MUTATED                       0                              0
  DDX5 WILD-TYPE                   106                             10
D288V10, multiclass
                                clus
vv                               DDX5 MUTATED DDX5 WILD-TYPE
  COLON ADENOCARCINOMA                      6            309
  COLON MUCINOUS ADENOCARCINOMA             3             44
  RECTAL ADENOCARCINOMA                     0            106
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  DDX5 MUTATED     5   0   2   1
  DDX5 WILD-TYPE 340   4  29  24
D288V11, multiclass
    clus
vv   DDX5 MUTATED DDX5 WILD-TYPE
  R0            5            340
  R1            0              4
  R2            2             29
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D288V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DDX5 MUTATED                                  0     1
  DDX5 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  DDX5 MUTATED                           1     3
  DDX5 WILD-TYPE                        21   223
D288V13, multiclass
                                  clus
vv                                 DDX5 MUTATED DDX5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                       3            223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(289) Variable = PTPDC1 MUTATION ANALYSIS
D289V1, survival
                  sevent
clus2                0   1
  PTPDC1 MUTATED     9   1
  PTPDC1 WILD-TYPE 369  92
  PTPDC1 MUTATED PTPDC1 WILD-TYPE 
              10              461 
  PTPDC1 MUTATED PTPDC1 WILD-TYPE 
               1               92 
$`PTPDC1 MUTATED`
TCGA-AA-3553 TCGA-AA-3554 TCGA-AD-6895 TCGA-AU-6004 TCGA-CM-4743 TCGA-CM-6675 
       24.00        17.95         0.72        27.09        23.05        13.05 
TCGA-DM-A1DA TCGA-G4-6588 TCGA-AG-3612 TCGA-AG-A002 
        7.50        26.17        19.99        20.98 

$`PTPDC1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       21.01        13.02        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
       56.55         0.79         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
        0.20        14.50        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
      124.27        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6676 TCGA-CM-6677 
       15.02        14.04        11.01        12.95        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB 
       92.75        49.91        13.32        12.59       140.38        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       35.80        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3726 
        6.05         0.99        15.95        19.99        13.94         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  PTPDC1 MUTATED PTPDC1 WILD-TYPE 
            0.72             0.00 
  PTPDC1 MUTATED PTPDC1 WILD-TYPE 
           27.09           148.01 
  PTPDC1 MUTATED PTPDC1 WILD-TYPE 
          20.485           20.190 
[1] "0.7 - 27.1 (20.5)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.4"
D289V2, continuous
D289V3, binary
                  cls
clus                 0   1
  PTPDC1 MUTATED     8   2
  PTPDC1 WILD-TYPE 358 117
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PTPDC1 MUTATED      8    2
  PTPDC1 WILD-TYPE  358  117
        clus
vv       PTPDC1 MUTATED PTPDC1 WILD-TYPE
  COLON               8              358
  RECTUM              2              117
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PTPDC1 MUTATED         3        0        0         3         0         0
  PTPDC1 WILD-TYPE      88        1       32       135        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PTPDC1 MUTATED           0          0          1          1        0
  PTPDC1 WILD-TYPE        24         11         58         41       48
                  vv
clus               STAGE IVA STAGE IVB
  PTPDC1 MUTATED           0         1
  PTPDC1 WILD-TYPE        18         0
D289V4, multiclass
            clus
vv           PTPDC1 MUTATED PTPDC1 WILD-TYPE
  STAGE I                 3               88
  STAGE IA                0                1
  STAGE II                0               32
  STAGE IIA               3              135
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              1               58
  STAGE IIIC              1               41
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               1                0
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  PTPDC1 MUTATED     0   3   7   0
  PTPDC1 WILD-TYPE  17  89 322  50
D289V5, multiclass
    clus
vv   PTPDC1 MUTATED PTPDC1 WILD-TYPE
  T1              0               17
  T2              3               89
  T3              7              322
  T4              0               50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  PTPDC1 MUTATED     6   2   2
  PTPDC1 WILD-TYPE 281 111  85
D289V6, multiclass
    clus
vv   PTPDC1 MUTATED PTPDC1 WILD-TYPE
  N0              6              281
  N1              2              111
  N2              2               85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D289V7, binary
                  cls
clus                 0   1
  PTPDC1 MUTATED     8   1
  PTPDC1 WILD-TYPE 367  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PTPDC1 MUTATED      8    1
  PTPDC1 WILD-TYPE  367   64
   clus
vv  PTPDC1 MUTATED PTPDC1 WILD-TYPE
  0              8              367
  1              1               64
[1] 2 2
[1] FALSE
D289V8, binary
                  cls
clus                 0   1
  PTPDC1 MUTATED     6   4
  PTPDC1 WILD-TYPE 219 260
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PTPDC1 MUTATED      6    4
  PTPDC1 WILD-TYPE  219  260
        clus
vv       PTPDC1 MUTATED PTPDC1 WILD-TYPE
  FEMALE              6              219
  MALE                4              260
[1] 2 2
[1] FALSE
D289V9, binary
                  cls
clus                 0   1
  PTPDC1 MUTATED     7   0
  PTPDC1 WILD-TYPE 343  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PTPDC1 MUTATED      7    0
  PTPDC1 WILD-TYPE  343   22
     clus
vv    PTPDC1 MUTATED PTPDC1 WILD-TYPE
  NO               7              343
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PTPDC1 MUTATED                      8                             0
  PTPDC1 WILD-TYPE                  307                            47
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PTPDC1 MUTATED                       2                              0
  PTPDC1 WILD-TYPE                   104                             10
D289V10, multiclass
                                clus
vv                               PTPDC1 MUTATED PTPDC1 WILD-TYPE
  COLON ADENOCARCINOMA                        8              307
  COLON MUCINOUS ADENOCARCINOMA               0               47
  RECTAL ADENOCARCINOMA                       2              104
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  PTPDC1 MUTATED     8   0   0   0
  PTPDC1 WILD-TYPE 337   4  31  25
D289V11, multiclass
    clus
vv   PTPDC1 MUTATED PTPDC1 WILD-TYPE
  R0              8              337
  R1              0                4
  R2              0               31
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D289V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PTPDC1 MUTATED                                  0     0
  PTPDC1 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  PTPDC1 MUTATED                           1     5
  PTPDC1 WILD-TYPE                        21   221
D289V13, multiclass
                                  clus
vv                                 PTPDC1 MUTATED PTPDC1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                         5              221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(290) Variable = BAG4 MUTATION ANALYSIS
D290V1, survival
                sevent
clus2              0   1
  BAG4 MUTATED     8   0
  BAG4 WILD-TYPE 370  93
  BAG4 MUTATED BAG4 WILD-TYPE 
             8            463 
  BAG4 MUTATED BAG4 WILD-TYPE 
             0             93 
$`BAG4 MUTATED`
TCGA-A6-5665 TCGA-AA-3555 TCGA-AA-3977 TCGA-AD-6890 TCGA-CA-6717 TCGA-CK-4952 
       22.06        29.95        25.02         0.79        12.76        15.62 
TCGA-CM-4744 TCGA-G4-6323 
       20.02        13.78 

$`BAG4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       13.02        24.00        17.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07        12.20        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 
       14.30        17.56       148.01        85.45        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6586 
       85.48        63.62        61.91        36.00        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  BAG4 MUTATED BAG4 WILD-TYPE 
          0.79           0.00 
  BAG4 MUTATED BAG4 WILD-TYPE 
         29.95         148.01 
  BAG4 MUTATED BAG4 WILD-TYPE 
         17.82          20.28 
[1] "0.8 - 29.9 (17.8)"  "0.0 - 148.0 (20.3)"
[1] "hr="     "9100000"
D290V2, continuous
D290V3, binary
                cls
clus               0   1
  BAG4 MUTATED     8   0
  BAG4 WILD-TYPE 358 119
[1] "tbl2"
                cls
clus             [,1] [,2]
  BAG4 MUTATED      8    0
  BAG4 WILD-TYPE  358  119
        clus
vv       BAG4 MUTATED BAG4 WILD-TYPE
  COLON             8            358
  RECTUM            0            119
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  BAG4 MUTATED         1        1        0         3         0         0
  BAG4 WILD-TYPE      90        0       32       135        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  BAG4 MUTATED           0          0          0          1        0         0
  BAG4 WILD-TYPE        24         11         59         41       48        18
                vv
clus             STAGE IVB
  BAG4 MUTATED           0
  BAG4 WILD-TYPE         1
D290V4, multiclass
            clus
vv           BAG4 MUTATED BAG4 WILD-TYPE
  STAGE I               1             90
  STAGE IA              1              0
  STAGE II              0             32
  STAGE IIA             3            135
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            0             59
  STAGE IIIC            1             41
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  BAG4 MUTATED     1   2   3   1
  BAG4 WILD-TYPE  16  90 326  49
D290V5, multiclass
    clus
vv   BAG4 MUTATED BAG4 WILD-TYPE
  T1            1             16
  T2            2             90
  T3            3            326
  T4            1             49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  BAG4 MUTATED     7   0   1
  BAG4 WILD-TYPE 280 113  86
D290V6, multiclass
    clus
vv   BAG4 MUTATED BAG4 WILD-TYPE
  N0            7            280
  N1            0            113
  N2            1             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D290V7, binary
                cls
clus               0   1
  BAG4 MUTATED     5   0
  BAG4 WILD-TYPE 370  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  BAG4 MUTATED      5    0
  BAG4 WILD-TYPE  370   65
   clus
vv  BAG4 MUTATED BAG4 WILD-TYPE
  0            5            370
  1            0             65
[1] 2 2
[1] FALSE
D290V8, binary
                cls
clus               0   1
  BAG4 MUTATED     3   5
  BAG4 WILD-TYPE 222 259
[1] "tbl2"
                cls
clus             [,1] [,2]
  BAG4 MUTATED      3    5
  BAG4 WILD-TYPE  222  259
        clus
vv       BAG4 MUTATED BAG4 WILD-TYPE
  FEMALE            3            222
  MALE              5            259
[1] 2 2
[1] FALSE
D290V9, binary
                cls
clus               0   1
  BAG4 MUTATED     6   0
  BAG4 WILD-TYPE 344  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  BAG4 MUTATED      6    0
  BAG4 WILD-TYPE  344   22
     clus
vv    BAG4 MUTATED BAG4 WILD-TYPE
  NO             6            344
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  BAG4 MUTATED                      5                             3
  BAG4 WILD-TYPE                  310                            44
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  BAG4 MUTATED                       0                              0
  BAG4 WILD-TYPE                   106                             10
D290V10, multiclass
                                clus
vv                               BAG4 MUTATED BAG4 WILD-TYPE
  COLON ADENOCARCINOMA                      5            310
  COLON MUCINOUS ADENOCARCINOMA             3             44
  RECTAL ADENOCARCINOMA                     0            106
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  BAG4 MUTATED     4   0   0   2
  BAG4 WILD-TYPE 341   4  31  23
D290V11, multiclass
    clus
vv   BAG4 MUTATED BAG4 WILD-TYPE
  R0            4            341
  R1            0              4
  R2            0             31
  RX            2             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D290V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  BAG4 MUTATED                                  0     1
  BAG4 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  BAG4 MUTATED                           1     4
  BAG4 WILD-TYPE                        21   222
D290V13, multiclass
                                  clus
vv                                 BAG4 MUTATED BAG4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                       4            222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(291) Variable = BAZ1B MUTATION ANALYSIS
D291V1, survival
                 sevent
clus2               0   1
  BAZ1B MUTATED    20   6
  BAZ1B WILD-TYPE 358  87
  BAZ1B MUTATED BAZ1B WILD-TYPE 
             26             445 
  BAZ1B MUTATED BAZ1B WILD-TYPE 
              6              87 
$`BAZ1B MUTATED`
TCGA-AA-3663 TCGA-AA-3713 TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-A00A TCGA-AA-A00N 
        6.97        19.04         2.01        33.01        38.04         4.01 
TCGA-AD-5900 TCGA-AZ-6598 TCGA-AZ-6601 TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-6162 
        0.07        49.41       100.01        12.76        10.06        12.00 
TCGA-CM-6171 TCGA-D5-6532 TCGA-D5-6540 TCGA-D5-6898 TCGA-D5-6926 TCGA-D5-6930 
       14.04        18.25        16.14         1.48         9.04         1.51 
TCGA-DM-A1D6 TCGA-G4-6588 TCGA-AF-2693 TCGA-AG-A002 TCGA-CI-6624 TCGA-CL-5917 
       49.91        26.17        19.10        20.98         4.73        78.12 
TCGA-EI-6510 TCGA-F5-6571 
       18.28        31.30 

$`BAZ1B WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.05        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3939 
       24.03        27.02        29.98        18.05        31.00        12.99 
TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
        7.96        27.02        13.94        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 
        0.92        41.00        39.98        18.05        40.96        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 
        5.13       106.75        22.36        62.79        88.21         6.77 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
       12.10        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 
       15.02        15.02        17.03        15.02         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       55.92        20.19         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6922 
        4.80        17.13        12.49        15.58         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6931 
       12.43        14.30         9.44        11.64         4.80        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       92.75        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       35.80        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       43.04        13.55        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
       33.17         6.97         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-F5-6464 
       32.61         0.49        20.55        19.96        20.91         9.96 
TCGA-F5-6465 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       49.51        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  BAZ1B MUTATED BAZ1B WILD-TYPE 
           0.07            0.00 
  BAZ1B MUTATED BAZ1B WILD-TYPE 
         100.01          148.01 
  BAZ1B MUTATED BAZ1B WILD-TYPE 
         17.195          20.980 
[1] "0.1 - 100.0 (17.2)" "0.0 - 148.0 (21.0)"
[1] "hr=" "1.3"
D291V2, continuous
D291V3, binary
                 cls
clus                0   1
  BAZ1B MUTATED    21   5
  BAZ1B WILD-TYPE 345 114
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BAZ1B MUTATED     21    5
  BAZ1B WILD-TYPE  345  114
        clus
vv       BAZ1B MUTATED BAZ1B WILD-TYPE
  COLON             21             345
  RECTUM             5             114
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  BAZ1B MUTATED         7        0        3         9         2         0
  BAZ1B WILD-TYPE      84        1       29       129         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  BAZ1B MUTATED           0          0          2          1        2         1
  BAZ1B WILD-TYPE        24         11         57         41       46        17
                 vv
clus              STAGE IVB
  BAZ1B MUTATED           0
  BAZ1B WILD-TYPE         1
D291V4, multiclass
            clus
vv           BAZ1B MUTATED BAZ1B WILD-TYPE
  STAGE I                7              84
  STAGE IA               0               1
  STAGE II               3              29
  STAGE IIA              9             129
  STAGE IIB              2               8
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             2              57
  STAGE IIIC             1              41
  STAGE IV               2              46
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  BAZ1B MUTATED     0   8  16   3
  BAZ1B WILD-TYPE  17  84 313  47
D291V5, multiclass
    clus
vv   BAZ1B MUTATED BAZ1B WILD-TYPE
  T1             0              17
  T2             8              84
  T3            16             313
  T4             3              47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  BAZ1B MUTATED    23   2   2
  BAZ1B WILD-TYPE 264 111  85
D291V6, multiclass
    clus
vv   BAZ1B MUTATED BAZ1B WILD-TYPE
  N0            23             264
  N1             2             111
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D291V7, binary
                 cls
clus                0   1
  BAZ1B MUTATED    20   2
  BAZ1B WILD-TYPE 355  63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BAZ1B MUTATED     20    2
  BAZ1B WILD-TYPE  355   63
   clus
vv  BAZ1B MUTATED BAZ1B WILD-TYPE
  0            20             355
  1             2              63
[1] 2 2
[1] FALSE
D291V8, binary
                 cls
clus                0   1
  BAZ1B MUTATED    11  16
  BAZ1B WILD-TYPE 214 248
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BAZ1B MUTATED     11   16
  BAZ1B WILD-TYPE  214  248
        clus
vv       BAZ1B MUTATED BAZ1B WILD-TYPE
  FEMALE            11             214
  MALE              16             248
[1] 2 2
[1] FALSE
D291V9, binary
                 cls
clus                0   1
  BAZ1B MUTATED    18   2
  BAZ1B WILD-TYPE 332  20
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BAZ1B MUTATED     18    2
  BAZ1B WILD-TYPE  332   20
     clus
vv    BAZ1B MUTATED BAZ1B WILD-TYPE
  NO             18             332
  YES             2              20
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  BAZ1B MUTATED                     13                             8
  BAZ1B WILD-TYPE                  302                            39
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  BAZ1B MUTATED                       5                              0
  BAZ1B WILD-TYPE                   101                             10
D291V10, multiclass
                                clus
vv                               BAZ1B MUTATED BAZ1B WILD-TYPE
  COLON ADENOCARCINOMA                      13             302
  COLON MUCINOUS ADENOCARCINOMA              8              39
  RECTAL ADENOCARCINOMA                      5             101
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  BAZ1B MUTATED    17   0   2   3
  BAZ1B WILD-TYPE 328   4  29  22
D291V11, multiclass
    clus
vv   BAZ1B MUTATED BAZ1B WILD-TYPE
  R0            17             328
  R1             0               4
  R2             2              29
  RX             3              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D291V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  BAZ1B MUTATED                                  0     2
  BAZ1B WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  BAZ1B MUTATED                           0    17
  BAZ1B WILD-TYPE                        22   209
D291V13, multiclass
                                  clus
vv                                 BAZ1B MUTATED BAZ1B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               9
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                       17             209
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(292) Variable = PAQR5 MUTATION ANALYSIS
D292V1, survival
                 sevent
clus2               0   1
  PAQR5 MUTATED     6   2
  PAQR5 WILD-TYPE 372  91
  PAQR5 MUTATED PAQR5 WILD-TYPE 
              8             463 
  PAQR5 MUTATED PAQR5 WILD-TYPE 
              2              91 
$`PAQR5 MUTATED`
TCGA-A6-4105 TCGA-AA-3663 TCGA-AD-6895 TCGA-AY-5543 TCGA-CK-5912 TCGA-D5-5541 
       14.53         6.97         0.72        33.01        49.08        55.92 
TCGA-D5-6540 TCGA-D5-6541 
       16.14        15.58 

$`PAQR5 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 
       16.57        34.65        33.34        32.75        36.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
       56.55         0.79         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6197 
        0.20        14.50        27.09        16.31         0.95        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       19.59        56.09        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6898 
       15.12        17.85         4.80        17.13        12.49         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  PAQR5 MUTATED PAQR5 WILD-TYPE 
           0.72            0.00 
  PAQR5 MUTATED PAQR5 WILD-TYPE 
          55.92          148.01 
  PAQR5 MUTATED PAQR5 WILD-TYPE 
          15.86           20.28 
[1] "0.7 - 55.9 (15.9)"  "0.0 - 148.0 (20.3)"
[1] "hr=" "1.3"
D292V2, continuous
D292V3, binary
                 cls
clus                0   1
  PAQR5 MUTATED     8   0
  PAQR5 WILD-TYPE 358 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PAQR5 MUTATED      8    0
  PAQR5 WILD-TYPE  358  119
        clus
vv       PAQR5 MUTATED PAQR5 WILD-TYPE
  COLON              8             358
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PAQR5 MUTATED         2        0        1         2         0         0
  PAQR5 WILD-TYPE      89        1       31       136        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PAQR5 MUTATED           0          0          1          0        0         1
  PAQR5 WILD-TYPE        24         11         58         42       48        17
                 vv
clus              STAGE IVB
  PAQR5 MUTATED           0
  PAQR5 WILD-TYPE         1
D292V4, multiclass
            clus
vv           PAQR5 MUTATED PAQR5 WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              2             136
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PAQR5 MUTATED     0   2   6   0
  PAQR5 WILD-TYPE  17  90 323  50
D292V5, multiclass
    clus
vv   PAQR5 MUTATED PAQR5 WILD-TYPE
  T1             0              17
  T2             2              90
  T3             6             323
  T4             0              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  PAQR5 MUTATED     5   3   0
  PAQR5 WILD-TYPE 282 110  87
D292V6, multiclass
    clus
vv   PAQR5 MUTATED PAQR5 WILD-TYPE
  N0             5             282
  N1             3             110
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D292V7, binary
                 cls
clus                0   1
  PAQR5 MUTATED     5   1
  PAQR5 WILD-TYPE 370  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PAQR5 MUTATED      5    1
  PAQR5 WILD-TYPE  370   64
   clus
vv  PAQR5 MUTATED PAQR5 WILD-TYPE
  0             5             370
  1             1              64
[1] 2 2
[1] FALSE
D292V8, binary
                 cls
clus                0   1
  PAQR5 MUTATED     1   7
  PAQR5 WILD-TYPE 224 257
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PAQR5 MUTATED      1    7
  PAQR5 WILD-TYPE  224  257
        clus
vv       PAQR5 MUTATED PAQR5 WILD-TYPE
  FEMALE             1             224
  MALE               7             257
[1] 2 2
[1] FALSE
D292V9, binary
                 cls
clus                0   1
  PAQR5 MUTATED     7   0
  PAQR5 WILD-TYPE 343  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PAQR5 MUTATED      7    0
  PAQR5 WILD-TYPE  343   22
     clus
vv    PAQR5 MUTATED PAQR5 WILD-TYPE
  NO              7             343
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PAQR5 MUTATED                      7                             1
  PAQR5 WILD-TYPE                  308                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PAQR5 MUTATED                       0                              0
  PAQR5 WILD-TYPE                   106                             10
D292V10, multiclass
                                clus
vv                               PAQR5 MUTATED PAQR5 WILD-TYPE
  COLON ADENOCARCINOMA                       7             308
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  PAQR5 MUTATED     5   0   0   1
  PAQR5 WILD-TYPE 340   4  31  24
D292V11, multiclass
    clus
vv   PAQR5 MUTATED PAQR5 WILD-TYPE
  R0             5             340
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D292V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PAQR5 MUTATED                                  0     0
  PAQR5 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PAQR5 MUTATED                           1     6
  PAQR5 WILD-TYPE                        21   220
D292V13, multiclass
                                  clus
vv                                 PAQR5 MUTATED PAQR5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        6             220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(293) Variable = KDM3B MUTATION ANALYSIS
D293V1, survival
                 sevent
clus2               0   1
  KDM3B MUTATED    28   3
  KDM3B WILD-TYPE 350  90
  KDM3B MUTATED KDM3B WILD-TYPE 
             31             440 
  KDM3B MUTATED KDM3B WILD-TYPE 
              3              90 
$`KDM3B MUTATED`
TCGA-A6-5661 TCGA-A6-5665 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3555 TCGA-AA-3672 
       33.53        22.06        19.66        20.28        29.95         0.92 
TCGA-AA-3950 TCGA-AA-3966 TCGA-AA-3977 TCGA-AA-A010 TCGA-AA-A01Q TCGA-AD-6895 
       24.00         2.01        25.02        34.98         1.02         0.72 
TCGA-AD-6963 TCGA-AZ-6598 TCGA-AZ-6605 TCGA-CA-6717 TCGA-CA-6719 TCGA-CM-5341 
       27.42        49.41         5.23        12.76        14.30        29.06 
TCGA-CM-5344 TCGA-CM-6163 TCGA-CM-6168 TCGA-CM-6171 TCGA-CM-6676 TCGA-D5-6923 
       22.03         2.96        12.99        14.04        11.08        12.43 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A28H TCGA-F4-6703 TCGA-G4-6321 TCGA-AG-A002 
       12.59       140.38       117.07        47.87        22.09        20.98 
TCGA-EI-6510 
       18.28 

$`KDM3B WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
        7.04         3.02         1.02        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       78.08         6.05         6.97        54.02         2.01        14.01 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
        2.01        20.98        34.03        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
       38.07        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 
        0.07        21.37        15.52        56.55         0.79         5.79 
TCGA-AD-6901 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 
        5.13       106.75        22.36        62.79        88.21         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
       12.10       100.01        29.56        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       10.06        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5348 
       23.05        20.02        37.02        25.02        13.02        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       17.03        15.02        12.00        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       14.99        13.02        15.02        11.01        12.95        13.05 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6924 
       16.14        15.58         1.48         3.68         4.41        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       92.75        49.91        13.32         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
       60.79        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       36.00        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-F5-6464 
       32.61         0.49        20.55        19.96        20.91         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  KDM3B MUTATED KDM3B WILD-TYPE 
           0.72            0.00 
  KDM3B MUTATED KDM3B WILD-TYPE 
         140.38          148.01 
  KDM3B MUTATED KDM3B WILD-TYPE 
         20.280          20.155 
[1] "0.7 - 140.4 (20.3)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.9"
D293V2, continuous
D293V3, binary
                 cls
clus                0   1
  KDM3B MUTATED    32   2
  KDM3B WILD-TYPE 334 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM3B MUTATED     32    2
  KDM3B WILD-TYPE  334  117
        clus
vv       KDM3B MUTATED KDM3B WILD-TYPE
  COLON             32             334
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KDM3B MUTATED         5        0        2        12         2         0
  KDM3B WILD-TYPE      86        1       30       126         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  KDM3B MUTATED           2          1          2          3        0         1
  KDM3B WILD-TYPE        22         10         57         39       48        17
                 vv
clus              STAGE IVB
  KDM3B MUTATED           0
  KDM3B WILD-TYPE         1
D293V4, multiclass
            clus
vv           KDM3B MUTATED KDM3B WILD-TYPE
  STAGE I                5              86
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA             12             126
  STAGE IIB              2               8
  STAGE IIC              0               1
  STAGE III              2              22
  STAGE IIIA             1              10
  STAGE IIIB             2              57
  STAGE IIIC             3              39
  STAGE IV               0              48
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  KDM3B MUTATED     1   8  21   4
  KDM3B WILD-TYPE  16  84 308  46
D293V5, multiclass
    clus
vv   KDM3B MUTATED KDM3B WILD-TYPE
  T1             1              16
  T2             8              84
  T3            21             308
  T4             4              46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  KDM3B MUTATED    24   8   2
  KDM3B WILD-TYPE 263 105  85
D293V6, multiclass
    clus
vv   KDM3B MUTATED KDM3B WILD-TYPE
  N0            24             263
  N1             8             105
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D293V7, binary
                 cls
clus                0   1
  KDM3B MUTATED    24   0
  KDM3B WILD-TYPE 351  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM3B MUTATED     24    0
  KDM3B WILD-TYPE  351   65
   clus
vv  KDM3B MUTATED KDM3B WILD-TYPE
  0            24             351
  1             0              65
[1] 2 2
[1] FALSE
D293V8, binary
                 cls
clus                0   1
  KDM3B MUTATED    19  15
  KDM3B WILD-TYPE 206 249
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM3B MUTATED     19   15
  KDM3B WILD-TYPE  206  249
        clus
vv       KDM3B MUTATED KDM3B WILD-TYPE
  FEMALE            19             206
  MALE              15             249
[1] 2 2
[1] FALSE
D293V9, binary
                 cls
clus                0   1
  KDM3B MUTATED    25   0
  KDM3B WILD-TYPE 325  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM3B MUTATED     25    0
  KDM3B WILD-TYPE  325   22
     clus
vv    KDM3B MUTATED KDM3B WILD-TYPE
  NO             25             325
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  KDM3B MUTATED                     26                             6
  KDM3B WILD-TYPE                  289                            41
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  KDM3B MUTATED                       2                              0
  KDM3B WILD-TYPE                   104                             10
D293V10, multiclass
                                clus
vv                               KDM3B MUTATED KDM3B WILD-TYPE
  COLON ADENOCARCINOMA                      26             289
  COLON MUCINOUS ADENOCARCINOMA              6              41
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  KDM3B MUTATED    22   0   0   2
  KDM3B WILD-TYPE 323   4  31  23
D293V11, multiclass
    clus
vv   KDM3B MUTATED KDM3B WILD-TYPE
  R0            22             323
  R1             0               4
  R2             0              31
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D293V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KDM3B MUTATED                                  0     2
  KDM3B WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  KDM3B MUTATED                           2    20
  KDM3B WILD-TYPE                        20   206
D293V13, multiclass
                                  clus
vv                                 KDM3B MUTATED KDM3B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               9
  BLACK OR AFRICAN AMERICAN                    2              20
  WHITE                                       20             206
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(294) Variable = FAHD2B MUTATION ANALYSIS
D294V1, survival
                  sevent
clus2                0   1
  FAHD2B MUTATED     5   0
  FAHD2B WILD-TYPE 373  93
  FAHD2B MUTATED FAHD2B WILD-TYPE 
               5              466 
  FAHD2B MUTATED FAHD2B WILD-TYPE 
               0               93 
$`FAHD2B MUTATED`
TCGA-A6-5665 TCGA-A6-6780 TCGA-AD-5900 TCGA-AU-6004 TCGA-CM-5861 
       22.06        20.12         0.07        27.09        15.02 

$`FAHD2B WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       39.98        18.05        40.96        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
        0.20        14.50        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 
       29.06        22.03        22.98        30.08        32.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  FAHD2B MUTATED FAHD2B WILD-TYPE 
            0.07             0.00 
  FAHD2B MUTATED FAHD2B WILD-TYPE 
           27.09           148.01 
  FAHD2B MUTATED FAHD2B WILD-TYPE 
          20.120           20.235 
[1] "0.1 - 27.1 (20.1)"  "0.0 - 148.0 (20.2)"
[1] "hr="     "3300000"
D294V2, continuous
D294V3, binary
                  cls
clus                 0   1
  FAHD2B MUTATED     6   0
  FAHD2B WILD-TYPE 360 119
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAHD2B MUTATED      6    0
  FAHD2B WILD-TYPE  360  119
        clus
vv       FAHD2B MUTATED FAHD2B WILD-TYPE
  COLON               6              360
  RECTUM              0              119
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FAHD2B MUTATED         2        0        0         3         1         0
  FAHD2B WILD-TYPE      89        1       32       135         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FAHD2B MUTATED           0          0          0          0        0
  FAHD2B WILD-TYPE        24         11         59         42       48
                  vv
clus               STAGE IVA STAGE IVB
  FAHD2B MUTATED           0         0
  FAHD2B WILD-TYPE        18         1
D294V4, multiclass
            clus
vv           FAHD2B MUTATED FAHD2B WILD-TYPE
  STAGE I                 2               89
  STAGE IA                0                1
  STAGE II                0               32
  STAGE IIA               3              135
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              0               59
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  FAHD2B MUTATED     0   2   3   1
  FAHD2B WILD-TYPE  17  90 326  49
D294V5, multiclass
    clus
vv   FAHD2B MUTATED FAHD2B WILD-TYPE
  T1              0               17
  T2              2               90
  T3              3              326
  T4              1               49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  FAHD2B MUTATED     6   0   0
  FAHD2B WILD-TYPE 281 113  87
D294V6, multiclass
    clus
vv   FAHD2B MUTATED FAHD2B WILD-TYPE
  N0              6              281
  N1              0              113
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D294V7, binary
                  cls
clus                 0   1
  FAHD2B MUTATED     3   0
  FAHD2B WILD-TYPE 372  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAHD2B MUTATED      3    0
  FAHD2B WILD-TYPE  372   65
   clus
vv  FAHD2B MUTATED FAHD2B WILD-TYPE
  0              3              372
  1              0               65
[1] 2 2
[1] FALSE
D294V8, binary
                  cls
clus                 0   1
  FAHD2B MUTATED     4   2
  FAHD2B WILD-TYPE 221 262
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAHD2B MUTATED      4    2
  FAHD2B WILD-TYPE  221  262
        clus
vv       FAHD2B MUTATED FAHD2B WILD-TYPE
  FEMALE              4              221
  MALE                2              262
[1] 2 2
[1] FALSE
D294V9, binary
                  cls
clus                 0   1
  FAHD2B MUTATED     3   0
  FAHD2B WILD-TYPE 347  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAHD2B MUTATED      3    0
  FAHD2B WILD-TYPE  347   22
     clus
vv    FAHD2B MUTATED FAHD2B WILD-TYPE
  NO               3              347
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  FAHD2B MUTATED                      4                             2
  FAHD2B WILD-TYPE                  311                            45
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  FAHD2B MUTATED                       0                              0
  FAHD2B WILD-TYPE                   106                             10
D294V10, multiclass
                                clus
vv                               FAHD2B MUTATED FAHD2B WILD-TYPE
  COLON ADENOCARCINOMA                        4              311
  COLON MUCINOUS ADENOCARCINOMA               2               45
  RECTAL ADENOCARCINOMA                       0              106
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  FAHD2B MUTATED     4   0   0   1
  FAHD2B WILD-TYPE 341   4  31  24
D294V11, multiclass
    clus
vv   FAHD2B MUTATED FAHD2B WILD-TYPE
  R0              4              341
  R1              0                4
  R2              0               31
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D294V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FAHD2B MUTATED                                  0     0
  FAHD2B WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  FAHD2B MUTATED                           0     6
  FAHD2B WILD-TYPE                        22   220
D294V13, multiclass
                                  clus
vv                                 FAHD2B MUTATED FAHD2B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         6              220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(295) Variable = ZCCHC6 MUTATION ANALYSIS
D295V1, survival
                  sevent
clus2                0   1
  ZCCHC6 MUTATED    17   3
  ZCCHC6 WILD-TYPE 361  90
  ZCCHC6 MUTATED ZCCHC6 WILD-TYPE 
              20              451 
  ZCCHC6 MUTATED ZCCHC6 WILD-TYPE 
               3               90 
$`ZCCHC6 MUTATED`
TCGA-AA-3516 TCGA-AA-3532 TCGA-AA-3663 TCGA-AA-3681 TCGA-AA-3821 TCGA-AA-3950 
       13.02        29.00         6.97         5.98         1.02        24.00 
TCGA-AA-A017 TCGA-AA-A02J TCGA-AD-6889 TCGA-AY-6197 TCGA-AZ-6598 TCGA-CA-6717 
        1.02         5.03        56.55        21.44        49.41        12.76 
TCGA-CK-4952 TCGA-CM-6680 TCGA-DM-A28K TCGA-G4-6309 TCGA-G4-6323 TCGA-G4-6628 
       15.62        12.03        98.24        85.48        13.78        79.69 
TCGA-AG-A002 TCGA-AG-A01W 
       20.98        70.03 

$`ZCCHC6 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        1.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3534 TCGA-AA-3538 
       19.07         0.00        19.07        34.03        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
       11.01        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
        0.99        25.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       26.01         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99        34.98        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       51.98        39.98         2.01        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        88.21         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07        12.20        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
       17.56       148.01        85.45        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       10.06        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
       60.79       117.07         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 
       65.85        53.62        44.68        55.04        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        35.80        26.17        91.79        46.75 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01Y 
       37.02        15.95        36.03         9.07        12.00        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  ZCCHC6 MUTATED ZCCHC6 WILD-TYPE 
            1.02             0.00 
  ZCCHC6 MUTATED ZCCHC6 WILD-TYPE 
           98.24           148.01 
  ZCCHC6 MUTATED ZCCHC6 WILD-TYPE 
           18.30            20.19 
[1] "1.0 - 98.2 (18.3)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.6"
D295V2, continuous
D295V3, binary
                  cls
clus                 0   1
  ZCCHC6 MUTATED    18   2
  ZCCHC6 WILD-TYPE 348 117
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZCCHC6 MUTATED     18    2
  ZCCHC6 WILD-TYPE  348  117
        clus
vv       ZCCHC6 MUTATED ZCCHC6 WILD-TYPE
  COLON              18              348
  RECTUM              2              117
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZCCHC6 MUTATED         3        1        3         7         0         0
  ZCCHC6 WILD-TYPE      88        0       29       131        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZCCHC6 MUTATED           2          0          2          1        1
  ZCCHC6 WILD-TYPE        22         11         57         41       47
                  vv
clus               STAGE IVA STAGE IVB
  ZCCHC6 MUTATED           0         0
  ZCCHC6 WILD-TYPE        18         1
D295V4, multiclass
            clus
vv           ZCCHC6 MUTATED ZCCHC6 WILD-TYPE
  STAGE I                 3               88
  STAGE IA                1                0
  STAGE II                3               29
  STAGE IIA               7              131
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               2               22
  STAGE IIIA              0               11
  STAGE IIIB              2               57
  STAGE IIIC              1               41
  STAGE IV                1               47
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZCCHC6 MUTATED     0   3  15   1
  ZCCHC6 WILD-TYPE  17  89 314  49
D295V5, multiclass
    clus
vv   ZCCHC6 MUTATED ZCCHC6 WILD-TYPE
  T1              0               17
  T2              3               89
  T3             15              314
  T4              1               49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  ZCCHC6 MUTATED    15   2   3
  ZCCHC6 WILD-TYPE 272 111  84
D295V6, multiclass
    clus
vv   ZCCHC6 MUTATED ZCCHC6 WILD-TYPE
  N0             15              272
  N1              2              111
  N2              3               84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D295V7, binary
                  cls
clus                 0   1
  ZCCHC6 MUTATED    16   1
  ZCCHC6 WILD-TYPE 359  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZCCHC6 MUTATED     16    1
  ZCCHC6 WILD-TYPE  359   64
   clus
vv  ZCCHC6 MUTATED ZCCHC6 WILD-TYPE
  0             16              359
  1              1               64
[1] 2 2
[1] FALSE
D295V8, binary
                  cls
clus                 0   1
  ZCCHC6 MUTATED    11   9
  ZCCHC6 WILD-TYPE 214 255
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZCCHC6 MUTATED     11    9
  ZCCHC6 WILD-TYPE  214  255
        clus
vv       ZCCHC6 MUTATED ZCCHC6 WILD-TYPE
  FEMALE             11              214
  MALE                9              255
[1] 2 2
[1] FALSE
D295V9, binary
                  cls
clus                 0   1
  ZCCHC6 MUTATED    14   0
  ZCCHC6 WILD-TYPE 336  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZCCHC6 MUTATED     14    0
  ZCCHC6 WILD-TYPE  336   22
     clus
vv    ZCCHC6 MUTATED ZCCHC6 WILD-TYPE
  NO              14              336
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ZCCHC6 MUTATED                     12                             6
  ZCCHC6 WILD-TYPE                  303                            41
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ZCCHC6 MUTATED                       2                              0
  ZCCHC6 WILD-TYPE                   104                             10
D295V10, multiclass
                                clus
vv                               ZCCHC6 MUTATED ZCCHC6 WILD-TYPE
  COLON ADENOCARCINOMA                       12              303
  COLON MUCINOUS ADENOCARCINOMA               6               41
  RECTAL ADENOCARCINOMA                       2              104
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ZCCHC6 MUTATED    13   0   1   2
  ZCCHC6 WILD-TYPE 332   4  30  23
D295V11, multiclass
    clus
vv   ZCCHC6 MUTATED ZCCHC6 WILD-TYPE
  R0             13              332
  R1              0                4
  R2              1               30
  RX              2               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D295V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZCCHC6 MUTATED                                  0     2
  ZCCHC6 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZCCHC6 MUTATED                           2     6
  ZCCHC6 WILD-TYPE                        20   220
D295V13, multiclass
                                  clus
vv                                 ZCCHC6 MUTATED ZCCHC6 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                9
  BLACK OR AFRICAN AMERICAN                     2               20
  WHITE                                         6              220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(296) Variable = TNMD MUTATION ANALYSIS
D296V1, survival
                sevent
clus2              0   1
  TNMD MUTATED     9   2
  TNMD WILD-TYPE 369  91
  TNMD MUTATED TNMD WILD-TYPE 
            11            460 
  TNMD MUTATED TNMD WILD-TYPE 
             2             91 
$`TNMD MUTATED`
TCGA-A6-5665 TCGA-A6-6141 TCGA-AA-3502 TCGA-AA-3542 TCGA-AA-3815 TCGA-AA-3864 
       22.06         8.38        35.01        12.99        33.04        53.00 
TCGA-AA-3977 TCGA-AZ-6598 TCGA-CK-5916 TCGA-D5-6930 TCGA-G4-6586 
       25.02        49.41        21.14         1.51        35.80 

$`TNMD WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 
       22.09        32.71        27.09        22.52        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3510 
       19.66        20.28         7.04         3.02         1.02        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3543 
       19.07        34.03        29.00        29.00        26.01         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
       26.99        19.04        19.04        10.06        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       30.05        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 
        5.13       106.75        22.36        62.79        88.21         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 
       85.45        15.62        49.08        51.32         9.99        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        4.80        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  TNMD MUTATED TNMD WILD-TYPE 
          1.51           0.00 
  TNMD MUTATED TNMD WILD-TYPE 
         53.00         148.01 
  TNMD MUTATED TNMD WILD-TYPE 
        25.020         20.035 
[1] "1.5 - 53.0 (25.0)"  "0.0 - 148.0 (20.0)"
[1] "hr=" "1.1"
D296V2, continuous
D296V3, binary
                cls
clus               0   1
  TNMD MUTATED    11   0
  TNMD WILD-TYPE 355 119
[1] "tbl2"
                cls
clus             [,1] [,2]
  TNMD MUTATED     11    0
  TNMD WILD-TYPE  355  119
        clus
vv       TNMD MUTATED TNMD WILD-TYPE
  COLON            11            355
  RECTUM            0            119
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TNMD MUTATED         2        0        2         5         0         0
  TNMD WILD-TYPE      89        1       30       133        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TNMD MUTATED           0          0          0          1        0         0
  TNMD WILD-TYPE        24         11         59         41       48        18
                vv
clus             STAGE IVB
  TNMD MUTATED           0
  TNMD WILD-TYPE         1
D296V4, multiclass
            clus
vv           TNMD MUTATED TNMD WILD-TYPE
  STAGE I               2             89
  STAGE IA              0              1
  STAGE II              2             30
  STAGE IIA             5            133
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            0             59
  STAGE IIIC            1             41
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  TNMD MUTATED     1   2   8   0
  TNMD WILD-TYPE  16  90 321  50
D296V5, multiclass
    clus
vv   TNMD MUTATED TNMD WILD-TYPE
  T1            1             16
  T2            2             90
  T3            8            321
  T4            0             50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  TNMD MUTATED    10   0   1
  TNMD WILD-TYPE 277 113  86
D296V6, multiclass
    clus
vv   TNMD MUTATED TNMD WILD-TYPE
  N0           10            277
  N1            0            113
  N2            1             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D296V7, binary
                cls
clus               0   1
  TNMD MUTATED     9   0
  TNMD WILD-TYPE 366  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  TNMD MUTATED      9    0
  TNMD WILD-TYPE  366   65
   clus
vv  TNMD MUTATED TNMD WILD-TYPE
  0            9            366
  1            0             65
[1] 2 2
[1] FALSE
D296V8, binary
                cls
clus               0   1
  TNMD MUTATED     5   6
  TNMD WILD-TYPE 220 258
[1] "tbl2"
                cls
clus             [,1] [,2]
  TNMD MUTATED      5    6
  TNMD WILD-TYPE  220  258
        clus
vv       TNMD MUTATED TNMD WILD-TYPE
  FEMALE            5            220
  MALE              6            258
[1] 2 2
[1] FALSE
D296V9, binary
                cls
clus               0   1
  TNMD MUTATED    10   0
  TNMD WILD-TYPE 340  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  TNMD MUTATED     10    0
  TNMD WILD-TYPE  340   22
     clus
vv    TNMD MUTATED TNMD WILD-TYPE
  NO            10            340
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  TNMD MUTATED                     10                             1
  TNMD WILD-TYPE                  305                            46
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  TNMD MUTATED                       0                              0
  TNMD WILD-TYPE                   106                             10
D296V10, multiclass
                                clus
vv                               TNMD MUTATED TNMD WILD-TYPE
  COLON ADENOCARCINOMA                     10            305
  COLON MUCINOUS ADENOCARCINOMA             1             46
  RECTAL ADENOCARCINOMA                     0            106
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  TNMD MUTATED     7   0   0   1
  TNMD WILD-TYPE 338   4  31  24
D296V11, multiclass
    clus
vv   TNMD MUTATED TNMD WILD-TYPE
  R0            7            338
  R1            0              4
  R2            0             31
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D296V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TNMD MUTATED                                  0     0
  TNMD WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  TNMD MUTATED                           1     5
  TNMD WILD-TYPE                        21   221
D296V13, multiclass
                                  clus
vv                                 TNMD MUTATED TNMD WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                       5            221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(297) Variable = RNF182 MUTATION ANALYSIS
D297V1, survival
                  sevent
clus2                0   1
  RNF182 MUTATED    14   2
  RNF182 WILD-TYPE 364  91
  RNF182 MUTATED RNF182 WILD-TYPE 
              16              455 
  RNF182 MUTATED RNF182 WILD-TYPE 
               2               91 
$`RNF182 MUTATED`
TCGA-A6-3810 TCGA-AA-3558 TCGA-AA-3655 TCGA-AA-3713 TCGA-AD-6888 TCGA-AZ-4315 
       36.53        20.98        61.02        19.04        15.52        58.39 
TCGA-AZ-5407 TCGA-D5-5540 TCGA-D5-6540 TCGA-D5-6931 TCGA-DM-A1HB TCGA-DM-A282 
       88.21        56.09        16.14        12.00       135.65       139.17 
TCGA-F4-6809 TCGA-AG-A002 TCGA-DC-6682 TCGA-EI-6506 
       13.25        20.98         4.01        20.55 

$`RNF182 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        32.75        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3560 
       13.02        24.00        17.95        29.95        23.01        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       13.94        19.99        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       85.05        26.99        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
       40.96         0.07        21.37        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6598 
        1.41         5.13       106.75        22.36        62.79        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5541 
       10.06        12.03        45.40        12.26        19.59        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
        4.80        17.13        12.49        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        4.80         1.51        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A285 TCGA-DM-A28C 
      140.38         7.50        44.32       131.51         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       41.42        16.24        33.67         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
       19.99         5.95         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6507 
       57.24        24.13        51.48        32.61         0.49        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  RNF182 MUTATED RNF182 WILD-TYPE 
            4.01             0.00 
  RNF182 MUTATED RNF182 WILD-TYPE 
          139.17           148.01 
  RNF182 MUTATED RNF182 WILD-TYPE 
           20.98            20.05 
[1] "4.0 - 139.2 (21.0)" "0.0 - 148.0 (20.1)"
[1] "hr=" "2.6"
D297V2, continuous
D297V3, binary
                  cls
clus                 0   1
  RNF182 MUTATED    13   3
  RNF182 WILD-TYPE 353 116
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF182 MUTATED     13    3
  RNF182 WILD-TYPE  353  116
        clus
vv       RNF182 MUTATED RNF182 WILD-TYPE
  COLON              13              353
  RECTUM              3              116
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RNF182 MUTATED         4        0        1         6         0         0
  RNF182 WILD-TYPE      87        1       31       132        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RNF182 MUTATED           0          0          2          1        1
  RNF182 WILD-TYPE        24         11         57         41       47
                  vv
clus               STAGE IVA STAGE IVB
  RNF182 MUTATED           1         0
  RNF182 WILD-TYPE        17         1
D297V4, multiclass
            clus
vv           RNF182 MUTATED RNF182 WILD-TYPE
  STAGE I                 4               87
  STAGE IA                0                1
  STAGE II                1               31
  STAGE IIA               6              132
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              2               57
  STAGE IIIC              1               41
  STAGE IV                1               47
  STAGE IVA               1               17
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  RNF182 MUTATED     1   3  11   1
  RNF182 WILD-TYPE  16  89 318  49
D297V5, multiclass
    clus
vv   RNF182 MUTATED RNF182 WILD-TYPE
  T1              1               16
  T2              3               89
  T3             11              318
  T4              1               49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  RNF182 MUTATED    12   3   1
  RNF182 WILD-TYPE 275 110  86
D297V6, multiclass
    clus
vv   RNF182 MUTATED RNF182 WILD-TYPE
  N0             12              275
  N1              3              110
  N2              1               86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D297V7, binary
                  cls
clus                 0   1
  RNF182 MUTATED    14   2
  RNF182 WILD-TYPE 361  63
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF182 MUTATED     14    2
  RNF182 WILD-TYPE  361   63
   clus
vv  RNF182 MUTATED RNF182 WILD-TYPE
  0             14              361
  1              2               63
[1] 2 2
[1] FALSE
D297V8, binary
                  cls
clus                 0   1
  RNF182 MUTATED     4  12
  RNF182 WILD-TYPE 221 252
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF182 MUTATED      4   12
  RNF182 WILD-TYPE  221  252
        clus
vv       RNF182 MUTATED RNF182 WILD-TYPE
  FEMALE              4              221
  MALE               12              252
[1] 2 2
[1] FALSE
D297V9, binary
                  cls
clus                 0   1
  RNF182 MUTATED    12   1
  RNF182 WILD-TYPE 338  21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF182 MUTATED     12    1
  RNF182 WILD-TYPE  338   21
     clus
vv    RNF182 MUTATED RNF182 WILD-TYPE
  NO              12              338
  YES              1               21
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  RNF182 MUTATED                     11                             1
  RNF182 WILD-TYPE                  304                            46
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  RNF182 MUTATED                       3                              0
  RNF182 WILD-TYPE                   103                             10
D297V10, multiclass
                                clus
vv                               RNF182 MUTATED RNF182 WILD-TYPE
  COLON ADENOCARCINOMA                       11              304
  COLON MUCINOUS ADENOCARCINOMA               1               46
  RECTAL ADENOCARCINOMA                       3              103
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  RNF182 MUTATED    11   0   2   0
  RNF182 WILD-TYPE 334   4  29  25
D297V11, multiclass
    clus
vv   RNF182 MUTATED RNF182 WILD-TYPE
  R0             11              334
  R1              0                4
  R2              2               29
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D297V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RNF182 MUTATED                                  0     0
  RNF182 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  RNF182 MUTATED                           0    12
  RNF182 WILD-TYPE                        22   214
D297V13, multiclass
                                  clus
vv                                 RNF182 MUTATED RNF182 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                        12              214
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(298) Variable = ERCC5 MUTATION ANALYSIS
D298V1, survival
                 sevent
clus2               0   1
  ERCC5 MUTATED    15   8
  ERCC5 WILD-TYPE 363  85
  ERCC5 MUTATED ERCC5 WILD-TYPE 
             23             448 
  ERCC5 MUTATED ERCC5 WILD-TYPE 
              8              85 
$`ERCC5 MUTATED`
TCGA-A6-2672 TCGA-A6-5665 TCGA-A6-6780 TCGA-AA-3492 TCGA-AA-3655 TCGA-AA-3815 
       46.65        22.06        20.12         3.02        61.02        33.04 
TCGA-AA-A00N TCGA-AZ-4315 TCGA-AZ-6598 TCGA-AZ-6608 TCGA-CM-5861 TCGA-CM-6171 
        4.01        58.39        49.41         1.61        15.02        14.04 
TCGA-CM-6674 TCGA-D5-5537 TCGA-D5-5540 TCGA-DM-A0XD TCGA-DM-A282 TCGA-DM-A28F 
       12.95        45.40        56.09        24.43       139.17        35.97 
TCGA-F4-6806 TCGA-F4-6809 TCGA-AG-3742 TCGA-AG-3892 TCGA-AG-A002 
       41.42        13.25         0.99        13.02        20.98 

$`ERCC5 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6781 
       24.16        21.76        24.69        24.39        23.87        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
       20.28         7.04         1.02        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       78.08         6.05         6.97        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
       19.04        19.04        10.06        35.05         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        33.01        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 
      106.75        22.36        62.79        88.21         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 
      100.01        29.56         5.23        11.74         3.19        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 
       29.06        22.03        22.98        30.08        32.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       15.02        11.01        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6529 
       10.06        12.03        12.26        19.59        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A285 
      140.38         7.50        44.32       131.51       135.65         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
       81.37       119.93        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       16.24        33.67         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3878 TCGA-AG-3881 
        7.99         0.99        37.02        32.98         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 
       19.99         1.02        17.95        36.95        17.03        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  ERCC5 MUTATED ERCC5 WILD-TYPE 
           0.99            0.00 
  ERCC5 MUTATED ERCC5 WILD-TYPE 
         139.17          148.01 
  ERCC5 MUTATED ERCC5 WILD-TYPE 
         22.060          20.035 
[1] "1.0 - 139.2 (22.1)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.5"
D298V2, continuous
D298V3, binary
                 cls
clus                0   1
  ERCC5 MUTATED    20   3
  ERCC5 WILD-TYPE 346 116
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERCC5 MUTATED     20    3
  ERCC5 WILD-TYPE  346  116
        clus
vv       ERCC5 MUTATED ERCC5 WILD-TYPE
  COLON             20             346
  RECTUM             3             116
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ERCC5 MUTATED         5        0        3        10         1         0
  ERCC5 WILD-TYPE      86        1       29       128         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ERCC5 MUTATED           0          1          2          0        0         1
  ERCC5 WILD-TYPE        24         10         57         42       48        17
                 vv
clus              STAGE IVB
  ERCC5 MUTATED           0
  ERCC5 WILD-TYPE         1
D298V4, multiclass
            clus
vv           ERCC5 MUTATED ERCC5 WILD-TYPE
  STAGE I                5              86
  STAGE IA               0               1
  STAGE II               3              29
  STAGE IIA             10             128
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             1              10
  STAGE IIIB             2              57
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ERCC5 MUTATED     2   4  16   1
  ERCC5 WILD-TYPE  15  88 313  49
D298V5, multiclass
    clus
vv   ERCC5 MUTATED ERCC5 WILD-TYPE
  T1             2              15
  T2             4              88
  T3            16             313
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  ERCC5 MUTATED    18   4   1
  ERCC5 WILD-TYPE 269 109  86
D298V6, multiclass
    clus
vv   ERCC5 MUTATED ERCC5 WILD-TYPE
  N0            18             269
  N1             4             109
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D298V7, binary
                 cls
clus                0   1
  ERCC5 MUTATED    19   1
  ERCC5 WILD-TYPE 356  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERCC5 MUTATED     19    1
  ERCC5 WILD-TYPE  356   64
   clus
vv  ERCC5 MUTATED ERCC5 WILD-TYPE
  0            19             356
  1             1              64
[1] 2 2
[1] FALSE
D298V8, binary
                 cls
clus                0   1
  ERCC5 MUTATED    13  10
  ERCC5 WILD-TYPE 212 254
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERCC5 MUTATED     13   10
  ERCC5 WILD-TYPE  212  254
        clus
vv       ERCC5 MUTATED ERCC5 WILD-TYPE
  FEMALE            13             212
  MALE              10             254
[1] 2 2
[1] FALSE
D298V9, binary
                 cls
clus                0   1
  ERCC5 MUTATED    18   0
  ERCC5 WILD-TYPE 332  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERCC5 MUTATED     18    0
  ERCC5 WILD-TYPE  332   22
     clus
vv    ERCC5 MUTATED ERCC5 WILD-TYPE
  NO             18             332
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ERCC5 MUTATED                     18                             2
  ERCC5 WILD-TYPE                  297                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ERCC5 MUTATED                       3                              0
  ERCC5 WILD-TYPE                   103                             10
D298V10, multiclass
                                clus
vv                               ERCC5 MUTATED ERCC5 WILD-TYPE
  COLON ADENOCARCINOMA                      18             297
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      3             103
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  ERCC5 MUTATED    16   0   0   1
  ERCC5 WILD-TYPE 329   4  31  24
D298V11, multiclass
    clus
vv   ERCC5 MUTATED ERCC5 WILD-TYPE
  R0            16             329
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D298V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ERCC5 MUTATED                                  0     0
  ERCC5 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ERCC5 MUTATED                           0    16
  ERCC5 WILD-TYPE                        22   210
D298V13, multiclass
                                  clus
vv                                 ERCC5 MUTATED ERCC5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                       16             210
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(299) Variable = JAK3 MUTATION ANALYSIS
D299V1, survival
                sevent
clus2              0   1
  JAK3 MUTATED    22   4
  JAK3 WILD-TYPE 356  89
  JAK3 MUTATED JAK3 WILD-TYPE 
            26            445 
  JAK3 MUTATED JAK3 WILD-TYPE 
             4             89 
$`JAK3 MUTATED`
TCGA-A6-5662 TCGA-A6-6648 TCGA-A6-6651 TCGA-AA-3555 TCGA-AA-3662 TCGA-AA-3877 
       23.61        25.18        21.76        29.95         6.05        31.00 
TCGA-AA-3977 TCGA-AA-A00E TCGA-AU-6004 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
       25.02        30.02        27.09        62.79        88.21        49.41 
TCGA-CA-6717 TCGA-CK-4952 TCGA-CK-5913 TCGA-CM-4752 TCGA-D5-6537 TCGA-DM-A28H 
       12.76        15.62        51.32        13.02         4.80       117.07 
TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6586 TCGA-G4-6588 TCGA-AG-3608 TCGA-AG-3742 
       55.04        63.62        35.80        26.17        15.95         0.99 
TCGA-AG-A02N TCGA-DY-A1DG 
       61.97        51.48 

$`JAK3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        33.53        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6649 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       24.16        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       17.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       61.02        78.08         6.97        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       18.05         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       38.04        19.00        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       10.88         0.20        14.50        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       22.36         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07        12.20        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
      148.01        85.45        49.08         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6539 
        1.32        43.27        15.12        17.85        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28K TCGA-F4-6459 
       81.37       119.93        35.97        60.79        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6625 
       85.48        61.91        36.00        22.09        13.78        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
       32.98         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 
      126.44        41.36        57.24        24.13        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  JAK3 MUTATED JAK3 WILD-TYPE 
          0.99           0.00 
  JAK3 MUTATED JAK3 WILD-TYPE 
        117.07         148.01 
  JAK3 MUTATED JAK3 WILD-TYPE 
         28.52          19.99 
[1] "1.0 - 117.1 (28.5)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.9"
D299V2, continuous
D299V3, binary
                cls
clus               0   1
  JAK3 MUTATED    24   4
  JAK3 WILD-TYPE 342 115
[1] "tbl2"
                cls
clus             [,1] [,2]
  JAK3 MUTATED     24    4
  JAK3 WILD-TYPE  342  115
        clus
vv       JAK3 MUTATED JAK3 WILD-TYPE
  COLON            24            342
  RECTUM            4            115
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  JAK3 MUTATED         5        0        4         8         0         0
  JAK3 WILD-TYPE      86        1       28       130        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  JAK3 MUTATED           0          0          4          2        1         3
  JAK3 WILD-TYPE        24         11         55         40       47        15
                vv
clus             STAGE IVB
  JAK3 MUTATED           0
  JAK3 WILD-TYPE         1
D299V4, multiclass
            clus
vv           JAK3 MUTATED JAK3 WILD-TYPE
  STAGE I               5             86
  STAGE IA              0              1
  STAGE II              4             28
  STAGE IIA             8            130
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            4             55
  STAGE IIIC            2             40
  STAGE IV              1             47
  STAGE IVA             3             15
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  JAK3 MUTATED     3   3  19   3
  JAK3 WILD-TYPE  14  89 310  47
D299V5, multiclass
    clus
vv   JAK3 MUTATED JAK3 WILD-TYPE
  T1            3             14
  T2            3             89
  T3           19            310
  T4            3             47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  JAK3 MUTATED    19   5   4
  JAK3 WILD-TYPE 268 108  83
D299V6, multiclass
    clus
vv   JAK3 MUTATED JAK3 WILD-TYPE
  N0           19            268
  N1            5            108
  N2            4             83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D299V7, binary
                cls
clus               0   1
  JAK3 MUTATED    17   4
  JAK3 WILD-TYPE 358  61
[1] "tbl2"
                cls
clus             [,1] [,2]
  JAK3 MUTATED     17    4
  JAK3 WILD-TYPE  358   61
   clus
vv  JAK3 MUTATED JAK3 WILD-TYPE
  0           17            358
  1            4             61
[1] 2 2
[1] FALSE
D299V8, binary
                cls
clus               0   1
  JAK3 MUTATED    15  13
  JAK3 WILD-TYPE 210 251
[1] "tbl2"
                cls
clus             [,1] [,2]
  JAK3 MUTATED     15   13
  JAK3 WILD-TYPE  210  251
        clus
vv       JAK3 MUTATED JAK3 WILD-TYPE
  FEMALE           15            210
  MALE             13            251
[1] 2 2
[1] FALSE
D299V9, binary
                cls
clus               0   1
  JAK3 MUTATED    19   1
  JAK3 WILD-TYPE 331  21
[1] "tbl2"
                cls
clus             [,1] [,2]
  JAK3 MUTATED     19    1
  JAK3 WILD-TYPE  331   21
     clus
vv    JAK3 MUTATED JAK3 WILD-TYPE
  NO            19            331
  YES            1             21
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  JAK3 MUTATED                     20                             4
  JAK3 WILD-TYPE                  295                            43
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  JAK3 MUTATED                       4                              0
  JAK3 WILD-TYPE                   102                             10
D299V10, multiclass
                                clus
vv                               JAK3 MUTATED JAK3 WILD-TYPE
  COLON ADENOCARCINOMA                     20            295
  COLON MUCINOUS ADENOCARCINOMA             4             43
  RECTAL ADENOCARCINOMA                     4            102
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  JAK3 MUTATED    14   0   1   4
  JAK3 WILD-TYPE 331   4  30  21
D299V11, multiclass
    clus
vv   JAK3 MUTATED JAK3 WILD-TYPE
  R0           14            331
  R1            0              4
  R2            1             30
  RX            4             21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D299V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  JAK3 MUTATED                                  0     1
  JAK3 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  JAK3 MUTATED                           1    17
  JAK3 WILD-TYPE                        21   209
D299V13, multiclass
                                  clus
vv                                 JAK3 MUTATED JAK3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                      17            209
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(300) Variable = HM13 MUTATION ANALYSIS
D300V1, survival
                sevent
clus2              0   1
  HM13 MUTATED     4   1
  HM13 WILD-TYPE 374  92
  HM13 MUTATED HM13 WILD-TYPE 
             5            466 
  HM13 MUTATED HM13 WILD-TYPE 
             1             92 
$`HM13 MUTATED`
TCGA-AA-3555 TCGA-D5-6536 TCGA-D5-6539 TCGA-F4-6459 TCGA-F4-6703 
       29.95        17.85        12.49         8.61        47.87 

$`HM13 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 
       21.01        13.02        24.00        17.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
        4.80        17.13        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6704 
      117.07        98.24        31.96        35.74         6.18         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  HM13 MUTATED HM13 WILD-TYPE 
          8.61           0.00 
  HM13 MUTATED HM13 WILD-TYPE 
         47.87         148.01 
  HM13 MUTATED HM13 WILD-TYPE 
        17.850         20.235 
[1] "8.6 - 47.9 (17.9)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.1"
D300V2, continuous
D300V3, binary
                cls
clus               0   1
  HM13 MUTATED     5   0
  HM13 WILD-TYPE 361 119
[1] "tbl2"
                cls
clus             [,1] [,2]
  HM13 MUTATED      5    0
  HM13 WILD-TYPE  361  119
        clus
vv       HM13 MUTATED HM13 WILD-TYPE
  COLON             5            361
  RECTUM            0            119
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  HM13 MUTATED         0        0        0         3         0         0
  HM13 WILD-TYPE      91        1       32       135        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  HM13 MUTATED           0          1          1          0        0         0
  HM13 WILD-TYPE        24         10         58         42       48        18
                vv
clus             STAGE IVB
  HM13 MUTATED           0
  HM13 WILD-TYPE         1
D300V4, multiclass
            clus
vv           HM13 MUTATED HM13 WILD-TYPE
  STAGE I               0             91
  STAGE IA              0              1
  STAGE II              0             32
  STAGE IIA             3            135
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            1             10
  STAGE IIIB            1             58
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  HM13 MUTATED     0   0   5   0
  HM13 WILD-TYPE  17  92 324  50
D300V5, multiclass
    clus
vv   HM13 MUTATED HM13 WILD-TYPE
  T1            0             17
  T2            0             92
  T3            5            324
  T4            0             50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  HM13 MUTATED     4   0   1
  HM13 WILD-TYPE 283 113  86
D300V6, multiclass
    clus
vv   HM13 MUTATED HM13 WILD-TYPE
  N0            4            283
  N1            0            113
  N2            1             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D300V7, binary
                cls
clus               0   1
  HM13 MUTATED     5   0
  HM13 WILD-TYPE 370  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  HM13 MUTATED      5    0
  HM13 WILD-TYPE  370   65
   clus
vv  HM13 MUTATED HM13 WILD-TYPE
  0            5            370
  1            0             65
[1] 2 2
[1] FALSE
D300V8, binary
                cls
clus               0   1
  HM13 MUTATED     3   2
  HM13 WILD-TYPE 222 262
[1] "tbl2"
                cls
clus             [,1] [,2]
  HM13 MUTATED      3    2
  HM13 WILD-TYPE  222  262
        clus
vv       HM13 MUTATED HM13 WILD-TYPE
  FEMALE            3            222
  MALE              2            262
[1] 2 2
[1] FALSE
D300V9, binary
                cls
clus               0   1
  HM13 MUTATED     5   0
  HM13 WILD-TYPE 345  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  HM13 MUTATED      5    0
  HM13 WILD-TYPE  345   22
     clus
vv    HM13 MUTATED HM13 WILD-TYPE
  NO             5            345
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  HM13 MUTATED                      4                             1
  HM13 WILD-TYPE                  311                            46
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  HM13 MUTATED                       0                              0
  HM13 WILD-TYPE                   106                             10
D300V10, multiclass
                                clus
vv                               HM13 MUTATED HM13 WILD-TYPE
  COLON ADENOCARCINOMA                      4            311
  COLON MUCINOUS ADENOCARCINOMA             1             46
  RECTAL ADENOCARCINOMA                     0            106
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  HM13 MUTATED     5   0   0   0
  HM13 WILD-TYPE 340   4  31  25
D300V11, multiclass
    clus
vv   HM13 MUTATED HM13 WILD-TYPE
  R0            5            340
  R1            0              4
  R2            0             31
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D300V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HM13 MUTATED                                  0     0
  HM13 WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  HM13 MUTATED                           0     4
  HM13 WILD-TYPE                        22   222
D300V13, multiclass
                                  clus
vv                                 HM13 MUTATED HM13 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       4            222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(301) Variable = RBM10 MUTATION ANALYSIS
D301V1, survival
                 sevent
clus2               0   1
  RBM10 MUTATED    12   5
  RBM10 WILD-TYPE 366  88
  RBM10 MUTATED RBM10 WILD-TYPE 
             17             454 
  RBM10 MUTATED RBM10 WILD-TYPE 
              5              88 
$`RBM10 MUTATED`
TCGA-A6-5661 TCGA-A6-5666 TCGA-AA-3672 TCGA-AA-3811 TCGA-AA-3941 TCGA-AD-6965 
       33.53        32.71         0.92        10.06        24.00         0.20 
TCGA-AU-6004 TCGA-AY-6197 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-CM-5868 TCGA-AF-2689 
       27.09        21.44        49.41         6.77        17.03        39.48 
TCGA-AG-3583 TCGA-AG-3902 TCGA-AG-3999 TCGA-AG-A002 TCGA-EI-6510 
       20.05        32.02        28.04        20.98        18.28 

$`RBM10 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       22.06        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
       54.02         2.01        14.01        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3815 
       85.05        26.99        19.04        19.04        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3947 
       29.98        18.05        31.00         2.01        12.99        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AU-3779 TCGA-AY-4070 
        5.79        22.42        27.42        10.88        14.50        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        33.01        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6600 TCGA-AZ-6601 
      106.75        22.36        62.79        88.21        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
        5.03        15.02        15.02        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       79.69        24.13        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3909 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       19.99        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       20.91         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  RBM10 MUTATED RBM10 WILD-TYPE 
            0.2             0.0 
  RBM10 MUTATED RBM10 WILD-TYPE 
          49.41          148.01 
  RBM10 MUTATED RBM10 WILD-TYPE 
          21.44           20.07 
[1] "0.2 - 49.4 (21.4)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.8"
D301V2, continuous
D301V3, binary
                 cls
clus                0   1
  RBM10 MUTATED    12   6
  RBM10 WILD-TYPE 354 113
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM10 MUTATED     12    6
  RBM10 WILD-TYPE  354  113
        clus
vv       RBM10 MUTATED RBM10 WILD-TYPE
  COLON             12             354
  RECTUM             6             113
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RBM10 MUTATED         3        0        2         3         0         1
  RBM10 WILD-TYPE      88        1       30       135        10         0
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RBM10 MUTATED           2          0          0          1        2         3
  RBM10 WILD-TYPE        22         11         59         41       46        15
                 vv
clus              STAGE IVB
  RBM10 MUTATED           0
  RBM10 WILD-TYPE         1
D301V4, multiclass
            clus
vv           RBM10 MUTATED RBM10 WILD-TYPE
  STAGE I                3              88
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA              3             135
  STAGE IIB              0              10
  STAGE IIC              1               0
  STAGE III              2              22
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             1              41
  STAGE IV               2              46
  STAGE IVA              3              15
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  RBM10 MUTATED     0   4   9   5
  RBM10 WILD-TYPE  17  88 320  45
D301V5, multiclass
    clus
vv   RBM10 MUTATED RBM10 WILD-TYPE
  T1             0              17
  T2             4              88
  T3             9             320
  T4             5              45
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  RBM10 MUTATED    10   3   5
  RBM10 WILD-TYPE 277 110  82
D301V6, multiclass
    clus
vv   RBM10 MUTATED RBM10 WILD-TYPE
  N0            10             277
  N1             3             110
  N2             5              82
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D301V7, binary
                 cls
clus                0   1
  RBM10 MUTATED     9   4
  RBM10 WILD-TYPE 366  61
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM10 MUTATED      9    4
  RBM10 WILD-TYPE  366   61
   clus
vv  RBM10 MUTATED RBM10 WILD-TYPE
  0             9             366
  1             4              61
[1] 2 2
[1] FALSE
D301V8, binary
                 cls
clus                0   1
  RBM10 MUTATED    11   7
  RBM10 WILD-TYPE 214 257
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM10 MUTATED     11    7
  RBM10 WILD-TYPE  214  257
        clus
vv       RBM10 MUTATED RBM10 WILD-TYPE
  FEMALE            11             214
  MALE               7             257
[1] 2 2
[1] FALSE
D301V9, binary
                 cls
clus                0   1
  RBM10 MUTATED    15   0
  RBM10 WILD-TYPE 335  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM10 MUTATED     15    0
  RBM10 WILD-TYPE  335   22
     clus
vv    RBM10 MUTATED RBM10 WILD-TYPE
  NO             15             335
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  RBM10 MUTATED                     12                             0
  RBM10 WILD-TYPE                  303                            47
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  RBM10 MUTATED                       5                              1
  RBM10 WILD-TYPE                   101                              9
D301V10, multiclass
                                clus
vv                               RBM10 MUTATED RBM10 WILD-TYPE
  COLON ADENOCARCINOMA                      12             303
  COLON MUCINOUS ADENOCARCINOMA              0              47
  RECTAL ADENOCARCINOMA                      5             101
  RECTAL MUCINOUS ADENOCARCINOMA             1               9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  RBM10 MUTATED    13   0   1   0
  RBM10 WILD-TYPE 332   4  30  25
D301V11, multiclass
    clus
vv   RBM10 MUTATED RBM10 WILD-TYPE
  R0            13             332
  R1             0               4
  R2             1              30
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D301V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RBM10 MUTATED                                  0     0
  RBM10 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  RBM10 MUTATED                           1     9
  RBM10 WILD-TYPE                        21   217
D301V13, multiclass
                                  clus
vv                                 RBM10 MUTATED RBM10 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        9             217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(302) Variable = TRPM7 MUTATION ANALYSIS
D302V1, survival
                 sevent
clus2               0   1
  TRPM7 MUTATED    21   7
  TRPM7 WILD-TYPE 357  86
  TRPM7 MUTATED TRPM7 WILD-TYPE 
             28             443 
  TRPM7 MUTATED TRPM7 WILD-TYPE 
              7              86 
$`TRPM7 MUTATED`
TCGA-A6-5660 TCGA-A6-5666 TCGA-A6-6649 TCGA-A6-6653 TCGA-AA-3672 TCGA-AA-3947 
       29.19        32.71        24.16        24.39         0.92        33.01 
TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01V TCGA-AD-5900 TCGA-AD-6964 
       25.02         4.01        34.98        35.01         0.07        10.88 
TCGA-AZ-4681 TCGA-AZ-6600 TCGA-AZ-6607 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4952 
      106.75        12.10         3.19        12.76        10.06        15.62 
TCGA-D5-5538 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6928 TCGA-DM-A1D4 TCGA-DM-A1DB 
       12.26        43.27        17.85        11.64        92.75        44.32 
TCGA-DM-A1HB TCGA-DM-A28H TCGA-AG-3892 TCGA-AG-A002 
      135.65       117.07        13.02        20.98 

$`TRPM7 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       22.06        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       21.76        24.69        23.87        20.12        19.66        20.28 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
        7.04         3.02         1.02        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
       14.01        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 
       18.05        31.00         2.01        12.99        24.00        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
       40.96        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        1.41         5.13        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6608 
        6.77       100.01        29.56         5.23        11.74         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 
       14.30        17.56       148.01        85.45        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5539 TCGA-D5-5540 
       11.01        10.06        12.03        45.40        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6537 
       55.92        20.19        18.25         1.32        15.12         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 
        4.41        12.43        14.30         9.04         9.44         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
       38.20       130.65        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
        7.50       131.51       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       35.97        60.79        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  TRPM7 MUTATED TRPM7 WILD-TYPE 
           0.07            0.00 
  TRPM7 MUTATED TRPM7 WILD-TYPE 
         135.65          148.01 
  TRPM7 MUTATED TRPM7 WILD-TYPE 
          22.57           20.12 
[1] "0.1 - 135.7 (22.6)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.1"
D302V2, continuous
D302V3, binary
                 cls
clus                0   1
  TRPM7 MUTATED    28   2
  TRPM7 WILD-TYPE 338 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRPM7 MUTATED     28    2
  TRPM7 WILD-TYPE  338  117
        clus
vv       TRPM7 MUTATED TRPM7 WILD-TYPE
  COLON             28             338
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TRPM7 MUTATED         5        0        0         9         3         1
  TRPM7 WILD-TYPE      86        1       32       129         7         0
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TRPM7 MUTATED           1          0          3          4        2         0
  TRPM7 WILD-TYPE        23         11         56         38       46        18
                 vv
clus              STAGE IVB
  TRPM7 MUTATED           0
  TRPM7 WILD-TYPE         1
D302V4, multiclass
            clus
vv           TRPM7 MUTATED TRPM7 WILD-TYPE
  STAGE I                5              86
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              9             129
  STAGE IIB              3               7
  STAGE IIC              1               0
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             3              56
  STAGE IIIC             4              38
  STAGE IV               2              46
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  TRPM7 MUTATED     1   5  16   8
  TRPM7 WILD-TYPE  16  87 313  42
D302V5, multiclass
    clus
vv   TRPM7 MUTATED TRPM7 WILD-TYPE
  T1             1              16
  T2             5              87
  T3            16             313
  T4             8              42
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  TRPM7 MUTATED    19   5   6
  TRPM7 WILD-TYPE 268 108  81
D302V6, multiclass
    clus
vv   TRPM7 MUTATED TRPM7 WILD-TYPE
  N0            19             268
  N1             5             108
  N2             6              81
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D302V7, binary
                 cls
clus                0   1
  TRPM7 MUTATED    24   2
  TRPM7 WILD-TYPE 351  63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRPM7 MUTATED     24    2
  TRPM7 WILD-TYPE  351   63
   clus
vv  TRPM7 MUTATED TRPM7 WILD-TYPE
  0            24             351
  1             2              63
[1] 2 2
[1] FALSE
D302V8, binary
                 cls
clus                0   1
  TRPM7 MUTATED     9  21
  TRPM7 WILD-TYPE 216 243
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRPM7 MUTATED      9   21
  TRPM7 WILD-TYPE  216  243
        clus
vv       TRPM7 MUTATED TRPM7 WILD-TYPE
  FEMALE             9             216
  MALE              21             243
[1] 2 2
[1] FALSE
D302V9, binary
                 cls
clus                0   1
  TRPM7 MUTATED    19   0
  TRPM7 WILD-TYPE 331  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRPM7 MUTATED     19    0
  TRPM7 WILD-TYPE  331   22
     clus
vv    TRPM7 MUTATED TRPM7 WILD-TYPE
  NO             19             331
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  TRPM7 MUTATED                     19                             8
  TRPM7 WILD-TYPE                  296                            39
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  TRPM7 MUTATED                       2                              0
  TRPM7 WILD-TYPE                   104                             10
D302V10, multiclass
                                clus
vv                               TRPM7 MUTATED TRPM7 WILD-TYPE
  COLON ADENOCARCINOMA                      19             296
  COLON MUCINOUS ADENOCARCINOMA              8              39
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  TRPM7 MUTATED    15   0   0   3
  TRPM7 WILD-TYPE 330   4  31  22
D302V11, multiclass
    clus
vv   TRPM7 MUTATED TRPM7 WILD-TYPE
  R0            15             330
  R1             0               4
  R2             0              31
  RX             3              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D302V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TRPM7 MUTATED                                  0     2
  TRPM7 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  TRPM7 MUTATED                           2    17
  TRPM7 WILD-TYPE                        20   209
D302V13, multiclass
                                  clus
vv                                 TRPM7 MUTATED TRPM7 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               9
  BLACK OR AFRICAN AMERICAN                    2              20
  WHITE                                       17             209
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(303) Variable = CAMSAP1L1 MUTATION ANALYSIS
D303V1, survival
                     sevent
clus2                   0   1
  CAMSAP1L1 MUTATED    19   3
  CAMSAP1L1 WILD-TYPE 359  90
  CAMSAP1L1 MUTATED CAMSAP1L1 WILD-TYPE 
                 22                 449 
  CAMSAP1L1 MUTATED CAMSAP1L1 WILD-TYPE 
                  3                  90 
$`CAMSAP1L1 MUTATED`
TCGA-A6-3809 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5664 TCGA-AA-3496 TCGA-AA-3715 
       32.75        30.44        33.53        22.09         1.02        19.04 
TCGA-AA-3815 TCGA-AA-3877 TCGA-AU-6004 TCGA-AZ-4315 TCGA-AZ-6599 TCGA-CA-6717 
       33.04        31.00        27.09        58.39         6.77        12.76 
TCGA-CM-6162 TCGA-D5-6927 TCGA-D5-6930 TCGA-F4-6570 TCGA-G4-6304 TCGA-G4-6309 
       12.00         9.44         1.51         6.18        53.62        85.48 
TCGA-G4-6315 TCGA-G4-6586 TCGA-AH-6549 TCGA-CI-6624 
       61.91        35.80        17.49         4.73 

$`CAMSAP1L1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 
       31.63        29.19        23.61        22.06        32.71        27.09 
TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 
       22.52         8.38        25.08        25.18        24.16        21.76 
TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       24.69        24.39        23.87        20.12        19.66        20.28 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
        7.04         3.02        35.01        63.98         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
       13.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       36.03         8.05        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       78.08         6.05         6.97        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       19.04        10.06        35.05         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 
       17.03        24.03        27.02        29.98        18.05         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       10.88         0.20        14.50        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        88.21        49.41        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07        12.20        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       15.02        17.03        15.02         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       11.64         4.80        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 
      117.07        98.24         8.61        31.96        35.74        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       44.68        55.04        63.62        36.00        22.09        13.78 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 
       38.04       117.11        38.56         1.45         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
        6.05        33.17         6.97        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  CAMSAP1L1 MUTATED CAMSAP1L1 WILD-TYPE 
               1.02                0.00 
  CAMSAP1L1 MUTATED CAMSAP1L1 WILD-TYPE 
              85.48              148.01 
  CAMSAP1L1 MUTATED CAMSAP1L1 WILD-TYPE 
              24.59               20.12 
[1] "1.0 - 85.5 (24.6)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.5"
D303V2, continuous
D303V3, binary
                     cls
clus                    0   1
  CAMSAP1L1 MUTATED    21   2
  CAMSAP1L1 WILD-TYPE 345 117
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  CAMSAP1L1 MUTATED     21    2
  CAMSAP1L1 WILD-TYPE  345  117
        clus
vv       CAMSAP1L1 MUTATED CAMSAP1L1 WILD-TYPE
  COLON                 21                 345
  RECTUM                 2                 117
[1] 2 2
[1] FALSE
                     vv
clus                  STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CAMSAP1L1 MUTATED         5        0        2         8         2         0
  CAMSAP1L1 WILD-TYPE      86        1       30       130         8         1
                     vv
clus                  STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CAMSAP1L1 MUTATED           0          0          2          2        1
  CAMSAP1L1 WILD-TYPE        24         11         57         40       47
                     vv
clus                  STAGE IVA STAGE IVB
  CAMSAP1L1 MUTATED           0         0
  CAMSAP1L1 WILD-TYPE        18         1
D303V4, multiclass
            clus
vv           CAMSAP1L1 MUTATED CAMSAP1L1 WILD-TYPE
  STAGE I                    5                  86
  STAGE IA                   0                   1
  STAGE II                   2                  30
  STAGE IIA                  8                 130
  STAGE IIB                  2                   8
  STAGE IIC                  0                   1
  STAGE III                  0                  24
  STAGE IIIA                 0                  11
  STAGE IIIB                 2                  57
  STAGE IIIC                 2                  40
  STAGE IV                   1                  47
  STAGE IVA                  0                  18
  STAGE IVB                  0                   1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                   T1  T2  T3  T4
  CAMSAP1L1 MUTATED     1   4  15   3
  CAMSAP1L1 WILD-TYPE  16  88 314  47
D303V5, multiclass
    clus
vv   CAMSAP1L1 MUTATED CAMSAP1L1 WILD-TYPE
  T1                 1                  16
  T2                 4                  88
  T3                15                 314
  T4                 3                  47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                   N0  N1  N2
  CAMSAP1L1 MUTATED    17   3   2
  CAMSAP1L1 WILD-TYPE 270 110  85
D303V6, multiclass
    clus
vv   CAMSAP1L1 MUTATED CAMSAP1L1 WILD-TYPE
  N0                17                 270
  N1                 3                 110
  N2                 2                  85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D303V7, binary
                     cls
clus                    0   1
  CAMSAP1L1 MUTATED    18   1
  CAMSAP1L1 WILD-TYPE 357  64
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  CAMSAP1L1 MUTATED     18    1
  CAMSAP1L1 WILD-TYPE  357   64
   clus
vv  CAMSAP1L1 MUTATED CAMSAP1L1 WILD-TYPE
  0                18                 357
  1                 1                  64
[1] 2 2
[1] FALSE
D303V8, binary
                     cls
clus                    0   1
  CAMSAP1L1 MUTATED    12  11
  CAMSAP1L1 WILD-TYPE 213 253
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  CAMSAP1L1 MUTATED     12   11
  CAMSAP1L1 WILD-TYPE  213  253
        clus
vv       CAMSAP1L1 MUTATED CAMSAP1L1 WILD-TYPE
  FEMALE                12                 213
  MALE                  11                 253
[1] 2 2
[1] FALSE
D303V9, binary
                     cls
clus                    0   1
  CAMSAP1L1 MUTATED    18   0
  CAMSAP1L1 WILD-TYPE 332  22
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  CAMSAP1L1 MUTATED     18    0
  CAMSAP1L1 WILD-TYPE  332   22
     clus
vv    CAMSAP1L1 MUTATED CAMSAP1L1 WILD-TYPE
  NO                 18                 332
  YES                 0                  22
[1] 2 2
[1] FALSE
                     vv
clus                  COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CAMSAP1L1 MUTATED                     15                             6
  CAMSAP1L1 WILD-TYPE                  300                            41
                     vv
clus                  RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CAMSAP1L1 MUTATED                       2                              0
  CAMSAP1L1 WILD-TYPE                   104                             10
D303V10, multiclass
                                clus
vv                               CAMSAP1L1 MUTATED CAMSAP1L1 WILD-TYPE
  COLON ADENOCARCINOMA                          15                 300
  COLON MUCINOUS ADENOCARCINOMA                  6                  41
  RECTAL ADENOCARCINOMA                          2                 104
  RECTAL MUCINOUS ADENOCARCINOMA                 0                  10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                   R0  R1  R2  RX
  CAMSAP1L1 MUTATED    18   0   0   2
  CAMSAP1L1 WILD-TYPE 327   4  31  23
D303V11, multiclass
    clus
vv   CAMSAP1L1 MUTATED CAMSAP1L1 WILD-TYPE
  R0                18                 327
  R1                 0                   4
  R2                 0                  31
  RX                 2                  23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D303V12, continuous
                     vv
clus                  AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CAMSAP1L1 MUTATED                                  0     1
  CAMSAP1L1 WILD-TYPE                                1    10
                     vv
clus                  BLACK OR AFRICAN AMERICAN WHITE
  CAMSAP1L1 MUTATED                           3    15
  CAMSAP1L1 WILD-TYPE                        19   211
D303V13, multiclass
                                  clus
vv                                 CAMSAP1L1 MUTATED CAMSAP1L1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                 0                   1
  ASIAN                                            1                  10
  BLACK OR AFRICAN AMERICAN                        3                  19
  WHITE                                           15                 211
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(304) Variable = SLC33A1 MUTATION ANALYSIS
D304V1, survival
                   sevent
clus2                 0   1
  SLC33A1 MUTATED     7   2
  SLC33A1 WILD-TYPE 371  91
  SLC33A1 MUTATED SLC33A1 WILD-TYPE 
                9               462 
  SLC33A1 MUTATED SLC33A1 WILD-TYPE 
                2                91 
$`SLC33A1 MUTATED`
TCGA-AD-6901 TCGA-AZ-4315 TCGA-AZ-6599 TCGA-CK-6751 TCGA-CM-6680 TCGA-D5-6536 
       22.42        58.39         6.77       124.27        12.03        17.85 
TCGA-D5-6539 TCGA-G4-6315 TCGA-AG-A002 
       12.49        61.91        20.98 

$`SLC33A1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        33.01        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 
      106.75        22.36        62.79        88.21        49.41        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
        1.91        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.08        11.01        10.06        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 
       43.27        15.12         4.80        17.13        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       85.48        63.62        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  SLC33A1 MUTATED SLC33A1 WILD-TYPE 
             6.77              0.00 
  SLC33A1 MUTATED SLC33A1 WILD-TYPE 
           124.27            148.01 
  SLC33A1 MUTATED SLC33A1 WILD-TYPE 
           20.980            20.155 
[1] "6.8 - 124.3 (21.0)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.2"
D304V2, continuous
D304V3, binary
                   cls
clus                  0   1
  SLC33A1 MUTATED     9   1
  SLC33A1 WILD-TYPE 357 118
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC33A1 MUTATED      9    1
  SLC33A1 WILD-TYPE  357  118
        clus
vv       SLC33A1 MUTATED SLC33A1 WILD-TYPE
  COLON                9               357
  RECTUM               1               118
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SLC33A1 MUTATED         3        0        0         3         0         0
  SLC33A1 WILD-TYPE      88        1       32       135        10         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC33A1 MUTATED           0          1          1          0        1
  SLC33A1 WILD-TYPE        24         10         58         42       47
                   vv
clus                STAGE IVA STAGE IVB
  SLC33A1 MUTATED           0         0
  SLC33A1 WILD-TYPE        18         1
D304V4, multiclass
            clus
vv           SLC33A1 MUTATED SLC33A1 WILD-TYPE
  STAGE I                  3                88
  STAGE IA                 0                 1
  STAGE II                 0                32
  STAGE IIA                3               135
  STAGE IIB                0                10
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               1                10
  STAGE IIIB               1                58
  STAGE IIIC               0                42
  STAGE IV                 1                47
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  SLC33A1 MUTATED     0   3   7   0
  SLC33A1 WILD-TYPE  17  89 322  50
D304V5, multiclass
    clus
vv   SLC33A1 MUTATED SLC33A1 WILD-TYPE
  T1               0                17
  T2               3                89
  T3               7               322
  T4               0                50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  SLC33A1 MUTATED     8   1   1
  SLC33A1 WILD-TYPE 279 112  86
D304V6, multiclass
    clus
vv   SLC33A1 MUTATED SLC33A1 WILD-TYPE
  N0               8               279
  N1               1               112
  N2               1                86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D304V7, binary
                   cls
clus                  0   1
  SLC33A1 MUTATED     6   1
  SLC33A1 WILD-TYPE 369  64
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC33A1 MUTATED      6    1
  SLC33A1 WILD-TYPE  369   64
   clus
vv  SLC33A1 MUTATED SLC33A1 WILD-TYPE
  0               6               369
  1               1                64
[1] 2 2
[1] FALSE
D304V8, binary
                   cls
clus                  0   1
  SLC33A1 MUTATED     4   6
  SLC33A1 WILD-TYPE 221 258
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC33A1 MUTATED      4    6
  SLC33A1 WILD-TYPE  221  258
        clus
vv       SLC33A1 MUTATED SLC33A1 WILD-TYPE
  FEMALE               4               221
  MALE                 6               258
[1] 2 2
[1] FALSE
D304V9, binary
                   cls
clus                  0   1
  SLC33A1 MUTATED     9   0
  SLC33A1 WILD-TYPE 341  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC33A1 MUTATED      9    0
  SLC33A1 WILD-TYPE  341   22
     clus
vv    SLC33A1 MUTATED SLC33A1 WILD-TYPE
  NO                9               341
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SLC33A1 MUTATED                      8                             1
  SLC33A1 WILD-TYPE                  307                            46
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SLC33A1 MUTATED                       1                              0
  SLC33A1 WILD-TYPE                   105                             10
D304V10, multiclass
                                clus
vv                               SLC33A1 MUTATED SLC33A1 WILD-TYPE
  COLON ADENOCARCINOMA                         8               307
  COLON MUCINOUS ADENOCARCINOMA                1                46
  RECTAL ADENOCARCINOMA                        1               105
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  SLC33A1 MUTATED     7   0   0   1
  SLC33A1 WILD-TYPE 338   4  31  24
D304V11, multiclass
    clus
vv   SLC33A1 MUTATED SLC33A1 WILD-TYPE
  R0               7               338
  R1               0                 4
  R2               0                31
  RX               1                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D304V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SLC33A1 MUTATED                                  0     0
  SLC33A1 WILD-TYPE                                1    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  SLC33A1 MUTATED                           0     8
  SLC33A1 WILD-TYPE                        22   218
D304V13, multiclass
                                  clus
vv                                 SLC33A1 MUTATED SLC33A1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                      0                22
  WHITE                                          8               218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(305) Variable = F2RL1 MUTATION ANALYSIS
D305V1, survival
                 sevent
clus2               0   1
  F2RL1 MUTATED     7   0
  F2RL1 WILD-TYPE 371  93
  F2RL1 MUTATED F2RL1 WILD-TYPE 
              7             464 
  F2RL1 MUTATED F2RL1 WILD-TYPE 
              0              93 
$`F2RL1 MUTATED`
TCGA-AZ-4315 TCGA-CM-4744 TCGA-CM-6163 TCGA-CM-6677 TCGA-CM-6678 TCGA-D5-5539 
       58.39        20.02         2.96        11.08        11.01        19.59 
TCGA-AG-A002 
       20.98 

$`F2RL1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
       16.31         0.95        33.01        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4746 
       21.14        82.95         1.91       124.27        23.05        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       15.02        12.00        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       13.05        11.08        10.06        12.03        45.40        12.26 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  F2RL1 MUTATED F2RL1 WILD-TYPE 
           2.96            0.00 
  F2RL1 MUTATED F2RL1 WILD-TYPE 
          58.39          148.01 
  F2RL1 MUTATED F2RL1 WILD-TYPE 
         19.590          20.415 
[1] "3.0 - 58.4 (19.6)"  "0.0 - 148.0 (20.4)"
[1] "hr="     "9100000"
D305V2, continuous
D305V3, binary
                 cls
clus                0   1
  F2RL1 MUTATED     7   1
  F2RL1 WILD-TYPE 359 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  F2RL1 MUTATED      7    1
  F2RL1 WILD-TYPE  359  118
        clus
vv       F2RL1 MUTATED F2RL1 WILD-TYPE
  COLON              7             359
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  F2RL1 MUTATED         4        0        0         2         0         0
  F2RL1 WILD-TYPE      87        1       32       136        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  F2RL1 MUTATED           0          1          0          0        0         1
  F2RL1 WILD-TYPE        24         10         59         42       48        17
                 vv
clus              STAGE IVB
  F2RL1 MUTATED           0
  F2RL1 WILD-TYPE         1
D305V4, multiclass
            clus
vv           F2RL1 MUTATED F2RL1 WILD-TYPE
  STAGE I                4              87
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              2             136
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             1              10
  STAGE IIIB             0              59
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  F2RL1 MUTATED     1   3   3   1
  F2RL1 WILD-TYPE  16  89 326  49
D305V5, multiclass
    clus
vv   F2RL1 MUTATED F2RL1 WILD-TYPE
  T1             1              16
  T2             3              89
  T3             3             326
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  F2RL1 MUTATED     6   2   0
  F2RL1 WILD-TYPE 281 111  87
D305V6, multiclass
    clus
vv   F2RL1 MUTATED F2RL1 WILD-TYPE
  N0             6             281
  N1             2             111
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D305V7, binary
                 cls
clus                0   1
  F2RL1 MUTATED     6   1
  F2RL1 WILD-TYPE 369  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  F2RL1 MUTATED      6    1
  F2RL1 WILD-TYPE  369   64
   clus
vv  F2RL1 MUTATED F2RL1 WILD-TYPE
  0             6             369
  1             1              64
[1] 2 2
[1] FALSE
D305V8, binary
                 cls
clus                0   1
  F2RL1 MUTATED     2   6
  F2RL1 WILD-TYPE 223 258
[1] "tbl2"
                 cls
clus              [,1] [,2]
  F2RL1 MUTATED      2    6
  F2RL1 WILD-TYPE  223  258
        clus
vv       F2RL1 MUTATED F2RL1 WILD-TYPE
  FEMALE             2             223
  MALE               6             258
[1] 2 2
[1] FALSE
D305V9, binary
                 cls
clus                0   1
  F2RL1 MUTATED     7   0
  F2RL1 WILD-TYPE 343  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  F2RL1 MUTATED      7    0
  F2RL1 WILD-TYPE  343   22
     clus
vv    F2RL1 MUTATED F2RL1 WILD-TYPE
  NO              7             343
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  F2RL1 MUTATED                      6                             1
  F2RL1 WILD-TYPE                  309                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  F2RL1 MUTATED                       1                              0
  F2RL1 WILD-TYPE                   105                             10
D305V10, multiclass
                                clus
vv                               F2RL1 MUTATED F2RL1 WILD-TYPE
  COLON ADENOCARCINOMA                       6             309
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  F2RL1 MUTATED     7   0   0   1
  F2RL1 WILD-TYPE 338   4  31  24
D305V11, multiclass
    clus
vv   F2RL1 MUTATED F2RL1 WILD-TYPE
  R0             7             338
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D305V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  F2RL1 MUTATED                                  0     0
  F2RL1 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  F2RL1 MUTATED                           0     7
  F2RL1 WILD-TYPE                        22   219
D305V13, multiclass
                                  clus
vv                                 F2RL1 MUTATED F2RL1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        7             219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(306) Variable = USP26 MUTATION ANALYSIS
D306V1, survival
                 sevent
clus2               0   1
  USP26 MUTATED    21   2
  USP26 WILD-TYPE 357  91
  USP26 MUTATED USP26 WILD-TYPE 
             23             448 
  USP26 MUTATED USP26 WILD-TYPE 
              2              91 
$`USP26 MUTATED`
TCGA-A6-2672 TCGA-A6-5665 TCGA-A6-6653 TCGA-A6-6781 TCGA-AA-3510 TCGA-AA-3663 
       46.65        22.06        24.39        19.66        63.98         6.97 
TCGA-AA-3864 TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-A00E TCGA-AA-A010 TCGA-AU-6004 
       53.00        33.01        24.00        30.02        34.98        27.09 
TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-6599 TCGA-CA-6717 TCGA-CM-6171 TCGA-D5-6928 
       21.44        58.39         6.77        12.76        14.04        11.64 
TCGA-D5-6932 TCGA-F4-6570 TCGA-F4-6806 TCGA-F4-6856 TCGA-AG-3892 
       11.38         6.18        41.42        35.31        13.02 

$`USP26 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 
       24.16        21.76        24.69        23.87        20.12        20.28 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 
        7.04         3.02         1.02        35.01         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
       13.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       36.03         8.05        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
       78.08         6.05        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 
        2.01        12.99        24.00        26.01         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
       16.31         0.95        33.01        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 
      106.75        22.36        62.79        88.21        49.41        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       13.02        15.02        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
       14.30         9.04         9.44         4.80         1.51        12.00 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6807 TCGA-F4-6808 
       35.74        47.87         1.55        34.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
       13.25         0.53        47.41       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 
        1.02        17.95        36.95        17.03        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  USP26 MUTATED USP26 WILD-TYPE 
           6.18            0.00 
  USP26 MUTATED USP26 WILD-TYPE 
          63.98          148.01 
  USP26 MUTATED USP26 WILD-TYPE 
         24.000          20.035 
[1] "6.2 - 64.0 (24.0)"  "0.0 - 148.0 (20.0)"
[1] "hr=" "2.5"
D306V2, continuous
D306V3, binary
                 cls
clus                0   1
  USP26 MUTATED    23   1
  USP26 WILD-TYPE 343 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP26 MUTATED     23    1
  USP26 WILD-TYPE  343  118
        clus
vv       USP26 MUTATED USP26 WILD-TYPE
  COLON             23             343
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  USP26 MUTATED         7        0        3        10         2         0
  USP26 WILD-TYPE      84        1       29       128         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  USP26 MUTATED           0          0          1          1        0         0
  USP26 WILD-TYPE        24         11         58         41       48        18
                 vv
clus              STAGE IVB
  USP26 MUTATED           0
  USP26 WILD-TYPE         1
D306V4, multiclass
            clus
vv           USP26 MUTATED USP26 WILD-TYPE
  STAGE I                7              84
  STAGE IA               0               1
  STAGE II               3              29
  STAGE IIA             10             128
  STAGE IIB              2               8
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             1              41
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  USP26 MUTATED     1   6  14   3
  USP26 WILD-TYPE  16  86 315  47
D306V5, multiclass
    clus
vv   USP26 MUTATED USP26 WILD-TYPE
  T1             1              16
  T2             6              86
  T3            14             315
  T4             3              47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  USP26 MUTATED    22   2   0
  USP26 WILD-TYPE 265 111  87
D306V6, multiclass
    clus
vv   USP26 MUTATED USP26 WILD-TYPE
  N0            22             265
  N1             2             111
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D306V7, binary
                 cls
clus                0   1
  USP26 MUTATED    21   0
  USP26 WILD-TYPE 354  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP26 MUTATED     21    0
  USP26 WILD-TYPE  354   65
   clus
vv  USP26 MUTATED USP26 WILD-TYPE
  0            21             354
  1             0              65
[1] 2 2
[1] FALSE
D306V8, binary
                 cls
clus                0   1
  USP26 MUTATED    11  13
  USP26 WILD-TYPE 214 251
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP26 MUTATED     11   13
  USP26 WILD-TYPE  214  251
        clus
vv       USP26 MUTATED USP26 WILD-TYPE
  FEMALE            11             214
  MALE              13             251
[1] 2 2
[1] FALSE
D306V9, binary
                 cls
clus                0   1
  USP26 MUTATED    22   0
  USP26 WILD-TYPE 328  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP26 MUTATED     22    0
  USP26 WILD-TYPE  328   22
     clus
vv    USP26 MUTATED USP26 WILD-TYPE
  NO             22             328
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  USP26 MUTATED                     17                             6
  USP26 WILD-TYPE                  298                            41
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  USP26 MUTATED                       1                              0
  USP26 WILD-TYPE                   105                             10
D306V10, multiclass
                                clus
vv                               USP26 MUTATED USP26 WILD-TYPE
  COLON ADENOCARCINOMA                      17             298
  COLON MUCINOUS ADENOCARCINOMA              6              41
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  USP26 MUTATED    21   0   0   1
  USP26 WILD-TYPE 324   4  31  24
D306V11, multiclass
    clus
vv   USP26 MUTATED USP26 WILD-TYPE
  R0            21             324
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D306V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  USP26 MUTATED                                  0     1
  USP26 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  USP26 MUTATED                           0    14
  USP26 WILD-TYPE                        22   212
D306V13, multiclass
                                  clus
vv                                 USP26 MUTATED USP26 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                       14             212
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(307) Variable = WEE1 MUTATION ANALYSIS
D307V1, survival
                sevent
clus2              0   1
  WEE1 MUTATED     8   3
  WEE1 WILD-TYPE 370  90
  WEE1 MUTATED WEE1 WILD-TYPE 
            11            460 
  WEE1 MUTATED WEE1 WILD-TYPE 
             3             90 
$`WEE1 MUTATED`
TCGA-AA-3510 TCGA-AA-3821 TCGA-AU-6004 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-AZ-6599 
       63.98         1.02        27.09        58.39        49.41         6.77 
TCGA-CA-5254 TCGA-CM-5348 TCGA-CM-5861 TCGA-DM-A28C TCGA-G4-6293 
       12.69        22.98        15.02        81.37       133.18 

$`WEE1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 
       10.06        35.05        33.04         0.99        25.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       10.88         0.20        14.50        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       62.79        88.21        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
       11.74         3.19         1.61         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5349 
       37.02        25.02        13.02        29.06        22.03        30.08 
TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       32.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
      139.17         6.12       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
        0.53        47.41        35.31        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  WEE1 MUTATED WEE1 WILD-TYPE 
          1.02           0.00 
  WEE1 MUTATED WEE1 WILD-TYPE 
        133.18         148.01 
  WEE1 MUTATED WEE1 WILD-TYPE 
        27.090         20.085 
[1] "1.0 - 133.2 (27.1)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.2"
D307V2, continuous
D307V3, binary
                cls
clus               0   1
  WEE1 MUTATED    12   0
  WEE1 WILD-TYPE 354 119
[1] "tbl2"
                cls
clus             [,1] [,2]
  WEE1 MUTATED     12    0
  WEE1 WILD-TYPE  354  119
        clus
vv       WEE1 MUTATED WEE1 WILD-TYPE
  COLON            12            354
  RECTUM            0            119
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  WEE1 MUTATED         3        0        3         4         0         0
  WEE1 WILD-TYPE      88        1       29       134        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  WEE1 MUTATED           1          0          1          0        0         0
  WEE1 WILD-TYPE        23         11         58         42       48        18
                vv
clus             STAGE IVB
  WEE1 MUTATED           0
  WEE1 WILD-TYPE         1
D307V4, multiclass
            clus
vv           WEE1 MUTATED WEE1 WILD-TYPE
  STAGE I               3             88
  STAGE IA              0              1
  STAGE II              3             29
  STAGE IIA             4            134
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             1             23
  STAGE IIIA            0             11
  STAGE IIIB            1             58
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  WEE1 MUTATED     0   3   8   1
  WEE1 WILD-TYPE  17  89 321  49
D307V5, multiclass
    clus
vv   WEE1 MUTATED WEE1 WILD-TYPE
  T1            0             17
  T2            3             89
  T3            8            321
  T4            1             49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  WEE1 MUTATED    10   2   0
  WEE1 WILD-TYPE 277 111  87
D307V6, multiclass
    clus
vv   WEE1 MUTATED WEE1 WILD-TYPE
  N0           10            277
  N1            2            111
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D307V7, binary
                cls
clus               0   1
  WEE1 MUTATED    10   0
  WEE1 WILD-TYPE 365  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  WEE1 MUTATED     10    0
  WEE1 WILD-TYPE  365   65
   clus
vv  WEE1 MUTATED WEE1 WILD-TYPE
  0           10            365
  1            0             65
[1] 2 2
[1] FALSE
D307V8, binary
                cls
clus               0   1
  WEE1 MUTATED     7   5
  WEE1 WILD-TYPE 218 259
[1] "tbl2"
                cls
clus             [,1] [,2]
  WEE1 MUTATED      7    5
  WEE1 WILD-TYPE  218  259
        clus
vv       WEE1 MUTATED WEE1 WILD-TYPE
  FEMALE            7            218
  MALE              5            259
[1] 2 2
[1] FALSE
D307V9, binary
                cls
clus               0   1
  WEE1 MUTATED     9   0
  WEE1 WILD-TYPE 341  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  WEE1 MUTATED      9    0
  WEE1 WILD-TYPE  341   22
     clus
vv    WEE1 MUTATED WEE1 WILD-TYPE
  NO             9            341
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  WEE1 MUTATED                     11                             1
  WEE1 WILD-TYPE                  304                            46
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  WEE1 MUTATED                       0                              0
  WEE1 WILD-TYPE                   106                             10
D307V10, multiclass
                                clus
vv                               WEE1 MUTATED WEE1 WILD-TYPE
  COLON ADENOCARCINOMA                     11            304
  COLON MUCINOUS ADENOCARCINOMA             1             46
  RECTAL ADENOCARCINOMA                     0            106
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  WEE1 MUTATED     8   0   0   1
  WEE1 WILD-TYPE 337   4  31  24
D307V11, multiclass
    clus
vv   WEE1 MUTATED WEE1 WILD-TYPE
  R0            8            337
  R1            0              4
  R2            0             31
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D307V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  WEE1 MUTATED                                  0     1
  WEE1 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  WEE1 MUTATED                           0     8
  WEE1 WILD-TYPE                        22   218
D307V13, multiclass
                                  clus
vv                                 WEE1 MUTATED WEE1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       8            218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(308) Variable = ERBB2IP MUTATION ANALYSIS
D308V1, survival
                   sevent
clus2                 0   1
  ERBB2IP MUTATED    16   1
  ERBB2IP WILD-TYPE 362  92
  ERBB2IP MUTATED ERBB2IP WILD-TYPE 
               17               454 
  ERBB2IP MUTATED ERBB2IP WILD-TYPE 
                1                92 
$`ERBB2IP MUTATED`
TCGA-A6-6142 TCGA-AA-3510 TCGA-AA-3655 TCGA-AA-3864 TCGA-AA-3977 TCGA-AA-A00N 
       25.08        63.98        61.02        53.00        25.02         4.01 
TCGA-AA-A010 TCGA-AU-6004 TCGA-CA-6717 TCGA-CM-6674 TCGA-CM-6677 TCGA-DM-A1HA 
       34.98        27.09        12.76        12.95        11.08       131.51 
TCGA-F4-6856 TCGA-G4-6628 TCGA-AG-3892 TCGA-AG-A002 TCGA-AH-6644 
       35.31        79.69        13.02        20.98         0.72 

$`ERBB2IP WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       13.94        19.99        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        31.07        30.05        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 
       27.42        10.88         0.20        14.50        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.20        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6675 
       12.99        13.02        15.02        14.04        11.01        13.05 
TCGA-CM-6676 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
        7.50        44.32       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 
       35.80        26.17        91.79        46.75        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-CI-6619 TCGA-CI-6620 
       38.56         1.45        17.49         0.69         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  ERBB2IP MUTATED ERBB2IP WILD-TYPE 
             0.72              0.00 
  ERBB2IP MUTATED ERBB2IP WILD-TYPE 
           131.51            148.01 
  ERBB2IP MUTATED ERBB2IP WILD-TYPE 
           25.080            20.035 
[1] "0.7 - 131.5 (25.1)" "0.0 - 148.0 (20.0)"
[1] "hr=" "4.7"
D308V2, continuous
D308V3, binary
                   cls
clus                  0   1
  ERBB2IP MUTATED    15   3
  ERBB2IP WILD-TYPE 351 116
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ERBB2IP MUTATED     15    3
  ERBB2IP WILD-TYPE  351  116
        clus
vv       ERBB2IP MUTATED ERBB2IP WILD-TYPE
  COLON               15               351
  RECTUM               3               116
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ERBB2IP MUTATED         5        0        3         3         3         0
  ERBB2IP WILD-TYPE      86        1       29       135         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ERBB2IP MUTATED           0          0          0          1        0
  ERBB2IP WILD-TYPE        24         11         59         41       48
                   vv
clus                STAGE IVA STAGE IVB
  ERBB2IP MUTATED           1         0
  ERBB2IP WILD-TYPE        17         1
D308V4, multiclass
            clus
vv           ERBB2IP MUTATED ERBB2IP WILD-TYPE
  STAGE I                  5                86
  STAGE IA                 0                 1
  STAGE II                 3                29
  STAGE IIA                3               135
  STAGE IIB                3                 7
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               0                11
  STAGE IIIB               0                59
  STAGE IIIC               1                41
  STAGE IV                 0                48
  STAGE IVA                1                17
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  ERBB2IP MUTATED     1   5   9   3
  ERBB2IP WILD-TYPE  16  87 320  47
D308V5, multiclass
    clus
vv   ERBB2IP MUTATED ERBB2IP WILD-TYPE
  T1               1                16
  T2               5                87
  T3               9               320
  T4               3                47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  ERBB2IP MUTATED    15   1   1
  ERBB2IP WILD-TYPE 272 112  86
D308V6, multiclass
    clus
vv   ERBB2IP MUTATED ERBB2IP WILD-TYPE
  N0              15               272
  N1               1               112
  N2               1                86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D308V7, binary
                   cls
clus                  0   1
  ERBB2IP MUTATED    14   1
  ERBB2IP WILD-TYPE 361  64
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ERBB2IP MUTATED     14    1
  ERBB2IP WILD-TYPE  361   64
   clus
vv  ERBB2IP MUTATED ERBB2IP WILD-TYPE
  0              14               361
  1               1                64
[1] 2 2
[1] FALSE
D308V8, binary
                   cls
clus                  0   1
  ERBB2IP MUTATED     6  12
  ERBB2IP WILD-TYPE 219 252
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ERBB2IP MUTATED      6   12
  ERBB2IP WILD-TYPE  219  252
        clus
vv       ERBB2IP MUTATED ERBB2IP WILD-TYPE
  FEMALE               6               219
  MALE                12               252
[1] 2 2
[1] FALSE
D308V9, binary
                   cls
clus                  0   1
  ERBB2IP MUTATED    13   0
  ERBB2IP WILD-TYPE 337  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ERBB2IP MUTATED     13    0
  ERBB2IP WILD-TYPE  337   22
     clus
vv    ERBB2IP MUTATED ERBB2IP WILD-TYPE
  NO               13               337
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ERBB2IP MUTATED                     12                             3
  ERBB2IP WILD-TYPE                  303                            44
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ERBB2IP MUTATED                       3                              0
  ERBB2IP WILD-TYPE                   103                             10
D308V10, multiclass
                                clus
vv                               ERBB2IP MUTATED ERBB2IP WILD-TYPE
  COLON ADENOCARCINOMA                        12               303
  COLON MUCINOUS ADENOCARCINOMA                3                44
  RECTAL ADENOCARCINOMA                        3               103
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  ERBB2IP MUTATED    12   0   0   2
  ERBB2IP WILD-TYPE 333   4  31  23
D308V11, multiclass
    clus
vv   ERBB2IP MUTATED ERBB2IP WILD-TYPE
  R0              12               333
  R1               0                 4
  R2               0                31
  RX               2                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D308V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ERBB2IP MUTATED                                  0     1
  ERBB2IP WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  ERBB2IP MUTATED                           0     9
  ERBB2IP WILD-TYPE                        22   217
D308V13, multiclass
                                  clus
vv                                 ERBB2IP MUTATED ERBB2IP WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                10
  BLACK OR AFRICAN AMERICAN                      0                22
  WHITE                                          9               217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(309) Variable = B4GALNT4 MUTATION ANALYSIS
D309V1, survival
                    sevent
clus2                  0   1
  B4GALNT4 MUTATED     7   3
  B4GALNT4 WILD-TYPE 371  90
  B4GALNT4 MUTATED B4GALNT4 WILD-TYPE 
                10                461 
  B4GALNT4 MUTATED B4GALNT4 WILD-TYPE 
                 3                 90 
$`B4GALNT4 MUTATED`
TCGA-A6-2672 TCGA-AA-3510 TCGA-AD-6964 TCGA-AU-6004 TCGA-AZ-6598 TCGA-CK-5916 
       46.65        63.98        10.88        27.09        49.41        21.14 
TCGA-CM-4743 TCGA-D5-6928 TCGA-DM-A1HB TCGA-G4-6588 
       23.05        11.64       135.65        26.17 

$`B4GALNT4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
        0.20        14.50        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        88.21         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 
       51.32         9.99        82.95         1.91       124.27        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
        9.44         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 
       61.91        36.00        22.09        13.78        35.80        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  B4GALNT4 MUTATED B4GALNT4 WILD-TYPE 
             10.88               0.00 
  B4GALNT4 MUTATED B4GALNT4 WILD-TYPE 
            135.65             148.01 
  B4GALNT4 MUTATED B4GALNT4 WILD-TYPE 
             26.63              20.02 
[1] "10.9 - 135.7 (26.6)" "0.0 - 148.0 (20.0)" 
[1] "hr=" "1"  
D309V2, continuous
D309V3, binary
                    cls
clus                   0   1
  B4GALNT4 MUTATED    11   0
  B4GALNT4 WILD-TYPE 355 119
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  B4GALNT4 MUTATED     11    0
  B4GALNT4 WILD-TYPE  355  119
        clus
vv       B4GALNT4 MUTATED B4GALNT4 WILD-TYPE
  COLON                11                355
  RECTUM                0                119
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  B4GALNT4 MUTATED         2        0        2         3         1         0
  B4GALNT4 WILD-TYPE      89        1       30       135         9         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  B4GALNT4 MUTATED           0          0          2          0        0
  B4GALNT4 WILD-TYPE        24         11         57         42       48
                    vv
clus                 STAGE IVA STAGE IVB
  B4GALNT4 MUTATED           0         0
  B4GALNT4 WILD-TYPE        18         1
D309V4, multiclass
            clus
vv           B4GALNT4 MUTATED B4GALNT4 WILD-TYPE
  STAGE I                   2                 89
  STAGE IA                  0                  1
  STAGE II                  2                 30
  STAGE IIA                 3                135
  STAGE IIB                 1                  9
  STAGE IIC                 0                  1
  STAGE III                 0                 24
  STAGE IIIA                0                 11
  STAGE IIIB                2                 57
  STAGE IIIC                0                 42
  STAGE IV                  0                 48
  STAGE IVA                 0                 18
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  B4GALNT4 MUTATED     1   1   7   2
  B4GALNT4 WILD-TYPE  16  91 322  48
D309V5, multiclass
    clus
vv   B4GALNT4 MUTATED B4GALNT4 WILD-TYPE
  T1                1                 16
  T2                1                 91
  T3                7                322
  T4                2                 48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  B4GALNT4 MUTATED     8   2   1
  B4GALNT4 WILD-TYPE 279 111  86
D309V6, multiclass
    clus
vv   B4GALNT4 MUTATED B4GALNT4 WILD-TYPE
  N0                8                279
  N1                2                111
  N2                1                 86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D309V7, binary
                    cls
clus                   0   1
  B4GALNT4 MUTATED     8   0
  B4GALNT4 WILD-TYPE 367  65
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  B4GALNT4 MUTATED      8    0
  B4GALNT4 WILD-TYPE  367   65
   clus
vv  B4GALNT4 MUTATED B4GALNT4 WILD-TYPE
  0                8                367
  1                0                 65
[1] 2 2
[1] FALSE
D309V8, binary
                    cls
clus                   0   1
  B4GALNT4 MUTATED     6   5
  B4GALNT4 WILD-TYPE 219 259
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  B4GALNT4 MUTATED      6    5
  B4GALNT4 WILD-TYPE  219  259
        clus
vv       B4GALNT4 MUTATED B4GALNT4 WILD-TYPE
  FEMALE                6                219
  MALE                  5                259
[1] 2 2
[1] FALSE
D309V9, binary
                    cls
clus                   0   1
  B4GALNT4 MUTATED     8   0
  B4GALNT4 WILD-TYPE 342  22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  B4GALNT4 MUTATED      8    0
  B4GALNT4 WILD-TYPE  342   22
     clus
vv    B4GALNT4 MUTATED B4GALNT4 WILD-TYPE
  NO                 8                342
  YES                0                 22
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  B4GALNT4 MUTATED                      9                             1
  B4GALNT4 WILD-TYPE                  306                            46
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  B4GALNT4 MUTATED                       0                              0
  B4GALNT4 WILD-TYPE                   106                             10
D309V10, multiclass
                                clus
vv                               B4GALNT4 MUTATED B4GALNT4 WILD-TYPE
  COLON ADENOCARCINOMA                          9                306
  COLON MUCINOUS ADENOCARCINOMA                 1                 46
  RECTAL ADENOCARCINOMA                         0                106
  RECTAL MUCINOUS ADENOCARCINOMA                0                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  B4GALNT4 MUTATED     6   0   0   2
  B4GALNT4 WILD-TYPE 339   4  31  23
D309V11, multiclass
    clus
vv   B4GALNT4 MUTATED B4GALNT4 WILD-TYPE
  R0                6                339
  R1                0                  4
  R2                0                 31
  RX                2                 23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D309V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  B4GALNT4 MUTATED                                  0     0
  B4GALNT4 WILD-TYPE                                1    11
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  B4GALNT4 MUTATED                           0    10
  B4GALNT4 WILD-TYPE                        22   216
D309V13, multiclass
                                  clus
vv                                 B4GALNT4 MUTATED B4GALNT4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 11
  BLACK OR AFRICAN AMERICAN                       0                 22
  WHITE                                          10                216
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(310) Variable = NSUN6 MUTATION ANALYSIS
D310V1, survival
                 sevent
clus2               0   1
  NSUN6 MUTATED     8   2
  NSUN6 WILD-TYPE 370  91
  NSUN6 MUTATED NSUN6 WILD-TYPE 
             10             461 
  NSUN6 MUTATED NSUN6 WILD-TYPE 
              2              91 
$`NSUN6 MUTATED`
TCGA-A6-6781 TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-A010 TCGA-AD-5900 TCGA-AZ-6607 
       19.66         3.02        63.98        34.98         0.07         3.19 
TCGA-CM-5861 TCGA-D5-6540 TCGA-AG-A002 TCGA-DY-A0XA 
       15.02        16.14        20.98       126.44 

$`NSUN6 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 
       23.87        20.12        20.28         7.04         1.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
       40.96        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       22.98        30.08        32.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 
       17.85         4.80        17.13        12.49        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD 
        5.95         4.01         5.03         5.29        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  NSUN6 MUTATED NSUN6 WILD-TYPE 
           0.07            0.00 
  NSUN6 MUTATED NSUN6 WILD-TYPE 
         126.44          148.01 
  NSUN6 MUTATED NSUN6 WILD-TYPE 
          17.90           20.28 
[1] "0.1 - 126.4 (17.9)" "0.0 - 148.0 (20.3)"
[1] "hr=" "1.1"
D310V2, continuous
D310V3, binary
                 cls
clus                0   1
  NSUN6 MUTATED     8   2
  NSUN6 WILD-TYPE 358 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NSUN6 MUTATED      8    2
  NSUN6 WILD-TYPE  358  117
        clus
vv       NSUN6 MUTATED NSUN6 WILD-TYPE
  COLON              8             358
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NSUN6 MUTATED         3        0        2         2         1         0
  NSUN6 WILD-TYPE      88        1       30       136         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NSUN6 MUTATED           0          0          0          1        1         0
  NSUN6 WILD-TYPE        24         11         59         41       47        18
                 vv
clus              STAGE IVB
  NSUN6 MUTATED           0
  NSUN6 WILD-TYPE         1
D310V4, multiclass
            clus
vv           NSUN6 MUTATED NSUN6 WILD-TYPE
  STAGE I                3              88
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA              2             136
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             1              41
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  NSUN6 MUTATED     0   3   4   3
  NSUN6 WILD-TYPE  17  89 325  47
D310V5, multiclass
    clus
vv   NSUN6 MUTATED NSUN6 WILD-TYPE
  T1             0              17
  T2             3              89
  T3             4             325
  T4             3              47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  NSUN6 MUTATED     8   1   1
  NSUN6 WILD-TYPE 279 112  86
D310V6, multiclass
    clus
vv   NSUN6 MUTATED NSUN6 WILD-TYPE
  N0             8             279
  N1             1             112
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D310V7, binary
                 cls
clus                0   1
  NSUN6 MUTATED     7   1
  NSUN6 WILD-TYPE 368  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NSUN6 MUTATED      7    1
  NSUN6 WILD-TYPE  368   64
   clus
vv  NSUN6 MUTATED NSUN6 WILD-TYPE
  0             7             368
  1             1              64
[1] 2 2
[1] FALSE
D310V8, binary
                 cls
clus                0   1
  NSUN6 MUTATED     4   6
  NSUN6 WILD-TYPE 221 258
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NSUN6 MUTATED      4    6
  NSUN6 WILD-TYPE  221  258
        clus
vv       NSUN6 MUTATED NSUN6 WILD-TYPE
  FEMALE             4             221
  MALE               6             258
[1] 2 2
[1] FALSE
D310V9, binary
                 cls
clus                0   1
  NSUN6 MUTATED     8   0
  NSUN6 WILD-TYPE 342  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NSUN6 MUTATED      8    0
  NSUN6 WILD-TYPE  342   22
     clus
vv    NSUN6 MUTATED NSUN6 WILD-TYPE
  NO              8             342
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  NSUN6 MUTATED                      5                             3
  NSUN6 WILD-TYPE                  310                            44
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  NSUN6 MUTATED                       2                              0
  NSUN6 WILD-TYPE                   104                             10
D310V10, multiclass
                                clus
vv                               NSUN6 MUTATED NSUN6 WILD-TYPE
  COLON ADENOCARCINOMA                       5             310
  COLON MUCINOUS ADENOCARCINOMA              3              44
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  NSUN6 MUTATED     8   0   0   0
  NSUN6 WILD-TYPE 337   4  31  25
D310V11, multiclass
    clus
vv   NSUN6 MUTATED NSUN6 WILD-TYPE
  R0             8             337
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D310V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NSUN6 MUTATED                                  0     0
  NSUN6 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  NSUN6 MUTATED                           0     6
  NSUN6 WILD-TYPE                        22   220
D310V13, multiclass
                                  clus
vv                                 NSUN6 MUTATED NSUN6 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        6             220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(311) Variable = KDM5B MUTATION ANALYSIS
D311V1, survival
                 sevent
clus2               0   1
  KDM5B MUTATED    18   9
  KDM5B WILD-TYPE 360  84
  KDM5B MUTATED KDM5B WILD-TYPE 
             27             444 
  KDM5B MUTATED KDM5B WILD-TYPE 
              9              84 
$`KDM5B MUTATED`
TCGA-A6-3809 TCGA-A6-5661 TCGA-AA-3510 TCGA-AA-3715 TCGA-AA-3818 TCGA-AA-3864 
       32.75        33.53        63.98        19.04         0.99        53.00 
TCGA-AA-3877 TCGA-AA-3947 TCGA-AY-6197 TCGA-AZ-6601 TCGA-CA-6717 TCGA-CM-6161 
       31.00        33.01        21.44       100.01        12.76        15.02 
TCGA-CM-6677 TCGA-D5-5541 TCGA-DM-A0XD TCGA-DM-A1D4 TCGA-DM-A1D9 TCGA-DM-A1DA 
       11.08        55.92        24.43        92.75       140.38         7.50 
TCGA-DM-A28H TCGA-F4-6570 TCGA-G4-6304 TCGA-G4-6626 TCGA-AF-2693 TCGA-AG-3575 
      117.07         6.18        53.62        46.75        19.10        12.00 
TCGA-AG-3726 TCGA-AG-4007 TCGA-DY-A1DD 
        7.99         1.02        57.24 

$`KDM5B WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       31.63        30.44        29.19        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       85.05        26.99        19.04        10.06        35.05        33.04 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       30.05        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
        2.01        12.99        24.00        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       33.01        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07        12.20        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        15.02        17.03        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6678 
       14.04        11.01        12.95        13.05        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
      119.70        38.20       130.65        49.91        13.32        12.59 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
      119.93        35.97        60.79        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       35.74        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       74.56        65.85        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       91.79        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       10.39        36.03        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       13.94        19.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4008 
       32.02        19.99        28.04        36.03        14.04        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       41.36        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  KDM5B MUTATED KDM5B WILD-TYPE 
           0.99            0.00 
  KDM5B MUTATED KDM5B WILD-TYPE 
         140.38          148.01 
  KDM5B MUTATED KDM5B WILD-TYPE 
         31.000          20.035 
[1] "1.0 - 140.4 (31.0)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.2"
D311V2, continuous
D311V3, binary
                 cls
clus                0   1
  KDM5B MUTATED    23   4
  KDM5B WILD-TYPE 343 115
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM5B MUTATED     23    4
  KDM5B WILD-TYPE  343  115
        clus
vv       KDM5B MUTATED KDM5B WILD-TYPE
  COLON             23             343
  RECTUM             4             115
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KDM5B MUTATED         4        0        5        11         3         0
  KDM5B WILD-TYPE      87        1       27       127         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  KDM5B MUTATED           0          0          2          2        1         0
  KDM5B WILD-TYPE        24         11         57         40       47        18
                 vv
clus              STAGE IVB
  KDM5B MUTATED           0
  KDM5B WILD-TYPE         1
D311V4, multiclass
            clus
vv           KDM5B MUTATED KDM5B WILD-TYPE
  STAGE I                4              87
  STAGE IA               0               1
  STAGE II               5              27
  STAGE IIA             11             127
  STAGE IIB              3               7
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             2              57
  STAGE IIIC             2              40
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  KDM5B MUTATED     1   3  20   4
  KDM5B WILD-TYPE  16  89 309  46
D311V5, multiclass
    clus
vv   KDM5B MUTATED KDM5B WILD-TYPE
  T1             1              16
  T2             3              89
  T3            20             309
  T4             4              46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  KDM5B MUTATED    23   2   3
  KDM5B WILD-TYPE 264 111  84
D311V6, multiclass
    clus
vv   KDM5B MUTATED KDM5B WILD-TYPE
  N0            23             264
  N1             2             111
  N2             3              84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D311V7, binary
                 cls
clus                0   1
  KDM5B MUTATED    25   1
  KDM5B WILD-TYPE 350  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM5B MUTATED     25    1
  KDM5B WILD-TYPE  350   64
   clus
vv  KDM5B MUTATED KDM5B WILD-TYPE
  0            25             350
  1             1              64
[1] 2 2
[1] FALSE
D311V8, binary
                 cls
clus                0   1
  KDM5B MUTATED    14  14
  KDM5B WILD-TYPE 211 250
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM5B MUTATED     14   14
  KDM5B WILD-TYPE  211  250
        clus
vv       KDM5B MUTATED KDM5B WILD-TYPE
  FEMALE            14             211
  MALE              14             250
[1] 2 2
[1] FALSE
D311V9, binary
                 cls
clus                0   1
  KDM5B MUTATED    19   0
  KDM5B WILD-TYPE 331  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM5B MUTATED     19    0
  KDM5B WILD-TYPE  331   22
     clus
vv    KDM5B MUTATED KDM5B WILD-TYPE
  NO             19             331
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  KDM5B MUTATED                     19                             4
  KDM5B WILD-TYPE                  296                            43
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  KDM5B MUTATED                       4                              0
  KDM5B WILD-TYPE                   102                             10
D311V10, multiclass
                                clus
vv                               KDM5B MUTATED KDM5B WILD-TYPE
  COLON ADENOCARCINOMA                      19             296
  COLON MUCINOUS ADENOCARCINOMA              4              43
  RECTAL ADENOCARCINOMA                      4             102
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  KDM5B MUTATED    18   0   1   1
  KDM5B WILD-TYPE 327   4  30  24
D311V11, multiclass
    clus
vv   KDM5B MUTATED KDM5B WILD-TYPE
  R0            18             327
  R1             0               4
  R2             1              30
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D311V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KDM5B MUTATED                                  0     1
  KDM5B WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  KDM5B MUTATED                           1    16
  KDM5B WILD-TYPE                        21   210
D311V13, multiclass
                                  clus
vv                                 KDM5B MUTATED KDM5B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                       16             210
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(312) Variable = KRAS MUTATION ANALYSIS
D312V1, survival
                sevent
clus2              0   1
  KRAS MUTATED   183  43
  KRAS WILD-TYPE 195  50
  KRAS MUTATED KRAS WILD-TYPE 
           226            245 
  KRAS MUTATED KRAS WILD-TYPE 
            43             50 
$`KRAS MUTATED`
TCGA-A6-2683 TCGA-A6-3808 TCGA-A6-4105 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 
       16.57        33.34        14.53        31.63        30.44        33.53 
TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6138 TCGA-A6-6141 
       23.61        22.09        22.06        32.71        22.52         8.38 
TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6782 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3520 
       24.39        23.87        20.28        35.01         6.97        24.03 
TCGA-AA-3522 TCGA-AA-3530 TCGA-AA-3532 TCGA-AA-3548 TCGA-AA-3555 TCGA-AA-3556 
       37.05        19.07        29.00        33.99        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       20.98        19.99        13.94        61.02        78.08         6.97 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3696 TCGA-AA-3713 
        0.92        50.04        11.01         5.98         5.03        19.04 
TCGA-AA-3715 TCGA-AA-3818 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       19.04         0.99        38.99        37.02        14.93         0.00 
TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3861 TCGA-AA-3864 
       10.06        33.07         0.00        36.03        30.05        53.00 
TCGA-AA-3870 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3975 TCGA-AA-3977 
       29.98         2.01        12.99        24.00        34.06        25.02 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A00K TCGA-AA-A00N 
       24.00        19.07        27.02        38.04        18.05         4.01 
TCGA-AA-A00Q TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01R 
       42.02        32.02        12.00        31.00        31.00        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       26.01        37.02        51.98        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6889 TCGA-AD-6895 
       39.98        18.05        40.96        21.37        56.55         0.72 
TCGA-AD-6901 TCGA-AD-6964 TCGA-AD-6965 TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4315 
       22.42        10.88         0.20        33.01        17.82        58.39 
TCGA-AZ-4616 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
        5.13        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19         1.61         3.06         3.25 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-6748 
       12.20        10.06        17.56       148.01        85.45         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-5862 
      124.27        23.05        20.02        37.02        25.02         5.03 
TCGA-CM-5863 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6166 TCGA-CM-6167 
       15.02        15.02         2.96        29.03        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6678 TCGA-D5-5537 TCGA-D5-5538 
       12.99        14.04        12.95        11.01        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6535 TCGA-D5-6536 
       19.59        56.09        20.19        18.25        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6923 TCGA-D5-6927 
        4.80        17.13        12.49        15.58        12.43         9.44 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28E TCGA-DM-A28G 
       44.32       131.51       139.17         6.12       119.93        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
      117.07        98.24        47.87        34.42        41.42        16.24 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6323 
        0.53        47.41        35.31        53.62        44.68        13.78 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       35.80        91.79        46.75        39.48        43.04        13.55 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3575 TCGA-AG-3580 
       14.50        16.83        20.02        10.39        12.00         8.02 
TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3594 TCGA-AG-3599 TCGA-AG-3605 
        7.07        20.05         1.02         2.01        12.03         0.99 
TCGA-AG-3611 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 
       13.94         7.99         0.99        37.02         0.99         0.99 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3896 TCGA-AG-3902 TCGA-AG-3909 
       17.95        36.95        13.02         1.02        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       28.04        14.04        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01W TCGA-AG-A020 TCGA-AG-A025 
       23.01        15.95        36.03        70.03        10.98        49.97 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6549 TCGA-AH-6644 
       61.97        41.00        38.04        38.56        17.49         0.72 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CL-5917 TCGA-DC-6155 TCGA-DC-6160 TCGA-DC-6683 
       33.17         6.97        78.12        13.97        19.99         5.03 
TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6510 
       24.13        32.61         0.49        20.55        19.96        18.28 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6812 TCGA-G5-6235 
       31.30        28.57         0.66        55.76 

$`KRAS WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5660 TCGA-A6-6137 
       34.65        32.75        36.53        32.91        29.19        27.09 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6780 
       25.08        25.18        24.16        21.76        24.69        20.12 
TCGA-A6-6781 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3510 TCGA-AA-3514 
       19.66         7.04         3.02         1.02        63.98         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3524 TCGA-AA-3525 
       13.02        38.99         1.02         9.07        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3531 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        34.03        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
        0.99        14.01        21.01        13.02        24.00        17.95 
TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3678 
       19.99         6.05        54.02         2.01        14.01        47.01 
TCGA-AA-3679 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3710 
       15.02        37.05        19.00        36.00        85.05        26.99 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       10.06        35.05        33.04        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3846 TCGA-AA-3850 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       15.95        17.03         0.00        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       31.07        17.03        24.03        27.02        18.05        31.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3976 
        2.01        21.99        16.08        50.99        13.05        26.01 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00E 
       27.02        27.02         7.96        13.94        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00U 
       34.03        18.05        38.04        27.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01P 
       14.99        21.99        34.98         1.02        10.98        38.07 
TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A024 TCGA-AA-A02F 
        1.02         1.02        33.04        35.01        39.06        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AD-5900 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6899 
        2.01         5.03         0.07        15.52         0.79         5.79 
TCGA-AD-6963 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6197 
       27.42        14.50        27.09        16.31         0.95        21.44 
TCGA-AZ-4323 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6603 TCGA-CA-5254 
        1.41       106.75        22.36        62.79        29.56        12.69 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4952 TCGA-CK-5912 
        3.29         0.07        12.76        14.30        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CM-4752 TCGA-CM-5341 
       51.32         9.99        21.14        82.95        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5864 
       22.03        22.98        30.08        32.02        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 
       17.03        12.00        16.04        13.02        15.02        11.01 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5541 
       13.05        11.08        11.08        10.06        12.03        55.92 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6540 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
        1.32        43.27        16.14         1.48         3.68         4.41 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6929 TCGA-DM-A0XF TCGA-DM-A1DA 
       14.30         9.04        11.64         4.80        38.20         7.50 
TCGA-DM-A1HB TCGA-DM-A28C TCGA-DM-A28F TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
      135.65        81.37        35.97         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6704 TCGA-F4-6808 TCGA-F4-6809 TCGA-G4-6293 TCGA-G4-6299 
        6.18         1.55        33.67        13.25       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       65.85        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6588 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2693 TCGA-AF-3400 
       22.09        26.17        79.69        24.13        19.10        34.49 
TCGA-AF-3913 TCGA-AF-6136 TCGA-AG-3574 TCGA-AG-3578 TCGA-AG-3582 TCGA-AG-3584 
       10.39        15.39        36.03        32.02        36.03        24.00 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3598 TCGA-AG-3600 TCGA-AG-3608 TCGA-AG-3609 
       46.03        34.03        50.04         6.05        15.95        19.99 
TCGA-AG-3612 TCGA-AG-3732 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3890 
       19.99        32.98        19.04        19.99         1.02        17.03 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-A002 
       35.01        14.01        48.03        36.03         1.02        20.98 
TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01Y TCGA-AG-A026 TCGA-AG-A02G 
       37.02         9.07        12.00        64.01         1.94        38.96 
TCGA-AG-A036 TCGA-AH-6547 TCGA-AH-6643 TCGA-CI-6619 TCGA-CI-6624 TCGA-CL-5918 
      117.11         1.45         0.69         6.05         4.73         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6681 TCGA-DC-6682 
       15.02         5.03        27.95        10.98         5.95         4.01 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DG TCGA-EI-6508 
        5.29       126.44        41.36        57.24        51.48        20.91 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6811 TCGA-F5-6813 TCGA-G5-6641 
        9.96        49.51        32.19         0.69        26.43 

  KRAS MUTATED KRAS WILD-TYPE 
             0              0 
  KRAS MUTATED KRAS WILD-TYPE 
        148.01         135.65 
  KRAS MUTATED KRAS WILD-TYPE 
        20.035         20.980 
[1] "0.0 - 148.0 (20.0)" "0.0 - 135.7 (21.0)"
[1] "hr=" "1.2"
D312V2, continuous
D312V3, binary
                cls
clus               0   1
  KRAS MUTATED   168  61
  KRAS WILD-TYPE 198  58
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED    168   61
  KRAS WILD-TYPE  198   58
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  COLON           168            198
  RECTUM           61             58
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KRAS MUTATED        44        1       17        72         5         1
  KRAS WILD-TYPE      47        0       15        66         5         0
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  KRAS MUTATED           9          7         21         15       20        10
  KRAS WILD-TYPE        15          4         38         27       28         8
                vv
clus             STAGE IVB
  KRAS MUTATED           0
  KRAS WILD-TYPE         1
D312V4, multiclass
            clus
vv           KRAS MUTATED KRAS WILD-TYPE
  STAGE I              44             47
  STAGE IA              1              0
  STAGE II             17             15
  STAGE IIA            72             66
  STAGE IIB             5              5
  STAGE IIC             1              0
  STAGE III             9             15
  STAGE IIIA            7              4
  STAGE IIIB           21             38
  STAGE IIIC           15             27
  STAGE IV             20             28
  STAGE IVA            10              8
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  KRAS MUTATED     8  45 152  25
  KRAS WILD-TYPE   9  47 177  25
D312V5, multiclass
    clus
vv   KRAS MUTATED KRAS WILD-TYPE
  T1            8              9
  T2           45             47
  T3          152            177
  T4           25             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  KRAS MUTATED   145  47  37
  KRAS WILD-TYPE 142  66  50
D312V6, multiclass
    clus
vv   KRAS MUTATED KRAS WILD-TYPE
  N0          145            142
  N1           47             66
  N2           37             50
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D312V7, binary
                cls
clus               0   1
  KRAS MUTATED   181  28
  KRAS WILD-TYPE 194  37
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED    181   28
  KRAS WILD-TYPE  194   37
   clus
vv  KRAS MUTATED KRAS WILD-TYPE
  0          181            194
  1           28             37
[1] 2 2
[1] FALSE
D312V8, binary
                cls
clus               0   1
  KRAS MUTATED   100 131
  KRAS WILD-TYPE 125 133
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED    100  131
  KRAS WILD-TYPE  125  133
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  FEMALE          100            125
  MALE            131            133
[1] 2 2
[1] FALSE
D312V9, binary
                cls
clus               0   1
  KRAS MUTATED   167  10
  KRAS WILD-TYPE 183  12
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED    167   10
  KRAS WILD-TYPE  183   12
     clus
vv    KRAS MUTATED KRAS WILD-TYPE
  NO           167            183
  YES           10             12
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  KRAS MUTATED                    146                            20
  KRAS WILD-TYPE                  169                            27
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  KRAS MUTATED                      53                              6
  KRAS WILD-TYPE                    53                              4
D312V10, multiclass
                                clus
vv                               KRAS MUTATED KRAS WILD-TYPE
  COLON ADENOCARCINOMA                    146            169
  COLON MUCINOUS ADENOCARCINOMA            20             27
  RECTAL ADENOCARCINOMA                    53             53
  RECTAL MUCINOUS ADENOCARCINOMA            6              4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  KRAS MUTATED   160   2  10  11
  KRAS WILD-TYPE 185   2  21  14
D312V11, multiclass
    clus
vv   KRAS MUTATED KRAS WILD-TYPE
  R0          160            185
  R1            2              2
  R2           10             21
  RX           11             14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D312V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KRAS MUTATED                                  0     5
  KRAS WILD-TYPE                                1     6
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  KRAS MUTATED                          12   114
  KRAS WILD-TYPE                        10   112
D312V13, multiclass
                                  clus
vv                                 KRAS MUTATED KRAS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       5              6
  BLACK OR AFRICAN AMERICAN                  12             10
  WHITE                                     114            112
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(313) Variable = GATA3 MUTATION ANALYSIS
D313V1, survival
                 sevent
clus2               0   1
  GATA3 MUTATED     9   4
  GATA3 WILD-TYPE 369  89
  GATA3 MUTATED GATA3 WILD-TYPE 
             13             458 
  GATA3 MUTATED GATA3 WILD-TYPE 
              4              89 
$`GATA3 MUTATED`
TCGA-A6-5665 TCGA-A6-6141 TCGA-AA-3492 TCGA-AA-3821 TCGA-AA-3930 TCGA-AA-A00Q 
       22.06         8.38         3.02         1.02         2.01        42.02 
TCGA-AD-6895 TCGA-AD-6901 TCGA-AY-6197 TCGA-AZ-6601 TCGA-DM-A0X9 TCGA-G4-6293 
        0.72        22.42        21.44       100.01       119.70       133.18 
TCGA-G4-6307 
       55.04 

$`GATA3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 
       22.09        32.71        27.09        22.52        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       19.66        20.28         7.04         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
       33.04         0.99        25.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       29.98        18.05        31.00        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R 
       18.05        18.05        38.04         4.01        27.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6963 
       21.37        15.52        56.55         0.79         5.79        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       33.01        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0XD TCGA-DM-A0XF 
        1.51        12.00        11.38        10.26        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       47.41        35.31        74.56        65.85        53.62        44.68 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  GATA3 MUTATED GATA3 WILD-TYPE 
           0.72            0.00 
  GATA3 MUTATED GATA3 WILD-TYPE 
         133.18          148.01 
  GATA3 MUTATED GATA3 WILD-TYPE 
         22.060          20.085 
[1] "0.7 - 133.2 (22.1)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.1"
D313V2, continuous
D313V3, binary
                 cls
clus                0   1
  GATA3 MUTATED    16   0
  GATA3 WILD-TYPE 350 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GATA3 MUTATED     16    0
  GATA3 WILD-TYPE  350  119
        clus
vv       GATA3 MUTATED GATA3 WILD-TYPE
  COLON             16             350
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GATA3 MUTATED         2        0        2         4         1         0
  GATA3 WILD-TYPE      89        1       30       134         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  GATA3 MUTATED           2          0          2          0        1         0
  GATA3 WILD-TYPE        22         11         57         42       47        18
                 vv
clus              STAGE IVB
  GATA3 MUTATED           0
  GATA3 WILD-TYPE         1
D313V4, multiclass
            clus
vv           GATA3 MUTATED GATA3 WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA              4             134
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              2              22
  STAGE IIIA             0              11
  STAGE IIIB             2              57
  STAGE IIIC             0              42
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  GATA3 MUTATED     0   2  12   2
  GATA3 WILD-TYPE  17  90 317  48
D313V5, multiclass
    clus
vv   GATA3 MUTATED GATA3 WILD-TYPE
  T1             0              17
  T2             2              90
  T3            12             317
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  GATA3 MUTATED    10   4   2
  GATA3 WILD-TYPE 277 109  85
D313V6, multiclass
    clus
vv   GATA3 MUTATED GATA3 WILD-TYPE
  N0            10             277
  N1             4             109
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D313V7, binary
                 cls
clus                0   1
  GATA3 MUTATED    10   1
  GATA3 WILD-TYPE 365  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GATA3 MUTATED     10    1
  GATA3 WILD-TYPE  365   64
   clus
vv  GATA3 MUTATED GATA3 WILD-TYPE
  0            10             365
  1             1              64
[1] 2 2
[1] FALSE
D313V8, binary
                 cls
clus                0   1
  GATA3 MUTATED     8   8
  GATA3 WILD-TYPE 217 256
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GATA3 MUTATED      8    8
  GATA3 WILD-TYPE  217  256
        clus
vv       GATA3 MUTATED GATA3 WILD-TYPE
  FEMALE             8             217
  MALE               8             256
[1] 2 2
[1] FALSE
D313V9, binary
                 cls
clus                0   1
  GATA3 MUTATED    11   0
  GATA3 WILD-TYPE 339  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GATA3 MUTATED     11    0
  GATA3 WILD-TYPE  339   22
     clus
vv    GATA3 MUTATED GATA3 WILD-TYPE
  NO             11             339
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  GATA3 MUTATED                     15                             1
  GATA3 WILD-TYPE                  300                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  GATA3 MUTATED                       0                              0
  GATA3 WILD-TYPE                   106                             10
D313V10, multiclass
                                clus
vv                               GATA3 MUTATED GATA3 WILD-TYPE
  COLON ADENOCARCINOMA                      15             300
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  GATA3 MUTATED     8   0   1   2
  GATA3 WILD-TYPE 337   4  30  23
D313V11, multiclass
    clus
vv   GATA3 MUTATED GATA3 WILD-TYPE
  R0             8             337
  R1             0               4
  R2             1              30
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D313V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GATA3 MUTATED                                  0     0
  GATA3 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  GATA3 MUTATED                           1    10
  GATA3 WILD-TYPE                        21   216
D313V13, multiclass
                                  clus
vv                                 GATA3 MUTATED GATA3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                       10             216
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(314) Variable = OVCH1 MUTATION ANALYSIS
D314V1, survival
                 sevent
clus2               0   1
  OVCH1 MUTATED    17   8
  OVCH1 WILD-TYPE 361  85
  OVCH1 MUTATED OVCH1 WILD-TYPE 
             25             446 
  OVCH1 MUTATED OVCH1 WILD-TYPE 
              8              85 
$`OVCH1 MUTATED`
TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3492 TCGA-AA-3680 TCGA-AA-3710 TCGA-AA-3977 
       20.12        19.66         3.02        11.01        26.99        25.02 
TCGA-AA-A00N TCGA-AA-A010 TCGA-AD-6901 TCGA-AU-3779 TCGA-CA-5796 TCGA-CA-6717 
        4.01        34.98        22.42        14.50         3.25        12.76 
TCGA-CM-5864 TCGA-CM-6164 TCGA-CM-6171 TCGA-D5-6923 TCGA-DM-A1DB TCGA-DM-A1HB 
       15.02        29.03        14.04        12.43        44.32       135.65 
TCGA-F4-6570 TCGA-G4-6303 TCGA-G4-6588 TCGA-AG-3894 TCGA-AG-A002 TCGA-DY-A0XA 
        6.18        65.85        26.17        14.01        20.98       126.44 
TCGA-DY-A1DG 
       51.48 

$`OVCH1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       23.87        20.28         7.04         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6964 
       56.55         0.79         0.72         5.79        27.42        10.88 
TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
        0.20        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.06         3.29         0.07        12.20        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6165 TCGA-CM-6166 
       17.03        15.02        12.00         2.96        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 
       14.99        12.99        13.02        15.02        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
        4.41        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
      140.38         7.50       131.51       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       31.96        35.74        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
      133.18        74.56        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       35.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1H8 
        5.03         5.29        41.36        57.24        24.13        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  OVCH1 MUTATED OVCH1 WILD-TYPE 
           3.02            0.00 
  OVCH1 MUTATED OVCH1 WILD-TYPE 
         135.65          148.01 
  OVCH1 MUTATED OVCH1 WILD-TYPE 
         20.120          20.235 
[1] "3.0 - 135.7 (20.1)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.5"
D314V2, continuous
D314V3, binary
                 cls
clus                0   1
  OVCH1 MUTATED    22   4
  OVCH1 WILD-TYPE 344 115
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OVCH1 MUTATED     22    4
  OVCH1 WILD-TYPE  344  115
        clus
vv       OVCH1 MUTATED OVCH1 WILD-TYPE
  COLON             22             344
  RECTUM             4             115
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  OVCH1 MUTATED         4        0        1        12         2         0
  OVCH1 WILD-TYPE      87        1       31       126         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  OVCH1 MUTATED           0          0          1          1        2         1
  OVCH1 WILD-TYPE        24         11         58         41       46        17
                 vv
clus              STAGE IVB
  OVCH1 MUTATED           0
  OVCH1 WILD-TYPE         1
D314V4, multiclass
            clus
vv           OVCH1 MUTATED OVCH1 WILD-TYPE
  STAGE I                4              87
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA             12             126
  STAGE IIB              2               8
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             1              41
  STAGE IV               2              46
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  OVCH1 MUTATED     0   5  17   4
  OVCH1 WILD-TYPE  17  87 312  46
D314V5, multiclass
    clus
vv   OVCH1 MUTATED OVCH1 WILD-TYPE
  T1             0              17
  T2             5              87
  T3            17             312
  T4             4              46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  OVCH1 MUTATED    21   4   1
  OVCH1 WILD-TYPE 266 109  86
D314V6, multiclass
    clus
vv   OVCH1 MUTATED OVCH1 WILD-TYPE
  N0            21             266
  N1             4             109
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D314V7, binary
                 cls
clus                0   1
  OVCH1 MUTATED    19   3
  OVCH1 WILD-TYPE 356  62
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OVCH1 MUTATED     19    3
  OVCH1 WILD-TYPE  356   62
   clus
vv  OVCH1 MUTATED OVCH1 WILD-TYPE
  0            19             356
  1             3              62
[1] 2 2
[1] FALSE
D314V8, binary
                 cls
clus                0   1
  OVCH1 MUTATED    13  13
  OVCH1 WILD-TYPE 212 251
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OVCH1 MUTATED     13   13
  OVCH1 WILD-TYPE  212  251
        clus
vv       OVCH1 MUTATED OVCH1 WILD-TYPE
  FEMALE            13             212
  MALE              13             251
[1] 2 2
[1] FALSE
D314V9, binary
                 cls
clus                0   1
  OVCH1 MUTATED    19   1
  OVCH1 WILD-TYPE 331  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OVCH1 MUTATED     19    1
  OVCH1 WILD-TYPE  331   21
     clus
vv    OVCH1 MUTATED OVCH1 WILD-TYPE
  NO             19             331
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  OVCH1 MUTATED                     16                             5
  OVCH1 WILD-TYPE                  299                            42
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  OVCH1 MUTATED                       4                              0
  OVCH1 WILD-TYPE                   102                             10
D314V10, multiclass
                                clus
vv                               OVCH1 MUTATED OVCH1 WILD-TYPE
  COLON ADENOCARCINOMA                      16             299
  COLON MUCINOUS ADENOCARCINOMA              5              42
  RECTAL ADENOCARCINOMA                      4             102
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  OVCH1 MUTATED    17   0   1   1
  OVCH1 WILD-TYPE 328   4  30  24
D314V11, multiclass
    clus
vv   OVCH1 MUTATED OVCH1 WILD-TYPE
  R0            17             328
  R1             0               4
  R2             1              30
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D314V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OVCH1 MUTATED                                  0     2
  OVCH1 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  OVCH1 MUTATED                           0    15
  OVCH1 WILD-TYPE                        22   211
D314V13, multiclass
                                  clus
vv                                 OVCH1 MUTATED OVCH1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               9
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                       15             211
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(315) Variable = MUC17 MUTATION ANALYSIS
D315V1, survival
                 sevent
clus2               0   1
  MUC17 MUTATED    46   7
  MUC17 WILD-TYPE 332  86
  MUC17 MUTATED MUC17 WILD-TYPE 
             53             418 
  MUC17 MUTATED MUC17 WILD-TYPE 
              7              86 
$`MUC17 MUTATED`
TCGA-A6-2672 TCGA-A6-3807 TCGA-A6-5661 TCGA-A6-5665 TCGA-A6-6649 TCGA-A6-6781 
       46.65        34.65        33.53        22.06        24.16        19.66 
TCGA-A6-6782 TCGA-AA-3510 TCGA-AA-3516 TCGA-AA-3660 TCGA-AA-3696 TCGA-AA-3697 
       20.28        63.98        13.02        78.08         5.03        85.05 
TCGA-AA-3713 TCGA-AA-3815 TCGA-AA-3864 TCGA-AA-3950 TCGA-AA-3977 TCGA-AA-3980 
       19.04        33.04        53.00        24.00        25.02        27.02 
TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01I TCGA-AA-A029 TCGA-AD-6889 TCGA-AD-6895 
        4.01        34.98        31.00        51.98        56.55         0.72 
TCGA-AD-6899 TCGA-AZ-4315 TCGA-AZ-4681 TCGA-AZ-5407 TCGA-AZ-6600 TCGA-CA-6716 
        5.79        58.39       106.75        88.21        12.10        12.20 
TCGA-CK-5916 TCGA-CM-6161 TCGA-CM-6674 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6922 
       21.14        15.02        12.95        17.13        16.14         4.41 
TCGA-D5-6928 TCGA-D5-6929 TCGA-DM-A28H TCGA-DM-A28K TCGA-G4-6321 TCGA-G4-6586 
       11.64         4.80       117.07        98.24        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6626 TCGA-AG-3742 TCGA-AG-3894 TCGA-AG-3902 TCGA-AG-A002 
       26.17        46.75         0.99        14.01        32.02        20.98 
TCGA-AG-A01W TCGA-CI-6624 TCGA-EF-5830 TCGA-EI-6507 TCGA-EI-6510 
       70.03         4.73         0.49        19.96        18.28 

$`MUC17 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5657 
       33.34        32.75        36.53        14.53        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 
       30.44        29.19        23.61        22.09        32.71        27.09 
TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 
       22.52         8.38        25.08        25.18        21.76        24.69 
TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       24.39        23.87        20.12         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
       35.01         6.97         1.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3710 TCGA-AA-3715 
        5.98        37.05        19.00        36.00        26.99        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       10.06        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 
        0.99        31.07        31.07        30.05        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        33.01        26.01         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       26.01        24.00        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A02F TCGA-AA-A02H 
       35.01        26.01        37.02        39.06        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6901 
       40.96         0.07        21.37        15.52         0.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        33.01        21.44        17.82         1.41         5.13 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6603 
       22.36        62.79        49.41         6.77       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
        9.99        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       17.03        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6923 TCGA-D5-6924 
       12.49        15.58         1.48         3.68        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
        9.04         9.44         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       60.79         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6625 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       36.00        13.78        91.79        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3878 TCGA-AG-3881 
        7.99         0.99        37.02        32.98         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
       35.01         1.02        48.03        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CL-5917 
        0.69         0.72         6.05        33.17         6.97        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EI-6506 
       41.36        57.24        24.13        51.48        32.61        20.55 
TCGA-EI-6508 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       20.91         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  MUC17 MUTATED MUC17 WILD-TYPE 
           0.49            0.00 
  MUC17 MUTATED MUC17 WILD-TYPE 
         117.07          148.01 
  MUC17 MUTATED MUC17 WILD-TYPE 
         22.090          20.005 
[1] "0.5 - 117.1 (22.1)" "0.0 - 148.0 (20.0)"
[1] "hr=" "2"  
D315V2, continuous
D315V3, binary
                 cls
clus                0   1
  MUC17 MUTATED    46   9
  MUC17 WILD-TYPE 320 110
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MUC17 MUTATED     46    9
  MUC17 WILD-TYPE  320  110
        clus
vv       MUC17 MUTATED MUC17 WILD-TYPE
  COLON             46             320
  RECTUM             9             110
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MUC17 MUTATED         9        0        5        18         5         0
  MUC17 WILD-TYPE      82        1       27       120         5         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MUC17 MUTATED           3          1          3          4        4         1
  MUC17 WILD-TYPE        21         10         56         38       44        17
                 vv
clus              STAGE IVB
  MUC17 MUTATED           0
  MUC17 WILD-TYPE         1
D315V4, multiclass
            clus
vv           MUC17 MUTATED MUC17 WILD-TYPE
  STAGE I                9              82
  STAGE IA               0               1
  STAGE II               5              27
  STAGE IIA             18             120
  STAGE IIB              5               5
  STAGE IIC              0               1
  STAGE III              3              21
  STAGE IIIA             1              10
  STAGE IIIB             3              56
  STAGE IIIC             4              38
  STAGE IV               4              44
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  MUC17 MUTATED     3   9  35   8
  MUC17 WILD-TYPE  14  83 294  42
D315V5, multiclass
    clus
vv   MUC17 MUTATED MUC17 WILD-TYPE
  T1             3              14
  T2             9              83
  T3            35             294
  T4             8              42
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  MUC17 MUTATED    41   9   5
  MUC17 WILD-TYPE 246 104  82
D315V6, multiclass
    clus
vv   MUC17 MUTATED MUC17 WILD-TYPE
  N0            41             246
  N1             9             104
  N2             5              82
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D315V7, binary
                 cls
clus                0   1
  MUC17 MUTATED    43   4
  MUC17 WILD-TYPE 332  61
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MUC17 MUTATED     43    4
  MUC17 WILD-TYPE  332   61
   clus
vv  MUC17 MUTATED MUC17 WILD-TYPE
  0            43             332
  1             4              61
[1] 2 2
[1] FALSE
D315V8, binary
                 cls
clus                0   1
  MUC17 MUTATED    26  29
  MUC17 WILD-TYPE 199 235
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MUC17 MUTATED     26   29
  MUC17 WILD-TYPE  199  235
        clus
vv       MUC17 MUTATED MUC17 WILD-TYPE
  FEMALE            26             199
  MALE              29             235
[1] 2 2
[1] FALSE
D315V9, binary
                 cls
clus                0   1
  MUC17 MUTATED    39   2
  MUC17 WILD-TYPE 311  20
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MUC17 MUTATED     39    2
  MUC17 WILD-TYPE  311   20
     clus
vv    MUC17 MUTATED MUC17 WILD-TYPE
  NO             39             311
  YES             2              20
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MUC17 MUTATED                     38                             8
  MUC17 WILD-TYPE                  277                            39
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MUC17 MUTATED                       9                              0
  MUC17 WILD-TYPE                    97                             10
D315V10, multiclass
                                clus
vv                               MUC17 MUTATED MUC17 WILD-TYPE
  COLON ADENOCARCINOMA                      38             277
  COLON MUCINOUS ADENOCARCINOMA              8              39
  RECTAL ADENOCARCINOMA                      9              97
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  MUC17 MUTATED    37   0   2   3
  MUC17 WILD-TYPE 308   4  29  22
D315V11, multiclass
    clus
vv   MUC17 MUTATED MUC17 WILD-TYPE
  R0            37             308
  R1             0               4
  R2             2              29
  RX             3              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D315V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MUC17 MUTATED                                  0     2
  MUC17 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  MUC17 MUTATED                           2    30
  MUC17 WILD-TYPE                        20   196
D315V13, multiclass
                                  clus
vv                                 MUC17 MUTATED MUC17 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               9
  BLACK OR AFRICAN AMERICAN                    2              20
  WHITE                                       30             196
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(316) Variable = GTF2B MUTATION ANALYSIS
D316V1, survival
                 sevent
clus2               0   1
  GTF2B MUTATED    10   1
  GTF2B WILD-TYPE 368  92
  GTF2B MUTATED GTF2B WILD-TYPE 
             11             460 
  GTF2B MUTATED GTF2B WILD-TYPE 
              1              92 
$`GTF2B MUTATED`
TCGA-AA-3510 TCGA-AA-3660 TCGA-AA-3713 TCGA-AA-3877 TCGA-AZ-4315 TCGA-AZ-4681 
       63.98        78.08        19.04        31.00        58.39       106.75 
TCGA-CM-5344 TCGA-DM-A1HB TCGA-G4-6323 TCGA-G4-6586 TCGA-DY-A1DF 
       22.03       135.65        13.78        35.80        24.13 

$`GTF2B WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 
       19.99        13.94        19.99        61.02         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       27.02        29.98        18.05         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
       17.82         1.41         5.13        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5348 
       20.02        37.02        25.02        13.02        29.06        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      131.51       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6588 TCGA-G4-6625 
       63.62        61.91        36.00        22.09        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  GTF2B MUTATED GTF2B WILD-TYPE 
          13.78            0.00 
  GTF2B MUTATED GTF2B WILD-TYPE 
         135.65          148.01 
  GTF2B MUTATED GTF2B WILD-TYPE 
          35.80           20.02 
[1] "13.8 - 135.7 (35.8)" "0.0 - 148.0 (20.0)" 
[1] "hr=" "4.3"
D316V2, continuous
D316V3, binary
                 cls
clus                0   1
  GTF2B MUTATED    11   1
  GTF2B WILD-TYPE 355 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GTF2B MUTATED     11    1
  GTF2B WILD-TYPE  355  118
        clus
vv       GTF2B MUTATED GTF2B WILD-TYPE
  COLON             11             355
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GTF2B MUTATED         1        1        2         3         1         0
  GTF2B WILD-TYPE      90        0       30       135         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  GTF2B MUTATED           0          0          2          1        1         0
  GTF2B WILD-TYPE        24         11         57         41       47        18
                 vv
clus              STAGE IVB
  GTF2B MUTATED           0
  GTF2B WILD-TYPE         1
D316V4, multiclass
            clus
vv           GTF2B MUTATED GTF2B WILD-TYPE
  STAGE I                1              90
  STAGE IA               1               0
  STAGE II               2              30
  STAGE IIA              3             135
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             2              57
  STAGE IIIC             1              41
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  GTF2B MUTATED     1   0   9   1
  GTF2B WILD-TYPE  16  92 320  49
D316V5, multiclass
    clus
vv   GTF2B MUTATED GTF2B WILD-TYPE
  T1             1              16
  T2             0              92
  T3             9             320
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  GTF2B MUTATED     9   2   1
  GTF2B WILD-TYPE 278 111  86
D316V6, multiclass
    clus
vv   GTF2B MUTATED GTF2B WILD-TYPE
  N0             9             278
  N1             2             111
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D316V7, binary
                 cls
clus                0   1
  GTF2B MUTATED     9   1
  GTF2B WILD-TYPE 366  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GTF2B MUTATED      9    1
  GTF2B WILD-TYPE  366   64
   clus
vv  GTF2B MUTATED GTF2B WILD-TYPE
  0             9             366
  1             1              64
[1] 2 2
[1] FALSE
D316V8, binary
                 cls
clus                0   1
  GTF2B MUTATED     7   5
  GTF2B WILD-TYPE 218 259
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GTF2B MUTATED      7    5
  GTF2B WILD-TYPE  218  259
        clus
vv       GTF2B MUTATED GTF2B WILD-TYPE
  FEMALE             7             218
  MALE               5             259
[1] 2 2
[1] FALSE
D316V9, binary
                 cls
clus                0   1
  GTF2B MUTATED     8   1
  GTF2B WILD-TYPE 342  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GTF2B MUTATED      8    1
  GTF2B WILD-TYPE  342   21
     clus
vv    GTF2B MUTATED GTF2B WILD-TYPE
  NO              8             342
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  GTF2B MUTATED                      9                             1
  GTF2B WILD-TYPE                  306                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  GTF2B MUTATED                       1                              0
  GTF2B WILD-TYPE                   105                             10
D316V10, multiclass
                                clus
vv                               GTF2B MUTATED GTF2B WILD-TYPE
  COLON ADENOCARCINOMA                       9             306
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  GTF2B MUTATED     8   0   1   1
  GTF2B WILD-TYPE 337   4  30  24
D316V11, multiclass
    clus
vv   GTF2B MUTATED GTF2B WILD-TYPE
  R0             8             337
  R1             0               4
  R2             1              30
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D316V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GTF2B MUTATED                                  0     0
  GTF2B WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  GTF2B MUTATED                           1     7
  GTF2B WILD-TYPE                        21   219
D316V13, multiclass
                                  clus
vv                                 GTF2B MUTATED GTF2B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        7             219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(317) Variable = RUNX1 MUTATION ANALYSIS
D317V1, survival
                 sevent
clus2               0   1
  RUNX1 MUTATED    33   7
  RUNX1 WILD-TYPE 345  86
  RUNX1 MUTATED RUNX1 WILD-TYPE 
             40             431 
  RUNX1 MUTATED RUNX1 WILD-TYPE 
              7              86 
$`RUNX1 MUTATED`
TCGA-A6-4105 TCGA-A6-5657 TCGA-A6-6781 TCGA-AA-3672 TCGA-AA-3697 TCGA-AA-3713 
       14.53        31.63        19.66         0.92        85.05        19.04 
TCGA-AA-3818 TCGA-AA-3861 TCGA-AA-3950 TCGA-AA-A01T TCGA-AD-6889 TCGA-AY-5543 
        0.99        30.05        24.00        33.04        56.55        33.01 
TCGA-AZ-4315 TCGA-AZ-4681 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6603 TCGA-CK-4950 
       58.39       106.75        49.41         6.77        29.56        85.45 
TCGA-CK-4952 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-6168 TCGA-CM-6171 
       15.62        30.08        32.02        15.02        12.99        14.04 
TCGA-D5-6533 TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6569 
        1.32        44.32       135.65       117.07        98.24        35.74 
TCGA-G4-6293 TCGA-G4-6304 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6626 TCGA-G4-6628 
      133.18        53.62        36.00        13.78        46.75        79.69 
TCGA-AH-6549 TCGA-CI-6619 TCGA-EF-5830 TCGA-G5-6235 
       17.49         6.05         0.49        55.76 

$`RUNX1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 
       16.57        34.65        33.34        32.75        36.53        32.91 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       30.44        29.19        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
        2.01        14.01        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 
        5.98        37.05        19.00        36.00         5.03        26.99 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3819 TCGA-AA-3821 
       19.04        10.06        35.05        33.04        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 
       32.05         0.99        31.07        31.07        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 
       12.99        24.00        33.01        26.01         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V 
       31.00        38.07         1.02        35.01         1.02        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 
       40.96         0.07        21.37        15.52         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
       27.09        16.31         0.95        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6600 TCGA-AZ-6601 
        5.13        22.36        62.79        88.21        12.10       100.01 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
       14.30        17.56       148.01        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6169 
        2.96        29.03        16.04        21.99        14.99        13.02 
TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       15.02        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 
       56.09        55.92        20.19        18.25        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HA 
       49.91        13.32        12.59       140.38         7.50       131.51 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
        8.61        31.96         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       35.31        74.56        65.85        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       63.62        61.91        22.09        35.80        26.17        91.79 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.69         0.72        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EI-6506 
       41.36        57.24        24.13        51.48        32.61        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        26.43 

  RUNX1 MUTATED RUNX1 WILD-TYPE 
           0.49            0.00 
  RUNX1 MUTATED RUNX1 WILD-TYPE 
         135.65          148.01 
  RUNX1 MUTATED RUNX1 WILD-TYPE 
         31.825          19.990 
[1] "0.5 - 135.7 (31.8)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.8"
D317V2, continuous
D317V3, binary
                 cls
clus                0   1
  RUNX1 MUTATED    37   4
  RUNX1 WILD-TYPE 329 115
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RUNX1 MUTATED     37    4
  RUNX1 WILD-TYPE  329  115
        clus
vv       RUNX1 MUTATED RUNX1 WILD-TYPE
  COLON             37             329
  RECTUM             4             115
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RUNX1 MUTATED         4        1        1        14         2         0
  RUNX1 WILD-TYPE      87        0       31       124         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RUNX1 MUTATED           5          0          5          4        2         1
  RUNX1 WILD-TYPE        19         11         54         38       46        17
                 vv
clus              STAGE IVB
  RUNX1 MUTATED           0
  RUNX1 WILD-TYPE         1
D317V4, multiclass
            clus
vv           RUNX1 MUTATED RUNX1 WILD-TYPE
  STAGE I                4              87
  STAGE IA               1               0
  STAGE II               1              31
  STAGE IIA             14             124
  STAGE IIB              2               8
  STAGE IIC              0               1
  STAGE III              5              19
  STAGE IIIA             0              11
  STAGE IIIB             5              54
  STAGE IIIC             4              38
  STAGE IV               2              46
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  RUNX1 MUTATED     0   5  30   5
  RUNX1 WILD-TYPE  17  87 299  45
D317V5, multiclass
    clus
vv   RUNX1 MUTATED RUNX1 WILD-TYPE
  T1             0              17
  T2             5              87
  T3            30             299
  T4             5              45
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  RUNX1 MUTATED    25  11   4
  RUNX1 WILD-TYPE 262 102  83
D317V6, multiclass
    clus
vv   RUNX1 MUTATED RUNX1 WILD-TYPE
  N0            25             262
  N1            11             102
  N2             4              83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D317V7, binary
                 cls
clus                0   1
  RUNX1 MUTATED    30   3
  RUNX1 WILD-TYPE 345  62
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RUNX1 MUTATED     30    3
  RUNX1 WILD-TYPE  345   62
   clus
vv  RUNX1 MUTATED RUNX1 WILD-TYPE
  0            30             345
  1             3              62
[1] 2 2
[1] FALSE
D317V8, binary
                 cls
clus                0   1
  RUNX1 MUTATED    18  23
  RUNX1 WILD-TYPE 207 241
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RUNX1 MUTATED     18   23
  RUNX1 WILD-TYPE  207  241
        clus
vv       RUNX1 MUTATED RUNX1 WILD-TYPE
  FEMALE            18             207
  MALE              23             241
[1] 2 2
[1] FALSE
D317V9, binary
                 cls
clus                0   1
  RUNX1 MUTATED    29   1
  RUNX1 WILD-TYPE 321  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RUNX1 MUTATED     29    1
  RUNX1 WILD-TYPE  321   21
     clus
vv    RUNX1 MUTATED RUNX1 WILD-TYPE
  NO             29             321
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  RUNX1 MUTATED                     32                             4
  RUNX1 WILD-TYPE                  283                            43
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  RUNX1 MUTATED                       4                              0
  RUNX1 WILD-TYPE                   102                             10
D317V10, multiclass
                                clus
vv                               RUNX1 MUTATED RUNX1 WILD-TYPE
  COLON ADENOCARCINOMA                      32             283
  COLON MUCINOUS ADENOCARCINOMA              4              43
  RECTAL ADENOCARCINOMA                      4             102
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  RUNX1 MUTATED    26   2   1   2
  RUNX1 WILD-TYPE 319   2  30  23
D317V11, multiclass
    clus
vv   RUNX1 MUTATED RUNX1 WILD-TYPE
  R0            26             319
  R1             2               2
  R2             1              30
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D317V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RUNX1 MUTATED                                  0     1
  RUNX1 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  RUNX1 MUTATED                           5    27
  RUNX1 WILD-TYPE                        17   199
D317V13, multiclass
                                  clus
vv                                 RUNX1 MUTATED RUNX1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    5              17
  WHITE                                       27             199
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(318) Variable = C9ORF84 MUTATION ANALYSIS
D318V1, survival
                   sevent
clus2                 0   1
  C9ORF84 MUTATED    15   5
  C9ORF84 WILD-TYPE 363  88
  C9ORF84 MUTATED C9ORF84 WILD-TYPE 
               20               451 
  C9ORF84 MUTATED C9ORF84 WILD-TYPE 
                5                88 
$`C9ORF84 MUTATED`
TCGA-A6-6781 TCGA-AA-3489 TCGA-AA-3715 TCGA-AA-3845 TCGA-AA-A00J TCGA-AA-A010 
       19.66         7.04        19.04         0.00        18.05        34.98 
TCGA-AD-5900 TCGA-AD-6889 TCGA-CA-5796 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-6751 
        0.07        56.55         3.25        12.76        10.06       124.27 
TCGA-CM-4746 TCGA-D5-6923 TCGA-F4-6809 TCGA-F4-6856 TCGA-G4-6304 TCGA-G4-6307 
       37.02        12.43        13.25        35.31        53.62        55.04 
TCGA-G4-6310 TCGA-AG-A002 
       63.62        20.98 

$`C9ORF84 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       23.87        20.12        20.28         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       38.99        37.02        14.93        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 
        0.92        41.00        39.98        18.05        40.96        21.37 
TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       15.52         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        1.61        12.69         3.06         3.29         0.07        12.20 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CM-4743 
       51.32         9.99        21.14        82.95         1.91        23.05 
TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       20.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        1.48         3.68         4.41        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
       33.67         0.53        47.41       133.18        74.56        65.85 
TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       44.68        85.48        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  C9ORF84 MUTATED C9ORF84 WILD-TYPE 
                0                 0 
  C9ORF84 MUTATED C9ORF84 WILD-TYPE 
           124.27            148.01 
  C9ORF84 MUTATED C9ORF84 WILD-TYPE 
            19.35             20.28 
[1] "0.0 - 124.3 (19.4)" "0.0 - 148.0 (20.3)"
[1] "hr=" "1.1"
D318V2, continuous
D318V3, binary
                   cls
clus                  0   1
  C9ORF84 MUTATED    20   1
  C9ORF84 WILD-TYPE 346 118
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C9ORF84 MUTATED     20    1
  C9ORF84 WILD-TYPE  346  118
        clus
vv       C9ORF84 MUTATED C9ORF84 WILD-TYPE
  COLON               20               346
  RECTUM               1               118
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  C9ORF84 MUTATED         6        0        2         6         2         0
  C9ORF84 WILD-TYPE      85        1       30       132         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C9ORF84 MUTATED           0          0          3          1        0
  C9ORF84 WILD-TYPE        24         11         56         41       48
                   vv
clus                STAGE IVA STAGE IVB
  C9ORF84 MUTATED           1         0
  C9ORF84 WILD-TYPE        17         1
D318V4, multiclass
            clus
vv           C9ORF84 MUTATED C9ORF84 WILD-TYPE
  STAGE I                  6                85
  STAGE IA                 0                 1
  STAGE II                 2                30
  STAGE IIA                6               132
  STAGE IIB                2                 8
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               0                11
  STAGE IIIB               3                56
  STAGE IIIC               1                41
  STAGE IV                 0                48
  STAGE IVA                1                17
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  C9ORF84 MUTATED     0   6  11   4
  C9ORF84 WILD-TYPE  17  86 318  46
D318V5, multiclass
    clus
vv   C9ORF84 MUTATED C9ORF84 WILD-TYPE
  T1               0                17
  T2               6                86
  T3              11               318
  T4               4                46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  C9ORF84 MUTATED    16   5   0
  C9ORF84 WILD-TYPE 271 108  87
D318V6, multiclass
    clus
vv   C9ORF84 MUTATED C9ORF84 WILD-TYPE
  N0              16               271
  N1               5               108
  N2               0                87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D318V7, binary
                   cls
clus                  0   1
  C9ORF84 MUTATED    17   1
  C9ORF84 WILD-TYPE 358  64
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C9ORF84 MUTATED     17    1
  C9ORF84 WILD-TYPE  358   64
   clus
vv  C9ORF84 MUTATED C9ORF84 WILD-TYPE
  0              17               358
  1               1                64
[1] 2 2
[1] FALSE
D318V8, binary
                   cls
clus                  0   1
  C9ORF84 MUTATED     8  13
  C9ORF84 WILD-TYPE 217 251
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C9ORF84 MUTATED      8   13
  C9ORF84 WILD-TYPE  217  251
        clus
vv       C9ORF84 MUTATED C9ORF84 WILD-TYPE
  FEMALE               8               217
  MALE                13               251
[1] 2 2
[1] FALSE
D318V9, binary
                   cls
clus                  0   1
  C9ORF84 MUTATED    16   1
  C9ORF84 WILD-TYPE 334  21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C9ORF84 MUTATED     16    1
  C9ORF84 WILD-TYPE  334   21
     clus
vv    C9ORF84 MUTATED C9ORF84 WILD-TYPE
  NO               16               334
  YES               1                21
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  C9ORF84 MUTATED                     13                             7
  C9ORF84 WILD-TYPE                  302                            40
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  C9ORF84 MUTATED                       1                              0
  C9ORF84 WILD-TYPE                   105                             10
D318V10, multiclass
                                clus
vv                               C9ORF84 MUTATED C9ORF84 WILD-TYPE
  COLON ADENOCARCINOMA                        13               302
  COLON MUCINOUS ADENOCARCINOMA                7                40
  RECTAL ADENOCARCINOMA                        1               105
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  C9ORF84 MUTATED    17   0   0   3
  C9ORF84 WILD-TYPE 328   4  31  22
D318V11, multiclass
    clus
vv   C9ORF84 MUTATED C9ORF84 WILD-TYPE
  R0              17               328
  R1               0                 4
  R2               0                31
  RX               3                22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D318V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C9ORF84 MUTATED                                  0     4
  C9ORF84 WILD-TYPE                                1     7
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  C9ORF84 MUTATED                           1     9
  C9ORF84 WILD-TYPE                        21   217
D318V13, multiclass
                                  clus
vv                                 C9ORF84 MUTATED C9ORF84 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          4                 7
  BLACK OR AFRICAN AMERICAN                      1                21
  WHITE                                          9               217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(319) Variable = NR4A2 MUTATION ANALYSIS
D319V1, survival
                 sevent
clus2               0   1
  NR4A2 MUTATED    11   2
  NR4A2 WILD-TYPE 367  91
  NR4A2 MUTATED NR4A2 WILD-TYPE 
             13             458 
  NR4A2 MUTATED NR4A2 WILD-TYPE 
              2              91 
$`NR4A2 MUTATED`
TCGA-A6-2676 TCGA-A6-6781 TCGA-AA-3713 TCGA-AA-3821 TCGA-AA-3966 TCGA-AA-A01Q 
       42.90        19.66        19.04         1.02         2.01         1.02 
TCGA-AD-6889 TCGA-AZ-4315 TCGA-CM-5861 TCGA-D5-6533 TCGA-AG-A002 TCGA-AG-A00Y 
       56.55        58.39        15.02         1.32        20.98        23.01 
TCGA-DY-A1DD 
       57.24 

$`NR4A2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
       33.04         0.99        25.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       21.37        15.52         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        33.01        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       32.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       18.25        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       25.97        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
        5.29       126.44        41.36        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  NR4A2 MUTATED NR4A2 WILD-TYPE 
           1.02            0.00 
  NR4A2 MUTATED NR4A2 WILD-TYPE 
          58.39          148.01 
  NR4A2 MUTATED NR4A2 WILD-TYPE 
         19.660          20.235 
[1] "1.0 - 58.4 (19.7)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.3"
D319V2, continuous
D319V3, binary
                 cls
clus                0   1
  NR4A2 MUTATED    10   3
  NR4A2 WILD-TYPE 356 116
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NR4A2 MUTATED     10    3
  NR4A2 WILD-TYPE  356  116
        clus
vv       NR4A2 MUTATED NR4A2 WILD-TYPE
  COLON             10             356
  RECTUM             3             116
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NR4A2 MUTATED         2        0        1         5         1         0
  NR4A2 WILD-TYPE      89        1       31       133         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NR4A2 MUTATED           0          0          2          1        1         0
  NR4A2 WILD-TYPE        24         11         57         41       47        18
                 vv
clus              STAGE IVB
  NR4A2 MUTATED           0
  NR4A2 WILD-TYPE         1
D319V4, multiclass
            clus
vv           NR4A2 MUTATED NR4A2 WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              5             133
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             2              57
  STAGE IIIC             1              41
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  NR4A2 MUTATED     0   2   8   3
  NR4A2 WILD-TYPE  17  90 321  47
D319V5, multiclass
    clus
vv   NR4A2 MUTATED NR4A2 WILD-TYPE
  T1             0              17
  T2             2              90
  T3             8             321
  T4             3              47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  NR4A2 MUTATED    11   2   0
  NR4A2 WILD-TYPE 276 111  87
D319V6, multiclass
    clus
vv   NR4A2 MUTATED NR4A2 WILD-TYPE
  N0            11             276
  N1             2             111
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D319V7, binary
                 cls
clus                0   1
  NR4A2 MUTATED    11   1
  NR4A2 WILD-TYPE 364  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NR4A2 MUTATED     11    1
  NR4A2 WILD-TYPE  364   64
   clus
vv  NR4A2 MUTATED NR4A2 WILD-TYPE
  0            11             364
  1             1              64
[1] 2 2
[1] FALSE
D319V8, binary
                 cls
clus                0   1
  NR4A2 MUTATED     7   6
  NR4A2 WILD-TYPE 218 258
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NR4A2 MUTATED      7    6
  NR4A2 WILD-TYPE  218  258
        clus
vv       NR4A2 MUTATED NR4A2 WILD-TYPE
  FEMALE             7             218
  MALE               6             258
[1] 2 2
[1] FALSE
D319V9, binary
                 cls
clus                0   1
  NR4A2 MUTATED     7   1
  NR4A2 WILD-TYPE 343  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NR4A2 MUTATED      7    1
  NR4A2 WILD-TYPE  343   21
     clus
vv    NR4A2 MUTATED NR4A2 WILD-TYPE
  NO              7             343
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  NR4A2 MUTATED                      7                             3
  NR4A2 WILD-TYPE                  308                            44
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  NR4A2 MUTATED                       3                              0
  NR4A2 WILD-TYPE                   103                             10
D319V10, multiclass
                                clus
vv                               NR4A2 MUTATED NR4A2 WILD-TYPE
  COLON ADENOCARCINOMA                       7             308
  COLON MUCINOUS ADENOCARCINOMA              3              44
  RECTAL ADENOCARCINOMA                      3             103
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  NR4A2 MUTATED     9   0   1   0
  NR4A2 WILD-TYPE 336   4  30  25
D319V11, multiclass
    clus
vv   NR4A2 MUTATED NR4A2 WILD-TYPE
  R0             9             336
  R1             0               4
  R2             1              30
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D319V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NR4A2 MUTATED                                  0     1
  NR4A2 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  NR4A2 MUTATED                           0     6
  NR4A2 WILD-TYPE                        22   220
D319V13, multiclass
                                  clus
vv                                 NR4A2 MUTATED NR4A2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        6             220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(320) Variable = LATS1 MUTATION ANALYSIS
D320V1, survival
                 sevent
clus2               0   1
  LATS1 MUTATED    11   9
  LATS1 WILD-TYPE 367  84
  LATS1 MUTATED LATS1 WILD-TYPE 
             20             451 
  LATS1 MUTATED LATS1 WILD-TYPE 
              9              84 
$`LATS1 MUTATED`
TCGA-A6-2676 TCGA-AA-3492 TCGA-AA-3516 TCGA-AA-3681 TCGA-AA-A00N TCGA-AA-A02H 
       42.90         3.02        13.02         5.98         4.01         2.01 
TCGA-AD-6889 TCGA-AD-6964 TCGA-AZ-6598 TCGA-CK-4950 TCGA-CK-5916 TCGA-CM-6168 
       56.55        10.88        49.41        85.45        21.14        12.99 
TCGA-D5-6536 TCGA-DM-A1HB TCGA-F4-6570 TCGA-G4-6321 TCGA-G4-6588 TCGA-AG-A002 
       17.85       135.65         6.18        22.09        26.17        20.98 
TCGA-CI-6624 TCGA-CL-5918 
        4.73         7.17 

$`LATS1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 
       20.12        19.66        20.28         7.04         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
       63.98         6.97         1.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
       11.01        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02J TCGA-AA-A02K 
       37.02        39.06        51.98        39.98         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       21.37        15.52         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 
      106.75        22.36        62.79        88.21         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 
       12.76        10.06        14.30        17.56       148.01        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       49.08        51.32         9.99        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6169 TCGA-CM-6170 
       29.03        16.04        21.99        14.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       15.12         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      131.51       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 
       61.91        36.00        13.78        35.80        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CL-5917 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
       78.12        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  LATS1 MUTATED LATS1 WILD-TYPE 
           2.01            0.00 
  LATS1 MUTATED LATS1 WILD-TYPE 
         135.65          148.01 
  LATS1 MUTATED LATS1 WILD-TYPE 
         15.435          20.280 
[1] "2.0 - 135.7 (15.4)" "0.0 - 148.0 (20.3)"
[1] "hr=" "2.4"
D320V2, continuous
D320V3, binary
                 cls
clus                0   1
  LATS1 MUTATED    18   3
  LATS1 WILD-TYPE 348 116
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LATS1 MUTATED     18    3
  LATS1 WILD-TYPE  348  116
        clus
vv       LATS1 MUTATED LATS1 WILD-TYPE
  COLON             18             348
  RECTUM             3             116
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  LATS1 MUTATED         3        0        2         7         2         0
  LATS1 WILD-TYPE      88        1       30       131         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  LATS1 MUTATED           3          0          2          0        1         0
  LATS1 WILD-TYPE        21         11         57         42       47        18
                 vv
clus              STAGE IVB
  LATS1 MUTATED           0
  LATS1 WILD-TYPE         1
D320V4, multiclass
            clus
vv           LATS1 MUTATED LATS1 WILD-TYPE
  STAGE I                3              88
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA              7             131
  STAGE IIB              2               8
  STAGE IIC              0               1
  STAGE III              3              21
  STAGE IIIA             0              11
  STAGE IIIB             2              57
  STAGE IIIC             0              42
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  LATS1 MUTATED     1   3  14   3
  LATS1 WILD-TYPE  16  89 315  47
D320V5, multiclass
    clus
vv   LATS1 MUTATED LATS1 WILD-TYPE
  T1             1              16
  T2             3              89
  T3            14             315
  T4             3              47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  LATS1 MUTATED    14   4   3
  LATS1 WILD-TYPE 273 109  84
D320V6, multiclass
    clus
vv   LATS1 MUTATED LATS1 WILD-TYPE
  N0            14             273
  N1             4             109
  N2             3              84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D320V7, binary
                 cls
clus                0   1
  LATS1 MUTATED    16   1
  LATS1 WILD-TYPE 359  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LATS1 MUTATED     16    1
  LATS1 WILD-TYPE  359   64
   clus
vv  LATS1 MUTATED LATS1 WILD-TYPE
  0            16             359
  1             1              64
[1] 2 2
[1] FALSE
D320V8, binary
                 cls
clus                0   1
  LATS1 MUTATED    15   6
  LATS1 WILD-TYPE 210 258
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LATS1 MUTATED     15    6
  LATS1 WILD-TYPE  210  258
        clus
vv       LATS1 MUTATED LATS1 WILD-TYPE
  FEMALE            15             210
  MALE               6             258
[1] 2 2
[1] FALSE
D320V9, binary
                 cls
clus                0   1
  LATS1 MUTATED    15   0
  LATS1 WILD-TYPE 335  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LATS1 MUTATED     15    0
  LATS1 WILD-TYPE  335   22
     clus
vv    LATS1 MUTATED LATS1 WILD-TYPE
  NO             15             335
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  LATS1 MUTATED                     15                             2
  LATS1 WILD-TYPE                  300                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  LATS1 MUTATED                       3                              0
  LATS1 WILD-TYPE                   103                             10
D320V10, multiclass
                                clus
vv                               LATS1 MUTATED LATS1 WILD-TYPE
  COLON ADENOCARCINOMA                      15             300
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      3             103
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  LATS1 MUTATED    11   1   1   2
  LATS1 WILD-TYPE 334   3  30  23
D320V11, multiclass
    clus
vv   LATS1 MUTATED LATS1 WILD-TYPE
  R0            11             334
  R1             1               3
  R2             1              30
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D320V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  LATS1 MUTATED                                  0     1
  LATS1 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  LATS1 MUTATED                           2    11
  LATS1 WILD-TYPE                        20   215
D320V13, multiclass
                                  clus
vv                                 LATS1 MUTATED LATS1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    2              20
  WHITE                                       11             215
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(321) Variable = THAP9 MUTATION ANALYSIS
D321V1, survival
                 sevent
clus2               0   1
  THAP9 MUTATED    12   4
  THAP9 WILD-TYPE 366  89
  THAP9 MUTATED THAP9 WILD-TYPE 
             16             455 
  THAP9 MUTATED THAP9 WILD-TYPE 
              4              89 
$`THAP9 MUTATED`
TCGA-A6-5666 TCGA-AA-3713 TCGA-AA-3848 TCGA-AA-3877 TCGA-AA-3947 TCGA-AA-A00N 
       32.71        19.04        10.06        31.00        33.01         4.01 
TCGA-AA-A010 TCGA-AA-A01Q TCGA-AY-6386 TCGA-AZ-5407 TCGA-D5-6929 TCGA-DM-A1DA 
       34.98         1.02        17.82        88.21         4.80         7.50 
TCGA-AG-3892 TCGA-AG-A002 TCGA-AG-A032 TCGA-DY-A1DG 
       13.02        20.98        38.04        51.48 

$`THAP9 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        22.06        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       27.02        29.98        18.05         2.01        12.99        24.00 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01R TCGA-AA-A01S 
       12.00        31.00        31.00        38.07        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       33.01        21.44        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 
       12.43        14.30         9.04         9.44        11.64         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       36.95        17.03        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       57.24        24.13        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  THAP9 MUTATED THAP9 WILD-TYPE 
           1.02            0.00 
  THAP9 MUTATED THAP9 WILD-TYPE 
          88.21          148.01 
  THAP9 MUTATED THAP9 WILD-TYPE 
          20.01           20.19 
[1] "1.0 - 88.2 (20.0)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.4"
D321V2, continuous
D321V3, binary
                 cls
clus                0   1
  THAP9 MUTATED    12   4
  THAP9 WILD-TYPE 354 115
[1] "tbl2"
                 cls
clus              [,1] [,2]
  THAP9 MUTATED     12    4
  THAP9 WILD-TYPE  354  115
        clus
vv       THAP9 MUTATED THAP9 WILD-TYPE
  COLON             12             354
  RECTUM             4             115
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  THAP9 MUTATED         4        0        1         0         3         1
  THAP9 WILD-TYPE      87        1       31       138         7         0
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  THAP9 MUTATED           0          0          2          2        2         1
  THAP9 WILD-TYPE        24         11         57         40       46        17
                 vv
clus              STAGE IVB
  THAP9 MUTATED           0
  THAP9 WILD-TYPE         1
D321V4, multiclass
            clus
vv           THAP9 MUTATED THAP9 WILD-TYPE
  STAGE I                4              87
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              0             138
  STAGE IIB              3               7
  STAGE IIC              1               0
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             2              57
  STAGE IIIC             2              40
  STAGE IV               2              46
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  THAP9 MUTATED     3   1   8   4
  THAP9 WILD-TYPE  14  91 321  46
D321V5, multiclass
    clus
vv   THAP9 MUTATED THAP9 WILD-TYPE
  T1             3              14
  T2             1              91
  T3             8             321
  T4             4              46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  THAP9 MUTATED    10   4   2
  THAP9 WILD-TYPE 277 109  85
D321V6, multiclass
    clus
vv   THAP9 MUTATED THAP9 WILD-TYPE
  N0            10             277
  N1             4             109
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D321V7, binary
                 cls
clus                0   1
  THAP9 MUTATED    13   3
  THAP9 WILD-TYPE 362  62
[1] "tbl2"
                 cls
clus              [,1] [,2]
  THAP9 MUTATED     13    3
  THAP9 WILD-TYPE  362   62
   clus
vv  THAP9 MUTATED THAP9 WILD-TYPE
  0            13             362
  1             3              62
[1] 2 2
[1] FALSE
D321V8, binary
                 cls
clus                0   1
  THAP9 MUTATED    10   6
  THAP9 WILD-TYPE 215 258
[1] "tbl2"
                 cls
clus              [,1] [,2]
  THAP9 MUTATED     10    6
  THAP9 WILD-TYPE  215  258
        clus
vv       THAP9 MUTATED THAP9 WILD-TYPE
  FEMALE            10             215
  MALE               6             258
[1] 2 2
[1] FALSE
D321V9, binary
                 cls
clus                0   1
  THAP9 MUTATED     9   2
  THAP9 WILD-TYPE 341  20
[1] "tbl2"
                 cls
clus              [,1] [,2]
  THAP9 MUTATED      9    2
  THAP9 WILD-TYPE  341   20
     clus
vv    THAP9 MUTATED THAP9 WILD-TYPE
  NO              9             341
  YES             2              20
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  THAP9 MUTATED                      9                             3
  THAP9 WILD-TYPE                  306                            44
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  THAP9 MUTATED                       4                              0
  THAP9 WILD-TYPE                   102                             10
D321V10, multiclass
                                clus
vv                               THAP9 MUTATED THAP9 WILD-TYPE
  COLON ADENOCARCINOMA                       9             306
  COLON MUCINOUS ADENOCARCINOMA              3              44
  RECTAL ADENOCARCINOMA                      4             102
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  THAP9 MUTATED    11   0   1   0
  THAP9 WILD-TYPE 334   4  30  25
D321V11, multiclass
    clus
vv   THAP9 MUTATED THAP9 WILD-TYPE
  R0            11             334
  R1             0               4
  R2             1              30
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D321V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  THAP9 MUTATED                                  0     0
  THAP9 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  THAP9 MUTATED                           1     5
  THAP9 WILD-TYPE                        21   221
D321V13, multiclass
                                  clus
vv                                 THAP9 MUTATED THAP9 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        5             221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(322) Variable = ZNF449 MUTATION ANALYSIS
D322V1, survival
                  sevent
clus2                0   1
  ZNF449 MUTATED    13   1
  ZNF449 WILD-TYPE 365  92
  ZNF449 MUTATED ZNF449 WILD-TYPE 
              14              457 
  ZNF449 MUTATED ZNF449 WILD-TYPE 
               1               92 
$`ZNF449 MUTATED`
TCGA-A6-5661 TCGA-A6-5665 TCGA-AA-3663 TCGA-AA-A01Q TCGA-AD-5900 TCGA-AU-6004 
       33.53        22.06         6.97         1.02         0.07        27.09 
TCGA-CA-6716 TCGA-D5-6931 TCGA-F4-6805 TCGA-G4-6588 TCGA-AG-3892 TCGA-AG-A002 
       12.20        12.00        34.42        26.17        13.02        20.98 
TCGA-DY-A1DD TCGA-F5-6571 
       57.24        31.30 

$`ZNF449 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       31.00        38.07        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
       40.96        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6932 TCGA-D5-7000 
        9.44        11.64         4.80         1.51        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
        6.18        47.87         1.55        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 
       61.91        36.00        22.09        13.78        35.80        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 
        1.02        17.95        36.95        17.03        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
        5.29       126.44        41.36        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       49.51        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  ZNF449 MUTATED ZNF449 WILD-TYPE 
            0.07             0.00 
  ZNF449 MUTATED ZNF449 WILD-TYPE 
           57.24           148.01 
  ZNF449 MUTATED ZNF449 WILD-TYPE 
           21.52            20.12 
[1] "0.1 - 57.2 (21.5)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "2.2"
D322V2, continuous
D322V3, binary
                  cls
clus                 0   1
  ZNF449 MUTATED    10   4
  ZNF449 WILD-TYPE 356 115
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF449 MUTATED     10    4
  ZNF449 WILD-TYPE  356  115
        clus
vv       ZNF449 MUTATED ZNF449 WILD-TYPE
  COLON              10              356
  RECTUM              4              115
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZNF449 MUTATED         4        0        2         6         0         0
  ZNF449 WILD-TYPE      87        1       30       132        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF449 MUTATED           0          0          1          1        0
  ZNF449 WILD-TYPE        24         11         58         41       48
                  vv
clus               STAGE IVA STAGE IVB
  ZNF449 MUTATED           0         0
  ZNF449 WILD-TYPE        18         1
D322V4, multiclass
            clus
vv           ZNF449 MUTATED ZNF449 WILD-TYPE
  STAGE I                 4               87
  STAGE IA                0                1
  STAGE II                2               30
  STAGE IIA               6              132
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              1               58
  STAGE IIIC              1               41
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZNF449 MUTATED     1   3   9   1
  ZNF449 WILD-TYPE  16  89 320  49
D322V5, multiclass
    clus
vv   ZNF449 MUTATED ZNF449 WILD-TYPE
  T1              1               16
  T2              3               89
  T3              9              320
  T4              1               49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  ZNF449 MUTATED    12   1   1
  ZNF449 WILD-TYPE 275 112  86
D322V6, multiclass
    clus
vv   ZNF449 MUTATED ZNF449 WILD-TYPE
  N0             12              275
  N1              1              112
  N2              1               86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D322V7, binary
                  cls
clus                 0   1
  ZNF449 MUTATED    13   0
  ZNF449 WILD-TYPE 362  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF449 MUTATED     13    0
  ZNF449 WILD-TYPE  362   65
   clus
vv  ZNF449 MUTATED ZNF449 WILD-TYPE
  0             13              362
  1              0               65
[1] 2 2
[1] FALSE
D322V8, binary
                  cls
clus                 0   1
  ZNF449 MUTATED     9   5
  ZNF449 WILD-TYPE 216 259
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF449 MUTATED      9    5
  ZNF449 WILD-TYPE  216  259
        clus
vv       ZNF449 MUTATED ZNF449 WILD-TYPE
  FEMALE              9              216
  MALE                5              259
[1] 2 2
[1] FALSE
D322V9, binary
                  cls
clus                 0   1
  ZNF449 MUTATED    10   0
  ZNF449 WILD-TYPE 340  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF449 MUTATED     10    0
  ZNF449 WILD-TYPE  340   22
     clus
vv    ZNF449 MUTATED ZNF449 WILD-TYPE
  NO              10              340
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ZNF449 MUTATED                      9                             1
  ZNF449 WILD-TYPE                  306                            46
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ZNF449 MUTATED                       4                              0
  ZNF449 WILD-TYPE                   102                             10
D322V10, multiclass
                                clus
vv                               ZNF449 MUTATED ZNF449 WILD-TYPE
  COLON ADENOCARCINOMA                        9              306
  COLON MUCINOUS ADENOCARCINOMA               1               46
  RECTAL ADENOCARCINOMA                       4              102
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ZNF449 MUTATED    12   0   0   1
  ZNF449 WILD-TYPE 333   4  31  24
D322V11, multiclass
    clus
vv   ZNF449 MUTATED ZNF449 WILD-TYPE
  R0             12              333
  R1              0                4
  R2              0               31
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D322V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF449 MUTATED                                  0     1
  ZNF449 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZNF449 MUTATED                           1     8
  ZNF449 WILD-TYPE                        21   218
D322V13, multiclass
                                  clus
vv                                 ZNF449 MUTATED ZNF449 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                         8              218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(323) Variable = PRDM1 MUTATION ANALYSIS
D323V1, survival
                 sevent
clus2               0   1
  PRDM1 MUTATED    17   4
  PRDM1 WILD-TYPE 361  89
  PRDM1 MUTATED PRDM1 WILD-TYPE 
             21             450 
  PRDM1 MUTATED PRDM1 WILD-TYPE 
              4              89 
$`PRDM1 MUTATED`
TCGA-A6-5666 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3968 TCGA-AA-A00J TCGA-AA-A00N 
       32.71         6.05         6.97        21.99        18.05         4.01 
TCGA-AU-6004 TCGA-AY-6197 TCGA-AZ-6599 TCGA-CK-4950 TCGA-CM-4746 TCGA-CM-6164 
       27.09        21.44         6.77        85.45        37.02        29.03 
TCGA-CM-6171 TCGA-D5-5541 TCGA-D5-6540 TCGA-DM-A1D6 TCGA-F4-6570 TCGA-G4-6293 
       14.04        55.92        16.14        49.91         6.18       133.18 
TCGA-G4-6307 TCGA-AG-3882 TCGA-AG-A002 
       55.04        19.99        20.98 

$`PRDM1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        22.06        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 
       19.99        13.94        19.99        61.02        78.08        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       34.03        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 
       22.42        27.42        10.88         0.20        14.50        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        33.01        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 
      106.75        22.36        62.79        88.21        49.41        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 
       12.76        10.06        14.30        17.56       148.01        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
      124.27        23.05        20.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
        4.80        17.13        12.49        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D7 TCGA-DM-A1D8 
       24.43        38.20       130.65        92.75        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 
       98.24         8.61        31.96        35.74        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       47.41        35.31        74.56        65.85        53.62        44.68 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
        0.99        19.04         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  PRDM1 MUTATED PRDM1 WILD-TYPE 
           4.01            0.00 
  PRDM1 MUTATED PRDM1 WILD-TYPE 
         133.18          148.01 
  PRDM1 MUTATED PRDM1 WILD-TYPE 
         21.440          20.085 
[1] "4.0 - 133.2 (21.4)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.2"
D323V2, continuous
D323V3, binary
                 cls
clus                0   1
  PRDM1 MUTATED    20   2
  PRDM1 WILD-TYPE 346 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRDM1 MUTATED     20    2
  PRDM1 WILD-TYPE  346  117
        clus
vv       PRDM1 MUTATED PRDM1 WILD-TYPE
  COLON             20             346
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PRDM1 MUTATED         8        0        1         4         2         1
  PRDM1 WILD-TYPE      83        1       31       134         8         0
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PRDM1 MUTATED           1          0          4          0        1         0
  PRDM1 WILD-TYPE        23         11         55         42       47        18
                 vv
clus              STAGE IVB
  PRDM1 MUTATED           0
  PRDM1 WILD-TYPE         1
D323V4, multiclass
            clus
vv           PRDM1 MUTATED PRDM1 WILD-TYPE
  STAGE I                8              83
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              4             134
  STAGE IIB              2               8
  STAGE IIC              1               0
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             4              55
  STAGE IIIC             0              42
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PRDM1 MUTATED     0   8   9   5
  PRDM1 WILD-TYPE  17  84 320  45
D323V5, multiclass
    clus
vv   PRDM1 MUTATED PRDM1 WILD-TYPE
  T1             0              17
  T2             8              84
  T3             9             320
  T4             5              45
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  PRDM1 MUTATED    16   5   1
  PRDM1 WILD-TYPE 271 108  86
D323V6, multiclass
    clus
vv   PRDM1 MUTATED PRDM1 WILD-TYPE
  N0            16             271
  N1             5             108
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D323V7, binary
                 cls
clus                0   1
  PRDM1 MUTATED    18   1
  PRDM1 WILD-TYPE 357  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRDM1 MUTATED     18    1
  PRDM1 WILD-TYPE  357   64
   clus
vv  PRDM1 MUTATED PRDM1 WILD-TYPE
  0            18             357
  1             1              64
[1] 2 2
[1] FALSE
D323V8, binary
                 cls
clus                0   1
  PRDM1 MUTATED    11  11
  PRDM1 WILD-TYPE 214 253
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRDM1 MUTATED     11   11
  PRDM1 WILD-TYPE  214  253
        clus
vv       PRDM1 MUTATED PRDM1 WILD-TYPE
  FEMALE            11             214
  MALE              11             253
[1] 2 2
[1] FALSE
D323V9, binary
                 cls
clus                0   1
  PRDM1 MUTATED    18   0
  PRDM1 WILD-TYPE 332  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRDM1 MUTATED     18    0
  PRDM1 WILD-TYPE  332   22
     clus
vv    PRDM1 MUTATED PRDM1 WILD-TYPE
  NO             18             332
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PRDM1 MUTATED                     16                             4
  PRDM1 WILD-TYPE                  299                            43
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PRDM1 MUTATED                       2                              0
  PRDM1 WILD-TYPE                   104                             10
D323V10, multiclass
                                clus
vv                               PRDM1 MUTATED PRDM1 WILD-TYPE
  COLON ADENOCARCINOMA                      16             299
  COLON MUCINOUS ADENOCARCINOMA              4              43
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  PRDM1 MUTATED    16   1   1   1
  PRDM1 WILD-TYPE 329   3  30  24
D323V11, multiclass
    clus
vv   PRDM1 MUTATED PRDM1 WILD-TYPE
  R0            16             329
  R1             1               3
  R2             1              30
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D323V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PRDM1 MUTATED                                  0     0
  PRDM1 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PRDM1 MUTATED                           2    13
  PRDM1 WILD-TYPE                        20   213
D323V13, multiclass
                                  clus
vv                                 PRDM1 MUTATED PRDM1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    2              20
  WHITE                                       13             213
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(324) Variable = MBTD1 MUTATION ANALYSIS
D324V1, survival
                 sevent
clus2               0   1
  MBTD1 MUTATED     9   2
  MBTD1 WILD-TYPE 369  91
  MBTD1 MUTATED MBTD1 WILD-TYPE 
             11             460 
  MBTD1 MUTATED MBTD1 WILD-TYPE 
              2              91 
$`MBTD1 MUTATED`
TCGA-AA-3492 TCGA-AD-6889 TCGA-AZ-6601 TCGA-CK-4948 TCGA-CK-5913 TCGA-CK-6747 
        3.02        56.55       100.01       148.01        51.32        82.95 
TCGA-D5-5539 TCGA-D5-6922 TCGA-G4-6628 TCGA-CI-6622 TCGA-DY-A0XA 
       19.59         4.41        79.69         6.97       126.44 

$`MBTD1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       15.52         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
       12.10        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4952 
       12.76        10.06        14.30        17.56        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       49.08         9.99        21.14         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 
       11.01        10.06        12.03        45.40        12.26        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        1.48         3.68        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       26.17        91.79        46.75        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
        6.05        33.17         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        4.01         5.03         5.29        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  MBTD1 MUTATED MBTD1 WILD-TYPE 
           3.02            0.00 
  MBTD1 MUTATED MBTD1 WILD-TYPE 
         148.01          140.38 
  MBTD1 MUTATED MBTD1 WILD-TYPE 
         56.550          20.085 
[1] "3.0 - 148.0 (56.5)" "0.0 - 140.4 (20.1)"
[1] "hr=" "2.4"
D324V2, continuous
D324V3, binary
                 cls
clus                0   1
  MBTD1 MUTATED     9   2
  MBTD1 WILD-TYPE 357 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MBTD1 MUTATED      9    2
  MBTD1 WILD-TYPE  357  117
        clus
vv       MBTD1 MUTATED MBTD1 WILD-TYPE
  COLON              9             357
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MBTD1 MUTATED         1        0        2         4         1         0
  MBTD1 WILD-TYPE      90        1       30       134         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MBTD1 MUTATED           1          2          0          0        0         0
  MBTD1 WILD-TYPE        23          9         59         42       48        18
                 vv
clus              STAGE IVB
  MBTD1 MUTATED           0
  MBTD1 WILD-TYPE         1
D324V4, multiclass
            clus
vv           MBTD1 MUTATED MBTD1 WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA              4             134
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             2               9
  STAGE IIIB             0              59
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  MBTD1 MUTATED     0   1   9   1
  MBTD1 WILD-TYPE  17  91 320  49
D324V5, multiclass
    clus
vv   MBTD1 MUTATED MBTD1 WILD-TYPE
  T1             0              17
  T2             1              91
  T3             9             320
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  MBTD1 MUTATED     8   3   0
  MBTD1 WILD-TYPE 279 110  87
D324V6, multiclass
    clus
vv   MBTD1 MUTATED MBTD1 WILD-TYPE
  N0             8             279
  N1             3             110
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D324V7, binary
                 cls
clus                0   1
  MBTD1 MUTATED     9   0
  MBTD1 WILD-TYPE 366  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MBTD1 MUTATED      9    0
  MBTD1 WILD-TYPE  366   65
   clus
vv  MBTD1 MUTATED MBTD1 WILD-TYPE
  0             9             366
  1             0              65
[1] 2 2
[1] FALSE
D324V8, binary
                 cls
clus                0   1
  MBTD1 MUTATED     5   6
  MBTD1 WILD-TYPE 220 258
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MBTD1 MUTATED      5    6
  MBTD1 WILD-TYPE  220  258
        clus
vv       MBTD1 MUTATED MBTD1 WILD-TYPE
  FEMALE             5             220
  MALE               6             258
[1] 2 2
[1] FALSE
D324V9, binary
                 cls
clus                0   1
  MBTD1 MUTATED     7   0
  MBTD1 WILD-TYPE 343  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MBTD1 MUTATED      7    0
  MBTD1 WILD-TYPE  343   22
     clus
vv    MBTD1 MUTATED MBTD1 WILD-TYPE
  NO              7             343
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MBTD1 MUTATED                      8                             1
  MBTD1 WILD-TYPE                  307                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MBTD1 MUTATED                       2                              0
  MBTD1 WILD-TYPE                   104                             10
D324V10, multiclass
                                clus
vv                               MBTD1 MUTATED MBTD1 WILD-TYPE
  COLON ADENOCARCINOMA                       8             307
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  MBTD1 MUTATED     5   0   0   2
  MBTD1 WILD-TYPE 340   4  31  23
D324V11, multiclass
    clus
vv   MBTD1 MUTATED MBTD1 WILD-TYPE
  R0             5             340
  R1             0               4
  R2             0              31
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D324V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MBTD1 MUTATED                                  0     1
  MBTD1 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  MBTD1 MUTATED                           0     9
  MBTD1 WILD-TYPE                        22   217
D324V13, multiclass
                                  clus
vv                                 MBTD1 MUTATED MBTD1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        9             217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(325) Variable = MKL2 MUTATION ANALYSIS
D325V1, survival
                sevent
clus2              0   1
  MKL2 MUTATED     7   4
  MKL2 WILD-TYPE 371  89
  MKL2 MUTATED MKL2 WILD-TYPE 
            11            460 
  MKL2 MUTATED MKL2 WILD-TYPE 
             4             89 
$`MKL2 MUTATED`
TCGA-A6-5665 TCGA-AA-3492 TCGA-AA-3518 TCGA-AD-5900 TCGA-AD-6963 TCGA-AD-6964 
       22.06         3.02         1.02         0.07        27.42        10.88 
TCGA-AU-6004 TCGA-CK-5916 TCGA-F4-6570 TCGA-G4-6307 TCGA-AG-A002 
       27.09        21.14         6.18        55.04        20.98 

$`MKL2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 
       20.12        19.66        20.28         7.04         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3519 
       63.98         6.97         1.02        13.02        38.99         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       18.05        40.96        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 
        0.72         5.79        22.42         0.20        14.50        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       65.85        53.62        44.68        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  MKL2 MUTATED MKL2 WILD-TYPE 
          0.07           0.00 
  MKL2 MUTATED MKL2 WILD-TYPE 
         55.04         148.01 
  MKL2 MUTATED MKL2 WILD-TYPE 
        20.980         20.155 
[1] "0.1 - 55.0 (21.0)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "2.7"
D325V2, continuous
D325V3, binary
                cls
clus               0   1
  MKL2 MUTATED    10   1
  MKL2 WILD-TYPE 356 118
[1] "tbl2"
                cls
clus             [,1] [,2]
  MKL2 MUTATED     10    1
  MKL2 WILD-TYPE  356  118
        clus
vv       MKL2 MUTATED MKL2 WILD-TYPE
  COLON            10            356
  RECTUM            1            118
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MKL2 MUTATED         4        0        1         3         0         0
  MKL2 WILD-TYPE      87        1       31       135        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MKL2 MUTATED           0          0          1          0        0         0
  MKL2 WILD-TYPE        24         11         58         42       48        18
                vv
clus             STAGE IVB
  MKL2 MUTATED           0
  MKL2 WILD-TYPE         1
D325V4, multiclass
            clus
vv           MKL2 MUTATED MKL2 WILD-TYPE
  STAGE I               4             87
  STAGE IA              0              1
  STAGE II              1             31
  STAGE IIA             3            135
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            1             58
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  MKL2 MUTATED     1   3   6   1
  MKL2 WILD-TYPE  16  89 323  49
D325V5, multiclass
    clus
vv   MKL2 MUTATED MKL2 WILD-TYPE
  T1            1             16
  T2            3             89
  T3            6            323
  T4            1             49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  MKL2 MUTATED     9   1   1
  MKL2 WILD-TYPE 278 112  86
D325V6, multiclass
    clus
vv   MKL2 MUTATED MKL2 WILD-TYPE
  N0            9            278
  N1            1            112
  N2            1             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D325V7, binary
                cls
clus               0   1
  MKL2 MUTATED     8   0
  MKL2 WILD-TYPE 367  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  MKL2 MUTATED      8    0
  MKL2 WILD-TYPE  367   65
   clus
vv  MKL2 MUTATED MKL2 WILD-TYPE
  0            8            367
  1            0             65
[1] 2 2
[1] FALSE
D325V8, binary
                cls
clus               0   1
  MKL2 MUTATED     7   4
  MKL2 WILD-TYPE 218 260
[1] "tbl2"
                cls
clus             [,1] [,2]
  MKL2 MUTATED      7    4
  MKL2 WILD-TYPE  218  260
        clus
vv       MKL2 MUTATED MKL2 WILD-TYPE
  FEMALE            7            218
  MALE              4            260
[1] 2 2
[1] FALSE
D325V9, binary
                cls
clus               0   1
  MKL2 MUTATED     8   0
  MKL2 WILD-TYPE 342  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  MKL2 MUTATED      8    0
  MKL2 WILD-TYPE  342   22
     clus
vv    MKL2 MUTATED MKL2 WILD-TYPE
  NO             8            342
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MKL2 MUTATED                      9                             1
  MKL2 WILD-TYPE                  306                            46
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MKL2 MUTATED                       1                              0
  MKL2 WILD-TYPE                   105                             10
D325V10, multiclass
                                clus
vv                               MKL2 MUTATED MKL2 WILD-TYPE
  COLON ADENOCARCINOMA                      9            306
  COLON MUCINOUS ADENOCARCINOMA             1             46
  RECTAL ADENOCARCINOMA                     1            105
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  MKL2 MUTATED     8   0   0   1
  MKL2 WILD-TYPE 337   4  31  24
D325V11, multiclass
    clus
vv   MKL2 MUTATED MKL2 WILD-TYPE
  R0            8            337
  R1            0              4
  R2            0             31
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D325V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MKL2 MUTATED                                  0     0
  MKL2 WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  MKL2 MUTATED                           0     8
  MKL2 WILD-TYPE                        22   218
D325V13, multiclass
                                  clus
vv                                 MKL2 MUTATED MKL2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       8            218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(326) Variable = LIG1 MUTATION ANALYSIS
D326V1, survival
                sevent
clus2              0   1
  LIG1 MUTATED    14   5
  LIG1 WILD-TYPE 364  88
  LIG1 MUTATED LIG1 WILD-TYPE 
            19            452 
  LIG1 MUTATED LIG1 WILD-TYPE 
             5             88 
$`LIG1 MUTATED`
TCGA-A6-5665 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-A00N TCGA-AA-A010 TCGA-AZ-6600 
       22.06        30.05        53.00         4.01        34.98        12.10 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CM-6171 TCGA-D5-6536 TCGA-D5-6540 TCGA-F4-6460 
        3.19         1.61        14.04        17.85        16.14        31.96 
TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6306 TCGA-AG-3732 TCGA-DC-6155 TCGA-EI-6507 
       35.31        74.56        44.68        32.98        13.97        19.96 
TCGA-EI-6510 
       18.28 

$`LIG1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3866 TCGA-AA-3867 
       32.05         0.99        31.07        31.07        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       88.21        49.41         6.77       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
       11.74        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 
       14.99        12.99        13.02        15.02        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 
       18.25         1.32        43.27        15.12         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       12.49        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
        8.61        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-G4-6293 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
      133.18        65.85        53.62        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
        0.99        37.02         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
        5.03        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6508 TCGA-F5-6464 
       51.48        32.61         0.49        20.55        20.91         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  LIG1 MUTATED LIG1 WILD-TYPE 
          1.61           0.00 
  LIG1 MUTATED LIG1 WILD-TYPE 
         74.56         148.01 
  LIG1 MUTATED LIG1 WILD-TYPE 
        19.960         20.235 
[1] "1.6 - 74.6 (20.0)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.4"
D326V2, continuous
D326V3, binary
                cls
clus               0   1
  LIG1 MUTATED    16   4
  LIG1 WILD-TYPE 350 115
[1] "tbl2"
                cls
clus             [,1] [,2]
  LIG1 MUTATED     16    4
  LIG1 WILD-TYPE  350  115
        clus
vv       LIG1 MUTATED LIG1 WILD-TYPE
  COLON            16            350
  RECTUM            4            115
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  LIG1 MUTATED         4        0        2         5         2         0
  LIG1 WILD-TYPE      87        1       30       133         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  LIG1 MUTATED           0          2          1          1        2         1
  LIG1 WILD-TYPE        24          9         58         41       46        17
                vv
clus             STAGE IVB
  LIG1 MUTATED           0
  LIG1 WILD-TYPE         1
D326V4, multiclass
            clus
vv           LIG1 MUTATED LIG1 WILD-TYPE
  STAGE I               4             87
  STAGE IA              0              1
  STAGE II              2             30
  STAGE IIA             5            133
  STAGE IIB             2              8
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            2              9
  STAGE IIIB            1             58
  STAGE IIIC            1             41
  STAGE IV              2             46
  STAGE IVA             1             17
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  LIG1 MUTATED     0   8   7   5
  LIG1 WILD-TYPE  17  84 322  45
D326V5, multiclass
    clus
vv   LIG1 MUTATED LIG1 WILD-TYPE
  T1            0             17
  T2            8             84
  T3            7            322
  T4            5             45
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  LIG1 MUTATED    14   4   2
  LIG1 WILD-TYPE 273 109  85
D326V6, multiclass
    clus
vv   LIG1 MUTATED LIG1 WILD-TYPE
  N0           14            273
  N1            4            109
  N2            2             85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D326V7, binary
                cls
clus               0   1
  LIG1 MUTATED    17   2
  LIG1 WILD-TYPE 358  63
[1] "tbl2"
                cls
clus             [,1] [,2]
  LIG1 MUTATED     17    2
  LIG1 WILD-TYPE  358   63
   clus
vv  LIG1 MUTATED LIG1 WILD-TYPE
  0           17            358
  1            2             63
[1] 2 2
[1] FALSE
D326V8, binary
                cls
clus               0   1
  LIG1 MUTATED     9  11
  LIG1 WILD-TYPE 216 253
[1] "tbl2"
                cls
clus             [,1] [,2]
  LIG1 MUTATED      9   11
  LIG1 WILD-TYPE  216  253
        clus
vv       LIG1 MUTATED LIG1 WILD-TYPE
  FEMALE            9            216
  MALE             11            253
[1] 2 2
[1] FALSE
D326V9, binary
                cls
clus               0   1
  LIG1 MUTATED    17   0
  LIG1 WILD-TYPE 333  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  LIG1 MUTATED     17    0
  LIG1 WILD-TYPE  333   22
     clus
vv    LIG1 MUTATED LIG1 WILD-TYPE
  NO            17            333
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  LIG1 MUTATED                     13                             3
  LIG1 WILD-TYPE                  302                            44
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  LIG1 MUTATED                       4                              0
  LIG1 WILD-TYPE                   102                             10
D326V10, multiclass
                                clus
vv                               LIG1 MUTATED LIG1 WILD-TYPE
  COLON ADENOCARCINOMA                     13            302
  COLON MUCINOUS ADENOCARCINOMA             3             44
  RECTAL ADENOCARCINOMA                     4            102
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  LIG1 MUTATED    17   0   0   0
  LIG1 WILD-TYPE 328   4  31  25
D326V11, multiclass
    clus
vv   LIG1 MUTATED LIG1 WILD-TYPE
  R0           17            328
  R1            0              4
  R2            0             31
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D326V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  LIG1 MUTATED                                  0     0
  LIG1 WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  LIG1 MUTATED                           1    13
  LIG1 WILD-TYPE                        21   213
D326V13, multiclass
                                  clus
vv                                 LIG1 MUTATED LIG1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                      13            213
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(327) Variable = ZNF708 MUTATION ANALYSIS
D327V1, survival
                  sevent
clus2                0   1
  ZNF708 MUTATED     7   4
  ZNF708 WILD-TYPE 371  89
  ZNF708 MUTATED ZNF708 WILD-TYPE 
              11              460 
  ZNF708 MUTATED ZNF708 WILD-TYPE 
               4               89 
$`ZNF708 MUTATED`
TCGA-A6-5666 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-A00N TCGA-AA-A010 TCGA-AD-6964 
       32.71        85.05        19.04         4.01        34.98        10.88 
TCGA-AY-5543 TCGA-CA-6718 TCGA-D5-6928 TCGA-DM-A28G TCGA-AG-A002 
       33.01        10.06        11.64        60.79        20.98 

$`ZNF708 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        22.06        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       36.00         5.03        26.99        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       16.31         0.95        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07        12.20        12.76        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28H 
      139.17         6.12        81.37       119.93        35.97       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  ZNF708 MUTATED ZNF708 WILD-TYPE 
            4.01             0.00 
  ZNF708 MUTATED ZNF708 WILD-TYPE 
           85.05           148.01 
  ZNF708 MUTATED ZNF708 WILD-TYPE 
          20.980           20.155 
[1] "4.0 - 85.0 (21.0)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.7"
D327V2, continuous
D327V3, binary
                  cls
clus                 0   1
  ZNF708 MUTATED    12   1
  ZNF708 WILD-TYPE 354 118
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF708 MUTATED     12    1
  ZNF708 WILD-TYPE  354  118
        clus
vv       ZNF708 MUTATED ZNF708 WILD-TYPE
  COLON              12              354
  RECTUM              1              118
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZNF708 MUTATED         2        0        0         4         2         1
  ZNF708 WILD-TYPE      89        1       32       134         8         0
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF708 MUTATED           1          0          0          0        1
  ZNF708 WILD-TYPE        23         11         59         42       47
                  vv
clus               STAGE IVA STAGE IVB
  ZNF708 MUTATED           1         0
  ZNF708 WILD-TYPE        17         1
D327V4, multiclass
            clus
vv           ZNF708 MUTATED ZNF708 WILD-TYPE
  STAGE I                 2               89
  STAGE IA                0                1
  STAGE II                0               32
  STAGE IIA               4              134
  STAGE IIB               2                8
  STAGE IIC               1                0
  STAGE III               1               23
  STAGE IIIA              0               11
  STAGE IIIB              0               59
  STAGE IIIC              0               42
  STAGE IV                1               47
  STAGE IVA               1               17
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZNF708 MUTATED     0   2   7   4
  ZNF708 WILD-TYPE  17  90 322  46
D327V5, multiclass
    clus
vv   ZNF708 MUTATED ZNF708 WILD-TYPE
  T1              0               17
  T2              2               90
  T3              7              322
  T4              4               46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  ZNF708 MUTATED    11   1   1
  ZNF708 WILD-TYPE 276 112  86
D327V6, multiclass
    clus
vv   ZNF708 MUTATED ZNF708 WILD-TYPE
  N0             11              276
  N1              1              112
  N2              1               86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D327V7, binary
                  cls
clus                 0   1
  ZNF708 MUTATED     9   2
  ZNF708 WILD-TYPE 366  63
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF708 MUTATED      9    2
  ZNF708 WILD-TYPE  366   63
   clus
vv  ZNF708 MUTATED ZNF708 WILD-TYPE
  0              9              366
  1              2               63
[1] 2 2
[1] FALSE
D327V8, binary
                  cls
clus                 0   1
  ZNF708 MUTATED     3  10
  ZNF708 WILD-TYPE 222 254
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF708 MUTATED      3   10
  ZNF708 WILD-TYPE  222  254
        clus
vv       ZNF708 MUTATED ZNF708 WILD-TYPE
  FEMALE              3              222
  MALE               10              254
[1] 2 2
[1] FALSE
D327V9, binary
                  cls
clus                 0   1
  ZNF708 MUTATED     8   1
  ZNF708 WILD-TYPE 342  21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF708 MUTATED      8    1
  ZNF708 WILD-TYPE  342   21
     clus
vv    ZNF708 MUTATED ZNF708 WILD-TYPE
  NO               8              342
  YES              1               21
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ZNF708 MUTATED                     10                             2
  ZNF708 WILD-TYPE                  305                            45
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ZNF708 MUTATED                       1                              0
  ZNF708 WILD-TYPE                   105                             10
D327V10, multiclass
                                clus
vv                               ZNF708 MUTATED ZNF708 WILD-TYPE
  COLON ADENOCARCINOMA                       10              305
  COLON MUCINOUS ADENOCARCINOMA               2               45
  RECTAL ADENOCARCINOMA                       1              105
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ZNF708 MUTATED     7   0   1   2
  ZNF708 WILD-TYPE 338   4  30  23
D327V11, multiclass
    clus
vv   ZNF708 MUTATED ZNF708 WILD-TYPE
  R0              7              338
  R1              0                4
  R2              1               30
  RX              2               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D327V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF708 MUTATED                                  0     1
  ZNF708 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZNF708 MUTATED                           1     5
  ZNF708 WILD-TYPE                        21   221
D327V13, multiclass
                                  clus
vv                                 ZNF708 MUTATED ZNF708 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                         5              221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(328) Variable = IL13RA2 MUTATION ANALYSIS
D328V1, survival
                   sevent
clus2                 0   1
  IL13RA2 MUTATED    14   2
  IL13RA2 WILD-TYPE 364  91
  IL13RA2 MUTATED IL13RA2 WILD-TYPE 
               16               455 
  IL13RA2 MUTATED IL13RA2 WILD-TYPE 
                2                91 
$`IL13RA2 MUTATED`
TCGA-A6-5660 TCGA-AA-3510 TCGA-AA-3662 TCGA-AA-3697 TCGA-AA-A00E TCGA-AA-A010 
       29.19        63.98         6.05        85.05        30.02        34.98 
TCGA-CM-6165 TCGA-D5-6536 TCGA-D5-6920 TCGA-DM-A1DB TCGA-DM-A285 TCGA-DM-A28H 
       16.04        17.85         3.68        44.32         6.12       117.07 
TCGA-G4-6315 TCGA-G4-6588 TCGA-AG-A00C TCGA-EI-6506 
       61.91        26.17         6.02        20.55 

$`IL13RA2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00F 
        7.96        27.02        13.94        38.04        19.00        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
       12.59       140.38         7.50       131.51       135.65       139.17 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28K TCGA-F4-6459 
       81.37       119.93        35.97        60.79        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       55.04        85.48        63.62        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       35.80        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       20.98        13.94        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6507 
       57.24        24.13        51.48        32.61         0.49        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  IL13RA2 MUTATED IL13RA2 WILD-TYPE 
             3.68              0.00 
  IL13RA2 MUTATED IL13RA2 WILD-TYPE 
           117.07            148.01 
  IL13RA2 MUTATED IL13RA2 WILD-TYPE 
            27.68             20.05 
[1] "3.7 - 117.1 (27.7)" "0.0 - 148.0 (20.1)"
[1] "hr=" "2.2"
D328V2, continuous
D328V3, binary
                   cls
clus                  0   1
  IL13RA2 MUTATED    14   2
  IL13RA2 WILD-TYPE 352 117
[1] "tbl2"
                   cls
clus                [,1] [,2]
  IL13RA2 MUTATED     14    2
  IL13RA2 WILD-TYPE  352  117
        clus
vv       IL13RA2 MUTATED IL13RA2 WILD-TYPE
  COLON               14               352
  RECTUM               2               117
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  IL13RA2 MUTATED         0        0        1         7         1         0
  IL13RA2 WILD-TYPE      91        1       31       131         9         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  IL13RA2 MUTATED           1          0          1          2        3
  IL13RA2 WILD-TYPE        23         11         58         40       45
                   vv
clus                STAGE IVA STAGE IVB
  IL13RA2 MUTATED           0         0
  IL13RA2 WILD-TYPE        18         1
D328V4, multiclass
            clus
vv           IL13RA2 MUTATED IL13RA2 WILD-TYPE
  STAGE I                  0                91
  STAGE IA                 0                 1
  STAGE II                 1                31
  STAGE IIA                7               131
  STAGE IIB                1                 9
  STAGE IIC                0                 1
  STAGE III                1                23
  STAGE IIIA               0                11
  STAGE IIIB               1                58
  STAGE IIIC               2                40
  STAGE IV                 3                45
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  IL13RA2 MUTATED     0   0  14   2
  IL13RA2 WILD-TYPE  17  92 315  48
D328V5, multiclass
    clus
vv   IL13RA2 MUTATED IL13RA2 WILD-TYPE
  T1               0                17
  T2               0                92
  T3              14               315
  T4               2                48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  IL13RA2 MUTATED    10   2   4
  IL13RA2 WILD-TYPE 277 111  83
D328V6, multiclass
    clus
vv   IL13RA2 MUTATED IL13RA2 WILD-TYPE
  N0              10               277
  N1               2               111
  N2               4                83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D328V7, binary
                   cls
clus                  0   1
  IL13RA2 MUTATED    13   3
  IL13RA2 WILD-TYPE 362  62
[1] "tbl2"
                   cls
clus                [,1] [,2]
  IL13RA2 MUTATED     13    3
  IL13RA2 WILD-TYPE  362   62
   clus
vv  IL13RA2 MUTATED IL13RA2 WILD-TYPE
  0              13               362
  1               3                62
[1] 2 2
[1] FALSE
D328V8, binary
                   cls
clus                  0   1
  IL13RA2 MUTATED     7   9
  IL13RA2 WILD-TYPE 218 255
[1] "tbl2"
                   cls
clus                [,1] [,2]
  IL13RA2 MUTATED      7    9
  IL13RA2 WILD-TYPE  218  255
        clus
vv       IL13RA2 MUTATED IL13RA2 WILD-TYPE
  FEMALE               7               218
  MALE                 9               255
[1] 2 2
[1] FALSE
D328V9, binary
                   cls
clus                  0   1
  IL13RA2 MUTATED    11   1
  IL13RA2 WILD-TYPE 339  21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  IL13RA2 MUTATED     11    1
  IL13RA2 WILD-TYPE  339   21
     clus
vv    IL13RA2 MUTATED IL13RA2 WILD-TYPE
  NO               11               339
  YES               1                21
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  IL13RA2 MUTATED                     13                             1
  IL13RA2 WILD-TYPE                  302                            46
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  IL13RA2 MUTATED                       2                              0
  IL13RA2 WILD-TYPE                   104                             10
D328V10, multiclass
                                clus
vv                               IL13RA2 MUTATED IL13RA2 WILD-TYPE
  COLON ADENOCARCINOMA                        13               302
  COLON MUCINOUS ADENOCARCINOMA                1                46
  RECTAL ADENOCARCINOMA                        2               104
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  IL13RA2 MUTATED    11   0   1   0
  IL13RA2 WILD-TYPE 334   4  30  25
D328V11, multiclass
    clus
vv   IL13RA2 MUTATED IL13RA2 WILD-TYPE
  R0              11               334
  R1               0                 4
  R2               1                30
  RX               0                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D328V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  IL13RA2 MUTATED                                  0     0
  IL13RA2 WILD-TYPE                                1    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  IL13RA2 MUTATED                           1     9
  IL13RA2 WILD-TYPE                        21   217
D328V13, multiclass
                                  clus
vv                                 IL13RA2 MUTATED IL13RA2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                      1                21
  WHITE                                          9               217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(329) Variable = FGFR3 MUTATION ANALYSIS
D329V1, survival
                 sevent
clus2               0   1
  FGFR3 MUTATED    19   4
  FGFR3 WILD-TYPE 359  89
  FGFR3 MUTATED FGFR3 WILD-TYPE 
             23             448 
  FGFR3 MUTATED FGFR3 WILD-TYPE 
              4              89 
$`FGFR3 MUTATED`
TCGA-A6-5665 TCGA-AA-3939 TCGA-AA-A01R TCGA-AD-6889 TCGA-AD-6895 TCGA-AD-6963 
       22.06        12.99        35.01        56.55         0.72        27.42 
TCGA-AD-6964 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-CA-6719 TCGA-CM-5860 
       10.88        58.39        49.41         6.77        14.30        32.02 
TCGA-CM-6162 TCGA-CM-6167 TCGA-D5-6534 TCGA-D5-6540 TCGA-D5-6541 TCGA-DM-A1D7 
       12.00        14.99        43.27        16.14        15.58        13.32 
TCGA-F4-6703 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6310 TCGA-DC-6155 
       47.87        35.31       133.18        63.62        13.97 

$`FGFR3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
        2.01        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T 
       31.00        31.00        38.07         1.02         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 
       18.05        40.96         0.07        21.37        15.52         0.79 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
        5.79        22.42         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        33.01        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6600 TCGA-AZ-6601 
      106.75        22.36        62.79        88.21        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       10.06        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.03        22.98        30.08        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       15.02        17.03        15.02         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       21.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       20.19        18.25         1.32        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       17.13        12.49         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
      130.65        92.75        49.91        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       31.96        35.74         6.18         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6299 
       16.24        33.67        13.25         0.53        47.41        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6315 
       65.85        53.62        44.68        55.04        85.48        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
        5.03        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  FGFR3 MUTATED FGFR3 WILD-TYPE 
           0.72            0.00 
  FGFR3 MUTATED FGFR3 WILD-TYPE 
         133.18          148.01 
  FGFR3 MUTATED FGFR3 WILD-TYPE 
         22.060          20.155 
[1] "0.7 - 133.2 (22.1)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.4"
D329V2, continuous
D329V3, binary
                 cls
clus                0   1
  FGFR3 MUTATED    22   1
  FGFR3 WILD-TYPE 344 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FGFR3 MUTATED     22    1
  FGFR3 WILD-TYPE  344  118
        clus
vv       FGFR3 MUTATED FGFR3 WILD-TYPE
  COLON             22             344
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FGFR3 MUTATED         3        0        1        10         0         0
  FGFR3 WILD-TYPE      88        1       31       128        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  FGFR3 MUTATED           2          1          2          1        0         0
  FGFR3 WILD-TYPE        22         10         57         41       48        18
                 vv
clus              STAGE IVB
  FGFR3 MUTATED           0
  FGFR3 WILD-TYPE         1
D329V4, multiclass
            clus
vv           FGFR3 MUTATED FGFR3 WILD-TYPE
  STAGE I                3              88
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA             10             128
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              2              22
  STAGE IIIA             1              10
  STAGE IIIB             2              57
  STAGE IIIC             1              41
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  FGFR3 MUTATED     0   4  18   1
  FGFR3 WILD-TYPE  17  88 311  49
D329V5, multiclass
    clus
vv   FGFR3 MUTATED FGFR3 WILD-TYPE
  T1             0              17
  T2             4              88
  T3            18             311
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  FGFR3 MUTATED    15   5   3
  FGFR3 WILD-TYPE 272 108  84
D329V6, multiclass
    clus
vv   FGFR3 MUTATED FGFR3 WILD-TYPE
  N0            15             272
  N1             5             108
  N2             3              84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D329V7, binary
                 cls
clus                0   1
  FGFR3 MUTATED    18   0
  FGFR3 WILD-TYPE 357  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FGFR3 MUTATED     18    0
  FGFR3 WILD-TYPE  357   65
   clus
vv  FGFR3 MUTATED FGFR3 WILD-TYPE
  0            18             357
  1             0              65
[1] 2 2
[1] FALSE
D329V8, binary
                 cls
clus                0   1
  FGFR3 MUTATED     7  16
  FGFR3 WILD-TYPE 218 248
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FGFR3 MUTATED      7   16
  FGFR3 WILD-TYPE  218  248
        clus
vv       FGFR3 MUTATED FGFR3 WILD-TYPE
  FEMALE             7             218
  MALE              16             248
[1] 2 2
[1] FALSE
D329V9, binary
                 cls
clus                0   1
  FGFR3 MUTATED    18   2
  FGFR3 WILD-TYPE 332  20
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FGFR3 MUTATED     18    2
  FGFR3 WILD-TYPE  332   20
     clus
vv    FGFR3 MUTATED FGFR3 WILD-TYPE
  NO             18             332
  YES             2              20
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  FGFR3 MUTATED                     16                             5
  FGFR3 WILD-TYPE                  299                            42
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  FGFR3 MUTATED                       1                              0
  FGFR3 WILD-TYPE                   105                             10
D329V10, multiclass
                                clus
vv                               FGFR3 MUTATED FGFR3 WILD-TYPE
  COLON ADENOCARCINOMA                      16             299
  COLON MUCINOUS ADENOCARCINOMA              5              42
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  FGFR3 MUTATED    15   0   0   1
  FGFR3 WILD-TYPE 330   4  31  24
D329V11, multiclass
    clus
vv   FGFR3 MUTATED FGFR3 WILD-TYPE
  R0            15             330
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D329V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FGFR3 MUTATED                                  0     2
  FGFR3 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  FGFR3 MUTATED                           1    18
  FGFR3 WILD-TYPE                        21   208
D329V13, multiclass
                                  clus
vv                                 FGFR3 MUTATED FGFR3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               9
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                       18             208
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(330) Variable = PTPN12 MUTATION ANALYSIS
D330V1, survival
                  sevent
clus2                0   1
  PTPN12 MUTATED    15   3
  PTPN12 WILD-TYPE 363  90
  PTPN12 MUTATED PTPN12 WILD-TYPE 
              18              453 
  PTPN12 MUTATED PTPN12 WILD-TYPE 
               3               90 
$`PTPN12 MUTATED`
TCGA-A6-6781 TCGA-AA-3510 TCGA-AA-3525 TCGA-AA-3663 TCGA-AA-3672 TCGA-AA-3710 
       19.66        63.98         8.05         6.97         0.92        26.99 
TCGA-AA-3950 TCGA-AA-3955 TCGA-AA-A00N TCGA-AA-A010 TCGA-AD-6964 TCGA-AZ-6598 
       24.00        20.98         4.01        34.98        10.88        49.41 
TCGA-CA-6717 TCGA-G4-6586 TCGA-AG-3892 TCGA-AG-A002 TCGA-CL-5917 TCGA-DY-A0XA 
       12.76        35.80        13.02        20.98        78.12       126.44 

$`PTPN12 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3529 
        9.07        24.03        37.05        36.03        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02        78.08         6.05        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
       14.01        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 
       37.05        19.00        36.00         5.03        85.05        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3952 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
        2.01        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
        0.72         5.79        22.42        27.42         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       88.21         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07        12.20        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
       33.17         6.97         4.73         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.03         5.29        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  PTPN12 MUTATED PTPN12 WILD-TYPE 
            0.92             0.00 
  PTPN12 MUTATED PTPN12 WILD-TYPE 
          126.44           148.01 
  PTPN12 MUTATED PTPN12 WILD-TYPE 
           20.98            20.12 
[1] "0.9 - 126.4 (21.0)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.4"
D330V2, continuous
D330V3, binary
                  cls
clus                 0   1
  PTPN12 MUTATED    17   4
  PTPN12 WILD-TYPE 349 115
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PTPN12 MUTATED     17    4
  PTPN12 WILD-TYPE  349  115
        clus
vv       PTPN12 MUTATED PTPN12 WILD-TYPE
  COLON              17              349
  RECTUM              4              115
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PTPN12 MUTATED         2        0        4         6         3         0
  PTPN12 WILD-TYPE      89        1       28       132         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PTPN12 MUTATED           1          0          2          2        0
  PTPN12 WILD-TYPE        23         11         57         40       48
                  vv
clus               STAGE IVA STAGE IVB
  PTPN12 MUTATED           0         0
  PTPN12 WILD-TYPE        18         1
D330V4, multiclass
            clus
vv           PTPN12 MUTATED PTPN12 WILD-TYPE
  STAGE I                 2               89
  STAGE IA                0                1
  STAGE II                4               28
  STAGE IIA               6              132
  STAGE IIB               3                7
  STAGE IIC               0                1
  STAGE III               1               23
  STAGE IIIA              0               11
  STAGE IIIB              2               57
  STAGE IIIC              2               40
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  PTPN12 MUTATED     1   2  12   6
  PTPN12 WILD-TYPE  16  90 317  44
D330V5, multiclass
    clus
vv   PTPN12 MUTATED PTPN12 WILD-TYPE
  T1              1               16
  T2              2               90
  T3             12              317
  T4              6               44
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  PTPN12 MUTATED    15   3   3
  PTPN12 WILD-TYPE 272 110  84
D330V6, multiclass
    clus
vv   PTPN12 MUTATED PTPN12 WILD-TYPE
  N0             15              272
  N1              3              110
  N2              3               84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D330V7, binary
                  cls
clus                 0   1
  PTPN12 MUTATED    16   0
  PTPN12 WILD-TYPE 359  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PTPN12 MUTATED     16    0
  PTPN12 WILD-TYPE  359   65
   clus
vv  PTPN12 MUTATED PTPN12 WILD-TYPE
  0             16              359
  1              0               65
[1] 2 2
[1] FALSE
D330V8, binary
                  cls
clus                 0   1
  PTPN12 MUTATED    12   9
  PTPN12 WILD-TYPE 213 255
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PTPN12 MUTATED     12    9
  PTPN12 WILD-TYPE  213  255
        clus
vv       PTPN12 MUTATED PTPN12 WILD-TYPE
  FEMALE             12              213
  MALE                9              255
[1] 2 2
[1] FALSE
D330V9, binary
                  cls
clus                 0   1
  PTPN12 MUTATED    16   0
  PTPN12 WILD-TYPE 334  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PTPN12 MUTATED     16    0
  PTPN12 WILD-TYPE  334   22
     clus
vv    PTPN12 MUTATED PTPN12 WILD-TYPE
  NO              16              334
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PTPN12 MUTATED                     13                             4
  PTPN12 WILD-TYPE                  302                            43
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PTPN12 MUTATED                       4                              0
  PTPN12 WILD-TYPE                   102                             10
D330V10, multiclass
                                clus
vv                               PTPN12 MUTATED PTPN12 WILD-TYPE
  COLON ADENOCARCINOMA                       13              302
  COLON MUCINOUS ADENOCARCINOMA               4               43
  RECTAL ADENOCARCINOMA                       4              102
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  PTPN12 MUTATED    15   0   0   3
  PTPN12 WILD-TYPE 330   4  31  22
D330V11, multiclass
    clus
vv   PTPN12 MUTATED PTPN12 WILD-TYPE
  R0             15              330
  R1              0                4
  R2              0               31
  RX              3               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D330V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PTPN12 MUTATED                                  0     1
  PTPN12 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  PTPN12 MUTATED                           0     7
  PTPN12 WILD-TYPE                        22   219
D330V13, multiclass
                                  clus
vv                                 PTPN12 MUTATED PTPN12 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         7              219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(331) Variable = TUBE1 MUTATION ANALYSIS
D331V1, survival
                 sevent
clus2               0   1
  TUBE1 MUTATED     9   3
  TUBE1 WILD-TYPE 369  90
  TUBE1 MUTATED TUBE1 WILD-TYPE 
             12             459 
  TUBE1 MUTATED TUBE1 WILD-TYPE 
              3              90 
$`TUBE1 MUTATED`
TCGA-A6-2677 TCGA-A6-5661 TCGA-AA-3516 TCGA-AA-3663 TCGA-AA-A010 TCGA-CA-6717 
       24.33        33.53        13.02         6.97        34.98        12.76 
TCGA-CK-4950 TCGA-CM-6162 TCGA-CM-6171 TCGA-DM-A1HB TCGA-DM-A28G TCGA-AG-A002 
       85.45        12.00        14.04       135.65        60.79        20.98 

$`TUBE1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        42.90        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       31.63        30.44        29.19        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
       63.98         6.97         1.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02        78.08         6.05        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07        12.20        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
       17.56       148.01        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       17.03        15.02         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 
       14.99        12.99        13.02        15.02        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 
       12.59       140.38         7.50        44.32       131.51       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28H TCGA-DM-A28K 
        6.12        81.37       119.93        35.97       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  TUBE1 MUTATED TUBE1 WILD-TYPE 
           6.97            0.00 
  TUBE1 MUTATED TUBE1 WILD-TYPE 
         135.65          148.01 
  TUBE1 MUTATED TUBE1 WILD-TYPE 
         22.655          20.120 
[1] "7.0 - 135.7 (22.7)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1"  
D331V2, continuous
D331V3, binary
                 cls
clus                0   1
  TUBE1 MUTATED    11   1
  TUBE1 WILD-TYPE 355 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TUBE1 MUTATED     11    1
  TUBE1 WILD-TYPE  355  118
        clus
vv       TUBE1 MUTATED TUBE1 WILD-TYPE
  COLON             11             355
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TUBE1 MUTATED         2        0        1         3         1         0
  TUBE1 WILD-TYPE      89        1       31       135         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TUBE1 MUTATED           1          0          3          1        0         0
  TUBE1 WILD-TYPE        23         11         56         41       48        18
                 vv
clus              STAGE IVB
  TUBE1 MUTATED           0
  TUBE1 WILD-TYPE         1
D331V4, multiclass
            clus
vv           TUBE1 MUTATED TUBE1 WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              3             135
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             3              56
  STAGE IIIC             1              41
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  TUBE1 MUTATED     0   2   9   1
  TUBE1 WILD-TYPE  17  90 320  49
D331V5, multiclass
    clus
vv   TUBE1 MUTATED TUBE1 WILD-TYPE
  T1             0              17
  T2             2              90
  T3             9             320
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  TUBE1 MUTATED     7   3   2
  TUBE1 WILD-TYPE 280 110  85
D331V6, multiclass
    clus
vv   TUBE1 MUTATED TUBE1 WILD-TYPE
  N0             7             280
  N1             3             110
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D331V7, binary
                 cls
clus                0   1
  TUBE1 MUTATED    12   0
  TUBE1 WILD-TYPE 363  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TUBE1 MUTATED     12    0
  TUBE1 WILD-TYPE  363   65
   clus
vv  TUBE1 MUTATED TUBE1 WILD-TYPE
  0            12             363
  1             0              65
[1] 2 2
[1] FALSE
D331V8, binary
                 cls
clus                0   1
  TUBE1 MUTATED     7   5
  TUBE1 WILD-TYPE 218 259
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TUBE1 MUTATED      7    5
  TUBE1 WILD-TYPE  218  259
        clus
vv       TUBE1 MUTATED TUBE1 WILD-TYPE
  FEMALE             7             218
  MALE               5             259
[1] 2 2
[1] FALSE
D331V9, binary
                 cls
clus                0   1
  TUBE1 MUTATED    10   0
  TUBE1 WILD-TYPE 340  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TUBE1 MUTATED     10    0
  TUBE1 WILD-TYPE  340   22
     clus
vv    TUBE1 MUTATED TUBE1 WILD-TYPE
  NO             10             340
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  TUBE1 MUTATED                      7                             3
  TUBE1 WILD-TYPE                  308                            44
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  TUBE1 MUTATED                       1                              0
  TUBE1 WILD-TYPE                   105                             10
D331V10, multiclass
                                clus
vv                               TUBE1 MUTATED TUBE1 WILD-TYPE
  COLON ADENOCARCINOMA                       7             308
  COLON MUCINOUS ADENOCARCINOMA              3              44
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  TUBE1 MUTATED     7   1   0   1
  TUBE1 WILD-TYPE 338   3  31  24
D331V11, multiclass
    clus
vv   TUBE1 MUTATED TUBE1 WILD-TYPE
  R0             7             338
  R1             1               3
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D331V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TUBE1 MUTATED                                  0     1
  TUBE1 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  TUBE1 MUTATED                           2     5
  TUBE1 WILD-TYPE                        20   221
D331V13, multiclass
                                  clus
vv                                 TUBE1 MUTATED TUBE1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    2              20
  WHITE                                        5             221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(332) Variable = TGFBR2 MUTATION ANALYSIS
D332V1, survival
                  sevent
clus2                0   1
  TGFBR2 MUTATED    17   6
  TGFBR2 WILD-TYPE 361  87
  TGFBR2 MUTATED TGFBR2 WILD-TYPE 
              23              448 
  TGFBR2 MUTATED TGFBR2 WILD-TYPE 
               6               87 
$`TGFBR2 MUTATED`
TCGA-A6-3808 TCGA-A6-6141 TCGA-AA-3492 TCGA-AA-3514 TCGA-AA-3968 TCGA-AA-A010 
       33.34         8.38         3.02         1.02        21.99        34.98 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A029 TCGA-AA-A03F TCGA-AD-6964 TCGA-CK-4952 
        1.02        35.01        51.98        18.05        10.88        15.62 
TCGA-CM-4743 TCGA-CM-6161 TCGA-CM-6674 TCGA-D5-5540 TCGA-D5-6931 TCGA-DM-A1HB 
       23.05        15.02        12.95        56.09        12.00       135.65 
TCGA-F4-6460 TCGA-G4-6303 TCGA-G4-6588 TCGA-CL-5918 TCGA-DY-A1DC 
       31.96        65.85        26.17         7.17        41.36 

$`TGFBR2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 
       22.06        32.71        27.09        22.52        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       19.66        20.28         7.04         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        6.97        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
        2.01        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01S 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A02F 
       33.04        35.01        26.01        37.02        39.06        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
        0.72         5.79        22.42        27.42         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 
       14.30        17.56       148.01        85.45        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 
        9.99        21.14        82.95         1.91       124.27        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       17.03        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       45.40        12.26        19.59        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
        1.51        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
        7.50        44.32       131.51       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
      133.18        74.56        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-DC-5337 
        6.05        33.17         6.97         4.73        78.12        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DD TCGA-DY-A1DF 
        4.01         5.03         5.29       126.44        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  TGFBR2 MUTATED TGFBR2 WILD-TYPE 
            1.02             0.00 
  TGFBR2 MUTATED TGFBR2 WILD-TYPE 
          135.65           148.01 
  TGFBR2 MUTATED TGFBR2 WILD-TYPE 
          21.990           20.155 
[1] "1.0 - 135.7 (22.0)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.3"
D332V2, continuous
D332V3, binary
                  cls
clus                 0   1
  TGFBR2 MUTATED    21   2
  TGFBR2 WILD-TYPE 345 117
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TGFBR2 MUTATED     21    2
  TGFBR2 WILD-TYPE  345  117
        clus
vv       TGFBR2 MUTATED TGFBR2 WILD-TYPE
  COLON              21              345
  RECTUM              2              117
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TGFBR2 MUTATED         3        0        3         8         1         0
  TGFBR2 WILD-TYPE      88        1       29       130         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TGFBR2 MUTATED           2          0          2          2        1
  TGFBR2 WILD-TYPE        22         11         57         40       47
                  vv
clus               STAGE IVA STAGE IVB
  TGFBR2 MUTATED           0         0
  TGFBR2 WILD-TYPE        18         1
D332V4, multiclass
            clus
vv           TGFBR2 MUTATED TGFBR2 WILD-TYPE
  STAGE I                 3               88
  STAGE IA                0                1
  STAGE II                3               29
  STAGE IIA               8              130
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               2               22
  STAGE IIIA              0               11
  STAGE IIIB              2               57
  STAGE IIIC              2               40
  STAGE IV                1               47
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  TGFBR2 MUTATED     0   3  16   4
  TGFBR2 WILD-TYPE  17  89 313  46
D332V5, multiclass
    clus
vv   TGFBR2 MUTATED TGFBR2 WILD-TYPE
  T1              0               17
  T2              3               89
  T3             16              313
  T4              4               46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  TGFBR2 MUTATED    15   3   5
  TGFBR2 WILD-TYPE 272 110  82
D332V6, multiclass
    clus
vv   TGFBR2 MUTATED TGFBR2 WILD-TYPE
  N0             15              272
  N1              3              110
  N2              5               82
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D332V7, binary
                  cls
clus                 0   1
  TGFBR2 MUTATED    20   1
  TGFBR2 WILD-TYPE 355  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TGFBR2 MUTATED     20    1
  TGFBR2 WILD-TYPE  355   64
   clus
vv  TGFBR2 MUTATED TGFBR2 WILD-TYPE
  0             20              355
  1              1               64
[1] 2 2
[1] FALSE
D332V8, binary
                  cls
clus                 0   1
  TGFBR2 MUTATED    13  10
  TGFBR2 WILD-TYPE 212 254
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TGFBR2 MUTATED     13   10
  TGFBR2 WILD-TYPE  212  254
        clus
vv       TGFBR2 MUTATED TGFBR2 WILD-TYPE
  FEMALE             13              212
  MALE               10              254
[1] 2 2
[1] FALSE
D332V9, binary
                  cls
clus                 0   1
  TGFBR2 MUTATED    17   1
  TGFBR2 WILD-TYPE 333  21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TGFBR2 MUTATED     17    1
  TGFBR2 WILD-TYPE  333   21
     clus
vv    TGFBR2 MUTATED TGFBR2 WILD-TYPE
  NO              17              333
  YES              1               21
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  TGFBR2 MUTATED                     17                             3
  TGFBR2 WILD-TYPE                  298                            44
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  TGFBR2 MUTATED                       2                              0
  TGFBR2 WILD-TYPE                   104                             10
D332V10, multiclass
                                clus
vv                               TGFBR2 MUTATED TGFBR2 WILD-TYPE
  COLON ADENOCARCINOMA                       17              298
  COLON MUCINOUS ADENOCARCINOMA               3               44
  RECTAL ADENOCARCINOMA                       2              104
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  TGFBR2 MUTATED    17   0   0   2
  TGFBR2 WILD-TYPE 328   4  31  23
D332V11, multiclass
    clus
vv   TGFBR2 MUTATED TGFBR2 WILD-TYPE
  R0             17              328
  R1              0                4
  R2              0               31
  RX              2               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D332V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TGFBR2 MUTATED                                  0     0
  TGFBR2 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  TGFBR2 MUTATED                           1    14
  TGFBR2 WILD-TYPE                        21   212
D332V13, multiclass
                                  clus
vv                                 TGFBR2 MUTATED TGFBR2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                        14              212
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(333) Variable = OR1J2 MUTATION ANALYSIS
D333V1, survival
                 sevent
clus2               0   1
  OR1J2 MUTATED    12   0
  OR1J2 WILD-TYPE 366  93
  OR1J2 MUTATED OR1J2 WILD-TYPE 
             12             459 
  OR1J2 MUTATED OR1J2 WILD-TYPE 
              0              93 
$`OR1J2 MUTATED`
TCGA-A6-6780 TCGA-AA-3663 TCGA-AY-5543 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
       20.12         6.97        33.01         3.25         3.29         0.07 
TCGA-CK-5914 TCGA-CK-6747 TCGA-CM-6170 TCGA-AG-3732 TCGA-AG-3892 TCGA-AG-A002 
        9.99        82.95        15.02        32.98        13.02        20.98 

$`OR1J2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.69         3.06        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5916 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       21.14         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       14.99        12.99        13.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
        0.99        37.02         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 
        1.02        17.95        36.95        17.03        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  OR1J2 MUTATED OR1J2 WILD-TYPE 
           0.07            0.00 
  OR1J2 MUTATED OR1J2 WILD-TYPE 
          82.95          148.01 
  OR1J2 MUTATED OR1J2 WILD-TYPE 
          14.02           20.55 
[1] "0.1 - 83.0 (14.0)"  "0.0 - 148.0 (20.6)"
[1] "hr="     "9200000"
D333V2, continuous
D333V3, binary
                 cls
clus                0   1
  OR1J2 MUTATED    10   3
  OR1J2 WILD-TYPE 356 116
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR1J2 MUTATED     10    3
  OR1J2 WILD-TYPE  356  116
        clus
vv       OR1J2 MUTATED OR1J2 WILD-TYPE
  COLON             10             356
  RECTUM             3             116
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  OR1J2 MUTATED         4        0        1         4         0         0
  OR1J2 WILD-TYPE      87        1       31       134        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  OR1J2 MUTATED           1          0          2          0        0         1
  OR1J2 WILD-TYPE        23         11         57         42       48        17
                 vv
clus              STAGE IVB
  OR1J2 MUTATED           0
  OR1J2 WILD-TYPE         1
D333V4, multiclass
            clus
vv           OR1J2 MUTATED OR1J2 WILD-TYPE
  STAGE I                4              87
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              4             134
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             2              57
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  OR1J2 MUTATED     1   3   9   0
  OR1J2 WILD-TYPE  16  89 320  50
D333V5, multiclass
    clus
vv   OR1J2 MUTATED OR1J2 WILD-TYPE
  T1             1              16
  T2             3              89
  T3             9             320
  T4             0              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  OR1J2 MUTATED     9   3   1
  OR1J2 WILD-TYPE 278 110  86
D333V6, multiclass
    clus
vv   OR1J2 MUTATED OR1J2 WILD-TYPE
  N0             9             278
  N1             3             110
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D333V7, binary
                 cls
clus                0   1
  OR1J2 MUTATED     9   1
  OR1J2 WILD-TYPE 366  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR1J2 MUTATED      9    1
  OR1J2 WILD-TYPE  366   64
   clus
vv  OR1J2 MUTATED OR1J2 WILD-TYPE
  0             9             366
  1             1              64
[1] 2 2
[1] FALSE
D333V8, binary
                 cls
clus                0   1
  OR1J2 MUTATED     6   7
  OR1J2 WILD-TYPE 219 257
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR1J2 MUTATED      6    7
  OR1J2 WILD-TYPE  219  257
        clus
vv       OR1J2 MUTATED OR1J2 WILD-TYPE
  FEMALE             6             219
  MALE               7             257
[1] 2 2
[1] FALSE
D333V9, binary
                 cls
clus                0   1
  OR1J2 MUTATED    10   0
  OR1J2 WILD-TYPE 340  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR1J2 MUTATED     10    0
  OR1J2 WILD-TYPE  340   22
     clus
vv    OR1J2 MUTATED OR1J2 WILD-TYPE
  NO             10             340
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  OR1J2 MUTATED                      8                             2
  OR1J2 WILD-TYPE                  307                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  OR1J2 MUTATED                       3                              0
  OR1J2 WILD-TYPE                   103                             10
D333V10, multiclass
                                clus
vv                               OR1J2 MUTATED OR1J2 WILD-TYPE
  COLON ADENOCARCINOMA                       8             307
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      3             103
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  OR1J2 MUTATED     9   0   0   3
  OR1J2 WILD-TYPE 336   4  31  22
D333V11, multiclass
    clus
vv   OR1J2 MUTATED OR1J2 WILD-TYPE
  R0             9             336
  R1             0               4
  R2             0              31
  RX             3              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D333V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OR1J2 MUTATED                                  0     3
  OR1J2 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  OR1J2 MUTATED                           1     4
  OR1J2 WILD-TYPE                        21   222
D333V13, multiclass
                                  clus
vv                                 OR1J2 MUTATED OR1J2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        3               8
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        4             222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(334) Variable = SPR MUTATION ANALYSIS
D334V1, survival
               sevent
clus2             0   1
  SPR MUTATED     4   3
  SPR WILD-TYPE 374  90
  SPR MUTATED SPR WILD-TYPE 
            7           464 
  SPR MUTATED SPR WILD-TYPE 
            3            90 
$`SPR MUTATED`
TCGA-A6-4105 TCGA-AA-3492 TCGA-AZ-6599 TCGA-CK-4952 TCGA-CK-5913 TCGA-D5-6928 
       14.53         3.02         6.77        15.62        51.32        11.64 
TCGA-G4-6293 
      133.18 

$`SPR WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 
       16.57        34.65        33.34        32.75        36.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 
       20.12        19.66        20.28         7.04         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 
      106.75        22.36        62.79        88.21        49.41        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       49.08         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
       14.30         9.04         9.44         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
       35.31        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  SPR MUTATED SPR WILD-TYPE 
         3.02          0.00 
  SPR MUTATED SPR WILD-TYPE 
       133.18        148.01 
  SPR MUTATED SPR WILD-TYPE 
       14.530        20.415 
[1] "3.0 - 133.2 (14.5)" "0.0 - 148.0 (20.4)"
[1] "hr=" "1.9"
D334V2, continuous
D334V3, binary
               cls
clus              0   1
  SPR MUTATED     7   0
  SPR WILD-TYPE 359 119
[1] "tbl2"
               cls
clus            [,1] [,2]
  SPR MUTATED      7    0
  SPR WILD-TYPE  359  119
        clus
vv       SPR MUTATED SPR WILD-TYPE
  COLON            7           359
  RECTUM           0           119
[1] 2 2
[1] FALSE
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SPR MUTATED         1        0        1         3         0         0
  SPR WILD-TYPE      90        1       31       135        10         1
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SPR MUTATED           1          0          0          1        0         0
  SPR WILD-TYPE        23         11         59         41       48        18
               vv
clus            STAGE IVB
  SPR MUTATED           0
  SPR WILD-TYPE         1
D334V4, multiclass
            clus
vv           SPR MUTATED SPR WILD-TYPE
  STAGE I              1            90
  STAGE IA             0             1
  STAGE II             1            31
  STAGE IIA            3           135
  STAGE IIB            0            10
  STAGE IIC            0             1
  STAGE III            1            23
  STAGE IIIA           0            11
  STAGE IIIB           0            59
  STAGE IIIC           1            41
  STAGE IV             0            48
  STAGE IVA            0            18
  STAGE IVB            0             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  SPR MUTATED     0   1   5   1
  SPR WILD-TYPE  17  91 324  49
D334V5, multiclass
    clus
vv   SPR MUTATED SPR WILD-TYPE
  T1           0            17
  T2           1            91
  T3           5           324
  T4           1            49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2
  SPR MUTATED     5   1   1
  SPR WILD-TYPE 282 112  86
D334V6, multiclass
    clus
vv   SPR MUTATED SPR WILD-TYPE
  N0           5           282
  N1           1           112
  N2           1            86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D334V7, binary
               cls
clus              0   1
  SPR MUTATED     5   0
  SPR WILD-TYPE 370  65
[1] "tbl2"
               cls
clus            [,1] [,2]
  SPR MUTATED      5    0
  SPR WILD-TYPE  370   65
   clus
vv  SPR MUTATED SPR WILD-TYPE
  0           5           370
  1           0            65
[1] 2 2
[1] FALSE
D334V8, binary
               cls
clus              0   1
  SPR MUTATED     4   3
  SPR WILD-TYPE 221 261
[1] "tbl2"
               cls
clus            [,1] [,2]
  SPR MUTATED      4    3
  SPR WILD-TYPE  221  261
        clus
vv       SPR MUTATED SPR WILD-TYPE
  FEMALE           4           221
  MALE             3           261
[1] 2 2
[1] FALSE
D334V9, binary
               cls
clus              0   1
  SPR MUTATED     6   0
  SPR WILD-TYPE 344  22
[1] "tbl2"
               cls
clus            [,1] [,2]
  SPR MUTATED      6    0
  SPR WILD-TYPE  344   22
     clus
vv    SPR MUTATED SPR WILD-TYPE
  NO            6           344
  YES           0            22
[1] 2 2
[1] FALSE
               vv
clus            COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SPR MUTATED                      5                             2
  SPR WILD-TYPE                  310                            45
               vv
clus            RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SPR MUTATED                       0                              0
  SPR WILD-TYPE                   106                             10
D334V10, multiclass
                                clus
vv                               SPR MUTATED SPR WILD-TYPE
  COLON ADENOCARCINOMA                     5           310
  COLON MUCINOUS ADENOCARCINOMA            2            45
  RECTAL ADENOCARCINOMA                    0           106
  RECTAL MUCINOUS ADENOCARCINOMA           0            10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             R0  R1  R2  RX
  SPR MUTATED     3   0   0   2
  SPR WILD-TYPE 342   4  31  23
D334V11, multiclass
    clus
vv   SPR MUTATED SPR WILD-TYPE
  R0           3           342
  R1           0             4
  R2           0            31
  RX           2            23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D334V12, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SPR MUTATED                                  0     0
  SPR WILD-TYPE                                1    11
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  SPR MUTATED                           0     6
  SPR WILD-TYPE                        22   220
D334V13, multiclass
                                  clus
vv                                 SPR MUTATED SPR WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      0            11
  BLACK OR AFRICAN AMERICAN                  0            22
  WHITE                                      6           220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(335) Variable = TRIM32 MUTATION ANALYSIS
D335V1, survival
                  sevent
clus2                0   1
  TRIM32 MUTATED     9   3
  TRIM32 WILD-TYPE 369  90
  TRIM32 MUTATED TRIM32 WILD-TYPE 
              12              459 
  TRIM32 MUTATED TRIM32 WILD-TYPE 
               3               90 
$`TRIM32 MUTATED`
TCGA-AA-3516 TCGA-AA-3522 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3968 TCGA-AA-A01R 
       13.02        37.05        26.99        19.04        21.99        35.01 
TCGA-AZ-5403 TCGA-F4-6808 TCGA-G4-6299 TCGA-G4-6304 TCGA-G4-6315 TCGA-G4-6628 
       62.79        33.67        74.56        53.62        61.91        79.69 

$`TRIM32 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        1.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        1.02         9.07        24.03        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
        5.03        85.05        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
        2.01        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
        1.02         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6598 
        1.41         5.13       106.75        22.36        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       16.24        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6317 
       65.85        44.68        55.04        85.48        63.62        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  TRIM32 MUTATED TRIM32 WILD-TYPE 
           13.02             0.00 
  TRIM32 MUTATED TRIM32 WILD-TYPE 
           79.69           148.01 
  TRIM32 MUTATED TRIM32 WILD-TYPE 
           36.03            20.02 
[1] "13.0 - 79.7 (36.0)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.3"
D335V2, continuous
D335V3, binary
                  cls
clus                 0   1
  TRIM32 MUTATED    12   0
  TRIM32 WILD-TYPE 354 119
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIM32 MUTATED     12    0
  TRIM32 WILD-TYPE  354  119
        clus
vv       TRIM32 MUTATED TRIM32 WILD-TYPE
  COLON              12              354
  RECTUM              0              119
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TRIM32 MUTATED         3        0        2         2         1         0
  TRIM32 WILD-TYPE      88        1       30       136         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TRIM32 MUTATED           2          0          0          1        1
  TRIM32 WILD-TYPE        22         11         59         41       47
                  vv
clus               STAGE IVA STAGE IVB
  TRIM32 MUTATED           0         0
  TRIM32 WILD-TYPE        18         1
D335V4, multiclass
            clus
vv           TRIM32 MUTATED TRIM32 WILD-TYPE
  STAGE I                 3               88
  STAGE IA                0                1
  STAGE II                2               30
  STAGE IIA               2              136
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               2               22
  STAGE IIIA              0               11
  STAGE IIIB              0               59
  STAGE IIIC              1               41
  STAGE IV                1               47
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  TRIM32 MUTATED     1   2   8   1
  TRIM32 WILD-TYPE  16  90 321  49
D335V5, multiclass
    clus
vv   TRIM32 MUTATED TRIM32 WILD-TYPE
  T1              1               16
  T2              2               90
  T3              8              321
  T4              1               49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  TRIM32 MUTATED     8   1   3
  TRIM32 WILD-TYPE 279 112  84
D335V6, multiclass
    clus
vv   TRIM32 MUTATED TRIM32 WILD-TYPE
  N0              8              279
  N1              1              112
  N2              3               84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D335V7, binary
                  cls
clus                 0   1
  TRIM32 MUTATED    10   1
  TRIM32 WILD-TYPE 365  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIM32 MUTATED     10    1
  TRIM32 WILD-TYPE  365   64
   clus
vv  TRIM32 MUTATED TRIM32 WILD-TYPE
  0             10              365
  1              1               64
[1] 2 2
[1] FALSE
D335V8, binary
                  cls
clus                 0   1
  TRIM32 MUTATED     5   7
  TRIM32 WILD-TYPE 220 257
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIM32 MUTATED      5    7
  TRIM32 WILD-TYPE  220  257
        clus
vv       TRIM32 MUTATED TRIM32 WILD-TYPE
  FEMALE              5              220
  MALE                7              257
[1] 2 2
[1] FALSE
D335V9, binary
                  cls
clus                 0   1
  TRIM32 MUTATED    11   1
  TRIM32 WILD-TYPE 339  21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIM32 MUTATED     11    1
  TRIM32 WILD-TYPE  339   21
     clus
vv    TRIM32 MUTATED TRIM32 WILD-TYPE
  NO              11              339
  YES              1               21
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  TRIM32 MUTATED                     10                             2
  TRIM32 WILD-TYPE                  305                            45
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  TRIM32 MUTATED                       0                              0
  TRIM32 WILD-TYPE                   106                             10
D335V10, multiclass
                                clus
vv                               TRIM32 MUTATED TRIM32 WILD-TYPE
  COLON ADENOCARCINOMA                       10              305
  COLON MUCINOUS ADENOCARCINOMA               2               45
  RECTAL ADENOCARCINOMA                       0              106
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  TRIM32 MUTATED    10   0   0   0
  TRIM32 WILD-TYPE 335   4  31  25
D335V11, multiclass
    clus
vv   TRIM32 MUTATED TRIM32 WILD-TYPE
  R0             10              335
  R1              0                4
  R2              0               31
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D335V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TRIM32 MUTATED                                  0     0
  TRIM32 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  TRIM32 MUTATED                           0     6
  TRIM32 WILD-TYPE                        22   220
D335V13, multiclass
                                  clus
vv                                 TRIM32 MUTATED TRIM32 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         6              220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(336) Variable = TWISTNB MUTATION ANALYSIS
D336V1, survival
                   sevent
clus2                 0   1
  TWISTNB MUTATED     8   1
  TWISTNB WILD-TYPE 370  92
  TWISTNB MUTATED TWISTNB WILD-TYPE 
                9               462 
  TWISTNB MUTATED TWISTNB WILD-TYPE 
                1                92 
$`TWISTNB MUTATED`
TCGA-AA-3977 TCGA-AZ-6603 TCGA-CM-4743 TCGA-CM-5344 TCGA-D5-6926 TCGA-DM-A28H 
       25.02        29.56        23.05        22.03         9.04       117.07 
TCGA-G4-6309 TCGA-G4-6625 TCGA-AG-A002 
       85.48        91.79        20.98 

$`TWISTNB WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77        12.10       100.01         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
       82.95         1.91       124.27        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       13.02        29.06        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       12.43        14.30         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28K TCGA-F4-6459 
       81.37       119.93        35.97        60.79        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       55.04        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       35.80        26.17        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  TWISTNB MUTATED TWISTNB WILD-TYPE 
             9.04              0.00 
  TWISTNB MUTATED TWISTNB WILD-TYPE 
           117.07            148.01 
  TWISTNB MUTATED TWISTNB WILD-TYPE 
            25.02             20.02 
[1] "9.0 - 117.1 (25.0)" "0.0 - 148.0 (20.0)"
[1] "hr=" "3"  
D336V2, continuous
D336V3, binary
                   cls
clus                  0   1
  TWISTNB MUTATED     8   1
  TWISTNB WILD-TYPE 358 118
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TWISTNB MUTATED      8    1
  TWISTNB WILD-TYPE  358  118
        clus
vv       TWISTNB MUTATED TWISTNB WILD-TYPE
  COLON                8               358
  RECTUM               1               118
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TWISTNB MUTATED         1        0        0         2         0         0
  TWISTNB WILD-TYPE      90        1       32       136        10         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TWISTNB MUTATED           0          0          3          1        0
  TWISTNB WILD-TYPE        24         11         56         41       48
                   vv
clus                STAGE IVA STAGE IVB
  TWISTNB MUTATED           0         0
  TWISTNB WILD-TYPE        18         1
D336V4, multiclass
            clus
vv           TWISTNB MUTATED TWISTNB WILD-TYPE
  STAGE I                  1                90
  STAGE IA                 0                 1
  STAGE II                 0                32
  STAGE IIA                2               136
  STAGE IIB                0                10
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               0                11
  STAGE IIIB               3                56
  STAGE IIIC               1                41
  STAGE IV                 0                48
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  TWISTNB MUTATED     0   3   5   1
  TWISTNB WILD-TYPE  17  89 324  49
D336V5, multiclass
    clus
vv   TWISTNB MUTATED TWISTNB WILD-TYPE
  T1               0                17
  T2               3                89
  T3               5               324
  T4               1                49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  TWISTNB MUTATED     4   4   1
  TWISTNB WILD-TYPE 283 109  86
D336V6, multiclass
    clus
vv   TWISTNB MUTATED TWISTNB WILD-TYPE
  N0               4               283
  N1               4               109
  N2               1                86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D336V7, binary
                   cls
clus                  0   1
  TWISTNB MUTATED     7   0
  TWISTNB WILD-TYPE 368  65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TWISTNB MUTATED      7    0
  TWISTNB WILD-TYPE  368   65
   clus
vv  TWISTNB MUTATED TWISTNB WILD-TYPE
  0               7               368
  1               0                65
[1] 2 2
[1] FALSE
D336V8, binary
                   cls
clus                  0   1
  TWISTNB MUTATED     4   5
  TWISTNB WILD-TYPE 221 259
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TWISTNB MUTATED      4    5
  TWISTNB WILD-TYPE  221  259
        clus
vv       TWISTNB MUTATED TWISTNB WILD-TYPE
  FEMALE               4               221
  MALE                 5               259
[1] 2 2
[1] FALSE
D336V9, binary
                   cls
clus                  0   1
  TWISTNB MUTATED     7   1
  TWISTNB WILD-TYPE 343  21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TWISTNB MUTATED      7    1
  TWISTNB WILD-TYPE  343   21
     clus
vv    TWISTNB MUTATED TWISTNB WILD-TYPE
  NO                7               343
  YES               1                21
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  TWISTNB MUTATED                      8                             0
  TWISTNB WILD-TYPE                  307                            47
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  TWISTNB MUTATED                       1                              0
  TWISTNB WILD-TYPE                   105                             10
D336V10, multiclass
                                clus
vv                               TWISTNB MUTATED TWISTNB WILD-TYPE
  COLON ADENOCARCINOMA                         8               307
  COLON MUCINOUS ADENOCARCINOMA                0                47
  RECTAL ADENOCARCINOMA                        1               105
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  TWISTNB MUTATED     6   0   0   0
  TWISTNB WILD-TYPE 339   4  31  25
D336V11, multiclass
    clus
vv   TWISTNB MUTATED TWISTNB WILD-TYPE
  R0               6               339
  R1               0                 4
  R2               0                31
  RX               0                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D336V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TWISTNB MUTATED                                  0     0
  TWISTNB WILD-TYPE                                1    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  TWISTNB MUTATED                           1     6
  TWISTNB WILD-TYPE                        21   220
D336V13, multiclass
                                  clus
vv                                 TWISTNB MUTATED TWISTNB WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                      1                21
  WHITE                                          6               220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(337) Variable = PKDREJ MUTATION ANALYSIS
D337V1, survival
                  sevent
clus2                0   1
  PKDREJ MUTATED    29   5
  PKDREJ WILD-TYPE 349  88
  PKDREJ MUTATED PKDREJ WILD-TYPE 
              34              437 
  PKDREJ MUTATED PKDREJ WILD-TYPE 
               5               88 
$`PKDREJ MUTATED`
TCGA-A6-5666 TCGA-A6-6781 TCGA-AA-3663 TCGA-AA-3688 TCGA-AA-3950 TCGA-AA-3977 
       32.71        19.66         6.97        19.00        24.00        25.02 
TCGA-AA-A00J TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A017 TCGA-AD-6889 TCGA-AU-6004 
       18.05         4.01        34.98         1.02        56.55        27.09 
TCGA-AY-6197 TCGA-AZ-4315 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4952 TCGA-CK-5913 
       21.44        58.39        12.76        10.06        15.62        51.32 
TCGA-CM-5349 TCGA-CM-5868 TCGA-CM-6162 TCGA-D5-6535 TCGA-D5-6540 TCGA-D5-6898 
       30.08        17.03        12.00        15.12        16.14         1.48 
TCGA-DM-A0XD TCGA-F4-6570 TCGA-G4-6299 TCGA-G4-6304 TCGA-G4-6628 TCGA-AG-A002 
       24.43         6.18        74.56        53.62        79.69        20.98 
TCGA-AH-6544 TCGA-CI-6624 TCGA-DY-A1DF TCGA-F5-6465 
       38.56         4.73        24.13        49.51 

$`PKDREJ WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        22.06        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
       11.01         5.98        37.05        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       33.01        26.01         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       21.99        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 
       40.96         0.07        21.37        15.52         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
       16.31         0.95        33.01        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 
       12.20        14.30        17.56       148.01        85.45        49.08 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       22.98        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       15.02         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       18.25         1.32        43.27        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       12.49        15.58         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       11.38        10.26       119.70        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       35.74        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       65.85        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       46.75        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6547 TCGA-AH-6549 
       61.97        41.00        38.04       117.11         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CL-5917 
        0.69         0.72         6.05        33.17         6.97        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       41.36        57.24        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6571 TCGA-F5-6702 
       19.96        20.91        18.28         9.96        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  PKDREJ MUTATED PKDREJ WILD-TYPE 
            1.02             0.00 
  PKDREJ MUTATED PKDREJ WILD-TYPE 
           79.69           148.01 
  PKDREJ MUTATED PKDREJ WILD-TYPE 
           21.21            20.12 
[1] "1.0 - 79.7 (21.2)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.4"
D337V2, continuous
D337V3, binary
                  cls
clus                 0   1
  PKDREJ MUTATED    31   5
  PKDREJ WILD-TYPE 335 114
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PKDREJ MUTATED     31    5
  PKDREJ WILD-TYPE  335  114
        clus
vv       PKDREJ MUTATED PKDREJ WILD-TYPE
  COLON              31              335
  RECTUM              5              114
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PKDREJ MUTATED         6        0        1        13         3         1
  PKDREJ WILD-TYPE      85        1       31       125         7         0
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PKDREJ MUTATED           1          0          3          4        1
  PKDREJ WILD-TYPE        23         11         56         38       47
                  vv
clus               STAGE IVA STAGE IVB
  PKDREJ MUTATED           1         0
  PKDREJ WILD-TYPE        17         1
D337V4, multiclass
            clus
vv           PKDREJ MUTATED PKDREJ WILD-TYPE
  STAGE I                 6               85
  STAGE IA                0                1
  STAGE II                1               31
  STAGE IIA              13              125
  STAGE IIB               3                7
  STAGE IIC               1                0
  STAGE III               1               23
  STAGE IIIA              0               11
  STAGE IIIB              3               56
  STAGE IIIC              4               38
  STAGE IV                1               47
  STAGE IVA               1               17
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  PKDREJ MUTATED     0   7  21   8
  PKDREJ WILD-TYPE  17  85 308  42
D337V5, multiclass
    clus
vv   PKDREJ MUTATED PKDREJ WILD-TYPE
  T1              0               17
  T2              7               85
  T3             21              308
  T4              8               42
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  PKDREJ MUTATED    25   7   4
  PKDREJ WILD-TYPE 262 106  83
D337V6, multiclass
    clus
vv   PKDREJ MUTATED PKDREJ WILD-TYPE
  N0             25              262
  N1              7              106
  N2              4               83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D337V7, binary
                  cls
clus                 0   1
  PKDREJ MUTATED    28   3
  PKDREJ WILD-TYPE 347  62
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PKDREJ MUTATED     28    3
  PKDREJ WILD-TYPE  347   62
   clus
vv  PKDREJ MUTATED PKDREJ WILD-TYPE
  0             28              347
  1              3               62
[1] 2 2
[1] FALSE
D337V8, binary
                  cls
clus                 0   1
  PKDREJ MUTATED    17  19
  PKDREJ WILD-TYPE 208 245
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PKDREJ MUTATED     17   19
  PKDREJ WILD-TYPE  208  245
        clus
vv       PKDREJ MUTATED PKDREJ WILD-TYPE
  FEMALE             17              208
  MALE               19              245
[1] 2 2
[1] FALSE
D337V9, binary
                  cls
clus                 0   1
  PKDREJ MUTATED    25   0
  PKDREJ WILD-TYPE 325  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PKDREJ MUTATED     25    0
  PKDREJ WILD-TYPE  325   22
     clus
vv    PKDREJ MUTATED PKDREJ WILD-TYPE
  NO              25              325
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PKDREJ MUTATED                     23                             8
  PKDREJ WILD-TYPE                  292                            39
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PKDREJ MUTATED                       5                              0
  PKDREJ WILD-TYPE                   101                             10
D337V10, multiclass
                                clus
vv                               PKDREJ MUTATED PKDREJ WILD-TYPE
  COLON ADENOCARCINOMA                       23              292
  COLON MUCINOUS ADENOCARCINOMA               8               39
  RECTAL ADENOCARCINOMA                       5              101
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  PKDREJ MUTATED    23   0   1   5
  PKDREJ WILD-TYPE 322   4  30  20
D337V11, multiclass
    clus
vv   PKDREJ MUTATED PKDREJ WILD-TYPE
  R0             23              322
  R1              0                4
  R2              1               30
  RX              5               20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D337V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PKDREJ MUTATED                                  0     3
  PKDREJ WILD-TYPE                                1     8
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  PKDREJ MUTATED                           0    22
  PKDREJ WILD-TYPE                        22   204
D337V13, multiclass
                                  clus
vv                                 PKDREJ MUTATED PKDREJ WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         3                8
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                        22              204
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(338) Variable = SYNE1 MUTATION ANALYSIS
D338V1, survival
                 sevent
clus2               0   1
  SYNE1 MUTATED   107  31
  SYNE1 WILD-TYPE 271  62
  SYNE1 MUTATED SYNE1 WILD-TYPE 
            138             333 
  SYNE1 MUTATED SYNE1 WILD-TYPE 
             31              62 
$`SYNE1 MUTATED`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2683 TCGA-A6-3808 
       43.76        46.65        42.90        24.33        16.57        33.34 
TCGA-A6-4105 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6141 
       14.53        29.19        33.53        22.06        32.71         8.38 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3492 
       25.18        24.16        21.76        19.66        20.28         3.02 
TCGA-AA-3510 TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3522 TCGA-AA-3525 TCGA-AA-3543 
       63.98        13.02         1.02        37.05         8.05         0.99 
TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3562 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       29.95        20.98        19.99         6.97        54.02         2.01 
TCGA-AA-3672 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3833 TCGA-AA-3845 
        0.92        85.05        26.99        19.04        15.95         0.00 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3875 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3977 
        0.00        36.03        18.05        26.01        24.00        25.02 
TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A00E TCGA-AA-A00N TCGA-AA-A00U 
       27.02         7.96        27.02        30.02         4.01        17.03 
TCGA-AA-A010 TCGA-AA-A01Q TCGA-AA-A02K TCGA-AA-A02W TCGA-AD-5900 TCGA-AD-6888 
       34.98         1.02        14.01        41.00         0.07        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AU-6004 TCGA-AY-5543 TCGA-AY-6197 
       56.55         0.79         0.72        27.09        33.01        21.44 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-CA-5797 
       58.39         1.41        88.21        49.41         6.77         3.29 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4952 TCGA-CK-6751 
       12.20        12.76        10.06        14.30        15.62       124.27 
TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       23.05        37.02        13.02        29.06        22.03        22.98 
TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6171 
       15.02        15.02        15.02        15.02        12.00        14.04 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-5541 
       11.01        10.06        12.03        12.26        56.09        55.92 
TCGA-D5-6534 TCGA-D5-6539 TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       43.27        12.49        14.30         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-DM-A0XF TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HB 
        1.51        12.00        38.20       140.38        44.32       135.65 
TCGA-DM-A285 TCGA-DM-A28F TCGA-F4-6460 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6809 
        6.12        35.97        31.96         6.18        47.87        13.25 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6626 
       85.48        63.62        22.09        35.80        26.17        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2691 TCGA-AF-6672 TCGA-AG-3594 TCGA-AG-3731 
       79.69        24.13        43.04        10.39         2.01        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-A002 TCGA-AG-A015 
       32.98         0.99        13.02        14.01        20.98        36.03 
TCGA-AG-A025 TCGA-AG-A02N TCGA-AG-A036 TCGA-AH-6644 TCGA-CI-6624 TCGA-DY-A1DF 
       49.97        61.97       117.11         0.72         4.73        24.13 
TCGA-DY-A1DG TCGA-EF-5830 TCGA-EI-6507 TCGA-EI-6510 TCGA-F5-6464 TCGA-G5-6235 
       51.48         0.49        19.96        18.28         9.96        55.76 

$`SYNE1 WILD-TYPE`
TCGA-A6-2674 TCGA-A6-2678 TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 
       43.76        42.28        34.65        32.75        36.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-6137 TCGA-A6-6138 
       31.63        30.44        23.61        22.09        27.09        22.52 
TCGA-A6-6142 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-AA-3489 
       25.08        24.69        24.39        23.87        20.12         7.04 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3519 
        1.02        35.01         6.97         1.02        38.99         9.07 
TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       24.03        36.03        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 
       29.00        29.00        26.01        12.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 
       21.01        13.02        24.00        17.95        23.01        19.99 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3667 TCGA-AA-3673 
       13.94        61.02        78.08         6.05        14.01        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       36.00         5.03        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3837 TCGA-AA-3842 
        0.99        25.02         1.02        17.98        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3855 
       14.93        17.03        10.06         0.00        33.07        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       24.03        27.02        29.98        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3986 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       24.00        27.02        19.07        13.94        38.04        19.00 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
        0.99        14.99        21.99         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01R TCGA-AA-A01S 
       12.00        31.00        31.00        38.07        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02Y TCGA-AA-A03F 
       39.98         2.01         5.03         0.92        39.98        18.05 
TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
       40.96        21.37         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6386 TCGA-AZ-4616 
        0.20        14.50        16.31         0.95        17.82         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
      106.75        22.36        62.79        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-6715 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 
        3.25         0.07        17.56       148.01        85.45        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CM-4744 
       51.32         9.99        21.14        82.95         1.91        20.02 
TCGA-CM-4747 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5868 TCGA-CM-6163 
       25.02        30.08        32.02         5.03        17.03         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       15.02        11.01        12.95        13.05        11.08        11.08 
TCGA-D5-5537 TCGA-D5-5539 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6535 
       45.40        19.59        20.19        18.25         1.32        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
       17.85         4.80        17.13        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 TCGA-D5-6932 TCGA-D5-7000 
        3.68         4.41        12.43         9.04        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
      119.70        24.43       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A28C TCGA-DM-A28E 
       12.59         7.50       131.51       139.17        81.37       119.93 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6569 TCGA-F4-6704 
       60.79       117.07        98.24         8.61        35.74         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6854 TCGA-F4-6855 
       34.42        41.42        16.24        33.67         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6625 TCGA-AF-2689 
       55.04        61.91        36.00        13.78        91.79        39.48 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       15.39        20.02        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
       34.03        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3878 
       19.99        13.94        19.99         7.99         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       35.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A016 TCGA-AG-A01L 
       25.97        23.01        37.02        15.95         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X 
       70.03        64.01        10.98         1.94        38.96        41.00 
TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-CI-6619 
       38.04        38.56         1.45        17.49         0.69         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
       33.17         6.97        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1H8 
        5.03         5.29       126.44        41.36        57.24        32.61 
TCGA-EI-6506 TCGA-EI-6508 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       20.55        20.91        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6641 
        0.66         0.69        26.43 

  SYNE1 MUTATED SYNE1 WILD-TYPE 
              0               0 
  SYNE1 MUTATED SYNE1 WILD-TYPE 
         140.38          148.01 
  SYNE1 MUTATED SYNE1 WILD-TYPE 
          20.98           20.05 
[1] "0.0 - 140.4 (21.0)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.2"
D338V2, continuous
D338V3, binary
                 cls
clus                0   1
  SYNE1 MUTATED   118  24
  SYNE1 WILD-TYPE 248  95
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SYNE1 MUTATED    118   24
  SYNE1 WILD-TYPE  248   95
        clus
vv       SYNE1 MUTATED SYNE1 WILD-TYPE
  COLON            118             248
  RECTUM            24              95
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SYNE1 MUTATED        23        0        8        43         6         1
  SYNE1 WILD-TYPE      68        1       24        95         4         0
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SYNE1 MUTATED           6          2         23         10       10         6
  SYNE1 WILD-TYPE        18          9         36         32       38        12
                 vv
clus              STAGE IVB
  SYNE1 MUTATED           0
  SYNE1 WILD-TYPE         1
D338V4, multiclass
            clus
vv           SYNE1 MUTATED SYNE1 WILD-TYPE
  STAGE I               23              68
  STAGE IA               0               1
  STAGE II               8              24
  STAGE IIA             43              95
  STAGE IIB              6               4
  STAGE IIC              1               0
  STAGE III              6              18
  STAGE IIIA             2               9
  STAGE IIIB            23              36
  STAGE IIIC            10              32
  STAGE IV              10              38
  STAGE IVA              6              12
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  SYNE1 MUTATED     8  20  96  18
  SYNE1 WILD-TYPE   9  72 233  32
D338V5, multiclass
    clus
vv   SYNE1 MUTATED SYNE1 WILD-TYPE
  T1             8               9
  T2            20              72
  T3            96             233
  T4            18              32
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  SYNE1 MUTATED    88  35  18
  SYNE1 WILD-TYPE 199  78  69
D338V6, multiclass
    clus
vv   SYNE1 MUTATED SYNE1 WILD-TYPE
  N0            88             199
  N1            35              78
  N2            18              69
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D338V7, binary
                 cls
clus                0   1
  SYNE1 MUTATED   111  14
  SYNE1 WILD-TYPE 264  51
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SYNE1 MUTATED    111   14
  SYNE1 WILD-TYPE  264   51
   clus
vv  SYNE1 MUTATED SYNE1 WILD-TYPE
  0           111             264
  1            14              51
[1] 2 2
[1] FALSE
D338V8, binary
                 cls
clus                0   1
  SYNE1 MUTATED    65  77
  SYNE1 WILD-TYPE 160 187
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SYNE1 MUTATED     65   77
  SYNE1 WILD-TYPE  160  187
        clus
vv       SYNE1 MUTATED SYNE1 WILD-TYPE
  FEMALE            65             160
  MALE              77             187
[1] 2 2
[1] FALSE
D338V9, binary
                 cls
clus                0   1
  SYNE1 MUTATED   105   5
  SYNE1 WILD-TYPE 245  17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SYNE1 MUTATED    105    5
  SYNE1 WILD-TYPE  245   17
     clus
vv    SYNE1 MUTATED SYNE1 WILD-TYPE
  NO            105             245
  YES             5              17
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SYNE1 MUTATED                     96                            20
  SYNE1 WILD-TYPE                  219                            27
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SYNE1 MUTATED                      23                              1
  SYNE1 WILD-TYPE                    83                              9
D338V10, multiclass
                                clus
vv                               SYNE1 MUTATED SYNE1 WILD-TYPE
  COLON ADENOCARCINOMA                      96             219
  COLON MUCINOUS ADENOCARCINOMA             20              27
  RECTAL ADENOCARCINOMA                     23              83
  RECTAL MUCINOUS ADENOCARCINOMA             1               9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  SYNE1 MUTATED    99   1   6   7
  SYNE1 WILD-TYPE 246   3  25  18
D338V11, multiclass
    clus
vv   SYNE1 MUTATED SYNE1 WILD-TYPE
  R0            99             246
  R1             1               3
  R2             6              25
  RX             7              18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D338V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SYNE1 MUTATED                                  0     6
  SYNE1 WILD-TYPE                                1     5
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  SYNE1 MUTATED                           7    80
  SYNE1 WILD-TYPE                        15   146
D338V13, multiclass
                                  clus
vv                                 SYNE1 MUTATED SYNE1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        6               5
  BLACK OR AFRICAN AMERICAN                    7              15
  WHITE                                       80             146
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(339) Variable = WNT16 MUTATION ANALYSIS
D339V1, survival
                 sevent
clus2               0   1
  WNT16 MUTATED     5   2
  WNT16 WILD-TYPE 373  91
  WNT16 MUTATED WNT16 WILD-TYPE 
              7             464 
  WNT16 MUTATED WNT16 WILD-TYPE 
              2              91 
$`WNT16 MUTATED`
TCGA-A6-6781 TCGA-AA-3492 TCGA-AA-3660 TCGA-AA-A010 TCGA-AZ-4315 TCGA-AZ-5403 
       19.66         3.02        78.08        34.98        58.39        62.79 
TCGA-D5-6928 
       11.64 

$`WNT16 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 
       23.87        20.12        20.28         7.04         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       13.94        19.99        61.02         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5407 
       17.82         1.41         5.13       106.75        22.36        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.04         9.44         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  WNT16 MUTATED WNT16 WILD-TYPE 
           3.02            0.00 
  WNT16 MUTATED WNT16 WILD-TYPE 
          78.08          148.01 
  WNT16 MUTATED WNT16 WILD-TYPE 
         34.980          20.155 
[1] "3.0 - 78.1 (35.0)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.1"
D339V2, continuous
D339V3, binary
                 cls
clus                0   1
  WNT16 MUTATED     8   0
  WNT16 WILD-TYPE 358 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WNT16 MUTATED      8    0
  WNT16 WILD-TYPE  358  119
        clus
vv       WNT16 MUTATED WNT16 WILD-TYPE
  COLON              8             358
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  WNT16 MUTATED         0        0        3         2         2         0
  WNT16 WILD-TYPE      91        1       29       136         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  WNT16 MUTATED           0          0          0          1        0         0
  WNT16 WILD-TYPE        24         11         59         41       48        18
                 vv
clus              STAGE IVB
  WNT16 MUTATED           0
  WNT16 WILD-TYPE         1
D339V4, multiclass
            clus
vv           WNT16 MUTATED WNT16 WILD-TYPE
  STAGE I                0              91
  STAGE IA               0               1
  STAGE II               3              29
  STAGE IIA              2             136
  STAGE IIB              2               8
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             1              41
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  WNT16 MUTATED     0   0   5   3
  WNT16 WILD-TYPE  17  92 324  47
D339V5, multiclass
    clus
vv   WNT16 MUTATED WNT16 WILD-TYPE
  T1             0              17
  T2             0              92
  T3             5             324
  T4             3              47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  WNT16 MUTATED     7   1   0
  WNT16 WILD-TYPE 280 112  87
D339V6, multiclass
    clus
vv   WNT16 MUTATED WNT16 WILD-TYPE
  N0             7             280
  N1             1             112
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D339V7, binary
                 cls
clus                0   1
  WNT16 MUTATED     5   0
  WNT16 WILD-TYPE 370  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WNT16 MUTATED      5    0
  WNT16 WILD-TYPE  370   65
   clus
vv  WNT16 MUTATED WNT16 WILD-TYPE
  0             5             370
  1             0              65
[1] 2 2
[1] FALSE
D339V8, binary
                 cls
clus                0   1
  WNT16 MUTATED     4   4
  WNT16 WILD-TYPE 221 260
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WNT16 MUTATED      4    4
  WNT16 WILD-TYPE  221  260
        clus
vv       WNT16 MUTATED WNT16 WILD-TYPE
  FEMALE             4             221
  MALE               4             260
[1] 2 2
[1] FALSE
D339V9, binary
                 cls
clus                0   1
  WNT16 MUTATED     7   0
  WNT16 WILD-TYPE 343  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WNT16 MUTATED      7    0
  WNT16 WILD-TYPE  343   22
     clus
vv    WNT16 MUTATED WNT16 WILD-TYPE
  NO              7             343
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  WNT16 MUTATED                      6                             2
  WNT16 WILD-TYPE                  309                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  WNT16 MUTATED                       0                              0
  WNT16 WILD-TYPE                   106                             10
D339V10, multiclass
                                clus
vv                               WNT16 MUTATED WNT16 WILD-TYPE
  COLON ADENOCARCINOMA                       6             309
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  WNT16 MUTATED     6   0   0   1
  WNT16 WILD-TYPE 339   4  31  24
D339V11, multiclass
    clus
vv   WNT16 MUTATED WNT16 WILD-TYPE
  R0             6             339
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D339V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  WNT16 MUTATED                                  0     0
  WNT16 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  WNT16 MUTATED                           0     5
  WNT16 WILD-TYPE                        22   221
D339V13, multiclass
                                  clus
vv                                 WNT16 MUTATED WNT16 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        5             221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(340) Variable = ZNF189 MUTATION ANALYSIS
D340V1, survival
                  sevent
clus2                0   1
  ZNF189 MUTATED    18   1
  ZNF189 WILD-TYPE 360  92
  ZNF189 MUTATED ZNF189 WILD-TYPE 
              19              452 
  ZNF189 MUTATED ZNF189 WILD-TYPE 
               1               92 
$`ZNF189 MUTATED`
TCGA-A6-5659 TCGA-A6-5665 TCGA-A6-6781 TCGA-AA-3510 TCGA-AA-3815 TCGA-AD-5900 
       30.44        22.06        19.66        63.98        33.04         0.07 
TCGA-AZ-4315 TCGA-AZ-4681 TCGA-CA-6716 TCGA-CA-6717 TCGA-CM-6164 TCGA-CM-6168 
       58.39       106.75        12.20        12.76        29.03        12.99 
TCGA-CM-6172 TCGA-D5-6532 TCGA-D5-6541 TCGA-D5-6926 TCGA-G4-6317 TCGA-AF-5654 
       11.01        18.25        15.58         9.04        36.00        16.83 
TCGA-AG-A002 
       20.98 

$`ZNF189 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        29.19        33.53        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 
       20.28         7.04         3.02         1.02        35.01         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
       26.99        19.04        19.04        10.06        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
       16.31         0.95        33.01        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
        5.13        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6169 TCGA-CM-6170 
        2.96        16.04        21.99        14.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       14.04        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       55.92        20.19         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6898 TCGA-D5-6920 
        4.80        17.13        12.49        16.14         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
        4.41        12.43        14.30         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       34.49        10.39        14.50        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  ZNF189 MUTATED ZNF189 WILD-TYPE 
            0.07             0.00 
  ZNF189 MUTATED ZNF189 WILD-TYPE 
          106.75           148.01 
  ZNF189 MUTATED ZNF189 WILD-TYPE 
          19.660           20.235 
[1] "0.1 - 106.8 (19.7)" "0.0 - 148.0 (20.2)"
[1] "hr=" "4.1"
D340V2, continuous
D340V3, binary
                  cls
clus                 0   1
  ZNF189 MUTATED    17   2
  ZNF189 WILD-TYPE 349 117
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF189 MUTATED     17    2
  ZNF189 WILD-TYPE  349  117
        clus
vv       ZNF189 MUTATED ZNF189 WILD-TYPE
  COLON              17              349
  RECTUM              2              117
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZNF189 MUTATED         4        0        1        10         0         0
  ZNF189 WILD-TYPE      87        1       31       128        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF189 MUTATED           0          0          2          2        0
  ZNF189 WILD-TYPE        24         11         57         40       48
                  vv
clus               STAGE IVA STAGE IVB
  ZNF189 MUTATED           0         0
  ZNF189 WILD-TYPE        18         1
D340V4, multiclass
            clus
vv           ZNF189 MUTATED ZNF189 WILD-TYPE
  STAGE I                 4               87
  STAGE IA                0                1
  STAGE II                1               31
  STAGE IIA              10              128
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              2               57
  STAGE IIIC              2               40
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZNF189 MUTATED     0   4  13   2
  ZNF189 WILD-TYPE  17  88 316  48
D340V5, multiclass
    clus
vv   ZNF189 MUTATED ZNF189 WILD-TYPE
  T1              0               17
  T2              4               88
  T3             13              316
  T4              2               48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  ZNF189 MUTATED    15   3   1
  ZNF189 WILD-TYPE 272 110  86
D340V6, multiclass
    clus
vv   ZNF189 MUTATED ZNF189 WILD-TYPE
  N0             15              272
  N1              3              110
  N2              1               86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D340V7, binary
                  cls
clus                 0   1
  ZNF189 MUTATED    16   0
  ZNF189 WILD-TYPE 359  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF189 MUTATED     16    0
  ZNF189 WILD-TYPE  359   65
   clus
vv  ZNF189 MUTATED ZNF189 WILD-TYPE
  0             16              359
  1              0               65
[1] 2 2
[1] FALSE
D340V8, binary
                  cls
clus                 0   1
  ZNF189 MUTATED     8  11
  ZNF189 WILD-TYPE 217 253
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF189 MUTATED      8   11
  ZNF189 WILD-TYPE  217  253
        clus
vv       ZNF189 MUTATED ZNF189 WILD-TYPE
  FEMALE              8              217
  MALE               11              253
[1] 2 2
[1] FALSE
D340V9, binary
                  cls
clus                 0   1
  ZNF189 MUTATED    17   1
  ZNF189 WILD-TYPE 333  21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF189 MUTATED     17    1
  ZNF189 WILD-TYPE  333   21
     clus
vv    ZNF189 MUTATED ZNF189 WILD-TYPE
  NO              17              333
  YES              1               21
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ZNF189 MUTATED                     14                             3
  ZNF189 WILD-TYPE                  301                            44
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ZNF189 MUTATED                       2                              0
  ZNF189 WILD-TYPE                   104                             10
D340V10, multiclass
                                clus
vv                               ZNF189 MUTATED ZNF189 WILD-TYPE
  COLON ADENOCARCINOMA                       14              301
  COLON MUCINOUS ADENOCARCINOMA               3               44
  RECTAL ADENOCARCINOMA                       2              104
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ZNF189 MUTATED    17   0   0   2
  ZNF189 WILD-TYPE 328   4  31  23
D340V11, multiclass
    clus
vv   ZNF189 MUTATED ZNF189 WILD-TYPE
  R0             17              328
  R1              0                4
  R2              0               31
  RX              2               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D340V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF189 MUTATED                                  0     2
  ZNF189 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZNF189 MUTATED                           1    13
  ZNF189 WILD-TYPE                        21   213
D340V13, multiclass
                                  clus
vv                                 ZNF189 MUTATED ZNF189 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                9
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                        13              213
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(341) Variable = TRRAP MUTATION ANALYSIS
D341V1, survival
                 sevent
clus2               0   1
  TRRAP MUTATED    40  13
  TRRAP WILD-TYPE 338  80
  TRRAP MUTATED TRRAP WILD-TYPE 
             53             418 
  TRRAP MUTATED TRRAP WILD-TYPE 
             13              80 
$`TRRAP MUTATED`
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-6138 
       42.90        42.28        31.63        29.19        23.61        22.52 
TCGA-A6-6781 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3510 TCGA-AA-3552 TCGA-AA-3663 
       19.66         3.02         1.02        63.98        13.02         6.97 
TCGA-AA-3672 TCGA-AA-3678 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3815 
        0.92        47.01        26.99        19.04        10.06        33.04 
TCGA-AA-A00A TCGA-AA-A010 TCGA-AA-A01P TCGA-AA-A01R TCGA-AD-6901 TCGA-AZ-4315 
       38.04        34.98        38.07        35.01        22.42        58.39 
TCGA-AZ-4681 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4952 
      106.75        88.21         6.77        10.06        17.56        15.62 
TCGA-CK-5913 TCGA-CK-5916 TCGA-CM-4752 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-6171 
       51.32        21.14        13.02        32.02        15.02        14.04 
TCGA-D5-5539 TCGA-D5-6535 TCGA-D5-6930 TCGA-DM-A1D4 TCGA-DM-A1HA TCGA-F4-6808 
       19.59        15.12         1.51        92.75       131.51        33.67 
TCGA-G4-6306 TCGA-G4-6586 TCGA-G4-6628 TCGA-AG-3892 TCGA-AG-A002 TCGA-AG-A02N 
       44.68        35.80        79.69        13.02        20.98        61.97 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DY-A1DG TCGA-F5-6571 TCGA-F5-6813 
       10.98        19.99        51.48        31.30         0.69 

$`TRRAP WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2683 TCGA-A6-3807 
       43.76        46.65        43.76        24.33        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5659 
       33.34        32.75        36.53        14.53        32.91        30.44 
TCGA-A6-5661 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6141 
       33.53        22.09        22.06        32.71        27.09         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3502 TCGA-AA-3511 
       23.87        20.12        20.28         7.04        35.01         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       14.01        33.99        21.01        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
       78.08         6.05        54.02         2.01        14.01        50.04 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
        5.03        85.05        19.04        35.05         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       13.94        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       31.00        31.00         1.02         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        0.72         5.79        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6600 
        1.41         5.13        22.36        62.79        49.41        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5914 
       12.76        14.30       148.01        85.45        49.08         9.99 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5862 
       25.02        29.06        22.03        22.98        30.08         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       15.02        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 
       11.01        10.06        12.03        45.40        12.26        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 
       55.92        20.19        18.25         1.32        43.27        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       11.64         4.80        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       24.43        38.20       130.65        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
      140.38         7.50        44.32       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       34.42        41.42        16.24        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6307 
       35.31       133.18        74.56        65.85        53.62        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       26.17        91.79        46.75        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 
       19.99         1.02        17.95        36.95        17.03        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       38.96        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       27.95         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       41.36        57.24        24.13        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6702 
       19.96        20.91        18.28         9.96        49.51        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66        55.76        26.43 

  TRRAP MUTATED TRRAP WILD-TYPE 
           0.69            0.00 
  TRRAP MUTATED TRRAP WILD-TYPE 
         131.51          148.01 
  TRRAP MUTATED TRRAP WILD-TYPE 
         23.610          20.005 
[1] "0.7 - 131.5 (23.6)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1"  
D341V2, continuous
D341V3, binary
                 cls
clus                0   1
  TRRAP MUTATED    49   8
  TRRAP WILD-TYPE 317 111
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRRAP MUTATED     49    8
  TRRAP WILD-TYPE  317  111
        clus
vv       TRRAP MUTATED TRRAP WILD-TYPE
  COLON             49             317
  RECTUM             8             111
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TRRAP MUTATED        12        0        7        16         3         0
  TRRAP WILD-TYPE      79        1       25       122         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TRRAP MUTATED           5          1          4          6        0         2
  TRRAP WILD-TYPE        19         10         55         36       48        16
                 vv
clus              STAGE IVB
  TRRAP MUTATED           0
  TRRAP WILD-TYPE         1
D341V4, multiclass
            clus
vv           TRRAP MUTATED TRRAP WILD-TYPE
  STAGE I               12              79
  STAGE IA               0               1
  STAGE II               7              25
  STAGE IIA             16             122
  STAGE IIB              3               7
  STAGE IIC              0               1
  STAGE III              5              19
  STAGE IIIA             1              10
  STAGE IIIB             4              55
  STAGE IIIC             6              36
  STAGE IV               0              48
  STAGE IVA              2              16
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  TRRAP MUTATED     4  10  35   8
  TRRAP WILD-TYPE  13  82 294  42
D341V5, multiclass
    clus
vv   TRRAP MUTATED TRRAP WILD-TYPE
  T1             4              13
  T2            10              82
  T3            35             294
  T4             8              42
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  TRRAP MUTATED    39  10   8
  TRRAP WILD-TYPE 248 103  79
D341V6, multiclass
    clus
vv   TRRAP MUTATED TRRAP WILD-TYPE
  N0            39             248
  N1            10             103
  N2             8              79
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D341V7, binary
                 cls
clus                0   1
  TRRAP MUTATED    48   2
  TRRAP WILD-TYPE 327  63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRRAP MUTATED     48    2
  TRRAP WILD-TYPE  327   63
   clus
vv  TRRAP MUTATED TRRAP WILD-TYPE
  0            48             327
  1             2              63
[1] 2 2
[1] FALSE
D341V8, binary
                 cls
clus                0   1
  TRRAP MUTATED    27  30
  TRRAP WILD-TYPE 198 234
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRRAP MUTATED     27   30
  TRRAP WILD-TYPE  198  234
        clus
vv       TRRAP MUTATED TRRAP WILD-TYPE
  FEMALE            27             198
  MALE              30             234
[1] 2 2
[1] FALSE
D341V9, binary
                 cls
clus                0   1
  TRRAP MUTATED    43   1
  TRRAP WILD-TYPE 307  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRRAP MUTATED     43    1
  TRRAP WILD-TYPE  307   21
     clus
vv    TRRAP MUTATED TRRAP WILD-TYPE
  NO             43             307
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  TRRAP MUTATED                     44                             5
  TRRAP WILD-TYPE                  271                            42
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  TRRAP MUTATED                       8                              0
  TRRAP WILD-TYPE                    98                             10
D341V10, multiclass
                                clus
vv                               TRRAP MUTATED TRRAP WILD-TYPE
  COLON ADENOCARCINOMA                      44             271
  COLON MUCINOUS ADENOCARCINOMA              5              42
  RECTAL ADENOCARCINOMA                      8              98
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  TRRAP MUTATED    40   0   0   8
  TRRAP WILD-TYPE 305   4  31  17
D341V11, multiclass
    clus
vv   TRRAP MUTATED TRRAP WILD-TYPE
  R0            40             305
  R1             0               4
  R2             0              31
  RX             8              17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D341V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TRRAP MUTATED                                  0     1
  TRRAP WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  TRRAP MUTATED                           3    33
  TRRAP WILD-TYPE                        19   193
D341V13, multiclass
                                  clus
vv                                 TRRAP MUTATED TRRAP WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    3              19
  WHITE                                       33             193
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(342) Variable = C14ORF43 MUTATION ANALYSIS
D342V1, survival
                    sevent
clus2                  0   1
  C14ORF43 MUTATED    17   3
  C14ORF43 WILD-TYPE 361  90
  C14ORF43 MUTATED C14ORF43 WILD-TYPE 
                20                451 
  C14ORF43 MUTATED C14ORF43 WILD-TYPE 
                 3                 90 
$`C14ORF43 MUTATED`
TCGA-A6-3809 TCGA-AA-3518 TCGA-AA-3663 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3864 
       32.75         1.02         6.97        26.99        19.04        53.00 
TCGA-AD-5900 TCGA-AD-6889 TCGA-AZ-6598 TCGA-AZ-6601 TCGA-CA-6717 TCGA-CK-5916 
        0.07        56.55        49.41       100.01        12.76        21.14 
TCGA-CM-6170 TCGA-CM-6171 TCGA-D5-6930 TCGA-G4-6309 TCGA-G4-6588 TCGA-G4-6625 
       15.02        14.04         1.51        85.48        26.17        91.79 
TCGA-AG-3896 TCGA-EI-6507 
        1.02        19.96 

$`C14ORF43 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       85.05        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       30.05        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 
        0.92        41.00        39.98        18.05        40.96        21.37 
TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       15.52         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 
      106.75        22.36        62.79        88.21         6.77        12.10 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07        12.20        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       51.32         9.99        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6172 
       16.04        21.99        14.99        12.99        13.02        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       11.64         4.80        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 
       65.85        53.62        44.68        55.04        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6626 TCGA-G4-6628 
       36.00        22.09        13.78        35.80        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3898 
       36.95        17.03        13.02        35.01        14.01        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
        0.49        20.55        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  C14ORF43 MUTATED C14ORF43 WILD-TYPE 
              0.07               0.00 
  C14ORF43 MUTATED C14ORF43 WILD-TYPE 
            100.01             148.01 
  C14ORF43 MUTATED C14ORF43 WILD-TYPE 
             20.55              20.19 
[1] "0.1 - 100.0 (20.6)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.7"
D342V2, continuous
D342V3, binary
                    cls
clus                   0   1
  C14ORF43 MUTATED    18   2
  C14ORF43 WILD-TYPE 348 117
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C14ORF43 MUTATED     18    2
  C14ORF43 WILD-TYPE  348  117
        clus
vv       C14ORF43 MUTATED C14ORF43 WILD-TYPE
  COLON                18                348
  RECTUM                2                117
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  C14ORF43 MUTATED         5        0        4         8         1         0
  C14ORF43 WILD-TYPE      86        1       28       130         9         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C14ORF43 MUTATED           0          0          1          0        1
  C14ORF43 WILD-TYPE        24         11         58         42       47
                    vv
clus                 STAGE IVA STAGE IVB
  C14ORF43 MUTATED           0         0
  C14ORF43 WILD-TYPE        18         1
D342V4, multiclass
            clus
vv           C14ORF43 MUTATED C14ORF43 WILD-TYPE
  STAGE I                   5                 86
  STAGE IA                  0                  1
  STAGE II                  4                 28
  STAGE IIA                 8                130
  STAGE IIB                 1                  9
  STAGE IIC                 0                  1
  STAGE III                 0                 24
  STAGE IIIA                0                 11
  STAGE IIIB                1                 58
  STAGE IIIC                0                 42
  STAGE IV                  1                 47
  STAGE IVA                 0                 18
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  C14ORF43 MUTATED     1   4  14   1
  C14ORF43 WILD-TYPE  16  88 315  49
D342V5, multiclass
    clus
vv   C14ORF43 MUTATED C14ORF43 WILD-TYPE
  T1                1                 16
  T2                4                 88
  T3               14                315
  T4                1                 49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  C14ORF43 MUTATED    19   1   0
  C14ORF43 WILD-TYPE 268 112  87
D342V6, multiclass
    clus
vv   C14ORF43 MUTATED C14ORF43 WILD-TYPE
  N0               19                268
  N1                1                112
  N2                0                 87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D342V7, binary
                    cls
clus                   0   1
  C14ORF43 MUTATED    17   1
  C14ORF43 WILD-TYPE 358  64
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C14ORF43 MUTATED     17    1
  C14ORF43 WILD-TYPE  358   64
   clus
vv  C14ORF43 MUTATED C14ORF43 WILD-TYPE
  0               17                358
  1                1                 64
[1] 2 2
[1] FALSE
D342V8, binary
                    cls
clus                   0   1
  C14ORF43 MUTATED    11   9
  C14ORF43 WILD-TYPE 214 255
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C14ORF43 MUTATED     11    9
  C14ORF43 WILD-TYPE  214  255
        clus
vv       C14ORF43 MUTATED C14ORF43 WILD-TYPE
  FEMALE               11                214
  MALE                  9                255
[1] 2 2
[1] FALSE
D342V9, binary
                    cls
clus                   0   1
  C14ORF43 MUTATED    14   1
  C14ORF43 WILD-TYPE 336  21
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C14ORF43 MUTATED     14    1
  C14ORF43 WILD-TYPE  336   21
     clus
vv    C14ORF43 MUTATED C14ORF43 WILD-TYPE
  NO                14                336
  YES                1                 21
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  C14ORF43 MUTATED                     14                             4
  C14ORF43 WILD-TYPE                  301                            43
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  C14ORF43 MUTATED                       2                              0
  C14ORF43 WILD-TYPE                   104                             10
D342V10, multiclass
                                clus
vv                               C14ORF43 MUTATED C14ORF43 WILD-TYPE
  COLON ADENOCARCINOMA                         14                301
  COLON MUCINOUS ADENOCARCINOMA                 4                 43
  RECTAL ADENOCARCINOMA                         2                104
  RECTAL MUCINOUS ADENOCARCINOMA                0                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  C14ORF43 MUTATED    14   0   1   2
  C14ORF43 WILD-TYPE 331   4  30  23
D342V11, multiclass
    clus
vv   C14ORF43 MUTATED C14ORF43 WILD-TYPE
  R0               14                331
  R1                0                  4
  R2                1                 30
  RX                2                 23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D342V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C14ORF43 MUTATED                                  0     2
  C14ORF43 WILD-TYPE                                1     9
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  C14ORF43 MUTATED                           1    11
  C14ORF43 WILD-TYPE                        21   215
D342V13, multiclass
                                  clus
vv                                 C14ORF43 MUTATED C14ORF43 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           2                  9
  BLACK OR AFRICAN AMERICAN                       1                 21
  WHITE                                          11                215
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(343) Variable = LHCGR MUTATION ANALYSIS
D343V1, survival
                 sevent
clus2               0   1
  LHCGR MUTATED    18   5
  LHCGR WILD-TYPE 360  88
  LHCGR MUTATED LHCGR WILD-TYPE 
             23             448 
  LHCGR MUTATED LHCGR WILD-TYPE 
              5              88 
$`LHCGR MUTATED`
TCGA-A6-3808 TCGA-AA-3510 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-A00O TCGA-AA-A029 
       33.34        63.98        61.02         6.05        27.02        51.98 
TCGA-AD-6965 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-CA-6716 TCGA-CA-6717 
        0.20        58.39        49.41         6.77        12.20        12.76 
TCGA-CA-6718 TCGA-CK-6748 TCGA-CM-5344 TCGA-CM-5860 TCGA-CM-6166 TCGA-D5-6541 
       10.06         1.91        22.03        32.02        21.99        15.58 
TCGA-D5-6932 TCGA-DM-A28G TCGA-F4-6570 TCGA-F4-6807 TCGA-G4-6586 
       11.38        60.79         6.18        16.24        35.80 

$`LHCGR WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        19.99        78.08         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04         4.01        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       37.02        39.06        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        10.88        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        33.01        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6600 TCGA-AZ-6601 
      106.75        22.36        62.79        88.21        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6719 TCGA-CK-4947 
        3.06         3.25         3.29         0.07        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       21.14        82.95       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5861 
       25.02        13.02        29.06        22.98        30.08        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
        2.96        29.03        16.04        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       16.14         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       35.97       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6808 TCGA-F4-6809 
       47.87         1.55        34.42        41.42        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  LHCGR MUTATED LHCGR WILD-TYPE 
            0.2             0.0 
  LHCGR MUTATED LHCGR WILD-TYPE 
          63.98          148.01 
  LHCGR MUTATED LHCGR WILD-TYPE 
         21.990          20.155 
[1] "0.2 - 64.0 (22.0)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1"  
D343V2, continuous
D343V3, binary
                 cls
clus                0   1
  LHCGR MUTATED    24   0
  LHCGR WILD-TYPE 342 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LHCGR MUTATED     24    0
  LHCGR WILD-TYPE  342  119
        clus
vv       LHCGR MUTATED LHCGR WILD-TYPE
  COLON             24             342
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  LHCGR MUTATED         2        0        4        12         0         0
  LHCGR WILD-TYPE      89        1       28       126        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  LHCGR MUTATED           0          0          1          2        2         0
  LHCGR WILD-TYPE        24         11         58         40       46        18
                 vv
clus              STAGE IVB
  LHCGR MUTATED           0
  LHCGR WILD-TYPE         1
D343V4, multiclass
            clus
vv           LHCGR MUTATED LHCGR WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               4              28
  STAGE IIA             12             126
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             2              40
  STAGE IV               2              46
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  LHCGR MUTATED     0   2  20   2
  LHCGR WILD-TYPE  17  90 309  48
D343V5, multiclass
    clus
vv   LHCGR MUTATED LHCGR WILD-TYPE
  T1             0              17
  T2             2              90
  T3            20             309
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  LHCGR MUTATED    18   2   4
  LHCGR WILD-TYPE 269 111  83
D343V6, multiclass
    clus
vv   LHCGR MUTATED LHCGR WILD-TYPE
  N0            18             269
  N1             2             111
  N2             4              83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D343V7, binary
                 cls
clus                0   1
  LHCGR MUTATED    19   2
  LHCGR WILD-TYPE 356  63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LHCGR MUTATED     19    2
  LHCGR WILD-TYPE  356   63
   clus
vv  LHCGR MUTATED LHCGR WILD-TYPE
  0            19             356
  1             2              63
[1] 2 2
[1] FALSE
D343V8, binary
                 cls
clus                0   1
  LHCGR MUTATED    10  14
  LHCGR WILD-TYPE 215 250
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LHCGR MUTATED     10   14
  LHCGR WILD-TYPE  215  250
        clus
vv       LHCGR MUTATED LHCGR WILD-TYPE
  FEMALE            10             215
  MALE              14             250
[1] 2 2
[1] FALSE
D343V9, binary
                 cls
clus                0   1
  LHCGR MUTATED    21   0
  LHCGR WILD-TYPE 329  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LHCGR MUTATED     21    0
  LHCGR WILD-TYPE  329   22
     clus
vv    LHCGR MUTATED LHCGR WILD-TYPE
  NO             21             329
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  LHCGR MUTATED                     22                             2
  LHCGR WILD-TYPE                  293                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  LHCGR MUTATED                       0                              0
  LHCGR WILD-TYPE                   106                             10
D343V10, multiclass
                                clus
vv                               LHCGR MUTATED LHCGR WILD-TYPE
  COLON ADENOCARCINOMA                      22             293
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  LHCGR MUTATED    15   0   1   4
  LHCGR WILD-TYPE 330   4  30  21
D343V11, multiclass
    clus
vv   LHCGR MUTATED LHCGR WILD-TYPE
  R0            15             330
  R1             0               4
  R2             1              30
  RX             4              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D343V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  LHCGR MUTATED                                  0     3
  LHCGR WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  LHCGR MUTATED                           0    15
  LHCGR WILD-TYPE                        22   211
D343V13, multiclass
                                  clus
vv                                 LHCGR MUTATED LHCGR WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        3               8
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                       15             211
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(344) Variable = ZC3H13 MUTATION ANALYSIS
D344V1, survival
                  sevent
clus2                0   1
  ZC3H13 MUTATED    32   8
  ZC3H13 WILD-TYPE 346  85
  ZC3H13 MUTATED ZC3H13 WILD-TYPE 
              40              431 
  ZC3H13 MUTATED ZC3H13 WILD-TYPE 
               8               85 
$`ZC3H13 MUTATED`
TCGA-A6-2677 TCGA-A6-5661 TCGA-A6-5665 TCGA-AA-3510 TCGA-AA-3516 TCGA-AA-3525 
       24.33        33.53        22.06        63.98        13.02         8.05 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3713 TCGA-AA-3815 TCGA-AA-3864 
       17.95        29.95        23.01        19.04        33.04        53.00 
TCGA-AA-3947 TCGA-AA-3956 TCGA-AA-3977 TCGA-AA-A00J TCGA-AA-A00N TCGA-AA-A00R 
       33.01        34.03        25.02        18.05         4.01         0.99 
TCGA-AA-A010 TCGA-AA-A01F TCGA-AA-A01Q TCGA-AA-A01R TCGA-AZ-4315 TCGA-CA-6717 
       34.98        32.02         1.02        35.01        58.39        12.76 
TCGA-CK-5916 TCGA-CM-5341 TCGA-D5-5539 TCGA-D5-6922 TCGA-DM-A0XF TCGA-DM-A28K 
       21.14        29.06        19.59         4.41        38.20        98.24 
TCGA-F4-6569 TCGA-F4-6570 TCGA-G4-6304 TCGA-G4-6626 TCGA-AF-2691 TCGA-AG-3892 
       35.74         6.18        53.62        46.75        43.04        13.02 
TCGA-AG-A002 TCGA-AG-A02N TCGA-DC-6682 TCGA-DY-A1H8 
       20.98        61.97         4.01        32.61 

$`ZC3H13 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        42.90        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 
       31.63        30.44        29.19        23.61        22.09        32.71 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       27.09        22.52         8.38        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 
       20.28         7.04         3.02         1.02        35.01         6.97 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
        1.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
       36.03        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       21.01        13.02        24.00        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
       85.05        26.99        19.04        10.06        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       30.05        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 
       31.00         2.01        12.99        24.00        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
        2.01        20.98         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       30.02        34.03        18.05        38.04        27.02        42.02 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01G 
       17.03        14.99        21.99         1.02        10.98        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       31.00        31.00        38.07         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07        12.20        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
        9.99        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       37.02        25.02        13.02        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       12.03        45.40        12.26        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-F4-6459 
       81.37       119.93        35.97        60.79       117.07         8.61 
TCGA-F4-6460 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       31.96        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       74.56        65.85        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2692 TCGA-AF-2693 
       91.79        79.69        24.13        39.48        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       17.95        36.95        17.03        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X 
       64.01        10.98        49.97         1.94        38.96        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
       19.99         5.95         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       57.24        24.13        51.48         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  ZC3H13 MUTATED ZC3H13 WILD-TYPE 
            0.99             0.00 
  ZC3H13 MUTATED ZC3H13 WILD-TYPE 
           98.24           148.01 
  ZC3H13 MUTATED ZC3H13 WILD-TYPE 
           27.04            19.99 
[1] "1.0 - 98.2 (27.0)"  "0.0 - 148.0 (20.0)"
[1] "hr=" "1.1"
D344V2, continuous
D344V3, binary
                  cls
clus                 0   1
  ZC3H13 MUTATED    34   6
  ZC3H13 WILD-TYPE 332 113
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZC3H13 MUTATED     34    6
  ZC3H13 WILD-TYPE  332  113
        clus
vv       ZC3H13 MUTATED ZC3H13 WILD-TYPE
  COLON              34              332
  RECTUM              6              113
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZC3H13 MUTATED         7        0        4        12         4         0
  ZC3H13 WILD-TYPE      84        1       28       126         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZC3H13 MUTATED           2          4          3          2        1
  ZC3H13 WILD-TYPE        22          7         56         40       47
                  vv
clus               STAGE IVA STAGE IVB
  ZC3H13 MUTATED           0         0
  ZC3H13 WILD-TYPE        18         1
D344V4, multiclass
            clus
vv           ZC3H13 MUTATED ZC3H13 WILD-TYPE
  STAGE I                 7               84
  STAGE IA                0                1
  STAGE II                4               28
  STAGE IIA              12              126
  STAGE IIB               4                6
  STAGE IIC               0                1
  STAGE III               2               22
  STAGE IIIA              4                7
  STAGE IIIB              3               56
  STAGE IIIC              2               40
  STAGE IV                1               47
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZC3H13 MUTATED     3   7  25   5
  ZC3H13 WILD-TYPE  14  85 304  45
D344V5, multiclass
    clus
vv   ZC3H13 MUTATED ZC3H13 WILD-TYPE
  T1              3               14
  T2              7               85
  T3             25              304
  T4              5               45
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  ZC3H13 MUTATED    29   7   4
  ZC3H13 WILD-TYPE 258 106  83
D344V6, multiclass
    clus
vv   ZC3H13 MUTATED ZC3H13 WILD-TYPE
  N0             29              258
  N1              7              106
  N2              4               83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D344V7, binary
                  cls
clus                 0   1
  ZC3H13 MUTATED    38   1
  ZC3H13 WILD-TYPE 337  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZC3H13 MUTATED     38    1
  ZC3H13 WILD-TYPE  337   64
   clus
vv  ZC3H13 MUTATED ZC3H13 WILD-TYPE
  0             38              337
  1              1               64
[1] 2 2
[1] FALSE
D344V8, binary
                  cls
clus                 0   1
  ZC3H13 MUTATED    19  21
  ZC3H13 WILD-TYPE 206 243
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZC3H13 MUTATED     19   21
  ZC3H13 WILD-TYPE  206  243
        clus
vv       ZC3H13 MUTATED ZC3H13 WILD-TYPE
  FEMALE             19              206
  MALE               21              243
[1] 2 2
[1] FALSE
D344V9, binary
                  cls
clus                 0   1
  ZC3H13 MUTATED    29   2
  ZC3H13 WILD-TYPE 321  20
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZC3H13 MUTATED     29    2
  ZC3H13 WILD-TYPE  321   20
     clus
vv    ZC3H13 MUTATED ZC3H13 WILD-TYPE
  NO              29              321
  YES              2               20
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ZC3H13 MUTATED                     23                             9
  ZC3H13 WILD-TYPE                  292                            38
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ZC3H13 MUTATED                       6                              0
  ZC3H13 WILD-TYPE                   100                             10
D344V10, multiclass
                                clus
vv                               ZC3H13 MUTATED ZC3H13 WILD-TYPE
  COLON ADENOCARCINOMA                       23              292
  COLON MUCINOUS ADENOCARCINOMA               9               38
  RECTAL ADENOCARCINOMA                       6              100
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ZC3H13 MUTATED    32   0   1   2
  ZC3H13 WILD-TYPE 313   4  30  23
D344V11, multiclass
    clus
vv   ZC3H13 MUTATED ZC3H13 WILD-TYPE
  R0             32              313
  R1              0                4
  R2              1               30
  RX              2               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D344V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZC3H13 MUTATED                                  0     1
  ZC3H13 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZC3H13 MUTATED                           1    16
  ZC3H13 WILD-TYPE                        21   210
D344V13, multiclass
                                  clus
vv                                 ZC3H13 MUTATED ZC3H13 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                        16              210
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(345) Variable = PRKCH MUTATION ANALYSIS
D345V1, survival
                 sevent
clus2               0   1
  PRKCH MUTATED    10   3
  PRKCH WILD-TYPE 368  90
  PRKCH MUTATED PRKCH WILD-TYPE 
             13             458 
  PRKCH MUTATED PRKCH WILD-TYPE 
              3              90 
$`PRKCH MUTATED`
TCGA-A6-5665 TCGA-AA-3502 TCGA-AA-3989 TCGA-AD-6889 TCGA-AU-6004 TCGA-AZ-6601 
       22.06        35.01         7.96        56.55        27.09       100.01 
TCGA-CA-6717 TCGA-CM-5864 TCGA-CM-6167 TCGA-D5-5540 TCGA-F4-6460 TCGA-G4-6586 
       12.76        15.02        14.99        56.09        31.96        35.80 
TCGA-AG-A002 
       20.98 

$`PRKCH WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       27.02        19.07        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 
       18.05        40.96         0.07        21.37        15.52         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       14.50        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 
       88.21        49.41         6.77        12.10        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07        12.20        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5868 
       30.08        32.02        15.02         5.03        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       45.40        12.26        19.59        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
       98.24         8.61        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       22.09        13.78        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  PRKCH MUTATED PRKCH WILD-TYPE 
           7.96            0.00 
  PRKCH MUTATED PRKCH WILD-TYPE 
         100.01          148.01 
  PRKCH MUTATED PRKCH WILD-TYPE 
         27.090          20.035 
[1] "8.0 - 100.0 (27.1)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.1"
D345V2, continuous
D345V3, binary
                 cls
clus                0   1
  PRKCH MUTATED    13   1
  PRKCH WILD-TYPE 353 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRKCH MUTATED     13    1
  PRKCH WILD-TYPE  353  118
        clus
vv       PRKCH MUTATED PRKCH WILD-TYPE
  COLON             13             353
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PRKCH MUTATED         4        0        1         6         0         0
  PRKCH WILD-TYPE      87        1       31       132        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PRKCH MUTATED           0          0          1          1        1         0
  PRKCH WILD-TYPE        24         11         58         41       47        18
                 vv
clus              STAGE IVB
  PRKCH MUTATED           0
  PRKCH WILD-TYPE         1
D345V4, multiclass
            clus
vv           PRKCH MUTATED PRKCH WILD-TYPE
  STAGE I                4              87
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              6             132
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             1              41
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PRKCH MUTATED     0   4  10   0
  PRKCH WILD-TYPE  17  88 319  50
D345V5, multiclass
    clus
vv   PRKCH MUTATED PRKCH WILD-TYPE
  T1             0              17
  T2             4              88
  T3            10             319
  T4             0              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  PRKCH MUTATED    11   1   2
  PRKCH WILD-TYPE 276 112  85
D345V6, multiclass
    clus
vv   PRKCH MUTATED PRKCH WILD-TYPE
  N0            11             276
  N1             1             112
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D345V7, binary
                 cls
clus                0   1
  PRKCH MUTATED    13   1
  PRKCH WILD-TYPE 362  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRKCH MUTATED     13    1
  PRKCH WILD-TYPE  362   64
   clus
vv  PRKCH MUTATED PRKCH WILD-TYPE
  0            13             362
  1             1              64
[1] 2 2
[1] FALSE
D345V8, binary
                 cls
clus                0   1
  PRKCH MUTATED     6   8
  PRKCH WILD-TYPE 219 256
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRKCH MUTATED      6    8
  PRKCH WILD-TYPE  219  256
        clus
vv       PRKCH MUTATED PRKCH WILD-TYPE
  FEMALE             6             219
  MALE               8             256
[1] 2 2
[1] FALSE
D345V9, binary
                 cls
clus                0   1
  PRKCH MUTATED    11   0
  PRKCH WILD-TYPE 339  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRKCH MUTATED     11    0
  PRKCH WILD-TYPE  339   22
     clus
vv    PRKCH MUTATED PRKCH WILD-TYPE
  NO             11             339
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PRKCH MUTATED                     12                             1
  PRKCH WILD-TYPE                  303                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PRKCH MUTATED                       1                              0
  PRKCH WILD-TYPE                   105                             10
D345V10, multiclass
                                clus
vv                               PRKCH MUTATED PRKCH WILD-TYPE
  COLON ADENOCARCINOMA                      12             303
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  PRKCH MUTATED    10   0   1   1
  PRKCH WILD-TYPE 335   4  30  24
D345V11, multiclass
    clus
vv   PRKCH MUTATED PRKCH WILD-TYPE
  R0            10             335
  R1             0               4
  R2             1              30
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D345V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PRKCH MUTATED                                  0     2
  PRKCH WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PRKCH MUTATED                           1     7
  PRKCH WILD-TYPE                        21   219
D345V13, multiclass
                                  clus
vv                                 PRKCH MUTATED PRKCH WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               9
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        7             219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(346) Variable = FNDC7 MUTATION ANALYSIS
D346V1, survival
                 sevent
clus2               0   1
  FNDC7 MUTATED     8   1
  FNDC7 WILD-TYPE 370  92
  FNDC7 MUTATED FNDC7 WILD-TYPE 
              9             462 
  FNDC7 MUTATED FNDC7 WILD-TYPE 
              1              92 
$`FNDC7 MUTATED`
TCGA-A6-5660 TCGA-A6-5665 TCGA-AA-3663 TCGA-AA-3947 TCGA-AD-6895 TCGA-AZ-4315 
       29.19        22.06         6.97        33.01         0.72        58.39 
TCGA-AZ-6599 TCGA-CM-6162 TCGA-CM-6164 
        6.77        12.00        29.03 

$`FNDC7 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        33.53        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       49.41        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       17.03        15.02         2.96        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  FNDC7 MUTATED FNDC7 WILD-TYPE 
           0.72            0.00 
  FNDC7 MUTATED FNDC7 WILD-TYPE 
          58.39          148.01 
  FNDC7 MUTATED FNDC7 WILD-TYPE 
         22.060          20.155 
[1] "0.7 - 58.4 (22.1)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.5"
D346V2, continuous
D346V3, binary
                 cls
clus                0   1
  FNDC7 MUTATED     9   0
  FNDC7 WILD-TYPE 357 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FNDC7 MUTATED      9    0
  FNDC7 WILD-TYPE  357  119
        clus
vv       FNDC7 MUTATED FNDC7 WILD-TYPE
  COLON              9             357
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FNDC7 MUTATED         1        0        1         3         1         0
  FNDC7 WILD-TYPE      90        1       31       135         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  FNDC7 MUTATED           0          0          1          1        0         0
  FNDC7 WILD-TYPE        24         11         58         41       48        18
                 vv
clus              STAGE IVB
  FNDC7 MUTATED           0
  FNDC7 WILD-TYPE         1
D346V4, multiclass
            clus
vv           FNDC7 MUTATED FNDC7 WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              3             135
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             1              41
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  FNDC7 MUTATED     0   1   7   1
  FNDC7 WILD-TYPE  17  91 322  49
D346V5, multiclass
    clus
vv   FNDC7 MUTATED FNDC7 WILD-TYPE
  T1             0              17
  T2             1              91
  T3             7             322
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  FNDC7 MUTATED     6   2   1
  FNDC7 WILD-TYPE 281 111  86
D346V6, multiclass
    clus
vv   FNDC7 MUTATED FNDC7 WILD-TYPE
  N0             6             281
  N1             2             111
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D346V7, binary
                 cls
clus                0   1
  FNDC7 MUTATED     7   0
  FNDC7 WILD-TYPE 368  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FNDC7 MUTATED      7    0
  FNDC7 WILD-TYPE  368   65
   clus
vv  FNDC7 MUTATED FNDC7 WILD-TYPE
  0             7             368
  1             0              65
[1] 2 2
[1] FALSE
D346V8, binary
                 cls
clus                0   1
  FNDC7 MUTATED     4   5
  FNDC7 WILD-TYPE 221 259
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FNDC7 MUTATED      4    5
  FNDC7 WILD-TYPE  221  259
        clus
vv       FNDC7 MUTATED FNDC7 WILD-TYPE
  FEMALE             4             221
  MALE               5             259
[1] 2 2
[1] FALSE
D346V9, binary
                 cls
clus                0   1
  FNDC7 MUTATED     8   0
  FNDC7 WILD-TYPE 342  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FNDC7 MUTATED      8    0
  FNDC7 WILD-TYPE  342   22
     clus
vv    FNDC7 MUTATED FNDC7 WILD-TYPE
  NO              8             342
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  FNDC7 MUTATED                      7                             2
  FNDC7 WILD-TYPE                  308                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  FNDC7 MUTATED                       0                              0
  FNDC7 WILD-TYPE                   106                             10
D346V10, multiclass
                                clus
vv                               FNDC7 MUTATED FNDC7 WILD-TYPE
  COLON ADENOCARCINOMA                       7             308
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  FNDC7 MUTATED     6   0   0   0
  FNDC7 WILD-TYPE 339   4  31  25
D346V11, multiclass
    clus
vv   FNDC7 MUTATED FNDC7 WILD-TYPE
  R0             6             339
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D346V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FNDC7 MUTATED                                  0     0
  FNDC7 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  FNDC7 MUTATED                           1     6
  FNDC7 WILD-TYPE                        21   220
D346V13, multiclass
                                  clus
vv                                 FNDC7 MUTATED FNDC7 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        6             220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(347) Variable = ZNF438 MUTATION ANALYSIS
D347V1, survival
                  sevent
clus2                0   1
  ZNF438 MUTATED     8   3
  ZNF438 WILD-TYPE 370  90
  ZNF438 MUTATED ZNF438 WILD-TYPE 
              11              460 
  ZNF438 MUTATED ZNF438 WILD-TYPE 
               3               90 
$`ZNF438 MUTATED`
TCGA-A6-2671 TCGA-A6-6137 TCGA-AA-3845 TCGA-AA-A00N TCGA-CA-6717 TCGA-CK-4952 
       43.76        27.09         0.00         4.01        12.76        15.62 
TCGA-CM-6167 TCGA-D5-6541 TCGA-D5-6927 TCGA-G4-6588 TCGA-AG-A002 
       14.99        15.58         9.44        26.17        20.98 

$`ZNF438 WILD-TYPE`
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       46.65        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       22.06        32.71        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 
       15.95        38.99        37.02        14.93        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07        12.20        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 
       14.30        17.56       148.01        85.45        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       16.04        21.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6898 
       17.85         4.80        17.13        12.49        16.14         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6928 
        3.68         4.41        12.43        14.30         9.04        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 
       61.91        36.00        22.09        13.78        35.80        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  ZNF438 MUTATED ZNF438 WILD-TYPE 
               0                0 
  ZNF438 MUTATED ZNF438 WILD-TYPE 
           43.76           148.01 
  ZNF438 MUTATED ZNF438 WILD-TYPE 
          15.580           20.415 
[1] "0.0 - 43.8 (15.6)"  "0.0 - 148.0 (20.4)"
[1] "hr=" "2.1"
D347V2, continuous
D347V3, binary
                  cls
clus                 0   1
  ZNF438 MUTATED    12   1
  ZNF438 WILD-TYPE 354 118
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF438 MUTATED     12    1
  ZNF438 WILD-TYPE  354  118
        clus
vv       ZNF438 MUTATED ZNF438 WILD-TYPE
  COLON              12              354
  RECTUM              1              118
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZNF438 MUTATED         2        0        0         5         1         0
  ZNF438 WILD-TYPE      89        1       32       133         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF438 MUTATED           1          0          1          2        1
  ZNF438 WILD-TYPE        23         11         58         40       47
                  vv
clus               STAGE IVA STAGE IVB
  ZNF438 MUTATED           0         0
  ZNF438 WILD-TYPE        18         1
D347V4, multiclass
            clus
vv           ZNF438 MUTATED ZNF438 WILD-TYPE
  STAGE I                 2               89
  STAGE IA                0                1
  STAGE II                0               32
  STAGE IIA               5              133
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               1               23
  STAGE IIIA              0               11
  STAGE IIIB              1               58
  STAGE IIIC              2               40
  STAGE IV                1               47
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZNF438 MUTATED     0   2   9   2
  ZNF438 WILD-TYPE  17  90 320  48
D347V5, multiclass
    clus
vv   ZNF438 MUTATED ZNF438 WILD-TYPE
  T1              0               17
  T2              2               90
  T3              9              320
  T4              2               48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  ZNF438 MUTATED     8   1   4
  ZNF438 WILD-TYPE 279 112  83
D347V6, multiclass
    clus
vv   ZNF438 MUTATED ZNF438 WILD-TYPE
  N0              8              279
  N1              1              112
  N2              4               83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D347V7, binary
                  cls
clus                 0   1
  ZNF438 MUTATED    11   1
  ZNF438 WILD-TYPE 364  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF438 MUTATED     11    1
  ZNF438 WILD-TYPE  364   64
   clus
vv  ZNF438 MUTATED ZNF438 WILD-TYPE
  0             11              364
  1              1               64
[1] 2 2
[1] FALSE
D347V8, binary
                  cls
clus                 0   1
  ZNF438 MUTATED     4   9
  ZNF438 WILD-TYPE 221 255
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF438 MUTATED      4    9
  ZNF438 WILD-TYPE  221  255
        clus
vv       ZNF438 MUTATED ZNF438 WILD-TYPE
  FEMALE              4              221
  MALE                9              255
[1] 2 2
[1] FALSE
D347V9, binary
                  cls
clus                 0   1
  ZNF438 MUTATED     8   0
  ZNF438 WILD-TYPE 342  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF438 MUTATED      8    0
  ZNF438 WILD-TYPE  342   22
     clus
vv    ZNF438 MUTATED ZNF438 WILD-TYPE
  NO               8              342
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ZNF438 MUTATED                      9                             3
  ZNF438 WILD-TYPE                  306                            44
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ZNF438 MUTATED                       1                              0
  ZNF438 WILD-TYPE                   105                             10
D347V10, multiclass
                                clus
vv                               ZNF438 MUTATED ZNF438 WILD-TYPE
  COLON ADENOCARCINOMA                        9              306
  COLON MUCINOUS ADENOCARCINOMA               3               44
  RECTAL ADENOCARCINOMA                       1              105
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ZNF438 MUTATED     9   0   0   3
  ZNF438 WILD-TYPE 336   4  31  22
D347V11, multiclass
    clus
vv   ZNF438 MUTATED ZNF438 WILD-TYPE
  R0              9              336
  R1              0                4
  R2              0               31
  RX              3               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D347V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF438 MUTATED                                  0     1
  ZNF438 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZNF438 MUTATED                           1     7
  ZNF438 WILD-TYPE                        21   219
D347V13, multiclass
                                  clus
vv                                 ZNF438 MUTATED ZNF438 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                         7              219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(348) Variable = NRAS MUTATION ANALYSIS
D348V1, survival
                sevent
clus2              0   1
  NRAS MUTATED    37   7
  NRAS WILD-TYPE 341  86
  NRAS MUTATED NRAS WILD-TYPE 
            44            427 
  NRAS MUTATED NRAS WILD-TYPE 
             7             86 
$`NRAS MUTATED`
TCGA-A6-2678 TCGA-A6-5656 TCGA-A6-5666 TCGA-AA-3549 TCGA-AA-3558 TCGA-AA-3666 
       42.28        32.91        32.71        21.01        20.98         2.01 
TCGA-AA-3713 TCGA-AA-3819 TCGA-AA-3850 TCGA-AA-3864 TCGA-AA-3972 TCGA-AA-3973 
       19.04        25.02         0.00        53.00        50.99        13.05 
TCGA-AA-3976 TCGA-AA-A00F TCGA-AA-A00N TCGA-AA-A01V TCGA-AA-A024 TCGA-AA-A02F 
       26.01        34.03         4.01        35.01        39.06        39.98 
TCGA-AY-5543 TCGA-CA-5797 TCGA-CM-5864 TCGA-CM-6162 TCGA-CM-6680 TCGA-D5-5538 
       33.01         3.29        15.02        12.00        12.03        12.26 
TCGA-D5-6539 TCGA-D5-6922 TCGA-D5-6932 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-F4-6809 
       12.49         4.41        11.38       140.38         7.50        13.25 
TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6315 TCGA-AF-2691 TCGA-AF-3913 TCGA-AF-6136 
       53.62        55.04        61.91        43.04        10.39        15.39 
TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-A01L TCGA-DC-5337 TCGA-DC-6160 TCGA-DC-6682 
       13.02        14.01        12.00        15.02        19.99         4.01 
TCGA-EI-6510 TCGA-F5-6465 
       18.28        49.51 

$`NRAS WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2683 
       43.76        46.65        43.76        42.90        24.33        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5657 
       34.65        33.34        32.75        36.53        14.53        31.63 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       30.44        29.19        33.53        23.61        22.09        22.06 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       27.09        22.52         8.38        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
        0.99        14.01        33.99        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       29.95        23.01        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3672 
       78.08         6.05         6.97        54.02        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3821 TCGA-AA-3831 
       10.06        35.05        33.04         0.99         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
       10.06        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        31.07        30.05        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3979 
        2.01        21.99        16.08        34.06        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       38.04        19.00        30.02        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       26.01        37.02        51.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       16.31         0.95        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-6715 
        3.19         1.61        12.69         3.06         3.25         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5868 TCGA-CM-6161 
       32.02        15.02         5.03        15.02        17.03        15.02 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-D5-5537 TCGA-D5-5539 
       11.08        11.08        11.01        10.06        45.40        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 
       15.12        17.85         4.80        17.13        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        1.48         3.68        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 
       11.64         4.80         1.51        12.00        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
       12.59        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6854 TCGA-F4-6855 
       34.42        41.42        16.24        33.67         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6309 
       35.31       133.18        74.56        65.85        44.68        85.48 
TCGA-G4-6310 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       63.62        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2692 
       91.79        46.75        79.69        24.13        39.48        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 
       19.10        34.49        14.50        16.83        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       36.95        17.03        35.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       15.95        36.03         9.07        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6681 TCGA-DC-6683 
        5.03        13.97        27.95        10.98         5.95         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-F5-6464 
       32.61         0.49        20.55        19.96        20.91         9.96 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  NRAS MUTATED NRAS WILD-TYPE 
             0              0 
  NRAS MUTATED NRAS WILD-TYPE 
        140.38         148.01 
  NRAS MUTATED NRAS WILD-TYPE 
         18.66          20.55 
[1] "0.0 - 140.4 (18.7)" "0.0 - 148.0 (20.6)"
[1] "hr=" "1.3"
D348V2, continuous
D348V3, binary
                cls
clus               0   1
  NRAS MUTATED    33  11
  NRAS WILD-TYPE 333 108
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRAS MUTATED     33   11
  NRAS WILD-TYPE  333  108
        clus
vv       NRAS MUTATED NRAS WILD-TYPE
  COLON            33            333
  RECTUM           11            108
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NRAS MUTATED        10        0        2         7         2         1
  NRAS WILD-TYPE      81        1       30       131         8         0
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NRAS MUTATED           1          3          7          2        6         3
  NRAS WILD-TYPE        23          8         52         40       42        15
                vv
clus             STAGE IVB
  NRAS MUTATED           0
  NRAS WILD-TYPE         1
D348V4, multiclass
            clus
vv           NRAS MUTATED NRAS WILD-TYPE
  STAGE I              10             81
  STAGE IA              0              1
  STAGE II              2             30
  STAGE IIA             7            131
  STAGE IIB             2              8
  STAGE IIC             1              0
  STAGE III             1             23
  STAGE IIIA            3              8
  STAGE IIIB            7             52
  STAGE IIIC            2             40
  STAGE IV              6             42
  STAGE IVA             3             15
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  NRAS MUTATED     3   9  28   4
  NRAS WILD-TYPE  14  83 301  46
D348V5, multiclass
    clus
vv   NRAS MUTATED NRAS WILD-TYPE
  T1            3             14
  T2            9             83
  T3           28            301
  T4            4             46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  NRAS MUTATED    25  16   3
  NRAS WILD-TYPE 262  97  84
D348V6, multiclass
    clus
vv   NRAS MUTATED NRAS WILD-TYPE
  N0           25            262
  N1           16             97
  N2            3             84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D348V7, binary
                cls
clus               0   1
  NRAS MUTATED    34   8
  NRAS WILD-TYPE 341  57
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRAS MUTATED     34    8
  NRAS WILD-TYPE  341   57
   clus
vv  NRAS MUTATED NRAS WILD-TYPE
  0           34            341
  1            8             57
[1] 2 2
[1] FALSE
D348V8, binary
                cls
clus               0   1
  NRAS MUTATED    18  26
  NRAS WILD-TYPE 207 238
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRAS MUTATED     18   26
  NRAS WILD-TYPE  207  238
        clus
vv       NRAS MUTATED NRAS WILD-TYPE
  FEMALE           18            207
  MALE             26            238
[1] 2 2
[1] FALSE
D348V9, binary
                cls
clus               0   1
  NRAS MUTATED    30   4
  NRAS WILD-TYPE 320  18
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRAS MUTATED     30    4
  NRAS WILD-TYPE  320   18
     clus
vv    NRAS MUTATED NRAS WILD-TYPE
  NO            30            320
  YES            4             18
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  NRAS MUTATED                     30                             3
  NRAS WILD-TYPE                  285                            44
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  NRAS MUTATED                      11                              0
  NRAS WILD-TYPE                    95                             10
D348V10, multiclass
                                clus
vv                               NRAS MUTATED NRAS WILD-TYPE
  COLON ADENOCARCINOMA                     30            285
  COLON MUCINOUS ADENOCARCINOMA             3             44
  RECTAL ADENOCARCINOMA                    11             95
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  NRAS MUTATED    34   0   5   0
  NRAS WILD-TYPE 311   4  26  25
D348V11, multiclass
    clus
vv   NRAS MUTATED NRAS WILD-TYPE
  R0           34            311
  R1            0              4
  R2            5             26
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D348V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NRAS MUTATED                                  0     1
  NRAS WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  NRAS MUTATED                           2    23
  NRAS WILD-TYPE                        20   203
D348V13, multiclass
                                  clus
vv                                 NRAS MUTATED NRAS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   2             20
  WHITE                                      23            203
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(349) Variable = HIST1H1E MUTATION ANALYSIS
D349V1, survival
                    sevent
clus2                  0   1
  HIST1H1E MUTATED     5   1
  HIST1H1E WILD-TYPE 373  92
  HIST1H1E MUTATED HIST1H1E WILD-TYPE 
                 6                465 
  HIST1H1E MUTATED HIST1H1E WILD-TYPE 
                 1                 92 
$`HIST1H1E MUTATED`
TCGA-A6-5665 TCGA-AZ-6598 TCGA-CA-6717 TCGA-CM-4746 TCGA-CM-5861 TCGA-CM-6169 
       22.06        49.41        12.76        37.02        15.02        13.02 

$`HIST1H1E WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 
        5.13       106.75        22.36        62.79        88.21         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.20        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4752 
        1.91       124.27        23.05        20.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 
       29.06        22.03        22.98        30.08        32.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6170 
       29.03        16.04        21.99        14.99        12.99        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  HIST1H1E MUTATED HIST1H1E WILD-TYPE 
             12.76               0.00 
  HIST1H1E MUTATED HIST1H1E WILD-TYPE 
             49.41             148.01 
  HIST1H1E MUTATED HIST1H1E WILD-TYPE 
             18.54              20.19 
[1] "12.8 - 49.4 (18.5)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.2"
D349V2, continuous
D349V3, binary
                    cls
clus                   0   1
  HIST1H1E MUTATED     6   0
  HIST1H1E WILD-TYPE 360 119
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HIST1H1E MUTATED      6    0
  HIST1H1E WILD-TYPE  360  119
        clus
vv       HIST1H1E MUTATED HIST1H1E WILD-TYPE
  COLON                 6                360
  RECTUM                0                119
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  HIST1H1E MUTATED         1        0        1         4         0         0
  HIST1H1E WILD-TYPE      90        1       31       134        10         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HIST1H1E MUTATED           0          0          0          0        0
  HIST1H1E WILD-TYPE        24         11         59         42       48
                    vv
clus                 STAGE IVA STAGE IVB
  HIST1H1E MUTATED           0         0
  HIST1H1E WILD-TYPE        18         1
D349V4, multiclass
            clus
vv           HIST1H1E MUTATED HIST1H1E WILD-TYPE
  STAGE I                   1                 90
  STAGE IA                  0                  1
  STAGE II                  1                 31
  STAGE IIA                 4                134
  STAGE IIB                 0                 10
  STAGE IIC                 0                  1
  STAGE III                 0                 24
  STAGE IIIA                0                 11
  STAGE IIIB                0                 59
  STAGE IIIC                0                 42
  STAGE IV                  0                 48
  STAGE IVA                 0                 18
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  HIST1H1E MUTATED     0   1   5   0
  HIST1H1E WILD-TYPE  17  91 324  50
D349V5, multiclass
    clus
vv   HIST1H1E MUTATED HIST1H1E WILD-TYPE
  T1                0                 17
  T2                1                 91
  T3                5                324
  T4                0                 50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  HIST1H1E MUTATED     6   0   0
  HIST1H1E WILD-TYPE 281 113  87
D349V6, multiclass
    clus
vv   HIST1H1E MUTATED HIST1H1E WILD-TYPE
  N0                6                281
  N1                0                113
  N2                0                 87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D349V7, binary
                    cls
clus                   0   1
  HIST1H1E MUTATED     5   0
  HIST1H1E WILD-TYPE 370  65
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HIST1H1E MUTATED      5    0
  HIST1H1E WILD-TYPE  370   65
   clus
vv  HIST1H1E MUTATED HIST1H1E WILD-TYPE
  0                5                370
  1                0                 65
[1] 2 2
[1] FALSE
D349V8, binary
                    cls
clus                   0   1
  HIST1H1E MUTATED     3   3
  HIST1H1E WILD-TYPE 222 261
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HIST1H1E MUTATED      3    3
  HIST1H1E WILD-TYPE  222  261
        clus
vv       HIST1H1E MUTATED HIST1H1E WILD-TYPE
  FEMALE                3                222
  MALE                  3                261
[1] 2 2
[1] FALSE
D349V9, binary
                    cls
clus                   0   1
  HIST1H1E MUTATED     6   0
  HIST1H1E WILD-TYPE 344  22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HIST1H1E MUTATED      6    0
  HIST1H1E WILD-TYPE  344   22
     clus
vv    HIST1H1E MUTATED HIST1H1E WILD-TYPE
  NO                 6                344
  YES                0                 22
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  HIST1H1E MUTATED                      5                             1
  HIST1H1E WILD-TYPE                  310                            46
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  HIST1H1E MUTATED                       0                              0
  HIST1H1E WILD-TYPE                   106                             10
D349V10, multiclass
                                clus
vv                               HIST1H1E MUTATED HIST1H1E WILD-TYPE
  COLON ADENOCARCINOMA                          5                310
  COLON MUCINOUS ADENOCARCINOMA                 1                 46
  RECTAL ADENOCARCINOMA                         0                106
  RECTAL MUCINOUS ADENOCARCINOMA                0                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  HIST1H1E MUTATED     4   0   0   1
  HIST1H1E WILD-TYPE 341   4  31  24
D349V11, multiclass
    clus
vv   HIST1H1E MUTATED HIST1H1E WILD-TYPE
  R0                4                341
  R1                0                  4
  R2                0                 31
  RX                1                 24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D349V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HIST1H1E MUTATED                                  0     1
  HIST1H1E WILD-TYPE                                1    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  HIST1H1E MUTATED                           2     3
  HIST1H1E WILD-TYPE                        20   223
D349V13, multiclass
                                  clus
vv                                 HIST1H1E MUTATED HIST1H1E WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                 10
  BLACK OR AFRICAN AMERICAN                       2                 20
  WHITE                                           3                223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(350) Variable = ZAK MUTATION ANALYSIS
D350V1, survival
               sevent
clus2             0   1
  ZAK MUTATED     9   0
  ZAK WILD-TYPE 369  93
  ZAK MUTATED ZAK WILD-TYPE 
            9           462 
  ZAK MUTATED ZAK WILD-TYPE 
            0            93 
$`ZAK MUTATED`
TCGA-AA-3710 TCGA-AA-3977 TCGA-AA-A010 TCGA-CK-6747 TCGA-CM-5349 TCGA-D5-5539 
       26.99        25.02        34.98        82.95        30.08        19.59 
TCGA-AG-3731 TCGA-AG-A002 TCGA-EI-6510 
       37.02        20.98        18.28 

$`ZAK WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
       19.00        36.00         5.03        85.05        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6748 
       15.62        49.08        51.32         9.99        21.14         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       29.06        22.03        22.98        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3732 TCGA-AG-3742 
       13.94        19.99         7.99         0.99        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       20.55        19.96        20.91         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  ZAK MUTATED ZAK WILD-TYPE 
        18.28          0.00 
  ZAK MUTATED ZAK WILD-TYPE 
        82.95        148.01 
  ZAK MUTATED ZAK WILD-TYPE 
       26.990        20.035 
[1] "18.3 - 83.0 (27.0)" "0.0 - 148.0 (20.0)"
[1] "hr="     "9200000"
D350V2, continuous
D350V3, binary
               cls
clus              0   1
  ZAK MUTATED     6   3
  ZAK WILD-TYPE 360 116
[1] "tbl2"
               cls
clus            [,1] [,2]
  ZAK MUTATED      6    3
  ZAK WILD-TYPE  360  116
        clus
vv       ZAK MUTATED ZAK WILD-TYPE
  COLON            6           360
  RECTUM           3           116
[1] 2 2
[1] FALSE
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZAK MUTATED         1        0        0         3         1         0
  ZAK WILD-TYPE      90        1       32       135         9         1
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ZAK MUTATED           0          1          0          0        1         1
  ZAK WILD-TYPE        24         10         59         42       47        17
               vv
clus            STAGE IVB
  ZAK MUTATED           0
  ZAK WILD-TYPE         1
D350V4, multiclass
            clus
vv           ZAK MUTATED ZAK WILD-TYPE
  STAGE I              1            90
  STAGE IA             0             1
  STAGE II             0            32
  STAGE IIA            3           135
  STAGE IIB            1             9
  STAGE IIC            0             1
  STAGE III            0            24
  STAGE IIIA           1            10
  STAGE IIIB           0            59
  STAGE IIIC           0            42
  STAGE IV             1            47
  STAGE IVA            1            17
  STAGE IVB            0             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  ZAK MUTATED     0   3   5   1
  ZAK WILD-TYPE  17  89 324  49
D350V5, multiclass
    clus
vv   ZAK MUTATED ZAK WILD-TYPE
  T1           0            17
  T2           3            89
  T3           5           324
  T4           1            49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2
  ZAK MUTATED     7   2   0
  ZAK WILD-TYPE 280 111  87
D350V6, multiclass
    clus
vv   ZAK MUTATED ZAK WILD-TYPE
  N0           7           280
  N1           2           111
  N2           0            87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D350V7, binary
               cls
clus              0   1
  ZAK MUTATED     5   1
  ZAK WILD-TYPE 370  64
[1] "tbl2"
               cls
clus            [,1] [,2]
  ZAK MUTATED      5    1
  ZAK WILD-TYPE  370   64
   clus
vv  ZAK MUTATED ZAK WILD-TYPE
  0           5           370
  1           1            64
[1] 2 2
[1] FALSE
D350V8, binary
               cls
clus              0   1
  ZAK MUTATED     5   4
  ZAK WILD-TYPE 220 260
[1] "tbl2"
               cls
clus            [,1] [,2]
  ZAK MUTATED      5    4
  ZAK WILD-TYPE  220  260
        clus
vv       ZAK MUTATED ZAK WILD-TYPE
  FEMALE           5           220
  MALE             4           260
[1] 2 2
[1] FALSE
D350V9, binary
               cls
clus              0   1
  ZAK MUTATED     9   0
  ZAK WILD-TYPE 341  22
[1] "tbl2"
               cls
clus            [,1] [,2]
  ZAK MUTATED      9    0
  ZAK WILD-TYPE  341   22
     clus
vv    ZAK MUTATED ZAK WILD-TYPE
  NO            9           341
  YES           0            22
[1] 2 2
[1] FALSE
               vv
clus            COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ZAK MUTATED                      5                             1
  ZAK WILD-TYPE                  310                            46
               vv
clus            RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ZAK MUTATED                       3                              0
  ZAK WILD-TYPE                   103                             10
D350V10, multiclass
                                clus
vv                               ZAK MUTATED ZAK WILD-TYPE
  COLON ADENOCARCINOMA                     5           310
  COLON MUCINOUS ADENOCARCINOMA            1            46
  RECTAL ADENOCARCINOMA                    3           103
  RECTAL MUCINOUS ADENOCARCINOMA           0            10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             R0  R1  R2  RX
  ZAK MUTATED     6   0   1   1
  ZAK WILD-TYPE 339   4  30  24
D350V11, multiclass
    clus
vv   ZAK MUTATED ZAK WILD-TYPE
  R0           6           339
  R1           0             4
  R2           1            30
  RX           1            24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D350V12, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZAK MUTATED                                  0     0
  ZAK WILD-TYPE                                1    11
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  ZAK MUTATED                           0     4
  ZAK WILD-TYPE                        22   222
D350V13, multiclass
                                  clus
vv                                 ZAK MUTATED ZAK WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      0            11
  BLACK OR AFRICAN AMERICAN                  0            22
  WHITE                                      4           222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(351) Variable = SLC24A2 MUTATION ANALYSIS
D351V1, survival
                   sevent
clus2                 0   1
  SLC24A2 MUTATED    12   6
  SLC24A2 WILD-TYPE 366  87
  SLC24A2 MUTATED SLC24A2 WILD-TYPE 
               18               453 
  SLC24A2 MUTATED SLC24A2 WILD-TYPE 
                6                87 
$`SLC24A2 MUTATED`
TCGA-A6-6780 TCGA-AA-3492 TCGA-AA-3713 TCGA-AA-3947 TCGA-AA-3977 TCGA-AA-A00A 
       20.12         3.02        19.04        33.01        25.02        38.04 
TCGA-AA-A010 TCGA-AY-4070 TCGA-AZ-4315 TCGA-AZ-6603 TCGA-CA-6717 TCGA-CA-6718 
       34.98        16.31        58.39        29.56        12.76        10.06 
TCGA-D5-6540 TCGA-D5-6930 TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-AG-3578 
       16.14         1.51        13.32       140.38        44.32        32.02 

$`SLC24A2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 
       23.87        19.66        20.28         7.04         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       27.02        13.94        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4071 
       27.42        10.88         0.20        14.50        27.09         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       33.01        21.44        17.82         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
      100.01         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 
        3.06         3.25         3.29         0.07        12.20        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 
       15.12        17.85         4.80        17.13        12.49        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
        9.44        11.64         4.80        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
       12.59         7.50       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       10.39        36.03        12.00         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  SLC24A2 MUTATED SLC24A2 WILD-TYPE 
             1.51              0.00 
  SLC24A2 MUTATED SLC24A2 WILD-TYPE 
           140.38            148.01 
  SLC24A2 MUTATED SLC24A2 WILD-TYPE 
            22.57             20.19 
[1] "1.5 - 140.4 (22.6)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.6"
D351V2, continuous
D351V3, binary
                   cls
clus                  0   1
  SLC24A2 MUTATED    17   2
  SLC24A2 WILD-TYPE 349 117
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC24A2 MUTATED     17    2
  SLC24A2 WILD-TYPE  349  117
        clus
vv       SLC24A2 MUTATED SLC24A2 WILD-TYPE
  COLON               17               349
  RECTUM               2               117
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SLC24A2 MUTATED         1        0        1        10         2         0
  SLC24A2 WILD-TYPE      90        1       31       128         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC24A2 MUTATED           0          0          1          1        1
  SLC24A2 WILD-TYPE        24         11         58         41       47
                   vv
clus                STAGE IVA STAGE IVB
  SLC24A2 MUTATED           0         0
  SLC24A2 WILD-TYPE        18         1
D351V4, multiclass
            clus
vv           SLC24A2 MUTATED SLC24A2 WILD-TYPE
  STAGE I                  1                90
  STAGE IA                 0                 1
  STAGE II                 1                31
  STAGE IIA               10               128
  STAGE IIB                2                 8
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               0                11
  STAGE IIIB               1                58
  STAGE IIIC               1                41
  STAGE IV                 1                47
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  SLC24A2 MUTATED     0   3  14   2
  SLC24A2 WILD-TYPE  17  89 315  48
D351V5, multiclass
    clus
vv   SLC24A2 MUTATED SLC24A2 WILD-TYPE
  T1               0                17
  T2               3                89
  T3              14               315
  T4               2                48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  SLC24A2 MUTATED    16   2   1
  SLC24A2 WILD-TYPE 271 111  86
D351V6, multiclass
    clus
vv   SLC24A2 MUTATED SLC24A2 WILD-TYPE
  N0              16               271
  N1               2               111
  N2               1                86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D351V7, binary
                   cls
clus                  0   1
  SLC24A2 MUTATED    15   1
  SLC24A2 WILD-TYPE 360  64
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC24A2 MUTATED     15    1
  SLC24A2 WILD-TYPE  360   64
   clus
vv  SLC24A2 MUTATED SLC24A2 WILD-TYPE
  0              15               360
  1               1                64
[1] 2 2
[1] FALSE
D351V8, binary
                   cls
clus                  0   1
  SLC24A2 MUTATED     8  11
  SLC24A2 WILD-TYPE 217 253
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC24A2 MUTATED      8   11
  SLC24A2 WILD-TYPE  217  253
        clus
vv       SLC24A2 MUTATED SLC24A2 WILD-TYPE
  FEMALE               8               217
  MALE                11               253
[1] 2 2
[1] FALSE
D351V9, binary
                   cls
clus                  0   1
  SLC24A2 MUTATED    13   1
  SLC24A2 WILD-TYPE 337  21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC24A2 MUTATED     13    1
  SLC24A2 WILD-TYPE  337   21
     clus
vv    SLC24A2 MUTATED SLC24A2 WILD-TYPE
  NO               13               337
  YES               1                21
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SLC24A2 MUTATED                     11                             5
  SLC24A2 WILD-TYPE                  304                            42
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SLC24A2 MUTATED                       0                              2
  SLC24A2 WILD-TYPE                   106                              8
D351V10, multiclass
                                clus
vv                               SLC24A2 MUTATED SLC24A2 WILD-TYPE
  COLON ADENOCARCINOMA                        11               304
  COLON MUCINOUS ADENOCARCINOMA                5                42
  RECTAL ADENOCARCINOMA                        0               106
  RECTAL MUCINOUS ADENOCARCINOMA               2                 8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  SLC24A2 MUTATED     9   1   1   2
  SLC24A2 WILD-TYPE 336   3  30  23
D351V11, multiclass
    clus
vv   SLC24A2 MUTATED SLC24A2 WILD-TYPE
  R0               9               336
  R1               1                 3
  R2               1                30
  RX               2                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D351V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SLC24A2 MUTATED                                  0     2
  SLC24A2 WILD-TYPE                                1     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  SLC24A2 MUTATED                           1     8
  SLC24A2 WILD-TYPE                        21   218
D351V13, multiclass
                                  clus
vv                                 SLC24A2 MUTATED SLC24A2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          2                 9
  BLACK OR AFRICAN AMERICAN                      1                21
  WHITE                                          8               218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(352) Variable = HORMAD1 MUTATION ANALYSIS
D352V1, survival
                   sevent
clus2                 0   1
  HORMAD1 MUTATED     9   4
  HORMAD1 WILD-TYPE 369  89
  HORMAD1 MUTATED HORMAD1 WILD-TYPE 
               13               458 
  HORMAD1 MUTATED HORMAD1 WILD-TYPE 
                4                89 
$`HORMAD1 MUTATED`
TCGA-A6-6653 TCGA-AA-A00N TCGA-AA-A010 TCGA-AD-6895 TCGA-AZ-6607 TCGA-CK-4950 
       24.39         4.01        34.98         0.72         3.19        85.45 
TCGA-DM-A1D0 TCGA-DM-A1HA TCGA-DM-A28F TCGA-F4-6570 TCGA-F4-6806 TCGA-G4-6309 
      130.65       131.51        35.97         6.18        41.42        85.48 
TCGA-G4-6628 
       79.69 

$`HORMAD1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
       25.08        25.18        24.16        21.76        24.69        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.79         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       14.30        17.56       148.01        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D4 
       11.38        10.26       119.70        24.43        38.20        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G 
      135.65       139.17         6.12        81.37       119.93        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 
      117.07        98.24         8.61        31.96        35.74        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
        1.55        34.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       44.68        55.04        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 
       13.78        35.80        26.17        91.79        46.75        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  HORMAD1 MUTATED HORMAD1 WILD-TYPE 
             0.72              0.00 
  HORMAD1 MUTATED HORMAD1 WILD-TYPE 
           131.51            148.01 
  HORMAD1 MUTATED HORMAD1 WILD-TYPE 
           35.970            20.035 
[1] "0.7 - 131.5 (36.0)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.1"
D352V2, continuous
D352V3, binary
                   cls
clus                  0   1
  HORMAD1 MUTATED    13   0
  HORMAD1 WILD-TYPE 353 119
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HORMAD1 MUTATED     13    0
  HORMAD1 WILD-TYPE  353  119
        clus
vv       HORMAD1 MUTATED HORMAD1 WILD-TYPE
  COLON               13               353
  RECTUM               0               119
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  HORMAD1 MUTATED         3        0        0         2         2         0
  HORMAD1 WILD-TYPE      88        1       32       136         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HORMAD1 MUTATED           0          0          3          1        1
  HORMAD1 WILD-TYPE        24         11         56         41       47
                   vv
clus                STAGE IVA STAGE IVB
  HORMAD1 MUTATED           0         0
  HORMAD1 WILD-TYPE        18         1
D352V4, multiclass
            clus
vv           HORMAD1 MUTATED HORMAD1 WILD-TYPE
  STAGE I                  3                88
  STAGE IA                 0                 1
  STAGE II                 0                32
  STAGE IIA                2               136
  STAGE IIB                2                 8
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               0                11
  STAGE IIIB               3                56
  STAGE IIIC               1                41
  STAGE IV                 1                47
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  HORMAD1 MUTATED     0   3   7   3
  HORMAD1 WILD-TYPE  17  89 322  47
D352V5, multiclass
    clus
vv   HORMAD1 MUTATED HORMAD1 WILD-TYPE
  T1               0                17
  T2               3                89
  T3               7               322
  T4               3                47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  HORMAD1 MUTATED     7   4   2
  HORMAD1 WILD-TYPE 280 109  85
D352V6, multiclass
    clus
vv   HORMAD1 MUTATED HORMAD1 WILD-TYPE
  N0               7               280
  N1               4               109
  N2               2                85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D352V7, binary
                   cls
clus                  0   1
  HORMAD1 MUTATED    11   1
  HORMAD1 WILD-TYPE 364  64
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HORMAD1 MUTATED     11    1
  HORMAD1 WILD-TYPE  364   64
   clus
vv  HORMAD1 MUTATED HORMAD1 WILD-TYPE
  0              11               364
  1               1                64
[1] 2 2
[1] FALSE
D352V8, binary
                   cls
clus                  0   1
  HORMAD1 MUTATED     6   7
  HORMAD1 WILD-TYPE 219 257
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HORMAD1 MUTATED      6    7
  HORMAD1 WILD-TYPE  219  257
        clus
vv       HORMAD1 MUTATED HORMAD1 WILD-TYPE
  FEMALE               6               219
  MALE                 7               257
[1] 2 2
[1] FALSE
D352V9, binary
                   cls
clus                  0   1
  HORMAD1 MUTATED     8   0
  HORMAD1 WILD-TYPE 342  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HORMAD1 MUTATED      8    0
  HORMAD1 WILD-TYPE  342   22
     clus
vv    HORMAD1 MUTATED HORMAD1 WILD-TYPE
  NO                8               342
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  HORMAD1 MUTATED                     12                             1
  HORMAD1 WILD-TYPE                  303                            46
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  HORMAD1 MUTATED                       0                              0
  HORMAD1 WILD-TYPE                   106                             10
D352V10, multiclass
                                clus
vv                               HORMAD1 MUTATED HORMAD1 WILD-TYPE
  COLON ADENOCARCINOMA                        12               303
  COLON MUCINOUS ADENOCARCINOMA                1                46
  RECTAL ADENOCARCINOMA                        0               106
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  HORMAD1 MUTATED     6   1   0   0
  HORMAD1 WILD-TYPE 339   3  31  25
D352V11, multiclass
    clus
vv   HORMAD1 MUTATED HORMAD1 WILD-TYPE
  R0               6               339
  R1               1                 3
  R2               0                31
  RX               0                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D352V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HORMAD1 MUTATED                                  0     0
  HORMAD1 WILD-TYPE                                1    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  HORMAD1 MUTATED                           2     9
  HORMAD1 WILD-TYPE                        20   217
D352V13, multiclass
                                  clus
vv                                 HORMAD1 MUTATED HORMAD1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                      2                20
  WHITE                                          9               217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(353) Variable = BRAF MUTATION ANALYSIS
D353V1, survival
                sevent
clus2              0   1
  BRAF MUTATED    79  25
  BRAF WILD-TYPE 299  68
  BRAF MUTATED BRAF WILD-TYPE 
           104            367 
  BRAF MUTATED BRAF WILD-TYPE 
            25             68 
$`BRAF MUTATED`
TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-3809 TCGA-A6-5657 TCGA-A6-5661 TCGA-A6-5664 
       46.65        42.90        32.75        31.63        33.53        22.09 
TCGA-A6-5665 TCGA-A6-6649 TCGA-A6-6653 TCGA-AA-3492 TCGA-AA-3516 TCGA-AA-3525 
       22.06        24.16        24.39         3.02        13.02         8.05 
TCGA-AA-3543 TCGA-AA-3664 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3815 TCGA-AA-3821 
        0.99        54.02        19.04        19.04        33.04         1.02 
TCGA-AA-3833 TCGA-AA-3877 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3966 
       15.95        31.00        33.01        26.01        24.00         2.01 
TCGA-AA-A00D TCGA-AA-A00J TCGA-AA-A01D TCGA-AA-A01P TCGA-AD-5900 TCGA-AD-6889 
       19.00        18.05        10.98        38.07         0.07        56.55 
TCGA-AD-6895 TCGA-AD-6963 TCGA-AD-6964 TCGA-AU-6004 TCGA-AZ-5407 TCGA-AZ-6598 
        0.72        27.42        10.88        27.09        88.21        49.41 
TCGA-AZ-6603 TCGA-AZ-6606 TCGA-CA-5796 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 
       29.56        11.74         3.25        12.76        10.06        17.56 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CM-4744 
       85.45        15.62        51.32         9.99        82.95        20.02 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5864 TCGA-CM-5868 
       22.98        30.08        32.02        15.02        15.02        17.03 
TCGA-CM-6162 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6674 
       12.00        12.99        13.02        15.02        14.04        12.95 
TCGA-CM-6675 TCGA-D5-5538 TCGA-D5-6529 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       13.05        12.26        20.19        43.27        15.12        17.85 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6928 TCGA-D5-6930 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.49        16.14        11.64         1.51        24.43        38.20 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1DA TCGA-DM-A1HB TCGA-DM-A285 
       92.75        49.91        13.32         7.50       135.65         6.12 
TCGA-DM-A28C TCGA-F4-6460 TCGA-F4-6570 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6310 
       81.37        31.96         6.18        74.56        65.85        63.62 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AG-3578 TCGA-AG-3885 TCGA-AG-A002 TCGA-DC-6158 TCGA-DC-6160 
       79.69        32.02        17.95        20.98        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DD TCGA-EF-5830 TCGA-EI-6508 
        5.95         5.03         5.29        57.24         0.49        20.91 
TCGA-EI-6510 TCGA-F5-6811 
       18.28        32.19 

$`BRAF WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       43.76        43.76        24.33        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 
       33.34        36.53        14.53        32.91        30.44        29.19 
TCGA-A6-5662 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       23.61        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       25.18        21.76        24.69        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
       20.28         7.04         1.02        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
        1.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
       36.03        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       29.00        26.01        12.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
        6.97         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
        5.03        85.05        26.99        10.06        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       25.02        17.98        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 
       17.03        24.03        27.02        29.98        18.05         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 
       12.99        24.00         2.01        20.98        34.03        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L 
       13.94        38.04        30.02        34.03        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99        34.98         1.02        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       31.00         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        21.37        15.52         0.79         5.79        22.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
        0.20        14.50        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6607 
       62.79         6.77        12.10       100.01         5.23         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        1.61        12.69         3.06         3.29         0.07        12.20 
TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-5912 TCGA-CK-5916 TCGA-CK-6748 TCGA-CK-6751 
       14.30       148.01        49.08        21.14         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       23.05        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
        5.03        15.02        15.02         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6172 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       21.99        14.99        11.01        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       10.06        12.03        45.40        19.59        56.09        55.92 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6541 TCGA-D5-6898 
       18.25         1.32         4.80        17.13        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A1D0 
        4.80        12.00        11.38        10.26       119.70       130.65 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A28E 
       12.59       140.38        44.32       131.51       139.17       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6569 
       35.97        60.79       117.07        98.24         8.61        35.74 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6304 
       13.25         0.53        47.41        35.31       133.18        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6317 TCGA-AF-2687 
       44.68        55.04        85.48        61.91        36.00        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       12.00         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.04        19.99         1.02        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6682 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.03        13.97        27.95         4.01       126.44        41.36 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EI-6506 TCGA-EI-6507 TCGA-F5-6464 
       24.13        51.48        32.61        20.55        19.96         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       49.51        31.30        28.57         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  BRAF MUTATED BRAF WILD-TYPE 
          0.07           0.00 
  BRAF MUTATED BRAF WILD-TYPE 
        135.65         148.01 
  BRAF MUTATED BRAF WILD-TYPE 
        20.005         20.550 
[1] "0.1 - 135.7 (20.0)" "0.0 - 148.0 (20.6)"
[1] "hr=" "1.2"
D353V2, continuous
D353V3, binary
                cls
clus               0   1
  BRAF MUTATED    96  13
  BRAF WILD-TYPE 270 106
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRAF MUTATED     96   13
  BRAF WILD-TYPE  270  106
        clus
vv       BRAF MUTATED BRAF WILD-TYPE
  COLON            96            270
  RECTUM           13            106
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  BRAF MUTATED        17        1        6        35         5         0
  BRAF WILD-TYPE      74        0       26       103         5         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  BRAF MUTATED           4          1         20          7        5         3
  BRAF WILD-TYPE        20         10         39         35       43        15
                vv
clus             STAGE IVB
  BRAF MUTATED           1
  BRAF WILD-TYPE         0
D353V4, multiclass
            clus
vv           BRAF MUTATED BRAF WILD-TYPE
  STAGE I              17             74
  STAGE IA              1              0
  STAGE II              6             26
  STAGE IIA            35            103
  STAGE IIB             5              5
  STAGE IIC             0              1
  STAGE III             4             20
  STAGE IIIA            1             10
  STAGE IIIB           20             39
  STAGE IIIC            7             35
  STAGE IV              5             43
  STAGE IVA             3             15
  STAGE IVB             1              0
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  BRAF MUTATED     2  18  74  14
  BRAF WILD-TYPE  15  74 255  36
D353V5, multiclass
    clus
vv   BRAF MUTATED BRAF WILD-TYPE
  T1            2             15
  T2           18             74
  T3           74            255
  T4           14             36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  BRAF MUTATED    68  26  15
  BRAF WILD-TYPE 219  87  72
D353V6, multiclass
    clus
vv   BRAF MUTATED BRAF WILD-TYPE
  N0           68            219
  N1           26             87
  N2           15             72
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D353V7, binary
                cls
clus               0   1
  BRAF MUTATED    85   8
  BRAF WILD-TYPE 290  57
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRAF MUTATED     85    8
  BRAF WILD-TYPE  290   57
   clus
vv  BRAF MUTATED BRAF WILD-TYPE
  0           85            290
  1            8             57
[1] 2 2
[1] FALSE
D353V8, binary
                cls
clus               0   1
  BRAF MUTATED    59  50
  BRAF WILD-TYPE 166 214
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRAF MUTATED     59   50
  BRAF WILD-TYPE  166  214
        clus
vv       BRAF MUTATED BRAF WILD-TYPE
  FEMALE           59            166
  MALE             50            214
[1] 2 2
[1] FALSE
D353V9, binary
                cls
clus               0   1
  BRAF MUTATED    79   3
  BRAF WILD-TYPE 271  19
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRAF MUTATED     79    3
  BRAF WILD-TYPE  271   19
     clus
vv    BRAF MUTATED BRAF WILD-TYPE
  NO            79            271
  YES            3             19
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  BRAF MUTATED                     69                            24
  BRAF WILD-TYPE                  246                            23
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  BRAF MUTATED                      11                              2
  BRAF WILD-TYPE                    95                              8
D353V10, multiclass
                                clus
vv                               BRAF MUTATED BRAF WILD-TYPE
  COLON ADENOCARCINOMA                     69            246
  COLON MUCINOUS ADENOCARCINOMA            24             23
  RECTAL ADENOCARCINOMA                    11             95
  RECTAL MUCINOUS ADENOCARCINOMA            2              8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  BRAF MUTATED    72   1   2  10
  BRAF WILD-TYPE 273   3  29  15
D353V11, multiclass
    clus
vv   BRAF MUTATED BRAF WILD-TYPE
  R0           72            273
  R1            1              3
  R2            2             29
  RX           10             15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D353V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  BRAF MUTATED                                  0     5
  BRAF WILD-TYPE                                1     6
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  BRAF MUTATED                           8    71
  BRAF WILD-TYPE                        14   155
D353V13, multiclass
                                  clus
vv                                 BRAF MUTATED BRAF WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       5              6
  BLACK OR AFRICAN AMERICAN                   8             14
  WHITE                                      71            155
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(354) Variable = DDX59 MUTATION ANALYSIS
D354V1, survival
                 sevent
clus2               0   1
  DDX59 MUTATED    12   1
  DDX59 WILD-TYPE 366  92
  DDX59 MUTATED DDX59 WILD-TYPE 
             13             458 
  DDX59 MUTATED DDX59 WILD-TYPE 
              1              92 
$`DDX59 MUTATED`
TCGA-A6-5665 TCGA-AA-3510 TCGA-AD-6895 TCGA-AZ-4315 TCGA-AZ-6600 TCGA-CA-6717 
       22.06        63.98         0.72        58.39        12.10        12.76 
TCGA-CK-4947 TCGA-D5-6540 TCGA-D5-6930 TCGA-G4-6306 TCGA-G4-6586 TCGA-AG-3609 
       17.56        16.14         1.51        44.68        35.80        19.99 
TCGA-EI-6507 
       19.96 

$`DDX59 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
       56.55         0.79         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        88.21        49.41         6.77       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07        12.20        10.06        14.30 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 
       17.85         4.80        17.13        12.49        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       11.64         4.80        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       65.85        53.62        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
       32.61         0.49        20.55        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  DDX59 MUTATED DDX59 WILD-TYPE 
           0.72            0.00 
  DDX59 MUTATED DDX59 WILD-TYPE 
          63.98          148.01 
  DDX59 MUTATED DDX59 WILD-TYPE 
         19.960          20.415 
[1] "0.7 - 64.0 (20.0)"  "0.0 - 148.0 (20.4)"
[1] "hr=" "2.6"
D354V2, continuous
D354V3, binary
                 cls
clus                0   1
  DDX59 MUTATED    11   2
  DDX59 WILD-TYPE 355 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX59 MUTATED     11    2
  DDX59 WILD-TYPE  355  117
        clus
vv       DDX59 MUTATED DDX59 WILD-TYPE
  COLON             11             355
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DDX59 MUTATED         1        0        1         7         0         0
  DDX59 WILD-TYPE      90        1       31       131        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DDX59 MUTATED           0          0          1          1        1         0
  DDX59 WILD-TYPE        24         11         58         41       47        18
                 vv
clus              STAGE IVB
  DDX59 MUTATED           0
  DDX59 WILD-TYPE         1
D354V4, multiclass
            clus
vv           DDX59 MUTATED DDX59 WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              7             131
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             1              41
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  DDX59 MUTATED     0   2   9   2
  DDX59 WILD-TYPE  17  90 320  48
D354V5, multiclass
    clus
vv   DDX59 MUTATED DDX59 WILD-TYPE
  T1             0              17
  T2             2              90
  T3             9             320
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  DDX59 MUTATED     9   3   1
  DDX59 WILD-TYPE 278 110  86
D354V6, multiclass
    clus
vv   DDX59 MUTATED DDX59 WILD-TYPE
  N0             9             278
  N1             3             110
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D354V7, binary
                 cls
clus                0   1
  DDX59 MUTATED    11   1
  DDX59 WILD-TYPE 364  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX59 MUTATED     11    1
  DDX59 WILD-TYPE  364   64
   clus
vv  DDX59 MUTATED DDX59 WILD-TYPE
  0            11             364
  1             1              64
[1] 2 2
[1] FALSE
D354V8, binary
                 cls
clus                0   1
  DDX59 MUTATED     4   9
  DDX59 WILD-TYPE 221 255
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX59 MUTATED      4    9
  DDX59 WILD-TYPE  221  255
        clus
vv       DDX59 MUTATED DDX59 WILD-TYPE
  FEMALE             4             221
  MALE               9             255
[1] 2 2
[1] FALSE
D354V9, binary
                 cls
clus                0   1
  DDX59 MUTATED    10   0
  DDX59 WILD-TYPE 340  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX59 MUTATED     10    0
  DDX59 WILD-TYPE  340   22
     clus
vv    DDX59 MUTATED DDX59 WILD-TYPE
  NO             10             340
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  DDX59 MUTATED                      8                             3
  DDX59 WILD-TYPE                  307                            44
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  DDX59 MUTATED                       2                              0
  DDX59 WILD-TYPE                   104                             10
D354V10, multiclass
                                clus
vv                               DDX59 MUTATED DDX59 WILD-TYPE
  COLON ADENOCARCINOMA                       8             307
  COLON MUCINOUS ADENOCARCINOMA              3              44
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  DDX59 MUTATED     9   0   0   2
  DDX59 WILD-TYPE 336   4  31  23
D354V11, multiclass
    clus
vv   DDX59 MUTATED DDX59 WILD-TYPE
  R0             9             336
  R1             0               4
  R2             0              31
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D354V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DDX59 MUTATED                                  0     1
  DDX59 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  DDX59 MUTATED                           1     9
  DDX59 WILD-TYPE                        21   217
D354V13, multiclass
                                  clus
vv                                 DDX59 MUTATED DDX59 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        9             217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(355) Variable = NLRP13 MUTATION ANALYSIS
D355V1, survival
                  sevent
clus2                0   1
  NLRP13 MUTATED    24   3
  NLRP13 WILD-TYPE 354  90
  NLRP13 MUTATED NLRP13 WILD-TYPE 
              27              444 
  NLRP13 MUTATED NLRP13 WILD-TYPE 
               3               90 
$`NLRP13 MUTATED`
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6781 TCGA-AA-3510 TCGA-AA-3525 TCGA-AA-3860 
       32.71        27.09        19.66        63.98         8.05        31.07 
TCGA-AA-3877 TCGA-AA-3950 TCGA-AA-A010 TCGA-AA-A01K TCGA-AD-6890 TCGA-AD-6899 
       31.00        24.00        34.98        31.00         0.79         5.79 
TCGA-AZ-4315 TCGA-AZ-5403 TCGA-CA-6717 TCGA-CM-5344 TCGA-CM-5861 TCGA-D5-6541 
       58.39        62.79        12.76        22.03        15.02        15.58 
TCGA-D5-6930 TCGA-DM-A1DB TCGA-G4-6299 TCGA-G4-6309 TCGA-G4-6586 TCGA-AF-2693 
        1.51        44.32        74.56        85.48        35.80        19.10 
TCGA-AG-3892 TCGA-AG-A002 TCGA-CI-6620 
       13.02        20.98        33.17 

$`NLRP13 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       22.09        22.06        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 
       20.28         7.04         3.02         1.02        35.01         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       37.05        36.03        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       78.08         6.05         6.97        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 
        0.00        36.03        32.05         0.99        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 
        2.01        12.99        24.00        33.01        26.01         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6895 
       40.96         0.07        21.37        15.52        56.55         0.72 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
       16.31         0.95        33.01        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
        5.13       106.75        22.36        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.20        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 
       13.02        29.06        22.98        30.08        32.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       16.14         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 
        9.04         9.44        11.64         4.80        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HA 
       49.91        13.32        12.59       140.38         7.50       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 
       65.85        53.62        44.68        55.04        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 
       79.69        24.13        39.48        43.04        13.55        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       36.95        17.03        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        0.72         6.05         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  NLRP13 MUTATED NLRP13 WILD-TYPE 
            0.79             0.00 
  NLRP13 MUTATED NLRP13 WILD-TYPE 
           85.48           148.01 
  NLRP13 MUTATED NLRP13 WILD-TYPE 
           27.09            20.02 
[1] "0.8 - 85.5 (27.1)"  "0.0 - 148.0 (20.0)"
[1] "hr=" "2.1"
D355V2, continuous
D355V3, binary
                  cls
clus                 0   1
  NLRP13 MUTATED    27   3
  NLRP13 WILD-TYPE 339 116
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NLRP13 MUTATED     27    3
  NLRP13 WILD-TYPE  339  116
        clus
vv       NLRP13 MUTATED NLRP13 WILD-TYPE
  COLON              27              339
  RECTUM              3              116
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NLRP13 MUTATED         4        0        2         9         1         1
  NLRP13 WILD-TYPE      87        1       30       129         9         0
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NLRP13 MUTATED           1          0          5          5        1
  NLRP13 WILD-TYPE        23         11         54         37       47
                  vv
clus               STAGE IVA STAGE IVB
  NLRP13 MUTATED           1         0
  NLRP13 WILD-TYPE        17         1
D355V4, multiclass
            clus
vv           NLRP13 MUTATED NLRP13 WILD-TYPE
  STAGE I                 4               87
  STAGE IA                0                1
  STAGE II                2               30
  STAGE IIA               9              129
  STAGE IIB               1                9
  STAGE IIC               1                0
  STAGE III               1               23
  STAGE IIIA              0               11
  STAGE IIIB              5               54
  STAGE IIIC              5               37
  STAGE IV                1               47
  STAGE IVA               1               17
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  NLRP13 MUTATED     3   2  22   4
  NLRP13 WILD-TYPE  14  90 307  46
D355V5, multiclass
    clus
vv   NLRP13 MUTATED NLRP13 WILD-TYPE
  T1              3               14
  T2              2               90
  T3             22              307
  T4              4               46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  NLRP13 MUTATED    18   7   6
  NLRP13 WILD-TYPE 269 106  81
D355V6, multiclass
    clus
vv   NLRP13 MUTATED NLRP13 WILD-TYPE
  N0             18              269
  N1              7              106
  N2              6               81
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D355V7, binary
                  cls
clus                 0   1
  NLRP13 MUTATED    23   2
  NLRP13 WILD-TYPE 352  63
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NLRP13 MUTATED     23    2
  NLRP13 WILD-TYPE  352   63
   clus
vv  NLRP13 MUTATED NLRP13 WILD-TYPE
  0             23              352
  1              2               63
[1] 2 2
[1] FALSE
D355V8, binary
                  cls
clus                 0   1
  NLRP13 MUTATED    13  18
  NLRP13 WILD-TYPE 212 246
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NLRP13 MUTATED     13   18
  NLRP13 WILD-TYPE  212  246
        clus
vv       NLRP13 MUTATED NLRP13 WILD-TYPE
  FEMALE             13              212
  MALE               18              246
[1] 2 2
[1] FALSE
D355V9, binary
                  cls
clus                 0   1
  NLRP13 MUTATED    24   0
  NLRP13 WILD-TYPE 326  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NLRP13 MUTATED     24    0
  NLRP13 WILD-TYPE  326   22
     clus
vv    NLRP13 MUTATED NLRP13 WILD-TYPE
  NO              24              326
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  NLRP13 MUTATED                     20                             7
  NLRP13 WILD-TYPE                  295                            40
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  NLRP13 MUTATED                       3                              0
  NLRP13 WILD-TYPE                   103                             10
D355V10, multiclass
                                clus
vv                               NLRP13 MUTATED NLRP13 WILD-TYPE
  COLON ADENOCARCINOMA                       20              295
  COLON MUCINOUS ADENOCARCINOMA               7               40
  RECTAL ADENOCARCINOMA                       3              103
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  NLRP13 MUTATED    21   0   1   1
  NLRP13 WILD-TYPE 324   4  30  24
D355V11, multiclass
    clus
vv   NLRP13 MUTATED NLRP13 WILD-TYPE
  R0             21              324
  R1              0                4
  R2              1               30
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D355V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NLRP13 MUTATED                                  0     1
  NLRP13 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  NLRP13 MUTATED                           1    17
  NLRP13 WILD-TYPE                        21   209
D355V13, multiclass
                                  clus
vv                                 NLRP13 MUTATED NLRP13 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                        17              209
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(356) Variable = MKI67 MUTATION ANALYSIS
D356V1, survival
                 sevent
clus2               0   1
  MKI67 MUTATED    35   8
  MKI67 WILD-TYPE 343  85
  MKI67 MUTATED MKI67 WILD-TYPE 
             43             428 
  MKI67 MUTATED MKI67 WILD-TYPE 
              8              85 
$`MKI67 MUTATED`
TCGA-A6-2676 TCGA-A6-3809 TCGA-A6-5660 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       42.90        32.75        29.19        24.39        23.87        20.12 
TCGA-AA-3510 TCGA-AA-3525 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3815 TCGA-AA-3845 
       63.98         8.05        85.05        19.04        33.04         0.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3966 TCGA-AA-3977 TCGA-AA-A00A TCGA-AA-A00E 
       33.01        26.01         2.01        25.02        38.04        30.02 
TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01Q TCGA-AU-3779 TCGA-AU-6004 TCGA-AZ-6598 
        4.01        34.98         1.02        14.50        27.09        49.41 
TCGA-CA-6718 TCGA-CK-4952 TCGA-CM-5349 TCGA-CM-6162 TCGA-D5-6924 TCGA-DM-A1DB 
       10.06        15.62        30.08        12.00        14.30        44.32 
TCGA-DM-A28K TCGA-F4-6570 TCGA-F4-6703 TCGA-G4-6315 TCGA-G4-6628 TCGA-AF-2693 
       98.24         6.18        47.87        61.91        79.69        19.10 
TCGA-AG-3593 TCGA-AG-3731 TCGA-AG-A002 TCGA-AG-A02N TCGA-CI-6624 TCGA-EI-6507 
       34.03        37.02        20.98        61.97         4.73        19.96 
TCGA-EI-6508 
       20.91 

$`MKI67 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5657 
       34.65        33.34        36.53        14.53        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 
       30.44        33.53        23.61        22.09        22.06        32.71 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       27.09        22.52         8.38        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       21.76        24.69        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3526 
        1.02         9.07        24.03        37.05        36.03        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
        5.03        26.99        19.04        10.06        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
       14.93        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3950 TCGA-AA-3952 
       31.00         2.01        12.99        24.00        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       20.98        34.03        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00J 
        7.96        27.02        13.94        19.00        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        31.00        38.07        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
        0.20        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       88.21         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07        12.20        12.76        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
      148.01        85.45        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5860 
       25.02        13.02        29.06        22.03        22.98        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       12.43         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
        7.50       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-F4-6459 TCGA-F4-6460 
      119.93        35.97        60.79       117.07         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.74         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 
       46.75        24.13        39.48        43.04        13.55        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3594 TCGA-AG-3598 
       20.05        24.00         1.02        46.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
       19.99         7.99         0.99        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
       49.97         1.94        38.96        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
       33.17         6.97        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6510 TCGA-F5-6464 
       51.48        32.61         0.49        20.55        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  MKI67 MUTATED MKI67 WILD-TYPE 
              0               0 
  MKI67 MUTATED MKI67 WILD-TYPE 
          98.24          148.01 
  MKI67 MUTATED MKI67 WILD-TYPE 
          26.01           19.99 
[1] "0.0 - 98.2 (26.0)"  "0.0 - 148.0 (20.0)"
[1] "hr=" "1.2"
D356V2, continuous
D356V3, binary
                 cls
clus                0   1
  MKI67 MUTATED    36   7
  MKI67 WILD-TYPE 330 112
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MKI67 MUTATED     36    7
  MKI67 WILD-TYPE  330  112
        clus
vv       MKI67 MUTATED MKI67 WILD-TYPE
  COLON             36             330
  RECTUM             7             112
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MKI67 MUTATED         6        0        5        17         5         0
  MKI67 WILD-TYPE      85        1       27       121         5         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MKI67 MUTATED           1          0          5          2        2         0
  MKI67 WILD-TYPE        23         11         54         40       46        18
                 vv
clus              STAGE IVB
  MKI67 MUTATED           0
  MKI67 WILD-TYPE         1
D356V4, multiclass
            clus
vv           MKI67 MUTATED MKI67 WILD-TYPE
  STAGE I                6              85
  STAGE IA               0               1
  STAGE II               5              27
  STAGE IIA             17             121
  STAGE IIB              5               5
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             5              54
  STAGE IIIC             2              40
  STAGE IV               2              46
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  MKI67 MUTATED     0   7  31   6
  MKI67 WILD-TYPE  17  85 298  44
D356V5, multiclass
    clus
vv   MKI67 MUTATED MKI67 WILD-TYPE
  T1             0              17
  T2             7              85
  T3            31             298
  T4             6              44
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  MKI67 MUTATED    35   7   2
  MKI67 WILD-TYPE 252 106  85
D356V6, multiclass
    clus
vv   MKI67 MUTATED MKI67 WILD-TYPE
  N0            35             252
  N1             7             106
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D356V7, binary
                 cls
clus                0   1
  MKI67 MUTATED    38   2
  MKI67 WILD-TYPE 337  63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MKI67 MUTATED     38    2
  MKI67 WILD-TYPE  337   63
   clus
vv  MKI67 MUTATED MKI67 WILD-TYPE
  0            38             337
  1             2              63
[1] 2 2
[1] FALSE
D356V8, binary
                 cls
clus                0   1
  MKI67 MUTATED    21  23
  MKI67 WILD-TYPE 204 241
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MKI67 MUTATED     21   23
  MKI67 WILD-TYPE  204  241
        clus
vv       MKI67 MUTATED MKI67 WILD-TYPE
  FEMALE            21             204
  MALE              23             241
[1] 2 2
[1] FALSE
D356V9, binary
                 cls
clus                0   1
  MKI67 MUTATED    32   1
  MKI67 WILD-TYPE 318  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MKI67 MUTATED     32    1
  MKI67 WILD-TYPE  318   21
     clus
vv    MKI67 MUTATED MKI67 WILD-TYPE
  NO             32             318
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MKI67 MUTATED                     27                             9
  MKI67 WILD-TYPE                  288                            38
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MKI67 MUTATED                       7                              0
  MKI67 WILD-TYPE                    99                             10
D356V10, multiclass
                                clus
vv                               MKI67 MUTATED MKI67 WILD-TYPE
  COLON ADENOCARCINOMA                      27             288
  COLON MUCINOUS ADENOCARCINOMA              9              38
  RECTAL ADENOCARCINOMA                      7              99
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  MKI67 MUTATED    30   0   1   2
  MKI67 WILD-TYPE 315   4  30  23
D356V11, multiclass
    clus
vv   MKI67 MUTATED MKI67 WILD-TYPE
  R0            30             315
  R1             0               4
  R2             1              30
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D356V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MKI67 MUTATED                                  0     1
  MKI67 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  MKI67 MUTATED                           1    22
  MKI67 WILD-TYPE                        21   204
D356V13, multiclass
                                  clus
vv                                 MKI67 MUTATED MKI67 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                       22             204
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(357) Variable = MET MUTATION ANALYSIS
D357V1, survival
               sevent
clus2             0   1
  MET MUTATED    34  14
  MET WILD-TYPE 344  79
  MET MUTATED MET WILD-TYPE 
           48           423 
  MET MUTATED MET WILD-TYPE 
           14            79 
$`MET MUTATED`
TCGA-A6-4105 TCGA-A6-5666 TCGA-A6-6141 TCGA-AA-3662 TCGA-AA-3713 TCGA-AA-3950 
       14.53        32.71         8.38         6.05        19.04        24.00 
TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A02K TCGA-AD-6889 TCGA-AD-6890 TCGA-AU-3779 
        4.01        34.98        14.01        56.55         0.79        14.50 
TCGA-AY-6197 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-CA-6715 TCGA-CA-6718 
       21.44        49.41        12.10        29.56         0.07        10.06 
TCGA-CA-6719 TCGA-CK-4952 TCGA-CM-4743 TCGA-CM-5341 TCGA-CM-5864 TCGA-CM-6167 
       14.30        15.62        23.05        29.06        15.02        14.99 
TCGA-CM-6170 TCGA-CM-6674 TCGA-CM-6675 TCGA-D5-6533 TCGA-D5-6924 TCGA-DM-A1D8 
       15.02        12.95        13.05         1.32        14.30        12.59 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A285 TCGA-DM-A28H TCGA-F4-6459 TCGA-F4-6460 
        7.50        44.32         6.12       117.07         8.61        31.96 
TCGA-G4-6293 TCGA-G4-6304 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6628 TCGA-AG-3892 
      133.18        53.62        63.62        22.09        79.69        13.02 
TCGA-CI-6620 TCGA-DC-5337 TCGA-DY-A0XA TCGA-F5-6464 TCGA-F5-6812 TCGA-G5-6235 
       33.17        15.02       126.44         9.96         0.66        55.76 

$`MET WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 
       16.57        34.65        33.34        32.75        36.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       22.06        27.09        22.52        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02        78.08         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       26.99        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       26.01         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
       39.98         2.01         5.03         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 
       18.05        40.96         0.07        21.37        15.52         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-6004 
        5.79        22.42        27.42        10.88         0.20        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       16.31         0.95        33.01        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 
        5.13       106.75        22.36        62.79        88.21         6.77 
TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
      100.01         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6716 TCGA-CA-6717 TCGA-CK-4947 
        3.06         3.25         3.29        12.20        12.76        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
      148.01        85.45        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
       82.95         1.91       124.27        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       13.02        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
        5.03        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6171 
       29.03        16.04        21.99        12.99        13.02        14.04 
TCGA-CM-6172 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       11.01        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       18.25        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       12.43         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A1HA 
      130.65        92.75        49.91        13.32       140.38       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      135.65       139.17        81.37       119.93        35.97        60.79 
TCGA-DM-A28K TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       98.24        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       35.31        74.56        65.85        44.68        55.04        85.48 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       61.91        36.00        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       46.75        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       17.95        36.95        17.03        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6622 TCGA-CI-6624 
       17.49         0.69         0.72         6.05         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
       78.12         7.17         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC 
       19.99         5.95         4.01         5.03         5.29        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       19.96        20.91        18.28        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6813 TCGA-G5-6641 
       32.19         0.69        26.43 

  MET MUTATED MET WILD-TYPE 
         0.07          0.00 
  MET MUTATED MET WILD-TYPE 
       133.18        148.01 
  MET MUTATED MET WILD-TYPE 
        15.02         20.98 
[1] "0.1 - 133.2 (15.0)" "0.0 - 148.0 (21.0)"
[1] "hr=" "1.5"
D357V2, continuous
D357V3, binary
               cls
clus              0   1
  MET MUTATED    42   7
  MET WILD-TYPE 324 112
[1] "tbl2"
               cls
clus            [,1] [,2]
  MET MUTATED     42    7
  MET WILD-TYPE  324  112
        clus
vv       MET MUTATED MET WILD-TYPE
  COLON           42           324
  RECTUM           7           112
[1] 2 2
[1] FALSE
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MET MUTATED         5        0        1        15         3         1
  MET WILD-TYPE      86        1       31       123         7         0
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MET MUTATED           2          1          6          5        5         1
  MET WILD-TYPE        22         10         53         37       43        17
               vv
clus            STAGE IVB
  MET MUTATED           1
  MET WILD-TYPE         0
D357V4, multiclass
            clus
vv           MET MUTATED MET WILD-TYPE
  STAGE I              5            86
  STAGE IA             0             1
  STAGE II             1            31
  STAGE IIA           15           123
  STAGE IIB            3             7
  STAGE IIC            1             0
  STAGE III            2            22
  STAGE IIIA           1            10
  STAGE IIIB           6            53
  STAGE IIIC           5            37
  STAGE IV             5            43
  STAGE IVA            1            17
  STAGE IVB            1             0
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  MET MUTATED     3   6  30  10
  MET WILD-TYPE  14  86 299  40
D357V5, multiclass
    clus
vv   MET MUTATED MET WILD-TYPE
  T1           3            14
  T2           6            86
  T3          30           299
  T4          10            40
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2
  MET MUTATED    28  11  10
  MET WILD-TYPE 259 102  77
D357V6, multiclass
    clus
vv   MET MUTATED MET WILD-TYPE
  N0          28           259
  N1          11           102
  N2          10            77
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D357V7, binary
               cls
clus              0   1
  MET MUTATED    35   7
  MET WILD-TYPE 340  58
[1] "tbl2"
               cls
clus            [,1] [,2]
  MET MUTATED     35    7
  MET WILD-TYPE  340   58
   clus
vv  MET MUTATED MET WILD-TYPE
  0          35           340
  1           7            58
[1] 2 2
[1] FALSE
D357V8, binary
               cls
clus              0   1
  MET MUTATED    24  25
  MET WILD-TYPE 201 239
[1] "tbl2"
               cls
clus            [,1] [,2]
  MET MUTATED     24   25
  MET WILD-TYPE  201  239
        clus
vv       MET MUTATED MET WILD-TYPE
  FEMALE          24           201
  MALE            25           239
[1] 2 2
[1] FALSE
D357V9, binary
               cls
clus              0   1
  MET MUTATED    32   2
  MET WILD-TYPE 318  20
[1] "tbl2"
               cls
clus            [,1] [,2]
  MET MUTATED     32    2
  MET WILD-TYPE  318   20
     clus
vv    MET MUTATED MET WILD-TYPE
  NO           32           318
  YES           2            20
[1] 2 2
[1] FALSE
               vv
clus            COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MET MUTATED                     38                             4
  MET WILD-TYPE                  277                            43
               vv
clus            RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MET MUTATED                       7                              0
  MET WILD-TYPE                    99                             10
D357V10, multiclass
                                clus
vv                               MET MUTATED MET WILD-TYPE
  COLON ADENOCARCINOMA                    38           277
  COLON MUCINOUS ADENOCARCINOMA            4            43
  RECTAL ADENOCARCINOMA                    7            99
  RECTAL MUCINOUS ADENOCARCINOMA           0            10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             R0  R1  R2  RX
  MET MUTATED    26   1   3   4
  MET WILD-TYPE 319   3  28  21
D357V11, multiclass
    clus
vv   MET MUTATED MET WILD-TYPE
  R0          26           319
  R1           1             3
  R2           3            28
  RX           4            21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D357V12, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MET MUTATED                                  0     4
  MET WILD-TYPE                                1     7
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  MET MUTATED                           4    33
  MET WILD-TYPE                        18   193
D357V13, multiclass
                                  clus
vv                                 MET MUTATED MET WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      4             7
  BLACK OR AFRICAN AMERICAN                  4            18
  WHITE                                     33           193
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(358) Variable = PIK3C2A MUTATION ANALYSIS
D358V1, survival
                   sevent
clus2                 0   1
  PIK3C2A MUTATED    20   2
  PIK3C2A WILD-TYPE 358  91
  PIK3C2A MUTATED PIK3C2A WILD-TYPE 
               22               449 
  PIK3C2A MUTATED PIK3C2A WILD-TYPE 
                2                91 
$`PIK3C2A MUTATED`
TCGA-A6-5660 TCGA-A6-6141 TCGA-AA-3496 TCGA-AA-3660 TCGA-AA-3877 TCGA-AA-3977 
       29.19         8.38         1.02        78.08        31.00        25.02 
TCGA-AZ-6598 TCGA-CA-6717 TCGA-CK-4950 TCGA-CM-5861 TCGA-CM-6674 TCGA-D5-6540 
       49.41        12.76        85.45        15.02        12.95        16.14 
TCGA-G4-6309 TCGA-G4-6315 TCGA-AF-3400 TCGA-AF-3913 TCGA-AG-A002 TCGA-DY-A0XA 
       85.48        61.91        34.49        10.39        20.98       126.44 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       20.55        19.96        20.91        18.28 

$`PIK3C2A WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 
       22.06        32.71        27.09        22.52        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3510 
       19.66        20.28         7.04         3.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       29.98        18.05         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07        12.20        10.06        14.30        17.56       148.01 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6676 
       13.02        15.02        14.04        11.01        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       55.04        63.62        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       43.04        13.55        19.10        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.03         5.29        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       32.61         0.49         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  PIK3C2A MUTATED PIK3C2A WILD-TYPE 
             1.02              0.00 
  PIK3C2A MUTATED PIK3C2A WILD-TYPE 
           126.44            148.01 
  PIK3C2A MUTATED PIK3C2A WILD-TYPE 
           20.945            20.050 
[1] "1.0 - 126.4 (20.9)" "0.0 - 148.0 (20.1)"
[1] "hr=" "3"  
D358V2, continuous
D358V3, binary
                   cls
clus                  0   1
  PIK3C2A MUTATED    14   8
  PIK3C2A WILD-TYPE 352 111
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PIK3C2A MUTATED     14    8
  PIK3C2A WILD-TYPE  352  111
        clus
vv       PIK3C2A MUTATED PIK3C2A WILD-TYPE
  COLON               14               352
  RECTUM               8               111
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PIK3C2A MUTATED         3        0        3         8         0         0
  PIK3C2A WILD-TYPE      88        1       29       130        10         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PIK3C2A MUTATED           0          0          3          1        2
  PIK3C2A WILD-TYPE        24         11         56         41       46
                   vv
clus                STAGE IVA STAGE IVB
  PIK3C2A MUTATED           1         0
  PIK3C2A WILD-TYPE        17         1
D358V4, multiclass
            clus
vv           PIK3C2A MUTATED PIK3C2A WILD-TYPE
  STAGE I                  3                88
  STAGE IA                 0                 1
  STAGE II                 3                29
  STAGE IIA                8               130
  STAGE IIB                0                10
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               0                11
  STAGE IIIB               3                56
  STAGE IIIC               1                41
  STAGE IV                 2                46
  STAGE IVA                1                17
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  PIK3C2A MUTATED     1   4  17   0
  PIK3C2A WILD-TYPE  16  88 312  50
D358V5, multiclass
    clus
vv   PIK3C2A MUTATED PIK3C2A WILD-TYPE
  T1               1                16
  T2               4                88
  T3              17               312
  T4               0                50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  PIK3C2A MUTATED    16   5   1
  PIK3C2A WILD-TYPE 271 108  86
D358V6, multiclass
    clus
vv   PIK3C2A MUTATED PIK3C2A WILD-TYPE
  N0              16               271
  N1               5               108
  N2               1                86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D358V7, binary
                   cls
clus                  0   1
  PIK3C2A MUTATED    17   2
  PIK3C2A WILD-TYPE 358  63
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PIK3C2A MUTATED     17    2
  PIK3C2A WILD-TYPE  358   63
   clus
vv  PIK3C2A MUTATED PIK3C2A WILD-TYPE
  0              17               358
  1               2                63
[1] 2 2
[1] FALSE
D358V8, binary
                   cls
clus                  0   1
  PIK3C2A MUTATED    11  11
  PIK3C2A WILD-TYPE 214 253
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PIK3C2A MUTATED     11   11
  PIK3C2A WILD-TYPE  214  253
        clus
vv       PIK3C2A MUTATED PIK3C2A WILD-TYPE
  FEMALE              11               214
  MALE                11               253
[1] 2 2
[1] FALSE
D358V9, binary
                   cls
clus                  0   1
  PIK3C2A MUTATED    19   1
  PIK3C2A WILD-TYPE 331  21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PIK3C2A MUTATED     19    1
  PIK3C2A WILD-TYPE  331   21
     clus
vv    PIK3C2A MUTATED PIK3C2A WILD-TYPE
  NO               19               331
  YES               1                21
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PIK3C2A MUTATED                     11                             3
  PIK3C2A WILD-TYPE                  304                            44
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PIK3C2A MUTATED                       7                              1
  PIK3C2A WILD-TYPE                    99                              9
D358V10, multiclass
                                clus
vv                               PIK3C2A MUTATED PIK3C2A WILD-TYPE
  COLON ADENOCARCINOMA                        11               304
  COLON MUCINOUS ADENOCARCINOMA                3                44
  RECTAL ADENOCARCINOMA                        7                99
  RECTAL MUCINOUS ADENOCARCINOMA               1                 9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  PIK3C2A MUTATED    15   1   0   1
  PIK3C2A WILD-TYPE 330   3  31  24
D358V11, multiclass
    clus
vv   PIK3C2A MUTATED PIK3C2A WILD-TYPE
  R0              15               330
  R1               1                 3
  R2               0                31
  RX               1                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D358V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PIK3C2A MUTATED                                  0     1
  PIK3C2A WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  PIK3C2A MUTATED                           5    11
  PIK3C2A WILD-TYPE                        17   215
D358V13, multiclass
                                  clus
vv                                 PIK3C2A MUTATED PIK3C2A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                10
  BLACK OR AFRICAN AMERICAN                      5                17
  WHITE                                         11               215
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(359) Variable = ERBB3 MUTATION ANALYSIS
D359V1, survival
                 sevent
clus2               0   1
  ERBB3 MUTATED    26   2
  ERBB3 WILD-TYPE 352  91
  ERBB3 MUTATED ERBB3 WILD-TYPE 
             28             443 
  ERBB3 MUTATED ERBB3 WILD-TYPE 
              2              91 
$`ERBB3 MUTATED`
TCGA-A6-5657 TCGA-AA-3519 TCGA-AA-3672 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3819 
       31.63         9.07         0.92        19.04        19.04        25.02 
TCGA-AA-3864 TCGA-AA-3950 TCGA-AA-3976 TCGA-AA-A00A TCGA-AA-A00R TCGA-AA-A010 
       53.00        24.00        26.01        38.04         0.99        34.98 
TCGA-AD-6890 TCGA-AY-6197 TCGA-CA-5254 TCGA-CK-4947 TCGA-CM-4746 TCGA-CM-5348 
        0.79        21.44        12.69        17.56        37.02        22.98 
TCGA-CM-5349 TCGA-D5-6534 TCGA-D5-6928 TCGA-D5-6931 TCGA-F4-6856 TCGA-G4-6304 
       30.08        43.27        11.64        12.00        35.31        53.62 
TCGA-AG-3600 TCGA-AG-3726 TCGA-AG-A02N TCGA-F5-6464 
        6.05         7.99        61.97         9.96 

$`ERBB3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        1.02        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
       54.02         2.01        14.01        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       85.05        26.99        10.06        35.05        33.04         0.99 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 
        2.01        12.99        24.00        33.01        26.01         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00E 
       19.07         7.96        27.02        13.94        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
       42.02        17.03        14.99        21.99         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       21.37        15.52        56.55         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        33.01        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        1.61         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       12.76        10.06        14.30       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
      124.27        23.05        20.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       22.03        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6536 
       55.92        20.19        18.25         1.32        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        4.80         1.51        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 
        0.53        47.41       133.18        74.56        65.85        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       50.04        12.03         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
       19.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 
       10.98        49.97         1.94        38.96        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       19.96        20.91        18.28        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  ERBB3 MUTATED ERBB3 WILD-TYPE 
           0.79            0.00 
  ERBB3 MUTATED ERBB3 WILD-TYPE 
          61.97          148.01 
  ERBB3 MUTATED ERBB3 WILD-TYPE 
          22.21           20.12 
[1] "0.8 - 62.0 (22.2)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "2.6"
D359V2, continuous
D359V3, binary
                 cls
clus                0   1
  ERBB3 MUTATED    26   4
  ERBB3 WILD-TYPE 340 115
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERBB3 MUTATED     26    4
  ERBB3 WILD-TYPE  340  115
        clus
vv       ERBB3 MUTATED ERBB3 WILD-TYPE
  COLON             26             340
  RECTUM             4             115
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ERBB3 MUTATED         4        0        4         8         2         0
  ERBB3 WILD-TYPE      87        1       28       130         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ERBB3 MUTATED           2          1          3          3        2         0
  ERBB3 WILD-TYPE        22         10         56         39       46        18
                 vv
clus              STAGE IVB
  ERBB3 MUTATED           0
  ERBB3 WILD-TYPE         1
D359V4, multiclass
            clus
vv           ERBB3 MUTATED ERBB3 WILD-TYPE
  STAGE I                4              87
  STAGE IA               0               1
  STAGE II               4              28
  STAGE IIA              8             130
  STAGE IIB              2               8
  STAGE IIC              0               1
  STAGE III              2              22
  STAGE IIIA             1              10
  STAGE IIIB             3              56
  STAGE IIIC             3              39
  STAGE IV               2              46
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ERBB3 MUTATED     1   5  18   6
  ERBB3 WILD-TYPE  16  87 311  44
D359V5, multiclass
    clus
vv   ERBB3 MUTATED ERBB3 WILD-TYPE
  T1             1              16
  T2             5              87
  T3            18             311
  T4             6              44
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  ERBB3 MUTATED    20   6   4
  ERBB3 WILD-TYPE 267 107  83
D359V6, multiclass
    clus
vv   ERBB3 MUTATED ERBB3 WILD-TYPE
  N0            20             267
  N1             6             107
  N2             4              83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D359V7, binary
                 cls
clus                0   1
  ERBB3 MUTATED    26   2
  ERBB3 WILD-TYPE 349  63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERBB3 MUTATED     26    2
  ERBB3 WILD-TYPE  349   63
   clus
vv  ERBB3 MUTATED ERBB3 WILD-TYPE
  0            26             349
  1             2              63
[1] 2 2
[1] FALSE
D359V8, binary
                 cls
clus                0   1
  ERBB3 MUTATED    14  16
  ERBB3 WILD-TYPE 211 248
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERBB3 MUTATED     14   16
  ERBB3 WILD-TYPE  211  248
        clus
vv       ERBB3 MUTATED ERBB3 WILD-TYPE
  FEMALE            14             211
  MALE              16             248
[1] 2 2
[1] FALSE
D359V9, binary
                 cls
clus                0   1
  ERBB3 MUTATED    23   2
  ERBB3 WILD-TYPE 327  20
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERBB3 MUTATED     23    2
  ERBB3 WILD-TYPE  327   20
     clus
vv    ERBB3 MUTATED ERBB3 WILD-TYPE
  NO             23             327
  YES             2              20
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ERBB3 MUTATED                     22                             4
  ERBB3 WILD-TYPE                  293                            43
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ERBB3 MUTATED                       4                              0
  ERBB3 WILD-TYPE                   102                             10
D359V10, multiclass
                                clus
vv                               ERBB3 MUTATED ERBB3 WILD-TYPE
  COLON ADENOCARCINOMA                      22             293
  COLON MUCINOUS ADENOCARCINOMA              4              43
  RECTAL ADENOCARCINOMA                      4             102
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  ERBB3 MUTATED    25   0   2   2
  ERBB3 WILD-TYPE 320   4  29  23
D359V11, multiclass
    clus
vv   ERBB3 MUTATED ERBB3 WILD-TYPE
  R0            25             320
  R1             0               4
  R2             2              29
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D359V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ERBB3 MUTATED                                  0     1
  ERBB3 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ERBB3 MUTATED                           2    11
  ERBB3 WILD-TYPE                        20   215
D359V13, multiclass
                                  clus
vv                                 ERBB3 MUTATED ERBB3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    2              20
  WHITE                                       11             215
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(360) Variable = CENPF MUTATION ANALYSIS
D360V1, survival
                 sevent
clus2               0   1
  CENPF MUTATED    41   5
  CENPF WILD-TYPE 337  88
  CENPF MUTATED CENPF WILD-TYPE 
             46             425 
  CENPF MUTATED CENPF WILD-TYPE 
              5              88 
$`CENPF MUTATED`
TCGA-A6-2676 TCGA-A6-3809 TCGA-A6-5656 TCGA-A6-5661 TCGA-A6-6648 TCGA-AA-3510 
       42.90        32.75        32.91        33.53        25.18        63.98 
TCGA-AA-3525 TCGA-AA-3555 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3815 TCGA-AA-3845 
        8.05        29.95        78.08         6.97        33.04         0.00 
TCGA-AA-3977 TCGA-AA-A00J TCGA-AA-A00N TCGA-AA-A00R TCGA-AA-A010 TCGA-AA-A01Q 
       25.02        18.05         4.01         0.99        34.98         1.02 
TCGA-AA-A02O TCGA-AD-5900 TCGA-AZ-4315 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4952 
        0.92         0.07        58.39        12.76        14.30        15.62 
TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4752 TCGA-CM-5861 TCGA-CM-6162 TCGA-CM-6675 
       82.95       124.27        13.02        15.02        12.00        13.05 
TCGA-D5-6535 TCGA-D5-6540 TCGA-D5-6898 TCGA-DM-A1D7 TCGA-F4-6569 TCGA-F4-6808 
       15.12        16.14         1.48        13.32        35.74        33.67 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6303 TCGA-G4-6307 TCGA-G4-6625 TCGA-AF-2687 
       35.31       133.18        65.85        55.04        91.79        24.13 
TCGA-AF-6136 TCGA-AG-3892 TCGA-AG-3902 TCGA-AG-A002 
       15.39        13.02        32.02        20.98 

$`CENPF WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5657 TCGA-A6-5659 
       34.65        33.34        36.53        14.53        31.63        30.44 
TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 
       29.19        23.61        22.09        22.06        32.71        27.09 
TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 
       22.52         8.38        25.08        24.16        21.76        24.69 
TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 
       24.39        23.87        20.12        19.66        20.28         7.04 
TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        3.02         1.02        35.01         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       13.02        24.00        17.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 
       13.94        19.99        61.02         6.05        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
       26.99        19.04        19.04        10.06        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
       14.93        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L 
       38.04        19.00        30.02        34.03        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       27.02        42.02        17.03        14.99        21.99         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 
       41.00        39.98        18.05        40.96        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       33.01        21.44        17.82         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 
       10.06        17.56       148.01        85.45        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6748 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        9.99        21.14         1.91        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       25.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 
        5.03        15.02        15.02        17.03        15.02         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6676 TCGA-CM-6677 
       15.02        14.04        11.01        12.95        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6920 
       17.85         4.80        17.13        12.49        15.58         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D8 
       24.43        38.20       130.65        92.75        49.91        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
       98.24         8.61        31.96         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       34.42        41.42        16.24        13.25         0.53        47.41 
TCGA-G4-6299 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       74.56        53.62        44.68        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6626 
       36.00        22.09        13.78        35.80        26.17        46.75 
TCGA-G4-6628 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       79.69        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       10.39        14.50        16.83        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3909 
       17.03        35.01        14.01         1.02        48.03        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  CENPF MUTATED CENPF WILD-TYPE 
              0               0 
  CENPF MUTATED CENPF WILD-TYPE 
         133.18          148.01 
  CENPF MUTATED CENPF WILD-TYPE 
         22.555          20.120 
[1] "0.0 - 133.2 (22.6)" "0.0 - 148.0 (20.1)"
[1] "hr=" "2.2"
D360V2, continuous
D360V3, binary
                 cls
clus                0   1
  CENPF MUTATED    41   5
  CENPF WILD-TYPE 325 114
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CENPF MUTATED     41    5
  CENPF WILD-TYPE  325  114
        clus
vv       CENPF MUTATED CENPF WILD-TYPE
  COLON             41             325
  RECTUM             5             114
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CENPF MUTATED        11        0        5        13         4         0
  CENPF WILD-TYPE      80        1       27       125         6         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CENPF MUTATED           1          0          6          2        1         1
  CENPF WILD-TYPE        23         11         53         40       47        17
                 vv
clus              STAGE IVB
  CENPF MUTATED           1
  CENPF WILD-TYPE         0
D360V4, multiclass
            clus
vv           CENPF MUTATED CENPF WILD-TYPE
  STAGE I               11              80
  STAGE IA               0               1
  STAGE II               5              27
  STAGE IIA             13             125
  STAGE IIB              4               6
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             6              53
  STAGE IIIC             2              40
  STAGE IV               1              47
  STAGE IVA              1              17
  STAGE IVB              1               0
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CENPF MUTATED     2  10  28   6
  CENPF WILD-TYPE  15  82 301  44
D360V5, multiclass
    clus
vv   CENPF MUTATED CENPF WILD-TYPE
  T1             2              15
  T2            10              82
  T3            28             301
  T4             6              44
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  CENPF MUTATED    35   8   3
  CENPF WILD-TYPE 252 105  84
D360V6, multiclass
    clus
vv   CENPF MUTATED CENPF WILD-TYPE
  N0            35             252
  N1             8             105
  N2             3              84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D360V7, binary
                 cls
clus                0   1
  CENPF MUTATED    37   3
  CENPF WILD-TYPE 338  62
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CENPF MUTATED     37    3
  CENPF WILD-TYPE  338   62
   clus
vv  CENPF MUTATED CENPF WILD-TYPE
  0            37             338
  1             3              62
[1] 2 2
[1] FALSE
D360V8, binary
                 cls
clus                0   1
  CENPF MUTATED    24  22
  CENPF WILD-TYPE 201 242
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CENPF MUTATED     24   22
  CENPF WILD-TYPE  201  242
        clus
vv       CENPF MUTATED CENPF WILD-TYPE
  FEMALE            24             201
  MALE              22             242
[1] 2 2
[1] FALSE
D360V9, binary
                 cls
clus                0   1
  CENPF MUTATED    35   2
  CENPF WILD-TYPE 315  20
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CENPF MUTATED     35    2
  CENPF WILD-TYPE  315   20
     clus
vv    CENPF MUTATED CENPF WILD-TYPE
  NO             35             315
  YES             2              20
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CENPF MUTATED                     29                            11
  CENPF WILD-TYPE                  286                            36
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CENPF MUTATED                       5                              0
  CENPF WILD-TYPE                   101                             10
D360V10, multiclass
                                clus
vv                               CENPF MUTATED CENPF WILD-TYPE
  COLON ADENOCARCINOMA                      29             286
  COLON MUCINOUS ADENOCARCINOMA             11              36
  RECTAL ADENOCARCINOMA                      5             101
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  CENPF MUTATED    35   0   0   6
  CENPF WILD-TYPE 310   4  31  19
D360V11, multiclass
    clus
vv   CENPF MUTATED CENPF WILD-TYPE
  R0            35             310
  R1             0               4
  R2             0              31
  RX             6              19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D360V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CENPF MUTATED                                  0     2
  CENPF WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CENPF MUTATED                           3    24
  CENPF WILD-TYPE                        19   202
D360V13, multiclass
                                  clus
vv                                 CENPF MUTATED CENPF WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               9
  BLACK OR AFRICAN AMERICAN                    3              19
  WHITE                                       24             202
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(361) Variable = TXNDC15 MUTATION ANALYSIS
D361V1, survival
                   sevent
clus2                 0   1
  TXNDC15 MUTATED     5   2
  TXNDC15 WILD-TYPE 373  91
  TXNDC15 MUTATED TXNDC15 WILD-TYPE 
                7               464 
  TXNDC15 MUTATED TXNDC15 WILD-TYPE 
                2                91 
$`TXNDC15 MUTATED`
TCGA-AA-3950 TCGA-AA-A00N TCGA-CM-4746 TCGA-CM-6163 TCGA-DM-A285 TCGA-G4-6307 
       24.00         4.01        37.02         2.96         6.12        55.04 
TCGA-AG-A002 
       20.98 

$`TXNDC15 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4747 
       82.95         1.91       124.27        23.05        20.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
       12.00        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       44.68        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  TXNDC15 MUTATED TXNDC15 WILD-TYPE 
             2.96              0.00 
  TXNDC15 MUTATED TXNDC15 WILD-TYPE 
            55.04            148.01 
  TXNDC15 MUTATED TXNDC15 WILD-TYPE 
           20.980            20.155 
[1] "3.0 - 55.0 (21.0)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.7"
D361V2, continuous
D361V3, binary
                   cls
clus                  0   1
  TXNDC15 MUTATED     6   1
  TXNDC15 WILD-TYPE 360 118
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TXNDC15 MUTATED      6    1
  TXNDC15 WILD-TYPE  360  118
        clus
vv       TXNDC15 MUTATED TXNDC15 WILD-TYPE
  COLON                6               360
  RECTUM               1               118
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TXNDC15 MUTATED         3        0        0         1         1         0
  TXNDC15 WILD-TYPE      88        1       32       137         9         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TXNDC15 MUTATED           0          0          1          0        1
  TXNDC15 WILD-TYPE        24         11         58         42       47
                   vv
clus                STAGE IVA STAGE IVB
  TXNDC15 MUTATED           0         0
  TXNDC15 WILD-TYPE        18         1
D361V4, multiclass
            clus
vv           TXNDC15 MUTATED TXNDC15 WILD-TYPE
  STAGE I                  3                88
  STAGE IA                 0                 1
  STAGE II                 0                32
  STAGE IIA                1               137
  STAGE IIB                1                 9
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               0                11
  STAGE IIIB               1                58
  STAGE IIIC               0                42
  STAGE IV                 1                47
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  TXNDC15 MUTATED     1   2   3   1
  TXNDC15 WILD-TYPE  16  90 326  49
D361V5, multiclass
    clus
vv   TXNDC15 MUTATED TXNDC15 WILD-TYPE
  T1               1                16
  T2               2                90
  T3               3               326
  T4               1                49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  TXNDC15 MUTATED     5   1   1
  TXNDC15 WILD-TYPE 282 112  86
D361V6, multiclass
    clus
vv   TXNDC15 MUTATED TXNDC15 WILD-TYPE
  N0               5               282
  N1               1               112
  N2               1                86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D361V7, binary
                   cls
clus                  0   1
  TXNDC15 MUTATED     6   1
  TXNDC15 WILD-TYPE 369  64
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TXNDC15 MUTATED      6    1
  TXNDC15 WILD-TYPE  369   64
   clus
vv  TXNDC15 MUTATED TXNDC15 WILD-TYPE
  0               6               369
  1               1                64
[1] 2 2
[1] FALSE
D361V8, binary
                   cls
clus                  0   1
  TXNDC15 MUTATED     3   4
  TXNDC15 WILD-TYPE 222 260
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TXNDC15 MUTATED      3    4
  TXNDC15 WILD-TYPE  222  260
        clus
vv       TXNDC15 MUTATED TXNDC15 WILD-TYPE
  FEMALE               3               222
  MALE                 4               260
[1] 2 2
[1] FALSE
D361V9, binary
                   cls
clus                  0   1
  TXNDC15 MUTATED     5   0
  TXNDC15 WILD-TYPE 345  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TXNDC15 MUTATED      5    0
  TXNDC15 WILD-TYPE  345   22
     clus
vv    TXNDC15 MUTATED TXNDC15 WILD-TYPE
  NO                5               345
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  TXNDC15 MUTATED                      3                             3
  TXNDC15 WILD-TYPE                  312                            44
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  TXNDC15 MUTATED                       1                              0
  TXNDC15 WILD-TYPE                   105                             10
D361V10, multiclass
                                clus
vv                               TXNDC15 MUTATED TXNDC15 WILD-TYPE
  COLON ADENOCARCINOMA                         3               312
  COLON MUCINOUS ADENOCARCINOMA                3                44
  RECTAL ADENOCARCINOMA                        1               105
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  TXNDC15 MUTATED     6   0   0   0
  TXNDC15 WILD-TYPE 339   4  31  25
D361V11, multiclass
    clus
vv   TXNDC15 MUTATED TXNDC15 WILD-TYPE
  R0               6               339
  R1               0                 4
  R2               0                31
  RX               0                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D361V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TXNDC15 MUTATED                                  0     0
  TXNDC15 WILD-TYPE                                1    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  TXNDC15 MUTATED                           1     3
  TXNDC15 WILD-TYPE                        21   223
D361V13, multiclass
                                  clus
vv                                 TXNDC15 MUTATED TXNDC15 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                      1                21
  WHITE                                          3               223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(362) Variable = TSHR MUTATION ANALYSIS
D362V1, survival
                sevent
clus2              0   1
  TSHR MUTATED    35  13
  TSHR WILD-TYPE 343  80
  TSHR MUTATED TSHR WILD-TYPE 
            48            423 
  TSHR MUTATED TSHR WILD-TYPE 
            13             80 
$`TSHR MUTATED`
TCGA-A6-5665 TCGA-A6-6141 TCGA-AA-3516 TCGA-AA-3555 TCGA-AA-3660 TCGA-AA-3663 
       22.06         8.38        13.02        29.95        78.08         6.97 
TCGA-AA-3947 TCGA-AA-A010 TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A02K TCGA-AD-6890 
       33.01        34.98        38.07         1.02        14.01         0.79 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6603 
       17.82        58.39        62.79        49.41         6.77        29.56 
TCGA-CA-6717 TCGA-CK-5912 TCGA-CM-5868 TCGA-CM-6164 TCGA-CM-6172 TCGA-D5-5538 
       12.76        49.08        17.03        29.03        11.01        12.26 
TCGA-D5-6536 TCGA-D5-6541 TCGA-D5-6926 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0XF 
       17.85        15.58         9.04        12.00        10.26        38.20 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28H TCGA-F4-6460 TCGA-F4-6703 
      139.17         6.12        81.37       117.07        31.96        47.87 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 
       44.68        55.04        85.48        13.78        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2691 TCGA-CL-5918 TCGA-DT-5265 TCGA-F5-6465 
       46.75        79.69        43.04         7.17         5.29        49.51 

$`TSHR WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 
       22.09        32.71        27.09        22.52        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
       63.98         6.97         1.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       17.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
       61.02         6.05        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 
       31.00         2.01        12.99        24.00        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       31.00        31.00        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
        5.03         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6895 TCGA-AD-6899 
        0.07        21.37        15.52        56.55         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AZ-4323 TCGA-AZ-4616 
       16.31         0.95        33.01        21.44         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6605 
      106.75        22.36        88.21        12.10       100.01         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07        12.20        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
      148.01        85.45        15.62        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6161 
       32.02        15.02         5.03        15.02        15.02        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
       12.00         2.96        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       13.02        15.02        14.04        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5539 
       11.08        11.01        10.06        12.03        45.40        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6898 
       15.12         4.80        17.13        12.49        16.14         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6928 
        3.68         4.41        12.43        14.30         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6932 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A1D0 
        4.80         1.51        11.38       119.70        24.43       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
       44.32       131.51       135.65       119.93        35.97        60.79 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6704 TCGA-F4-6805 
       98.24         8.61        35.74         6.18         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6310 
       35.31       133.18        74.56        65.85        53.62        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6586 TCGA-AF-2687 TCGA-AF-2689 
       61.91        36.00        22.09        35.80        24.13        39.48 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-DC-5337 
        6.05        33.17         6.97         4.73        78.12        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        4.01         5.03       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
       18.28         9.96        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  TSHR MUTATED TSHR WILD-TYPE 
          0.79           0.00 
  TSHR MUTATED TSHR WILD-TYPE 
        139.17         148.01 
  TSHR MUTATED TSHR WILD-TYPE 
        29.295         20.020 
[1] "0.8 - 139.2 (29.3)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1"  
D362V2, continuous
D362V3, binary
                cls
clus               0   1
  TSHR MUTATED    44   4
  TSHR WILD-TYPE 322 115
[1] "tbl2"
                cls
clus             [,1] [,2]
  TSHR MUTATED     44    4
  TSHR WILD-TYPE  322  115
        clus
vv       TSHR MUTATED TSHR WILD-TYPE
  COLON            44            322
  RECTUM            4            115
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TSHR MUTATED         5        1        6        17         2         0
  TSHR WILD-TYPE      86        0       26       121         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TSHR MUTATED           2          0          7          3        2         1
  TSHR WILD-TYPE        22         11         52         39       46        17
                vv
clus             STAGE IVB
  TSHR MUTATED           0
  TSHR WILD-TYPE         1
D362V4, multiclass
            clus
vv           TSHR MUTATED TSHR WILD-TYPE
  STAGE I               5             86
  STAGE IA              1              0
  STAGE II              6             26
  STAGE IIA            17            121
  STAGE IIB             2              8
  STAGE IIC             0              1
  STAGE III             2             22
  STAGE IIIA            0             11
  STAGE IIIB            7             52
  STAGE IIIC            3             39
  STAGE IV              2             46
  STAGE IVA             1             17
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  TSHR MUTATED     2   6  33   6
  TSHR WILD-TYPE  15  86 296  44
D362V5, multiclass
    clus
vv   TSHR MUTATED TSHR WILD-TYPE
  T1            2             15
  T2            6             86
  T3           33            296
  T4            6             44
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  TSHR MUTATED    32  10   6
  TSHR WILD-TYPE 255 103  81
D362V6, multiclass
    clus
vv   TSHR MUTATED TSHR WILD-TYPE
  N0           32            255
  N1           10            103
  N2            6             81
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D362V7, binary
                cls
clus               0   1
  TSHR MUTATED    37   3
  TSHR WILD-TYPE 338  62
[1] "tbl2"
                cls
clus             [,1] [,2]
  TSHR MUTATED     37    3
  TSHR WILD-TYPE  338   62
   clus
vv  TSHR MUTATED TSHR WILD-TYPE
  0           37            338
  1            3             62
[1] 2 2
[1] FALSE
D362V8, binary
                cls
clus               0   1
  TSHR MUTATED    27  21
  TSHR WILD-TYPE 198 243
[1] "tbl2"
                cls
clus             [,1] [,2]
  TSHR MUTATED     27   21
  TSHR WILD-TYPE  198  243
        clus
vv       TSHR MUTATED TSHR WILD-TYPE
  FEMALE           27            198
  MALE             21            243
[1] 2 2
[1] FALSE
D362V9, binary
                cls
clus               0   1
  TSHR MUTATED    40   1
  TSHR WILD-TYPE 310  21
[1] "tbl2"
                cls
clus             [,1] [,2]
  TSHR MUTATED     40    1
  TSHR WILD-TYPE  310   21
     clus
vv    TSHR MUTATED TSHR WILD-TYPE
  NO            40            310
  YES            1             21
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  TSHR MUTATED                     37                             6
  TSHR WILD-TYPE                  278                            41
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  TSHR MUTATED                       3                              1
  TSHR WILD-TYPE                   103                              9
D362V10, multiclass
                                clus
vv                               TSHR MUTATED TSHR WILD-TYPE
  COLON ADENOCARCINOMA                     37            278
  COLON MUCINOUS ADENOCARCINOMA             6             41
  RECTAL ADENOCARCINOMA                     3            103
  RECTAL MUCINOUS ADENOCARCINOMA            1              9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  TSHR MUTATED    31   0   1   4
  TSHR WILD-TYPE 314   4  30  21
D362V11, multiclass
    clus
vv   TSHR MUTATED TSHR WILD-TYPE
  R0           31            314
  R1            0              4
  R2            1             30
  RX            4             21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D362V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TSHR MUTATED                                  0     2
  TSHR WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  TSHR MUTATED                           4    33
  TSHR WILD-TYPE                        18   193
D362V13, multiclass
                                  clus
vv                                 TSHR MUTATED TSHR WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              9
  BLACK OR AFRICAN AMERICAN                   4             18
  WHITE                                      33            193
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(363) Variable = KIAA1012 MUTATION ANALYSIS
D363V1, survival
                    sevent
clus2                  0   1
  KIAA1012 MUTATED    18   5
  KIAA1012 WILD-TYPE 360  88
  KIAA1012 MUTATED KIAA1012 WILD-TYPE 
                23                448 
  KIAA1012 MUTATED KIAA1012 WILD-TYPE 
                 5                 88 
$`KIAA1012 MUTATED`
TCGA-A6-6781 TCGA-AA-3663 TCGA-AA-3672 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3815 
       19.66         6.97         0.92        19.04        10.06        33.04 
TCGA-AA-3989 TCGA-AA-A010 TCGA-AU-3779 TCGA-AZ-4315 TCGA-AZ-4682 TCGA-CA-6717 
        7.96        34.98        14.50        58.39        22.36        12.76 
TCGA-CK-5913 TCGA-CM-5344 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-6162 TCGA-D5-5539 
       51.32        22.03        32.02        15.02        12.00        19.59 
TCGA-D5-6536 TCGA-G4-6588 TCGA-G4-6626 TCGA-AG-A002 TCGA-EI-6510 
       17.85        26.17        46.75        20.98        18.28 

$`KIAA1012 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
       54.02         2.01        14.01        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
       85.05        26.99        19.04        35.05         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3994 TCGA-AA-A004 
       24.00        27.02        27.02        19.07        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       10.88         0.20        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-5403 
       21.44        17.82         1.41         5.13       106.75        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07        12.20        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 
       17.56       148.01        85.45        15.62        49.08         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5349 
       37.02        25.02        13.02        29.06        22.98        30.08 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 
        5.03        15.02        15.02        17.03        15.02         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       15.12         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       35.80        91.79        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       20.91         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  KIAA1012 MUTATED KIAA1012 WILD-TYPE 
              0.92               0.00 
  KIAA1012 MUTATED KIAA1012 WILD-TYPE 
             58.39             148.01 
  KIAA1012 MUTATED KIAA1012 WILD-TYPE 
            19.590             20.415 
[1] "0.9 - 58.4 (19.6)"  "0.0 - 148.0 (20.4)"
[1] "hr=" "1.3"
D363V2, continuous
D363V3, binary
                    cls
clus                   0   1
  KIAA1012 MUTATED    23   2
  KIAA1012 WILD-TYPE 343 117
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1012 MUTATED     23    2
  KIAA1012 WILD-TYPE  343  117
        clus
vv       KIAA1012 MUTATED KIAA1012 WILD-TYPE
  COLON                23                343
  RECTUM                2                117
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KIAA1012 MUTATED         2        0        2        10         1         0
  KIAA1012 WILD-TYPE      89        1       30       128         9         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIAA1012 MUTATED           2          1          2          2        1
  KIAA1012 WILD-TYPE        22         10         57         40       47
                    vv
clus                 STAGE IVA STAGE IVB
  KIAA1012 MUTATED           2         0
  KIAA1012 WILD-TYPE        16         1
D363V4, multiclass
            clus
vv           KIAA1012 MUTATED KIAA1012 WILD-TYPE
  STAGE I                   2                 89
  STAGE IA                  0                  1
  STAGE II                  2                 30
  STAGE IIA                10                128
  STAGE IIB                 1                  9
  STAGE IIC                 0                  1
  STAGE III                 2                 22
  STAGE IIIA                1                 10
  STAGE IIIB                2                 57
  STAGE IIIC                2                 40
  STAGE IV                  1                 47
  STAGE IVA                 2                 16
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  KIAA1012 MUTATED     0   3  20   2
  KIAA1012 WILD-TYPE  17  89 309  48
D363V5, multiclass
    clus
vv   KIAA1012 MUTATED KIAA1012 WILD-TYPE
  T1                0                 17
  T2                3                 89
  T3               20                309
  T4                2                 48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  KIAA1012 MUTATED    17   5   3
  KIAA1012 WILD-TYPE 270 108  84
D363V6, multiclass
    clus
vv   KIAA1012 MUTATED KIAA1012 WILD-TYPE
  N0               17                270
  N1                5                108
  N2                3                 84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D363V7, binary
                    cls
clus                   0   1
  KIAA1012 MUTATED    18   2
  KIAA1012 WILD-TYPE 357  63
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1012 MUTATED     18    2
  KIAA1012 WILD-TYPE  357   63
   clus
vv  KIAA1012 MUTATED KIAA1012 WILD-TYPE
  0               18                357
  1                2                 63
[1] 2 2
[1] FALSE
D363V8, binary
                    cls
clus                   0   1
  KIAA1012 MUTATED    11  14
  KIAA1012 WILD-TYPE 214 250
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1012 MUTATED     11   14
  KIAA1012 WILD-TYPE  214  250
        clus
vv       KIAA1012 MUTATED KIAA1012 WILD-TYPE
  FEMALE               11                214
  MALE                 14                250
[1] 2 2
[1] FALSE
D363V9, binary
                    cls
clus                   0   1
  KIAA1012 MUTATED    23   0
  KIAA1012 WILD-TYPE 327  22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1012 MUTATED     23    0
  KIAA1012 WILD-TYPE  327   22
     clus
vv    KIAA1012 MUTATED KIAA1012 WILD-TYPE
  NO                23                327
  YES                0                 22
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  KIAA1012 MUTATED                     18                             5
  KIAA1012 WILD-TYPE                  297                            42
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  KIAA1012 MUTATED                       2                              0
  KIAA1012 WILD-TYPE                   104                             10
D363V10, multiclass
                                clus
vv                               KIAA1012 MUTATED KIAA1012 WILD-TYPE
  COLON ADENOCARCINOMA                         18                297
  COLON MUCINOUS ADENOCARCINOMA                 5                 42
  RECTAL ADENOCARCINOMA                         2                104
  RECTAL MUCINOUS ADENOCARCINOMA                0                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  KIAA1012 MUTATED    21   0   1   3
  KIAA1012 WILD-TYPE 324   4  30  22
D363V11, multiclass
    clus
vv   KIAA1012 MUTATED KIAA1012 WILD-TYPE
  R0               21                324
  R1                0                  4
  R2                1                 30
  RX                3                 22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D363V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KIAA1012 MUTATED                                  0     1
  KIAA1012 WILD-TYPE                                1    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  KIAA1012 MUTATED                           0    16
  KIAA1012 WILD-TYPE                        22   210
D363V13, multiclass
                                  clus
vv                                 KIAA1012 MUTATED KIAA1012 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                 10
  BLACK OR AFRICAN AMERICAN                       0                 22
  WHITE                                          16                210
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(364) Variable = CHML MUTATION ANALYSIS
D364V1, survival
                sevent
clus2              0   1
  CHML MUTATED    18   6
  CHML WILD-TYPE 360  87
  CHML MUTATED CHML WILD-TYPE 
            24            447 
  CHML MUTATED CHML WILD-TYPE 
             6             87 
$`CHML MUTATED`
TCGA-A6-3809 TCGA-A6-6138 TCGA-A6-6141 TCGA-AA-3492 TCGA-AA-3525 TCGA-AA-3662 
       32.75        22.52         8.38         3.02         8.05         6.05 
TCGA-AA-3672 TCGA-AA-3947 TCGA-AD-6964 TCGA-AU-6004 TCGA-AZ-6601 TCGA-CM-5348 
        0.92        33.01        10.88        27.09       100.01        22.98 
TCGA-CM-6162 TCGA-D5-5537 TCGA-D5-6923 TCGA-D5-6928 TCGA-D5-6929 TCGA-F4-6460 
       12.00        45.40        12.43        11.64         4.80        31.96 
TCGA-G4-6323 TCGA-G4-6625 TCGA-AF-6136 TCGA-AG-3890 TCGA-DC-6158 TCGA-F5-6812 
       13.78        91.79        15.39        17.03        10.98         0.66 

$`CHML WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       22.06        32.71        27.09        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
       20.28         7.04         1.02        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       37.05        36.03        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
       78.08         6.97        54.02         2.01        14.01        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
        2.01        12.99        24.00        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
        0.20        14.50        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 
       62.79        88.21        49.41         6.77        12.10        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.03        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       15.02        17.03        15.02         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       10.06        12.03        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6930 
        3.68         4.41        14.30         9.04         9.44         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
        8.61        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       35.80        26.17        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       16.83        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 
       19.99         1.02        17.95        36.95        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
        5.03        13.97        27.95        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  CHML MUTATED CHML WILD-TYPE 
          0.66           0.00 
  CHML MUTATED CHML WILD-TYPE 
        100.01         148.01 
  CHML MUTATED CHML WILD-TYPE 
        13.105         20.910 
[1] "0.7 - 100.0 (13.1)" "0.0 - 148.0 (20.9)"
[1] "hr=" "1.5"
D364V2, continuous
D364V3, binary
                cls
clus               0   1
  CHML MUTATED    20   4
  CHML WILD-TYPE 346 115
[1] "tbl2"
                cls
clus             [,1] [,2]
  CHML MUTATED     20    4
  CHML WILD-TYPE  346  115
        clus
vv       CHML MUTATED CHML WILD-TYPE
  COLON            20            346
  RECTUM            4            115
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CHML MUTATED         5        1        2         5         2         0
  CHML WILD-TYPE      86        0       30       133         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CHML MUTATED           1          0          5          0        2         0
  CHML WILD-TYPE        23         11         54         42       46        18
                vv
clus             STAGE IVB
  CHML MUTATED           0
  CHML WILD-TYPE         1
D364V4, multiclass
            clus
vv           CHML MUTATED CHML WILD-TYPE
  STAGE I               5             86
  STAGE IA              1              0
  STAGE II              2             30
  STAGE IIA             5            133
  STAGE IIB             2              8
  STAGE IIC             0              1
  STAGE III             1             23
  STAGE IIIA            0             11
  STAGE IIIB            5             54
  STAGE IIIC            0             42
  STAGE IV              2             46
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  CHML MUTATED     0   5  14   4
  CHML WILD-TYPE  17  87 315  46
D364V5, multiclass
    clus
vv   CHML MUTATED CHML WILD-TYPE
  T1            0             17
  T2            5             87
  T3           14            315
  T4            4             46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  CHML MUTATED    14   7   3
  CHML WILD-TYPE 273 106  84
D364V6, multiclass
    clus
vv   CHML MUTATED CHML WILD-TYPE
  N0           14            273
  N1            7            106
  N2            3             84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D364V7, binary
                cls
clus               0   1
  CHML MUTATED    18   2
  CHML WILD-TYPE 357  63
[1] "tbl2"
                cls
clus             [,1] [,2]
  CHML MUTATED     18    2
  CHML WILD-TYPE  357   63
   clus
vv  CHML MUTATED CHML WILD-TYPE
  0           18            357
  1            2             63
[1] 2 2
[1] FALSE
D364V8, binary
                cls
clus               0   1
  CHML MUTATED    11  13
  CHML WILD-TYPE 214 251
[1] "tbl2"
                cls
clus             [,1] [,2]
  CHML MUTATED     11   13
  CHML WILD-TYPE  214  251
        clus
vv       CHML MUTATED CHML WILD-TYPE
  FEMALE           11            214
  MALE             13            251
[1] 2 2
[1] FALSE
D364V9, binary
                cls
clus               0   1
  CHML MUTATED    20   1
  CHML WILD-TYPE 330  21
[1] "tbl2"
                cls
clus             [,1] [,2]
  CHML MUTATED     20    1
  CHML WILD-TYPE  330   21
     clus
vv    CHML MUTATED CHML WILD-TYPE
  NO            20            330
  YES            1             21
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CHML MUTATED                     16                             4
  CHML WILD-TYPE                  299                            43
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CHML MUTATED                       4                              0
  CHML WILD-TYPE                   102                             10
D364V10, multiclass
                                clus
vv                               CHML MUTATED CHML WILD-TYPE
  COLON ADENOCARCINOMA                     16            299
  COLON MUCINOUS ADENOCARCINOMA             4             43
  RECTAL ADENOCARCINOMA                     4            102
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  CHML MUTATED    17   0   1   1
  CHML WILD-TYPE 328   4  30  24
D364V11, multiclass
    clus
vv   CHML MUTATED CHML WILD-TYPE
  R0           17            328
  R1            0              4
  R2            1             30
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D364V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CHML MUTATED                                  0     0
  CHML WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  CHML MUTATED                           2    16
  CHML WILD-TYPE                        20   210
D364V13, multiclass
                                  clus
vv                                 CHML MUTATED CHML WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   2             20
  WHITE                                      16            210
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(365) Variable = TGFBR1 MUTATION ANALYSIS
D365V1, survival
                  sevent
clus2                0   1
  TGFBR1 MUTATED    15   2
  TGFBR1 WILD-TYPE 363  91
  TGFBR1 MUTATED TGFBR1 WILD-TYPE 
              17              454 
  TGFBR1 MUTATED TGFBR1 WILD-TYPE 
               2               91 
$`TGFBR1 MUTATED`
TCGA-A6-6138 TCGA-A6-6653 TCGA-AA-3492 TCGA-AA-3663 TCGA-AA-A00J TCGA-AA-A00N 
       22.52        24.39         3.02         6.97        18.05         4.01 
TCGA-AA-A00R TCGA-AA-A010 TCGA-AZ-4315 TCGA-CA-6717 TCGA-CK-6751 TCGA-D5-5541 
        0.99        34.98        58.39        12.76       124.27        55.92 
TCGA-D5-6927 TCGA-F4-6806 TCGA-AG-3598 TCGA-AG-3892 TCGA-AG-A02N 
        9.44        41.42        50.04        13.02        61.97 

$`TGFBR1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6141 TCGA-A6-6142 
       22.09        22.06        32.71        27.09         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 
       25.18        24.16        21.76        24.69        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       19.66        20.28         7.04         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02        78.08         6.05        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00U 
       34.03        18.05        38.04        27.02        42.02        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       33.01        21.44        17.82         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       19.59        56.09        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.04        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6807 
       35.74         6.18        47.87         1.55        34.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3599 TCGA-AG-3600 
        1.02        46.03        34.03         2.01        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 
       19.99         1.02        17.95        36.95        17.03        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
        1.94        38.96        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  TGFBR1 MUTATED TGFBR1 WILD-TYPE 
            0.99             0.00 
  TGFBR1 MUTATED TGFBR1 WILD-TYPE 
          124.27           148.01 
  TGFBR1 MUTATED TGFBR1 WILD-TYPE 
          22.520           20.155 
[1] "1.0 - 124.3 (22.5)" "0.0 - 148.0 (20.2)"
[1] "hr=" "2.1"
D365V2, continuous
D365V3, binary
                  cls
clus                 0   1
  TGFBR1 MUTATED    14   3
  TGFBR1 WILD-TYPE 352 116
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TGFBR1 MUTATED     14    3
  TGFBR1 WILD-TYPE  352  116
        clus
vv       TGFBR1 MUTATED TGFBR1 WILD-TYPE
  COLON              14              352
  RECTUM              3              116
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TGFBR1 MUTATED         6        0        3         4         2         0
  TGFBR1 WILD-TYPE      85        1       29       134         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TGFBR1 MUTATED           0          0          2          0        0
  TGFBR1 WILD-TYPE        24         11         57         42       48
                  vv
clus               STAGE IVA STAGE IVB
  TGFBR1 MUTATED           0         0
  TGFBR1 WILD-TYPE        18         1
D365V4, multiclass
            clus
vv           TGFBR1 MUTATED TGFBR1 WILD-TYPE
  STAGE I                 6               85
  STAGE IA                0                1
  STAGE II                3               29
  STAGE IIA               4              134
  STAGE IIB               2                8
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              2               57
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  TGFBR1 MUTATED     1   5   8   3
  TGFBR1 WILD-TYPE  16  87 321  47
D365V5, multiclass
    clus
vv   TGFBR1 MUTATED TGFBR1 WILD-TYPE
  T1              1               16
  T2              5               87
  T3              8              321
  T4              3               47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  TGFBR1 MUTATED    15   2   0
  TGFBR1 WILD-TYPE 272 111  87
D365V6, multiclass
    clus
vv   TGFBR1 MUTATED TGFBR1 WILD-TYPE
  N0             15              272
  N1              2              111
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D365V7, binary
                  cls
clus                 0   1
  TGFBR1 MUTATED    16   0
  TGFBR1 WILD-TYPE 359  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TGFBR1 MUTATED     16    0
  TGFBR1 WILD-TYPE  359   65
   clus
vv  TGFBR1 MUTATED TGFBR1 WILD-TYPE
  0             16              359
  1              0               65
[1] 2 2
[1] FALSE
D365V8, binary
                  cls
clus                 0   1
  TGFBR1 MUTATED     6  11
  TGFBR1 WILD-TYPE 219 253
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TGFBR1 MUTATED      6   11
  TGFBR1 WILD-TYPE  219  253
        clus
vv       TGFBR1 MUTATED TGFBR1 WILD-TYPE
  FEMALE              6              219
  MALE               11              253
[1] 2 2
[1] FALSE
D365V9, binary
                  cls
clus                 0   1
  TGFBR1 MUTATED    14   0
  TGFBR1 WILD-TYPE 336  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TGFBR1 MUTATED     14    0
  TGFBR1 WILD-TYPE  336   22
     clus
vv    TGFBR1 MUTATED TGFBR1 WILD-TYPE
  NO              14              336
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  TGFBR1 MUTATED                     10                             4
  TGFBR1 WILD-TYPE                  305                            43
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  TGFBR1 MUTATED                       3                              0
  TGFBR1 WILD-TYPE                   103                             10
D365V10, multiclass
                                clus
vv                               TGFBR1 MUTATED TGFBR1 WILD-TYPE
  COLON ADENOCARCINOMA                       10              305
  COLON MUCINOUS ADENOCARCINOMA               4               43
  RECTAL ADENOCARCINOMA                       3              103
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  TGFBR1 MUTATED    13   0   0   2
  TGFBR1 WILD-TYPE 332   4  31  23
D365V11, multiclass
    clus
vv   TGFBR1 MUTATED TGFBR1 WILD-TYPE
  R0             13              332
  R1              0                4
  R2              0               31
  RX              2               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D365V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TGFBR1 MUTATED                                  0     1
  TGFBR1 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  TGFBR1 MUTATED                           0     7
  TGFBR1 WILD-TYPE                        22   219
D365V13, multiclass
                                  clus
vv                                 TGFBR1 MUTATED TGFBR1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         7              219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(366) Variable = ETAA1 MUTATION ANALYSIS
D366V1, survival
                 sevent
clus2               0   1
  ETAA1 MUTATED    16   2
  ETAA1 WILD-TYPE 362  91
  ETAA1 MUTATED ETAA1 WILD-TYPE 
             18             453 
  ETAA1 MUTATED ETAA1 WILD-TYPE 
              2              91 
$`ETAA1 MUTATED`
TCGA-AA-3492 TCGA-AA-3525 TCGA-AA-3663 TCGA-AA-3866 TCGA-AA-3977 TCGA-AA-A010 
        3.02         8.05         6.97        17.03        25.02        34.98 
TCGA-AD-5900 TCGA-AZ-4315 TCGA-AZ-5407 TCGA-CA-6717 TCGA-D5-5541 TCGA-D5-6539 
        0.07        58.39        88.21        12.76        55.92        12.49 
TCGA-D5-6927 TCGA-DM-A1HA TCGA-F4-6459 TCGA-G4-6588 TCGA-AG-3892 TCGA-AG-A002 
        9.44       131.51         8.61        26.17        13.02        20.98 

$`ETAA1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3526 
        1.02         9.07        24.03        37.05        36.03        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3867 TCGA-AA-3869 
       31.07        31.07        30.05        53.00        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 
        0.92        41.00        39.98        18.05        40.96        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        33.01        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
      106.75        22.36        62.79        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       12.26        19.59        56.09        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 
       43.27        15.12        17.85         4.80        17.13        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.04        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
       60.79       117.07        98.24        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 
       61.91        36.00        22.09        13.78        35.80        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 
        1.02        17.95        36.95        17.03        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  ETAA1 MUTATED ETAA1 WILD-TYPE 
           0.07            0.00 
  ETAA1 MUTATED ETAA1 WILD-TYPE 
         131.51          148.01 
  ETAA1 MUTATED ETAA1 WILD-TYPE 
         15.025          20.280 
[1] "0.1 - 131.5 (15.0)" "0.0 - 148.0 (20.3)"
[1] "hr=" "2"  
D366V2, continuous
D366V3, binary
                 cls
clus                0   1
  ETAA1 MUTATED    16   2
  ETAA1 WILD-TYPE 350 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ETAA1 MUTATED     16    2
  ETAA1 WILD-TYPE  350  117
        clus
vv       ETAA1 MUTATED ETAA1 WILD-TYPE
  COLON             16             350
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ETAA1 MUTATED         5        0        2         4         1         0
  ETAA1 WILD-TYPE      86        1       30       134         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ETAA1 MUTATED           0          1          3          1        0         0
  ETAA1 WILD-TYPE        24         10         56         41       48        18
                 vv
clus              STAGE IVB
  ETAA1 MUTATED           0
  ETAA1 WILD-TYPE         1
D366V4, multiclass
            clus
vv           ETAA1 MUTATED ETAA1 WILD-TYPE
  STAGE I                5              86
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA              4             134
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             1              10
  STAGE IIIB             3              56
  STAGE IIIC             1              41
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ETAA1 MUTATED     2   4  11   1
  ETAA1 WILD-TYPE  15  88 318  49
D366V5, multiclass
    clus
vv   ETAA1 MUTATED ETAA1 WILD-TYPE
  T1             2              15
  T2             4              88
  T3            11             318
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  ETAA1 MUTATED    14   2   2
  ETAA1 WILD-TYPE 273 111  85
D366V6, multiclass
    clus
vv   ETAA1 MUTATED ETAA1 WILD-TYPE
  N0            14             273
  N1             2             111
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D366V7, binary
                 cls
clus                0   1
  ETAA1 MUTATED    16   0
  ETAA1 WILD-TYPE 359  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ETAA1 MUTATED     16    0
  ETAA1 WILD-TYPE  359   65
   clus
vv  ETAA1 MUTATED ETAA1 WILD-TYPE
  0            16             359
  1             0              65
[1] 2 2
[1] FALSE
D366V8, binary
                 cls
clus                0   1
  ETAA1 MUTATED     8  10
  ETAA1 WILD-TYPE 217 254
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ETAA1 MUTATED      8   10
  ETAA1 WILD-TYPE  217  254
        clus
vv       ETAA1 MUTATED ETAA1 WILD-TYPE
  FEMALE             8             217
  MALE              10             254
[1] 2 2
[1] FALSE
D366V9, binary
                 cls
clus                0   1
  ETAA1 MUTATED    16   0
  ETAA1 WILD-TYPE 334  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ETAA1 MUTATED     16    0
  ETAA1 WILD-TYPE  334   22
     clus
vv    ETAA1 MUTATED ETAA1 WILD-TYPE
  NO             16             334
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ETAA1 MUTATED                     14                             2
  ETAA1 WILD-TYPE                  301                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ETAA1 MUTATED                       2                              0
  ETAA1 WILD-TYPE                   104                             10
D366V10, multiclass
                                clus
vv                               ETAA1 MUTATED ETAA1 WILD-TYPE
  COLON ADENOCARCINOMA                      14             301
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  ETAA1 MUTATED    14   0   0   1
  ETAA1 WILD-TYPE 331   4  31  24
D366V11, multiclass
    clus
vv   ETAA1 MUTATED ETAA1 WILD-TYPE
  R0            14             331
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D366V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ETAA1 MUTATED                                  0     1
  ETAA1 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ETAA1 MUTATED                           0     9
  ETAA1 WILD-TYPE                        22   217
D366V13, multiclass
                                  clus
vv                                 ETAA1 MUTATED ETAA1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        9             217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(367) Variable = DEPDC5 MUTATION ANALYSIS
D367V1, survival
                  sevent
clus2                0   1
  DEPDC5 MUTATED    19   3
  DEPDC5 WILD-TYPE 359  90
  DEPDC5 MUTATED DEPDC5 WILD-TYPE 
              22              449 
  DEPDC5 MUTATED DEPDC5 WILD-TYPE 
               3               90 
$`DEPDC5 MUTATED`
TCGA-A6-5661 TCGA-A6-6141 TCGA-A6-6781 TCGA-AA-3715 TCGA-AA-3819 TCGA-AA-A00N 
       33.53         8.38        19.66        19.04        25.02         4.01 
TCGA-AA-A01R TCGA-AD-6895 TCGA-AU-6004 TCGA-AY-6197 TCGA-CM-4744 TCGA-CM-4746 
       35.01         0.72        27.09        21.44        20.02        37.02 
TCGA-CM-6171 TCGA-D5-6927 TCGA-DM-A28F TCGA-G4-6586 TCGA-G4-6625 TCGA-AG-3742 
       14.04         9.44        35.97        35.80        91.79         0.99 
TCGA-AG-3892 TCGA-AG-A002 TCGA-DC-6157 TCGA-EF-5830 
       13.02        20.98        27.95         0.49 

$`DEPDC5 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 
       22.06        32.71        27.09        22.52        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       85.05        26.99        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
        0.99         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       15.52        56.55         0.79         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       10.88         0.20        14.50        16.31         0.95        33.01 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
      124.27        23.05        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G 
      135.65       139.17         6.12        81.37       119.93        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6626 
       61.91        36.00        22.09        13.78        26.17        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
       32.98         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       36.95        17.03        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6158 TCGA-DC-6160 
        7.17        15.02         5.03        13.97        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EI-6506 TCGA-EI-6507 
       57.24        24.13        51.48        32.61        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  DEPDC5 MUTATED DEPDC5 WILD-TYPE 
            0.49             0.00 
  DEPDC5 MUTATED DEPDC5 WILD-TYPE 
           91.79           148.01 
  DEPDC5 MUTATED DEPDC5 WILD-TYPE 
           20.50            20.19 
[1] "0.5 - 91.8 (20.5)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.2"
D367V2, continuous
D367V3, binary
                  cls
clus                 0   1
  DEPDC5 MUTATED    19   5
  DEPDC5 WILD-TYPE 347 114
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DEPDC5 MUTATED     19    5
  DEPDC5 WILD-TYPE  347  114
        clus
vv       DEPDC5 MUTATED DEPDC5 WILD-TYPE
  COLON              19              347
  RECTUM              5              114
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEPDC5 MUTATED         9        0        1         7         2         0
  DEPDC5 WILD-TYPE      82        1       31       131         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DEPDC5 MUTATED           1          0          1          2        0
  DEPDC5 WILD-TYPE        23         11         58         40       48
                  vv
clus               STAGE IVA STAGE IVB
  DEPDC5 MUTATED           0         0
  DEPDC5 WILD-TYPE        18         1
D367V4, multiclass
            clus
vv           DEPDC5 MUTATED DEPDC5 WILD-TYPE
  STAGE I                 9               82
  STAGE IA                0                1
  STAGE II                1               31
  STAGE IIA               7              131
  STAGE IIB               2                8
  STAGE IIC               0                1
  STAGE III               1               23
  STAGE IIIA              0               11
  STAGE IIIB              1               58
  STAGE IIIC              2               40
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  DEPDC5 MUTATED     2   7  12   3
  DEPDC5 WILD-TYPE  15  85 317  47
D367V5, multiclass
    clus
vv   DEPDC5 MUTATED DEPDC5 WILD-TYPE
  T1              2               15
  T2              7               85
  T3             12              317
  T4              3               47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  DEPDC5 MUTATED    19   3   2
  DEPDC5 WILD-TYPE 268 110  85
D367V6, multiclass
    clus
vv   DEPDC5 MUTATED DEPDC5 WILD-TYPE
  N0             19              268
  N1              3              110
  N2              2               85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D367V7, binary
                  cls
clus                 0   1
  DEPDC5 MUTATED    19   0
  DEPDC5 WILD-TYPE 356  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DEPDC5 MUTATED     19    0
  DEPDC5 WILD-TYPE  356   65
   clus
vv  DEPDC5 MUTATED DEPDC5 WILD-TYPE
  0             19              356
  1              0               65
[1] 2 2
[1] FALSE
D367V8, binary
                  cls
clus                 0   1
  DEPDC5 MUTATED     8  16
  DEPDC5 WILD-TYPE 217 248
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DEPDC5 MUTATED      8   16
  DEPDC5 WILD-TYPE  217  248
        clus
vv       DEPDC5 MUTATED DEPDC5 WILD-TYPE
  FEMALE              8              217
  MALE               16              248
[1] 2 2
[1] FALSE
D367V9, binary
                  cls
clus                 0   1
  DEPDC5 MUTATED    14   1
  DEPDC5 WILD-TYPE 336  21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DEPDC5 MUTATED     14    1
  DEPDC5 WILD-TYPE  336   21
     clus
vv    DEPDC5 MUTATED DEPDC5 WILD-TYPE
  NO              14              336
  YES              1               21
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  DEPDC5 MUTATED                     15                             4
  DEPDC5 WILD-TYPE                  300                            43
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  DEPDC5 MUTATED                       5                              0
  DEPDC5 WILD-TYPE                   101                             10
D367V10, multiclass
                                clus
vv                               DEPDC5 MUTATED DEPDC5 WILD-TYPE
  COLON ADENOCARCINOMA                       15              300
  COLON MUCINOUS ADENOCARCINOMA               4               43
  RECTAL ADENOCARCINOMA                       5              101
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  DEPDC5 MUTATED    20   0   0   1
  DEPDC5 WILD-TYPE 325   4  31  24
D367V11, multiclass
    clus
vv   DEPDC5 MUTATED DEPDC5 WILD-TYPE
  R0             20              325
  R1              0                4
  R2              0               31
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D367V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEPDC5 MUTATED                                  0     0
  DEPDC5 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  DEPDC5 MUTATED                           4    13
  DEPDC5 WILD-TYPE                        18   213
D367V13, multiclass
                                  clus
vv                                 DEPDC5 MUTATED DEPDC5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     4               18
  WHITE                                        13              213
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(368) Variable = DPCR1 MUTATION ANALYSIS
D368V1, survival
                 sevent
clus2               0   1
  DPCR1 MUTATED    14   1
  DPCR1 WILD-TYPE 364  92
  DPCR1 MUTATED DPCR1 WILD-TYPE 
             15             456 
  DPCR1 MUTATED DPCR1 WILD-TYPE 
              1              92 
$`DPCR1 MUTATED`
TCGA-A6-6141 TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3510 TCGA-AA-A010 TCGA-AD-6963 
        8.38        20.12        19.66        63.98        34.98        27.42 
TCGA-CM-5861 TCGA-CM-5868 TCGA-D5-5541 TCGA-D5-6534 TCGA-F4-6570 TCGA-F4-6856 
       15.02        17.03        55.92        43.27         6.18        35.31 
TCGA-AG-A002 TCGA-DC-6157 TCGA-DC-6160 
       20.98        27.95        19.99 

$`DPCR1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 
       22.09        22.06        32.71        27.09        22.52        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 
       20.28         7.04         3.02         1.02        35.01         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       22.98        30.08        32.02         5.03        15.02        15.02 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-6529 
       12.03        45.40        12.26        19.59        56.09        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       18.25         1.32        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 
       98.24         8.61        31.96        35.74        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       47.41       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6158 
       78.12         7.17        15.02         5.03        13.97        10.98 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  DPCR1 MUTATED DPCR1 WILD-TYPE 
           6.18            0.00 
  DPCR1 MUTATED DPCR1 WILD-TYPE 
          63.98          148.01 
  DPCR1 MUTATED DPCR1 WILD-TYPE 
          20.98           20.12 
[1] "6.2 - 64.0 (21.0)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "3.2"
D368V2, continuous
D368V3, binary
                 cls
clus                0   1
  DPCR1 MUTATED    12   3
  DPCR1 WILD-TYPE 354 116
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DPCR1 MUTATED     12    3
  DPCR1 WILD-TYPE  354  116
        clus
vv       DPCR1 MUTATED DPCR1 WILD-TYPE
  COLON             12             354
  RECTUM             3             116
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DPCR1 MUTATED         4        0        1         5         1         0
  DPCR1 WILD-TYPE      87        1       31       133         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DPCR1 MUTATED           0          0          1          1        0         1
  DPCR1 WILD-TYPE        24         11         58         41       48        17
                 vv
clus              STAGE IVB
  DPCR1 MUTATED           0
  DPCR1 WILD-TYPE         1
D368V4, multiclass
            clus
vv           DPCR1 MUTATED DPCR1 WILD-TYPE
  STAGE I                4              87
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              5             133
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             1              41
  STAGE IV               0              48
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  DPCR1 MUTATED     0   4   8   3
  DPCR1 WILD-TYPE  17  88 321  47
D368V5, multiclass
    clus
vv   DPCR1 MUTATED DPCR1 WILD-TYPE
  T1             0              17
  T2             4              88
  T3             8             321
  T4             3              47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  DPCR1 MUTATED    12   3   0
  DPCR1 WILD-TYPE 275 110  87
D368V6, multiclass
    clus
vv   DPCR1 MUTATED DPCR1 WILD-TYPE
  N0            12             275
  N1             3             110
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D368V7, binary
                 cls
clus                0   1
  DPCR1 MUTATED    11   1
  DPCR1 WILD-TYPE 364  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DPCR1 MUTATED     11    1
  DPCR1 WILD-TYPE  364   64
   clus
vv  DPCR1 MUTATED DPCR1 WILD-TYPE
  0            11             364
  1             1              64
[1] 2 2
[1] FALSE
D368V8, binary
                 cls
clus                0   1
  DPCR1 MUTATED     5  10
  DPCR1 WILD-TYPE 220 254
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DPCR1 MUTATED      5   10
  DPCR1 WILD-TYPE  220  254
        clus
vv       DPCR1 MUTATED DPCR1 WILD-TYPE
  FEMALE             5             220
  MALE              10             254
[1] 2 2
[1] FALSE
D368V9, binary
                 cls
clus                0   1
  DPCR1 MUTATED    13   0
  DPCR1 WILD-TYPE 337  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DPCR1 MUTATED     13    0
  DPCR1 WILD-TYPE  337   22
     clus
vv    DPCR1 MUTATED DPCR1 WILD-TYPE
  NO             13             337
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  DPCR1 MUTATED                      8                             4
  DPCR1 WILD-TYPE                  307                            43
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  DPCR1 MUTATED                       3                              0
  DPCR1 WILD-TYPE                   103                             10
D368V10, multiclass
                                clus
vv                               DPCR1 MUTATED DPCR1 WILD-TYPE
  COLON ADENOCARCINOMA                       8             307
  COLON MUCINOUS ADENOCARCINOMA              4              43
  RECTAL ADENOCARCINOMA                      3             103
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  DPCR1 MUTATED    12   0   0   0
  DPCR1 WILD-TYPE 333   4  31  25
D368V11, multiclass
    clus
vv   DPCR1 MUTATED DPCR1 WILD-TYPE
  R0            12             333
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D368V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DPCR1 MUTATED                                  0     0
  DPCR1 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  DPCR1 MUTATED                           2    10
  DPCR1 WILD-TYPE                        20   216
D368V13, multiclass
                                  clus
vv                                 DPCR1 MUTATED DPCR1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    2              20
  WHITE                                       10             216
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(369) Variable = NOTCH2NL MUTATION ANALYSIS
D369V1, survival
                    sevent
clus2                  0   1
  NOTCH2NL MUTATED     5   1
  NOTCH2NL WILD-TYPE 373  92
  NOTCH2NL MUTATED NOTCH2NL WILD-TYPE 
                 6                465 
  NOTCH2NL MUTATED NOTCH2NL WILD-TYPE 
                 1                 92 
$`NOTCH2NL MUTATED`
TCGA-A6-6649 TCGA-AA-3520 TCGA-AA-A00N TCGA-AZ-4315 TCGA-D5-6923 TCGA-G4-6588 
       24.16        24.03         4.01        58.39        12.43        26.17 

$`NOTCH2NL WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.08        25.18        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        1.02         9.07        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       22.09        13.78        35.80        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  NOTCH2NL MUTATED NOTCH2NL WILD-TYPE 
              4.01               0.00 
  NOTCH2NL MUTATED NOTCH2NL WILD-TYPE 
             58.39             148.01 
  NOTCH2NL MUTATED NOTCH2NL WILD-TYPE 
            24.095             20.120 
[1] "4.0 - 58.4 (24.1)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.2"
D369V2, continuous
D369V3, binary
                    cls
clus                   0   1
  NOTCH2NL MUTATED     6   0
  NOTCH2NL WILD-TYPE 360 119
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  NOTCH2NL MUTATED      6    0
  NOTCH2NL WILD-TYPE  360  119
        clus
vv       NOTCH2NL MUTATED NOTCH2NL WILD-TYPE
  COLON                 6                360
  RECTUM                0                119
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NOTCH2NL MUTATED         1        0        1         2         1         0
  NOTCH2NL WILD-TYPE      90        1       31       136         9         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NOTCH2NL MUTATED           0          0          1          0        0
  NOTCH2NL WILD-TYPE        24         11         58         42       48
                    vv
clus                 STAGE IVA STAGE IVB
  NOTCH2NL MUTATED           0         0
  NOTCH2NL WILD-TYPE        18         1
D369V4, multiclass
            clus
vv           NOTCH2NL MUTATED NOTCH2NL WILD-TYPE
  STAGE I                   1                 90
  STAGE IA                  0                  1
  STAGE II                  1                 31
  STAGE IIA                 2                136
  STAGE IIB                 1                  9
  STAGE IIC                 0                  1
  STAGE III                 0                 24
  STAGE IIIA                0                 11
  STAGE IIIB                1                 58
  STAGE IIIC                0                 42
  STAGE IV                  0                 48
  STAGE IVA                 0                 18
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  NOTCH2NL MUTATED     0   1   4   1
  NOTCH2NL WILD-TYPE  17  91 325  49
D369V5, multiclass
    clus
vv   NOTCH2NL MUTATED NOTCH2NL WILD-TYPE
  T1                0                 17
  T2                1                 91
  T3                4                325
  T4                1                 49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  NOTCH2NL MUTATED     5   1   0
  NOTCH2NL WILD-TYPE 282 112  87
D369V6, multiclass
    clus
vv   NOTCH2NL MUTATED NOTCH2NL WILD-TYPE
  N0                5                282
  N1                1                112
  N2                0                 87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D369V7, binary
                    cls
clus                   0   1
  NOTCH2NL MUTATED     6   0
  NOTCH2NL WILD-TYPE 369  65
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  NOTCH2NL MUTATED      6    0
  NOTCH2NL WILD-TYPE  369   65
   clus
vv  NOTCH2NL MUTATED NOTCH2NL WILD-TYPE
  0                6                369
  1                0                 65
[1] 2 2
[1] FALSE
D369V8, binary
                    cls
clus                   0   1
  NOTCH2NL MUTATED     2   4
  NOTCH2NL WILD-TYPE 223 260
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  NOTCH2NL MUTATED      2    4
  NOTCH2NL WILD-TYPE  223  260
        clus
vv       NOTCH2NL MUTATED NOTCH2NL WILD-TYPE
  FEMALE                2                223
  MALE                  4                260
[1] 2 2
[1] FALSE
D369V9, binary
                    cls
clus                   0   1
  NOTCH2NL MUTATED     5   0
  NOTCH2NL WILD-TYPE 345  22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  NOTCH2NL MUTATED      5    0
  NOTCH2NL WILD-TYPE  345   22
     clus
vv    NOTCH2NL MUTATED NOTCH2NL WILD-TYPE
  NO                 5                345
  YES                0                 22
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  NOTCH2NL MUTATED                      5                             1
  NOTCH2NL WILD-TYPE                  310                            46
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  NOTCH2NL MUTATED                       0                              0
  NOTCH2NL WILD-TYPE                   106                             10
D369V10, multiclass
                                clus
vv                               NOTCH2NL MUTATED NOTCH2NL WILD-TYPE
  COLON ADENOCARCINOMA                          5                310
  COLON MUCINOUS ADENOCARCINOMA                 1                 46
  RECTAL ADENOCARCINOMA                         0                106
  RECTAL MUCINOUS ADENOCARCINOMA                0                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  NOTCH2NL MUTATED     5   0   0   0
  NOTCH2NL WILD-TYPE 340   4  31  25
D369V11, multiclass
    clus
vv   NOTCH2NL MUTATED NOTCH2NL WILD-TYPE
  R0                5                340
  R1                0                  4
  R2                0                 31
  RX                0                 25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D369V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NOTCH2NL MUTATED                                  0     0
  NOTCH2NL WILD-TYPE                                1    11
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  NOTCH2NL MUTATED                           0     4
  NOTCH2NL WILD-TYPE                        22   222
D369V13, multiclass
                                  clus
vv                                 NOTCH2NL MUTATED NOTCH2NL WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 11
  BLACK OR AFRICAN AMERICAN                       0                 22
  WHITE                                           4                222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(370) Variable = RNF160 MUTATION ANALYSIS
D370V1, survival
                  sevent
clus2                0   1
  RNF160 MUTATED    15   3
  RNF160 WILD-TYPE 363  90
  RNF160 MUTATED RNF160 WILD-TYPE 
              18              453 
  RNF160 MUTATED RNF160 WILD-TYPE 
               3               90 
$`RNF160 MUTATED`
TCGA-A6-5657 TCGA-AA-3949 TCGA-AA-A00A TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A01R 
       31.63        26.01        38.04         4.01        27.02        35.01 
TCGA-AD-6965 TCGA-AZ-4681 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4948 TCGA-CK-6747 
        0.20       106.75        12.76        10.06       148.01        82.95 
TCGA-CM-5861 TCGA-DM-A1DB TCGA-G4-6293 TCGA-G4-6315 TCGA-AG-A002 TCGA-DC-6682 
       15.02        44.32       133.18        61.91        20.98         4.01 

$`RNF160 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-3952 
        2.01        12.99        24.00        33.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00D 
       27.02        19.07         7.96        27.02        13.94        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00Q 
       30.02        34.03        18.05        18.05        38.04        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
        1.02         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        10.88        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
        5.13        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       12.20        14.30        17.56        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       51.32         9.99        21.14         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       22.98        30.08        32.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HA 
       49.91        13.32        12.59       140.38         7.50       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6299 
       33.67        13.25         0.53        47.41        35.31        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 
       13.97        27.95        10.98        19.99         5.95         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  RNF160 MUTATED RNF160 WILD-TYPE 
             0.2              0.0 
  RNF160 MUTATED RNF160 WILD-TYPE 
          148.01           140.38 
  RNF160 MUTATED RNF160 WILD-TYPE 
          29.325           20.020 
[1] "0.2 - 148.0 (29.3)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1.8"
D370V2, continuous
D370V3, binary
                  cls
clus                 0   1
  RNF160 MUTATED    16   2
  RNF160 WILD-TYPE 350 117
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF160 MUTATED     16    2
  RNF160 WILD-TYPE  350  117
        clus
vv       RNF160 MUTATED RNF160 WILD-TYPE
  COLON              16              350
  RECTUM              2              117
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RNF160 MUTATED         1        0        0         8         1         0
  RNF160 WILD-TYPE      90        1       32       130         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RNF160 MUTATED           3          0          2          1        1
  RNF160 WILD-TYPE        21         11         57         41       47
                  vv
clus               STAGE IVA STAGE IVB
  RNF160 MUTATED           0         0
  RNF160 WILD-TYPE        18         1
D370V4, multiclass
            clus
vv           RNF160 MUTATED RNF160 WILD-TYPE
  STAGE I                 1               90
  STAGE IA                0                1
  STAGE II                0               32
  STAGE IIA               8              130
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               3               21
  STAGE IIIA              0               11
  STAGE IIIB              2               57
  STAGE IIIC              1               41
  STAGE IV                1               47
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  RNF160 MUTATED     0   1  15   2
  RNF160 WILD-TYPE  17  91 314  48
D370V5, multiclass
    clus
vv   RNF160 MUTATED RNF160 WILD-TYPE
  T1              0               17
  T2              1               91
  T3             15              314
  T4              2               48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  RNF160 MUTATED    10   5   3
  RNF160 WILD-TYPE 277 108  84
D370V6, multiclass
    clus
vv   RNF160 MUTATED RNF160 WILD-TYPE
  N0             10              277
  N1              5              108
  N2              3               84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D370V7, binary
                  cls
clus                 0   1
  RNF160 MUTATED    15   1
  RNF160 WILD-TYPE 360  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF160 MUTATED     15    1
  RNF160 WILD-TYPE  360   64
   clus
vv  RNF160 MUTATED RNF160 WILD-TYPE
  0             15              360
  1              1               64
[1] 2 2
[1] FALSE
D370V8, binary
                  cls
clus                 0   1
  RNF160 MUTATED     7  11
  RNF160 WILD-TYPE 218 253
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF160 MUTATED      7   11
  RNF160 WILD-TYPE  218  253
        clus
vv       RNF160 MUTATED RNF160 WILD-TYPE
  FEMALE              7              218
  MALE               11              253
[1] 2 2
[1] FALSE
D370V9, binary
                  cls
clus                 0   1
  RNF160 MUTATED    13   1
  RNF160 WILD-TYPE 337  21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF160 MUTATED     13    1
  RNF160 WILD-TYPE  337   21
     clus
vv    RNF160 MUTATED RNF160 WILD-TYPE
  NO              13              337
  YES              1               21
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  RNF160 MUTATED                     12                             4
  RNF160 WILD-TYPE                  303                            43
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  RNF160 MUTATED                       2                              0
  RNF160 WILD-TYPE                   104                             10
D370V10, multiclass
                                clus
vv                               RNF160 MUTATED RNF160 WILD-TYPE
  COLON ADENOCARCINOMA                       12              303
  COLON MUCINOUS ADENOCARCINOMA               4               43
  RECTAL ADENOCARCINOMA                       2              104
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  RNF160 MUTATED    13   0   0   3
  RNF160 WILD-TYPE 332   4  31  22
D370V11, multiclass
    clus
vv   RNF160 MUTATED RNF160 WILD-TYPE
  R0             13              332
  R1              0                4
  R2              0               31
  RX              3               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D370V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RNF160 MUTATED                                  0     2
  RNF160 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  RNF160 MUTATED                           1     9
  RNF160 WILD-TYPE                        21   217
D370V13, multiclass
                                  clus
vv                                 RNF160 MUTATED RNF160 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                9
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                         9              217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(371) Variable = MYO3B MUTATION ANALYSIS
D371V1, survival
                 sevent
clus2               0   1
  MYO3B MUTATED    26   7
  MYO3B WILD-TYPE 352  86
  MYO3B MUTATED MYO3B WILD-TYPE 
             33             438 
  MYO3B MUTATED MYO3B WILD-TYPE 
              7              86 
$`MYO3B MUTATED`
TCGA-A6-2671 TCGA-A6-6141 TCGA-A6-6781 TCGA-AA-3662 TCGA-AA-3697 TCGA-AA-3713 
       43.76         8.38        19.66         6.05        85.05        19.04 
TCGA-AA-3845 TCGA-AA-A00N TCGA-AD-6964 TCGA-AU-3779 TCGA-AY-5543 TCGA-AZ-4315 
        0.00         4.01        10.88        14.50        33.01        58.39 
TCGA-AZ-6607 TCGA-CA-6717 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4752 TCGA-CM-5860 
        3.19        12.76       124.27        23.05        13.02        32.02 
TCGA-CM-6166 TCGA-CM-6169 TCGA-CM-6674 TCGA-CM-6676 TCGA-D5-6532 TCGA-D5-6927 
       21.99        13.02        12.95        11.08        18.25         9.44 
TCGA-D5-6931 TCGA-F4-6570 TCGA-F4-6856 TCGA-G4-6315 TCGA-G4-6321 TCGA-G4-6586 
       12.00         6.18        35.31        61.91        22.09        35.80 
TCGA-AG-A002 TCGA-DY-A0XA TCGA-DY-A1DG 
       20.98       126.44        51.48 

$`MYO3B WILD-TYPE`
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       46.65        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 
       22.06        32.71        27.09        22.52        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02        78.08         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 
        5.98        37.05        19.00        36.00         5.03        26.99 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6197 TCGA-AY-6386 
        0.20        27.09        16.31         0.95        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
       11.74         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07        12.20        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-5341 
       82.95         1.91        20.02        37.02        25.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.03        22.98        30.08        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       16.04        14.99        12.99        15.02        14.04        11.01 
TCGA-CM-6675 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       13.05        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6533 
       12.26        19.59        56.09        55.92        20.19         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6932 
       14.30         9.04        11.64         4.80         1.51        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       35.74        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 
       33.67        13.25         0.53        47.41       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       36.00        13.78        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       41.36        57.24        24.13        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  MYO3B MUTATED MYO3B WILD-TYPE 
              0               0 
  MYO3B MUTATED MYO3B WILD-TYPE 
         126.44          148.01 
  MYO3B MUTATED MYO3B WILD-TYPE 
         19.040          20.415 
[1] "0.0 - 126.4 (19.0)" "0.0 - 148.0 (20.4)"
[1] "hr=" "1"  
D371V2, continuous
D371V3, binary
                 cls
clus                0   1
  MYO3B MUTATED    31   3
  MYO3B WILD-TYPE 335 116
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYO3B MUTATED     31    3
  MYO3B WILD-TYPE  335  116
        clus
vv       MYO3B MUTATED MYO3B WILD-TYPE
  COLON             31             335
  RECTUM             3             116
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MYO3B MUTATED         5        0        0        15         1         0
  MYO3B WILD-TYPE      86        1       32       123         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MYO3B MUTATED           3          0          0          2        5         2
  MYO3B WILD-TYPE        21         11         59         40       43        16
                 vv
clus              STAGE IVB
  MYO3B MUTATED           0
  MYO3B WILD-TYPE         1
D371V4, multiclass
            clus
vv           MYO3B MUTATED MYO3B WILD-TYPE
  STAGE I                5              86
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA             15             123
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              3              21
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             2              40
  STAGE IV               5              43
  STAGE IVA              2              16
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  MYO3B MUTATED     0   6  22   6
  MYO3B WILD-TYPE  17  86 307  44
D371V5, multiclass
    clus
vv   MYO3B MUTATED MYO3B WILD-TYPE
  T1             0              17
  T2             6              86
  T3            22             307
  T4             6              44
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  MYO3B MUTATED    23   5   6
  MYO3B WILD-TYPE 264 108  81
D371V6, multiclass
    clus
vv   MYO3B MUTATED MYO3B WILD-TYPE
  N0            23             264
  N1             5             108
  N2             6              81
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D371V7, binary
                 cls
clus                0   1
  MYO3B MUTATED    23   7
  MYO3B WILD-TYPE 352  58
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYO3B MUTATED     23    7
  MYO3B WILD-TYPE  352   58
   clus
vv  MYO3B MUTATED MYO3B WILD-TYPE
  0            23             352
  1             7              58
[1] 2 2
[1] FALSE
D371V8, binary
                 cls
clus                0   1
  MYO3B MUTATED    10  24
  MYO3B WILD-TYPE 215 240
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYO3B MUTATED     10   24
  MYO3B WILD-TYPE  215  240
        clus
vv       MYO3B MUTATED MYO3B WILD-TYPE
  FEMALE            10             215
  MALE              24             240
[1] 2 2
[1] FALSE
D371V9, binary
                 cls
clus                0   1
  MYO3B MUTATED    28   1
  MYO3B WILD-TYPE 322  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYO3B MUTATED     28    1
  MYO3B WILD-TYPE  322   21
     clus
vv    MYO3B MUTATED MYO3B WILD-TYPE
  NO             28             322
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MYO3B MUTATED                     26                             5
  MYO3B WILD-TYPE                  289                            42
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MYO3B MUTATED                       3                              0
  MYO3B WILD-TYPE                   103                             10
D371V10, multiclass
                                clus
vv                               MYO3B MUTATED MYO3B WILD-TYPE
  COLON ADENOCARCINOMA                      26             289
  COLON MUCINOUS ADENOCARCINOMA              5              42
  RECTAL ADENOCARCINOMA                      3             103
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  MYO3B MUTATED    25   0   2   2
  MYO3B WILD-TYPE 320   4  29  23
D371V11, multiclass
    clus
vv   MYO3B MUTATED MYO3B WILD-TYPE
  R0            25             320
  R1             0               4
  R2             2              29
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D371V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MYO3B MUTATED                                  0     1
  MYO3B WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  MYO3B MUTATED                           4    22
  MYO3B WILD-TYPE                        18   204
D371V13, multiclass
                                  clus
vv                                 MYO3B MUTATED MYO3B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    4              18
  WHITE                                       22             204
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(372) Variable = TRIM23 MUTATION ANALYSIS
D372V1, survival
                  sevent
clus2                0   1
  TRIM23 MUTATED    10   2
  TRIM23 WILD-TYPE 368  91
  TRIM23 MUTATED TRIM23 WILD-TYPE 
              12              459 
  TRIM23 MUTATED TRIM23 WILD-TYPE 
               2               91 
$`TRIM23 MUTATED`
TCGA-AA-3496 TCGA-AA-3949 TCGA-AA-3977 TCGA-AZ-6598 TCGA-CM-6171 TCGA-DM-A1D6 
        1.02        26.01        25.02        49.41        14.04        49.91 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6315 TCGA-G4-6317 TCGA-AG-A002 TCGA-DC-6682 
      133.18        74.56        61.91        36.00        20.98         4.01 

$`TRIM23 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-3952 
        2.01        12.99        24.00        33.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        88.21         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       13.02        15.02        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
      130.65        92.75        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       35.31        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       63.62        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 
       13.97        27.95        10.98        19.99         5.95         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  TRIM23 MUTATED TRIM23 WILD-TYPE 
            1.02             0.00 
  TRIM23 MUTATED TRIM23 WILD-TYPE 
          133.18           148.01 
  TRIM23 MUTATED TRIM23 WILD-TYPE 
          31.005           20.020 
[1] "1.0 - 133.2 (31.0)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.9"
D372V2, continuous
D372V3, binary
                  cls
clus                 0   1
  TRIM23 MUTATED    11   2
  TRIM23 WILD-TYPE 355 117
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIM23 MUTATED     11    2
  TRIM23 WILD-TYPE  355  117
        clus
vv       TRIM23 MUTATED TRIM23 WILD-TYPE
  COLON              11              355
  RECTUM              2              117
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TRIM23 MUTATED         2        0        2         3         0         0
  TRIM23 WILD-TYPE      89        1       30       135        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TRIM23 MUTATED           1          0          1          2        1
  TRIM23 WILD-TYPE        23         11         58         40       47
                  vv
clus               STAGE IVA STAGE IVB
  TRIM23 MUTATED           0         0
  TRIM23 WILD-TYPE        18         1
D372V4, multiclass
            clus
vv           TRIM23 MUTATED TRIM23 WILD-TYPE
  STAGE I                 2               89
  STAGE IA                0                1
  STAGE II                2               30
  STAGE IIA               3              135
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               1               23
  STAGE IIIA              0               11
  STAGE IIIB              1               58
  STAGE IIIC              2               40
  STAGE IV                1               47
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  TRIM23 MUTATED     0   3  10   0
  TRIM23 WILD-TYPE  17  89 319  50
D372V5, multiclass
    clus
vv   TRIM23 MUTATED TRIM23 WILD-TYPE
  T1              0               17
  T2              3               89
  T3             10              319
  T4              0               50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  TRIM23 MUTATED     8   3   2
  TRIM23 WILD-TYPE 279 110  85
D372V6, multiclass
    clus
vv   TRIM23 MUTATED TRIM23 WILD-TYPE
  N0              8              279
  N1              3              110
  N2              2               85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D372V7, binary
                  cls
clus                 0   1
  TRIM23 MUTATED     9   1
  TRIM23 WILD-TYPE 366  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIM23 MUTATED      9    1
  TRIM23 WILD-TYPE  366   64
   clus
vv  TRIM23 MUTATED TRIM23 WILD-TYPE
  0              9              366
  1              1               64
[1] 2 2
[1] FALSE
D372V8, binary
                  cls
clus                 0   1
  TRIM23 MUTATED     7   6
  TRIM23 WILD-TYPE 218 258
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIM23 MUTATED      7    6
  TRIM23 WILD-TYPE  218  258
        clus
vv       TRIM23 MUTATED TRIM23 WILD-TYPE
  FEMALE              7              218
  MALE                6              258
[1] 2 2
[1] FALSE
D372V9, binary
                  cls
clus                 0   1
  TRIM23 MUTATED     9   0
  TRIM23 WILD-TYPE 341  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIM23 MUTATED      9    0
  TRIM23 WILD-TYPE  341   22
     clus
vv    TRIM23 MUTATED TRIM23 WILD-TYPE
  NO               9              341
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  TRIM23 MUTATED                      9                             2
  TRIM23 WILD-TYPE                  306                            45
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  TRIM23 MUTATED                       2                              0
  TRIM23 WILD-TYPE                   104                             10
D372V10, multiclass
                                clus
vv                               TRIM23 MUTATED TRIM23 WILD-TYPE
  COLON ADENOCARCINOMA                        9              306
  COLON MUCINOUS ADENOCARCINOMA               2               45
  RECTAL ADENOCARCINOMA                       2              104
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  TRIM23 MUTATED    10   0   0   0
  TRIM23 WILD-TYPE 335   4  31  25
D372V11, multiclass
    clus
vv   TRIM23 MUTATED TRIM23 WILD-TYPE
  R0             10              335
  R1              0                4
  R2              0               31
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D372V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TRIM23 MUTATED                                  0     0
  TRIM23 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  TRIM23 MUTATED                           0     8
  TRIM23 WILD-TYPE                        22   218
D372V13, multiclass
                                  clus
vv                                 TRIM23 MUTATED TRIM23 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         8              218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(373) Variable = AGFG1 MUTATION ANALYSIS
D373V1, survival
                 sevent
clus2               0   1
  AGFG1 MUTATED     8   4
  AGFG1 WILD-TYPE 370  89
  AGFG1 MUTATED AGFG1 WILD-TYPE 
             12             459 
  AGFG1 MUTATED AGFG1 WILD-TYPE 
              4              89 
$`AGFG1 MUTATED`
TCGA-A6-5665 TCGA-AA-3510 TCGA-AA-3968 TCGA-AA-A00N TCGA-AA-A010 TCGA-AD-6895 
       22.06        63.98        21.99         4.01        34.98         0.72 
TCGA-AZ-4682 TCGA-AZ-6598 TCGA-CA-6718 TCGA-CM-5349 TCGA-DM-A0X9 TCGA-AF-2693 
       22.36        49.41        10.06        30.08       119.70        19.10 

$`AGFG1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       20.98        34.03         2.01        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 
        0.07        21.37        15.52        56.55         0.79         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 
        1.41         5.13       106.75        62.79        88.21         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.20        12.76        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5861 
       13.02        29.06        22.03        22.98        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0XD TCGA-DM-A0XF 
        1.51        12.00        11.38        10.26        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 
       79.69        24.13        39.48        43.04        13.55        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  AGFG1 MUTATED AGFG1 WILD-TYPE 
           0.72            0.00 
  AGFG1 MUTATED AGFG1 WILD-TYPE 
         119.70          148.01 
  AGFG1 MUTATED AGFG1 WILD-TYPE 
          22.21           20.05 
[1] "0.7 - 119.7 (22.2)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.4"
D373V2, continuous
D373V3, binary
                 cls
clus                0   1
  AGFG1 MUTATED    15   0
  AGFG1 WILD-TYPE 351 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AGFG1 MUTATED     15    0
  AGFG1 WILD-TYPE  351  119
        clus
vv       AGFG1 MUTATED AGFG1 WILD-TYPE
  COLON             15             351
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  AGFG1 MUTATED         2        0        3         4         3         0
  AGFG1 WILD-TYPE      89        1       29       134         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AGFG1 MUTATED           1          0          0          1        0         1
  AGFG1 WILD-TYPE        23         11         59         41       48        17
                 vv
clus              STAGE IVB
  AGFG1 MUTATED           0
  AGFG1 WILD-TYPE         1
D373V4, multiclass
            clus
vv           AGFG1 MUTATED AGFG1 WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               3              29
  STAGE IIA              4             134
  STAGE IIB              3               7
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             1              41
  STAGE IV               0              48
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  AGFG1 MUTATED     0   2  11   3
  AGFG1 WILD-TYPE  17  90 318  47
D373V5, multiclass
    clus
vv   AGFG1 MUTATED AGFG1 WILD-TYPE
  T1             0              17
  T2             2              90
  T3            11             318
  T4             3              47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  AGFG1 MUTATED    13   1   2
  AGFG1 WILD-TYPE 274 112  85
D373V6, multiclass
    clus
vv   AGFG1 MUTATED AGFG1 WILD-TYPE
  N0            13             274
  N1             1             112
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D373V7, binary
                 cls
clus                0   1
  AGFG1 MUTATED    10   1
  AGFG1 WILD-TYPE 365  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AGFG1 MUTATED     10    1
  AGFG1 WILD-TYPE  365   64
   clus
vv  AGFG1 MUTATED AGFG1 WILD-TYPE
  0            10             365
  1             1              64
[1] 2 2
[1] FALSE
D373V8, binary
                 cls
clus                0   1
  AGFG1 MUTATED     7   9
  AGFG1 WILD-TYPE 218 255
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AGFG1 MUTATED      7    9
  AGFG1 WILD-TYPE  218  255
        clus
vv       AGFG1 MUTATED AGFG1 WILD-TYPE
  FEMALE             7             218
  MALE               9             255
[1] 2 2
[1] FALSE
D373V9, binary
                 cls
clus                0   1
  AGFG1 MUTATED     9   0
  AGFG1 WILD-TYPE 341  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AGFG1 MUTATED      9    0
  AGFG1 WILD-TYPE  341   22
     clus
vv    AGFG1 MUTATED AGFG1 WILD-TYPE
  NO              9             341
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  AGFG1 MUTATED                     13                             2
  AGFG1 WILD-TYPE                  302                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  AGFG1 MUTATED                       0                              0
  AGFG1 WILD-TYPE                   106                             10
D373V10, multiclass
                                clus
vv                               AGFG1 MUTATED AGFG1 WILD-TYPE
  COLON ADENOCARCINOMA                      13             302
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  AGFG1 MUTATED    10   0   0   2
  AGFG1 WILD-TYPE 335   4  31  23
D373V11, multiclass
    clus
vv   AGFG1 MUTATED AGFG1 WILD-TYPE
  R0            10             335
  R1             0               4
  R2             0              31
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D373V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AGFG1 MUTATED                                  0     1
  AGFG1 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  AGFG1 MUTATED                           0     9
  AGFG1 WILD-TYPE                        22   217
D373V13, multiclass
                                  clus
vv                                 AGFG1 MUTATED AGFG1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        9             217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(374) Variable = KCNS3 MUTATION ANALYSIS
D374V1, survival
                 sevent
clus2               0   1
  KCNS3 MUTATED    18   3
  KCNS3 WILD-TYPE 360  90
  KCNS3 MUTATED KCNS3 WILD-TYPE 
             21             450 
  KCNS3 MUTATED KCNS3 WILD-TYPE 
              3              90 
$`KCNS3 MUTATED`
TCGA-A6-3809 TCGA-A6-6780 TCGA-AA-3496 TCGA-AA-3812 TCGA-AA-A010 TCGA-AD-5900 
       32.75        20.12         1.02        35.05        34.98         0.07 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-CM-4746 TCGA-CM-4752 
       33.01        21.44        49.41         6.77        37.02        13.02 
TCGA-CM-5864 TCGA-CM-6678 TCGA-D5-5540 TCGA-D5-6533 TCGA-DM-A28C TCGA-G4-6299 
       15.02        11.01        56.09         1.32        81.37        74.56 
TCGA-G4-6628 TCGA-AG-3731 TCGA-AG-3902 
       79.69        37.02        32.02 

$`KCNS3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3510 
       19.66        20.28         7.04         3.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3815 
       85.05        26.99        19.04        19.04        10.06        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       16.31         0.95        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6600 TCGA-AZ-6601 
      106.75        22.36        62.79        88.21        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-5341 TCGA-CM-5344 
      124.27        23.05        20.02        25.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6679 
       11.01        12.95        13.05        11.08        11.08        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6529 
       12.03        45.40        12.26        19.59        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       18.25        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
        6.12       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       47.41        35.31       133.18        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 
       13.78        35.80        26.17        91.79        46.75        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
       19.99         7.99         0.99        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3909 
       13.02        35.01        14.01         1.02        48.03        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  KCNS3 MUTATED KCNS3 WILD-TYPE 
           0.07            0.00 
  KCNS3 MUTATED KCNS3 WILD-TYPE 
          81.37          148.01 
  KCNS3 MUTATED KCNS3 WILD-TYPE 
          32.75           20.02 
[1] "0.1 - 81.4 (32.8)"  "0.0 - 148.0 (20.0)"
[1] "hr=" "1.7"
D374V2, continuous
D374V3, binary
                 cls
clus                0   1
  KCNS3 MUTATED    19   2
  KCNS3 WILD-TYPE 347 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNS3 MUTATED     19    2
  KCNS3 WILD-TYPE  347  117
        clus
vv       KCNS3 MUTATED KCNS3 WILD-TYPE
  COLON             19             347
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KCNS3 MUTATED         5        0        2         7         2         0
  KCNS3 WILD-TYPE      86        1       30       131         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  KCNS3 MUTATED           0          0          1          1        1         2
  KCNS3 WILD-TYPE        24         11         58         41       47        16
                 vv
clus              STAGE IVB
  KCNS3 MUTATED           0
  KCNS3 WILD-TYPE         1
D374V4, multiclass
            clus
vv           KCNS3 MUTATED KCNS3 WILD-TYPE
  STAGE I                5              86
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA              7             131
  STAGE IIB              2               8
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             1              41
  STAGE IV               1              47
  STAGE IVA              2              16
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  KCNS3 MUTATED     0   5  12   4
  KCNS3 WILD-TYPE  17  87 317  46
D374V5, multiclass
    clus
vv   KCNS3 MUTATED KCNS3 WILD-TYPE
  T1             0              17
  T2             5              87
  T3            12             317
  T4             4              46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  KCNS3 MUTATED    17   3   1
  KCNS3 WILD-TYPE 270 110  86
D374V6, multiclass
    clus
vv   KCNS3 MUTATED KCNS3 WILD-TYPE
  N0            17             270
  N1             3             110
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D374V7, binary
                 cls
clus                0   1
  KCNS3 MUTATED    13   3
  KCNS3 WILD-TYPE 362  62
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNS3 MUTATED     13    3
  KCNS3 WILD-TYPE  362   62
   clus
vv  KCNS3 MUTATED KCNS3 WILD-TYPE
  0            13             362
  1             3              62
[1] 2 2
[1] FALSE
D374V8, binary
                 cls
clus                0   1
  KCNS3 MUTATED     8  13
  KCNS3 WILD-TYPE 217 251
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNS3 MUTATED      8   13
  KCNS3 WILD-TYPE  217  251
        clus
vv       KCNS3 MUTATED KCNS3 WILD-TYPE
  FEMALE             8             217
  MALE              13             251
[1] 2 2
[1] FALSE
D374V9, binary
                 cls
clus                0   1
  KCNS3 MUTATED    17   0
  KCNS3 WILD-TYPE 333  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNS3 MUTATED     17    0
  KCNS3 WILD-TYPE  333   22
     clus
vv    KCNS3 MUTATED KCNS3 WILD-TYPE
  NO             17             333
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  KCNS3 MUTATED                     16                             3
  KCNS3 WILD-TYPE                  299                            44
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  KCNS3 MUTATED                       2                              0
  KCNS3 WILD-TYPE                   104                             10
D374V10, multiclass
                                clus
vv                               KCNS3 MUTATED KCNS3 WILD-TYPE
  COLON ADENOCARCINOMA                      16             299
  COLON MUCINOUS ADENOCARCINOMA              3              44
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  KCNS3 MUTATED    16   0   1   0
  KCNS3 WILD-TYPE 329   4  30  25
D374V11, multiclass
    clus
vv   KCNS3 MUTATED KCNS3 WILD-TYPE
  R0            16             329
  R1             0               4
  R2             1              30
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D374V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KCNS3 MUTATED                                  0     0
  KCNS3 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  KCNS3 MUTATED                           3    13
  KCNS3 WILD-TYPE                        19   213
D374V13, multiclass
                                  clus
vv                                 KCNS3 MUTATED KCNS3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    3              19
  WHITE                                       13             213
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(375) Variable = GPR112 MUTATION ANALYSIS
D375V1, survival
                  sevent
clus2                0   1
  GPR112 MUTATED    28  10
  GPR112 WILD-TYPE 350  83
  GPR112 MUTATED GPR112 WILD-TYPE 
              38              433 
  GPR112 MUTATED GPR112 WILD-TYPE 
              10               83 
$`GPR112 MUTATED`
TCGA-A6-2672 TCGA-A6-2678 TCGA-A6-3809 TCGA-A6-5665 TCGA-A6-6781 TCGA-AA-3510 
       46.65        42.28        32.75        22.06        19.66        63.98 
TCGA-AA-3555 TCGA-AA-3678 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3950 TCGA-AA-3977 
       29.95        47.01        26.99        10.06        24.00        25.02 
TCGA-AA-A00N TCGA-AA-A02J TCGA-AD-6889 TCGA-AD-6890 TCGA-AZ-4315 TCGA-AZ-5407 
        4.01         5.03        56.55         0.79        58.39        88.21 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-5349 TCGA-CM-5864 
      100.01        29.56        12.76        10.06        30.08        15.02 
TCGA-CM-6161 TCGA-CM-6169 TCGA-CM-6678 TCGA-DM-A285 TCGA-DM-A28F TCGA-G4-6303 
       15.02        13.02        11.01         6.12        35.97        65.85 
TCGA-AG-3578 TCGA-AG-3608 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3892 TCGA-AG-A002 
       32.02        15.95        37.02        32.98        13.02        20.98 
TCGA-AG-A026 TCGA-EI-6508 
        1.94        20.91 

$`GPR112 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2683 TCGA-A6-3807 
       43.76        43.76        42.90        24.33        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        36.53        14.53        32.91        31.63        30.44 
TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 
       29.19        33.53        23.61        22.09        32.71        27.09 
TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 
       22.52         8.38        25.08        25.18        24.16        21.76 
TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 
       24.69        24.39        23.87        20.12        20.28         7.04 
TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        3.02         1.02        35.01         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 
       21.01        13.02        24.00        17.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3815 
        5.03        85.05        19.04        19.04        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       33.01        26.01         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       51.98        39.98         2.01        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       49.41         6.77        12.10         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       12.20        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       29.06        22.03        22.98        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5868 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       15.02        17.03        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       21.99        14.99        12.99        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6679 TCGA-CM-6680 
       12.95        13.05        11.08        11.08        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
      139.17        81.37       119.93        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6304 TCGA-G4-6306 
       47.41        35.31       133.18        74.56        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       36.03        12.00         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
       12.03         6.05         0.99        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
        7.99         0.99         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 
        1.02        17.95        36.95        17.03        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A02G TCGA-AG-A02N 
       70.03        64.01        10.98        49.97        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
        0.49        20.55        19.96        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  GPR112 MUTATED GPR112 WILD-TYPE 
            0.79             0.00 
  GPR112 MUTATED GPR112 WILD-TYPE 
          100.01           148.01 
  GPR112 MUTATED GPR112 WILD-TYPE 
           24.51            20.02 
[1] "0.8 - 100.0 (24.5)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.2"
D375V2, continuous
D375V3, binary
                  cls
clus                 0   1
  GPR112 MUTATED    30   8
  GPR112 WILD-TYPE 336 111
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR112 MUTATED     30    8
  GPR112 WILD-TYPE  336  111
        clus
vv       GPR112 MUTATED GPR112 WILD-TYPE
  COLON              30              336
  RECTUM              8              111
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GPR112 MUTATED         6        0        3        12         2         0
  GPR112 WILD-TYPE      85        1       29       126         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GPR112 MUTATED           2          0          4          1        4
  GPR112 WILD-TYPE        22         11         55         41       44
                  vv
clus               STAGE IVA STAGE IVB
  GPR112 MUTATED           1         0
  GPR112 WILD-TYPE        17         1
D375V4, multiclass
            clus
vv           GPR112 MUTATED GPR112 WILD-TYPE
  STAGE I                 6               85
  STAGE IA                0                1
  STAGE II                3               29
  STAGE IIA              12              126
  STAGE IIB               2                8
  STAGE IIC               0                1
  STAGE III               2               22
  STAGE IIIA              0               11
  STAGE IIIB              4               55
  STAGE IIIC              1               41
  STAGE IV                4               44
  STAGE IVA               1               17
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  GPR112 MUTATED     3   7  23   5
  GPR112 WILD-TYPE  14  85 306  45
D375V5, multiclass
    clus
vv   GPR112 MUTATED GPR112 WILD-TYPE
  T1              3               14
  T2              7               85
  T3             23              306
  T4              5               45
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  GPR112 MUTATED    26  10   2
  GPR112 WILD-TYPE 261 103  85
D375V6, multiclass
    clus
vv   GPR112 MUTATED GPR112 WILD-TYPE
  N0             26              261
  N1             10              103
  N2              2               85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D375V7, binary
                  cls
clus                 0   1
  GPR112 MUTATED    29   5
  GPR112 WILD-TYPE 346  60
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR112 MUTATED     29    5
  GPR112 WILD-TYPE  346   60
   clus
vv  GPR112 MUTATED GPR112 WILD-TYPE
  0             29              346
  1              5               60
[1] 2 2
[1] FALSE
D375V8, binary
                  cls
clus                 0   1
  GPR112 MUTATED    22  16
  GPR112 WILD-TYPE 203 248
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR112 MUTATED     22   16
  GPR112 WILD-TYPE  203  248
        clus
vv       GPR112 MUTATED GPR112 WILD-TYPE
  FEMALE             22              203
  MALE               16              248
[1] 2 2
[1] FALSE
D375V9, binary
                  cls
clus                 0   1
  GPR112 MUTATED    31   0
  GPR112 WILD-TYPE 319  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR112 MUTATED     31    0
  GPR112 WILD-TYPE  319   22
     clus
vv    GPR112 MUTATED GPR112 WILD-TYPE
  NO              31              319
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  GPR112 MUTATED                     23                             7
  GPR112 WILD-TYPE                  292                            40
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  GPR112 MUTATED                       7                              1
  GPR112 WILD-TYPE                    99                              9
D375V10, multiclass
                                clus
vv                               GPR112 MUTATED GPR112 WILD-TYPE
  COLON ADENOCARCINOMA                       23              292
  COLON MUCINOUS ADENOCARCINOMA               7               40
  RECTAL ADENOCARCINOMA                       7               99
  RECTAL MUCINOUS ADENOCARCINOMA              1                9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  GPR112 MUTATED    25   1   2   2
  GPR112 WILD-TYPE 320   3  29  23
D375V11, multiclass
    clus
vv   GPR112 MUTATED GPR112 WILD-TYPE
  R0             25              320
  R1              1                3
  R2              2               29
  RX              2               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D375V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GPR112 MUTATED                                  0     3
  GPR112 WILD-TYPE                                1     8
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  GPR112 MUTATED                           1    18
  GPR112 WILD-TYPE                        21   208
D375V13, multiclass
                                  clus
vv                                 GPR112 MUTATED GPR112 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         3                8
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                        18              208
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(376) Variable = PTPRK MUTATION ANALYSIS
D376V1, survival
                 sevent
clus2               0   1
  PTPRK MUTATED    33   4
  PTPRK WILD-TYPE 345  89
  PTPRK MUTATED PTPRK WILD-TYPE 
             37             434 
  PTPRK MUTATED PTPRK WILD-TYPE 
              4              89 
$`PTPRK MUTATED`
TCGA-A6-3809 TCGA-A6-5665 TCGA-A6-6141 TCGA-AA-3510 TCGA-AA-3555 TCGA-AA-3663 
       32.75        22.06         8.38        63.98        29.95         6.97 
TCGA-AA-3715 TCGA-AA-3815 TCGA-AA-3867 TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-3977 
       19.04        33.04        24.03        33.01        24.00        25.02 
TCGA-AA-A00N TCGA-AA-A01R TCGA-AA-A01V TCGA-AD-6895 TCGA-AU-6004 TCGA-AY-6197 
        4.01        35.01        35.01         0.72        27.09        21.44 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CM-4743 TCGA-CM-5349 TCGA-CM-6165 TCGA-CM-6674 
       15.62        51.32        23.05        30.08        16.04        12.95 
TCGA-D5-6532 TCGA-DM-A0XD TCGA-DM-A1D8 TCGA-F4-6854 TCGA-F4-6856 TCGA-G4-6304 
       18.25        24.43        12.59         0.53        35.31        53.62 
TCGA-G4-6310 TCGA-G4-6588 TCGA-AG-3731 TCGA-AG-A02N TCGA-AH-6549 TCGA-DC-5869 
       63.62        26.17        37.02        61.97        17.49         5.03 
TCGA-EI-6507 
       19.96 

$`PTPRK WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       32.71        27.09        22.52        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 
       20.28         7.04         3.02         1.02        35.01         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
       78.08         6.05        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       10.06        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        26.01         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S 
       12.00        31.00        31.00        38.07         1.02         1.02 
TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       33.04        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.79         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4315 
       14.50        16.31         0.95        33.01        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 
       17.56       148.01        85.45        49.08         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
       82.95         1.91       124.27        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5861 
       13.02        29.06        22.03        22.98        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
        2.96        29.03        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       15.02        14.04        11.01        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       56.09        55.92        20.19         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
       10.26       119.70        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       13.32       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 
       13.25        47.41       133.18        74.56        65.85        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       55.04        85.48        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       35.80        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        7.99         0.99        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
       49.97         1.94        38.96        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
       38.56         1.45         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-6155 
        6.97         4.73        78.12         7.17        15.02        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
       32.61         0.49        20.55        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  PTPRK MUTATED PTPRK WILD-TYPE 
           0.53            0.00 
  PTPRK MUTATED PTPRK WILD-TYPE 
          63.98          148.01 
  PTPRK MUTATED PTPRK WILD-TYPE 
         24.030          20.005 
[1] "0.5 - 64.0 (24.0)"  "0.0 - 148.0 (20.0)"
[1] "hr=" "1.9"
D376V2, continuous
D376V3, binary
                 cls
clus                0   1
  PTPRK MUTATED    33   5
  PTPRK WILD-TYPE 333 114
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPRK MUTATED     33    5
  PTPRK WILD-TYPE  333  114
        clus
vv       PTPRK MUTATED PTPRK WILD-TYPE
  COLON             33             333
  RECTUM             5             114
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PTPRK MUTATED         3        0        4        16         4         0
  PTPRK WILD-TYPE      88        1       28       122         6         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PTPRK MUTATED           1          0          2          1        3         0
  PTPRK WILD-TYPE        23         11         57         41       45        18
                 vv
clus              STAGE IVB
  PTPRK MUTATED           0
  PTPRK WILD-TYPE         1
D376V4, multiclass
            clus
vv           PTPRK MUTATED PTPRK WILD-TYPE
  STAGE I                3              88
  STAGE IA               0               1
  STAGE II               4              28
  STAGE IIA             16             122
  STAGE IIB              4               6
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             2              57
  STAGE IIIC             1              41
  STAGE IV               3              45
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PTPRK MUTATED     0   4  28   6
  PTPRK WILD-TYPE  17  88 301  44
D376V5, multiclass
    clus
vv   PTPRK MUTATED PTPRK WILD-TYPE
  T1             0              17
  T2             4              88
  T3            28             301
  T4             6              44
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  PTPRK MUTATED    28   5   4
  PTPRK WILD-TYPE 259 108  83
D376V6, multiclass
    clus
vv   PTPRK MUTATED PTPRK WILD-TYPE
  N0            28             259
  N1             5             108
  N2             4              83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D376V7, binary
                 cls
clus                0   1
  PTPRK MUTATED    29   3
  PTPRK WILD-TYPE 346  62
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPRK MUTATED     29    3
  PTPRK WILD-TYPE  346   62
   clus
vv  PTPRK MUTATED PTPRK WILD-TYPE
  0            29             346
  1             3              62
[1] 2 2
[1] FALSE
D376V8, binary
                 cls
clus                0   1
  PTPRK MUTATED    16  22
  PTPRK WILD-TYPE 209 242
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPRK MUTATED     16   22
  PTPRK WILD-TYPE  209  242
        clus
vv       PTPRK MUTATED PTPRK WILD-TYPE
  FEMALE            16             209
  MALE              22             242
[1] 2 2
[1] FALSE
D376V9, binary
                 cls
clus                0   1
  PTPRK MUTATED    26   2
  PTPRK WILD-TYPE 324  20
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPRK MUTATED     26    2
  PTPRK WILD-TYPE  324   20
     clus
vv    PTPRK MUTATED PTPRK WILD-TYPE
  NO             26             324
  YES             2              20
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PTPRK MUTATED                     24                             9
  PTPRK WILD-TYPE                  291                            38
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PTPRK MUTATED                       5                              0
  PTPRK WILD-TYPE                   101                             10
D376V10, multiclass
                                clus
vv                               PTPRK MUTATED PTPRK WILD-TYPE
  COLON ADENOCARCINOMA                      24             291
  COLON MUCINOUS ADENOCARCINOMA              9              38
  RECTAL ADENOCARCINOMA                      5             101
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  PTPRK MUTATED    27   0   3   3
  PTPRK WILD-TYPE 318   4  28  22
D376V11, multiclass
    clus
vv   PTPRK MUTATED PTPRK WILD-TYPE
  R0            27             318
  R1             0               4
  R2             3              28
  RX             3              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D376V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PTPRK MUTATED                                  0     0
  PTPRK WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PTPRK MUTATED                           2    21
  PTPRK WILD-TYPE                        20   205
D376V13, multiclass
                                  clus
vv                                 PTPRK MUTATED PTPRK WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    2              20
  WHITE                                       21             205
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(377) Variable = DCAF6 MUTATION ANALYSIS
D377V1, survival
                 sevent
clus2               0   1
  DCAF6 MUTATED    14   3
  DCAF6 WILD-TYPE 364  90
  DCAF6 MUTATED DCAF6 WILD-TYPE 
             17             454 
  DCAF6 MUTATED DCAF6 WILD-TYPE 
              3              90 
$`DCAF6 MUTATED`
TCGA-A6-2676 TCGA-A6-5661 TCGA-AA-3815 TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A010 
       42.90        33.53        33.04        25.02         4.01        34.98 
TCGA-AD-6889 TCGA-AD-6895 TCGA-AY-6197 TCGA-CA-5254 TCGA-CA-6718 TCGA-CM-6163 
       56.55         0.72        21.44        12.69        10.06         2.96 
TCGA-CM-6677 TCGA-D5-6540 TCGA-AG-A002 TCGA-CI-6622 TCGA-F5-6465 
       11.08        16.14        20.98         6.97        49.51 

$`DCAF6 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       31.63        30.44        29.19        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       35.05         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       21.37        15.52         0.79         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       33.01        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6164 
       15.02        15.02        17.03        15.02        12.00        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6678 
       14.04        11.01        12.95        13.05        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 
       17.85         4.80        17.13        12.49        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
        6.05        33.17         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       20.91        18.28         9.96        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  DCAF6 MUTATED DCAF6 WILD-TYPE 
           0.72            0.00 
  DCAF6 MUTATED DCAF6 WILD-TYPE 
          56.55          148.01 
  DCAF6 MUTATED DCAF6 WILD-TYPE 
         20.980          20.155 
[1] "0.7 - 56.5 (21.0)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1"  
D377V2, continuous
D377V3, binary
                 cls
clus                0   1
  DCAF6 MUTATED    15   3
  DCAF6 WILD-TYPE 351 116
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DCAF6 MUTATED     15    3
  DCAF6 WILD-TYPE  351  116
        clus
vv       DCAF6 MUTATED DCAF6 WILD-TYPE
  COLON             15             351
  RECTUM             3             116
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DCAF6 MUTATED         3        0        0         9         4         0
  DCAF6 WILD-TYPE      88        1       32       129         6         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DCAF6 MUTATED           0          0          0          0        0         0
  DCAF6 WILD-TYPE        24         11         59         42       48        18
                 vv
clus              STAGE IVB
  DCAF6 MUTATED           0
  DCAF6 WILD-TYPE         1
D377V4, multiclass
            clus
vv           DCAF6 MUTATED DCAF6 WILD-TYPE
  STAGE I                3              88
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              9             129
  STAGE IIB              4               6
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  DCAF6 MUTATED     1   3  10   4
  DCAF6 WILD-TYPE  16  89 319  46
D377V5, multiclass
    clus
vv   DCAF6 MUTATED DCAF6 WILD-TYPE
  T1             1              16
  T2             3              89
  T3            10             319
  T4             4              46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  DCAF6 MUTATED    17   1   0
  DCAF6 WILD-TYPE 270 112  87
D377V6, multiclass
    clus
vv   DCAF6 MUTATED DCAF6 WILD-TYPE
  N0            17             270
  N1             1             112
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D377V7, binary
                 cls
clus                0   1
  DCAF6 MUTATED    15   0
  DCAF6 WILD-TYPE 360  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DCAF6 MUTATED     15    0
  DCAF6 WILD-TYPE  360   65
   clus
vv  DCAF6 MUTATED DCAF6 WILD-TYPE
  0            15             360
  1             0              65
[1] 2 2
[1] FALSE
D377V8, binary
                 cls
clus                0   1
  DCAF6 MUTATED     8  10
  DCAF6 WILD-TYPE 217 254
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DCAF6 MUTATED      8   10
  DCAF6 WILD-TYPE  217  254
        clus
vv       DCAF6 MUTATED DCAF6 WILD-TYPE
  FEMALE             8             217
  MALE              10             254
[1] 2 2
[1] FALSE
D377V9, binary
                 cls
clus                0   1
  DCAF6 MUTATED    13   0
  DCAF6 WILD-TYPE 337  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DCAF6 MUTATED     13    0
  DCAF6 WILD-TYPE  337   22
     clus
vv    DCAF6 MUTATED DCAF6 WILD-TYPE
  NO             13             337
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  DCAF6 MUTATED                     13                             2
  DCAF6 WILD-TYPE                  302                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  DCAF6 MUTATED                       3                              0
  DCAF6 WILD-TYPE                   103                             10
D377V10, multiclass
                                clus
vv                               DCAF6 MUTATED DCAF6 WILD-TYPE
  COLON ADENOCARCINOMA                      13             302
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      3             103
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  DCAF6 MUTATED    12   0   0   2
  DCAF6 WILD-TYPE 333   4  31  23
D377V11, multiclass
    clus
vv   DCAF6 MUTATED DCAF6 WILD-TYPE
  R0            12             333
  R1             0               4
  R2             0              31
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D377V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DCAF6 MUTATED                                  0     3
  DCAF6 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  DCAF6 MUTATED                           1     8
  DCAF6 WILD-TYPE                        21   218
D377V13, multiclass
                                  clus
vv                                 DCAF6 MUTATED DCAF6 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        3               8
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        8             218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(378) Variable = CCDC18 MUTATION ANALYSIS
D378V1, survival
                  sevent
clus2                0   1
  CCDC18 MUTATED    10   2
  CCDC18 WILD-TYPE 368  91
  CCDC18 MUTATED CCDC18 WILD-TYPE 
              12              459 
  CCDC18 MUTATED CCDC18 WILD-TYPE 
               2               91 
$`CCDC18 MUTATED`
TCGA-AA-3660 TCGA-AA-3977 TCGA-AA-A010 TCGA-AD-6899 TCGA-CA-6717 TCGA-CM-4743 
       78.08        25.02        34.98         5.79        12.76        23.05 
TCGA-CM-6166 TCGA-CM-6677 TCGA-D5-6929 TCGA-DM-A28C TCGA-AG-A002 TCGA-F5-6812 
       21.99        11.08         4.80        81.37        20.98         0.66 

$`CCDC18 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 
       20.98        19.99        13.94        19.99        61.02         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.79         0.72        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07        12.20        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       16.04        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6678 TCGA-CM-6679 
       11.01        12.95        13.05        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       11.64         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
      139.17         6.12       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  CCDC18 MUTATED CCDC18 WILD-TYPE 
            0.66             0.00 
  CCDC18 MUTATED CCDC18 WILD-TYPE 
           81.37           148.01 
  CCDC18 MUTATED CCDC18 WILD-TYPE 
          21.485           20.120 
[1] "0.7 - 81.4 (21.5)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.2"
D378V2, continuous
D378V3, binary
                  cls
clus                 0   1
  CCDC18 MUTATED    11   2
  CCDC18 WILD-TYPE 355 117
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC18 MUTATED     11    2
  CCDC18 WILD-TYPE  355  117
        clus
vv       CCDC18 MUTATED CCDC18 WILD-TYPE
  COLON              11              355
  RECTUM              2              117
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CCDC18 MUTATED         2        0        1         6         1         0
  CCDC18 WILD-TYPE      89        1       31       132         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CCDC18 MUTATED           0          0          0          1        1
  CCDC18 WILD-TYPE        24         11         59         41       47
                  vv
clus               STAGE IVA STAGE IVB
  CCDC18 MUTATED           0         0
  CCDC18 WILD-TYPE        18         1
D378V4, multiclass
            clus
vv           CCDC18 MUTATED CCDC18 WILD-TYPE
  STAGE I                 2               89
  STAGE IA                0                1
  STAGE II                1               31
  STAGE IIA               6              132
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              0               59
  STAGE IIIC              1               41
  STAGE IV                1               47
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  CCDC18 MUTATED     0   3   8   2
  CCDC18 WILD-TYPE  17  89 321  48
D378V5, multiclass
    clus
vv   CCDC18 MUTATED CCDC18 WILD-TYPE
  T1              0               17
  T2              3               89
  T3              8              321
  T4              2               48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  CCDC18 MUTATED    11   1   1
  CCDC18 WILD-TYPE 276 112  86
D378V6, multiclass
    clus
vv   CCDC18 MUTATED CCDC18 WILD-TYPE
  N0             11              276
  N1              1              112
  N2              1               86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D378V7, binary
                  cls
clus                 0   1
  CCDC18 MUTATED    10   1
  CCDC18 WILD-TYPE 365  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC18 MUTATED     10    1
  CCDC18 WILD-TYPE  365   64
   clus
vv  CCDC18 MUTATED CCDC18 WILD-TYPE
  0             10              365
  1              1               64
[1] 2 2
[1] FALSE
D378V8, binary
                  cls
clus                 0   1
  CCDC18 MUTATED     6   7
  CCDC18 WILD-TYPE 219 257
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC18 MUTATED      6    7
  CCDC18 WILD-TYPE  219  257
        clus
vv       CCDC18 MUTATED CCDC18 WILD-TYPE
  FEMALE              6              219
  MALE                7              257
[1] 2 2
[1] FALSE
D378V9, binary
                  cls
clus                 0   1
  CCDC18 MUTATED     9   0
  CCDC18 WILD-TYPE 341  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC18 MUTATED      9    0
  CCDC18 WILD-TYPE  341   22
     clus
vv    CCDC18 MUTATED CCDC18 WILD-TYPE
  NO               9              341
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CCDC18 MUTATED                      9                             2
  CCDC18 WILD-TYPE                  306                            45
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CCDC18 MUTATED                       2                              0
  CCDC18 WILD-TYPE                   104                             10
D378V10, multiclass
                                clus
vv                               CCDC18 MUTATED CCDC18 WILD-TYPE
  COLON ADENOCARCINOMA                        9              306
  COLON MUCINOUS ADENOCARCINOMA               2               45
  RECTAL ADENOCARCINOMA                       2              104
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  CCDC18 MUTATED     9   0   0   1
  CCDC18 WILD-TYPE 336   4  31  24
D378V11, multiclass
    clus
vv   CCDC18 MUTATED CCDC18 WILD-TYPE
  R0              9              336
  R1              0                4
  R2              0               31
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D378V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CCDC18 MUTATED                                  0     1
  CCDC18 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  CCDC18 MUTATED                           0     7
  CCDC18 WILD-TYPE                        22   219
D378V13, multiclass
                                  clus
vv                                 CCDC18 MUTATED CCDC18 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         7              219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(379) Variable = RAB28 MUTATION ANALYSIS
D379V1, survival
                 sevent
clus2               0   1
  RAB28 MUTATED     5   2
  RAB28 WILD-TYPE 373  91
  RAB28 MUTATED RAB28 WILD-TYPE 
              7             464 
  RAB28 MUTATED RAB28 WILD-TYPE 
              2              91 
$`RAB28 MUTATED`
TCGA-AY-6197 TCGA-AZ-6598 TCGA-D5-6541 TCGA-DM-A28G TCGA-F4-6856 TCGA-G4-6588 
       21.44        49.41        15.58        60.79        35.31        26.17 
TCGA-AG-A002 
       20.98 

$`RAB28 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       16.31         0.95        33.01        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 
        5.13       106.75        22.36        62.79        88.21         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6898 TCGA-D5-6920 
        4.80        17.13        12.49        16.14         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28H 
      139.17         6.12        81.37       119.93        35.97       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
        0.53        47.41       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       22.09        13.78        35.80        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  RAB28 MUTATED RAB28 WILD-TYPE 
          15.58            0.00 
  RAB28 MUTATED RAB28 WILD-TYPE 
          60.79          148.01 
  RAB28 MUTATED RAB28 WILD-TYPE 
         26.170          20.035 
[1] "15.6 - 60.8 (26.2)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.1"
D379V2, continuous
D379V3, binary
                 cls
clus                0   1
  RAB28 MUTATED     6   1
  RAB28 WILD-TYPE 360 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RAB28 MUTATED      6    1
  RAB28 WILD-TYPE  360  118
        clus
vv       RAB28 MUTATED RAB28 WILD-TYPE
  COLON              6             360
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RAB28 MUTATED         2        0        1         4         0         0
  RAB28 WILD-TYPE      89        1       31       134        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RAB28 MUTATED           0          0          0          0        0         0
  RAB28 WILD-TYPE        24         11         59         42       48        18
                 vv
clus              STAGE IVB
  RAB28 MUTATED           0
  RAB28 WILD-TYPE         1
D379V4, multiclass
            clus
vv           RAB28 MUTATED RAB28 WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              4             134
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  RAB28 MUTATED     0   2   5   0
  RAB28 WILD-TYPE  17  90 324  50
D379V5, multiclass
    clus
vv   RAB28 MUTATED RAB28 WILD-TYPE
  T1             0              17
  T2             2              90
  T3             5             324
  T4             0              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  RAB28 MUTATED     7   0   0
  RAB28 WILD-TYPE 280 113  87
D379V6, multiclass
    clus
vv   RAB28 MUTATED RAB28 WILD-TYPE
  N0             7             280
  N1             0             113
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D379V7, binary
                 cls
clus                0   1
  RAB28 MUTATED     5   0
  RAB28 WILD-TYPE 370  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RAB28 MUTATED      5    0
  RAB28 WILD-TYPE  370   65
   clus
vv  RAB28 MUTATED RAB28 WILD-TYPE
  0             5             370
  1             0              65
[1] 2 2
[1] FALSE
D379V8, binary
                 cls
clus                0   1
  RAB28 MUTATED     2   5
  RAB28 WILD-TYPE 223 259
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RAB28 MUTATED      2    5
  RAB28 WILD-TYPE  223  259
        clus
vv       RAB28 MUTATED RAB28 WILD-TYPE
  FEMALE             2             223
  MALE               5             259
[1] 2 2
[1] FALSE
D379V9, binary
                 cls
clus                0   1
  RAB28 MUTATED     6   0
  RAB28 WILD-TYPE 344  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RAB28 MUTATED      6    0
  RAB28 WILD-TYPE  344   22
     clus
vv    RAB28 MUTATED RAB28 WILD-TYPE
  NO              6             344
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  RAB28 MUTATED                      5                             1
  RAB28 WILD-TYPE                  310                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  RAB28 MUTATED                       1                              0
  RAB28 WILD-TYPE                   105                             10
D379V10, multiclass
                                clus
vv                               RAB28 MUTATED RAB28 WILD-TYPE
  COLON ADENOCARCINOMA                       5             310
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  RAB28 MUTATED     5   0   0   0
  RAB28 WILD-TYPE 340   4  31  25
D379V11, multiclass
    clus
vv   RAB28 MUTATED RAB28 WILD-TYPE
  R0             5             340
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D379V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RAB28 MUTATED                                  0     0
  RAB28 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  RAB28 MUTATED                           0     6
  RAB28 WILD-TYPE                        22   220
D379V13, multiclass
                                  clus
vv                                 RAB28 MUTATED RAB28 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        6             220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(380) Variable = ARHGEF10 MUTATION ANALYSIS
D380V1, survival
                    sevent
clus2                  0   1
  ARHGEF10 MUTATED    21   3
  ARHGEF10 WILD-TYPE 357  90
  ARHGEF10 MUTATED ARHGEF10 WILD-TYPE 
                24                447 
  ARHGEF10 MUTATED ARHGEF10 WILD-TYPE 
                 3                 90 
$`ARHGEF10 MUTATED`
TCGA-A6-6141 TCGA-A6-6780 TCGA-AA-3496 TCGA-AA-3518 TCGA-AA-3672 TCGA-AA-3710 
        8.38        20.12         1.02         1.02         0.92        26.99 
TCGA-AA-3713 TCGA-AA-3864 TCGA-AA-3950 TCGA-AA-3966 TCGA-AA-3977 TCGA-AA-A01P 
       19.04        53.00        24.00         2.01        25.02        38.07 
TCGA-AD-5900 TCGA-AZ-4315 TCGA-AZ-6603 TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-4743 
        0.07        58.39        29.56        12.76        10.06        23.05 
TCGA-CM-6171 TCGA-CM-6172 TCGA-D5-6536 TCGA-D5-6541 TCGA-D5-6928 TCGA-AG-A002 
       14.04        11.01        17.85        15.58        11.64        20.98 

$`ARHGEF10 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 
       22.09        22.06        32.71        27.09        22.52        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3510 
       19.66        20.28         7.04         3.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3520 
        6.97         1.02        13.02        38.99         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
       14.01        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3715 
       37.05        19.00        36.00         5.03        85.05        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 
       32.05         0.99        31.07        31.07        30.05        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 
       12.99        24.00        33.01        26.01         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
       34.03        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01Q 
       10.98        32.02        12.00        31.00        31.00         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 
        0.92        41.00        39.98        18.05        40.96        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        33.01        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
       12.10       100.01         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 
       20.19        18.25         1.32        43.27        15.12         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       17.13        12.49        16.14         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6930 
       12.43        14.30         9.04         9.44         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  ARHGEF10 MUTATED ARHGEF10 WILD-TYPE 
              0.07               0.00 
  ARHGEF10 MUTATED ARHGEF10 WILD-TYPE 
             58.39             148.01 
  ARHGEF10 MUTATED ARHGEF10 WILD-TYPE 
            16.715             20.910 
[1] "0.1 - 58.4 (16.7)"  "0.0 - 148.0 (20.9)"
[1] "hr=" "1.2"
D380V2, continuous
D380V3, binary
                    cls
clus                   0   1
  ARHGEF10 MUTATED    23   1
  ARHGEF10 WILD-TYPE 343 118
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ARHGEF10 MUTATED     23    1
  ARHGEF10 WILD-TYPE  343  118
        clus
vv       ARHGEF10 MUTATED ARHGEF10 WILD-TYPE
  COLON                23                343
  RECTUM                1                118
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ARHGEF10 MUTATED         3        0        2        13         0         0
  ARHGEF10 WILD-TYPE      88        1       30       125        10         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ARHGEF10 MUTATED           2          0          1          0        1
  ARHGEF10 WILD-TYPE        22         11         58         42       47
                    vv
clus                 STAGE IVA STAGE IVB
  ARHGEF10 MUTATED           0         0
  ARHGEF10 WILD-TYPE        18         1
D380V4, multiclass
            clus
vv           ARHGEF10 MUTATED ARHGEF10 WILD-TYPE
  STAGE I                   3                 88
  STAGE IA                  0                  1
  STAGE II                  2                 30
  STAGE IIA                13                125
  STAGE IIB                 0                 10
  STAGE IIC                 0                  1
  STAGE III                 2                 22
  STAGE IIIA                0                 11
  STAGE IIIB                1                 58
  STAGE IIIC                0                 42
  STAGE IV                  1                 47
  STAGE IVA                 0                 18
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  ARHGEF10 MUTATED     0   5  19   0
  ARHGEF10 WILD-TYPE  17  87 310  50
D380V5, multiclass
    clus
vv   ARHGEF10 MUTATED ARHGEF10 WILD-TYPE
  T1                0                 17
  T2                5                 87
  T3               19                310
  T4                0                 50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  ARHGEF10 MUTATED    20   4   0
  ARHGEF10 WILD-TYPE 267 109  87
D380V6, multiclass
    clus
vv   ARHGEF10 MUTATED ARHGEF10 WILD-TYPE
  N0               20                267
  N1                4                109
  N2                0                 87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D380V7, binary
                    cls
clus                   0   1
  ARHGEF10 MUTATED    19   1
  ARHGEF10 WILD-TYPE 356  64
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ARHGEF10 MUTATED     19    1
  ARHGEF10 WILD-TYPE  356   64
   clus
vv  ARHGEF10 MUTATED ARHGEF10 WILD-TYPE
  0               19                356
  1                1                 64
[1] 2 2
[1] FALSE
D380V8, binary
                    cls
clus                   0   1
  ARHGEF10 MUTATED    10  14
  ARHGEF10 WILD-TYPE 215 250
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ARHGEF10 MUTATED     10   14
  ARHGEF10 WILD-TYPE  215  250
        clus
vv       ARHGEF10 MUTATED ARHGEF10 WILD-TYPE
  FEMALE               10                215
  MALE                 14                250
[1] 2 2
[1] FALSE
D380V9, binary
                    cls
clus                   0   1
  ARHGEF10 MUTATED    19   1
  ARHGEF10 WILD-TYPE 331  21
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ARHGEF10 MUTATED     19    1
  ARHGEF10 WILD-TYPE  331   21
     clus
vv    ARHGEF10 MUTATED ARHGEF10 WILD-TYPE
  NO                19                331
  YES                1                 21
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ARHGEF10 MUTATED                     17                             6
  ARHGEF10 WILD-TYPE                  298                            41
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ARHGEF10 MUTATED                       1                              0
  ARHGEF10 WILD-TYPE                   105                             10
D380V10, multiclass
                                clus
vv                               ARHGEF10 MUTATED ARHGEF10 WILD-TYPE
  COLON ADENOCARCINOMA                         17                298
  COLON MUCINOUS ADENOCARCINOMA                 6                 41
  RECTAL ADENOCARCINOMA                         1                105
  RECTAL MUCINOUS ADENOCARCINOMA                0                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  ARHGEF10 MUTATED    16   0   1   2
  ARHGEF10 WILD-TYPE 329   4  30  23
D380V11, multiclass
    clus
vv   ARHGEF10 MUTATED ARHGEF10 WILD-TYPE
  R0               16                329
  R1                0                  4
  R2                1                 30
  RX                2                 23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D380V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ARHGEF10 MUTATED                                  0     2
  ARHGEF10 WILD-TYPE                                1     9
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  ARHGEF10 MUTATED                           1    10
  ARHGEF10 WILD-TYPE                        21   216
D380V13, multiclass
                                  clus
vv                                 ARHGEF10 MUTATED ARHGEF10 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           2                  9
  BLACK OR AFRICAN AMERICAN                       1                 21
  WHITE                                          10                216
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(381) Variable = HEPACAM2 MUTATION ANALYSIS
D381V1, survival
                    sevent
clus2                  0   1
  HEPACAM2 MUTATED    11   3
  HEPACAM2 WILD-TYPE 367  90
  HEPACAM2 MUTATED HEPACAM2 WILD-TYPE 
                14                457 
  HEPACAM2 MUTATED HEPACAM2 WILD-TYPE 
                 3                 90 
$`HEPACAM2 MUTATED`
TCGA-A6-3809 TCGA-A6-6781 TCGA-AA-3845 TCGA-AA-3977 TCGA-AU-6004 TCGA-AZ-6600 
       32.75        19.66         0.00        25.02        27.09        12.10 
TCGA-CA-6718 TCGA-CK-4952 TCGA-CM-4743 TCGA-CM-5348 TCGA-D5-6930 TCGA-G4-6315 
       10.06        15.62        23.05        22.98         1.51        61.91 
TCGA-G4-6628 TCGA-AG-A002 
       79.69        20.98 

$`HEPACAM2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 
       15.95        38.99        37.02        14.93        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       14.50        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       88.21        49.41         6.77       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07        12.20        12.76        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
      148.01        85.45        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
       82.95         1.91       124.27        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       13.02        29.06        22.03        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6317 TCGA-G4-6321 
       44.68        55.04        85.48        63.62        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 
       13.78        35.80        26.17        91.79        46.75        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  HEPACAM2 MUTATED HEPACAM2 WILD-TYPE 
                 0                  0 
  HEPACAM2 MUTATED HEPACAM2 WILD-TYPE 
             79.69             148.01 
  HEPACAM2 MUTATED HEPACAM2 WILD-TYPE 
             21.98              20.12 
[1] "0.0 - 79.7 (22.0)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.1"
D381V2, continuous
D381V3, binary
                    cls
clus                   0   1
  HEPACAM2 MUTATED    13   1
  HEPACAM2 WILD-TYPE 353 118
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HEPACAM2 MUTATED     13    1
  HEPACAM2 WILD-TYPE  353  118
        clus
vv       HEPACAM2 MUTATED HEPACAM2 WILD-TYPE
  COLON                13                353
  RECTUM                1                118
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  HEPACAM2 MUTATED         3        0        0         4         1         0
  HEPACAM2 WILD-TYPE      88        1       32       134         9         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HEPACAM2 MUTATED           0          0          1          2        2
  HEPACAM2 WILD-TYPE        24         11         58         40       46
                    vv
clus                 STAGE IVA STAGE IVB
  HEPACAM2 MUTATED           0         0
  HEPACAM2 WILD-TYPE        18         1
D381V4, multiclass
            clus
vv           HEPACAM2 MUTATED HEPACAM2 WILD-TYPE
  STAGE I                   3                 88
  STAGE IA                  0                  1
  STAGE II                  0                 32
  STAGE IIA                 4                134
  STAGE IIB                 1                  9
  STAGE IIC                 0                  1
  STAGE III                 0                 24
  STAGE IIIA                0                 11
  STAGE IIIB                1                 58
  STAGE IIIC                2                 40
  STAGE IV                  2                 46
  STAGE IVA                 0                 18
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  HEPACAM2 MUTATED     0   4   6   4
  HEPACAM2 WILD-TYPE  17  88 323  46
D381V5, multiclass
    clus
vv   HEPACAM2 MUTATED HEPACAM2 WILD-TYPE
  T1                0                 17
  T2                4                 88
  T3                6                323
  T4                4                 46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  HEPACAM2 MUTATED     9   4   1
  HEPACAM2 WILD-TYPE 278 109  86
D381V6, multiclass
    clus
vv   HEPACAM2 MUTATED HEPACAM2 WILD-TYPE
  N0                9                278
  N1                4                109
  N2                1                 86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D381V7, binary
                    cls
clus                   0   1
  HEPACAM2 MUTATED    10   2
  HEPACAM2 WILD-TYPE 365  63
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HEPACAM2 MUTATED     10    2
  HEPACAM2 WILD-TYPE  365   63
   clus
vv  HEPACAM2 MUTATED HEPACAM2 WILD-TYPE
  0               10                365
  1                2                 63
[1] 2 2
[1] FALSE
D381V8, binary
                    cls
clus                   0   1
  HEPACAM2 MUTATED     4  10
  HEPACAM2 WILD-TYPE 221 254
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HEPACAM2 MUTATED      4   10
  HEPACAM2 WILD-TYPE  221  254
        clus
vv       HEPACAM2 MUTATED HEPACAM2 WILD-TYPE
  FEMALE                4                221
  MALE                 10                254
[1] 2 2
[1] FALSE
D381V9, binary
                    cls
clus                   0   1
  HEPACAM2 MUTATED     9   0
  HEPACAM2 WILD-TYPE 341  22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HEPACAM2 MUTATED      9    0
  HEPACAM2 WILD-TYPE  341   22
     clus
vv    HEPACAM2 MUTATED HEPACAM2 WILD-TYPE
  NO                 9                341
  YES                0                 22
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  HEPACAM2 MUTATED                      9                             4
  HEPACAM2 WILD-TYPE                  306                            43
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  HEPACAM2 MUTATED                       1                              0
  HEPACAM2 WILD-TYPE                   105                             10
D381V10, multiclass
                                clus
vv                               HEPACAM2 MUTATED HEPACAM2 WILD-TYPE
  COLON ADENOCARCINOMA                          9                306
  COLON MUCINOUS ADENOCARCINOMA                 4                 43
  RECTAL ADENOCARCINOMA                         1                105
  RECTAL MUCINOUS ADENOCARCINOMA                0                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  HEPACAM2 MUTATED    10   0   0   2
  HEPACAM2 WILD-TYPE 335   4  31  23
D381V11, multiclass
    clus
vv   HEPACAM2 MUTATED HEPACAM2 WILD-TYPE
  R0               10                335
  R1                0                  4
  R2                0                 31
  RX                2                 23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D381V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HEPACAM2 MUTATED                                  0     1
  HEPACAM2 WILD-TYPE                                1    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  HEPACAM2 MUTATED                           1     9
  HEPACAM2 WILD-TYPE                        21   217
D381V13, multiclass
                                  clus
vv                                 HEPACAM2 MUTATED HEPACAM2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                 10
  BLACK OR AFRICAN AMERICAN                       1                 21
  WHITE                                           9                217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(382) Variable = KCNH7 MUTATION ANALYSIS
D382V1, survival
                 sevent
clus2               0   1
  KCNH7 MUTATED    26  11
  KCNH7 WILD-TYPE 352  82
  KCNH7 MUTATED KCNH7 WILD-TYPE 
             37             434 
  KCNH7 MUTATED KCNH7 WILD-TYPE 
             11              82 
$`KCNH7 MUTATED`
TCGA-A6-2676 TCGA-AA-3510 TCGA-AA-3554 TCGA-AA-3715 TCGA-AA-3845 TCGA-AA-3941 
       42.90        63.98        17.95        19.04         0.00        24.00 
TCGA-AA-3966 TCGA-AA-A00N TCGA-AA-A01R TCGA-AU-3779 TCGA-AY-4071 TCGA-AZ-5403 
        2.01         4.01        35.01        14.50         0.95        62.79 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4950 TCGA-CK-5916 TCGA-CM-5348 TCGA-CM-5349 
       12.76        10.06        85.45        21.14        22.98        30.08 
TCGA-CM-6161 TCGA-CM-6170 TCGA-CM-6674 TCGA-CM-6678 TCGA-D5-6535 TCGA-D5-6930 
       15.02        15.02        12.95        11.01        15.12         1.51 
TCGA-DM-A1D0 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6856 TCGA-G4-6317 TCGA-G4-6586 
      130.65        35.74         6.18        35.31        36.00        35.80 
TCGA-G4-6626 TCGA-AF-2687 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A02X TCGA-F5-6464 
       46.75        24.13        20.98        13.94        41.00         9.96 
TCGA-F5-6465 
       49.51 

$`KCNH7 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       24.00        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       85.05        26.99        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02        14.93        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3947 TCGA-AA-3949 
       18.05        31.00         2.01        12.99        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 
       24.00         2.01        20.98        34.03        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T 
       31.00        31.00        38.07         1.02         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
        0.20        27.09        16.31        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5407 
       58.39         1.41         5.13       106.75        22.36        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        3.29         0.07        12.20        14.30        17.56       148.01 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 
       15.62        49.08        51.32         9.99        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       29.06        22.03        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       15.02        17.03        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6171 TCGA-CM-6172 
       21.99        14.99        12.99        13.02        14.04        11.01 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       13.05        11.08        11.08        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
        1.32        43.27        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6931 
       14.30         9.04         9.44        11.64         4.80        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D4 
       11.38        10.26       119.70        24.43        38.20        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
       13.25         0.53        47.41       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-AF-2689 
       22.09        13.78        26.17        91.79        79.69        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
        1.94        38.96        61.97        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       18.28        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  KCNH7 MUTATED KCNH7 WILD-TYPE 
              0               0 
  KCNH7 MUTATED KCNH7 WILD-TYPE 
         130.65          148.01 
  KCNH7 MUTATED KCNH7 WILD-TYPE 
         20.980          20.155 
[1] "0.0 - 130.7 (21.0)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.5"
D382V2, continuous
D382V3, binary
                 cls
clus                0   1
  KCNH7 MUTATED    31   6
  KCNH7 WILD-TYPE 335 113
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNH7 MUTATED     31    6
  KCNH7 WILD-TYPE  335  113
        clus
vv       KCNH7 MUTATED KCNH7 WILD-TYPE
  COLON             31             335
  RECTUM             6             113
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KCNH7 MUTATED         9        0        3        15         2         0
  KCNH7 WILD-TYPE      82        1       29       123         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  KCNH7 MUTATED           1          0          3          3        0         2
  KCNH7 WILD-TYPE        23         11         56         39       48        16
                 vv
clus              STAGE IVB
  KCNH7 MUTATED           0
  KCNH7 WILD-TYPE         1
D382V4, multiclass
            clus
vv           KCNH7 MUTATED KCNH7 WILD-TYPE
  STAGE I                9              82
  STAGE IA               0               1
  STAGE II               3              29
  STAGE IIA             15             123
  STAGE IIB              2               8
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             3              56
  STAGE IIIC             3              39
  STAGE IV               0              48
  STAGE IVA              2              16
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  KCNH7 MUTATED     2   7  24   5
  KCNH7 WILD-TYPE  15  85 305  45
D382V5, multiclass
    clus
vv   KCNH7 MUTATED KCNH7 WILD-TYPE
  T1             2              15
  T2             7              85
  T3            24             305
  T4             5              45
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  KCNH7 MUTATED    29   5   4
  KCNH7 WILD-TYPE 258 108  83
D382V6, multiclass
    clus
vv   KCNH7 MUTATED KCNH7 WILD-TYPE
  N0            29             258
  N1             5             108
  N2             4              83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D382V7, binary
                 cls
clus                0   1
  KCNH7 MUTATED    32   2
  KCNH7 WILD-TYPE 343  63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNH7 MUTATED     32    2
  KCNH7 WILD-TYPE  343   63
   clus
vv  KCNH7 MUTATED KCNH7 WILD-TYPE
  0            32             343
  1             2              63
[1] 2 2
[1] FALSE
D382V8, binary
                 cls
clus                0   1
  KCNH7 MUTATED    22  16
  KCNH7 WILD-TYPE 203 248
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNH7 MUTATED     22   16
  KCNH7 WILD-TYPE  203  248
        clus
vv       KCNH7 MUTATED KCNH7 WILD-TYPE
  FEMALE            22             203
  MALE              16             248
[1] 2 2
[1] FALSE
D382V9, binary
                 cls
clus                0   1
  KCNH7 MUTATED    29   2
  KCNH7 WILD-TYPE 321  20
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNH7 MUTATED     29    2
  KCNH7 WILD-TYPE  321   20
     clus
vv    KCNH7 MUTATED KCNH7 WILD-TYPE
  NO             29             321
  YES             2              20
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  KCNH7 MUTATED                     25                             6
  KCNH7 WILD-TYPE                  290                            41
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  KCNH7 MUTATED                       5                              1
  KCNH7 WILD-TYPE                   101                              9
D382V10, multiclass
                                clus
vv                               KCNH7 MUTATED KCNH7 WILD-TYPE
  COLON ADENOCARCINOMA                      25             290
  COLON MUCINOUS ADENOCARCINOMA              6              41
  RECTAL ADENOCARCINOMA                      5             101
  RECTAL MUCINOUS ADENOCARCINOMA             1               9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  KCNH7 MUTATED    30   1   0   4
  KCNH7 WILD-TYPE 315   3  31  21
D382V11, multiclass
    clus
vv   KCNH7 MUTATED KCNH7 WILD-TYPE
  R0            30             315
  R1             1               3
  R2             0              31
  RX             4              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D382V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KCNH7 MUTATED                                  0     2
  KCNH7 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  KCNH7 MUTATED                           1    23
  KCNH7 WILD-TYPE                        21   203
D382V13, multiclass
                                  clus
vv                                 KCNH7 MUTATED KCNH7 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               9
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                       23             203
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(383) Variable = AGBL2 MUTATION ANALYSIS
D383V1, survival
                 sevent
clus2               0   1
  AGBL2 MUTATED    11   2
  AGBL2 WILD-TYPE 367  91
  AGBL2 MUTATED AGBL2 WILD-TYPE 
             13             458 
  AGBL2 MUTATED AGBL2 WILD-TYPE 
              2              91 
$`AGBL2 MUTATED`
TCGA-A6-4105 TCGA-A6-5665 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-A00K TCGA-AA-A00N 
       14.53        22.06         6.05         6.97        18.05         4.01 
TCGA-AA-A010 TCGA-AD-5900 TCGA-AZ-4315 TCGA-CK-4948 TCGA-CM-5861 TCGA-G4-6315 
       34.98         0.07        58.39       148.01        15.02        61.91 
TCGA-AG-A002 
       20.98 

$`AGBL2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 
       16.57        34.65        33.34        32.75        36.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 
       13.94        19.99        61.02        78.08        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       34.03        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 
       41.00        39.98        18.05        40.96        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       33.01        21.44        17.82         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4952 
       12.76        10.06        14.30        17.56        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 
       29.06        22.03        22.98        30.08        32.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6317 TCGA-G4-6321 
       44.68        55.04        85.48        63.62        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  AGBL2 MUTATED AGBL2 WILD-TYPE 
           0.07            0.00 
  AGBL2 MUTATED AGBL2 WILD-TYPE 
         148.01          140.38 
  AGBL2 MUTATED AGBL2 WILD-TYPE 
         18.050          20.235 
[1] "0.1 - 148.0 (18.1)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.4"
D383V2, continuous
D383V3, binary
                 cls
clus                0   1
  AGBL2 MUTATED    14   1
  AGBL2 WILD-TYPE 352 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AGBL2 MUTATED     14    1
  AGBL2 WILD-TYPE  352  118
        clus
vv       AGBL2 MUTATED AGBL2 WILD-TYPE
  COLON             14             352
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  AGBL2 MUTATED         2        0        1         6         3         0
  AGBL2 WILD-TYPE      89        1       31       132         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AGBL2 MUTATED           1          0          0          0        2         0
  AGBL2 WILD-TYPE        23         11         59         42       46        18
                 vv
clus              STAGE IVB
  AGBL2 MUTATED           0
  AGBL2 WILD-TYPE         1
D383V4, multiclass
            clus
vv           AGBL2 MUTATED AGBL2 WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              6             132
  STAGE IIB              3               7
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             0              42
  STAGE IV               2              46
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  AGBL2 MUTATED     0   2   9   4
  AGBL2 WILD-TYPE  17  90 320  46
D383V5, multiclass
    clus
vv   AGBL2 MUTATED AGBL2 WILD-TYPE
  T1             0              17
  T2             2              90
  T3             9             320
  T4             4              46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  AGBL2 MUTATED    12   2   1
  AGBL2 WILD-TYPE 275 111  86
D383V6, multiclass
    clus
vv   AGBL2 MUTATED AGBL2 WILD-TYPE
  N0            12             275
  N1             2             111
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D383V7, binary
                 cls
clus                0   1
  AGBL2 MUTATED    11   2
  AGBL2 WILD-TYPE 364  63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AGBL2 MUTATED     11    2
  AGBL2 WILD-TYPE  364   63
   clus
vv  AGBL2 MUTATED AGBL2 WILD-TYPE
  0            11             364
  1             2              63
[1] 2 2
[1] FALSE
D383V8, binary
                 cls
clus                0   1
  AGBL2 MUTATED     7   8
  AGBL2 WILD-TYPE 218 256
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AGBL2 MUTATED      7    8
  AGBL2 WILD-TYPE  218  256
        clus
vv       AGBL2 MUTATED AGBL2 WILD-TYPE
  FEMALE             7             218
  MALE               8             256
[1] 2 2
[1] FALSE
D383V9, binary
                 cls
clus                0   1
  AGBL2 MUTATED    10   0
  AGBL2 WILD-TYPE 340  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AGBL2 MUTATED     10    0
  AGBL2 WILD-TYPE  340   22
     clus
vv    AGBL2 MUTATED AGBL2 WILD-TYPE
  NO             10             340
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  AGBL2 MUTATED                     12                             2
  AGBL2 WILD-TYPE                  303                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  AGBL2 MUTATED                       1                              0
  AGBL2 WILD-TYPE                   105                             10
D383V10, multiclass
                                clus
vv                               AGBL2 MUTATED AGBL2 WILD-TYPE
  COLON ADENOCARCINOMA                      12             303
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  AGBL2 MUTATED    12   0   1   1
  AGBL2 WILD-TYPE 333   4  30  24
D383V11, multiclass
    clus
vv   AGBL2 MUTATED AGBL2 WILD-TYPE
  R0            12             333
  R1             0               4
  R2             1              30
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D383V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AGBL2 MUTATED                                  0     0
  AGBL2 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  AGBL2 MUTATED                           0     8
  AGBL2 WILD-TYPE                        22   218
D383V13, multiclass
                                  clus
vv                                 AGBL2 MUTATED AGBL2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        8             218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(384) Variable = ACP6 MUTATION ANALYSIS
D384V1, survival
                sevent
clus2              0   1
  ACP6 MUTATED     4   2
  ACP6 WILD-TYPE 374  91
  ACP6 MUTATED ACP6 WILD-TYPE 
             6            465 
  ACP6 MUTATED ACP6 WILD-TYPE 
             2             91 
$`ACP6 MUTATED`
TCGA-A6-6648 TCGA-AA-3713 TCGA-AD-6964 TCGA-CK-4948 TCGA-F4-6460 TCGA-G4-6588 
       25.18        19.04        10.88       148.01        31.96        26.17 

$`ACP6 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.08        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4952 
       12.76        10.06        14.30        17.56        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
       98.24         8.61        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       22.09        13.78        35.80        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  ACP6 MUTATED ACP6 WILD-TYPE 
         10.88           0.00 
  ACP6 MUTATED ACP6 WILD-TYPE 
        148.01         140.38 
  ACP6 MUTATED ACP6 WILD-TYPE 
        25.675         20.120 
[1] "10.9 - 148.0 (25.7)" "0.0 - 140.4 (20.1)" 
[1] "hr=" "1.3"
D384V2, continuous
D384V3, binary
                cls
clus               0   1
  ACP6 MUTATED     6   0
  ACP6 WILD-TYPE 360 119
[1] "tbl2"
                cls
clus             [,1] [,2]
  ACP6 MUTATED      6    0
  ACP6 WILD-TYPE  360  119
        clus
vv       ACP6 MUTATED ACP6 WILD-TYPE
  COLON             6            360
  RECTUM            0            119
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ACP6 MUTATED         0        0        0         1         0         0
  ACP6 WILD-TYPE      91        1       32       137        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ACP6 MUTATED           1          0          1          0        1         1
  ACP6 WILD-TYPE        23         11         58         42       47        17
                vv
clus             STAGE IVB
  ACP6 MUTATED           0
  ACP6 WILD-TYPE         1
D384V4, multiclass
            clus
vv           ACP6 MUTATED ACP6 WILD-TYPE
  STAGE I               0             91
  STAGE IA              0              1
  STAGE II              0             32
  STAGE IIA             1            137
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             1             23
  STAGE IIIA            0             11
  STAGE IIIB            1             58
  STAGE IIIC            0             42
  STAGE IV              1             47
  STAGE IVA             1             17
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  ACP6 MUTATED     0   0   5   1
  ACP6 WILD-TYPE  17  92 324  49
D384V5, multiclass
    clus
vv   ACP6 MUTATED ACP6 WILD-TYPE
  T1            0             17
  T2            0             92
  T3            5            324
  T4            1             49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  ACP6 MUTATED     3   2   1
  ACP6 WILD-TYPE 284 111  86
D384V6, multiclass
    clus
vv   ACP6 MUTATED ACP6 WILD-TYPE
  N0            3            284
  N1            2            111
  N2            1             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D384V7, binary
                cls
clus               0   1
  ACP6 MUTATED     3   2
  ACP6 WILD-TYPE 372  63
[1] "tbl2"
                cls
clus             [,1] [,2]
  ACP6 MUTATED      3    2
  ACP6 WILD-TYPE  372   63
   clus
vv  ACP6 MUTATED ACP6 WILD-TYPE
  0            3            372
  1            2             63
[1] 2 2
[1] FALSE
D384V8, binary
                cls
clus               0   1
  ACP6 MUTATED     3   3
  ACP6 WILD-TYPE 222 261
[1] "tbl2"
                cls
clus             [,1] [,2]
  ACP6 MUTATED      3    3
  ACP6 WILD-TYPE  222  261
        clus
vv       ACP6 MUTATED ACP6 WILD-TYPE
  FEMALE            3            222
  MALE              3            261
[1] 2 2
[1] FALSE
D384V9, binary
                cls
clus               0   1
  ACP6 MUTATED     5   1
  ACP6 WILD-TYPE 345  21
[1] "tbl2"
                cls
clus             [,1] [,2]
  ACP6 MUTATED      5    1
  ACP6 WILD-TYPE  345   21
     clus
vv    ACP6 MUTATED ACP6 WILD-TYPE
  NO             5            345
  YES            1             21
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ACP6 MUTATED                      6                             0
  ACP6 WILD-TYPE                  309                            47
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ACP6 MUTATED                       0                              0
  ACP6 WILD-TYPE                   106                             10
D384V10, multiclass
                                clus
vv                               ACP6 MUTATED ACP6 WILD-TYPE
  COLON ADENOCARCINOMA                      6            309
  COLON MUCINOUS ADENOCARCINOMA             0             47
  RECTAL ADENOCARCINOMA                     0            106
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  ACP6 MUTATED     3   0   1   0
  ACP6 WILD-TYPE 342   4  30  25
D384V11, multiclass
    clus
vv   ACP6 MUTATED ACP6 WILD-TYPE
  R0            3            342
  R1            0              4
  R2            1             30
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D384V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ACP6 MUTATED                                  0     0
  ACP6 WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  ACP6 MUTATED                           0     5
  ACP6 WILD-TYPE                        22   221
D384V13, multiclass
                                  clus
vv                                 ACP6 MUTATED ACP6 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       5            221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(385) Variable = UBC MUTATION ANALYSIS
D385V1, survival
               sevent
clus2             0   1
  UBC MUTATED     5   0
  UBC WILD-TYPE 373  93
  UBC MUTATED UBC WILD-TYPE 
            5           466 
  UBC MUTATED UBC WILD-TYPE 
            0            93 
$`UBC MUTATED`
TCGA-A6-6652 TCGA-CM-5349 TCGA-CM-6162 TCGA-G4-6315 TCGA-F5-6812 
       24.69        30.08        12.00        61.91         0.66 

$`UBC WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6654 
       25.08        25.18        24.16        21.76        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       15.02         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.69        55.76        26.43 

  UBC MUTATED UBC WILD-TYPE 
         0.66          0.00 
  UBC MUTATED UBC WILD-TYPE 
        61.91        148.01 
  UBC MUTATED UBC WILD-TYPE 
       24.690        20.155 
[1] "0.7 - 61.9 (24.7)"  "0.0 - 148.0 (20.2)"
[1] "hr="     "9100000"
D385V2, continuous
D385V3, binary
               cls
clus              0   1
  UBC MUTATED     4   1
  UBC WILD-TYPE 362 118
[1] "tbl2"
               cls
clus            [,1] [,2]
  UBC MUTATED      4    1
  UBC WILD-TYPE  362  118
        clus
vv       UBC MUTATED UBC WILD-TYPE
  COLON            4           362
  RECTUM           1           118
[1] 2 2
[1] FALSE
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  UBC MUTATED         0        0        0         2         0         0
  UBC WILD-TYPE      91        1       32       136        10         1
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  UBC MUTATED           0          0          1          0        1         1
  UBC WILD-TYPE        24         11         58         42       47        17
               vv
clus            STAGE IVB
  UBC MUTATED           0
  UBC WILD-TYPE         1
D385V4, multiclass
            clus
vv           UBC MUTATED UBC WILD-TYPE
  STAGE I              0            91
  STAGE IA             0             1
  STAGE II             0            32
  STAGE IIA            2           136
  STAGE IIB            0            10
  STAGE IIC            0             1
  STAGE III            0            24
  STAGE IIIA           0            11
  STAGE IIIB           1            58
  STAGE IIIC           0            42
  STAGE IV             1            47
  STAGE IVA            1            17
  STAGE IVB            0             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  UBC MUTATED     0   0   5   0
  UBC WILD-TYPE  17  92 324  50
D385V5, multiclass
    clus
vv   UBC MUTATED UBC WILD-TYPE
  T1           0            17
  T2           0            92
  T3           5           324
  T4           0            50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2
  UBC MUTATED     3   2   0
  UBC WILD-TYPE 284 111  87
D385V6, multiclass
    clus
vv   UBC MUTATED UBC WILD-TYPE
  N0           3           284
  N1           2           111
  N2           0            87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D385V7, binary
               cls
clus              0   1
  UBC MUTATED     3   2
  UBC WILD-TYPE 372  63
[1] "tbl2"
               cls
clus            [,1] [,2]
  UBC MUTATED      3    2
  UBC WILD-TYPE  372   63
   clus
vv  UBC MUTATED UBC WILD-TYPE
  0           3           372
  1           2            63
[1] 2 2
[1] FALSE
D385V8, binary
               cls
clus              0   1
  UBC MUTATED     2   3
  UBC WILD-TYPE 223 261
[1] "tbl2"
               cls
clus            [,1] [,2]
  UBC MUTATED      2    3
  UBC WILD-TYPE  223  261
        clus
vv       UBC MUTATED UBC WILD-TYPE
  FEMALE           2           223
  MALE             3           261
[1] 2 2
[1] FALSE
D385V9, binary
               cls
clus              0   1
  UBC MUTATED     4   0
  UBC WILD-TYPE 346  22
[1] "tbl2"
               cls
clus            [,1] [,2]
  UBC MUTATED      4    0
  UBC WILD-TYPE  346   22
     clus
vv    UBC MUTATED UBC WILD-TYPE
  NO            4           346
  YES           0            22
[1] 2 2
[1] FALSE
               vv
clus            COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  UBC MUTATED                      3                             1
  UBC WILD-TYPE                  312                            46
               vv
clus            RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  UBC MUTATED                       1                              0
  UBC WILD-TYPE                   105                             10
D385V10, multiclass
                                clus
vv                               UBC MUTATED UBC WILD-TYPE
  COLON ADENOCARCINOMA                     3           312
  COLON MUCINOUS ADENOCARCINOMA            1            46
  RECTAL ADENOCARCINOMA                    1           105
  RECTAL MUCINOUS ADENOCARCINOMA           0            10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             R0  R1  R2  RX
  UBC MUTATED     4   0   0   0
  UBC WILD-TYPE 341   4  31  25
D385V11, multiclass
    clus
vv   UBC MUTATED UBC WILD-TYPE
  R0           4           341
  R1           0             4
  R2           0            31
  RX           0            25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D385V12, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  UBC MUTATED                                  0     0
  UBC WILD-TYPE                                1    11
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  UBC MUTATED                           1     4
  UBC WILD-TYPE                        21   222
D385V13, multiclass
                                  clus
vv                                 UBC MUTATED UBC WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      0            11
  BLACK OR AFRICAN AMERICAN                  1            21
  WHITE                                      4           222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(386) Variable = BRCA2 MUTATION ANALYSIS
D386V1, survival
                 sevent
clus2               0   1
  BRCA2 MUTATED    46  10
  BRCA2 WILD-TYPE 332  83
  BRCA2 MUTATED BRCA2 WILD-TYPE 
             56             415 
  BRCA2 MUTATED BRCA2 WILD-TYPE 
             10              83 
$`BRCA2 MUTATED`
TCGA-A6-5656 TCGA-A6-5665 TCGA-A6-6654 TCGA-AA-3496 TCGA-AA-3510 TCGA-AA-3518 
       32.91        22.06        23.87         1.02        63.98         1.02 
TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.99         6.05         6.97        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-A00N TCGA-AA-A010 TCGA-AD-6964 TCGA-AU-6004 TCGA-AZ-4315 
       19.04         4.01        34.98        10.88        27.09        58.39 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 
       49.41         6.77       100.01         0.07        12.76        10.06 
TCGA-CK-5913 TCGA-CM-4743 TCGA-CM-4752 TCGA-CM-5863 TCGA-CM-5868 TCGA-CM-6162 
       51.32        23.05        13.02        15.02        17.03        12.00 
TCGA-CM-6172 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-D5-6536 TCGA-D5-6540 
       11.01        11.08        11.01        10.06        17.85        16.14 
TCGA-D5-6923 TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6930 TCGA-DM-A0XD TCGA-DM-A1D9 
       12.43         9.04         4.80         1.51        24.43       140.38 
TCGA-F4-6460 TCGA-G4-6307 TCGA-G4-6588 TCGA-G4-6628 TCGA-AF-5654 TCGA-AG-3892 
       31.96        55.04        26.17        79.69        16.83        13.02 
TCGA-AG-A002 TCGA-AG-A00C TCGA-AH-6643 TCGA-CI-6622 TCGA-CI-6624 TCGA-DC-6155 
       20.98         6.02         0.69         6.97         4.73        13.97 
TCGA-EI-6507 TCGA-EI-6508 
       19.96        20.91 

$`BRCA2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 
       24.16        21.76        24.69        24.39        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 
       20.28         7.04         3.02        35.01         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       13.02        38.99         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 
       20.98        19.99        13.94        61.02        78.08        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
        0.79         0.72         5.79        22.42        27.42         0.20 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       14.50        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
       12.10        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6716 TCGA-CA-6719 
       12.69         3.06         3.25         3.29        12.20        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 
       17.56       148.01        85.45        15.62        49.08         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 
       21.14        82.95         1.91       124.27        20.02        37.02 
TCGA-CM-4747 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       25.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 
       15.02         5.03        15.02        15.02         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6680 TCGA-D5-5537 
       14.04        12.95        13.05        11.08        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
        1.32        43.27        15.12         4.80        17.13        12.49 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6924 TCGA-D5-6927 
       15.58         1.48         3.68         4.41        14.30         9.44 
TCGA-D5-6928 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XF 
       11.64        12.00        11.38        10.26       119.70        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1DA 
      130.65        92.75        49.91        13.32        12.59         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 
      133.18        74.56        65.85        53.62        44.68        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       91.79        46.75        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6655 
       19.10        34.49        10.39        14.50        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       17.95        36.95        17.03        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
        1.02        17.03        13.94        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6644 
       38.04       117.11        38.56         1.45        17.49         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.05        33.17        78.12         7.17        15.02         5.03 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       32.61         0.49        20.55        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  BRCA2 MUTATED BRCA2 WILD-TYPE 
           0.07            0.00 
  BRCA2 MUTATED BRCA2 WILD-TYPE 
         140.38          148.01 
  BRCA2 MUTATED BRCA2 WILD-TYPE 
         16.485          21.370 
[1] "0.1 - 140.4 (16.5)" "0.0 - 148.0 (21.4)"
[1] "hr=" "1"  
D386V2, continuous
D386V3, binary
                 cls
clus                0   1
  BRCA2 MUTATED    47  11
  BRCA2 WILD-TYPE 319 108
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BRCA2 MUTATED     47   11
  BRCA2 WILD-TYPE  319  108
        clus
vv       BRCA2 MUTATED BRCA2 WILD-TYPE
  COLON             47             319
  RECTUM            11             108
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  BRCA2 MUTATED        10        0        6        17         3         0
  BRCA2 WILD-TYPE      81        1       26       121         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  BRCA2 MUTATED           2          1         11          2        3         2
  BRCA2 WILD-TYPE        22         10         48         40       45        16
                 vv
clus              STAGE IVB
  BRCA2 MUTATED           0
  BRCA2 WILD-TYPE         1
D386V4, multiclass
            clus
vv           BRCA2 MUTATED BRCA2 WILD-TYPE
  STAGE I               10              81
  STAGE IA               0               1
  STAGE II               6              26
  STAGE IIA             17             121
  STAGE IIB              3               7
  STAGE IIC              0               1
  STAGE III              2              22
  STAGE IIIA             1              10
  STAGE IIIB            11              48
  STAGE IIIC             2              40
  STAGE IV               3              45
  STAGE IVA              2              16
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  BRCA2 MUTATED     1  10  38   9
  BRCA2 WILD-TYPE  16  82 291  41
D386V5, multiclass
    clus
vv   BRCA2 MUTATED BRCA2 WILD-TYPE
  T1             1              16
  T2            10              82
  T3            38             291
  T4             9              41
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  BRCA2 MUTATED    38  15   5
  BRCA2 WILD-TYPE 249  98  82
D386V6, multiclass
    clus
vv   BRCA2 MUTATED BRCA2 WILD-TYPE
  N0            38             249
  N1            15              98
  N2             5              82
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D386V7, binary
                 cls
clus                0   1
  BRCA2 MUTATED    49   5
  BRCA2 WILD-TYPE 326  60
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BRCA2 MUTATED     49    5
  BRCA2 WILD-TYPE  326   60
   clus
vv  BRCA2 MUTATED BRCA2 WILD-TYPE
  0            49             326
  1             5              60
[1] 2 2
[1] FALSE
D386V8, binary
                 cls
clus                0   1
  BRCA2 MUTATED    27  31
  BRCA2 WILD-TYPE 198 233
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BRCA2 MUTATED     27   31
  BRCA2 WILD-TYPE  198  233
        clus
vv       BRCA2 MUTATED BRCA2 WILD-TYPE
  FEMALE            27             198
  MALE              31             233
[1] 2 2
[1] FALSE
D386V9, binary
                 cls
clus                0   1
  BRCA2 MUTATED    41   3
  BRCA2 WILD-TYPE 309  19
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BRCA2 MUTATED     41    3
  BRCA2 WILD-TYPE  309   19
     clus
vv    BRCA2 MUTATED BRCA2 WILD-TYPE
  NO             41             309
  YES             3              19
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  BRCA2 MUTATED                     41                             6
  BRCA2 WILD-TYPE                  274                            41
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  BRCA2 MUTATED                      11                              0
  BRCA2 WILD-TYPE                    95                             10
D386V10, multiclass
                                clus
vv                               BRCA2 MUTATED BRCA2 WILD-TYPE
  COLON ADENOCARCINOMA                      41             274
  COLON MUCINOUS ADENOCARCINOMA              6              41
  RECTAL ADENOCARCINOMA                     11              95
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  BRCA2 MUTATED    41   0   3   4
  BRCA2 WILD-TYPE 304   4  28  21
D386V11, multiclass
    clus
vv   BRCA2 MUTATED BRCA2 WILD-TYPE
  R0            41             304
  R1             0               4
  R2             3              28
  RX             4              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D386V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  BRCA2 MUTATED                                  0     3
  BRCA2 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  BRCA2 MUTATED                           1    37
  BRCA2 WILD-TYPE                        21   189
D386V13, multiclass
                                  clus
vv                                 BRCA2 MUTATED BRCA2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        3               8
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                       37             189
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(387) Variable = EZH2 MUTATION ANALYSIS
D387V1, survival
                sevent
clus2              0   1
  EZH2 MUTATED    33  11
  EZH2 WILD-TYPE 345  82
  EZH2 MUTATED EZH2 WILD-TYPE 
            44            427 
  EZH2 MUTATED EZH2 WILD-TYPE 
            11             82 
$`EZH2 MUTATED`
TCGA-A6-2676 TCGA-A6-3809 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5665 TCGA-A6-6141 
       42.90        32.75        29.19        33.53        22.06         8.38 
TCGA-A6-6653 TCGA-A6-6781 TCGA-AA-3510 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3672 
       24.39        19.66        63.98         6.05         6.97         0.92 
TCGA-AA-3713 TCGA-AA-A00N TCGA-AA-A010 TCGA-AD-6964 TCGA-AY-6197 TCGA-AZ-6599 
       19.04         4.01        34.98        10.88        21.44         6.77 
TCGA-AZ-6608 TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-5344 TCGA-CM-5863 TCGA-CM-5864 
        1.61        12.76        10.06        22.03        15.02        15.02 
TCGA-D5-5540 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6540 TCGA-D5-6541 
       56.09        15.12        17.85         4.80        16.14        15.58 
TCGA-D5-6920 TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A28F TCGA-F4-6808 TCGA-G4-6303 
        3.68        44.32       135.65        35.97        33.67        65.85 
TCGA-G4-6306 TCGA-G4-6317 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6626 TCGA-G4-6628 
       44.68        36.00        35.80        26.17        46.75        79.69 
TCGA-AF-6672 TCGA-AH-6544 
       10.39        38.56 

$`EZH2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5657 
       34.65        33.34        36.53        14.53        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 
       30.44        23.61        22.09        32.71        27.09        22.52 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
       25.08        25.18        24.16        21.76        24.69        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       19.99        61.02        78.08        54.02         2.01        14.01 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
        0.79         0.72         5.79        22.42        27.42         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 
       14.50        27.09        16.31         0.95        33.01        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       88.21        49.41        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
       11.74         3.19        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.07        12.20        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       13.02        29.06        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
        5.03        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6538 
       55.92        20.19        18.25         1.32        43.27        17.13 
TCGA-D5-6539 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
       12.49         1.48         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HA 
       49.91        13.32        12.59       140.38         7.50       131.51 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H 
      139.17         6.12        81.37       119.93        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6854 
        1.55        34.42        41.42        16.24        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6304 TCGA-G4-6307 
       47.41        35.31       133.18        74.56        53.62        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6625 
       85.48        63.62        61.91        22.09        13.78        91.79 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AG-3574 
       10.39        14.50        16.83        15.39        20.02        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       41.00        38.04       117.11         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  EZH2 MUTATED EZH2 WILD-TYPE 
          0.92           0.00 
  EZH2 MUTATED EZH2 WILD-TYPE 
        135.65         148.01 
  EZH2 MUTATED EZH2 WILD-TYPE 
        21.735         20.120 
[1] "0.9 - 135.7 (21.7)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.3"
D387V2, continuous
D387V3, binary
                cls
clus               0   1
  EZH2 MUTATED    44   2
  EZH2 WILD-TYPE 322 117
[1] "tbl2"
                cls
clus             [,1] [,2]
  EZH2 MUTATED     44    2
  EZH2 WILD-TYPE  322  117
        clus
vv       EZH2 MUTATED EZH2 WILD-TYPE
  COLON            44            322
  RECTUM            2            117
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  EZH2 MUTATED         6        0        2        15         4         0
  EZH2 WILD-TYPE      85        1       30       123         6         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  EZH2 MUTATED           2          1          6          4        4         0
  EZH2 WILD-TYPE        22         10         53         38       44        18
                vv
clus             STAGE IVB
  EZH2 MUTATED           0
  EZH2 WILD-TYPE         1
D387V4, multiclass
            clus
vv           EZH2 MUTATED EZH2 WILD-TYPE
  STAGE I               6             85
  STAGE IA              0              1
  STAGE II              2             30
  STAGE IIA            15            123
  STAGE IIB             4              6
  STAGE IIC             0              1
  STAGE III             2             22
  STAGE IIIA            1             10
  STAGE IIIB            6             53
  STAGE IIIC            4             38
  STAGE IV              4             44
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  EZH2 MUTATED     1   7  30   8
  EZH2 WILD-TYPE  16  85 299  42
D387V5, multiclass
    clus
vv   EZH2 MUTATED EZH2 WILD-TYPE
  T1            1             16
  T2            7             85
  T3           30            299
  T4            8             42
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  EZH2 MUTATED    28  11   7
  EZH2 WILD-TYPE 259 102  80
D387V6, multiclass
    clus
vv   EZH2 MUTATED EZH2 WILD-TYPE
  N0           28            259
  N1           11            102
  N2            7             80
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D387V7, binary
                cls
clus               0   1
  EZH2 MUTATED    33   4
  EZH2 WILD-TYPE 342  61
[1] "tbl2"
                cls
clus             [,1] [,2]
  EZH2 MUTATED     33    4
  EZH2 WILD-TYPE  342   61
   clus
vv  EZH2 MUTATED EZH2 WILD-TYPE
  0           33            342
  1            4             61
[1] 2 2
[1] FALSE
D387V8, binary
                cls
clus               0   1
  EZH2 MUTATED    17  29
  EZH2 WILD-TYPE 208 235
[1] "tbl2"
                cls
clus             [,1] [,2]
  EZH2 MUTATED     17   29
  EZH2 WILD-TYPE  208  235
        clus
vv       EZH2 MUTATED EZH2 WILD-TYPE
  FEMALE           17            208
  MALE             29            235
[1] 2 2
[1] FALSE
D387V9, binary
                cls
clus               0   1
  EZH2 MUTATED    37   2
  EZH2 WILD-TYPE 313  20
[1] "tbl2"
                cls
clus             [,1] [,2]
  EZH2 MUTATED     37    2
  EZH2 WILD-TYPE  313   20
     clus
vv    EZH2 MUTATED EZH2 WILD-TYPE
  NO            37            313
  YES            2             20
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  EZH2 MUTATED                     36                             7
  EZH2 WILD-TYPE                  279                            40
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  EZH2 MUTATED                       2                              0
  EZH2 WILD-TYPE                   104                             10
D387V10, multiclass
                                clus
vv                               EZH2 MUTATED EZH2 WILD-TYPE
  COLON ADENOCARCINOMA                     36            279
  COLON MUCINOUS ADENOCARCINOMA             7             40
  RECTAL ADENOCARCINOMA                     2            104
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  EZH2 MUTATED    30   0   2   3
  EZH2 WILD-TYPE 315   4  29  22
D387V11, multiclass
    clus
vv   EZH2 MUTATED EZH2 WILD-TYPE
  R0           30            315
  R1            0              4
  R2            2             29
  RX            3             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D387V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  EZH2 MUTATED                                  0     2
  EZH2 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  EZH2 MUTATED                           3    33
  EZH2 WILD-TYPE                        19   193
D387V13, multiclass
                                  clus
vv                                 EZH2 MUTATED EZH2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              9
  BLACK OR AFRICAN AMERICAN                   3             19
  WHITE                                      33            193
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(388) Variable = OR5B2 MUTATION ANALYSIS
D388V1, survival
                 sevent
clus2               0   1
  OR5B2 MUTATED    11   2
  OR5B2 WILD-TYPE 367  91
  OR5B2 MUTATED OR5B2 WILD-TYPE 
             13             458 
  OR5B2 MUTATED OR5B2 WILD-TYPE 
              2              91 
$`OR5B2 MUTATED`
TCGA-AA-3510 TCGA-AA-3977 TCGA-AA-A010 TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-6605 
       63.98        25.02        34.98        21.44        58.39         5.23 
TCGA-CM-6166 TCGA-CM-6676 TCGA-D5-6537 TCGA-DM-A0X9 TCGA-AF-6672 TCGA-DC-6683 
       21.99        11.08         4.80       119.70        10.39         5.03 
TCGA-F5-6812 
        0.66 

$`OR5B2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       16.04        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       11.01        12.95        13.05        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0XD 
        4.80         1.51        12.00        11.38        10.26        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       20.02        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6813 
        9.96        49.51        31.30        28.57        32.19         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  OR5B2 MUTATED OR5B2 WILD-TYPE 
           0.66            0.00 
  OR5B2 MUTATED OR5B2 WILD-TYPE 
         119.70          148.01 
  OR5B2 MUTATED OR5B2 WILD-TYPE 
         21.440          20.155 
[1] "0.7 - 119.7 (21.4)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.4"
D388V2, continuous
D388V3, binary
                 cls
clus                0   1
  OR5B2 MUTATED    12   3
  OR5B2 WILD-TYPE 354 116
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR5B2 MUTATED     12    3
  OR5B2 WILD-TYPE  354  116
        clus
vv       OR5B2 MUTATED OR5B2 WILD-TYPE
  COLON             12             354
  RECTUM             3             116
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  OR5B2 MUTATED         2        0        1         4         1         0
  OR5B2 WILD-TYPE      89        1       31       134         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  OR5B2 MUTATED           1          0          3          1        1         0
  OR5B2 WILD-TYPE        23         11         56         41       47        18
                 vv
clus              STAGE IVB
  OR5B2 MUTATED           0
  OR5B2 WILD-TYPE         1
D388V4, multiclass
            clus
vv           OR5B2 MUTATED OR5B2 WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              4             134
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             3              56
  STAGE IIIC             1              41
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  OR5B2 MUTATED     0   3   9   3
  OR5B2 WILD-TYPE  17  89 320  47
D388V5, multiclass
    clus
vv   OR5B2 MUTATED OR5B2 WILD-TYPE
  T1             0              17
  T2             3              89
  T3             9             320
  T4             3              47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  OR5B2 MUTATED     9   3   3
  OR5B2 WILD-TYPE 278 110  84
D388V6, multiclass
    clus
vv   OR5B2 MUTATED OR5B2 WILD-TYPE
  N0             9             278
  N1             3             110
  N2             3              84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D388V7, binary
                 cls
clus                0   1
  OR5B2 MUTATED    10   0
  OR5B2 WILD-TYPE 365  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR5B2 MUTATED     10    0
  OR5B2 WILD-TYPE  365   65
   clus
vv  OR5B2 MUTATED OR5B2 WILD-TYPE
  0            10             365
  1             0              65
[1] 2 2
[1] FALSE
D388V8, binary
                 cls
clus                0   1
  OR5B2 MUTATED     3  12
  OR5B2 WILD-TYPE 222 252
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR5B2 MUTATED      3   12
  OR5B2 WILD-TYPE  222  252
        clus
vv       OR5B2 MUTATED OR5B2 WILD-TYPE
  FEMALE             3             222
  MALE              12             252
[1] 2 2
[1] FALSE
D388V9, binary
                 cls
clus                0   1
  OR5B2 MUTATED     9   1
  OR5B2 WILD-TYPE 341  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR5B2 MUTATED      9    1
  OR5B2 WILD-TYPE  341   21
     clus
vv    OR5B2 MUTATED OR5B2 WILD-TYPE
  NO              9             341
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  OR5B2 MUTATED                     11                             1
  OR5B2 WILD-TYPE                  304                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  OR5B2 MUTATED                       3                              0
  OR5B2 WILD-TYPE                   103                             10
D388V10, multiclass
                                clus
vv                               OR5B2 MUTATED OR5B2 WILD-TYPE
  COLON ADENOCARCINOMA                      11             304
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      3             103
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  OR5B2 MUTATED    11   0   0   0
  OR5B2 WILD-TYPE 334   4  31  25
D388V11, multiclass
    clus
vv   OR5B2 MUTATED OR5B2 WILD-TYPE
  R0            11             334
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D388V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OR5B2 MUTATED                                  0     0
  OR5B2 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  OR5B2 MUTATED                           0    11
  OR5B2 WILD-TYPE                        22   215
D388V13, multiclass
                                  clus
vv                                 OR5B2 MUTATED OR5B2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                       11             215
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(389) Variable = GABRA6 MUTATION ANALYSIS
D389V1, survival
                  sevent
clus2                0   1
  GABRA6 MUTATED    17   3
  GABRA6 WILD-TYPE 361  90
  GABRA6 MUTATED GABRA6 WILD-TYPE 
              20              451 
  GABRA6 MUTATED GABRA6 WILD-TYPE 
               3               90 
$`GABRA6 MUTATED`
TCGA-AA-3510 TCGA-AA-3663 TCGA-AA-3681 TCGA-AA-3715 TCGA-AA-3864 TCGA-AA-A010 
       63.98         6.97         5.98        19.04        53.00        34.98 
TCGA-AY-5543 TCGA-AZ-5407 TCGA-CK-6751 TCGA-CM-6164 TCGA-D5-6923 TCGA-D5-6928 
       33.01        88.21       124.27        29.03        12.43        11.64 
TCGA-D5-6930 TCGA-D5-6931 TCGA-DM-A285 TCGA-F4-6703 TCGA-G4-6304 TCGA-G4-6310 
        1.51        12.00         6.12        47.87        53.62        63.62 
TCGA-G4-6588 TCGA-F5-6464 
       26.17         9.96 

$`GABRA6 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       15.02        11.01        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       85.05        26.99        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       31.07        30.05        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       16.31         0.95        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 
        5.13       106.75        22.36        62.79        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
       82.95         1.91        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
       12.00         2.96        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6932 TCGA-D5-7000 
       14.30         9.04         9.44         4.80        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      135.65       139.17        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       44.68        55.04        85.48        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       13.78        35.80        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6465 
        0.49        20.55        19.96        20.91        18.28        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  GABRA6 MUTATED GABRA6 WILD-TYPE 
            1.51             0.00 
  GABRA6 MUTATED GABRA6 WILD-TYPE 
          124.27           148.01 
  GABRA6 MUTATED GABRA6 WILD-TYPE 
           27.60            20.12 
[1] "1.5 - 124.3 (27.6)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.8"
D389V2, continuous
D389V3, binary
                  cls
clus                 0   1
  GABRA6 MUTATED    19   2
  GABRA6 WILD-TYPE 347 117
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GABRA6 MUTATED     19    2
  GABRA6 WILD-TYPE  347  117
        clus
vv       GABRA6 MUTATED GABRA6 WILD-TYPE
  COLON              19              347
  RECTUM              2              117
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GABRA6 MUTATED         3        0        4         5         2         0
  GABRA6 WILD-TYPE      88        1       28       133         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GABRA6 MUTATED           1          0          2          2        1
  GABRA6 WILD-TYPE        23         11         57         40       47
                  vv
clus               STAGE IVA STAGE IVB
  GABRA6 MUTATED           1         0
  GABRA6 WILD-TYPE        17         1
D389V4, multiclass
            clus
vv           GABRA6 MUTATED GABRA6 WILD-TYPE
  STAGE I                 3               88
  STAGE IA                0                1
  STAGE II                4               28
  STAGE IIA               5              133
  STAGE IIB               2                8
  STAGE IIC               0                1
  STAGE III               1               23
  STAGE IIIA              0               11
  STAGE IIIB              2               57
  STAGE IIIC              2               40
  STAGE IV                1               47
  STAGE IVA               1               17
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  GABRA6 MUTATED     1   2  13   5
  GABRA6 WILD-TYPE  16  90 316  45
D389V5, multiclass
    clus
vv   GABRA6 MUTATED GABRA6 WILD-TYPE
  T1              1               16
  T2              2               90
  T3             13              316
  T4              5               45
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  GABRA6 MUTATED    14   4   3
  GABRA6 WILD-TYPE 273 109  84
D389V6, multiclass
    clus
vv   GABRA6 MUTATED GABRA6 WILD-TYPE
  N0             14              273
  N1              4              109
  N2              3               84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D389V7, binary
                  cls
clus                 0   1
  GABRA6 MUTATED    18   2
  GABRA6 WILD-TYPE 357  63
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GABRA6 MUTATED     18    2
  GABRA6 WILD-TYPE  357   63
   clus
vv  GABRA6 MUTATED GABRA6 WILD-TYPE
  0             18              357
  1              2               63
[1] 2 2
[1] FALSE
D389V8, binary
                  cls
clus                 0   1
  GABRA6 MUTATED    10  11
  GABRA6 WILD-TYPE 215 253
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GABRA6 MUTATED     10   11
  GABRA6 WILD-TYPE  215  253
        clus
vv       GABRA6 MUTATED GABRA6 WILD-TYPE
  FEMALE             10              215
  MALE               11              253
[1] 2 2
[1] FALSE
D389V9, binary
                  cls
clus                 0   1
  GABRA6 MUTATED    17   1
  GABRA6 WILD-TYPE 333  21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GABRA6 MUTATED     17    1
  GABRA6 WILD-TYPE  333   21
     clus
vv    GABRA6 MUTATED GABRA6 WILD-TYPE
  NO              17              333
  YES              1               21
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  GABRA6 MUTATED                     15                             4
  GABRA6 WILD-TYPE                  300                            43
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  GABRA6 MUTATED                       2                              0
  GABRA6 WILD-TYPE                   104                             10
D389V10, multiclass
                                clus
vv                               GABRA6 MUTATED GABRA6 WILD-TYPE
  COLON ADENOCARCINOMA                       15              300
  COLON MUCINOUS ADENOCARCINOMA               4               43
  RECTAL ADENOCARCINOMA                       2              104
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  GABRA6 MUTATED    17   0   1   1
  GABRA6 WILD-TYPE 328   4  30  24
D389V11, multiclass
    clus
vv   GABRA6 MUTATED GABRA6 WILD-TYPE
  R0             17              328
  R1              0                4
  R2              1               30
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D389V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GABRA6 MUTATED                                  0     0
  GABRA6 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  GABRA6 MUTATED                           1    13
  GABRA6 WILD-TYPE                        21   213
D389V13, multiclass
                                  clus
vv                                 GABRA6 MUTATED GABRA6 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                        13              213
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(390) Variable = LYST MUTATION ANALYSIS
D390V1, survival
                sevent
clus2              0   1
  LYST MUTATED    31   8
  LYST WILD-TYPE 347  85
  LYST MUTATED LYST WILD-TYPE 
            39            432 
  LYST MUTATED LYST WILD-TYPE 
             8             85 
$`LYST MUTATED`
TCGA-A6-2676 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5666 TCGA-A6-6141 TCGA-A6-6652 
       42.90        33.53        23.61        32.71         8.38        24.69 
TCGA-A6-6781 TCGA-AA-3514 TCGA-AA-3525 TCGA-AA-3555 TCGA-AA-3663 TCGA-AA-3715 
       19.66         1.02         8.05        29.95         6.97        19.04 
TCGA-AA-3877 TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-3977 TCGA-AA-A00A TCGA-AA-A00N 
       31.00        33.01        24.00        25.02        38.04         4.01 
TCGA-AA-A010 TCGA-AA-A02W TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AU-6004 
       34.98        41.00        15.52         0.72        10.88        27.09 
TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-CA-6717 TCGA-CK-4952 TCGA-CM-6167 
       21.44        58.39        49.41        12.76        15.62        14.99 
TCGA-CM-6171 TCGA-D5-6928 TCGA-G4-6586 TCGA-AG-3892 TCGA-AG-A002 TCGA-DY-A0XA 
       14.04        11.64        35.80        13.02        20.98       126.44 
TCGA-DY-A1DG TCGA-F5-6464 TCGA-F5-6702 
       51.48         9.96        28.57 

$`LYST WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 
       31.63        30.44        29.19        22.09        22.06        27.09 
TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6653 
       22.52        25.08        25.18        24.16        21.76        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01        63.98         6.97        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3529 
        9.07        24.03        37.05        36.03        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       17.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       61.02        78.08         6.05        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 
        2.01        12.99        24.00        26.01         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
        7.96        27.02        13.94        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6889 
       39.98        18.05        40.96         0.07        21.37        56.55 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
        0.79         5.79        22.42        27.42         0.20        14.50 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
       16.31         0.95        33.01        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 
      106.75        22.36        62.79        88.21         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 
       10.06        14.30        17.56       148.01        85.45        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       29.03        16.04        21.99        12.99        13.02        15.02 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
        9.44         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 
       63.62        61.91        36.00        22.09        13.78        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 
       19.99         1.02        17.95        36.95        17.03        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1H8 
        5.03         5.29        41.36        57.24        24.13        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6465 
        0.49        20.55        19.96        20.91        18.28        49.51 
TCGA-F5-6571 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       31.30        32.19         0.66         0.69        55.76        26.43 

  LYST MUTATED LYST WILD-TYPE 
          0.72           0.00 
  LYST MUTATED LYST WILD-TYPE 
        126.44         148.01 
  LYST MUTATED LYST WILD-TYPE 
        23.610         20.035 
[1] "0.7 - 126.4 (23.6)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.1"
D390V2, continuous
D390V3, binary
                cls
clus               0   1
  LYST MUTATED    34   6
  LYST WILD-TYPE 332 113
[1] "tbl2"
                cls
clus             [,1] [,2]
  LYST MUTATED     34    6
  LYST WILD-TYPE  332  113
        clus
vv       LYST MUTATED LYST WILD-TYPE
  COLON            34            332
  RECTUM            6            113
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  LYST MUTATED         7        0        3        12         4         1
  LYST WILD-TYPE      84        1       29       126         6         0
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  LYST MUTATED           0          0          2          4        0         4
  LYST WILD-TYPE        24         11         57         38       48        14
                vv
clus             STAGE IVB
  LYST MUTATED           0
  LYST WILD-TYPE         1
D390V4, multiclass
            clus
vv           LYST MUTATED LYST WILD-TYPE
  STAGE I               7             84
  STAGE IA              0              1
  STAGE II              3             29
  STAGE IIA            12            126
  STAGE IIB             4              6
  STAGE IIC             1              0
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            2             57
  STAGE IIIC            4             38
  STAGE IV              0             48
  STAGE IVA             4             14
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  LYST MUTATED     2   6  23   9
  LYST WILD-TYPE  15  86 306  41
D390V5, multiclass
    clus
vv   LYST MUTATED LYST WILD-TYPE
  T1            2             15
  T2            6             86
  T3           23            306
  T4            9             41
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  LYST MUTATED    29   6   5
  LYST WILD-TYPE 258 107  82
D390V6, multiclass
    clus
vv   LYST MUTATED LYST WILD-TYPE
  N0           29            258
  N1            6            107
  N2            5             82
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D390V7, binary
                cls
clus               0   1
  LYST MUTATED    30   4
  LYST WILD-TYPE 345  61
[1] "tbl2"
                cls
clus             [,1] [,2]
  LYST MUTATED     30    4
  LYST WILD-TYPE  345   61
   clus
vv  LYST MUTATED LYST WILD-TYPE
  0           30            345
  1            4             61
[1] 2 2
[1] FALSE
D390V8, binary
                cls
clus               0   1
  LYST MUTATED    19  21
  LYST WILD-TYPE 206 243
[1] "tbl2"
                cls
clus             [,1] [,2]
  LYST MUTATED     19   21
  LYST WILD-TYPE  206  243
        clus
vv       LYST MUTATED LYST WILD-TYPE
  FEMALE           19            206
  MALE             21            243
[1] 2 2
[1] FALSE
D390V9, binary
                cls
clus               0   1
  LYST MUTATED    33   0
  LYST WILD-TYPE 317  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  LYST MUTATED     33    0
  LYST WILD-TYPE  317   22
     clus
vv    LYST MUTATED LYST WILD-TYPE
  NO            33            317
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  LYST MUTATED                     25                             9
  LYST WILD-TYPE                  290                            38
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  LYST MUTATED                       6                              0
  LYST WILD-TYPE                   100                             10
D390V10, multiclass
                                clus
vv                               LYST MUTATED LYST WILD-TYPE
  COLON ADENOCARCINOMA                     25            290
  COLON MUCINOUS ADENOCARCINOMA             9             38
  RECTAL ADENOCARCINOMA                     6            100
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  LYST MUTATED    28   0   0   2
  LYST WILD-TYPE 317   4  31  23
D390V11, multiclass
    clus
vv   LYST MUTATED LYST WILD-TYPE
  R0           28            317
  R1            0              4
  R2            0             31
  RX            2             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D390V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  LYST MUTATED                                  0     1
  LYST WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  LYST MUTATED                           4    19
  LYST WILD-TYPE                        18   207
D390V13, multiclass
                                  clus
vv                                 LYST MUTATED LYST WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   4             18
  WHITE                                      19            207
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(391) Variable = PPP2R1A MUTATION ANALYSIS
D391V1, survival
                   sevent
clus2                 0   1
  PPP2R1A MUTATED    12   2
  PPP2R1A WILD-TYPE 366  91
  PPP2R1A MUTATED PPP2R1A WILD-TYPE 
               14               457 
  PPP2R1A MUTATED PPP2R1A WILD-TYPE 
                2                91 
$`PPP2R1A MUTATED`
TCGA-A6-6653 TCGA-AA-3514 TCGA-AA-3663 TCGA-AA-3846 TCGA-AA-A01R TCGA-AA-A02O 
       24.39         1.02         6.97        17.03        35.01         0.92 
TCGA-AD-5900 TCGA-AZ-5407 TCGA-AZ-6601 TCGA-CK-4952 TCGA-D5-6540 TCGA-D5-6928 
        0.07        88.21       100.01        15.62        16.14        11.64 
TCGA-G4-6588 TCGA-G4-6626 
       26.17        46.75 

$`PPP2R1A WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
       25.08        25.18        24.16        21.76        24.69        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01        63.98         6.97        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3848 TCGA-AA-3850 
       38.99        37.02        14.93         0.00        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
       38.07         1.02         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 
       14.01        41.00        39.98        18.05        40.96        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 
        5.13       106.75        22.36        62.79        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
       12.10        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       12.49        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
       14.30         9.04         9.44         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       13.78        35.80        91.79        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  PPP2R1A MUTATED PPP2R1A WILD-TYPE 
             0.07              0.00 
  PPP2R1A MUTATED PPP2R1A WILD-TYPE 
           100.01            148.01 
  PPP2R1A MUTATED PPP2R1A WILD-TYPE 
           16.585            20.280 
[1] "0.1 - 100.0 (16.6)" "0.0 - 148.0 (20.3)"
[1] "hr=" "1.5"
D391V2, continuous
D391V3, binary
                   cls
clus                  0   1
  PPP2R1A MUTATED    14   0
  PPP2R1A WILD-TYPE 352 119
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PPP2R1A MUTATED     14    0
  PPP2R1A WILD-TYPE  352  119
        clus
vv       PPP2R1A MUTATED PPP2R1A WILD-TYPE
  COLON               14               352
  RECTUM               0               119
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PPP2R1A MUTATED         5        0        3         4         0         0
  PPP2R1A WILD-TYPE      86        1       29       134        10         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PPP2R1A MUTATED           1          0          0          1        0
  PPP2R1A WILD-TYPE        23         11         59         41       48
                   vv
clus                STAGE IVA STAGE IVB
  PPP2R1A MUTATED           0         0
  PPP2R1A WILD-TYPE        18         1
D391V4, multiclass
            clus
vv           PPP2R1A MUTATED PPP2R1A WILD-TYPE
  STAGE I                  5                86
  STAGE IA                 0                 1
  STAGE II                 3                29
  STAGE IIA                4               134
  STAGE IIB                0                10
  STAGE IIC                0                 1
  STAGE III                1                23
  STAGE IIIA               0                11
  STAGE IIIB               0                59
  STAGE IIIC               1                41
  STAGE IV                 0                48
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  PPP2R1A MUTATED     1   4   8   1
  PPP2R1A WILD-TYPE  16  88 321  49
D391V5, multiclass
    clus
vv   PPP2R1A MUTATED PPP2R1A WILD-TYPE
  T1               1                16
  T2               4                88
  T3               8               321
  T4               1                49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  PPP2R1A MUTATED    12   0   2
  PPP2R1A WILD-TYPE 275 113  85
D391V6, multiclass
    clus
vv   PPP2R1A MUTATED PPP2R1A WILD-TYPE
  N0              12               275
  N1               0               113
  N2               2                85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D391V7, binary
                   cls
clus                  0   1
  PPP2R1A MUTATED    13   0
  PPP2R1A WILD-TYPE 362  65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PPP2R1A MUTATED     13    0
  PPP2R1A WILD-TYPE  362   65
   clus
vv  PPP2R1A MUTATED PPP2R1A WILD-TYPE
  0              13               362
  1               0                65
[1] 2 2
[1] FALSE
D391V8, binary
                   cls
clus                  0   1
  PPP2R1A MUTATED     5   9
  PPP2R1A WILD-TYPE 220 255
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PPP2R1A MUTATED      5    9
  PPP2R1A WILD-TYPE  220  255
        clus
vv       PPP2R1A MUTATED PPP2R1A WILD-TYPE
  FEMALE               5               220
  MALE                 9               255
[1] 2 2
[1] FALSE
D391V9, binary
                   cls
clus                  0   1
  PPP2R1A MUTATED    10   1
  PPP2R1A WILD-TYPE 340  21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PPP2R1A MUTATED     10    1
  PPP2R1A WILD-TYPE  340   21
     clus
vv    PPP2R1A MUTATED PPP2R1A WILD-TYPE
  NO               10               340
  YES               1                21
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PPP2R1A MUTATED                      9                             5
  PPP2R1A WILD-TYPE                  306                            42
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PPP2R1A MUTATED                       0                              0
  PPP2R1A WILD-TYPE                   106                             10
D391V10, multiclass
                                clus
vv                               PPP2R1A MUTATED PPP2R1A WILD-TYPE
  COLON ADENOCARCINOMA                         9               306
  COLON MUCINOUS ADENOCARCINOMA                5                42
  RECTAL ADENOCARCINOMA                        0               106
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  PPP2R1A MUTATED    10   0   0   1
  PPP2R1A WILD-TYPE 335   4  31  24
D391V11, multiclass
    clus
vv   PPP2R1A MUTATED PPP2R1A WILD-TYPE
  R0              10               335
  R1               0                 4
  R2               0                31
  RX               1                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D391V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PPP2R1A MUTATED                                  0     0
  PPP2R1A WILD-TYPE                                1    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  PPP2R1A MUTATED                           0     9
  PPP2R1A WILD-TYPE                        22   217
D391V13, multiclass
                                  clus
vv                                 PPP2R1A MUTATED PPP2R1A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                      0                22
  WHITE                                          9               217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(392) Variable = NUP54 MUTATION ANALYSIS
D392V1, survival
                 sevent
clus2               0   1
  NUP54 MUTATED     8   2
  NUP54 WILD-TYPE 370  91
  NUP54 MUTATED NUP54 WILD-TYPE 
             10             461 
  NUP54 MUTATED NUP54 WILD-TYPE 
              2              91 
$`NUP54 MUTATED`
TCGA-A6-6141 TCGA-AA-3510 TCGA-AA-A010 TCGA-AZ-6600 TCGA-CM-5864 TCGA-CM-6678 
        8.38        63.98        34.98        12.10        15.02        11.01 
TCGA-DM-A1D4 TCGA-G4-6321 TCGA-AG-A002 TCGA-EI-6507 
       92.75        22.09        20.98        19.96 

$`NUP54 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 
       22.09        22.06        32.71        27.09        22.52        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 
       22.36        62.79        88.21        49.41         6.77       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
        5.03        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.08        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6586 
       85.48        63.62        61.91        36.00        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  NUP54 MUTATED NUP54 WILD-TYPE 
           8.38            0.00 
  NUP54 MUTATED NUP54 WILD-TYPE 
          92.75          148.01 
  NUP54 MUTATED NUP54 WILD-TYPE 
          20.47           20.19 
[1] "8.4 - 92.8 (20.5)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.2"
D392V2, continuous
D392V3, binary
                 cls
clus                0   1
  NUP54 MUTATED     8   2
  NUP54 WILD-TYPE 358 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NUP54 MUTATED      8    2
  NUP54 WILD-TYPE  358  117
        clus
vv       NUP54 MUTATED NUP54 WILD-TYPE
  COLON              8             358
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NUP54 MUTATED         2        0        1         3         1         0
  NUP54 WILD-TYPE      89        1       31       135         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NUP54 MUTATED           1          0          0          0        1         1
  NUP54 WILD-TYPE        23         11         59         42       47        17
                 vv
clus              STAGE IVB
  NUP54 MUTATED           0
  NUP54 WILD-TYPE         1
D392V4, multiclass
            clus
vv           NUP54 MUTATED NUP54 WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              3             135
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             0              42
  STAGE IV               1              47
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  NUP54 MUTATED     0   3   4   3
  NUP54 WILD-TYPE  17  89 325  47
D392V5, multiclass
    clus
vv   NUP54 MUTATED NUP54 WILD-TYPE
  T1             0              17
  T2             3              89
  T3             4             325
  T4             3              47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  NUP54 MUTATED     7   3   0
  NUP54 WILD-TYPE 280 110  87
D392V6, multiclass
    clus
vv   NUP54 MUTATED NUP54 WILD-TYPE
  N0             7             280
  N1             3             110
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D392V7, binary
                 cls
clus                0   1
  NUP54 MUTATED     7   2
  NUP54 WILD-TYPE 368  63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NUP54 MUTATED      7    2
  NUP54 WILD-TYPE  368   63
   clus
vv  NUP54 MUTATED NUP54 WILD-TYPE
  0             7             368
  1             2              63
[1] 2 2
[1] FALSE
D392V8, binary
                 cls
clus                0   1
  NUP54 MUTATED     3   7
  NUP54 WILD-TYPE 222 257
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NUP54 MUTATED      3    7
  NUP54 WILD-TYPE  222  257
        clus
vv       NUP54 MUTATED NUP54 WILD-TYPE
  FEMALE             3             222
  MALE               7             257
[1] 2 2
[1] FALSE
D392V9, binary
                 cls
clus                0   1
  NUP54 MUTATED     8   0
  NUP54 WILD-TYPE 342  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NUP54 MUTATED      8    0
  NUP54 WILD-TYPE  342   22
     clus
vv    NUP54 MUTATED NUP54 WILD-TYPE
  NO              8             342
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  NUP54 MUTATED                      8                             0
  NUP54 WILD-TYPE                  307                            47
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  NUP54 MUTATED                       2                              0
  NUP54 WILD-TYPE                   104                             10
D392V10, multiclass
                                clus
vv                               NUP54 MUTATED NUP54 WILD-TYPE
  COLON ADENOCARCINOMA                       8             307
  COLON MUCINOUS ADENOCARCINOMA              0              47
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  NUP54 MUTATED     7   0   0   0
  NUP54 WILD-TYPE 338   4  31  25
D392V11, multiclass
    clus
vv   NUP54 MUTATED NUP54 WILD-TYPE
  R0             7             338
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D392V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NUP54 MUTATED                                  0     0
  NUP54 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  NUP54 MUTATED                           2     5
  NUP54 WILD-TYPE                        20   221
D392V13, multiclass
                                  clus
vv                                 NUP54 MUTATED NUP54 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    2              20
  WHITE                                        5             221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(393) Variable = OR11G2 MUTATION ANALYSIS
D393V1, survival
                  sevent
clus2                0   1
  OR11G2 MUTATED     4   2
  OR11G2 WILD-TYPE 374  91
  OR11G2 MUTATED OR11G2 WILD-TYPE 
               6              465 
  OR11G2 MUTATED OR11G2 WILD-TYPE 
               2               91 
$`OR11G2 MUTATED`
TCGA-AA-3489 TCGA-AA-A00N TCGA-D5-5541 TCGA-DM-A28E TCGA-G4-6307 TCGA-AG-A002 
        7.04         4.01        55.92       119.93        55.04        20.98 

$`OR11G2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-6529 
       12.03        45.40        12.26        19.59        56.09        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
      139.17         6.12        81.37        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       53.62        44.68        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  OR11G2 MUTATED OR11G2 WILD-TYPE 
            4.01             0.00 
  OR11G2 MUTATED OR11G2 WILD-TYPE 
          119.93           148.01 
  OR11G2 MUTATED OR11G2 WILD-TYPE 
           38.01            20.12 
[1] "4.0 - 119.9 (38.0)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1"  
D393V2, continuous
D393V3, binary
                  cls
clus                 0   1
  OR11G2 MUTATED     5   1
  OR11G2 WILD-TYPE 361 118
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR11G2 MUTATED      5    1
  OR11G2 WILD-TYPE  361  118
        clus
vv       OR11G2 MUTATED OR11G2 WILD-TYPE
  COLON               5              361
  RECTUM              1              118
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  OR11G2 MUTATED         1        0        1         1         1         0
  OR11G2 WILD-TYPE      90        1       31       137         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  OR11G2 MUTATED           0          0          2          0        0
  OR11G2 WILD-TYPE        24         11         57         42       48
                  vv
clus               STAGE IVA STAGE IVB
  OR11G2 MUTATED           0         0
  OR11G2 WILD-TYPE        18         1
D393V4, multiclass
            clus
vv           OR11G2 MUTATED OR11G2 WILD-TYPE
  STAGE I                 1               90
  STAGE IA                0                1
  STAGE II                1               31
  STAGE IIA               1              137
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              2               57
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  OR11G2 MUTATED     0   1   4   1
  OR11G2 WILD-TYPE  17  91 325  49
D393V5, multiclass
    clus
vv   OR11G2 MUTATED OR11G2 WILD-TYPE
  T1              0               17
  T2              1               91
  T3              4              325
  T4              1               49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  OR11G2 MUTATED     4   2   0
  OR11G2 WILD-TYPE 283 111  87
D393V6, multiclass
    clus
vv   OR11G2 MUTATED OR11G2 WILD-TYPE
  N0              4              283
  N1              2              111
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D393V7, binary
                  cls
clus                 0   1
  OR11G2 MUTATED     6   0
  OR11G2 WILD-TYPE 369  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR11G2 MUTATED      6    0
  OR11G2 WILD-TYPE  369   65
   clus
vv  OR11G2 MUTATED OR11G2 WILD-TYPE
  0              6              369
  1              0               65
[1] 2 2
[1] FALSE
D393V8, binary
                  cls
clus                 0   1
  OR11G2 MUTATED     2   4
  OR11G2 WILD-TYPE 223 260
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR11G2 MUTATED      2    4
  OR11G2 WILD-TYPE  223  260
        clus
vv       OR11G2 MUTATED OR11G2 WILD-TYPE
  FEMALE              2              223
  MALE                4              260
[1] 2 2
[1] FALSE
D393V9, binary
                  cls
clus                 0   1
  OR11G2 MUTATED     4   0
  OR11G2 WILD-TYPE 346  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR11G2 MUTATED      4    0
  OR11G2 WILD-TYPE  346   22
     clus
vv    OR11G2 MUTATED OR11G2 WILD-TYPE
  NO               4              346
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  OR11G2 MUTATED                      4                             1
  OR11G2 WILD-TYPE                  311                            46
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  OR11G2 MUTATED                       1                              0
  OR11G2 WILD-TYPE                   105                             10
D393V10, multiclass
                                clus
vv                               OR11G2 MUTATED OR11G2 WILD-TYPE
  COLON ADENOCARCINOMA                        4              311
  COLON MUCINOUS ADENOCARCINOMA               1               46
  RECTAL ADENOCARCINOMA                       1              105
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  OR11G2 MUTATED     5   0   0   0
  OR11G2 WILD-TYPE 340   4  31  25
D393V11, multiclass
    clus
vv   OR11G2 MUTATED OR11G2 WILD-TYPE
  R0              5              340
  R1              0                4
  R2              0               31
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D393V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OR11G2 MUTATED                                  0     0
  OR11G2 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  OR11G2 MUTATED                           0     3
  OR11G2 WILD-TYPE                        22   223
D393V13, multiclass
                                  clus
vv                                 OR11G2 MUTATED OR11G2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         3              223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(394) Variable = FUBP3 MUTATION ANALYSIS
D394V1, survival
                 sevent
clus2               0   1
  FUBP3 MUTATED     8   1
  FUBP3 WILD-TYPE 370  92
  FUBP3 MUTATED FUBP3 WILD-TYPE 
              9             462 
  FUBP3 MUTATED FUBP3 WILD-TYPE 
              1              92 
$`FUBP3 MUTATED`
TCGA-AA-3663 TCGA-AA-3950 TCGA-AA-A010 TCGA-AD-5900 TCGA-AD-6895 TCGA-AZ-4315 
        6.97        24.00        34.98         0.07         0.72        58.39 
TCGA-CM-6162 TCGA-F4-6570 TCGA-F4-6856 
       12.00         6.18        35.31 

$`FUBP3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.05        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 
        2.01        12.99        24.00        33.01        26.01         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       18.05        40.96        21.37        15.52        56.55         0.79 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       15.02        17.03        15.02         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       35.74        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 
       33.67        13.25         0.53        47.41       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  FUBP3 MUTATED FUBP3 WILD-TYPE 
           0.07            0.00 
  FUBP3 MUTATED FUBP3 WILD-TYPE 
          58.39          148.01 
  FUBP3 MUTATED FUBP3 WILD-TYPE 
         12.000          20.235 
[1] "0.1 - 58.4 (12.0)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.3"
D394V2, continuous
D394V3, binary
                 cls
clus                0   1
  FUBP3 MUTATED     9   0
  FUBP3 WILD-TYPE 357 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FUBP3 MUTATED      9    0
  FUBP3 WILD-TYPE  357  119
        clus
vv       FUBP3 MUTATED FUBP3 WILD-TYPE
  COLON              9             357
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FUBP3 MUTATED         2        0        1         3         1         0
  FUBP3 WILD-TYPE      89        1       31       135         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  FUBP3 MUTATED           0          0          1          0        0         0
  FUBP3 WILD-TYPE        24         11         58         42       48        18
                 vv
clus              STAGE IVB
  FUBP3 MUTATED           0
  FUBP3 WILD-TYPE         1
D394V4, multiclass
            clus
vv           FUBP3 MUTATED FUBP3 WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              3             135
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  FUBP3 MUTATED     0   2   6   1
  FUBP3 WILD-TYPE  17  90 323  49
D394V5, multiclass
    clus
vv   FUBP3 MUTATED FUBP3 WILD-TYPE
  T1             0              17
  T2             2              90
  T3             6             323
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  FUBP3 MUTATED     7   2   0
  FUBP3 WILD-TYPE 280 111  87
D394V6, multiclass
    clus
vv   FUBP3 MUTATED FUBP3 WILD-TYPE
  N0             7             280
  N1             2             111
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D394V7, binary
                 cls
clus                0   1
  FUBP3 MUTATED     7   0
  FUBP3 WILD-TYPE 368  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FUBP3 MUTATED      7    0
  FUBP3 WILD-TYPE  368   65
   clus
vv  FUBP3 MUTATED FUBP3 WILD-TYPE
  0             7             368
  1             0              65
[1] 2 2
[1] FALSE
D394V8, binary
                 cls
clus                0   1
  FUBP3 MUTATED     4   5
  FUBP3 WILD-TYPE 221 259
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FUBP3 MUTATED      4    5
  FUBP3 WILD-TYPE  221  259
        clus
vv       FUBP3 MUTATED FUBP3 WILD-TYPE
  FEMALE             4             221
  MALE               5             259
[1] 2 2
[1] FALSE
D394V9, binary
                 cls
clus                0   1
  FUBP3 MUTATED     7   0
  FUBP3 WILD-TYPE 343  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FUBP3 MUTATED      7    0
  FUBP3 WILD-TYPE  343   22
     clus
vv    FUBP3 MUTATED FUBP3 WILD-TYPE
  NO              7             343
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  FUBP3 MUTATED                      5                             4
  FUBP3 WILD-TYPE                  310                            43
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  FUBP3 MUTATED                       0                              0
  FUBP3 WILD-TYPE                   106                             10
D394V10, multiclass
                                clus
vv                               FUBP3 MUTATED FUBP3 WILD-TYPE
  COLON ADENOCARCINOMA                       5             310
  COLON MUCINOUS ADENOCARCINOMA              4              43
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  FUBP3 MUTATED     8   0   0   0
  FUBP3 WILD-TYPE 337   4  31  25
D394V11, multiclass
    clus
vv   FUBP3 MUTATED FUBP3 WILD-TYPE
  R0             8             337
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D394V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FUBP3 MUTATED                                  0     0
  FUBP3 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  FUBP3 MUTATED                           0     6
  FUBP3 WILD-TYPE                        22   220
D394V13, multiclass
                                  clus
vv                                 FUBP3 MUTATED FUBP3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        6             220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(395) Variable = TOB1 MUTATION ANALYSIS
D395V1, survival
                sevent
clus2              0   1
  TOB1 MUTATED     8   0
  TOB1 WILD-TYPE 370  93
  TOB1 MUTATED TOB1 WILD-TYPE 
             8            463 
  TOB1 MUTATED TOB1 WILD-TYPE 
             0             93 
$`TOB1 MUTATED`
TCGA-A6-6780 TCGA-CK-4952 TCGA-CK-6751 TCGA-CM-5863 TCGA-G4-6310 TCGA-G4-6586 
       20.12        15.62       124.27        15.02        63.62        35.80 
TCGA-AG-3892 TCGA-AG-A002 
       13.02        20.98 

$`TOB1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
      148.01        85.45        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
       82.95         1.91        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
       15.02         5.03        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6317 
       53.62        44.68        55.04        85.48        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       22.09        13.78        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       36.95        17.03        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  TOB1 MUTATED TOB1 WILD-TYPE 
         13.02           0.00 
  TOB1 MUTATED TOB1 WILD-TYPE 
        124.27         148.01 
  TOB1 MUTATED TOB1 WILD-TYPE 
         20.55          20.19 
[1] "13.0 - 124.3 (20.6)" "0.0 - 148.0 (20.2)" 
[1] "hr="     "9300000"
D395V2, continuous
D395V3, binary
                cls
clus               0   1
  TOB1 MUTATED     6   2
  TOB1 WILD-TYPE 360 117
[1] "tbl2"
                cls
clus             [,1] [,2]
  TOB1 MUTATED      6    2
  TOB1 WILD-TYPE  360  117
        clus
vv       TOB1 MUTATED TOB1 WILD-TYPE
  COLON             6            360
  RECTUM            2            117
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TOB1 MUTATED         3        0        0         2         0         0
  TOB1 WILD-TYPE      88        1       32       136        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TOB1 MUTATED           0          0          2          1        0         0
  TOB1 WILD-TYPE        24         11         57         41       48        18
                vv
clus             STAGE IVB
  TOB1 MUTATED           0
  TOB1 WILD-TYPE         1
D395V4, multiclass
            clus
vv           TOB1 MUTATED TOB1 WILD-TYPE
  STAGE I               3             88
  STAGE IA              0              1
  STAGE II              0             32
  STAGE IIA             2            136
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            2             57
  STAGE IIIC            1             41
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  TOB1 MUTATED     1   2   4   1
  TOB1 WILD-TYPE  16  90 325  49
D395V5, multiclass
    clus
vv   TOB1 MUTATED TOB1 WILD-TYPE
  T1            1             16
  T2            2             90
  T3            4            325
  T4            1             49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  TOB1 MUTATED     5   2   1
  TOB1 WILD-TYPE 282 111  86
D395V6, multiclass
    clus
vv   TOB1 MUTATED TOB1 WILD-TYPE
  N0            5            282
  N1            2            111
  N2            1             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D395V7, binary
                cls
clus               0   1
  TOB1 MUTATED     6   0
  TOB1 WILD-TYPE 369  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  TOB1 MUTATED      6    0
  TOB1 WILD-TYPE  369   65
   clus
vv  TOB1 MUTATED TOB1 WILD-TYPE
  0            6            369
  1            0             65
[1] 2 2
[1] FALSE
D395V8, binary
                cls
clus               0   1
  TOB1 MUTATED     5   3
  TOB1 WILD-TYPE 220 261
[1] "tbl2"
                cls
clus             [,1] [,2]
  TOB1 MUTATED      5    3
  TOB1 WILD-TYPE  220  261
        clus
vv       TOB1 MUTATED TOB1 WILD-TYPE
  FEMALE            5            220
  MALE              3            261
[1] 2 2
[1] FALSE
D395V9, binary
                cls
clus               0   1
  TOB1 MUTATED     6   1
  TOB1 WILD-TYPE 344  21
[1] "tbl2"
                cls
clus             [,1] [,2]
  TOB1 MUTATED      6    1
  TOB1 WILD-TYPE  344   21
     clus
vv    TOB1 MUTATED TOB1 WILD-TYPE
  NO             6            344
  YES            1             21
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  TOB1 MUTATED                      2                             4
  TOB1 WILD-TYPE                  313                            43
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  TOB1 MUTATED                       2                              0
  TOB1 WILD-TYPE                   104                             10
D395V10, multiclass
                                clus
vv                               TOB1 MUTATED TOB1 WILD-TYPE
  COLON ADENOCARCINOMA                      2            313
  COLON MUCINOUS ADENOCARCINOMA             4             43
  RECTAL ADENOCARCINOMA                     2            104
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  TOB1 MUTATED     5   0   0   2
  TOB1 WILD-TYPE 340   4  31  23
D395V11, multiclass
    clus
vv   TOB1 MUTATED TOB1 WILD-TYPE
  R0            5            340
  R1            0              4
  R2            0             31
  RX            2             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D395V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TOB1 MUTATED                                  0     0
  TOB1 WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  TOB1 MUTATED                           0     6
  TOB1 WILD-TYPE                        22   220
D395V13, multiclass
                                  clus
vv                                 TOB1 MUTATED TOB1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       6            220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(396) Variable = DAXX MUTATION ANALYSIS
D396V1, survival
                sevent
clus2              0   1
  DAXX MUTATED    13   2
  DAXX WILD-TYPE 365  91
  DAXX MUTATED DAXX WILD-TYPE 
            15            456 
  DAXX MUTATED DAXX WILD-TYPE 
             2             91 
$`DAXX MUTATED`
TCGA-A6-5657 TCGA-A6-5661 TCGA-AU-6004 TCGA-CK-5916 TCGA-CM-5862 TCGA-CM-5868 
       31.63        33.53        27.09        21.14         5.03        17.03 
TCGA-CM-6166 TCGA-D5-6536 TCGA-G4-6309 TCGA-G4-6317 TCGA-G4-6586 TCGA-AG-A015 
       21.99        17.85        85.48        36.00        35.80        36.03 
TCGA-CI-6624 TCGA-CL-5918 TCGA-F5-6702 
        4.73         7.17        28.57 

$`DAXX WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       32.91        30.44        29.19        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       10.88         0.20        14.50        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 
       15.62        49.08        51.32         9.99        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        15.02        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       16.04        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 
       74.56        65.85        53.62        44.68        55.04        63.62 
TCGA-G4-6315 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       61.91        22.09        13.78        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A016 TCGA-AG-A01L 
       25.97        23.01        37.02        15.95         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CL-5917 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
       78.12        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       31.30        32.19         0.66         0.69        55.76        26.43 

  DAXX MUTATED DAXX WILD-TYPE 
          4.73           0.00 
  DAXX MUTATED DAXX WILD-TYPE 
         85.48         148.01 
  DAXX MUTATED DAXX WILD-TYPE 
        27.090         20.035 
[1] "4.7 - 85.5 (27.1)"  "0.0 - 148.0 (20.0)"
[1] "hr=" "1.4"
D396V2, continuous
D396V3, binary
                cls
clus               0   1
  DAXX MUTATED    12   4
  DAXX WILD-TYPE 354 115
[1] "tbl2"
                cls
clus             [,1] [,2]
  DAXX MUTATED     12    4
  DAXX WILD-TYPE  354  115
        clus
vv       DAXX MUTATED DAXX WILD-TYPE
  COLON            12            354
  RECTUM            4            115
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DAXX MUTATED         5        0        0         4         0         0
  DAXX WILD-TYPE      86        1       32       134        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DAXX MUTATED           1          0          2          1        0         3
  DAXX WILD-TYPE        23         11         57         41       48        15
                vv
clus             STAGE IVB
  DAXX MUTATED           0
  DAXX WILD-TYPE         1
D396V4, multiclass
            clus
vv           DAXX MUTATED DAXX WILD-TYPE
  STAGE I               5             86
  STAGE IA              0              1
  STAGE II              0             32
  STAGE IIA             4            134
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             1             23
  STAGE IIIA            0             11
  STAGE IIIB            2             57
  STAGE IIIC            1             41
  STAGE IV              0             48
  STAGE IVA             3             15
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  DAXX MUTATED     2   3  10   1
  DAXX WILD-TYPE  15  89 319  49
D396V5, multiclass
    clus
vv   DAXX MUTATED DAXX WILD-TYPE
  T1            2             15
  T2            3             89
  T3           10            319
  T4            1             49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  DAXX MUTATED     9   5   2
  DAXX WILD-TYPE 278 108  85
D396V6, multiclass
    clus
vv   DAXX MUTATED DAXX WILD-TYPE
  N0            9            278
  N1            5            108
  N2            2             85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D396V7, binary
                cls
clus               0   1
  DAXX MUTATED    11   3
  DAXX WILD-TYPE 364  62
[1] "tbl2"
                cls
clus             [,1] [,2]
  DAXX MUTATED     11    3
  DAXX WILD-TYPE  364   62
   clus
vv  DAXX MUTATED DAXX WILD-TYPE
  0           11            364
  1            3             62
[1] 2 2
[1] FALSE
D396V8, binary
                cls
clus               0   1
  DAXX MUTATED    11   5
  DAXX WILD-TYPE 214 259
[1] "tbl2"
                cls
clus             [,1] [,2]
  DAXX MUTATED     11    5
  DAXX WILD-TYPE  214  259
        clus
vv       DAXX MUTATED DAXX WILD-TYPE
  FEMALE           11            214
  MALE              5            259
[1] 2 2
[1] FALSE
D396V9, binary
                cls
clus               0   1
  DAXX MUTATED    13   0
  DAXX WILD-TYPE 337  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  DAXX MUTATED     13    0
  DAXX WILD-TYPE  337   22
     clus
vv    DAXX MUTATED DAXX WILD-TYPE
  NO            13            337
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  DAXX MUTATED                     12                             0
  DAXX WILD-TYPE                  303                            47
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  DAXX MUTATED                       4                              0
  DAXX WILD-TYPE                   102                             10
D396V10, multiclass
                                clus
vv                               DAXX MUTATED DAXX WILD-TYPE
  COLON ADENOCARCINOMA                     12            303
  COLON MUCINOUS ADENOCARCINOMA             0             47
  RECTAL ADENOCARCINOMA                     4            102
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  DAXX MUTATED    13   0   0   2
  DAXX WILD-TYPE 332   4  31  23
D396V11, multiclass
    clus
vv   DAXX MUTATED DAXX WILD-TYPE
  R0           13            332
  R1            0              4
  R2            0             31
  RX            2             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D396V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DAXX MUTATED                                  0     0
  DAXX WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  DAXX MUTATED                           3    11
  DAXX WILD-TYPE                        19   215
D396V13, multiclass
                                  clus
vv                                 DAXX MUTATED DAXX WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   3             19
  WHITE                                      11            215
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(397) Variable = MARK1 MUTATION ANALYSIS
D397V1, survival
                 sevent
clus2               0   1
  MARK1 MUTATED    23   5
  MARK1 WILD-TYPE 355  88
  MARK1 MUTATED MARK1 WILD-TYPE 
             28             443 
  MARK1 MUTATED MARK1 WILD-TYPE 
              5              88 
$`MARK1 MUTATED`
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5665 TCGA-AA-3510 TCGA-AA-3555 TCGA-AA-3710 
       31.63        30.44        22.06        63.98        29.95        26.99 
TCGA-AA-3821 TCGA-AA-3977 TCGA-AA-A024 TCGA-AU-3779 TCGA-AZ-4315 TCGA-AZ-4681 
        1.02        25.02        39.06        14.50        58.39       106.75 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-CA-6717 TCGA-CK-4947 TCGA-CM-4747 TCGA-CM-6166 
        6.77        12.10        12.76        17.56        25.02        21.99 
TCGA-D5-5537 TCGA-D5-6539 TCGA-D5-6923 TCGA-DM-A28H TCGA-G4-6299 TCGA-G4-6309 
       45.40        12.49        12.43       117.07        74.56        85.48 
TCGA-AG-3726 TCGA-AG-A002 TCGA-AG-A02N TCGA-DY-A1DG 
        7.99        20.98        61.97        51.48 

$`MARK1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 
       32.91        29.19        33.53        23.61        22.09        32.71 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       27.09        22.52         8.38        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 
       20.28         7.04         3.02         1.02        35.01         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       78.08         6.05         6.97        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 
       37.05        19.00        36.00         5.03        85.05        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02F 
       33.04        35.01        26.01        37.02        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
        0.20        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
       17.82         1.41         5.13        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       49.41       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       12.20        10.06        14.30       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4752 TCGA-CM-5341 
      124.27        23.05        20.02        37.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       29.03        16.04        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       11.01        10.06        12.03        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
       17.85         4.80        17.13        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        3.68         4.41        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6303 TCGA-G4-6304 
        0.53        47.41        35.31       133.18        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       44.68        55.04        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       13.94        19.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 
       10.98        49.97         1.94        38.96        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       57.24        24.13        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  MARK1 MUTATED MARK1 WILD-TYPE 
           1.02            0.00 
  MARK1 MUTATED MARK1 WILD-TYPE 
         117.07          148.01 
  MARK1 MUTATED MARK1 WILD-TYPE 
         26.005          19.990 
[1] "1.0 - 117.1 (26.0)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.6"
D397V2, continuous
D397V3, binary
                 cls
clus                0   1
  MARK1 MUTATED    25   4
  MARK1 WILD-TYPE 341 115
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MARK1 MUTATED     25    4
  MARK1 WILD-TYPE  341  115
        clus
vv       MARK1 MUTATED MARK1 WILD-TYPE
  COLON             25             341
  RECTUM             4             115
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MARK1 MUTATED         7        0        3         9         0         0
  MARK1 WILD-TYPE      84        1       29       129        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MARK1 MUTATED           0          1          3          2        1         2
  MARK1 WILD-TYPE        24         10         56         40       47        16
                 vv
clus              STAGE IVB
  MARK1 MUTATED           0
  MARK1 WILD-TYPE         1
D397V4, multiclass
            clus
vv           MARK1 MUTATED MARK1 WILD-TYPE
  STAGE I                7              84
  STAGE IA               0               1
  STAGE II               3              29
  STAGE IIA              9             129
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             1              10
  STAGE IIIB             3              56
  STAGE IIIC             2              40
  STAGE IV               1              47
  STAGE IVA              2              16
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  MARK1 MUTATED     0   8  18   3
  MARK1 WILD-TYPE  17  84 311  47
D397V5, multiclass
    clus
vv   MARK1 MUTATED MARK1 WILD-TYPE
  T1             0              17
  T2             8              84
  T3            18             311
  T4             3              47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  MARK1 MUTATED    20   6   3
  MARK1 WILD-TYPE 267 107  84
D397V6, multiclass
    clus
vv   MARK1 MUTATED MARK1 WILD-TYPE
  N0            20             267
  N1             6             107
  N2             3              84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D397V7, binary
                 cls
clus                0   1
  MARK1 MUTATED    23   3
  MARK1 WILD-TYPE 352  62
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MARK1 MUTATED     23    3
  MARK1 WILD-TYPE  352   62
   clus
vv  MARK1 MUTATED MARK1 WILD-TYPE
  0            23             352
  1             3              62
[1] 2 2
[1] FALSE
D397V8, binary
                 cls
clus                0   1
  MARK1 MUTATED    12  17
  MARK1 WILD-TYPE 213 247
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MARK1 MUTATED     12   17
  MARK1 WILD-TYPE  213  247
        clus
vv       MARK1 MUTATED MARK1 WILD-TYPE
  FEMALE            12             213
  MALE              17             247
[1] 2 2
[1] FALSE
D397V9, binary
                 cls
clus                0   1
  MARK1 MUTATED    24   0
  MARK1 WILD-TYPE 326  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MARK1 MUTATED     24    0
  MARK1 WILD-TYPE  326   22
     clus
vv    MARK1 MUTATED MARK1 WILD-TYPE
  NO             24             326
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MARK1 MUTATED                     21                             4
  MARK1 WILD-TYPE                  294                            43
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MARK1 MUTATED                       4                              0
  MARK1 WILD-TYPE                   102                             10
D397V10, multiclass
                                clus
vv                               MARK1 MUTATED MARK1 WILD-TYPE
  COLON ADENOCARCINOMA                      21             294
  COLON MUCINOUS ADENOCARCINOMA              4              43
  RECTAL ADENOCARCINOMA                      4             102
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  MARK1 MUTATED    21   0   0   3
  MARK1 WILD-TYPE 324   4  31  22
D397V11, multiclass
    clus
vv   MARK1 MUTATED MARK1 WILD-TYPE
  R0            21             324
  R1             0               4
  R2             0              31
  RX             3              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D397V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MARK1 MUTATED                                  0     1
  MARK1 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  MARK1 MUTATED                           3    15
  MARK1 WILD-TYPE                        19   211
D397V13, multiclass
                                  clus
vv                                 MARK1 MUTATED MARK1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    3              19
  WHITE                                       15             211
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(398) Variable = USP25 MUTATION ANALYSIS
D398V1, survival
                 sevent
clus2               0   1
  USP25 MUTATED    21   2
  USP25 WILD-TYPE 357  91
  USP25 MUTATED USP25 WILD-TYPE 
             23             448 
  USP25 MUTATED USP25 WILD-TYPE 
              2              91 
$`USP25 MUTATED`
TCGA-A6-5656 TCGA-A6-6654 TCGA-AA-3977 TCGA-AA-A00N TCGA-AD-6889 TCGA-AD-6895 
       32.91        23.87        25.02         4.01        56.55         0.72 
TCGA-AU-3779 TCGA-AZ-4315 TCGA-AZ-6603 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6719 
       14.50        58.39        29.56         0.07        12.76        14.30 
TCGA-CK-6751 TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-6164 TCGA-CM-6172 TCGA-D5-6540 
      124.27        22.98        32.02        29.03        11.01        16.14 
TCGA-D5-6920 TCGA-AG-A002 TCGA-AG-A00C TCGA-AG-A036 TCGA-DY-A0XA 
        3.68        20.98         6.02       117.11       126.44 

$`USP25 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 
       25.18        24.16        21.76        24.69        24.39        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6899 
       40.96         0.07        21.37        15.52         0.79         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        10.88         0.20        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        33.01        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
       12.10       100.01         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6716 TCGA-CA-6718 
       12.69         3.06         3.25         3.29        12.20        10.06 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CM-4743 TCGA-CM-4744 
        9.99        21.14        82.95         1.91        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5349 
       37.02        25.02        13.02        29.06        22.03        30.08 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
       12.00         2.96        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       13.02        15.02        14.04        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
       15.58         1.48         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       17.03        13.94        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        4.01         5.03         5.29        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  USP25 MUTATED USP25 WILD-TYPE 
           0.07            0.00 
  USP25 MUTATED USP25 WILD-TYPE 
         126.44          148.01 
  USP25 MUTATED USP25 WILD-TYPE 
         22.980          20.085 
[1] "0.1 - 126.4 (23.0)" "0.0 - 148.0 (20.1)"
[1] "hr=" "2.8"
D398V2, continuous
D398V3, binary
                 cls
clus                0   1
  USP25 MUTATED    19   4
  USP25 WILD-TYPE 347 115
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP25 MUTATED     19    4
  USP25 WILD-TYPE  347  115
        clus
vv       USP25 MUTATED USP25 WILD-TYPE
  COLON             19             347
  RECTUM             4             115
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  USP25 MUTATED         4        0        0         9         1         0
  USP25 WILD-TYPE      87        1       32       129         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  USP25 MUTATED           1          0          5          0        0         0
  USP25 WILD-TYPE        23         11         54         42       48        18
                 vv
clus              STAGE IVB
  USP25 MUTATED           0
  USP25 WILD-TYPE         1
D398V4, multiclass
            clus
vv           USP25 MUTATED USP25 WILD-TYPE
  STAGE I                4              87
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              9             129
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             5              54
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  USP25 MUTATED     0   6  16   1
  USP25 WILD-TYPE  17  86 313  49
D398V5, multiclass
    clus
vv   USP25 MUTATED USP25 WILD-TYPE
  T1             0              17
  T2             6              86
  T3            16             313
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  USP25 MUTATED    15   7   1
  USP25 WILD-TYPE 272 106  86
D398V6, multiclass
    clus
vv   USP25 MUTATED USP25 WILD-TYPE
  N0            15             272
  N1             7             106
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D398V7, binary
                 cls
clus                0   1
  USP25 MUTATED    19   0
  USP25 WILD-TYPE 356  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP25 MUTATED     19    0
  USP25 WILD-TYPE  356   65
   clus
vv  USP25 MUTATED USP25 WILD-TYPE
  0            19             356
  1             0              65
[1] 2 2
[1] FALSE
D398V8, binary
                 cls
clus                0   1
  USP25 MUTATED     9  14
  USP25 WILD-TYPE 216 250
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP25 MUTATED      9   14
  USP25 WILD-TYPE  216  250
        clus
vv       USP25 MUTATED USP25 WILD-TYPE
  FEMALE             9             216
  MALE              14             250
[1] 2 2
[1] FALSE
D398V9, binary
                 cls
clus                0   1
  USP25 MUTATED    15   2
  USP25 WILD-TYPE 335  20
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP25 MUTATED     15    2
  USP25 WILD-TYPE  335   20
     clus
vv    USP25 MUTATED USP25 WILD-TYPE
  NO             15             335
  YES             2              20
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  USP25 MUTATED                     15                             4
  USP25 WILD-TYPE                  300                            43
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  USP25 MUTATED                       4                              0
  USP25 WILD-TYPE                   102                             10
D398V10, multiclass
                                clus
vv                               USP25 MUTATED USP25 WILD-TYPE
  COLON ADENOCARCINOMA                      15             300
  COLON MUCINOUS ADENOCARCINOMA              4              43
  RECTAL ADENOCARCINOMA                      4             102
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  USP25 MUTATED    12   0   0   4
  USP25 WILD-TYPE 333   4  31  21
D398V11, multiclass
    clus
vv   USP25 MUTATED USP25 WILD-TYPE
  R0            12             333
  R1             0               4
  R2             0              31
  RX             4              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D398V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  USP25 MUTATED                                  0     4
  USP25 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  USP25 MUTATED                           0    14
  USP25 WILD-TYPE                        22   212
D398V13, multiclass
                                  clus
vv                                 USP25 MUTATED USP25 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        4               7
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                       14             212
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(399) Variable = TOPORS MUTATION ANALYSIS
D399V1, survival
                  sevent
clus2                0   1
  TOPORS MUTATED    16   5
  TOPORS WILD-TYPE 362  88
  TOPORS MUTATED TOPORS WILD-TYPE 
              21              450 
  TOPORS MUTATED TOPORS WILD-TYPE 
               5               88 
$`TOPORS MUTATED`
TCGA-AA-3713 TCGA-AA-3815 TCGA-AA-3966 TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A024 
       19.04        33.04         2.01        25.02         4.01        39.06 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-CM-5862 TCGA-DM-A28F TCGA-G4-6307 
        0.95        33.01        21.44         5.03        35.97        55.04 
TCGA-G4-6323 TCGA-AF-6655 TCGA-AG-3732 TCGA-AG-3892 TCGA-AG-A002 TCGA-AG-A014 
       13.78        20.02        32.98        13.02        20.98        15.95 
TCGA-DC-5869 TCGA-EI-6507 TCGA-G5-6235 
        5.03        19.96        55.76 

$`TOPORS WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       10.06        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       20.98        34.03        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       37.02        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       16.31        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
       15.02        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
        6.12        81.37       119.93        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       44.68        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       14.50        16.83        15.39        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        7.99         0.99        37.02         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 
       19.99         1.02        17.95        36.95        17.03        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       25.97        23.01        37.02        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-6155 TCGA-DC-6157 
        4.73        78.12         7.17        15.02        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
        0.49        20.55        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6641 
       31.30        28.57        32.19         0.66         0.69        26.43 

  TOPORS MUTATED TOPORS WILD-TYPE 
            0.95             0.00 
  TOPORS MUTATED TOPORS WILD-TYPE 
           55.76           148.01 
  TOPORS MUTATED TOPORS WILD-TYPE 
          20.020           20.235 
[1] "0.9 - 55.8 (20.0)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.4"
D399V2, continuous
D399V3, binary
                  cls
clus                 0   1
  TOPORS MUTATED    13   8
  TOPORS WILD-TYPE 353 111
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TOPORS MUTATED     13    8
  TOPORS WILD-TYPE  353  111
        clus
vv       TOPORS MUTATED TOPORS WILD-TYPE
  COLON              13              353
  RECTUM              8              111
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TOPORS MUTATED         5        1        1         5         1         0
  TOPORS WILD-TYPE      86        0       31       133         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TOPORS MUTATED           0          1          4          0        1
  TOPORS WILD-TYPE        24         10         55         42       47
                  vv
clus               STAGE IVA STAGE IVB
  TOPORS MUTATED           2         0
  TOPORS WILD-TYPE        16         1
D399V4, multiclass
            clus
vv           TOPORS MUTATED TOPORS WILD-TYPE
  STAGE I                 5               86
  STAGE IA                1                0
  STAGE II                1               31
  STAGE IIA               5              133
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              1               10
  STAGE IIIB              4               55
  STAGE IIIC              0               42
  STAGE IV                1               47
  STAGE IVA               2               16
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  TOPORS MUTATED     2   5  13   1
  TOPORS WILD-TYPE  15  87 316  49
D399V5, multiclass
    clus
vv   TOPORS MUTATED TOPORS WILD-TYPE
  T1              2               15
  T2              5               87
  T3             13              316
  T4              1               49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  TOPORS MUTATED    15   7   0
  TOPORS WILD-TYPE 272 106  87
D399V6, multiclass
    clus
vv   TOPORS MUTATED TOPORS WILD-TYPE
  N0             15              272
  N1              7              106
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D399V7, binary
                  cls
clus                 0   1
  TOPORS MUTATED    14   3
  TOPORS WILD-TYPE 361  62
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TOPORS MUTATED     14    3
  TOPORS WILD-TYPE  361   62
   clus
vv  TOPORS MUTATED TOPORS WILD-TYPE
  0             14              361
  1              3               62
[1] 2 2
[1] FALSE
D399V8, binary
                  cls
clus                 0   1
  TOPORS MUTATED     9  13
  TOPORS WILD-TYPE 216 251
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TOPORS MUTATED      9   13
  TOPORS WILD-TYPE  216  251
        clus
vv       TOPORS MUTATED TOPORS WILD-TYPE
  FEMALE              9              216
  MALE               13              251
[1] 2 2
[1] FALSE
D399V9, binary
                  cls
clus                 0   1
  TOPORS MUTATED    15   1
  TOPORS WILD-TYPE 335  21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TOPORS MUTATED     15    1
  TOPORS WILD-TYPE  335   21
     clus
vv    TOPORS MUTATED TOPORS WILD-TYPE
  NO              15              335
  YES              1               21
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  TOPORS MUTATED                     10                             3
  TOPORS WILD-TYPE                  305                            44
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  TOPORS MUTATED                       8                              0
  TOPORS WILD-TYPE                    98                             10
D399V10, multiclass
                                clus
vv                               TOPORS MUTATED TOPORS WILD-TYPE
  COLON ADENOCARCINOMA                       10              305
  COLON MUCINOUS ADENOCARCINOMA               3               44
  RECTAL ADENOCARCINOMA                       8               98
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  TOPORS MUTATED    17   1   1   0
  TOPORS WILD-TYPE 328   3  30  25
D399V11, multiclass
    clus
vv   TOPORS MUTATED TOPORS WILD-TYPE
  R0             17              328
  R1              1                3
  R2              1               30
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D399V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TOPORS MUTATED                                  0     0
  TOPORS WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  TOPORS MUTATED                           3     8
  TOPORS WILD-TYPE                        19   218
D399V13, multiclass
                                  clus
vv                                 TOPORS MUTATED TOPORS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     3               19
  WHITE                                         8              218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(400) Variable = ENPEP MUTATION ANALYSIS
D400V1, survival
                 sevent
clus2               0   1
  ENPEP MUTATED    15   8
  ENPEP WILD-TYPE 363  85
  ENPEP MUTATED ENPEP WILD-TYPE 
             23             448 
  ENPEP MUTATED ENPEP WILD-TYPE 
              8              85 
$`ENPEP MUTATED`
TCGA-A6-2672 TCGA-A6-5661 TCGA-A6-6141 TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3516 
       46.65        33.53         8.38         3.02        63.98        13.02 
TCGA-AA-3664 TCGA-AA-3977 TCGA-AA-A00U TCGA-AA-A010 TCGA-AD-6890 TCGA-AD-6964 
       54.02        25.02        17.03        34.98         0.79        10.88 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-CA-5796 TCGA-CA-6717 TCGA-D5-5538 
        6.77        12.10       100.01         3.25        12.76        12.26 
TCGA-D5-6536 TCGA-DM-A1D7 TCGA-F4-6809 TCGA-AG-3883 TCGA-AG-A002 
       17.85        13.32        13.25         1.02        20.98 

$`ENPEP WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       31.63        30.44        29.19        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       32.71        27.09        22.52        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 
       20.28         7.04         1.02        35.01         6.97         1.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.05         6.97         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00W TCGA-AA-A00Z 
        4.01        27.02        42.02         0.99        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6895 
       40.96         0.07        21.37        15.52        56.55         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
       49.41        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
       12.69         3.06         3.29         0.07        12.20        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5539 
       11.08        11.01        10.06        12.03        45.40        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       15.12         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       49.91        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       33.67         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
       19.99        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  ENPEP MUTATED ENPEP WILD-TYPE 
           0.79            0.00 
  ENPEP MUTATED ENPEP WILD-TYPE 
         100.01          148.01 
  ENPEP MUTATED ENPEP WILD-TYPE 
         13.250          20.945 
[1] "0.8 - 100.0 (13.2)" "0.0 - 148.0 (20.9)"
[1] "hr=" "2"  
D400V2, continuous
D400V3, binary
                 cls
clus                0   1
  ENPEP MUTATED    21   2
  ENPEP WILD-TYPE 345 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ENPEP MUTATED     21    2
  ENPEP WILD-TYPE  345  117
        clus
vv       ENPEP MUTATED ENPEP WILD-TYPE
  COLON             21             345
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ENPEP MUTATED         3        0        4         6         1         0
  ENPEP WILD-TYPE      88        1       28       132         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ENPEP MUTATED           1          0          3          0        1         1
  ENPEP WILD-TYPE        23         11         56         42       47        17
                 vv
clus              STAGE IVB
  ENPEP MUTATED           0
  ENPEP WILD-TYPE         1
D400V4, multiclass
            clus
vv           ENPEP MUTATED ENPEP WILD-TYPE
  STAGE I                3              88
  STAGE IA               0               1
  STAGE II               4              28
  STAGE IIA              6             132
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             3              56
  STAGE IIIC             0              42
  STAGE IV               1              47
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ENPEP MUTATED     1   4  15   3
  ENPEP WILD-TYPE  16  88 314  47
D400V5, multiclass
    clus
vv   ENPEP MUTATED ENPEP WILD-TYPE
  T1             1              16
  T2             4              88
  T3            15             314
  T4             3              47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  ENPEP MUTATED    16   5   2
  ENPEP WILD-TYPE 271 108  85
D400V6, multiclass
    clus
vv   ENPEP MUTATED ENPEP WILD-TYPE
  N0            16             271
  N1             5             108
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D400V7, binary
                 cls
clus                0   1
  ENPEP MUTATED    17   2
  ENPEP WILD-TYPE 358  63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ENPEP MUTATED     17    2
  ENPEP WILD-TYPE  358   63
   clus
vv  ENPEP MUTATED ENPEP WILD-TYPE
  0            17             358
  1             2              63
[1] 2 2
[1] FALSE
D400V8, binary
                 cls
clus                0   1
  ENPEP MUTATED     9  14
  ENPEP WILD-TYPE 216 250
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ENPEP MUTATED      9   14
  ENPEP WILD-TYPE  216  250
        clus
vv       ENPEP MUTATED ENPEP WILD-TYPE
  FEMALE             9             216
  MALE              14             250
[1] 2 2
[1] FALSE
D400V9, binary
                 cls
clus                0   1
  ENPEP MUTATED    19   0
  ENPEP WILD-TYPE 331  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ENPEP MUTATED     19    0
  ENPEP WILD-TYPE  331   22
     clus
vv    ENPEP MUTATED ENPEP WILD-TYPE
  NO             19             331
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ENPEP MUTATED                     17                             3
  ENPEP WILD-TYPE                  298                            44
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ENPEP MUTATED                       2                              0
  ENPEP WILD-TYPE                   104                             10
D400V10, multiclass
                                clus
vv                               ENPEP MUTATED ENPEP WILD-TYPE
  COLON ADENOCARCINOMA                      17             298
  COLON MUCINOUS ADENOCARCINOMA              3              44
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  ENPEP MUTATED    13   0   0   1
  ENPEP WILD-TYPE 332   4  31  24
D400V11, multiclass
    clus
vv   ENPEP MUTATED ENPEP WILD-TYPE
  R0            13             332
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D400V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ENPEP MUTATED                                  0     2
  ENPEP WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ENPEP MUTATED                           3     9
  ENPEP WILD-TYPE                        19   217
D400V13, multiclass
                                  clus
vv                                 ENPEP MUTATED ENPEP WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               9
  BLACK OR AFRICAN AMERICAN                    3              19
  WHITE                                        9             217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(401) Variable = RING1 MUTATION ANALYSIS
D401V1, survival
                 sevent
clus2               0   1
  RING1 MUTATED     9   0
  RING1 WILD-TYPE 369  93
  RING1 MUTATED RING1 WILD-TYPE 
              9             462 
  RING1 MUTATED RING1 WILD-TYPE 
              0              93 
$`RING1 MUTATED`
TCGA-A6-6141 TCGA-AA-3713 TCGA-AZ-4315 TCGA-CM-4743 TCGA-CM-6171 TCGA-D5-6930 
        8.38        19.04        58.39        23.05        14.04         1.51 
TCGA-DM-A1HA TCGA-G4-6586 TCGA-DC-5337 
      131.51        35.80        15.02 

$`RING1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 
       22.09        22.06        32.71        27.09        22.52        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       33.01        21.44        17.82         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
        1.91       124.27        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       13.02        15.02        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6931 
       14.30         9.04         9.44        11.64         4.80        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
       44.32       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
        7.17         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  RING1 MUTATED RING1 WILD-TYPE 
           1.51            0.00 
  RING1 MUTATED RING1 WILD-TYPE 
         131.51          148.01 
  RING1 MUTATED RING1 WILD-TYPE 
         19.040          20.235 
[1] "1.5 - 131.5 (19.0)" "0.0 - 148.0 (20.2)"
[1] "hr="     "9300000"
D401V2, continuous
D401V3, binary
                 cls
clus                0   1
  RING1 MUTATED    10   1
  RING1 WILD-TYPE 356 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RING1 MUTATED     10    1
  RING1 WILD-TYPE  356  118
        clus
vv       RING1 MUTATED RING1 WILD-TYPE
  COLON             10             356
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RING1 MUTATED         2        0        0         6         1         0
  RING1 WILD-TYPE      89        1       32       132         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RING1 MUTATED           0          0          0          1        1         0
  RING1 WILD-TYPE        24         11         59         41       47        18
                 vv
clus              STAGE IVB
  RING1 MUTATED           0
  RING1 WILD-TYPE         1
D401V4, multiclass
            clus
vv           RING1 MUTATED RING1 WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              6             132
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             1              41
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  RING1 MUTATED     1   1   8   1
  RING1 WILD-TYPE  16  91 321  49
D401V5, multiclass
    clus
vv   RING1 MUTATED RING1 WILD-TYPE
  T1             1              16
  T2             1              91
  T3             8             321
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  RING1 MUTATED    10   0   1
  RING1 WILD-TYPE 277 113  86
D401V6, multiclass
    clus
vv   RING1 MUTATED RING1 WILD-TYPE
  N0            10             277
  N1             0             113
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D401V7, binary
                 cls
clus                0   1
  RING1 MUTATED     9   1
  RING1 WILD-TYPE 366  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RING1 MUTATED      9    1
  RING1 WILD-TYPE  366   64
   clus
vv  RING1 MUTATED RING1 WILD-TYPE
  0             9             366
  1             1              64
[1] 2 2
[1] FALSE
D401V8, binary
                 cls
clus                0   1
  RING1 MUTATED     4   7
  RING1 WILD-TYPE 221 257
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RING1 MUTATED      4    7
  RING1 WILD-TYPE  221  257
        clus
vv       RING1 MUTATED RING1 WILD-TYPE
  FEMALE             4             221
  MALE               7             257
[1] 2 2
[1] FALSE
D401V9, binary
                 cls
clus                0   1
  RING1 MUTATED     6   1
  RING1 WILD-TYPE 344  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RING1 MUTATED      6    1
  RING1 WILD-TYPE  344   21
     clus
vv    RING1 MUTATED RING1 WILD-TYPE
  NO              6             344
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  RING1 MUTATED                      9                             1
  RING1 WILD-TYPE                  306                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  RING1 MUTATED                       1                              0
  RING1 WILD-TYPE                   105                             10
D401V10, multiclass
                                clus
vv                               RING1 MUTATED RING1 WILD-TYPE
  COLON ADENOCARCINOMA                       9             306
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  RING1 MUTATED     7   0   1   1
  RING1 WILD-TYPE 338   4  30  24
D401V11, multiclass
    clus
vv   RING1 MUTATED RING1 WILD-TYPE
  R0             7             338
  R1             0               4
  R2             1              30
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D401V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RING1 MUTATED                                  0     0
  RING1 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  RING1 MUTATED                           1     8
  RING1 WILD-TYPE                        21   218
D401V13, multiclass
                                  clus
vv                                 RING1 MUTATED RING1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        8             218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(402) Variable = NGEF MUTATION ANALYSIS
D402V1, survival
                sevent
clus2              0   1
  NGEF MUTATED    14   3
  NGEF WILD-TYPE 364  90
  NGEF MUTATED NGEF WILD-TYPE 
            17            454 
  NGEF MUTATED NGEF WILD-TYPE 
             3             90 
$`NGEF MUTATED`
TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6653 TCGA-AA-3660 TCGA-AA-3850 TCGA-AD-6899 
       22.06        27.09        24.39        78.08         0.00         5.79 
TCGA-AU-3779 TCGA-AZ-4315 TCGA-CM-5344 TCGA-D5-6536 TCGA-D5-6540 TCGA-D5-6926 
       14.50        58.39        22.03        17.85        16.14         9.04 
TCGA-DM-A1DB TCGA-G4-6299 TCGA-G4-6317 TCGA-EF-5830 TCGA-EI-6506 
       44.32        74.56        36.00         0.49        20.55 

$`NGEF WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       22.09        32.71        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       24.16        21.76        24.69        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 
       37.02        14.93         0.00        17.03        10.06        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        10.88         0.20        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        33.01        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       25.02        13.02        29.06        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 
       18.25         1.32        43.27        15.12         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       12.49        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
       14.30         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
      133.18        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       63.62        61.91        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EI-6507 TCGA-EI-6508 
       57.24        24.13        51.48        32.61        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  NGEF MUTATED NGEF WILD-TYPE 
             0              0 
  NGEF MUTATED NGEF WILD-TYPE 
         78.08         148.01 
  NGEF MUTATED NGEF WILD-TYPE 
        22.030         20.085 
[1] "0.0 - 78.1 (22.0)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.2"
D402V2, continuous
D402V3, binary
                cls
clus               0   1
  NGEF MUTATED    16   2
  NGEF WILD-TYPE 350 117
[1] "tbl2"
                cls
clus             [,1] [,2]
  NGEF MUTATED     16    2
  NGEF WILD-TYPE  350  117
        clus
vv       NGEF MUTATED NGEF WILD-TYPE
  COLON            16            350
  RECTUM            2            117
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NGEF MUTATED         3        0        1         6         1         0
  NGEF WILD-TYPE      88        1       31       132         9         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NGEF MUTATED           1          0          3          3        0         0
  NGEF WILD-TYPE        23         11         56         39       48        18
                vv
clus             STAGE IVB
  NGEF MUTATED           0
  NGEF WILD-TYPE         1
D402V4, multiclass
            clus
vv           NGEF MUTATED NGEF WILD-TYPE
  STAGE I               3             88
  STAGE IA              0              1
  STAGE II              1             31
  STAGE IIA             6            132
  STAGE IIB             1              9
  STAGE IIC             0              1
  STAGE III             1             23
  STAGE IIIA            0             11
  STAGE IIIB            3             56
  STAGE IIIC            3             39
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  NGEF MUTATED     0   3  12   3
  NGEF WILD-TYPE  17  89 317  47
D402V5, multiclass
    clus
vv   NGEF MUTATED NGEF WILD-TYPE
  T1            0             17
  T2            3             89
  T3           12            317
  T4            3             47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  NGEF MUTATED    11   3   4
  NGEF WILD-TYPE 276 110  83
D402V6, multiclass
    clus
vv   NGEF MUTATED NGEF WILD-TYPE
  N0           11            276
  N1            3            110
  N2            4             83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D402V7, binary
                cls
clus               0   1
  NGEF MUTATED    16   0
  NGEF WILD-TYPE 359  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  NGEF MUTATED     16    0
  NGEF WILD-TYPE  359   65
   clus
vv  NGEF MUTATED NGEF WILD-TYPE
  0           16            359
  1            0             65
[1] 2 2
[1] FALSE
D402V8, binary
                cls
clus               0   1
  NGEF MUTATED     6  12
  NGEF WILD-TYPE 219 252
[1] "tbl2"
                cls
clus             [,1] [,2]
  NGEF MUTATED      6   12
  NGEF WILD-TYPE  219  252
        clus
vv       NGEF MUTATED NGEF WILD-TYPE
  FEMALE            6            219
  MALE             12            252
[1] 2 2
[1] FALSE
D402V9, binary
                cls
clus               0   1
  NGEF MUTATED    13   1
  NGEF WILD-TYPE 337  21
[1] "tbl2"
                cls
clus             [,1] [,2]
  NGEF MUTATED     13    1
  NGEF WILD-TYPE  337   21
     clus
vv    NGEF MUTATED NGEF WILD-TYPE
  NO            13            337
  YES            1             21
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  NGEF MUTATED                     14                             2
  NGEF WILD-TYPE                  301                            45
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  NGEF MUTATED                       2                              0
  NGEF WILD-TYPE                   104                             10
D402V10, multiclass
                                clus
vv                               NGEF MUTATED NGEF WILD-TYPE
  COLON ADENOCARCINOMA                     14            301
  COLON MUCINOUS ADENOCARCINOMA             2             45
  RECTAL ADENOCARCINOMA                     2            104
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  NGEF MUTATED    14   0   0   0
  NGEF WILD-TYPE 331   4  31  25
D402V11, multiclass
    clus
vv   NGEF MUTATED NGEF WILD-TYPE
  R0           14            331
  R1            0              4
  R2            0             31
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D402V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NGEF MUTATED                                  0     0
  NGEF WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  NGEF MUTATED                           0    15
  NGEF WILD-TYPE                        22   211
D402V13, multiclass
                                  clus
vv                                 NGEF MUTATED NGEF WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                      15            211
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(403) Variable = MMAA MUTATION ANALYSIS
D403V1, survival
                sevent
clus2              0   1
  MMAA MUTATED    10   2
  MMAA WILD-TYPE 368  91
  MMAA MUTATED MMAA WILD-TYPE 
            12            459 
  MMAA MUTATED MMAA WILD-TYPE 
             2             91 
$`MMAA MUTATED`
TCGA-A6-6141 TCGA-A6-6782 TCGA-AA-3663 TCGA-AA-A00N TCGA-AZ-4315 TCGA-AZ-6607 
        8.38        20.28         6.97         4.01        58.39         3.19 
TCGA-CA-6717 TCGA-CM-5341 TCGA-CM-5349 TCGA-AG-3727 TCGA-AG-A002 TCGA-AH-6643 
       12.76        29.06        30.08         0.99        20.98         0.69 

$`MMAA WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 
       22.09        22.06        32.71        27.09        22.52        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        19.66         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07        12.20        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5860 
       37.02        25.02        13.02        22.03        22.98        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
        1.45        17.49         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  MMAA MUTATED MMAA WILD-TYPE 
          0.69           0.00 
  MMAA MUTATED MMAA WILD-TYPE 
         58.39         148.01 
  MMAA MUTATED MMAA WILD-TYPE 
         10.57          20.55 
[1] "0.7 - 58.4 (10.6)"  "0.0 - 148.0 (20.6)"
[1] "hr=" "1.3"
D403V2, continuous
D403V3, binary
                cls
clus               0   1
  MMAA MUTATED     9   3
  MMAA WILD-TYPE 357 116
[1] "tbl2"
                cls
clus             [,1] [,2]
  MMAA MUTATED      9    3
  MMAA WILD-TYPE  357  116
        clus
vv       MMAA MUTATED MMAA WILD-TYPE
  COLON             9            357
  RECTUM            3            116
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MMAA MUTATED         1        0        1         4         2         0
  MMAA WILD-TYPE      90        1       31       134         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MMAA MUTATED           1          1          0          1        1         0
  MMAA WILD-TYPE        23         10         59         41       47        18
                vv
clus             STAGE IVB
  MMAA MUTATED           0
  MMAA WILD-TYPE         1
D403V4, multiclass
            clus
vv           MMAA MUTATED MMAA WILD-TYPE
  STAGE I               1             90
  STAGE IA              0              1
  STAGE II              1             31
  STAGE IIA             4            134
  STAGE IIB             2              8
  STAGE IIC             0              1
  STAGE III             1             23
  STAGE IIIA            1             10
  STAGE IIIB            0             59
  STAGE IIIC            1             41
  STAGE IV              1             47
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  MMAA MUTATED     0   2   7   3
  MMAA WILD-TYPE  17  90 322  47
D403V5, multiclass
    clus
vv   MMAA MUTATED MMAA WILD-TYPE
  T1            0             17
  T2            2             90
  T3            7            322
  T4            3             47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  MMAA MUTATED     8   2   2
  MMAA WILD-TYPE 279 111  85
D403V6, multiclass
    clus
vv   MMAA MUTATED MMAA WILD-TYPE
  N0            8            279
  N1            2            111
  N2            2             85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D403V7, binary
                cls
clus               0   1
  MMAA MUTATED    10   1
  MMAA WILD-TYPE 365  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  MMAA MUTATED     10    1
  MMAA WILD-TYPE  365   64
   clus
vv  MMAA MUTATED MMAA WILD-TYPE
  0           10            365
  1            1             64
[1] 2 2
[1] FALSE
D403V8, binary
                cls
clus               0   1
  MMAA MUTATED     3   9
  MMAA WILD-TYPE 222 255
[1] "tbl2"
                cls
clus             [,1] [,2]
  MMAA MUTATED      3    9
  MMAA WILD-TYPE  222  255
        clus
vv       MMAA MUTATED MMAA WILD-TYPE
  FEMALE            3            222
  MALE              9            255
[1] 2 2
[1] FALSE
D403V9, binary
                cls
clus               0   1
  MMAA MUTATED     9   0
  MMAA WILD-TYPE 341  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  MMAA MUTATED      9    0
  MMAA WILD-TYPE  341   22
     clus
vv    MMAA MUTATED MMAA WILD-TYPE
  NO             9            341
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MMAA MUTATED                      7                             2
  MMAA WILD-TYPE                  308                            45
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MMAA MUTATED                       3                              0
  MMAA WILD-TYPE                   103                             10
D403V10, multiclass
                                clus
vv                               MMAA MUTATED MMAA WILD-TYPE
  COLON ADENOCARCINOMA                      7            308
  COLON MUCINOUS ADENOCARCINOMA             2             45
  RECTAL ADENOCARCINOMA                     3            103
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  MMAA MUTATED     8   0   0   1
  MMAA WILD-TYPE 337   4  31  24
D403V11, multiclass
    clus
vv   MMAA MUTATED MMAA WILD-TYPE
  R0            8            337
  R1            0              4
  R2            0             31
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D403V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MMAA MUTATED                                  0     1
  MMAA WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  MMAA MUTATED                           1     6
  MMAA WILD-TYPE                        21   220
D403V13, multiclass
                                  clus
vv                                 MMAA MUTATED MMAA WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                       6            220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(404) Variable = ZNF630 MUTATION ANALYSIS
D404V1, survival
                  sevent
clus2                0   1
  ZNF630 MUTATED     8   0
  ZNF630 WILD-TYPE 370  93
  ZNF630 MUTATED ZNF630 WILD-TYPE 
               8              463 
  ZNF630 MUTATED ZNF630 WILD-TYPE 
               0               93 
$`ZNF630 MUTATED`
TCGA-AA-3555 TCGA-AZ-4315 TCGA-AZ-4681 TCGA-CM-6164 TCGA-D5-5540 TCGA-G4-6588 
       29.95        58.39       106.75        29.03        56.09        26.17 
TCGA-AF-6136 TCGA-AG-A002 
       15.39        20.98 

$`ZNF630 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 
       21.01        13.02        24.00        17.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        33.01        21.44        17.82         1.41         5.13 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
       12.00         2.96        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       12.26        19.59        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       22.09        13.78        35.80        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       10.39        14.50        16.83        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  ZNF630 MUTATED ZNF630 WILD-TYPE 
           15.39             0.00 
  ZNF630 MUTATED ZNF630 WILD-TYPE 
          106.75           148.01 
  ZNF630 MUTATED ZNF630 WILD-TYPE 
           29.49            20.02 
[1] "15.4 - 106.8 (29.5)" "0.0 - 148.0 (20.0)" 
[1] "hr="     "9400000"
D404V2, continuous
D404V3, binary
                  cls
clus                 0   1
  ZNF630 MUTATED     7   2
  ZNF630 WILD-TYPE 359 117
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF630 MUTATED      7    2
  ZNF630 WILD-TYPE  359  117
        clus
vv       ZNF630 MUTATED ZNF630 WILD-TYPE
  COLON               7              359
  RECTUM              2              117
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZNF630 MUTATED         1        0        0         7         0         0
  ZNF630 WILD-TYPE      90        1       32       131        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF630 MUTATED           0          0          1          0        0
  ZNF630 WILD-TYPE        24         11         58         42       48
                  vv
clus               STAGE IVA STAGE IVB
  ZNF630 MUTATED           0         0
  ZNF630 WILD-TYPE        18         1
D404V4, multiclass
            clus
vv           ZNF630 MUTATED ZNF630 WILD-TYPE
  STAGE I                 1               90
  STAGE IA                0                1
  STAGE II                0               32
  STAGE IIA               7              131
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              1               58
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZNF630 MUTATED     0   1   8   0
  ZNF630 WILD-TYPE  17  91 321  50
D404V5, multiclass
    clus
vv   ZNF630 MUTATED ZNF630 WILD-TYPE
  T1              0               17
  T2              1               91
  T3              8              321
  T4              0               50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  ZNF630 MUTATED     8   1   0
  ZNF630 WILD-TYPE 279 112  87
D404V6, multiclass
    clus
vv   ZNF630 MUTATED ZNF630 WILD-TYPE
  N0              8              279
  N1              1              112
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D404V7, binary
                  cls
clus                 0   1
  ZNF630 MUTATED     8   0
  ZNF630 WILD-TYPE 367  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF630 MUTATED      8    0
  ZNF630 WILD-TYPE  367   65
   clus
vv  ZNF630 MUTATED ZNF630 WILD-TYPE
  0              8              367
  1              0               65
[1] 2 2
[1] FALSE
D404V8, binary
                  cls
clus                 0   1
  ZNF630 MUTATED     6   3
  ZNF630 WILD-TYPE 219 261
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF630 MUTATED      6    3
  ZNF630 WILD-TYPE  219  261
        clus
vv       ZNF630 MUTATED ZNF630 WILD-TYPE
  FEMALE              6              219
  MALE                3              261
[1] 2 2
[1] FALSE
D404V9, binary
                  cls
clus                 0   1
  ZNF630 MUTATED     7   1
  ZNF630 WILD-TYPE 343  21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF630 MUTATED      7    1
  ZNF630 WILD-TYPE  343   21
     clus
vv    ZNF630 MUTATED ZNF630 WILD-TYPE
  NO               7              343
  YES              1               21
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ZNF630 MUTATED                      6                             1
  ZNF630 WILD-TYPE                  309                            46
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ZNF630 MUTATED                       2                              0
  ZNF630 WILD-TYPE                   104                             10
D404V10, multiclass
                                clus
vv                               ZNF630 MUTATED ZNF630 WILD-TYPE
  COLON ADENOCARCINOMA                        6              309
  COLON MUCINOUS ADENOCARCINOMA               1               46
  RECTAL ADENOCARCINOMA                       2              104
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ZNF630 MUTATED     8   0   0   0
  ZNF630 WILD-TYPE 337   4  31  25
D404V11, multiclass
    clus
vv   ZNF630 MUTATED ZNF630 WILD-TYPE
  R0              8              337
  R1              0                4
  R2              0               31
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D404V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF630 MUTATED                                  0     0
  ZNF630 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZNF630 MUTATED                           0     6
  ZNF630 WILD-TYPE                        22   220
D404V13, multiclass
                                  clus
vv                                 ZNF630 MUTATED ZNF630 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         6              220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(405) Variable = KIR2DL3 MUTATION ANALYSIS
D405V1, survival
                   sevent
clus2                 0   1
  KIR2DL3 MUTATED    13   5
  KIR2DL3 WILD-TYPE 365  88
  KIR2DL3 MUTATED KIR2DL3 WILD-TYPE 
               18               453 
  KIR2DL3 MUTATED KIR2DL3 WILD-TYPE 
                5                88 
$`KIR2DL3 MUTATED`
TCGA-A6-4105 TCGA-A6-5665 TCGA-A6-6648 TCGA-A6-6651 TCGA-AA-3496 TCGA-AA-3815 
       14.53        22.06        25.18        21.76         1.02        33.04 
TCGA-AY-5543 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6601 TCGA-CM-4747 TCGA-CM-4752 
       33.01        22.36        62.79       100.01        25.02        13.02 
TCGA-CM-5341 TCGA-CM-6163 TCGA-CM-6168 TCGA-D5-6537 TCGA-D5-6928 TCGA-DM-A28H 
       29.06         2.96        12.99         4.80        11.64       117.07 

$`KIR2DL3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 
       16.57        34.65        33.34        32.75        36.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6649 
       32.71        27.09        22.52         8.38        25.08        24.16 
TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       24.69        24.39        23.87        20.12        19.66        20.28 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
        7.04         3.02        35.01        63.98         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
       13.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       36.03         8.05        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       78.08         6.05         6.97        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
       19.04        19.04        10.06        35.05         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       16.31         0.95        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
        5.13       106.75        88.21        49.41         6.77        12.10 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-5344 TCGA-CM-5348 
      124.27        23.05        20.02        37.02        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       17.03        15.02        12.00        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       14.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6538 
       18.25         1.32        43.27        15.12        17.85        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6930 
       12.43        14.30         9.04         9.44         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28K TCGA-F4-6459 
       81.37       119.93        35.97        60.79        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  KIR2DL3 MUTATED KIR2DL3 WILD-TYPE 
             1.02              0.00 
  KIR2DL3 MUTATED KIR2DL3 WILD-TYPE 
           117.07            148.01 
  KIR2DL3 MUTATED KIR2DL3 WILD-TYPE 
            22.21             20.05 
[1] "1.0 - 117.1 (22.2)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.3"
D405V2, continuous
D405V3, binary
                   cls
clus                  0   1
  KIR2DL3 MUTATED    19   0
  KIR2DL3 WILD-TYPE 347 119
[1] "tbl2"
                   cls
clus                [,1] [,2]
  KIR2DL3 MUTATED     19    0
  KIR2DL3 WILD-TYPE  347  119
        clus
vv       KIR2DL3 MUTATED KIR2DL3 WILD-TYPE
  COLON               19               347
  RECTUM               0               119
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KIR2DL3 MUTATED         1        0        3         7         0         0
  KIR2DL3 WILD-TYPE      90        1       29       131        10         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIR2DL3 MUTATED           0          1          2          1        0
  KIR2DL3 WILD-TYPE        24         10         57         41       48
                   vv
clus                STAGE IVA STAGE IVB
  KIR2DL3 MUTATED           4         0
  KIR2DL3 WILD-TYPE        14         1
D405V4, multiclass
            clus
vv           KIR2DL3 MUTATED KIR2DL3 WILD-TYPE
  STAGE I                  1                90
  STAGE IA                 0                 1
  STAGE II                 3                29
  STAGE IIA                7               131
  STAGE IIB                0                10
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               1                10
  STAGE IIIB               2                57
  STAGE IIIC               1                41
  STAGE IV                 0                48
  STAGE IVA                4                14
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  KIR2DL3 MUTATED     1   1  16   1
  KIR2DL3 WILD-TYPE  16  91 313  49
D405V5, multiclass
    clus
vv   KIR2DL3 MUTATED KIR2DL3 WILD-TYPE
  T1               1                16
  T2               1                91
  T3              16               313
  T4               1                49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  KIR2DL3 MUTATED    13   5   1
  KIR2DL3 WILD-TYPE 274 108  86
D405V6, multiclass
    clus
vv   KIR2DL3 MUTATED KIR2DL3 WILD-TYPE
  N0              13               274
  N1               5               108
  N2               1                86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D405V7, binary
                   cls
clus                  0   1
  KIR2DL3 MUTATED    12   4
  KIR2DL3 WILD-TYPE 363  61
[1] "tbl2"
                   cls
clus                [,1] [,2]
  KIR2DL3 MUTATED     12    4
  KIR2DL3 WILD-TYPE  363   61
   clus
vv  KIR2DL3 MUTATED KIR2DL3 WILD-TYPE
  0              12               363
  1               4                61
[1] 2 2
[1] FALSE
D405V8, binary
                   cls
clus                  0   1
  KIR2DL3 MUTATED     8  11
  KIR2DL3 WILD-TYPE 217 253
[1] "tbl2"
                   cls
clus                [,1] [,2]
  KIR2DL3 MUTATED      8   11
  KIR2DL3 WILD-TYPE  217  253
        clus
vv       KIR2DL3 MUTATED KIR2DL3 WILD-TYPE
  FEMALE               8               217
  MALE                11               253
[1] 2 2
[1] FALSE
D405V9, binary
                   cls
clus                  0   1
  KIR2DL3 MUTATED    16   0
  KIR2DL3 WILD-TYPE 334  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  KIR2DL3 MUTATED     16    0
  KIR2DL3 WILD-TYPE  334   22
     clus
vv    KIR2DL3 MUTATED KIR2DL3 WILD-TYPE
  NO               16               334
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  KIR2DL3 MUTATED                     18                             1
  KIR2DL3 WILD-TYPE                  297                            46
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  KIR2DL3 MUTATED                       0                              0
  KIR2DL3 WILD-TYPE                   106                             10
D405V10, multiclass
                                clus
vv                               KIR2DL3 MUTATED KIR2DL3 WILD-TYPE
  COLON ADENOCARCINOMA                        18               297
  COLON MUCINOUS ADENOCARCINOMA                1                46
  RECTAL ADENOCARCINOMA                        0               106
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  KIR2DL3 MUTATED    13   0   0   0
  KIR2DL3 WILD-TYPE 332   4  31  25
D405V11, multiclass
    clus
vv   KIR2DL3 MUTATED KIR2DL3 WILD-TYPE
  R0              13               332
  R1               0                 4
  R2               0                31
  RX               0                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D405V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KIR2DL3 MUTATED                                  0     0
  KIR2DL3 WILD-TYPE                                1    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  KIR2DL3 MUTATED                           3    13
  KIR2DL3 WILD-TYPE                        19   213
D405V13, multiclass
                                  clus
vv                                 KIR2DL3 MUTATED KIR2DL3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                      3                19
  WHITE                                         13               213
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(406) Variable = SLC7A6 MUTATION ANALYSIS
D406V1, survival
                  sevent
clus2                0   1
  SLC7A6 MUTATED     6   0
  SLC7A6 WILD-TYPE 372  93
  SLC7A6 MUTATED SLC7A6 WILD-TYPE 
               6              465 
  SLC7A6 MUTATED SLC7A6 WILD-TYPE 
               0               93 
$`SLC7A6 MUTATED`
TCGA-AA-3660 TCGA-AZ-5407 TCGA-CA-5797 TCGA-CM-6680 TCGA-DM-A1HB TCGA-F4-6855 
       78.08        88.21         3.29        12.03       135.65        47.41 

$`SLC7A6 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 
       20.98        19.99        13.94        19.99        61.02         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 
        5.13       106.75        22.36        62.79        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6716 
        1.61        12.69         3.06         3.25         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-D5-5537 
       13.05        11.08        11.08        11.01        10.06        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 
      140.38         7.50        44.32       131.51       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  SLC7A6 MUTATED SLC7A6 WILD-TYPE 
            3.29             0.00 
  SLC7A6 MUTATED SLC7A6 WILD-TYPE 
          135.65           148.01 
  SLC7A6 MUTATED SLC7A6 WILD-TYPE 
          62.745           20.120 
[1] "3.3 - 135.7 (62.7)" "0.0 - 148.0 (20.1)"
[1] "hr="     "9500000"
D406V2, continuous
D406V3, binary
                  cls
clus                 0   1
  SLC7A6 MUTATED     6   1
  SLC7A6 WILD-TYPE 360 118
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLC7A6 MUTATED      6    1
  SLC7A6 WILD-TYPE  360  118
        clus
vv       SLC7A6 MUTATED SLC7A6 WILD-TYPE
  COLON               6              360
  RECTUM              1              118
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SLC7A6 MUTATED         1        0        1         2         0         0
  SLC7A6 WILD-TYPE      90        1       31       136        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC7A6 MUTATED           1          0          2          0        0
  SLC7A6 WILD-TYPE        23         11         57         42       48
                  vv
clus               STAGE IVA STAGE IVB
  SLC7A6 MUTATED           0         0
  SLC7A6 WILD-TYPE        18         1
D406V4, multiclass
            clus
vv           SLC7A6 MUTATED SLC7A6 WILD-TYPE
  STAGE I                 1               90
  STAGE IA                0                1
  STAGE II                1               31
  STAGE IIA               2              136
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               1               23
  STAGE IIIA              0               11
  STAGE IIIB              2               57
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  SLC7A6 MUTATED     1   0   6   0
  SLC7A6 WILD-TYPE  16  92 323  50
D406V5, multiclass
    clus
vv   SLC7A6 MUTATED SLC7A6 WILD-TYPE
  T1              1               16
  T2              0               92
  T3              6              323
  T4              0               50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  SLC7A6 MUTATED     4   2   1
  SLC7A6 WILD-TYPE 283 111  86
D406V6, multiclass
    clus
vv   SLC7A6 MUTATED SLC7A6 WILD-TYPE
  N0              4              283
  N1              2              111
  N2              1               86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D406V7, binary
                  cls
clus                 0   1
  SLC7A6 MUTATED     6   0
  SLC7A6 WILD-TYPE 369  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLC7A6 MUTATED      6    0
  SLC7A6 WILD-TYPE  369   65
   clus
vv  SLC7A6 MUTATED SLC7A6 WILD-TYPE
  0              6              369
  1              0               65
[1] 2 2
[1] FALSE
D406V8, binary
                  cls
clus                 0   1
  SLC7A6 MUTATED     4   3
  SLC7A6 WILD-TYPE 221 261
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLC7A6 MUTATED      4    3
  SLC7A6 WILD-TYPE  221  261
        clus
vv       SLC7A6 MUTATED SLC7A6 WILD-TYPE
  FEMALE              4              221
  MALE                3              261
[1] 2 2
[1] FALSE
D406V9, binary
                  cls
clus                 0   1
  SLC7A6 MUTATED     5   0
  SLC7A6 WILD-TYPE 345  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLC7A6 MUTATED      5    0
  SLC7A6 WILD-TYPE  345   22
     clus
vv    SLC7A6 MUTATED SLC7A6 WILD-TYPE
  NO               5              345
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SLC7A6 MUTATED                      5                             0
  SLC7A6 WILD-TYPE                  310                            47
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SLC7A6 MUTATED                       1                              0
  SLC7A6 WILD-TYPE                   105                             10
D406V10, multiclass
                                clus
vv                               SLC7A6 MUTATED SLC7A6 WILD-TYPE
  COLON ADENOCARCINOMA                        5              310
  COLON MUCINOUS ADENOCARCINOMA               0               47
  RECTAL ADENOCARCINOMA                       1              105
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  SLC7A6 MUTATED     4   0   0   0
  SLC7A6 WILD-TYPE 341   4  31  25
D406V11, multiclass
    clus
vv   SLC7A6 MUTATED SLC7A6 WILD-TYPE
  R0              4              341
  R1              0                4
  R2              0               31
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D406V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SLC7A6 MUTATED                                  0     1
  SLC7A6 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  SLC7A6 MUTATED                           0     5
  SLC7A6 WILD-TYPE                        22   221
D406V13, multiclass
                                  clus
vv                                 SLC7A6 MUTATED SLC7A6 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         5              221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(407) Variable = JMJD1C MUTATION ANALYSIS
D407V1, survival
                  sevent
clus2                0   1
  JMJD1C MUTATED    23   3
  JMJD1C WILD-TYPE 355  90
  JMJD1C MUTATED JMJD1C WILD-TYPE 
              26              445 
  JMJD1C MUTATED JMJD1C WILD-TYPE 
               3               90 
$`JMJD1C MUTATED`
TCGA-A6-6781 TCGA-AA-3510 TCGA-AA-3672 TCGA-AA-3866 TCGA-AA-3949 TCGA-AA-3977 
       19.66        63.98         0.92        17.03        26.01        25.02 
TCGA-AA-A010 TCGA-AA-A01K TCGA-AD-6964 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       34.98        31.00        10.88        21.44        17.82        58.39 
TCGA-CA-6717 TCGA-CK-4952 TCGA-CM-4744 TCGA-CM-6169 TCGA-CM-6674 TCGA-CM-6678 
       12.76        15.62        20.02        13.02        12.95        11.01 
TCGA-D5-6538 TCGA-D5-6541 TCGA-D5-6928 TCGA-G4-6293 TCGA-G4-6323 TCGA-AG-3883 
       17.13        15.58        11.64       133.18        13.78         1.02 
TCGA-DY-A1DC TCGA-DY-A1DG 
       41.36        51.48 

$`JMJD1C WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
       54.02         2.01        14.01        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3867 TCGA-AA-3869 
       31.07        31.07        30.05        53.00        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       33.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       12.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07        12.20        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
      148.01        85.45        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-4747 
       82.95         1.91       124.27        23.05        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6676 
       12.99        15.02        14.04        11.01        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.08        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6898 
       15.12        17.85         4.80        12.49        16.14         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6303 
       13.25         0.53        47.41        35.31        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3885 
       32.98         0.99         0.99        19.04        19.99        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 
        5.29       126.44        57.24        24.13        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  JMJD1C MUTATED JMJD1C WILD-TYPE 
            0.92             0.00 
  JMJD1C MUTATED JMJD1C WILD-TYPE 
          133.18           148.01 
  JMJD1C MUTATED JMJD1C WILD-TYPE 
          17.475           20.910 
[1] "0.9 - 133.2 (17.5)" "0.0 - 148.0 (20.9)"
[1] "hr=" "1.8"
D407V2, continuous
D407V3, binary
                  cls
clus                 0   1
  JMJD1C MUTATED    24   3
  JMJD1C WILD-TYPE 342 116
[1] "tbl2"
                  cls
clus               [,1] [,2]
  JMJD1C MUTATED     24    3
  JMJD1C WILD-TYPE  342  116
        clus
vv       JMJD1C MUTATED JMJD1C WILD-TYPE
  COLON              24              342
  RECTUM              3              116
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  JMJD1C MUTATED         3        1        1         9         1         0
  JMJD1C WILD-TYPE      88        0       31       129         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  JMJD1C MUTATED           2          0          3          3        0
  JMJD1C WILD-TYPE        22         11         56         39       48
                  vv
clus               STAGE IVA STAGE IVB
  JMJD1C MUTATED           2         0
  JMJD1C WILD-TYPE        16         1
D407V4, multiclass
            clus
vv           JMJD1C MUTATED JMJD1C WILD-TYPE
  STAGE I                 3               88
  STAGE IA                1                0
  STAGE II                1               31
  STAGE IIA               9              129
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               2               22
  STAGE IIIA              0               11
  STAGE IIIB              3               56
  STAGE IIIC              3               39
  STAGE IV                0               48
  STAGE IVA               2               16
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  JMJD1C MUTATED     0   4  17   5
  JMJD1C WILD-TYPE  17  88 312  45
D407V5, multiclass
    clus
vv   JMJD1C MUTATED JMJD1C WILD-TYPE
  T1              0               17
  T2              4               88
  T3             17              312
  T4              5               45
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  JMJD1C MUTATED    16   7   4
  JMJD1C WILD-TYPE 271 106  83
D407V6, multiclass
    clus
vv   JMJD1C MUTATED JMJD1C WILD-TYPE
  N0             16              271
  N1              7              106
  N2              4               83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D407V7, binary
                  cls
clus                 0   1
  JMJD1C MUTATED    20   2
  JMJD1C WILD-TYPE 355  63
[1] "tbl2"
                  cls
clus               [,1] [,2]
  JMJD1C MUTATED     20    2
  JMJD1C WILD-TYPE  355   63
   clus
vv  JMJD1C MUTATED JMJD1C WILD-TYPE
  0             20              355
  1              2               63
[1] 2 2
[1] FALSE
D407V8, binary
                  cls
clus                 0   1
  JMJD1C MUTATED    12  15
  JMJD1C WILD-TYPE 213 249
[1] "tbl2"
                  cls
clus               [,1] [,2]
  JMJD1C MUTATED     12   15
  JMJD1C WILD-TYPE  213  249
        clus
vv       JMJD1C MUTATED JMJD1C WILD-TYPE
  FEMALE             12              213
  MALE               15              249
[1] 2 2
[1] FALSE
D407V9, binary
                  cls
clus                 0   1
  JMJD1C MUTATED    22   0
  JMJD1C WILD-TYPE 328  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  JMJD1C MUTATED     22    0
  JMJD1C WILD-TYPE  328   22
     clus
vv    JMJD1C MUTATED JMJD1C WILD-TYPE
  NO              22              328
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  JMJD1C MUTATED                     19                             5
  JMJD1C WILD-TYPE                  296                            42
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  JMJD1C MUTATED                       3                              0
  JMJD1C WILD-TYPE                   103                             10
D407V10, multiclass
                                clus
vv                               JMJD1C MUTATED JMJD1C WILD-TYPE
  COLON ADENOCARCINOMA                       19              296
  COLON MUCINOUS ADENOCARCINOMA               5               42
  RECTAL ADENOCARCINOMA                       3              103
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  JMJD1C MUTATED    21   0   0   2
  JMJD1C WILD-TYPE 324   4  31  23
D407V11, multiclass
    clus
vv   JMJD1C MUTATED JMJD1C WILD-TYPE
  R0             21              324
  R1              0                4
  R2              0               31
  RX              2               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D407V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  JMJD1C MUTATED                                  0     1
  JMJD1C WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  JMJD1C MUTATED                           3    14
  JMJD1C WILD-TYPE                        19   212
D407V13, multiclass
                                  clus
vv                                 JMJD1C MUTATED JMJD1C WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     3               19
  WHITE                                        14              212
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(408) Variable = C6ORF170 MUTATION ANALYSIS
D408V1, survival
                    sevent
clus2                  0   1
  C6ORF170 MUTATED    17   5
  C6ORF170 WILD-TYPE 361  88
  C6ORF170 MUTATED C6ORF170 WILD-TYPE 
                22                449 
  C6ORF170 MUTATED C6ORF170 WILD-TYPE 
                 5                 88 
$`C6ORF170 MUTATED`
TCGA-A6-6142 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3977 
       25.08        63.98         6.97        26.99        19.04        25.02 
TCGA-AA-A010 TCGA-AD-6901 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-CA-6717 TCGA-CA-6718 
       34.98        22.42        58.39        49.41        12.76        10.06 
TCGA-CM-5864 TCGA-CM-6162 TCGA-D5-6898 TCGA-DM-A28F TCGA-F4-6704 TCGA-AF-2693 
       15.02        12.00         1.48        35.97         1.55        19.10 
TCGA-AG-3885 TCGA-AG-A002 TCGA-DT-5265 TCGA-EI-6508 
       17.95        20.98         5.29        20.91 

$`C6ORF170 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
       35.01         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       85.05        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6963 
       15.52        56.55         0.79         0.72         5.79        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       33.01        21.44        17.82         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        88.21         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 
        3.06         3.25         3.29         0.07        12.20        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       17.03        15.02         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 
        4.80        17.13        12.49        16.14        15.58         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H 
      139.17         6.12        81.37       119.93        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 
       79.69        24.13        39.48        43.04        13.55        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 
        0.99         0.99        19.04        19.99         1.02        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC 
       19.99         5.95         4.01         5.03       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       19.96        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  C6ORF170 MUTATED C6ORF170 WILD-TYPE 
              1.48               0.00 
  C6ORF170 MUTATED C6ORF170 WILD-TYPE 
             63.98             148.01 
  C6ORF170 MUTATED C6ORF170 WILD-TYPE 
            20.005             20.190 
[1] "1.5 - 64.0 (20.0)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.3"
D408V2, continuous
D408V3, binary
                    cls
clus                   0   1
  C6ORF170 MUTATED    18   4
  C6ORF170 WILD-TYPE 348 115
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C6ORF170 MUTATED     18    4
  C6ORF170 WILD-TYPE  348  115
        clus
vv       C6ORF170 MUTATED C6ORF170 WILD-TYPE
  COLON                18                348
  RECTUM                4                115
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  C6ORF170 MUTATED         4        0        5         5         1         0
  C6ORF170 WILD-TYPE      87        1       27       133         9         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C6ORF170 MUTATED           0          0          4          1        0
  C6ORF170 WILD-TYPE        24         11         55         41       48
                    vv
clus                 STAGE IVA STAGE IVB
  C6ORF170 MUTATED           1         0
  C6ORF170 WILD-TYPE        17         1
D408V4, multiclass
            clus
vv           C6ORF170 MUTATED C6ORF170 WILD-TYPE
  STAGE I                   4                 87
  STAGE IA                  0                  1
  STAGE II                  5                 27
  STAGE IIA                 5                133
  STAGE IIB                 1                  9
  STAGE IIC                 0                  1
  STAGE III                 0                 24
  STAGE IIIA                0                 11
  STAGE IIIB                4                 55
  STAGE IIIC                1                 41
  STAGE IV                  0                 48
  STAGE IVA                 1                 17
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  C6ORF170 MUTATED     0   5  16   2
  C6ORF170 WILD-TYPE  17  87 313  48
D408V5, multiclass
    clus
vv   C6ORF170 MUTATED C6ORF170 WILD-TYPE
  T1                0                 17
  T2                5                 87
  T3               16                313
  T4                2                 48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  C6ORF170 MUTATED    17   5   1
  C6ORF170 WILD-TYPE 270 108  86
D408V6, multiclass
    clus
vv   C6ORF170 MUTATED C6ORF170 WILD-TYPE
  N0               17                270
  N1                5                108
  N2                1                 86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D408V7, binary
                    cls
clus                   0   1
  C6ORF170 MUTATED    17   1
  C6ORF170 WILD-TYPE 358  64
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C6ORF170 MUTATED     17    1
  C6ORF170 WILD-TYPE  358   64
   clus
vv  C6ORF170 MUTATED C6ORF170 WILD-TYPE
  0               17                358
  1                1                 64
[1] 2 2
[1] FALSE
D408V8, binary
                    cls
clus                   0   1
  C6ORF170 MUTATED     9  14
  C6ORF170 WILD-TYPE 216 250
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C6ORF170 MUTATED      9   14
  C6ORF170 WILD-TYPE  216  250
        clus
vv       C6ORF170 MUTATED C6ORF170 WILD-TYPE
  FEMALE                9                216
  MALE                 14                250
[1] 2 2
[1] FALSE
D408V9, binary
                    cls
clus                   0   1
  C6ORF170 MUTATED    18   1
  C6ORF170 WILD-TYPE 332  21
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C6ORF170 MUTATED     18    1
  C6ORF170 WILD-TYPE  332   21
     clus
vv    C6ORF170 MUTATED C6ORF170 WILD-TYPE
  NO                18                332
  YES                1                 21
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  C6ORF170 MUTATED                     15                             3
  C6ORF170 WILD-TYPE                  300                            44
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  C6ORF170 MUTATED                       3                              1
  C6ORF170 WILD-TYPE                   103                              9
D408V10, multiclass
                                clus
vv                               C6ORF170 MUTATED C6ORF170 WILD-TYPE
  COLON ADENOCARCINOMA                         15                300
  COLON MUCINOUS ADENOCARCINOMA                 3                 44
  RECTAL ADENOCARCINOMA                         3                103
  RECTAL MUCINOUS ADENOCARCINOMA                1                  9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  C6ORF170 MUTATED    14   0   0   3
  C6ORF170 WILD-TYPE 331   4  31  22
D408V11, multiclass
    clus
vv   C6ORF170 MUTATED C6ORF170 WILD-TYPE
  R0               14                331
  R1                0                  4
  R2                0                 31
  RX                3                 22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D408V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C6ORF170 MUTATED                                  1     3
  C6ORF170 WILD-TYPE                                0     8
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  C6ORF170 MUTATED                           0    10
  C6ORF170 WILD-TYPE                        22   216
D408V13, multiclass
                                  clus
vv                                 C6ORF170 MUTATED C6ORF170 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                           3                  8
  BLACK OR AFRICAN AMERICAN                       0                 22
  WHITE                                          10                216
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(409) Variable = MSH2 MUTATION ANALYSIS
D409V1, survival
                sevent
clus2              0   1
  MSH2 MUTATED    29   7
  MSH2 WILD-TYPE 349  86
  MSH2 MUTATED MSH2 WILD-TYPE 
            36            435 
  MSH2 MUTATED MSH2 WILD-TYPE 
             7             86 
$`MSH2 MUTATED`
TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3968 TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A010 
        3.02         1.02        21.99        25.02         4.01        34.98 
TCGA-AD-6889 TCGA-AD-6895 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-6197 TCGA-AY-6386 
       56.55         0.72        14.50        27.09        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4681 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       58.39       106.75        49.41         6.77        12.10       100.01 
TCGA-AZ-6605 TCGA-CA-6717 TCGA-CK-5914 TCGA-CM-4746 TCGA-CM-5348 TCGA-CM-6162 
        5.23        12.76         9.99        37.02        22.98        12.00 
TCGA-CM-6172 TCGA-CM-6674 TCGA-D5-6930 TCGA-DM-A1HB TCGA-DM-A28H TCGA-F4-6806 
       11.01        12.95         1.51       135.65       117.07        41.42 
TCGA-G4-6307 TCGA-G4-6315 TCGA-AF-2687 TCGA-AG-3892 TCGA-AG-A002 TCGA-EF-5830 
       55.04        61.91        24.13        13.02        20.98         0.49 

$`MSH2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3502 
       23.87        20.12        19.66        20.28         7.04        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       20.98        34.03         2.01        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       21.37        15.52         0.79         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AZ-4323 
       10.88         0.20        16.31         0.95        33.01         1.41 
TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6603 TCGA-AZ-6606 
        5.13        22.36        62.79        88.21        29.56        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07        12.20        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 
       85.45        15.62        49.08        51.32        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4752 
        1.91       124.27        23.05        20.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       29.06        22.03        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 
       15.02        15.02        17.03        15.02         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       14.04        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       11.64         4.80        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 
       12.59       140.38         7.50        44.32       131.51       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28K 
        6.12        81.37       119.93        35.97        60.79        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       34.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       85.48        63.62        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2689 TCGA-AF-2691 
       26.17        91.79        46.75        79.69        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 
       19.99         1.02        17.95        36.95        17.03        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       51.48        32.61        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  MSH2 MUTATED MSH2 WILD-TYPE 
          0.49           0.00 
  MSH2 MUTATED MSH2 WILD-TYPE 
        135.65         148.01 
  MSH2 MUTATED MSH2 WILD-TYPE 
         21.21          20.12 
[1] "0.5 - 135.7 (21.2)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.2"
D409V2, continuous
D409V3, binary
                cls
clus               0   1
  MSH2 MUTATED    33   4
  MSH2 WILD-TYPE 333 115
[1] "tbl2"
                cls
clus             [,1] [,2]
  MSH2 MUTATED     33    4
  MSH2 WILD-TYPE  333  115
        clus
vv       MSH2 MUTATED MSH2 WILD-TYPE
  COLON            33            333
  RECTUM            4            115
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MSH2 MUTATED         7        0        4         8         3         0
  MSH2 WILD-TYPE      84        1       28       130         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MSH2 MUTATED           1          0          8          2        2         0
  MSH2 WILD-TYPE        23         11         51         40       46        18
                vv
clus             STAGE IVB
  MSH2 MUTATED           0
  MSH2 WILD-TYPE         1
D409V4, multiclass
            clus
vv           MSH2 MUTATED MSH2 WILD-TYPE
  STAGE I               7             84
  STAGE IA              0              1
  STAGE II              4             28
  STAGE IIA             8            130
  STAGE IIB             3              7
  STAGE IIC             0              1
  STAGE III             1             23
  STAGE IIIA            0             11
  STAGE IIIB            8             51
  STAGE IIIC            2             40
  STAGE IV              2             46
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  MSH2 MUTATED     1   7  24   5
  MSH2 WILD-TYPE  16  85 305  45
D409V5, multiclass
    clus
vv   MSH2 MUTATED MSH2 WILD-TYPE
  T1            1             16
  T2            7             85
  T3           24            305
  T4            5             45
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  MSH2 MUTATED    23  11   3
  MSH2 WILD-TYPE 264 102  84
D409V6, multiclass
    clus
vv   MSH2 MUTATED MSH2 WILD-TYPE
  N0           23            264
  N1           11            102
  N2            3             84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D409V7, binary
                cls
clus               0   1
  MSH2 MUTATED    29   2
  MSH2 WILD-TYPE 346  63
[1] "tbl2"
                cls
clus             [,1] [,2]
  MSH2 MUTATED     29    2
  MSH2 WILD-TYPE  346   63
   clus
vv  MSH2 MUTATED MSH2 WILD-TYPE
  0           29            346
  1            2             63
[1] 2 2
[1] FALSE
D409V8, binary
                cls
clus               0   1
  MSH2 MUTATED    14  23
  MSH2 WILD-TYPE 211 241
[1] "tbl2"
                cls
clus             [,1] [,2]
  MSH2 MUTATED     14   23
  MSH2 WILD-TYPE  211  241
        clus
vv       MSH2 MUTATED MSH2 WILD-TYPE
  FEMALE           14            211
  MALE             23            241
[1] 2 2
[1] FALSE
D409V9, binary
                cls
clus               0   1
  MSH2 MUTATED    24   1
  MSH2 WILD-TYPE 326  21
[1] "tbl2"
                cls
clus             [,1] [,2]
  MSH2 MUTATED     24    1
  MSH2 WILD-TYPE  326   21
     clus
vv    MSH2 MUTATED MSH2 WILD-TYPE
  NO            24            326
  YES            1             21
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MSH2 MUTATED                     28                             4
  MSH2 WILD-TYPE                  287                            43
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MSH2 MUTATED                       4                              0
  MSH2 WILD-TYPE                   102                             10
D409V10, multiclass
                                clus
vv                               MSH2 MUTATED MSH2 WILD-TYPE
  COLON ADENOCARCINOMA                     28            287
  COLON MUCINOUS ADENOCARCINOMA             4             43
  RECTAL ADENOCARCINOMA                     4            102
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  MSH2 MUTATED    25   0   0   2
  MSH2 WILD-TYPE 320   4  31  23
D409V11, multiclass
    clus
vv   MSH2 MUTATED MSH2 WILD-TYPE
  R0           25            320
  R1            0              4
  R2            0             31
  RX            2             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D409V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MSH2 MUTATED                                  0     2
  MSH2 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  MSH2 MUTATED                           3    23
  MSH2 WILD-TYPE                        19   203
D409V13, multiclass
                                  clus
vv                                 MSH2 MUTATED MSH2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              9
  BLACK OR AFRICAN AMERICAN                   3             19
  WHITE                                      23            203
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(410) Variable = EP300 MUTATION ANALYSIS
D410V1, survival
                 sevent
clus2               0   1
  EP300 MUTATED    42   3
  EP300 WILD-TYPE 336  90
  EP300 MUTATED EP300 WILD-TYPE 
             45             426 
  EP300 MUTATED EP300 WILD-TYPE 
              3              90 
$`EP300 MUTATED`
TCGA-A6-5659 TCGA-A6-6141 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3554 
       30.44         8.38        24.39        20.12        19.66        17.95 
TCGA-AA-3555 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3715 TCGA-AA-3864 TCGA-AA-3877 
       29.95        61.02         6.05        19.04        53.00        31.00 
TCGA-AA-A00J TCGA-AA-A00N TCGA-AA-A00R TCGA-AA-A010 TCGA-AA-A01G TCGA-AD-6889 
       18.05         4.01         0.99        34.98        12.00        56.55 
TCGA-AU-6004 TCGA-AY-6386 TCGA-CA-5796 TCGA-CA-6717 TCGA-CK-5913 TCGA-CM-4743 
       27.09        17.82         3.25        12.76        51.32        23.05 
TCGA-CM-4752 TCGA-CM-5868 TCGA-CM-6162 TCGA-D5-5540 TCGA-D5-6539 TCGA-D5-6920 
       13.02        17.03        12.00        56.09        12.49         3.68 
TCGA-D5-6931 TCGA-DM-A1D0 TCGA-DM-A1DA TCGA-G4-6323 TCGA-G4-6628 TCGA-AF-2687 
       12.00       130.65         7.50        13.78        79.69        24.13 
TCGA-AG-3732 TCGA-AG-A002 TCGA-CI-6619 TCGA-DC-6682 TCGA-EI-6507 TCGA-EI-6510 
       32.98        20.98         6.05         4.01        19.96        18.28 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

$`EP300 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 
       22.06        32.71        27.09        22.52        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6782 TCGA-AA-3489 
       24.16        21.76        24.69        23.87        20.28         7.04 
TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
        3.02         1.02        35.01        63.98         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
       13.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       36.03         8.05        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3556 TCGA-AA-3558 
       33.99        21.01        13.02        24.00        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       19.99        13.94        19.99        78.08         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       85.05        26.99        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       31.07        30.05        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       18.05         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       38.04        27.02        42.02        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
        1.02        10.98        32.02        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
        0.07        21.37        15.52         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 
       22.42        27.42        10.88         0.20        14.50        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        33.01        21.44        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        1.61        12.69         3.06         3.29         0.07        12.20 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       49.08         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       20.02        37.02        25.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       15.02         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       45.40        12.26        19.59        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       16.14        15.58         1.48         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6932 
        9.04         9.44        11.64         4.80         1.51        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D4 TCGA-DM-A1D6 
       10.26       119.70        24.43        38.20        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       13.32        12.59       140.38        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       61.91        36.00        22.09        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       46.75        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 
       13.94        19.99         7.99         0.99        37.02         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        0.72        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        5.95         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6508 
       24.13        51.48        32.61         0.49        20.55        20.91 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 

  EP300 MUTATED EP300 WILD-TYPE 
           0.69            0.00 
  EP300 MUTATED EP300 WILD-TYPE 
         130.65          148.01 
  EP300 MUTATED EP300 WILD-TYPE 
         19.040          20.945 
[1] "0.7 - 130.7 (19.0)" "0.0 - 148.0 (20.9)"
[1] "hr=" "3.1"
D410V2, continuous
D410V3, binary
                 cls
clus                0   1
  EP300 MUTATED    36  10
  EP300 WILD-TYPE 330 109
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EP300 MUTATED     36   10
  EP300 WILD-TYPE  330  109
        clus
vv       EP300 MUTATED EP300 WILD-TYPE
  COLON             36             330
  RECTUM            10             109
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  EP300 MUTATED         8        1        3        17         2         0
  EP300 WILD-TYPE      83        0       29       121         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  EP300 MUTATED           0          2          4          5        2         2
  EP300 WILD-TYPE        24          9         55         37       46        16
                 vv
clus              STAGE IVB
  EP300 MUTATED           0
  EP300 WILD-TYPE         1
D410V4, multiclass
            clus
vv           EP300 MUTATED EP300 WILD-TYPE
  STAGE I                8              83
  STAGE IA               1               0
  STAGE II               3              29
  STAGE IIA             17             121
  STAGE IIB              2               8
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             2               9
  STAGE IIIB             4              55
  STAGE IIIC             5              37
  STAGE IV               2              46
  STAGE IVA              2              16
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  EP300 MUTATED     2   8  27   8
  EP300 WILD-TYPE  15  84 302  42
D410V5, multiclass
    clus
vv   EP300 MUTATED EP300 WILD-TYPE
  T1             2              15
  T2             8              84
  T3            27             302
  T4             8              42
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  EP300 MUTATED    33   8   5
  EP300 WILD-TYPE 254 105  82
D410V6, multiclass
    clus
vv   EP300 MUTATED EP300 WILD-TYPE
  N0            33             254
  N1             8             105
  N2             5              82
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D410V7, binary
                 cls
clus                0   1
  EP300 MUTATED    36   3
  EP300 WILD-TYPE 339  62
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EP300 MUTATED     36    3
  EP300 WILD-TYPE  339   62
   clus
vv  EP300 MUTATED EP300 WILD-TYPE
  0            36             339
  1             3              62
[1] 2 2
[1] FALSE
D410V8, binary
                 cls
clus                0   1
  EP300 MUTATED    19  27
  EP300 WILD-TYPE 206 237
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EP300 MUTATED     19   27
  EP300 WILD-TYPE  206  237
        clus
vv       EP300 MUTATED EP300 WILD-TYPE
  FEMALE            19             206
  MALE              27             237
[1] 2 2
[1] FALSE
D410V9, binary
                 cls
clus                0   1
  EP300 MUTATED    34   1
  EP300 WILD-TYPE 316  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EP300 MUTATED     34    1
  EP300 WILD-TYPE  316   21
     clus
vv    EP300 MUTATED EP300 WILD-TYPE
  NO             34             316
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  EP300 MUTATED                     26                            10
  EP300 WILD-TYPE                  289                            37
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  EP300 MUTATED                       9                              1
  EP300 WILD-TYPE                    97                              9
D410V10, multiclass
                                clus
vv                               EP300 MUTATED EP300 WILD-TYPE
  COLON ADENOCARCINOMA                      26             289
  COLON MUCINOUS ADENOCARCINOMA             10              37
  RECTAL ADENOCARCINOMA                      9              97
  RECTAL MUCINOUS ADENOCARCINOMA             1               9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  EP300 MUTATED    35   1   1   2
  EP300 WILD-TYPE 310   3  30  23
D410V11, multiclass
    clus
vv   EP300 MUTATED EP300 WILD-TYPE
  R0            35             310
  R1             1               3
  R2             1              30
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D410V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  EP300 MUTATED                                  0     3
  EP300 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  EP300 MUTATED                           4    24
  EP300 WILD-TYPE                        18   202
D410V13, multiclass
                                  clus
vv                                 EP300 MUTATED EP300 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        3               8
  BLACK OR AFRICAN AMERICAN                    4              18
  WHITE                                       24             202
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(411) Variable = SKIL MUTATION ANALYSIS
D411V1, survival
                sevent
clus2              0   1
  SKIL MUTATED     6   3
  SKIL WILD-TYPE 372  90
  SKIL MUTATED SKIL WILD-TYPE 
             9            462 
  SKIL MUTATED SKIL WILD-TYPE 
             3             90 
$`SKIL MUTATED`
TCGA-AA-3663 TCGA-CM-6164 TCGA-CM-6675 TCGA-DM-A1D6 TCGA-DM-A28F TCGA-F4-6856 
        6.97        29.03        13.05        49.91        35.97        35.31 
TCGA-G4-6303 TCGA-AF-6672 TCGA-AG-A002 
       65.85        10.39        20.98 

$`SKIL WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.05        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6165 TCGA-CM-6166 
       17.03        15.02        12.00         2.96        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       12.95        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D7 TCGA-DM-A1D8 
       24.43        38.20       130.65        92.75        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
        6.12        81.37       119.93        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
       47.41       133.18        74.56        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AG-3574 TCGA-AG-3575 
       14.50        16.83        15.39        20.02        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  SKIL MUTATED SKIL WILD-TYPE 
          6.97           0.00 
  SKIL MUTATED SKIL WILD-TYPE 
         65.85         148.01 
  SKIL MUTATED SKIL WILD-TYPE 
        29.030         20.085 
[1] "7.0 - 65.8 (29.0)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.5"
D411V2, continuous
D411V3, binary
                cls
clus               0   1
  SKIL MUTATED     7   2
  SKIL WILD-TYPE 359 117
[1] "tbl2"
                cls
clus             [,1] [,2]
  SKIL MUTATED      7    2
  SKIL WILD-TYPE  359  117
        clus
vv       SKIL MUTATED SKIL WILD-TYPE
  COLON             7            359
  RECTUM            2            117
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SKIL MUTATED         2        0        1         2         0         0
  SKIL WILD-TYPE      89        1       31       136        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SKIL MUTATED           0          0          1          0        2         0
  SKIL WILD-TYPE        24         11         58         42       46        18
                vv
clus             STAGE IVB
  SKIL MUTATED           1
  SKIL WILD-TYPE         0
D411V4, multiclass
            clus
vv           SKIL MUTATED SKIL WILD-TYPE
  STAGE I               2             89
  STAGE IA              0              1
  STAGE II              1             31
  STAGE IIA             2            136
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            1             58
  STAGE IIIC            0             42
  STAGE IV              2             46
  STAGE IVA             0             18
  STAGE IVB             1              0
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  SKIL MUTATED     0   2   6   1
  SKIL WILD-TYPE  17  90 323  49
D411V5, multiclass
    clus
vv   SKIL MUTATED SKIL WILD-TYPE
  T1            0             17
  T2            2             90
  T3            6            323
  T4            1             49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  SKIL MUTATED     5   2   2
  SKIL WILD-TYPE 282 111  85
D411V6, multiclass
    clus
vv   SKIL MUTATED SKIL WILD-TYPE
  N0            5            282
  N1            2            111
  N2            2             85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D411V7, binary
                cls
clus               0   1
  SKIL MUTATED     6   2
  SKIL WILD-TYPE 369  63
[1] "tbl2"
                cls
clus             [,1] [,2]
  SKIL MUTATED      6    2
  SKIL WILD-TYPE  369   63
   clus
vv  SKIL MUTATED SKIL WILD-TYPE
  0            6            369
  1            2             63
[1] 2 2
[1] FALSE
D411V8, binary
                cls
clus               0   1
  SKIL MUTATED     2   7
  SKIL WILD-TYPE 223 257
[1] "tbl2"
                cls
clus             [,1] [,2]
  SKIL MUTATED      2    7
  SKIL WILD-TYPE  223  257
        clus
vv       SKIL MUTATED SKIL WILD-TYPE
  FEMALE            2            223
  MALE              7            257
[1] 2 2
[1] FALSE
D411V9, binary
                cls
clus               0   1
  SKIL MUTATED     6   1
  SKIL WILD-TYPE 344  21
[1] "tbl2"
                cls
clus             [,1] [,2]
  SKIL MUTATED      6    1
  SKIL WILD-TYPE  344   21
     clus
vv    SKIL MUTATED SKIL WILD-TYPE
  NO             6            344
  YES            1             21
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SKIL MUTATED                      5                             2
  SKIL WILD-TYPE                  310                            45
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SKIL MUTATED                       2                              0
  SKIL WILD-TYPE                   104                             10
D411V10, multiclass
                                clus
vv                               SKIL MUTATED SKIL WILD-TYPE
  COLON ADENOCARCINOMA                      5            310
  COLON MUCINOUS ADENOCARCINOMA             2             45
  RECTAL ADENOCARCINOMA                     2            104
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  SKIL MUTATED     6   0   0   0
  SKIL WILD-TYPE 339   4  31  25
D411V11, multiclass
    clus
vv   SKIL MUTATED SKIL WILD-TYPE
  R0            6            339
  R1            0              4
  R2            0             31
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D411V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SKIL MUTATED                                  0     0
  SKIL WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  SKIL MUTATED                           1     6
  SKIL WILD-TYPE                        21   220
D411V13, multiclass
                                  clus
vv                                 SKIL MUTATED SKIL WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                       6            220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(412) Variable = TIAL1 MUTATION ANALYSIS
D412V1, survival
                 sevent
clus2               0   1
  TIAL1 MUTATED     8   4
  TIAL1 WILD-TYPE 370  89
  TIAL1 MUTATED TIAL1 WILD-TYPE 
             12             459 
  TIAL1 MUTATED TIAL1 WILD-TYPE 
              4              89 
$`TIAL1 MUTATED`
TCGA-AA-3663 TCGA-AA-3715 TCGA-AA-3864 TCGA-AA-A00J TCGA-AZ-6599 TCGA-CA-6718 
        6.97        19.04        53.00        18.05         6.77        10.06 
TCGA-CM-5862 TCGA-CM-6675 TCGA-D5-6920 TCGA-D5-6928 TCGA-DM-A1HB TCGA-AG-3892 
        5.03        13.05         3.68        11.64       135.65        13.02 

$`TIAL1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.05        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 
       36.00         5.03        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 
        0.99        31.07        31.07        30.05        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        88.21        49.41        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 
        3.25         3.29         0.07        12.20        12.76        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5864 
       22.98        30.08        32.02        15.02        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       11.01        12.95        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 
        4.41        12.43        14.30         9.04         9.44         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 
      140.38         7.50        44.32       131.51       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       17.95        36.95        17.03        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  TIAL1 MUTATED TIAL1 WILD-TYPE 
           3.68            0.00 
  TIAL1 MUTATED TIAL1 WILD-TYPE 
         135.65          148.01 
  TIAL1 MUTATED TIAL1 WILD-TYPE 
          12.33           20.98 
[1] "3.7 - 135.7 (12.3)" "0.0 - 148.0 (21.0)"
[1] "hr=" "1.9"
D412V2, continuous
D412V3, binary
                 cls
clus                0   1
  TIAL1 MUTATED    12   1
  TIAL1 WILD-TYPE 354 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TIAL1 MUTATED     12    1
  TIAL1 WILD-TYPE  354  118
        clus
vv       TIAL1 MUTATED TIAL1 WILD-TYPE
  COLON             12             354
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TIAL1 MUTATED         2        0        3         3         1         0
  TIAL1 WILD-TYPE      89        1       29       135         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TIAL1 MUTATED           0          0          2          0        0         1
  TIAL1 WILD-TYPE        24         11         57         42       48        17
                 vv
clus              STAGE IVB
  TIAL1 MUTATED           1
  TIAL1 WILD-TYPE         0
D412V4, multiclass
            clus
vv           TIAL1 MUTATED TIAL1 WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               3              29
  STAGE IIA              3             135
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             2              57
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              1              17
  STAGE IVB              1               0
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  TIAL1 MUTATED     1   1   9   2
  TIAL1 WILD-TYPE  16  91 320  48
D412V5, multiclass
    clus
vv   TIAL1 MUTATED TIAL1 WILD-TYPE
  T1             1              16
  T2             1              91
  T3             9             320
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  TIAL1 MUTATED     9   3   1
  TIAL1 WILD-TYPE 278 110  86
D412V6, multiclass
    clus
vv   TIAL1 MUTATED TIAL1 WILD-TYPE
  N0             9             278
  N1             3             110
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D412V7, binary
                 cls
clus                0   1
  TIAL1 MUTATED     9   2
  TIAL1 WILD-TYPE 366  63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TIAL1 MUTATED      9    2
  TIAL1 WILD-TYPE  366   63
   clus
vv  TIAL1 MUTATED TIAL1 WILD-TYPE
  0             9             366
  1             2              63
[1] 2 2
[1] FALSE
D412V8, binary
                 cls
clus                0   1
  TIAL1 MUTATED     3  10
  TIAL1 WILD-TYPE 222 254
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TIAL1 MUTATED      3   10
  TIAL1 WILD-TYPE  222  254
        clus
vv       TIAL1 MUTATED TIAL1 WILD-TYPE
  FEMALE             3             222
  MALE              10             254
[1] 2 2
[1] FALSE
D412V9, binary
                 cls
clus                0   1
  TIAL1 MUTATED    10   0
  TIAL1 WILD-TYPE 340  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TIAL1 MUTATED     10    0
  TIAL1 WILD-TYPE  340   22
     clus
vv    TIAL1 MUTATED TIAL1 WILD-TYPE
  NO             10             340
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  TIAL1 MUTATED                      9                             2
  TIAL1 WILD-TYPE                  306                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  TIAL1 MUTATED                       1                              0
  TIAL1 WILD-TYPE                   105                             10
D412V10, multiclass
                                clus
vv                               TIAL1 MUTATED TIAL1 WILD-TYPE
  COLON ADENOCARCINOMA                       9             306
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  TIAL1 MUTATED     9   0   0   2
  TIAL1 WILD-TYPE 336   4  31  23
D412V11, multiclass
    clus
vv   TIAL1 MUTATED TIAL1 WILD-TYPE
  R0             9             336
  R1             0               4
  R2             0              31
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D412V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TIAL1 MUTATED                                  0     1
  TIAL1 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  TIAL1 MUTATED                           1     6
  TIAL1 WILD-TYPE                        21   220
D412V13, multiclass
                                  clus
vv                                 TIAL1 MUTATED TIAL1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        6             220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(413) Variable = OR2T33 MUTATION ANALYSIS
D413V1, survival
                  sevent
clus2                0   1
  OR2T33 MUTATED    13   4
  OR2T33 WILD-TYPE 365  89
  OR2T33 MUTATED OR2T33 WILD-TYPE 
              17              454 
  OR2T33 MUTATED OR2T33 WILD-TYPE 
               4               89 
$`OR2T33 MUTATED`
TCGA-A6-6780 TCGA-AA-3492 TCGA-AA-3662 TCGA-AA-3715 TCGA-AA-3977 TCGA-AA-A010 
       20.12         3.02         6.05        19.04        25.02        34.98 
TCGA-AA-A03J TCGA-AZ-4315 TCGA-AZ-6600 TCGA-CA-6717 TCGA-CM-5349 TCGA-CM-6168 
       40.96        58.39        12.10        12.76        30.08        12.99 
TCGA-D5-6532 TCGA-DM-A1DB TCGA-G4-6625 TCGA-AG-3892 TCGA-F5-6811 
       18.25        44.32        91.79        13.02        32.19 

$`OR2T33 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 
       23.87        19.66        20.28         7.04         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       85.05        26.99        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6548 
        0.92        41.00        39.98        18.05         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        33.01        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       29.06        22.03        22.98        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6169 TCGA-CM-6170 
       29.03        16.04        21.99        14.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       56.09        55.92        20.19         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HA 
       49.91        13.32        12.59       140.38         7.50       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       26.17        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 
       19.99         1.02        17.95        36.95        17.03        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  OR2T33 MUTATED OR2T33 WILD-TYPE 
            3.02             0.00 
  OR2T33 MUTATED OR2T33 WILD-TYPE 
           91.79           148.01 
  OR2T33 MUTATED OR2T33 WILD-TYPE 
          20.120           20.235 
[1] "3.0 - 91.8 (20.1)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.1"
D413V2, continuous
D413V3, binary
                  cls
clus                 0   1
  OR2T33 MUTATED    16   2
  OR2T33 WILD-TYPE 350 117
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR2T33 MUTATED     16    2
  OR2T33 WILD-TYPE  350  117
        clus
vv       OR2T33 MUTATED OR2T33 WILD-TYPE
  COLON              16              350
  RECTUM              2              117
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  OR2T33 MUTATED         2        0        2        10         1         0
  OR2T33 WILD-TYPE      89        1       30       128         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  OR2T33 MUTATED           0          0          0          0        2
  OR2T33 WILD-TYPE        24         11         59         42       46
                  vv
clus               STAGE IVA STAGE IVB
  OR2T33 MUTATED           0         0
  OR2T33 WILD-TYPE        18         1
D413V4, multiclass
            clus
vv           OR2T33 MUTATED OR2T33 WILD-TYPE
  STAGE I                 2               89
  STAGE IA                0                1
  STAGE II                2               30
  STAGE IIA              10              128
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              0               59
  STAGE IIIC              0               42
  STAGE IV                2               46
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  OR2T33 MUTATED     1   2  12   3
  OR2T33 WILD-TYPE  16  90 317  47
D413V5, multiclass
    clus
vv   OR2T33 MUTATED OR2T33 WILD-TYPE
  T1              1               16
  T2              2               90
  T3             12              317
  T4              3               47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  OR2T33 MUTATED    16   1   1
  OR2T33 WILD-TYPE 271 112  86
D413V6, multiclass
    clus
vv   OR2T33 MUTATED OR2T33 WILD-TYPE
  N0             16              271
  N1              1              112
  N2              1               86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D413V7, binary
                  cls
clus                 0   1
  OR2T33 MUTATED    14   2
  OR2T33 WILD-TYPE 361  63
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR2T33 MUTATED     14    2
  OR2T33 WILD-TYPE  361   63
   clus
vv  OR2T33 MUTATED OR2T33 WILD-TYPE
  0             14              361
  1              2               63
[1] 2 2
[1] FALSE
D413V8, binary
                  cls
clus                 0   1
  OR2T33 MUTATED    10   8
  OR2T33 WILD-TYPE 215 256
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR2T33 MUTATED     10    8
  OR2T33 WILD-TYPE  215  256
        clus
vv       OR2T33 MUTATED OR2T33 WILD-TYPE
  FEMALE             10              215
  MALE                8              256
[1] 2 2
[1] FALSE
D413V9, binary
                  cls
clus                 0   1
  OR2T33 MUTATED    15   0
  OR2T33 WILD-TYPE 335  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR2T33 MUTATED     15    0
  OR2T33 WILD-TYPE  335   22
     clus
vv    OR2T33 MUTATED OR2T33 WILD-TYPE
  NO              15              335
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  OR2T33 MUTATED                     14                             2
  OR2T33 WILD-TYPE                  301                            45
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  OR2T33 MUTATED                       2                              0
  OR2T33 WILD-TYPE                   104                             10
D413V10, multiclass
                                clus
vv                               OR2T33 MUTATED OR2T33 WILD-TYPE
  COLON ADENOCARCINOMA                       14              301
  COLON MUCINOUS ADENOCARCINOMA               2               45
  RECTAL ADENOCARCINOMA                       2              104
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  OR2T33 MUTATED    11   0   1   1
  OR2T33 WILD-TYPE 334   4  30  24
D413V11, multiclass
    clus
vv   OR2T33 MUTATED OR2T33 WILD-TYPE
  R0             11              334
  R1              0                4
  R2              1               30
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D413V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OR2T33 MUTATED                                  0     1
  OR2T33 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  OR2T33 MUTATED                           2     7
  OR2T33 WILD-TYPE                        20   219
D413V13, multiclass
                                  clus
vv                                 OR2T33 MUTATED OR2T33 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     2               20
  WHITE                                         7              219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(414) Variable = SMC2 MUTATION ANALYSIS
D414V1, survival
                sevent
clus2              0   1
  SMC2 MUTATED    19   9
  SMC2 WILD-TYPE 359  84
  SMC2 MUTATED SMC2 WILD-TYPE 
            28            443 
  SMC2 MUTATED SMC2 WILD-TYPE 
             9             84 
$`SMC2 MUTATED`
TCGA-AA-3492 TCGA-AA-3819 TCGA-AA-3979 TCGA-AA-A01Z TCGA-AD-6889 TCGA-AD-6890 
        3.02        25.02        24.00        37.02        56.55         0.79 
TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-6598 TCGA-CA-6716 TCGA-CA-6717 
       33.01        17.82         1.41        49.41        12.20        12.76 
TCGA-CM-4743 TCGA-CM-5862 TCGA-CM-6168 TCGA-D5-6533 TCGA-D5-6537 TCGA-D5-6540 
       23.05         5.03        12.99         1.32         4.80        16.14 
TCGA-D5-6920 TCGA-DM-A1D6 TCGA-DM-A28F TCGA-F4-6570 TCGA-G4-6293 TCGA-G4-6626 
        3.68        49.91        35.97         6.18       133.18        46.75 
TCGA-AG-3892 TCGA-AG-A002 TCGA-CI-6624 TCGA-DC-5869 
       13.02        20.98         4.73         5.03 

$`SMC2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3821 TCGA-AA-3831 
       10.06        35.05        33.04         0.99         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        25.02        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       35.01        26.01        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6899 
       40.96         0.07        21.37        15.52         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-4616 TCGA-AZ-4681 
       16.31         0.95        21.44        58.39         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        88.21         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6718 TCGA-CA-6719 
        3.06         3.25         3.29         0.07        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 
        9.99        21.14        82.95         1.91       124.27        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       30.08        32.02        15.02        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       14.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6539 
       18.25        43.27        15.12        17.85        17.13        12.49 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
       15.58         1.48         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G 
      135.65       139.17         6.12        81.37       119.93        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 
      117.07        98.24         8.61        31.96        35.74        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
        0.53        47.41        35.31        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 
       22.09        13.78        35.80        26.17        91.79        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       36.95        17.03        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CL-5917 TCGA-CL-5918 
        0.72         6.05        33.17         6.97        78.12         7.17 
TCGA-DC-5337 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
       15.02        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  SMC2 MUTATED SMC2 WILD-TYPE 
          0.79           0.00 
  SMC2 MUTATED SMC2 WILD-TYPE 
        133.18         148.01 
  SMC2 MUTATED SMC2 WILD-TYPE 
         14.58          20.55 
[1] "0.8 - 133.2 (14.6)" "0.0 - 148.0 (20.6)"
[1] "hr=" "1.9"
D414V2, continuous
D414V3, binary
                cls
clus               0   1
  SMC2 MUTATED    25   4
  SMC2 WILD-TYPE 341 115
[1] "tbl2"
                cls
clus             [,1] [,2]
  SMC2 MUTATED     25    4
  SMC2 WILD-TYPE  341  115
        clus
vv       SMC2 MUTATED SMC2 WILD-TYPE
  COLON            25            341
  RECTUM            4            115
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SMC2 MUTATED         4        0        3        11         1         0
  SMC2 WILD-TYPE      87        1       29       127         9         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SMC2 MUTATED           1          0          5          0        1         2
  SMC2 WILD-TYPE        23         11         54         42       47        16
                vv
clus             STAGE IVB
  SMC2 MUTATED           0
  SMC2 WILD-TYPE         1
D414V4, multiclass
            clus
vv           SMC2 MUTATED SMC2 WILD-TYPE
  STAGE I               4             87
  STAGE IA              0              1
  STAGE II              3             29
  STAGE IIA            11            127
  STAGE IIB             1              9
  STAGE IIC             0              1
  STAGE III             1             23
  STAGE IIIA            0             11
  STAGE IIIB            5             54
  STAGE IIIC            0             42
  STAGE IV              1             47
  STAGE IVA             2             16
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  SMC2 MUTATED     2   3  21   3
  SMC2 WILD-TYPE  15  89 308  47
D414V5, multiclass
    clus
vv   SMC2 MUTATED SMC2 WILD-TYPE
  T1            2             15
  T2            3             89
  T3           21            308
  T4            3             47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  SMC2 MUTATED    21   7   1
  SMC2 WILD-TYPE 266 106  86
D414V6, multiclass
    clus
vv   SMC2 MUTATED SMC2 WILD-TYPE
  N0           21            266
  N1            7            106
  N2            1             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D414V7, binary
                cls
clus               0   1
  SMC2 MUTATED    22   3
  SMC2 WILD-TYPE 353  62
[1] "tbl2"
                cls
clus             [,1] [,2]
  SMC2 MUTATED     22    3
  SMC2 WILD-TYPE  353   62
   clus
vv  SMC2 MUTATED SMC2 WILD-TYPE
  0           22            353
  1            3             62
[1] 2 2
[1] FALSE
D414V8, binary
                cls
clus               0   1
  SMC2 MUTATED    14  15
  SMC2 WILD-TYPE 211 249
[1] "tbl2"
                cls
clus             [,1] [,2]
  SMC2 MUTATED     14   15
  SMC2 WILD-TYPE  211  249
        clus
vv       SMC2 MUTATED SMC2 WILD-TYPE
  FEMALE           14            211
  MALE             15            249
[1] 2 2
[1] FALSE
D414V9, binary
                cls
clus               0   1
  SMC2 MUTATED    20   0
  SMC2 WILD-TYPE 330  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  SMC2 MUTATED     20    0
  SMC2 WILD-TYPE  330   22
     clus
vv    SMC2 MUTATED SMC2 WILD-TYPE
  NO            20            330
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SMC2 MUTATED                     22                             3
  SMC2 WILD-TYPE                  293                            44
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SMC2 MUTATED                       4                              0
  SMC2 WILD-TYPE                   102                             10
D414V10, multiclass
                                clus
vv                               SMC2 MUTATED SMC2 WILD-TYPE
  COLON ADENOCARCINOMA                     22            293
  COLON MUCINOUS ADENOCARCINOMA             3             44
  RECTAL ADENOCARCINOMA                     4            102
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  SMC2 MUTATED    19   0   0   3
  SMC2 WILD-TYPE 326   4  31  22
D414V11, multiclass
    clus
vv   SMC2 MUTATED SMC2 WILD-TYPE
  R0           19            326
  R1            0              4
  R2            0             31
  RX            3             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D414V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SMC2 MUTATED                                  0     3
  SMC2 WILD-TYPE                                1     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  SMC2 MUTATED                           4    16
  SMC2 WILD-TYPE                        18   210
D414V13, multiclass
                                  clus
vv                                 SMC2 MUTATED SMC2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       3              8
  BLACK OR AFRICAN AMERICAN                   4             18
  WHITE                                      16            210
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(415) Variable = C14ORF159 MUTATION ANALYSIS
D415V1, survival
                     sevent
clus2                   0   1
  C14ORF159 MUTATED     8   1
  C14ORF159 WILD-TYPE 370  92
  C14ORF159 MUTATED C14ORF159 WILD-TYPE 
                  9                 462 
  C14ORF159 MUTATED C14ORF159 WILD-TYPE 
                  1                  92 
$`C14ORF159 MUTATED`
TCGA-A6-5660 TCGA-AA-A010 TCGA-AU-3779 TCGA-AZ-6601 TCGA-D5-6927 TCGA-DM-A1D9 
       29.19        34.98        14.50       100.01         9.44       140.38 
TCGA-DM-A1HB TCGA-F4-6808 TCGA-AG-A002 
      135.65        33.67        20.98 

$`C14ORF159 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       10.88         0.20        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       12.43        14.30         9.04        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1DA 
      130.65        92.75        49.91        13.32        12.59         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
       44.32       131.51       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       16.24        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  C14ORF159 MUTATED C14ORF159 WILD-TYPE 
               9.44                0.00 
  C14ORF159 MUTATED C14ORF159 WILD-TYPE 
             140.38              148.01 
  C14ORF159 MUTATED C14ORF159 WILD-TYPE 
             33.670              20.035 
[1] "9.4 - 140.4 (33.7)" "0.0 - 148.0 (20.0)"
[1] "hr=" "3.3"
D415V2, continuous
D415V3, binary
                     cls
clus                    0   1
  C14ORF159 MUTATED     9   1
  C14ORF159 WILD-TYPE 357 118
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  C14ORF159 MUTATED      9    1
  C14ORF159 WILD-TYPE  357  118
        clus
vv       C14ORF159 MUTATED C14ORF159 WILD-TYPE
  COLON                  9                 357
  RECTUM                 1                 118
[1] 2 2
[1] FALSE
                     vv
clus                  STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  C14ORF159 MUTATED         3        0        1         3         1         0
  C14ORF159 WILD-TYPE      88        1       31       135         9         1
                     vv
clus                  STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C14ORF159 MUTATED           0          0          1          1        0
  C14ORF159 WILD-TYPE        24         11         58         41       48
                     vv
clus                  STAGE IVA STAGE IVB
  C14ORF159 MUTATED           0         0
  C14ORF159 WILD-TYPE        18         1
D415V4, multiclass
            clus
vv           C14ORF159 MUTATED C14ORF159 WILD-TYPE
  STAGE I                    3                  88
  STAGE IA                   0                   1
  STAGE II                   1                  31
  STAGE IIA                  3                 135
  STAGE IIB                  1                   9
  STAGE IIC                  0                   1
  STAGE III                  0                  24
  STAGE IIIA                 0                  11
  STAGE IIIB                 1                  58
  STAGE IIIC                 1                  41
  STAGE IV                   0                  48
  STAGE IVA                  0                  18
  STAGE IVB                  0                   1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                   T1  T2  T3  T4
  C14ORF159 MUTATED     1   2   6   1
  C14ORF159 WILD-TYPE  16  90 323  49
D415V5, multiclass
    clus
vv   C14ORF159 MUTATED C14ORF159 WILD-TYPE
  T1                 1                  16
  T2                 2                  90
  T3                 6                 323
  T4                 1                  49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                   N0  N1  N2
  C14ORF159 MUTATED     8   1   1
  C14ORF159 WILD-TYPE 279 112  86
D415V6, multiclass
    clus
vv   C14ORF159 MUTATED C14ORF159 WILD-TYPE
  N0                 8                 279
  N1                 1                 112
  N2                 1                  86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D415V7, binary
                     cls
clus                    0   1
  C14ORF159 MUTATED     9   0
  C14ORF159 WILD-TYPE 366  65
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  C14ORF159 MUTATED      9    0
  C14ORF159 WILD-TYPE  366   65
   clus
vv  C14ORF159 MUTATED C14ORF159 WILD-TYPE
  0                 9                 366
  1                 0                  65
[1] 2 2
[1] FALSE
D415V8, binary
                     cls
clus                    0   1
  C14ORF159 MUTATED     4   6
  C14ORF159 WILD-TYPE 221 258
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  C14ORF159 MUTATED      4    6
  C14ORF159 WILD-TYPE  221  258
        clus
vv       C14ORF159 MUTATED C14ORF159 WILD-TYPE
  FEMALE                 4                 221
  MALE                   6                 258
[1] 2 2
[1] FALSE
D415V9, binary
                     cls
clus                    0   1
  C14ORF159 MUTATED     7   0
  C14ORF159 WILD-TYPE 343  22
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  C14ORF159 MUTATED      7    0
  C14ORF159 WILD-TYPE  343   22
     clus
vv    C14ORF159 MUTATED C14ORF159 WILD-TYPE
  NO                  7                 343
  YES                 0                  22
[1] 2 2
[1] FALSE
                     vv
clus                  COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  C14ORF159 MUTATED                      8                             0
  C14ORF159 WILD-TYPE                  307                            47
                     vv
clus                  RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  C14ORF159 MUTATED                       1                              0
  C14ORF159 WILD-TYPE                   105                             10
D415V10, multiclass
                                clus
vv                               C14ORF159 MUTATED C14ORF159 WILD-TYPE
  COLON ADENOCARCINOMA                           8                 307
  COLON MUCINOUS ADENOCARCINOMA                  0                  47
  RECTAL ADENOCARCINOMA                          1                 105
  RECTAL MUCINOUS ADENOCARCINOMA                 0                  10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                   R0  R1  R2  RX
  C14ORF159 MUTATED     5   0   0   1
  C14ORF159 WILD-TYPE 340   4  31  24
D415V11, multiclass
    clus
vv   C14ORF159 MUTATED C14ORF159 WILD-TYPE
  R0                 5                 340
  R1                 0                   4
  R2                 0                  31
  RX                 1                  24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D415V12, continuous
                     vv
clus                  AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C14ORF159 MUTATED                                  0     0
  C14ORF159 WILD-TYPE                                1    11
                     vv
clus                  BLACK OR AFRICAN AMERICAN WHITE
  C14ORF159 MUTATED                           1     7
  C14ORF159 WILD-TYPE                        21   219
D415V13, multiclass
                                  clus
vv                                 C14ORF159 MUTATED C14ORF159 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                 0                   1
  ASIAN                                            0                  11
  BLACK OR AFRICAN AMERICAN                        1                  21
  WHITE                                            7                 219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(416) Variable = IQGAP2 MUTATION ANALYSIS
D416V1, survival
                  sevent
clus2                0   1
  IQGAP2 MUTATED    19   7
  IQGAP2 WILD-TYPE 359  86
  IQGAP2 MUTATED IQGAP2 WILD-TYPE 
              26              445 
  IQGAP2 MUTATED IQGAP2 WILD-TYPE 
               7               86 
$`IQGAP2 MUTATED`
TCGA-A6-2676 TCGA-AA-3543 TCGA-AA-3549 TCGA-AA-3950 TCGA-AA-3977 TCGA-AA-A00E 
       42.90         0.99        21.01        24.00        25.02        30.02 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AZ-4315 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6606 
       38.04         4.01        58.39        62.79        49.41        11.74 
TCGA-CA-6717 TCGA-CK-5913 TCGA-CM-6169 TCGA-CM-6674 TCGA-D5-6931 TCGA-DM-A1DB 
       12.76        51.32        13.02        12.95        12.00        44.32 
TCGA-F4-6570 TCGA-F4-6703 TCGA-AF-4110 TCGA-AG-3593 TCGA-AG-A002 TCGA-CI-6622 
        6.18        47.87        14.50        34.03        20.98         6.97 
TCGA-DC-6683 TCGA-EI-6507 
        5.03        19.96 

$`IQGAP2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3552 TCGA-AA-3553 
       26.01        12.99        14.01        33.99        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        33.01        26.01         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00J 
       27.02        13.94        38.04        19.00        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       18.05        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       33.01        21.44        17.82         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       22.36        88.21         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07        12.20        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 
      148.01        85.45        15.62        49.08         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6675 
       14.99        12.99        15.02        14.04        11.01        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
        1.51        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
        7.50       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       31.96        35.74         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-5654 
       43.04        13.55        19.10        34.49        10.39        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       46.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DT-5265 
       27.95        10.98        19.99         5.95         4.01         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
        0.49        20.55        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  IQGAP2 MUTATED IQGAP2 WILD-TYPE 
            0.99             0.00 
  IQGAP2 MUTATED IQGAP2 WILD-TYPE 
           62.79           148.01 
  IQGAP2 MUTATED IQGAP2 WILD-TYPE 
          20.995           20.120 
[1] "1.0 - 62.8 (21.0)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.3"
D416V2, continuous
D416V3, binary
                  cls
clus                 0   1
  IQGAP2 MUTATED    21   5
  IQGAP2 WILD-TYPE 345 114
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IQGAP2 MUTATED     21    5
  IQGAP2 WILD-TYPE  345  114
        clus
vv       IQGAP2 MUTATED IQGAP2 WILD-TYPE
  COLON              21              345
  RECTUM              5              114
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  IQGAP2 MUTATED         3        0        2        13         3         0
  IQGAP2 WILD-TYPE      88        1       30       125         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  IQGAP2 MUTATED           0          0          1          1        2
  IQGAP2 WILD-TYPE        24         11         58         41       46
                  vv
clus               STAGE IVA STAGE IVB
  IQGAP2 MUTATED           1         0
  IQGAP2 WILD-TYPE        17         1
D416V4, multiclass
            clus
vv           IQGAP2 MUTATED IQGAP2 WILD-TYPE
  STAGE I                 3               88
  STAGE IA                0                1
  STAGE II                2               30
  STAGE IIA              13              125
  STAGE IIB               3                7
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              1               58
  STAGE IIIC              1               41
  STAGE IV                2               46
  STAGE IVA               1               17
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  IQGAP2 MUTATED     0   4  17   6
  IQGAP2 WILD-TYPE  17  88 312  44
D416V5, multiclass
    clus
vv   IQGAP2 MUTATED IQGAP2 WILD-TYPE
  T1              0               17
  T2              4               88
  T3             17              312
  T4              6               44
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  IQGAP2 MUTATED    22   1   4
  IQGAP2 WILD-TYPE 265 112  83
D416V6, multiclass
    clus
vv   IQGAP2 MUTATED IQGAP2 WILD-TYPE
  N0             22              265
  N1              1              112
  N2              4               83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D416V7, binary
                  cls
clus                 0   1
  IQGAP2 MUTATED    20   2
  IQGAP2 WILD-TYPE 355  63
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IQGAP2 MUTATED     20    2
  IQGAP2 WILD-TYPE  355   63
   clus
vv  IQGAP2 MUTATED IQGAP2 WILD-TYPE
  0             20              355
  1              2               63
[1] 2 2
[1] FALSE
D416V8, binary
                  cls
clus                 0   1
  IQGAP2 MUTATED     7  20
  IQGAP2 WILD-TYPE 218 244
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IQGAP2 MUTATED      7   20
  IQGAP2 WILD-TYPE  218  244
        clus
vv       IQGAP2 MUTATED IQGAP2 WILD-TYPE
  FEMALE              7              218
  MALE               20              244
[1] 2 2
[1] FALSE
D416V9, binary
                  cls
clus                 0   1
  IQGAP2 MUTATED    20   2
  IQGAP2 WILD-TYPE 330  20
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IQGAP2 MUTATED     20    2
  IQGAP2 WILD-TYPE  330   20
     clus
vv    IQGAP2 MUTATED IQGAP2 WILD-TYPE
  NO              20              330
  YES              2               20
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  IQGAP2 MUTATED                     17                             4
  IQGAP2 WILD-TYPE                  298                            43
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  IQGAP2 MUTATED                       5                              0
  IQGAP2 WILD-TYPE                   101                             10
D416V10, multiclass
                                clus
vv                               IQGAP2 MUTATED IQGAP2 WILD-TYPE
  COLON ADENOCARCINOMA                       17              298
  COLON MUCINOUS ADENOCARCINOMA               4               43
  RECTAL ADENOCARCINOMA                       5              101
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  IQGAP2 MUTATED    18   0   1   2
  IQGAP2 WILD-TYPE 327   4  30  23
D416V11, multiclass
    clus
vv   IQGAP2 MUTATED IQGAP2 WILD-TYPE
  R0             18              327
  R1              0                4
  R2              1               30
  RX              2               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D416V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  IQGAP2 MUTATED                                  0     1
  IQGAP2 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  IQGAP2 MUTATED                           1    15
  IQGAP2 WILD-TYPE                        21   211
D416V13, multiclass
                                  clus
vv                                 IQGAP2 MUTATED IQGAP2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                        15              211
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(417) Variable = DNAH11 MUTATION ANALYSIS
D417V1, survival
                  sevent
clus2                0   1
  DNAH11 MUTATED    58  16
  DNAH11 WILD-TYPE 320  77
  DNAH11 MUTATED DNAH11 WILD-TYPE 
              74              397 
  DNAH11 MUTATED DNAH11 WILD-TYPE 
              16               77 
$`DNAH11 MUTATED`
TCGA-A6-3809 TCGA-A6-6141 TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3489 TCGA-AA-3496 
       32.75         8.38        20.12        19.66         7.04         1.02 
TCGA-AA-3510 TCGA-AA-3530 TCGA-AA-3672 TCGA-AA-3678 TCGA-AA-3697 TCGA-AA-3715 
       63.98        19.07         0.92        47.01        85.05        19.04 
TCGA-AA-3811 TCGA-AA-3815 TCGA-AA-3854 TCGA-AA-3864 TCGA-AA-3870 TCGA-AA-3950 
       10.06        33.04        36.03        53.00        29.98        24.00 
TCGA-AA-3977 TCGA-AA-3989 TCGA-AA-A00N TCGA-AA-A010 TCGA-AD-6889 TCGA-AD-6895 
       25.02         7.96         4.01        34.98        56.55         0.72 
TCGA-AD-6963 TCGA-AU-6004 TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-5407 TCGA-AZ-6600 
       27.42        27.09        21.44        58.39        88.21        12.10 
TCGA-AZ-6606 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-5916 TCGA-CK-6751 TCGA-CM-5341 
       11.74        12.76        10.06        21.14       124.27        29.06 
TCGA-CM-5344 TCGA-CM-5862 TCGA-CM-6162 TCGA-CM-6163 TCGA-D5-5540 TCGA-D5-6535 
       22.03         5.03        12.00         2.96        56.09        15.12 
TCGA-D5-6536 TCGA-D5-6898 TCGA-D5-6923 TCGA-D5-6928 TCGA-D5-6931 TCGA-DM-A1D9 
       17.85         1.48        12.43        11.64        12.00       140.38 
TCGA-DM-A1DA TCGA-DM-A1HB TCGA-DM-A28E TCGA-DM-A28G TCGA-F4-6459 TCGA-F4-6855 
        7.50       135.65       119.93        60.79         8.61        47.41 
TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6306 TCGA-G4-6321 TCGA-G4-6626 TCGA-AF-2687 
       35.31        74.56        44.68        22.09        46.75        24.13 
TCGA-AF-3913 TCGA-AF-6136 TCGA-AG-3885 TCGA-AG-3892 TCGA-AG-4005 TCGA-AG-A002 
       10.39        15.39        17.95        13.02        14.04        20.98 
TCGA-AG-A026 TCGA-AH-6644 TCGA-CI-6624 TCGA-DC-6157 TCGA-DC-6683 TCGA-EI-6506 
        1.94         0.72         4.73        27.95         5.03        20.55 
TCGA-F5-6813 TCGA-G5-6641 
        0.69        26.43 

$`DNAH11 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 
       22.06        32.71        27.09        22.52        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6782 
       24.16        21.76        24.69        24.39        23.87        20.28 
TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        3.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
       19.07         0.00        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3679 TCGA-AA-3680 
       54.02         2.01        14.01        50.04        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 
        5.98        37.05        19.00        36.00         5.03        26.99 
TCGA-AA-3713 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       19.04        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3855 TCGA-AA-3856 
       10.06         0.00        33.07         0.00        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        31.07        30.05        17.03        24.03        27.02 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       26.01         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        27.02        19.07        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6899 
       40.96         0.07        21.37        15.52         0.79         5.79 
TCGA-AD-6901 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 
       22.42        10.88         0.20        14.50        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       33.01        17.82         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       62.79        49.41         6.77       100.01        29.56         5.23 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.07        12.20        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 
       15.62        49.08        51.32         9.99        82.95         1.91 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5348 
       23.05        20.02        37.02        25.02        13.02        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       30.08        32.02        15.02        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
       15.02        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       12.26        19.59        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       43.27         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 
        3.68         4.41        14.30         9.04         9.44         4.80 
TCGA-D5-6930 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
        1.51        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1DB 
      130.65        92.75        49.91        13.32        12.59        44.32 
TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28F TCGA-DM-A28H 
      131.51       139.17         6.12        81.37        35.97       117.07 
TCGA-DM-A28K TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
       98.24        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-G4-6293 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
      133.18        65.85        53.62        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       61.91        36.00        13.78        35.80        26.17        91.79 
TCGA-G4-6628 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       79.69        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       14.50        16.83        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 
       19.04        19.99         1.02        36.95        17.03        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       36.03         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A02G TCGA-AG-A02N 
       70.03        64.01        10.98        49.97        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CL-5917 TCGA-CL-5918 
        0.69         6.05        33.17         6.97        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
       15.02         5.03        13.97        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        4.01         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       51.48        32.61         0.49        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-G5-6235 
       55.76 

  DNAH11 MUTATED DNAH11 WILD-TYPE 
            0.69             0.00 
  DNAH11 MUTATED DNAH11 WILD-TYPE 
          140.38           148.01 
  DNAH11 MUTATED DNAH11 WILD-TYPE 
          20.335           20.190 
[1] "0.7 - 140.4 (20.3)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1"  
D417V2, continuous
D417V3, binary
                  cls
clus                 0   1
  DNAH11 MUTATED    60  15
  DNAH11 WILD-TYPE 306 104
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DNAH11 MUTATED     60   15
  DNAH11 WILD-TYPE  306  104
        clus
vv       DNAH11 MUTATED DNAH11 WILD-TYPE
  COLON              60              306
  RECTUM             15              104
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DNAH11 MUTATED        14        0        6        20         3         0
  DNAH11 WILD-TYPE      77        1       26       118         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DNAH11 MUTATED           5          2          8          6        6
  DNAH11 WILD-TYPE        19          9         51         36       42
                  vv
clus               STAGE IVA STAGE IVB
  DNAH11 MUTATED           1         0
  DNAH11 WILD-TYPE        17         1
D417V4, multiclass
            clus
vv           DNAH11 MUTATED DNAH11 WILD-TYPE
  STAGE I                14               77
  STAGE IA                0                1
  STAGE II                6               26
  STAGE IIA              20              118
  STAGE IIB               3                7
  STAGE IIC               0                1
  STAGE III               5               19
  STAGE IIIA              2                9
  STAGE IIIB              8               51
  STAGE IIIC              6               36
  STAGE IV                6               42
  STAGE IVA               1               17
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  DNAH11 MUTATED     5  15  46   9
  DNAH11 WILD-TYPE  12  77 283  41
D417V5, multiclass
    clus
vv   DNAH11 MUTATED DNAH11 WILD-TYPE
  T1              5               12
  T2             15               77
  T3             46              283
  T4              9               41
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  DNAH11 MUTATED    46  17  11
  DNAH11 WILD-TYPE 241  96  76
D417V6, multiclass
    clus
vv   DNAH11 MUTATED DNAH11 WILD-TYPE
  N0             46              241
  N1             17               96
  N2             11               76
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D417V7, binary
                  cls
clus                 0   1
  DNAH11 MUTATED    56   7
  DNAH11 WILD-TYPE 319  58
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DNAH11 MUTATED     56    7
  DNAH11 WILD-TYPE  319   58
   clus
vv  DNAH11 MUTATED DNAH11 WILD-TYPE
  0             56              319
  1              7               58
[1] 2 2
[1] FALSE
D417V8, binary
                  cls
clus                 0   1
  DNAH11 MUTATED    31  44
  DNAH11 WILD-TYPE 194 220
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DNAH11 MUTATED     31   44
  DNAH11 WILD-TYPE  194  220
        clus
vv       DNAH11 MUTATED DNAH11 WILD-TYPE
  FEMALE             31              194
  MALE               44              220
[1] 2 2
[1] FALSE
D417V9, binary
                  cls
clus                 0   1
  DNAH11 MUTATED    52   3
  DNAH11 WILD-TYPE 298  19
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DNAH11 MUTATED     52    3
  DNAH11 WILD-TYPE  298   19
     clus
vv    DNAH11 MUTATED DNAH11 WILD-TYPE
  NO              52              298
  YES              3               19
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  DNAH11 MUTATED                     48                            11
  DNAH11 WILD-TYPE                  267                            36
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  DNAH11 MUTATED                      14                              1
  DNAH11 WILD-TYPE                    92                              9
D417V10, multiclass
                                clus
vv                               DNAH11 MUTATED DNAH11 WILD-TYPE
  COLON ADENOCARCINOMA                       48              267
  COLON MUCINOUS ADENOCARCINOMA              11               36
  RECTAL ADENOCARCINOMA                      14               92
  RECTAL MUCINOUS ADENOCARCINOMA              1                9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  DNAH11 MUTATED    51   1   1   5
  DNAH11 WILD-TYPE 294   3  30  20
D417V11, multiclass
    clus
vv   DNAH11 MUTATED DNAH11 WILD-TYPE
  R0             51              294
  R1              1                3
  R2              1               30
  RX              5               20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D417V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DNAH11 MUTATED                                  0     3
  DNAH11 WILD-TYPE                                1     8
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  DNAH11 MUTATED                           4    44
  DNAH11 WILD-TYPE                        18   182
D417V13, multiclass
                                  clus
vv                                 DNAH11 MUTATED DNAH11 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         3                8
  BLACK OR AFRICAN AMERICAN                     4               18
  WHITE                                        44              182
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(418) Variable = EPHA7 MUTATION ANALYSIS
D418V1, survival
                 sevent
clus2               0   1
  EPHA7 MUTATED    29  11
  EPHA7 WILD-TYPE 349  82
  EPHA7 MUTATED EPHA7 WILD-TYPE 
             40             431 
  EPHA7 MUTATED EPHA7 WILD-TYPE 
             11              82 
$`EPHA7 MUTATED`
TCGA-A6-3809 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3555 TCGA-AA-3663 TCGA-AA-3710 
       32.75         3.02         1.02        29.95         6.97        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3815 TCGA-AA-3858 TCGA-AA-3966 TCGA-AA-A00N 
       19.04        19.04        33.04        31.07         2.01         4.01 
TCGA-AA-A010 TCGA-AD-5900 TCGA-AD-6901 TCGA-AD-6964 TCGA-AZ-4315 TCGA-AZ-6605 
       34.98         0.07        22.42        10.88        58.39         5.23 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-6751 TCGA-CM-5349 TCGA-CM-6162 
       12.76        10.06        17.56       124.27        30.08        12.00 
TCGA-CM-6171 TCGA-D5-6536 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6930 TCGA-DM-A1D6 
       14.04        17.85        12.49        15.58         1.51        49.91 
TCGA-DM-A1DA TCGA-DM-A28G TCGA-G4-6321 TCGA-AF-2693 TCGA-AG-3892 TCGA-AG-A002 
        7.50        60.79        22.09        19.10        13.02        20.98 
TCGA-AG-A026 TCGA-CI-6624 TCGA-DC-6682 TCGA-G5-6235 
        1.94         4.73         4.01        55.76 

$`EPHA7 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3502 TCGA-AA-3510 
       20.12        19.66        20.28         7.04        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       17.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       61.02        78.08         6.05        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3811 
       37.05        19.00        36.00         5.03        85.05        10.06 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       35.05         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 
       41.00        39.98        18.05        40.96        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6965 
       56.55         0.79         0.72         5.79        27.42         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-4950 
        3.29         0.07        12.20        14.30       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
        1.91        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       29.06        22.03        22.98        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 
       15.02        15.02        17.03        15.02         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
        4.80        17.13        16.14         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB 
      130.65        92.75        13.32        12.59       140.38        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       35.97       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       63.62        61.91        36.00        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       13.55        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 
        1.02        17.95        36.95        17.03        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A02G TCGA-AG-A02N 
       70.03        64.01        10.98        49.97        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CL-5917 
        0.69         0.72         6.05        33.17         6.97        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
       19.99         5.95         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        26.43 

  EPHA7 MUTATED EPHA7 WILD-TYPE 
           0.07            0.00 
  EPHA7 MUTATED EPHA7 WILD-TYPE 
         124.27          148.01 
  EPHA7 MUTATED EPHA7 WILD-TYPE 
          16.57           20.98 
[1] "0.1 - 124.3 (16.6)" "0.0 - 148.0 (21.0)"
[1] "hr=" "1.8"
D418V2, continuous
D418V3, binary
                 cls
clus                0   1
  EPHA7 MUTATED    35   6
  EPHA7 WILD-TYPE 331 113
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPHA7 MUTATED     35    6
  EPHA7 WILD-TYPE  331  113
        clus
vv       EPHA7 MUTATED EPHA7 WILD-TYPE
  COLON             35             331
  RECTUM             6             113
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  EPHA7 MUTATED         8        0        5        14         3         0
  EPHA7 WILD-TYPE      83        1       27       124         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  EPHA7 MUTATED           2          1          4          2        1         0
  EPHA7 WILD-TYPE        22         10         55         40       47        18
                 vv
clus              STAGE IVB
  EPHA7 MUTATED           0
  EPHA7 WILD-TYPE         1
D418V4, multiclass
            clus
vv           EPHA7 MUTATED EPHA7 WILD-TYPE
  STAGE I                8              83
  STAGE IA               0               1
  STAGE II               5              27
  STAGE IIA             14             124
  STAGE IIB              3               7
  STAGE IIC              0               1
  STAGE III              2              22
  STAGE IIIA             1              10
  STAGE IIIB             4              55
  STAGE IIIC             2              40
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  EPHA7 MUTATED     1   8  26   7
  EPHA7 WILD-TYPE  16  84 303  43
D418V5, multiclass
    clus
vv   EPHA7 MUTATED EPHA7 WILD-TYPE
  T1             1              16
  T2             8              84
  T3            26             303
  T4             7              43
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  EPHA7 MUTATED    33   5   4
  EPHA7 WILD-TYPE 254 108  83
D418V6, multiclass
    clus
vv   EPHA7 MUTATED EPHA7 WILD-TYPE
  N0            33             254
  N1             5             108
  N2             4              83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D418V7, binary
                 cls
clus                0   1
  EPHA7 MUTATED    33   1
  EPHA7 WILD-TYPE 342  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPHA7 MUTATED     33    1
  EPHA7 WILD-TYPE  342   64
   clus
vv  EPHA7 MUTATED EPHA7 WILD-TYPE
  0            33             342
  1             1              64
[1] 2 2
[1] FALSE
D418V8, binary
                 cls
clus                0   1
  EPHA7 MUTATED    18  24
  EPHA7 WILD-TYPE 207 240
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPHA7 MUTATED     18   24
  EPHA7 WILD-TYPE  207  240
        clus
vv       EPHA7 MUTATED EPHA7 WILD-TYPE
  FEMALE            18             207
  MALE              24             240
[1] 2 2
[1] FALSE
D418V9, binary
                 cls
clus                0   1
  EPHA7 MUTATED    28   1
  EPHA7 WILD-TYPE 322  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPHA7 MUTATED     28    1
  EPHA7 WILD-TYPE  322   21
     clus
vv    EPHA7 MUTATED EPHA7 WILD-TYPE
  NO             28             322
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  EPHA7 MUTATED                     24                            11
  EPHA7 WILD-TYPE                  291                            36
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  EPHA7 MUTATED                       6                              0
  EPHA7 WILD-TYPE                   100                             10
D418V10, multiclass
                                clus
vv                               EPHA7 MUTATED EPHA7 WILD-TYPE
  COLON ADENOCARCINOMA                      24             291
  COLON MUCINOUS ADENOCARCINOMA             11              36
  RECTAL ADENOCARCINOMA                      6             100
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  EPHA7 MUTATED    26   2   1   4
  EPHA7 WILD-TYPE 319   2  30  21
D418V11, multiclass
    clus
vv   EPHA7 MUTATED EPHA7 WILD-TYPE
  R0            26             319
  R1             2               2
  R2             1              30
  RX             4              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D418V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  EPHA7 MUTATED                                  0     2
  EPHA7 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  EPHA7 MUTATED                           0    24
  EPHA7 WILD-TYPE                        22   202
D418V13, multiclass
                                  clus
vv                                 EPHA7 MUTATED EPHA7 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               9
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                       24             202
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(419) Variable = DNAH8 MUTATION ANALYSIS
D419V1, survival
                 sevent
clus2               0   1
  DNAH8 MUTATED    57   8
  DNAH8 WILD-TYPE 321  85
  DNAH8 MUTATED DNAH8 WILD-TYPE 
             65             406 
  DNAH8 MUTATED DNAH8 WILD-TYPE 
              8              85 
$`DNAH8 MUTATED`
TCGA-A6-2671 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5660 TCGA-A6-5664 
       43.76        32.75        36.53        14.53        29.19        22.09 
TCGA-A6-5665 TCGA-A6-6141 TCGA-A6-6653 TCGA-A6-6781 TCGA-AA-3510 TCGA-AA-3672 
       22.06         8.38        24.39        19.66        63.98         0.92 
TCGA-AA-3713 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3947 TCGA-AA-3956 TCGA-AA-3966 
       19.04        30.05        53.00        33.01        34.03         2.01 
TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00N TCGA-AA-A010 
       34.06        25.02        30.02        18.05         4.01        34.98 
TCGA-AA-A01R TCGA-AD-6889 TCGA-AD-6964 TCGA-AU-3779 TCGA-AY-6197 TCGA-AZ-4315 
       35.01        56.55        10.88        14.50        21.44        58.39 
TCGA-AZ-4682 TCGA-AZ-6598 TCGA-CA-5797 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       22.36        49.41         3.29        12.20        12.76        10.06 
TCGA-CK-4950 TCGA-CM-5344 TCGA-CM-6161 TCGA-CM-6168 TCGA-CM-6171 TCGA-D5-5538 
       85.45        22.03        15.02        12.99        14.04        12.26 
TCGA-D5-6539 TCGA-D5-6926 TCGA-D5-6932 TCGA-DM-A1D9 TCGA-DM-A1HA TCGA-F4-6570 
       12.49         9.04        11.38       140.38       131.51         6.18 
TCGA-F4-6703 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6856 TCGA-G4-6304 TCGA-G4-6306 
       47.87        16.24        33.67        35.31        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6588 TCGA-G4-6628 TCGA-AG-3605 TCGA-AG-3732 TCGA-AG-3892 
       55.04        26.17        79.69         0.99        32.98        13.02 
TCGA-AG-3902 TCGA-AG-A002 TCGA-AG-A020 TCGA-EI-6510 TCGA-F5-6812 
       32.02        20.98        10.98        18.28         0.66 

$`DNAH8 WILD-TYPE`
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       46.65        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 
       34.65        33.34        32.91        31.63        30.44        33.53 
TCGA-A6-5662 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 
       23.61        32.71        27.09        22.52        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 
       24.16        21.76        24.69        23.87        20.12        20.28 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 
        7.04         3.02         1.02        35.01         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
       13.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       36.03         8.05        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       78.08         6.05         6.97        54.02         2.01        14.01 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3866 TCGA-AA-3867 
       32.05         0.99        31.07        31.07        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3968 
       24.00        26.01        24.00         2.01        20.98        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       16.08        50.99        13.05        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       19.00        34.03        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       15.52         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 
        0.20        27.09        16.31         0.95        33.01        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 
        1.41         5.13       106.75        62.79        88.21         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6719 
        1.61        12.69         3.06         3.25         0.07        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
       17.56       148.01        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5349 
       37.02        25.02        13.02        29.06        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       13.02        15.02        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5539 
       11.08        11.01        10.06        12.03        45.40        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 
       15.12        17.85         4.80        17.13        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6927 
        1.48         3.68         4.41        12.43        14.30         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 
       11.64         4.80         1.51        12.00        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
       12.59         7.50        44.32       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
        8.61        31.96        35.74         1.55        34.42        41.42 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
       13.25         0.53        47.41       133.18        74.56        65.85 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       35.80        91.79        46.75        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       37.02         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       17.95        36.95        17.03        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       48.03        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       19.96        20.91         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.69        55.76        26.43 

  DNAH8 MUTATED DNAH8 WILD-TYPE 
           0.66            0.00 
  DNAH8 MUTATED DNAH8 WILD-TYPE 
         140.38          148.01 
  DNAH8 MUTATED DNAH8 WILD-TYPE 
         22.090          20.005 
[1] "0.7 - 140.4 (22.1)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.9"
D419V2, continuous
D419V3, binary
                 cls
clus                0   1
  DNAH8 MUTATED    59   8
  DNAH8 WILD-TYPE 307 111
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DNAH8 MUTATED     59    8
  DNAH8 WILD-TYPE  307  111
        clus
vv       DNAH8 MUTATED DNAH8 WILD-TYPE
  COLON             59             307
  RECTUM             8             111
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DNAH8 MUTATED        10        0        3        26         6         0
  DNAH8 WILD-TYPE      81        1       29       112         4         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DNAH8 MUTATED           3          1          6          5        3         2
  DNAH8 WILD-TYPE        21         10         53         37       45        16
                 vv
clus              STAGE IVB
  DNAH8 MUTATED           0
  DNAH8 WILD-TYPE         1
D419V4, multiclass
            clus
vv           DNAH8 MUTATED DNAH8 WILD-TYPE
  STAGE I               10              81
  STAGE IA               0               1
  STAGE II               3              29
  STAGE IIA             26             112
  STAGE IIB              6               4
  STAGE IIC              0               1
  STAGE III              3              21
  STAGE IIIA             1              10
  STAGE IIIB             6              53
  STAGE IIIC             5              37
  STAGE IV               3              45
  STAGE IVA              2              16
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  DNAH8 MUTATED     2  11  43  11
  DNAH8 WILD-TYPE  15  81 286  39
D419V5, multiclass
    clus
vv   DNAH8 MUTATED DNAH8 WILD-TYPE
  T1             2              15
  T2            11              81
  T3            43             286
  T4            11              39
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  DNAH8 MUTATED    50  10   7
  DNAH8 WILD-TYPE 237 103  80
D419V6, multiclass
    clus
vv   DNAH8 MUTATED DNAH8 WILD-TYPE
  N0            50             237
  N1            10             103
  N2             7              80
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D419V7, binary
                 cls
clus                0   1
  DNAH8 MUTATED    55   4
  DNAH8 WILD-TYPE 320  61
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DNAH8 MUTATED     55    4
  DNAH8 WILD-TYPE  320   61
   clus
vv  DNAH8 MUTATED DNAH8 WILD-TYPE
  0            55             320
  1             4              61
[1] 2 2
[1] FALSE
D419V8, binary
                 cls
clus                0   1
  DNAH8 MUTATED    29  38
  DNAH8 WILD-TYPE 196 226
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DNAH8 MUTATED     29   38
  DNAH8 WILD-TYPE  196  226
        clus
vv       DNAH8 MUTATED DNAH8 WILD-TYPE
  FEMALE            29             196
  MALE              38             226
[1] 2 2
[1] FALSE
D419V9, binary
                 cls
clus                0   1
  DNAH8 MUTATED    54   3
  DNAH8 WILD-TYPE 296  19
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DNAH8 MUTATED     54    3
  DNAH8 WILD-TYPE  296   19
     clus
vv    DNAH8 MUTATED DNAH8 WILD-TYPE
  NO             54             296
  YES             3              19
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  DNAH8 MUTATED                     50                             9
  DNAH8 WILD-TYPE                  265                            38
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  DNAH8 MUTATED                       7                              1
  DNAH8 WILD-TYPE                    99                              9
D419V10, multiclass
                                clus
vv                               DNAH8 MUTATED DNAH8 WILD-TYPE
  COLON ADENOCARCINOMA                      50             265
  COLON MUCINOUS ADENOCARCINOMA              9              38
  RECTAL ADENOCARCINOMA                      7              99
  RECTAL MUCINOUS ADENOCARCINOMA             1               9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  DNAH8 MUTATED    48   1   2   4
  DNAH8 WILD-TYPE 297   3  29  21
D419V11, multiclass
    clus
vv   DNAH8 MUTATED DNAH8 WILD-TYPE
  R0            48             297
  R1             1               3
  R2             2              29
  RX             4              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D419V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DNAH8 MUTATED                                  0     5
  DNAH8 WILD-TYPE                                1     6
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  DNAH8 MUTATED                           5    35
  DNAH8 WILD-TYPE                        17   191
D419V13, multiclass
                                  clus
vv                                 DNAH8 MUTATED DNAH8 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        5               6
  BLACK OR AFRICAN AMERICAN                    5              17
  WHITE                                       35             191
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(420) Variable = MACF1 MUTATION ANALYSIS
D420V1, survival
                 sevent
clus2               0   1
  MACF1 MUTATED    51  13
  MACF1 WILD-TYPE 327  80
  MACF1 MUTATED MACF1 WILD-TYPE 
             64             407 
  MACF1 MUTATED MACF1 WILD-TYPE 
             13              80 
$`MACF1 MUTATED`
TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-5665 TCGA-A6-6653 TCGA-A6-6780 
       46.65        42.90        42.28        22.06        24.39        20.12 
TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3516 TCGA-AA-3554 TCGA-AA-3662 TCGA-AA-3713 
        3.02        63.98        13.02        17.95         6.05        19.04 
TCGA-AA-3811 TCGA-AA-3815 TCGA-AA-3850 TCGA-AA-3864 TCGA-AA-3949 TCGA-AA-3966 
       10.06        33.04         0.00        53.00        26.01         2.01 
TCGA-AA-3977 TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00N TCGA-AA-A00R 
       25.02        38.04        30.02        18.05         4.01         0.99 
TCGA-AA-A010 TCGA-AA-A01R TCGA-AD-6895 TCGA-AD-6899 TCGA-AY-6197 TCGA-AZ-4315 
       34.98        35.01         0.72         5.79        21.44        58.39 
TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-CA-5796 TCGA-CA-6717 
       62.79        49.41        12.10       100.01         3.25        12.76 
TCGA-CK-4952 TCGA-CK-6751 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-6162 TCGA-CM-6165 
       15.62       124.27        15.02         5.03        12.00        16.04 
TCGA-CM-6171 TCGA-CM-6674 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6926 TCGA-D5-6927 
       14.04        12.95        15.12        17.85         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6930 TCGA-F4-6570 TCGA-F4-6703 TCGA-G4-6315 TCGA-G4-6586 
       11.64         1.51         6.18        47.87        61.91        35.80 
TCGA-G4-6588 TCGA-G4-6628 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3727 TCGA-AG-3885 
       26.17        79.69        20.02        10.39         0.99        17.95 
TCGA-AG-3892 TCGA-AG-A002 TCGA-AG-A011 TCGA-F5-6812 
       13.02        20.98        37.02         0.66 

$`MACF1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 
       43.76        43.76        24.33        16.57        34.65        33.34 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       32.75        36.53        14.53        32.91        31.63        30.44 
TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 
       29.19        33.53        23.61        22.09        32.71        27.09 
TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 
       22.52         8.38        25.08        25.18        24.16        21.76 
TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       24.69        23.87        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
       35.01         6.97         1.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       61.02        78.08         6.97        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       19.04        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
       10.06        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        31.07        30.05        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 
       33.01        24.00         2.01        20.98        34.03        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       19.00        34.03        18.05        38.04        27.02        42.02 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S 
       12.00        31.00        31.00        38.07         1.02         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
       56.55         0.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 
       14.50        27.09        16.31         0.95        33.01        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6599 
        1.41         5.13       106.75        22.36        88.21         6.77 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.06         3.29         0.07        12.20        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
       17.56       148.01        85.45        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       21.14        82.95         1.91        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 
       32.02        15.02        15.02        17.03        15.02         2.96 
TCGA-CM-6164 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       29.03        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       11.01        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6537 TCGA-D5-6538 
       20.19        18.25         1.32        43.27         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       12.43        14.30         4.80        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6317 
       53.62        44.68        55.04        85.48        63.62        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 
       22.09        13.78        91.79        46.75        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       16.83        15.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3731 
       15.95        19.99        13.94        19.99         7.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       36.95        17.03        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A014 
       17.03        13.94         6.02        25.97        23.01        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.69        55.76        26.43 

  MACF1 MUTATED MACF1 WILD-TYPE 
              0               0 
  MACF1 MUTATED MACF1 WILD-TYPE 
         124.27          148.01 
  MACF1 MUTATED MACF1 WILD-TYPE 
          17.95           20.98 
[1] "0.0 - 124.3 (17.9)" "0.0 - 148.0 (21.0)"
[1] "hr=" "1.1"
D420V2, continuous
D420V3, binary
                 cls
clus                0   1
  MACF1 MUTATED    58   8
  MACF1 WILD-TYPE 308 111
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MACF1 MUTATED     58    8
  MACF1 WILD-TYPE  308  111
        clus
vv       MACF1 MUTATED MACF1 WILD-TYPE
  COLON             58             308
  RECTUM             8             111
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MACF1 MUTATED         8        0        6        25         3         0
  MACF1 WILD-TYPE      83        1       26       113         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MACF1 MUTATED           5          1          8          2        5         1
  MACF1 WILD-TYPE        19         10         51         40       43        17
                 vv
clus              STAGE IVB
  MACF1 MUTATED           0
  MACF1 WILD-TYPE         1
D420V4, multiclass
            clus
vv           MACF1 MUTATED MACF1 WILD-TYPE
  STAGE I                8              83
  STAGE IA               0               1
  STAGE II               6              26
  STAGE IIA             25             113
  STAGE IIB              3               7
  STAGE IIC              0               1
  STAGE III              5              19
  STAGE IIIA             1              10
  STAGE IIIB             8              51
  STAGE IIIC             2              40
  STAGE IV               5              43
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  MACF1 MUTATED     1   9  46  10
  MACF1 WILD-TYPE  16  83 283  40
D420V5, multiclass
    clus
vv   MACF1 MUTATED MACF1 WILD-TYPE
  T1             1              16
  T2             9              83
  T3            46             283
  T4            10              40
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  MACF1 MUTATED    44  14   8
  MACF1 WILD-TYPE 243  99  79
D420V6, multiclass
    clus
vv   MACF1 MUTATED MACF1 WILD-TYPE
  N0            44             243
  N1            14              99
  N2             8              79
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D420V7, binary
                 cls
clus                0   1
  MACF1 MUTATED    51   5
  MACF1 WILD-TYPE 324  60
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MACF1 MUTATED     51    5
  MACF1 WILD-TYPE  324   60
   clus
vv  MACF1 MUTATED MACF1 WILD-TYPE
  0            51             324
  1             5              60
[1] 2 2
[1] FALSE
D420V8, binary
                 cls
clus                0   1
  MACF1 MUTATED    29  37
  MACF1 WILD-TYPE 196 227
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MACF1 MUTATED     29   37
  MACF1 WILD-TYPE  196  227
        clus
vv       MACF1 MUTATED MACF1 WILD-TYPE
  FEMALE            29             196
  MALE              37             227
[1] 2 2
[1] FALSE
D420V9, binary
                 cls
clus                0   1
  MACF1 MUTATED    49   5
  MACF1 WILD-TYPE 301  17
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MACF1 MUTATED     49    5
  MACF1 WILD-TYPE  301   17
     clus
vv    MACF1 MUTATED MACF1 WILD-TYPE
  NO             49             301
  YES             5              17
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MACF1 MUTATED                     43                            15
  MACF1 WILD-TYPE                  272                            32
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MACF1 MUTATED                       8                              0
  MACF1 WILD-TYPE                    98                             10
D420V10, multiclass
                                clus
vv                               MACF1 MUTATED MACF1 WILD-TYPE
  COLON ADENOCARCINOMA                      43             272
  COLON MUCINOUS ADENOCARCINOMA             15              32
  RECTAL ADENOCARCINOMA                      8              98
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  MACF1 MUTATED    48   0   2   4
  MACF1 WILD-TYPE 297   4  29  21
D420V11, multiclass
    clus
vv   MACF1 MUTATED MACF1 WILD-TYPE
  R0            48             297
  R1             0               4
  R2             2              29
  RX             4              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D420V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MACF1 MUTATED                                  0     2
  MACF1 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  MACF1 MUTATED                           1    36
  MACF1 WILD-TYPE                        21   190
D420V13, multiclass
                                  clus
vv                                 MACF1 MUTATED MACF1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               9
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                       36             190
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(421) Variable = IL1RAPL1 MUTATION ANALYSIS
D421V1, survival
                    sevent
clus2                  0   1
  IL1RAPL1 MUTATED    19   6
  IL1RAPL1 WILD-TYPE 359  87
  IL1RAPL1 MUTATED IL1RAPL1 WILD-TYPE 
                25                446 
  IL1RAPL1 MUTATED IL1RAPL1 WILD-TYPE 
                 6                 87 
$`IL1RAPL1 MUTATED`
TCGA-A6-5661 TCGA-AA-3518 TCGA-AA-3554 TCGA-AA-3663 TCGA-AA-3977 TCGA-AZ-6598 
       33.53         1.02        17.95         6.97        25.02        49.41 
TCGA-AZ-6607 TCGA-CA-6717 TCGA-CM-6162 TCGA-CM-6164 TCGA-D5-6532 TCGA-D5-6533 
        3.19        12.76        12.00        29.03        18.25         1.32 
TCGA-DM-A1DA TCGA-DM-A285 TCGA-DM-A28E TCGA-DM-A28G TCGA-F4-6855 TCGA-G4-6304 
        7.50         6.12       119.93        60.79        47.41        53.62 
TCGA-G4-6307 TCGA-G4-6628 TCGA-AG-3892 TCGA-AG-A002 TCGA-AH-6544 TCGA-DC-6158 
       55.04        79.69        13.02        20.98        38.56        10.98 
TCGA-DT-5265 
        5.29 

$`IL1RAPL1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       24.00        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02        78.08         6.05        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       88.21         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
       11.74         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07        12.20        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
       15.02         2.96        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6534 
       12.26        19.59        56.09        55.92        20.19        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB 
       92.75        49.91        13.32        12.59       140.38        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A28C TCGA-DM-A28F TCGA-DM-A28H 
      131.51       135.65       139.17        81.37        35.97       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 
        0.53        35.31       133.18        74.56        65.85        44.68 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 
       35.80        26.17        91.79        46.75        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       13.97        27.95        19.99         5.95         4.01         5.03 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  IL1RAPL1 MUTATED IL1RAPL1 WILD-TYPE 
              1.02               0.00 
  IL1RAPL1 MUTATED IL1RAPL1 WILD-TYPE 
            119.93             148.01 
  IL1RAPL1 MUTATED IL1RAPL1 WILD-TYPE 
            18.250             20.235 
[1] "1.0 - 119.9 (18.2)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.1"
D421V2, continuous
D421V3, binary
                    cls
clus                   0   1
  IL1RAPL1 MUTATED    23   5
  IL1RAPL1 WILD-TYPE 343 114
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  IL1RAPL1 MUTATED     23    5
  IL1RAPL1 WILD-TYPE  343  114
        clus
vv       IL1RAPL1 MUTATED IL1RAPL1 WILD-TYPE
  COLON                23                343
  RECTUM                5                114
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  IL1RAPL1 MUTATED         4        0        3        11         2         0
  IL1RAPL1 WILD-TYPE      87        1       29       127         8         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  IL1RAPL1 MUTATED           0          0          3          1        2
  IL1RAPL1 WILD-TYPE        24         11         56         41       46
                    vv
clus                 STAGE IVA STAGE IVB
  IL1RAPL1 MUTATED           0         0
  IL1RAPL1 WILD-TYPE        18         1
D421V4, multiclass
            clus
vv           IL1RAPL1 MUTATED IL1RAPL1 WILD-TYPE
  STAGE I                   4                 87
  STAGE IA                  0                  1
  STAGE II                  3                 29
  STAGE IIA                11                127
  STAGE IIB                 2                  8
  STAGE IIC                 0                  1
  STAGE III                 0                 24
  STAGE IIIA                0                 11
  STAGE IIIB                3                 56
  STAGE IIIC                1                 41
  STAGE IV                  2                 46
  STAGE IVA                 0                 18
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  IL1RAPL1 MUTATED     1   4  19   4
  IL1RAPL1 WILD-TYPE  16  88 310  46
D421V5, multiclass
    clus
vv   IL1RAPL1 MUTATED IL1RAPL1 WILD-TYPE
  T1                1                 16
  T2                4                 88
  T3               19                310
  T4                4                 46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  IL1RAPL1 MUTATED    22   3   3
  IL1RAPL1 WILD-TYPE 265 110  84
D421V6, multiclass
    clus
vv   IL1RAPL1 MUTATED IL1RAPL1 WILD-TYPE
  N0               22                265
  N1                3                110
  N2                3                 84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D421V7, binary
                    cls
clus                   0   1
  IL1RAPL1 MUTATED    22   3
  IL1RAPL1 WILD-TYPE 353  62
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  IL1RAPL1 MUTATED     22    3
  IL1RAPL1 WILD-TYPE  353   62
   clus
vv  IL1RAPL1 MUTATED IL1RAPL1 WILD-TYPE
  0               22                353
  1                3                 62
[1] 2 2
[1] FALSE
D421V8, binary
                    cls
clus                   0   1
  IL1RAPL1 MUTATED    17  11
  IL1RAPL1 WILD-TYPE 208 253
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  IL1RAPL1 MUTATED     17   11
  IL1RAPL1 WILD-TYPE  208  253
        clus
vv       IL1RAPL1 MUTATED IL1RAPL1 WILD-TYPE
  FEMALE               17                208
  MALE                 11                253
[1] 2 2
[1] FALSE
D421V9, binary
                    cls
clus                   0   1
  IL1RAPL1 MUTATED    19   0
  IL1RAPL1 WILD-TYPE 331  22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  IL1RAPL1 MUTATED     19    0
  IL1RAPL1 WILD-TYPE  331   22
     clus
vv    IL1RAPL1 MUTATED IL1RAPL1 WILD-TYPE
  NO                19                331
  YES                0                 22
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  IL1RAPL1 MUTATED                     20                             3
  IL1RAPL1 WILD-TYPE                  295                            44
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  IL1RAPL1 MUTATED                       4                              1
  IL1RAPL1 WILD-TYPE                   102                              9
D421V10, multiclass
                                clus
vv                               IL1RAPL1 MUTATED IL1RAPL1 WILD-TYPE
  COLON ADENOCARCINOMA                         20                295
  COLON MUCINOUS ADENOCARCINOMA                 3                 44
  RECTAL ADENOCARCINOMA                         4                102
  RECTAL MUCINOUS ADENOCARCINOMA                1                  9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  IL1RAPL1 MUTATED    17   0   0   3
  IL1RAPL1 WILD-TYPE 328   4  31  22
D421V11, multiclass
    clus
vv   IL1RAPL1 MUTATED IL1RAPL1 WILD-TYPE
  R0               17                328
  R1                0                  4
  R2                0                 31
  RX                3                 22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D421V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  IL1RAPL1 MUTATED                                  0     2
  IL1RAPL1 WILD-TYPE                                1     9
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  IL1RAPL1 MUTATED                           1    17
  IL1RAPL1 WILD-TYPE                        21   209
D421V13, multiclass
                                  clus
vv                                 IL1RAPL1 MUTATED IL1RAPL1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           2                  9
  BLACK OR AFRICAN AMERICAN                       1                 21
  WHITE                                          17                209
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(422) Variable = WDR78 MUTATION ANALYSIS
D422V1, survival
                 sevent
clus2               0   1
  WDR78 MUTATED    14   2
  WDR78 WILD-TYPE 364  91
  WDR78 MUTATED WDR78 WILD-TYPE 
             16             455 
  WDR78 MUTATED WDR78 WILD-TYPE 
              2              91 
$`WDR78 MUTATED`
TCGA-AA-3672 TCGA-AA-3680 TCGA-AA-3713 TCGA-AA-3977 TCGA-AZ-4315 TCGA-CA-6717 
        0.92        11.01        19.04        25.02        58.39        12.76 
TCGA-CA-6718 TCGA-D5-5540 TCGA-D5-6529 TCGA-D5-6923 TCGA-G4-6304 TCGA-G4-6307 
       10.06        56.09        20.19        12.43        53.62        55.04 
TCGA-AG-3600 TCGA-AG-3742 TCGA-AG-A002 TCGA-EI-6507 
        6.05         0.99        20.98        19.96 

$`WDR78 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
        6.05         6.97        54.02         2.01        14.01        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       47.01        15.02         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 
        3.25         3.29         0.07        12.20        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5541 
       10.06        12.03        45.40        12.26        19.59        55.92 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
        4.41        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       44.68        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       50.04        12.03         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3878 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  WDR78 MUTATED WDR78 WILD-TYPE 
           0.92            0.00 
  WDR78 MUTATED WDR78 WILD-TYPE 
          58.39          148.01 
  WDR78 MUTATED WDR78 WILD-TYPE 
          19.50           20.55 
[1] "0.9 - 58.4 (19.5)"  "0.0 - 148.0 (20.6)"
[1] "hr=" "1.6"
D422V2, continuous
D422V3, binary
                 cls
clus                0   1
  WDR78 MUTATED    12   4
  WDR78 WILD-TYPE 354 115
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WDR78 MUTATED     12    4
  WDR78 WILD-TYPE  354  115
        clus
vv       WDR78 MUTATED WDR78 WILD-TYPE
  COLON             12             354
  RECTUM             4             115
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  WDR78 MUTATED         3        0        0         6         1         0
  WDR78 WILD-TYPE      88        1       32       132         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  WDR78 MUTATED           1          0          1          1        2         0
  WDR78 WILD-TYPE        23         11         58         41       46        18
                 vv
clus              STAGE IVB
  WDR78 MUTATED           0
  WDR78 WILD-TYPE         1
D422V4, multiclass
            clus
vv           WDR78 MUTATED WDR78 WILD-TYPE
  STAGE I                3              88
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              6             132
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             1              41
  STAGE IV               2              46
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  WDR78 MUTATED     1   3  10   2
  WDR78 WILD-TYPE  16  89 319  48
D422V5, multiclass
    clus
vv   WDR78 MUTATED WDR78 WILD-TYPE
  T1             1              16
  T2             3              89
  T3            10             319
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  WDR78 MUTATED    12   2   2
  WDR78 WILD-TYPE 275 111  85
D422V6, multiclass
    clus
vv   WDR78 MUTATED WDR78 WILD-TYPE
  N0            12             275
  N1             2             111
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D422V7, binary
                 cls
clus                0   1
  WDR78 MUTATED    13   2
  WDR78 WILD-TYPE 362  63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WDR78 MUTATED     13    2
  WDR78 WILD-TYPE  362   63
   clus
vv  WDR78 MUTATED WDR78 WILD-TYPE
  0            13             362
  1             2              63
[1] 2 2
[1] FALSE
D422V8, binary
                 cls
clus                0   1
  WDR78 MUTATED     5  11
  WDR78 WILD-TYPE 220 253
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WDR78 MUTATED      5   11
  WDR78 WILD-TYPE  220  253
        clus
vv       WDR78 MUTATED WDR78 WILD-TYPE
  FEMALE             5             220
  MALE              11             253
[1] 2 2
[1] FALSE
D422V9, binary
                 cls
clus                0   1
  WDR78 MUTATED    13   2
  WDR78 WILD-TYPE 337  20
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WDR78 MUTATED     13    2
  WDR78 WILD-TYPE  337   20
     clus
vv    WDR78 MUTATED WDR78 WILD-TYPE
  NO             13             337
  YES             2              20
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  WDR78 MUTATED                     11                             1
  WDR78 WILD-TYPE                  304                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  WDR78 MUTATED                       4                              0
  WDR78 WILD-TYPE                   102                             10
D422V10, multiclass
                                clus
vv                               WDR78 MUTATED WDR78 WILD-TYPE
  COLON ADENOCARCINOMA                      11             304
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      4             102
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  WDR78 MUTATED    11   0   2   2
  WDR78 WILD-TYPE 334   4  29  23
D422V11, multiclass
    clus
vv   WDR78 MUTATED WDR78 WILD-TYPE
  R0            11             334
  R1             0               4
  R2             2              29
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D422V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  WDR78 MUTATED                                  0     2
  WDR78 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  WDR78 MUTATED                           0     7
  WDR78 WILD-TYPE                        22   219
D422V13, multiclass
                                  clus
vv                                 WDR78 MUTATED WDR78 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               9
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        7             219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(423) Variable = TRIM13 MUTATION ANALYSIS
D423V1, survival
                  sevent
clus2                0   1
  TRIM13 MUTATED     7   1
  TRIM13 WILD-TYPE 371  92
  TRIM13 MUTATED TRIM13 WILD-TYPE 
               8              463 
  TRIM13 MUTATED TRIM13 WILD-TYPE 
               1               92 
$`TRIM13 MUTATED`
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3848 TCGA-AA-3950 TCGA-AA-3977 TCGA-AY-5543 
       78.08         6.05        10.06        24.00        25.02        33.01 
TCGA-G4-6293 TCGA-AG-A002 
      133.18        20.98 

$`TRIM13 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3663 
       20.98        19.99        13.94        19.99        61.02         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        33.01        26.01         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       27.09        16.31         0.95        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
       35.31        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  TRIM13 MUTATED TRIM13 WILD-TYPE 
            6.05             0.00 
  TRIM13 MUTATED TRIM13 WILD-TYPE 
          133.18           148.01 
  TRIM13 MUTATED TRIM13 WILD-TYPE 
           24.51            20.05 
[1] "6.0 - 133.2 (24.5)" "0.0 - 148.0 (20.1)"
[1] "hr=" "2.2"
D423V2, continuous
D423V3, binary
                  cls
clus                 0   1
  TRIM13 MUTATED     7   1
  TRIM13 WILD-TYPE 359 118
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIM13 MUTATED      7    1
  TRIM13 WILD-TYPE  359  118
        clus
vv       TRIM13 MUTATED TRIM13 WILD-TYPE
  COLON               7              359
  RECTUM              1              118
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TRIM13 MUTATED         1        0        1         1         0         0
  TRIM13 WILD-TYPE      90        1       31       137        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TRIM13 MUTATED           1          0          0          1        1
  TRIM13 WILD-TYPE        23         11         59         41       47
                  vv
clus               STAGE IVA STAGE IVB
  TRIM13 MUTATED           1         0
  TRIM13 WILD-TYPE        17         1
D423V4, multiclass
            clus
vv           TRIM13 MUTATED TRIM13 WILD-TYPE
  STAGE I                 1               90
  STAGE IA                0                1
  STAGE II                1               31
  STAGE IIA               1              137
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               1               23
  STAGE IIIA              0               11
  STAGE IIIB              0               59
  STAGE IIIC              1               41
  STAGE IV                1               47
  STAGE IVA               1               17
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  TRIM13 MUTATED     0   2   5   1
  TRIM13 WILD-TYPE  17  90 324  49
D423V5, multiclass
    clus
vv   TRIM13 MUTATED TRIM13 WILD-TYPE
  T1              0               17
  T2              2               90
  T3              5              324
  T4              1               49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  TRIM13 MUTATED     4   2   2
  TRIM13 WILD-TYPE 283 111  85
D423V6, multiclass
    clus
vv   TRIM13 MUTATED TRIM13 WILD-TYPE
  N0              4              283
  N1              2              111
  N2              2               85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D423V7, binary
                  cls
clus                 0   1
  TRIM13 MUTATED     5   2
  TRIM13 WILD-TYPE 370  63
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIM13 MUTATED      5    2
  TRIM13 WILD-TYPE  370   63
   clus
vv  TRIM13 MUTATED TRIM13 WILD-TYPE
  0              5              370
  1              2               63
[1] 2 2
[1] FALSE
D423V8, binary
                  cls
clus                 0   1
  TRIM13 MUTATED     6   2
  TRIM13 WILD-TYPE 219 262
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIM13 MUTATED      6    2
  TRIM13 WILD-TYPE  219  262
        clus
vv       TRIM13 MUTATED TRIM13 WILD-TYPE
  FEMALE              6              219
  MALE                2              262
[1] 2 2
[1] FALSE
D423V9, binary
                  cls
clus                 0   1
  TRIM13 MUTATED     8   0
  TRIM13 WILD-TYPE 342  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIM13 MUTATED      8    0
  TRIM13 WILD-TYPE  342   22
     clus
vv    TRIM13 MUTATED TRIM13 WILD-TYPE
  NO               8              342
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  TRIM13 MUTATED                      6                             1
  TRIM13 WILD-TYPE                  309                            46
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  TRIM13 MUTATED                       1                              0
  TRIM13 WILD-TYPE                   105                             10
D423V10, multiclass
                                clus
vv                               TRIM13 MUTATED TRIM13 WILD-TYPE
  COLON ADENOCARCINOMA                        6              309
  COLON MUCINOUS ADENOCARCINOMA               1               46
  RECTAL ADENOCARCINOMA                       1              105
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  TRIM13 MUTATED     6   0   1   0
  TRIM13 WILD-TYPE 339   4  30  25
D423V11, multiclass
    clus
vv   TRIM13 MUTATED TRIM13 WILD-TYPE
  R0              6              339
  R1              0                4
  R2              1               30
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D423V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TRIM13 MUTATED                                  0     0
  TRIM13 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  TRIM13 MUTATED                           1     1
  TRIM13 WILD-TYPE                        21   225
D423V13, multiclass
[1] "Remove cluster labels:" "TRIM13 MUTATED"        
clus
  TRIM13 MUTATED TRIM13 WILD-TYPE 
               2              258 
      TCGA-A6-2671       TCGA-A6-2672       TCGA-A6-2674       TCGA-A6-2676 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-A6-2677       TCGA-A6-2678       TCGA-A6-2683       TCGA-A6-3807 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-A6-3808       TCGA-A6-3809       TCGA-A6-3810       TCGA-A6-4105 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-A6-5656       TCGA-A6-5657       TCGA-A6-5659       TCGA-A6-5660 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-A6-5661       TCGA-A6-5662       TCGA-A6-5664       TCGA-A6-5665 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-A6-5666       TCGA-A6-6137       TCGA-A6-6138       TCGA-A6-6141 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-A6-6142       TCGA-A6-6648       TCGA-A6-6649       TCGA-A6-6651 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-A6-6652       TCGA-A6-6653       TCGA-A6-6654       TCGA-A6-6780 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-A6-6781       TCGA-A6-6782       TCGA-AD-5900       TCGA-AD-6548 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-AD-6888       TCGA-AD-6889       TCGA-AD-6890       TCGA-AD-6895 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-AD-6899       TCGA-AD-6901       TCGA-AD-6963       TCGA-AD-6964 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-AD-6965       TCGA-AU-3779       TCGA-AU-6004       TCGA-AY-4070 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-AY-4071       TCGA-AY-6196       TCGA-AY-6197       TCGA-AY-6386 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-AZ-4315       TCGA-AZ-4323       TCGA-AZ-4616       TCGA-AZ-4681 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-AZ-4682       TCGA-AZ-5403       TCGA-AZ-5407       TCGA-AZ-6598 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-AZ-6599       TCGA-AZ-6600       TCGA-AZ-6601       TCGA-AZ-6603 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-AZ-6605       TCGA-AZ-6606       TCGA-AZ-6607       TCGA-AZ-6608 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-CA-5254       TCGA-CA-5255       TCGA-CA-5796       TCGA-CA-5797 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-CA-6715       TCGA-CA-6716       TCGA-CA-6717       TCGA-CA-6718 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-CA-6719       TCGA-CK-4947       TCGA-CK-4948       TCGA-CK-4950 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-CK-4952       TCGA-CK-5912       TCGA-CK-5913       TCGA-CK-5914 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-CK-5915       TCGA-CK-5916       TCGA-CK-6746       TCGA-CK-6747 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-CK-6748       TCGA-CK-6751       TCGA-CM-4743       TCGA-CM-4744 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-CM-4746       TCGA-CM-4747       TCGA-CM-4752       TCGA-CM-5341 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-CM-5344       TCGA-CM-5348       TCGA-CM-5349       TCGA-CM-5860 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-CM-5861       TCGA-CM-5862       TCGA-CM-5863       TCGA-CM-5864 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-CM-5868       TCGA-CM-6161       TCGA-CM-6162       TCGA-CM-6163 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-CM-6164       TCGA-CM-6165       TCGA-CM-6166       TCGA-CM-6167 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-CM-6168       TCGA-CM-6169       TCGA-CM-6170       TCGA-CM-6171 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-CM-6172       TCGA-CM-6674       TCGA-CM-6675       TCGA-CM-6676 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-CM-6677       TCGA-CM-6678       TCGA-CM-6679       TCGA-CM-6680 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-D5-5537       TCGA-D5-5538       TCGA-D5-5539       TCGA-D5-5540 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-D5-5541       TCGA-D5-6529       TCGA-D5-6532       TCGA-D5-6533 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-D5-6534       TCGA-D5-6535       TCGA-D5-6536       TCGA-D5-6537 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-D5-6538       TCGA-D5-6539       TCGA-D5-6540       TCGA-D5-6541 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-D5-6898       TCGA-D5-6920       TCGA-D5-6922       TCGA-D5-6923 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-D5-6924       TCGA-D5-6926       TCGA-D5-6927       TCGA-D5-6928 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-D5-6929       TCGA-D5-6930       TCGA-D5-6931       TCGA-D5-6932 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-D5-7000       TCGA-DM-A0X9       TCGA-DM-A0XD       TCGA-DM-A0XF 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-DM-A1D0       TCGA-DM-A1D4       TCGA-DM-A1D6       TCGA-DM-A1D7 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-DM-A1D8       TCGA-DM-A1D9       TCGA-DM-A1DA       TCGA-DM-A1DB 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-DM-A1HA       TCGA-DM-A1HB       TCGA-DM-A282       TCGA-DM-A285 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-DM-A28C       TCGA-DM-A28E       TCGA-DM-A28F       TCGA-DM-A28G 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-DM-A28H       TCGA-DM-A28K       TCGA-F4-6459       TCGA-F4-6460 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-F4-6569       TCGA-F4-6570       TCGA-F4-6703       TCGA-F4-6704 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-F4-6805       TCGA-F4-6806       TCGA-F4-6807       TCGA-F4-6808 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-F4-6809       TCGA-F4-6854       TCGA-F4-6855       TCGA-F4-6856 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-G4-6299       TCGA-G4-6303       TCGA-G4-6304       TCGA-G4-6306 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-G4-6307       TCGA-G4-6309       TCGA-G4-6310       TCGA-G4-6315 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-G4-6317       TCGA-G4-6321       TCGA-G4-6323       TCGA-G4-6586 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-G4-6588       TCGA-G4-6625       TCGA-G4-6626       TCGA-G4-6628 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-AF-2687       TCGA-AF-2689       TCGA-AF-2691       TCGA-AF-2692 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-AF-2693       TCGA-AF-3400       TCGA-AF-3913       TCGA-AF-4110 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-AF-5654       TCGA-AF-6136       TCGA-AF-6655       TCGA-AF-6672 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-AH-6544       TCGA-AH-6547       TCGA-AH-6549       TCGA-AH-6643 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-AH-6644       TCGA-CI-6619       TCGA-CI-6620       TCGA-CI-6621 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-CI-6622       TCGA-CI-6624       TCGA-CL-5917       TCGA-CL-5918 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-DC-5337       TCGA-DC-5869       TCGA-DC-6155       TCGA-DC-6157 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-DC-6158       TCGA-DC-6160       TCGA-DC-6681       TCGA-DC-6682 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-DC-6683       TCGA-DT-5265       TCGA-DY-A0XA       TCGA-DY-A1DC 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-DY-A1DD       TCGA-DY-A1DF       TCGA-DY-A1DG       TCGA-DY-A1H8 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-EF-5830       TCGA-EI-6506       TCGA-EI-6507       TCGA-EI-6508 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-EI-6510       TCGA-F5-6464       TCGA-F5-6465       TCGA-F5-6571 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-F5-6702       TCGA-F5-6811       TCGA-F5-6812       TCGA-F5-6813 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 
      TCGA-G5-6235       TCGA-G5-6641 
"TRIM13 WILD-TYPE" "TRIM13 WILD-TYPE" 

Clustering(424) Variable = OR1I1 MUTATION ANALYSIS
D424V1, survival
                 sevent
clus2               0   1
  OR1I1 MUTATED    10   1
  OR1I1 WILD-TYPE 368  92
  OR1I1 MUTATED OR1I1 WILD-TYPE 
             11             460 
  OR1I1 MUTATED OR1I1 WILD-TYPE 
              1              92 
$`OR1I1 MUTATED`
TCGA-A6-5659 TCGA-AA-3864 TCGA-AU-3779 TCGA-AZ-6601 TCGA-CA-6717 TCGA-CM-5861 
       30.44        53.00        14.50       100.01        12.76        15.02 
TCGA-D5-6930 TCGA-F4-6569 TCGA-G4-6293 TCGA-G4-6625 TCGA-AG-A002 
        1.51        35.74       133.18        91.79        20.98 

$`OR1I1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 
       32.05         0.99        31.07        31.07        30.05        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       10.88         0.20        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07        12.20        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 
       22.03        22.98        30.08        32.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 
        9.04         9.44        11.64         4.80        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6299 
       33.67        13.25         0.53        47.41        35.31        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  OR1I1 MUTATED OR1I1 WILD-TYPE 
           1.51            0.00 
  OR1I1 MUTATED OR1I1 WILD-TYPE 
         133.18          148.01 
  OR1I1 MUTATED OR1I1 WILD-TYPE 
         30.440          20.085 
[1] "1.5 - 133.2 (30.4)" "0.0 - 148.0 (20.1)"
[1] "hr=" "3.6"
D424V2, continuous
D424V3, binary
                 cls
clus                0   1
  OR1I1 MUTATED    10   1
  OR1I1 WILD-TYPE 356 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR1I1 MUTATED     10    1
  OR1I1 WILD-TYPE  356  118
        clus
vv       OR1I1 MUTATED OR1I1 WILD-TYPE
  COLON             10             356
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  OR1I1 MUTATED         3        0        2         5         0         0
  OR1I1 WILD-TYPE      88        1       30       133        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  OR1I1 MUTATED           1          0          0          0        0         0
  OR1I1 WILD-TYPE        23         11         59         42       48        18
                 vv
clus              STAGE IVB
  OR1I1 MUTATED           0
  OR1I1 WILD-TYPE         1
D424V4, multiclass
            clus
vv           OR1I1 MUTATED OR1I1 WILD-TYPE
  STAGE I                3              88
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA              5             133
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  OR1I1 MUTATED     0   3   8   0
  OR1I1 WILD-TYPE  17  89 321  50
D424V5, multiclass
    clus
vv   OR1I1 MUTATED OR1I1 WILD-TYPE
  T1             0              17
  T2             3              89
  T3             8             321
  T4             0              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  OR1I1 MUTATED    10   1   0
  OR1I1 WILD-TYPE 277 112  87
D424V6, multiclass
    clus
vv   OR1I1 MUTATED OR1I1 WILD-TYPE
  N0            10             277
  N1             1             112
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D424V7, binary
                 cls
clus                0   1
  OR1I1 MUTATED    11   0
  OR1I1 WILD-TYPE 364  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR1I1 MUTATED     11    0
  OR1I1 WILD-TYPE  364   65
   clus
vv  OR1I1 MUTATED OR1I1 WILD-TYPE
  0            11             364
  1             0              65
[1] 2 2
[1] FALSE
D424V8, binary
                 cls
clus                0   1
  OR1I1 MUTATED     4   7
  OR1I1 WILD-TYPE 221 257
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR1I1 MUTATED      4    7
  OR1I1 WILD-TYPE  221  257
        clus
vv       OR1I1 MUTATED OR1I1 WILD-TYPE
  FEMALE             4             221
  MALE               7             257
[1] 2 2
[1] FALSE
D424V9, binary
                 cls
clus                0   1
  OR1I1 MUTATED    10   0
  OR1I1 WILD-TYPE 340  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR1I1 MUTATED     10    0
  OR1I1 WILD-TYPE  340   22
     clus
vv    OR1I1 MUTATED OR1I1 WILD-TYPE
  NO             10             340
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  OR1I1 MUTATED                      8                             2
  OR1I1 WILD-TYPE                  307                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  OR1I1 MUTATED                       1                              0
  OR1I1 WILD-TYPE                   105                             10
D424V10, multiclass
                                clus
vv                               OR1I1 MUTATED OR1I1 WILD-TYPE
  COLON ADENOCARCINOMA                       8             307
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  OR1I1 MUTATED     9   0   0   1
  OR1I1 WILD-TYPE 336   4  31  24
D424V11, multiclass
    clus
vv   OR1I1 MUTATED OR1I1 WILD-TYPE
  R0             9             336
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D424V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OR1I1 MUTATED                                  0     1
  OR1I1 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  OR1I1 MUTATED                           0     8
  OR1I1 WILD-TYPE                        22   218
D424V13, multiclass
                                  clus
vv                                 OR1I1 MUTATED OR1I1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        8             218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(425) Variable = ACOT9 MUTATION ANALYSIS
D425V1, survival
                 sevent
clus2               0   1
  ACOT9 MUTATED     5   0
  ACOT9 WILD-TYPE 373  93
  ACOT9 MUTATED ACOT9 WILD-TYPE 
              5             466 
  ACOT9 MUTATED ACOT9 WILD-TYPE 
              0              93 
$`ACOT9 MUTATED`
TCGA-A6-5665 TCGA-AA-3697 TCGA-AA-3864 TCGA-CK-4948 TCGA-AG-3892 
       22.06        85.05        53.00       148.01        13.02 

$`ACOT9 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 
        0.99        31.07        31.07        30.05        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4952 
       12.76        10.06        14.30        17.56        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 
        1.02        17.95        36.95        17.03        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  ACOT9 MUTATED ACOT9 WILD-TYPE 
          13.02            0.00 
  ACOT9 MUTATED ACOT9 WILD-TYPE 
         148.01          140.38 
  ACOT9 MUTATED ACOT9 WILD-TYPE 
         53.000          20.085 
[1] "13.0 - 148.0 (53.0)" "0.0 - 140.4 (20.1)" 
[1] "hr="     "9400000"
D425V2, continuous
D425V3, binary
                 cls
clus                0   1
  ACOT9 MUTATED     4   1
  ACOT9 WILD-TYPE 362 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ACOT9 MUTATED      4    1
  ACOT9 WILD-TYPE  362  118
        clus
vv       ACOT9 MUTATED ACOT9 WILD-TYPE
  COLON              4             362
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ACOT9 MUTATED         1        0        1         1         0         0
  ACOT9 WILD-TYPE      90        1       31       137        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ACOT9 MUTATED           2          0          0          0        0         0
  ACOT9 WILD-TYPE        22         11         59         42       48        18
                 vv
clus              STAGE IVB
  ACOT9 MUTATED           0
  ACOT9 WILD-TYPE         1
D425V4, multiclass
            clus
vv           ACOT9 MUTATED ACOT9 WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              1             137
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              2              22
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ACOT9 MUTATED     1   0   4   0
  ACOT9 WILD-TYPE  16  92 325  50
D425V5, multiclass
    clus
vv   ACOT9 MUTATED ACOT9 WILD-TYPE
  T1             1              16
  T2             0              92
  T3             4             325
  T4             0              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  ACOT9 MUTATED     4   1   0
  ACOT9 WILD-TYPE 283 112  87
D425V6, multiclass
    clus
vv   ACOT9 MUTATED ACOT9 WILD-TYPE
  N0             4             283
  N1             1             112
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D425V7, binary
                 cls
clus                0   1
  ACOT9 MUTATED     5   0
  ACOT9 WILD-TYPE 370  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ACOT9 MUTATED      5    0
  ACOT9 WILD-TYPE  370   65
   clus
vv  ACOT9 MUTATED ACOT9 WILD-TYPE
  0             5             370
  1             0              65
[1] 2 2
[1] FALSE
D425V8, binary
                 cls
clus                0   1
  ACOT9 MUTATED     3   2
  ACOT9 WILD-TYPE 222 262
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ACOT9 MUTATED      3    2
  ACOT9 WILD-TYPE  222  262
        clus
vv       ACOT9 MUTATED ACOT9 WILD-TYPE
  FEMALE             3             222
  MALE               2             262
[1] 2 2
[1] FALSE
D425V9, binary
                 cls
clus                0   1
  ACOT9 MUTATED     5   0
  ACOT9 WILD-TYPE 345  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ACOT9 MUTATED      5    0
  ACOT9 WILD-TYPE  345   22
     clus
vv    ACOT9 MUTATED ACOT9 WILD-TYPE
  NO              5             345
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ACOT9 MUTATED                      4                             0
  ACOT9 WILD-TYPE                  311                            47
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ACOT9 MUTATED                       1                              0
  ACOT9 WILD-TYPE                   105                             10
D425V10, multiclass
                                clus
vv                               ACOT9 MUTATED ACOT9 WILD-TYPE
  COLON ADENOCARCINOMA                       4             311
  COLON MUCINOUS ADENOCARCINOMA              0              47
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  ACOT9 MUTATED     5   0   0   0
  ACOT9 WILD-TYPE 340   4  31  25
D425V11, multiclass
    clus
vv   ACOT9 MUTATED ACOT9 WILD-TYPE
  R0             5             340
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D425V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ACOT9 MUTATED                                  0     0
  ACOT9 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ACOT9 MUTATED                           0     2
  ACOT9 WILD-TYPE                        22   224
D425V13, multiclass
[1] "Remove cluster labels:" "ACOT9 MUTATED"         
clus
  ACOT9 MUTATED ACOT9 WILD-TYPE 
              2             258 
     TCGA-A6-2671      TCGA-A6-2672      TCGA-A6-2674      TCGA-A6-2676 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-A6-2677      TCGA-A6-2678      TCGA-A6-2683      TCGA-A6-3807 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-A6-3808      TCGA-A6-3809      TCGA-A6-3810      TCGA-A6-4105 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-A6-5656      TCGA-A6-5657      TCGA-A6-5659      TCGA-A6-5660 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-A6-5661      TCGA-A6-5662      TCGA-A6-5664      TCGA-A6-5666 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-A6-6137      TCGA-A6-6138      TCGA-A6-6141      TCGA-A6-6142 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-A6-6648      TCGA-A6-6649      TCGA-A6-6651      TCGA-A6-6652 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-A6-6653      TCGA-A6-6654      TCGA-A6-6780      TCGA-A6-6781 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-A6-6782      TCGA-AD-5900      TCGA-AD-6548      TCGA-AD-6888 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-AD-6889      TCGA-AD-6890      TCGA-AD-6895      TCGA-AD-6899 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-AD-6901      TCGA-AD-6963      TCGA-AD-6964      TCGA-AD-6965 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-AU-3779      TCGA-AU-6004      TCGA-AY-4070      TCGA-AY-4071 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-AY-5543      TCGA-AY-6196      TCGA-AY-6197      TCGA-AY-6386 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-AZ-4315      TCGA-AZ-4323      TCGA-AZ-4616      TCGA-AZ-4681 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-AZ-4682      TCGA-AZ-5403      TCGA-AZ-5407      TCGA-AZ-6598 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-AZ-6599      TCGA-AZ-6600      TCGA-AZ-6601      TCGA-AZ-6603 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-AZ-6605      TCGA-AZ-6606      TCGA-AZ-6607      TCGA-AZ-6608 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-CA-5254      TCGA-CA-5255      TCGA-CA-5796      TCGA-CA-5797 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-CA-6715      TCGA-CA-6716      TCGA-CA-6717      TCGA-CA-6718 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-CA-6719      TCGA-CK-4947      TCGA-CK-4950      TCGA-CK-4952 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-CK-5912      TCGA-CK-5913      TCGA-CK-5914      TCGA-CK-5915 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-CK-5916      TCGA-CK-6746      TCGA-CK-6747      TCGA-CK-6748 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-CK-6751      TCGA-CM-4743      TCGA-CM-4744      TCGA-CM-4746 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-CM-4747      TCGA-CM-4752      TCGA-CM-5341      TCGA-CM-5344 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-CM-5348      TCGA-CM-5349      TCGA-CM-5860      TCGA-CM-5861 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-CM-5862      TCGA-CM-5863      TCGA-CM-5864      TCGA-CM-5868 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-CM-6161      TCGA-CM-6162      TCGA-CM-6163      TCGA-CM-6164 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-CM-6165      TCGA-CM-6166      TCGA-CM-6167      TCGA-CM-6168 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-CM-6169      TCGA-CM-6170      TCGA-CM-6171      TCGA-CM-6172 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-CM-6674      TCGA-CM-6675      TCGA-CM-6676      TCGA-CM-6677 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-CM-6678      TCGA-CM-6679      TCGA-CM-6680      TCGA-D5-5537 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-D5-5538      TCGA-D5-5539      TCGA-D5-5540      TCGA-D5-5541 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-D5-6529      TCGA-D5-6532      TCGA-D5-6533      TCGA-D5-6534 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-D5-6535      TCGA-D5-6536      TCGA-D5-6537      TCGA-D5-6538 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-D5-6539      TCGA-D5-6540      TCGA-D5-6541      TCGA-D5-6898 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-D5-6920      TCGA-D5-6922      TCGA-D5-6923      TCGA-D5-6924 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-D5-6926      TCGA-D5-6927      TCGA-D5-6928      TCGA-D5-6929 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-D5-6930      TCGA-D5-6931      TCGA-D5-6932      TCGA-D5-7000 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-DM-A0X9      TCGA-DM-A0XD      TCGA-DM-A0XF      TCGA-DM-A1D0 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-DM-A1D4      TCGA-DM-A1D6      TCGA-DM-A1D7      TCGA-DM-A1D8 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-DM-A1D9      TCGA-DM-A1DA      TCGA-DM-A1DB      TCGA-DM-A1HA 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-DM-A1HB      TCGA-DM-A282      TCGA-DM-A285      TCGA-DM-A28C 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-DM-A28E      TCGA-DM-A28F      TCGA-DM-A28G      TCGA-DM-A28H 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-DM-A28K      TCGA-F4-6459      TCGA-F4-6460      TCGA-F4-6569 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-F4-6570      TCGA-F4-6703      TCGA-F4-6704      TCGA-F4-6805 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-F4-6806      TCGA-F4-6807      TCGA-F4-6808      TCGA-F4-6809 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-F4-6854      TCGA-F4-6855      TCGA-F4-6856      TCGA-G4-6293 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-G4-6299      TCGA-G4-6303      TCGA-G4-6304      TCGA-G4-6306 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-G4-6307      TCGA-G4-6309      TCGA-G4-6310      TCGA-G4-6315 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-G4-6317      TCGA-G4-6321      TCGA-G4-6323      TCGA-G4-6586 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-G4-6588      TCGA-G4-6625      TCGA-G4-6626      TCGA-G4-6628 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-AF-2687      TCGA-AF-2689      TCGA-AF-2691      TCGA-AF-2692 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-AF-2693      TCGA-AF-3400      TCGA-AF-3913      TCGA-AF-4110 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-AF-5654      TCGA-AF-6136      TCGA-AF-6655      TCGA-AF-6672 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-AH-6544      TCGA-AH-6547      TCGA-AH-6549      TCGA-AH-6643 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-AH-6644      TCGA-CI-6619      TCGA-CI-6620      TCGA-CI-6621 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-CI-6622      TCGA-CI-6624      TCGA-CL-5917      TCGA-CL-5918 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-DC-5337      TCGA-DC-5869      TCGA-DC-6155      TCGA-DC-6157 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-DC-6158      TCGA-DC-6160      TCGA-DC-6681      TCGA-DC-6682 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-DC-6683      TCGA-DT-5265      TCGA-DY-A0XA      TCGA-DY-A1DC 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-DY-A1DD      TCGA-DY-A1DF      TCGA-DY-A1DG      TCGA-DY-A1H8 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-EF-5830      TCGA-EI-6506      TCGA-EI-6507      TCGA-EI-6508 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-EI-6510      TCGA-F5-6464      TCGA-F5-6465      TCGA-F5-6571 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-F5-6702      TCGA-F5-6811      TCGA-F5-6812      TCGA-F5-6813 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 
     TCGA-G5-6235      TCGA-G5-6641 
"ACOT9 WILD-TYPE" "ACOT9 WILD-TYPE" 

Clustering(426) Variable = GPX6 MUTATION ANALYSIS
D426V1, survival
                sevent
clus2              0   1
  GPX6 MUTATED     6   3
  GPX6 WILD-TYPE 372  90
  GPX6 MUTATED GPX6 WILD-TYPE 
             9            462 
  GPX6 MUTATED GPX6 WILD-TYPE 
             3             90 
$`GPX6 MUTATED`
TCGA-A6-6649 TCGA-AA-3510 TCGA-AA-3845 TCGA-AA-A010 TCGA-CK-5914 TCGA-DM-A1DB 
       24.16        63.98         0.00        34.98         9.99        44.32 
TCGA-G4-6303 TCGA-G4-6628 TCGA-AG-3892 
       65.85        79.69        13.02 

$`GPX6 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.08        25.18        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 
       15.95        38.99        37.02        14.93        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       49.08        51.32        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
        7.50       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
       35.31       133.18        74.56        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 
       35.80        26.17        91.79        46.75        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  GPX6 MUTATED GPX6 WILD-TYPE 
             0              0 
  GPX6 MUTATED GPX6 WILD-TYPE 
         79.69         148.01 
  GPX6 MUTATED GPX6 WILD-TYPE 
        34.980         20.085 
[1] "0.0 - 79.7 (35.0)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.1"
D426V2, continuous
D426V3, binary
                cls
clus               0   1
  GPX6 MUTATED     9   1
  GPX6 WILD-TYPE 357 118
[1] "tbl2"
                cls
clus             [,1] [,2]
  GPX6 MUTATED      9    1
  GPX6 WILD-TYPE  357  118
        clus
vv       GPX6 MUTATED GPX6 WILD-TYPE
  COLON             9            357
  RECTUM            1            118
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GPX6 MUTATED         2        0        1         2         2         0
  GPX6 WILD-TYPE      89        1       31       136         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  GPX6 MUTATED           0          0          2          0        1         0
  GPX6 WILD-TYPE        24         11         57         42       47        18
                vv
clus             STAGE IVB
  GPX6 MUTATED           0
  GPX6 WILD-TYPE         1
D426V4, multiclass
            clus
vv           GPX6 MUTATED GPX6 WILD-TYPE
  STAGE I               2             89
  STAGE IA              0              1
  STAGE II              1             31
  STAGE IIA             2            136
  STAGE IIB             2              8
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            2             57
  STAGE IIIC            0             42
  STAGE IV              1             47
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  GPX6 MUTATED     1   1   6   2
  GPX6 WILD-TYPE  16  91 323  48
D426V5, multiclass
    clus
vv   GPX6 MUTATED GPX6 WILD-TYPE
  T1            1             16
  T2            1             91
  T3            6            323
  T4            2             48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  GPX6 MUTATED     7   3   0
  GPX6 WILD-TYPE 280 110  87
D426V6, multiclass
    clus
vv   GPX6 MUTATED GPX6 WILD-TYPE
  N0            7            280
  N1            3            110
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D426V7, binary
                cls
clus               0   1
  GPX6 MUTATED     7   1
  GPX6 WILD-TYPE 368  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  GPX6 MUTATED      7    1
  GPX6 WILD-TYPE  368   64
   clus
vv  GPX6 MUTATED GPX6 WILD-TYPE
  0            7            368
  1            1             64
[1] 2 2
[1] FALSE
D426V8, binary
                cls
clus               0   1
  GPX6 MUTATED     5   5
  GPX6 WILD-TYPE 220 259
[1] "tbl2"
                cls
clus             [,1] [,2]
  GPX6 MUTATED      5    5
  GPX6 WILD-TYPE  220  259
        clus
vv       GPX6 MUTATED GPX6 WILD-TYPE
  FEMALE            5            220
  MALE              5            259
[1] 2 2
[1] FALSE
D426V9, binary
                cls
clus               0   1
  GPX6 MUTATED     6   0
  GPX6 WILD-TYPE 344  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  GPX6 MUTATED      6    0
  GPX6 WILD-TYPE  344   22
     clus
vv    GPX6 MUTATED GPX6 WILD-TYPE
  NO             6            344
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  GPX6 MUTATED                      9                             0
  GPX6 WILD-TYPE                  306                            47
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  GPX6 MUTATED                       1                              0
  GPX6 WILD-TYPE                   105                             10
D426V10, multiclass
                                clus
vv                               GPX6 MUTATED GPX6 WILD-TYPE
  COLON ADENOCARCINOMA                      9            306
  COLON MUCINOUS ADENOCARCINOMA             0             47
  RECTAL ADENOCARCINOMA                     1            105
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  GPX6 MUTATED     6   0   0   2
  GPX6 WILD-TYPE 339   4  31  23
D426V11, multiclass
    clus
vv   GPX6 MUTATED GPX6 WILD-TYPE
  R0            6            339
  R1            0              4
  R2            0             31
  RX            2             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D426V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GPX6 MUTATED                                  0     0
  GPX6 WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  GPX6 MUTATED                           0     6
  GPX6 WILD-TYPE                        22   220
D426V13, multiclass
                                  clus
vv                                 GPX6 MUTATED GPX6 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       6            220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(427) Variable = KIAA1797 MUTATION ANALYSIS
D427V1, survival
                    sevent
clus2                  0   1
  KIAA1797 MUTATED    20   4
  KIAA1797 WILD-TYPE 358  89
  KIAA1797 MUTATED KIAA1797 WILD-TYPE 
                24                447 
  KIAA1797 MUTATED KIAA1797 WILD-TYPE 
                 4                 89 
$`KIAA1797 MUTATED`
TCGA-A6-5665 TCGA-A6-6141 TCGA-AA-3492 TCGA-AA-3864 TCGA-AA-A00N TCGA-AA-A00O 
       22.06         8.38         3.02        53.00         4.01        27.02 
TCGA-AA-A01Q TCGA-AD-5900 TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-CA-6717 
        1.02         0.07        21.44        58.39        49.41        12.76 
TCGA-CM-6169 TCGA-CM-6172 TCGA-D5-6532 TCGA-D5-6535 TCGA-D5-6540 TCGA-F4-6703 
       13.02        11.01        18.25        15.12        16.14        47.87 
TCGA-G4-6293 TCGA-G4-6626 TCGA-AF-6655 TCGA-AG-3892 TCGA-AG-A002 TCGA-EI-6507 
      133.18        46.75        20.02        13.02        20.98        19.96 

$`KIAA1797 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 
       22.09        32.71        27.09        22.52        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       19.66        20.28         7.04         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        31.07        30.05        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00Q TCGA-AA-A00R 
       34.03        18.05        18.05        38.04        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01R 
       32.02        12.00        31.00        31.00        38.07        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 
       41.00        39.98        18.05        40.96        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       33.01        17.82         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        88.21         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07        12.20        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6170 TCGA-CM-6171 
       16.04        21.99        14.99        12.99        15.02        14.04 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       20.19         1.32        43.27        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       12.49        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6704 TCGA-F4-6805 
        8.61        31.96        35.74         6.18         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
       35.31        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       35.80        26.17        91.79        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       16.83        15.39        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 
       19.99         1.02        17.95        36.95        17.03        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6510 
       51.48        32.61         0.49        20.55        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  KIAA1797 MUTATED KIAA1797 WILD-TYPE 
              0.07               0.00 
  KIAA1797 MUTATED KIAA1797 WILD-TYPE 
            133.18             148.01 
  KIAA1797 MUTATED KIAA1797 WILD-TYPE 
            19.105             20.550 
[1] "0.1 - 133.2 (19.1)" "0.0 - 148.0 (20.6)"
[1] "hr=" "1.2"
D427V2, continuous
D427V3, binary
                    cls
clus                   0   1
  KIAA1797 MUTATED    20   4
  KIAA1797 WILD-TYPE 346 115
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1797 MUTATED     20    4
  KIAA1797 WILD-TYPE  346  115
        clus
vv       KIAA1797 MUTATED KIAA1797 WILD-TYPE
  COLON                20                346
  RECTUM                4                115
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KIAA1797 MUTATED         4        0        4        10         1         0
  KIAA1797 WILD-TYPE      87        1       28       128         9         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIAA1797 MUTATED           1          1          2          1        0
  KIAA1797 WILD-TYPE        23         10         57         41       48
                    vv
clus                 STAGE IVA STAGE IVB
  KIAA1797 MUTATED           0         0
  KIAA1797 WILD-TYPE        18         1
D427V4, multiclass
            clus
vv           KIAA1797 MUTATED KIAA1797 WILD-TYPE
  STAGE I                   4                 87
  STAGE IA                  0                  1
  STAGE II                  4                 28
  STAGE IIA                10                128
  STAGE IIB                 1                  9
  STAGE IIC                 0                  1
  STAGE III                 1                 23
  STAGE IIIA                1                 10
  STAGE IIIB                2                 57
  STAGE IIIC                1                 41
  STAGE IV                  0                 48
  STAGE IVA                 0                 18
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  KIAA1797 MUTATED     1   4  18   1
  KIAA1797 WILD-TYPE  16  88 311  49
D427V5, multiclass
    clus
vv   KIAA1797 MUTATED KIAA1797 WILD-TYPE
  T1                1                 16
  T2                4                 88
  T3               18                311
  T4                1                 49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  KIAA1797 MUTATED    19   4   1
  KIAA1797 WILD-TYPE 268 109  86
D427V6, multiclass
    clus
vv   KIAA1797 MUTATED KIAA1797 WILD-TYPE
  N0               19                268
  N1                4                109
  N2                1                 86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D427V7, binary
                    cls
clus                   0   1
  KIAA1797 MUTATED    20   0
  KIAA1797 WILD-TYPE 355  65
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1797 MUTATED     20    0
  KIAA1797 WILD-TYPE  355   65
   clus
vv  KIAA1797 MUTATED KIAA1797 WILD-TYPE
  0               20                355
  1                0                 65
[1] 2 2
[1] FALSE
D427V8, binary
                    cls
clus                   0   1
  KIAA1797 MUTATED     9  15
  KIAA1797 WILD-TYPE 216 249
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1797 MUTATED      9   15
  KIAA1797 WILD-TYPE  216  249
        clus
vv       KIAA1797 MUTATED KIAA1797 WILD-TYPE
  FEMALE                9                216
  MALE                 15                249
[1] 2 2
[1] FALSE
D427V9, binary
                    cls
clus                   0   1
  KIAA1797 MUTATED    21   0
  KIAA1797 WILD-TYPE 329  22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1797 MUTATED     21    0
  KIAA1797 WILD-TYPE  329   22
     clus
vv    KIAA1797 MUTATED KIAA1797 WILD-TYPE
  NO                21                329
  YES                0                 22
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  KIAA1797 MUTATED                     16                             4
  KIAA1797 WILD-TYPE                  299                            43
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  KIAA1797 MUTATED                       4                              0
  KIAA1797 WILD-TYPE                   102                             10
D427V10, multiclass
                                clus
vv                               KIAA1797 MUTATED KIAA1797 WILD-TYPE
  COLON ADENOCARCINOMA                         16                299
  COLON MUCINOUS ADENOCARCINOMA                 4                 43
  RECTAL ADENOCARCINOMA                         4                102
  RECTAL MUCINOUS ADENOCARCINOMA                0                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  KIAA1797 MUTATED    20   0   0   2
  KIAA1797 WILD-TYPE 325   4  31  23
D427V11, multiclass
    clus
vv   KIAA1797 MUTATED KIAA1797 WILD-TYPE
  R0               20                325
  R1                0                  4
  R2                0                 31
  RX                2                 23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D427V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KIAA1797 MUTATED                                  0     1
  KIAA1797 WILD-TYPE                                1    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  KIAA1797 MUTATED                           2    14
  KIAA1797 WILD-TYPE                        20   212
D427V13, multiclass
                                  clus
vv                                 KIAA1797 MUTATED KIAA1797 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                 10
  BLACK OR AFRICAN AMERICAN                       2                 20
  WHITE                                          14                212
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(428) Variable = ODZ1 MUTATION ANALYSIS
D428V1, survival
                sevent
clus2              0   1
  ODZ1 MUTATED    59  15
  ODZ1 WILD-TYPE 319  78
  ODZ1 MUTATED ODZ1 WILD-TYPE 
            74            397 
  ODZ1 MUTATED ODZ1 WILD-TYPE 
            15             78 
$`ODZ1 MUTATED`
TCGA-A6-5657 TCGA-A6-5661 TCGA-A6-6652 TCGA-AA-3502 TCGA-AA-3516 TCGA-AA-3553 
       31.63        33.53        24.69        35.01        13.02        24.00 
TCGA-AA-3555 TCGA-AA-3560 TCGA-AA-3662 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
       29.95        19.99         6.05        19.04        19.04        10.06 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3821 TCGA-AA-3837 TCGA-AA-3845 TCGA-AA-3947 
       33.04         0.99         1.02        38.99         0.00        33.01 
TCGA-AA-3980 TCGA-AA-A00Q TCGA-AA-A01P TCGA-AA-A03F TCGA-AD-6889 TCGA-AU-3779 
       27.02        42.02        38.07        18.05        56.55        14.50 
TCGA-AY-4071 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4681 TCGA-CA-6717 TCGA-CA-6718 
        0.95        17.82        58.39       106.75        12.76        10.06 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-6747 TCGA-CM-5344 TCGA-CM-5861 
       85.45        15.62        51.32        82.95        22.03        15.02 
TCGA-CM-6161 TCGA-CM-6167 TCGA-CM-6674 TCGA-CM-6677 TCGA-CM-6678 TCGA-D5-5538 
       15.02        14.99        12.95        11.08        11.01        12.26 
TCGA-D5-5540 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6931 TCGA-D5-6932 TCGA-DM-A1D8 
       56.09        16.14        15.58        12.00        11.38        12.59 
TCGA-DM-A1DB TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6808 TCGA-G4-6293 TCGA-G4-6304 
       44.32         6.18        47.87        33.67       133.18        53.62 
TCGA-G4-6307 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-AF-2689 TCGA-AG-3605 
       55.04        13.78        35.80        26.17        39.48         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3881 TCGA-AG-A002 TCGA-AG-A020 TCGA-CL-5917 
       37.02        32.98        19.04        20.98        10.98        78.12 
TCGA-DC-5337 TCGA-DY-A0XA TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EI-6506 TCGA-EI-6507 
       15.02       126.44        24.13        51.48        20.55        19.96 
TCGA-F5-6811 TCGA-G5-6641 
       32.19        26.43 

$`ODZ1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       32.91        30.44        29.19        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       24.16        21.76        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3510 TCGA-AA-3511 
       20.28         7.04         3.02         1.02        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
        1.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       36.03         8.05        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 
       33.99        21.01        13.02        17.95        23.01        20.98 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3812 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 
       85.05        26.99        35.05        25.02        17.98        15.95 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02        14.93        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 
       18.05        31.00         2.01        12.99        24.00        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       24.00        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04         4.01        27.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        31.00         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 
       40.96         0.07        21.37        15.52         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-6004 
        5.79        22.42        27.42        10.88         0.20        27.09 
TCGA-AY-4070 TCGA-AY-5543 TCGA-AY-6197 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 
       16.31        33.01        21.44         1.41         5.13        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 
        3.06         3.25         3.29         0.07        12.20        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6748 
       17.56       148.01        49.08         9.99        21.14         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 
       29.06        22.98        30.08        32.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       15.02        17.03        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       21.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5539 
       13.05        11.08        10.06        12.03        45.40        19.59 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6898 TCGA-D5-6920 
       17.85         4.80        17.13        12.49         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
        4.80         1.51        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A1DA 
      130.65        92.75        49.91        13.32       140.38         7.50 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6809 
       35.74         1.55        34.42        41.42        16.24        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 
        0.53        47.41        35.31        74.56        65.85        44.68 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6625 
       85.48        63.62        61.91        36.00        22.09        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       46.75        79.69        24.13        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3608 TCGA-AG-3609 
        2.01        50.04        12.03         6.05        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3742 TCGA-AG-3878 
       13.94        19.99         7.99         0.99         0.99         0.99 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A025 TCGA-AG-A026 
        9.07        12.00        70.03        64.01        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5918 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
        6.97         4.73         7.17         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6508 TCGA-EI-6510 
       41.36        57.24        32.61         0.49        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6812 TCGA-F5-6813 
        9.96        49.51        31.30        28.57         0.66         0.69 
TCGA-G5-6235 
       55.76 

  ODZ1 MUTATED ODZ1 WILD-TYPE 
             0              0 
  ODZ1 MUTATED ODZ1 WILD-TYPE 
        133.18         148.01 
  ODZ1 MUTATED ODZ1 WILD-TYPE 
        21.505         20.050 
[1] "0.0 - 133.2 (21.5)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.1"
D428V2, continuous
D428V3, binary
                cls
clus               0   1
  ODZ1 MUTATED    60  16
  ODZ1 WILD-TYPE 306 103
[1] "tbl2"
                cls
clus             [,1] [,2]
  ODZ1 MUTATED     60   16
  ODZ1 WILD-TYPE  306  103
        clus
vv       ODZ1 MUTATED ODZ1 WILD-TYPE
  COLON            60            306
  RECTUM           16            103
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ODZ1 MUTATED        11        1        1        31         3         0
  ODZ1 WILD-TYPE      80        0       31       107         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ODZ1 MUTATED           6          1          7          7        5         3
  ODZ1 WILD-TYPE        18         10         52         35       43        15
                vv
clus             STAGE IVB
  ODZ1 MUTATED           0
  ODZ1 WILD-TYPE         1
D428V4, multiclass
            clus
vv           ODZ1 MUTATED ODZ1 WILD-TYPE
  STAGE I              11             80
  STAGE IA              1              0
  STAGE II              1             31
  STAGE IIA            31            107
  STAGE IIB             3              7
  STAGE IIC             0              1
  STAGE III             6             18
  STAGE IIIA            1             10
  STAGE IIIB            7             52
  STAGE IIIC            7             35
  STAGE IV              5             43
  STAGE IVA             3             15
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  ODZ1 MUTATED     4   8  56   8
  ODZ1 WILD-TYPE  13  84 273  42
D428V5, multiclass
    clus
vv   ODZ1 MUTATED ODZ1 WILD-TYPE
  T1            4             13
  T2            8             84
  T3           56            273
  T4            8             42
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  ODZ1 MUTATED    49  16  12
  ODZ1 WILD-TYPE 238  97  75
D428V6, multiclass
    clus
vv   ODZ1 MUTATED ODZ1 WILD-TYPE
  N0           49            238
  N1           16             97
  N2           12             75
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D428V7, binary
                cls
clus               0   1
  ODZ1 MUTATED    60   8
  ODZ1 WILD-TYPE 315  57
[1] "tbl2"
                cls
clus             [,1] [,2]
  ODZ1 MUTATED     60    8
  ODZ1 WILD-TYPE  315   57
   clus
vv  ODZ1 MUTATED ODZ1 WILD-TYPE
  0           60            315
  1            8             57
[1] 2 2
[1] FALSE
D428V8, binary
                cls
clus               0   1
  ODZ1 MUTATED    51  26
  ODZ1 WILD-TYPE 174 238
[1] "tbl2"
                cls
clus             [,1] [,2]
  ODZ1 MUTATED     51   26
  ODZ1 WILD-TYPE  174  238
        clus
vv       ODZ1 MUTATED ODZ1 WILD-TYPE
  FEMALE           51            174
  MALE             26            238
[1] 2 2
[1] FALSE
D428V9, binary
                cls
clus               0   1
  ODZ1 MUTATED    61   1
  ODZ1 WILD-TYPE 289  21
[1] "tbl2"
                cls
clus             [,1] [,2]
  ODZ1 MUTATED     61    1
  ODZ1 WILD-TYPE  289   21
     clus
vv    ODZ1 MUTATED ODZ1 WILD-TYPE
  NO            61            289
  YES            1             21
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ODZ1 MUTATED                     50                            10
  ODZ1 WILD-TYPE                  265                            37
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ODZ1 MUTATED                      13                              2
  ODZ1 WILD-TYPE                    93                              8
D428V10, multiclass
                                clus
vv                               ODZ1 MUTATED ODZ1 WILD-TYPE
  COLON ADENOCARCINOMA                     50            265
  COLON MUCINOUS ADENOCARCINOMA            10             37
  RECTAL ADENOCARCINOMA                    13             93
  RECTAL MUCINOUS ADENOCARCINOMA            2              8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  ODZ1 MUTATED    54   1   4   7
  ODZ1 WILD-TYPE 291   3  27  18
D428V11, multiclass
    clus
vv   ODZ1 MUTATED ODZ1 WILD-TYPE
  R0           54            291
  R1            1              3
  R2            4             27
  RX            7             18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D428V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ODZ1 MUTATED                                  0     3
  ODZ1 WILD-TYPE                                1     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  ODZ1 MUTATED                           7    41
  ODZ1 WILD-TYPE                        15   185
D428V13, multiclass
                                  clus
vv                                 ODZ1 MUTATED ODZ1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       3              8
  BLACK OR AFRICAN AMERICAN                   7             15
  WHITE                                      41            185
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(429) Variable = KPNA5 MUTATION ANALYSIS
D429V1, survival
                 sevent
clus2               0   1
  KPNA5 MUTATED     7   3
  KPNA5 WILD-TYPE 371  90
  KPNA5 MUTATED KPNA5 WILD-TYPE 
             10             461 
  KPNA5 MUTATED KPNA5 WILD-TYPE 
              3              90 
$`KPNA5 MUTATED`
TCGA-AA-3524 TCGA-AA-3713 TCGA-AA-3973 TCGA-AA-A00N TCGA-AZ-6608 TCGA-CK-5913 
       36.03        19.04        13.05         4.01         1.61        51.32 
TCGA-D5-6930 TCGA-DM-A28E TCGA-G4-6315 TCGA-G4-6626 
        1.51       119.93        61.91        46.75 

$`KPNA5 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3525 
       38.99         1.02         9.07        24.03        37.05         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 
        9.04         9.44        11.64         4.80        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28F 
      131.51       135.65       139.17         6.12        81.37        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       63.62        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       91.79        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  KPNA5 MUTATED KPNA5 WILD-TYPE 
           1.51            0.00 
  KPNA5 MUTATED KPNA5 WILD-TYPE 
         119.93          148.01 
  KPNA5 MUTATED KPNA5 WILD-TYPE 
         27.535          20.190 
[1] "1.5 - 119.9 (27.5)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.1"
D429V2, continuous
D429V3, binary
                 cls
clus                0   1
  KPNA5 MUTATED    11   0
  KPNA5 WILD-TYPE 355 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KPNA5 MUTATED     11    0
  KPNA5 WILD-TYPE  355  119
        clus
vv       KPNA5 MUTATED KPNA5 WILD-TYPE
  COLON             11             355
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KPNA5 MUTATED         0        0        1         4         2         0
  KPNA5 WILD-TYPE      91        1       31       134         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  KPNA5 MUTATED           0          1          0          0        3         0
  KPNA5 WILD-TYPE        24         10         59         42       45        18
                 vv
clus              STAGE IVB
  KPNA5 MUTATED           0
  KPNA5 WILD-TYPE         1
D429V4, multiclass
            clus
vv           KPNA5 MUTATED KPNA5 WILD-TYPE
  STAGE I                0              91
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              4             134
  STAGE IIB              2               8
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             1              10
  STAGE IIIB             0              59
  STAGE IIIC             0              42
  STAGE IV               3              45
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  KPNA5 MUTATED     0   1   7   3
  KPNA5 WILD-TYPE  17  91 322  47
D429V5, multiclass
    clus
vv   KPNA5 MUTATED KPNA5 WILD-TYPE
  T1             0              17
  T2             1              91
  T3             7             322
  T4             3              47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  KPNA5 MUTATED     8   3   0
  KPNA5 WILD-TYPE 279 110  87
D429V6, multiclass
    clus
vv   KPNA5 MUTATED KPNA5 WILD-TYPE
  N0             8             279
  N1             3             110
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D429V7, binary
                 cls
clus                0   1
  KPNA5 MUTATED     6   3
  KPNA5 WILD-TYPE 369  62
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KPNA5 MUTATED      6    3
  KPNA5 WILD-TYPE  369   62
   clus
vv  KPNA5 MUTATED KPNA5 WILD-TYPE
  0             6             369
  1             3              62
[1] 2 2
[1] FALSE
D429V8, binary
                 cls
clus                0   1
  KPNA5 MUTATED     4   7
  KPNA5 WILD-TYPE 221 257
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KPNA5 MUTATED      4    7
  KPNA5 WILD-TYPE  221  257
        clus
vv       KPNA5 MUTATED KPNA5 WILD-TYPE
  FEMALE             4             221
  MALE               7             257
[1] 2 2
[1] FALSE
D429V9, binary
                 cls
clus                0   1
  KPNA5 MUTATED     6   1
  KPNA5 WILD-TYPE 344  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KPNA5 MUTATED      6    1
  KPNA5 WILD-TYPE  344   21
     clus
vv    KPNA5 MUTATED KPNA5 WILD-TYPE
  NO              6             344
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  KPNA5 MUTATED                      9                             2
  KPNA5 WILD-TYPE                  306                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  KPNA5 MUTATED                       0                              0
  KPNA5 WILD-TYPE                   106                             10
D429V10, multiclass
                                clus
vv                               KPNA5 MUTATED KPNA5 WILD-TYPE
  COLON ADENOCARCINOMA                       9             306
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  KPNA5 MUTATED     5   0   2   2
  KPNA5 WILD-TYPE 340   4  29  23
D429V11, multiclass
    clus
vv   KPNA5 MUTATED KPNA5 WILD-TYPE
  R0             5             340
  R1             0               4
  R2             2              29
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D429V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KPNA5 MUTATED                                  0     0
  KPNA5 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  KPNA5 MUTATED                           0     7
  KPNA5 WILD-TYPE                        22   219
D429V13, multiclass
                                  clus
vv                                 KPNA5 MUTATED KPNA5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        7             219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(430) Variable = DMRTB1 MUTATION ANALYSIS
D430V1, survival
                  sevent
clus2                0   1
  DMRTB1 MUTATED     5   1
  DMRTB1 WILD-TYPE 373  92
  DMRTB1 MUTATED DMRTB1 WILD-TYPE 
               6              465 
  DMRTB1 MUTATED DMRTB1 WILD-TYPE 
               1               92 
$`DMRTB1 MUTATED`
TCGA-AA-3713 TCGA-AA-3846 TCGA-CK-5916 TCGA-CM-5341 TCGA-D5-6928 TCGA-G4-6588 
       19.04        17.03        21.14        29.06        11.64        26.17 

$`DMRTB1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 
       85.45        15.62        49.08        51.32         9.99        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       13.02        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6930 
       12.43        14.30         9.04         9.44         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       22.09        13.78        35.80        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  DMRTB1 MUTATED DMRTB1 WILD-TYPE 
           11.64             0.00 
  DMRTB1 MUTATED DMRTB1 WILD-TYPE 
           29.06           148.01 
  DMRTB1 MUTATED DMRTB1 WILD-TYPE 
           20.09            20.19 
[1] "11.6 - 29.1 (20.1)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.1"
D430V2, continuous
D430V3, binary
                  cls
clus                 0   1
  DMRTB1 MUTATED     6   0
  DMRTB1 WILD-TYPE 360 119
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DMRTB1 MUTATED      6    0
  DMRTB1 WILD-TYPE  360  119
        clus
vv       DMRTB1 MUTATED DMRTB1 WILD-TYPE
  COLON               6              360
  RECTUM              0              119
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DMRTB1 MUTATED         1        0        0         3         0         0
  DMRTB1 WILD-TYPE      90        1       32       135        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DMRTB1 MUTATED           0          1          0          0        1
  DMRTB1 WILD-TYPE        24         10         59         42       47
                  vv
clus               STAGE IVA STAGE IVB
  DMRTB1 MUTATED           0         0
  DMRTB1 WILD-TYPE        18         1
D430V4, multiclass
            clus
vv           DMRTB1 MUTATED DMRTB1 WILD-TYPE
  STAGE I                 1               90
  STAGE IA                0                1
  STAGE II                0               32
  STAGE IIA               3              135
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              1               10
  STAGE IIIB              0               59
  STAGE IIIC              0               42
  STAGE IV                1               47
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  DMRTB1 MUTATED     1   1   4   0
  DMRTB1 WILD-TYPE  16  91 325  50
D430V5, multiclass
    clus
vv   DMRTB1 MUTATED DMRTB1 WILD-TYPE
  T1              1               16
  T2              1               91
  T3              4              325
  T4              0               50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  DMRTB1 MUTATED     5   1   0
  DMRTB1 WILD-TYPE 282 112  87
D430V6, multiclass
    clus
vv   DMRTB1 MUTATED DMRTB1 WILD-TYPE
  N0              5              282
  N1              1              112
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D430V7, binary
                  cls
clus                 0   1
  DMRTB1 MUTATED     5   1
  DMRTB1 WILD-TYPE 370  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DMRTB1 MUTATED      5    1
  DMRTB1 WILD-TYPE  370   64
   clus
vv  DMRTB1 MUTATED DMRTB1 WILD-TYPE
  0              5              370
  1              1               64
[1] 2 2
[1] FALSE
D430V8, binary
                  cls
clus                 0   1
  DMRTB1 MUTATED     4   2
  DMRTB1 WILD-TYPE 221 262
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DMRTB1 MUTATED      4    2
  DMRTB1 WILD-TYPE  221  262
        clus
vv       DMRTB1 MUTATED DMRTB1 WILD-TYPE
  FEMALE              4              221
  MALE                2              262
[1] 2 2
[1] FALSE
D430V9, binary
                  cls
clus                 0   1
  DMRTB1 MUTATED     5   1
  DMRTB1 WILD-TYPE 345  21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DMRTB1 MUTATED      5    1
  DMRTB1 WILD-TYPE  345   21
     clus
vv    DMRTB1 MUTATED DMRTB1 WILD-TYPE
  NO               5              345
  YES              1               21
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  DMRTB1 MUTATED                      5                             1
  DMRTB1 WILD-TYPE                  310                            46
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  DMRTB1 MUTATED                       0                              0
  DMRTB1 WILD-TYPE                   106                             10
D430V10, multiclass
                                clus
vv                               DMRTB1 MUTATED DMRTB1 WILD-TYPE
  COLON ADENOCARCINOMA                        5              310
  COLON MUCINOUS ADENOCARCINOMA               1               46
  RECTAL ADENOCARCINOMA                       0              106
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  DMRTB1 MUTATED     4   0   1   1
  DMRTB1 WILD-TYPE 341   4  30  24
D430V11, multiclass
    clus
vv   DMRTB1 MUTATED DMRTB1 WILD-TYPE
  R0              4              341
  R1              0                4
  R2              1               30
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D430V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DMRTB1 MUTATED                                  0     0
  DMRTB1 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  DMRTB1 MUTATED                           0     4
  DMRTB1 WILD-TYPE                        22   222
D430V13, multiclass
                                  clus
vv                                 DMRTB1 MUTATED DMRTB1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         4              222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(431) Variable = NUP160 MUTATION ANALYSIS
D431V1, survival
                  sevent
clus2                0   1
  NUP160 MUTATED     8   2
  NUP160 WILD-TYPE 370  91
  NUP160 MUTATED NUP160 WILD-TYPE 
              10              461 
  NUP160 MUTATED NUP160 WILD-TYPE 
               2               91 
$`NUP160 MUTATED`
TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-A00J TCGA-CM-4743 TCGA-D5-6537 TCGA-D5-6923 
       25.02        27.02        18.05        23.05         4.80        12.43 
TCGA-D5-6930 TCGA-DM-A1DA TCGA-G4-6309 TCGA-G4-6323 
        1.51         7.50        85.48        13.78 

$`NUP160 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       19.00        30.02        34.03        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
        1.91       124.27        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6539 
        1.32        43.27        15.12        17.85        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6924 
       16.14        15.58         1.48         3.68         4.41        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 
        9.04         9.44        11.64         4.80        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA 
       49.91        13.32        12.59       140.38        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 
       74.56        65.85        53.62        44.68        55.04        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       61.91        36.00        22.09        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  NUP160 MUTATED NUP160 WILD-TYPE 
            1.51             0.00 
  NUP160 MUTATED NUP160 WILD-TYPE 
           85.48           148.01 
  NUP160 MUTATED NUP160 WILD-TYPE 
          15.915           20.280 
[1] "1.5 - 85.5 (15.9)"  "0.0 - 148.0 (20.3)"
[1] "hr=" "1.2"
D431V2, continuous
D431V3, binary
                  cls
clus                 0   1
  NUP160 MUTATED    11   0
  NUP160 WILD-TYPE 355 119
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NUP160 MUTATED     11    0
  NUP160 WILD-TYPE  355  119
        clus
vv       NUP160 MUTATED NUP160 WILD-TYPE
  COLON              11              355
  RECTUM              0              119
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NUP160 MUTATED         2        1        1         2         0         0
  NUP160 WILD-TYPE      89        0       31       136        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NUP160 MUTATED           0          0          3          1        0
  NUP160 WILD-TYPE        24         11         56         41       48
                  vv
clus               STAGE IVA STAGE IVB
  NUP160 MUTATED           0         0
  NUP160 WILD-TYPE        18         1
D431V4, multiclass
            clus
vv           NUP160 MUTATED NUP160 WILD-TYPE
  STAGE I                 2               89
  STAGE IA                1                0
  STAGE II                1               31
  STAGE IIA               2              136
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              3               56
  STAGE IIIC              1               41
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  NUP160 MUTATED     0   3   5   2
  NUP160 WILD-TYPE  17  89 324  48
D431V5, multiclass
    clus
vv   NUP160 MUTATED NUP160 WILD-TYPE
  T1              0               17
  T2              3               89
  T3              5              324
  T4              2               48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  NUP160 MUTATED     7   3   1
  NUP160 WILD-TYPE 280 110  86
D431V6, multiclass
    clus
vv   NUP160 MUTATED NUP160 WILD-TYPE
  N0              7              280
  N1              3              110
  N2              1               86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D431V7, binary
                  cls
clus                 0   1
  NUP160 MUTATED     8   0
  NUP160 WILD-TYPE 367  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NUP160 MUTATED      8    0
  NUP160 WILD-TYPE  367   65
   clus
vv  NUP160 MUTATED NUP160 WILD-TYPE
  0              8              367
  1              0               65
[1] 2 2
[1] FALSE
D431V8, binary
                  cls
clus                 0   1
  NUP160 MUTATED     4   7
  NUP160 WILD-TYPE 221 257
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NUP160 MUTATED      4    7
  NUP160 WILD-TYPE  221  257
        clus
vv       NUP160 MUTATED NUP160 WILD-TYPE
  FEMALE              4              221
  MALE                7              257
[1] 2 2
[1] FALSE
D431V9, binary
                  cls
clus                 0   1
  NUP160 MUTATED     8   0
  NUP160 WILD-TYPE 342  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NUP160 MUTATED      8    0
  NUP160 WILD-TYPE  342   22
     clus
vv    NUP160 MUTATED NUP160 WILD-TYPE
  NO               8              342
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  NUP160 MUTATED                      9                             2
  NUP160 WILD-TYPE                  306                            45
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  NUP160 MUTATED                       0                              0
  NUP160 WILD-TYPE                   106                             10
D431V10, multiclass
                                clus
vv                               NUP160 MUTATED NUP160 WILD-TYPE
  COLON ADENOCARCINOMA                        9              306
  COLON MUCINOUS ADENOCARCINOMA               2               45
  RECTAL ADENOCARCINOMA                       0              106
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  NUP160 MUTATED     8   0   0   0
  NUP160 WILD-TYPE 337   4  31  25
D431V11, multiclass
    clus
vv   NUP160 MUTATED NUP160 WILD-TYPE
  R0              8              337
  R1              0                4
  R2              0               31
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D431V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NUP160 MUTATED                                  0     0
  NUP160 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  NUP160 MUTATED                           2     5
  NUP160 WILD-TYPE                        20   221
D431V13, multiclass
                                  clus
vv                                 NUP160 MUTATED NUP160 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     2               20
  WHITE                                         5              221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(432) Variable = GRIA4 MUTATION ANALYSIS
D432V1, survival
                 sevent
clus2               0   1
  GRIA4 MUTATED    33   4
  GRIA4 WILD-TYPE 345  89
  GRIA4 MUTATED GRIA4 WILD-TYPE 
             37             434 
  GRIA4 MUTATED GRIA4 WILD-TYPE 
              4              89 
$`GRIA4 MUTATED`
TCGA-A6-2676 TCGA-A6-5661 TCGA-A6-6782 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3554 
       42.90        33.53        20.28        63.98         6.97        17.95 
TCGA-AA-3678 TCGA-AA-3851 TCGA-AA-3867 TCGA-AA-3877 TCGA-AA-A010 TCGA-AA-A01Z 
       47.01        33.07        24.03        31.00        34.98        37.02 
TCGA-AZ-4315 TCGA-CA-6715 TCGA-CA-6717 TCGA-CM-4744 TCGA-CM-5348 TCGA-CM-5349 
       58.39         0.07        12.76        20.02        22.98        30.08 
TCGA-CM-5868 TCGA-CM-6675 TCGA-D5-6924 TCGA-DM-A1HB TCGA-DM-A28C TCGA-F4-6460 
       17.03        13.05        14.30       135.65        81.37        31.96 
TCGA-F4-6805 TCGA-F4-6808 TCGA-F4-6856 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6317 
       34.42        33.67        35.31        55.04        63.62        36.00 
TCGA-AF-5654 TCGA-AG-3883 TCGA-AG-3898 TCGA-AG-A002 TCGA-AG-A036 TCGA-DC-6682 
       16.83         1.02        48.03        20.98       117.11         4.01 
TCGA-F5-6702 
       28.57 

$`GRIA4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       31.63        30.44        29.19        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3514 
       19.66         7.04         3.02         1.02        35.01         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
       13.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       36.03         8.05        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3556 
       33.99        21.01        13.02        24.00        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       50.04        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       17.03        10.06         0.00         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       27.02        29.98        18.05         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
       16.31         0.95        33.01        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.20        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
        1.91       124.27        23.05        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       29.06        22.03        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       15.02        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       11.01        12.95        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        3.68         4.41        12.43         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 
       12.59       140.38         7.50        44.32       131.51       139.17 
TCGA-DM-A285 TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
        6.12       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6806 
        8.61        35.74         6.18        47.87         1.55        41.42 
TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 
       16.24        13.25         0.53        47.41       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6321 
       65.85        53.62        44.68        85.48        61.91        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       10.39        14.50        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
        0.99        19.04        19.99        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3902 TCGA-AG-3909 
       13.02        35.01        14.01         1.02        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 
        1.94        38.96        61.97        41.00        38.04        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 
       13.97        27.95        10.98        19.99         5.95         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
        9.96        49.51        31.30        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  GRIA4 MUTATED GRIA4 WILD-TYPE 
           0.07            0.00 
  GRIA4 MUTATED GRIA4 WILD-TYPE 
         135.65          148.01 
  GRIA4 MUTATED GRIA4 WILD-TYPE 
          31.96           19.99 
[1] "0.1 - 135.7 (32.0)" "0.0 - 148.0 (20.0)"
[1] "hr=" "2.5"
D432V2, continuous
D432V3, binary
                 cls
clus                0   1
  GRIA4 MUTATED    30   7
  GRIA4 WILD-TYPE 336 112
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GRIA4 MUTATED     30    7
  GRIA4 WILD-TYPE  336  112
        clus
vv       GRIA4 MUTATED GRIA4 WILD-TYPE
  COLON             30             336
  RECTUM             7             112
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GRIA4 MUTATED         7        0        3        11         3         0
  GRIA4 WILD-TYPE      84        1       29       127         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  GRIA4 MUTATED           2          0          6          1        1         2
  GRIA4 WILD-TYPE        22         11         53         41       47        16
                 vv
clus              STAGE IVB
  GRIA4 MUTATED           1
  GRIA4 WILD-TYPE         0
D432V4, multiclass
            clus
vv           GRIA4 MUTATED GRIA4 WILD-TYPE
  STAGE I                7              84
  STAGE IA               0               1
  STAGE II               3              29
  STAGE IIA             11             127
  STAGE IIB              3               7
  STAGE IIC              0               1
  STAGE III              2              22
  STAGE IIIA             0              11
  STAGE IIIB             6              53
  STAGE IIIC             1              41
  STAGE IV               1              47
  STAGE IVA              2              16
  STAGE IVB              1               0
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  GRIA4 MUTATED     2   6  24   5
  GRIA4 WILD-TYPE  15  86 305  45
D432V5, multiclass
    clus
vv   GRIA4 MUTATED GRIA4 WILD-TYPE
  T1             2              15
  T2             6              86
  T3            24             305
  T4             5              45
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  GRIA4 MUTATED    24   9   4
  GRIA4 WILD-TYPE 263 104  83
D432V6, multiclass
    clus
vv   GRIA4 MUTATED GRIA4 WILD-TYPE
  N0            24             263
  N1             9             104
  N2             4              83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D432V7, binary
                 cls
clus                0   1
  GRIA4 MUTATED    31   4
  GRIA4 WILD-TYPE 344  61
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GRIA4 MUTATED     31    4
  GRIA4 WILD-TYPE  344   61
   clus
vv  GRIA4 MUTATED GRIA4 WILD-TYPE
  0            31             344
  1             4              61
[1] 2 2
[1] FALSE
D432V8, binary
                 cls
clus                0   1
  GRIA4 MUTATED    14  23
  GRIA4 WILD-TYPE 211 241
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GRIA4 MUTATED     14   23
  GRIA4 WILD-TYPE  211  241
        clus
vv       GRIA4 MUTATED GRIA4 WILD-TYPE
  FEMALE            14             211
  MALE              23             241
[1] 2 2
[1] FALSE
D432V9, binary
                 cls
clus                0   1
  GRIA4 MUTATED    30   2
  GRIA4 WILD-TYPE 320  20
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GRIA4 MUTATED     30    2
  GRIA4 WILD-TYPE  320   20
     clus
vv    GRIA4 MUTATED GRIA4 WILD-TYPE
  NO             30             320
  YES             2              20
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  GRIA4 MUTATED                     26                             3
  GRIA4 WILD-TYPE                  289                            44
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  GRIA4 MUTATED                       7                              0
  GRIA4 WILD-TYPE                    99                             10
D432V10, multiclass
                                clus
vv                               GRIA4 MUTATED GRIA4 WILD-TYPE
  COLON ADENOCARCINOMA                      26             289
  COLON MUCINOUS ADENOCARCINOMA              3              44
  RECTAL ADENOCARCINOMA                      7              99
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  GRIA4 MUTATED    31   0   1   2
  GRIA4 WILD-TYPE 314   4  30  23
D432V11, multiclass
    clus
vv   GRIA4 MUTATED GRIA4 WILD-TYPE
  R0            31             314
  R1             0               4
  R2             1              30
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D432V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GRIA4 MUTATED                                  0     2
  GRIA4 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  GRIA4 MUTATED                           2    20
  GRIA4 WILD-TYPE                        20   206
D432V13, multiclass
                                  clus
vv                                 GRIA4 MUTATED GRIA4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               9
  BLACK OR AFRICAN AMERICAN                    2              20
  WHITE                                       20             206
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(433) Variable = FBLN5 MUTATION ANALYSIS
D433V1, survival
                 sevent
clus2               0   1
  FBLN5 MUTATED     6   4
  FBLN5 WILD-TYPE 372  89
  FBLN5 MUTATED FBLN5 WILD-TYPE 
             10             461 
  FBLN5 MUTATED FBLN5 WILD-TYPE 
              4              89 
$`FBLN5 MUTATED`
TCGA-AY-5543 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-CA-6717 TCGA-CK-4952 TCGA-DM-A0XF 
       33.01        88.21        49.41        12.76        15.62        38.20 
TCGA-DM-A1DB TCGA-G4-6626 TCGA-AG-A002 TCGA-F5-6465 
       44.32        46.75        20.98        49.51 

$`FBLN5 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       16.31         0.95        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6599 TCGA-AZ-6600 
        5.13       106.75        22.36        62.79         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 
       10.06        14.30        17.56       148.01        85.45        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A1D0 
       12.00        11.38        10.26       119.70        24.43       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       35.80        26.17        91.79        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6571 TCGA-F5-6702 
       19.96        20.91        18.28         9.96        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  FBLN5 MUTATED FBLN5 WILD-TYPE 
          12.76            0.00 
  FBLN5 MUTATED FBLN5 WILD-TYPE 
          88.21          148.01 
  FBLN5 MUTATED FBLN5 WILD-TYPE 
          41.26           20.02 
[1] "12.8 - 88.2 (41.3)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.3"
D433V2, continuous
D433V3, binary
                 cls
clus                0   1
  FBLN5 MUTATED     8   2
  FBLN5 WILD-TYPE 358 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FBLN5 MUTATED      8    2
  FBLN5 WILD-TYPE  358  117
        clus
vv       FBLN5 MUTATED FBLN5 WILD-TYPE
  COLON              8             358
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FBLN5 MUTATED         2        0        1         4         0         0
  FBLN5 WILD-TYPE      89        1       31       134        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  FBLN5 MUTATED           0          0          0          2        0         1
  FBLN5 WILD-TYPE        24         11         59         40       48        17
                 vv
clus              STAGE IVB
  FBLN5 MUTATED           0
  FBLN5 WILD-TYPE         1
D433V4, multiclass
            clus
vv           FBLN5 MUTATED FBLN5 WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              4             134
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             2              40
  STAGE IV               0              48
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  FBLN5 MUTATED     1   1   7   1
  FBLN5 WILD-TYPE  16  91 322  49
D433V5, multiclass
    clus
vv   FBLN5 MUTATED FBLN5 WILD-TYPE
  T1             1              16
  T2             1              91
  T3             7             322
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  FBLN5 MUTATED     7   1   2
  FBLN5 WILD-TYPE 280 112  85
D433V6, multiclass
    clus
vv   FBLN5 MUTATED FBLN5 WILD-TYPE
  N0             7             280
  N1             1             112
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D433V7, binary
                 cls
clus                0   1
  FBLN5 MUTATED     8   1
  FBLN5 WILD-TYPE 367  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FBLN5 MUTATED      8    1
  FBLN5 WILD-TYPE  367   64
   clus
vv  FBLN5 MUTATED FBLN5 WILD-TYPE
  0             8             367
  1             1              64
[1] 2 2
[1] FALSE
D433V8, binary
                 cls
clus                0   1
  FBLN5 MUTATED     6   4
  FBLN5 WILD-TYPE 219 260
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FBLN5 MUTATED      6    4
  FBLN5 WILD-TYPE  219  260
        clus
vv       FBLN5 MUTATED FBLN5 WILD-TYPE
  FEMALE             6             219
  MALE               4             260
[1] 2 2
[1] FALSE
D433V9, binary
                 cls
clus                0   1
  FBLN5 MUTATED     7   0
  FBLN5 WILD-TYPE 343  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FBLN5 MUTATED      7    0
  FBLN5 WILD-TYPE  343   22
     clus
vv    FBLN5 MUTATED FBLN5 WILD-TYPE
  NO              7             343
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  FBLN5 MUTATED                      5                             2
  FBLN5 WILD-TYPE                  310                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  FBLN5 MUTATED                       2                              0
  FBLN5 WILD-TYPE                   104                             10
D433V10, multiclass
                                clus
vv                               FBLN5 MUTATED FBLN5 WILD-TYPE
  COLON ADENOCARCINOMA                       5             310
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  FBLN5 MUTATED     4   0   0   2
  FBLN5 WILD-TYPE 341   4  31  23
D433V11, multiclass
    clus
vv   FBLN5 MUTATED FBLN5 WILD-TYPE
  R0             4             341
  R1             0               4
  R2             0              31
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D433V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FBLN5 MUTATED                                  0     1
  FBLN5 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  FBLN5 MUTATED                           1     7
  FBLN5 WILD-TYPE                        21   219
D433V13, multiclass
                                  clus
vv                                 FBLN5 MUTATED FBLN5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        7             219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(434) Variable = FBXO34 MUTATION ANALYSIS
D434V1, survival
                  sevent
clus2                0   1
  FBXO34 MUTATED     8   4
  FBXO34 WILD-TYPE 370  89
  FBXO34 MUTATED FBXO34 WILD-TYPE 
              12              459 
  FBXO34 MUTATED FBXO34 WILD-TYPE 
               4               89 
$`FBXO34 MUTATED`
TCGA-AA-3663 TCGA-AA-3672 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-CA-6718 TCGA-CK-6747 
        6.97         0.92        58.39        49.41        10.06        82.95 
TCGA-CM-6171 TCGA-D5-6537 TCGA-DM-A1D4 TCGA-AG-3892 TCGA-AG-A002 TCGA-AH-6544 
       14.04         4.80        92.75        13.02        20.98        38.56 

$`FBXO34 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 
        6.05        54.02         2.01        14.01        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       33.01        21.44        17.82         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        88.21         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       51.32         9.99        21.14         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
       17.85        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-DM-A1D7 
      119.70        24.43        38.20       130.65        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 
       19.99         1.02        17.95        36.95        17.03        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6547 
       38.96        61.97        41.00        38.04       117.11         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  FBXO34 MUTATED FBXO34 WILD-TYPE 
            0.92             0.00 
  FBXO34 MUTATED FBXO34 WILD-TYPE 
           92.75           148.01 
  FBXO34 MUTATED FBXO34 WILD-TYPE 
           17.51            20.19 
[1] "0.9 - 92.8 (17.5)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.3"
D434V2, continuous
D434V3, binary
                  cls
clus                 0   1
  FBXO34 MUTATED     9   3
  FBXO34 WILD-TYPE 357 116
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FBXO34 MUTATED      9    3
  FBXO34 WILD-TYPE  357  116
        clus
vv       FBXO34 MUTATED FBXO34 WILD-TYPE
  COLON               9              357
  RECTUM              3              116
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FBXO34 MUTATED         3        0        2         4         0         0
  FBXO34 WILD-TYPE      88        1       30       134        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FBXO34 MUTATED           1          0          1          0        0
  FBXO34 WILD-TYPE        23         11         58         42       48
                  vv
clus               STAGE IVA STAGE IVB
  FBXO34 MUTATED           0         0
  FBXO34 WILD-TYPE        18         1
D434V4, multiclass
            clus
vv           FBXO34 MUTATED FBXO34 WILD-TYPE
  STAGE I                 3               88
  STAGE IA                0                1
  STAGE II                2               30
  STAGE IIA               4              134
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               1               23
  STAGE IIIA              0               11
  STAGE IIIB              1               58
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  FBXO34 MUTATED     1   2   9   0
  FBXO34 WILD-TYPE  16  90 320  50
D434V5, multiclass
    clus
vv   FBXO34 MUTATED FBXO34 WILD-TYPE
  T1              1               16
  T2              2               90
  T3              9              320
  T4              0               50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  FBXO34 MUTATED     9   3   0
  FBXO34 WILD-TYPE 278 110  87
D434V6, multiclass
    clus
vv   FBXO34 MUTATED FBXO34 WILD-TYPE
  N0              9              278
  N1              3              110
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D434V7, binary
                  cls
clus                 0   1
  FBXO34 MUTATED     8   1
  FBXO34 WILD-TYPE 367  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FBXO34 MUTATED      8    1
  FBXO34 WILD-TYPE  367   64
   clus
vv  FBXO34 MUTATED FBXO34 WILD-TYPE
  0              8              367
  1              1               64
[1] 2 2
[1] FALSE
D434V8, binary
                  cls
clus                 0   1
  FBXO34 MUTATED     5   7
  FBXO34 WILD-TYPE 220 257
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FBXO34 MUTATED      5    7
  FBXO34 WILD-TYPE  220  257
        clus
vv       FBXO34 MUTATED FBXO34 WILD-TYPE
  FEMALE              5              220
  MALE                7              257
[1] 2 2
[1] FALSE
D434V9, binary
                  cls
clus                 0   1
  FBXO34 MUTATED    11   0
  FBXO34 WILD-TYPE 339  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FBXO34 MUTATED     11    0
  FBXO34 WILD-TYPE  339   22
     clus
vv    FBXO34 MUTATED FBXO34 WILD-TYPE
  NO              11              339
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  FBXO34 MUTATED                      9                             0
  FBXO34 WILD-TYPE                  306                            47
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  FBXO34 MUTATED                       3                              0
  FBXO34 WILD-TYPE                   103                             10
D434V10, multiclass
                                clus
vv                               FBXO34 MUTATED FBXO34 WILD-TYPE
  COLON ADENOCARCINOMA                        9              306
  COLON MUCINOUS ADENOCARCINOMA               0               47
  RECTAL ADENOCARCINOMA                       3              103
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  FBXO34 MUTATED     7   0   0   2
  FBXO34 WILD-TYPE 338   4  31  23
D434V11, multiclass
    clus
vv   FBXO34 MUTATED FBXO34 WILD-TYPE
  R0              7              338
  R1              0                4
  R2              0               31
  RX              2               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D434V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FBXO34 MUTATED                                  0     1
  FBXO34 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  FBXO34 MUTATED                           0     7
  FBXO34 WILD-TYPE                        22   219
D434V13, multiclass
                                  clus
vv                                 FBXO34 MUTATED FBXO34 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         7              219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(435) Variable = BRCA1 MUTATION ANALYSIS
D435V1, survival
                 sevent
clus2               0   1
  BRCA1 MUTATED    20   8
  BRCA1 WILD-TYPE 358  85
  BRCA1 MUTATED BRCA1 WILD-TYPE 
             28             443 
  BRCA1 MUTATED BRCA1 WILD-TYPE 
              8              85 
$`BRCA1 MUTATED`
TCGA-A6-3809 TCGA-A6-6782 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3510 TCGA-AA-3715 
       32.75        20.28         3.02         1.02        63.98        19.04 
TCGA-AA-3977 TCGA-AA-A00E TCGA-AA-A010 TCGA-AD-6889 TCGA-AZ-6598 TCGA-AZ-6599 
       25.02        30.02        34.98        56.55        49.41         6.77 
TCGA-CA-5797 TCGA-CA-6717 TCGA-CK-4948 TCGA-CK-4952 TCGA-CM-5862 TCGA-CM-5864 
        3.29        12.76       148.01        15.62         5.03        15.02 
TCGA-CM-6171 TCGA-D5-5537 TCGA-D5-6928 TCGA-DM-A1D6 TCGA-DM-A1HB TCGA-F4-6570 
       14.04        45.40        11.64        49.91       135.65         6.18 
TCGA-G4-6317 TCGA-AG-A002 TCGA-CI-6619 TCGA-EI-6506 
       36.00        20.98         6.05        20.55 

$`BRCA1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3489 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 
       20.12        19.66         7.04        35.01         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
       13.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       36.03         8.05        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       78.08         6.05         6.97        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       38.04        19.00        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 
       18.05        40.96         0.07        21.37        15.52         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       62.79        88.21        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 
        0.07        12.20        10.06        14.30        17.56        85.45 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5863 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       10.06        12.03        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D7 TCGA-DM-A1D8 
       24.43        38.20       130.65        92.75        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 
      140.38         7.50        44.32       131.51       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
        8.61        31.96        35.74        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6321 TCGA-G4-6323 
       55.04        85.48        63.62        61.91        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        0.72        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6507 
       57.24        24.13        51.48        32.61         0.49        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  BRCA1 MUTATED BRCA1 WILD-TYPE 
           1.02            0.00 
  BRCA1 MUTATED BRCA1 WILD-TYPE 
         148.01          140.38 
  BRCA1 MUTATED BRCA1 WILD-TYPE 
         20.415          20.120 
[1] "1.0 - 148.0 (20.4)" "0.0 - 140.4 (20.1)"
[1] "hr=" "1.3"
D435V2, continuous
D435V3, binary
                 cls
clus                0   1
  BRCA1 MUTATED    26   3
  BRCA1 WILD-TYPE 340 116
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BRCA1 MUTATED     26    3
  BRCA1 WILD-TYPE  340  116
        clus
vv       BRCA1 MUTATED BRCA1 WILD-TYPE
  COLON             26             340
  RECTUM             3             116
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  BRCA1 MUTATED         4        0        5        10         3         0
  BRCA1 WILD-TYPE      87        1       27       128         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  BRCA1 MUTATED           1          0          1          2        1         1
  BRCA1 WILD-TYPE        23         11         58         40       47        17
                 vv
clus              STAGE IVB
  BRCA1 MUTATED           0
  BRCA1 WILD-TYPE         1
D435V4, multiclass
            clus
vv           BRCA1 MUTATED BRCA1 WILD-TYPE
  STAGE I                4              87
  STAGE IA               0               1
  STAGE II               5              27
  STAGE IIA             10             128
  STAGE IIB              3               7
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             2              40
  STAGE IV               1              47
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  BRCA1 MUTATED     0   5  20   4
  BRCA1 WILD-TYPE  17  87 309  46
D435V5, multiclass
    clus
vv   BRCA1 MUTATED BRCA1 WILD-TYPE
  T1             0              17
  T2             5              87
  T3            20             309
  T4             4              46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  BRCA1 MUTATED    22   4   3
  BRCA1 WILD-TYPE 265 109  84
D435V6, multiclass
    clus
vv   BRCA1 MUTATED BRCA1 WILD-TYPE
  N0            22             265
  N1             4             109
  N2             3              84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D435V7, binary
                 cls
clus                0   1
  BRCA1 MUTATED    21   2
  BRCA1 WILD-TYPE 354  63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BRCA1 MUTATED     21    2
  BRCA1 WILD-TYPE  354   63
   clus
vv  BRCA1 MUTATED BRCA1 WILD-TYPE
  0            21             354
  1             2              63
[1] 2 2
[1] FALSE
D435V8, binary
                 cls
clus                0   1
  BRCA1 MUTATED    12  17
  BRCA1 WILD-TYPE 213 247
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BRCA1 MUTATED     12   17
  BRCA1 WILD-TYPE  213  247
        clus
vv       BRCA1 MUTATED BRCA1 WILD-TYPE
  FEMALE            12             213
  MALE              17             247
[1] 2 2
[1] FALSE
D435V9, binary
                 cls
clus                0   1
  BRCA1 MUTATED    22   0
  BRCA1 WILD-TYPE 328  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BRCA1 MUTATED     22    0
  BRCA1 WILD-TYPE  328   22
     clus
vv    BRCA1 MUTATED BRCA1 WILD-TYPE
  NO             22             328
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  BRCA1 MUTATED                     20                             5
  BRCA1 WILD-TYPE                  295                            42
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  BRCA1 MUTATED                       3                              0
  BRCA1 WILD-TYPE                   103                             10
D435V10, multiclass
                                clus
vv                               BRCA1 MUTATED BRCA1 WILD-TYPE
  COLON ADENOCARCINOMA                      20             295
  COLON MUCINOUS ADENOCARCINOMA              5              42
  RECTAL ADENOCARCINOMA                      3             103
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  BRCA1 MUTATED    18   0   0   3
  BRCA1 WILD-TYPE 327   4  31  22
D435V11, multiclass
    clus
vv   BRCA1 MUTATED BRCA1 WILD-TYPE
  R0            18             327
  R1             0               4
  R2             0              31
  RX             3              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D435V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  BRCA1 MUTATED                                  0     3
  BRCA1 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  BRCA1 MUTATED                           0    17
  BRCA1 WILD-TYPE                        22   209
D435V13, multiclass
                                  clus
vv                                 BRCA1 MUTATED BRCA1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        3               8
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                       17             209
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(436) Variable = INSRR MUTATION ANALYSIS
D436V1, survival
                 sevent
clus2               0   1
  INSRR MUTATED    25   6
  INSRR WILD-TYPE 353  87
  INSRR MUTATED INSRR WILD-TYPE 
             31             440 
  INSRR MUTATED INSRR WILD-TYPE 
              6              87 
$`INSRR MUTATED`
TCGA-A6-2676 TCGA-A6-6648 TCGA-AA-3518 TCGA-AA-3666 TCGA-AA-3941 TCGA-AA-3950 
       42.90        25.18         1.02         2.01        24.00        24.00 
TCGA-AA-3977 TCGA-AD-6895 TCGA-AU-3779 TCGA-AZ-6601 TCGA-CA-6717 TCGA-CA-6718 
       25.02         0.72        14.50       100.01        12.76        10.06 
TCGA-CK-4948 TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-5868 TCGA-CM-6162 TCGA-D5-6533 
      148.01        23.05        37.02        17.03        12.00         1.32 
TCGA-D5-6538 TCGA-D5-6929 TCGA-DM-A285 TCGA-F4-6570 TCGA-G4-6304 TCGA-G4-6588 
       17.13         4.80         6.12         6.18        53.62        26.17 
TCGA-G4-6628 TCGA-AG-A002 TCGA-AH-6544 TCGA-AH-6643 TCGA-CI-6620 TCGA-DC-6157 
       79.69        20.98        38.56         0.69        33.17        27.95 
TCGA-EI-6507 
       19.96 

$`INSRR WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3519 
       63.98         6.97         1.02        13.02        38.99         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3947 
       29.98        18.05        31.00         2.01        12.99        33.01 
TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       26.01         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       15.52        56.55         0.79         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       10.88         0.20        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 
        3.06         3.25         3.29         0.07        12.20        14.30 
TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
       17.56        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4747 
       21.14        82.95         1.91       124.27        20.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6163 
       15.02         5.03        15.02        15.02        15.02         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6534 
       19.59        56.09        55.92        20.19        18.25        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       15.12        17.85         4.80        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
        9.44        11.64         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      135.65       139.17        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 
      117.07        98.24         8.61        31.96        35.74        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 
       22.09        13.78        35.80        91.79        46.75        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6644 TCGA-CI-6619 
       38.04       117.11         1.45        17.49         0.72         6.05 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       13.97        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
       32.61         0.49        20.55        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  INSRR MUTATED INSRR WILD-TYPE 
           0.69            0.00 
  INSRR MUTATED INSRR WILD-TYPE 
         148.01          140.38 
  INSRR MUTATED INSRR WILD-TYPE 
         20.980          20.155 
[1] "0.7 - 148.0 (21.0)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1"  
D436V2, continuous
D436V3, binary
                 cls
clus                0   1
  INSRR MUTATED    26   6
  INSRR WILD-TYPE 340 113
[1] "tbl2"
                 cls
clus              [,1] [,2]
  INSRR MUTATED     26    6
  INSRR WILD-TYPE  340  113
        clus
vv       INSRR MUTATED INSRR WILD-TYPE
  COLON             26             340
  RECTUM             6             113
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  INSRR MUTATED         4        0        2         9         2         0
  INSRR WILD-TYPE      87        1       30       129         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  INSRR MUTATED           2          0          3          1        2         4
  INSRR WILD-TYPE        22         11         56         41       46        14
                 vv
clus              STAGE IVB
  INSRR MUTATED           0
  INSRR WILD-TYPE         1
D436V4, multiclass
            clus
vv           INSRR MUTATED INSRR WILD-TYPE
  STAGE I                4              87
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA              9             129
  STAGE IIB              2               8
  STAGE IIC              0               1
  STAGE III              2              22
  STAGE IIIA             0              11
  STAGE IIIB             3              56
  STAGE IIIC             1              41
  STAGE IV               2              46
  STAGE IVA              4              14
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  INSRR MUTATED     0   5  21   6
  INSRR WILD-TYPE  17  87 308  44
D436V5, multiclass
    clus
vv   INSRR MUTATED INSRR WILD-TYPE
  T1             0              17
  T2             5              87
  T3            21             308
  T4             6              44
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  INSRR MUTATED    20   9   3
  INSRR WILD-TYPE 267 104  84
D436V6, multiclass
    clus
vv   INSRR MUTATED INSRR WILD-TYPE
  N0            20             267
  N1             9             104
  N2             3              84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D436V7, binary
                 cls
clus                0   1
  INSRR MUTATED    23   7
  INSRR WILD-TYPE 352  58
[1] "tbl2"
                 cls
clus              [,1] [,2]
  INSRR MUTATED     23    7
  INSRR WILD-TYPE  352   58
   clus
vv  INSRR MUTATED INSRR WILD-TYPE
  0            23             352
  1             7              58
[1] 2 2
[1] FALSE
D436V8, binary
                 cls
clus                0   1
  INSRR MUTATED    17  15
  INSRR WILD-TYPE 208 249
[1] "tbl2"
                 cls
clus              [,1] [,2]
  INSRR MUTATED     17   15
  INSRR WILD-TYPE  208  249
        clus
vv       INSRR MUTATED INSRR WILD-TYPE
  FEMALE            17             208
  MALE              15             249
[1] 2 2
[1] FALSE
D436V9, binary
                 cls
clus                0   1
  INSRR MUTATED    23   0
  INSRR WILD-TYPE 327  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  INSRR MUTATED     23    0
  INSRR WILD-TYPE  327   22
     clus
vv    INSRR MUTATED INSRR WILD-TYPE
  NO             23             327
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  INSRR MUTATED                     22                             4
  INSRR WILD-TYPE                  293                            43
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  INSRR MUTATED                       6                              0
  INSRR WILD-TYPE                   100                             10
D436V10, multiclass
                                clus
vv                               INSRR MUTATED INSRR WILD-TYPE
  COLON ADENOCARCINOMA                      22             293
  COLON MUCINOUS ADENOCARCINOMA              4              43
  RECTAL ADENOCARCINOMA                      6             100
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  INSRR MUTATED    23   0   0   2
  INSRR WILD-TYPE 322   4  31  23
D436V11, multiclass
    clus
vv   INSRR MUTATED INSRR WILD-TYPE
  R0            23             322
  R1             0               4
  R2             0              31
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D436V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  INSRR MUTATED                                  0     2
  INSRR WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  INSRR MUTATED                           2    21
  INSRR WILD-TYPE                        20   205
D436V13, multiclass
                                  clus
vv                                 INSRR MUTATED INSRR WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               9
  BLACK OR AFRICAN AMERICAN                    2              20
  WHITE                                       21             205
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(437) Variable = FBN2 MUTATION ANALYSIS
D437V1, survival
                sevent
clus2              0   1
  FBN2 MUTATED    31  13
  FBN2 WILD-TYPE 347  80
  FBN2 MUTATED FBN2 WILD-TYPE 
            44            427 
  FBN2 MUTATED FBN2 WILD-TYPE 
            13             80 
$`FBN2 MUTATED`
TCGA-A6-3809 TCGA-A6-4105 TCGA-A6-5665 TCGA-A6-6649 TCGA-A6-6653 TCGA-AA-3510 
       32.75        14.53        22.06        24.16        24.39        63.98 
TCGA-AA-3516 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3864 
       13.02         0.99        13.02        17.95        29.95        53.00 
TCGA-AA-3947 TCGA-AA-3966 TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01G 
       33.01         2.01        25.02         4.01        34.98        12.00 
TCGA-AA-A01Q TCGA-AA-A01V TCGA-AA-A03F TCGA-AD-5900 TCGA-AY-4071 TCGA-AZ-4315 
        1.02        35.01        18.05         0.07         0.95        58.39 
TCGA-AZ-6601 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-5914 TCGA-CK-6751 TCGA-CM-6169 
      100.01        12.76        10.06         9.99       124.27        13.02 
TCGA-CM-6674 TCGA-D5-6898 TCGA-D5-6928 TCGA-DM-A0XF TCGA-DM-A28F TCGA-F4-6460 
       12.95         1.48        11.64        38.20        35.97        31.96 
TCGA-F4-6570 TCGA-F4-6704 TCGA-G4-6315 TCGA-G4-6321 TCGA-G4-6588 TCGA-AG-A002 
        6.18         1.55        61.91        22.09        26.17        20.98 
TCGA-DY-A1DD TCGA-F5-6811 
       57.24        32.19 

$`FBN2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 
       16.57        34.65        33.34        36.53        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 
       30.44        29.19        33.53        23.61        22.09        32.71 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 
       27.09        22.52         8.38        25.08        25.18        21.76 
TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 
       24.69        23.87        20.12        19.66        20.28         7.04 
TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02         1.02        35.01         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 
       26.01        12.99        14.01        33.99        21.01        24.00 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       78.08         6.05         6.97        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       30.05        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 
       31.00         2.01        12.99        24.00        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
        2.01        20.98        34.03        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01R 
       10.98        32.02        31.00        31.00        38.07        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
        1.02        33.04        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       39.98        40.96        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       14.50        27.09        16.31        33.01        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       49.41         6.77        12.10        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.07        12.20        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        49.08        51.32        21.14        82.95         1.91 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6170 
       29.03        16.04        21.99        14.99        12.99        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       14.04        11.01        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       24.43       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
        6.12        81.37       119.93        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        8.61        35.74        47.87        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 
       63.62        36.00        13.78        35.80        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
        5.29       126.44        41.36        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       49.51        31.30        28.57         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  FBN2 MUTATED FBN2 WILD-TYPE 
          0.07           0.00 
  FBN2 MUTATED FBN2 WILD-TYPE 
        124.27         148.01 
  FBN2 MUTATED FBN2 WILD-TYPE 
         21.52          20.12 
[1] "0.1 - 124.3 (21.5)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.6"
D437V2, continuous
D437V3, binary
                cls
clus               0   1
  FBN2 MUTATED    42   3
  FBN2 WILD-TYPE 324 116
[1] "tbl2"
                cls
clus             [,1] [,2]
  FBN2 MUTATED     42    3
  FBN2 WILD-TYPE  324  116
        clus
vv       FBN2 MUTATED FBN2 WILD-TYPE
  COLON            42            324
  RECTUM            3            116
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FBN2 MUTATED         8        0        4        16         4         0
  FBN2 WILD-TYPE      83        1       28       122         6         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  FBN2 MUTATED           3          0          5          4        1         0
  FBN2 WILD-TYPE        21         11         54         38       47        18
                vv
clus             STAGE IVB
  FBN2 MUTATED           0
  FBN2 WILD-TYPE         1
D437V4, multiclass
            clus
vv           FBN2 MUTATED FBN2 WILD-TYPE
  STAGE I               8             83
  STAGE IA              0              1
  STAGE II              4             28
  STAGE IIA            16            122
  STAGE IIB             4              6
  STAGE IIC             0              1
  STAGE III             3             21
  STAGE IIIA            0             11
  STAGE IIIB            5             54
  STAGE IIIC            4             38
  STAGE IV              1             47
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  FBN2 MUTATED     1   9  32   4
  FBN2 WILD-TYPE  16  83 297  46
D437V5, multiclass
    clus
vv   FBN2 MUTATED FBN2 WILD-TYPE
  T1            1             16
  T2            9             83
  T3           32            297
  T4            4             46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  FBN2 MUTATED    33   7   6
  FBN2 WILD-TYPE 254 106  81
D437V6, multiclass
    clus
vv   FBN2 MUTATED FBN2 WILD-TYPE
  N0           33            254
  N1            7            106
  N2            6             81
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D437V7, binary
                cls
clus               0   1
  FBN2 MUTATED    37   1
  FBN2 WILD-TYPE 338  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  FBN2 MUTATED     37    1
  FBN2 WILD-TYPE  338   64
   clus
vv  FBN2 MUTATED FBN2 WILD-TYPE
  0           37            338
  1            1             64
[1] 2 2
[1] FALSE
D437V8, binary
                cls
clus               0   1
  FBN2 MUTATED    21  25
  FBN2 WILD-TYPE 204 239
[1] "tbl2"
                cls
clus             [,1] [,2]
  FBN2 MUTATED     21   25
  FBN2 WILD-TYPE  204  239
        clus
vv       FBN2 MUTATED FBN2 WILD-TYPE
  FEMALE           21            204
  MALE             25            239
[1] 2 2
[1] FALSE
D437V9, binary
                cls
clus               0   1
  FBN2 MUTATED    32   0
  FBN2 WILD-TYPE 318  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  FBN2 MUTATED     32    0
  FBN2 WILD-TYPE  318   22
     clus
vv    FBN2 MUTATED FBN2 WILD-TYPE
  NO            32            318
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  FBN2 MUTATED                     26                            15
  FBN2 WILD-TYPE                  289                            32
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  FBN2 MUTATED                       3                              0
  FBN2 WILD-TYPE                   103                             10
D437V10, multiclass
                                clus
vv                               FBN2 MUTATED FBN2 WILD-TYPE
  COLON ADENOCARCINOMA                     26            289
  COLON MUCINOUS ADENOCARCINOMA            15             32
  RECTAL ADENOCARCINOMA                     3            103
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  FBN2 MUTATED    31   0   0   4
  FBN2 WILD-TYPE 314   4  31  21
D437V11, multiclass
    clus
vv   FBN2 MUTATED FBN2 WILD-TYPE
  R0           31            314
  R1            0              4
  R2            0             31
  RX            4             21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D437V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FBN2 MUTATED                                  1     2
  FBN2 WILD-TYPE                                0     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  FBN2 MUTATED                           1    24
  FBN2 WILD-TYPE                        21   202
D437V13, multiclass
                                  clus
vv                                 FBN2 MUTATED FBN2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            1              0
  ASIAN                                       2              9
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                      24            202
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(438) Variable = STAB2 MUTATION ANALYSIS
D438V1, survival
                 sevent
clus2               0   1
  STAB2 MUTATED    31   4
  STAB2 WILD-TYPE 347  89
  STAB2 MUTATED STAB2 WILD-TYPE 
             35             436 
  STAB2 MUTATED STAB2 WILD-TYPE 
              4              89 
$`STAB2 MUTATED`
TCGA-A6-2672 TCGA-A6-3809 TCGA-A6-6141 TCGA-A6-6653 TCGA-A6-6780 TCGA-AA-3492 
       46.65        32.75         8.38        24.39        20.12         3.02 
TCGA-AA-3510 TCGA-AA-3554 TCGA-AA-3845 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3947 
       63.98        17.95         0.00        31.07        53.00        33.01 
TCGA-AA-3949 TCGA-AA-3977 TCGA-AA-A00K TCGA-AA-A010 TCGA-AA-A01T TCGA-AZ-4315 
       26.01        25.02        18.05        34.98        33.04        58.39 
TCGA-AZ-6600 TCGA-CA-5797 TCGA-CA-6717 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6679 
       12.10         3.29        12.76        21.99        14.99        10.06 
TCGA-D5-6536 TCGA-D5-6538 TCGA-DM-A0XD TCGA-DM-A1HB TCGA-DM-A28K TCGA-F4-6703 
       17.85        17.13        24.43       135.65        98.24        47.87 
TCGA-G4-6323 TCGA-AG-3892 TCGA-AG-A002 TCGA-AG-A02N TCGA-F5-6811 
       13.78        13.02        20.98        61.97        32.19 

$`STAB2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5657 
       34.65        33.34        36.53        14.53        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       30.44        29.19        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       32.71        27.09        22.52        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 
       21.76        24.69        23.87        19.66        20.28         7.04 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       13.02        24.00        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 
       15.95        38.99        37.02        14.93        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       31.07        30.05        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3950 
       18.05        31.00         2.01        12.99        24.00        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00L TCGA-AA-A00N 
       19.00        30.02        34.03        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01X 
       38.07         1.02        35.01         1.02        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       49.41         6.77       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-6715 
        3.19         1.61        12.69         3.06         3.25         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.20        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6168 TCGA-CM-6169 
       12.00         2.96        29.03        16.04        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.08        11.01        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
       15.12         4.80        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
      119.70        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 
       12.59       140.38         7.50        44.32       131.51       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6704 TCGA-F4-6805 
        8.61        31.96        35.74         6.18         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       17.03        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
       49.97         1.94        38.96        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  STAB2 MUTATED STAB2 WILD-TYPE 
              0               0 
  STAB2 MUTATED STAB2 WILD-TYPE 
         135.65          148.01 
  STAB2 MUTATED STAB2 WILD-TYPE 
          24.39           20.02 
[1] "0.0 - 135.7 (24.4)" "0.0 - 148.0 (20.0)"
[1] "hr=" "2.1"
D438V2, continuous
D438V3, binary
                 cls
clus                0   1
  STAB2 MUTATED    32   4
  STAB2 WILD-TYPE 334 115
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STAB2 MUTATED     32    4
  STAB2 WILD-TYPE  334  115
        clus
vv       STAB2 MUTATED STAB2 WILD-TYPE
  COLON             32             334
  RECTUM             4             115
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  STAB2 MUTATED         6        1        4        14         3         0
  STAB2 WILD-TYPE      85        0       28       124         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  STAB2 MUTATED           1          0          4          1        1         0
  STAB2 WILD-TYPE        23         11         55         41       47        18
                 vv
clus              STAGE IVB
  STAB2 MUTATED           0
  STAB2 WILD-TYPE         1
D438V4, multiclass
            clus
vv           STAB2 MUTATED STAB2 WILD-TYPE
  STAGE I                6              85
  STAGE IA               1               0
  STAGE II               4              28
  STAGE IIA             14             124
  STAGE IIB              3               7
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             4              55
  STAGE IIIC             1              41
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  STAB2 MUTATED     1   6  24   4
  STAB2 WILD-TYPE  16  86 305  46
D438V5, multiclass
    clus
vv   STAB2 MUTATED STAB2 WILD-TYPE
  T1             1              16
  T2             6              86
  T3            24             305
  T4             4              46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  STAB2 MUTATED    29   5   2
  STAB2 WILD-TYPE 258 108  85
D438V6, multiclass
    clus
vv   STAB2 MUTATED STAB2 WILD-TYPE
  N0            29             258
  N1             5             108
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D438V7, binary
                 cls
clus                0   1
  STAB2 MUTATED    31   1
  STAB2 WILD-TYPE 344  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STAB2 MUTATED     31    1
  STAB2 WILD-TYPE  344   64
   clus
vv  STAB2 MUTATED STAB2 WILD-TYPE
  0            31             344
  1             1              64
[1] 2 2
[1] FALSE
D438V8, binary
                 cls
clus                0   1
  STAB2 MUTATED    14  22
  STAB2 WILD-TYPE 211 242
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STAB2 MUTATED     14   22
  STAB2 WILD-TYPE  211  242
        clus
vv       STAB2 MUTATED STAB2 WILD-TYPE
  FEMALE            14             211
  MALE              22             242
[1] 2 2
[1] FALSE
D438V9, binary
                 cls
clus                0   1
  STAB2 MUTATED    28   0
  STAB2 WILD-TYPE 322  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STAB2 MUTATED     28    0
  STAB2 WILD-TYPE  322   22
     clus
vv    STAB2 MUTATED STAB2 WILD-TYPE
  NO             28             322
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  STAB2 MUTATED                     25                             6
  STAB2 WILD-TYPE                  290                            41
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  STAB2 MUTATED                       4                              0
  STAB2 WILD-TYPE                   102                             10
D438V10, multiclass
                                clus
vv                               STAB2 MUTATED STAB2 WILD-TYPE
  COLON ADENOCARCINOMA                      25             290
  COLON MUCINOUS ADENOCARCINOMA              6              41
  RECTAL ADENOCARCINOMA                      4             102
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  STAB2 MUTATED    25   0   0   2
  STAB2 WILD-TYPE 320   4  31  23
D438V11, multiclass
    clus
vv   STAB2 MUTATED STAB2 WILD-TYPE
  R0            25             320
  R1             0               4
  R2             0              31
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D438V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  STAB2 MUTATED                                  0     2
  STAB2 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  STAB2 MUTATED                           4    15
  STAB2 WILD-TYPE                        18   211
D438V13, multiclass
                                  clus
vv                                 STAB2 MUTATED STAB2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               9
  BLACK OR AFRICAN AMERICAN                    4              18
  WHITE                                       15             211
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(439) Variable = ATP6V1A MUTATION ANALYSIS
D439V1, survival
                   sevent
clus2                 0   1
  ATP6V1A MUTATED     9   2
  ATP6V1A WILD-TYPE 369  91
  ATP6V1A MUTATED ATP6V1A WILD-TYPE 
               11               460 
  ATP6V1A MUTATED ATP6V1A WILD-TYPE 
                2                91 
$`ATP6V1A MUTATED`
TCGA-A6-6781 TCGA-AA-3811 TCGA-AA-3977 TCGA-AZ-6603 TCGA-CA-6717 TCGA-CM-5344 
       19.66        10.06        25.02        29.56        12.76        22.03 
TCGA-D5-6923 TCGA-D5-6930 TCGA-DM-A1D0 TCGA-AF-2693 TCGA-CI-6624 
       12.43         1.51       130.65        19.10         4.73 

$`ATP6V1A WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
      100.01         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07        12.20        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6924 TCGA-D5-6926 
       15.58         1.48         3.68         4.41        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
        9.44        11.64         4.80        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
      119.70        24.43        38.20        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       13.55        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
       33.17         6.97        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  ATP6V1A MUTATED ATP6V1A WILD-TYPE 
             1.51              0.00 
  ATP6V1A MUTATED ATP6V1A WILD-TYPE 
           130.65            148.01 
  ATP6V1A MUTATED ATP6V1A WILD-TYPE 
           19.100            20.415 
[1] "1.5 - 130.7 (19.1)" "0.0 - 148.0 (20.4)"
[1] "hr=" "1"  
D439V2, continuous
D439V3, binary
                   cls
clus                  0   1
  ATP6V1A MUTATED     9   1
  ATP6V1A WILD-TYPE 357 118
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ATP6V1A MUTATED      9    1
  ATP6V1A WILD-TYPE  357  118
        clus
vv       ATP6V1A MUTATED ATP6V1A WILD-TYPE
  COLON                9               357
  RECTUM               1               118
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ATP6V1A MUTATED         3        0        0         3         0         0
  ATP6V1A WILD-TYPE      88        1       32       135        10         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ATP6V1A MUTATED           1          0          1          1        0
  ATP6V1A WILD-TYPE        23         11         58         41       48
                   vv
clus                STAGE IVA STAGE IVB
  ATP6V1A MUTATED           0         0
  ATP6V1A WILD-TYPE        18         1
D439V4, multiclass
            clus
vv           ATP6V1A MUTATED ATP6V1A WILD-TYPE
  STAGE I                  3                88
  STAGE IA                 0                 1
  STAGE II                 0                32
  STAGE IIA                3               135
  STAGE IIB                0                10
  STAGE IIC                0                 1
  STAGE III                1                23
  STAGE IIIA               0                11
  STAGE IIIB               1                58
  STAGE IIIC               1                41
  STAGE IV                 0                48
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  ATP6V1A MUTATED     0   5   5   1
  ATP6V1A WILD-TYPE  17  87 324  49
D439V5, multiclass
    clus
vv   ATP6V1A MUTATED ATP6V1A WILD-TYPE
  T1               0                17
  T2               5                87
  T3               5               324
  T4               1                49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  ATP6V1A MUTATED     7   3   1
  ATP6V1A WILD-TYPE 280 110  86
D439V6, multiclass
    clus
vv   ATP6V1A MUTATED ATP6V1A WILD-TYPE
  N0               7               280
  N1               3               110
  N2               1                86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D439V7, binary
                   cls
clus                  0   1
  ATP6V1A MUTATED     7   0
  ATP6V1A WILD-TYPE 368  65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ATP6V1A MUTATED      7    0
  ATP6V1A WILD-TYPE  368   65
   clus
vv  ATP6V1A MUTATED ATP6V1A WILD-TYPE
  0               7               368
  1               0                65
[1] 2 2
[1] FALSE
D439V8, binary
                   cls
clus                  0   1
  ATP6V1A MUTATED     5   6
  ATP6V1A WILD-TYPE 220 258
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ATP6V1A MUTATED      5    6
  ATP6V1A WILD-TYPE  220  258
        clus
vv       ATP6V1A MUTATED ATP6V1A WILD-TYPE
  FEMALE               5               220
  MALE                 6               258
[1] 2 2
[1] FALSE
D439V9, binary
                   cls
clus                  0   1
  ATP6V1A MUTATED     8   0
  ATP6V1A WILD-TYPE 342  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ATP6V1A MUTATED      8    0
  ATP6V1A WILD-TYPE  342   22
     clus
vv    ATP6V1A MUTATED ATP6V1A WILD-TYPE
  NO                8               342
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ATP6V1A MUTATED                      6                             3
  ATP6V1A WILD-TYPE                  309                            44
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ATP6V1A MUTATED                       1                              0
  ATP6V1A WILD-TYPE                   105                             10
D439V10, multiclass
                                clus
vv                               ATP6V1A MUTATED ATP6V1A WILD-TYPE
  COLON ADENOCARCINOMA                         6               309
  COLON MUCINOUS ADENOCARCINOMA                3                44
  RECTAL ADENOCARCINOMA                        1               105
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  ATP6V1A MUTATED     5   0   0   1
  ATP6V1A WILD-TYPE 340   4  31  24
D439V11, multiclass
    clus
vv   ATP6V1A MUTATED ATP6V1A WILD-TYPE
  R0               5               340
  R1               0                 4
  R2               0                31
  RX               1                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D439V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ATP6V1A MUTATED                                  0     1
  ATP6V1A WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  ATP6V1A MUTATED                           0     8
  ATP6V1A WILD-TYPE                        22   218
D439V13, multiclass
                                  clus
vv                                 ATP6V1A MUTATED ATP6V1A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                10
  BLACK OR AFRICAN AMERICAN                      0                22
  WHITE                                          8               218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(440) Variable = DUSP19 MUTATION ANALYSIS
D440V1, survival
                  sevent
clus2                0   1
  DUSP19 MUTATED    10   2
  DUSP19 WILD-TYPE 368  91
  DUSP19 MUTATED DUSP19 WILD-TYPE 
              12              459 
  DUSP19 MUTATED DUSP19 WILD-TYPE 
               2               91 
$`DUSP19 MUTATED`
TCGA-A6-5665 TCGA-AA-A00N TCGA-AZ-4315 TCGA-CA-6719 TCGA-CM-4752 TCGA-D5-5538 
       22.06         4.01        58.39        14.30        13.02        12.26 
TCGA-D5-6537 TCGA-D5-6923 TCGA-D5-6930 TCGA-AG-A002 TCGA-EI-6506 TCGA-EI-6510 
        4.80        12.43         1.51        20.98        20.55        18.28 

$`DUSP19 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       33.01        21.44        17.82         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       12.76        10.06        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-5341 
      124.27        23.05        20.02        37.02        25.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5539 
       11.08        11.01        10.06        12.03        45.40        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       15.12        17.85        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        1.48         3.68         4.41        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       11.64         4.80        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6507 TCGA-EI-6508 
       24.13        51.48        32.61         0.49        19.96        20.91 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  DUSP19 MUTATED DUSP19 WILD-TYPE 
            1.51             0.00 
  DUSP19 MUTATED DUSP19 WILD-TYPE 
           58.39           148.01 
  DUSP19 MUTATED DUSP19 WILD-TYPE 
           13.66            20.91 
[1] "1.5 - 58.4 (13.7)"  "0.0 - 148.0 (20.9)"
[1] "hr=" "1.2"
D440V2, continuous
D440V3, binary
                  cls
clus                 0   1
  DUSP19 MUTATED     9   3
  DUSP19 WILD-TYPE 357 116
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DUSP19 MUTATED      9    3
  DUSP19 WILD-TYPE  357  116
        clus
vv       DUSP19 MUTATED DUSP19 WILD-TYPE
  COLON               9              357
  RECTUM              3              116
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DUSP19 MUTATED         2        0        0         6         1         0
  DUSP19 WILD-TYPE      89        1       32       132         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DUSP19 MUTATED           0          0          2          0        0
  DUSP19 WILD-TYPE        24         11         57         42       48
                  vv
clus               STAGE IVA STAGE IVB
  DUSP19 MUTATED           1         0
  DUSP19 WILD-TYPE        17         1
D440V4, multiclass
            clus
vv           DUSP19 MUTATED DUSP19 WILD-TYPE
  STAGE I                 2               89
  STAGE IA                0                1
  STAGE II                0               32
  STAGE IIA               6              132
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              2               57
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               1               17
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  DUSP19 MUTATED     0   3   8   1
  DUSP19 WILD-TYPE  17  89 321  49
D440V5, multiclass
    clus
vv   DUSP19 MUTATED DUSP19 WILD-TYPE
  T1              0               17
  T2              3               89
  T3              8              321
  T4              1               49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  DUSP19 MUTATED    10   2   0
  DUSP19 WILD-TYPE 277 111  87
D440V6, multiclass
    clus
vv   DUSP19 MUTATED DUSP19 WILD-TYPE
  N0             10              277
  N1              2              111
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D440V7, binary
                  cls
clus                 0   1
  DUSP19 MUTATED    10   0
  DUSP19 WILD-TYPE 365  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DUSP19 MUTATED     10    0
  DUSP19 WILD-TYPE  365   65
   clus
vv  DUSP19 MUTATED DUSP19 WILD-TYPE
  0             10              365
  1              0               65
[1] 2 2
[1] FALSE
D440V8, binary
                  cls
clus                 0   1
  DUSP19 MUTATED     4   8
  DUSP19 WILD-TYPE 221 256
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DUSP19 MUTATED      4    8
  DUSP19 WILD-TYPE  221  256
        clus
vv       DUSP19 MUTATED DUSP19 WILD-TYPE
  FEMALE              4              221
  MALE                8              256
[1] 2 2
[1] FALSE
D440V9, binary
                  cls
clus                 0   1
  DUSP19 MUTATED    10   0
  DUSP19 WILD-TYPE 340  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DUSP19 MUTATED     10    0
  DUSP19 WILD-TYPE  340   22
     clus
vv    DUSP19 MUTATED DUSP19 WILD-TYPE
  NO              10              340
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  DUSP19 MUTATED                      7                             2
  DUSP19 WILD-TYPE                  308                            45
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  DUSP19 MUTATED                       3                              0
  DUSP19 WILD-TYPE                   103                             10
D440V10, multiclass
                                clus
vv                               DUSP19 MUTATED DUSP19 WILD-TYPE
  COLON ADENOCARCINOMA                        7              308
  COLON MUCINOUS ADENOCARCINOMA               2               45
  RECTAL ADENOCARCINOMA                       3              103
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  DUSP19 MUTATED    11   0   0   1
  DUSP19 WILD-TYPE 334   4  31  24
D440V11, multiclass
    clus
vv   DUSP19 MUTATED DUSP19 WILD-TYPE
  R0             11              334
  R1              0                4
  R2              0               31
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D440V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DUSP19 MUTATED                                  0     1
  DUSP19 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  DUSP19 MUTATED                           1     8
  DUSP19 WILD-TYPE                        21   218
D440V13, multiclass
                                  clus
vv                                 DUSP19 MUTATED DUSP19 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                         8              218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(441) Variable = MRPS5 MUTATION ANALYSIS
D441V1, survival
                 sevent
clus2               0   1
  MRPS5 MUTATED     8   4
  MRPS5 WILD-TYPE 370  89
  MRPS5 MUTATED MRPS5 WILD-TYPE 
             12             459 
  MRPS5 MUTATED MRPS5 WILD-TYPE 
              4              89 
$`MRPS5 MUTATED`
TCGA-AA-3672 TCGA-AA-A00N TCGA-AD-6890 TCGA-AY-6197 TCGA-AZ-6599 TCGA-AZ-6600 
        0.92         4.01         0.79        21.44         6.77        12.10 
TCGA-CA-5796 TCGA-CM-6165 TCGA-D5-6532 TCGA-D5-6537 TCGA-G4-6304 TCGA-EI-6507 
        3.25        16.04        18.25         4.80        53.62        19.96 

$`MRPS5 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
        6.05         6.97        54.02         2.01        14.01        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
       56.55         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       62.79        88.21        49.41       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5797 
       11.74         3.19         1.61        12.69         3.06         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6166 
       17.03        15.02        12.00         2.96        29.03        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6538 
       20.19         1.32        43.27        15.12        17.85        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6510 
       51.48        32.61         0.49        20.55        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  MRPS5 MUTATED MRPS5 WILD-TYPE 
           0.79            0.00 
  MRPS5 MUTATED MRPS5 WILD-TYPE 
          53.62          148.01 
  MRPS5 MUTATED MRPS5 WILD-TYPE 
          9.435          20.980 
[1] "0.8 - 53.6 (9.4)"   "0.0 - 148.0 (21.0)"
[1] "hr=" "3.1"
D441V2, continuous
D441V3, binary
                 cls
clus                0   1
  MRPS5 MUTATED    11   1
  MRPS5 WILD-TYPE 355 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MRPS5 MUTATED     11    1
  MRPS5 WILD-TYPE  355  118
        clus
vv       MRPS5 MUTATED MRPS5 WILD-TYPE
  COLON             11             355
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MRPS5 MUTATED         1        0        0         5         2         0
  MRPS5 WILD-TYPE      90        1       32       133         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MRPS5 MUTATED           1          0          1          0        1         0
  MRPS5 WILD-TYPE        23         11         58         42       47        18
                 vv
clus              STAGE IVB
  MRPS5 MUTATED           0
  MRPS5 WILD-TYPE         1
D441V4, multiclass
            clus
vv           MRPS5 MUTATED MRPS5 WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              5             133
  STAGE IIB              2               8
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             0              42
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  MRPS5 MUTATED     1   1   7   3
  MRPS5 WILD-TYPE  16  91 322  47
D441V5, multiclass
    clus
vv   MRPS5 MUTATED MRPS5 WILD-TYPE
  T1             1              16
  T2             1              91
  T3             7             322
  T4             3              47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  MRPS5 MUTATED     9   3   0
  MRPS5 WILD-TYPE 278 110  87
D441V6, multiclass
    clus
vv   MRPS5 MUTATED MRPS5 WILD-TYPE
  N0             9             278
  N1             3             110
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D441V7, binary
                 cls
clus                0   1
  MRPS5 MUTATED     7   1
  MRPS5 WILD-TYPE 368  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MRPS5 MUTATED      7    1
  MRPS5 WILD-TYPE  368   64
   clus
vv  MRPS5 MUTATED MRPS5 WILD-TYPE
  0             7             368
  1             1              64
[1] 2 2
[1] FALSE
D441V8, binary
                 cls
clus                0   1
  MRPS5 MUTATED     3   9
  MRPS5 WILD-TYPE 222 255
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MRPS5 MUTATED      3    9
  MRPS5 WILD-TYPE  222  255
        clus
vv       MRPS5 MUTATED MRPS5 WILD-TYPE
  FEMALE             3             222
  MALE               9             255
[1] 2 2
[1] FALSE
D441V9, binary
                 cls
clus                0   1
  MRPS5 MUTATED     9   0
  MRPS5 WILD-TYPE 341  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MRPS5 MUTATED      9    0
  MRPS5 WILD-TYPE  341   22
     clus
vv    MRPS5 MUTATED MRPS5 WILD-TYPE
  NO              9             341
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MRPS5 MUTATED                      9                             2
  MRPS5 WILD-TYPE                  306                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MRPS5 MUTATED                       1                              0
  MRPS5 WILD-TYPE                   105                             10
D441V10, multiclass
                                clus
vv                               MRPS5 MUTATED MRPS5 WILD-TYPE
  COLON ADENOCARCINOMA                       9             306
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  MRPS5 MUTATED     9   0   0   0
  MRPS5 WILD-TYPE 336   4  31  25
D441V11, multiclass
    clus
vv   MRPS5 MUTATED MRPS5 WILD-TYPE
  R0             9             336
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D441V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MRPS5 MUTATED                                  0     1
  MRPS5 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  MRPS5 MUTATED                           1     8
  MRPS5 WILD-TYPE                        21   218
D441V13, multiclass
                                  clus
vv                                 MRPS5 MUTATED MRPS5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        8             218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(442) Variable = UIMC1 MUTATION ANALYSIS
D442V1, survival
                 sevent
clus2               0   1
  UIMC1 MUTATED     6   3
  UIMC1 WILD-TYPE 372  90
  UIMC1 MUTATED UIMC1 WILD-TYPE 
              9             462 
  UIMC1 MUTATED UIMC1 WILD-TYPE 
              3              90 
$`UIMC1 MUTATED`
TCGA-AA-A01P TCGA-CA-6717 TCGA-CK-4948 TCGA-CM-5862 TCGA-D5-6927 TCGA-G4-6323 
       38.07        12.76       148.01         5.03         9.44        13.78 
TCGA-AG-A002 TCGA-AG-A032 TCGA-DY-A1DC 
       20.98        38.04        41.36 

$`UIMC1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01Q TCGA-AA-A01R 
       32.02        12.00        31.00        31.00         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 
        0.07        12.20        10.06        14.30        17.56        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
       15.02        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       12.43        14.30         9.04        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       22.09        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       41.00       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  UIMC1 MUTATED UIMC1 WILD-TYPE 
           5.03            0.00 
  UIMC1 MUTATED UIMC1 WILD-TYPE 
         148.01          140.38 
  UIMC1 MUTATED UIMC1 WILD-TYPE 
         20.980          20.155 
[1] "5.0 - 148.0 (21.0)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.5"
D442V2, continuous
D442V3, binary
                 cls
clus                0   1
  UIMC1 MUTATED     6   3
  UIMC1 WILD-TYPE 360 116
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UIMC1 MUTATED      6    3
  UIMC1 WILD-TYPE  360  116
        clus
vv       UIMC1 MUTATED UIMC1 WILD-TYPE
  COLON              6             360
  RECTUM             3             116
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  UIMC1 MUTATED         1        1        0         3         0         0
  UIMC1 WILD-TYPE      90        0       32       135        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  UIMC1 MUTATED           2          0          1          0        0         1
  UIMC1 WILD-TYPE        22         11         58         42       48        17
                 vv
clus              STAGE IVB
  UIMC1 MUTATED           0
  UIMC1 WILD-TYPE         1
D442V4, multiclass
            clus
vv           UIMC1 MUTATED UIMC1 WILD-TYPE
  STAGE I                1              90
  STAGE IA               1               0
  STAGE II               0              32
  STAGE IIA              3             135
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              2              22
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  UIMC1 MUTATED     0   1   7   0
  UIMC1 WILD-TYPE  17  91 322  50
D442V5, multiclass
    clus
vv   UIMC1 MUTATED UIMC1 WILD-TYPE
  T1             0              17
  T2             1              91
  T3             7             322
  T4             0              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  UIMC1 MUTATED     5   4   0
  UIMC1 WILD-TYPE 282 109  87
D442V6, multiclass
    clus
vv   UIMC1 MUTATED UIMC1 WILD-TYPE
  N0             5             282
  N1             4             109
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D442V7, binary
                 cls
clus                0   1
  UIMC1 MUTATED     7   1
  UIMC1 WILD-TYPE 368  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UIMC1 MUTATED      7    1
  UIMC1 WILD-TYPE  368   64
   clus
vv  UIMC1 MUTATED UIMC1 WILD-TYPE
  0             7             368
  1             1              64
[1] 2 2
[1] FALSE
D442V8, binary
                 cls
clus                0   1
  UIMC1 MUTATED     3   6
  UIMC1 WILD-TYPE 222 258
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UIMC1 MUTATED      3    6
  UIMC1 WILD-TYPE  222  258
        clus
vv       UIMC1 MUTATED UIMC1 WILD-TYPE
  FEMALE             3             222
  MALE               6             258
[1] 2 2
[1] FALSE
D442V9, binary
                 cls
clus                0   1
  UIMC1 MUTATED     7   1
  UIMC1 WILD-TYPE 343  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UIMC1 MUTATED      7    1
  UIMC1 WILD-TYPE  343   21
     clus
vv    UIMC1 MUTATED UIMC1 WILD-TYPE
  NO              7             343
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  UIMC1 MUTATED                      5                             1
  UIMC1 WILD-TYPE                  310                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  UIMC1 MUTATED                       3                              0
  UIMC1 WILD-TYPE                   103                             10
D442V10, multiclass
                                clus
vv                               UIMC1 MUTATED UIMC1 WILD-TYPE
  COLON ADENOCARCINOMA                       5             310
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      3             103
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  UIMC1 MUTATED     7   0   0   1
  UIMC1 WILD-TYPE 338   4  31  24
D442V11, multiclass
    clus
vv   UIMC1 MUTATED UIMC1 WILD-TYPE
  R0             7             338
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D442V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  UIMC1 MUTATED                                  0     1
  UIMC1 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  UIMC1 MUTATED                           1     4
  UIMC1 WILD-TYPE                        21   222
D442V13, multiclass
                                  clus
vv                                 UIMC1 MUTATED UIMC1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        4             222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(443) Variable = LRP2 MUTATION ANALYSIS
D443V1, survival
                sevent
clus2              0   1
  LRP2 MUTATED    70  14
  LRP2 WILD-TYPE 308  79
  LRP2 MUTATED LRP2 WILD-TYPE 
            84            387 
  LRP2 MUTATED LRP2 WILD-TYPE 
            14             79 
$`LRP2 MUTATED`
TCGA-A6-5657 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6654 
       31.63        22.06        32.71         8.38        25.08        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3555 TCGA-AA-3662 
       20.12        19.66        13.02         1.02        29.95         6.05 
TCGA-AA-3663 TCGA-AA-3672 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3833 TCGA-AA-3845 
        6.97         0.92        85.05        19.04        15.95         0.00 
TCGA-AA-3855 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3877 TCGA-AA-3947 TCGA-AA-3949 
       32.05        53.00        17.03        31.00        33.01        26.01 
TCGA-AA-3973 TCGA-AA-3977 TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00L TCGA-AA-A00N 
       13.05        25.02        34.03        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A010 TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01T 
       27.02        34.98        38.07         1.02        35.01        33.04 
TCGA-AA-A02O TCGA-AD-5900 TCGA-AD-6895 TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-6598 
        0.92         0.07         0.72        21.44        58.39        49.41 
TCGA-AZ-6601 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4952 TCGA-CK-5912 
      100.01        12.76        10.06        14.30        15.62        49.08 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5864 
       29.06        22.03        22.98        32.02        15.02        15.02 
TCGA-CM-6163 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6677 TCGA-D5-5540 
        2.96        14.04        11.01        13.05        11.08        56.09 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6540 TCGA-DM-A0XD TCGA-DM-A0XF 
       20.19        18.25         1.32        16.14        24.43        38.20 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A28G TCGA-DM-A28H TCGA-F4-6703 TCGA-F4-6854 
      131.51       135.65        60.79       117.07        47.87         0.53 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6588 TCGA-G4-6628 TCGA-AF-4110 TCGA-AG-3883 
       65.85        53.62        26.17        79.69        14.50         1.02 
TCGA-AG-3892 TCGA-AG-A002 TCGA-AG-A014 TCGA-AG-A02G TCGA-CI-6624 TCGA-G5-6235 
       13.02        20.98        15.95        38.96         4.73        55.76 

$`LRP2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 
       27.09        22.52        25.18        24.16        21.76        24.69 
TCGA-A6-6653 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       24.39        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3520 
       63.98         6.97         1.02        38.99         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 
       78.08        54.02         2.01        14.01        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
        5.03        26.99        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3837 TCGA-AA-3842 
        0.99        25.02         1.02        17.98        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
       14.93        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3867 
       36.03         0.99        31.07        31.07        30.05        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       27.02        29.98        18.05         2.01        12.99        24.00 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       16.08        50.99        34.06        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00K TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       19.00        30.02        18.05        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       31.00        31.00         1.02        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 
       41.00        39.98        18.05        40.96        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
       56.55         0.79         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       88.21         6.77        12.10        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5913 
        0.07        12.20        17.56       148.01        85.45        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5349 TCGA-CM-5862 
       20.02        37.02        25.02        13.02        30.08         5.03 
TCGA-CM-5863 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6164 TCGA-CM-6165 
       15.02        17.03        15.02        12.00        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6674 
       21.99        14.99        12.99        13.02        15.02        12.95 
TCGA-CM-6676 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       19.59        55.92        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       17.13        12.49        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A1D0 
        1.51        12.00        11.38        10.26       119.70       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
       44.32       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6704 
       98.24         8.61        31.96        35.74         6.18         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6855 
       34.42        41.42        16.24        33.67        13.25        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       35.31       133.18        74.56        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       91.79        46.75        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       19.10        34.49        10.39        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3885 
       32.98         0.99         0.99        19.04        19.99        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       36.95        17.03        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
       49.97         1.94        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
       33.17         6.97        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6641 
        0.66         0.69        26.43 

  LRP2 MUTATED LRP2 WILD-TYPE 
             0              0 
  LRP2 MUTATED LRP2 WILD-TYPE 
        135.65         148.01 
  LRP2 MUTATED LRP2 WILD-TYPE 
        21.735         20.020 
[1] "0.0 - 135.7 (21.7)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.3"
D443V2, continuous
D443V3, binary
                cls
clus               0   1
  LRP2 MUTATED    77   9
  LRP2 WILD-TYPE 289 110
[1] "tbl2"
                cls
clus             [,1] [,2]
  LRP2 MUTATED     77    9
  LRP2 WILD-TYPE  289  110
        clus
vv       LRP2 MUTATED LRP2 WILD-TYPE
  COLON            77            289
  RECTUM            9            110
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  LRP2 MUTATED        15        0        7        26         4         1
  LRP2 WILD-TYPE      76        1       25       112         6         0
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  LRP2 MUTATED           6          1         10          8        4         2
  LRP2 WILD-TYPE        18         10         49         34       44        16
                vv
clus             STAGE IVB
  LRP2 MUTATED           1
  LRP2 WILD-TYPE         0
D443V4, multiclass
            clus
vv           LRP2 MUTATED LRP2 WILD-TYPE
  STAGE I              15             76
  STAGE IA              0              1
  STAGE II              7             25
  STAGE IIA            26            112
  STAGE IIB             4              6
  STAGE IIC             1              0
  STAGE III             6             18
  STAGE IIIA            1             10
  STAGE IIIB           10             49
  STAGE IIIC            8             34
  STAGE IV              4             44
  STAGE IVA             2             16
  STAGE IVB             1              0
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  LRP2 MUTATED     3  15  57  12
  LRP2 WILD-TYPE  14  77 272  38
D443V5, multiclass
    clus
vv   LRP2 MUTATED LRP2 WILD-TYPE
  T1            3             14
  T2           15             77
  T3           57            272
  T4           12             38
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  LRP2 MUTATED    56  19  12
  LRP2 WILD-TYPE 231  94  75
D443V6, multiclass
    clus
vv   LRP2 MUTATED LRP2 WILD-TYPE
  N0           56            231
  N1           19             94
  N2           12             75
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D443V7, binary
                cls
clus               0   1
  LRP2 MUTATED    71   6
  LRP2 WILD-TYPE 304  59
[1] "tbl2"
                cls
clus             [,1] [,2]
  LRP2 MUTATED     71    6
  LRP2 WILD-TYPE  304   59
   clus
vv  LRP2 MUTATED LRP2 WILD-TYPE
  0           71            304
  1            6             59
[1] 2 2
[1] FALSE
D443V8, binary
                cls
clus               0   1
  LRP2 MUTATED    38  49
  LRP2 WILD-TYPE 187 215
[1] "tbl2"
                cls
clus             [,1] [,2]
  LRP2 MUTATED     38   49
  LRP2 WILD-TYPE  187  215
        clus
vv       LRP2 MUTATED LRP2 WILD-TYPE
  FEMALE           38            187
  MALE             49            215
[1] 2 2
[1] FALSE
D443V9, binary
                cls
clus               0   1
  LRP2 MUTATED    65   1
  LRP2 WILD-TYPE 285  21
[1] "tbl2"
                cls
clus             [,1] [,2]
  LRP2 MUTATED     65    1
  LRP2 WILD-TYPE  285   21
     clus
vv    LRP2 MUTATED LRP2 WILD-TYPE
  NO            65            285
  YES            1             21
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  LRP2 MUTATED                     61                            14
  LRP2 WILD-TYPE                  254                            33
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  LRP2 MUTATED                       9                              0
  LRP2 WILD-TYPE                    97                             10
D443V10, multiclass
                                clus
vv                               LRP2 MUTATED LRP2 WILD-TYPE
  COLON ADENOCARCINOMA                     61            254
  COLON MUCINOUS ADENOCARCINOMA            14             33
  RECTAL ADENOCARCINOMA                     9             97
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  LRP2 MUTATED    61   1   3   5
  LRP2 WILD-TYPE 284   3  28  20
D443V11, multiclass
    clus
vv   LRP2 MUTATED LRP2 WILD-TYPE
  R0           61            284
  R1            1              3
  R2            3             28
  RX            5             20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D443V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  LRP2 MUTATED                                  0     3
  LRP2 WILD-TYPE                                1     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  LRP2 MUTATED                           3    44
  LRP2 WILD-TYPE                        19   182
D443V13, multiclass
                                  clus
vv                                 LRP2 MUTATED LRP2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       3              8
  BLACK OR AFRICAN AMERICAN                   3             19
  WHITE                                      44            182
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(444) Variable = FUT10 MUTATION ANALYSIS
D444V1, survival
                 sevent
clus2               0   1
  FUT10 MUTATED     6   0
  FUT10 WILD-TYPE 372  93
  FUT10 MUTATED FUT10 WILD-TYPE 
              6             465 
  FUT10 MUTATED FUT10 WILD-TYPE 
              0              93 
$`FUT10 MUTATED`
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-6649 TCGA-AD-6963 TCGA-G4-6586 TCGA-AG-A002 
       33.53        23.61        24.16        27.42        35.80        20.98 

$`FUT10 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5664 TCGA-A6-5665 
       32.91        31.63        30.44        29.19        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6964 TCGA-AD-6965 
        0.79         0.72         5.79        22.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  FUT10 MUTATED FUT10 WILD-TYPE 
          20.98            0.00 
  FUT10 MUTATED FUT10 WILD-TYPE 
          35.80          148.01 
  FUT10 MUTATED FUT10 WILD-TYPE 
          25.79           20.02 
[1] "21.0 - 35.8 (25.8)" "0.0 - 148.0 (20.0)"
[1] "hr="     "9100000"
D444V2, continuous
D444V3, binary
                 cls
clus                0   1
  FUT10 MUTATED     6   1
  FUT10 WILD-TYPE 360 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FUT10 MUTATED      6    1
  FUT10 WILD-TYPE  360  118
        clus
vv       FUT10 MUTATED FUT10 WILD-TYPE
  COLON              6             360
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FUT10 MUTATED         1        0        0         3         0         0
  FUT10 WILD-TYPE      90        1       32       135        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  FUT10 MUTATED           0          0          1          0        0         1
  FUT10 WILD-TYPE        24         11         58         42       48        17
                 vv
clus              STAGE IVB
  FUT10 MUTATED           0
  FUT10 WILD-TYPE         1
D444V4, multiclass
            clus
vv           FUT10 MUTATED FUT10 WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              3             135
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  FUT10 MUTATED     0   1   6   0
  FUT10 WILD-TYPE  17  91 323  50
D444V5, multiclass
    clus
vv   FUT10 MUTATED FUT10 WILD-TYPE
  T1             0              17
  T2             1              91
  T3             6             323
  T4             0              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  FUT10 MUTATED     5   1   1
  FUT10 WILD-TYPE 282 112  86
D444V6, multiclass
    clus
vv   FUT10 MUTATED FUT10 WILD-TYPE
  N0             5             282
  N1             1             112
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D444V7, binary
                 cls
clus                0   1
  FUT10 MUTATED     5   1
  FUT10 WILD-TYPE 370  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FUT10 MUTATED      5    1
  FUT10 WILD-TYPE  370   64
   clus
vv  FUT10 MUTATED FUT10 WILD-TYPE
  0             5             370
  1             1              64
[1] 2 2
[1] FALSE
D444V8, binary
                 cls
clus                0   1
  FUT10 MUTATED     3   4
  FUT10 WILD-TYPE 222 260
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FUT10 MUTATED      3    4
  FUT10 WILD-TYPE  222  260
        clus
vv       FUT10 MUTATED FUT10 WILD-TYPE
  FEMALE             3             222
  MALE               4             260
[1] 2 2
[1] FALSE
D444V9, binary
                 cls
clus                0   1
  FUT10 MUTATED     6   0
  FUT10 WILD-TYPE 344  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FUT10 MUTATED      6    0
  FUT10 WILD-TYPE  344   22
     clus
vv    FUT10 MUTATED FUT10 WILD-TYPE
  NO              6             344
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  FUT10 MUTATED                      6                             0
  FUT10 WILD-TYPE                  309                            47
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  FUT10 MUTATED                       1                              0
  FUT10 WILD-TYPE                   105                             10
D444V10, multiclass
                                clus
vv                               FUT10 MUTATED FUT10 WILD-TYPE
  COLON ADENOCARCINOMA                       6             309
  COLON MUCINOUS ADENOCARCINOMA              0              47
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  FUT10 MUTATED     4   0   0   0
  FUT10 WILD-TYPE 341   4  31  25
D444V11, multiclass
    clus
vv   FUT10 MUTATED FUT10 WILD-TYPE
  R0             4             341
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D444V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FUT10 MUTATED                                  0     0
  FUT10 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  FUT10 MUTATED                           1     4
  FUT10 WILD-TYPE                        21   222
D444V13, multiclass
                                  clus
vv                                 FUT10 MUTATED FUT10 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        4             222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(445) Variable = GAB2 MUTATION ANALYSIS
D445V1, survival
                sevent
clus2              0   1
  GAB2 MUTATED    10   0
  GAB2 WILD-TYPE 368  93
  GAB2 MUTATED GAB2 WILD-TYPE 
            10            461 
  GAB2 MUTATED GAB2 WILD-TYPE 
             0             93 
$`GAB2 MUTATED`
TCGA-A6-6781 TCGA-AA-3861 TCGA-AA-A01Q TCGA-CM-4752 TCGA-CM-5861 TCGA-CM-6169 
       19.66        30.05         1.02        13.02        15.02        13.02 
TCGA-CM-6171 TCGA-DM-A282 TCGA-G4-6306 TCGA-DC-6681 
       14.04       139.17        44.68         5.95 

$`GAB2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 
       32.05         0.99        31.07        31.07        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        31.00        38.07        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 
       29.06        22.03        22.98        30.08        32.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6170 
       29.03        16.04        21.99        14.99        12.99        15.02 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      131.51       135.65         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       74.56        65.85        53.62        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  GAB2 MUTATED GAB2 WILD-TYPE 
          1.02           0.00 
  GAB2 MUTATED GAB2 WILD-TYPE 
        139.17         148.01 
  GAB2 MUTATED GAB2 WILD-TYPE 
         14.53          20.55 
[1] "1.0 - 139.2 (14.5)" "0.0 - 148.0 (20.6)"
[1] "hr="     "9200000"
D445V2, continuous
D445V3, binary
                cls
clus               0   1
  GAB2 MUTATED     9   1
  GAB2 WILD-TYPE 357 118
[1] "tbl2"
                cls
clus             [,1] [,2]
  GAB2 MUTATED      9    1
  GAB2 WILD-TYPE  357  118
        clus
vv       GAB2 MUTATED GAB2 WILD-TYPE
  COLON             9            357
  RECTUM            1            118
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GAB2 MUTATED         1        0        1         6         0         0
  GAB2 WILD-TYPE      90        1       31       132        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  GAB2 MUTATED           0          0          0          1        0         1
  GAB2 WILD-TYPE        24         11         59         41       48        17
                vv
clus             STAGE IVB
  GAB2 MUTATED           0
  GAB2 WILD-TYPE         1
D445V4, multiclass
            clus
vv           GAB2 MUTATED GAB2 WILD-TYPE
  STAGE I               1             90
  STAGE IA              0              1
  STAGE II              1             31
  STAGE IIA             6            132
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            0             59
  STAGE IIIC            1             41
  STAGE IV              0             48
  STAGE IVA             1             17
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  GAB2 MUTATED     0   2   7   1
  GAB2 WILD-TYPE  17  90 322  49
D445V5, multiclass
    clus
vv   GAB2 MUTATED GAB2 WILD-TYPE
  T1            0             17
  T2            2             90
  T3            7            322
  T4            1             49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  GAB2 MUTATED     8   1   1
  GAB2 WILD-TYPE 279 112  86
D445V6, multiclass
    clus
vv   GAB2 MUTATED GAB2 WILD-TYPE
  N0            8            279
  N1            1            112
  N2            1             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D445V7, binary
                cls
clus               0   1
  GAB2 MUTATED     8   1
  GAB2 WILD-TYPE 367  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  GAB2 MUTATED      8    1
  GAB2 WILD-TYPE  367   64
   clus
vv  GAB2 MUTATED GAB2 WILD-TYPE
  0            8            367
  1            1             64
[1] 2 2
[1] FALSE
D445V8, binary
                cls
clus               0   1
  GAB2 MUTATED     5   5
  GAB2 WILD-TYPE 220 259
[1] "tbl2"
                cls
clus             [,1] [,2]
  GAB2 MUTATED      5    5
  GAB2 WILD-TYPE  220  259
        clus
vv       GAB2 MUTATED GAB2 WILD-TYPE
  FEMALE            5            220
  MALE              5            259
[1] 2 2
[1] FALSE
D445V9, binary
                cls
clus               0   1
  GAB2 MUTATED     7   0
  GAB2 WILD-TYPE 343  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  GAB2 MUTATED      7    0
  GAB2 WILD-TYPE  343   22
     clus
vv    GAB2 MUTATED GAB2 WILD-TYPE
  NO             7            343
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  GAB2 MUTATED                      8                             1
  GAB2 WILD-TYPE                  307                            46
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  GAB2 MUTATED                       1                              0
  GAB2 WILD-TYPE                   105                             10
D445V10, multiclass
                                clus
vv                               GAB2 MUTATED GAB2 WILD-TYPE
  COLON ADENOCARCINOMA                      8            307
  COLON MUCINOUS ADENOCARCINOMA             1             46
  RECTAL ADENOCARCINOMA                     1            105
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  GAB2 MUTATED     9   0   0   0
  GAB2 WILD-TYPE 336   4  31  25
D445V11, multiclass
    clus
vv   GAB2 MUTATED GAB2 WILD-TYPE
  R0            9            336
  R1            0              4
  R2            0             31
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D445V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GAB2 MUTATED                                  0     0
  GAB2 WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  GAB2 MUTATED                           2     6
  GAB2 WILD-TYPE                        20   220
D445V13, multiclass
                                  clus
vv                                 GAB2 MUTATED GAB2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   2             20
  WHITE                                       6            220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(446) Variable = DSG1 MUTATION ANALYSIS
D446V1, survival
                sevent
clus2              0   1
  DSG1 MUTATED    17   4
  DSG1 WILD-TYPE 361  89
  DSG1 MUTATED DSG1 WILD-TYPE 
            21            450 
  DSG1 MUTATED DSG1 WILD-TYPE 
             4             89 
$`DSG1 MUTATED`
TCGA-AA-3510 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3966 TCGA-AA-A00N TCGA-AA-A010 
       63.98        26.01        24.00         2.01         4.01        34.98 
TCGA-AA-A01F TCGA-AA-A01R TCGA-AU-6004 TCGA-AZ-4315 TCGA-CA-6717 TCGA-CA-6718 
       32.02        35.01        27.09        58.39        12.76        10.06 
TCGA-CM-6169 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6931 TCGA-G4-6307 TCGA-G4-6586 
       13.02        12.49        15.58        12.00        55.04        35.80 
TCGA-AG-A002 TCGA-DC-6158 TCGA-DY-A1H8 
       20.98        10.98        32.61 

$`DSG1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3952 TCGA-AA-3955 
        2.01        12.99        24.00        33.01         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
       34.03        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99         1.02        10.98 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S 
       12.00        31.00        31.00        38.07         1.02         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       10.88         0.20        14.50        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 
        3.06         3.25         3.29         0.07        12.20        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6170 TCGA-CM-6171 
       16.04        21.99        14.99        12.99        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6898 TCGA-D5-6920 
       17.85         4.80        17.13        16.14         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        4.80         1.51        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       53.62        44.68        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       22.09        13.78        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EF-5830 TCGA-EI-6506 
       41.36        57.24        24.13        51.48         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  DSG1 MUTATED DSG1 WILD-TYPE 
          2.01           0.00 
  DSG1 MUTATED DSG1 WILD-TYPE 
         63.98         148.01 
  DSG1 MUTATED DSG1 WILD-TYPE 
        24.000         20.085 
[1] "2.0 - 64.0 (24.0)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1"  
D446V2, continuous
D446V3, binary
                cls
clus               0   1
  DSG1 MUTATED    18   3
  DSG1 WILD-TYPE 348 116
[1] "tbl2"
                cls
clus             [,1] [,2]
  DSG1 MUTATED     18    3
  DSG1 WILD-TYPE  348  116
        clus
vv       DSG1 MUTATED DSG1 WILD-TYPE
  COLON            18            348
  RECTUM            3            116
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DSG1 MUTATED         3        0        1         8         2         0
  DSG1 WILD-TYPE      88        1       31       130         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DSG1 MUTATED           1          2          3          1        0         0
  DSG1 WILD-TYPE        23          9         56         41       48        18
                vv
clus             STAGE IVB
  DSG1 MUTATED           0
  DSG1 WILD-TYPE         1
D446V4, multiclass
            clus
vv           DSG1 MUTATED DSG1 WILD-TYPE
  STAGE I               3             88
  STAGE IA              0              1
  STAGE II              1             31
  STAGE IIA             8            130
  STAGE IIB             2              8
  STAGE IIC             0              1
  STAGE III             1             23
  STAGE IIIA            2              9
  STAGE IIIB            3             56
  STAGE IIIC            1             41
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  DSG1 MUTATED     0   4  14   3
  DSG1 WILD-TYPE  17  88 315  47
D446V5, multiclass
    clus
vv   DSG1 MUTATED DSG1 WILD-TYPE
  T1            0             17
  T2            4             88
  T3           14            315
  T4            3             47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  DSG1 MUTATED    15   4   2
  DSG1 WILD-TYPE 272 109  85
D446V6, multiclass
    clus
vv   DSG1 MUTATED DSG1 WILD-TYPE
  N0           15            272
  N1            4            109
  N2            2             85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D446V7, binary
                cls
clus               0   1
  DSG1 MUTATED    21   0
  DSG1 WILD-TYPE 354  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  DSG1 MUTATED     21    0
  DSG1 WILD-TYPE  354   65
   clus
vv  DSG1 MUTATED DSG1 WILD-TYPE
  0           21            354
  1            0             65
[1] 2 2
[1] FALSE
D446V8, binary
                cls
clus               0   1
  DSG1 MUTATED     9  12
  DSG1 WILD-TYPE 216 252
[1] "tbl2"
                cls
clus             [,1] [,2]
  DSG1 MUTATED      9   12
  DSG1 WILD-TYPE  216  252
        clus
vv       DSG1 MUTATED DSG1 WILD-TYPE
  FEMALE            9            216
  MALE             12            252
[1] 2 2
[1] FALSE
D446V9, binary
                cls
clus               0   1
  DSG1 MUTATED    16   1
  DSG1 WILD-TYPE 334  21
[1] "tbl2"
                cls
clus             [,1] [,2]
  DSG1 MUTATED     16    1
  DSG1 WILD-TYPE  334   21
     clus
vv    DSG1 MUTATED DSG1 WILD-TYPE
  NO            16            334
  YES            1             21
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  DSG1 MUTATED                     12                             6
  DSG1 WILD-TYPE                  303                            41
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  DSG1 MUTATED                       3                              0
  DSG1 WILD-TYPE                   103                             10
D446V10, multiclass
                                clus
vv                               DSG1 MUTATED DSG1 WILD-TYPE
  COLON ADENOCARCINOMA                     12            303
  COLON MUCINOUS ADENOCARCINOMA             6             41
  RECTAL ADENOCARCINOMA                     3            103
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  DSG1 MUTATED    17   0   0   2
  DSG1 WILD-TYPE 328   4  31  23
D446V11, multiclass
    clus
vv   DSG1 MUTATED DSG1 WILD-TYPE
  R0           17            328
  R1            0              4
  R2            0             31
  RX            2             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D446V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DSG1 MUTATED                                  0     2
  DSG1 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  DSG1 MUTATED                           1     9
  DSG1 WILD-TYPE                        21   217
D446V13, multiclass
                                  clus
vv                                 DSG1 MUTATED DSG1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              9
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                       9            217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(447) Variable = DKK2 MUTATION ANALYSIS
D447V1, survival
                sevent
clus2              0   1
  DKK2 MUTATED    20   5
  DKK2 WILD-TYPE 358  88
  DKK2 MUTATED DKK2 WILD-TYPE 
            25            446 
  DKK2 MUTATED DKK2 WILD-TYPE 
             5             88 
$`DKK2 MUTATED`
TCGA-A6-2676 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-6782 TCGA-AA-3554 TCGA-AA-3672 
       42.90        30.44        33.53        20.28        17.95         0.92 
TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3971 TCGA-AD-6964 TCGA-AY-5543 TCGA-AZ-4315 
       85.05        19.04        16.08        10.88        33.01        58.39 
TCGA-CK-4952 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6930 TCGA-D5-6932 TCGA-F4-6805 
       15.62        15.58         1.48         1.51        11.38        34.42 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6588 TCGA-G4-6626 TCGA-AG-3582 TCGA-F5-6571 
       85.48        63.62        26.17        46.75        36.03        31.30 
TCGA-G5-6235 
       55.76 

$`DKK2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 
       31.63        29.19        23.61        22.09        22.06        32.71 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       27.09        22.52         8.38        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
        7.04         3.02         1.02        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3555 
       14.01        33.99        21.01        13.02        24.00        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       78.08         6.05         6.97        54.02         2.01        14.01 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 
       19.00        36.00         5.03        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3972 TCGA-AA-3973 
       20.98        34.03         2.01        21.99        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
        0.79         0.72         5.79        22.42        27.42         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6197 TCGA-AY-6386 
       14.50        27.09        16.31         0.95        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
       17.56       148.01        85.45        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6920 
       17.85         4.80        17.13        12.49        16.14         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
        4.80        12.00        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       55.04        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6625 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       91.79        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
        7.07        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
       18.28         9.96        49.51        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6641 
        0.69        26.43 

  DKK2 MUTATED DKK2 WILD-TYPE 
          0.92           0.00 
  DKK2 MUTATED DKK2 WILD-TYPE 
         85.48         148.01 
  DKK2 MUTATED DKK2 WILD-TYPE 
        30.440         20.035 
[1] "0.9 - 85.5 (30.4)"  "0.0 - 148.0 (20.0)"
[1] "hr=" "1.2"
D447V2, continuous
D447V3, binary
                cls
clus               0   1
  DKK2 MUTATED    23   3
  DKK2 WILD-TYPE 343 116
[1] "tbl2"
                cls
clus             [,1] [,2]
  DKK2 MUTATED     23    3
  DKK2 WILD-TYPE  343  116
        clus
vv       DKK2 MUTATED DKK2 WILD-TYPE
  COLON            23            343
  RECTUM            3            116
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DKK2 MUTATED         2        0        1        10         2         0
  DKK2 WILD-TYPE      89        1       31       128         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DKK2 MUTATED           3          0          3          2        1         1
  DKK2 WILD-TYPE        21         11         56         40       47        17
                vv
clus             STAGE IVB
  DKK2 MUTATED           0
  DKK2 WILD-TYPE         1
D447V4, multiclass
            clus
vv           DKK2 MUTATED DKK2 WILD-TYPE
  STAGE I               2             89
  STAGE IA              0              1
  STAGE II              1             31
  STAGE IIA            10            128
  STAGE IIB             2              8
  STAGE IIC             0              1
  STAGE III             3             21
  STAGE IIIA            0             11
  STAGE IIIB            3             56
  STAGE IIIC            2             40
  STAGE IV              1             47
  STAGE IVA             1             17
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  DKK2 MUTATED     0   2  20   4
  DKK2 WILD-TYPE  17  90 309  46
D447V5, multiclass
    clus
vv   DKK2 MUTATED DKK2 WILD-TYPE
  T1            0             17
  T2            2             90
  T3           20            309
  T4            4             46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  DKK2 MUTATED    16   7   3
  DKK2 WILD-TYPE 271 106  84
D447V6, multiclass
    clus
vv   DKK2 MUTATED DKK2 WILD-TYPE
  N0           16            271
  N1            7            106
  N2            3             84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D447V7, binary
                cls
clus               0   1
  DKK2 MUTATED    20   2
  DKK2 WILD-TYPE 355  63
[1] "tbl2"
                cls
clus             [,1] [,2]
  DKK2 MUTATED     20    2
  DKK2 WILD-TYPE  355   63
   clus
vv  DKK2 MUTATED DKK2 WILD-TYPE
  0           20            355
  1            2             63
[1] 2 2
[1] FALSE
D447V8, binary
                cls
clus               0   1
  DKK2 MUTATED    11  15
  DKK2 WILD-TYPE 214 249
[1] "tbl2"
                cls
clus             [,1] [,2]
  DKK2 MUTATED     11   15
  DKK2 WILD-TYPE  214  249
        clus
vv       DKK2 MUTATED DKK2 WILD-TYPE
  FEMALE           11            214
  MALE             15            249
[1] 2 2
[1] FALSE
D447V9, binary
                cls
clus               0   1
  DKK2 MUTATED    21   1
  DKK2 WILD-TYPE 329  21
[1] "tbl2"
                cls
clus             [,1] [,2]
  DKK2 MUTATED     21    1
  DKK2 WILD-TYPE  329   21
     clus
vv    DKK2 MUTATED DKK2 WILD-TYPE
  NO            21            329
  YES            1             21
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  DKK2 MUTATED                     20                             3
  DKK2 WILD-TYPE                  295                            44
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  DKK2 MUTATED                       3                              0
  DKK2 WILD-TYPE                   103                             10
D447V10, multiclass
                                clus
vv                               DKK2 MUTATED DKK2 WILD-TYPE
  COLON ADENOCARCINOMA                     20            295
  COLON MUCINOUS ADENOCARCINOMA             3             44
  RECTAL ADENOCARCINOMA                     3            103
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  DKK2 MUTATED    21   1   1   1
  DKK2 WILD-TYPE 324   3  30  24
D447V11, multiclass
    clus
vv   DKK2 MUTATED DKK2 WILD-TYPE
  R0           21            324
  R1            1              3
  R2            1             30
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D447V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DKK2 MUTATED                                  0     0
  DKK2 WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  DKK2 MUTATED                           3    17
  DKK2 WILD-TYPE                        19   209
D447V13, multiclass
                                  clus
vv                                 DKK2 MUTATED DKK2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   3             19
  WHITE                                      17            209
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(448) Variable = COX15 MUTATION ANALYSIS
D448V1, survival
                 sevent
clus2               0   1
  COX15 MUTATED     5   2
  COX15 WILD-TYPE 373  91
  COX15 MUTATED COX15 WILD-TYPE 
              7             464 
  COX15 MUTATED COX15 WILD-TYPE 
              2              91 
$`COX15 MUTATED`
TCGA-A6-5665 TCGA-AA-3492 TCGA-AA-3950 TCGA-AA-A00N TCGA-CM-5868 TCGA-AG-A002 
       22.06         3.02        24.00         4.01        17.03        20.98 
TCGA-AH-6643 
        0.69 

$`COX15 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 
       20.12        19.66        20.28         7.04         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 
       12.99        24.00        33.01        26.01         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
        5.03        15.02        15.02        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
       17.49         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  COX15 MUTATED COX15 WILD-TYPE 
           0.69            0.00 
  COX15 MUTATED COX15 WILD-TYPE 
          24.00          148.01 
  COX15 MUTATED COX15 WILD-TYPE 
         17.030          20.235 
[1] "0.7 - 24.0 (17.0)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "2.9"
D448V2, continuous
D448V3, binary
                 cls
clus                0   1
  COX15 MUTATED     5   2
  COX15 WILD-TYPE 361 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  COX15 MUTATED      5    2
  COX15 WILD-TYPE  361  117
        clus
vv       COX15 MUTATED COX15 WILD-TYPE
  COLON              5             361
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  COX15 MUTATED         1        0        1         2         1         0
  COX15 WILD-TYPE      90        1       31       136         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  COX15 MUTATED           0          0          0          1        0         1
  COX15 WILD-TYPE        24         11         59         41       48        17
                 vv
clus              STAGE IVB
  COX15 MUTATED           0
  COX15 WILD-TYPE         1
D448V4, multiclass
            clus
vv           COX15 MUTATED COX15 WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              2             136
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             1              41
  STAGE IV               0              48
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  COX15 MUTATED     0   1   4   2
  COX15 WILD-TYPE  17  91 325  48
D448V5, multiclass
    clus
vv   COX15 MUTATED COX15 WILD-TYPE
  T1             0              17
  T2             1              91
  T3             4             325
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  COX15 MUTATED     5   1   1
  COX15 WILD-TYPE 282 112  86
D448V6, multiclass
    clus
vv   COX15 MUTATED COX15 WILD-TYPE
  N0             5             282
  N1             1             112
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D448V7, binary
                 cls
clus                0   1
  COX15 MUTATED     6   1
  COX15 WILD-TYPE 369  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  COX15 MUTATED      6    1
  COX15 WILD-TYPE  369   64
   clus
vv  COX15 MUTATED COX15 WILD-TYPE
  0             6             369
  1             1              64
[1] 2 2
[1] FALSE
D448V8, binary
                 cls
clus                0   1
  COX15 MUTATED     4   3
  COX15 WILD-TYPE 221 261
[1] "tbl2"
                 cls
clus              [,1] [,2]
  COX15 MUTATED      4    3
  COX15 WILD-TYPE  221  261
        clus
vv       COX15 MUTATED COX15 WILD-TYPE
  FEMALE             4             221
  MALE               3             261
[1] 2 2
[1] FALSE
D448V9, binary
                 cls
clus                0   1
  COX15 MUTATED     5   0
  COX15 WILD-TYPE 345  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  COX15 MUTATED      5    0
  COX15 WILD-TYPE  345   22
     clus
vv    COX15 MUTATED COX15 WILD-TYPE
  NO              5             345
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  COX15 MUTATED                      3                             2
  COX15 WILD-TYPE                  312                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  COX15 MUTATED                       2                              0
  COX15 WILD-TYPE                   104                             10
D448V10, multiclass
                                clus
vv                               COX15 MUTATED COX15 WILD-TYPE
  COLON ADENOCARCINOMA                       3             312
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  COX15 MUTATED     7   0   0   0
  COX15 WILD-TYPE 338   4  31  25
D448V11, multiclass
    clus
vv   COX15 MUTATED COX15 WILD-TYPE
  R0             7             338
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D448V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  COX15 MUTATED                                  0     0
  COX15 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  COX15 MUTATED                           0     3
  COX15 WILD-TYPE                        22   223
D448V13, multiclass
                                  clus
vv                                 COX15 MUTATED COX15 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        3             223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(449) Variable = JAK2 MUTATION ANALYSIS
D449V1, survival
                sevent
clus2              0   1
  JAK2 MUTATED    35   8
  JAK2 WILD-TYPE 343  85
  JAK2 MUTATED JAK2 WILD-TYPE 
            43            428 
  JAK2 MUTATED JAK2 WILD-TYPE 
             8             85 
$`JAK2 MUTATED`
TCGA-A6-5662 TCGA-A6-5666 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3713 TCGA-AA-3815 
       23.61        32.71        78.08         6.05        19.04        33.04 
TCGA-AA-3950 TCGA-AA-3966 TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A02K TCGA-AU-6004 
       24.00         2.01         4.01        34.98        14.01        27.09 
TCGA-AY-5543 TCGA-AZ-4616 TCGA-AZ-6598 TCGA-AZ-6606 TCGA-CA-6717 TCGA-CA-6718 
       33.01         5.13        49.41        11.74        12.76        10.06 
TCGA-CA-6719 TCGA-CM-4746 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5868 TCGA-CM-6161 
       14.30        37.02        32.02         5.03        17.03        15.02 
TCGA-CM-6169 TCGA-CM-6170 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6541 TCGA-D5-6929 
       13.02        15.02        18.25         1.32        15.58         4.80 
TCGA-DM-A0XD TCGA-F4-6569 TCGA-F4-6704 TCGA-F4-6807 TCGA-G4-6293 TCGA-G4-6309 
       24.43        35.74         1.55        16.24       133.18        85.48 
TCGA-G4-6625 TCGA-AF-6672 TCGA-AG-A002 TCGA-DC-5869 TCGA-DC-6683 TCGA-EF-5830 
       91.79        10.39        20.98         5.03         5.03         0.49 
TCGA-EI-6508 
       20.91 

$`JAK2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        33.53        22.09 
TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       22.06        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        19.99        61.02         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
       26.99        19.04        10.06        35.05         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
        2.01        20.98        34.03        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
        5.03         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       16.31         0.95        21.44        17.82        58.39         1.41 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 
      106.75        22.36        62.79        88.21         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
      100.01        29.56         5.23         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CK-4947 
        3.06         3.25         3.29         0.07        12.20        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        15.02        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6171 TCGA-CM-6172 
       16.04        21.99        14.99        12.99        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       20.19        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       12.49        16.14         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 
       14.30         9.04         9.44        11.64         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       11.38        10.26       119.70        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6808 TCGA-F4-6809 
        6.18        47.87        34.42        41.42        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
        0.53        47.41        35.31        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       44.68        55.04        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       13.78        35.80        26.17        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AG-3574 TCGA-AG-3575 
       14.50        16.83        15.39        20.02        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
       15.02        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        4.01         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6510 TCGA-F5-6464 
       51.48        32.61        20.55        19.96        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  JAK2 MUTATED JAK2 WILD-TYPE 
          0.49           0.00 
  JAK2 MUTATED JAK2 WILD-TYPE 
        133.18         148.01 
  JAK2 MUTATED JAK2 WILD-TYPE 
         16.24          20.98 
[1] "0.5 - 133.2 (16.2)" "0.0 - 148.0 (21.0)"
[1] "hr=" "1.1"
D449V2, continuous
D449V3, binary
                cls
clus               0   1
  JAK2 MUTATED    40   6
  JAK2 WILD-TYPE 326 113
[1] "tbl2"
                cls
clus             [,1] [,2]
  JAK2 MUTATED     40    6
  JAK2 WILD-TYPE  326  113
        clus
vv       JAK2 MUTATED JAK2 WILD-TYPE
  COLON            40            326
  RECTUM            6            113
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  JAK2 MUTATED         6        0        2        13         4         1
  JAK2 WILD-TYPE      85        1       30       125         6         0
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  JAK2 MUTATED           1          0          5          3        7         4
  JAK2 WILD-TYPE        23         11         54         39       41        14
                vv
clus             STAGE IVB
  JAK2 MUTATED           0
  JAK2 WILD-TYPE         1
D449V4, multiclass
            clus
vv           JAK2 MUTATED JAK2 WILD-TYPE
  STAGE I               6             85
  STAGE IA              0              1
  STAGE II              2             30
  STAGE IIA            13            125
  STAGE IIB             4              6
  STAGE IIC             1              0
  STAGE III             1             23
  STAGE IIIA            0             11
  STAGE IIIB            5             54
  STAGE IIIC            3             39
  STAGE IV              7             41
  STAGE IVA             4             14
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  JAK2 MUTATED     0   6  29  11
  JAK2 WILD-TYPE  17  86 300  39
D449V5, multiclass
    clus
vv   JAK2 MUTATED JAK2 WILD-TYPE
  T1            0             17
  T2            6             86
  T3           29            300
  T4           11             39
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  JAK2 MUTATED    28   9   9
  JAK2 WILD-TYPE 259 104  78
D449V6, multiclass
    clus
vv   JAK2 MUTATED JAK2 WILD-TYPE
  N0           28            259
  N1            9            104
  N2            9             78
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D449V7, binary
                cls
clus               0   1
  JAK2 MUTATED    31  10
  JAK2 WILD-TYPE 344  55
[1] "tbl2"
                cls
clus             [,1] [,2]
  JAK2 MUTATED     31   10
  JAK2 WILD-TYPE  344   55
   clus
vv  JAK2 MUTATED JAK2 WILD-TYPE
  0           31            344
  1           10             55
[1] 2 2
[1] FALSE
D449V8, binary
                cls
clus               0   1
  JAK2 MUTATED    23  23
  JAK2 WILD-TYPE 202 241
[1] "tbl2"
                cls
clus             [,1] [,2]
  JAK2 MUTATED     23   23
  JAK2 WILD-TYPE  202  241
        clus
vv       JAK2 MUTATED JAK2 WILD-TYPE
  FEMALE           23            202
  MALE             23            241
[1] 2 2
[1] FALSE
D449V9, binary
                cls
clus               0   1
  JAK2 MUTATED    31   2
  JAK2 WILD-TYPE 319  20
[1] "tbl2"
                cls
clus             [,1] [,2]
  JAK2 MUTATED     31    2
  JAK2 WILD-TYPE  319   20
     clus
vv    JAK2 MUTATED JAK2 WILD-TYPE
  NO            31            319
  YES            2             20
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  JAK2 MUTATED                     34                             6
  JAK2 WILD-TYPE                  281                            41
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  JAK2 MUTATED                       6                              0
  JAK2 WILD-TYPE                   100                             10
D449V10, multiclass
                                clus
vv                               JAK2 MUTATED JAK2 WILD-TYPE
  COLON ADENOCARCINOMA                     34            281
  COLON MUCINOUS ADENOCARCINOMA             6             41
  RECTAL ADENOCARCINOMA                     6            100
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  JAK2 MUTATED    31   0   3   4
  JAK2 WILD-TYPE 314   4  28  21
D449V11, multiclass
    clus
vv   JAK2 MUTATED JAK2 WILD-TYPE
  R0           31            314
  R1            0              4
  R2            3             28
  RX            4             21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D449V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  JAK2 MUTATED                                  1     3
  JAK2 WILD-TYPE                                0     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  JAK2 MUTATED                           5    26
  JAK2 WILD-TYPE                        17   200
D449V13, multiclass
                                  clus
vv                                 JAK2 MUTATED JAK2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            1              0
  ASIAN                                       3              8
  BLACK OR AFRICAN AMERICAN                   5             17
  WHITE                                      26            200
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(450) Variable = HIVEP2 MUTATION ANALYSIS
D450V1, survival
                  sevent
clus2                0   1
  HIVEP2 MUTATED    19   4
  HIVEP2 WILD-TYPE 359  89
  HIVEP2 MUTATED HIVEP2 WILD-TYPE 
              23              448 
  HIVEP2 MUTATED HIVEP2 WILD-TYPE 
               4               89 
$`HIVEP2 MUTATED`
TCGA-A6-6781 TCGA-AA-3510 TCGA-AA-3664 TCGA-AA-3710 TCGA-AA-3821 TCGA-AA-3877 
       19.66        63.98        54.02        26.99         1.02        31.00 
TCGA-AA-3950 TCGA-AD-6889 TCGA-AZ-6607 TCGA-CA-6717 TCGA-CM-4744 TCGA-CM-5344 
       24.00        56.55         3.19        12.76        20.02        22.03 
TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-6169 TCGA-CM-6678 TCGA-DM-A1HB TCGA-G4-6626 
        5.03        15.02        13.02        11.01       135.65        46.75 
TCGA-AF-2687 TCGA-AF-3913 TCGA-AG-3892 TCGA-AG-A002 TCGA-AG-A02N 
       24.13        10.39        13.02        20.98        61.97 

$`HIVEP2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       85.05        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
        0.99        25.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       18.05         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       15.52         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6608 
       12.10       100.01        29.56         5.23        11.74         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
      124.27        23.05        37.02        25.02        13.02        29.06 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5868 
       22.98        30.08        32.02        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       14.99        12.99        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       13.05        11.08        11.08        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 
      140.38         7.50        44.32       131.51       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 
       22.09        13.78        35.80        26.17        91.79        79.69 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-4110 
       39.48        43.04        13.55        19.10        34.49        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
        1.94        38.96        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  HIVEP2 MUTATED HIVEP2 WILD-TYPE 
            1.02             0.00 
  HIVEP2 MUTATED HIVEP2 WILD-TYPE 
          135.65           148.01 
  HIVEP2 MUTATED HIVEP2 WILD-TYPE 
          20.980           20.155 
[1] "1.0 - 135.7 (21.0)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.3"
D450V2, continuous
D450V3, binary
                  cls
clus                 0   1
  HIVEP2 MUTATED    19   5
  HIVEP2 WILD-TYPE 347 114
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HIVEP2 MUTATED     19    5
  HIVEP2 WILD-TYPE  347  114
        clus
vv       HIVEP2 MUTATED HIVEP2 WILD-TYPE
  COLON              19              347
  RECTUM              5              114
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  HIVEP2 MUTATED         6        0        3         7         0         0
  HIVEP2 WILD-TYPE      85        1       29       131        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HIVEP2 MUTATED           0          0          2          2        2
  HIVEP2 WILD-TYPE        24         11         57         40       46
                  vv
clus               STAGE IVA STAGE IVB
  HIVEP2 MUTATED           2         0
  HIVEP2 WILD-TYPE        16         1
D450V4, multiclass
            clus
vv           HIVEP2 MUTATED HIVEP2 WILD-TYPE
  STAGE I                 6               85
  STAGE IA                0                1
  STAGE II                3               29
  STAGE IIA               7              131
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              2               57
  STAGE IIIC              2               40
  STAGE IV                2               46
  STAGE IVA               2               16
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  HIVEP2 MUTATED     2   4  15   3
  HIVEP2 WILD-TYPE  15  88 314  47
D450V5, multiclass
    clus
vv   HIVEP2 MUTATED HIVEP2 WILD-TYPE
  T1              2               15
  T2              4               88
  T3             15              314
  T4              3               47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  HIVEP2 MUTATED    16   6   2
  HIVEP2 WILD-TYPE 271 107  85
D450V6, multiclass
    clus
vv   HIVEP2 MUTATED HIVEP2 WILD-TYPE
  N0             16              271
  N1              6              107
  N2              2               85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D450V7, binary
                  cls
clus                 0   1
  HIVEP2 MUTATED    19   4
  HIVEP2 WILD-TYPE 356  61
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HIVEP2 MUTATED     19    4
  HIVEP2 WILD-TYPE  356   61
   clus
vv  HIVEP2 MUTATED HIVEP2 WILD-TYPE
  0             19              356
  1              4               61
[1] 2 2
[1] FALSE
D450V8, binary
                  cls
clus                 0   1
  HIVEP2 MUTATED     9  15
  HIVEP2 WILD-TYPE 216 249
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HIVEP2 MUTATED      9   15
  HIVEP2 WILD-TYPE  216  249
        clus
vv       HIVEP2 MUTATED HIVEP2 WILD-TYPE
  FEMALE              9              216
  MALE               15              249
[1] 2 2
[1] FALSE
D450V9, binary
                  cls
clus                 0   1
  HIVEP2 MUTATED    19   1
  HIVEP2 WILD-TYPE 331  21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HIVEP2 MUTATED     19    1
  HIVEP2 WILD-TYPE  331   21
     clus
vv    HIVEP2 MUTATED HIVEP2 WILD-TYPE
  NO              19              331
  YES              1               21
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  HIVEP2 MUTATED                     13                             5
  HIVEP2 WILD-TYPE                  302                            42
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  HIVEP2 MUTATED                       5                              0
  HIVEP2 WILD-TYPE                   101                             10
D450V10, multiclass
                                clus
vv                               HIVEP2 MUTATED HIVEP2 WILD-TYPE
  COLON ADENOCARCINOMA                       13              302
  COLON MUCINOUS ADENOCARCINOMA               5               42
  RECTAL ADENOCARCINOMA                       5              101
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  HIVEP2 MUTATED    20   0   0   1
  HIVEP2 WILD-TYPE 325   4  31  24
D450V11, multiclass
    clus
vv   HIVEP2 MUTATED HIVEP2 WILD-TYPE
  R0             20              325
  R1              0                4
  R2              0               31
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D450V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HIVEP2 MUTATED                                  0     2
  HIVEP2 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  HIVEP2 MUTATED                           2    10
  HIVEP2 WILD-TYPE                        20   216
D450V13, multiclass
                                  clus
vv                                 HIVEP2 MUTATED HIVEP2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                9
  BLACK OR AFRICAN AMERICAN                     2               20
  WHITE                                        10              216
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(451) Variable = RELN MUTATION ANALYSIS
D451V1, survival
                sevent
clus2              0   1
  RELN MUTATED    51  16
  RELN WILD-TYPE 327  77
  RELN MUTATED RELN WILD-TYPE 
            67            404 
  RELN MUTATED RELN WILD-TYPE 
            16             77 
$`RELN MUTATED`
TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-5661 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6141 
       34.65        32.75        33.53        22.06        32.71         8.38 
TCGA-A6-6652 TCGA-AA-3516 TCGA-AA-3525 TCGA-AA-3532 TCGA-AA-3555 TCGA-AA-3664 
       24.69        13.02         8.05        29.00        29.95        54.02 
TCGA-AA-3672 TCGA-AA-3680 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3818 TCGA-AA-3837 
        0.92        11.01        19.04        19.04         0.99        38.99 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A010 
       33.01        26.01        24.00        25.02         4.01        34.98 
TCGA-AD-6889 TCGA-AD-6901 TCGA-AD-6964 TCGA-AZ-4315 TCGA-AZ-5407 TCGA-AZ-6601 
       56.55        22.42        10.88        58.39        88.21       100.01 
TCGA-CA-5796 TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-5348 
        3.25        12.76        10.06        23.05        20.02        22.98 
TCGA-CM-5349 TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6674 TCGA-CM-6675 
       30.08         5.03        15.02        17.03        12.95        13.05 
TCGA-D5-6532 TCGA-D5-6537 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6923 TCGA-D5-6928 
       18.25         4.80        12.49        15.58        12.43        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-DM-A0XF TCGA-DM-A1D4 TCGA-DM-A1DA TCGA-DM-A1DB 
        4.80         1.51        38.20        92.75         7.50        44.32 
TCGA-DM-A28E TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6586 TCGA-G4-6588 
      119.93        55.04        85.48        63.62        35.80        26.17 
TCGA-G4-6628 TCGA-AG-3609 TCGA-AG-3892 TCGA-AG-A002 TCGA-DC-6681 TCGA-DY-A1DC 
       79.69        19.99        13.02        20.98         5.95        41.36 
TCGA-EI-6507 
       19.96 

$`RELN WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5657 
       16.57        33.34        36.53        14.53        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-6137 TCGA-A6-6138 
       30.44        29.19        23.61        22.09        27.09        22.52 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6654 
       25.08        25.18        24.16        21.76        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3529 
        9.07        24.03        37.05        36.03        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       19.07        34.03        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
       78.08         6.05         6.97         2.01        14.01        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       47.01        15.02         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
        5.03        85.05        26.99        10.06        35.05        33.04 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3842 TCGA-AA-3844 
       25.02         1.02        17.98        15.95        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3952 TCGA-AA-3955 
       31.00         2.01        12.99        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6963 
       21.37        15.52         0.79         0.72         5.79        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 
       62.79        49.41         6.77        12.10        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5797 
       11.74         3.19         1.61        12.69         3.06         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.07        12.20        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
        1.91       124.27        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-6161 TCGA-CM-6162 
       22.03        32.02        15.02        15.02        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6676 TCGA-CM-6677 
       13.02        15.02        14.04        11.01        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       56.09        55.92        20.19         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       17.85        17.13        16.14         1.48         3.68         4.41 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       14.30         9.04         9.44        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
      119.70        24.43       130.65        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
      140.38       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6315 
      133.18        74.56        65.85        53.62        44.68        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 
       36.00        22.09        13.78        91.79        46.75        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3611 TCGA-AG-3612 
       12.03         6.05         0.99        15.95        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6682 
        5.03        13.97        27.95        10.98        19.99         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.03         5.29       126.44        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
       32.61         0.49        20.55        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  RELN MUTATED RELN WILD-TYPE 
          0.92           0.00 
  RELN MUTATED RELN WILD-TYPE 
        119.93         148.01 
  RELN MUTATED RELN WILD-TYPE 
        22.060         20.085 
[1] "0.9 - 119.9 (22.1)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.1"
D451V2, continuous
D451V3, binary
                cls
clus               0   1
  RELN MUTATED    65   6
  RELN WILD-TYPE 301 113
[1] "tbl2"
                cls
clus             [,1] [,2]
  RELN MUTATED     65    6
  RELN WILD-TYPE  301  113
        clus
vv       RELN MUTATED RELN WILD-TYPE
  COLON            65            301
  RECTUM            6            113
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RELN MUTATED         7        0        3        28         5         1
  RELN WILD-TYPE      84        1       29       110         5         0
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RELN MUTATED           2          1          7          5        4         4
  RELN WILD-TYPE        22         10         52         37       44        14
                vv
clus             STAGE IVB
  RELN MUTATED           1
  RELN WILD-TYPE         0
D451V4, multiclass
            clus
vv           RELN MUTATED RELN WILD-TYPE
  STAGE I               7             84
  STAGE IA              0              1
  STAGE II              3             29
  STAGE IIA            28            110
  STAGE IIB             5              5
  STAGE IIC             1              0
  STAGE III             2             22
  STAGE IIIA            1             10
  STAGE IIIB            7             52
  STAGE IIIC            5             37
  STAGE IV              4             44
  STAGE IVA             4             14
  STAGE IVB             1              0
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  RELN MUTATED     2   6  54   9
  RELN WILD-TYPE  15  86 275  41
D451V5, multiclass
    clus
vv   RELN MUTATED RELN WILD-TYPE
  T1            2             15
  T2            6             86
  T3           54            275
  T4            9             41
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  RELN MUTATED    49  11  11
  RELN WILD-TYPE 238 102  76
D451V6, multiclass
    clus
vv   RELN MUTATED RELN WILD-TYPE
  N0           49            238
  N1           11            102
  N2           11             76
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D451V7, binary
                cls
clus               0   1
  RELN MUTATED    56   9
  RELN WILD-TYPE 319  56
[1] "tbl2"
                cls
clus             [,1] [,2]
  RELN MUTATED     56    9
  RELN WILD-TYPE  319   56
   clus
vv  RELN MUTATED RELN WILD-TYPE
  0           56            319
  1            9             56
[1] 2 2
[1] FALSE
D451V8, binary
                cls
clus               0   1
  RELN MUTATED    34  37
  RELN WILD-TYPE 191 227
[1] "tbl2"
                cls
clus             [,1] [,2]
  RELN MUTATED     34   37
  RELN WILD-TYPE  191  227
        clus
vv       RELN MUTATED RELN WILD-TYPE
  FEMALE           34            191
  MALE             37            227
[1] 2 2
[1] FALSE
D451V9, binary
                cls
clus               0   1
  RELN MUTATED    53   2
  RELN WILD-TYPE 297  20
[1] "tbl2"
                cls
clus             [,1] [,2]
  RELN MUTATED     53    2
  RELN WILD-TYPE  297   20
     clus
vv    RELN MUTATED RELN WILD-TYPE
  NO            53            297
  YES            2             20
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  RELN MUTATED                     51                            13
  RELN WILD-TYPE                  264                            34
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  RELN MUTATED                       6                              0
  RELN WILD-TYPE                   100                             10
D451V10, multiclass
                                clus
vv                               RELN MUTATED RELN WILD-TYPE
  COLON ADENOCARCINOMA                     51            264
  COLON MUCINOUS ADENOCARCINOMA            13             34
  RECTAL ADENOCARCINOMA                     6            100
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  RELN MUTATED    49   0   3   3
  RELN WILD-TYPE 296   4  28  22
D451V11, multiclass
    clus
vv   RELN MUTATED RELN WILD-TYPE
  R0           49            296
  R1            0              4
  R2            3             28
  RX            3             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D451V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RELN MUTATED                                  0     4
  RELN WILD-TYPE                                1     7
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  RELN MUTATED                           5    40
  RELN WILD-TYPE                        17   186
D451V13, multiclass
                                  clus
vv                                 RELN MUTATED RELN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       4              7
  BLACK OR AFRICAN AMERICAN                   5             17
  WHITE                                      40            186
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(452) Variable = FLG2 MUTATION ANALYSIS
D452V1, survival
                sevent
clus2              0   1
  FLG2 MUTATED    24   8
  FLG2 WILD-TYPE 354  85
  FLG2 MUTATED FLG2 WILD-TYPE 
            32            439 
  FLG2 MUTATED FLG2 WILD-TYPE 
             8             85 
$`FLG2 MUTATED`
TCGA-AA-3496 TCGA-AA-3510 TCGA-AA-3525 TCGA-AA-3532 TCGA-AA-3663 TCGA-AA-3710 
        1.02        63.98         8.05        29.00         6.97        26.99 
TCGA-AA-3837 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3986 TCGA-AA-A00N 
       38.99        31.00         2.01        33.01        19.07         4.01 
TCGA-AU-6004 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-AZ-6606 TCGA-CA-6717 TCGA-CA-6718 
       27.09        58.39        49.41        11.74        12.76        10.06 
TCGA-CK-5913 TCGA-CM-4747 TCGA-CM-6167 TCGA-CM-6675 TCGA-D5-5540 TCGA-D5-6529 
       51.32        25.02        14.99        13.05        56.09        20.19 
TCGA-DM-A1D4 TCGA-F4-6570 TCGA-G4-6309 TCGA-AG-3731 TCGA-AG-4005 TCGA-AG-A002 
       92.75         6.18        85.48        37.02        14.04        20.98 
TCGA-AH-6549 TCGA-DY-A1DG 
       17.49        51.48 

$`FLG2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3529 
        9.07        24.03        37.05        36.03        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       19.07        34.03        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       61.02        78.08         6.05        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 
       37.05        19.00        36.00         5.03        85.05        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
        1.02        17.98        15.95        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3939 
       17.03        24.03        27.02        29.98        18.05        12.99 
TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       26.01        25.02        24.00        27.02        27.02         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 
       22.42        27.42        10.88         0.20        14.50        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        33.01        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 
      106.75        22.36        62.79        88.21         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
      100.01        29.56         5.23         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 
        3.06         3.25         3.29         0.07        12.20        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 
       17.56       148.01        85.45        15.62        49.08         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       37.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       12.26        19.59        55.92        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       35.74        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 
       74.56        65.85        53.62        44.68        55.04        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
        0.99        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       36.03         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 
      126.44        41.36        57.24        24.13        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  FLG2 MUTATED FLG2 WILD-TYPE 
          1.02           0.00 
  FLG2 MUTATED FLG2 WILD-TYPE 
         92.75         148.01 
  FLG2 MUTATED FLG2 WILD-TYPE 
         23.00          20.05 
[1] "1.0 - 92.8 (23.0)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.1"
D452V2, continuous
D452V3, binary
                cls
clus               0   1
  FLG2 MUTATED    28   5
  FLG2 WILD-TYPE 338 114
[1] "tbl2"
                cls
clus             [,1] [,2]
  FLG2 MUTATED     28    5
  FLG2 WILD-TYPE  338  114
        clus
vv       FLG2 MUTATED FLG2 WILD-TYPE
  COLON            28            338
  RECTUM            5            114
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FLG2 MUTATED         4        0        4        12         2         0
  FLG2 WILD-TYPE      87        1       28       126         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  FLG2 MUTATED           0          0          2          1        4         2
  FLG2 WILD-TYPE        24         11         57         41       44        16
                vv
clus             STAGE IVB
  FLG2 MUTATED           1
  FLG2 WILD-TYPE         0
D452V4, multiclass
            clus
vv           FLG2 MUTATED FLG2 WILD-TYPE
  STAGE I               4             87
  STAGE IA              0              1
  STAGE II              4             28
  STAGE IIA            12            126
  STAGE IIB             2              8
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            2             57
  STAGE IIIC            1             41
  STAGE IV              4             44
  STAGE IVA             2             16
  STAGE IVB             1              0
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  FLG2 MUTATED     1   3  25   4
  FLG2 WILD-TYPE  16  89 304  46
D452V5, multiclass
    clus
vv   FLG2 MUTATED FLG2 WILD-TYPE
  T1            1             16
  T2            3             89
  T3           25            304
  T4            4             46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  FLG2 MUTATED    22   5   5
  FLG2 WILD-TYPE 265 108  82
D452V6, multiclass
    clus
vv   FLG2 MUTATED FLG2 WILD-TYPE
  N0           22            265
  N1            5            108
  N2            5             82
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D452V7, binary
                cls
clus               0   1
  FLG2 MUTATED    23   7
  FLG2 WILD-TYPE 352  58
[1] "tbl2"
                cls
clus             [,1] [,2]
  FLG2 MUTATED     23    7
  FLG2 WILD-TYPE  352   58
   clus
vv  FLG2 MUTATED FLG2 WILD-TYPE
  0           23            352
  1            7             58
[1] 2 2
[1] FALSE
D452V8, binary
                cls
clus               0   1
  FLG2 MUTATED    11  22
  FLG2 WILD-TYPE 214 242
[1] "tbl2"
                cls
clus             [,1] [,2]
  FLG2 MUTATED     11   22
  FLG2 WILD-TYPE  214  242
        clus
vv       FLG2 MUTATED FLG2 WILD-TYPE
  FEMALE           11            214
  MALE             22            242
[1] 2 2
[1] FALSE
D452V9, binary
                cls
clus               0   1
  FLG2 MUTATED    27   0
  FLG2 WILD-TYPE 323  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  FLG2 MUTATED     27    0
  FLG2 WILD-TYPE  323   22
     clus
vv    FLG2 MUTATED FLG2 WILD-TYPE
  NO            27            323
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  FLG2 MUTATED                     23                             5
  FLG2 WILD-TYPE                  292                            42
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  FLG2 MUTATED                       5                              0
  FLG2 WILD-TYPE                   101                             10
D452V10, multiclass
                                clus
vv                               FLG2 MUTATED FLG2 WILD-TYPE
  COLON ADENOCARCINOMA                     23            292
  COLON MUCINOUS ADENOCARCINOMA             5             42
  RECTAL ADENOCARCINOMA                     5            101
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  FLG2 MUTATED    23   0   2   4
  FLG2 WILD-TYPE 322   4  29  21
D452V11, multiclass
    clus
vv   FLG2 MUTATED FLG2 WILD-TYPE
  R0           23            322
  R1            0              4
  R2            2             29
  RX            4             21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D452V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FLG2 MUTATED                                  0     2
  FLG2 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  FLG2 MUTATED                           3    12
  FLG2 WILD-TYPE                        19   214
D452V13, multiclass
                                  clus
vv                                 FLG2 MUTATED FLG2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              9
  BLACK OR AFRICAN AMERICAN                   3             19
  WHITE                                      12            214
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(453) Variable = HMCN1 MUTATION ANALYSIS
D453V1, survival
                 sevent
clus2               0   1
  HMCN1 MUTATED    65  14
  HMCN1 WILD-TYPE 313  79
  HMCN1 MUTATED HMCN1 WILD-TYPE 
             79             392 
  HMCN1 MUTATED HMCN1 WILD-TYPE 
             14              79 
$`HMCN1 MUTATED`
TCGA-A6-2674 TCGA-A6-3809 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5665 TCGA-A6-6651 
       43.76        32.75        29.19        33.53        22.06        21.76 
TCGA-A6-6781 TCGA-AA-3510 TCGA-AA-3525 TCGA-AA-3554 TCGA-AA-3672 TCGA-AA-3713 
       19.66        63.98         8.05        17.95         0.92        19.04 
TCGA-AA-3815 TCGA-AA-3845 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3947 TCGA-AA-3949 
       33.04         0.00        31.07        53.00        33.01        26.01 
TCGA-AA-3956 TCGA-AA-3977 TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00E 
       34.03        25.02         7.96        13.94        38.04        30.02 
TCGA-AA-A00J TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A024 TCGA-AA-A03J TCGA-AD-6895 
       18.05         4.01        34.98        39.06        40.96         0.72 
TCGA-AU-6004 TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-5407 TCGA-AZ-6601 TCGA-CA-5797 
       27.09        21.44        58.39        88.21       100.01         3.29 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4952 TCGA-CK-5914 TCGA-CK-6751 TCGA-CM-4743 
       12.76        10.06        15.62         9.99       124.27        23.05 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-6674 
       22.98        30.08        32.02        15.02         5.03        12.95 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-6529 TCGA-D5-6536 TCGA-D5-6541 
       10.06        12.03        45.40        20.19        17.85        15.58 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-DM-A1DB 
        4.41        12.43         1.51        12.00        11.38        44.32 
TCGA-DM-A1HB TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6570 TCGA-F4-6703 TCGA-G4-6307 
      135.65         8.61        31.96         6.18        47.87        55.04 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-AF-2693 TCGA-AG-3575 TCGA-AG-3583 
       22.09        35.80        26.17        19.10        12.00        20.05 
TCGA-AG-3609 TCGA-AG-3878 TCGA-AG-3892 TCGA-AG-A002 TCGA-AG-A02N TCGA-AG-A02X 
       19.99         0.99        13.02        20.98        61.97        41.00 
TCGA-DY-A1H8 
       32.61 

$`HMCN1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5657 
       34.65        33.34        36.53        14.53        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 
       30.44        23.61        22.09        32.71        27.09        22.52 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        24.16        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3529 
        9.07        24.03        37.05        36.03        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
       14.01        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       19.04        10.06        35.05         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 
       17.98        15.95        38.99        37.02        14.93        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
        0.99        31.07        30.05        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       24.00         2.01        20.98         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3994 TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00K 
       27.02        19.07        27.02        19.00        34.03        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       35.01        26.01        37.02        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 
        0.07        21.37        15.52        56.55         0.79         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 
       22.42        27.42        10.88         0.20        14.50        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
        0.95        33.01        17.82         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 
       22.36        62.79        49.41         6.77        12.10        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        3.25         0.07        12.20        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       85.45        49.08        51.32        21.14        82.95         1.91 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       15.02        14.04        11.01        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6532 
       11.01        12.26        19.59        56.09        55.92        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
        1.32        43.27        15.12         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       16.14         1.48         3.68        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       11.64         4.80        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
        7.50       131.51       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6569 TCGA-F4-6704 
       35.97        60.79       117.07        98.24        35.74         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 
       44.68        85.48        63.62        61.91        36.00        13.78 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       13.55        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       20.02        10.39        36.03        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       36.03        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3611 
       50.04        12.03         6.05         0.99        15.95        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
        1.94        38.96        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  HMCN1 MUTATED HMCN1 WILD-TYPE 
              0               0 
  HMCN1 MUTATED HMCN1 WILD-TYPE 
         135.65          148.01 
  HMCN1 MUTATED HMCN1 WILD-TYPE 
         21.760          20.005 
[1] "0.0 - 135.7 (21.8)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.2"
D453V2, continuous
D453V3, binary
                 cls
clus                0   1
  HMCN1 MUTATED    72   9
  HMCN1 WILD-TYPE 294 110
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HMCN1 MUTATED     72    9
  HMCN1 WILD-TYPE  294  110
        clus
vv       HMCN1 MUTATED HMCN1 WILD-TYPE
  COLON             72             294
  RECTUM             9             110
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  HMCN1 MUTATED        11        0        6        32         5         0
  HMCN1 WILD-TYPE      80        1       26       106         5         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  HMCN1 MUTATED           3          2         11          5        4         1
  HMCN1 WILD-TYPE        21          9         48         37       44        17
                 vv
clus              STAGE IVB
  HMCN1 MUTATED           0
  HMCN1 WILD-TYPE         1
D453V4, multiclass
            clus
vv           HMCN1 MUTATED HMCN1 WILD-TYPE
  STAGE I               11              80
  STAGE IA               0               1
  STAGE II               6              26
  STAGE IIA             32             106
  STAGE IIB              5               5
  STAGE IIC              0               1
  STAGE III              3              21
  STAGE IIIA             2               9
  STAGE IIIB            11              48
  STAGE IIIC             5              37
  STAGE IV               4              44
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  HMCN1 MUTATED     2  12  59   9
  HMCN1 WILD-TYPE  15  80 270  41
D453V5, multiclass
    clus
vv   HMCN1 MUTATED HMCN1 WILD-TYPE
  T1             2              15
  T2            12              80
  T3            59             270
  T4             9              41
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  HMCN1 MUTATED    55  16  11
  HMCN1 WILD-TYPE 232  97  76
D453V6, multiclass
    clus
vv   HMCN1 MUTATED HMCN1 WILD-TYPE
  N0            55             232
  N1            16              97
  N2            11              76
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D453V7, binary
                 cls
clus                0   1
  HMCN1 MUTATED    66   5
  HMCN1 WILD-TYPE 309  60
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HMCN1 MUTATED     66    5
  HMCN1 WILD-TYPE  309   60
   clus
vv  HMCN1 MUTATED HMCN1 WILD-TYPE
  0            66             309
  1             5              60
[1] 2 2
[1] FALSE
D453V8, binary
                 cls
clus                0   1
  HMCN1 MUTATED    31  51
  HMCN1 WILD-TYPE 194 213
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HMCN1 MUTATED     31   51
  HMCN1 WILD-TYPE  194  213
        clus
vv       HMCN1 MUTATED HMCN1 WILD-TYPE
  FEMALE            31             194
  MALE              51             213
[1] 2 2
[1] FALSE
D453V9, binary
                 cls
clus                0   1
  HMCN1 MUTATED    64   1
  HMCN1 WILD-TYPE 286  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HMCN1 MUTATED     64    1
  HMCN1 WILD-TYPE  286   21
     clus
vv    HMCN1 MUTATED HMCN1 WILD-TYPE
  NO             64             286
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  HMCN1 MUTATED                     59                            12
  HMCN1 WILD-TYPE                  256                            35
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  HMCN1 MUTATED                       8                              1
  HMCN1 WILD-TYPE                    98                              9
D453V10, multiclass
                                clus
vv                               HMCN1 MUTATED HMCN1 WILD-TYPE
  COLON ADENOCARCINOMA                      59             256
  COLON MUCINOUS ADENOCARCINOMA             12              35
  RECTAL ADENOCARCINOMA                      8              98
  RECTAL MUCINOUS ADENOCARCINOMA             1               9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  HMCN1 MUTATED    62   0   3   7
  HMCN1 WILD-TYPE 283   4  28  18
D453V11, multiclass
    clus
vv   HMCN1 MUTATED HMCN1 WILD-TYPE
  R0            62             283
  R1             0               4
  R2             3              28
  RX             7              18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D453V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HMCN1 MUTATED                                  0     3
  HMCN1 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  HMCN1 MUTATED                           2    45
  HMCN1 WILD-TYPE                        20   181
D453V13, multiclass
                                  clus
vv                                 HMCN1 MUTATED HMCN1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        3               8
  BLACK OR AFRICAN AMERICAN                    2              20
  WHITE                                       45             181
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(454) Variable = PIK3CA MUTATION ANALYSIS
D454V1, survival
                  sevent
clus2                0   1
  PIK3CA MUTATED   164  43
  PIK3CA WILD-TYPE 214  50
  PIK3CA MUTATED PIK3CA WILD-TYPE 
             207              264 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              43               50 
$`PIK3CA MUTATED`
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       33.34        32.75        14.53        32.91        31.63        30.44 
TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6141 
       29.19        33.53        23.61        22.06        32.71         8.38 
TCGA-A6-6649 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 
       24.16        24.69        23.87        20.12        20.28         7.04 
TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3655 
        3.02         1.02        35.01        63.98         6.97        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3673 TCGA-AA-3696 TCGA-AA-3697 
       78.08         6.05         6.97        50.04         5.03        85.05 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3837 
       19.04        19.04        35.05        33.04         0.99        38.99 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
       10.06         0.00         0.00        30.05        53.00        17.03 
TCGA-AA-3877 TCGA-AA-3939 TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-3956 TCGA-AA-3977 
       31.00        12.99        33.01        24.00        34.03        25.02 
TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01V TCGA-AA-A02O 
        4.01        34.98        31.00        31.00        35.01         0.92 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6890 
       39.98        18.05        40.96         0.07        21.37         0.79 
TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4616 TCGA-AZ-4682 
       33.01        21.44        17.82        58.39         5.13        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6606 
       62.79        88.21        49.41         6.77       100.01        11.74 
TCGA-AZ-6608 TCGA-CA-5255 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        1.61         3.06        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 
      148.01        85.45        15.62        49.08         9.99        21.14 
TCGA-CK-6747 TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5344 
       82.95        23.05        37.02        25.02        13.02        22.03 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-6161 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-6162 TCGA-CM-6164 TCGA-CM-6166 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6171 
       12.00        29.03        21.99        12.99        13.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6676 TCGA-CM-6678 TCGA-CM-6680 TCGA-D5-5538 
       11.01        12.95        11.08        11.01        12.03        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6534 
       19.59        56.09        55.92        20.19        18.25        43.27 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
       17.85         4.80        17.13        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6923 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6931 
        3.68        12.43         9.04         9.44         4.80        12.00 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D7 TCGA-DM-A1D8 
       10.26       119.70        24.43        38.20        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A285 TCGA-DM-A28C 
      140.38        44.32       131.51       135.65         6.12        81.37 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       35.97        60.79       117.07         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        6.18        47.87        34.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       53.62        44.68        55.04        63.62        61.91        36.00 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-AF-2687 
       13.78        35.80        26.17        91.79        79.69        24.13 
TCGA-AF-2693 TCGA-AF-6136 TCGA-AF-6672 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 
       19.10        15.39        10.39        37.02         0.99         0.99 
TCGA-AG-3887 TCGA-AG-A00H TCGA-AG-A020 TCGA-AG-A02N TCGA-AH-6544 TCGA-AH-6643 
       36.95        25.97        10.98        61.97        38.56         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        0.72         6.05         6.97         4.73        78.12         7.17 
TCGA-DC-5869 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
        5.03        27.95        10.98         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DG TCGA-EF-5830 TCGA-EI-6507 TCGA-F5-6571 
      126.44        41.36        51.48         0.49        19.96        31.30 
TCGA-F5-6811 TCGA-F5-6813 TCGA-G5-6235 
       32.19         0.69        55.76 

$`PIK3CA WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-5664 TCGA-A6-6137 TCGA-A6-6138 
       16.57        34.65        36.53        22.09        27.09        22.52 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6781 TCGA-AA-3514 
       25.08        25.18        21.76        24.39        19.66         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
       13.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       36.03         8.05        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3664 
       23.01        20.98        19.99        13.94        19.99        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
        2.01        14.01         0.92        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3710 TCGA-AA-3811 
        5.98        37.05        19.00        36.00        26.99        10.06 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3842 TCGA-AA-3844 
       25.02         1.02        17.98        15.95        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        17.03        33.07        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       31.07        31.07        24.03        27.02        29.98        18.05 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3966 
        2.01        24.00        26.01         2.01        20.98         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01X 
       38.07         1.02        35.01         1.02        33.04        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02W TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6895 TCGA-AD-6901 
       14.01        41.00        15.52        56.55         0.72        22.42 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AZ-4323 TCGA-AZ-4681 TCGA-AZ-6600 TCGA-AZ-6603 
       16.31         0.95         1.41       106.75        12.10        29.56 
TCGA-AZ-6605 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        5.23         3.19        12.69         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CK-5913 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-5341 
       12.20        51.32         1.91       124.27        20.02        29.06 
TCGA-CM-5348 TCGA-CM-5863 TCGA-CM-5868 TCGA-CM-6163 TCGA-CM-6165 TCGA-CM-6167 
       22.98        15.02        17.03         2.96        16.04        14.99 
TCGA-CM-6170 TCGA-CM-6675 TCGA-CM-6677 TCGA-CM-6679 TCGA-D5-5537 TCGA-D5-6533 
       15.02        13.05        11.08        10.06        45.40         1.32 
TCGA-D5-6535 TCGA-D5-6539 TCGA-D5-6922 TCGA-D5-6924 TCGA-D5-6928 TCGA-D5-6930 
       15.12        12.49         4.41        14.30        11.64         1.51 
TCGA-D5-6932 TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1DA TCGA-DM-A282 
       11.38       130.65        92.75        49.91         7.50       139.17 
TCGA-DM-A28E TCGA-DM-A28K TCGA-F4-6704 TCGA-F4-6806 TCGA-G4-6309 TCGA-G4-6321 
      119.93        98.24         1.55        41.42        85.48        22.09 
TCGA-G4-6626 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3913 
       46.75        39.48        43.04        13.55        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6655 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       14.50        16.83        20.02        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3732 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99        32.98        19.04        19.99         1.02        17.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 
       17.03        20.98        13.94         6.02        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
       49.97         1.94        38.96        41.00        38.04       117.11 
TCGA-AH-6547 TCGA-AH-6549 TCGA-CI-6620 TCGA-DC-5337 TCGA-DC-6155 TCGA-DC-6160 
        1.45        17.49        33.17        15.02        13.97        19.99 
TCGA-DC-6681 TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EI-6506 TCGA-EI-6508 
        5.95        57.24        24.13        32.61        20.55        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6702 TCGA-F5-6812 TCGA-G5-6641 
       18.28         9.96        49.51        28.57         0.66        26.43 

  PIK3CA MUTATED PIK3CA WILD-TYPE 
               0                0 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
          148.01           139.17 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
           21.99            19.99 
[1] "0.0 - 148.0 (22.0)" "0.0 - 139.2 (20.0)"
[1] "hr=" "1.1"
D454V2, continuous
D454V3, binary
                  cls
clus                 0   1
  PIK3CA MUTATED   175  35
  PIK3CA WILD-TYPE 191  84
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED    175   35
  PIK3CA WILD-TYPE  191   84
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  COLON             175              191
  RECTUM             35               84
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PIK3CA MUTATED        37        1       17        66         9         1
  PIK3CA WILD-TYPE      54        0       15        72         1         0
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PIK3CA MUTATED           6          2         27         16       12
  PIK3CA WILD-TYPE        18          9         32         26       36
                  vv
clus               STAGE IVA STAGE IVB
  PIK3CA MUTATED           9         0
  PIK3CA WILD-TYPE         9         1
D454V4, multiclass
            clus
vv           PIK3CA MUTATED PIK3CA WILD-TYPE
  STAGE I                37               54
  STAGE IA                1                0
  STAGE II               17               15
  STAGE IIA              66               72
  STAGE IIB               9                1
  STAGE IIC               1                0
  STAGE III               6               18
  STAGE IIIA              2                9
  STAGE IIIB             27               32
  STAGE IIIC             16               26
  STAGE IV               12               36
  STAGE IVA               9                9
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  PIK3CA MUTATED     6  35 145  24
  PIK3CA WILD-TYPE  11  57 184  26
D454V5, multiclass
    clus
vv   PIK3CA MUTATED PIK3CA WILD-TYPE
  T1              6               11
  T2             35               57
  T3            145              184
  T4             24               26
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  PIK3CA MUTATED   138  43  29
  PIK3CA WILD-TYPE 149  70  58
D454V6, multiclass
    clus
vv   PIK3CA MUTATED PIK3CA WILD-TYPE
  N0            138              149
  N1             43               70
  N2             29               58
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D454V7, binary
                  cls
clus                 0   1
  PIK3CA MUTATED   162  21
  PIK3CA WILD-TYPE 213  44
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED    162   21
  PIK3CA WILD-TYPE  213   44
   clus
vv  PIK3CA MUTATED PIK3CA WILD-TYPE
  0            162              213
  1             21               44
[1] 2 2
[1] FALSE
D454V8, binary
                  cls
clus                 0   1
  PIK3CA MUTATED    92 119
  PIK3CA WILD-TYPE 133 145
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED     92  119
  PIK3CA WILD-TYPE  133  145
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  FEMALE             92              133
  MALE              119              145
[1] 2 2
[1] FALSE
D454V9, binary
                  cls
clus                 0   1
  PIK3CA MUTATED   149   9
  PIK3CA WILD-TYPE 201  13
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED    149    9
  PIK3CA WILD-TYPE  201   13
     clus
vv    PIK3CA MUTATED PIK3CA WILD-TYPE
  NO             149              201
  YES              9               13
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PIK3CA MUTATED                    152                            20
  PIK3CA WILD-TYPE                  163                            27
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PIK3CA MUTATED                      31                              4
  PIK3CA WILD-TYPE                    75                              6
D454V10, multiclass
                                clus
vv                               PIK3CA MUTATED PIK3CA WILD-TYPE
  COLON ADENOCARCINOMA                      152              163
  COLON MUCINOUS ADENOCARCINOMA              20               27
  RECTAL ADENOCARCINOMA                      31               75
  RECTAL MUCINOUS ADENOCARCINOMA              4                6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  PIK3CA MUTATED   140   2   4  14
  PIK3CA WILD-TYPE 205   2  27  11
D454V11, multiclass
    clus
vv   PIK3CA MUTATED PIK3CA WILD-TYPE
  R0            140              205
  R1              2                2
  R2              4               27
  RX             14               11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D454V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PIK3CA MUTATED                                  0     5
  PIK3CA WILD-TYPE                                1     6
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  PIK3CA MUTATED                          15   141
  PIK3CA WILD-TYPE                         7    85
D454V13, multiclass
                                  clus
vv                                 PIK3CA MUTATED PIK3CA WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         5                6
  BLACK OR AFRICAN AMERICAN                    15                7
  WHITE                                       141               85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(455) Variable = PRKD1 MUTATION ANALYSIS
D455V1, survival
                 sevent
clus2               0   1
  PRKD1 MUTATED    24   4
  PRKD1 WILD-TYPE 354  89
  PRKD1 MUTATED PRKD1 WILD-TYPE 
             28             443 
  PRKD1 MUTATED PRKD1 WILD-TYPE 
              4              89 
$`PRKD1 MUTATED`
TCGA-AA-3510 TCGA-AA-3655 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3821 TCGA-AA-3845 
       63.98        61.02        26.99        19.04         1.02         0.00 
TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-A010 TCGA-AA-A02J TCGA-AD-5900 TCGA-AZ-4315 
       34.06        25.02        34.98         5.03         0.07        58.39 
TCGA-AZ-6599 TCGA-AZ-6605 TCGA-CA-6717 TCGA-CM-5861 TCGA-CM-5864 TCGA-D5-6533 
        6.77         5.23        12.76        15.02        15.02         1.32 
TCGA-D5-6534 TCGA-D5-6538 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6628 TCGA-AG-3581 
       43.27        17.13        47.41       133.18        79.69         7.07 
TCGA-AG-4005 TCGA-AG-A002 TCGA-AG-A036 TCGA-G5-6235 
       14.04        20.98       117.11        55.76 

$`PRKD1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       19.99        13.94        19.99        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
        5.03        85.05        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
        0.99        25.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
       14.93        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       16.08        50.99        13.05        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        2.01        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
       40.96        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6606 TCGA-AZ-6607 
       49.41        12.10       100.01        29.56        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.20        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
        5.03        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6535 
       19.59        56.09        55.92        20.19        18.25        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
       17.85         4.80        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6303 
       33.67        13.25         0.53        35.31        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       46.75        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3582 
       10.39        36.03        12.00        32.02         8.02        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4007 
       48.03        32.02        19.99        28.04        36.03         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
       38.04        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        26.43 

  PRKD1 MUTATED PRKD1 WILD-TYPE 
              0               0 
  PRKD1 MUTATED PRKD1 WILD-TYPE 
         133.18          148.01 
  PRKD1 MUTATED PRKD1 WILD-TYPE 
          20.01           20.19 
[1] "0.0 - 133.2 (20.0)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.8"
D455V2, continuous
D455V3, binary
                 cls
clus                0   1
  PRKD1 MUTATED    24   5
  PRKD1 WILD-TYPE 342 114
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRKD1 MUTATED     24    5
  PRKD1 WILD-TYPE  342  114
        clus
vv       PRKD1 MUTATED PRKD1 WILD-TYPE
  COLON             24             342
  RECTUM             5             114
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PRKD1 MUTATED         8        0        2         8         1         0
  PRKD1 WILD-TYPE      83        1       30       130         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PRKD1 MUTATED           2          0          4          0        3         0
  PRKD1 WILD-TYPE        22         11         55         42       45        18
                 vv
clus              STAGE IVB
  PRKD1 MUTATED           0
  PRKD1 WILD-TYPE         1
D455V4, multiclass
            clus
vv           PRKD1 MUTATED PRKD1 WILD-TYPE
  STAGE I                8              83
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA              8             130
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              2              22
  STAGE IIIA             0              11
  STAGE IIIB             4              55
  STAGE IIIC             0              42
  STAGE IV               3              45
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PRKD1 MUTATED     0   9  17   3
  PRKD1 WILD-TYPE  17  83 312  47
D455V5, multiclass
    clus
vv   PRKD1 MUTATED PRKD1 WILD-TYPE
  T1             0              17
  T2             9              83
  T3            17             312
  T4             3              47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  PRKD1 MUTATED    23   3   3
  PRKD1 WILD-TYPE 264 110  84
D455V6, multiclass
    clus
vv   PRKD1 MUTATED PRKD1 WILD-TYPE
  N0            23             264
  N1             3             110
  N2             3              84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D455V7, binary
                 cls
clus                0   1
  PRKD1 MUTATED    22   3
  PRKD1 WILD-TYPE 353  62
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRKD1 MUTATED     22    3
  PRKD1 WILD-TYPE  353   62
   clus
vv  PRKD1 MUTATED PRKD1 WILD-TYPE
  0            22             353
  1             3              62
[1] 2 2
[1] FALSE
D455V8, binary
                 cls
clus                0   1
  PRKD1 MUTATED    12  17
  PRKD1 WILD-TYPE 213 247
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRKD1 MUTATED     12   17
  PRKD1 WILD-TYPE  213  247
        clus
vv       PRKD1 MUTATED PRKD1 WILD-TYPE
  FEMALE            12             213
  MALE              17             247
[1] 2 2
[1] FALSE
D455V9, binary
                 cls
clus                0   1
  PRKD1 MUTATED    22   2
  PRKD1 WILD-TYPE 328  20
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRKD1 MUTATED     22    2
  PRKD1 WILD-TYPE  328   20
     clus
vv    PRKD1 MUTATED PRKD1 WILD-TYPE
  NO             22             328
  YES             2              20
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PRKD1 MUTATED                     20                             4
  PRKD1 WILD-TYPE                  295                            43
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PRKD1 MUTATED                       5                              0
  PRKD1 WILD-TYPE                   101                             10
D455V10, multiclass
                                clus
vv                               PRKD1 MUTATED PRKD1 WILD-TYPE
  COLON ADENOCARCINOMA                      20             295
  COLON MUCINOUS ADENOCARCINOMA              4              43
  RECTAL ADENOCARCINOMA                      5             101
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  PRKD1 MUTATED    22   1   2   1
  PRKD1 WILD-TYPE 323   3  29  24
D455V11, multiclass
    clus
vv   PRKD1 MUTATED PRKD1 WILD-TYPE
  R0            22             323
  R1             1               3
  R2             2              29
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D455V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PRKD1 MUTATED                                  0     1
  PRKD1 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PRKD1 MUTATED                           0    13
  PRKD1 WILD-TYPE                        22   213
D455V13, multiclass
                                  clus
vv                                 PRKD1 MUTATED PRKD1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                       13             213
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(456) Variable = ADAMTS19 MUTATION ANALYSIS
D456V1, survival
                    sevent
clus2                  0   1
  ADAMTS19 MUTATED    18   7
  ADAMTS19 WILD-TYPE 360  86
  ADAMTS19 MUTATED ADAMTS19 WILD-TYPE 
                25                446 
  ADAMTS19 MUTATED ADAMTS19 WILD-TYPE 
                 7                 86 
$`ADAMTS19 MUTATED`
TCGA-A6-2676 TCGA-A6-6780 TCGA-AA-A00J TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01P 
       42.90        20.12        18.05         4.01        34.98        38.07 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-6599 TCGA-AZ-6605 
       14.50        27.09        21.44        58.39         6.77         5.23 
TCGA-CM-4743 TCGA-CM-5349 TCGA-CM-6678 TCGA-D5-6534 TCGA-DM-A1HB TCGA-DM-A28F 
       23.05        30.08        11.01        43.27       135.65        35.97 
TCGA-G4-6293 TCGA-AF-6655 TCGA-AG-3599 TCGA-AG-3742 TCGA-AG-A002 TCGA-DY-A1H8 
      133.18        20.02        12.03         0.99        20.98        32.61 
TCGA-G5-6641 
       26.43 

$`ADAMTS19 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       19.00        30.02        34.03        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01Q 
       10.98        32.02        12.00        31.00        31.00         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AY-4070 TCGA-AY-4071 
       22.42        27.42        10.88         0.20        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       33.01        17.82         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        88.21        49.41        12.10       100.01        29.56 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 
        9.99        21.14        82.95         1.91       124.27        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6679 TCGA-CM-6680 
       12.95        13.05        11.08        11.08        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       18.25         1.32        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 
      140.38         7.50        44.32       131.51       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
       81.37       119.93        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
       35.31        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       14.50        16.83        15.39        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3600 
        1.02        46.03        34.03         2.01        50.04         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
        0.99        37.02        32.98         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       51.48         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 
        0.69        55.76 

  ADAMTS19 MUTATED ADAMTS19 WILD-TYPE 
              0.99               0.00 
  ADAMTS19 MUTATED ADAMTS19 WILD-TYPE 
            135.65             148.01 
  ADAMTS19 MUTATED ADAMTS19 WILD-TYPE 
            23.050             20.005 
[1] "1.0 - 135.7 (23.1)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.3"
D456V2, continuous
D456V3, binary
                    cls
clus                   0   1
  ADAMTS19 MUTATED    19   6
  ADAMTS19 WILD-TYPE 347 113
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ADAMTS19 MUTATED     19    6
  ADAMTS19 WILD-TYPE  347  113
        clus
vv       ADAMTS19 MUTATED ADAMTS19 WILD-TYPE
  COLON                19                347
  RECTUM                6                113
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ADAMTS19 MUTATED         5        0        0         7         3         0
  ADAMTS19 WILD-TYPE      86        1       32       131         7         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ADAMTS19 MUTATED           2          3          4          0        0
  ADAMTS19 WILD-TYPE        22          8         55         42       48
                    vv
clus                 STAGE IVA STAGE IVB
  ADAMTS19 MUTATED           1         0
  ADAMTS19 WILD-TYPE        17         1
D456V4, multiclass
            clus
vv           ADAMTS19 MUTATED ADAMTS19 WILD-TYPE
  STAGE I                   5                 86
  STAGE IA                  0                  1
  STAGE II                  0                 32
  STAGE IIA                 7                131
  STAGE IIB                 3                  7
  STAGE IIC                 0                  1
  STAGE III                 2                 22
  STAGE IIIA                3                  8
  STAGE IIIB                4                 55
  STAGE IIIC                0                 42
  STAGE IV                  0                 48
  STAGE IVA                 1                 17
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  ADAMTS19 MUTATED     2   6  11   6
  ADAMTS19 WILD-TYPE  15  86 318  44
D456V5, multiclass
    clus
vv   ADAMTS19 MUTATED ADAMTS19 WILD-TYPE
  T1                2                 15
  T2                6                 86
  T3               11                318
  T4                6                 44
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  ADAMTS19 MUTATED    15  10   0
  ADAMTS19 WILD-TYPE 272 103  87
D456V6, multiclass
    clus
vv   ADAMTS19 MUTATED ADAMTS19 WILD-TYPE
  N0               15                272
  N1               10                103
  N2                0                 87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D456V7, binary
                    cls
clus                   0   1
  ADAMTS19 MUTATED    20   1
  ADAMTS19 WILD-TYPE 355  64
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ADAMTS19 MUTATED     20    1
  ADAMTS19 WILD-TYPE  355   64
   clus
vv  ADAMTS19 MUTATED ADAMTS19 WILD-TYPE
  0               20                355
  1                1                 64
[1] 2 2
[1] FALSE
D456V8, binary
                    cls
clus                   0   1
  ADAMTS19 MUTATED    11  14
  ADAMTS19 WILD-TYPE 214 250
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ADAMTS19 MUTATED     11   14
  ADAMTS19 WILD-TYPE  214  250
        clus
vv       ADAMTS19 MUTATED ADAMTS19 WILD-TYPE
  FEMALE               11                214
  MALE                 14                250
[1] 2 2
[1] FALSE
D456V9, binary
                    cls
clus                   0   1
  ADAMTS19 MUTATED    19   0
  ADAMTS19 WILD-TYPE 331  22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ADAMTS19 MUTATED     19    0
  ADAMTS19 WILD-TYPE  331   22
     clus
vv    ADAMTS19 MUTATED ADAMTS19 WILD-TYPE
  NO                19                331
  YES                0                 22
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ADAMTS19 MUTATED                     14                             4
  ADAMTS19 WILD-TYPE                  301                            43
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ADAMTS19 MUTATED                       4                              1
  ADAMTS19 WILD-TYPE                   102                              9
D456V10, multiclass
                                clus
vv                               ADAMTS19 MUTATED ADAMTS19 WILD-TYPE
  COLON ADENOCARCINOMA                         14                301
  COLON MUCINOUS ADENOCARCINOMA                 4                 43
  RECTAL ADENOCARCINOMA                         4                102
  RECTAL MUCINOUS ADENOCARCINOMA                1                  9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  ADAMTS19 MUTATED    19   0   0   0
  ADAMTS19 WILD-TYPE 326   4  31  25
D456V11, multiclass
    clus
vv   ADAMTS19 MUTATED ADAMTS19 WILD-TYPE
  R0               19                326
  R1                0                  4
  R2                0                 31
  RX                0                 25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D456V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ADAMTS19 MUTATED                                  0     0
  ADAMTS19 WILD-TYPE                                1    11
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  ADAMTS19 MUTATED                           0    18
  ADAMTS19 WILD-TYPE                        22   208
D456V13, multiclass
                                  clus
vv                                 ADAMTS19 MUTATED ADAMTS19 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 11
  BLACK OR AFRICAN AMERICAN                       0                 22
  WHITE                                          18                208
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(457) Variable = CLVS2 MUTATION ANALYSIS
D457V1, survival
                 sevent
clus2               0   1
  CLVS2 MUTATED     9   0
  CLVS2 WILD-TYPE 369  93
  CLVS2 MUTATED CLVS2 WILD-TYPE 
              9             462 
  CLVS2 MUTATED CLVS2 WILD-TYPE 
              0              93 
$`CLVS2 MUTATED`
TCGA-AA-3713 TCGA-AA-3864 TCGA-AA-A01Q TCGA-AD-6889 TCGA-CM-5348 TCGA-D5-6532 
       19.04        53.00         1.02        56.55        22.98        18.25 
TCGA-D5-6533 TCGA-D5-6540 TCGA-AG-A002 
        1.32        16.14        20.98 

$`CLVS2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 
       32.05         0.99        31.07        31.07        30.05        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        31.00        38.07        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 
       18.05        40.96         0.07        21.37        15.52         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       29.06        22.03        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6534 TCGA-D5-6535 
       19.59        56.09        55.92        20.19        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 
       17.85         4.80        17.13        12.49        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  CLVS2 MUTATED CLVS2 WILD-TYPE 
           1.02            0.00 
  CLVS2 MUTATED CLVS2 WILD-TYPE 
          56.55          148.01 
  CLVS2 MUTATED CLVS2 WILD-TYPE 
         19.040          20.235 
[1] "1.0 - 56.5 (19.0)"  "0.0 - 148.0 (20.2)"
[1] "hr="     "9200000"
D457V2, continuous
D457V3, binary
                 cls
clus                0   1
  CLVS2 MUTATED     9   1
  CLVS2 WILD-TYPE 357 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CLVS2 MUTATED      9    1
  CLVS2 WILD-TYPE  357  118
        clus
vv       CLVS2 MUTATED CLVS2 WILD-TYPE
  COLON              9             357
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CLVS2 MUTATED         3        0        2         2         0         0
  CLVS2 WILD-TYPE      88        1       30       136        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CLVS2 MUTATED           0          0          2          0        1         0
  CLVS2 WILD-TYPE        24         11         57         42       47        18
                 vv
clus              STAGE IVB
  CLVS2 MUTATED           0
  CLVS2 WILD-TYPE         1
D457V4, multiclass
            clus
vv           CLVS2 MUTATED CLVS2 WILD-TYPE
  STAGE I                3              88
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA              2             136
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             2              57
  STAGE IIIC             0              42
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CLVS2 MUTATED     0   3   6   1
  CLVS2 WILD-TYPE  17  89 323  49
D457V5, multiclass
    clus
vv   CLVS2 MUTATED CLVS2 WILD-TYPE
  T1             0              17
  T2             3              89
  T3             6             323
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  CLVS2 MUTATED     9   1   0
  CLVS2 WILD-TYPE 278 112  87
D457V6, multiclass
    clus
vv   CLVS2 MUTATED CLVS2 WILD-TYPE
  N0             9             278
  N1             1             112
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D457V7, binary
                 cls
clus                0   1
  CLVS2 MUTATED     8   1
  CLVS2 WILD-TYPE 367  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CLVS2 MUTATED      8    1
  CLVS2 WILD-TYPE  367   64
   clus
vv  CLVS2 MUTATED CLVS2 WILD-TYPE
  0             8             367
  1             1              64
[1] 2 2
[1] FALSE
D457V8, binary
                 cls
clus                0   1
  CLVS2 MUTATED     2   8
  CLVS2 WILD-TYPE 223 256
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CLVS2 MUTATED      2    8
  CLVS2 WILD-TYPE  223  256
        clus
vv       CLVS2 MUTATED CLVS2 WILD-TYPE
  FEMALE             2             223
  MALE               8             256
[1] 2 2
[1] FALSE
D457V9, binary
                 cls
clus                0   1
  CLVS2 MUTATED     5   1
  CLVS2 WILD-TYPE 345  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CLVS2 MUTATED      5    1
  CLVS2 WILD-TYPE  345   21
     clus
vv    CLVS2 MUTATED CLVS2 WILD-TYPE
  NO              5             345
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CLVS2 MUTATED                      8                             1
  CLVS2 WILD-TYPE                  307                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CLVS2 MUTATED                       1                              0
  CLVS2 WILD-TYPE                   105                             10
D457V10, multiclass
                                clus
vv                               CLVS2 MUTATED CLVS2 WILD-TYPE
  COLON ADENOCARCINOMA                       8             307
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  CLVS2 MUTATED     7   0   1   1
  CLVS2 WILD-TYPE 338   4  30  24
D457V11, multiclass
    clus
vv   CLVS2 MUTATED CLVS2 WILD-TYPE
  R0             7             338
  R1             0               4
  R2             1              30
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D457V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CLVS2 MUTATED                                  0     1
  CLVS2 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CLVS2 MUTATED                           0     5
  CLVS2 WILD-TYPE                        22   221
D457V13, multiclass
                                  clus
vv                                 CLVS2 MUTATED CLVS2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        5             221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(458) Variable = GTF3C3 MUTATION ANALYSIS
D458V1, survival
                  sevent
clus2                0   1
  GTF3C3 MUTATED    13   4
  GTF3C3 WILD-TYPE 365  89
  GTF3C3 MUTATED GTF3C3 WILD-TYPE 
              17              454 
  GTF3C3 MUTATED GTF3C3 WILD-TYPE 
               4               89 
$`GTF3C3 MUTATED`
TCGA-A6-5661 TCGA-AA-3496 TCGA-AA-3977 TCGA-AA-A010 TCGA-AD-6964 TCGA-AZ-4315 
       33.53         1.02        25.02        34.98        10.88        58.39 
TCGA-AZ-6598 TCGA-CA-6715 TCGA-CA-6717 TCGA-CM-6163 TCGA-CM-6674 TCGA-DM-A0XD 
       49.41         0.07        12.76         2.96        12.95        24.43 
TCGA-DM-A1D6 TCGA-F4-6807 TCGA-G4-6628 TCGA-AG-3892 TCGA-AG-A002 
       49.91        16.24        79.69        13.02        20.98 

$`GTF3C3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 
       20.12        19.66        20.28         7.04         3.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
        0.72         5.79        22.42        27.42         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.20        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
       12.00        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6676 
       13.02        15.02        14.04        11.01        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XF TCGA-DM-A1D0 
       12.00        11.38        10.26       119.70        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       92.75        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       26.17        91.79        46.75        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 
       19.99         1.02        17.95        36.95        17.03        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  GTF3C3 MUTATED GTF3C3 WILD-TYPE 
            0.07             0.00 
  GTF3C3 MUTATED GTF3C3 WILD-TYPE 
           79.69           148.01 
  GTF3C3 MUTATED GTF3C3 WILD-TYPE 
          20.980           20.155 
[1] "0.1 - 79.7 (21.0)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.2"
D458V2, continuous
D458V3, binary
                  cls
clus                 0   1
  GTF3C3 MUTATED    15   3
  GTF3C3 WILD-TYPE 351 116
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GTF3C3 MUTATED     15    3
  GTF3C3 WILD-TYPE  351  116
        clus
vv       GTF3C3 MUTATED GTF3C3 WILD-TYPE
  COLON              15              351
  RECTUM              3              116
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GTF3C3 MUTATED         4        0        2         7         1         0
  GTF3C3 WILD-TYPE      87        1       30       131         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GTF3C3 MUTATED           0          0          1          1        0
  GTF3C3 WILD-TYPE        24         11         58         41       48
                  vv
clus               STAGE IVA STAGE IVB
  GTF3C3 MUTATED           0         0
  GTF3C3 WILD-TYPE        18         1
D458V4, multiclass
            clus
vv           GTF3C3 MUTATED GTF3C3 WILD-TYPE
  STAGE I                 4               87
  STAGE IA                0                1
  STAGE II                2               30
  STAGE IIA               7              131
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              1               58
  STAGE IIIC              1               41
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  GTF3C3 MUTATED     2   3  11   2
  GTF3C3 WILD-TYPE  15  89 318  48
D458V5, multiclass
    clus
vv   GTF3C3 MUTATED GTF3C3 WILD-TYPE
  T1              2               15
  T2              3               89
  T3             11              318
  T4              2               48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  GTF3C3 MUTATED    15   1   2
  GTF3C3 WILD-TYPE 272 112  85
D458V6, multiclass
    clus
vv   GTF3C3 MUTATED GTF3C3 WILD-TYPE
  N0             15              272
  N1              1              112
  N2              2               85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D458V7, binary
                  cls
clus                 0   1
  GTF3C3 MUTATED    15   0
  GTF3C3 WILD-TYPE 360  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GTF3C3 MUTATED     15    0
  GTF3C3 WILD-TYPE  360   65
   clus
vv  GTF3C3 MUTATED GTF3C3 WILD-TYPE
  0             15              360
  1              0               65
[1] 2 2
[1] FALSE
D458V8, binary
                  cls
clus                 0   1
  GTF3C3 MUTATED     7  11
  GTF3C3 WILD-TYPE 218 253
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GTF3C3 MUTATED      7   11
  GTF3C3 WILD-TYPE  218  253
        clus
vv       GTF3C3 MUTATED GTF3C3 WILD-TYPE
  FEMALE              7              218
  MALE               11              253
[1] 2 2
[1] FALSE
D458V9, binary
                  cls
clus                 0   1
  GTF3C3 MUTATED    13   0
  GTF3C3 WILD-TYPE 337  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GTF3C3 MUTATED     13    0
  GTF3C3 WILD-TYPE  337   22
     clus
vv    GTF3C3 MUTATED GTF3C3 WILD-TYPE
  NO              13              337
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  GTF3C3 MUTATED                     13                             2
  GTF3C3 WILD-TYPE                  302                            45
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  GTF3C3 MUTATED                       3                              0
  GTF3C3 WILD-TYPE                   103                             10
D458V10, multiclass
                                clus
vv                               GTF3C3 MUTATED GTF3C3 WILD-TYPE
  COLON ADENOCARCINOMA                       13              302
  COLON MUCINOUS ADENOCARCINOMA               2               45
  RECTAL ADENOCARCINOMA                       3              103
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  GTF3C3 MUTATED    11   0   0   2
  GTF3C3 WILD-TYPE 334   4  31  23
D458V11, multiclass
    clus
vv   GTF3C3 MUTATED GTF3C3 WILD-TYPE
  R0             11              334
  R1              0                4
  R2              0               31
  RX              2               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D458V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GTF3C3 MUTATED                                  0     2
  GTF3C3 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  GTF3C3 MUTATED                           1     9
  GTF3C3 WILD-TYPE                        21   217
D458V13, multiclass
                                  clus
vv                                 GTF3C3 MUTATED GTF3C3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                9
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                         9              217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(459) Variable = BAI3 MUTATION ANALYSIS
D459V1, survival
                sevent
clus2              0   1
  BAI3 MUTATED    38  11
  BAI3 WILD-TYPE 340  82
  BAI3 MUTATED BAI3 WILD-TYPE 
            49            422 
  BAI3 MUTATED BAI3 WILD-TYPE 
            11             82 
$`BAI3 MUTATED`
TCGA-A6-5656 TCGA-AA-3510 TCGA-AA-3516 TCGA-AA-3526 TCGA-AA-3554 TCGA-AA-3555 
       32.91        63.98        13.02        19.07        17.95        29.95 
TCGA-AA-3663 TCGA-AA-3679 TCGA-AA-3815 TCGA-AA-3821 TCGA-AA-3947 TCGA-AA-A00N 
        6.97        15.02        33.04         1.02        33.01         4.01 
TCGA-AA-A010 TCGA-AA-A01G TCGA-AU-6004 TCGA-AZ-6598 TCGA-AZ-6606 TCGA-CA-6717 
       34.98        12.00        27.09        49.41        11.74        12.76 
TCGA-CA-6718 TCGA-CK-4952 TCGA-CK-5913 TCGA-CM-5861 TCGA-CM-5868 TCGA-CM-6166 
       10.06        15.62        51.32        15.02        17.03        21.99 
TCGA-CM-6170 TCGA-D5-5537 TCGA-D5-6533 TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6541 
       15.02        45.40         1.32        17.85        17.13        15.58 
TCGA-DM-A1D4 TCGA-DM-A1D8 TCGA-DM-A28G TCGA-G4-6306 TCGA-G4-6315 TCGA-G4-6321 
       92.75        12.59        60.79        44.68        61.91        22.09 
TCGA-G4-6625 TCGA-G4-6628 TCGA-AF-6672 TCGA-AG-3612 TCGA-AG-3896 TCGA-AG-A002 
       91.79        79.69        10.39        19.99         1.02        20.98 
TCGA-AG-A00Y TCGA-AG-A02N TCGA-AH-6544 TCGA-AH-6643 TCGA-AH-6644 TCGA-DY-A1DF 
       23.01        61.97        38.56         0.69         0.72        24.13 
TCGA-F5-6464 
        9.96 

$`BAI3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
       35.01         6.97         1.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3529 TCGA-AA-3530 
       24.03        37.05        36.03         8.05         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3556 
       14.01        33.99        21.01        13.02        24.00        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.05        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       47.01        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
       35.05         0.99        25.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99         1.02        10.98        32.02 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       10.88         0.20        14.50        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        88.21         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
       29.56         5.23         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 
        3.25         3.29         0.07        12.20        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
      148.01        85.45        49.08         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
        5.03        15.02        15.02        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6171 
       29.03        16.04        14.99        12.99        13.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       10.06        12.03        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6539 
       20.19        18.25        43.27        15.12         4.80        12.49 
TCGA-D5-6540 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       16.14         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       49.91        13.32       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6317 
       65.85        53.62        55.04        85.48        63.62        36.00 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 
       13.78        35.80        26.17        46.75        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       16.83        15.39        20.02        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3726 TCGA-AG-3727 
        0.99        15.95        19.99        13.94         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
       14.01        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X 
       64.01        10.98        49.97         1.94        38.96        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6547 TCGA-AH-6549 TCGA-CI-6619 TCGA-CI-6620 
       38.04       117.11         1.45        17.49         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DG 
        5.03         5.29       126.44        41.36        57.24        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  BAI3 MUTATED BAI3 WILD-TYPE 
          0.69           0.00 
  BAI3 MUTATED BAI3 WILD-TYPE 
         92.75         148.01 
  BAI3 MUTATED BAI3 WILD-TYPE 
        19.070         20.415 
[1] "0.7 - 92.8 (19.1)"  "0.0 - 148.0 (20.4)"
[1] "hr=" "1.1"
D459V2, continuous
D459V3, binary
                cls
clus               0   1
  BAI3 MUTATED    43  11
  BAI3 WILD-TYPE 323 108
[1] "tbl2"
                cls
clus             [,1] [,2]
  BAI3 MUTATED     43   11
  BAI3 WILD-TYPE  323  108
        clus
vv       BAI3 MUTATED BAI3 WILD-TYPE
  COLON            43            323
  RECTUM           11            108
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  BAI3 MUTATED        10        0        5        17         3         0
  BAI3 WILD-TYPE      81        1       27       121         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  BAI3 MUTATED           2          0          3          5        5         1
  BAI3 WILD-TYPE        22         11         56         37       43        17
                vv
clus             STAGE IVB
  BAI3 MUTATED           0
  BAI3 WILD-TYPE         1
D459V4, multiclass
            clus
vv           BAI3 MUTATED BAI3 WILD-TYPE
  STAGE I              10             81
  STAGE IA              0              1
  STAGE II              5             27
  STAGE IIA            17            121
  STAGE IIB             3              7
  STAGE IIC             0              1
  STAGE III             2             22
  STAGE IIIA            0             11
  STAGE IIIB            3             56
  STAGE IIIC            5             37
  STAGE IV              5             43
  STAGE IVA             1             17
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  BAI3 MUTATED     0  12  32  10
  BAI3 WILD-TYPE  17  80 297  40
D459V5, multiclass
    clus
vv   BAI3 MUTATED BAI3 WILD-TYPE
  T1            0             17
  T2           12             80
  T3           32            297
  T4           10             40
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  BAI3 MUTATED    35   6  12
  BAI3 WILD-TYPE 252 107  75
D459V6, multiclass
    clus
vv   BAI3 MUTATED BAI3 WILD-TYPE
  N0           35            252
  N1            6            107
  N2           12             75
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D459V7, binary
                cls
clus               0   1
  BAI3 MUTATED    39   6
  BAI3 WILD-TYPE 336  59
[1] "tbl2"
                cls
clus             [,1] [,2]
  BAI3 MUTATED     39    6
  BAI3 WILD-TYPE  336   59
   clus
vv  BAI3 MUTATED BAI3 WILD-TYPE
  0           39            336
  1            6             59
[1] 2 2
[1] FALSE
D459V8, binary
                cls
clus               0   1
  BAI3 MUTATED    25  29
  BAI3 WILD-TYPE 200 235
[1] "tbl2"
                cls
clus             [,1] [,2]
  BAI3 MUTATED     25   29
  BAI3 WILD-TYPE  200  235
        clus
vv       BAI3 MUTATED BAI3 WILD-TYPE
  FEMALE           25            200
  MALE             29            235
[1] 2 2
[1] FALSE
D459V9, binary
                cls
clus               0   1
  BAI3 MUTATED    36   1
  BAI3 WILD-TYPE 314  21
[1] "tbl2"
                cls
clus             [,1] [,2]
  BAI3 MUTATED     36    1
  BAI3 WILD-TYPE  314   21
     clus
vv    BAI3 MUTATED BAI3 WILD-TYPE
  NO            36            314
  YES            1             21
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  BAI3 MUTATED                     34                             9
  BAI3 WILD-TYPE                  281                            38
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  BAI3 MUTATED                      11                              0
  BAI3 WILD-TYPE                    95                             10
D459V10, multiclass
                                clus
vv                               BAI3 MUTATED BAI3 WILD-TYPE
  COLON ADENOCARCINOMA                     34            281
  COLON MUCINOUS ADENOCARCINOMA             9             38
  RECTAL ADENOCARCINOMA                    11             95
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  BAI3 MUTATED    35   0   2   6
  BAI3 WILD-TYPE 310   4  29  19
D459V11, multiclass
    clus
vv   BAI3 MUTATED BAI3 WILD-TYPE
  R0           35            310
  R1            0              4
  R2            2             29
  RX            6             19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D459V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  BAI3 MUTATED                                  0     2
  BAI3 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  BAI3 MUTATED                           0    31
  BAI3 WILD-TYPE                        22   195
D459V13, multiclass
                                  clus
vv                                 BAI3 MUTATED BAI3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              9
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                      31            195
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(460) Variable = AURKA MUTATION ANALYSIS
D460V1, survival
                 sevent
clus2               0   1
  AURKA MUTATED     4   3
  AURKA WILD-TYPE 374  90
  AURKA MUTATED AURKA WILD-TYPE 
              7             464 
  AURKA MUTATED AURKA WILD-TYPE 
              3              90 
$`AURKA MUTATED`
TCGA-AA-3864 TCGA-AA-A00J TCGA-AZ-6605 TCGA-AZ-6608 TCGA-CM-6674 TCGA-CM-6677 
       53.00        18.05         5.23         1.61        12.95        11.08 
TCGA-G4-6626 
       46.75 

$`AURKA WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L 
       38.04        19.00        30.02        34.03        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 
       12.10       100.01        29.56        11.74         3.19        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6676 
       13.02        15.02        14.04        11.01        13.05        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-AF-2687 
       13.78        35.80        26.17        91.79        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  AURKA MUTATED AURKA WILD-TYPE 
           1.61            0.00 
  AURKA MUTATED AURKA WILD-TYPE 
          53.00          148.01 
  AURKA MUTATED AURKA WILD-TYPE 
         12.950          20.415 
[1] "1.6 - 53.0 (12.9)"  "0.0 - 148.0 (20.4)"
[1] "hr=" "2.4"
D460V2, continuous
D460V3, binary
                 cls
clus                0   1
  AURKA MUTATED     7   0
  AURKA WILD-TYPE 359 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AURKA MUTATED      7    0
  AURKA WILD-TYPE  359  119
        clus
vv       AURKA MUTATED AURKA WILD-TYPE
  COLON              7             359
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  AURKA MUTATED         0        0        1         3         0         0
  AURKA WILD-TYPE      91        1       31       135        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AURKA MUTATED           0          1          2          0        0         0
  AURKA WILD-TYPE        24         10         57         42       48        18
                 vv
clus              STAGE IVB
  AURKA MUTATED           0
  AURKA WILD-TYPE         1
D460V4, multiclass
            clus
vv           AURKA MUTATED AURKA WILD-TYPE
  STAGE I                0              91
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              3             135
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             1              10
  STAGE IIIB             2              57
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  AURKA MUTATED     0   1   4   2
  AURKA WILD-TYPE  17  91 325  48
D460V5, multiclass
    clus
vv   AURKA MUTATED AURKA WILD-TYPE
  T1             0              17
  T2             1              91
  T3             4             325
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  AURKA MUTATED     4   3   0
  AURKA WILD-TYPE 283 110  87
D460V6, multiclass
    clus
vv   AURKA MUTATED AURKA WILD-TYPE
  N0             4             283
  N1             3             110
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D460V7, binary
                 cls
clus                0   1
  AURKA MUTATED     7   0
  AURKA WILD-TYPE 368  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AURKA MUTATED      7    0
  AURKA WILD-TYPE  368   65
   clus
vv  AURKA MUTATED AURKA WILD-TYPE
  0             7             368
  1             0              65
[1] 2 2
[1] FALSE
D460V8, binary
                 cls
clus                0   1
  AURKA MUTATED     2   5
  AURKA WILD-TYPE 223 259
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AURKA MUTATED      2    5
  AURKA WILD-TYPE  223  259
        clus
vv       AURKA MUTATED AURKA WILD-TYPE
  FEMALE             2             223
  MALE               5             259
[1] 2 2
[1] FALSE
D460V9, binary
                 cls
clus                0   1
  AURKA MUTATED     7   0
  AURKA WILD-TYPE 343  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AURKA MUTATED      7    0
  AURKA WILD-TYPE  343   22
     clus
vv    AURKA MUTATED AURKA WILD-TYPE
  NO              7             343
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  AURKA MUTATED                      6                             1
  AURKA WILD-TYPE                  309                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  AURKA MUTATED                       0                              0
  AURKA WILD-TYPE                   106                             10
D460V10, multiclass
                                clus
vv                               AURKA MUTATED AURKA WILD-TYPE
  COLON ADENOCARCINOMA                       6             309
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  AURKA MUTATED     5   0   0   0
  AURKA WILD-TYPE 340   4  31  25
D460V11, multiclass
    clus
vv   AURKA MUTATED AURKA WILD-TYPE
  R0             5             340
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D460V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AURKA MUTATED                                  0     0
  AURKA WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  AURKA MUTATED                           0     5
  AURKA WILD-TYPE                        22   221
D460V13, multiclass
                                  clus
vv                                 AURKA MUTATED AURKA WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        5             221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(461) Variable = RBM7 MUTATION ANALYSIS
D461V1, survival
                sevent
clus2              0   1
  RBM7 MUTATED     7   4
  RBM7 WILD-TYPE 371  89
  RBM7 MUTATED RBM7 WILD-TYPE 
            11            460 
  RBM7 MUTATED RBM7 WILD-TYPE 
             4             89 
$`RBM7 MUTATED`
TCGA-AA-3837 TCGA-AA-A00N TCGA-AZ-4315 TCGA-AZ-6599 TCGA-AZ-6603 TCGA-CA-6717 
       38.99         4.01        58.39         6.77        29.56        12.76 
TCGA-CK-4952 TCGA-CM-6678 TCGA-D5-6535 TCGA-G4-6303 TCGA-CI-6622 
       15.62        11.01        15.12        65.85         6.97 

$`RBM7 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
        1.02        17.98        15.95        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       33.01        21.44        17.82         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        88.21        49.41        12.10       100.01 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07        12.20        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
       17.56       148.01        85.45        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6679 
       11.01        12.95        13.05        11.08        11.08        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 
       20.19        18.25         1.32        43.27        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
       33.17         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  RBM7 MUTATED RBM7 WILD-TYPE 
          4.01           0.00 
  RBM7 MUTATED RBM7 WILD-TYPE 
         65.85         148.01 
  RBM7 MUTATED RBM7 WILD-TYPE 
        15.120         20.415 
[1] "4.0 - 65.8 (15.1)"  "0.0 - 148.0 (20.4)"
[1] "hr=" "1.9"
D461V2, continuous
D461V3, binary
                cls
clus               0   1
  RBM7 MUTATED    10   1
  RBM7 WILD-TYPE 356 118
[1] "tbl2"
                cls
clus             [,1] [,2]
  RBM7 MUTATED     10    1
  RBM7 WILD-TYPE  356  118
        clus
vv       RBM7 MUTATED RBM7 WILD-TYPE
  COLON            10            356
  RECTUM            1            118
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RBM7 MUTATED         1        0        0         3         2         0
  RBM7 WILD-TYPE      90        1       32       135         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RBM7 MUTATED           0          0          1          1        1         1
  RBM7 WILD-TYPE        24         11         58         41       47        17
                vv
clus             STAGE IVB
  RBM7 MUTATED           0
  RBM7 WILD-TYPE         1
D461V4, multiclass
            clus
vv           RBM7 MUTATED RBM7 WILD-TYPE
  STAGE I               1             90
  STAGE IA              0              1
  STAGE II              0             32
  STAGE IIA             3            135
  STAGE IIB             2              8
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            1             58
  STAGE IIIC            1             41
  STAGE IV              1             47
  STAGE IVA             1             17
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  RBM7 MUTATED     0   2   5   4
  RBM7 WILD-TYPE  17  90 324  46
D461V5, multiclass
    clus
vv   RBM7 MUTATED RBM7 WILD-TYPE
  T1            0             17
  T2            2             90
  T3            5            324
  T4            4             46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  RBM7 MUTATED     6   4   1
  RBM7 WILD-TYPE 281 109  86
D461V6, multiclass
    clus
vv   RBM7 MUTATED RBM7 WILD-TYPE
  N0            6            281
  N1            4            109
  N2            1             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D461V7, binary
                cls
clus               0   1
  RBM7 MUTATED     6   2
  RBM7 WILD-TYPE 369  63
[1] "tbl2"
                cls
clus             [,1] [,2]
  RBM7 MUTATED      6    2
  RBM7 WILD-TYPE  369   63
   clus
vv  RBM7 MUTATED RBM7 WILD-TYPE
  0            6            369
  1            2             63
[1] 2 2
[1] FALSE
D461V8, binary
                cls
clus               0   1
  RBM7 MUTATED     5   6
  RBM7 WILD-TYPE 220 258
[1] "tbl2"
                cls
clus             [,1] [,2]
  RBM7 MUTATED      5    6
  RBM7 WILD-TYPE  220  258
        clus
vv       RBM7 MUTATED RBM7 WILD-TYPE
  FEMALE            5            220
  MALE              6            258
[1] 2 2
[1] FALSE
D461V9, binary
                cls
clus               0   1
  RBM7 MUTATED     8   0
  RBM7 WILD-TYPE 342  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  RBM7 MUTATED      8    0
  RBM7 WILD-TYPE  342   22
     clus
vv    RBM7 MUTATED RBM7 WILD-TYPE
  NO             8            342
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  RBM7 MUTATED                      6                             4
  RBM7 WILD-TYPE                  309                            43
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  RBM7 MUTATED                       1                              0
  RBM7 WILD-TYPE                   105                             10
D461V10, multiclass
                                clus
vv                               RBM7 MUTATED RBM7 WILD-TYPE
  COLON ADENOCARCINOMA                      6            309
  COLON MUCINOUS ADENOCARCINOMA             4             43
  RECTAL ADENOCARCINOMA                     1            105
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  RBM7 MUTATED     5   0   0   3
  RBM7 WILD-TYPE 340   4  31  22
D461V11, multiclass
    clus
vv   RBM7 MUTATED RBM7 WILD-TYPE
  R0            5            340
  R1            0              4
  R2            0             31
  RX            3             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D461V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RBM7 MUTATED                                  0     1
  RBM7 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  RBM7 MUTATED                           0     8
  RBM7 WILD-TYPE                        22   218
D461V13, multiclass
                                  clus
vv                                 RBM7 MUTATED RBM7 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       8            218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(462) Variable = CNTNAP5 MUTATION ANALYSIS
D462V1, survival
                   sevent
clus2                 0   1
  CNTNAP5 MUTATED    36  10
  CNTNAP5 WILD-TYPE 342  83
  CNTNAP5 MUTATED CNTNAP5 WILD-TYPE 
               46               425 
  CNTNAP5 MUTATED CNTNAP5 WILD-TYPE 
               10                83 
$`CNTNAP5 MUTATED`
TCGA-A6-2671 TCGA-A6-5661 TCGA-A6-5665 TCGA-A6-6141 TCGA-A6-6654 TCGA-A6-6780 
       43.76        33.53        22.06         8.38        23.87        20.12 
TCGA-AA-3660 TCGA-AA-3947 TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01R 
       78.08        33.01        25.02         4.01        34.98        35.01 
TCGA-AA-A01Z TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6901 TCGA-AD-6964 TCGA-AU-6004 
       37.02         0.07        56.55        22.42        10.88        27.09 
TCGA-AZ-4315 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6608 TCGA-CA-6716 TCGA-CA-6717 
       58.39        62.79        49.41         1.61        12.20        12.76 
TCGA-CA-6718 TCGA-CK-5914 TCGA-CM-4746 TCGA-CM-5341 TCGA-CM-6166 TCGA-D5-6532 
       10.06         9.99        37.02        29.06        21.99        18.25 
TCGA-D5-6930 TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-F4-6569 TCGA-F4-6570 TCGA-G4-6309 
        1.51       130.65        49.91        35.74         6.18        85.48 
TCGA-G4-6315 TCGA-G4-6323 TCGA-G4-6628 TCGA-AG-3882 TCGA-AG-A002 TCGA-CI-6624 
       61.91        13.78        79.69        19.99        20.98         4.73 
TCGA-DC-6683 TCGA-DT-5265 TCGA-EI-6510 TCGA-F5-6811 
        5.03         5.29        18.28        32.19 

$`CNTNAP5 WILD-TYPE`
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       46.65        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 
       31.63        30.44        29.19        23.61        22.09        32.71 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 
       27.09        22.52        25.08        25.18        24.16        21.76 
TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       24.69        24.39        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 
       20.98        19.99        13.94        19.99        61.02         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
        2.01        12.99        24.00        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A024 
        1.02         1.02        33.04        35.01        26.01        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 
       41.00        39.98        18.05        40.96        21.37        15.52 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
        0.79         0.72         5.79        27.42         0.20        14.50 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
       16.31         0.95        33.01        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 
        5.13       106.75        22.36        88.21         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 
      100.01        29.56         5.23        11.74         3.19        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6719 TCGA-CK-4947 
        3.06         3.25         3.29         0.07        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5916 
      148.01        85.45        15.62        49.08        51.32        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4747 
       82.95         1.91       124.27        23.05        20.02        25.02 
TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       13.02        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
        2.96        29.03        16.04        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6534 
       19.59        56.09        55.92        20.19         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 
        9.04         9.44        11.64         4.80        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D4 TCGA-DM-A1D7 
       10.26       119.70        24.43        38.20        92.75        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6703 TCGA-F4-6704 
      117.07        98.24         8.61        31.96        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6586 
       44.68        55.04        63.62        36.00        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       26.17        91.79        46.75        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        6.97        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DY-A0XA 
       27.95        10.98        19.99         5.95         4.01       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       20.55        19.96        20.91         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57         0.66         0.69        55.76        26.43 

  CNTNAP5 MUTATED CNTNAP5 WILD-TYPE 
             0.07              0.00 
  CNTNAP5 MUTATED CNTNAP5 WILD-TYPE 
           130.65            148.01 
  CNTNAP5 MUTATED CNTNAP5 WILD-TYPE 
           23.145            19.990 
[1] "0.1 - 130.7 (23.1)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1"  
D462V2, continuous
D462V3, binary
                   cls
clus                  0   1
  CNTNAP5 MUTATED    40   7
  CNTNAP5 WILD-TYPE 326 112
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CNTNAP5 MUTATED     40    7
  CNTNAP5 WILD-TYPE  326  112
        clus
vv       CNTNAP5 MUTATED CNTNAP5 WILD-TYPE
  COLON               40               326
  RECTUM               7               112
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CNTNAP5 MUTATED         9        1        5        16         3         0
  CNTNAP5 WILD-TYPE      82        0       27       122         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CNTNAP5 MUTATED           1          2          4          0        2
  CNTNAP5 WILD-TYPE        23          9         55         42       46
                   vv
clus                STAGE IVA STAGE IVB
  CNTNAP5 MUTATED           1         0
  CNTNAP5 WILD-TYPE        17         1
D462V4, multiclass
            clus
vv           CNTNAP5 MUTATED CNTNAP5 WILD-TYPE
  STAGE I                  9                82
  STAGE IA                 1                 0
  STAGE II                 5                27
  STAGE IIA               16               122
  STAGE IIB                3                 7
  STAGE IIC                0                 1
  STAGE III                1                23
  STAGE IIIA               2                 9
  STAGE IIIB               4                55
  STAGE IIIC               0                42
  STAGE IV                 2                46
  STAGE IVA                1                17
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  CNTNAP5 MUTATED     0  13  29   4
  CNTNAP5 WILD-TYPE  17  79 300  46
D462V5, multiclass
    clus
vv   CNTNAP5 MUTATED CNTNAP5 WILD-TYPE
  T1               0                17
  T2              13                79
  T3              29               300
  T4               4                46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  CNTNAP5 MUTATED    37   7   3
  CNTNAP5 WILD-TYPE 250 106  84
D462V6, multiclass
    clus
vv   CNTNAP5 MUTATED CNTNAP5 WILD-TYPE
  N0              37               250
  N1               7               106
  N2               3                84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D462V7, binary
                   cls
clus                  0   1
  CNTNAP5 MUTATED    35   2
  CNTNAP5 WILD-TYPE 340  63
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CNTNAP5 MUTATED     35    2
  CNTNAP5 WILD-TYPE  340   63
   clus
vv  CNTNAP5 MUTATED CNTNAP5 WILD-TYPE
  0              35               340
  1               2                63
[1] 2 2
[1] FALSE
D462V8, binary
                   cls
clus                  0   1
  CNTNAP5 MUTATED    19  28
  CNTNAP5 WILD-TYPE 206 236
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CNTNAP5 MUTATED     19   28
  CNTNAP5 WILD-TYPE  206  236
        clus
vv       CNTNAP5 MUTATED CNTNAP5 WILD-TYPE
  FEMALE              19               206
  MALE                28               236
[1] 2 2
[1] FALSE
D462V9, binary
                   cls
clus                  0   1
  CNTNAP5 MUTATED    35   1
  CNTNAP5 WILD-TYPE 315  21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CNTNAP5 MUTATED     35    1
  CNTNAP5 WILD-TYPE  315   21
     clus
vv    CNTNAP5 MUTATED CNTNAP5 WILD-TYPE
  NO               35               315
  YES               1                21
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CNTNAP5 MUTATED                     32                             8
  CNTNAP5 WILD-TYPE                  283                            39
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CNTNAP5 MUTATED                       6                              1
  CNTNAP5 WILD-TYPE                   100                              9
D462V10, multiclass
                                clus
vv                               CNTNAP5 MUTATED CNTNAP5 WILD-TYPE
  COLON ADENOCARCINOMA                        32               283
  COLON MUCINOUS ADENOCARCINOMA                8                39
  RECTAL ADENOCARCINOMA                        6               100
  RECTAL MUCINOUS ADENOCARCINOMA               1                 9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  CNTNAP5 MUTATED    28   0   0   5
  CNTNAP5 WILD-TYPE 317   4  31  20
D462V11, multiclass
    clus
vv   CNTNAP5 MUTATED CNTNAP5 WILD-TYPE
  R0              28               317
  R1               0                 4
  R2               0                31
  RX               5                20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D462V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CNTNAP5 MUTATED                                  0     5
  CNTNAP5 WILD-TYPE                                1     6
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  CNTNAP5 MUTATED                           5    27
  CNTNAP5 WILD-TYPE                        17   199
D462V13, multiclass
                                  clus
vv                                 CNTNAP5 MUTATED CNTNAP5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          5                 6
  BLACK OR AFRICAN AMERICAN                      5                17
  WHITE                                         27               199
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(463) Variable = TMPRSS15 MUTATION ANALYSIS
D463V1, survival
                    sevent
clus2                  0   1
  TMPRSS15 MUTATED    19   7
  TMPRSS15 WILD-TYPE 359  86
  TMPRSS15 MUTATED TMPRSS15 WILD-TYPE 
                26                445 
  TMPRSS15 MUTATED TMPRSS15 WILD-TYPE 
                 7                 86 
$`TMPRSS15 MUTATED`
TCGA-A6-6137 TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3715 
       27.09        13.02         1.02        29.95        20.98        19.04 
TCGA-AA-3864 TCGA-AA-A010 TCGA-AD-6888 TCGA-AY-6386 TCGA-AZ-6598 TCGA-AZ-6599 
       53.00        34.98        15.52        17.82        49.41         6.77 
TCGA-CA-5797 TCGA-CA-6718 TCGA-CK-6748 TCGA-CM-4746 TCGA-CM-4752 TCGA-CM-6166 
        3.29        10.06         1.91        37.02        13.02        21.99 
TCGA-D5-6536 TCGA-D5-6931 TCGA-DM-A28F TCGA-G4-6309 TCGA-AF-6655 TCGA-AG-A002 
       17.85        12.00        35.97        85.48        20.02        20.98 
TCGA-AG-A02N TCGA-F5-6571 
       61.97        31.30 

$`TMPRSS15 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        22.06        32.71        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3519 
       35.01        63.98         6.97         1.02        38.99         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       17.95        23.01        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       78.08         6.05         6.97        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6889 
       39.98        18.05        40.96         0.07        21.37        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       62.79        88.21        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07        12.20        12.76        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-5341 
       82.95       124.27        23.05        20.02        25.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       29.03        16.04        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       15.12         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6932 TCGA-D5-7000 
        9.44        11.64         4.80         1.51        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G 
      135.65       139.17         6.12        81.37       119.93        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 
       65.85        53.62        44.68        55.04        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       49.51        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  TMPRSS15 MUTATED TMPRSS15 WILD-TYPE 
              1.02               0.00 
  TMPRSS15 MUTATED TMPRSS15 WILD-TYPE 
             85.48             148.01 
  TMPRSS15 MUTATED TMPRSS15 WILD-TYPE 
             20.50              20.19 
[1] "1.0 - 85.5 (20.5)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.4"
D463V2, continuous
D463V3, binary
                    cls
clus                   0   1
  TMPRSS15 MUTATED    22   4
  TMPRSS15 WILD-TYPE 344 115
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  TMPRSS15 MUTATED     22    4
  TMPRSS15 WILD-TYPE  344  115
        clus
vv       TMPRSS15 MUTATED TMPRSS15 WILD-TYPE
  COLON                22                344
  RECTUM                4                115
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TMPRSS15 MUTATED         5        0        4         7         1         0
  TMPRSS15 WILD-TYPE      86        1       28       131         9         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TMPRSS15 MUTATED           1          1          5          1        1
  TMPRSS15 WILD-TYPE        23         10         54         41       47
                    vv
clus                 STAGE IVA STAGE IVB
  TMPRSS15 MUTATED           0         0
  TMPRSS15 WILD-TYPE        18         1
D463V4, multiclass
            clus
vv           TMPRSS15 MUTATED TMPRSS15 WILD-TYPE
  STAGE I                   5                 86
  STAGE IA                  0                  1
  STAGE II                  4                 28
  STAGE IIA                 7                131
  STAGE IIB                 1                  9
  STAGE IIC                 0                  1
  STAGE III                 1                 23
  STAGE IIIA                1                 10
  STAGE IIIB                5                 54
  STAGE IIIC                1                 41
  STAGE IV                  1                 47
  STAGE IVA                 0                 18
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  TMPRSS15 MUTATED     0   6  18   2
  TMPRSS15 WILD-TYPE  17  86 311  48
D463V5, multiclass
    clus
vv   TMPRSS15 MUTATED TMPRSS15 WILD-TYPE
  T1                0                 17
  T2                6                 86
  T3               18                311
  T4                2                 48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  TMPRSS15 MUTATED    17   7   2
  TMPRSS15 WILD-TYPE 270 106  85
D463V6, multiclass
    clus
vv   TMPRSS15 MUTATED TMPRSS15 WILD-TYPE
  N0               17                270
  N1                7                106
  N2                2                 85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D463V7, binary
                    cls
clus                   0   1
  TMPRSS15 MUTATED    23   1
  TMPRSS15 WILD-TYPE 352  64
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  TMPRSS15 MUTATED     23    1
  TMPRSS15 WILD-TYPE  352   64
   clus
vv  TMPRSS15 MUTATED TMPRSS15 WILD-TYPE
  0               23                352
  1                1                 64
[1] 2 2
[1] FALSE
D463V8, binary
                    cls
clus                   0   1
  TMPRSS15 MUTATED    10  16
  TMPRSS15 WILD-TYPE 215 248
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  TMPRSS15 MUTATED     10   16
  TMPRSS15 WILD-TYPE  215  248
        clus
vv       TMPRSS15 MUTATED TMPRSS15 WILD-TYPE
  FEMALE               10                215
  MALE                 16                248
[1] 2 2
[1] FALSE
D463V9, binary
                    cls
clus                   0   1
  TMPRSS15 MUTATED    23   0
  TMPRSS15 WILD-TYPE 327  22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  TMPRSS15 MUTATED     23    0
  TMPRSS15 WILD-TYPE  327   22
     clus
vv    TMPRSS15 MUTATED TMPRSS15 WILD-TYPE
  NO                23                327
  YES                0                 22
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  TMPRSS15 MUTATED                     19                             3
  TMPRSS15 WILD-TYPE                  296                            44
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  TMPRSS15 MUTATED                       4                              0
  TMPRSS15 WILD-TYPE                   102                             10
D463V10, multiclass
                                clus
vv                               TMPRSS15 MUTATED TMPRSS15 WILD-TYPE
  COLON ADENOCARCINOMA                         19                296
  COLON MUCINOUS ADENOCARCINOMA                 3                 44
  RECTAL ADENOCARCINOMA                         4                102
  RECTAL MUCINOUS ADENOCARCINOMA                0                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  TMPRSS15 MUTATED    18   0   1   2
  TMPRSS15 WILD-TYPE 327   4  30  23
D463V11, multiclass
    clus
vv   TMPRSS15 MUTATED TMPRSS15 WILD-TYPE
  R0               18                327
  R1                0                  4
  R2                1                 30
  RX                2                 23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D463V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TMPRSS15 MUTATED                                  0     2
  TMPRSS15 WILD-TYPE                                1     9
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  TMPRSS15 MUTATED                           4    11
  TMPRSS15 WILD-TYPE                        18   215
D463V13, multiclass
                                  clus
vv                                 TMPRSS15 MUTATED TMPRSS15 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           2                  9
  BLACK OR AFRICAN AMERICAN                       4                 18
  WHITE                                          11                215
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(464) Variable = EGFR MUTATION ANALYSIS
D464V1, survival
                sevent
clus2              0   1
  EGFR MUTATED    57  24
  EGFR WILD-TYPE 321  69
  EGFR MUTATED EGFR WILD-TYPE 
            81            390 
  EGFR MUTATED EGFR WILD-TYPE 
            24             69 
$`EGFR MUTATED`
TCGA-A6-3809 TCGA-A6-5660 TCGA-AA-3502 TCGA-AA-3518 TCGA-AA-3542 TCGA-AA-3663 
       32.75        29.19        35.01         1.02        12.99         6.97 
TCGA-AA-3697 TCGA-AA-3811 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3982 TCGA-AA-A00E 
       85.05        10.06         2.01        21.99        27.02        30.02 
TCGA-AA-A00N TCGA-AA-A00R TCGA-AA-A01R TCGA-AA-A02K TCGA-AD-5900 TCGA-AD-6901 
        4.01         0.99        35.01        14.01         0.07        22.42 
TCGA-AD-6964 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-5543 TCGA-AZ-5403 TCGA-AZ-5407 
       10.88        14.50        27.09        33.01        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6608 
       49.41         6.77        12.10       100.01        29.56         1.61 
TCGA-CA-6717 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-5344 
       12.76        51.32         9.99         1.91       124.27        22.03 
TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-6162 TCGA-CM-6166 TCGA-CM-6168 TCGA-CM-6169 
       32.02         5.03        12.00        21.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6680 TCGA-D5-5539 TCGA-D5-5540 
       15.02        11.08        11.08        12.03        19.59        56.09 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
        1.32        43.27        17.85         4.80        17.13        12.49 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6928 TCGA-DM-A1D8 TCGA-DM-A1DB TCGA-DM-A1HB 
        1.48         3.68        11.64        12.59        44.32       135.65 
TCGA-DM-A285 TCGA-DM-A28F TCGA-F4-6460 TCGA-F4-6808 TCGA-F4-6809 TCGA-G4-6299 
        6.12        35.97        31.96        33.67        13.25        74.56 
TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6588 
       65.85        44.68        55.04        61.91        36.00        26.17 
TCGA-AF-2687 TCGA-AG-3742 TCGA-AG-A002 TCGA-DY-A0XA TCGA-DY-A1DD TCGA-DY-A1DF 
       24.13         0.99        20.98       126.44        57.24        24.13 
TCGA-DY-A1DG TCGA-EF-5830 TCGA-F5-6465 
       51.48         0.49        49.51 

$`EGFR WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       31.63        30.44        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3510 
       19.66        20.28         7.04         3.02         1.02        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3520 
        6.97         1.02        13.02        38.99         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3543 TCGA-AA-3544 
       34.03        29.00        29.00        26.01         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
       78.08         6.05        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       19.00        36.00         5.03        26.99        19.04        19.04 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
       20.98        34.03        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3986 TCGA-AA-3989 
       26.01        25.02        24.00        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00J 
       27.02        13.94        38.04        19.00        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W 
       18.05        38.04        27.02        42.02        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T 
       31.00        31.00        38.07         1.02         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        2.01         5.03         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
       40.96        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6965 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6197 
        5.79        27.42         0.20        16.31         0.95        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07        12.20        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5916 TCGA-CK-6747 
      148.01        85.45        15.62        49.08        21.14        82.95 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       22.98        30.08        15.02        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6171 
       15.02         2.96        29.03        16.04        14.99        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6678 TCGA-CM-6679 TCGA-D5-5537 
       11.01        12.95        13.05        11.01        10.06        45.40 
TCGA-D5-5538 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6535 TCGA-D5-6540 
       12.26        55.92        20.19        18.25        15.12        16.14 
TCGA-D5-6541 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       15.58         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A28C TCGA-DM-A28E 
      140.38         7.50       131.51       139.17        81.37       119.93 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6569 TCGA-F4-6570 
       60.79       117.07        98.24         8.61        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6854 
       47.87         1.55        34.42        41.42        16.24         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6304 TCGA-G4-6309 TCGA-G4-6310 
       47.41        35.31       133.18        53.62        85.48        63.62 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       22.09        13.78        35.80        91.79        46.75        79.69 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3878 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1H8 
        5.95         4.01         5.03         5.29        41.36        32.61 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6571 
       20.55        19.96        20.91        18.28         9.96        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  EGFR MUTATED EGFR WILD-TYPE 
          0.07           0.00 
  EGFR MUTATED EGFR WILD-TYPE 
        135.65         148.01 
  EGFR MUTATED EGFR WILD-TYPE 
        21.990         20.085 
[1] "0.1 - 135.7 (22.0)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.5"
D464V2, continuous
D464V3, binary
                cls
clus               0   1
  EGFR MUTATED    75   9
  EGFR WILD-TYPE 291 110
[1] "tbl2"
                cls
clus             [,1] [,2]
  EGFR MUTATED     75    9
  EGFR WILD-TYPE  291  110
        clus
vv       EGFR MUTATED EGFR WILD-TYPE
  COLON            75            291
  RECTUM            9            110
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  EGFR MUTATED        16        0        4        20         3         0
  EGFR WILD-TYPE      75        1       28       118         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  EGFR MUTATED           4          3         13          7        6         4
  EGFR WILD-TYPE        20          8         46         35       42        14
                vv
clus             STAGE IVB
  EGFR MUTATED           0
  EGFR WILD-TYPE         1
D464V4, multiclass
            clus
vv           EGFR MUTATED EGFR WILD-TYPE
  STAGE I              16             75
  STAGE IA              0              1
  STAGE II              4             28
  STAGE IIA            20            118
  STAGE IIB             3              7
  STAGE IIC             0              1
  STAGE III             4             20
  STAGE IIIA            3              8
  STAGE IIIB           13             46
  STAGE IIIC            7             35
  STAGE IV              6             42
  STAGE IVA             4             14
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  EGFR MUTATED     3  16  58   7
  EGFR WILD-TYPE  14  76 271  43
D464V5, multiclass
    clus
vv   EGFR MUTATED EGFR WILD-TYPE
  T1            3             14
  T2           16             76
  T3           58            271
  T4            7             43
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  EGFR MUTATED    47  22  15
  EGFR WILD-TYPE 240  91  72
D464V6, multiclass
    clus
vv   EGFR MUTATED EGFR WILD-TYPE
  N0           47            240
  N1           22             91
  N2           15             72
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D464V7, binary
                cls
clus               0   1
  EGFR MUTATED    59  10
  EGFR WILD-TYPE 316  55
[1] "tbl2"
                cls
clus             [,1] [,2]
  EGFR MUTATED     59   10
  EGFR WILD-TYPE  316   55
   clus
vv  EGFR MUTATED EGFR WILD-TYPE
  0           59            316
  1           10             55
[1] 2 2
[1] FALSE
D464V8, binary
                cls
clus               0   1
  EGFR MUTATED    43  41
  EGFR WILD-TYPE 182 223
[1] "tbl2"
                cls
clus             [,1] [,2]
  EGFR MUTATED     43   41
  EGFR WILD-TYPE  182  223
        clus
vv       EGFR MUTATED EGFR WILD-TYPE
  FEMALE           43            182
  MALE             41            223
[1] 2 2
[1] FALSE
D464V9, binary
                cls
clus               0   1
  EGFR MUTATED    57   2
  EGFR WILD-TYPE 293  20
[1] "tbl2"
                cls
clus             [,1] [,2]
  EGFR MUTATED     57    2
  EGFR WILD-TYPE  293   20
     clus
vv    EGFR MUTATED EGFR WILD-TYPE
  NO            57            293
  YES            2             20
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  EGFR MUTATED                     60                            14
  EGFR WILD-TYPE                  255                            33
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  EGFR MUTATED                       9                              0
  EGFR WILD-TYPE                    97                             10
D464V10, multiclass
                                clus
vv                               EGFR MUTATED EGFR WILD-TYPE
  COLON ADENOCARCINOMA                     60            255
  COLON MUCINOUS ADENOCARCINOMA            14             33
  RECTAL ADENOCARCINOMA                     9             97
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  EGFR MUTATED    55   0   1   6
  EGFR WILD-TYPE 290   4  30  19
D464V11, multiclass
    clus
vv   EGFR MUTATED EGFR WILD-TYPE
  R0           55            290
  R1            0              4
  R2            1             30
  RX            6             19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D464V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  EGFR MUTATED                                  0     1
  EGFR WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  EGFR MUTATED                           5    61
  EGFR WILD-TYPE                        17   165
D464V13, multiclass
                                  clus
vv                                 EGFR MUTATED EGFR WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   5             17
  WHITE                                      61            165
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(465) Variable = CTBP2 MUTATION ANALYSIS
D465V1, survival
                 sevent
clus2               0   1
  CTBP2 MUTATED     5   1
  CTBP2 WILD-TYPE 373  92
  CTBP2 MUTATED CTBP2 WILD-TYPE 
              6             465 
  CTBP2 MUTATED CTBP2 WILD-TYPE 
              1              92 
$`CTBP2 MUTATED`
TCGA-AA-3713 TCGA-AD-6964 TCGA-CM-6168 TCGA-D5-6931 TCGA-DM-A1HB TCGA-DC-5869 
       19.04        10.88        12.99        12.00       135.65         5.03 

$`CTBP2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       14.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        4.80         1.51        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 
      140.38         7.50        44.32       131.51       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-6155 
        6.97         4.73        78.12         7.17        15.02        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  CTBP2 MUTATED CTBP2 WILD-TYPE 
           5.03            0.00 
  CTBP2 MUTATED CTBP2 WILD-TYPE 
         135.65          148.01 
  CTBP2 MUTATED CTBP2 WILD-TYPE 
         12.495          20.550 
[1] "5.0 - 135.7 (12.5)" "0.0 - 148.0 (20.6)"
[1] "hr=" "1.2"
D465V2, continuous
D465V3, binary
                 cls
clus                0   1
  CTBP2 MUTATED     6   1
  CTBP2 WILD-TYPE 360 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CTBP2 MUTATED      6    1
  CTBP2 WILD-TYPE  360  118
        clus
vv       CTBP2 MUTATED CTBP2 WILD-TYPE
  COLON              6             360
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CTBP2 MUTATED         0        0        0         1         1         0
  CTBP2 WILD-TYPE      91        1       32       137         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CTBP2 MUTATED           0          0          2          1        1         0
  CTBP2 WILD-TYPE        24         11         57         41       47        18
                 vv
clus              STAGE IVB
  CTBP2 MUTATED           0
  CTBP2 WILD-TYPE         1
D465V4, multiclass
            clus
vv           CTBP2 MUTATED CTBP2 WILD-TYPE
  STAGE I                0              91
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              1             137
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             2              57
  STAGE IIIC             1              41
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CTBP2 MUTATED     0   0   4   3
  CTBP2 WILD-TYPE  17  92 325  47
D465V5, multiclass
    clus
vv   CTBP2 MUTATED CTBP2 WILD-TYPE
  T1             0              17
  T2             0              92
  T3             4             325
  T4             3              47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  CTBP2 MUTATED     3   2   2
  CTBP2 WILD-TYPE 284 111  85
D465V6, multiclass
    clus
vv   CTBP2 MUTATED CTBP2 WILD-TYPE
  N0             3             284
  N1             2             111
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D465V7, binary
                 cls
clus                0   1
  CTBP2 MUTATED     4   1
  CTBP2 WILD-TYPE 371  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CTBP2 MUTATED      4    1
  CTBP2 WILD-TYPE  371   64
   clus
vv  CTBP2 MUTATED CTBP2 WILD-TYPE
  0             4             371
  1             1              64
[1] 2 2
[1] FALSE
D465V8, binary
                 cls
clus                0   1
  CTBP2 MUTATED     3   4
  CTBP2 WILD-TYPE 222 260
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CTBP2 MUTATED      3    4
  CTBP2 WILD-TYPE  222  260
        clus
vv       CTBP2 MUTATED CTBP2 WILD-TYPE
  FEMALE             3             222
  MALE               4             260
[1] 2 2
[1] FALSE
D465V9, binary
                 cls
clus                0   1
  CTBP2 MUTATED     3   1
  CTBP2 WILD-TYPE 347  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CTBP2 MUTATED      3    1
  CTBP2 WILD-TYPE  347   21
     clus
vv    CTBP2 MUTATED CTBP2 WILD-TYPE
  NO              3             347
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CTBP2 MUTATED                      5                             0
  CTBP2 WILD-TYPE                  310                            47
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CTBP2 MUTATED                       1                              0
  CTBP2 WILD-TYPE                   105                             10
D465V10, multiclass
                                clus
vv                               CTBP2 MUTATED CTBP2 WILD-TYPE
  COLON ADENOCARCINOMA                       5             310
  COLON MUCINOUS ADENOCARCINOMA              0              47
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  CTBP2 MUTATED     3   0   1   1
  CTBP2 WILD-TYPE 342   4  30  24
D465V11, multiclass
    clus
vv   CTBP2 MUTATED CTBP2 WILD-TYPE
  R0             3             342
  R1             0               4
  R2             1              30
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D465V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CTBP2 MUTATED                                  0     0
  CTBP2 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CTBP2 MUTATED                           2     4
  CTBP2 WILD-TYPE                        20   222
D465V13, multiclass
                                  clus
vv                                 CTBP2 MUTATED CTBP2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    2              20
  WHITE                                        4             222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(466) Variable = APOB MUTATION ANALYSIS
D466V1, survival
                sevent
clus2              0   1
  APOB MUTATED    53   9
  APOB WILD-TYPE 325  84
  APOB MUTATED APOB WILD-TYPE 
            62            409 
  APOB MUTATED APOB WILD-TYPE 
             9             84 
$`APOB MUTATED`
TCGA-A6-2672 TCGA-A6-3809 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5665 TCGA-AA-3489 
       46.65        32.75        29.19        23.61        22.06         7.04 
TCGA-AA-3525 TCGA-AA-3549 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3710 TCGA-AA-3713 
        8.05        21.01        29.95        23.01        26.99        19.04 
TCGA-AA-3950 TCGA-AA-A00J TCGA-AA-A00N TCGA-AA-A00U TCGA-AA-A010 TCGA-AA-A01P 
       24.00        18.05         4.01        17.03        34.98        38.07 
TCGA-AA-A01Q TCGA-AA-A02F TCGA-AD-6964 TCGA-AU-6004 TCGA-AZ-4315 TCGA-AZ-5403 
        1.02        39.98        10.88        27.09        58.39        62.79 
TCGA-AZ-6598 TCGA-AZ-6607 TCGA-CA-5797 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 
       49.41         3.19         3.29        12.20        12.76        14.30 
TCGA-CK-4947 TCGA-CK-5913 TCGA-CK-5914 TCGA-CM-4743 TCGA-CM-5348 TCGA-CM-5860 
       17.56        51.32         9.99        23.05        22.98        32.02 
TCGA-CM-5861 TCGA-CM-6168 TCGA-D5-5538 TCGA-D5-5541 TCGA-D5-6538 TCGA-D5-6927 
       15.02        12.99        12.26        55.92        17.13         9.44 
TCGA-D5-6931 TCGA-DM-A0X9 TCGA-DM-A1D0 TCGA-F4-6460 TCGA-F4-6854 TCGA-F4-6855 
       12.00       119.70       130.65        31.96         0.53        47.41 
TCGA-G4-6586 TCGA-G4-6628 TCGA-AF-5654 TCGA-AF-6672 TCGA-AG-3742 TCGA-AG-3892 
       35.80        79.69        16.83        10.39         0.99        13.02 
TCGA-AG-4005 TCGA-AG-A002 TCGA-AG-A02N TCGA-AH-6643 TCGA-CI-6619 TCGA-DC-6683 
       14.04        20.98        61.97         0.69         6.05         5.03 
TCGA-EF-5830 TCGA-EI-6510 
        0.49        18.28 

$`APOB WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5657 
       34.65        33.34        36.53        14.53        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 
       30.44        33.53        22.09        32.71        27.09        22.52 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 
        8.38        25.08        25.18        24.16        21.76        24.69 
TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3492 
       24.39        23.87        20.12        19.66        20.28         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3552 
       26.01        12.99         0.99        14.01        33.99        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       24.00        17.95        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L 
       38.04        19.00        30.02        34.03        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       27.02        42.02         0.99        14.99        21.99         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01R 
       10.98        32.02        12.00        31.00        31.00        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       51.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
        0.20        14.50        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5407 
       17.82         1.41         5.13       106.75        22.36        88.21 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6718 
        1.61        12.69         3.06         3.25         0.07        10.06 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5916 TCGA-CK-6747 
      148.01        85.45        15.62        49.08        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
        1.91       124.27        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       29.06        22.03        30.08         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       21.99        14.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-6529 TCGA-D5-6532 
       12.03        45.40        19.59        56.09        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6539 
        1.32        43.27        15.12        17.85         4.80        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6932 
       14.30         9.04        11.64         4.80         1.51        11.38 
TCGA-D5-7000 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       10.26        24.43        38.20        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
      117.07        98.24         8.61        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 
       13.78        26.17        91.79        46.75        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       15.39        20.02        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       37.02        32.98         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       17.95        36.95        17.03        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4007 
       48.03        32.02        19.99        28.04        36.03         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 
       10.98        49.97         1.94        38.96        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6644 TCGA-CI-6620 
      117.11        38.56         1.45        17.49         0.72        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-F5-6464 TCGA-F5-6465 
       32.61        20.55        19.96        20.91         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  APOB MUTATED APOB WILD-TYPE 
          0.49           0.00 
  APOB MUTATED APOB WILD-TYPE 
        130.65         148.01 
  APOB MUTATED APOB WILD-TYPE 
         18.66          20.28 
[1] "0.5 - 130.7 (18.7)" "0.0 - 148.0 (20.3)"
[1] "hr=" "1.4"
D466V2, continuous
D466V3, binary
                cls
clus               0   1
  APOB MUTATED    54  13
  APOB WILD-TYPE 312 106
[1] "tbl2"
                cls
clus             [,1] [,2]
  APOB MUTATED     54   13
  APOB WILD-TYPE  312  106
        clus
vv       APOB MUTATED APOB WILD-TYPE
  COLON            54            312
  RECTUM           13            106
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  APOB MUTATED         8        0        6        21         5         0
  APOB WILD-TYPE      83        1       26       117         5         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  APOB MUTATED           1          0         12          5        6         2
  APOB WILD-TYPE        23         11         47         37       42        16
                vv
clus             STAGE IVB
  APOB MUTATED           0
  APOB WILD-TYPE         1
D466V4, multiclass
            clus
vv           APOB MUTATED APOB WILD-TYPE
  STAGE I               8             83
  STAGE IA              0              1
  STAGE II              6             26
  STAGE IIA            21            117
  STAGE IIB             5              5
  STAGE IIC             0              1
  STAGE III             1             23
  STAGE IIIA            0             11
  STAGE IIIB           12             47
  STAGE IIIC            5             37
  STAGE IV              6             42
  STAGE IVA             2             16
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  APOB MUTATED     2   7  46  12
  APOB WILD-TYPE  15  85 283  38
D466V5, multiclass
    clus
vv   APOB MUTATED APOB WILD-TYPE
  T1            2             15
  T2            7             85
  T3           46            283
  T4           12             38
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  APOB MUTATED    42  14  11
  APOB WILD-TYPE 245  99  76
D466V6, multiclass
    clus
vv   APOB MUTATED APOB WILD-TYPE
  N0           42            245
  N1           14             99
  N2           11             76
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D466V7, binary
                cls
clus               0   1
  APOB MUTATED    52   6
  APOB WILD-TYPE 323  59
[1] "tbl2"
                cls
clus             [,1] [,2]
  APOB MUTATED     52    6
  APOB WILD-TYPE  323   59
   clus
vv  APOB MUTATED APOB WILD-TYPE
  0           52            323
  1            6             59
[1] 2 2
[1] FALSE
D466V8, binary
                cls
clus               0   1
  APOB MUTATED    32  35
  APOB WILD-TYPE 193 229
[1] "tbl2"
                cls
clus             [,1] [,2]
  APOB MUTATED     32   35
  APOB WILD-TYPE  193  229
        clus
vv       APOB MUTATED APOB WILD-TYPE
  FEMALE           32            193
  MALE             35            229
[1] 2 2
[1] FALSE
D466V9, binary
                cls
clus               0   1
  APOB MUTATED    47   3
  APOB WILD-TYPE 303  19
[1] "tbl2"
                cls
clus             [,1] [,2]
  APOB MUTATED     47    3
  APOB WILD-TYPE  303   19
     clus
vv    APOB MUTATED APOB WILD-TYPE
  NO            47            303
  YES            3             19
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  APOB MUTATED                     46                             7
  APOB WILD-TYPE                  269                            40
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  APOB MUTATED                      13                              0
  APOB WILD-TYPE                    93                             10
D466V10, multiclass
                                clus
vv                               APOB MUTATED APOB WILD-TYPE
  COLON ADENOCARCINOMA                     46            269
  COLON MUCINOUS ADENOCARCINOMA             7             40
  RECTAL ADENOCARCINOMA                    13             93
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  APOB MUTATED    48   0   2   7
  APOB WILD-TYPE 297   4  29  18
D466V11, multiclass
    clus
vv   APOB MUTATED APOB WILD-TYPE
  R0           48            297
  R1            0              4
  R2            2             29
  RX            7             18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D466V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  APOB MUTATED                                  0     4
  APOB WILD-TYPE                                1     7
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  APOB MUTATED                           2    38
  APOB WILD-TYPE                        20   188
D466V13, multiclass
                                  clus
vv                                 APOB MUTATED APOB WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       4              7
  BLACK OR AFRICAN AMERICAN                   2             20
  WHITE                                      38            188
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(467) Variable = EPHA3 MUTATION ANALYSIS
D467V1, survival
                 sevent
clus2               0   1
  EPHA3 MUTATED    47  16
  EPHA3 WILD-TYPE 331  77
  EPHA3 MUTATED EPHA3 WILD-TYPE 
             63             408 
  EPHA3 MUTATED EPHA3 WILD-TYPE 
             16              77 
$`EPHA3 MUTATED`
TCGA-A6-5660 TCGA-A6-5661 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3516 
       29.19        33.53         3.02        35.01        63.98        13.02 
TCGA-AA-3544 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3688 TCGA-AA-3713 TCGA-AA-3811 
       14.01        13.94        61.02        19.00        19.04        10.06 
TCGA-AA-3833 TCGA-AA-3845 TCGA-AA-3861 TCGA-AA-3869 TCGA-AA-3949 TCGA-AA-3950 
       15.95         0.00        30.05        27.02        26.01        24.00 
TCGA-AA-3966 TCGA-AA-A00E TCGA-AA-A010 TCGA-AD-6889 TCGA-AD-6899 TCGA-AD-6965 
        2.01        30.02        34.98        56.55         5.79         0.20 
TCGA-AU-6004 TCGA-AY-5543 TCGA-AZ-5403 TCGA-AZ-6600 TCGA-CA-6717 TCGA-CK-4952 
       27.09        33.01        62.79        12.10        12.76        15.62 
TCGA-CK-5913 TCGA-CK-5916 TCGA-CM-5344 TCGA-CM-6162 TCGA-CM-6171 TCGA-CM-6674 
       51.32        21.14        22.03        12.00        14.04        12.95 
TCGA-CM-6680 TCGA-D5-5538 TCGA-D5-6533 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6926 
       12.03        12.26         1.32        16.14        15.58         9.04 
TCGA-D5-6928 TCGA-D5-6930 TCGA-DM-A1D0 TCGA-DM-A1D7 TCGA-DM-A1HB TCGA-DM-A28G 
       11.64         1.51       130.65        13.32       135.65        60.79 
TCGA-F4-6460 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6321 TCGA-G4-6588 
       31.96        65.85        44.68        85.48        22.09        26.17 
TCGA-G4-6626 TCGA-AF-2687 TCGA-AG-3600 TCGA-AG-3609 TCGA-AG-3892 TCGA-DY-A1DC 
       46.75        24.13         6.05        19.99        13.02        41.36 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6507 
       32.61         0.49        19.96 

$`EPHA3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       32.91        31.63        30.44        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3511 TCGA-AA-3514 
       19.66        20.28         7.04         1.02         6.97         1.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3548 TCGA-AA-3549 
       29.00        26.01        12.99         0.99        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        19.99        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
       11.01         5.98        37.05        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       26.99        19.04        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 
        1.02        17.98        38.99        37.02        14.93        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
        0.99        31.07        31.07        53.00        17.03        24.03 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 
       33.01         2.01        20.98        34.03        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       38.04        19.00        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 
       18.05        40.96         0.07        21.37        15.52         0.79 
TCGA-AD-6895 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AU-3779 TCGA-AY-4070 
        0.72        22.42        27.42        10.88        14.50        16.31 
TCGA-AY-4071 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 
      106.75        22.36        88.21        49.41         6.77       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07        12.20        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5914 
       14.30        17.56       148.01        85.45        49.08         9.99 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       25.02        13.02        29.06        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       13.02        15.02        11.01        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-D5-5537 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       11.01        10.06        45.40        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       20.19        18.25        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       17.13        12.49         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       14.30         9.44         4.80        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D8 
      119.70        24.43        38.20        92.75        49.91        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 
      140.38         7.50        44.32       131.51       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
       81.37       119.93        35.97       117.07        98.24         8.61 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 
      133.18        74.56        53.62        55.04        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-AF-2689 
       36.00        13.78        35.80        91.79        79.69        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
        0.99        15.95        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 
        1.02        17.95        36.95        17.03        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.03         5.29       126.44        57.24        24.13        51.48 
TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       20.55        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  EPHA3 MUTATED EPHA3 WILD-TYPE 
              0               0 
  EPHA3 MUTATED EPHA3 WILD-TYPE 
         135.65          148.01 
  EPHA3 MUTATED EPHA3 WILD-TYPE 
         19.990          20.235 
[1] "0.0 - 135.7 (20.0)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.3"
D467V2, continuous
D467V3, binary
                 cls
clus                0   1
  EPHA3 MUTATED    57   8
  EPHA3 WILD-TYPE 309 111
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPHA3 MUTATED     57    8
  EPHA3 WILD-TYPE  309  111
        clus
vv       EPHA3 MUTATED EPHA3 WILD-TYPE
  COLON             57             309
  RECTUM             8             111
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  EPHA3 MUTATED         7        0        4        24         3         0
  EPHA3 WILD-TYPE      84        1       28       114         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  EPHA3 MUTATED           3          1         10          6        5         1
  EPHA3 WILD-TYPE        21         10         49         36       43        17
                 vv
clus              STAGE IVB
  EPHA3 MUTATED           0
  EPHA3 WILD-TYPE         1
D467V4, multiclass
            clus
vv           EPHA3 MUTATED EPHA3 WILD-TYPE
  STAGE I                7              84
  STAGE IA               0               1
  STAGE II               4              28
  STAGE IIA             24             114
  STAGE IIB              3               7
  STAGE IIC              0               1
  STAGE III              3              21
  STAGE IIIA             1              10
  STAGE IIIB            10              49
  STAGE IIIC             6              36
  STAGE IV               5              43
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  EPHA3 MUTATED     2   8  45  10
  EPHA3 WILD-TYPE  15  84 284  40
D467V5, multiclass
    clus
vv   EPHA3 MUTATED EPHA3 WILD-TYPE
  T1             2              15
  T2             8              84
  T3            45             284
  T4            10              40
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  EPHA3 MUTATED    40  14  11
  EPHA3 WILD-TYPE 247  99  76
D467V6, multiclass
    clus
vv   EPHA3 MUTATED EPHA3 WILD-TYPE
  N0            40             247
  N1            14              99
  N2            11              76
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D467V7, binary
                 cls
clus                0   1
  EPHA3 MUTATED    53   6
  EPHA3 WILD-TYPE 322  59
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPHA3 MUTATED     53    6
  EPHA3 WILD-TYPE  322   59
   clus
vv  EPHA3 MUTATED EPHA3 WILD-TYPE
  0            53             322
  1             6              59
[1] 2 2
[1] FALSE
D467V8, binary
                 cls
clus                0   1
  EPHA3 MUTATED    33  32
  EPHA3 WILD-TYPE 192 232
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPHA3 MUTATED     33   32
  EPHA3 WILD-TYPE  192  232
        clus
vv       EPHA3 MUTATED EPHA3 WILD-TYPE
  FEMALE            33             192
  MALE              32             232
[1] 2 2
[1] FALSE
D467V9, binary
                 cls
clus                0   1
  EPHA3 MUTATED    43   4
  EPHA3 WILD-TYPE 307  18
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPHA3 MUTATED     43    4
  EPHA3 WILD-TYPE  307   18
     clus
vv    EPHA3 MUTATED EPHA3 WILD-TYPE
  NO             43             307
  YES             4              18
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  EPHA3 MUTATED                     44                            11
  EPHA3 WILD-TYPE                  271                            36
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  EPHA3 MUTATED                       8                              0
  EPHA3 WILD-TYPE                    98                             10
D467V10, multiclass
                                clus
vv                               EPHA3 MUTATED EPHA3 WILD-TYPE
  COLON ADENOCARCINOMA                      44             271
  COLON MUCINOUS ADENOCARCINOMA             11              36
  RECTAL ADENOCARCINOMA                      8              98
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  EPHA3 MUTATED    43   0   3   5
  EPHA3 WILD-TYPE 302   4  28  20
D467V11, multiclass
    clus
vv   EPHA3 MUTATED EPHA3 WILD-TYPE
  R0            43             302
  R1             0               4
  R2             3              28
  RX             5              20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D467V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  EPHA3 MUTATED                                  0     2
  EPHA3 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  EPHA3 MUTATED                           5    35
  EPHA3 WILD-TYPE                        17   191
D467V13, multiclass
                                  clus
vv                                 EPHA3 MUTATED EPHA3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               9
  BLACK OR AFRICAN AMERICAN                    5              17
  WHITE                                       35             191
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(468) Variable = PTPN11 MUTATION ANALYSIS
D468V1, survival
                  sevent
clus2                0   1
  PTPN11 MUTATED    25  12
  PTPN11 WILD-TYPE 353  81
  PTPN11 MUTATED PTPN11 WILD-TYPE 
              37              434 
  PTPN11 MUTATED PTPN11 WILD-TYPE 
              12               81 
$`PTPN11 MUTATED`
TCGA-AA-3555 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3697 TCGA-AA-3977 TCGA-AD-6964 
       29.95        61.02        78.08        85.05        25.02        10.88 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CA-6718 TCGA-CK-5914 
       49.41         6.77       100.01         1.61        10.06         9.99 
TCGA-CK-6747 TCGA-CM-5862 TCGA-CM-6675 TCGA-CM-6676 TCGA-D5-6534 TCGA-D5-6535 
       82.95         5.03        13.05        11.08        43.27        15.12 
TCGA-D5-6538 TCGA-DM-A0X9 TCGA-DM-A1HA TCGA-DM-A28F TCGA-G4-6299 TCGA-G4-6303 
       17.13       119.70       131.51        35.97        74.56        65.85 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6588 TCGA-AF-2693 TCGA-AF-4110 
       44.68        55.04        63.62        26.17        19.10        14.50 
TCGA-AG-A002 TCGA-AG-A036 TCGA-AH-6643 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
       20.98       117.11         0.69       126.44        41.36        57.24 
TCGA-DY-A1H8 
       32.61 

$`PTPN11 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 
       21.01        13.02        24.00        17.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        13.94        19.99         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 
       12.10        29.56         5.23        11.74         3.19        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       51.32        21.14         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       30.08        32.02        15.02        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       12.95        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
        1.32        17.85         4.80        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
       10.26        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HB 
       13.32        12.59       140.38         7.50        44.32       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H 
      139.17         6.12        81.37       119.93        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6304 TCGA-G4-6309 
        0.53        47.41        35.31       133.18        53.62        85.48 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 
       61.91        36.00        22.09        13.78        35.80        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       34.49        10.39        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6644 
       41.00        38.04        38.56         1.45        17.49         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DF TCGA-DY-A1DG 
        5.95         4.01         5.03         5.29        24.13        51.48 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  PTPN11 MUTATED PTPN11 WILD-TYPE 
            0.69             0.00 
  PTPN11 MUTATED PTPN11 WILD-TYPE 
          131.51           148.01 
  PTPN11 MUTATED PTPN11 WILD-TYPE 
           35.97            19.99 
[1] "0.7 - 131.5 (36.0)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1"  
D468V2, continuous
D468V3, binary
                  cls
clus                 0   1
  PTPN11 MUTATED    30   8
  PTPN11 WILD-TYPE 336 111
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PTPN11 MUTATED     30    8
  PTPN11 WILD-TYPE  336  111
        clus
vv       PTPN11 MUTATED PTPN11 WILD-TYPE
  COLON              30              336
  RECTUM              8              111
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PTPN11 MUTATED         5        0        4        10         0         0
  PTPN11 WILD-TYPE      86        1       28       128        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PTPN11 MUTATED           3          2          7          3        1
  PTPN11 WILD-TYPE        21          9         52         39       47
                  vv
clus               STAGE IVA STAGE IVB
  PTPN11 MUTATED           2         1
  PTPN11 WILD-TYPE        16         0
D468V4, multiclass
            clus
vv           PTPN11 MUTATED PTPN11 WILD-TYPE
  STAGE I                 5               86
  STAGE IA                0                1
  STAGE II                4               28
  STAGE IIA              10              128
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               3               21
  STAGE IIIA              2                9
  STAGE IIIB              7               52
  STAGE IIIC              3               39
  STAGE IV                1               47
  STAGE IVA               2               16
  STAGE IVB               1                0
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  PTPN11 MUTATED     0   9  29   2
  PTPN11 WILD-TYPE  17  83 300  48
D468V5, multiclass
    clus
vv   PTPN11 MUTATED PTPN11 WILD-TYPE
  T1              0               17
  T2              9               83
  T3             29              300
  T4              2               48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  PTPN11 MUTATED    21  10   9
  PTPN11 WILD-TYPE 266 103  78
D468V6, multiclass
    clus
vv   PTPN11 MUTATED PTPN11 WILD-TYPE
  N0             21              266
  N1             10              103
  N2              9               78
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D468V7, binary
                  cls
clus                 0   1
  PTPN11 MUTATED    27   3
  PTPN11 WILD-TYPE 348  62
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PTPN11 MUTATED     27    3
  PTPN11 WILD-TYPE  348   62
   clus
vv  PTPN11 MUTATED PTPN11 WILD-TYPE
  0             27              348
  1              3               62
[1] 2 2
[1] FALSE
D468V8, binary
                  cls
clus                 0   1
  PTPN11 MUTATED    17  23
  PTPN11 WILD-TYPE 208 241
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PTPN11 MUTATED     17   23
  PTPN11 WILD-TYPE  208  241
        clus
vv       PTPN11 MUTATED PTPN11 WILD-TYPE
  FEMALE             17              208
  MALE               23              241
[1] 2 2
[1] FALSE
D468V9, binary
                  cls
clus                 0   1
  PTPN11 MUTATED    26   2
  PTPN11 WILD-TYPE 324  20
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PTPN11 MUTATED     26    2
  PTPN11 WILD-TYPE  324   20
     clus
vv    PTPN11 MUTATED PTPN11 WILD-TYPE
  NO              26              324
  YES              2               20
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PTPN11 MUTATED                     28                             2
  PTPN11 WILD-TYPE                  287                            45
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PTPN11 MUTATED                       8                              0
  PTPN11 WILD-TYPE                    98                             10
D468V10, multiclass
                                clus
vv                               PTPN11 MUTATED PTPN11 WILD-TYPE
  COLON ADENOCARCINOMA                       28              287
  COLON MUCINOUS ADENOCARCINOMA               2               45
  RECTAL ADENOCARCINOMA                       8               98
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  PTPN11 MUTATED    21   0   0   5
  PTPN11 WILD-TYPE 324   4  31  20
D468V11, multiclass
    clus
vv   PTPN11 MUTATED PTPN11 WILD-TYPE
  R0             21              324
  R1              0                4
  R2              0               31
  RX              5               20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D468V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PTPN11 MUTATED                                  0     1
  PTPN11 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  PTPN11 MUTATED                           1    29
  PTPN11 WILD-TYPE                        21   197
D468V13, multiclass
                                  clus
vv                                 PTPN11 MUTATED PTPN11 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                        29              197
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(469) Variable = KIAA1409 MUTATION ANALYSIS
D469V1, survival
                    sevent
clus2                  0   1
  KIAA1409 MUTATED    34   8
  KIAA1409 WILD-TYPE 344  85
  KIAA1409 MUTATED KIAA1409 WILD-TYPE 
                42                429 
  KIAA1409 MUTATED KIAA1409 WILD-TYPE 
                 8                 85 
$`KIAA1409 MUTATED`
TCGA-A6-2672 TCGA-A6-5659 TCGA-A6-5662 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3510 
       46.65        30.44        23.61         3.02         1.02        63.98 
TCGA-AA-3525 TCGA-AA-3556 TCGA-AA-3660 TCGA-AA-3672 TCGA-AA-3680 TCGA-AA-3713 
        8.05        23.01        78.08         0.92        11.01        19.04 
TCGA-AA-3811 TCGA-AA-3815 TCGA-AA-3845 TCGA-AA-3864 TCGA-AA-3977 TCGA-AA-A00J 
       10.06        33.04         0.00        53.00        25.02        18.05 
TCGA-AA-A00N TCGA-AA-A010 TCGA-AD-5900 TCGA-AU-6004 TCGA-AZ-4315 TCGA-AZ-6600 
        4.01        34.98         0.07        27.09        58.39        12.10 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4952 TCGA-CM-6162 TCGA-CM-6164 TCGA-CM-6676 
       12.76        10.06        15.62        12.00        29.03        11.08 
TCGA-CM-6680 TCGA-D5-6536 TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 
       12.03        17.85         9.04        11.64         1.51        12.00 
TCGA-DM-A1D7 TCGA-G4-6304 TCGA-AF-4110 TCGA-AG-A002 TCGA-EI-6507 TCGA-EI-6510 
       13.32        53.62        14.50        20.98        19.96        18.28 

$`KIAA1409 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 
       31.63        29.19        33.53        22.09        22.06        32.71 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       27.09        22.52         8.38        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
       20.28         7.04        35.01         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3560 
       13.02        24.00        17.95        29.95        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       13.94        19.99        61.02         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3681 
        2.01        14.01        50.04        47.01        15.02         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       19.04        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 
       15.95        38.99        37.02        14.93        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        31.07        30.05        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       39.98        18.05        40.96        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
        0.20        14.50        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       88.21        49.41         6.77       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        3.29         0.07        12.20        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       85.45        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6163 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
        2.96        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6677 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       11.01        10.06        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6929 
        3.68         4.41        12.43        14.30         9.44         4.80 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       92.75        49.91        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
      133.18        74.56        65.85        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-5654 
       43.04        13.55        19.10        34.49        10.39        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6508 
       24.13        51.48        32.61         0.49        20.55        20.91 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  KIAA1409 MUTATED KIAA1409 WILD-TYPE 
                 0                  0 
  KIAA1409 MUTATED KIAA1409 WILD-TYPE 
             78.08             148.01 
  KIAA1409 MUTATED KIAA1409 WILD-TYPE 
             15.06              21.01 
[1] "0.0 - 78.1 (15.1)"  "0.0 - 148.0 (21.0)"
[1] "hr=" "1.2"
D469V2, continuous
D469V3, binary
                    cls
clus                   0   1
  KIAA1409 MUTATED    39   3
  KIAA1409 WILD-TYPE 327 116
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1409 MUTATED     39    3
  KIAA1409 WILD-TYPE  327  116
        clus
vv       KIAA1409 MUTATED KIAA1409 WILD-TYPE
  COLON                39                327
  RECTUM                3                116
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KIAA1409 MUTATED         6        0        5        11         3         0
  KIAA1409 WILD-TYPE      85        1       27       127         7         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIAA1409 MUTATED           2          0          6          2        4
  KIAA1409 WILD-TYPE        22         11         53         40       44
                    vv
clus                 STAGE IVA STAGE IVB
  KIAA1409 MUTATED           3         0
  KIAA1409 WILD-TYPE        15         1
D469V4, multiclass
            clus
vv           KIAA1409 MUTATED KIAA1409 WILD-TYPE
  STAGE I                   6                 85
  STAGE IA                  0                  1
  STAGE II                  5                 27
  STAGE IIA                11                127
  STAGE IIB                 3                  7
  STAGE IIC                 0                  1
  STAGE III                 2                 22
  STAGE IIIA                0                 11
  STAGE IIIB                6                 53
  STAGE IIIC                2                 40
  STAGE IV                  4                 44
  STAGE IVA                 3                 15
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  KIAA1409 MUTATED     0   8  25  10
  KIAA1409 WILD-TYPE  17  84 304  40
D469V5, multiclass
    clus
vv   KIAA1409 MUTATED KIAA1409 WILD-TYPE
  T1                0                 17
  T2                8                 84
  T3               25                304
  T4               10                 40
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  KIAA1409 MUTATED    28   7   8
  KIAA1409 WILD-TYPE 259 106  79
D469V6, multiclass
    clus
vv   KIAA1409 MUTATED KIAA1409 WILD-TYPE
  N0               28                259
  N1                7                106
  N2                8                 79
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D469V7, binary
                    cls
clus                   0   1
  KIAA1409 MUTATED    34   5
  KIAA1409 WILD-TYPE 341  60
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1409 MUTATED     34    5
  KIAA1409 WILD-TYPE  341   60
   clus
vv  KIAA1409 MUTATED KIAA1409 WILD-TYPE
  0               34                341
  1                5                 60
[1] 2 2
[1] FALSE
D469V8, binary
                    cls
clus                   0   1
  KIAA1409 MUTATED    18  25
  KIAA1409 WILD-TYPE 207 239
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1409 MUTATED     18   25
  KIAA1409 WILD-TYPE  207  239
        clus
vv       KIAA1409 MUTATED KIAA1409 WILD-TYPE
  FEMALE               18                207
  MALE                 25                239
[1] 2 2
[1] FALSE
D469V9, binary
                    cls
clus                   0   1
  KIAA1409 MUTATED    31   2
  KIAA1409 WILD-TYPE 319  20
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1409 MUTATED     31    2
  KIAA1409 WILD-TYPE  319   20
     clus
vv    KIAA1409 MUTATED KIAA1409 WILD-TYPE
  NO                31                319
  YES                2                 20
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  KIAA1409 MUTATED                     29                             8
  KIAA1409 WILD-TYPE                  286                            39
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  KIAA1409 MUTATED                       3                              0
  KIAA1409 WILD-TYPE                   103                             10
D469V10, multiclass
                                clus
vv                               KIAA1409 MUTATED KIAA1409 WILD-TYPE
  COLON ADENOCARCINOMA                         29                286
  COLON MUCINOUS ADENOCARCINOMA                 8                 39
  RECTAL ADENOCARCINOMA                         3                103
  RECTAL MUCINOUS ADENOCARCINOMA                0                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  KIAA1409 MUTATED    33   0   3   3
  KIAA1409 WILD-TYPE 312   4  28  22
D469V11, multiclass
    clus
vv   KIAA1409 MUTATED KIAA1409 WILD-TYPE
  R0               33                312
  R1                0                  4
  R2                3                 28
  RX                3                 22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D469V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KIAA1409 MUTATED                                  0     2
  KIAA1409 WILD-TYPE                                1     9
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  KIAA1409 MUTATED                           1    21
  KIAA1409 WILD-TYPE                        21   205
D469V13, multiclass
                                  clus
vv                                 KIAA1409 MUTATED KIAA1409 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           2                  9
  BLACK OR AFRICAN AMERICAN                       1                 21
  WHITE                                          21                205
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(470) Variable = DOCK1 MUTATION ANALYSIS
D470V1, survival
                 sevent
clus2               0   1
  DOCK1 MUTATED    21   4
  DOCK1 WILD-TYPE 357  89
  DOCK1 MUTATED DOCK1 WILD-TYPE 
             25             446 
  DOCK1 MUTATED DOCK1 WILD-TYPE 
              4              89 
$`DOCK1 MUTATED`
TCGA-A6-5661 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3715 TCGA-AA-3950 TCGA-AA-A004 
       33.53        78.08        54.02        19.04        24.00        13.94 
TCGA-AA-A010 TCGA-AD-5900 TCGA-AD-6889 TCGA-AU-3779 TCGA-AZ-4315 TCGA-CA-6717 
       34.98         0.07        56.55        14.50        58.39        12.76 
TCGA-CK-4948 TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-6166 TCGA-CM-6171 TCGA-D5-6537 
      148.01        23.05        37.02        21.99        14.04         4.80 
TCGA-DM-A0XD TCGA-F4-6570 TCGA-G4-6307 TCGA-G4-6588 TCGA-AG-A002 TCGA-AH-6549 
       24.43         6.18        55.04        26.17        20.98        17.49 
TCGA-EI-6510 
       18.28 

$`DOCK1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 
       19.99        13.94        19.99        61.02         6.05         6.97 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       85.05        26.99        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       33.01        26.01         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       27.02        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 
       41.00        39.98        18.05        40.96        21.37        15.52 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
        0.20        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07        12.20        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
       17.56        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4747 
       21.14        82.95         1.91       124.27        20.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6168 
       12.00         2.96        29.03        16.04        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       13.02        15.02        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       43.27        15.12        17.85        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       11.38        10.26       119.70        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       35.74        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6310 
       74.56        65.85        53.62        44.68        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 
       61.91        36.00        22.09        13.78        35.80        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
        1.45         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-F5-6464 
       32.61         0.49        20.55        19.96        20.91         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  DOCK1 MUTATED DOCK1 WILD-TYPE 
           0.07            0.00 
  DOCK1 MUTATED DOCK1 WILD-TYPE 
         148.01          140.38 
  DOCK1 MUTATED DOCK1 WILD-TYPE 
         23.050          20.035 
[1] "0.1 - 148.0 (23.1)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1.5"
D470V2, continuous
D470V3, binary
                 cls
clus                0   1
  DOCK1 MUTATED    24   3
  DOCK1 WILD-TYPE 342 116
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DOCK1 MUTATED     24    3
  DOCK1 WILD-TYPE  342  116
        clus
vv       DOCK1 MUTATED DOCK1 WILD-TYPE
  COLON             24             342
  RECTUM             3             116
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DOCK1 MUTATED         5        0        3        12         1         0
  DOCK1 WILD-TYPE      86        1       29       126         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DOCK1 MUTATED           1          0          2          1        0         1
  DOCK1 WILD-TYPE        23         11         57         41       48        17
                 vv
clus              STAGE IVB
  DOCK1 MUTATED           0
  DOCK1 WILD-TYPE         1
D470V4, multiclass
            clus
vv           DOCK1 MUTATED DOCK1 WILD-TYPE
  STAGE I                5              86
  STAGE IA               0               1
  STAGE II               3              29
  STAGE IIA             12             126
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             2              57
  STAGE IIIC             1              41
  STAGE IV               0              48
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  DOCK1 MUTATED     0   6  20   1
  DOCK1 WILD-TYPE  17  86 309  49
D470V5, multiclass
    clus
vv   DOCK1 MUTATED DOCK1 WILD-TYPE
  T1             0              17
  T2             6              86
  T3            20             309
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  DOCK1 MUTATED    22   3   1
  DOCK1 WILD-TYPE 265 110  86
D470V6, multiclass
    clus
vv   DOCK1 MUTATED DOCK1 WILD-TYPE
  N0            22             265
  N1             3             110
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D470V7, binary
                 cls
clus                0   1
  DOCK1 MUTATED    22   0
  DOCK1 WILD-TYPE 353  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DOCK1 MUTATED     22    0
  DOCK1 WILD-TYPE  353   65
   clus
vv  DOCK1 MUTATED DOCK1 WILD-TYPE
  0            22             353
  1             0              65
[1] 2 2
[1] FALSE
D470V8, binary
                 cls
clus                0   1
  DOCK1 MUTATED    14  13
  DOCK1 WILD-TYPE 211 251
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DOCK1 MUTATED     14   13
  DOCK1 WILD-TYPE  211  251
        clus
vv       DOCK1 MUTATED DOCK1 WILD-TYPE
  FEMALE            14             211
  MALE              13             251
[1] 2 2
[1] FALSE
D470V9, binary
                 cls
clus                0   1
  DOCK1 MUTATED    22   0
  DOCK1 WILD-TYPE 328  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DOCK1 MUTATED     22    0
  DOCK1 WILD-TYPE  328   22
     clus
vv    DOCK1 MUTATED DOCK1 WILD-TYPE
  NO             22             328
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  DOCK1 MUTATED                     20                             4
  DOCK1 WILD-TYPE                  295                            43
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  DOCK1 MUTATED                       3                              0
  DOCK1 WILD-TYPE                   103                             10
D470V10, multiclass
                                clus
vv                               DOCK1 MUTATED DOCK1 WILD-TYPE
  COLON ADENOCARCINOMA                      20             295
  COLON MUCINOUS ADENOCARCINOMA              4              43
  RECTAL ADENOCARCINOMA                      3             103
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  DOCK1 MUTATED    23   0   0   2
  DOCK1 WILD-TYPE 322   4  31  23
D470V11, multiclass
    clus
vv   DOCK1 MUTATED DOCK1 WILD-TYPE
  R0            23             322
  R1             0               4
  R2             0              31
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D470V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DOCK1 MUTATED                                  0     2
  DOCK1 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  DOCK1 MUTATED                           2    15
  DOCK1 WILD-TYPE                        20   211
D470V13, multiclass
                                  clus
vv                                 DOCK1 MUTATED DOCK1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               9
  BLACK OR AFRICAN AMERICAN                    2              20
  WHITE                                       15             211
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(471) Variable = GRM8 MUTATION ANALYSIS
D471V1, survival
                sevent
clus2              0   1
  GRM8 MUTATED    13   7
  GRM8 WILD-TYPE 365  86
  GRM8 MUTATED GRM8 WILD-TYPE 
            20            451 
  GRM8 MUTATED GRM8 WILD-TYPE 
             7             86 
$`GRM8 MUTATED`
TCGA-A6-5661 TCGA-A6-5665 TCGA-AA-3489 TCGA-AA-3715 TCGA-AA-3977 TCGA-AA-A00N 
       33.53        22.06         7.04        19.04        25.02         4.01 
TCGA-AA-A010 TCGA-AZ-4315 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-CA-6717 TCGA-CA-6718 
       34.98        58.39        62.79        49.41        12.76        10.06 
TCGA-CM-5860 TCGA-CM-6677 TCGA-D5-6927 TCGA-F4-6805 TCGA-F4-6856 TCGA-G4-6303 
       32.02        11.08         9.44        34.42        35.31        65.85 
TCGA-G4-6309 TCGA-AG-A002 
       85.48        20.98 

$`GRM8 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       19.66        20.28         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       85.05        26.99        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        33.01        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
      106.75        22.36        88.21         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 
        3.06         3.25         3.29         0.07        12.20        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       22.98        30.08        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6678 TCGA-CM-6679 
       11.01        12.95        13.05        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6928 
        3.68         4.41        12.43        14.30         9.04        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
       47.87         1.55        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6304 TCGA-G4-6306 
        0.53        47.41       133.18        74.56        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       55.04        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  GRM8 MUTATED GRM8 WILD-TYPE 
          4.01           0.00 
  GRM8 MUTATED GRM8 WILD-TYPE 
         85.48         148.01 
  GRM8 MUTATED GRM8 WILD-TYPE 
         28.52          20.02 
[1] "4.0 - 85.5 (28.5)"  "0.0 - 148.0 (20.0)"
[1] "hr=" "1.5"
D471V2, continuous
D471V3, binary
                cls
clus               0   1
  GRM8 MUTATED    21   1
  GRM8 WILD-TYPE 345 118
[1] "tbl2"
                cls
clus             [,1] [,2]
  GRM8 MUTATED     21    1
  GRM8 WILD-TYPE  345  118
        clus
vv       GRM8 MUTATED GRM8 WILD-TYPE
  COLON            21            345
  RECTUM            1            118
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GRM8 MUTATED         2        0        4         9         3         0
  GRM8 WILD-TYPE      89        1       28       129         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  GRM8 MUTATED           0          0          1          1        1         0
  GRM8 WILD-TYPE        24         11         58         41       47        18
                vv
clus             STAGE IVB
  GRM8 MUTATED           0
  GRM8 WILD-TYPE         1
D471V4, multiclass
            clus
vv           GRM8 MUTATED GRM8 WILD-TYPE
  STAGE I               2             89
  STAGE IA              0              1
  STAGE II              4             28
  STAGE IIA             9            129
  STAGE IIB             3              7
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            1             58
  STAGE IIIC            1             41
  STAGE IV              1             47
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  GRM8 MUTATED     0   3  16   3
  GRM8 WILD-TYPE  17  89 313  47
D471V5, multiclass
    clus
vv   GRM8 MUTATED GRM8 WILD-TYPE
  T1            0             17
  T2            3             89
  T3           16            313
  T4            3             47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  GRM8 MUTATED    19   2   1
  GRM8 WILD-TYPE 268 111  86
D471V6, multiclass
    clus
vv   GRM8 MUTATED GRM8 WILD-TYPE
  N0           19            268
  N1            2            111
  N2            1             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D471V7, binary
                cls
clus               0   1
  GRM8 MUTATED    16   1
  GRM8 WILD-TYPE 359  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  GRM8 MUTATED     16    1
  GRM8 WILD-TYPE  359   64
   clus
vv  GRM8 MUTATED GRM8 WILD-TYPE
  0           16            359
  1            1             64
[1] 2 2
[1] FALSE
D471V8, binary
                cls
clus               0   1
  GRM8 MUTATED     9  13
  GRM8 WILD-TYPE 216 251
[1] "tbl2"
                cls
clus             [,1] [,2]
  GRM8 MUTATED      9   13
  GRM8 WILD-TYPE  216  251
        clus
vv       GRM8 MUTATED GRM8 WILD-TYPE
  FEMALE            9            216
  MALE             13            251
[1] 2 2
[1] FALSE
D471V9, binary
                cls
clus               0   1
  GRM8 MUTATED    19   0
  GRM8 WILD-TYPE 331  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  GRM8 MUTATED     19    0
  GRM8 WILD-TYPE  331   22
     clus
vv    GRM8 MUTATED GRM8 WILD-TYPE
  NO            19            331
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  GRM8 MUTATED                     17                             4
  GRM8 WILD-TYPE                  298                            43
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  GRM8 MUTATED                       1                              0
  GRM8 WILD-TYPE                   105                             10
D471V10, multiclass
                                clus
vv                               GRM8 MUTATED GRM8 WILD-TYPE
  COLON ADENOCARCINOMA                     17            298
  COLON MUCINOUS ADENOCARCINOMA             4             43
  RECTAL ADENOCARCINOMA                     1            105
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  GRM8 MUTATED    16   0   0   3
  GRM8 WILD-TYPE 329   4  31  22
D471V11, multiclass
    clus
vv   GRM8 MUTATED GRM8 WILD-TYPE
  R0           16            329
  R1            0              4
  R2            0             31
  RX            3             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D471V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GRM8 MUTATED                                  0     2
  GRM8 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  GRM8 MUTATED                           2    12
  GRM8 WILD-TYPE                        20   214
D471V13, multiclass
                                  clus
vv                                 GRM8 MUTATED GRM8 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              9
  BLACK OR AFRICAN AMERICAN                   2             20
  WHITE                                      12            214
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(472) Variable = NTRK3 MUTATION ANALYSIS
D472V1, survival
                 sevent
clus2               0   1
  NTRK3 MUTATED    25   4
  NTRK3 WILD-TYPE 353  89
  NTRK3 MUTATED NTRK3 WILD-TYPE 
             29             442 
  NTRK3 MUTATED NTRK3 WILD-TYPE 
              4              89 
$`NTRK3 MUTATED`
TCGA-A6-5657 TCGA-A6-6781 TCGA-AA-3664 TCGA-AA-3713 TCGA-AA-3815 TCGA-AA-3833 
       31.63        19.66        54.02        19.04        33.04        15.95 
TCGA-AA-3877 TCGA-AA-3941 TCGA-AA-A010 TCGA-AD-5900 TCGA-AZ-4682 TCGA-AZ-6599 
       31.00        24.00        34.98         0.07        22.36         6.77 
TCGA-CA-6718 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-6161 TCGA-CM-6166 
       10.06        30.08        32.02        15.02        15.02        21.99 
TCGA-D5-6931 TCGA-DM-A1D9 TCGA-G4-6303 TCGA-G4-6315 TCGA-G4-6586 TCGA-AF-6136 
       12.00       140.38        65.85        61.91        35.80        15.39 
TCGA-AG-A002 TCGA-AG-A01L TCGA-EF-5830 TCGA-EI-6508 TCGA-G5-6235 
       20.98        12.00         0.49        20.91        55.76 

$`NTRK3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
       85.05        26.99        19.04        10.06        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
       25.02         1.02        17.98        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
        2.01        12.99        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       18.05        40.96        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-5403 
       17.82        58.39         1.41         5.13       106.75        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       88.21        49.41        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07        12.20        12.76        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6162 TCGA-CM-6163 
        5.03        15.02        15.02        17.03        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       29.03        16.04        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6932 
        9.04         9.44        11.64         4.80         1.51        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       49.91        13.32        12.59         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       74.56        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 
       34.49        10.39        14.50        16.83        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01W TCGA-AG-A01Y 
       37.02        15.95        36.03         9.07        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EI-6506 
       41.36        57.24        24.13        51.48        32.61        20.55 
TCGA-EI-6507 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       19.96        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6641 
       32.19         0.66         0.69        26.43 

  NTRK3 MUTATED NTRK3 WILD-TYPE 
           0.07            0.00 
  NTRK3 MUTATED NTRK3 WILD-TYPE 
         140.38          148.01 
  NTRK3 MUTATED NTRK3 WILD-TYPE 
         21.990          20.035 
[1] "0.1 - 140.4 (22.0)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.6"
D472V2, continuous
D472V3, binary
                 cls
clus                0   1
  NTRK3 MUTATED    25   6
  NTRK3 WILD-TYPE 341 113
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NTRK3 MUTATED     25    6
  NTRK3 WILD-TYPE  341  113
        clus
vv       NTRK3 MUTATED NTRK3 WILD-TYPE
  COLON             25             341
  RECTUM             6             113
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NTRK3 MUTATED         6        0        2         9         2         0
  NTRK3 WILD-TYPE      85        1       30       129         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NTRK3 MUTATED           0          0          5          2        3         2
  NTRK3 WILD-TYPE        24         11         54         40       45        16
                 vv
clus              STAGE IVB
  NTRK3 MUTATED           0
  NTRK3 WILD-TYPE         1
D472V4, multiclass
            clus
vv           NTRK3 MUTATED NTRK3 WILD-TYPE
  STAGE I                6              85
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA              9             129
  STAGE IIB              2               8
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             5              54
  STAGE IIIC             2              40
  STAGE IV               3              45
  STAGE IVA              2              16
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  NTRK3 MUTATED     1   5  19   6
  NTRK3 WILD-TYPE  16  87 310  44
D472V5, multiclass
    clus
vv   NTRK3 MUTATED NTRK3 WILD-TYPE
  T1             1              16
  T2             5              87
  T3            19             310
  T4             6              44
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  NTRK3 MUTATED    21   9   1
  NTRK3 WILD-TYPE 266 104  86
D472V6, multiclass
    clus
vv   NTRK3 MUTATED NTRK3 WILD-TYPE
  N0            21             266
  N1             9             104
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D472V7, binary
                 cls
clus                0   1
  NTRK3 MUTATED    21   5
  NTRK3 WILD-TYPE 354  60
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NTRK3 MUTATED     21    5
  NTRK3 WILD-TYPE  354   60
   clus
vv  NTRK3 MUTATED NTRK3 WILD-TYPE
  0            21             354
  1             5              60
[1] 2 2
[1] FALSE
D472V8, binary
                 cls
clus                0   1
  NTRK3 MUTATED    17  14
  NTRK3 WILD-TYPE 208 250
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NTRK3 MUTATED     17   14
  NTRK3 WILD-TYPE  208  250
        clus
vv       NTRK3 MUTATED NTRK3 WILD-TYPE
  FEMALE            17             208
  MALE              14             250
[1] 2 2
[1] FALSE
D472V9, binary
                 cls
clus                0   1
  NTRK3 MUTATED    23   2
  NTRK3 WILD-TYPE 327  20
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NTRK3 MUTATED     23    2
  NTRK3 WILD-TYPE  327   20
     clus
vv    NTRK3 MUTATED NTRK3 WILD-TYPE
  NO             23             327
  YES             2              20
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  NTRK3 MUTATED                     22                             3
  NTRK3 WILD-TYPE                  293                            44
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  NTRK3 MUTATED                       6                              0
  NTRK3 WILD-TYPE                   100                             10
D472V10, multiclass
                                clus
vv                               NTRK3 MUTATED NTRK3 WILD-TYPE
  COLON ADENOCARCINOMA                      22             293
  COLON MUCINOUS ADENOCARCINOMA              3              44
  RECTAL ADENOCARCINOMA                      6             100
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  NTRK3 MUTATED    25   1   1   1
  NTRK3 WILD-TYPE 320   3  30  24
D472V11, multiclass
    clus
vv   NTRK3 MUTATED NTRK3 WILD-TYPE
  R0            25             320
  R1             1               3
  R2             1              30
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D472V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NTRK3 MUTATED                                  0     1
  NTRK3 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  NTRK3 MUTATED                           1    18
  NTRK3 WILD-TYPE                        21   208
D472V13, multiclass
                                  clus
vv                                 NTRK3 MUTATED NTRK3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                       18             208
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(473) Variable = ANKRD30A MUTATION ANALYSIS
D473V1, survival
                    sevent
clus2                  0   1
  ANKRD30A MUTATED    26   6
  ANKRD30A WILD-TYPE 352  87
  ANKRD30A MUTATED ANKRD30A WILD-TYPE 
                32                439 
  ANKRD30A MUTATED ANKRD30A WILD-TYPE 
                 6                 87 
$`ANKRD30A MUTATED`
TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-AA-3660 
       14.53        32.91        22.52         8.38        25.08        78.08 
TCGA-AA-3977 TCGA-AA-A010 TCGA-AA-A01Z TCGA-AD-5900 TCGA-AU-3779 TCGA-AZ-4315 
       25.02        34.98        37.02         0.07        14.50        58.39 
TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-6751 TCGA-CM-5862 TCGA-CM-6164 
        0.07        12.76        10.06       124.27         5.03        29.03 
TCGA-CM-6168 TCGA-D5-5537 TCGA-D5-6931 TCGA-DM-A28E TCGA-DM-A28F TCGA-F4-6703 
       12.99        45.40        12.00       119.93        35.97        47.87 
TCGA-G4-6303 TCGA-G4-6307 TCGA-G4-6588 TCGA-AF-6672 TCGA-AG-A002 TCGA-AG-A01W 
       65.85        55.04        26.17        10.39        20.98        70.03 
TCGA-AG-A02N TCGA-F5-6571 
       61.97        31.30 

$`ANKRD30A WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5657 
       16.57        34.65        33.34        32.75        36.53        31.63 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       30.44        29.19        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 
       32.71        27.09        25.18        24.16        21.76        24.69 
TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 
       24.39        23.87        20.12        19.66        20.28         7.04 
TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
        3.02         1.02        35.01        63.98         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
       13.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       36.03         8.05        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       33.04        35.01        26.01        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       18.05        40.96        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        3.29        12.20        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
        1.91        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       16.04        21.99        14.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       10.06        12.03        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       11.64         4.80         1.51        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
      139.17         6.12        81.37        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6704 TCGA-F4-6805 
        8.61        31.96        35.74         6.18         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 
       35.31       133.18        74.56        53.62        44.68        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       15.39        20.02        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       12.00        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       49.51        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  ANKRD30A MUTATED ANKRD30A WILD-TYPE 
              0.07               0.00 
  ANKRD30A MUTATED ANKRD30A WILD-TYPE 
            124.27             148.01 
  ANKRD30A MUTATED ANKRD30A WILD-TYPE 
             27.60              19.99 
[1] "0.1 - 124.3 (27.6)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.5"
D473V2, continuous
D473V3, binary
                    cls
clus                   0   1
  ANKRD30A MUTATED    28   5
  ANKRD30A WILD-TYPE 338 114
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ANKRD30A MUTATED     28    5
  ANKRD30A WILD-TYPE  338  114
        clus
vv       ANKRD30A MUTATED ANKRD30A WILD-TYPE
  COLON                28                338
  RECTUM                5                114
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ANKRD30A MUTATED         5        0        4        13         1         0
  ANKRD30A WILD-TYPE      86        1       28       125         9         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ANKRD30A MUTATED           1          0          3          1        2
  ANKRD30A WILD-TYPE        23         11         56         41       46
                    vv
clus                 STAGE IVA STAGE IVB
  ANKRD30A MUTATED           2         0
  ANKRD30A WILD-TYPE        16         1
D473V4, multiclass
            clus
vv           ANKRD30A MUTATED ANKRD30A WILD-TYPE
  STAGE I                   5                 86
  STAGE IA                  0                  1
  STAGE II                  4                 28
  STAGE IIA                13                125
  STAGE IIB                 1                  9
  STAGE IIC                 0                  1
  STAGE III                 1                 23
  STAGE IIIA                0                 11
  STAGE IIIB                3                 56
  STAGE IIIC                1                 41
  STAGE IV                  2                 46
  STAGE IVA                 2                 16
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  ANKRD30A MUTATED     0   6  24   3
  ANKRD30A WILD-TYPE  17  86 305  47
D473V5, multiclass
    clus
vv   ANKRD30A MUTATED ANKRD30A WILD-TYPE
  T1                0                 17
  T2                6                 86
  T3               24                305
  T4                3                 47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  ANKRD30A MUTATED    23   6   4
  ANKRD30A WILD-TYPE 264 107  83
D473V6, multiclass
    clus
vv   ANKRD30A MUTATED ANKRD30A WILD-TYPE
  N0               23                264
  N1                6                107
  N2                4                 83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D473V7, binary
                    cls
clus                   0   1
  ANKRD30A MUTATED    25   3
  ANKRD30A WILD-TYPE 350  62
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ANKRD30A MUTATED     25    3
  ANKRD30A WILD-TYPE  350   62
   clus
vv  ANKRD30A MUTATED ANKRD30A WILD-TYPE
  0               25                350
  1                3                 62
[1] 2 2
[1] FALSE
D473V8, binary
                    cls
clus                   0   1
  ANKRD30A MUTATED    13  20
  ANKRD30A WILD-TYPE 212 244
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ANKRD30A MUTATED     13   20
  ANKRD30A WILD-TYPE  212  244
        clus
vv       ANKRD30A MUTATED ANKRD30A WILD-TYPE
  FEMALE               13                212
  MALE                 20                244
[1] 2 2
[1] FALSE
D473V9, binary
                    cls
clus                   0   1
  ANKRD30A MUTATED    25   1
  ANKRD30A WILD-TYPE 325  21
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ANKRD30A MUTATED     25    1
  ANKRD30A WILD-TYPE  325   21
     clus
vv    ANKRD30A MUTATED ANKRD30A WILD-TYPE
  NO                25                325
  YES                1                 21
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ANKRD30A MUTATED                     25                             3
  ANKRD30A WILD-TYPE                  290                            44
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ANKRD30A MUTATED                       5                              0
  ANKRD30A WILD-TYPE                   101                             10
D473V10, multiclass
                                clus
vv                               ANKRD30A MUTATED ANKRD30A WILD-TYPE
  COLON ADENOCARCINOMA                         25                290
  COLON MUCINOUS ADENOCARCINOMA                 3                 44
  RECTAL ADENOCARCINOMA                         5                101
  RECTAL MUCINOUS ADENOCARCINOMA                0                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  ANKRD30A MUTATED    19   0   0   5
  ANKRD30A WILD-TYPE 326   4  31  20
D473V11, multiclass
    clus
vv   ANKRD30A MUTATED ANKRD30A WILD-TYPE
  R0               19                326
  R1                0                  4
  R2                0                 31
  RX                5                 20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D473V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ANKRD30A MUTATED                                  0     3
  ANKRD30A WILD-TYPE                                1     8
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  ANKRD30A MUTATED                           2    20
  ANKRD30A WILD-TYPE                        20   206
D473V13, multiclass
                                  clus
vv                                 ANKRD30A MUTATED ANKRD30A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           3                  8
  BLACK OR AFRICAN AMERICAN                       2                 20
  WHITE                                          20                206
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(474) Variable = MYH1 MUTATION ANALYSIS
D474V1, survival
                sevent
clus2              0   1
  MYH1 MUTATED    28   7
  MYH1 WILD-TYPE 350  86
  MYH1 MUTATED MYH1 WILD-TYPE 
            35            436 
  MYH1 MUTATED MYH1 WILD-TYPE 
             7             86 
$`MYH1 MUTATED`
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5666 TCGA-AA-3492 TCGA-AA-3818 
       30.44        29.19        33.53        32.71         3.02         0.99 
TCGA-AA-3966 TCGA-AA-3977 TCGA-AA-A00J TCGA-AA-A010 TCGA-AD-6889 TCGA-AD-6890 
        2.01        25.02        18.05        34.98        56.55         0.79 
TCGA-AZ-4315 TCGA-AZ-6601 TCGA-AZ-6605 TCGA-CA-6717 TCGA-CK-4948 TCGA-CK-5913 
       58.39       100.01         5.23        12.76       148.01        51.32 
TCGA-CM-4743 TCGA-CM-5863 TCGA-CM-6162 TCGA-CM-6167 TCGA-CM-6676 TCGA-D5-6535 
       23.05        15.02        12.00        14.99        11.08        15.12 
TCGA-D5-6922 TCGA-D5-6923 TCGA-DM-A1D8 TCGA-DM-A28F TCGA-G4-6306 TCGA-G4-6586 
        4.41        12.43        12.59        35.97        44.68        35.80 
TCGA-G4-6626 TCGA-AG-3605 TCGA-AG-3727 TCGA-AG-A002 TCGA-CI-6624 
       46.75         0.99         0.99        20.98         4.73 

$`MYH1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 
       32.91        31.63        23.61        22.09        22.06        27.09 
TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 
       22.52         8.38        25.08        25.18        24.16        21.76 
TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       24.69        24.39        23.87        20.12        19.66        20.28 
TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
        7.04         1.02        35.01        63.98         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
       13.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       36.03         8.05        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       78.08         6.05         6.97        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3819 
       19.04        19.04        10.06        35.05        33.04        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 
       24.00         2.01        20.98        34.03        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       19.00        30.02        34.03        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6899 
       40.96         0.07        21.37        15.52         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
       16.31         0.95        33.01        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
        6.77        12.10        29.56        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       10.06        14.30        17.56        85.45        15.62        49.08 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 
        9.99        21.14        82.95         1.91       124.27        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-5868 
       30.08        32.02        15.02         5.03        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6168 
       15.02         2.96        29.03        16.04        21.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       43.27        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       15.58         1.48         3.68        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       13.32       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H 
      139.17         6.12        81.37       119.93        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       53.62        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-AF-2687 
       22.09        13.78        26.17        91.79        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
       12.03         6.05        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        7.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
       33.17         6.97        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  MYH1 MUTATED MYH1 WILD-TYPE 
          0.79           0.00 
  MYH1 MUTATED MYH1 WILD-TYPE 
        148.01         140.38 
  MYH1 MUTATED MYH1 WILD-TYPE 
        18.050         20.235 
[1] "0.8 - 148.0 (18.1)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1"  
D474V2, continuous
D474V3, binary
                cls
clus               0   1
  MYH1 MUTATED    32   4
  MYH1 WILD-TYPE 334 115
[1] "tbl2"
                cls
clus             [,1] [,2]
  MYH1 MUTATED     32    4
  MYH1 WILD-TYPE  334  115
        clus
vv       MYH1 MUTATED MYH1 WILD-TYPE
  COLON            32            334
  RECTUM            4            115
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MYH1 MUTATED         5        0        2        12         1         1
  MYH1 WILD-TYPE      86        1       30       126         9         0
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MYH1 MUTATED           2          1          6          2        1         0
  MYH1 WILD-TYPE        22         10         53         40       47        18
                vv
clus             STAGE IVB
  MYH1 MUTATED           0
  MYH1 WILD-TYPE         1
D474V4, multiclass
            clus
vv           MYH1 MUTATED MYH1 WILD-TYPE
  STAGE I               5             86
  STAGE IA              0              1
  STAGE II              2             30
  STAGE IIA            12            126
  STAGE IIB             1              9
  STAGE IIC             1              0
  STAGE III             2             22
  STAGE IIIA            1             10
  STAGE IIIB            6             53
  STAGE IIIC            2             40
  STAGE IV              1             47
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  MYH1 MUTATED     1   7  24   4
  MYH1 WILD-TYPE  16  85 305  46
D474V5, multiclass
    clus
vv   MYH1 MUTATED MYH1 WILD-TYPE
  T1            1             16
  T2            7             85
  T3           24            305
  T4            4             46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  MYH1 MUTATED    23  11   2
  MYH1 WILD-TYPE 264 102  85
D474V6, multiclass
    clus
vv   MYH1 MUTATED MYH1 WILD-TYPE
  N0           23            264
  N1           11            102
  N2            2             85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D474V7, binary
                cls
clus               0   1
  MYH1 MUTATED    30   1
  MYH1 WILD-TYPE 345  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  MYH1 MUTATED     30    1
  MYH1 WILD-TYPE  345   64
   clus
vv  MYH1 MUTATED MYH1 WILD-TYPE
  0           30            345
  1            1             64
[1] 2 2
[1] FALSE
D474V8, binary
                cls
clus               0   1
  MYH1 MUTATED    17  19
  MYH1 WILD-TYPE 208 245
[1] "tbl2"
                cls
clus             [,1] [,2]
  MYH1 MUTATED     17   19
  MYH1 WILD-TYPE  208  245
        clus
vv       MYH1 MUTATED MYH1 WILD-TYPE
  FEMALE           17            208
  MALE             19            245
[1] 2 2
[1] FALSE
D474V9, binary
                cls
clus               0   1
  MYH1 MUTATED    25   0
  MYH1 WILD-TYPE 325  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  MYH1 MUTATED     25    0
  MYH1 WILD-TYPE  325   22
     clus
vv    MYH1 MUTATED MYH1 WILD-TYPE
  NO            25            325
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MYH1 MUTATED                     27                             5
  MYH1 WILD-TYPE                  288                            42
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MYH1 MUTATED                       4                              0
  MYH1 WILD-TYPE                   102                             10
D474V10, multiclass
                                clus
vv                               MYH1 MUTATED MYH1 WILD-TYPE
  COLON ADENOCARCINOMA                     27            288
  COLON MUCINOUS ADENOCARCINOMA             5             42
  RECTAL ADENOCARCINOMA                     4            102
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  MYH1 MUTATED    21   0   1   3
  MYH1 WILD-TYPE 324   4  30  22
D474V11, multiclass
    clus
vv   MYH1 MUTATED MYH1 WILD-TYPE
  R0           21            324
  R1            0              4
  R2            1             30
  RX            3             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D474V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MYH1 MUTATED                                  0     2
  MYH1 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  MYH1 MUTATED                           3    21
  MYH1 WILD-TYPE                        19   205
D474V13, multiclass
                                  clus
vv                                 MYH1 MUTATED MYH1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              9
  BLACK OR AFRICAN AMERICAN                   3             19
  WHITE                                      21            205
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(475) Variable = PHF3 MUTATION ANALYSIS
D475V1, survival
                sevent
clus2              0   1
  PHF3 MUTATED    20   3
  PHF3 WILD-TYPE 358  90
  PHF3 MUTATED PHF3 WILD-TYPE 
            23            448 
  PHF3 MUTATED PHF3 WILD-TYPE 
             3             90 
$`PHF3 MUTATED`
TCGA-A6-5660 TCGA-A6-6142 TCGA-A6-6781 TCGA-AA-3510 TCGA-AA-3710 TCGA-AA-3947 
       29.19        25.08        19.66        63.98        26.99        33.01 
TCGA-AA-3966 TCGA-AA-A00A TCGA-AA-A00N TCGA-AA-A010 TCGA-AD-5900 TCGA-AU-6004 
        2.01        38.04         4.01        34.98         0.07        27.09 
TCGA-AY-6197 TCGA-CA-5797 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4948 TCGA-CM-6169 
       21.44         3.29        12.76        10.06       148.01        13.02 
TCGA-D5-6541 TCGA-DM-A28F TCGA-AG-A002 TCGA-AH-6549 TCGA-F5-6813 
       15.58        35.97        20.98        17.49         0.69 

$`PHF3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6648 
       22.06        32.71        27.09        22.52         8.38        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 
       20.28         7.04         3.02         1.02        35.01         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 
       18.05        31.00         2.01        12.99        24.00        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 
       24.00         2.01        20.98        34.03        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
       40.96        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       16.31         0.95        33.01        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-6715 
        3.19         1.61        12.69         3.06         3.25         0.07 
TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       12.20        14.30        17.56        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6170 
       29.03        16.04        21.99        14.99        12.99        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
      117.11        38.56         1.45         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66        55.76        26.43 

  PHF3 MUTATED PHF3 WILD-TYPE 
          0.07           0.00 
  PHF3 MUTATED PHF3 WILD-TYPE 
        148.01         140.38 
  PHF3 MUTATED PHF3 WILD-TYPE 
        20.980         20.155 
[1] "0.1 - 148.0 (21.0)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.4"
D475V2, continuous
D475V3, binary
                cls
clus               0   1
  PHF3 MUTATED    23   3
  PHF3 WILD-TYPE 343 116
[1] "tbl2"
                cls
clus             [,1] [,2]
  PHF3 MUTATED     23    3
  PHF3 WILD-TYPE  343  116
        clus
vv       PHF3 MUTATED PHF3 WILD-TYPE
  COLON            23            343
  RECTUM            3            116
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PHF3 MUTATED         3        0        2         9         3         0
  PHF3 WILD-TYPE      88        1       30       129         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PHF3 MUTATED           2          0          1          3        1         1
  PHF3 WILD-TYPE        22         11         58         39       47        17
                vv
clus             STAGE IVB
  PHF3 MUTATED           0
  PHF3 WILD-TYPE         1
D475V4, multiclass
            clus
vv           PHF3 MUTATED PHF3 WILD-TYPE
  STAGE I               3             88
  STAGE IA              0              1
  STAGE II              2             30
  STAGE IIA             9            129
  STAGE IIB             3              7
  STAGE IIC             0              1
  STAGE III             2             22
  STAGE IIIA            0             11
  STAGE IIIB            1             58
  STAGE IIIC            3             39
  STAGE IV              1             47
  STAGE IVA             1             17
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  PHF3 MUTATED     0   3  17   6
  PHF3 WILD-TYPE  17  89 312  44
D475V5, multiclass
    clus
vv   PHF3 MUTATED PHF3 WILD-TYPE
  T1            0             17
  T2            3             89
  T3           17            312
  T4            6             44
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  PHF3 MUTATED    17   4   4
  PHF3 WILD-TYPE 270 109  83
D475V6, multiclass
    clus
vv   PHF3 MUTATED PHF3 WILD-TYPE
  N0           17            270
  N1            4            109
  N2            4             83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D475V7, binary
                cls
clus               0   1
  PHF3 MUTATED    20   2
  PHF3 WILD-TYPE 355  63
[1] "tbl2"
                cls
clus             [,1] [,2]
  PHF3 MUTATED     20    2
  PHF3 WILD-TYPE  355   63
   clus
vv  PHF3 MUTATED PHF3 WILD-TYPE
  0           20            355
  1            2             63
[1] 2 2
[1] FALSE
D475V8, binary
                cls
clus               0   1
  PHF3 MUTATED     9  17
  PHF3 WILD-TYPE 216 247
[1] "tbl2"
                cls
clus             [,1] [,2]
  PHF3 MUTATED      9   17
  PHF3 WILD-TYPE  216  247
        clus
vv       PHF3 MUTATED PHF3 WILD-TYPE
  FEMALE            9            216
  MALE             17            247
[1] 2 2
[1] FALSE
D475V9, binary
                cls
clus               0   1
  PHF3 MUTATED    17   0
  PHF3 WILD-TYPE 333  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  PHF3 MUTATED     17    0
  PHF3 WILD-TYPE  333   22
     clus
vv    PHF3 MUTATED PHF3 WILD-TYPE
  NO            17            333
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PHF3 MUTATED                     17                             6
  PHF3 WILD-TYPE                  298                            41
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PHF3 MUTATED                       3                              0
  PHF3 WILD-TYPE                   103                             10
D475V10, multiclass
                                clus
vv                               PHF3 MUTATED PHF3 WILD-TYPE
  COLON ADENOCARCINOMA                     17            298
  COLON MUCINOUS ADENOCARCINOMA             6             41
  RECTAL ADENOCARCINOMA                     3            103
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  PHF3 MUTATED    18   0   1   3
  PHF3 WILD-TYPE 327   4  30  22
D475V11, multiclass
    clus
vv   PHF3 MUTATED PHF3 WILD-TYPE
  R0           18            327
  R1            0              4
  R2            1             30
  RX            3             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D475V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PHF3 MUTATED                                  0     3
  PHF3 WILD-TYPE                                1     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  PHF3 MUTATED                           2    10
  PHF3 WILD-TYPE                        20   216
D475V13, multiclass
                                  clus
vv                                 PHF3 MUTATED PHF3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       3              8
  BLACK OR AFRICAN AMERICAN                   2             20
  WHITE                                      10            216
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(476) Variable = PLCB2 MUTATION ANALYSIS
D476V1, survival
                 sevent
clus2               0   1
  PLCB2 MUTATED     6   4
  PLCB2 WILD-TYPE 372  89
  PLCB2 MUTATED PLCB2 WILD-TYPE 
             10             461 
  PLCB2 MUTATED PLCB2 WILD-TYPE 
              4              89 
$`PLCB2 MUTATED`
TCGA-AA-3672 TCGA-AA-3949 TCGA-AA-3977 TCGA-AZ-4315 TCGA-AZ-6608 TCGA-CK-5914 
        0.92        26.01        25.02        58.39         1.61         9.99 
TCGA-D5-6536 TCGA-DM-A1D6 TCGA-DM-A1DB TCGA-AF-5654 
       17.85        49.91        44.32        16.83 

$`PLCB2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
        6.05         6.97        54.02         2.01        14.01        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-3952 
        2.01        12.99        24.00        33.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       51.32        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       15.12         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A1HB 
       13.32        12.59       140.38         7.50       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-6136 
       13.55        19.10        34.49        10.39        14.50        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  PLCB2 MUTATED PLCB2 WILD-TYPE 
           0.92            0.00 
  PLCB2 MUTATED PLCB2 WILD-TYPE 
          58.39          148.01 
  PLCB2 MUTATED PLCB2 WILD-TYPE 
         21.435          20.190 
[1] "0.9 - 58.4 (21.4)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "2"  
D476V2, continuous
D476V3, binary
                 cls
clus                0   1
  PLCB2 MUTATED     9   1
  PLCB2 WILD-TYPE 357 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PLCB2 MUTATED      9    1
  PLCB2 WILD-TYPE  357  118
        clus
vv       PLCB2 MUTATED PLCB2 WILD-TYPE
  COLON              9             357
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PLCB2 MUTATED         1        0        0         4         0         0
  PLCB2 WILD-TYPE      90        1       32       134        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PLCB2 MUTATED           1          1          2          0        0         0
  PLCB2 WILD-TYPE        23         10         57         42       48        18
                 vv
clus              STAGE IVB
  PLCB2 MUTATED           0
  PLCB2 WILD-TYPE         1
D476V4, multiclass
            clus
vv           PLCB2 MUTATED PLCB2 WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              4             134
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             1              10
  STAGE IIIB             2              57
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PLCB2 MUTATED     0   3   7   0
  PLCB2 WILD-TYPE  17  89 322  50
D476V5, multiclass
    clus
vv   PLCB2 MUTATED PLCB2 WILD-TYPE
  T1             0              17
  T2             3              89
  T3             7             322
  T4             0              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  PLCB2 MUTATED     6   4   0
  PLCB2 WILD-TYPE 281 109  87
D476V6, multiclass
    clus
vv   PLCB2 MUTATED PLCB2 WILD-TYPE
  N0             6             281
  N1             4             109
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D476V7, binary
                 cls
clus                0   1
  PLCB2 MUTATED     8   0
  PLCB2 WILD-TYPE 367  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PLCB2 MUTATED      8    0
  PLCB2 WILD-TYPE  367   65
   clus
vv  PLCB2 MUTATED PLCB2 WILD-TYPE
  0             8             367
  1             0              65
[1] 2 2
[1] FALSE
D476V8, binary
                 cls
clus                0   1
  PLCB2 MUTATED     4   6
  PLCB2 WILD-TYPE 221 258
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PLCB2 MUTATED      4    6
  PLCB2 WILD-TYPE  221  258
        clus
vv       PLCB2 MUTATED PLCB2 WILD-TYPE
  FEMALE             4             221
  MALE               6             258
[1] 2 2
[1] FALSE
D476V9, binary
                 cls
clus                0   1
  PLCB2 MUTATED     7   0
  PLCB2 WILD-TYPE 343  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PLCB2 MUTATED      7    0
  PLCB2 WILD-TYPE  343   22
     clus
vv    PLCB2 MUTATED PLCB2 WILD-TYPE
  NO              7             343
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PLCB2 MUTATED                      7                             2
  PLCB2 WILD-TYPE                  308                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PLCB2 MUTATED                       1                              0
  PLCB2 WILD-TYPE                   105                             10
D476V10, multiclass
                                clus
vv                               PLCB2 MUTATED PLCB2 WILD-TYPE
  COLON ADENOCARCINOMA                       7             308
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  PLCB2 MUTATED     5   0   0   1
  PLCB2 WILD-TYPE 340   4  31  24
D476V11, multiclass
    clus
vv   PLCB2 MUTATED PLCB2 WILD-TYPE
  R0             5             340
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D476V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PLCB2 MUTATED                                  0     0
  PLCB2 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PLCB2 MUTATED                           0     7
  PLCB2 WILD-TYPE                        22   219
D476V13, multiclass
                                  clus
vv                                 PLCB2 MUTATED PLCB2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        7             219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(477) Variable = PTPRD MUTATION ANALYSIS
D477V1, survival
                 sevent
clus2               0   1
  PTPRD MUTATED    29   7
  PTPRD WILD-TYPE 349  86
  PTPRD MUTATED PTPRD WILD-TYPE 
             36             435 
  PTPRD MUTATED PTPRD WILD-TYPE 
              7              86 
$`PTPRD MUTATED`
TCGA-A6-2677 TCGA-A6-5659 TCGA-A6-5660 TCGA-AA-3660 TCGA-AA-3811 TCGA-AA-3947 
       24.33        30.44        29.19        78.08        10.06        33.01 
TCGA-AA-3966 TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01P TCGA-AZ-5403 
        2.01        25.02         4.01        34.98        38.07        62.79 
TCGA-AZ-5407 TCGA-CA-6717 TCGA-CK-5912 TCGA-CK-5913 TCGA-CM-4743 TCGA-CM-4752 
       88.21        12.76        49.08        51.32        23.05        13.02 
TCGA-CM-5344 TCGA-CM-5860 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6171 TCGA-CM-6674 
       22.03        32.02        12.00         2.96        14.04        12.95 
TCGA-D5-5539 TCGA-D5-5540 TCGA-DM-A28E TCGA-DM-A28K TCGA-G4-6304 TCGA-G4-6588 
       19.59        56.09       119.93        98.24        53.62        26.17 
TCGA-AF-6136 TCGA-AG-3881 TCGA-AG-A002 TCGA-DC-5337 TCGA-DY-A1DG TCGA-EI-6508 
       15.39        19.04        20.98        15.02        51.48        20.91 

$`PTPRD WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        42.90        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 
       31.63        33.53        23.61        22.09        22.06        32.71 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       27.09        22.52         8.38        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       26.99        19.04        19.04        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 
       18.05        31.00         2.01        12.99        24.00        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 
       24.00         2.01        20.98        34.03        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-6598 
       58.39         1.41         5.13       106.75        22.36        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07        12.20        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       85.45        15.62         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-5341 TCGA-CM-5348 
      124.27        20.02        37.02        25.02        29.06        22.98 
TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       30.08        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
       15.02        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       13.02        15.02        11.01        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5541 
       11.01        10.06        12.03        45.40        12.26        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28F TCGA-DM-A28G 
      135.65       139.17         6.12        81.37        35.97        60.79 
TCGA-DM-A28H TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
      117.07         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       22.09        13.78        35.80        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       10.39        14.50        16.83        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
        0.99        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6510 
       24.13        32.61         0.49        20.55        19.96        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  PTPRD MUTATED PTPRD WILD-TYPE 
           2.01            0.00 
  PTPRD MUTATED PTPRD WILD-TYPE 
         119.93          148.01 
  PTPRD MUTATED PTPRD WILD-TYPE 
         24.675          19.990 
[1] "2.0 - 119.9 (24.7)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.3"
D477V2, continuous
D477V3, binary
                 cls
clus                0   1
  PTPRD MUTATED    32   6
  PTPRD WILD-TYPE 334 113
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPRD MUTATED     32    6
  PTPRD WILD-TYPE  334  113
        clus
vv       PTPRD MUTATED PTPRD WILD-TYPE
  COLON             32             334
  RECTUM             6             113
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PTPRD MUTATED         7        0        2        13         4         0
  PTPRD WILD-TYPE      84        1       30       125         6         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PTPRD MUTATED           2          1          4          3        0         1
  PTPRD WILD-TYPE        22         10         55         39       48        17
                 vv
clus              STAGE IVB
  PTPRD MUTATED           0
  PTPRD WILD-TYPE         1
D477V4, multiclass
            clus
vv           PTPRD MUTATED PTPRD WILD-TYPE
  STAGE I                7              84
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA             13             125
  STAGE IIB              4               6
  STAGE IIC              0               1
  STAGE III              2              22
  STAGE IIIA             1              10
  STAGE IIIB             4              55
  STAGE IIIC             3              39
  STAGE IV               0              48
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PTPRD MUTATED     3   5  26   4
  PTPRD WILD-TYPE  14  87 303  46
D477V5, multiclass
    clus
vv   PTPRD MUTATED PTPRD WILD-TYPE
  T1             3              14
  T2             5              87
  T3            26             303
  T4             4              46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  PTPRD MUTATED    27   7   4
  PTPRD WILD-TYPE 260 106  83
D477V6, multiclass
    clus
vv   PTPRD MUTATED PTPRD WILD-TYPE
  N0            27             260
  N1             7             106
  N2             4              83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D477V7, binary
                 cls
clus                0   1
  PTPRD MUTATED    31   1
  PTPRD WILD-TYPE 344  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPRD MUTATED     31    1
  PTPRD WILD-TYPE  344   64
   clus
vv  PTPRD MUTATED PTPRD WILD-TYPE
  0            31             344
  1             1              64
[1] 2 2
[1] FALSE
D477V8, binary
                 cls
clus                0   1
  PTPRD MUTATED    19  19
  PTPRD WILD-TYPE 206 245
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPRD MUTATED     19   19
  PTPRD WILD-TYPE  206  245
        clus
vv       PTPRD MUTATED PTPRD WILD-TYPE
  FEMALE            19             206
  MALE              19             245
[1] 2 2
[1] FALSE
D477V9, binary
                 cls
clus                0   1
  PTPRD MUTATED    30   1
  PTPRD WILD-TYPE 320  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPRD MUTATED     30    1
  PTPRD WILD-TYPE  320   21
     clus
vv    PTPRD MUTATED PTPRD WILD-TYPE
  NO             30             320
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PTPRD MUTATED                     24                             8
  PTPRD WILD-TYPE                  291                            39
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PTPRD MUTATED                       5                              0
  PTPRD WILD-TYPE                   101                             10
D477V10, multiclass
                                clus
vv                               PTPRD MUTATED PTPRD WILD-TYPE
  COLON ADENOCARCINOMA                      24             291
  COLON MUCINOUS ADENOCARCINOMA              8              39
  RECTAL ADENOCARCINOMA                      5             101
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  PTPRD MUTATED    25   0   0   3
  PTPRD WILD-TYPE 320   4  31  22
D477V11, multiclass
    clus
vv   PTPRD MUTATED PTPRD WILD-TYPE
  R0            25             320
  R1             0               4
  R2             0              31
  RX             3              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D477V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PTPRD MUTATED                                  0     1
  PTPRD WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PTPRD MUTATED                           2    24
  PTPRD WILD-TYPE                        20   202
D477V13, multiclass
                                  clus
vv                                 PTPRD MUTATED PTPRD WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    2              20
  WHITE                                       24             202
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(478) Variable = CSMD3 MUTATION ANALYSIS
D478V1, survival
                 sevent
clus2               0   1
  CSMD3 MUTATED    85  20
  CSMD3 WILD-TYPE 293  73
  CSMD3 MUTATED CSMD3 WILD-TYPE 
            105             366 
  CSMD3 MUTATED CSMD3 WILD-TYPE 
             20              73 
$`CSMD3 MUTATED`
TCGA-A6-2676 TCGA-A6-3809 TCGA-A6-5660 TCGA-A6-6137 TCGA-A6-6141 TCGA-A6-6653 
       42.90        32.75        29.19        27.09         8.38        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3511 
       23.87        20.12        19.66         3.02        63.98         6.97 
TCGA-AA-3516 TCGA-AA-3525 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3660 TCGA-AA-3692 
       13.02         8.05        17.95        29.95        78.08        36.00 
TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3821 TCGA-AA-3861 TCGA-AA-3950 
       85.05        19.04        19.04         1.02        30.05        24.00 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3973 TCGA-AA-3977 TCGA-AA-A00E TCGA-AA-A00J 
        2.01        21.99        13.05        25.02        30.02        18.05 
TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01Q TCGA-AA-A01Z TCGA-AD-6889 TCGA-AD-6895 
        4.01        34.98         1.02        37.02        56.55         0.72 
TCGA-AY-5543 TCGA-AZ-4315 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6603 
       33.01        58.39        88.21         6.77       100.01        29.56 
TCGA-CA-5254 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.69         3.29         0.07        12.20        12.76        10.06 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-5916 TCGA-CM-4744 TCGA-CM-4752 TCGA-CM-5348 
       17.56       148.01        21.14        20.02        13.02        22.98 
TCGA-CM-5860 TCGA-CM-6167 TCGA-CM-6171 TCGA-CM-6674 TCGA-D5-6533 TCGA-D5-6535 
       32.02        14.99        14.04        12.95         1.32        15.12 
TCGA-D5-6540 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A1D0 
       16.14        11.64         4.80        10.26       119.70       130.65 
TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A285 TCGA-DM-A28H TCGA-DM-A28K 
       12.59         7.50        44.32         6.12       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6807 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6303 TCGA-G4-6304 
        8.61        16.24        47.41        35.31        65.85        53.62 
TCGA-G4-6307 TCGA-G4-6317 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6626 TCGA-G4-6628 
       55.04        36.00        35.80        26.17        46.75        79.69 
TCGA-AF-2693 TCGA-AF-6655 TCGA-AG-3731 TCGA-AG-3892 TCGA-AG-3898 TCGA-AG-4007 
       19.10        20.02        37.02        13.02        48.03         1.02 
TCGA-AG-A002 TCGA-AG-A011 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A02N TCGA-AH-6549 
       20.98        37.02        12.00        70.03        61.97        17.49 
TCGA-CI-6624 TCGA-DC-5337 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-EI-6506 
        4.73        15.02         5.03       126.44        41.36        20.55 
TCGA-F5-6464 TCGA-F5-6702 TCGA-G5-6641 
        9.96        28.57        26.43 

$`CSMD3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5657 
       34.65        33.34        36.53        14.53        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 
       30.44        33.53        23.61        22.09        22.06        32.71 
TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 
       22.52        25.08        25.18        24.16        21.76        24.69 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3514 TCGA-AA-3517 
       20.28         7.04         1.02        35.01         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3526 
        1.02         9.07        24.03        37.05        36.03        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       24.00        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       61.02         6.05         6.97        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
       37.05        19.00         5.03        26.99        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
       33.04         0.99        25.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       31.07        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3972 
       26.01         2.01        20.98        34.03        16.08        50.99 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00F 
        7.96        27.02        13.94        38.04        19.00        34.03 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        31.00        38.07        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       35.01        26.01        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6899 
       40.96         0.07        21.37        15.52         0.79         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
       16.31         0.95        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6605 
      106.75        22.36        62.79        49.41        12.10         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-6719 
       11.74         3.19         1.61         3.06         3.25        14.30 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 
       85.45        15.62        49.08        51.32         9.99        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-5341 
        1.91       124.27        23.05        37.02        25.02        29.06 
TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       22.03        30.08        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6675 
       21.99        12.99        13.02        15.02        11.01        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 
       43.27        17.85         4.80        17.13        12.49        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-DM-A0XD TCGA-DM-A0XF 
        9.44         1.51        12.00        11.38        24.43        38.20 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A1HA TCGA-DM-A1HB 
       92.75        49.91        13.32       140.38       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-F4-6460 
      139.17        81.37       119.93        35.97        60.79        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6306 
       33.67        13.25         0.53       133.18        74.56        44.68 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6625 
       85.48        63.62        61.91        22.09        13.78        91.79 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3913 
       24.13        39.48        43.04        13.55        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       14.50        16.83        15.39        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        7.99         0.99        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 
       19.99         1.02        17.95        36.95        17.03        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
       14.01         1.02        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       14.04        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
       15.95        36.03         9.07        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
        1.94        38.96        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
        1.45         0.69         0.72         6.05        33.17         6.97 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
       78.12         7.17         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DT-5265 TCGA-DY-A1DD TCGA-DY-A1DF 
       19.99         5.95         4.01         5.29        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       51.48        32.61         0.49        19.96        20.91        18.28 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       49.51        31.30        32.19         0.66         0.69        55.76 

  CSMD3 MUTATED CSMD3 WILD-TYPE 
           0.07            0.00 
  CSMD3 MUTATED CSMD3 WILD-TYPE 
         148.01          140.38 
  CSMD3 MUTATED CSMD3 WILD-TYPE 
          20.98           20.02 
[1] "0.1 - 148.0 (21.0)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1.3"
D478V2, continuous
D478V3, binary
                 cls
clus                0   1
  CSMD3 MUTATED    86  21
  CSMD3 WILD-TYPE 280  98
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CSMD3 MUTATED     86   21
  CSMD3 WILD-TYPE  280   98
        clus
vv       CSMD3 MUTATED CSMD3 WILD-TYPE
  COLON             86             280
  RECTUM            21              98
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CSMD3 MUTATED        17        0       11        34         5         0
  CSMD3 WILD-TYPE      74        1       21       104         5         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CSMD3 MUTATED           3          2         13          8        8         2
  CSMD3 WILD-TYPE        21          9         46         34       40        16
                 vv
clus              STAGE IVB
  CSMD3 MUTATED           0
  CSMD3 WILD-TYPE         1
D478V4, multiclass
            clus
vv           CSMD3 MUTATED CSMD3 WILD-TYPE
  STAGE I               17              74
  STAGE IA               0               1
  STAGE II              11              21
  STAGE IIA             34             104
  STAGE IIB              5               5
  STAGE IIC              0               1
  STAGE III              3              21
  STAGE IIIA             2               9
  STAGE IIIB            13              46
  STAGE IIIC             8              34
  STAGE IV               8              40
  STAGE IVA              2              16
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CSMD3 MUTATED     5  16  73  14
  CSMD3 WILD-TYPE  12  76 256  36
D478V5, multiclass
    clus
vv   CSMD3 MUTATED CSMD3 WILD-TYPE
  T1             5              12
  T2            16              76
  T3            73             256
  T4            14              36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  CSMD3 MUTATED    71  24  12
  CSMD3 WILD-TYPE 216  89  75
D478V6, multiclass
    clus
vv   CSMD3 MUTATED CSMD3 WILD-TYPE
  N0            71             216
  N1            24              89
  N2            12              75
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D478V7, binary
                 cls
clus                0   1
  CSMD3 MUTATED    86  10
  CSMD3 WILD-TYPE 289  55
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CSMD3 MUTATED     86   10
  CSMD3 WILD-TYPE  289   55
   clus
vv  CSMD3 MUTATED CSMD3 WILD-TYPE
  0            86             289
  1            10              55
[1] 2 2
[1] FALSE
D478V8, binary
                 cls
clus                0   1
  CSMD3 MUTATED    52  56
  CSMD3 WILD-TYPE 173 208
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CSMD3 MUTATED     52   56
  CSMD3 WILD-TYPE  173  208
        clus
vv       CSMD3 MUTATED CSMD3 WILD-TYPE
  FEMALE            52             173
  MALE              56             208
[1] 2 2
[1] FALSE
D478V9, binary
                 cls
clus                0   1
  CSMD3 MUTATED    79   2
  CSMD3 WILD-TYPE 271  20
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CSMD3 MUTATED     79    2
  CSMD3 WILD-TYPE  271   20
     clus
vv    CSMD3 MUTATED CSMD3 WILD-TYPE
  NO             79             271
  YES             2              20
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CSMD3 MUTATED                     68                            18
  CSMD3 WILD-TYPE                  247                            29
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CSMD3 MUTATED                      20                              1
  CSMD3 WILD-TYPE                    86                              9
D478V10, multiclass
                                clus
vv                               CSMD3 MUTATED CSMD3 WILD-TYPE
  COLON ADENOCARCINOMA                      68             247
  COLON MUCINOUS ADENOCARCINOMA             18              29
  RECTAL ADENOCARCINOMA                     20              86
  RECTAL MUCINOUS ADENOCARCINOMA             1               9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  CSMD3 MUTATED    67   0   5   9
  CSMD3 WILD-TYPE 278   4  26  16
D478V11, multiclass
    clus
vv   CSMD3 MUTATED CSMD3 WILD-TYPE
  R0            67             278
  R1             0               4
  R2             5              26
  RX             9              16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D478V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CSMD3 MUTATED                                  0     7
  CSMD3 WILD-TYPE                                1     4
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CSMD3 MUTATED                           5    59
  CSMD3 WILD-TYPE                        17   167
D478V13, multiclass
                                  clus
vv                                 CSMD3 MUTATED CSMD3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        7               4
  BLACK OR AFRICAN AMERICAN                    5              17
  WHITE                                       59             167
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(479) Variable = USH2A MUTATION ANALYSIS
D479V1, survival
                 sevent
clus2               0   1
  USH2A MUTATED    68  16
  USH2A WILD-TYPE 310  77
  USH2A MUTATED USH2A WILD-TYPE 
             84             387 
  USH2A MUTATED USH2A WILD-TYPE 
             16              77 
$`USH2A MUTATED`
TCGA-A6-5660 TCGA-A6-6141 TCGA-A6-6649 TCGA-A6-6654 TCGA-A6-6781 TCGA-AA-3489 
       29.19         8.38        24.16        23.87        19.66         7.04 
TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3560 
        3.02        63.98         6.97         8.05        19.07        19.99 
TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3672 TCGA-AA-3710 TCGA-AA-3715 
       61.02         6.05         6.97         0.92        26.99        19.04 
TCGA-AA-3821 TCGA-AA-3846 TCGA-AA-3855 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3877 
        1.02        17.03        32.05        30.05        53.00        31.00 
TCGA-AA-3952 TCGA-AA-3966 TCGA-AA-3977 TCGA-AA-A004 TCGA-AA-A00N TCGA-AA-A00R 
        2.01         2.01        25.02        13.94         4.01         0.99 
TCGA-AA-A00U TCGA-AA-A010 TCGA-AA-A01Q TCGA-AA-A02H TCGA-AD-6895 TCGA-AD-6964 
       17.03        34.98         1.02         2.01         0.72        10.88 
TCGA-AZ-4315 TCGA-AZ-5407 TCGA-AZ-6600 TCGA-AZ-6607 TCGA-CA-6717 TCGA-CA-6718 
       58.39        88.21        12.10         3.19        12.76        10.06 
TCGA-CK-4952 TCGA-CK-5916 TCGA-CK-6751 TCGA-CM-4746 TCGA-CM-5349 TCGA-CM-5861 
       15.62        21.14       124.27        37.02        30.08        15.02 
TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6164 TCGA-CM-6171 TCGA-D5-5538 TCGA-D5-5539 
       15.02        15.02        29.03        14.04        12.26        19.59 
TCGA-D5-5540 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6541 
       56.09        15.12        17.85         4.80        17.13        15.58 
TCGA-DM-A1D8 TCGA-DM-A1HB TCGA-DM-A282 TCGA-F4-6570 TCGA-F4-6704 TCGA-F4-6807 
       12.59       135.65       139.17         6.18         1.55        16.24 
TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6315 TCGA-G4-6586 TCGA-G4-6628 TCGA-AF-2693 
       47.41       133.18        61.91        35.80        79.69        19.10 
TCGA-AF-4110 TCGA-AG-3892 TCGA-AG-3896 TCGA-AG-A002 TCGA-AH-6547 TCGA-CI-6622 
       14.50        13.02         1.02        20.98         1.45         6.97 
TCGA-CI-6624 TCGA-DY-A1DC TCGA-DY-A1DG TCGA-EF-5830 TCGA-EI-6506 TCGA-G5-6235 
        4.73        41.36        51.48         0.49        20.55        55.76 

$`USH2A WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 
       22.06        32.71        27.09        22.52        25.08        25.18 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3496 
       21.76        24.69        24.39        20.12        20.28         1.02 
TCGA-AA-3502 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
       35.01         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       24.03        37.05        36.03         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3664 
       23.01        20.98        13.94        19.99        78.08        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
        2.01        14.01        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3856 
       10.06         0.00        33.07         0.00        36.03         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       31.07        31.07        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       18.05         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       24.00        20.98        34.03        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
       19.07         7.96        27.02        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        31.00        38.07        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
       16.31         0.95        33.01        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 
        5.13       106.75        22.36        62.79        49.41         6.77 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5254 
      100.01        29.56         5.23        11.74         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 
        3.06         3.25         3.29         0.07        12.20        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
       17.56       148.01        85.45        49.08        51.32         9.99 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4752 
       82.95         1.91        23.05        20.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 
       29.06        22.03        22.98        32.02         5.03        15.02 
TCGA-CM-5868 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       17.03        12.00         2.96        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       12.99        13.02        15.02        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6539 
       55.92        20.19        18.25         1.32        43.27        12.49 
TCGA-D5-6540 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       16.14         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       92.75        49.91        13.32       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      131.51         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 
      117.07        98.24         8.61        31.96        35.74        47.87 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6856 
       34.42        41.42        33.67        13.25         0.53        35.31 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 
       63.62        36.00        22.09        13.78        26.17        91.79 
TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 
       46.75        24.13        39.48        43.04        13.55        34.49 
TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       10.39        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       17.03        35.01        14.01        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
       38.56        17.49         0.69         0.72         6.05        33.17 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EI-6507 TCGA-EI-6508 
      126.44        57.24        24.13        32.61        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6641 
        0.66         0.69        26.43 

  USH2A MUTATED USH2A WILD-TYPE 
           0.49            0.00 
  USH2A MUTATED USH2A WILD-TYPE 
         139.17          148.01 
  USH2A MUTATED USH2A WILD-TYPE 
         16.635          21.990 
[1] "0.5 - 139.2 (16.6)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1"  
D479V2, continuous
D479V3, binary
                 cls
clus                0   1
  USH2A MUTATED    74  12
  USH2A WILD-TYPE 292 107
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USH2A MUTATED     74   12
  USH2A WILD-TYPE  292  107
        clus
vv       USH2A MUTATED USH2A WILD-TYPE
  COLON             74             292
  RECTUM            12             107
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  USH2A MUTATED        18        0        9        22         4         0
  USH2A WILD-TYPE      73        1       23       116         6         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  USH2A MUTATED           3          1         11          8        5         2
  USH2A WILD-TYPE        21         10         48         34       43        16
                 vv
clus              STAGE IVB
  USH2A MUTATED           0
  USH2A WILD-TYPE         1
D479V4, multiclass
            clus
vv           USH2A MUTATED USH2A WILD-TYPE
  STAGE I               18              73
  STAGE IA               0               1
  STAGE II               9              23
  STAGE IIA             22             116
  STAGE IIB              4               6
  STAGE IIC              0               1
  STAGE III              3              21
  STAGE IIIA             1              10
  STAGE IIIB            11              48
  STAGE IIIC             8              34
  STAGE IV               5              43
  STAGE IVA              2              16
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  USH2A MUTATED     4  15  56  13
  USH2A WILD-TYPE  13  77 273  37
D479V5, multiclass
    clus
vv   USH2A MUTATED USH2A WILD-TYPE
  T1             4              13
  T2            15              77
  T3            56             273
  T4            13              37
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  USH2A MUTATED    55  19  14
  USH2A WILD-TYPE 232  94  73
D479V6, multiclass
    clus
vv   USH2A MUTATED USH2A WILD-TYPE
  N0            55             232
  N1            19              94
  N2            14              73
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D479V7, binary
                 cls
clus                0   1
  USH2A MUTATED    68   6
  USH2A WILD-TYPE 307  59
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USH2A MUTATED     68    6
  USH2A WILD-TYPE  307   59
   clus
vv  USH2A MUTATED USH2A WILD-TYPE
  0            68             307
  1             6              59
[1] 2 2
[1] FALSE
D479V8, binary
                 cls
clus                0   1
  USH2A MUTATED    40  48
  USH2A WILD-TYPE 185 216
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USH2A MUTATED     40   48
  USH2A WILD-TYPE  185  216
        clus
vv       USH2A MUTATED USH2A WILD-TYPE
  FEMALE            40             185
  MALE              48             216
[1] 2 2
[1] FALSE
D479V9, binary
                 cls
clus                0   1
  USH2A MUTATED    64   0
  USH2A WILD-TYPE 286  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USH2A MUTATED     64    0
  USH2A WILD-TYPE  286   22
     clus
vv    USH2A MUTATED USH2A WILD-TYPE
  NO             64             286
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  USH2A MUTATED                     62                            11
  USH2A WILD-TYPE                  253                            36
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  USH2A MUTATED                      12                              0
  USH2A WILD-TYPE                    94                             10
D479V10, multiclass
                                clus
vv                               USH2A MUTATED USH2A WILD-TYPE
  COLON ADENOCARCINOMA                      62             253
  COLON MUCINOUS ADENOCARCINOMA             11              36
  RECTAL ADENOCARCINOMA                     12              94
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  USH2A MUTATED    58   1   3   6
  USH2A WILD-TYPE 287   3  28  19
D479V11, multiclass
    clus
vv   USH2A MUTATED USH2A WILD-TYPE
  R0            58             287
  R1             1               3
  R2             3              28
  RX             6              19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D479V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  USH2A MUTATED                                  1     2
  USH2A WILD-TYPE                                0     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  USH2A MUTATED                           4    46
  USH2A WILD-TYPE                        18   180
D479V13, multiclass
                                  clus
vv                                 USH2A MUTATED USH2A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             1               0
  ASIAN                                        2               9
  BLACK OR AFRICAN AMERICAN                    4              18
  WHITE                                       46             180
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(480) Variable = MYEOV MUTATION ANALYSIS
D480V1, survival
                 sevent
clus2               0   1
  MYEOV MUTATED     7   0
  MYEOV WILD-TYPE 371  93
  MYEOV MUTATED MYEOV WILD-TYPE 
              7             464 
  MYEOV MUTATED MYEOV WILD-TYPE 
              0              93 
$`MYEOV MUTATED`
TCGA-A6-5661 TCGA-AA-A00E TCGA-AD-6889 TCGA-AU-6004 TCGA-D5-6923 TCGA-G4-6588 
       33.53        30.02        56.55        27.09        12.43        26.17 
TCGA-EF-5830 
        0.49 

$`MYEOV WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       38.04        19.00        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
        0.20        14.50        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       22.09        13.78        35.80        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
       32.61        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  MYEOV MUTATED MYEOV WILD-TYPE 
           0.49            0.00 
  MYEOV MUTATED MYEOV WILD-TYPE 
          56.55          148.01 
  MYEOV MUTATED MYEOV WILD-TYPE 
         27.090          20.085 
[1] "0.5 - 56.5 (27.1)"  "0.0 - 148.0 (20.1)"
[1] "hr="     "9100000"
D480V2, continuous
D480V3, binary
                 cls
clus                0   1
  MYEOV MUTATED     6   1
  MYEOV WILD-TYPE 360 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYEOV MUTATED      6    1
  MYEOV WILD-TYPE  360  118
        clus
vv       MYEOV MUTATED MYEOV WILD-TYPE
  COLON              6             360
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MYEOV MUTATED         2        0        0         4         1         0
  MYEOV WILD-TYPE      89        1       32       134         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MYEOV MUTATED           0          0          0          0        0         0
  MYEOV WILD-TYPE        24         11         59         42       48        18
                 vv
clus              STAGE IVB
  MYEOV MUTATED           0
  MYEOV WILD-TYPE         1
D480V4, multiclass
            clus
vv           MYEOV MUTATED MYEOV WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              4             134
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  MYEOV MUTATED     0   2   4   1
  MYEOV WILD-TYPE  17  90 325  49
D480V5, multiclass
    clus
vv   MYEOV MUTATED MYEOV WILD-TYPE
  T1             0              17
  T2             2              90
  T3             4             325
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  MYEOV MUTATED     7   0   0
  MYEOV WILD-TYPE 280 113  87
D480V6, multiclass
    clus
vv   MYEOV MUTATED MYEOV WILD-TYPE
  N0             7             280
  N1             0             113
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D480V7, binary
                 cls
clus                0   1
  MYEOV MUTATED     7   0
  MYEOV WILD-TYPE 368  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYEOV MUTATED      7    0
  MYEOV WILD-TYPE  368   65
   clus
vv  MYEOV MUTATED MYEOV WILD-TYPE
  0             7             368
  1             0              65
[1] 2 2
[1] FALSE
D480V8, binary
                 cls
clus                0   1
  MYEOV MUTATED     3   4
  MYEOV WILD-TYPE 222 260
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYEOV MUTATED      3    4
  MYEOV WILD-TYPE  222  260
        clus
vv       MYEOV MUTATED MYEOV WILD-TYPE
  FEMALE             3             222
  MALE               4             260
[1] 2 2
[1] FALSE
D480V9, binary
                 cls
clus                0   1
  MYEOV MUTATED     4   0
  MYEOV WILD-TYPE 346  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYEOV MUTATED      4    0
  MYEOV WILD-TYPE  346   22
     clus
vv    MYEOV MUTATED MYEOV WILD-TYPE
  NO              4             346
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MYEOV MUTATED                      6                             0
  MYEOV WILD-TYPE                  309                            47
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MYEOV MUTATED                       1                              0
  MYEOV WILD-TYPE                   105                             10
D480V10, multiclass
                                clus
vv                               MYEOV MUTATED MYEOV WILD-TYPE
  COLON ADENOCARCINOMA                       6             309
  COLON MUCINOUS ADENOCARCINOMA              0              47
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  MYEOV MUTATED     6   0   0   0
  MYEOV WILD-TYPE 339   4  31  25
D480V11, multiclass
    clus
vv   MYEOV MUTATED MYEOV WILD-TYPE
  R0             6             339
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D480V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MYEOV MUTATED                                  0     1
  MYEOV WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  MYEOV MUTATED                           1     4
  MYEOV WILD-TYPE                        21   222
D480V13, multiclass
                                  clus
vv                                 MYEOV MUTATED MYEOV WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        4             222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(481) Variable = BRE MUTATION ANALYSIS
D481V1, survival
               sevent
clus2             0   1
  BRE MUTATED     8   4
  BRE WILD-TYPE 370  89
  BRE MUTATED BRE WILD-TYPE 
           12           459 
  BRE MUTATED BRE WILD-TYPE 
            4            89 
$`BRE MUTATED`
TCGA-A6-2676 TCGA-A6-5665 TCGA-AA-3492 TCGA-AA-3815 TCGA-AZ-6598 TCGA-AZ-6606 
       42.90        22.06         3.02        33.04        49.41        11.74 
TCGA-CM-4746 TCGA-CM-4752 TCGA-CM-6677 TCGA-G4-6293 TCGA-AG-A025 TCGA-DC-5869 
       37.02        13.02        11.08       133.18        49.97         5.03 

$`BRE WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       19.66        20.28         7.04         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        88.21         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       20.02        25.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       12.95        13.05        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6303 
       13.25         0.53        47.41        35.31        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A026 
        9.07        12.00        70.03        64.01        10.98         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-6155 
        6.97         4.73        78.12         7.17        15.02        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  BRE MUTATED BRE WILD-TYPE 
         3.02          0.00 
  BRE MUTATED BRE WILD-TYPE 
       133.18        148.01 
  BRE MUTATED BRE WILD-TYPE 
        27.55         20.12 
[1] "3.0 - 133.2 (27.5)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.4"
D481V2, continuous
D481V3, binary
               cls
clus              0   1
  BRE MUTATED    10   2
  BRE WILD-TYPE 356 117
[1] "tbl2"
               cls
clus            [,1] [,2]
  BRE MUTATED     10    2
  BRE WILD-TYPE  356  117
        clus
vv       BRE MUTATED BRE WILD-TYPE
  COLON           10           356
  RECTUM           2           117
[1] 2 2
[1] FALSE
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  BRE MUTATED         2        0        2         4         1         0
  BRE WILD-TYPE      89        1       30       134         9         1
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  BRE MUTATED           1          0          1          0        1         0
  BRE WILD-TYPE        23         11         58         42       47        18
               vv
clus            STAGE IVB
  BRE MUTATED           0
  BRE WILD-TYPE         1
D481V4, multiclass
            clus
vv           BRE MUTATED BRE WILD-TYPE
  STAGE I              2            89
  STAGE IA             0             1
  STAGE II             2            30
  STAGE IIA            4           134
  STAGE IIB            1             9
  STAGE IIC            0             1
  STAGE III            1            23
  STAGE IIIA           0            11
  STAGE IIIB           1            58
  STAGE IIIC           0            42
  STAGE IV             1            47
  STAGE IVA            0            18
  STAGE IVB            0             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  BRE MUTATED     1   1   8   2
  BRE WILD-TYPE  16  91 321  48
D481V5, multiclass
    clus
vv   BRE MUTATED BRE WILD-TYPE
  T1           1            16
  T2           1            91
  T3           8           321
  T4           2            48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2
  BRE MUTATED     9   2   1
  BRE WILD-TYPE 278 111  86
D481V6, multiclass
    clus
vv   BRE MUTATED BRE WILD-TYPE
  N0           9           278
  N1           2           111
  N2           1            86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D481V7, binary
               cls
clus              0   1
  BRE MUTATED    10   1
  BRE WILD-TYPE 365  64
[1] "tbl2"
               cls
clus            [,1] [,2]
  BRE MUTATED     10    1
  BRE WILD-TYPE  365   64
   clus
vv  BRE MUTATED BRE WILD-TYPE
  0          10           365
  1           1            64
[1] 2 2
[1] FALSE
D481V8, binary
               cls
clus              0   1
  BRE MUTATED     9   3
  BRE WILD-TYPE 216 261
[1] "tbl2"
               cls
clus            [,1] [,2]
  BRE MUTATED      9    3
  BRE WILD-TYPE  216  261
        clus
vv       BRE MUTATED BRE WILD-TYPE
  FEMALE           9           216
  MALE             3           261
[1] 2 2
[1] FALSE
D481V9, binary
               cls
clus              0   1
  BRE MUTATED    10   0
  BRE WILD-TYPE 340  22
[1] "tbl2"
               cls
clus            [,1] [,2]
  BRE MUTATED     10    0
  BRE WILD-TYPE  340   22
     clus
vv    BRE MUTATED BRE WILD-TYPE
  NO           10           340
  YES           0            22
[1] 2 2
[1] FALSE
               vv
clus            COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  BRE MUTATED                     10                             0
  BRE WILD-TYPE                  305                            47
               vv
clus            RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  BRE MUTATED                       2                              0
  BRE WILD-TYPE                   104                             10
D481V10, multiclass
                                clus
vv                               BRE MUTATED BRE WILD-TYPE
  COLON ADENOCARCINOMA                    10           305
  COLON MUCINOUS ADENOCARCINOMA            0            47
  RECTAL ADENOCARCINOMA                    2           104
  RECTAL MUCINOUS ADENOCARCINOMA           0            10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             R0  R1  R2  RX
  BRE MUTATED    10   0   0   0
  BRE WILD-TYPE 335   4  31  25
D481V11, multiclass
    clus
vv   BRE MUTATED BRE WILD-TYPE
  R0          10           335
  R1           0             4
  R2           0            31
  RX           0            25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D481V12, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  BRE MUTATED                                  0     0
  BRE WILD-TYPE                                1    11
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  BRE MUTATED                           3     6
  BRE WILD-TYPE                        19   220
D481V13, multiclass
                                  clus
vv                                 BRE MUTATED BRE WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      0            11
  BLACK OR AFRICAN AMERICAN                  3            19
  WHITE                                      6           220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(482) Variable = SCN3A MUTATION ANALYSIS
D482V1, survival
                 sevent
clus2               0   1
  SCN3A MUTATED    36  10
  SCN3A WILD-TYPE 342  83
  SCN3A MUTATED SCN3A WILD-TYPE 
             46             425 
  SCN3A MUTATED SCN3A WILD-TYPE 
             10              83 
$`SCN3A MUTATED`
TCGA-A6-2671 TCGA-A6-3809 TCGA-A6-5661 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6652 
       43.76        32.75        33.53        22.06        32.71        24.69 
TCGA-A6-6781 TCGA-AA-3510 TCGA-AA-3556 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3877 
       19.66        63.98        23.01        19.04        19.04        31.00 
TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A02F 
       33.01        24.00        25.02         4.01        34.98        39.98 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-CA-6717 
       17.82        58.39        62.79        49.41         6.77        12.76 
TCGA-CM-5344 TCGA-CM-6674 TCGA-CM-6678 TCGA-CM-6679 TCGA-D5-5541 TCGA-D5-6533 
       22.03        12.95        11.01        10.06        55.92         1.32 
TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6930 TCGA-D5-6931 TCGA-DM-A1D9 TCGA-DM-A1HB 
       15.12         4.80         1.51        12.00       140.38       135.65 
TCGA-F4-6459 TCGA-G4-6321 TCGA-G4-6323 TCGA-AG-A002 TCGA-AG-A02X TCGA-CI-6620 
        8.61        22.09        13.78        20.98        41.00        33.17 
TCGA-DC-6160 TCGA-DC-6682 TCGA-DY-A1DF TCGA-F5-6464 
       19.99         4.01        24.13         9.96 

$`SCN3A WILD-TYPE`
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       46.65        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5657 
       34.65        33.34        36.53        14.53        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-6137 TCGA-A6-6138 
       30.44        29.19        23.61        22.09        27.09        22.52 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6653 
        8.38        25.08        25.18        24.16        21.76        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       24.00        17.95        29.95        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       85.05        26.99        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3952 
       18.05         2.01        12.99        24.00        26.01         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       37.02        39.06        51.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AZ-4323 TCGA-AZ-4616 
       16.31         0.95        33.01        21.44         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
      106.75        22.36        88.21        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07        12.20        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5348 
       20.02        37.02        25.02        13.02        29.06        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6680 TCGA-D5-5537 
       11.01        13.05        11.08        11.08        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6534 
       12.26        19.59        56.09        20.19        18.25        43.27 
TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
       17.85        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       11.64         4.80        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
        7.50        44.32       131.51       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6460 
      119.93        35.97        60.79       117.07        98.24        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6586 TCGA-G4-6588 
       85.48        63.62        61.91        36.00        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
        1.94        38.96        61.97        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6622 
        1.45        17.49         0.69         0.72         6.05         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       27.95        10.98         5.95         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       41.36        57.24        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       19.96        20.91        18.28        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  SCN3A MUTATED SCN3A WILD-TYPE 
           1.32            0.00 
  SCN3A MUTATED SCN3A WILD-TYPE 
         140.38          148.01 
  SCN3A MUTATED SCN3A WILD-TYPE 
         22.075          20.020 
[1] "1.3 - 140.4 (22.1)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1"  
D482V2, continuous
D482V3, binary
                 cls
clus                0   1
  SCN3A MUTATED    42   7
  SCN3A WILD-TYPE 324 112
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SCN3A MUTATED     42    7
  SCN3A WILD-TYPE  324  112
        clus
vv       SCN3A MUTATED SCN3A WILD-TYPE
  COLON             42             324
  RECTUM             7             112
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SCN3A MUTATED         6        1        5        11         4         1
  SCN3A WILD-TYPE      85        0       27       127         6         0
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SCN3A MUTATED           2          0          8          4        3         3
  SCN3A WILD-TYPE        22         11         51         38       45        15
                 vv
clus              STAGE IVB
  SCN3A MUTATED           0
  SCN3A WILD-TYPE         1
D482V4, multiclass
            clus
vv           SCN3A MUTATED SCN3A WILD-TYPE
  STAGE I                6              85
  STAGE IA               1               0
  STAGE II               5              27
  STAGE IIA             11             127
  STAGE IIB              4               6
  STAGE IIC              1               0
  STAGE III              2              22
  STAGE IIIA             0              11
  STAGE IIIB             8              51
  STAGE IIIC             4              38
  STAGE IV               3              45
  STAGE IVA              3              15
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  SCN3A MUTATED     1   7  29  11
  SCN3A WILD-TYPE  16  85 300  39
D482V5, multiclass
    clus
vv   SCN3A MUTATED SCN3A WILD-TYPE
  T1             1              16
  T2             7              85
  T3            29             300
  T4            11              39
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  SCN3A MUTATED    32  11   6
  SCN3A WILD-TYPE 255 102  81
D482V6, multiclass
    clus
vv   SCN3A MUTATED SCN3A WILD-TYPE
  N0            32             255
  N1            11             102
  N2             6              81
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D482V7, binary
                 cls
clus                0   1
  SCN3A MUTATED    34   6
  SCN3A WILD-TYPE 341  59
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SCN3A MUTATED     34    6
  SCN3A WILD-TYPE  341   59
   clus
vv  SCN3A MUTATED SCN3A WILD-TYPE
  0            34             341
  1             6              59
[1] 2 2
[1] FALSE
D482V8, binary
                 cls
clus                0   1
  SCN3A MUTATED    22  27
  SCN3A WILD-TYPE 203 237
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SCN3A MUTATED     22   27
  SCN3A WILD-TYPE  203  237
        clus
vv       SCN3A MUTATED SCN3A WILD-TYPE
  FEMALE            22             203
  MALE              27             237
[1] 2 2
[1] FALSE
D482V9, binary
                 cls
clus                0   1
  SCN3A MUTATED    36   1
  SCN3A WILD-TYPE 314  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SCN3A MUTATED     36    1
  SCN3A WILD-TYPE  314   21
     clus
vv    SCN3A MUTATED SCN3A WILD-TYPE
  NO             36             314
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SCN3A MUTATED                     32                             8
  SCN3A WILD-TYPE                  283                            39
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SCN3A MUTATED                       7                              0
  SCN3A WILD-TYPE                    99                             10
D482V10, multiclass
                                clus
vv                               SCN3A MUTATED SCN3A WILD-TYPE
  COLON ADENOCARCINOMA                      32             283
  COLON MUCINOUS ADENOCARCINOMA              8              39
  RECTAL ADENOCARCINOMA                      7              99
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  SCN3A MUTATED    35   0   2   2
  SCN3A WILD-TYPE 310   4  29  23
D482V11, multiclass
    clus
vv   SCN3A MUTATED SCN3A WILD-TYPE
  R0            35             310
  R1             0               4
  R2             2              29
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D482V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SCN3A MUTATED                                  0     1
  SCN3A WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  SCN3A MUTATED                           4    28
  SCN3A WILD-TYPE                        18   198
D482V13, multiclass
                                  clus
vv                                 SCN3A MUTATED SCN3A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    4              18
  WHITE                                       28             198
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(483) Variable = FKTN MUTATION ANALYSIS
D483V1, survival
                sevent
clus2              0   1
  FKTN MUTATED     8   1
  FKTN WILD-TYPE 370  92
  FKTN MUTATED FKTN WILD-TYPE 
             9            462 
  FKTN MUTATED FKTN WILD-TYPE 
             1             92 
$`FKTN MUTATED`
TCGA-AA-3811 TCGA-AA-3950 TCGA-AA-A010 TCGA-AZ-4315 TCGA-D5-5540 TCGA-DM-A1HB 
       10.06        24.00        34.98        58.39        56.09       135.65 
TCGA-G4-6586 TCGA-AG-A002 TCGA-EI-6510 
       35.80        20.98        18.28 

$`FKTN WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       19.04        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 
        2.01        12.99        24.00        33.01        26.01         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       12.26        19.59        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
        7.50        44.32       131.51       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       13.78        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       20.55        19.96        20.91         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  FKTN MUTATED FKTN WILD-TYPE 
         10.06           0.00 
  FKTN MUTATED FKTN WILD-TYPE 
        135.65         148.01 
  FKTN MUTATED FKTN WILD-TYPE 
        34.980         20.035 
[1] "10.1 - 135.7 (35.0)" "0.0 - 148.0 (20.0)" 
[1] "hr=" "2.7"
D483V2, continuous
D483V3, binary
                cls
clus               0   1
  FKTN MUTATED     7   2
  FKTN WILD-TYPE 359 117
[1] "tbl2"
                cls
clus             [,1] [,2]
  FKTN MUTATED      7    2
  FKTN WILD-TYPE  359  117
        clus
vv       FKTN MUTATED FKTN WILD-TYPE
  COLON             7            359
  RECTUM            2            117
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FKTN MUTATED         1        0        0         4         1         0
  FKTN WILD-TYPE      90        1       32       134         9         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  FKTN MUTATED           1          0          1          0        0         1
  FKTN WILD-TYPE        23         11         58         42       48        17
                vv
clus             STAGE IVB
  FKTN MUTATED           0
  FKTN WILD-TYPE         1
D483V4, multiclass
            clus
vv           FKTN MUTATED FKTN WILD-TYPE
  STAGE I               1             90
  STAGE IA              0              1
  STAGE II              0             32
  STAGE IIA             4            134
  STAGE IIB             1              9
  STAGE IIC             0              1
  STAGE III             1             23
  STAGE IIIA            0             11
  STAGE IIIB            1             58
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             1             17
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  FKTN MUTATED     0   2   6   1
  FKTN WILD-TYPE  17  90 323  49
D483V5, multiclass
    clus
vv   FKTN MUTATED FKTN WILD-TYPE
  T1            0             17
  T2            2             90
  T3            6            323
  T4            1             49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  FKTN MUTATED     7   1   1
  FKTN WILD-TYPE 280 112  86
D483V6, multiclass
    clus
vv   FKTN MUTATED FKTN WILD-TYPE
  N0            7            280
  N1            1            112
  N2            1             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D483V7, binary
                cls
clus               0   1
  FKTN MUTATED     8   0
  FKTN WILD-TYPE 367  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  FKTN MUTATED      8    0
  FKTN WILD-TYPE  367   65
   clus
vv  FKTN MUTATED FKTN WILD-TYPE
  0            8            367
  1            0             65
[1] 2 2
[1] FALSE
D483V8, binary
                cls
clus               0   1
  FKTN MUTATED     5   4
  FKTN WILD-TYPE 220 260
[1] "tbl2"
                cls
clus             [,1] [,2]
  FKTN MUTATED      5    4
  FKTN WILD-TYPE  220  260
        clus
vv       FKTN MUTATED FKTN WILD-TYPE
  FEMALE            5            220
  MALE              4            260
[1] 2 2
[1] FALSE
D483V9, binary
                cls
clus               0   1
  FKTN MUTATED     8   0
  FKTN WILD-TYPE 342  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  FKTN MUTATED      8    0
  FKTN WILD-TYPE  342   22
     clus
vv    FKTN MUTATED FKTN WILD-TYPE
  NO             8            342
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  FKTN MUTATED                      5                             1
  FKTN WILD-TYPE                  310                            46
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  FKTN MUTATED                       2                              0
  FKTN WILD-TYPE                   104                             10
D483V10, multiclass
                                clus
vv                               FKTN MUTATED FKTN WILD-TYPE
  COLON ADENOCARCINOMA                      5            310
  COLON MUCINOUS ADENOCARCINOMA             1             46
  RECTAL ADENOCARCINOMA                     2            104
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  FKTN MUTATED     8   0   0   0
  FKTN WILD-TYPE 337   4  31  25
D483V11, multiclass
    clus
vv   FKTN MUTATED FKTN WILD-TYPE
  R0            8            337
  R1            0              4
  R2            0             31
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D483V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FKTN MUTATED                                  0     0
  FKTN WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  FKTN MUTATED                           0     5
  FKTN WILD-TYPE                        22   221
D483V13, multiclass
                                  clus
vv                                 FKTN MUTATED FKTN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       5            221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(484) Variable = MIER1 MUTATION ANALYSIS
D484V1, survival
                 sevent
clus2               0   1
  MIER1 MUTATED     7   1
  MIER1 WILD-TYPE 371  92
  MIER1 MUTATED MIER1 WILD-TYPE 
              8             463 
  MIER1 MUTATED MIER1 WILD-TYPE 
              1              92 
$`MIER1 MUTATED`
TCGA-A6-5659 TCGA-AA-A010 TCGA-CA-6717 TCGA-DM-A28E TCGA-DM-A28F TCGA-G4-6588 
       30.44        34.98        12.76       119.93        35.97        26.17 
TCGA-AG-A002 TCGA-AH-6549 
       20.98        17.49 

$`MIER1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.20        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
      139.17         6.12        81.37        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       22.09        13.78        35.80        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 
       41.00        38.04       117.11        38.56         1.45         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  MIER1 MUTATED MIER1 WILD-TYPE 
          12.76            0.00 
  MIER1 MUTATED MIER1 WILD-TYPE 
         119.93          148.01 
  MIER1 MUTATED MIER1 WILD-TYPE 
         28.305          20.050 
[1] "12.8 - 119.9 (28.3)" "0.0 - 148.0 (20.1)" 
[1] "hr=" "2"  
D484V2, continuous
D484V3, binary
                 cls
clus                0   1
  MIER1 MUTATED     6   2
  MIER1 WILD-TYPE 360 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MIER1 MUTATED      6    2
  MIER1 WILD-TYPE  360  117
        clus
vv       MIER1 MUTATED MIER1 WILD-TYPE
  COLON              6             360
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MIER1 MUTATED         2        0        0         3         1         0
  MIER1 WILD-TYPE      89        1       32       135         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MIER1 MUTATED           0          0          1          0        0         0
  MIER1 WILD-TYPE        24         11         58         42       48        18
                 vv
clus              STAGE IVB
  MIER1 MUTATED           0
  MIER1 WILD-TYPE         1
D484V4, multiclass
            clus
vv           MIER1 MUTATED MIER1 WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              3             135
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  MIER1 MUTATED     0   2   5   1
  MIER1 WILD-TYPE  17  90 324  49
D484V5, multiclass
    clus
vv   MIER1 MUTATED MIER1 WILD-TYPE
  T1             0              17
  T2             2              90
  T3             5             324
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  MIER1 MUTATED     6   1   0
  MIER1 WILD-TYPE 281 112  87
D484V6, multiclass
    clus
vv   MIER1 MUTATED MIER1 WILD-TYPE
  N0             6             281
  N1             1             112
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D484V7, binary
                 cls
clus                0   1
  MIER1 MUTATED     7   0
  MIER1 WILD-TYPE 368  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MIER1 MUTATED      7    0
  MIER1 WILD-TYPE  368   65
   clus
vv  MIER1 MUTATED MIER1 WILD-TYPE
  0             7             368
  1             0              65
[1] 2 2
[1] FALSE
D484V8, binary
                 cls
clus                0   1
  MIER1 MUTATED     3   5
  MIER1 WILD-TYPE 222 259
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MIER1 MUTATED      3    5
  MIER1 WILD-TYPE  222  259
        clus
vv       MIER1 MUTATED MIER1 WILD-TYPE
  FEMALE             3             222
  MALE               5             259
[1] 2 2
[1] FALSE
D484V9, binary
                 cls
clus                0   1
  MIER1 MUTATED     6   0
  MIER1 WILD-TYPE 344  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MIER1 MUTATED      6    0
  MIER1 WILD-TYPE  344   22
     clus
vv    MIER1 MUTATED MIER1 WILD-TYPE
  NO              6             344
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MIER1 MUTATED                      5                             1
  MIER1 WILD-TYPE                  310                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MIER1 MUTATED                       2                              0
  MIER1 WILD-TYPE                   104                             10
D484V10, multiclass
                                clus
vv                               MIER1 MUTATED MIER1 WILD-TYPE
  COLON ADENOCARCINOMA                       5             310
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  MIER1 MUTATED     4   0   0   2
  MIER1 WILD-TYPE 341   4  31  23
D484V11, multiclass
    clus
vv   MIER1 MUTATED MIER1 WILD-TYPE
  R0             4             341
  R1             0               4
  R2             0              31
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D484V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MIER1 MUTATED                                  0     1
  MIER1 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  MIER1 MUTATED                           0     5
  MIER1 WILD-TYPE                        22   221
D484V13, multiclass
                                  clus
vv                                 MIER1 MUTATED MIER1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        5             221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(485) Variable = KIRREL2 MUTATION ANALYSIS
D485V1, survival
                   sevent
clus2                 0   1
  KIRREL2 MUTATED    13   2
  KIRREL2 WILD-TYPE 365  91
  KIRREL2 MUTATED KIRREL2 WILD-TYPE 
               15               456 
  KIRREL2 MUTATED KIRREL2 WILD-TYPE 
                2                91 
$`KIRREL2 MUTATED`
TCGA-A6-5661 TCGA-A6-5665 TCGA-A6-6781 TCGA-AA-3663 TCGA-AA-3715 TCGA-AA-3831 
       33.53        22.06        19.66         6.97        19.04        17.98 
TCGA-AA-3864 TCGA-AA-A010 TCGA-AD-5900 TCGA-CM-4743 TCGA-D5-6540 TCGA-G4-6588 
       53.00        34.98         0.07        23.05        16.14        26.17 
TCGA-AF-3913 TCGA-DC-5869 TCGA-F5-6465 
       10.39         5.03        49.51 

$`KIRREL2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02        78.08         6.05        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       26.99        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
       25.02         1.02        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       39.98        18.05        40.96        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
        1.91       124.27        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       12.49        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       22.09        13.78        35.80        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
       78.12         7.17        15.02        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6571 
       20.55        19.96        20.91        18.28         9.96        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  KIRREL2 MUTATED KIRREL2 WILD-TYPE 
             0.07              0.00 
  KIRREL2 MUTATED KIRREL2 WILD-TYPE 
            53.00            148.01 
  KIRREL2 MUTATED KIRREL2 WILD-TYPE 
           19.660            20.235 
[1] "0.1 - 53.0 (19.7)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.3"
D485V2, continuous
D485V3, binary
                   cls
clus                  0   1
  KIRREL2 MUTATED    12   3
  KIRREL2 WILD-TYPE 354 116
[1] "tbl2"
                   cls
clus                [,1] [,2]
  KIRREL2 MUTATED     12    3
  KIRREL2 WILD-TYPE  354  116
        clus
vv       KIRREL2 MUTATED KIRREL2 WILD-TYPE
  COLON               12               354
  RECTUM               3               116
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KIRREL2 MUTATED         2        0        3         6         1         0
  KIRREL2 WILD-TYPE      89        1       29       132         9         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIRREL2 MUTATED           0          0          1          1        1
  KIRREL2 WILD-TYPE        24         11         58         41       47
                   vv
clus                STAGE IVA STAGE IVB
  KIRREL2 MUTATED           0         0
  KIRREL2 WILD-TYPE        18         1
D485V4, multiclass
            clus
vv           KIRREL2 MUTATED KIRREL2 WILD-TYPE
  STAGE I                  2                89
  STAGE IA                 0                 1
  STAGE II                 3                29
  STAGE IIA                6               132
  STAGE IIB                1                 9
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               0                11
  STAGE IIIB               1                58
  STAGE IIIC               1                41
  STAGE IV                 1                47
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  KIRREL2 MUTATED     0   2  11   2
  KIRREL2 WILD-TYPE  17  90 318  48
D485V5, multiclass
    clus
vv   KIRREL2 MUTATED KIRREL2 WILD-TYPE
  T1               0                17
  T2               2                90
  T3              11               318
  T4               2                48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  KIRREL2 MUTATED    12   3   0
  KIRREL2 WILD-TYPE 275 110  87
D485V6, multiclass
    clus
vv   KIRREL2 MUTATED KIRREL2 WILD-TYPE
  N0              12               275
  N1               3               110
  N2               0                87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D485V7, binary
                   cls
clus                  0   1
  KIRREL2 MUTATED    12   1
  KIRREL2 WILD-TYPE 363  64
[1] "tbl2"
                   cls
clus                [,1] [,2]
  KIRREL2 MUTATED     12    1
  KIRREL2 WILD-TYPE  363   64
   clus
vv  KIRREL2 MUTATED KIRREL2 WILD-TYPE
  0              12               363
  1               1                64
[1] 2 2
[1] FALSE
D485V8, binary
                   cls
clus                  0   1
  KIRREL2 MUTATED     6   9
  KIRREL2 WILD-TYPE 219 255
[1] "tbl2"
                   cls
clus                [,1] [,2]
  KIRREL2 MUTATED      6    9
  KIRREL2 WILD-TYPE  219  255
        clus
vv       KIRREL2 MUTATED KIRREL2 WILD-TYPE
  FEMALE               6               219
  MALE                 9               255
[1] 2 2
[1] FALSE
D485V9, binary
                   cls
clus                  0   1
  KIRREL2 MUTATED    13   0
  KIRREL2 WILD-TYPE 337  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  KIRREL2 MUTATED     13    0
  KIRREL2 WILD-TYPE  337   22
     clus
vv    KIRREL2 MUTATED KIRREL2 WILD-TYPE
  NO               13               337
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  KIRREL2 MUTATED                      9                             3
  KIRREL2 WILD-TYPE                  306                            44
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  KIRREL2 MUTATED                       3                              0
  KIRREL2 WILD-TYPE                   103                             10
D485V10, multiclass
                                clus
vv                               KIRREL2 MUTATED KIRREL2 WILD-TYPE
  COLON ADENOCARCINOMA                         9               306
  COLON MUCINOUS ADENOCARCINOMA                3                44
  RECTAL ADENOCARCINOMA                        3               103
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  KIRREL2 MUTATED    15   0   0   0
  KIRREL2 WILD-TYPE 330   4  31  25
D485V11, multiclass
    clus
vv   KIRREL2 MUTATED KIRREL2 WILD-TYPE
  R0              15               330
  R1               0                 4
  R2               0                31
  RX               0                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D485V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KIRREL2 MUTATED                                  0     0
  KIRREL2 WILD-TYPE                                1    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  KIRREL2 MUTATED                           3     7
  KIRREL2 WILD-TYPE                        19   219
D485V13, multiclass
                                  clus
vv                                 KIRREL2 MUTATED KIRREL2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                      3                19
  WHITE                                          7               219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(486) Variable = PAK3 MUTATION ANALYSIS
D486V1, survival
                sevent
clus2              0   1
  PAK3 MUTATED    17   3
  PAK3 WILD-TYPE 361  90
  PAK3 MUTATED PAK3 WILD-TYPE 
            20            451 
  PAK3 MUTATED PAK3 WILD-TYPE 
             3             90 
$`PAK3 MUTATED`
TCGA-A6-2676 TCGA-AA-3510 TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3681 TCGA-AA-3977 
       42.90        63.98        61.02         6.97         5.98        25.02 
TCGA-CA-6718 TCGA-CM-6164 TCGA-CM-6171 TCGA-CM-6676 TCGA-D5-6536 TCGA-D5-6541 
       10.06        29.03        14.04        11.08        17.85        15.58 
TCGA-DM-A1HB TCGA-DM-A28K TCGA-F4-6569 TCGA-G4-6586 TCGA-G4-6625 TCGA-AG-4007 
      135.65        98.24        35.74        35.80        91.79         1.02 
TCGA-AG-A002 TCGA-DY-A1DF 
       20.98        24.13 

$`PAK3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 
       13.94        19.99        78.08         6.05        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07        12.20        12.76        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6165 TCGA-CM-6166 
       17.03        15.02        12.00         2.96        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 
       14.99        12.99        13.02        15.02        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       13.05        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
        1.32        43.27        15.12         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       16.14         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
       44.32       131.51       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6570 
       35.97        60.79       117.07         8.61        31.96         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6626 
       61.91        36.00        22.09        13.78        26.17        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       14.04        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
      126.44        41.36        57.24        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  PAK3 MUTATED PAK3 WILD-TYPE 
          1.02           0.00 
  PAK3 MUTATED PAK3 WILD-TYPE 
        135.65         148.01 
  PAK3 MUTATED PAK3 WILD-TYPE 
        24.575         20.050 
[1] "1.0 - 135.7 (24.6)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.8"
D486V2, continuous
D486V3, binary
                cls
clus               0   1
  PAK3 MUTATED    17   3
  PAK3 WILD-TYPE 349 116
[1] "tbl2"
                cls
clus             [,1] [,2]
  PAK3 MUTATED     17    3
  PAK3 WILD-TYPE  349  116
        clus
vv       PAK3 MUTATED PAK3 WILD-TYPE
  COLON            17            349
  RECTUM            3            116
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PAK3 MUTATED         4        0        3         7         1         0
  PAK3 WILD-TYPE      87        1       29       131         9         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PAK3 MUTATED           1          0          1          1        1         0
  PAK3 WILD-TYPE        23         11         58         41       47        18
                vv
clus             STAGE IVB
  PAK3 MUTATED           0
  PAK3 WILD-TYPE         1
D486V4, multiclass
            clus
vv           PAK3 MUTATED PAK3 WILD-TYPE
  STAGE I               4             87
  STAGE IA              0              1
  STAGE II              3             29
  STAGE IIA             7            131
  STAGE IIB             1              9
  STAGE IIC             0              1
  STAGE III             1             23
  STAGE IIIA            0             11
  STAGE IIIB            1             58
  STAGE IIIC            1             41
  STAGE IV              1             47
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  PAK3 MUTATED     0   5  13   2
  PAK3 WILD-TYPE  17  87 316  48
D486V5, multiclass
    clus
vv   PAK3 MUTATED PAK3 WILD-TYPE
  T1            0             17
  T2            5             87
  T3           13            316
  T4            2             48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  PAK3 MUTATED    16   2   2
  PAK3 WILD-TYPE 271 111  85
D486V6, multiclass
    clus
vv   PAK3 MUTATED PAK3 WILD-TYPE
  N0           16            271
  N1            2            111
  N2            2             85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D486V7, binary
                cls
clus               0   1
  PAK3 MUTATED    18   1
  PAK3 WILD-TYPE 357  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  PAK3 MUTATED     18    1
  PAK3 WILD-TYPE  357   64
   clus
vv  PAK3 MUTATED PAK3 WILD-TYPE
  0           18            357
  1            1             64
[1] 2 2
[1] FALSE
D486V8, binary
                cls
clus               0   1
  PAK3 MUTATED     7  13
  PAK3 WILD-TYPE 218 251
[1] "tbl2"
                cls
clus             [,1] [,2]
  PAK3 MUTATED      7   13
  PAK3 WILD-TYPE  218  251
        clus
vv       PAK3 MUTATED PAK3 WILD-TYPE
  FEMALE            7            218
  MALE             13            251
[1] 2 2
[1] FALSE
D486V9, binary
                cls
clus               0   1
  PAK3 MUTATED    16   0
  PAK3 WILD-TYPE 334  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  PAK3 MUTATED     16    0
  PAK3 WILD-TYPE  334   22
     clus
vv    PAK3 MUTATED PAK3 WILD-TYPE
  NO            16            334
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PAK3 MUTATED                     15                             1
  PAK3 WILD-TYPE                  300                            46
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PAK3 MUTATED                       3                              0
  PAK3 WILD-TYPE                   103                             10
D486V10, multiclass
                                clus
vv                               PAK3 MUTATED PAK3 WILD-TYPE
  COLON ADENOCARCINOMA                     15            300
  COLON MUCINOUS ADENOCARCINOMA             1             46
  RECTAL ADENOCARCINOMA                     3            103
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  PAK3 MUTATED    14   0   1   1
  PAK3 WILD-TYPE 331   4  30  24
D486V11, multiclass
    clus
vv   PAK3 MUTATED PAK3 WILD-TYPE
  R0           14            331
  R1            0              4
  R2            1             30
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D486V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PAK3 MUTATED                                  0     1
  PAK3 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  PAK3 MUTATED                           0    12
  PAK3 WILD-TYPE                        22   214
D486V13, multiclass
                                  clus
vv                                 PAK3 MUTATED PAK3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                      12            214
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(487) Variable = RAF1 MUTATION ANALYSIS
D487V1, survival
                sevent
clus2              0   1
  RAF1 MUTATED    13   2
  RAF1 WILD-TYPE 365  91
  RAF1 MUTATED RAF1 WILD-TYPE 
            15            456 
  RAF1 MUTATED RAF1 WILD-TYPE 
             2             91 
$`RAF1 MUTATED`
TCGA-AA-3510 TCGA-AA-3516 TCGA-AA-3562 TCGA-AA-A00N TCGA-AA-A01V TCGA-AZ-4315 
       63.98        13.02        19.99         4.01        35.01        58.39 
TCGA-AZ-5407 TCGA-CA-6717 TCGA-CM-4746 TCGA-CM-6162 TCGA-DM-A28H TCGA-F4-6856 
       88.21        12.76        37.02        12.00       117.07        35.31 
TCGA-G4-6306 TCGA-AG-A002 TCGA-DC-6155 
       44.68        20.98        13.97 

$`RAF1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 
        1.02        35.01         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       13.94        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01X 
       38.07         1.02        35.01         1.02        33.04        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6598 
        1.41         5.13       106.75        22.36        62.79        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07        12.20        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4747 
       82.95         1.91       124.27        23.05        20.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28K 
        6.12        81.37       119.93        35.97        60.79        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6307 
       47.41       133.18        74.56        65.85        53.62        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
        7.17        15.02         5.03        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  RAF1 MUTATED RAF1 WILD-TYPE 
          4.01           0.00 
  RAF1 MUTATED RAF1 WILD-TYPE 
        117.07         148.01 
  RAF1 MUTATED RAF1 WILD-TYPE 
        35.010         20.085 
[1] "4.0 - 117.1 (35.0)" "0.0 - 148.0 (20.1)"
[1] "hr=" "2.2"
D487V2, continuous
D487V3, binary
                cls
clus               0   1
  RAF1 MUTATED    13   2
  RAF1 WILD-TYPE 353 117
[1] "tbl2"
                cls
clus             [,1] [,2]
  RAF1 MUTATED     13    2
  RAF1 WILD-TYPE  353  117
        clus
vv       RAF1 MUTATED RAF1 WILD-TYPE
  COLON            13            353
  RECTUM            2            117
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RAF1 MUTATED         5        0        1         3         1         0
  RAF1 WILD-TYPE      86        1       31       135         9         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RAF1 MUTATED           1          1          1          2        0         0
  RAF1 WILD-TYPE        23         10         58         40       48        18
                vv
clus             STAGE IVB
  RAF1 MUTATED           0
  RAF1 WILD-TYPE         1
D487V4, multiclass
            clus
vv           RAF1 MUTATED RAF1 WILD-TYPE
  STAGE I               5             86
  STAGE IA              0              1
  STAGE II              1             31
  STAGE IIA             3            135
  STAGE IIB             1              9
  STAGE IIC             0              1
  STAGE III             1             23
  STAGE IIIA            1             10
  STAGE IIIB            1             58
  STAGE IIIC            2             40
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  RAF1 MUTATED     1   6   7   1
  RAF1 WILD-TYPE  16  86 322  49
D487V5, multiclass
    clus
vv   RAF1 MUTATED RAF1 WILD-TYPE
  T1            1             16
  T2            6             86
  T3            7            322
  T4            1             49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  RAF1 MUTATED    10   2   3
  RAF1 WILD-TYPE 277 111  84
D487V6, multiclass
    clus
vv   RAF1 MUTATED RAF1 WILD-TYPE
  N0           10            277
  N1            2            111
  N2            3             84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D487V7, binary
                cls
clus               0   1
  RAF1 MUTATED    15   0
  RAF1 WILD-TYPE 360  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  RAF1 MUTATED     15    0
  RAF1 WILD-TYPE  360   65
   clus
vv  RAF1 MUTATED RAF1 WILD-TYPE
  0           15            360
  1            0             65
[1] 2 2
[1] FALSE
D487V8, binary
                cls
clus               0   1
  RAF1 MUTATED     4  11
  RAF1 WILD-TYPE 221 253
[1] "tbl2"
                cls
clus             [,1] [,2]
  RAF1 MUTATED      4   11
  RAF1 WILD-TYPE  221  253
        clus
vv       RAF1 MUTATED RAF1 WILD-TYPE
  FEMALE            4            221
  MALE             11            253
[1] 2 2
[1] FALSE
D487V9, binary
                cls
clus               0   1
  RAF1 MUTATED    12   0
  RAF1 WILD-TYPE 338  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  RAF1 MUTATED     12    0
  RAF1 WILD-TYPE  338   22
     clus
vv    RAF1 MUTATED RAF1 WILD-TYPE
  NO            12            338
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  RAF1 MUTATED                      8                             5
  RAF1 WILD-TYPE                  307                            42
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  RAF1 MUTATED                       2                              0
  RAF1 WILD-TYPE                   104                             10
D487V10, multiclass
                                clus
vv                               RAF1 MUTATED RAF1 WILD-TYPE
  COLON ADENOCARCINOMA                      8            307
  COLON MUCINOUS ADENOCARCINOMA             5             42
  RECTAL ADENOCARCINOMA                     2            104
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  RAF1 MUTATED    11   0   0   1
  RAF1 WILD-TYPE 334   4  31  24
D487V11, multiclass
    clus
vv   RAF1 MUTATED RAF1 WILD-TYPE
  R0           11            334
  R1            0              4
  R2            0             31
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D487V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RAF1 MUTATED                                  0     1
  RAF1 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  RAF1 MUTATED                           1     7
  RAF1 WILD-TYPE                        21   219
D487V13, multiclass
                                  clus
vv                                 RAF1 MUTATED RAF1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                       7            219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(488) Variable = ASNSD1 MUTATION ANALYSIS
D488V1, survival
                  sevent
clus2                0   1
  ASNSD1 MUTATED     6   2
  ASNSD1 WILD-TYPE 372  91
  ASNSD1 MUTATED ASNSD1 WILD-TYPE 
               8              463 
  ASNSD1 MUTATED ASNSD1 WILD-TYPE 
               2               91 
$`ASNSD1 MUTATED`
TCGA-A6-6780 TCGA-AA-3510 TCGA-AA-3715 TCGA-AA-3864 TCGA-AA-3947 TCGA-AD-6964 
       20.12        63.98        19.04        53.00        33.01        10.88 
TCGA-CA-6717 TCGA-F5-6813 
       12.76         0.69 

$`ASNSD1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        31.07        30.05        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07        12.20        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-G5-6235 
       49.51        31.30        28.57        32.19         0.66        55.76 
TCGA-G5-6641 
       26.43 

  ASNSD1 MUTATED ASNSD1 WILD-TYPE 
            0.69             0.00 
  ASNSD1 MUTATED ASNSD1 WILD-TYPE 
           63.98           148.01 
  ASNSD1 MUTATED ASNSD1 WILD-TYPE 
           19.58            20.28 
[1] "0.7 - 64.0 (19.6)"  "0.0 - 148.0 (20.3)"
[1] "hr=" "1.2"
D488V2, continuous
D488V3, binary
                  cls
clus                 0   1
  ASNSD1 MUTATED     9   1
  ASNSD1 WILD-TYPE 357 118
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ASNSD1 MUTATED      9    1
  ASNSD1 WILD-TYPE  357  118
        clus
vv       ASNSD1 MUTATED ASNSD1 WILD-TYPE
  COLON               9              357
  RECTUM              1              118
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ASNSD1 MUTATED         0        0        3         3         1         0
  ASNSD1 WILD-TYPE      91        1       29       135         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ASNSD1 MUTATED           0          0          0          2        0
  ASNSD1 WILD-TYPE        24         11         59         40       48
                  vv
clus               STAGE IVA STAGE IVB
  ASNSD1 MUTATED           0         0
  ASNSD1 WILD-TYPE        18         1
D488V4, multiclass
            clus
vv           ASNSD1 MUTATED ASNSD1 WILD-TYPE
  STAGE I                 0               91
  STAGE IA                0                1
  STAGE II                3               29
  STAGE IIA               3              135
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              0               59
  STAGE IIIC              2               40
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ASNSD1 MUTATED     0   0   7   3
  ASNSD1 WILD-TYPE  17  92 322  47
D488V5, multiclass
    clus
vv   ASNSD1 MUTATED ASNSD1 WILD-TYPE
  T1              0               17
  T2              0               92
  T3              7              322
  T4              3               47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  ASNSD1 MUTATED     7   0   3
  ASNSD1 WILD-TYPE 280 113  84
D488V6, multiclass
    clus
vv   ASNSD1 MUTATED ASNSD1 WILD-TYPE
  N0              7              280
  N1              0              113
  N2              3               84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D488V7, binary
                  cls
clus                 0   1
  ASNSD1 MUTATED     7   0
  ASNSD1 WILD-TYPE 368  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ASNSD1 MUTATED      7    0
  ASNSD1 WILD-TYPE  368   65
   clus
vv  ASNSD1 MUTATED ASNSD1 WILD-TYPE
  0              7              368
  1              0               65
[1] 2 2
[1] FALSE
D488V8, binary
                  cls
clus                 0   1
  ASNSD1 MUTATED     2   8
  ASNSD1 WILD-TYPE 223 256
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ASNSD1 MUTATED      2    8
  ASNSD1 WILD-TYPE  223  256
        clus
vv       ASNSD1 MUTATED ASNSD1 WILD-TYPE
  FEMALE              2              223
  MALE                8              256
[1] 2 2
[1] FALSE
D488V9, binary
                  cls
clus                 0   1
  ASNSD1 MUTATED     7   0
  ASNSD1 WILD-TYPE 343  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ASNSD1 MUTATED      7    0
  ASNSD1 WILD-TYPE  343   22
     clus
vv    ASNSD1 MUTATED ASNSD1 WILD-TYPE
  NO               7              343
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ASNSD1 MUTATED                      5                             4
  ASNSD1 WILD-TYPE                  310                            43
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ASNSD1 MUTATED                       1                              0
  ASNSD1 WILD-TYPE                   105                             10
D488V10, multiclass
                                clus
vv                               ASNSD1 MUTATED ASNSD1 WILD-TYPE
  COLON ADENOCARCINOMA                        5              310
  COLON MUCINOUS ADENOCARCINOMA               4               43
  RECTAL ADENOCARCINOMA                       1              105
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ASNSD1 MUTATED     7   0   0   1
  ASNSD1 WILD-TYPE 338   4  31  24
D488V11, multiclass
    clus
vv   ASNSD1 MUTATED ASNSD1 WILD-TYPE
  R0              7              338
  R1              0                4
  R2              0               31
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D488V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ASNSD1 MUTATED                                  0     1
  ASNSD1 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ASNSD1 MUTATED                           0     4
  ASNSD1 WILD-TYPE                        22   222
D488V13, multiclass
                                  clus
vv                                 ASNSD1 MUTATED ASNSD1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         4              222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(489) Variable = ABCC4 MUTATION ANALYSIS
D489V1, survival
                 sevent
clus2               0   1
  ABCC4 MUTATED    13   4
  ABCC4 WILD-TYPE 365  89
  ABCC4 MUTATED ABCC4 WILD-TYPE 
             17             454 
  ABCC4 MUTATED ABCC4 WILD-TYPE 
              4              89 
$`ABCC4 MUTATED`
TCGA-A6-5666 TCGA-AA-3516 TCGA-AA-3534 TCGA-AA-3955 TCGA-AA-A00N TCGA-AA-A010 
       32.71        13.02        29.00        20.98         4.01        34.98 
TCGA-AA-A01R TCGA-AU-6004 TCGA-AZ-4315 TCGA-AZ-6601 TCGA-CA-5797 TCGA-CK-6747 
       35.01        27.09        58.39       100.01         3.29        82.95 
TCGA-CM-4743 TCGA-D5-5539 TCGA-D5-6534 TCGA-DM-A285 TCGA-G4-6306 
       23.05        19.59        43.27         6.12        44.68 

$`ABCC4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        22.06        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3538 TCGA-AA-3542 
        0.00        19.07        34.03        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3956 
       24.00        33.01        26.01        24.00         2.01        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 
       27.42        10.88         0.20        14.50        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       33.01        21.44        17.82         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.06         3.25         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 
       51.32         9.99        21.14         1.91       124.27        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-5541 
       10.06        12.03        45.40        12.26        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       20.19        18.25         1.32        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
      139.17        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       53.62        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  ABCC4 MUTATED ABCC4 WILD-TYPE 
           3.29            0.00 
  ABCC4 MUTATED ABCC4 WILD-TYPE 
         100.01          148.01 
  ABCC4 MUTATED ABCC4 WILD-TYPE 
          29.00           20.02 
[1] "3.3 - 100.0 (29.0)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.1"
D489V2, continuous
D489V3, binary
                 cls
clus                0   1
  ABCC4 MUTATED    20   0
  ABCC4 WILD-TYPE 346 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCC4 MUTATED     20    0
  ABCC4 WILD-TYPE  346  119
        clus
vv       ABCC4 MUTATED ABCC4 WILD-TYPE
  COLON             20             346
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ABCC4 MUTATED         1        0        2         8         3         1
  ABCC4 WILD-TYPE      90        1       30       130         7         0
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ABCC4 MUTATED           2          1          1          0        1         0
  ABCC4 WILD-TYPE        22         10         58         42       47        18
                 vv
clus              STAGE IVB
  ABCC4 MUTATED           0
  ABCC4 WILD-TYPE         1
D489V4, multiclass
            clus
vv           ABCC4 MUTATED ABCC4 WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA              8             130
  STAGE IIB              3               7
  STAGE IIC              1               0
  STAGE III              2              22
  STAGE IIIA             1              10
  STAGE IIIB             1              58
  STAGE IIIC             0              42
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ABCC4 MUTATED     0   3  12   5
  ABCC4 WILD-TYPE  17  89 317  45
D489V5, multiclass
    clus
vv   ABCC4 MUTATED ABCC4 WILD-TYPE
  T1             0              17
  T2             3              89
  T3            12             317
  T4             5              45
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  ABCC4 MUTATED    15   1   4
  ABCC4 WILD-TYPE 272 112  83
D489V6, multiclass
    clus
vv   ABCC4 MUTATED ABCC4 WILD-TYPE
  N0            15             272
  N1             1             112
  N2             4              83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D489V7, binary
                 cls
clus                0   1
  ABCC4 MUTATED    17   1
  ABCC4 WILD-TYPE 358  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCC4 MUTATED     17    1
  ABCC4 WILD-TYPE  358   64
   clus
vv  ABCC4 MUTATED ABCC4 WILD-TYPE
  0            17             358
  1             1              64
[1] 2 2
[1] FALSE
D489V8, binary
                 cls
clus                0   1
  ABCC4 MUTATED    10  10
  ABCC4 WILD-TYPE 215 254
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCC4 MUTATED     10   10
  ABCC4 WILD-TYPE  215  254
        clus
vv       ABCC4 MUTATED ABCC4 WILD-TYPE
  FEMALE            10             215
  MALE              10             254
[1] 2 2
[1] FALSE
D489V9, binary
                 cls
clus                0   1
  ABCC4 MUTATED    13   1
  ABCC4 WILD-TYPE 337  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCC4 MUTATED     13    1
  ABCC4 WILD-TYPE  337   21
     clus
vv    ABCC4 MUTATED ABCC4 WILD-TYPE
  NO             13             337
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ABCC4 MUTATED                     14                             6
  ABCC4 WILD-TYPE                  301                            41
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ABCC4 MUTATED                       0                              0
  ABCC4 WILD-TYPE                   106                             10
D489V10, multiclass
                                clus
vv                               ABCC4 MUTATED ABCC4 WILD-TYPE
  COLON ADENOCARCINOMA                      14             301
  COLON MUCINOUS ADENOCARCINOMA              6              41
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  ABCC4 MUTATED    14   0   0   2
  ABCC4 WILD-TYPE 331   4  31  23
D489V11, multiclass
    clus
vv   ABCC4 MUTATED ABCC4 WILD-TYPE
  R0            14             331
  R1             0               4
  R2             0              31
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D489V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ABCC4 MUTATED                                  0     1
  ABCC4 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ABCC4 MUTATED                           0    11
  ABCC4 WILD-TYPE                        22   215
D489V13, multiclass
                                  clus
vv                                 ABCC4 MUTATED ABCC4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                       11             215
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(490) Variable = CYLC1 MUTATION ANALYSIS
D490V1, survival
                 sevent
clus2               0   1
  CYLC1 MUTATED    26   6
  CYLC1 WILD-TYPE 352  87
  CYLC1 MUTATED CYLC1 WILD-TYPE 
             32             439 
  CYLC1 MUTATED CYLC1 WILD-TYPE 
              6              87 
$`CYLC1 MUTATED`
TCGA-A6-3809 TCGA-A6-5665 TCGA-A6-6653 TCGA-AA-3511 TCGA-AA-A010 TCGA-AA-A01P 
       32.75        22.06        24.39         6.97        34.98        38.07 
TCGA-AD-6548 TCGA-AD-6889 TCGA-AD-6899 TCGA-AZ-4315 TCGA-AZ-4616 TCGA-CA-6717 
       21.37        56.55         5.79        58.39         5.13        12.76 
TCGA-CM-5860 TCGA-CM-6167 TCGA-D5-5537 TCGA-D5-5540 TCGA-D5-6929 TCGA-DM-A1DA 
       32.02        14.99        45.40        56.09         4.80         7.50 
TCGA-DM-A28E TCGA-F4-6570 TCGA-F4-6805 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6315 
      119.93         6.18        34.42       133.18        74.56        61.91 
TCGA-G4-6317 TCGA-G4-6588 TCGA-AF-2692 TCGA-AF-6136 TCGA-AG-3892 TCGA-AG-A002 
       36.00        26.17        13.55        15.39        13.02        20.98 
TCGA-EI-6506 TCGA-F5-6465 
       20.55        49.51 

$`CYLC1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       24.16        21.76        24.69        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01Q 
       10.98        32.02        12.00        31.00        31.00         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
       15.52         0.79         0.72        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       21.44        17.82         1.41       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07        12.20        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       22.98        30.08        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       21.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.03        12.26        19.59        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 
       12.43        14.30         9.04         9.44        11.64         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.74        47.87         1.55        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6303 TCGA-G4-6304 
       13.25         0.53        47.41        35.31        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6323 
       44.68        55.04        85.48        63.62        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       35.80        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       43.04        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 
        1.02        17.95        36.95        17.03        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
       32.61         0.49        19.96        20.91        18.28         9.96 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  CYLC1 MUTATED CYLC1 WILD-TYPE 
            4.8             0.0 
  CYLC1 MUTATED CYLC1 WILD-TYPE 
         133.18          148.01 
  CYLC1 MUTATED CYLC1 WILD-TYPE 
          25.28           19.99 
[1] "4.8 - 133.2 (25.3)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.4"
D490V2, continuous
D490V3, binary
                 cls
clus                0   1
  CYLC1 MUTATED    27   6
  CYLC1 WILD-TYPE 339 113
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CYLC1 MUTATED     27    6
  CYLC1 WILD-TYPE  339  113
        clus
vv       CYLC1 MUTATED CYLC1 WILD-TYPE
  COLON             27             339
  RECTUM             6             113
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CYLC1 MUTATED         4        0        1        14         3         0
  CYLC1 WILD-TYPE      87        1       31       124         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CYLC1 MUTATED           2          0          2          5        3         0
  CYLC1 WILD-TYPE        22         11         57         37       45        18
                 vv
clus              STAGE IVB
  CYLC1 MUTATED           0
  CYLC1 WILD-TYPE         1
D490V4, multiclass
            clus
vv           CYLC1 MUTATED CYLC1 WILD-TYPE
  STAGE I                4              87
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA             14             124
  STAGE IIB              3               7
  STAGE IIC              0               1
  STAGE III              2              22
  STAGE IIIA             0              11
  STAGE IIIB             2              57
  STAGE IIIC             5              37
  STAGE IV               3              45
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CYLC1 MUTATED     1   3  25   5
  CYLC1 WILD-TYPE  16  89 304  45
D490V5, multiclass
    clus
vv   CYLC1 MUTATED CYLC1 WILD-TYPE
  T1             1              16
  T2             3              89
  T3            25             304
  T4             5              45
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  CYLC1 MUTATED    21   6   7
  CYLC1 WILD-TYPE 266 107  80
D490V6, multiclass
    clus
vv   CYLC1 MUTATED CYLC1 WILD-TYPE
  N0            21             266
  N1             6             107
  N2             7              80
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D490V7, binary
                 cls
clus                0   1
  CYLC1 MUTATED    26   3
  CYLC1 WILD-TYPE 349  62
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CYLC1 MUTATED     26    3
  CYLC1 WILD-TYPE  349   62
   clus
vv  CYLC1 MUTATED CYLC1 WILD-TYPE
  0            26             349
  1             3              62
[1] 2 2
[1] FALSE
D490V8, binary
                 cls
clus                0   1
  CYLC1 MUTATED    22  12
  CYLC1 WILD-TYPE 203 252
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CYLC1 MUTATED     22   12
  CYLC1 WILD-TYPE  203  252
        clus
vv       CYLC1 MUTATED CYLC1 WILD-TYPE
  FEMALE            22             203
  MALE              12             252
[1] 2 2
[1] FALSE
D490V9, binary
                 cls
clus                0   1
  CYLC1 MUTATED    27   1
  CYLC1 WILD-TYPE 323  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CYLC1 MUTATED     27    1
  CYLC1 WILD-TYPE  323   21
     clus
vv    CYLC1 MUTATED CYLC1 WILD-TYPE
  NO             27             323
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CYLC1 MUTATED                     24                             3
  CYLC1 WILD-TYPE                  291                            44
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CYLC1 MUTATED                       5                              1
  CYLC1 WILD-TYPE                   101                              9
D490V10, multiclass
                                clus
vv                               CYLC1 MUTATED CYLC1 WILD-TYPE
  COLON ADENOCARCINOMA                      24             291
  COLON MUCINOUS ADENOCARCINOMA              3              44
  RECTAL ADENOCARCINOMA                      5             101
  RECTAL MUCINOUS ADENOCARCINOMA             1               9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  CYLC1 MUTATED    24   0   0   3
  CYLC1 WILD-TYPE 321   4  31  22
D490V11, multiclass
    clus
vv   CYLC1 MUTATED CYLC1 WILD-TYPE
  R0            24             321
  R1             0               4
  R2             0              31
  RX             3              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D490V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CYLC1 MUTATED                                  0     2
  CYLC1 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CYLC1 MUTATED                           1    25
  CYLC1 WILD-TYPE                        21   201
D490V13, multiclass
                                  clus
vv                                 CYLC1 MUTATED CYLC1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               9
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                       25             201
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(491) Variable = RNF111 MUTATION ANALYSIS
D491V1, survival
                  sevent
clus2                0   1
  RNF111 MUTATED    12   3
  RNF111 WILD-TYPE 366  90
  RNF111 MUTATED RNF111 WILD-TYPE 
              15              456 
  RNF111 MUTATED RNF111 WILD-TYPE 
               3               90 
$`RNF111 MUTATED`
TCGA-A6-3809 TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3710 TCGA-AA-3815 TCGA-AA-3852 
       32.75        20.12        19.66        26.99        33.04         0.00 
TCGA-AA-A00R TCGA-AZ-4315 TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-5861 TCGA-D5-6532 
        0.99        58.39        12.76        10.06        15.02        18.25 
TCGA-G4-6626 TCGA-AG-3892 TCGA-AG-A002 
       46.75        13.02        20.98 

$`RNF111 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
       85.05        19.04        19.04        10.06        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00U 
       18.05        38.04         4.01        27.02        42.02        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        33.01        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       12.20        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 
       29.06        22.03        22.98        30.08        32.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6534 
       19.59        56.09        55.92        20.19         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-AF-2687 
       13.78        35.80        26.17        91.79        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       17.03        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  RNF111 MUTATED RNF111 WILD-TYPE 
               0                0 
  RNF111 MUTATED RNF111 WILD-TYPE 
           58.39           148.01 
  RNF111 MUTATED RNF111 WILD-TYPE 
          19.660           20.415 
[1] "0.0 - 58.4 (19.7)"  "0.0 - 148.0 (20.4)"
[1] "hr=" "1.2"
D491V2, continuous
D491V3, binary
                  cls
clus                 0   1
  RNF111 MUTATED    14   2
  RNF111 WILD-TYPE 352 117
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF111 MUTATED     14    2
  RNF111 WILD-TYPE  352  117
        clus
vv       RNF111 MUTATED RNF111 WILD-TYPE
  COLON              14              352
  RECTUM              2              117
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RNF111 MUTATED         3        0        0        10         1         0
  RNF111 WILD-TYPE      88        1       32       128         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RNF111 MUTATED           1          0          0          1        0
  RNF111 WILD-TYPE        23         11         59         41       48
                  vv
clus               STAGE IVA STAGE IVB
  RNF111 MUTATED           0         0
  RNF111 WILD-TYPE        18         1
D491V4, multiclass
            clus
vv           RNF111 MUTATED RNF111 WILD-TYPE
  STAGE I                 3               88
  STAGE IA                0                1
  STAGE II                0               32
  STAGE IIA              10              128
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               1               23
  STAGE IIIA              0               11
  STAGE IIIB              0               59
  STAGE IIIC              1               41
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  RNF111 MUTATED     1   2  11   2
  RNF111 WILD-TYPE  16  90 318  48
D491V5, multiclass
    clus
vv   RNF111 MUTATED RNF111 WILD-TYPE
  T1              1               16
  T2              2               90
  T3             11              318
  T4              2               48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  RNF111 MUTATED    14   1   1
  RNF111 WILD-TYPE 273 112  86
D491V6, multiclass
    clus
vv   RNF111 MUTATED RNF111 WILD-TYPE
  N0             14              273
  N1              1              112
  N2              1               86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D491V7, binary
                  cls
clus                 0   1
  RNF111 MUTATED    14   0
  RNF111 WILD-TYPE 361  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF111 MUTATED     14    0
  RNF111 WILD-TYPE  361   65
   clus
vv  RNF111 MUTATED RNF111 WILD-TYPE
  0             14              361
  1              0               65
[1] 2 2
[1] FALSE
D491V8, binary
                  cls
clus                 0   1
  RNF111 MUTATED     6  10
  RNF111 WILD-TYPE 219 254
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF111 MUTATED      6   10
  RNF111 WILD-TYPE  219  254
        clus
vv       RNF111 MUTATED RNF111 WILD-TYPE
  FEMALE              6              219
  MALE               10              254
[1] 2 2
[1] FALSE
D491V9, binary
                  cls
clus                 0   1
  RNF111 MUTATED    13   0
  RNF111 WILD-TYPE 337  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF111 MUTATED     13    0
  RNF111 WILD-TYPE  337   22
     clus
vv    RNF111 MUTATED RNF111 WILD-TYPE
  NO              13              337
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  RNF111 MUTATED                      9                             5
  RNF111 WILD-TYPE                  306                            42
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  RNF111 MUTATED                       2                              0
  RNF111 WILD-TYPE                   104                             10
D491V10, multiclass
                                clus
vv                               RNF111 MUTATED RNF111 WILD-TYPE
  COLON ADENOCARCINOMA                        9              306
  COLON MUCINOUS ADENOCARCINOMA               5               42
  RECTAL ADENOCARCINOMA                       2              104
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  RNF111 MUTATED    13   0   0   2
  RNF111 WILD-TYPE 332   4  31  23
D491V11, multiclass
    clus
vv   RNF111 MUTATED RNF111 WILD-TYPE
  R0             13              332
  R1              0                4
  R2              0               31
  RX              2               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D491V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RNF111 MUTATED                                  0     2
  RNF111 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  RNF111 MUTATED                           0     7
  RNF111 WILD-TYPE                        22   219
D491V13, multiclass
                                  clus
vv                                 RNF111 MUTATED RNF111 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                9
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         7              219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(492) Variable = CLIP4 MUTATION ANALYSIS
D492V1, survival
                 sevent
clus2               0   1
  CLIP4 MUTATED     8   5
  CLIP4 WILD-TYPE 370  88
  CLIP4 MUTATED CLIP4 WILD-TYPE 
             13             458 
  CLIP4 MUTATED CLIP4 WILD-TYPE 
              5              88 
$`CLIP4 MUTATED`
TCGA-AA-3510 TCGA-AA-3555 TCGA-AA-3662 TCGA-AA-3815 TCGA-AA-3977 TCGA-AA-A00N 
       63.98        29.95         6.05        33.04        25.02         4.01 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6964 TCGA-AY-6386 TCGA-AZ-6598 TCGA-CM-6677 
       18.05        40.96        10.88        17.82        49.41        11.08 
TCGA-DM-A1D4 
       92.75 

$`CLIP4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       13.02        24.00        17.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
        0.92        41.00        39.98         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        88.21         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  CLIP4 MUTATED CLIP4 WILD-TYPE 
           4.01            0.00 
  CLIP4 MUTATED CLIP4 WILD-TYPE 
          92.75          148.01 
  CLIP4 MUTATED CLIP4 WILD-TYPE 
         25.020          20.155 
[1] "4.0 - 92.8 (25.0)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.6"
D492V2, continuous
D492V3, binary
                 cls
clus                0   1
  CLIP4 MUTATED    14   0
  CLIP4 WILD-TYPE 352 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CLIP4 MUTATED     14    0
  CLIP4 WILD-TYPE  352  119
        clus
vv       CLIP4 MUTATED CLIP4 WILD-TYPE
  COLON             14             352
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CLIP4 MUTATED         1        0        2         5         1         0
  CLIP4 WILD-TYPE      90        1       30       133         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CLIP4 MUTATED           1          0          1          0        1         0
  CLIP4 WILD-TYPE        23         11         58         42       47        18
                 vv
clus              STAGE IVB
  CLIP4 MUTATED           0
  CLIP4 WILD-TYPE         1
D492V4, multiclass
            clus
vv           CLIP4 MUTATED CLIP4 WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA              5             133
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             0              42
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CLIP4 MUTATED     0   2   9   3
  CLIP4 WILD-TYPE  17  90 320  47
D492V5, multiclass
    clus
vv   CLIP4 MUTATED CLIP4 WILD-TYPE
  T1             0              17
  T2             2              90
  T3             9             320
  T4             3              47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  CLIP4 MUTATED    10   1   3
  CLIP4 WILD-TYPE 277 112  84
D492V6, multiclass
    clus
vv   CLIP4 MUTATED CLIP4 WILD-TYPE
  N0            10             277
  N1             1             112
  N2             3              84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D492V7, binary
                 cls
clus                0   1
  CLIP4 MUTATED    10   1
  CLIP4 WILD-TYPE 365  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CLIP4 MUTATED     10    1
  CLIP4 WILD-TYPE  365   64
   clus
vv  CLIP4 MUTATED CLIP4 WILD-TYPE
  0            10             365
  1             1              64
[1] 2 2
[1] FALSE
D492V8, binary
                 cls
clus                0   1
  CLIP4 MUTATED     9   5
  CLIP4 WILD-TYPE 216 259
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CLIP4 MUTATED      9    5
  CLIP4 WILD-TYPE  216  259
        clus
vv       CLIP4 MUTATED CLIP4 WILD-TYPE
  FEMALE             9             216
  MALE               5             259
[1] 2 2
[1] FALSE
D492V9, binary
                 cls
clus                0   1
  CLIP4 MUTATED    10   0
  CLIP4 WILD-TYPE 340  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CLIP4 MUTATED     10    0
  CLIP4 WILD-TYPE  340   22
     clus
vv    CLIP4 MUTATED CLIP4 WILD-TYPE
  NO             10             340
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CLIP4 MUTATED                     11                             3
  CLIP4 WILD-TYPE                  304                            44
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CLIP4 MUTATED                       0                              0
  CLIP4 WILD-TYPE                   106                             10
D492V10, multiclass
                                clus
vv                               CLIP4 MUTATED CLIP4 WILD-TYPE
  COLON ADENOCARCINOMA                      11             304
  COLON MUCINOUS ADENOCARCINOMA              3              44
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  CLIP4 MUTATED     9   0   1   0
  CLIP4 WILD-TYPE 336   4  30  25
D492V11, multiclass
    clus
vv   CLIP4 MUTATED CLIP4 WILD-TYPE
  R0             9             336
  R1             0               4
  R2             1              30
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D492V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CLIP4 MUTATED                                  0     0
  CLIP4 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CLIP4 MUTATED                           1     4
  CLIP4 WILD-TYPE                        21   222
D492V13, multiclass
                                  clus
vv                                 CLIP4 MUTATED CLIP4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        4             222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(493) Variable = SULT6B1 MUTATION ANALYSIS
D493V1, survival
                   sevent
clus2                 0   1
  SULT6B1 MUTATED     9   1
  SULT6B1 WILD-TYPE 369  92
  SULT6B1 MUTATED SULT6B1 WILD-TYPE 
               10               461 
  SULT6B1 MUTATED SULT6B1 WILD-TYPE 
                1                92 
$`SULT6B1 MUTATED`
TCGA-AA-3510 TCGA-AA-A010 TCGA-AZ-4315 TCGA-CM-4743 TCGA-D5-6539 TCGA-DM-A1DB 
       63.98        34.98        58.39        23.05        12.49        44.32 
TCGA-G4-6310 TCGA-AG-3731 TCGA-AG-A002 TCGA-EF-5830 
       63.62        37.02        20.98         0.49 

$`SULT6B1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       33.01        21.44        17.82         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
        1.91       124.27        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
        7.50       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       55.04        85.48        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
       19.99         7.99         0.99        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EI-6506 TCGA-EI-6507 
       57.24        24.13        51.48        32.61        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  SULT6B1 MUTATED SULT6B1 WILD-TYPE 
             0.49              0.00 
  SULT6B1 MUTATED SULT6B1 WILD-TYPE 
            63.98            148.01 
  SULT6B1 MUTATED SULT6B1 WILD-TYPE 
            36.00             20.02 
[1] "0.5 - 64.0 (36.0)"  "0.0 - 148.0 (20.0)"
[1] "hr=" "2.9"
D493V2, continuous
D493V3, binary
                   cls
clus                  0   1
  SULT6B1 MUTATED     9   3
  SULT6B1 WILD-TYPE 357 116
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SULT6B1 MUTATED      9    3
  SULT6B1 WILD-TYPE  357  116
        clus
vv       SULT6B1 MUTATED SULT6B1 WILD-TYPE
  COLON                9               357
  RECTUM               3               116
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SULT6B1 MUTATED         1        0        1         4         2         0
  SULT6B1 WILD-TYPE      90        1       31       134         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SULT6B1 MUTATED           0          1          1          1        1
  SULT6B1 WILD-TYPE        24         10         58         41       47
                   vv
clus                STAGE IVA STAGE IVB
  SULT6B1 MUTATED           0         0
  SULT6B1 WILD-TYPE        18         1
D493V4, multiclass
            clus
vv           SULT6B1 MUTATED SULT6B1 WILD-TYPE
  STAGE I                  1                90
  STAGE IA                 0                 1
  STAGE II                 1                31
  STAGE IIA                4               134
  STAGE IIB                2                 8
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               1                10
  STAGE IIIB               1                58
  STAGE IIIC               1                41
  STAGE IV                 1                47
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  SULT6B1 MUTATED     0   1   9   2
  SULT6B1 WILD-TYPE  17  91 320  48
D493V5, multiclass
    clus
vv   SULT6B1 MUTATED SULT6B1 WILD-TYPE
  T1               0                17
  T2               1                91
  T3               9               320
  T4               2                48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  SULT6B1 MUTATED     9   2   1
  SULT6B1 WILD-TYPE 278 111  86
D493V6, multiclass
    clus
vv   SULT6B1 MUTATED SULT6B1 WILD-TYPE
  N0               9               278
  N1               2               111
  N2               1                86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D493V7, binary
                   cls
clus                  0   1
  SULT6B1 MUTATED    10   1
  SULT6B1 WILD-TYPE 365  64
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SULT6B1 MUTATED     10    1
  SULT6B1 WILD-TYPE  365   64
   clus
vv  SULT6B1 MUTATED SULT6B1 WILD-TYPE
  0              10               365
  1               1                64
[1] 2 2
[1] FALSE
D493V8, binary
                   cls
clus                  0   1
  SULT6B1 MUTATED     3   9
  SULT6B1 WILD-TYPE 222 255
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SULT6B1 MUTATED      3    9
  SULT6B1 WILD-TYPE  222  255
        clus
vv       SULT6B1 MUTATED SULT6B1 WILD-TYPE
  FEMALE               3               222
  MALE                 9               255
[1] 2 2
[1] FALSE
D493V9, binary
                   cls
clus                  0   1
  SULT6B1 MUTATED     7   1
  SULT6B1 WILD-TYPE 343  21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SULT6B1 MUTATED      7    1
  SULT6B1 WILD-TYPE  343   21
     clus
vv    SULT6B1 MUTATED SULT6B1 WILD-TYPE
  NO                7               343
  YES               1                21
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SULT6B1 MUTATED                      8                             1
  SULT6B1 WILD-TYPE                  307                            46
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SULT6B1 MUTATED                       3                              0
  SULT6B1 WILD-TYPE                   103                             10
D493V10, multiclass
                                clus
vv                               SULT6B1 MUTATED SULT6B1 WILD-TYPE
  COLON ADENOCARCINOMA                         8               307
  COLON MUCINOUS ADENOCARCINOMA                1                46
  RECTAL ADENOCARCINOMA                        3               103
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  SULT6B1 MUTATED    10   0   1   0
  SULT6B1 WILD-TYPE 335   4  30  25
D493V11, multiclass
    clus
vv   SULT6B1 MUTATED SULT6B1 WILD-TYPE
  R0              10               335
  R1               0                 4
  R2               1                30
  RX               0                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D493V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SULT6B1 MUTATED                                  0     0
  SULT6B1 WILD-TYPE                                1    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  SULT6B1 MUTATED                           0     7
  SULT6B1 WILD-TYPE                        22   219
D493V13, multiclass
                                  clus
vv                                 SULT6B1 MUTATED SULT6B1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                      0                22
  WHITE                                          7               219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(494) Variable = PLA2G4E MUTATION ANALYSIS
D494V1, survival
                   sevent
clus2                 0   1
  PLA2G4E MUTATED     8   2
  PLA2G4E WILD-TYPE 370  91
  PLA2G4E MUTATED PLA2G4E WILD-TYPE 
               10               461 
  PLA2G4E MUTATED PLA2G4E WILD-TYPE 
                2                91 
$`PLA2G4E MUTATED`
TCGA-A6-6780 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3697 TCGA-AU-6004 TCGA-AZ-6598 
       20.12        61.02         6.05        85.05        27.09        49.41 
TCGA-CA-6717 TCGA-CK-5916 TCGA-G4-6588 TCGA-AG-A002 
       12.76        21.14        26.17        20.98 

$`PLA2G4E WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       19.99        13.94        19.99        78.08         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       14.50        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       88.21         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07        12.20        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  PLA2G4E MUTATED PLA2G4E WILD-TYPE 
             6.05              0.00 
  PLA2G4E MUTATED PLA2G4E WILD-TYPE 
            85.05            148.01 
  PLA2G4E MUTATED PLA2G4E WILD-TYPE 
           23.655            20.020 
[1] "6.0 - 85.0 (23.7)"  "0.0 - 148.0 (20.0)"
[1] "hr=" "1.3"
D494V2, continuous
D494V3, binary
                   cls
clus                  0   1
  PLA2G4E MUTATED    10   1
  PLA2G4E WILD-TYPE 356 118
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLA2G4E MUTATED     10    1
  PLA2G4E WILD-TYPE  356  118
        clus
vv       PLA2G4E MUTATED PLA2G4E WILD-TYPE
  COLON               10               356
  RECTUM               1               118
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PLA2G4E MUTATED         3        0        2         3         0         0
  PLA2G4E WILD-TYPE      88        1       30       135        10         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PLA2G4E MUTATED           2          0          0          0        1
  PLA2G4E WILD-TYPE        22         11         59         42       47
                   vv
clus                STAGE IVA STAGE IVB
  PLA2G4E MUTATED           0         0
  PLA2G4E WILD-TYPE        18         1
D494V4, multiclass
            clus
vv           PLA2G4E MUTATED PLA2G4E WILD-TYPE
  STAGE I                  3                88
  STAGE IA                 0                 1
  STAGE II                 2                30
  STAGE IIA                3               135
  STAGE IIB                0                10
  STAGE IIC                0                 1
  STAGE III                2                22
  STAGE IIIA               0                11
  STAGE IIIB               0                59
  STAGE IIIC               0                42
  STAGE IV                 1                47
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  PLA2G4E MUTATED     1   2   7   1
  PLA2G4E WILD-TYPE  16  90 322  49
D494V5, multiclass
    clus
vv   PLA2G4E MUTATED PLA2G4E WILD-TYPE
  T1               1                16
  T2               2                90
  T3               7               322
  T4               1                49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  PLA2G4E MUTATED     9   0   2
  PLA2G4E WILD-TYPE 278 113  85
D494V6, multiclass
    clus
vv   PLA2G4E MUTATED PLA2G4E WILD-TYPE
  N0               9               278
  N1               0               113
  N2               2                85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D494V7, binary
                   cls
clus                  0   1
  PLA2G4E MUTATED     8   1
  PLA2G4E WILD-TYPE 367  64
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLA2G4E MUTATED      8    1
  PLA2G4E WILD-TYPE  367   64
   clus
vv  PLA2G4E MUTATED PLA2G4E WILD-TYPE
  0               8               367
  1               1                64
[1] 2 2
[1] FALSE
D494V8, binary
                   cls
clus                  0   1
  PLA2G4E MUTATED     5   6
  PLA2G4E WILD-TYPE 220 258
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLA2G4E MUTATED      5    6
  PLA2G4E WILD-TYPE  220  258
        clus
vv       PLA2G4E MUTATED PLA2G4E WILD-TYPE
  FEMALE               5               220
  MALE                 6               258
[1] 2 2
[1] FALSE
D494V9, binary
                   cls
clus                  0   1
  PLA2G4E MUTATED     9   0
  PLA2G4E WILD-TYPE 341  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLA2G4E MUTATED      9    0
  PLA2G4E WILD-TYPE  341   22
     clus
vv    PLA2G4E MUTATED PLA2G4E WILD-TYPE
  NO                9               341
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PLA2G4E MUTATED                      8                             2
  PLA2G4E WILD-TYPE                  307                            45
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PLA2G4E MUTATED                       1                              0
  PLA2G4E WILD-TYPE                   105                             10
D494V10, multiclass
                                clus
vv                               PLA2G4E MUTATED PLA2G4E WILD-TYPE
  COLON ADENOCARCINOMA                         8               307
  COLON MUCINOUS ADENOCARCINOMA                2                45
  RECTAL ADENOCARCINOMA                        1               105
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  PLA2G4E MUTATED     6   0   1   2
  PLA2G4E WILD-TYPE 339   4  30  23
D494V11, multiclass
    clus
vv   PLA2G4E MUTATED PLA2G4E WILD-TYPE
  R0               6               339
  R1               0                 4
  R2               1                30
  RX               2                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D494V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PLA2G4E MUTATED                                  0     1
  PLA2G4E WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  PLA2G4E MUTATED                           0     5
  PLA2G4E WILD-TYPE                        22   221
D494V13, multiclass
                                  clus
vv                                 PLA2G4E MUTATED PLA2G4E WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                10
  BLACK OR AFRICAN AMERICAN                      0                22
  WHITE                                          5               221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(495) Variable = CLCNKA MUTATION ANALYSIS
D495V1, survival
                  sevent
clus2                0   1
  CLCNKA MUTATED     6   3
  CLCNKA WILD-TYPE 372  90
  CLCNKA MUTATED CLCNKA WILD-TYPE 
               9              462 
  CLCNKA MUTATED CLCNKA WILD-TYPE 
               3               90 
$`CLCNKA MUTATED`
TCGA-AA-3492 TCGA-AA-3663 TCGA-AA-3672 TCGA-AY-6197 TCGA-AZ-6598 TCGA-DM-A1D6 
        3.02         6.97         0.92        21.44        49.41        49.91 
TCGA-DM-A1D9 TCGA-F4-6856 TCGA-G4-6628 
      140.38        35.31        79.69 

$`CLCNKA WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
       54.02         2.01        14.01        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        88.21         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A1DB 
      130.65        92.75        13.32        12.59         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 
       16.24        33.67        13.25         0.53        47.41       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       26.17        91.79        46.75        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  CLCNKA MUTATED CLCNKA WILD-TYPE 
            0.92             0.00 
  CLCNKA MUTATED CLCNKA WILD-TYPE 
          140.38           148.01 
  CLCNKA MUTATED CLCNKA WILD-TYPE 
          35.310           20.085 
[1] "0.9 - 140.4 (35.3)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.1"
D495V2, continuous
D495V3, binary
                  cls
clus                 0   1
  CLCNKA MUTATED    10   0
  CLCNKA WILD-TYPE 356 119
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CLCNKA MUTATED     10    0
  CLCNKA WILD-TYPE  356  119
        clus
vv       CLCNKA MUTATED CLCNKA WILD-TYPE
  COLON              10              356
  RECTUM              0              119
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CLCNKA MUTATED         3        0        3         3         0         0
  CLCNKA WILD-TYPE      88        1       29       135        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CLCNKA MUTATED           1          0          0          0        0
  CLCNKA WILD-TYPE        23         11         59         42       48
                  vv
clus               STAGE IVA STAGE IVB
  CLCNKA MUTATED           0         0
  CLCNKA WILD-TYPE        18         1
D495V4, multiclass
            clus
vv           CLCNKA MUTATED CLCNKA WILD-TYPE
  STAGE I                 3               88
  STAGE IA                0                1
  STAGE II                3               29
  STAGE IIA               3              135
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               1               23
  STAGE IIIA              0               11
  STAGE IIIB              0               59
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  CLCNKA MUTATED     0   3   7   0
  CLCNKA WILD-TYPE  17  89 322  50
D495V5, multiclass
    clus
vv   CLCNKA MUTATED CLCNKA WILD-TYPE
  T1              0               17
  T2              3               89
  T3              7              322
  T4              0               50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  CLCNKA MUTATED     9   1   0
  CLCNKA WILD-TYPE 278 112  87
D495V6, multiclass
    clus
vv   CLCNKA MUTATED CLCNKA WILD-TYPE
  N0              9              278
  N1              1              112
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D495V7, binary
                  cls
clus                 0   1
  CLCNKA MUTATED     7   0
  CLCNKA WILD-TYPE 368  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CLCNKA MUTATED      7    0
  CLCNKA WILD-TYPE  368   65
   clus
vv  CLCNKA MUTATED CLCNKA WILD-TYPE
  0              7              368
  1              0               65
[1] 2 2
[1] FALSE
D495V8, binary
                  cls
clus                 0   1
  CLCNKA MUTATED     4   6
  CLCNKA WILD-TYPE 221 258
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CLCNKA MUTATED      4    6
  CLCNKA WILD-TYPE  221  258
        clus
vv       CLCNKA MUTATED CLCNKA WILD-TYPE
  FEMALE              4              221
  MALE                6              258
[1] 2 2
[1] FALSE
D495V9, binary
                  cls
clus                 0   1
  CLCNKA MUTATED     7   0
  CLCNKA WILD-TYPE 343  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CLCNKA MUTATED      7    0
  CLCNKA WILD-TYPE  343   22
     clus
vv    CLCNKA MUTATED CLCNKA WILD-TYPE
  NO               7              343
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CLCNKA MUTATED                      8                             2
  CLCNKA WILD-TYPE                  307                            45
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CLCNKA MUTATED                       0                              0
  CLCNKA WILD-TYPE                   106                             10
D495V10, multiclass
                                clus
vv                               CLCNKA MUTATED CLCNKA WILD-TYPE
  COLON ADENOCARCINOMA                        8              307
  COLON MUCINOUS ADENOCARCINOMA               2               45
  RECTAL ADENOCARCINOMA                       0              106
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  CLCNKA MUTATED     6   0   0   1
  CLCNKA WILD-TYPE 339   4  31  24
D495V11, multiclass
    clus
vv   CLCNKA MUTATED CLCNKA WILD-TYPE
  R0              6              339
  R1              0                4
  R2              0               31
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D495V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CLCNKA MUTATED                                  0     0
  CLCNKA WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  CLCNKA MUTATED                           0     7
  CLCNKA WILD-TYPE                        22   219
D495V13, multiclass
                                  clus
vv                                 CLCNKA MUTATED CLCNKA WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         7              219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(496) Variable = ERCC6 MUTATION ANALYSIS
D496V1, survival
                 sevent
clus2               0   1
  ERCC6 MUTATED    25   7
  ERCC6 WILD-TYPE 353  86
  ERCC6 MUTATED ERCC6 WILD-TYPE 
             32             439 
  ERCC6 MUTATED ERCC6 WILD-TYPE 
              7              86 
$`ERCC6 MUTATED`
TCGA-A6-2676 TCGA-A6-5665 TCGA-A6-6141 TCGA-A6-6652 TCGA-AA-3496 TCGA-AA-3510 
       42.90        22.06         8.38        24.69         1.02        63.98 
TCGA-AA-3554 TCGA-AA-3663 TCGA-AA-3666 TCGA-AA-3697 TCGA-AA-3977 TCGA-AA-A00J 
       17.95         6.97         2.01        85.05        25.02        18.05 
TCGA-AA-A00N TCGA-AA-A010 TCGA-AD-6964 TCGA-AY-6197 TCGA-AZ-4315 TCGA-CA-6717 
        4.01        34.98        10.88        21.44        58.39        12.76 
TCGA-CK-5913 TCGA-D5-6540 TCGA-DM-A1D4 TCGA-DM-A1HA TCGA-DM-A28H TCGA-F4-6703 
       51.32        16.14        92.75       131.51       117.07        47.87 
TCGA-F4-6856 TCGA-G4-6303 TCGA-G4-6586 TCGA-AG-A002 TCGA-AG-A02G TCGA-DY-A0XA 
       35.31        65.85        35.80        20.98        38.96       126.44 
TCGA-EI-6506 TCGA-G5-6235 
       20.55        55.76 

$`ERCC6 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       32.71        27.09        22.52        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       21.76        24.39        23.87        20.12        19.66        20.28 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        7.04         3.02        35.01         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       21.01        13.02        24.00        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
       54.02        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07        12.20        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 
       17.56       148.01        85.45        15.62        49.08         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 
       17.85         4.80        17.13        12.49        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-DM-A1D7 
      119.70        24.43        38.20       130.65        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A282 
       12.59       140.38         7.50        44.32       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28K 
        6.12        81.37       119.93        35.97        60.79        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6704 TCGA-F4-6805 
        8.61        31.96        35.74         6.18         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
      133.18        74.56        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 
       63.62        61.91        36.00        22.09        13.78        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
        1.94        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.03         5.29        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
       32.61         0.49        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6641 
       26.43 

  ERCC6 MUTATED ERCC6 WILD-TYPE 
           1.02            0.00 
  ERCC6 MUTATED ERCC6 WILD-TYPE 
         131.51          148.01 
  ERCC6 MUTATED ERCC6 WILD-TYPE 
          30.00           19.99 
[1] "1.0 - 131.5 (30.0)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.4"
D496V2, continuous
D496V3, binary
                 cls
clus                0   1
  ERCC6 MUTATED    28   5
  ERCC6 WILD-TYPE 338 114
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERCC6 MUTATED     28    5
  ERCC6 WILD-TYPE  338  114
        clus
vv       ERCC6 MUTATED ERCC6 WILD-TYPE
  COLON             28             338
  RECTUM             5             114
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ERCC6 MUTATED         3        0        4        12         3         0
  ERCC6 WILD-TYPE      88        1       28       126         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ERCC6 MUTATED           2          0          2          2        2         1
  ERCC6 WILD-TYPE        22         11         57         40       46        17
                 vv
clus              STAGE IVB
  ERCC6 MUTATED           0
  ERCC6 WILD-TYPE         1
D496V4, multiclass
            clus
vv           ERCC6 MUTATED ERCC6 WILD-TYPE
  STAGE I                3              88
  STAGE IA               0               1
  STAGE II               4              28
  STAGE IIA             12             126
  STAGE IIB              3               7
  STAGE IIC              0               1
  STAGE III              2              22
  STAGE IIIA             0              11
  STAGE IIIB             2              57
  STAGE IIIC             2              40
  STAGE IV               2              46
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ERCC6 MUTATED     0   5  22   6
  ERCC6 WILD-TYPE  17  87 307  44
D496V5, multiclass
    clus
vv   ERCC6 MUTATED ERCC6 WILD-TYPE
  T1             0              17
  T2             5              87
  T3            22             307
  T4             6              44
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  ERCC6 MUTATED    25   5   3
  ERCC6 WILD-TYPE 262 108  84
D496V6, multiclass
    clus
vv   ERCC6 MUTATED ERCC6 WILD-TYPE
  N0            25             262
  N1             5             108
  N2             3              84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D496V7, binary
                 cls
clus                0   1
  ERCC6 MUTATED    25   3
  ERCC6 WILD-TYPE 350  62
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERCC6 MUTATED     25    3
  ERCC6 WILD-TYPE  350   62
   clus
vv  ERCC6 MUTATED ERCC6 WILD-TYPE
  0            25             350
  1             3              62
[1] 2 2
[1] FALSE
D496V8, binary
                 cls
clus                0   1
  ERCC6 MUTATED    11  22
  ERCC6 WILD-TYPE 214 242
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERCC6 MUTATED     11   22
  ERCC6 WILD-TYPE  214  242
        clus
vv       ERCC6 MUTATED ERCC6 WILD-TYPE
  FEMALE            11             214
  MALE              22             242
[1] 2 2
[1] FALSE
D496V9, binary
                 cls
clus                0   1
  ERCC6 MUTATED    25   0
  ERCC6 WILD-TYPE 325  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERCC6 MUTATED     25    0
  ERCC6 WILD-TYPE  325   22
     clus
vv    ERCC6 MUTATED ERCC6 WILD-TYPE
  NO             25             325
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ERCC6 MUTATED                     23                             5
  ERCC6 WILD-TYPE                  292                            42
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ERCC6 MUTATED                       5                              0
  ERCC6 WILD-TYPE                   101                             10
D496V10, multiclass
                                clus
vv                               ERCC6 MUTATED ERCC6 WILD-TYPE
  COLON ADENOCARCINOMA                      23             292
  COLON MUCINOUS ADENOCARCINOMA              5              42
  RECTAL ADENOCARCINOMA                      5             101
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  ERCC6 MUTATED    21   1   1   2
  ERCC6 WILD-TYPE 324   3  30  23
D496V11, multiclass
    clus
vv   ERCC6 MUTATED ERCC6 WILD-TYPE
  R0            21             324
  R1             1               3
  R2             1              30
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D496V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ERCC6 MUTATED                                  0     1
  ERCC6 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ERCC6 MUTATED                           2    17
  ERCC6 WILD-TYPE                        20   209
D496V13, multiclass
                                  clus
vv                                 ERCC6 MUTATED ERCC6 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    2              20
  WHITE                                       17             209
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(497) Variable = ALG2 MUTATION ANALYSIS
D497V1, survival
                sevent
clus2              0   1
  ALG2 MUTATED     5   3
  ALG2 WILD-TYPE 373  90
  ALG2 MUTATED ALG2 WILD-TYPE 
             8            463 
  ALG2 MUTATED ALG2 WILD-TYPE 
             3             90 
$`ALG2 MUTATED`
TCGA-AA-3518 TCGA-AA-A00N TCGA-AA-A010 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-CM-5349 
        1.02         4.01        34.98        62.79        88.21        30.08 
TCGA-D5-6537 TCGA-G4-6588 
        4.80        26.17 

$`ALG2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
       38.99         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       22.36        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.03        22.98        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       15.12        17.85        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       35.80        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  ALG2 MUTATED ALG2 WILD-TYPE 
          1.02           0.00 
  ALG2 MUTATED ALG2 WILD-TYPE 
         88.21         148.01 
  ALG2 MUTATED ALG2 WILD-TYPE 
        28.125         20.120 
[1] "1.0 - 88.2 (28.1)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.6"
D497V2, continuous
D497V3, binary
                cls
clus               0   1
  ALG2 MUTATED     8   0
  ALG2 WILD-TYPE 358 119
[1] "tbl2"
                cls
clus             [,1] [,2]
  ALG2 MUTATED      8    0
  ALG2 WILD-TYPE  358  119
        clus
vv       ALG2 MUTATED ALG2 WILD-TYPE
  COLON             8            358
  RECTUM            0            119
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ALG2 MUTATED         1        0        1         3         2         0
  ALG2 WILD-TYPE      90        1       31       135         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ALG2 MUTATED           0          0          1          0        0         0
  ALG2 WILD-TYPE        24         11         58         42       48        18
                vv
clus             STAGE IVB
  ALG2 MUTATED           0
  ALG2 WILD-TYPE         1
D497V4, multiclass
            clus
vv           ALG2 MUTATED ALG2 WILD-TYPE
  STAGE I               1             90
  STAGE IA              0              1
  STAGE II              1             31
  STAGE IIA             3            135
  STAGE IIB             2              8
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            1             58
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  ALG2 MUTATED     1   0   5   2
  ALG2 WILD-TYPE  16  92 324  48
D497V5, multiclass
    clus
vv   ALG2 MUTATED ALG2 WILD-TYPE
  T1            1             16
  T2            0             92
  T3            5            324
  T4            2             48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  ALG2 MUTATED     7   1   0
  ALG2 WILD-TYPE 280 112  87
D497V6, multiclass
    clus
vv   ALG2 MUTATED ALG2 WILD-TYPE
  N0            7            280
  N1            1            112
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D497V7, binary
                cls
clus               0   1
  ALG2 MUTATED     6   0
  ALG2 WILD-TYPE 369  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  ALG2 MUTATED      6    0
  ALG2 WILD-TYPE  369   65
   clus
vv  ALG2 MUTATED ALG2 WILD-TYPE
  0            6            369
  1            0             65
[1] 2 2
[1] FALSE
D497V8, binary
                cls
clus               0   1
  ALG2 MUTATED     5   3
  ALG2 WILD-TYPE 220 261
[1] "tbl2"
                cls
clus             [,1] [,2]
  ALG2 MUTATED      5    3
  ALG2 WILD-TYPE  220  261
        clus
vv       ALG2 MUTATED ALG2 WILD-TYPE
  FEMALE            5            220
  MALE              3            261
[1] 2 2
[1] FALSE
D497V9, binary
                cls
clus               0   1
  ALG2 MUTATED     6   0
  ALG2 WILD-TYPE 344  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  ALG2 MUTATED      6    0
  ALG2 WILD-TYPE  344   22
     clus
vv    ALG2 MUTATED ALG2 WILD-TYPE
  NO             6            344
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ALG2 MUTATED                      7                             1
  ALG2 WILD-TYPE                  308                            46
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ALG2 MUTATED                       0                              0
  ALG2 WILD-TYPE                   106                             10
D497V10, multiclass
                                clus
vv                               ALG2 MUTATED ALG2 WILD-TYPE
  COLON ADENOCARCINOMA                      7            308
  COLON MUCINOUS ADENOCARCINOMA             1             46
  RECTAL ADENOCARCINOMA                     0            106
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  ALG2 MUTATED     6   0   0   0
  ALG2 WILD-TYPE 339   4  31  25
D497V11, multiclass
    clus
vv   ALG2 MUTATED ALG2 WILD-TYPE
  R0            6            339
  R1            0              4
  R2            0             31
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D497V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ALG2 MUTATED                                  0     0
  ALG2 WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  ALG2 MUTATED                           0     5
  ALG2 WILD-TYPE                        22   221
D497V13, multiclass
                                  clus
vv                                 ALG2 MUTATED ALG2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       5            221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(498) Variable = C9ORF131 MUTATION ANALYSIS
D498V1, survival
                    sevent
clus2                  0   1
  C9ORF131 MUTATED     9   2
  C9ORF131 WILD-TYPE 369  91
  C9ORF131 MUTATED C9ORF131 WILD-TYPE 
                11                460 
  C9ORF131 MUTATED C9ORF131 WILD-TYPE 
                 2                 91 
$`C9ORF131 MUTATED`
TCGA-A6-5665 TCGA-AA-3555 TCGA-AA-A00N TCGA-AA-A010 TCGA-AD-6895 TCGA-AU-6004 
       22.06        29.95         4.01        34.98         0.72        27.09 
TCGA-AZ-6598 TCGA-CA-6717 TCGA-CK-5913 TCGA-D5-6540 TCGA-G4-6628 
       49.41        12.76        51.32        16.14        79.69 

$`C9ORF131 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       13.02        24.00        17.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07        12.20        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       85.45        15.62        49.08         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       17.13        12.49        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       46.75        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  C9ORF131 MUTATED C9ORF131 WILD-TYPE 
              0.72               0.00 
  C9ORF131 MUTATED C9ORF131 WILD-TYPE 
             79.69             148.01 
  C9ORF131 MUTATED C9ORF131 WILD-TYPE 
            27.090             20.085 
[1] "0.7 - 79.7 (27.1)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.3"
D498V2, continuous
D498V3, binary
                    cls
clus                   0   1
  C9ORF131 MUTATED    13   0
  C9ORF131 WILD-TYPE 353 119
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C9ORF131 MUTATED     13    0
  C9ORF131 WILD-TYPE  353  119
        clus
vv       C9ORF131 MUTATED C9ORF131 WILD-TYPE
  COLON                13                353
  RECTUM                0                119
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  C9ORF131 MUTATED         3        0        1         5         3         0
  C9ORF131 WILD-TYPE      88        1       31       133         7         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C9ORF131 MUTATED           0          0          0          0        0
  C9ORF131 WILD-TYPE        24         11         59         42       48
                    vv
clus                 STAGE IVA STAGE IVB
  C9ORF131 MUTATED           0         0
  C9ORF131 WILD-TYPE        18         1
D498V4, multiclass
            clus
vv           C9ORF131 MUTATED C9ORF131 WILD-TYPE
  STAGE I                   3                 88
  STAGE IA                  0                  1
  STAGE II                  1                 31
  STAGE IIA                 5                133
  STAGE IIB                 3                  7
  STAGE IIC                 0                  1
  STAGE III                 0                 24
  STAGE IIIA                0                 11
  STAGE IIIB                0                 59
  STAGE IIIC                0                 42
  STAGE IV                  0                 48
  STAGE IVA                 0                 18
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  C9ORF131 MUTATED     0   3   7   3
  C9ORF131 WILD-TYPE  17  89 322  47
D498V5, multiclass
    clus
vv   C9ORF131 MUTATED C9ORF131 WILD-TYPE
  T1                0                 17
  T2                3                 89
  T3                7                322
  T4                3                 47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  C9ORF131 MUTATED    12   1   0
  C9ORF131 WILD-TYPE 275 112  87
D498V6, multiclass
    clus
vv   C9ORF131 MUTATED C9ORF131 WILD-TYPE
  N0               12                275
  N1                1                112
  N2                0                 87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D498V7, binary
                    cls
clus                   0   1
  C9ORF131 MUTATED     9   0
  C9ORF131 WILD-TYPE 366  65
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C9ORF131 MUTATED      9    0
  C9ORF131 WILD-TYPE  366   65
   clus
vv  C9ORF131 MUTATED C9ORF131 WILD-TYPE
  0                9                366
  1                0                 65
[1] 2 2
[1] FALSE
D498V8, binary
                    cls
clus                   0   1
  C9ORF131 MUTATED     8   5
  C9ORF131 WILD-TYPE 217 259
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C9ORF131 MUTATED      8    5
  C9ORF131 WILD-TYPE  217  259
        clus
vv       C9ORF131 MUTATED C9ORF131 WILD-TYPE
  FEMALE                8                217
  MALE                  5                259
[1] 2 2
[1] FALSE
D498V9, binary
                    cls
clus                   0   1
  C9ORF131 MUTATED     8   0
  C9ORF131 WILD-TYPE 342  22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C9ORF131 MUTATED      8    0
  C9ORF131 WILD-TYPE  342   22
     clus
vv    C9ORF131 MUTATED C9ORF131 WILD-TYPE
  NO                 8                342
  YES                0                 22
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  C9ORF131 MUTATED                      9                             4
  C9ORF131 WILD-TYPE                  306                            43
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  C9ORF131 MUTATED                       0                              0
  C9ORF131 WILD-TYPE                   106                             10
D498V10, multiclass
                                clus
vv                               C9ORF131 MUTATED C9ORF131 WILD-TYPE
  COLON ADENOCARCINOMA                          9                306
  COLON MUCINOUS ADENOCARCINOMA                 4                 43
  RECTAL ADENOCARCINOMA                         0                106
  RECTAL MUCINOUS ADENOCARCINOMA                0                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  C9ORF131 MUTATED     8   0   0   3
  C9ORF131 WILD-TYPE 337   4  31  22
D498V11, multiclass
    clus
vv   C9ORF131 MUTATED C9ORF131 WILD-TYPE
  R0                8                337
  R1                0                  4
  R2                0                 31
  RX                3                 22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D498V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C9ORF131 MUTATED                                  0     1
  C9ORF131 WILD-TYPE                                1    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  C9ORF131 MUTATED                           0     8
  C9ORF131 WILD-TYPE                        22   218
D498V13, multiclass
                                  clus
vv                                 C9ORF131 MUTATED C9ORF131 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                 10
  BLACK OR AFRICAN AMERICAN                       0                 22
  WHITE                                           8                218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(499) Variable = EXT1 MUTATION ANALYSIS
D499V1, survival
                sevent
clus2              0   1
  EXT1 MUTATED    16   4
  EXT1 WILD-TYPE 362  89
  EXT1 MUTATED EXT1 WILD-TYPE 
            20            451 
  EXT1 MUTATED EXT1 WILD-TYPE 
             4             89 
$`EXT1 MUTATED`
TCGA-A6-5656 TCGA-AA-3517 TCGA-AA-3555 TCGA-AA-3666 TCGA-AA-3715 TCGA-AA-3977 
       32.91        38.99        29.95         2.01        19.04        25.02 
TCGA-AA-A00A TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01R TCGA-AD-5900 TCGA-AD-6963 
       38.04         4.01        34.98        35.01         0.07        27.42 
TCGA-AY-6197 TCGA-AY-6386 TCGA-CK-5912 TCGA-CK-6751 TCGA-CM-6676 TCGA-D5-6536 
       21.44        17.82        49.08       124.27        11.08        17.85 
TCGA-AG-A011 TCGA-DC-6160 
       37.02        19.99 

$`EXT1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        13.02         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       24.00        17.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       26.99        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       13.94        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       31.00        38.07         1.02         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
       40.96        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       16.31         0.95        33.01        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       85.45        15.62        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
        1.91        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       43.27        15.12         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       23.01        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       10.98         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  EXT1 MUTATED EXT1 WILD-TYPE 
          0.07           0.00 
  EXT1 MUTATED EXT1 WILD-TYPE 
        124.27         148.01 
  EXT1 MUTATED EXT1 WILD-TYPE 
         26.22          20.05 
[1] "0.1 - 124.3 (26.2)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1"  
D499V2, continuous
D499V3, binary
                cls
clus               0   1
  EXT1 MUTATED    18   2
  EXT1 WILD-TYPE 348 117
[1] "tbl2"
                cls
clus             [,1] [,2]
  EXT1 MUTATED     18    2
  EXT1 WILD-TYPE  348  117
        clus
vv       EXT1 MUTATED EXT1 WILD-TYPE
  COLON            18            348
  RECTUM            2            117
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  EXT1 MUTATED         6        0        1         6         2         0
  EXT1 WILD-TYPE      85        1       31       132         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  EXT1 MUTATED           2          0          1          0        0         0
  EXT1 WILD-TYPE        22         11         58         42       48        18
                vv
clus             STAGE IVB
  EXT1 MUTATED           0
  EXT1 WILD-TYPE         1
D499V4, multiclass
            clus
vv           EXT1 MUTATED EXT1 WILD-TYPE
  STAGE I               6             85
  STAGE IA              0              1
  STAGE II              1             31
  STAGE IIA             6            132
  STAGE IIB             2              8
  STAGE IIC             0              1
  STAGE III             2             22
  STAGE IIIA            0             11
  STAGE IIIB            1             58
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  EXT1 MUTATED     0   7  11   2
  EXT1 WILD-TYPE  17  85 318  48
D499V5, multiclass
    clus
vv   EXT1 MUTATED EXT1 WILD-TYPE
  T1            0             17
  T2            7             85
  T3           11            318
  T4            2             48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  EXT1 MUTATED    17   2   1
  EXT1 WILD-TYPE 270 111  86
D499V6, multiclass
    clus
vv   EXT1 MUTATED EXT1 WILD-TYPE
  N0           17            270
  N1            2            111
  N2            1             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D499V7, binary
                cls
clus               0   1
  EXT1 MUTATED    14   0
  EXT1 WILD-TYPE 361  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  EXT1 MUTATED     14    0
  EXT1 WILD-TYPE  361   65
   clus
vv  EXT1 MUTATED EXT1 WILD-TYPE
  0           14            361
  1            0             65
[1] 2 2
[1] FALSE
D499V8, binary
                cls
clus               0   1
  EXT1 MUTATED     4  16
  EXT1 WILD-TYPE 221 248
[1] "tbl2"
                cls
clus             [,1] [,2]
  EXT1 MUTATED      4   16
  EXT1 WILD-TYPE  221  248
        clus
vv       EXT1 MUTATED EXT1 WILD-TYPE
  FEMALE            4            221
  MALE             16            248
[1] 2 2
[1] FALSE
D499V9, binary
                cls
clus               0   1
  EXT1 MUTATED    15   1
  EXT1 WILD-TYPE 335  21
[1] "tbl2"
                cls
clus             [,1] [,2]
  EXT1 MUTATED     15    1
  EXT1 WILD-TYPE  335   21
     clus
vv    EXT1 MUTATED EXT1 WILD-TYPE
  NO            15            335
  YES            1             21
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  EXT1 MUTATED                     13                             5
  EXT1 WILD-TYPE                  302                            42
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  EXT1 MUTATED                       2                              0
  EXT1 WILD-TYPE                   104                             10
D499V10, multiclass
                                clus
vv                               EXT1 MUTATED EXT1 WILD-TYPE
  COLON ADENOCARCINOMA                     13            302
  COLON MUCINOUS ADENOCARCINOMA             5             42
  RECTAL ADENOCARCINOMA                     2            104
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  EXT1 MUTATED    15   0   0   2
  EXT1 WILD-TYPE 330   4  31  23
D499V11, multiclass
    clus
vv   EXT1 MUTATED EXT1 WILD-TYPE
  R0           15            330
  R1            0              4
  R2            0             31
  RX            2             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D499V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  EXT1 MUTATED                                  0     0
  EXT1 WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  EXT1 MUTATED                           1     9
  EXT1 WILD-TYPE                        21   217
D499V13, multiclass
                                  clus
vv                                 EXT1 MUTATED EXT1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                       9            217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(500) Variable = IGFBP7 MUTATION ANALYSIS
D500V1, survival
                  sevent
clus2                0   1
  IGFBP7 MUTATED     5   0
  IGFBP7 WILD-TYPE 373  93
  IGFBP7 MUTATED IGFBP7 WILD-TYPE 
               5              466 
  IGFBP7 MUTATED IGFBP7 WILD-TYPE 
               0               93 
$`IGFBP7 MUTATED`
TCGA-A6-5657 TCGA-AA-3815 TCGA-D5-5541 TCGA-F4-6808 TCGA-EF-5830 
       31.63        33.04        55.92        33.67         0.49 

$`IGFBP7 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       10.06        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-6529 
       12.03        45.40        12.26        19.59        56.09        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6809 
       47.87         1.55        34.42        41.42        16.24        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       24.13        51.48        32.61        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  IGFBP7 MUTATED IGFBP7 WILD-TYPE 
            0.49             0.00 
  IGFBP7 MUTATED IGFBP7 WILD-TYPE 
           55.92           148.01 
  IGFBP7 MUTATED IGFBP7 WILD-TYPE 
          33.040           20.085 
[1] "0.5 - 55.9 (33.0)"  "0.0 - 148.0 (20.1)"
[1] "hr="     "9100000"
D500V2, continuous
D500V3, binary
                  cls
clus                 0   1
  IGFBP7 MUTATED     4   1
  IGFBP7 WILD-TYPE 362 118
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IGFBP7 MUTATED      4    1
  IGFBP7 WILD-TYPE  362  118
        clus
vv       IGFBP7 MUTATED IGFBP7 WILD-TYPE
  COLON               4              362
  RECTUM              1              118
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  IGFBP7 MUTATED         1        0        0         1         1         0
  IGFBP7 WILD-TYPE      90        1       32       137         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  IGFBP7 MUTATED           0          0          2          0        0
  IGFBP7 WILD-TYPE        24         11         57         42       48
                  vv
clus               STAGE IVA STAGE IVB
  IGFBP7 MUTATED           0         0
  IGFBP7 WILD-TYPE        18         1
D500V4, multiclass
            clus
vv           IGFBP7 MUTATED IGFBP7 WILD-TYPE
  STAGE I                 1               90
  STAGE IA                0                1
  STAGE II                0               32
  STAGE IIA               1              137
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              2               57
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  IGFBP7 MUTATED     1   0   3   1
  IGFBP7 WILD-TYPE  16  92 326  49
D500V5, multiclass
    clus
vv   IGFBP7 MUTATED IGFBP7 WILD-TYPE
  T1              1               16
  T2              0               92
  T3              3              326
  T4              1               49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  IGFBP7 MUTATED     3   2   0
  IGFBP7 WILD-TYPE 284 111  87
D500V6, multiclass
    clus
vv   IGFBP7 MUTATED IGFBP7 WILD-TYPE
  N0              3              284
  N1              2              111
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D500V7, binary
                  cls
clus                 0   1
  IGFBP7 MUTATED     5   0
  IGFBP7 WILD-TYPE 370  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IGFBP7 MUTATED      5    0
  IGFBP7 WILD-TYPE  370   65
   clus
vv  IGFBP7 MUTATED IGFBP7 WILD-TYPE
  0              5              370
  1              0               65
[1] 2 2
[1] FALSE
D500V8, binary
                  cls
clus                 0   1
  IGFBP7 MUTATED     2   3
  IGFBP7 WILD-TYPE 223 261
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IGFBP7 MUTATED      2    3
  IGFBP7 WILD-TYPE  223  261
        clus
vv       IGFBP7 MUTATED IGFBP7 WILD-TYPE
  FEMALE              2              223
  MALE                3              261
[1] 2 2
[1] FALSE
D500V9, binary
                  cls
clus                 0   1
  IGFBP7 MUTATED     4   0
  IGFBP7 WILD-TYPE 346  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IGFBP7 MUTATED      4    0
  IGFBP7 WILD-TYPE  346   22
     clus
vv    IGFBP7 MUTATED IGFBP7 WILD-TYPE
  NO               4              346
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  IGFBP7 MUTATED                      4                             0
  IGFBP7 WILD-TYPE                  311                            47
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  IGFBP7 MUTATED                       1                              0
  IGFBP7 WILD-TYPE                   105                             10
D500V10, multiclass
                                clus
vv                               IGFBP7 MUTATED IGFBP7 WILD-TYPE
  COLON ADENOCARCINOMA                        4              311
  COLON MUCINOUS ADENOCARCINOMA               0               47
  RECTAL ADENOCARCINOMA                       1              105
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  IGFBP7 MUTATED     5   0   0   0
  IGFBP7 WILD-TYPE 340   4  31  25
D500V11, multiclass
    clus
vv   IGFBP7 MUTATED IGFBP7 WILD-TYPE
  R0              5              340
  R1              0                4
  R2              0               31
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D500V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  IGFBP7 MUTATED                                  0     0
  IGFBP7 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  IGFBP7 MUTATED                           1     3
  IGFBP7 WILD-TYPE                        21   223
D500V13, multiclass
                                  clus
vv                                 IGFBP7 MUTATED IGFBP7 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                         3              223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(501) Variable = C6ORF89 MUTATION ANALYSIS
D501V1, survival
                   sevent
clus2                 0   1
  C6ORF89 MUTATED     3   2
  C6ORF89 WILD-TYPE 375  91
  C6ORF89 MUTATED C6ORF89 WILD-TYPE 
                5               466 
  C6ORF89 MUTATED C6ORF89 WILD-TYPE 
                2                91 
$`C6ORF89 MUTATED`
TCGA-AA-3811 TCGA-AA-3977 TCGA-CM-6678 TCGA-F4-6809 TCGA-AG-A002 
       10.06        25.02        11.01        13.25        20.98 

$`C6ORF89 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       19.04        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6679 TCGA-CM-6680 
       12.95        13.05        11.08        11.08        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  C6ORF89 MUTATED C6ORF89 WILD-TYPE 
            10.06              0.00 
  C6ORF89 MUTATED C6ORF89 WILD-TYPE 
            25.02            148.01 
  C6ORF89 MUTATED C6ORF89 WILD-TYPE 
           13.250            20.235 
[1] "10.1 - 25.0 (13.2)" "0.0 - 148.0 (20.2)"
[1] "hr=" "3.2"
D501V2, continuous
D501V3, binary
                   cls
clus                  0   1
  C6ORF89 MUTATED     6   1
  C6ORF89 WILD-TYPE 360 118
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C6ORF89 MUTATED      6    1
  C6ORF89 WILD-TYPE  360  118
        clus
vv       C6ORF89 MUTATED C6ORF89 WILD-TYPE
  COLON                6               360
  RECTUM               1               118
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  C6ORF89 MUTATED         1        0        0         1         0         0
  C6ORF89 WILD-TYPE      90        1       32       137        10         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C6ORF89 MUTATED           1          0          0          1        0
  C6ORF89 WILD-TYPE        23         11         59         41       48
                   vv
clus                STAGE IVA STAGE IVB
  C6ORF89 MUTATED           2         0
  C6ORF89 WILD-TYPE        16         1
D501V4, multiclass
            clus
vv           C6ORF89 MUTATED C6ORF89 WILD-TYPE
  STAGE I                  1                90
  STAGE IA                 0                 1
  STAGE II                 0                32
  STAGE IIA                1               137
  STAGE IIB                0                10
  STAGE IIC                0                 1
  STAGE III                1                23
  STAGE IIIA               0                11
  STAGE IIIB               0                59
  STAGE IIIC               1                41
  STAGE IV                 0                48
  STAGE IVA                2                16
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  C6ORF89 MUTATED     0   2   4   1
  C6ORF89 WILD-TYPE  17  90 325  49
D501V5, multiclass
    clus
vv   C6ORF89 MUTATED C6ORF89 WILD-TYPE
  T1               0                17
  T2               2                90
  T3               4               325
  T4               1                49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  C6ORF89 MUTATED     3   2   2
  C6ORF89 WILD-TYPE 284 111  85
D501V6, multiclass
    clus
vv   C6ORF89 MUTATED C6ORF89 WILD-TYPE
  N0               3               284
  N1               2               111
  N2               2                85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D501V7, binary
                   cls
clus                  0   1
  C6ORF89 MUTATED     3   2
  C6ORF89 WILD-TYPE 372  63
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C6ORF89 MUTATED      3    2
  C6ORF89 WILD-TYPE  372   63
   clus
vv  C6ORF89 MUTATED C6ORF89 WILD-TYPE
  0               3               372
  1               2                63
[1] 2 2
[1] FALSE
D501V8, binary
                   cls
clus                  0   1
  C6ORF89 MUTATED     4   3
  C6ORF89 WILD-TYPE 221 261
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C6ORF89 MUTATED      4    3
  C6ORF89 WILD-TYPE  221  261
        clus
vv       C6ORF89 MUTATED C6ORF89 WILD-TYPE
  FEMALE               4               221
  MALE                 3               261
[1] 2 2
[1] FALSE
D501V9, binary
                   cls
clus                  0   1
  C6ORF89 MUTATED     5   0
  C6ORF89 WILD-TYPE 345  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C6ORF89 MUTATED      5    0
  C6ORF89 WILD-TYPE  345   22
     clus
vv    C6ORF89 MUTATED C6ORF89 WILD-TYPE
  NO                5               345
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  C6ORF89 MUTATED                      5                             1
  C6ORF89 WILD-TYPE                  310                            46
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  C6ORF89 MUTATED                       1                              0
  C6ORF89 WILD-TYPE                   105                             10
D501V10, multiclass
                                clus
vv                               C6ORF89 MUTATED C6ORF89 WILD-TYPE
  COLON ADENOCARCINOMA                         5               310
  COLON MUCINOUS ADENOCARCINOMA                1                46
  RECTAL ADENOCARCINOMA                        1               105
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  C6ORF89 MUTATED     6   0   0   0
  C6ORF89 WILD-TYPE 339   4  31  25
D501V11, multiclass
    clus
vv   C6ORF89 MUTATED C6ORF89 WILD-TYPE
  R0               6               339
  R1               0                 4
  R2               0                31
  RX               0                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D501V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C6ORF89 MUTATED                                  0     0
  C6ORF89 WILD-TYPE                                1    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  C6ORF89 MUTATED                           0     3
  C6ORF89 WILD-TYPE                        22   223
D501V13, multiclass
                                  clus
vv                                 C6ORF89 MUTATED C6ORF89 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                      0                22
  WHITE                                          3               223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(502) Variable = ART5 MUTATION ANALYSIS
D502V1, survival
                sevent
clus2              0   1
  ART5 MUTATED     8   2
  ART5 WILD-TYPE 370  91
  ART5 MUTATED ART5 WILD-TYPE 
            10            461 
  ART5 MUTATED ART5 WILD-TYPE 
             2             91 
$`ART5 MUTATED`
TCGA-A6-6780 TCGA-AA-3864 TCGA-AD-6889 TCGA-AD-6964 TCGA-AY-6197 TCGA-AZ-4315 
       20.12        53.00        56.55        10.88        21.44        58.39 
TCGA-AZ-6598 TCGA-CM-4752 TCGA-D5-6928 TCGA-AG-3726 
       49.41        13.02        11.64         7.99 

$`ART5 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 
       32.05         0.99        31.07        31.07        30.05        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
        0.79         0.72         5.79        22.42        27.42         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 
       14.50        27.09        16.31         0.95        33.01        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       37.02        25.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3727 
        0.99        15.95        19.99        13.94        19.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  ART5 MUTATED ART5 WILD-TYPE 
          7.99           0.00 
  ART5 MUTATED ART5 WILD-TYPE 
         58.39         148.01 
  ART5 MUTATED ART5 WILD-TYPE 
         20.78          20.19 
[1] "8.0 - 58.4 (20.8)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.3"
D502V2, continuous
D502V3, binary
                cls
clus               0   1
  ART5 MUTATED     9   1
  ART5 WILD-TYPE 357 118
[1] "tbl2"
                cls
clus             [,1] [,2]
  ART5 MUTATED      9    1
  ART5 WILD-TYPE  357  118
        clus
vv       ART5 MUTATED ART5 WILD-TYPE
  COLON             9            357
  RECTUM            1            118
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ART5 MUTATED         1        0        2         6         0         0
  ART5 WILD-TYPE      90        1       30       132        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ART5 MUTATED           0          0          0          0        0         0
  ART5 WILD-TYPE        24         11         59         42       48        18
                vv
clus             STAGE IVB
  ART5 MUTATED           0
  ART5 WILD-TYPE         1
D502V4, multiclass
            clus
vv           ART5 MUTATED ART5 WILD-TYPE
  STAGE I               1             90
  STAGE IA              0              1
  STAGE II              2             30
  STAGE IIA             6            132
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            0             59
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  ART5 MUTATED     0   1   8   1
  ART5 WILD-TYPE  17  91 321  49
D502V5, multiclass
    clus
vv   ART5 MUTATED ART5 WILD-TYPE
  T1            0             17
  T2            1             91
  T3            8            321
  T4            1             49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  ART5 MUTATED     9   0   1
  ART5 WILD-TYPE 278 113  86
D502V6, multiclass
    clus
vv   ART5 MUTATED ART5 WILD-TYPE
  N0            9            278
  N1            0            113
  N2            1             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D502V7, binary
                cls
clus               0   1
  ART5 MUTATED     6   0
  ART5 WILD-TYPE 369  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  ART5 MUTATED      6    0
  ART5 WILD-TYPE  369   65
   clus
vv  ART5 MUTATED ART5 WILD-TYPE
  0            6            369
  1            0             65
[1] 2 2
[1] FALSE
D502V8, binary
                cls
clus               0   1
  ART5 MUTATED     2   8
  ART5 WILD-TYPE 223 256
[1] "tbl2"
                cls
clus             [,1] [,2]
  ART5 MUTATED      2    8
  ART5 WILD-TYPE  223  256
        clus
vv       ART5 MUTATED ART5 WILD-TYPE
  FEMALE            2            223
  MALE              8            256
[1] 2 2
[1] FALSE
D502V9, binary
                cls
clus               0   1
  ART5 MUTATED     9   0
  ART5 WILD-TYPE 341  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  ART5 MUTATED      9    0
  ART5 WILD-TYPE  341   22
     clus
vv    ART5 MUTATED ART5 WILD-TYPE
  NO             9            341
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ART5 MUTATED                      7                             2
  ART5 WILD-TYPE                  308                            45
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ART5 MUTATED                       1                              0
  ART5 WILD-TYPE                   105                             10
D502V10, multiclass
                                clus
vv                               ART5 MUTATED ART5 WILD-TYPE
  COLON ADENOCARCINOMA                      7            308
  COLON MUCINOUS ADENOCARCINOMA             2             45
  RECTAL ADENOCARCINOMA                     1            105
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  ART5 MUTATED     6   0   0   0
  ART5 WILD-TYPE 339   4  31  25
D502V11, multiclass
    clus
vv   ART5 MUTATED ART5 WILD-TYPE
  R0            6            339
  R1            0              4
  R2            0             31
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D502V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ART5 MUTATED                                  0     1
  ART5 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  ART5 MUTATED                           1     6
  ART5 WILD-TYPE                        21   220
D502V13, multiclass
                                  clus
vv                                 ART5 MUTATED ART5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                       6            220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(503) Variable = CUL2 MUTATION ANALYSIS
D503V1, survival
                sevent
clus2              0   1
  CUL2 MUTATED    13   1
  CUL2 WILD-TYPE 365  92
  CUL2 MUTATED CUL2 WILD-TYPE 
            14            457 
  CUL2 MUTATED CUL2 WILD-TYPE 
             1             92 
$`CUL2 MUTATED`
TCGA-AA-3555 TCGA-AA-3966 TCGA-AA-A010 TCGA-AA-A01Q TCGA-AD-6889 TCGA-AZ-4315 
       29.95         2.01        34.98         1.02        56.55        58.39 
TCGA-AZ-6598 TCGA-CA-6717 TCGA-CM-4743 TCGA-D5-6532 TCGA-D5-6538 TCGA-D5-6928 
       49.41        12.76        23.05        18.25        17.13        11.64 
TCGA-G4-6628 TCGA-AG-A002 
       79.69        20.98 

$`CUL2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 
       21.01        13.02        24.00        17.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
        2.01        20.98        34.03        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       31.00        38.07        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 
       40.96         0.07        21.37        15.52         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07        12.20        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
       82.95         1.91       124.27        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6539 
        1.32        43.27        15.12        17.85         4.80        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
       14.30         9.04         9.44         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 
       13.78        35.80        26.17        91.79        46.75        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  CUL2 MUTATED CUL2 WILD-TYPE 
          1.02           0.00 
  CUL2 MUTATED CUL2 WILD-TYPE 
         79.69         148.01 
  CUL2 MUTATED CUL2 WILD-TYPE 
        22.015         20.120 
[1] "1.0 - 79.7 (22.0)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "3.3"
D503V2, continuous
D503V3, binary
                cls
clus               0   1
  CUL2 MUTATED    14   1
  CUL2 WILD-TYPE 352 118
[1] "tbl2"
                cls
clus             [,1] [,2]
  CUL2 MUTATED     14    1
  CUL2 WILD-TYPE  352  118
        clus
vv       CUL2 MUTATED CUL2 WILD-TYPE
  COLON            14            352
  RECTUM            1            118
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CUL2 MUTATED         2        0        2         8         2         0
  CUL2 WILD-TYPE      89        1       30       130         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CUL2 MUTATED           0          0          1          0        0         0
  CUL2 WILD-TYPE        24         11         58         42       48        18
                vv
clus             STAGE IVB
  CUL2 MUTATED           0
  CUL2 WILD-TYPE         1
D503V4, multiclass
            clus
vv           CUL2 MUTATED CUL2 WILD-TYPE
  STAGE I               2             89
  STAGE IA              0              1
  STAGE II              2             30
  STAGE IIA             8            130
  STAGE IIB             2              8
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            1             58
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  CUL2 MUTATED     0   2  11   2
  CUL2 WILD-TYPE  17  90 318  48
D503V5, multiclass
    clus
vv   CUL2 MUTATED CUL2 WILD-TYPE
  T1            0             17
  T2            2             90
  T3           11            318
  T4            2             48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  CUL2 MUTATED    14   0   1
  CUL2 WILD-TYPE 273 113  86
D503V6, multiclass
    clus
vv   CUL2 MUTATED CUL2 WILD-TYPE
  N0           14            273
  N1            0            113
  N2            1             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D503V7, binary
                cls
clus               0   1
  CUL2 MUTATED    13   0
  CUL2 WILD-TYPE 362  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  CUL2 MUTATED     13    0
  CUL2 WILD-TYPE  362   65
   clus
vv  CUL2 MUTATED CUL2 WILD-TYPE
  0           13            362
  1            0             65
[1] 2 2
[1] FALSE
D503V8, binary
                cls
clus               0   1
  CUL2 MUTATED     7   8
  CUL2 WILD-TYPE 218 256
[1] "tbl2"
                cls
clus             [,1] [,2]
  CUL2 MUTATED      7    8
  CUL2 WILD-TYPE  218  256
        clus
vv       CUL2 MUTATED CUL2 WILD-TYPE
  FEMALE            7            218
  MALE              8            256
[1] 2 2
[1] FALSE
D503V9, binary
                cls
clus               0   1
  CUL2 MUTATED    11   0
  CUL2 WILD-TYPE 339  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  CUL2 MUTATED     11    0
  CUL2 WILD-TYPE  339   22
     clus
vv    CUL2 MUTATED CUL2 WILD-TYPE
  NO            11            339
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CUL2 MUTATED                     10                             4
  CUL2 WILD-TYPE                  305                            43
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CUL2 MUTATED                       1                              0
  CUL2 WILD-TYPE                   105                             10
D503V10, multiclass
                                clus
vv                               CUL2 MUTATED CUL2 WILD-TYPE
  COLON ADENOCARCINOMA                     10            305
  COLON MUCINOUS ADENOCARCINOMA             4             43
  RECTAL ADENOCARCINOMA                     1            105
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  CUL2 MUTATED    10   0   0   2
  CUL2 WILD-TYPE 335   4  31  23
D503V11, multiclass
    clus
vv   CUL2 MUTATED CUL2 WILD-TYPE
  R0           10            335
  R1            0              4
  R2            0             31
  RX            2             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D503V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CUL2 MUTATED                                  0     2
  CUL2 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  CUL2 MUTATED                           0     8
  CUL2 WILD-TYPE                        22   218
D503V13, multiclass
                                  clus
vv                                 CUL2 MUTATED CUL2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              9
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       8            218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(504) Variable = CDC6 MUTATION ANALYSIS
D504V1, survival
                sevent
clus2              0   1
  CDC6 MUTATED     8   2
  CDC6 WILD-TYPE 370  91
  CDC6 MUTATED CDC6 WILD-TYPE 
            10            461 
  CDC6 MUTATED CDC6 WILD-TYPE 
             2             91 
$`CDC6 MUTATED`
TCGA-A6-4105 TCGA-A6-5666 TCGA-AA-3510 TCGA-CA-5796 TCGA-CA-6717 TCGA-CA-6718 
       14.53        32.71        63.98         3.25        12.76        10.06 
TCGA-AG-3732 TCGA-AG-A002 TCGA-AH-6544 TCGA-F5-6811 
       32.98        20.98        38.56        32.19 

$`CDC6 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 
       16.57        34.65        33.34        32.75        36.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       22.06        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 
       12.69         3.06         3.29         0.07        12.20        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 
       13.94        19.99         7.99         0.99        37.02         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
       38.04       117.11         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57         0.66         0.69        55.76        26.43 

  CDC6 MUTATED CDC6 WILD-TYPE 
          3.25           0.00 
  CDC6 MUTATED CDC6 WILD-TYPE 
         63.98         148.01 
  CDC6 MUTATED CDC6 WILD-TYPE 
        26.585         20.120 
[1] "3.2 - 64.0 (26.6)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1"  
D504V2, continuous
D504V3, binary
                cls
clus               0   1
  CDC6 MUTATED     6   4
  CDC6 WILD-TYPE 360 115
[1] "tbl2"
                cls
clus             [,1] [,2]
  CDC6 MUTATED      6    4
  CDC6 WILD-TYPE  360  115
        clus
vv       CDC6 MUTATED CDC6 WILD-TYPE
  COLON             6            360
  RECTUM            4            115
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CDC6 MUTATED         2        0        1         5         0         1
  CDC6 WILD-TYPE      89        1       31       133        10         0
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CDC6 MUTATED           0          0          0          0        0         0
  CDC6 WILD-TYPE        24         11         59         42       48        18
                vv
clus             STAGE IVB
  CDC6 MUTATED           0
  CDC6 WILD-TYPE         1
D504V4, multiclass
            clus
vv           CDC6 MUTATED CDC6 WILD-TYPE
  STAGE I               2             89
  STAGE IA              0              1
  STAGE II              1             31
  STAGE IIA             5            133
  STAGE IIB             0             10
  STAGE IIC             1              0
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            0             59
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  CDC6 MUTATED     0   2   7   1
  CDC6 WILD-TYPE  17  90 322  49
D504V5, multiclass
    clus
vv   CDC6 MUTATED CDC6 WILD-TYPE
  T1            0             17
  T2            2             90
  T3            7            322
  T4            1             49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  CDC6 MUTATED     9   1   0
  CDC6 WILD-TYPE 278 112  87
D504V6, multiclass
    clus
vv   CDC6 MUTATED CDC6 WILD-TYPE
  N0            9            278
  N1            1            112
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D504V7, binary
                cls
clus               0   1
  CDC6 MUTATED     9   1
  CDC6 WILD-TYPE 366  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  CDC6 MUTATED      9    1
  CDC6 WILD-TYPE  366   64
   clus
vv  CDC6 MUTATED CDC6 WILD-TYPE
  0            9            366
  1            1             64
[1] 2 2
[1] FALSE
D504V8, binary
                cls
clus               0   1
  CDC6 MUTATED     3   7
  CDC6 WILD-TYPE 222 257
[1] "tbl2"
                cls
clus             [,1] [,2]
  CDC6 MUTATED      3    7
  CDC6 WILD-TYPE  222  257
        clus
vv       CDC6 MUTATED CDC6 WILD-TYPE
  FEMALE            3            222
  MALE              7            257
[1] 2 2
[1] FALSE
D504V9, binary
                cls
clus               0   1
  CDC6 MUTATED    10   0
  CDC6 WILD-TYPE 340  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  CDC6 MUTATED     10    0
  CDC6 WILD-TYPE  340   22
     clus
vv    CDC6 MUTATED CDC6 WILD-TYPE
  NO            10            340
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CDC6 MUTATED                      4                             2
  CDC6 WILD-TYPE                  311                            45
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CDC6 MUTATED                       4                              0
  CDC6 WILD-TYPE                   102                             10
D504V10, multiclass
                                clus
vv                               CDC6 MUTATED CDC6 WILD-TYPE
  COLON ADENOCARCINOMA                      4            311
  COLON MUCINOUS ADENOCARCINOMA             2             45
  RECTAL ADENOCARCINOMA                     4            102
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  CDC6 MUTATED     4   0   0   2
  CDC6 WILD-TYPE 341   4  31  23
D504V11, multiclass
    clus
vv   CDC6 MUTATED CDC6 WILD-TYPE
  R0            4            341
  R1            0              4
  R2            0             31
  RX            2             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D504V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CDC6 MUTATED                                  0     3
  CDC6 WILD-TYPE                                1     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  CDC6 MUTATED                           0     4
  CDC6 WILD-TYPE                        22   222
D504V13, multiclass
                                  clus
vv                                 CDC6 MUTATED CDC6 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       3              8
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       4            222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(505) Variable = SOX7 MUTATION ANALYSIS
D505V1, survival
                sevent
clus2              0   1
  SOX7 MUTATED     9   3
  SOX7 WILD-TYPE 369  90
  SOX7 MUTATED SOX7 WILD-TYPE 
            12            459 
  SOX7 MUTATED SOX7 WILD-TYPE 
             3             90 
$`SOX7 MUTATED`
TCGA-A6-6780 TCGA-AA-3672 TCGA-AA-3815 TCGA-AA-3947 TCGA-AA-A010 TCGA-AY-6197 
       20.12         0.92        33.04        33.01        34.98        21.44 
TCGA-AZ-4315 TCGA-AZ-6598 TCGA-CA-6717 TCGA-CM-6171 TCGA-DM-A1D7 TCGA-DY-A1DG 
       58.39        49.41        12.76        14.04        13.32        51.48 

$`SOX7 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 
        6.97        54.02         2.01        14.01        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       35.05         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4323 
       27.09        16.31         0.95        33.01        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 
        5.13       106.75        22.36        62.79        88.21         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.20        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       12.99        13.02        15.02        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D8 TCGA-DM-A1D9 
       38.20       130.65        92.75        49.91        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  SOX7 MUTATED SOX7 WILD-TYPE 
          0.92           0.00 
  SOX7 MUTATED SOX7 WILD-TYPE 
         58.39         148.01 
  SOX7 MUTATED SOX7 WILD-TYPE 
        27.225         20.050 
[1] "0.9 - 58.4 (27.2)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.1"
D505V2, continuous
D505V3, binary
                cls
clus               0   1
  SOX7 MUTATED    11   1
  SOX7 WILD-TYPE 355 118
[1] "tbl2"
                cls
clus             [,1] [,2]
  SOX7 MUTATED     11    1
  SOX7 WILD-TYPE  355  118
        clus
vv       SOX7 MUTATED SOX7 WILD-TYPE
  COLON            11            355
  RECTUM            1            118
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SOX7 MUTATED         1        0        1         6         2         0
  SOX7 WILD-TYPE      90        1       31       132         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SOX7 MUTATED           1          0          0          0        0         1
  SOX7 WILD-TYPE        23         11         59         42       48        17
                vv
clus             STAGE IVB
  SOX7 MUTATED           0
  SOX7 WILD-TYPE         1
D505V4, multiclass
            clus
vv           SOX7 MUTATED SOX7 WILD-TYPE
  STAGE I               1             90
  STAGE IA              0              1
  STAGE II              1             31
  STAGE IIA             6            132
  STAGE IIB             2              8
  STAGE IIC             0              1
  STAGE III             1             23
  STAGE IIIA            0             11
  STAGE IIIB            0             59
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             1             17
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  SOX7 MUTATED     0   1   9   2
  SOX7 WILD-TYPE  17  91 320  48
D505V5, multiclass
    clus
vv   SOX7 MUTATED SOX7 WILD-TYPE
  T1            0             17
  T2            1             91
  T3            9            320
  T4            2             48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  SOX7 MUTATED    10   2   0
  SOX7 WILD-TYPE 277 111  87
D505V6, multiclass
    clus
vv   SOX7 MUTATED SOX7 WILD-TYPE
  N0           10            277
  N1            2            111
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D505V7, binary
                cls
clus               0   1
  SOX7 MUTATED     8   1
  SOX7 WILD-TYPE 367  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  SOX7 MUTATED      8    1
  SOX7 WILD-TYPE  367   64
   clus
vv  SOX7 MUTATED SOX7 WILD-TYPE
  0            8            367
  1            1             64
[1] 2 2
[1] FALSE
D505V8, binary
                cls
clus               0   1
  SOX7 MUTATED     6   6
  SOX7 WILD-TYPE 219 258
[1] "tbl2"
                cls
clus             [,1] [,2]
  SOX7 MUTATED      6    6
  SOX7 WILD-TYPE  219  258
        clus
vv       SOX7 MUTATED SOX7 WILD-TYPE
  FEMALE            6            219
  MALE              6            258
[1] 2 2
[1] FALSE
D505V9, binary
                cls
clus               0   1
  SOX7 MUTATED    10   0
  SOX7 WILD-TYPE 340  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  SOX7 MUTATED     10    0
  SOX7 WILD-TYPE  340   22
     clus
vv    SOX7 MUTATED SOX7 WILD-TYPE
  NO            10            340
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SOX7 MUTATED                      7                             3
  SOX7 WILD-TYPE                  308                            44
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SOX7 MUTATED                       1                              0
  SOX7 WILD-TYPE                   105                             10
D505V10, multiclass
                                clus
vv                               SOX7 MUTATED SOX7 WILD-TYPE
  COLON ADENOCARCINOMA                      7            308
  COLON MUCINOUS ADENOCARCINOMA             3             44
  RECTAL ADENOCARCINOMA                     1            105
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  SOX7 MUTATED     7   0   0   1
  SOX7 WILD-TYPE 338   4  31  24
D505V11, multiclass
    clus
vv   SOX7 MUTATED SOX7 WILD-TYPE
  R0            7            338
  R1            0              4
  R2            0             31
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D505V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SOX7 MUTATED                                  0     1
  SOX7 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  SOX7 MUTATED                           0     7
  SOX7 WILD-TYPE                        22   219
D505V13, multiclass
                                  clus
vv                                 SOX7 MUTATED SOX7 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       7            219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(506) Variable = ZNF644 MUTATION ANALYSIS
D506V1, survival
                  sevent
clus2                0   1
  ZNF644 MUTATED    20   1
  ZNF644 WILD-TYPE 358  92
  ZNF644 MUTATED ZNF644 WILD-TYPE 
              21              450 
  ZNF644 MUTATED ZNF644 WILD-TYPE 
               1               92 
$`ZNF644 MUTATED`
TCGA-A6-2672 TCGA-A6-5657 TCGA-A6-5661 TCGA-AA-3510 TCGA-AA-3663 TCGA-AA-3821 
       46.65        31.63        33.53        63.98         6.97         1.02 
TCGA-AA-3947 TCGA-AA-3977 TCGA-AZ-4315 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       33.01        25.02        58.39        12.76        10.06        14.30 
TCGA-CM-4744 TCGA-CM-4747 TCGA-D5-6536 TCGA-DM-A28H TCGA-G4-6588 TCGA-AF-6136 
       20.02        25.02        17.85       117.07        26.17        15.39 
TCGA-AG-A002 TCGA-CI-6624 TCGA-EI-6510 
       20.98         4.73        18.28 

$`ZNF644 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 
       30.44        29.19        23.61        22.09        22.06        32.71 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       27.09        22.52         8.38        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 
       20.28         7.04         3.02         1.02        35.01         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       61.02        78.08         6.05        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
       25.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 
       31.00         2.01        12.99        24.00        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       33.01        21.44        17.82         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4746 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       37.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 
       20.19        18.25         1.32        43.27        15.12         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        35.80        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 
       34.49        10.39        14.50        16.83        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CL-5917 
        0.69         0.72         6.05        33.17         6.97        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       20.55        19.96        20.91         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  ZNF644 MUTATED ZNF644 WILD-TYPE 
            1.02             0.00 
  ZNF644 MUTATED ZNF644 WILD-TYPE 
          117.07           148.01 
  ZNF644 MUTATED ZNF644 WILD-TYPE 
          20.980           20.155 
[1] "1.0 - 117.1 (21.0)" "0.0 - 148.0 (20.2)"
[1] "hr=" "4.6"
D506V2, continuous
D506V3, binary
                  cls
clus                 0   1
  ZNF644 MUTATED    17   4
  ZNF644 WILD-TYPE 349 115
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF644 MUTATED     17    4
  ZNF644 WILD-TYPE  349  115
        clus
vv       ZNF644 MUTATED ZNF644 WILD-TYPE
  COLON              17              349
  RECTUM              4              115
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZNF644 MUTATED         4        0        2         7         1         0
  ZNF644 WILD-TYPE      87        1       30       131         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF644 MUTATED           0          0          3          1        0
  ZNF644 WILD-TYPE        24         11         56         41       48
                  vv
clus               STAGE IVA STAGE IVB
  ZNF644 MUTATED           2         0
  ZNF644 WILD-TYPE        16         1
D506V4, multiclass
            clus
vv           ZNF644 MUTATED ZNF644 WILD-TYPE
  STAGE I                 4               87
  STAGE IA                0                1
  STAGE II                2               30
  STAGE IIA               7              131
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              3               56
  STAGE IIIC              1               41
  STAGE IV                0               48
  STAGE IVA               2               16
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZNF644 MUTATED     0   6  13   2
  ZNF644 WILD-TYPE  17  86 316  48
D506V5, multiclass
    clus
vv   ZNF644 MUTATED ZNF644 WILD-TYPE
  T1              0               17
  T2              6               86
  T3             13              316
  T4              2               48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  ZNF644 MUTATED    16   4   1
  ZNF644 WILD-TYPE 271 109  86
D506V6, multiclass
    clus
vv   ZNF644 MUTATED ZNF644 WILD-TYPE
  N0             16              271
  N1              4              109
  N2              1               86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D506V7, binary
                  cls
clus                 0   1
  ZNF644 MUTATED    17   1
  ZNF644 WILD-TYPE 358  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF644 MUTATED     17    1
  ZNF644 WILD-TYPE  358   64
   clus
vv  ZNF644 MUTATED ZNF644 WILD-TYPE
  0             17              358
  1              1               64
[1] 2 2
[1] FALSE
D506V8, binary
                  cls
clus                 0   1
  ZNF644 MUTATED     8  13
  ZNF644 WILD-TYPE 217 251
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF644 MUTATED      8   13
  ZNF644 WILD-TYPE  217  251
        clus
vv       ZNF644 MUTATED ZNF644 WILD-TYPE
  FEMALE              8              217
  MALE               13              251
[1] 2 2
[1] FALSE
D506V9, binary
                  cls
clus                 0   1
  ZNF644 MUTATED    18   1
  ZNF644 WILD-TYPE 332  21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF644 MUTATED     18    1
  ZNF644 WILD-TYPE  332   21
     clus
vv    ZNF644 MUTATED ZNF644 WILD-TYPE
  NO              18              332
  YES              1               21
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ZNF644 MUTATED                     14                             3
  ZNF644 WILD-TYPE                  301                            44
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ZNF644 MUTATED                       4                              0
  ZNF644 WILD-TYPE                   102                             10
D506V10, multiclass
                                clus
vv                               ZNF644 MUTATED ZNF644 WILD-TYPE
  COLON ADENOCARCINOMA                       14              301
  COLON MUCINOUS ADENOCARCINOMA               3               44
  RECTAL ADENOCARCINOMA                       4              102
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ZNF644 MUTATED    14   0   0   3
  ZNF644 WILD-TYPE 331   4  31  22
D506V11, multiclass
    clus
vv   ZNF644 MUTATED ZNF644 WILD-TYPE
  R0             14              331
  R1              0                4
  R2              0               31
  RX              3               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D506V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF644 MUTATED                                  0     3
  ZNF644 WILD-TYPE                                1     8
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZNF644 MUTATED                           2    10
  ZNF644 WILD-TYPE                        20   216
D506V13, multiclass
                                  clus
vv                                 ZNF644 MUTATED ZNF644 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         3                8
  BLACK OR AFRICAN AMERICAN                     2               20
  WHITE                                        10              216
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(507) Variable = XPOT MUTATION ANALYSIS
D507V1, survival
                sevent
clus2              0   1
  XPOT MUTATED     8   2
  XPOT WILD-TYPE 370  91
  XPOT MUTATED XPOT WILD-TYPE 
            10            461 
  XPOT MUTATED XPOT WILD-TYPE 
             2             91 
$`XPOT MUTATED`
TCGA-AA-A00N TCGA-AA-A00R TCGA-AZ-6598 TCGA-CA-6717 TCGA-CK-4947 TCGA-G4-6586 
        4.01         0.99        49.41        12.76        17.56        35.80 
TCGA-G4-6588 TCGA-AH-6544 TCGA-CI-6624 TCGA-EI-6510 
       26.17        38.56         4.73        18.28 

$`XPOT WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W 
       18.05        38.04        27.02        42.02        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 
      106.75        22.36        62.79        88.21         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       10.06        14.30       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       22.09        13.78        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       41.00        38.04       117.11         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CL-5917 TCGA-CL-5918 
        0.72         6.05        33.17         6.97        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       19.96        20.91         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  XPOT MUTATED XPOT WILD-TYPE 
          0.99           0.00 
  XPOT MUTATED XPOT WILD-TYPE 
         49.41         148.01 
  XPOT MUTATED XPOT WILD-TYPE 
         17.92          20.28 
[1] "1.0 - 49.4 (17.9)"  "0.0 - 148.0 (20.3)"
[1] "hr=" "1.3"
D507V2, continuous
D507V3, binary
                cls
clus               0   1
  XPOT MUTATED     8   3
  XPOT WILD-TYPE 358 116
[1] "tbl2"
                cls
clus             [,1] [,2]
  XPOT MUTATED      8    3
  XPOT WILD-TYPE  358  116
        clus
vv       XPOT MUTATED XPOT WILD-TYPE
  COLON             8            358
  RECTUM            3            116
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  XPOT MUTATED         2        0        1         4         1         0
  XPOT WILD-TYPE      89        1       31       134         9         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  XPOT MUTATED           0          0          1          0        0         1
  XPOT WILD-TYPE        24         11         58         42       48        17
                vv
clus             STAGE IVB
  XPOT MUTATED           0
  XPOT WILD-TYPE         1
D507V4, multiclass
            clus
vv           XPOT MUTATED XPOT WILD-TYPE
  STAGE I               2             89
  STAGE IA              0              1
  STAGE II              1             31
  STAGE IIA             4            134
  STAGE IIB             1              9
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            1             58
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             1             17
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  XPOT MUTATED     0   3   6   2
  XPOT WILD-TYPE  17  89 323  48
D507V5, multiclass
    clus
vv   XPOT MUTATED XPOT WILD-TYPE
  T1            0             17
  T2            3             89
  T3            6            323
  T4            2             48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  XPOT MUTATED     9   2   0
  XPOT WILD-TYPE 278 111  87
D507V6, multiclass
    clus
vv   XPOT MUTATED XPOT WILD-TYPE
  N0            9            278
  N1            2            111
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D507V7, binary
                cls
clus               0   1
  XPOT MUTATED     8   1
  XPOT WILD-TYPE 367  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  XPOT MUTATED      8    1
  XPOT WILD-TYPE  367   64
   clus
vv  XPOT MUTATED XPOT WILD-TYPE
  0            8            367
  1            1             64
[1] 2 2
[1] FALSE
D507V8, binary
                cls
clus               0   1
  XPOT MUTATED     8   3
  XPOT WILD-TYPE 217 261
[1] "tbl2"
                cls
clus             [,1] [,2]
  XPOT MUTATED      8    3
  XPOT WILD-TYPE  217  261
        clus
vv       XPOT MUTATED XPOT WILD-TYPE
  FEMALE            8            217
  MALE              3            261
[1] 2 2
[1] FALSE
D507V9, binary
                cls
clus               0   1
  XPOT MUTATED     7   0
  XPOT WILD-TYPE 343  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  XPOT MUTATED      7    0
  XPOT WILD-TYPE  343   22
     clus
vv    XPOT MUTATED XPOT WILD-TYPE
  NO             7            343
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  XPOT MUTATED                      6                             2
  XPOT WILD-TYPE                  309                            45
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  XPOT MUTATED                       3                              0
  XPOT WILD-TYPE                   103                             10
D507V10, multiclass
                                clus
vv                               XPOT MUTATED XPOT WILD-TYPE
  COLON ADENOCARCINOMA                      6            309
  COLON MUCINOUS ADENOCARCINOMA             2             45
  RECTAL ADENOCARCINOMA                     3            103
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  XPOT MUTATED     6   0   0   2
  XPOT WILD-TYPE 339   4  31  23
D507V11, multiclass
    clus
vv   XPOT MUTATED XPOT WILD-TYPE
  R0            6            339
  R1            0              4
  R2            0             31
  RX            2             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D507V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  XPOT MUTATED                                  0     1
  XPOT WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  XPOT MUTATED                           0     7
  XPOT WILD-TYPE                        22   219
D507V13, multiclass
                                  clus
vv                                 XPOT MUTATED XPOT WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       7            219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(508) Variable = TIFA MUTATION ANALYSIS
D508V1, survival
                sevent
clus2              0   1
  TIFA MUTATED     5   0
  TIFA WILD-TYPE 373  93
  TIFA MUTATED TIFA WILD-TYPE 
             5            466 
  TIFA MUTATED TIFA WILD-TYPE 
             0             93 
$`TIFA MUTATED`
TCGA-AA-3663 TCGA-CA-6715 TCGA-CM-5348 TCGA-D5-5541 TCGA-G4-6317 
        6.97         0.07        22.98        55.92        36.00 

$`TIFA WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.05        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5860 
       25.02        13.02        29.06        22.03        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-6529 TCGA-D5-6532 
       45.40        12.26        19.59        56.09        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  TIFA MUTATED TIFA WILD-TYPE 
          0.07           0.00 
  TIFA MUTATED TIFA WILD-TYPE 
         55.92         148.01 
  TIFA MUTATED TIFA WILD-TYPE 
        22.980         20.155 
[1] "0.1 - 55.9 (23.0)"  "0.0 - 148.0 (20.2)"
[1] "hr="     "3300000"
D508V2, continuous
D508V3, binary
                cls
clus               0   1
  TIFA MUTATED     6   0
  TIFA WILD-TYPE 360 119
[1] "tbl2"
                cls
clus             [,1] [,2]
  TIFA MUTATED      6    0
  TIFA WILD-TYPE  360  119
        clus
vv       TIFA MUTATED TIFA WILD-TYPE
  COLON             6            360
  RECTUM            0            119
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TIFA MUTATED         0        0        1         1         0         0
  TIFA WILD-TYPE      91        1       31       137        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TIFA MUTATED           0          0          3          1        0         0
  TIFA WILD-TYPE        24         11         56         41       48        18
                vv
clus             STAGE IVB
  TIFA MUTATED           0
  TIFA WILD-TYPE         1
D508V4, multiclass
            clus
vv           TIFA MUTATED TIFA WILD-TYPE
  STAGE I               0             91
  STAGE IA              0              1
  STAGE II              1             31
  STAGE IIA             1            137
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            3             56
  STAGE IIIC            1             41
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  TIFA MUTATED     0   0   6   0
  TIFA WILD-TYPE  17  92 323  50
D508V5, multiclass
    clus
vv   TIFA MUTATED TIFA WILD-TYPE
  T1            0             17
  T2            0             92
  T3            6            323
  T4            0             50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  TIFA MUTATED     2   3   1
  TIFA WILD-TYPE 285 110  86
D508V6, multiclass
    clus
vv   TIFA MUTATED TIFA WILD-TYPE
  N0            2            285
  N1            3            110
  N2            1             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D508V7, binary
                cls
clus               0   1
  TIFA MUTATED     5   0
  TIFA WILD-TYPE 370  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  TIFA MUTATED      5    0
  TIFA WILD-TYPE  370   65
   clus
vv  TIFA MUTATED TIFA WILD-TYPE
  0            5            370
  1            0             65
[1] 2 2
[1] FALSE
D508V8, binary
                cls
clus               0   1
  TIFA MUTATED     2   4
  TIFA WILD-TYPE 223 260
[1] "tbl2"
                cls
clus             [,1] [,2]
  TIFA MUTATED      2    4
  TIFA WILD-TYPE  223  260
        clus
vv       TIFA MUTATED TIFA WILD-TYPE
  FEMALE            2            223
  MALE              4            260
[1] 2 2
[1] FALSE
D508V9, binary
                cls
clus               0   1
  TIFA MUTATED     4   0
  TIFA WILD-TYPE 346  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  TIFA MUTATED      4    0
  TIFA WILD-TYPE  346   22
     clus
vv    TIFA MUTATED TIFA WILD-TYPE
  NO             4            346
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  TIFA MUTATED                      6                             0
  TIFA WILD-TYPE                  309                            47
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  TIFA MUTATED                       0                              0
  TIFA WILD-TYPE                   106                             10
D508V10, multiclass
                                clus
vv                               TIFA MUTATED TIFA WILD-TYPE
  COLON ADENOCARCINOMA                      6            309
  COLON MUCINOUS ADENOCARCINOMA             0             47
  RECTAL ADENOCARCINOMA                     0            106
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  TIFA MUTATED     5   0   0   1
  TIFA WILD-TYPE 340   4  31  24
D508V11, multiclass
    clus
vv   TIFA MUTATED TIFA WILD-TYPE
  R0            5            340
  R1            0              4
  R2            0             31
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D508V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TIFA MUTATED                                  0     1
  TIFA WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  TIFA MUTATED                           0     3
  TIFA WILD-TYPE                        22   223
D508V13, multiclass
                                  clus
vv                                 TIFA MUTATED TIFA WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       3            223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(509) Variable = STK38L MUTATION ANALYSIS
D509V1, survival
                  sevent
clus2                0   1
  STK38L MUTATED     9   1
  STK38L WILD-TYPE 369  92
  STK38L MUTATED STK38L WILD-TYPE 
              10              461 
  STK38L MUTATED STK38L WILD-TYPE 
               1               92 
$`STK38L MUTATED`
TCGA-AA-A00N TCGA-AA-A010 TCGA-AD-6963 TCGA-AY-6386 TCGA-CM-5348 TCGA-D5-6539 
        4.01        34.98        27.42        17.82        22.98        12.49 
TCGA-G4-6323 TCGA-AG-A002 TCGA-AH-6549 TCGA-F5-6465 
       13.78        20.98        17.49        49.51 

$`STK38L WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6964 
       56.55         0.79         0.72         5.79        22.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       29.06        22.03        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 
       43.27        15.12        17.85         4.80        17.13        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 
       38.04       117.11        38.56         1.45         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6571 TCGA-F5-6702 
       19.96        20.91        18.28         9.96        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  STK38L MUTATED STK38L WILD-TYPE 
            4.01             0.00 
  STK38L MUTATED STK38L WILD-TYPE 
           49.51           148.01 
  STK38L MUTATED STK38L WILD-TYPE 
           19.40            20.19 
[1] "4.0 - 49.5 (19.4)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.7"
D509V2, continuous
D509V3, binary
                  cls
clus                 0   1
  STK38L MUTATED     7   3
  STK38L WILD-TYPE 359 116
[1] "tbl2"
                  cls
clus               [,1] [,2]
  STK38L MUTATED      7    3
  STK38L WILD-TYPE  359  116
        clus
vv       STK38L MUTATED STK38L WILD-TYPE
  COLON               7              359
  RECTUM              3              116
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  STK38L MUTATED         1        1        0         1         2         0
  STK38L WILD-TYPE      90        0       32       137         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  STK38L MUTATED           0          1          2          0        0
  STK38L WILD-TYPE        24         10         57         42       48
                  vv
clus               STAGE IVA STAGE IVB
  STK38L MUTATED           0         0
  STK38L WILD-TYPE        18         1
D509V4, multiclass
            clus
vv           STK38L MUTATED STK38L WILD-TYPE
  STAGE I                 1               90
  STAGE IA                1                0
  STAGE II                0               32
  STAGE IIA               1              137
  STAGE IIB               2                8
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              1               10
  STAGE IIIB              2               57
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  STK38L MUTATED     0   1   6   2
  STK38L WILD-TYPE  17  91 323  48
D509V5, multiclass
    clus
vv   STK38L MUTATED STK38L WILD-TYPE
  T1              0               17
  T2              1               91
  T3              6              323
  T4              2               48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  STK38L MUTATED     7   2   0
  STK38L WILD-TYPE 280 111  87
D509V6, multiclass
    clus
vv   STK38L MUTATED STK38L WILD-TYPE
  N0              7              280
  N1              2              111
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D509V7, binary
                  cls
clus                 0   1
  STK38L MUTATED     7   0
  STK38L WILD-TYPE 368  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  STK38L MUTATED      7    0
  STK38L WILD-TYPE  368   65
   clus
vv  STK38L MUTATED STK38L WILD-TYPE
  0              7              368
  1              0               65
[1] 2 2
[1] FALSE
D509V8, binary
                  cls
clus                 0   1
  STK38L MUTATED     4   6
  STK38L WILD-TYPE 221 258
[1] "tbl2"
                  cls
clus               [,1] [,2]
  STK38L MUTATED      4    6
  STK38L WILD-TYPE  221  258
        clus
vv       STK38L MUTATED STK38L WILD-TYPE
  FEMALE              4              221
  MALE                6              258
[1] 2 2
[1] FALSE
D509V9, binary
                  cls
clus                 0   1
  STK38L MUTATED     9   0
  STK38L WILD-TYPE 341  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  STK38L MUTATED      9    0
  STK38L WILD-TYPE  341   22
     clus
vv    STK38L MUTATED STK38L WILD-TYPE
  NO               9              341
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  STK38L MUTATED                      6                             1
  STK38L WILD-TYPE                  309                            46
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  STK38L MUTATED                       3                              0
  STK38L WILD-TYPE                   103                             10
D509V10, multiclass
                                clus
vv                               STK38L MUTATED STK38L WILD-TYPE
  COLON ADENOCARCINOMA                        6              309
  COLON MUCINOUS ADENOCARCINOMA               1               46
  RECTAL ADENOCARCINOMA                       3              103
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  STK38L MUTATED     8   0   0   1
  STK38L WILD-TYPE 337   4  31  24
D509V11, multiclass
    clus
vv   STK38L MUTATED STK38L WILD-TYPE
  R0              8              337
  R1              0                4
  R2              0               31
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D509V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  STK38L MUTATED                                  0     0
  STK38L WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  STK38L MUTATED                           2     5
  STK38L WILD-TYPE                        20   221
D509V13, multiclass
                                  clus
vv                                 STK38L MUTATED STK38L WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     2               20
  WHITE                                         5              221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(510) Variable = SMARCA4 MUTATION ANALYSIS
D510V1, survival
                   sevent
clus2                 0   1
  SMARCA4 MUTATED    26   6
  SMARCA4 WILD-TYPE 352  87
  SMARCA4 MUTATED SMARCA4 WILD-TYPE 
               32               439 
  SMARCA4 MUTATED SMARCA4 WILD-TYPE 
                6                87 
$`SMARCA4 MUTATED`
TCGA-A6-6653 TCGA-A6-6781 TCGA-AA-3492 TCGA-AA-3518 TCGA-AA-3524 TCGA-AA-3529 
       24.39        19.66         3.02         1.02        36.03         0.00 
TCGA-AA-3558 TCGA-AA-3663 TCGA-AA-3815 TCGA-AA-3977 TCGA-AA-A010 TCGA-AD-6889 
       20.98         6.97        33.04        25.02        34.98        56.55 
TCGA-AD-6964 TCGA-AY-6197 TCGA-AZ-6598 TCGA-AZ-6601 TCGA-CA-6717 TCGA-CK-4950 
       10.88        21.44        49.41       100.01        12.76        85.45 
TCGA-CM-4746 TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-6161 TCGA-CM-6674 
       37.02        13.02        22.03        22.98        15.02        12.95 
TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6928 TCGA-G4-6310 TCGA-G4-6588 TCGA-AG-4007 
       43.27        17.85        11.64        63.62        26.17         1.02 
TCGA-CI-6620 TCGA-DY-A1DG 
       33.17        51.48 

$`SMARCA4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
       25.08        25.18        24.16        21.76        24.69        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.12        20.28         7.04         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3520 
        6.97         1.02        13.02        38.99         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
       37.05         8.05        19.07        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       35.05         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
        0.07        21.37        15.52         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        33.01        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 
      106.75        22.36        62.79        88.21         6.77        12.10 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07        12.20        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       14.30        17.56       148.01        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-5341 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       20.02        25.02        29.06        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6162 TCGA-CM-6163 
        5.03        15.02        15.02        17.03        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       15.02        14.04        11.01        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6535 
       56.09        55.92        20.19        18.25         1.32        15.12 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6315 
       65.85        53.62        44.68        55.04        85.48        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        35.80        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6622 TCGA-CI-6624 
       17.49         0.69         0.72         6.05         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 
      126.44        41.36        57.24        24.13        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  SMARCA4 MUTATED SMARCA4 WILD-TYPE 
                0                 0 
  SMARCA4 MUTATED SMARCA4 WILD-TYPE 
           100.01            148.01 
  SMARCA4 MUTATED SMARCA4 WILD-TYPE 
           22.505            20.020 
[1] "0.0 - 100.0 (22.5)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.2"
D510V2, continuous
D510V3, binary
                   cls
clus                  0   1
  SMARCA4 MUTATED    30   3
  SMARCA4 WILD-TYPE 336 116
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SMARCA4 MUTATED     30    3
  SMARCA4 WILD-TYPE  336  116
        clus
vv       SMARCA4 MUTATED SMARCA4 WILD-TYPE
  COLON               30               336
  RECTUM               3               116
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SMARCA4 MUTATED         4        0        5        11         1         0
  SMARCA4 WILD-TYPE      87        1       27       127         9         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SMARCA4 MUTATED           1          0          4          2        1
  SMARCA4 WILD-TYPE        23         11         55         40       47
                   vv
clus                STAGE IVA STAGE IVB
  SMARCA4 MUTATED           2         0
  SMARCA4 WILD-TYPE        16         1
D510V4, multiclass
            clus
vv           SMARCA4 MUTATED SMARCA4 WILD-TYPE
  STAGE I                  4                87
  STAGE IA                 0                 1
  STAGE II                 5                27
  STAGE IIA               11               127
  STAGE IIB                1                 9
  STAGE IIC                0                 1
  STAGE III                1                23
  STAGE IIIA               0                11
  STAGE IIIB               4                55
  STAGE IIIC               2                40
  STAGE IV                 1                47
  STAGE IVA                2                16
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  SMARCA4 MUTATED     0   5  24   4
  SMARCA4 WILD-TYPE  17  87 305  46
D510V5, multiclass
    clus
vv   SMARCA4 MUTATED SMARCA4 WILD-TYPE
  T1               0                17
  T2               5                87
  T3              24               305
  T4               4                46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  SMARCA4 MUTATED    22   7   4
  SMARCA4 WILD-TYPE 265 106  83
D510V6, multiclass
    clus
vv   SMARCA4 MUTATED SMARCA4 WILD-TYPE
  N0              22               265
  N1               7               106
  N2               4                83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D510V7, binary
                   cls
clus                  0   1
  SMARCA4 MUTATED    25   3
  SMARCA4 WILD-TYPE 350  62
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SMARCA4 MUTATED     25    3
  SMARCA4 WILD-TYPE  350   62
   clus
vv  SMARCA4 MUTATED SMARCA4 WILD-TYPE
  0              25               350
  1               3                62
[1] 2 2
[1] FALSE
D510V8, binary
                   cls
clus                  0   1
  SMARCA4 MUTATED    12  21
  SMARCA4 WILD-TYPE 213 243
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SMARCA4 MUTATED     12   21
  SMARCA4 WILD-TYPE  213  243
        clus
vv       SMARCA4 MUTATED SMARCA4 WILD-TYPE
  FEMALE              12               213
  MALE                21               243
[1] 2 2
[1] FALSE
D510V9, binary
                   cls
clus                  0   1
  SMARCA4 MUTATED    26   1
  SMARCA4 WILD-TYPE 324  21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SMARCA4 MUTATED     26    1
  SMARCA4 WILD-TYPE  324   21
     clus
vv    SMARCA4 MUTATED SMARCA4 WILD-TYPE
  NO               26               324
  YES               1                21
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SMARCA4 MUTATED                     26                             4
  SMARCA4 WILD-TYPE                  289                            43
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SMARCA4 MUTATED                       3                              0
  SMARCA4 WILD-TYPE                   103                             10
D510V10, multiclass
                                clus
vv                               SMARCA4 MUTATED SMARCA4 WILD-TYPE
  COLON ADENOCARCINOMA                        26               289
  COLON MUCINOUS ADENOCARCINOMA                4                43
  RECTAL ADENOCARCINOMA                        3               103
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  SMARCA4 MUTATED    21   1   2   1
  SMARCA4 WILD-TYPE 324   3  29  24
D510V11, multiclass
    clus
vv   SMARCA4 MUTATED SMARCA4 WILD-TYPE
  R0              21               324
  R1               1                 3
  R2               2                29
  RX               1                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D510V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SMARCA4 MUTATED                                  0     2
  SMARCA4 WILD-TYPE                                1     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  SMARCA4 MUTATED                           3    17
  SMARCA4 WILD-TYPE                        19   209
D510V13, multiclass
                                  clus
vv                                 SMARCA4 MUTATED SMARCA4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          2                 9
  BLACK OR AFRICAN AMERICAN                      3                19
  WHITE                                         17               209
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(511) Variable = ZNF691 MUTATION ANALYSIS
D511V1, survival
                  sevent
clus2                0   1
  ZNF691 MUTATED     6   2
  ZNF691 WILD-TYPE 372  91
  ZNF691 MUTATED ZNF691 WILD-TYPE 
               8              463 
  ZNF691 MUTATED ZNF691 WILD-TYPE 
               2               91 
$`ZNF691 MUTATED`
TCGA-AA-3516 TCGA-AZ-6598 TCGA-CK-4952 TCGA-CM-4743 TCGA-D5-6536 TCGA-DM-A282 
       13.02        49.41        15.62        23.05        17.85       139.17 
TCGA-G4-6315 TCGA-AG-3608 
       61.91        15.95 

$`ZNF691 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        1.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 
        5.13       106.75        22.36        62.79        88.21         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       85.45        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
        1.91       124.27        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
        1.32        43.27        15.12         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A285 TCGA-DM-A28C 
        7.50        44.32       131.51       135.65         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       55.04        85.48        63.62        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
       12.03         6.05         0.99        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  ZNF691 MUTATED ZNF691 WILD-TYPE 
           13.02             0.00 
  ZNF691 MUTATED ZNF691 WILD-TYPE 
          139.17           148.01 
  ZNF691 MUTATED ZNF691 WILD-TYPE 
           20.45            20.19 
[1] "13.0 - 139.2 (20.5)" "0.0 - 148.0 (20.2)" 
[1] "hr=" "1.2"
D511V2, continuous
D511V3, binary
                  cls
clus                 0   1
  ZNF691 MUTATED     7   1
  ZNF691 WILD-TYPE 359 118
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF691 MUTATED      7    1
  ZNF691 WILD-TYPE  359  118
        clus
vv       ZNF691 MUTATED ZNF691 WILD-TYPE
  COLON               7              359
  RECTUM              1              118
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZNF691 MUTATED         0        0        1         4         0         0
  ZNF691 WILD-TYPE      91        1       31       134        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF691 MUTATED           1          0          0          1        1
  ZNF691 WILD-TYPE        23         11         59         41       47
                  vv
clus               STAGE IVA STAGE IVB
  ZNF691 MUTATED           0         0
  ZNF691 WILD-TYPE        18         1
D511V4, multiclass
            clus
vv           ZNF691 MUTATED ZNF691 WILD-TYPE
  STAGE I                 0               91
  STAGE IA                0                1
  STAGE II                1               31
  STAGE IIA               4              134
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               1               23
  STAGE IIIA              0               11
  STAGE IIIB              0               59
  STAGE IIIC              1               41
  STAGE IV                1               47
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZNF691 MUTATED     0   0   7   1
  ZNF691 WILD-TYPE  17  92 322  49
D511V5, multiclass
    clus
vv   ZNF691 MUTATED ZNF691 WILD-TYPE
  T1              0               17
  T2              0               92
  T3              7              322
  T4              1               49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  ZNF691 MUTATED     5   1   2
  ZNF691 WILD-TYPE 282 112  85
D511V6, multiclass
    clus
vv   ZNF691 MUTATED ZNF691 WILD-TYPE
  N0              5              282
  N1              1              112
  N2              2               85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D511V7, binary
                  cls
clus                 0   1
  ZNF691 MUTATED     6   1
  ZNF691 WILD-TYPE 369  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF691 MUTATED      6    1
  ZNF691 WILD-TYPE  369   64
   clus
vv  ZNF691 MUTATED ZNF691 WILD-TYPE
  0              6              369
  1              1               64
[1] 2 2
[1] FALSE
D511V8, binary
                  cls
clus                 0   1
  ZNF691 MUTATED     5   3
  ZNF691 WILD-TYPE 220 261
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF691 MUTATED      5    3
  ZNF691 WILD-TYPE  220  261
        clus
vv       ZNF691 MUTATED ZNF691 WILD-TYPE
  FEMALE              5              220
  MALE                3              261
[1] 2 2
[1] FALSE
D511V9, binary
                  cls
clus                 0   1
  ZNF691 MUTATED     6   0
  ZNF691 WILD-TYPE 344  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF691 MUTATED      6    0
  ZNF691 WILD-TYPE  344   22
     clus
vv    ZNF691 MUTATED ZNF691 WILD-TYPE
  NO               6              344
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ZNF691 MUTATED                      5                             2
  ZNF691 WILD-TYPE                  310                            45
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ZNF691 MUTATED                       1                              0
  ZNF691 WILD-TYPE                   105                             10
D511V10, multiclass
                                clus
vv                               ZNF691 MUTATED ZNF691 WILD-TYPE
  COLON ADENOCARCINOMA                        5              310
  COLON MUCINOUS ADENOCARCINOMA               2               45
  RECTAL ADENOCARCINOMA                       1              105
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ZNF691 MUTATED     4   0   0   1
  ZNF691 WILD-TYPE 341   4  31  24
D511V11, multiclass
    clus
vv   ZNF691 MUTATED ZNF691 WILD-TYPE
  R0              4              341
  R1              0                4
  R2              0               31
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D511V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF691 MUTATED                                  0     0
  ZNF691 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZNF691 MUTATED                           0     6
  ZNF691 WILD-TYPE                        22   220
D511V13, multiclass
                                  clus
vv                                 ZNF691 MUTATED ZNF691 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         6              220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(512) Variable = UBR4 MUTATION ANALYSIS
D512V1, survival
                sevent
clus2              0   1
  UBR4 MUTATED    38   7
  UBR4 WILD-TYPE 340  86
  UBR4 MUTATED UBR4 WILD-TYPE 
            45            426 
  UBR4 MUTATED UBR4 WILD-TYPE 
             7             86 
$`UBR4 MUTATED`
TCGA-A6-2676 TCGA-A6-5660 TCGA-A6-6780 TCGA-AA-3516 TCGA-AA-3542 TCGA-AA-3663 
       42.90        29.19        20.12        13.02        12.99         6.97 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3864 TCGA-AA-3950 
       85.05        26.99        19.04        10.06        53.00        24.00 
TCGA-AA-A010 TCGA-AA-A02K TCGA-AD-6895 TCGA-AD-6963 TCGA-AD-6964 TCGA-AY-5543 
       34.98        14.01         0.72        27.42        10.88        33.01 
TCGA-AZ-4315 TCGA-AZ-6601 TCGA-CA-6717 TCGA-CM-4743 TCGA-CM-5863 TCGA-CM-6171 
       58.39       100.01        12.76        23.05        15.02        14.04 
TCGA-CM-6674 TCGA-CM-6676 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6540 
       12.95        11.08        18.25         1.32        15.12        16.14 
TCGA-D5-6927 TCGA-D5-7000 TCGA-DM-A1HB TCGA-F4-6570 TCGA-F4-6856 TCGA-G4-6304 
        9.44        10.26       135.65         6.18        35.31        53.62 
TCGA-G4-6588 TCGA-AG-3598 TCGA-AG-A002 TCGA-AG-A01Y TCGA-AG-A02N TCGA-DC-5337 
       26.17        50.04        20.98        64.01        61.97        15.02 
TCGA-DT-5265 TCGA-EI-6507 TCGA-F5-6811 
        5.29        19.96        32.19 

$`UBR4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       31.63        30.44        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6781 
       24.16        21.76        24.69        24.39        23.87        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        6.97         1.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3543 TCGA-AA-3544 
       34.03        29.00        29.00        26.01         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
       78.08         6.05        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3815 
       19.00        36.00         5.03        19.04        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       31.07        30.05        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       26.01         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02W 
       51.98        39.98         2.01         5.03         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6965 TCGA-AU-3779 
       56.55         0.79         5.79        22.42         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
       27.09        16.31         0.95        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77        12.10        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.20        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
        1.91       124.27        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
        5.03        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       15.02        11.01        13.05        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       20.19        43.27        17.85         4.80        17.13        12.49 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.04        11.64         4.80         1.51        12.00        11.38 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 
      117.07        98.24         8.61        31.96        35.74        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 
        0.53        47.41       133.18        74.56        65.85        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       13.78        35.80        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3599 
       24.00         1.02        46.03        34.03         2.01        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A020 TCGA-AG-A025 
       36.03         9.07        12.00        70.03        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
        1.94        38.96        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5869 TCGA-DC-6155 
        6.97         4.73        78.12         7.17         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
        0.49        20.55        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       31.30        28.57         0.66         0.69        55.76        26.43 

  UBR4 MUTATED UBR4 WILD-TYPE 
          0.72           0.00 
  UBR4 MUTATED UBR4 WILD-TYPE 
        135.65         148.01 
  UBR4 MUTATED UBR4 WILD-TYPE 
        19.960         20.415 
[1] "0.7 - 135.7 (20.0)" "0.0 - 148.0 (20.4)"
[1] "hr=" "1.5"
D512V2, continuous
D512V3, binary
                cls
clus               0   1
  UBR4 MUTATED    39   8
  UBR4 WILD-TYPE 327 111
[1] "tbl2"
                cls
clus             [,1] [,2]
  UBR4 MUTATED     39    8
  UBR4 WILD-TYPE  327  111
        clus
vv       UBR4 MUTATED UBR4 WILD-TYPE
  COLON            39            327
  RECTUM            8            111
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  UBR4 MUTATED         7        0        6        15         4         0
  UBR4 WILD-TYPE      84        1       26       123         6         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  UBR4 MUTATED           3          0          4          2        2         1
  UBR4 WILD-TYPE        21         11         55         40       46        17
                vv
clus             STAGE IVB
  UBR4 MUTATED           0
  UBR4 WILD-TYPE         1
D512V4, multiclass
            clus
vv           UBR4 MUTATED UBR4 WILD-TYPE
  STAGE I               7             84
  STAGE IA              0              1
  STAGE II              6             26
  STAGE IIA            15            123
  STAGE IIB             4              6
  STAGE IIC             0              1
  STAGE III             3             21
  STAGE IIIA            0             11
  STAGE IIIB            4             55
  STAGE IIIC            2             40
  STAGE IV              2             46
  STAGE IVA             1             17
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  UBR4 MUTATED     1   6  33   7
  UBR4 WILD-TYPE  16  86 296  43
D512V5, multiclass
    clus
vv   UBR4 MUTATED UBR4 WILD-TYPE
  T1            1             16
  T2            6             86
  T3           33            296
  T4            7             43
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  UBR4 MUTATED    36   5   6
  UBR4 WILD-TYPE 251 108  81
D512V6, multiclass
    clus
vv   UBR4 MUTATED UBR4 WILD-TYPE
  N0           36            251
  N1            5            108
  N2            6             81
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D512V7, binary
                cls
clus               0   1
  UBR4 MUTATED    38   3
  UBR4 WILD-TYPE 337  62
[1] "tbl2"
                cls
clus             [,1] [,2]
  UBR4 MUTATED     38    3
  UBR4 WILD-TYPE  337   62
   clus
vv  UBR4 MUTATED UBR4 WILD-TYPE
  0           38            337
  1            3             62
[1] 2 2
[1] FALSE
D512V8, binary
                cls
clus               0   1
  UBR4 MUTATED    19  28
  UBR4 WILD-TYPE 206 236
[1] "tbl2"
                cls
clus             [,1] [,2]
  UBR4 MUTATED     19   28
  UBR4 WILD-TYPE  206  236
        clus
vv       UBR4 MUTATED UBR4 WILD-TYPE
  FEMALE           19            206
  MALE             28            236
[1] 2 2
[1] FALSE
D512V9, binary
                cls
clus               0   1
  UBR4 MUTATED    39   1
  UBR4 WILD-TYPE 311  21
[1] "tbl2"
                cls
clus             [,1] [,2]
  UBR4 MUTATED     39    1
  UBR4 WILD-TYPE  311   21
     clus
vv    UBR4 MUTATED UBR4 WILD-TYPE
  NO            39            311
  YES            1             21
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  UBR4 MUTATED                     30                             8
  UBR4 WILD-TYPE                  285                            39
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  UBR4 MUTATED                       7                              1
  UBR4 WILD-TYPE                    99                              9
D512V10, multiclass
                                clus
vv                               UBR4 MUTATED UBR4 WILD-TYPE
  COLON ADENOCARCINOMA                     30            285
  COLON MUCINOUS ADENOCARCINOMA             8             39
  RECTAL ADENOCARCINOMA                     7             99
  RECTAL MUCINOUS ADENOCARCINOMA            1              9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  UBR4 MUTATED    32   0   2   4
  UBR4 WILD-TYPE 313   4  29  21
D512V11, multiclass
    clus
vv   UBR4 MUTATED UBR4 WILD-TYPE
  R0           32            313
  R1            0              4
  R2            2             29
  RX            4             21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D512V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  UBR4 MUTATED                                  0     2
  UBR4 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  UBR4 MUTATED                           2    27
  UBR4 WILD-TYPE                        20   199
D512V13, multiclass
                                  clus
vv                                 UBR4 MUTATED UBR4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              9
  BLACK OR AFRICAN AMERICAN                   2             20
  WHITE                                      27            199
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(513) Variable = LPCAT3 MUTATION ANALYSIS
D513V1, survival
                  sevent
clus2                0   1
  LPCAT3 MUTATED     4   1
  LPCAT3 WILD-TYPE 374  92
  LPCAT3 MUTATED LPCAT3 WILD-TYPE 
               5              466 
  LPCAT3 MUTATED LPCAT3 WILD-TYPE 
               1               92 
$`LPCAT3 MUTATED`
TCGA-AA-3542 TCGA-AA-A01Q TCGA-AZ-6598 TCGA-D5-6536 TCGA-G4-6628 
       12.99         1.02        49.41        17.85        79.69 

$`LPCAT3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       29.00        26.01         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01R TCGA-AA-A01S 
       12.00        31.00        31.00        38.07        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 
      106.75        22.36        62.79        88.21         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 
       18.25         1.32        43.27        15.12         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       46.75        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  LPCAT3 MUTATED LPCAT3 WILD-TYPE 
            1.02             0.00 
  LPCAT3 MUTATED LPCAT3 WILD-TYPE 
           79.69           148.01 
  LPCAT3 MUTATED LPCAT3 WILD-TYPE 
          17.850           20.235 
[1] "1.0 - 79.7 (17.9)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.3"
D513V2, continuous
D513V3, binary
                  cls
clus                 0   1
  LPCAT3 MUTATED     5   0
  LPCAT3 WILD-TYPE 361 119
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LPCAT3 MUTATED      5    0
  LPCAT3 WILD-TYPE  361  119
        clus
vv       LPCAT3 MUTATED LPCAT3 WILD-TYPE
  COLON               5              361
  RECTUM              0              119
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  LPCAT3 MUTATED         1        0        2         1         0         0
  LPCAT3 WILD-TYPE      90        1       30       137        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  LPCAT3 MUTATED           0          0          0          1        0
  LPCAT3 WILD-TYPE        24         11         59         41       48
                  vv
clus               STAGE IVA STAGE IVB
  LPCAT3 MUTATED           0         0
  LPCAT3 WILD-TYPE        18         1
D513V4, multiclass
            clus
vv           LPCAT3 MUTATED LPCAT3 WILD-TYPE
  STAGE I                 1               90
  STAGE IA                0                1
  STAGE II                2               30
  STAGE IIA               1              137
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              0               59
  STAGE IIIC              1               41
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  LPCAT3 MUTATED     0   1   4   0
  LPCAT3 WILD-TYPE  17  91 325  50
D513V5, multiclass
    clus
vv   LPCAT3 MUTATED LPCAT3 WILD-TYPE
  T1              0               17
  T2              1               91
  T3              4              325
  T4              0               50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  LPCAT3 MUTATED     4   0   1
  LPCAT3 WILD-TYPE 283 113  86
D513V6, multiclass
    clus
vv   LPCAT3 MUTATED LPCAT3 WILD-TYPE
  N0              4              283
  N1              0              113
  N2              1               86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D513V7, binary
                  cls
clus                 0   1
  LPCAT3 MUTATED     4   0
  LPCAT3 WILD-TYPE 371  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LPCAT3 MUTATED      4    0
  LPCAT3 WILD-TYPE  371   65
   clus
vv  LPCAT3 MUTATED LPCAT3 WILD-TYPE
  0              4              371
  1              0               65
[1] 2 2
[1] FALSE
D513V8, binary
                  cls
clus                 0   1
  LPCAT3 MUTATED     2   3
  LPCAT3 WILD-TYPE 223 261
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LPCAT3 MUTATED      2    3
  LPCAT3 WILD-TYPE  223  261
        clus
vv       LPCAT3 MUTATED LPCAT3 WILD-TYPE
  FEMALE              2              223
  MALE                3              261
[1] 2 2
[1] FALSE
D513V9, binary
                  cls
clus                 0   1
  LPCAT3 MUTATED     4   0
  LPCAT3 WILD-TYPE 346  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LPCAT3 MUTATED      4    0
  LPCAT3 WILD-TYPE  346   22
     clus
vv    LPCAT3 MUTATED LPCAT3 WILD-TYPE
  NO               4              346
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  LPCAT3 MUTATED                      5                             0
  LPCAT3 WILD-TYPE                  310                            47
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  LPCAT3 MUTATED                       0                              0
  LPCAT3 WILD-TYPE                   106                             10
D513V10, multiclass
                                clus
vv                               LPCAT3 MUTATED LPCAT3 WILD-TYPE
  COLON ADENOCARCINOMA                        5              310
  COLON MUCINOUS ADENOCARCINOMA               0               47
  RECTAL ADENOCARCINOMA                       0              106
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  LPCAT3 MUTATED     4   0   0   0
  LPCAT3 WILD-TYPE 341   4  31  25
D513V11, multiclass
    clus
vv   LPCAT3 MUTATED LPCAT3 WILD-TYPE
  R0              4              341
  R1              0                4
  R2              0               31
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D513V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  LPCAT3 MUTATED                                  0     0
  LPCAT3 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  LPCAT3 MUTATED                           0     3
  LPCAT3 WILD-TYPE                        22   223
D513V13, multiclass
                                  clus
vv                                 LPCAT3 MUTATED LPCAT3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         3              223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(514) Variable = STX7 MUTATION ANALYSIS
D514V1, survival
                sevent
clus2              0   1
  STX7 MUTATED     3   1
  STX7 WILD-TYPE 375  92
  STX7 MUTATED STX7 WILD-TYPE 
             4            467 
  STX7 MUTATED STX7 WILD-TYPE 
             1             92 
$`STX7 MUTATED`
TCGA-AA-3815 TCGA-AA-A00N TCGA-CA-6717 TCGA-AG-3892 
       33.04         4.01        12.76        13.02 

$`STX7 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       19.04        10.06        35.05         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.20        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 
       19.99         1.02        17.95        36.95        17.03        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  STX7 MUTATED STX7 WILD-TYPE 
          4.01           0.00 
  STX7 MUTATED STX7 WILD-TYPE 
         33.04         148.01 
  STX7 MUTATED STX7 WILD-TYPE 
         12.89          20.28 
[1] "4.0 - 33.0 (12.9)"  "0.0 - 148.0 (20.3)"
[1] "hr=" "2.1"
D514V2, continuous
D514V3, binary
                cls
clus               0   1
  STX7 MUTATED     4   1
  STX7 WILD-TYPE 362 118
[1] "tbl2"
                cls
clus             [,1] [,2]
  STX7 MUTATED      4    1
  STX7 WILD-TYPE  362  118
        clus
vv       STX7 MUTATED STX7 WILD-TYPE
  COLON             4            362
  RECTUM            1            118
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  STX7 MUTATED         1        0        0         3         1         0
  STX7 WILD-TYPE      90        1       32       135         9         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  STX7 MUTATED           0          0          0          0        0         0
  STX7 WILD-TYPE        24         11         59         42       48        18
                vv
clus             STAGE IVB
  STX7 MUTATED           0
  STX7 WILD-TYPE         1
D514V4, multiclass
            clus
vv           STX7 MUTATED STX7 WILD-TYPE
  STAGE I               1             90
  STAGE IA              0              1
  STAGE II              0             32
  STAGE IIA             3            135
  STAGE IIB             1              9
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            0             59
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  STX7 MUTATED     1   0   3   1
  STX7 WILD-TYPE  16  92 326  49
D514V5, multiclass
    clus
vv   STX7 MUTATED STX7 WILD-TYPE
  T1            1             16
  T2            0             92
  T3            3            326
  T4            1             49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  STX7 MUTATED     5   0   0
  STX7 WILD-TYPE 282 113  87
D514V6, multiclass
    clus
vv   STX7 MUTATED STX7 WILD-TYPE
  N0            5            282
  N1            0            113
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D514V7, binary
                cls
clus               0   1
  STX7 MUTATED     5   0
  STX7 WILD-TYPE 370  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  STX7 MUTATED      5    0
  STX7 WILD-TYPE  370   65
   clus
vv  STX7 MUTATED STX7 WILD-TYPE
  0            5            370
  1            0             65
[1] 2 2
[1] FALSE
D514V8, binary
                cls
clus               0   1
  STX7 MUTATED     3   2
  STX7 WILD-TYPE 222 262
[1] "tbl2"
                cls
clus             [,1] [,2]
  STX7 MUTATED      3    2
  STX7 WILD-TYPE  222  262
        clus
vv       STX7 MUTATED STX7 WILD-TYPE
  FEMALE            3            222
  MALE              2            262
[1] 2 2
[1] FALSE
D514V9, binary
                cls
clus               0   1
  STX7 MUTATED     3   0
  STX7 WILD-TYPE 347  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  STX7 MUTATED      3    0
  STX7 WILD-TYPE  347   22
     clus
vv    STX7 MUTATED STX7 WILD-TYPE
  NO             3            347
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  STX7 MUTATED                      2                             2
  STX7 WILD-TYPE                  313                            45
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  STX7 MUTATED                       1                              0
  STX7 WILD-TYPE                   105                             10
D514V10, multiclass
                                clus
vv                               STX7 MUTATED STX7 WILD-TYPE
  COLON ADENOCARCINOMA                      2            313
  COLON MUCINOUS ADENOCARCINOMA             2             45
  RECTAL ADENOCARCINOMA                     1            105
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  STX7 MUTATED     4   0   0   1
  STX7 WILD-TYPE 341   4  31  24
D514V11, multiclass
    clus
vv   STX7 MUTATED STX7 WILD-TYPE
  R0            4            341
  R1            0              4
  R2            0             31
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D514V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  STX7 MUTATED                                  0     1
  STX7 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  STX7 MUTATED                           0     0
  STX7 WILD-TYPE                        22   226
D514V13, multiclass
[1] "Remove cluster labels:" "STX7 MUTATED"          
clus
  STX7 MUTATED STX7 WILD-TYPE 
             1            259 
    TCGA-A6-2671     TCGA-A6-2672     TCGA-A6-2674     TCGA-A6-2676 
"STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" 
    TCGA-A6-2677     TCGA-A6-2678     TCGA-A6-2683     TCGA-A6-3807 
"STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" 
    TCGA-A6-3808     TCGA-A6-3809     TCGA-A6-3810     TCGA-A6-4105 
"STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" 
    TCGA-A6-5656     TCGA-A6-5657     TCGA-A6-5659     TCGA-A6-5660 
"STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" 
    TCGA-A6-5661     TCGA-A6-5662     TCGA-A6-5664     TCGA-A6-5665 
"STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" 
    TCGA-A6-5666     TCGA-A6-6137     TCGA-A6-6138     TCGA-A6-6141 
"STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" 
    TCGA-A6-6142     TCGA-A6-6648     TCGA-A6-6649     TCGA-A6-6651 
"STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" 
    TCGA-A6-6652     TCGA-A6-6653     TCGA-A6-6654     TCGA-A6-6780 
"STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" 
    TCGA-A6-6781     TCGA-A6-6782     TCGA-AD-5900     TCGA-AD-6548 
"STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" 
    TCGA-AD-6888     TCGA-AD-6889     TCGA-AD-6890     TCGA-AD-6895 
"STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" 
    TCGA-AD-6899     TCGA-AD-6901     TCGA-AD-6963     TCGA-AD-6964 
"STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" 
    TCGA-AD-6965     TCGA-AU-3779     TCGA-AU-6004     TCGA-AY-4070 
"STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" 
    TCGA-AY-4071     TCGA-AY-5543     TCGA-AY-6196     TCGA-AY-6197 
"STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" 
    TCGA-AY-6386     TCGA-AZ-4315     TCGA-AZ-4323     TCGA-AZ-4616 
"STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" 
    TCGA-AZ-4681     TCGA-AZ-4682     TCGA-AZ-5403     TCGA-AZ-5407 
"STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" 
    TCGA-AZ-6598     TCGA-AZ-6599     TCGA-AZ-6600     TCGA-AZ-6601 
"STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" 
    TCGA-AZ-6603     TCGA-AZ-6605     TCGA-AZ-6606     TCGA-AZ-6607 
"STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" 
    TCGA-AZ-6608     TCGA-CA-5254     TCGA-CA-5255     TCGA-CA-5796 
"STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" 
    TCGA-CA-5797     TCGA-CA-6715     TCGA-CA-6716     TCGA-CA-6718 
"STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" 
    TCGA-CA-6719     TCGA-CK-4947     TCGA-CK-4948     TCGA-CK-4950 
"STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" 
    TCGA-CK-4952     TCGA-CK-5912     TCGA-CK-5913     TCGA-CK-5914 
"STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" 
    TCGA-CK-5915     TCGA-CK-5916     TCGA-CK-6746     TCGA-CK-6747 
"STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" 
    TCGA-CK-6748     TCGA-CK-6751     TCGA-CM-4743     TCGA-CM-4744 
"STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" 
    TCGA-CM-4746     TCGA-CM-4747     TCGA-CM-4752     TCGA-CM-5341 
"STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" 
    TCGA-CM-5344     TCGA-CM-5348     TCGA-CM-5349     TCGA-CM-5860 
"STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" 
    TCGA-CM-5861     TCGA-CM-5862     TCGA-CM-5863     TCGA-CM-5864 
"STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" 
    TCGA-CM-5868     TCGA-CM-6161     TCGA-CM-6162     TCGA-CM-6163 
"STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" 
    TCGA-CM-6164     TCGA-CM-6165     TCGA-CM-6166     TCGA-CM-6167 
"STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" 
    TCGA-CM-6168     TCGA-CM-6169     TCGA-CM-6170     TCGA-CM-6171 
"STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" 
    TCGA-CM-6172     TCGA-CM-6674     TCGA-CM-6675     TCGA-CM-6676 
"STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" 
    TCGA-CM-6677     TCGA-CM-6678     TCGA-CM-6679     TCGA-CM-6680 
"STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" 
    TCGA-D5-5537     TCGA-D5-5538     TCGA-D5-5539     TCGA-D5-5540 
"STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" 
    TCGA-D5-5541     TCGA-D5-6529     TCGA-D5-6532     TCGA-D5-6533 
"STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" 
    TCGA-D5-6534     TCGA-D5-6535     TCGA-D5-6536     TCGA-D5-6537 
"STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" 
    TCGA-D5-6538     TCGA-D5-6539     TCGA-D5-6540     TCGA-D5-6541 
"STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" 
    TCGA-D5-6898     TCGA-D5-6920     TCGA-D5-6922     TCGA-D5-6923 
"STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" 
    TCGA-D5-6924     TCGA-D5-6926     TCGA-D5-6927     TCGA-D5-6928 
"STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" 
    TCGA-D5-6929     TCGA-D5-6930     TCGA-D5-6931     TCGA-D5-6932 
"STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" 
    TCGA-D5-7000     TCGA-DM-A0X9     TCGA-DM-A0XD     TCGA-DM-A0XF 
"STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" 
    TCGA-DM-A1D0     TCGA-DM-A1D4     TCGA-DM-A1D6     TCGA-DM-A1D7 
"STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" 
    TCGA-DM-A1D8     TCGA-DM-A1D9     TCGA-DM-A1DA     TCGA-DM-A1DB 
"STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" 
    TCGA-DM-A1HA     TCGA-DM-A1HB     TCGA-DM-A282     TCGA-DM-A285 
"STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" 
    TCGA-DM-A28C     TCGA-DM-A28E     TCGA-DM-A28F     TCGA-DM-A28G 
"STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" 
    TCGA-DM-A28H     TCGA-DM-A28K     TCGA-F4-6459     TCGA-F4-6460 
"STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" 
    TCGA-F4-6569     TCGA-F4-6570     TCGA-F4-6703     TCGA-F4-6704 
"STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" 
    TCGA-F4-6805     TCGA-F4-6806     TCGA-F4-6807     TCGA-F4-6808 
"STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" 
    TCGA-F4-6809     TCGA-F4-6854     TCGA-F4-6855     TCGA-F4-6856 
"STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" 
    TCGA-G4-6293     TCGA-G4-6299     TCGA-G4-6303     TCGA-G4-6304 
"STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" 
    TCGA-G4-6306     TCGA-G4-6307     TCGA-G4-6309     TCGA-G4-6310 
"STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" 
    TCGA-G4-6315     TCGA-G4-6317     TCGA-G4-6321     TCGA-G4-6323 
"STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" 
    TCGA-G4-6586     TCGA-G4-6588     TCGA-G4-6625     TCGA-G4-6626 
"STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" 
    TCGA-G4-6628     TCGA-AF-2687     TCGA-AF-2689     TCGA-AF-2691 
"STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" 
    TCGA-AF-2692     TCGA-AF-2693     TCGA-AF-3400     TCGA-AF-3913 
"STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" 
    TCGA-AF-4110     TCGA-AF-5654     TCGA-AF-6136     TCGA-AF-6655 
"STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" 
    TCGA-AF-6672     TCGA-AH-6544     TCGA-AH-6547     TCGA-AH-6549 
"STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" 
    TCGA-AH-6643     TCGA-AH-6644     TCGA-CI-6619     TCGA-CI-6620 
"STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" 
    TCGA-CI-6621     TCGA-CI-6622     TCGA-CI-6624     TCGA-CL-5917 
"STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" 
    TCGA-CL-5918     TCGA-DC-5337     TCGA-DC-5869     TCGA-DC-6155 
"STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" 
    TCGA-DC-6157     TCGA-DC-6158     TCGA-DC-6160     TCGA-DC-6681 
"STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" 
    TCGA-DC-6682     TCGA-DC-6683     TCGA-DT-5265     TCGA-DY-A0XA 
"STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" 
    TCGA-DY-A1DC     TCGA-DY-A1DD     TCGA-DY-A1DF     TCGA-DY-A1DG 
"STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" 
    TCGA-DY-A1H8     TCGA-EF-5830     TCGA-EI-6506     TCGA-EI-6507 
"STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" 
    TCGA-EI-6508     TCGA-EI-6510     TCGA-F5-6464     TCGA-F5-6465 
"STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" 
    TCGA-F5-6571     TCGA-F5-6702     TCGA-F5-6811     TCGA-F5-6812 
"STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" 
    TCGA-F5-6813     TCGA-G5-6235     TCGA-G5-6641 
"STX7 WILD-TYPE" "STX7 WILD-TYPE" "STX7 WILD-TYPE" 

Clustering(515) Variable = SLC2A3 MUTATION ANALYSIS
D515V1, survival
                  sevent
clus2                0   1
  SLC2A3 MUTATED    10   1
  SLC2A3 WILD-TYPE 368  92
  SLC2A3 MUTATED SLC2A3 WILD-TYPE 
              11              460 
  SLC2A3 MUTATED SLC2A3 WILD-TYPE 
               1               92 
$`SLC2A3 MUTATED`
TCGA-A6-5665 TCGA-A6-6141 TCGA-A6-6781 TCGA-AA-A01D TCGA-AY-5543 TCGA-AZ-4315 
       22.06         8.38        19.66        10.98        33.01        58.39 
TCGA-CK-4950 TCGA-CM-6676 TCGA-DM-A1HA TCGA-G4-6588 TCGA-G4-6628 
       85.45        11.08       131.51        26.17        79.69 

$`SLC2A3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 
       22.09        32.71        27.09        22.52        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       34.98         1.02        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6197 TCGA-AY-6386 
       14.50        27.09        16.31         0.95        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
       17.56       148.01        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       11.01        12.95        13.05        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HB 
       13.32        12.59       140.38         7.50        44.32       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 
       61.91        36.00        22.09        13.78        35.80        91.79 
TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       46.75        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  SLC2A3 MUTATED SLC2A3 WILD-TYPE 
            8.38             0.00 
  SLC2A3 MUTATED SLC2A3 WILD-TYPE 
          131.51           148.01 
  SLC2A3 MUTATED SLC2A3 WILD-TYPE 
          26.170           20.085 
[1] "8.4 - 131.5 (26.2)" "0.0 - 148.0 (20.1)"
[1] "hr=" "3.5"
D515V2, continuous
D515V3, binary
                  cls
clus                 0   1
  SLC2A3 MUTATED    11   1
  SLC2A3 WILD-TYPE 355 118
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLC2A3 MUTATED     11    1
  SLC2A3 WILD-TYPE  355  118
        clus
vv       SLC2A3 MUTATED SLC2A3 WILD-TYPE
  COLON              11              355
  RECTUM              1              118
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SLC2A3 MUTATED         2        0        0         4         0         0
  SLC2A3 WILD-TYPE      89        1       32       134        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC2A3 MUTATED           1          0          1          3        0
  SLC2A3 WILD-TYPE        23         11         58         39       48
                  vv
clus               STAGE IVA STAGE IVB
  SLC2A3 MUTATED           1         0
  SLC2A3 WILD-TYPE        17         1
D515V4, multiclass
            clus
vv           SLC2A3 MUTATED SLC2A3 WILD-TYPE
  STAGE I                 2               89
  STAGE IA                0                1
  STAGE II                0               32
  STAGE IIA               4              134
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               1               23
  STAGE IIIA              0               11
  STAGE IIIB              1               58
  STAGE IIIC              3               39
  STAGE IV                0               48
  STAGE IVA               1               17
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  SLC2A3 MUTATED     0   2   9   1
  SLC2A3 WILD-TYPE  17  90 320  49
D515V5, multiclass
    clus
vv   SLC2A3 MUTATED SLC2A3 WILD-TYPE
  T1              0               17
  T2              2               90
  T3              9              320
  T4              1               49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  SLC2A3 MUTATED     6   4   2
  SLC2A3 WILD-TYPE 281 109  85
D515V6, multiclass
    clus
vv   SLC2A3 MUTATED SLC2A3 WILD-TYPE
  N0              6              281
  N1              4              109
  N2              2               85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D515V7, binary
                  cls
clus                 0   1
  SLC2A3 MUTATED     9   1
  SLC2A3 WILD-TYPE 366  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLC2A3 MUTATED      9    1
  SLC2A3 WILD-TYPE  366   64
   clus
vv  SLC2A3 MUTATED SLC2A3 WILD-TYPE
  0              9              366
  1              1               64
[1] 2 2
[1] FALSE
D515V8, binary
                  cls
clus                 0   1
  SLC2A3 MUTATED     5   7
  SLC2A3 WILD-TYPE 220 257
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLC2A3 MUTATED      5    7
  SLC2A3 WILD-TYPE  220  257
        clus
vv       SLC2A3 MUTATED SLC2A3 WILD-TYPE
  FEMALE              5              220
  MALE                7              257
[1] 2 2
[1] FALSE
D515V9, binary
                  cls
clus                 0   1
  SLC2A3 MUTATED    10   0
  SLC2A3 WILD-TYPE 340  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLC2A3 MUTATED     10    0
  SLC2A3 WILD-TYPE  340   22
     clus
vv    SLC2A3 MUTATED SLC2A3 WILD-TYPE
  NO              10              340
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SLC2A3 MUTATED                      9                             2
  SLC2A3 WILD-TYPE                  306                            45
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SLC2A3 MUTATED                       1                              0
  SLC2A3 WILD-TYPE                   105                             10
D515V10, multiclass
                                clus
vv                               SLC2A3 MUTATED SLC2A3 WILD-TYPE
  COLON ADENOCARCINOMA                        9              306
  COLON MUCINOUS ADENOCARCINOMA               2               45
  RECTAL ADENOCARCINOMA                       1              105
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  SLC2A3 MUTATED     8   1   0   0
  SLC2A3 WILD-TYPE 337   3  31  25
D515V11, multiclass
    clus
vv   SLC2A3 MUTATED SLC2A3 WILD-TYPE
  R0              8              337
  R1              1                3
  R2              0               31
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D515V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SLC2A3 MUTATED                                  0     0
  SLC2A3 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  SLC2A3 MUTATED                           3     8
  SLC2A3 WILD-TYPE                        19   218
D515V13, multiclass
                                  clus
vv                                 SLC2A3 MUTATED SLC2A3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     3               19
  WHITE                                         8              218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(516) Variable = HDAC1 MUTATION ANALYSIS
D516V1, survival
                 sevent
clus2               0   1
  HDAC1 MUTATED     4   1
  HDAC1 WILD-TYPE 374  92
  HDAC1 MUTATED HDAC1 WILD-TYPE 
              5             466 
  HDAC1 MUTATED HDAC1 WILD-TYPE 
              1              92 
$`HDAC1 MUTATED`
TCGA-A6-5661 TCGA-A6-6780 TCGA-AA-A01Q TCGA-AA-A02K TCGA-D5-6535 
       33.53        20.12         1.02        14.01        15.12 

$`HDAC1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        31.00        38.07        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        2.01         5.03         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
        1.32        43.27        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  HDAC1 MUTATED HDAC1 WILD-TYPE 
           1.02            0.00 
  HDAC1 MUTATED HDAC1 WILD-TYPE 
          33.53          148.01 
  HDAC1 MUTATED HDAC1 WILD-TYPE 
         15.120          20.415 
[1] "1.0 - 33.5 (15.1)"  "0.0 - 148.0 (20.4)"
[1] "hr=" "1.6"
D516V2, continuous
D516V3, binary
                 cls
clus                0   1
  HDAC1 MUTATED     5   0
  HDAC1 WILD-TYPE 361 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HDAC1 MUTATED      5    0
  HDAC1 WILD-TYPE  361  119
        clus
vv       HDAC1 MUTATED HDAC1 WILD-TYPE
  COLON              5             361
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  HDAC1 MUTATED         0        0        1         2         0         0
  HDAC1 WILD-TYPE      91        1       31       136        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  HDAC1 MUTATED           0          0          1          0        1         0
  HDAC1 WILD-TYPE        24         11         58         42       47        18
                 vv
clus              STAGE IVB
  HDAC1 MUTATED           0
  HDAC1 WILD-TYPE         1
D516V4, multiclass
            clus
vv           HDAC1 MUTATED HDAC1 WILD-TYPE
  STAGE I                0              91
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              2             136
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             0              42
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  HDAC1 MUTATED     0   0   4   1
  HDAC1 WILD-TYPE  17  92 325  49
D516V5, multiclass
    clus
vv   HDAC1 MUTATED HDAC1 WILD-TYPE
  T1             0              17
  T2             0              92
  T3             4             325
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  HDAC1 MUTATED     3   1   1
  HDAC1 WILD-TYPE 284 112  86
D516V6, multiclass
    clus
vv   HDAC1 MUTATED HDAC1 WILD-TYPE
  N0             3             284
  N1             1             112
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D516V7, binary
                 cls
clus                0   1
  HDAC1 MUTATED     2   1
  HDAC1 WILD-TYPE 373  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HDAC1 MUTATED      2    1
  HDAC1 WILD-TYPE  373   64
   clus
vv  HDAC1 MUTATED HDAC1 WILD-TYPE
  0             2             373
  1             1              64
[1] 2 2
[1] FALSE
D516V8, binary
                 cls
clus                0   1
  HDAC1 MUTATED     3   2
  HDAC1 WILD-TYPE 222 262
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HDAC1 MUTATED      3    2
  HDAC1 WILD-TYPE  222  262
        clus
vv       HDAC1 MUTATED HDAC1 WILD-TYPE
  FEMALE             3             222
  MALE               2             262
[1] 2 2
[1] FALSE
D516V9, binary
                 cls
clus                0   1
  HDAC1 MUTATED     4   0
  HDAC1 WILD-TYPE 346  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HDAC1 MUTATED      4    0
  HDAC1 WILD-TYPE  346   22
     clus
vv    HDAC1 MUTATED HDAC1 WILD-TYPE
  NO              4             346
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  HDAC1 MUTATED                      4                             1
  HDAC1 WILD-TYPE                  311                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  HDAC1 MUTATED                       0                              0
  HDAC1 WILD-TYPE                   106                             10
D516V10, multiclass
                                clus
vv                               HDAC1 MUTATED HDAC1 WILD-TYPE
  COLON ADENOCARCINOMA                       4             311
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  HDAC1 MUTATED     2   0   1   1
  HDAC1 WILD-TYPE 343   4  30  24
D516V11, multiclass
    clus
vv   HDAC1 MUTATED HDAC1 WILD-TYPE
  R0             2             343
  R1             0               4
  R2             1              30
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D516V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HDAC1 MUTATED                                  0     0
  HDAC1 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  HDAC1 MUTATED                           1     2
  HDAC1 WILD-TYPE                        21   224
D516V13, multiclass
                                  clus
vv                                 HDAC1 MUTATED HDAC1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        2             224
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(517) Variable = RUFY1 MUTATION ANALYSIS
D517V1, survival
                 sevent
clus2               0   1
  RUFY1 MUTATED    12   2
  RUFY1 WILD-TYPE 366  91
  RUFY1 MUTATED RUFY1 WILD-TYPE 
             14             457 
  RUFY1 MUTATED RUFY1 WILD-TYPE 
              2              91 
$`RUFY1 MUTATED`
TCGA-A6-5665 TCGA-A6-5666 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AY-6386 
       22.06        32.71        61.02        78.08         6.97        17.82 
TCGA-AZ-4315 TCGA-CA-5254 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6931 TCGA-DM-A1DB 
       58.39        12.69        12.49        16.14        12.00        44.32 
TCGA-G4-6309 TCGA-AF-3913 
       85.48        10.39 

$`RUFY1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       22.09        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       13.94        19.99         6.05        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AZ-4323 
       27.09        16.31         0.95        33.01        21.44         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        3.19         1.61         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
        4.80        17.13        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
        1.51        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
        7.50       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       55.04        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-4110 
       39.48        43.04        13.55        19.10        34.49        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  RUFY1 MUTATED RUFY1 WILD-TYPE 
           6.97            0.00 
  RUFY1 MUTATED RUFY1 WILD-TYPE 
          85.48          148.01 
  RUFY1 MUTATED RUFY1 WILD-TYPE 
          19.94           20.19 
[1] "7.0 - 85.5 (19.9)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.9"
D517V2, continuous
D517V3, binary
                 cls
clus                0   1
  RUFY1 MUTATED    13   1
  RUFY1 WILD-TYPE 353 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RUFY1 MUTATED     13    1
  RUFY1 WILD-TYPE  353  118
        clus
vv       RUFY1 MUTATED RUFY1 WILD-TYPE
  COLON             13             353
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RUFY1 MUTATED         1        0        3         4         0         1
  RUFY1 WILD-TYPE      90        1       29       134        10         0
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RUFY1 MUTATED           0          1          2          1        1         0
  RUFY1 WILD-TYPE        24         10         57         41       47        18
                 vv
clus              STAGE IVB
  RUFY1 MUTATED           0
  RUFY1 WILD-TYPE         1
D517V4, multiclass
            clus
vv           RUFY1 MUTATED RUFY1 WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               3              29
  STAGE IIA              4             134
  STAGE IIB              0              10
  STAGE IIC              1               0
  STAGE III              0              24
  STAGE IIIA             1              10
  STAGE IIIB             2              57
  STAGE IIIC             1              41
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  RUFY1 MUTATED     0   1  11   2
  RUFY1 WILD-TYPE  17  91 318  48
D517V5, multiclass
    clus
vv   RUFY1 MUTATED RUFY1 WILD-TYPE
  T1             0              17
  T2             1              91
  T3            11             318
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  RUFY1 MUTATED    10   3   1
  RUFY1 WILD-TYPE 277 110  86
D517V6, multiclass
    clus
vv   RUFY1 MUTATED RUFY1 WILD-TYPE
  N0            10             277
  N1             3             110
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D517V7, binary
                 cls
clus                0   1
  RUFY1 MUTATED    13   1
  RUFY1 WILD-TYPE 362  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RUFY1 MUTATED     13    1
  RUFY1 WILD-TYPE  362   64
   clus
vv  RUFY1 MUTATED RUFY1 WILD-TYPE
  0            13             362
  1             1              64
[1] 2 2
[1] FALSE
D517V8, binary
                 cls
clus                0   1
  RUFY1 MUTATED     6   8
  RUFY1 WILD-TYPE 219 256
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RUFY1 MUTATED      6    8
  RUFY1 WILD-TYPE  219  256
        clus
vv       RUFY1 MUTATED RUFY1 WILD-TYPE
  FEMALE             6             219
  MALE               8             256
[1] 2 2
[1] FALSE
D517V9, binary
                 cls
clus                0   1
  RUFY1 MUTATED    13   0
  RUFY1 WILD-TYPE 337  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RUFY1 MUTATED     13    0
  RUFY1 WILD-TYPE  337   22
     clus
vv    RUFY1 MUTATED RUFY1 WILD-TYPE
  NO             13             337
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  RUFY1 MUTATED                     12                             1
  RUFY1 WILD-TYPE                  303                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  RUFY1 MUTATED                       1                              0
  RUFY1 WILD-TYPE                   105                             10
D517V10, multiclass
                                clus
vv                               RUFY1 MUTATED RUFY1 WILD-TYPE
  COLON ADENOCARCINOMA                      12             303
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  RUFY1 MUTATED    11   0   0   1
  RUFY1 WILD-TYPE 334   4  31  24
D517V11, multiclass
    clus
vv   RUFY1 MUTATED RUFY1 WILD-TYPE
  R0            11             334
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D517V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RUFY1 MUTATED                                  0     1
  RUFY1 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  RUFY1 MUTATED                           3     7
  RUFY1 WILD-TYPE                        19   219
D517V13, multiclass
                                  clus
vv                                 RUFY1 MUTATED RUFY1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    3              19
  WHITE                                        7             219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(518) Variable = PSD MUTATION ANALYSIS
D518V1, survival
               sevent
clus2             0   1
  PSD MUTATED    12   4
  PSD WILD-TYPE 366  89
  PSD MUTATED PSD WILD-TYPE 
           16           455 
  PSD MUTATED PSD WILD-TYPE 
            4            89 
$`PSD MUTATED`
TCGA-A6-5665 TCGA-AA-3516 TCGA-AA-3663 TCGA-AA-3696 TCGA-AA-3815 TCGA-AA-A00E 
       22.06        13.02         6.97         5.03        33.04        30.02 
TCGA-AZ-4315 TCGA-AZ-4681 TCGA-CA-6717 TCGA-CK-5913 TCGA-CK-5916 TCGA-CM-5860 
       58.39       106.75        12.76        51.32        21.14        32.02 
TCGA-D5-6540 TCGA-DM-A1D8 TCGA-G4-6309 TCGA-CL-5918 
       16.14        12.59        85.48         7.17 

$`PSD WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 
       11.01         5.98        37.05        19.00        36.00        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
       26.99        19.04        19.04        10.06        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00J 
       27.02        13.94        38.04        19.00        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
       16.31         0.95        33.01        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
        5.13        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.20        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       15.62        49.08         9.99        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.03        22.98        30.08        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 
       15.12        17.85         4.80        17.13        12.49        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       49.91        13.32       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 
       74.56        65.85        53.62        44.68        55.04        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-DC-5337 
        6.05        33.17         6.97         4.73        78.12        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  PSD MUTATED PSD WILD-TYPE 
         5.03          0.00 
  PSD MUTATED PSD WILD-TYPE 
       106.75        148.01 
  PSD MUTATED PSD WILD-TYPE 
        21.60         20.12 
[1] "5.0 - 106.8 (21.6)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1"  
D518V2, continuous
D518V3, binary
               cls
clus              0   1
  PSD MUTATED    16   1
  PSD WILD-TYPE 350 118
[1] "tbl2"
               cls
clus            [,1] [,2]
  PSD MUTATED     16    1
  PSD WILD-TYPE  350  118
        clus
vv       PSD MUTATED PSD WILD-TYPE
  COLON           16           350
  RECTUM           1           118
[1] 2 2
[1] FALSE
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PSD MUTATED         2        0        2         9         0         0
  PSD WILD-TYPE      89        1       30       129        10         1
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PSD MUTATED           1          0          1          0        1         0
  PSD WILD-TYPE        23         11         58         42       47        18
               vv
clus            STAGE IVB
  PSD MUTATED           0
  PSD WILD-TYPE         1
D518V4, multiclass
            clus
vv           PSD MUTATED PSD WILD-TYPE
  STAGE I              2            89
  STAGE IA             0             1
  STAGE II             2            30
  STAGE IIA            9           129
  STAGE IIB            0            10
  STAGE IIC            0             1
  STAGE III            1            23
  STAGE IIIA           0            11
  STAGE IIIB           1            58
  STAGE IIIC           0            42
  STAGE IV             1            47
  STAGE IVA            0            18
  STAGE IVB            0             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  PSD MUTATED     1   1  14   1
  PSD WILD-TYPE  16  91 315  49
D518V5, multiclass
    clus
vv   PSD MUTATED PSD WILD-TYPE
  T1           1            16
  T2           1            91
  T3          14           315
  T4           1            49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2
  PSD MUTATED    13   3   1
  PSD WILD-TYPE 274 110  86
D518V6, multiclass
    clus
vv   PSD MUTATED PSD WILD-TYPE
  N0          13           274
  N1           3           110
  N2           1            86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D518V7, binary
               cls
clus              0   1
  PSD MUTATED    13   1
  PSD WILD-TYPE 362  64
[1] "tbl2"
               cls
clus            [,1] [,2]
  PSD MUTATED     13    1
  PSD WILD-TYPE  362   64
   clus
vv  PSD MUTATED PSD WILD-TYPE
  0          13           362
  1           1            64
[1] 2 2
[1] FALSE
D518V8, binary
               cls
clus              0   1
  PSD MUTATED    11   6
  PSD WILD-TYPE 214 258
[1] "tbl2"
               cls
clus            [,1] [,2]
  PSD MUTATED     11    6
  PSD WILD-TYPE  214  258
        clus
vv       PSD MUTATED PSD WILD-TYPE
  FEMALE          11           214
  MALE             6           258
[1] 2 2
[1] FALSE
D518V9, binary
               cls
clus              0   1
  PSD MUTATED    15   0
  PSD WILD-TYPE 335  22
[1] "tbl2"
               cls
clus            [,1] [,2]
  PSD MUTATED     15    0
  PSD WILD-TYPE  335   22
     clus
vv    PSD MUTATED PSD WILD-TYPE
  NO           15           335
  YES           0            22
[1] 2 2
[1] FALSE
               vv
clus            COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PSD MUTATED                     13                             3
  PSD WILD-TYPE                  302                            44
               vv
clus            RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PSD MUTATED                       1                              0
  PSD WILD-TYPE                   105                             10
D518V10, multiclass
                                clus
vv                               PSD MUTATED PSD WILD-TYPE
  COLON ADENOCARCINOMA                    13           302
  COLON MUCINOUS ADENOCARCINOMA            3            44
  RECTAL ADENOCARCINOMA                    1           105
  RECTAL MUCINOUS ADENOCARCINOMA           0            10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             R0  R1  R2  RX
  PSD MUTATED    10   0   1   4
  PSD WILD-TYPE 335   4  30  21
D518V11, multiclass
    clus
vv   PSD MUTATED PSD WILD-TYPE
  R0          10           335
  R1           0             4
  R2           1            30
  RX           4            21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D518V12, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PSD MUTATED                                  0     1
  PSD WILD-TYPE                                1    10
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  PSD MUTATED                           1     9
  PSD WILD-TYPE                        21   217
D518V13, multiclass
                                  clus
vv                                 PSD MUTATED PSD WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      1            10
  BLACK OR AFRICAN AMERICAN                  1            21
  WHITE                                      9           217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(519) Variable = CDC5L MUTATION ANALYSIS
D519V1, survival
                 sevent
clus2               0   1
  CDC5L MUTATED     9   3
  CDC5L WILD-TYPE 369  90
  CDC5L MUTATED CDC5L WILD-TYPE 
             12             459 
  CDC5L MUTATED CDC5L WILD-TYPE 
              3              90 
$`CDC5L MUTATED`
TCGA-AA-3489 TCGA-AA-3510 TCGA-AA-3555 TCGA-AA-3713 TCGA-AD-6895 TCGA-AZ-4315 
        7.04        63.98        29.95        19.04         0.72        58.39 
TCGA-AZ-6601 TCGA-CA-6717 TCGA-D5-6923 TCGA-G4-6588 TCGA-DY-A1H8 TCGA-F5-6571 
      100.01        12.76        12.43        26.17        32.61        31.30 

$`CDC5L WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       24.00        17.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       85.05        26.99        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       49.41         6.77        12.10        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07        12.20        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        3.68         4.41        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 
       61.91        36.00        22.09        13.78        35.80        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       24.13        51.48         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
       18.28         9.96        49.51        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  CDC5L MUTATED CDC5L WILD-TYPE 
           0.72            0.00 
  CDC5L MUTATED CDC5L WILD-TYPE 
         100.01          148.01 
  CDC5L MUTATED CDC5L WILD-TYPE 
          28.06           20.12 
[1] "0.7 - 100.0 (28.1)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1"  
D519V2, continuous
D519V3, binary
                 cls
clus                0   1
  CDC5L MUTATED    11   2
  CDC5L WILD-TYPE 355 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDC5L MUTATED     11    2
  CDC5L WILD-TYPE  355  117
        clus
vv       CDC5L MUTATED CDC5L WILD-TYPE
  COLON             11             355
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CDC5L MUTATED         1        0        3         6         0         0
  CDC5L WILD-TYPE      90        1       29       132        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CDC5L MUTATED           0          1          0          0        1         0
  CDC5L WILD-TYPE        24         10         59         42       47        18
                 vv
clus              STAGE IVB
  CDC5L MUTATED           0
  CDC5L WILD-TYPE         1
D519V4, multiclass
            clus
vv           CDC5L MUTATED CDC5L WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               3              29
  STAGE IIA              6             132
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             1              10
  STAGE IIIB             0              59
  STAGE IIIC             0              42
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CDC5L MUTATED     0   2  11   0
  CDC5L WILD-TYPE  17  90 318  50
D519V5, multiclass
    clus
vv   CDC5L MUTATED CDC5L WILD-TYPE
  T1             0              17
  T2             2              90
  T3            11             318
  T4             0              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  CDC5L MUTATED    11   2   0
  CDC5L WILD-TYPE 276 111  87
D519V6, multiclass
    clus
vv   CDC5L MUTATED CDC5L WILD-TYPE
  N0            11             276
  N1             2             111
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D519V7, binary
                 cls
clus                0   1
  CDC5L MUTATED    11   1
  CDC5L WILD-TYPE 364  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDC5L MUTATED     11    1
  CDC5L WILD-TYPE  364   64
   clus
vv  CDC5L MUTATED CDC5L WILD-TYPE
  0            11             364
  1             1              64
[1] 2 2
[1] FALSE
D519V8, binary
                 cls
clus                0   1
  CDC5L MUTATED     5   8
  CDC5L WILD-TYPE 220 256
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDC5L MUTATED      5    8
  CDC5L WILD-TYPE  220  256
        clus
vv       CDC5L MUTATED CDC5L WILD-TYPE
  FEMALE             5             220
  MALE               8             256
[1] 2 2
[1] FALSE
D519V9, binary
                 cls
clus                0   1
  CDC5L MUTATED     9   1
  CDC5L WILD-TYPE 341  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDC5L MUTATED      9    1
  CDC5L WILD-TYPE  341   21
     clus
vv    CDC5L MUTATED CDC5L WILD-TYPE
  NO              9             341
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CDC5L MUTATED                      9                             2
  CDC5L WILD-TYPE                  306                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CDC5L MUTATED                       2                              0
  CDC5L WILD-TYPE                   104                             10
D519V10, multiclass
                                clus
vv                               CDC5L MUTATED CDC5L WILD-TYPE
  COLON ADENOCARCINOMA                       9             306
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  CDC5L MUTATED     8   0   1   1
  CDC5L WILD-TYPE 337   4  30  24
D519V11, multiclass
    clus
vv   CDC5L MUTATED CDC5L WILD-TYPE
  R0             8             337
  R1             0               4
  R2             1              30
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D519V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CDC5L MUTATED                                  0     1
  CDC5L WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CDC5L MUTATED                           0     7
  CDC5L WILD-TYPE                        22   219
D519V13, multiclass
                                  clus
vv                                 CDC5L MUTATED CDC5L WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        7             219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(520) Variable = ARID2 MUTATION ANALYSIS
D520V1, survival
                 sevent
clus2               0   1
  ARID2 MUTATED    28   6
  ARID2 WILD-TYPE 350  87
  ARID2 MUTATED ARID2 WILD-TYPE 
             34             437 
  ARID2 MUTATED ARID2 WILD-TYPE 
              6              87 
$`ARID2 MUTATED`
TCGA-A6-5657 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6654 TCGA-AA-3672 TCGA-AA-3697 
       31.63        27.09        22.52        23.87         0.92        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3845 TCGA-AA-3867 TCGA-AA-3977 
       26.99        19.04        19.04         0.00        24.03        25.02 
TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01Q TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4315 
        4.01        34.98         1.02         0.72        10.88        58.39 
TCGA-CA-6718 TCGA-CK-5914 TCGA-CM-5348 TCGA-CM-6168 TCGA-CM-6171 TCGA-D5-6928 
       10.06         9.99        22.98        12.99        14.04        11.64 
TCGA-DM-A1HB TCGA-F4-6570 TCGA-G4-6586 TCGA-G4-6628 TCGA-AG-4001 TCGA-AG-A002 
      135.65         6.18        35.80        79.69        36.03        20.98 
TCGA-AG-A011 TCGA-AG-A032 TCGA-CI-6619 TCGA-DC-6682 
       37.02        38.04         6.05         4.01 

$`ARID2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       22.06        32.71         8.38        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       21.76        24.69        24.39        20.12        19.66        20.28 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
        7.04         3.02         1.02        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
       14.01        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3811 TCGA-AA-3812 
       37.05        19.00        36.00         5.03        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       38.99        37.02        14.93        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3870 
       31.07        30.05        53.00        17.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        31.00        38.07        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
        0.79         5.79        22.42        27.42         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07        12.20        12.76        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5916 
      148.01        85.45        15.62        49.08        51.32        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5860 
       25.02        13.02        29.06        22.03        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       13.02        15.02        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
       14.30         9.04         9.44         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
       44.32       131.51       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       35.74        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 
       63.62        61.91        36.00        22.09        13.78        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       91.79        46.75        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       23.01        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       41.00       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        0.72        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        5.95         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  ARID2 MUTATED ARID2 WILD-TYPE 
              0               0 
  ARID2 MUTATED ARID2 WILD-TYPE 
         135.65          148.01 
  ARID2 MUTATED ARID2 WILD-TYPE 
          21.75           20.12 
[1] "0.0 - 135.7 (21.8)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.1"
D520V2, continuous
D520V3, binary
                 cls
clus                0   1
  ARID2 MUTATED    31   6
  ARID2 WILD-TYPE 335 113
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ARID2 MUTATED     31    6
  ARID2 WILD-TYPE  335  113
        clus
vv       ARID2 MUTATED ARID2 WILD-TYPE
  COLON             31             335
  RECTUM             6             113
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ARID2 MUTATED         5        0        3        11         2         0
  ARID2 WILD-TYPE      86        1       29       127         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ARID2 MUTATED           2          0          7          0        4         0
  ARID2 WILD-TYPE        22         11         52         42       44        18
                 vv
clus              STAGE IVB
  ARID2 MUTATED           0
  ARID2 WILD-TYPE         1
D520V4, multiclass
            clus
vv           ARID2 MUTATED ARID2 WILD-TYPE
  STAGE I                5              86
  STAGE IA               0               1
  STAGE II               3              29
  STAGE IIA             11             127
  STAGE IIB              2               8
  STAGE IIC              0               1
  STAGE III              2              22
  STAGE IIIA             0              11
  STAGE IIIB             7              52
  STAGE IIIC             0              42
  STAGE IV               4              44
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ARID2 MUTATED     0   6  27   4
  ARID2 WILD-TYPE  17  86 302  46
D520V5, multiclass
    clus
vv   ARID2 MUTATED ARID2 WILD-TYPE
  T1             0              17
  T2             6              86
  T3            27             302
  T4             4              46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  ARID2 MUTATED    24  10   3
  ARID2 WILD-TYPE 263 103  84
D520V6, multiclass
    clus
vv   ARID2 MUTATED ARID2 WILD-TYPE
  N0            24             263
  N1            10             103
  N2             3              84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D520V7, binary
                 cls
clus                0   1
  ARID2 MUTATED    28   4
  ARID2 WILD-TYPE 347  61
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ARID2 MUTATED     28    4
  ARID2 WILD-TYPE  347   61
   clus
vv  ARID2 MUTATED ARID2 WILD-TYPE
  0            28             347
  1             4              61
[1] 2 2
[1] FALSE
D520V8, binary
                 cls
clus                0   1
  ARID2 MUTATED    13  24
  ARID2 WILD-TYPE 212 240
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ARID2 MUTATED     13   24
  ARID2 WILD-TYPE  212  240
        clus
vv       ARID2 MUTATED ARID2 WILD-TYPE
  FEMALE            13             212
  MALE              24             240
[1] 2 2
[1] FALSE
D520V9, binary
                 cls
clus                0   1
  ARID2 MUTATED    24   2
  ARID2 WILD-TYPE 326  20
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ARID2 MUTATED     24    2
  ARID2 WILD-TYPE  326   20
     clus
vv    ARID2 MUTATED ARID2 WILD-TYPE
  NO             24             326
  YES             2              20
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ARID2 MUTATED                     28                             2
  ARID2 WILD-TYPE                  287                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ARID2 MUTATED                       6                              0
  ARID2 WILD-TYPE                   100                             10
D520V10, multiclass
                                clus
vv                               ARID2 MUTATED ARID2 WILD-TYPE
  COLON ADENOCARCINOMA                      28             287
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      6             100
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  ARID2 MUTATED    23   0   3   3
  ARID2 WILD-TYPE 322   4  28  22
D520V11, multiclass
    clus
vv   ARID2 MUTATED ARID2 WILD-TYPE
  R0            23             322
  R1             0               4
  R2             3              28
  RX             3              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D520V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ARID2 MUTATED                                  0     1
  ARID2 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ARID2 MUTATED                           2    17
  ARID2 WILD-TYPE                        20   209
D520V13, multiclass
                                  clus
vv                                 ARID2 MUTATED ARID2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    2              20
  WHITE                                       17             209
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(521) Variable = SCLT1 MUTATION ANALYSIS
D521V1, survival
                 sevent
clus2               0   1
  SCLT1 MUTATED    14   4
  SCLT1 WILD-TYPE 364  89
  SCLT1 MUTATED SCLT1 WILD-TYPE 
             18             453 
  SCLT1 MUTATED SCLT1 WILD-TYPE 
              4              89 
$`SCLT1 MUTATED`
TCGA-A6-6782 TCGA-AA-3496 TCGA-AA-3663 TCGA-AA-3672 TCGA-AA-3845 TCGA-AA-3864 
       20.28         1.02         6.97         0.92         0.00        53.00 
TCGA-AA-A010 TCGA-AA-A01Q TCGA-AD-6889 TCGA-AZ-4315 TCGA-AZ-6601 TCGA-CA-6717 
       34.98         1.02        56.55        58.39       100.01        12.76 
TCGA-DM-A0XD TCGA-DM-A28F TCGA-G4-6299 TCGA-G4-6307 TCGA-G4-6588 TCGA-AG-3892 
       24.43        35.97        74.56        55.04        26.17        13.02 

$`SCLT1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 
       23.87        20.12        19.66         7.04         3.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
        2.01        14.01        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02        14.93        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       30.05        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01R TCGA-AA-A01S 
       12.00        31.00        31.00        38.07        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 
       62.79        88.21        49.41         6.77        12.10        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07        12.20        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       11.38        10.26       119.70        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       65.85        53.62        44.68        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        35.80        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       17.95        36.95        17.03        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  SCLT1 MUTATED SCLT1 WILD-TYPE 
              0               0 
  SCLT1 MUTATED SCLT1 WILD-TYPE 
         100.01          148.01 
  SCLT1 MUTATED SCLT1 WILD-TYPE 
          25.30           20.05 
[1] "0.0 - 100.0 (25.3)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.1"
D521V2, continuous
D521V3, binary
                 cls
clus                0   1
  SCLT1 MUTATED    18   1
  SCLT1 WILD-TYPE 348 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SCLT1 MUTATED     18    1
  SCLT1 WILD-TYPE  348  118
        clus
vv       SCLT1 MUTATED SCLT1 WILD-TYPE
  COLON             18             348
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SCLT1 MUTATED         1        0        5         6         3         0
  SCLT1 WILD-TYPE      90        1       27       132         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SCLT1 MUTATED           1          0          2          1        0         0
  SCLT1 WILD-TYPE        23         11         57         41       48        18
                 vv
clus              STAGE IVB
  SCLT1 MUTATED           0
  SCLT1 WILD-TYPE         1
D521V4, multiclass
            clus
vv           SCLT1 MUTATED SCLT1 WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               5              27
  STAGE IIA              6             132
  STAGE IIB              3               7
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             2              57
  STAGE IIIC             1              41
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  SCLT1 MUTATED     1   0  15   3
  SCLT1 WILD-TYPE  16  92 314  47
D521V5, multiclass
    clus
vv   SCLT1 MUTATED SCLT1 WILD-TYPE
  T1             1              16
  T2             0              92
  T3            15             314
  T4             3              47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  SCLT1 MUTATED    15   3   1
  SCLT1 WILD-TYPE 272 110  86
D521V6, multiclass
    clus
vv   SCLT1 MUTATED SCLT1 WILD-TYPE
  N0            15             272
  N1             3             110
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D521V7, binary
                 cls
clus                0   1
  SCLT1 MUTATED    17   0
  SCLT1 WILD-TYPE 358  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SCLT1 MUTATED     17    0
  SCLT1 WILD-TYPE  358   65
   clus
vv  SCLT1 MUTATED SCLT1 WILD-TYPE
  0            17             358
  1             0              65
[1] 2 2
[1] FALSE
D521V8, binary
                 cls
clus                0   1
  SCLT1 MUTATED     9  10
  SCLT1 WILD-TYPE 216 254
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SCLT1 MUTATED      9   10
  SCLT1 WILD-TYPE  216  254
        clus
vv       SCLT1 MUTATED SCLT1 WILD-TYPE
  FEMALE             9             216
  MALE              10             254
[1] 2 2
[1] FALSE
D521V9, binary
                 cls
clus                0   1
  SCLT1 MUTATED    12   0
  SCLT1 WILD-TYPE 338  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SCLT1 MUTATED     12    0
  SCLT1 WILD-TYPE  338   22
     clus
vv    SCLT1 MUTATED SCLT1 WILD-TYPE
  NO             12             338
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SCLT1 MUTATED                     17                             1
  SCLT1 WILD-TYPE                  298                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SCLT1 MUTATED                       1                              0
  SCLT1 WILD-TYPE                   105                             10
D521V10, multiclass
                                clus
vv                               SCLT1 MUTATED SCLT1 WILD-TYPE
  COLON ADENOCARCINOMA                      17             298
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  SCLT1 MUTATED    12   0   0   2
  SCLT1 WILD-TYPE 333   4  31  23
D521V11, multiclass
    clus
vv   SCLT1 MUTATED SCLT1 WILD-TYPE
  R0            12             333
  R1             0               4
  R2             0              31
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D521V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SCLT1 MUTATED                                  0     2
  SCLT1 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  SCLT1 MUTATED                           0     9
  SCLT1 WILD-TYPE                        22   217
D521V13, multiclass
                                  clus
vv                                 SCLT1 MUTATED SCLT1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               9
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        9             217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(522) Variable = ZFC3H1 MUTATION ANALYSIS
D522V1, survival
                  sevent
clus2                0   1
  ZFC3H1 MUTATED    14   6
  ZFC3H1 WILD-TYPE 364  87
  ZFC3H1 MUTATED ZFC3H1 WILD-TYPE 
              20              451 
  ZFC3H1 MUTATED ZFC3H1 WILD-TYPE 
               6               87 
$`ZFC3H1 MUTATED`
TCGA-A6-5661 TCGA-A6-5665 TCGA-AA-3663 TCGA-AA-3715 TCGA-AA-3815 TCGA-AA-3864 
       33.53        22.06         6.97        19.04        33.04        53.00 
TCGA-AA-3875 TCGA-AA-3950 TCGA-AA-3975 TCGA-AA-A010 TCGA-AY-6386 TCGA-AZ-6598 
       18.05        24.00        34.06        34.98        17.82        49.41 
TCGA-AZ-6600 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-5912 TCGA-CK-5916 TCGA-D5-6927 
       12.10        12.76        10.06        49.08        21.14         9.44 
TCGA-AG-A002 TCGA-AG-A02N 
       20.98        61.97 

$`ZFC3H1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
       85.05        26.99        19.04        10.06        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3877 
       30.05        17.03        24.03        27.02        29.98        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 
        2.01        12.99        24.00        33.01        26.01         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       88.21         6.77       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.07        12.20        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       15.62        51.32         9.99        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
       14.30         9.04        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X 
       64.01        10.98        49.97         1.94        38.96        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  ZFC3H1 MUTATED ZFC3H1 WILD-TYPE 
            6.97             0.00 
  ZFC3H1 MUTATED ZFC3H1 WILD-TYPE 
           61.97           148.01 
  ZFC3H1 MUTATED ZFC3H1 WILD-TYPE 
           21.60            20.05 
[1] "7.0 - 62.0 (21.6)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.5"
D522V2, continuous
D522V3, binary
                  cls
clus                 0   1
  ZFC3H1 MUTATED    19   2
  ZFC3H1 WILD-TYPE 347 117
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZFC3H1 MUTATED     19    2
  ZFC3H1 WILD-TYPE  347  117
        clus
vv       ZFC3H1 MUTATED ZFC3H1 WILD-TYPE
  COLON              19              347
  RECTUM              2              117
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZFC3H1 MUTATED         5        0        5         7         2         0
  ZFC3H1 WILD-TYPE      86        1       27       131         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZFC3H1 MUTATED           0          0          1          0        1
  ZFC3H1 WILD-TYPE        24         11         58         42       47
                  vv
clus               STAGE IVA STAGE IVB
  ZFC3H1 MUTATED           0         0
  ZFC3H1 WILD-TYPE        18         1
D522V4, multiclass
            clus
vv           ZFC3H1 MUTATED ZFC3H1 WILD-TYPE
  STAGE I                 5               86
  STAGE IA                0                1
  STAGE II                5               27
  STAGE IIA               7              131
  STAGE IIB               2                8
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              1               58
  STAGE IIIC              0               42
  STAGE IV                1               47
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZFC3H1 MUTATED     2   3  13   3
  ZFC3H1 WILD-TYPE  15  89 316  47
D522V5, multiclass
    clus
vv   ZFC3H1 MUTATED ZFC3H1 WILD-TYPE
  T1              2               15
  T2              3               89
  T3             13              316
  T4              3               47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  ZFC3H1 MUTATED    19   2   0
  ZFC3H1 WILD-TYPE 268 111  87
D522V6, multiclass
    clus
vv   ZFC3H1 MUTATED ZFC3H1 WILD-TYPE
  N0             19              268
  N1              2              111
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D522V7, binary
                  cls
clus                 0   1
  ZFC3H1 MUTATED    17   1
  ZFC3H1 WILD-TYPE 358  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZFC3H1 MUTATED     17    1
  ZFC3H1 WILD-TYPE  358   64
   clus
vv  ZFC3H1 MUTATED ZFC3H1 WILD-TYPE
  0             17              358
  1              1               64
[1] 2 2
[1] FALSE
D522V8, binary
                  cls
clus                 0   1
  ZFC3H1 MUTATED    10  11
  ZFC3H1 WILD-TYPE 215 253
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZFC3H1 MUTATED     10   11
  ZFC3H1 WILD-TYPE  215  253
        clus
vv       ZFC3H1 MUTATED ZFC3H1 WILD-TYPE
  FEMALE             10              215
  MALE               11              253
[1] 2 2
[1] FALSE
D522V9, binary
                  cls
clus                 0   1
  ZFC3H1 MUTATED    18   0
  ZFC3H1 WILD-TYPE 332  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZFC3H1 MUTATED     18    0
  ZFC3H1 WILD-TYPE  332   22
     clus
vv    ZFC3H1 MUTATED ZFC3H1 WILD-TYPE
  NO              18              332
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ZFC3H1 MUTATED                     17                             2
  ZFC3H1 WILD-TYPE                  298                            45
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ZFC3H1 MUTATED                       2                              0
  ZFC3H1 WILD-TYPE                   104                             10
D522V10, multiclass
                                clus
vv                               ZFC3H1 MUTATED ZFC3H1 WILD-TYPE
  COLON ADENOCARCINOMA                       17              298
  COLON MUCINOUS ADENOCARCINOMA               2               45
  RECTAL ADENOCARCINOMA                       2              104
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ZFC3H1 MUTATED    14   0   0   5
  ZFC3H1 WILD-TYPE 331   4  31  20
D522V11, multiclass
    clus
vv   ZFC3H1 MUTATED ZFC3H1 WILD-TYPE
  R0             14              331
  R1              0                4
  R2              0               31
  RX              5               20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D522V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZFC3H1 MUTATED                                  0     2
  ZFC3H1 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZFC3H1 MUTATED                           3     6
  ZFC3H1 WILD-TYPE                        19   220
D522V13, multiclass
                                  clus
vv                                 ZFC3H1 MUTATED ZFC3H1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                9
  BLACK OR AFRICAN AMERICAN                     3               19
  WHITE                                         6              220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(523) Variable = OR2M3 MUTATION ANALYSIS
D523V1, survival
                 sevent
clus2               0   1
  OR2M3 MUTATED    13   3
  OR2M3 WILD-TYPE 365  90
  OR2M3 MUTATED OR2M3 WILD-TYPE 
             16             455 
  OR2M3 MUTATED OR2M3 WILD-TYPE 
              3              90 
$`OR2M3 MUTATED`
TCGA-AA-3949 TCGA-AZ-4315 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-5912 TCGA-CM-4744 
       26.01        58.39        12.76        10.06        49.08        20.02 
TCGA-CM-5349 TCGA-CM-6163 TCGA-CM-6168 TCGA-D5-6540 TCGA-DM-A1D7 TCGA-F4-6805 
       30.08         2.96        12.99        16.14        13.32        34.42 
TCGA-F4-6855 TCGA-G4-6628 TCGA-AF-2693 TCGA-AG-A002 
       47.41        79.69        19.10        20.98 

$`OR2M3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3950 
       31.00         2.01        12.99        24.00        33.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        33.01        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       12.20        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       23.05        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       22.98        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       17.03        15.02        12.00        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       14.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       17.13        12.49        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D8 TCGA-DM-A1D9 
       38.20       130.65        92.75        49.91        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6856 
       41.42        16.24        33.67        13.25         0.53        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 
       35.80        26.17        91.79        46.75        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       43.04        13.55        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  OR2M3 MUTATED OR2M3 WILD-TYPE 
           2.96            0.00 
  OR2M3 MUTATED OR2M3 WILD-TYPE 
          79.69          148.01 
  OR2M3 MUTATED OR2M3 WILD-TYPE 
          20.50           20.19 
[1] "3.0 - 79.7 (20.5)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.2"
D523V2, continuous
D523V3, binary
                 cls
clus                0   1
  OR2M3 MUTATED    15   1
  OR2M3 WILD-TYPE 351 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR2M3 MUTATED     15    1
  OR2M3 WILD-TYPE  351  118
        clus
vv       OR2M3 MUTATED OR2M3 WILD-TYPE
  COLON             15             351
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  OR2M3 MUTATED         7        0        1         8         0         0
  OR2M3 WILD-TYPE      84        1       31       130        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  OR2M3 MUTATED           0          0          1          0        0         0
  OR2M3 WILD-TYPE        24         11         58         42       48        18
                 vv
clus              STAGE IVB
  OR2M3 MUTATED           0
  OR2M3 WILD-TYPE         1
D523V4, multiclass
            clus
vv           OR2M3 MUTATED OR2M3 WILD-TYPE
  STAGE I                7              84
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              8             130
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  OR2M3 MUTATED     1   6   9   1
  OR2M3 WILD-TYPE  16  86 320  49
D523V5, multiclass
    clus
vv   OR2M3 MUTATED OR2M3 WILD-TYPE
  T1             1              16
  T2             6              86
  T3             9             320
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  OR2M3 MUTATED    16   1   0
  OR2M3 WILD-TYPE 271 112  87
D523V6, multiclass
    clus
vv   OR2M3 MUTATED OR2M3 WILD-TYPE
  N0            16             271
  N1             1             112
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D523V7, binary
                 cls
clus                0   1
  OR2M3 MUTATED    15   0
  OR2M3 WILD-TYPE 360  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR2M3 MUTATED     15    0
  OR2M3 WILD-TYPE  360   65
   clus
vv  OR2M3 MUTATED OR2M3 WILD-TYPE
  0            15             360
  1             0              65
[1] 2 2
[1] FALSE
D523V8, binary
                 cls
clus                0   1
  OR2M3 MUTATED     6  11
  OR2M3 WILD-TYPE 219 253
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR2M3 MUTATED      6   11
  OR2M3 WILD-TYPE  219  253
        clus
vv       OR2M3 MUTATED OR2M3 WILD-TYPE
  FEMALE             6             219
  MALE              11             253
[1] 2 2
[1] FALSE
D523V9, binary
                 cls
clus                0   1
  OR2M3 MUTATED    15   0
  OR2M3 WILD-TYPE 335  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR2M3 MUTATED     15    0
  OR2M3 WILD-TYPE  335   22
     clus
vv    OR2M3 MUTATED OR2M3 WILD-TYPE
  NO             15             335
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  OR2M3 MUTATED                     11                             3
  OR2M3 WILD-TYPE                  304                            44
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  OR2M3 MUTATED                       1                              0
  OR2M3 WILD-TYPE                   105                             10
D523V10, multiclass
                                clus
vv                               OR2M3 MUTATED OR2M3 WILD-TYPE
  COLON ADENOCARCINOMA                      11             304
  COLON MUCINOUS ADENOCARCINOMA              3              44
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  OR2M3 MUTATED    12   0   0   3
  OR2M3 WILD-TYPE 333   4  31  22
D523V11, multiclass
    clus
vv   OR2M3 MUTATED OR2M3 WILD-TYPE
  R0            12             333
  R1             0               4
  R2             0              31
  RX             3              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D523V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OR2M3 MUTATED                                  0     2
  OR2M3 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  OR2M3 MUTATED                           1    11
  OR2M3 WILD-TYPE                        21   215
D523V13, multiclass
                                  clus
vv                                 OR2M3 MUTATED OR2M3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               9
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                       11             215
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(524) Variable = RNF145 MUTATION ANALYSIS
D524V1, survival
                  sevent
clus2                0   1
  RNF145 MUTATED    13   3
  RNF145 WILD-TYPE 365  90
  RNF145 MUTATED RNF145 WILD-TYPE 
              16              455 
  RNF145 MUTATED RNF145 WILD-TYPE 
               3               90 
$`RNF145 MUTATED`
TCGA-AA-3510 TCGA-AA-3950 TCGA-AD-6964 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-AZ-6601 
       63.98        24.00        10.88        58.39        49.41       100.01 
TCGA-CM-5348 TCGA-CM-6162 TCGA-DM-A1D9 TCGA-DM-A1HA TCGA-F4-6569 TCGA-F4-6856 
       22.98        12.00       140.38       131.51        35.74        35.31 
TCGA-G4-6628 TCGA-AG-A002 TCGA-DC-6681 TCGA-F5-6465 
       79.69        20.98         5.95        49.51 

$`RNF145 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 
        2.01        12.99        24.00        33.01        26.01         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 
       62.79        88.21         6.77        12.10        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       17.03        15.02         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A282 
       13.32        12.59         7.50        44.32       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
       98.24         8.61        31.96         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       47.41       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 
       13.78        35.80        26.17        91.79        46.75        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
       19.99         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6571 TCGA-F5-6702 
       19.96        20.91        18.28         9.96        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  RNF145 MUTATED RNF145 WILD-TYPE 
            5.95             0.00 
  RNF145 MUTATED RNF145 WILD-TYPE 
          140.38           148.01 
  RNF145 MUTATED RNF145 WILD-TYPE 
          42.575           19.990 
[1] "6.0 - 140.4 (42.6)" "0.0 - 148.0 (20.0)"
[1] "hr=" "2"  
D524V2, continuous
D524V3, binary
                  cls
clus                 0   1
  RNF145 MUTATED    14   3
  RNF145 WILD-TYPE 352 116
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF145 MUTATED     14    3
  RNF145 WILD-TYPE  352  116
        clus
vv       RNF145 MUTATED RNF145 WILD-TYPE
  COLON              14              352
  RECTUM              3              116
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RNF145 MUTATED         4        0        4         4         0         0
  RNF145 WILD-TYPE      87        1       28       134        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RNF145 MUTATED           0          0          2          1        0
  RNF145 WILD-TYPE        24         11         57         41       48
                  vv
clus               STAGE IVA STAGE IVB
  RNF145 MUTATED           1         0
  RNF145 WILD-TYPE        17         1
D524V4, multiclass
            clus
vv           RNF145 MUTATED RNF145 WILD-TYPE
  STAGE I                 4               87
  STAGE IA                0                1
  STAGE II                4               28
  STAGE IIA               4              134
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              2               57
  STAGE IIIC              1               41
  STAGE IV                0               48
  STAGE IVA               1               17
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  RNF145 MUTATED     0   4  11   2
  RNF145 WILD-TYPE  17  88 318  48
D524V5, multiclass
    clus
vv   RNF145 MUTATED RNF145 WILD-TYPE
  T1              0               17
  T2              4               88
  T3             11              318
  T4              2               48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  RNF145 MUTATED    12   2   3
  RNF145 WILD-TYPE 275 111  84
D524V6, multiclass
    clus
vv   RNF145 MUTATED RNF145 WILD-TYPE
  N0             12              275
  N1              2              111
  N2              3               84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D524V7, binary
                  cls
clus                 0   1
  RNF145 MUTATED    14   1
  RNF145 WILD-TYPE 361  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF145 MUTATED     14    1
  RNF145 WILD-TYPE  361   64
   clus
vv  RNF145 MUTATED RNF145 WILD-TYPE
  0             14              361
  1              1               64
[1] 2 2
[1] FALSE
D524V8, binary
                  cls
clus                 0   1
  RNF145 MUTATED     7  10
  RNF145 WILD-TYPE 218 254
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF145 MUTATED      7   10
  RNF145 WILD-TYPE  218  254
        clus
vv       RNF145 MUTATED RNF145 WILD-TYPE
  FEMALE              7              218
  MALE               10              254
[1] 2 2
[1] FALSE
D524V9, binary
                  cls
clus                 0   1
  RNF145 MUTATED    13   0
  RNF145 WILD-TYPE 337  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF145 MUTATED     13    0
  RNF145 WILD-TYPE  337   22
     clus
vv    RNF145 MUTATED RNF145 WILD-TYPE
  NO              13              337
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  RNF145 MUTATED                     11                             3
  RNF145 WILD-TYPE                  304                            44
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  RNF145 MUTATED                       3                              0
  RNF145 WILD-TYPE                   103                             10
D524V10, multiclass
                                clus
vv                               RNF145 MUTATED RNF145 WILD-TYPE
  COLON ADENOCARCINOMA                       11              304
  COLON MUCINOUS ADENOCARCINOMA               3               44
  RECTAL ADENOCARCINOMA                       3              103
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  RNF145 MUTATED    12   0   0   0
  RNF145 WILD-TYPE 333   4  31  25
D524V11, multiclass
    clus
vv   RNF145 MUTATED RNF145 WILD-TYPE
  R0             12              333
  R1              0                4
  R2              0               31
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D524V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RNF145 MUTATED                                  0     0
  RNF145 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  RNF145 MUTATED                           0    13
  RNF145 WILD-TYPE                        22   213
D524V13, multiclass
                                  clus
vv                                 RNF145 MUTATED RNF145 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                        13              213
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(525) Variable = TMEM169 MUTATION ANALYSIS
D525V1, survival
                   sevent
clus2                 0   1
  TMEM169 MUTATED     7   7
  TMEM169 WILD-TYPE 371  86
  TMEM169 MUTATED TMEM169 WILD-TYPE 
               14               457 
  TMEM169 MUTATED TMEM169 WILD-TYPE 
                7                86 
$`TMEM169 MUTATED`
TCGA-A6-4105 TCGA-AA-3489 TCGA-AA-3510 TCGA-AA-3713 TCGA-AD-6889 TCGA-CK-5916 
       14.53         7.04        63.98        19.04        56.55        21.14 
TCGA-CK-6751 TCGA-D5-6529 TCGA-D5-6539 TCGA-DM-A1D7 TCGA-DM-A28F TCGA-F4-6570 
      124.27        20.19        12.49        13.32        35.97         6.18 
TCGA-G4-6303 TCGA-AG-4007 
       65.85         1.02 

$`TMEM169 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 
       16.57        34.65        33.34        32.75        36.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        19.66        20.28         3.02         1.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       85.05        26.99        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 
       40.96         0.07        21.37        15.52         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CM-4743 TCGA-CM-4744 
       51.32         9.99        82.95         1.91        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       55.92        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
        4.80        17.13        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D8 
       24.43        38.20       130.65        92.75        49.91        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
        6.12        81.37       119.93        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
        8.61        31.96        35.74        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
       35.31       133.18        74.56        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4008 
       32.02        19.99        28.04        36.03        14.04        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  TMEM169 MUTATED TMEM169 WILD-TYPE 
             1.02              0.00 
  TMEM169 MUTATED TMEM169 WILD-TYPE 
           124.27            148.01 
  TMEM169 MUTATED TMEM169 WILD-TYPE 
           19.615            20.280 
[1] "1.0 - 124.3 (19.6)" "0.0 - 148.0 (20.3)"
[1] "hr=" "2.1"
D525V2, continuous
D525V3, binary
                   cls
clus                  0   1
  TMEM169 MUTATED    13   1
  TMEM169 WILD-TYPE 353 118
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM169 MUTATED     13    1
  TMEM169 WILD-TYPE  353  118
        clus
vv       TMEM169 MUTATED TMEM169 WILD-TYPE
  COLON               13               353
  RECTUM               1               118
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TMEM169 MUTATED         2        0        2         5         0         0
  TMEM169 WILD-TYPE      89        1       30       133        10         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TMEM169 MUTATED           0          1          1          0        3
  TMEM169 WILD-TYPE        24         10         58         42       45
                   vv
clus                STAGE IVA STAGE IVB
  TMEM169 MUTATED           0         0
  TMEM169 WILD-TYPE        18         1
D525V4, multiclass
            clus
vv           TMEM169 MUTATED TMEM169 WILD-TYPE
  STAGE I                  2                89
  STAGE IA                 0                 1
  STAGE II                 2                30
  STAGE IIA                5               133
  STAGE IIB                0                10
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               1                10
  STAGE IIIB               1                58
  STAGE IIIC               0                42
  STAGE IV                 3                45
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  TMEM169 MUTATED     1   1  11   1
  TMEM169 WILD-TYPE  16  91 318  49
D525V5, multiclass
    clus
vv   TMEM169 MUTATED TMEM169 WILD-TYPE
  T1               1                16
  T2               1                91
  T3              11               318
  T4               1                49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  TMEM169 MUTATED    11   2   1
  TMEM169 WILD-TYPE 276 111  86
D525V6, multiclass
    clus
vv   TMEM169 MUTATED TMEM169 WILD-TYPE
  N0              11               276
  N1               2               111
  N2               1                86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D525V7, binary
                   cls
clus                  0   1
  TMEM169 MUTATED    10   3
  TMEM169 WILD-TYPE 365  62
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM169 MUTATED     10    3
  TMEM169 WILD-TYPE  365   62
   clus
vv  TMEM169 MUTATED TMEM169 WILD-TYPE
  0              10               365
  1               3                62
[1] 2 2
[1] FALSE
D525V8, binary
                   cls
clus                  0   1
  TMEM169 MUTATED     5   9
  TMEM169 WILD-TYPE 220 255
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM169 MUTATED      5    9
  TMEM169 WILD-TYPE  220  255
        clus
vv       TMEM169 MUTATED TMEM169 WILD-TYPE
  FEMALE               5               220
  MALE                 9               255
[1] 2 2
[1] FALSE
D525V9, binary
                   cls
clus                  0   1
  TMEM169 MUTATED     9   1
  TMEM169 WILD-TYPE 341  21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM169 MUTATED      9    1
  TMEM169 WILD-TYPE  341   21
     clus
vv    TMEM169 MUTATED TMEM169 WILD-TYPE
  NO                9               341
  YES               1                21
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  TMEM169 MUTATED                     11                             1
  TMEM169 WILD-TYPE                  304                            46
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  TMEM169 MUTATED                       1                              0
  TMEM169 WILD-TYPE                   105                             10
D525V10, multiclass
                                clus
vv                               TMEM169 MUTATED TMEM169 WILD-TYPE
  COLON ADENOCARCINOMA                        11               304
  COLON MUCINOUS ADENOCARCINOMA                1                46
  RECTAL ADENOCARCINOMA                        1               105
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  TMEM169 MUTATED     6   0   2   2
  TMEM169 WILD-TYPE 339   4  29  23
D525V11, multiclass
    clus
vv   TMEM169 MUTATED TMEM169 WILD-TYPE
  R0               6               339
  R1               0                 4
  R2               2                29
  RX               2                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D525V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TMEM169 MUTATED                                  0     1
  TMEM169 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  TMEM169 MUTATED                           0     9
  TMEM169 WILD-TYPE                        22   217
D525V13, multiclass
                                  clus
vv                                 TMEM169 MUTATED TMEM169 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                10
  BLACK OR AFRICAN AMERICAN                      0                22
  WHITE                                          9               217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(526) Variable = NOX5 MUTATION ANALYSIS
D526V1, survival
                sevent
clus2              0   1
  NOX5 MUTATED     5   0
  NOX5 WILD-TYPE 373  93
  NOX5 MUTATED NOX5 WILD-TYPE 
             5            466 
  NOX5 MUTATED NOX5 WILD-TYPE 
             0             93 
$`NOX5 MUTATED`
TCGA-A6-6781 TCGA-AA-3713 TCGA-AA-3966 TCGA-CA-6717 TCGA-D5-6930 
       19.66        19.04         2.01        12.76         1.51 

$`NOX5 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       20.98        34.03        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  NOX5 MUTATED NOX5 WILD-TYPE 
          1.51           0.00 
  NOX5 MUTATED NOX5 WILD-TYPE 
         19.66         148.01 
  NOX5 MUTATED NOX5 WILD-TYPE 
         12.76          20.73 
[1] "1.5 - 19.7 (12.8)"  "0.0 - 148.0 (20.7)"
[1] "hr="     "3300000"
D526V2, continuous
D526V3, binary
                cls
clus               0   1
  NOX5 MUTATED     5   0
  NOX5 WILD-TYPE 361 119
[1] "tbl2"
                cls
clus             [,1] [,2]
  NOX5 MUTATED      5    0
  NOX5 WILD-TYPE  361  119
        clus
vv       NOX5 MUTATED NOX5 WILD-TYPE
  COLON             5            361
  RECTUM            0            119
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NOX5 MUTATED         0        0        0         3         0         0
  NOX5 WILD-TYPE      91        1       32       135        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NOX5 MUTATED           0          0          0          1        1         0
  NOX5 WILD-TYPE        24         11         59         41       47        18
                vv
clus             STAGE IVB
  NOX5 MUTATED           0
  NOX5 WILD-TYPE         1
D526V4, multiclass
            clus
vv           NOX5 MUTATED NOX5 WILD-TYPE
  STAGE I               0             91
  STAGE IA              0              1
  STAGE II              0             32
  STAGE IIA             3            135
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            0             59
  STAGE IIIC            1             41
  STAGE IV              1             47
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  NOX5 MUTATED     0   0   4   1
  NOX5 WILD-TYPE  17  92 325  49
D526V5, multiclass
    clus
vv   NOX5 MUTATED NOX5 WILD-TYPE
  T1            0             17
  T2            0             92
  T3            4            325
  T4            1             49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  NOX5 MUTATED     4   1   0
  NOX5 WILD-TYPE 283 112  87
D526V6, multiclass
    clus
vv   NOX5 MUTATED NOX5 WILD-TYPE
  N0            4            283
  N1            1            112
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D526V7, binary
                cls
clus               0   1
  NOX5 MUTATED     3   1
  NOX5 WILD-TYPE 372  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  NOX5 MUTATED      3    1
  NOX5 WILD-TYPE  372   64
   clus
vv  NOX5 MUTATED NOX5 WILD-TYPE
  0            3            372
  1            1             64
[1] 2 2
[1] FALSE
D526V8, binary
                cls
clus               0   1
  NOX5 MUTATED     1   4
  NOX5 WILD-TYPE 224 260
[1] "tbl2"
                cls
clus             [,1] [,2]
  NOX5 MUTATED      1    4
  NOX5 WILD-TYPE  224  260
        clus
vv       NOX5 MUTATED NOX5 WILD-TYPE
  FEMALE            1            224
  MALE              4            260
[1] 2 2
[1] FALSE
D526V9, binary
                cls
clus               0   1
  NOX5 MUTATED     2   1
  NOX5 WILD-TYPE 348  21
[1] "tbl2"
                cls
clus             [,1] [,2]
  NOX5 MUTATED      2    1
  NOX5 WILD-TYPE  348   21
     clus
vv    NOX5 MUTATED NOX5 WILD-TYPE
  NO             2            348
  YES            1             21
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  NOX5 MUTATED                      1                             4
  NOX5 WILD-TYPE                  314                            43
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  NOX5 MUTATED                       0                              0
  NOX5 WILD-TYPE                   106                             10
D526V10, multiclass
                                clus
vv                               NOX5 MUTATED NOX5 WILD-TYPE
  COLON ADENOCARCINOMA                      1            314
  COLON MUCINOUS ADENOCARCINOMA             4             43
  RECTAL ADENOCARCINOMA                     0            106
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  NOX5 MUTATED     2   0   1   1
  NOX5 WILD-TYPE 343   4  30  24
D526V11, multiclass
    clus
vv   NOX5 MUTATED NOX5 WILD-TYPE
  R0            2            343
  R1            0              4
  R2            1             30
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D526V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NOX5 MUTATED                                  0     1
  NOX5 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  NOX5 MUTATED                           0     2
  NOX5 WILD-TYPE                        22   224
D526V13, multiclass
                                  clus
vv                                 NOX5 MUTATED NOX5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       2            224
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(527) Variable = HAS2 MUTATION ANALYSIS
D527V1, survival
                sevent
clus2              0   1
  HAS2 MUTATED     8   2
  HAS2 WILD-TYPE 370  91
  HAS2 MUTATED HAS2 WILD-TYPE 
            10            461 
  HAS2 MUTATED HAS2 WILD-TYPE 
             2             91 
$`HAS2 MUTATED`
TCGA-A6-6780 TCGA-AA-3492 TCGA-AA-3821 TCGA-AA-A00N TCGA-AD-6889 TCGA-AY-6197 
       20.12         3.02         1.02         4.01        56.55        21.44 
TCGA-AY-6386 TCGA-CA-6716 TCGA-G4-6306 TCGA-AG-A002 
       17.82        12.20        44.68        20.98 

$`HAS2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 
       23.87        19.66        20.28         7.04         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 
       35.05        33.04         0.99        25.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 
       40.96         0.07        21.37        15.52         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AZ-4315 TCGA-AZ-4323 
       27.09        16.31         0.95        33.01        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       74.56        65.85        53.62        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  HAS2 MUTATED HAS2 WILD-TYPE 
          1.02           0.00 
  HAS2 MUTATED HAS2 WILD-TYPE 
         56.55         148.01 
  HAS2 MUTATED HAS2 WILD-TYPE 
         18.97          20.28 
[1] "1.0 - 56.5 (19.0)"  "0.0 - 148.0 (20.3)"
[1] "hr=" "1.2"
D527V2, continuous
D527V3, binary
                cls
clus               0   1
  HAS2 MUTATED     9   1
  HAS2 WILD-TYPE 357 118
[1] "tbl2"
                cls
clus             [,1] [,2]
  HAS2 MUTATED      9    1
  HAS2 WILD-TYPE  357  118
        clus
vv       HAS2 MUTATED HAS2 WILD-TYPE
  COLON             9            357
  RECTUM            1            118
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  HAS2 MUTATED         2        0        1         5         1         0
  HAS2 WILD-TYPE      89        1       31       133         9         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  HAS2 MUTATED           0          0          1          0        0         0
  HAS2 WILD-TYPE        24         11         58         42       48        18
                vv
clus             STAGE IVB
  HAS2 MUTATED           0
  HAS2 WILD-TYPE         1
D527V4, multiclass
            clus
vv           HAS2 MUTATED HAS2 WILD-TYPE
  STAGE I               2             89
  STAGE IA              0              1
  STAGE II              1             31
  STAGE IIA             5            133
  STAGE IIB             1              9
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            1             58
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  HAS2 MUTATED     0   3   6   1
  HAS2 WILD-TYPE  17  89 323  49
D527V5, multiclass
    clus
vv   HAS2 MUTATED HAS2 WILD-TYPE
  T1            0             17
  T2            3             89
  T3            6            323
  T4            1             49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  HAS2 MUTATED     9   1   0
  HAS2 WILD-TYPE 278 112  87
D527V6, multiclass
    clus
vv   HAS2 MUTATED HAS2 WILD-TYPE
  N0            9            278
  N1            1            112
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D527V7, binary
                cls
clus               0   1
  HAS2 MUTATED     8   0
  HAS2 WILD-TYPE 367  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  HAS2 MUTATED      8    0
  HAS2 WILD-TYPE  367   65
   clus
vv  HAS2 MUTATED HAS2 WILD-TYPE
  0            8            367
  1            0             65
[1] 2 2
[1] FALSE
D527V8, binary
                cls
clus               0   1
  HAS2 MUTATED     3   7
  HAS2 WILD-TYPE 222 257
[1] "tbl2"
                cls
clus             [,1] [,2]
  HAS2 MUTATED      3    7
  HAS2 WILD-TYPE  222  257
        clus
vv       HAS2 MUTATED HAS2 WILD-TYPE
  FEMALE            3            222
  MALE              7            257
[1] 2 2
[1] FALSE
D527V9, binary
                cls
clus               0   1
  HAS2 MUTATED     8   0
  HAS2 WILD-TYPE 342  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  HAS2 MUTATED      8    0
  HAS2 WILD-TYPE  342   22
     clus
vv    HAS2 MUTATED HAS2 WILD-TYPE
  NO             8            342
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  HAS2 MUTATED                      6                             3
  HAS2 WILD-TYPE                  309                            44
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  HAS2 MUTATED                       1                              0
  HAS2 WILD-TYPE                   105                             10
D527V10, multiclass
                                clus
vv                               HAS2 MUTATED HAS2 WILD-TYPE
  COLON ADENOCARCINOMA                      6            309
  COLON MUCINOUS ADENOCARCINOMA             3             44
  RECTAL ADENOCARCINOMA                     1            105
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  HAS2 MUTATED     7   0   0   1
  HAS2 WILD-TYPE 338   4  31  24
D527V11, multiclass
    clus
vv   HAS2 MUTATED HAS2 WILD-TYPE
  R0            7            338
  R1            0              4
  R2            0             31
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D527V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HAS2 MUTATED                                  0     2
  HAS2 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  HAS2 MUTATED                           1     3
  HAS2 WILD-TYPE                        21   223
D527V13, multiclass
                                  clus
vv                                 HAS2 MUTATED HAS2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              9
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                       3            223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(528) Variable = INSM2 MUTATION ANALYSIS
D528V1, survival
                 sevent
clus2               0   1
  INSM2 MUTATED    10   1
  INSM2 WILD-TYPE 368  92
  INSM2 MUTATED INSM2 WILD-TYPE 
             11             460 
  INSM2 MUTATED INSM2 WILD-TYPE 
              1              92 
$`INSM2 MUTATED`
TCGA-A6-6781 TCGA-AD-6895 TCGA-AY-6386 TCGA-AZ-6598 TCGA-CA-6717 TCGA-CK-4952 
       19.66         0.72        17.82        49.41        12.76        15.62 
TCGA-CM-4743 TCGA-CM-4744 TCGA-G4-6299 TCGA-G4-6628 TCGA-AG-A002 
       23.05        20.02        74.56        79.69        20.98 

$`INSM2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       15.52        56.55         0.79         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       33.01        21.44        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        88.21         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07        12.20        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 
       14.30        17.56       148.01        85.45        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4746 
        9.99        21.14        82.95         1.91       124.27        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       91.79        46.75        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  INSM2 MUTATED INSM2 WILD-TYPE 
           0.72            0.00 
  INSM2 MUTATED INSM2 WILD-TYPE 
          79.69          148.01 
  INSM2 MUTATED INSM2 WILD-TYPE 
         20.020          20.235 
[1] "0.7 - 79.7 (20.0)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "2.6"
D528V2, continuous
D528V3, binary
                 cls
clus                0   1
  INSM2 MUTATED    10   1
  INSM2 WILD-TYPE 356 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  INSM2 MUTATED     10    1
  INSM2 WILD-TYPE  356  118
        clus
vv       INSM2 MUTATED INSM2 WILD-TYPE
  COLON             10             356
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  INSM2 MUTATED         3        0        1         2         0         0
  INSM2 WILD-TYPE      88        1       31       136        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  INSM2 MUTATED           0          0          1          3        0         0
  INSM2 WILD-TYPE        24         11         58         39       48        18
                 vv
clus              STAGE IVB
  INSM2 MUTATED           0
  INSM2 WILD-TYPE         1
D528V4, multiclass
            clus
vv           INSM2 MUTATED INSM2 WILD-TYPE
  STAGE I                3              88
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              2             136
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             3              39
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  INSM2 MUTATED     0   3   6   2
  INSM2 WILD-TYPE  17  89 323  48
D528V5, multiclass
    clus
vv   INSM2 MUTATED INSM2 WILD-TYPE
  T1             0              17
  T2             3              89
  T3             6             323
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  INSM2 MUTATED     6   3   2
  INSM2 WILD-TYPE 281 110  85
D528V6, multiclass
    clus
vv   INSM2 MUTATED INSM2 WILD-TYPE
  N0             6             281
  N1             3             110
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D528V7, binary
                 cls
clus                0   1
  INSM2 MUTATED     8   0
  INSM2 WILD-TYPE 367  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  INSM2 MUTATED      8    0
  INSM2 WILD-TYPE  367   65
   clus
vv  INSM2 MUTATED INSM2 WILD-TYPE
  0             8             367
  1             0              65
[1] 2 2
[1] FALSE
D528V8, binary
                 cls
clus                0   1
  INSM2 MUTATED     3   8
  INSM2 WILD-TYPE 222 256
[1] "tbl2"
                 cls
clus              [,1] [,2]
  INSM2 MUTATED      3    8
  INSM2 WILD-TYPE  222  256
        clus
vv       INSM2 MUTATED INSM2 WILD-TYPE
  FEMALE             3             222
  MALE               8             256
[1] 2 2
[1] FALSE
D528V9, binary
                 cls
clus                0   1
  INSM2 MUTATED     9   0
  INSM2 WILD-TYPE 341  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  INSM2 MUTATED      9    0
  INSM2 WILD-TYPE  341   22
     clus
vv    INSM2 MUTATED INSM2 WILD-TYPE
  NO              9             341
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  INSM2 MUTATED                      7                             3
  INSM2 WILD-TYPE                  308                            44
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  INSM2 MUTATED                       1                              0
  INSM2 WILD-TYPE                   105                             10
D528V10, multiclass
                                clus
vv                               INSM2 MUTATED INSM2 WILD-TYPE
  COLON ADENOCARCINOMA                       7             308
  COLON MUCINOUS ADENOCARCINOMA              3              44
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  INSM2 MUTATED     7   0   0   2
  INSM2 WILD-TYPE 338   4  31  23
D528V11, multiclass
    clus
vv   INSM2 MUTATED INSM2 WILD-TYPE
  R0             7             338
  R1             0               4
  R2             0              31
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D528V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  INSM2 MUTATED                                  0     1
  INSM2 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  INSM2 MUTATED                           1     8
  INSM2 WILD-TYPE                        21   218
D528V13, multiclass
                                  clus
vv                                 INSM2 MUTATED INSM2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        8             218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(529) Variable = SCLY MUTATION ANALYSIS
D529V1, survival
                sevent
clus2              0   1
  SCLY MUTATED     9   3
  SCLY WILD-TYPE 369  90
  SCLY MUTATED SCLY WILD-TYPE 
            12            459 
  SCLY MUTATED SCLY WILD-TYPE 
             3             90 
$`SCLY MUTATED`
TCGA-A6-3809 TCGA-AA-3678 TCGA-AA-3877 TCGA-AZ-6598 TCGA-CK-5916 TCGA-CM-5349 
       32.75        47.01        31.00        49.41        21.14        30.08 
TCGA-CM-5861 TCGA-CM-5864 TCGA-D5-6930 TCGA-DM-A28F TCGA-F4-6703 TCGA-DY-A0XA 
       15.02        15.02         1.51        35.97        47.87       126.44 

$`SCLY WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 
       24.03        27.02        29.98        18.05         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        88.21         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       49.08        51.32         9.99        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5868 
       22.03        22.98        32.02         5.03        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       11.64         4.80        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H 
      139.17         6.12        81.37       119.93        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6704 
       98.24         8.61        31.96        35.74         6.18         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.03         5.29        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  SCLY MUTATED SCLY WILD-TYPE 
          1.51           0.00 
  SCLY MUTATED SCLY WILD-TYPE 
        126.44         148.01 
  SCLY MUTATED SCLY WILD-TYPE 
        31.875         20.020 
[1] "1.5 - 126.4 (31.9)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.1"
D529V2, continuous
D529V3, binary
                cls
clus               0   1
  SCLY MUTATED    11   1
  SCLY WILD-TYPE 355 118
[1] "tbl2"
                cls
clus             [,1] [,2]
  SCLY MUTATED     11    1
  SCLY WILD-TYPE  355  118
        clus
vv       SCLY MUTATED SCLY WILD-TYPE
  COLON            11            355
  RECTUM            1            118
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SCLY MUTATED         3        0        1         5         1         0
  SCLY WILD-TYPE      88        1       31       133         9         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SCLY MUTATED           1          0          1          0        0         0
  SCLY WILD-TYPE        23         11         58         42       48        18
                vv
clus             STAGE IVB
  SCLY MUTATED           0
  SCLY WILD-TYPE         1
D529V4, multiclass
            clus
vv           SCLY MUTATED SCLY WILD-TYPE
  STAGE I               3             88
  STAGE IA              0              1
  STAGE II              1             31
  STAGE IIA             5            133
  STAGE IIB             1              9
  STAGE IIC             0              1
  STAGE III             1             23
  STAGE IIIA            0             11
  STAGE IIIB            1             58
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  SCLY MUTATED     2   2   7   1
  SCLY WILD-TYPE  15  90 322  49
D529V5, multiclass
    clus
vv   SCLY MUTATED SCLY WILD-TYPE
  T1            2             15
  T2            2             90
  T3            7            322
  T4            1             49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  SCLY MUTATED    10   2   0
  SCLY WILD-TYPE 277 111  87
D529V6, multiclass
    clus
vv   SCLY MUTATED SCLY WILD-TYPE
  N0           10            277
  N1            2            111
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D529V7, binary
                cls
clus               0   1
  SCLY MUTATED    11   0
  SCLY WILD-TYPE 364  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  SCLY MUTATED     11    0
  SCLY WILD-TYPE  364   65
   clus
vv  SCLY MUTATED SCLY WILD-TYPE
  0           11            364
  1            0             65
[1] 2 2
[1] FALSE
D529V8, binary
                cls
clus               0   1
  SCLY MUTATED     8   4
  SCLY WILD-TYPE 217 260
[1] "tbl2"
                cls
clus             [,1] [,2]
  SCLY MUTATED      8    4
  SCLY WILD-TYPE  217  260
        clus
vv       SCLY MUTATED SCLY WILD-TYPE
  FEMALE            8            217
  MALE              4            260
[1] 2 2
[1] FALSE
D529V9, binary
                cls
clus               0   1
  SCLY MUTATED     9   0
  SCLY WILD-TYPE 341  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  SCLY MUTATED      9    0
  SCLY WILD-TYPE  341   22
     clus
vv    SCLY MUTATED SCLY WILD-TYPE
  NO             9            341
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SCLY MUTATED                      8                             3
  SCLY WILD-TYPE                  307                            44
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SCLY MUTATED                       1                              0
  SCLY WILD-TYPE                   105                             10
D529V10, multiclass
                                clus
vv                               SCLY MUTATED SCLY WILD-TYPE
  COLON ADENOCARCINOMA                      8            307
  COLON MUCINOUS ADENOCARCINOMA             3             44
  RECTAL ADENOCARCINOMA                     1            105
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  SCLY MUTATED     8   0   0   1
  SCLY WILD-TYPE 337   4  31  24
D529V11, multiclass
    clus
vv   SCLY MUTATED SCLY WILD-TYPE
  R0            8            337
  R1            0              4
  R2            0             31
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D529V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SCLY MUTATED                                  0     0
  SCLY WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  SCLY MUTATED                           0    10
  SCLY WILD-TYPE                        22   216
D529V13, multiclass
                                  clus
vv                                 SCLY MUTATED SCLY WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                      10            216
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(530) Variable = CDK17 MUTATION ANALYSIS
D530V1, survival
                 sevent
clus2               0   1
  CDK17 MUTATED     7   4
  CDK17 WILD-TYPE 371  89
  CDK17 MUTATED CDK17 WILD-TYPE 
             11             460 
  CDK17 MUTATED CDK17 WILD-TYPE 
              4              89 
$`CDK17 MUTATED`
TCGA-AA-3558 TCGA-AA-3994 TCGA-AA-A00N TCGA-AA-A010 TCGA-AD-6963 TCGA-AZ-6598 
       20.98        27.02         4.01        34.98        27.42        49.41 
TCGA-CA-6718 TCGA-CK-4950 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6626 
       10.06        85.45        13.78        26.17        46.75 

$`CDK17 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        27.02        19.07         7.96        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        0.72         5.79        22.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       88.21         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07        12.20        12.76        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
      148.01        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 
       63.62        61.91        36.00        22.09        35.80        91.79 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  CDK17 MUTATED CDK17 WILD-TYPE 
           4.01            0.00 
  CDK17 MUTATED CDK17 WILD-TYPE 
          85.45          148.01 
  CDK17 MUTATED CDK17 WILD-TYPE 
         27.020          20.035 
[1] "4.0 - 85.5 (27.0)"  "0.0 - 148.0 (20.0)"
[1] "hr=" "1.6"
D530V2, continuous
D530V3, binary
                 cls
clus                0   1
  CDK17 MUTATED    11   0
  CDK17 WILD-TYPE 355 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDK17 MUTATED     11    0
  CDK17 WILD-TYPE  355  119
        clus
vv       CDK17 MUTATED CDK17 WILD-TYPE
  COLON             11             355
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CDK17 MUTATED         1        1        1         3         2         0
  CDK17 WILD-TYPE      90        0       31       135         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CDK17 MUTATED           0          0          2          0        0         0
  CDK17 WILD-TYPE        24         11         57         42       48        18
                 vv
clus              STAGE IVB
  CDK17 MUTATED           0
  CDK17 WILD-TYPE         1
D530V4, multiclass
            clus
vv           CDK17 MUTATED CDK17 WILD-TYPE
  STAGE I                1              90
  STAGE IA               1               0
  STAGE II               1              31
  STAGE IIA              3             135
  STAGE IIB              2               8
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             2              57
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CDK17 MUTATED     0   1   7   2
  CDK17 WILD-TYPE  17  91 322  48
D530V5, multiclass
    clus
vv   CDK17 MUTATED CDK17 WILD-TYPE
  T1             0              17
  T2             1              91
  T3             7             322
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  CDK17 MUTATED     9   2   0
  CDK17 WILD-TYPE 278 111  87
D530V6, multiclass
    clus
vv   CDK17 MUTATED CDK17 WILD-TYPE
  N0             9             278
  N1             2             111
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D530V7, binary
                 cls
clus                0   1
  CDK17 MUTATED     8   0
  CDK17 WILD-TYPE 367  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDK17 MUTATED      8    0
  CDK17 WILD-TYPE  367   65
   clus
vv  CDK17 MUTATED CDK17 WILD-TYPE
  0             8             367
  1             0              65
[1] 2 2
[1] FALSE
D530V8, binary
                 cls
clus                0   1
  CDK17 MUTATED     4   7
  CDK17 WILD-TYPE 221 257
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDK17 MUTATED      4    7
  CDK17 WILD-TYPE  221  257
        clus
vv       CDK17 MUTATED CDK17 WILD-TYPE
  FEMALE             4             221
  MALE               7             257
[1] 2 2
[1] FALSE
D530V9, binary
                 cls
clus                0   1
  CDK17 MUTATED    10   0
  CDK17 WILD-TYPE 340  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDK17 MUTATED     10    0
  CDK17 WILD-TYPE  340   22
     clus
vv    CDK17 MUTATED CDK17 WILD-TYPE
  NO             10             340
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CDK17 MUTATED                      9                             2
  CDK17 WILD-TYPE                  306                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CDK17 MUTATED                       0                              0
  CDK17 WILD-TYPE                   106                             10
D530V10, multiclass
                                clus
vv                               CDK17 MUTATED CDK17 WILD-TYPE
  COLON ADENOCARCINOMA                       9             306
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  CDK17 MUTATED     6   1   1   1
  CDK17 WILD-TYPE 339   3  30  24
D530V11, multiclass
    clus
vv   CDK17 MUTATED CDK17 WILD-TYPE
  R0             6             339
  R1             1               3
  R2             1              30
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D530V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CDK17 MUTATED                                  0     1
  CDK17 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CDK17 MUTATED                           2     4
  CDK17 WILD-TYPE                        20   222
D530V13, multiclass
                                  clus
vv                                 CDK17 MUTATED CDK17 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    2              20
  WHITE                                        4             222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(531) Variable = GOLPH3L MUTATION ANALYSIS
D531V1, survival
                   sevent
clus2                 0   1
  GOLPH3L MUTATED     3   3
  GOLPH3L WILD-TYPE 375  90
  GOLPH3L MUTATED GOLPH3L WILD-TYPE 
                6               465 
  GOLPH3L MUTATED GOLPH3L WILD-TYPE 
                3                90 
$`GOLPH3L MUTATED`
TCGA-AA-3529 TCGA-AY-6386 TCGA-AZ-4315 TCGA-DM-A1D4 TCGA-G4-6303 TCGA-AG-A002 
        0.00        17.82        58.39        92.75        65.85        20.98 

$`GOLPH3L WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
        8.05        19.07        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
        0.95        33.01        21.44         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       24.43        38.20       130.65        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6304 
        0.53        47.41        35.31       133.18        74.56        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  GOLPH3L MUTATED GOLPH3L WILD-TYPE 
                0                 0 
  GOLPH3L MUTATED GOLPH3L WILD-TYPE 
            92.75            148.01 
  GOLPH3L MUTATED GOLPH3L WILD-TYPE 
           39.685            20.120 
[1] "0.0 - 92.8 (39.7)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.5"
D531V2, continuous
D531V3, binary
                   cls
clus                  0   1
  GOLPH3L MUTATED     5   1
  GOLPH3L WILD-TYPE 361 118
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GOLPH3L MUTATED      5    1
  GOLPH3L WILD-TYPE  361  118
        clus
vv       GOLPH3L MUTATED GOLPH3L WILD-TYPE
  COLON                5               361
  RECTUM               1               118
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GOLPH3L MUTATED         1        0        0         2         0         0
  GOLPH3L WILD-TYPE      90        1       32       136        10         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GOLPH3L MUTATED           0          0          1          1        1
  GOLPH3L WILD-TYPE        24         11         58         41       47
                   vv
clus                STAGE IVA STAGE IVB
  GOLPH3L MUTATED           0         0
  GOLPH3L WILD-TYPE        18         1
D531V4, multiclass
            clus
vv           GOLPH3L MUTATED GOLPH3L WILD-TYPE
  STAGE I                  1                90
  STAGE IA                 0                 1
  STAGE II                 0                32
  STAGE IIA                2               136
  STAGE IIB                0                10
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               0                11
  STAGE IIIB               1                58
  STAGE IIIC               1                41
  STAGE IV                 1                47
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  GOLPH3L MUTATED     0   1   5   0
  GOLPH3L WILD-TYPE  17  91 324  50
D531V5, multiclass
    clus
vv   GOLPH3L MUTATED GOLPH3L WILD-TYPE
  T1               0                17
  T2               1                91
  T3               5               324
  T4               0                50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  GOLPH3L MUTATED     3   2   1
  GOLPH3L WILD-TYPE 284 111  86
D531V6, multiclass
    clus
vv   GOLPH3L MUTATED GOLPH3L WILD-TYPE
  N0               3               284
  N1               2               111
  N2               1                86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D531V7, binary
                   cls
clus                  0   1
  GOLPH3L MUTATED     5   1
  GOLPH3L WILD-TYPE 370  64
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GOLPH3L MUTATED      5    1
  GOLPH3L WILD-TYPE  370   64
   clus
vv  GOLPH3L MUTATED GOLPH3L WILD-TYPE
  0               5               370
  1               1                64
[1] 2 2
[1] FALSE
D531V8, binary
                   cls
clus                  0   1
  GOLPH3L MUTATED     3   3
  GOLPH3L WILD-TYPE 222 261
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GOLPH3L MUTATED      3    3
  GOLPH3L WILD-TYPE  222  261
        clus
vv       GOLPH3L MUTATED GOLPH3L WILD-TYPE
  FEMALE               3               222
  MALE                 3               261
[1] 2 2
[1] FALSE
D531V9, binary
                   cls
clus                  0   1
  GOLPH3L MUTATED     4   0
  GOLPH3L WILD-TYPE 346  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GOLPH3L MUTATED      4    0
  GOLPH3L WILD-TYPE  346   22
     clus
vv    GOLPH3L MUTATED GOLPH3L WILD-TYPE
  NO                4               346
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  GOLPH3L MUTATED                      5                             0
  GOLPH3L WILD-TYPE                  310                            47
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  GOLPH3L MUTATED                       1                              0
  GOLPH3L WILD-TYPE                   105                             10
D531V10, multiclass
                                clus
vv                               GOLPH3L MUTATED GOLPH3L WILD-TYPE
  COLON ADENOCARCINOMA                         5               310
  COLON MUCINOUS ADENOCARCINOMA                0                47
  RECTAL ADENOCARCINOMA                        1               105
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  GOLPH3L MUTATED     5   0   0   0
  GOLPH3L WILD-TYPE 340   4  31  25
D531V11, multiclass
    clus
vv   GOLPH3L MUTATED GOLPH3L WILD-TYPE
  R0               5               340
  R1               0                 4
  R2               0                31
  RX               0                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D531V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GOLPH3L MUTATED                                  0     0
  GOLPH3L WILD-TYPE                                1    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  GOLPH3L MUTATED                           1     3
  GOLPH3L WILD-TYPE                        21   223
D531V13, multiclass
                                  clus
vv                                 GOLPH3L MUTATED GOLPH3L WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                      1                21
  WHITE                                          3               223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(532) Variable = GGTLC2 MUTATION ANALYSIS
D532V1, survival
                  sevent
clus2                0   1
  GGTLC2 MUTATED     6   0
  GGTLC2 WILD-TYPE 372  93
  GGTLC2 MUTATED GGTLC2 WILD-TYPE 
               6              465 
  GGTLC2 MUTATED GGTLC2 WILD-TYPE 
               0               93 
$`GGTLC2 MUTATED`
TCGA-AU-3779 TCGA-D5-6535 TCGA-G4-6306 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
       14.50        15.12        44.68        22.09        35.80        26.17 

$`GGTLC2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        10.88         0.20        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 
       55.92        20.19        18.25         1.32        43.27        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       74.56        65.85        53.62        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       61.91        36.00        13.78        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  GGTLC2 MUTATED GGTLC2 WILD-TYPE 
            14.5              0.0 
  GGTLC2 MUTATED GGTLC2 WILD-TYPE 
           44.68           148.01 
  GGTLC2 MUTATED GGTLC2 WILD-TYPE 
           24.13            20.12 
[1] "14.5 - 44.7 (24.1)" "0.0 - 148.0 (20.1)"
[1] "hr="     "9100000"
D532V2, continuous
D532V3, binary
                  cls
clus                 0   1
  GGTLC2 MUTATED     7   0
  GGTLC2 WILD-TYPE 359 119
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GGTLC2 MUTATED      7    0
  GGTLC2 WILD-TYPE  359  119
        clus
vv       GGTLC2 MUTATED GGTLC2 WILD-TYPE
  COLON               7              359
  RECTUM              0              119
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GGTLC2 MUTATED         0        0        0         4         1         0
  GGTLC2 WILD-TYPE      91        1       32       134         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GGTLC2 MUTATED           1          0          1          0        0
  GGTLC2 WILD-TYPE        23         11         58         42       48
                  vv
clus               STAGE IVA STAGE IVB
  GGTLC2 MUTATED           0         0
  GGTLC2 WILD-TYPE        18         1
D532V4, multiclass
            clus
vv           GGTLC2 MUTATED GGTLC2 WILD-TYPE
  STAGE I                 0               91
  STAGE IA                0                1
  STAGE II                0               32
  STAGE IIA               4              134
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               1               23
  STAGE IIIA              0               11
  STAGE IIIB              1               58
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  GGTLC2 MUTATED     0   2   4   1
  GGTLC2 WILD-TYPE  17  90 325  49
D532V5, multiclass
    clus
vv   GGTLC2 MUTATED GGTLC2 WILD-TYPE
  T1              0               17
  T2              2               90
  T3              4              325
  T4              1               49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  GGTLC2 MUTATED     5   2   0
  GGTLC2 WILD-TYPE 282 111  87
D532V6, multiclass
    clus
vv   GGTLC2 MUTATED GGTLC2 WILD-TYPE
  N0              5              282
  N1              2              111
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D532V7, binary
                  cls
clus                 0   1
  GGTLC2 MUTATED     4   0
  GGTLC2 WILD-TYPE 371  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GGTLC2 MUTATED      4    0
  GGTLC2 WILD-TYPE  371   65
   clus
vv  GGTLC2 MUTATED GGTLC2 WILD-TYPE
  0              4              371
  1              0               65
[1] 2 2
[1] FALSE
D532V8, binary
                  cls
clus                 0   1
  GGTLC2 MUTATED     6   1
  GGTLC2 WILD-TYPE 219 263
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GGTLC2 MUTATED      6    1
  GGTLC2 WILD-TYPE  219  263
        clus
vv       GGTLC2 MUTATED GGTLC2 WILD-TYPE
  FEMALE              6              219
  MALE                1              263
[1] 2 2
[1] FALSE
D532V9, binary
                  cls
clus                 0   1
  GGTLC2 MUTATED     6   0
  GGTLC2 WILD-TYPE 344  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GGTLC2 MUTATED      6    0
  GGTLC2 WILD-TYPE  344   22
     clus
vv    GGTLC2 MUTATED GGTLC2 WILD-TYPE
  NO               6              344
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  GGTLC2 MUTATED                      7                             0
  GGTLC2 WILD-TYPE                  308                            47
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  GGTLC2 MUTATED                       0                              0
  GGTLC2 WILD-TYPE                   106                             10
D532V10, multiclass
                                clus
vv                               GGTLC2 MUTATED GGTLC2 WILD-TYPE
  COLON ADENOCARCINOMA                        7              308
  COLON MUCINOUS ADENOCARCINOMA               0               47
  RECTAL ADENOCARCINOMA                       0              106
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  GGTLC2 MUTATED     5   0   0   2
  GGTLC2 WILD-TYPE 340   4  31  23
D532V11, multiclass
    clus
vv   GGTLC2 MUTATED GGTLC2 WILD-TYPE
  R0              5              340
  R1              0                4
  R2              0               31
  RX              2               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D532V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GGTLC2 MUTATED                                  0     0
  GGTLC2 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  GGTLC2 MUTATED                           0     7
  GGTLC2 WILD-TYPE                        22   219
D532V13, multiclass
                                  clus
vv                                 GGTLC2 MUTATED GGTLC2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         7              219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(533) Variable = SYNCRIP MUTATION ANALYSIS
D533V1, survival
                   sevent
clus2                 0   1
  SYNCRIP MUTATED     9   3
  SYNCRIP WILD-TYPE 369  90
  SYNCRIP MUTATED SYNCRIP WILD-TYPE 
               12               459 
  SYNCRIP MUTATED SYNCRIP WILD-TYPE 
                3                90 
$`SYNCRIP MUTATED`
TCGA-AA-A010 TCGA-AA-A017 TCGA-AZ-6599 TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-5348 
       34.98         1.02         6.77        12.76        10.06        22.98 
TCGA-CM-6171 TCGA-D5-6535 TCGA-D5-6536 TCGA-F4-6460 TCGA-AG-3892 TCGA-AG-A002 
       14.04        15.12        17.85        31.96        13.02        20.98 

$`SYNCRIP WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       17.03        14.99        21.99        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 
      106.75        22.36        62.79        88.21        49.41        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.03        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6537 
       55.92        20.19        18.25         1.32        43.27         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
      117.07        98.24         8.61        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 
        1.02        17.95        36.95        17.03        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  SYNCRIP MUTATED SYNCRIP WILD-TYPE 
             1.02              0.00 
  SYNCRIP MUTATED SYNCRIP WILD-TYPE 
            34.98            148.01 
  SYNCRIP MUTATED SYNCRIP WILD-TYPE 
            14.58             20.55 
[1] "1.0 - 35.0 (14.6)"  "0.0 - 148.0 (20.6)"
[1] "hr=" "2"  
D533V2, continuous
D533V3, binary
                   cls
clus                  0   1
  SYNCRIP MUTATED    10   2
  SYNCRIP WILD-TYPE 356 117
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SYNCRIP MUTATED     10    2
  SYNCRIP WILD-TYPE  356  117
        clus
vv       SYNCRIP MUTATED SYNCRIP WILD-TYPE
  COLON               10               356
  RECTUM               2               117
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SYNCRIP MUTATED         4        0        0         4         1         0
  SYNCRIP WILD-TYPE      87        1       32       134         9         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SYNCRIP MUTATED           0          0          3          0        0
  SYNCRIP WILD-TYPE        24         11         56         42       48
                   vv
clus                STAGE IVA STAGE IVB
  SYNCRIP MUTATED           0         0
  SYNCRIP WILD-TYPE        18         1
D533V4, multiclass
            clus
vv           SYNCRIP MUTATED SYNCRIP WILD-TYPE
  STAGE I                  4                87
  STAGE IA                 0                 1
  STAGE II                 0                32
  STAGE IIA                4               134
  STAGE IIB                1                 9
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               0                11
  STAGE IIIB               3                56
  STAGE IIIC               0                42
  STAGE IV                 0                48
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  SYNCRIP MUTATED     1   3   7   1
  SYNCRIP WILD-TYPE  16  89 322  49
D533V5, multiclass
    clus
vv   SYNCRIP MUTATED SYNCRIP WILD-TYPE
  T1               1                16
  T2               3                89
  T3               7               322
  T4               1                49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  SYNCRIP MUTATED     9   3   0
  SYNCRIP WILD-TYPE 278 110  87
D533V6, multiclass
    clus
vv   SYNCRIP MUTATED SYNCRIP WILD-TYPE
  N0               9               278
  N1               3               110
  N2               0                87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D533V7, binary
                   cls
clus                  0   1
  SYNCRIP MUTATED    10   0
  SYNCRIP WILD-TYPE 365  65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SYNCRIP MUTATED     10    0
  SYNCRIP WILD-TYPE  365   65
   clus
vv  SYNCRIP MUTATED SYNCRIP WILD-TYPE
  0              10               365
  1               0                65
[1] 2 2
[1] FALSE
D533V8, binary
                   cls
clus                  0   1
  SYNCRIP MUTATED     6   6
  SYNCRIP WILD-TYPE 219 258
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SYNCRIP MUTATED      6    6
  SYNCRIP WILD-TYPE  219  258
        clus
vv       SYNCRIP MUTATED SYNCRIP WILD-TYPE
  FEMALE               6               219
  MALE                 6               258
[1] 2 2
[1] FALSE
D533V9, binary
                   cls
clus                  0   1
  SYNCRIP MUTATED    11   0
  SYNCRIP WILD-TYPE 339  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SYNCRIP MUTATED     11    0
  SYNCRIP WILD-TYPE  339   22
     clus
vv    SYNCRIP MUTATED SYNCRIP WILD-TYPE
  NO               11               339
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SYNCRIP MUTATED                      9                             1
  SYNCRIP WILD-TYPE                  306                            46
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SYNCRIP MUTATED                       2                              0
  SYNCRIP WILD-TYPE                   104                             10
D533V10, multiclass
                                clus
vv                               SYNCRIP MUTATED SYNCRIP WILD-TYPE
  COLON ADENOCARCINOMA                         9               306
  COLON MUCINOUS ADENOCARCINOMA                1                46
  RECTAL ADENOCARCINOMA                        2               104
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  SYNCRIP MUTATED     8   0   0   3
  SYNCRIP WILD-TYPE 337   4  31  22
D533V11, multiclass
    clus
vv   SYNCRIP MUTATED SYNCRIP WILD-TYPE
  R0               8               337
  R1               0                 4
  R2               0                31
  RX               3                22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D533V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SYNCRIP MUTATED                                  0     2
  SYNCRIP WILD-TYPE                                1     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  SYNCRIP MUTATED                           0     6
  SYNCRIP WILD-TYPE                        22   220
D533V13, multiclass
                                  clus
vv                                 SYNCRIP MUTATED SYNCRIP WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          2                 9
  BLACK OR AFRICAN AMERICAN                      0                22
  WHITE                                          6               220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(534) Variable = IFITM3 MUTATION ANALYSIS
D534V1, survival
                  sevent
clus2                0   1
  IFITM3 MUTATED     8   0
  IFITM3 WILD-TYPE 370  93
  IFITM3 MUTATED IFITM3 WILD-TYPE 
               8              463 
  IFITM3 MUTATED IFITM3 WILD-TYPE 
               0               93 
$`IFITM3 MUTATED`
TCGA-AY-6197 TCGA-CM-5349 TCGA-CM-6165 TCGA-D5-5540 TCGA-D5-6529 TCGA-G4-6317 
       21.44        30.08        16.04        56.09        20.19        36.00 
TCGA-AF-4110 TCGA-EI-6506 
       14.50        20.55 

$`IFITM3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       16.31         0.95        33.01        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6166 TCGA-CM-6167 
       15.02        12.00         2.96        29.03        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6532 TCGA-D5-6533 
       45.40        12.26        19.59        55.92        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6321 
       44.68        55.04        85.48        63.62        61.91        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       10.39        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
        0.49        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  IFITM3 MUTATED IFITM3 WILD-TYPE 
            14.5              0.0 
  IFITM3 MUTATED IFITM3 WILD-TYPE 
           56.09           148.01 
  IFITM3 MUTATED IFITM3 WILD-TYPE 
          20.995           20.050 
[1] "14.5 - 56.1 (21.0)" "0.0 - 148.0 (20.1)"
[1] "hr="     "9200000"
D534V2, continuous
D534V3, binary
                  cls
clus                 0   1
  IFITM3 MUTATED     6   1
  IFITM3 WILD-TYPE 360 118
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IFITM3 MUTATED      6    1
  IFITM3 WILD-TYPE  360  118
        clus
vv       IFITM3 MUTATED IFITM3 WILD-TYPE
  COLON               6              360
  RECTUM              1              118
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  IFITM3 MUTATED         0        0        0         6         0         0
  IFITM3 WILD-TYPE      91        1       32       132        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  IFITM3 MUTATED           0          0          0          1        0
  IFITM3 WILD-TYPE        24         11         59         41       48
                  vv
clus               STAGE IVA STAGE IVB
  IFITM3 MUTATED           1         0
  IFITM3 WILD-TYPE        17         1
D534V4, multiclass
            clus
vv           IFITM3 MUTATED IFITM3 WILD-TYPE
  STAGE I                 0               91
  STAGE IA                0                1
  STAGE II                0               32
  STAGE IIA               6              132
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              0               59
  STAGE IIIC              1               41
  STAGE IV                0               48
  STAGE IVA               1               17
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  IFITM3 MUTATED     0   0   7   1
  IFITM3 WILD-TYPE  17  92 322  49
D534V5, multiclass
    clus
vv   IFITM3 MUTATED IFITM3 WILD-TYPE
  T1              0               17
  T2              0               92
  T3              7              322
  T4              1               49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  IFITM3 MUTATED     6   0   2
  IFITM3 WILD-TYPE 281 113  85
D534V6, multiclass
    clus
vv   IFITM3 MUTATED IFITM3 WILD-TYPE
  N0              6              281
  N1              0              113
  N2              2               85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D534V7, binary
                  cls
clus                 0   1
  IFITM3 MUTATED     5   0
  IFITM3 WILD-TYPE 370  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IFITM3 MUTATED      5    0
  IFITM3 WILD-TYPE  370   65
   clus
vv  IFITM3 MUTATED IFITM3 WILD-TYPE
  0              5              370
  1              0               65
[1] 2 2
[1] FALSE
D534V8, binary
                  cls
clus                 0   1
  IFITM3 MUTATED     3   5
  IFITM3 WILD-TYPE 222 259
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IFITM3 MUTATED      3    5
  IFITM3 WILD-TYPE  222  259
        clus
vv       IFITM3 MUTATED IFITM3 WILD-TYPE
  FEMALE              3              222
  MALE                5              259
[1] 2 2
[1] FALSE
D534V9, binary
                  cls
clus                 0   1
  IFITM3 MUTATED     8   0
  IFITM3 WILD-TYPE 342  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IFITM3 MUTATED      8    0
  IFITM3 WILD-TYPE  342   22
     clus
vv    IFITM3 MUTATED IFITM3 WILD-TYPE
  NO               8              342
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  IFITM3 MUTATED                      6                             0
  IFITM3 WILD-TYPE                  309                            47
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  IFITM3 MUTATED                       1                              0
  IFITM3 WILD-TYPE                   105                             10
D534V10, multiclass
                                clus
vv                               IFITM3 MUTATED IFITM3 WILD-TYPE
  COLON ADENOCARCINOMA                        6              309
  COLON MUCINOUS ADENOCARCINOMA               0               47
  RECTAL ADENOCARCINOMA                       1              105
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  IFITM3 MUTATED     8   0   0   0
  IFITM3 WILD-TYPE 337   4  31  25
D534V11, multiclass
    clus
vv   IFITM3 MUTATED IFITM3 WILD-TYPE
  R0              8              337
  R1              0                4
  R2              0               31
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D534V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  IFITM3 MUTATED                                  0     0
  IFITM3 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  IFITM3 MUTATED                           0     8
  IFITM3 WILD-TYPE                        22   218
D534V13, multiclass
                                  clus
vv                                 IFITM3 MUTATED IFITM3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         8              218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(535) Variable = SMG1 MUTATION ANALYSIS
D535V1, survival
                sevent
clus2              0   1
  SMG1 MUTATED    19   8
  SMG1 WILD-TYPE 359  85
  SMG1 MUTATED SMG1 WILD-TYPE 
            27            444 
  SMG1 MUTATED SMG1 WILD-TYPE 
             8             85 
$`SMG1 MUTATED`
TCGA-A6-6781 TCGA-AA-3492 TCGA-AA-3663 TCGA-AA-3833 TCGA-AA-3864 TCGA-AA-3947 
       19.66         3.02         6.97        15.95        53.00        33.01 
TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01I TCGA-AA-A01R TCGA-AY-5543 TCGA-AZ-6598 
        4.01        34.98        31.00        35.01        33.01        49.41 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CM-4746 
       12.76        10.06        17.56       148.01        85.45        37.02 
TCGA-CM-5344 TCGA-CM-5348 TCGA-D5-5538 TCGA-DM-A0XF TCGA-DM-A28G TCGA-F4-6460 
       22.03        22.98        12.26        38.20        60.79        31.96 
TCGA-G4-6626 TCGA-AG-A002 TCGA-EI-6507 
       46.75        20.98        19.96 

$`SMG1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 
       23.87        20.12        20.28         7.04         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3837 
       33.04         0.99        25.02         1.02        17.98        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       31.07        30.05        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 
       18.05        31.00         2.01        12.99        24.00        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       31.00        38.07         1.02         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6197 TCGA-AY-6386 
       14.50        27.09        16.31         0.95        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       88.21         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4952 TCGA-CK-5912 
        3.29         0.07        12.20        14.30        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5349 
       23.05        20.02        25.02        13.02        29.06        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       12.03        45.40        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       24.43       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28H TCGA-DM-A28K 
        6.12        81.37       119.93        35.97       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
        8.61        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-AF-2687 
       13.78        35.80        26.17        91.79        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       20.55        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  SMG1 MUTATED SMG1 WILD-TYPE 
          3.02           0.00 
  SMG1 MUTATED SMG1 WILD-TYPE 
        148.01         140.38 
  SMG1 MUTATED SMG1 WILD-TYPE 
         31.00          20.02 
[1] "3.0 - 148.0 (31.0)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1.3"
D535V2, continuous
D535V3, binary
                cls
clus               0   1
  SMG1 MUTATED    25   2
  SMG1 WILD-TYPE 341 117
[1] "tbl2"
                cls
clus             [,1] [,2]
  SMG1 MUTATED     25    2
  SMG1 WILD-TYPE  341  117
        clus
vv       SMG1 MUTATED SMG1 WILD-TYPE
  COLON            25            341
  RECTUM            2            117
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SMG1 MUTATED         3        0        4         6         3         0
  SMG1 WILD-TYPE      88        1       28       132         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SMG1 MUTATED           2          0          6          2        0         1
  SMG1 WILD-TYPE        22         11         53         40       48        17
                vv
clus             STAGE IVB
  SMG1 MUTATED           0
  SMG1 WILD-TYPE         1
D535V4, multiclass
            clus
vv           SMG1 MUTATED SMG1 WILD-TYPE
  STAGE I               3             88
  STAGE IA              0              1
  STAGE II              4             28
  STAGE IIA             6            132
  STAGE IIB             3              7
  STAGE IIC             0              1
  STAGE III             2             22
  STAGE IIIA            0             11
  STAGE IIIB            6             53
  STAGE IIIC            2             40
  STAGE IV              0             48
  STAGE IVA             1             17
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  SMG1 MUTATED     0   3  19   5
  SMG1 WILD-TYPE  17  89 310  45
D535V5, multiclass
    clus
vv   SMG1 MUTATED SMG1 WILD-TYPE
  T1            0             17
  T2            3             89
  T3           19            310
  T4            5             45
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  SMG1 MUTATED    16   9   2
  SMG1 WILD-TYPE 271 104  85
D535V6, multiclass
    clus
vv   SMG1 MUTATED SMG1 WILD-TYPE
  N0           16            271
  N1            9            104
  N2            2             85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D535V7, binary
                cls
clus               0   1
  SMG1 MUTATED    24   1
  SMG1 WILD-TYPE 351  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  SMG1 MUTATED     24    1
  SMG1 WILD-TYPE  351   64
   clus
vv  SMG1 MUTATED SMG1 WILD-TYPE
  0           24            351
  1            1             64
[1] 2 2
[1] FALSE
D535V8, binary
                cls
clus               0   1
  SMG1 MUTATED    13  14
  SMG1 WILD-TYPE 212 250
[1] "tbl2"
                cls
clus             [,1] [,2]
  SMG1 MUTATED     13   14
  SMG1 WILD-TYPE  212  250
        clus
vv       SMG1 MUTATED SMG1 WILD-TYPE
  FEMALE           13            212
  MALE             14            250
[1] 2 2
[1] FALSE
D535V9, binary
                cls
clus               0   1
  SMG1 MUTATED    23   1
  SMG1 WILD-TYPE 327  21
[1] "tbl2"
                cls
clus             [,1] [,2]
  SMG1 MUTATED     23    1
  SMG1 WILD-TYPE  327   21
     clus
vv    SMG1 MUTATED SMG1 WILD-TYPE
  NO            23            327
  YES            1             21
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SMG1 MUTATED                     19                             5
  SMG1 WILD-TYPE                  296                            42
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SMG1 MUTATED                       2                              0
  SMG1 WILD-TYPE                   104                             10
D535V10, multiclass
                                clus
vv                               SMG1 MUTATED SMG1 WILD-TYPE
  COLON ADENOCARCINOMA                     19            296
  COLON MUCINOUS ADENOCARCINOMA             5             42
  RECTAL ADENOCARCINOMA                     2            104
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  SMG1 MUTATED    20   1   0   3
  SMG1 WILD-TYPE 325   3  31  22
D535V11, multiclass
    clus
vv   SMG1 MUTATED SMG1 WILD-TYPE
  R0           20            325
  R1            1              3
  R2            0             31
  RX            3             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D535V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SMG1 MUTATED                                  0     2
  SMG1 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  SMG1 MUTATED                           3    12
  SMG1 WILD-TYPE                        19   214
D535V13, multiclass
                                  clus
vv                                 SMG1 MUTATED SMG1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              9
  BLACK OR AFRICAN AMERICAN                   3             19
  WHITE                                      12            214
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(536) Variable = RBL2 MUTATION ANALYSIS
D536V1, survival
                sevent
clus2              0   1
  RBL2 MUTATED    19   3
  RBL2 WILD-TYPE 359  90
  RBL2 MUTATED RBL2 WILD-TYPE 
            22            449 
  RBL2 MUTATED RBL2 WILD-TYPE 
             3             90 
$`RBL2 MUTATED`
TCGA-A6-3809 TCGA-A6-5665 TCGA-AA-3554 TCGA-AA-3558 TCGA-AA-3811 TCGA-AA-3864 
       32.75        22.06        17.95        20.98        10.06        53.00 
TCGA-AA-3977 TCGA-AA-A010 TCGA-AA-A01Q TCGA-AD-5900 TCGA-AD-6895 TCGA-AZ-4315 
       25.02        34.98         1.02         0.07         0.72        58.39 
TCGA-AZ-6605 TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-5861 TCGA-CM-5864 TCGA-CM-6169 
        5.23        12.76        10.06        15.02        15.02        13.02 
TCGA-D5-5538 TCGA-G4-6588 TCGA-AF-4110 TCGA-AG-3742 
       12.26        26.17        14.50         0.99 

$`RBL2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       24.00        29.95        23.01        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       26.99        19.04        19.04        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       30.05        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        31.00        38.07        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       18.05        40.96        21.37        15.52        56.55         0.79 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6606 
       49.41         6.77        12.10       100.01        29.56        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.07        12.20        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
        5.03        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6170 
       29.03        16.04        21.99        14.99        12.99        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5539 TCGA-D5-5540 
       11.01        10.06        12.03        45.40        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       35.80        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-5654 
       43.04        13.55        19.10        34.49        10.39        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
        0.99        37.02        32.98         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  RBL2 MUTATED RBL2 WILD-TYPE 
          0.07           0.00 
  RBL2 MUTATED RBL2 WILD-TYPE 
         58.39         148.01 
  RBL2 MUTATED RBL2 WILD-TYPE 
         14.76          20.91 
[1] "0.1 - 58.4 (14.8)"  "0.0 - 148.0 (20.9)"
[1] "hr=" "1.1"
D536V2, continuous
D536V3, binary
                cls
clus               0   1
  RBL2 MUTATED    21   1
  RBL2 WILD-TYPE 345 118
[1] "tbl2"
                cls
clus             [,1] [,2]
  RBL2 MUTATED     21    1
  RBL2 WILD-TYPE  345  118
        clus
vv       RBL2 MUTATED RBL2 WILD-TYPE
  COLON            21            345
  RECTUM            1            118
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RBL2 MUTATED         4        0        3         8         2         0
  RBL2 WILD-TYPE      87        1       29       130         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RBL2 MUTATED           1          0          2          0        0         1
  RBL2 WILD-TYPE        23         11         57         42       48        17
                vv
clus             STAGE IVB
  RBL2 MUTATED           0
  RBL2 WILD-TYPE         1
D536V4, multiclass
            clus
vv           RBL2 MUTATED RBL2 WILD-TYPE
  STAGE I               4             87
  STAGE IA              0              1
  STAGE II              3             29
  STAGE IIA             8            130
  STAGE IIB             2              8
  STAGE IIC             0              1
  STAGE III             1             23
  STAGE IIIA            0             11
  STAGE IIIB            2             57
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             1             17
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  RBL2 MUTATED     1   4  13   5
  RBL2 WILD-TYPE  16  88 316  45
D536V5, multiclass
    clus
vv   RBL2 MUTATED RBL2 WILD-TYPE
  T1            1             16
  T2            4             88
  T3           13            316
  T4            5             45
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  RBL2 MUTATED    18   3   2
  RBL2 WILD-TYPE 269 110  85
D536V6, multiclass
    clus
vv   RBL2 MUTATED RBL2 WILD-TYPE
  N0           18            269
  N1            3            110
  N2            2             85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D536V7, binary
                cls
clus               0   1
  RBL2 MUTATED    19   0
  RBL2 WILD-TYPE 356  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  RBL2 MUTATED     19    0
  RBL2 WILD-TYPE  356   65
   clus
vv  RBL2 MUTATED RBL2 WILD-TYPE
  0           19            356
  1            0             65
[1] 2 2
[1] FALSE
D536V8, binary
                cls
clus               0   1
  RBL2 MUTATED    11  12
  RBL2 WILD-TYPE 214 252
[1] "tbl2"
                cls
clus             [,1] [,2]
  RBL2 MUTATED     11   12
  RBL2 WILD-TYPE  214  252
        clus
vv       RBL2 MUTATED RBL2 WILD-TYPE
  FEMALE           11            214
  MALE             12            252
[1] 2 2
[1] FALSE
D536V9, binary
                cls
clus               0   1
  RBL2 MUTATED    18   0
  RBL2 WILD-TYPE 332  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  RBL2 MUTATED     18    0
  RBL2 WILD-TYPE  332   22
     clus
vv    RBL2 MUTATED RBL2 WILD-TYPE
  NO            18            332
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  RBL2 MUTATED                     18                             3
  RBL2 WILD-TYPE                  297                            44
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  RBL2 MUTATED                       1                              0
  RBL2 WILD-TYPE                   105                             10
D536V10, multiclass
                                clus
vv                               RBL2 MUTATED RBL2 WILD-TYPE
  COLON ADENOCARCINOMA                     18            297
  COLON MUCINOUS ADENOCARCINOMA             3             44
  RECTAL ADENOCARCINOMA                     1            105
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  RBL2 MUTATED    17   0   1   2
  RBL2 WILD-TYPE 328   4  30  23
D536V11, multiclass
    clus
vv   RBL2 MUTATED RBL2 WILD-TYPE
  R0           17            328
  R1            0              4
  R2            1             30
  RX            2             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D536V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RBL2 MUTATED                                  0     2
  RBL2 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  RBL2 MUTATED                           1    11
  RBL2 WILD-TYPE                        21   215
D536V13, multiclass
                                  clus
vv                                 RBL2 MUTATED RBL2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              9
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                      11            215
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(537) Variable = CASC1 MUTATION ANALYSIS
D537V1, survival
                 sevent
clus2               0   1
  CASC1 MUTATED    12   2
  CASC1 WILD-TYPE 366  91
  CASC1 MUTATED CASC1 WILD-TYPE 
             14             457 
  CASC1 MUTATED CASC1 WILD-TYPE 
              2              91 
$`CASC1 MUTATED`
TCGA-AA-3520 TCGA-AA-3966 TCGA-AA-3977 TCGA-AA-A010 TCGA-AZ-6599 TCGA-AZ-6603 
       24.03         2.01        25.02        34.98         6.77        29.56 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CK-4952 TCGA-CM-6676 TCGA-D5-6539 TCGA-F4-6856 
       12.20        12.76        15.62        11.08        12.49        35.31 
TCGA-AG-3892 TCGA-AG-A002 
       13.02        20.98 

$`CASC1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
       38.99         1.02         9.07        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
        2.01        20.98        34.03        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6605 
       62.79        88.21        49.41        12.10       100.01         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        3.29         0.07        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       85.45        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       13.05        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       47.41       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       36.95        17.03        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  CASC1 MUTATED CASC1 WILD-TYPE 
           2.01            0.00 
  CASC1 MUTATED CASC1 WILD-TYPE 
          35.31          148.01 
  CASC1 MUTATED CASC1 WILD-TYPE 
          14.32           20.28 
[1] "2.0 - 35.3 (14.3)"  "0.0 - 148.0 (20.3)"
[1] "hr=" "1.1"
D537V2, continuous
D537V3, binary
                 cls
clus                0   1
  CASC1 MUTATED    12   2
  CASC1 WILD-TYPE 354 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASC1 MUTATED     12    2
  CASC1 WILD-TYPE  354  117
        clus
vv       CASC1 MUTATED CASC1 WILD-TYPE
  COLON             12             354
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CASC1 MUTATED         5        0        1         3         1         0
  CASC1 WILD-TYPE      86        1       31       135         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CASC1 MUTATED           0          1          0          1        0         0
  CASC1 WILD-TYPE        24         10         59         41       48        18
                 vv
clus              STAGE IVB
  CASC1 MUTATED           0
  CASC1 WILD-TYPE         1
D537V4, multiclass
            clus
vv           CASC1 MUTATED CASC1 WILD-TYPE
  STAGE I                5              86
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              3             135
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             1              10
  STAGE IIIB             0              59
  STAGE IIIC             1              41
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CASC1 MUTATED     1   6   5   2
  CASC1 WILD-TYPE  16  86 324  48
D537V5, multiclass
    clus
vv   CASC1 MUTATED CASC1 WILD-TYPE
  T1             1              16
  T2             6              86
  T3             5             324
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  CASC1 MUTATED    12   1   1
  CASC1 WILD-TYPE 275 112  86
D537V6, multiclass
    clus
vv   CASC1 MUTATED CASC1 WILD-TYPE
  N0            12             275
  N1             1             112
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D537V7, binary
                 cls
clus                0   1
  CASC1 MUTATED    11   0
  CASC1 WILD-TYPE 364  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASC1 MUTATED     11    0
  CASC1 WILD-TYPE  364   65
   clus
vv  CASC1 MUTATED CASC1 WILD-TYPE
  0            11             364
  1             0              65
[1] 2 2
[1] FALSE
D537V8, binary
                 cls
clus                0   1
  CASC1 MUTATED     7   7
  CASC1 WILD-TYPE 218 257
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASC1 MUTATED      7    7
  CASC1 WILD-TYPE  218  257
        clus
vv       CASC1 MUTATED CASC1 WILD-TYPE
  FEMALE             7             218
  MALE               7             257
[1] 2 2
[1] FALSE
D537V9, binary
                 cls
clus                0   1
  CASC1 MUTATED    12   0
  CASC1 WILD-TYPE 338  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASC1 MUTATED     12    0
  CASC1 WILD-TYPE  338   22
     clus
vv    CASC1 MUTATED CASC1 WILD-TYPE
  NO             12             338
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CASC1 MUTATED                      8                             4
  CASC1 WILD-TYPE                  307                            43
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CASC1 MUTATED                       2                              0
  CASC1 WILD-TYPE                   104                             10
D537V10, multiclass
                                clus
vv                               CASC1 MUTATED CASC1 WILD-TYPE
  COLON ADENOCARCINOMA                       8             307
  COLON MUCINOUS ADENOCARCINOMA              4              43
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  CASC1 MUTATED     7   0   0   3
  CASC1 WILD-TYPE 338   4  31  22
D537V11, multiclass
    clus
vv   CASC1 MUTATED CASC1 WILD-TYPE
  R0             7             338
  R1             0               4
  R2             0              31
  RX             3              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D537V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CASC1 MUTATED                                  0     2
  CASC1 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CASC1 MUTATED                           0     6
  CASC1 WILD-TYPE                        22   220
D537V13, multiclass
                                  clus
vv                                 CASC1 MUTATED CASC1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               9
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        6             220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(538) Variable = LNX2 MUTATION ANALYSIS
D538V1, survival
                sevent
clus2              0   1
  LNX2 MUTATED    13   5
  LNX2 WILD-TYPE 365  88
  LNX2 MUTATED LNX2 WILD-TYPE 
            18            453 
  LNX2 MUTATED LNX2 WILD-TYPE 
             5             88 
$`LNX2 MUTATED`
TCGA-A6-5665 TCGA-AA-3811 TCGA-AA-3818 TCGA-AA-3821 TCGA-AA-3949 TCGA-AA-A00N 
       22.06        10.06         0.99         1.02        26.01         4.01 
TCGA-AA-A00R TCGA-AA-A01R TCGA-AU-6004 TCGA-CA-6718 TCGA-CM-5348 TCGA-CM-6166 
        0.99        35.01        27.09        10.06        22.98        21.99 
TCGA-D5-5541 TCGA-D5-6533 TCGA-D5-6930 TCGA-DM-A1D4 TCGA-AG-A002 TCGA-DY-A0XA 
       55.92         1.32         1.51        92.75        20.98       126.44 

$`LNX2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
       35.05        33.04        25.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       33.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00U 
       18.05        18.05        38.04        27.02        42.02        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S 
       12.00        31.00        31.00        38.07         1.02         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       10.88         0.20        14.50        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       12.76        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       29.06        22.03        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       29.03        16.04        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       56.09        20.19        18.25        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       11.64         4.80        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       24.43        38.20       130.65        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.03         5.29        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  LNX2 MUTATED LNX2 WILD-TYPE 
          0.99           0.00 
  LNX2 MUTATED LNX2 WILD-TYPE 
        126.44         148.01 
  LNX2 MUTATED LNX2 WILD-TYPE 
        21.485         20.120 
[1] "1.0 - 126.4 (21.5)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.5"
D538V2, continuous
D538V3, binary
                cls
clus               0   1
  LNX2 MUTATED    16   2
  LNX2 WILD-TYPE 350 117
[1] "tbl2"
                cls
clus             [,1] [,2]
  LNX2 MUTATED     16    2
  LNX2 WILD-TYPE  350  117
        clus
vv       LNX2 MUTATED LNX2 WILD-TYPE
  COLON            16            350
  RECTUM            2            117
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  LNX2 MUTATED         5        0        0         6         1         0
  LNX2 WILD-TYPE      86        1       32       132         9         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  LNX2 MUTATED           2          0          4          0        0         0
  LNX2 WILD-TYPE        22         11         55         42       48        18
                vv
clus             STAGE IVB
  LNX2 MUTATED           0
  LNX2 WILD-TYPE         1
D538V4, multiclass
            clus
vv           LNX2 MUTATED LNX2 WILD-TYPE
  STAGE I               5             86
  STAGE IA              0              1
  STAGE II              0             32
  STAGE IIA             6            132
  STAGE IIB             1              9
  STAGE IIC             0              1
  STAGE III             2             22
  STAGE IIIA            0             11
  STAGE IIIB            4             55
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  LNX2 MUTATED     0   5  11   2
  LNX2 WILD-TYPE  17  87 318  48
D538V5, multiclass
    clus
vv   LNX2 MUTATED LNX2 WILD-TYPE
  T1            0             17
  T2            5             87
  T3           11            318
  T4            2             48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  LNX2 MUTATED    13   3   2
  LNX2 WILD-TYPE 274 110  85
D538V6, multiclass
    clus
vv   LNX2 MUTATED LNX2 WILD-TYPE
  N0           13            274
  N1            3            110
  N2            2             85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D538V7, binary
                cls
clus               0   1
  LNX2 MUTATED    18   0
  LNX2 WILD-TYPE 357  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  LNX2 MUTATED     18    0
  LNX2 WILD-TYPE  357   65
   clus
vv  LNX2 MUTATED LNX2 WILD-TYPE
  0           18            357
  1            0             65
[1] 2 2
[1] FALSE
D538V8, binary
                cls
clus               0   1
  LNX2 MUTATED    10   8
  LNX2 WILD-TYPE 215 256
[1] "tbl2"
                cls
clus             [,1] [,2]
  LNX2 MUTATED     10    8
  LNX2 WILD-TYPE  215  256
        clus
vv       LNX2 MUTATED LNX2 WILD-TYPE
  FEMALE           10            215
  MALE              8            256
[1] 2 2
[1] FALSE
D538V9, binary
                cls
clus               0   1
  LNX2 MUTATED     9   1
  LNX2 WILD-TYPE 341  21
[1] "tbl2"
                cls
clus             [,1] [,2]
  LNX2 MUTATED      9    1
  LNX2 WILD-TYPE  341   21
     clus
vv    LNX2 MUTATED LNX2 WILD-TYPE
  NO             9            341
  YES            1             21
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  LNX2 MUTATED                     11                             5
  LNX2 WILD-TYPE                  304                            42
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  LNX2 MUTATED                       2                              0
  LNX2 WILD-TYPE                   104                             10
D538V10, multiclass
                                clus
vv                               LNX2 MUTATED LNX2 WILD-TYPE
  COLON ADENOCARCINOMA                     11            304
  COLON MUCINOUS ADENOCARCINOMA             5             42
  RECTAL ADENOCARCINOMA                     2            104
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  LNX2 MUTATED    15   0   0   1
  LNX2 WILD-TYPE 330   4  31  24
D538V11, multiclass
    clus
vv   LNX2 MUTATED LNX2 WILD-TYPE
  R0           15            330
  R1            0              4
  R2            0             31
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D538V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  LNX2 MUTATED                                  0     1
  LNX2 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  LNX2 MUTATED                           0     9
  LNX2 WILD-TYPE                        22   217
D538V13, multiclass
                                  clus
vv                                 LNX2 MUTATED LNX2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       9            217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(539) Variable = N4BP2 MUTATION ANALYSIS
D539V1, survival
                 sevent
clus2               0   1
  N4BP2 MUTATED    20   6
  N4BP2 WILD-TYPE 358  87
  N4BP2 MUTATED N4BP2 WILD-TYPE 
             26             445 
  N4BP2 MUTATED N4BP2 WILD-TYPE 
              6              87 
$`N4BP2 MUTATED`
TCGA-A6-2676 TCGA-A6-3809 TCGA-A6-5666 TCGA-A6-6648 TCGA-A6-6651 TCGA-AA-3819 
       42.90        32.75        32.71        25.18        21.76        25.02 
TCGA-AA-A00E TCGA-AA-A010 TCGA-AD-5900 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-CA-6717 
       30.02        34.98         0.07        58.39        49.41        12.76 
TCGA-CA-6718 TCGA-CK-5916 TCGA-CK-6747 TCGA-CM-6162 TCGA-CM-6171 TCGA-CM-6675 
       10.06        21.14        82.95        12.00        14.04        13.05 
TCGA-D5-5537 TCGA-D5-6538 TCGA-DM-A28C TCGA-F4-6704 TCGA-G4-6588 TCGA-AG-3742 
       45.40        17.13        81.37         1.55        26.17         0.99 
TCGA-AG-A002 TCGA-EI-6507 
       20.98        19.96 

$`N4BP2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5657 
       34.65        33.34        36.53        14.53        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       30.44        29.19        33.53        23.61        22.09        22.06 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6649 TCGA-A6-6652 
       27.09        22.52         8.38        25.08        24.16        24.69 
TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 
       24.39        23.87        20.12        19.66        20.28         7.04 
TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
        3.02         1.02        35.01        63.98         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
       13.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       36.03         8.05        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       78.08         6.05         6.97        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       13.94        38.04        19.00        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       39.98        18.05        40.96        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        88.21         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 
        3.25         3.29         0.07        12.20        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6676 TCGA-CM-6677 
       13.02        15.02        11.01        12.95        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       11.01        10.06        12.03        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
       17.85         4.80        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      135.65       139.17         6.12       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
       47.87        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        35.80        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
       32.98         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
        0.49        20.55        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  N4BP2 MUTATED N4BP2 WILD-TYPE 
           0.07            0.00 
  N4BP2 MUTATED N4BP2 WILD-TYPE 
          82.95          148.01 
  N4BP2 MUTATED N4BP2 WILD-TYPE 
          23.39           20.02 
[1] "0.1 - 83.0 (23.4)"  "0.0 - 148.0 (20.0)"
[1] "hr=" "1.1"
D539V2, continuous
D539V3, binary
                 cls
clus                0   1
  N4BP2 MUTATED    24   3
  N4BP2 WILD-TYPE 342 116
[1] "tbl2"
                 cls
clus              [,1] [,2]
  N4BP2 MUTATED     24    3
  N4BP2 WILD-TYPE  342  116
        clus
vv       N4BP2 MUTATED N4BP2 WILD-TYPE
  COLON             24             342
  RECTUM             3             116
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  N4BP2 MUTATED         5        0        1        11         3         1
  N4BP2 WILD-TYPE      86        1       31       127         7         0
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  N4BP2 MUTATED           0          0          3          1        0         1
  N4BP2 WILD-TYPE        24         11         56         41       48        17
                 vv
clus              STAGE IVB
  N4BP2 MUTATED           1
  N4BP2 WILD-TYPE         0
D539V4, multiclass
            clus
vv           N4BP2 MUTATED N4BP2 WILD-TYPE
  STAGE I                5              86
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA             11             127
  STAGE IIB              3               7
  STAGE IIC              1               0
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             3              56
  STAGE IIIC             1              41
  STAGE IV               0              48
  STAGE IVA              1              17
  STAGE IVB              1               0
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  N4BP2 MUTATED     2   3  18   4
  N4BP2 WILD-TYPE  15  89 311  46
D539V5, multiclass
    clus
vv   N4BP2 MUTATED N4BP2 WILD-TYPE
  T1             2              15
  T2             3              89
  T3            18             311
  T4             4              46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  N4BP2 MUTATED    21   2   4
  N4BP2 WILD-TYPE 266 111  83
D539V6, multiclass
    clus
vv   N4BP2 MUTATED N4BP2 WILD-TYPE
  N0            21             266
  N1             2             111
  N2             4              83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D539V7, binary
                 cls
clus                0   1
  N4BP2 MUTATED    19   2
  N4BP2 WILD-TYPE 356  63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  N4BP2 MUTATED     19    2
  N4BP2 WILD-TYPE  356   63
   clus
vv  N4BP2 MUTATED N4BP2 WILD-TYPE
  0            19             356
  1             2              63
[1] 2 2
[1] FALSE
D539V8, binary
                 cls
clus                0   1
  N4BP2 MUTATED    14  13
  N4BP2 WILD-TYPE 211 251
[1] "tbl2"
                 cls
clus              [,1] [,2]
  N4BP2 MUTATED     14   13
  N4BP2 WILD-TYPE  211  251
        clus
vv       N4BP2 MUTATED N4BP2 WILD-TYPE
  FEMALE            14             211
  MALE              13             251
[1] 2 2
[1] FALSE
D539V9, binary
                 cls
clus                0   1
  N4BP2 MUTATED    22   0
  N4BP2 WILD-TYPE 328  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  N4BP2 MUTATED     22    0
  N4BP2 WILD-TYPE  328   22
     clus
vv    N4BP2 MUTATED N4BP2 WILD-TYPE
  NO             22             328
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  N4BP2 MUTATED                     19                             5
  N4BP2 WILD-TYPE                  296                            42
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  N4BP2 MUTATED                       3                              0
  N4BP2 WILD-TYPE                   103                             10
D539V10, multiclass
                                clus
vv                               N4BP2 MUTATED N4BP2 WILD-TYPE
  COLON ADENOCARCINOMA                      19             296
  COLON MUCINOUS ADENOCARCINOMA              5              42
  RECTAL ADENOCARCINOMA                      3             103
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  N4BP2 MUTATED    17   0   0   5
  N4BP2 WILD-TYPE 328   4  31  20
D539V11, multiclass
    clus
vv   N4BP2 MUTATED N4BP2 WILD-TYPE
  R0            17             328
  R1             0               4
  R2             0              31
  RX             5              20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D539V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  N4BP2 MUTATED                                  1     2
  N4BP2 WILD-TYPE                                0     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  N4BP2 MUTATED                           1    17
  N4BP2 WILD-TYPE                        21   209
D539V13, multiclass
                                  clus
vv                                 N4BP2 MUTATED N4BP2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             1               0
  ASIAN                                        2               9
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                       17             209
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(540) Variable = KRT14 MUTATION ANALYSIS
D540V1, survival
                 sevent
clus2               0   1
  KRT14 MUTATED     6   3
  KRT14 WILD-TYPE 372  90
  KRT14 MUTATED KRT14 WILD-TYPE 
              9             462 
  KRT14 MUTATED KRT14 WILD-TYPE 
              3              90 
$`KRT14 MUTATED`
TCGA-A6-5665 TCGA-AA-3662 TCGA-AD-6964 TCGA-AZ-4682 TCGA-AZ-6599 TCGA-CM-6674 
       22.06         6.05        10.88        22.36         6.77        12.95 
TCGA-DM-A28E TCGA-G4-6588 TCGA-AG-A002 
      119.93        26.17        20.98 

$`KRT14 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       19.99        13.94        19.99        61.02        78.08         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        88.21        49.41        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       15.02        14.04        11.01        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       35.80        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  KRT14 MUTATED KRT14 WILD-TYPE 
           6.05            0.00 
  KRT14 MUTATED KRT14 WILD-TYPE 
         119.93          148.01 
  KRT14 MUTATED KRT14 WILD-TYPE 
         20.980          20.155 
[1] "6.0 - 119.9 (21.0)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.8"
D540V2, continuous
D540V3, binary
                 cls
clus                0   1
  KRT14 MUTATED     8   1
  KRT14 WILD-TYPE 358 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KRT14 MUTATED      8    1
  KRT14 WILD-TYPE  358  118
        clus
vv       KRT14 MUTATED KRT14 WILD-TYPE
  COLON              8             358
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KRT14 MUTATED         2        0        0         4         0         0
  KRT14 WILD-TYPE      89        1       32       134        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  KRT14 MUTATED           0          0          0          0        1         1
  KRT14 WILD-TYPE        24         11         59         42       47        17
                 vv
clus              STAGE IVB
  KRT14 MUTATED           0
  KRT14 WILD-TYPE         1
D540V4, multiclass
            clus
vv           KRT14 MUTATED KRT14 WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              4             134
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             0              42
  STAGE IV               1              47
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  KRT14 MUTATED     0   2   5   2
  KRT14 WILD-TYPE  17  90 324  48
D540V5, multiclass
    clus
vv   KRT14 MUTATED KRT14 WILD-TYPE
  T1             0              17
  T2             2              90
  T3             5             324
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  KRT14 MUTATED     7   0   2
  KRT14 WILD-TYPE 280 113  85
D540V6, multiclass
    clus
vv   KRT14 MUTATED KRT14 WILD-TYPE
  N0             7             280
  N1             0             113
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D540V7, binary
                 cls
clus                0   1
  KRT14 MUTATED     5   2
  KRT14 WILD-TYPE 370  63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KRT14 MUTATED      5    2
  KRT14 WILD-TYPE  370   63
   clus
vv  KRT14 MUTATED KRT14 WILD-TYPE
  0             5             370
  1             2              63
[1] 2 2
[1] FALSE
D540V8, binary
                 cls
clus                0   1
  KRT14 MUTATED     4   5
  KRT14 WILD-TYPE 221 259
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KRT14 MUTATED      4    5
  KRT14 WILD-TYPE  221  259
        clus
vv       KRT14 MUTATED KRT14 WILD-TYPE
  FEMALE             4             221
  MALE               5             259
[1] 2 2
[1] FALSE
D540V9, binary
                 cls
clus                0   1
  KRT14 MUTATED     8   0
  KRT14 WILD-TYPE 342  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KRT14 MUTATED      8    0
  KRT14 WILD-TYPE  342   22
     clus
vv    KRT14 MUTATED KRT14 WILD-TYPE
  NO              8             342
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  KRT14 MUTATED                      8                             0
  KRT14 WILD-TYPE                  307                            47
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  KRT14 MUTATED                       1                              0
  KRT14 WILD-TYPE                   105                             10
D540V10, multiclass
                                clus
vv                               KRT14 MUTATED KRT14 WILD-TYPE
  COLON ADENOCARCINOMA                       8             307
  COLON MUCINOUS ADENOCARCINOMA              0              47
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  KRT14 MUTATED     5   0   1   0
  KRT14 WILD-TYPE 340   4  30  25
D540V11, multiclass
    clus
vv   KRT14 MUTATED KRT14 WILD-TYPE
  R0             5             340
  R1             0               4
  R2             1              30
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D540V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KRT14 MUTATED                                  0     0
  KRT14 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  KRT14 MUTATED                           0     7
  KRT14 WILD-TYPE                        22   219
D540V13, multiclass
                                  clus
vv                                 KRT14 MUTATED KRT14 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        7             219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(541) Variable = LNPEP MUTATION ANALYSIS
D541V1, survival
                 sevent
clus2               0   1
  LNPEP MUTATED    13   5
  LNPEP WILD-TYPE 365  88
  LNPEP MUTATED LNPEP WILD-TYPE 
             18             453 
  LNPEP MUTATED LNPEP WILD-TYPE 
              5              88 
$`LNPEP MUTATED`
TCGA-AA-3492 TCGA-AA-3663 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3966 TCGA-AA-A00A 
        3.02         6.97        19.04        19.04         2.01        38.04 
TCGA-AA-A00J TCGA-AA-A010 TCGA-AZ-4315 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-CA-6718 
       18.05        34.98        58.39        88.21        49.41        10.06 
TCGA-CK-6747 TCGA-D5-6536 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6626 TCGA-AG-A002 
       82.95        17.85        85.48        63.62        46.75        20.98 

$`LNPEP WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
        5.03        85.05        26.99        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K 
       27.02        13.94        19.00        30.02        34.03        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       33.01        21.44        17.82         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       22.36        62.79         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 
        3.25         3.29         0.07        12.20        12.76        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
        9.99        21.14         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6315 
       74.56        65.85        53.62        44.68        55.04        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  LNPEP MUTATED LNPEP WILD-TYPE 
           2.01            0.00 
  LNPEP MUTATED LNPEP WILD-TYPE 
          88.21          148.01 
  LNPEP MUTATED LNPEP WILD-TYPE 
          27.98           20.12 
[1] "2.0 - 88.2 (28.0)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1"  
D541V2, continuous
D541V3, binary
                 cls
clus                0   1
  LNPEP MUTATED    18   1
  LNPEP WILD-TYPE 348 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LNPEP MUTATED     18    1
  LNPEP WILD-TYPE  348  118
        clus
vv       LNPEP MUTATED LNPEP WILD-TYPE
  COLON             18             348
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  LNPEP MUTATED         2        0        4         8         1         0
  LNPEP WILD-TYPE      89        1       28       130         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  LNPEP MUTATED           0          0          3          0        1         0
  LNPEP WILD-TYPE        24         11         56         42       47        18
                 vv
clus              STAGE IVB
  LNPEP MUTATED           0
  LNPEP WILD-TYPE         1
D541V4, multiclass
            clus
vv           LNPEP MUTATED LNPEP WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               4              28
  STAGE IIA              8             130
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             3              56
  STAGE IIIC             0              42
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  LNPEP MUTATED     1   1  15   2
  LNPEP WILD-TYPE  16  91 314  48
D541V5, multiclass
    clus
vv   LNPEP MUTATED LNPEP WILD-TYPE
  T1             1              16
  T2             1              91
  T3            15             314
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  LNPEP MUTATED    16   3   0
  LNPEP WILD-TYPE 271 110  87
D541V6, multiclass
    clus
vv   LNPEP MUTATED LNPEP WILD-TYPE
  N0            16             271
  N1             3             110
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D541V7, binary
                 cls
clus                0   1
  LNPEP MUTATED    16   1
  LNPEP WILD-TYPE 359  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LNPEP MUTATED     16    1
  LNPEP WILD-TYPE  359   64
   clus
vv  LNPEP MUTATED LNPEP WILD-TYPE
  0            16             359
  1             1              64
[1] 2 2
[1] FALSE
D541V8, binary
                 cls
clus                0   1
  LNPEP MUTATED     8  11
  LNPEP WILD-TYPE 217 253
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LNPEP MUTATED      8   11
  LNPEP WILD-TYPE  217  253
        clus
vv       LNPEP MUTATED LNPEP WILD-TYPE
  FEMALE             8             217
  MALE              11             253
[1] 2 2
[1] FALSE
D541V9, binary
                 cls
clus                0   1
  LNPEP MUTATED    15   2
  LNPEP WILD-TYPE 335  20
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LNPEP MUTATED     15    2
  LNPEP WILD-TYPE  335   20
     clus
vv    LNPEP MUTATED LNPEP WILD-TYPE
  NO             15             335
  YES             2              20
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  LNPEP MUTATED                     16                             2
  LNPEP WILD-TYPE                  299                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  LNPEP MUTATED                       1                              0
  LNPEP WILD-TYPE                   105                             10
D541V10, multiclass
                                clus
vv                               LNPEP MUTATED LNPEP WILD-TYPE
  COLON ADENOCARCINOMA                      16             299
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  LNPEP MUTATED    13   0   1   2
  LNPEP WILD-TYPE 332   4  30  23
D541V11, multiclass
    clus
vv   LNPEP MUTATED LNPEP WILD-TYPE
  R0            13             332
  R1             0               4
  R2             1              30
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D541V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  LNPEP MUTATED                                  0     1
  LNPEP WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  LNPEP MUTATED                           1     7
  LNPEP WILD-TYPE                        21   219
D541V13, multiclass
                                  clus
vv                                 LNPEP MUTATED LNPEP WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        7             219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(542) Variable = SP110 MUTATION ANALYSIS
D542V1, survival
                 sevent
clus2               0   1
  SP110 MUTATED     8   2
  SP110 WILD-TYPE 370  91
  SP110 MUTATED SP110 WILD-TYPE 
             10             461 
  SP110 MUTATED SP110 WILD-TYPE 
              2              91 
$`SP110 MUTATED`
TCGA-AA-3710 TCGA-AD-6899 TCGA-AU-3779 TCGA-CM-5861 TCGA-CM-6166 TCGA-CM-6172 
       26.99         5.79        14.50        15.02        21.99        11.01 
TCGA-CM-6676 TCGA-D5-6539 TCGA-D5-6930 TCGA-DM-A1DA 
       11.08        12.49         1.51         7.50 

$`SP110 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
       19.00        36.00         5.03        85.05        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6901 TCGA-AD-6963 
       15.52        56.55         0.79         0.72        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       10.88         0.20        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
        2.96        29.03        16.04        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6677 TCGA-CM-6678 
       15.02        14.04        12.95        13.05        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
       17.85         4.80        17.13        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       11.64         4.80        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
       12.59       140.38        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  SP110 MUTATED SP110 WILD-TYPE 
           1.51            0.00 
  SP110 MUTATED SP110 WILD-TYPE 
          26.99          148.01 
  SP110 MUTATED SP110 WILD-TYPE 
         11.785          20.910 
[1] "1.5 - 27.0 (11.8)"  "0.0 - 148.0 (20.9)"
[1] "hr=" "2"  
D542V2, continuous
D542V3, binary
                 cls
clus                0   1
  SP110 MUTATED    10   0
  SP110 WILD-TYPE 356 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SP110 MUTATED     10    0
  SP110 WILD-TYPE  356  119
        clus
vv       SP110 MUTATED SP110 WILD-TYPE
  COLON             10             356
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SP110 MUTATED         2        0        0         4         0         0
  SP110 WILD-TYPE      89        1       32       134        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SP110 MUTATED           0          1          1          2        0         0
  SP110 WILD-TYPE        24         10         58         40       48        18
                 vv
clus              STAGE IVB
  SP110 MUTATED           0
  SP110 WILD-TYPE         1
D542V4, multiclass
            clus
vv           SP110 MUTATED SP110 WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              4             134
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             1              10
  STAGE IIIB             1              58
  STAGE IIIC             2              40
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  SP110 MUTATED     0   2   7   1
  SP110 WILD-TYPE  17  90 322  49
D542V5, multiclass
    clus
vv   SP110 MUTATED SP110 WILD-TYPE
  T1             0              17
  T2             2              90
  T3             7             322
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  SP110 MUTATED     7   1   2
  SP110 WILD-TYPE 280 112  85
D542V6, multiclass
    clus
vv   SP110 MUTATED SP110 WILD-TYPE
  N0             7             280
  N1             1             112
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D542V7, binary
                 cls
clus                0   1
  SP110 MUTATED     9   0
  SP110 WILD-TYPE 366  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SP110 MUTATED      9    0
  SP110 WILD-TYPE  366   65
   clus
vv  SP110 MUTATED SP110 WILD-TYPE
  0             9             366
  1             0              65
[1] 2 2
[1] FALSE
D542V8, binary
                 cls
clus                0   1
  SP110 MUTATED     7   3
  SP110 WILD-TYPE 218 261
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SP110 MUTATED      7    3
  SP110 WILD-TYPE  218  261
        clus
vv       SP110 MUTATED SP110 WILD-TYPE
  FEMALE             7             218
  MALE               3             261
[1] 2 2
[1] FALSE
D542V9, binary
                 cls
clus                0   1
  SP110 MUTATED     8   0
  SP110 WILD-TYPE 342  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SP110 MUTATED      8    0
  SP110 WILD-TYPE  342   22
     clus
vv    SP110 MUTATED SP110 WILD-TYPE
  NO              8             342
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SP110 MUTATED                      8                             2
  SP110 WILD-TYPE                  307                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SP110 MUTATED                       0                              0
  SP110 WILD-TYPE                   106                             10
D542V10, multiclass
                                clus
vv                               SP110 MUTATED SP110 WILD-TYPE
  COLON ADENOCARCINOMA                       8             307
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  SP110 MUTATED     8   0   0   0
  SP110 WILD-TYPE 337   4  31  25
D542V11, multiclass
    clus
vv   SP110 MUTATED SP110 WILD-TYPE
  R0             8             337
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D542V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SP110 MUTATED                                  0     0
  SP110 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  SP110 MUTATED                           0     9
  SP110 WILD-TYPE                        22   217
D542V13, multiclass
                                  clus
vv                                 SP110 MUTATED SP110 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        9             217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(543) Variable = C5ORF34 MUTATION ANALYSIS
D543V1, survival
                   sevent
clus2                 0   1
  C5ORF34 MUTATED    10   2
  C5ORF34 WILD-TYPE 368  91
  C5ORF34 MUTATED C5ORF34 WILD-TYPE 
               12               459 
  C5ORF34 MUTATED C5ORF34 WILD-TYPE 
                2                91 
$`C5ORF34 MUTATED`
TCGA-A6-6137 TCGA-AA-3815 TCGA-AA-A00N TCGA-AU-6004 TCGA-CA-6717 TCGA-D5-5539 
       27.09        33.04         4.01        27.09        12.76        19.59 
TCGA-D5-6540 TCGA-D5-6930 TCGA-DM-A1DA TCGA-G4-6588 TCGA-AG-A002 TCGA-DC-5337 
       16.14         1.51         7.50        26.17        20.98        15.02 

$`C5ORF34 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        22.06        32.71        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       10.06        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
        0.20        14.50        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07        12.20        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 
       15.12        17.85         4.80        17.13        12.49        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
        9.44        11.64         4.80        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       13.32        12.59       140.38        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 
       61.91        36.00        22.09        13.78        35.80        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5869 TCGA-DC-6155 
        6.97         4.73        78.12         7.17         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  C5ORF34 MUTATED C5ORF34 WILD-TYPE 
             1.51              0.00 
  C5ORF34 MUTATED C5ORF34 WILD-TYPE 
            33.04            148.01 
  C5ORF34 MUTATED C5ORF34 WILD-TYPE 
           17.865            20.280 
[1] "1.5 - 33.0 (17.9)"  "0.0 - 148.0 (20.3)"
[1] "hr=" "1.3"
D543V2, continuous
D543V3, binary
                   cls
clus                  0   1
  C5ORF34 MUTATED    10   2
  C5ORF34 WILD-TYPE 356 117
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C5ORF34 MUTATED     10    2
  C5ORF34 WILD-TYPE  356  117
        clus
vv       C5ORF34 MUTATED C5ORF34 WILD-TYPE
  COLON               10               356
  RECTUM               2               117
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  C5ORF34 MUTATED         4        0        0         4         1         0
  C5ORF34 WILD-TYPE      87        1       32       134         9         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C5ORF34 MUTATED           0          1          1          1        0
  C5ORF34 WILD-TYPE        24         10         58         41       48
                   vv
clus                STAGE IVA STAGE IVB
  C5ORF34 MUTATED           0         0
  C5ORF34 WILD-TYPE        18         1
D543V4, multiclass
            clus
vv           C5ORF34 MUTATED C5ORF34 WILD-TYPE
  STAGE I                  4                87
  STAGE IA                 0                 1
  STAGE II                 0                32
  STAGE IIA                4               134
  STAGE IIB                1                 9
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               1                10
  STAGE IIIB               1                58
  STAGE IIIC               1                41
  STAGE IV                 0                48
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  C5ORF34 MUTATED     1   3   7   1
  C5ORF34 WILD-TYPE  16  89 322  49
D543V5, multiclass
    clus
vv   C5ORF34 MUTATED C5ORF34 WILD-TYPE
  T1               1                16
  T2               3                89
  T3               7               322
  T4               1                49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  C5ORF34 MUTATED     9   2   1
  C5ORF34 WILD-TYPE 278 111  86
D543V6, multiclass
    clus
vv   C5ORF34 MUTATED C5ORF34 WILD-TYPE
  N0               9               278
  N1               2               111
  N2               1                86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D543V7, binary
                   cls
clus                  0   1
  C5ORF34 MUTATED    12   0
  C5ORF34 WILD-TYPE 363  65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C5ORF34 MUTATED     12    0
  C5ORF34 WILD-TYPE  363   65
   clus
vv  C5ORF34 MUTATED C5ORF34 WILD-TYPE
  0              12               363
  1               0                65
[1] 2 2
[1] FALSE
D543V8, binary
                   cls
clus                  0   1
  C5ORF34 MUTATED     4   8
  C5ORF34 WILD-TYPE 221 256
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C5ORF34 MUTATED      4    8
  C5ORF34 WILD-TYPE  221  256
        clus
vv       C5ORF34 MUTATED C5ORF34 WILD-TYPE
  FEMALE               4               221
  MALE                 8               256
[1] 2 2
[1] FALSE
D543V9, binary
                   cls
clus                  0   1
  C5ORF34 MUTATED     8   0
  C5ORF34 WILD-TYPE 342  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C5ORF34 MUTATED      8    0
  C5ORF34 WILD-TYPE  342   22
     clus
vv    C5ORF34 MUTATED C5ORF34 WILD-TYPE
  NO                8               342
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  C5ORF34 MUTATED                      5                             5
  C5ORF34 WILD-TYPE                  310                            42
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  C5ORF34 MUTATED                       2                              0
  C5ORF34 WILD-TYPE                   104                             10
D543V10, multiclass
                                clus
vv                               C5ORF34 MUTATED C5ORF34 WILD-TYPE
  COLON ADENOCARCINOMA                         5               310
  COLON MUCINOUS ADENOCARCINOMA                5                42
  RECTAL ADENOCARCINOMA                        2               104
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  C5ORF34 MUTATED     9   0   0   1
  C5ORF34 WILD-TYPE 336   4  31  24
D543V11, multiclass
    clus
vv   C5ORF34 MUTATED C5ORF34 WILD-TYPE
  R0               9               336
  R1               0                 4
  R2               0                31
  RX               1                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D543V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C5ORF34 MUTATED                                  0     1
  C5ORF34 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  C5ORF34 MUTATED                           0     8
  C5ORF34 WILD-TYPE                        22   218
D543V13, multiclass
                                  clus
vv                                 C5ORF34 MUTATED C5ORF34 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                10
  BLACK OR AFRICAN AMERICAN                      0                22
  WHITE                                          8               218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(544) Variable = ADORA3 MUTATION ANALYSIS
D544V1, survival
                  sevent
clus2                0   1
  ADORA3 MUTATED     9   6
  ADORA3 WILD-TYPE 369  87
  ADORA3 MUTATED ADORA3 WILD-TYPE 
              15              456 
  ADORA3 MUTATED ADORA3 WILD-TYPE 
               6               87 
$`ADORA3 MUTATED`
TCGA-A6-3807 TCGA-AA-3864 TCGA-AA-3955 TCGA-AU-3779 TCGA-CA-6718 TCGA-CK-5916 
       34.65        53.00        20.98        14.50        10.06        21.14 
TCGA-CK-6751 TCGA-CM-5348 TCGA-CM-6676 TCGA-DM-A1D8 TCGA-F4-6570 TCGA-F4-6809 
      124.27        22.98        11.08        12.59         6.18        13.25 
TCGA-F4-6855 TCGA-G4-6588 TCGA-DY-A1DG 
       47.41        26.17        51.48 

$`ADORA3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 
       32.05         0.99        31.07        31.07        30.05        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
        0.20        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CM-4743 TCGA-CM-4744 
       51.32         9.99        82.95         1.91        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5349 
       37.02        25.02        13.02        29.06        22.03        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       12.95        13.05        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 
       98.24         8.61        31.96        35.74        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6854 TCGA-F4-6856 
       34.42        41.42        16.24        33.67         0.53        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       35.80        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       41.36        57.24        24.13        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  ADORA3 MUTATED ADORA3 WILD-TYPE 
            6.18             0.00 
  ADORA3 MUTATED ADORA3 WILD-TYPE 
          124.27           148.01 
  ADORA3 MUTATED ADORA3 WILD-TYPE 
          21.140           20.085 
[1] "6.2 - 124.3 (21.1)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.8"
D544V2, continuous
D544V3, binary
                  cls
clus                 0   1
  ADORA3 MUTATED    14   1
  ADORA3 WILD-TYPE 352 118
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ADORA3 MUTATED     14    1
  ADORA3 WILD-TYPE  352  118
        clus
vv       ADORA3 MUTATED ADORA3 WILD-TYPE
  COLON              14              352
  RECTUM              1              118
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ADORA3 MUTATED         3        0        1         5         0         0
  ADORA3 WILD-TYPE      88        1       31       133        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ADORA3 MUTATED           0          0          2          1        0
  ADORA3 WILD-TYPE        24         11         57         41       48
                  vv
clus               STAGE IVA STAGE IVB
  ADORA3 MUTATED           2         0
  ADORA3 WILD-TYPE        16         1
D544V4, multiclass
            clus
vv           ADORA3 MUTATED ADORA3 WILD-TYPE
  STAGE I                 3               88
  STAGE IA                0                1
  STAGE II                1               31
  STAGE IIA               5              133
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              2               57
  STAGE IIIC              1               41
  STAGE IV                0               48
  STAGE IVA               2               16
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ADORA3 MUTATED     1   3  11   0
  ADORA3 WILD-TYPE  16  89 318  50
D544V5, multiclass
    clus
vv   ADORA3 MUTATED ADORA3 WILD-TYPE
  T1              1               16
  T2              3               89
  T3             11              318
  T4              0               50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  ADORA3 MUTATED     9   4   2
  ADORA3 WILD-TYPE 278 109  85
D544V6, multiclass
    clus
vv   ADORA3 MUTATED ADORA3 WILD-TYPE
  N0              9              278
  N1              4              109
  N2              2               85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D544V7, binary
                  cls
clus                 0   1
  ADORA3 MUTATED    11   2
  ADORA3 WILD-TYPE 364  63
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ADORA3 MUTATED     11    2
  ADORA3 WILD-TYPE  364   63
   clus
vv  ADORA3 MUTATED ADORA3 WILD-TYPE
  0             11              364
  1              2               63
[1] 2 2
[1] FALSE
D544V8, binary
                  cls
clus                 0   1
  ADORA3 MUTATED     9   6
  ADORA3 WILD-TYPE 216 258
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ADORA3 MUTATED      9    6
  ADORA3 WILD-TYPE  216  258
        clus
vv       ADORA3 MUTATED ADORA3 WILD-TYPE
  FEMALE              9              216
  MALE                6              258
[1] 2 2
[1] FALSE
D544V9, binary
                  cls
clus                 0   1
  ADORA3 MUTATED    13   0
  ADORA3 WILD-TYPE 337  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ADORA3 MUTATED     13    0
  ADORA3 WILD-TYPE  337   22
     clus
vv    ADORA3 MUTATED ADORA3 WILD-TYPE
  NO              13              337
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ADORA3 MUTATED                     13                             1
  ADORA3 WILD-TYPE                  302                            46
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ADORA3 MUTATED                       1                              0
  ADORA3 WILD-TYPE                   105                             10
D544V10, multiclass
                                clus
vv                               ADORA3 MUTATED ADORA3 WILD-TYPE
  COLON ADENOCARCINOMA                       13              302
  COLON MUCINOUS ADENOCARCINOMA               1               46
  RECTAL ADENOCARCINOMA                       1              105
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ADORA3 MUTATED    10   0   0   3
  ADORA3 WILD-TYPE 335   4  31  22
D544V11, multiclass
    clus
vv   ADORA3 MUTATED ADORA3 WILD-TYPE
  R0             10              335
  R1              0                4
  R2              0               31
  RX              3               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D544V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ADORA3 MUTATED                                  0     1
  ADORA3 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ADORA3 MUTATED                           0    12
  ADORA3 WILD-TYPE                        22   214
D544V13, multiclass
                                  clus
vv                                 ADORA3 MUTATED ADORA3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                        12              214
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(545) Variable = MAP2K4 MUTATION ANALYSIS
D545V1, survival
                  sevent
clus2                0   1
  MAP2K4 MUTATED    22   9
  MAP2K4 WILD-TYPE 356  84
  MAP2K4 MUTATED MAP2K4 WILD-TYPE 
              31              440 
  MAP2K4 MUTATED MAP2K4 WILD-TYPE 
               9               84 
$`MAP2K4 MUTATED`
TCGA-A6-5666 TCGA-A6-6141 TCGA-AA-3492 TCGA-AA-3672 TCGA-AA-3845 TCGA-AA-3861 
       32.71         8.38         3.02         0.92         0.00        30.05 
TCGA-AA-3864 TCGA-AA-3952 TCGA-AA-3966 TCGA-AA-3986 TCGA-AA-A00N TCGA-AA-A010 
       53.00         2.01         2.01        19.07         4.01        34.98 
TCGA-AD-6548 TCGA-AD-6899 TCGA-AD-6901 TCGA-AZ-6598 TCGA-CA-6716 TCGA-CA-6718 
       21.37         5.79        22.42        49.41        12.20        10.06 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 TCGA-CM-6171 TCGA-CM-6172 TCGA-D5-6535 
       17.56       148.01        15.62        14.04        11.01        15.12 
TCGA-D5-6539 TCGA-DM-A1DA TCGA-G4-6628 TCGA-AG-3727 TCGA-AG-A00Y TCGA-DC-5337 
       12.49         7.50        79.69         0.99        23.01        15.02 
TCGA-F5-6812 
        0.66 

$`MAP2K4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 
       22.09        22.06        27.09        22.52        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       19.66        20.28         7.04         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
        2.01        14.01        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02        14.93        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       20.98        34.03        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6963 TCGA-AD-6964 
       15.52        56.55         0.79         0.72        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        88.21         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6719 
        3.06         3.25         3.29         0.07        12.76        14.30 
TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       85.45        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       12.99        13.02        15.02        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 
       43.27        17.85         4.80        17.13        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA 
       49.91        13.32        12.59       140.38        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       26.17        91.79        46.75        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
        6.02        25.97        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5869 TCGA-DC-6155 
        6.97         4.73        78.12         7.17         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6813 
        9.96        49.51        31.30        28.57        32.19         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  MAP2K4 MUTATED MAP2K4 WILD-TYPE 
               0                0 
  MAP2K4 MUTATED MAP2K4 WILD-TYPE 
          148.01           140.38 
  MAP2K4 MUTATED MAP2K4 WILD-TYPE 
           14.04            20.98 
[1] "0.0 - 148.0 (14.0)" "0.0 - 140.4 (21.0)"
[1] "hr=" "1.9"
D545V2, continuous
D545V3, binary
                  cls
clus                 0   1
  MAP2K4 MUTATED    30   4
  MAP2K4 WILD-TYPE 336 115
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP2K4 MUTATED     30    4
  MAP2K4 WILD-TYPE  336  115
        clus
vv       MAP2K4 MUTATED MAP2K4 WILD-TYPE
  COLON              30              336
  RECTUM              4              115
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MAP2K4 MUTATED         5        0        3         9         3         1
  MAP2K4 WILD-TYPE      86        1       29       129         7         0
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MAP2K4 MUTATED           3          1          3          5        0
  MAP2K4 WILD-TYPE        21         10         56         37       48
                  vv
clus               STAGE IVA STAGE IVB
  MAP2K4 MUTATED           0         0
  MAP2K4 WILD-TYPE        18         1
D545V4, multiclass
            clus
vv           MAP2K4 MUTATED MAP2K4 WILD-TYPE
  STAGE I                 5               86
  STAGE IA                0                1
  STAGE II                3               29
  STAGE IIA               9              129
  STAGE IIB               3                7
  STAGE IIC               1                0
  STAGE III               3               21
  STAGE IIIA              1               10
  STAGE IIIB              3               56
  STAGE IIIC              5               37
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  MAP2K4 MUTATED     1   4  22   7
  MAP2K4 WILD-TYPE  16  88 307  43
D545V5, multiclass
    clus
vv   MAP2K4 MUTATED MAP2K4 WILD-TYPE
  T1              1               16
  T2              4               88
  T3             22              307
  T4              7               43
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  MAP2K4 MUTATED    23   6   5
  MAP2K4 WILD-TYPE 264 107  82
D545V6, multiclass
    clus
vv   MAP2K4 MUTATED MAP2K4 WILD-TYPE
  N0             23              264
  N1              6              107
  N2              5               82
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D545V7, binary
                  cls
clus                 0   1
  MAP2K4 MUTATED    28   0
  MAP2K4 WILD-TYPE 347  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP2K4 MUTATED     28    0
  MAP2K4 WILD-TYPE  347   65
   clus
vv  MAP2K4 MUTATED MAP2K4 WILD-TYPE
  0             28              347
  1              0               65
[1] 2 2
[1] FALSE
D545V8, binary
                  cls
clus                 0   1
  MAP2K4 MUTATED    18  16
  MAP2K4 WILD-TYPE 207 248
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP2K4 MUTATED     18   16
  MAP2K4 WILD-TYPE  207  248
        clus
vv       MAP2K4 MUTATED MAP2K4 WILD-TYPE
  FEMALE             18              207
  MALE               16              248
[1] 2 2
[1] FALSE
D545V9, binary
                  cls
clus                 0   1
  MAP2K4 MUTATED    23   0
  MAP2K4 WILD-TYPE 327  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP2K4 MUTATED     23    0
  MAP2K4 WILD-TYPE  327   22
     clus
vv    MAP2K4 MUTATED MAP2K4 WILD-TYPE
  NO              23              327
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MAP2K4 MUTATED                     25                             5
  MAP2K4 WILD-TYPE                  290                            42
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MAP2K4 MUTATED                       4                              0
  MAP2K4 WILD-TYPE                   102                             10
D545V10, multiclass
                                clus
vv                               MAP2K4 MUTATED MAP2K4 WILD-TYPE
  COLON ADENOCARCINOMA                       25              290
  COLON MUCINOUS ADENOCARCINOMA               5               42
  RECTAL ADENOCARCINOMA                       4              102
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  MAP2K4 MUTATED    21   0   0   6
  MAP2K4 WILD-TYPE 324   4  31  19
D545V11, multiclass
    clus
vv   MAP2K4 MUTATED MAP2K4 WILD-TYPE
  R0             21              324
  R1              0                4
  R2              0               31
  RX              6               19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D545V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MAP2K4 MUTATED                                  0     2
  MAP2K4 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  MAP2K4 MUTATED                           1    18
  MAP2K4 WILD-TYPE                        21   208
D545V13, multiclass
                                  clus
vv                                 MAP2K4 MUTATED MAP2K4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                9
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                        18              208
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(546) Variable = OVGP1 MUTATION ANALYSIS
D546V1, survival
                 sevent
clus2               0   1
  OVGP1 MUTATED    16   1
  OVGP1 WILD-TYPE 362  92
  OVGP1 MUTATED OVGP1 WILD-TYPE 
             17             454 
  OVGP1 MUTATED OVGP1 WILD-TYPE 
              1              92 
$`OVGP1 MUTATED`
TCGA-A6-5666 TCGA-AA-3510 TCGA-AA-3663 TCGA-AA-3864 TCGA-AA-A00A TCGA-AD-5900 
       32.71        63.98         6.97        53.00        38.04         0.07 
TCGA-AD-6889 TCGA-AD-6899 TCGA-AU-3779 TCGA-AY-6386 TCGA-AZ-4681 TCGA-CM-6163 
       56.55         5.79        14.50        17.82       106.75         2.96 
TCGA-CM-6679 TCGA-D5-6536 TCGA-AG-3742 TCGA-AG-A002 TCGA-DC-6681 
       10.06        17.85         0.99        20.98         5.95 

$`OVGP1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        22.06        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        31.07        30.05        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
        7.96        27.02        13.94        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6901 TCGA-AD-6963 
       21.37        15.52         0.79         0.72        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       10.88         0.20        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5403 
       21.44        58.39         1.41         5.13        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6164 
       15.02        15.02        17.03        15.02        12.00        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       11.01        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3878 TCGA-AG-3881 
        7.99         0.99        37.02        32.98         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6682 
        5.03        13.97        27.95        10.98        19.99         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  OVGP1 MUTATED OVGP1 WILD-TYPE 
           0.07            0.00 
  OVGP1 MUTATED OVGP1 WILD-TYPE 
         106.75          148.01 
  OVGP1 MUTATED OVGP1 WILD-TYPE 
         17.820          20.415 
[1] "0.1 - 106.8 (17.8)" "0.0 - 148.0 (20.4)"
[1] "hr=" "3.7"
D546V2, continuous
D546V3, binary
                 cls
clus                0   1
  OVGP1 MUTATED    14   3
  OVGP1 WILD-TYPE 352 116
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OVGP1 MUTATED     14    3
  OVGP1 WILD-TYPE  352  116
        clus
vv       OVGP1 MUTATED OVGP1 WILD-TYPE
  COLON             14             352
  RECTUM             3             116
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  OVGP1 MUTATED         4        0        3         6         0         1
  OVGP1 WILD-TYPE      87        1       29       132        10         0
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  OVGP1 MUTATED           0          0          1          1        0         1
  OVGP1 WILD-TYPE        24         11         58         41       48        17
                 vv
clus              STAGE IVB
  OVGP1 MUTATED           0
  OVGP1 WILD-TYPE         1
D546V4, multiclass
            clus
vv           OVGP1 MUTATED OVGP1 WILD-TYPE
  STAGE I                4              87
  STAGE IA               0               1
  STAGE II               3              29
  STAGE IIA              6             132
  STAGE IIB              0              10
  STAGE IIC              1               0
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             1              41
  STAGE IV               0              48
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  OVGP1 MUTATED     2   2  11   2
  OVGP1 WILD-TYPE  15  90 318  48
D546V5, multiclass
    clus
vv   OVGP1 MUTATED OVGP1 WILD-TYPE
  T1             2              15
  T2             2              90
  T3            11             318
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  OVGP1 MUTATED    14   1   2
  OVGP1 WILD-TYPE 273 112  85
D546V6, multiclass
    clus
vv   OVGP1 MUTATED OVGP1 WILD-TYPE
  N0            14             273
  N1             1             112
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D546V7, binary
                 cls
clus                0   1
  OVGP1 MUTATED    14   1
  OVGP1 WILD-TYPE 361  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OVGP1 MUTATED     14    1
  OVGP1 WILD-TYPE  361   64
   clus
vv  OVGP1 MUTATED OVGP1 WILD-TYPE
  0            14             361
  1             1              64
[1] 2 2
[1] FALSE
D546V8, binary
                 cls
clus                0   1
  OVGP1 MUTATED     5  12
  OVGP1 WILD-TYPE 220 252
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OVGP1 MUTATED      5   12
  OVGP1 WILD-TYPE  220  252
        clus
vv       OVGP1 MUTATED OVGP1 WILD-TYPE
  FEMALE             5             220
  MALE              12             252
[1] 2 2
[1] FALSE
D546V9, binary
                 cls
clus                0   1
  OVGP1 MUTATED    13   0
  OVGP1 WILD-TYPE 337  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OVGP1 MUTATED     13    0
  OVGP1 WILD-TYPE  337   22
     clus
vv    OVGP1 MUTATED OVGP1 WILD-TYPE
  NO             13             337
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  OVGP1 MUTATED                     12                             2
  OVGP1 WILD-TYPE                  303                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  OVGP1 MUTATED                       3                              0
  OVGP1 WILD-TYPE                   103                             10
D546V10, multiclass
                                clus
vv                               OVGP1 MUTATED OVGP1 WILD-TYPE
  COLON ADENOCARCINOMA                      12             303
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      3             103
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  OVGP1 MUTATED    14   0   0   0
  OVGP1 WILD-TYPE 331   4  31  25
D546V11, multiclass
    clus
vv   OVGP1 MUTATED OVGP1 WILD-TYPE
  R0            14             331
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D546V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OVGP1 MUTATED                                  0     1
  OVGP1 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  OVGP1 MUTATED                           1     9
  OVGP1 WILD-TYPE                        21   217
D546V13, multiclass
                                  clus
vv                                 OVGP1 MUTATED OVGP1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        9             217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(547) Variable = GOLGB1 MUTATION ANALYSIS
D547V1, survival
                  sevent
clus2                0   1
  GOLGB1 MUTATED    32   9
  GOLGB1 WILD-TYPE 346  84
  GOLGB1 MUTATED GOLGB1 WILD-TYPE 
              41              430 
  GOLGB1 MUTATED GOLGB1 WILD-TYPE 
               9               84 
$`GOLGB1 MUTATED`
TCGA-A6-5659 TCGA-A6-6141 TCGA-A6-6780 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3555 
       30.44         8.38        20.12        35.01        63.98        29.95 
TCGA-AA-3561 TCGA-AA-3710 TCGA-AA-3864 TCGA-AA-3977 TCGA-AA-A00J TCGA-AA-A00N 
       13.94        26.99        53.00        25.02        18.05         4.01 
TCGA-AA-A010 TCGA-AD-6901 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-AZ-6606 TCGA-CA-6716 
       34.98        22.42        58.39        49.41        11.74        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-4746 TCGA-CM-6162 TCGA-CM-6170 TCGA-CM-6680 
       12.76        10.06        37.02        12.00        15.02        12.03 
TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6927 
       17.85        17.13        16.14        15.58         1.48         9.44 
TCGA-DM-A0XF TCGA-DM-A282 TCGA-F4-6570 TCGA-F4-6809 TCGA-G4-6307 TCGA-G4-6317 
       38.20       139.17         6.18        13.25        55.04        36.00 
TCGA-G4-6588 TCGA-AF-2692 TCGA-AG-3732 TCGA-AG-A002 TCGA-F5-6464 
       26.17        13.55        32.98        20.98         9.96 

$`GOLGB1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 
       22.06        32.71        27.09        22.52        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6781 
       24.16        21.76        24.69        24.39        23.87        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3511 TCGA-AA-3514 
       20.28         7.04         3.02         1.02         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
       13.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       36.03         8.05        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 
       33.99        21.01        13.02        24.00        17.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       20.98        19.99        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        85.05        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 
        0.99        31.07        31.07        30.05        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       34.03        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6963 
       15.52        56.55         0.79         0.72         5.79        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       33.01        21.44        17.82         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        88.21         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
       29.56         5.23         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        3.25         3.29         0.07        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4747 
       82.95         1.91       124.27        23.05        20.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       13.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.08        11.01        10.06        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6539 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       15.12         4.80        12.49         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
       14.30         9.04        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A1D0 TCGA-DM-A1D4 
       11.38        10.26       119.70        24.43       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      131.51       135.65         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6321 
       53.62        44.68        85.48        63.62        61.91        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       13.78        35.80        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       39.48        43.04        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        7.99         0.99        37.02         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       20.91        18.28        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  GOLGB1 MUTATED GOLGB1 WILD-TYPE 
            1.48             0.00 
  GOLGB1 MUTATED GOLGB1 WILD-TYPE 
          139.17           148.01 
  GOLGB1 MUTATED GOLGB1 WILD-TYPE 
          18.050           20.415 
[1] "1.5 - 139.2 (18.1)" "0.0 - 148.0 (20.4)"
[1] "hr=" "1.1"
D547V2, continuous
D547V3, binary
                  cls
clus                 0   1
  GOLGB1 MUTATED    38   3
  GOLGB1 WILD-TYPE 328 116
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GOLGB1 MUTATED     38    3
  GOLGB1 WILD-TYPE  328  116
        clus
vv       GOLGB1 MUTATED GOLGB1 WILD-TYPE
  COLON              38              328
  RECTUM              3              116
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GOLGB1 MUTATED         8        0        3        17         2         0
  GOLGB1 WILD-TYPE      83        1       29       121         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GOLGB1 MUTATED           0          0          5          3        1
  GOLGB1 WILD-TYPE        24         11         54         39       47
                  vv
clus               STAGE IVA STAGE IVB
  GOLGB1 MUTATED           1         0
  GOLGB1 WILD-TYPE        17         1
D547V4, multiclass
            clus
vv           GOLGB1 MUTATED GOLGB1 WILD-TYPE
  STAGE I                 8               83
  STAGE IA                0                1
  STAGE II                3               29
  STAGE IIA              17              121
  STAGE IIB               2                8
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              5               54
  STAGE IIIC              3               39
  STAGE IV                1               47
  STAGE IVA               1               17
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  GOLGB1 MUTATED     0   9  28   5
  GOLGB1 WILD-TYPE  17  83 301  45
D547V5, multiclass
    clus
vv   GOLGB1 MUTATED GOLGB1 WILD-TYPE
  T1              0               17
  T2              9               83
  T3             28              301
  T4              5               45
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  GOLGB1 MUTATED    32   4   6
  GOLGB1 WILD-TYPE 255 109  81
D547V6, multiclass
    clus
vv   GOLGB1 MUTATED GOLGB1 WILD-TYPE
  N0             32              255
  N1              4              109
  N2              6               81
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D547V7, binary
                  cls
clus                 0   1
  GOLGB1 MUTATED    35   2
  GOLGB1 WILD-TYPE 340  63
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GOLGB1 MUTATED     35    2
  GOLGB1 WILD-TYPE  340   63
   clus
vv  GOLGB1 MUTATED GOLGB1 WILD-TYPE
  0             35              340
  1              2               63
[1] 2 2
[1] FALSE
D547V8, binary
                  cls
clus                 0   1
  GOLGB1 MUTATED    20  22
  GOLGB1 WILD-TYPE 205 242
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GOLGB1 MUTATED     20   22
  GOLGB1 WILD-TYPE  205  242
        clus
vv       GOLGB1 MUTATED GOLGB1 WILD-TYPE
  FEMALE             20              205
  MALE               22              242
[1] 2 2
[1] FALSE
D547V9, binary
                  cls
clus                 0   1
  GOLGB1 MUTATED    37   0
  GOLGB1 WILD-TYPE 313  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GOLGB1 MUTATED     37    0
  GOLGB1 WILD-TYPE  313   22
     clus
vv    GOLGB1 MUTATED GOLGB1 WILD-TYPE
  NO              37              313
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  GOLGB1 MUTATED                     30                             7
  GOLGB1 WILD-TYPE                  285                            40
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  GOLGB1 MUTATED                       3                              0
  GOLGB1 WILD-TYPE                   103                             10
D547V10, multiclass
                                clus
vv                               GOLGB1 MUTATED GOLGB1 WILD-TYPE
  COLON ADENOCARCINOMA                       30              285
  COLON MUCINOUS ADENOCARCINOMA               7               40
  RECTAL ADENOCARCINOMA                       3              103
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  GOLGB1 MUTATED    31   0   0   3
  GOLGB1 WILD-TYPE 314   4  31  22
D547V11, multiclass
    clus
vv   GOLGB1 MUTATED GOLGB1 WILD-TYPE
  R0             31              314
  R1              0                4
  R2              0               31
  RX              3               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D547V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GOLGB1 MUTATED                                  0     3
  GOLGB1 WILD-TYPE                                1     8
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  GOLGB1 MUTATED                           2    24
  GOLGB1 WILD-TYPE                        20   202
D547V13, multiclass
                                  clus
vv                                 GOLGB1 MUTATED GOLGB1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         3                8
  BLACK OR AFRICAN AMERICAN                     2               20
  WHITE                                        24              202
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(548) Variable = SYT1 MUTATION ANALYSIS
D548V1, survival
                sevent
clus2              0   1
  SYT1 MUTATED    12   1
  SYT1 WILD-TYPE 366  92
  SYT1 MUTATED SYT1 WILD-TYPE 
            13            458 
  SYT1 MUTATED SYT1 WILD-TYPE 
             1             92 
$`SYT1 MUTATED`
TCGA-A6-5660 TCGA-AA-3510 TCGA-AA-3697 TCGA-AA-A010 TCGA-CA-6717 TCGA-CK-6751 
       29.19        63.98        85.05        34.98        12.76       124.27 
TCGA-CM-4743 TCGA-CM-5861 TCGA-CM-6680 TCGA-D5-6529 TCGA-G4-6323 TCGA-G4-6586 
       23.05        15.02        12.03        20.19        13.78        35.80 
TCGA-G4-6626 
       46.75 

$`SYT1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07        12.20        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CM-4744 
       51.32         9.99        21.14        82.95         1.91        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       30.08        32.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6532 
       45.40        12.26        19.59        56.09        55.92        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-AF-2687 
       36.00        22.09        26.17        91.79        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  SYT1 MUTATED SYT1 WILD-TYPE 
         12.03           0.00 
  SYT1 MUTATED SYT1 WILD-TYPE 
        124.27         148.01 
  SYT1 MUTATED SYT1 WILD-TYPE 
        29.190         20.035 
[1] "12.0 - 124.3 (29.2)" "0.0 - 148.0 (20.0)" 
[1] "hr=" "3.8"
D548V2, continuous
D548V3, binary
                cls
clus               0   1
  SYT1 MUTATED    13   0
  SYT1 WILD-TYPE 353 119
[1] "tbl2"
                cls
clus             [,1] [,2]
  SYT1 MUTATED     13    0
  SYT1 WILD-TYPE  353  119
        clus
vv       SYT1 MUTATED SYT1 WILD-TYPE
  COLON            13            353
  RECTUM            0            119
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SYT1 MUTATED         1        1        1         6         1         0
  SYT1 WILD-TYPE      90        0       31       132         9         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SYT1 MUTATED           1          0          1          1        0         0
  SYT1 WILD-TYPE        23         11         58         41       48        18
                vv
clus             STAGE IVB
  SYT1 MUTATED           0
  SYT1 WILD-TYPE         1
D548V4, multiclass
            clus
vv           SYT1 MUTATED SYT1 WILD-TYPE
  STAGE I               1             90
  STAGE IA              1              0
  STAGE II              1             31
  STAGE IIA             6            132
  STAGE IIB             1              9
  STAGE IIC             0              1
  STAGE III             1             23
  STAGE IIIA            0             11
  STAGE IIIB            1             58
  STAGE IIIC            1             41
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  SYT1 MUTATED     0   1  10   1
  SYT1 WILD-TYPE  17  91 319  49
D548V5, multiclass
    clus
vv   SYT1 MUTATED SYT1 WILD-TYPE
  T1            0             17
  T2            1             91
  T3           10            319
  T4            1             49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  SYT1 MUTATED    11   0   2
  SYT1 WILD-TYPE 276 113  85
D548V6, multiclass
    clus
vv   SYT1 MUTATED SYT1 WILD-TYPE
  N0           11            276
  N1            0            113
  N2            2             85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D548V7, binary
                cls
clus               0   1
  SYT1 MUTATED    11   0
  SYT1 WILD-TYPE 364  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  SYT1 MUTATED     11    0
  SYT1 WILD-TYPE  364   65
   clus
vv  SYT1 MUTATED SYT1 WILD-TYPE
  0           11            364
  1            0             65
[1] 2 2
[1] FALSE
D548V8, binary
                cls
clus               0   1
  SYT1 MUTATED     5   8
  SYT1 WILD-TYPE 220 256
[1] "tbl2"
                cls
clus             [,1] [,2]
  SYT1 MUTATED      5    8
  SYT1 WILD-TYPE  220  256
        clus
vv       SYT1 MUTATED SYT1 WILD-TYPE
  FEMALE            5            220
  MALE              8            256
[1] 2 2
[1] FALSE
D548V9, binary
                cls
clus               0   1
  SYT1 MUTATED    13   0
  SYT1 WILD-TYPE 337  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  SYT1 MUTATED     13    0
  SYT1 WILD-TYPE  337   22
     clus
vv    SYT1 MUTATED SYT1 WILD-TYPE
  NO            13            337
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SYT1 MUTATED                     11                             2
  SYT1 WILD-TYPE                  304                            45
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SYT1 MUTATED                       0                              0
  SYT1 WILD-TYPE                   106                             10
D548V10, multiclass
                                clus
vv                               SYT1 MUTATED SYT1 WILD-TYPE
  COLON ADENOCARCINOMA                     11            304
  COLON MUCINOUS ADENOCARCINOMA             2             45
  RECTAL ADENOCARCINOMA                     0            106
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  SYT1 MUTATED    10   0   0   2
  SYT1 WILD-TYPE 335   4  31  23
D548V11, multiclass
    clus
vv   SYT1 MUTATED SYT1 WILD-TYPE
  R0           10            335
  R1            0              4
  R2            0             31
  RX            2             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D548V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SYT1 MUTATED                                  0     1
  SYT1 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  SYT1 MUTATED                           2     7
  SYT1 WILD-TYPE                        20   219
D548V13, multiclass
                                  clus
vv                                 SYT1 MUTATED SYT1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   2             20
  WHITE                                       7            219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(549) Variable = UVRAG MUTATION ANALYSIS
D549V1, survival
                 sevent
clus2               0   1
  UVRAG MUTATED     9   1
  UVRAG WILD-TYPE 369  92
  UVRAG MUTATED UVRAG WILD-TYPE 
             10             461 
  UVRAG MUTATED UVRAG WILD-TYPE 
              1              92 
$`UVRAG MUTATED`
TCGA-AA-3510 TCGA-AA-3697 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-D5-6929 
       63.98        85.05        12.76        10.06        14.30         4.80 
TCGA-AF-2687 TCGA-AG-A002 TCGA-EI-6508 TCGA-F5-6813 
       24.13        20.98        20.91         0.69 

$`UVRAG WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       12.20        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 
       14.30         9.04         9.44        11.64         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       20.55        19.96        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66        55.76        26.43 

  UVRAG MUTATED UVRAG WILD-TYPE 
           0.69            0.00 
  UVRAG MUTATED UVRAG WILD-TYPE 
          85.05          148.01 
  UVRAG MUTATED UVRAG WILD-TYPE 
         17.605          20.190 
[1] "0.7 - 85.0 (17.6)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "2"  
D549V2, continuous
D549V3, binary
                 cls
clus                0   1
  UVRAG MUTATED     7   4
  UVRAG WILD-TYPE 359 115
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UVRAG MUTATED      7    4
  UVRAG WILD-TYPE  359  115
        clus
vv       UVRAG MUTATED UVRAG WILD-TYPE
  COLON              7             359
  RECTUM             4             115
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  UVRAG MUTATED         1        0        1         4         0         0
  UVRAG WILD-TYPE      90        1       31       134        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  UVRAG MUTATED           1          0          1          2        1         0
  UVRAG WILD-TYPE        23         11         58         40       47        18
                 vv
clus              STAGE IVB
  UVRAG MUTATED           0
  UVRAG WILD-TYPE         1
D549V4, multiclass
            clus
vv           UVRAG MUTATED UVRAG WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              4             134
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             2              40
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  UVRAG MUTATED     0   1   9   1
  UVRAG WILD-TYPE  17  91 320  49
D549V5, multiclass
    clus
vv   UVRAG MUTATED UVRAG WILD-TYPE
  T1             0              17
  T2             1              91
  T3             9             320
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  UVRAG MUTATED     7   2   2
  UVRAG WILD-TYPE 280 111  85
D549V6, multiclass
    clus
vv   UVRAG MUTATED UVRAG WILD-TYPE
  N0             7             280
  N1             2             111
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D549V7, binary
                 cls
clus                0   1
  UVRAG MUTATED    10   1
  UVRAG WILD-TYPE 365  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UVRAG MUTATED     10    1
  UVRAG WILD-TYPE  365   64
   clus
vv  UVRAG MUTATED UVRAG WILD-TYPE
  0            10             365
  1             1              64
[1] 2 2
[1] FALSE
D549V8, binary
                 cls
clus                0   1
  UVRAG MUTATED     3   8
  UVRAG WILD-TYPE 222 256
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UVRAG MUTATED      3    8
  UVRAG WILD-TYPE  222  256
        clus
vv       UVRAG MUTATED UVRAG WILD-TYPE
  FEMALE             3             222
  MALE               8             256
[1] 2 2
[1] FALSE
D549V9, binary
                 cls
clus                0   1
  UVRAG MUTATED     7   1
  UVRAG WILD-TYPE 343  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UVRAG MUTATED      7    1
  UVRAG WILD-TYPE  343   21
     clus
vv    UVRAG MUTATED UVRAG WILD-TYPE
  NO              7             343
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  UVRAG MUTATED                      6                             1
  UVRAG WILD-TYPE                  309                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  UVRAG MUTATED                       4                              0
  UVRAG WILD-TYPE                   102                             10
D549V10, multiclass
                                clus
vv                               UVRAG MUTATED UVRAG WILD-TYPE
  COLON ADENOCARCINOMA                       6             309
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      4             102
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  UVRAG MUTATED     8   0   0   3
  UVRAG WILD-TYPE 337   4  31  22
D549V11, multiclass
    clus
vv   UVRAG MUTATED UVRAG WILD-TYPE
  R0             8             337
  R1             0               4
  R2             0              31
  RX             3              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D549V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  UVRAG MUTATED                                  0     3
  UVRAG WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  UVRAG MUTATED                           0     4
  UVRAG WILD-TYPE                        22   222
D549V13, multiclass
                                  clus
vv                                 UVRAG MUTATED UVRAG WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        3               8
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        4             222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(550) Variable = CLVS1 MUTATION ANALYSIS
D550V1, survival
                 sevent
clus2               0   1
  CLVS1 MUTATED    10   2
  CLVS1 WILD-TYPE 368  91
  CLVS1 MUTATED CLVS1 WILD-TYPE 
             12             459 
  CLVS1 MUTATED CLVS1 WILD-TYPE 
              2              91 
$`CLVS1 MUTATED`
TCGA-A6-5666 TCGA-AA-3510 TCGA-AA-3516 TCGA-AA-3864 TCGA-AA-A01Z TCGA-CA-6717 
       32.71        63.98        13.02        53.00        37.02        12.76 
TCGA-CM-6168 TCGA-CM-6676 TCGA-D5-6532 TCGA-DM-A1D8 TCGA-AG-3885 TCGA-DC-6682 
       12.99        11.08        18.25        12.59        17.95         4.01 

$`CLVS1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        22.06        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
       35.01         6.97         1.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        31.07        30.05        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       26.01        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07        12.20        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       16.04        21.99        14.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       11.01        12.95        13.05        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       20.19         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
        1.02        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 
       13.97        27.95        10.98        19.99         5.95         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  CLVS1 MUTATED CLVS1 WILD-TYPE 
           4.01            0.00 
  CLVS1 MUTATED CLVS1 WILD-TYPE 
          63.98          148.01 
  CLVS1 MUTATED CLVS1 WILD-TYPE 
         15.485          20.550 
[1] "4.0 - 64.0 (15.5)"  "0.0 - 148.0 (20.6)"
[1] "hr=" "1.2"
D550V2, continuous
D550V3, binary
                 cls
clus                0   1
  CLVS1 MUTATED    10   2
  CLVS1 WILD-TYPE 356 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CLVS1 MUTATED     10    2
  CLVS1 WILD-TYPE  356  117
        clus
vv       CLVS1 MUTATED CLVS1 WILD-TYPE
  COLON             10             356
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CLVS1 MUTATED         1        0        3         4         0         1
  CLVS1 WILD-TYPE      90        1       29       134        10         0
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CLVS1 MUTATED           1          0          1          0        0         0
  CLVS1 WILD-TYPE        23         11         58         42       48        18
                 vv
clus              STAGE IVB
  CLVS1 MUTATED           0
  CLVS1 WILD-TYPE         1
D550V4, multiclass
            clus
vv           CLVS1 MUTATED CLVS1 WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               3              29
  STAGE IIA              4             134
  STAGE IIB              0              10
  STAGE IIC              1               0
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CLVS1 MUTATED     0   1  10   1
  CLVS1 WILD-TYPE  17  91 319  49
D550V5, multiclass
    clus
vv   CLVS1 MUTATED CLVS1 WILD-TYPE
  T1             0              17
  T2             1              91
  T3            10             319
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  CLVS1 MUTATED     9   2   1
  CLVS1 WILD-TYPE 278 111  86
D550V6, multiclass
    clus
vv   CLVS1 MUTATED CLVS1 WILD-TYPE
  N0             9             278
  N1             2             111
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D550V7, binary
                 cls
clus                0   1
  CLVS1 MUTATED    11   0
  CLVS1 WILD-TYPE 364  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CLVS1 MUTATED     11    0
  CLVS1 WILD-TYPE  364   65
   clus
vv  CLVS1 MUTATED CLVS1 WILD-TYPE
  0            11             364
  1             0              65
[1] 2 2
[1] FALSE
D550V8, binary
                 cls
clus                0   1
  CLVS1 MUTATED     4   8
  CLVS1 WILD-TYPE 221 256
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CLVS1 MUTATED      4    8
  CLVS1 WILD-TYPE  221  256
        clus
vv       CLVS1 MUTATED CLVS1 WILD-TYPE
  FEMALE             4             221
  MALE               8             256
[1] 2 2
[1] FALSE
D550V9, binary
                 cls
clus                0   1
  CLVS1 MUTATED     9   1
  CLVS1 WILD-TYPE 341  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CLVS1 MUTATED      9    1
  CLVS1 WILD-TYPE  341   21
     clus
vv    CLVS1 MUTATED CLVS1 WILD-TYPE
  NO              9             341
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CLVS1 MUTATED                      8                             2
  CLVS1 WILD-TYPE                  307                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CLVS1 MUTATED                       2                              0
  CLVS1 WILD-TYPE                   104                             10
D550V10, multiclass
                                clus
vv                               CLVS1 MUTATED CLVS1 WILD-TYPE
  COLON ADENOCARCINOMA                       8             307
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  CLVS1 MUTATED     8   0   0   1
  CLVS1 WILD-TYPE 337   4  31  24
D550V11, multiclass
    clus
vv   CLVS1 MUTATED CLVS1 WILD-TYPE
  R0             8             337
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D550V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CLVS1 MUTATED                                  0     1
  CLVS1 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CLVS1 MUTATED                           1     5
  CLVS1 WILD-TYPE                        21   221
D550V13, multiclass
                                  clus
vv                                 CLVS1 MUTATED CLVS1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        5             221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(551) Variable = TTF1 MUTATION ANALYSIS
D551V1, survival
                sevent
clus2              0   1
  TTF1 MUTATED     8   2
  TTF1 WILD-TYPE 370  91
  TTF1 MUTATED TTF1 WILD-TYPE 
            10            461 
  TTF1 MUTATED TTF1 WILD-TYPE 
             2             91 
$`TTF1 MUTATED`
TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-6141 TCGA-AA-3492 TCGA-CA-6717 TCGA-CA-6718 
       30.44        33.53         8.38         3.02        12.76        10.06 
TCGA-CM-5861 TCGA-CM-6680 TCGA-AG-3892 TCGA-AG-A002 
       15.02        12.03        13.02        20.98 

$`TTF1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       32.91        31.63        29.19        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       32.71        27.09        22.52        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
       20.28         7.04         1.02        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 
        3.06         3.25         3.29         0.07        12.20        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       22.98        30.08        32.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       10.06        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  TTF1 MUTATED TTF1 WILD-TYPE 
          3.02           0.00 
  TTF1 MUTATED TTF1 WILD-TYPE 
         33.53         148.01 
  TTF1 MUTATED TTF1 WILD-TYPE 
         12.89          20.55 
[1] "3.0 - 33.5 (12.9)"  "0.0 - 148.0 (20.6)"
[1] "hr=" "1.7"
D551V2, continuous
D551V3, binary
                cls
clus               0   1
  TTF1 MUTATED     9   2
  TTF1 WILD-TYPE 357 117
[1] "tbl2"
                cls
clus             [,1] [,2]
  TTF1 MUTATED      9    2
  TTF1 WILD-TYPE  357  117
        clus
vv       TTF1 MUTATED TTF1 WILD-TYPE
  COLON             9            357
  RECTUM            2            117
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TTF1 MUTATED         3        0        1         5         1         0
  TTF1 WILD-TYPE      88        1       31       133         9         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TTF1 MUTATED           0          0          1          0        0         0
  TTF1 WILD-TYPE        24         11         58         42       48        18
                vv
clus             STAGE IVB
  TTF1 MUTATED           0
  TTF1 WILD-TYPE         1
D551V4, multiclass
            clus
vv           TTF1 MUTATED TTF1 WILD-TYPE
  STAGE I               3             88
  STAGE IA              0              1
  STAGE II              1             31
  STAGE IIA             5            133
  STAGE IIB             1              9
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            1             58
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  TTF1 MUTATED     1   2   7   1
  TTF1 WILD-TYPE  16  90 322  49
D551V5, multiclass
    clus
vv   TTF1 MUTATED TTF1 WILD-TYPE
  T1            1             16
  T2            2             90
  T3            7            322
  T4            1             49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  TTF1 MUTATED    10   0   1
  TTF1 WILD-TYPE 277 113  86
D551V6, multiclass
    clus
vv   TTF1 MUTATED TTF1 WILD-TYPE
  N0           10            277
  N1            0            113
  N2            1             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D551V7, binary
                cls
clus               0   1
  TTF1 MUTATED    10   0
  TTF1 WILD-TYPE 365  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  TTF1 MUTATED     10    0
  TTF1 WILD-TYPE  365   65
   clus
vv  TTF1 MUTATED TTF1 WILD-TYPE
  0           10            365
  1            0             65
[1] 2 2
[1] FALSE
D551V8, binary
                cls
clus               0   1
  TTF1 MUTATED     6   5
  TTF1 WILD-TYPE 219 259
[1] "tbl2"
                cls
clus             [,1] [,2]
  TTF1 MUTATED      6    5
  TTF1 WILD-TYPE  219  259
        clus
vv       TTF1 MUTATED TTF1 WILD-TYPE
  FEMALE            6            219
  MALE              5            259
[1] 2 2
[1] FALSE
D551V9, binary
                cls
clus               0   1
  TTF1 MUTATED    10   0
  TTF1 WILD-TYPE 340  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  TTF1 MUTATED     10    0
  TTF1 WILD-TYPE  340   22
     clus
vv    TTF1 MUTATED TTF1 WILD-TYPE
  NO            10            340
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  TTF1 MUTATED                      8                             1
  TTF1 WILD-TYPE                  307                            46
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  TTF1 MUTATED                       2                              0
  TTF1 WILD-TYPE                   104                             10
D551V10, multiclass
                                clus
vv                               TTF1 MUTATED TTF1 WILD-TYPE
  COLON ADENOCARCINOMA                      8            307
  COLON MUCINOUS ADENOCARCINOMA             1             46
  RECTAL ADENOCARCINOMA                     2            104
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  TTF1 MUTATED     7   0   0   3
  TTF1 WILD-TYPE 338   4  31  22
D551V11, multiclass
    clus
vv   TTF1 MUTATED TTF1 WILD-TYPE
  R0            7            338
  R1            0              4
  R2            0             31
  RX            3             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D551V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TTF1 MUTATED                                  0     2
  TTF1 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  TTF1 MUTATED                           2     4
  TTF1 WILD-TYPE                        20   222
D551V13, multiclass
                                  clus
vv                                 TTF1 MUTATED TTF1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              9
  BLACK OR AFRICAN AMERICAN                   2             20
  WHITE                                       4            222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(552) Variable = FGFR1 MUTATION ANALYSIS
D552V1, survival
                 sevent
clus2               0   1
  FGFR1 MUTATED    15   2
  FGFR1 WILD-TYPE 363  91
  FGFR1 MUTATED FGFR1 WILD-TYPE 
             17             454 
  FGFR1 MUTATED FGFR1 WILD-TYPE 
              2              91 
$`FGFR1 MUTATED`
TCGA-AA-3510 TCGA-AA-3715 TCGA-AZ-4681 TCGA-CA-6717 TCGA-CK-4950 TCGA-CM-4744 
       63.98        19.04       106.75        12.76        85.45        20.02 
TCGA-CM-6171 TCGA-CM-6680 TCGA-D5-6931 TCGA-DM-A1HB TCGA-DM-A28K TCGA-F4-6806 
       14.04        12.03        12.00       135.65        98.24        41.42 
TCGA-G4-6303 TCGA-G4-6309 TCGA-G4-6315 TCGA-AG-A002 TCGA-DY-A0XA 
       65.85        85.48        61.91        20.98       126.44 

$`FGFR1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 
       36.00         5.03        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5912 
       10.06        14.30        17.56       148.01        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       23.05        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       10.06        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       11.64         4.80         1.51        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 
       12.59       140.38         7.50        44.32       131.51       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       34.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
       35.31       133.18        74.56        53.62        44.68        55.04 
TCGA-G4-6310 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       63.62        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        4.01         5.03         5.29        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  FGFR1 MUTATED FGFR1 WILD-TYPE 
             12               0 
  FGFR1 MUTATED FGFR1 WILD-TYPE 
         135.65          148.01 
  FGFR1 MUTATED FGFR1 WILD-TYPE 
         61.910          20.035 
[1] "12.0 - 135.7 (61.9)" "0.0 - 148.0 (20.0)" 
[1] "hr=" "3.8"
D552V2, continuous
D552V3, binary
                 cls
clus                0   1
  FGFR1 MUTATED    17   2
  FGFR1 WILD-TYPE 349 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FGFR1 MUTATED     17    2
  FGFR1 WILD-TYPE  349  117
        clus
vv       FGFR1 MUTATED FGFR1 WILD-TYPE
  COLON             17             349
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FGFR1 MUTATED         4        0        2         5         0         0
  FGFR1 WILD-TYPE      87        1       30       133        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  FGFR1 MUTATED           1          0          4          1        2         0
  FGFR1 WILD-TYPE        23         11         55         41       46        18
                 vv
clus              STAGE IVB
  FGFR1 MUTATED           0
  FGFR1 WILD-TYPE         1
D552V4, multiclass
            clus
vv           FGFR1 MUTATED FGFR1 WILD-TYPE
  STAGE I                4              87
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA              5             133
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             4              55
  STAGE IIIC             1              41
  STAGE IV               2              46
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  FGFR1 MUTATED     0   4  14   1
  FGFR1 WILD-TYPE  17  88 315  49
D552V5, multiclass
    clus
vv   FGFR1 MUTATED FGFR1 WILD-TYPE
  T1             0              17
  T2             4              88
  T3            14             315
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  FGFR1 MUTATED    11   5   3
  FGFR1 WILD-TYPE 276 108  84
D552V6, multiclass
    clus
vv   FGFR1 MUTATED FGFR1 WILD-TYPE
  N0            11             276
  N1             5             108
  N2             3              84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D552V7, binary
                 cls
clus                0   1
  FGFR1 MUTATED    17   2
  FGFR1 WILD-TYPE 358  63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FGFR1 MUTATED     17    2
  FGFR1 WILD-TYPE  358   63
   clus
vv  FGFR1 MUTATED FGFR1 WILD-TYPE
  0            17             358
  1             2              63
[1] 2 2
[1] FALSE
D552V8, binary
                 cls
clus                0   1
  FGFR1 MUTATED     9  10
  FGFR1 WILD-TYPE 216 254
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FGFR1 MUTATED      9   10
  FGFR1 WILD-TYPE  216  254
        clus
vv       FGFR1 MUTATED FGFR1 WILD-TYPE
  FEMALE             9             216
  MALE              10             254
[1] 2 2
[1] FALSE
D552V9, binary
                 cls
clus                0   1
  FGFR1 MUTATED    14   0
  FGFR1 WILD-TYPE 336  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FGFR1 MUTATED     14    0
  FGFR1 WILD-TYPE  336   22
     clus
vv    FGFR1 MUTATED FGFR1 WILD-TYPE
  NO             14             336
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  FGFR1 MUTATED                     14                             2
  FGFR1 WILD-TYPE                  301                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  FGFR1 MUTATED                       2                              0
  FGFR1 WILD-TYPE                   104                             10
D552V10, multiclass
                                clus
vv                               FGFR1 MUTATED FGFR1 WILD-TYPE
  COLON ADENOCARCINOMA                      14             301
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  FGFR1 MUTATED    14   1   0   1
  FGFR1 WILD-TYPE 331   3  31  24
D552V11, multiclass
    clus
vv   FGFR1 MUTATED FGFR1 WILD-TYPE
  R0            14             331
  R1             1               3
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D552V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FGFR1 MUTATED                                  0     1
  FGFR1 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  FGFR1 MUTATED                           2    11
  FGFR1 WILD-TYPE                        20   215
D552V13, multiclass
                                  clus
vv                                 FGFR1 MUTATED FGFR1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    2              20
  WHITE                                       11             215
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(553) Variable = OSMR MUTATION ANALYSIS
D553V1, survival
                sevent
clus2              0   1
  OSMR MUTATED    14   8
  OSMR WILD-TYPE 364  85
  OSMR MUTATED OSMR WILD-TYPE 
            22            449 
  OSMR MUTATED OSMR WILD-TYPE 
             8             85 
$`OSMR MUTATED`
TCGA-A6-5665 TCGA-A6-6781 TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3818 TCGA-AA-3864 
       22.06        19.66         3.02        63.98         0.99        53.00 
TCGA-AA-3972 TCGA-AA-A00N TCGA-AY-6197 TCGA-AZ-6599 TCGA-AZ-6607 TCGA-CA-6717 
       50.99         4.01        21.44         6.77         3.19        12.76 
TCGA-CA-6718 TCGA-CM-4744 TCGA-CM-6171 TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6540 
       10.06        20.02        14.04        17.85        17.13        16.14 
TCGA-DM-A28H TCGA-G4-6303 TCGA-AG-3583 TCGA-AG-A01L 
      117.07        65.85        20.05        12.00 

$`OSMR WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 
       20.12        20.28         7.04         1.02        35.01         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       30.05        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       16.08        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       33.01        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        88.21        49.41        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 
        3.25         3.29         0.07        12.20        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4746 
       21.14        82.95         1.91       124.27        23.05        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 
       14.99        12.99        13.02        15.02        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6539 
       18.25         1.32        43.27        15.12         4.80        12.49 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
      119.93        35.97        60.79        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
      133.18        74.56        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3584 TCGA-AG-3586 
       32.02         8.02         7.07        36.03        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
       36.03         9.07        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  OSMR MUTATED OSMR WILD-TYPE 
          0.99           0.00 
  OSMR MUTATED OSMR WILD-TYPE 
        117.07         148.01 
  OSMR MUTATED OSMR WILD-TYPE 
         17.49          20.98 
[1] "1.0 - 117.1 (17.5)" "0.0 - 148.0 (21.0)"
[1] "hr=" "1.8"
D553V2, continuous
D553V3, binary
                cls
clus               0   1
  OSMR MUTATED    20   2
  OSMR WILD-TYPE 346 117
[1] "tbl2"
                cls
clus             [,1] [,2]
  OSMR MUTATED     20    2
  OSMR WILD-TYPE  346  117
        clus
vv       OSMR MUTATED OSMR WILD-TYPE
  COLON            20            346
  RECTUM            2            117
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  OSMR MUTATED         4        0        3         6         1         0
  OSMR WILD-TYPE      87        1       29       132         9         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  OSMR MUTATED           0          0          2          2        4         0
  OSMR WILD-TYPE        24         11         57         40       44        18
                vv
clus             STAGE IVB
  OSMR MUTATED           0
  OSMR WILD-TYPE         1
D553V4, multiclass
            clus
vv           OSMR MUTATED OSMR WILD-TYPE
  STAGE I               4             87
  STAGE IA              0              1
  STAGE II              3             29
  STAGE IIA             6            132
  STAGE IIB             1              9
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            2             57
  STAGE IIIC            2             40
  STAGE IV              4             44
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  OSMR MUTATED     0   4  15   3
  OSMR WILD-TYPE  17  88 314  47
D553V5, multiclass
    clus
vv   OSMR MUTATED OSMR WILD-TYPE
  T1            0             17
  T2            4             88
  T3           15            314
  T4            3             47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  OSMR MUTATED    14   4   4
  OSMR WILD-TYPE 273 109  83
D553V6, multiclass
    clus
vv   OSMR MUTATED OSMR WILD-TYPE
  N0           14            273
  N1            4            109
  N2            4             83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D553V7, binary
                cls
clus               0   1
  OSMR MUTATED    15   4
  OSMR WILD-TYPE 360  61
[1] "tbl2"
                cls
clus             [,1] [,2]
  OSMR MUTATED     15    4
  OSMR WILD-TYPE  360   61
   clus
vv  OSMR MUTATED OSMR WILD-TYPE
  0           15            360
  1            4             61
[1] 2 2
[1] FALSE
D553V8, binary
                cls
clus               0   1
  OSMR MUTATED     6  16
  OSMR WILD-TYPE 219 248
[1] "tbl2"
                cls
clus             [,1] [,2]
  OSMR MUTATED      6   16
  OSMR WILD-TYPE  219  248
        clus
vv       OSMR MUTATED OSMR WILD-TYPE
  FEMALE            6            219
  MALE             16            248
[1] 2 2
[1] FALSE
D553V9, binary
                cls
clus               0   1
  OSMR MUTATED    18   0
  OSMR WILD-TYPE 332  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  OSMR MUTATED     18    0
  OSMR WILD-TYPE  332   22
     clus
vv    OSMR MUTATED OSMR WILD-TYPE
  NO            18            332
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  OSMR MUTATED                     16                             4
  OSMR WILD-TYPE                  299                            43
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  OSMR MUTATED                       1                              1
  OSMR WILD-TYPE                   105                              9
D553V10, multiclass
                                clus
vv                               OSMR MUTATED OSMR WILD-TYPE
  COLON ADENOCARCINOMA                     16            299
  COLON MUCINOUS ADENOCARCINOMA             4             43
  RECTAL ADENOCARCINOMA                     1            105
  RECTAL MUCINOUS ADENOCARCINOMA            1              9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  OSMR MUTATED    15   0   2   2
  OSMR WILD-TYPE 330   4  29  23
D553V11, multiclass
    clus
vv   OSMR MUTATED OSMR WILD-TYPE
  R0           15            330
  R1            0              4
  R2            2             29
  RX            2             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D553V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OSMR MUTATED                                  0     2
  OSMR WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  OSMR MUTATED                           0    12
  OSMR WILD-TYPE                        22   214
D553V13, multiclass
                                  clus
vv                                 OSMR MUTATED OSMR WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              9
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                      12            214
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(554) Variable = LASS3 MUTATION ANALYSIS
D554V1, survival
                 sevent
clus2               0   1
  LASS3 MUTATED    15   2
  LASS3 WILD-TYPE 363  91
  LASS3 MUTATED LASS3 WILD-TYPE 
             17             454 
  LASS3 MUTATED LASS3 WILD-TYPE 
              2              91 
$`LASS3 MUTATED`
TCGA-AA-3510 TCGA-AA-3664 TCGA-AA-3672 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3977 
       63.98        54.02         0.92        26.99        19.04        25.02 
TCGA-AA-A010 TCGA-AA-A01I TCGA-AY-6386 TCGA-CM-5348 TCGA-D5-6533 TCGA-D5-6535 
       34.98        31.00        17.82        22.98         1.32        15.12 
TCGA-D5-6538 TCGA-F4-6459 TCGA-AG-3892 TCGA-AG-A002 TCGA-AG-A026 
       17.13         8.61        13.02        20.98         1.94 

$`LASS3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        6.97         2.01        14.01        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       85.05        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       12.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       33.01        21.44        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       13.02        29.06        22.03        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       43.27        17.85         4.80        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6460 TCGA-F4-6569 
       35.97        60.79       117.07        98.24        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  LASS3 MUTATED LASS3 WILD-TYPE 
           0.92            0.00 
  LASS3 MUTATED LASS3 WILD-TYPE 
          63.98          148.01 
  LASS3 MUTATED LASS3 WILD-TYPE 
         19.040          20.235 
[1] "0.9 - 64.0 (19.0)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.5"
D554V2, continuous
D554V3, binary
                 cls
clus                0   1
  LASS3 MUTATED    14   3
  LASS3 WILD-TYPE 352 116
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LASS3 MUTATED     14    3
  LASS3 WILD-TYPE  352  116
        clus
vv       LASS3 MUTATED LASS3 WILD-TYPE
  COLON             14             352
  RECTUM             3             116
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  LASS3 MUTATED         3        0        3         1         1         0
  LASS3 WILD-TYPE      88        1       29       137         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  LASS3 MUTATED           1          0          6          0        1         0
  LASS3 WILD-TYPE        23         11         53         42       47        18
                 vv
clus              STAGE IVB
  LASS3 MUTATED           0
  LASS3 WILD-TYPE         1
D554V4, multiclass
            clus
vv           LASS3 MUTATED LASS3 WILD-TYPE
  STAGE I                3              88
  STAGE IA               0               1
  STAGE II               3              29
  STAGE IIA              1             137
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             6              53
  STAGE IIIC             0              42
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  LASS3 MUTATED     1   3  10   3
  LASS3 WILD-TYPE  16  89 319  47
D554V5, multiclass
    clus
vv   LASS3 MUTATED LASS3 WILD-TYPE
  T1             1              16
  T2             3              89
  T3            10             319
  T4             3              47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  LASS3 MUTATED    11   4   2
  LASS3 WILD-TYPE 276 109  85
D554V6, multiclass
    clus
vv   LASS3 MUTATED LASS3 WILD-TYPE
  N0            11             276
  N1             4             109
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D554V7, binary
                 cls
clus                0   1
  LASS3 MUTATED    14   1
  LASS3 WILD-TYPE 361  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LASS3 MUTATED     14    1
  LASS3 WILD-TYPE  361   64
   clus
vv  LASS3 MUTATED LASS3 WILD-TYPE
  0            14             361
  1             1              64
[1] 2 2
[1] FALSE
D554V8, binary
                 cls
clus                0   1
  LASS3 MUTATED    10   7
  LASS3 WILD-TYPE 215 257
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LASS3 MUTATED     10    7
  LASS3 WILD-TYPE  215  257
        clus
vv       LASS3 MUTATED LASS3 WILD-TYPE
  FEMALE            10             215
  MALE               7             257
[1] 2 2
[1] FALSE
D554V9, binary
                 cls
clus                0   1
  LASS3 MUTATED    14   1
  LASS3 WILD-TYPE 336  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LASS3 MUTATED     14    1
  LASS3 WILD-TYPE  336   21
     clus
vv    LASS3 MUTATED LASS3 WILD-TYPE
  NO             14             336
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  LASS3 MUTATED                     14                             0
  LASS3 WILD-TYPE                  301                            47
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  LASS3 MUTATED                       3                              0
  LASS3 WILD-TYPE                   103                             10
D554V10, multiclass
                                clus
vv                               LASS3 MUTATED LASS3 WILD-TYPE
  COLON ADENOCARCINOMA                      14             301
  COLON MUCINOUS ADENOCARCINOMA              0              47
  RECTAL ADENOCARCINOMA                      3             103
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  LASS3 MUTATED    13   1   1   1
  LASS3 WILD-TYPE 332   3  30  24
D554V11, multiclass
    clus
vv   LASS3 MUTATED LASS3 WILD-TYPE
  R0            13             332
  R1             1               3
  R2             1              30
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D554V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  LASS3 MUTATED                                  0     0
  LASS3 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  LASS3 MUTATED                           1     5
  LASS3 WILD-TYPE                        21   221
D554V13, multiclass
                                  clus
vv                                 LASS3 MUTATED LASS3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        5             221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(555) Variable = HGS MUTATION ANALYSIS
D555V1, survival
               sevent
clus2             0   1
  HGS MUTATED     7   3
  HGS WILD-TYPE 371  90
  HGS MUTATED HGS WILD-TYPE 
           10           461 
  HGS MUTATED HGS WILD-TYPE 
            3            90 
$`HGS MUTATED`
TCGA-AA-3496 TCGA-AY-6197 TCGA-AZ-6598 TCGA-AZ-6601 TCGA-CK-5913 TCGA-CK-6751 
        1.02        21.44        49.41       100.01        51.32       124.27 
TCGA-CM-5861 TCGA-D5-5540 TCGA-D5-6540 TCGA-F4-6570 
       15.02        56.09        16.14         6.18 

$`HGS WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        33.01        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 
      106.75        22.36        62.79        88.21         6.77        12.10 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CM-4743 
       49.08         9.99        21.14        82.95         1.91        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       22.98        30.08        32.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5541 
       10.06        12.03        45.40        12.26        19.59        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
        4.80        17.13        12.49        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 
      117.07        98.24         8.61        31.96        35.74        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  HGS MUTATED HGS WILD-TYPE 
         1.02          0.00 
  HGS MUTATED HGS WILD-TYPE 
       124.27        148.01 
  HGS MUTATED HGS WILD-TYPE 
       35.425        20.120 
[1] "1.0 - 124.3 (35.4)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.1"
D555V2, continuous
D555V3, binary
               cls
clus              0   1
  HGS MUTATED    10   0
  HGS WILD-TYPE 356 119
[1] "tbl2"
               cls
clus            [,1] [,2]
  HGS MUTATED     10    0
  HGS WILD-TYPE  356  119
        clus
vv       HGS MUTATED HGS WILD-TYPE
  COLON           10           356
  RECTUM           0           119
[1] 2 2
[1] FALSE
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  HGS MUTATED         2        0        3         5         0         0
  HGS WILD-TYPE      89        1       29       133        10         1
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  HGS MUTATED           0          0          0          0        0         0
  HGS WILD-TYPE        24         11         59         42       48        18
               vv
clus            STAGE IVB
  HGS MUTATED           0
  HGS WILD-TYPE         1
D555V4, multiclass
            clus
vv           HGS MUTATED HGS WILD-TYPE
  STAGE I              2            89
  STAGE IA             0             1
  STAGE II             3            29
  STAGE IIA            5           133
  STAGE IIB            0            10
  STAGE IIC            0             1
  STAGE III            0            24
  STAGE IIIA           0            11
  STAGE IIIB           0            59
  STAGE IIIC           0            42
  STAGE IV             0            48
  STAGE IVA            0            18
  STAGE IVB            0             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  HGS MUTATED     0   2   8   0
  HGS WILD-TYPE  17  90 321  50
D555V5, multiclass
    clus
vv   HGS MUTATED HGS WILD-TYPE
  T1           0            17
  T2           2            90
  T3           8           321
  T4           0            50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2
  HGS MUTATED    10   0   0
  HGS WILD-TYPE 277 113  87
D555V6, multiclass
    clus
vv   HGS MUTATED HGS WILD-TYPE
  N0          10           277
  N1           0           113
  N2           0            87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D555V7, binary
               cls
clus              0   1
  HGS MUTATED     6   0
  HGS WILD-TYPE 369  65
[1] "tbl2"
               cls
clus            [,1] [,2]
  HGS MUTATED      6    0
  HGS WILD-TYPE  369   65
   clus
vv  HGS MUTATED HGS WILD-TYPE
  0           6           369
  1           0            65
[1] 2 2
[1] FALSE
D555V8, binary
               cls
clus              0   1
  HGS MUTATED     6   4
  HGS WILD-TYPE 219 260
[1] "tbl2"
               cls
clus            [,1] [,2]
  HGS MUTATED      6    4
  HGS WILD-TYPE  219  260
        clus
vv       HGS MUTATED HGS WILD-TYPE
  FEMALE           6           219
  MALE             4           260
[1] 2 2
[1] FALSE
D555V9, binary
               cls
clus              0   1
  HGS MUTATED     9   0
  HGS WILD-TYPE 341  22
[1] "tbl2"
               cls
clus            [,1] [,2]
  HGS MUTATED      9    0
  HGS WILD-TYPE  341   22
     clus
vv    HGS MUTATED HGS WILD-TYPE
  NO            9           341
  YES           0            22
[1] 2 2
[1] FALSE
               vv
clus            COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  HGS MUTATED                      8                             2
  HGS WILD-TYPE                  307                            45
               vv
clus            RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  HGS MUTATED                       0                              0
  HGS WILD-TYPE                   106                             10
D555V10, multiclass
                                clus
vv                               HGS MUTATED HGS WILD-TYPE
  COLON ADENOCARCINOMA                     8           307
  COLON MUCINOUS ADENOCARCINOMA            2            45
  RECTAL ADENOCARCINOMA                    0           106
  RECTAL MUCINOUS ADENOCARCINOMA           0            10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             R0  R1  R2  RX
  HGS MUTATED     6   0   0   2
  HGS WILD-TYPE 339   4  31  23
D555V11, multiclass
    clus
vv   HGS MUTATED HGS WILD-TYPE
  R0           6           339
  R1           0             4
  R2           0            31
  RX           2            23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D555V12, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HGS MUTATED                                  0     0
  HGS WILD-TYPE                                1    11
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  HGS MUTATED                           0     9
  HGS WILD-TYPE                        22   217
D555V13, multiclass
                                  clus
vv                                 HGS MUTATED HGS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      0            11
  BLACK OR AFRICAN AMERICAN                  0            22
  WHITE                                      9           217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(556) Variable = PLEKHA6 MUTATION ANALYSIS
D556V1, survival
                   sevent
clus2                 0   1
  PLEKHA6 MUTATED    17   2
  PLEKHA6 WILD-TYPE 361  91
  PLEKHA6 MUTATED PLEKHA6 WILD-TYPE 
               19               452 
  PLEKHA6 MUTATED PLEKHA6 WILD-TYPE 
                2                91 
$`PLEKHA6 MUTATED`
TCGA-A6-6653 TCGA-A6-6781 TCGA-AA-3663 TCGA-AA-3672 TCGA-AA-3713 TCGA-AA-3715 
       24.39        19.66         6.97         0.92        19.04        19.04 
TCGA-AA-3815 TCGA-AA-3821 TCGA-AA-3966 TCGA-AA-A00A TCGA-AD-6889 TCGA-AU-6004 
       33.04         1.02         2.01        38.04        56.55        27.09 
TCGA-AY-6197 TCGA-AZ-6598 TCGA-CM-5861 TCGA-D5-6540 TCGA-D5-6928 TCGA-F4-6856 
       21.44        49.41        15.02        16.14        11.64        35.31 
TCGA-AG-A02N 
       61.97 

$`PLEKHA6 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
       25.08        25.18        24.16        21.76        24.69        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
        2.01        14.01        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 
       26.99        10.06        35.05         0.99        25.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       20.98        34.03        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00E 
       19.07         7.96        27.02        13.94        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 
       40.96         0.07        21.37        15.52         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       16.31         0.95        33.01        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 
        5.13       106.75        22.36        62.79        88.21         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       32.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       17.13        12.49        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6930 
       12.43        14.30         9.04         9.44         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       47.41       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  PLEKHA6 MUTATED PLEKHA6 WILD-TYPE 
             0.92              0.00 
  PLEKHA6 MUTATED PLEKHA6 WILD-TYPE 
            61.97            148.01 
  PLEKHA6 MUTATED PLEKHA6 WILD-TYPE 
           19.660            20.235 
[1] "0.9 - 62.0 (19.7)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.8"
D556V2, continuous
D556V3, binary
                   cls
clus                  0   1
  PLEKHA6 MUTATED    19   1
  PLEKHA6 WILD-TYPE 347 118
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLEKHA6 MUTATED     19    1
  PLEKHA6 WILD-TYPE  347  118
        clus
vv       PLEKHA6 MUTATED PLEKHA6 WILD-TYPE
  COLON               19               347
  RECTUM               1               118
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PLEKHA6 MUTATED         5        0        4         8         0         0
  PLEKHA6 WILD-TYPE      86        1       28       130        10         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PLEKHA6 MUTATED           1          0          0          1        1
  PLEKHA6 WILD-TYPE        23         11         59         41       47
                   vv
clus                STAGE IVA STAGE IVB
  PLEKHA6 MUTATED           0         0
  PLEKHA6 WILD-TYPE        18         1
D556V4, multiclass
            clus
vv           PLEKHA6 MUTATED PLEKHA6 WILD-TYPE
  STAGE I                  5                86
  STAGE IA                 0                 1
  STAGE II                 4                28
  STAGE IIA                8               130
  STAGE IIB                0                10
  STAGE IIC                0                 1
  STAGE III                1                23
  STAGE IIIA               0                11
  STAGE IIIB               0                59
  STAGE IIIC               1                41
  STAGE IV                 1                47
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  PLEKHA6 MUTATED     0   5  14   1
  PLEKHA6 WILD-TYPE  17  87 315  49
D556V5, multiclass
    clus
vv   PLEKHA6 MUTATED PLEKHA6 WILD-TYPE
  T1               0                17
  T2               5                87
  T3              14               315
  T4               1                49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  PLEKHA6 MUTATED    18   2   0
  PLEKHA6 WILD-TYPE 269 111  87
D556V6, multiclass
    clus
vv   PLEKHA6 MUTATED PLEKHA6 WILD-TYPE
  N0              18               269
  N1               2               111
  N2               0                87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D556V7, binary
                   cls
clus                  0   1
  PLEKHA6 MUTATED    16   1
  PLEKHA6 WILD-TYPE 359  64
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLEKHA6 MUTATED     16    1
  PLEKHA6 WILD-TYPE  359   64
   clus
vv  PLEKHA6 MUTATED PLEKHA6 WILD-TYPE
  0              16               359
  1               1                64
[1] 2 2
[1] FALSE
D556V8, binary
                   cls
clus                  0   1
  PLEKHA6 MUTATED     8  12
  PLEKHA6 WILD-TYPE 217 252
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLEKHA6 MUTATED      8   12
  PLEKHA6 WILD-TYPE  217  252
        clus
vv       PLEKHA6 MUTATED PLEKHA6 WILD-TYPE
  FEMALE               8               217
  MALE                12               252
[1] 2 2
[1] FALSE
D556V9, binary
                   cls
clus                  0   1
  PLEKHA6 MUTATED    14   1
  PLEKHA6 WILD-TYPE 336  21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLEKHA6 MUTATED     14    1
  PLEKHA6 WILD-TYPE  336   21
     clus
vv    PLEKHA6 MUTATED PLEKHA6 WILD-TYPE
  NO               14               336
  YES               1                21
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PLEKHA6 MUTATED                     13                             6
  PLEKHA6 WILD-TYPE                  302                            41
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PLEKHA6 MUTATED                       1                              0
  PLEKHA6 WILD-TYPE                   105                             10
D556V10, multiclass
                                clus
vv                               PLEKHA6 MUTATED PLEKHA6 WILD-TYPE
  COLON ADENOCARCINOMA                        13               302
  COLON MUCINOUS ADENOCARCINOMA                6                41
  RECTAL ADENOCARCINOMA                        1               105
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  PLEKHA6 MUTATED    15   0   1   0
  PLEKHA6 WILD-TYPE 330   4  30  25
D556V11, multiclass
    clus
vv   PLEKHA6 MUTATED PLEKHA6 WILD-TYPE
  R0              15               330
  R1               0                 4
  R2               1                30
  RX               0                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D556V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PLEKHA6 MUTATED                                  0     1
  PLEKHA6 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  PLEKHA6 MUTATED                           0     9
  PLEKHA6 WILD-TYPE                        22   217
D556V13, multiclass
                                  clus
vv                                 PLEKHA6 MUTATED PLEKHA6 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                10
  BLACK OR AFRICAN AMERICAN                      0                22
  WHITE                                          9               217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(557) Variable = MAP7D1 MUTATION ANALYSIS
D557V1, survival
                  sevent
clus2                0   1
  MAP7D1 MUTATED    12   2
  MAP7D1 WILD-TYPE 366  91
  MAP7D1 MUTATED MAP7D1 WILD-TYPE 
              14              457 
  MAP7D1 MUTATED MAP7D1 WILD-TYPE 
               2               91 
$`MAP7D1 MUTATED`
TCGA-A6-6781 TCGA-AA-A00N TCGA-AD-5900 TCGA-AU-6004 TCGA-CA-6719 TCGA-CK-5913 
       19.66         4.01         0.07        27.09        14.30        51.32 
TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-6162 TCGA-D5-6930 TCGA-DM-A1D8 TCGA-G4-6309 
       30.08        15.02        12.00         1.51        12.59        85.48 
TCGA-G4-6586 TCGA-G4-6628 
       35.80        79.69 

$`MAP7D1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       39.98        18.05        40.96        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
        0.20        14.50        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       10.06        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       22.98        32.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       15.02         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        4.80        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D9 
       38.20       130.65        92.75        49.91        13.32       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       44.68        55.04        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 
       13.78        26.17        91.79        46.75        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  MAP7D1 MUTATED MAP7D1 WILD-TYPE 
            0.07             0.00 
  MAP7D1 MUTATED MAP7D1 WILD-TYPE 
           85.48           148.01 
  MAP7D1 MUTATED MAP7D1 WILD-TYPE 
           17.34            20.28 
[1] "0.1 - 85.5 (17.3)"  "0.0 - 148.0 (20.3)"
[1] "hr=" "1.5"
D557V2, continuous
D557V3, binary
                  cls
clus                 0   1
  MAP7D1 MUTATED    15   0
  MAP7D1 WILD-TYPE 351 119
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP7D1 MUTATED     15    0
  MAP7D1 WILD-TYPE  351  119
        clus
vv       MAP7D1 MUTATED MAP7D1 WILD-TYPE
  COLON              15              351
  RECTUM              0              119
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MAP7D1 MUTATED         3        0        0         6         2         0
  MAP7D1 WILD-TYPE      88        1       32       132         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MAP7D1 MUTATED           0          0          2          1        0
  MAP7D1 WILD-TYPE        24         11         57         41       48
                  vv
clus               STAGE IVA STAGE IVB
  MAP7D1 MUTATED           0         0
  MAP7D1 WILD-TYPE        18         1
D557V4, multiclass
            clus
vv           MAP7D1 MUTATED MAP7D1 WILD-TYPE
  STAGE I                 3               88
  STAGE IA                0                1
  STAGE II                0               32
  STAGE IIA               6              132
  STAGE IIB               2                8
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              2               57
  STAGE IIIC              1               41
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  MAP7D1 MUTATED     0   3   9   3
  MAP7D1 WILD-TYPE  17  89 320  47
D557V5, multiclass
    clus
vv   MAP7D1 MUTATED MAP7D1 WILD-TYPE
  T1              0               17
  T2              3               89
  T3              9              320
  T4              3               47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  MAP7D1 MUTATED    11   4   0
  MAP7D1 WILD-TYPE 276 109  87
D557V6, multiclass
    clus
vv   MAP7D1 MUTATED MAP7D1 WILD-TYPE
  N0             11              276
  N1              4              109
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D557V7, binary
                  cls
clus                 0   1
  MAP7D1 MUTATED    10   0
  MAP7D1 WILD-TYPE 365  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP7D1 MUTATED     10    0
  MAP7D1 WILD-TYPE  365   65
   clus
vv  MAP7D1 MUTATED MAP7D1 WILD-TYPE
  0             10              365
  1              0               65
[1] 2 2
[1] FALSE
D557V8, binary
                  cls
clus                 0   1
  MAP7D1 MUTATED     9   6
  MAP7D1 WILD-TYPE 216 258
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP7D1 MUTATED      9    6
  MAP7D1 WILD-TYPE  216  258
        clus
vv       MAP7D1 MUTATED MAP7D1 WILD-TYPE
  FEMALE              9              216
  MALE                6              258
[1] 2 2
[1] FALSE
D557V9, binary
                  cls
clus                 0   1
  MAP7D1 MUTATED     9   0
  MAP7D1 WILD-TYPE 341  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP7D1 MUTATED      9    0
  MAP7D1 WILD-TYPE  341   22
     clus
vv    MAP7D1 MUTATED MAP7D1 WILD-TYPE
  NO               9              341
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MAP7D1 MUTATED                     10                             5
  MAP7D1 WILD-TYPE                  305                            42
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MAP7D1 MUTATED                       0                              0
  MAP7D1 WILD-TYPE                   106                             10
D557V10, multiclass
                                clus
vv                               MAP7D1 MUTATED MAP7D1 WILD-TYPE
  COLON ADENOCARCINOMA                       10              305
  COLON MUCINOUS ADENOCARCINOMA               5               42
  RECTAL ADENOCARCINOMA                       0              106
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  MAP7D1 MUTATED    11   0   0   3
  MAP7D1 WILD-TYPE 334   4  31  22
D557V11, multiclass
    clus
vv   MAP7D1 MUTATED MAP7D1 WILD-TYPE
  R0             11              334
  R1              0                4
  R2              0               31
  RX              3               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D557V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MAP7D1 MUTATED                                  0     1
  MAP7D1 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  MAP7D1 MUTATED                           1    12
  MAP7D1 WILD-TYPE                        21   214
D557V13, multiclass
                                  clus
vv                                 MAP7D1 MUTATED MAP7D1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                        12              214
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(558) Variable = MPO MUTATION ANALYSIS
D558V1, survival
               sevent
clus2             0   1
  MPO MUTATED    12   3
  MPO WILD-TYPE 366  90
  MPO MUTATED MPO WILD-TYPE 
           15           456 
  MPO MUTATED MPO WILD-TYPE 
            3            90 
$`MPO MUTATED`
TCGA-A6-6780 TCGA-AA-3877 TCGA-AA-3977 TCGA-AA-A02K TCGA-AZ-4315 TCGA-CA-6717 
       20.12        31.00        25.02        14.01        58.39        12.76 
TCGA-CM-6164 TCGA-CM-6167 TCGA-DM-A1HB TCGA-F4-6807 TCGA-F4-6809 TCGA-AF-6136 
       29.03        14.99       135.65        16.24        13.25        15.39 
TCGA-AG-3892 TCGA-AG-A002 TCGA-DY-A1DG 
       13.02        20.98        51.48 

$`MPO WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 
       17.03        24.03        27.02        29.98        18.05         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        2.01         5.03         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07        12.20        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6165 
       15.02        17.03        15.02        12.00         2.96        16.04 
TCGA-CM-6166 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       21.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6808 TCGA-F4-6854 
       47.87         1.55        34.42        41.42        33.67         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 
       34.49        10.39        14.50        16.83        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       36.95        17.03        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       41.36        57.24        24.13        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  MPO MUTATED MPO WILD-TYPE 
        12.76          0.00 
  MPO MUTATED MPO WILD-TYPE 
       135.65        148.01 
  MPO MUTATED MPO WILD-TYPE 
       20.120        20.235 
[1] "12.8 - 135.7 (20.1)" "0.0 - 148.0 (20.2)" 
[1] "hr=" "1.1"
D558V2, continuous
D558V3, binary
               cls
clus              0   1
  MPO MUTATED    12   4
  MPO WILD-TYPE 354 115
[1] "tbl2"
               cls
clus            [,1] [,2]
  MPO MUTATED     12    4
  MPO WILD-TYPE  354  115
        clus
vv       MPO MUTATED MPO WILD-TYPE
  COLON           12           354
  RECTUM           4           115
[1] 2 2
[1] FALSE
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MPO MUTATED         3        0        0         5         0         0
  MPO WILD-TYPE      88        1       32       133        10         1
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MPO MUTATED           0          0          2          2        1         2
  MPO WILD-TYPE        24         11         57         40       47        16
               vv
clus            STAGE IVB
  MPO MUTATED           0
  MPO WILD-TYPE         1
D558V4, multiclass
            clus
vv           MPO MUTATED MPO WILD-TYPE
  STAGE I              3            88
  STAGE IA             0             1
  STAGE II             0            32
  STAGE IIA            5           133
  STAGE IIB            0            10
  STAGE IIC            0             1
  STAGE III            0            24
  STAGE IIIA           0            11
  STAGE IIIB           2            57
  STAGE IIIC           2            40
  STAGE IV             1            47
  STAGE IVA            2            16
  STAGE IVB            0             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  MPO MUTATED     2   2  11   1
  MPO WILD-TYPE  15  90 318  49
D558V5, multiclass
    clus
vv   MPO MUTATED MPO WILD-TYPE
  T1           2            15
  T2           2            90
  T3          11           318
  T4           1            49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2
  MPO MUTATED     9   4   3
  MPO WILD-TYPE 278 109  84
D558V6, multiclass
    clus
vv   MPO MUTATED MPO WILD-TYPE
  N0           9           278
  N1           4           109
  N2           3            84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D558V7, binary
               cls
clus              0   1
  MPO MUTATED    10   3
  MPO WILD-TYPE 365  62
[1] "tbl2"
               cls
clus            [,1] [,2]
  MPO MUTATED     10    3
  MPO WILD-TYPE  365   62
   clus
vv  MPO MUTATED MPO WILD-TYPE
  0          10           365
  1           3            62
[1] 2 2
[1] FALSE
D558V8, binary
               cls
clus              0   1
  MPO MUTATED     8   8
  MPO WILD-TYPE 217 256
[1] "tbl2"
               cls
clus            [,1] [,2]
  MPO MUTATED      8    8
  MPO WILD-TYPE  217  256
        clus
vv       MPO MUTATED MPO WILD-TYPE
  FEMALE           8           217
  MALE             8           256
[1] 2 2
[1] FALSE
D558V9, binary
               cls
clus              0   1
  MPO MUTATED    12   1
  MPO WILD-TYPE 338  21
[1] "tbl2"
               cls
clus            [,1] [,2]
  MPO MUTATED     12    1
  MPO WILD-TYPE  338   21
     clus
vv    MPO MUTATED MPO WILD-TYPE
  NO           12           338
  YES           1            21
[1] 2 2
[1] FALSE
               vv
clus            COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MPO MUTATED                      8                             3
  MPO WILD-TYPE                  307                            44
               vv
clus            RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MPO MUTATED                       4                              0
  MPO WILD-TYPE                   102                             10
D558V10, multiclass
                                clus
vv                               MPO MUTATED MPO WILD-TYPE
  COLON ADENOCARCINOMA                     8           307
  COLON MUCINOUS ADENOCARCINOMA            3            44
  RECTAL ADENOCARCINOMA                    4           102
  RECTAL MUCINOUS ADENOCARCINOMA           0            10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             R0  R1  R2  RX
  MPO MUTATED     9   0   1   1
  MPO WILD-TYPE 336   4  30  24
D558V11, multiclass
    clus
vv   MPO MUTATED MPO WILD-TYPE
  R0           9           336
  R1           0             4
  R2           1            30
  RX           1            24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D558V12, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MPO MUTATED                                  0     1
  MPO WILD-TYPE                                1    10
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  MPO MUTATED                           1     8
  MPO WILD-TYPE                        21   218
D558V13, multiclass
                                  clus
vv                                 MPO MUTATED MPO WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      1            10
  BLACK OR AFRICAN AMERICAN                  1            21
  WHITE                                      8           218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(559) Variable = WBP11 MUTATION ANALYSIS
D559V1, survival
                 sevent
clus2               0   1
  WBP11 MUTATED     6   1
  WBP11 WILD-TYPE 372  92
  WBP11 MUTATED WBP11 WILD-TYPE 
              7             464 
  WBP11 MUTATED WBP11 WILD-TYPE 
              1              92 
$`WBP11 MUTATED`
TCGA-A6-5665 TCGA-AA-3713 TCGA-CK-4950 TCGA-D5-6540 TCGA-D5-6541 TCGA-DM-A28G 
       22.06        19.04        85.45        16.14        15.58        60.79 
TCGA-G4-6309 
       85.48 

$`WBP11 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       17.13        12.49         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
       81.37       119.93        35.97       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       55.04        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  WBP11 MUTATED WBP11 WILD-TYPE 
          15.58            0.00 
  WBP11 MUTATED WBP11 WILD-TYPE 
          85.48          148.01 
  WBP11 MUTATED WBP11 WILD-TYPE 
         22.060          20.155 
[1] "15.6 - 85.5 (22.1)" "0.0 - 148.0 (20.2)"
[1] "hr=" "2.4"
D559V2, continuous
D559V3, binary
                 cls
clus                0   1
  WBP11 MUTATED     8   0
  WBP11 WILD-TYPE 358 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WBP11 MUTATED      8    0
  WBP11 WILD-TYPE  358  119
        clus
vv       WBP11 MUTATED WBP11 WILD-TYPE
  COLON              8             358
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  WBP11 MUTATED         1        0        0         4         0         0
  WBP11 WILD-TYPE      90        1       32       134        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  WBP11 MUTATED           0          0          2          0        1         0
  WBP11 WILD-TYPE        24         11         57         42       47        18
                 vv
clus              STAGE IVB
  WBP11 MUTATED           0
  WBP11 WILD-TYPE         1
D559V4, multiclass
            clus
vv           WBP11 MUTATED WBP11 WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              4             134
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             2              57
  STAGE IIIC             0              42
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  WBP11 MUTATED     0   1   7   0
  WBP11 WILD-TYPE  17  91 322  50
D559V5, multiclass
    clus
vv   WBP11 MUTATED WBP11 WILD-TYPE
  T1             0              17
  T2             1              91
  T3             7             322
  T4             0              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  WBP11 MUTATED     6   2   0
  WBP11 WILD-TYPE 281 111  87
D559V6, multiclass
    clus
vv   WBP11 MUTATED WBP11 WILD-TYPE
  N0             6             281
  N1             2             111
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D559V7, binary
                 cls
clus                0   1
  WBP11 MUTATED     7   1
  WBP11 WILD-TYPE 368  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WBP11 MUTATED      7    1
  WBP11 WILD-TYPE  368   64
   clus
vv  WBP11 MUTATED WBP11 WILD-TYPE
  0             7             368
  1             1              64
[1] 2 2
[1] FALSE
D559V8, binary
                 cls
clus                0   1
  WBP11 MUTATED     4   4
  WBP11 WILD-TYPE 221 260
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WBP11 MUTATED      4    4
  WBP11 WILD-TYPE  221  260
        clus
vv       WBP11 MUTATED WBP11 WILD-TYPE
  FEMALE             4             221
  MALE               4             260
[1] 2 2
[1] FALSE
D559V9, binary
                 cls
clus                0   1
  WBP11 MUTATED     5   1
  WBP11 WILD-TYPE 345  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WBP11 MUTATED      5    1
  WBP11 WILD-TYPE  345   21
     clus
vv    WBP11 MUTATED WBP11 WILD-TYPE
  NO              5             345
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  WBP11 MUTATED                      7                             1
  WBP11 WILD-TYPE                  308                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  WBP11 MUTATED                       0                              0
  WBP11 WILD-TYPE                   106                             10
D559V10, multiclass
                                clus
vv                               WBP11 MUTATED WBP11 WILD-TYPE
  COLON ADENOCARCINOMA                       7             308
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  WBP11 MUTATED     5   1   1   0
  WBP11 WILD-TYPE 340   3  30  25
D559V11, multiclass
    clus
vv   WBP11 MUTATED WBP11 WILD-TYPE
  R0             5             340
  R1             1               3
  R2             1              30
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D559V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  WBP11 MUTATED                                  0     0
  WBP11 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  WBP11 MUTATED                           2     4
  WBP11 WILD-TYPE                        20   222
D559V13, multiclass
                                  clus
vv                                 WBP11 MUTATED WBP11 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    2              20
  WHITE                                        4             222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(560) Variable = RASA2 MUTATION ANALYSIS
D560V1, survival
                 sevent
clus2               0   1
  RASA2 MUTATED    14   2
  RASA2 WILD-TYPE 364  91
  RASA2 MUTATED RASA2 WILD-TYPE 
             16             455 
  RASA2 MUTATED RASA2 WILD-TYPE 
              2              91 
$`RASA2 MUTATED`
TCGA-A6-6141 TCGA-AA-3510 TCGA-AA-3655 TCGA-AA-3697 TCGA-AA-A010 TCGA-AD-5900 
        8.38        63.98        61.02        85.05        34.98         0.07 
TCGA-AD-6889 TCGA-AD-6964 TCGA-AZ-4315 TCGA-CK-6751 TCGA-CM-5344 TCGA-D5-6926 
       56.55        10.88        58.39       124.27        22.03         9.04 
TCGA-DM-A1D6 TCGA-F4-6703 TCGA-G4-6321 TCGA-AG-A002 
       49.91        47.87        22.09        20.98 

$`RASA2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 
       22.09        22.06        32.71        27.09        22.52        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       13.94        19.99        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       21.37        15.52         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       33.01        21.44        17.82         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
        1.91        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       29.06        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
       14.30         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       92.75        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       35.74         6.18         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       63.62        61.91        36.00        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  RASA2 MUTATED RASA2 WILD-TYPE 
           0.07            0.00 
  RASA2 MUTATED RASA2 WILD-TYPE 
         124.27          148.01 
  RASA2 MUTATED RASA2 WILD-TYPE 
         41.425          20.020 
[1] "0.1 - 124.3 (41.4)" "0.0 - 148.0 (20.0)"
[1] "hr=" "2.7"
D560V2, continuous
D560V3, binary
                 cls
clus                0   1
  RASA2 MUTATED    15   2
  RASA2 WILD-TYPE 351 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RASA2 MUTATED     15    2
  RASA2 WILD-TYPE  351  117
        clus
vv       RASA2 MUTATED RASA2 WILD-TYPE
  COLON             15             351
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RASA2 MUTATED         3        0        2         6         1         0
  RASA2 WILD-TYPE      88        1       30       132         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RASA2 MUTATED           2          0          2          0        0         0
  RASA2 WILD-TYPE        22         11         57         42       48        18
                 vv
clus              STAGE IVB
  RASA2 MUTATED           0
  RASA2 WILD-TYPE         1
D560V4, multiclass
            clus
vv           RASA2 MUTATED RASA2 WILD-TYPE
  STAGE I                3              88
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA              6             132
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              2              22
  STAGE IIIA             0              11
  STAGE IIIB             2              57
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  RASA2 MUTATED     0   4  10   3
  RASA2 WILD-TYPE  17  88 319  47
D560V5, multiclass
    clus
vv   RASA2 MUTATED RASA2 WILD-TYPE
  T1             0              17
  T2             4              88
  T3            10             319
  T4             3              47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  RASA2 MUTATED    13   3   1
  RASA2 WILD-TYPE 274 110  86
D560V6, multiclass
    clus
vv   RASA2 MUTATED RASA2 WILD-TYPE
  N0            13             274
  N1             3             110
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D560V7, binary
                 cls
clus                0   1
  RASA2 MUTATED    13   0
  RASA2 WILD-TYPE 362  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RASA2 MUTATED     13    0
  RASA2 WILD-TYPE  362   65
   clus
vv  RASA2 MUTATED RASA2 WILD-TYPE
  0            13             362
  1             0              65
[1] 2 2
[1] FALSE
D560V8, binary
                 cls
clus                0   1
  RASA2 MUTATED     5  12
  RASA2 WILD-TYPE 220 252
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RASA2 MUTATED      5   12
  RASA2 WILD-TYPE  220  252
        clus
vv       RASA2 MUTATED RASA2 WILD-TYPE
  FEMALE             5             220
  MALE              12             252
[1] 2 2
[1] FALSE
D560V9, binary
                 cls
clus                0   1
  RASA2 MUTATED    12   1
  RASA2 WILD-TYPE 338  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RASA2 MUTATED     12    1
  RASA2 WILD-TYPE  338   21
     clus
vv    RASA2 MUTATED RASA2 WILD-TYPE
  NO             12             338
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  RASA2 MUTATED                     12                             3
  RASA2 WILD-TYPE                  303                            44
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  RASA2 MUTATED                       2                              0
  RASA2 WILD-TYPE                   104                             10
D560V10, multiclass
                                clus
vv                               RASA2 MUTATED RASA2 WILD-TYPE
  COLON ADENOCARCINOMA                      12             303
  COLON MUCINOUS ADENOCARCINOMA              3              44
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  RASA2 MUTATED    12   0   0   1
  RASA2 WILD-TYPE 333   4  31  24
D560V11, multiclass
    clus
vv   RASA2 MUTATED RASA2 WILD-TYPE
  R0            12             333
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D560V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RASA2 MUTATED                                  0     1
  RASA2 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  RASA2 MUTATED                           1     9
  RASA2 WILD-TYPE                        21   217
D560V13, multiclass
                                  clus
vv                                 RASA2 MUTATED RASA2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        9             217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(561) Variable = PLCH2 MUTATION ANALYSIS
D561V1, survival
                 sevent
clus2               0   1
  PLCH2 MUTATED    14   5
  PLCH2 WILD-TYPE 364  88
  PLCH2 MUTATED PLCH2 WILD-TYPE 
             19             452 
  PLCH2 MUTATED PLCH2 WILD-TYPE 
              5              88 
$`PLCH2 MUTATED`
TCGA-A6-6782 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3994 TCGA-AZ-6599 TCGA-AZ-6600 
       20.28        35.01         6.97        27.02         6.77        12.10 
TCGA-AZ-6603 TCGA-CK-4947 TCGA-CK-4952 TCGA-CM-6167 TCGA-D5-6928 TCGA-DM-A1D0 
       29.56        17.56        15.62        14.99        11.64       130.65 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A28F TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6303 
      131.51       135.65        35.97        47.41        35.31        65.85 
TCGA-G4-6628 
       79.69 

$`PLCH2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        19.66         7.04         3.02         1.02 
TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
       63.98         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
       19.07         7.96        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6606 
       62.79        88.21        49.41       100.01         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4948 
        0.07        12.20        12.76        10.06        14.30       148.01 
TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       85.45        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6168 
       12.00         2.96        29.03        16.04        21.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6930 
       12.43        14.30         9.04         9.44         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G 
       44.32       139.17         6.12        81.37       119.93        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6304 TCGA-G4-6306 
       13.25         0.53       133.18        74.56        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 
       13.78        35.80        26.17        91.79        46.75        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  PLCH2 MUTATED PLCH2 WILD-TYPE 
           6.77            0.00 
  PLCH2 MUTATED PLCH2 WILD-TYPE 
         135.65          148.01 
  PLCH2 MUTATED PLCH2 WILD-TYPE 
         29.560          20.035 
[1] "6.8 - 135.7 (29.6)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.1"
D561V2, continuous
D561V3, binary
                 cls
clus                0   1
  PLCH2 MUTATED    19   0
  PLCH2 WILD-TYPE 347 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PLCH2 MUTATED     19    0
  PLCH2 WILD-TYPE  347  119
        clus
vv       PLCH2 MUTATED PLCH2 WILD-TYPE
  COLON             19             347
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PLCH2 MUTATED         4        0        1         3         1         0
  PLCH2 WILD-TYPE      87        1       31       135         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PLCH2 MUTATED           0          0          4          3        2         0
  PLCH2 WILD-TYPE        24         11         55         39       46        18
                 vv
clus              STAGE IVB
  PLCH2 MUTATED           0
  PLCH2 WILD-TYPE         1
D561V4, multiclass
            clus
vv           PLCH2 MUTATED PLCH2 WILD-TYPE
  STAGE I                4              87
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              3             135
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             4              55
  STAGE IIIC             3              39
  STAGE IV               2              46
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PLCH2 MUTATED     0   5   9   5
  PLCH2 WILD-TYPE  17  87 320  45
D561V5, multiclass
    clus
vv   PLCH2 MUTATED PLCH2 WILD-TYPE
  T1             0              17
  T2             5              87
  T3             9             320
  T4             5              45
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  PLCH2 MUTATED     9   7   3
  PLCH2 WILD-TYPE 278 106  84
D561V6, multiclass
    clus
vv   PLCH2 MUTATED PLCH2 WILD-TYPE
  N0             9             278
  N1             7             106
  N2             3              84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D561V7, binary
                 cls
clus                0   1
  PLCH2 MUTATED    14   2
  PLCH2 WILD-TYPE 361  63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PLCH2 MUTATED     14    2
  PLCH2 WILD-TYPE  361   63
   clus
vv  PLCH2 MUTATED PLCH2 WILD-TYPE
  0            14             361
  1             2              63
[1] 2 2
[1] FALSE
D561V8, binary
                 cls
clus                0   1
  PLCH2 MUTATED     7  12
  PLCH2 WILD-TYPE 218 252
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PLCH2 MUTATED      7   12
  PLCH2 WILD-TYPE  218  252
        clus
vv       PLCH2 MUTATED PLCH2 WILD-TYPE
  FEMALE             7             218
  MALE              12             252
[1] 2 2
[1] FALSE
D561V9, binary
                 cls
clus                0   1
  PLCH2 MUTATED    13   0
  PLCH2 WILD-TYPE 337  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PLCH2 MUTATED     13    0
  PLCH2 WILD-TYPE  337   22
     clus
vv    PLCH2 MUTATED PLCH2 WILD-TYPE
  NO             13             337
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PLCH2 MUTATED                     14                             4
  PLCH2 WILD-TYPE                  301                            43
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PLCH2 MUTATED                       0                              0
  PLCH2 WILD-TYPE                   106                             10
D561V10, multiclass
                                clus
vv                               PLCH2 MUTATED PLCH2 WILD-TYPE
  COLON ADENOCARCINOMA                      14             301
  COLON MUCINOUS ADENOCARCINOMA              4              43
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  PLCH2 MUTATED     9   0   0   2
  PLCH2 WILD-TYPE 336   4  31  23
D561V11, multiclass
    clus
vv   PLCH2 MUTATED PLCH2 WILD-TYPE
  R0             9             336
  R1             0               4
  R2             0              31
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D561V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PLCH2 MUTATED                                  0     0
  PLCH2 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PLCH2 MUTATED                           2    14
  PLCH2 WILD-TYPE                        20   212
D561V13, multiclass
                                  clus
vv                                 PLCH2 MUTATED PLCH2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    2              20
  WHITE                                       14             212
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(562) Variable = C1ORF59 MUTATION ANALYSIS
D562V1, survival
                   sevent
clus2                 0   1
  C1ORF59 MUTATED     7   3
  C1ORF59 WILD-TYPE 371  90
  C1ORF59 MUTATED C1ORF59 WILD-TYPE 
               10               461 
  C1ORF59 MUTATED C1ORF59 WILD-TYPE 
                3                90 
$`C1ORF59 MUTATED`
TCGA-A6-5660 TCGA-A6-6781 TCGA-AA-A00N TCGA-AZ-4315 TCGA-AZ-5403 TCGA-CA-6719 
       29.19        19.66         4.01        58.39        62.79        14.30 
TCGA-CM-4752 TCGA-CM-5348 TCGA-D5-5540 TCGA-DM-A0XD 
       13.02        22.98        56.09        24.43 

$`C1ORF59 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13       106.75        22.36 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5349 
       20.02        37.02        25.02        29.06        22.03        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6529 
       12.03        45.40        12.26        19.59        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  C1ORF59 MUTATED C1ORF59 WILD-TYPE 
             4.01              0.00 
  C1ORF59 MUTATED C1ORF59 WILD-TYPE 
            62.79            148.01 
  C1ORF59 MUTATED C1ORF59 WILD-TYPE 
           23.705            20.120 
[1] "4.0 - 62.8 (23.7)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.2"
D562V2, continuous
D562V3, binary
                   cls
clus                  0   1
  C1ORF59 MUTATED    10   0
  C1ORF59 WILD-TYPE 356 119
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C1ORF59 MUTATED     10    0
  C1ORF59 WILD-TYPE  356  119
        clus
vv       C1ORF59 MUTATED C1ORF59 WILD-TYPE
  COLON               10               356
  RECTUM               0               119
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  C1ORF59 MUTATED         0        0        1         5         1         0
  C1ORF59 WILD-TYPE      91        1       31       133         9         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C1ORF59 MUTATED           0          0          1          2        0
  C1ORF59 WILD-TYPE        24         11         58         40       48
                   vv
clus                STAGE IVA STAGE IVB
  C1ORF59 MUTATED           0         0
  C1ORF59 WILD-TYPE        18         1
D562V4, multiclass
            clus
vv           C1ORF59 MUTATED C1ORF59 WILD-TYPE
  STAGE I                  0                91
  STAGE IA                 0                 1
  STAGE II                 1                31
  STAGE IIA                5               133
  STAGE IIB                1                 9
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               0                11
  STAGE IIIB               1                58
  STAGE IIIC               2                40
  STAGE IV                 0                48
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  C1ORF59 MUTATED     0   0   8   2
  C1ORF59 WILD-TYPE  17  92 321  48
D562V5, multiclass
    clus
vv   C1ORF59 MUTATED C1ORF59 WILD-TYPE
  T1               0                17
  T2               0                92
  T3               8               321
  T4               2                48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  C1ORF59 MUTATED     7   2   1
  C1ORF59 WILD-TYPE 280 111  86
D562V6, multiclass
    clus
vv   C1ORF59 MUTATED C1ORF59 WILD-TYPE
  N0               7               280
  N1               2               111
  N2               1                86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D562V7, binary
                   cls
clus                  0   1
  C1ORF59 MUTATED     8   0
  C1ORF59 WILD-TYPE 367  65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C1ORF59 MUTATED      8    0
  C1ORF59 WILD-TYPE  367   65
   clus
vv  C1ORF59 MUTATED C1ORF59 WILD-TYPE
  0               8               367
  1               0                65
[1] 2 2
[1] FALSE
D562V8, binary
                   cls
clus                  0   1
  C1ORF59 MUTATED     0  10
  C1ORF59 WILD-TYPE 225 254
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C1ORF59 MUTATED      0   10
  C1ORF59 WILD-TYPE  225  254
        clus
vv       C1ORF59 MUTATED C1ORF59 WILD-TYPE
  FEMALE               0               225
  MALE                10               254
[1] 2 2
[1] FALSE
D562V9, binary
                   cls
clus                  0   1
  C1ORF59 MUTATED     8   0
  C1ORF59 WILD-TYPE 342  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C1ORF59 MUTATED      8    0
  C1ORF59 WILD-TYPE  342   22
     clus
vv    C1ORF59 MUTATED C1ORF59 WILD-TYPE
  NO                8               342
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  C1ORF59 MUTATED                      8                             2
  C1ORF59 WILD-TYPE                  307                            45
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  C1ORF59 MUTATED                       0                              0
  C1ORF59 WILD-TYPE                   106                             10
D562V10, multiclass
                                clus
vv                               C1ORF59 MUTATED C1ORF59 WILD-TYPE
  COLON ADENOCARCINOMA                         8               307
  COLON MUCINOUS ADENOCARCINOMA                2                45
  RECTAL ADENOCARCINOMA                        0               106
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  C1ORF59 MUTATED     6   0   0   1
  C1ORF59 WILD-TYPE 339   4  31  24
D562V11, multiclass
    clus
vv   C1ORF59 MUTATED C1ORF59 WILD-TYPE
  R0               6               339
  R1               0                 4
  R2               0                31
  RX               1                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D562V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C1ORF59 MUTATED                                  0     1
  C1ORF59 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  C1ORF59 MUTATED                           2     6
  C1ORF59 WILD-TYPE                        20   220
D562V13, multiclass
                                  clus
vv                                 C1ORF59 MUTATED C1ORF59 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                10
  BLACK OR AFRICAN AMERICAN                      2                20
  WHITE                                          6               220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(563) Variable = MEPE MUTATION ANALYSIS
D563V1, survival
                sevent
clus2              0   1
  MEPE MUTATED    14   4
  MEPE WILD-TYPE 364  89
  MEPE MUTATED MEPE WILD-TYPE 
            18            453 
  MEPE MUTATED MEPE WILD-TYPE 
             4             89 
$`MEPE MUTATED`
TCGA-A6-5665 TCGA-A6-6141 TCGA-AA-3555 TCGA-AA-3697 TCGA-AA-A00N TCGA-AA-A01P 
       22.06         8.38        29.95        85.05         4.01        38.07 
TCGA-AD-6889 TCGA-AU-6004 TCGA-AZ-6605 TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-5868 
       56.55        27.09         5.23        12.76        10.06        17.03 
TCGA-D5-6924 TCGA-D5-6930 TCGA-F4-6703 TCGA-AG-3885 TCGA-AG-4008 TCGA-AG-A002 
       14.30         1.51        47.87        17.95        17.03        20.98 

$`MEPE WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 
       22.09        32.71        27.09        22.52        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       24.00        17.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01Q 
       10.98        32.02        12.00        31.00        31.00         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       21.37        15.52         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 
       27.42        10.88         0.20        14.50        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
       12.10       100.01        29.56        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        15.02        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 
       15.58         1.48         3.68         4.41        12.43         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
        9.44        11.64         4.80        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
        6.18         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
       19.99         1.02        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       36.03        14.04         1.02        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  MEPE MUTATED MEPE WILD-TYPE 
          1.51           0.00 
  MEPE MUTATED MEPE WILD-TYPE 
         85.05         148.01 
  MEPE MUTATED MEPE WILD-TYPE 
         17.49          20.28 
[1] "1.5 - 85.0 (17.5)"  "0.0 - 148.0 (20.3)"
[1] "hr=" "1.2"
D563V2, continuous
D563V3, binary
                cls
clus               0   1
  MEPE MUTATED    15   3
  MEPE WILD-TYPE 351 116
[1] "tbl2"
                cls
clus             [,1] [,2]
  MEPE MUTATED     15    3
  MEPE WILD-TYPE  351  116
        clus
vv       MEPE MUTATED MEPE WILD-TYPE
  COLON            15            351
  RECTUM            3            116
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MEPE MUTATED         2        0        0        10         1         0
  MEPE WILD-TYPE      89        1       32       128         9         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MEPE MUTATED           2          0          2          0        0         1
  MEPE WILD-TYPE        22         11         57         42       48        17
                vv
clus             STAGE IVB
  MEPE MUTATED           0
  MEPE WILD-TYPE         1
D563V4, multiclass
            clus
vv           MEPE MUTATED MEPE WILD-TYPE
  STAGE I               2             89
  STAGE IA              0              1
  STAGE II              0             32
  STAGE IIA            10            128
  STAGE IIB             1              9
  STAGE IIC             0              1
  STAGE III             2             22
  STAGE IIIA            0             11
  STAGE IIIB            2             57
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             1             17
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  MEPE MUTATED     0   2  13   3
  MEPE WILD-TYPE  17  90 316  47
D563V5, multiclass
    clus
vv   MEPE MUTATED MEPE WILD-TYPE
  T1            0             17
  T2            2             90
  T3           13            316
  T4            3             47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  MEPE MUTATED    14   4   0
  MEPE WILD-TYPE 273 109  87
D563V6, multiclass
    clus
vv   MEPE MUTATED MEPE WILD-TYPE
  N0           14            273
  N1            4            109
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D563V7, binary
                cls
clus               0   1
  MEPE MUTATED    17   1
  MEPE WILD-TYPE 358  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  MEPE MUTATED     17    1
  MEPE WILD-TYPE  358   64
   clus
vv  MEPE MUTATED MEPE WILD-TYPE
  0           17            358
  1            1             64
[1] 2 2
[1] FALSE
D563V8, binary
                cls
clus               0   1
  MEPE MUTATED     6  12
  MEPE WILD-TYPE 219 252
[1] "tbl2"
                cls
clus             [,1] [,2]
  MEPE MUTATED      6   12
  MEPE WILD-TYPE  219  252
        clus
vv       MEPE MUTATED MEPE WILD-TYPE
  FEMALE            6            219
  MALE             12            252
[1] 2 2
[1] FALSE
D563V9, binary
                cls
clus               0   1
  MEPE MUTATED    13   1
  MEPE WILD-TYPE 337  21
[1] "tbl2"
                cls
clus             [,1] [,2]
  MEPE MUTATED     13    1
  MEPE WILD-TYPE  337   21
     clus
vv    MEPE MUTATED MEPE WILD-TYPE
  NO            13            337
  YES            1             21
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MEPE MUTATED                     11                             4
  MEPE WILD-TYPE                  304                            43
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MEPE MUTATED                       3                              0
  MEPE WILD-TYPE                   103                             10
D563V10, multiclass
                                clus
vv                               MEPE MUTATED MEPE WILD-TYPE
  COLON ADENOCARCINOMA                     11            304
  COLON MUCINOUS ADENOCARCINOMA             4             43
  RECTAL ADENOCARCINOMA                     3            103
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  MEPE MUTATED    13   0   0   2
  MEPE WILD-TYPE 332   4  31  23
D563V11, multiclass
    clus
vv   MEPE MUTATED MEPE WILD-TYPE
  R0           13            332
  R1            0              4
  R2            0             31
  RX            2             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D563V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MEPE MUTATED                                  0     3
  MEPE WILD-TYPE                                1     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  MEPE MUTATED                           1     7
  MEPE WILD-TYPE                        21   219
D563V13, multiclass
                                  clus
vv                                 MEPE MUTATED MEPE WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       3              8
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                       7            219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(564) Variable = RNASEL MUTATION ANALYSIS
D564V1, survival
                  sevent
clus2                0   1
  RNASEL MUTATED    10   4
  RNASEL WILD-TYPE 368  89
  RNASEL MUTATED RNASEL WILD-TYPE 
              14              457 
  RNASEL MUTATED RNASEL WILD-TYPE 
               4               89 
$`RNASEL MUTATED`
TCGA-A6-3809 TCGA-AA-3517 TCGA-AA-A00N TCGA-AD-5900 TCGA-AD-6895 TCGA-AZ-4315 
       32.75        38.99         4.01         0.07         0.72        58.39 
TCGA-AZ-6600 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-5916 TCGA-D5-6922 TCGA-F4-6808 
       12.10        12.76        10.06        21.14         4.41        33.67 
TCGA-AG-3892 TCGA-AH-6544 
       13.02        38.56 

$`RNASEL WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        13.02         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       18.05        40.96        21.37        15.52        56.55         0.79 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       49.41         6.77       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.07        12.20        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 
       15.62        49.08        51.32         9.99        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6923 
       12.49        16.14        15.58         1.48         3.68        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       34.42        41.42        16.24        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       36.95        17.03        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       41.00        38.04       117.11         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  RNASEL MUTATED RNASEL WILD-TYPE 
            0.07             0.00 
  RNASEL MUTATED RNASEL WILD-TYPE 
           58.39           148.01 
  RNASEL MUTATED RNASEL WILD-TYPE 
           12.89            20.28 
[1] "0.1 - 58.4 (12.9)"  "0.0 - 148.0 (20.3)"
[1] "hr=" "1.9"
D564V2, continuous
D564V3, binary
                  cls
clus                 0   1
  RNASEL MUTATED    12   2
  RNASEL WILD-TYPE 354 117
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNASEL MUTATED     12    2
  RNASEL WILD-TYPE  354  117
        clus
vv       RNASEL MUTATED RNASEL WILD-TYPE
  COLON              12              354
  RECTUM              2              117
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RNASEL MUTATED         4        0        0         4         2         0
  RNASEL WILD-TYPE      87        1       32       134         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RNASEL MUTATED           0          1          0          0        1
  RNASEL WILD-TYPE        24         10         59         42       47
                  vv
clus               STAGE IVA STAGE IVB
  RNASEL MUTATED           0         0
  RNASEL WILD-TYPE        18         1
D564V4, multiclass
            clus
vv           RNASEL MUTATED RNASEL WILD-TYPE
  STAGE I                 4               87
  STAGE IA                0                1
  STAGE II                0               32
  STAGE IIA               4              134
  STAGE IIB               2                8
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              1               10
  STAGE IIIB              0               59
  STAGE IIIC              0               42
  STAGE IV                1               47
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  RNASEL MUTATED     3   1   7   3
  RNASEL WILD-TYPE  14  91 322  47
D564V5, multiclass
    clus
vv   RNASEL MUTATED RNASEL WILD-TYPE
  T1              3               14
  T2              1               91
  T3              7              322
  T4              3               47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  RNASEL MUTATED    10   4   0
  RNASEL WILD-TYPE 277 109  87
D564V6, multiclass
    clus
vv   RNASEL MUTATED RNASEL WILD-TYPE
  N0             10              277
  N1              4              109
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D564V7, binary
                  cls
clus                 0   1
  RNASEL MUTATED    10   2
  RNASEL WILD-TYPE 365  63
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNASEL MUTATED     10    2
  RNASEL WILD-TYPE  365   63
   clus
vv  RNASEL MUTATED RNASEL WILD-TYPE
  0             10              365
  1              2               63
[1] 2 2
[1] FALSE
D564V8, binary
                  cls
clus                 0   1
  RNASEL MUTATED     4  10
  RNASEL WILD-TYPE 221 254
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNASEL MUTATED      4   10
  RNASEL WILD-TYPE  221  254
        clus
vv       RNASEL MUTATED RNASEL WILD-TYPE
  FEMALE              4              221
  MALE               10              254
[1] 2 2
[1] FALSE
D564V9, binary
                  cls
clus                 0   1
  RNASEL MUTATED     9   0
  RNASEL WILD-TYPE 341  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNASEL MUTATED      9    0
  RNASEL WILD-TYPE  341   22
     clus
vv    RNASEL MUTATED RNASEL WILD-TYPE
  NO               9              341
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  RNASEL MUTATED                      8                             4
  RNASEL WILD-TYPE                  307                            43
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  RNASEL MUTATED                       2                              0
  RNASEL WILD-TYPE                   104                             10
D564V10, multiclass
                                clus
vv                               RNASEL MUTATED RNASEL WILD-TYPE
  COLON ADENOCARCINOMA                        8              307
  COLON MUCINOUS ADENOCARCINOMA               4               43
  RECTAL ADENOCARCINOMA                       2              104
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  RNASEL MUTATED     8   0   0   3
  RNASEL WILD-TYPE 337   4  31  22
D564V11, multiclass
    clus
vv   RNASEL MUTATED RNASEL WILD-TYPE
  R0              8              337
  R1              0                4
  R2              0               31
  RX              3               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D564V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RNASEL MUTATED                                  0     2
  RNASEL WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  RNASEL MUTATED                           1     8
  RNASEL WILD-TYPE                        21   218
D564V13, multiclass
                                  clus
vv                                 RNASEL MUTATED RNASEL WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                9
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                         8              218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(565) Variable = ESCO2 MUTATION ANALYSIS
D565V1, survival
                 sevent
clus2               0   1
  ESCO2 MUTATED    11   3
  ESCO2 WILD-TYPE 367  90
  ESCO2 MUTATED ESCO2 WILD-TYPE 
             14             457 
  ESCO2 MUTATED ESCO2 WILD-TYPE 
              3              90 
$`ESCO2 MUTATED`
TCGA-AA-3663 TCGA-AA-3811 TCGA-AA-A00N TCGA-AA-A010 TCGA-AY-6197 TCGA-AZ-4315 
        6.97        10.06         4.01        34.98        21.44        58.39 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-4743 TCGA-CM-5349 TCGA-AG-3609 TCGA-CL-5918 
       12.76        10.06        23.05        30.08        19.99         7.17 
TCGA-DC-5337 TCGA-F5-6812 
       15.02         0.66 

$`ESCO2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.05        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 
       14.50        27.09        16.31         0.95        33.01        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        3.29         0.07        12.20        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
       82.95         1.91       124.27        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5861 
       13.02        29.06        22.03        22.98        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       15.95        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
        6.97         4.73        78.12         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6813 TCGA-G5-6235 
       49.51        31.30        28.57        32.19         0.69        55.76 
TCGA-G5-6641 
       26.43 

  ESCO2 MUTATED ESCO2 WILD-TYPE 
           0.66            0.00 
  ESCO2 MUTATED ESCO2 WILD-TYPE 
          58.39          148.01 
  ESCO2 MUTATED ESCO2 WILD-TYPE 
          13.89           20.55 
[1] "0.7 - 58.4 (13.9)"  "0.0 - 148.0 (20.6)"
[1] "hr=" "1.6"
D565V2, continuous
D565V3, binary
                 cls
clus                0   1
  ESCO2 MUTATED    10   4
  ESCO2 WILD-TYPE 356 115
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ESCO2 MUTATED     10    4
  ESCO2 WILD-TYPE  356  115
        clus
vv       ESCO2 MUTATED ESCO2 WILD-TYPE
  COLON             10             356
  RECTUM             4             115
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ESCO2 MUTATED         1        0        1         8         2         0
  ESCO2 WILD-TYPE      90        1       31       130         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ESCO2 MUTATED           1          0          0          1        0         0
  ESCO2 WILD-TYPE        23         11         59         41       48        18
                 vv
clus              STAGE IVB
  ESCO2 MUTATED           0
  ESCO2 WILD-TYPE         1
D565V4, multiclass
            clus
vv           ESCO2 MUTATED ESCO2 WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              8             130
  STAGE IIB              2               8
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             1              41
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ESCO2 MUTATED     1   0  11   2
  ESCO2 WILD-TYPE  16  92 318  48
D565V5, multiclass
    clus
vv   ESCO2 MUTATED ESCO2 WILD-TYPE
  T1             1              16
  T2             0              92
  T3            11             318
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  ESCO2 MUTATED    12   0   2
  ESCO2 WILD-TYPE 275 113  85
D565V6, multiclass
    clus
vv   ESCO2 MUTATED ESCO2 WILD-TYPE
  N0            12             275
  N1             0             113
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D565V7, binary
                 cls
clus                0   1
  ESCO2 MUTATED    12   0
  ESCO2 WILD-TYPE 363  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ESCO2 MUTATED     12    0
  ESCO2 WILD-TYPE  363   65
   clus
vv  ESCO2 MUTATED ESCO2 WILD-TYPE
  0            12             363
  1             0              65
[1] 2 2
[1] FALSE
D565V8, binary
                 cls
clus                0   1
  ESCO2 MUTATED     5   9
  ESCO2 WILD-TYPE 220 255
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ESCO2 MUTATED      5    9
  ESCO2 WILD-TYPE  220  255
        clus
vv       ESCO2 MUTATED ESCO2 WILD-TYPE
  FEMALE             5             220
  MALE               9             255
[1] 2 2
[1] FALSE
D565V9, binary
                 cls
clus                0   1
  ESCO2 MUTATED    12   0
  ESCO2 WILD-TYPE 338  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ESCO2 MUTATED     12    0
  ESCO2 WILD-TYPE  338   22
     clus
vv    ESCO2 MUTATED ESCO2 WILD-TYPE
  NO             12             338
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ESCO2 MUTATED                      8                             2
  ESCO2 WILD-TYPE                  307                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ESCO2 MUTATED                       4                              0
  ESCO2 WILD-TYPE                   102                             10
D565V10, multiclass
                                clus
vv                               ESCO2 MUTATED ESCO2 WILD-TYPE
  COLON ADENOCARCINOMA                       8             307
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      4             102
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  ESCO2 MUTATED    11   0   0   3
  ESCO2 WILD-TYPE 334   4  31  22
D565V11, multiclass
    clus
vv   ESCO2 MUTATED ESCO2 WILD-TYPE
  R0            11             334
  R1             0               4
  R2             0              31
  RX             3              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D565V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ESCO2 MUTATED                                  0     2
  ESCO2 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ESCO2 MUTATED                           0     7
  ESCO2 WILD-TYPE                        22   219
D565V13, multiclass
                                  clus
vv                                 ESCO2 MUTATED ESCO2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               9
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        7             219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(566) Variable = CCDC88A MUTATION ANALYSIS
D566V1, survival
                   sevent
clus2                 0   1
  CCDC88A MUTATED    27   6
  CCDC88A WILD-TYPE 351  87
  CCDC88A MUTATED CCDC88A WILD-TYPE 
               33               438 
  CCDC88A MUTATED CCDC88A WILD-TYPE 
                6                87 
$`CCDC88A MUTATED`
TCGA-A6-2676 TCGA-A6-3809 TCGA-A6-5665 TCGA-A6-6653 TCGA-A6-6781 TCGA-AA-3510 
       42.90        32.75        22.06        24.39        19.66        63.98 
TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3524 TCGA-AA-3555 TCGA-AA-3663 TCGA-AA-3977 
       13.02         1.02        36.03        29.95         6.97        25.02 
TCGA-AA-A00U TCGA-AA-A010 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-6603 TCGA-CA-6717 
       17.03        34.98        58.39         1.41        29.56        12.76 
TCGA-CA-6718 TCGA-CM-4746 TCGA-CM-5348 TCGA-D5-5540 TCGA-DM-A0XD TCGA-DM-A1HA 
       10.06        37.02        22.98        56.09        24.43       131.51 
TCGA-DM-A28K TCGA-G4-6586 TCGA-G4-6628 TCGA-AF-2687 TCGA-AG-3593 TCGA-AG-A002 
       98.24        35.80        79.69        24.13        34.03        20.98 
TCGA-CI-6624 TCGA-EI-6507 TCGA-F5-6812 
        4.73        19.96         0.66 

$`CCDC88A WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5657 
       34.65        33.34        36.53        14.53        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 
       30.44        29.19        33.53        23.61        22.09        32.71 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       27.09        22.52         8.38        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 
       21.76        24.69        23.87        20.12        20.28         7.04 
TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        3.02         1.02        35.01         6.97         1.02        38.99 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
        9.07        24.03        37.05         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       17.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       61.02        78.08         6.05        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       33.01        21.44        17.82         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 
        3.25         3.29         0.07        12.20        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5860 
       25.02        13.02        29.06        22.03        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       45.40        12.26        19.59        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XF 
        1.51        12.00        11.38        10.26       119.70        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
        7.50        44.32       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-F4-6459 TCGA-F4-6460 
      119.93        35.97        60.79       117.07         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       26.17        91.79        46.75        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
        0.49        20.55        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       31.30        28.57        32.19         0.69        55.76        26.43 

  CCDC88A MUTATED CCDC88A WILD-TYPE 
             0.66              0.00 
  CCDC88A MUTATED CCDC88A WILD-TYPE 
           131.51            148.01 
  CCDC88A MUTATED CCDC88A WILD-TYPE 
            24.43             19.99 
[1] "0.7 - 131.5 (24.4)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.3"
D566V2, continuous
D566V3, binary
                   cls
clus                  0   1
  CCDC88A MUTATED    30   6
  CCDC88A WILD-TYPE 336 113
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC88A MUTATED     30    6
  CCDC88A WILD-TYPE  336  113
        clus
vv       CCDC88A MUTATED CCDC88A WILD-TYPE
  COLON               30               336
  RECTUM               6               113
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CCDC88A MUTATED         5        0        3        14         4         0
  CCDC88A WILD-TYPE      86        1       29       124         6         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CCDC88A MUTATED           1          0          2          3        2
  CCDC88A WILD-TYPE        23         11         57         39       46
                   vv
clus                STAGE IVA STAGE IVB
  CCDC88A MUTATED           0         0
  CCDC88A WILD-TYPE        18         1
D566V4, multiclass
            clus
vv           CCDC88A MUTATED CCDC88A WILD-TYPE
  STAGE I                  5                86
  STAGE IA                 0                 1
  STAGE II                 3                29
  STAGE IIA               14               124
  STAGE IIB                4                 6
  STAGE IIC                0                 1
  STAGE III                1                23
  STAGE IIIA               0                11
  STAGE IIIB               2                57
  STAGE IIIC               3                39
  STAGE IV                 2                46
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  CCDC88A MUTATED     0   7  23   6
  CCDC88A WILD-TYPE  17  85 306  44
D566V5, multiclass
    clus
vv   CCDC88A MUTATED CCDC88A WILD-TYPE
  T1               0                17
  T2               7                85
  T3              23               306
  T4               6                44
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  CCDC88A MUTATED    27   4   5
  CCDC88A WILD-TYPE 260 109  82
D566V6, multiclass
    clus
vv   CCDC88A MUTATED CCDC88A WILD-TYPE
  N0              27               260
  N1               4               109
  N2               5                82
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D566V7, binary
                   cls
clus                  0   1
  CCDC88A MUTATED    30   2
  CCDC88A WILD-TYPE 345  63
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC88A MUTATED     30    2
  CCDC88A WILD-TYPE  345   63
   clus
vv  CCDC88A MUTATED CCDC88A WILD-TYPE
  0              30               345
  1               2                63
[1] 2 2
[1] FALSE
D566V8, binary
                   cls
clus                  0   1
  CCDC88A MUTATED    14  22
  CCDC88A WILD-TYPE 211 242
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC88A MUTATED     14   22
  CCDC88A WILD-TYPE  211  242
        clus
vv       CCDC88A MUTATED CCDC88A WILD-TYPE
  FEMALE              14               211
  MALE                22               242
[1] 2 2
[1] FALSE
D566V9, binary
                   cls
clus                  0   1
  CCDC88A MUTATED    25   2
  CCDC88A WILD-TYPE 325  20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC88A MUTATED     25    2
  CCDC88A WILD-TYPE  325   20
     clus
vv    CCDC88A MUTATED CCDC88A WILD-TYPE
  NO               25               325
  YES               2                20
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CCDC88A MUTATED                     24                             6
  CCDC88A WILD-TYPE                  291                            41
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CCDC88A MUTATED                       6                              0
  CCDC88A WILD-TYPE                   100                             10
D566V10, multiclass
                                clus
vv                               CCDC88A MUTATED CCDC88A WILD-TYPE
  COLON ADENOCARCINOMA                        24               291
  COLON MUCINOUS ADENOCARCINOMA                6                41
  RECTAL ADENOCARCINOMA                        6               100
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  CCDC88A MUTATED    23   0   1   3
  CCDC88A WILD-TYPE 322   4  30  22
D566V11, multiclass
    clus
vv   CCDC88A MUTATED CCDC88A WILD-TYPE
  R0              23               322
  R1               0                 4
  R2               1                30
  RX               3                22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D566V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CCDC88A MUTATED                                  0     2
  CCDC88A WILD-TYPE                                1     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  CCDC88A MUTATED                           1    20
  CCDC88A WILD-TYPE                        21   206
D566V13, multiclass
                                  clus
vv                                 CCDC88A MUTATED CCDC88A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          2                 9
  BLACK OR AFRICAN AMERICAN                      1                21
  WHITE                                         20               206
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(567) Variable = ATP8B1 MUTATION ANALYSIS
D567V1, survival
                  sevent
clus2                0   1
  ATP8B1 MUTATED    23   4
  ATP8B1 WILD-TYPE 355  89
  ATP8B1 MUTATED ATP8B1 WILD-TYPE 
              27              444 
  ATP8B1 MUTATED ATP8B1 WILD-TYPE 
               4               89 
$`ATP8B1 MUTATED`
TCGA-A6-5665 TCGA-A6-6780 TCGA-AA-3554 TCGA-AA-3672 TCGA-AA-3877 TCGA-AA-A010 
       22.06        20.12        17.95         0.92        31.00        34.98 
TCGA-AA-A01K TCGA-AD-5900 TCGA-AY-6197 TCGA-AZ-6598 TCGA-AZ-6601 TCGA-CA-6717 
       31.00         0.07        21.44        49.41       100.01        12.76 
TCGA-CA-6718 TCGA-CM-4752 TCGA-CM-5349 TCGA-CM-6165 TCGA-CM-6674 TCGA-D5-6529 
       10.06        13.02        30.08        16.04        12.95        20.19 
TCGA-D5-6534 TCGA-DM-A28H TCGA-G4-6625 TCGA-G4-6626 TCGA-AG-3605 TCGA-AG-3892 
       43.27       117.07        91.79        46.75         0.99        13.02 
TCGA-AG-A002 TCGA-AH-6643 TCGA-F5-6812 
       20.98         0.69         0.66 

$`ATP8B1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       24.00        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
        2.01        14.01        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       29.98        18.05         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       32.02        12.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 
       41.00        39.98        18.05        40.96        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       33.01        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 
       22.36        62.79        88.21         6.77        12.10        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 
        3.25         3.29         0.07        12.20        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5860 
       37.02        25.02        29.06        22.03        22.98        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
       12.00         2.96        29.03        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6676 
       13.02        15.02        14.04        11.01        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6535 
       19.59        56.09        55.92        18.25         1.32        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       35.97        60.79        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       26.17        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3608 
       34.03         2.01        50.04        12.03         6.05        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       17.95        36.95        17.03        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       31.30        28.57        32.19         0.69        55.76        26.43 

  ATP8B1 MUTATED ATP8B1 WILD-TYPE 
            0.07             0.00 
  ATP8B1 MUTATED ATP8B1 WILD-TYPE 
          117.07           148.01 
  ATP8B1 MUTATED ATP8B1 WILD-TYPE 
          20.190           20.165 
[1] "0.1 - 117.1 (20.2)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.4"
D567V2, continuous
D567V3, binary
                  cls
clus                 0   1
  ATP8B1 MUTATED    23   5
  ATP8B1 WILD-TYPE 343 114
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP8B1 MUTATED     23    5
  ATP8B1 WILD-TYPE  343  114
        clus
vv       ATP8B1 MUTATED ATP8B1 WILD-TYPE
  COLON              23              343
  RECTUM              5              114
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ATP8B1 MUTATED         4        0        2        16         1         0
  ATP8B1 WILD-TYPE      87        1       30       122         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ATP8B1 MUTATED           1          0          0          3        1
  ATP8B1 WILD-TYPE        23         11         59         39       47
                  vv
clus               STAGE IVA STAGE IVB
  ATP8B1 MUTATED           0         0
  ATP8B1 WILD-TYPE        18         1
D567V4, multiclass
            clus
vv           ATP8B1 MUTATED ATP8B1 WILD-TYPE
  STAGE I                 4               87
  STAGE IA                0                1
  STAGE II                2               30
  STAGE IIA              16              122
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               1               23
  STAGE IIIA              0               11
  STAGE IIIB              0               59
  STAGE IIIC              3               39
  STAGE IV                1               47
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ATP8B1 MUTATED     2   2  23   1
  ATP8B1 WILD-TYPE  15  90 306  49
D567V5, multiclass
    clus
vv   ATP8B1 MUTATED ATP8B1 WILD-TYPE
  T1              2               15
  T2              2               90
  T3             23              306
  T4              1               49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  ATP8B1 MUTATED    23   2   3
  ATP8B1 WILD-TYPE 264 111  84
D567V6, multiclass
    clus
vv   ATP8B1 MUTATED ATP8B1 WILD-TYPE
  N0             23              264
  N1              2              111
  N2              3               84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D567V7, binary
                  cls
clus                 0   1
  ATP8B1 MUTATED    23   1
  ATP8B1 WILD-TYPE 352  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP8B1 MUTATED     23    1
  ATP8B1 WILD-TYPE  352   64
   clus
vv  ATP8B1 MUTATED ATP8B1 WILD-TYPE
  0             23              352
  1              1               64
[1] 2 2
[1] FALSE
D567V8, binary
                  cls
clus                 0   1
  ATP8B1 MUTATED    13  15
  ATP8B1 WILD-TYPE 212 249
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP8B1 MUTATED     13   15
  ATP8B1 WILD-TYPE  212  249
        clus
vv       ATP8B1 MUTATED ATP8B1 WILD-TYPE
  FEMALE             13              212
  MALE               15              249
[1] 2 2
[1] FALSE
D567V9, binary
                  cls
clus                 0   1
  ATP8B1 MUTATED    22   0
  ATP8B1 WILD-TYPE 328  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP8B1 MUTATED     22    0
  ATP8B1 WILD-TYPE  328   22
     clus
vv    ATP8B1 MUTATED ATP8B1 WILD-TYPE
  NO              22              328
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ATP8B1 MUTATED                     18                             5
  ATP8B1 WILD-TYPE                  297                            42
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ATP8B1 MUTATED                       5                              0
  ATP8B1 WILD-TYPE                   101                             10
D567V10, multiclass
                                clus
vv                               ATP8B1 MUTATED ATP8B1 WILD-TYPE
  COLON ADENOCARCINOMA                       18              297
  COLON MUCINOUS ADENOCARCINOMA               5               42
  RECTAL ADENOCARCINOMA                       5              101
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ATP8B1 MUTATED    21   0   1   2
  ATP8B1 WILD-TYPE 324   4  30  23
D567V11, multiclass
    clus
vv   ATP8B1 MUTATED ATP8B1 WILD-TYPE
  R0             21              324
  R1              0                4
  R2              1               30
  RX              2               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D567V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ATP8B1 MUTATED                                  0     2
  ATP8B1 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ATP8B1 MUTATED                           1    16
  ATP8B1 WILD-TYPE                        21   210
D567V13, multiclass
                                  clus
vv                                 ATP8B1 MUTATED ATP8B1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                9
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                        16              210
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(568) Variable = LAMC1 MUTATION ANALYSIS
D568V1, survival
                 sevent
clus2               0   1
  LAMC1 MUTATED    18   5
  LAMC1 WILD-TYPE 360  88
  LAMC1 MUTATED LAMC1 WILD-TYPE 
             23             448 
  LAMC1 MUTATED LAMC1 WILD-TYPE 
              5              88 
$`LAMC1 MUTATED`
TCGA-A6-4105 TCGA-A6-5660 TCGA-AA-3510 TCGA-AA-3715 TCGA-AA-3864 TCGA-AA-3977 
       14.53        29.19        63.98        19.04        53.00        25.02 
TCGA-AA-A00E TCGA-AA-A00U TCGA-AA-A010 TCGA-AA-A017 TCGA-AY-6197 TCGA-AZ-4315 
       30.02        17.03        34.98         1.02        21.44        58.39 
TCGA-AZ-6603 TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5864 TCGA-CM-6162 TCGA-D5-6920 
       29.56        22.03        30.08        15.02        12.00         3.68 
TCGA-D5-6930 TCGA-DM-A1D7 TCGA-F4-6570 TCGA-AG-3731 TCGA-AG-A002 
        1.51        13.32         6.18        37.02        20.98 

$`LAMC1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 
       16.57        34.65        33.34        32.75        36.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       31.63        30.44        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       85.05        26.99        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       31.07        30.05        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       13.94        38.04        19.00        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00W 
       38.04         4.01        27.02        42.02         0.99        14.99 
TCGA-AA-A00Z TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       21.99        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 
       14.50        27.09        16.31         0.95        33.01        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6606 
       49.41         6.77        12.10       100.01         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5860 
       37.02        25.02        13.02        29.06        22.98        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 
       15.02         5.03        15.02        17.03        15.02         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       16.14        15.58         1.48         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 
        9.04         9.44        11.64         4.80        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       49.91        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
        0.99        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  LAMC1 MUTATED LAMC1 WILD-TYPE 
           1.02            0.00 
  LAMC1 MUTATED LAMC1 WILD-TYPE 
          63.98          148.01 
  LAMC1 MUTATED LAMC1 WILD-TYPE 
         21.440          20.085 
[1] "1.0 - 64.0 (21.4)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.2"
D568V2, continuous
D568V3, binary
                 cls
clus                0   1
  LAMC1 MUTATED    21   2
  LAMC1 WILD-TYPE 345 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LAMC1 MUTATED     21    2
  LAMC1 WILD-TYPE  345  117
        clus
vv       LAMC1 MUTATED LAMC1 WILD-TYPE
  COLON             21             345
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  LAMC1 MUTATED         2        0        3        10         1         0
  LAMC1 WILD-TYPE      89        1       29       128         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  LAMC1 MUTATED           0          0          3          1        1         0
  LAMC1 WILD-TYPE        24         11         56         41       47        18
                 vv
clus              STAGE IVB
  LAMC1 MUTATED           0
  LAMC1 WILD-TYPE         1
D568V4, multiclass
            clus
vv           LAMC1 MUTATED LAMC1 WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               3              29
  STAGE IIA             10             128
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             3              56
  STAGE IIIC             1              41
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  LAMC1 MUTATED     0   4  18   1
  LAMC1 WILD-TYPE  17  88 311  49
D568V5, multiclass
    clus
vv   LAMC1 MUTATED LAMC1 WILD-TYPE
  T1             0              17
  T2             4              88
  T3            18             311
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  LAMC1 MUTATED    17   5   1
  LAMC1 WILD-TYPE 270 108  86
D568V6, multiclass
    clus
vv   LAMC1 MUTATED LAMC1 WILD-TYPE
  N0            17             270
  N1             5             108
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D568V7, binary
                 cls
clus                0   1
  LAMC1 MUTATED    19   1
  LAMC1 WILD-TYPE 356  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LAMC1 MUTATED     19    1
  LAMC1 WILD-TYPE  356   64
   clus
vv  LAMC1 MUTATED LAMC1 WILD-TYPE
  0            19             356
  1             1              64
[1] 2 2
[1] FALSE
D568V8, binary
                 cls
clus                0   1
  LAMC1 MUTATED     8  15
  LAMC1 WILD-TYPE 217 249
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LAMC1 MUTATED      8   15
  LAMC1 WILD-TYPE  217  249
        clus
vv       LAMC1 MUTATED LAMC1 WILD-TYPE
  FEMALE             8             217
  MALE              15             249
[1] 2 2
[1] FALSE
D568V9, binary
                 cls
clus                0   1
  LAMC1 MUTATED    19   0
  LAMC1 WILD-TYPE 331  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LAMC1 MUTATED     19    0
  LAMC1 WILD-TYPE  331   22
     clus
vv    LAMC1 MUTATED LAMC1 WILD-TYPE
  NO             19             331
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  LAMC1 MUTATED                     18                             2
  LAMC1 WILD-TYPE                  297                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  LAMC1 MUTATED                       2                              0
  LAMC1 WILD-TYPE                   104                             10
D568V10, multiclass
                                clus
vv                               LAMC1 MUTATED LAMC1 WILD-TYPE
  COLON ADENOCARCINOMA                      18             297
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  LAMC1 MUTATED    17   0   1   0
  LAMC1 WILD-TYPE 328   4  30  25
D568V11, multiclass
    clus
vv   LAMC1 MUTATED LAMC1 WILD-TYPE
  R0            17             328
  R1             0               4
  R2             1              30
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D568V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  LAMC1 MUTATED                                  0     0
  LAMC1 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  LAMC1 MUTATED                           1    12
  LAMC1 WILD-TYPE                        21   214
D568V13, multiclass
                                  clus
vv                                 LAMC1 MUTATED LAMC1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                       12             214
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(569) Variable = SLFN12L MUTATION ANALYSIS
D569V1, survival
                   sevent
clus2                 0   1
  SLFN12L MUTATED     6   2
  SLFN12L WILD-TYPE 372  91
  SLFN12L MUTATED SLFN12L WILD-TYPE 
                8               463 
  SLFN12L MUTATED SLFN12L WILD-TYPE 
                2                91 
$`SLFN12L MUTATED`
TCGA-AA-3681 TCGA-AA-3811 TCGA-AA-3815 TCGA-AZ-4315 TCGA-CA-6717 TCGA-CA-6718 
        5.98        10.06        33.04        58.39        12.76        10.06 
TCGA-CK-4948 TCGA-G4-6315 
      148.01        61.91 

$`SLFN12L WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3685 TCGA-AA-3688 
       50.04        47.01        15.02        11.01        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       35.05         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 
        3.06         3.25         3.29         0.07        12.20        14.30 
TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
       17.56        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       85.48        63.62        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  SLFN12L MUTATED SLFN12L WILD-TYPE 
             5.98              0.00 
  SLFN12L MUTATED SLFN12L WILD-TYPE 
           148.01            140.38 
  SLFN12L MUTATED SLFN12L WILD-TYPE 
            22.90             20.19 
[1] "6.0 - 148.0 (22.9)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.1"
D569V2, continuous
D569V3, binary
                   cls
clus                  0   1
  SLFN12L MUTATED     8   0
  SLFN12L WILD-TYPE 358 119
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLFN12L MUTATED      8    0
  SLFN12L WILD-TYPE  358  119
        clus
vv       SLFN12L MUTATED SLFN12L WILD-TYPE
  COLON                8               358
  RECTUM               0               119
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SLFN12L MUTATED         0        0        0         4         0         0
  SLFN12L WILD-TYPE      91        1       32       134        10         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLFN12L MUTATED           3          0          0          0        1
  SLFN12L WILD-TYPE        21         11         59         42       47
                   vv
clus                STAGE IVA STAGE IVB
  SLFN12L MUTATED           0         0
  SLFN12L WILD-TYPE        18         1
D569V4, multiclass
            clus
vv           SLFN12L MUTATED SLFN12L WILD-TYPE
  STAGE I                  0                91
  STAGE IA                 0                 1
  STAGE II                 0                32
  STAGE IIA                4               134
  STAGE IIB                0                10
  STAGE IIC                0                 1
  STAGE III                3                21
  STAGE IIIA               0                11
  STAGE IIIB               0                59
  STAGE IIIC               0                42
  STAGE IV                 1                47
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  SLFN12L MUTATED     0   0   8   0
  SLFN12L WILD-TYPE  17  92 321  50
D569V5, multiclass
    clus
vv   SLFN12L MUTATED SLFN12L WILD-TYPE
  T1               0                17
  T2               0                92
  T3               8               321
  T4               0                50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  SLFN12L MUTATED     4   3   1
  SLFN12L WILD-TYPE 283 110  86
D569V6, multiclass
    clus
vv   SLFN12L MUTATED SLFN12L WILD-TYPE
  N0               4               283
  N1               3               110
  N2               1                86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D569V7, binary
                   cls
clus                  0   1
  SLFN12L MUTATED     7   1
  SLFN12L WILD-TYPE 368  64
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLFN12L MUTATED      7    1
  SLFN12L WILD-TYPE  368   64
   clus
vv  SLFN12L MUTATED SLFN12L WILD-TYPE
  0               7               368
  1               1                64
[1] 2 2
[1] FALSE
D569V8, binary
                   cls
clus                  0   1
  SLFN12L MUTATED     4   4
  SLFN12L WILD-TYPE 221 260
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLFN12L MUTATED      4    4
  SLFN12L WILD-TYPE  221  260
        clus
vv       SLFN12L MUTATED SLFN12L WILD-TYPE
  FEMALE               4               221
  MALE                 4               260
[1] 2 2
[1] FALSE
D569V9, binary
                   cls
clus                  0   1
  SLFN12L MUTATED     8   0
  SLFN12L WILD-TYPE 342  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLFN12L MUTATED      8    0
  SLFN12L WILD-TYPE  342   22
     clus
vv    SLFN12L MUTATED SLFN12L WILD-TYPE
  NO                8               342
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SLFN12L MUTATED                      7                             1
  SLFN12L WILD-TYPE                  308                            46
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SLFN12L MUTATED                       0                              0
  SLFN12L WILD-TYPE                   106                             10
D569V10, multiclass
                                clus
vv                               SLFN12L MUTATED SLFN12L WILD-TYPE
  COLON ADENOCARCINOMA                         7               308
  COLON MUCINOUS ADENOCARCINOMA                1                46
  RECTAL ADENOCARCINOMA                        0               106
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  SLFN12L MUTATED     6   0   0   2
  SLFN12L WILD-TYPE 339   4  31  23
D569V11, multiclass
    clus
vv   SLFN12L MUTATED SLFN12L WILD-TYPE
  R0               6               339
  R1               0                 4
  R2               0                31
  RX               2                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D569V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SLFN12L MUTATED                                  0     2
  SLFN12L WILD-TYPE                                1     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  SLFN12L MUTATED                           0     3
  SLFN12L WILD-TYPE                        22   223
D569V13, multiclass
                                  clus
vv                                 SLFN12L MUTATED SLFN12L WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          2                 9
  BLACK OR AFRICAN AMERICAN                      0                22
  WHITE                                          3               223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(570) Variable = PLXNA3 MUTATION ANALYSIS
D570V1, survival
                  sevent
clus2                0   1
  PLXNA3 MUTATED    17   2
  PLXNA3 WILD-TYPE 361  91
  PLXNA3 MUTATED PLXNA3 WILD-TYPE 
              19              452 
  PLXNA3 MUTATED PLXNA3 WILD-TYPE 
               2               91 
$`PLXNA3 MUTATED`
TCGA-A6-5661 TCGA-A6-5665 TCGA-AA-3663 TCGA-AA-3713 TCGA-AA-3947 TCGA-AD-5900 
       33.53        22.06         6.97        19.04        33.01         0.07 
TCGA-AU-6004 TCGA-AY-6197 TCGA-AY-6386 TCGA-CA-5797 TCGA-CK-5916 TCGA-CM-4746 
       27.09        21.44        17.82         3.29        21.14        37.02 
TCGA-CM-5861 TCGA-CM-6171 TCGA-F4-6460 TCGA-G4-6309 TCGA-G4-6628 TCGA-AG-3887 
       15.02        14.04        31.96        85.48        79.69        36.95 
TCGA-DY-A0XA 
      126.44 

$`PLXNA3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       85.05        26.99        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 
       22.42        27.42        10.88         0.20        14.50        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
        0.95        33.01        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
       12.69         3.06         3.25         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       49.08        51.32         9.99        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       23.05        20.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       22.98        30.08        32.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 
       21.99        14.99        12.99        13.02        15.02        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6569 TCGA-F4-6570 
       60.79       117.07        98.24         8.61        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 
       65.85        53.62        44.68        55.04        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       46.75        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       17.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
        5.29        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  PLXNA3 MUTATED PLXNA3 WILD-TYPE 
            0.07             0.00 
  PLXNA3 MUTATED PLXNA3 WILD-TYPE 
          126.44           148.01 
  PLXNA3 MUTATED PLXNA3 WILD-TYPE 
          22.060           20.035 
[1] "0.1 - 126.4 (22.1)" "0.0 - 148.0 (20.0)"
[1] "hr=" "2.2"
D570V2, continuous
D570V3, binary
                  cls
clus                 0   1
  PLXNA3 MUTATED    17   2
  PLXNA3 WILD-TYPE 349 117
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PLXNA3 MUTATED     17    2
  PLXNA3 WILD-TYPE  349  117
        clus
vv       PLXNA3 MUTATED PLXNA3 WILD-TYPE
  COLON              17              349
  RECTUM              2              117
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PLXNA3 MUTATED         6        0        1         7         1         0
  PLXNA3 WILD-TYPE      85        1       31       131         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PLXNA3 MUTATED           0          0          3          0        1
  PLXNA3 WILD-TYPE        24         11         56         42       47
                  vv
clus               STAGE IVA STAGE IVB
  PLXNA3 MUTATED           0         0
  PLXNA3 WILD-TYPE        18         1
D570V4, multiclass
            clus
vv           PLXNA3 MUTATED PLXNA3 WILD-TYPE
  STAGE I                 6               85
  STAGE IA                0                1
  STAGE II                1               31
  STAGE IIA               7              131
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              3               56
  STAGE IIIC              0               42
  STAGE IV                1               47
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  PLXNA3 MUTATED     1   5  12   1
  PLXNA3 WILD-TYPE  16  87 317  49
D570V5, multiclass
    clus
vv   PLXNA3 MUTATED PLXNA3 WILD-TYPE
  T1              1               16
  T2              5               87
  T3             12              317
  T4              1               49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  PLXNA3 MUTATED    16   3   0
  PLXNA3 WILD-TYPE 271 110  87
D570V6, multiclass
    clus
vv   PLXNA3 MUTATED PLXNA3 WILD-TYPE
  N0             16              271
  N1              3              110
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D570V7, binary
                  cls
clus                 0   1
  PLXNA3 MUTATED    16   1
  PLXNA3 WILD-TYPE 359  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PLXNA3 MUTATED     16    1
  PLXNA3 WILD-TYPE  359   64
   clus
vv  PLXNA3 MUTATED PLXNA3 WILD-TYPE
  0             16              359
  1              1               64
[1] 2 2
[1] FALSE
D570V8, binary
                  cls
clus                 0   1
  PLXNA3 MUTATED    11   8
  PLXNA3 WILD-TYPE 214 256
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PLXNA3 MUTATED     11    8
  PLXNA3 WILD-TYPE  214  256
        clus
vv       PLXNA3 MUTATED PLXNA3 WILD-TYPE
  FEMALE             11              214
  MALE                8              256
[1] 2 2
[1] FALSE
D570V9, binary
                  cls
clus                 0   1
  PLXNA3 MUTATED    14   2
  PLXNA3 WILD-TYPE 336  20
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PLXNA3 MUTATED     14    2
  PLXNA3 WILD-TYPE  336   20
     clus
vv    PLXNA3 MUTATED PLXNA3 WILD-TYPE
  NO              14              336
  YES              2               20
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PLXNA3 MUTATED                     15                             2
  PLXNA3 WILD-TYPE                  300                            45
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PLXNA3 MUTATED                       1                              1
  PLXNA3 WILD-TYPE                   105                              9
D570V10, multiclass
                                clus
vv                               PLXNA3 MUTATED PLXNA3 WILD-TYPE
  COLON ADENOCARCINOMA                       15              300
  COLON MUCINOUS ADENOCARCINOMA               2               45
  RECTAL ADENOCARCINOMA                       1              105
  RECTAL MUCINOUS ADENOCARCINOMA              1                9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  PLXNA3 MUTATED    16   0   1   1
  PLXNA3 WILD-TYPE 329   4  30  24
D570V11, multiclass
    clus
vv   PLXNA3 MUTATED PLXNA3 WILD-TYPE
  R0             16              329
  R1              0                4
  R2              1               30
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D570V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PLXNA3 MUTATED                                  0     1
  PLXNA3 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  PLXNA3 MUTATED                           4    10
  PLXNA3 WILD-TYPE                        18   216
D570V13, multiclass
                                  clus
vv                                 PLXNA3 MUTATED PLXNA3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     4               18
  WHITE                                        10              216
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(571) Variable = ITGAV MUTATION ANALYSIS
D571V1, survival
                 sevent
clus2               0   1
  ITGAV MUTATED    14   3
  ITGAV WILD-TYPE 364  90
  ITGAV MUTATED ITGAV WILD-TYPE 
             17             454 
  ITGAV MUTATED ITGAV WILD-TYPE 
              3              90 
$`ITGAV MUTATED`
TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3950 TCGA-AY-4070 TCGA-AY-6197 TCGA-AZ-4315 
       61.02         6.97        24.00        16.31        21.44        58.39 
TCGA-AZ-6601 TCGA-CA-6717 TCGA-CK-4948 TCGA-CM-5861 TCGA-CM-6674 TCGA-D5-6923 
      100.01        12.76       148.01        15.02        12.95        12.43 
TCGA-F4-6856 TCGA-G4-6306 TCGA-G4-6628 TCGA-AG-A002 TCGA-AG-A02G 
       35.31        44.68        79.69        20.98        38.96 

$`ITGAV WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 
       20.98        19.99        13.94        19.99        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 
       12.99        24.00        33.01        26.01         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 
        0.20        14.50        27.09         0.95        33.01        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       49.41         6.77        12.10        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 
        0.07        12.20        10.06        14.30        17.56        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6676 
       13.02        15.02        14.04        11.01        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6924 
       16.14        15.58         1.48         3.68         4.41        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 
      133.18        74.56        65.85        53.62        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       26.17        91.79        46.75        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
        1.94        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  ITGAV MUTATED ITGAV WILD-TYPE 
           6.97            0.00 
  ITGAV MUTATED ITGAV WILD-TYPE 
         148.01          140.38 
  ITGAV MUTATED ITGAV WILD-TYPE 
         24.000          20.035 
[1] "7.0 - 148.0 (24.0)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1.7"
D571V2, continuous
D571V3, binary
                 cls
clus                0   1
  ITGAV MUTATED    15   2
  ITGAV WILD-TYPE 351 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITGAV MUTATED     15    2
  ITGAV WILD-TYPE  351  117
        clus
vv       ITGAV MUTATED ITGAV WILD-TYPE
  COLON             15             351
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ITGAV MUTATED         4        0        3         7         0         0
  ITGAV WILD-TYPE      87        1       29       131        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ITGAV MUTATED           1          0          0          1        1         0
  ITGAV WILD-TYPE        23         11         59         41       47        18
                 vv
clus              STAGE IVB
  ITGAV MUTATED           0
  ITGAV WILD-TYPE         1
D571V4, multiclass
            clus
vv           ITGAV MUTATED ITGAV WILD-TYPE
  STAGE I                4              87
  STAGE IA               0               1
  STAGE II               3              29
  STAGE IIA              7             131
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             1              41
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ITGAV MUTATED     0   6  11   0
  ITGAV WILD-TYPE  17  86 318  50
D571V5, multiclass
    clus
vv   ITGAV MUTATED ITGAV WILD-TYPE
  T1             0              17
  T2             6              86
  T3            11             318
  T4             0              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  ITGAV MUTATED    14   2   1
  ITGAV WILD-TYPE 273 111  86
D571V6, multiclass
    clus
vv   ITGAV MUTATED ITGAV WILD-TYPE
  N0            14             273
  N1             2             111
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D571V7, binary
                 cls
clus                0   1
  ITGAV MUTATED    15   1
  ITGAV WILD-TYPE 360  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITGAV MUTATED     15    1
  ITGAV WILD-TYPE  360   64
   clus
vv  ITGAV MUTATED ITGAV WILD-TYPE
  0            15             360
  1             1              64
[1] 2 2
[1] FALSE
D571V8, binary
                 cls
clus                0   1
  ITGAV MUTATED     4  13
  ITGAV WILD-TYPE 221 251
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITGAV MUTATED      4   13
  ITGAV WILD-TYPE  221  251
        clus
vv       ITGAV MUTATED ITGAV WILD-TYPE
  FEMALE             4             221
  MALE              13             251
[1] 2 2
[1] FALSE
D571V9, binary
                 cls
clus                0   1
  ITGAV MUTATED    17   0
  ITGAV WILD-TYPE 333  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITGAV MUTATED     17    0
  ITGAV WILD-TYPE  333   22
     clus
vv    ITGAV MUTATED ITGAV WILD-TYPE
  NO             17             333
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ITGAV MUTATED                     12                             3
  ITGAV WILD-TYPE                  303                            44
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ITGAV MUTATED                       2                              0
  ITGAV WILD-TYPE                   104                             10
D571V10, multiclass
                                clus
vv                               ITGAV MUTATED ITGAV WILD-TYPE
  COLON ADENOCARCINOMA                      12             303
  COLON MUCINOUS ADENOCARCINOMA              3              44
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  ITGAV MUTATED    13   1   1   1
  ITGAV WILD-TYPE 332   3  30  24
D571V11, multiclass
    clus
vv   ITGAV MUTATED ITGAV WILD-TYPE
  R0            13             332
  R1             1               3
  R2             1              30
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D571V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ITGAV MUTATED                                  0     1
  ITGAV WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ITGAV MUTATED                           1    10
  ITGAV WILD-TYPE                        21   216
D571V13, multiclass
                                  clus
vv                                 ITGAV MUTATED ITGAV WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                       10             216
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(572) Variable = TAF12 MUTATION ANALYSIS
D572V1, survival
                 sevent
clus2               0   1
  TAF12 MUTATED     4   0
  TAF12 WILD-TYPE 374  93
  TAF12 MUTATED TAF12 WILD-TYPE 
              4             467 
  TAF12 MUTATED TAF12 WILD-TYPE 
              0              93 
$`TAF12 MUTATED`
TCGA-AA-3662 TCGA-CM-5349 TCGA-CM-6165 TCGA-EI-6506 
        6.05        30.08        16.04        20.55 

$`TAF12 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6166 TCGA-CM-6167 
       15.02        12.00         2.96        29.03        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6507 
       57.24        24.13        51.48        32.61         0.49        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  TAF12 MUTATED TAF12 WILD-TYPE 
           6.05            0.00 
  TAF12 MUTATED TAF12 WILD-TYPE 
          30.08          148.01 
  TAF12 MUTATED TAF12 WILD-TYPE 
         18.295          20.190 
[1] "6.0 - 30.1 (18.3)"  "0.0 - 148.0 (20.2)"
[1] "hr="     "3300000"
D572V2, continuous
D572V3, binary
                 cls
clus                0   1
  TAF12 MUTATED     3   1
  TAF12 WILD-TYPE 363 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TAF12 MUTATED      3    1
  TAF12 WILD-TYPE  363  118
        clus
vv       TAF12 MUTATED TAF12 WILD-TYPE
  COLON              3             363
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TAF12 MUTATED         0        0        0         3         0         0
  TAF12 WILD-TYPE      91        1       32       135        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TAF12 MUTATED           0          0          0          0        1         0
  TAF12 WILD-TYPE        24         11         59         42       47        18
                 vv
clus              STAGE IVB
  TAF12 MUTATED           0
  TAF12 WILD-TYPE         1
D572V4, multiclass
            clus
vv           TAF12 MUTATED TAF12 WILD-TYPE
  STAGE I                0              91
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              3             135
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             0              42
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  TAF12 MUTATED     0   0   3   1
  TAF12 WILD-TYPE  17  92 326  49
D572V5, multiclass
    clus
vv   TAF12 MUTATED TAF12 WILD-TYPE
  T1             0              17
  T2             0              92
  T3             3             326
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  TAF12 MUTATED     3   0   1
  TAF12 WILD-TYPE 284 113  86
D572V6, multiclass
    clus
vv   TAF12 MUTATED TAF12 WILD-TYPE
  N0             3             284
  N1             0             113
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D572V7, binary
                 cls
clus                0   1
  TAF12 MUTATED     3   1
  TAF12 WILD-TYPE 372  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TAF12 MUTATED      3    1
  TAF12 WILD-TYPE  372   64
   clus
vv  TAF12 MUTATED TAF12 WILD-TYPE
  0             3             372
  1             1              64
[1] 2 2
[1] FALSE
D572V8, binary
                 cls
clus                0   1
  TAF12 MUTATED     3   1
  TAF12 WILD-TYPE 222 263
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TAF12 MUTATED      3    1
  TAF12 WILD-TYPE  222  263
        clus
vv       TAF12 MUTATED TAF12 WILD-TYPE
  FEMALE             3             222
  MALE               1             263
[1] 2 2
[1] FALSE
D572V9, binary
                 cls
clus                0   1
  TAF12 MUTATED     4   0
  TAF12 WILD-TYPE 346  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TAF12 MUTATED      4    0
  TAF12 WILD-TYPE  346   22
     clus
vv    TAF12 MUTATED TAF12 WILD-TYPE
  NO              4             346
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  TAF12 MUTATED                      3                             0
  TAF12 WILD-TYPE                  312                            47
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  TAF12 MUTATED                       1                              0
  TAF12 WILD-TYPE                   105                             10
D572V10, multiclass
                                clus
vv                               TAF12 MUTATED TAF12 WILD-TYPE
  COLON ADENOCARCINOMA                       3             312
  COLON MUCINOUS ADENOCARCINOMA              0              47
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  TAF12 MUTATED     3   0   1   0
  TAF12 WILD-TYPE 342   4  30  25
D572V11, multiclass
    clus
vv   TAF12 MUTATED TAF12 WILD-TYPE
  R0             3             342
  R1             0               4
  R2             1              30
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D572V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TAF12 MUTATED                                  0     0
  TAF12 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  TAF12 MUTATED                           0     3
  TAF12 WILD-TYPE                        22   223
D572V13, multiclass
                                  clus
vv                                 TAF12 MUTATED TAF12 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        3             223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(573) Variable = ZNF473 MUTATION ANALYSIS
D573V1, survival
                  sevent
clus2                0   1
  ZNF473 MUTATED    12   3
  ZNF473 WILD-TYPE 366  90
  ZNF473 MUTATED ZNF473 WILD-TYPE 
              15              456 
  ZNF473 MUTATED ZNF473 WILD-TYPE 
               3               90 
$`ZNF473 MUTATED`
TCGA-A6-2676 TCGA-A6-6141 TCGA-AA-3949 TCGA-AA-3975 TCGA-AA-A00N TCGA-CA-6718 
       42.90         8.38        26.01        34.06         4.01        10.06 
TCGA-CK-4950 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5864 TCGA-CM-6678 TCGA-D5-5540 
       85.45        30.08        32.02        15.02        11.01        56.09 
TCGA-G4-6588 TCGA-AG-A002 TCGA-AH-6644 
       26.17        20.98         0.72 

$`ZNF473 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 
       22.06        32.71        27.09        22.52        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       12.99        24.00        33.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 
        3.25         3.29         0.07        12.20        12.76        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
       17.56       148.01        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
       15.02         5.03        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.08        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       19.59        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       13.78        35.80        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  ZNF473 MUTATED ZNF473 WILD-TYPE 
            0.72             0.00 
  ZNF473 MUTATED ZNF473 WILD-TYPE 
           85.45           148.01 
  ZNF473 MUTATED ZNF473 WILD-TYPE 
          26.010           20.085 
[1] "0.7 - 85.5 (26.0)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1"  
D573V2, continuous
D573V3, binary
                  cls
clus                 0   1
  ZNF473 MUTATED    14   2
  ZNF473 WILD-TYPE 352 117
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF473 MUTATED     14    2
  ZNF473 WILD-TYPE  352  117
        clus
vv       ZNF473 MUTATED ZNF473 WILD-TYPE
  COLON              14              352
  RECTUM              2              117
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZNF473 MUTATED         3        0        0         7         2         0
  ZNF473 WILD-TYPE      88        1       32       131         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF473 MUTATED           0          0          2          0        0
  ZNF473 WILD-TYPE        24         11         57         42       48
                  vv
clus               STAGE IVA STAGE IVB
  ZNF473 MUTATED           1         0
  ZNF473 WILD-TYPE        17         1
D573V4, multiclass
            clus
vv           ZNF473 MUTATED ZNF473 WILD-TYPE
  STAGE I                 3               88
  STAGE IA                0                1
  STAGE II                0               32
  STAGE IIA               7              131
  STAGE IIB               2                8
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              2               57
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               1               17
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZNF473 MUTATED     0   3  10   3
  ZNF473 WILD-TYPE  17  89 319  47
D573V5, multiclass
    clus
vv   ZNF473 MUTATED ZNF473 WILD-TYPE
  T1              0               17
  T2              3               89
  T3             10              319
  T4              3               47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  ZNF473 MUTATED    12   3   0
  ZNF473 WILD-TYPE 275 110  87
D573V6, multiclass
    clus
vv   ZNF473 MUTATED ZNF473 WILD-TYPE
  N0             12              275
  N1              3              110
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D573V7, binary
                  cls
clus                 0   1
  ZNF473 MUTATED    14   1
  ZNF473 WILD-TYPE 361  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF473 MUTATED     14    1
  ZNF473 WILD-TYPE  361   64
   clus
vv  ZNF473 MUTATED ZNF473 WILD-TYPE
  0             14              361
  1              1               64
[1] 2 2
[1] FALSE
D573V8, binary
                  cls
clus                 0   1
  ZNF473 MUTATED     7   9
  ZNF473 WILD-TYPE 218 255
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF473 MUTATED      7    9
  ZNF473 WILD-TYPE  218  255
        clus
vv       ZNF473 MUTATED ZNF473 WILD-TYPE
  FEMALE              7              218
  MALE                9              255
[1] 2 2
[1] FALSE
D573V9, binary
                  cls
clus                 0   1
  ZNF473 MUTATED    13   0
  ZNF473 WILD-TYPE 337  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF473 MUTATED     13    0
  ZNF473 WILD-TYPE  337   22
     clus
vv    ZNF473 MUTATED ZNF473 WILD-TYPE
  NO              13              337
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ZNF473 MUTATED                     12                             2
  ZNF473 WILD-TYPE                  303                            45
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ZNF473 MUTATED                       2                              0
  ZNF473 WILD-TYPE                   104                             10
D573V10, multiclass
                                clus
vv                               ZNF473 MUTATED ZNF473 WILD-TYPE
  COLON ADENOCARCINOMA                       12              303
  COLON MUCINOUS ADENOCARCINOMA               2               45
  RECTAL ADENOCARCINOMA                       2              104
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ZNF473 MUTATED    12   1   0   1
  ZNF473 WILD-TYPE 333   3  31  24
D573V11, multiclass
    clus
vv   ZNF473 MUTATED ZNF473 WILD-TYPE
  R0             12              333
  R1              1                3
  R2              0               31
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D573V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF473 MUTATED                                  0     1
  ZNF473 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZNF473 MUTATED                           2     8
  ZNF473 WILD-TYPE                        20   218
D573V13, multiclass
                                  clus
vv                                 ZNF473 MUTATED ZNF473 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     2               20
  WHITE                                         8              218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(574) Variable = ENPP3 MUTATION ANALYSIS
D574V1, survival
                 sevent
clus2               0   1
  ENPP3 MUTATED     8   3
  ENPP3 WILD-TYPE 370  90
  ENPP3 MUTATED ENPP3 WILD-TYPE 
             11             460 
  ENPP3 MUTATED ENPP3 WILD-TYPE 
              3              90 
$`ENPP3 MUTATED`
TCGA-AA-3555 TCGA-AA-3713 TCGA-AA-A00N TCGA-AD-6964 TCGA-AZ-6598 TCGA-CA-6717 
       29.95        19.04         4.01        10.88        49.41        12.76 
TCGA-CM-5344 TCGA-D5-6928 TCGA-DM-A1HB TCGA-AG-A002 TCGA-EI-6507 
       22.03        11.64       135.65        20.98        19.96 

$`ENPP3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 
       21.01        13.02        24.00        17.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
        0.79         0.72         5.79        22.42        27.42         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        88.21         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07        12.20        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5348 
       20.02        37.02        25.02        13.02        29.06        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
        9.44         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6508 
       24.13        51.48        32.61         0.49        20.55        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  ENPP3 MUTATED ENPP3 WILD-TYPE 
           4.01            0.00 
  ENPP3 MUTATED ENPP3 WILD-TYPE 
         135.65          148.01 
  ENPP3 MUTATED ENPP3 WILD-TYPE 
         19.960          20.235 
[1] "4.0 - 135.7 (20.0)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.3"
D574V2, continuous
D574V3, binary
                 cls
clus                0   1
  ENPP3 MUTATED     9   2
  ENPP3 WILD-TYPE 357 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ENPP3 MUTATED      9    2
  ENPP3 WILD-TYPE  357  117
        clus
vv       ENPP3 MUTATED ENPP3 WILD-TYPE
  COLON              9             357
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ENPP3 MUTATED         1        0        1         4         1         0
  ENPP3 WILD-TYPE      90        1       31       134         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ENPP3 MUTATED           0          0          2          0        1         0
  ENPP3 WILD-TYPE        24         11         57         42       47        18
                 vv
clus              STAGE IVB
  ENPP3 MUTATED           0
  ENPP3 WILD-TYPE         1
D574V4, multiclass
            clus
vv           ENPP3 MUTATED ENPP3 WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              4             134
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             2              57
  STAGE IIIC             0              42
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ENPP3 MUTATED     0   1   8   2
  ENPP3 WILD-TYPE  17  91 321  48
D574V5, multiclass
    clus
vv   ENPP3 MUTATED ENPP3 WILD-TYPE
  T1             0              17
  T2             1              91
  T3             8             321
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  ENPP3 MUTATED     8   2   1
  ENPP3 WILD-TYPE 279 111  86
D574V6, multiclass
    clus
vv   ENPP3 MUTATED ENPP3 WILD-TYPE
  N0             8             279
  N1             2             111
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D574V7, binary
                 cls
clus                0   1
  ENPP3 MUTATED     8   1
  ENPP3 WILD-TYPE 367  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ENPP3 MUTATED      8    1
  ENPP3 WILD-TYPE  367   64
   clus
vv  ENPP3 MUTATED ENPP3 WILD-TYPE
  0             8             367
  1             1              64
[1] 2 2
[1] FALSE
D574V8, binary
                 cls
clus                0   1
  ENPP3 MUTATED     3   8
  ENPP3 WILD-TYPE 222 256
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ENPP3 MUTATED      3    8
  ENPP3 WILD-TYPE  222  256
        clus
vv       ENPP3 MUTATED ENPP3 WILD-TYPE
  FEMALE             3             222
  MALE               8             256
[1] 2 2
[1] FALSE
D574V9, binary
                 cls
clus                0   1
  ENPP3 MUTATED     8   1
  ENPP3 WILD-TYPE 342  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ENPP3 MUTATED      8    1
  ENPP3 WILD-TYPE  342   21
     clus
vv    ENPP3 MUTATED ENPP3 WILD-TYPE
  NO              8             342
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ENPP3 MUTATED                      4                             4
  ENPP3 WILD-TYPE                  311                            43
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ENPP3 MUTATED                       2                              0
  ENPP3 WILD-TYPE                   104                             10
D574V10, multiclass
                                clus
vv                               ENPP3 MUTATED ENPP3 WILD-TYPE
  COLON ADENOCARCINOMA                       4             311
  COLON MUCINOUS ADENOCARCINOMA              4              43
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  ENPP3 MUTATED     6   0   1   1
  ENPP3 WILD-TYPE 339   4  30  24
D574V11, multiclass
    clus
vv   ENPP3 MUTATED ENPP3 WILD-TYPE
  R0             6             339
  R1             0               4
  R2             1              30
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D574V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ENPP3 MUTATED                                  0     1
  ENPP3 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ENPP3 MUTATED                           0     6
  ENPP3 WILD-TYPE                        22   220
D574V13, multiclass
                                  clus
vv                                 ENPP3 MUTATED ENPP3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        6             220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(575) Variable = OR4N4 MUTATION ANALYSIS
D575V1, survival
                 sevent
clus2               0   1
  OR4N4 MUTATED    13   5
  OR4N4 WILD-TYPE 365  88
  OR4N4 MUTATED OR4N4 WILD-TYPE 
             18             453 
  OR4N4 MUTATED OR4N4 WILD-TYPE 
              5              88 
$`OR4N4 MUTATED`
TCGA-A6-6137 TCGA-AA-3655 TCGA-AA-3715 TCGA-AA-A00N TCGA-AA-A010 TCGA-CM-6162 
       27.09        61.02        19.04         4.01        34.98        12.00 
TCGA-CM-6676 TCGA-DM-A0XF TCGA-DM-A1HB TCGA-F4-6460 TCGA-G4-6303 TCGA-G4-6586 
       11.08        38.20       135.65        31.96        65.85        35.80 
TCGA-AF-2693 TCGA-AG-3892 TCGA-AG-A002 TCGA-AH-6643 TCGA-EI-6508 TCGA-F5-6465 
       19.10        13.02        20.98         0.69        20.91        49.51 

$`OR4N4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        22.06        32.71        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       19.99        13.94        19.99        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 
       15.02        15.02        17.03        15.02         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6677 TCGA-CM-6678 
       14.04        11.01        12.95        13.05        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
       10.26       119.70        24.43       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
      117.07        98.24         8.61        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6304 
        0.53        47.41        35.31       133.18        74.56        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       22.09        13.78        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3913 
       24.13        39.48        43.04        13.55        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       17.03        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6644 TCGA-CI-6619 
      117.11        38.56         1.45        17.49         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
       18.28         9.96        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  OR4N4 MUTATED OR4N4 WILD-TYPE 
           0.69            0.00 
  OR4N4 MUTATED OR4N4 WILD-TYPE 
         135.65          148.01 
  OR4N4 MUTATED OR4N4 WILD-TYPE 
         24.035          20.050 
[1] "0.7 - 135.7 (24.0)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.2"
D575V2, continuous
D575V3, binary
                 cls
clus                0   1
  OR4N4 MUTATED    12   5
  OR4N4 WILD-TYPE 354 114
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR4N4 MUTATED     12    5
  OR4N4 WILD-TYPE  354  114
        clus
vv       OR4N4 MUTATED OR4N4 WILD-TYPE
  COLON             12             354
  RECTUM             5             114
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  OR4N4 MUTATED         4        0        2         2         2         0
  OR4N4 WILD-TYPE      87        1       30       136         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  OR4N4 MUTATED           0          0          5          2        1         0
  OR4N4 WILD-TYPE        24         11         54         40       47        18
                 vv
clus              STAGE IVB
  OR4N4 MUTATED           0
  OR4N4 WILD-TYPE         1
D575V4, multiclass
            clus
vv           OR4N4 MUTATED OR4N4 WILD-TYPE
  STAGE I                4              87
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA              2             136
  STAGE IIB              2               8
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             5              54
  STAGE IIIC             2              40
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  OR4N4 MUTATED     1   3  12   2
  OR4N4 WILD-TYPE  16  89 317  48
D575V5, multiclass
    clus
vv   OR4N4 MUTATED OR4N4 WILD-TYPE
  T1             1              16
  T2             3              89
  T3            12             317
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  OR4N4 MUTATED    10   6   2
  OR4N4 WILD-TYPE 277 107  85
D575V6, multiclass
    clus
vv   OR4N4 MUTATED OR4N4 WILD-TYPE
  N0            10             277
  N1             6             107
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D575V7, binary
                 cls
clus                0   1
  OR4N4 MUTATED    16   1
  OR4N4 WILD-TYPE 359  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR4N4 MUTATED     16    1
  OR4N4 WILD-TYPE  359   64
   clus
vv  OR4N4 MUTATED OR4N4 WILD-TYPE
  0            16             359
  1             1              64
[1] 2 2
[1] FALSE
D575V8, binary
                 cls
clus                0   1
  OR4N4 MUTATED     9   9
  OR4N4 WILD-TYPE 216 255
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR4N4 MUTATED      9    9
  OR4N4 WILD-TYPE  216  255
        clus
vv       OR4N4 MUTATED OR4N4 WILD-TYPE
  FEMALE             9             216
  MALE               9             255
[1] 2 2
[1] FALSE
D575V9, binary
                 cls
clus                0   1
  OR4N4 MUTATED    14   0
  OR4N4 WILD-TYPE 336  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR4N4 MUTATED     14    0
  OR4N4 WILD-TYPE  336   22
     clus
vv    OR4N4 MUTATED OR4N4 WILD-TYPE
  NO             14             336
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  OR4N4 MUTATED                      8                             2
  OR4N4 WILD-TYPE                  307                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  OR4N4 MUTATED                       5                              0
  OR4N4 WILD-TYPE                   101                             10
D575V10, multiclass
                                clus
vv                               OR4N4 MUTATED OR4N4 WILD-TYPE
  COLON ADENOCARCINOMA                       8             307
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      5             101
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  OR4N4 MUTATED    14   0   0   0
  OR4N4 WILD-TYPE 331   4  31  25
D575V11, multiclass
    clus
vv   OR4N4 MUTATED OR4N4 WILD-TYPE
  R0            14             331
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D575V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OR4N4 MUTATED                                  0     0
  OR4N4 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  OR4N4 MUTATED                           0    12
  OR4N4 WILD-TYPE                        22   214
D575V13, multiclass
                                  clus
vv                                 OR4N4 MUTATED OR4N4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                       12             214
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(576) Variable = CHEK2 MUTATION ANALYSIS
D576V1, survival
                 sevent
clus2               0   1
  CHEK2 MUTATED     8   2
  CHEK2 WILD-TYPE 370  91
  CHEK2 MUTATED CHEK2 WILD-TYPE 
             10             461 
  CHEK2 MUTATED CHEK2 WILD-TYPE 
              2              91 
$`CHEK2 MUTATED`
TCGA-A6-6653 TCGA-AA-3815 TCGA-AA-A01Q TCGA-AZ-6608 TCGA-CA-6717 TCGA-CA-6718 
       24.39        33.04         1.02         1.61        12.76        10.06 
TCGA-CM-4743 TCGA-D5-6529 TCGA-D5-6928 TCGA-G4-6317 
       23.05        20.19        11.64        36.00 

$`CHEK2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
       25.08        25.18        24.16        21.76        24.69        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       10.06        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        31.00        38.07        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 
      100.01        29.56         5.23        11.74         3.19        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 
        3.06         3.25         3.29         0.07        12.20        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 
        9.99        21.14        82.95         1.91       124.27        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       55.92        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       61.91        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  CHEK2 MUTATED CHEK2 WILD-TYPE 
           1.02            0.00 
  CHEK2 MUTATED CHEK2 WILD-TYPE 
          36.00          148.01 
  CHEK2 MUTATED CHEK2 WILD-TYPE 
         16.475          20.280 
[1] "1.0 - 36.0 (16.5)"  "0.0 - 148.0 (20.3)"
[1] "hr=" "1.6"
D576V2, continuous
D576V3, binary
                 cls
clus                0   1
  CHEK2 MUTATED    10   0
  CHEK2 WILD-TYPE 356 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CHEK2 MUTATED     10    0
  CHEK2 WILD-TYPE  356  119
        clus
vv       CHEK2 MUTATED CHEK2 WILD-TYPE
  COLON             10             356
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CHEK2 MUTATED         1        0        1         6         0         0
  CHEK2 WILD-TYPE      90        1       31       132        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CHEK2 MUTATED           0          1          0          1        0         0
  CHEK2 WILD-TYPE        24         10         59         41       48        18
                 vv
clus              STAGE IVB
  CHEK2 MUTATED           0
  CHEK2 WILD-TYPE         1
D576V4, multiclass
            clus
vv           CHEK2 MUTATED CHEK2 WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              6             132
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             1              10
  STAGE IIIB             0              59
  STAGE IIIC             1              41
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CHEK2 MUTATED     0   2   8   0
  CHEK2 WILD-TYPE  17  90 321  50
D576V5, multiclass
    clus
vv   CHEK2 MUTATED CHEK2 WILD-TYPE
  T1             0              17
  T2             2              90
  T3             8             321
  T4             0              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  CHEK2 MUTATED     8   1   1
  CHEK2 WILD-TYPE 279 112  86
D576V6, multiclass
    clus
vv   CHEK2 MUTATED CHEK2 WILD-TYPE
  N0             8             279
  N1             1             112
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D576V7, binary
                 cls
clus                0   1
  CHEK2 MUTATED     9   0
  CHEK2 WILD-TYPE 366  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CHEK2 MUTATED      9    0
  CHEK2 WILD-TYPE  366   65
   clus
vv  CHEK2 MUTATED CHEK2 WILD-TYPE
  0             9             366
  1             0              65
[1] 2 2
[1] FALSE
D576V8, binary
                 cls
clus                0   1
  CHEK2 MUTATED     4   6
  CHEK2 WILD-TYPE 221 258
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CHEK2 MUTATED      4    6
  CHEK2 WILD-TYPE  221  258
        clus
vv       CHEK2 MUTATED CHEK2 WILD-TYPE
  FEMALE             4             221
  MALE               6             258
[1] 2 2
[1] FALSE
D576V9, binary
                 cls
clus                0   1
  CHEK2 MUTATED     9   0
  CHEK2 WILD-TYPE 341  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CHEK2 MUTATED      9    0
  CHEK2 WILD-TYPE  341   22
     clus
vv    CHEK2 MUTATED CHEK2 WILD-TYPE
  NO              9             341
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CHEK2 MUTATED                      8                             2
  CHEK2 WILD-TYPE                  307                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CHEK2 MUTATED                       0                              0
  CHEK2 WILD-TYPE                   106                             10
D576V10, multiclass
                                clus
vv                               CHEK2 MUTATED CHEK2 WILD-TYPE
  COLON ADENOCARCINOMA                       8             307
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  CHEK2 MUTATED     6   0   0   2
  CHEK2 WILD-TYPE 339   4  31  23
D576V11, multiclass
    clus
vv   CHEK2 MUTATED CHEK2 WILD-TYPE
  R0             6             339
  R1             0               4
  R2             0              31
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D576V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CHEK2 MUTATED                                  0     2
  CHEK2 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CHEK2 MUTATED                           0     6
  CHEK2 WILD-TYPE                        22   220
D576V13, multiclass
                                  clus
vv                                 CHEK2 MUTATED CHEK2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               9
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        6             220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(577) Variable = GTF2IRD2 MUTATION ANALYSIS
D577V1, survival
                    sevent
clus2                  0   1
  GTF2IRD2 MUTATED     6   0
  GTF2IRD2 WILD-TYPE 372  93
  GTF2IRD2 MUTATED GTF2IRD2 WILD-TYPE 
                 6                465 
  GTF2IRD2 MUTATED GTF2IRD2 WILD-TYPE 
                 0                 93 
$`GTF2IRD2 MUTATED`
TCGA-CA-5797 TCGA-CA-6717 TCGA-CM-5860 TCGA-CM-6165 TCGA-F4-6856 TCGA-G4-6588 
        3.29        12.76        32.02        16.04        35.31        26.17 

$`GTF2IRD2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07        12.20        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
       12.00         2.96        29.03        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
        0.53        47.41       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       22.09        13.78        35.80        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  GTF2IRD2 MUTATED GTF2IRD2 WILD-TYPE 
              3.29               0.00 
  GTF2IRD2 MUTATED GTF2IRD2 WILD-TYPE 
             35.31             148.01 
  GTF2IRD2 MUTATED GTF2IRD2 WILD-TYPE 
            21.105             20.190 
[1] "3.3 - 35.3 (21.1)"  "0.0 - 148.0 (20.2)"
[1] "hr="     "3300000"
D577V2, continuous
D577V3, binary
                    cls
clus                   0   1
  GTF2IRD2 MUTATED     6   0
  GTF2IRD2 WILD-TYPE 360 119
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  GTF2IRD2 MUTATED      6    0
  GTF2IRD2 WILD-TYPE  360  119
        clus
vv       GTF2IRD2 MUTATED GTF2IRD2 WILD-TYPE
  COLON                 6                360
  RECTUM                0                119
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GTF2IRD2 MUTATED         1        0        0         5         0         0
  GTF2IRD2 WILD-TYPE      90        1       32       133        10         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GTF2IRD2 MUTATED           0          0          0          0        0
  GTF2IRD2 WILD-TYPE        24         11         59         42       48
                    vv
clus                 STAGE IVA STAGE IVB
  GTF2IRD2 MUTATED           0         0
  GTF2IRD2 WILD-TYPE        18         1
D577V4, multiclass
            clus
vv           GTF2IRD2 MUTATED GTF2IRD2 WILD-TYPE
  STAGE I                   1                 90
  STAGE IA                  0                  1
  STAGE II                  0                 32
  STAGE IIA                 5                133
  STAGE IIB                 0                 10
  STAGE IIC                 0                  1
  STAGE III                 0                 24
  STAGE IIIA                0                 11
  STAGE IIIB                0                 59
  STAGE IIIC                0                 42
  STAGE IV                  0                 48
  STAGE IVA                 0                 18
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  GTF2IRD2 MUTATED     0   1   5   0
  GTF2IRD2 WILD-TYPE  17  91 324  50
D577V5, multiclass
    clus
vv   GTF2IRD2 MUTATED GTF2IRD2 WILD-TYPE
  T1                0                 17
  T2                1                 91
  T3                5                324
  T4                0                 50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  GTF2IRD2 MUTATED     6   0   0
  GTF2IRD2 WILD-TYPE 281 113  87
D577V6, multiclass
    clus
vv   GTF2IRD2 MUTATED GTF2IRD2 WILD-TYPE
  N0                6                281
  N1                0                113
  N2                0                 87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D577V7, binary
                    cls
clus                   0   1
  GTF2IRD2 MUTATED     6   0
  GTF2IRD2 WILD-TYPE 369  65
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  GTF2IRD2 MUTATED      6    0
  GTF2IRD2 WILD-TYPE  369   65
   clus
vv  GTF2IRD2 MUTATED GTF2IRD2 WILD-TYPE
  0                6                369
  1                0                 65
[1] 2 2
[1] FALSE
D577V8, binary
                    cls
clus                   0   1
  GTF2IRD2 MUTATED     1   5
  GTF2IRD2 WILD-TYPE 224 259
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  GTF2IRD2 MUTATED      1    5
  GTF2IRD2 WILD-TYPE  224  259
        clus
vv       GTF2IRD2 MUTATED GTF2IRD2 WILD-TYPE
  FEMALE                1                224
  MALE                  5                259
[1] 2 2
[1] FALSE
D577V9, binary
                    cls
clus                   0   1
  GTF2IRD2 MUTATED     6   0
  GTF2IRD2 WILD-TYPE 344  22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  GTF2IRD2 MUTATED      6    0
  GTF2IRD2 WILD-TYPE  344   22
     clus
vv    GTF2IRD2 MUTATED GTF2IRD2 WILD-TYPE
  NO                 6                344
  YES                0                 22
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  GTF2IRD2 MUTATED                      4                             2
  GTF2IRD2 WILD-TYPE                  311                            45
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  GTF2IRD2 MUTATED                       0                              0
  GTF2IRD2 WILD-TYPE                   106                             10
D577V10, multiclass
                                clus
vv                               GTF2IRD2 MUTATED GTF2IRD2 WILD-TYPE
  COLON ADENOCARCINOMA                          4                311
  COLON MUCINOUS ADENOCARCINOMA                 2                 45
  RECTAL ADENOCARCINOMA                         0                106
  RECTAL MUCINOUS ADENOCARCINOMA                0                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  GTF2IRD2 MUTATED     5   0   0   1
  GTF2IRD2 WILD-TYPE 340   4  31  24
D577V11, multiclass
    clus
vv   GTF2IRD2 MUTATED GTF2IRD2 WILD-TYPE
  R0                5                340
  R1                0                  4
  R2                0                 31
  RX                1                 24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D577V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GTF2IRD2 MUTATED                                  0     2
  GTF2IRD2 WILD-TYPE                                1     9
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  GTF2IRD2 MUTATED                           0     4
  GTF2IRD2 WILD-TYPE                        22   222
D577V13, multiclass
                                  clus
vv                                 GTF2IRD2 MUTATED GTF2IRD2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           2                  9
  BLACK OR AFRICAN AMERICAN                       0                 22
  WHITE                                           4                222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(578) Variable = AKAP9 MUTATION ANALYSIS
D578V1, survival
                 sevent
clus2               0   1
  AKAP9 MUTATED    37  11
  AKAP9 WILD-TYPE 341  82
  AKAP9 MUTATED AKAP9 WILD-TYPE 
             48             423 
  AKAP9 MUTATED AKAP9 WILD-TYPE 
             11              82 
$`AKAP9 MUTATED`
TCGA-A6-2676 TCGA-A6-5661 TCGA-A6-5665 TCGA-A6-6138 TCGA-A6-6142 TCGA-AA-3492 
       42.90        33.53        22.06        22.52        25.08         3.02 
TCGA-AA-3510 TCGA-AA-3532 TCGA-AA-3543 TCGA-AA-3555 TCGA-AA-3660 TCGA-AA-3672 
       63.98        29.00         0.99        29.95        78.08         0.92 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3864 TCGA-AA-3877 
       85.05        26.99        19.04        19.04        53.00        31.00 
TCGA-AA-3947 TCGA-AA-A00N TCGA-AA-A010 TCGA-AD-6964 TCGA-AY-6197 TCGA-AZ-4315 
       33.01         4.01        34.98        10.88        21.44        58.39 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        6.77        12.10       100.01        12.20        12.76        10.06 
TCGA-CK-4947 TCGA-CM-4743 TCGA-CM-5861 TCGA-D5-6534 TCGA-D5-6923 TCGA-D5-6926 
       17.56        23.05        15.02        43.27        12.43         9.04 
TCGA-DM-A1DB TCGA-F4-6570 TCGA-G4-6310 TCGA-G4-6588 TCGA-G4-6628 TCGA-AF-2693 
       44.32         6.18        63.62        26.17        79.69        19.10 
TCGA-AF-4110 TCGA-AG-3892 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A02N TCGA-CL-5918 
       14.50        13.02        20.98        13.94        61.97         7.17 

$`AKAP9 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 
       31.63        30.44        29.19        23.61        22.09        32.71 
TCGA-A6-6137 TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 
       27.09         8.38        25.18        24.16        21.76        24.69 
TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 
       24.39        23.87        20.12        19.66        20.28         7.04 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3534 TCGA-AA-3538 
       19.07         0.00        19.07        34.03        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
       12.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       17.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       61.02         6.05         6.97        54.02         2.01        14.01 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       19.00        36.00         5.03        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       31.07        30.05        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 
       18.05         2.01        12.99        24.00        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
        0.79         0.72         5.79        22.42        27.42         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 
       14.50        27.09        16.31         0.95        33.01        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
       49.41        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6719 
       12.69         3.06         3.25         3.29         0.07        14.30 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 
       21.14        82.95         1.91       124.27        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       32.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       18.25         1.32        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
       14.30         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       35.74        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 
       61.91        36.00        22.09        13.78        35.80        91.79 
TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 
       46.75        24.13        39.48        43.04        13.55        34.49 
TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       10.39        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       17.03        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
        1.94        38.96        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        6.97         4.73        78.12        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  AKAP9 MUTATED AKAP9 WILD-TYPE 
           0.92            0.00 
  AKAP9 MUTATED AKAP9 WILD-TYPE 
         100.01          148.01 
  AKAP9 MUTATED AKAP9 WILD-TYPE 
          21.75           20.05 
[1] "0.9 - 100.0 (21.8)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1"  
D578V2, continuous
D578V3, binary
                 cls
clus                0   1
  AKAP9 MUTATED    43   5
  AKAP9 WILD-TYPE 323 114
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AKAP9 MUTATED     43    5
  AKAP9 WILD-TYPE  323  114
        clus
vv       AKAP9 MUTATED AKAP9 WILD-TYPE
  COLON             43             323
  RECTUM             5             114
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  AKAP9 MUTATED        10        0        7        18         4         0
  AKAP9 WILD-TYPE      81        1       25       120         6         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AKAP9 MUTATED           2          0          3          0        3         2
  AKAP9 WILD-TYPE        22         11         56         42       45        16
                 vv
clus              STAGE IVB
  AKAP9 MUTATED           0
  AKAP9 WILD-TYPE         1
D578V4, multiclass
            clus
vv           AKAP9 MUTATED AKAP9 WILD-TYPE
  STAGE I               10              81
  STAGE IA               0               1
  STAGE II               7              25
  STAGE IIA             18             120
  STAGE IIB              4               6
  STAGE IIC              0               1
  STAGE III              2              22
  STAGE IIIA             0              11
  STAGE IIIB             3              56
  STAGE IIIC             0              42
  STAGE IV               3              45
  STAGE IVA              2              16
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  AKAP9 MUTATED     2   8  30  10
  AKAP9 WILD-TYPE  15  84 299  40
D578V5, multiclass
    clus
vv   AKAP9 MUTATED AKAP9 WILD-TYPE
  T1             2              15
  T2             8              84
  T3            30             299
  T4            10              40
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  AKAP9 MUTATED    41   6   3
  AKAP9 WILD-TYPE 246 107  84
D578V6, multiclass
    clus
vv   AKAP9 MUTATED AKAP9 WILD-TYPE
  N0            41             246
  N1             6             107
  N2             3              84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D578V7, binary
                 cls
clus                0   1
  AKAP9 MUTATED    40   4
  AKAP9 WILD-TYPE 335  61
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AKAP9 MUTATED     40    4
  AKAP9 WILD-TYPE  335   61
   clus
vv  AKAP9 MUTATED AKAP9 WILD-TYPE
  0            40             335
  1             4              61
[1] 2 2
[1] FALSE
D578V8, binary
                 cls
clus                0   1
  AKAP9 MUTATED    22  28
  AKAP9 WILD-TYPE 203 236
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AKAP9 MUTATED     22   28
  AKAP9 WILD-TYPE  203  236
        clus
vv       AKAP9 MUTATED AKAP9 WILD-TYPE
  FEMALE            22             203
  MALE              28             236
[1] 2 2
[1] FALSE
D578V9, binary
                 cls
clus                0   1
  AKAP9 MUTATED    41   3
  AKAP9 WILD-TYPE 309  19
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AKAP9 MUTATED     41    3
  AKAP9 WILD-TYPE  309   19
     clus
vv    AKAP9 MUTATED AKAP9 WILD-TYPE
  NO             41             309
  YES             3              19
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  AKAP9 MUTATED                     35                             8
  AKAP9 WILD-TYPE                  280                            39
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  AKAP9 MUTATED                       4                              1
  AKAP9 WILD-TYPE                   102                              9
D578V10, multiclass
                                clus
vv                               AKAP9 MUTATED AKAP9 WILD-TYPE
  COLON ADENOCARCINOMA                      35             280
  COLON MUCINOUS ADENOCARCINOMA              8              39
  RECTAL ADENOCARCINOMA                      4             102
  RECTAL MUCINOUS ADENOCARCINOMA             1               9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  AKAP9 MUTATED    35   0   2   5
  AKAP9 WILD-TYPE 310   4  29  20
D578V11, multiclass
    clus
vv   AKAP9 MUTATED AKAP9 WILD-TYPE
  R0            35             310
  R1             0               4
  R2             2              29
  RX             5              20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D578V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AKAP9 MUTATED                                  0     3
  AKAP9 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  AKAP9 MUTATED                           2    23
  AKAP9 WILD-TYPE                        20   203
D578V13, multiclass
                                  clus
vv                                 AKAP9 MUTATED AKAP9 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        3               8
  BLACK OR AFRICAN AMERICAN                    2              20
  WHITE                                       23             203
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(579) Variable = ABI3BP MUTATION ANALYSIS
D579V1, survival
                  sevent
clus2                0   1
  ABI3BP MUTATED    16   6
  ABI3BP WILD-TYPE 362  87
  ABI3BP MUTATED ABI3BP WILD-TYPE 
              22              449 
  ABI3BP MUTATED ABI3BP WILD-TYPE 
               6               87 
$`ABI3BP MUTATED`
TCGA-A6-6654 TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01R TCGA-AY-4071 
       23.87        25.02         4.01        34.98        35.01         0.95 
TCGA-AZ-6598 TCGA-AZ-6601 TCGA-CA-6717 TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-6164 
       49.41       100.01        12.76        13.02        22.03        29.03 
TCGA-D5-6536 TCGA-D5-6926 TCGA-D5-6929 TCGA-DM-A0XF TCGA-F4-6570 TCGA-G4-6307 
       17.85         9.04         4.80        38.20         6.18        55.04 
TCGA-G4-6317 TCGA-G4-6586 TCGA-AG-A02N TCGA-EI-6510 
       36.00        35.80        61.97        18.28 

$`ABI3BP WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
       38.07         1.02         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       27.09        16.31        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77        12.10        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.20        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       29.06        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       15.12         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6927 
        1.48         3.68         4.41        12.43        14.30         9.44 
TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       11.64         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       24.43       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 
       98.24         8.61        31.96        35.74        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6321 TCGA-G4-6323 
       44.68        85.48        63.62        61.91        22.09        13.78 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 
       10.98        49.97         1.94        38.96        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       19.96        20.91         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  ABI3BP MUTATED ABI3BP WILD-TYPE 
            0.95             0.00 
  ABI3BP MUTATED ABI3BP WILD-TYPE 
          100.01           148.01 
  ABI3BP MUTATED ABI3BP WILD-TYPE 
          24.445           20.050 
[1] "0.9 - 100.0 (24.4)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.3"
D579V2, continuous
D579V3, binary
                  cls
clus                 0   1
  ABI3BP MUTATED    20   2
  ABI3BP WILD-TYPE 346 117
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ABI3BP MUTATED     20    2
  ABI3BP WILD-TYPE  346  117
        clus
vv       ABI3BP MUTATED ABI3BP WILD-TYPE
  COLON              20              346
  RECTUM              2              117
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ABI3BP MUTATED         1        0        3         7         2         0
  ABI3BP WILD-TYPE      90        1       29       131         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ABI3BP MUTATED           1          0          4          2        1
  ABI3BP WILD-TYPE        23         11         55         40       47
                  vv
clus               STAGE IVA STAGE IVB
  ABI3BP MUTATED           1         0
  ABI3BP WILD-TYPE        17         1
D579V4, multiclass
            clus
vv           ABI3BP MUTATED ABI3BP WILD-TYPE
  STAGE I                 1               90
  STAGE IA                0                1
  STAGE II                3               29
  STAGE IIA               7              131
  STAGE IIB               2                8
  STAGE IIC               0                1
  STAGE III               1               23
  STAGE IIIA              0               11
  STAGE IIIB              4               55
  STAGE IIIC              2               40
  STAGE IV                1               47
  STAGE IVA               1               17
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ABI3BP MUTATED     1   2  17   3
  ABI3BP WILD-TYPE  16  90 312  47
D579V5, multiclass
    clus
vv   ABI3BP MUTATED ABI3BP WILD-TYPE
  T1              1               16
  T2              2               90
  T3             17              312
  T4              3               47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  ABI3BP MUTATED    15   5   3
  ABI3BP WILD-TYPE 272 108  84
D579V6, multiclass
    clus
vv   ABI3BP MUTATED ABI3BP WILD-TYPE
  N0             15              272
  N1              5              108
  N2              3               84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D579V7, binary
                  cls
clus                 0   1
  ABI3BP MUTATED    17   1
  ABI3BP WILD-TYPE 358  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ABI3BP MUTATED     17    1
  ABI3BP WILD-TYPE  358   64
   clus
vv  ABI3BP MUTATED ABI3BP WILD-TYPE
  0             17              358
  1              1               64
[1] 2 2
[1] FALSE
D579V8, binary
                  cls
clus                 0   1
  ABI3BP MUTATED    14   9
  ABI3BP WILD-TYPE 211 255
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ABI3BP MUTATED     14    9
  ABI3BP WILD-TYPE  211  255
        clus
vv       ABI3BP MUTATED ABI3BP WILD-TYPE
  FEMALE             14              211
  MALE                9              255
[1] 2 2
[1] FALSE
D579V9, binary
                  cls
clus                 0   1
  ABI3BP MUTATED    16   2
  ABI3BP WILD-TYPE 334  20
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ABI3BP MUTATED     16    2
  ABI3BP WILD-TYPE  334   20
     clus
vv    ABI3BP MUTATED ABI3BP WILD-TYPE
  NO              16              334
  YES              2               20
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ABI3BP MUTATED                     16                             3
  ABI3BP WILD-TYPE                  299                            44
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ABI3BP MUTATED                       2                              0
  ABI3BP WILD-TYPE                   104                             10
D579V10, multiclass
                                clus
vv                               ABI3BP MUTATED ABI3BP WILD-TYPE
  COLON ADENOCARCINOMA                       16              299
  COLON MUCINOUS ADENOCARCINOMA               3               44
  RECTAL ADENOCARCINOMA                       2              104
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ABI3BP MUTATED    17   0   0   1
  ABI3BP WILD-TYPE 328   4  31  24
D579V11, multiclass
    clus
vv   ABI3BP MUTATED ABI3BP WILD-TYPE
  R0             17              328
  R1              0                4
  R2              0               31
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D579V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ABI3BP MUTATED                                  0     1
  ABI3BP WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ABI3BP MUTATED                           1    15
  ABI3BP WILD-TYPE                        21   211
D579V13, multiclass
                                  clus
vv                                 ABI3BP MUTATED ABI3BP WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                        15              211
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(580) Variable = ENTPD4 MUTATION ANALYSIS
D580V1, survival
                  sevent
clus2                0   1
  ENTPD4 MUTATED    14   3
  ENTPD4 WILD-TYPE 364  90
  ENTPD4 MUTATED ENTPD4 WILD-TYPE 
              17              454 
  ENTPD4 MUTATED ENTPD4 WILD-TYPE 
               3               90 
$`ENTPD4 MUTATED`
TCGA-A6-6649 TCGA-AA-3489 TCGA-AA-3715 TCGA-AA-3949 TCGA-AA-A010 TCGA-AA-A01P 
       24.16         7.04        19.04        26.01        34.98        38.07 
TCGA-AD-6889 TCGA-AD-6895 TCGA-CM-6170 TCGA-D5-6929 TCGA-D5-6930 TCGA-DM-A1HB 
       56.55         0.72        15.02         4.80         1.51       135.65 
TCGA-F4-6856 TCGA-G4-6315 TCGA-G4-6588 TCGA-G4-6628 TCGA-DC-6160 
       35.31        61.91        26.17        79.69        19.99 

$`ENTPD4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.08        25.18        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        19.66        20.28         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        33.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01Q 
       10.98        32.02        12.00        31.00        31.00         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       21.37        15.52         0.79         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       14.99        12.99        13.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
        7.50        44.32       131.51       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       85.48        63.62        36.00        22.09        13.78        35.80 
TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       91.79        46.75        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6681 TCGA-DC-6682 
        5.03        13.97        27.95        10.98         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  ENTPD4 MUTATED ENTPD4 WILD-TYPE 
            0.72             0.00 
  ENTPD4 MUTATED ENTPD4 WILD-TYPE 
          135.65           148.01 
  ENTPD4 MUTATED ENTPD4 WILD-TYPE 
          26.010           20.085 
[1] "0.7 - 135.7 (26.0)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.4"
D580V2, continuous
D580V3, binary
                  cls
clus                 0   1
  ENTPD4 MUTATED    17   1
  ENTPD4 WILD-TYPE 349 118
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ENTPD4 MUTATED     17    1
  ENTPD4 WILD-TYPE  349  118
        clus
vv       ENTPD4 MUTATED ENTPD4 WILD-TYPE
  COLON              17              349
  RECTUM              1              118
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ENTPD4 MUTATED         4        0        3         3         1         0
  ENTPD4 WILD-TYPE      87        1       29       135         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ENTPD4 MUTATED           1          0          3          0        2
  ENTPD4 WILD-TYPE        23         11         56         42       46
                  vv
clus               STAGE IVA STAGE IVB
  ENTPD4 MUTATED           0         0
  ENTPD4 WILD-TYPE        18         1
D580V4, multiclass
            clus
vv           ENTPD4 MUTATED ENTPD4 WILD-TYPE
  STAGE I                 4               87
  STAGE IA                0                1
  STAGE II                3               29
  STAGE IIA               3              135
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               1               23
  STAGE IIIA              0               11
  STAGE IIIB              3               56
  STAGE IIIC              0               42
  STAGE IV                2               46
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ENTPD4 MUTATED     0   4  12   2
  ENTPD4 WILD-TYPE  17  88 317  48
D580V5, multiclass
    clus
vv   ENTPD4 MUTATED ENTPD4 WILD-TYPE
  T1              0               17
  T2              4               88
  T3             12              317
  T4              2               48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  ENTPD4 MUTATED    11   7   0
  ENTPD4 WILD-TYPE 276 106  87
D580V6, multiclass
    clus
vv   ENTPD4 MUTATED ENTPD4 WILD-TYPE
  N0             11              276
  N1              7              106
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D580V7, binary
                  cls
clus                 0   1
  ENTPD4 MUTATED    15   2
  ENTPD4 WILD-TYPE 360  63
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ENTPD4 MUTATED     15    2
  ENTPD4 WILD-TYPE  360   63
   clus
vv  ENTPD4 MUTATED ENTPD4 WILD-TYPE
  0             15              360
  1              2               63
[1] 2 2
[1] FALSE
D580V8, binary
                  cls
clus                 0   1
  ENTPD4 MUTATED     7  11
  ENTPD4 WILD-TYPE 218 253
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ENTPD4 MUTATED      7   11
  ENTPD4 WILD-TYPE  218  253
        clus
vv       ENTPD4 MUTATED ENTPD4 WILD-TYPE
  FEMALE              7              218
  MALE               11              253
[1] 2 2
[1] FALSE
D580V9, binary
                  cls
clus                 0   1
  ENTPD4 MUTATED    11   0
  ENTPD4 WILD-TYPE 339  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ENTPD4 MUTATED     11    0
  ENTPD4 WILD-TYPE  339   22
     clus
vv    ENTPD4 MUTATED ENTPD4 WILD-TYPE
  NO              11              339
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ENTPD4 MUTATED                     13                             3
  ENTPD4 WILD-TYPE                  302                            44
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ENTPD4 MUTATED                       1                              0
  ENTPD4 WILD-TYPE                   105                             10
D580V10, multiclass
                                clus
vv                               ENTPD4 MUTATED ENTPD4 WILD-TYPE
  COLON ADENOCARCINOMA                       13              302
  COLON MUCINOUS ADENOCARCINOMA               3               44
  RECTAL ADENOCARCINOMA                       1              105
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ENTPD4 MUTATED    14   0   0   0
  ENTPD4 WILD-TYPE 331   4  31  25
D580V11, multiclass
    clus
vv   ENTPD4 MUTATED ENTPD4 WILD-TYPE
  R0             14              331
  R1              0                4
  R2              0               31
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D580V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ENTPD4 MUTATED                                  0     1
  ENTPD4 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ENTPD4 MUTATED                           0    11
  ENTPD4 WILD-TYPE                        22   215
D580V13, multiclass
                                  clus
vv                                 ENTPD4 MUTATED ENTPD4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                        11              215
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(581) Variable = HFE2 MUTATION ANALYSIS
D581V1, survival
                sevent
clus2              0   1
  HFE2 MUTATED     6   2
  HFE2 WILD-TYPE 372  91
  HFE2 MUTATED HFE2 WILD-TYPE 
             8            463 
  HFE2 MUTATED HFE2 WILD-TYPE 
             2             91 
$`HFE2 MUTATED`
TCGA-AA-3815 TCGA-AA-A03J TCGA-AZ-6601 TCGA-CK-5914 TCGA-G4-6306 TCGA-G4-6315 
       33.04        40.96       100.01         9.99        44.68        61.91 
TCGA-AF-5654 TCGA-AG-A002 
       16.83        20.98 

$`HFE2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       19.04        10.06        35.05         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       41.00        39.98        18.05         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
       12.10        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        49.08        51.32        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6317 TCGA-G4-6321 
       53.62        55.04        85.48        63.62        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       10.39        14.50        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  HFE2 MUTATED HFE2 WILD-TYPE 
          9.99           0.00 
  HFE2 MUTATED HFE2 WILD-TYPE 
        100.01         148.01 
  HFE2 MUTATED HFE2 WILD-TYPE 
         37.00          20.05 
[1] "10.0 - 100.0 (37.0)" "0.0 - 148.0 (20.1)" 
[1] "hr=" "1.3"
D581V2, continuous
D581V3, binary
                cls
clus               0   1
  HFE2 MUTATED     8   2
  HFE2 WILD-TYPE 358 117
[1] "tbl2"
                cls
clus             [,1] [,2]
  HFE2 MUTATED      8    2
  HFE2 WILD-TYPE  358  117
        clus
vv       HFE2 MUTATED HFE2 WILD-TYPE
  COLON             8            358
  RECTUM            2            117
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  HFE2 MUTATED         4        0        2         2         0         0
  HFE2 WILD-TYPE      87        1       30       136        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  HFE2 MUTATED           0          0          1          0        1         0
  HFE2 WILD-TYPE        24         11         58         42       47        18
                vv
clus             STAGE IVB
  HFE2 MUTATED           0
  HFE2 WILD-TYPE         1
D581V4, multiclass
            clus
vv           HFE2 MUTATED HFE2 WILD-TYPE
  STAGE I               4             87
  STAGE IA              0              1
  STAGE II              2             30
  STAGE IIA             2            136
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            1             58
  STAGE IIIC            0             42
  STAGE IV              1             47
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  HFE2 MUTATED     0   5   4   1
  HFE2 WILD-TYPE  17  87 325  49
D581V5, multiclass
    clus
vv   HFE2 MUTATED HFE2 WILD-TYPE
  T1            0             17
  T2            5             87
  T3            4            325
  T4            1             49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  HFE2 MUTATED     8   2   0
  HFE2 WILD-TYPE 279 111  87
D581V6, multiclass
    clus
vv   HFE2 MUTATED HFE2 WILD-TYPE
  N0            8            279
  N1            2            111
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D581V7, binary
                cls
clus               0   1
  HFE2 MUTATED     7   1
  HFE2 WILD-TYPE 368  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  HFE2 MUTATED      7    1
  HFE2 WILD-TYPE  368   64
   clus
vv  HFE2 MUTATED HFE2 WILD-TYPE
  0            7            368
  1            1             64
[1] 2 2
[1] FALSE
D581V8, binary
                cls
clus               0   1
  HFE2 MUTATED     4   6
  HFE2 WILD-TYPE 221 258
[1] "tbl2"
                cls
clus             [,1] [,2]
  HFE2 MUTATED      4    6
  HFE2 WILD-TYPE  221  258
        clus
vv       HFE2 MUTATED HFE2 WILD-TYPE
  FEMALE            4            221
  MALE              6            258
[1] 2 2
[1] FALSE
D581V9, binary
                cls
clus               0   1
  HFE2 MUTATED     7   0
  HFE2 WILD-TYPE 343  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  HFE2 MUTATED      7    0
  HFE2 WILD-TYPE  343   22
     clus
vv    HFE2 MUTATED HFE2 WILD-TYPE
  NO             7            343
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  HFE2 MUTATED                      8                             0
  HFE2 WILD-TYPE                  307                            47
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  HFE2 MUTATED                       2                              0
  HFE2 WILD-TYPE                   104                             10
D581V10, multiclass
                                clus
vv                               HFE2 MUTATED HFE2 WILD-TYPE
  COLON ADENOCARCINOMA                      8            307
  COLON MUCINOUS ADENOCARCINOMA             0             47
  RECTAL ADENOCARCINOMA                     2            104
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  HFE2 MUTATED     7   0   0   2
  HFE2 WILD-TYPE 338   4  31  23
D581V11, multiclass
    clus
vv   HFE2 MUTATED HFE2 WILD-TYPE
  R0            7            338
  R1            0              4
  R2            0             31
  RX            2             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D581V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HFE2 MUTATED                                  0     0
  HFE2 WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  HFE2 MUTATED                           0     6
  HFE2 WILD-TYPE                        22   220
D581V13, multiclass
                                  clus
vv                                 HFE2 MUTATED HFE2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       6            220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(582) Variable = SPCS2 MUTATION ANALYSIS
D582V1, survival
                 sevent
clus2               0   1
  SPCS2 MUTATED     3   2
  SPCS2 WILD-TYPE 375  91
  SPCS2 MUTATED SPCS2 WILD-TYPE 
              5             466 
  SPCS2 MUTATED SPCS2 WILD-TYPE 
              2              91 
$`SPCS2 MUTATED`
TCGA-AA-3697 TCGA-AZ-6608 TCGA-CK-6751 TCGA-D5-6923 TCGA-DM-A28C 
       85.05         1.61       124.27        12.43        81.37 

$`SPCS2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       19.00        36.00         5.03        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        3.19        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
       82.95         1.91        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
        4.41        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
        6.12       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  SPCS2 MUTATED SPCS2 WILD-TYPE 
           1.61            0.00 
  SPCS2 MUTATED SPCS2 WILD-TYPE 
         124.27          148.01 
  SPCS2 MUTATED SPCS2 WILD-TYPE 
         81.370          20.155 
[1] "1.6 - 124.3 (81.4)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.1"
D582V2, continuous
D582V3, binary
                 cls
clus                0   1
  SPCS2 MUTATED     5   0
  SPCS2 WILD-TYPE 361 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SPCS2 MUTATED      5    0
  SPCS2 WILD-TYPE  361  119
        clus
vv       SPCS2 MUTATED SPCS2 WILD-TYPE
  COLON              5             361
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SPCS2 MUTATED         2        0        0         1         0         0
  SPCS2 WILD-TYPE      89        1       32       137        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SPCS2 MUTATED           1          1          0          0        0         0
  SPCS2 WILD-TYPE        23         10         59         42       48        18
                 vv
clus              STAGE IVB
  SPCS2 MUTATED           0
  SPCS2 WILD-TYPE         1
D582V4, multiclass
            clus
vv           SPCS2 MUTATED SPCS2 WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              1             137
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             1              10
  STAGE IIIB             0              59
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  SPCS2 MUTATED     0   3   2   0
  SPCS2 WILD-TYPE  17  89 327  50
D582V5, multiclass
    clus
vv   SPCS2 MUTATED SPCS2 WILD-TYPE
  T1             0              17
  T2             3              89
  T3             2             327
  T4             0              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  SPCS2 MUTATED     4   1   0
  SPCS2 WILD-TYPE 283 112  87
D582V6, multiclass
    clus
vv   SPCS2 MUTATED SPCS2 WILD-TYPE
  N0             4             283
  N1             1             112
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D582V7, binary
                 cls
clus                0   1
  SPCS2 MUTATED     4   0
  SPCS2 WILD-TYPE 371  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SPCS2 MUTATED      4    0
  SPCS2 WILD-TYPE  371   65
   clus
vv  SPCS2 MUTATED SPCS2 WILD-TYPE
  0             4             371
  1             0              65
[1] 2 2
[1] FALSE
D582V8, binary
                 cls
clus                0   1
  SPCS2 MUTATED     2   3
  SPCS2 WILD-TYPE 223 261
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SPCS2 MUTATED      2    3
  SPCS2 WILD-TYPE  223  261
        clus
vv       SPCS2 MUTATED SPCS2 WILD-TYPE
  FEMALE             2             223
  MALE               3             261
[1] 2 2
[1] FALSE
D582V9, binary
                 cls
clus                0   1
  SPCS2 MUTATED     4   0
  SPCS2 WILD-TYPE 346  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SPCS2 MUTATED      4    0
  SPCS2 WILD-TYPE  346   22
     clus
vv    SPCS2 MUTATED SPCS2 WILD-TYPE
  NO              4             346
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SPCS2 MUTATED                      4                             1
  SPCS2 WILD-TYPE                  311                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SPCS2 MUTATED                       0                              0
  SPCS2 WILD-TYPE                   106                             10
D582V10, multiclass
                                clus
vv                               SPCS2 MUTATED SPCS2 WILD-TYPE
  COLON ADENOCARCINOMA                       4             311
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  SPCS2 MUTATED     2   0   0   1
  SPCS2 WILD-TYPE 343   4  31  24
D582V11, multiclass
    clus
vv   SPCS2 MUTATED SPCS2 WILD-TYPE
  R0             2             343
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D582V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SPCS2 MUTATED                                  0     0
  SPCS2 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  SPCS2 MUTATED                           0     4
  SPCS2 WILD-TYPE                        22   222
D582V13, multiclass
                                  clus
vv                                 SPCS2 MUTATED SPCS2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        4             222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(583) Variable = RAD51AP2 MUTATION ANALYSIS
D583V1, survival
                    sevent
clus2                  0   1
  RAD51AP2 MUTATED    16   2
  RAD51AP2 WILD-TYPE 362  91
  RAD51AP2 MUTATED RAD51AP2 WILD-TYPE 
                18                453 
  RAD51AP2 MUTATED RAD51AP2 WILD-TYPE 
                 2                 91 
$`RAD51AP2 MUTATED`
TCGA-A6-3809 TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3713 TCGA-AA-3815 TCGA-AA-A00N 
       32.75        20.12        19.66        19.04        33.04         4.01 
TCGA-AA-A010 TCGA-AD-6895 TCGA-AY-6197 TCGA-AZ-4315 TCGA-D5-5537 TCGA-F4-6856 
       34.98         0.72        21.44        58.39        45.40        35.31 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 TCGA-AG-3892 TCGA-AG-A002 TCGA-CI-6624 
       35.80        26.17        79.69        13.02        20.98         4.73 

$`RAD51AP2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
       85.05        26.99        19.04        10.06        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       15.52        56.55         0.79         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       33.01        17.82         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5538 
       11.08        11.08        11.01        10.06        12.03        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       47.41       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       13.78        91.79        46.75        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 
       19.99         1.02        17.95        36.95        17.03        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        6.97        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  RAD51AP2 MUTATED RAD51AP2 WILD-TYPE 
              0.72               0.00 
  RAD51AP2 MUTATED RAD51AP2 WILD-TYPE 
             79.69             148.01 
  RAD51AP2 MUTATED RAD51AP2 WILD-TYPE 
            23.805             20.020 
[1] "0.7 - 79.7 (23.8)"  "0.0 - 148.0 (20.0)"
[1] "hr=" "1.9"
D583V2, continuous
D583V3, binary
                    cls
clus                   0   1
  RAD51AP2 MUTATED    16   3
  RAD51AP2 WILD-TYPE 350 116
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  RAD51AP2 MUTATED     16    3
  RAD51AP2 WILD-TYPE  350  116
        clus
vv       RAD51AP2 MUTATED RAD51AP2 WILD-TYPE
  COLON                16                350
  RECTUM                3                116
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RAD51AP2 MUTATED         5        0        0         8         3         0
  RAD51AP2 WILD-TYPE      86        1       32       130         7         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RAD51AP2 MUTATED           0          0          0          1        1
  RAD51AP2 WILD-TYPE        24         11         59         41       47
                    vv
clus                 STAGE IVA STAGE IVB
  RAD51AP2 MUTATED           0         0
  RAD51AP2 WILD-TYPE        18         1
D583V4, multiclass
            clus
vv           RAD51AP2 MUTATED RAD51AP2 WILD-TYPE
  STAGE I                   5                 86
  STAGE IA                  0                  1
  STAGE II                  0                 32
  STAGE IIA                 8                130
  STAGE IIB                 3                  7
  STAGE IIC                 0                  1
  STAGE III                 0                 24
  STAGE IIIA                0                 11
  STAGE IIIB                0                 59
  STAGE IIIC                1                 41
  STAGE IV                  1                 47
  STAGE IVA                 0                 18
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  RAD51AP2 MUTATED     1   4  10   4
  RAD51AP2 WILD-TYPE  16  88 319  46
D583V5, multiclass
    clus
vv   RAD51AP2 MUTATED RAD51AP2 WILD-TYPE
  T1                1                 16
  T2                4                 88
  T3               10                319
  T4                4                 46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  RAD51AP2 MUTATED    16   2   1
  RAD51AP2 WILD-TYPE 271 111  86
D583V6, multiclass
    clus
vv   RAD51AP2 MUTATED RAD51AP2 WILD-TYPE
  N0               16                271
  N1                2                111
  N2                1                 86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D583V7, binary
                    cls
clus                   0   1
  RAD51AP2 MUTATED    13   1
  RAD51AP2 WILD-TYPE 362  64
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  RAD51AP2 MUTATED     13    1
  RAD51AP2 WILD-TYPE  362   64
   clus
vv  RAD51AP2 MUTATED RAD51AP2 WILD-TYPE
  0               13                362
  1                1                 64
[1] 2 2
[1] FALSE
D583V8, binary
                    cls
clus                   0   1
  RAD51AP2 MUTATED     8  11
  RAD51AP2 WILD-TYPE 217 253
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  RAD51AP2 MUTATED      8   11
  RAD51AP2 WILD-TYPE  217  253
        clus
vv       RAD51AP2 MUTATED RAD51AP2 WILD-TYPE
  FEMALE                8                217
  MALE                 11                253
[1] 2 2
[1] FALSE
D583V9, binary
                    cls
clus                   0   1
  RAD51AP2 MUTATED    14   1
  RAD51AP2 WILD-TYPE 336  21
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  RAD51AP2 MUTATED     14    1
  RAD51AP2 WILD-TYPE  336   21
     clus
vv    RAD51AP2 MUTATED RAD51AP2 WILD-TYPE
  NO                14                336
  YES                1                 21
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  RAD51AP2 MUTATED                     11                             5
  RAD51AP2 WILD-TYPE                  304                            42
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  RAD51AP2 MUTATED                       3                              0
  RAD51AP2 WILD-TYPE                   103                             10
D583V10, multiclass
                                clus
vv                               RAD51AP2 MUTATED RAD51AP2 WILD-TYPE
  COLON ADENOCARCINOMA                         11                304
  COLON MUCINOUS ADENOCARCINOMA                 5                 42
  RECTAL ADENOCARCINOMA                         3                103
  RECTAL MUCINOUS ADENOCARCINOMA                0                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  RAD51AP2 MUTATED    14   0   1   1
  RAD51AP2 WILD-TYPE 331   4  30  24
D583V11, multiclass
    clus
vv   RAD51AP2 MUTATED RAD51AP2 WILD-TYPE
  R0               14                331
  R1                0                  4
  R2                1                 30
  RX                1                 24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D583V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RAD51AP2 MUTATED                                  0     0
  RAD51AP2 WILD-TYPE                                1    11
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  RAD51AP2 MUTATED                           0    12
  RAD51AP2 WILD-TYPE                        22   214
D583V13, multiclass
                                  clus
vv                                 RAD51AP2 MUTATED RAD51AP2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 11
  BLACK OR AFRICAN AMERICAN                       0                 22
  WHITE                                          12                214
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(584) Variable = BMPR1A MUTATION ANALYSIS
D584V1, survival
                  sevent
clus2                0   1
  BMPR1A MUTATED    16   2
  BMPR1A WILD-TYPE 362  91
  BMPR1A MUTATED BMPR1A WILD-TYPE 
              18              453 
  BMPR1A MUTATED BMPR1A WILD-TYPE 
               2               91 
$`BMPR1A MUTATED`
TCGA-AA-3510 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3833 TCGA-AA-3950 TCGA-AA-3966 
       63.98         6.97        54.02        15.95        24.00         2.01 
TCGA-AA-A00J TCGA-AD-6964 TCGA-AY-6386 TCGA-AZ-6601 TCGA-CM-4743 TCGA-CM-5344 
       18.05        10.88        17.82       100.01        23.05        22.03 
TCGA-CM-6162 TCGA-D5-6539 TCGA-DM-A1D9 TCGA-DM-A28K TCGA-F4-6704 TCGA-G4-6317 
       12.00        12.49       140.38        98.24         1.55        36.00 

$`BMPR1A WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3837 
       33.04         0.99        25.02         1.02        17.98        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 
       33.01        26.01         2.01        20.98        34.03        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       33.01        21.44        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
      124.27        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       15.02        17.03        15.02         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
       17.85         4.80        17.13        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       13.32        12.59         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
      117.07         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6321 
       44.68        55.04        85.48        63.62        61.91        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  BMPR1A MUTATED BMPR1A WILD-TYPE 
            1.55             0.00 
  BMPR1A MUTATED BMPR1A WILD-TYPE 
          140.38           148.01 
  BMPR1A MUTATED BMPR1A WILD-TYPE 
           20.04            20.19 
[1] "1.6 - 140.4 (20.0)" "0.0 - 148.0 (20.2)"
[1] "hr=" "2.5"
D584V2, continuous
D584V3, binary
                  cls
clus                 0   1
  BMPR1A MUTATED    18   0
  BMPR1A WILD-TYPE 348 119
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BMPR1A MUTATED     18    0
  BMPR1A WILD-TYPE  348  119
        clus
vv       BMPR1A MUTATED BMPR1A WILD-TYPE
  COLON              18              348
  RECTUM              0              119
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  BMPR1A MUTATED         0        0        4         6         0         0
  BMPR1A WILD-TYPE      91        1       28       132        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  BMPR1A MUTATED           0          1          4          2        0
  BMPR1A WILD-TYPE        24         10         55         40       48
                  vv
clus               STAGE IVA STAGE IVB
  BMPR1A MUTATED           0         0
  BMPR1A WILD-TYPE        18         1
D584V4, multiclass
            clus
vv           BMPR1A MUTATED BMPR1A WILD-TYPE
  STAGE I                 0               91
  STAGE IA                0                1
  STAGE II                4               28
  STAGE IIA               6              132
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              1               10
  STAGE IIIB              4               55
  STAGE IIIC              2               40
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  BMPR1A MUTATED     0   0  16   2
  BMPR1A WILD-TYPE  17  92 313  48
D584V5, multiclass
    clus
vv   BMPR1A MUTATED BMPR1A WILD-TYPE
  T1              0               17
  T2              0               92
  T3             16              313
  T4              2               48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  BMPR1A MUTATED    11   4   3
  BMPR1A WILD-TYPE 276 109  84
D584V6, multiclass
    clus
vv   BMPR1A MUTATED BMPR1A WILD-TYPE
  N0             11              276
  N1              4              109
  N2              3               84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D584V7, binary
                  cls
clus                 0   1
  BMPR1A MUTATED    15   0
  BMPR1A WILD-TYPE 360  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BMPR1A MUTATED     15    0
  BMPR1A WILD-TYPE  360   65
   clus
vv  BMPR1A MUTATED BMPR1A WILD-TYPE
  0             15              360
  1              0               65
[1] 2 2
[1] FALSE
D584V8, binary
                  cls
clus                 0   1
  BMPR1A MUTATED    10   8
  BMPR1A WILD-TYPE 215 256
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BMPR1A MUTATED     10    8
  BMPR1A WILD-TYPE  215  256
        clus
vv       BMPR1A MUTATED BMPR1A WILD-TYPE
  FEMALE             10              215
  MALE                8              256
[1] 2 2
[1] FALSE
D584V9, binary
                  cls
clus                 0   1
  BMPR1A MUTATED    14   0
  BMPR1A WILD-TYPE 336  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BMPR1A MUTATED     14    0
  BMPR1A WILD-TYPE  336   22
     clus
vv    BMPR1A MUTATED BMPR1A WILD-TYPE
  NO              14              336
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  BMPR1A MUTATED                     12                             6
  BMPR1A WILD-TYPE                  303                            41
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  BMPR1A MUTATED                       0                              0
  BMPR1A WILD-TYPE                   106                             10
D584V10, multiclass
                                clus
vv                               BMPR1A MUTATED BMPR1A WILD-TYPE
  COLON ADENOCARCINOMA                       12              303
  COLON MUCINOUS ADENOCARCINOMA               6               41
  RECTAL ADENOCARCINOMA                       0              106
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  BMPR1A MUTATED    13   0   0   0
  BMPR1A WILD-TYPE 332   4  31  25
D584V11, multiclass
    clus
vv   BMPR1A MUTATED BMPR1A WILD-TYPE
  R0             13              332
  R1              0                4
  R2              0               31
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D584V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  BMPR1A MUTATED                                  1     0
  BMPR1A WILD-TYPE                                0    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  BMPR1A MUTATED                           1     9
  BMPR1A WILD-TYPE                        21   217
D584V13, multiclass
                                  clus
vv                                 BMPR1A MUTATED BMPR1A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              1                0
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                         9              217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(585) Variable = MLL4 MUTATION ANALYSIS
D585V1, survival
                sevent
clus2              0   1
  MLL4 MUTATED    31   7
  MLL4 WILD-TYPE 347  86
  MLL4 MUTATED MLL4 WILD-TYPE 
            38            433 
  MLL4 MUTATED MLL4 WILD-TYPE 
             7             86 
$`MLL4 MUTATED`
TCGA-A6-5661 TCGA-A6-6653 TCGA-AA-3492 TCGA-AA-3663 TCGA-AA-3685 TCGA-AA-3713 
       33.53        24.39         3.02         6.97        37.05        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3864 TCGA-AA-3950 
       19.04        10.06        17.98        15.95        53.00        24.00 
TCGA-AA-A010 TCGA-AY-6386 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-CA-5255 TCGA-CA-6718 
       34.98        17.82        88.21        49.41         3.06        10.06 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5916 TCGA-CM-4743 TCGA-CM-5861 TCGA-CM-5862 
       15.62        51.32        21.14        23.05        15.02         5.03 
TCGA-CM-6171 TCGA-CM-6674 TCGA-D5-6540 TCGA-DM-A1D9 TCGA-G4-6299 TCGA-G4-6304 
       14.04        12.95        16.14       140.38        74.56        53.62 
TCGA-G4-6588 TCGA-G4-6628 TCGA-AG-3726 TCGA-AG-A002 TCGA-AG-A02N TCGA-DC-5337 
       26.17        79.69         7.99        20.98        61.97        15.02 
TCGA-DC-6157 TCGA-EI-6507 
       27.95        19.96 

$`MLL4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 
       25.18        24.16        21.76        24.69        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       19.66        20.28         7.04         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02        78.08         6.05        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
        5.98        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3837 
       35.05        33.04         0.99        25.02         1.02        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       31.07        30.05        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       26.01         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        33.01        21.44        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
      106.75        22.36        62.79         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 
        3.25         3.29         0.07        12.20        12.76        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-6747 
       17.56       148.01        85.45        49.08         9.99        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
        1.91       124.27        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5863 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       11.01        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
        4.80        17.13        12.49        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
       12.59         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6303 TCGA-G4-6306 
        0.53        47.41        35.31       133.18        65.85        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 
       13.78        35.80        91.79        46.75        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
        1.94        38.96        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5869 TCGA-DC-6155 
        6.97         4.73        78.12         7.17         5.03        13.97 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
        0.49        20.55        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  MLL4 MUTATED MLL4 WILD-TYPE 
          3.02           0.00 
  MLL4 MUTATED MLL4 WILD-TYPE 
        140.38         148.01 
  MLL4 MUTATED MLL4 WILD-TYPE 
         20.47          20.19 
[1] "3.0 - 140.4 (20.5)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.3"
D585V2, continuous
D585V3, binary
                cls
clus               0   1
  MLL4 MUTATED    33   6
  MLL4 WILD-TYPE 333 113
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL4 MUTATED     33    6
  MLL4 WILD-TYPE  333  113
        clus
vv       MLL4 MUTATED MLL4 WILD-TYPE
  COLON            33            333
  RECTUM            6            113
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MLL4 MUTATED        10        0        7        14         2         0
  MLL4 WILD-TYPE      81        1       25       124         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MLL4 MUTATED           1          0          1          2        1         1
  MLL4 WILD-TYPE        23         11         58         40       47        17
                vv
clus             STAGE IVB
  MLL4 MUTATED           0
  MLL4 WILD-TYPE         1
D585V4, multiclass
            clus
vv           MLL4 MUTATED MLL4 WILD-TYPE
  STAGE I              10             81
  STAGE IA              0              1
  STAGE II              7             25
  STAGE IIA            14            124
  STAGE IIB             2              8
  STAGE IIC             0              1
  STAGE III             1             23
  STAGE IIIA            0             11
  STAGE IIIB            1             58
  STAGE IIIC            2             40
  STAGE IV              1             47
  STAGE IVA             1             17
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  MLL4 MUTATED     3   7  26   3
  MLL4 WILD-TYPE  14  85 303  47
D585V5, multiclass
    clus
vv   MLL4 MUTATED MLL4 WILD-TYPE
  T1            3             14
  T2            7             85
  T3           26            303
  T4            3             47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  MLL4 MUTATED    34   2   3
  MLL4 WILD-TYPE 253 111  84
D585V6, multiclass
    clus
vv   MLL4 MUTATED MLL4 WILD-TYPE
  N0           34            253
  N1            2            111
  N2            3             84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D585V7, binary
                cls
clus               0   1
  MLL4 MUTATED    35   2
  MLL4 WILD-TYPE 340  63
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL4 MUTATED     35    2
  MLL4 WILD-TYPE  340   63
   clus
vv  MLL4 MUTATED MLL4 WILD-TYPE
  0           35            340
  1            2             63
[1] 2 2
[1] FALSE
D585V8, binary
                cls
clus               0   1
  MLL4 MUTATED    19  20
  MLL4 WILD-TYPE 206 244
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL4 MUTATED     19   20
  MLL4 WILD-TYPE  206  244
        clus
vv       MLL4 MUTATED MLL4 WILD-TYPE
  FEMALE           19            206
  MALE             20            244
[1] 2 2
[1] FALSE
D585V9, binary
                cls
clus               0   1
  MLL4 MUTATED    32   2
  MLL4 WILD-TYPE 318  20
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL4 MUTATED     32    2
  MLL4 WILD-TYPE  318   20
     clus
vv    MLL4 MUTATED MLL4 WILD-TYPE
  NO            32            318
  YES            2             20
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MLL4 MUTATED                     30                             3
  MLL4 WILD-TYPE                  285                            44
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MLL4 MUTATED                       6                              0
  MLL4 WILD-TYPE                   100                             10
D585V10, multiclass
                                clus
vv                               MLL4 MUTATED MLL4 WILD-TYPE
  COLON ADENOCARCINOMA                     30            285
  COLON MUCINOUS ADENOCARCINOMA             3             44
  RECTAL ADENOCARCINOMA                     6            100
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  MLL4 MUTATED    29   0   1   5
  MLL4 WILD-TYPE 316   4  30  20
D585V11, multiclass
    clus
vv   MLL4 MUTATED MLL4 WILD-TYPE
  R0           29            316
  R1            0              4
  R2            1             30
  RX            5             20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D585V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MLL4 MUTATED                                  0     2
  MLL4 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  MLL4 MUTATED                           3    19
  MLL4 WILD-TYPE                        19   207
D585V13, multiclass
                                  clus
vv                                 MLL4 MUTATED MLL4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              9
  BLACK OR AFRICAN AMERICAN                   3             19
  WHITE                                      19            207
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(586) Variable = KIF21A MUTATION ANALYSIS
D586V1, survival
                  sevent
clus2                0   1
  KIF21A MUTATED    23   5
  KIF21A WILD-TYPE 355  88
  KIF21A MUTATED KIF21A WILD-TYPE 
              28              443 
  KIF21A MUTATED KIF21A WILD-TYPE 
               5               88 
$`KIF21A MUTATED`
TCGA-A6-5665 TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3492 TCGA-AA-3663 TCGA-AA-3815 
       22.06        20.12        19.66         3.02         6.97        33.04 
TCGA-AA-3845 TCGA-AA-3867 TCGA-AA-3977 TCGA-AA-A00N TCGA-AD-6890 TCGA-AY-6197 
        0.00        24.03        25.02         4.01         0.79        21.44 
TCGA-AZ-4315 TCGA-AZ-6598 TCGA-CA-6717 TCGA-CK-4952 TCGA-CM-6162 TCGA-CM-6169 
       58.39        49.41        12.76        15.62        12.00        13.02 
TCGA-D5-6926 TCGA-D5-6928 TCGA-F4-6570 TCGA-G4-6299 TCGA-G4-6309 TCGA-AG-3892 
        9.04        11.64         6.18        74.56        85.48        13.02 
TCGA-AG-A002 TCGA-CI-6624 TCGA-CL-5917 TCGA-DC-6682 
       20.98         4.73        78.12         4.01 

$`KIF21A WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
       20.28         7.04         1.02        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       61.02        78.08         6.05        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
       19.04        19.04        10.06        35.05         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       17.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6895 
       40.96         0.07        21.37        15.52        56.55         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4323 
       27.09        16.31         0.95        33.01        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 
        5.13       106.75        22.36        62.79        88.21         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.20        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 
        5.03        15.02        15.02        17.03        15.02         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6170 
       29.03        16.04        21.99        14.99        12.99        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
        9.44         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6303 
       13.25         0.53        47.41        35.31       133.18        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       53.62        44.68        55.04        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       17.95        36.95        17.03        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CL-5918 
        0.69         0.72         6.05        33.17         6.97         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        5.95         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  KIF21A MUTATED KIF21A WILD-TYPE 
               0                0 
  KIF21A MUTATED KIF21A WILD-TYPE 
           85.48           148.01 
  KIF21A MUTATED KIF21A WILD-TYPE 
           14.32            20.91 
[1] "0.0 - 85.5 (14.3)"  "0.0 - 148.0 (20.9)"
[1] "hr=" "1"  
D586V2, continuous
D586V3, binary
                  cls
clus                 0   1
  KIF21A MUTATED    24   5
  KIF21A WILD-TYPE 342 114
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KIF21A MUTATED     24    5
  KIF21A WILD-TYPE  342  114
        clus
vv       KIF21A MUTATED KIF21A WILD-TYPE
  COLON              24              342
  RECTUM              5              114
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KIF21A MUTATED         3        0        3        12         1         0
  KIF21A WILD-TYPE      88        1       29       126         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIF21A MUTATED           0          0          3          4        1
  KIF21A WILD-TYPE        24         11         56         38       47
                  vv
clus               STAGE IVA STAGE IVB
  KIF21A MUTATED           0         0
  KIF21A WILD-TYPE        18         1
D586V4, multiclass
            clus
vv           KIF21A MUTATED KIF21A WILD-TYPE
  STAGE I                 3               88
  STAGE IA                0                1
  STAGE II                3               29
  STAGE IIA              12              126
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              3               56
  STAGE IIIC              4               38
  STAGE IV                1               47
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  KIF21A MUTATED     2   3  20   4
  KIF21A WILD-TYPE  15  89 309  46
D586V5, multiclass
    clus
vv   KIF21A MUTATED KIF21A WILD-TYPE
  T1              2               15
  T2              3               89
  T3             20              309
  T4              4               46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  KIF21A MUTATED    21   4   4
  KIF21A WILD-TYPE 266 109  83
D586V6, multiclass
    clus
vv   KIF21A MUTATED KIF21A WILD-TYPE
  N0             21              266
  N1              4              109
  N2              4               83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D586V7, binary
                  cls
clus                 0   1
  KIF21A MUTATED    21   1
  KIF21A WILD-TYPE 354  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KIF21A MUTATED     21    1
  KIF21A WILD-TYPE  354   64
   clus
vv  KIF21A MUTATED KIF21A WILD-TYPE
  0             21              354
  1              1               64
[1] 2 2
[1] FALSE
D586V8, binary
                  cls
clus                 0   1
  KIF21A MUTATED    13  16
  KIF21A WILD-TYPE 212 248
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KIF21A MUTATED     13   16
  KIF21A WILD-TYPE  212  248
        clus
vv       KIF21A MUTATED KIF21A WILD-TYPE
  FEMALE             13              212
  MALE               16              248
[1] 2 2
[1] FALSE
D586V9, binary
                  cls
clus                 0   1
  KIF21A MUTATED    21   1
  KIF21A WILD-TYPE 329  21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KIF21A MUTATED     21    1
  KIF21A WILD-TYPE  329   21
     clus
vv    KIF21A MUTATED KIF21A WILD-TYPE
  NO              21              329
  YES              1               21
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  KIF21A MUTATED                     17                             7
  KIF21A WILD-TYPE                  298                            40
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  KIF21A MUTATED                       5                              0
  KIF21A WILD-TYPE                   101                             10
D586V10, multiclass
                                clus
vv                               KIF21A MUTATED KIF21A WILD-TYPE
  COLON ADENOCARCINOMA                       17              298
  COLON MUCINOUS ADENOCARCINOMA               7               40
  RECTAL ADENOCARCINOMA                       5              101
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  KIF21A MUTATED    20   0   1   3
  KIF21A WILD-TYPE 325   4  30  22
D586V11, multiclass
    clus
vv   KIF21A MUTATED KIF21A WILD-TYPE
  R0             20              325
  R1              0                4
  R2              1               30
  RX              3               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D586V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KIF21A MUTATED                                  0     1
  KIF21A WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  KIF21A MUTATED                           2    16
  KIF21A WILD-TYPE                        20   210
D586V13, multiclass
                                  clus
vv                                 KIF21A MUTATED KIF21A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     2               20
  WHITE                                        16              210
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(587) Variable = ZNF286A MUTATION ANALYSIS
D587V1, survival
                   sevent
clus2                 0   1
  ZNF286A MUTATED     7   1
  ZNF286A WILD-TYPE 371  92
  ZNF286A MUTATED ZNF286A WILD-TYPE 
                8               463 
  ZNF286A MUTATED ZNF286A WILD-TYPE 
                1                92 
$`ZNF286A MUTATED`
TCGA-A6-6141 TCGA-AA-A010 TCGA-AD-5900 TCGA-AZ-4315 TCGA-AZ-6601 TCGA-CA-6717 
        8.38        34.98         0.07        58.39       100.01        12.76 
TCGA-AG-3731 TCGA-AG-A002 
       37.02        20.98 

$`ZNF286A WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 
       22.09        22.06        32.71        27.09        22.52        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       39.98        18.05        40.96        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 
       62.79        88.21        49.41         6.77        12.10        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07        12.20        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3732 TCGA-AG-3742 
       13.94        19.99         7.99         0.99        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  ZNF286A MUTATED ZNF286A WILD-TYPE 
             0.07              0.00 
  ZNF286A MUTATED ZNF286A WILD-TYPE 
           100.01            148.01 
  ZNF286A MUTATED ZNF286A WILD-TYPE 
            27.98             20.12 
[1] "0.1 - 100.0 (28.0)" "0.0 - 148.0 (20.1)"
[1] "hr=" "2.1"
D587V2, continuous
D587V3, binary
                   cls
clus                  0   1
  ZNF286A MUTATED     7   2
  ZNF286A WILD-TYPE 359 117
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZNF286A MUTATED      7    2
  ZNF286A WILD-TYPE  359  117
        clus
vv       ZNF286A MUTATED ZNF286A WILD-TYPE
  COLON                7               359
  RECTUM               2               117
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZNF286A MUTATED         2        0        1         4         1         0
  ZNF286A WILD-TYPE      89        1       31       134         9         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF286A MUTATED           0          0          0          0        1
  ZNF286A WILD-TYPE        24         11         59         42       47
                   vv
clus                STAGE IVA STAGE IVB
  ZNF286A MUTATED           0         0
  ZNF286A WILD-TYPE        18         1
D587V4, multiclass
            clus
vv           ZNF286A MUTATED ZNF286A WILD-TYPE
  STAGE I                  2                89
  STAGE IA                 0                 1
  STAGE II                 1                31
  STAGE IIA                4               134
  STAGE IIB                1                 9
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               0                11
  STAGE IIIB               0                59
  STAGE IIIC               0                42
  STAGE IV                 1                47
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  ZNF286A MUTATED     0   2   6   1
  ZNF286A WILD-TYPE  17  90 323  49
D587V5, multiclass
    clus
vv   ZNF286A MUTATED ZNF286A WILD-TYPE
  T1               0                17
  T2               2                90
  T3               6               323
  T4               1                49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  ZNF286A MUTATED     8   1   0
  ZNF286A WILD-TYPE 279 112  87
D587V6, multiclass
    clus
vv   ZNF286A MUTATED ZNF286A WILD-TYPE
  N0               8               279
  N1               1               112
  N2               0                87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D587V7, binary
                   cls
clus                  0   1
  ZNF286A MUTATED     7   1
  ZNF286A WILD-TYPE 368  64
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZNF286A MUTATED      7    1
  ZNF286A WILD-TYPE  368   64
   clus
vv  ZNF286A MUTATED ZNF286A WILD-TYPE
  0               7               368
  1               1                64
[1] 2 2
[1] FALSE
D587V8, binary
                   cls
clus                  0   1
  ZNF286A MUTATED     2   7
  ZNF286A WILD-TYPE 223 257
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZNF286A MUTATED      2    7
  ZNF286A WILD-TYPE  223  257
        clus
vv       ZNF286A MUTATED ZNF286A WILD-TYPE
  FEMALE               2               223
  MALE                 7               257
[1] 2 2
[1] FALSE
D587V9, binary
                   cls
clus                  0   1
  ZNF286A MUTATED     7   0
  ZNF286A WILD-TYPE 343  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZNF286A MUTATED      7    0
  ZNF286A WILD-TYPE  343   22
     clus
vv    ZNF286A MUTATED ZNF286A WILD-TYPE
  NO                7               343
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ZNF286A MUTATED                      5                             2
  ZNF286A WILD-TYPE                  310                            45
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ZNF286A MUTATED                       2                              0
  ZNF286A WILD-TYPE                   104                             10
D587V10, multiclass
                                clus
vv                               ZNF286A MUTATED ZNF286A WILD-TYPE
  COLON ADENOCARCINOMA                         5               310
  COLON MUCINOUS ADENOCARCINOMA                2                45
  RECTAL ADENOCARCINOMA                        2               104
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  ZNF286A MUTATED     5   0   1   1
  ZNF286A WILD-TYPE 340   4  30  24
D587V11, multiclass
    clus
vv   ZNF286A MUTATED ZNF286A WILD-TYPE
  R0               5               340
  R1               0                 4
  R2               1                30
  RX               1                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D587V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF286A MUTATED                                  0     1
  ZNF286A WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  ZNF286A MUTATED                           1     3
  ZNF286A WILD-TYPE                        21   223
D587V13, multiclass
                                  clus
vv                                 ZNF286A MUTATED ZNF286A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                10
  BLACK OR AFRICAN AMERICAN                      1                21
  WHITE                                          3               223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(588) Variable = AK3L1 MUTATION ANALYSIS
D588V1, survival
                 sevent
clus2               0   1
  AK3L1 MUTATED     4   0
  AK3L1 WILD-TYPE 374  93
  AK3L1 MUTATED AK3L1 WILD-TYPE 
              4             467 
  AK3L1 MUTATED AK3L1 WILD-TYPE 
              0              93 
$`AK3L1 MUTATED`
TCGA-A6-6781 TCGA-CM-6168 TCGA-G4-6321 TCGA-DC-5337 
       19.66        12.99        22.09        15.02 

$`AK3L1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       21.99        14.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       63.62        61.91        36.00        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  AK3L1 MUTATED AK3L1 WILD-TYPE 
          12.99            0.00 
  AK3L1 MUTATED AK3L1 WILD-TYPE 
          22.09          148.01 
  AK3L1 MUTATED AK3L1 WILD-TYPE 
          17.34           20.28 
[1] "13.0 - 22.1 (17.3)" "0.0 - 148.0 (20.3)"
[1] "hr="     "3300000"
D588V2, continuous
D588V3, binary
                 cls
clus                0   1
  AK3L1 MUTATED     3   1
  AK3L1 WILD-TYPE 363 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AK3L1 MUTATED      3    1
  AK3L1 WILD-TYPE  363  118
        clus
vv       AK3L1 MUTATED AK3L1 WILD-TYPE
  COLON              3             363
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  AK3L1 MUTATED         1        0        0         1         0         0
  AK3L1 WILD-TYPE      90        1       32       137        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AK3L1 MUTATED           1          0          0          1        0         0
  AK3L1 WILD-TYPE        23         11         59         41       48        18
                 vv
clus              STAGE IVB
  AK3L1 MUTATED           0
  AK3L1 WILD-TYPE         1
D588V4, multiclass
            clus
vv           AK3L1 MUTATED AK3L1 WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              1             137
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             1              41
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  AK3L1 MUTATED     1   1   1   1
  AK3L1 WILD-TYPE  16  91 328  49
D588V5, multiclass
    clus
vv   AK3L1 MUTATED AK3L1 WILD-TYPE
  T1             1              16
  T2             1              91
  T3             1             328
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  AK3L1 MUTATED     2   2   0
  AK3L1 WILD-TYPE 285 111  87
D588V6, multiclass
    clus
vv   AK3L1 MUTATED AK3L1 WILD-TYPE
  N0             2             285
  N1             2             111
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D588V7, binary
                 cls
clus                0   1
  AK3L1 MUTATED     2   0
  AK3L1 WILD-TYPE 373  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AK3L1 MUTATED      2    0
  AK3L1 WILD-TYPE  373   65
   clus
vv  AK3L1 MUTATED AK3L1 WILD-TYPE
  0             2             373
  1             0              65
[1] 2 2
[1] FALSE
D588V8, binary
                 cls
clus                0   1
  AK3L1 MUTATED     2   2
  AK3L1 WILD-TYPE 223 262
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AK3L1 MUTATED      2    2
  AK3L1 WILD-TYPE  223  262
        clus
vv       AK3L1 MUTATED AK3L1 WILD-TYPE
  FEMALE             2             223
  MALE               2             262
[1] 2 2
[1] FALSE
D588V9, binary
                 cls
clus                0   1
  AK3L1 MUTATED     4   0
  AK3L1 WILD-TYPE 346  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AK3L1 MUTATED      4    0
  AK3L1 WILD-TYPE  346   22
     clus
vv    AK3L1 MUTATED AK3L1 WILD-TYPE
  NO              4             346
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  AK3L1 MUTATED                      2                             1
  AK3L1 WILD-TYPE                  313                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  AK3L1 MUTATED                       1                              0
  AK3L1 WILD-TYPE                   105                             10
D588V10, multiclass
                                clus
vv                               AK3L1 MUTATED AK3L1 WILD-TYPE
  COLON ADENOCARCINOMA                       2             313
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  AK3L1 MUTATED     4   0   0   0
  AK3L1 WILD-TYPE 341   4  31  25
D588V11, multiclass
    clus
vv   AK3L1 MUTATED AK3L1 WILD-TYPE
  R0             4             341
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D588V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AK3L1 MUTATED                                  0     0
  AK3L1 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  AK3L1 MUTATED                           1     3
  AK3L1 WILD-TYPE                        21   223
D588V13, multiclass
                                  clus
vv                                 AK3L1 MUTATED AK3L1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        3             223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(589) Variable = PIK3C3 MUTATION ANALYSIS
D589V1, survival
                  sevent
clus2                0   1
  PIK3C3 MUTATED    21   4
  PIK3C3 WILD-TYPE 357  89
  PIK3C3 MUTATED PIK3C3 WILD-TYPE 
              25              446 
  PIK3C3 MUTATED PIK3C3 WILD-TYPE 
               4               89 
$`PIK3C3 MUTATED`
TCGA-A6-5665 TCGA-AA-3492 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3660 TCGA-AA-3864 
       22.06         3.02        17.95        29.95        78.08        53.00 
TCGA-AA-A00J TCGA-AD-6888 TCGA-AD-6889 TCGA-AU-6004 TCGA-AY-6197 TCGA-AZ-6601 
       18.05        15.52        56.55        27.09        21.44       100.01 
TCGA-CA-6717 TCGA-CK-6748 TCGA-CM-4752 TCGA-CM-6168 TCGA-D5-6533 TCGA-D5-6536 
       12.76         1.91        13.02        12.99         1.32        17.85 
TCGA-D5-6540 TCGA-F4-6703 TCGA-G4-6586 TCGA-G4-6626 TCGA-AF-4110 TCGA-AG-A002 
       16.14        47.87        35.80        46.75        14.50        20.98 
TCGA-DY-A0XA 
      126.44 

$`PIK3C3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 
       20.12        19.66        20.28         7.04         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       24.00        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       61.02         6.05         6.97        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       30.05        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 
        0.20        14.50        16.31         0.95        33.01        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 
       88.21        49.41         6.77        12.10        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07        12.20        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       21.14        82.95       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       25.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 
       43.27        15.12         4.80        17.13        12.49        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       35.74         6.18         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 
       63.62        61.91        36.00        22.09        13.78        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       91.79        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       19.10        34.49        10.39        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
        5.29        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  PIK3C3 MUTATED PIK3C3 WILD-TYPE 
            1.32             0.00 
  PIK3C3 MUTATED PIK3C3 WILD-TYPE 
          126.44           148.01 
  PIK3C3 MUTATED PIK3C3 WILD-TYPE 
          20.980           20.155 
[1] "1.3 - 126.4 (21.0)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.5"
D589V2, continuous
D589V3, binary
                  cls
clus                 0   1
  PIK3C3 MUTATED    23   2
  PIK3C3 WILD-TYPE 343 117
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3C3 MUTATED     23    2
  PIK3C3 WILD-TYPE  343  117
        clus
vv       PIK3C3 MUTATED PIK3C3 WILD-TYPE
  COLON              23              343
  RECTUM              2              117
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PIK3C3 MUTATED         3        0        5        13         0         0
  PIK3C3 WILD-TYPE      88        1       27       125        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PIK3C3 MUTATED           0          0          3          0        1
  PIK3C3 WILD-TYPE        24         11         56         42       47
                  vv
clus               STAGE IVA STAGE IVB
  PIK3C3 MUTATED           1         0
  PIK3C3 WILD-TYPE        17         1
D589V4, multiclass
            clus
vv           PIK3C3 MUTATED PIK3C3 WILD-TYPE
  STAGE I                 3               88
  STAGE IA                0                1
  STAGE II                5               27
  STAGE IIA              13              125
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              3               56
  STAGE IIIC              0               42
  STAGE IV                1               47
  STAGE IVA               1               17
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  PIK3C3 MUTATED     0   3  19   4
  PIK3C3 WILD-TYPE  17  89 310  46
D589V5, multiclass
    clus
vv   PIK3C3 MUTATED PIK3C3 WILD-TYPE
  T1              0               17
  T2              3               89
  T3             19              310
  T4              4               46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  PIK3C3 MUTATED    22   3   1
  PIK3C3 WILD-TYPE 265 110  86
D589V6, multiclass
    clus
vv   PIK3C3 MUTATED PIK3C3 WILD-TYPE
  N0             22              265
  N1              3              110
  N2              1               86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D589V7, binary
                  cls
clus                 0   1
  PIK3C3 MUTATED    23   1
  PIK3C3 WILD-TYPE 352  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3C3 MUTATED     23    1
  PIK3C3 WILD-TYPE  352   64
   clus
vv  PIK3C3 MUTATED PIK3C3 WILD-TYPE
  0             23              352
  1              1               64
[1] 2 2
[1] FALSE
D589V8, binary
                  cls
clus                 0   1
  PIK3C3 MUTATED    12  14
  PIK3C3 WILD-TYPE 213 250
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3C3 MUTATED     12   14
  PIK3C3 WILD-TYPE  213  250
        clus
vv       PIK3C3 MUTATED PIK3C3 WILD-TYPE
  FEMALE             12              213
  MALE               14              250
[1] 2 2
[1] FALSE
D589V9, binary
                  cls
clus                 0   1
  PIK3C3 MUTATED    21   0
  PIK3C3 WILD-TYPE 329  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3C3 MUTATED     21    0
  PIK3C3 WILD-TYPE  329   22
     clus
vv    PIK3C3 MUTATED PIK3C3 WILD-TYPE
  NO              21              329
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PIK3C3 MUTATED                     18                             5
  PIK3C3 WILD-TYPE                  297                            42
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PIK3C3 MUTATED                       2                              0
  PIK3C3 WILD-TYPE                   104                             10
D589V10, multiclass
                                clus
vv                               PIK3C3 MUTATED PIK3C3 WILD-TYPE
  COLON ADENOCARCINOMA                       18              297
  COLON MUCINOUS ADENOCARCINOMA               5               42
  RECTAL ADENOCARCINOMA                       2              104
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  PIK3C3 MUTATED    21   0   0   2
  PIK3C3 WILD-TYPE 324   4  31  23
D589V11, multiclass
    clus
vv   PIK3C3 MUTATED PIK3C3 WILD-TYPE
  R0             21              324
  R1              0                4
  R2              0               31
  RX              2               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D589V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PIK3C3 MUTATED                                  0     2
  PIK3C3 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  PIK3C3 MUTATED                           2    14
  PIK3C3 WILD-TYPE                        20   212
D589V13, multiclass
                                  clus
vv                                 PIK3C3 MUTATED PIK3C3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                9
  BLACK OR AFRICAN AMERICAN                     2               20
  WHITE                                        14              212
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(590) Variable = POLE MUTATION ANALYSIS
D590V1, survival
                sevent
clus2              0   1
  POLE MUTATED    25   7
  POLE WILD-TYPE 353  86
  POLE MUTATED POLE WILD-TYPE 
            32            439 
  POLE MUTATED POLE WILD-TYPE 
             7             86 
$`POLE MUTATED`
TCGA-A6-4105 TCGA-A6-6141 TCGA-A6-6781 TCGA-AA-3510 TCGA-AA-3518 TCGA-AA-3525 
       14.53         8.38        19.66        63.98         1.02         8.05 
TCGA-AA-3555 TCGA-AA-3660 TCGA-AA-3678 TCGA-AA-3710 TCGA-AA-3815 TCGA-AA-3833 
       29.95        78.08        47.01        26.99        33.04        15.95 
TCGA-AA-3864 TCGA-AA-3977 TCGA-AA-A00J TCGA-AA-A00N TCGA-AA-A010 TCGA-AD-6964 
       53.00        25.02        18.05         4.01        34.98        10.88 
TCGA-AZ-4315 TCGA-AZ-6598 TCGA-AZ-6601 TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-5861 
       58.39        49.41       100.01        12.76        10.06        15.02 
TCGA-CM-6675 TCGA-CM-6678 TCGA-D5-6540 TCGA-DM-A28K TCGA-G4-6303 TCGA-AG-3892 
       13.05        11.01        16.14        98.24        65.85        13.02 
TCGA-AG-A002 TCGA-AG-A01W 
       20.98        70.03 

$`POLE WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 
       16.57        34.65        33.34        32.75        36.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 
       22.06        32.71        27.09        22.52        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 
       20.28         7.04         3.02         1.02        35.01         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
        1.02        13.02        38.99         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
       36.03        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 
       21.01        13.02        24.00        17.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 
       19.99        13.94        19.99        61.02         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3679 
       54.02         2.01        14.01         0.92        50.04        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
       85.05        19.04        19.04        10.06        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
       25.02         1.02        17.98        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       19.00        30.02        34.03        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
       16.31         0.95        33.01        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 
        5.13       106.75        22.36        62.79        88.21         6.77 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
       12.10        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 
       22.03        22.98        30.08        32.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6679 
       14.04        11.01        12.95        11.08        11.08        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
        4.80        17.13        12.49        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
      117.07         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6304 
        0.53        47.41        35.31       133.18        74.56        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       17.95        36.95        17.03        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01Y 
       37.02        15.95        36.03         9.07        12.00        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  POLE MUTATED POLE WILD-TYPE 
          1.02           0.00 
  POLE MUTATED POLE WILD-TYPE 
        100.01         148.01 
  POLE MUTATED POLE WILD-TYPE 
         20.32          20.19 
[1] "1.0 - 100.0 (20.3)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.2"
D590V2, continuous
D590V3, binary
                cls
clus               0   1
  POLE MUTATED    31   3
  POLE WILD-TYPE 335 116
[1] "tbl2"
                cls
clus             [,1] [,2]
  POLE MUTATED     31    3
  POLE WILD-TYPE  335  116
        clus
vv       POLE MUTATED POLE WILD-TYPE
  COLON            31            335
  RECTUM            3            116
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  POLE MUTATED         4        0        6        13         2         0
  POLE WILD-TYPE      87        1       26       125         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  POLE MUTATED           1          0          2          1        1         1
  POLE WILD-TYPE        23         11         57         41       47        17
                vv
clus             STAGE IVB
  POLE MUTATED           1
  POLE WILD-TYPE         0
D590V4, multiclass
            clus
vv           POLE MUTATED POLE WILD-TYPE
  STAGE I               4             87
  STAGE IA              0              1
  STAGE II              6             26
  STAGE IIA            13            125
  STAGE IIB             2              8
  STAGE IIC             0              1
  STAGE III             1             23
  STAGE IIIA            0             11
  STAGE IIIB            2             57
  STAGE IIIC            1             41
  STAGE IV              1             47
  STAGE IVA             1             17
  STAGE IVB             1              0
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  POLE MUTATED     1   5  22   6
  POLE WILD-TYPE  16  87 307  44
D590V5, multiclass
    clus
vv   POLE MUTATED POLE WILD-TYPE
  T1            1             16
  T2            5             87
  T3           22            307
  T4            6             44
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  POLE MUTATED    26   6   2
  POLE WILD-TYPE 261 107  85
D590V6, multiclass
    clus
vv   POLE MUTATED POLE WILD-TYPE
  N0           26            261
  N1            6            107
  N2            2             85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D590V7, binary
                cls
clus               0   1
  POLE MUTATED    26   3
  POLE WILD-TYPE 349  62
[1] "tbl2"
                cls
clus             [,1] [,2]
  POLE MUTATED     26    3
  POLE WILD-TYPE  349   62
   clus
vv  POLE MUTATED POLE WILD-TYPE
  0           26            349
  1            3             62
[1] 2 2
[1] FALSE
D590V8, binary
                cls
clus               0   1
  POLE MUTATED    15  19
  POLE WILD-TYPE 210 245
[1] "tbl2"
                cls
clus             [,1] [,2]
  POLE MUTATED     15   19
  POLE WILD-TYPE  210  245
        clus
vv       POLE MUTATED POLE WILD-TYPE
  FEMALE           15            210
  MALE             19            245
[1] 2 2
[1] FALSE
D590V9, binary
                cls
clus               0   1
  POLE MUTATED    28   0
  POLE WILD-TYPE 322  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  POLE MUTATED     28    0
  POLE WILD-TYPE  322   22
     clus
vv    POLE MUTATED POLE WILD-TYPE
  NO            28            322
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  POLE MUTATED                     24                             7
  POLE WILD-TYPE                  291                            40
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  POLE MUTATED                       3                              0
  POLE WILD-TYPE                   103                             10
D590V10, multiclass
                                clus
vv                               POLE MUTATED POLE WILD-TYPE
  COLON ADENOCARCINOMA                     24            291
  COLON MUCINOUS ADENOCARCINOMA             7             40
  RECTAL ADENOCARCINOMA                     3            103
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  POLE MUTATED    24   0   0   3
  POLE WILD-TYPE 321   4  31  22
D590V11, multiclass
    clus
vv   POLE MUTATED POLE WILD-TYPE
  R0           24            321
  R1            0              4
  R2            0             31
  RX            3             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D590V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  POLE MUTATED                                  0     2
  POLE WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  POLE MUTATED                           2    12
  POLE WILD-TYPE                        20   214
D590V13, multiclass
                                  clus
vv                                 POLE MUTATED POLE WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              9
  BLACK OR AFRICAN AMERICAN                   2             20
  WHITE                                      12            214
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(591) Variable = PNP MUTATION ANALYSIS
D591V1, survival
               sevent
clus2             0   1
  PNP MUTATED     0   3
  PNP WILD-TYPE 378  90
  PNP MUTATED PNP WILD-TYPE 
            3           468 
  PNP MUTATED PNP WILD-TYPE 
            3            90 
$`PNP MUTATED`
TCGA-AA-3492 TCGA-AA-3845 TCGA-AZ-6598 
        3.02         0.00        49.41 

$`PNP WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 
       17.98        15.95        38.99        37.02        14.93        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 
      106.75        22.36        62.79        88.21         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  PNP MUTATED PNP WILD-TYPE 
            0             0 
  PNP MUTATED PNP WILD-TYPE 
        49.41        148.01 
  PNP MUTATED PNP WILD-TYPE 
        3.020        20.235 
[1] "0.0 - 49.4 (3.0)"   "0.0 - 148.0 (20.2)"
[1] "hr=" "6.8"
D591V2, continuous
D591V3, binary
               cls
clus              0   1
  PNP MUTATED     4   0
  PNP WILD-TYPE 362 119
[1] "tbl2"
               cls
clus            [,1] [,2]
  PNP MUTATED      4    0
  PNP WILD-TYPE  362  119
        clus
vv       PNP MUTATED PNP WILD-TYPE
  COLON            4           362
  RECTUM           0           119
[1] 2 2
[1] FALSE
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PNP MUTATED         1        0        2         1         0         0
  PNP WILD-TYPE      90        1       30       137        10         1
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PNP MUTATED           0          0          0          0        0         0
  PNP WILD-TYPE        24         11         59         42       48        18
               vv
clus            STAGE IVB
  PNP MUTATED           0
  PNP WILD-TYPE         1
D591V4, multiclass
            clus
vv           PNP MUTATED PNP WILD-TYPE
  STAGE I              1            90
  STAGE IA             0             1
  STAGE II             2            30
  STAGE IIA            1           137
  STAGE IIB            0            10
  STAGE IIC            0             1
  STAGE III            0            24
  STAGE IIIA           0            11
  STAGE IIIB           0            59
  STAGE IIIC           0            42
  STAGE IV             0            48
  STAGE IVA            0            18
  STAGE IVB            0             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  PNP MUTATED     0   1   3   0
  PNP WILD-TYPE  17  91 326  50
D591V5, multiclass
    clus
vv   PNP MUTATED PNP WILD-TYPE
  T1           0            17
  T2           1            91
  T3           3           326
  T4           0            50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2
  PNP MUTATED     4   0   0
  PNP WILD-TYPE 283 113  87
D591V6, multiclass
    clus
vv   PNP MUTATED PNP WILD-TYPE
  N0           4           283
  N1           0           113
  N2           0            87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D591V7, binary
               cls
clus              0   1
  PNP MUTATED     2   0
  PNP WILD-TYPE 373  65
[1] "tbl2"
               cls
clus            [,1] [,2]
  PNP MUTATED      2    0
  PNP WILD-TYPE  373   65
   clus
vv  PNP MUTATED PNP WILD-TYPE
  0           2           373
  1           0            65
[1] 2 2
[1] FALSE
D591V8, binary
               cls
clus              0   1
  PNP MUTATED     3   1
  PNP WILD-TYPE 222 263
[1] "tbl2"
               cls
clus            [,1] [,2]
  PNP MUTATED      3    1
  PNP WILD-TYPE  222  263
        clus
vv       PNP MUTATED PNP WILD-TYPE
  FEMALE           3           222
  MALE             1           263
[1] 2 2
[1] FALSE
D591V9, binary
               cls
clus              0   1
  PNP MUTATED     2   0
  PNP WILD-TYPE 348  22
[1] "tbl2"
               cls
clus            [,1] [,2]
  PNP MUTATED      2    0
  PNP WILD-TYPE  348   22
     clus
vv    PNP MUTATED PNP WILD-TYPE
  NO            2           348
  YES           0            22
[1] 2 2
[1] FALSE
               vv
clus            COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PNP MUTATED                      4                             0
  PNP WILD-TYPE                  311                            47
               vv
clus            RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PNP MUTATED                       0                              0
  PNP WILD-TYPE                   106                             10
D591V10, multiclass
                                clus
vv                               PNP MUTATED PNP WILD-TYPE
  COLON ADENOCARCINOMA                     4           311
  COLON MUCINOUS ADENOCARCINOMA            0            47
  RECTAL ADENOCARCINOMA                    0           106
  RECTAL MUCINOUS ADENOCARCINOMA           0            10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             R0  R1  R2  RX
  PNP MUTATED     2   0   0   1
  PNP WILD-TYPE 343   4  31  24
D591V11, multiclass
    clus
vv   PNP MUTATED PNP WILD-TYPE
  R0           2           343
  R1           0             4
  R2           0            31
  RX           1            24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D591V12, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PNP MUTATED                                  0     0
  PNP WILD-TYPE                                1    11
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  PNP MUTATED                           0     2
  PNP WILD-TYPE                        22   224
D591V13, multiclass
[1] "Remove cluster labels:" "PNP MUTATED"           
clus
  PNP MUTATED PNP WILD-TYPE 
            2           258 
   TCGA-A6-2671    TCGA-A6-2672    TCGA-A6-2674    TCGA-A6-2676    TCGA-A6-2677 
"PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" 
   TCGA-A6-2678    TCGA-A6-2683    TCGA-A6-3807    TCGA-A6-3808    TCGA-A6-3809 
"PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" 
   TCGA-A6-3810    TCGA-A6-4105    TCGA-A6-5656    TCGA-A6-5657    TCGA-A6-5659 
"PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" 
   TCGA-A6-5660    TCGA-A6-5661    TCGA-A6-5662    TCGA-A6-5664    TCGA-A6-5665 
"PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" 
   TCGA-A6-5666    TCGA-A6-6137    TCGA-A6-6138    TCGA-A6-6141    TCGA-A6-6142 
"PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" 
   TCGA-A6-6648    TCGA-A6-6649    TCGA-A6-6651    TCGA-A6-6652    TCGA-A6-6653 
"PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" 
   TCGA-A6-6654    TCGA-A6-6780    TCGA-A6-6781    TCGA-A6-6782    TCGA-AD-5900 
"PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" 
   TCGA-AD-6548    TCGA-AD-6888    TCGA-AD-6889    TCGA-AD-6890    TCGA-AD-6895 
"PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" 
   TCGA-AD-6899    TCGA-AD-6901    TCGA-AD-6963    TCGA-AD-6964    TCGA-AD-6965 
"PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" 
   TCGA-AU-3779    TCGA-AU-6004    TCGA-AY-4070    TCGA-AY-4071    TCGA-AY-5543 
"PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" 
   TCGA-AY-6196    TCGA-AY-6197    TCGA-AY-6386    TCGA-AZ-4315    TCGA-AZ-4323 
"PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" 
   TCGA-AZ-4616    TCGA-AZ-4681    TCGA-AZ-4682    TCGA-AZ-5403    TCGA-AZ-5407 
"PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" 
   TCGA-AZ-6599    TCGA-AZ-6600    TCGA-AZ-6601    TCGA-AZ-6603    TCGA-AZ-6605 
"PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" 
   TCGA-AZ-6606    TCGA-AZ-6607    TCGA-AZ-6608    TCGA-CA-5254    TCGA-CA-5255 
"PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" 
   TCGA-CA-5796    TCGA-CA-5797    TCGA-CA-6715    TCGA-CA-6716    TCGA-CA-6717 
"PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" 
   TCGA-CA-6718    TCGA-CA-6719    TCGA-CK-4947    TCGA-CK-4948    TCGA-CK-4950 
"PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" 
   TCGA-CK-4952    TCGA-CK-5912    TCGA-CK-5913    TCGA-CK-5914    TCGA-CK-5916 
"PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" 
   TCGA-CK-6746    TCGA-CK-6747    TCGA-CK-6748    TCGA-CK-6751    TCGA-CM-4743 
"PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" 
   TCGA-CM-4744    TCGA-CM-4746    TCGA-CM-4747    TCGA-CM-4752    TCGA-CM-5341 
"PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" 
   TCGA-CM-5344    TCGA-CM-5348    TCGA-CM-5349    TCGA-CM-5860    TCGA-CM-5861 
"PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" 
   TCGA-CM-5862    TCGA-CM-5863    TCGA-CM-5864    TCGA-CM-5868    TCGA-CM-6161 
"PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" 
   TCGA-CM-6162    TCGA-CM-6163    TCGA-CM-6164    TCGA-CM-6165    TCGA-CM-6166 
"PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" 
   TCGA-CM-6167    TCGA-CM-6168    TCGA-CM-6169    TCGA-CM-6170    TCGA-CM-6171 
"PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" 
   TCGA-CM-6172    TCGA-CM-6674    TCGA-CM-6675    TCGA-CM-6676    TCGA-CM-6677 
"PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" 
   TCGA-CM-6678    TCGA-CM-6679    TCGA-CM-6680    TCGA-D5-5537    TCGA-D5-5538 
"PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" 
   TCGA-D5-5539    TCGA-D5-5540    TCGA-D5-5541    TCGA-D5-6529    TCGA-D5-6532 
"PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" 
   TCGA-D5-6533    TCGA-D5-6534    TCGA-D5-6535    TCGA-D5-6536    TCGA-D5-6537 
"PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" 
   TCGA-D5-6538    TCGA-D5-6539    TCGA-D5-6540    TCGA-D5-6541    TCGA-D5-6898 
"PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" 
   TCGA-D5-6920    TCGA-D5-6922    TCGA-D5-6923    TCGA-D5-6924    TCGA-D5-6926 
"PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" 
   TCGA-D5-6927    TCGA-D5-6928    TCGA-D5-6929    TCGA-D5-6930    TCGA-D5-6931 
"PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" 
   TCGA-D5-6932    TCGA-D5-7000    TCGA-DM-A0X9    TCGA-DM-A0XD    TCGA-DM-A0XF 
"PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" 
   TCGA-DM-A1D0    TCGA-DM-A1D4    TCGA-DM-A1D6    TCGA-DM-A1D7    TCGA-DM-A1D8 
"PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" 
   TCGA-DM-A1D9    TCGA-DM-A1DA    TCGA-DM-A1DB    TCGA-DM-A1HA    TCGA-DM-A1HB 
"PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" 
   TCGA-DM-A282    TCGA-DM-A285    TCGA-DM-A28C    TCGA-DM-A28E    TCGA-DM-A28F 
"PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" 
   TCGA-DM-A28G    TCGA-DM-A28H    TCGA-DM-A28K    TCGA-F4-6459    TCGA-F4-6460 
"PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" 
   TCGA-F4-6569    TCGA-F4-6570    TCGA-F4-6703    TCGA-F4-6704    TCGA-F4-6805 
"PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" 
   TCGA-F4-6806    TCGA-F4-6807    TCGA-F4-6808    TCGA-F4-6809    TCGA-F4-6854 
"PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" 
   TCGA-F4-6855    TCGA-F4-6856    TCGA-G4-6293    TCGA-G4-6299    TCGA-G4-6303 
"PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" 
   TCGA-G4-6304    TCGA-G4-6306    TCGA-G4-6307    TCGA-G4-6309    TCGA-G4-6310 
"PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" 
   TCGA-G4-6315    TCGA-G4-6317    TCGA-G4-6321    TCGA-G4-6323    TCGA-G4-6586 
"PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" 
   TCGA-G4-6588    TCGA-G4-6625    TCGA-G4-6626    TCGA-G4-6628    TCGA-AF-2687 
"PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" 
   TCGA-AF-2689    TCGA-AF-2691    TCGA-AF-2692    TCGA-AF-2693    TCGA-AF-3400 
"PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" 
   TCGA-AF-3913    TCGA-AF-4110    TCGA-AF-5654    TCGA-AF-6136    TCGA-AF-6655 
"PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" 
   TCGA-AF-6672    TCGA-AH-6544    TCGA-AH-6547    TCGA-AH-6549    TCGA-AH-6643 
"PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" 
   TCGA-AH-6644    TCGA-CI-6619    TCGA-CI-6620    TCGA-CI-6621    TCGA-CI-6622 
"PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" 
   TCGA-CI-6624    TCGA-CL-5917    TCGA-CL-5918    TCGA-DC-5337    TCGA-DC-5869 
"PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" 
   TCGA-DC-6155    TCGA-DC-6157    TCGA-DC-6158    TCGA-DC-6160    TCGA-DC-6681 
"PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" 
   TCGA-DC-6682    TCGA-DC-6683    TCGA-DT-5265    TCGA-DY-A0XA    TCGA-DY-A1DC 
"PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" 
   TCGA-DY-A1DD    TCGA-DY-A1DF    TCGA-DY-A1DG    TCGA-DY-A1H8    TCGA-EF-5830 
"PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" 
   TCGA-EI-6506    TCGA-EI-6507    TCGA-EI-6508    TCGA-EI-6510    TCGA-F5-6464 
"PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" 
   TCGA-F5-6465    TCGA-F5-6571    TCGA-F5-6702    TCGA-F5-6811    TCGA-F5-6812 
"PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" 
   TCGA-F5-6813    TCGA-G5-6235    TCGA-G5-6641 
"PNP WILD-TYPE" "PNP WILD-TYPE" "PNP WILD-TYPE" 

Clustering(592) Variable = ZNF570 MUTATION ANALYSIS
D592V1, survival
                  sevent
clus2                0   1
  ZNF570 MUTATED     9   1
  ZNF570 WILD-TYPE 369  92
  ZNF570 MUTATED ZNF570 WILD-TYPE 
              10              461 
  ZNF570 MUTATED ZNF570 WILD-TYPE 
               1               92 
$`ZNF570 MUTATED`
TCGA-A6-3810 TCGA-AA-3815 TCGA-AA-3833 TCGA-CK-5916 TCGA-CK-6751 TCGA-CM-5868 
       36.53        33.04        15.95        21.14       124.27        17.03 
TCGA-D5-6540 TCGA-G4-6309 TCGA-AG-A002 TCGA-CI-6624 
       16.14        85.48        20.98         4.73 

$`ZNF570 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        32.75        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       10.06        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 
       15.62        49.08        51.32         9.99        82.95         1.91 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        15.02        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 
       15.12        17.85         4.80        17.13        12.49        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
        6.05        33.17         6.97        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  ZNF570 MUTATED ZNF570 WILD-TYPE 
            4.73             0.00 
  ZNF570 MUTATED ZNF570 WILD-TYPE 
          124.27           148.01 
  ZNF570 MUTATED ZNF570 WILD-TYPE 
           21.06            20.12 
[1] "4.7 - 124.3 (21.1)" "0.0 - 148.0 (20.1)"
[1] "hr=" "2.6"
D592V2, continuous
D592V3, binary
                  cls
clus                 0   1
  ZNF570 MUTATED     9   2
  ZNF570 WILD-TYPE 357 117
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF570 MUTATED      9    2
  ZNF570 WILD-TYPE  357  117
        clus
vv       ZNF570 MUTATED ZNF570 WILD-TYPE
  COLON               9              357
  RECTUM              2              117
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZNF570 MUTATED         5        0        0         3         1         0
  ZNF570 WILD-TYPE      86        1       32       135         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF570 MUTATED           0          0          1          0        0
  ZNF570 WILD-TYPE        24         11         58         42       48
                  vv
clus               STAGE IVA STAGE IVB
  ZNF570 MUTATED           1         0
  ZNF570 WILD-TYPE        17         1
D592V4, multiclass
            clus
vv           ZNF570 MUTATED ZNF570 WILD-TYPE
  STAGE I                 5               86
  STAGE IA                0                1
  STAGE II                0               32
  STAGE IIA               3              135
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              1               58
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               1               17
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZNF570 MUTATED     1   4   4   2
  ZNF570 WILD-TYPE  16  88 325  48
D592V5, multiclass
    clus
vv   ZNF570 MUTATED ZNF570 WILD-TYPE
  T1              1               16
  T2              4               88
  T3              4              325
  T4              2               48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  ZNF570 MUTATED     9   2   0
  ZNF570 WILD-TYPE 278 111  87
D592V6, multiclass
    clus
vv   ZNF570 MUTATED ZNF570 WILD-TYPE
  N0              9              278
  N1              2              111
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D592V7, binary
                  cls
clus                 0   1
  ZNF570 MUTATED     8   1
  ZNF570 WILD-TYPE 367  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF570 MUTATED      8    1
  ZNF570 WILD-TYPE  367   64
   clus
vv  ZNF570 MUTATED ZNF570 WILD-TYPE
  0              8              367
  1              1               64
[1] 2 2
[1] FALSE
D592V8, binary
                  cls
clus                 0   1
  ZNF570 MUTATED     8   3
  ZNF570 WILD-TYPE 217 261
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF570 MUTATED      8    3
  ZNF570 WILD-TYPE  217  261
        clus
vv       ZNF570 MUTATED ZNF570 WILD-TYPE
  FEMALE              8              217
  MALE                3              261
[1] 2 2
[1] FALSE
D592V9, binary
                  cls
clus                 0   1
  ZNF570 MUTATED     9   0
  ZNF570 WILD-TYPE 341  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF570 MUTATED      9    0
  ZNF570 WILD-TYPE  341   22
     clus
vv    ZNF570 MUTATED ZNF570 WILD-TYPE
  NO               9              341
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ZNF570 MUTATED                      7                             2
  ZNF570 WILD-TYPE                  308                            45
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ZNF570 MUTATED                       2                              0
  ZNF570 WILD-TYPE                   104                             10
D592V10, multiclass
                                clus
vv                               ZNF570 MUTATED ZNF570 WILD-TYPE
  COLON ADENOCARCINOMA                        7              308
  COLON MUCINOUS ADENOCARCINOMA               2               45
  RECTAL ADENOCARCINOMA                       2              104
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ZNF570 MUTATED     7   0   0   3
  ZNF570 WILD-TYPE 338   4  31  22
D592V11, multiclass
    clus
vv   ZNF570 MUTATED ZNF570 WILD-TYPE
  R0              7              338
  R1              0                4
  R2              0               31
  RX              3               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D592V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF570 MUTATED                                  0     0
  ZNF570 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZNF570 MUTATED                           1     7
  ZNF570 WILD-TYPE                        21   219
D592V13, multiclass
                                  clus
vv                                 ZNF570 MUTATED ZNF570 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                         7              219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(593) Variable = TNPO1 MUTATION ANALYSIS
D593V1, survival
                 sevent
clus2               0   1
  TNPO1 MUTATED    14   2
  TNPO1 WILD-TYPE 364  91
  TNPO1 MUTATED TNPO1 WILD-TYPE 
             16             455 
  TNPO1 MUTATED TNPO1 WILD-TYPE 
              2              91 
$`TNPO1 MUTATED`
TCGA-A6-3809 TCGA-A6-6141 TCGA-AA-3510 TCGA-AA-3518 TCGA-AA-3966 TCGA-AA-3977 
       32.75         8.38        63.98         1.02         2.01        25.02 
TCGA-AA-A010 TCGA-AU-6004 TCGA-AZ-6598 TCGA-CK-5914 TCGA-CK-5916 TCGA-CM-6678 
       34.98        27.09        49.41         9.99        21.14        11.01 
TCGA-D5-6929 TCGA-G4-6323 TCGA-G4-6586 TCGA-AG-3586 
        4.80        13.78        35.80         1.02 

$`TNPO1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 
       22.06        32.71        27.09        22.52        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3520 
        6.97         1.02        13.02        38.99         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 
       27.42        10.88         0.20        14.50        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 
      106.75        22.36        62.79        88.21         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       15.62        49.08        51.32        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.08        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.04         9.44        11.64         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6588 
       85.48        63.62        61.91        36.00        22.09        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3587 
        8.02         7.07        36.03        20.05        24.00        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  TNPO1 MUTATED TNPO1 WILD-TYPE 
           1.02            0.00 
  TNPO1 MUTATED TNPO1 WILD-TYPE 
          63.98          148.01 
  TNPO1 MUTATED TNPO1 WILD-TYPE 
          17.46           20.19 
[1] "1.0 - 64.0 (17.5)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.3"
D593V2, continuous
D593V3, binary
                 cls
clus                0   1
  TNPO1 MUTATED    16   1
  TNPO1 WILD-TYPE 350 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TNPO1 MUTATED     16    1
  TNPO1 WILD-TYPE  350  118
        clus
vv       TNPO1 MUTATED TNPO1 WILD-TYPE
  COLON             16             350
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TNPO1 MUTATED         2        1        2         5         2         0
  TNPO1 WILD-TYPE      89        0       30       133         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TNPO1 MUTATED           1          0          1          0        1         1
  TNPO1 WILD-TYPE        23         11         58         42       47        17
                 vv
clus              STAGE IVB
  TNPO1 MUTATED           0
  TNPO1 WILD-TYPE         1
D593V4, multiclass
            clus
vv           TNPO1 MUTATED TNPO1 WILD-TYPE
  STAGE I                2              89
  STAGE IA               1               0
  STAGE II               2              30
  STAGE IIA              5             133
  STAGE IIB              2               8
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             0              42
  STAGE IV               1              47
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  TNPO1 MUTATED     1   2  10   3
  TNPO1 WILD-TYPE  16  90 319  47
D593V5, multiclass
    clus
vv   TNPO1 MUTATED TNPO1 WILD-TYPE
  T1             1              16
  T2             2              90
  T3            10             319
  T4             3              47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  TNPO1 MUTATED    13   3   1
  TNPO1 WILD-TYPE 274 110  86
D593V6, multiclass
    clus
vv   TNPO1 MUTATED TNPO1 WILD-TYPE
  N0            13             274
  N1             3             110
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D593V7, binary
                 cls
clus                0   1
  TNPO1 MUTATED    11   2
  TNPO1 WILD-TYPE 364  63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TNPO1 MUTATED     11    2
  TNPO1 WILD-TYPE  364   63
   clus
vv  TNPO1 MUTATED TNPO1 WILD-TYPE
  0            11             364
  1             2              63
[1] 2 2
[1] FALSE
D593V8, binary
                 cls
clus                0   1
  TNPO1 MUTATED    12   5
  TNPO1 WILD-TYPE 213 259
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TNPO1 MUTATED     12    5
  TNPO1 WILD-TYPE  213  259
        clus
vv       TNPO1 MUTATED TNPO1 WILD-TYPE
  FEMALE            12             213
  MALE               5             259
[1] 2 2
[1] FALSE
D593V9, binary
                 cls
clus                0   1
  TNPO1 MUTATED    10   0
  TNPO1 WILD-TYPE 340  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TNPO1 MUTATED     10    0
  TNPO1 WILD-TYPE  340   22
     clus
vv    TNPO1 MUTATED TNPO1 WILD-TYPE
  NO             10             340
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  TNPO1 MUTATED                     14                             2
  TNPO1 WILD-TYPE                  301                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  TNPO1 MUTATED                       0                              0
  TNPO1 WILD-TYPE                   106                             10
D593V10, multiclass
                                clus
vv                               TNPO1 MUTATED TNPO1 WILD-TYPE
  COLON ADENOCARCINOMA                      14             301
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  TNPO1 MUTATED    11   0   0   2
  TNPO1 WILD-TYPE 334   4  31  23
D593V11, multiclass
    clus
vv   TNPO1 MUTATED TNPO1 WILD-TYPE
  R0            11             334
  R1             0               4
  R2             0              31
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D593V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TNPO1 MUTATED                                  0     0
  TNPO1 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  TNPO1 MUTATED                           2     8
  TNPO1 WILD-TYPE                        20   218
D593V13, multiclass
                                  clus
vv                                 TNPO1 MUTATED TNPO1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    2              20
  WHITE                                        8             218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(594) Variable = MAP9 MUTATION ANALYSIS
D594V1, survival
                sevent
clus2              0   1
  MAP9 MUTATED    14   4
  MAP9 WILD-TYPE 364  89
  MAP9 MUTATED MAP9 WILD-TYPE 
            18            453 
  MAP9 MUTATED MAP9 WILD-TYPE 
             4             89 
$`MAP9 MUTATED`
TCGA-A6-5665 TCGA-AA-3662 TCGA-AA-3837 TCGA-AA-3845 TCGA-AA-3977 TCGA-AU-6004 
       22.06         6.05        38.99         0.00        25.02        27.09 
TCGA-AZ-6598 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-5913 TCGA-CM-4743 TCGA-CM-5348 
       49.41        12.76        10.06        51.32        23.05        22.98 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6922 TCGA-D5-6929 TCGA-F5-6465 TCGA-F5-6702 
        4.80        17.13         4.41         4.80        49.51        28.57 

$`MAP9 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       19.99        13.94        19.99        61.02        78.08         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       15.95        37.02        14.93        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.07        12.20        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        49.08         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
      124.27        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.03        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
       15.12        17.85        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        3.68        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6571 TCGA-F5-6811 TCGA-F5-6812 
       20.91        18.28         9.96        31.30        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  MAP9 MUTATED MAP9 WILD-TYPE 
             0              0 
  MAP9 MUTATED MAP9 WILD-TYPE 
         51.32         148.01 
  MAP9 MUTATED MAP9 WILD-TYPE 
         22.52          20.12 
[1] "0.0 - 51.3 (22.5)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.3"
D594V2, continuous
D594V3, binary
                cls
clus               0   1
  MAP9 MUTATED    16   2
  MAP9 WILD-TYPE 350 117
[1] "tbl2"
                cls
clus             [,1] [,2]
  MAP9 MUTATED     16    2
  MAP9 WILD-TYPE  350  117
        clus
vv       MAP9 MUTATED MAP9 WILD-TYPE
  COLON            16            350
  RECTUM            2            117
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MAP9 MUTATED         1        0        1         8         0         0
  MAP9 WILD-TYPE      90        1       31       130        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MAP9 MUTATED           0          1          3          0        2         1
  MAP9 WILD-TYPE        24         10         56         42       46        17
                vv
clus             STAGE IVB
  MAP9 MUTATED           0
  MAP9 WILD-TYPE         1
D594V4, multiclass
            clus
vv           MAP9 MUTATED MAP9 WILD-TYPE
  STAGE I               1             90
  STAGE IA              0              1
  STAGE II              1             31
  STAGE IIA             8            130
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            1             10
  STAGE IIIB            3             56
  STAGE IIIC            0             42
  STAGE IV              2             46
  STAGE IVA             1             17
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  MAP9 MUTATED     0   2  15   1
  MAP9 WILD-TYPE  17  90 314  49
D594V5, multiclass
    clus
vv   MAP9 MUTATED MAP9 WILD-TYPE
  T1            0             17
  T2            2             90
  T3           15            314
  T4            1             49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  MAP9 MUTATED    11   5   2
  MAP9 WILD-TYPE 276 108  85
D594V6, multiclass
    clus
vv   MAP9 MUTATED MAP9 WILD-TYPE
  N0           11            276
  N1            5            108
  N2            2             85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D594V7, binary
                cls
clus               0   1
  MAP9 MUTATED    11   3
  MAP9 WILD-TYPE 364  62
[1] "tbl2"
                cls
clus             [,1] [,2]
  MAP9 MUTATED     11    3
  MAP9 WILD-TYPE  364   62
   clus
vv  MAP9 MUTATED MAP9 WILD-TYPE
  0           11            364
  1            3             62
[1] 2 2
[1] FALSE
D594V8, binary
                cls
clus               0   1
  MAP9 MUTATED     9   9
  MAP9 WILD-TYPE 216 255
[1] "tbl2"
                cls
clus             [,1] [,2]
  MAP9 MUTATED      9    9
  MAP9 WILD-TYPE  216  255
        clus
vv       MAP9 MUTATED MAP9 WILD-TYPE
  FEMALE            9            216
  MALE              9            255
[1] 2 2
[1] FALSE
D594V9, binary
                cls
clus               0   1
  MAP9 MUTATED    14   0
  MAP9 WILD-TYPE 336  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  MAP9 MUTATED     14    0
  MAP9 WILD-TYPE  336   22
     clus
vv    MAP9 MUTATED MAP9 WILD-TYPE
  NO            14            336
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MAP9 MUTATED                     14                             2
  MAP9 WILD-TYPE                  301                            45
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MAP9 MUTATED                       2                              0
  MAP9 WILD-TYPE                   104                             10
D594V10, multiclass
                                clus
vv                               MAP9 MUTATED MAP9 WILD-TYPE
  COLON ADENOCARCINOMA                     14            301
  COLON MUCINOUS ADENOCARCINOMA             2             45
  RECTAL ADENOCARCINOMA                     2            104
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  MAP9 MUTATED    12   0   1   3
  MAP9 WILD-TYPE 333   4  30  22
D594V11, multiclass
    clus
vv   MAP9 MUTATED MAP9 WILD-TYPE
  R0           12            333
  R1            0              4
  R2            1             30
  RX            3             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D594V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MAP9 MUTATED                                  0     2
  MAP9 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  MAP9 MUTATED                           0    12
  MAP9 WILD-TYPE                        22   214
D594V13, multiclass
                                  clus
vv                                 MAP9 MUTATED MAP9 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              9
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                      12            214
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(595) Variable = ITPR1 MUTATION ANALYSIS
D595V1, survival
                 sevent
clus2               0   1
  ITPR1 MUTATED    29  10
  ITPR1 WILD-TYPE 349  83
  ITPR1 MUTATED ITPR1 WILD-TYPE 
             39             432 
  ITPR1 MUTATED ITPR1 WILD-TYPE 
             10              83 
$`ITPR1 MUTATED`
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5661 TCGA-A6-5665 TCGA-A6-6781 TCGA-AA-3510 
       32.91        31.63        33.53        22.06        19.66        63.98 
TCGA-AA-3664 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3815 TCGA-AA-3833 TCGA-AA-3845 
       54.02        85.05        19.04        33.04        15.95         0.00 
TCGA-AA-3864 TCGA-AA-3994 TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A02Y TCGA-AD-6895 
       53.00        27.02         4.01        34.98        39.98         0.72 
TCGA-AZ-4315 TCGA-AZ-4682 TCGA-AZ-6598 TCGA-AZ-6601 TCGA-CA-6717 TCGA-CA-6718 
       58.39        22.36        49.41       100.01        12.76        10.06 
TCGA-CK-5913 TCGA-CM-5861 TCGA-CM-6171 TCGA-D5-6533 TCGA-D5-6536 TCGA-DM-A1DB 
       51.32        15.02        14.04         1.32        17.85        44.32 
TCGA-DM-A28F TCGA-F4-6570 TCGA-F4-6703 TCGA-G4-6309 TCGA-G4-6628 TCGA-AG-3892 
       35.97         6.18        47.87        85.48        79.69        13.02 
TCGA-AG-A002 TCGA-AH-6549 TCGA-DC-6160 
       20.98        17.49        19.99 

$`ITPR1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 
       30.44        29.19        23.61        22.09        32.71        27.09 
TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 
       22.52         8.38        25.08        25.18        24.16        21.76 
TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 
       24.69        24.39        23.87        20.12        20.28         7.04 
TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        3.02         1.02        35.01         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.05         6.97         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 
       36.00         5.03        26.99        19.04        10.06        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3837 TCGA-AA-3842 
        0.99        25.02         1.02        17.98        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
       14.93        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        27.02        19.07         7.96        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A03F TCGA-AA-A03J 
        5.03        14.01         0.92        41.00        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 
        0.07        21.37        15.52        56.55         0.79         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
       16.31         0.95        33.01        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 
        5.13       106.75        62.79        88.21         6.77        12.10 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 
        3.06         3.25         3.29         0.07        12.20        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 
       17.56       148.01        85.45        15.62        49.08         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       30.08        32.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 
       14.99        12.99        13.02        15.02        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       18.25        43.27        15.12         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
        7.50       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
      119.93        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.74         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 
       65.85        53.62        44.68        55.04        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       46.75        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       17.95        36.95        17.03        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 
       41.00        38.04       117.11        38.56         1.45         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  ITPR1 MUTATED ITPR1 WILD-TYPE 
              0               0 
  ITPR1 MUTATED ITPR1 WILD-TYPE 
         100.01          148.01 
  ITPR1 MUTATED ITPR1 WILD-TYPE 
          27.02           20.02 
[1] "0.0 - 100.0 (27.0)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1"  
D595V2, continuous
D595V3, binary
                 cls
clus                0   1
  ITPR1 MUTATED    37   4
  ITPR1 WILD-TYPE 329 115
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITPR1 MUTATED     37    4
  ITPR1 WILD-TYPE  329  115
        clus
vv       ITPR1 MUTATED ITPR1 WILD-TYPE
  COLON             37             329
  RECTUM             4             115
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ITPR1 MUTATED         7        0        6        14         2         0
  ITPR1 WILD-TYPE      84        1       26       124         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ITPR1 MUTATED           2          0          5          1        1         1
  ITPR1 WILD-TYPE        22         11         54         41       47        17
                 vv
clus              STAGE IVB
  ITPR1 MUTATED           0
  ITPR1 WILD-TYPE         1
D595V4, multiclass
            clus
vv           ITPR1 MUTATED ITPR1 WILD-TYPE
  STAGE I                7              84
  STAGE IA               0               1
  STAGE II               6              26
  STAGE IIA             14             124
  STAGE IIB              2               8
  STAGE IIC              0               1
  STAGE III              2              22
  STAGE IIIA             0              11
  STAGE IIIB             5              54
  STAGE IIIC             1              41
  STAGE IV               1              47
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ITPR1 MUTATED     1   6  30   4
  ITPR1 WILD-TYPE  16  86 299  46
D595V5, multiclass
    clus
vv   ITPR1 MUTATED ITPR1 WILD-TYPE
  T1             1              16
  T2             6              86
  T3            30             299
  T4             4              46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  ITPR1 MUTATED    32   6   2
  ITPR1 WILD-TYPE 255 107  85
D595V6, multiclass
    clus
vv   ITPR1 MUTATED ITPR1 WILD-TYPE
  N0            32             255
  N1             6             107
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D595V7, binary
                 cls
clus                0   1
  ITPR1 MUTATED    34   2
  ITPR1 WILD-TYPE 341  63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITPR1 MUTATED     34    2
  ITPR1 WILD-TYPE  341   63
   clus
vv  ITPR1 MUTATED ITPR1 WILD-TYPE
  0            34             341
  1             2              63
[1] 2 2
[1] FALSE
D595V8, binary
                 cls
clus                0   1
  ITPR1 MUTATED    16  25
  ITPR1 WILD-TYPE 209 239
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITPR1 MUTATED     16   25
  ITPR1 WILD-TYPE  209  239
        clus
vv       ITPR1 MUTATED ITPR1 WILD-TYPE
  FEMALE            16             209
  MALE              25             239
[1] 2 2
[1] FALSE
D595V9, binary
                 cls
clus                0   1
  ITPR1 MUTATED    32   0
  ITPR1 WILD-TYPE 318  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITPR1 MUTATED     32    0
  ITPR1 WILD-TYPE  318   22
     clus
vv    ITPR1 MUTATED ITPR1 WILD-TYPE
  NO             32             318
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ITPR1 MUTATED                     33                             4
  ITPR1 WILD-TYPE                  282                            43
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ITPR1 MUTATED                       4                              0
  ITPR1 WILD-TYPE                   102                             10
D595V10, multiclass
                                clus
vv                               ITPR1 MUTATED ITPR1 WILD-TYPE
  COLON ADENOCARCINOMA                      33             282
  COLON MUCINOUS ADENOCARCINOMA              4              43
  RECTAL ADENOCARCINOMA                      4             102
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  ITPR1 MUTATED    30   0   1   4
  ITPR1 WILD-TYPE 315   4  30  21
D595V11, multiclass
    clus
vv   ITPR1 MUTATED ITPR1 WILD-TYPE
  R0            30             315
  R1             0               4
  R2             1              30
  RX             4              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D595V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ITPR1 MUTATED                                  0     2
  ITPR1 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ITPR1 MUTATED                           3    20
  ITPR1 WILD-TYPE                        19   206
D595V13, multiclass
                                  clus
vv                                 ITPR1 MUTATED ITPR1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               9
  BLACK OR AFRICAN AMERICAN                    3              19
  WHITE                                       20             206
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(596) Variable = NME7 MUTATION ANALYSIS
D596V1, survival
                sevent
clus2              0   1
  NME7 MUTATED     5   3
  NME7 WILD-TYPE 373  90
  NME7 MUTATED NME7 WILD-TYPE 
             8            463 
  NME7 MUTATED NME7 WILD-TYPE 
             3             90 
$`NME7 MUTATED`
TCGA-AA-A00N TCGA-AA-A010 TCGA-AZ-4315 TCGA-AZ-5403 TCGA-CM-4743 TCGA-AG-3574 
        4.01        34.98        58.39        62.79        23.05        36.03 
TCGA-AG-A002 TCGA-EI-6510 
       20.98        18.28 

$`NME7 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       33.01        21.44        17.82         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
      124.27        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       10.39        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-F5-6464 TCGA-F5-6465 
        0.49        20.55        19.96        20.91         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  NME7 MUTATED NME7 WILD-TYPE 
          4.01           0.00 
  NME7 MUTATED NME7 WILD-TYPE 
         62.79         148.01 
  NME7 MUTATED NME7 WILD-TYPE 
        29.015         20.050 
[1] "4.0 - 62.8 (29.0)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.5"
D596V2, continuous
D596V3, binary
                cls
clus               0   1
  NME7 MUTATED     6   3
  NME7 WILD-TYPE 360 116
[1] "tbl2"
                cls
clus             [,1] [,2]
  NME7 MUTATED      6    3
  NME7 WILD-TYPE  360  116
        clus
vv       NME7 MUTATED NME7 WILD-TYPE
  COLON             6            360
  RECTUM            3            116
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NME7 MUTATED         1        0        3         2         2         0
  NME7 WILD-TYPE      90        1       29       136         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NME7 MUTATED           0          0          0          0        0         1
  NME7 WILD-TYPE        24         11         59         42       48        17
                vv
clus             STAGE IVB
  NME7 MUTATED           0
  NME7 WILD-TYPE         1
D596V4, multiclass
            clus
vv           NME7 MUTATED NME7 WILD-TYPE
  STAGE I               1             90
  STAGE IA              0              1
  STAGE II              3             29
  STAGE IIA             2            136
  STAGE IIB             2              8
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            0             59
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             1             17
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  NME7 MUTATED     0   2   4   3
  NME7 WILD-TYPE  17  90 325  47
D596V5, multiclass
    clus
vv   NME7 MUTATED NME7 WILD-TYPE
  T1            0             17
  T2            2             90
  T3            4            325
  T4            3             47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  NME7 MUTATED     9   0   0
  NME7 WILD-TYPE 278 113  87
D596V6, multiclass
    clus
vv   NME7 MUTATED NME7 WILD-TYPE
  N0            9            278
  N1            0            113
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D596V7, binary
                cls
clus               0   1
  NME7 MUTATED     7   0
  NME7 WILD-TYPE 368  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  NME7 MUTATED      7    0
  NME7 WILD-TYPE  368   65
   clus
vv  NME7 MUTATED NME7 WILD-TYPE
  0            7            368
  1            0             65
[1] 2 2
[1] FALSE
D596V8, binary
                cls
clus               0   1
  NME7 MUTATED     4   5
  NME7 WILD-TYPE 221 259
[1] "tbl2"
                cls
clus             [,1] [,2]
  NME7 MUTATED      4    5
  NME7 WILD-TYPE  221  259
        clus
vv       NME7 MUTATED NME7 WILD-TYPE
  FEMALE            4            221
  MALE              5            259
[1] 2 2
[1] FALSE
D596V9, binary
                cls
clus               0   1
  NME7 MUTATED     7   0
  NME7 WILD-TYPE 343  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  NME7 MUTATED      7    0
  NME7 WILD-TYPE  343   22
     clus
vv    NME7 MUTATED NME7 WILD-TYPE
  NO             7            343
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  NME7 MUTATED                      5                             1
  NME7 WILD-TYPE                  310                            46
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  NME7 MUTATED                       3                              0
  NME7 WILD-TYPE                   103                             10
D596V10, multiclass
                                clus
vv                               NME7 MUTATED NME7 WILD-TYPE
  COLON ADENOCARCINOMA                      5            310
  COLON MUCINOUS ADENOCARCINOMA             1             46
  RECTAL ADENOCARCINOMA                     3            103
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  NME7 MUTATED     8   0   0   0
  NME7 WILD-TYPE 337   4  31  25
D596V11, multiclass
    clus
vv   NME7 MUTATED NME7 WILD-TYPE
  R0            8            337
  R1            0              4
  R2            0             31
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D596V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NME7 MUTATED                                  0     0
  NME7 WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  NME7 MUTATED                           0     4
  NME7 WILD-TYPE                        22   222
D596V13, multiclass
                                  clus
vv                                 NME7 MUTATED NME7 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       4            222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(597) Variable = TNFAIP3 MUTATION ANALYSIS
D597V1, survival
                   sevent
clus2                 0   1
  TNFAIP3 MUTATED    33   4
  TNFAIP3 WILD-TYPE 345  89
  TNFAIP3 MUTATED TNFAIP3 WILD-TYPE 
               37               434 
  TNFAIP3 MUTATED TNFAIP3 WILD-TYPE 
                4                89 
$`TNFAIP3 MUTATED`
TCGA-A6-5661 TCGA-A6-5665 TCGA-A6-6138 TCGA-AA-3510 TCGA-AA-3713 TCGA-AA-3811 
       33.53        22.06        22.52        63.98        19.04        10.06 
TCGA-AA-3950 TCGA-AA-3975 TCGA-AD-6895 TCGA-AU-3779 TCGA-AZ-4315 TCGA-AZ-5407 
       24.00        34.06         0.72        14.50        58.39        88.21 
TCGA-AZ-6599 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5914 
        6.77        12.76        10.06        85.45        15.62         9.99 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-6169 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       23.05        20.02        13.02        15.12        17.85         4.80 
TCGA-D5-6541 TCGA-D5-6929 TCGA-DM-A1HB TCGA-DM-A28K TCGA-G4-6293 TCGA-G4-6299 
       15.58         4.80       135.65        98.24       133.18        74.56 
TCGA-G4-6315 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6628 TCGA-AG-3609 TCGA-AG-3732 
       61.91        13.78        35.80        79.69        19.99        32.98 
TCGA-DT-5265 
        5.29 

$`TNFAIP3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       32.71        27.09         8.38        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 
       20.28         7.04         3.02         1.02        35.01         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       26.99        19.04        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
       56.55         0.79         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
        0.20        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       49.41        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-5912 
        0.07        12.20        14.30        17.56       148.01        49.08 
TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4746 
       51.32        21.14        82.95         1.91       124.27        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       14.99        12.99        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       18.25         1.32        43.27        17.13        12.49        16.14 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
        9.44        11.64         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
      117.07         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
        0.53        47.41        35.31        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6588 
       55.04        85.48        63.62        36.00        22.09        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       91.79        46.75        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       15.95        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  TNFAIP3 MUTATED TNFAIP3 WILD-TYPE 
             0.72              0.00 
  TNFAIP3 MUTATED TNFAIP3 WILD-TYPE 
           135.65            148.01 
  TNFAIP3 MUTATED TNFAIP3 WILD-TYPE 
           20.020            20.235 
[1] "0.7 - 135.7 (20.0)" "0.0 - 148.0 (20.2)"
[1] "hr=" "2.6"
D597V2, continuous
D597V3, binary
                   cls
clus                  0   1
  TNFAIP3 MUTATED    34   3
  TNFAIP3 WILD-TYPE 332 116
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TNFAIP3 MUTATED     34    3
  TNFAIP3 WILD-TYPE  332  116
        clus
vv       TNFAIP3 MUTATED TNFAIP3 WILD-TYPE
  COLON               34               332
  RECTUM               3               116
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TNFAIP3 MUTATED         7        1        2        13         0         0
  TNFAIP3 WILD-TYPE      84        0       30       125        10         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TNFAIP3 MUTATED           2          0          5          3        3
  TNFAIP3 WILD-TYPE        22         11         54         39       45
                   vv
clus                STAGE IVA STAGE IVB
  TNFAIP3 MUTATED           0         0
  TNFAIP3 WILD-TYPE        18         1
D597V4, multiclass
            clus
vv           TNFAIP3 MUTATED TNFAIP3 WILD-TYPE
  STAGE I                  7                84
  STAGE IA                 1                 0
  STAGE II                 2                30
  STAGE IIA               13               125
  STAGE IIB                0                10
  STAGE IIC                0                 1
  STAGE III                2                22
  STAGE IIIA               0                11
  STAGE IIIB               5                54
  STAGE IIIC               3                39
  STAGE IV                 3                45
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  TNFAIP3 MUTATED     1   6  28   1
  TNFAIP3 WILD-TYPE  16  86 301  49
D597V5, multiclass
    clus
vv   TNFAIP3 MUTATED TNFAIP3 WILD-TYPE
  T1               1                16
  T2               6                86
  T3              28               301
  T4               1                49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  TNFAIP3 MUTATED    24   9   4
  TNFAIP3 WILD-TYPE 263 104  83
D597V6, multiclass
    clus
vv   TNFAIP3 MUTATED TNFAIP3 WILD-TYPE
  N0              24               263
  N1               9               104
  N2               4                83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D597V7, binary
                   cls
clus                  0   1
  TNFAIP3 MUTATED    28   3
  TNFAIP3 WILD-TYPE 347  62
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TNFAIP3 MUTATED     28    3
  TNFAIP3 WILD-TYPE  347   62
   clus
vv  TNFAIP3 MUTATED TNFAIP3 WILD-TYPE
  0              28               347
  1               3                62
[1] 2 2
[1] FALSE
D597V8, binary
                   cls
clus                  0   1
  TNFAIP3 MUTATED    14  23
  TNFAIP3 WILD-TYPE 211 241
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TNFAIP3 MUTATED     14   23
  TNFAIP3 WILD-TYPE  211  241
        clus
vv       TNFAIP3 MUTATED TNFAIP3 WILD-TYPE
  FEMALE              14               211
  MALE                23               241
[1] 2 2
[1] FALSE
D597V9, binary
                   cls
clus                  0   1
  TNFAIP3 MUTATED    30   1
  TNFAIP3 WILD-TYPE 320  21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TNFAIP3 MUTATED     30    1
  TNFAIP3 WILD-TYPE  320   21
     clus
vv    TNFAIP3 MUTATED TNFAIP3 WILD-TYPE
  NO               30               320
  YES               1                21
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  TNFAIP3 MUTATED                     29                             4
  TNFAIP3 WILD-TYPE                  286                            43
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  TNFAIP3 MUTATED                       2                              1
  TNFAIP3 WILD-TYPE                   104                              9
D597V10, multiclass
                                clus
vv                               TNFAIP3 MUTATED TNFAIP3 WILD-TYPE
  COLON ADENOCARCINOMA                        29               286
  COLON MUCINOUS ADENOCARCINOMA                4                43
  RECTAL ADENOCARCINOMA                        2               104
  RECTAL MUCINOUS ADENOCARCINOMA               1                 9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  TNFAIP3 MUTATED    23   1   1   6
  TNFAIP3 WILD-TYPE 322   3  30  19
D597V11, multiclass
    clus
vv   TNFAIP3 MUTATED TNFAIP3 WILD-TYPE
  R0              23               322
  R1               1                 3
  R2               1                30
  RX               6                19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D597V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TNFAIP3 MUTATED                                  0     3
  TNFAIP3 WILD-TYPE                                1     8
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  TNFAIP3 MUTATED                           4    23
  TNFAIP3 WILD-TYPE                        18   203
D597V13, multiclass
                                  clus
vv                                 TNFAIP3 MUTATED TNFAIP3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          3                 8
  BLACK OR AFRICAN AMERICAN                      4                18
  WHITE                                         23               203
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(598) Variable = DDX3X MUTATION ANALYSIS
D598V1, survival
                 sevent
clus2               0   1
  DDX3X MUTATED     6   3
  DDX3X WILD-TYPE 372  90
  DDX3X MUTATED DDX3X WILD-TYPE 
              9             462 
  DDX3X MUTATED DDX3X WILD-TYPE 
              3              90 
$`DDX3X MUTATED`
TCGA-AA-3492 TCGA-AA-3662 TCGA-AA-A010 TCGA-AD-6964 TCGA-AU-6004 TCGA-CA-6717 
        3.02         6.05        34.98        10.88        27.09        12.76 
TCGA-CK-4950 TCGA-CM-5344 TCGA-G4-6626 
       85.45        22.03        46.75 

$`DDX3X WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       19.99        13.94        19.99        61.02        78.08         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
        0.79         0.72         5.79        22.42        27.42         0.20 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       14.50        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07        12.20        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
       17.56       148.01        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5349 
       37.02        25.02        13.02        29.06        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       26.17        91.79        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  DDX3X MUTATED DDX3X WILD-TYPE 
           3.02            0.00 
  DDX3X MUTATED DDX3X WILD-TYPE 
          85.45          148.01 
  DDX3X MUTATED DDX3X WILD-TYPE 
         22.030          20.155 
[1] "3.0 - 85.5 (22.0)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.6"
D598V2, continuous
D598V3, binary
                 cls
clus                0   1
  DDX3X MUTATED    10   0
  DDX3X WILD-TYPE 356 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX3X MUTATED     10    0
  DDX3X WILD-TYPE  356  119
        clus
vv       DDX3X MUTATED DDX3X WILD-TYPE
  COLON             10             356
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DDX3X MUTATED         1        0        1         3         1         0
  DDX3X WILD-TYPE      90        1       31       135         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DDX3X MUTATED           0          0          2          0        1         0
  DDX3X WILD-TYPE        24         11         57         42       47        18
                 vv
clus              STAGE IVB
  DDX3X MUTATED           0
  DDX3X WILD-TYPE         1
D598V4, multiclass
            clus
vv           DDX3X MUTATED DDX3X WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              3             135
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             2              57
  STAGE IIIC             0              42
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  DDX3X MUTATED     0   1   6   3
  DDX3X WILD-TYPE  17  91 323  47
D598V5, multiclass
    clus
vv   DDX3X MUTATED DDX3X WILD-TYPE
  T1             0              17
  T2             1              91
  T3             6             323
  T4             3              47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  DDX3X MUTATED     6   2   2
  DDX3X WILD-TYPE 281 111  85
D598V6, multiclass
    clus
vv   DDX3X MUTATED DDX3X WILD-TYPE
  N0             6             281
  N1             2             111
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D598V7, binary
                 cls
clus                0   1
  DDX3X MUTATED     8   1
  DDX3X WILD-TYPE 367  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX3X MUTATED      8    1
  DDX3X WILD-TYPE  367   64
   clus
vv  DDX3X MUTATED DDX3X WILD-TYPE
  0             8             367
  1             1              64
[1] 2 2
[1] FALSE
D598V8, binary
                 cls
clus                0   1
  DDX3X MUTATED     7   3
  DDX3X WILD-TYPE 218 261
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX3X MUTATED      7    3
  DDX3X WILD-TYPE  218  261
        clus
vv       DDX3X MUTATED DDX3X WILD-TYPE
  FEMALE             7             218
  MALE               3             261
[1] 2 2
[1] FALSE
D598V9, binary
                 cls
clus                0   1
  DDX3X MUTATED     8   0
  DDX3X WILD-TYPE 342  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX3X MUTATED      8    0
  DDX3X WILD-TYPE  342   22
     clus
vv    DDX3X MUTATED DDX3X WILD-TYPE
  NO              8             342
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  DDX3X MUTATED                      9                             1
  DDX3X WILD-TYPE                  306                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  DDX3X MUTATED                       0                              0
  DDX3X WILD-TYPE                   106                             10
D598V10, multiclass
                                clus
vv                               DDX3X MUTATED DDX3X WILD-TYPE
  COLON ADENOCARCINOMA                       9             306
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  DDX3X MUTATED     6   1   1   1
  DDX3X WILD-TYPE 339   3  30  24
D598V11, multiclass
    clus
vv   DDX3X MUTATED DDX3X WILD-TYPE
  R0             6             339
  R1             1               3
  R2             1              30
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D598V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DDX3X MUTATED                                  0     1
  DDX3X WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  DDX3X MUTATED                           1     4
  DDX3X WILD-TYPE                        21   222
D598V13, multiclass
                                  clus
vv                                 DDX3X MUTATED DDX3X WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        4             222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(599) Variable = ETV1 MUTATION ANALYSIS
D599V1, survival
                sevent
clus2              0   1
  ETV1 MUTATED    11   3
  ETV1 WILD-TYPE 367  90
  ETV1 MUTATED ETV1 WILD-TYPE 
            14            457 
  ETV1 MUTATED ETV1 WILD-TYPE 
             3             90 
$`ETV1 MUTATED`
TCGA-A6-5661 TCGA-A6-6654 TCGA-AA-3715 TCGA-AA-A00N TCGA-AA-A010 TCGA-AZ-6598 
       33.53        23.87        19.04         4.01        34.98        49.41 
TCGA-CA-6717 TCGA-CM-6677 TCGA-D5-6536 TCGA-D5-6926 TCGA-G4-6304 TCGA-G4-6628 
       12.76        11.08        17.85         9.04        53.62        79.69 
TCGA-AG-A002 TCGA-DC-5337 
       20.98        15.02 

$`ETV1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 
       25.18        24.16        21.76        24.69        24.39        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       88.21         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07        12.20        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6678 TCGA-CM-6679 
       11.01        12.95        13.05        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 
       20.19        18.25         1.32        43.27        15.12         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
        4.41        12.43        14.30         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
       78.12         7.17         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  ETV1 MUTATED ETV1 WILD-TYPE 
          4.01           0.00 
  ETV1 MUTATED ETV1 WILD-TYPE 
         79.69         148.01 
  ETV1 MUTATED ETV1 WILD-TYPE 
         20.01          20.19 
[1] "4.0 - 79.7 (20.0)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1"  
D599V2, continuous
D599V3, binary
                cls
clus               0   1
  ETV1 MUTATED    13   2
  ETV1 WILD-TYPE 353 117
[1] "tbl2"
                cls
clus             [,1] [,2]
  ETV1 MUTATED     13    2
  ETV1 WILD-TYPE  353  117
        clus
vv       ETV1 MUTATED ETV1 WILD-TYPE
  COLON            13            353
  RECTUM            2            117
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ETV1 MUTATED         3        0        2         5         3         0
  ETV1 WILD-TYPE      88        1       30       133         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ETV1 MUTATED           0          0          2          0        0         0
  ETV1 WILD-TYPE        24         11         57         42       48        18
                vv
clus             STAGE IVB
  ETV1 MUTATED           0
  ETV1 WILD-TYPE         1
D599V4, multiclass
            clus
vv           ETV1 MUTATED ETV1 WILD-TYPE
  STAGE I               3             88
  STAGE IA              0              1
  STAGE II              2             30
  STAGE IIA             5            133
  STAGE IIB             3              7
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            2             57
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  ETV1 MUTATED     1   2   8   4
  ETV1 WILD-TYPE  16  90 321  46
D599V5, multiclass
    clus
vv   ETV1 MUTATED ETV1 WILD-TYPE
  T1            1             16
  T2            2             90
  T3            8            321
  T4            4             46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  ETV1 MUTATED    13   2   0
  ETV1 WILD-TYPE 274 111  87
D599V6, multiclass
    clus
vv   ETV1 MUTATED ETV1 WILD-TYPE
  N0           13            274
  N1            2            111
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D599V7, binary
                cls
clus               0   1
  ETV1 MUTATED    14   0
  ETV1 WILD-TYPE 361  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  ETV1 MUTATED     14    0
  ETV1 WILD-TYPE  361   65
   clus
vv  ETV1 MUTATED ETV1 WILD-TYPE
  0           14            361
  1            0             65
[1] 2 2
[1] FALSE
D599V8, binary
                cls
clus               0   1
  ETV1 MUTATED     7   8
  ETV1 WILD-TYPE 218 256
[1] "tbl2"
                cls
clus             [,1] [,2]
  ETV1 MUTATED      7    8
  ETV1 WILD-TYPE  218  256
        clus
vv       ETV1 MUTATED ETV1 WILD-TYPE
  FEMALE            7            218
  MALE              8            256
[1] 2 2
[1] FALSE
D599V9, binary
                cls
clus               0   1
  ETV1 MUTATED    12   1
  ETV1 WILD-TYPE 338  21
[1] "tbl2"
                cls
clus             [,1] [,2]
  ETV1 MUTATED     12    1
  ETV1 WILD-TYPE  338   21
     clus
vv    ETV1 MUTATED ETV1 WILD-TYPE
  NO            12            338
  YES            1             21
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ETV1 MUTATED                     11                             2
  ETV1 WILD-TYPE                  304                            45
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ETV1 MUTATED                       2                              0
  ETV1 WILD-TYPE                   104                             10
D599V10, multiclass
                                clus
vv                               ETV1 MUTATED ETV1 WILD-TYPE
  COLON ADENOCARCINOMA                     11            304
  COLON MUCINOUS ADENOCARCINOMA             2             45
  RECTAL ADENOCARCINOMA                     2            104
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  ETV1 MUTATED    12   0   0   1
  ETV1 WILD-TYPE 333   4  31  24
D599V11, multiclass
    clus
vv   ETV1 MUTATED ETV1 WILD-TYPE
  R0           12            333
  R1            0              4
  R2            0             31
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D599V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ETV1 MUTATED                                  0     1
  ETV1 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  ETV1 MUTATED                           1     8
  ETV1 WILD-TYPE                        21   218
D599V13, multiclass
                                  clus
vv                                 ETV1 MUTATED ETV1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                       8            218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(600) Variable = ACVR2A MUTATION ANALYSIS
D600V1, survival
                  sevent
clus2                0   1
  ACVR2A MUTATED    12   5
  ACVR2A WILD-TYPE 366  88
  ACVR2A MUTATED ACVR2A WILD-TYPE 
              17              454 
  ACVR2A MUTATED ACVR2A WILD-TYPE 
               5               88 
$`ACVR2A MUTATED`
TCGA-A6-2672 TCGA-A6-5665 TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3710 TCGA-AA-A010 
       46.65        22.06         3.02        63.98        26.99        34.98 
TCGA-AA-A01V TCGA-AA-A02F TCGA-AD-6901 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-CA-6717 
       35.01        39.98        22.42        88.21        49.41        12.76 
TCGA-CA-6718 TCGA-CK-6751 TCGA-CM-6677 TCGA-DM-A1DA TCGA-AG-A002 
       10.06       124.27        11.08         7.50        20.98 

$`ACVR2A WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 
       19.66        20.28         7.04         1.02        35.01         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
       35.01         1.02        33.04        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       51.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6964 
       56.55         0.79         0.72         5.79        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       22.36        62.79         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 
        3.25         3.29         0.07        12.20        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       21.14        82.95         1.91        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       12.95        13.05        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
       12.59       140.38        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  ACVR2A MUTATED ACVR2A WILD-TYPE 
            3.02             0.00 
  ACVR2A MUTATED ACVR2A WILD-TYPE 
          124.27           148.01 
  ACVR2A MUTATED ACVR2A WILD-TYPE 
           26.99            20.02 
[1] "3.0 - 124.3 (27.0)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.1"
D600V2, continuous
D600V3, binary
                  cls
clus                 0   1
  ACVR2A MUTATED    17   1
  ACVR2A WILD-TYPE 349 118
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ACVR2A MUTATED     17    1
  ACVR2A WILD-TYPE  349  118
        clus
vv       ACVR2A MUTATED ACVR2A WILD-TYPE
  COLON              17              349
  RECTUM              1              118
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ACVR2A MUTATED         4        0        3         6         1         0
  ACVR2A WILD-TYPE      87        1       29       132         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ACVR2A MUTATED           0          0          1          1        1
  ACVR2A WILD-TYPE        24         11         58         41       47
                  vv
clus               STAGE IVA STAGE IVB
  ACVR2A MUTATED           0         0
  ACVR2A WILD-TYPE        18         1
D600V4, multiclass
            clus
vv           ACVR2A MUTATED ACVR2A WILD-TYPE
  STAGE I                 4               87
  STAGE IA                0                1
  STAGE II                3               29
  STAGE IIA               6              132
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              1               58
  STAGE IIIC              1               41
  STAGE IV                1               47
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ACVR2A MUTATED     1   3  13   1
  ACVR2A WILD-TYPE  16  89 316  49
D600V5, multiclass
    clus
vv   ACVR2A MUTATED ACVR2A WILD-TYPE
  T1              1               16
  T2              3               89
  T3             13              316
  T4              1               49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  ACVR2A MUTATED    15   2   1
  ACVR2A WILD-TYPE 272 111  86
D600V6, multiclass
    clus
vv   ACVR2A MUTATED ACVR2A WILD-TYPE
  N0             15              272
  N1              2              111
  N2              1               86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D600V7, binary
                  cls
clus                 0   1
  ACVR2A MUTATED    14   1
  ACVR2A WILD-TYPE 361  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ACVR2A MUTATED     14    1
  ACVR2A WILD-TYPE  361   64
   clus
vv  ACVR2A MUTATED ACVR2A WILD-TYPE
  0             14              361
  1              1               64
[1] 2 2
[1] FALSE
D600V8, binary
                  cls
clus                 0   1
  ACVR2A MUTATED    12   6
  ACVR2A WILD-TYPE 213 258
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ACVR2A MUTATED     12    6
  ACVR2A WILD-TYPE  213  258
        clus
vv       ACVR2A MUTATED ACVR2A WILD-TYPE
  FEMALE             12              213
  MALE                6              258
[1] 2 2
[1] FALSE
D600V9, binary
                  cls
clus                 0   1
  ACVR2A MUTATED    15   0
  ACVR2A WILD-TYPE 335  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ACVR2A MUTATED     15    0
  ACVR2A WILD-TYPE  335   22
     clus
vv    ACVR2A MUTATED ACVR2A WILD-TYPE
  NO              15              335
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ACVR2A MUTATED                     15                             2
  ACVR2A WILD-TYPE                  300                            45
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ACVR2A MUTATED                       1                              0
  ACVR2A WILD-TYPE                   105                             10
D600V10, multiclass
                                clus
vv                               ACVR2A MUTATED ACVR2A WILD-TYPE
  COLON ADENOCARCINOMA                       15              300
  COLON MUCINOUS ADENOCARCINOMA               2               45
  RECTAL ADENOCARCINOMA                       1              105
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ACVR2A MUTATED    10   0   1   3
  ACVR2A WILD-TYPE 335   4  30  22
D600V11, multiclass
    clus
vv   ACVR2A MUTATED ACVR2A WILD-TYPE
  R0             10              335
  R1              0                4
  R2              1               30
  RX              3               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D600V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ACVR2A MUTATED                                  0     2
  ACVR2A WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ACVR2A MUTATED                           0     8
  ACVR2A WILD-TYPE                        22   218
D600V13, multiclass
                                  clus
vv                                 ACVR2A MUTATED ACVR2A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                9
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         8              218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(601) Variable = RNF20 MUTATION ANALYSIS
D601V1, survival
                 sevent
clus2               0   1
  RNF20 MUTATED    18   3
  RNF20 WILD-TYPE 360  90
  RNF20 MUTATED RNF20 WILD-TYPE 
             21             450 
  RNF20 MUTATED RNF20 WILD-TYPE 
              3              90 
$`RNF20 MUTATED`
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3543 TCGA-AA-3680 TCGA-AA-3685 
       23.87        20.12        19.66         0.99        11.01        37.05 
TCGA-AA-3947 TCGA-AA-A01I TCGA-AD-6964 TCGA-AU-6004 TCGA-AY-6197 TCGA-AZ-6598 
       33.01        31.00        10.88        27.09        21.44        49.41 
TCGA-CM-4746 TCGA-CM-6162 TCGA-CM-6677 TCGA-D5-6928 TCGA-DM-A28H TCGA-G4-6628 
       37.02        12.00        11.08        11.64       117.07        79.69 
TCGA-AG-A002 TCGA-DY-A0XA TCGA-EI-6510 
       20.98       126.44        18.28 

$`RNF20 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3681 
       14.01         0.92        50.04        47.01        15.02         5.98 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 
       31.00         2.01        12.99        24.00        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       12.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 
        0.20        14.50        16.31         0.95        33.01        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       88.21         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       20.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       17.03        15.02         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       12.95        13.05        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 
        4.41        12.43        14.30         9.04         9.44         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28K 
        6.12        81.37       119.93        35.97        60.79        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       20.55        19.96        20.91         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  RNF20 MUTATED RNF20 WILD-TYPE 
           0.99            0.00 
  RNF20 MUTATED RNF20 WILD-TYPE 
         126.44          148.01 
  RNF20 MUTATED RNF20 WILD-TYPE 
         21.440          20.035 
[1] "1.0 - 126.4 (21.4)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.7"
D601V2, continuous
D601V3, binary
                 cls
clus                0   1
  RNF20 MUTATED    18   3
  RNF20 WILD-TYPE 348 116
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RNF20 MUTATED     18    3
  RNF20 WILD-TYPE  348  116
        clus
vv       RNF20 MUTATED RNF20 WILD-TYPE
  COLON             18             348
  RECTUM             3             116
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RNF20 MUTATED         6        0        2         5         1         0
  RNF20 WILD-TYPE      85        1       30       133         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RNF20 MUTATED           0          0          2          2        1         1
  RNF20 WILD-TYPE        24         11         57         40       47        17
                 vv
clus              STAGE IVB
  RNF20 MUTATED           0
  RNF20 WILD-TYPE         1
D601V4, multiclass
            clus
vv           RNF20 MUTATED RNF20 WILD-TYPE
  STAGE I                6              85
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA              5             133
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             2              57
  STAGE IIIC             2              40
  STAGE IV               1              47
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  RNF20 MUTATED     0   7  10   4
  RNF20 WILD-TYPE  17  85 319  46
D601V5, multiclass
    clus
vv   RNF20 MUTATED RNF20 WILD-TYPE
  T1             0              17
  T2             7              85
  T3            10             319
  T4             4              46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  RNF20 MUTATED    15   3   3
  RNF20 WILD-TYPE 272 110  84
D601V6, multiclass
    clus
vv   RNF20 MUTATED RNF20 WILD-TYPE
  N0            15             272
  N1             3             110
  N2             3              84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D601V7, binary
                 cls
clus                0   1
  RNF20 MUTATED    14   1
  RNF20 WILD-TYPE 361  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RNF20 MUTATED     14    1
  RNF20 WILD-TYPE  361   64
   clus
vv  RNF20 MUTATED RNF20 WILD-TYPE
  0            14             361
  1             1              64
[1] 2 2
[1] FALSE
D601V8, binary
                 cls
clus                0   1
  RNF20 MUTATED     9  12
  RNF20 WILD-TYPE 216 252
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RNF20 MUTATED      9   12
  RNF20 WILD-TYPE  216  252
        clus
vv       RNF20 MUTATED RNF20 WILD-TYPE
  FEMALE             9             216
  MALE              12             252
[1] 2 2
[1] FALSE
D601V9, binary
                 cls
clus                0   1
  RNF20 MUTATED    18   0
  RNF20 WILD-TYPE 332  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RNF20 MUTATED     18    0
  RNF20 WILD-TYPE  332   22
     clus
vv    RNF20 MUTATED RNF20 WILD-TYPE
  NO             18             332
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  RNF20 MUTATED                     12                             6
  RNF20 WILD-TYPE                  303                            41
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  RNF20 MUTATED                       3                              0
  RNF20 WILD-TYPE                   103                             10
D601V10, multiclass
                                clus
vv                               RNF20 MUTATED RNF20 WILD-TYPE
  COLON ADENOCARCINOMA                      12             303
  COLON MUCINOUS ADENOCARCINOMA              6              41
  RECTAL ADENOCARCINOMA                      3             103
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  RNF20 MUTATED    14   0   1   0
  RNF20 WILD-TYPE 331   4  30  25
D601V11, multiclass
    clus
vv   RNF20 MUTATED RNF20 WILD-TYPE
  R0            14             331
  R1             0               4
  R2             1              30
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D601V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RNF20 MUTATED                                  0     0
  RNF20 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  RNF20 MUTATED                           1    14
  RNF20 WILD-TYPE                        21   212
D601V13, multiclass
                                  clus
vv                                 RNF20 MUTATED RNF20 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                       14             212
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(602) Variable = ATG2B MUTATION ANALYSIS
D602V1, survival
                 sevent
clus2               0   1
  ATG2B MUTATED    12   5
  ATG2B WILD-TYPE 366  88
  ATG2B MUTATED ATG2B WILD-TYPE 
             17             454 
  ATG2B MUTATED ATG2B WILD-TYPE 
              5              88 
$`ATG2B MUTATED`
TCGA-A6-6780 TCGA-AA-3492 TCGA-AA-3663 TCGA-AA-3681 TCGA-AA-3811 TCGA-AA-3819 
       20.12         3.02         6.97         5.98        10.06        25.02 
TCGA-AA-A00N TCGA-AA-A010 TCGA-AZ-6608 TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-5861 
        4.01        34.98         1.61        12.76        10.06        15.02 
TCGA-CM-6171 TCGA-G4-6628 TCGA-AG-A002 TCGA-AG-A02X TCGA-AH-6544 
       14.04        79.69        20.98        41.00        38.56 

$`ATG2B WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 
       23.87        19.66        20.28         7.04         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
       11.01        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       26.99        19.04        19.04        35.05        33.04         0.99 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 
       22.03        22.98        30.08        32.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 
       35.80        26.17        91.79        46.75        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A032 TCGA-AG-A036 
       49.97         1.94        38.96        61.97        38.04       117.11 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  ATG2B MUTATED ATG2B WILD-TYPE 
           1.61            0.00 
  ATG2B MUTATED ATG2B WILD-TYPE 
          79.69          148.01 
  ATG2B MUTATED ATG2B WILD-TYPE 
          14.04           20.73 
[1] "1.6 - 79.7 (14.0)"  "0.0 - 148.0 (20.7)"
[1] "hr=" "2"  
D602V2, continuous
D602V3, binary
                 cls
clus                0   1
  ATG2B MUTATED    15   3
  ATG2B WILD-TYPE 351 116
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ATG2B MUTATED     15    3
  ATG2B WILD-TYPE  351  116
        clus
vv       ATG2B MUTATED ATG2B WILD-TYPE
  COLON             15             351
  RECTUM             3             116
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ATG2B MUTATED         4        0        2         6         2         0
  ATG2B WILD-TYPE      87        1       30       132         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ATG2B MUTATED           2          1          0          0        0         0
  ATG2B WILD-TYPE        22         10         59         42       48        18
                 vv
clus              STAGE IVB
  ATG2B MUTATED           0
  ATG2B WILD-TYPE         1
D602V4, multiclass
            clus
vv           ATG2B MUTATED ATG2B WILD-TYPE
  STAGE I                4              87
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA              6             132
  STAGE IIB              2               8
  STAGE IIC              0               1
  STAGE III              2              22
  STAGE IIIA             1              10
  STAGE IIIB             0              59
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ATG2B MUTATED     0   5  11   2
  ATG2B WILD-TYPE  17  87 318  48
D602V5, multiclass
    clus
vv   ATG2B MUTATED ATG2B WILD-TYPE
  T1             0              17
  T2             5              87
  T3            11             318
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  ATG2B MUTATED    14   3   1
  ATG2B WILD-TYPE 273 110  86
D602V6, multiclass
    clus
vv   ATG2B MUTATED ATG2B WILD-TYPE
  N0            14             273
  N1             3             110
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D602V7, binary
                 cls
clus                0   1
  ATG2B MUTATED    16   1
  ATG2B WILD-TYPE 359  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ATG2B MUTATED     16    1
  ATG2B WILD-TYPE  359   64
   clus
vv  ATG2B MUTATED ATG2B WILD-TYPE
  0            16             359
  1             1              64
[1] 2 2
[1] FALSE
D602V8, binary
                 cls
clus                0   1
  ATG2B MUTATED     9   9
  ATG2B WILD-TYPE 216 255
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ATG2B MUTATED      9    9
  ATG2B WILD-TYPE  216  255
        clus
vv       ATG2B MUTATED ATG2B WILD-TYPE
  FEMALE             9             216
  MALE               9             255
[1] 2 2
[1] FALSE
D602V9, binary
                 cls
clus                0   1
  ATG2B MUTATED    15   0
  ATG2B WILD-TYPE 335  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ATG2B MUTATED     15    0
  ATG2B WILD-TYPE  335   22
     clus
vv    ATG2B MUTATED ATG2B WILD-TYPE
  NO             15             335
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ATG2B MUTATED                     12                             3
  ATG2B WILD-TYPE                  303                            44
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ATG2B MUTATED                       3                              0
  ATG2B WILD-TYPE                   103                             10
D602V10, multiclass
                                clus
vv                               ATG2B MUTATED ATG2B WILD-TYPE
  COLON ADENOCARCINOMA                      12             303
  COLON MUCINOUS ADENOCARCINOMA              3              44
  RECTAL ADENOCARCINOMA                      3             103
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  ATG2B MUTATED    13   0   0   2
  ATG2B WILD-TYPE 332   4  31  23
D602V11, multiclass
    clus
vv   ATG2B MUTATED ATG2B WILD-TYPE
  R0            13             332
  R1             0               4
  R2             0              31
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D602V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ATG2B MUTATED                                  0     2
  ATG2B WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ATG2B MUTATED                           0     6
  ATG2B WILD-TYPE                        22   220
D602V13, multiclass
                                  clus
vv                                 ATG2B MUTATED ATG2B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               9
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        6             220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(603) Variable = FRY MUTATION ANALYSIS
D603V1, survival
               sevent
clus2             0   1
  FRY MUTATED    33   8
  FRY WILD-TYPE 345  85
  FRY MUTATED FRY WILD-TYPE 
           41           430 
  FRY MUTATED FRY WILD-TYPE 
            8            85 
$`FRY MUTATED`
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-4105 TCGA-A6-5661 TCGA-A6-5665 TCGA-A6-6141 
       33.34        32.75        14.53        33.53        22.06         8.38 
TCGA-AA-3492 TCGA-AA-3663 TCGA-AA-3864 TCGA-AA-3877 TCGA-AA-3947 TCGA-AA-3977 
        3.02         6.97        53.00        31.00        33.01        25.02 
TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01P TCGA-AA-A01R TCGA-AA-A02O TCGA-AA-A03F 
        4.01        34.98        38.07        35.01         0.92        18.05 
TCGA-AD-5900 TCGA-AU-6004 TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-CA-6717 
        0.07        27.09        21.44        58.39        49.41        12.76 
TCGA-CA-6718 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-6168 
       10.06        37.02        25.02        32.02        15.02        12.99 
TCGA-D5-6538 TCGA-DM-A0X9 TCGA-DM-A1DA TCGA-F4-6703 TCGA-F4-6806 TCGA-F4-6855 
       17.13       119.70         7.50        47.87        41.42        47.41 
TCGA-G4-6307 TCGA-G4-6628 TCGA-AG-3892 TCGA-AG-A002 TCGA-F5-6702 
       55.04        79.69        13.02        20.98        28.57 

$`FRY WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       16.57        34.65        36.53        32.91        31.63        30.44 
TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 
       29.19        23.61        22.09        32.71        27.09        22.52 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 
        0.99        31.07        31.07        30.05        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       27.02        29.98        18.05         2.01        12.99        24.00 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       31.00        31.00         1.02         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03J TCGA-AD-6548 
        5.03        14.01        41.00        39.98        40.96        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 
       27.42        10.88         0.20        14.50        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       33.01        17.82         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        88.21         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 
        3.25         3.29         0.07        12.20        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5862 
       13.02        29.06        22.03        22.98        30.08         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6169 TCGA-CM-6170 
       29.03        16.04        21.99        14.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       15.12        17.85         4.80        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
       10.26        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       13.32        12.59       140.38        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
        1.55        34.42        16.24        33.67        13.25         0.53 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 
       35.80        26.17        91.79        46.75        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6811 
       20.91        18.28         9.96        49.51        31.30        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  FRY MUTATED FRY WILD-TYPE 
         0.07          0.00 
  FRY MUTATED FRY WILD-TYPE 
       119.70        148.01 
  FRY MUTATED FRY WILD-TYPE 
        27.09         19.99 
[1] "0.1 - 119.7 (27.1)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.1"
D603V2, continuous
D603V3, binary
               cls
clus              0   1
  FRY MUTATED    38   3
  FRY WILD-TYPE 328 116
[1] "tbl2"
               cls
clus            [,1] [,2]
  FRY MUTATED     38    3
  FRY WILD-TYPE  328  116
        clus
vv       FRY MUTATED FRY WILD-TYPE
  COLON           38           328
  RECTUM           3           116
[1] 2 2
[1] FALSE
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FRY MUTATED         8        0        5        15         4         0
  FRY WILD-TYPE      83        1       27       123         6         1
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  FRY MUTATED           3          0          2          1        0         2
  FRY WILD-TYPE        21         11         57         41       48        16
               vv
clus            STAGE IVB
  FRY MUTATED           0
  FRY WILD-TYPE         1
D603V4, multiclass
            clus
vv           FRY MUTATED FRY WILD-TYPE
  STAGE I              8            83
  STAGE IA             0             1
  STAGE II             5            27
  STAGE IIA           15           123
  STAGE IIB            4             6
  STAGE IIC            0             1
  STAGE III            3            21
  STAGE IIIA           0            11
  STAGE IIIB           2            57
  STAGE IIIC           1            41
  STAGE IV             0            48
  STAGE IVA            2            16
  STAGE IVB            0             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  FRY MUTATED     2   7  27   5
  FRY WILD-TYPE  15  85 302  45
D603V5, multiclass
    clus
vv   FRY MUTATED FRY WILD-TYPE
  T1           2            15
  T2           7            85
  T3          27           302
  T4           5            45
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2
  FRY MUTATED    33   4   4
  FRY WILD-TYPE 254 109  83
D603V6, multiclass
    clus
vv   FRY MUTATED FRY WILD-TYPE
  N0          33           254
  N1           4           109
  N2           4            83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D603V7, binary
               cls
clus              0   1
  FRY MUTATED    35   2
  FRY WILD-TYPE 340  63
[1] "tbl2"
               cls
clus            [,1] [,2]
  FRY MUTATED     35    2
  FRY WILD-TYPE  340   63
   clus
vv  FRY MUTATED FRY WILD-TYPE
  0          35           340
  1           2            63
[1] 2 2
[1] FALSE
D603V8, binary
               cls
clus              0   1
  FRY MUTATED    20  21
  FRY WILD-TYPE 205 243
[1] "tbl2"
               cls
clus            [,1] [,2]
  FRY MUTATED     20   21
  FRY WILD-TYPE  205  243
        clus
vv       FRY MUTATED FRY WILD-TYPE
  FEMALE          20           205
  MALE            21           243
[1] 2 2
[1] FALSE
D603V9, binary
               cls
clus              0   1
  FRY MUTATED    33   1
  FRY WILD-TYPE 317  21
[1] "tbl2"
               cls
clus            [,1] [,2]
  FRY MUTATED     33    1
  FRY WILD-TYPE  317   21
     clus
vv    FRY MUTATED FRY WILD-TYPE
  NO           33           317
  YES           1            21
[1] 2 2
[1] FALSE
               vv
clus            COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  FRY MUTATED                     30                             8
  FRY WILD-TYPE                  285                            39
               vv
clus            RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  FRY MUTATED                       3                              0
  FRY WILD-TYPE                   103                             10
D603V10, multiclass
                                clus
vv                               FRY MUTATED FRY WILD-TYPE
  COLON ADENOCARCINOMA                    30           285
  COLON MUCINOUS ADENOCARCINOMA            8            39
  RECTAL ADENOCARCINOMA                    3           103
  RECTAL MUCINOUS ADENOCARCINOMA           0            10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             R0  R1  R2  RX
  FRY MUTATED    33   0   0   2
  FRY WILD-TYPE 312   4  31  23
D603V11, multiclass
    clus
vv   FRY MUTATED FRY WILD-TYPE
  R0          33           312
  R1           0             4
  R2           0            31
  RX           2            23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D603V12, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FRY MUTATED                                  0     2
  FRY WILD-TYPE                                1     9
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  FRY MUTATED                           4    21
  FRY WILD-TYPE                        18   205
D603V13, multiclass
                                  clus
vv                                 FRY MUTATED FRY WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      2             9
  BLACK OR AFRICAN AMERICAN                  4            18
  WHITE                                     21           205
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(604) Variable = SCN2A MUTATION ANALYSIS
D604V1, survival
                 sevent
clus2               0   1
  SCN2A MUTATED    42   7
  SCN2A WILD-TYPE 336  86
  SCN2A MUTATED SCN2A WILD-TYPE 
             49             422 
  SCN2A MUTATED SCN2A WILD-TYPE 
              7              86 
$`SCN2A MUTATED`
TCGA-A6-2671 TCGA-A6-2676 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-6137 
       43.76        42.90        32.91        31.63        29.19        27.09 
TCGA-A6-6141 TCGA-A6-6651 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3663 TCGA-AA-3875 
        8.38        21.76         3.02         1.02         6.97        18.05 
TCGA-AA-3877 TCGA-AA-3947 TCGA-AA-3977 TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A00R 
       31.00        33.01        25.02        27.02        38.04         0.99 
TCGA-AA-A010 TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01Z TCGA-AA-A02K TCGA-AD-5900 
       34.98         1.02        35.01        37.02        14.01         0.07 
TCGA-AU-3779 TCGA-AZ-4315 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       14.50        58.39        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-5914 TCGA-CM-4743 TCGA-CM-5861 TCGA-CM-6163 TCGA-CM-6166 
       17.56         9.99        23.05        15.02         2.96        21.99 
TCGA-CM-6676 TCGA-D5-6540 TCGA-D5-6930 TCGA-DM-A28G TCGA-DM-A28K TCGA-G4-6306 
       11.08        16.14         1.51        60.79        98.24        44.68 
TCGA-G4-6315 TCGA-G4-6628 TCGA-AG-3574 TCGA-AG-A002 TCGA-AG-A02N TCGA-CI-6622 
       61.91        79.69        36.03        20.98        61.97         6.97 
TCGA-F5-6811 
       32.19 

$`SCN2A WILD-TYPE`
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       46.65        43.76        24.33        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5659 TCGA-A6-5661 
       33.34        32.75        36.53        14.53        30.44        33.53 
TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6138 TCGA-A6-6142 
       23.61        22.09        22.06        32.71        22.52        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       25.18        24.16        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
       19.66        20.28         7.04        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       61.02        78.08         6.05        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
        2.01        12.99        24.00        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       19.07         7.96        13.94        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01S TCGA-AA-A01T 
       12.00        31.00        31.00        38.07         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       35.01        26.01        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
        5.03         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        10.88         0.20        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        33.01        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5916 
      148.01        85.45        15.62        49.08        51.32        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
       82.95         1.91       124.27        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       29.03        16.04        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6677 TCGA-CM-6678 
       14.04        11.01        12.95        13.05        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 
       17.85         4.80        17.13        12.49        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       11.64         4.80        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28H 
      139.17         6.12        81.37       119.93        35.97       117.07 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       55.04        85.48        63.62        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 
       35.80        26.17        91.79        46.75        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3575 TCGA-AG-3578 
       16.83        15.39        20.02        10.39        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
        1.94        38.96        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6812 TCGA-F5-6813 
        9.96        49.51        31.30        28.57         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  SCN2A MUTATED SCN2A WILD-TYPE 
           0.07            0.00 
  SCN2A MUTATED SCN2A WILD-TYPE 
          98.24          148.01 
  SCN2A MUTATED SCN2A WILD-TYPE 
         21.990          20.035 
[1] "0.1 - 98.2 (22.0)"  "0.0 - 148.0 (20.0)"
[1] "hr=" "1.4"
D604V2, continuous
D604V3, binary
                 cls
clus                0   1
  SCN2A MUTATED    45   5
  SCN2A WILD-TYPE 321 114
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SCN2A MUTATED     45    5
  SCN2A WILD-TYPE  321  114
        clus
vv       SCN2A MUTATED SCN2A WILD-TYPE
  COLON             45             321
  RECTUM             5             114
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SCN2A MUTATED        11        0        7        15         5         0
  SCN2A WILD-TYPE      80        1       25       123         5         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SCN2A MUTATED           1          0          6          1        3         0
  SCN2A WILD-TYPE        23         11         53         41       45        18
                 vv
clus              STAGE IVB
  SCN2A MUTATED           0
  SCN2A WILD-TYPE         1
D604V4, multiclass
            clus
vv           SCN2A MUTATED SCN2A WILD-TYPE
  STAGE I               11              80
  STAGE IA               0               1
  STAGE II               7              25
  STAGE IIA             15             123
  STAGE IIB              5               5
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             6              53
  STAGE IIIC             1              41
  STAGE IV               3              45
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  SCN2A MUTATED     3  10  30   7
  SCN2A WILD-TYPE  14  82 299  43
D604V5, multiclass
    clus
vv   SCN2A MUTATED SCN2A WILD-TYPE
  T1             3              14
  T2            10              82
  T3            30             299
  T4             7              43
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  SCN2A MUTATED    39   7   4
  SCN2A WILD-TYPE 248 106  83
D604V6, multiclass
    clus
vv   SCN2A MUTATED SCN2A WILD-TYPE
  N0            39             248
  N1             7             106
  N2             4              83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D604V7, binary
                 cls
clus                0   1
  SCN2A MUTATED    42   3
  SCN2A WILD-TYPE 333  62
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SCN2A MUTATED     42    3
  SCN2A WILD-TYPE  333   62
   clus
vv  SCN2A MUTATED SCN2A WILD-TYPE
  0            42             333
  1             3              62
[1] 2 2
[1] FALSE
D604V8, binary
                 cls
clus                0   1
  SCN2A MUTATED    17  33
  SCN2A WILD-TYPE 208 231
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SCN2A MUTATED     17   33
  SCN2A WILD-TYPE  208  231
        clus
vv       SCN2A MUTATED SCN2A WILD-TYPE
  FEMALE            17             208
  MALE              33             231
[1] 2 2
[1] FALSE
D604V9, binary
                 cls
clus                0   1
  SCN2A MUTATED    38   1
  SCN2A WILD-TYPE 312  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SCN2A MUTATED     38    1
  SCN2A WILD-TYPE  312   21
     clus
vv    SCN2A MUTATED SCN2A WILD-TYPE
  NO             38             312
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SCN2A MUTATED                     36                             9
  SCN2A WILD-TYPE                  279                            38
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SCN2A MUTATED                       5                              0
  SCN2A WILD-TYPE                   101                             10
D604V10, multiclass
                                clus
vv                               SCN2A MUTATED SCN2A WILD-TYPE
  COLON ADENOCARCINOMA                      36             279
  COLON MUCINOUS ADENOCARCINOMA              9              38
  RECTAL ADENOCARCINOMA                      5             101
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  SCN2A MUTATED    32   0   1   7
  SCN2A WILD-TYPE 313   4  30  18
D604V11, multiclass
    clus
vv   SCN2A MUTATED SCN2A WILD-TYPE
  R0            32             313
  R1             0               4
  R2             1              30
  RX             7              18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D604V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SCN2A MUTATED                                  0     4
  SCN2A WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  SCN2A MUTATED                           3    25
  SCN2A WILD-TYPE                        19   201
D604V13, multiclass
                                  clus
vv                                 SCN2A MUTATED SCN2A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        4               7
  BLACK OR AFRICAN AMERICAN                    3              19
  WHITE                                       25             201
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(605) Variable = ALK MUTATION ANALYSIS
D605V1, survival
               sevent
clus2             0   1
  ALK MUTATED    29  10
  ALK WILD-TYPE 349  83
  ALK MUTATED ALK WILD-TYPE 
           39           432 
  ALK MUTATED ALK WILD-TYPE 
           10            83 
$`ALK MUTATED`
TCGA-A6-2676 TCGA-A6-4105 TCGA-A6-5666 TCGA-AA-3496 TCGA-AA-3510 TCGA-AA-3518 
       42.90        14.53        32.71         1.02        63.98         1.02 
TCGA-AA-3562 TCGA-AA-3663 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3818 
       19.99         6.97        26.99        19.04        19.04         0.99 
TCGA-AA-3845 TCGA-AA-3950 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A01R 
        0.00        24.00        26.01        25.02         4.01        35.01 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CA-6717 TCGA-CM-4752 TCGA-CM-6162 TCGA-CM-6163 
      100.01         1.61        12.76        13.02        12.00         2.96 
TCGA-CM-6165 TCGA-CM-6170 TCGA-D5-6540 TCGA-D5-6930 TCGA-DM-A1D7 TCGA-DM-A1D8 
       16.04        15.02        16.14         1.51        13.32        12.59 
TCGA-DM-A1HA TCGA-F4-6703 TCGA-G4-6304 TCGA-G4-6307 TCGA-AF-6136 TCGA-AG-3609 
      131.51        47.87        53.62        55.04        15.39        19.99 
TCGA-AG-A002 TCGA-AH-6643 TCGA-F5-6465 
       20.98         0.69        49.51 

$`ALK WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 
       34.65        33.34        32.75        36.53        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       30.44        29.19        33.53        23.61        22.09        22.06 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       27.09        22.52         8.38        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 
       20.28         7.04         3.02        35.01         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       13.02        38.99         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       20.98        19.99        13.94        61.02        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3819 
        5.03        85.05        10.06        35.05        33.04        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 
        2.01        12.99        24.00        33.01        26.01         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       13.05        34.06        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
        1.02         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       49.41         6.77        12.10        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        3.19        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.20        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6164 
        5.03        15.02        15.02        17.03        15.02        29.03 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6171 TCGA-CM-6172 
       21.99        14.99        12.99        13.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
        4.80        17.13        12.49        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        4.80        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D9 TCGA-DM-A1DA 
       38.20       130.65        92.75        49.91       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
       44.32       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       35.74         6.18         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       74.56        65.85        44.68        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6655 
       19.10        34.49        10.39        14.50        16.83        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6571 
       20.55        19.96        20.91        18.28         9.96        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  ALK MUTATED ALK WILD-TYPE 
            0             0 
  ALK MUTATED ALK WILD-TYPE 
       131.51        148.01 
  ALK MUTATED ALK WILD-TYPE 
        16.14         20.98 
[1] "0.0 - 131.5 (16.1)" "0.0 - 148.0 (21.0)"
[1] "hr=" "1.4"
D605V2, continuous
D605V3, binary
               cls
clus              0   1
  ALK MUTATED    35   5
  ALK WILD-TYPE 331 114
[1] "tbl2"
               cls
clus            [,1] [,2]
  ALK MUTATED     35    5
  ALK WILD-TYPE  331  114
        clus
vv       ALK MUTATED ALK WILD-TYPE
  COLON           35           331
  RECTUM           5           114
[1] 2 2
[1] FALSE
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ALK MUTATED         4        0        5        13         3         1
  ALK WILD-TYPE      87        1       27       125         7         0
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ALK MUTATED           2          2          3          4        1         0
  ALK WILD-TYPE        22          9         56         38       47        18
               vv
clus            STAGE IVB
  ALK MUTATED           0
  ALK WILD-TYPE         1
D605V4, multiclass
            clus
vv           ALK MUTATED ALK WILD-TYPE
  STAGE I              4            87
  STAGE IA             0             1
  STAGE II             5            27
  STAGE IIA           13           125
  STAGE IIB            3             7
  STAGE IIC            1             0
  STAGE III            2            22
  STAGE IIIA           2             9
  STAGE IIIB           3            56
  STAGE IIIC           4            38
  STAGE IV             1            47
  STAGE IVA            0            18
  STAGE IVB            0             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  ALK MUTATED     1   6  29   4
  ALK WILD-TYPE  16  86 300  46
D605V5, multiclass
    clus
vv   ALK MUTATED ALK WILD-TYPE
  T1           1            16
  T2           6            86
  T3          29           300
  T4           4            46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2
  ALK MUTATED    28   6   6
  ALK WILD-TYPE 259 107  81
D605V6, multiclass
    clus
vv   ALK MUTATED ALK WILD-TYPE
  N0          28           259
  N1           6           107
  N2           6            81
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D605V7, binary
               cls
clus              0   1
  ALK MUTATED    36   1
  ALK WILD-TYPE 339  64
[1] "tbl2"
               cls
clus            [,1] [,2]
  ALK MUTATED     36    1
  ALK WILD-TYPE  339   64
   clus
vv  ALK MUTATED ALK WILD-TYPE
  0          36           339
  1           1            64
[1] 2 2
[1] FALSE
D605V8, binary
               cls
clus              0   1
  ALK MUTATED    16  24
  ALK WILD-TYPE 209 240
[1] "tbl2"
               cls
clus            [,1] [,2]
  ALK MUTATED     16   24
  ALK WILD-TYPE  209  240
        clus
vv       ALK MUTATED ALK WILD-TYPE
  FEMALE          16           209
  MALE            24           240
[1] 2 2
[1] FALSE
D605V9, binary
               cls
clus              0   1
  ALK MUTATED    26   3
  ALK WILD-TYPE 324  19
[1] "tbl2"
               cls
clus            [,1] [,2]
  ALK MUTATED     26    3
  ALK WILD-TYPE  324   19
     clus
vv    ALK MUTATED ALK WILD-TYPE
  NO           26           324
  YES           3            19
[1] 2 2
[1] FALSE
               vv
clus            COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ALK MUTATED                     27                             7
  ALK WILD-TYPE                  288                            40
               vv
clus            RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ALK MUTATED                       5                              0
  ALK WILD-TYPE                   101                             10
D605V10, multiclass
                                clus
vv                               ALK MUTATED ALK WILD-TYPE
  COLON ADENOCARCINOMA                    27           288
  COLON MUCINOUS ADENOCARCINOMA            7            40
  RECTAL ADENOCARCINOMA                    5           101
  RECTAL MUCINOUS ADENOCARCINOMA           0            10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             R0  R1  R2  RX
  ALK MUTATED    29   0   1   1
  ALK WILD-TYPE 316   4  30  24
D605V11, multiclass
    clus
vv   ALK MUTATED ALK WILD-TYPE
  R0          29           316
  R1           0             4
  R2           1            30
  RX           1            24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D605V12, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ALK MUTATED                                  0     1
  ALK WILD-TYPE                                1    10
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  ALK MUTATED                           1    20
  ALK WILD-TYPE                        21   206
D605V13, multiclass
                                  clus
vv                                 ALK MUTATED ALK WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      1            10
  BLACK OR AFRICAN AMERICAN                  1            21
  WHITE                                     20           206
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(606) Variable = SP4 MUTATION ANALYSIS
D606V1, survival
               sevent
clus2             0   1
  SP4 MUTATED     8   4
  SP4 WILD-TYPE 370  89
  SP4 MUTATED SP4 WILD-TYPE 
           12           459 
  SP4 MUTATED SP4 WILD-TYPE 
            4            89 
$`SP4 MUTATED`
TCGA-AA-3966 TCGA-AA-A010 TCGA-AA-A01Q TCGA-AD-6964 TCGA-AU-6004 TCGA-AY-6386 
        2.01        34.98         1.02        10.88        27.09        17.82 
TCGA-AZ-6598 TCGA-AZ-6600 TCGA-CK-4950 TCGA-D5-5540 TCGA-D5-6541 TCGA-DM-A1DB 
       49.41        12.10        85.45        56.09        15.58        44.32 

$`SP4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 
       24.00         2.01        20.98        34.03        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        31.00        38.07        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
        0.79         0.72         5.79        22.42        27.42         0.20 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AZ-4315 
       14.50        16.31         0.95        33.01        21.44        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       45.40        12.26        19.59        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       12.49        16.14         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
        7.50       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  SP4 MUTATED SP4 WILD-TYPE 
         1.02          0.00 
  SP4 MUTATED SP4 WILD-TYPE 
        85.45        148.01 
  SP4 MUTATED SP4 WILD-TYPE 
       22.455        20.190 
[1] "1.0 - 85.5 (22.5)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.5"
D606V2, continuous
D606V3, binary
               cls
clus              0   1
  SP4 MUTATED    12   0
  SP4 WILD-TYPE 354 119
[1] "tbl2"
               cls
clus            [,1] [,2]
  SP4 MUTATED     12    0
  SP4 WILD-TYPE  354  119
        clus
vv       SP4 MUTATED SP4 WILD-TYPE
  COLON           12           354
  RECTUM           0           119
[1] 2 2
[1] FALSE
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SP4 MUTATED         1        0        2         4         1         0
  SP4 WILD-TYPE      90        1       30       134         9         1
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SP4 MUTATED           0          0          2          0        1         0
  SP4 WILD-TYPE        24         11         57         42       47        18
               vv
clus            STAGE IVB
  SP4 MUTATED           0
  SP4 WILD-TYPE         1
D606V4, multiclass
            clus
vv           SP4 MUTATED SP4 WILD-TYPE
  STAGE I              1            90
  STAGE IA             0             1
  STAGE II             2            30
  STAGE IIA            4           134
  STAGE IIB            1             9
  STAGE IIC            0             1
  STAGE III            0            24
  STAGE IIIA           0            11
  STAGE IIIB           2            57
  STAGE IIIC           0            42
  STAGE IV             1            47
  STAGE IVA            0            18
  STAGE IVB            0             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  SP4 MUTATED     0   1   8   3
  SP4 WILD-TYPE  17  91 321  47
D606V5, multiclass
    clus
vv   SP4 MUTATED SP4 WILD-TYPE
  T1           0            17
  T2           1            91
  T3           8           321
  T4           3            47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2
  SP4 MUTATED     8   3   1
  SP4 WILD-TYPE 279 110  86
D606V6, multiclass
    clus
vv   SP4 MUTATED SP4 WILD-TYPE
  N0           8           279
  N1           3           110
  N2           1            86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D606V7, binary
               cls
clus              0   1
  SP4 MUTATED     9   1
  SP4 WILD-TYPE 366  64
[1] "tbl2"
               cls
clus            [,1] [,2]
  SP4 MUTATED      9    1
  SP4 WILD-TYPE  366   64
   clus
vv  SP4 MUTATED SP4 WILD-TYPE
  0           9           366
  1           1            64
[1] 2 2
[1] FALSE
D606V8, binary
               cls
clus              0   1
  SP4 MUTATED     7   5
  SP4 WILD-TYPE 218 259
[1] "tbl2"
               cls
clus            [,1] [,2]
  SP4 MUTATED      7    5
  SP4 WILD-TYPE  218  259
        clus
vv       SP4 MUTATED SP4 WILD-TYPE
  FEMALE           7           218
  MALE             5           259
[1] 2 2
[1] FALSE
D606V9, binary
               cls
clus              0   1
  SP4 MUTATED     7   0
  SP4 WILD-TYPE 343  22
[1] "tbl2"
               cls
clus            [,1] [,2]
  SP4 MUTATED      7    0
  SP4 WILD-TYPE  343   22
     clus
vv    SP4 MUTATED SP4 WILD-TYPE
  NO            7           343
  YES           0            22
[1] 2 2
[1] FALSE
               vv
clus            COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SP4 MUTATED                     11                             1
  SP4 WILD-TYPE                  304                            46
               vv
clus            RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SP4 MUTATED                       0                              0
  SP4 WILD-TYPE                   106                             10
D606V10, multiclass
                                clus
vv                               SP4 MUTATED SP4 WILD-TYPE
  COLON ADENOCARCINOMA                    11           304
  COLON MUCINOUS ADENOCARCINOMA            1            46
  RECTAL ADENOCARCINOMA                    0           106
  RECTAL MUCINOUS ADENOCARCINOMA           0            10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             R0  R1  R2  RX
  SP4 MUTATED     6   1   0   0
  SP4 WILD-TYPE 339   3  31  25
D606V11, multiclass
    clus
vv   SP4 MUTATED SP4 WILD-TYPE
  R0           6           339
  R1           1             3
  R2           0            31
  RX           0            25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D606V12, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SP4 MUTATED                                  0     0
  SP4 WILD-TYPE                                1    11
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  SP4 MUTATED                           3     6
  SP4 WILD-TYPE                        19   220
D606V13, multiclass
                                  clus
vv                                 SP4 MUTATED SP4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      0            11
  BLACK OR AFRICAN AMERICAN                  3            19
  WHITE                                      6           220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(607) Variable = IQSEC2 MUTATION ANALYSIS
D607V1, survival
                  sevent
clus2                0   1
  IQSEC2 MUTATED    15   1
  IQSEC2 WILD-TYPE 363  92
  IQSEC2 MUTATED IQSEC2 WILD-TYPE 
              16              455 
  IQSEC2 MUTATED IQSEC2 WILD-TYPE 
               1               92 
$`IQSEC2 MUTATED`
TCGA-A6-5665 TCGA-AA-3560 TCGA-AA-3662 TCGA-AA-3821 TCGA-AA-3877 TCGA-AA-3947 
       22.06        19.99         6.05         1.02        31.00        33.01 
TCGA-AY-5543 TCGA-AZ-6598 TCGA-CK-5913 TCGA-CM-4743 TCGA-CM-6171 TCGA-D5-6535 
       33.01        49.41        51.32        23.05        14.04        15.12 
TCGA-DM-A1HB TCGA-F4-6856 TCGA-G4-6588 TCGA-AG-A02N 
      135.65        35.31        26.17        61.97 

$`IQSEC2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
       33.04         0.99        25.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 
       29.98        18.05         2.01        12.99        24.00        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       16.31         0.95        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 
        5.13       106.75        22.36        62.79        88.21         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       85.45        15.62        49.08         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
        1.91       124.27        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       13.02        15.02        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       43.27        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
       44.32       131.51       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 
       16.24        33.67        13.25         0.53        47.41       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
       49.97         1.94        38.96        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  IQSEC2 MUTATED IQSEC2 WILD-TYPE 
            1.02             0.00 
  IQSEC2 MUTATED IQSEC2 WILD-TYPE 
          135.65           148.01 
  IQSEC2 MUTATED IQSEC2 WILD-TYPE 
          28.585           20.020 
[1] "1.0 - 135.7 (28.6)" "0.0 - 148.0 (20.0)"
[1] "hr=" "4.1"
D607V2, continuous
D607V3, binary
                  cls
clus                 0   1
  IQSEC2 MUTATED    16   1
  IQSEC2 WILD-TYPE 350 118
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IQSEC2 MUTATED     16    1
  IQSEC2 WILD-TYPE  350  118
        clus
vv       IQSEC2 MUTATED IQSEC2 WILD-TYPE
  COLON              16              350
  RECTUM              1              118
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  IQSEC2 MUTATED         4        0        2         4         2         0
  IQSEC2 WILD-TYPE      87        1       30       134         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  IQSEC2 MUTATED           0          0          2          1        1
  IQSEC2 WILD-TYPE        24         11         57         41       47
                  vv
clus               STAGE IVA STAGE IVB
  IQSEC2 MUTATED           1         0
  IQSEC2 WILD-TYPE        17         1
D607V4, multiclass
            clus
vv           IQSEC2 MUTATED IQSEC2 WILD-TYPE
  STAGE I                 4               87
  STAGE IA                0                1
  STAGE II                2               30
  STAGE IIA               4              134
  STAGE IIB               2                8
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              2               57
  STAGE IIIC              1               41
  STAGE IV                1               47
  STAGE IVA               1               17
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  IQSEC2 MUTATED     1   3  10   3
  IQSEC2 WILD-TYPE  16  89 319  47
D607V5, multiclass
    clus
vv   IQSEC2 MUTATED IQSEC2 WILD-TYPE
  T1              1               16
  T2              3               89
  T3             10              319
  T4              3               47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  IQSEC2 MUTATED    12   3   2
  IQSEC2 WILD-TYPE 275 110  85
D607V6, multiclass
    clus
vv   IQSEC2 MUTATED IQSEC2 WILD-TYPE
  N0             12              275
  N1              3              110
  N2              2               85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D607V7, binary
                  cls
clus                 0   1
  IQSEC2 MUTATED    11   2
  IQSEC2 WILD-TYPE 364  63
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IQSEC2 MUTATED     11    2
  IQSEC2 WILD-TYPE  364   63
   clus
vv  IQSEC2 MUTATED IQSEC2 WILD-TYPE
  0             11              364
  1              2               63
[1] 2 2
[1] FALSE
D607V8, binary
                  cls
clus                 0   1
  IQSEC2 MUTATED    13   4
  IQSEC2 WILD-TYPE 212 260
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IQSEC2 MUTATED     13    4
  IQSEC2 WILD-TYPE  212  260
        clus
vv       IQSEC2 MUTATED IQSEC2 WILD-TYPE
  FEMALE             13              212
  MALE                4              260
[1] 2 2
[1] FALSE
D607V9, binary
                  cls
clus                 0   1
  IQSEC2 MUTATED    14   0
  IQSEC2 WILD-TYPE 336  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IQSEC2 MUTATED     14    0
  IQSEC2 WILD-TYPE  336   22
     clus
vv    IQSEC2 MUTATED IQSEC2 WILD-TYPE
  NO              14              336
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  IQSEC2 MUTATED                     11                             4
  IQSEC2 WILD-TYPE                  304                            43
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  IQSEC2 MUTATED                       1                              0
  IQSEC2 WILD-TYPE                   105                             10
D607V10, multiclass
                                clus
vv                               IQSEC2 MUTATED IQSEC2 WILD-TYPE
  COLON ADENOCARCINOMA                       11              304
  COLON MUCINOUS ADENOCARCINOMA               4               43
  RECTAL ADENOCARCINOMA                       1              105
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  IQSEC2 MUTATED    11   0   1   3
  IQSEC2 WILD-TYPE 334   4  30  22
D607V11, multiclass
    clus
vv   IQSEC2 MUTATED IQSEC2 WILD-TYPE
  R0             11              334
  R1              0                4
  R2              1               30
  RX              3               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D607V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  IQSEC2 MUTATED                                  0     0
  IQSEC2 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  IQSEC2 MUTATED                           1    10
  IQSEC2 WILD-TYPE                        21   216
D607V13, multiclass
                                  clus
vv                                 IQSEC2 MUTATED IQSEC2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                        10              216
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(608) Variable = PPP1R12B MUTATION ANALYSIS
D608V1, survival
                    sevent
clus2                  0   1
  PPP1R12B MUTATED    13   2
  PPP1R12B WILD-TYPE 365  91
  PPP1R12B MUTATED PPP1R12B WILD-TYPE 
                15                456 
  PPP1R12B MUTATED PPP1R12B WILD-TYPE 
                 2                 91 
$`PPP1R12B MUTATED`
TCGA-AA-3842 TCGA-AA-3867 TCGA-AA-A00N TCGA-AZ-4315 TCGA-CM-5344 TCGA-CM-5348 
       37.02        24.03         4.01        58.39        22.03        22.98 
TCGA-CM-6162 TCGA-D5-6529 TCGA-D5-6536 TCGA-DM-A1D4 TCGA-G4-6310 TCGA-G4-6588 
       12.00        20.19        17.85        92.75        63.62        26.17 
TCGA-AG-3892 TCGA-AG-4008 TCGA-AG-A002 
       13.02        17.03        20.98 

$`PPP1R12B WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3844 TCGA-AA-3845 
        1.02        17.98        15.95        38.99        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       17.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       29.06        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       15.02        17.03        15.02         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 
       55.92        18.25         1.32        43.27        15.12         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       24.43        38.20       130.65        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6317 
       53.62        44.68        55.04        85.48        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       22.09        13.78        35.80        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       36.95        17.03        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  PPP1R12B MUTATED PPP1R12B WILD-TYPE 
              4.01               0.00 
  PPP1R12B MUTATED PPP1R12B WILD-TYPE 
             92.75             148.01 
  PPP1R12B MUTATED PPP1R12B WILD-TYPE 
            22.030             20.035 
[1] "4.0 - 92.8 (22.0)"  "0.0 - 148.0 (20.0)"
[1] "hr=" "1.8"
D608V2, continuous
D608V3, binary
                    cls
clus                   0   1
  PPP1R12B MUTATED    12   3
  PPP1R12B WILD-TYPE 354 116
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  PPP1R12B MUTATED     12    3
  PPP1R12B WILD-TYPE  354  116
        clus
vv       PPP1R12B MUTATED PPP1R12B WILD-TYPE
  COLON                12                354
  RECTUM                3                116
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PPP1R12B MUTATED         2        0        0         6         1         0
  PPP1R12B WILD-TYPE      89        1       32       132         9         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PPP1R12B MUTATED           0          1          4          0        1
  PPP1R12B WILD-TYPE        24         10         55         42       47
                    vv
clus                 STAGE IVA STAGE IVB
  PPP1R12B MUTATED           0         0
  PPP1R12B WILD-TYPE        18         1
D608V4, multiclass
            clus
vv           PPP1R12B MUTATED PPP1R12B WILD-TYPE
  STAGE I                   2                 89
  STAGE IA                  0                  1
  STAGE II                  0                 32
  STAGE IIA                 6                132
  STAGE IIB                 1                  9
  STAGE IIC                 0                  1
  STAGE III                 0                 24
  STAGE IIIA                1                 10
  STAGE IIIB                4                 55
  STAGE IIIC                0                 42
  STAGE IV                  1                 47
  STAGE IVA                 0                 18
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  PPP1R12B MUTATED     1   2  11   1
  PPP1R12B WILD-TYPE  16  90 318  49
D608V5, multiclass
    clus
vv   PPP1R12B MUTATED PPP1R12B WILD-TYPE
  T1                1                 16
  T2                2                 90
  T3               11                318
  T4                1                 49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  PPP1R12B MUTATED     9   5   1
  PPP1R12B WILD-TYPE 278 108  86
D608V6, multiclass
    clus
vv   PPP1R12B MUTATED PPP1R12B WILD-TYPE
  N0                9                278
  N1                5                108
  N2                1                 86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D608V7, binary
                    cls
clus                   0   1
  PPP1R12B MUTATED    14   1
  PPP1R12B WILD-TYPE 361  64
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  PPP1R12B MUTATED     14    1
  PPP1R12B WILD-TYPE  361   64
   clus
vv  PPP1R12B MUTATED PPP1R12B WILD-TYPE
  0               14                361
  1                1                 64
[1] 2 2
[1] FALSE
D608V8, binary
                    cls
clus                   0   1
  PPP1R12B MUTATED     4  11
  PPP1R12B WILD-TYPE 221 253
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  PPP1R12B MUTATED      4   11
  PPP1R12B WILD-TYPE  221  253
        clus
vv       PPP1R12B MUTATED PPP1R12B WILD-TYPE
  FEMALE                4                221
  MALE                 11                253
[1] 2 2
[1] FALSE
D608V9, binary
                    cls
clus                   0   1
  PPP1R12B MUTATED    12   1
  PPP1R12B WILD-TYPE 338  21
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  PPP1R12B MUTATED     12    1
  PPP1R12B WILD-TYPE  338   21
     clus
vv    PPP1R12B MUTATED PPP1R12B WILD-TYPE
  NO                12                338
  YES                1                 21
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PPP1R12B MUTATED                     10                             2
  PPP1R12B WILD-TYPE                  305                            45
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PPP1R12B MUTATED                       3                              0
  PPP1R12B WILD-TYPE                   103                             10
D608V10, multiclass
                                clus
vv                               PPP1R12B MUTATED PPP1R12B WILD-TYPE
  COLON ADENOCARCINOMA                         10                305
  COLON MUCINOUS ADENOCARCINOMA                 2                 45
  RECTAL ADENOCARCINOMA                         3                103
  RECTAL MUCINOUS ADENOCARCINOMA                0                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  PPP1R12B MUTATED    13   0   1   0
  PPP1R12B WILD-TYPE 332   4  30  25
D608V11, multiclass
    clus
vv   PPP1R12B MUTATED PPP1R12B WILD-TYPE
  R0               13                332
  R1                0                  4
  R2                1                 30
  RX                0                 25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D608V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PPP1R12B MUTATED                                  0     0
  PPP1R12B WILD-TYPE                                1    11
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  PPP1R12B MUTATED                           0     9
  PPP1R12B WILD-TYPE                        22   217
D608V13, multiclass
                                  clus
vv                                 PPP1R12B MUTATED PPP1R12B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 11
  BLACK OR AFRICAN AMERICAN                       0                 22
  WHITE                                           9                217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(609) Variable = WWTR1 MUTATION ANALYSIS
D609V1, survival
                 sevent
clus2               0   1
  WWTR1 MUTATED     6   1
  WWTR1 WILD-TYPE 372  92
  WWTR1 MUTATED WWTR1 WILD-TYPE 
              7             464 
  WWTR1 MUTATED WWTR1 WILD-TYPE 
              1              92 
$`WWTR1 MUTATED`
TCGA-A6-6138 TCGA-A6-6780 TCGA-AA-3538 TCGA-AA-3555 TCGA-AY-6197 TCGA-CK-5916 
       22.52        20.12        26.01        29.95        21.44        21.14 
TCGA-EI-6507 
       19.96 

$`WWTR1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6141 TCGA-A6-6142 
       22.09        22.06        32.71        27.09         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3542 
        0.00        19.07        34.03        29.00        29.00        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       17.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 
       14.50        27.09        16.31         0.95        33.01        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       51.32         9.99        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
       32.61         0.49        20.55        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  WWTR1 MUTATED WWTR1 WILD-TYPE 
          19.96            0.00 
  WWTR1 MUTATED WWTR1 WILD-TYPE 
          29.95          148.01 
  WWTR1 MUTATED WWTR1 WILD-TYPE 
         21.440          20.035 
[1] "20.0 - 29.9 (21.4)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.2"
D609V2, continuous
D609V3, binary
                 cls
clus                0   1
  WWTR1 MUTATED     6   1
  WWTR1 WILD-TYPE 360 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WWTR1 MUTATED      6    1
  WWTR1 WILD-TYPE  360  118
        clus
vv       WWTR1 MUTATED WWTR1 WILD-TYPE
  COLON              6             360
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  WWTR1 MUTATED         3        0        0         4         0         0
  WWTR1 WILD-TYPE      88        1       32       134        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  WWTR1 MUTATED           0          0          0          0        0         0
  WWTR1 WILD-TYPE        24         11         59         42       48        18
                 vv
clus              STAGE IVB
  WWTR1 MUTATED           0
  WWTR1 WILD-TYPE         1
D609V4, multiclass
            clus
vv           WWTR1 MUTATED WWTR1 WILD-TYPE
  STAGE I                3              88
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              4             134
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  WWTR1 MUTATED     1   2   4   0
  WWTR1 WILD-TYPE  16  90 325  50
D609V5, multiclass
    clus
vv   WWTR1 MUTATED WWTR1 WILD-TYPE
  T1             1              16
  T2             2              90
  T3             4             325
  T4             0              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  WWTR1 MUTATED     7   0   0
  WWTR1 WILD-TYPE 280 113  87
D609V6, multiclass
    clus
vv   WWTR1 MUTATED WWTR1 WILD-TYPE
  N0             7             280
  N1             0             113
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D609V7, binary
                 cls
clus                0   1
  WWTR1 MUTATED     5   0
  WWTR1 WILD-TYPE 370  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WWTR1 MUTATED      5    0
  WWTR1 WILD-TYPE  370   65
   clus
vv  WWTR1 MUTATED WWTR1 WILD-TYPE
  0             5             370
  1             0              65
[1] 2 2
[1] FALSE
D609V8, binary
                 cls
clus                0   1
  WWTR1 MUTATED     3   4
  WWTR1 WILD-TYPE 222 260
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WWTR1 MUTATED      3    4
  WWTR1 WILD-TYPE  222  260
        clus
vv       WWTR1 MUTATED WWTR1 WILD-TYPE
  FEMALE             3             222
  MALE               4             260
[1] 2 2
[1] FALSE
D609V9, binary
                 cls
clus                0   1
  WWTR1 MUTATED     7   0
  WWTR1 WILD-TYPE 343  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WWTR1 MUTATED      7    0
  WWTR1 WILD-TYPE  343   22
     clus
vv    WWTR1 MUTATED WWTR1 WILD-TYPE
  NO              7             343
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  WWTR1 MUTATED                      4                             2
  WWTR1 WILD-TYPE                  311                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  WWTR1 MUTATED                       1                              0
  WWTR1 WILD-TYPE                   105                             10
D609V10, multiclass
                                clus
vv                               WWTR1 MUTATED WWTR1 WILD-TYPE
  COLON ADENOCARCINOMA                       4             311
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  WWTR1 MUTATED     4   0   0   1
  WWTR1 WILD-TYPE 341   4  31  24
D609V11, multiclass
    clus
vv   WWTR1 MUTATED WWTR1 WILD-TYPE
  R0             4             341
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D609V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  WWTR1 MUTATED                                  0     0
  WWTR1 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  WWTR1 MUTATED                           0     5
  WWTR1 WILD-TYPE                        22   221
D609V13, multiclass
                                  clus
vv                                 WWTR1 MUTATED WWTR1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        5             221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(610) Variable = ABLIM3 MUTATION ANALYSIS
D610V1, survival
                  sevent
clus2                0   1
  ABLIM3 MUTATED    10   7
  ABLIM3 WILD-TYPE 368  86
  ABLIM3 MUTATED ABLIM3 WILD-TYPE 
              17              454 
  ABLIM3 MUTATED ABLIM3 WILD-TYPE 
               7               86 
$`ABLIM3 MUTATED`
TCGA-AA-3516 TCGA-AA-3526 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3833 
       13.02        19.07        26.99        19.04        19.04        15.95 
TCGA-AD-6888 TCGA-AD-6895 TCGA-AU-6004 TCGA-AZ-6598 TCGA-CA-6717 TCGA-CK-5916 
       15.52         0.72        27.09        49.41        12.76        21.14 
TCGA-D5-6532 TCGA-DM-A28F TCGA-G4-6303 TCGA-AF-6655 TCGA-DC-6160 
       18.25        35.97        65.85        20.02        19.99 

$`ABLIM3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        1.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
        5.03        85.05        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
       25.02         1.02        17.98        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       21.37        56.55         0.79         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       10.88         0.20        14.50        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        88.21         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07        12.20        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       51.32         9.99        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       56.09        55.92        20.19         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       74.56        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       15.39        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6681 TCGA-DC-6682 
        5.03        13.97        27.95        10.98         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  ABLIM3 MUTATED ABLIM3 WILD-TYPE 
            0.72             0.00 
  ABLIM3 MUTATED ABLIM3 WILD-TYPE 
           65.85           148.01 
  ABLIM3 MUTATED ABLIM3 WILD-TYPE 
           19.07            20.73 
[1] "0.7 - 65.8 (19.1)"  "0.0 - 148.0 (20.7)"
[1] "hr=" "2.3"
D610V2, continuous
D610V3, binary
                  cls
clus                 0   1
  ABLIM3 MUTATED    16   2
  ABLIM3 WILD-TYPE 350 117
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ABLIM3 MUTATED     16    2
  ABLIM3 WILD-TYPE  350  117
        clus
vv       ABLIM3 MUTATED ABLIM3 WILD-TYPE
  COLON              16              350
  RECTUM              2              117
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ABLIM3 MUTATED         4        0        2         5         0         0
  ABLIM3 WILD-TYPE      87        1       30       133        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ABLIM3 MUTATED           1          1          2          0        2
  ABLIM3 WILD-TYPE        23         10         57         42       46
                  vv
clus               STAGE IVA STAGE IVB
  ABLIM3 MUTATED           0         0
  ABLIM3 WILD-TYPE        18         1
D610V4, multiclass
            clus
vv           ABLIM3 MUTATED ABLIM3 WILD-TYPE
  STAGE I                 4               87
  STAGE IA                0                1
  STAGE II                2               30
  STAGE IIA               5              133
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               1               23
  STAGE IIIA              1               10
  STAGE IIIB              2               57
  STAGE IIIC              0               42
  STAGE IV                2               46
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ABLIM3 MUTATED     1   4  13   0
  ABLIM3 WILD-TYPE  16  88 316  50
D610V5, multiclass
    clus
vv   ABLIM3 MUTATED ABLIM3 WILD-TYPE
  T1              1               16
  T2              4               88
  T3             13              316
  T4              0               50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  ABLIM3 MUTATED    12   5   1
  ABLIM3 WILD-TYPE 275 108  86
D610V6, multiclass
    clus
vv   ABLIM3 MUTATED ABLIM3 WILD-TYPE
  N0             12              275
  N1              5              108
  N2              1               86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D610V7, binary
                  cls
clus                 0   1
  ABLIM3 MUTATED    14   2
  ABLIM3 WILD-TYPE 361  63
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ABLIM3 MUTATED     14    2
  ABLIM3 WILD-TYPE  361   63
   clus
vv  ABLIM3 MUTATED ABLIM3 WILD-TYPE
  0             14              361
  1              2               63
[1] 2 2
[1] FALSE
D610V8, binary
                  cls
clus                 0   1
  ABLIM3 MUTATED     8  10
  ABLIM3 WILD-TYPE 217 254
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ABLIM3 MUTATED      8   10
  ABLIM3 WILD-TYPE  217  254
        clus
vv       ABLIM3 MUTATED ABLIM3 WILD-TYPE
  FEMALE              8              217
  MALE               10              254
[1] 2 2
[1] FALSE
D610V9, binary
                  cls
clus                 0   1
  ABLIM3 MUTATED    12   1
  ABLIM3 WILD-TYPE 338  21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ABLIM3 MUTATED     12    1
  ABLIM3 WILD-TYPE  338   21
     clus
vv    ABLIM3 MUTATED ABLIM3 WILD-TYPE
  NO              12              338
  YES              1               21
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ABLIM3 MUTATED                     14                             2
  ABLIM3 WILD-TYPE                  301                            45
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ABLIM3 MUTATED                       2                              0
  ABLIM3 WILD-TYPE                   104                             10
D610V10, multiclass
                                clus
vv                               ABLIM3 MUTATED ABLIM3 WILD-TYPE
  COLON ADENOCARCINOMA                       14              301
  COLON MUCINOUS ADENOCARCINOMA               2               45
  RECTAL ADENOCARCINOMA                       2              104
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ABLIM3 MUTATED    11   0   1   2
  ABLIM3 WILD-TYPE 334   4  30  23
D610V11, multiclass
    clus
vv   ABLIM3 MUTATED ABLIM3 WILD-TYPE
  R0             11              334
  R1              0                4
  R2              1               30
  RX              2               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D610V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ABLIM3 MUTATED                                  0     1
  ABLIM3 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ABLIM3 MUTATED                           0    10
  ABLIM3 WILD-TYPE                        22   216
D610V13, multiclass
                                  clus
vv                                 ABLIM3 MUTATED ABLIM3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                        10              216
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(611) Variable = SNTN MUTATION ANALYSIS
D611V1, survival
                sevent
clus2              0   1
  SNTN MUTATED     6   0
  SNTN WILD-TYPE 372  93
  SNTN MUTATED SNTN WILD-TYPE 
             6            465 
  SNTN MUTATED SNTN WILD-TYPE 
             0             93 
$`SNTN MUTATED`
TCGA-AA-3496 TCGA-CA-6716 TCGA-CM-6676 TCGA-DM-A1HA TCGA-F4-6806 TCGA-DC-6157 
        1.02        12.20        11.08       131.51        41.42        27.95 

$`SNTN WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       12.95        13.05        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A282 
       12.59       140.38         7.50        44.32       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
        1.55        34.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       13.97        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  SNTN MUTATED SNTN WILD-TYPE 
          1.02           0.00 
  SNTN MUTATED SNTN WILD-TYPE 
        131.51         148.01 
  SNTN MUTATED SNTN WILD-TYPE 
        20.075         20.190 
[1] "1.0 - 131.5 (20.1)" "0.0 - 148.0 (20.2)"
[1] "hr="     "9200000"
D611V2, continuous
D611V3, binary
                cls
clus               0   1
  SNTN MUTATED     6   1
  SNTN WILD-TYPE 360 118
[1] "tbl2"
                cls
clus             [,1] [,2]
  SNTN MUTATED      6    1
  SNTN WILD-TYPE  360  118
        clus
vv       SNTN MUTATED SNTN WILD-TYPE
  COLON             6            360
  RECTUM            1            118
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SNTN MUTATED         3        0        1         1         1         0
  SNTN WILD-TYPE      88        1       31       137         9         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SNTN MUTATED           0          0          0          1        0         0
  SNTN WILD-TYPE        24         11         59         41       48        18
                vv
clus             STAGE IVB
  SNTN MUTATED           0
  SNTN WILD-TYPE         1
D611V4, multiclass
            clus
vv           SNTN MUTATED SNTN WILD-TYPE
  STAGE I               3             88
  STAGE IA              0              1
  STAGE II              1             31
  STAGE IIA             1            137
  STAGE IIB             1              9
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            0             59
  STAGE IIIC            1             41
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  SNTN MUTATED     0   3   3   1
  SNTN WILD-TYPE  17  89 326  49
D611V5, multiclass
    clus
vv   SNTN MUTATED SNTN WILD-TYPE
  T1            0             17
  T2            3             89
  T3            3            326
  T4            1             49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  SNTN MUTATED     6   0   1
  SNTN WILD-TYPE 281 113  86
D611V6, multiclass
    clus
vv   SNTN MUTATED SNTN WILD-TYPE
  N0            6            281
  N1            0            113
  N2            1             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D611V7, binary
                cls
clus               0   1
  SNTN MUTATED     6   0
  SNTN WILD-TYPE 369  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  SNTN MUTATED      6    0
  SNTN WILD-TYPE  369   65
   clus
vv  SNTN MUTATED SNTN WILD-TYPE
  0            6            369
  1            0             65
[1] 2 2
[1] FALSE
D611V8, binary
                cls
clus               0   1
  SNTN MUTATED     3   4
  SNTN WILD-TYPE 222 260
[1] "tbl2"
                cls
clus             [,1] [,2]
  SNTN MUTATED      3    4
  SNTN WILD-TYPE  222  260
        clus
vv       SNTN MUTATED SNTN WILD-TYPE
  FEMALE            3            222
  MALE              4            260
[1] 2 2
[1] FALSE
D611V9, binary
                cls
clus               0   1
  SNTN MUTATED     3   0
  SNTN WILD-TYPE 347  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  SNTN MUTATED      3    0
  SNTN WILD-TYPE  347   22
     clus
vv    SNTN MUTATED SNTN WILD-TYPE
  NO             3            347
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SNTN MUTATED                      6                             0
  SNTN WILD-TYPE                  309                            47
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SNTN MUTATED                       1                              0
  SNTN WILD-TYPE                   105                             10
D611V10, multiclass
                                clus
vv                               SNTN MUTATED SNTN WILD-TYPE
  COLON ADENOCARCINOMA                      6            309
  COLON MUCINOUS ADENOCARCINOMA             0             47
  RECTAL ADENOCARCINOMA                     1            105
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  SNTN MUTATED     4   0   0   2
  SNTN WILD-TYPE 341   4  31  23
D611V11, multiclass
    clus
vv   SNTN MUTATED SNTN WILD-TYPE
  R0            4            341
  R1            0              4
  R2            0             31
  RX            2             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D611V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SNTN MUTATED                                  0     1
  SNTN WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  SNTN MUTATED                           1     4
  SNTN WILD-TYPE                        21   222
D611V13, multiclass
                                  clus
vv                                 SNTN MUTATED SNTN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                       4            222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(612) Variable = DSG4 MUTATION ANALYSIS
D612V1, survival
                sevent
clus2              0   1
  DSG4 MUTATED    21   2
  DSG4 WILD-TYPE 357  91
  DSG4 MUTATED DSG4 WILD-TYPE 
            23            448 
  DSG4 MUTATED DSG4 WILD-TYPE 
             2             91 
$`DSG4 MUTATED`
TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3510 TCGA-AA-3555 TCGA-AA-3660 TCGA-AA-3672 
       20.12        19.66        63.98        29.95        78.08         0.92 
TCGA-AA-3864 TCGA-AA-3950 TCGA-AA-A00J TCGA-AY-6386 TCGA-CA-6718 TCGA-CK-4950 
       53.00        24.00        18.05        17.82        10.06        85.45 
TCGA-D5-6533 TCGA-D5-6540 TCGA-D5-6920 TCGA-D5-6929 TCGA-DM-A282 TCGA-F4-6570 
        1.32        16.14         3.68         4.80       139.17         6.18 
TCGA-F4-6703 TCGA-G4-6321 TCGA-AG-3892 TCGA-AG-A002 TCGA-DC-5337 
       47.87        22.09        13.02        20.98        15.02 

$`DSG4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       23.87        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       17.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       61.02         6.05         6.97        54.02         2.01        14.01 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 
        2.01        12.99        24.00        33.01        26.01         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       19.00        30.02        34.03        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       14.30        17.56       148.01        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 
       56.09        55.92        20.19        18.25        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 
       17.85         4.80        17.13        12.49        15.58         1.48 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A285 
      140.38         7.50        44.32       131.51       135.65         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
        8.61        31.96        35.74         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6586 
       85.48        63.62        61.91        36.00        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5869 
       33.17         6.97         4.73        78.12         7.17         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  DSG4 MUTATED DSG4 WILD-TYPE 
          0.92           0.00 
  DSG4 MUTATED DSG4 WILD-TYPE 
        139.17         148.01 
  DSG4 MUTATED DSG4 WILD-TYPE 
        19.660         20.415 
[1] "0.9 - 139.2 (19.7)" "0.0 - 148.0 (20.4)"
[1] "hr=" "2.7"
D612V2, continuous
D612V3, binary
                cls
clus               0   1
  DSG4 MUTATED    21   3
  DSG4 WILD-TYPE 345 116
[1] "tbl2"
                cls
clus             [,1] [,2]
  DSG4 MUTATED     21    3
  DSG4 WILD-TYPE  345  116
        clus
vv       DSG4 MUTATED DSG4 WILD-TYPE
  COLON            21            345
  RECTUM            3            116
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DSG4 MUTATED         4        0        3         8         0         0
  DSG4 WILD-TYPE      87        1       29       130        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DSG4 MUTATED           2          0          4          2        1         0
  DSG4 WILD-TYPE        22         11         55         40       47        18
                vv
clus             STAGE IVB
  DSG4 MUTATED           0
  DSG4 WILD-TYPE         1
D612V4, multiclass
            clus
vv           DSG4 MUTATED DSG4 WILD-TYPE
  STAGE I               4             87
  STAGE IA              0              1
  STAGE II              3             29
  STAGE IIA             8            130
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             2             22
  STAGE IIIA            0             11
  STAGE IIIB            4             55
  STAGE IIIC            2             40
  STAGE IV              1             47
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  DSG4 MUTATED     2   3  16   3
  DSG4 WILD-TYPE  15  89 313  47
D612V5, multiclass
    clus
vv   DSG4 MUTATED DSG4 WILD-TYPE
  T1            2             15
  T2            3             89
  T3           16            313
  T4            3             47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  DSG4 MUTATED    16   7   1
  DSG4 WILD-TYPE 271 106  86
D612V6, multiclass
    clus
vv   DSG4 MUTATED DSG4 WILD-TYPE
  N0           16            271
  N1            7            106
  N2            1             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D612V7, binary
                cls
clus               0   1
  DSG4 MUTATED    19   1
  DSG4 WILD-TYPE 356  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  DSG4 MUTATED     19    1
  DSG4 WILD-TYPE  356   64
   clus
vv  DSG4 MUTATED DSG4 WILD-TYPE
  0           19            356
  1            1             64
[1] 2 2
[1] FALSE
D612V8, binary
                cls
clus               0   1
  DSG4 MUTATED    13  11
  DSG4 WILD-TYPE 212 253
[1] "tbl2"
                cls
clus             [,1] [,2]
  DSG4 MUTATED     13   11
  DSG4 WILD-TYPE  212  253
        clus
vv       DSG4 MUTATED DSG4 WILD-TYPE
  FEMALE           13            212
  MALE             11            253
[1] 2 2
[1] FALSE
D612V9, binary
                cls
clus               0   1
  DSG4 MUTATED    19   0
  DSG4 WILD-TYPE 331  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  DSG4 MUTATED     19    0
  DSG4 WILD-TYPE  331   22
     clus
vv    DSG4 MUTATED DSG4 WILD-TYPE
  NO            19            331
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  DSG4 MUTATED                     14                             7
  DSG4 WILD-TYPE                  301                            40
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  DSG4 MUTATED                       3                              0
  DSG4 WILD-TYPE                   103                             10
D612V10, multiclass
                                clus
vv                               DSG4 MUTATED DSG4 WILD-TYPE
  COLON ADENOCARCINOMA                     14            301
  COLON MUCINOUS ADENOCARCINOMA             7             40
  RECTAL ADENOCARCINOMA                     3            103
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  DSG4 MUTATED    20   1   0   1
  DSG4 WILD-TYPE 325   3  31  24
D612V11, multiclass
    clus
vv   DSG4 MUTATED DSG4 WILD-TYPE
  R0           20            325
  R1            1              3
  R2            0             31
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D612V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DSG4 MUTATED                                  0     1
  DSG4 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  DSG4 MUTATED                           2    12
  DSG4 WILD-TYPE                        20   214
D612V13, multiclass
                                  clus
vv                                 DSG4 MUTATED DSG4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   2             20
  WHITE                                      12            214
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(613) Variable = PCDH12 MUTATION ANALYSIS
D613V1, survival
                  sevent
clus2                0   1
  PCDH12 MUTATED    18   2
  PCDH12 WILD-TYPE 360  91
  PCDH12 MUTATED PCDH12 WILD-TYPE 
              20              451 
  PCDH12 MUTATED PCDH12 WILD-TYPE 
               2               91 
$`PCDH12 MUTATED`
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5665 TCGA-AA-3672 TCGA-AA-3713 TCGA-AA-3821 
       33.53        23.61        22.06         0.92        19.04         1.02 
TCGA-AA-3864 TCGA-AA-3877 TCGA-AA-A010 TCGA-AD-6964 TCGA-AZ-6598 TCGA-CA-6715 
       53.00        31.00        34.98        10.88        49.41         0.07 
TCGA-CA-6717 TCGA-CK-5913 TCGA-CM-6171 TCGA-D5-6927 TCGA-D5-6928 TCGA-AG-3609 
       12.76        51.32        14.04         9.44        11.64        19.99 
TCGA-AG-3885 TCGA-AG-A002 
       17.95        20.98 

$`PCDH12 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5664 TCGA-A6-5666 
       32.91        31.63        30.44        29.19        22.09        32.71 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       27.09        22.52         8.38        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
        2.01        14.01        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       26.99        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
       25.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 
       17.03        24.03        27.02        29.98        18.05         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
        0.79         0.72         5.79        22.42        27.42         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        88.21         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.25         3.29        12.20        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 
      148.01        85.45        15.62        49.08         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 
       14.99        12.99        13.02        15.02        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6930 
        4.41        12.43        14.30         9.04         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 
        0.99         0.99        19.04        19.99         1.02        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  PCDH12 MUTATED PCDH12 WILD-TYPE 
            0.07             0.00 
  PCDH12 MUTATED PCDH12 WILD-TYPE 
           53.00           148.01 
  PCDH12 MUTATED PCDH12 WILD-TYPE 
          19.515           20.280 
[1] "0.1 - 53.0 (19.5)"  "0.0 - 148.0 (20.3)"
[1] "hr=" "1.7"
D613V2, continuous
D613V3, binary
                  cls
clus                 0   1
  PCDH12 MUTATED    17   3
  PCDH12 WILD-TYPE 349 116
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PCDH12 MUTATED     17    3
  PCDH12 WILD-TYPE  349  116
        clus
vv       PCDH12 MUTATED PCDH12 WILD-TYPE
  COLON              17              349
  RECTUM              3              116
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PCDH12 MUTATED         4        0        2         6         1         0
  PCDH12 WILD-TYPE      87        1       30       132         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PCDH12 MUTATED           1          0          2          1        1
  PCDH12 WILD-TYPE        23         11         57         41       47
                  vv
clus               STAGE IVA STAGE IVB
  PCDH12 MUTATED           1         0
  PCDH12 WILD-TYPE        17         1
D613V4, multiclass
            clus
vv           PCDH12 MUTATED PCDH12 WILD-TYPE
  STAGE I                 4               87
  STAGE IA                0                1
  STAGE II                2               30
  STAGE IIA               6              132
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               1               23
  STAGE IIIA              0               11
  STAGE IIIB              2               57
  STAGE IIIC              1               41
  STAGE IV                1               47
  STAGE IVA               1               17
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  PCDH12 MUTATED     1   3  14   2
  PCDH12 WILD-TYPE  16  89 315  48
D613V5, multiclass
    clus
vv   PCDH12 MUTATED PCDH12 WILD-TYPE
  T1              1               16
  T2              3               89
  T3             14              315
  T4              2               48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  PCDH12 MUTATED    14   3   3
  PCDH12 WILD-TYPE 273 110  84
D613V6, multiclass
    clus
vv   PCDH12 MUTATED PCDH12 WILD-TYPE
  N0             14              273
  N1              3              110
  N2              3               84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D613V7, binary
                  cls
clus                 0   1
  PCDH12 MUTATED    15   2
  PCDH12 WILD-TYPE 360  63
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PCDH12 MUTATED     15    2
  PCDH12 WILD-TYPE  360   63
   clus
vv  PCDH12 MUTATED PCDH12 WILD-TYPE
  0             15              360
  1              2               63
[1] 2 2
[1] FALSE
D613V8, binary
                  cls
clus                 0   1
  PCDH12 MUTATED    11   9
  PCDH12 WILD-TYPE 214 255
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PCDH12 MUTATED     11    9
  PCDH12 WILD-TYPE  214  255
        clus
vv       PCDH12 MUTATED PCDH12 WILD-TYPE
  FEMALE             11              214
  MALE                9              255
[1] 2 2
[1] FALSE
D613V9, binary
                  cls
clus                 0   1
  PCDH12 MUTATED    17   2
  PCDH12 WILD-TYPE 333  20
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PCDH12 MUTATED     17    2
  PCDH12 WILD-TYPE  333   20
     clus
vv    PCDH12 MUTATED PCDH12 WILD-TYPE
  NO              17              333
  YES              2               20
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PCDH12 MUTATED                     13                             4
  PCDH12 WILD-TYPE                  302                            43
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PCDH12 MUTATED                       3                              0
  PCDH12 WILD-TYPE                   103                             10
D613V10, multiclass
                                clus
vv                               PCDH12 MUTATED PCDH12 WILD-TYPE
  COLON ADENOCARCINOMA                       13              302
  COLON MUCINOUS ADENOCARCINOMA               4               43
  RECTAL ADENOCARCINOMA                       3              103
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  PCDH12 MUTATED    13   0   1   3
  PCDH12 WILD-TYPE 332   4  30  22
D613V11, multiclass
    clus
vv   PCDH12 MUTATED PCDH12 WILD-TYPE
  R0             13              332
  R1              0                4
  R2              1               30
  RX              3               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D613V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PCDH12 MUTATED                                  0     2
  PCDH12 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  PCDH12 MUTATED                           1     8
  PCDH12 WILD-TYPE                        21   218
D613V13, multiclass
                                  clus
vv                                 PCDH12 MUTATED PCDH12 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                9
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                         8              218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(614) Variable = EAPP MUTATION ANALYSIS
D614V1, survival
                sevent
clus2              0   1
  EAPP MUTATED     3   2
  EAPP WILD-TYPE 375  91
  EAPP MUTATED EAPP WILD-TYPE 
             5            466 
  EAPP MUTATED EAPP WILD-TYPE 
             2             91 
$`EAPP MUTATED`
TCGA-A6-4105 TCGA-AA-A03F TCGA-D5-6535 TCGA-AG-4007 TCGA-AG-A002 
       14.53        18.05        15.12         1.02        20.98 

$`EAPP WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 
       16.57        34.65        33.34        32.75        36.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       41.00        39.98        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 
       20.19        18.25         1.32        43.27        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       28.04        36.03        14.04        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  EAPP MUTATED EAPP WILD-TYPE 
          1.02           0.00 
  EAPP MUTATED EAPP WILD-TYPE 
         20.98         148.01 
  EAPP MUTATED EAPP WILD-TYPE 
        15.120         20.415 
[1] "1.0 - 21.0 (15.1)"  "0.0 - 148.0 (20.4)"
[1] "hr=" "3.6"
D614V2, continuous
D614V3, binary
                cls
clus               0   1
  EAPP MUTATED     4   2
  EAPP WILD-TYPE 362 117
[1] "tbl2"
                cls
clus             [,1] [,2]
  EAPP MUTATED      4    2
  EAPP WILD-TYPE  362  117
        clus
vv       EAPP MUTATED EAPP WILD-TYPE
  COLON             4            362
  RECTUM            2            117
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  EAPP MUTATED         1        0        0         1         0         0
  EAPP WILD-TYPE      90        1       32       137        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  EAPP MUTATED           2          0          1          0        1         0
  EAPP WILD-TYPE        22         11         58         42       47        18
                vv
clus             STAGE IVB
  EAPP MUTATED           0
  EAPP WILD-TYPE         1
D614V4, multiclass
            clus
vv           EAPP MUTATED EAPP WILD-TYPE
  STAGE I               1             90
  STAGE IA              0              1
  STAGE II              0             32
  STAGE IIA             1            137
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             2             22
  STAGE IIIA            0             11
  STAGE IIIB            1             58
  STAGE IIIC            0             42
  STAGE IV              1             47
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  EAPP MUTATED     0   1   4   1
  EAPP WILD-TYPE  17  91 325  49
D614V5, multiclass
    clus
vv   EAPP MUTATED EAPP WILD-TYPE
  T1            0             17
  T2            1             91
  T3            4            325
  T4            1             49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  EAPP MUTATED     2   1   3
  EAPP WILD-TYPE 285 112  84
D614V6, multiclass
    clus
vv   EAPP MUTATED EAPP WILD-TYPE
  N0            2            285
  N1            1            112
  N2            3             84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D614V7, binary
                cls
clus               0   1
  EAPP MUTATED     4   1
  EAPP WILD-TYPE 371  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  EAPP MUTATED      4    1
  EAPP WILD-TYPE  371   64
   clus
vv  EAPP MUTATED EAPP WILD-TYPE
  0            4            371
  1            1             64
[1] 2 2
[1] FALSE
D614V8, binary
                cls
clus               0   1
  EAPP MUTATED     2   4
  EAPP WILD-TYPE 223 260
[1] "tbl2"
                cls
clus             [,1] [,2]
  EAPP MUTATED      2    4
  EAPP WILD-TYPE  223  260
        clus
vv       EAPP MUTATED EAPP WILD-TYPE
  FEMALE            2            223
  MALE              4            260
[1] 2 2
[1] FALSE
D614V9, binary
                cls
clus               0   1
  EAPP MUTATED     3   0
  EAPP WILD-TYPE 347  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  EAPP MUTATED      3    0
  EAPP WILD-TYPE  347   22
     clus
vv    EAPP MUTATED EAPP WILD-TYPE
  NO             3            347
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  EAPP MUTATED                      3                             1
  EAPP WILD-TYPE                  312                            46
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  EAPP MUTATED                       2                              0
  EAPP WILD-TYPE                   104                             10
D614V10, multiclass
                                clus
vv                               EAPP MUTATED EAPP WILD-TYPE
  COLON ADENOCARCINOMA                      3            312
  COLON MUCINOUS ADENOCARCINOMA             1             46
  RECTAL ADENOCARCINOMA                     2            104
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  EAPP MUTATED     3   0   1   1
  EAPP WILD-TYPE 342   4  30  24
D614V11, multiclass
    clus
vv   EAPP MUTATED EAPP WILD-TYPE
  R0            3            342
  R1            0              4
  R2            1             30
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D614V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  EAPP MUTATED                                  0     0
  EAPP WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  EAPP MUTATED                           0     2
  EAPP WILD-TYPE                        22   224
D614V13, multiclass
[1] "Remove cluster labels:" "EAPP MUTATED"          
clus
  EAPP MUTATED EAPP WILD-TYPE 
             2            258 
    TCGA-A6-2671     TCGA-A6-2672     TCGA-A6-2674     TCGA-A6-2676 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-A6-2677     TCGA-A6-2678     TCGA-A6-2683     TCGA-A6-3807 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-A6-3808     TCGA-A6-3809     TCGA-A6-3810     TCGA-A6-5656 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-A6-5657     TCGA-A6-5659     TCGA-A6-5660     TCGA-A6-5661 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-A6-5662     TCGA-A6-5664     TCGA-A6-5665     TCGA-A6-5666 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-A6-6137     TCGA-A6-6138     TCGA-A6-6141     TCGA-A6-6142 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-A6-6648     TCGA-A6-6649     TCGA-A6-6651     TCGA-A6-6652 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-A6-6653     TCGA-A6-6654     TCGA-A6-6780     TCGA-A6-6781 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-A6-6782     TCGA-AD-5900     TCGA-AD-6548     TCGA-AD-6888 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-AD-6889     TCGA-AD-6890     TCGA-AD-6895     TCGA-AD-6899 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-AD-6901     TCGA-AD-6963     TCGA-AD-6964     TCGA-AD-6965 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-AU-3779     TCGA-AU-6004     TCGA-AY-4070     TCGA-AY-4071 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-AY-5543     TCGA-AY-6196     TCGA-AY-6197     TCGA-AY-6386 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-AZ-4315     TCGA-AZ-4323     TCGA-AZ-4616     TCGA-AZ-4681 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-AZ-4682     TCGA-AZ-5403     TCGA-AZ-5407     TCGA-AZ-6598 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-AZ-6599     TCGA-AZ-6600     TCGA-AZ-6601     TCGA-AZ-6603 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-AZ-6605     TCGA-AZ-6606     TCGA-AZ-6607     TCGA-AZ-6608 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-CA-5254     TCGA-CA-5255     TCGA-CA-5796     TCGA-CA-5797 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-CA-6715     TCGA-CA-6716     TCGA-CA-6717     TCGA-CA-6718 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-CA-6719     TCGA-CK-4947     TCGA-CK-4948     TCGA-CK-4950 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-CK-4952     TCGA-CK-5912     TCGA-CK-5913     TCGA-CK-5914 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-CK-5915     TCGA-CK-5916     TCGA-CK-6746     TCGA-CK-6747 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-CK-6748     TCGA-CK-6751     TCGA-CM-4743     TCGA-CM-4744 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-CM-4746     TCGA-CM-4747     TCGA-CM-4752     TCGA-CM-5341 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-CM-5344     TCGA-CM-5348     TCGA-CM-5349     TCGA-CM-5860 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-CM-5861     TCGA-CM-5862     TCGA-CM-5863     TCGA-CM-5864 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-CM-5868     TCGA-CM-6161     TCGA-CM-6162     TCGA-CM-6163 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-CM-6164     TCGA-CM-6165     TCGA-CM-6166     TCGA-CM-6167 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-CM-6168     TCGA-CM-6169     TCGA-CM-6170     TCGA-CM-6171 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-CM-6172     TCGA-CM-6674     TCGA-CM-6675     TCGA-CM-6676 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-CM-6677     TCGA-CM-6678     TCGA-CM-6679     TCGA-CM-6680 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-D5-5537     TCGA-D5-5538     TCGA-D5-5539     TCGA-D5-5540 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-D5-5541     TCGA-D5-6529     TCGA-D5-6532     TCGA-D5-6533 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-D5-6534     TCGA-D5-6536     TCGA-D5-6537     TCGA-D5-6538 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-D5-6539     TCGA-D5-6540     TCGA-D5-6541     TCGA-D5-6898 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-D5-6920     TCGA-D5-6922     TCGA-D5-6923     TCGA-D5-6924 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-D5-6926     TCGA-D5-6927     TCGA-D5-6928     TCGA-D5-6929 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-D5-6930     TCGA-D5-6931     TCGA-D5-6932     TCGA-D5-7000 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-DM-A0X9     TCGA-DM-A0XD     TCGA-DM-A0XF     TCGA-DM-A1D0 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-DM-A1D4     TCGA-DM-A1D6     TCGA-DM-A1D7     TCGA-DM-A1D8 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-DM-A1D9     TCGA-DM-A1DA     TCGA-DM-A1DB     TCGA-DM-A1HA 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-DM-A1HB     TCGA-DM-A282     TCGA-DM-A285     TCGA-DM-A28C 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-DM-A28E     TCGA-DM-A28F     TCGA-DM-A28G     TCGA-DM-A28H 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-DM-A28K     TCGA-F4-6459     TCGA-F4-6460     TCGA-F4-6569 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-F4-6570     TCGA-F4-6703     TCGA-F4-6704     TCGA-F4-6805 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-F4-6806     TCGA-F4-6807     TCGA-F4-6808     TCGA-F4-6809 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-F4-6854     TCGA-F4-6855     TCGA-F4-6856     TCGA-G4-6293 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-G4-6299     TCGA-G4-6303     TCGA-G4-6304     TCGA-G4-6306 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-G4-6307     TCGA-G4-6309     TCGA-G4-6310     TCGA-G4-6315 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-G4-6317     TCGA-G4-6321     TCGA-G4-6323     TCGA-G4-6586 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-G4-6588     TCGA-G4-6625     TCGA-G4-6626     TCGA-G4-6628 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-AF-2687     TCGA-AF-2689     TCGA-AF-2691     TCGA-AF-2692 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-AF-2693     TCGA-AF-3400     TCGA-AF-3913     TCGA-AF-4110 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-AF-5654     TCGA-AF-6136     TCGA-AF-6655     TCGA-AF-6672 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-AH-6544     TCGA-AH-6547     TCGA-AH-6549     TCGA-AH-6643 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-AH-6644     TCGA-CI-6619     TCGA-CI-6620     TCGA-CI-6621 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-CI-6622     TCGA-CI-6624     TCGA-CL-5917     TCGA-CL-5918 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-DC-5337     TCGA-DC-5869     TCGA-DC-6155     TCGA-DC-6157 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-DC-6158     TCGA-DC-6160     TCGA-DC-6681     TCGA-DC-6682 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-DC-6683     TCGA-DT-5265     TCGA-DY-A0XA     TCGA-DY-A1DC 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-DY-A1DD     TCGA-DY-A1DF     TCGA-DY-A1DG     TCGA-DY-A1H8 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-EF-5830     TCGA-EI-6506     TCGA-EI-6507     TCGA-EI-6508 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-EI-6510     TCGA-F5-6464     TCGA-F5-6465     TCGA-F5-6571 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-F5-6702     TCGA-F5-6811     TCGA-F5-6812     TCGA-F5-6813 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" "EAPP WILD-TYPE" 
    TCGA-G5-6235     TCGA-G5-6641 
"EAPP WILD-TYPE" "EAPP WILD-TYPE" 

Clustering(615) Variable = SLC7A10 MUTATION ANALYSIS
D615V1, survival
                   sevent
clus2                 0   1
  SLC7A10 MUTATED     5   2
  SLC7A10 WILD-TYPE 373  91
  SLC7A10 MUTATED SLC7A10 WILD-TYPE 
                7               464 
  SLC7A10 MUTATED SLC7A10 WILD-TYPE 
                2                91 
$`SLC7A10 MUTATED`
TCGA-AA-3664 TCGA-AA-3715 TCGA-AD-6889 TCGA-AU-6004 TCGA-AZ-6598 TCGA-CM-6674 
       54.02        19.04        56.55        27.09        49.41        12.95 
TCGA-D5-6928 
       11.64 

$`SLC7A10 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.05         6.97         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 
       36.00         5.03        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
        0.20        14.50        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        88.21         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       15.02        14.04        11.01        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.04         9.44         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  SLC7A10 MUTATED SLC7A10 WILD-TYPE 
            11.64              0.00 
  SLC7A10 MUTATED SLC7A10 WILD-TYPE 
            56.55            148.01 
  SLC7A10 MUTATED SLC7A10 WILD-TYPE 
           27.090            20.155 
[1] "11.6 - 56.5 (27.1)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.1"
D615V2, continuous
D615V3, binary
                   cls
clus                  0   1
  SLC7A10 MUTATED     8   0
  SLC7A10 WILD-TYPE 358 119
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC7A10 MUTATED      8    0
  SLC7A10 WILD-TYPE  358  119
        clus
vv       SLC7A10 MUTATED SLC7A10 WILD-TYPE
  COLON                8               358
  RECTUM               0               119
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SLC7A10 MUTATED         1        0        3         3         1         0
  SLC7A10 WILD-TYPE      90        1       29       135         9         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC7A10 MUTATED           0          0          0          0        0
  SLC7A10 WILD-TYPE        24         11         59         42       48
                   vv
clus                STAGE IVA STAGE IVB
  SLC7A10 MUTATED           0         0
  SLC7A10 WILD-TYPE        18         1
D615V4, multiclass
            clus
vv           SLC7A10 MUTATED SLC7A10 WILD-TYPE
  STAGE I                  1                90
  STAGE IA                 0                 1
  STAGE II                 3                29
  STAGE IIA                3               135
  STAGE IIB                1                 9
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               0                11
  STAGE IIIB               0                59
  STAGE IIIC               0                42
  STAGE IV                 0                48
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  SLC7A10 MUTATED     0   1   6   1
  SLC7A10 WILD-TYPE  17  91 323  49
D615V5, multiclass
    clus
vv   SLC7A10 MUTATED SLC7A10 WILD-TYPE
  T1               0                17
  T2               1                91
  T3               6               323
  T4               1                49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  SLC7A10 MUTATED     8   0   0
  SLC7A10 WILD-TYPE 279 113  87
D615V6, multiclass
    clus
vv   SLC7A10 MUTATED SLC7A10 WILD-TYPE
  N0               8               279
  N1               0               113
  N2               0                87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D615V7, binary
                   cls
clus                  0   1
  SLC7A10 MUTATED     6   0
  SLC7A10 WILD-TYPE 369  65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC7A10 MUTATED      6    0
  SLC7A10 WILD-TYPE  369   65
   clus
vv  SLC7A10 MUTATED SLC7A10 WILD-TYPE
  0               6               369
  1               0                65
[1] 2 2
[1] FALSE
D615V8, binary
                   cls
clus                  0   1
  SLC7A10 MUTATED     4   4
  SLC7A10 WILD-TYPE 221 260
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC7A10 MUTATED      4    4
  SLC7A10 WILD-TYPE  221  260
        clus
vv       SLC7A10 MUTATED SLC7A10 WILD-TYPE
  FEMALE               4               221
  MALE                 4               260
[1] 2 2
[1] FALSE
D615V9, binary
                   cls
clus                  0   1
  SLC7A10 MUTATED     5   0
  SLC7A10 WILD-TYPE 345  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC7A10 MUTATED      5    0
  SLC7A10 WILD-TYPE  345   22
     clus
vv    SLC7A10 MUTATED SLC7A10 WILD-TYPE
  NO                5               345
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SLC7A10 MUTATED                      7                             1
  SLC7A10 WILD-TYPE                  308                            46
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SLC7A10 MUTATED                       0                              0
  SLC7A10 WILD-TYPE                   106                             10
D615V10, multiclass
                                clus
vv                               SLC7A10 MUTATED SLC7A10 WILD-TYPE
  COLON ADENOCARCINOMA                         7               308
  COLON MUCINOUS ADENOCARCINOMA                1                46
  RECTAL ADENOCARCINOMA                        0               106
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  SLC7A10 MUTATED     5   0   0   1
  SLC7A10 WILD-TYPE 340   4  31  24
D615V11, multiclass
    clus
vv   SLC7A10 MUTATED SLC7A10 WILD-TYPE
  R0               5               340
  R1               0                 4
  R2               0                31
  RX               1                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D615V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SLC7A10 MUTATED                                  0     1
  SLC7A10 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  SLC7A10 MUTATED                           0     5
  SLC7A10 WILD-TYPE                        22   221
D615V13, multiclass
                                  clus
vv                                 SLC7A10 MUTATED SLC7A10 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                10
  BLACK OR AFRICAN AMERICAN                      0                22
  WHITE                                          5               221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(616) Variable = ZNF711 MUTATION ANALYSIS
D616V1, survival
                  sevent
clus2                0   1
  ZNF711 MUTATED     8   2
  ZNF711 WILD-TYPE 370  91
  ZNF711 MUTATED ZNF711 WILD-TYPE 
              10              461 
  ZNF711 MUTATED ZNF711 WILD-TYPE 
               2               91 
$`ZNF711 MUTATED`
TCGA-A6-6138 TCGA-A6-6651 TCGA-AA-3492 TCGA-AA-A01Q TCGA-AU-6004 TCGA-D5-5541 
       22.52        21.76         3.02         1.02        27.09        55.92 
TCGA-D5-6539 TCGA-D5-6928 TCGA-F4-6570 TCGA-AG-3742 
       12.49        11.64         6.18         0.99 

$`ZNF711 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6141 TCGA-A6-6142 
       22.09        22.06        32.71        27.09         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       25.18        24.16        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       19.66        20.28         7.04         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       31.00        38.07        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       14.50        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       19.59        56.09        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 
       15.12        17.85         4.80        17.13        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
        9.44         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
        0.99        37.02        32.98         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  ZNF711 MUTATED ZNF711 WILD-TYPE 
            0.99             0.00 
  ZNF711 MUTATED ZNF711 WILD-TYPE 
           55.92           148.01 
  ZNF711 MUTATED ZNF711 WILD-TYPE 
          12.065           20.280 
[1] "1.0 - 55.9 (12.1)"  "0.0 - 148.0 (20.3)"
[1] "hr=" "1.5"
D616V2, continuous
D616V3, binary
                  cls
clus                 0   1
  ZNF711 MUTATED    10   1
  ZNF711 WILD-TYPE 356 118
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF711 MUTATED     10    1
  ZNF711 WILD-TYPE  356  118
        clus
vv       ZNF711 MUTATED ZNF711 WILD-TYPE
  COLON              10              356
  RECTUM              1              118
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZNF711 MUTATED         3        0        2         2         0         0
  ZNF711 WILD-TYPE      88        1       30       136        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF711 MUTATED           0          1          2          0        1
  ZNF711 WILD-TYPE        24         10         57         42       47
                  vv
clus               STAGE IVA STAGE IVB
  ZNF711 MUTATED           0         0
  ZNF711 WILD-TYPE        18         1
D616V4, multiclass
            clus
vv           ZNF711 MUTATED ZNF711 WILD-TYPE
  STAGE I                 3               88
  STAGE IA                0                1
  STAGE II                2               30
  STAGE IIA               2              136
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              1               10
  STAGE IIIB              2               57
  STAGE IIIC              0               42
  STAGE IV                1               47
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZNF711 MUTATED     1   2   7   1
  ZNF711 WILD-TYPE  16  90 322  49
D616V5, multiclass
    clus
vv   ZNF711 MUTATED ZNF711 WILD-TYPE
  T1              1               16
  T2              2               90
  T3              7              322
  T4              1               49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  ZNF711 MUTATED     8   2   1
  ZNF711 WILD-TYPE 279 111  86
D616V6, multiclass
    clus
vv   ZNF711 MUTATED ZNF711 WILD-TYPE
  N0              8              279
  N1              2              111
  N2              1               86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D616V7, binary
                  cls
clus                 0   1
  ZNF711 MUTATED     9   1
  ZNF711 WILD-TYPE 366  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF711 MUTATED      9    1
  ZNF711 WILD-TYPE  366   64
   clus
vv  ZNF711 MUTATED ZNF711 WILD-TYPE
  0              9              366
  1              1               64
[1] 2 2
[1] FALSE
D616V8, binary
                  cls
clus                 0   1
  ZNF711 MUTATED     7   4
  ZNF711 WILD-TYPE 218 260
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF711 MUTATED      7    4
  ZNF711 WILD-TYPE  218  260
        clus
vv       ZNF711 MUTATED ZNF711 WILD-TYPE
  FEMALE              7              218
  MALE                4              260
[1] 2 2
[1] FALSE
D616V9, binary
                  cls
clus                 0   1
  ZNF711 MUTATED     7   0
  ZNF711 WILD-TYPE 343  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF711 MUTATED      7    0
  ZNF711 WILD-TYPE  343   22
     clus
vv    ZNF711 MUTATED ZNF711 WILD-TYPE
  NO               7              343
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ZNF711 MUTATED                      9                             1
  ZNF711 WILD-TYPE                  306                            46
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ZNF711 MUTATED                       1                              0
  ZNF711 WILD-TYPE                   105                             10
D616V10, multiclass
                                clus
vv                               ZNF711 MUTATED ZNF711 WILD-TYPE
  COLON ADENOCARCINOMA                        9              306
  COLON MUCINOUS ADENOCARCINOMA               1               46
  RECTAL ADENOCARCINOMA                       1              105
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ZNF711 MUTATED     8   0   1   0
  ZNF711 WILD-TYPE 337   4  30  25
D616V11, multiclass
    clus
vv   ZNF711 MUTATED ZNF711 WILD-TYPE
  R0              8              337
  R1              0                4
  R2              1               30
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D616V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF711 MUTATED                                  0     0
  ZNF711 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZNF711 MUTATED                           0     7
  ZNF711 WILD-TYPE                        22   219
D616V13, multiclass
                                  clus
vv                                 ZNF711 MUTATED ZNF711 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         7              219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(617) Variable = REXO4 MUTATION ANALYSIS
D617V1, survival
                 sevent
clus2               0   1
  REXO4 MUTATED     3   2
  REXO4 WILD-TYPE 375  91
  REXO4 MUTATED REXO4 WILD-TYPE 
              5             466 
  REXO4 MUTATED REXO4 WILD-TYPE 
              2              91 
$`REXO4 MUTATED`
TCGA-AA-3715 TCGA-AA-A00J TCGA-CK-6747 TCGA-CM-5861 TCGA-F4-6570 
       19.04        18.05        82.95        15.02         6.18 

$`REXO4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L 
       38.04        19.00        30.02        34.03        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 
       98.24         8.61        31.96        35.74        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  REXO4 MUTATED REXO4 WILD-TYPE 
           6.18            0.00 
  REXO4 MUTATED REXO4 WILD-TYPE 
          82.95          148.01 
  REXO4 MUTATED REXO4 WILD-TYPE 
         18.050          20.415 
[1] "6.2 - 83.0 (18.1)"  "0.0 - 148.0 (20.4)"
[1] "hr=" "1.8"
D617V2, continuous
D617V3, binary
                 cls
clus                0   1
  REXO4 MUTATED     5   0
  REXO4 WILD-TYPE 361 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  REXO4 MUTATED      5    0
  REXO4 WILD-TYPE  361  119
        clus
vv       REXO4 MUTATED REXO4 WILD-TYPE
  COLON              5             361
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  REXO4 MUTATED         0        0        1         3         0         0
  REXO4 WILD-TYPE      91        1       31       135        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  REXO4 MUTATED           0          0          1          0        0         0
  REXO4 WILD-TYPE        24         11         58         42       48        18
                 vv
clus              STAGE IVB
  REXO4 MUTATED           0
  REXO4 WILD-TYPE         1
D617V4, multiclass
            clus
vv           REXO4 MUTATED REXO4 WILD-TYPE
  STAGE I                0              91
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              3             135
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  REXO4 MUTATED     0   0   4   1
  REXO4 WILD-TYPE  17  92 325  49
D617V5, multiclass
    clus
vv   REXO4 MUTATED REXO4 WILD-TYPE
  T1             0              17
  T2             0              92
  T3             4             325
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  REXO4 MUTATED     4   1   0
  REXO4 WILD-TYPE 283 112  87
D617V6, multiclass
    clus
vv   REXO4 MUTATED REXO4 WILD-TYPE
  N0             4             283
  N1             1             112
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D617V7, binary
                 cls
clus                0   1
  REXO4 MUTATED     4   0
  REXO4 WILD-TYPE 371  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  REXO4 MUTATED      4    0
  REXO4 WILD-TYPE  371   65
   clus
vv  REXO4 MUTATED REXO4 WILD-TYPE
  0             4             371
  1             0              65
[1] 2 2
[1] FALSE
D617V8, binary
                 cls
clus                0   1
  REXO4 MUTATED     3   2
  REXO4 WILD-TYPE 222 262
[1] "tbl2"
                 cls
clus              [,1] [,2]
  REXO4 MUTATED      3    2
  REXO4 WILD-TYPE  222  262
        clus
vv       REXO4 MUTATED REXO4 WILD-TYPE
  FEMALE             3             222
  MALE               2             262
[1] 2 2
[1] FALSE
D617V9, binary
                 cls
clus                0   1
  REXO4 MUTATED     5   0
  REXO4 WILD-TYPE 345  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  REXO4 MUTATED      5    0
  REXO4 WILD-TYPE  345   22
     clus
vv    REXO4 MUTATED REXO4 WILD-TYPE
  NO              5             345
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  REXO4 MUTATED                      4                             1
  REXO4 WILD-TYPE                  311                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  REXO4 MUTATED                       0                              0
  REXO4 WILD-TYPE                   106                             10
D617V10, multiclass
                                clus
vv                               REXO4 MUTATED REXO4 WILD-TYPE
  COLON ADENOCARCINOMA                       4             311
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  REXO4 MUTATED     4   0   0   1
  REXO4 WILD-TYPE 341   4  31  24
D617V11, multiclass
    clus
vv   REXO4 MUTATED REXO4 WILD-TYPE
  R0             4             341
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D617V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  REXO4 MUTATED                                  0     0
  REXO4 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  REXO4 MUTATED                           0     3
  REXO4 WILD-TYPE                        22   223
D617V13, multiclass
                                  clus
vv                                 REXO4 MUTATED REXO4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        3             223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(618) Variable = ABCB4 MUTATION ANALYSIS
D618V1, survival
                 sevent
clus2               0   1
  ABCB4 MUTATED    21   5
  ABCB4 WILD-TYPE 357  88
  ABCB4 MUTATED ABCB4 WILD-TYPE 
             26             445 
  ABCB4 MUTATED ABCB4 WILD-TYPE 
              5              88 
$`ABCB4 MUTATED`
TCGA-A6-5666 TCGA-A6-6781 TCGA-AA-3510 TCGA-AA-3525 TCGA-AA-3680 TCGA-AA-3811 
       32.71        19.66        63.98         8.05        11.01        10.06 
TCGA-AA-A004 TCGA-AA-A00R TCGA-AA-A010 TCGA-AD-5900 TCGA-AD-6889 TCGA-AU-3779 
       13.94         0.99        34.98         0.07        56.55        14.50 
TCGA-AZ-4315 TCGA-AZ-6598 TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-4746 TCGA-D5-6540 
       58.39        49.41        12.76        10.06        37.02        16.14 
TCGA-D5-6541 TCGA-D5-6928 TCGA-D5-6930 TCGA-AG-3892 TCGA-AG-A002 TCGA-AG-A036 
       15.58        11.64         1.51        13.02        20.98       117.11 
TCGA-DY-A1DD TCGA-EI-6510 
       57.24        18.28 

$`ABCB4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        22.06        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       24.03        37.05        36.03        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3681 
       14.01         0.92        50.04        47.01        15.02         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        19.04        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W 
       38.04         4.01        27.02        42.02        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 
       18.05        40.96        21.37        15.52         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-6004 
        5.79        22.42        27.42        10.88         0.20        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
       16.31         0.95        33.01        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 
        5.13       106.75        22.36        62.79        88.21         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       12.20        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
      124.27        23.05        20.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        9.44         4.80        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 
       19.99         1.02        17.95        36.95        17.03        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 
       38.96        61.97        41.00        38.04        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
        5.29       126.44        41.36        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-F5-6464 TCGA-F5-6465 
        0.49        20.55        19.96        20.91         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  ABCB4 MUTATED ABCB4 WILD-TYPE 
           0.07            0.00 
  ABCB4 MUTATED ABCB4 WILD-TYPE 
         117.11          148.01 
  ABCB4 MUTATED ABCB4 WILD-TYPE 
          15.86           20.91 
[1] "0.1 - 117.1 (15.9)" "0.0 - 148.0 (20.9)"
[1] "hr=" "1.1"
D618V2, continuous
D618V3, binary
                 cls
clus                0   1
  ABCB4 MUTATED    22   5
  ABCB4 WILD-TYPE 344 114
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCB4 MUTATED     22    5
  ABCB4 WILD-TYPE  344  114
        clus
vv       ABCB4 MUTATED ABCB4 WILD-TYPE
  COLON             22             344
  RECTUM             5             114
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ABCB4 MUTATED         6        0        3         9         1         1
  ABCB4 WILD-TYPE      85        1       29       129         9         0
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ABCB4 MUTATED           2          0          2          1        1         1
  ABCB4 WILD-TYPE        22         11         57         41       47        17
                 vv
clus              STAGE IVB
  ABCB4 MUTATED           0
  ABCB4 WILD-TYPE         1
D618V4, multiclass
            clus
vv           ABCB4 MUTATED ABCB4 WILD-TYPE
  STAGE I                6              85
  STAGE IA               0               1
  STAGE II               3              29
  STAGE IIA              9             129
  STAGE IIB              1               9
  STAGE IIC              1               0
  STAGE III              2              22
  STAGE IIIA             0              11
  STAGE IIIB             2              57
  STAGE IIIC             1              41
  STAGE IV               1              47
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ABCB4 MUTATED     1   6  15   5
  ABCB4 WILD-TYPE  16  86 314  45
D618V5, multiclass
    clus
vv   ABCB4 MUTATED ABCB4 WILD-TYPE
  T1             1              16
  T2             6              86
  T3            15             314
  T4             5              45
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  ABCB4 MUTATED    21   3   3
  ABCB4 WILD-TYPE 266 110  84
D618V6, multiclass
    clus
vv   ABCB4 MUTATED ABCB4 WILD-TYPE
  N0            21             266
  N1             3             110
  N2             3              84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D618V7, binary
                 cls
clus                0   1
  ABCB4 MUTATED    22   1
  ABCB4 WILD-TYPE 353  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCB4 MUTATED     22    1
  ABCB4 WILD-TYPE  353   64
   clus
vv  ABCB4 MUTATED ABCB4 WILD-TYPE
  0            22             353
  1             1              64
[1] 2 2
[1] FALSE
D618V8, binary
                 cls
clus                0   1
  ABCB4 MUTATED    10  17
  ABCB4 WILD-TYPE 215 247
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCB4 MUTATED     10   17
  ABCB4 WILD-TYPE  215  247
        clus
vv       ABCB4 MUTATED ABCB4 WILD-TYPE
  FEMALE            10             215
  MALE              17             247
[1] 2 2
[1] FALSE
D618V9, binary
                 cls
clus                0   1
  ABCB4 MUTATED    20   1
  ABCB4 WILD-TYPE 330  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCB4 MUTATED     20    1
  ABCB4 WILD-TYPE  330   21
     clus
vv    ABCB4 MUTATED ABCB4 WILD-TYPE
  NO             20             330
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ABCB4 MUTATED                     16                             6
  ABCB4 WILD-TYPE                  299                            41
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ABCB4 MUTATED                       5                              0
  ABCB4 WILD-TYPE                   101                             10
D618V10, multiclass
                                clus
vv                               ABCB4 MUTATED ABCB4 WILD-TYPE
  COLON ADENOCARCINOMA                      16             299
  COLON MUCINOUS ADENOCARCINOMA              6              41
  RECTAL ADENOCARCINOMA                      5             101
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  ABCB4 MUTATED    20   0   1   2
  ABCB4 WILD-TYPE 325   4  30  23
D618V11, multiclass
    clus
vv   ABCB4 MUTATED ABCB4 WILD-TYPE
  R0            20             325
  R1             0               4
  R2             1              30
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D618V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ABCB4 MUTATED                                  0     3
  ABCB4 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ABCB4 MUTATED                           1    12
  ABCB4 WILD-TYPE                        21   214
D618V13, multiclass
                                  clus
vv                                 ABCB4 MUTATED ABCB4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        3               8
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                       12             214
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(619) Variable = FAAH2 MUTATION ANALYSIS
D619V1, survival
                 sevent
clus2               0   1
  FAAH2 MUTATED    11   3
  FAAH2 WILD-TYPE 367  90
  FAAH2 MUTATED FAAH2 WILD-TYPE 
             14             457 
  FAAH2 MUTATED FAAH2 WILD-TYPE 
              3              90 
$`FAAH2 MUTATED`
TCGA-AA-3516 TCGA-AA-3525 TCGA-AA-3815 TCGA-AA-A00F TCGA-AA-A017 TCGA-AY-5543 
       13.02         8.05        33.04        34.03         1.02        33.01 
TCGA-AZ-6599 TCGA-CK-4947 TCGA-CM-6676 TCGA-D5-6535 TCGA-G4-6315 TCGA-DY-A0XA 
        6.77        17.56        11.08        15.12        61.91       126.44 
TCGA-DY-A1DG TCGA-F5-6465 
       51.48        49.51 

$`FAAH2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        1.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3526 
        1.02         9.07        24.03        37.05        36.03        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       35.05         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       30.02        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       27.09        16.31         0.95        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       49.41        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4948 
        0.07        12.20        12.76        10.06        14.30       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       12.95        13.05        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       18.25         1.32        43.27        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6317 
       53.62        44.68        55.04        85.48        63.62        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1H8 
        5.03         5.29        41.36        57.24        24.13        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  FAAH2 MUTATED FAAH2 WILD-TYPE 
           1.02            0.00 
  FAAH2 MUTATED FAAH2 WILD-TYPE 
         126.44          148.01 
  FAAH2 MUTATED FAAH2 WILD-TYPE 
         25.285          20.190 
[1] "1.0 - 126.4 (25.3)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.1"
D619V2, continuous
D619V3, binary
                 cls
clus                0   1
  FAAH2 MUTATED    11   3
  FAAH2 WILD-TYPE 355 116
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FAAH2 MUTATED     11    3
  FAAH2 WILD-TYPE  355  116
        clus
vv       FAAH2 MUTATED FAAH2 WILD-TYPE
  COLON             11             355
  RECTUM             3             116
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FAAH2 MUTATED         2        0        0         4         0         0
  FAAH2 WILD-TYPE      89        1       32       134        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  FAAH2 MUTATED           1          0          3          1        1         2
  FAAH2 WILD-TYPE        23         11         56         41       47        16
                 vv
clus              STAGE IVB
  FAAH2 MUTATED           0
  FAAH2 WILD-TYPE         1
D619V4, multiclass
            clus
vv           FAAH2 MUTATED FAAH2 WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              4             134
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             3              56
  STAGE IIIC             1              41
  STAGE IV               1              47
  STAGE IVA              2              16
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  FAAH2 MUTATED     0   2  11   1
  FAAH2 WILD-TYPE  17  90 318  49
D619V5, multiclass
    clus
vv   FAAH2 MUTATED FAAH2 WILD-TYPE
  T1             0              17
  T2             2              90
  T3            11             318
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  FAAH2 MUTATED     6   6   2
  FAAH2 WILD-TYPE 281 107  85
D619V6, multiclass
    clus
vv   FAAH2 MUTATED FAAH2 WILD-TYPE
  N0             6             281
  N1             6             107
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D619V7, binary
                 cls
clus                0   1
  FAAH2 MUTATED     9   3
  FAAH2 WILD-TYPE 366  62
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FAAH2 MUTATED      9    3
  FAAH2 WILD-TYPE  366   62
   clus
vv  FAAH2 MUTATED FAAH2 WILD-TYPE
  0             9             366
  1             3              62
[1] 2 2
[1] FALSE
D619V8, binary
                 cls
clus                0   1
  FAAH2 MUTATED     8   6
  FAAH2 WILD-TYPE 217 258
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FAAH2 MUTATED      8    6
  FAAH2 WILD-TYPE  217  258
        clus
vv       FAAH2 MUTATED FAAH2 WILD-TYPE
  FEMALE             8             217
  MALE               6             258
[1] 2 2
[1] FALSE
D619V9, binary
                 cls
clus                0   1
  FAAH2 MUTATED    11   0
  FAAH2 WILD-TYPE 339  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FAAH2 MUTATED     11    0
  FAAH2 WILD-TYPE  339   22
     clus
vv    FAAH2 MUTATED FAAH2 WILD-TYPE
  NO             11             339
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  FAAH2 MUTATED                     10                             1
  FAAH2 WILD-TYPE                  305                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  FAAH2 MUTATED                       3                              0
  FAAH2 WILD-TYPE                   103                             10
D619V10, multiclass
                                clus
vv                               FAAH2 MUTATED FAAH2 WILD-TYPE
  COLON ADENOCARCINOMA                      10             305
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      3             103
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  FAAH2 MUTATED     8   0   0   2
  FAAH2 WILD-TYPE 337   4  31  23
D619V11, multiclass
    clus
vv   FAAH2 MUTATED FAAH2 WILD-TYPE
  R0             8             337
  R1             0               4
  R2             0              31
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D619V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FAAH2 MUTATED                                  0     0
  FAAH2 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  FAAH2 MUTATED                           1     8
  FAAH2 WILD-TYPE                        21   218
D619V13, multiclass
                                  clus
vv                                 FAAH2 MUTATED FAAH2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        8             218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(620) Variable = RASAL2 MUTATION ANALYSIS
D620V1, survival
                  sevent
clus2                0   1
  RASAL2 MUTATED    10   5
  RASAL2 WILD-TYPE 368  88
  RASAL2 MUTATED RASAL2 WILD-TYPE 
              15              456 
  RASAL2 MUTATED RASAL2 WILD-TYPE 
               5               88 
$`RASAL2 MUTATED`
TCGA-AA-3655 TCGA-AA-3815 TCGA-AA-3947 TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01Q 
       61.02        33.04        33.01         4.01        34.98         1.02 
TCGA-AY-4071 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-5916 TCGA-CM-5862 TCGA-CM-6161 
        0.95        12.76        10.06        21.14         5.03        15.02 
TCGA-CM-6162 TCGA-DM-A28K TCGA-AG-3593 
       12.00        98.24        34.03 

$`RASAL2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 
       20.98        19.99        13.94        19.99        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       10.06        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       12.99        24.00        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       16.31        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.07        12.20        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 
       15.62        49.08        51.32         9.99        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       15.02        15.02        17.03         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       35.97        60.79       117.07         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
        1.02        46.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  RASAL2 MUTATED RASAL2 WILD-TYPE 
            0.95             0.00 
  RASAL2 MUTATED RASAL2 WILD-TYPE 
           98.24           148.01 
  RASAL2 MUTATED RASAL2 WILD-TYPE 
          15.020           20.235 
[1] "0.9 - 98.2 (15.0)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.9"
D620V2, continuous
D620V3, binary
                  cls
clus                 0   1
  RASAL2 MUTATED    14   1
  RASAL2 WILD-TYPE 352 118
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RASAL2 MUTATED     14    1
  RASAL2 WILD-TYPE  352  118
        clus
vv       RASAL2 MUTATED RASAL2 WILD-TYPE
  COLON              14              352
  RECTUM              1              118
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RASAL2 MUTATED         3        0        2         5         3         0
  RASAL2 WILD-TYPE      88        1       30       133         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RASAL2 MUTATED           0          0          1          0        1
  RASAL2 WILD-TYPE        24         11         58         42       47
                  vv
clus               STAGE IVA STAGE IVB
  RASAL2 MUTATED           1         0
  RASAL2 WILD-TYPE        17         1
D620V4, multiclass
            clus
vv           RASAL2 MUTATED RASAL2 WILD-TYPE
  STAGE I                 3               88
  STAGE IA                0                1
  STAGE II                2               30
  STAGE IIA               5              133
  STAGE IIB               3                7
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              1               58
  STAGE IIIC              0               42
  STAGE IV                1               47
  STAGE IVA               1               17
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  RASAL2 MUTATED     2   1   9   4
  RASAL2 WILD-TYPE  15  91 320  46
D620V5, multiclass
    clus
vv   RASAL2 MUTATED RASAL2 WILD-TYPE
  T1              2               15
  T2              1               91
  T3              9              320
  T4              4               46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  RASAL2 MUTATED    13   2   1
  RASAL2 WILD-TYPE 274 111  86
D620V6, multiclass
    clus
vv   RASAL2 MUTATED RASAL2 WILD-TYPE
  N0             13              274
  N1              2              111
  N2              1               86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D620V7, binary
                  cls
clus                 0   1
  RASAL2 MUTATED    13   2
  RASAL2 WILD-TYPE 362  63
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RASAL2 MUTATED     13    2
  RASAL2 WILD-TYPE  362   63
   clus
vv  RASAL2 MUTATED RASAL2 WILD-TYPE
  0             13              362
  1              2               63
[1] 2 2
[1] FALSE
D620V8, binary
                  cls
clus                 0   1
  RASAL2 MUTATED     9   7
  RASAL2 WILD-TYPE 216 257
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RASAL2 MUTATED      9    7
  RASAL2 WILD-TYPE  216  257
        clus
vv       RASAL2 MUTATED RASAL2 WILD-TYPE
  FEMALE              9              216
  MALE                7              257
[1] 2 2
[1] FALSE
D620V9, binary
                  cls
clus                 0   1
  RASAL2 MUTATED    11   1
  RASAL2 WILD-TYPE 339  21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RASAL2 MUTATED     11    1
  RASAL2 WILD-TYPE  339   21
     clus
vv    RASAL2 MUTATED RASAL2 WILD-TYPE
  NO              11              339
  YES              1               21
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  RASAL2 MUTATED                      9                             5
  RASAL2 WILD-TYPE                  306                            42
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  RASAL2 MUTATED                       1                              0
  RASAL2 WILD-TYPE                   105                             10
D620V10, multiclass
                                clus
vv                               RASAL2 MUTATED RASAL2 WILD-TYPE
  COLON ADENOCARCINOMA                        9              306
  COLON MUCINOUS ADENOCARCINOMA               5               42
  RECTAL ADENOCARCINOMA                       1              105
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  RASAL2 MUTATED    11   0   1   3
  RASAL2 WILD-TYPE 334   4  30  22
D620V11, multiclass
    clus
vv   RASAL2 MUTATED RASAL2 WILD-TYPE
  R0             11              334
  R1              0                4
  R2              1               30
  RX              3               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D620V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RASAL2 MUTATED                                  0     2
  RASAL2 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  RASAL2 MUTATED                           0     6
  RASAL2 WILD-TYPE                        22   220
D620V13, multiclass
                                  clus
vv                                 RASAL2 MUTATED RASAL2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                9
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         6              220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(621) Variable = ATAD5 MUTATION ANALYSIS
D621V1, survival
                 sevent
clus2               0   1
  ATAD5 MUTATED    19   5
  ATAD5 WILD-TYPE 359  88
  ATAD5 MUTATED ATAD5 WILD-TYPE 
             24             447 
  ATAD5 MUTATED ATAD5 WILD-TYPE 
              5              88 
$`ATAD5 MUTATED`
TCGA-A6-5661 TCGA-AA-3555 TCGA-AA-3663 TCGA-AA-3864 TCGA-AA-3947 TCGA-AA-3966 
       33.53        29.95         6.97        53.00        33.01         2.01 
TCGA-AA-A010 TCGA-AA-A01P TCGA-AD-6889 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-CA-6717 
       34.98        38.07        56.55        88.21        49.41        12.76 
TCGA-CA-6718 TCGA-F4-6570 TCGA-F4-6854 TCGA-F4-6856 TCGA-G4-6309 TCGA-G4-6588 
       10.06         6.18         0.53        35.31        85.48        26.17 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AG-3732 TCGA-AG-3892 TCGA-AG-A002 TCGA-CI-6624 
       46.75        79.69        32.98        13.02        20.98         4.73 

$`ATAD5 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       13.02        24.00        17.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        31.07        30.05        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 
       26.01        24.00         2.01        20.98        34.03        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       12.00        31.00        31.00         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       22.36        62.79         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 
        3.25         3.29         0.07        12.20        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       35.74        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
       33.67        13.25        47.41       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       53.62        44.68        55.04        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-AF-2687 TCGA-AF-2689 
       22.09        13.78        35.80        91.79        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        7.99         0.99        37.02         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 
       19.99         1.02        17.95        36.95        17.03        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        6.97        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  ATAD5 MUTATED ATAD5 WILD-TYPE 
           0.53            0.00 
  ATAD5 MUTATED ATAD5 WILD-TYPE 
          88.21          148.01 
  ATAD5 MUTATED ATAD5 WILD-TYPE 
         32.995          20.020 
[1] "0.5 - 88.2 (33.0)"  "0.0 - 148.0 (20.0)"
[1] "hr=" "1.2"
D621V2, continuous
D621V3, binary
                 cls
clus                0   1
  ATAD5 MUTATED    21   4
  ATAD5 WILD-TYPE 345 115
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ATAD5 MUTATED     21    4
  ATAD5 WILD-TYPE  345  115
        clus
vv       ATAD5 MUTATED ATAD5 WILD-TYPE
  COLON             21             345
  RECTUM             4             115
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ATAD5 MUTATED         7        0        3        11         2         0
  ATAD5 WILD-TYPE      84        1       29       127         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ATAD5 MUTATED           1          0          1          0        0         0
  ATAD5 WILD-TYPE        23         11         58         42       48        18
                 vv
clus              STAGE IVB
  ATAD5 MUTATED           0
  ATAD5 WILD-TYPE         1
D621V4, multiclass
            clus
vv           ATAD5 MUTATED ATAD5 WILD-TYPE
  STAGE I                7              84
  STAGE IA               0               1
  STAGE II               3              29
  STAGE IIA             11             127
  STAGE IIB              2               8
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ATAD5 MUTATED     2   5  16   2
  ATAD5 WILD-TYPE  15  87 313  48
D621V5, multiclass
    clus
vv   ATAD5 MUTATED ATAD5 WILD-TYPE
  T1             2              15
  T2             5              87
  T3            16             313
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  ATAD5 MUTATED    23   2   0
  ATAD5 WILD-TYPE 264 111  87
D621V6, multiclass
    clus
vv   ATAD5 MUTATED ATAD5 WILD-TYPE
  N0            23             264
  N1             2             111
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D621V7, binary
                 cls
clus                0   1
  ATAD5 MUTATED    24   0
  ATAD5 WILD-TYPE 351  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ATAD5 MUTATED     24    0
  ATAD5 WILD-TYPE  351   65
   clus
vv  ATAD5 MUTATED ATAD5 WILD-TYPE
  0            24             351
  1             0              65
[1] 2 2
[1] FALSE
D621V8, binary
                 cls
clus                0   1
  ATAD5 MUTATED    16   9
  ATAD5 WILD-TYPE 209 255
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ATAD5 MUTATED     16    9
  ATAD5 WILD-TYPE  209  255
        clus
vv       ATAD5 MUTATED ATAD5 WILD-TYPE
  FEMALE            16             209
  MALE               9             255
[1] 2 2
[1] FALSE
D621V9, binary
                 cls
clus                0   1
  ATAD5 MUTATED    21   0
  ATAD5 WILD-TYPE 329  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ATAD5 MUTATED     21    0
  ATAD5 WILD-TYPE  329   22
     clus
vv    ATAD5 MUTATED ATAD5 WILD-TYPE
  NO             21             329
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ATAD5 MUTATED                     16                             5
  ATAD5 WILD-TYPE                  299                            42
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ATAD5 MUTATED                       4                              0
  ATAD5 WILD-TYPE                   102                             10
D621V10, multiclass
                                clus
vv                               ATAD5 MUTATED ATAD5 WILD-TYPE
  COLON ADENOCARCINOMA                      16             299
  COLON MUCINOUS ADENOCARCINOMA              5              42
  RECTAL ADENOCARCINOMA                      4             102
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  ATAD5 MUTATED    18   0   0   2
  ATAD5 WILD-TYPE 327   4  31  23
D621V11, multiclass
    clus
vv   ATAD5 MUTATED ATAD5 WILD-TYPE
  R0            18             327
  R1             0               4
  R2             0              31
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D621V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ATAD5 MUTATED                                  0     3
  ATAD5 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ATAD5 MUTATED                           2     9
  ATAD5 WILD-TYPE                        20   217
D621V13, multiclass
                                  clus
vv                                 ATAD5 MUTATED ATAD5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        3               8
  BLACK OR AFRICAN AMERICAN                    2              20
  WHITE                                        9             217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(622) Variable = ZNF14 MUTATION ANALYSIS
D622V1, survival
                 sevent
clus2               0   1
  ZNF14 MUTATED    10   3
  ZNF14 WILD-TYPE 368  90
  ZNF14 MUTATED ZNF14 WILD-TYPE 
             13             458 
  ZNF14 MUTATED ZNF14 WILD-TYPE 
              3              90 
$`ZNF14 MUTATED`
TCGA-A6-5665 TCGA-A6-6141 TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01X TCGA-AD-6901 
       22.06         8.38         4.01        34.98        26.01        22.42 
TCGA-AZ-5407 TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-5860 TCGA-D5-6539 TCGA-D5-6924 
       88.21        12.76        10.06        32.02        12.49        14.30 
TCGA-AG-A002 
       20.98 

$`ZNF14 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 
       22.09        32.71        27.09        22.52        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6598 
        1.41         5.13       106.75        22.36        62.79        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.07        12.20        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5861 
       13.02        29.06        22.03        22.98        30.08        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  ZNF14 MUTATED ZNF14 WILD-TYPE 
           4.01            0.00 
  ZNF14 MUTATED ZNF14 WILD-TYPE 
          88.21          148.01 
  ZNF14 MUTATED ZNF14 WILD-TYPE 
         20.980          20.155 
[1] "4.0 - 88.2 (21.0)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.4"
D622V2, continuous
D622V3, binary
                 cls
clus                0   1
  ZNF14 MUTATED    13   1
  ZNF14 WILD-TYPE 353 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZNF14 MUTATED     13    1
  ZNF14 WILD-TYPE  353  118
        clus
vv       ZNF14 MUTATED ZNF14 WILD-TYPE
  COLON             13             353
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZNF14 MUTATED         2        0        0         7         2         0
  ZNF14 WILD-TYPE      89        1       32       131         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ZNF14 MUTATED           1          1          0          0        0         0
  ZNF14 WILD-TYPE        23         10         59         42       48        18
                 vv
clus              STAGE IVB
  ZNF14 MUTATED           0
  ZNF14 WILD-TYPE         1
D622V4, multiclass
            clus
vv           ZNF14 MUTATED ZNF14 WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              7             131
  STAGE IIB              2               8
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             1              10
  STAGE IIIB             0              59
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ZNF14 MUTATED     1   2   9   2
  ZNF14 WILD-TYPE  16  90 320  48
D622V5, multiclass
    clus
vv   ZNF14 MUTATED ZNF14 WILD-TYPE
  T1             1              16
  T2             2              90
  T3             9             320
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  ZNF14 MUTATED    13   1   0
  ZNF14 WILD-TYPE 274 112  87
D622V6, multiclass
    clus
vv   ZNF14 MUTATED ZNF14 WILD-TYPE
  N0            13             274
  N1             1             112
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D622V7, binary
                 cls
clus                0   1
  ZNF14 MUTATED    13   0
  ZNF14 WILD-TYPE 362  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZNF14 MUTATED     13    0
  ZNF14 WILD-TYPE  362   65
   clus
vv  ZNF14 MUTATED ZNF14 WILD-TYPE
  0            13             362
  1             0              65
[1] 2 2
[1] FALSE
D622V8, binary
                 cls
clus                0   1
  ZNF14 MUTATED     6   8
  ZNF14 WILD-TYPE 219 256
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZNF14 MUTATED      6    8
  ZNF14 WILD-TYPE  219  256
        clus
vv       ZNF14 MUTATED ZNF14 WILD-TYPE
  FEMALE             6             219
  MALE               8             256
[1] 2 2
[1] FALSE
D622V9, binary
                 cls
clus                0   1
  ZNF14 MUTATED    12   0
  ZNF14 WILD-TYPE 338  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZNF14 MUTATED     12    0
  ZNF14 WILD-TYPE  338   22
     clus
vv    ZNF14 MUTATED ZNF14 WILD-TYPE
  NO             12             338
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ZNF14 MUTATED                     11                             2
  ZNF14 WILD-TYPE                  304                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ZNF14 MUTATED                       1                              0
  ZNF14 WILD-TYPE                   105                             10
D622V10, multiclass
                                clus
vv                               ZNF14 MUTATED ZNF14 WILD-TYPE
  COLON ADENOCARCINOMA                      11             304
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  ZNF14 MUTATED     8   0   0   3
  ZNF14 WILD-TYPE 337   4  31  22
D622V11, multiclass
    clus
vv   ZNF14 MUTATED ZNF14 WILD-TYPE
  R0             8             337
  R1             0               4
  R2             0              31
  RX             3              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D622V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF14 MUTATED                                  0     2
  ZNF14 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ZNF14 MUTATED                           1     6
  ZNF14 WILD-TYPE                        21   220
D622V13, multiclass
                                  clus
vv                                 ZNF14 MUTATED ZNF14 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               9
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        6             220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(623) Variable = NAP1L1 MUTATION ANALYSIS
D623V1, survival
                  sevent
clus2                0   1
  NAP1L1 MUTATED     8   1
  NAP1L1 WILD-TYPE 370  92
  NAP1L1 MUTATED NAP1L1 WILD-TYPE 
               9              462 
  NAP1L1 MUTATED NAP1L1 WILD-TYPE 
               1               92 
$`NAP1L1 MUTATED`
TCGA-A6-4105 TCGA-A6-5666 TCGA-AA-3977 TCGA-AD-6890 TCGA-AZ-4315 TCGA-CA-6717 
       14.53        32.71        25.02         0.79        58.39        12.76 
TCGA-DM-A1HB TCGA-AH-6643 TCGA-CI-6622 
      135.65         0.69         6.97 

$`NAP1L1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 
       16.57        34.65        33.34        32.75        36.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       22.06        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07        12.20        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
       44.32       131.51       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        0.72         6.05        33.17         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  NAP1L1 MUTATED NAP1L1 WILD-TYPE 
            0.69             0.00 
  NAP1L1 MUTATED NAP1L1 WILD-TYPE 
          135.65           148.01 
  NAP1L1 MUTATED NAP1L1 WILD-TYPE 
          14.530           20.235 
[1] "0.7 - 135.7 (14.5)" "0.0 - 148.0 (20.2)"
[1] "hr=" "2"  
D623V2, continuous
D623V3, binary
                  cls
clus                 0   1
  NAP1L1 MUTATED     7   2
  NAP1L1 WILD-TYPE 359 117
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NAP1L1 MUTATED      7    2
  NAP1L1 WILD-TYPE  359  117
        clus
vv       NAP1L1 MUTATED NAP1L1 WILD-TYPE
  COLON               7              359
  RECTUM              2              117
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NAP1L1 MUTATED         0        0        0         3         1         1
  NAP1L1 WILD-TYPE      91        1       32       135         9         0
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NAP1L1 MUTATED           0          0          1          1        0
  NAP1L1 WILD-TYPE        24         11         58         41       48
                  vv
clus               STAGE IVA STAGE IVB
  NAP1L1 MUTATED           0         0
  NAP1L1 WILD-TYPE        18         1
D623V4, multiclass
            clus
vv           NAP1L1 MUTATED NAP1L1 WILD-TYPE
  STAGE I                 0               91
  STAGE IA                0                1
  STAGE II                0               32
  STAGE IIA               3              135
  STAGE IIB               1                9
  STAGE IIC               1                0
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              1               58
  STAGE IIIC              1               41
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  NAP1L1 MUTATED     1   1   5   2
  NAP1L1 WILD-TYPE  16  91 324  48
D623V5, multiclass
    clus
vv   NAP1L1 MUTATED NAP1L1 WILD-TYPE
  T1              1               16
  T2              1               91
  T3              5              324
  T4              2               48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  NAP1L1 MUTATED     7   1   1
  NAP1L1 WILD-TYPE 280 112  86
D623V6, multiclass
    clus
vv   NAP1L1 MUTATED NAP1L1 WILD-TYPE
  N0              7              280
  N1              1              112
  N2              1               86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D623V7, binary
                  cls
clus                 0   1
  NAP1L1 MUTATED     7   0
  NAP1L1 WILD-TYPE 368  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NAP1L1 MUTATED      7    0
  NAP1L1 WILD-TYPE  368   65
   clus
vv  NAP1L1 MUTATED NAP1L1 WILD-TYPE
  0              7              368
  1              0               65
[1] 2 2
[1] FALSE
D623V8, binary
                  cls
clus                 0   1
  NAP1L1 MUTATED     0   9
  NAP1L1 WILD-TYPE 225 255
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NAP1L1 MUTATED      0    9
  NAP1L1 WILD-TYPE  225  255
        clus
vv       NAP1L1 MUTATED NAP1L1 WILD-TYPE
  FEMALE              0              225
  MALE                9              255
[1] 2 2
[1] FALSE
D623V9, binary
                  cls
clus                 0   1
  NAP1L1 MUTATED     5   0
  NAP1L1 WILD-TYPE 345  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NAP1L1 MUTATED      5    0
  NAP1L1 WILD-TYPE  345   22
     clus
vv    NAP1L1 MUTATED NAP1L1 WILD-TYPE
  NO               5              345
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  NAP1L1 MUTATED                      5                             1
  NAP1L1 WILD-TYPE                  310                            46
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  NAP1L1 MUTATED                       2                              0
  NAP1L1 WILD-TYPE                   104                             10
D623V10, multiclass
                                clus
vv                               NAP1L1 MUTATED NAP1L1 WILD-TYPE
  COLON ADENOCARCINOMA                        5              310
  COLON MUCINOUS ADENOCARCINOMA               1               46
  RECTAL ADENOCARCINOMA                       2              104
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  NAP1L1 MUTATED     2   0   0   1
  NAP1L1 WILD-TYPE 343   4  31  24
D623V11, multiclass
    clus
vv   NAP1L1 MUTATED NAP1L1 WILD-TYPE
  R0              2              343
  R1              0                4
  R2              0               31
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D623V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NAP1L1 MUTATED                                  0     1
  NAP1L1 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  NAP1L1 MUTATED                           0     7
  NAP1L1 WILD-TYPE                        22   219
D623V13, multiclass
                                  clus
vv                                 NAP1L1 MUTATED NAP1L1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         7              219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(624) Variable = CHRM3 MUTATION ANALYSIS
D624V1, survival
                 sevent
clus2               0   1
  CHRM3 MUTATED     9   6
  CHRM3 WILD-TYPE 369  87
  CHRM3 MUTATED CHRM3 WILD-TYPE 
             15             456 
  CHRM3 MUTATED CHRM3 WILD-TYPE 
              6              87 
$`CHRM3 MUTATED`
TCGA-AA-3864 TCGA-AA-A00N TCGA-AA-A01R TCGA-AD-6901 TCGA-AZ-5407 TCGA-CA-6717 
       53.00         4.01        35.01        22.42        88.21        12.76 
TCGA-CA-6718 TCGA-CM-5349 TCGA-CM-6166 TCGA-D5-6931 TCGA-DM-A1D6 TCGA-F4-6570 
       10.06        30.08        21.99        12.00        49.91         6.18 
TCGA-G4-6303 TCGA-AG-3731 TCGA-DC-6682 
       65.85        37.02         4.01 

$`CHRM3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T 
       31.00        31.00        38.07         1.02         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.79         0.72         5.79        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 
        3.25         3.29         0.07        12.20        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6167 
       15.02        12.00         2.96        29.03        16.04        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        4.80         1.51        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
       38.20       130.65        92.75        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
        8.61        31.96        35.74        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
       35.31       133.18        74.56        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
       19.99         7.99         0.99        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
       19.99         5.95         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  CHRM3 MUTATED CHRM3 WILD-TYPE 
           4.01            0.00 
  CHRM3 MUTATED CHRM3 WILD-TYPE 
          88.21          148.01 
  CHRM3 MUTATED CHRM3 WILD-TYPE 
         22.420          20.085 
[1] "4.0 - 88.2 (22.4)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.8"
D624V2, continuous
D624V3, binary
                 cls
clus                0   1
  CHRM3 MUTATED    13   2
  CHRM3 WILD-TYPE 353 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CHRM3 MUTATED     13    2
  CHRM3 WILD-TYPE  353  117
        clus
vv       CHRM3 MUTATED CHRM3 WILD-TYPE
  COLON             13             353
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CHRM3 MUTATED         2        0        1         6         1         0
  CHRM3 WILD-TYPE      89        1       31       132         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CHRM3 MUTATED           1          0          0          1        2         0
  CHRM3 WILD-TYPE        23         11         59         41       46        18
                 vv
clus              STAGE IVB
  CHRM3 MUTATED           0
  CHRM3 WILD-TYPE         1
D624V4, multiclass
            clus
vv           CHRM3 MUTATED CHRM3 WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              6             132
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             1              41
  STAGE IV               2              46
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CHRM3 MUTATED     1   1  11   2
  CHRM3 WILD-TYPE  16  91 318  48
D624V5, multiclass
    clus
vv   CHRM3 MUTATED CHRM3 WILD-TYPE
  T1             1              16
  T2             1              91
  T3            11             318
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  CHRM3 MUTATED    11   2   2
  CHRM3 WILD-TYPE 276 111  85
D624V6, multiclass
    clus
vv   CHRM3 MUTATED CHRM3 WILD-TYPE
  N0            11             276
  N1             2             111
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D624V7, binary
                 cls
clus                0   1
  CHRM3 MUTATED    12   2
  CHRM3 WILD-TYPE 363  63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CHRM3 MUTATED     12    2
  CHRM3 WILD-TYPE  363   63
   clus
vv  CHRM3 MUTATED CHRM3 WILD-TYPE
  0            12             363
  1             2              63
[1] 2 2
[1] FALSE
D624V8, binary
                 cls
clus                0   1
  CHRM3 MUTATED     5  10
  CHRM3 WILD-TYPE 220 254
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CHRM3 MUTATED      5   10
  CHRM3 WILD-TYPE  220  254
        clus
vv       CHRM3 MUTATED CHRM3 WILD-TYPE
  FEMALE             5             220
  MALE              10             254
[1] 2 2
[1] FALSE
D624V9, binary
                 cls
clus                0   1
  CHRM3 MUTATED    11   1
  CHRM3 WILD-TYPE 339  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CHRM3 MUTATED     11    1
  CHRM3 WILD-TYPE  339   21
     clus
vv    CHRM3 MUTATED CHRM3 WILD-TYPE
  NO             11             339
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CHRM3 MUTATED                      9                             4
  CHRM3 WILD-TYPE                  306                            43
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CHRM3 MUTATED                       2                              0
  CHRM3 WILD-TYPE                   104                             10
D624V10, multiclass
                                clus
vv                               CHRM3 MUTATED CHRM3 WILD-TYPE
  COLON ADENOCARCINOMA                       9             306
  COLON MUCINOUS ADENOCARCINOMA              4              43
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  CHRM3 MUTATED     9   0   1   2
  CHRM3 WILD-TYPE 336   4  30  23
D624V11, multiclass
    clus
vv   CHRM3 MUTATED CHRM3 WILD-TYPE
  R0             9             336
  R1             0               4
  R2             1              30
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D624V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CHRM3 MUTATED                                  0     2
  CHRM3 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CHRM3 MUTATED                           0     9
  CHRM3 WILD-TYPE                        22   217
D624V13, multiclass
                                  clus
vv                                 CHRM3 MUTATED CHRM3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               9
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        9             217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(625) Variable = GPR87 MUTATION ANALYSIS
D625V1, survival
                 sevent
clus2               0   1
  GPR87 MUTATED     9   1
  GPR87 WILD-TYPE 369  92
  GPR87 MUTATED GPR87 WILD-TYPE 
             10             461 
  GPR87 MUTATED GPR87 WILD-TYPE 
              1              92 
$`GPR87 MUTATED`
TCGA-AA-3555 TCGA-AA-3977 TCGA-AA-A01Z TCGA-AU-6004 TCGA-CA-6717 TCGA-CM-5862 
       29.95        25.02        37.02        27.09        12.76         5.03 
TCGA-CM-6674 TCGA-D5-6540 TCGA-F4-6806 TCGA-AG-3892 
       12.95        16.14        41.42        13.02 

$`GPR87 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 
       21.01        13.02        24.00        17.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       33.04        35.01        26.01        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
        0.20        14.50        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07        12.20        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 
       22.03        22.98        30.08        32.02        15.02        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       14.04        11.01        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 
       17.85         4.80        17.13        12.49        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6807 TCGA-F4-6808 
        6.18        47.87         1.55        34.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 
       19.99         1.02        17.95        36.95        17.03        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  GPR87 MUTATED GPR87 WILD-TYPE 
           5.03            0.00 
  GPR87 MUTATED GPR87 WILD-TYPE 
          41.42          148.01 
  GPR87 MUTATED GPR87 WILD-TYPE 
          20.58           20.19 
[1] "5.0 - 41.4 (20.6)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.7"
D625V2, continuous
D625V3, binary
                 cls
clus                0   1
  GPR87 MUTATED    10   1
  GPR87 WILD-TYPE 356 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPR87 MUTATED     10    1
  GPR87 WILD-TYPE  356  118
        clus
vv       GPR87 MUTATED GPR87 WILD-TYPE
  COLON             10             356
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GPR87 MUTATED         4        0        1         3         0         0
  GPR87 WILD-TYPE      87        1       31       135        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  GPR87 MUTATED           0          0          0          0        1         1
  GPR87 WILD-TYPE        24         11         59         42       47        17
                 vv
clus              STAGE IVB
  GPR87 MUTATED           0
  GPR87 WILD-TYPE         1
D625V4, multiclass
            clus
vv           GPR87 MUTATED GPR87 WILD-TYPE
  STAGE I                4              87
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              3             135
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             0              42
  STAGE IV               1              47
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  GPR87 MUTATED     1   4   5   1
  GPR87 WILD-TYPE  16  88 324  49
D625V5, multiclass
    clus
vv   GPR87 MUTATED GPR87 WILD-TYPE
  T1             1              16
  T2             4              88
  T3             5             324
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  GPR87 MUTATED     9   1   1
  GPR87 WILD-TYPE 278 112  86
D625V6, multiclass
    clus
vv   GPR87 MUTATED GPR87 WILD-TYPE
  N0             9             278
  N1             1             112
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D625V7, binary
                 cls
clus                0   1
  GPR87 MUTATED     8   2
  GPR87 WILD-TYPE 367  63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPR87 MUTATED      8    2
  GPR87 WILD-TYPE  367   63
   clus
vv  GPR87 MUTATED GPR87 WILD-TYPE
  0             8             367
  1             2              63
[1] 2 2
[1] FALSE
D625V8, binary
                 cls
clus                0   1
  GPR87 MUTATED     5   6
  GPR87 WILD-TYPE 220 258
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPR87 MUTATED      5    6
  GPR87 WILD-TYPE  220  258
        clus
vv       GPR87 MUTATED GPR87 WILD-TYPE
  FEMALE             5             220
  MALE               6             258
[1] 2 2
[1] FALSE
D625V9, binary
                 cls
clus                0   1
  GPR87 MUTATED     9   0
  GPR87 WILD-TYPE 341  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPR87 MUTATED      9    0
  GPR87 WILD-TYPE  341   22
     clus
vv    GPR87 MUTATED GPR87 WILD-TYPE
  NO              9             341
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  GPR87 MUTATED                      6                             4
  GPR87 WILD-TYPE                  309                            43
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  GPR87 MUTATED                       1                              0
  GPR87 WILD-TYPE                   105                             10
D625V10, multiclass
                                clus
vv                               GPR87 MUTATED GPR87 WILD-TYPE
  COLON ADENOCARCINOMA                       6             309
  COLON MUCINOUS ADENOCARCINOMA              4              43
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  GPR87 MUTATED     8   0   1   1
  GPR87 WILD-TYPE 337   4  30  24
D625V11, multiclass
    clus
vv   GPR87 MUTATED GPR87 WILD-TYPE
  R0             8             337
  R1             0               4
  R2             1              30
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D625V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GPR87 MUTATED                                  0     1
  GPR87 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  GPR87 MUTATED                           0     5
  GPR87 WILD-TYPE                        22   221
D625V13, multiclass
                                  clus
vv                                 GPR87 MUTATED GPR87 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        5             221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(626) Variable = AKR1C4 MUTATION ANALYSIS
D626V1, survival
                  sevent
clus2                0   1
  AKR1C4 MUTATED     8   3
  AKR1C4 WILD-TYPE 370  90
  AKR1C4 MUTATED AKR1C4 WILD-TYPE 
              11              460 
  AKR1C4 MUTATED AKR1C4 WILD-TYPE 
               3               90 
$`AKR1C4 MUTATED`
TCGA-AA-3660 TCGA-AA-A00O TCGA-AA-A01R TCGA-CA-6718 TCGA-CK-4950 TCGA-D5-6535 
       78.08        27.02        35.01        10.06        85.45        15.12 
TCGA-DM-A0XF TCGA-F4-6809 TCGA-G4-6306 TCGA-AG-3892 TCGA-CI-6620 
       38.20        13.25        44.68        13.02        33.17 

$`AKR1C4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 
       20.98        19.99        13.94        19.99        61.02         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04         4.01        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T 
       31.00        31.00        38.07         1.02         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5912 
       12.76        14.30        17.56       148.01        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       43.27        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A1D0 TCGA-DM-A1D4 
       11.38        10.26       119.70        24.43       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       16.24        33.67         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       74.56        65.85        53.62        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 
       19.99         1.02        17.95        36.95        17.03        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  AKR1C4 MUTATED AKR1C4 WILD-TYPE 
           10.06             0.00 
  AKR1C4 MUTATED AKR1C4 WILD-TYPE 
           85.45           148.01 
  AKR1C4 MUTATED AKR1C4 WILD-TYPE 
          33.170           20.085 
[1] "10.1 - 85.5 (33.2)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1"  
D626V2, continuous
D626V3, binary
                  cls
clus                 0   1
  AKR1C4 MUTATED     9   2
  AKR1C4 WILD-TYPE 357 117
[1] "tbl2"
                  cls
clus               [,1] [,2]
  AKR1C4 MUTATED      9    2
  AKR1C4 WILD-TYPE  357  117
        clus
vv       AKR1C4 MUTATED AKR1C4 WILD-TYPE
  COLON               9              357
  RECTUM              2              117
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  AKR1C4 MUTATED         1        0        1         2         0         0
  AKR1C4 WILD-TYPE      90        1       31       136        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  AKR1C4 MUTATED           1          0          2          2        0
  AKR1C4 WILD-TYPE        23         11         57         40       48
                  vv
clus               STAGE IVA STAGE IVB
  AKR1C4 MUTATED           2         0
  AKR1C4 WILD-TYPE        16         1
D626V4, multiclass
            clus
vv           AKR1C4 MUTATED AKR1C4 WILD-TYPE
  STAGE I                 1               90
  STAGE IA                0                1
  STAGE II                1               31
  STAGE IIA               2              136
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               1               23
  STAGE IIIA              0               11
  STAGE IIIB              2               57
  STAGE IIIC              2               40
  STAGE IV                0               48
  STAGE IVA               2               16
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  AKR1C4 MUTATED     1   1   9   0
  AKR1C4 WILD-TYPE  16  91 320  50
D626V5, multiclass
    clus
vv   AKR1C4 MUTATED AKR1C4 WILD-TYPE
  T1              1               16
  T2              1               91
  T3              9              320
  T4              0               50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  AKR1C4 MUTATED     4   4   3
  AKR1C4 WILD-TYPE 283 109  84
D626V6, multiclass
    clus
vv   AKR1C4 MUTATED AKR1C4 WILD-TYPE
  N0              4              283
  N1              4              109
  N2              3               84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D626V7, binary
                  cls
clus                 0   1
  AKR1C4 MUTATED     8   2
  AKR1C4 WILD-TYPE 367  63
[1] "tbl2"
                  cls
clus               [,1] [,2]
  AKR1C4 MUTATED      8    2
  AKR1C4 WILD-TYPE  367   63
   clus
vv  AKR1C4 MUTATED AKR1C4 WILD-TYPE
  0              8              367
  1              2               63
[1] 2 2
[1] FALSE
D626V8, binary
                  cls
clus                 0   1
  AKR1C4 MUTATED     8   3
  AKR1C4 WILD-TYPE 217 261
[1] "tbl2"
                  cls
clus               [,1] [,2]
  AKR1C4 MUTATED      8    3
  AKR1C4 WILD-TYPE  217  261
        clus
vv       AKR1C4 MUTATED AKR1C4 WILD-TYPE
  FEMALE              8              217
  MALE                3              261
[1] 2 2
[1] FALSE
D626V9, binary
                  cls
clus                 0   1
  AKR1C4 MUTATED     9   1
  AKR1C4 WILD-TYPE 341  21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  AKR1C4 MUTATED      9    1
  AKR1C4 WILD-TYPE  341   21
     clus
vv    AKR1C4 MUTATED AKR1C4 WILD-TYPE
  NO               9              341
  YES              1               21
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  AKR1C4 MUTATED                      7                             1
  AKR1C4 WILD-TYPE                  308                            46
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  AKR1C4 MUTATED                       2                              0
  AKR1C4 WILD-TYPE                   104                             10
D626V10, multiclass
                                clus
vv                               AKR1C4 MUTATED AKR1C4 WILD-TYPE
  COLON ADENOCARCINOMA                        7              308
  COLON MUCINOUS ADENOCARCINOMA               1               46
  RECTAL ADENOCARCINOMA                       2              104
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  AKR1C4 MUTATED     6   1   0   2
  AKR1C4 WILD-TYPE 339   3  31  23
D626V11, multiclass
    clus
vv   AKR1C4 MUTATED AKR1C4 WILD-TYPE
  R0              6              339
  R1              1                3
  R2              0               31
  RX              2               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D626V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AKR1C4 MUTATED                                  0     1
  AKR1C4 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  AKR1C4 MUTATED                           1     5
  AKR1C4 WILD-TYPE                        21   221
D626V13, multiclass
                                  clus
vv                                 AKR1C4 MUTATED AKR1C4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                         5              221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(627) Variable = E2F6 MUTATION ANALYSIS
D627V1, survival
                sevent
clus2              0   1
  E2F6 MUTATED     3   1
  E2F6 WILD-TYPE 375  92
  E2F6 MUTATED E2F6 WILD-TYPE 
             4            467 
  E2F6 MUTATED E2F6 WILD-TYPE 
             1             92 
$`E2F6 MUTATED`
TCGA-AZ-6603 TCGA-CI-6624 TCGA-DC-6155 TCGA-F5-6811 
       29.56         4.73        13.97        32.19 

$`E2F6 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6606 
       49.41         6.77        12.10       100.01         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CL-5917 
        0.69         0.72         6.05        33.17         6.97        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
        7.17        15.02         5.03        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57         0.66         0.69        55.76        26.43 

  E2F6 MUTATED E2F6 WILD-TYPE 
          4.73           0.00 
  E2F6 MUTATED E2F6 WILD-TYPE 
         32.19         148.01 
  E2F6 MUTATED E2F6 WILD-TYPE 
        21.765         20.190 
[1] "4.7 - 32.2 (21.8)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.8"
D627V2, continuous
D627V3, binary
                cls
clus               0   1
  E2F6 MUTATED     1   3
  E2F6 WILD-TYPE 365 116
[1] "tbl2"
                cls
clus             [,1] [,2]
  E2F6 MUTATED      1    3
  E2F6 WILD-TYPE  365  116
        clus
vv       E2F6 MUTATED E2F6 WILD-TYPE
  COLON             1            365
  RECTUM            3            116
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  E2F6 MUTATED         1        0        0         1         0         0
  E2F6 WILD-TYPE      90        1       32       137        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  E2F6 MUTATED           0          1          0          0        0         0
  E2F6 WILD-TYPE        24         10         59         42       48        18
                vv
clus             STAGE IVB
  E2F6 MUTATED           0
  E2F6 WILD-TYPE         1
D627V4, multiclass
            clus
vv           E2F6 MUTATED E2F6 WILD-TYPE
  STAGE I               1             90
  STAGE IA              0              1
  STAGE II              0             32
  STAGE IIA             1            137
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            1             10
  STAGE IIIB            0             59
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  E2F6 MUTATED     0   3   1   0
  E2F6 WILD-TYPE  17  89 328  50
D627V5, multiclass
    clus
vv   E2F6 MUTATED E2F6 WILD-TYPE
  T1            0             17
  T2            3             89
  T3            1            328
  T4            0             50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  E2F6 MUTATED     2   2   0
  E2F6 WILD-TYPE 285 111  87
D627V6, multiclass
    clus
vv   E2F6 MUTATED E2F6 WILD-TYPE
  N0            2            285
  N1            2            111
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D627V7, binary
                cls
clus               0   1
  E2F6 MUTATED     3   0
  E2F6 WILD-TYPE 372  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  E2F6 MUTATED      3    0
  E2F6 WILD-TYPE  372   65
   clus
vv  E2F6 MUTATED E2F6 WILD-TYPE
  0            3            372
  1            0             65
[1] 2 2
[1] FALSE
D627V8, binary
                cls
clus               0   1
  E2F6 MUTATED     4   0
  E2F6 WILD-TYPE 221 264
[1] "tbl2"
                cls
clus             [,1] [,2]
  E2F6 MUTATED      4    0
  E2F6 WILD-TYPE  221  264
        clus
vv       E2F6 MUTATED E2F6 WILD-TYPE
  FEMALE            4            221
  MALE              0            264
[1] 2 2
[1] FALSE
D627V9, binary
                cls
clus               0   1
  E2F6 MUTATED     3   0
  E2F6 WILD-TYPE 347  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  E2F6 MUTATED      3    0
  E2F6 WILD-TYPE  347   22
     clus
vv    E2F6 MUTATED E2F6 WILD-TYPE
  NO             3            347
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  E2F6 MUTATED                      1                             0
  E2F6 WILD-TYPE                  314                            47
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  E2F6 MUTATED                       3                              0
  E2F6 WILD-TYPE                   103                             10
D627V10, multiclass
                                clus
vv                               E2F6 MUTATED E2F6 WILD-TYPE
  COLON ADENOCARCINOMA                      1            314
  COLON MUCINOUS ADENOCARCINOMA             0             47
  RECTAL ADENOCARCINOMA                     3            103
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  E2F6 MUTATED     1   0   0   0
  E2F6 WILD-TYPE 344   4  31  25
D627V11, multiclass
[1] "Remove cluster labels:" "E2F6 MUTATED"          
clus
  E2F6 MUTATED E2F6 WILD-TYPE 
             1            404 
    TCGA-A6-2671     TCGA-A6-2672     TCGA-A6-2674     TCGA-A6-2676 
"E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" 
    TCGA-A6-2677     TCGA-A6-2678     TCGA-A6-2683     TCGA-A6-3807 
"E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" 
    TCGA-A6-3808     TCGA-A6-3809     TCGA-A6-3810     TCGA-A6-5657 
"E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" 
    TCGA-A6-5659     TCGA-A6-5661     TCGA-A6-5665     TCGA-A6-6781 
"E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" 
    TCGA-AA-3489     TCGA-AA-3492     TCGA-AA-3496     TCGA-AA-3502 
"E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" 
    TCGA-AA-3510     TCGA-AA-3511     TCGA-AA-3514     TCGA-AA-3517 
"E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" 
    TCGA-AA-3518     TCGA-AA-3519     TCGA-AA-3520     TCGA-AA-3521 
"E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" 
    TCGA-AA-3522     TCGA-AA-3524     TCGA-AA-3525     TCGA-AA-3526 
"E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" 
    TCGA-AA-3527     TCGA-AA-3529     TCGA-AA-3530     TCGA-AA-3531 
"E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" 
    TCGA-AA-3532     TCGA-AA-3534     TCGA-AA-3538     TCGA-AA-3542 
"E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" 
    TCGA-AA-3543     TCGA-AA-3544     TCGA-AA-3548     TCGA-AA-3549 
"E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" 
    TCGA-AA-3552     TCGA-AA-3553     TCGA-AA-3554     TCGA-AA-3555 
"E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" 
    TCGA-AA-3556     TCGA-AA-3558     TCGA-AA-3560     TCGA-AA-3561 
"E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" 
    TCGA-AA-3562     TCGA-AA-3655     TCGA-AA-3660     TCGA-AA-3662 
"E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" 
    TCGA-AA-3663     TCGA-AA-3664     TCGA-AA-3666     TCGA-AA-3667 
"E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" 
    TCGA-AA-3672     TCGA-AA-3673     TCGA-AA-3678     TCGA-AA-3679 
"E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" 
    TCGA-AA-3680     TCGA-AA-3681     TCGA-AA-3684     TCGA-AA-3685 
"E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" 
    TCGA-AA-3688     TCGA-AA-3692     TCGA-AA-3693     TCGA-AA-3695 
"E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" 
    TCGA-AA-3696     TCGA-AA-3697     TCGA-AA-3710     TCGA-AA-3712 
"E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" 
    TCGA-AA-3713     TCGA-AA-3715     TCGA-AA-3811     TCGA-AA-3812 
"E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" 
    TCGA-AA-3814     TCGA-AA-3815     TCGA-AA-3818     TCGA-AA-3819 
"E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" 
    TCGA-AA-3821     TCGA-AA-3831     TCGA-AA-3833     TCGA-AA-3837 
"E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" 
    TCGA-AA-3842     TCGA-AA-3844     TCGA-AA-3845     TCGA-AA-3846 
"E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" 
    TCGA-AA-3848     TCGA-AA-3850     TCGA-AA-3851     TCGA-AA-3852 
"E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" 
    TCGA-AA-3854     TCGA-AA-3855     TCGA-AA-3856     TCGA-AA-3858 
"E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" 
    TCGA-AA-3860     TCGA-AA-3861     TCGA-AA-3864     TCGA-AA-3866 
"E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" 
    TCGA-AA-3867     TCGA-AA-3869     TCGA-AA-3870     TCGA-AA-3872 
"E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" 
    TCGA-AA-3875     TCGA-AA-3877     TCGA-AA-3930     TCGA-AA-3939 
"E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" 
    TCGA-AA-3941     TCGA-AA-3947     TCGA-AA-3949     TCGA-AA-3950 
"E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" 
    TCGA-AA-3952     TCGA-AA-3955     TCGA-AA-3956     TCGA-AA-3968 
"E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" 
    TCGA-AA-3971     TCGA-AA-3972     TCGA-AA-3973     TCGA-AA-3975 
"E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" 
    TCGA-AA-3976     TCGA-AA-3979     TCGA-AA-3984     TCGA-AA-3986 
"E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" 
    TCGA-AA-3989     TCGA-AA-3994     TCGA-AA-A004     TCGA-AA-A00A 
"E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" 
    TCGA-AA-A00D     TCGA-AA-A00E     TCGA-AA-A00F     TCGA-AA-A00J 
"E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" 
    TCGA-AA-A00K     TCGA-AA-A00L     TCGA-AA-A00N     TCGA-AA-A00O 
"E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" 
    TCGA-AA-A00Q     TCGA-AA-A00R     TCGA-AA-A00U     TCGA-AA-A00W 
"E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" 
    TCGA-AA-A00Z     TCGA-AA-A010     TCGA-AA-A017     TCGA-AA-A01D 
"E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" 
    TCGA-AA-A01F     TCGA-AA-A01G     TCGA-AA-A01I     TCGA-AA-A01K 
"E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" 
    TCGA-AA-A01P     TCGA-AA-A01Q     TCGA-AA-A01R     TCGA-AA-A01S 
"E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" 
    TCGA-AA-A01T     TCGA-AA-A01V     TCGA-AA-A01X     TCGA-AA-A01Z 
"E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" 
    TCGA-AA-A022     TCGA-AA-A024     TCGA-AA-A029     TCGA-AA-A02F 
"E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" 
    TCGA-AA-A02H     TCGA-AA-A02J     TCGA-AA-A02K     TCGA-AA-A02O 
"E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" 
    TCGA-AA-A02W     TCGA-AA-A02Y     TCGA-AA-A03F     TCGA-AA-A03J 
"E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" 
    TCGA-AD-5900     TCGA-AD-6548     TCGA-AD-6888     TCGA-AU-3779 
"E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" 
    TCGA-AU-6004     TCGA-AY-4070     TCGA-AY-4071     TCGA-AY-5543 
"E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" 
    TCGA-AY-6196     TCGA-AY-6197     TCGA-AY-6386     TCGA-AZ-4315 
"E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" 
    TCGA-AZ-4681     TCGA-AZ-4682     TCGA-CA-5254     TCGA-CA-5255 
"E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" 
    TCGA-CA-5796     TCGA-CA-5797     TCGA-CA-6715     TCGA-CA-6716 
"E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" 
    TCGA-CA-6717     TCGA-CA-6718     TCGA-CA-6719     TCGA-CK-4947 
"E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" 
    TCGA-CK-4948     TCGA-CK-4950     TCGA-CK-4952     TCGA-CK-5912 
"E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" 
    TCGA-CK-5913     TCGA-CK-5914     TCGA-CK-5915     TCGA-CK-5916 
"E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" 
    TCGA-CK-6746     TCGA-CK-6747     TCGA-CK-6748     TCGA-CK-6751 
"E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" 
    TCGA-CM-4743     TCGA-CM-4744     TCGA-CM-4746     TCGA-CM-4747 
"E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" 
    TCGA-CM-4752     TCGA-CM-5341     TCGA-CM-5344     TCGA-CM-5348 
"E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" 
    TCGA-CM-5349     TCGA-CM-5860     TCGA-CM-5861     TCGA-CM-5862 
"E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" 
    TCGA-CM-5863     TCGA-CM-5864     TCGA-CM-5868     TCGA-CM-6161 
"E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" 
    TCGA-CM-6162     TCGA-CM-6163     TCGA-CM-6164     TCGA-CM-6165 
"E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" 
    TCGA-CM-6166     TCGA-CM-6167     TCGA-CM-6168     TCGA-CM-6169 
"E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" 
    TCGA-CM-6170     TCGA-CM-6171     TCGA-CM-6172     TCGA-CM-6674 
"E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" 
    TCGA-CM-6675     TCGA-CM-6676     TCGA-CM-6677     TCGA-CM-6678 
"E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" 
    TCGA-CM-6679     TCGA-CM-6680     TCGA-D5-5537     TCGA-D5-5538 
"E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" 
    TCGA-D5-5539     TCGA-D5-5540     TCGA-D5-5541     TCGA-D5-6529 
"E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" 
    TCGA-D5-6532     TCGA-D5-6533     TCGA-D5-6534     TCGA-D5-6535 
"E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" 
    TCGA-D5-6536     TCGA-D5-6537     TCGA-D5-6538     TCGA-D5-6539 
"E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" 
    TCGA-D5-6540     TCGA-D5-6541     TCGA-D5-6898     TCGA-D5-6920 
"E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" 
    TCGA-D5-6922     TCGA-D5-6923     TCGA-D5-6924     TCGA-D5-6926 
"E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" 
    TCGA-D5-6927     TCGA-D5-6928     TCGA-D5-6929     TCGA-D5-6930 
"E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" 
    TCGA-D5-6931     TCGA-D5-6932     TCGA-D5-7000     TCGA-F4-6459 
"E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" 
    TCGA-F4-6460     TCGA-F4-6569     TCGA-F4-6570     TCGA-F4-6703 
"E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" 
    TCGA-F4-6704     TCGA-F4-6805     TCGA-F4-6806     TCGA-F4-6807 
"E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" 
    TCGA-F4-6808     TCGA-F4-6809     TCGA-F4-6854     TCGA-F4-6855 
"E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" 
    TCGA-F4-6856     TCGA-G4-6293     TCGA-G4-6299     TCGA-G4-6303 
"E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" 
    TCGA-G4-6304     TCGA-G4-6306     TCGA-G4-6307     TCGA-G4-6309 
"E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" 
    TCGA-G4-6310     TCGA-G4-6315     TCGA-G4-6317     TCGA-G4-6321 
"E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" 
    TCGA-G4-6323     TCGA-G4-6586     TCGA-G4-6588     TCGA-G4-6625 
"E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" 
    TCGA-G4-6626     TCGA-G4-6628     TCGA-AF-2687     TCGA-AF-2689 
"E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" 
    TCGA-AF-2691     TCGA-AF-2692     TCGA-AF-3400     TCGA-AF-3913 
"E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" 
    TCGA-AF-4110     TCGA-AF-5654     TCGA-AF-6655     TCGA-AG-3574 
"E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" 
    TCGA-AG-3575     TCGA-AG-3578     TCGA-AG-3580     TCGA-AG-3581 
"E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" 
    TCGA-AG-3582     TCGA-AG-3583     TCGA-AG-3584     TCGA-AG-3586 
"E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" 
    TCGA-AG-3587     TCGA-AG-3593     TCGA-AG-3594     TCGA-AG-3598 
"E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" 
    TCGA-AG-3599     TCGA-AG-3600     TCGA-AG-3601     TCGA-AG-3602 
"E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" 
    TCGA-AG-3605     TCGA-AG-3608     TCGA-AG-3609     TCGA-AG-3611 
"E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" 
    TCGA-AG-3612     TCGA-AG-3726     TCGA-AG-3727     TCGA-AG-3731 
"E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" 
    TCGA-AG-3732     TCGA-AG-3742     TCGA-AG-3878     TCGA-AG-3882 
"E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" 
    TCGA-AG-3883     TCGA-AG-3885     TCGA-AG-3887     TCGA-AG-3890 
"E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" 
    TCGA-AG-3892     TCGA-AG-3893     TCGA-AG-3894     TCGA-AG-3896 
"E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" 
    TCGA-AG-3898     TCGA-AG-3901     TCGA-AG-3902     TCGA-AG-3909 
"E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" 
    TCGA-AG-3999     TCGA-AG-4001     TCGA-AG-4005     TCGA-AG-4007 
"E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" 
    TCGA-AG-4008     TCGA-AG-4015     TCGA-AG-A002     TCGA-AG-A008 
"E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" 
    TCGA-AG-A00C     TCGA-AG-A00H     TCGA-AG-A00Y     TCGA-AG-A011 
"E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" 
    TCGA-AG-A014     TCGA-AG-A015     TCGA-AG-A016     TCGA-AG-A01L 
"E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" 
    TCGA-AG-A01W     TCGA-AG-A01Y     TCGA-AG-A020     TCGA-AG-A025 
"E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" 
    TCGA-AG-A026     TCGA-AG-A02G     TCGA-AG-A02N     TCGA-AG-A02X 
"E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" 
    TCGA-AG-A032     TCGA-AG-A036     TCGA-AH-6549     TCGA-AH-6643 
"E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" 
    TCGA-CL-5917     TCGA-CL-5918     TCGA-DC-5337     TCGA-DC-5869 
"E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" 
    TCGA-DC-6157     TCGA-DC-6158     TCGA-DC-6160     TCGA-DC-6681 
"E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" 
    TCGA-DC-6682     TCGA-DC-6683     TCGA-DT-5265     TCGA-EF-5830 
"E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" 
    TCGA-EI-6506     TCGA-EI-6507     TCGA-EI-6508     TCGA-EI-6510 
"E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" 
    TCGA-F5-6464     TCGA-F5-6465     TCGA-F5-6571     TCGA-F5-6702 
"E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" 
    TCGA-F5-6812     TCGA-F5-6813     TCGA-G5-6235     TCGA-G5-6641 
"E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" "E2F6 WILD-TYPE" 
D627V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  E2F6 MUTATED                                  0     0
  E2F6 WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  E2F6 MUTATED                           0     4
  E2F6 WILD-TYPE                        22   222
D627V13, multiclass
                                  clus
vv                                 E2F6 MUTATED E2F6 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       4            222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(628) Variable = PRKCI MUTATION ANALYSIS
D628V1, survival
                 sevent
clus2               0   1
  PRKCI MUTATED    16   3
  PRKCI WILD-TYPE 362  90
  PRKCI MUTATED PRKCI WILD-TYPE 
             19             452 
  PRKCI MUTATED PRKCI WILD-TYPE 
              3              90 
$`PRKCI MUTATED`
TCGA-A6-6141 TCGA-A6-6780 TCGA-AA-3510 TCGA-AA-3555 TCGA-AA-3663 TCGA-AA-3815 
        8.38        20.12        63.98        29.95         6.97        33.04 
TCGA-AA-3977 TCGA-AA-A010 TCGA-AZ-4315 TCGA-AZ-6599 TCGA-CM-6169 TCGA-CM-6171 
       25.02        34.98        58.39         6.77        13.02        14.04 
TCGA-D5-5540 TCGA-D5-6535 TCGA-D5-6540 TCGA-DM-A1D4 TCGA-G4-6586 TCGA-DY-A1DD 
       56.09        15.12        16.14        92.75        35.80        57.24 
TCGA-F5-6702 
       28.57 

$`PRKCI WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 
       22.09        22.06        32.71        27.09        22.52        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       17.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       61.02        78.08         6.05        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
       19.04        19.04        10.06        35.05         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       33.01        21.44        17.82         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        88.21        49.41        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       15.02        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 
       55.92        20.19        18.25         1.32        43.27        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
        4.80        17.13        12.49        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       24.43        38.20       130.65        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DF TCGA-DY-A1DG 
        5.03         5.29       126.44        41.36        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
        9.96        49.51        31.30        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  PRKCI MUTATED PRKCI WILD-TYPE 
           6.77            0.00 
  PRKCI MUTATED PRKCI WILD-TYPE 
          92.75          148.01 
  PRKCI MUTATED PRKCI WILD-TYPE 
         28.570          20.035 
[1] "6.8 - 92.8 (28.6)"  "0.0 - 148.0 (20.0)"
[1] "hr=" "1.6"
D628V2, continuous
D628V3, binary
                 cls
clus                0   1
  PRKCI MUTATED    18   2
  PRKCI WILD-TYPE 348 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRKCI MUTATED     18    2
  PRKCI WILD-TYPE  348  117
        clus
vv       PRKCI MUTATED PRKCI WILD-TYPE
  COLON             18             348
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PRKCI MUTATED         3        0        2        10         1         0
  PRKCI WILD-TYPE      88        1       30       128         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PRKCI MUTATED           0          0          2          0        0         1
  PRKCI WILD-TYPE        24         11         57         42       48        17
                 vv
clus              STAGE IVB
  PRKCI MUTATED           0
  PRKCI WILD-TYPE         1
D628V4, multiclass
            clus
vv           PRKCI MUTATED PRKCI WILD-TYPE
  STAGE I                3              88
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA             10             128
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             2              57
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PRKCI MUTATED     0   4  15   1
  PRKCI WILD-TYPE  17  88 314  49
D628V5, multiclass
    clus
vv   PRKCI MUTATED PRKCI WILD-TYPE
  T1             0              17
  T2             4              88
  T3            15             314
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  PRKCI MUTATED    17   3   0
  PRKCI WILD-TYPE 270 110  87
D628V6, multiclass
    clus
vv   PRKCI MUTATED PRKCI WILD-TYPE
  N0            17             270
  N1             3             110
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D628V7, binary
                 cls
clus                0   1
  PRKCI MUTATED    15   1
  PRKCI WILD-TYPE 360  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRKCI MUTATED     15    1
  PRKCI WILD-TYPE  360   64
   clus
vv  PRKCI MUTATED PRKCI WILD-TYPE
  0            15             360
  1             1              64
[1] 2 2
[1] FALSE
D628V8, binary
                 cls
clus                0   1
  PRKCI MUTATED     8  12
  PRKCI WILD-TYPE 217 252
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRKCI MUTATED      8   12
  PRKCI WILD-TYPE  217  252
        clus
vv       PRKCI MUTATED PRKCI WILD-TYPE
  FEMALE             8             217
  MALE              12             252
[1] 2 2
[1] FALSE
D628V9, binary
                 cls
clus                0   1
  PRKCI MUTATED    17   0
  PRKCI WILD-TYPE 333  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRKCI MUTATED     17    0
  PRKCI WILD-TYPE  333   22
     clus
vv    PRKCI MUTATED PRKCI WILD-TYPE
  NO             17             333
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PRKCI MUTATED                     15                             3
  PRKCI WILD-TYPE                  300                            44
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PRKCI MUTATED                       2                              0
  PRKCI WILD-TYPE                   104                             10
D628V10, multiclass
                                clus
vv                               PRKCI MUTATED PRKCI WILD-TYPE
  COLON ADENOCARCINOMA                      15             300
  COLON MUCINOUS ADENOCARCINOMA              3              44
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  PRKCI MUTATED    13   0   0   1
  PRKCI WILD-TYPE 332   4  31  24
D628V11, multiclass
    clus
vv   PRKCI MUTATED PRKCI WILD-TYPE
  R0            13             332
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D628V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PRKCI MUTATED                                  0     0
  PRKCI WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PRKCI MUTATED                           2    11
  PRKCI WILD-TYPE                        20   215
D628V13, multiclass
                                  clus
vv                                 PRKCI MUTATED PRKCI WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    2              20
  WHITE                                       11             215
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(629) Variable = SEC31A MUTATION ANALYSIS
D629V1, survival
                  sevent
clus2                0   1
  SEC31A MUTATED    13   2
  SEC31A WILD-TYPE 365  91
  SEC31A MUTATED SEC31A WILD-TYPE 
              15              456 
  SEC31A MUTATED SEC31A WILD-TYPE 
               2               91 
$`SEC31A MUTATED`
TCGA-A6-5665 TCGA-AA-3543 TCGA-AA-3662 TCGA-AA-3710 TCGA-AA-3819 TCGA-AD-6889 
       22.06         0.99         6.05        26.99        25.02        56.55 
TCGA-AD-6895 TCGA-CA-6717 TCGA-CM-6167 TCGA-F4-6570 TCGA-F4-6856 TCGA-G4-6309 
        0.72        12.76        14.99         6.18        35.31        85.48 
TCGA-G4-6626 TCGA-EI-6507 TCGA-G5-6235 
       46.75        19.96        55.76 

$`SEC31A WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       26.01        12.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       85.05        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
        0.99         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
        0.07        21.37        15.52         0.79         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07        12.20        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 
      117.07        98.24         8.61        31.96        35.74        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
        0.53        47.41       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       44.68        55.04        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-AF-2687 
       13.78        35.80        26.17        91.79        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
        0.49        20.55        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6641 
       31.30        28.57        32.19         0.66         0.69        26.43 

  SEC31A MUTATED SEC31A WILD-TYPE 
            0.72             0.00 
  SEC31A MUTATED SEC31A WILD-TYPE 
           85.48           148.01 
  SEC31A MUTATED SEC31A WILD-TYPE 
          22.060           20.155 
[1] "0.7 - 85.5 (22.1)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.6"
D629V2, continuous
D629V3, binary
                  cls
clus                 0   1
  SEC31A MUTATED    13   2
  SEC31A WILD-TYPE 353 117
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SEC31A MUTATED     13    2
  SEC31A WILD-TYPE  353  117
        clus
vv       SEC31A MUTATED SEC31A WILD-TYPE
  COLON              13              353
  RECTUM              2              117
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SEC31A MUTATED         2        0        0         8         0         0
  SEC31A WILD-TYPE      89        1       32       130        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SEC31A MUTATED           0          0          2          1        1
  SEC31A WILD-TYPE        24         11         57         41       47
                  vv
clus               STAGE IVA STAGE IVB
  SEC31A MUTATED           0         0
  SEC31A WILD-TYPE        18         1
D629V4, multiclass
            clus
vv           SEC31A MUTATED SEC31A WILD-TYPE
  STAGE I                 2               89
  STAGE IA                0                1
  STAGE II                0               32
  STAGE IIA               8              130
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              2               57
  STAGE IIIC              1               41
  STAGE IV                1               47
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  SEC31A MUTATED     0   2  12   1
  SEC31A WILD-TYPE  17  90 317  49
D629V5, multiclass
    clus
vv   SEC31A MUTATED SEC31A WILD-TYPE
  T1              0               17
  T2              2               90
  T3             12              317
  T4              1               49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  SEC31A MUTATED    10   3   2
  SEC31A WILD-TYPE 277 110  85
D629V6, multiclass
    clus
vv   SEC31A MUTATED SEC31A WILD-TYPE
  N0             10              277
  N1              3              110
  N2              2               85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D629V7, binary
                  cls
clus                 0   1
  SEC31A MUTATED    12   1
  SEC31A WILD-TYPE 363  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SEC31A MUTATED     12    1
  SEC31A WILD-TYPE  363   64
   clus
vv  SEC31A MUTATED SEC31A WILD-TYPE
  0             12              363
  1              1               64
[1] 2 2
[1] FALSE
D629V8, binary
                  cls
clus                 0   1
  SEC31A MUTATED     7   8
  SEC31A WILD-TYPE 218 256
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SEC31A MUTATED      7    8
  SEC31A WILD-TYPE  218  256
        clus
vv       SEC31A MUTATED SEC31A WILD-TYPE
  FEMALE              7              218
  MALE                8              256
[1] 2 2
[1] FALSE
D629V9, binary
                  cls
clus                 0   1
  SEC31A MUTATED    13   0
  SEC31A WILD-TYPE 337  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SEC31A MUTATED     13    0
  SEC31A WILD-TYPE  337   22
     clus
vv    SEC31A MUTATED SEC31A WILD-TYPE
  NO              13              337
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SEC31A MUTATED                     10                             3
  SEC31A WILD-TYPE                  305                            44
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SEC31A MUTATED                       2                              0
  SEC31A WILD-TYPE                   104                             10
D629V10, multiclass
                                clus
vv                               SEC31A MUTATED SEC31A WILD-TYPE
  COLON ADENOCARCINOMA                       10              305
  COLON MUCINOUS ADENOCARCINOMA               3               44
  RECTAL ADENOCARCINOMA                       2              104
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  SEC31A MUTATED    10   1   1   1
  SEC31A WILD-TYPE 335   3  30  24
D629V11, multiclass
    clus
vv   SEC31A MUTATED SEC31A WILD-TYPE
  R0             10              335
  R1              1                3
  R2              1               30
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D629V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SEC31A MUTATED                                  0     2
  SEC31A WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  SEC31A MUTATED                           2     7
  SEC31A WILD-TYPE                        20   219
D629V13, multiclass
                                  clus
vv                                 SEC31A MUTATED SEC31A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                9
  BLACK OR AFRICAN AMERICAN                     2               20
  WHITE                                         7              219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(630) Variable = KIAA0319L MUTATION ANALYSIS
D630V1, survival
                     sevent
clus2                   0   1
  KIAA0319L MUTATED    16   4
  KIAA0319L WILD-TYPE 362  89
  KIAA0319L MUTATED KIAA0319L WILD-TYPE 
                 20                 451 
  KIAA0319L MUTATED KIAA0319L WILD-TYPE 
                  4                  89 
$`KIAA0319L MUTATED`
TCGA-A6-2676 TCGA-A6-5659 TCGA-A6-6781 TCGA-AA-3492 TCGA-AA-3819 TCGA-AA-3877 
       42.90        30.44        19.66         3.02        25.02        31.00 
TCGA-AA-3977 TCGA-AA-A010 TCGA-AA-A01Q TCGA-AZ-4315 TCGA-AZ-6598 TCGA-CA-6717 
       25.02        34.98         1.02        58.39        49.41        12.76 
TCGA-CK-4947 TCGA-CM-4746 TCGA-D5-6927 TCGA-DM-A1HB TCGA-F4-6570 TCGA-G4-6307 
       17.56        37.02         9.44       135.65         6.18        55.04 
TCGA-G4-6588 TCGA-EI-6507 
       26.17        19.96 

$`KIAA0319L WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       31.63        29.19        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
       20.28         7.04         1.02        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
        0.99         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       18.05         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        31.00        38.07        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        88.21         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07        12.20        10.06        14.30 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6928 
        3.68         4.41        12.43        14.30         9.04        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 
       12.59       140.38         7.50        44.32       131.51       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 
       98.24         8.61        31.96        35.74        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       44.68        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       13.78        35.80        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
        0.49        20.55        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  KIAA0319L MUTATED KIAA0319L WILD-TYPE 
               1.02                0.00 
  KIAA0319L MUTATED KIAA0319L WILD-TYPE 
             135.65              148.01 
  KIAA0319L MUTATED KIAA0319L WILD-TYPE 
             25.595              20.050 
[1] "1.0 - 135.7 (25.6)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.2"
D630V2, continuous
D630V3, binary
                     cls
clus                    0   1
  KIAA0319L MUTATED    19   1
  KIAA0319L WILD-TYPE 347 118
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  KIAA0319L MUTATED     19    1
  KIAA0319L WILD-TYPE  347  118
        clus
vv       KIAA0319L MUTATED KIAA0319L WILD-TYPE
  COLON                 19                 347
  RECTUM                 1                 118
[1] 2 2
[1] FALSE
                     vv
clus                  STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KIAA0319L MUTATED         3        0        3         7         2         0
  KIAA0319L WILD-TYPE      88        1       29       131         8         1
                     vv
clus                  STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIAA0319L MUTATED           0          0          3          1        0
  KIAA0319L WILD-TYPE        24         11         56         41       48
                     vv
clus                  STAGE IVA STAGE IVB
  KIAA0319L MUTATED           0         0
  KIAA0319L WILD-TYPE        18         1
D630V4, multiclass
            clus
vv           KIAA0319L MUTATED KIAA0319L WILD-TYPE
  STAGE I                    3                  88
  STAGE IA                   0                   1
  STAGE II                   3                  29
  STAGE IIA                  7                 131
  STAGE IIB                  2                   8
  STAGE IIC                  0                   1
  STAGE III                  0                  24
  STAGE IIIA                 0                  11
  STAGE IIIB                 3                  56
  STAGE IIIC                 1                  41
  STAGE IV                   0                  48
  STAGE IVA                  0                  18
  STAGE IVB                  0                   1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                   T1  T2  T3  T4
  KIAA0319L MUTATED     1   3  12   4
  KIAA0319L WILD-TYPE  16  89 317  46
D630V5, multiclass
    clus
vv   KIAA0319L MUTATED KIAA0319L WILD-TYPE
  T1                 1                  16
  T2                 3                  89
  T3                12                 317
  T4                 4                  46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                   N0  N1  N2
  KIAA0319L MUTATED    16   4   0
  KIAA0319L WILD-TYPE 271 109  87
D630V6, multiclass
    clus
vv   KIAA0319L MUTATED KIAA0319L WILD-TYPE
  N0                16                 271
  N1                 4                 109
  N2                 0                  87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D630V7, binary
                     cls
clus                    0   1
  KIAA0319L MUTATED    17   0
  KIAA0319L WILD-TYPE 358  65
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  KIAA0319L MUTATED     17    0
  KIAA0319L WILD-TYPE  358   65
   clus
vv  KIAA0319L MUTATED KIAA0319L WILD-TYPE
  0                17                 358
  1                 0                  65
[1] 2 2
[1] FALSE
D630V8, binary
                     cls
clus                    0   1
  KIAA0319L MUTATED    11   9
  KIAA0319L WILD-TYPE 214 255
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  KIAA0319L MUTATED     11    9
  KIAA0319L WILD-TYPE  214  255
        clus
vv       KIAA0319L MUTATED KIAA0319L WILD-TYPE
  FEMALE                11                 214
  MALE                   9                 255
[1] 2 2
[1] FALSE
D630V9, binary
                     cls
clus                    0   1
  KIAA0319L MUTATED    18   0
  KIAA0319L WILD-TYPE 332  22
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  KIAA0319L MUTATED     18    0
  KIAA0319L WILD-TYPE  332   22
     clus
vv    KIAA0319L MUTATED KIAA0319L WILD-TYPE
  NO                 18                 332
  YES                 0                  22
[1] 2 2
[1] FALSE
                     vv
clus                  COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  KIAA0319L MUTATED                     15                             3
  KIAA0319L WILD-TYPE                  300                            44
                     vv
clus                  RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  KIAA0319L MUTATED                       1                              0
  KIAA0319L WILD-TYPE                   105                             10
D630V10, multiclass
                                clus
vv                               KIAA0319L MUTATED KIAA0319L WILD-TYPE
  COLON ADENOCARCINOMA                          15                 300
  COLON MUCINOUS ADENOCARCINOMA                  3                  44
  RECTAL ADENOCARCINOMA                          1                 105
  RECTAL MUCINOUS ADENOCARCINOMA                 0                  10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                   R0  R1  R2  RX
  KIAA0319L MUTATED    15   0   0   2
  KIAA0319L WILD-TYPE 330   4  31  23
D630V11, multiclass
    clus
vv   KIAA0319L MUTATED KIAA0319L WILD-TYPE
  R0                15                 330
  R1                 0                   4
  R2                 0                  31
  RX                 2                  23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D630V12, continuous
                     vv
clus                  AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KIAA0319L MUTATED                                  0     1
  KIAA0319L WILD-TYPE                                1    10
                     vv
clus                  BLACK OR AFRICAN AMERICAN WHITE
  KIAA0319L MUTATED                           1    12
  KIAA0319L WILD-TYPE                        21   214
D630V13, multiclass
                                  clus
vv                                 KIAA0319L MUTATED KIAA0319L WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                 0                   1
  ASIAN                                            1                  10
  BLACK OR AFRICAN AMERICAN                        1                  21
  WHITE                                           12                 214
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(631) Variable = BACE2 MUTATION ANALYSIS
D631V1, survival
                 sevent
clus2               0   1
  BACE2 MUTATED    11   0
  BACE2 WILD-TYPE 367  93
  BACE2 MUTATED BACE2 WILD-TYPE 
             11             460 
  BACE2 MUTATED BACE2 WILD-TYPE 
              0              93 
$`BACE2 MUTATED`
TCGA-A6-2672 TCGA-A6-6648 TCGA-A6-6651 TCGA-AA-3994 TCGA-AA-A010 TCGA-AD-6895 
       46.65        25.18        21.76        27.02        34.98         0.72 
TCGA-AY-6386 TCGA-CK-4952 TCGA-CM-6679 TCGA-G4-6309 TCGA-EI-6507 
       17.82        15.62        10.06        85.48        19.96 

$`BACE2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6649 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       24.16        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
       19.07         7.96        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 
        0.07        21.37        15.52        56.55         0.79         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-4323 
       16.31         0.95        33.01        21.44        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
      148.01        85.45        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6680 
       12.95        13.05        11.08        11.08        11.01        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 
       65.85        53.62        44.68        55.04        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6508 
       24.13        51.48        32.61         0.49        20.55        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  BACE2 MUTATED BACE2 WILD-TYPE 
           0.72            0.00 
  BACE2 MUTATED BACE2 WILD-TYPE 
          85.48          148.01 
  BACE2 MUTATED BACE2 WILD-TYPE 
         21.760          20.155 
[1] "0.7 - 85.5 (21.8)"  "0.0 - 148.0 (20.2)"
[1] "hr="     "9300000"
D631V2, continuous
D631V3, binary
                 cls
clus                0   1
  BACE2 MUTATED    10   1
  BACE2 WILD-TYPE 356 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BACE2 MUTATED     10    1
  BACE2 WILD-TYPE  356  118
        clus
vv       BACE2 MUTATED BACE2 WILD-TYPE
  COLON             10             356
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  BACE2 MUTATED         0        0        0         2         1         0
  BACE2 WILD-TYPE      91        1       32       136         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  BACE2 MUTATED           0          0          5          1        0         1
  BACE2 WILD-TYPE        24         11         54         41       48        17
                 vv
clus              STAGE IVB
  BACE2 MUTATED           0
  BACE2 WILD-TYPE         1
D631V4, multiclass
            clus
vv           BACE2 MUTATED BACE2 WILD-TYPE
  STAGE I                0              91
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              2             136
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             5              54
  STAGE IIIC             1              41
  STAGE IV               0              48
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  BACE2 MUTATED     0   0   9   2
  BACE2 WILD-TYPE  17  92 320  48
D631V5, multiclass
    clus
vv   BACE2 MUTATED BACE2 WILD-TYPE
  T1             0              17
  T2             0              92
  T3             9             320
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  BACE2 MUTATED     4   6   1
  BACE2 WILD-TYPE 283 107  86
D631V6, multiclass
    clus
vv   BACE2 MUTATED BACE2 WILD-TYPE
  N0             4             283
  N1             6             107
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D631V7, binary
                 cls
clus                0   1
  BACE2 MUTATED     8   1
  BACE2 WILD-TYPE 367  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BACE2 MUTATED      8    1
  BACE2 WILD-TYPE  367   64
   clus
vv  BACE2 MUTATED BACE2 WILD-TYPE
  0             8             367
  1             1              64
[1] 2 2
[1] FALSE
D631V8, binary
                 cls
clus                0   1
  BACE2 MUTATED     6   5
  BACE2 WILD-TYPE 219 259
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BACE2 MUTATED      6    5
  BACE2 WILD-TYPE  219  259
        clus
vv       BACE2 MUTATED BACE2 WILD-TYPE
  FEMALE             6             219
  MALE               5             259
[1] 2 2
[1] FALSE
D631V9, binary
                 cls
clus                0   1
  BACE2 MUTATED     9   0
  BACE2 WILD-TYPE 341  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BACE2 MUTATED      9    0
  BACE2 WILD-TYPE  341   22
     clus
vv    BACE2 MUTATED BACE2 WILD-TYPE
  NO              9             341
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  BACE2 MUTATED                      8                             2
  BACE2 WILD-TYPE                  307                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  BACE2 MUTATED                       1                              0
  BACE2 WILD-TYPE                   105                             10
D631V10, multiclass
                                clus
vv                               BACE2 MUTATED BACE2 WILD-TYPE
  COLON ADENOCARCINOMA                       8             307
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  BACE2 MUTATED     7   0   0   1
  BACE2 WILD-TYPE 338   4  31  24
D631V11, multiclass
    clus
vv   BACE2 MUTATED BACE2 WILD-TYPE
  R0             7             338
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D631V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  BACE2 MUTATED                                  0     0
  BACE2 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  BACE2 MUTATED                           2     7
  BACE2 WILD-TYPE                        20   219
D631V13, multiclass
                                  clus
vv                                 BACE2 MUTATED BACE2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    2              20
  WHITE                                        7             219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(632) Variable = VAV2 MUTATION ANALYSIS
D632V1, survival
                sevent
clus2              0   1
  VAV2 MUTATED    16   3
  VAV2 WILD-TYPE 362  90
  VAV2 MUTATED VAV2 WILD-TYPE 
            19            452 
  VAV2 MUTATED VAV2 WILD-TYPE 
             3             90 
$`VAV2 MUTATED`
TCGA-A6-6781 TCGA-AA-3534 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-A01R TCGA-CK-4947 
       19.66        29.00         6.05         6.97        35.01        17.56 
TCGA-CM-4743 TCGA-CM-5861 TCGA-CM-5862 TCGA-D5-6533 TCGA-D5-6536 TCGA-D5-6537 
       23.05        15.02         5.03         1.32        17.85         4.80 
TCGA-D5-6541 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AG-A002 
       15.58        35.80        91.79        46.75        79.69        20.98 
TCGA-AG-A02N 
       61.97 

$`VAV2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3538 
       19.07         0.00        19.07        34.03        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 
       13.94        19.99        61.02        78.08        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
       38.07         1.02         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       14.30       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 
        9.99        21.14        82.95         1.91       124.27        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       30.08        32.02        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       18.25        43.27        15.12        17.13        12.49        16.14 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6588 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       26.17        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  VAV2 MUTATED VAV2 WILD-TYPE 
          1.32           0.00 
  VAV2 MUTATED VAV2 WILD-TYPE 
         91.79         148.01 
  VAV2 MUTATED VAV2 WILD-TYPE 
        19.660         20.235 
[1] "1.3 - 91.8 (19.7)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.3"
D632V2, continuous
D632V3, binary
                cls
clus               0   1
  VAV2 MUTATED    17   2
  VAV2 WILD-TYPE 349 117
[1] "tbl2"
                cls
clus             [,1] [,2]
  VAV2 MUTATED     17    2
  VAV2 WILD-TYPE  349  117
        clus
vv       VAV2 MUTATED VAV2 WILD-TYPE
  COLON            17            349
  RECTUM            2            117
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  VAV2 MUTATED         2        0        2         8         0         0
  VAV2 WILD-TYPE      89        1       30       130        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  VAV2 MUTATED           1          0          3          1        1         1
  VAV2 WILD-TYPE        23         11         56         41       47        17
                vv
clus             STAGE IVB
  VAV2 MUTATED           0
  VAV2 WILD-TYPE         1
D632V4, multiclass
            clus
vv           VAV2 MUTATED VAV2 WILD-TYPE
  STAGE I               2             89
  STAGE IA              0              1
  STAGE II              2             30
  STAGE IIA             8            130
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             1             23
  STAGE IIIA            0             11
  STAGE IIIB            3             56
  STAGE IIIC            1             41
  STAGE IV              1             47
  STAGE IVA             1             17
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  VAV2 MUTATED     0   2  13   4
  VAV2 WILD-TYPE  17  90 316  46
D632V5, multiclass
    clus
vv   VAV2 MUTATED VAV2 WILD-TYPE
  T1            0             17
  T2            2             90
  T3           13            316
  T4            4             46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  VAV2 MUTATED    13   4   2
  VAV2 WILD-TYPE 274 109  85
D632V6, multiclass
    clus
vv   VAV2 MUTATED VAV2 WILD-TYPE
  N0           13            274
  N1            4            109
  N2            2             85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D632V7, binary
                cls
clus               0   1
  VAV2 MUTATED    15   2
  VAV2 WILD-TYPE 360  63
[1] "tbl2"
                cls
clus             [,1] [,2]
  VAV2 MUTATED     15    2
  VAV2 WILD-TYPE  360   63
   clus
vv  VAV2 MUTATED VAV2 WILD-TYPE
  0           15            360
  1            2             63
[1] 2 2
[1] FALSE
D632V8, binary
                cls
clus               0   1
  VAV2 MUTATED     7  12
  VAV2 WILD-TYPE 218 252
[1] "tbl2"
                cls
clus             [,1] [,2]
  VAV2 MUTATED      7   12
  VAV2 WILD-TYPE  218  252
        clus
vv       VAV2 MUTATED VAV2 WILD-TYPE
  FEMALE            7            218
  MALE             12            252
[1] 2 2
[1] FALSE
D632V9, binary
                cls
clus               0   1
  VAV2 MUTATED    16   1
  VAV2 WILD-TYPE 334  21
[1] "tbl2"
                cls
clus             [,1] [,2]
  VAV2 MUTATED     16    1
  VAV2 WILD-TYPE  334   21
     clus
vv    VAV2 MUTATED VAV2 WILD-TYPE
  NO            16            334
  YES            1             21
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  VAV2 MUTATED                     15                             2
  VAV2 WILD-TYPE                  300                            45
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  VAV2 MUTATED                       2                              0
  VAV2 WILD-TYPE                   104                             10
D632V10, multiclass
                                clus
vv                               VAV2 MUTATED VAV2 WILD-TYPE
  COLON ADENOCARCINOMA                     15            300
  COLON MUCINOUS ADENOCARCINOMA             2             45
  RECTAL ADENOCARCINOMA                     2            104
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  VAV2 MUTATED    17   0   1   1
  VAV2 WILD-TYPE 328   4  30  24
D632V11, multiclass
    clus
vv   VAV2 MUTATED VAV2 WILD-TYPE
  R0           17            328
  R1            0              4
  R2            1             30
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D632V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  VAV2 MUTATED                                  0     0
  VAV2 WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  VAV2 MUTATED                           0    13
  VAV2 WILD-TYPE                        22   213
D632V13, multiclass
                                  clus
vv                                 VAV2 MUTATED VAV2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                      13            213
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(633) Variable = GAB1 MUTATION ANALYSIS
D633V1, survival
                sevent
clus2              0   1
  GAB1 MUTATED     8   6
  GAB1 WILD-TYPE 370  87
  GAB1 MUTATED GAB1 WILD-TYPE 
            14            457 
  GAB1 MUTATED GAB1 WILD-TYPE 
             6             87 
$`GAB1 MUTATED`
TCGA-A6-2676 TCGA-A6-5665 TCGA-AA-3492 TCGA-AA-3715 TCGA-AA-3854 TCGA-AA-A00N 
       42.90        22.06         3.02        19.04        36.03         4.01 
TCGA-AA-A010 TCGA-AD-6889 TCGA-AZ-6605 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-6679 
       34.98        56.55         5.23        30.08        32.02        10.06 
TCGA-DM-A28C TCGA-G4-6588 
       81.37        26.17 

$`GAB1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       19.66        20.28         7.04         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       85.05        26.99        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
       33.07         0.00        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       15.52         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
       12.10       100.01        29.56        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5861 TCGA-CM-5862 
       13.02        29.06        22.03        22.98        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.08        11.01        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28E 
       44.32       131.51       135.65       139.17         6.12       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       35.80        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  GAB1 MUTATED GAB1 WILD-TYPE 
          3.02           0.00 
  GAB1 MUTATED GAB1 WILD-TYPE 
         81.37         148.01 
  GAB1 MUTATED GAB1 WILD-TYPE 
        28.125         20.050 
[1] "3.0 - 81.4 (28.1)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "2.1"
D633V2, continuous
D633V3, binary
                cls
clus               0   1
  GAB1 MUTATED    15   0
  GAB1 WILD-TYPE 351 119
[1] "tbl2"
                cls
clus             [,1] [,2]
  GAB1 MUTATED     15    0
  GAB1 WILD-TYPE  351  119
        clus
vv       GAB1 MUTATED GAB1 WILD-TYPE
  COLON            15            351
  RECTUM            0            119
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GAB1 MUTATED         1        0        2         8         3         0
  GAB1 WILD-TYPE      90        1       30       130         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  GAB1 MUTATED           0          0          1          0        0         0
  GAB1 WILD-TYPE        24         11         58         42       48        18
                vv
clus             STAGE IVB
  GAB1 MUTATED           0
  GAB1 WILD-TYPE         1
D633V4, multiclass
            clus
vv           GAB1 MUTATED GAB1 WILD-TYPE
  STAGE I               1             90
  STAGE IA              0              1
  STAGE II              2             30
  STAGE IIA             8            130
  STAGE IIB             3              7
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            1             58
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  GAB1 MUTATED     0   1  10   4
  GAB1 WILD-TYPE  17  91 319  46
D633V5, multiclass
    clus
vv   GAB1 MUTATED GAB1 WILD-TYPE
  T1            0             17
  T2            1             91
  T3           10            319
  T4            4             46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  GAB1 MUTATED    14   1   0
  GAB1 WILD-TYPE 273 112  87
D633V6, multiclass
    clus
vv   GAB1 MUTATED GAB1 WILD-TYPE
  N0           14            273
  N1            1            112
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D633V7, binary
                cls
clus               0   1
  GAB1 MUTATED    15   0
  GAB1 WILD-TYPE 360  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  GAB1 MUTATED     15    0
  GAB1 WILD-TYPE  360   65
   clus
vv  GAB1 MUTATED GAB1 WILD-TYPE
  0           15            360
  1            0             65
[1] 2 2
[1] FALSE
D633V8, binary
                cls
clus               0   1
  GAB1 MUTATED     8   7
  GAB1 WILD-TYPE 217 257
[1] "tbl2"
                cls
clus             [,1] [,2]
  GAB1 MUTATED      8    7
  GAB1 WILD-TYPE  217  257
        clus
vv       GAB1 MUTATED GAB1 WILD-TYPE
  FEMALE            8            217
  MALE              7            257
[1] 2 2
[1] FALSE
D633V9, binary
                cls
clus               0   1
  GAB1 MUTATED    11   0
  GAB1 WILD-TYPE 339  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  GAB1 MUTATED     11    0
  GAB1 WILD-TYPE  339   22
     clus
vv    GAB1 MUTATED GAB1 WILD-TYPE
  NO            11            339
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  GAB1 MUTATED                     13                             2
  GAB1 WILD-TYPE                  302                            45
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  GAB1 MUTATED                       0                              0
  GAB1 WILD-TYPE                   106                             10
D633V10, multiclass
                                clus
vv                               GAB1 MUTATED GAB1 WILD-TYPE
  COLON ADENOCARCINOMA                     13            302
  COLON MUCINOUS ADENOCARCINOMA             2             45
  RECTAL ADENOCARCINOMA                     0            106
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  GAB1 MUTATED    12   0   0   0
  GAB1 WILD-TYPE 333   4  31  25
D633V11, multiclass
    clus
vv   GAB1 MUTATED GAB1 WILD-TYPE
  R0           12            333
  R1            0              4
  R2            0             31
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D633V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GAB1 MUTATED                                  0     1
  GAB1 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  GAB1 MUTATED                           0     8
  GAB1 WILD-TYPE                        22   218
D633V13, multiclass
                                  clus
vv                                 GAB1 MUTATED GAB1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       8            218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(634) Variable = RPA3 MUTATION ANALYSIS
D634V1, survival
                sevent
clus2              0   1
  RPA3 MUTATED     4   0
  RPA3 WILD-TYPE 374  93
  RPA3 MUTATED RPA3 WILD-TYPE 
             4            467 
  RPA3 MUTATED RPA3 WILD-TYPE 
             0             93 
$`RPA3 MUTATED`
TCGA-AA-3496 TCGA-AA-3511 TCGA-CM-6676 TCGA-G4-6309 
        1.02         6.97        11.08        85.48 

$`RPA3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01        63.98         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       12.95        13.05        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 
       65.85        53.62        44.68        55.04        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  RPA3 MUTATED RPA3 WILD-TYPE 
          1.02           0.00 
  RPA3 MUTATED RPA3 WILD-TYPE 
         85.48         148.01 
  RPA3 MUTATED RPA3 WILD-TYPE 
         9.025         20.280 
[1] "1.0 - 85.5 (9.0)"   "0.0 - 148.0 (20.3)"
[1] "hr="     "3300000"
D634V2, continuous
D634V3, binary
                cls
clus               0   1
  RPA3 MUTATED     4   0
  RPA3 WILD-TYPE 362 119
[1] "tbl2"
                cls
clus             [,1] [,2]
  RPA3 MUTATED      4    0
  RPA3 WILD-TYPE  362  119
        clus
vv       RPA3 MUTATED RPA3 WILD-TYPE
  COLON             4            362
  RECTUM            0            119
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RPA3 MUTATED         1        0        2         0         0         0
  RPA3 WILD-TYPE      90        1       30       138        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RPA3 MUTATED           0          0          1          0        0         0
  RPA3 WILD-TYPE        24         11         58         42       48        18
                vv
clus             STAGE IVB
  RPA3 MUTATED           0
  RPA3 WILD-TYPE         1
D634V4, multiclass
            clus
vv           RPA3 MUTATED RPA3 WILD-TYPE
  STAGE I               1             90
  STAGE IA              0              1
  STAGE II              2             30
  STAGE IIA             0            138
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            1             58
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  RPA3 MUTATED     0   1   2   1
  RPA3 WILD-TYPE  17  91 327  49
D634V5, multiclass
    clus
vv   RPA3 MUTATED RPA3 WILD-TYPE
  T1            0             17
  T2            1             91
  T3            2            327
  T4            1             49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  RPA3 MUTATED     3   1   0
  RPA3 WILD-TYPE 284 112  87
D634V6, multiclass
    clus
vv   RPA3 MUTATED RPA3 WILD-TYPE
  N0            3            284
  N1            1            112
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D634V7, binary
                cls
clus               0   1
  RPA3 MUTATED     4   0
  RPA3 WILD-TYPE 371  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  RPA3 MUTATED      4    0
  RPA3 WILD-TYPE  371   65
   clus
vv  RPA3 MUTATED RPA3 WILD-TYPE
  0            4            371
  1            0             65
[1] 2 2
[1] FALSE
D634V8, binary
                cls
clus               0   1
  RPA3 MUTATED     2   2
  RPA3 WILD-TYPE 223 262
[1] "tbl2"
                cls
clus             [,1] [,2]
  RPA3 MUTATED      2    2
  RPA3 WILD-TYPE  223  262
        clus
vv       RPA3 MUTATED RPA3 WILD-TYPE
  FEMALE            2            223
  MALE              2            262
[1] 2 2
[1] FALSE
D634V9, binary
                cls
clus               0   1
  RPA3 MUTATED     3   0
  RPA3 WILD-TYPE 347  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  RPA3 MUTATED      3    0
  RPA3 WILD-TYPE  347   22
     clus
vv    RPA3 MUTATED RPA3 WILD-TYPE
  NO             3            347
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  RPA3 MUTATED                      4                             0
  RPA3 WILD-TYPE                  311                            47
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  RPA3 MUTATED                       0                              0
  RPA3 WILD-TYPE                   106                             10
D634V10, multiclass
                                clus
vv                               RPA3 MUTATED RPA3 WILD-TYPE
  COLON ADENOCARCINOMA                      4            311
  COLON MUCINOUS ADENOCARCINOMA             0             47
  RECTAL ADENOCARCINOMA                     0            106
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  RPA3 MUTATED     4   0   0   0
  RPA3 WILD-TYPE 341   4  31  25
D634V11, multiclass
    clus
vv   RPA3 MUTATED RPA3 WILD-TYPE
  R0            4            341
  R1            0              4
  R2            0             31
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D634V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RPA3 MUTATED                                  0     0
  RPA3 WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  RPA3 MUTATED                           1     1
  RPA3 WILD-TYPE                        21   225
D634V13, multiclass
[1] "Remove cluster labels:" "RPA3 MUTATED"          
clus
  RPA3 MUTATED RPA3 WILD-TYPE 
             2            258 
    TCGA-A6-2671     TCGA-A6-2672     TCGA-A6-2674     TCGA-A6-2676 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-A6-2677     TCGA-A6-2678     TCGA-A6-2683     TCGA-A6-3807 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-A6-3808     TCGA-A6-3809     TCGA-A6-3810     TCGA-A6-4105 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-A6-5656     TCGA-A6-5657     TCGA-A6-5659     TCGA-A6-5660 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-A6-5661     TCGA-A6-5662     TCGA-A6-5664     TCGA-A6-5665 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-A6-5666     TCGA-A6-6137     TCGA-A6-6138     TCGA-A6-6141 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-A6-6142     TCGA-A6-6648     TCGA-A6-6649     TCGA-A6-6651 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-A6-6652     TCGA-A6-6653     TCGA-A6-6654     TCGA-A6-6780 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-A6-6781     TCGA-A6-6782     TCGA-AD-5900     TCGA-AD-6548 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-AD-6888     TCGA-AD-6889     TCGA-AD-6890     TCGA-AD-6895 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-AD-6899     TCGA-AD-6901     TCGA-AD-6963     TCGA-AD-6964 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-AD-6965     TCGA-AU-3779     TCGA-AU-6004     TCGA-AY-4070 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-AY-4071     TCGA-AY-5543     TCGA-AY-6196     TCGA-AY-6197 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-AY-6386     TCGA-AZ-4315     TCGA-AZ-4323     TCGA-AZ-4616 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-AZ-4681     TCGA-AZ-4682     TCGA-AZ-5403     TCGA-AZ-5407 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-AZ-6598     TCGA-AZ-6599     TCGA-AZ-6600     TCGA-AZ-6601 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-AZ-6603     TCGA-AZ-6605     TCGA-AZ-6606     TCGA-AZ-6607 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-AZ-6608     TCGA-CA-5254     TCGA-CA-5255     TCGA-CA-5796 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-CA-5797     TCGA-CA-6715     TCGA-CA-6716     TCGA-CA-6717 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-CA-6718     TCGA-CA-6719     TCGA-CK-4947     TCGA-CK-4948 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-CK-4950     TCGA-CK-4952     TCGA-CK-5912     TCGA-CK-5913 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-CK-5914     TCGA-CK-5915     TCGA-CK-5916     TCGA-CK-6746 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-CK-6747     TCGA-CK-6748     TCGA-CK-6751     TCGA-CM-4743 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-CM-4744     TCGA-CM-4746     TCGA-CM-4747     TCGA-CM-4752 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-CM-5341     TCGA-CM-5344     TCGA-CM-5348     TCGA-CM-5349 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-CM-5860     TCGA-CM-5861     TCGA-CM-5862     TCGA-CM-5863 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-CM-5864     TCGA-CM-5868     TCGA-CM-6161     TCGA-CM-6162 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-CM-6163     TCGA-CM-6164     TCGA-CM-6165     TCGA-CM-6166 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-CM-6167     TCGA-CM-6168     TCGA-CM-6169     TCGA-CM-6170 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-CM-6171     TCGA-CM-6172     TCGA-CM-6674     TCGA-CM-6675 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-CM-6677     TCGA-CM-6678     TCGA-CM-6679     TCGA-CM-6680 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-D5-5537     TCGA-D5-5538     TCGA-D5-5539     TCGA-D5-5540 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-D5-5541     TCGA-D5-6529     TCGA-D5-6532     TCGA-D5-6533 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-D5-6534     TCGA-D5-6535     TCGA-D5-6536     TCGA-D5-6537 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-D5-6538     TCGA-D5-6539     TCGA-D5-6540     TCGA-D5-6541 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-D5-6898     TCGA-D5-6920     TCGA-D5-6922     TCGA-D5-6923 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-D5-6924     TCGA-D5-6926     TCGA-D5-6927     TCGA-D5-6928 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-D5-6929     TCGA-D5-6930     TCGA-D5-6931     TCGA-D5-6932 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-D5-7000     TCGA-DM-A0X9     TCGA-DM-A0XD     TCGA-DM-A0XF 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-DM-A1D0     TCGA-DM-A1D4     TCGA-DM-A1D6     TCGA-DM-A1D7 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-DM-A1D8     TCGA-DM-A1D9     TCGA-DM-A1DA     TCGA-DM-A1DB 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-DM-A1HA     TCGA-DM-A1HB     TCGA-DM-A282     TCGA-DM-A285 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-DM-A28C     TCGA-DM-A28E     TCGA-DM-A28F     TCGA-DM-A28G 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-DM-A28H     TCGA-DM-A28K     TCGA-F4-6459     TCGA-F4-6460 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-F4-6569     TCGA-F4-6570     TCGA-F4-6703     TCGA-F4-6704 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-F4-6805     TCGA-F4-6806     TCGA-F4-6807     TCGA-F4-6808 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-F4-6809     TCGA-F4-6854     TCGA-F4-6855     TCGA-F4-6856 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-G4-6293     TCGA-G4-6299     TCGA-G4-6303     TCGA-G4-6304 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-G4-6306     TCGA-G4-6307     TCGA-G4-6310     TCGA-G4-6315 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-G4-6317     TCGA-G4-6321     TCGA-G4-6323     TCGA-G4-6586 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-G4-6588     TCGA-G4-6625     TCGA-G4-6626     TCGA-G4-6628 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-AF-2687     TCGA-AF-2689     TCGA-AF-2691     TCGA-AF-2692 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-AF-2693     TCGA-AF-3400     TCGA-AF-3913     TCGA-AF-4110 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-AF-5654     TCGA-AF-6136     TCGA-AF-6655     TCGA-AF-6672 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-AH-6544     TCGA-AH-6547     TCGA-AH-6549     TCGA-AH-6643 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-AH-6644     TCGA-CI-6619     TCGA-CI-6620     TCGA-CI-6621 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-CI-6622     TCGA-CI-6624     TCGA-CL-5917     TCGA-CL-5918 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-DC-5337     TCGA-DC-5869     TCGA-DC-6155     TCGA-DC-6157 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-DC-6158     TCGA-DC-6160     TCGA-DC-6681     TCGA-DC-6682 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-DC-6683     TCGA-DT-5265     TCGA-DY-A0XA     TCGA-DY-A1DC 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-DY-A1DD     TCGA-DY-A1DF     TCGA-DY-A1DG     TCGA-DY-A1H8 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-EF-5830     TCGA-EI-6506     TCGA-EI-6507     TCGA-EI-6508 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-EI-6510     TCGA-F5-6464     TCGA-F5-6465     TCGA-F5-6571 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-F5-6702     TCGA-F5-6811     TCGA-F5-6812     TCGA-F5-6813 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 
    TCGA-G5-6235     TCGA-G5-6641 
"RPA3 WILD-TYPE" "RPA3 WILD-TYPE" 

Clustering(635) Variable = GPR61 MUTATION ANALYSIS
D635V1, survival
                 sevent
clus2               0   1
  GPR61 MUTATED     9   2
  GPR61 WILD-TYPE 369  91
  GPR61 MUTATED GPR61 WILD-TYPE 
             11             460 
  GPR61 MUTATED GPR61 WILD-TYPE 
              2              91 
$`GPR61 MUTATED`
TCGA-AA-3492 TCGA-AA-3667 TCGA-AA-3715 TCGA-AA-3980 TCGA-AZ-4315 TCGA-CM-5860 
        3.02        14.01        19.04        27.02        58.39        32.02 
TCGA-D5-6536 TCGA-G4-6299 TCGA-AF-6672 TCGA-CL-5918 TCGA-EI-6507 
       17.85        74.56        10.39         7.17        19.96 

$`GPR61 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
        6.97        54.02         2.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        25.02        24.00        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.03        22.98        30.08        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       15.12         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
      133.18        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       16.83        15.39        20.02        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-DC-5337 
        6.05        33.17         6.97         4.73        78.12        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6508 
       24.13        51.48        32.61         0.49        20.55        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  GPR61 MUTATED GPR61 WILD-TYPE 
           3.02            0.00 
  GPR61 MUTATED GPR61 WILD-TYPE 
          74.56          148.01 
  GPR61 MUTATED GPR61 WILD-TYPE 
         19.040          20.415 
[1] "3.0 - 74.6 (19.0)"  "0.0 - 148.0 (20.4)"
[1] "hr=" "1.1"
D635V2, continuous
D635V3, binary
                 cls
clus                0   1
  GPR61 MUTATED     9   3
  GPR61 WILD-TYPE 357 116
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPR61 MUTATED      9    3
  GPR61 WILD-TYPE  357  116
        clus
vv       GPR61 MUTATED GPR61 WILD-TYPE
  COLON              9             357
  RECTUM             3             116
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GPR61 MUTATED         2        0        2         6         0         0
  GPR61 WILD-TYPE      89        1       30       132        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  GPR61 MUTATED           0          0          0          1        1         0
  GPR61 WILD-TYPE        24         11         59         41       47        18
                 vv
clus              STAGE IVB
  GPR61 MUTATED           0
  GPR61 WILD-TYPE         1
D635V4, multiclass
            clus
vv           GPR61 MUTATED GPR61 WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA              6             132
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             1              41
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  GPR61 MUTATED     0   2   9   1
  GPR61 WILD-TYPE  17  90 320  49
D635V5, multiclass
    clus
vv   GPR61 MUTATED GPR61 WILD-TYPE
  T1             0              17
  T2             2              90
  T3             9             320
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  GPR61 MUTATED    10   0   2
  GPR61 WILD-TYPE 277 113  85
D635V6, multiclass
    clus
vv   GPR61 MUTATED GPR61 WILD-TYPE
  N0            10             277
  N1             0             113
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D635V7, binary
                 cls
clus                0   1
  GPR61 MUTATED    10   0
  GPR61 WILD-TYPE 365  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPR61 MUTATED     10    0
  GPR61 WILD-TYPE  365   65
   clus
vv  GPR61 MUTATED GPR61 WILD-TYPE
  0            10             365
  1             0              65
[1] 2 2
[1] FALSE
D635V8, binary
                 cls
clus                0   1
  GPR61 MUTATED     5   7
  GPR61 WILD-TYPE 220 257
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPR61 MUTATED      5    7
  GPR61 WILD-TYPE  220  257
        clus
vv       GPR61 MUTATED GPR61 WILD-TYPE
  FEMALE             5             220
  MALE               7             257
[1] 2 2
[1] FALSE
D635V9, binary
                 cls
clus                0   1
  GPR61 MUTATED    10   1
  GPR61 WILD-TYPE 340  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPR61 MUTATED     10    1
  GPR61 WILD-TYPE  340   21
     clus
vv    GPR61 MUTATED GPR61 WILD-TYPE
  NO             10             340
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  GPR61 MUTATED                      9                             0
  GPR61 WILD-TYPE                  306                            47
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  GPR61 MUTATED                       3                              0
  GPR61 WILD-TYPE                   103                             10
D635V10, multiclass
                                clus
vv                               GPR61 MUTATED GPR61 WILD-TYPE
  COLON ADENOCARCINOMA                       9             306
  COLON MUCINOUS ADENOCARCINOMA              0              47
  RECTAL ADENOCARCINOMA                      3             103
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  GPR61 MUTATED     9   0   0   1
  GPR61 WILD-TYPE 336   4  31  24
D635V11, multiclass
    clus
vv   GPR61 MUTATED GPR61 WILD-TYPE
  R0             9             336
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D635V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GPR61 MUTATED                                  0     0
  GPR61 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  GPR61 MUTATED                           0     7
  GPR61 WILD-TYPE                        22   219
D635V13, multiclass
                                  clus
vv                                 GPR61 MUTATED GPR61 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        7             219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(636) Variable = OAS1 MUTATION ANALYSIS
D636V1, survival
                sevent
clus2              0   1
  OAS1 MUTATED     5   3
  OAS1 WILD-TYPE 373  90
  OAS1 MUTATED OAS1 WILD-TYPE 
             8            463 
  OAS1 MUTATED OAS1 WILD-TYPE 
             3             90 
$`OAS1 MUTATED`
TCGA-AA-3660 TCGA-AA-3845 TCGA-AA-3950 TCGA-AZ-4315 TCGA-D5-6534 TCGA-DM-A285 
       78.08         0.00        24.00        58.39        43.27         6.12 
TCGA-G4-6307 TCGA-DY-A1DG 
       55.04        51.48 

$`OAS1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 
       20.98        19.99        13.94        19.99        61.02         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 
       17.98        15.95        38.99        37.02        14.93        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 
       12.99        24.00        33.01        26.01         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
        1.32        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A28C 
        7.50        44.32       131.51       135.65       139.17        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 
      126.44        41.36        57.24        24.13        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  OAS1 MUTATED OAS1 WILD-TYPE 
             0              0 
  OAS1 MUTATED OAS1 WILD-TYPE 
         78.08         148.01 
  OAS1 MUTATED OAS1 WILD-TYPE 
        47.375         20.050 
[1] "0.0 - 78.1 (47.4)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.2"
D636V2, continuous
D636V3, binary
                cls
clus               0   1
  OAS1 MUTATED     8   1
  OAS1 WILD-TYPE 358 118
[1] "tbl2"
                cls
clus             [,1] [,2]
  OAS1 MUTATED      8    1
  OAS1 WILD-TYPE  358  118
        clus
vv       OAS1 MUTATED OAS1 WILD-TYPE
  COLON             8            358
  RECTUM            1            118
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  OAS1 MUTATED         0        0        1         5         0         0
  OAS1 WILD-TYPE      91        1       31       133        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  OAS1 MUTATED           0          0          1          0        1         1
  OAS1 WILD-TYPE        24         11         58         42       47        17
                vv
clus             STAGE IVB
  OAS1 MUTATED           0
  OAS1 WILD-TYPE         1
D636V4, multiclass
            clus
vv           OAS1 MUTATED OAS1 WILD-TYPE
  STAGE I               0             91
  STAGE IA              0              1
  STAGE II              1             31
  STAGE IIA             5            133
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            1             58
  STAGE IIIC            0             42
  STAGE IV              1             47
  STAGE IVA             1             17
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  OAS1 MUTATED     0   0   9   0
  OAS1 WILD-TYPE  17  92 320  50
D636V5, multiclass
    clus
vv   OAS1 MUTATED OAS1 WILD-TYPE
  T1            0             17
  T2            0             92
  T3            9            320
  T4            0             50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  OAS1 MUTATED     6   2   1
  OAS1 WILD-TYPE 281 111  86
D636V6, multiclass
    clus
vv   OAS1 MUTATED OAS1 WILD-TYPE
  N0            6            281
  N1            2            111
  N2            1             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D636V7, binary
                cls
clus               0   1
  OAS1 MUTATED     7   2
  OAS1 WILD-TYPE 368  63
[1] "tbl2"
                cls
clus             [,1] [,2]
  OAS1 MUTATED      7    2
  OAS1 WILD-TYPE  368   63
   clus
vv  OAS1 MUTATED OAS1 WILD-TYPE
  0            7            368
  1            2             63
[1] 2 2
[1] FALSE
D636V8, binary
                cls
clus               0   1
  OAS1 MUTATED     7   2
  OAS1 WILD-TYPE 218 262
[1] "tbl2"
                cls
clus             [,1] [,2]
  OAS1 MUTATED      7    2
  OAS1 WILD-TYPE  218  262
        clus
vv       OAS1 MUTATED OAS1 WILD-TYPE
  FEMALE            7            218
  MALE              2            262
[1] 2 2
[1] FALSE
D636V9, binary
                cls
clus               0   1
  OAS1 MUTATED     5   0
  OAS1 WILD-TYPE 345  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  OAS1 MUTATED      5    0
  OAS1 WILD-TYPE  345   22
     clus
vv    OAS1 MUTATED OAS1 WILD-TYPE
  NO             5            345
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  OAS1 MUTATED                      5                             3
  OAS1 WILD-TYPE                  310                            44
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  OAS1 MUTATED                       1                              0
  OAS1 WILD-TYPE                   105                             10
D636V10, multiclass
                                clus
vv                               OAS1 MUTATED OAS1 WILD-TYPE
  COLON ADENOCARCINOMA                      5            310
  COLON MUCINOUS ADENOCARCINOMA             3             44
  RECTAL ADENOCARCINOMA                     1            105
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  OAS1 MUTATED     7   0   0   0
  OAS1 WILD-TYPE 338   4  31  25
D636V11, multiclass
    clus
vv   OAS1 MUTATED OAS1 WILD-TYPE
  R0            7            338
  R1            0              4
  R2            0             31
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D636V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OAS1 MUTATED                                  0     0
  OAS1 WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  OAS1 MUTATED                           0     5
  OAS1 WILD-TYPE                        22   221
D636V13, multiclass
                                  clus
vv                                 OAS1 MUTATED OAS1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       5            221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(637) Variable = OLR1 MUTATION ANALYSIS
D637V1, survival
                sevent
clus2              0   1
  OLR1 MUTATED     9   1
  OLR1 WILD-TYPE 369  92
  OLR1 MUTATED OLR1 WILD-TYPE 
            10            461 
  OLR1 MUTATED OLR1 WILD-TYPE 
             1             92 
$`OLR1 MUTATED`
TCGA-A6-5665 TCGA-A6-6649 TCGA-AA-A01R TCGA-AD-5900 TCGA-CM-4752 TCGA-D5-5539 
       22.06        24.16        35.01         0.07        13.02        19.59 
TCGA-DM-A1D7 TCGA-DM-A1HA TCGA-G4-6307 TCGA-AG-3892 
       13.32       131.51        55.04        13.02 

$`OLR1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       25.18        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T 
       31.00        31.00        38.07         1.02         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       18.05        40.96        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-5341 
      124.27        23.05        20.02        37.02        25.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       92.75        49.91        12.59       140.38         7.50        44.32 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6310 
       74.56        65.85        53.62        44.68        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 
       19.99         1.02        17.95        36.95        17.03        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  OLR1 MUTATED OLR1 WILD-TYPE 
          0.07           0.00 
  OLR1 MUTATED OLR1 WILD-TYPE 
        131.51         148.01 
  OLR1 MUTATED OLR1 WILD-TYPE 
        20.825         20.190 
[1] "0.1 - 131.5 (20.8)" "0.0 - 148.0 (20.2)"
[1] "hr=" "2.3"
D637V2, continuous
D637V3, binary
                cls
clus               0   1
  OLR1 MUTATED     9   1
  OLR1 WILD-TYPE 357 118
[1] "tbl2"
                cls
clus             [,1] [,2]
  OLR1 MUTATED      9    1
  OLR1 WILD-TYPE  357  118
        clus
vv       OLR1 MUTATED OLR1 WILD-TYPE
  COLON             9            357
  RECTUM            1            118
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  OLR1 MUTATED         2        0        0         3         0         0
  OLR1 WILD-TYPE      89        1       32       135        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  OLR1 MUTATED           1          1          2          1        0         0
  OLR1 WILD-TYPE        23         10         57         41       48        18
                vv
clus             STAGE IVB
  OLR1 MUTATED           0
  OLR1 WILD-TYPE         1
D637V4, multiclass
            clus
vv           OLR1 MUTATED OLR1 WILD-TYPE
  STAGE I               2             89
  STAGE IA              0              1
  STAGE II              0             32
  STAGE IIA             3            135
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             1             23
  STAGE IIIA            1             10
  STAGE IIIB            2             57
  STAGE IIIC            1             41
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  OLR1 MUTATED     1   1   8   0
  OLR1 WILD-TYPE  16  91 321  50
D637V5, multiclass
    clus
vv   OLR1 MUTATED OLR1 WILD-TYPE
  T1            1             16
  T2            1             91
  T3            8            321
  T4            0             50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  OLR1 MUTATED     5   3   2
  OLR1 WILD-TYPE 282 110  85
D637V6, multiclass
    clus
vv   OLR1 MUTATED OLR1 WILD-TYPE
  N0            5            282
  N1            3            110
  N2            2             85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D637V7, binary
                cls
clus               0   1
  OLR1 MUTATED     9   0
  OLR1 WILD-TYPE 366  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  OLR1 MUTATED      9    0
  OLR1 WILD-TYPE  366   65
   clus
vv  OLR1 MUTATED OLR1 WILD-TYPE
  0            9            366
  1            0             65
[1] 2 2
[1] FALSE
D637V8, binary
                cls
clus               0   1
  OLR1 MUTATED     3   7
  OLR1 WILD-TYPE 222 257
[1] "tbl2"
                cls
clus             [,1] [,2]
  OLR1 MUTATED      3    7
  OLR1 WILD-TYPE  222  257
        clus
vv       OLR1 MUTATED OLR1 WILD-TYPE
  FEMALE            3            222
  MALE              7            257
[1] 2 2
[1] FALSE
D637V9, binary
                cls
clus               0   1
  OLR1 MUTATED     6   1
  OLR1 WILD-TYPE 344  21
[1] "tbl2"
                cls
clus             [,1] [,2]
  OLR1 MUTATED      6    1
  OLR1 WILD-TYPE  344   21
     clus
vv    OLR1 MUTATED OLR1 WILD-TYPE
  NO             6            344
  YES            1             21
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  OLR1 MUTATED                      5                             3
  OLR1 WILD-TYPE                  310                            44
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  OLR1 MUTATED                       1                              0
  OLR1 WILD-TYPE                   105                             10
D637V10, multiclass
                                clus
vv                               OLR1 MUTATED OLR1 WILD-TYPE
  COLON ADENOCARCINOMA                      5            310
  COLON MUCINOUS ADENOCARCINOMA             3             44
  RECTAL ADENOCARCINOMA                     1            105
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  OLR1 MUTATED     7   0   0   0
  OLR1 WILD-TYPE 338   4  31  25
D637V11, multiclass
    clus
vv   OLR1 MUTATED OLR1 WILD-TYPE
  R0            7            338
  R1            0              4
  R2            0             31
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D637V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OLR1 MUTATED                                  0     0
  OLR1 WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  OLR1 MUTATED                           1     7
  OLR1 WILD-TYPE                        21   219
D637V13, multiclass
                                  clus
vv                                 OLR1 MUTATED OLR1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                       7            219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(638) Variable = ELFN2 MUTATION ANALYSIS
D638V1, survival
                 sevent
clus2               0   1
  ELFN2 MUTATED     8   1
  ELFN2 WILD-TYPE 370  92
  ELFN2 MUTATED ELFN2 WILD-TYPE 
              9             462 
  ELFN2 MUTATED ELFN2 WILD-TYPE 
              1              92 
$`ELFN2 MUTATED`
TCGA-AA-3979 TCGA-AD-6895 TCGA-CK-4947 TCGA-CM-5860 TCGA-D5-6533 TCGA-D5-6535 
       24.00         0.72        17.56        32.02         1.32        15.12 
TCGA-D5-6537 TCGA-D5-6927 TCGA-G4-6315 
        4.80         9.44        61.91 

$`ELFN2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       15.52        56.55         0.79         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-4950 
       12.20        12.76        10.06        14.30       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5861 
       13.02        29.06        22.03        22.98        30.08        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       43.27        17.85        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       63.62        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  ELFN2 MUTATED ELFN2 WILD-TYPE 
           0.72            0.00 
  ELFN2 MUTATED ELFN2 WILD-TYPE 
          61.91          148.01 
  ELFN2 MUTATED ELFN2 WILD-TYPE 
         15.120          20.415 
[1] "0.7 - 61.9 (15.1)"  "0.0 - 148.0 (20.4)"
[1] "hr=" "1.3"
D638V2, continuous
D638V3, binary
                 cls
clus                0   1
  ELFN2 MUTATED     9   0
  ELFN2 WILD-TYPE 357 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ELFN2 MUTATED      9    0
  ELFN2 WILD-TYPE  357  119
        clus
vv       ELFN2 MUTATED ELFN2 WILD-TYPE
  COLON              9             357
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ELFN2 MUTATED         0        0        0         3         0         0
  ELFN2 WILD-TYPE      91        1       32       135        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ELFN2 MUTATED           0          0          4          0        1         0
  ELFN2 WILD-TYPE        24         11         55         42       47        18
                 vv
clus              STAGE IVB
  ELFN2 MUTATED           0
  ELFN2 WILD-TYPE         1
D638V4, multiclass
            clus
vv           ELFN2 MUTATED ELFN2 WILD-TYPE
  STAGE I                0              91
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              3             135
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             4              55
  STAGE IIIC             0              42
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ELFN2 MUTATED     0   0   7   2
  ELFN2 WILD-TYPE  17  92 322  48
D638V5, multiclass
    clus
vv   ELFN2 MUTATED ELFN2 WILD-TYPE
  T1             0              17
  T2             0              92
  T3             7             322
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  ELFN2 MUTATED     4   5   0
  ELFN2 WILD-TYPE 283 108  87
D638V6, multiclass
    clus
vv   ELFN2 MUTATED ELFN2 WILD-TYPE
  N0             4             283
  N1             5             108
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D638V7, binary
                 cls
clus                0   1
  ELFN2 MUTATED     5   1
  ELFN2 WILD-TYPE 370  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ELFN2 MUTATED      5    1
  ELFN2 WILD-TYPE  370   64
   clus
vv  ELFN2 MUTATED ELFN2 WILD-TYPE
  0             5             370
  1             1              64
[1] 2 2
[1] FALSE
D638V8, binary
                 cls
clus                0   1
  ELFN2 MUTATED     3   6
  ELFN2 WILD-TYPE 222 258
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ELFN2 MUTATED      3    6
  ELFN2 WILD-TYPE  222  258
        clus
vv       ELFN2 MUTATED ELFN2 WILD-TYPE
  FEMALE             3             222
  MALE               6             258
[1] 2 2
[1] FALSE
D638V9, binary
                 cls
clus                0   1
  ELFN2 MUTATED     7   0
  ELFN2 WILD-TYPE 343  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ELFN2 MUTATED      7    0
  ELFN2 WILD-TYPE  343   22
     clus
vv    ELFN2 MUTATED ELFN2 WILD-TYPE
  NO              7             343
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ELFN2 MUTATED                      9                             0
  ELFN2 WILD-TYPE                  306                            47
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ELFN2 MUTATED                       0                              0
  ELFN2 WILD-TYPE                   106                             10
D638V10, multiclass
                                clus
vv                               ELFN2 MUTATED ELFN2 WILD-TYPE
  COLON ADENOCARCINOMA                       9             306
  COLON MUCINOUS ADENOCARCINOMA              0              47
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  ELFN2 MUTATED     6   0   0   2
  ELFN2 WILD-TYPE 339   4  31  23
D638V11, multiclass
    clus
vv   ELFN2 MUTATED ELFN2 WILD-TYPE
  R0             6             339
  R1             0               4
  R2             0              31
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D638V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ELFN2 MUTATED                                  0     0
  ELFN2 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ELFN2 MUTATED                           0     8
  ELFN2 WILD-TYPE                        22   218
D638V13, multiclass
                                  clus
vv                                 ELFN2 MUTATED ELFN2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        8             218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(639) Variable = ANAPC4 MUTATION ANALYSIS
D639V1, survival
                  sevent
clus2                0   1
  ANAPC4 MUTATED    10   2
  ANAPC4 WILD-TYPE 368  91
  ANAPC4 MUTATED ANAPC4 WILD-TYPE 
              12              459 
  ANAPC4 MUTATED ANAPC4 WILD-TYPE 
               2               91 
$`ANAPC4 MUTATED`
TCGA-A6-6141 TCGA-AA-3697 TCGA-AA-A00N TCGA-AD-5900 TCGA-CA-6717 TCGA-CK-4950 
        8.38        85.05         4.01         0.07        12.76        85.45 
TCGA-CM-6676 TCGA-D5-6538 TCGA-DM-A1D4 TCGA-G4-6315 TCGA-AG-A002 TCGA-F5-6812 
       11.08        17.13        92.75        61.91        20.98         0.66 

$`ANAPC4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 
       22.09        22.06        32.71        27.09        22.52        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       18.05        40.96        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07        12.20        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       14.30        17.56       148.01        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6677 TCGA-CM-6678 
       14.04        11.01        12.95        13.05        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
       17.85         4.80        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-DM-A1D7 
      119.70        24.43        38.20       130.65        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  ANAPC4 MUTATED ANAPC4 WILD-TYPE 
            0.07             0.00 
  ANAPC4 MUTATED ANAPC4 WILD-TYPE 
           92.75           148.01 
  ANAPC4 MUTATED ANAPC4 WILD-TYPE 
          14.945           20.280 
[1] "0.1 - 92.8 (14.9)"  "0.0 - 148.0 (20.3)"
[1] "hr=" "1.6"
D639V2, continuous
D639V3, binary
                  cls
clus                 0   1
  ANAPC4 MUTATED    10   2
  ANAPC4 WILD-TYPE 356 117
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ANAPC4 MUTATED     10    2
  ANAPC4 WILD-TYPE  356  117
        clus
vv       ANAPC4 MUTATED ANAPC4 WILD-TYPE
  COLON              10              356
  RECTUM              2              117
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ANAPC4 MUTATED         3        0        0         4         1         0
  ANAPC4 WILD-TYPE      88        1       32       134         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ANAPC4 MUTATED           1          0          2          0        1
  ANAPC4 WILD-TYPE        23         11         57         42       47
                  vv
clus               STAGE IVA STAGE IVB
  ANAPC4 MUTATED           0         0
  ANAPC4 WILD-TYPE        18         1
D639V4, multiclass
            clus
vv           ANAPC4 MUTATED ANAPC4 WILD-TYPE
  STAGE I                 3               88
  STAGE IA                0                1
  STAGE II                0               32
  STAGE IIA               4              134
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               1               23
  STAGE IIIA              0               11
  STAGE IIIB              2               57
  STAGE IIIC              0               42
  STAGE IV                1               47
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ANAPC4 MUTATED     0   3   8   1
  ANAPC4 WILD-TYPE  17  89 321  49
D639V5, multiclass
    clus
vv   ANAPC4 MUTATED ANAPC4 WILD-TYPE
  T1              0               17
  T2              3               89
  T3              8              321
  T4              1               49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  ANAPC4 MUTATED     9   2   1
  ANAPC4 WILD-TYPE 278 111  86
D639V6, multiclass
    clus
vv   ANAPC4 MUTATED ANAPC4 WILD-TYPE
  N0              9              278
  N1              2              111
  N2              1               86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D639V7, binary
                  cls
clus                 0   1
  ANAPC4 MUTATED    10   1
  ANAPC4 WILD-TYPE 365  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ANAPC4 MUTATED     10    1
  ANAPC4 WILD-TYPE  365   64
   clus
vv  ANAPC4 MUTATED ANAPC4 WILD-TYPE
  0             10              365
  1              1               64
[1] 2 2
[1] FALSE
D639V8, binary
                  cls
clus                 0   1
  ANAPC4 MUTATED     2  10
  ANAPC4 WILD-TYPE 223 254
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ANAPC4 MUTATED      2   10
  ANAPC4 WILD-TYPE  223  254
        clus
vv       ANAPC4 MUTATED ANAPC4 WILD-TYPE
  FEMALE              2              223
  MALE               10              254
[1] 2 2
[1] FALSE
D639V9, binary
                  cls
clus                 0   1
  ANAPC4 MUTATED     8   0
  ANAPC4 WILD-TYPE 342  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ANAPC4 MUTATED      8    0
  ANAPC4 WILD-TYPE  342   22
     clus
vv    ANAPC4 MUTATED ANAPC4 WILD-TYPE
  NO               8              342
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ANAPC4 MUTATED                      7                             3
  ANAPC4 WILD-TYPE                  308                            44
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ANAPC4 MUTATED                       2                              0
  ANAPC4 WILD-TYPE                   104                             10
D639V10, multiclass
                                clus
vv                               ANAPC4 MUTATED ANAPC4 WILD-TYPE
  COLON ADENOCARCINOMA                        7              308
  COLON MUCINOUS ADENOCARCINOMA               3               44
  RECTAL ADENOCARCINOMA                       2              104
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ANAPC4 MUTATED     8   1   0   1
  ANAPC4 WILD-TYPE 337   3  31  24
D639V11, multiclass
    clus
vv   ANAPC4 MUTATED ANAPC4 WILD-TYPE
  R0              8              337
  R1              1                3
  R2              0               31
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D639V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ANAPC4 MUTATED                                  0     1
  ANAPC4 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ANAPC4 MUTATED                           2     6
  ANAPC4 WILD-TYPE                        20   220
D639V13, multiclass
                                  clus
vv                                 ANAPC4 MUTATED ANAPC4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     2               20
  WHITE                                         6              220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(640) Variable = ITGB8 MUTATION ANALYSIS
D640V1, survival
                 sevent
clus2               0   1
  ITGB8 MUTATED     9   2
  ITGB8 WILD-TYPE 369  91
  ITGB8 MUTATED ITGB8 WILD-TYPE 
             11             460 
  ITGB8 MUTATED ITGB8 WILD-TYPE 
              2              91 
$`ITGB8 MUTATED`
TCGA-AA-3713 TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-3977 TCGA-AA-A00N TCGA-AZ-4315 
       19.04        33.01        24.00        25.02         4.01        58.39 
TCGA-AZ-6603 TCGA-G4-6588 TCGA-AG-A002 TCGA-CI-6619 TCGA-EI-6507 
       29.56        26.17        20.98         6.05        19.96 

$`ITGB8 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 
        2.01        12.99        24.00        26.01         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6606 
       49.41         6.77        12.10       100.01         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       35.80        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6508 
       24.13        51.48        32.61         0.49        20.55        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  ITGB8 MUTATED ITGB8 WILD-TYPE 
           4.01            0.00 
  ITGB8 MUTATED ITGB8 WILD-TYPE 
          58.39          148.01 
  ITGB8 MUTATED ITGB8 WILD-TYPE 
         24.000          20.085 
[1] "4.0 - 58.4 (24.0)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1"  
D640V2, continuous
D640V3, binary
                 cls
clus                0   1
  ITGB8 MUTATED     9   3
  ITGB8 WILD-TYPE 357 116
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITGB8 MUTATED      9    3
  ITGB8 WILD-TYPE  357  116
        clus
vv       ITGB8 MUTATED ITGB8 WILD-TYPE
  COLON              9             357
  RECTUM             3             116
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ITGB8 MUTATED         1        0        0         5         2         0
  ITGB8 WILD-TYPE      90        1       32       133         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ITGB8 MUTATED           0          0          0          0        2         0
  ITGB8 WILD-TYPE        24         11         59         42       46        18
                 vv
clus              STAGE IVB
  ITGB8 MUTATED           0
  ITGB8 WILD-TYPE         1
D640V4, multiclass
            clus
vv           ITGB8 MUTATED ITGB8 WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              5             133
  STAGE IIB              2               8
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             0              42
  STAGE IV               2              46
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ITGB8 MUTATED     0   3   7   2
  ITGB8 WILD-TYPE  17  89 322  48
D640V5, multiclass
    clus
vv   ITGB8 MUTATED ITGB8 WILD-TYPE
  T1             0              17
  T2             3              89
  T3             7             322
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  ITGB8 MUTATED    10   2   0
  ITGB8 WILD-TYPE 277 111  87
D640V6, multiclass
    clus
vv   ITGB8 MUTATED ITGB8 WILD-TYPE
  N0            10             277
  N1             2             111
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D640V7, binary
                 cls
clus                0   1
  ITGB8 MUTATED     8   2
  ITGB8 WILD-TYPE 367  63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITGB8 MUTATED      8    2
  ITGB8 WILD-TYPE  367   63
   clus
vv  ITGB8 MUTATED ITGB8 WILD-TYPE
  0             8             367
  1             2              63
[1] 2 2
[1] FALSE
D640V8, binary
                 cls
clus                0   1
  ITGB8 MUTATED     5   7
  ITGB8 WILD-TYPE 220 257
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITGB8 MUTATED      5    7
  ITGB8 WILD-TYPE  220  257
        clus
vv       ITGB8 MUTATED ITGB8 WILD-TYPE
  FEMALE             5             220
  MALE               7             257
[1] 2 2
[1] FALSE
D640V9, binary
                 cls
clus                0   1
  ITGB8 MUTATED     8   1
  ITGB8 WILD-TYPE 342  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITGB8 MUTATED      8    1
  ITGB8 WILD-TYPE  342   21
     clus
vv    ITGB8 MUTATED ITGB8 WILD-TYPE
  NO              8             342
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ITGB8 MUTATED                      6                             3
  ITGB8 WILD-TYPE                  309                            44
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ITGB8 MUTATED                       3                              0
  ITGB8 WILD-TYPE                   103                             10
D640V10, multiclass
                                clus
vv                               ITGB8 MUTATED ITGB8 WILD-TYPE
  COLON ADENOCARCINOMA                       6             309
  COLON MUCINOUS ADENOCARCINOMA              3              44
  RECTAL ADENOCARCINOMA                      3             103
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  ITGB8 MUTATED     8   0   1   0
  ITGB8 WILD-TYPE 337   4  30  25
D640V11, multiclass
    clus
vv   ITGB8 MUTATED ITGB8 WILD-TYPE
  R0             8             337
  R1             0               4
  R2             1              30
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D640V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ITGB8 MUTATED                                  0     0
  ITGB8 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ITGB8 MUTATED                           0     5
  ITGB8 WILD-TYPE                        22   221
D640V13, multiclass
                                  clus
vv                                 ITGB8 MUTATED ITGB8 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        5             221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(641) Variable = PAXIP1 MUTATION ANALYSIS
D641V1, survival
                  sevent
clus2                0   1
  PAXIP1 MUTATED    13   7
  PAXIP1 WILD-TYPE 365  86
  PAXIP1 MUTATED PAXIP1 WILD-TYPE 
              20              451 
  PAXIP1 MUTATED PAXIP1 WILD-TYPE 
               7               86 
$`PAXIP1 MUTATED`
TCGA-A6-6141 TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3811 TCGA-AA-3877 TCGA-AA-3977 
        8.38        20.12        19.66        10.06        31.00        25.02 
TCGA-AA-A00N TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-6601 TCGA-AZ-6607 TCGA-CK-4952 
        4.01        15.52        10.88       100.01         3.19        15.62 
TCGA-CM-6674 TCGA-D5-5539 TCGA-D5-6533 TCGA-DM-A1D4 TCGA-AG-A02N TCGA-DC-6157 
       12.95        19.59         1.32        92.75        61.97        27.95 
TCGA-EI-6507 TCGA-F5-6571 
       19.96        31.30 

$`PAXIP1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 
       22.09        22.06        32.71        27.09        22.52        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3815 
       85.05        26.99        19.04        19.04        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       29.98        18.05         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 
       14.30        17.56       148.01        85.45        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       14.04        11.01        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-5541 
       10.06        12.03        45.40        12.26        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       20.19        18.25        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       24.43        38.20       130.65        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
        1.94        38.96        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       13.97        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
       32.61         0.49        20.55        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       49.51        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  PAXIP1 MUTATED PAXIP1 WILD-TYPE 
            1.32             0.00 
  PAXIP1 MUTATED PAXIP1 WILD-TYPE 
          100.01           148.01 
  PAXIP1 MUTATED PAXIP1 WILD-TYPE 
          19.625           20.910 
[1] "1.3 - 100.0 (19.6)" "0.0 - 148.0 (20.9)"
[1] "hr=" "1.8"
D641V2, continuous
D641V3, binary
                  cls
clus                 0   1
  PAXIP1 MUTATED    16   4
  PAXIP1 WILD-TYPE 350 115
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PAXIP1 MUTATED     16    4
  PAXIP1 WILD-TYPE  350  115
        clus
vv       PAXIP1 MUTATED PAXIP1 WILD-TYPE
  COLON              16              350
  RECTUM              4              115
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PAXIP1 MUTATED         2        0        2         6         1         0
  PAXIP1 WILD-TYPE      89        1       30       132         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PAXIP1 MUTATED           1          1          2          2        1
  PAXIP1 WILD-TYPE        23         10         57         40       47
                  vv
clus               STAGE IVA STAGE IVB
  PAXIP1 MUTATED           0         0
  PAXIP1 WILD-TYPE        18         1
D641V4, multiclass
            clus
vv           PAXIP1 MUTATED PAXIP1 WILD-TYPE
  STAGE I                 2               89
  STAGE IA                0                1
  STAGE II                2               30
  STAGE IIA               6              132
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               1               23
  STAGE IIIA              1               10
  STAGE IIIB              2               57
  STAGE IIIC              2               40
  STAGE IV                1               47
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  PAXIP1 MUTATED     1   2  11   6
  PAXIP1 WILD-TYPE  16  90 318  44
D641V5, multiclass
    clus
vv   PAXIP1 MUTATED PAXIP1 WILD-TYPE
  T1              1               16
  T2              2               90
  T3             11              318
  T4              6               44
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  PAXIP1 MUTATED    13   3   4
  PAXIP1 WILD-TYPE 274 110  83
D641V6, multiclass
    clus
vv   PAXIP1 MUTATED PAXIP1 WILD-TYPE
  N0             13              274
  N1              3              110
  N2              4               83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D641V7, binary
                  cls
clus                 0   1
  PAXIP1 MUTATED    15   1
  PAXIP1 WILD-TYPE 360  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PAXIP1 MUTATED     15    1
  PAXIP1 WILD-TYPE  360   64
   clus
vv  PAXIP1 MUTATED PAXIP1 WILD-TYPE
  0             15              360
  1              1               64
[1] 2 2
[1] FALSE
D641V8, binary
                  cls
clus                 0   1
  PAXIP1 MUTATED     5  15
  PAXIP1 WILD-TYPE 220 249
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PAXIP1 MUTATED      5   15
  PAXIP1 WILD-TYPE  220  249
        clus
vv       PAXIP1 MUTATED PAXIP1 WILD-TYPE
  FEMALE              5              220
  MALE               15              249
[1] 2 2
[1] FALSE
D641V9, binary
                  cls
clus                 0   1
  PAXIP1 MUTATED    14   0
  PAXIP1 WILD-TYPE 336  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PAXIP1 MUTATED     14    0
  PAXIP1 WILD-TYPE  336   22
     clus
vv    PAXIP1 MUTATED PAXIP1 WILD-TYPE
  NO              14              336
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PAXIP1 MUTATED                     10                             6
  PAXIP1 WILD-TYPE                  305                            41
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PAXIP1 MUTATED                       4                              0
  PAXIP1 WILD-TYPE                   102                             10
D641V10, multiclass
                                clus
vv                               PAXIP1 MUTATED PAXIP1 WILD-TYPE
  COLON ADENOCARCINOMA                       10              305
  COLON MUCINOUS ADENOCARCINOMA               6               41
  RECTAL ADENOCARCINOMA                       4              102
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  PAXIP1 MUTATED    12   0   0   1
  PAXIP1 WILD-TYPE 333   4  31  24
D641V11, multiclass
    clus
vv   PAXIP1 MUTATED PAXIP1 WILD-TYPE
  R0             12              333
  R1              0                4
  R2              0               31
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D641V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PAXIP1 MUTATED                                  0     0
  PAXIP1 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  PAXIP1 MUTATED                           2    13
  PAXIP1 WILD-TYPE                        20   213
D641V13, multiclass
                                  clus
vv                                 PAXIP1 MUTATED PAXIP1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     2               20
  WHITE                                        13              213
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(642) Variable = HIST1H1C MUTATION ANALYSIS
D642V1, survival
                    sevent
clus2                  0   1
  HIST1H1C MUTATED     4   0
  HIST1H1C WILD-TYPE 374  93
  HIST1H1C MUTATED HIST1H1C WILD-TYPE 
                 4                467 
  HIST1H1C MUTATED HIST1H1C WILD-TYPE 
                 0                 93 
$`HIST1H1C MUTATED`
TCGA-AA-3510 TCGA-AA-A01V TCGA-AD-6895 TCGA-DM-A0X9 
       63.98        35.01         0.72       119.70 

$`HIST1H1C WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
        1.02        33.04        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
       56.55         0.79         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0XD 
        4.80         1.51        12.00        11.38        10.26        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  HIST1H1C MUTATED HIST1H1C WILD-TYPE 
              0.72               0.00 
  HIST1H1C MUTATED HIST1H1C WILD-TYPE 
            119.70             148.01 
  HIST1H1C MUTATED HIST1H1C WILD-TYPE 
            49.495             20.120 
[1] "0.7 - 119.7 (49.5)" "0.0 - 148.0 (20.1)"
[1] "hr="     "9300000"
D642V2, continuous
D642V3, binary
                    cls
clus                   0   1
  HIST1H1C MUTATED     4   0
  HIST1H1C WILD-TYPE 362 119
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HIST1H1C MUTATED      4    0
  HIST1H1C WILD-TYPE  362  119
        clus
vv       HIST1H1C MUTATED HIST1H1C WILD-TYPE
  COLON                 4                362
  RECTUM                0                119
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  HIST1H1C MUTATED         1        0        1         1         0         0
  HIST1H1C WILD-TYPE      90        1       31       137        10         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HIST1H1C MUTATED           0          0          0          0        0
  HIST1H1C WILD-TYPE        24         11         59         42       48
                    vv
clus                 STAGE IVA STAGE IVB
  HIST1H1C MUTATED           0         0
  HIST1H1C WILD-TYPE        18         1
D642V4, multiclass
            clus
vv           HIST1H1C MUTATED HIST1H1C WILD-TYPE
  STAGE I                   1                 90
  STAGE IA                  0                  1
  STAGE II                  1                 31
  STAGE IIA                 1                137
  STAGE IIB                 0                 10
  STAGE IIC                 0                  1
  STAGE III                 0                 24
  STAGE IIIA                0                 11
  STAGE IIIB                0                 59
  STAGE IIIC                0                 42
  STAGE IV                  0                 48
  STAGE IVA                 0                 18
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  HIST1H1C MUTATED     0   1   3   0
  HIST1H1C WILD-TYPE  17  91 326  50
D642V5, multiclass
    clus
vv   HIST1H1C MUTATED HIST1H1C WILD-TYPE
  T1                0                 17
  T2                1                 91
  T3                3                326
  T4                0                 50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  HIST1H1C MUTATED     3   1   0
  HIST1H1C WILD-TYPE 284 112  87
D642V6, multiclass
    clus
vv   HIST1H1C MUTATED HIST1H1C WILD-TYPE
  N0                3                284
  N1                1                112
  N2                0                 87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D642V7, binary
                    cls
clus                   0   1
  HIST1H1C MUTATED     3   0
  HIST1H1C WILD-TYPE 372  65
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HIST1H1C MUTATED      3    0
  HIST1H1C WILD-TYPE  372   65
   clus
vv  HIST1H1C MUTATED HIST1H1C WILD-TYPE
  0                3                372
  1                0                 65
[1] 2 2
[1] FALSE
D642V8, binary
                    cls
clus                   0   1
  HIST1H1C MUTATED     1   3
  HIST1H1C WILD-TYPE 224 261
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HIST1H1C MUTATED      1    3
  HIST1H1C WILD-TYPE  224  261
        clus
vv       HIST1H1C MUTATED HIST1H1C WILD-TYPE
  FEMALE                1                224
  MALE                  3                261
[1] 2 2
[1] FALSE
D642V9, binary
                    cls
clus                   0   1
  HIST1H1C MUTATED     1   0
  HIST1H1C WILD-TYPE 349  22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HIST1H1C MUTATED      1    0
  HIST1H1C WILD-TYPE  349   22
     clus
vv    HIST1H1C MUTATED HIST1H1C WILD-TYPE
  NO                 1                349
  YES                0                 22
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  HIST1H1C MUTATED                      4                             0
  HIST1H1C WILD-TYPE                  311                            47
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  HIST1H1C MUTATED                       0                              0
  HIST1H1C WILD-TYPE                   106                             10
D642V10, multiclass
                                clus
vv                               HIST1H1C MUTATED HIST1H1C WILD-TYPE
  COLON ADENOCARCINOMA                          4                311
  COLON MUCINOUS ADENOCARCINOMA                 0                 47
  RECTAL ADENOCARCINOMA                         0                106
  RECTAL MUCINOUS ADENOCARCINOMA                0                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  HIST1H1C MUTATED     2   0   0   0
  HIST1H1C WILD-TYPE 343   4  31  25
D642V11, multiclass
[1] "Remove cluster labels:" "HIST1H1C MUTATED"      
clus
  HIST1H1C MUTATED HIST1H1C WILD-TYPE 
                 2                403 
        TCGA-A6-2671         TCGA-A6-2672         TCGA-A6-2674 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-A6-2676         TCGA-A6-2677         TCGA-A6-2678 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-A6-2683         TCGA-A6-3807         TCGA-A6-3808 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-A6-3809         TCGA-A6-3810         TCGA-A6-5657 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-A6-5659         TCGA-A6-5661         TCGA-A6-5665 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-A6-6781         TCGA-AA-3489         TCGA-AA-3492 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-AA-3496         TCGA-AA-3502         TCGA-AA-3511 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-AA-3514         TCGA-AA-3517         TCGA-AA-3518 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-AA-3519         TCGA-AA-3520         TCGA-AA-3521 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-AA-3522         TCGA-AA-3524         TCGA-AA-3525 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-AA-3526         TCGA-AA-3527         TCGA-AA-3529 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-AA-3530         TCGA-AA-3531         TCGA-AA-3532 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-AA-3534         TCGA-AA-3538         TCGA-AA-3542 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-AA-3543         TCGA-AA-3544         TCGA-AA-3548 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-AA-3549         TCGA-AA-3552         TCGA-AA-3553 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-AA-3554         TCGA-AA-3555         TCGA-AA-3556 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-AA-3558         TCGA-AA-3560         TCGA-AA-3561 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-AA-3562         TCGA-AA-3655         TCGA-AA-3660 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-AA-3662         TCGA-AA-3663         TCGA-AA-3664 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-AA-3666         TCGA-AA-3667         TCGA-AA-3672 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-AA-3673         TCGA-AA-3678         TCGA-AA-3679 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-AA-3680         TCGA-AA-3681         TCGA-AA-3684 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-AA-3685         TCGA-AA-3688         TCGA-AA-3692 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-AA-3693         TCGA-AA-3695         TCGA-AA-3696 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-AA-3697         TCGA-AA-3710         TCGA-AA-3712 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-AA-3713         TCGA-AA-3715         TCGA-AA-3811 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-AA-3812         TCGA-AA-3814         TCGA-AA-3815 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-AA-3818         TCGA-AA-3819         TCGA-AA-3821 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-AA-3831         TCGA-AA-3833         TCGA-AA-3837 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-AA-3842         TCGA-AA-3844         TCGA-AA-3845 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-AA-3846         TCGA-AA-3848         TCGA-AA-3850 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-AA-3851         TCGA-AA-3852         TCGA-AA-3854 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-AA-3855         TCGA-AA-3856         TCGA-AA-3858 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-AA-3860         TCGA-AA-3861         TCGA-AA-3864 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-AA-3866         TCGA-AA-3867         TCGA-AA-3869 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-AA-3870         TCGA-AA-3872         TCGA-AA-3875 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-AA-3877         TCGA-AA-3930         TCGA-AA-3939 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-AA-3941         TCGA-AA-3947         TCGA-AA-3949 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-AA-3950         TCGA-AA-3952         TCGA-AA-3955 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-AA-3956         TCGA-AA-3968         TCGA-AA-3971 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-AA-3972         TCGA-AA-3973         TCGA-AA-3975 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-AA-3976         TCGA-AA-3979         TCGA-AA-3984 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-AA-3986         TCGA-AA-3989         TCGA-AA-3994 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-AA-A004         TCGA-AA-A00A         TCGA-AA-A00D 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-AA-A00E         TCGA-AA-A00F         TCGA-AA-A00J 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-AA-A00K         TCGA-AA-A00L         TCGA-AA-A00N 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-AA-A00O         TCGA-AA-A00Q         TCGA-AA-A00R 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-AA-A00U         TCGA-AA-A00W         TCGA-AA-A00Z 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-AA-A010         TCGA-AA-A017         TCGA-AA-A01D 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-AA-A01F         TCGA-AA-A01G         TCGA-AA-A01I 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-AA-A01K         TCGA-AA-A01P         TCGA-AA-A01Q 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-AA-A01R         TCGA-AA-A01S         TCGA-AA-A01T 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-AA-A01X         TCGA-AA-A01Z         TCGA-AA-A022 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-AA-A024         TCGA-AA-A029         TCGA-AA-A02F 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-AA-A02H         TCGA-AA-A02J         TCGA-AA-A02K 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-AA-A02O         TCGA-AA-A02W         TCGA-AA-A02Y 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-AA-A03F         TCGA-AA-A03J         TCGA-AD-5900 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-AD-6548         TCGA-AD-6888         TCGA-AU-3779 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-AU-6004         TCGA-AY-4070         TCGA-AY-4071 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-AY-5543         TCGA-AY-6196         TCGA-AY-6197 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-AY-6386         TCGA-AZ-4315         TCGA-AZ-4681 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-AZ-4682         TCGA-CA-5254         TCGA-CA-5255 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-CA-5796         TCGA-CA-5797         TCGA-CA-6715 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-CA-6716         TCGA-CA-6717         TCGA-CA-6718 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-CA-6719         TCGA-CK-4947         TCGA-CK-4948 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-CK-4950         TCGA-CK-4952         TCGA-CK-5912 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-CK-5913         TCGA-CK-5914         TCGA-CK-5915 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-CK-5916         TCGA-CK-6746         TCGA-CK-6747 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-CK-6748         TCGA-CK-6751         TCGA-CM-4743 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-CM-4744         TCGA-CM-4746         TCGA-CM-4747 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-CM-4752         TCGA-CM-5341         TCGA-CM-5344 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-CM-5348         TCGA-CM-5349         TCGA-CM-5860 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-CM-5861         TCGA-CM-5862         TCGA-CM-5863 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-CM-5864         TCGA-CM-5868         TCGA-CM-6161 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-CM-6162         TCGA-CM-6163         TCGA-CM-6164 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-CM-6165         TCGA-CM-6166         TCGA-CM-6167 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-CM-6168         TCGA-CM-6169         TCGA-CM-6170 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-CM-6171         TCGA-CM-6172         TCGA-CM-6674 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-CM-6675         TCGA-CM-6676         TCGA-CM-6677 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-CM-6678         TCGA-CM-6679         TCGA-CM-6680 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-D5-5537         TCGA-D5-5538         TCGA-D5-5539 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-D5-5540         TCGA-D5-5541         TCGA-D5-6529 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-D5-6532         TCGA-D5-6533         TCGA-D5-6534 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-D5-6535         TCGA-D5-6536         TCGA-D5-6537 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-D5-6538         TCGA-D5-6539         TCGA-D5-6540 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-D5-6541         TCGA-D5-6898         TCGA-D5-6920 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-D5-6922         TCGA-D5-6923         TCGA-D5-6924 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-D5-6926         TCGA-D5-6927         TCGA-D5-6928 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-D5-6929         TCGA-D5-6930         TCGA-D5-6931 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-D5-6932         TCGA-D5-7000         TCGA-F4-6459 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-F4-6460         TCGA-F4-6569         TCGA-F4-6570 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-F4-6703         TCGA-F4-6704         TCGA-F4-6805 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-F4-6806         TCGA-F4-6807         TCGA-F4-6808 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-F4-6809         TCGA-F4-6854         TCGA-F4-6855 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-F4-6856         TCGA-G4-6293         TCGA-G4-6299 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-G4-6303         TCGA-G4-6304         TCGA-G4-6306 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-G4-6307         TCGA-G4-6309         TCGA-G4-6310 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-G4-6315         TCGA-G4-6317         TCGA-G4-6321 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-G4-6323         TCGA-G4-6586         TCGA-G4-6588 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-G4-6625         TCGA-G4-6626         TCGA-G4-6628 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2691 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-AF-2692         TCGA-AF-3400         TCGA-AF-3913 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6655 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-AG-3574         TCGA-AG-3575         TCGA-AG-3578 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-AG-3580         TCGA-AG-3581         TCGA-AG-3582 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-AG-3583         TCGA-AG-3584         TCGA-AG-3586 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-AG-3587         TCGA-AG-3593         TCGA-AG-3594 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-AG-3598         TCGA-AG-3599         TCGA-AG-3600 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-AG-3601         TCGA-AG-3602         TCGA-AG-3605 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-AG-3608         TCGA-AG-3609         TCGA-AG-3611 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-AG-3612         TCGA-AG-3726         TCGA-AG-3727 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3732         TCGA-AG-3742 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-AG-3878         TCGA-AG-3882         TCGA-AG-3883 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-AG-3885         TCGA-AG-3887         TCGA-AG-3890 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-AG-3892         TCGA-AG-3893         TCGA-AG-3894 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-AG-3896         TCGA-AG-3898         TCGA-AG-3901 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-AG-3902         TCGA-AG-3909         TCGA-AG-3999 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-AG-4001         TCGA-AG-4005         TCGA-AG-4007 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4015         TCGA-AG-A002 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01L 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-AG-A01W         TCGA-AG-A01Y         TCGA-AG-A020 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-AG-A036         TCGA-AH-6549         TCGA-AH-6643 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-CL-5917         TCGA-CL-5918         TCGA-DC-5337 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6155         TCGA-DC-6157 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-DC-6158         TCGA-DC-6160         TCGA-DC-6681 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-DC-6682         TCGA-DC-6683         TCGA-DT-5265 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-EF-5830         TCGA-EI-6506         TCGA-EI-6507 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-EI-6508         TCGA-EI-6510         TCGA-F5-6464 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-F5-6465         TCGA-F5-6571         TCGA-F5-6702 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-G5-6235 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-G5-6641 
"HIST1H1C WILD-TYPE" 
D642V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HIST1H1C MUTATED                                  0     0
  HIST1H1C WILD-TYPE                                1    11
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  HIST1H1C MUTATED                           0     2
  HIST1H1C WILD-TYPE                        22   224
D642V13, multiclass
[1] "Remove cluster labels:" "HIST1H1C MUTATED"      
clus
  HIST1H1C MUTATED HIST1H1C WILD-TYPE 
                 2                258 
        TCGA-A6-2671         TCGA-A6-2672         TCGA-A6-2674 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-A6-2676         TCGA-A6-2677         TCGA-A6-2678 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-A6-2683         TCGA-A6-3807         TCGA-A6-3808 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-A6-3809         TCGA-A6-3810         TCGA-A6-4105 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-A6-5656         TCGA-A6-5657         TCGA-A6-5659 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-A6-5660         TCGA-A6-5661         TCGA-A6-5662 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-A6-5664         TCGA-A6-5665         TCGA-A6-5666 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-A6-6137         TCGA-A6-6138         TCGA-A6-6141 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-A6-6142         TCGA-A6-6648         TCGA-A6-6649 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-A6-6651         TCGA-A6-6652         TCGA-A6-6653 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-A6-6654         TCGA-A6-6780         TCGA-A6-6781 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-A6-6782         TCGA-AD-5900         TCGA-AD-6548 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-AD-6888         TCGA-AD-6889         TCGA-AD-6890 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-AD-6899         TCGA-AD-6901         TCGA-AD-6963 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-AD-6964         TCGA-AD-6965         TCGA-AU-3779 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-AU-6004         TCGA-AY-4070         TCGA-AY-4071 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-AY-5543         TCGA-AY-6196         TCGA-AY-6197 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-AY-6386         TCGA-AZ-4315         TCGA-AZ-4323 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-AZ-4616         TCGA-AZ-4681         TCGA-AZ-4682 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-AZ-5403         TCGA-AZ-5407         TCGA-AZ-6598 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-AZ-6599         TCGA-AZ-6600         TCGA-AZ-6601 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-AZ-6603         TCGA-AZ-6605         TCGA-AZ-6606 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-AZ-6607         TCGA-AZ-6608         TCGA-CA-5254 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-CA-5255         TCGA-CA-5796         TCGA-CA-5797 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-CA-6715         TCGA-CA-6716         TCGA-CA-6717 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-CA-6718         TCGA-CA-6719         TCGA-CK-4947 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-CK-4948         TCGA-CK-4950         TCGA-CK-4952 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-CK-5912         TCGA-CK-5913         TCGA-CK-5914 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-CK-5915         TCGA-CK-5916         TCGA-CK-6746 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-CK-6747         TCGA-CK-6748         TCGA-CK-6751 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-CM-4743         TCGA-CM-4744         TCGA-CM-4746 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-CM-4747         TCGA-CM-4752         TCGA-CM-5341 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-CM-5344         TCGA-CM-5348         TCGA-CM-5349 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-CM-5860         TCGA-CM-5861         TCGA-CM-5862 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-CM-5863         TCGA-CM-5864         TCGA-CM-5868 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-CM-6161         TCGA-CM-6162         TCGA-CM-6163 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-CM-6164         TCGA-CM-6165         TCGA-CM-6166 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-CM-6167         TCGA-CM-6168         TCGA-CM-6169 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-CM-6170         TCGA-CM-6171         TCGA-CM-6172 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-CM-6674         TCGA-CM-6675         TCGA-CM-6676 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-CM-6677         TCGA-CM-6678         TCGA-CM-6679 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-CM-6680         TCGA-D5-5537         TCGA-D5-5538 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-D5-5539         TCGA-D5-5540         TCGA-D5-5541 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-D5-6529         TCGA-D5-6532         TCGA-D5-6533 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-D5-6534         TCGA-D5-6535         TCGA-D5-6536 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-D5-6537         TCGA-D5-6538         TCGA-D5-6539 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-D5-6540         TCGA-D5-6541         TCGA-D5-6898 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-D5-6920         TCGA-D5-6922         TCGA-D5-6923 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-D5-6924         TCGA-D5-6926         TCGA-D5-6927 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-D5-6928         TCGA-D5-6929         TCGA-D5-6930 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-D5-6931         TCGA-D5-6932         TCGA-D5-7000 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-DM-A0XD         TCGA-DM-A0XF         TCGA-DM-A1D0 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-DM-A1D4         TCGA-DM-A1D6         TCGA-DM-A1D7 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-DM-A1D8         TCGA-DM-A1D9         TCGA-DM-A1DA 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-DM-A1DB         TCGA-DM-A1HA         TCGA-DM-A1HB 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-DM-A282         TCGA-DM-A285         TCGA-DM-A28C 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-DM-A28E         TCGA-DM-A28F         TCGA-DM-A28G 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-DM-A28H         TCGA-DM-A28K         TCGA-F4-6459 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-F4-6460         TCGA-F4-6569         TCGA-F4-6570 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-F4-6703         TCGA-F4-6704         TCGA-F4-6805 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-F4-6806         TCGA-F4-6807         TCGA-F4-6808 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-F4-6809         TCGA-F4-6854         TCGA-F4-6855 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-F4-6856         TCGA-G4-6293         TCGA-G4-6299 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-G4-6303         TCGA-G4-6304         TCGA-G4-6306 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-G4-6307         TCGA-G4-6309         TCGA-G4-6310 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-G4-6315         TCGA-G4-6317         TCGA-G4-6321 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-G4-6323         TCGA-G4-6586         TCGA-G4-6588 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-G4-6625         TCGA-G4-6626         TCGA-G4-6628 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2691 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-AF-2692         TCGA-AF-2693         TCGA-AF-3400 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-AF-3913         TCGA-AF-4110         TCGA-AF-5654 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-AF-6136         TCGA-AF-6655         TCGA-AF-6672 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6549 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-AH-6643         TCGA-AH-6644         TCGA-CI-6619 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-CI-6620         TCGA-CI-6621         TCGA-CI-6622 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-CI-6624         TCGA-CL-5917         TCGA-CL-5918 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-DC-5337         TCGA-DC-5869         TCGA-DC-6155 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-DC-6157         TCGA-DC-6158         TCGA-DC-6160 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-DC-6681         TCGA-DC-6682         TCGA-DC-6683 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-DT-5265         TCGA-DY-A0XA         TCGA-DY-A1DC 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-DY-A1DD         TCGA-DY-A1DF         TCGA-DY-A1DG 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-DY-A1H8         TCGA-EF-5830         TCGA-EI-6506 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6510 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-F5-6464         TCGA-F5-6465         TCGA-F5-6571 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6811         TCGA-F5-6812 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 
        TCGA-F5-6813         TCGA-G5-6235         TCGA-G5-6641 
"HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" "HIST1H1C WILD-TYPE" 

Clustering(643) Variable = IL18R1 MUTATION ANALYSIS
D643V1, survival
                  sevent
clus2                0   1
  IL18R1 MUTATED    14   2
  IL18R1 WILD-TYPE 364  91
  IL18R1 MUTATED IL18R1 WILD-TYPE 
              16              455 
  IL18R1 MUTATED IL18R1 WILD-TYPE 
               2               91 
$`IL18R1 MUTATED`
TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3516 TCGA-AA-3672 TCGA-AA-3815 TCGA-AA-3877 
        3.02        63.98        13.02         0.92        33.04        31.00 
TCGA-AA-3955 TCGA-AA-3971 TCGA-AA-A010 TCGA-AA-A02O TCGA-CK-6751 TCGA-F4-6703 
       20.98        16.08        34.98         0.92       124.27        47.87 
TCGA-G4-6306 TCGA-AF-2687 TCGA-AG-3892 TCGA-AG-A002 
       44.68        24.13        13.02        20.98 

$`IL18R1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
       35.01         6.97         1.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
        2.01        14.01        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
       26.99        19.04        19.04        10.06        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       18.05         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3972 
       24.00         2.01        34.03         2.01        21.99        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        2.01         5.03        14.01        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6704 TCGA-F4-6805 
        8.61        31.96        35.74         6.18         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6307 
       35.31       133.18        74.56        65.85        53.62        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2689 
       35.80        26.17        91.79        46.75        79.69        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  IL18R1 MUTATED IL18R1 WILD-TYPE 
            0.92             0.00 
  IL18R1 MUTATED IL18R1 WILD-TYPE 
          124.27           148.01 
  IL18R1 MUTATED IL18R1 WILD-TYPE 
          22.555           20.050 
[1] "0.9 - 124.3 (22.6)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.8"
D643V2, continuous
D643V3, binary
                  cls
clus                 0   1
  IL18R1 MUTATED    13   3
  IL18R1 WILD-TYPE 353 116
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IL18R1 MUTATED     13    3
  IL18R1 WILD-TYPE  353  116
        clus
vv       IL18R1 MUTATED IL18R1 WILD-TYPE
  COLON              13              353
  RECTUM              3              116
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  IL18R1 MUTATED         4        0        3         3         1         0
  IL18R1 WILD-TYPE      87        1       29       135         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  IL18R1 MUTATED           3          0          1          1        0
  IL18R1 WILD-TYPE        21         11         58         41       48
                  vv
clus               STAGE IVA STAGE IVB
  IL18R1 MUTATED           0         0
  IL18R1 WILD-TYPE        18         1
D643V4, multiclass
            clus
vv           IL18R1 MUTATED IL18R1 WILD-TYPE
  STAGE I                 4               87
  STAGE IA                0                1
  STAGE II                3               29
  STAGE IIA               3              135
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               3               21
  STAGE IIIA              0               11
  STAGE IIIB              1               58
  STAGE IIIC              1               41
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  IL18R1 MUTATED     2   4   9   1
  IL18R1 WILD-TYPE  15  88 320  49
D643V5, multiclass
    clus
vv   IL18R1 MUTATED IL18R1 WILD-TYPE
  T1              2               15
  T2              4               88
  T3              9              320
  T4              1               49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  IL18R1 MUTATED    11   2   3
  IL18R1 WILD-TYPE 276 111  84
D643V6, multiclass
    clus
vv   IL18R1 MUTATED IL18R1 WILD-TYPE
  N0             11              276
  N1              2              111
  N2              3               84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D643V7, binary
                  cls
clus                 0   1
  IL18R1 MUTATED    15   0
  IL18R1 WILD-TYPE 360  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IL18R1 MUTATED     15    0
  IL18R1 WILD-TYPE  360   65
   clus
vv  IL18R1 MUTATED IL18R1 WILD-TYPE
  0             15              360
  1              0               65
[1] 2 2
[1] FALSE
D643V8, binary
                  cls
clus                 0   1
  IL18R1 MUTATED     8   8
  IL18R1 WILD-TYPE 217 256
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IL18R1 MUTATED      8    8
  IL18R1 WILD-TYPE  217  256
        clus
vv       IL18R1 MUTATED IL18R1 WILD-TYPE
  FEMALE              8              217
  MALE                8              256
[1] 2 2
[1] FALSE
D643V9, binary
                  cls
clus                 0   1
  IL18R1 MUTATED    14   1
  IL18R1 WILD-TYPE 336  21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IL18R1 MUTATED     14    1
  IL18R1 WILD-TYPE  336   21
     clus
vv    IL18R1 MUTATED IL18R1 WILD-TYPE
  NO              14              336
  YES              1               21
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  IL18R1 MUTATED                     10                             3
  IL18R1 WILD-TYPE                  305                            44
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  IL18R1 MUTATED                       3                              0
  IL18R1 WILD-TYPE                   103                             10
D643V10, multiclass
                                clus
vv                               IL18R1 MUTATED IL18R1 WILD-TYPE
  COLON ADENOCARCINOMA                       10              305
  COLON MUCINOUS ADENOCARCINOMA               3               44
  RECTAL ADENOCARCINOMA                       3              103
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  IL18R1 MUTATED    14   0   0   1
  IL18R1 WILD-TYPE 331   4  31  24
D643V11, multiclass
    clus
vv   IL18R1 MUTATED IL18R1 WILD-TYPE
  R0             14              331
  R1              0                4
  R2              0               31
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D643V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  IL18R1 MUTATED                                  0     0
  IL18R1 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  IL18R1 MUTATED                           0     4
  IL18R1 WILD-TYPE                        22   222
D643V13, multiclass
                                  clus
vv                                 IL18R1 MUTATED IL18R1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         4              222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(644) Variable = IBTK MUTATION ANALYSIS
D644V1, survival
                sevent
clus2              0   1
  IBTK MUTATED    16   6
  IBTK WILD-TYPE 362  87
  IBTK MUTATED IBTK WILD-TYPE 
            22            449 
  IBTK MUTATED IBTK WILD-TYPE 
             6             87 
$`IBTK MUTATED`
TCGA-A6-5661 TCGA-AA-3516 TCGA-AA-3543 TCGA-AA-3663 TCGA-AA-3672 TCGA-AA-3715 
       33.53        13.02         0.99         6.97         0.92        19.04 
TCGA-AA-3815 TCGA-AA-A010 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-AZ-6603 TCGA-AZ-6607 
       33.04        34.98        58.39        49.41        29.56         3.19 
TCGA-CK-5913 TCGA-CK-6748 TCGA-DM-A1D0 TCGA-F4-6459 TCGA-F4-6806 TCGA-G4-6321 
       51.32         1.91       130.65         8.61        41.42        22.09 
TCGA-G4-6628 TCGA-AG-3892 TCGA-AG-A002 TCGA-F5-6571 
       79.69        13.02        20.98        31.30 

$`IBTK WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
       12.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02        78.08         6.05        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
       14.01        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       19.04        10.06        35.05         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       33.01        21.44        17.82         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        88.21         6.77        12.10       100.01 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 
       17.56       148.01        85.45        15.62        49.08         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       21.14        82.95       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
      119.70        24.43        38.20        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
      117.07        98.24        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
        1.55        34.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 
       13.78        35.80        26.17        91.79        46.75        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       17.03        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6702 
       19.96        20.91        18.28         9.96        49.51        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  IBTK MUTATED IBTK WILD-TYPE 
          0.92           0.00 
  IBTK MUTATED IBTK WILD-TYPE 
        130.65         148.01 
  IBTK MUTATED IBTK WILD-TYPE 
        25.825         20.050 
[1] "0.9 - 130.7 (25.8)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.2"
D644V2, continuous
D644V3, binary
                cls
clus               0   1
  IBTK MUTATED    19   4
  IBTK WILD-TYPE 347 115
[1] "tbl2"
                cls
clus             [,1] [,2]
  IBTK MUTATED     19    4
  IBTK WILD-TYPE  347  115
        clus
vv       IBTK MUTATED IBTK WILD-TYPE
  COLON            19            347
  RECTUM            4            115
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  IBTK MUTATED         5        0        3         6         1         0
  IBTK WILD-TYPE      86        1       29       132         9         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  IBTK MUTATED           4          0          1          0        2         0
  IBTK WILD-TYPE        20         11         58         42       46        18
                vv
clus             STAGE IVB
  IBTK MUTATED           0
  IBTK WILD-TYPE         1
D644V4, multiclass
            clus
vv           IBTK MUTATED IBTK WILD-TYPE
  STAGE I               5             86
  STAGE IA              0              1
  STAGE II              3             29
  STAGE IIA             6            132
  STAGE IIB             1              9
  STAGE IIC             0              1
  STAGE III             4             20
  STAGE IIIA            0             11
  STAGE IIIB            1             58
  STAGE IIIC            0             42
  STAGE IV              2             46
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  IBTK MUTATED     1   6  14   2
  IBTK WILD-TYPE  16  86 315  48
D644V5, multiclass
    clus
vv   IBTK MUTATED IBTK WILD-TYPE
  T1            1             16
  T2            6             86
  T3           14            315
  T4            2             48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  IBTK MUTATED    15   5   3
  IBTK WILD-TYPE 272 108  84
D644V6, multiclass
    clus
vv   IBTK MUTATED IBTK WILD-TYPE
  N0           15            272
  N1            5            108
  N2            3             84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D644V7, binary
                cls
clus               0   1
  IBTK MUTATED    16   2
  IBTK WILD-TYPE 359  63
[1] "tbl2"
                cls
clus             [,1] [,2]
  IBTK MUTATED     16    2
  IBTK WILD-TYPE  359   63
   clus
vv  IBTK MUTATED IBTK WILD-TYPE
  0           16            359
  1            2             63
[1] 2 2
[1] FALSE
D644V8, binary
                cls
clus               0   1
  IBTK MUTATED    15   8
  IBTK WILD-TYPE 210 256
[1] "tbl2"
                cls
clus             [,1] [,2]
  IBTK MUTATED     15    8
  IBTK WILD-TYPE  210  256
        clus
vv       IBTK MUTATED IBTK WILD-TYPE
  FEMALE           15            210
  MALE              8            256
[1] 2 2
[1] FALSE
D644V9, binary
                cls
clus               0   1
  IBTK MUTATED    21   0
  IBTK WILD-TYPE 329  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  IBTK MUTATED     21    0
  IBTK WILD-TYPE  329   22
     clus
vv    IBTK MUTATED IBTK WILD-TYPE
  NO            21            329
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  IBTK MUTATED                     16                             3
  IBTK WILD-TYPE                  299                            44
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  IBTK MUTATED                       4                              0
  IBTK WILD-TYPE                   102                             10
D644V10, multiclass
                                clus
vv                               IBTK MUTATED IBTK WILD-TYPE
  COLON ADENOCARCINOMA                     16            299
  COLON MUCINOUS ADENOCARCINOMA             3             44
  RECTAL ADENOCARCINOMA                     4            102
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  IBTK MUTATED    15   0   0   2
  IBTK WILD-TYPE 330   4  31  23
D644V11, multiclass
    clus
vv   IBTK MUTATED IBTK WILD-TYPE
  R0           15            330
  R1            0              4
  R2            0             31
  RX            2             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D644V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  IBTK MUTATED                                  0     0
  IBTK WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  IBTK MUTATED                           1    13
  IBTK WILD-TYPE                        21   213
D644V13, multiclass
                                  clus
vv                                 IBTK MUTATED IBTK WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                      13            213
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(645) Variable = RTP3 MUTATION ANALYSIS
D645V1, survival
                sevent
clus2              0   1
  RTP3 MUTATED     2   3
  RTP3 WILD-TYPE 376  90
  RTP3 MUTATED RTP3 WILD-TYPE 
             5            466 
  RTP3 MUTATED RTP3 WILD-TYPE 
             3             90 
$`RTP3 MUTATED`
TCGA-AZ-6598 TCGA-AZ-6603 TCGA-AZ-6608 TCGA-CK-4948 TCGA-D5-6532 
       49.41        29.56         1.61       148.01        18.25 

$`RTP3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77        12.10       100.01         5.23        11.74         3.19 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4952 
       12.76        10.06        14.30        17.56        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6533 
       12.26        19.59        56.09        55.92        20.19         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  RTP3 MUTATED RTP3 WILD-TYPE 
          1.61           0.00 
  RTP3 MUTATED RTP3 WILD-TYPE 
        148.01         140.38 
  RTP3 MUTATED RTP3 WILD-TYPE 
        29.560         20.155 
[1] "1.6 - 148.0 (29.6)" "0.0 - 140.4 (20.2)"
[1] "hr=" "2"  
D645V2, continuous
D645V3, binary
                cls
clus               0   1
  RTP3 MUTATED     5   0
  RTP3 WILD-TYPE 361 119
[1] "tbl2"
                cls
clus             [,1] [,2]
  RTP3 MUTATED      5    0
  RTP3 WILD-TYPE  361  119
        clus
vv       RTP3 MUTATED RTP3 WILD-TYPE
  COLON             5            361
  RECTUM            0            119
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RTP3 MUTATED         0        0        1         1         0         0
  RTP3 WILD-TYPE      91        1       31       137        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RTP3 MUTATED           1          1          0          0        0         0
  RTP3 WILD-TYPE        23         10         59         42       48        18
                vv
clus             STAGE IVB
  RTP3 MUTATED           0
  RTP3 WILD-TYPE         1
D645V4, multiclass
            clus
vv           RTP3 MUTATED RTP3 WILD-TYPE
  STAGE I               0             91
  STAGE IA              0              1
  STAGE II              1             31
  STAGE IIA             1            137
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             1             23
  STAGE IIIA            1             10
  STAGE IIIB            0             59
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  RTP3 MUTATED     0   2   3   0
  RTP3 WILD-TYPE  17  90 326  50
D645V5, multiclass
    clus
vv   RTP3 MUTATED RTP3 WILD-TYPE
  T1            0             17
  T2            2             90
  T3            3            326
  T4            0             50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  RTP3 MUTATED     2   3   0
  RTP3 WILD-TYPE 285 110  87
D645V6, multiclass
    clus
vv   RTP3 MUTATED RTP3 WILD-TYPE
  N0            2            285
  N1            3            110
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D645V7, binary
                cls
clus               0   1
  RTP3 MUTATED     3   0
  RTP3 WILD-TYPE 372  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  RTP3 MUTATED      3    0
  RTP3 WILD-TYPE  372   65
   clus
vv  RTP3 MUTATED RTP3 WILD-TYPE
  0            3            372
  1            0             65
[1] 2 2
[1] FALSE
D645V8, binary
                cls
clus               0   1
  RTP3 MUTATED     4   1
  RTP3 WILD-TYPE 221 263
[1] "tbl2"
                cls
clus             [,1] [,2]
  RTP3 MUTATED      4    1
  RTP3 WILD-TYPE  221  263
        clus
vv       RTP3 MUTATED RTP3 WILD-TYPE
  FEMALE            4            221
  MALE              1            263
[1] 2 2
[1] FALSE
D645V9, binary
                cls
clus               0   1
  RTP3 MUTATED     5   0
  RTP3 WILD-TYPE 345  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  RTP3 MUTATED      5    0
  RTP3 WILD-TYPE  345   22
     clus
vv    RTP3 MUTATED RTP3 WILD-TYPE
  NO             5            345
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  RTP3 MUTATED                      5                             0
  RTP3 WILD-TYPE                  310                            47
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  RTP3 MUTATED                       0                              0
  RTP3 WILD-TYPE                   106                             10
D645V10, multiclass
                                clus
vv                               RTP3 MUTATED RTP3 WILD-TYPE
  COLON ADENOCARCINOMA                      5            310
  COLON MUCINOUS ADENOCARCINOMA             0             47
  RECTAL ADENOCARCINOMA                     0            106
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  RTP3 MUTATED     2   0   0   0
  RTP3 WILD-TYPE 343   4  31  25
D645V11, multiclass
[1] "Remove cluster labels:" "RTP3 MUTATED"          
clus
  RTP3 MUTATED RTP3 WILD-TYPE 
             2            403 
    TCGA-A6-2671     TCGA-A6-2672     TCGA-A6-2674     TCGA-A6-2676 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-A6-2677     TCGA-A6-2678     TCGA-A6-2683     TCGA-A6-3807 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-A6-3808     TCGA-A6-3809     TCGA-A6-3810     TCGA-A6-5657 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-A6-5659     TCGA-A6-5661     TCGA-A6-5665     TCGA-A6-6781 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-AA-3489     TCGA-AA-3492     TCGA-AA-3496     TCGA-AA-3502 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-AA-3510     TCGA-AA-3511     TCGA-AA-3514     TCGA-AA-3517 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-AA-3518     TCGA-AA-3519     TCGA-AA-3520     TCGA-AA-3521 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-AA-3522     TCGA-AA-3524     TCGA-AA-3525     TCGA-AA-3526 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-AA-3527     TCGA-AA-3529     TCGA-AA-3530     TCGA-AA-3531 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-AA-3532     TCGA-AA-3534     TCGA-AA-3538     TCGA-AA-3542 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-AA-3543     TCGA-AA-3544     TCGA-AA-3548     TCGA-AA-3549 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-AA-3552     TCGA-AA-3553     TCGA-AA-3554     TCGA-AA-3555 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-AA-3556     TCGA-AA-3558     TCGA-AA-3560     TCGA-AA-3561 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-AA-3562     TCGA-AA-3655     TCGA-AA-3660     TCGA-AA-3662 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-AA-3663     TCGA-AA-3664     TCGA-AA-3666     TCGA-AA-3667 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-AA-3672     TCGA-AA-3673     TCGA-AA-3678     TCGA-AA-3679 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-AA-3680     TCGA-AA-3681     TCGA-AA-3684     TCGA-AA-3685 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-AA-3688     TCGA-AA-3692     TCGA-AA-3693     TCGA-AA-3695 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-AA-3696     TCGA-AA-3697     TCGA-AA-3710     TCGA-AA-3712 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-AA-3713     TCGA-AA-3715     TCGA-AA-3811     TCGA-AA-3812 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-AA-3814     TCGA-AA-3815     TCGA-AA-3818     TCGA-AA-3819 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-AA-3821     TCGA-AA-3831     TCGA-AA-3833     TCGA-AA-3837 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-AA-3842     TCGA-AA-3844     TCGA-AA-3845     TCGA-AA-3846 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-AA-3848     TCGA-AA-3850     TCGA-AA-3851     TCGA-AA-3852 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-AA-3854     TCGA-AA-3855     TCGA-AA-3856     TCGA-AA-3858 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-AA-3860     TCGA-AA-3861     TCGA-AA-3864     TCGA-AA-3866 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-AA-3867     TCGA-AA-3869     TCGA-AA-3870     TCGA-AA-3872 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-AA-3875     TCGA-AA-3877     TCGA-AA-3930     TCGA-AA-3939 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-AA-3941     TCGA-AA-3947     TCGA-AA-3949     TCGA-AA-3950 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-AA-3952     TCGA-AA-3955     TCGA-AA-3956     TCGA-AA-3968 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-AA-3971     TCGA-AA-3972     TCGA-AA-3973     TCGA-AA-3975 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-AA-3976     TCGA-AA-3979     TCGA-AA-3984     TCGA-AA-3986 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-AA-3989     TCGA-AA-3994     TCGA-AA-A004     TCGA-AA-A00A 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-AA-A00D     TCGA-AA-A00E     TCGA-AA-A00F     TCGA-AA-A00J 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-AA-A00K     TCGA-AA-A00L     TCGA-AA-A00N     TCGA-AA-A00O 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-AA-A00Q     TCGA-AA-A00R     TCGA-AA-A00U     TCGA-AA-A00W 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-AA-A00Z     TCGA-AA-A010     TCGA-AA-A017     TCGA-AA-A01D 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-AA-A01F     TCGA-AA-A01G     TCGA-AA-A01I     TCGA-AA-A01K 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-AA-A01P     TCGA-AA-A01Q     TCGA-AA-A01R     TCGA-AA-A01S 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-AA-A01T     TCGA-AA-A01V     TCGA-AA-A01X     TCGA-AA-A01Z 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-AA-A022     TCGA-AA-A024     TCGA-AA-A029     TCGA-AA-A02F 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-AA-A02H     TCGA-AA-A02J     TCGA-AA-A02K     TCGA-AA-A02O 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-AA-A02W     TCGA-AA-A02Y     TCGA-AA-A03F     TCGA-AA-A03J 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-AD-5900     TCGA-AD-6548     TCGA-AD-6888     TCGA-AU-3779 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-AU-6004     TCGA-AY-4070     TCGA-AY-4071     TCGA-AY-5543 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-AY-6196     TCGA-AY-6197     TCGA-AY-6386     TCGA-AZ-4315 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-AZ-4681     TCGA-AZ-4682     TCGA-CA-5254     TCGA-CA-5255 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-CA-5796     TCGA-CA-5797     TCGA-CA-6715     TCGA-CA-6716 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-CA-6717     TCGA-CA-6718     TCGA-CA-6719     TCGA-CK-4947 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-CK-4950     TCGA-CK-4952     TCGA-CK-5912     TCGA-CK-5913 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-CK-5914     TCGA-CK-5915     TCGA-CK-5916     TCGA-CK-6746 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-CK-6747     TCGA-CK-6748     TCGA-CK-6751     TCGA-CM-4743 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-CM-4744     TCGA-CM-4746     TCGA-CM-4747     TCGA-CM-4752 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-CM-5341     TCGA-CM-5344     TCGA-CM-5348     TCGA-CM-5349 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-CM-5860     TCGA-CM-5861     TCGA-CM-5862     TCGA-CM-5863 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-CM-5864     TCGA-CM-5868     TCGA-CM-6161     TCGA-CM-6162 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-CM-6163     TCGA-CM-6164     TCGA-CM-6165     TCGA-CM-6166 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-CM-6167     TCGA-CM-6168     TCGA-CM-6169     TCGA-CM-6170 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-CM-6171     TCGA-CM-6172     TCGA-CM-6674     TCGA-CM-6675 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-CM-6676     TCGA-CM-6677     TCGA-CM-6678     TCGA-CM-6679 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-CM-6680     TCGA-D5-5537     TCGA-D5-5538     TCGA-D5-5539 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-D5-5540     TCGA-D5-5541     TCGA-D5-6529     TCGA-D5-6533 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-D5-6534     TCGA-D5-6535     TCGA-D5-6536     TCGA-D5-6537 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-D5-6538     TCGA-D5-6539     TCGA-D5-6540     TCGA-D5-6541 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-D5-6898     TCGA-D5-6920     TCGA-D5-6922     TCGA-D5-6923 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-D5-6924     TCGA-D5-6926     TCGA-D5-6927     TCGA-D5-6928 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-D5-6929     TCGA-D5-6930     TCGA-D5-6931     TCGA-D5-6932 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-D5-7000     TCGA-F4-6459     TCGA-F4-6460     TCGA-F4-6569 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-F4-6570     TCGA-F4-6703     TCGA-F4-6704     TCGA-F4-6805 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-F4-6806     TCGA-F4-6807     TCGA-F4-6808     TCGA-F4-6809 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-F4-6854     TCGA-F4-6855     TCGA-F4-6856     TCGA-G4-6293 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-G4-6299     TCGA-G4-6303     TCGA-G4-6304     TCGA-G4-6306 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-G4-6307     TCGA-G4-6309     TCGA-G4-6310     TCGA-G4-6315 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-G4-6317     TCGA-G4-6321     TCGA-G4-6323     TCGA-G4-6586 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-G4-6588     TCGA-G4-6625     TCGA-G4-6626     TCGA-G4-6628 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-AF-2687     TCGA-AF-2689     TCGA-AF-2691     TCGA-AF-2692 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-AF-3400     TCGA-AF-3913     TCGA-AF-4110     TCGA-AF-5654 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-AF-6655     TCGA-AG-3574     TCGA-AG-3575     TCGA-AG-3578 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-AG-3580     TCGA-AG-3581     TCGA-AG-3582     TCGA-AG-3583 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-AG-3584     TCGA-AG-3586     TCGA-AG-3587     TCGA-AG-3593 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-AG-3594     TCGA-AG-3598     TCGA-AG-3599     TCGA-AG-3600 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-AG-3601     TCGA-AG-3602     TCGA-AG-3605     TCGA-AG-3608 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-AG-3609     TCGA-AG-3611     TCGA-AG-3612     TCGA-AG-3726 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-AG-3727     TCGA-AG-3731     TCGA-AG-3732     TCGA-AG-3742 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-AG-3878     TCGA-AG-3882     TCGA-AG-3883     TCGA-AG-3885 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-AG-3887     TCGA-AG-3890     TCGA-AG-3892     TCGA-AG-3893 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-AG-3894     TCGA-AG-3896     TCGA-AG-3898     TCGA-AG-3901 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-AG-3902     TCGA-AG-3909     TCGA-AG-3999     TCGA-AG-4001 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-AG-4005     TCGA-AG-4007     TCGA-AG-4008     TCGA-AG-4015 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-AG-A002     TCGA-AG-A008     TCGA-AG-A00C     TCGA-AG-A00H 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-AG-A00Y     TCGA-AG-A011     TCGA-AG-A014     TCGA-AG-A015 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-AG-A016     TCGA-AG-A01L     TCGA-AG-A01W     TCGA-AG-A01Y 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-AG-A020     TCGA-AG-A025     TCGA-AG-A026     TCGA-AG-A02G 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-AG-A02N     TCGA-AG-A02X     TCGA-AG-A032     TCGA-AG-A036 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-AH-6549     TCGA-AH-6643     TCGA-CL-5917     TCGA-CL-5918 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-DC-5337     TCGA-DC-5869     TCGA-DC-6155     TCGA-DC-6157 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-DC-6158     TCGA-DC-6160     TCGA-DC-6681     TCGA-DC-6682 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-DC-6683     TCGA-DT-5265     TCGA-EF-5830     TCGA-EI-6506 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-EI-6507     TCGA-EI-6508     TCGA-EI-6510     TCGA-F5-6464 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-F5-6465     TCGA-F5-6571     TCGA-F5-6702     TCGA-F5-6812 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
    TCGA-F5-6813     TCGA-G5-6235     TCGA-G5-6641 
"RTP3 WILD-TYPE" "RTP3 WILD-TYPE" "RTP3 WILD-TYPE" 
D645V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RTP3 MUTATED                                  0     0
  RTP3 WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  RTP3 MUTATED                           0     5
  RTP3 WILD-TYPE                        22   221
D645V13, multiclass
                                  clus
vv                                 RTP3 MUTATED RTP3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       5            221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(646) Variable = TAOK3 MUTATION ANALYSIS
D646V1, survival
                 sevent
clus2               0   1
  TAOK3 MUTATED    16   3
  TAOK3 WILD-TYPE 362  90
  TAOK3 MUTATED TAOK3 WILD-TYPE 
             19             452 
  TAOK3 MUTATED TAOK3 WILD-TYPE 
              3              90 
$`TAOK3 MUTATED`
TCGA-A6-3809 TCGA-A6-5665 TCGA-A6-6781 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3977 
       32.75        22.06        19.66         7.04         3.02        25.02 
TCGA-AA-A00N TCGA-AA-A010 TCGA-CA-6717 TCGA-CK-4952 TCGA-CK-5913 TCGA-CM-5861 
        4.01        34.98        12.76        15.62        51.32        15.02 
TCGA-CM-6169 TCGA-CM-6171 TCGA-D5-6532 TCGA-D5-6540 TCGA-D5-6927 TCGA-D5-6929 
       13.02        14.04        18.25        16.14         9.44         4.80 
TCGA-G4-6307 
       55.04 

$`TAOK3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6782 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
       20.28         1.02        35.01        63.98         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
       13.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       36.03         8.05        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       78.08         6.05         6.97        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.20        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       49.08         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 
       22.03        22.98        30.08        32.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6170 TCGA-CM-6172 
       16.04        21.99        14.99        12.99        15.02        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       20.19         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       17.13        12.49        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 
       12.43        14.30         9.04        11.64         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  TAOK3 MUTATED TAOK3 WILD-TYPE 
           3.02            0.00 
  TAOK3 MUTATED TAOK3 WILD-TYPE 
          55.04          148.01 
  TAOK3 MUTATED TAOK3 WILD-TYPE 
         15.620          20.945 
[1] "3.0 - 55.0 (15.6)"  "0.0 - 148.0 (20.9)"
[1] "hr=" "1"  
D646V2, continuous
D646V3, binary
                 cls
clus                0   1
  TAOK3 MUTATED    20   0
  TAOK3 WILD-TYPE 346 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TAOK3 MUTATED     20    0
  TAOK3 WILD-TYPE  346  119
        clus
vv       TAOK3 MUTATED TAOK3 WILD-TYPE
  COLON             20             346
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TAOK3 MUTATED         2        0        2         8         3         0
  TAOK3 WILD-TYPE      89        1       30       130         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TAOK3 MUTATED           0          0          1          2        1         0
  TAOK3 WILD-TYPE        24         11         58         40       47        18
                 vv
clus              STAGE IVB
  TAOK3 MUTATED           0
  TAOK3 WILD-TYPE         1
D646V4, multiclass
            clus
vv           TAOK3 MUTATED TAOK3 WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA              8             130
  STAGE IIB              3               7
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             2              40
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  TAOK3 MUTATED     0   3  12   5
  TAOK3 WILD-TYPE  17  89 317  45
D646V5, multiclass
    clus
vv   TAOK3 MUTATED TAOK3 WILD-TYPE
  T1             0              17
  T2             3              89
  T3            12             317
  T4             5              45
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  TAOK3 MUTATED    16   3   1
  TAOK3 WILD-TYPE 271 110  86
D646V6, multiclass
    clus
vv   TAOK3 MUTATED TAOK3 WILD-TYPE
  N0            16             271
  N1             3             110
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D646V7, binary
                 cls
clus                0   1
  TAOK3 MUTATED    16   1
  TAOK3 WILD-TYPE 359  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TAOK3 MUTATED     16    1
  TAOK3 WILD-TYPE  359   64
   clus
vv  TAOK3 MUTATED TAOK3 WILD-TYPE
  0            16             359
  1             1              64
[1] 2 2
[1] FALSE
D646V8, binary
                 cls
clus                0   1
  TAOK3 MUTATED    11   9
  TAOK3 WILD-TYPE 214 255
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TAOK3 MUTATED     11    9
  TAOK3 WILD-TYPE  214  255
        clus
vv       TAOK3 MUTATED TAOK3 WILD-TYPE
  FEMALE            11             214
  MALE               9             255
[1] 2 2
[1] FALSE
D646V9, binary
                 cls
clus                0   1
  TAOK3 MUTATED    16   0
  TAOK3 WILD-TYPE 334  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TAOK3 MUTATED     16    0
  TAOK3 WILD-TYPE  334   22
     clus
vv    TAOK3 MUTATED TAOK3 WILD-TYPE
  NO             16             334
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  TAOK3 MUTATED                     14                             6
  TAOK3 WILD-TYPE                  301                            41
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  TAOK3 MUTATED                       0                              0
  TAOK3 WILD-TYPE                   106                             10
D646V10, multiclass
                                clus
vv                               TAOK3 MUTATED TAOK3 WILD-TYPE
  COLON ADENOCARCINOMA                      14             301
  COLON MUCINOUS ADENOCARCINOMA              6              41
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  TAOK3 MUTATED    16   0   0   3
  TAOK3 WILD-TYPE 329   4  31  22
D646V11, multiclass
    clus
vv   TAOK3 MUTATED TAOK3 WILD-TYPE
  R0            16             329
  R1             0               4
  R2             0              31
  RX             3              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D646V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TAOK3 MUTATED                                  0     1
  TAOK3 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  TAOK3 MUTATED                           1    12
  TAOK3 WILD-TYPE                        21   214
D646V13, multiclass
                                  clus
vv                                 TAOK3 MUTATED TAOK3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                       12             214
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(647) Variable = RAE1 MUTATION ANALYSIS
D647V1, survival
                sevent
clus2              0   1
  RAE1 MUTATED     5   2
  RAE1 WILD-TYPE 373  91
  RAE1 MUTATED RAE1 WILD-TYPE 
             7            464 
  RAE1 MUTATED RAE1 WILD-TYPE 
             2             91 
$`RAE1 MUTATED`
TCGA-A6-3809 TCGA-A6-6652 TCGA-A6-6780 TCGA-AA-A00A TCGA-DM-A1DA TCGA-AG-3574 
       32.75        24.69        20.12        38.04         7.50        36.03 
TCGA-AG-A002 
       20.98 

$`RAE1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6781 
       25.18        24.16        21.76        24.39        23.87        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00E 
       19.07         7.96        27.02        13.94        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
      140.38        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       10.39        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  RAE1 MUTATED RAE1 WILD-TYPE 
           7.5            0.0 
  RAE1 MUTATED RAE1 WILD-TYPE 
         38.04         148.01 
  RAE1 MUTATED RAE1 WILD-TYPE 
        24.690         20.035 
[1] "7.5 - 38.0 (24.7)"  "0.0 - 148.0 (20.0)"
[1] "hr=" "1.6"
D647V2, continuous
D647V3, binary
                cls
clus               0   1
  RAE1 MUTATED     6   2
  RAE1 WILD-TYPE 360 117
[1] "tbl2"
                cls
clus             [,1] [,2]
  RAE1 MUTATED      6    2
  RAE1 WILD-TYPE  360  117
        clus
vv       RAE1 MUTATED RAE1 WILD-TYPE
  COLON             6            360
  RECTUM            2            117
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RAE1 MUTATED         1        0        1         2         2         0
  RAE1 WILD-TYPE      90        1       31       136         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RAE1 MUTATED           0          0          0          1        0         1
  RAE1 WILD-TYPE        24         11         59         41       48        17
                vv
clus             STAGE IVB
  RAE1 MUTATED           0
  RAE1 WILD-TYPE         1
D647V4, multiclass
            clus
vv           RAE1 MUTATED RAE1 WILD-TYPE
  STAGE I               1             90
  STAGE IA              0              1
  STAGE II              1             31
  STAGE IIA             2            136
  STAGE IIB             2              8
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            0             59
  STAGE IIIC            1             41
  STAGE IV              0             48
  STAGE IVA             1             17
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  RAE1 MUTATED     0   1   5   2
  RAE1 WILD-TYPE  17  91 324  48
D647V5, multiclass
    clus
vv   RAE1 MUTATED RAE1 WILD-TYPE
  T1            0             17
  T2            1             91
  T3            5            324
  T4            2             48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  RAE1 MUTATED     7   0   1
  RAE1 WILD-TYPE 280 113  86
D647V6, multiclass
    clus
vv   RAE1 MUTATED RAE1 WILD-TYPE
  N0            7            280
  N1            0            113
  N2            1             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D647V7, binary
                cls
clus               0   1
  RAE1 MUTATED     5   1
  RAE1 WILD-TYPE 370  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  RAE1 MUTATED      5    1
  RAE1 WILD-TYPE  370   64
   clus
vv  RAE1 MUTATED RAE1 WILD-TYPE
  0            5            370
  1            1             64
[1] 2 2
[1] FALSE
D647V8, binary
                cls
clus               0   1
  RAE1 MUTATED     4   4
  RAE1 WILD-TYPE 221 260
[1] "tbl2"
                cls
clus             [,1] [,2]
  RAE1 MUTATED      4    4
  RAE1 WILD-TYPE  221  260
        clus
vv       RAE1 MUTATED RAE1 WILD-TYPE
  FEMALE            4            221
  MALE              4            260
[1] 2 2
[1] FALSE
D647V9, binary
                cls
clus               0   1
  RAE1 MUTATED     6   0
  RAE1 WILD-TYPE 344  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  RAE1 MUTATED      6    0
  RAE1 WILD-TYPE  344   22
     clus
vv    RAE1 MUTATED RAE1 WILD-TYPE
  NO             6            344
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  RAE1 MUTATED                      4                             2
  RAE1 WILD-TYPE                  311                            45
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  RAE1 MUTATED                       2                              0
  RAE1 WILD-TYPE                   104                             10
D647V10, multiclass
                                clus
vv                               RAE1 MUTATED RAE1 WILD-TYPE
  COLON ADENOCARCINOMA                      4            311
  COLON MUCINOUS ADENOCARCINOMA             2             45
  RECTAL ADENOCARCINOMA                     2            104
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  RAE1 MUTATED     4   0   0   1
  RAE1 WILD-TYPE 341   4  31  24
D647V11, multiclass
    clus
vv   RAE1 MUTATED RAE1 WILD-TYPE
  R0            4            341
  R1            0              4
  R2            0             31
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D647V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RAE1 MUTATED                                  0     0
  RAE1 WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  RAE1 MUTATED                           1     4
  RAE1 WILD-TYPE                        21   222
D647V13, multiclass
                                  clus
vv                                 RAE1 MUTATED RAE1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                       4            222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(648) Variable = KIF2C MUTATION ANALYSIS
D648V1, survival
                 sevent
clus2               0   1
  KIF2C MUTATED     8   4
  KIF2C WILD-TYPE 370  89
  KIF2C MUTATED KIF2C WILD-TYPE 
             12             459 
  KIF2C MUTATED KIF2C WILD-TYPE 
              4              89 
$`KIF2C MUTATED`
TCGA-A6-2676 TCGA-AA-A010 TCGA-AA-A01Z TCGA-AD-6895 TCGA-D5-6540 TCGA-DM-A0X9 
       42.90        34.98        37.02         0.72        16.14       119.70 
TCGA-DM-A1D6 TCGA-F4-6703 TCGA-AG-3892 TCGA-AG-A002 TCGA-DY-A1DD TCGA-DY-A1DG 
       49.91        47.87        13.02        20.98        57.24        51.48 

$`KIF2C WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       33.04        35.01        26.01        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.79         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       12.49        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       12.00        11.38        10.26        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       92.75        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       35.74         6.18         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DF 
        4.01         5.03         5.29       126.44        41.36        24.13 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  KIF2C MUTATED KIF2C WILD-TYPE 
           0.72            0.00 
  KIF2C MUTATED KIF2C WILD-TYPE 
         119.70          148.01 
  KIF2C MUTATED KIF2C WILD-TYPE 
          39.96           20.02 
[1] "0.7 - 119.7 (40.0)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.1"
D648V2, continuous
D648V3, binary
                 cls
clus                0   1
  KIF2C MUTATED     8   4
  KIF2C WILD-TYPE 358 115
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KIF2C MUTATED      8    4
  KIF2C WILD-TYPE  358  115
        clus
vv       KIF2C MUTATED KIF2C WILD-TYPE
  COLON              8             358
  RECTUM             4             115
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KIF2C MUTATED         3        0        1         3         2         0
  KIF2C WILD-TYPE      88        1       31       135         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  KIF2C MUTATED           0          0          1          0        0         1
  KIF2C WILD-TYPE        24         11         58         42       48        17
                 vv
clus              STAGE IVB
  KIF2C MUTATED           0
  KIF2C WILD-TYPE         1
D648V4, multiclass
            clus
vv           KIF2C MUTATED KIF2C WILD-TYPE
  STAGE I                3              88
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              3             135
  STAGE IIB              2               8
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  KIF2C MUTATED     1   2   7   2
  KIF2C WILD-TYPE  16  90 322  48
D648V5, multiclass
    clus
vv   KIF2C MUTATED KIF2C WILD-TYPE
  T1             1              16
  T2             2              90
  T3             7             322
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  KIF2C MUTATED     9   3   0
  KIF2C WILD-TYPE 278 110  87
D648V6, multiclass
    clus
vv   KIF2C MUTATED KIF2C WILD-TYPE
  N0             9             278
  N1             3             110
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D648V7, binary
                 cls
clus                0   1
  KIF2C MUTATED    10   1
  KIF2C WILD-TYPE 365  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KIF2C MUTATED     10    1
  KIF2C WILD-TYPE  365   64
   clus
vv  KIF2C MUTATED KIF2C WILD-TYPE
  0            10             365
  1             1              64
[1] 2 2
[1] FALSE
D648V8, binary
                 cls
clus                0   1
  KIF2C MUTATED     5   7
  KIF2C WILD-TYPE 220 257
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KIF2C MUTATED      5    7
  KIF2C WILD-TYPE  220  257
        clus
vv       KIF2C MUTATED KIF2C WILD-TYPE
  FEMALE             5             220
  MALE               7             257
[1] 2 2
[1] FALSE
D648V9, binary
                 cls
clus                0   1
  KIF2C MUTATED     7   0
  KIF2C WILD-TYPE 343  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KIF2C MUTATED      7    0
  KIF2C WILD-TYPE  343   22
     clus
vv    KIF2C MUTATED KIF2C WILD-TYPE
  NO              7             343
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  KIF2C MUTATED                      6                             2
  KIF2C WILD-TYPE                  309                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  KIF2C MUTATED                       4                              0
  KIF2C WILD-TYPE                   102                             10
D648V10, multiclass
                                clus
vv                               KIF2C MUTATED KIF2C WILD-TYPE
  COLON ADENOCARCINOMA                       6             309
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      4             102
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  KIF2C MUTATED     7   0   0   0
  KIF2C WILD-TYPE 338   4  31  25
D648V11, multiclass
    clus
vv   KIF2C MUTATED KIF2C WILD-TYPE
  R0             7             338
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D648V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KIF2C MUTATED                                  0     0
  KIF2C WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  KIF2C MUTATED                           0     8
  KIF2C WILD-TYPE                        22   218
D648V13, multiclass
                                  clus
vv                                 KIF2C MUTATED KIF2C WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        8             218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(649) Variable = C7ORF58 MUTATION ANALYSIS
D649V1, survival
                   sevent
clus2                 0   1
  C7ORF58 MUTATED    20   5
  C7ORF58 WILD-TYPE 358  88
  C7ORF58 MUTATED C7ORF58 WILD-TYPE 
               25               446 
  C7ORF58 MUTATED C7ORF58 WILD-TYPE 
                5                88 
$`C7ORF58 MUTATED`
TCGA-A6-2676 TCGA-A6-5662 TCGA-A6-6649 TCGA-A6-6780 TCGA-AA-3672 TCGA-AA-3697 
       42.90        23.61        24.16        20.12         0.92        85.05 
TCGA-AA-3949 TCGA-AA-A00N TCGA-AA-A010 TCGA-AU-6004 TCGA-AZ-4315 TCGA-AZ-6601 
       26.01         4.01        34.98        27.09        58.39       100.01 
TCGA-CA-5254 TCGA-CA-6717 TCGA-CA-6718 TCGA-D5-6922 TCGA-D5-6930 TCGA-DM-A28H 
       12.69        12.76        10.06         4.41         1.51       117.07 
TCGA-F4-6856 TCGA-G4-6309 TCGA-AG-3892 TCGA-AG-A002 TCGA-CI-6619 TCGA-CL-5917 
       35.31        85.48        13.02        20.98         6.05        78.12 
TCGA-DY-A1DG 
       51.48 

$`C7ORF58 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5664 TCGA-A6-5665 
       31.63        30.44        29.19        33.53        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 
       21.76        24.69        24.39        23.87        19.66        20.28 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
        7.04         3.02         1.02        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
       14.01        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 
       37.05        19.00        36.00         5.03        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3950 
       31.00         2.01        12.99        24.00        33.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
        0.20        14.50        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 
       88.21        49.41         6.77        12.10        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
       11.74         3.19         1.61         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.07        12.20        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28K TCGA-F4-6459 
       81.37       119.93        35.97        60.79        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6620 
       38.56         1.45        17.49         0.69         0.72        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        6.97         4.73         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1H8 
        5.29       126.44        41.36        57.24        24.13        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  C7ORF58 MUTATED C7ORF58 WILD-TYPE 
             0.92              0.00 
  C7ORF58 MUTATED C7ORF58 WILD-TYPE 
           117.07            148.01 
  C7ORF58 MUTATED C7ORF58 WILD-TYPE 
            24.16             20.02 
[1] "0.9 - 117.1 (24.2)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.3"
D649V2, continuous
D649V3, binary
                   cls
clus                  0   1
  C7ORF58 MUTATED    21   5
  C7ORF58 WILD-TYPE 345 114
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C7ORF58 MUTATED     21    5
  C7ORF58 WILD-TYPE  345  114
        clus
vv       C7ORF58 MUTATED C7ORF58 WILD-TYPE
  COLON               21               345
  RECTUM               5               114
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  C7ORF58 MUTATED         4        0        1         6         3         0
  C7ORF58 WILD-TYPE      87        1       31       132         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C7ORF58 MUTATED           3          1          3          2        1
  C7ORF58 WILD-TYPE        21         10         56         40       47
                   vv
clus                STAGE IVA STAGE IVB
  C7ORF58 MUTATED           2         0
  C7ORF58 WILD-TYPE        16         1
D649V4, multiclass
            clus
vv           C7ORF58 MUTATED C7ORF58 WILD-TYPE
  STAGE I                  4                87
  STAGE IA                 0                 1
  STAGE II                 1                31
  STAGE IIA                6               132
  STAGE IIB                3                 7
  STAGE IIC                0                 1
  STAGE III                3                21
  STAGE IIIA               1                10
  STAGE IIIB               3                56
  STAGE IIIC               2                40
  STAGE IV                 1                47
  STAGE IVA                2                16
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  C7ORF58 MUTATED     1   3  19   3
  C7ORF58 WILD-TYPE  16  89 310  47
D649V5, multiclass
    clus
vv   C7ORF58 MUTATED C7ORF58 WILD-TYPE
  T1               1                16
  T2               3                89
  T3              19               310
  T4               3                47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  C7ORF58 MUTATED    15   7   4
  C7ORF58 WILD-TYPE 272 106  83
D649V6, multiclass
    clus
vv   C7ORF58 MUTATED C7ORF58 WILD-TYPE
  N0              15               272
  N1               7               106
  N2               4                83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D649V7, binary
                   cls
clus                  0   1
  C7ORF58 MUTATED    21   3
  C7ORF58 WILD-TYPE 354  62
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C7ORF58 MUTATED     21    3
  C7ORF58 WILD-TYPE  354   62
   clus
vv  C7ORF58 MUTATED C7ORF58 WILD-TYPE
  0              21               354
  1               3                62
[1] 2 2
[1] FALSE
D649V8, binary
                   cls
clus                  0   1
  C7ORF58 MUTATED     9  17
  C7ORF58 WILD-TYPE 216 247
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C7ORF58 MUTATED      9   17
  C7ORF58 WILD-TYPE  216  247
        clus
vv       C7ORF58 MUTATED C7ORF58 WILD-TYPE
  FEMALE               9               216
  MALE                17               247
[1] 2 2
[1] FALSE
D649V9, binary
                   cls
clus                  0   1
  C7ORF58 MUTATED    18   0
  C7ORF58 WILD-TYPE 332  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C7ORF58 MUTATED     18    0
  C7ORF58 WILD-TYPE  332   22
     clus
vv    C7ORF58 MUTATED C7ORF58 WILD-TYPE
  NO               18               332
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  C7ORF58 MUTATED                     15                             6
  C7ORF58 WILD-TYPE                  300                            41
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  C7ORF58 MUTATED                       5                              0
  C7ORF58 WILD-TYPE                   101                             10
D649V10, multiclass
                                clus
vv                               C7ORF58 MUTATED C7ORF58 WILD-TYPE
  COLON ADENOCARCINOMA                        15               300
  COLON MUCINOUS ADENOCARCINOMA                6                41
  RECTAL ADENOCARCINOMA                        5               101
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  C7ORF58 MUTATED    15   0   0   4
  C7ORF58 WILD-TYPE 330   4  31  21
D649V11, multiclass
    clus
vv   C7ORF58 MUTATED C7ORF58 WILD-TYPE
  R0              15               330
  R1               0                 4
  R2               0                31
  RX               4                21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D649V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C7ORF58 MUTATED                                  0     3
  C7ORF58 WILD-TYPE                                1     8
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  C7ORF58 MUTATED                           1    14
  C7ORF58 WILD-TYPE                        21   212
D649V13, multiclass
                                  clus
vv                                 C7ORF58 MUTATED C7ORF58 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          3                 8
  BLACK OR AFRICAN AMERICAN                      1                21
  WHITE                                         14               212
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(650) Variable = PVRL4 MUTATION ANALYSIS
D650V1, survival
                 sevent
clus2               0   1
  PVRL4 MUTATED     9   1
  PVRL4 WILD-TYPE 369  92
  PVRL4 MUTATED PVRL4 WILD-TYPE 
             10             461 
  PVRL4 MUTATED PVRL4 WILD-TYPE 
              1              92 
$`PVRL4 MUTATED`
TCGA-A6-6141 TCGA-AA-3715 TCGA-AA-3877 TCGA-AA-3966 TCGA-AA-A00J TCGA-CM-5349 
        8.38        19.04        31.00         2.01        18.05        30.08 
TCGA-CM-5868 TCGA-DM-A1HB TCGA-G4-6293 TCGA-CL-5918 
       17.03       135.65       133.18         7.17 

$`PVRL4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 
       22.09        22.06        32.71        27.09        22.52        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 
       36.00         5.03        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 
       24.03        27.02        29.98        18.05         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
       34.03        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.03        22.98        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       15.02        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      131.51       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6299 
       33.67        13.25         0.53        47.41        35.31        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-DC-5337 
        6.05        33.17         6.97         4.73        78.12        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  PVRL4 MUTATED PVRL4 WILD-TYPE 
           2.01            0.00 
  PVRL4 MUTATED PVRL4 WILD-TYPE 
         135.65          148.01 
  PVRL4 MUTATED PVRL4 WILD-TYPE 
         18.545          20.280 
[1] "2.0 - 135.7 (18.5)" "0.0 - 148.0 (20.3)"
[1] "hr=" "2.5"
D650V2, continuous
D650V3, binary
                 cls
clus                0   1
  PVRL4 MUTATED     9   1
  PVRL4 WILD-TYPE 357 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PVRL4 MUTATED      9    1
  PVRL4 WILD-TYPE  357  118
        clus
vv       PVRL4 MUTATED PVRL4 WILD-TYPE
  COLON              9             357
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PVRL4 MUTATED         1        0        1         4         0         0
  PVRL4 WILD-TYPE      90        1       31       134        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PVRL4 MUTATED           1          0          2          0        0         1
  PVRL4 WILD-TYPE        23         11         57         42       48        17
                 vv
clus              STAGE IVB
  PVRL4 MUTATED           0
  PVRL4 WILD-TYPE         1
D650V4, multiclass
            clus
vv           PVRL4 MUTATED PVRL4 WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              4             134
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             2              57
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PVRL4 MUTATED     1   0   7   2
  PVRL4 WILD-TYPE  16  92 322  48
D650V5, multiclass
    clus
vv   PVRL4 MUTATED PVRL4 WILD-TYPE
  T1             1              16
  T2             0              92
  T3             7             322
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  PVRL4 MUTATED     6   4   0
  PVRL4 WILD-TYPE 281 109  87
D650V6, multiclass
    clus
vv   PVRL4 MUTATED PVRL4 WILD-TYPE
  N0             6             281
  N1             4             109
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D650V7, binary
                 cls
clus                0   1
  PVRL4 MUTATED     8   1
  PVRL4 WILD-TYPE 367  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PVRL4 MUTATED      8    1
  PVRL4 WILD-TYPE  367   64
   clus
vv  PVRL4 MUTATED PVRL4 WILD-TYPE
  0             8             367
  1             1              64
[1] 2 2
[1] FALSE
D650V8, binary
                 cls
clus                0   1
  PVRL4 MUTATED     6   4
  PVRL4 WILD-TYPE 219 260
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PVRL4 MUTATED      6    4
  PVRL4 WILD-TYPE  219  260
        clus
vv       PVRL4 MUTATED PVRL4 WILD-TYPE
  FEMALE             6             219
  MALE               4             260
[1] 2 2
[1] FALSE
D650V9, binary
                 cls
clus                0   1
  PVRL4 MUTATED     8   0
  PVRL4 WILD-TYPE 342  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PVRL4 MUTATED      8    0
  PVRL4 WILD-TYPE  342   22
     clus
vv    PVRL4 MUTATED PVRL4 WILD-TYPE
  NO              8             342
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PVRL4 MUTATED                      5                             3
  PVRL4 WILD-TYPE                  310                            44
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PVRL4 MUTATED                       1                              0
  PVRL4 WILD-TYPE                   105                             10
D650V10, multiclass
                                clus
vv                               PVRL4 MUTATED PVRL4 WILD-TYPE
  COLON ADENOCARCINOMA                       5             310
  COLON MUCINOUS ADENOCARCINOMA              3              44
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  PVRL4 MUTATED     6   0   0   1
  PVRL4 WILD-TYPE 339   4  31  24
D650V11, multiclass
    clus
vv   PVRL4 MUTATED PVRL4 WILD-TYPE
  R0             6             339
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D650V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PVRL4 MUTATED                                  0     0
  PVRL4 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PVRL4 MUTATED                           1     5
  PVRL4 WILD-TYPE                        21   221
D650V13, multiclass
                                  clus
vv                                 PVRL4 MUTATED PVRL4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        5             221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(651) Variable = MTDH MUTATION ANALYSIS
D651V1, survival
                sevent
clus2              0   1
  MTDH MUTATED    10   2
  MTDH WILD-TYPE 368  91
  MTDH MUTATED MTDH WILD-TYPE 
            12            459 
  MTDH MUTATED MTDH WILD-TYPE 
             2             91 
$`MTDH MUTATED`
TCGA-A6-2676 TCGA-AA-3511 TCGA-AA-3979 TCGA-AA-A010 TCGA-AD-6889 TCGA-AD-6895 
       42.90         6.97        24.00        34.98        56.55         0.72 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4950 TCGA-CM-4744 TCGA-G4-6310 TCGA-AG-A002 
       12.76        10.06        85.45        20.02        63.62        20.98 

$`MTDH WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01        63.98         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        25.02        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6899 
       40.96         0.07        21.37        15.52         0.79         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        3.29         0.07        12.20        14.30        17.56       148.01 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
        1.91       124.27        23.05        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6317 
       53.62        44.68        55.04        85.48        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  MTDH MUTATED MTDH WILD-TYPE 
          0.72           0.00 
  MTDH MUTATED MTDH WILD-TYPE 
         85.45         148.01 
  MTDH MUTATED MTDH WILD-TYPE 
         22.49          20.12 
[1] "0.7 - 85.5 (22.5)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.5"
D651V2, continuous
D651V3, binary
                cls
clus               0   1
  MTDH MUTATED    12   1
  MTDH WILD-TYPE 354 118
[1] "tbl2"
                cls
clus             [,1] [,2]
  MTDH MUTATED     12    1
  MTDH WILD-TYPE  354  118
        clus
vv       MTDH MUTATED MTDH WILD-TYPE
  COLON            12            354
  RECTUM            1            118
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MTDH MUTATED         2        0        1         4         3         0
  MTDH WILD-TYPE      89        1       31       134         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MTDH MUTATED           0          0          2          0        0         0
  MTDH WILD-TYPE        24         11         57         42       48        18
                vv
clus             STAGE IVB
  MTDH MUTATED           0
  MTDH WILD-TYPE         1
D651V4, multiclass
            clus
vv           MTDH MUTATED MTDH WILD-TYPE
  STAGE I               2             89
  STAGE IA              0              1
  STAGE II              1             31
  STAGE IIA             4            134
  STAGE IIB             3              7
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            2             57
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  MTDH MUTATED     0   2   7   4
  MTDH WILD-TYPE  17  90 322  46
D651V5, multiclass
    clus
vv   MTDH MUTATED MTDH WILD-TYPE
  T1            0             17
  T2            2             90
  T3            7            322
  T4            4             46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  MTDH MUTATED    10   3   0
  MTDH WILD-TYPE 277 110  87
D651V6, multiclass
    clus
vv   MTDH MUTATED MTDH WILD-TYPE
  N0           10            277
  N1            3            110
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D651V7, binary
                cls
clus               0   1
  MTDH MUTATED    11   0
  MTDH WILD-TYPE 364  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  MTDH MUTATED     11    0
  MTDH WILD-TYPE  364   65
   clus
vv  MTDH MUTATED MTDH WILD-TYPE
  0           11            364
  1            0             65
[1] 2 2
[1] FALSE
D651V8, binary
                cls
clus               0   1
  MTDH MUTATED     4   9
  MTDH WILD-TYPE 221 255
[1] "tbl2"
                cls
clus             [,1] [,2]
  MTDH MUTATED      4    9
  MTDH WILD-TYPE  221  255
        clus
vv       MTDH MUTATED MTDH WILD-TYPE
  FEMALE            4            221
  MALE              9            255
[1] 2 2
[1] FALSE
D651V9, binary
                cls
clus               0   1
  MTDH MUTATED     9   1
  MTDH WILD-TYPE 341  21
[1] "tbl2"
                cls
clus             [,1] [,2]
  MTDH MUTATED      9    1
  MTDH WILD-TYPE  341   21
     clus
vv    MTDH MUTATED MTDH WILD-TYPE
  NO             9            341
  YES            1             21
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MTDH MUTATED                     11                             1
  MTDH WILD-TYPE                  304                            46
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MTDH MUTATED                       1                              0
  MTDH WILD-TYPE                   105                             10
D651V10, multiclass
                                clus
vv                               MTDH MUTATED MTDH WILD-TYPE
  COLON ADENOCARCINOMA                     11            304
  COLON MUCINOUS ADENOCARCINOMA             1             46
  RECTAL ADENOCARCINOMA                     1            105
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  MTDH MUTATED     7   1   0   3
  MTDH WILD-TYPE 338   3  31  22
D651V11, multiclass
    clus
vv   MTDH MUTATED MTDH WILD-TYPE
  R0            7            338
  R1            1              3
  R2            0             31
  RX            3             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D651V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MTDH MUTATED                                  0     3
  MTDH WILD-TYPE                                1     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  MTDH MUTATED                           1     5
  MTDH WILD-TYPE                        21   221
D651V13, multiclass
                                  clus
vv                                 MTDH MUTATED MTDH WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       3              8
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                       5            221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(652) Variable = AIFM1 MUTATION ANALYSIS
D652V1, survival
                 sevent
clus2               0   1
  AIFM1 MUTATED    11   2
  AIFM1 WILD-TYPE 367  91
  AIFM1 MUTATED AIFM1 WILD-TYPE 
             13             458 
  AIFM1 MUTATED AIFM1 WILD-TYPE 
              2              91 
$`AIFM1 MUTATED`
TCGA-A6-5659 TCGA-AA-A00J TCGA-AD-6895 TCGA-CA-6718 TCGA-CM-5348 TCGA-CM-5862 
       30.44        18.05         0.72        10.06        22.98         5.03 
TCGA-CM-5863 TCGA-D5-6931 TCGA-DM-A1HB TCGA-G4-6315 TCGA-G4-6321 TCGA-AG-3892 
       15.02        12.00       135.65        61.91        22.09        13.02 
TCGA-DY-A0XA 
      126.44 

$`AIFM1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L 
       38.04        19.00        30.02        34.03        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
       56.55         0.79         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       12.76        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5864 
       29.06        22.03        30.08        32.02        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6932 TCGA-D5-7000 
        9.44        11.64         4.80         1.51        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       36.00        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       17.95        36.95        17.03        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
        5.29        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  AIFM1 MUTATED AIFM1 WILD-TYPE 
           0.72            0.00 
  AIFM1 MUTATED AIFM1 WILD-TYPE 
         135.65          148.01 
  AIFM1 MUTATED AIFM1 WILD-TYPE 
         18.050          20.235 
[1] "0.7 - 135.7 (18.1)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.6"
D652V2, continuous
D652V3, binary
                 cls
clus                0   1
  AIFM1 MUTATED    11   2
  AIFM1 WILD-TYPE 355 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AIFM1 MUTATED     11    2
  AIFM1 WILD-TYPE  355  117
        clus
vv       AIFM1 MUTATED AIFM1 WILD-TYPE
  COLON             11             355
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  AIFM1 MUTATED         2        0        0         2         0         0
  AIFM1 WILD-TYPE      89        1       32       136        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AIFM1 MUTATED           1          0          4          1        1         1
  AIFM1 WILD-TYPE        23         11         55         41       47        17
                 vv
clus              STAGE IVB
  AIFM1 MUTATED           0
  AIFM1 WILD-TYPE         1
D652V4, multiclass
            clus
vv           AIFM1 MUTATED AIFM1 WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              2             136
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             4              55
  STAGE IIIC             1              41
  STAGE IV               1              47
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  AIFM1 MUTATED     1   2   8   2
  AIFM1 WILD-TYPE  16  90 321  48
D652V5, multiclass
    clus
vv   AIFM1 MUTATED AIFM1 WILD-TYPE
  T1             1              16
  T2             2              90
  T3             8             321
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  AIFM1 MUTATED     4   8   1
  AIFM1 WILD-TYPE 283 105  86
D652V6, multiclass
    clus
vv   AIFM1 MUTATED AIFM1 WILD-TYPE
  N0             4             283
  N1             8             105
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D652V7, binary
                 cls
clus                0   1
  AIFM1 MUTATED     9   2
  AIFM1 WILD-TYPE 366  63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AIFM1 MUTATED      9    2
  AIFM1 WILD-TYPE  366   63
   clus
vv  AIFM1 MUTATED AIFM1 WILD-TYPE
  0             9             366
  1             2              63
[1] 2 2
[1] FALSE
D652V8, binary
                 cls
clus                0   1
  AIFM1 MUTATED     4   9
  AIFM1 WILD-TYPE 221 255
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AIFM1 MUTATED      4    9
  AIFM1 WILD-TYPE  221  255
        clus
vv       AIFM1 MUTATED AIFM1 WILD-TYPE
  FEMALE             4             221
  MALE               9             255
[1] 2 2
[1] FALSE
D652V9, binary
                 cls
clus                0   1
  AIFM1 MUTATED    10   0
  AIFM1 WILD-TYPE 340  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AIFM1 MUTATED     10    0
  AIFM1 WILD-TYPE  340   22
     clus
vv    AIFM1 MUTATED AIFM1 WILD-TYPE
  NO             10             340
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  AIFM1 MUTATED                      8                             2
  AIFM1 WILD-TYPE                  307                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  AIFM1 MUTATED                       2                              0
  AIFM1 WILD-TYPE                   104                             10
D652V10, multiclass
                                clus
vv                               AIFM1 MUTATED AIFM1 WILD-TYPE
  COLON ADENOCARCINOMA                       8             307
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  AIFM1 MUTATED     9   0   0   1
  AIFM1 WILD-TYPE 336   4  31  24
D652V11, multiclass
    clus
vv   AIFM1 MUTATED AIFM1 WILD-TYPE
  R0             9             336
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D652V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AIFM1 MUTATED                                  0     1
  AIFM1 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  AIFM1 MUTATED                           0    10
  AIFM1 WILD-TYPE                        22   216
D652V13, multiclass
                                  clus
vv                                 AIFM1 MUTATED AIFM1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                       10             216
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(653) Variable = WNK4 MUTATION ANALYSIS
D653V1, survival
                sevent
clus2              0   1
  WNK4 MUTATED    11   1
  WNK4 WILD-TYPE 367  92
  WNK4 MUTATED WNK4 WILD-TYPE 
            12            459 
  WNK4 MUTATED WNK4 WILD-TYPE 
             1             92 
$`WNK4 MUTATED`
TCGA-A6-6653 TCGA-AA-3492 TCGA-AA-3663 TCGA-AA-3864 TCGA-AA-3877 TCGA-AA-3950 
       24.39         3.02         6.97        53.00        31.00        24.00 
TCGA-AU-6004 TCGA-AZ-4315 TCGA-CK-6747 TCGA-D5-6928 TCGA-D5-6930 TCGA-AH-6644 
       27.09        58.39        82.95        11.64         1.51         0.72 

$`WNK4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
       25.08        25.18        24.16        21.76        24.69        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 
       20.12        19.66        20.28         7.04         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        31.07        30.05        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       29.98        18.05         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       26.01         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 
       22.42        27.42        10.88         0.20        14.50        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        33.01        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 
        4.41        12.43        14.30         9.04         9.44         4.80 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
        1.45        17.49         0.69         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  WNK4 MUTATED WNK4 WILD-TYPE 
          0.72           0.00 
  WNK4 MUTATED WNK4 WILD-TYPE 
         82.95         148.01 
  WNK4 MUTATED WNK4 WILD-TYPE 
        24.195         20.120 
[1] "0.7 - 83.0 (24.2)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "2.6"
D653V2, continuous
D653V3, binary
                cls
clus               0   1
  WNK4 MUTATED    11   1
  WNK4 WILD-TYPE 355 118
[1] "tbl2"
                cls
clus             [,1] [,2]
  WNK4 MUTATED     11    1
  WNK4 WILD-TYPE  355  118
        clus
vv       WNK4 MUTATED WNK4 WILD-TYPE
  COLON            11            355
  RECTUM            1            118
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  WNK4 MUTATED         3        0        3         5         0         0
  WNK4 WILD-TYPE      88        1       29       133        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  WNK4 MUTATED           0          0          0          0        0         0
  WNK4 WILD-TYPE        24         11         59         42       48        18
                vv
clus             STAGE IVB
  WNK4 MUTATED           0
  WNK4 WILD-TYPE         1
D653V4, multiclass
            clus
vv           WNK4 MUTATED WNK4 WILD-TYPE
  STAGE I               3             88
  STAGE IA              0              1
  STAGE II              3             29
  STAGE IIA             5            133
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            0             59
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  WNK4 MUTATED     1   2   9   0
  WNK4 WILD-TYPE  16  90 320  50
D653V5, multiclass
    clus
vv   WNK4 MUTATED WNK4 WILD-TYPE
  T1            1             16
  T2            2             90
  T3            9            320
  T4            0             50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  WNK4 MUTATED    11   0   0
  WNK4 WILD-TYPE 276 113  87
D653V6, multiclass
    clus
vv   WNK4 MUTATED WNK4 WILD-TYPE
  N0           11            276
  N1            0            113
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D653V7, binary
                cls
clus               0   1
  WNK4 MUTATED    10   0
  WNK4 WILD-TYPE 365  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  WNK4 MUTATED     10    0
  WNK4 WILD-TYPE  365   65
   clus
vv  WNK4 MUTATED WNK4 WILD-TYPE
  0           10            365
  1            0             65
[1] 2 2
[1] FALSE
D653V8, binary
                cls
clus               0   1
  WNK4 MUTATED     5   7
  WNK4 WILD-TYPE 220 257
[1] "tbl2"
                cls
clus             [,1] [,2]
  WNK4 MUTATED      5    7
  WNK4 WILD-TYPE  220  257
        clus
vv       WNK4 MUTATED WNK4 WILD-TYPE
  FEMALE            5            220
  MALE              7            257
[1] 2 2
[1] FALSE
D653V9, binary
                cls
clus               0   1
  WNK4 MUTATED     9   0
  WNK4 WILD-TYPE 341  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  WNK4 MUTATED      9    0
  WNK4 WILD-TYPE  341   22
     clus
vv    WNK4 MUTATED WNK4 WILD-TYPE
  NO             9            341
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  WNK4 MUTATED                      7                             4
  WNK4 WILD-TYPE                  308                            43
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  WNK4 MUTATED                       1                              0
  WNK4 WILD-TYPE                   105                             10
D653V10, multiclass
                                clus
vv                               WNK4 MUTATED WNK4 WILD-TYPE
  COLON ADENOCARCINOMA                      7            308
  COLON MUCINOUS ADENOCARCINOMA             4             43
  RECTAL ADENOCARCINOMA                     1            105
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  WNK4 MUTATED     9   0   0   1
  WNK4 WILD-TYPE 336   4  31  24
D653V11, multiclass
    clus
vv   WNK4 MUTATED WNK4 WILD-TYPE
  R0            9            336
  R1            0              4
  R2            0             31
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D653V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  WNK4 MUTATED                                  0     0
  WNK4 WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  WNK4 MUTATED                           0     7
  WNK4 WILD-TYPE                        22   219
D653V13, multiclass
                                  clus
vv                                 WNK4 MUTATED WNK4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       7            219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(654) Variable = POLM MUTATION ANALYSIS
D654V1, survival
                sevent
clus2              0   1
  POLM MUTATED    10   1
  POLM WILD-TYPE 368  92
  POLM MUTATED POLM WILD-TYPE 
            11            460 
  POLM MUTATED POLM WILD-TYPE 
             1             92 
$`POLM MUTATED`
TCGA-A6-6781 TCGA-AA-3672 TCGA-AZ-4682 TCGA-CK-5913 TCGA-CM-5861 TCGA-D5-6535 
       19.66         0.92        22.36        51.32        15.02        15.12 
TCGA-D5-6927 TCGA-D5-6930 TCGA-DM-A1HB TCGA-G4-6293 TCGA-AG-A02N 
        9.44         1.51       135.65       133.18        61.97 

$`POLM WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 
        6.97        54.02         2.01        14.01        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
      106.75        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        49.08         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 
       29.06        22.03        22.98        30.08        32.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       43.27        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
        9.04        11.64         4.80        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6303 
       13.25         0.53        47.41        35.31        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
        1.94        38.96        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  POLM MUTATED POLM WILD-TYPE 
          0.92           0.00 
  POLM MUTATED POLM WILD-TYPE 
        135.65         148.01 
  POLM MUTATED POLM WILD-TYPE 
        19.660         20.235 
[1] "0.9 - 135.7 (19.7)" "0.0 - 148.0 (20.2)"
[1] "hr=" "3.2"
D654V2, continuous
D654V3, binary
                cls
clus               0   1
  POLM MUTATED    11   1
  POLM WILD-TYPE 355 118
[1] "tbl2"
                cls
clus             [,1] [,2]
  POLM MUTATED     11    1
  POLM WILD-TYPE  355  118
        clus
vv       POLM MUTATED POLM WILD-TYPE
  COLON            11            355
  RECTUM            1            118
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  POLM MUTATED         0        0        1         4         1         0
  POLM WILD-TYPE      91        1       31       134         9         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  POLM MUTATED           2          0          2          1        0         1
  POLM WILD-TYPE        22         11         57         41       48        17
                vv
clus             STAGE IVB
  POLM MUTATED           0
  POLM WILD-TYPE         1
D654V4, multiclass
            clus
vv           POLM MUTATED POLM WILD-TYPE
  STAGE I               0             91
  STAGE IA              0              1
  STAGE II              1             31
  STAGE IIA             4            134
  STAGE IIB             1              9
  STAGE IIC             0              1
  STAGE III             2             22
  STAGE IIIA            0             11
  STAGE IIIB            2             57
  STAGE IIIC            1             41
  STAGE IV              0             48
  STAGE IVA             1             17
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  POLM MUTATED     0   0  10   2
  POLM WILD-TYPE  17  92 319  48
D654V5, multiclass
    clus
vv   POLM MUTATED POLM WILD-TYPE
  T1            0             17
  T2            0             92
  T3           10            319
  T4            2             48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  POLM MUTATED     7   5   0
  POLM WILD-TYPE 280 108  87
D654V6, multiclass
    clus
vv   POLM MUTATED POLM WILD-TYPE
  N0            7            280
  N1            5            108
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D654V7, binary
                cls
clus               0   1
  POLM MUTATED     7   1
  POLM WILD-TYPE 368  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  POLM MUTATED      7    1
  POLM WILD-TYPE  368   64
   clus
vv  POLM MUTATED POLM WILD-TYPE
  0            7            368
  1            1             64
[1] 2 2
[1] FALSE
D654V8, binary
                cls
clus               0   1
  POLM MUTATED     6   6
  POLM WILD-TYPE 219 258
[1] "tbl2"
                cls
clus             [,1] [,2]
  POLM MUTATED      6    6
  POLM WILD-TYPE  219  258
        clus
vv       POLM MUTATED POLM WILD-TYPE
  FEMALE            6            219
  MALE              6            258
[1] 2 2
[1] FALSE
D654V9, binary
                cls
clus               0   1
  POLM MUTATED     8   0
  POLM WILD-TYPE 342  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  POLM MUTATED      8    0
  POLM WILD-TYPE  342   22
     clus
vv    POLM MUTATED POLM WILD-TYPE
  NO             8            342
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  POLM MUTATED                      8                             2
  POLM WILD-TYPE                  307                            45
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  POLM MUTATED                       1                              0
  POLM WILD-TYPE                   105                             10
D654V10, multiclass
                                clus
vv                               POLM MUTATED POLM WILD-TYPE
  COLON ADENOCARCINOMA                      8            307
  COLON MUCINOUS ADENOCARCINOMA             2             45
  RECTAL ADENOCARCINOMA                     1            105
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  POLM MUTATED     8   0   0   3
  POLM WILD-TYPE 337   4  31  22
D654V11, multiclass
    clus
vv   POLM MUTATED POLM WILD-TYPE
  R0            8            337
  R1            0              4
  R2            0             31
  RX            3             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D654V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  POLM MUTATED                                  0     0
  POLM WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  POLM MUTATED                           0    10
  POLM WILD-TYPE                        22   216
D654V13, multiclass
                                  clus
vv                                 POLM MUTATED POLM WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                      10            216
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(655) Variable = RCSD1 MUTATION ANALYSIS
D655V1, survival
                 sevent
clus2               0   1
  RCSD1 MUTATED    11   5
  RCSD1 WILD-TYPE 367  88
  RCSD1 MUTATED RCSD1 WILD-TYPE 
             16             455 
  RCSD1 MUTATED RCSD1 WILD-TYPE 
              5              88 
$`RCSD1 MUTATED`
TCGA-A6-2672 TCGA-AA-3542 TCGA-AA-3713 TCGA-AA-A00J TCGA-AD-6899 TCGA-AU-6004 
       46.65        12.99        19.04        18.05         5.79        27.09 
TCGA-AZ-6598 TCGA-AZ-6600 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-5913 TCGA-CK-5914 
       49.41        12.10        10.06        14.30        51.32         9.99 
TCGA-D5-6930 TCGA-G4-6303 TCGA-AG-3892 TCGA-AG-A02N 
        1.51        65.85        13.02        61.97 

$`RCSD1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       26.01         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        0.72        22.42        27.42        10.88         0.20        14.50 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       12.20        12.76        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       49.08        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 
        9.04         9.44        11.64         4.80        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
      133.18        74.56        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
       49.97         1.94        38.96        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  RCSD1 MUTATED RCSD1 WILD-TYPE 
           1.51            0.00 
  RCSD1 MUTATED RCSD1 WILD-TYPE 
          65.85          148.01 
  RCSD1 MUTATED RCSD1 WILD-TYPE 
         16.175          20.550 
[1] "1.5 - 65.8 (16.2)"  "0.0 - 148.0 (20.6)"
[1] "hr=" "1.5"
D655V2, continuous
D655V3, binary
                 cls
clus                0   1
  RCSD1 MUTATED    14   2
  RCSD1 WILD-TYPE 352 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RCSD1 MUTATED     14    2
  RCSD1 WILD-TYPE  352  117
        clus
vv       RCSD1 MUTATED RCSD1 WILD-TYPE
  COLON             14             352
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RCSD1 MUTATED         2        0        2         4         0         0
  RCSD1 WILD-TYPE      89        1       30       134        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RCSD1 MUTATED           0          0          3          2        3         0
  RCSD1 WILD-TYPE        24         11         56         40       45        18
                 vv
clus              STAGE IVB
  RCSD1 MUTATED           0
  RCSD1 WILD-TYPE         1
D655V4, multiclass
            clus
vv           RCSD1 MUTATED RCSD1 WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA              4             134
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             3              56
  STAGE IIIC             2              40
  STAGE IV               3              45
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  RCSD1 MUTATED     1   1  11   3
  RCSD1 WILD-TYPE  16  91 318  47
D655V5, multiclass
    clus
vv   RCSD1 MUTATED RCSD1 WILD-TYPE
  T1             1              16
  T2             1              91
  T3            11             318
  T4             3              47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  RCSD1 MUTATED     9   5   2
  RCSD1 WILD-TYPE 278 108  85
D655V6, multiclass
    clus
vv   RCSD1 MUTATED RCSD1 WILD-TYPE
  N0             9             278
  N1             5             108
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D655V7, binary
                 cls
clus                0   1
  RCSD1 MUTATED     9   3
  RCSD1 WILD-TYPE 366  62
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RCSD1 MUTATED      9    3
  RCSD1 WILD-TYPE  366   62
   clus
vv  RCSD1 MUTATED RCSD1 WILD-TYPE
  0             9             366
  1             3              62
[1] 2 2
[1] FALSE
D655V8, binary
                 cls
clus                0   1
  RCSD1 MUTATED     6  10
  RCSD1 WILD-TYPE 219 254
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RCSD1 MUTATED      6   10
  RCSD1 WILD-TYPE  219  254
        clus
vv       RCSD1 MUTATED RCSD1 WILD-TYPE
  FEMALE             6             219
  MALE              10             254
[1] 2 2
[1] FALSE
D655V9, binary
                 cls
clus                0   1
  RCSD1 MUTATED    10   1
  RCSD1 WILD-TYPE 340  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RCSD1 MUTATED     10    1
  RCSD1 WILD-TYPE  340   21
     clus
vv    RCSD1 MUTATED RCSD1 WILD-TYPE
  NO             10             340
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  RCSD1 MUTATED                     11                             3
  RCSD1 WILD-TYPE                  304                            44
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  RCSD1 MUTATED                       2                              0
  RCSD1 WILD-TYPE                   104                             10
D655V10, multiclass
                                clus
vv                               RCSD1 MUTATED RCSD1 WILD-TYPE
  COLON ADENOCARCINOMA                      11             304
  COLON MUCINOUS ADENOCARCINOMA              3              44
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  RCSD1 MUTATED     8   0   1   4
  RCSD1 WILD-TYPE 337   4  30  21
D655V11, multiclass
    clus
vv   RCSD1 MUTATED RCSD1 WILD-TYPE
  R0             8             337
  R1             0               4
  R2             1              30
  RX             4              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D655V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RCSD1 MUTATED                                  0     2
  RCSD1 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  RCSD1 MUTATED                           1     8
  RCSD1 WILD-TYPE                        21   218
D655V13, multiclass
                                  clus
vv                                 RCSD1 MUTATED RCSD1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               9
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        8             218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(656) Variable = CSNK1D MUTATION ANALYSIS
D656V1, survival
                  sevent
clus2                0   1
  CSNK1D MUTATED    14   1
  CSNK1D WILD-TYPE 364  92
  CSNK1D MUTATED CSNK1D WILD-TYPE 
              15              456 
  CSNK1D MUTATED CSNK1D WILD-TYPE 
               1               92 
$`CSNK1D MUTATED`
TCGA-A6-5661 TCGA-A6-5662 TCGA-AA-3821 TCGA-AA-3864 TCGA-AA-A00R TCGA-AY-5543 
       33.53        23.61         1.02        53.00         0.99        33.01 
TCGA-AZ-4315 TCGA-AZ-6605 TCGA-CA-6717 TCGA-CM-5861 TCGA-CM-6679 TCGA-D5-6533 
       58.39         5.23        12.76        15.02        10.06         1.32 
TCGA-D5-6928 TCGA-G4-6628 TCGA-AG-A002 
       11.64        79.69        20.98 

$`CSNK1D WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5664 TCGA-A6-5665 
       32.91        31.63        30.44        29.19        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 
       35.05        33.04         0.99        25.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        31.07        30.05        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
       42.02        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
       27.09        16.31         0.95        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77        12.10       100.01        29.56        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.20        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.08        11.01        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6534 
       19.59        56.09        55.92        20.19        18.25        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.04         9.44         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 
       35.80        26.17        91.79        46.75        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  CSNK1D MUTATED CSNK1D WILD-TYPE 
            0.99             0.00 
  CSNK1D MUTATED CSNK1D WILD-TYPE 
           79.69           148.01 
  CSNK1D MUTATED CSNK1D WILD-TYPE 
          15.020           20.235 
[1] "1.0 - 79.7 (15.0)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "2.8"
D656V2, continuous
D656V3, binary
                  cls
clus                 0   1
  CSNK1D MUTATED    14   1
  CSNK1D WILD-TYPE 352 118
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CSNK1D MUTATED     14    1
  CSNK1D WILD-TYPE  352  118
        clus
vv       CSNK1D MUTATED CSNK1D WILD-TYPE
  COLON              14              352
  RECTUM              1              118
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CSNK1D MUTATED         4        0        1         6         0         0
  CSNK1D WILD-TYPE      87        1       31       132        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CSNK1D MUTATED           0          0          2          0        0
  CSNK1D WILD-TYPE        24         11         57         42       48
                  vv
clus               STAGE IVA STAGE IVB
  CSNK1D MUTATED           2         0
  CSNK1D WILD-TYPE        16         1
D656V4, multiclass
            clus
vv           CSNK1D MUTATED CSNK1D WILD-TYPE
  STAGE I                 4               87
  STAGE IA                0                1
  STAGE II                1               31
  STAGE IIA               6              132
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              2               57
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               2               16
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  CSNK1D MUTATED     0   4   9   2
  CSNK1D WILD-TYPE  17  88 320  48
D656V5, multiclass
    clus
vv   CSNK1D MUTATED CSNK1D WILD-TYPE
  T1              0               17
  T2              4               88
  T3              9              320
  T4              2               48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  CSNK1D MUTATED    12   2   1
  CSNK1D WILD-TYPE 275 111  86
D656V6, multiclass
    clus
vv   CSNK1D MUTATED CSNK1D WILD-TYPE
  N0             12              275
  N1              2              111
  N2              1               86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D656V7, binary
                  cls
clus                 0   1
  CSNK1D MUTATED    13   2
  CSNK1D WILD-TYPE 362  63
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CSNK1D MUTATED     13    2
  CSNK1D WILD-TYPE  362   63
   clus
vv  CSNK1D MUTATED CSNK1D WILD-TYPE
  0             13              362
  1              2               63
[1] 2 2
[1] FALSE
D656V8, binary
                  cls
clus                 0   1
  CSNK1D MUTATED     6   9
  CSNK1D WILD-TYPE 219 255
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CSNK1D MUTATED      6    9
  CSNK1D WILD-TYPE  219  255
        clus
vv       CSNK1D MUTATED CSNK1D WILD-TYPE
  FEMALE              6              219
  MALE                9              255
[1] 2 2
[1] FALSE
D656V9, binary
                  cls
clus                 0   1
  CSNK1D MUTATED    13   0
  CSNK1D WILD-TYPE 337  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CSNK1D MUTATED     13    0
  CSNK1D WILD-TYPE  337   22
     clus
vv    CSNK1D MUTATED CSNK1D WILD-TYPE
  NO              13              337
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CSNK1D MUTATED                     11                             3
  CSNK1D WILD-TYPE                  304                            44
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CSNK1D MUTATED                       1                              0
  CSNK1D WILD-TYPE                   105                             10
D656V10, multiclass
                                clus
vv                               CSNK1D MUTATED CSNK1D WILD-TYPE
  COLON ADENOCARCINOMA                       11              304
  COLON MUCINOUS ADENOCARCINOMA               3               44
  RECTAL ADENOCARCINOMA                       1              105
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  CSNK1D MUTATED    12   0   0   1
  CSNK1D WILD-TYPE 333   4  31  24
D656V11, multiclass
    clus
vv   CSNK1D MUTATED CSNK1D WILD-TYPE
  R0             12              333
  R1              0                4
  R2              0               31
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D656V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CSNK1D MUTATED                                  0     1
  CSNK1D WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  CSNK1D MUTATED                           2     8
  CSNK1D WILD-TYPE                        20   218
D656V13, multiclass
                                  clus
vv                                 CSNK1D MUTATED CSNK1D WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     2               20
  WHITE                                         8              218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(657) Variable = GPNMB MUTATION ANALYSIS
D657V1, survival
                 sevent
clus2               0   1
  GPNMB MUTATED     8   4
  GPNMB WILD-TYPE 370  89
  GPNMB MUTATED GPNMB WILD-TYPE 
             12             459 
  GPNMB MUTATED GPNMB WILD-TYPE 
              4              89 
$`GPNMB MUTATED`
TCGA-AA-3496 TCGA-AA-3672 TCGA-AA-3977 TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-5868 
        1.02         0.92        25.02        12.76        10.06        17.03 
TCGA-D5-6536 TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A28C TCGA-DM-A28H TCGA-DY-A1DG 
       17.85        44.32       135.65        81.37       117.07        51.48 

$`GPNMB WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 
        6.97        54.02         2.01        14.01        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        15.02        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       15.12         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HA 
       49.91        13.32        12.59       140.38         7.50       131.51 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28K 
      139.17         6.12       119.93        35.97        60.79        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  GPNMB MUTATED GPNMB WILD-TYPE 
           0.92            0.00 
  GPNMB MUTATED GPNMB WILD-TYPE 
         135.65          148.01 
  GPNMB MUTATED GPNMB WILD-TYPE 
         21.435          20.190 
[1] "0.9 - 135.7 (21.4)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.1"
D657V2, continuous
D657V3, binary
                 cls
clus                0   1
  GPNMB MUTATED    13   1
  GPNMB WILD-TYPE 353 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPNMB MUTATED     13    1
  GPNMB WILD-TYPE  353  118
        clus
vv       GPNMB MUTATED GPNMB WILD-TYPE
  COLON             13             353
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GPNMB MUTATED         0        0        1         5         1         0
  GPNMB WILD-TYPE      91        1       31       133         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  GPNMB MUTATED           2          0          1          1        0         2
  GPNMB WILD-TYPE        22         11         58         41       48        16
                 vv
clus              STAGE IVB
  GPNMB MUTATED           0
  GPNMB WILD-TYPE         1
D657V4, multiclass
            clus
vv           GPNMB MUTATED GPNMB WILD-TYPE
  STAGE I                0              91
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              5             133
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              2              22
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             1              41
  STAGE IV               0              48
  STAGE IVA              2              16
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  GPNMB MUTATED     0   1  11   2
  GPNMB WILD-TYPE  17  91 318  48
D657V5, multiclass
    clus
vv   GPNMB MUTATED GPNMB WILD-TYPE
  T1             0              17
  T2             1              91
  T3            11             318
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  GPNMB MUTATED     8   4   2
  GPNMB WILD-TYPE 279 109  85
D657V6, multiclass
    clus
vv   GPNMB MUTATED GPNMB WILD-TYPE
  N0             8             279
  N1             4             109
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D657V7, binary
                 cls
clus                0   1
  GPNMB MUTATED    10   2
  GPNMB WILD-TYPE 365  63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPNMB MUTATED     10    2
  GPNMB WILD-TYPE  365   63
   clus
vv  GPNMB MUTATED GPNMB WILD-TYPE
  0            10             365
  1             2              63
[1] 2 2
[1] FALSE
D657V8, binary
                 cls
clus                0   1
  GPNMB MUTATED     4  10
  GPNMB WILD-TYPE 221 254
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPNMB MUTATED      4   10
  GPNMB WILD-TYPE  221  254
        clus
vv       GPNMB MUTATED GPNMB WILD-TYPE
  FEMALE             4             221
  MALE              10             254
[1] 2 2
[1] FALSE
D657V9, binary
                 cls
clus                0   1
  GPNMB MUTATED     6   0
  GPNMB WILD-TYPE 344  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPNMB MUTATED      6    0
  GPNMB WILD-TYPE  344   22
     clus
vv    GPNMB MUTATED GPNMB WILD-TYPE
  NO              6             344
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  GPNMB MUTATED                     11                             1
  GPNMB WILD-TYPE                  304                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  GPNMB MUTATED                       1                              0
  GPNMB WILD-TYPE                   105                             10
D657V10, multiclass
                                clus
vv                               GPNMB MUTATED GPNMB WILD-TYPE
  COLON ADENOCARCINOMA                      11             304
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  GPNMB MUTATED     5   0   0   3
  GPNMB WILD-TYPE 340   4  31  22
D657V11, multiclass
    clus
vv   GPNMB MUTATED GPNMB WILD-TYPE
  R0             5             340
  R1             0               4
  R2             0              31
  RX             3              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D657V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GPNMB MUTATED                                  0     2
  GPNMB WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  GPNMB MUTATED                           0     8
  GPNMB WILD-TYPE                        22   218
D657V13, multiclass
                                  clus
vv                                 GPNMB MUTATED GPNMB WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               9
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        8             218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(658) Variable = ATP11C MUTATION ANALYSIS
D658V1, survival
                  sevent
clus2                0   1
  ATP11C MUTATED    22   6
  ATP11C WILD-TYPE 356  87
  ATP11C MUTATED ATP11C WILD-TYPE 
              28              443 
  ATP11C MUTATED ATP11C WILD-TYPE 
               6               87 
$`ATP11C MUTATED`
TCGA-A6-4105 TCGA-A6-5661 TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3660 
       14.53        33.53        23.87        19.66        20.28        78.08 
TCGA-AA-3947 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-A00N TCGA-AA-A00R TCGA-AA-A010 
       33.01        25.02        27.02         4.01         0.99        34.98 
TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-CA-6717 TCGA-CA-6718 
       21.44        58.39        12.10       100.01        12.76        10.06 
TCGA-CK-4947 TCGA-D5-6535 TCGA-DM-A1HA TCGA-DM-A28F TCGA-G4-6586 TCGA-G4-6588 
       17.56        15.12       131.51        35.97        35.80        26.17 
TCGA-AF-2692 TCGA-AG-3893 TCGA-CI-6619 TCGA-EI-6510 
       13.55        35.01         6.05        18.28 

$`ATP11C WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 
       16.57        34.65        33.34        32.75        36.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       31.63        30.44        29.19        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 TCGA-AA-3489 
       24.16        21.76        24.69        24.39        20.12         7.04 
TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
        3.02         1.02        35.01        63.98         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
       13.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       36.03         8.05        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 
       31.00         2.01        12.99        24.00        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3982 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
       42.02        17.03        14.99        21.99         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
       16.31         0.95        33.01        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 
        3.06         3.25         3.29         0.07        12.20        14.30 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 
       55.92        20.19        18.25         1.32        43.27        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HB 
       13.32        12.59       140.38         7.50        44.32       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H 
      139.17         6.12        81.37       119.93        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       36.00        22.09        13.78        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       24.13        39.48        43.04        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       17.03        13.02        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        0.72        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       19.96        20.91         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  ATP11C MUTATED ATP11C WILD-TYPE 
            0.99             0.00 
  ATP11C MUTATED ATP11C WILD-TYPE 
          131.51           148.01 
  ATP11C MUTATED ATP11C WILD-TYPE 
          22.655           20.050 
[1] "1.0 - 131.5 (22.7)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1"  
D658V2, continuous
D658V3, binary
                  cls
clus                 0   1
  ATP11C MUTATED    25   3
  ATP11C WILD-TYPE 341 116
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP11C MUTATED     25    3
  ATP11C WILD-TYPE  341  116
        clus
vv       ATP11C MUTATED ATP11C WILD-TYPE
  COLON              25              341
  RECTUM              3              116
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ATP11C MUTATED         2        0        2        10         4         0
  ATP11C WILD-TYPE      89        1       30       128         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ATP11C MUTATED           0          0          5          2        2
  ATP11C WILD-TYPE        24         11         54         40       46
                  vv
clus               STAGE IVA STAGE IVB
  ATP11C MUTATED           1         0
  ATP11C WILD-TYPE        17         1
D658V4, multiclass
            clus
vv           ATP11C MUTATED ATP11C WILD-TYPE
  STAGE I                 2               89
  STAGE IA                0                1
  STAGE II                2               30
  STAGE IIA              10              128
  STAGE IIB               4                6
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              5               54
  STAGE IIIC              2               40
  STAGE IV                2               46
  STAGE IVA               1               17
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ATP11C MUTATED     0   4  18   7
  ATP11C WILD-TYPE  17  88 311  43
D658V5, multiclass
    clus
vv   ATP11C MUTATED ATP11C WILD-TYPE
  T1              0               17
  T2              4               88
  T3             18              311
  T4              7               43
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  ATP11C MUTATED    20   8   1
  ATP11C WILD-TYPE 267 105  86
D658V6, multiclass
    clus
vv   ATP11C MUTATED ATP11C WILD-TYPE
  N0             20              267
  N1              8              105
  N2              1               86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D658V7, binary
                  cls
clus                 0   1
  ATP11C MUTATED    21   2
  ATP11C WILD-TYPE 354  63
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP11C MUTATED     21    2
  ATP11C WILD-TYPE  354   63
   clus
vv  ATP11C MUTATED ATP11C WILD-TYPE
  0             21              354
  1              2               63
[1] 2 2
[1] FALSE
D658V8, binary
                  cls
clus                 0   1
  ATP11C MUTATED    14  15
  ATP11C WILD-TYPE 211 249
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP11C MUTATED     14   15
  ATP11C WILD-TYPE  211  249
        clus
vv       ATP11C MUTATED ATP11C WILD-TYPE
  FEMALE             14              211
  MALE               15              249
[1] 2 2
[1] FALSE
D658V9, binary
                  cls
clus                 0   1
  ATP11C MUTATED    22   0
  ATP11C WILD-TYPE 328  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP11C MUTATED     22    0
  ATP11C WILD-TYPE  328   22
     clus
vv    ATP11C MUTATED ATP11C WILD-TYPE
  NO              22              328
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ATP11C MUTATED                     21                             4
  ATP11C WILD-TYPE                  294                            43
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ATP11C MUTATED                       3                              0
  ATP11C WILD-TYPE                   103                             10
D658V10, multiclass
                                clus
vv                               ATP11C MUTATED ATP11C WILD-TYPE
  COLON ADENOCARCINOMA                       21              294
  COLON MUCINOUS ADENOCARCINOMA               4               43
  RECTAL ADENOCARCINOMA                       3              103
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ATP11C MUTATED    15   0   0   4
  ATP11C WILD-TYPE 330   4  31  21
D658V11, multiclass
    clus
vv   ATP11C MUTATED ATP11C WILD-TYPE
  R0             15              330
  R1              0                4
  R2              0               31
  RX              4               21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D658V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ATP11C MUTATED                                  0     2
  ATP11C WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ATP11C MUTATED                           2    16
  ATP11C WILD-TYPE                        20   210
D658V13, multiclass
                                  clus
vv                                 ATP11C MUTATED ATP11C WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                9
  BLACK OR AFRICAN AMERICAN                     2               20
  WHITE                                        16              210
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(659) Variable = IQGAP1 MUTATION ANALYSIS
D659V1, survival
                  sevent
clus2                0   1
  IQGAP1 MUTATED    19   4
  IQGAP1 WILD-TYPE 359  89
  IQGAP1 MUTATED IQGAP1 WILD-TYPE 
              23              448 
  IQGAP1 MUTATED IQGAP1 WILD-TYPE 
               4               89 
$`IQGAP1 MUTATED`
TCGA-A6-2676 TCGA-A6-5665 TCGA-AA-3496 TCGA-AA-3555 TCGA-AA-3833 TCGA-AA-3947 
       42.90        22.06         1.02        29.95        15.95        33.01 
TCGA-AA-3950 TCGA-AA-3966 TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A00R TCGA-AA-A01Q 
       24.00         2.01        25.02         4.01         0.99         1.02 
TCGA-AD-6964 TCGA-AY-5543 TCGA-CA-6717 TCGA-CM-4743 TCGA-CM-5344 TCGA-CM-5860 
       10.88        33.01        12.76        23.05        22.03        32.02 
TCGA-F4-6570 TCGA-AG-3732 TCGA-AG-A002 TCGA-DC-5337 TCGA-DC-6155 
        6.18        32.98        20.98        15.02        13.97 

$`IQGAP1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3510 
       19.66        20.28         7.04         3.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       17.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3837 TCGA-AA-3842 
        0.99        25.02         1.02        17.98        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 
       18.05        31.00         2.01        12.99        24.00        26.01 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
        2.01        20.98        34.03        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
       42.02        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.20        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
        1.91       124.27        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       29.06        22.98        30.08        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       31.96        35.74        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 
       19.99         7.99         0.99        37.02         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5869 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
        5.03        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  IQGAP1 MUTATED IQGAP1 WILD-TYPE 
            0.99             0.00 
  IQGAP1 MUTATED IQGAP1 WILD-TYPE 
           42.90           148.01 
  IQGAP1 MUTATED IQGAP1 WILD-TYPE 
          20.980           20.155 
[1] "1.0 - 42.9 (21.0)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.3"
D659V2, continuous
D659V3, binary
                  cls
clus                 0   1
  IQGAP1 MUTATED    20   4
  IQGAP1 WILD-TYPE 346 115
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IQGAP1 MUTATED     20    4
  IQGAP1 WILD-TYPE  346  115
        clus
vv       IQGAP1 MUTATED IQGAP1 WILD-TYPE
  COLON              20              346
  RECTUM              4              115
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  IQGAP1 MUTATED         4        0        2         9         4         0
  IQGAP1 WILD-TYPE      87        1       30       129         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  IQGAP1 MUTATED           0          1          1          0        0
  IQGAP1 WILD-TYPE        24         10         58         42       48
                  vv
clus               STAGE IVA STAGE IVB
  IQGAP1 MUTATED           1         0
  IQGAP1 WILD-TYPE        17         1
D659V4, multiclass
            clus
vv           IQGAP1 MUTATED IQGAP1 WILD-TYPE
  STAGE I                 4               87
  STAGE IA                0                1
  STAGE II                2               30
  STAGE IIA               9              129
  STAGE IIB               4                6
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              1               10
  STAGE IIIB              1               58
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               1               17
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  IQGAP1 MUTATED     1   5  13   5
  IQGAP1 WILD-TYPE  16  87 316  45
D659V5, multiclass
    clus
vv   IQGAP1 MUTATED IQGAP1 WILD-TYPE
  T1              1               16
  T2              5               87
  T3             13              316
  T4              5               45
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  IQGAP1 MUTATED    20   3   1
  IQGAP1 WILD-TYPE 267 110  86
D659V6, multiclass
    clus
vv   IQGAP1 MUTATED IQGAP1 WILD-TYPE
  N0             20              267
  N1              3              110
  N2              1               86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D659V7, binary
                  cls
clus                 0   1
  IQGAP1 MUTATED    20   1
  IQGAP1 WILD-TYPE 355  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IQGAP1 MUTATED     20    1
  IQGAP1 WILD-TYPE  355   64
   clus
vv  IQGAP1 MUTATED IQGAP1 WILD-TYPE
  0             20              355
  1              1               64
[1] 2 2
[1] FALSE
D659V8, binary
                  cls
clus                 0   1
  IQGAP1 MUTATED    16   8
  IQGAP1 WILD-TYPE 209 256
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IQGAP1 MUTATED     16    8
  IQGAP1 WILD-TYPE  209  256
        clus
vv       IQGAP1 MUTATED IQGAP1 WILD-TYPE
  FEMALE             16              209
  MALE                8              256
[1] 2 2
[1] FALSE
D659V9, binary
                  cls
clus                 0   1
  IQGAP1 MUTATED    18   0
  IQGAP1 WILD-TYPE 332  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IQGAP1 MUTATED     18    0
  IQGAP1 WILD-TYPE  332   22
     clus
vv    IQGAP1 MUTATED IQGAP1 WILD-TYPE
  NO              18              332
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  IQGAP1 MUTATED                     14                             6
  IQGAP1 WILD-TYPE                  301                            41
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  IQGAP1 MUTATED                       4                              0
  IQGAP1 WILD-TYPE                   102                             10
D659V10, multiclass
                                clus
vv                               IQGAP1 MUTATED IQGAP1 WILD-TYPE
  COLON ADENOCARCINOMA                       14              301
  COLON MUCINOUS ADENOCARCINOMA               6               41
  RECTAL ADENOCARCINOMA                       4              102
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  IQGAP1 MUTATED    19   0   0   2
  IQGAP1 WILD-TYPE 326   4  31  23
D659V11, multiclass
    clus
vv   IQGAP1 MUTATED IQGAP1 WILD-TYPE
  R0             19              326
  R1              0                4
  R2              0               31
  RX              2               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D659V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  IQGAP1 MUTATED                                  0     1
  IQGAP1 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  IQGAP1 MUTATED                           1    10
  IQGAP1 WILD-TYPE                        21   216
D659V13, multiclass
                                  clus
vv                                 IQGAP1 MUTATED IQGAP1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                        10              216
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(660) Variable = TRMT5 MUTATION ANALYSIS
D660V1, survival
                 sevent
clus2               0   1
  TRMT5 MUTATED     6   2
  TRMT5 WILD-TYPE 372  91
  TRMT5 MUTATED TRMT5 WILD-TYPE 
              8             463 
  TRMT5 MUTATED TRMT5 WILD-TYPE 
              2              91 
$`TRMT5 MUTATED`
TCGA-AA-3697 TCGA-AA-A00N TCGA-AZ-6600 TCGA-CM-5861 TCGA-CM-6161 TCGA-D5-6927 
       85.05         4.01        12.10        15.02        15.02         9.44 
TCGA-AG-A002 TCGA-DT-5265 
       20.98         5.29 

$`TRMT5 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       19.00        36.00         5.03        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6162 TCGA-CM-6163 
        5.03        15.02        15.02        17.03        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
       14.30         9.04        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A0XA 
       10.98        19.99         5.95         4.01         5.03       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  TRMT5 MUTATED TRMT5 WILD-TYPE 
           4.01            0.00 
  TRMT5 MUTATED TRMT5 WILD-TYPE 
          85.05          148.01 
  TRMT5 MUTATED TRMT5 WILD-TYPE 
          13.56           20.55 
[1] "4.0 - 85.0 (13.6)"  "0.0 - 148.0 (20.6)"
[1] "hr=" "1.6"
D660V2, continuous
D660V3, binary
                 cls
clus                0   1
  TRMT5 MUTATED     6   2
  TRMT5 WILD-TYPE 360 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRMT5 MUTATED      6    2
  TRMT5 WILD-TYPE  360  117
        clus
vv       TRMT5 MUTATED TRMT5 WILD-TYPE
  COLON              6             360
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TRMT5 MUTATED         2        0        1         2         1         0
  TRMT5 WILD-TYPE      89        1       31       136         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TRMT5 MUTATED           1          0          0          0        1         0
  TRMT5 WILD-TYPE        23         11         59         42       47        18
                 vv
clus              STAGE IVB
  TRMT5 MUTATED           0
  TRMT5 WILD-TYPE         1
D660V4, multiclass
            clus
vv           TRMT5 MUTATED TRMT5 WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              2             136
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             0              42
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  TRMT5 MUTATED     0   2   4   2
  TRMT5 WILD-TYPE  17  90 325  48
D660V5, multiclass
    clus
vv   TRMT5 MUTATED TRMT5 WILD-TYPE
  T1             0              17
  T2             2              90
  T3             4             325
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  TRMT5 MUTATED     7   1   0
  TRMT5 WILD-TYPE 280 112  87
D660V6, multiclass
    clus
vv   TRMT5 MUTATED TRMT5 WILD-TYPE
  N0             7             280
  N1             1             112
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D660V7, binary
                 cls
clus                0   1
  TRMT5 MUTATED     7   1
  TRMT5 WILD-TYPE 368  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRMT5 MUTATED      7    1
  TRMT5 WILD-TYPE  368   64
   clus
vv  TRMT5 MUTATED TRMT5 WILD-TYPE
  0             7             368
  1             1              64
[1] 2 2
[1] FALSE
D660V8, binary
                 cls
clus                0   1
  TRMT5 MUTATED     2   6
  TRMT5 WILD-TYPE 223 258
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRMT5 MUTATED      2    6
  TRMT5 WILD-TYPE  223  258
        clus
vv       TRMT5 MUTATED TRMT5 WILD-TYPE
  FEMALE             2             223
  MALE               6             258
[1] 2 2
[1] FALSE
D660V9, binary
                 cls
clus                0   1
  TRMT5 MUTATED     6   0
  TRMT5 WILD-TYPE 344  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRMT5 MUTATED      6    0
  TRMT5 WILD-TYPE  344   22
     clus
vv    TRMT5 MUTATED TRMT5 WILD-TYPE
  NO              6             344
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  TRMT5 MUTATED                      5                             1
  TRMT5 WILD-TYPE                  310                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  TRMT5 MUTATED                       1                              1
  TRMT5 WILD-TYPE                   105                              9
D660V10, multiclass
                                clus
vv                               TRMT5 MUTATED TRMT5 WILD-TYPE
  COLON ADENOCARCINOMA                       5             310
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             1               9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  TRMT5 MUTATED     6   0   0   1
  TRMT5 WILD-TYPE 339   4  31  24
D660V11, multiclass
    clus
vv   TRMT5 MUTATED TRMT5 WILD-TYPE
  R0             6             339
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D660V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TRMT5 MUTATED                                  0     1
  TRMT5 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  TRMT5 MUTATED                           1     3
  TRMT5 WILD-TYPE                        21   223
D660V13, multiclass
                                  clus
vv                                 TRMT5 MUTATED TRMT5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        3             223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(661) Variable = MAP7D3 MUTATION ANALYSIS
D661V1, survival
                  sevent
clus2                0   1
  MAP7D3 MUTATED    17   5
  MAP7D3 WILD-TYPE 361  88
  MAP7D3 MUTATED MAP7D3 WILD-TYPE 
              22              449 
  MAP7D3 MUTATED MAP7D3 WILD-TYPE 
               5               88 
$`MAP7D3 MUTATED`
TCGA-A6-5665 TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3660 TCGA-AA-3710 TCGA-AA-3941 
       22.06         3.02        63.98        78.08        26.99        24.00 
TCGA-AA-A03J TCGA-AZ-4315 TCGA-AZ-4616 TCGA-CA-6717 TCGA-D5-6930 TCGA-DM-A28E 
       40.96        58.39         5.13        12.76         1.51       119.93 
TCGA-F4-6570 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-AF-2693 TCGA-AG-3892 
        6.18        35.80        26.17        91.79        19.10        13.02 
TCGA-AG-A002 TCGA-AG-A02N TCGA-DC-6158 TCGA-F5-6464 
       20.98        61.97        10.98         9.96 

$`MAP7D3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 
       20.12        19.66        20.28         7.04         1.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3947 TCGA-AA-3949 
       18.05        31.00         2.01        12.99        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6548 
        0.92        41.00        39.98        18.05         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4681 
        0.95        33.01        21.44        17.82         1.41       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
       81.37        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       31.96        35.74        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       17.95        36.95        17.03        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X 
       64.01        10.98        49.97         1.94        38.96        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6160 
        7.17        15.02         5.03        13.97        27.95        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       19.96        20.91        18.28        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  MAP7D3 MUTATED MAP7D3 WILD-TYPE 
            1.51             0.00 
  MAP7D3 MUTATED MAP7D3 WILD-TYPE 
          119.93           148.01 
  MAP7D3 MUTATED MAP7D3 WILD-TYPE 
           23.03            20.05 
[1] "1.5 - 119.9 (23.0)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.1"
D661V2, continuous
D661V3, binary
                  cls
clus                 0   1
  MAP7D3 MUTATED    17   5
  MAP7D3 WILD-TYPE 349 114
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP7D3 MUTATED     17    5
  MAP7D3 WILD-TYPE  349  114
        clus
vv       MAP7D3 MUTATED MAP7D3 WILD-TYPE
  COLON              17              349
  RECTUM              5              114
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MAP7D3 MUTATED         5        0        4        11         0         0
  MAP7D3 WILD-TYPE      86        1       28       127        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MAP7D3 MUTATED           0          0          0          1        1
  MAP7D3 WILD-TYPE        24         11         59         41       47
                  vv
clus               STAGE IVA STAGE IVB
  MAP7D3 MUTATED           1         0
  MAP7D3 WILD-TYPE        17         1
D661V4, multiclass
            clus
vv           MAP7D3 MUTATED MAP7D3 WILD-TYPE
  STAGE I                 5               86
  STAGE IA                0                1
  STAGE II                4               28
  STAGE IIA              11              127
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              0               59
  STAGE IIIC              1               41
  STAGE IV                1               47
  STAGE IVA               1               17
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  MAP7D3 MUTATED     1   4  16   2
  MAP7D3 WILD-TYPE  16  88 313  48
D661V5, multiclass
    clus
vv   MAP7D3 MUTATED MAP7D3 WILD-TYPE
  T1              1               16
  T2              4               88
  T3             16              313
  T4              2               48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  MAP7D3 MUTATED    20   1   2
  MAP7D3 WILD-TYPE 267 112  85
D661V6, multiclass
    clus
vv   MAP7D3 MUTATED MAP7D3 WILD-TYPE
  N0             20              267
  N1              1              112
  N2              2               85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D661V7, binary
                  cls
clus                 0   1
  MAP7D3 MUTATED    20   2
  MAP7D3 WILD-TYPE 355  63
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP7D3 MUTATED     20    2
  MAP7D3 WILD-TYPE  355   63
   clus
vv  MAP7D3 MUTATED MAP7D3 WILD-TYPE
  0             20              355
  1              2               63
[1] 2 2
[1] FALSE
D661V8, binary
                  cls
clus                 0   1
  MAP7D3 MUTATED    15   8
  MAP7D3 WILD-TYPE 210 256
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP7D3 MUTATED     15    8
  MAP7D3 WILD-TYPE  210  256
        clus
vv       MAP7D3 MUTATED MAP7D3 WILD-TYPE
  FEMALE             15              210
  MALE                8              256
[1] 2 2
[1] FALSE
D661V9, binary
                  cls
clus                 0   1
  MAP7D3 MUTATED    19   0
  MAP7D3 WILD-TYPE 331  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP7D3 MUTATED     19    0
  MAP7D3 WILD-TYPE  331   22
     clus
vv    MAP7D3 MUTATED MAP7D3 WILD-TYPE
  NO              19              331
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MAP7D3 MUTATED                     15                             2
  MAP7D3 WILD-TYPE                  300                            45
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MAP7D3 MUTATED                       5                              0
  MAP7D3 WILD-TYPE                   101                             10
D661V10, multiclass
                                clus
vv                               MAP7D3 MUTATED MAP7D3 WILD-TYPE
  COLON ADENOCARCINOMA                       15              300
  COLON MUCINOUS ADENOCARCINOMA               2               45
  RECTAL ADENOCARCINOMA                       5              101
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  MAP7D3 MUTATED    19   0   0   1
  MAP7D3 WILD-TYPE 326   4  31  24
D661V11, multiclass
    clus
vv   MAP7D3 MUTATED MAP7D3 WILD-TYPE
  R0             19              326
  R1              0                4
  R2              0               31
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D661V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MAP7D3 MUTATED                                  0     1
  MAP7D3 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  MAP7D3 MUTATED                           0    12
  MAP7D3 WILD-TYPE                        22   214
D661V13, multiclass
                                  clus
vv                                 MAP7D3 MUTATED MAP7D3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                        12              214
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(662) Variable = BFAR MUTATION ANALYSIS
D662V1, survival
                sevent
clus2              0   1
  BFAR MUTATED     8   1
  BFAR WILD-TYPE 370  92
  BFAR MUTATED BFAR WILD-TYPE 
             9            462 
  BFAR MUTATED BFAR WILD-TYPE 
             1             92 
$`BFAR MUTATED`
TCGA-AA-3672 TCGA-AD-6963 TCGA-AU-6004 TCGA-AZ-4681 TCGA-CA-6717 TCGA-CA-6718 
        0.92        27.42        27.09       106.75        12.76        10.06 
TCGA-CK-4947 TCGA-G4-6321 TCGA-AF-6136 
       17.56        22.09        15.39 

$`BFAR WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
        6.05         6.97        54.02         2.01        14.01        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       10.88         0.20        14.50        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 
       21.44        17.82        58.39         1.41         5.13        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 
        3.06         3.25         3.29         0.07        12.20        14.30 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6586 
       85.48        63.62        61.91        36.00        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       16.83        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  BFAR MUTATED BFAR WILD-TYPE 
          0.92           0.00 
  BFAR MUTATED BFAR WILD-TYPE 
        106.75         148.01 
  BFAR MUTATED BFAR WILD-TYPE 
        17.560         20.235 
[1] "0.9 - 106.8 (17.6)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.8"
D662V2, continuous
D662V3, binary
                cls
clus               0   1
  BFAR MUTATED     8   1
  BFAR WILD-TYPE 358 118
[1] "tbl2"
                cls
clus             [,1] [,2]
  BFAR MUTATED      8    1
  BFAR WILD-TYPE  358  118
        clus
vv       BFAR MUTATED BFAR WILD-TYPE
  COLON             8            358
  RECTUM            1            118
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  BFAR MUTATED         1        0        0         3         0         0
  BFAR WILD-TYPE      90        1       32       135        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  BFAR MUTATED           2          0          2          0        0         0
  BFAR WILD-TYPE        22         11         57         42       48        18
                vv
clus             STAGE IVB
  BFAR MUTATED           0
  BFAR WILD-TYPE         1
D662V4, multiclass
            clus
vv           BFAR MUTATED BFAR WILD-TYPE
  STAGE I               1             90
  STAGE IA              0              1
  STAGE II              0             32
  STAGE IIA             3            135
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             2             22
  STAGE IIIA            0             11
  STAGE IIIB            2             57
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  BFAR MUTATED     0   2   6   1
  BFAR WILD-TYPE  17  90 323  49
D662V5, multiclass
    clus
vv   BFAR MUTATED BFAR WILD-TYPE
  T1            0             17
  T2            2             90
  T3            6            323
  T4            1             49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  BFAR MUTATED     5   4   0
  BFAR WILD-TYPE 282 109  87
D662V6, multiclass
    clus
vv   BFAR MUTATED BFAR WILD-TYPE
  N0            5            282
  N1            4            109
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D662V7, binary
                cls
clus               0   1
  BFAR MUTATED     6   0
  BFAR WILD-TYPE 369  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  BFAR MUTATED      6    0
  BFAR WILD-TYPE  369   65
   clus
vv  BFAR MUTATED BFAR WILD-TYPE
  0            6            369
  1            0             65
[1] 2 2
[1] FALSE
D662V8, binary
                cls
clus               0   1
  BFAR MUTATED     6   3
  BFAR WILD-TYPE 219 261
[1] "tbl2"
                cls
clus             [,1] [,2]
  BFAR MUTATED      6    3
  BFAR WILD-TYPE  219  261
        clus
vv       BFAR MUTATED BFAR WILD-TYPE
  FEMALE            6            219
  MALE              3            261
[1] 2 2
[1] FALSE
D662V9, binary
                cls
clus               0   1
  BFAR MUTATED     7   1
  BFAR WILD-TYPE 343  21
[1] "tbl2"
                cls
clus             [,1] [,2]
  BFAR MUTATED      7    1
  BFAR WILD-TYPE  343   21
     clus
vv    BFAR MUTATED BFAR WILD-TYPE
  NO             7            343
  YES            1             21
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  BFAR MUTATED                      7                             1
  BFAR WILD-TYPE                  308                            46
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  BFAR MUTATED                       1                              0
  BFAR WILD-TYPE                   105                             10
D662V10, multiclass
                                clus
vv                               BFAR MUTATED BFAR WILD-TYPE
  COLON ADENOCARCINOMA                      7            308
  COLON MUCINOUS ADENOCARCINOMA             1             46
  RECTAL ADENOCARCINOMA                     1            105
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  BFAR MUTATED     4   0   0   3
  BFAR WILD-TYPE 341   4  31  22
D662V11, multiclass
    clus
vv   BFAR MUTATED BFAR WILD-TYPE
  R0            4            341
  R1            0              4
  R2            0             31
  RX            3             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D662V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  BFAR MUTATED                                  0     2
  BFAR WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  BFAR MUTATED                           0     6
  BFAR WILD-TYPE                        22   220
D662V13, multiclass
                                  clus
vv                                 BFAR MUTATED BFAR WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              9
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       6            220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(663) Variable = KCTD16 MUTATION ANALYSIS
D663V1, survival
                  sevent
clus2                0   1
  KCTD16 MUTATED     7   7
  KCTD16 WILD-TYPE 371  86
  KCTD16 MUTATED KCTD16 WILD-TYPE 
              14              457 
  KCTD16 MUTATED KCTD16 WILD-TYPE 
               7               86 
$`KCTD16 MUTATED`
TCGA-A6-2676 TCGA-AA-3549 TCGA-AA-3697 TCGA-AD-6964 TCGA-AZ-6601 TCGA-AZ-6605 
       42.90        21.01        85.05        10.88       100.01         5.23 
TCGA-CM-5864 TCGA-DM-A1D4 TCGA-DM-A1DA TCGA-DM-A28K TCGA-F4-6460 TCGA-G4-6306 
       15.02        92.75         7.50        98.24        31.96        44.68 
TCGA-AG-A002 TCGA-CI-6619 
       20.98         6.05 

$`KCTD16 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3552 
       26.01        12.99         0.99        14.01        33.99        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
        0.79         0.72         5.79        22.42        27.42         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 
       62.79        88.21        49.41         6.77        12.10        29.56 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D6 
       10.26       119.70        24.43        38.20       130.65        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       13.32        12.59       140.38        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-F4-6459 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
      117.07         8.61        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.69         0.72        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  KCTD16 MUTATED KCTD16 WILD-TYPE 
            5.23             0.00 
  KCTD16 MUTATED KCTD16 WILD-TYPE 
          100.01           148.01 
  KCTD16 MUTATED KCTD16 WILD-TYPE 
          26.485           20.050 
[1] "5.2 - 100.0 (26.5)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.7"
D663V2, continuous
D663V3, binary
                  cls
clus                 0   1
  KCTD16 MUTATED    12   2
  KCTD16 WILD-TYPE 354 117
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KCTD16 MUTATED     12    2
  KCTD16 WILD-TYPE  354  117
        clus
vv       KCTD16 MUTATED KCTD16 WILD-TYPE
  COLON              12              354
  RECTUM              2              117
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KCTD16 MUTATED         3        0        1         3         1         0
  KCTD16 WILD-TYPE      88        1       31       135         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KCTD16 MUTATED           1          0          2          1        1
  KCTD16 WILD-TYPE        23         11         57         41       47
                  vv
clus               STAGE IVA STAGE IVB
  KCTD16 MUTATED           0         0
  KCTD16 WILD-TYPE        18         1
D663V4, multiclass
            clus
vv           KCTD16 MUTATED KCTD16 WILD-TYPE
  STAGE I                 3               88
  STAGE IA                0                1
  STAGE II                1               31
  STAGE IIA               3              135
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               1               23
  STAGE IIIA              0               11
  STAGE IIIB              2               57
  STAGE IIIC              1               41
  STAGE IV                1               47
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  KCTD16 MUTATED     0   4   7   3
  KCTD16 WILD-TYPE  17  88 322  47
D663V5, multiclass
    clus
vv   KCTD16 MUTATED KCTD16 WILD-TYPE
  T1              0               17
  T2              4               88
  T3              7              322
  T4              3               47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  KCTD16 MUTATED     9   3   2
  KCTD16 WILD-TYPE 278 110  85
D663V6, multiclass
    clus
vv   KCTD16 MUTATED KCTD16 WILD-TYPE
  N0              9              278
  N1              3              110
  N2              2               85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D663V7, binary
                  cls
clus                 0   1
  KCTD16 MUTATED    12   1
  KCTD16 WILD-TYPE 363  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KCTD16 MUTATED     12    1
  KCTD16 WILD-TYPE  363   64
   clus
vv  KCTD16 MUTATED KCTD16 WILD-TYPE
  0             12              363
  1              1               64
[1] 2 2
[1] FALSE
D663V8, binary
                  cls
clus                 0   1
  KCTD16 MUTATED     3  11
  KCTD16 WILD-TYPE 222 253
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KCTD16 MUTATED      3   11
  KCTD16 WILD-TYPE  222  253
        clus
vv       KCTD16 MUTATED KCTD16 WILD-TYPE
  FEMALE              3              222
  MALE               11              253
[1] 2 2
[1] FALSE
D663V9, binary
                  cls
clus                 0   1
  KCTD16 MUTATED     9   1
  KCTD16 WILD-TYPE 341  21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KCTD16 MUTATED      9    1
  KCTD16 WILD-TYPE  341   21
     clus
vv    KCTD16 MUTATED KCTD16 WILD-TYPE
  NO               9              341
  YES              1               21
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  KCTD16 MUTATED                     11                             1
  KCTD16 WILD-TYPE                  304                            46
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  KCTD16 MUTATED                       2                              0
  KCTD16 WILD-TYPE                   104                             10
D663V10, multiclass
                                clus
vv                               KCTD16 MUTATED KCTD16 WILD-TYPE
  COLON ADENOCARCINOMA                       11              304
  COLON MUCINOUS ADENOCARCINOMA               1               46
  RECTAL ADENOCARCINOMA                       2              104
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  KCTD16 MUTATED     7   0   0   0
  KCTD16 WILD-TYPE 338   4  31  25
D663V11, multiclass
    clus
vv   KCTD16 MUTATED KCTD16 WILD-TYPE
  R0              7              338
  R1              0                4
  R2              0               31
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D663V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KCTD16 MUTATED                                  0     0
  KCTD16 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  KCTD16 MUTATED                           0    11
  KCTD16 WILD-TYPE                        22   215
D663V13, multiclass
                                  clus
vv                                 KCTD16 MUTATED KCTD16 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                        11              215
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(664) Variable = MFN1 MUTATION ANALYSIS
D664V1, survival
                sevent
clus2              0   1
  MFN1 MUTATED    10   4
  MFN1 WILD-TYPE 368  89
  MFN1 MUTATED MFN1 WILD-TYPE 
            14            457 
  MFN1 MUTATED MFN1 WILD-TYPE 
             4             89 
$`MFN1 MUTATED`
TCGA-A6-5665 TCGA-A6-6780 TCGA-AA-3516 TCGA-AD-6895 TCGA-AZ-6601 TCGA-CA-6715 
       22.06        20.12        13.02         0.72       100.01         0.07 
TCGA-CK-5916 TCGA-D5-6532 TCGA-D5-6922 TCGA-D5-6930 TCGA-DM-A1DA TCGA-F4-6808 
       21.14        18.25         4.41         1.51         7.50        33.67 
TCGA-G4-6299 TCGA-AG-A002 
       74.56        20.98 

$`MFN1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
       63.98         6.97         1.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.79         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 
       62.79        88.21        49.41         6.77        12.10        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
        9.99        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       55.92        20.19         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        3.68        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        4.80        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
      140.38        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       34.42        41.42        16.24        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
       35.31       133.18        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  MFN1 MUTATED MFN1 WILD-TYPE 
          0.07           0.00 
  MFN1 MUTATED MFN1 WILD-TYPE 
        100.01         148.01 
  MFN1 MUTATED MFN1 WILD-TYPE 
        19.185         20.280 
[1] "0.1 - 100.0 (19.2)" "0.0 - 148.0 (20.3)"
[1] "hr=" "1.6"
D664V2, continuous
D664V3, binary
                cls
clus               0   1
  MFN1 MUTATED    13   1
  MFN1 WILD-TYPE 353 118
[1] "tbl2"
                cls
clus             [,1] [,2]
  MFN1 MUTATED     13    1
  MFN1 WILD-TYPE  353  118
        clus
vv       MFN1 MUTATED MFN1 WILD-TYPE
  COLON            13            353
  RECTUM            1            118
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MFN1 MUTATED         3        0        1         4         0         0
  MFN1 WILD-TYPE      88        1       31       134        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MFN1 MUTATED           1          1          1          2        0         0
  MFN1 WILD-TYPE        23         10         58         40       48        18
                vv
clus             STAGE IVB
  MFN1 MUTATED           0
  MFN1 WILD-TYPE         1
D664V4, multiclass
            clus
vv           MFN1 MUTATED MFN1 WILD-TYPE
  STAGE I               3             88
  STAGE IA              0              1
  STAGE II              1             31
  STAGE IIA             4            134
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             1             23
  STAGE IIIA            1             10
  STAGE IIIB            1             58
  STAGE IIIC            2             40
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  MFN1 MUTATED     2   1  11   0
  MFN1 WILD-TYPE  15  91 318  50
D664V5, multiclass
    clus
vv   MFN1 MUTATED MFN1 WILD-TYPE
  T1            2             15
  T2            1             91
  T3           11            318
  T4            0             50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  MFN1 MUTATED     8   3   3
  MFN1 WILD-TYPE 279 110  84
D664V6, multiclass
    clus
vv   MFN1 MUTATED MFN1 WILD-TYPE
  N0            8            279
  N1            3            110
  N2            3             84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D664V7, binary
                cls
clus               0   1
  MFN1 MUTATED    12   0
  MFN1 WILD-TYPE 363  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  MFN1 MUTATED     12    0
  MFN1 WILD-TYPE  363   65
   clus
vv  MFN1 MUTATED MFN1 WILD-TYPE
  0           12            363
  1            0             65
[1] 2 2
[1] FALSE
D664V8, binary
                cls
clus               0   1
  MFN1 MUTATED     5   9
  MFN1 WILD-TYPE 220 255
[1] "tbl2"
                cls
clus             [,1] [,2]
  MFN1 MUTATED      5    9
  MFN1 WILD-TYPE  220  255
        clus
vv       MFN1 MUTATED MFN1 WILD-TYPE
  FEMALE            5            220
  MALE              9            255
[1] 2 2
[1] FALSE
D664V9, binary
                cls
clus               0   1
  MFN1 MUTATED     9   0
  MFN1 WILD-TYPE 341  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  MFN1 MUTATED      9    0
  MFN1 WILD-TYPE  341   22
     clus
vv    MFN1 MUTATED MFN1 WILD-TYPE
  NO             9            341
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MFN1 MUTATED                     10                             3
  MFN1 WILD-TYPE                  305                            44
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MFN1 MUTATED                       1                              0
  MFN1 WILD-TYPE                   105                             10
D664V10, multiclass
                                clus
vv                               MFN1 MUTATED MFN1 WILD-TYPE
  COLON ADENOCARCINOMA                     10            305
  COLON MUCINOUS ADENOCARCINOMA             3             44
  RECTAL ADENOCARCINOMA                     1            105
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  MFN1 MUTATED     7   0   0   2
  MFN1 WILD-TYPE 338   4  31  23
D664V11, multiclass
    clus
vv   MFN1 MUTATED MFN1 WILD-TYPE
  R0            7            338
  R1            0              4
  R2            0             31
  RX            2             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D664V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MFN1 MUTATED                                  0     1
  MFN1 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  MFN1 MUTATED                           0    11
  MFN1 WILD-TYPE                        22   215
D664V13, multiclass
                                  clus
vv                                 MFN1 MUTATED MFN1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                      11            215
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(665) Variable = ELF3 MUTATION ANALYSIS
D665V1, survival
                sevent
clus2              0   1
  ELF3 MUTATED     9   0
  ELF3 WILD-TYPE 369  93
  ELF3 MUTATED ELF3 WILD-TYPE 
             9            462 
  ELF3 MUTATED ELF3 WILD-TYPE 
             0             93 
$`ELF3 MUTATED`
TCGA-A6-2678 TCGA-AA-3979 TCGA-G4-6293 TCGA-G4-6306 TCGA-G4-6586 TCGA-AG-3599 
       42.28        24.00       133.18        44.68        35.80        12.03 
TCGA-AG-3892 TCGA-AG-3902 TCGA-AH-6643 
       13.02        32.02         0.69 

$`ELF3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2683 
       43.76        46.65        43.76        42.90        24.33        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        25.02        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6299 
       33.67        13.25         0.53        47.41        35.31        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       65.85        53.62        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
        2.01        50.04         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       36.95        17.03        35.01        14.01         1.02        48.03 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6644 
       38.04       117.11        38.56         1.45        17.49         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  ELF3 MUTATED ELF3 WILD-TYPE 
          0.69           0.00 
  ELF3 MUTATED ELF3 WILD-TYPE 
        133.18         148.01 
  ELF3 MUTATED ELF3 WILD-TYPE 
        32.020         20.085 
[1] "0.7 - 133.2 (32.0)" "0.0 - 148.0 (20.1)"
[1] "hr="     "9300000"
D665V2, continuous
D665V3, binary
                cls
clus               0   1
  ELF3 MUTATED     6   4
  ELF3 WILD-TYPE 360 115
[1] "tbl2"
                cls
clus             [,1] [,2]
  ELF3 MUTATED      6    4
  ELF3 WILD-TYPE  360  115
        clus
vv       ELF3 MUTATED ELF3 WILD-TYPE
  COLON             6            360
  RECTUM            4            115
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ELF3 MUTATED         2        0        0         4         0         0
  ELF3 WILD-TYPE      89        1       32       134        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ELF3 MUTATED           1          0          1          1        1         0
  ELF3 WILD-TYPE        23         11         58         41       47        18
                vv
clus             STAGE IVB
  ELF3 MUTATED           0
  ELF3 WILD-TYPE         1
D665V4, multiclass
            clus
vv           ELF3 MUTATED ELF3 WILD-TYPE
  STAGE I               2             89
  STAGE IA              0              1
  STAGE II              0             32
  STAGE IIA             4            134
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             1             23
  STAGE IIIA            0             11
  STAGE IIIB            1             58
  STAGE IIIC            1             41
  STAGE IV              1             47
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  ELF3 MUTATED     1   2   6   1
  ELF3 WILD-TYPE  16  90 323  49
D665V5, multiclass
    clus
vv   ELF3 MUTATED ELF3 WILD-TYPE
  T1            1             16
  T2            2             90
  T3            6            323
  T4            1             49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  ELF3 MUTATED     6   2   2
  ELF3 WILD-TYPE 281 111  85
D665V6, multiclass
    clus
vv   ELF3 MUTATED ELF3 WILD-TYPE
  N0            6            281
  N1            2            111
  N2            2             85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D665V7, binary
                cls
clus               0   1
  ELF3 MUTATED     9   1
  ELF3 WILD-TYPE 366  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  ELF3 MUTATED      9    1
  ELF3 WILD-TYPE  366   64
   clus
vv  ELF3 MUTATED ELF3 WILD-TYPE
  0            9            366
  1            1             64
[1] 2 2
[1] FALSE
D665V8, binary
                cls
clus               0   1
  ELF3 MUTATED     4   6
  ELF3 WILD-TYPE 221 258
[1] "tbl2"
                cls
clus             [,1] [,2]
  ELF3 MUTATED      4    6
  ELF3 WILD-TYPE  221  258
        clus
vv       ELF3 MUTATED ELF3 WILD-TYPE
  FEMALE            4            221
  MALE              6            258
[1] 2 2
[1] FALSE
D665V9, binary
                cls
clus               0   1
  ELF3 MUTATED     8   0
  ELF3 WILD-TYPE 342  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  ELF3 MUTATED      8    0
  ELF3 WILD-TYPE  342   22
     clus
vv    ELF3 MUTATED ELF3 WILD-TYPE
  NO             8            342
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ELF3 MUTATED                      6                             0
  ELF3 WILD-TYPE                  309                            47
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ELF3 MUTATED                       3                              0
  ELF3 WILD-TYPE                   103                             10
D665V10, multiclass
                                clus
vv                               ELF3 MUTATED ELF3 WILD-TYPE
  COLON ADENOCARCINOMA                      6            309
  COLON MUCINOUS ADENOCARCINOMA             0             47
  RECTAL ADENOCARCINOMA                     3            103
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  ELF3 MUTATED     9   0   1   0
  ELF3 WILD-TYPE 336   4  30  25
D665V11, multiclass
    clus
vv   ELF3 MUTATED ELF3 WILD-TYPE
  R0            9            336
  R1            0              4
  R2            1             30
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D665V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ELF3 MUTATED                                  0     0
  ELF3 WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  ELF3 MUTATED                           0     5
  ELF3 WILD-TYPE                        22   221
D665V13, multiclass
                                  clus
vv                                 ELF3 MUTATED ELF3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       5            221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(666) Variable = TAPBP MUTATION ANALYSIS
D666V1, survival
                 sevent
clus2               0   1
  TAPBP MUTATED     4   1
  TAPBP WILD-TYPE 374  92
  TAPBP MUTATED TAPBP WILD-TYPE 
              5             466 
  TAPBP MUTATED TAPBP WILD-TYPE 
              1              92 
$`TAPBP MUTATED`
TCGA-AA-3833 TCGA-AA-A00J TCGA-CM-5862 TCGA-AG-3593 TCGA-AG-3892 
       15.95        18.05         5.03        34.03        13.02 

$`TAPBP WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
        1.02        17.98        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L 
       38.04        19.00        30.02        34.03        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       32.02        15.02        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       46.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 
        1.02        17.95        36.95        17.03        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  TAPBP MUTATED TAPBP WILD-TYPE 
           5.03            0.00 
  TAPBP MUTATED TAPBP WILD-TYPE 
          34.03          148.01 
  TAPBP MUTATED TAPBP WILD-TYPE 
         15.950          20.415 
[1] "5.0 - 34.0 (15.9)"  "0.0 - 148.0 (20.4)"
[1] "hr=" "1.6"
D666V2, continuous
D666V3, binary
                 cls
clus                0   1
  TAPBP MUTATED     3   2
  TAPBP WILD-TYPE 363 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TAPBP MUTATED      3    2
  TAPBP WILD-TYPE  363  117
        clus
vv       TAPBP MUTATED TAPBP WILD-TYPE
  COLON              3             363
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TAPBP MUTATED         1        0        0         2         0         0
  TAPBP WILD-TYPE      90        1       32       136        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TAPBP MUTATED           0          0          1          0        0         1
  TAPBP WILD-TYPE        24         11         58         42       48        17
                 vv
clus              STAGE IVB
  TAPBP MUTATED           0
  TAPBP WILD-TYPE         1
D666V4, multiclass
            clus
vv           TAPBP MUTATED TAPBP WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              2             136
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  TAPBP MUTATED     1   0   3   1
  TAPBP WILD-TYPE  16  92 326  49
D666V5, multiclass
    clus
vv   TAPBP MUTATED TAPBP WILD-TYPE
  T1             1              16
  T2             0              92
  T3             3             326
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  TAPBP MUTATED     3   2   0
  TAPBP WILD-TYPE 284 111  87
D666V6, multiclass
    clus
vv   TAPBP MUTATED TAPBP WILD-TYPE
  N0             3             284
  N1             2             111
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D666V7, binary
                 cls
clus                0   1
  TAPBP MUTATED     4   1
  TAPBP WILD-TYPE 371  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TAPBP MUTATED      4    1
  TAPBP WILD-TYPE  371   64
   clus
vv  TAPBP MUTATED TAPBP WILD-TYPE
  0             4             371
  1             1              64
[1] 2 2
[1] FALSE
D666V8, binary
                 cls
clus                0   1
  TAPBP MUTATED     3   2
  TAPBP WILD-TYPE 222 262
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TAPBP MUTATED      3    2
  TAPBP WILD-TYPE  222  262
        clus
vv       TAPBP MUTATED TAPBP WILD-TYPE
  FEMALE             3             222
  MALE               2             262
[1] 2 2
[1] FALSE
D666V9, binary
                 cls
clus                0   1
  TAPBP MUTATED     4   1
  TAPBP WILD-TYPE 346  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TAPBP MUTATED      4    1
  TAPBP WILD-TYPE  346   21
     clus
vv    TAPBP MUTATED TAPBP WILD-TYPE
  NO              4             346
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  TAPBP MUTATED                      2                             1
  TAPBP WILD-TYPE                  313                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  TAPBP MUTATED                       2                              0
  TAPBP WILD-TYPE                   104                             10
D666V10, multiclass
                                clus
vv                               TAPBP MUTATED TAPBP WILD-TYPE
  COLON ADENOCARCINOMA                       2             313
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  TAPBP MUTATED     5   0   0   0
  TAPBP WILD-TYPE 340   4  31  25
D666V11, multiclass
    clus
vv   TAPBP MUTATED TAPBP WILD-TYPE
  R0             5             340
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D666V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TAPBP MUTATED                                  0     0
  TAPBP WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  TAPBP MUTATED                           0     1
  TAPBP WILD-TYPE                        22   225
D666V13, multiclass
[1] "Remove cluster labels:" "TAPBP MUTATED"         
clus
  TAPBP MUTATED TAPBP WILD-TYPE 
              1             259 
     TCGA-A6-2671      TCGA-A6-2672      TCGA-A6-2674      TCGA-A6-2676 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-A6-2677      TCGA-A6-2678      TCGA-A6-2683      TCGA-A6-3807 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-A6-3808      TCGA-A6-3809      TCGA-A6-3810      TCGA-A6-4105 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-A6-5656      TCGA-A6-5657      TCGA-A6-5659      TCGA-A6-5660 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-A6-5661      TCGA-A6-5662      TCGA-A6-5664      TCGA-A6-5665 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-A6-5666      TCGA-A6-6137      TCGA-A6-6138      TCGA-A6-6141 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-A6-6142      TCGA-A6-6648      TCGA-A6-6649      TCGA-A6-6651 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-A6-6652      TCGA-A6-6653      TCGA-A6-6654      TCGA-A6-6780 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-A6-6781      TCGA-A6-6782      TCGA-AD-5900      TCGA-AD-6548 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-AD-6888      TCGA-AD-6889      TCGA-AD-6890      TCGA-AD-6895 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-AD-6899      TCGA-AD-6901      TCGA-AD-6963      TCGA-AD-6964 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-AD-6965      TCGA-AU-3779      TCGA-AU-6004      TCGA-AY-4070 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-AY-4071      TCGA-AY-5543      TCGA-AY-6196      TCGA-AY-6197 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-AY-6386      TCGA-AZ-4315      TCGA-AZ-4323      TCGA-AZ-4616 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-AZ-4681      TCGA-AZ-4682      TCGA-AZ-5403      TCGA-AZ-5407 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-AZ-6598      TCGA-AZ-6599      TCGA-AZ-6600      TCGA-AZ-6601 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-AZ-6603      TCGA-AZ-6605      TCGA-AZ-6606      TCGA-AZ-6607 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-AZ-6608      TCGA-CA-5254      TCGA-CA-5255      TCGA-CA-5796 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-CA-5797      TCGA-CA-6715      TCGA-CA-6716      TCGA-CA-6717 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-CA-6718      TCGA-CA-6719      TCGA-CK-4947      TCGA-CK-4948 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-CK-4950      TCGA-CK-4952      TCGA-CK-5912      TCGA-CK-5913 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-CK-5914      TCGA-CK-5915      TCGA-CK-5916      TCGA-CK-6746 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-CK-6747      TCGA-CK-6748      TCGA-CK-6751      TCGA-CM-4743 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-CM-4744      TCGA-CM-4746      TCGA-CM-4747      TCGA-CM-4752 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-CM-5341      TCGA-CM-5344      TCGA-CM-5348      TCGA-CM-5349 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-CM-5860      TCGA-CM-5861      TCGA-CM-5863      TCGA-CM-5864 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-CM-5868      TCGA-CM-6161      TCGA-CM-6162      TCGA-CM-6163 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-CM-6164      TCGA-CM-6165      TCGA-CM-6166      TCGA-CM-6167 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-CM-6168      TCGA-CM-6169      TCGA-CM-6170      TCGA-CM-6171 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-CM-6172      TCGA-CM-6674      TCGA-CM-6675      TCGA-CM-6676 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-CM-6677      TCGA-CM-6678      TCGA-CM-6679      TCGA-CM-6680 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-D5-5537      TCGA-D5-5538      TCGA-D5-5539      TCGA-D5-5540 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-D5-5541      TCGA-D5-6529      TCGA-D5-6532      TCGA-D5-6533 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-D5-6534      TCGA-D5-6535      TCGA-D5-6536      TCGA-D5-6537 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-D5-6538      TCGA-D5-6539      TCGA-D5-6540      TCGA-D5-6541 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-D5-6898      TCGA-D5-6920      TCGA-D5-6922      TCGA-D5-6923 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-D5-6924      TCGA-D5-6926      TCGA-D5-6927      TCGA-D5-6928 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-D5-6929      TCGA-D5-6930      TCGA-D5-6931      TCGA-D5-6932 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-D5-7000      TCGA-DM-A0X9      TCGA-DM-A0XD      TCGA-DM-A0XF 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-DM-A1D0      TCGA-DM-A1D4      TCGA-DM-A1D6      TCGA-DM-A1D7 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-DM-A1D8      TCGA-DM-A1D9      TCGA-DM-A1DA      TCGA-DM-A1DB 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-DM-A1HA      TCGA-DM-A1HB      TCGA-DM-A282      TCGA-DM-A285 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-DM-A28C      TCGA-DM-A28E      TCGA-DM-A28F      TCGA-DM-A28G 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-DM-A28H      TCGA-DM-A28K      TCGA-F4-6459      TCGA-F4-6460 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-F4-6569      TCGA-F4-6570      TCGA-F4-6703      TCGA-F4-6704 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-F4-6805      TCGA-F4-6806      TCGA-F4-6807      TCGA-F4-6808 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-F4-6809      TCGA-F4-6854      TCGA-F4-6855      TCGA-F4-6856 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-G4-6293      TCGA-G4-6299      TCGA-G4-6303      TCGA-G4-6304 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-G4-6306      TCGA-G4-6307      TCGA-G4-6309      TCGA-G4-6310 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-G4-6315      TCGA-G4-6317      TCGA-G4-6321      TCGA-G4-6323 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-G4-6586      TCGA-G4-6588      TCGA-G4-6625      TCGA-G4-6626 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-G4-6628      TCGA-AF-2687      TCGA-AF-2689      TCGA-AF-2691 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-AF-2692      TCGA-AF-2693      TCGA-AF-3400      TCGA-AF-3913 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-AF-4110      TCGA-AF-5654      TCGA-AF-6136      TCGA-AF-6655 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-AF-6672      TCGA-AH-6544      TCGA-AH-6547      TCGA-AH-6549 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-AH-6643      TCGA-AH-6644      TCGA-CI-6619      TCGA-CI-6620 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-CI-6621      TCGA-CI-6622      TCGA-CI-6624      TCGA-CL-5917 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-CL-5918      TCGA-DC-5337      TCGA-DC-5869      TCGA-DC-6155 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-DC-6157      TCGA-DC-6158      TCGA-DC-6160      TCGA-DC-6681 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-DC-6682      TCGA-DC-6683      TCGA-DT-5265      TCGA-DY-A0XA 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-DY-A1DC      TCGA-DY-A1DD      TCGA-DY-A1DF      TCGA-DY-A1DG 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-DY-A1H8      TCGA-EF-5830      TCGA-EI-6506      TCGA-EI-6507 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-EI-6508      TCGA-EI-6510      TCGA-F5-6464      TCGA-F5-6465 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-F5-6571      TCGA-F5-6702      TCGA-F5-6811      TCGA-F5-6812 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 
     TCGA-F5-6813      TCGA-G5-6235      TCGA-G5-6641 
"TAPBP WILD-TYPE" "TAPBP WILD-TYPE" "TAPBP WILD-TYPE" 

Clustering(667) Variable = RBM19 MUTATION ANALYSIS
D667V1, survival
                 sevent
clus2               0   1
  RBM19 MUTATED    14   7
  RBM19 WILD-TYPE 364  86
  RBM19 MUTATED RBM19 WILD-TYPE 
             21             450 
  RBM19 MUTATED RBM19 WILD-TYPE 
              7              86 
$`RBM19 MUTATED`
TCGA-A6-5660 TCGA-AA-3492 TCGA-AA-3516 TCGA-AA-3672 TCGA-AA-3947 TCGA-AA-3977 
       29.19         3.02        13.02         0.92        33.01        25.02 
TCGA-AA-A00J TCGA-AA-A00N TCGA-AD-6964 TCGA-AU-3779 TCGA-AZ-4315 TCGA-AZ-6601 
       18.05         4.01        10.88        14.50        58.39       100.01 
TCGA-CK-5916 TCGA-CM-5860 TCGA-CM-6161 TCGA-CM-6162 TCGA-D5-5539 TCGA-D5-6537 
       21.14        32.02        15.02        12.00        19.59         4.80 
TCGA-G4-6299 TCGA-G4-6310 TCGA-G4-6317 
       74.56        63.62        36.00 

$`RBM19 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 
       20.12        19.66        20.28         7.04         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
       63.98         6.97         1.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
        2.01        14.01        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
        0.20        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 
       88.21        49.41         6.77        12.10        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
        9.99        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       30.08        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       12.26        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       43.27        15.12        17.85        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
       35.31       133.18        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       85.48        61.91        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  RBM19 MUTATED RBM19 WILD-TYPE 
           0.92            0.00 
  RBM19 MUTATED RBM19 WILD-TYPE 
         100.01          148.01 
  RBM19 MUTATED RBM19 WILD-TYPE 
         19.590          20.235 
[1] "0.9 - 100.0 (19.6)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.6"
D667V2, continuous
D667V3, binary
                 cls
clus                0   1
  RBM19 MUTATED    21   0
  RBM19 WILD-TYPE 345 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM19 MUTATED     21    0
  RBM19 WILD-TYPE  345  119
        clus
vv       RBM19 MUTATED RBM19 WILD-TYPE
  COLON             21             345
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RBM19 MUTATED         2        0        2         3         2         0
  RBM19 WILD-TYPE      89        1       30       135         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RBM19 MUTATED           2          1          4          3        0         0
  RBM19 WILD-TYPE        22         10         55         39       48        18
                 vv
clus              STAGE IVB
  RBM19 MUTATED           0
  RBM19 WILD-TYPE         1
D667V4, multiclass
            clus
vv           RBM19 MUTATED RBM19 WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA              3             135
  STAGE IIB              2               8
  STAGE IIC              0               1
  STAGE III              2              22
  STAGE IIIA             1              10
  STAGE IIIB             4              55
  STAGE IIIC             3              39
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  RBM19 MUTATED     1   2  14   4
  RBM19 WILD-TYPE  16  90 315  46
D667V5, multiclass
    clus
vv   RBM19 MUTATED RBM19 WILD-TYPE
  T1             1              16
  T2             2              90
  T3            14             315
  T4             4              46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  RBM19 MUTATED    10   6   5
  RBM19 WILD-TYPE 277 107  82
D667V6, multiclass
    clus
vv   RBM19 MUTATED RBM19 WILD-TYPE
  N0            10             277
  N1             6             107
  N2             5              82
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D667V7, binary
                 cls
clus                0   1
  RBM19 MUTATED    17   0
  RBM19 WILD-TYPE 358  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM19 MUTATED     17    0
  RBM19 WILD-TYPE  358   65
   clus
vv  RBM19 MUTATED RBM19 WILD-TYPE
  0            17             358
  1             0              65
[1] 2 2
[1] FALSE
D667V8, binary
                 cls
clus                0   1
  RBM19 MUTATED     9  12
  RBM19 WILD-TYPE 216 252
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM19 MUTATED      9   12
  RBM19 WILD-TYPE  216  252
        clus
vv       RBM19 MUTATED RBM19 WILD-TYPE
  FEMALE             9             216
  MALE              12             252
[1] 2 2
[1] FALSE
D667V9, binary
                 cls
clus                0   1
  RBM19 MUTATED    19   1
  RBM19 WILD-TYPE 331  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM19 MUTATED     19    1
  RBM19 WILD-TYPE  331   21
     clus
vv    RBM19 MUTATED RBM19 WILD-TYPE
  NO             19             331
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  RBM19 MUTATED                     15                             6
  RBM19 WILD-TYPE                  300                            41
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  RBM19 MUTATED                       0                              0
  RBM19 WILD-TYPE                   106                             10
D667V10, multiclass
                                clus
vv                               RBM19 MUTATED RBM19 WILD-TYPE
  COLON ADENOCARCINOMA                      15             300
  COLON MUCINOUS ADENOCARCINOMA              6              41
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  RBM19 MUTATED    15   0   0   1
  RBM19 WILD-TYPE 330   4  31  24
D667V11, multiclass
    clus
vv   RBM19 MUTATED RBM19 WILD-TYPE
  R0            15             330
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D667V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RBM19 MUTATED                                  0     0
  RBM19 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  RBM19 MUTATED                           1    13
  RBM19 WILD-TYPE                        21   213
D667V13, multiclass
                                  clus
vv                                 RBM19 MUTATED RBM19 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                       13             213
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(668) Variable = MSH4 MUTATION ANALYSIS
D668V1, survival
                sevent
clus2              0   1
  MSH4 MUTATED    12   2
  MSH4 WILD-TYPE 366  91
  MSH4 MUTATED MSH4 WILD-TYPE 
            14            457 
  MSH4 MUTATED MSH4 WILD-TYPE 
             2             91 
$`MSH4 MUTATED`
TCGA-A6-2678 TCGA-AA-3510 TCGA-AA-A010 TCGA-AZ-4315 TCGA-AZ-4681 TCGA-AZ-6598 
       42.28        63.98        34.98        58.39       106.75        49.41 
TCGA-CA-6717 TCGA-CK-4948 TCGA-CM-5348 TCGA-G4-6303 TCGA-G4-6586 TCGA-AG-3892 
       12.76       148.01        22.98        65.85        35.80        13.02 
TCGA-AH-6644 TCGA-CI-6624 
        0.72         4.73 

$`MSH4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2683 
       43.76        46.65        43.76        42.90        24.33        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5403 
       21.44        17.82         1.41         5.13        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       88.21         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07        12.20        10.06        14.30        17.56 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5860 
       25.02        13.02        29.06        22.03        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       17.95        36.95        17.03        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CL-5917 
       17.49         0.69         6.05        33.17         6.97        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  MSH4 MUTATED MSH4 WILD-TYPE 
          0.72           0.00 
  MSH4 MUTATED MSH4 WILD-TYPE 
        148.01         140.38 
  MSH4 MUTATED MSH4 WILD-TYPE 
         39.04          20.02 
[1] "0.7 - 148.0 (39.0)" "0.0 - 140.4 (20.0)"
[1] "hr=" "2.4"
D668V2, continuous
D668V3, binary
                cls
clus               0   1
  MSH4 MUTATED    12   3
  MSH4 WILD-TYPE 354 116
[1] "tbl2"
                cls
clus             [,1] [,2]
  MSH4 MUTATED     12    3
  MSH4 WILD-TYPE  354  116
        clus
vv       MSH4 MUTATED MSH4 WILD-TYPE
  COLON            12            354
  RECTUM            3            116
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MSH4 MUTATED         2        0        2         5         1         0
  MSH4 WILD-TYPE      89        1       30       133         9         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MSH4 MUTATED           1          0          2          0        1         0
  MSH4 WILD-TYPE        23         11         57         42       47        18
                vv
clus             STAGE IVB
  MSH4 MUTATED           0
  MSH4 WILD-TYPE         1
D668V4, multiclass
            clus
vv           MSH4 MUTATED MSH4 WILD-TYPE
  STAGE I               2             89
  STAGE IA              0              1
  STAGE II              2             30
  STAGE IIA             5            133
  STAGE IIB             1              9
  STAGE IIC             0              1
  STAGE III             1             23
  STAGE IIIA            0             11
  STAGE IIIB            2             57
  STAGE IIIC            0             42
  STAGE IV              1             47
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  MSH4 MUTATED     1   1  12   1
  MSH4 WILD-TYPE  16  91 317  49
D668V5, multiclass
    clus
vv   MSH4 MUTATED MSH4 WILD-TYPE
  T1            1             16
  T2            1             91
  T3           12            317
  T4            1             49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  MSH4 MUTATED    10   4   0
  MSH4 WILD-TYPE 277 109  87
D668V6, multiclass
    clus
vv   MSH4 MUTATED MSH4 WILD-TYPE
  N0           10            277
  N1            4            109
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D668V7, binary
                cls
clus               0   1
  MSH4 MUTATED    12   1
  MSH4 WILD-TYPE 363  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  MSH4 MUTATED     12    1
  MSH4 WILD-TYPE  363   64
   clus
vv  MSH4 MUTATED MSH4 WILD-TYPE
  0           12            363
  1            1             64
[1] 2 2
[1] FALSE
D668V8, binary
                cls
clus               0   1
  MSH4 MUTATED    10   5
  MSH4 WILD-TYPE 215 259
[1] "tbl2"
                cls
clus             [,1] [,2]
  MSH4 MUTATED     10    5
  MSH4 WILD-TYPE  215  259
        clus
vv       MSH4 MUTATED MSH4 WILD-TYPE
  FEMALE           10            215
  MALE              5            259
[1] 2 2
[1] FALSE
D668V9, binary
                cls
clus               0   1
  MSH4 MUTATED    12   0
  MSH4 WILD-TYPE 338  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  MSH4 MUTATED     12    0
  MSH4 WILD-TYPE  338   22
     clus
vv    MSH4 MUTATED MSH4 WILD-TYPE
  NO            12            338
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MSH4 MUTATED                     11                             1
  MSH4 WILD-TYPE                  304                            46
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MSH4 MUTATED                       3                              0
  MSH4 WILD-TYPE                   103                             10
D668V10, multiclass
                                clus
vv                               MSH4 MUTATED MSH4 WILD-TYPE
  COLON ADENOCARCINOMA                     11            304
  COLON MUCINOUS ADENOCARCINOMA             1             46
  RECTAL ADENOCARCINOMA                     3            103
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  MSH4 MUTATED    11   0   0   1
  MSH4 WILD-TYPE 334   4  31  24
D668V11, multiclass
    clus
vv   MSH4 MUTATED MSH4 WILD-TYPE
  R0           11            334
  R1            0              4
  R2            0             31
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D668V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MSH4 MUTATED                                  0     1
  MSH4 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  MSH4 MUTATED                           0    10
  MSH4 WILD-TYPE                        22   216
D668V13, multiclass
                                  clus
vv                                 MSH4 MUTATED MSH4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                      10            216
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(669) Variable = ADAMTS4 MUTATION ANALYSIS
D669V1, survival
                   sevent
clus2                 0   1
  ADAMTS4 MUTATED    15   3
  ADAMTS4 WILD-TYPE 363  90
  ADAMTS4 MUTATED ADAMTS4 WILD-TYPE 
               18               453 
  ADAMTS4 MUTATED ADAMTS4 WILD-TYPE 
                3                90 
$`ADAMTS4 MUTATED`
TCGA-A6-5661 TCGA-A6-5665 TCGA-A6-6780 TCGA-AA-3660 TCGA-AA-A010 TCGA-AZ-6598 
       33.53        22.06        20.12        78.08        34.98        49.41 
TCGA-CK-4952 TCGA-CK-5916 TCGA-CM-4743 TCGA-CM-5861 TCGA-CM-6171 TCGA-D5-6538 
       15.62        21.14        23.05        15.02        14.04        17.13 
TCGA-DM-A0XD TCGA-F4-6856 TCGA-AG-3609 TCGA-AG-A002 TCGA-DC-5337 TCGA-DT-5265 
       24.43        35.31        19.99        20.98        15.02         5.29 

$`ADAMTS4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6781 
       24.16        21.76        24.69        24.39        23.87        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       88.21         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
       17.56       148.01        85.45        49.08        51.32         9.99 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
       82.95         1.91       124.27        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       13.02        15.02        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6539 TCGA-D5-6540 
       43.27        15.12        17.85         4.80        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       11.38        10.26       119.70        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 
       16.24        33.67        13.25         0.53        47.41       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        6.05         0.99        15.95        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5869 
       33.17         6.97         4.73        78.12         7.17         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.03       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  ADAMTS4 MUTATED ADAMTS4 WILD-TYPE 
             5.29              0.00 
  ADAMTS4 MUTATED ADAMTS4 WILD-TYPE 
            78.08            148.01 
  ADAMTS4 MUTATED ADAMTS4 WILD-TYPE 
            21.06             20.05 
[1] "5.3 - 78.1 (21.1)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.2"
D669V2, continuous
D669V3, binary
                   cls
clus                  0   1
  ADAMTS4 MUTATED    14   4
  ADAMTS4 WILD-TYPE 352 115
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ADAMTS4 MUTATED     14    4
  ADAMTS4 WILD-TYPE  352  115
        clus
vv       ADAMTS4 MUTATED ADAMTS4 WILD-TYPE
  COLON               14               352
  RECTUM               4               115
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ADAMTS4 MUTATED         5        0        3         6         1         0
  ADAMTS4 WILD-TYPE      86        1       29       132         9         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ADAMTS4 MUTATED           0          0          1          2        0
  ADAMTS4 WILD-TYPE        24         11         58         40       48
                   vv
clus                STAGE IVA STAGE IVB
  ADAMTS4 MUTATED           0         0
  ADAMTS4 WILD-TYPE        18         1
D669V4, multiclass
            clus
vv           ADAMTS4 MUTATED ADAMTS4 WILD-TYPE
  STAGE I                  5                86
  STAGE IA                 0                 1
  STAGE II                 3                29
  STAGE IIA                6               132
  STAGE IIB                1                 9
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               0                11
  STAGE IIIB               1                58
  STAGE IIIC               2                40
  STAGE IV                 0                48
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  ADAMTS4 MUTATED     2   3  11   2
  ADAMTS4 WILD-TYPE  15  89 318  48
D669V5, multiclass
    clus
vv   ADAMTS4 MUTATED ADAMTS4 WILD-TYPE
  T1               2                15
  T2               3                89
  T3              11               318
  T4               2                48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  ADAMTS4 MUTATED    15   0   3
  ADAMTS4 WILD-TYPE 272 113  84
D669V6, multiclass
    clus
vv   ADAMTS4 MUTATED ADAMTS4 WILD-TYPE
  N0              15               272
  N1               0               113
  N2               3                84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D669V7, binary
                   cls
clus                  0   1
  ADAMTS4 MUTATED    16   0
  ADAMTS4 WILD-TYPE 359  65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ADAMTS4 MUTATED     16    0
  ADAMTS4 WILD-TYPE  359   65
   clus
vv  ADAMTS4 MUTATED ADAMTS4 WILD-TYPE
  0              16               359
  1               0                65
[1] 2 2
[1] FALSE
D669V8, binary
                   cls
clus                  0   1
  ADAMTS4 MUTATED    11   7
  ADAMTS4 WILD-TYPE 214 257
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ADAMTS4 MUTATED     11    7
  ADAMTS4 WILD-TYPE  214  257
        clus
vv       ADAMTS4 MUTATED ADAMTS4 WILD-TYPE
  FEMALE              11               214
  MALE                 7               257
[1] 2 2
[1] FALSE
D669V9, binary
                   cls
clus                  0   1
  ADAMTS4 MUTATED    16   0
  ADAMTS4 WILD-TYPE 334  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ADAMTS4 MUTATED     16    0
  ADAMTS4 WILD-TYPE  334   22
     clus
vv    ADAMTS4 MUTATED ADAMTS4 WILD-TYPE
  NO               16               334
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ADAMTS4 MUTATED                     11                             3
  ADAMTS4 WILD-TYPE                  304                            44
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ADAMTS4 MUTATED                       3                              1
  ADAMTS4 WILD-TYPE                   103                              9
D669V10, multiclass
                                clus
vv                               ADAMTS4 MUTATED ADAMTS4 WILD-TYPE
  COLON ADENOCARCINOMA                        11               304
  COLON MUCINOUS ADENOCARCINOMA                3                44
  RECTAL ADENOCARCINOMA                        3               103
  RECTAL MUCINOUS ADENOCARCINOMA               1                 9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  ADAMTS4 MUTATED    12   0   0   3
  ADAMTS4 WILD-TYPE 333   4  31  22
D669V11, multiclass
    clus
vv   ADAMTS4 MUTATED ADAMTS4 WILD-TYPE
  R0              12               333
  R1               0                 4
  R2               0                31
  RX               3                22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D669V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ADAMTS4 MUTATED                                  0     1
  ADAMTS4 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  ADAMTS4 MUTATED                           1    12
  ADAMTS4 WILD-TYPE                        21   214
D669V13, multiclass
                                  clus
vv                                 ADAMTS4 MUTATED ADAMTS4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                10
  BLACK OR AFRICAN AMERICAN                      1                21
  WHITE                                         12               214
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(670) Variable = ASPM MUTATION ANALYSIS
D670V1, survival
                sevent
clus2              0   1
  ASPM MUTATED    38   8
  ASPM WILD-TYPE 340  85
  ASPM MUTATED ASPM WILD-TYPE 
            46            425 
  ASPM MUTATED ASPM WILD-TYPE 
             8             85 
$`ASPM MUTATED`
TCGA-A6-5665 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3510 TCGA-AA-3543 
       22.06        24.39        20.12        19.66        63.98         0.99 
TCGA-AA-3555 TCGA-AA-3811 TCGA-AA-3864 TCGA-AA-3947 TCGA-AA-3977 TCGA-AA-A00E 
       29.95        10.06        53.00        33.01        25.02        30.02 
TCGA-AA-A00J TCGA-AA-A00N TCGA-AA-A00Q TCGA-AA-A00Z TCGA-AA-A010 TCGA-AD-6889 
       18.05         4.01        42.02        21.99        34.98        56.55 
TCGA-AD-6895 TCGA-AD-6901 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-CA-6715 TCGA-CA-6716 
        0.72        22.42        58.39         1.41         0.07        12.20 
TCGA-CA-6717 TCGA-CK-5916 TCGA-CK-6748 TCGA-CM-6161 TCGA-CM-6171 TCGA-CM-6678 
       12.76        21.14         1.91        15.02        14.04        11.01 
TCGA-D5-6540 TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6929 TCGA-DM-A1HB TCGA-DM-A285 
       16.14         9.04        11.64         4.80       135.65         6.12 
TCGA-DM-A28C TCGA-F4-6703 TCGA-F4-6856 TCGA-G4-6588 TCGA-G4-6628 TCGA-AG-A002 
       81.37        47.87        35.31        26.17        79.69        20.98 
TCGA-AG-A02N TCGA-CI-6620 TCGA-DY-A1DD TCGA-G5-6235 
       61.97        33.17        57.24        55.76 

$`ASPM WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6782 
       25.18        24.16        21.76        24.69        23.87        20.28 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 
        7.04         3.02         1.02        35.01         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
       13.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       36.03         8.05        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 
       29.00        29.00        26.01        12.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 
       21.01        13.02        24.00        17.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 
        0.99        31.07        31.07        30.05        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00K 
       27.02        13.94        38.04        19.00        34.03        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 
       38.04        27.02         0.99        17.03        14.99         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6963 
        0.07        21.37        15.52         0.79         5.79        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       33.01        21.44        17.82         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.06         3.25         3.29        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
       82.95       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6162 
       15.02         5.03        15.02        15.02        17.03        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       13.02        15.02        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.08        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 
       15.12        17.85         4.80        17.13        12.49        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6927 
        1.48         3.68         4.41        12.43        14.30         9.44 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A28E 
      140.38         7.50        44.32       131.51       139.17       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       35.74         6.18         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 
       33.67        13.25         0.53        47.41       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 
       61.91        36.00        22.09        13.78        35.80        91.79 
TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       46.75        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.69         0.72         6.05         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       41.36        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        26.43 

  ASPM MUTATED ASPM WILD-TYPE 
          0.07           0.00 
  ASPM MUTATED ASPM WILD-TYPE 
        135.65         148.01 
  ASPM MUTATED ASPM WILD-TYPE 
        22.025         20.020 
[1] "0.1 - 135.7 (22.0)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.3"
D670V2, continuous
D670V3, binary
                cls
clus               0   1
  ASPM MUTATED    42   5
  ASPM WILD-TYPE 324 114
[1] "tbl2"
                cls
clus             [,1] [,2]
  ASPM MUTATED     42    5
  ASPM WILD-TYPE  324  114
        clus
vv       ASPM MUTATED ASPM WILD-TYPE
  COLON            42            324
  RECTUM            5            114
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ASPM MUTATED         9        0        3        14         3         0
  ASPM WILD-TYPE      82        1       29       124         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ASPM MUTATED           1          0          7          1        4         2
  ASPM WILD-TYPE        23         11         52         41       44        16
                vv
clus             STAGE IVB
  ASPM MUTATED           0
  ASPM WILD-TYPE         1
D670V4, multiclass
            clus
vv           ASPM MUTATED ASPM WILD-TYPE
  STAGE I               9             82
  STAGE IA              0              1
  STAGE II              3             29
  STAGE IIA            14            124
  STAGE IIB             3              7
  STAGE IIC             0              1
  STAGE III             1             23
  STAGE IIIA            0             11
  STAGE IIIB            7             52
  STAGE IIIC            1             41
  STAGE IV              4             44
  STAGE IVA             2             16
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  ASPM MUTATED     1   9  28   9
  ASPM WILD-TYPE  16  83 301  41
D670V5, multiclass
    clus
vv   ASPM MUTATED ASPM WILD-TYPE
  T1            1             16
  T2            9             83
  T3           28            301
  T4            9             41
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  ASPM MUTATED    31  13   3
  ASPM WILD-TYPE 256 100  84
D670V6, multiclass
    clus
vv   ASPM MUTATED ASPM WILD-TYPE
  N0           31            256
  N1           13            100
  N2            3             84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D670V7, binary
                cls
clus               0   1
  ASPM MUTATED    35   6
  ASPM WILD-TYPE 340  59
[1] "tbl2"
                cls
clus             [,1] [,2]
  ASPM MUTATED     35    6
  ASPM WILD-TYPE  340   59
   clus
vv  ASPM MUTATED ASPM WILD-TYPE
  0           35            340
  1            6             59
[1] 2 2
[1] FALSE
D670V8, binary
                cls
clus               0   1
  ASPM MUTATED    17  30
  ASPM WILD-TYPE 208 234
[1] "tbl2"
                cls
clus             [,1] [,2]
  ASPM MUTATED     17   30
  ASPM WILD-TYPE  208  234
        clus
vv       ASPM MUTATED ASPM WILD-TYPE
  FEMALE           17            208
  MALE             30            234
[1] 2 2
[1] FALSE
D670V9, binary
                cls
clus               0   1
  ASPM MUTATED    35   1
  ASPM WILD-TYPE 315  21
[1] "tbl2"
                cls
clus             [,1] [,2]
  ASPM MUTATED     35    1
  ASPM WILD-TYPE  315   21
     clus
vv    ASPM MUTATED ASPM WILD-TYPE
  NO            35            315
  YES            1             21
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ASPM MUTATED                     28                            13
  ASPM WILD-TYPE                  287                            34
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ASPM MUTATED                       5                              0
  ASPM WILD-TYPE                   101                             10
D670V10, multiclass
                                clus
vv                               ASPM MUTATED ASPM WILD-TYPE
  COLON ADENOCARCINOMA                     28            287
  COLON MUCINOUS ADENOCARCINOMA            13             34
  RECTAL ADENOCARCINOMA                     5            101
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  ASPM MUTATED    29   1   0   5
  ASPM WILD-TYPE 316   3  31  20
D670V11, multiclass
    clus
vv   ASPM MUTATED ASPM WILD-TYPE
  R0           29            316
  R1            1              3
  R2            0             31
  RX            5             20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D670V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ASPM MUTATED                                  0     4
  ASPM WILD-TYPE                                1     7
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  ASPM MUTATED                           0    27
  ASPM WILD-TYPE                        22   199
D670V13, multiclass
                                  clus
vv                                 ASPM MUTATED ASPM WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       4              7
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                      27            199
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(671) Variable = ZNF180 MUTATION ANALYSIS
D671V1, survival
                  sevent
clus2                0   1
  ZNF180 MUTATED    14   3
  ZNF180 WILD-TYPE 364  90
  ZNF180 MUTATED ZNF180 WILD-TYPE 
              17              454 
  ZNF180 MUTATED ZNF180 WILD-TYPE 
               3               90 
$`ZNF180 MUTATED`
TCGA-A6-3809 TCGA-AA-3510 TCGA-AA-3660 TCGA-AA-3713 TCGA-AA-3864 TCGA-AA-3866 
       32.75        63.98        78.08        19.04        53.00        17.03 
TCGA-AA-3977 TCGA-AA-A00N TCGA-AY-6197 TCGA-AZ-6600 TCGA-CA-6717 TCGA-CM-5348 
       25.02         4.01        21.44        12.10        12.76        22.98 
TCGA-D5-6537 TCGA-AF-6672 TCGA-AG-3892 TCGA-AG-A002 TCGA-CI-6622 
        4.80        10.39        13.02        20.98         6.97 

$`ZNF180 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       13.94        19.99        61.02         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       85.05        26.99        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       31.07        30.05        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       33.01        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 
       22.36        62.79        88.21        49.41         6.77       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07        12.20        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.03        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       15.12        17.85        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AG-3574 TCGA-AG-3575 
       14.50        16.83        15.39        20.02        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
       33.17         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  ZNF180 MUTATED ZNF180 WILD-TYPE 
            4.01             0.00 
  ZNF180 MUTATED ZNF180 WILD-TYPE 
           78.08           148.01 
  ZNF180 MUTATED ZNF180 WILD-TYPE 
          19.040           20.235 
[1] "4.0 - 78.1 (19.0)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.1"
D671V2, continuous
D671V3, binary
                  cls
clus                 0   1
  ZNF180 MUTATED    14   4
  ZNF180 WILD-TYPE 352 115
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF180 MUTATED     14    4
  ZNF180 WILD-TYPE  352  115
        clus
vv       ZNF180 MUTATED ZNF180 WILD-TYPE
  COLON              14              352
  RECTUM              4              115
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZNF180 MUTATED         3        0        3         3         3         0
  ZNF180 WILD-TYPE      88        1       29       135         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF180 MUTATED           0          0          2          0        3
  ZNF180 WILD-TYPE        24         11         57         42       45
                  vv
clus               STAGE IVA STAGE IVB
  ZNF180 MUTATED           0         0
  ZNF180 WILD-TYPE        18         1
D671V4, multiclass
            clus
vv           ZNF180 MUTATED ZNF180 WILD-TYPE
  STAGE I                 3               88
  STAGE IA                0                1
  STAGE II                3               29
  STAGE IIA               3              135
  STAGE IIB               3                7
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              2               57
  STAGE IIIC              0               42
  STAGE IV                3               45
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZNF180 MUTATED     1   3   9   5
  ZNF180 WILD-TYPE  16  89 320  45
D671V5, multiclass
    clus
vv   ZNF180 MUTATED ZNF180 WILD-TYPE
  T1              1               16
  T2              3               89
  T3              9              320
  T4              5               45
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  ZNF180 MUTATED    14   3   1
  ZNF180 WILD-TYPE 273 110  86
D671V6, multiclass
    clus
vv   ZNF180 MUTATED ZNF180 WILD-TYPE
  N0             14              273
  N1              3              110
  N2              1               86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D671V7, binary
                  cls
clus                 0   1
  ZNF180 MUTATED    12   2
  ZNF180 WILD-TYPE 363  63
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF180 MUTATED     12    2
  ZNF180 WILD-TYPE  363   63
   clus
vv  ZNF180 MUTATED ZNF180 WILD-TYPE
  0             12              363
  1              2               63
[1] 2 2
[1] FALSE
D671V8, binary
                  cls
clus                 0   1
  ZNF180 MUTATED     5  13
  ZNF180 WILD-TYPE 220 251
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF180 MUTATED      5   13
  ZNF180 WILD-TYPE  220  251
        clus
vv       ZNF180 MUTATED ZNF180 WILD-TYPE
  FEMALE              5              220
  MALE               13              251
[1] 2 2
[1] FALSE
D671V9, binary
                  cls
clus                 0   1
  ZNF180 MUTATED    12   2
  ZNF180 WILD-TYPE 338  20
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF180 MUTATED     12    2
  ZNF180 WILD-TYPE  338   20
     clus
vv    ZNF180 MUTATED ZNF180 WILD-TYPE
  NO              12              338
  YES              2               20
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ZNF180 MUTATED                     11                             3
  ZNF180 WILD-TYPE                  304                            44
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ZNF180 MUTATED                       4                              0
  ZNF180 WILD-TYPE                   102                             10
D671V10, multiclass
                                clus
vv                               ZNF180 MUTATED ZNF180 WILD-TYPE
  COLON ADENOCARCINOMA                       11              304
  COLON MUCINOUS ADENOCARCINOMA               3               44
  RECTAL ADENOCARCINOMA                       4              102
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ZNF180 MUTATED    12   0   1   1
  ZNF180 WILD-TYPE 333   4  30  24
D671V11, multiclass
    clus
vv   ZNF180 MUTATED ZNF180 WILD-TYPE
  R0             12              333
  R1              0                4
  R2              1               30
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D671V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF180 MUTATED                                  0     1
  ZNF180 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZNF180 MUTATED                           1     6
  ZNF180 WILD-TYPE                        21   220
D671V13, multiclass
                                  clus
vv                                 ZNF180 MUTATED ZNF180 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                         6              220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(672) Variable = HYDIN MUTATION ANALYSIS
D672V1, survival
                 sevent
clus2               0   1
  HYDIN MUTATED    68  20
  HYDIN WILD-TYPE 310  73
  HYDIN MUTATED HYDIN WILD-TYPE 
             88             383 
  HYDIN MUTATED HYDIN WILD-TYPE 
             20              73 
$`HYDIN MUTATED`
TCGA-A6-3809 TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5665 
       32.75        32.91        30.44        29.19        33.53        22.06 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6653 TCGA-A6-6782 TCGA-AA-3492 TCGA-AA-3510 
        8.38        25.08        24.39        20.28         3.02        63.98 
TCGA-AA-3518 TCGA-AA-3524 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3666 
        1.02        36.03        61.02         6.05         6.97         2.01 
TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3815 TCGA-AA-3833 TCGA-AA-3846 TCGA-AA-3854 
       26.99        19.04        33.04        15.95        17.03        36.03 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3877 TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-3972 
       30.05        53.00        31.00        33.01        24.00        50.99 
TCGA-AA-3977 TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A03F TCGA-AD-5900 
       25.02        18.05         4.01        34.98        18.05         0.07 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6965 TCGA-AU-6004 
       15.52        56.55         0.72         5.79         0.20        27.09 
TCGA-AZ-4315 TCGA-AZ-4682 TCGA-AZ-6598 TCGA-AZ-6601 TCGA-AZ-6606 TCGA-AZ-6607 
       58.39        22.36        49.41       100.01        11.74         3.19 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-6747 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-6162 
       12.76        10.06        82.95        37.02        25.02        12.00 
TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       14.04        12.95        13.05        12.03        45.40        12.26 
TCGA-D5-6535 TCGA-D5-6538 TCGA-D5-6541 TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6932 
       15.12        17.13        15.58        14.30         9.44        11.38 
TCGA-DM-A1D9 TCGA-DM-A282 TCGA-DM-A28G TCGA-F4-6570 TCGA-F4-6855 TCGA-G4-6317 
      140.38       139.17        60.79         6.18        47.41        36.00 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 TCGA-AF-5654 TCGA-AG-3582 TCGA-AG-3881 
       35.80        26.17        79.69        16.83        36.03        19.04 
TCGA-AG-3885 TCGA-AG-3892 TCGA-AG-3896 TCGA-AG-4007 TCGA-AG-A002 TCGA-DC-6155 
       17.95        13.02         1.02         1.02        20.98        13.97 
TCGA-DC-6158 TCGA-DY-A1DC TCGA-EI-6506 TCGA-EI-6510 
       10.98        41.36        20.55        18.28 

$`HYDIN WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5657 
       16.57        34.65        33.34        36.53        14.53        31.63 
TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6648 
       23.61        22.09        32.71        27.09        22.52        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       24.16        21.76        24.69        23.87        20.12        19.66 
TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        7.04         1.02        35.01         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3525 TCGA-AA-3526 
       38.99         9.07        24.03        37.05         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3672 
       13.94        19.99        78.08        54.02        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3811 
       19.00        36.00         5.03        85.05        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3837 
       35.05         0.99        25.02         1.02        17.98        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02        14.93         0.00        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3866 
        0.00        32.05         0.99        31.07        31.07        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 
       24.03        27.02        29.98        18.05         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        26.01         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       21.99        16.08        13.05        34.06        26.01        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00L 
       38.04        19.00        30.02        34.03        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03J 
        5.03        14.01         0.92        41.00        39.98        40.96 
TCGA-AD-6548 TCGA-AD-6890 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AU-3779 
       21.37         0.79        22.42        27.42        10.88        14.50 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
       16.31         0.95        33.01        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 
        5.13       106.75        62.79        88.21         6.77        12.10 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       29.56         5.23         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        3.29         0.07        12.20        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4752 TCGA-CM-5341 
        1.91       124.27        23.05        20.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 
       15.02        15.02        17.03        15.02         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6172 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-D5-5539 
       11.01        11.08        11.08        11.01        10.06        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6898 TCGA-D5-6920 
       17.85         4.80        12.49        16.14         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
        4.41        12.43         9.04        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       12.00        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A1DB 
       92.75        49.91        13.32        12.59         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      131.51       135.65         6.12        81.37       119.93        35.97 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 
      117.07        98.24         8.61        31.96        35.74        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
        0.53        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6321 
       44.68        55.04        85.48        63.62        61.91        22.09 
TCGA-G4-6323 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       13.78        91.79        46.75        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-6136 
       13.55        19.10        34.49        10.39        14.50        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
        7.07        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 
       32.98         0.99         0.99        19.99         1.02        36.95 
TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       17.03        35.01        14.01        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       28.04        36.03        14.04        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6157 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       27.95        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
      126.44        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6507 TCGA-EI-6508 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       19.96        20.91         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  HYDIN MUTATED HYDIN WILD-TYPE 
           0.07            0.00 
  HYDIN MUTATED HYDIN WILD-TYPE 
         140.38          148.01 
  HYDIN MUTATED HYDIN WILD-TYPE 
         20.415          20.120 
[1] "0.1 - 140.4 (20.4)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.1"
D672V2, continuous
D672V3, binary
                 cls
clus                0   1
  HYDIN MUTATED    80  13
  HYDIN WILD-TYPE 286 106
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HYDIN MUTATED     80   13
  HYDIN WILD-TYPE  286  106
        clus
vv       HYDIN MUTATED HYDIN WILD-TYPE
  COLON             80             286
  RECTUM            13             106
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  HYDIN MUTATED        15        0       10        33         6         0
  HYDIN WILD-TYPE      76        1       22       105         4         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  HYDIN MUTATED           3          1          7          4        6         4
  HYDIN WILD-TYPE        21         10         52         38       42        14
                 vv
clus              STAGE IVB
  HYDIN MUTATED           1
  HYDIN WILD-TYPE         0
D672V4, multiclass
            clus
vv           HYDIN MUTATED HYDIN WILD-TYPE
  STAGE I               15              76
  STAGE IA               0               1
  STAGE II              10              22
  STAGE IIA             33             105
  STAGE IIB              6               4
  STAGE IIC              0               1
  STAGE III              3              21
  STAGE IIIA             1              10
  STAGE IIIB             7              52
  STAGE IIIC             4              38
  STAGE IV               6              42
  STAGE IVA              4              14
  STAGE IVB              1               0
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  HYDIN MUTATED     2  16  61  14
  HYDIN WILD-TYPE  15  76 268  36
D672V5, multiclass
    clus
vv   HYDIN MUTATED HYDIN WILD-TYPE
  T1             2              15
  T2            16              76
  T3            61             268
  T4            14              36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  HYDIN MUTATED    66  12  15
  HYDIN WILD-TYPE 221 101  72
D672V6, multiclass
    clus
vv   HYDIN MUTATED HYDIN WILD-TYPE
  N0            66             221
  N1            12             101
  N2            15              72
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D672V7, binary
                 cls
clus                0   1
  HYDIN MUTATED    69  10
  HYDIN WILD-TYPE 306  55
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HYDIN MUTATED     69   10
  HYDIN WILD-TYPE  306   55
   clus
vv  HYDIN MUTATED HYDIN WILD-TYPE
  0            69             306
  1            10              55
[1] 2 2
[1] FALSE
D672V8, binary
                 cls
clus                0   1
  HYDIN MUTATED    45  48
  HYDIN WILD-TYPE 180 216
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HYDIN MUTATED     45   48
  HYDIN WILD-TYPE  180  216
        clus
vv       HYDIN MUTATED HYDIN WILD-TYPE
  FEMALE            45             180
  MALE              48             216
[1] 2 2
[1] FALSE
D672V9, binary
                 cls
clus                0   1
  HYDIN MUTATED    71   1
  HYDIN WILD-TYPE 279  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HYDIN MUTATED     71    1
  HYDIN WILD-TYPE  279   21
     clus
vv    HYDIN MUTATED HYDIN WILD-TYPE
  NO             71             279
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  HYDIN MUTATED                     68                            12
  HYDIN WILD-TYPE                  247                            35
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  HYDIN MUTATED                      12                              0
  HYDIN WILD-TYPE                    94                             10
D672V10, multiclass
                                clus
vv                               HYDIN MUTATED HYDIN WILD-TYPE
  COLON ADENOCARCINOMA                      68             247
  COLON MUCINOUS ADENOCARCINOMA             12              35
  RECTAL ADENOCARCINOMA                     12              94
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  HYDIN MUTATED    63   0   4   6
  HYDIN WILD-TYPE 282   4  27  19
D672V11, multiclass
    clus
vv   HYDIN MUTATED HYDIN WILD-TYPE
  R0            63             282
  R1             0               4
  R2             4              27
  RX             6              19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D672V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HYDIN MUTATED                                  0     3
  HYDIN WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  HYDIN MUTATED                           5    50
  HYDIN WILD-TYPE                        17   176
D672V13, multiclass
                                  clus
vv                                 HYDIN MUTATED HYDIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        3               8
  BLACK OR AFRICAN AMERICAN                    5              17
  WHITE                                       50             176
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(673) Variable = NCOA3 MUTATION ANALYSIS
D673V1, survival
                 sevent
clus2               0   1
  NCOA3 MUTATED    14   2
  NCOA3 WILD-TYPE 364  91
  NCOA3 MUTATED NCOA3 WILD-TYPE 
             16             455 
  NCOA3 MUTATED NCOA3 WILD-TYPE 
              2              91 
$`NCOA3 MUTATED`
TCGA-A6-5666 TCGA-AA-3821 TCGA-AA-3864 TCGA-AA-3956 TCGA-AA-A00N TCGA-AA-A00O 
       32.71         1.02        53.00        34.03         4.01        27.02 
TCGA-CA-5254 TCGA-CA-6717 TCGA-D5-6540 TCGA-D5-6927 TCGA-DM-A1DB TCGA-DM-A28E 
       12.69        12.76        16.14         9.44        44.32       119.93 
TCGA-F4-6856 TCGA-AF-2687 TCGA-AG-A002 TCGA-EF-5830 
       35.31        24.13        20.98         0.49 

$`NCOA3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        22.06        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 
       10.06        35.05        33.04         0.99        25.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 
        0.99        31.07        31.07        30.05        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00Q TCGA-AA-A00R 
       34.03        18.05        18.05        38.04        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
       11.74         3.19         1.61         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07        12.20        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
        4.80        17.13        12.49        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6929 
        4.41        12.43        14.30         9.04        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
      140.38         7.50       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
       81.37        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2689 
       35.80        26.17        91.79        46.75        79.69        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EI-6506 TCGA-EI-6507 
       57.24        24.13        51.48        32.61        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  NCOA3 MUTATED NCOA3 WILD-TYPE 
           0.49            0.00 
  NCOA3 MUTATED NCOA3 WILD-TYPE 
         119.93          148.01 
  NCOA3 MUTATED NCOA3 WILD-TYPE 
         22.555          20.120 
[1] "0.5 - 119.9 (22.6)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.6"
D673V2, continuous
D673V3, binary
                 cls
clus                0   1
  NCOA3 MUTATED    14   3
  NCOA3 WILD-TYPE 352 116
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NCOA3 MUTATED     14    3
  NCOA3 WILD-TYPE  352  116
        clus
vv       NCOA3 MUTATED NCOA3 WILD-TYPE
  COLON             14             352
  RECTUM             3             116
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NCOA3 MUTATED         4        0        2         6         2         1
  NCOA3 WILD-TYPE      87        1       30       132         8         0
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NCOA3 MUTATED           0          0          0          2        0         0
  NCOA3 WILD-TYPE        24         11         59         40       48        18
                 vv
clus              STAGE IVB
  NCOA3 MUTATED           0
  NCOA3 WILD-TYPE         1
D673V4, multiclass
            clus
vv           NCOA3 MUTATED NCOA3 WILD-TYPE
  STAGE I                4              87
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA              6             132
  STAGE IIB              2               8
  STAGE IIC              1               0
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             2              40
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  NCOA3 MUTATED     0   4   9   4
  NCOA3 WILD-TYPE  17  88 320  46
D673V5, multiclass
    clus
vv   NCOA3 MUTATED NCOA3 WILD-TYPE
  T1             0              17
  T2             4              88
  T3             9             320
  T4             4              46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  NCOA3 MUTATED    15   0   2
  NCOA3 WILD-TYPE 272 113  85
D673V6, multiclass
    clus
vv   NCOA3 MUTATED NCOA3 WILD-TYPE
  N0            15             272
  N1             0             113
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D673V7, binary
                 cls
clus                0   1
  NCOA3 MUTATED    17   0
  NCOA3 WILD-TYPE 358  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NCOA3 MUTATED     17    0
  NCOA3 WILD-TYPE  358   65
   clus
vv  NCOA3 MUTATED NCOA3 WILD-TYPE
  0            17             358
  1             0              65
[1] 2 2
[1] FALSE
D673V8, binary
                 cls
clus                0   1
  NCOA3 MUTATED     5  12
  NCOA3 WILD-TYPE 220 252
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NCOA3 MUTATED      5   12
  NCOA3 WILD-TYPE  220  252
        clus
vv       NCOA3 MUTATED NCOA3 WILD-TYPE
  FEMALE             5             220
  MALE              12             252
[1] 2 2
[1] FALSE
D673V9, binary
                 cls
clus                0   1
  NCOA3 MUTATED    11   1
  NCOA3 WILD-TYPE 339  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NCOA3 MUTATED     11    1
  NCOA3 WILD-TYPE  339   21
     clus
vv    NCOA3 MUTATED NCOA3 WILD-TYPE
  NO             11             339
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  NCOA3 MUTATED                      9                             5
  NCOA3 WILD-TYPE                  306                            42
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  NCOA3 MUTATED                       3                              0
  NCOA3 WILD-TYPE                   103                             10
D673V10, multiclass
                                clus
vv                               NCOA3 MUTATED NCOA3 WILD-TYPE
  COLON ADENOCARCINOMA                       9             306
  COLON MUCINOUS ADENOCARCINOMA              5              42
  RECTAL ADENOCARCINOMA                      3             103
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  NCOA3 MUTATED    12   0   0   2
  NCOA3 WILD-TYPE 333   4  31  23
D673V11, multiclass
    clus
vv   NCOA3 MUTATED NCOA3 WILD-TYPE
  R0            12             333
  R1             0               4
  R2             0              31
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D673V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NCOA3 MUTATED                                  0     2
  NCOA3 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  NCOA3 MUTATED                           0     8
  NCOA3 WILD-TYPE                        22   218
D673V13, multiclass
                                  clus
vv                                 NCOA3 MUTATED NCOA3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               9
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        8             218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(674) Variable = ARMCX5 MUTATION ANALYSIS
D674V1, survival
                  sevent
clus2                0   1
  ARMCX5 MUTATED     5   2
  ARMCX5 WILD-TYPE 373  91
  ARMCX5 MUTATED ARMCX5 WILD-TYPE 
               7              464 
  ARMCX5 MUTATED ARMCX5 WILD-TYPE 
               2               91 
$`ARMCX5 MUTATED`
TCGA-A6-2672 TCGA-AA-3660 TCGA-AA-3815 TCGA-AA-A00N TCGA-AZ-6598 TCGA-CM-5860 
       46.65        78.08        33.04         4.01        49.41        32.02 
TCGA-G4-6588 
       26.17 

$`ARMCX5 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 
       19.99        13.94        19.99        61.02         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       35.05         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        88.21         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.03        22.98        30.08        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       13.78        35.80        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  ARMCX5 MUTATED ARMCX5 WILD-TYPE 
            4.01             0.00 
  ARMCX5 MUTATED ARMCX5 WILD-TYPE 
           78.08           148.01 
  ARMCX5 MUTATED ARMCX5 WILD-TYPE 
          33.040           20.035 
[1] "4.0 - 78.1 (33.0)"  "0.0 - 148.0 (20.0)"
[1] "hr=" "1"  
D674V2, continuous
D674V3, binary
                  cls
clus                 0   1
  ARMCX5 MUTATED     8   0
  ARMCX5 WILD-TYPE 358 119
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARMCX5 MUTATED      8    0
  ARMCX5 WILD-TYPE  358  119
        clus
vv       ARMCX5 MUTATED ARMCX5 WILD-TYPE
  COLON               8              358
  RECTUM              0              119
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ARMCX5 MUTATED         0        0        2         3         1         0
  ARMCX5 WILD-TYPE      91        1       30       135         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ARMCX5 MUTATED           0          0          1          0        1
  ARMCX5 WILD-TYPE        24         11         58         42       47
                  vv
clus               STAGE IVA STAGE IVB
  ARMCX5 MUTATED           0         0
  ARMCX5 WILD-TYPE        18         1
D674V4, multiclass
            clus
vv           ARMCX5 MUTATED ARMCX5 WILD-TYPE
  STAGE I                 0               91
  STAGE IA                0                1
  STAGE II                2               30
  STAGE IIA               3              135
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              1               58
  STAGE IIIC              0               42
  STAGE IV                1               47
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ARMCX5 MUTATED     0   0   7   1
  ARMCX5 WILD-TYPE  17  92 322  49
D674V5, multiclass
    clus
vv   ARMCX5 MUTATED ARMCX5 WILD-TYPE
  T1              0               17
  T2              0               92
  T3              7              322
  T4              1               49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  ARMCX5 MUTATED     6   1   1
  ARMCX5 WILD-TYPE 281 112  86
D674V6, multiclass
    clus
vv   ARMCX5 MUTATED ARMCX5 WILD-TYPE
  N0              6              281
  N1              1              112
  N2              1               86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D674V7, binary
                  cls
clus                 0   1
  ARMCX5 MUTATED     6   1
  ARMCX5 WILD-TYPE 369  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARMCX5 MUTATED      6    1
  ARMCX5 WILD-TYPE  369   64
   clus
vv  ARMCX5 MUTATED ARMCX5 WILD-TYPE
  0              6              369
  1              1               64
[1] 2 2
[1] FALSE
D674V8, binary
                  cls
clus                 0   1
  ARMCX5 MUTATED     6   2
  ARMCX5 WILD-TYPE 219 262
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARMCX5 MUTATED      6    2
  ARMCX5 WILD-TYPE  219  262
        clus
vv       ARMCX5 MUTATED ARMCX5 WILD-TYPE
  FEMALE              6              219
  MALE                2              262
[1] 2 2
[1] FALSE
D674V9, binary
                  cls
clus                 0   1
  ARMCX5 MUTATED     6   0
  ARMCX5 WILD-TYPE 344  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARMCX5 MUTATED      6    0
  ARMCX5 WILD-TYPE  344   22
     clus
vv    ARMCX5 MUTATED ARMCX5 WILD-TYPE
  NO               6              344
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ARMCX5 MUTATED                      7                             1
  ARMCX5 WILD-TYPE                  308                            46
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ARMCX5 MUTATED                       0                              0
  ARMCX5 WILD-TYPE                   106                             10
D674V10, multiclass
                                clus
vv                               ARMCX5 MUTATED ARMCX5 WILD-TYPE
  COLON ADENOCARCINOMA                        7              308
  COLON MUCINOUS ADENOCARCINOMA               1               46
  RECTAL ADENOCARCINOMA                       0              106
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ARMCX5 MUTATED     6   0   1   0
  ARMCX5 WILD-TYPE 339   4  30  25
D674V11, multiclass
    clus
vv   ARMCX5 MUTATED ARMCX5 WILD-TYPE
  R0              6              339
  R1              0                4
  R2              1               30
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D674V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ARMCX5 MUTATED                                  0     0
  ARMCX5 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ARMCX5 MUTATED                           0     4
  ARMCX5 WILD-TYPE                        22   222
D674V13, multiclass
                                  clus
vv                                 ARMCX5 MUTATED ARMCX5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         4              222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(675) Variable = YLPM1 MUTATION ANALYSIS
D675V1, survival
                 sevent
clus2               0   1
  YLPM1 MUTATED    19   4
  YLPM1 WILD-TYPE 359  89
  YLPM1 MUTATED YLPM1 WILD-TYPE 
             23             448 
  YLPM1 MUTATED YLPM1 WILD-TYPE 
              4              89 
$`YLPM1 MUTATED`
TCGA-A6-6781 TCGA-AA-3510 TCGA-AA-3663 TCGA-AA-3692 TCGA-AA-3713 TCGA-AA-3815 
       19.66        63.98         6.97        36.00        19.04        33.04 
TCGA-AA-3818 TCGA-AA-3821 TCGA-AA-3972 TCGA-AA-A010 TCGA-AA-A01P TCGA-AY-6386 
        0.99         1.02        50.99        34.98        38.07        17.82 
TCGA-CA-6717 TCGA-CK-5913 TCGA-CK-5916 TCGA-CM-4743 TCGA-CM-5861 TCGA-CM-6171 
       12.76        51.32        21.14        23.05        15.02        14.04 
TCGA-D5-6540 TCGA-G4-6309 TCGA-G4-6586 TCGA-AG-3892 TCGA-AG-A002 
       16.14        85.48        35.80        13.02        20.98 

$`YLPM1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3696 TCGA-AA-3697 
       11.01         5.98        37.05        19.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3819 TCGA-AA-3831 
       26.99        19.04        10.06        35.05        25.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 
       20.98        34.03         2.01        21.99        16.08        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AZ-4315 
       27.09        16.31         0.95        33.01        21.44        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07        12.20        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-6747 
      148.01        85.45        15.62        49.08         9.99        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
        1.91       124.27        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 
       29.06        22.03        22.98        30.08        32.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       15.02        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 
       15.12        17.85         4.80        17.13        12.49        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 
       63.62        61.91        36.00        22.09        13.78        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 
       19.99         1.02        17.95        36.95        17.03        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  YLPM1 MUTATED YLPM1 WILD-TYPE 
           0.99            0.00 
  YLPM1 MUTATED YLPM1 WILD-TYPE 
          85.48          148.01 
  YLPM1 MUTATED YLPM1 WILD-TYPE 
         20.980          20.155 
[1] "1.0 - 85.5 (21.0)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.2"
D675V2, continuous
D675V3, binary
                 cls
clus                0   1
  YLPM1 MUTATED    22   2
  YLPM1 WILD-TYPE 344 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  YLPM1 MUTATED     22    2
  YLPM1 WILD-TYPE  344  117
        clus
vv       YLPM1 MUTATED YLPM1 WILD-TYPE
  COLON             22             344
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  YLPM1 MUTATED         6        0        2         8         1         0
  YLPM1 WILD-TYPE      85        1       30       130         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  YLPM1 MUTATED           1          0          2          1        3         0
  YLPM1 WILD-TYPE        23         11         57         41       45        18
                 vv
clus              STAGE IVB
  YLPM1 MUTATED           0
  YLPM1 WILD-TYPE         1
D675V4, multiclass
            clus
vv           YLPM1 MUTATED YLPM1 WILD-TYPE
  STAGE I                6              85
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA              8             130
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             2              57
  STAGE IIIC             1              41
  STAGE IV               3              45
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  YLPM1 MUTATED     2   4  16   2
  YLPM1 WILD-TYPE  15  88 313  48
D675V5, multiclass
    clus
vv   YLPM1 MUTATED YLPM1 WILD-TYPE
  T1             2              15
  T2             4              88
  T3            16             313
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  YLPM1 MUTATED    18   5   1
  YLPM1 WILD-TYPE 269 108  86
D675V6, multiclass
    clus
vv   YLPM1 MUTATED YLPM1 WILD-TYPE
  N0            18             269
  N1             5             108
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D675V7, binary
                 cls
clus                0   1
  YLPM1 MUTATED    19   3
  YLPM1 WILD-TYPE 356  62
[1] "tbl2"
                 cls
clus              [,1] [,2]
  YLPM1 MUTATED     19    3
  YLPM1 WILD-TYPE  356   62
   clus
vv  YLPM1 MUTATED YLPM1 WILD-TYPE
  0            19             356
  1             3              62
[1] 2 2
[1] FALSE
D675V8, binary
                 cls
clus                0   1
  YLPM1 MUTATED    15   9
  YLPM1 WILD-TYPE 210 255
[1] "tbl2"
                 cls
clus              [,1] [,2]
  YLPM1 MUTATED     15    9
  YLPM1 WILD-TYPE  210  255
        clus
vv       YLPM1 MUTATED YLPM1 WILD-TYPE
  FEMALE            15             210
  MALE               9             255
[1] 2 2
[1] FALSE
D675V9, binary
                 cls
clus                0   1
  YLPM1 MUTATED    20   2
  YLPM1 WILD-TYPE 330  20
[1] "tbl2"
                 cls
clus              [,1] [,2]
  YLPM1 MUTATED     20    2
  YLPM1 WILD-TYPE  330   20
     clus
vv    YLPM1 MUTATED YLPM1 WILD-TYPE
  NO             20             330
  YES             2              20
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  YLPM1 MUTATED                     17                             5
  YLPM1 WILD-TYPE                  298                            42
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  YLPM1 MUTATED                       2                              0
  YLPM1 WILD-TYPE                   104                             10
D675V10, multiclass
                                clus
vv                               YLPM1 MUTATED YLPM1 WILD-TYPE
  COLON ADENOCARCINOMA                      17             298
  COLON MUCINOUS ADENOCARCINOMA              5              42
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  YLPM1 MUTATED    18   0   3   3
  YLPM1 WILD-TYPE 327   4  28  22
D675V11, multiclass
    clus
vv   YLPM1 MUTATED YLPM1 WILD-TYPE
  R0            18             327
  R1             0               4
  R2             3              28
  RX             3              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D675V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  YLPM1 MUTATED                                  0     1
  YLPM1 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  YLPM1 MUTATED                           2     8
  YLPM1 WILD-TYPE                        20   218
D675V13, multiclass
                                  clus
vv                                 YLPM1 MUTATED YLPM1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    2              20
  WHITE                                        8             218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(676) Variable = PLEK MUTATION ANALYSIS
D676V1, survival
                sevent
clus2              0   1
  PLEK MUTATED    13   1
  PLEK WILD-TYPE 365  92
  PLEK MUTATED PLEK WILD-TYPE 
            14            457 
  PLEK MUTATED PLEK WILD-TYPE 
             1             92 
$`PLEK MUTATED`
TCGA-A6-6653 TCGA-AA-3518 TCGA-AA-3555 TCGA-AA-3662 TCGA-AA-3815 TCGA-AA-A00N 
       24.39         1.02        29.95         6.05        33.04         4.01 
TCGA-AA-A010 TCGA-AD-5900 TCGA-AZ-4315 TCGA-CA-6717 TCGA-CK-5914 TCGA-D5-6931 
       34.98         0.07        58.39        12.76         9.99        12.00 
TCGA-AG-3892 TCGA-AG-4007 
       13.02         1.02 

$`PLEK WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
       25.08        25.18        24.16        21.76        24.69        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       24.00        17.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02        78.08         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
       26.99        19.04        19.04        10.06        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 
       41.00        39.98        18.05        40.96        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       33.01        21.44        17.82         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       49.08        51.32        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       36.95        17.03        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4008 
       32.02        19.99        28.04        36.03        14.04        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  PLEK MUTATED PLEK WILD-TYPE 
          0.07           0.00 
  PLEK MUTATED PLEK WILD-TYPE 
         58.39         148.01 
  PLEK MUTATED PLEK WILD-TYPE 
         12.38          20.55 
[1] "0.1 - 58.4 (12.4)"  "0.0 - 148.0 (20.6)"
[1] "hr=" "1.8"
D676V2, continuous
D676V3, binary
                cls
clus               0   1
  PLEK MUTATED    12   2
  PLEK WILD-TYPE 354 117
[1] "tbl2"
                cls
clus             [,1] [,2]
  PLEK MUTATED     12    2
  PLEK WILD-TYPE  354  117
        clus
vv       PLEK MUTATED PLEK WILD-TYPE
  COLON            12            354
  RECTUM            2            117
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PLEK MUTATED         3        0        0         5         2         0
  PLEK WILD-TYPE      88        1       32       133         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PLEK MUTATED           0          0          1          1        2         0
  PLEK WILD-TYPE        24         11         58         41       46        18
                vv
clus             STAGE IVB
  PLEK MUTATED           0
  PLEK WILD-TYPE         1
D676V4, multiclass
            clus
vv           PLEK MUTATED PLEK WILD-TYPE
  STAGE I               3             88
  STAGE IA              0              1
  STAGE II              0             32
  STAGE IIA             5            133
  STAGE IIB             2              8
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            1             58
  STAGE IIIC            1             41
  STAGE IV              2             46
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  PLEK MUTATED     1   2   6   5
  PLEK WILD-TYPE  16  90 323  45
D676V5, multiclass
    clus
vv   PLEK MUTATED PLEK WILD-TYPE
  T1            1             16
  T2            2             90
  T3            6            323
  T4            5             45
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  PLEK MUTATED    10   1   3
  PLEK WILD-TYPE 277 112  84
D676V6, multiclass
    clus
vv   PLEK MUTATED PLEK WILD-TYPE
  N0           10            277
  N1            1            112
  N2            3             84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D676V7, binary
                cls
clus               0   1
  PLEK MUTATED    10   2
  PLEK WILD-TYPE 365  63
[1] "tbl2"
                cls
clus             [,1] [,2]
  PLEK MUTATED     10    2
  PLEK WILD-TYPE  365   63
   clus
vv  PLEK MUTATED PLEK WILD-TYPE
  0           10            365
  1            2             63
[1] 2 2
[1] FALSE
D676V8, binary
                cls
clus               0   1
  PLEK MUTATED     6   8
  PLEK WILD-TYPE 219 256
[1] "tbl2"
                cls
clus             [,1] [,2]
  PLEK MUTATED      6    8
  PLEK WILD-TYPE  219  256
        clus
vv       PLEK MUTATED PLEK WILD-TYPE
  FEMALE            6            219
  MALE              8            256
[1] 2 2
[1] FALSE
D676V9, binary
                cls
clus               0   1
  PLEK MUTATED     9   0
  PLEK WILD-TYPE 341  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  PLEK MUTATED      9    0
  PLEK WILD-TYPE  341   22
     clus
vv    PLEK MUTATED PLEK WILD-TYPE
  NO             9            341
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PLEK MUTATED                      8                             4
  PLEK WILD-TYPE                  307                            43
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PLEK MUTATED                       2                              0
  PLEK WILD-TYPE                   104                             10
D676V10, multiclass
                                clus
vv                               PLEK MUTATED PLEK WILD-TYPE
  COLON ADENOCARCINOMA                      8            307
  COLON MUCINOUS ADENOCARCINOMA             4             43
  RECTAL ADENOCARCINOMA                     2            104
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  PLEK MUTATED     9   0   2   2
  PLEK WILD-TYPE 336   4  29  23
D676V11, multiclass
    clus
vv   PLEK MUTATED PLEK WILD-TYPE
  R0            9            336
  R1            0              4
  R2            2             29
  RX            2             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D676V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PLEK MUTATED                                  0     1
  PLEK WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  PLEK MUTATED                           0     5
  PLEK WILD-TYPE                        22   221
D676V13, multiclass
                                  clus
vv                                 PLEK MUTATED PLEK WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       5            221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(677) Variable = MST4 MUTATION ANALYSIS
D677V1, survival
                sevent
clus2              0   1
  MST4 MUTATED     6   2
  MST4 WILD-TYPE 372  91
  MST4 MUTATED MST4 WILD-TYPE 
             8            463 
  MST4 MUTATED MST4 WILD-TYPE 
             2             91 
$`MST4 MUTATED`
TCGA-A6-4105 TCGA-A6-5661 TCGA-A6-5662 TCGA-AA-3496 TCGA-AA-A00N TCGA-AU-6004 
       14.53        33.53        23.61         1.02         4.01        27.09 
TCGA-DM-A28K TCGA-EI-6510 
       98.24        18.28 

$`MST4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 
       16.57        34.65        33.34        32.75        36.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 
       31.63        30.44        29.19        22.09        22.06        32.71 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       27.09        22.52         8.38        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
       20.28         7.04         3.02        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-F4-6459 TCGA-F4-6460 
      119.93        35.97        60.79       117.07         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-F5-6464 TCGA-F5-6465 
        0.49        20.55        19.96        20.91         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  MST4 MUTATED MST4 WILD-TYPE 
          1.02           0.00 
  MST4 MUTATED MST4 WILD-TYPE 
         98.24         148.01 
  MST4 MUTATED MST4 WILD-TYPE 
        20.945         20.190 
[1] "1.0 - 98.2 (20.9)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.3"
D677V2, continuous
D677V3, binary
                cls
clus               0   1
  MST4 MUTATED     7   1
  MST4 WILD-TYPE 359 118
[1] "tbl2"
                cls
clus             [,1] [,2]
  MST4 MUTATED      7    1
  MST4 WILD-TYPE  359  118
        clus
vv       MST4 MUTATED MST4 WILD-TYPE
  COLON             7            359
  RECTUM            1            118
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MST4 MUTATED         1        0        1         3         1         0
  MST4 WILD-TYPE      90        1       31       135         9         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MST4 MUTATED           0          0          0          0        0         2
  MST4 WILD-TYPE        24         11         59         42       48        16
                vv
clus             STAGE IVB
  MST4 MUTATED           0
  MST4 WILD-TYPE         1
D677V4, multiclass
            clus
vv           MST4 MUTATED MST4 WILD-TYPE
  STAGE I               1             90
  STAGE IA              0              1
  STAGE II              1             31
  STAGE IIA             3            135
  STAGE IIB             1              9
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            0             59
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             2             16
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  MST4 MUTATED     0   2   5   1
  MST4 WILD-TYPE  17  90 324  49
D677V5, multiclass
    clus
vv   MST4 MUTATED MST4 WILD-TYPE
  T1            0             17
  T2            2             90
  T3            5            324
  T4            1             49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  MST4 MUTATED     7   0   1
  MST4 WILD-TYPE 280 113  86
D677V6, multiclass
    clus
vv   MST4 MUTATED MST4 WILD-TYPE
  N0            7            280
  N1            0            113
  N2            1             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D677V7, binary
                cls
clus               0   1
  MST4 MUTATED     6   1
  MST4 WILD-TYPE 369  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  MST4 MUTATED      6    1
  MST4 WILD-TYPE  369   64
   clus
vv  MST4 MUTATED MST4 WILD-TYPE
  0            6            369
  1            1             64
[1] 2 2
[1] FALSE
D677V8, binary
                cls
clus               0   1
  MST4 MUTATED     4   4
  MST4 WILD-TYPE 221 260
[1] "tbl2"
                cls
clus             [,1] [,2]
  MST4 MUTATED      4    4
  MST4 WILD-TYPE  221  260
        clus
vv       MST4 MUTATED MST4 WILD-TYPE
  FEMALE            4            221
  MALE              4            260
[1] 2 2
[1] FALSE
D677V9, binary
                cls
clus               0   1
  MST4 MUTATED     4   0
  MST4 WILD-TYPE 346  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  MST4 MUTATED      4    0
  MST4 WILD-TYPE  346   22
     clus
vv    MST4 MUTATED MST4 WILD-TYPE
  NO             4            346
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MST4 MUTATED                      5                             2
  MST4 WILD-TYPE                  310                            45
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MST4 MUTATED                       1                              0
  MST4 WILD-TYPE                   105                             10
D677V10, multiclass
                                clus
vv                               MST4 MUTATED MST4 WILD-TYPE
  COLON ADENOCARCINOMA                      5            310
  COLON MUCINOUS ADENOCARCINOMA             2             45
  RECTAL ADENOCARCINOMA                     1            105
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  MST4 MUTATED     5   0   0   0
  MST4 WILD-TYPE 340   4  31  25
D677V11, multiclass
    clus
vv   MST4 MUTATED MST4 WILD-TYPE
  R0            5            340
  R1            0              4
  R2            0             31
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D677V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MST4 MUTATED                                  0     0
  MST4 WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  MST4 MUTATED                           1     5
  MST4 WILD-TYPE                        21   221
D677V13, multiclass
                                  clus
vv                                 MST4 MUTATED MST4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                       5            221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(678) Variable = MYL1 MUTATION ANALYSIS
D678V1, survival
                sevent
clus2              0   1
  MYL1 MUTATED     5   2
  MYL1 WILD-TYPE 373  91
  MYL1 MUTATED MYL1 WILD-TYPE 
             7            464 
  MYL1 MUTATED MYL1 WILD-TYPE 
             2             91 
$`MYL1 MUTATED`
TCGA-A6-5662 TCGA-AA-3979 TCGA-CK-5916 TCGA-CM-5862 TCGA-CM-6163 TCGA-CM-6172 
       23.61        24.00        21.14         5.03         2.96        11.01 
TCGA-D5-5540 
       56.09 

$`MYL1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        33.53        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        25.02        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 
       85.45        15.62        49.08        51.32         9.99        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
       15.02        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       15.02        14.04        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  MYL1 MUTATED MYL1 WILD-TYPE 
          2.96           0.00 
  MYL1 MUTATED MYL1 WILD-TYPE 
         56.09         148.01 
  MYL1 MUTATED MYL1 WILD-TYPE 
        21.140         20.155 
[1] "3.0 - 56.1 (21.1)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.8"
D678V2, continuous
D678V3, binary
                cls
clus               0   1
  MYL1 MUTATED     8   0
  MYL1 WILD-TYPE 358 119
[1] "tbl2"
                cls
clus             [,1] [,2]
  MYL1 MUTATED      8    0
  MYL1 WILD-TYPE  358  119
        clus
vv       MYL1 MUTATED MYL1 WILD-TYPE
  COLON             8            358
  RECTUM            0            119
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MYL1 MUTATED         3        0        0         2         0         0
  MYL1 WILD-TYPE      88        1       32       136        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MYL1 MUTATED           0          0          1          0        0         2
  MYL1 WILD-TYPE        24         11         58         42       48        16
                vv
clus             STAGE IVB
  MYL1 MUTATED           0
  MYL1 WILD-TYPE         1
D678V4, multiclass
            clus
vv           MYL1 MUTATED MYL1 WILD-TYPE
  STAGE I               3             88
  STAGE IA              0              1
  STAGE II              0             32
  STAGE IIA             2            136
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            1             58
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             2             16
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  MYL1 MUTATED     2   1   5   0
  MYL1 WILD-TYPE  15  91 324  50
D678V5, multiclass
    clus
vv   MYL1 MUTATED MYL1 WILD-TYPE
  T1            2             15
  T2            1             91
  T3            5            324
  T4            0             50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  MYL1 MUTATED     5   2   1
  MYL1 WILD-TYPE 282 111  86
D678V6, multiclass
    clus
vv   MYL1 MUTATED MYL1 WILD-TYPE
  N0            5            282
  N1            2            111
  N2            1             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D678V7, binary
                cls
clus               0   1
  MYL1 MUTATED     5   2
  MYL1 WILD-TYPE 370  63
[1] "tbl2"
                cls
clus             [,1] [,2]
  MYL1 MUTATED      5    2
  MYL1 WILD-TYPE  370   63
   clus
vv  MYL1 MUTATED MYL1 WILD-TYPE
  0            5            370
  1            2             63
[1] 2 2
[1] FALSE
D678V8, binary
                cls
clus               0   1
  MYL1 MUTATED     2   6
  MYL1 WILD-TYPE 223 258
[1] "tbl2"
                cls
clus             [,1] [,2]
  MYL1 MUTATED      2    6
  MYL1 WILD-TYPE  223  258
        clus
vv       MYL1 MUTATED MYL1 WILD-TYPE
  FEMALE            2            223
  MALE              6            258
[1] 2 2
[1] FALSE
D678V9, binary
                cls
clus               0   1
  MYL1 MUTATED     7   0
  MYL1 WILD-TYPE 343  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  MYL1 MUTATED      7    0
  MYL1 WILD-TYPE  343   22
     clus
vv    MYL1 MUTATED MYL1 WILD-TYPE
  NO             7            343
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MYL1 MUTATED                      8                             0
  MYL1 WILD-TYPE                  307                            47
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MYL1 MUTATED                       0                              0
  MYL1 WILD-TYPE                   106                             10
D678V10, multiclass
                                clus
vv                               MYL1 MUTATED MYL1 WILD-TYPE
  COLON ADENOCARCINOMA                      8            307
  COLON MUCINOUS ADENOCARCINOMA             0             47
  RECTAL ADENOCARCINOMA                     0            106
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  MYL1 MUTATED     5   0   0   2
  MYL1 WILD-TYPE 340   4  31  23
D678V11, multiclass
    clus
vv   MYL1 MUTATED MYL1 WILD-TYPE
  R0            5            340
  R1            0              4
  R2            0             31
  RX            2             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D678V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MYL1 MUTATED                                  0     0
  MYL1 WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  MYL1 MUTATED                           0     7
  MYL1 WILD-TYPE                        22   219
D678V13, multiclass
                                  clus
vv                                 MYL1 MUTATED MYL1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       7            219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(679) Variable = ANKHD1 MUTATION ANALYSIS
D679V1, survival
                  sevent
clus2                0   1
  ANKHD1 MUTATED    27   6
  ANKHD1 WILD-TYPE 351  87
  ANKHD1 MUTATED ANKHD1 WILD-TYPE 
              33              438 
  ANKHD1 MUTATED ANKHD1 WILD-TYPE 
               6               87 
$`ANKHD1 MUTATED`
TCGA-A6-3807 TCGA-A6-5666 TCGA-A6-6141 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3510 
       34.65        32.71         8.38         7.04         1.02        63.98 
TCGA-AA-3549 TCGA-AA-3660 TCGA-AA-3950 TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A010 
       21.01        78.08        24.00        25.02         4.01        34.98 
TCGA-AD-5900 TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 
        0.07        21.44        58.39        49.41         6.77       100.01 
TCGA-CA-6717 TCGA-CM-5348 TCGA-CM-6162 TCGA-CM-6674 TCGA-D5-6533 TCGA-DM-A1D7 
       12.76        22.98        12.00        12.95         1.32        13.32 
TCGA-G4-6304 TCGA-G4-6309 TCGA-G4-6323 TCGA-G4-6588 TCGA-AG-3892 TCGA-AG-A002 
       53.62        85.48        13.78        26.17        13.02        20.98 
TCGA-DY-A0XA TCGA-EI-6507 TCGA-F5-6465 
      126.44        19.96        49.51 

$`ANKHD1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       22.06        27.09        22.52        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
       20.28         3.02        35.01         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 
       19.99        13.94        19.99        61.02         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 
       12.99        24.00        33.01        26.01         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 
        0.92        41.00        39.98        18.05        40.96        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
        0.95        33.01        17.82         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 
       22.36        62.79        88.21        12.10        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07        12.20        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5349 
       37.02        25.02        13.02        29.06        22.03        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       15.02         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6675 
       12.99        13.02        15.02        14.04        11.01        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
      130.65        92.75        49.91        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 
       35.31       133.18        74.56        65.85        44.68        55.04 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 
       63.62        61.91        36.00        22.09        35.80        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 
        1.02        17.95        36.95        17.03        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
        5.29        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6571 
        0.49        20.55        20.91        18.28         9.96        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  ANKHD1 MUTATED ANKHD1 WILD-TYPE 
            0.07             0.00 
  ANKHD1 MUTATED ANKHD1 WILD-TYPE 
          126.44           148.01 
  ANKHD1 MUTATED ANKHD1 WILD-TYPE 
          21.440           20.035 
[1] "0.1 - 126.4 (21.4)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.4"
D679V2, continuous
D679V3, binary
                  cls
clus                 0   1
  ANKHD1 MUTATED    29   5
  ANKHD1 WILD-TYPE 337 114
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ANKHD1 MUTATED     29    5
  ANKHD1 WILD-TYPE  337  114
        clus
vv       ANKHD1 MUTATED ANKHD1 WILD-TYPE
  COLON              29              337
  RECTUM              5              114
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ANKHD1 MUTATED         5        1        6        12         3         1
  ANKHD1 WILD-TYPE      86        0       26       126         7         0
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ANKHD1 MUTATED           0          0          4          1        0
  ANKHD1 WILD-TYPE        24         11         55         41       48
                  vv
clus               STAGE IVA STAGE IVB
  ANKHD1 MUTATED           0         0
  ANKHD1 WILD-TYPE        18         1
D679V4, multiclass
            clus
vv           ANKHD1 MUTATED ANKHD1 WILD-TYPE
  STAGE I                 5               86
  STAGE IA                1                0
  STAGE II                6               26
  STAGE IIA              12              126
  STAGE IIB               3                7
  STAGE IIC               1                0
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              4               55
  STAGE IIIC              1               41
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ANKHD1 MUTATED     1   5  22   5
  ANKHD1 WILD-TYPE  16  87 307  45
D679V5, multiclass
    clus
vv   ANKHD1 MUTATED ANKHD1 WILD-TYPE
  T1              1               16
  T2              5               87
  T3             22              307
  T4              5               45
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  ANKHD1 MUTATED    30   3   1
  ANKHD1 WILD-TYPE 257 110  86
D679V6, multiclass
    clus
vv   ANKHD1 MUTATED ANKHD1 WILD-TYPE
  N0             30              257
  N1              3              110
  N2              1               86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D679V7, binary
                  cls
clus                 0   1
  ANKHD1 MUTATED    28   0
  ANKHD1 WILD-TYPE 347  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ANKHD1 MUTATED     28    0
  ANKHD1 WILD-TYPE  347   65
   clus
vv  ANKHD1 MUTATED ANKHD1 WILD-TYPE
  0             28              347
  1              0               65
[1] 2 2
[1] FALSE
D679V8, binary
                  cls
clus                 0   1
  ANKHD1 MUTATED    15  19
  ANKHD1 WILD-TYPE 210 245
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ANKHD1 MUTATED     15   19
  ANKHD1 WILD-TYPE  210  245
        clus
vv       ANKHD1 MUTATED ANKHD1 WILD-TYPE
  FEMALE             15              210
  MALE               19              245
[1] 2 2
[1] FALSE
D679V9, binary
                  cls
clus                 0   1
  ANKHD1 MUTATED    26   1
  ANKHD1 WILD-TYPE 324  21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ANKHD1 MUTATED     26    1
  ANKHD1 WILD-TYPE  324   21
     clus
vv    ANKHD1 MUTATED ANKHD1 WILD-TYPE
  NO              26              324
  YES              1               21
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ANKHD1 MUTATED                     23                             5
  ANKHD1 WILD-TYPE                  292                            42
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ANKHD1 MUTATED                       5                              0
  ANKHD1 WILD-TYPE                   101                             10
D679V10, multiclass
                                clus
vv                               ANKHD1 MUTATED ANKHD1 WILD-TYPE
  COLON ADENOCARCINOMA                       23              292
  COLON MUCINOUS ADENOCARCINOMA               5               42
  RECTAL ADENOCARCINOMA                       5              101
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ANKHD1 MUTATED    25   0   0   1
  ANKHD1 WILD-TYPE 320   4  31  24
D679V11, multiclass
    clus
vv   ANKHD1 MUTATED ANKHD1 WILD-TYPE
  R0             25              320
  R1              0                4
  R2              0               31
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D679V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ANKHD1 MUTATED                                  0     1
  ANKHD1 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ANKHD1 MUTATED                           3    18
  ANKHD1 WILD-TYPE                        19   208
D679V13, multiclass
                                  clus
vv                                 ANKHD1 MUTATED ANKHD1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     3               19
  WHITE                                        18              208
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(680) Variable = CEPT1 MUTATION ANALYSIS
D680V1, survival
                 sevent
clus2               0   1
  CEPT1 MUTATED     5   1
  CEPT1 WILD-TYPE 373  92
  CEPT1 MUTATED CEPT1 WILD-TYPE 
              6             465 
  CEPT1 MUTATED CEPT1 WILD-TYPE 
              1              92 
$`CEPT1 MUTATED`
TCGA-AA-3877 TCGA-CA-6717 TCGA-CA-6718 TCGA-DM-A1D9 TCGA-G4-6586 TCGA-EI-6507 
       31.00        12.76        10.06       140.38        35.80        19.96 

$`CEPT1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.07        12.20        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
       12.59         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6510 
       51.48        32.61         0.49        20.55        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  CEPT1 MUTATED CEPT1 WILD-TYPE 
          10.06            0.00 
  CEPT1 MUTATED CEPT1 WILD-TYPE 
         140.38          148.01 
  CEPT1 MUTATED CEPT1 WILD-TYPE 
          25.48           20.19 
[1] "10.1 - 140.4 (25.5)" "0.0 - 148.0 (20.2)" 
[1] "hr=" "1.5"
D680V2, continuous
D680V3, binary
                 cls
clus                0   1
  CEPT1 MUTATED     5   1
  CEPT1 WILD-TYPE 361 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CEPT1 MUTATED      5    1
  CEPT1 WILD-TYPE  361  118
        clus
vv       CEPT1 MUTATED CEPT1 WILD-TYPE
  COLON              5             361
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CEPT1 MUTATED         1        0        0         5         0         0
  CEPT1 WILD-TYPE      90        1       32       133        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CEPT1 MUTATED           0          0          0          0        0         0
  CEPT1 WILD-TYPE        24         11         59         42       48        18
                 vv
clus              STAGE IVB
  CEPT1 MUTATED           0
  CEPT1 WILD-TYPE         1
D680V4, multiclass
            clus
vv           CEPT1 MUTATED CEPT1 WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              5             133
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CEPT1 MUTATED     1   0   5   0
  CEPT1 WILD-TYPE  16  92 324  50
D680V5, multiclass
    clus
vv   CEPT1 MUTATED CEPT1 WILD-TYPE
  T1             1              16
  T2             0              92
  T3             5             324
  T4             0              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  CEPT1 MUTATED     6   0   0
  CEPT1 WILD-TYPE 281 113  87
D680V6, multiclass
    clus
vv   CEPT1 MUTATED CEPT1 WILD-TYPE
  N0             6             281
  N1             0             113
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D680V7, binary
                 cls
clus                0   1
  CEPT1 MUTATED     6   0
  CEPT1 WILD-TYPE 369  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CEPT1 MUTATED      6    0
  CEPT1 WILD-TYPE  369   65
   clus
vv  CEPT1 MUTATED CEPT1 WILD-TYPE
  0             6             369
  1             0              65
[1] 2 2
[1] FALSE
D680V8, binary
                 cls
clus                0   1
  CEPT1 MUTATED     3   3
  CEPT1 WILD-TYPE 222 261
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CEPT1 MUTATED      3    3
  CEPT1 WILD-TYPE  222  261
        clus
vv       CEPT1 MUTATED CEPT1 WILD-TYPE
  FEMALE             3             222
  MALE               3             261
[1] 2 2
[1] FALSE
D680V9, binary
                 cls
clus                0   1
  CEPT1 MUTATED     5   0
  CEPT1 WILD-TYPE 345  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CEPT1 MUTATED      5    0
  CEPT1 WILD-TYPE  345   22
     clus
vv    CEPT1 MUTATED CEPT1 WILD-TYPE
  NO              5             345
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CEPT1 MUTATED                      3                             2
  CEPT1 WILD-TYPE                  312                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CEPT1 MUTATED                       1                              0
  CEPT1 WILD-TYPE                   105                             10
D680V10, multiclass
                                clus
vv                               CEPT1 MUTATED CEPT1 WILD-TYPE
  COLON ADENOCARCINOMA                       3             312
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  CEPT1 MUTATED     3   0   0   2
  CEPT1 WILD-TYPE 342   4  31  23
D680V11, multiclass
    clus
vv   CEPT1 MUTATED CEPT1 WILD-TYPE
  R0             3             342
  R1             0               4
  R2             0              31
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D680V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CEPT1 MUTATED                                  0     2
  CEPT1 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CEPT1 MUTATED                           0     3
  CEPT1 WILD-TYPE                        22   223
D680V13, multiclass
                                  clus
vv                                 CEPT1 MUTATED CEPT1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               9
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        3             223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(681) Variable = TNFRSF9 MUTATION ANALYSIS
D681V1, survival
                   sevent
clus2                 0   1
  TNFRSF9 MUTATED     9   1
  TNFRSF9 WILD-TYPE 369  92
  TNFRSF9 MUTATED TNFRSF9 WILD-TYPE 
               10               461 
  TNFRSF9 MUTATED TNFRSF9 WILD-TYPE 
                1                92 
$`TNFRSF9 MUTATED`
TCGA-A6-5666 TCGA-A6-6653 TCGA-AA-A00J TCGA-AA-A01P TCGA-CA-5796 TCGA-CA-6717 
       32.71        24.39        18.05        38.07         3.25        12.76 
TCGA-CM-5341 TCGA-CM-6167 TCGA-D5-6538 TCGA-AG-A002 
       29.06        14.99        17.13        20.98 

$`TNFRSF9 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        22.06        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 
       25.18        24.16        21.76        24.69        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       19.00        30.02        34.03        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       31.00         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.06         3.29         0.07        12.20        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-5348 
       20.02        37.02        25.02        13.02        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       21.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
        4.80        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  TNFRSF9 MUTATED TNFRSF9 WILD-TYPE 
             3.25              0.00 
  TNFRSF9 MUTATED TNFRSF9 WILD-TYPE 
            38.07            148.01 
  TNFRSF9 MUTATED TNFRSF9 WILD-TYPE 
           19.515            20.190 
[1] "3.2 - 38.1 (19.5)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.6"
D681V2, continuous
D681V3, binary
                   cls
clus                  0   1
  TNFRSF9 MUTATED     9   1
  TNFRSF9 WILD-TYPE 357 118
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TNFRSF9 MUTATED      9    1
  TNFRSF9 WILD-TYPE  357  118
        clus
vv       TNFRSF9 MUTATED TNFRSF9 WILD-TYPE
  COLON                9               357
  RECTUM               1               118
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TNFRSF9 MUTATED         2        0        0         2         0         1
  TNFRSF9 WILD-TYPE      89        1       32       136        10         0
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TNFRSF9 MUTATED           1          1          2          1        0
  TNFRSF9 WILD-TYPE        23         10         57         41       48
                   vv
clus                STAGE IVA STAGE IVB
  TNFRSF9 MUTATED           0         0
  TNFRSF9 WILD-TYPE        18         1
D681V4, multiclass
            clus
vv           TNFRSF9 MUTATED TNFRSF9 WILD-TYPE
  STAGE I                  2                89
  STAGE IA                 0                 1
  STAGE II                 0                32
  STAGE IIA                2               136
  STAGE IIB                0                10
  STAGE IIC                1                 0
  STAGE III                1                23
  STAGE IIIA               1                10
  STAGE IIIB               2                57
  STAGE IIIC               1                41
  STAGE IV                 0                48
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  TNFRSF9 MUTATED     0   3   5   2
  TNFRSF9 WILD-TYPE  17  89 324  48
D681V5, multiclass
    clus
vv   TNFRSF9 MUTATED TNFRSF9 WILD-TYPE
  T1               0                17
  T2               3                89
  T3               5               324
  T4               2                48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  TNFRSF9 MUTATED     5   3   2
  TNFRSF9 WILD-TYPE 282 110  85
D681V6, multiclass
    clus
vv   TNFRSF9 MUTATED TNFRSF9 WILD-TYPE
  N0               5               282
  N1               3               110
  N2               2                85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D681V7, binary
                   cls
clus                  0   1
  TNFRSF9 MUTATED    10   0
  TNFRSF9 WILD-TYPE 365  65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TNFRSF9 MUTATED     10    0
  TNFRSF9 WILD-TYPE  365   65
   clus
vv  TNFRSF9 MUTATED TNFRSF9 WILD-TYPE
  0              10               365
  1               0                65
[1] 2 2
[1] FALSE
D681V8, binary
                   cls
clus                  0   1
  TNFRSF9 MUTATED     5   5
  TNFRSF9 WILD-TYPE 220 259
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TNFRSF9 MUTATED      5    5
  TNFRSF9 WILD-TYPE  220  259
        clus
vv       TNFRSF9 MUTATED TNFRSF9 WILD-TYPE
  FEMALE               5               220
  MALE                 5               259
[1] 2 2
[1] FALSE
D681V9, binary
                   cls
clus                  0   1
  TNFRSF9 MUTATED    10   0
  TNFRSF9 WILD-TYPE 340  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TNFRSF9 MUTATED     10    0
  TNFRSF9 WILD-TYPE  340   22
     clus
vv    TNFRSF9 MUTATED TNFRSF9 WILD-TYPE
  NO               10               340
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  TNFRSF9 MUTATED                      6                             3
  TNFRSF9 WILD-TYPE                  309                            44
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  TNFRSF9 MUTATED                       1                              0
  TNFRSF9 WILD-TYPE                   105                             10
D681V10, multiclass
                                clus
vv                               TNFRSF9 MUTATED TNFRSF9 WILD-TYPE
  COLON ADENOCARCINOMA                         6               309
  COLON MUCINOUS ADENOCARCINOMA                3                44
  RECTAL ADENOCARCINOMA                        1               105
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  TNFRSF9 MUTATED     7   0   0   1
  TNFRSF9 WILD-TYPE 338   4  31  24
D681V11, multiclass
    clus
vv   TNFRSF9 MUTATED TNFRSF9 WILD-TYPE
  R0               7               338
  R1               0                 4
  R2               0                31
  RX               1                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D681V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TNFRSF9 MUTATED                                  0     2
  TNFRSF9 WILD-TYPE                                1     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  TNFRSF9 MUTATED                           1     4
  TNFRSF9 WILD-TYPE                        21   222
D681V13, multiclass
                                  clus
vv                                 TNFRSF9 MUTATED TNFRSF9 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          2                 9
  BLACK OR AFRICAN AMERICAN                      1                21
  WHITE                                          4               222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(682) Variable = KDM5C MUTATION ANALYSIS
D682V1, survival
                 sevent
clus2               0   1
  KDM5C MUTATED    18   4
  KDM5C WILD-TYPE 360  89
  KDM5C MUTATED KDM5C WILD-TYPE 
             22             449 
  KDM5C MUTATED KDM5C WILD-TYPE 
              4              89 
$`KDM5C MUTATED`
TCGA-A6-2672 TCGA-A6-2676 TCGA-AA-3516 TCGA-AA-3555 TCGA-AA-3697 TCGA-AA-3710 
       46.65        42.90        13.02        29.95        85.05        26.99 
TCGA-AA-3947 TCGA-AA-3977 TCGA-AA-3979 TCGA-CM-4752 TCGA-CM-5348 TCGA-CM-5861 
       33.01        25.02        24.00        13.02        22.98        15.02 
TCGA-CM-5863 TCGA-CM-5868 TCGA-D5-7000 TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-F4-6809 
       15.02        17.03        10.26       130.65        92.75        13.25 
TCGA-G4-6293 TCGA-G4-6304 TCGA-AF-2693 TCGA-CI-6622 
      133.18        53.62        19.10         6.97 

$`KDM5C WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       43.76        43.76        24.33        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5657 
       33.34        32.75        36.53        14.53        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       30.44        29.19        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
       63.98         6.97         1.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       17.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3713 
        5.98        37.05        19.00        36.00         5.03        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 
       31.00         2.01        12.99        24.00        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3980 TCGA-AA-3982 
       50.99        13.05        34.06        26.01        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5864 
       29.06        22.03        30.08        32.02         5.03        15.02 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-DM-A0X9 
       11.64         4.80         1.51        12.00        11.38       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
       24.43        38.20        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6854 TCGA-F4-6855 
       34.42        41.42        16.24        33.67         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       35.31        74.56        65.85        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       43.04        13.55        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
        6.05        33.17         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  KDM5C MUTATED KDM5C WILD-TYPE 
           6.97            0.00 
  KDM5C MUTATED KDM5C WILD-TYPE 
         133.18          148.01 
  KDM5C MUTATED KDM5C WILD-TYPE 
          24.51           20.05 
[1] "7.0 - 133.2 (24.5)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.6"
D682V2, continuous
D682V3, binary
                 cls
clus                0   1
  KDM5C MUTATED    21   1
  KDM5C WILD-TYPE 345 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM5C MUTATED     21    1
  KDM5C WILD-TYPE  345  118
        clus
vv       KDM5C MUTATED KDM5C WILD-TYPE
  COLON             21             345
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KDM5C MUTATED         2        0        0         7         5         0
  KDM5C WILD-TYPE      89        1       32       131         5         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  KDM5C MUTATED           3          0          3          0        0         2
  KDM5C WILD-TYPE        21         11         56         42       48        16
                 vv
clus              STAGE IVB
  KDM5C MUTATED           0
  KDM5C WILD-TYPE         1
D682V4, multiclass
            clus
vv           KDM5C MUTATED KDM5C WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              7             131
  STAGE IIB              5               5
  STAGE IIC              0               1
  STAGE III              3              21
  STAGE IIIA             0              11
  STAGE IIIB             3              56
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              2              16
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  KDM5C MUTATED     0   3  14   6
  KDM5C WILD-TYPE  17  89 315  44
D682V5, multiclass
    clus
vv   KDM5C MUTATED KDM5C WILD-TYPE
  T1             0              17
  T2             3              89
  T3            14             315
  T4             6              44
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  KDM5C MUTATED    16   6   1
  KDM5C WILD-TYPE 271 107  86
D682V6, multiclass
    clus
vv   KDM5C MUTATED KDM5C WILD-TYPE
  N0            16             271
  N1             6             107
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D682V7, binary
                 cls
clus                0   1
  KDM5C MUTATED    18   2
  KDM5C WILD-TYPE 357  63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM5C MUTATED     18    2
  KDM5C WILD-TYPE  357   63
   clus
vv  KDM5C MUTATED KDM5C WILD-TYPE
  0            18             357
  1             2              63
[1] 2 2
[1] FALSE
D682V8, binary
                 cls
clus                0   1
  KDM5C MUTATED    15   8
  KDM5C WILD-TYPE 210 256
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM5C MUTATED     15    8
  KDM5C WILD-TYPE  210  256
        clus
vv       KDM5C MUTATED KDM5C WILD-TYPE
  FEMALE            15             210
  MALE               8             256
[1] 2 2
[1] FALSE
D682V9, binary
                 cls
clus                0   1
  KDM5C MUTATED    19   0
  KDM5C WILD-TYPE 331  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM5C MUTATED     19    0
  KDM5C WILD-TYPE  331   22
     clus
vv    KDM5C MUTATED KDM5C WILD-TYPE
  NO             19             331
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  KDM5C MUTATED                     16                             5
  KDM5C WILD-TYPE                  299                            42
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  KDM5C MUTATED                       1                              0
  KDM5C WILD-TYPE                   105                             10
D682V10, multiclass
                                clus
vv                               KDM5C MUTATED KDM5C WILD-TYPE
  COLON ADENOCARCINOMA                      16             299
  COLON MUCINOUS ADENOCARCINOMA              5              42
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  KDM5C MUTATED    16   0   0   1
  KDM5C WILD-TYPE 329   4  31  24
D682V11, multiclass
    clus
vv   KDM5C MUTATED KDM5C WILD-TYPE
  R0            16             329
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D682V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KDM5C MUTATED                                  0     0
  KDM5C WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  KDM5C MUTATED                           1    15
  KDM5C WILD-TYPE                        21   211
D682V13, multiclass
                                  clus
vv                                 KDM5C MUTATED KDM5C WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                       15             211
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(683) Variable = IFIT2 MUTATION ANALYSIS
D683V1, survival
                 sevent
clus2               0   1
  IFIT2 MUTATED     6   2
  IFIT2 WILD-TYPE 372  91
  IFIT2 MUTATED IFIT2 WILD-TYPE 
              8             463 
  IFIT2 MUTATED IFIT2 WILD-TYPE 
              2              91 
$`IFIT2 MUTATED`
TCGA-AA-3492 TCGA-AA-3950 TCGA-AA-3977 TCGA-CA-6717 TCGA-CA-6718 TCGA-D5-6534 
        3.02        24.00        25.02        12.76        10.06        43.27 
TCGA-G4-6309 TCGA-AG-A002 
       85.48        20.98 

$`IFIT2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 
        2.01        12.99        24.00        33.01        26.01         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       55.04        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  IFIT2 MUTATED IFIT2 WILD-TYPE 
           3.02            0.00 
  IFIT2 MUTATED IFIT2 WILD-TYPE 
          85.48          148.01 
  IFIT2 MUTATED IFIT2 WILD-TYPE 
          22.49           20.12 
[1] "3.0 - 85.5 (22.5)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.2"
D683V2, continuous
D683V3, binary
                 cls
clus                0   1
  IFIT2 MUTATED     7   1
  IFIT2 WILD-TYPE 359 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IFIT2 MUTATED      7    1
  IFIT2 WILD-TYPE  359  118
        clus
vv       IFIT2 MUTATED IFIT2 WILD-TYPE
  COLON              7             359
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  IFIT2 MUTATED         1        0        1         4         0         0
  IFIT2 WILD-TYPE      90        1       31       134        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  IFIT2 MUTATED           0          0          1          0        0         0
  IFIT2 WILD-TYPE        24         11         58         42       48        18
                 vv
clus              STAGE IVB
  IFIT2 MUTATED           0
  IFIT2 WILD-TYPE         1
D683V4, multiclass
            clus
vv           IFIT2 MUTATED IFIT2 WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              4             134
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  IFIT2 MUTATED     0   2   6   0
  IFIT2 WILD-TYPE  17  90 323  50
D683V5, multiclass
    clus
vv   IFIT2 MUTATED IFIT2 WILD-TYPE
  T1             0              17
  T2             2              90
  T3             6             323
  T4             0              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  IFIT2 MUTATED     7   1   0
  IFIT2 WILD-TYPE 280 112  87
D683V6, multiclass
    clus
vv   IFIT2 MUTATED IFIT2 WILD-TYPE
  N0             7             280
  N1             1             112
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D683V7, binary
                 cls
clus                0   1
  IFIT2 MUTATED     7   0
  IFIT2 WILD-TYPE 368  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IFIT2 MUTATED      7    0
  IFIT2 WILD-TYPE  368   65
   clus
vv  IFIT2 MUTATED IFIT2 WILD-TYPE
  0             7             368
  1             0              65
[1] 2 2
[1] FALSE
D683V8, binary
                 cls
clus                0   1
  IFIT2 MUTATED     4   4
  IFIT2 WILD-TYPE 221 260
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IFIT2 MUTATED      4    4
  IFIT2 WILD-TYPE  221  260
        clus
vv       IFIT2 MUTATED IFIT2 WILD-TYPE
  FEMALE             4             221
  MALE               4             260
[1] 2 2
[1] FALSE
D683V9, binary
                 cls
clus                0   1
  IFIT2 MUTATED     8   0
  IFIT2 WILD-TYPE 342  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IFIT2 MUTATED      8    0
  IFIT2 WILD-TYPE  342   22
     clus
vv    IFIT2 MUTATED IFIT2 WILD-TYPE
  NO              8             342
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  IFIT2 MUTATED                      4                             3
  IFIT2 WILD-TYPE                  311                            44
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  IFIT2 MUTATED                       1                              0
  IFIT2 WILD-TYPE                   105                             10
D683V10, multiclass
                                clus
vv                               IFIT2 MUTATED IFIT2 WILD-TYPE
  COLON ADENOCARCINOMA                       4             311
  COLON MUCINOUS ADENOCARCINOMA              3              44
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  IFIT2 MUTATED     5   0   0   2
  IFIT2 WILD-TYPE 340   4  31  23
D683V11, multiclass
    clus
vv   IFIT2 MUTATED IFIT2 WILD-TYPE
  R0             5             340
  R1             0               4
  R2             0              31
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D683V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  IFIT2 MUTATED                                  0     2
  IFIT2 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  IFIT2 MUTATED                           1     1
  IFIT2 WILD-TYPE                        21   225
D683V13, multiclass
                                  clus
vv                                 IFIT2 MUTATED IFIT2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               9
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        1             225
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(684) Variable = NUDCD1 MUTATION ANALYSIS
D684V1, survival
                  sevent
clus2                0   1
  NUDCD1 MUTATED     7   2
  NUDCD1 WILD-TYPE 371  91
  NUDCD1 MUTATED NUDCD1 WILD-TYPE 
               9              462 
  NUDCD1 MUTATED NUDCD1 WILD-TYPE 
               2               91 
$`NUDCD1 MUTATED`
TCGA-A6-6654 TCGA-AA-3710 TCGA-AA-A00N TCGA-CM-5868 TCGA-D5-6536 TCGA-DM-A1D8 
       23.87        26.99         4.01        17.03        17.85        12.59 
TCGA-DM-A1HB TCGA-G4-6588 TCGA-DC-6683 
      135.65        26.17         5.03 

$`NUDCD1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        85.05        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6162 
       15.02         5.03        15.02        15.02        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
        1.32        43.27        15.12         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A1DA 
      130.65        92.75        49.91        13.32       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
       44.32       131.51       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       35.80        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
       19.99         5.95         4.01         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  NUDCD1 MUTATED NUDCD1 WILD-TYPE 
            4.01             0.00 
  NUDCD1 MUTATED NUDCD1 WILD-TYPE 
          135.65           148.01 
  NUDCD1 MUTATED NUDCD1 WILD-TYPE 
          17.850           20.235 
[1] "4.0 - 135.7 (17.9)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.1"
D684V2, continuous
D684V3, binary
                  cls
clus                 0   1
  NUDCD1 MUTATED     9   1
  NUDCD1 WILD-TYPE 357 118
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NUDCD1 MUTATED      9    1
  NUDCD1 WILD-TYPE  357  118
        clus
vv       NUDCD1 MUTATED NUDCD1 WILD-TYPE
  COLON               9              357
  RECTUM              1              118
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NUDCD1 MUTATED         0        0        0         4         1         0
  NUDCD1 WILD-TYPE      91        1       32       134         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NUDCD1 MUTATED           0          0          3          0        0
  NUDCD1 WILD-TYPE        24         11         56         42       48
                  vv
clus               STAGE IVA STAGE IVB
  NUDCD1 MUTATED           1         0
  NUDCD1 WILD-TYPE        17         1
D684V4, multiclass
            clus
vv           NUDCD1 MUTATED NUDCD1 WILD-TYPE
  STAGE I                 0               91
  STAGE IA                0                1
  STAGE II                0               32
  STAGE IIA               4              134
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              3               56
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               1               17
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  NUDCD1 MUTATED     0   0   8   2
  NUDCD1 WILD-TYPE  17  92 321  48
D684V5, multiclass
    clus
vv   NUDCD1 MUTATED NUDCD1 WILD-TYPE
  T1              0               17
  T2              0               92
  T3              8              321
  T4              2               48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  NUDCD1 MUTATED     5   5   0
  NUDCD1 WILD-TYPE 282 108  87
D684V6, multiclass
    clus
vv   NUDCD1 MUTATED NUDCD1 WILD-TYPE
  N0              5              282
  N1              5              108
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D684V7, binary
                  cls
clus                 0   1
  NUDCD1 MUTATED     8   1
  NUDCD1 WILD-TYPE 367  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NUDCD1 MUTATED      8    1
  NUDCD1 WILD-TYPE  367   64
   clus
vv  NUDCD1 MUTATED NUDCD1 WILD-TYPE
  0              8              367
  1              1               64
[1] 2 2
[1] FALSE
D684V8, binary
                  cls
clus                 0   1
  NUDCD1 MUTATED     6   4
  NUDCD1 WILD-TYPE 219 260
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NUDCD1 MUTATED      6    4
  NUDCD1 WILD-TYPE  219  260
        clus
vv       NUDCD1 MUTATED NUDCD1 WILD-TYPE
  FEMALE              6              219
  MALE                4              260
[1] 2 2
[1] FALSE
D684V9, binary
                  cls
clus                 0   1
  NUDCD1 MUTATED     5   0
  NUDCD1 WILD-TYPE 345  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NUDCD1 MUTATED      5    0
  NUDCD1 WILD-TYPE  345   22
     clus
vv    NUDCD1 MUTATED NUDCD1 WILD-TYPE
  NO               5              345
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  NUDCD1 MUTATED                      7                             1
  NUDCD1 WILD-TYPE                  308                            46
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  NUDCD1 MUTATED                       1                              0
  NUDCD1 WILD-TYPE                   105                             10
D684V10, multiclass
                                clus
vv                               NUDCD1 MUTATED NUDCD1 WILD-TYPE
  COLON ADENOCARCINOMA                        7              308
  COLON MUCINOUS ADENOCARCINOMA               1               46
  RECTAL ADENOCARCINOMA                       1              105
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  NUDCD1 MUTATED     7   0   0   0
  NUDCD1 WILD-TYPE 338   4  31  25
D684V11, multiclass
    clus
vv   NUDCD1 MUTATED NUDCD1 WILD-TYPE
  R0              7              338
  R1              0                4
  R2              0               31
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D684V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NUDCD1 MUTATED                                  0     0
  NUDCD1 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  NUDCD1 MUTATED                           0     7
  NUDCD1 WILD-TYPE                        22   219
D684V13, multiclass
                                  clus
vv                                 NUDCD1 MUTATED NUDCD1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         7              219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(685) Variable = RBPMS MUTATION ANALYSIS
D685V1, survival
                 sevent
clus2               0   1
  RBPMS MUTATED     4   0
  RBPMS WILD-TYPE 374  93
  RBPMS MUTATED RBPMS WILD-TYPE 
              4             467 
  RBPMS MUTATED RBPMS WILD-TYPE 
              0              93 
$`RBPMS MUTATED`
TCGA-AA-3510 TCGA-AA-3713 TCGA-F4-6805 TCGA-AG-A002 
       63.98        19.04        34.42        20.98 

$`RBPMS WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
        6.18        47.87         1.55        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  RBPMS MUTATED RBPMS WILD-TYPE 
          19.04            0.00 
  RBPMS MUTATED RBPMS WILD-TYPE 
          63.98          148.01 
  RBPMS MUTATED RBPMS WILD-TYPE 
          27.70           20.12 
[1] "19.0 - 64.0 (27.7)" "0.0 - 148.0 (20.1)"
[1] "hr="     "9100000"
D685V2, continuous
D685V3, binary
                 cls
clus                0   1
  RBPMS MUTATED     3   1
  RBPMS WILD-TYPE 363 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBPMS MUTATED      3    1
  RBPMS WILD-TYPE  363  118
        clus
vv       RBPMS MUTATED RBPMS WILD-TYPE
  COLON              3             363
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RBPMS MUTATED         1        0        1         1         0         0
  RBPMS WILD-TYPE      90        1       31       137        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RBPMS MUTATED           0          0          0          0        1         0
  RBPMS WILD-TYPE        24         11         59         42       47        18
                 vv
clus              STAGE IVB
  RBPMS MUTATED           0
  RBPMS WILD-TYPE         1
D685V4, multiclass
            clus
vv           RBPMS MUTATED RBPMS WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              1             137
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             0              42
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  RBPMS MUTATED     0   1   3   0
  RBPMS WILD-TYPE  17  91 326  50
D685V5, multiclass
    clus
vv   RBPMS MUTATED RBPMS WILD-TYPE
  T1             0              17
  T2             1              91
  T3             3             326
  T4             0              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  RBPMS MUTATED     4   0   0
  RBPMS WILD-TYPE 283 113  87
D685V6, multiclass
    clus
vv   RBPMS MUTATED RBPMS WILD-TYPE
  N0             4             283
  N1             0             113
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D685V7, binary
                 cls
clus                0   1
  RBPMS MUTATED     3   1
  RBPMS WILD-TYPE 372  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBPMS MUTATED      3    1
  RBPMS WILD-TYPE  372   64
   clus
vv  RBPMS MUTATED RBPMS WILD-TYPE
  0             3             372
  1             1              64
[1] 2 2
[1] FALSE
D685V8, binary
                 cls
clus                0   1
  RBPMS MUTATED     1   3
  RBPMS WILD-TYPE 224 261
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBPMS MUTATED      1    3
  RBPMS WILD-TYPE  224  261
        clus
vv       RBPMS MUTATED RBPMS WILD-TYPE
  FEMALE             1             224
  MALE               3             261
[1] 2 2
[1] FALSE
D685V9, binary
                 cls
clus                0   1
  RBPMS MUTATED     3   1
  RBPMS WILD-TYPE 347  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBPMS MUTATED      3    1
  RBPMS WILD-TYPE  347   21
     clus
vv    RBPMS MUTATED RBPMS WILD-TYPE
  NO              3             347
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  RBPMS MUTATED                      3                             0
  RBPMS WILD-TYPE                  312                            47
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  RBPMS MUTATED                       1                              0
  RBPMS WILD-TYPE                   105                             10
D685V10, multiclass
                                clus
vv                               RBPMS MUTATED RBPMS WILD-TYPE
  COLON ADENOCARCINOMA                       3             312
  COLON MUCINOUS ADENOCARCINOMA              0              47
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  RBPMS MUTATED     3   0   1   0
  RBPMS WILD-TYPE 342   4  30  25
D685V11, multiclass
    clus
vv   RBPMS MUTATED RBPMS WILD-TYPE
  R0             3             342
  R1             0               4
  R2             1              30
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D685V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RBPMS MUTATED                                  0     0
  RBPMS WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  RBPMS MUTATED                           0     1
  RBPMS WILD-TYPE                        22   225
D685V13, multiclass
[1] "Remove cluster labels:" "RBPMS MUTATED"         
clus
  RBPMS MUTATED RBPMS WILD-TYPE 
              1             259 
     TCGA-A6-2671      TCGA-A6-2672      TCGA-A6-2674      TCGA-A6-2676 
"RBPMS WILD-TYPE" "RBPMS WILD-TYPE" "RBPMS WILD-TYPE" "RBPMS WILD-TYPE" 
     TCGA-A6-2677      TCGA-A6-2678      TCGA-A6-2683      TCGA-A6-3807 
"RBPMS WILD-TYPE" "RBPMS WILD-TYPE" "RBPMS WILD-TYPE" "RBPMS WILD-TYPE" 
     TCGA-A6-3808      TCGA-A6-3809      TCGA-A6-3810      TCGA-A6-4105 
"RBPMS WILD-TYPE" "RBPMS WILD-TYPE" "RBPMS WILD-TYPE" "RBPMS WILD-TYPE" 
     TCGA-A6-5656      TCGA-A6-5657      TCGA-A6-5659      TCGA-A6-5660 
"RBPMS WILD-TYPE" "RBPMS WILD-TYPE" "RBPMS WILD-TYPE" "RBPMS WILD-TYPE" 
     TCGA-A6-5661      TCGA-A6-5662      TCGA-A6-5664      TCGA-A6-5665 
"RBPMS WILD-TYPE" "RBPMS WILD-TYPE" "RBPMS WILD-TYPE" "RBPMS WILD-TYPE" 
     TCGA-A6-5666      TCGA-A6-6137      TCGA-A6-6138      TCGA-A6-6141 
"RBPMS WILD-TYPE" "RBPMS WILD-TYPE" "RBPMS WILD-TYPE" "RBPMS WILD-TYPE" 
     TCGA-A6-6142      TCGA-A6-6648      TCGA-A6-6649      TCGA-A6-6651 
"RBPMS WILD-TYPE" "RBPMS WILD-TYPE" "RBPMS WILD-TYPE" "RBPMS WILD-TYPE" 
     TCGA-A6-6652      TCGA-A6-6653      TCGA-A6-6654      TCGA-A6-6780 
"RBPMS WILD-TYPE" "RBPMS WILD-TYPE" "RBPMS WILD-TYPE" "RBPMS WILD-TYPE" 
     TCGA-A6-6781      TCGA-A6-6782      TCGA-AD-5900      TCGA-AD-6548 
"RBPMS WILD-TYPE" "RBPMS WILD-TYPE" "RBPMS WILD-TYPE" "RBPMS WILD-TYPE" 
     TCGA-AD-6888      TCGA-AD-6889      TCGA-AD-6890      TCGA-AD-6895 
"RBPMS WILD-TYPE" "RBPMS WILD-TYPE" "RBPMS WILD-TYPE" "RBPMS WILD-TYPE" 
     TCGA-AD-6899      TCGA-AD-6901      TCGA-AD-6963      TCGA-AD-6964 
"RBPMS WILD-TYPE" "RBPMS WILD-TYPE" "RBPMS WILD-TYPE" "RBPMS WILD-TYPE" 
     TCGA-AD-6965      TCGA-AU-3779      TCGA-AU-6004      TCGA-AY-4070 
"RBPMS WILD-TYPE" "RBPMS WILD-TYPE" "RBPMS WILD-TYPE" "RBPMS WILD-TYPE" 
     TCGA-AY-4071      TCGA-AY-5543      TCGA-AY-6196      TCGA-AY-6197 
"RBPMS WILD-TYPE" "RBPMS WILD-TYPE" "RBPMS WILD-TYPE" "RBPMS WILD-TYPE" 
     TCGA-AY-6386      TCGA-AZ-4315      TCGA-AZ-4323      TCGA-AZ-4616 
"RBPMS WILD-TYPE" "RBPMS WILD-TYPE" "RBPMS WILD-TYPE" "RBPMS WILD-TYPE" 
     TCGA-AZ-4681      TCGA-AZ-4682      TCGA-AZ-5403      TCGA-AZ-5407 
"RBPMS WILD-TYPE" "RBPMS WILD-TYPE" "RBPMS WILD-TYPE" "RBPMS WILD-TYPE" 
     TCGA-AZ-6598      TCGA-AZ-6599      TCGA-AZ-6600      TCGA-AZ-6601 
"RBPMS WILD-TYPE" "RBPMS WILD-TYPE" "RBPMS WILD-TYPE" "RBPMS WILD-TYPE" 
     TCGA-AZ-6603      TCGA-AZ-6605      TCGA-AZ-6606      TCGA-AZ-6607 
"RBPMS WILD-TYPE" "RBPMS WILD-TYPE" "RBPMS WILD-TYPE" "RBPMS WILD-TYPE" 
     TCGA-AZ-6608      TCGA-CA-5254      TCGA-CA-5255      TCGA-CA-5796 
"RBPMS WILD-TYPE" "RBPMS WILD-TYPE" "RBPMS WILD-TYPE" "RBPMS WILD-TYPE" 
     TCGA-CA-5797      TCGA-CA-6715      TCGA-CA-6716      TCGA-CA-6717 
"RBPMS WILD-TYPE" "RBPMS WILD-TYPE" "RBPMS WILD-TYPE" "RBPMS WILD-TYPE" 
     TCGA-CA-6718      TCGA-CA-6719      TCGA-CK-4947      TCGA-CK-4948 
"RBPMS WILD-TYPE" "RBPMS WILD-TYPE" "RBPMS WILD-TYPE" "RBPMS WILD-TYPE" 
     TCGA-CK-4950      TCGA-CK-4952      TCGA-CK-5912      TCGA-CK-5913 
"RBPMS WILD-TYPE" "RBPMS WILD-TYPE" "RBPMS WILD-TYPE" "RBPMS WILD-TYPE" 
     TCGA-CK-5914      TCGA-CK-5915      TCGA-CK-5916      TCGA-CK-6746 
"RBPMS WILD-TYPE" "RBPMS WILD-TYPE" "RBPMS WILD-TYPE" "RBPMS WILD-TYPE" 
     TCGA-CK-6747      TCGA-CK-6748      TCGA-CK-6751      TCGA-CM-4743 
"RBPMS WILD-TYPE" "RBPMS WILD-TYPE" "RBPMS WILD-TYPE" "RBPMS WILD-TYPE" 
     TCGA-CM-4744      TCGA-CM-4746      TCGA-CM-4747      TCGA-CM-4752 
"RBPMS WILD-TYPE" "RBPMS WILD-TYPE" "RBPMS WILD-TYPE" "RBPMS WILD-TYPE" 
     TCGA-CM-5341      TCGA-CM-5344      TCGA-CM-5348      TCGA-CM-5349 
"RBPMS WILD-TYPE" "RBPMS WILD-TYPE" "RBPMS WILD-TYPE" "RBPMS WILD-TYPE" 
     TCGA-CM-5860      TCGA-CM-5861      TCGA-CM-5862      TCGA-CM-5863 
"RBPMS WILD-TYPE" "RBPMS WILD-TYPE" "RBPMS WILD-TYPE" "RBPMS WILD-TYPE" 
     TCGA-CM-5864      TCGA-CM-5868      TCGA-CM-6161      TCGA-CM-6162 
"RBPMS WILD-TYPE" "RBPMS WILD-TYPE" "RBPMS WILD-TYPE" "RBPMS WILD-TYPE" 
     TCGA-CM-6163      TCGA-CM-6164      TCGA-CM-6165      TCGA-CM-6166 
"RBPMS WILD-TYPE" "RBPMS WILD-TYPE" "RBPMS WILD-TYPE" "RBPMS WILD-TYPE" 
     TCGA-CM-6167      TCGA-CM-6168      TCGA-CM-6169      TCGA-CM-6170 
"RBPMS WILD-TYPE" "RBPMS WILD-TYPE" "RBPMS WILD-TYPE" "RBPMS WILD-TYPE" 
     TCGA-CM-6171      TCGA-CM-6172      TCGA-CM-6674      TCGA-CM-6675 
"RBPMS WILD-TYPE" "RBPMS WILD-TYPE" "RBPMS WILD-TYPE" "RBPMS WILD-TYPE" 
     TCGA-CM-6676      TCGA-CM-6677      TCGA-CM-6678      TCGA-CM-6679 
"RBPMS WILD-TYPE" "RBPMS WILD-TYPE" "RBPMS WILD-TYPE" "RBPMS WILD-TYPE" 
     TCGA-CM-6680      TCGA-D5-5537      TCGA-D5-5538      TCGA-D5-5539 
"RBPMS WILD-TYPE" "RBPMS WILD-TYPE" "RBPMS WILD-TYPE" "RBPMS WILD-TYPE" 
     TCGA-D5-5540      TCGA-D5-5541      TCGA-D5-6529      TCGA-D5-6532 
"RBPMS WILD-TYPE" "RBPMS WILD-TYPE" "RBPMS WILD-TYPE" "RBPMS WILD-TYPE" 
     TCGA-D5-6533      TCGA-D5-6534      TCGA-D5-6535      TCGA-D5-6536 
"RBPMS WILD-TYPE" "RBPMS WILD-TYPE" "RBPMS WILD-TYPE" "RBPMS WILD-TYPE" 
     TCGA-D5-6537      TCGA-D5-6538      TCGA-D5-6539      TCGA-D5-6540 
"RBPMS WILD-TYPE" "RBPMS WILD-TYPE" "RBPMS WILD-TYPE" "RBPMS WILD-TYPE" 
     TCGA-D5-6541      TCGA-D5-6898      TCGA-D5-6920      TCGA-D5-6922 
"RBPMS WILD-TYPE" "RBPMS WILD-TYPE" "RBPMS WILD-TYPE" "RBPMS WILD-TYPE" 
     TCGA-D5-6923      TCGA-D5-6924      TCGA-D5-6926      TCGA-D5-6927 
"RBPMS WILD-TYPE" "RBPMS WILD-TYPE" "RBPMS WILD-TYPE" "RBPMS WILD-TYPE" 
     TCGA-D5-6928      TCGA-D5-6929      TCGA-D5-6930      TCGA-D5-6931 
"RBPMS WILD-TYPE" "RBPMS WILD-TYPE" "RBPMS WILD-TYPE" "RBPMS WILD-TYPE" 
     TCGA-D5-6932      TCGA-D5-7000      TCGA-DM-A0X9      TCGA-DM-A0XD 
"RBPMS WILD-TYPE" "RBPMS WILD-TYPE" "RBPMS WILD-TYPE" "RBPMS WILD-TYPE" 
     TCGA-DM-A0XF      TCGA-DM-A1D0      TCGA-DM-A1D4      TCGA-DM-A1D6 
"RBPMS WILD-TYPE" "RBPMS WILD-TYPE" "RBPMS WILD-TYPE" "RBPMS WILD-TYPE" 
     TCGA-DM-A1D7      TCGA-DM-A1D8      TCGA-DM-A1D9      TCGA-DM-A1DA 
"RBPMS WILD-TYPE" "RBPMS WILD-TYPE" "RBPMS WILD-TYPE" "RBPMS WILD-TYPE" 
     TCGA-DM-A1DB      TCGA-DM-A1HA      TCGA-DM-A1HB      TCGA-DM-A282 
"RBPMS WILD-TYPE" "RBPMS WILD-TYPE" "RBPMS WILD-TYPE" "RBPMS WILD-TYPE" 
     TCGA-DM-A285      TCGA-DM-A28C      TCGA-DM-A28E      TCGA-DM-A28F 
"RBPMS WILD-TYPE" "RBPMS WILD-TYPE" "RBPMS WILD-TYPE" "RBPMS WILD-TYPE" 
     TCGA-DM-A28G      TCGA-DM-A28H      TCGA-DM-A28K      TCGA-F4-6459 
"RBPMS WILD-TYPE" "RBPMS WILD-TYPE" "RBPMS WILD-TYPE" "RBPMS WILD-TYPE" 
     TCGA-F4-6460      TCGA-F4-6569      TCGA-F4-6570      TCGA-F4-6703 
"RBPMS WILD-TYPE" "RBPMS WILD-TYPE" "RBPMS WILD-TYPE" "RBPMS WILD-TYPE" 
     TCGA-F4-6704      TCGA-F4-6806      TCGA-F4-6807      TCGA-F4-6808 
"RBPMS WILD-TYPE" "RBPMS WILD-TYPE" "RBPMS WILD-TYPE" "RBPMS WILD-TYPE" 
     TCGA-F4-6809      TCGA-F4-6854      TCGA-F4-6855      TCGA-F4-6856 
"RBPMS WILD-TYPE" "RBPMS WILD-TYPE" "RBPMS WILD-TYPE" "RBPMS WILD-TYPE" 
     TCGA-G4-6293      TCGA-G4-6299      TCGA-G4-6303      TCGA-G4-6304 
"RBPMS WILD-TYPE" "RBPMS WILD-TYPE" "RBPMS WILD-TYPE" "RBPMS WILD-TYPE" 
     TCGA-G4-6306      TCGA-G4-6307      TCGA-G4-6309      TCGA-G4-6310 
"RBPMS WILD-TYPE" "RBPMS WILD-TYPE" "RBPMS WILD-TYPE" "RBPMS WILD-TYPE" 
     TCGA-G4-6315      TCGA-G4-6317      TCGA-G4-6321      TCGA-G4-6323 
"RBPMS WILD-TYPE" "RBPMS WILD-TYPE" "RBPMS WILD-TYPE" "RBPMS WILD-TYPE" 
     TCGA-G4-6586      TCGA-G4-6588      TCGA-G4-6625      TCGA-G4-6626 
"RBPMS WILD-TYPE" "RBPMS WILD-TYPE" "RBPMS WILD-TYPE" "RBPMS WILD-TYPE" 
     TCGA-G4-6628      TCGA-AF-2687      TCGA-AF-2689      TCGA-AF-2691 
"RBPMS WILD-TYPE" "RBPMS WILD-TYPE" "RBPMS WILD-TYPE" "RBPMS WILD-TYPE" 
     TCGA-AF-2692      TCGA-AF-2693      TCGA-AF-3400      TCGA-AF-3913 
"RBPMS WILD-TYPE" "RBPMS WILD-TYPE" "RBPMS WILD-TYPE" "RBPMS WILD-TYPE" 
     TCGA-AF-4110      TCGA-AF-5654      TCGA-AF-6136      TCGA-AF-6655 
"RBPMS WILD-TYPE" "RBPMS WILD-TYPE" "RBPMS WILD-TYPE" "RBPMS WILD-TYPE" 
     TCGA-AF-6672      TCGA-AH-6544      TCGA-AH-6547      TCGA-AH-6549 
"RBPMS WILD-TYPE" "RBPMS WILD-TYPE" "RBPMS WILD-TYPE" "RBPMS WILD-TYPE" 
     TCGA-AH-6643      TCGA-AH-6644      TCGA-CI-6619      TCGA-CI-6620 
"RBPMS WILD-TYPE" "RBPMS WILD-TYPE" "RBPMS WILD-TYPE" "RBPMS WILD-TYPE" 
     TCGA-CI-6621      TCGA-CI-6622      TCGA-CI-6624      TCGA-CL-5917 
"RBPMS WILD-TYPE" "RBPMS WILD-TYPE" "RBPMS WILD-TYPE" "RBPMS WILD-TYPE" 
     TCGA-CL-5918      TCGA-DC-5337      TCGA-DC-5869      TCGA-DC-6155 
"RBPMS WILD-TYPE" "RBPMS WILD-TYPE" "RBPMS WILD-TYPE" "RBPMS WILD-TYPE" 
     TCGA-DC-6157      TCGA-DC-6158      TCGA-DC-6160      TCGA-DC-6681 
"RBPMS WILD-TYPE" "RBPMS WILD-TYPE" "RBPMS WILD-TYPE" "RBPMS WILD-TYPE" 
     TCGA-DC-6682      TCGA-DC-6683      TCGA-DT-5265      TCGA-DY-A0XA 
"RBPMS WILD-TYPE" "RBPMS WILD-TYPE" "RBPMS WILD-TYPE" "RBPMS WILD-TYPE" 
     TCGA-DY-A1DC      TCGA-DY-A1DD      TCGA-DY-A1DF      TCGA-DY-A1DG 
"RBPMS WILD-TYPE" "RBPMS WILD-TYPE" "RBPMS WILD-TYPE" "RBPMS WILD-TYPE" 
     TCGA-DY-A1H8      TCGA-EF-5830      TCGA-EI-6506      TCGA-EI-6507 
"RBPMS WILD-TYPE" "RBPMS WILD-TYPE" "RBPMS WILD-TYPE" "RBPMS WILD-TYPE" 
     TCGA-EI-6508      TCGA-EI-6510      TCGA-F5-6464      TCGA-F5-6465 
"RBPMS WILD-TYPE" "RBPMS WILD-TYPE" "RBPMS WILD-TYPE" "RBPMS WILD-TYPE" 
     TCGA-F5-6571      TCGA-F5-6702      TCGA-F5-6811      TCGA-F5-6812 
"RBPMS WILD-TYPE" "RBPMS WILD-TYPE" "RBPMS WILD-TYPE" "RBPMS WILD-TYPE" 
     TCGA-F5-6813      TCGA-G5-6235      TCGA-G5-6641 
"RBPMS WILD-TYPE" "RBPMS WILD-TYPE" "RBPMS WILD-TYPE" 

Clustering(686) Variable = ZNF197 MUTATION ANALYSIS
D686V1, survival
                  sevent
clus2                0   1
  ZNF197 MUTATED    10   2
  ZNF197 WILD-TYPE 368  91
  ZNF197 MUTATED ZNF197 WILD-TYPE 
              12              459 
  ZNF197 MUTATED ZNF197 WILD-TYPE 
               2               91 
$`ZNF197 MUTATED`
TCGA-A6-6141 TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3663 TCGA-AA-3977 TCGA-AA-A010 
        8.38         3.02        63.98         6.97        25.02        34.98 
TCGA-CM-4743 TCGA-D5-6540 TCGA-DM-A0XD TCGA-AG-3726 TCGA-AG-A002 TCGA-F5-6812 
       23.05        16.14        24.43         7.99        20.98         0.66 

$`ZNF197 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 
       22.09        22.06        32.71        27.09        22.52        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 
       20.12        19.66        20.28         7.04         1.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02        78.08         6.05        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 
        9.99        21.14        82.95         1.91       124.27        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 
       17.85         4.80        17.13        12.49        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
      119.70        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3727 
        0.99        15.95        19.99        13.94        19.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  ZNF197 MUTATED ZNF197 WILD-TYPE 
            0.66             0.00 
  ZNF197 MUTATED ZNF197 WILD-TYPE 
           63.98           148.01 
  ZNF197 MUTATED ZNF197 WILD-TYPE 
           18.56            20.19 
[1] "0.7 - 64.0 (18.6)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.1"
D686V2, continuous
D686V3, binary
                  cls
clus                 0   1
  ZNF197 MUTATED     9   3
  ZNF197 WILD-TYPE 357 116
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF197 MUTATED      9    3
  ZNF197 WILD-TYPE  357  116
        clus
vv       ZNF197 MUTATED ZNF197 WILD-TYPE
  COLON               9              357
  RECTUM              3              116
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZNF197 MUTATED         3        0        3         4         1         0
  ZNF197 WILD-TYPE      88        1       29       134         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF197 MUTATED           0          0          0          0        0
  ZNF197 WILD-TYPE        24         11         59         42       48
                  vv
clus               STAGE IVA STAGE IVB
  ZNF197 MUTATED           0         0
  ZNF197 WILD-TYPE        18         1
D686V4, multiclass
            clus
vv           ZNF197 MUTATED ZNF197 WILD-TYPE
  STAGE I                 3               88
  STAGE IA                0                1
  STAGE II                3               29
  STAGE IIA               4              134
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              0               59
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZNF197 MUTATED     0   4   7   1
  ZNF197 WILD-TYPE  17  88 322  49
D686V5, multiclass
    clus
vv   ZNF197 MUTATED ZNF197 WILD-TYPE
  T1              0               17
  T2              4               88
  T3              7              322
  T4              1               49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  ZNF197 MUTATED    12   0   0
  ZNF197 WILD-TYPE 275 113  87
D686V6, multiclass
    clus
vv   ZNF197 MUTATED ZNF197 WILD-TYPE
  N0             12              275
  N1              0              113
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D686V7, binary
                  cls
clus                 0   1
  ZNF197 MUTATED    11   0
  ZNF197 WILD-TYPE 364  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF197 MUTATED     11    0
  ZNF197 WILD-TYPE  364   65
   clus
vv  ZNF197 MUTATED ZNF197 WILD-TYPE
  0             11              364
  1              0               65
[1] 2 2
[1] FALSE
D686V8, binary
                  cls
clus                 0   1
  ZNF197 MUTATED     3   9
  ZNF197 WILD-TYPE 222 255
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF197 MUTATED      3    9
  ZNF197 WILD-TYPE  222  255
        clus
vv       ZNF197 MUTATED ZNF197 WILD-TYPE
  FEMALE              3              222
  MALE                9              255
[1] 2 2
[1] FALSE
D686V9, binary
                  cls
clus                 0   1
  ZNF197 MUTATED    10   0
  ZNF197 WILD-TYPE 340  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF197 MUTATED     10    0
  ZNF197 WILD-TYPE  340   22
     clus
vv    ZNF197 MUTATED ZNF197 WILD-TYPE
  NO              10              340
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ZNF197 MUTATED                      8                             1
  ZNF197 WILD-TYPE                  307                            46
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ZNF197 MUTATED                       3                              0
  ZNF197 WILD-TYPE                   103                             10
D686V10, multiclass
                                clus
vv                               ZNF197 MUTATED ZNF197 WILD-TYPE
  COLON ADENOCARCINOMA                        8              307
  COLON MUCINOUS ADENOCARCINOMA               1               46
  RECTAL ADENOCARCINOMA                       3              103
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ZNF197 MUTATED     9   0   0   0
  ZNF197 WILD-TYPE 336   4  31  25
D686V11, multiclass
    clus
vv   ZNF197 MUTATED ZNF197 WILD-TYPE
  R0              9              336
  R1              0                4
  R2              0               31
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D686V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF197 MUTATED                                  0     0
  ZNF197 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZNF197 MUTATED                           1     4
  ZNF197 WILD-TYPE                        21   222
D686V13, multiclass
                                  clus
vv                                 ZNF197 MUTATED ZNF197 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                         4              222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(687) Variable = DOCK5 MUTATION ANALYSIS
D687V1, survival
                 sevent
clus2               0   1
  DOCK5 MUTATED    23   6
  DOCK5 WILD-TYPE 355  87
  DOCK5 MUTATED DOCK5 WILD-TYPE 
             29             442 
  DOCK5 MUTATED DOCK5 WILD-TYPE 
              6              87 
$`DOCK5 MUTATED`
TCGA-A6-5660 TCGA-A6-6780 TCGA-AA-3555 TCGA-AA-3672 TCGA-AA-3713 TCGA-AA-3715 
       29.19        20.12        29.95         0.92        19.04        19.04 
TCGA-AA-3864 TCGA-AA-3877 TCGA-AA-3950 TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00N 
       53.00        31.00        24.00        30.02        18.05         4.01 
TCGA-AA-A010 TCGA-AD-5900 TCGA-AD-6964 TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-6599 
       34.98         0.07        10.88        21.44        58.39         6.77 
TCGA-AZ-6601 TCGA-CA-6717 TCGA-CM-5861 TCGA-CM-6161 TCGA-DM-A0XF TCGA-F4-6856 
      100.01        12.76        15.02        15.02        38.20        35.31 
TCGA-G4-6304 TCGA-G4-6628 TCGA-AG-3742 TCGA-AG-A002 TCGA-EI-6507 
       53.62        79.69         0.99        20.98        19.96 

$`DOCK5 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       24.00        17.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
        2.01        14.01        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       26.99        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 
       17.03        24.03        27.02        29.98        18.05         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 
       12.99        24.00        33.01        26.01         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       34.03        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 
       41.00        39.98        18.05        40.96        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       88.21        49.41        12.10        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07        12.20        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6162 
       32.02         5.03        15.02        15.02        17.03        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 
       47.41       133.18        74.56        65.85        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 
       35.80        26.17        91.79        46.75        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3878 TCGA-AG-3881 
        7.99         0.99        37.02        32.98         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6508 
       24.13        51.48        32.61         0.49        20.55        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  DOCK5 MUTATED DOCK5 WILD-TYPE 
           0.07            0.00 
  DOCK5 MUTATED DOCK5 WILD-TYPE 
         100.01          148.01 
  DOCK5 MUTATED DOCK5 WILD-TYPE 
          20.98           20.12 
[1] "0.1 - 100.0 (21.0)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1"  
D687V2, continuous
D687V3, binary
                 cls
clus                0   1
  DOCK5 MUTATED    26   3
  DOCK5 WILD-TYPE 340 116
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DOCK5 MUTATED     26    3
  DOCK5 WILD-TYPE  340  116
        clus
vv       DOCK5 MUTATED DOCK5 WILD-TYPE
  COLON             26             340
  RECTUM             3             116
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DOCK5 MUTATED         8        0        3         9         3         0
  DOCK5 WILD-TYPE      83        1       29       129         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DOCK5 MUTATED           1          0          1          2        1         0
  DOCK5 WILD-TYPE        23         11         58         40       47        18
                 vv
clus              STAGE IVB
  DOCK5 MUTATED           0
  DOCK5 WILD-TYPE         1
D687V4, multiclass
            clus
vv           DOCK5 MUTATED DOCK5 WILD-TYPE
  STAGE I                8              83
  STAGE IA               0               1
  STAGE II               3              29
  STAGE IIA              9             129
  STAGE IIB              3               7
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             2              40
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  DOCK5 MUTATED     2   6  16   5
  DOCK5 WILD-TYPE  15  86 313  45
D687V5, multiclass
    clus
vv   DOCK5 MUTATED DOCK5 WILD-TYPE
  T1             2              15
  T2             6              86
  T3            16             313
  T4             5              45
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  DOCK5 MUTATED    24   2   3
  DOCK5 WILD-TYPE 263 111  84
D687V6, multiclass
    clus
vv   DOCK5 MUTATED DOCK5 WILD-TYPE
  N0            24             263
  N1             2             111
  N2             3              84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D687V7, binary
                 cls
clus                0   1
  DOCK5 MUTATED    23   1
  DOCK5 WILD-TYPE 352  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DOCK5 MUTATED     23    1
  DOCK5 WILD-TYPE  352   64
   clus
vv  DOCK5 MUTATED DOCK5 WILD-TYPE
  0            23             352
  1             1              64
[1] 2 2
[1] FALSE
D687V8, binary
                 cls
clus                0   1
  DOCK5 MUTATED    10  19
  DOCK5 WILD-TYPE 215 245
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DOCK5 MUTATED     10   19
  DOCK5 WILD-TYPE  215  245
        clus
vv       DOCK5 MUTATED DOCK5 WILD-TYPE
  FEMALE            10             215
  MALE              19             245
[1] 2 2
[1] FALSE
D687V9, binary
                 cls
clus                0   1
  DOCK5 MUTATED    24   1
  DOCK5 WILD-TYPE 326  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DOCK5 MUTATED     24    1
  DOCK5 WILD-TYPE  326   21
     clus
vv    DOCK5 MUTATED DOCK5 WILD-TYPE
  NO             24             326
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  DOCK5 MUTATED                     16                             9
  DOCK5 WILD-TYPE                  299                            38
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  DOCK5 MUTATED                       3                              0
  DOCK5 WILD-TYPE                   103                             10
D687V10, multiclass
                                clus
vv                               DOCK5 MUTATED DOCK5 WILD-TYPE
  COLON ADENOCARCINOMA                      16             299
  COLON MUCINOUS ADENOCARCINOMA              9              38
  RECTAL ADENOCARCINOMA                      3             103
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  DOCK5 MUTATED    21   0   1   1
  DOCK5 WILD-TYPE 324   4  30  24
D687V11, multiclass
    clus
vv   DOCK5 MUTATED DOCK5 WILD-TYPE
  R0            21             324
  R1             0               4
  R2             1              30
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D687V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DOCK5 MUTATED                                  0     1
  DOCK5 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  DOCK5 MUTATED                           1    14
  DOCK5 WILD-TYPE                        21   212
D687V13, multiclass
                                  clus
vv                                 DOCK5 MUTATED DOCK5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                       14             212
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(688) Variable = TNRC6C MUTATION ANALYSIS
D688V1, survival
                  sevent
clus2                0   1
  TNRC6C MUTATED    14   4
  TNRC6C WILD-TYPE 364  89
  TNRC6C MUTATED TNRC6C WILD-TYPE 
              18              453 
  TNRC6C MUTATED TNRC6C WILD-TYPE 
               4               89 
$`TNRC6C MUTATED`
TCGA-A6-3809 TCGA-A6-5665 TCGA-AA-3492 TCGA-AA-3815 TCGA-AA-3845 TCGA-AA-3950 
       32.75        22.06         3.02        33.04         0.00        24.00 
TCGA-AA-3966 TCGA-AA-A01P TCGA-AD-5900 TCGA-AU-6004 TCGA-AY-6197 TCGA-CA-6717 
        2.01        38.07         0.07        27.09        21.44        12.76 
TCGA-CK-5913 TCGA-CM-6171 TCGA-F4-6570 TCGA-F4-6856 TCGA-AG-3898 TCGA-AG-A002 
       51.32        14.04         6.18        35.31        48.03        20.98 

$`TNRC6C WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       19.66        20.28         7.04         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02        14.93        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 
       26.01         2.01        20.98        34.03        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       12.00        31.00        31.00         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       39.98        18.05        40.96        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 
        0.20        14.50        16.31         0.95        33.01        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07        12.20        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 
       17.56       148.01        85.45        15.62        49.08         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 
       21.99        14.99        12.99        13.02        15.02        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
       13.25         0.53        47.41       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
       14.01         1.02        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  TNRC6C MUTATED TNRC6C WILD-TYPE 
               0                0 
  TNRC6C MUTATED TNRC6C WILD-TYPE 
           51.32           148.01 
  TNRC6C MUTATED TNRC6C WILD-TYPE 
           21.75            20.05 
[1] "0.0 - 51.3 (21.8)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.4"
D688V2, continuous
D688V3, binary
                  cls
clus                 0   1
  TNRC6C MUTATED    18   2
  TNRC6C WILD-TYPE 348 117
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TNRC6C MUTATED     18    2
  TNRC6C WILD-TYPE  348  117
        clus
vv       TNRC6C MUTATED TNRC6C WILD-TYPE
  COLON              18              348
  RECTUM              2              117
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TNRC6C MUTATED         5        0        1        11         2         0
  TNRC6C WILD-TYPE      86        1       31       127         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TNRC6C MUTATED           1          0          0          0        0
  TNRC6C WILD-TYPE        23         11         59         42       48
                  vv
clus               STAGE IVA STAGE IVB
  TNRC6C MUTATED           0         0
  TNRC6C WILD-TYPE        18         1
D688V4, multiclass
            clus
vv           TNRC6C MUTATED TNRC6C WILD-TYPE
  STAGE I                 5               86
  STAGE IA                0                1
  STAGE II                1               31
  STAGE IIA              11              127
  STAGE IIB               2                8
  STAGE IIC               0                1
  STAGE III               1               23
  STAGE IIIA              0               11
  STAGE IIIB              0               59
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  TNRC6C MUTATED     0   5  13   2
  TNRC6C WILD-TYPE  17  87 316  48
D688V5, multiclass
    clus
vv   TNRC6C MUTATED TNRC6C WILD-TYPE
  T1              0               17
  T2              5               87
  T3             13              316
  T4              2               48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  TNRC6C MUTATED    19   1   0
  TNRC6C WILD-TYPE 268 112  87
D688V6, multiclass
    clus
vv   TNRC6C MUTATED TNRC6C WILD-TYPE
  N0             19              268
  N1              1              112
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D688V7, binary
                  cls
clus                 0   1
  TNRC6C MUTATED    16   0
  TNRC6C WILD-TYPE 359  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TNRC6C MUTATED     16    0
  TNRC6C WILD-TYPE  359   65
   clus
vv  TNRC6C MUTATED TNRC6C WILD-TYPE
  0             16              359
  1              0               65
[1] 2 2
[1] FALSE
D688V8, binary
                  cls
clus                 0   1
  TNRC6C MUTATED    14   6
  TNRC6C WILD-TYPE 211 258
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TNRC6C MUTATED     14    6
  TNRC6C WILD-TYPE  211  258
        clus
vv       TNRC6C MUTATED TNRC6C WILD-TYPE
  FEMALE             14              211
  MALE                6              258
[1] 2 2
[1] FALSE
D688V9, binary
                  cls
clus                 0   1
  TNRC6C MUTATED    14   0
  TNRC6C WILD-TYPE 336  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TNRC6C MUTATED     14    0
  TNRC6C WILD-TYPE  336   22
     clus
vv    TNRC6C MUTATED TNRC6C WILD-TYPE
  NO              14              336
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  TNRC6C MUTATED                     12                             6
  TNRC6C WILD-TYPE                  303                            41
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  TNRC6C MUTATED                       2                              0
  TNRC6C WILD-TYPE                   104                             10
D688V10, multiclass
                                clus
vv                               TNRC6C MUTATED TNRC6C WILD-TYPE
  COLON ADENOCARCINOMA                       12              303
  COLON MUCINOUS ADENOCARCINOMA               6               41
  RECTAL ADENOCARCINOMA                       2              104
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  TNRC6C MUTATED    16   0   0   3
  TNRC6C WILD-TYPE 329   4  31  22
D688V11, multiclass
    clus
vv   TNRC6C MUTATED TNRC6C WILD-TYPE
  R0             16              329
  R1              0                4
  R2              0               31
  RX              3               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D688V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TNRC6C MUTATED                                  0     1
  TNRC6C WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  TNRC6C MUTATED                           0    10
  TNRC6C WILD-TYPE                        22   216
D688V13, multiclass
                                  clus
vv                                 TNRC6C MUTATED TNRC6C WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                        10              216
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(689) Variable = NIPA2 MUTATION ANALYSIS
D689V1, survival
                 sevent
clus2               0   1
  NIPA2 MUTATED     7   1
  NIPA2 WILD-TYPE 371  92
  NIPA2 MUTATED NIPA2 WILD-TYPE 
              8             463 
  NIPA2 MUTATED NIPA2 WILD-TYPE 
              1              92 
$`NIPA2 MUTATED`
TCGA-AA-3524 TCGA-AA-3663 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3977 TCGA-CM-4746 
       36.03         6.97        26.99        19.04        25.02        37.02 
TCGA-DM-A1HB TCGA-AG-3726 
      135.65         7.99 

$`NIPA2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3525 
       38.99         1.02         9.07        24.03        37.05         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
        5.03        85.05        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       23.05        20.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
       44.32       131.51       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
       19.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  NIPA2 MUTATED NIPA2 WILD-TYPE 
           6.97            0.00 
  NIPA2 MUTATED NIPA2 WILD-TYPE 
         135.65          148.01 
  NIPA2 MUTATED NIPA2 WILD-TYPE 
         26.005          20.120 
[1] "7.0 - 135.7 (26.0)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.9"
D689V2, continuous
D689V3, binary
                 cls
clus                0   1
  NIPA2 MUTATED     7   1
  NIPA2 WILD-TYPE 359 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NIPA2 MUTATED      7    1
  NIPA2 WILD-TYPE  359  118
        clus
vv       NIPA2 MUTATED NIPA2 WILD-TYPE
  COLON              7             359
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NIPA2 MUTATED         2        0        3         1         0         0
  NIPA2 WILD-TYPE      89        1       29       137        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NIPA2 MUTATED           0          0          1          0        0         0
  NIPA2 WILD-TYPE        24         11         58         42       48        18
                 vv
clus              STAGE IVB
  NIPA2 MUTATED           0
  NIPA2 WILD-TYPE         1
D689V4, multiclass
            clus
vv           NIPA2 MUTATED NIPA2 WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               3              29
  STAGE IIA              1             137
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  NIPA2 MUTATED     0   3   5   0
  NIPA2 WILD-TYPE  17  89 324  50
D689V5, multiclass
    clus
vv   NIPA2 MUTATED NIPA2 WILD-TYPE
  T1             0              17
  T2             3              89
  T3             5             324
  T4             0              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  NIPA2 MUTATED     7   1   0
  NIPA2 WILD-TYPE 280 112  87
D689V6, multiclass
    clus
vv   NIPA2 MUTATED NIPA2 WILD-TYPE
  N0             7             280
  N1             1             112
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D689V7, binary
                 cls
clus                0   1
  NIPA2 MUTATED     7   0
  NIPA2 WILD-TYPE 368  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NIPA2 MUTATED      7    0
  NIPA2 WILD-TYPE  368   65
   clus
vv  NIPA2 MUTATED NIPA2 WILD-TYPE
  0             7             368
  1             0              65
[1] 2 2
[1] FALSE
D689V8, binary
                 cls
clus                0   1
  NIPA2 MUTATED     2   6
  NIPA2 WILD-TYPE 223 258
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NIPA2 MUTATED      2    6
  NIPA2 WILD-TYPE  223  258
        clus
vv       NIPA2 MUTATED NIPA2 WILD-TYPE
  FEMALE             2             223
  MALE               6             258
[1] 2 2
[1] FALSE
D689V9, binary
                 cls
clus                0   1
  NIPA2 MUTATED     7   0
  NIPA2 WILD-TYPE 343  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NIPA2 MUTATED      7    0
  NIPA2 WILD-TYPE  343   22
     clus
vv    NIPA2 MUTATED NIPA2 WILD-TYPE
  NO              7             343
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  NIPA2 MUTATED                      6                             0
  NIPA2 WILD-TYPE                  309                            47
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  NIPA2 MUTATED                       1                              0
  NIPA2 WILD-TYPE                   105                             10
D689V10, multiclass
                                clus
vv                               NIPA2 MUTATED NIPA2 WILD-TYPE
  COLON ADENOCARCINOMA                       6             309
  COLON MUCINOUS ADENOCARCINOMA              0              47
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  NIPA2 MUTATED     6   0   0   0
  NIPA2 WILD-TYPE 339   4  31  25
D689V11, multiclass
    clus
vv   NIPA2 MUTATED NIPA2 WILD-TYPE
  R0             6             339
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D689V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NIPA2 MUTATED                                  0     0
  NIPA2 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  NIPA2 MUTATED                           1     1
  NIPA2 WILD-TYPE                        21   225
D689V13, multiclass
[1] "Remove cluster labels:" "NIPA2 MUTATED"         
clus
  NIPA2 MUTATED NIPA2 WILD-TYPE 
              2             258 
     TCGA-A6-2671      TCGA-A6-2672      TCGA-A6-2674      TCGA-A6-2676 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-A6-2677      TCGA-A6-2678      TCGA-A6-2683      TCGA-A6-3807 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-A6-3808      TCGA-A6-3809      TCGA-A6-3810      TCGA-A6-4105 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-A6-5656      TCGA-A6-5657      TCGA-A6-5659      TCGA-A6-5660 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-A6-5661      TCGA-A6-5662      TCGA-A6-5664      TCGA-A6-5665 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-A6-5666      TCGA-A6-6137      TCGA-A6-6138      TCGA-A6-6141 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-A6-6142      TCGA-A6-6648      TCGA-A6-6649      TCGA-A6-6651 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-A6-6652      TCGA-A6-6653      TCGA-A6-6654      TCGA-A6-6780 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-A6-6781      TCGA-A6-6782      TCGA-AD-5900      TCGA-AD-6548 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-AD-6888      TCGA-AD-6889      TCGA-AD-6890      TCGA-AD-6895 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-AD-6899      TCGA-AD-6901      TCGA-AD-6963      TCGA-AD-6964 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-AD-6965      TCGA-AU-3779      TCGA-AU-6004      TCGA-AY-4070 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-AY-4071      TCGA-AY-5543      TCGA-AY-6196      TCGA-AY-6197 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-AY-6386      TCGA-AZ-4315      TCGA-AZ-4323      TCGA-AZ-4616 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-AZ-4681      TCGA-AZ-4682      TCGA-AZ-5403      TCGA-AZ-5407 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-AZ-6598      TCGA-AZ-6599      TCGA-AZ-6600      TCGA-AZ-6601 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-AZ-6603      TCGA-AZ-6605      TCGA-AZ-6606      TCGA-AZ-6607 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-AZ-6608      TCGA-CA-5254      TCGA-CA-5255      TCGA-CA-5796 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-CA-5797      TCGA-CA-6715      TCGA-CA-6716      TCGA-CA-6717 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-CA-6718      TCGA-CA-6719      TCGA-CK-4947      TCGA-CK-4948 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-CK-4950      TCGA-CK-4952      TCGA-CK-5912      TCGA-CK-5913 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-CK-5914      TCGA-CK-5915      TCGA-CK-5916      TCGA-CK-6746 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-CK-6747      TCGA-CK-6748      TCGA-CK-6751      TCGA-CM-4743 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-CM-4744      TCGA-CM-4747      TCGA-CM-4752      TCGA-CM-5341 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-CM-5344      TCGA-CM-5348      TCGA-CM-5349      TCGA-CM-5860 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-CM-5861      TCGA-CM-5862      TCGA-CM-5863      TCGA-CM-5864 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-CM-5868      TCGA-CM-6161      TCGA-CM-6162      TCGA-CM-6163 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-CM-6164      TCGA-CM-6165      TCGA-CM-6166      TCGA-CM-6167 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-CM-6168      TCGA-CM-6169      TCGA-CM-6170      TCGA-CM-6171 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-CM-6172      TCGA-CM-6674      TCGA-CM-6675      TCGA-CM-6676 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-CM-6677      TCGA-CM-6678      TCGA-CM-6679      TCGA-CM-6680 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-D5-5537      TCGA-D5-5538      TCGA-D5-5539      TCGA-D5-5540 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-D5-5541      TCGA-D5-6529      TCGA-D5-6532      TCGA-D5-6533 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-D5-6534      TCGA-D5-6535      TCGA-D5-6536      TCGA-D5-6537 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-D5-6538      TCGA-D5-6539      TCGA-D5-6540      TCGA-D5-6541 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-D5-6898      TCGA-D5-6920      TCGA-D5-6922      TCGA-D5-6923 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-D5-6924      TCGA-D5-6926      TCGA-D5-6927      TCGA-D5-6928 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-D5-6929      TCGA-D5-6930      TCGA-D5-6931      TCGA-D5-6932 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-D5-7000      TCGA-DM-A0X9      TCGA-DM-A0XD      TCGA-DM-A0XF 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-DM-A1D0      TCGA-DM-A1D4      TCGA-DM-A1D6      TCGA-DM-A1D7 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-DM-A1D8      TCGA-DM-A1D9      TCGA-DM-A1DA      TCGA-DM-A1DB 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-DM-A1HA      TCGA-DM-A282      TCGA-DM-A285      TCGA-DM-A28C 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-DM-A28E      TCGA-DM-A28F      TCGA-DM-A28G      TCGA-DM-A28H 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-DM-A28K      TCGA-F4-6459      TCGA-F4-6460      TCGA-F4-6569 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-F4-6570      TCGA-F4-6703      TCGA-F4-6704      TCGA-F4-6805 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-F4-6806      TCGA-F4-6807      TCGA-F4-6808      TCGA-F4-6809 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-F4-6854      TCGA-F4-6855      TCGA-F4-6856      TCGA-G4-6293 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-G4-6299      TCGA-G4-6303      TCGA-G4-6304      TCGA-G4-6306 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-G4-6307      TCGA-G4-6309      TCGA-G4-6310      TCGA-G4-6315 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-G4-6317      TCGA-G4-6321      TCGA-G4-6323      TCGA-G4-6586 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-G4-6588      TCGA-G4-6625      TCGA-G4-6626      TCGA-G4-6628 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-AF-2687      TCGA-AF-2689      TCGA-AF-2691      TCGA-AF-2692 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-AF-2693      TCGA-AF-3400      TCGA-AF-3913      TCGA-AF-4110 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-AF-5654      TCGA-AF-6136      TCGA-AF-6655      TCGA-AF-6672 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-AH-6544      TCGA-AH-6547      TCGA-AH-6549      TCGA-AH-6643 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-AH-6644      TCGA-CI-6619      TCGA-CI-6620      TCGA-CI-6621 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-CI-6622      TCGA-CI-6624      TCGA-CL-5917      TCGA-CL-5918 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-DC-5337      TCGA-DC-5869      TCGA-DC-6155      TCGA-DC-6157 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-DC-6158      TCGA-DC-6160      TCGA-DC-6681      TCGA-DC-6682 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-DC-6683      TCGA-DT-5265      TCGA-DY-A0XA      TCGA-DY-A1DC 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-DY-A1DD      TCGA-DY-A1DF      TCGA-DY-A1DG      TCGA-DY-A1H8 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-EF-5830      TCGA-EI-6506      TCGA-EI-6507      TCGA-EI-6508 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-EI-6510      TCGA-F5-6464      TCGA-F5-6465      TCGA-F5-6571 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-F5-6702      TCGA-F5-6811      TCGA-F5-6812      TCGA-F5-6813 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 
     TCGA-G5-6235      TCGA-G5-6641 
"NIPA2 WILD-TYPE" "NIPA2 WILD-TYPE" 

Clustering(690) Variable = NSUN2 MUTATION ANALYSIS
D690V1, survival
                 sevent
clus2               0   1
  NSUN2 MUTATED    10   2
  NSUN2 WILD-TYPE 368  91
  NSUN2 MUTATED NSUN2 WILD-TYPE 
             12             459 
  NSUN2 MUTATED NSUN2 WILD-TYPE 
              2              91 
$`NSUN2 MUTATED`
TCGA-A6-5659 TCGA-AA-3685 TCGA-AA-3833 TCGA-AA-3930 TCGA-AD-6964 TCGA-AZ-4315 
       30.44        37.05        15.95         2.01        10.88        58.39 
TCGA-CM-6674 TCGA-D5-5539 TCGA-D5-6541 TCGA-F4-6856 TCGA-G4-6304 TCGA-AG-A01Y 
       12.95        19.59        15.58        35.31        53.62        64.01 

$`NSUN2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3688 TCGA-AA-3692 
       47.01        15.02        11.01         5.98        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3939 TCGA-AA-3941 
       27.02        29.98        18.05        31.00        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
        0.72         5.79        22.42        27.42         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       14.04        11.01        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-5541 
       10.06        12.03        45.40        12.26        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6898 TCGA-D5-6920 
        4.80        17.13        12.49        16.14         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
       13.25         0.53        47.41       133.18        74.56        65.85 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       12.00        70.03        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  NSUN2 MUTATED NSUN2 WILD-TYPE 
           2.01            0.00 
  NSUN2 MUTATED NSUN2 WILD-TYPE 
          64.01          148.01 
  NSUN2 MUTATED NSUN2 WILD-TYPE 
         25.015          20.190 
[1] "2.0 - 64.0 (25.0)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.4"
D690V2, continuous
D690V3, binary
                 cls
clus                0   1
  NSUN2 MUTATED    11   1
  NSUN2 WILD-TYPE 355 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NSUN2 MUTATED     11    1
  NSUN2 WILD-TYPE  355  118
        clus
vv       NSUN2 MUTATED NSUN2 WILD-TYPE
  COLON             11             355
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NSUN2 MUTATED         2        0        2         4         1         0
  NSUN2 WILD-TYPE      89        1       30       134         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NSUN2 MUTATED           0          1          0          0        1         0
  NSUN2 WILD-TYPE        24         10         59         42       47        18
                 vv
clus              STAGE IVB
  NSUN2 MUTATED           0
  NSUN2 WILD-TYPE         1
D690V4, multiclass
            clus
vv           NSUN2 MUTATED NSUN2 WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA              4             134
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             1              10
  STAGE IIIB             0              59
  STAGE IIIC             0              42
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  NSUN2 MUTATED     0   2   8   2
  NSUN2 WILD-TYPE  17  90 321  48
D690V5, multiclass
    clus
vv   NSUN2 MUTATED NSUN2 WILD-TYPE
  T1             0              17
  T2             2              90
  T3             8             321
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  NSUN2 MUTATED     9   1   2
  NSUN2 WILD-TYPE 278 112  85
D690V6, multiclass
    clus
vv   NSUN2 MUTATED NSUN2 WILD-TYPE
  N0             9             278
  N1             1             112
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D690V7, binary
                 cls
clus                0   1
  NSUN2 MUTATED    10   1
  NSUN2 WILD-TYPE 365  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NSUN2 MUTATED     10    1
  NSUN2 WILD-TYPE  365   64
   clus
vv  NSUN2 MUTATED NSUN2 WILD-TYPE
  0            10             365
  1             1              64
[1] 2 2
[1] FALSE
D690V8, binary
                 cls
clus                0   1
  NSUN2 MUTATED     3   9
  NSUN2 WILD-TYPE 222 255
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NSUN2 MUTATED      3    9
  NSUN2 WILD-TYPE  222  255
        clus
vv       NSUN2 MUTATED NSUN2 WILD-TYPE
  FEMALE             3             222
  MALE               9             255
[1] 2 2
[1] FALSE
D690V9, binary
                 cls
clus                0   1
  NSUN2 MUTATED    11   0
  NSUN2 WILD-TYPE 339  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NSUN2 MUTATED     11    0
  NSUN2 WILD-TYPE  339   22
     clus
vv    NSUN2 MUTATED NSUN2 WILD-TYPE
  NO             11             339
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  NSUN2 MUTATED                      9                             2
  NSUN2 WILD-TYPE                  306                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  NSUN2 MUTATED                       1                              0
  NSUN2 WILD-TYPE                   105                             10
D690V10, multiclass
                                clus
vv                               NSUN2 MUTATED NSUN2 WILD-TYPE
  COLON ADENOCARCINOMA                       9             306
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  NSUN2 MUTATED    10   0   1   0
  NSUN2 WILD-TYPE 335   4  30  25
D690V11, multiclass
    clus
vv   NSUN2 MUTATED NSUN2 WILD-TYPE
  R0            10             335
  R1             0               4
  R2             1              30
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D690V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NSUN2 MUTATED                                  0     0
  NSUN2 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  NSUN2 MUTATED                           0     8
  NSUN2 WILD-TYPE                        22   218
D690V13, multiclass
                                  clus
vv                                 NSUN2 MUTATED NSUN2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        8             218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(691) Variable = CYP4X1 MUTATION ANALYSIS
D691V1, survival
                  sevent
clus2                0   1
  CYP4X1 MUTATED     5   1
  CYP4X1 WILD-TYPE 373  92
  CYP4X1 MUTATED CYP4X1 WILD-TYPE 
               6              465 
  CYP4X1 MUTATED CYP4X1 WILD-TYPE 
               1               92 
$`CYP4X1 MUTATED`
TCGA-AZ-5407 TCGA-CA-6717 TCGA-CK-4947 TCGA-F4-6809 TCGA-G4-6309 TCGA-CL-5918 
       88.21        12.76        17.56        13.25        85.48         7.17 

$`CYP4X1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6598 
        1.41         5.13       106.75        22.36        62.79        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-4950 
        0.07        12.20        10.06        14.30       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       53.62        44.68        55.04        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        6.97         4.73        78.12        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  CYP4X1 MUTATED CYP4X1 WILD-TYPE 
            7.17             0.00 
  CYP4X1 MUTATED CYP4X1 WILD-TYPE 
           88.21           148.01 
  CYP4X1 MUTATED CYP4X1 WILD-TYPE 
          15.405           20.280 
[1] "7.2 - 88.2 (15.4)"  "0.0 - 148.0 (20.3)"
[1] "hr=" "1.7"
D691V2, continuous
D691V3, binary
                  cls
clus                 0   1
  CYP4X1 MUTATED     5   1
  CYP4X1 WILD-TYPE 361 118
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CYP4X1 MUTATED      5    1
  CYP4X1 WILD-TYPE  361  118
        clus
vv       CYP4X1 MUTATED CYP4X1 WILD-TYPE
  COLON               5              361
  RECTUM              1              118
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CYP4X1 MUTATED         1        0        0         2         0         0
  CYP4X1 WILD-TYPE      90        1       32       136        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CYP4X1 MUTATED           0          0          2          0        0
  CYP4X1 WILD-TYPE        24         11         57         42       48
                  vv
clus               STAGE IVA STAGE IVB
  CYP4X1 MUTATED           1         0
  CYP4X1 WILD-TYPE        17         1
D691V4, multiclass
            clus
vv           CYP4X1 MUTATED CYP4X1 WILD-TYPE
  STAGE I                 1               90
  STAGE IA                0                1
  STAGE II                0               32
  STAGE IIA               2              136
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              2               57
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               1               17
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  CYP4X1 MUTATED     1   0   4   1
  CYP4X1 WILD-TYPE  16  92 325  49
D691V5, multiclass
    clus
vv   CYP4X1 MUTATED CYP4X1 WILD-TYPE
  T1              1               16
  T2              0               92
  T3              4              325
  T4              1               49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  CYP4X1 MUTATED     3   3   0
  CYP4X1 WILD-TYPE 284 110  87
D691V6, multiclass
    clus
vv   CYP4X1 MUTATED CYP4X1 WILD-TYPE
  N0              3              284
  N1              3              110
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D691V7, binary
                  cls
clus                 0   1
  CYP4X1 MUTATED     4   1
  CYP4X1 WILD-TYPE 371  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CYP4X1 MUTATED      4    1
  CYP4X1 WILD-TYPE  371   64
   clus
vv  CYP4X1 MUTATED CYP4X1 WILD-TYPE
  0              4              371
  1              1               64
[1] 2 2
[1] FALSE
D691V8, binary
                  cls
clus                 0   1
  CYP4X1 MUTATED     5   1
  CYP4X1 WILD-TYPE 220 263
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CYP4X1 MUTATED      5    1
  CYP4X1 WILD-TYPE  220  263
        clus
vv       CYP4X1 MUTATED CYP4X1 WILD-TYPE
  FEMALE              5              220
  MALE                1              263
[1] 2 2
[1] FALSE
D691V9, binary
                  cls
clus                 0   1
  CYP4X1 MUTATED     6   0
  CYP4X1 WILD-TYPE 344  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CYP4X1 MUTATED      6    0
  CYP4X1 WILD-TYPE  344   22
     clus
vv    CYP4X1 MUTATED CYP4X1 WILD-TYPE
  NO               6              344
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CYP4X1 MUTATED                      4                             1
  CYP4X1 WILD-TYPE                  311                            46
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CYP4X1 MUTATED                       1                              0
  CYP4X1 WILD-TYPE                   105                             10
D691V10, multiclass
                                clus
vv                               CYP4X1 MUTATED CYP4X1 WILD-TYPE
  COLON ADENOCARCINOMA                        4              311
  COLON MUCINOUS ADENOCARCINOMA               1               46
  RECTAL ADENOCARCINOMA                       1              105
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  CYP4X1 MUTATED     2   0   0   3
  CYP4X1 WILD-TYPE 343   4  31  22
D691V11, multiclass
    clus
vv   CYP4X1 MUTATED CYP4X1 WILD-TYPE
  R0              2              343
  R1              0                4
  R2              0               31
  RX              3               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D691V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CYP4X1 MUTATED                                  0     1
  CYP4X1 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  CYP4X1 MUTATED                           1     4
  CYP4X1 WILD-TYPE                        21   222
D691V13, multiclass
                                  clus
vv                                 CYP4X1 MUTATED CYP4X1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                         4              222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(692) Variable = C11ORF57 MUTATION ANALYSIS
D692V1, survival
                    sevent
clus2                  0   1
  C11ORF57 MUTATED    10   0
  C11ORF57 WILD-TYPE 368  93
  C11ORF57 MUTATED C11ORF57 WILD-TYPE 
                10                461 
  C11ORF57 MUTATED C11ORF57 WILD-TYPE 
                 0                 93 
$`C11ORF57 MUTATED`
TCGA-AA-3672 TCGA-AA-3950 TCGA-AA-A010 TCGA-AZ-4315 TCGA-CA-5254 TCGA-CA-6717 
        0.92        24.00        34.98        58.39        12.69        12.76 
TCGA-CM-5861 TCGA-G4-6588 TCGA-AG-3892 TCGA-AH-6644 
       15.02        26.17        13.02         0.72 

$`C11ORF57 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
        6.05         6.97        54.02         2.01        14.01        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 
        2.01        12.99        24.00        33.01        26.01         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5255 
       29.56         5.23        11.74         3.19         1.61         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07        12.20        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       22.98        30.08        32.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       35.80        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-CI-6619 
      117.11        38.56         1.45        17.49         0.69         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  C11ORF57 MUTATED C11ORF57 WILD-TYPE 
              0.72               0.00 
  C11ORF57 MUTATED C11ORF57 WILD-TYPE 
             58.39             148.01 
  C11ORF57 MUTATED C11ORF57 WILD-TYPE 
             14.02              20.28 
[1] "0.7 - 58.4 (14.0)"  "0.0 - 148.0 (20.3)"
[1] "hr="     "9200000"
D692V2, continuous
D692V3, binary
                    cls
clus                   0   1
  C11ORF57 MUTATED     8   3
  C11ORF57 WILD-TYPE 358 116
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C11ORF57 MUTATED      8    3
  C11ORF57 WILD-TYPE  358  116
        clus
vv       C11ORF57 MUTATED C11ORF57 WILD-TYPE
  COLON                 8                358
  RECTUM                3                116
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  C11ORF57 MUTATED         1        0        0         6         1         0
  C11ORF57 WILD-TYPE      90        1       32       132         9         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C11ORF57 MUTATED           1          0          1          0        0
  C11ORF57 WILD-TYPE        23         11         58         42       48
                    vv
clus                 STAGE IVA STAGE IVB
  C11ORF57 MUTATED           0         0
  C11ORF57 WILD-TYPE        18         1
D692V4, multiclass
            clus
vv           C11ORF57 MUTATED C11ORF57 WILD-TYPE
  STAGE I                   1                 90
  STAGE IA                  0                  1
  STAGE II                  0                 32
  STAGE IIA                 6                132
  STAGE IIB                 1                  9
  STAGE IIC                 0                  1
  STAGE III                 1                 23
  STAGE IIIA                0                 11
  STAGE IIIB                1                 58
  STAGE IIIC                0                 42
  STAGE IV                  0                 48
  STAGE IVA                 0                 18
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  C11ORF57 MUTATED     1   0   8   2
  C11ORF57 WILD-TYPE  16  92 321  48
D692V5, multiclass
    clus
vv   C11ORF57 MUTATED C11ORF57 WILD-TYPE
  T1                1                 16
  T2                0                 92
  T3                8                321
  T4                2                 48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  C11ORF57 MUTATED     8   2   0
  C11ORF57 WILD-TYPE 279 111  87
D692V6, multiclass
    clus
vv   C11ORF57 MUTATED C11ORF57 WILD-TYPE
  N0                8                279
  N1                2                111
  N2                0                 87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D692V7, binary
                    cls
clus                   0   1
  C11ORF57 MUTATED    10   0
  C11ORF57 WILD-TYPE 365  65
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C11ORF57 MUTATED     10    0
  C11ORF57 WILD-TYPE  365   65
   clus
vv  C11ORF57 MUTATED C11ORF57 WILD-TYPE
  0               10                365
  1                0                 65
[1] 2 2
[1] FALSE
D692V8, binary
                    cls
clus                   0   1
  C11ORF57 MUTATED     7   4
  C11ORF57 WILD-TYPE 218 260
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C11ORF57 MUTATED      7    4
  C11ORF57 WILD-TYPE  218  260
        clus
vv       C11ORF57 MUTATED C11ORF57 WILD-TYPE
  FEMALE                7                218
  MALE                  4                260
[1] 2 2
[1] FALSE
D692V9, binary
                    cls
clus                   0   1
  C11ORF57 MUTATED     9   0
  C11ORF57 WILD-TYPE 341  22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C11ORF57 MUTATED      9    0
  C11ORF57 WILD-TYPE  341   22
     clus
vv    C11ORF57 MUTATED C11ORF57 WILD-TYPE
  NO                 9                341
  YES                0                 22
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  C11ORF57 MUTATED                      6                             2
  C11ORF57 WILD-TYPE                  309                            45
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  C11ORF57 MUTATED                       3                              0
  C11ORF57 WILD-TYPE                   103                             10
D692V10, multiclass
                                clus
vv                               C11ORF57 MUTATED C11ORF57 WILD-TYPE
  COLON ADENOCARCINOMA                          6                309
  COLON MUCINOUS ADENOCARCINOMA                 2                 45
  RECTAL ADENOCARCINOMA                         3                103
  RECTAL MUCINOUS ADENOCARCINOMA                0                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  C11ORF57 MUTATED     7   0   1   2
  C11ORF57 WILD-TYPE 338   4  30  23
D692V11, multiclass
    clus
vv   C11ORF57 MUTATED C11ORF57 WILD-TYPE
  R0                7                338
  R1                0                  4
  R2                1                 30
  RX                2                 23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D692V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C11ORF57 MUTATED                                  0     2
  C11ORF57 WILD-TYPE                                1     9
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  C11ORF57 MUTATED                           0     4
  C11ORF57 WILD-TYPE                        22   222
D692V13, multiclass
                                  clus
vv                                 C11ORF57 MUTATED C11ORF57 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           2                  9
  BLACK OR AFRICAN AMERICAN                       0                 22
  WHITE                                           4                222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(693) Variable = ZNF439 MUTATION ANALYSIS
D693V1, survival
                  sevent
clus2                0   1
  ZNF439 MUTATED     5   0
  ZNF439 WILD-TYPE 373  93
  ZNF439 MUTATED ZNF439 WILD-TYPE 
               5              466 
  ZNF439 MUTATED ZNF439 WILD-TYPE 
               0               93 
$`ZNF439 MUTATED`
TCGA-AA-A010 TCGA-AZ-4315 TCGA-CA-6716 TCGA-CA-6717 TCGA-AG-A002 
       34.98        58.39        12.20        12.76        20.98 

$`ZNF439 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        33.01        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  ZNF439 MUTATED ZNF439 WILD-TYPE 
            12.2              0.0 
  ZNF439 MUTATED ZNF439 WILD-TYPE 
           58.39           148.01 
  ZNF439 MUTATED ZNF439 WILD-TYPE 
          20.980           20.155 
[1] "12.2 - 58.4 (21.0)" "0.0 - 148.0 (20.2)"
[1] "hr="     "9100000"
D693V2, continuous
D693V3, binary
                  cls
clus                 0   1
  ZNF439 MUTATED     4   1
  ZNF439 WILD-TYPE 362 118
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF439 MUTATED      4    1
  ZNF439 WILD-TYPE  362  118
        clus
vv       ZNF439 MUTATED ZNF439 WILD-TYPE
  COLON               4              362
  RECTUM              1              118
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZNF439 MUTATED         1        0        0         3         1         0
  ZNF439 WILD-TYPE      90        1       32       135         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF439 MUTATED           0          0          0          0        0
  ZNF439 WILD-TYPE        24         11         59         42       48
                  vv
clus               STAGE IVA STAGE IVB
  ZNF439 MUTATED           0         0
  ZNF439 WILD-TYPE        18         1
D693V4, multiclass
            clus
vv           ZNF439 MUTATED ZNF439 WILD-TYPE
  STAGE I                 1               90
  STAGE IA                0                1
  STAGE II                0               32
  STAGE IIA               3              135
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              0               59
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZNF439 MUTATED     0   1   3   1
  ZNF439 WILD-TYPE  17  91 326  49
D693V5, multiclass
    clus
vv   ZNF439 MUTATED ZNF439 WILD-TYPE
  T1              0               17
  T2              1               91
  T3              3              326
  T4              1               49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  ZNF439 MUTATED     5   0   0
  ZNF439 WILD-TYPE 282 113  87
D693V6, multiclass
    clus
vv   ZNF439 MUTATED ZNF439 WILD-TYPE
  N0              5              282
  N1              0              113
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D693V7, binary
                  cls
clus                 0   1
  ZNF439 MUTATED     5   0
  ZNF439 WILD-TYPE 370  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF439 MUTATED      5    0
  ZNF439 WILD-TYPE  370   65
   clus
vv  ZNF439 MUTATED ZNF439 WILD-TYPE
  0              5              370
  1              0               65
[1] 2 2
[1] FALSE
D693V8, binary
                  cls
clus                 0   1
  ZNF439 MUTATED     1   4
  ZNF439 WILD-TYPE 224 260
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF439 MUTATED      1    4
  ZNF439 WILD-TYPE  224  260
        clus
vv       ZNF439 MUTATED ZNF439 WILD-TYPE
  FEMALE              1              224
  MALE                4              260
[1] 2 2
[1] FALSE
D693V9, binary
                  cls
clus                 0   1
  ZNF439 MUTATED     5   0
  ZNF439 WILD-TYPE 345  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF439 MUTATED      5    0
  ZNF439 WILD-TYPE  345   22
     clus
vv    ZNF439 MUTATED ZNF439 WILD-TYPE
  NO               5              345
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ZNF439 MUTATED                      3                             1
  ZNF439 WILD-TYPE                  312                            46
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ZNF439 MUTATED                       1                              0
  ZNF439 WILD-TYPE                   105                             10
D693V10, multiclass
                                clus
vv                               ZNF439 MUTATED ZNF439 WILD-TYPE
  COLON ADENOCARCINOMA                        3              312
  COLON MUCINOUS ADENOCARCINOMA               1               46
  RECTAL ADENOCARCINOMA                       1              105
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ZNF439 MUTATED     3   0   0   2
  ZNF439 WILD-TYPE 342   4  31  23
D693V11, multiclass
    clus
vv   ZNF439 MUTATED ZNF439 WILD-TYPE
  R0              3              342
  R1              0                4
  R2              0               31
  RX              2               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D693V12, continuous
[1] "Remove cluster labels:" "ZNF439 MUTATED"        
clus
  ZNF439 MUTATED ZNF439 WILD-TYPE 
               2              456 
      TCGA-A6-2671       TCGA-A6-2672       TCGA-A6-2674       TCGA-A6-2676 
"ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" 
      TCGA-A6-2677       TCGA-A6-2678       TCGA-A6-2683       TCGA-A6-3807 
"ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" 
      TCGA-A6-3808       TCGA-A6-3809       TCGA-A6-3810       TCGA-A6-4105 
"ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" 
      TCGA-A6-5656       TCGA-A6-5657       TCGA-A6-5659       TCGA-A6-5660 
"ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" 
      TCGA-A6-5661       TCGA-A6-5662       TCGA-A6-5664       TCGA-A6-5665 
"ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" 
      TCGA-A6-5666       TCGA-A6-6137       TCGA-A6-6138       TCGA-A6-6141 
"ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" 
      TCGA-A6-6142       TCGA-A6-6648       TCGA-A6-6649       TCGA-A6-6651 
"ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" 
      TCGA-A6-6652       TCGA-A6-6653       TCGA-A6-6654       TCGA-A6-6780 
"ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" 
      TCGA-A6-6781       TCGA-A6-6782       TCGA-AA-3489       TCGA-AA-3492 
"ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" 
      TCGA-AA-3496       TCGA-AA-3502       TCGA-AA-3510       TCGA-AA-3511 
"ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" 
      TCGA-AA-3514       TCGA-AA-3516       TCGA-AA-3517       TCGA-AA-3518 
"ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" 
      TCGA-AA-3519       TCGA-AA-3520       TCGA-AA-3521       TCGA-AA-3522 
"ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" 
      TCGA-AA-3524       TCGA-AA-3525       TCGA-AA-3526       TCGA-AA-3527 
"ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" 
      TCGA-AA-3529       TCGA-AA-3530       TCGA-AA-3531       TCGA-AA-3532 
"ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" 
      TCGA-AA-3534       TCGA-AA-3538       TCGA-AA-3542       TCGA-AA-3543 
"ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" 
      TCGA-AA-3544       TCGA-AA-3548       TCGA-AA-3549       TCGA-AA-3552 
"ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" 
      TCGA-AA-3553       TCGA-AA-3554       TCGA-AA-3555       TCGA-AA-3556 
"ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" 
      TCGA-AA-3558       TCGA-AA-3560       TCGA-AA-3562       TCGA-AA-3655 
"ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" 
      TCGA-AA-3660       TCGA-AA-3662       TCGA-AA-3663       TCGA-AA-3664 
"ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" 
      TCGA-AA-3666       TCGA-AA-3667       TCGA-AA-3672       TCGA-AA-3673 
"ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" 
      TCGA-AA-3678       TCGA-AA-3679       TCGA-AA-3680       TCGA-AA-3681 
"ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" 
      TCGA-AA-3684       TCGA-AA-3685       TCGA-AA-3688       TCGA-AA-3692 
"ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" 
      TCGA-AA-3693       TCGA-AA-3695       TCGA-AA-3696       TCGA-AA-3697 
"ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" 
      TCGA-AA-3710       TCGA-AA-3712       TCGA-AA-3713       TCGA-AA-3715 
"ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" 
      TCGA-AA-3811       TCGA-AA-3812       TCGA-AA-3814       TCGA-AA-3815 
"ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" 
      TCGA-AA-3818       TCGA-AA-3819       TCGA-AA-3821       TCGA-AA-3831 
"ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" 
      TCGA-AA-3833       TCGA-AA-3837       TCGA-AA-3842       TCGA-AA-3844 
"ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" 
      TCGA-AA-3845       TCGA-AA-3846       TCGA-AA-3848       TCGA-AA-3850 
"ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" 
      TCGA-AA-3851       TCGA-AA-3852       TCGA-AA-3854       TCGA-AA-3855 
"ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" 
      TCGA-AA-3856       TCGA-AA-3858       TCGA-AA-3860       TCGA-AA-3861 
"ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" 
      TCGA-AA-3864       TCGA-AA-3866       TCGA-AA-3867       TCGA-AA-3869 
"ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" 
      TCGA-AA-3870       TCGA-AA-3872       TCGA-AA-3875       TCGA-AA-3877 
"ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" 
      TCGA-AA-3930       TCGA-AA-3939       TCGA-AA-3941       TCGA-AA-3947 
"ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" 
      TCGA-AA-3949       TCGA-AA-3950       TCGA-AA-3952       TCGA-AA-3955 
"ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" 
      TCGA-AA-3956       TCGA-AA-3966       TCGA-AA-3968       TCGA-AA-3971 
"ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" 
      TCGA-AA-3972       TCGA-AA-3973       TCGA-AA-3975       TCGA-AA-3976 
"ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" 
      TCGA-AA-3977       TCGA-AA-3979       TCGA-AA-3980       TCGA-AA-3982 
"ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" 
      TCGA-AA-3984       TCGA-AA-3986       TCGA-AA-3989       TCGA-AA-3994 
"ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" 
      TCGA-AA-A004       TCGA-AA-A00A       TCGA-AA-A00D       TCGA-AA-A00E 
"ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" 
      TCGA-AA-A00F       TCGA-AA-A00J       TCGA-AA-A00K       TCGA-AA-A00L 
"ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" 
      TCGA-AA-A00N       TCGA-AA-A00O       TCGA-AA-A00Q       TCGA-AA-A00R 
"ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" 
      TCGA-AA-A00U       TCGA-AA-A00W       TCGA-AA-A00Z       TCGA-AA-A017 
"ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" 
      TCGA-AA-A01D       TCGA-AA-A01F       TCGA-AA-A01G       TCGA-AA-A01I 
"ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" 
      TCGA-AA-A01K       TCGA-AA-A01P       TCGA-AA-A01Q       TCGA-AA-A01R 
"ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" 
      TCGA-AA-A01S       TCGA-AA-A01T       TCGA-AA-A01V       TCGA-AA-A01X 
"ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" 
      TCGA-AA-A01Z       TCGA-AA-A022       TCGA-AA-A024       TCGA-AA-A029 
"ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" 
      TCGA-AA-A02F       TCGA-AA-A02H       TCGA-AA-A02J       TCGA-AA-A02K 
"ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" 
      TCGA-AA-A02O       TCGA-AA-A02W       TCGA-AA-A02Y       TCGA-AA-A03F 
"ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" 
      TCGA-AA-A03J       TCGA-AD-5900       TCGA-AD-6548       TCGA-AD-6888 
"ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" 
      TCGA-AD-6889       TCGA-AD-6890       TCGA-AD-6895       TCGA-AD-6899 
"ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" 
      TCGA-AD-6901       TCGA-AD-6963       TCGA-AD-6964       TCGA-AD-6965 
"ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" 
      TCGA-AU-3779       TCGA-AU-6004       TCGA-AY-4070       TCGA-AY-4071 
"ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" 
      TCGA-AY-5543       TCGA-AY-6196       TCGA-AY-6197       TCGA-AY-6386 
"ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" 
      TCGA-AZ-4323       TCGA-AZ-4616       TCGA-AZ-4682       TCGA-AZ-5403 
"ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" 
      TCGA-AZ-5407       TCGA-AZ-6598       TCGA-AZ-6599       TCGA-AZ-6600 
"ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" 
      TCGA-AZ-6601       TCGA-AZ-6603       TCGA-AZ-6605       TCGA-AZ-6606 
"ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" 
      TCGA-AZ-6607       TCGA-AZ-6608       TCGA-CK-4947       TCGA-CK-4948 
"ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" 
      TCGA-CK-4950       TCGA-CK-4952       TCGA-CM-4743       TCGA-CM-4744 
"ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" 
      TCGA-CM-4746       TCGA-CM-4747       TCGA-CM-4752       TCGA-CM-5341 
"ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" 
      TCGA-CM-5344       TCGA-CM-5348       TCGA-CM-5349       TCGA-CM-5860 
"ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" 
      TCGA-CM-5861       TCGA-CM-5862       TCGA-CM-5863       TCGA-CM-5864 
"ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" 
      TCGA-CM-5868       TCGA-CM-6161       TCGA-CM-6162       TCGA-CM-6163 
"ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" 
      TCGA-CM-6164       TCGA-CM-6165       TCGA-CM-6166       TCGA-CM-6167 
"ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" 
      TCGA-CM-6168       TCGA-CM-6169       TCGA-CM-6170       TCGA-CM-6171 
"ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" 
      TCGA-CM-6172       TCGA-CM-6674       TCGA-CM-6675       TCGA-CM-6676 
"ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" 
      TCGA-CM-6677       TCGA-CM-6678       TCGA-CM-6679       TCGA-CM-6680 
"ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" 
      TCGA-D5-5537       TCGA-D5-5538       TCGA-D5-5539       TCGA-D5-5540 
"ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" 
      TCGA-D5-5541       TCGA-D5-6529       TCGA-D5-6532       TCGA-D5-6533 
"ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" 
      TCGA-D5-6534       TCGA-D5-6535       TCGA-D5-6536       TCGA-D5-6537 
"ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" 
      TCGA-D5-6538       TCGA-D5-6539       TCGA-D5-6540       TCGA-D5-6541 
"ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" 
      TCGA-D5-6898       TCGA-D5-6920       TCGA-D5-6922       TCGA-D5-6923 
"ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" 
      TCGA-D5-6924       TCGA-D5-6926       TCGA-D5-6927       TCGA-D5-6928 
"ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" 
      TCGA-D5-6929       TCGA-D5-6930       TCGA-D5-6931       TCGA-D5-6932 
"ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" 
      TCGA-D5-7000       TCGA-DM-A0X9       TCGA-DM-A0XD       TCGA-DM-A0XF 
"ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" 
      TCGA-DM-A1D0       TCGA-DM-A1D4       TCGA-DM-A1D6       TCGA-DM-A1D7 
"ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" 
      TCGA-DM-A1D8       TCGA-DM-A1D9       TCGA-DM-A1DA       TCGA-DM-A1DB 
"ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" 
      TCGA-DM-A1HA       TCGA-DM-A1HB       TCGA-DM-A282       TCGA-DM-A285 
"ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" 
      TCGA-DM-A28C       TCGA-DM-A28E       TCGA-DM-A28F       TCGA-DM-A28G 
"ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" 
      TCGA-DM-A28H       TCGA-DM-A28K       TCGA-F4-6459       TCGA-F4-6460 
"ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" 
      TCGA-F4-6569       TCGA-F4-6570       TCGA-F4-6703       TCGA-F4-6704 
"ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" 
      TCGA-F4-6806       TCGA-F4-6807       TCGA-F4-6808       TCGA-F4-6809 
"ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" 
      TCGA-F4-6854       TCGA-F4-6855       TCGA-F4-6856       TCGA-G4-6293 
"ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" 
      TCGA-G4-6299       TCGA-G4-6303       TCGA-G4-6304       TCGA-G4-6306 
"ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" 
      TCGA-G4-6307       TCGA-G4-6309       TCGA-G4-6310       TCGA-G4-6315 
"ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" 
      TCGA-G4-6317       TCGA-G4-6321       TCGA-G4-6323       TCGA-G4-6586 
"ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" 
      TCGA-G4-6588       TCGA-G4-6625       TCGA-G4-6626       TCGA-G4-6628 
"ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" 
      TCGA-AF-2687       TCGA-AF-2689       TCGA-AF-2691       TCGA-AF-2692 
"ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" 
      TCGA-AF-2693       TCGA-AF-3400       TCGA-AF-3913       TCGA-AF-4110 
"ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" 
      TCGA-AF-5654       TCGA-AF-6136       TCGA-AF-6655       TCGA-AF-6672 
"ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" 
      TCGA-AG-3574       TCGA-AG-3575       TCGA-AG-3578       TCGA-AG-3580 
"ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" 
      TCGA-AG-3581       TCGA-AG-3582       TCGA-AG-3583       TCGA-AG-3584 
"ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" 
      TCGA-AG-3586       TCGA-AG-3587       TCGA-AG-3593       TCGA-AG-3594 
"ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" 
      TCGA-AG-3598       TCGA-AG-3599       TCGA-AG-3600       TCGA-AG-3601 
"ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" 
      TCGA-AG-3602       TCGA-AG-3605       TCGA-AG-3608       TCGA-AG-3609 
"ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" 
      TCGA-AG-3611       TCGA-AG-3612       TCGA-AG-3726       TCGA-AG-3727 
"ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" 
      TCGA-AG-3731       TCGA-AG-3732       TCGA-AG-3742       TCGA-AG-3878 
"ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" 
      TCGA-AG-3881       TCGA-AG-3882       TCGA-AG-3883       TCGA-AG-3885 
"ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" 
      TCGA-AG-3887       TCGA-AG-3890       TCGA-AG-3892       TCGA-AG-3893 
"ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" 
      TCGA-AG-3894       TCGA-AG-3896       TCGA-AG-3898       TCGA-AG-3901 
"ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" 
      TCGA-AG-3902       TCGA-AG-3909       TCGA-AG-3999       TCGA-AG-4001 
"ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" 
      TCGA-AG-4005       TCGA-AG-4007       TCGA-AG-4008       TCGA-AG-4015 
"ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" 
      TCGA-AG-A008       TCGA-AG-A00C       TCGA-AG-A00H       TCGA-AG-A00Y 
"ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" 
      TCGA-AG-A011       TCGA-AG-A014       TCGA-AG-A015       TCGA-AG-A016 
"ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" 
      TCGA-AG-A01L       TCGA-AG-A01W       TCGA-AG-A01Y       TCGA-AG-A020 
"ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" 
      TCGA-AG-A025       TCGA-AG-A026       TCGA-AG-A02G       TCGA-AG-A02N 
"ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" 
      TCGA-AG-A02X       TCGA-AG-A032       TCGA-AG-A036       TCGA-AH-6544 
"ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" 
      TCGA-AH-6547       TCGA-AH-6643       TCGA-AH-6644       TCGA-CI-6622 
"ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" 
      TCGA-DC-5337       TCGA-DC-5869       TCGA-DC-6155       TCGA-DC-6157 
"ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" 
      TCGA-DC-6158       TCGA-DC-6160       TCGA-DC-6681       TCGA-DC-6682 
"ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" 
      TCGA-DC-6683       TCGA-DY-A0XA       TCGA-DY-A1DC       TCGA-DY-A1DD 
"ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" 
      TCGA-DY-A1DF       TCGA-DY-A1DG       TCGA-DY-A1H8       TCGA-EI-6506 
"ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" 
      TCGA-EI-6507       TCGA-EI-6508       TCGA-EI-6510       TCGA-F5-6464 
"ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" 
      TCGA-F5-6465       TCGA-F5-6571       TCGA-F5-6702       TCGA-F5-6811 
"ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" 
      TCGA-F5-6812       TCGA-F5-6813       TCGA-G5-6235       TCGA-G5-6641 
"ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" "ZNF439 WILD-TYPE" 
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF439 MUTATED                                  0     2
  ZNF439 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZNF439 MUTATED                           0     1
  ZNF439 WILD-TYPE                        22   225
D693V13, multiclass
                                  clus
vv                                 ZNF439 MUTATED ZNF439 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                9
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         1              225
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(694) Variable = UBA3 MUTATION ANALYSIS
D694V1, survival
                sevent
clus2              0   1
  UBA3 MUTATED     5   1
  UBA3 WILD-TYPE 373  92
  UBA3 MUTATED UBA3 WILD-TYPE 
             6            465 
  UBA3 MUTATED UBA3 WILD-TYPE 
             1             92 
$`UBA3 MUTATED`
TCGA-A6-3809 TCGA-AA-3489 TCGA-AA-3510 TCGA-AZ-5407 TCGA-CM-5349 TCGA-AG-A002 
       32.75         7.04        63.98        88.21        30.08        20.98 

$`UBA3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        19.66        20.28         3.02         1.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       29.06        22.03        22.98        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  UBA3 MUTATED UBA3 WILD-TYPE 
          7.04           0.00 
  UBA3 MUTATED UBA3 WILD-TYPE 
         88.21         148.01 
  UBA3 MUTATED UBA3 WILD-TYPE 
        31.415         20.050 
[1] "7.0 - 88.2 (31.4)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.8"
D694V2, continuous
D694V3, binary
                cls
clus               0   1
  UBA3 MUTATED     6   1
  UBA3 WILD-TYPE 360 118
[1] "tbl2"
                cls
clus             [,1] [,2]
  UBA3 MUTATED      6    1
  UBA3 WILD-TYPE  360  118
        clus
vv       UBA3 MUTATED UBA3 WILD-TYPE
  COLON             6            360
  RECTUM            1            118
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  UBA3 MUTATED         2        0        2         2         1         0
  UBA3 WILD-TYPE      89        1       30       136         9         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  UBA3 MUTATED           0          0          0          0        0         0
  UBA3 WILD-TYPE        24         11         59         42       48        18
                vv
clus             STAGE IVB
  UBA3 MUTATED           0
  UBA3 WILD-TYPE         1
D694V4, multiclass
            clus
vv           UBA3 MUTATED UBA3 WILD-TYPE
  STAGE I               2             89
  STAGE IA              0              1
  STAGE II              2             30
  STAGE IIA             2            136
  STAGE IIB             1              9
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            0             59
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  UBA3 MUTATED     1   1   4   1
  UBA3 WILD-TYPE  16  91 325  49
D694V5, multiclass
    clus
vv   UBA3 MUTATED UBA3 WILD-TYPE
  T1            1             16
  T2            1             91
  T3            4            325
  T4            1             49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  UBA3 MUTATED     7   0   0
  UBA3 WILD-TYPE 280 113  87
D694V6, multiclass
    clus
vv   UBA3 MUTATED UBA3 WILD-TYPE
  N0            7            280
  N1            0            113
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D694V7, binary
                cls
clus               0   1
  UBA3 MUTATED     7   0
  UBA3 WILD-TYPE 368  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  UBA3 MUTATED      7    0
  UBA3 WILD-TYPE  368   65
   clus
vv  UBA3 MUTATED UBA3 WILD-TYPE
  0            7            368
  1            0             65
[1] 2 2
[1] FALSE
D694V8, binary
                cls
clus               0   1
  UBA3 MUTATED     4   3
  UBA3 WILD-TYPE 221 261
[1] "tbl2"
                cls
clus             [,1] [,2]
  UBA3 MUTATED      4    3
  UBA3 WILD-TYPE  221  261
        clus
vv       UBA3 MUTATED UBA3 WILD-TYPE
  FEMALE            4            221
  MALE              3            261
[1] 2 2
[1] FALSE
D694V9, binary
                cls
clus               0   1
  UBA3 MUTATED     6   0
  UBA3 WILD-TYPE 344  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  UBA3 MUTATED      6    0
  UBA3 WILD-TYPE  344   22
     clus
vv    UBA3 MUTATED UBA3 WILD-TYPE
  NO             6            344
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  UBA3 MUTATED                      5                             1
  UBA3 WILD-TYPE                  310                            46
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  UBA3 MUTATED                       1                              0
  UBA3 WILD-TYPE                   105                             10
D694V10, multiclass
                                clus
vv                               UBA3 MUTATED UBA3 WILD-TYPE
  COLON ADENOCARCINOMA                      5            310
  COLON MUCINOUS ADENOCARCINOMA             1             46
  RECTAL ADENOCARCINOMA                     1            105
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  UBA3 MUTATED     6   0   0   0
  UBA3 WILD-TYPE 339   4  31  25
D694V11, multiclass
    clus
vv   UBA3 MUTATED UBA3 WILD-TYPE
  R0            6            339
  R1            0              4
  R2            0             31
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D694V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  UBA3 MUTATED                                  0     0
  UBA3 WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  UBA3 MUTATED                           0     3
  UBA3 WILD-TYPE                        22   223
D694V13, multiclass
                                  clus
vv                                 UBA3 MUTATED UBA3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       3            223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(695) Variable = KIAA0564 MUTATION ANALYSIS
D695V1, survival
                    sevent
clus2                  0   1
  KIAA0564 MUTATED    20   4
  KIAA0564 WILD-TYPE 358  89
  KIAA0564 MUTATED KIAA0564 WILD-TYPE 
                24                447 
  KIAA0564 MUTATED KIAA0564 WILD-TYPE 
                 4                 89 
$`KIAA0564 MUTATED`
TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3492 TCGA-AA-3525 
       24.39        20.12        19.66        20.28         3.02         8.05 
TCGA-AA-3554 TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A010 TCGA-AD-6889 TCGA-AY-6197 
       17.95        25.02         4.01        34.98        56.55        21.44 
TCGA-AZ-4315 TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-6171 TCGA-D5-6540 TCGA-DM-A1DB 
       58.39        12.76        10.06        14.04        16.14        44.32 
TCGA-DM-A1HA TCGA-G4-6588 TCGA-G4-6628 TCGA-AG-3902 TCGA-AG-A002 TCGA-AG-A01Y 
      131.51        26.17        79.69        32.02        20.98        64.01 

$`KIAA0564 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
       25.08        25.18        24.16        21.76        24.69        23.87 
TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
        7.04         1.02        35.01        63.98         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
       13.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
       36.03        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       21.01        13.02        24.00        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 
       40.96         0.07        21.37        15.52         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4323 
       27.09        16.31         0.95        33.01        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.07        12.20        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       12.99        13.02        15.02        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       12.49        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
        7.50       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       35.80        91.79        46.75        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3909 TCGA-AG-3999 
       35.01        14.01         1.02        48.03        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       12.00        70.03        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  KIAA0564 MUTATED KIAA0564 WILD-TYPE 
              3.02               0.00 
  KIAA0564 MUTATED KIAA0564 WILD-TYPE 
            131.51             148.01 
  KIAA0564 MUTATED KIAA0564 WILD-TYPE 
             21.21              20.02 
[1] "3.0 - 131.5 (21.2)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.4"
D695V2, continuous
D695V3, binary
                    cls
clus                   0   1
  KIAA0564 MUTATED    22   3
  KIAA0564 WILD-TYPE 344 116
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0564 MUTATED     22    3
  KIAA0564 WILD-TYPE  344  116
        clus
vv       KIAA0564 MUTATED KIAA0564 WILD-TYPE
  COLON                22                344
  RECTUM                3                116
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KIAA0564 MUTATED         5        0        2        11         3         0
  KIAA0564 WILD-TYPE      86        1       30       127         7         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIAA0564 MUTATED           0          0          1          2        0
  KIAA0564 WILD-TYPE        24         11         58         40       48
                    vv
clus                 STAGE IVA STAGE IVB
  KIAA0564 MUTATED           0         0
  KIAA0564 WILD-TYPE        18         1
D695V4, multiclass
            clus
vv           KIAA0564 MUTATED KIAA0564 WILD-TYPE
  STAGE I                   5                 86
  STAGE IA                  0                  1
  STAGE II                  2                 30
  STAGE IIA                11                127
  STAGE IIB                 3                  7
  STAGE IIC                 0                  1
  STAGE III                 0                 24
  STAGE IIIA                0                 11
  STAGE IIIB                1                 58
  STAGE IIIC                2                 40
  STAGE IV                  0                 48
  STAGE IVA                 0                 18
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  KIAA0564 MUTATED     0   6  15   4
  KIAA0564 WILD-TYPE  17  86 314  46
D695V5, multiclass
    clus
vv   KIAA0564 MUTATED KIAA0564 WILD-TYPE
  T1                0                 17
  T2                6                 86
  T3               15                314
  T4                4                 46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  KIAA0564 MUTATED    22   2   1
  KIAA0564 WILD-TYPE 265 111  86
D695V6, multiclass
    clus
vv   KIAA0564 MUTATED KIAA0564 WILD-TYPE
  N0               22                265
  N1                2                111
  N2                1                 86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D695V7, binary
                    cls
clus                   0   1
  KIAA0564 MUTATED    20   0
  KIAA0564 WILD-TYPE 355  65
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0564 MUTATED     20    0
  KIAA0564 WILD-TYPE  355   65
   clus
vv  KIAA0564 MUTATED KIAA0564 WILD-TYPE
  0               20                355
  1                0                 65
[1] 2 2
[1] FALSE
D695V8, binary
                    cls
clus                   0   1
  KIAA0564 MUTATED     7  18
  KIAA0564 WILD-TYPE 218 246
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0564 MUTATED      7   18
  KIAA0564 WILD-TYPE  218  246
        clus
vv       KIAA0564 MUTATED KIAA0564 WILD-TYPE
  FEMALE                7                218
  MALE                 18                246
[1] 2 2
[1] FALSE
D695V9, binary
                    cls
clus                   0   1
  KIAA0564 MUTATED    19   0
  KIAA0564 WILD-TYPE 331  22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0564 MUTATED     19    0
  KIAA0564 WILD-TYPE  331   22
     clus
vv    KIAA0564 MUTATED KIAA0564 WILD-TYPE
  NO                19                331
  YES                0                 22
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  KIAA0564 MUTATED                     17                             5
  KIAA0564 WILD-TYPE                  298                            42
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  KIAA0564 MUTATED                       3                              0
  KIAA0564 WILD-TYPE                   103                             10
D695V10, multiclass
                                clus
vv                               KIAA0564 MUTATED KIAA0564 WILD-TYPE
  COLON ADENOCARCINOMA                         17                298
  COLON MUCINOUS ADENOCARCINOMA                 5                 42
  RECTAL ADENOCARCINOMA                         3                103
  RECTAL MUCINOUS ADENOCARCINOMA                0                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  KIAA0564 MUTATED    16   0   0   2
  KIAA0564 WILD-TYPE 329   4  31  23
D695V11, multiclass
    clus
vv   KIAA0564 MUTATED KIAA0564 WILD-TYPE
  R0               16                329
  R1                0                  4
  R2                0                 31
  RX                2                 23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D695V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KIAA0564 MUTATED                                  0     3
  KIAA0564 WILD-TYPE                                1     8
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  KIAA0564 MUTATED                           0    12
  KIAA0564 WILD-TYPE                        22   214
D695V13, multiclass
                                  clus
vv                                 KIAA0564 MUTATED KIAA0564 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           3                  8
  BLACK OR AFRICAN AMERICAN                       0                 22
  WHITE                                          12                214
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(696) Variable = ATP8B2 MUTATION ANALYSIS
D696V1, survival
                  sevent
clus2                0   1
  ATP8B2 MUTATED    14   4
  ATP8B2 WILD-TYPE 364  89
  ATP8B2 MUTATED ATP8B2 WILD-TYPE 
              18              453 
  ATP8B2 MUTATED ATP8B2 WILD-TYPE 
               4               89 
$`ATP8B2 MUTATED`
TCGA-A6-5665 TCGA-AA-3663 TCGA-AA-3833 TCGA-AA-3950 TCGA-AA-3966 TCGA-AA-A010 
       22.06         6.97        15.95        24.00         2.01        34.98 
TCGA-CA-6717 TCGA-CK-5916 TCGA-CM-4746 TCGA-CM-4752 TCGA-CM-5861 TCGA-D5-6537 
       12.76        21.14        37.02        13.02        15.02         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-DM-A282 TCGA-DM-A28F TCGA-F4-6570 TCGA-AG-A002 
        1.51        12.00       139.17        35.97         6.18        20.98 

$`ATP8B2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        33.01        26.01         2.01        20.98        34.03 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07        12.20        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4747 
       82.95         1.91       124.27        23.05        20.02        25.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 
       29.06        22.03        22.98        30.08        32.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       43.27        15.12        17.85        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6932 TCGA-D5-7000 
        9.04         9.44        11.64         4.80        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H 
      135.65         6.12        81.37       119.93        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 
       98.24         8.61        31.96        35.74        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  ATP8B2 MUTATED ATP8B2 WILD-TYPE 
            1.51             0.00 
  ATP8B2 MUTATED ATP8B2 WILD-TYPE 
          139.17           148.01 
  ATP8B2 MUTATED ATP8B2 WILD-TYPE 
          15.485           20.280 
[1] "1.5 - 139.2 (15.5)" "0.0 - 148.0 (20.3)"
[1] "hr=" "1.4"
D696V2, continuous
D696V3, binary
                  cls
clus                 0   1
  ATP8B2 MUTATED    17   1
  ATP8B2 WILD-TYPE 349 118
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP8B2 MUTATED     17    1
  ATP8B2 WILD-TYPE  349  118
        clus
vv       ATP8B2 MUTATED ATP8B2 WILD-TYPE
  COLON              17              349
  RECTUM              1              118
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ATP8B2 MUTATED         3        0        1        10         1         0
  ATP8B2 WILD-TYPE      88        1       31       128         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ATP8B2 MUTATED           0          0          2          1        0
  ATP8B2 WILD-TYPE        24         11         57         41       48
                  vv
clus               STAGE IVA STAGE IVB
  ATP8B2 MUTATED           0         0
  ATP8B2 WILD-TYPE        18         1
D696V4, multiclass
            clus
vv           ATP8B2 MUTATED ATP8B2 WILD-TYPE
  STAGE I                 3               88
  STAGE IA                0                1
  STAGE II                1               31
  STAGE IIA              10              128
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              2               57
  STAGE IIIC              1               41
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ATP8B2 MUTATED     1   2  13   2
  ATP8B2 WILD-TYPE  16  90 316  48
D696V5, multiclass
    clus
vv   ATP8B2 MUTATED ATP8B2 WILD-TYPE
  T1              1               16
  T2              2               90
  T3             13              316
  T4              2               48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  ATP8B2 MUTATED    15   2   1
  ATP8B2 WILD-TYPE 272 111  86
D696V6, multiclass
    clus
vv   ATP8B2 MUTATED ATP8B2 WILD-TYPE
  N0             15              272
  N1              2              111
  N2              1               86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D696V7, binary
                  cls
clus                 0   1
  ATP8B2 MUTATED    17   0
  ATP8B2 WILD-TYPE 358  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP8B2 MUTATED     17    0
  ATP8B2 WILD-TYPE  358   65
   clus
vv  ATP8B2 MUTATED ATP8B2 WILD-TYPE
  0             17              358
  1              0               65
[1] 2 2
[1] FALSE
D696V8, binary
                  cls
clus                 0   1
  ATP8B2 MUTATED     9   9
  ATP8B2 WILD-TYPE 216 255
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP8B2 MUTATED      9    9
  ATP8B2 WILD-TYPE  216  255
        clus
vv       ATP8B2 MUTATED ATP8B2 WILD-TYPE
  FEMALE              9              216
  MALE                9              255
[1] 2 2
[1] FALSE
D696V9, binary
                  cls
clus                 0   1
  ATP8B2 MUTATED    14   0
  ATP8B2 WILD-TYPE 336  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP8B2 MUTATED     14    0
  ATP8B2 WILD-TYPE  336   22
     clus
vv    ATP8B2 MUTATED ATP8B2 WILD-TYPE
  NO              14              336
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ATP8B2 MUTATED                     13                             4
  ATP8B2 WILD-TYPE                  302                            43
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ATP8B2 MUTATED                       1                              0
  ATP8B2 WILD-TYPE                   105                             10
D696V10, multiclass
                                clus
vv                               ATP8B2 MUTATED ATP8B2 WILD-TYPE
  COLON ADENOCARCINOMA                       13              302
  COLON MUCINOUS ADENOCARCINOMA               4               43
  RECTAL ADENOCARCINOMA                       1              105
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ATP8B2 MUTATED    13   0   0   2
  ATP8B2 WILD-TYPE 332   4  31  23
D696V11, multiclass
    clus
vv   ATP8B2 MUTATED ATP8B2 WILD-TYPE
  R0             13              332
  R1              0                4
  R2              0               31
  RX              2               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D696V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ATP8B2 MUTATED                                  0     1
  ATP8B2 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ATP8B2 MUTATED                           2     9
  ATP8B2 WILD-TYPE                        20   217
D696V13, multiclass
                                  clus
vv                                 ATP8B2 MUTATED ATP8B2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     2               20
  WHITE                                         9              217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(697) Variable = PNPLA5 MUTATION ANALYSIS
D697V1, survival
                  sevent
clus2                0   1
  PNPLA5 MUTATED     9   1
  PNPLA5 WILD-TYPE 369  92
  PNPLA5 MUTATED PNPLA5 WILD-TYPE 
              10              461 
  PNPLA5 MUTATED PNPLA5 WILD-TYPE 
               1               92 
$`PNPLA5 MUTATED`
TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3877 TCGA-AU-6004 TCGA-CA-5254 TCGA-CK-5913 
        3.02        63.98        31.00        27.09        12.69        51.32 
TCGA-G4-6586 TCGA-G4-6628 TCGA-AG-3598 TCGA-EI-6507 
       35.80        79.69        50.04        19.96 

$`PNPLA5 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 
       24.03        27.02        29.98        18.05         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
        0.20        14.50        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5255 
       29.56         5.23        11.74         3.19         1.61         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 
       13.78        26.17        91.79        46.75        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3599 TCGA-AG-3600 
        1.02        46.03        34.03         2.01        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  PNPLA5 MUTATED PNPLA5 WILD-TYPE 
            3.02             0.00 
  PNPLA5 MUTATED PNPLA5 WILD-TYPE 
           79.69           148.01 
  PNPLA5 MUTATED PNPLA5 WILD-TYPE 
           33.40            20.05 
[1] "3.0 - 79.7 (33.4)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "3"  
D697V2, continuous
D697V3, binary
                  cls
clus                 0   1
  PNPLA5 MUTATED    10   2
  PNPLA5 WILD-TYPE 356 117
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PNPLA5 MUTATED     10    2
  PNPLA5 WILD-TYPE  356  117
        clus
vv       PNPLA5 MUTATED PNPLA5 WILD-TYPE
  COLON              10              356
  RECTUM              2              117
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PNPLA5 MUTATED         3        0        2         5         1         0
  PNPLA5 WILD-TYPE      88        1       30       133         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PNPLA5 MUTATED           0          0          0          0        1
  PNPLA5 WILD-TYPE        24         11         59         42       47
                  vv
clus               STAGE IVA STAGE IVB
  PNPLA5 MUTATED           0         0
  PNPLA5 WILD-TYPE        18         1
D697V4, multiclass
            clus
vv           PNPLA5 MUTATED PNPLA5 WILD-TYPE
  STAGE I                 3               88
  STAGE IA                0                1
  STAGE II                2               30
  STAGE IIA               5              133
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              0               59
  STAGE IIIC              0               42
  STAGE IV                1               47
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  PNPLA5 MUTATED     1   2   8   1
  PNPLA5 WILD-TYPE  16  90 321  49
D697V5, multiclass
    clus
vv   PNPLA5 MUTATED PNPLA5 WILD-TYPE
  T1              1               16
  T2              2               90
  T3              8              321
  T4              1               49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  PNPLA5 MUTATED    11   0   1
  PNPLA5 WILD-TYPE 276 113  86
D697V6, multiclass
    clus
vv   PNPLA5 MUTATED PNPLA5 WILD-TYPE
  N0             11              276
  N1              0              113
  N2              1               86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D697V7, binary
                  cls
clus                 0   1
  PNPLA5 MUTATED     9   1
  PNPLA5 WILD-TYPE 366  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PNPLA5 MUTATED      9    1
  PNPLA5 WILD-TYPE  366   64
   clus
vv  PNPLA5 MUTATED PNPLA5 WILD-TYPE
  0              9              366
  1              1               64
[1] 2 2
[1] FALSE
D697V8, binary
                  cls
clus                 0   1
  PNPLA5 MUTATED     8   4
  PNPLA5 WILD-TYPE 217 260
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PNPLA5 MUTATED      8    4
  PNPLA5 WILD-TYPE  217  260
        clus
vv       PNPLA5 MUTATED PNPLA5 WILD-TYPE
  FEMALE              8              217
  MALE                4              260
[1] 2 2
[1] FALSE
D697V9, binary
                  cls
clus                 0   1
  PNPLA5 MUTATED     9   0
  PNPLA5 WILD-TYPE 341  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PNPLA5 MUTATED      9    0
  PNPLA5 WILD-TYPE  341   22
     clus
vv    PNPLA5 MUTATED PNPLA5 WILD-TYPE
  NO               9              341
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PNPLA5 MUTATED                      9                             1
  PNPLA5 WILD-TYPE                  306                            46
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PNPLA5 MUTATED                       2                              0
  PNPLA5 WILD-TYPE                   104                             10
D697V10, multiclass
                                clus
vv                               PNPLA5 MUTATED PNPLA5 WILD-TYPE
  COLON ADENOCARCINOMA                        9              306
  COLON MUCINOUS ADENOCARCINOMA               1               46
  RECTAL ADENOCARCINOMA                       2              104
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  PNPLA5 MUTATED     8   0   1   3
  PNPLA5 WILD-TYPE 337   4  30  22
D697V11, multiclass
    clus
vv   PNPLA5 MUTATED PNPLA5 WILD-TYPE
  R0              8              337
  R1              0                4
  R2              1               30
  RX              3               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D697V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PNPLA5 MUTATED                                  0     1
  PNPLA5 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  PNPLA5 MUTATED                           0     6
  PNPLA5 WILD-TYPE                        22   220
D697V13, multiclass
                                  clus
vv                                 PNPLA5 MUTATED PNPLA5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         6              220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(698) Variable = VPS13B MUTATION ANALYSIS
D698V1, survival
                  sevent
clus2                0   1
  VPS13B MUTATED    45  13
  VPS13B WILD-TYPE 333  80
  VPS13B MUTATED VPS13B WILD-TYPE 
              58              413 
  VPS13B MUTATED VPS13B WILD-TYPE 
              13               80 
$`VPS13B MUTATED`
TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-6653 TCGA-A6-6781 TCGA-AA-3492 TCGA-AA-3496 
       29.19        33.53        24.39        19.66         3.02         1.02 
TCGA-AA-3516 TCGA-AA-3529 TCGA-AA-3555 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3713 
       13.02         0.00        29.95        14.01         0.92        19.04 
TCGA-AA-3715 TCGA-AA-3864 TCGA-AA-3956 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-A00N 
       19.04        53.00        34.03        25.02        27.02         4.01 
TCGA-AA-A010 TCGA-AA-A01R TCGA-AD-6964 TCGA-AY-4071 TCGA-AY-6197 TCGA-AZ-4315 
       34.98        35.01        10.88         0.95        21.44        58.39 
TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       62.79        49.41        12.10        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-5913 TCGA-CM-4746 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-6162 
       14.30        51.32        37.02        30.08        32.02        12.00 
TCGA-CM-6164 TCGA-CM-6171 TCGA-CM-6674 TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6535 
       29.03        14.04        12.95        19.59        55.92        15.12 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6927 TCGA-D5-6930 TCGA-D5-6931 TCGA-F4-6805 
       16.14        15.58         9.44         1.51        12.00        34.42 
TCGA-G4-6293 TCGA-G4-6628 TCGA-AG-3580 TCGA-AG-3605 TCGA-AG-A002 TCGA-AG-A026 
      133.18        79.69         8.02         0.99        20.98         1.94 
TCGA-AG-A02N TCGA-DC-6155 TCGA-DY-A0XA TCGA-DY-A1DD 
       61.97        13.97       126.44        57.24 

$`VPS13B WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       32.91        31.63        30.44        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 
       24.16        21.76        24.69        23.87        20.12        20.28 
TCGA-AA-3489 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        7.04        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
       19.07        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       24.00        17.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        2.01        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 
       32.05         0.99        31.07        31.07        30.05        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       20.98         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       34.06        26.01        24.00        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S 
       12.00        31.00        31.00        38.07         1.02         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-5543 TCGA-AY-6386 
        0.20        14.50        27.09        16.31        33.01        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6599 
        1.41         5.13       106.75        22.36        88.21         6.77 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CK-4947 
       12.69         3.06         3.25         3.29         0.07        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 
      148.01        85.45        15.62        49.08         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4747 
       82.95         1.91       124.27        23.05        20.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5861 TCGA-CM-5862 
       13.02        29.06        22.03        22.98        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6165 
       15.02        15.02        17.03        15.02         2.96        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 
       21.99        14.99        12.99        13.02        15.02        11.01 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       45.40        12.26        56.09        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6898 
       43.27        17.85         4.80        17.13        12.49         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6928 
        3.68         4.41        12.43        14.30         9.04        11.64 
TCGA-D5-6929 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
        4.80        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
       35.31        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 
       35.80        26.17        91.79        46.75        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
       32.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A02G 
       12.00        70.03        64.01        10.98        49.97        38.96 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6157 TCGA-DC-6158 
       78.12         7.17        15.02         5.03        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC 
       19.99         5.95         4.01         5.03         5.29        41.36 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  VPS13B MUTATED VPS13B WILD-TYPE 
               0                0 
  VPS13B MUTATED VPS13B WILD-TYPE 
          133.18           148.01 
  VPS13B MUTATED VPS13B WILD-TYPE 
          19.315           20.550 
[1] "0.0 - 133.2 (19.3)" "0.0 - 148.0 (20.6)"
[1] "hr=" "1.1"
D698V2, continuous
D698V3, binary
                  cls
clus                 0   1
  VPS13B MUTATED    51   8
  VPS13B WILD-TYPE 315 111
[1] "tbl2"
                  cls
clus               [,1] [,2]
  VPS13B MUTATED     51    8
  VPS13B WILD-TYPE  315  111
        clus
vv       VPS13B MUTATED VPS13B WILD-TYPE
  COLON              51              315
  RECTUM              8              111
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  VPS13B MUTATED        10        0        9        19         3         0
  VPS13B WILD-TYPE      81        1       23       119         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  VPS13B MUTATED           4          2          4          4        3
  VPS13B WILD-TYPE        20          9         55         38       45
                  vv
clus               STAGE IVA STAGE IVB
  VPS13B MUTATED           0         0
  VPS13B WILD-TYPE        18         1
D698V4, multiclass
            clus
vv           VPS13B MUTATED VPS13B WILD-TYPE
  STAGE I                10               81
  STAGE IA                0                1
  STAGE II                9               23
  STAGE IIA              19              119
  STAGE IIB               3                7
  STAGE IIC               0                1
  STAGE III               4               20
  STAGE IIIA              2                9
  STAGE IIIB              4               55
  STAGE IIIC              4               38
  STAGE IV                3               45
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  VPS13B MUTATED     2  10  39   9
  VPS13B WILD-TYPE  15  82 290  41
D698V5, multiclass
    clus
vv   VPS13B MUTATED VPS13B WILD-TYPE
  T1              2               15
  T2             10               82
  T3             39              290
  T4              9               41
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  VPS13B MUTATED    43  11   6
  VPS13B WILD-TYPE 244 102  81
D698V6, multiclass
    clus
vv   VPS13B MUTATED VPS13B WILD-TYPE
  N0             43              244
  N1             11              102
  N2              6               81
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D698V7, binary
                  cls
clus                 0   1
  VPS13B MUTATED    47   3
  VPS13B WILD-TYPE 328  62
[1] "tbl2"
                  cls
clus               [,1] [,2]
  VPS13B MUTATED     47    3
  VPS13B WILD-TYPE  328   62
   clus
vv  VPS13B MUTATED VPS13B WILD-TYPE
  0             47              328
  1              3               62
[1] 2 2
[1] FALSE
D698V8, binary
                  cls
clus                 0   1
  VPS13B MUTATED    26  34
  VPS13B WILD-TYPE 199 230
[1] "tbl2"
                  cls
clus               [,1] [,2]
  VPS13B MUTATED     26   34
  VPS13B WILD-TYPE  199  230
        clus
vv       VPS13B MUTATED VPS13B WILD-TYPE
  FEMALE             26              199
  MALE               34              230
[1] 2 2
[1] FALSE
D698V9, binary
                  cls
clus                 0   1
  VPS13B MUTATED    46   2
  VPS13B WILD-TYPE 304  20
[1] "tbl2"
                  cls
clus               [,1] [,2]
  VPS13B MUTATED     46    2
  VPS13B WILD-TYPE  304   20
     clus
vv    VPS13B MUTATED VPS13B WILD-TYPE
  NO              46              304
  YES              2               20
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  VPS13B MUTATED                     41                            10
  VPS13B WILD-TYPE                  274                            37
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  VPS13B MUTATED                       8                              0
  VPS13B WILD-TYPE                    98                             10
D698V10, multiclass
                                clus
vv                               VPS13B MUTATED VPS13B WILD-TYPE
  COLON ADENOCARCINOMA                       41              274
  COLON MUCINOUS ADENOCARCINOMA              10               37
  RECTAL ADENOCARCINOMA                       8               98
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  VPS13B MUTATED    39   1   2   7
  VPS13B WILD-TYPE 306   3  29  18
D698V11, multiclass
    clus
vv   VPS13B MUTATED VPS13B WILD-TYPE
  R0             39              306
  R1              1                3
  R2              2               29
  RX              7               18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D698V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  VPS13B MUTATED                                  0     4
  VPS13B WILD-TYPE                                1     7
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  VPS13B MUTATED                           4    30
  VPS13B WILD-TYPE                        18   196
D698V13, multiclass
                                  clus
vv                                 VPS13B MUTATED VPS13B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         4                7
  BLACK OR AFRICAN AMERICAN                     4               18
  WHITE                                        30              196
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(699) Variable = GPR22 MUTATION ANALYSIS
D699V1, survival
                 sevent
clus2               0   1
  GPR22 MUTATED     6   3
  GPR22 WILD-TYPE 372  90
  GPR22 MUTATED GPR22 WILD-TYPE 
              9             462 
  GPR22 MUTATED GPR22 WILD-TYPE 
              3              90 
$`GPR22 MUTATED`
TCGA-AA-3492 TCGA-AA-3713 TCGA-AA-3833 TCGA-AA-A00N TCGA-AU-6004 TCGA-CA-6717 
        3.02        19.04        15.95         4.01        27.09        12.76 
TCGA-CK-5916 TCGA-F4-6856 TCGA-G4-6306 
       21.14        35.31        44.68 

$`GPR22 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       14.50        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07        12.20        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
        9.99        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 
       16.24        33.67        13.25         0.53        47.41       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       74.56        65.85        53.62        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  GPR22 MUTATED GPR22 WILD-TYPE 
           3.02            0.00 
  GPR22 MUTATED GPR22 WILD-TYPE 
          44.68          148.01 
  GPR22 MUTATED GPR22 WILD-TYPE 
         19.040          20.235 
[1] "3.0 - 44.7 (19.0)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "2.2"
D699V2, continuous
D699V3, binary
                 cls
clus                0   1
  GPR22 MUTATED     9   0
  GPR22 WILD-TYPE 357 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPR22 MUTATED      9    0
  GPR22 WILD-TYPE  357  119
        clus
vv       GPR22 MUTATED GPR22 WILD-TYPE
  COLON              9             357
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GPR22 MUTATED         3        0        1         3         1         0
  GPR22 WILD-TYPE      88        1       31       135         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  GPR22 MUTATED           0          0          0          0        1         0
  GPR22 WILD-TYPE        24         11         59         42       47        18
                 vv
clus              STAGE IVB
  GPR22 MUTATED           0
  GPR22 WILD-TYPE         1
D699V4, multiclass
            clus
vv           GPR22 MUTATED GPR22 WILD-TYPE
  STAGE I                3              88
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              3             135
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             0              42
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  GPR22 MUTATED     1   3   4   1
  GPR22 WILD-TYPE  16  89 325  49
D699V5, multiclass
    clus
vv   GPR22 MUTATED GPR22 WILD-TYPE
  T1             1              16
  T2             3              89
  T3             4             325
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  GPR22 MUTATED     9   0   0
  GPR22 WILD-TYPE 278 113  87
D699V6, multiclass
    clus
vv   GPR22 MUTATED GPR22 WILD-TYPE
  N0             9             278
  N1             0             113
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D699V7, binary
                 cls
clus                0   1
  GPR22 MUTATED     8   1
  GPR22 WILD-TYPE 367  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPR22 MUTATED      8    1
  GPR22 WILD-TYPE  367   64
   clus
vv  GPR22 MUTATED GPR22 WILD-TYPE
  0             8             367
  1             1              64
[1] 2 2
[1] FALSE
D699V8, binary
                 cls
clus                0   1
  GPR22 MUTATED     4   5
  GPR22 WILD-TYPE 221 259
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPR22 MUTATED      4    5
  GPR22 WILD-TYPE  221  259
        clus
vv       GPR22 MUTATED GPR22 WILD-TYPE
  FEMALE             4             221
  MALE               5             259
[1] 2 2
[1] FALSE
D699V9, binary
                 cls
clus                0   1
  GPR22 MUTATED     6   1
  GPR22 WILD-TYPE 344  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPR22 MUTATED      6    1
  GPR22 WILD-TYPE  344   21
     clus
vv    GPR22 MUTATED GPR22 WILD-TYPE
  NO              6             344
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  GPR22 MUTATED                      6                             3
  GPR22 WILD-TYPE                  309                            44
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  GPR22 MUTATED                       0                              0
  GPR22 WILD-TYPE                   106                             10
D699V10, multiclass
                                clus
vv                               GPR22 MUTATED GPR22 WILD-TYPE
  COLON ADENOCARCINOMA                       6             309
  COLON MUCINOUS ADENOCARCINOMA              3              44
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  GPR22 MUTATED     6   0   1   2
  GPR22 WILD-TYPE 339   4  30  23
D699V11, multiclass
    clus
vv   GPR22 MUTATED GPR22 WILD-TYPE
  R0             6             339
  R1             0               4
  R2             1              30
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D699V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GPR22 MUTATED                                  0     1
  GPR22 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  GPR22 MUTATED                           0     4
  GPR22 WILD-TYPE                        22   222
D699V13, multiclass
                                  clus
vv                                 GPR22 MUTATED GPR22 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        4             222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(700) Variable = LRP6 MUTATION ANALYSIS
D700V1, survival
                sevent
clus2              0   1
  LRP6 MUTATED    24   2
  LRP6 WILD-TYPE 354  91
  LRP6 MUTATED LRP6 WILD-TYPE 
            26            445 
  LRP6 MUTATED LRP6 WILD-TYPE 
             2             91 
$`LRP6 MUTATED`
TCGA-AA-3524 TCGA-AA-3672 TCGA-AA-3864 TCGA-AA-3947 TCGA-AA-3966 TCGA-AA-3977 
       36.03         0.92        53.00        33.01         2.01        25.02 
TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01R TCGA-AD-5900 TCGA-AD-6889 TCGA-AZ-4315 
        4.01        34.98        35.01         0.07        56.55        58.39 
TCGA-AZ-6607 TCGA-CA-6717 TCGA-CM-5349 TCGA-CM-6674 TCGA-D5-6931 TCGA-G4-6307 
        3.19        12.76        30.08        12.95        12.00        55.04 
TCGA-G4-6323 TCGA-AG-3726 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3892 TCGA-AG-A002 
       13.78         7.99         0.99         0.99        13.02        20.98 
TCGA-EF-5830 TCGA-G5-6235 
        0.49        55.76 

$`LRP6 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3525 
       38.99         1.02         9.07        24.03        37.05         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 
        6.97        54.02         2.01        14.01        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 
        0.99        31.07        31.07        30.05        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T 
       31.00        31.00        38.07         1.02         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 
       18.05        40.96        21.37        15.52         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
       11.74         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07        12.20        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5860 
       25.02        13.02        29.06        22.03        22.98        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6675 
       12.99        13.02        15.02        14.04        11.01        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
        1.51        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       44.68        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3881 TCGA-AG-3882 
       19.99         0.99        37.02        32.98        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 
        1.02        17.95        36.95        17.03        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
       32.61        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6641 
       26.43 

  LRP6 MUTATED LRP6 WILD-TYPE 
          0.07           0.00 
  LRP6 MUTATED LRP6 WILD-TYPE 
         58.39         148.01 
  LRP6 MUTATED LRP6 WILD-TYPE 
         13.40          20.28 
[1] "0.1 - 58.4 (13.4)"  "0.0 - 148.0 (20.3)"
[1] "hr=" "2.3"
D700V2, continuous
D700V3, binary
                cls
clus               0   1
  LRP6 MUTATED    19   8
  LRP6 WILD-TYPE 347 111
[1] "tbl2"
                cls
clus             [,1] [,2]
  LRP6 MUTATED     19    8
  LRP6 WILD-TYPE  347  111
        clus
vv       LRP6 MUTATED LRP6 WILD-TYPE
  COLON            19            347
  RECTUM            8            111
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  LRP6 MUTATED         6        1        2         7         4         0
  LRP6 WILD-TYPE      85        0       30       131         6         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  LRP6 MUTATED           2          0          2          1        1         0
  LRP6 WILD-TYPE        22         11         57         41       47        18
                vv
clus             STAGE IVB
  LRP6 MUTATED           0
  LRP6 WILD-TYPE         1
D700V4, multiclass
            clus
vv           LRP6 MUTATED LRP6 WILD-TYPE
  STAGE I               6             85
  STAGE IA              1              0
  STAGE II              2             30
  STAGE IIA             7            131
  STAGE IIB             4              6
  STAGE IIC             0              1
  STAGE III             2             22
  STAGE IIIA            0             11
  STAGE IIIB            2             57
  STAGE IIIC            1             41
  STAGE IV              1             47
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  LRP6 MUTATED     2   5  13   6
  LRP6 WILD-TYPE  15  87 316  44
D700V5, multiclass
    clus
vv   LRP6 MUTATED LRP6 WILD-TYPE
  T1            2             15
  T2            5             87
  T3           13            316
  T4            6             44
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  LRP6 MUTATED    21   3   3
  LRP6 WILD-TYPE 266 110  84
D700V6, multiclass
    clus
vv   LRP6 MUTATED LRP6 WILD-TYPE
  N0           21            266
  N1            3            110
  N2            3             84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D700V7, binary
                cls
clus               0   1
  LRP6 MUTATED    22   1
  LRP6 WILD-TYPE 353  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  LRP6 MUTATED     22    1
  LRP6 WILD-TYPE  353   64
   clus
vv  LRP6 MUTATED LRP6 WILD-TYPE
  0           22            353
  1            1             64
[1] 2 2
[1] FALSE
D700V8, binary
                cls
clus               0   1
  LRP6 MUTATED    10  17
  LRP6 WILD-TYPE 215 247
[1] "tbl2"
                cls
clus             [,1] [,2]
  LRP6 MUTATED     10   17
  LRP6 WILD-TYPE  215  247
        clus
vv       LRP6 MUTATED LRP6 WILD-TYPE
  FEMALE           10            215
  MALE             17            247
[1] 2 2
[1] FALSE
D700V9, binary
                cls
clus               0   1
  LRP6 MUTATED    18   1
  LRP6 WILD-TYPE 332  21
[1] "tbl2"
                cls
clus             [,1] [,2]
  LRP6 MUTATED     18    1
  LRP6 WILD-TYPE  332   21
     clus
vv    LRP6 MUTATED LRP6 WILD-TYPE
  NO            18            332
  YES            1             21
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  LRP6 MUTATED                     13                             6
  LRP6 WILD-TYPE                  302                            41
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  LRP6 MUTATED                       8                              0
  LRP6 WILD-TYPE                    98                             10
D700V10, multiclass
                                clus
vv                               LRP6 MUTATED LRP6 WILD-TYPE
  COLON ADENOCARCINOMA                     13            302
  COLON MUCINOUS ADENOCARCINOMA             6             41
  RECTAL ADENOCARCINOMA                     8             98
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  LRP6 MUTATED    21   1   0   1
  LRP6 WILD-TYPE 324   3  31  24
D700V11, multiclass
    clus
vv   LRP6 MUTATED LRP6 WILD-TYPE
  R0           21            324
  R1            1              3
  R2            0             31
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D700V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  LRP6 MUTATED                                  0     2
  LRP6 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  LRP6 MUTATED                           1     9
  LRP6 WILD-TYPE                        21   217
D700V13, multiclass
                                  clus
vv                                 LRP6 MUTATED LRP6 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              9
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                       9            217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(701) Variable = EFHC1 MUTATION ANALYSIS
D701V1, survival
                 sevent
clus2               0   1
  EFHC1 MUTATED    10   1
  EFHC1 WILD-TYPE 368  92
  EFHC1 MUTATED EFHC1 WILD-TYPE 
             11             460 
  EFHC1 MUTATED EFHC1 WILD-TYPE 
              1              92 
$`EFHC1 MUTATED`
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3977 TCGA-AA-A010 TCGA-AU-6004 TCGA-CA-6718 
       20.98        34.03        25.02        34.98        27.09        10.06 
TCGA-CA-6719 TCGA-CM-6163 TCGA-G4-6628 TCGA-AG-A002 TCGA-F5-6571 
       14.30         2.96        79.69        20.98        31.30 

$`EFHC1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       24.00         2.01         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       14.50        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CK-4947 
        3.25         3.29         0.07        12.20        12.76        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       17.03        15.02        12.00        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       26.17        91.79        46.75        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6702 TCGA-F5-6811 
       20.91        18.28         9.96        49.51        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  EFHC1 MUTATED EFHC1 WILD-TYPE 
           2.96            0.00 
  EFHC1 MUTATED EFHC1 WILD-TYPE 
          79.69          148.01 
  EFHC1 MUTATED EFHC1 WILD-TYPE 
         25.020          20.035 
[1] "3.0 - 79.7 (25.0)"  "0.0 - 148.0 (20.0)"
[1] "hr=" "2.1"
D701V2, continuous
D701V3, binary
                 cls
clus                0   1
  EFHC1 MUTATED    11   2
  EFHC1 WILD-TYPE 355 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EFHC1 MUTATED     11    2
  EFHC1 WILD-TYPE  355  117
        clus
vv       EFHC1 MUTATED EFHC1 WILD-TYPE
  COLON             11             355
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  EFHC1 MUTATED         4        0        0         4         2         0
  EFHC1 WILD-TYPE      87        1       32       134         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  EFHC1 MUTATED           1          0          1          0        0         0
  EFHC1 WILD-TYPE        23         11         58         42       48        18
                 vv
clus              STAGE IVB
  EFHC1 MUTATED           0
  EFHC1 WILD-TYPE         1
D701V4, multiclass
            clus
vv           EFHC1 MUTATED EFHC1 WILD-TYPE
  STAGE I                4              87
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              4             134
  STAGE IIB              2               8
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  EFHC1 MUTATED     1   5   5   2
  EFHC1 WILD-TYPE  16  87 324  48
D701V5, multiclass
    clus
vv   EFHC1 MUTATED EFHC1 WILD-TYPE
  T1             1              16
  T2             5              87
  T3             5             324
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  EFHC1 MUTATED    11   0   2
  EFHC1 WILD-TYPE 276 113  85
D701V6, multiclass
    clus
vv   EFHC1 MUTATED EFHC1 WILD-TYPE
  N0            11             276
  N1             0             113
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D701V7, binary
                 cls
clus                0   1
  EFHC1 MUTATED    11   0
  EFHC1 WILD-TYPE 364  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EFHC1 MUTATED     11    0
  EFHC1 WILD-TYPE  364   65
   clus
vv  EFHC1 MUTATED EFHC1 WILD-TYPE
  0            11             364
  1             0              65
[1] 2 2
[1] FALSE
D701V8, binary
                 cls
clus                0   1
  EFHC1 MUTATED     4   9
  EFHC1 WILD-TYPE 221 255
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EFHC1 MUTATED      4    9
  EFHC1 WILD-TYPE  221  255
        clus
vv       EFHC1 MUTATED EFHC1 WILD-TYPE
  FEMALE             4             221
  MALE               9             255
[1] 2 2
[1] FALSE
D701V9, binary
                 cls
clus                0   1
  EFHC1 MUTATED    10   0
  EFHC1 WILD-TYPE 340  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EFHC1 MUTATED     10    0
  EFHC1 WILD-TYPE  340   22
     clus
vv    EFHC1 MUTATED EFHC1 WILD-TYPE
  NO             10             340
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  EFHC1 MUTATED                     11                             0
  EFHC1 WILD-TYPE                  304                            47
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  EFHC1 MUTATED                       2                              0
  EFHC1 WILD-TYPE                   104                             10
D701V10, multiclass
                                clus
vv                               EFHC1 MUTATED EFHC1 WILD-TYPE
  COLON ADENOCARCINOMA                      11             304
  COLON MUCINOUS ADENOCARCINOMA              0              47
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  EFHC1 MUTATED     9   0   0   3
  EFHC1 WILD-TYPE 336   4  31  22
D701V11, multiclass
    clus
vv   EFHC1 MUTATED EFHC1 WILD-TYPE
  R0             9             336
  R1             0               4
  R2             0              31
  RX             3              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D701V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  EFHC1 MUTATED                                  0     2
  EFHC1 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  EFHC1 MUTATED                           0     5
  EFHC1 WILD-TYPE                        22   221
D701V13, multiclass
                                  clus
vv                                 EFHC1 MUTATED EFHC1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               9
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        5             221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(702) Variable = CDC7 MUTATION ANALYSIS
D702V1, survival
                sevent
clus2              0   1
  CDC7 MUTATED     9   2
  CDC7 WILD-TYPE 369  91
  CDC7 MUTATED CDC7 WILD-TYPE 
            11            460 
  CDC7 MUTATED CDC7 WILD-TYPE 
             2             91 
$`CDC7 MUTATED`
TCGA-A6-2672 TCGA-AA-3496 TCGA-AA-3977 TCGA-AU-6004 TCGA-AZ-6599 TCGA-CA-5255 
       46.65         1.02        25.02        27.09         6.77         3.06 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-6676 TCGA-AG-A002 TCGA-DC-6681 
       12.76        10.06        11.08        20.98         5.95 

$`CDC7 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 
       20.12        19.66        20.28         7.04         3.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
        0.20        14.50        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        88.21        49.41        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5796 
        5.23        11.74         3.19         1.61        12.69         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        3.29         0.07        12.20        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       12.95        13.05        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6682 
        5.03        13.97        27.95        10.98        19.99         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  CDC7 MUTATED CDC7 WILD-TYPE 
          1.02           0.00 
  CDC7 MUTATED CDC7 WILD-TYPE 
         46.65         148.01 
  CDC7 MUTATED CDC7 WILD-TYPE 
        11.080         20.415 
[1] "1.0 - 46.6 (11.1)"  "0.0 - 148.0 (20.4)"
[1] "hr=" "1.5"
D702V2, continuous
D702V3, binary
                cls
clus               0   1
  CDC7 MUTATED    10   2
  CDC7 WILD-TYPE 356 117
[1] "tbl2"
                cls
clus             [,1] [,2]
  CDC7 MUTATED     10    2
  CDC7 WILD-TYPE  356  117
        clus
vv       CDC7 MUTATED CDC7 WILD-TYPE
  COLON            10            356
  RECTUM            2            117
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CDC7 MUTATED         5        0        1         3         0         0
  CDC7 WILD-TYPE      86        1       31       135        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CDC7 MUTATED           0          0          1          0        0         1
  CDC7 WILD-TYPE        24         11         58         42       48        17
                vv
clus             STAGE IVB
  CDC7 MUTATED           0
  CDC7 WILD-TYPE         1
D702V4, multiclass
            clus
vv           CDC7 MUTATED CDC7 WILD-TYPE
  STAGE I               5             86
  STAGE IA              0              1
  STAGE II              1             31
  STAGE IIA             3            135
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            1             58
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             1             17
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  CDC7 MUTATED     0   6   6   0
  CDC7 WILD-TYPE  17  86 323  50
D702V5, multiclass
    clus
vv   CDC7 MUTATED CDC7 WILD-TYPE
  T1            0             17
  T2            6             86
  T3            6            323
  T4            0             50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  CDC7 MUTATED    10   1   1
  CDC7 WILD-TYPE 277 112  86
D702V6, multiclass
    clus
vv   CDC7 MUTATED CDC7 WILD-TYPE
  N0           10            277
  N1            1            112
  N2            1             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D702V7, binary
                cls
clus               0   1
  CDC7 MUTATED     8   1
  CDC7 WILD-TYPE 367  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  CDC7 MUTATED      8    1
  CDC7 WILD-TYPE  367   64
   clus
vv  CDC7 MUTATED CDC7 WILD-TYPE
  0            8            367
  1            1             64
[1] 2 2
[1] FALSE
D702V8, binary
                cls
clus               0   1
  CDC7 MUTATED     4   8
  CDC7 WILD-TYPE 221 256
[1] "tbl2"
                cls
clus             [,1] [,2]
  CDC7 MUTATED      4    8
  CDC7 WILD-TYPE  221  256
        clus
vv       CDC7 MUTATED CDC7 WILD-TYPE
  FEMALE            4            221
  MALE              8            256
[1] 2 2
[1] FALSE
D702V9, binary
                cls
clus               0   1
  CDC7 MUTATED     7   1
  CDC7 WILD-TYPE 343  21
[1] "tbl2"
                cls
clus             [,1] [,2]
  CDC7 MUTATED      7    1
  CDC7 WILD-TYPE  343   21
     clus
vv    CDC7 MUTATED CDC7 WILD-TYPE
  NO             7            343
  YES            1             21
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CDC7 MUTATED                      9                             1
  CDC7 WILD-TYPE                  306                            46
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CDC7 MUTATED                       2                              0
  CDC7 WILD-TYPE                   104                             10
D702V10, multiclass
                                clus
vv                               CDC7 MUTATED CDC7 WILD-TYPE
  COLON ADENOCARCINOMA                      9            306
  COLON MUCINOUS ADENOCARCINOMA             1             46
  RECTAL ADENOCARCINOMA                     2            104
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  CDC7 MUTATED     6   0   0   4
  CDC7 WILD-TYPE 339   4  31  21
D702V11, multiclass
    clus
vv   CDC7 MUTATED CDC7 WILD-TYPE
  R0            6            339
  R1            0              4
  R2            0             31
  RX            4             21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D702V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CDC7 MUTATED                                  0     3
  CDC7 WILD-TYPE                                1     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  CDC7 MUTATED                           0     6
  CDC7 WILD-TYPE                        22   220
D702V13, multiclass
                                  clus
vv                                 CDC7 MUTATED CDC7 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       3              8
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       6            220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(703) Variable = ATP5J2 MUTATION ANALYSIS
D703V1, survival
                  sevent
clus2                0   1
  ATP5J2 MUTATED     4   1
  ATP5J2 WILD-TYPE 374  92
  ATP5J2 MUTATED ATP5J2 WILD-TYPE 
               5              466 
  ATP5J2 MUTATED ATP5J2 WILD-TYPE 
               1               92 
$`ATP5J2 MUTATED`
TCGA-AA-3977 TCGA-AZ-4315 TCGA-CM-4752 TCGA-CM-6161 TCGA-DY-A1DF 
       25.02        58.39        13.02        15.02        24.13 

$`ATP5J2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        33.01        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       25.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6162 
       15.02         5.03        15.02        15.02        17.03        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  ATP5J2 MUTATED ATP5J2 WILD-TYPE 
           13.02             0.00 
  ATP5J2 MUTATED ATP5J2 WILD-TYPE 
           58.39           148.01 
  ATP5J2 MUTATED ATP5J2 WILD-TYPE 
          24.130           20.155 
[1] "13.0 - 58.4 (24.1)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.1"
D703V2, continuous
D703V3, binary
                  cls
clus                 0   1
  ATP5J2 MUTATED     4   1
  ATP5J2 WILD-TYPE 362 118
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP5J2 MUTATED      4    1
  ATP5J2 WILD-TYPE  362  118
        clus
vv       ATP5J2 MUTATED ATP5J2 WILD-TYPE
  COLON               4              362
  RECTUM              1              118
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ATP5J2 MUTATED         1        0        0         2         0         0
  ATP5J2 WILD-TYPE      90        1       32       136        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ATP5J2 MUTATED           0          0          0          1        0
  ATP5J2 WILD-TYPE        24         11         59         41       48
                  vv
clus               STAGE IVA STAGE IVB
  ATP5J2 MUTATED           0         0
  ATP5J2 WILD-TYPE        18         1
D703V4, multiclass
            clus
vv           ATP5J2 MUTATED ATP5J2 WILD-TYPE
  STAGE I                 1               90
  STAGE IA                0                1
  STAGE II                0               32
  STAGE IIA               2              136
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              0               59
  STAGE IIIC              1               41
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ATP5J2 MUTATED     0   2   3   0
  ATP5J2 WILD-TYPE  17  90 326  50
D703V5, multiclass
    clus
vv   ATP5J2 MUTATED ATP5J2 WILD-TYPE
  T1              0               17
  T2              2               90
  T3              3              326
  T4              0               50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  ATP5J2 MUTATED     4   0   1
  ATP5J2 WILD-TYPE 283 113  86
D703V6, multiclass
    clus
vv   ATP5J2 MUTATED ATP5J2 WILD-TYPE
  N0              4              283
  N1              0              113
  N2              1               86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D703V7, binary
                  cls
clus                 0   1
  ATP5J2 MUTATED     4   0
  ATP5J2 WILD-TYPE 371  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP5J2 MUTATED      4    0
  ATP5J2 WILD-TYPE  371   65
   clus
vv  ATP5J2 MUTATED ATP5J2 WILD-TYPE
  0              4              371
  1              0               65
[1] 2 2
[1] FALSE
D703V8, binary
                  cls
clus                 0   1
  ATP5J2 MUTATED     2   3
  ATP5J2 WILD-TYPE 223 261
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP5J2 MUTATED      2    3
  ATP5J2 WILD-TYPE  223  261
        clus
vv       ATP5J2 MUTATED ATP5J2 WILD-TYPE
  FEMALE              2              223
  MALE                3              261
[1] 2 2
[1] FALSE
D703V9, binary
                  cls
clus                 0   1
  ATP5J2 MUTATED     4   0
  ATP5J2 WILD-TYPE 346  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP5J2 MUTATED      4    0
  ATP5J2 WILD-TYPE  346   22
     clus
vv    ATP5J2 MUTATED ATP5J2 WILD-TYPE
  NO               4              346
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ATP5J2 MUTATED                      4                             0
  ATP5J2 WILD-TYPE                  311                            47
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ATP5J2 MUTATED                       1                              0
  ATP5J2 WILD-TYPE                   105                             10
D703V10, multiclass
                                clus
vv                               ATP5J2 MUTATED ATP5J2 WILD-TYPE
  COLON ADENOCARCINOMA                        4              311
  COLON MUCINOUS ADENOCARCINOMA               0               47
  RECTAL ADENOCARCINOMA                       1              105
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ATP5J2 MUTATED     3   0   0   0
  ATP5J2 WILD-TYPE 342   4  31  25
D703V11, multiclass
    clus
vv   ATP5J2 MUTATED ATP5J2 WILD-TYPE
  R0              3              342
  R1              0                4
  R2              0               31
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D703V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ATP5J2 MUTATED                                  0     0
  ATP5J2 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ATP5J2 MUTATED                           1     3
  ATP5J2 WILD-TYPE                        21   223
D703V13, multiclass
                                  clus
vv                                 ATP5J2 MUTATED ATP5J2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                         3              223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(704) Variable = ADH1B MUTATION ANALYSIS
D704V1, survival
                 sevent
clus2               0   1
  ADH1B MUTATED     6   4
  ADH1B WILD-TYPE 372  89
  ADH1B MUTATED ADH1B WILD-TYPE 
             10             461 
  ADH1B MUTATED ADH1B WILD-TYPE 
              4              89 
$`ADH1B MUTATED`
TCGA-AA-3516 TCGA-AA-A02F TCGA-CK-5913 TCGA-CM-4746 TCGA-CM-5862 TCGA-D5-6540 
       13.02        39.98        51.32        37.02         5.03        16.14 
TCGA-F4-6570 TCGA-AG-3892 TCGA-DY-A1DG TCGA-EI-6510 
        6.18        13.02        51.48        18.28 

$`ADH1B WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        1.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       51.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       85.45        15.62        49.08         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4752 
        1.91       124.27        23.05        20.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       31.96        35.74        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       17.03        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       41.36        57.24        24.13        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       19.96        20.91         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  ADH1B MUTATED ADH1B WILD-TYPE 
           5.03            0.00 
  ADH1B MUTATED ADH1B WILD-TYPE 
          51.48          148.01 
  ADH1B MUTATED ADH1B WILD-TYPE 
          17.21           20.28 
[1] "5.0 - 51.5 (17.2)"  "0.0 - 148.0 (20.3)"
[1] "hr=" "2"  
D704V2, continuous
D704V3, binary
                 cls
clus                0   1
  ADH1B MUTATED     7   3
  ADH1B WILD-TYPE 359 116
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ADH1B MUTATED      7    3
  ADH1B WILD-TYPE  359  116
        clus
vv       ADH1B MUTATED ADH1B WILD-TYPE
  COLON              7             359
  RECTUM             3             116
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ADH1B MUTATED         3        0        0         2         0         0
  ADH1B WILD-TYPE      88        1       32       136        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ADH1B MUTATED           1          0          0          0        1         3
  ADH1B WILD-TYPE        23         11         59         42       47        15
                 vv
clus              STAGE IVB
  ADH1B MUTATED           0
  ADH1B WILD-TYPE         1
D704V4, multiclass
            clus
vv           ADH1B MUTATED ADH1B WILD-TYPE
  STAGE I                3              88
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              2             136
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             0              42
  STAGE IV               1              47
  STAGE IVA              3              15
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ADH1B MUTATED     1   3   6   0
  ADH1B WILD-TYPE  16  89 323  50
D704V5, multiclass
    clus
vv   ADH1B MUTATED ADH1B WILD-TYPE
  T1             1              16
  T2             3              89
  T3             6             323
  T4             0              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  ADH1B MUTATED     6   3   1
  ADH1B WILD-TYPE 281 110  86
D704V6, multiclass
    clus
vv   ADH1B MUTATED ADH1B WILD-TYPE
  N0             6             281
  N1             3             110
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D704V7, binary
                 cls
clus                0   1
  ADH1B MUTATED     5   3
  ADH1B WILD-TYPE 370  62
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ADH1B MUTATED      5    3
  ADH1B WILD-TYPE  370   62
   clus
vv  ADH1B MUTATED ADH1B WILD-TYPE
  0             5             370
  1             3              62
[1] 2 2
[1] FALSE
D704V8, binary
                 cls
clus                0   1
  ADH1B MUTATED     6   4
  ADH1B WILD-TYPE 219 260
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ADH1B MUTATED      6    4
  ADH1B WILD-TYPE  219  260
        clus
vv       ADH1B MUTATED ADH1B WILD-TYPE
  FEMALE             6             219
  MALE               4             260
[1] 2 2
[1] FALSE
D704V9, binary
                 cls
clus                0   1
  ADH1B MUTATED     9   0
  ADH1B WILD-TYPE 341  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ADH1B MUTATED      9    0
  ADH1B WILD-TYPE  341   22
     clus
vv    ADH1B MUTATED ADH1B WILD-TYPE
  NO              9             341
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ADH1B MUTATED                      5                             2
  ADH1B WILD-TYPE                  310                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ADH1B MUTATED                       3                              0
  ADH1B WILD-TYPE                   103                             10
D704V10, multiclass
                                clus
vv                               ADH1B MUTATED ADH1B WILD-TYPE
  COLON ADENOCARCINOMA                       5             310
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      3             103
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  ADH1B MUTATED     6   0   1   1
  ADH1B WILD-TYPE 339   4  30  24
D704V11, multiclass
    clus
vv   ADH1B MUTATED ADH1B WILD-TYPE
  R0             6             339
  R1             0               4
  R2             1              30
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D704V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ADH1B MUTATED                                  0     0
  ADH1B WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ADH1B MUTATED                           1     6
  ADH1B WILD-TYPE                        21   220
D704V13, multiclass
                                  clus
vv                                 ADH1B MUTATED ADH1B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        6             220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(705) Variable = PARP12 MUTATION ANALYSIS
D705V1, survival
                  sevent
clus2                0   1
  PARP12 MUTATED     8   2
  PARP12 WILD-TYPE 370  91
  PARP12 MUTATED PARP12 WILD-TYPE 
              10              461 
  PARP12 MUTATED PARP12 WILD-TYPE 
               2               91 
$`PARP12 MUTATED`
TCGA-A6-6780 TCGA-AA-3660 TCGA-AA-3950 TCGA-AA-3966 TCGA-AZ-6598 TCGA-CK-4947 
       20.12        78.08        24.00         2.01        49.41        17.56 
TCGA-F4-6460 TCGA-G4-6321 TCGA-G4-6628 TCGA-EF-5830 
       31.96        22.09        79.69         0.49 

$`PARP12 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 
       19.99        13.94        19.99        61.02         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 
       12.99        24.00        33.01        26.01         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
       34.03        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        88.21         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       14.30       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6586 
       85.48        63.62        61.91        36.00        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       26.17        91.79        46.75        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EI-6506 TCGA-EI-6507 
       57.24        24.13        51.48        32.61        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  PARP12 MUTATED PARP12 WILD-TYPE 
            0.49             0.00 
  PARP12 MUTATED PARP12 WILD-TYPE 
           79.69           148.01 
  PARP12 MUTATED PARP12 WILD-TYPE 
          23.045           20.050 
[1] "0.5 - 79.7 (23.0)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.2"
D705V2, continuous
D705V3, binary
                  cls
clus                 0   1
  PARP12 MUTATED     9   2
  PARP12 WILD-TYPE 357 117
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PARP12 MUTATED      9    2
  PARP12 WILD-TYPE  357  117
        clus
vv       PARP12 MUTATED PARP12 WILD-TYPE
  COLON               9              357
  RECTUM              2              117
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PARP12 MUTATED         1        0        2         4         1         0
  PARP12 WILD-TYPE      90        1       30       134         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PARP12 MUTATED           1          0          2          0        0
  PARP12 WILD-TYPE        23         11         57         42       48
                  vv
clus               STAGE IVA STAGE IVB
  PARP12 MUTATED           0         0
  PARP12 WILD-TYPE        18         1
D705V4, multiclass
            clus
vv           PARP12 MUTATED PARP12 WILD-TYPE
  STAGE I                 1               90
  STAGE IA                0                1
  STAGE II                2               30
  STAGE IIA               4              134
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               1               23
  STAGE IIIA              0               11
  STAGE IIIB              2               57
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  PARP12 MUTATED     0   2   7   2
  PARP12 WILD-TYPE  17  90 322  48
D705V5, multiclass
    clus
vv   PARP12 MUTATED PARP12 WILD-TYPE
  T1              0               17
  T2              2               90
  T3              7              322
  T4              2               48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  PARP12 MUTATED     8   3   0
  PARP12 WILD-TYPE 279 110  87
D705V6, multiclass
    clus
vv   PARP12 MUTATED PARP12 WILD-TYPE
  N0              8              279
  N1              3              110
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D705V7, binary
                  cls
clus                 0   1
  PARP12 MUTATED     8   0
  PARP12 WILD-TYPE 367  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PARP12 MUTATED      8    0
  PARP12 WILD-TYPE  367   65
   clus
vv  PARP12 MUTATED PARP12 WILD-TYPE
  0              8              367
  1              0               65
[1] 2 2
[1] FALSE
D705V8, binary
                  cls
clus                 0   1
  PARP12 MUTATED     8   3
  PARP12 WILD-TYPE 217 261
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PARP12 MUTATED      8    3
  PARP12 WILD-TYPE  217  261
        clus
vv       PARP12 MUTATED PARP12 WILD-TYPE
  FEMALE              8              217
  MALE                3              261
[1] 2 2
[1] FALSE
D705V9, binary
                  cls
clus                 0   1
  PARP12 MUTATED     8   0
  PARP12 WILD-TYPE 342  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PARP12 MUTATED      8    0
  PARP12 WILD-TYPE  342   22
     clus
vv    PARP12 MUTATED PARP12 WILD-TYPE
  NO               8              342
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PARP12 MUTATED                      6                             3
  PARP12 WILD-TYPE                  309                            44
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PARP12 MUTATED                       2                              0
  PARP12 WILD-TYPE                   104                             10
D705V10, multiclass
                                clus
vv                               PARP12 MUTATED PARP12 WILD-TYPE
  COLON ADENOCARCINOMA                        6              309
  COLON MUCINOUS ADENOCARCINOMA               3               44
  RECTAL ADENOCARCINOMA                       2              104
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  PARP12 MUTATED     7   0   0   1
  PARP12 WILD-TYPE 338   4  31  24
D705V11, multiclass
    clus
vv   PARP12 MUTATED PARP12 WILD-TYPE
  R0              7              338
  R1              0                4
  R2              0               31
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D705V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PARP12 MUTATED                                  0     0
  PARP12 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  PARP12 MUTATED                           0     7
  PARP12 WILD-TYPE                        22   219
D705V13, multiclass
                                  clus
vv                                 PARP12 MUTATED PARP12 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         7              219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(706) Variable = CD101 MUTATION ANALYSIS
D706V1, survival
                 sevent
clus2               0   1
  CD101 MUTATED    10   0
  CD101 WILD-TYPE 368  93
  CD101 MUTATED CD101 WILD-TYPE 
             10             461 
  CD101 MUTATED CD101 WILD-TYPE 
              0              93 
$`CD101 MUTATED`
TCGA-A6-6781 TCGA-AA-3977 TCGA-AA-A010 TCGA-AU-6004 TCGA-CA-6717 TCGA-DM-A1HA 
       19.66        25.02        34.98        27.09        12.76       131.51 
TCGA-G4-6588 TCGA-AF-4110 TCGA-AG-3892 TCGA-AG-A002 
       26.17        14.50        13.02        20.98 

$`CD101 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
        0.20        14.50        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07        12.20        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
        7.50        44.32       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       13.78        35.80        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  CD101 MUTATED CD101 WILD-TYPE 
          12.76            0.00 
  CD101 MUTATED CD101 WILD-TYPE 
         131.51          148.01 
  CD101 MUTATED CD101 WILD-TYPE 
          23.00           20.12 
[1] "12.8 - 131.5 (23.0)" "0.0 - 148.0 (20.1)" 
[1] "hr="     "9300000"
D706V2, continuous
D706V3, binary
                 cls
clus                0   1
  CD101 MUTATED     8   2
  CD101 WILD-TYPE 358 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CD101 MUTATED      8    2
  CD101 WILD-TYPE  358  117
        clus
vv       CD101 MUTATED CD101 WILD-TYPE
  COLON              8             358
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CD101 MUTATED         3        0        0         3         1         0
  CD101 WILD-TYPE      88        1       32       135         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CD101 MUTATED           0          0          0          2        0         1
  CD101 WILD-TYPE        24         11         59         40       48        17
                 vv
clus              STAGE IVB
  CD101 MUTATED           0
  CD101 WILD-TYPE         1
D706V4, multiclass
            clus
vv           CD101 MUTATED CD101 WILD-TYPE
  STAGE I                3              88
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              3             135
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             2              40
  STAGE IV               0              48
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CD101 MUTATED     1   3   4   3
  CD101 WILD-TYPE  16  89 325  47
D706V5, multiclass
    clus
vv   CD101 MUTATED CD101 WILD-TYPE
  T1             1              16
  T2             3              89
  T3             4             325
  T4             3              47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  CD101 MUTATED     8   1   2
  CD101 WILD-TYPE 279 112  85
D706V6, multiclass
    clus
vv   CD101 MUTATED CD101 WILD-TYPE
  N0             8             279
  N1             1             112
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D706V7, binary
                 cls
clus                0   1
  CD101 MUTATED     8   0
  CD101 WILD-TYPE 367  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CD101 MUTATED      8    0
  CD101 WILD-TYPE  367   65
   clus
vv  CD101 MUTATED CD101 WILD-TYPE
  0             8             367
  1             0              65
[1] 2 2
[1] FALSE
D706V8, binary
                 cls
clus                0   1
  CD101 MUTATED     5   6
  CD101 WILD-TYPE 220 258
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CD101 MUTATED      5    6
  CD101 WILD-TYPE  220  258
        clus
vv       CD101 MUTATED CD101 WILD-TYPE
  FEMALE             5             220
  MALE               6             258
[1] 2 2
[1] FALSE
D706V9, binary
                 cls
clus                0   1
  CD101 MUTATED     8   0
  CD101 WILD-TYPE 342  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CD101 MUTATED      8    0
  CD101 WILD-TYPE  342   22
     clus
vv    CD101 MUTATED CD101 WILD-TYPE
  NO              8             342
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CD101 MUTATED                      6                             2
  CD101 WILD-TYPE                  309                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CD101 MUTATED                       2                              0
  CD101 WILD-TYPE                   104                             10
D706V10, multiclass
                                clus
vv                               CD101 MUTATED CD101 WILD-TYPE
  COLON ADENOCARCINOMA                       6             309
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  CD101 MUTATED     8   0   0   1
  CD101 WILD-TYPE 337   4  31  24
D706V11, multiclass
    clus
vv   CD101 MUTATED CD101 WILD-TYPE
  R0             8             337
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D706V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CD101 MUTATED                                  0     1
  CD101 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CD101 MUTATED                           0     5
  CD101 WILD-TYPE                        22   221
D706V13, multiclass
                                  clus
vv                                 CD101 MUTATED CD101 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        5             221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(707) Variable = PTPRC MUTATION ANALYSIS
D707V1, survival
                 sevent
clus2               0   1
  PTPRC MUTATED    23   5
  PTPRC WILD-TYPE 355  88
  PTPRC MUTATED PTPRC WILD-TYPE 
             28             443 
  PTPRC MUTATED PTPRC WILD-TYPE 
              5              88 
$`PTPRC MUTATED`
TCGA-A6-5657 TCGA-A6-5661 TCGA-A6-6142 TCGA-A6-6780 TCGA-AA-3510 TCGA-AA-3660 
       31.63        33.53        25.08        20.12        63.98        78.08 
TCGA-AA-3710 TCGA-AA-3845 TCGA-AA-3877 TCGA-AA-3956 TCGA-AA-3977 TCGA-AA-A00J 
       26.99         0.00        31.00        34.03        25.02        18.05 
TCGA-AA-A010 TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6901 TCGA-AZ-4315 TCGA-CA-6717 
       34.98         0.07        56.55        22.42        58.39        12.76 
TCGA-CA-6718 TCGA-CM-5860 TCGA-DM-A1HB TCGA-F4-6460 TCGA-F4-6570 TCGA-G4-6628 
       10.06        32.02       135.65        31.96         6.18        79.69 
TCGA-AG-3892 TCGA-AG-A002 TCGA-AG-A02N TCGA-F5-6812 
       13.02        20.98        61.97         0.66 

$`PTPRC WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       32.91        30.44        29.19        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6649 
       32.71        27.09        22.52         8.38        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 
       21.76        24.69        24.39        23.87        19.66        20.28 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 
        7.04         3.02         1.02        35.01         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
       13.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       36.03         8.05        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
       19.00        36.00         5.03        85.05        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 
       17.98        15.95        38.99        37.02        14.93        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 
       24.03        27.02        29.98        18.05         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 
       41.00        39.98        18.05        40.96        21.37        15.52 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.79         0.72         5.79        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 
        3.25         3.29         0.07        12.20        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       30.08        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 
      117.07        98.24         8.61        35.74        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       36.95        17.03        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 
       10.98        49.97         1.94        38.96        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.69        55.76        26.43 

  PTPRC MUTATED PTPRC WILD-TYPE 
              0               0 
  PTPRC MUTATED PTPRC WILD-TYPE 
         135.65          148.01 
  PTPRC MUTATED PTPRC WILD-TYPE 
         28.995          19.990 
[1] "0.0 - 135.7 (29.0)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.4"
D707V2, continuous
D707V3, binary
                 cls
clus                0   1
  PTPRC MUTATED    25   4
  PTPRC WILD-TYPE 341 115
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPRC MUTATED     25    4
  PTPRC WILD-TYPE  341  115
        clus
vv       PTPRC MUTATED PTPRC WILD-TYPE
  COLON             25             341
  RECTUM             4             115
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PTPRC MUTATED         5        0        4        12         1         0
  PTPRC WILD-TYPE      86        1       28       126         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PTPRC MUTATED           0          0          4          0        0         1
  PTPRC WILD-TYPE        24         11         55         42       48        17
                 vv
clus              STAGE IVB
  PTPRC MUTATED           0
  PTPRC WILD-TYPE         1
D707V4, multiclass
            clus
vv           PTPRC MUTATED PTPRC WILD-TYPE
  STAGE I                5              86
  STAGE IA               0               1
  STAGE II               4              28
  STAGE IIA             12             126
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             4              55
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PTPRC MUTATED     2   4  20   3
  PTPRC WILD-TYPE  15  88 309  47
D707V5, multiclass
    clus
vv   PTPRC MUTATED PTPRC WILD-TYPE
  T1             2              15
  T2             4              88
  T3            20             309
  T4             3              47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  PTPRC MUTATED    24   5   0
  PTPRC WILD-TYPE 263 108  87
D707V6, multiclass
    clus
vv   PTPRC MUTATED PTPRC WILD-TYPE
  N0            24             263
  N1             5             108
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D707V7, binary
                 cls
clus                0   1
  PTPRC MUTATED    24   1
  PTPRC WILD-TYPE 351  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPRC MUTATED     24    1
  PTPRC WILD-TYPE  351   64
   clus
vv  PTPRC MUTATED PTPRC WILD-TYPE
  0            24             351
  1             1              64
[1] 2 2
[1] FALSE
D707V8, binary
                 cls
clus                0   1
  PTPRC MUTATED    11  18
  PTPRC WILD-TYPE 214 246
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPRC MUTATED     11   18
  PTPRC WILD-TYPE  214  246
        clus
vv       PTPRC MUTATED PTPRC WILD-TYPE
  FEMALE            11             214
  MALE              18             246
[1] 2 2
[1] FALSE
D707V9, binary
                 cls
clus                0   1
  PTPRC MUTATED    22   0
  PTPRC WILD-TYPE 328  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPRC MUTATED     22    0
  PTPRC WILD-TYPE  328   22
     clus
vv    PTPRC MUTATED PTPRC WILD-TYPE
  NO             22             328
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PTPRC MUTATED                     19                             5
  PTPRC WILD-TYPE                  296                            42
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PTPRC MUTATED                       4                              0
  PTPRC WILD-TYPE                   102                             10
D707V10, multiclass
                                clus
vv                               PTPRC MUTATED PTPRC WILD-TYPE
  COLON ADENOCARCINOMA                      19             296
  COLON MUCINOUS ADENOCARCINOMA              5              42
  RECTAL ADENOCARCINOMA                      4             102
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  PTPRC MUTATED    21   0   0   2
  PTPRC WILD-TYPE 324   4  31  23
D707V11, multiclass
    clus
vv   PTPRC MUTATED PTPRC WILD-TYPE
  R0            21             324
  R1             0               4
  R2             0              31
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D707V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PTPRC MUTATED                                  0     3
  PTPRC WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PTPRC MUTATED                           2    11
  PTPRC WILD-TYPE                        20   215
D707V13, multiclass
                                  clus
vv                                 PTPRC MUTATED PTPRC WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        3               8
  BLACK OR AFRICAN AMERICAN                    2              20
  WHITE                                       11             215
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(708) Variable = RIF1 MUTATION ANALYSIS
D708V1, survival
                sevent
clus2              0   1
  RIF1 MUTATED    32   6
  RIF1 WILD-TYPE 346  87
  RIF1 MUTATED RIF1 WILD-TYPE 
            38            433 
  RIF1 MUTATED RIF1 WILD-TYPE 
             6             87 
$`RIF1 MUTATED`
TCGA-A6-2672 TCGA-A6-3807 TCGA-A6-5665 TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3510 
       46.65        34.65        22.06        20.12        19.66        63.98 
TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3815 TCGA-AA-3821 
       61.02         6.05        19.04        19.04        33.04         1.02 
TCGA-AA-A00J TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01P TCGA-AY-5543 TCGA-AZ-4315 
       18.05         4.01        34.98        38.07        33.01        58.39 
TCGA-AZ-6603 TCGA-CA-5797 TCGA-CA-6718 TCGA-CK-4952 TCGA-CM-5868 TCGA-CM-6167 
       29.56         3.29        10.06        15.62        17.03        14.99 
TCGA-D5-6533 TCGA-D5-6541 TCGA-D5-6927 TCGA-F4-6570 TCGA-F4-6808 TCGA-G4-6293 
        1.32        15.58         9.44         6.18        33.67       133.18 
TCGA-G4-6304 TCGA-G4-6321 TCGA-G4-6628 TCGA-AG-3587 TCGA-AG-3892 TCGA-AG-A002 
       53.62        22.09        79.69        46.03        13.02        20.98 
TCGA-AG-A036 TCGA-AH-6644 
      117.11         0.72 

$`RIF1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5657 
       33.34        32.75        36.53        14.53        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 
       30.44        29.19        33.53        23.61        22.09        32.71 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       27.09        22.52         8.38        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6782 TCGA-AA-3489 
       21.76        24.69        24.39        23.87        20.28         7.04 
TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        3.02         1.02        35.01         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3663 
       20.98        19.99        13.94        19.99        78.08         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
        5.03        85.05        26.99        10.06        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
       25.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       31.00         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6197 TCGA-AY-6386 
       14.50        27.09        16.31         0.95        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6606 
       49.41         6.77        12.10       100.01         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-6715 
        3.19         1.61        12.69         3.06         3.25         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.20        12.76        14.30        17.56       148.01        85.45 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
        5.03        15.02        15.02        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       29.03        16.04        21.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 
       56.09        55.92        20.19        18.25        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6898 
       17.85         4.80        17.13        12.49        16.14         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6928 
        3.68         4.41        12.43        14.30         9.04        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 
      117.07        98.24         8.61        31.96        35.74        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6854 
        1.55        34.42        41.42        16.24        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 
       47.41        35.31        74.56        65.85        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6586 
       85.48        63.62        61.91        36.00        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       26.17        91.79        46.75        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 
        1.02        17.95        36.95        17.03        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       61.97        41.00        38.04        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.69         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  RIF1 MUTATED RIF1 WILD-TYPE 
          0.72           0.00 
  RIF1 MUTATED RIF1 WILD-TYPE 
        133.18         148.01 
  RIF1 MUTATED RIF1 WILD-TYPE 
         20.55          20.19 
[1] "0.7 - 133.2 (20.6)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.5"
D708V2, continuous
D708V3, binary
                cls
clus               0   1
  RIF1 MUTATED    35   6
  RIF1 WILD-TYPE 331 113
[1] "tbl2"
                cls
clus             [,1] [,2]
  RIF1 MUTATED     35    6
  RIF1 WILD-TYPE  331  113
        clus
vv       RIF1 MUTATED RIF1 WILD-TYPE
  COLON            35            331
  RECTUM            6            113
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RIF1 MUTATED         6        0        3         9         3         0
  RIF1 WILD-TYPE      85        1       29       129         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RIF1 MUTATED           6          0          3          5        2         2
  RIF1 WILD-TYPE        18         11         56         37       46        16
                vv
clus             STAGE IVB
  RIF1 MUTATED           0
  RIF1 WILD-TYPE         1
D708V4, multiclass
            clus
vv           RIF1 MUTATED RIF1 WILD-TYPE
  STAGE I               6             85
  STAGE IA              0              1
  STAGE II              3             29
  STAGE IIA             9            129
  STAGE IIB             3              7
  STAGE IIC             0              1
  STAGE III             6             18
  STAGE IIIA            0             11
  STAGE IIIB            3             56
  STAGE IIIC            5             37
  STAGE IV              2             46
  STAGE IVA             2             16
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  RIF1 MUTATED     2   6  24   9
  RIF1 WILD-TYPE  15  86 305  41
D708V5, multiclass
    clus
vv   RIF1 MUTATED RIF1 WILD-TYPE
  T1            2             15
  T2            6             86
  T3           24            305
  T4            9             41
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  RIF1 MUTATED    23  10   7
  RIF1 WILD-TYPE 264 103  80
D708V6, multiclass
    clus
vv   RIF1 MUTATED RIF1 WILD-TYPE
  N0           23            264
  N1           10            103
  N2            7             80
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D708V7, binary
                cls
clus               0   1
  RIF1 MUTATED    30   4
  RIF1 WILD-TYPE 345  61
[1] "tbl2"
                cls
clus             [,1] [,2]
  RIF1 MUTATED     30    4
  RIF1 WILD-TYPE  345   61
   clus
vv  RIF1 MUTATED RIF1 WILD-TYPE
  0           30            345
  1            4             61
[1] 2 2
[1] FALSE
D708V8, binary
                cls
clus               0   1
  RIF1 MUTATED    20  21
  RIF1 WILD-TYPE 205 243
[1] "tbl2"
                cls
clus             [,1] [,2]
  RIF1 MUTATED     20   21
  RIF1 WILD-TYPE  205  243
        clus
vv       RIF1 MUTATED RIF1 WILD-TYPE
  FEMALE           20            205
  MALE             21            243
[1] 2 2
[1] FALSE
D708V9, binary
                cls
clus               0   1
  RIF1 MUTATED    31   3
  RIF1 WILD-TYPE 319  19
[1] "tbl2"
                cls
clus             [,1] [,2]
  RIF1 MUTATED     31    3
  RIF1 WILD-TYPE  319   19
     clus
vv    RIF1 MUTATED RIF1 WILD-TYPE
  NO            31            319
  YES            3             19
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  RIF1 MUTATED                     28                             7
  RIF1 WILD-TYPE                  287                            40
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  RIF1 MUTATED                       6                              0
  RIF1 WILD-TYPE                   100                             10
D708V10, multiclass
                                clus
vv                               RIF1 MUTATED RIF1 WILD-TYPE
  COLON ADENOCARCINOMA                     28            287
  COLON MUCINOUS ADENOCARCINOMA             7             40
  RECTAL ADENOCARCINOMA                     6            100
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  RIF1 MUTATED    33   0   2   2
  RIF1 WILD-TYPE 312   4  29  23
D708V11, multiclass
    clus
vv   RIF1 MUTATED RIF1 WILD-TYPE
  R0           33            312
  R1            0              4
  R2            2             29
  RX            2             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D708V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RIF1 MUTATED                                  0     2
  RIF1 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  RIF1 MUTATED                           2    21
  RIF1 WILD-TYPE                        20   205
D708V13, multiclass
                                  clus
vv                                 RIF1 MUTATED RIF1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              9
  BLACK OR AFRICAN AMERICAN                   2             20
  WHITE                                      21            205
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(709) Variable = LAS1L MUTATION ANALYSIS
D709V1, survival
                 sevent
clus2               0   1
  LAS1L MUTATED    10   1
  LAS1L WILD-TYPE 368  92
  LAS1L MUTATED LAS1L WILD-TYPE 
             11             460 
  LAS1L MUTATED LAS1L WILD-TYPE 
              1              92 
$`LAS1L MUTATED`
TCGA-A6-2672 TCGA-A6-2676 TCGA-AU-3779 TCGA-AU-6004 TCGA-AZ-5407 TCGA-CM-6680 
       46.65        42.90        14.50        27.09        88.21        12.03 
TCGA-G4-6309 TCGA-G4-6321 TCGA-G4-6625 TCGA-AG-A00Y TCGA-EI-6507 
       85.48        22.09        91.79        23.01        19.96 

$`LAS1L WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       43.76        43.76        24.33        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5657 
       33.34        32.75        36.53        14.53        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       30.44        29.19        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       10.88         0.20        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.08        11.01        10.06        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6586 
       55.04        63.62        61.91        36.00        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       26.17        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
       13.94         6.02        25.97        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6508 
       24.13        51.48        32.61         0.49        20.55        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  LAS1L MUTATED LAS1L WILD-TYPE 
          12.03            0.00 
  LAS1L MUTATED LAS1L WILD-TYPE 
          91.79          148.01 
  LAS1L MUTATED LAS1L WILD-TYPE 
         27.090          20.035 
[1] "12.0 - 91.8 (27.1)" "0.0 - 148.0 (20.0)"
[1] "hr=" "3.6"
D709V2, continuous
D709V3, binary
                 cls
clus                0   1
  LAS1L MUTATED     9   2
  LAS1L WILD-TYPE 357 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LAS1L MUTATED      9    2
  LAS1L WILD-TYPE  357  117
        clus
vv       LAS1L MUTATED LAS1L WILD-TYPE
  COLON              9             357
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  LAS1L MUTATED         2        0        0         4         1         0
  LAS1L WILD-TYPE      89        1       32       134         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  LAS1L MUTATED           1          0          3          0        0         0
  LAS1L WILD-TYPE        23         11         56         42       48        18
                 vv
clus              STAGE IVB
  LAS1L MUTATED           0
  LAS1L WILD-TYPE         1
D709V4, multiclass
            clus
vv           LAS1L MUTATED LAS1L WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              4             134
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             3              56
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  LAS1L MUTATED     1   2   7   1
  LAS1L WILD-TYPE  16  90 322  49
D709V5, multiclass
    clus
vv   LAS1L MUTATED LAS1L WILD-TYPE
  T1             1              16
  T2             2              90
  T3             7             322
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  LAS1L MUTATED     7   3   1
  LAS1L WILD-TYPE 280 110  86
D709V6, multiclass
    clus
vv   LAS1L MUTATED LAS1L WILD-TYPE
  N0             7             280
  N1             3             110
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D709V7, binary
                 cls
clus                0   1
  LAS1L MUTATED    10   0
  LAS1L WILD-TYPE 365  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LAS1L MUTATED     10    0
  LAS1L WILD-TYPE  365   65
   clus
vv  LAS1L MUTATED LAS1L WILD-TYPE
  0            10             365
  1             0              65
[1] 2 2
[1] FALSE
D709V8, binary
                 cls
clus                0   1
  LAS1L MUTATED     9   2
  LAS1L WILD-TYPE 216 262
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LAS1L MUTATED      9    2
  LAS1L WILD-TYPE  216  262
        clus
vv       LAS1L MUTATED LAS1L WILD-TYPE
  FEMALE             9             216
  MALE               2             262
[1] 2 2
[1] FALSE
D709V9, binary
                 cls
clus                0   1
  LAS1L MUTATED    10   0
  LAS1L WILD-TYPE 340  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LAS1L MUTATED     10    0
  LAS1L WILD-TYPE  340   22
     clus
vv    LAS1L MUTATED LAS1L WILD-TYPE
  NO             10             340
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  LAS1L MUTATED                      9                             0
  LAS1L WILD-TYPE                  306                            47
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  LAS1L MUTATED                       2                              0
  LAS1L WILD-TYPE                   104                             10
D709V10, multiclass
                                clus
vv                               LAS1L MUTATED LAS1L WILD-TYPE
  COLON ADENOCARCINOMA                       9             306
  COLON MUCINOUS ADENOCARCINOMA              0              47
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  LAS1L MUTATED    10   0   0   0
  LAS1L WILD-TYPE 335   4  31  25
D709V11, multiclass
    clus
vv   LAS1L MUTATED LAS1L WILD-TYPE
  R0            10             335
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D709V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  LAS1L MUTATED                                  0     0
  LAS1L WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  LAS1L MUTATED                           1     9
  LAS1L WILD-TYPE                        21   217
D709V13, multiclass
                                  clus
vv                                 LAS1L MUTATED LAS1L WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        9             217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(710) Variable = HSD17B11 MUTATION ANALYSIS
D710V1, survival
                    sevent
clus2                  0   1
  HSD17B11 MUTATED     4   0
  HSD17B11 WILD-TYPE 374  93
  HSD17B11 MUTATED HSD17B11 WILD-TYPE 
                 4                467 
  HSD17B11 MUTATED HSD17B11 WILD-TYPE 
                 0                 93 
$`HSD17B11 MUTATED`
TCGA-CK-4952 TCGA-CM-5868 TCGA-D5-6529 TCGA-F4-6808 
       15.62        17.03        20.19        33.67 

$`HSD17B11 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
       17.56       148.01        85.45        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6809 
       47.87         1.55        34.42        41.42        16.24        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  HSD17B11 MUTATED HSD17B11 WILD-TYPE 
             15.62               0.00 
  HSD17B11 MUTATED HSD17B11 WILD-TYPE 
             33.67             148.01 
  HSD17B11 MUTATED HSD17B11 WILD-TYPE 
             18.61              20.28 
[1] "15.6 - 33.7 (18.6)" "0.0 - 148.0 (20.3)"
[1] "hr="     "3300000"
D710V2, continuous
D710V3, binary
                    cls
clus                   0   1
  HSD17B11 MUTATED     4   1
  HSD17B11 WILD-TYPE 362 118
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HSD17B11 MUTATED      4    1
  HSD17B11 WILD-TYPE  362  118
        clus
vv       HSD17B11 MUTATED HSD17B11 WILD-TYPE
  COLON                 4                362
  RECTUM                1                118
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  HSD17B11 MUTATED         1        0        0         1         0         0
  HSD17B11 WILD-TYPE      90        1       32       137        10         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HSD17B11 MUTATED           1          0          0          1        0
  HSD17B11 WILD-TYPE        23         11         59         41       48
                    vv
clus                 STAGE IVA STAGE IVB
  HSD17B11 MUTATED           1         0
  HSD17B11 WILD-TYPE        17         1
D710V4, multiclass
            clus
vv           HSD17B11 MUTATED HSD17B11 WILD-TYPE
  STAGE I                   1                 90
  STAGE IA                  0                  1
  STAGE II                  0                 32
  STAGE IIA                 1                137
  STAGE IIB                 0                 10
  STAGE IIC                 0                  1
  STAGE III                 1                 23
  STAGE IIIA                0                 11
  STAGE IIIB                0                 59
  STAGE IIIC                1                 41
  STAGE IV                  0                 48
  STAGE IVA                 1                 17
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  HSD17B11 MUTATED     1   0   2   2
  HSD17B11 WILD-TYPE  16  92 327  48
D710V5, multiclass
    clus
vv   HSD17B11 MUTATED HSD17B11 WILD-TYPE
  T1                1                 16
  T2                0                 92
  T3                2                327
  T4                2                 48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  HSD17B11 MUTATED     2   2   1
  HSD17B11 WILD-TYPE 285 111  86
D710V6, multiclass
    clus
vv   HSD17B11 MUTATED HSD17B11 WILD-TYPE
  N0                2                285
  N1                2                111
  N2                1                 86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D710V7, binary
                    cls
clus                   0   1
  HSD17B11 MUTATED     3   1
  HSD17B11 WILD-TYPE 372  64
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HSD17B11 MUTATED      3    1
  HSD17B11 WILD-TYPE  372   64
   clus
vv  HSD17B11 MUTATED HSD17B11 WILD-TYPE
  0                3                372
  1                1                 64
[1] 2 2
[1] FALSE
D710V8, binary
                    cls
clus                   0   1
  HSD17B11 MUTATED     3   2
  HSD17B11 WILD-TYPE 222 262
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HSD17B11 MUTATED      3    2
  HSD17B11 WILD-TYPE  222  262
        clus
vv       HSD17B11 MUTATED HSD17B11 WILD-TYPE
  FEMALE                3                222
  MALE                  2                262
[1] 2 2
[1] FALSE
D710V9, binary
                    cls
clus                   0   1
  HSD17B11 MUTATED     3   0
  HSD17B11 WILD-TYPE 347  22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HSD17B11 MUTATED      3    0
  HSD17B11 WILD-TYPE  347   22
     clus
vv    HSD17B11 MUTATED HSD17B11 WILD-TYPE
  NO                 3                347
  YES                0                 22
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  HSD17B11 MUTATED                      3                             1
  HSD17B11 WILD-TYPE                  312                            46
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  HSD17B11 MUTATED                       1                              0
  HSD17B11 WILD-TYPE                   105                             10
D710V10, multiclass
                                clus
vv                               HSD17B11 MUTATED HSD17B11 WILD-TYPE
  COLON ADENOCARCINOMA                          3                312
  COLON MUCINOUS ADENOCARCINOMA                 1                 46
  RECTAL ADENOCARCINOMA                         1                105
  RECTAL MUCINOUS ADENOCARCINOMA                0                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  HSD17B11 MUTATED     3   0   0   1
  HSD17B11 WILD-TYPE 342   4  31  24
D710V11, multiclass
    clus
vv   HSD17B11 MUTATED HSD17B11 WILD-TYPE
  R0                3                342
  R1                0                  4
  R2                0                 31
  RX                1                 24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D710V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HSD17B11 MUTATED                                  0     0
  HSD17B11 WILD-TYPE                                1    11
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  HSD17B11 MUTATED                           0     5
  HSD17B11 WILD-TYPE                        22   221
D710V13, multiclass
                                  clus
vv                                 HSD17B11 MUTATED HSD17B11 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 11
  BLACK OR AFRICAN AMERICAN                       0                 22
  WHITE                                           5                221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(711) Variable = RHEB MUTATION ANALYSIS
D711V1, survival
                sevent
clus2              0   1
  RHEB MUTATED     4   1
  RHEB WILD-TYPE 374  92
  RHEB MUTATED RHEB WILD-TYPE 
             5            466 
  RHEB MUTATED RHEB WILD-TYPE 
             1             92 
$`RHEB MUTATED`
TCGA-AZ-4315 TCGA-AZ-6599 TCGA-CK-5913 TCGA-G4-6625 TCGA-F5-6813 
       58.39         6.77        51.32        91.79         0.69 

$`RHEB WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
       16.31         0.95        33.01        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       85.45        15.62        49.08         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66        55.76        26.43 

  RHEB MUTATED RHEB WILD-TYPE 
          0.69           0.00 
  RHEB MUTATED RHEB WILD-TYPE 
         91.79         148.01 
  RHEB MUTATED RHEB WILD-TYPE 
        51.320         20.155 
[1] "0.7 - 91.8 (51.3)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.6"
D711V2, continuous
D711V3, binary
                cls
clus               0   1
  RHEB MUTATED     4   1
  RHEB WILD-TYPE 362 118
[1] "tbl2"
                cls
clus             [,1] [,2]
  RHEB MUTATED      4    1
  RHEB WILD-TYPE  362  118
        clus
vv       RHEB MUTATED RHEB WILD-TYPE
  COLON             4            362
  RECTUM            1            118
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RHEB MUTATED         1        0        0         3         0         0
  RHEB WILD-TYPE      90        1       32       135        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RHEB MUTATED           0          0          0          1        0         0
  RHEB WILD-TYPE        24         11         59         41       48        18
                vv
clus             STAGE IVB
  RHEB MUTATED           0
  RHEB WILD-TYPE         1
D711V4, multiclass
            clus
vv           RHEB MUTATED RHEB WILD-TYPE
  STAGE I               1             90
  STAGE IA              0              1
  STAGE II              0             32
  STAGE IIA             3            135
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            0             59
  STAGE IIIC            1             41
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  RHEB MUTATED     0   1   3   1
  RHEB WILD-TYPE  17  91 326  49
D711V5, multiclass
    clus
vv   RHEB MUTATED RHEB WILD-TYPE
  T1            0             17
  T2            1             91
  T3            3            326
  T4            1             49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  RHEB MUTATED     4   0   1
  RHEB WILD-TYPE 283 113  86
D711V6, multiclass
    clus
vv   RHEB MUTATED RHEB WILD-TYPE
  N0            4            283
  N1            0            113
  N2            1             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D711V7, binary
                cls
clus               0   1
  RHEB MUTATED     3   0
  RHEB WILD-TYPE 372  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  RHEB MUTATED      3    0
  RHEB WILD-TYPE  372   65
   clus
vv  RHEB MUTATED RHEB WILD-TYPE
  0            3            372
  1            0             65
[1] 2 2
[1] FALSE
D711V8, binary
                cls
clus               0   1
  RHEB MUTATED     2   3
  RHEB WILD-TYPE 223 261
[1] "tbl2"
                cls
clus             [,1] [,2]
  RHEB MUTATED      2    3
  RHEB WILD-TYPE  223  261
        clus
vv       RHEB MUTATED RHEB WILD-TYPE
  FEMALE            2            223
  MALE              3            261
[1] 2 2
[1] FALSE
D711V9, binary
                cls
clus               0   1
  RHEB MUTATED     4   0
  RHEB WILD-TYPE 346  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  RHEB MUTATED      4    0
  RHEB WILD-TYPE  346   22
     clus
vv    RHEB MUTATED RHEB WILD-TYPE
  NO             4            346
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  RHEB MUTATED                      4                             0
  RHEB WILD-TYPE                  311                            47
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  RHEB MUTATED                       1                              0
  RHEB WILD-TYPE                   105                             10
D711V10, multiclass
                                clus
vv                               RHEB MUTATED RHEB WILD-TYPE
  COLON ADENOCARCINOMA                      4            311
  COLON MUCINOUS ADENOCARCINOMA             0             47
  RECTAL ADENOCARCINOMA                     1            105
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  RHEB MUTATED     3   0   0   1
  RHEB WILD-TYPE 342   4  31  24
D711V11, multiclass
    clus
vv   RHEB MUTATED RHEB WILD-TYPE
  R0            3            342
  R1            0              4
  R2            0             31
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D711V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RHEB MUTATED                                  0     0
  RHEB WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  RHEB MUTATED                           0     5
  RHEB WILD-TYPE                        22   221
D711V13, multiclass
                                  clus
vv                                 RHEB MUTATED RHEB WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       5            221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(712) Variable = KIAA0406 MUTATION ANALYSIS
D712V1, survival
                    sevent
clus2                  0   1
  KIAA0406 MUTATED    11   4
  KIAA0406 WILD-TYPE 367  89
  KIAA0406 MUTATED KIAA0406 WILD-TYPE 
                15                456 
  KIAA0406 MUTATED KIAA0406 WILD-TYPE 
                 4                 89 
$`KIAA0406 MUTATED`
TCGA-A6-5661 TCGA-A6-6782 TCGA-AA-3663 TCGA-AA-3845 TCGA-AA-3950 TCGA-AA-3955 
       33.53        20.28         6.97         0.00        24.00        20.98 
TCGA-AA-A00F TCGA-AA-A01Q TCGA-AZ-6598 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       34.03         1.02        49.41        12.76        10.06        14.30 
TCGA-CM-4743 TCGA-F4-6570 TCGA-AG-4007 
       23.05         6.18         1.02 

$`KIAA0406 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        19.66         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       38.99        37.02        14.93        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01         2.01        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K 
       13.94        38.04        19.00        30.02        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01R TCGA-AA-A01S 
       12.00        31.00        31.00        38.07        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 
      106.75        22.36        62.79        88.21         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 
        9.99        21.14        82.95         1.91       124.27        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       35.74        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4008 TCGA-AG-A002 
       19.99        28.04        36.03        14.04        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  KIAA0406 MUTATED KIAA0406 WILD-TYPE 
                 0                  0 
  KIAA0406 MUTATED KIAA0406 WILD-TYPE 
             49.41             148.01 
  KIAA0406 MUTATED KIAA0406 WILD-TYPE 
             14.30              20.37 
[1] "0.0 - 49.4 (14.3)"  "0.0 - 148.0 (20.4)"
[1] "hr=" "2.1"
D712V2, continuous
D712V3, binary
                    cls
clus                   0   1
  KIAA0406 MUTATED    14   1
  KIAA0406 WILD-TYPE 352 118
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0406 MUTATED     14    1
  KIAA0406 WILD-TYPE  352  118
        clus
vv       KIAA0406 MUTATED KIAA0406 WILD-TYPE
  COLON                14                352
  RECTUM                1                118
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KIAA0406 MUTATED         0        0        3         8         1         0
  KIAA0406 WILD-TYPE      91        1       29       130         9         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIAA0406 MUTATED           0          0          1          1        1
  KIAA0406 WILD-TYPE        24         11         58         41       47
                    vv
clus                 STAGE IVA STAGE IVB
  KIAA0406 MUTATED           0         0
  KIAA0406 WILD-TYPE        18         1
D712V4, multiclass
            clus
vv           KIAA0406 MUTATED KIAA0406 WILD-TYPE
  STAGE I                   0                 91
  STAGE IA                  0                  1
  STAGE II                  3                 29
  STAGE IIA                 8                130
  STAGE IIB                 1                  9
  STAGE IIC                 0                  1
  STAGE III                 0                 24
  STAGE IIIA                0                 11
  STAGE IIIB                1                 58
  STAGE IIIC                1                 41
  STAGE IV                  1                 47
  STAGE IVA                 0                 18
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  KIAA0406 MUTATED     0   1  12   2
  KIAA0406 WILD-TYPE  17  91 317  48
D712V5, multiclass
    clus
vv   KIAA0406 MUTATED KIAA0406 WILD-TYPE
  T1                0                 17
  T2                1                 91
  T3               12                317
  T4                2                 48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  KIAA0406 MUTATED    12   0   3
  KIAA0406 WILD-TYPE 275 113  84
D712V6, multiclass
    clus
vv   KIAA0406 MUTATED KIAA0406 WILD-TYPE
  N0               12                275
  N1                0                113
  N2                3                 84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D712V7, binary
                    cls
clus                   0   1
  KIAA0406 MUTATED    12   1
  KIAA0406 WILD-TYPE 363  64
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0406 MUTATED     12    1
  KIAA0406 WILD-TYPE  363   64
   clus
vv  KIAA0406 MUTATED KIAA0406 WILD-TYPE
  0               12                363
  1                1                 64
[1] 2 2
[1] FALSE
D712V8, binary
                    cls
clus                   0   1
  KIAA0406 MUTATED     6   9
  KIAA0406 WILD-TYPE 219 255
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0406 MUTATED      6    9
  KIAA0406 WILD-TYPE  219  255
        clus
vv       KIAA0406 MUTATED KIAA0406 WILD-TYPE
  FEMALE                6                219
  MALE                  9                255
[1] 2 2
[1] FALSE
D712V9, binary
                    cls
clus                   0   1
  KIAA0406 MUTATED    12   0
  KIAA0406 WILD-TYPE 338  22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0406 MUTATED     12    0
  KIAA0406 WILD-TYPE  338   22
     clus
vv    KIAA0406 MUTATED KIAA0406 WILD-TYPE
  NO                12                338
  YES                0                 22
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  KIAA0406 MUTATED                     12                             2
  KIAA0406 WILD-TYPE                  303                            45
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  KIAA0406 MUTATED                       1                              0
  KIAA0406 WILD-TYPE                   105                             10
D712V10, multiclass
                                clus
vv                               KIAA0406 MUTATED KIAA0406 WILD-TYPE
  COLON ADENOCARCINOMA                         12                303
  COLON MUCINOUS ADENOCARCINOMA                 2                 45
  RECTAL ADENOCARCINOMA                         1                105
  RECTAL MUCINOUS ADENOCARCINOMA                0                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  KIAA0406 MUTATED     9   0   1   3
  KIAA0406 WILD-TYPE 336   4  30  22
D712V11, multiclass
    clus
vv   KIAA0406 MUTATED KIAA0406 WILD-TYPE
  R0                9                336
  R1                0                  4
  R2                1                 30
  RX                3                 22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D712V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KIAA0406 MUTATED                                  0     3
  KIAA0406 WILD-TYPE                                1     8
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  KIAA0406 MUTATED                           1     4
  KIAA0406 WILD-TYPE                        21   222
D712V13, multiclass
                                  clus
vv                                 KIAA0406 MUTATED KIAA0406 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           3                  8
  BLACK OR AFRICAN AMERICAN                       1                 21
  WHITE                                           4                222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(713) Variable = LRRC23 MUTATION ANALYSIS
D713V1, survival
                  sevent
clus2                0   1
  LRRC23 MUTATED     8   1
  LRRC23 WILD-TYPE 370  92
  LRRC23 MUTATED LRRC23 WILD-TYPE 
               9              462 
  LRRC23 MUTATED LRRC23 WILD-TYPE 
               1               92 
$`LRRC23 MUTATED`
TCGA-AD-6889 TCGA-AZ-5403 TCGA-CA-6717 TCGA-CM-5864 TCGA-CM-6163 TCGA-CM-6677 
       56.55        62.79        12.76        15.02         2.96        11.08 
TCGA-CM-6680 TCGA-D5-6923 TCGA-D5-6927 
       12.03        12.43         9.44 

$`LRRC23 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       21.37        15.52         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
        5.13       106.75        22.36        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.20        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
       15.02         5.03        15.02        17.03        15.02        12.00 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       11.01        10.06        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6928 
        1.48         3.68         4.41        14.30         9.04        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  LRRC23 MUTATED LRRC23 WILD-TYPE 
            2.96             0.00 
  LRRC23 MUTATED LRRC23 WILD-TYPE 
           62.79           148.01 
  LRRC23 MUTATED LRRC23 WILD-TYPE 
           12.43            20.73 
[1] "3.0 - 62.8 (12.4)"  "0.0 - 148.0 (20.7)"
[1] "hr=" "1.7"
D713V2, continuous
D713V3, binary
                  cls
clus                 0   1
  LRRC23 MUTATED     9   0
  LRRC23 WILD-TYPE 357 119
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LRRC23 MUTATED      9    0
  LRRC23 WILD-TYPE  357  119
        clus
vv       LRRC23 MUTATED LRRC23 WILD-TYPE
  COLON               9              357
  RECTUM              0              119
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  LRRC23 MUTATED         3        0        1         4         0         0
  LRRC23 WILD-TYPE      88        1       31       134        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  LRRC23 MUTATED           0          0          1          0        0
  LRRC23 WILD-TYPE        24         11         58         42       48
                  vv
clus               STAGE IVA STAGE IVB
  LRRC23 MUTATED           0         0
  LRRC23 WILD-TYPE        18         1
D713V4, multiclass
            clus
vv           LRRC23 MUTATED LRRC23 WILD-TYPE
  STAGE I                 3               88
  STAGE IA                0                1
  STAGE II                1               31
  STAGE IIA               4              134
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              1               58
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  LRRC23 MUTATED     1   2   6   0
  LRRC23 WILD-TYPE  16  90 323  50
D713V5, multiclass
    clus
vv   LRRC23 MUTATED LRRC23 WILD-TYPE
  T1              1               16
  T2              2               90
  T3              6              323
  T4              0               50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  LRRC23 MUTATED     8   0   1
  LRRC23 WILD-TYPE 279 113  86
D713V6, multiclass
    clus
vv   LRRC23 MUTATED LRRC23 WILD-TYPE
  N0              8              279
  N1              0              113
  N2              1               86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D713V7, binary
                  cls
clus                 0   1
  LRRC23 MUTATED     8   0
  LRRC23 WILD-TYPE 367  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LRRC23 MUTATED      8    0
  LRRC23 WILD-TYPE  367   65
   clus
vv  LRRC23 MUTATED LRRC23 WILD-TYPE
  0              8              367
  1              0               65
[1] 2 2
[1] FALSE
D713V8, binary
                  cls
clus                 0   1
  LRRC23 MUTATED     2   7
  LRRC23 WILD-TYPE 223 257
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LRRC23 MUTATED      2    7
  LRRC23 WILD-TYPE  223  257
        clus
vv       LRRC23 MUTATED LRRC23 WILD-TYPE
  FEMALE              2              223
  MALE                7              257
[1] 2 2
[1] FALSE
D713V9, binary
                  cls
clus                 0   1
  LRRC23 MUTATED     8   0
  LRRC23 WILD-TYPE 342  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LRRC23 MUTATED      8    0
  LRRC23 WILD-TYPE  342   22
     clus
vv    LRRC23 MUTATED LRRC23 WILD-TYPE
  NO               8              342
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  LRRC23 MUTATED                      8                             1
  LRRC23 WILD-TYPE                  307                            46
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  LRRC23 MUTATED                       0                              0
  LRRC23 WILD-TYPE                   106                             10
D713V10, multiclass
                                clus
vv                               LRRC23 MUTATED LRRC23 WILD-TYPE
  COLON ADENOCARCINOMA                        8              307
  COLON MUCINOUS ADENOCARCINOMA               1               46
  RECTAL ADENOCARCINOMA                       0              106
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  LRRC23 MUTATED     6   0   0   1
  LRRC23 WILD-TYPE 339   4  31  24
D713V11, multiclass
    clus
vv   LRRC23 MUTATED LRRC23 WILD-TYPE
  R0              6              339
  R1              0                4
  R2              0               31
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D713V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  LRRC23 MUTATED                                  0     2
  LRRC23 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  LRRC23 MUTATED                           0     7
  LRRC23 WILD-TYPE                        22   219
D713V13, multiclass
                                  clus
vv                                 LRRC23 MUTATED LRRC23 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                9
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         7              219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(714) Variable = FAM179A MUTATION ANALYSIS
D714V1, survival
                   sevent
clus2                 0   1
  FAM179A MUTATED    23   6
  FAM179A WILD-TYPE 355  87
  FAM179A MUTATED FAM179A WILD-TYPE 
               29               442 
  FAM179A MUTATED FAM179A WILD-TYPE 
                6                87 
$`FAM179A MUTATED`
TCGA-A6-3809 TCGA-A6-6137 TCGA-A6-6781 TCGA-AA-3510 TCGA-AA-3949 TCGA-AA-3950 
       32.75        27.09        19.66        63.98        26.01        24.00 
TCGA-AA-3977 TCGA-AA-A01R TCGA-AD-5900 TCGA-AD-6889 TCGA-AY-6197 TCGA-AZ-4315 
       25.02        35.01         0.07        56.55        21.44        58.39 
TCGA-AZ-6598 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-6717 TCGA-CK-4952 TCGA-CK-5916 
       49.41         3.19        12.69        12.76        15.62        21.14 
TCGA-CM-4743 TCGA-CM-6171 TCGA-D5-6541 TCGA-DM-A1D0 TCGA-DM-A1DA TCGA-DM-A28G 
       23.05        14.04        15.58       130.65         7.50        60.79 
TCGA-F4-6570 TCGA-F4-6807 TCGA-G4-6304 TCGA-AG-A002 TCGA-EI-6507 
        6.18        16.24        53.62        20.98        19.96 

$`FAM179A WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       22.06        32.71        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 
       20.28         7.04         3.02         1.02        35.01         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S 
       12.00        31.00        31.00        38.07         1.02         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 
       39.98        18.05        40.96        21.37        15.52         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 
       14.50        27.09        16.31         0.95        33.01        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6608 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        1.61         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 
       10.06        14.30        17.56       148.01        85.45        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 
       51.32         9.99        82.95         1.91       124.27        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 
       21.99        14.99        12.99        13.02        15.02        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6898 TCGA-D5-6920 
        4.80        17.13        12.49        16.14         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       24.43        38.20        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
      140.38        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
       81.37       119.93        35.97       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       31.96        35.74        47.87         1.55        34.42        41.42 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       74.56        65.85        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6508 
       24.13        51.48        32.61         0.49        20.55        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  FAM179A MUTATED FAM179A WILD-TYPE 
             0.07              0.00 
  FAM179A MUTATED FAM179A WILD-TYPE 
           130.65            148.01 
  FAM179A MUTATED FAM179A WILD-TYPE 
           21.440            20.035 
[1] "0.1 - 130.7 (21.4)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.1"
D714V2, continuous
D714V3, binary
                   cls
clus                  0   1
  FAM179A MUTATED    27   2
  FAM179A WILD-TYPE 339 117
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM179A MUTATED     27    2
  FAM179A WILD-TYPE  339  117
        clus
vv       FAM179A MUTATED FAM179A WILD-TYPE
  COLON               27               339
  RECTUM               2               117
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FAM179A MUTATED         4        0        2        12         2         0
  FAM179A WILD-TYPE      87        1       30       126         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FAM179A MUTATED           1          0          2          4        1
  FAM179A WILD-TYPE        23         11         57         38       47
                   vv
clus                STAGE IVA STAGE IVB
  FAM179A MUTATED           0         0
  FAM179A WILD-TYPE        18         1
D714V4, multiclass
            clus
vv           FAM179A MUTATED FAM179A WILD-TYPE
  STAGE I                  4                87
  STAGE IA                 0                 1
  STAGE II                 2                30
  STAGE IIA               12               126
  STAGE IIB                2                 8
  STAGE IIC                0                 1
  STAGE III                1                23
  STAGE IIIA               0                11
  STAGE IIIB               2                57
  STAGE IIIC               4                38
  STAGE IV                 1                47
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  FAM179A MUTATED     1   4  19   5
  FAM179A WILD-TYPE  16  88 310  45
D714V5, multiclass
    clus
vv   FAM179A MUTATED FAM179A WILD-TYPE
  T1               1                16
  T2               4                88
  T3              19               310
  T4               5                45
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  FAM179A MUTATED    21   3   5
  FAM179A WILD-TYPE 266 110  82
D714V6, multiclass
    clus
vv   FAM179A MUTATED FAM179A WILD-TYPE
  N0              21               266
  N1               3               110
  N2               5                82
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D714V7, binary
                   cls
clus                  0   1
  FAM179A MUTATED    23   1
  FAM179A WILD-TYPE 352  64
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM179A MUTATED     23    1
  FAM179A WILD-TYPE  352   64
   clus
vv  FAM179A MUTATED FAM179A WILD-TYPE
  0              23               352
  1               1                64
[1] 2 2
[1] FALSE
D714V8, binary
                   cls
clus                  0   1
  FAM179A MUTATED    13  16
  FAM179A WILD-TYPE 212 248
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM179A MUTATED     13   16
  FAM179A WILD-TYPE  212  248
        clus
vv       FAM179A MUTATED FAM179A WILD-TYPE
  FEMALE              13               212
  MALE                16               248
[1] 2 2
[1] FALSE
D714V9, binary
                   cls
clus                  0   1
  FAM179A MUTATED    22   1
  FAM179A WILD-TYPE 328  21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM179A MUTATED     22    1
  FAM179A WILD-TYPE  328   21
     clus
vv    FAM179A MUTATED FAM179A WILD-TYPE
  NO               22               328
  YES               1                21
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  FAM179A MUTATED                     19                             8
  FAM179A WILD-TYPE                  296                            39
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  FAM179A MUTATED                       2                              0
  FAM179A WILD-TYPE                   104                             10
D714V10, multiclass
                                clus
vv                               FAM179A MUTATED FAM179A WILD-TYPE
  COLON ADENOCARCINOMA                        19               296
  COLON MUCINOUS ADENOCARCINOMA                8                39
  RECTAL ADENOCARCINOMA                        2               104
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  FAM179A MUTATED    17   0   0   4
  FAM179A WILD-TYPE 328   4  31  21
D714V11, multiclass
    clus
vv   FAM179A MUTATED FAM179A WILD-TYPE
  R0              17               328
  R1               0                 4
  R2               0                31
  RX               4                21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D714V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FAM179A MUTATED                                  0     3
  FAM179A WILD-TYPE                                1     8
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  FAM179A MUTATED                           0    20
  FAM179A WILD-TYPE                        22   206
D714V13, multiclass
                                  clus
vv                                 FAM179A MUTATED FAM179A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          3                 8
  BLACK OR AFRICAN AMERICAN                      0                22
  WHITE                                         20               206
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(715) Variable = OR2V2 MUTATION ANALYSIS
D715V1, survival
                 sevent
clus2               0   1
  OR2V2 MUTATED     4   2
  OR2V2 WILD-TYPE 374  91
  OR2V2 MUTATED OR2V2 WILD-TYPE 
              6             465 
  OR2V2 MUTATED OR2V2 WILD-TYPE 
              2              91 
$`OR2V2 MUTATED`
TCGA-A6-3809 TCGA-A6-5661 TCGA-A6-6142 TCGA-A6-6648 TCGA-AZ-6598 TCGA-F4-6809 
       32.75        33.53        25.08        25.18        49.41        13.25 

$`OR2V2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       31.63        30.44        29.19        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6649 TCGA-A6-6651 
       32.71        27.09        22.52         8.38        24.16        21.76 
TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       24.69        24.39        23.87        20.12        19.66        20.28 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
        7.04         3.02         1.02        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        88.21         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6854 TCGA-F4-6855 
       34.42        41.42        16.24        33.67         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  OR2V2 MUTATED OR2V2 WILD-TYPE 
          13.25            0.00 
  OR2V2 MUTATED OR2V2 WILD-TYPE 
          49.41          148.01 
  OR2V2 MUTATED OR2V2 WILD-TYPE 
         28.965          20.050 
[1] "13.2 - 49.4 (29.0)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.5"
D715V2, continuous
D715V3, binary
                 cls
clus                0   1
  OR2V2 MUTATED     6   0
  OR2V2 WILD-TYPE 360 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR2V2 MUTATED      6    0
  OR2V2 WILD-TYPE  360  119
        clus
vv       OR2V2 MUTATED OR2V2 WILD-TYPE
  COLON              6             360
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  OR2V2 MUTATED         0        0        1         1         1         0
  OR2V2 WILD-TYPE      91        1       31       137         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  OR2V2 MUTATED           0          0          0          0        0         3
  OR2V2 WILD-TYPE        24         11         59         42       48        15
                 vv
clus              STAGE IVB
  OR2V2 MUTATED           0
  OR2V2 WILD-TYPE         1
D715V4, multiclass
            clus
vv           OR2V2 MUTATED OR2V2 WILD-TYPE
  STAGE I                0              91
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              1             137
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              3              15
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  OR2V2 MUTATED     0   0   5   1
  OR2V2 WILD-TYPE  17  92 324  49
D715V5, multiclass
    clus
vv   OR2V2 MUTATED OR2V2 WILD-TYPE
  T1             0              17
  T2             0              92
  T3             5             324
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  OR2V2 MUTATED     4   2   0
  OR2V2 WILD-TYPE 283 111  87
D715V6, multiclass
    clus
vv   OR2V2 MUTATED OR2V2 WILD-TYPE
  N0             4             283
  N1             2             111
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D715V7, binary
                 cls
clus                0   1
  OR2V2 MUTATED     2   3
  OR2V2 WILD-TYPE 373  62
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR2V2 MUTATED      2    3
  OR2V2 WILD-TYPE  373   62
   clus
vv  OR2V2 MUTATED OR2V2 WILD-TYPE
  0             2             373
  1             3              62
[1] 2 2
[1] FALSE
D715V8, binary
                 cls
clus                0   1
  OR2V2 MUTATED     5   1
  OR2V2 WILD-TYPE 220 263
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR2V2 MUTATED      5    1
  OR2V2 WILD-TYPE  220  263
        clus
vv       OR2V2 MUTATED OR2V2 WILD-TYPE
  FEMALE             5             220
  MALE               1             263
[1] 2 2
[1] FALSE
D715V9, binary
                 cls
clus                0   1
  OR2V2 MUTATED     6   0
  OR2V2 WILD-TYPE 344  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR2V2 MUTATED      6    0
  OR2V2 WILD-TYPE  344   22
     clus
vv    OR2V2 MUTATED OR2V2 WILD-TYPE
  NO              6             344
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  OR2V2 MUTATED                      5                             1
  OR2V2 WILD-TYPE                  310                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  OR2V2 MUTATED                       0                              0
  OR2V2 WILD-TYPE                   106                             10
D715V10, multiclass
                                clus
vv                               OR2V2 MUTATED OR2V2 WILD-TYPE
  COLON ADENOCARCINOMA                       5             310
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  OR2V2 MUTATED     3   0   0   0
  OR2V2 WILD-TYPE 342   4  31  25
D715V11, multiclass
    clus
vv   OR2V2 MUTATED OR2V2 WILD-TYPE
  R0             3             342
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D715V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OR2V2 MUTATED                                  0     0
  OR2V2 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  OR2V2 MUTATED                           1     5
  OR2V2 WILD-TYPE                        21   221
D715V13, multiclass
                                  clus
vv                                 OR2V2 MUTATED OR2V2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        5             221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(716) Variable = WNK1 MUTATION ANALYSIS
D716V1, survival
                sevent
clus2              0   1
  WNK1 MUTATED    17   4
  WNK1 WILD-TYPE 361  89
  WNK1 MUTATED WNK1 WILD-TYPE 
            21            450 
  WNK1 MUTATED WNK1 WILD-TYPE 
             4             89 
$`WNK1 MUTATED`
TCGA-A6-6648 TCGA-AA-3655 TCGA-AA-3815 TCGA-AA-3845 TCGA-AA-3977 TCGA-AA-A00N 
       25.18        61.02        33.04         0.00        25.02         4.01 
TCGA-AA-A010 TCGA-AA-A01R TCGA-AD-6895 TCGA-AZ-4315 TCGA-AZ-6608 TCGA-CA-5254 
       34.98        35.01         0.72        58.39         1.61        12.69 
TCGA-CM-5861 TCGA-CM-6168 TCGA-D5-6535 TCGA-DM-A28K TCGA-F4-6806 TCGA-G4-6588 
       15.02        12.99        15.12        98.24        41.42        26.17 
TCGA-AG-3587 TCGA-AG-3892 TCGA-DY-A1DD 
       46.03        13.02        57.24 

$`WNK1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.08        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       19.99        13.94        19.99        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       35.05         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       38.99        37.02        14.93        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S 
       12.00        31.00        31.00        38.07         1.02         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
       56.55         0.79         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5255 TCGA-CA-5796 
       29.56         5.23        11.74         3.19         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       22.98        30.08        32.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       21.99        14.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 
       20.19        18.25         1.32        43.27        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
      117.07         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
        1.55        34.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       22.09        13.78        35.80        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       20.05        24.00         1.02        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       17.03        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       41.36        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  WNK1 MUTATED WNK1 WILD-TYPE 
             0              0 
  WNK1 MUTATED WNK1 WILD-TYPE 
         98.24         148.01 
  WNK1 MUTATED WNK1 WILD-TYPE 
        25.180         20.085 
[1] "0.0 - 98.2 (25.2)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.2"
D716V2, continuous
D716V3, binary
                cls
clus               0   1
  WNK1 MUTATED    19   3
  WNK1 WILD-TYPE 347 116
[1] "tbl2"
                cls
clus             [,1] [,2]
  WNK1 MUTATED     19    3
  WNK1 WILD-TYPE  347  116
        clus
vv       WNK1 MUTATED WNK1 WILD-TYPE
  COLON            19            347
  RECTUM            3            116
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  WNK1 MUTATED         4        0        1         8         2         0
  WNK1 WILD-TYPE      87        1       31       130         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  WNK1 MUTATED           1          1          2          0        0         1
  WNK1 WILD-TYPE        23         10         57         42       48        17
                vv
clus             STAGE IVB
  WNK1 MUTATED           0
  WNK1 WILD-TYPE         1
D716V4, multiclass
            clus
vv           WNK1 MUTATED WNK1 WILD-TYPE
  STAGE I               4             87
  STAGE IA              0              1
  STAGE II              1             31
  STAGE IIA             8            130
  STAGE IIB             2              8
  STAGE IIC             0              1
  STAGE III             1             23
  STAGE IIIA            1             10
  STAGE IIIB            2             57
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             1             17
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  WNK1 MUTATED     1   5  14   2
  WNK1 WILD-TYPE  16  87 315  48
D716V5, multiclass
    clus
vv   WNK1 MUTATED WNK1 WILD-TYPE
  T1            1             16
  T2            5             87
  T3           14            315
  T4            2             48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  WNK1 MUTATED    17   4   1
  WNK1 WILD-TYPE 270 109  86
D716V6, multiclass
    clus
vv   WNK1 MUTATED WNK1 WILD-TYPE
  N0           17            270
  N1            4            109
  N2            1             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D716V7, binary
                cls
clus               0   1
  WNK1 MUTATED    17   1
  WNK1 WILD-TYPE 358  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  WNK1 MUTATED     17    1
  WNK1 WILD-TYPE  358   64
   clus
vv  WNK1 MUTATED WNK1 WILD-TYPE
  0           17            358
  1            1             64
[1] 2 2
[1] FALSE
D716V8, binary
                cls
clus               0   1
  WNK1 MUTATED    12  10
  WNK1 WILD-TYPE 213 254
[1] "tbl2"
                cls
clus             [,1] [,2]
  WNK1 MUTATED     12   10
  WNK1 WILD-TYPE  213  254
        clus
vv       WNK1 MUTATED WNK1 WILD-TYPE
  FEMALE           12            213
  MALE             10            254
[1] 2 2
[1] FALSE
D716V9, binary
                cls
clus               0   1
  WNK1 MUTATED    14   2
  WNK1 WILD-TYPE 336  20
[1] "tbl2"
                cls
clus             [,1] [,2]
  WNK1 MUTATED     14    2
  WNK1 WILD-TYPE  336   20
     clus
vv    WNK1 MUTATED WNK1 WILD-TYPE
  NO            14            336
  YES            2             20
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  WNK1 MUTATED                     16                             3
  WNK1 WILD-TYPE                  299                            44
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  WNK1 MUTATED                       3                              0
  WNK1 WILD-TYPE                   103                             10
D716V10, multiclass
                                clus
vv                               WNK1 MUTATED WNK1 WILD-TYPE
  COLON ADENOCARCINOMA                     16            299
  COLON MUCINOUS ADENOCARCINOMA             3             44
  RECTAL ADENOCARCINOMA                     3            103
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  WNK1 MUTATED    13   0   0   3
  WNK1 WILD-TYPE 332   4  31  22
D716V11, multiclass
    clus
vv   WNK1 MUTATED WNK1 WILD-TYPE
  R0           13            332
  R1            0              4
  R2            0             31
  RX            3             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D716V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  WNK1 MUTATED                                  0     1
  WNK1 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  WNK1 MUTATED                           1    11
  WNK1 WILD-TYPE                        21   215
D716V13, multiclass
                                  clus
vv                                 WNK1 MUTATED WNK1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                      11            215
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(717) Variable = FRS3 MUTATION ANALYSIS
D717V1, survival
                sevent
clus2              0   1
  FRS3 MUTATED     9   3
  FRS3 WILD-TYPE 369  90
  FRS3 MUTATED FRS3 WILD-TYPE 
            12            459 
  FRS3 MUTATED FRS3 WILD-TYPE 
             3             90 
$`FRS3 MUTATED`
TCGA-AA-3511 TCGA-AA-A01R TCGA-AA-A02K TCGA-AZ-4315 TCGA-AZ-6598 TCGA-CA-6717 
        6.97        35.01        14.01        58.39        49.41        12.76 
TCGA-CM-5349 TCGA-D5-6930 TCGA-DM-A1D9 TCGA-DM-A28K TCGA-AF-2687 TCGA-AF-3913 
       30.08         1.51       140.38        98.24        24.13        10.39 

$`FRS3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01        63.98         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S 
       12.00        31.00        31.00        38.07         1.02         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
       39.98         2.01         5.03         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        88.21         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07        12.20        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       22.98        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
        9.44        11.64         4.80        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       13.32        12.59         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
      117.07         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       46.75        79.69        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       34.49        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  FRS3 MUTATED FRS3 WILD-TYPE 
          1.51           0.00 
  FRS3 MUTATED FRS3 WILD-TYPE 
        140.38         148.01 
  FRS3 MUTATED FRS3 WILD-TYPE 
        27.105         20.120 
[1] "1.5 - 140.4 (27.1)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.1"
D717V2, continuous
D717V3, binary
                cls
clus               0   1
  FRS3 MUTATED    10   2
  FRS3 WILD-TYPE 356 117
[1] "tbl2"
                cls
clus             [,1] [,2]
  FRS3 MUTATED     10    2
  FRS3 WILD-TYPE  356  117
        clus
vv       FRS3 MUTATED FRS3 WILD-TYPE
  COLON            10            356
  RECTUM            2            117
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FRS3 MUTATED         0        0        2         6         0         0
  FRS3 WILD-TYPE      91        1       30       132        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  FRS3 MUTATED           1          0          0          1        2         0
  FRS3 WILD-TYPE        23         11         59         41       46        18
                vv
clus             STAGE IVB
  FRS3 MUTATED           0
  FRS3 WILD-TYPE         1
D717V4, multiclass
            clus
vv           FRS3 MUTATED FRS3 WILD-TYPE
  STAGE I               0             91
  STAGE IA              0              1
  STAGE II              2             30
  STAGE IIA             6            132
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             1             23
  STAGE IIIA            0             11
  STAGE IIIB            0             59
  STAGE IIIC            1             41
  STAGE IV              2             46
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  FRS3 MUTATED     0   0  10   2
  FRS3 WILD-TYPE  17  92 319  48
D717V5, multiclass
    clus
vv   FRS3 MUTATED FRS3 WILD-TYPE
  T1            0             17
  T2            0             92
  T3           10            319
  T4            2             48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  FRS3 MUTATED     8   1   3
  FRS3 WILD-TYPE 279 112  84
D717V6, multiclass
    clus
vv   FRS3 MUTATED FRS3 WILD-TYPE
  N0            8            279
  N1            1            112
  N2            3             84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D717V7, binary
                cls
clus               0   1
  FRS3 MUTATED     9   2
  FRS3 WILD-TYPE 366  63
[1] "tbl2"
                cls
clus             [,1] [,2]
  FRS3 MUTATED      9    2
  FRS3 WILD-TYPE  366   63
   clus
vv  FRS3 MUTATED FRS3 WILD-TYPE
  0            9            366
  1            2             63
[1] 2 2
[1] FALSE
D717V8, binary
                cls
clus               0   1
  FRS3 MUTATED     3   9
  FRS3 WILD-TYPE 222 255
[1] "tbl2"
                cls
clus             [,1] [,2]
  FRS3 MUTATED      3    9
  FRS3 WILD-TYPE  222  255
        clus
vv       FRS3 MUTATED FRS3 WILD-TYPE
  FEMALE            3            222
  MALE              9            255
[1] 2 2
[1] FALSE
D717V9, binary
                cls
clus               0   1
  FRS3 MUTATED     7   2
  FRS3 WILD-TYPE 343  20
[1] "tbl2"
                cls
clus             [,1] [,2]
  FRS3 MUTATED      7    2
  FRS3 WILD-TYPE  343   20
     clus
vv    FRS3 MUTATED FRS3 WILD-TYPE
  NO             7            343
  YES            2             20
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  FRS3 MUTATED                      6                             4
  FRS3 WILD-TYPE                  309                            43
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  FRS3 MUTATED                       2                              0
  FRS3 WILD-TYPE                   104                             10
D717V10, multiclass
                                clus
vv                               FRS3 MUTATED FRS3 WILD-TYPE
  COLON ADENOCARCINOMA                      6            309
  COLON MUCINOUS ADENOCARCINOMA             4             43
  RECTAL ADENOCARCINOMA                     2            104
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  FRS3 MUTATED     7   0   1   1
  FRS3 WILD-TYPE 338   4  30  24
D717V11, multiclass
    clus
vv   FRS3 MUTATED FRS3 WILD-TYPE
  R0            7            338
  R1            0              4
  R2            1             30
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D717V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FRS3 MUTATED                                  0     1
  FRS3 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  FRS3 MUTATED                           1     7
  FRS3 WILD-TYPE                        21   219
D717V13, multiclass
                                  clus
vv                                 FRS3 MUTATED FRS3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                       7            219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(718) Variable = EEF1D MUTATION ANALYSIS
D718V1, survival
                 sevent
clus2               0   1
  EEF1D MUTATED    10   1
  EEF1D WILD-TYPE 368  92
  EEF1D MUTATED EEF1D WILD-TYPE 
             11             460 
  EEF1D MUTATED EEF1D WILD-TYPE 
              1              92 
$`EEF1D MUTATED`
TCGA-AA-3713 TCGA-AZ-6601 TCGA-CM-5861 TCGA-D5-6920 TCGA-F4-6856 TCGA-G4-6310 
       19.04       100.01        15.02         3.68        35.31        63.62 
TCGA-G4-6588 TCGA-G4-6628 TCGA-DC-5337 TCGA-EI-6510 TCGA-G5-6235 
       26.17        79.69        15.02        18.28        55.76 

$`EEF1D WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77        12.10        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       32.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6922 
       17.13        12.49        16.14        15.58         1.48         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
        0.53        47.41       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       44.68        55.04        85.48        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 
       13.78        35.80        91.79        46.75        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
        7.17         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       19.96        20.91         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6641 
       32.19         0.66         0.69        26.43 

  EEF1D MUTATED EEF1D WILD-TYPE 
           3.68            0.00 
  EEF1D MUTATED EEF1D WILD-TYPE 
         100.01          148.01 
  EEF1D MUTATED EEF1D WILD-TYPE 
         26.170          20.155 
[1] "3.7 - 100.0 (26.2)" "0.0 - 148.0 (20.2)"
[1] "hr=" "3.4"
D718V2, continuous
D718V3, binary
                 cls
clus                0   1
  EEF1D MUTATED     9   3
  EEF1D WILD-TYPE 357 116
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EEF1D MUTATED      9    3
  EEF1D WILD-TYPE  357  116
        clus
vv       EEF1D MUTATED EEF1D WILD-TYPE
  COLON              9             357
  RECTUM             3             116
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  EEF1D MUTATED         3        0        1         3         0         0
  EEF1D WILD-TYPE      88        1       31       135        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  EEF1D MUTATED           0          0          2          1        1         1
  EEF1D WILD-TYPE        24         11         57         41       47        17
                 vv
clus              STAGE IVB
  EEF1D MUTATED           0
  EEF1D WILD-TYPE         1
D718V4, multiclass
            clus
vv           EEF1D MUTATED EEF1D WILD-TYPE
  STAGE I                3              88
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              3             135
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             2              57
  STAGE IIIC             1              41
  STAGE IV               1              47
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  EEF1D MUTATED     1   3   8   0
  EEF1D WILD-TYPE  16  89 321  50
D718V5, multiclass
    clus
vv   EEF1D MUTATED EEF1D WILD-TYPE
  T1             1              16
  T2             3              89
  T3             8             321
  T4             0              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  EEF1D MUTATED     9   2   1
  EEF1D WILD-TYPE 278 111  86
D718V6, multiclass
    clus
vv   EEF1D MUTATED EEF1D WILD-TYPE
  N0             9             278
  N1             2             111
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D718V7, binary
                 cls
clus                0   1
  EEF1D MUTATED     8   1
  EEF1D WILD-TYPE 367  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EEF1D MUTATED      8    1
  EEF1D WILD-TYPE  367   64
   clus
vv  EEF1D MUTATED EEF1D WILD-TYPE
  0             8             367
  1             1              64
[1] 2 2
[1] FALSE
D718V8, binary
                 cls
clus                0   1
  EEF1D MUTATED     4   8
  EEF1D WILD-TYPE 221 256
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EEF1D MUTATED      4    8
  EEF1D WILD-TYPE  221  256
        clus
vv       EEF1D MUTATED EEF1D WILD-TYPE
  FEMALE             4             221
  MALE               8             256
[1] 2 2
[1] FALSE
D718V9, binary
                 cls
clus                0   1
  EEF1D MUTATED     8   2
  EEF1D WILD-TYPE 342  20
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EEF1D MUTATED      8    2
  EEF1D WILD-TYPE  342   20
     clus
vv    EEF1D MUTATED EEF1D WILD-TYPE
  NO              8             342
  YES             2              20
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  EEF1D MUTATED                      7                             2
  EEF1D WILD-TYPE                  308                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  EEF1D MUTATED                       3                              0
  EEF1D WILD-TYPE                   103                             10
D718V10, multiclass
                                clus
vv                               EEF1D MUTATED EEF1D WILD-TYPE
  COLON ADENOCARCINOMA                       7             308
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      3             103
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  EEF1D MUTATED     9   1   1   0
  EEF1D WILD-TYPE 336   3  30  25
D718V11, multiclass
    clus
vv   EEF1D MUTATED EEF1D WILD-TYPE
  R0             9             336
  R1             1               3
  R2             1              30
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D718V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  EEF1D MUTATED                                  0     0
  EEF1D WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  EEF1D MUTATED                           0    11
  EEF1D WILD-TYPE                        22   215
D718V13, multiclass
                                  clus
vv                                 EEF1D MUTATED EEF1D WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                       11             215
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(719) Variable = DOCK10 MUTATION ANALYSIS
D719V1, survival
                  sevent
clus2                0   1
  DOCK10 MUTATED    19   7
  DOCK10 WILD-TYPE 359  86
  DOCK10 MUTATED DOCK10 WILD-TYPE 
              26              445 
  DOCK10 MUTATED DOCK10 WILD-TYPE 
               7               86 
$`DOCK10 MUTATED`
TCGA-A6-3809 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3697 
       32.75        24.16         1.02        14.01         0.92        85.05 
TCGA-AA-3713 TCGA-AA-3821 TCGA-AA-3977 TCGA-AA-3986 TCGA-AA-A00N TCGA-AA-A010 
       19.04         1.02        25.02        19.07         4.01        34.98 
TCGA-AD-5900 TCGA-AD-6901 TCGA-AY-6197 TCGA-AZ-6600 TCGA-CA-6717 TCGA-CA-6718 
        0.07        22.42        21.44        12.10        12.76        10.06 
TCGA-DM-A1D4 TCGA-DM-A1D8 TCGA-DM-A1HB TCGA-F4-6570 TCGA-G4-6307 TCGA-AG-A002 
       92.75        12.59       135.65         6.18        55.04        20.98 
TCGA-DC-6682 TCGA-G5-6235 
        4.01        55.76 

$`DOCK10 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       25.18        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3510 
       19.66        20.28         7.04         3.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        2.01        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3715 
       37.05        19.00        36.00         5.03        26.99        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 
       10.06        35.05        33.04         0.99        25.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 
        0.92        41.00        39.98        18.05        40.96        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6963 
       15.52        56.55         0.79         0.72         5.79        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       33.01        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 
       22.36        62.79        88.21        49.41         6.77       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 
        3.06         3.25         3.29         0.07        12.20        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       49.91        13.32       140.38         7.50        44.32       131.51 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 
      117.07        98.24         8.61        31.96        35.74        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       53.62        44.68        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 
       27.95        10.98        19.99         5.95         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6641 
       26.43 

  DOCK10 MUTATED DOCK10 WILD-TYPE 
            0.07             0.00 
  DOCK10 MUTATED DOCK10 WILD-TYPE 
          135.65           148.01 
  DOCK10 MUTATED DOCK10 WILD-TYPE 
          19.055           20.280 
[1] "0.1 - 135.7 (19.1)" "0.0 - 148.0 (20.3)"
[1] "hr=" "1.4"
D719V2, continuous
D719V3, binary
                  cls
clus                 0   1
  DOCK10 MUTATED    25   3
  DOCK10 WILD-TYPE 341 116
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DOCK10 MUTATED     25    3
  DOCK10 WILD-TYPE  341  116
        clus
vv       DOCK10 MUTATED DOCK10 WILD-TYPE
  COLON              25              341
  RECTUM              3              116
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DOCK10 MUTATED         5        0        2         7         3         0
  DOCK10 WILD-TYPE      86        1       30       131         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DOCK10 MUTATED           2          0          4          0        2
  DOCK10 WILD-TYPE        22         11         55         42       46
                  vv
clus               STAGE IVA STAGE IVB
  DOCK10 MUTATED           0         0
  DOCK10 WILD-TYPE        18         1
D719V4, multiclass
            clus
vv           DOCK10 MUTATED DOCK10 WILD-TYPE
  STAGE I                 5               86
  STAGE IA                0                1
  STAGE II                2               30
  STAGE IIA               7              131
  STAGE IIB               3                7
  STAGE IIC               0                1
  STAGE III               2               22
  STAGE IIIA              0               11
  STAGE IIIB              4               55
  STAGE IIIC              0               42
  STAGE IV                2               46
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  DOCK10 MUTATED     0   6  17   5
  DOCK10 WILD-TYPE  17  86 312  45
D719V5, multiclass
    clus
vv   DOCK10 MUTATED DOCK10 WILD-TYPE
  T1              0               17
  T2              6               86
  T3             17              312
  T4              5               45
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  DOCK10 MUTATED    21   7   0
  DOCK10 WILD-TYPE 266 106  87
D719V6, multiclass
    clus
vv   DOCK10 MUTATED DOCK10 WILD-TYPE
  N0             21              266
  N1              7              106
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D719V7, binary
                  cls
clus                 0   1
  DOCK10 MUTATED    20   2
  DOCK10 WILD-TYPE 355  63
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DOCK10 MUTATED     20    2
  DOCK10 WILD-TYPE  355   63
   clus
vv  DOCK10 MUTATED DOCK10 WILD-TYPE
  0             20              355
  1              2               63
[1] 2 2
[1] FALSE
D719V8, binary
                  cls
clus                 0   1
  DOCK10 MUTATED    11  17
  DOCK10 WILD-TYPE 214 247
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DOCK10 MUTATED     11   17
  DOCK10 WILD-TYPE  214  247
        clus
vv       DOCK10 MUTATED DOCK10 WILD-TYPE
  FEMALE             11              214
  MALE               17              247
[1] 2 2
[1] FALSE
D719V9, binary
                  cls
clus                 0   1
  DOCK10 MUTATED    17   1
  DOCK10 WILD-TYPE 333  21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DOCK10 MUTATED     17    1
  DOCK10 WILD-TYPE  333   21
     clus
vv    DOCK10 MUTATED DOCK10 WILD-TYPE
  NO              17              333
  YES              1               21
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  DOCK10 MUTATED                     19                             5
  DOCK10 WILD-TYPE                  296                            42
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  DOCK10 MUTATED                       3                              0
  DOCK10 WILD-TYPE                   103                             10
D719V10, multiclass
                                clus
vv                               DOCK10 MUTATED DOCK10 WILD-TYPE
  COLON ADENOCARCINOMA                       19              296
  COLON MUCINOUS ADENOCARCINOMA               5               42
  RECTAL ADENOCARCINOMA                       3              103
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  DOCK10 MUTATED    17   1   1   2
  DOCK10 WILD-TYPE 328   3  30  23
D719V11, multiclass
    clus
vv   DOCK10 MUTATED DOCK10 WILD-TYPE
  R0             17              328
  R1              1                3
  R2              1               30
  RX              2               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D719V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DOCK10 MUTATED                                  0     2
  DOCK10 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  DOCK10 MUTATED                           1    12
  DOCK10 WILD-TYPE                        21   214
D719V13, multiclass
                                  clus
vv                                 DOCK10 MUTATED DOCK10 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                9
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                        12              214
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(720) Variable = EXOC4 MUTATION ANALYSIS
D720V1, survival
                 sevent
clus2               0   1
  EXOC4 MUTATED    15   4
  EXOC4 WILD-TYPE 363  89
  EXOC4 MUTATED EXOC4 WILD-TYPE 
             19             452 
  EXOC4 MUTATED EXOC4 WILD-TYPE 
              4              89 
$`EXOC4 MUTATED`
TCGA-A6-5661 TCGA-A6-6141 TCGA-A6-6780 TCGA-AA-3713 TCGA-AA-3845 TCGA-AA-3854 
       33.53         8.38        20.12        19.04         0.00        36.03 
TCGA-AA-3864 TCGA-AD-6895 TCGA-AZ-4315 TCGA-AZ-6599 TCGA-CK-4948 TCGA-D5-6540 
       53.00         0.72        58.39         6.77       148.01        16.14 
TCGA-D5-6924 TCGA-DM-A0X9 TCGA-DM-A1DA TCGA-DM-A1HB TCGA-G4-6628 TCGA-AG-3583 
       14.30       119.70         7.50       135.65        79.69        20.05 
TCGA-AG-A002 
       20.98 

$`EXOC4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 
       22.06        32.71        27.09        22.52        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6781 
       24.16        21.76        24.69        24.39        23.87        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       85.05        26.99        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02        14.93        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
        0.00        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       15.52        56.55         0.79         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       33.01        21.44        17.82         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        88.21        49.41        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       10.06        14.30        17.56        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 
       15.58         1.48         3.68         4.41        12.43         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
       10.26        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 
       13.32        12.59       140.38        44.32       131.51       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       46.75        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       36.03        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  EXOC4 MUTATED EXOC4 WILD-TYPE 
              0               0 
  EXOC4 MUTATED EXOC4 WILD-TYPE 
         148.01          140.38 
  EXOC4 MUTATED EXOC4 WILD-TYPE 
         20.120          20.235 
[1] "0.0 - 148.0 (20.1)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.3"
D720V2, continuous
D720V3, binary
                 cls
clus                0   1
  EXOC4 MUTATED    18   2
  EXOC4 WILD-TYPE 348 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EXOC4 MUTATED     18    2
  EXOC4 WILD-TYPE  348  117
        clus
vv       EXOC4 MUTATED EXOC4 WILD-TYPE
  COLON             18             348
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  EXOC4 MUTATED         5        0        1         7         0         0
  EXOC4 WILD-TYPE      86        1       31       131        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  EXOC4 MUTATED           2          0          1          1        2         0
  EXOC4 WILD-TYPE        22         11         58         41       46        18
                 vv
clus              STAGE IVB
  EXOC4 MUTATED           0
  EXOC4 WILD-TYPE         1
D720V4, multiclass
            clus
vv           EXOC4 MUTATED EXOC4 WILD-TYPE
  STAGE I                5              86
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              7             131
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              2              22
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             1              41
  STAGE IV               2              46
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  EXOC4 MUTATED     0   5  15   0
  EXOC4 WILD-TYPE  17  87 314  50
D720V5, multiclass
    clus
vv   EXOC4 MUTATED EXOC4 WILD-TYPE
  T1             0              17
  T2             5              87
  T3            15             314
  T4             0              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  EXOC4 MUTATED    14   3   3
  EXOC4 WILD-TYPE 273 110  84
D720V6, multiclass
    clus
vv   EXOC4 MUTATED EXOC4 WILD-TYPE
  N0            14             273
  N1             3             110
  N2             3              84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D720V7, binary
                 cls
clus                0   1
  EXOC4 MUTATED    15   2
  EXOC4 WILD-TYPE 360  63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EXOC4 MUTATED     15    2
  EXOC4 WILD-TYPE  360   63
   clus
vv  EXOC4 MUTATED EXOC4 WILD-TYPE
  0            15             360
  1             2              63
[1] 2 2
[1] FALSE
D720V8, binary
                 cls
clus                0   1
  EXOC4 MUTATED     6  14
  EXOC4 WILD-TYPE 219 250
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EXOC4 MUTATED      6   14
  EXOC4 WILD-TYPE  219  250
        clus
vv       EXOC4 MUTATED EXOC4 WILD-TYPE
  FEMALE             6             219
  MALE              14             250
[1] 2 2
[1] FALSE
D720V9, binary
                 cls
clus                0   1
  EXOC4 MUTATED    13   1
  EXOC4 WILD-TYPE 337  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EXOC4 MUTATED     13    1
  EXOC4 WILD-TYPE  337   21
     clus
vv    EXOC4 MUTATED EXOC4 WILD-TYPE
  NO             13             337
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  EXOC4 MUTATED                     14                             3
  EXOC4 WILD-TYPE                  301                            44
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  EXOC4 MUTATED                       1                              1
  EXOC4 WILD-TYPE                   105                              9
D720V10, multiclass
                                clus
vv                               EXOC4 MUTATED EXOC4 WILD-TYPE
  COLON ADENOCARCINOMA                      14             301
  COLON MUCINOUS ADENOCARCINOMA              3              44
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             1               9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  EXOC4 MUTATED    11   0   2   0
  EXOC4 WILD-TYPE 334   4  29  25
D720V11, multiclass
    clus
vv   EXOC4 MUTATED EXOC4 WILD-TYPE
  R0            11             334
  R1             0               4
  R2             2              29
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D720V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  EXOC4 MUTATED                                  0     0
  EXOC4 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  EXOC4 MUTATED                           2    11
  EXOC4 WILD-TYPE                        20   215
D720V13, multiclass
                                  clus
vv                                 EXOC4 MUTATED EXOC4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    2              20
  WHITE                                       11             215
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(721) Variable = CEACAM1 MUTATION ANALYSIS
D721V1, survival
                   sevent
clus2                 0   1
  CEACAM1 MUTATED     4   1
  CEACAM1 WILD-TYPE 374  92
  CEACAM1 MUTATED CEACAM1 WILD-TYPE 
                5               466 
  CEACAM1 MUTATED CEACAM1 WILD-TYPE 
                1                92 
$`CEACAM1 MUTATED`
TCGA-AA-3525 TCGA-D5-6533 TCGA-F4-6459 TCGA-CI-6624 TCGA-F5-6812 
        8.05         1.32         8.61         4.73         0.66 

$`CEACAM1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       55.92        20.19        18.25        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
       60.79       117.07        98.24        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
        6.05        33.17         6.97        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.69        55.76        26.43 

  CEACAM1 MUTATED CEACAM1 WILD-TYPE 
             0.66              0.00 
  CEACAM1 MUTATED CEACAM1 WILD-TYPE 
             8.61            148.01 
  CEACAM1 MUTATED CEACAM1 WILD-TYPE 
             4.73             20.73 
[1] "0.7 - 8.6 (4.7)"    "0.0 - 148.0 (20.7)"
[1] "hr=" "5"  
D721V2, continuous
D721V3, binary
                   cls
clus                  0   1
  CEACAM1 MUTATED     3   2
  CEACAM1 WILD-TYPE 363 117
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CEACAM1 MUTATED      3    2
  CEACAM1 WILD-TYPE  363  117
        clus
vv       CEACAM1 MUTATED CEACAM1 WILD-TYPE
  COLON                3               363
  RECTUM               2               117
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CEACAM1 MUTATED         1        0        0         1         0         0
  CEACAM1 WILD-TYPE      90        1       32       137        10         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CEACAM1 MUTATED           0          0          3          0        0
  CEACAM1 WILD-TYPE        24         11         56         42       48
                   vv
clus                STAGE IVA STAGE IVB
  CEACAM1 MUTATED           0         0
  CEACAM1 WILD-TYPE        18         1
D721V4, multiclass
            clus
vv           CEACAM1 MUTATED CEACAM1 WILD-TYPE
  STAGE I                  1                90
  STAGE IA                 0                 1
  STAGE II                 0                32
  STAGE IIA                1               137
  STAGE IIB                0                10
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               0                11
  STAGE IIIB               3                56
  STAGE IIIC               0                42
  STAGE IV                 0                48
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  CEACAM1 MUTATED     0   1   3   1
  CEACAM1 WILD-TYPE  17  91 326  49
D721V5, multiclass
    clus
vv   CEACAM1 MUTATED CEACAM1 WILD-TYPE
  T1               0                17
  T2               1                91
  T3               3               326
  T4               1                49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  CEACAM1 MUTATED     3   1   1
  CEACAM1 WILD-TYPE 284 112  86
D721V6, multiclass
    clus
vv   CEACAM1 MUTATED CEACAM1 WILD-TYPE
  N0               3               284
  N1               1               112
  N2               1                86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D721V7, binary
                   cls
clus                  0   1
  CEACAM1 MUTATED     5   0
  CEACAM1 WILD-TYPE 370  65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CEACAM1 MUTATED      5    0
  CEACAM1 WILD-TYPE  370   65
   clus
vv  CEACAM1 MUTATED CEACAM1 WILD-TYPE
  0               5               370
  1               0                65
[1] 2 2
[1] FALSE
D721V8, binary
                   cls
clus                  0   1
  CEACAM1 MUTATED     3   2
  CEACAM1 WILD-TYPE 222 262
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CEACAM1 MUTATED      3    2
  CEACAM1 WILD-TYPE  222  262
        clus
vv       CEACAM1 MUTATED CEACAM1 WILD-TYPE
  FEMALE               3               222
  MALE                 2               262
[1] 2 2
[1] FALSE
D721V9, binary
                   cls
clus                  0   1
  CEACAM1 MUTATED     2   0
  CEACAM1 WILD-TYPE 348  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CEACAM1 MUTATED      2    0
  CEACAM1 WILD-TYPE  348   22
     clus
vv    CEACAM1 MUTATED CEACAM1 WILD-TYPE
  NO                2               348
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CEACAM1 MUTATED                      3                             0
  CEACAM1 WILD-TYPE                  312                            47
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CEACAM1 MUTATED                       2                              0
  CEACAM1 WILD-TYPE                   104                             10
D721V10, multiclass
                                clus
vv                               CEACAM1 MUTATED CEACAM1 WILD-TYPE
  COLON ADENOCARCINOMA                         3               312
  COLON MUCINOUS ADENOCARCINOMA                0                47
  RECTAL ADENOCARCINOMA                        2               104
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  CEACAM1 MUTATED     4   0   0   0
  CEACAM1 WILD-TYPE 341   4  31  25
D721V11, multiclass
    clus
vv   CEACAM1 MUTATED CEACAM1 WILD-TYPE
  R0               4               341
  R1               0                 4
  R2               0                31
  RX               0                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D721V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CEACAM1 MUTATED                                  0     0
  CEACAM1 WILD-TYPE                                1    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  CEACAM1 MUTATED                           0     4
  CEACAM1 WILD-TYPE                        22   222
D721V13, multiclass
                                  clus
vv                                 CEACAM1 MUTATED CEACAM1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                      0                22
  WHITE                                          4               222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(722) Variable = EIF5B MUTATION ANALYSIS
D722V1, survival
                 sevent
clus2               0   1
  EIF5B MUTATED    10   5
  EIF5B WILD-TYPE 368  88
  EIF5B MUTATED EIF5B WILD-TYPE 
             15             456 
  EIF5B MUTATED EIF5B WILD-TYPE 
              5              88 
$`EIF5B MUTATED`
TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3715 TCGA-AA-3977 TCGA-AD-6889 TCGA-AZ-6598 
        3.02        63.98        19.04        25.02        56.55        49.41 
TCGA-CA-6717 TCGA-CK-4950 TCGA-CK-5916 TCGA-D5-5538 TCGA-DM-A28K TCGA-F4-6570 
       12.76        85.45        21.14        12.26        98.24         6.18 
TCGA-F4-6856 TCGA-G4-6586 TCGA-G4-6588 
       35.31        35.80        26.17 

$`EIF5B WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 
       40.96         0.07        21.37        15.52         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       88.21         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07        12.20        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 
      148.01        15.62        49.08        51.32         9.99        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       45.40        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
        8.61        31.96        35.74        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  EIF5B MUTATED EIF5B WILD-TYPE 
           3.02            0.00 
  EIF5B MUTATED EIF5B WILD-TYPE 
          98.24          148.01 
  EIF5B MUTATED EIF5B WILD-TYPE 
         26.170          20.035 
[1] "3.0 - 98.2 (26.2)"  "0.0 - 148.0 (20.0)"
[1] "hr=" "1.2"
D722V2, continuous
D722V3, binary
                 cls
clus                0   1
  EIF5B MUTATED    16   0
  EIF5B WILD-TYPE 350 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EIF5B MUTATED     16    0
  EIF5B WILD-TYPE  350  119
        clus
vv       EIF5B MUTATED EIF5B WILD-TYPE
  COLON             16             350
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  EIF5B MUTATED         2        0        5         6         0         0
  EIF5B WILD-TYPE      89        1       27       132        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  EIF5B MUTATED           0          0          2          0        0         0
  EIF5B WILD-TYPE        24         11         57         42       48        18
                 vv
clus              STAGE IVB
  EIF5B MUTATED           0
  EIF5B WILD-TYPE         1
D722V4, multiclass
            clus
vv           EIF5B MUTATED EIF5B WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               5              27
  STAGE IIA              6             132
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             2              57
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  EIF5B MUTATED     1   2  12   1
  EIF5B WILD-TYPE  16  90 317  49
D722V5, multiclass
    clus
vv   EIF5B MUTATED EIF5B WILD-TYPE
  T1             1              16
  T2             2              90
  T3            12             317
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  EIF5B MUTATED    14   2   0
  EIF5B WILD-TYPE 273 111  87
D722V6, multiclass
    clus
vv   EIF5B MUTATED EIF5B WILD-TYPE
  N0            14             273
  N1             2             111
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D722V7, binary
                 cls
clus                0   1
  EIF5B MUTATED    14   0
  EIF5B WILD-TYPE 361  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EIF5B MUTATED     14    0
  EIF5B WILD-TYPE  361   65
   clus
vv  EIF5B MUTATED EIF5B WILD-TYPE
  0            14             361
  1             0              65
[1] 2 2
[1] FALSE
D722V8, binary
                 cls
clus                0   1
  EIF5B MUTATED     9   7
  EIF5B WILD-TYPE 216 257
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EIF5B MUTATED      9    7
  EIF5B WILD-TYPE  216  257
        clus
vv       EIF5B MUTATED EIF5B WILD-TYPE
  FEMALE             9             216
  MALE               7             257
[1] 2 2
[1] FALSE
D722V9, binary
                 cls
clus                0   1
  EIF5B MUTATED    13   0
  EIF5B WILD-TYPE 337  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EIF5B MUTATED     13    0
  EIF5B WILD-TYPE  337   22
     clus
vv    EIF5B MUTATED EIF5B WILD-TYPE
  NO             13             337
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  EIF5B MUTATED                     13                             3
  EIF5B WILD-TYPE                  302                            44
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  EIF5B MUTATED                       0                              0
  EIF5B WILD-TYPE                   106                             10
D722V10, multiclass
                                clus
vv                               EIF5B MUTATED EIF5B WILD-TYPE
  COLON ADENOCARCINOMA                      13             302
  COLON MUCINOUS ADENOCARCINOMA              3              44
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  EIF5B MUTATED     9   1   0   2
  EIF5B WILD-TYPE 336   3  31  23
D722V11, multiclass
    clus
vv   EIF5B MUTATED EIF5B WILD-TYPE
  R0             9             336
  R1             1               3
  R2             0              31
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D722V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  EIF5B MUTATED                                  0     2
  EIF5B WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  EIF5B MUTATED                           1     8
  EIF5B WILD-TYPE                        21   218
D722V13, multiclass
                                  clus
vv                                 EIF5B MUTATED EIF5B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               9
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        8             218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(723) Variable = PRAMEF12 MUTATION ANALYSIS
D723V1, survival
                    sevent
clus2                  0   1
  PRAMEF12 MUTATED     4   3
  PRAMEF12 WILD-TYPE 374  90
  PRAMEF12 MUTATED PRAMEF12 WILD-TYPE 
                 7                464 
  PRAMEF12 MUTATED PRAMEF12 WILD-TYPE 
                 3                 90 
$`PRAMEF12 MUTATED`
TCGA-AA-3715 TCGA-AZ-6603 TCGA-CM-6171 TCGA-DM-A28F TCGA-G4-6309 TCGA-AG-A002 
       19.04        29.56        14.04        35.97        85.48        20.98 
TCGA-F5-6812 
        0.66 

$`PRAMEF12 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77        12.10       100.01         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 
       14.99        12.99        13.02        15.02        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H 
      139.17         6.12        81.37       119.93        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       53.62        44.68        55.04        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6813 
        9.96        49.51        31.30        28.57        32.19         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  PRAMEF12 MUTATED PRAMEF12 WILD-TYPE 
              0.66               0.00 
  PRAMEF12 MUTATED PRAMEF12 WILD-TYPE 
             85.48             148.01 
  PRAMEF12 MUTATED PRAMEF12 WILD-TYPE 
            20.980             20.155 
[1] "0.7 - 85.5 (21.0)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "2.1"
D723V2, continuous
D723V3, binary
                    cls
clus                   0   1
  PRAMEF12 MUTATED     5   2
  PRAMEF12 WILD-TYPE 361 117
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  PRAMEF12 MUTATED      5    2
  PRAMEF12 WILD-TYPE  361  117
        clus
vv       PRAMEF12 MUTATED PRAMEF12 WILD-TYPE
  COLON                 5                361
  RECTUM                2                117
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PRAMEF12 MUTATED         2        0        1         1         0         0
  PRAMEF12 WILD-TYPE      89        1       31       137        10         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PRAMEF12 MUTATED           0          0          2          0        0
  PRAMEF12 WILD-TYPE        24         11         57         42       48
                    vv
clus                 STAGE IVA STAGE IVB
  PRAMEF12 MUTATED           0         0
  PRAMEF12 WILD-TYPE        18         1
D723V4, multiclass
            clus
vv           PRAMEF12 MUTATED PRAMEF12 WILD-TYPE
  STAGE I                   2                 89
  STAGE IA                  0                  1
  STAGE II                  1                 31
  STAGE IIA                 1                137
  STAGE IIB                 0                 10
  STAGE IIC                 0                  1
  STAGE III                 0                 24
  STAGE IIIA                0                 11
  STAGE IIIB                2                 57
  STAGE IIIC                0                 42
  STAGE IV                  0                 48
  STAGE IVA                 0                 18
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  PRAMEF12 MUTATED     0   3   4   0
  PRAMEF12 WILD-TYPE  17  89 325  50
D723V5, multiclass
    clus
vv   PRAMEF12 MUTATED PRAMEF12 WILD-TYPE
  T1                0                 17
  T2                3                 89
  T3                4                325
  T4                0                 50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  PRAMEF12 MUTATED     4   3   0
  PRAMEF12 WILD-TYPE 283 110  87
D723V6, multiclass
    clus
vv   PRAMEF12 MUTATED PRAMEF12 WILD-TYPE
  N0                4                283
  N1                3                110
  N2                0                 87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D723V7, binary
                    cls
clus                   0   1
  PRAMEF12 MUTATED     6   0
  PRAMEF12 WILD-TYPE 369  65
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  PRAMEF12 MUTATED      6    0
  PRAMEF12 WILD-TYPE  369   65
   clus
vv  PRAMEF12 MUTATED PRAMEF12 WILD-TYPE
  0                6                369
  1                0                 65
[1] 2 2
[1] FALSE
D723V8, binary
                    cls
clus                   0   1
  PRAMEF12 MUTATED     3   4
  PRAMEF12 WILD-TYPE 222 260
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  PRAMEF12 MUTATED      3    4
  PRAMEF12 WILD-TYPE  222  260
        clus
vv       PRAMEF12 MUTATED PRAMEF12 WILD-TYPE
  FEMALE                3                222
  MALE                  4                260
[1] 2 2
[1] FALSE
D723V9, binary
                    cls
clus                   0   1
  PRAMEF12 MUTATED     5   0
  PRAMEF12 WILD-TYPE 345  22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  PRAMEF12 MUTATED      5    0
  PRAMEF12 WILD-TYPE  345   22
     clus
vv    PRAMEF12 MUTATED PRAMEF12 WILD-TYPE
  NO                 5                345
  YES                0                 22
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PRAMEF12 MUTATED                      5                             0
  PRAMEF12 WILD-TYPE                  310                            47
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PRAMEF12 MUTATED                       2                              0
  PRAMEF12 WILD-TYPE                   104                             10
D723V10, multiclass
                                clus
vv                               PRAMEF12 MUTATED PRAMEF12 WILD-TYPE
  COLON ADENOCARCINOMA                          5                310
  COLON MUCINOUS ADENOCARCINOMA                 0                 47
  RECTAL ADENOCARCINOMA                         2                104
  RECTAL MUCINOUS ADENOCARCINOMA                0                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  PRAMEF12 MUTATED     5   0   0   0
  PRAMEF12 WILD-TYPE 340   4  31  25
D723V11, multiclass
    clus
vv   PRAMEF12 MUTATED PRAMEF12 WILD-TYPE
  R0                5                340
  R1                0                  4
  R2                0                 31
  RX                0                 25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D723V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PRAMEF12 MUTATED                                  0     0
  PRAMEF12 WILD-TYPE                                1    11
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  PRAMEF12 MUTATED                           1     4
  PRAMEF12 WILD-TYPE                        21   222
D723V13, multiclass
                                  clus
vv                                 PRAMEF12 MUTATED PRAMEF12 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 11
  BLACK OR AFRICAN AMERICAN                       1                 21
  WHITE                                           4                222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(724) Variable = SF1 MUTATION ANALYSIS
D724V1, survival
               sevent
clus2             0   1
  SF1 MUTATED    12   3
  SF1 WILD-TYPE 366  90
  SF1 MUTATED SF1 WILD-TYPE 
           15           456 
  SF1 MUTATED SF1 WILD-TYPE 
            3            90 
$`SF1 MUTATED`
TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-6142 TCGA-AA-3821 TCGA-AA-3947 TCGA-AA-3977 
       31.63        29.19        25.08         1.02        33.01        25.02 
TCGA-AA-A02Y TCGA-AD-6895 TCGA-AZ-6603 TCGA-CA-6718 TCGA-CM-4743 TCGA-CM-5868 
       39.98         0.72        29.56        10.06        23.05        17.03 
TCGA-DM-A1HB TCGA-AG-A002 TCGA-DY-A1DD 
      135.65        20.98        57.24 

$`SF1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       32.91        30.44        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6649 
       32.71        27.09        22.52         8.38        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
       33.04         0.99        25.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
        0.92        41.00        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       15.52        56.55         0.79         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
       12.10       100.01         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       12.76        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
      124.27        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        15.02        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
       44.32       131.51       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       41.36        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  SF1 MUTATED SF1 WILD-TYPE 
         0.72          0.00 
  SF1 MUTATED SF1 WILD-TYPE 
       135.65        148.01 
  SF1 MUTATED SF1 WILD-TYPE 
        25.08         20.02 
[1] "0.7 - 135.7 (25.1)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.1"
D724V2, continuous
D724V3, binary
               cls
clus              0   1
  SF1 MUTATED    14   2
  SF1 WILD-TYPE 352 117
[1] "tbl2"
               cls
clus            [,1] [,2]
  SF1 MUTATED     14    2
  SF1 WILD-TYPE  352  117
        clus
vv       SF1 MUTATED SF1 WILD-TYPE
  COLON           14           352
  RECTUM           2           117
[1] 2 2
[1] FALSE
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SF1 MUTATED         3        0        1         2         1         0
  SF1 WILD-TYPE      88        1       31       136         9         1
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SF1 MUTATED           0          0          3          1        0         2
  SF1 WILD-TYPE        24         11         56         41       48        16
               vv
clus            STAGE IVB
  SF1 MUTATED           0
  SF1 WILD-TYPE         1
D724V4, multiclass
            clus
vv           SF1 MUTATED SF1 WILD-TYPE
  STAGE I              3            88
  STAGE IA             0             1
  STAGE II             1            31
  STAGE IIA            2           136
  STAGE IIB            1             9
  STAGE IIC            0             1
  STAGE III            0            24
  STAGE IIIA           0            11
  STAGE IIIB           3            56
  STAGE IIIC           1            41
  STAGE IV             0            48
  STAGE IVA            2            16
  STAGE IVB            0             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  SF1 MUTATED     0   5   8   3
  SF1 WILD-TYPE  17  87 321  47
D724V5, multiclass
    clus
vv   SF1 MUTATED SF1 WILD-TYPE
  T1           0            17
  T2           5            87
  T3           8           321
  T4           3            47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2
  SF1 MUTATED     8   7   1
  SF1 WILD-TYPE 279 106  86
D724V6, multiclass
    clus
vv   SF1 MUTATED SF1 WILD-TYPE
  N0           8           279
  N1           7           106
  N2           1            86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D724V7, binary
               cls
clus              0   1
  SF1 MUTATED    11   2
  SF1 WILD-TYPE 364  63
[1] "tbl2"
               cls
clus            [,1] [,2]
  SF1 MUTATED     11    2
  SF1 WILD-TYPE  364   63
   clus
vv  SF1 MUTATED SF1 WILD-TYPE
  0          11           364
  1           2            63
[1] 2 2
[1] FALSE
D724V8, binary
               cls
clus              0   1
  SF1 MUTATED     7   9
  SF1 WILD-TYPE 218 255
[1] "tbl2"
               cls
clus            [,1] [,2]
  SF1 MUTATED      7    9
  SF1 WILD-TYPE  218  255
        clus
vv       SF1 MUTATED SF1 WILD-TYPE
  FEMALE           7           218
  MALE             9           255
[1] 2 2
[1] FALSE
D724V9, binary
               cls
clus              0   1
  SF1 MUTATED    12   0
  SF1 WILD-TYPE 338  22
[1] "tbl2"
               cls
clus            [,1] [,2]
  SF1 MUTATED     12    0
  SF1 WILD-TYPE  338   22
     clus
vv    SF1 MUTATED SF1 WILD-TYPE
  NO           12           338
  YES           0            22
[1] 2 2
[1] FALSE
               vv
clus            COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SF1 MUTATED                     11                             2
  SF1 WILD-TYPE                  304                            45
               vv
clus            RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SF1 MUTATED                       2                              0
  SF1 WILD-TYPE                   104                             10
D724V10, multiclass
                                clus
vv                               SF1 MUTATED SF1 WILD-TYPE
  COLON ADENOCARCINOMA                    11           304
  COLON MUCINOUS ADENOCARCINOMA            2            45
  RECTAL ADENOCARCINOMA                    2           104
  RECTAL MUCINOUS ADENOCARCINOMA           0            10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             R0  R1  R2  RX
  SF1 MUTATED     8   0   0   1
  SF1 WILD-TYPE 337   4  31  24
D724V11, multiclass
    clus
vv   SF1 MUTATED SF1 WILD-TYPE
  R0           8           337
  R1           0             4
  R2           0            31
  RX           1            24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D724V12, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SF1 MUTATED                                  0     1
  SF1 WILD-TYPE                                1    10
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  SF1 MUTATED                           2     7
  SF1 WILD-TYPE                        20   219
D724V13, multiclass
                                  clus
vv                                 SF1 MUTATED SF1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      1            10
  BLACK OR AFRICAN AMERICAN                  2            20
  WHITE                                      7           219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(725) Variable = BTNL3 MUTATION ANALYSIS
D725V1, survival
                 sevent
clus2               0   1
  BTNL3 MUTATED     8   0
  BTNL3 WILD-TYPE 370  93
  BTNL3 MUTATED BTNL3 WILD-TYPE 
              8             463 
  BTNL3 MUTATED BTNL3 WILD-TYPE 
              0              93 
$`BTNL3 MUTATED`
TCGA-A6-5665 TCGA-A6-6781 TCGA-CA-6717 TCGA-CM-4743 TCGA-CM-5861 TCGA-G4-6586 
       22.06        19.66        12.76        23.05        15.02        35.80 
TCGA-G4-6588 TCGA-AG-A002 
       26.17        20.98 

$`BTNL3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.20        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
        1.91       124.27        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 
       29.06        22.03        22.98        30.08        32.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       22.09        13.78        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  BTNL3 MUTATED BTNL3 WILD-TYPE 
          12.76            0.00 
  BTNL3 MUTATED BTNL3 WILD-TYPE 
          35.80          148.01 
  BTNL3 MUTATED BTNL3 WILD-TYPE 
          21.52           20.12 
[1] "12.8 - 35.8 (21.5)" "0.0 - 148.0 (20.1)"
[1] "hr="     "9200000"
D725V2, continuous
D725V3, binary
                 cls
clus                0   1
  BTNL3 MUTATED     7   1
  BTNL3 WILD-TYPE 359 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BTNL3 MUTATED      7    1
  BTNL3 WILD-TYPE  359  118
        clus
vv       BTNL3 MUTATED BTNL3 WILD-TYPE
  COLON              7             359
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  BTNL3 MUTATED         1        0        0         6         0         0
  BTNL3 WILD-TYPE      90        1       32       132        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  BTNL3 MUTATED           0          0          0          1        0         0
  BTNL3 WILD-TYPE        24         11         59         41       48        18
                 vv
clus              STAGE IVB
  BTNL3 MUTATED           0
  BTNL3 WILD-TYPE         1
D725V4, multiclass
            clus
vv           BTNL3 MUTATED BTNL3 WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              6             132
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             1              41
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  BTNL3 MUTATED     0   1   6   1
  BTNL3 WILD-TYPE  17  91 323  49
D725V5, multiclass
    clus
vv   BTNL3 MUTATED BTNL3 WILD-TYPE
  T1             0              17
  T2             1              91
  T3             6             323
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  BTNL3 MUTATED     7   1   0
  BTNL3 WILD-TYPE 280 112  87
D725V6, multiclass
    clus
vv   BTNL3 MUTATED BTNL3 WILD-TYPE
  N0             7             280
  N1             1             112
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D725V7, binary
                 cls
clus                0   1
  BTNL3 MUTATED     7   0
  BTNL3 WILD-TYPE 368  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BTNL3 MUTATED      7    0
  BTNL3 WILD-TYPE  368   65
   clus
vv  BTNL3 MUTATED BTNL3 WILD-TYPE
  0             7             368
  1             0              65
[1] 2 2
[1] FALSE
D725V8, binary
                 cls
clus                0   1
  BTNL3 MUTATED     4   4
  BTNL3 WILD-TYPE 221 260
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BTNL3 MUTATED      4    4
  BTNL3 WILD-TYPE  221  260
        clus
vv       BTNL3 MUTATED BTNL3 WILD-TYPE
  FEMALE             4             221
  MALE               4             260
[1] 2 2
[1] FALSE
D725V9, binary
                 cls
clus                0   1
  BTNL3 MUTATED     8   0
  BTNL3 WILD-TYPE 342  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BTNL3 MUTATED      8    0
  BTNL3 WILD-TYPE  342   22
     clus
vv    BTNL3 MUTATED BTNL3 WILD-TYPE
  NO              8             342
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  BTNL3 MUTATED                      5                             2
  BTNL3 WILD-TYPE                  310                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  BTNL3 MUTATED                       1                              0
  BTNL3 WILD-TYPE                   105                             10
D725V10, multiclass
                                clus
vv                               BTNL3 MUTATED BTNL3 WILD-TYPE
  COLON ADENOCARCINOMA                       5             310
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  BTNL3 MUTATED     7   0   0   1
  BTNL3 WILD-TYPE 338   4  31  24
D725V11, multiclass
    clus
vv   BTNL3 MUTATED BTNL3 WILD-TYPE
  R0             7             338
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D725V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  BTNL3 MUTATED                                  0     1
  BTNL3 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  BTNL3 MUTATED                           0     6
  BTNL3 WILD-TYPE                        22   220
D725V13, multiclass
                                  clus
vv                                 BTNL3 MUTATED BTNL3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        6             220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(726) Variable = EFCAB1 MUTATION ANALYSIS
D726V1, survival
                  sevent
clus2                0   1
  EFCAB1 MUTATED     4   1
  EFCAB1 WILD-TYPE 374  92
  EFCAB1 MUTATED EFCAB1 WILD-TYPE 
               5              466 
  EFCAB1 MUTATED EFCAB1 WILD-TYPE 
               1               92 
$`EFCAB1 MUTATED`
TCGA-AA-A00N TCGA-CK-4950 TCGA-AG-3893 TCGA-AG-A002 TCGA-DC-6683 
        4.01        85.45        35.01        20.98         5.03 

$`EFCAB1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
      148.01        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       13.02        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        4.01         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  EFCAB1 MUTATED EFCAB1 WILD-TYPE 
            4.01             0.00 
  EFCAB1 MUTATED EFCAB1 WILD-TYPE 
           85.45           148.01 
  EFCAB1 MUTATED EFCAB1 WILD-TYPE 
          20.980           20.155 
[1] "4.0 - 85.5 (21.0)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.1"
D726V2, continuous
D726V3, binary
                  cls
clus                 0   1
  EFCAB1 MUTATED     2   3
  EFCAB1 WILD-TYPE 364 116
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EFCAB1 MUTATED      2    3
  EFCAB1 WILD-TYPE  364  116
        clus
vv       EFCAB1 MUTATED EFCAB1 WILD-TYPE
  COLON               2              364
  RECTUM              3              116
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  EFCAB1 MUTATED         1        0        0         0         1         0
  EFCAB1 WILD-TYPE      90        1       32       138         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  EFCAB1 MUTATED           0          0          3          0        0
  EFCAB1 WILD-TYPE        24         11         56         42       48
                  vv
clus               STAGE IVA STAGE IVB
  EFCAB1 MUTATED           0         0
  EFCAB1 WILD-TYPE        18         1
D726V4, multiclass
            clus
vv           EFCAB1 MUTATED EFCAB1 WILD-TYPE
  STAGE I                 1               90
  STAGE IA                0                1
  STAGE II                0               32
  STAGE IIA               0              138
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              3               56
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  EFCAB1 MUTATED     0   1   3   1
  EFCAB1 WILD-TYPE  17  91 326  49
D726V5, multiclass
    clus
vv   EFCAB1 MUTATED EFCAB1 WILD-TYPE
  T1              0               17
  T2              1               91
  T3              3              326
  T4              1               49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  EFCAB1 MUTATED     2   3   0
  EFCAB1 WILD-TYPE 285 110  87
D726V6, multiclass
    clus
vv   EFCAB1 MUTATED EFCAB1 WILD-TYPE
  N0              2              285
  N1              3              110
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D726V7, binary
                  cls
clus                 0   1
  EFCAB1 MUTATED     5   0
  EFCAB1 WILD-TYPE 370  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EFCAB1 MUTATED      5    0
  EFCAB1 WILD-TYPE  370   65
   clus
vv  EFCAB1 MUTATED EFCAB1 WILD-TYPE
  0              5              370
  1              0               65
[1] 2 2
[1] FALSE
D726V8, binary
                  cls
clus                 0   1
  EFCAB1 MUTATED     1   4
  EFCAB1 WILD-TYPE 224 260
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EFCAB1 MUTATED      1    4
  EFCAB1 WILD-TYPE  224  260
        clus
vv       EFCAB1 MUTATED EFCAB1 WILD-TYPE
  FEMALE              1              224
  MALE                4              260
[1] 2 2
[1] FALSE
D726V9, binary
                  cls
clus                 0   1
  EFCAB1 MUTATED     3   0
  EFCAB1 WILD-TYPE 347  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EFCAB1 MUTATED      3    0
  EFCAB1 WILD-TYPE  347   22
     clus
vv    EFCAB1 MUTATED EFCAB1 WILD-TYPE
  NO               3              347
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  EFCAB1 MUTATED                      1                             1
  EFCAB1 WILD-TYPE                  314                            46
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  EFCAB1 MUTATED                       3                              0
  EFCAB1 WILD-TYPE                   103                             10
D726V10, multiclass
                                clus
vv                               EFCAB1 MUTATED EFCAB1 WILD-TYPE
  COLON ADENOCARCINOMA                        1              314
  COLON MUCINOUS ADENOCARCINOMA               1               46
  RECTAL ADENOCARCINOMA                       3              103
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  EFCAB1 MUTATED     4   1   0   0
  EFCAB1 WILD-TYPE 341   3  31  25
D726V11, multiclass
    clus
vv   EFCAB1 MUTATED EFCAB1 WILD-TYPE
  R0              4              341
  R1              1                3
  R2              0               31
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D726V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  EFCAB1 MUTATED                                  0     0
  EFCAB1 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  EFCAB1 MUTATED                           1     1
  EFCAB1 WILD-TYPE                        21   225
D726V13, multiclass
[1] "Remove cluster labels:" "EFCAB1 MUTATED"        
clus
  EFCAB1 MUTATED EFCAB1 WILD-TYPE 
               2              258 
      TCGA-A6-2671       TCGA-A6-2672       TCGA-A6-2674       TCGA-A6-2676 
"EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" 
      TCGA-A6-2677       TCGA-A6-2678       TCGA-A6-2683       TCGA-A6-3807 
"EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" 
      TCGA-A6-3808       TCGA-A6-3809       TCGA-A6-3810       TCGA-A6-4105 
"EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" 
      TCGA-A6-5656       TCGA-A6-5657       TCGA-A6-5659       TCGA-A6-5660 
"EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" 
      TCGA-A6-5661       TCGA-A6-5662       TCGA-A6-5664       TCGA-A6-5665 
"EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" 
      TCGA-A6-5666       TCGA-A6-6137       TCGA-A6-6138       TCGA-A6-6141 
"EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" 
      TCGA-A6-6142       TCGA-A6-6648       TCGA-A6-6649       TCGA-A6-6651 
"EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" 
      TCGA-A6-6652       TCGA-A6-6653       TCGA-A6-6654       TCGA-A6-6780 
"EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" 
      TCGA-A6-6781       TCGA-A6-6782       TCGA-AD-5900       TCGA-AD-6548 
"EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" 
      TCGA-AD-6888       TCGA-AD-6889       TCGA-AD-6890       TCGA-AD-6895 
"EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" 
      TCGA-AD-6899       TCGA-AD-6901       TCGA-AD-6963       TCGA-AD-6964 
"EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" 
      TCGA-AD-6965       TCGA-AU-3779       TCGA-AU-6004       TCGA-AY-4070 
"EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" 
      TCGA-AY-4071       TCGA-AY-5543       TCGA-AY-6196       TCGA-AY-6197 
"EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" 
      TCGA-AY-6386       TCGA-AZ-4315       TCGA-AZ-4323       TCGA-AZ-4616 
"EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" 
      TCGA-AZ-4681       TCGA-AZ-4682       TCGA-AZ-5403       TCGA-AZ-5407 
"EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" 
      TCGA-AZ-6598       TCGA-AZ-6599       TCGA-AZ-6600       TCGA-AZ-6601 
"EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" 
      TCGA-AZ-6603       TCGA-AZ-6605       TCGA-AZ-6606       TCGA-AZ-6607 
"EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" 
      TCGA-AZ-6608       TCGA-CA-5254       TCGA-CA-5255       TCGA-CA-5796 
"EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" 
      TCGA-CA-5797       TCGA-CA-6715       TCGA-CA-6716       TCGA-CA-6717 
"EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" 
      TCGA-CA-6718       TCGA-CA-6719       TCGA-CK-4947       TCGA-CK-4948 
"EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" 
      TCGA-CK-4952       TCGA-CK-5912       TCGA-CK-5913       TCGA-CK-5914 
"EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" 
      TCGA-CK-5915       TCGA-CK-5916       TCGA-CK-6746       TCGA-CK-6747 
"EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" 
      TCGA-CK-6748       TCGA-CK-6751       TCGA-CM-4743       TCGA-CM-4744 
"EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" 
      TCGA-CM-4746       TCGA-CM-4747       TCGA-CM-4752       TCGA-CM-5341 
"EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" 
      TCGA-CM-5344       TCGA-CM-5348       TCGA-CM-5349       TCGA-CM-5860 
"EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" 
      TCGA-CM-5861       TCGA-CM-5862       TCGA-CM-5863       TCGA-CM-5864 
"EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" 
      TCGA-CM-5868       TCGA-CM-6161       TCGA-CM-6162       TCGA-CM-6163 
"EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" 
      TCGA-CM-6164       TCGA-CM-6165       TCGA-CM-6166       TCGA-CM-6167 
"EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" 
      TCGA-CM-6168       TCGA-CM-6169       TCGA-CM-6170       TCGA-CM-6171 
"EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" 
      TCGA-CM-6172       TCGA-CM-6674       TCGA-CM-6675       TCGA-CM-6676 
"EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" 
      TCGA-CM-6677       TCGA-CM-6678       TCGA-CM-6679       TCGA-CM-6680 
"EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" 
      TCGA-D5-5537       TCGA-D5-5538       TCGA-D5-5539       TCGA-D5-5540 
"EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" 
      TCGA-D5-5541       TCGA-D5-6529       TCGA-D5-6532       TCGA-D5-6533 
"EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" 
      TCGA-D5-6534       TCGA-D5-6535       TCGA-D5-6536       TCGA-D5-6537 
"EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" 
      TCGA-D5-6538       TCGA-D5-6539       TCGA-D5-6540       TCGA-D5-6541 
"EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" 
      TCGA-D5-6898       TCGA-D5-6920       TCGA-D5-6922       TCGA-D5-6923 
"EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" 
      TCGA-D5-6924       TCGA-D5-6926       TCGA-D5-6927       TCGA-D5-6928 
"EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" 
      TCGA-D5-6929       TCGA-D5-6930       TCGA-D5-6931       TCGA-D5-6932 
"EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" 
      TCGA-D5-7000       TCGA-DM-A0X9       TCGA-DM-A0XD       TCGA-DM-A0XF 
"EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" 
      TCGA-DM-A1D0       TCGA-DM-A1D4       TCGA-DM-A1D6       TCGA-DM-A1D7 
"EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" 
      TCGA-DM-A1D8       TCGA-DM-A1D9       TCGA-DM-A1DA       TCGA-DM-A1DB 
"EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" 
      TCGA-DM-A1HA       TCGA-DM-A1HB       TCGA-DM-A282       TCGA-DM-A285 
"EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" 
      TCGA-DM-A28C       TCGA-DM-A28E       TCGA-DM-A28F       TCGA-DM-A28G 
"EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" 
      TCGA-DM-A28H       TCGA-DM-A28K       TCGA-F4-6459       TCGA-F4-6460 
"EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" 
      TCGA-F4-6569       TCGA-F4-6570       TCGA-F4-6703       TCGA-F4-6704 
"EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" 
      TCGA-F4-6805       TCGA-F4-6806       TCGA-F4-6807       TCGA-F4-6808 
"EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" 
      TCGA-F4-6809       TCGA-F4-6854       TCGA-F4-6855       TCGA-F4-6856 
"EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" 
      TCGA-G4-6293       TCGA-G4-6299       TCGA-G4-6303       TCGA-G4-6304 
"EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" 
      TCGA-G4-6306       TCGA-G4-6307       TCGA-G4-6309       TCGA-G4-6310 
"EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" 
      TCGA-G4-6315       TCGA-G4-6317       TCGA-G4-6321       TCGA-G4-6323 
"EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" 
      TCGA-G4-6586       TCGA-G4-6588       TCGA-G4-6625       TCGA-G4-6626 
"EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" 
      TCGA-G4-6628       TCGA-AF-2687       TCGA-AF-2689       TCGA-AF-2691 
"EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" 
      TCGA-AF-2692       TCGA-AF-2693       TCGA-AF-3400       TCGA-AF-3913 
"EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" 
      TCGA-AF-4110       TCGA-AF-5654       TCGA-AF-6136       TCGA-AF-6655 
"EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" 
      TCGA-AF-6672       TCGA-AH-6544       TCGA-AH-6547       TCGA-AH-6549 
"EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" 
      TCGA-AH-6643       TCGA-AH-6644       TCGA-CI-6619       TCGA-CI-6620 
"EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" 
      TCGA-CI-6621       TCGA-CI-6622       TCGA-CI-6624       TCGA-CL-5917 
"EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" 
      TCGA-CL-5918       TCGA-DC-5337       TCGA-DC-5869       TCGA-DC-6155 
"EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" 
      TCGA-DC-6157       TCGA-DC-6158       TCGA-DC-6160       TCGA-DC-6681 
"EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" 
      TCGA-DC-6682       TCGA-DT-5265       TCGA-DY-A0XA       TCGA-DY-A1DC 
"EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" 
      TCGA-DY-A1DD       TCGA-DY-A1DF       TCGA-DY-A1DG       TCGA-DY-A1H8 
"EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" 
      TCGA-EF-5830       TCGA-EI-6506       TCGA-EI-6507       TCGA-EI-6508 
"EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" 
      TCGA-EI-6510       TCGA-F5-6464       TCGA-F5-6465       TCGA-F5-6571 
"EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" 
      TCGA-F5-6702       TCGA-F5-6811       TCGA-F5-6812       TCGA-F5-6813 
"EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" 
      TCGA-G5-6235       TCGA-G5-6641 
"EFCAB1 WILD-TYPE" "EFCAB1 WILD-TYPE" 

Clustering(727) Variable = IKZF4 MUTATION ANALYSIS
D727V1, survival
                 sevent
clus2               0   1
  IKZF4 MUTATED     9   3
  IKZF4 WILD-TYPE 369  90
  IKZF4 MUTATED IKZF4 WILD-TYPE 
             12             459 
  IKZF4 MUTATED IKZF4 WILD-TYPE 
              3              90 
$`IKZF4 MUTATED`
TCGA-A6-6141 TCGA-A6-6654 TCGA-AA-3977 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-6600 
        8.38        23.87        25.02        21.44        17.82        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-CK-5914 TCGA-CM-5861 TCGA-D5-6924 TCGA-G4-6306 
      100.01        29.56         9.99        15.02        14.30        44.68 

$`IKZF4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 
       22.09        22.06        32.71        27.09        22.52        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 
       25.18        24.16        21.76        24.69        24.39        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       88.21        49.41         6.77         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 
       85.45        15.62        49.08        51.32        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       12.43         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  IKZF4 MUTATED IKZF4 WILD-TYPE 
           8.38            0.00 
  IKZF4 MUTATED IKZF4 WILD-TYPE 
         100.01          148.01 
  IKZF4 MUTATED IKZF4 WILD-TYPE 
          19.63           20.19 
[1] "8.4 - 100.0 (19.6)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.2"
D727V2, continuous
D727V3, binary
                 cls
clus                0   1
  IKZF4 MUTATED    13   0
  IKZF4 WILD-TYPE 353 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IKZF4 MUTATED     13    0
  IKZF4 WILD-TYPE  353  119
        clus
vv       IKZF4 MUTATED IKZF4 WILD-TYPE
  COLON             13             353
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  IKZF4 MUTATED         0        0        1         5         0         0
  IKZF4 WILD-TYPE      91        1       31       133        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  IKZF4 MUTATED           1          0          3          0        1         0
  IKZF4 WILD-TYPE        23         11         56         42       47        18
                 vv
clus              STAGE IVB
  IKZF4 MUTATED           0
  IKZF4 WILD-TYPE         1
D727V4, multiclass
            clus
vv           IKZF4 MUTATED IKZF4 WILD-TYPE
  STAGE I                0              91
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              5             133
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             3              56
  STAGE IIIC             0              42
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  IKZF4 MUTATED     0   3   9   1
  IKZF4 WILD-TYPE  17  89 320  49
D727V5, multiclass
    clus
vv   IKZF4 MUTATED IKZF4 WILD-TYPE
  T1             0              17
  T2             3              89
  T3             9             320
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  IKZF4 MUTATED     7   5   1
  IKZF4 WILD-TYPE 280 108  86
D727V6, multiclass
    clus
vv   IKZF4 MUTATED IKZF4 WILD-TYPE
  N0             7             280
  N1             5             108
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D727V7, binary
                 cls
clus                0   1
  IKZF4 MUTATED     8   1
  IKZF4 WILD-TYPE 367  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IKZF4 MUTATED      8    1
  IKZF4 WILD-TYPE  367   64
   clus
vv  IKZF4 MUTATED IKZF4 WILD-TYPE
  0             8             367
  1             1              64
[1] 2 2
[1] FALSE
D727V8, binary
                 cls
clus                0   1
  IKZF4 MUTATED     4   9
  IKZF4 WILD-TYPE 221 255
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IKZF4 MUTATED      4    9
  IKZF4 WILD-TYPE  221  255
        clus
vv       IKZF4 MUTATED IKZF4 WILD-TYPE
  FEMALE             4             221
  MALE               9             255
[1] 2 2
[1] FALSE
D727V9, binary
                 cls
clus                0   1
  IKZF4 MUTATED    10   0
  IKZF4 WILD-TYPE 340  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IKZF4 MUTATED     10    0
  IKZF4 WILD-TYPE  340   22
     clus
vv    IKZF4 MUTATED IKZF4 WILD-TYPE
  NO             10             340
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  IKZF4 MUTATED                     13                             0
  IKZF4 WILD-TYPE                  302                            47
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  IKZF4 MUTATED                       0                              0
  IKZF4 WILD-TYPE                   106                             10
D727V10, multiclass
                                clus
vv                               IKZF4 MUTATED IKZF4 WILD-TYPE
  COLON ADENOCARCINOMA                      13             302
  COLON MUCINOUS ADENOCARCINOMA              0              47
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  IKZF4 MUTATED     6   0   0   1
  IKZF4 WILD-TYPE 339   4  31  24
D727V11, multiclass
    clus
vv   IKZF4 MUTATED IKZF4 WILD-TYPE
  R0             6             339
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D727V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  IKZF4 MUTATED                                  0     0
  IKZF4 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  IKZF4 MUTATED                           3     8
  IKZF4 WILD-TYPE                        19   218
D727V13, multiclass
                                  clus
vv                                 IKZF4 MUTATED IKZF4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    3              19
  WHITE                                        8             218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(728) Variable = ZNF564 MUTATION ANALYSIS
D728V1, survival
                  sevent
clus2                0   1
  ZNF564 MUTATED     8   3
  ZNF564 WILD-TYPE 370  90
  ZNF564 MUTATED ZNF564 WILD-TYPE 
              11              460 
  ZNF564 MUTATED ZNF564 WILD-TYPE 
               3               90 
$`ZNF564 MUTATED`
TCGA-AA-3663 TCGA-AA-3864 TCGA-AA-A00N TCGA-AA-A010 TCGA-CA-6717 TCGA-CA-6718 
        6.97        53.00         4.01        34.98        12.76        10.06 
TCGA-CK-4952 TCGA-CM-5864 TCGA-DM-A1D6 TCGA-AG-A02N TCGA-DC-6682 
       15.62        15.02        49.91        61.97         4.01 

$`ZNF564 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.05        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 
       32.05         0.99        31.07        31.07        30.05        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 
        3.06         3.25         3.29         0.07        12.20        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
       17.56       148.01        85.45        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5868 
       30.08        32.02        15.02         5.03        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D7 
      119.70        24.43        38.20       130.65        92.75        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
       49.97         1.94        38.96        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  ZNF564 MUTATED ZNF564 WILD-TYPE 
            4.01             0.00 
  ZNF564 MUTATED ZNF564 WILD-TYPE 
           61.97           148.01 
  ZNF564 MUTATED ZNF564 WILD-TYPE 
          15.020           20.415 
[1] "4.0 - 62.0 (15.0)"  "0.0 - 148.0 (20.4)"
[1] "hr=" "1.4"
D728V2, continuous
D728V3, binary
                  cls
clus                 0   1
  ZNF564 MUTATED    10   2
  ZNF564 WILD-TYPE 356 117
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF564 MUTATED     10    2
  ZNF564 WILD-TYPE  356  117
        clus
vv       ZNF564 MUTATED ZNF564 WILD-TYPE
  COLON              10              356
  RECTUM              2              117
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZNF564 MUTATED         1        0        3         5         2         0
  ZNF564 WILD-TYPE      90        1       29       133         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF564 MUTATED           0          0          0          1        0
  ZNF564 WILD-TYPE        24         11         59         41       48
                  vv
clus               STAGE IVA STAGE IVB
  ZNF564 MUTATED           0         0
  ZNF564 WILD-TYPE        18         1
D728V4, multiclass
            clus
vv           ZNF564 MUTATED ZNF564 WILD-TYPE
  STAGE I                 1               90
  STAGE IA                0                1
  STAGE II                3               29
  STAGE IIA               5              133
  STAGE IIB               2                8
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              0               59
  STAGE IIIC              1               41
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZNF564 MUTATED     0   1   8   3
  ZNF564 WILD-TYPE  17  91 321  47
D728V5, multiclass
    clus
vv   ZNF564 MUTATED ZNF564 WILD-TYPE
  T1              0               17
  T2              1               91
  T3              8              321
  T4              3               47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  ZNF564 MUTATED    11   0   1
  ZNF564 WILD-TYPE 276 113  86
D728V6, multiclass
    clus
vv   ZNF564 MUTATED ZNF564 WILD-TYPE
  N0             11              276
  N1              0              113
  N2              1               86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D728V7, binary
                  cls
clus                 0   1
  ZNF564 MUTATED    12   0
  ZNF564 WILD-TYPE 363  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF564 MUTATED     12    0
  ZNF564 WILD-TYPE  363   65
   clus
vv  ZNF564 MUTATED ZNF564 WILD-TYPE
  0             12              363
  1              0               65
[1] 2 2
[1] FALSE
D728V8, binary
                  cls
clus                 0   1
  ZNF564 MUTATED     3   9
  ZNF564 WILD-TYPE 222 255
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF564 MUTATED      3    9
  ZNF564 WILD-TYPE  222  255
        clus
vv       ZNF564 MUTATED ZNF564 WILD-TYPE
  FEMALE              3              222
  MALE                9              255
[1] 2 2
[1] FALSE
D728V9, binary
                  cls
clus                 0   1
  ZNF564 MUTATED     6   0
  ZNF564 WILD-TYPE 344  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF564 MUTATED      6    0
  ZNF564 WILD-TYPE  344   22
     clus
vv    ZNF564 MUTATED ZNF564 WILD-TYPE
  NO               6              344
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ZNF564 MUTATED                      6                             4
  ZNF564 WILD-TYPE                  309                            43
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ZNF564 MUTATED                       2                              0
  ZNF564 WILD-TYPE                   104                             10
D728V10, multiclass
                                clus
vv                               ZNF564 MUTATED ZNF564 WILD-TYPE
  COLON ADENOCARCINOMA                        6              309
  COLON MUCINOUS ADENOCARCINOMA               4               43
  RECTAL ADENOCARCINOMA                       2              104
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ZNF564 MUTATED     8   0   0   3
  ZNF564 WILD-TYPE 337   4  31  22
D728V11, multiclass
    clus
vv   ZNF564 MUTATED ZNF564 WILD-TYPE
  R0              8              337
  R1              0                4
  R2              0               31
  RX              3               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D728V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF564 MUTATED                                  0     2
  ZNF564 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZNF564 MUTATED                           0     4
  ZNF564 WILD-TYPE                        22   222
D728V13, multiclass
                                  clus
vv                                 ZNF564 MUTATED ZNF564 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                9
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         4              222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(729) Variable = SLC46A3 MUTATION ANALYSIS
D729V1, survival
                   sevent
clus2                 0   1
  SLC46A3 MUTATED     8   1
  SLC46A3 WILD-TYPE 370  92
  SLC46A3 MUTATED SLC46A3 WILD-TYPE 
                9               462 
  SLC46A3 MUTATED SLC46A3 WILD-TYPE 
                1                92 
$`SLC46A3 MUTATED`
TCGA-A6-6781 TCGA-AA-3510 TCGA-AA-3544 TCGA-AA-3877 TCGA-AA-A010 TCGA-AU-6004 
       19.66        63.98        14.01        31.00        34.98        27.09 
TCGA-AZ-6599 TCGA-CA-6717 TCGA-AG-A002 
        6.77        12.76        20.98 

$`SLC46A3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
       12.99         0.99        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       27.02        29.98        18.05         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       49.41        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07        12.20        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  SLC46A3 MUTATED SLC46A3 WILD-TYPE 
             6.77              0.00 
  SLC46A3 MUTATED SLC46A3 WILD-TYPE 
            63.98            148.01 
  SLC46A3 MUTATED SLC46A3 WILD-TYPE 
           20.980            20.155 
[1] "6.8 - 64.0 (21.0)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.8"
D729V2, continuous
D729V3, binary
                   cls
clus                  0   1
  SLC46A3 MUTATED     8   1
  SLC46A3 WILD-TYPE 358 118
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC46A3 MUTATED      8    1
  SLC46A3 WILD-TYPE  358  118
        clus
vv       SLC46A3 MUTATED SLC46A3 WILD-TYPE
  COLON                8               358
  RECTUM               1               118
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SLC46A3 MUTATED         5        0        1         1         1         0
  SLC46A3 WILD-TYPE      86        1       31       137         9         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC46A3 MUTATED           0          0          0          1        0
  SLC46A3 WILD-TYPE        24         11         59         41       48
                   vv
clus                STAGE IVA STAGE IVB
  SLC46A3 MUTATED           0         0
  SLC46A3 WILD-TYPE        18         1
D729V4, multiclass
            clus
vv           SLC46A3 MUTATED SLC46A3 WILD-TYPE
  STAGE I                  5                86
  STAGE IA                 0                 1
  STAGE II                 1                31
  STAGE IIA                1               137
  STAGE IIB                1                 9
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               0                11
  STAGE IIIB               0                59
  STAGE IIIC               1                41
  STAGE IV                 0                48
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  SLC46A3 MUTATED     1   4   2   2
  SLC46A3 WILD-TYPE  16  88 327  48
D729V5, multiclass
    clus
vv   SLC46A3 MUTATED SLC46A3 WILD-TYPE
  T1               1                16
  T2               4                88
  T3               2               327
  T4               2                48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  SLC46A3 MUTATED     8   1   0
  SLC46A3 WILD-TYPE 279 112  87
D729V6, multiclass
    clus
vv   SLC46A3 MUTATED SLC46A3 WILD-TYPE
  N0               8               279
  N1               1               112
  N2               0                87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D729V7, binary
                   cls
clus                  0   1
  SLC46A3 MUTATED     7   0
  SLC46A3 WILD-TYPE 368  65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC46A3 MUTATED      7    0
  SLC46A3 WILD-TYPE  368   65
   clus
vv  SLC46A3 MUTATED SLC46A3 WILD-TYPE
  0               7               368
  1               0                65
[1] 2 2
[1] FALSE
D729V8, binary
                   cls
clus                  0   1
  SLC46A3 MUTATED     3   6
  SLC46A3 WILD-TYPE 222 258
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC46A3 MUTATED      3    6
  SLC46A3 WILD-TYPE  222  258
        clus
vv       SLC46A3 MUTATED SLC46A3 WILD-TYPE
  FEMALE               3               222
  MALE                 6               258
[1] 2 2
[1] FALSE
D729V9, binary
                   cls
clus                  0   1
  SLC46A3 MUTATED     8   0
  SLC46A3 WILD-TYPE 342  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC46A3 MUTATED      8    0
  SLC46A3 WILD-TYPE  342   22
     clus
vv    SLC46A3 MUTATED SLC46A3 WILD-TYPE
  NO                8               342
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SLC46A3 MUTATED                      5                             3
  SLC46A3 WILD-TYPE                  310                            44
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SLC46A3 MUTATED                       1                              0
  SLC46A3 WILD-TYPE                   105                             10
D729V10, multiclass
                                clus
vv                               SLC46A3 MUTATED SLC46A3 WILD-TYPE
  COLON ADENOCARCINOMA                         5               310
  COLON MUCINOUS ADENOCARCINOMA                3                44
  RECTAL ADENOCARCINOMA                        1               105
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  SLC46A3 MUTATED     7   0   0   1
  SLC46A3 WILD-TYPE 338   4  31  24
D729V11, multiclass
    clus
vv   SLC46A3 MUTATED SLC46A3 WILD-TYPE
  R0               7               338
  R1               0                 4
  R2               0                31
  RX               1                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D729V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SLC46A3 MUTATED                                  0     1
  SLC46A3 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  SLC46A3 MUTATED                           0     3
  SLC46A3 WILD-TYPE                        22   223
D729V13, multiclass
                                  clus
vv                                 SLC46A3 MUTATED SLC46A3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                10
  BLACK OR AFRICAN AMERICAN                      0                22
  WHITE                                          3               223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(730) Variable = VAV3 MUTATION ANALYSIS
D730V1, survival
                sevent
clus2              0   1
  VAV3 MUTATED    23   3
  VAV3 WILD-TYPE 355  90
  VAV3 MUTATED VAV3 WILD-TYPE 
            26            445 
  VAV3 MUTATED VAV3 WILD-TYPE 
             3             90 
$`VAV3 MUTATED`
TCGA-A6-2672 TCGA-A6-6141 TCGA-AA-3672 TCGA-AA-3713 TCGA-AA-3867 TCGA-AA-3949 
       46.65         8.38         0.92        19.04        24.03        26.01 
TCGA-AA-A010 TCGA-AA-A01R TCGA-AZ-4315 TCGA-AZ-6603 TCGA-CA-6717 TCGA-CA-6718 
       34.98        35.01        58.39        29.56        12.76        10.06 
TCGA-CK-4947 TCGA-CM-4743 TCGA-CM-5868 TCGA-CM-6171 TCGA-CM-6677 TCGA-D5-5539 
       17.56        23.05        17.03        14.04        11.08        19.59 
TCGA-D5-6539 TCGA-D5-6540 TCGA-DM-A1DB TCGA-G4-6304 TCGA-G4-6321 TCGA-AG-A002 
       12.49        16.14        44.32        53.62        22.09        20.98 
TCGA-AG-A01Y TCGA-AH-6547 
       64.01         1.45 

$`VAV3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 
       22.06        32.71        27.09        22.52        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
       54.02         2.01        14.01        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       85.05        26.99        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3870 
       31.07        30.05        53.00        17.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S 
       12.00        31.00        31.00        38.07         1.02         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       33.01        21.44        17.82         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
      100.01         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 
        3.06         3.25         3.29         0.07        12.20        14.30 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 
       21.14        82.95         1.91       124.27        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6161 
       32.02        15.02         5.03        15.02        15.02        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       12.99        13.02        15.02        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6541 TCGA-D5-6898 
       15.12        17.85         4.80        17.13        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A1HB 
       13.32        12.59       140.38         7.50       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       65.85        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       36.00        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       70.03        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6549 TCGA-AH-6643 
       41.00        38.04       117.11        38.56        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  VAV3 MUTATED VAV3 WILD-TYPE 
          0.92           0.00 
  VAV3 MUTATED VAV3 WILD-TYPE 
         64.01         148.01 
  VAV3 MUTATED VAV3 WILD-TYPE 
        20.285         20.190 
[1] "0.9 - 64.0 (20.3)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.7"
D730V2, continuous
D730V3, binary
                cls
clus               0   1
  VAV3 MUTATED    24   3
  VAV3 WILD-TYPE 342 116
[1] "tbl2"
                cls
clus             [,1] [,2]
  VAV3 MUTATED     24    3
  VAV3 WILD-TYPE  342  116
        clus
vv       VAV3 MUTATED VAV3 WILD-TYPE
  COLON            24            342
  RECTUM            3            116
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  VAV3 MUTATED         3        0        1         8         2         0
  VAV3 WILD-TYPE      88        1       31       130         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  VAV3 MUTATED           3          2          3          0        2         1
  VAV3 WILD-TYPE        21          9         56         42       46        17
                vv
clus             STAGE IVB
  VAV3 MUTATED           0
  VAV3 WILD-TYPE         1
D730V4, multiclass
            clus
vv           VAV3 MUTATED VAV3 WILD-TYPE
  STAGE I               3             88
  STAGE IA              0              1
  STAGE II              1             31
  STAGE IIA             8            130
  STAGE IIB             2              8
  STAGE IIC             0              1
  STAGE III             3             21
  STAGE IIIA            2              9
  STAGE IIIB            3             56
  STAGE IIIC            0             42
  STAGE IV              2             46
  STAGE IVA             1             17
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  VAV3 MUTATED     0   5  18   4
  VAV3 WILD-TYPE  17  87 311  46
D730V5, multiclass
    clus
vv   VAV3 MUTATED VAV3 WILD-TYPE
  T1            0             17
  T2            5             87
  T3           18            311
  T4            4             46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  VAV3 MUTATED    17   8   2
  VAV3 WILD-TYPE 270 105  85
D730V6, multiclass
    clus
vv   VAV3 MUTATED VAV3 WILD-TYPE
  N0           17            270
  N1            8            105
  N2            2             85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D730V7, binary
                cls
clus               0   1
  VAV3 MUTATED    21   3
  VAV3 WILD-TYPE 354  62
[1] "tbl2"
                cls
clus             [,1] [,2]
  VAV3 MUTATED     21    3
  VAV3 WILD-TYPE  354   62
   clus
vv  VAV3 MUTATED VAV3 WILD-TYPE
  0           21            354
  1            3             62
[1] 2 2
[1] FALSE
D730V8, binary
                cls
clus               0   1
  VAV3 MUTATED    15  12
  VAV3 WILD-TYPE 210 252
[1] "tbl2"
                cls
clus             [,1] [,2]
  VAV3 MUTATED     15   12
  VAV3 WILD-TYPE  210  252
        clus
vv       VAV3 MUTATED VAV3 WILD-TYPE
  FEMALE           15            210
  MALE             12            252
[1] 2 2
[1] FALSE
D730V9, binary
                cls
clus               0   1
  VAV3 MUTATED    21   2
  VAV3 WILD-TYPE 329  20
[1] "tbl2"
                cls
clus             [,1] [,2]
  VAV3 MUTATED     21    2
  VAV3 WILD-TYPE  329   20
     clus
vv    VAV3 MUTATED VAV3 WILD-TYPE
  NO            21            329
  YES            2             20
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  VAV3 MUTATED                     19                             5
  VAV3 WILD-TYPE                  296                            42
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  VAV3 MUTATED                       3                              0
  VAV3 WILD-TYPE                   103                             10
D730V10, multiclass
                                clus
vv                               VAV3 MUTATED VAV3 WILD-TYPE
  COLON ADENOCARCINOMA                     19            296
  COLON MUCINOUS ADENOCARCINOMA             5             42
  RECTAL ADENOCARCINOMA                     3            103
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  VAV3 MUTATED    18   0   2   3
  VAV3 WILD-TYPE 327   4  29  22
D730V11, multiclass
    clus
vv   VAV3 MUTATED VAV3 WILD-TYPE
  R0           18            327
  R1            0              4
  R2            2             29
  RX            3             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D730V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  VAV3 MUTATED                                  0     2
  VAV3 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  VAV3 MUTATED                           1    15
  VAV3 WILD-TYPE                        21   211
D730V13, multiclass
                                  clus
vv                                 VAV3 MUTATED VAV3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              9
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                      15            211
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(731) Variable = RPGRIP1L MUTATION ANALYSIS
D731V1, survival
                    sevent
clus2                  0   1
  RPGRIP1L MUTATED    14   3
  RPGRIP1L WILD-TYPE 364  90
  RPGRIP1L MUTATED RPGRIP1L WILD-TYPE 
                17                454 
  RPGRIP1L MUTATED RPGRIP1L WILD-TYPE 
                 3                 90 
$`RPGRIP1L MUTATED`
TCGA-A6-5661 TCGA-A6-6141 TCGA-A6-6648 TCGA-AA-3511 TCGA-AA-3680 TCGA-AA-3949 
       33.53         8.38        25.18         6.97        11.01        26.01 
TCGA-AA-3950 TCGA-AA-3966 TCGA-AA-A00N TCGA-AA-A010 TCGA-AD-6889 TCGA-AZ-6598 
       24.00         2.01         4.01        34.98        56.55        49.41 
TCGA-CM-4752 TCGA-D5-6536 TCGA-F4-6703 TCGA-F4-6808 TCGA-AG-A002 
       13.02        17.85        47.87        33.67        20.98 

$`RPGRIP1L WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6649 
       22.06        32.71        27.09        22.52        25.08        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3681 
       14.01         0.92        50.04        47.01        15.02         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
        2.01        20.98        34.03        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 
       40.96         0.07        21.37        15.52         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       88.21         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       20.02        37.02        25.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6809 
        6.18         1.55        34.42        41.42        16.24        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  RPGRIP1L MUTATED RPGRIP1L WILD-TYPE 
              2.01               0.00 
  RPGRIP1L MUTATED RPGRIP1L WILD-TYPE 
             56.55             148.01 
  RPGRIP1L MUTATED RPGRIP1L WILD-TYPE 
            24.000             20.085 
[1] "2.0 - 56.5 (24.0)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.1"
D731V2, continuous
D731V3, binary
                    cls
clus                   0   1
  RPGRIP1L MUTATED    17   1
  RPGRIP1L WILD-TYPE 349 118
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  RPGRIP1L MUTATED     17    1
  RPGRIP1L WILD-TYPE  349  118
        clus
vv       RPGRIP1L MUTATED RPGRIP1L WILD-TYPE
  COLON                17                349
  RECTUM                1                118
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RPGRIP1L MUTATED         2        0        2         9         2         0
  RPGRIP1L WILD-TYPE      89        1       30       129         8         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RPGRIP1L MUTATED           0          0          1          0        1
  RPGRIP1L WILD-TYPE        24         11         58         42       47
                    vv
clus                 STAGE IVA STAGE IVB
  RPGRIP1L MUTATED           1         0
  RPGRIP1L WILD-TYPE        17         1
D731V4, multiclass
            clus
vv           RPGRIP1L MUTATED RPGRIP1L WILD-TYPE
  STAGE I                   2                 89
  STAGE IA                  0                  1
  STAGE II                  2                 30
  STAGE IIA                 9                129
  STAGE IIB                 2                  8
  STAGE IIC                 0                  1
  STAGE III                 0                 24
  STAGE IIIA                0                 11
  STAGE IIIB                1                 58
  STAGE IIIC                0                 42
  STAGE IV                  1                 47
  STAGE IVA                 1                 17
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  RPGRIP1L MUTATED     1   1  12   4
  RPGRIP1L WILD-TYPE  16  91 317  46
D731V5, multiclass
    clus
vv   RPGRIP1L MUTATED RPGRIP1L WILD-TYPE
  T1                1                 16
  T2                1                 91
  T3               12                317
  T4                4                 46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  RPGRIP1L MUTATED    16   1   1
  RPGRIP1L WILD-TYPE 271 112  86
D731V6, multiclass
    clus
vv   RPGRIP1L MUTATED RPGRIP1L WILD-TYPE
  N0               16                271
  N1                1                112
  N2                1                 86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D731V7, binary
                    cls
clus                   0   1
  RPGRIP1L MUTATED    15   2
  RPGRIP1L WILD-TYPE 360  63
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  RPGRIP1L MUTATED     15    2
  RPGRIP1L WILD-TYPE  360   63
   clus
vv  RPGRIP1L MUTATED RPGRIP1L WILD-TYPE
  0               15                360
  1                2                 63
[1] 2 2
[1] FALSE
D731V8, binary
                    cls
clus                   0   1
  RPGRIP1L MUTATED     9   9
  RPGRIP1L WILD-TYPE 216 255
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  RPGRIP1L MUTATED      9    9
  RPGRIP1L WILD-TYPE  216  255
        clus
vv       RPGRIP1L MUTATED RPGRIP1L WILD-TYPE
  FEMALE                9                216
  MALE                  9                255
[1] 2 2
[1] FALSE
D731V9, binary
                    cls
clus                   0   1
  RPGRIP1L MUTATED    14   0
  RPGRIP1L WILD-TYPE 336  22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  RPGRIP1L MUTATED     14    0
  RPGRIP1L WILD-TYPE  336   22
     clus
vv    RPGRIP1L MUTATED RPGRIP1L WILD-TYPE
  NO                14                336
  YES                0                 22
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  RPGRIP1L MUTATED                     13                             4
  RPGRIP1L WILD-TYPE                  302                            43
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  RPGRIP1L MUTATED                       1                              0
  RPGRIP1L WILD-TYPE                   105                             10
D731V10, multiclass
                                clus
vv                               RPGRIP1L MUTATED RPGRIP1L WILD-TYPE
  COLON ADENOCARCINOMA                         13                302
  COLON MUCINOUS ADENOCARCINOMA                 4                 43
  RECTAL ADENOCARCINOMA                         1                105
  RECTAL MUCINOUS ADENOCARCINOMA                0                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  RPGRIP1L MUTATED    12   0   1   0
  RPGRIP1L WILD-TYPE 333   4  30  25
D731V11, multiclass
    clus
vv   RPGRIP1L MUTATED RPGRIP1L WILD-TYPE
  R0               12                333
  R1                0                  4
  R2                1                 30
  RX                0                 25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D731V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RPGRIP1L MUTATED                                  0     1
  RPGRIP1L WILD-TYPE                                1    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  RPGRIP1L MUTATED                           3     5
  RPGRIP1L WILD-TYPE                        19   221
D731V13, multiclass
                                  clus
vv                                 RPGRIP1L MUTATED RPGRIP1L WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                 10
  BLACK OR AFRICAN AMERICAN                       3                 19
  WHITE                                           5                221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(732) Variable = GATA1 MUTATION ANALYSIS
D732V1, survival
                 sevent
clus2               0   1
  GATA1 MUTATED    12   3
  GATA1 WILD-TYPE 366  90
  GATA1 MUTATED GATA1 WILD-TYPE 
             15             456 
  GATA1 MUTATED GATA1 WILD-TYPE 
              3              90 
$`GATA1 MUTATED`
TCGA-AA-3492 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-3966 
        3.02        78.08         6.97        33.01        24.00         2.01 
TCGA-AA-A01R TCGA-AD-5900 TCGA-AY-5543 TCGA-CK-4952 TCGA-CK-5914 TCGA-CM-6164 
       35.01         0.07        33.01        15.62         9.99        29.03 
TCGA-D5-6537 TCGA-G4-6303 TCGA-AG-A002 
        4.80        65.85        20.98 

$`GATA1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3664 
       19.99        13.94        19.99        61.02         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 
       24.00        26.01         2.01        20.98        34.03        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 
       41.00        39.98        18.05        40.96        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       49.08        51.32        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       15.12        17.85        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
      133.18        74.56        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  GATA1 MUTATED GATA1 WILD-TYPE 
           0.07            0.00 
  GATA1 MUTATED GATA1 WILD-TYPE 
          78.08          148.01 
  GATA1 MUTATED GATA1 WILD-TYPE 
         20.980          20.155 
[1] "0.1 - 78.1 (21.0)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.1"
D732V2, continuous
D732V3, binary
                 cls
clus                0   1
  GATA1 MUTATED    16   1
  GATA1 WILD-TYPE 350 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GATA1 MUTATED     16    1
  GATA1 WILD-TYPE  350  118
        clus
vv       GATA1 MUTATED GATA1 WILD-TYPE
  COLON             16             350
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GATA1 MUTATED         2        0        3         4         1         0
  GATA1 WILD-TYPE      89        1       29       134         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  GATA1 MUTATED           1          0          2          2        1         1
  GATA1 WILD-TYPE        23         11         57         40       47        17
                 vv
clus              STAGE IVB
  GATA1 MUTATED           0
  GATA1 WILD-TYPE         1
D732V4, multiclass
            clus
vv           GATA1 MUTATED GATA1 WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               3              29
  STAGE IIA              4             134
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             2              57
  STAGE IIIC             2              40
  STAGE IV               1              47
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  GATA1 MUTATED     0   2  13   2
  GATA1 WILD-TYPE  17  90 316  48
D732V5, multiclass
    clus
vv   GATA1 MUTATED GATA1 WILD-TYPE
  T1             0              17
  T2             2              90
  T3            13             316
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  GATA1 MUTATED    10   4   3
  GATA1 WILD-TYPE 277 109  84
D732V6, multiclass
    clus
vv   GATA1 MUTATED GATA1 WILD-TYPE
  N0            10             277
  N1             4             109
  N2             3              84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D732V7, binary
                 cls
clus                0   1
  GATA1 MUTATED    11   2
  GATA1 WILD-TYPE 364  63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GATA1 MUTATED     11    2
  GATA1 WILD-TYPE  364   63
   clus
vv  GATA1 MUTATED GATA1 WILD-TYPE
  0            11             364
  1             2              63
[1] 2 2
[1] FALSE
D732V8, binary
                 cls
clus                0   1
  GATA1 MUTATED    10   7
  GATA1 WILD-TYPE 215 257
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GATA1 MUTATED     10    7
  GATA1 WILD-TYPE  215  257
        clus
vv       GATA1 MUTATED GATA1 WILD-TYPE
  FEMALE            10             215
  MALE               7             257
[1] 2 2
[1] FALSE
D732V9, binary
                 cls
clus                0   1
  GATA1 MUTATED    10   1
  GATA1 WILD-TYPE 340  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GATA1 MUTATED     10    1
  GATA1 WILD-TYPE  340   21
     clus
vv    GATA1 MUTATED GATA1 WILD-TYPE
  NO             10             340
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  GATA1 MUTATED                      9                             7
  GATA1 WILD-TYPE                  306                            40
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  GATA1 MUTATED                       1                              0
  GATA1 WILD-TYPE                   105                             10
D732V10, multiclass
                                clus
vv                               GATA1 MUTATED GATA1 WILD-TYPE
  COLON ADENOCARCINOMA                       9             306
  COLON MUCINOUS ADENOCARCINOMA              7              40
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  GATA1 MUTATED    14   0   0   2
  GATA1 WILD-TYPE 331   4  31  23
D732V11, multiclass
    clus
vv   GATA1 MUTATED GATA1 WILD-TYPE
  R0            14             331
  R1             0               4
  R2             0              31
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D732V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GATA1 MUTATED                                  0     0
  GATA1 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  GATA1 MUTATED                           1     7
  GATA1 WILD-TYPE                        21   219
D732V13, multiclass
                                  clus
vv                                 GATA1 MUTATED GATA1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        7             219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(733) Variable = KIF21B MUTATION ANALYSIS
D733V1, survival
                  sevent
clus2                0   1
  KIF21B MUTATED    20   4
  KIF21B WILD-TYPE 358  89
  KIF21B MUTATED KIF21B WILD-TYPE 
              24              447 
  KIF21B MUTATED KIF21B WILD-TYPE 
               4               89 
$`KIF21B MUTATED`
TCGA-A6-5661 TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3555 TCGA-AA-3663 TCGA-AA-3845 
       33.53        20.12        19.66        29.95         6.97         0.00 
TCGA-AA-3864 TCGA-AA-A010 TCGA-AA-A01Q TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-6600 
       53.00        34.98         1.02        21.44        17.82        12.10 
TCGA-CM-5349 TCGA-CM-5861 TCGA-D5-6539 TCGA-D5-6930 TCGA-F4-6570 TCGA-F4-6703 
       30.08        15.02        12.49         1.51         6.18        47.87 
TCGA-F4-6808 TCGA-G4-6303 TCGA-G4-6586 TCGA-AG-3731 TCGA-CI-6619 TCGA-DC-6681 
       33.67        65.85        35.80        37.02         6.05         5.95 

$`KIF21B WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       17.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       61.02        78.08         6.05        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
       14.93        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        31.00        38.07        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       88.21        49.41         6.77       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       22.98        32.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
        4.80        17.13        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        4.80        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6704 TCGA-F4-6805 
       98.24         8.61        31.96        35.74         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       41.42        16.24        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
      133.18        74.56        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 
       63.62        61.91        36.00        22.09        13.78        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
        0.99        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6620 
       38.56         1.45        17.49         0.69         0.72        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6682 TCGA-DC-6683 
       13.97        27.95        10.98        19.99         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  KIF21B MUTATED KIF21B WILD-TYPE 
               0                0 
  KIF21B MUTATED KIF21B WILD-TYPE 
           65.85           148.01 
  KIF21B MUTATED KIF21B WILD-TYPE 
           19.89            20.28 
[1] "0.0 - 65.8 (19.9)"  "0.0 - 148.0 (20.3)"
[1] "hr=" "1"  
D733V2, continuous
D733V3, binary
                  cls
clus                 0   1
  KIF21B MUTATED    22   3
  KIF21B WILD-TYPE 344 116
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KIF21B MUTATED     22    3
  KIF21B WILD-TYPE  344  116
        clus
vv       KIF21B MUTATED KIF21B WILD-TYPE
  COLON              22              344
  RECTUM              3              116
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KIF21B MUTATED         1        0        3        11         2         0
  KIF21B WILD-TYPE      90        1       29       127         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIF21B MUTATED           0          1          1          1        4
  KIF21B WILD-TYPE        24         10         58         41       44
                  vv
clus               STAGE IVA STAGE IVB
  KIF21B MUTATED           1         0
  KIF21B WILD-TYPE        17         1
D733V4, multiclass
            clus
vv           KIF21B MUTATED KIF21B WILD-TYPE
  STAGE I                 1               90
  STAGE IA                0                1
  STAGE II                3               29
  STAGE IIA              11              127
  STAGE IIB               2                8
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              1               10
  STAGE IIIB              1               58
  STAGE IIIC              1               41
  STAGE IV                4               44
  STAGE IVA               1               17
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  KIF21B MUTATED     1   0  20   4
  KIF21B WILD-TYPE  16  92 309  46
D733V5, multiclass
    clus
vv   KIF21B MUTATED KIF21B WILD-TYPE
  T1              1               16
  T2              0               92
  T3             20              309
  T4              4               46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  KIF21B MUTATED    18   6   1
  KIF21B WILD-TYPE 269 107  86
D733V6, multiclass
    clus
vv   KIF21B MUTATED KIF21B WILD-TYPE
  N0             18              269
  N1              6              107
  N2              1               86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D733V7, binary
                  cls
clus                 0   1
  KIF21B MUTATED    16   5
  KIF21B WILD-TYPE 359  60
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KIF21B MUTATED     16    5
  KIF21B WILD-TYPE  359   60
   clus
vv  KIF21B MUTATED KIF21B WILD-TYPE
  0             16              359
  1              5               60
[1] 2 2
[1] FALSE
D733V8, binary
                  cls
clus                 0   1
  KIF21B MUTATED    15  10
  KIF21B WILD-TYPE 210 254
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KIF21B MUTATED     15   10
  KIF21B WILD-TYPE  210  254
        clus
vv       KIF21B MUTATED KIF21B WILD-TYPE
  FEMALE             15              210
  MALE               10              254
[1] 2 2
[1] FALSE
D733V9, binary
                  cls
clus                 0   1
  KIF21B MUTATED    18   0
  KIF21B WILD-TYPE 332  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KIF21B MUTATED     18    0
  KIF21B WILD-TYPE  332   22
     clus
vv    KIF21B MUTATED KIF21B WILD-TYPE
  NO              18              332
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  KIF21B MUTATED                     18                             4
  KIF21B WILD-TYPE                  297                            43
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  KIF21B MUTATED                       3                              0
  KIF21B WILD-TYPE                   103                             10
D733V10, multiclass
                                clus
vv                               KIF21B MUTATED KIF21B WILD-TYPE
  COLON ADENOCARCINOMA                       18              297
  COLON MUCINOUS ADENOCARCINOMA               4               43
  RECTAL ADENOCARCINOMA                       3              103
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  KIF21B MUTATED    20   0   1   1
  KIF21B WILD-TYPE 325   4  30  24
D733V11, multiclass
    clus
vv   KIF21B MUTATED KIF21B WILD-TYPE
  R0             20              325
  R1              0                4
  R2              1               30
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D733V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KIF21B MUTATED                                  0     0
  KIF21B WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  KIF21B MUTATED                           3    15
  KIF21B WILD-TYPE                        19   211
D733V13, multiclass
                                  clus
vv                                 KIF21B MUTATED KIF21B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     3               19
  WHITE                                        15              211
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(734) Variable = HELQ MUTATION ANALYSIS
D734V1, survival
                sevent
clus2              0   1
  HELQ MUTATED    14   4
  HELQ WILD-TYPE 364  89
  HELQ MUTATED HELQ WILD-TYPE 
            18            453 
  HELQ MUTATED HELQ WILD-TYPE 
             4             89 
$`HELQ MUTATED`
TCGA-AA-3510 TCGA-AA-3660 TCGA-AA-3821 TCGA-AA-3966 TCGA-AA-A00N TCGA-AA-A010 
       63.98        78.08         1.02         2.01         4.01        34.98 
TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-CA-6717 
        0.07        56.55         0.79        58.39        49.41        12.76 
TCGA-CM-5861 TCGA-CM-6165 TCGA-F4-6459 TCGA-G4-6628 TCGA-AG-A002 TCGA-DY-A1DG 
       15.02        16.04         8.61        79.69        20.98        51.48 

$`HELQ WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 
       19.99        13.94        19.99        61.02         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 
       35.05        33.04         0.99        25.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
       34.03        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 
        0.92        41.00        39.98        18.05        40.96        21.37 
TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
       15.52         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        88.21         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07        12.20        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       22.98        30.08        32.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6166 
       17.03        15.02        12.00         2.96        29.03        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
       60.79       117.07        98.24        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       91.79        46.75        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  HELQ MUTATED HELQ WILD-TYPE 
          0.07           0.00 
  HELQ MUTATED HELQ WILD-TYPE 
         79.69         148.01 
  HELQ MUTATED HELQ WILD-TYPE 
         18.51          20.19 
[1] "0.1 - 79.7 (18.5)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.1"
D734V2, continuous
D734V3, binary
                cls
clus               0   1
  HELQ MUTATED    18   2
  HELQ WILD-TYPE 348 117
[1] "tbl2"
                cls
clus             [,1] [,2]
  HELQ MUTATED     18    2
  HELQ WILD-TYPE  348  117
        clus
vv       HELQ MUTATED HELQ WILD-TYPE
  COLON            18            348
  RECTUM            2            117
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  HELQ MUTATED         4        0        3         6         3         0
  HELQ WILD-TYPE      87        1       29       132         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  HELQ MUTATED           1          0          1          0        0         1
  HELQ WILD-TYPE        23         11         58         42       48        17
                vv
clus             STAGE IVB
  HELQ MUTATED           0
  HELQ WILD-TYPE         1
D734V4, multiclass
            clus
vv           HELQ MUTATED HELQ WILD-TYPE
  STAGE I               4             87
  STAGE IA              0              1
  STAGE II              3             29
  STAGE IIA             6            132
  STAGE IIB             3              7
  STAGE IIC             0              1
  STAGE III             1             23
  STAGE IIIA            0             11
  STAGE IIIB            1             58
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             1             17
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  HELQ MUTATED     1   4  12   3
  HELQ WILD-TYPE  16  88 317  47
D734V5, multiclass
    clus
vv   HELQ MUTATED HELQ WILD-TYPE
  T1            1             16
  T2            4             88
  T3           12            317
  T4            3             47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  HELQ MUTATED    17   1   2
  HELQ WILD-TYPE 270 112  85
D734V6, multiclass
    clus
vv   HELQ MUTATED HELQ WILD-TYPE
  N0           17            270
  N1            1            112
  N2            2             85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D734V7, binary
                cls
clus               0   1
  HELQ MUTATED    15   1
  HELQ WILD-TYPE 360  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  HELQ MUTATED     15    1
  HELQ WILD-TYPE  360   64
   clus
vv  HELQ MUTATED HELQ WILD-TYPE
  0           15            360
  1            1             64
[1] 2 2
[1] FALSE
D734V8, binary
                cls
clus               0   1
  HELQ MUTATED     8  12
  HELQ WILD-TYPE 217 252
[1] "tbl2"
                cls
clus             [,1] [,2]
  HELQ MUTATED      8   12
  HELQ WILD-TYPE  217  252
        clus
vv       HELQ MUTATED HELQ WILD-TYPE
  FEMALE            8            217
  MALE             12            252
[1] 2 2
[1] FALSE
D734V9, binary
                cls
clus               0   1
  HELQ MUTATED    12   0
  HELQ WILD-TYPE 338  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  HELQ MUTATED     12    0
  HELQ WILD-TYPE  338   22
     clus
vv    HELQ MUTATED HELQ WILD-TYPE
  NO            12            338
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  HELQ MUTATED                     13                             5
  HELQ WILD-TYPE                  302                            42
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  HELQ MUTATED                       2                              0
  HELQ WILD-TYPE                   104                             10
D734V10, multiclass
                                clus
vv                               HELQ MUTATED HELQ WILD-TYPE
  COLON ADENOCARCINOMA                     13            302
  COLON MUCINOUS ADENOCARCINOMA             5             42
  RECTAL ADENOCARCINOMA                     2            104
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  HELQ MUTATED    13   0   0   2
  HELQ WILD-TYPE 332   4  31  23
D734V11, multiclass
    clus
vv   HELQ MUTATED HELQ WILD-TYPE
  R0           13            332
  R1            0              4
  R2            0             31
  RX            2             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D734V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HELQ MUTATED                                  0     2
  HELQ WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  HELQ MUTATED                           0    10
  HELQ WILD-TYPE                        22   216
D734V13, multiclass
                                  clus
vv                                 HELQ MUTATED HELQ WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              9
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                      10            216
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(735) Variable = ZNF799 MUTATION ANALYSIS
D735V1, survival
                  sevent
clus2                0   1
  ZNF799 MUTATED     6   1
  ZNF799 WILD-TYPE 372  92
  ZNF799 MUTATED ZNF799 WILD-TYPE 
               7              464 
  ZNF799 MUTATED ZNF799 WILD-TYPE 
               1               92 
$`ZNF799 MUTATED`
TCGA-AA-3662 TCGA-AA-A010 TCGA-AZ-4315 TCGA-AZ-5407 TCGA-D5-6532 TCGA-DM-A1DB 
        6.05        34.98        58.39        88.21        18.25        44.32 
TCGA-AG-A002 
       20.98 

$`ZNF799 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       33.01        21.44        17.82         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6533 
       12.26        19.59        56.09        55.92        20.19         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
        7.50       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  ZNF799 MUTATED ZNF799 WILD-TYPE 
            6.05             0.00 
  ZNF799 MUTATED ZNF799 WILD-TYPE 
           88.21           148.01 
  ZNF799 MUTATED ZNF799 WILD-TYPE 
          34.980           20.085 
[1] "6.0 - 88.2 (35.0)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "2.1"
D735V2, continuous
D735V3, binary
                  cls
clus                 0   1
  ZNF799 MUTATED     6   1
  ZNF799 WILD-TYPE 360 118
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF799 MUTATED      6    1
  ZNF799 WILD-TYPE  360  118
        clus
vv       ZNF799 MUTATED ZNF799 WILD-TYPE
  COLON               6              360
  RECTUM              1              118
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZNF799 MUTATED         2        0        0         3         1         0
  ZNF799 WILD-TYPE      89        1       32       135         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF799 MUTATED           0          0          0          0        1
  ZNF799 WILD-TYPE        24         11         59         42       47
                  vv
clus               STAGE IVA STAGE IVB
  ZNF799 MUTATED           0         0
  ZNF799 WILD-TYPE        18         1
D735V4, multiclass
            clus
vv           ZNF799 MUTATED ZNF799 WILD-TYPE
  STAGE I                 2               89
  STAGE IA                0                1
  STAGE II                0               32
  STAGE IIA               3              135
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              0               59
  STAGE IIIC              0               42
  STAGE IV                1               47
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZNF799 MUTATED     1   1   3   2
  ZNF799 WILD-TYPE  16  91 326  48
D735V5, multiclass
    clus
vv   ZNF799 MUTATED ZNF799 WILD-TYPE
  T1              1               16
  T2              1               91
  T3              3              326
  T4              2               48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  ZNF799 MUTATED     6   0   1
  ZNF799 WILD-TYPE 281 113  86
D735V6, multiclass
    clus
vv   ZNF799 MUTATED ZNF799 WILD-TYPE
  N0              6              281
  N1              0              113
  N2              1               86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D735V7, binary
                  cls
clus                 0   1
  ZNF799 MUTATED     6   1
  ZNF799 WILD-TYPE 369  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF799 MUTATED      6    1
  ZNF799 WILD-TYPE  369   64
   clus
vv  ZNF799 MUTATED ZNF799 WILD-TYPE
  0              6              369
  1              1               64
[1] 2 2
[1] FALSE
D735V8, binary
                  cls
clus                 0   1
  ZNF799 MUTATED     3   4
  ZNF799 WILD-TYPE 222 260
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF799 MUTATED      3    4
  ZNF799 WILD-TYPE  222  260
        clus
vv       ZNF799 MUTATED ZNF799 WILD-TYPE
  FEMALE              3              222
  MALE                4              260
[1] 2 2
[1] FALSE
D735V9, binary
                  cls
clus                 0   1
  ZNF799 MUTATED     6   0
  ZNF799 WILD-TYPE 344  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF799 MUTATED      6    0
  ZNF799 WILD-TYPE  344   22
     clus
vv    ZNF799 MUTATED ZNF799 WILD-TYPE
  NO               6              344
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ZNF799 MUTATED                      6                             0
  ZNF799 WILD-TYPE                  309                            47
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ZNF799 MUTATED                       1                              0
  ZNF799 WILD-TYPE                   105                             10
D735V10, multiclass
                                clus
vv                               ZNF799 MUTATED ZNF799 WILD-TYPE
  COLON ADENOCARCINOMA                        6              309
  COLON MUCINOUS ADENOCARCINOMA               0               47
  RECTAL ADENOCARCINOMA                       1              105
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ZNF799 MUTATED     4   0   1   0
  ZNF799 WILD-TYPE 341   4  30  25
D735V11, multiclass
    clus
vv   ZNF799 MUTATED ZNF799 WILD-TYPE
  R0              4              341
  R1              0                4
  R2              1               30
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D735V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF799 MUTATED                                  0     0
  ZNF799 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZNF799 MUTATED                           0     4
  ZNF799 WILD-TYPE                        22   222
D735V13, multiclass
                                  clus
vv                                 ZNF799 MUTATED ZNF799 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         4              222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(736) Variable = CACHD1 MUTATION ANALYSIS
D736V1, survival
                  sevent
clus2                0   1
  CACHD1 MUTATED    20   5
  CACHD1 WILD-TYPE 358  88
  CACHD1 MUTATED CACHD1 WILD-TYPE 
              25              446 
  CACHD1 MUTATED CACHD1 WILD-TYPE 
               5               88 
$`CACHD1 MUTATED`
TCGA-A6-2672 TCGA-A6-5665 TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6781 TCGA-AA-3516 
       46.65        22.06         8.38        25.18        19.66        13.02 
TCGA-AA-3950 TCGA-AA-3966 TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01I 
       24.00         2.01        25.02         4.01        34.98        31.00 
TCGA-AU-3779 TCGA-AZ-4315 TCGA-CA-6718 TCGA-CM-5349 TCGA-CM-5862 TCGA-CM-6162 
       14.50        58.39        10.06        30.08         5.03        12.00 
TCGA-D5-6538 TCGA-G4-6586 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-A002 TCGA-DY-A1DC 
       17.13        35.80        13.02        35.01        20.98        41.36 
TCGA-EI-6507 
       19.96 

$`CACHD1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6649 TCGA-A6-6651 
       32.71        27.09        22.52        25.08        24.16        21.76 
TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 
       24.69        24.39        23.87        20.12        20.28         7.04 
TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
        3.02         1.02        35.01        63.98         6.97         1.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
        2.01        20.98        34.03        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       10.98        32.02        12.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        10.88         0.20        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        33.01        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.20        12.76        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5861 
       13.02        29.06        22.03        22.98        32.02        15.02 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 
       15.02        15.02        17.03        15.02         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       15.12        17.85         4.80        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.03         5.29       126.44        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
       32.61         0.49        20.55        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  CACHD1 MUTATED CACHD1 WILD-TYPE 
            2.01             0.00 
  CACHD1 MUTATED CACHD1 WILD-TYPE 
           58.39           148.01 
  CACHD1 MUTATED CACHD1 WILD-TYPE 
          20.980           20.155 
[1] "2.0 - 58.4 (21.0)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.2"
D736V2, continuous
D736V3, binary
                  cls
clus                 0   1
  CACHD1 MUTATED    21   6
  CACHD1 WILD-TYPE 345 113
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CACHD1 MUTATED     21    6
  CACHD1 WILD-TYPE  345  113
        clus
vv       CACHD1 MUTATED CACHD1 WILD-TYPE
  COLON              21              345
  RECTUM              6              113
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CACHD1 MUTATED         3        0        0        12         2         0
  CACHD1 WILD-TYPE      88        1       32       126         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CACHD1 MUTATED           1          0          5          1        0
  CACHD1 WILD-TYPE        23         11         54         41       48
                  vv
clus               STAGE IVA STAGE IVB
  CACHD1 MUTATED           2         0
  CACHD1 WILD-TYPE        16         1
D736V4, multiclass
            clus
vv           CACHD1 MUTATED CACHD1 WILD-TYPE
  STAGE I                 3               88
  STAGE IA                0                1
  STAGE II                0               32
  STAGE IIA              12              126
  STAGE IIB               2                8
  STAGE IIC               0                1
  STAGE III               1               23
  STAGE IIIA              0               11
  STAGE IIIB              5               54
  STAGE IIIC              1               41
  STAGE IV                0               48
  STAGE IVA               2               16
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  CACHD1 MUTATED     1   3  19   4
  CACHD1 WILD-TYPE  16  89 310  46
D736V5, multiclass
    clus
vv   CACHD1 MUTATED CACHD1 WILD-TYPE
  T1              1               16
  T2              3               89
  T3             19              310
  T4              4               46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  CACHD1 MUTATED    19   6   2
  CACHD1 WILD-TYPE 268 107  85
D736V6, multiclass
    clus
vv   CACHD1 MUTATED CACHD1 WILD-TYPE
  N0             19              268
  N1              6              107
  N2              2               85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D736V7, binary
                  cls
clus                 0   1
  CACHD1 MUTATED    23   2
  CACHD1 WILD-TYPE 352  63
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CACHD1 MUTATED     23    2
  CACHD1 WILD-TYPE  352   63
   clus
vv  CACHD1 MUTATED CACHD1 WILD-TYPE
  0             23              352
  1              2               63
[1] 2 2
[1] FALSE
D736V8, binary
                  cls
clus                 0   1
  CACHD1 MUTATED    14  13
  CACHD1 WILD-TYPE 211 251
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CACHD1 MUTATED     14   13
  CACHD1 WILD-TYPE  211  251
        clus
vv       CACHD1 MUTATED CACHD1 WILD-TYPE
  FEMALE             14              211
  MALE               13              251
[1] 2 2
[1] FALSE
D736V9, binary
                  cls
clus                 0   1
  CACHD1 MUTATED    22   0
  CACHD1 WILD-TYPE 328  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CACHD1 MUTATED     22    0
  CACHD1 WILD-TYPE  328   22
     clus
vv    CACHD1 MUTATED CACHD1 WILD-TYPE
  NO              22              328
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CACHD1 MUTATED                     15                             6
  CACHD1 WILD-TYPE                  300                            41
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CACHD1 MUTATED                       6                              0
  CACHD1 WILD-TYPE                   100                             10
D736V10, multiclass
                                clus
vv                               CACHD1 MUTATED CACHD1 WILD-TYPE
  COLON ADENOCARCINOMA                       15              300
  COLON MUCINOUS ADENOCARCINOMA               6               41
  RECTAL ADENOCARCINOMA                       6              100
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  CACHD1 MUTATED    19   0   1   1
  CACHD1 WILD-TYPE 326   4  30  24
D736V11, multiclass
    clus
vv   CACHD1 MUTATED CACHD1 WILD-TYPE
  R0             19              326
  R1              0                4
  R2              1               30
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D736V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CACHD1 MUTATED                                  0     1
  CACHD1 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  CACHD1 MUTATED                           1    13
  CACHD1 WILD-TYPE                        21   213
D736V13, multiclass
                                  clus
vv                                 CACHD1 MUTATED CACHD1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                        13              213
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(737) Variable = CCDC93 MUTATION ANALYSIS
D737V1, survival
                  sevent
clus2                0   1
  CCDC93 MUTATED     8   3
  CCDC93 WILD-TYPE 370  90
  CCDC93 MUTATED CCDC93 WILD-TYPE 
              11              460 
  CCDC93 MUTATED CCDC93 WILD-TYPE 
               3               90 
$`CCDC93 MUTATED`
TCGA-A6-5665 TCGA-AA-3869 TCGA-AA-A010 TCGA-AD-6899 TCGA-AZ-6598 TCGA-CM-6163 
       22.06        27.02        34.98         5.79        49.41         2.96 
TCGA-CM-6171 TCGA-G4-6304 TCGA-AG-3586 TCGA-AG-A002 TCGA-DY-A0XA 
       14.04        53.62         1.02        20.98       126.44 

$`CCDC93 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       17.03        24.03        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.79         0.72        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        88.21         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6164 
       15.02        15.02        17.03        15.02        12.00        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
      133.18        74.56        65.85        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        4.01         5.03         5.29        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  CCDC93 MUTATED CCDC93 WILD-TYPE 
            1.02             0.00 
  CCDC93 MUTATED CCDC93 WILD-TYPE 
          126.44           148.01 
  CCDC93 MUTATED CCDC93 WILD-TYPE 
          22.060           20.085 
[1] "1.0 - 126.4 (22.1)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.2"
D737V2, continuous
D737V3, binary
                  cls
clus                 0   1
  CCDC93 MUTATED     9   3
  CCDC93 WILD-TYPE 357 116
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC93 MUTATED      9    3
  CCDC93 WILD-TYPE  357  116
        clus
vv       CCDC93 MUTATED CCDC93 WILD-TYPE
  COLON               9              357
  RECTUM              3              116
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CCDC93 MUTATED         3        0        1         3         2         0
  CCDC93 WILD-TYPE      88        1       31       135         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CCDC93 MUTATED           1          0          0          1        1
  CCDC93 WILD-TYPE        23         11         59         41       47
                  vv
clus               STAGE IVA STAGE IVB
  CCDC93 MUTATED           0         0
  CCDC93 WILD-TYPE        18         1
D737V4, multiclass
            clus
vv           CCDC93 MUTATED CCDC93 WILD-TYPE
  STAGE I                 3               88
  STAGE IA                0                1
  STAGE II                1               31
  STAGE IIA               3              135
  STAGE IIB               2                8
  STAGE IIC               0                1
  STAGE III               1               23
  STAGE IIIA              0               11
  STAGE IIIB              0               59
  STAGE IIIC              1               41
  STAGE IV                1               47
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  CCDC93 MUTATED     1   2   5   4
  CCDC93 WILD-TYPE  16  90 324  46
D737V5, multiclass
    clus
vv   CCDC93 MUTATED CCDC93 WILD-TYPE
  T1              1               16
  T2              2               90
  T3              5              324
  T4              4               46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  CCDC93 MUTATED     9   0   3
  CCDC93 WILD-TYPE 278 113  84
D737V6, multiclass
    clus
vv   CCDC93 MUTATED CCDC93 WILD-TYPE
  N0              9              278
  N1              0              113
  N2              3               84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D737V7, binary
                  cls
clus                 0   1
  CCDC93 MUTATED     9   1
  CCDC93 WILD-TYPE 366  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC93 MUTATED      9    1
  CCDC93 WILD-TYPE  366   64
   clus
vv  CCDC93 MUTATED CCDC93 WILD-TYPE
  0              9              366
  1              1               64
[1] 2 2
[1] FALSE
D737V8, binary
                  cls
clus                 0   1
  CCDC93 MUTATED     8   4
  CCDC93 WILD-TYPE 217 260
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC93 MUTATED      8    4
  CCDC93 WILD-TYPE  217  260
        clus
vv       CCDC93 MUTATED CCDC93 WILD-TYPE
  FEMALE              8              217
  MALE                4              260
[1] 2 2
[1] FALSE
D737V9, binary
                  cls
clus                 0   1
  CCDC93 MUTATED     9   0
  CCDC93 WILD-TYPE 341  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC93 MUTATED      9    0
  CCDC93 WILD-TYPE  341   22
     clus
vv    CCDC93 MUTATED CCDC93 WILD-TYPE
  NO               9              341
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CCDC93 MUTATED                      8                             1
  CCDC93 WILD-TYPE                  307                            46
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CCDC93 MUTATED                       2                              0
  CCDC93 WILD-TYPE                   104                             10
D737V10, multiclass
                                clus
vv                               CCDC93 MUTATED CCDC93 WILD-TYPE
  COLON ADENOCARCINOMA                        8              307
  COLON MUCINOUS ADENOCARCINOMA               1               46
  RECTAL ADENOCARCINOMA                       2              104
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  CCDC93 MUTATED     8   0   1   0
  CCDC93 WILD-TYPE 337   4  30  25
D737V11, multiclass
    clus
vv   CCDC93 MUTATED CCDC93 WILD-TYPE
  R0              8              337
  R1              0                4
  R2              1               30
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D737V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CCDC93 MUTATED                                  0     0
  CCDC93 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  CCDC93 MUTATED                           0     7
  CCDC93 WILD-TYPE                        22   219
D737V13, multiclass
                                  clus
vv                                 CCDC93 MUTATED CCDC93 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         7              219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(738) Variable = SYNRG MUTATION ANALYSIS
D738V1, survival
                 sevent
clus2               0   1
  SYNRG MUTATED    15   3
  SYNRG WILD-TYPE 363  90
  SYNRG MUTATED SYNRG WILD-TYPE 
             18             453 
  SYNRG MUTATED SYNRG WILD-TYPE 
              3              90 
$`SYNRG MUTATED`
TCGA-A6-6781 TCGA-AA-3525 TCGA-AA-3864 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-A00J 
       19.66         8.05        53.00        26.01        24.00        18.05 
TCGA-AU-6004 TCGA-AZ-6598 TCGA-AZ-6601 TCGA-CA-6717 TCGA-CK-6751 TCGA-CM-4752 
       27.09        49.41       100.01        12.76       124.27        13.02 
TCGA-D5-6539 TCGA-DM-A1D6 TCGA-DM-A1D9 TCGA-G4-6628 TCGA-DC-6681 TCGA-G5-6235 
       12.49        49.91       140.38        79.69         5.95        55.76 

$`SYNRG WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3526 
        1.02         9.07        24.03        37.05        36.03        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 
        0.99        31.07        31.07        30.05        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 
       22.42        27.42        10.88         0.20        14.50        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 
        5.13       106.75        22.36        62.79        88.21         6.77 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
       12.10        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-5341 TCGA-CM-5344 
       23.05        20.02        37.02        25.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 
       15.12        17.85         4.80        17.13        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       13.32        12.59         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       91.79        46.75        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6682 
        5.03        13.97        27.95        10.98        19.99         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6641 
        0.66         0.69        26.43 

  SYNRG MUTATED SYNRG WILD-TYPE 
           5.95            0.00 
  SYNRG MUTATED SYNRG WILD-TYPE 
         140.38          148.01 
  SYNRG MUTATED SYNRG WILD-TYPE 
          26.55           20.05 
[1] "6.0 - 140.4 (26.6)" "0.0 - 148.0 (20.1)"
[1] "hr=" "2.1"
D738V2, continuous
D738V3, binary
                 cls
clus                0   1
  SYNRG MUTATED    16   2
  SYNRG WILD-TYPE 350 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SYNRG MUTATED     16    2
  SYNRG WILD-TYPE  350  117
        clus
vv       SYNRG MUTATED SYNRG WILD-TYPE
  COLON             16             350
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SYNRG MUTATED         3        0        3         5         0         0
  SYNRG WILD-TYPE      88        1       29       133        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SYNRG MUTATED           0          1          4          1        0         1
  SYNRG WILD-TYPE        24         10         55         41       48        17
                 vv
clus              STAGE IVB
  SYNRG MUTATED           0
  SYNRG WILD-TYPE         1
D738V4, multiclass
            clus
vv           SYNRG MUTATED SYNRG WILD-TYPE
  STAGE I                3              88
  STAGE IA               0               1
  STAGE II               3              29
  STAGE IIA              5             133
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             1              10
  STAGE IIIB             4              55
  STAGE IIIC             1              41
  STAGE IV               0              48
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  SYNRG MUTATED     0   3  13   2
  SYNRG WILD-TYPE  17  89 316  48
D738V5, multiclass
    clus
vv   SYNRG MUTATED SYNRG WILD-TYPE
  T1             0              17
  T2             3              89
  T3            13             316
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  SYNRG MUTATED    12   5   1
  SYNRG WILD-TYPE 275 108  86
D738V6, multiclass
    clus
vv   SYNRG MUTATED SYNRG WILD-TYPE
  N0            12             275
  N1             5             108
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D738V7, binary
                 cls
clus                0   1
  SYNRG MUTATED    13   1
  SYNRG WILD-TYPE 362  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SYNRG MUTATED     13    1
  SYNRG WILD-TYPE  362   64
   clus
vv  SYNRG MUTATED SYNRG WILD-TYPE
  0            13             362
  1             1              64
[1] 2 2
[1] FALSE
D738V8, binary
                 cls
clus                0   1
  SYNRG MUTATED     8  10
  SYNRG WILD-TYPE 217 254
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SYNRG MUTATED      8   10
  SYNRG WILD-TYPE  217  254
        clus
vv       SYNRG MUTATED SYNRG WILD-TYPE
  FEMALE             8             217
  MALE              10             254
[1] 2 2
[1] FALSE
D738V9, binary
                 cls
clus                0   1
  SYNRG MUTATED    14   0
  SYNRG WILD-TYPE 336  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SYNRG MUTATED     14    0
  SYNRG WILD-TYPE  336   22
     clus
vv    SYNRG MUTATED SYNRG WILD-TYPE
  NO             14             336
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SYNRG MUTATED                      9                             7
  SYNRG WILD-TYPE                  306                            40
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SYNRG MUTATED                       2                              0
  SYNRG WILD-TYPE                   104                             10
D738V10, multiclass
                                clus
vv                               SYNRG MUTATED SYNRG WILD-TYPE
  COLON ADENOCARCINOMA                       9             306
  COLON MUCINOUS ADENOCARCINOMA              7              40
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  SYNRG MUTATED    11   1   0   2
  SYNRG WILD-TYPE 334   3  31  23
D738V11, multiclass
    clus
vv   SYNRG MUTATED SYNRG WILD-TYPE
  R0            11             334
  R1             1               3
  R2             0              31
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D738V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SYNRG MUTATED                                  0     1
  SYNRG WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  SYNRG MUTATED                           1    11
  SYNRG WILD-TYPE                        21   215
D738V13, multiclass
                                  clus
vv                                 SYNRG MUTATED SYNRG WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                       11             215
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(739) Variable = TRIM33 MUTATION ANALYSIS
D739V1, survival
                  sevent
clus2                0   1
  TRIM33 MUTATED    16   3
  TRIM33 WILD-TYPE 362  90
  TRIM33 MUTATED TRIM33 WILD-TYPE 
              19              452 
  TRIM33 MUTATED TRIM33 WILD-TYPE 
               3               90 
$`TRIM33 MUTATED`
TCGA-A6-5660 TCGA-A6-5661 TCGA-AA-3525 TCGA-AA-3811 TCGA-AA-3864 TCGA-AA-A010 
       29.19        33.53         8.05        10.06        53.00        34.98 
TCGA-AY-6197 TCGA-AZ-6598 TCGA-CK-5914 TCGA-CM-6171 TCGA-D5-6930 TCGA-F4-6856 
       21.44        49.41         9.99        14.04         1.51        35.31 
TCGA-G4-6307 TCGA-G4-6588 TCGA-AG-3894 TCGA-AG-A002 TCGA-AG-A00H TCGA-DY-A1DG 
       55.04        26.17        14.01        20.98        25.97        51.48 
TCGA-EI-6507 
       19.96 

$`TRIM33 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       32.91        31.63        30.44        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3529 
        9.07        24.03        37.05        36.03        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3815 
       85.05        26.99        19.04        19.04        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       31.07        30.05        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       16.31         0.95        33.01        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 
        5.13       106.75        22.36        62.79        88.21         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 
       85.45        15.62        49.08        51.32        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       12.99        13.02        15.02        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       47.41       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       35.80        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       13.02        35.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
        6.02        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
       32.61         0.49        20.55        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  TRIM33 MUTATED TRIM33 WILD-TYPE 
            1.51             0.00 
  TRIM33 MUTATED TRIM33 WILD-TYPE 
           55.04           148.01 
  TRIM33 MUTATED TRIM33 WILD-TYPE 
          25.970           20.035 
[1] "1.5 - 55.0 (26.0)"  "0.0 - 148.0 (20.0)"
[1] "hr=" "1.3"
D739V2, continuous
D739V3, binary
                  cls
clus                 0   1
  TRIM33 MUTATED    15   5
  TRIM33 WILD-TYPE 351 114
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIM33 MUTATED     15    5
  TRIM33 WILD-TYPE  351  114
        clus
vv       TRIM33 MUTATED TRIM33 WILD-TYPE
  COLON              15              351
  RECTUM              5              114
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TRIM33 MUTATED         3        0        2         7         2         0
  TRIM33 WILD-TYPE      88        1       30       131         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TRIM33 MUTATED           1          0          3          1        0
  TRIM33 WILD-TYPE        23         11         56         41       48
                  vv
clus               STAGE IVA STAGE IVB
  TRIM33 MUTATED           1         0
  TRIM33 WILD-TYPE        17         1
D739V4, multiclass
            clus
vv           TRIM33 MUTATED TRIM33 WILD-TYPE
  STAGE I                 3               88
  STAGE IA                0                1
  STAGE II                2               30
  STAGE IIA               7              131
  STAGE IIB               2                8
  STAGE IIC               0                1
  STAGE III               1               23
  STAGE IIIA              0               11
  STAGE IIIB              3               56
  STAGE IIIC              1               41
  STAGE IV                0               48
  STAGE IVA               1               17
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  TRIM33 MUTATED     0   3  15   2
  TRIM33 WILD-TYPE  17  89 314  48
D739V5, multiclass
    clus
vv   TRIM33 MUTATED TRIM33 WILD-TYPE
  T1              0               17
  T2              3               89
  T3             15              314
  T4              2               48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  TRIM33 MUTATED    14   4   2
  TRIM33 WILD-TYPE 273 109  85
D739V6, multiclass
    clus
vv   TRIM33 MUTATED TRIM33 WILD-TYPE
  N0             14              273
  N1              4              109
  N2              2               85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D739V7, binary
                  cls
clus                 0   1
  TRIM33 MUTATED    15   1
  TRIM33 WILD-TYPE 360  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIM33 MUTATED     15    1
  TRIM33 WILD-TYPE  360   64
   clus
vv  TRIM33 MUTATED TRIM33 WILD-TYPE
  0             15              360
  1              1               64
[1] 2 2
[1] FALSE
D739V8, binary
                  cls
clus                 0   1
  TRIM33 MUTATED     8  12
  TRIM33 WILD-TYPE 217 252
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIM33 MUTATED      8   12
  TRIM33 WILD-TYPE  217  252
        clus
vv       TRIM33 MUTATED TRIM33 WILD-TYPE
  FEMALE              8              217
  MALE               12              252
[1] 2 2
[1] FALSE
D739V9, binary
                  cls
clus                 0   1
  TRIM33 MUTATED    14   2
  TRIM33 WILD-TYPE 336  20
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIM33 MUTATED     14    2
  TRIM33 WILD-TYPE  336   20
     clus
vv    TRIM33 MUTATED TRIM33 WILD-TYPE
  NO              14              336
  YES              2               20
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  TRIM33 MUTATED                     13                             2
  TRIM33 WILD-TYPE                  302                            45
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  TRIM33 MUTATED                       5                              0
  TRIM33 WILD-TYPE                   101                             10
D739V10, multiclass
                                clus
vv                               TRIM33 MUTATED TRIM33 WILD-TYPE
  COLON ADENOCARCINOMA                       13              302
  COLON MUCINOUS ADENOCARCINOMA               2               45
  RECTAL ADENOCARCINOMA                       5              101
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  TRIM33 MUTATED    15   0   0   2
  TRIM33 WILD-TYPE 330   4  31  23
D739V11, multiclass
    clus
vv   TRIM33 MUTATED TRIM33 WILD-TYPE
  R0             15              330
  R1              0                4
  R2              0               31
  RX              2               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D739V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TRIM33 MUTATED                                  0     0
  TRIM33 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  TRIM33 MUTATED                           2    11
  TRIM33 WILD-TYPE                        20   215
D739V13, multiclass
                                  clus
vv                                 TRIM33 MUTATED TRIM33 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     2               20
  WHITE                                        11              215
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(740) Variable = LPIN2 MUTATION ANALYSIS
D740V1, survival
                 sevent
clus2               0   1
  LPIN2 MUTATED     8   1
  LPIN2 WILD-TYPE 370  92
  LPIN2 MUTATED LPIN2 WILD-TYPE 
              9             462 
  LPIN2 MUTATED LPIN2 WILD-TYPE 
              1              92 
$`LPIN2 MUTATED`
TCGA-AA-A010 TCGA-AA-A02J TCGA-AZ-4315 TCGA-CK-4948 TCGA-D5-6922 TCGA-F4-6703 
       34.98         5.03        58.39       148.01         4.41        47.87 
TCGA-F4-6856 TCGA-G4-6586 TCGA-AG-A002 
       35.31        35.80        20.98 

$`LPIN2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       51.98        39.98         2.01        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       33.01        21.44        17.82         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4952 
       12.76        10.06        14.30        17.56        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6923 
       12.49        16.14        15.58         1.48         3.68        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6704 TCGA-F4-6805 
        8.61        31.96        35.74         6.18         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  LPIN2 MUTATED LPIN2 WILD-TYPE 
           4.41            0.00 
  LPIN2 MUTATED LPIN2 WILD-TYPE 
         148.01          140.38 
  LPIN2 MUTATED LPIN2 WILD-TYPE 
         35.310          20.035 
[1] "4.4 - 148.0 (35.3)" "0.0 - 140.4 (20.0)"
[1] "hr=" "2.5"
D740V2, continuous
D740V3, binary
                 cls
clus                0   1
  LPIN2 MUTATED     9   1
  LPIN2 WILD-TYPE 357 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LPIN2 MUTATED      9    1
  LPIN2 WILD-TYPE  357  118
        clus
vv       LPIN2 MUTATED LPIN2 WILD-TYPE
  COLON              9             357
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  LPIN2 MUTATED         2        0        0         4         1         0
  LPIN2 WILD-TYPE      89        1       32       134         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  LPIN2 MUTATED           1          1          0          0        1         0
  LPIN2 WILD-TYPE        23         10         59         42       47        18
                 vv
clus              STAGE IVB
  LPIN2 MUTATED           0
  LPIN2 WILD-TYPE         1
D740V4, multiclass
            clus
vv           LPIN2 MUTATED LPIN2 WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              4             134
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             1              10
  STAGE IIIB             0              59
  STAGE IIIC             0              42
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  LPIN2 MUTATED     0   2   7   1
  LPIN2 WILD-TYPE  17  90 322  49
D740V5, multiclass
    clus
vv   LPIN2 MUTATED LPIN2 WILD-TYPE
  T1             0              17
  T2             2              90
  T3             7             322
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  LPIN2 MUTATED     8   2   0
  LPIN2 WILD-TYPE 279 111  87
D740V6, multiclass
    clus
vv   LPIN2 MUTATED LPIN2 WILD-TYPE
  N0             8             279
  N1             2             111
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D740V7, binary
                 cls
clus                0   1
  LPIN2 MUTATED     9   1
  LPIN2 WILD-TYPE 366  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LPIN2 MUTATED      9    1
  LPIN2 WILD-TYPE  366   64
   clus
vv  LPIN2 MUTATED LPIN2 WILD-TYPE
  0             9             366
  1             1              64
[1] 2 2
[1] FALSE
D740V8, binary
                 cls
clus                0   1
  LPIN2 MUTATED     5   5
  LPIN2 WILD-TYPE 220 259
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LPIN2 MUTATED      5    5
  LPIN2 WILD-TYPE  220  259
        clus
vv       LPIN2 MUTATED LPIN2 WILD-TYPE
  FEMALE             5             220
  MALE               5             259
[1] 2 2
[1] FALSE
D740V9, binary
                 cls
clus                0   1
  LPIN2 MUTATED     7   0
  LPIN2 WILD-TYPE 343  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LPIN2 MUTATED      7    0
  LPIN2 WILD-TYPE  343   22
     clus
vv    LPIN2 MUTATED LPIN2 WILD-TYPE
  NO              7             343
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  LPIN2 MUTATED                      8                             1
  LPIN2 WILD-TYPE                  307                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  LPIN2 MUTATED                       1                              0
  LPIN2 WILD-TYPE                   105                             10
D740V10, multiclass
                                clus
vv                               LPIN2 MUTATED LPIN2 WILD-TYPE
  COLON ADENOCARCINOMA                       8             307
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  LPIN2 MUTATED     9   0   1   0
  LPIN2 WILD-TYPE 336   4  30  25
D740V11, multiclass
    clus
vv   LPIN2 MUTATED LPIN2 WILD-TYPE
  R0             9             336
  R1             0               4
  R2             1              30
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D740V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  LPIN2 MUTATED                                  0     0
  LPIN2 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  LPIN2 MUTATED                           0     6
  LPIN2 WILD-TYPE                        22   220
D740V13, multiclass
                                  clus
vv                                 LPIN2 MUTATED LPIN2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        6             220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(741) Variable = ING1 MUTATION ANALYSIS
D741V1, survival
                sevent
clus2              0   1
  ING1 MUTATED     8   4
  ING1 WILD-TYPE 370  89
  ING1 MUTATED ING1 WILD-TYPE 
            12            459 
  ING1 MUTATED ING1 WILD-TYPE 
             4             89 
$`ING1 MUTATED`
TCGA-A6-2672 TCGA-AA-3502 TCGA-AA-3949 TCGA-AA-A010 TCGA-AA-A01F TCGA-AA-A03F 
       46.65        35.01        26.01        34.98        32.02        18.05 
TCGA-CK-4950 TCGA-DM-A28K TCGA-F4-6570 TCGA-G4-6586 TCGA-AF-3913 TCGA-DY-A1DD 
       85.45        98.24         6.18        35.80        10.39        57.24 

$`ING1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       12.99        24.00        33.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
        1.02        10.98        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03J TCGA-AD-5900 
       14.01         0.92        41.00        39.98        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
       17.56       148.01        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       35.97        60.79       117.07         8.61        31.96        35.74 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 
       61.91        36.00        22.09        13.78        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       19.10        34.49        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DF TCGA-DY-A1DG 
        5.03         5.29       126.44        41.36        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  ING1 MUTATED ING1 WILD-TYPE 
          6.18           0.00 
  ING1 MUTATED ING1 WILD-TYPE 
         98.24         148.01 
  ING1 MUTATED ING1 WILD-TYPE 
        34.995         20.020 
[1] "6.2 - 98.2 (35.0)"  "0.0 - 148.0 (20.0)"
[1] "hr=" "1.2"
D741V2, continuous
D741V3, binary
                cls
clus               0   1
  ING1 MUTATED    10   2
  ING1 WILD-TYPE 356 117
[1] "tbl2"
                cls
clus             [,1] [,2]
  ING1 MUTATED     10    2
  ING1 WILD-TYPE  356  117
        clus
vv       ING1 MUTATED ING1 WILD-TYPE
  COLON            10            356
  RECTUM            2            117
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ING1 MUTATED         1        0        0         3         1         0
  ING1 WILD-TYPE      90        1       32       135         9         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ING1 MUTATED           1          0          5          0        1         0
  ING1 WILD-TYPE        23         11         54         42       47        18
                vv
clus             STAGE IVB
  ING1 MUTATED           0
  ING1 WILD-TYPE         1
D741V4, multiclass
            clus
vv           ING1 MUTATED ING1 WILD-TYPE
  STAGE I               1             90
  STAGE IA              0              1
  STAGE II              0             32
  STAGE IIA             3            135
  STAGE IIB             1              9
  STAGE IIC             0              1
  STAGE III             1             23
  STAGE IIIA            0             11
  STAGE IIIB            5             54
  STAGE IIIC            0             42
  STAGE IV              1             47
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  ING1 MUTATED     0   1  10   1
  ING1 WILD-TYPE  17  91 319  49
D741V5, multiclass
    clus
vv   ING1 MUTATED ING1 WILD-TYPE
  T1            0             17
  T2            1             91
  T3           10            319
  T4            1             49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  ING1 MUTATED     5   6   1
  ING1 WILD-TYPE 282 107  86
D741V6, multiclass
    clus
vv   ING1 MUTATED ING1 WILD-TYPE
  N0            5            282
  N1            6            107
  N2            1             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D741V7, binary
                cls
clus               0   1
  ING1 MUTATED    11   1
  ING1 WILD-TYPE 364  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  ING1 MUTATED     11    1
  ING1 WILD-TYPE  364   64
   clus
vv  ING1 MUTATED ING1 WILD-TYPE
  0           11            364
  1            1             64
[1] 2 2
[1] FALSE
D741V8, binary
                cls
clus               0   1
  ING1 MUTATED     8   4
  ING1 WILD-TYPE 217 260
[1] "tbl2"
                cls
clus             [,1] [,2]
  ING1 MUTATED      8    4
  ING1 WILD-TYPE  217  260
        clus
vv       ING1 MUTATED ING1 WILD-TYPE
  FEMALE            8            217
  MALE              4            260
[1] 2 2
[1] FALSE
D741V9, binary
                cls
clus               0   1
  ING1 MUTATED     9   0
  ING1 WILD-TYPE 341  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  ING1 MUTATED      9    0
  ING1 WILD-TYPE  341   22
     clus
vv    ING1 MUTATED ING1 WILD-TYPE
  NO             9            341
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ING1 MUTATED                      7                             3
  ING1 WILD-TYPE                  308                            44
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ING1 MUTATED                       2                              0
  ING1 WILD-TYPE                   104                             10
D741V10, multiclass
                                clus
vv                               ING1 MUTATED ING1 WILD-TYPE
  COLON ADENOCARCINOMA                      7            308
  COLON MUCINOUS ADENOCARCINOMA             3             44
  RECTAL ADENOCARCINOMA                     2            104
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  ING1 MUTATED     9   1   0   0
  ING1 WILD-TYPE 336   3  31  25
D741V11, multiclass
    clus
vv   ING1 MUTATED ING1 WILD-TYPE
  R0            9            336
  R1            1              3
  R2            0             31
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D741V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ING1 MUTATED                                  0     0
  ING1 WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  ING1 MUTATED                           2     5
  ING1 WILD-TYPE                        20   221
D741V13, multiclass
                                  clus
vv                                 ING1 MUTATED ING1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   2             20
  WHITE                                       5            221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(742) Variable = TAB3 MUTATION ANALYSIS
D742V1, survival
                sevent
clus2              0   1
  TAB3 MUTATED     9   3
  TAB3 WILD-TYPE 369  90
  TAB3 MUTATED TAB3 WILD-TYPE 
            12            459 
  TAB3 MUTATED TAB3 WILD-TYPE 
             3             90 
$`TAB3 MUTATED`
TCGA-A6-5662 TCGA-AA-3966 TCGA-AA-A00N TCGA-AA-A01R TCGA-AZ-5403 TCGA-CA-6718 
       23.61         2.01         4.01        35.01        62.79        10.06 
TCGA-CM-5348 TCGA-F4-6807 TCGA-G4-6628 TCGA-AG-3892 TCGA-CI-6624 TCGA-DC-6155 
       22.98        16.24        79.69        13.02         4.73        13.97 

$`TAB3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        33.53        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
        2.01        20.98        34.03        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       31.00        38.07         1.02         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 
        3.25         3.29         0.07        12.20        12.76        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       26.17        91.79        46.75        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 
       19.99         1.02        17.95        36.95        17.03        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
       33.17         6.97        78.12         7.17        15.02         5.03 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  TAB3 MUTATED TAB3 WILD-TYPE 
          2.01           0.00 
  TAB3 MUTATED TAB3 WILD-TYPE 
         79.69         148.01 
  TAB3 MUTATED TAB3 WILD-TYPE 
        15.105         20.280 
[1] "2.0 - 79.7 (15.1)"  "0.0 - 148.0 (20.3)"
[1] "hr=" "1.4"
D742V2, continuous
D742V3, binary
                cls
clus               0   1
  TAB3 MUTATED    10   3
  TAB3 WILD-TYPE 356 116
[1] "tbl2"
                cls
clus             [,1] [,2]
  TAB3 MUTATED     10    3
  TAB3 WILD-TYPE  356  116
        clus
vv       TAB3 MUTATED TAB3 WILD-TYPE
  COLON            10            356
  RECTUM            3            116
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TAB3 MUTATED         3        0        1         2         1         0
  TAB3 WILD-TYPE      88        1       31       136         9         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TAB3 MUTATED           2          1          1          1        0         1
  TAB3 WILD-TYPE        22         10         58         41       48        17
                vv
clus             STAGE IVB
  TAB3 MUTATED           0
  TAB3 WILD-TYPE         1
D742V4, multiclass
            clus
vv           TAB3 MUTATED TAB3 WILD-TYPE
  STAGE I               3             88
  STAGE IA              0              1
  STAGE II              1             31
  STAGE IIA             2            136
  STAGE IIB             1              9
  STAGE IIC             0              1
  STAGE III             2             22
  STAGE IIIA            1             10
  STAGE IIIB            1             58
  STAGE IIIC            1             41
  STAGE IV              0             48
  STAGE IVA             1             17
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  TAB3 MUTATED     1   3   8   1
  TAB3 WILD-TYPE  16  89 321  49
D742V5, multiclass
    clus
vv   TAB3 MUTATED TAB3 WILD-TYPE
  T1            1             16
  T2            3             89
  T3            8            321
  T4            1             49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  TAB3 MUTATED     7   2   4
  TAB3 WILD-TYPE 280 111  83
D742V6, multiclass
    clus
vv   TAB3 MUTATED TAB3 WILD-TYPE
  N0            7            280
  N1            2            111
  N2            4             83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D742V7, binary
                cls
clus               0   1
  TAB3 MUTATED    11   1
  TAB3 WILD-TYPE 364  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  TAB3 MUTATED     11    1
  TAB3 WILD-TYPE  364   64
   clus
vv  TAB3 MUTATED TAB3 WILD-TYPE
  0           11            364
  1            1             64
[1] 2 2
[1] FALSE
D742V8, binary
                cls
clus               0   1
  TAB3 MUTATED     5   8
  TAB3 WILD-TYPE 220 256
[1] "tbl2"
                cls
clus             [,1] [,2]
  TAB3 MUTATED      5    8
  TAB3 WILD-TYPE  220  256
        clus
vv       TAB3 MUTATED TAB3 WILD-TYPE
  FEMALE            5            220
  MALE              8            256
[1] 2 2
[1] FALSE
D742V9, binary
                cls
clus               0   1
  TAB3 MUTATED     8   1
  TAB3 WILD-TYPE 342  21
[1] "tbl2"
                cls
clus             [,1] [,2]
  TAB3 MUTATED      8    1
  TAB3 WILD-TYPE  342   21
     clus
vv    TAB3 MUTATED TAB3 WILD-TYPE
  NO             8            342
  YES            1             21
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  TAB3 MUTATED                      7                             3
  TAB3 WILD-TYPE                  308                            44
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  TAB3 MUTATED                       3                              0
  TAB3 WILD-TYPE                   103                             10
D742V10, multiclass
                                clus
vv                               TAB3 MUTATED TAB3 WILD-TYPE
  COLON ADENOCARCINOMA                      7            308
  COLON MUCINOUS ADENOCARCINOMA             3             44
  RECTAL ADENOCARCINOMA                     3            103
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  TAB3 MUTATED     8   0   0   1
  TAB3 WILD-TYPE 337   4  31  24
D742V11, multiclass
    clus
vv   TAB3 MUTATED TAB3 WILD-TYPE
  R0            8            337
  R1            0              4
  R2            0             31
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D742V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TAB3 MUTATED                                  0     1
  TAB3 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  TAB3 MUTATED                           0     7
  TAB3 WILD-TYPE                        22   219
D742V13, multiclass
                                  clus
vv                                 TAB3 MUTATED TAB3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       7            219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(743) Variable = ZFP3 MUTATION ANALYSIS
D743V1, survival
                sevent
clus2              0   1
  ZFP3 MUTATED    11   1
  ZFP3 WILD-TYPE 367  92
  ZFP3 MUTATED ZFP3 WILD-TYPE 
            12            459 
  ZFP3 MUTATED ZFP3 WILD-TYPE 
             1             92 
$`ZFP3 MUTATED`
TCGA-A6-2672 TCGA-A6-5665 TCGA-AA-3510 TCGA-AA-3525 TCGA-AA-3555 TCGA-AA-3833 
       46.65        22.06        63.98         8.05        29.95        15.95 
TCGA-AA-3977 TCGA-AA-A010 TCGA-CA-6717 TCGA-DM-A1D4 TCGA-AG-3892 TCGA-AG-A002 
       25.02        34.98        12.76        92.75        13.02        20.98 

$`ZFP3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       24.03        37.05        36.03        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       78.08         6.05         6.97        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
       25.02         1.02        17.98        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.20        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       24.43        38.20       130.65        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 
        1.02        17.95        36.95        17.03        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  ZFP3 MUTATED ZFP3 WILD-TYPE 
          8.05           0.00 
  ZFP3 MUTATED ZFP3 WILD-TYPE 
         92.75         148.01 
  ZFP3 MUTATED ZFP3 WILD-TYPE 
         23.54          20.05 
[1] "8.1 - 92.8 (23.5)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "3"  
D743V2, continuous
D743V3, binary
                cls
clus               0   1
  ZFP3 MUTATED    10   2
  ZFP3 WILD-TYPE 356 117
[1] "tbl2"
                cls
clus             [,1] [,2]
  ZFP3 MUTATED     10    2
  ZFP3 WILD-TYPE  356  117
        clus
vv       ZFP3 MUTATED ZFP3 WILD-TYPE
  COLON            10            356
  RECTUM            2            117
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZFP3 MUTATED         2        0        1         5         1         0
  ZFP3 WILD-TYPE      89        1       31       133         9         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ZFP3 MUTATED           0          0          2          0        0         0
  ZFP3 WILD-TYPE        24         11         57         42       48        18
                vv
clus             STAGE IVB
  ZFP3 MUTATED           0
  ZFP3 WILD-TYPE         1
D743V4, multiclass
            clus
vv           ZFP3 MUTATED ZFP3 WILD-TYPE
  STAGE I               2             89
  STAGE IA              0              1
  STAGE II              1             31
  STAGE IIA             5            133
  STAGE IIB             1              9
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            2             57
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  ZFP3 MUTATED     1   2   8   1
  ZFP3 WILD-TYPE  16  90 321  49
D743V5, multiclass
    clus
vv   ZFP3 MUTATED ZFP3 WILD-TYPE
  T1            1             16
  T2            2             90
  T3            8            321
  T4            1             49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  ZFP3 MUTATED    10   2   0
  ZFP3 WILD-TYPE 277 111  87
D743V6, multiclass
    clus
vv   ZFP3 MUTATED ZFP3 WILD-TYPE
  N0           10            277
  N1            2            111
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D743V7, binary
                cls
clus               0   1
  ZFP3 MUTATED    11   0
  ZFP3 WILD-TYPE 364  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  ZFP3 MUTATED     11    0
  ZFP3 WILD-TYPE  364   65
   clus
vv  ZFP3 MUTATED ZFP3 WILD-TYPE
  0           11            364
  1            0             65
[1] 2 2
[1] FALSE
D743V8, binary
                cls
clus               0   1
  ZFP3 MUTATED     6   6
  ZFP3 WILD-TYPE 219 258
[1] "tbl2"
                cls
clus             [,1] [,2]
  ZFP3 MUTATED      6    6
  ZFP3 WILD-TYPE  219  258
        clus
vv       ZFP3 MUTATED ZFP3 WILD-TYPE
  FEMALE            6            219
  MALE              6            258
[1] 2 2
[1] FALSE
D743V9, binary
                cls
clus               0   1
  ZFP3 MUTATED    11   0
  ZFP3 WILD-TYPE 339  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  ZFP3 MUTATED     11    0
  ZFP3 WILD-TYPE  339   22
     clus
vv    ZFP3 MUTATED ZFP3 WILD-TYPE
  NO            11            339
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ZFP3 MUTATED                      8                             2
  ZFP3 WILD-TYPE                  307                            45
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ZFP3 MUTATED                       2                              0
  ZFP3 WILD-TYPE                   104                             10
D743V10, multiclass
                                clus
vv                               ZFP3 MUTATED ZFP3 WILD-TYPE
  COLON ADENOCARCINOMA                      8            307
  COLON MUCINOUS ADENOCARCINOMA             2             45
  RECTAL ADENOCARCINOMA                     2            104
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  ZFP3 MUTATED     9   0   0   1
  ZFP3 WILD-TYPE 336   4  31  24
D743V11, multiclass
    clus
vv   ZFP3 MUTATED ZFP3 WILD-TYPE
  R0            9            336
  R1            0              4
  R2            0             31
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D743V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZFP3 MUTATED                                  0     1
  ZFP3 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  ZFP3 MUTATED                           0     3
  ZFP3 WILD-TYPE                        22   223
D743V13, multiclass
                                  clus
vv                                 ZFP3 MUTATED ZFP3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       3            223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(744) Variable = ULK1 MUTATION ANALYSIS
D744V1, survival
                sevent
clus2              0   1
  ULK1 MUTATED     7   3
  ULK1 WILD-TYPE 371  90
  ULK1 MUTATED ULK1 WILD-TYPE 
            10            461 
  ULK1 MUTATED ULK1 WILD-TYPE 
             3             90 
$`ULK1 MUTATED`
TCGA-A6-6780 TCGA-AY-6197 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-CM-5349 
       20.12        21.44        62.79        49.41         6.77        30.08 
TCGA-D5-6928 TCGA-G4-6586 TCGA-G4-6588 TCGA-AG-3742 
       11.64        35.80        26.17         0.99 

$`ULK1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        33.01        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
      106.75        22.36        88.21        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.03        22.98        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.04         9.44         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
        0.99        37.02        32.98         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  ULK1 MUTATED ULK1 WILD-TYPE 
          0.99           0.00 
  ULK1 MUTATED ULK1 WILD-TYPE 
         62.79         148.01 
  ULK1 MUTATED ULK1 WILD-TYPE 
        23.805         20.050 
[1] "1.0 - 62.8 (23.8)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.5"
D744V2, continuous
D744V3, binary
                cls
clus               0   1
  ULK1 MUTATED    10   1
  ULK1 WILD-TYPE 356 118
[1] "tbl2"
                cls
clus             [,1] [,2]
  ULK1 MUTATED     10    1
  ULK1 WILD-TYPE  356  118
        clus
vv       ULK1 MUTATED ULK1 WILD-TYPE
  COLON            10            356
  RECTUM            1            118
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ULK1 MUTATED         2        0        2         6         1         0
  ULK1 WILD-TYPE      89        1       30       132         9         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ULK1 MUTATED           0          0          0          0        0         0
  ULK1 WILD-TYPE        24         11         59         42       48        18
                vv
clus             STAGE IVB
  ULK1 MUTATED           0
  ULK1 WILD-TYPE         1
D744V4, multiclass
            clus
vv           ULK1 MUTATED ULK1 WILD-TYPE
  STAGE I               2             89
  STAGE IA              0              1
  STAGE II              2             30
  STAGE IIA             6            132
  STAGE IIB             1              9
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            0             59
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  ULK1 MUTATED     1   1   8   1
  ULK1 WILD-TYPE  16  91 321  49
D744V5, multiclass
    clus
vv   ULK1 MUTATED ULK1 WILD-TYPE
  T1            1             16
  T2            1             91
  T3            8            321
  T4            1             49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  ULK1 MUTATED    11   0   0
  ULK1 WILD-TYPE 276 113  87
D744V6, multiclass
    clus
vv   ULK1 MUTATED ULK1 WILD-TYPE
  N0           11            276
  N1            0            113
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D744V7, binary
                cls
clus               0   1
  ULK1 MUTATED     5   0
  ULK1 WILD-TYPE 370  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  ULK1 MUTATED      5    0
  ULK1 WILD-TYPE  370   65
   clus
vv  ULK1 MUTATED ULK1 WILD-TYPE
  0            5            370
  1            0             65
[1] 2 2
[1] FALSE
D744V8, binary
                cls
clus               0   1
  ULK1 MUTATED     6   5
  ULK1 WILD-TYPE 219 259
[1] "tbl2"
                cls
clus             [,1] [,2]
  ULK1 MUTATED      6    5
  ULK1 WILD-TYPE  219  259
        clus
vv       ULK1 MUTATED ULK1 WILD-TYPE
  FEMALE            6            219
  MALE              5            259
[1] 2 2
[1] FALSE
D744V9, binary
                cls
clus               0   1
  ULK1 MUTATED     9   0
  ULK1 WILD-TYPE 341  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  ULK1 MUTATED      9    0
  ULK1 WILD-TYPE  341   22
     clus
vv    ULK1 MUTATED ULK1 WILD-TYPE
  NO             9            341
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ULK1 MUTATED                      8                             2
  ULK1 WILD-TYPE                  307                            45
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ULK1 MUTATED                       1                              0
  ULK1 WILD-TYPE                   105                             10
D744V10, multiclass
                                clus
vv                               ULK1 MUTATED ULK1 WILD-TYPE
  COLON ADENOCARCINOMA                      8            307
  COLON MUCINOUS ADENOCARCINOMA             2             45
  RECTAL ADENOCARCINOMA                     1            105
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  ULK1 MUTATED     6   0   0   1
  ULK1 WILD-TYPE 339   4  31  24
D744V11, multiclass
    clus
vv   ULK1 MUTATED ULK1 WILD-TYPE
  R0            6            339
  R1            0              4
  R2            0             31
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D744V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ULK1 MUTATED                                  0     0
  ULK1 WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  ULK1 MUTATED                           0    10
  ULK1 WILD-TYPE                        22   216
D744V13, multiclass
                                  clus
vv                                 ULK1 MUTATED ULK1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                      10            216
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(745) Variable = CLDN10 MUTATION ANALYSIS
D745V1, survival
                  sevent
clus2                0   1
  CLDN10 MUTATED    10   3
  CLDN10 WILD-TYPE 368  90
  CLDN10 MUTATED CLDN10 WILD-TYPE 
              13              458 
  CLDN10 MUTATED CLDN10 WILD-TYPE 
               3               90 
$`CLDN10 MUTATED`
TCGA-A6-6781 TCGA-AA-3510 TCGA-AA-3715 TCGA-AU-6004 TCGA-AZ-6598 TCGA-CM-4746 
       19.66        63.98        19.04        27.09        49.41        37.02 
TCGA-D5-6929 TCGA-DM-A0X9 TCGA-DM-A28E TCGA-F4-6570 TCGA-F4-6856 TCGA-AG-3598 
        4.80       119.70       119.93         6.18        35.31        50.04 
TCGA-AG-A002 
       20.98 

$`CLDN10 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
        0.20        14.50        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        88.21         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       23.05        20.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.04         9.44        11.64         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
       10.26        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28F TCGA-DM-A28G 
      135.65       139.17         6.12        81.37        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 
      117.07        98.24         8.61        31.96        35.74        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
        0.53        47.41       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
        2.01        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  CLDN10 MUTATED CLDN10 WILD-TYPE 
             4.8              0.0 
  CLDN10 MUTATED CLDN10 WILD-TYPE 
          119.93           148.01 
  CLDN10 MUTATED CLDN10 WILD-TYPE 
          35.310           20.035 
[1] "4.8 - 119.9 (35.3)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.4"
D745V2, continuous
D745V3, binary
                  cls
clus                 0   1
  CLDN10 MUTATED    11   2
  CLDN10 WILD-TYPE 355 117
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CLDN10 MUTATED     11    2
  CLDN10 WILD-TYPE  355  117
        clus
vv       CLDN10 MUTATED CLDN10 WILD-TYPE
  COLON              11              355
  RECTUM              2              117
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CLDN10 MUTATED         4        0        3         4         0         0
  CLDN10 WILD-TYPE      87        1       29       134        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CLDN10 MUTATED           0          0          0          1        1
  CLDN10 WILD-TYPE        24         11         59         41       47
                  vv
clus               STAGE IVA STAGE IVB
  CLDN10 MUTATED           0         0
  CLDN10 WILD-TYPE        18         1
D745V4, multiclass
            clus
vv           CLDN10 MUTATED CLDN10 WILD-TYPE
  STAGE I                 4               87
  STAGE IA                0                1
  STAGE II                3               29
  STAGE IIA               4              134
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              0               59
  STAGE IIIC              1               41
  STAGE IV                1               47
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  CLDN10 MUTATED     0   4   8   1
  CLDN10 WILD-TYPE  17  88 321  49
D745V5, multiclass
    clus
vv   CLDN10 MUTATED CLDN10 WILD-TYPE
  T1              0               17
  T2              4               88
  T3              8              321
  T4              1               49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  CLDN10 MUTATED    11   2   0
  CLDN10 WILD-TYPE 276 111  87
D745V6, multiclass
    clus
vv   CLDN10 MUTATED CLDN10 WILD-TYPE
  N0             11              276
  N1              2              111
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D745V7, binary
                  cls
clus                 0   1
  CLDN10 MUTATED    10   1
  CLDN10 WILD-TYPE 365  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CLDN10 MUTATED     10    1
  CLDN10 WILD-TYPE  365   64
   clus
vv  CLDN10 MUTATED CLDN10 WILD-TYPE
  0             10              365
  1              1               64
[1] 2 2
[1] FALSE
D745V8, binary
                  cls
clus                 0   1
  CLDN10 MUTATED     6   7
  CLDN10 WILD-TYPE 219 257
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CLDN10 MUTATED      6    7
  CLDN10 WILD-TYPE  219  257
        clus
vv       CLDN10 MUTATED CLDN10 WILD-TYPE
  FEMALE              6              219
  MALE                7              257
[1] 2 2
[1] FALSE
D745V9, binary
                  cls
clus                 0   1
  CLDN10 MUTATED     9   0
  CLDN10 WILD-TYPE 341  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CLDN10 MUTATED      9    0
  CLDN10 WILD-TYPE  341   22
     clus
vv    CLDN10 MUTATED CLDN10 WILD-TYPE
  NO               9              341
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CLDN10 MUTATED                      9                             2
  CLDN10 WILD-TYPE                  306                            45
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CLDN10 MUTATED                       2                              0
  CLDN10 WILD-TYPE                   104                             10
D745V10, multiclass
                                clus
vv                               CLDN10 MUTATED CLDN10 WILD-TYPE
  COLON ADENOCARCINOMA                        9              306
  COLON MUCINOUS ADENOCARCINOMA               2               45
  RECTAL ADENOCARCINOMA                       2              104
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  CLDN10 MUTATED    10   0   0   0
  CLDN10 WILD-TYPE 335   4  31  25
D745V11, multiclass
    clus
vv   CLDN10 MUTATED CLDN10 WILD-TYPE
  R0             10              335
  R1              0                4
  R2              0               31
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D745V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CLDN10 MUTATED                                  0     0
  CLDN10 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  CLDN10 MUTATED                           1     8
  CLDN10 WILD-TYPE                        21   218
D745V13, multiclass
                                  clus
vv                                 CLDN10 MUTATED CLDN10 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                         8              218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(746) Variable = RHPN2 MUTATION ANALYSIS
D746V1, survival
                 sevent
clus2               0   1
  RHPN2 MUTATED    13   5
  RHPN2 WILD-TYPE 365  88
  RHPN2 MUTATED RHPN2 WILD-TYPE 
             18             453 
  RHPN2 MUTATED RHPN2 WILD-TYPE 
              5              88 
$`RHPN2 MUTATED`
TCGA-A6-2676 TCGA-A6-4105 TCGA-A6-6648 TCGA-AA-3561 TCGA-AA-3949 TCGA-AA-A010 
       42.90        14.53        25.18        13.94        26.01        34.98 
TCGA-AU-6004 TCGA-AY-5543 TCGA-CA-5796 TCGA-CM-4743 TCGA-CM-6166 TCGA-D5-6537 
       27.09        33.01         3.25        23.05        21.99         4.80 
TCGA-D5-6541 TCGA-F4-6459 TCGA-G4-6293 TCGA-AG-A002 TCGA-DC-6158 TCGA-EI-6510 
       15.58         8.61       133.18        20.98        10.98        18.28 

$`RHPN2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 
       34.65        33.34        32.75        36.53        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       30.44        29.19        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6649 
       32.71        27.09        22.52         8.38        25.08        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3562 
       17.95        29.95        23.01        20.98        19.99        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       33.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 
       22.42        27.42        10.88         0.20        14.50        16.31 
TCGA-AY-4071 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        1.61        12.69         3.06         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
        1.91       124.27        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
        2.96        29.03        16.04        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       43.27        15.12        17.85        17.13        12.49        16.14 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6460 TCGA-F4-6569 
       35.97        60.79       117.07        98.24        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6299 
       33.67        13.25         0.53        47.41        35.31        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
        5.03        13.97        27.95        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  RHPN2 MUTATED RHPN2 WILD-TYPE 
           3.25            0.00 
  RHPN2 MUTATED RHPN2 WILD-TYPE 
         133.18          148.01 
  RHPN2 MUTATED RHPN2 WILD-TYPE 
         21.485          20.120 
[1] "3.2 - 133.2 (21.5)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.5"
D746V2, continuous
D746V3, binary
                 cls
clus                0   1
  RHPN2 MUTATED    15   3
  RHPN2 WILD-TYPE 351 116
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RHPN2 MUTATED     15    3
  RHPN2 WILD-TYPE  351  116
        clus
vv       RHPN2 MUTATED RHPN2 WILD-TYPE
  COLON             15             351
  RECTUM             3             116
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RHPN2 MUTATED         4        0        0         5         2         0
  RHPN2 WILD-TYPE      87        1       32       133         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RHPN2 MUTATED           1          0          3          0        0         3
  RHPN2 WILD-TYPE        23         11         56         42       48        15
                 vv
clus              STAGE IVB
  RHPN2 MUTATED           0
  RHPN2 WILD-TYPE         1
D746V4, multiclass
            clus
vv           RHPN2 MUTATED RHPN2 WILD-TYPE
  STAGE I                4              87
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              5             133
  STAGE IIB              2               8
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             3              56
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              3              15
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  RHPN2 MUTATED     0   5  11   2
  RHPN2 WILD-TYPE  17  87 318  48
D746V5, multiclass
    clus
vv   RHPN2 MUTATED RHPN2 WILD-TYPE
  T1             0              17
  T2             5              87
  T3            11             318
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  RHPN2 MUTATED    13   4   1
  RHPN2 WILD-TYPE 274 109  86
D746V6, multiclass
    clus
vv   RHPN2 MUTATED RHPN2 WILD-TYPE
  N0            13             274
  N1             4             109
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D746V7, binary
                 cls
clus                0   1
  RHPN2 MUTATED    14   2
  RHPN2 WILD-TYPE 361  63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RHPN2 MUTATED     14    2
  RHPN2 WILD-TYPE  361   63
   clus
vv  RHPN2 MUTATED RHPN2 WILD-TYPE
  0            14             361
  1             2              63
[1] 2 2
[1] FALSE
D746V8, binary
                 cls
clus                0   1
  RHPN2 MUTATED    10   8
  RHPN2 WILD-TYPE 215 256
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RHPN2 MUTATED     10    8
  RHPN2 WILD-TYPE  215  256
        clus
vv       RHPN2 MUTATED RHPN2 WILD-TYPE
  FEMALE            10             215
  MALE               8             256
[1] 2 2
[1] FALSE
D746V9, binary
                 cls
clus                0   1
  RHPN2 MUTATED    17   0
  RHPN2 WILD-TYPE 333  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RHPN2 MUTATED     17    0
  RHPN2 WILD-TYPE  333   22
     clus
vv    RHPN2 MUTATED RHPN2 WILD-TYPE
  NO             17             333
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  RHPN2 MUTATED                     13                             2
  RHPN2 WILD-TYPE                  302                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  RHPN2 MUTATED                       3                              0
  RHPN2 WILD-TYPE                   103                             10
D746V10, multiclass
                                clus
vv                               RHPN2 MUTATED RHPN2 WILD-TYPE
  COLON ADENOCARCINOMA                      13             302
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      3             103
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  RHPN2 MUTATED    16   0   0   0
  RHPN2 WILD-TYPE 329   4  31  25
D746V11, multiclass
    clus
vv   RHPN2 MUTATED RHPN2 WILD-TYPE
  R0            16             329
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D746V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RHPN2 MUTATED                                  0     1
  RHPN2 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  RHPN2 MUTATED                           1    12
  RHPN2 WILD-TYPE                        21   214
D746V13, multiclass
                                  clus
vv                                 RHPN2 MUTATED RHPN2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                       12             214
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(747) Variable = IL1RL1 MUTATION ANALYSIS
D747V1, survival
                  sevent
clus2                0   1
  IL1RL1 MUTATED    12   3
  IL1RL1 WILD-TYPE 366  90
  IL1RL1 MUTATED IL1RL1 WILD-TYPE 
              15              456 
  IL1RL1 MUTATED IL1RL1 WILD-TYPE 
               3               90 
$`IL1RL1 MUTATED`
TCGA-A6-5666 TCGA-A6-6782 TCGA-AA-3811 TCGA-AY-6197 TCGA-CA-6717 TCGA-CA-6718 
       32.71        20.28        10.06        21.44        12.76        10.06 
TCGA-CM-6674 TCGA-CM-6677 TCGA-D5-6930 TCGA-DM-A285 TCGA-F4-6569 TCGA-F4-6856 
       12.95        11.08         1.51         6.12        35.74        35.31 
TCGA-G4-6309 TCGA-AF-2693 TCGA-AG-A002 
       85.48        19.10        20.98 

$`IL1RL1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        22.06        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        19.66         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        19.04        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 
        3.06         3.25         3.29         0.07        12.20        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6678 TCGA-CM-6679 
       14.04        11.01        13.05        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       11.64         4.80        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
      139.17        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
       98.24         8.61        31.96         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       47.41       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       55.04        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       39.48        43.04        13.55        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  IL1RL1 MUTATED IL1RL1 WILD-TYPE 
            1.51             0.00 
  IL1RL1 MUTATED IL1RL1 WILD-TYPE 
           85.48           148.01 
  IL1RL1 MUTATED IL1RL1 WILD-TYPE 
           19.10            20.37 
[1] "1.5 - 85.5 (19.1)"  "0.0 - 148.0 (20.4)"
[1] "hr=" "1.3"
D747V2, continuous
D747V3, binary
                  cls
clus                 0   1
  IL1RL1 MUTATED    14   1
  IL1RL1 WILD-TYPE 352 118
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IL1RL1 MUTATED     14    1
  IL1RL1 WILD-TYPE  352  118
        clus
vv       IL1RL1 MUTATED IL1RL1 WILD-TYPE
  COLON              14              352
  RECTUM              1              118
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  IL1RL1 MUTATED         4        0        1         6         1         1
  IL1RL1 WILD-TYPE      87        1       31       132         9         0
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  IL1RL1 MUTATED           1          0          1          0        1
  IL1RL1 WILD-TYPE        23         11         58         42       47
                  vv
clus               STAGE IVA STAGE IVB
  IL1RL1 MUTATED           0         0
  IL1RL1 WILD-TYPE        18         1
D747V4, multiclass
            clus
vv           IL1RL1 MUTATED IL1RL1 WILD-TYPE
  STAGE I                 4               87
  STAGE IA                0                1
  STAGE II                1               31
  STAGE IIA               6              132
  STAGE IIB               1                9
  STAGE IIC               1                0
  STAGE III               1               23
  STAGE IIIA              0               11
  STAGE IIIB              1               58
  STAGE IIIC              0               42
  STAGE IV                1               47
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  IL1RL1 MUTATED     0   4   9   3
  IL1RL1 WILD-TYPE  17  88 320  47
D747V5, multiclass
    clus
vv   IL1RL1 MUTATED IL1RL1 WILD-TYPE
  T1              0               17
  T2              4               88
  T3              9              320
  T4              3               47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  IL1RL1 MUTATED    13   1   2
  IL1RL1 WILD-TYPE 274 112  85
D747V6, multiclass
    clus
vv   IL1RL1 MUTATED IL1RL1 WILD-TYPE
  N0             13              274
  N1              1              112
  N2              2               85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D747V7, binary
                  cls
clus                 0   1
  IL1RL1 MUTATED    12   1
  IL1RL1 WILD-TYPE 363  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IL1RL1 MUTATED     12    1
  IL1RL1 WILD-TYPE  363   64
   clus
vv  IL1RL1 MUTATED IL1RL1 WILD-TYPE
  0             12              363
  1              1               64
[1] 2 2
[1] FALSE
D747V8, binary
                  cls
clus                 0   1
  IL1RL1 MUTATED     5  11
  IL1RL1 WILD-TYPE 220 253
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IL1RL1 MUTATED      5   11
  IL1RL1 WILD-TYPE  220  253
        clus
vv       IL1RL1 MUTATED IL1RL1 WILD-TYPE
  FEMALE              5              220
  MALE               11              253
[1] 2 2
[1] FALSE
D747V9, binary
                  cls
clus                 0   1
  IL1RL1 MUTATED    13   0
  IL1RL1 WILD-TYPE 337  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IL1RL1 MUTATED     13    0
  IL1RL1 WILD-TYPE  337   22
     clus
vv    IL1RL1 MUTATED IL1RL1 WILD-TYPE
  NO              13              337
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  IL1RL1 MUTATED                     10                             4
  IL1RL1 WILD-TYPE                  305                            43
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  IL1RL1 MUTATED                       1                              0
  IL1RL1 WILD-TYPE                   105                             10
D747V10, multiclass
                                clus
vv                               IL1RL1 MUTATED IL1RL1 WILD-TYPE
  COLON ADENOCARCINOMA                       10              305
  COLON MUCINOUS ADENOCARCINOMA               4               43
  RECTAL ADENOCARCINOMA                       1              105
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  IL1RL1 MUTATED    10   0   0   2
  IL1RL1 WILD-TYPE 335   4  31  23
D747V11, multiclass
    clus
vv   IL1RL1 MUTATED IL1RL1 WILD-TYPE
  R0             10              335
  R1              0                4
  R2              0               31
  RX              2               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D747V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  IL1RL1 MUTATED                                  0     2
  IL1RL1 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  IL1RL1 MUTATED                           1    10
  IL1RL1 WILD-TYPE                        21   216
D747V13, multiclass
                                  clus
vv                                 IL1RL1 MUTATED IL1RL1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                9
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                        10              216
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(748) Variable = TOX MUTATION ANALYSIS
D748V1, survival
               sevent
clus2             0   1
  TOX MUTATED    15   3
  TOX WILD-TYPE 363  90
  TOX MUTATED TOX WILD-TYPE 
           18           453 
  TOX MUTATED TOX WILD-TYPE 
            3            90 
$`TOX MUTATED`
TCGA-A6-6780 TCGA-AA-3510 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3710 TCGA-AA-3950 
       20.12        63.98         6.97        54.02        26.99        24.00 
TCGA-AA-3968 TCGA-AA-3977 TCGA-AA-A00A TCGA-AA-A00J TCGA-AA-A010 TCGA-AZ-4315 
       21.99        25.02        38.04        18.05        34.98        58.39 
TCGA-AZ-6601 TCGA-DM-A28F TCGA-G4-6626 TCGA-AG-3593 TCGA-AG-A002 TCGA-G5-6235 
      100.01        35.97        46.75        34.03        20.98        55.76 

$`TOX WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3666 
       13.94        19.99        61.02        78.08         6.05         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3971 
       26.01         2.01        20.98        34.03         2.01        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00D 
       27.02        19.07         7.96        27.02        13.94        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       49.41         6.77        12.10        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       26.17        91.79        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       46.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6641 
        0.66         0.69        26.43 

  TOX MUTATED TOX WILD-TYPE 
         6.97          0.00 
  TOX MUTATED TOX WILD-TYPE 
       100.01        148.01 
  TOX MUTATED TOX WILD-TYPE 
       34.505        19.990 
[1] "7.0 - 100.0 (34.5)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.8"
D748V2, continuous
D748V3, binary
               cls
clus              0   1
  TOX MUTATED    15   3
  TOX WILD-TYPE 351 116
[1] "tbl2"
               cls
clus            [,1] [,2]
  TOX MUTATED     15    3
  TOX WILD-TYPE  351  116
        clus
vv       TOX MUTATED TOX WILD-TYPE
  COLON           15           351
  RECTUM           3           116
[1] 2 2
[1] FALSE
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TOX MUTATED         2        0        4         7         1         0
  TOX WILD-TYPE      89        1       28       131         9         1
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TOX MUTATED           0          0          3          0        0         0
  TOX WILD-TYPE        24         11         56         42       48        18
               vv
clus            STAGE IVB
  TOX MUTATED           0
  TOX WILD-TYPE         1
D748V4, multiclass
            clus
vv           TOX MUTATED TOX WILD-TYPE
  STAGE I              2            89
  STAGE IA             0             1
  STAGE II             4            28
  STAGE IIA            7           131
  STAGE IIB            1             9
  STAGE IIC            0             1
  STAGE III            0            24
  STAGE IIIA           0            11
  STAGE IIIB           3            56
  STAGE IIIC           0            42
  STAGE IV             0            48
  STAGE IVA            0            18
  STAGE IVB            0             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  TOX MUTATED     0   3  13   2
  TOX WILD-TYPE  17  89 316  48
D748V5, multiclass
    clus
vv   TOX MUTATED TOX WILD-TYPE
  T1           0            17
  T2           3            89
  T3          13           316
  T4           2            48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2
  TOX MUTATED    15   3   0
  TOX WILD-TYPE 272 110  87
D748V6, multiclass
    clus
vv   TOX MUTATED TOX WILD-TYPE
  N0          15           272
  N1           3           110
  N2           0            87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D748V7, binary
               cls
clus              0   1
  TOX MUTATED    15   0
  TOX WILD-TYPE 360  65
[1] "tbl2"
               cls
clus            [,1] [,2]
  TOX MUTATED     15    0
  TOX WILD-TYPE  360   65
   clus
vv  TOX MUTATED TOX WILD-TYPE
  0          15           360
  1           0            65
[1] 2 2
[1] FALSE
D748V8, binary
               cls
clus              0   1
  TOX MUTATED     6  12
  TOX WILD-TYPE 219 252
[1] "tbl2"
               cls
clus            [,1] [,2]
  TOX MUTATED      6   12
  TOX WILD-TYPE  219  252
        clus
vv       TOX MUTATED TOX WILD-TYPE
  FEMALE           6           219
  MALE            12           252
[1] 2 2
[1] FALSE
D748V9, binary
               cls
clus              0   1
  TOX MUTATED    16   1
  TOX WILD-TYPE 334  21
[1] "tbl2"
               cls
clus            [,1] [,2]
  TOX MUTATED     16    1
  TOX WILD-TYPE  334   21
     clus
vv    TOX MUTATED TOX WILD-TYPE
  NO           16           334
  YES           1            21
[1] 2 2
[1] FALSE
               vv
clus            COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  TOX MUTATED                     12                             3
  TOX WILD-TYPE                  303                            44
               vv
clus            RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  TOX MUTATED                       3                              0
  TOX WILD-TYPE                   103                             10
D748V10, multiclass
                                clus
vv                               TOX MUTATED TOX WILD-TYPE
  COLON ADENOCARCINOMA                    12           303
  COLON MUCINOUS ADENOCARCINOMA            3            44
  RECTAL ADENOCARCINOMA                    3           103
  RECTAL MUCINOUS ADENOCARCINOMA           0            10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             R0  R1  R2  RX
  TOX MUTATED    13   1   0   0
  TOX WILD-TYPE 332   3  31  25
D748V11, multiclass
    clus
vv   TOX MUTATED TOX WILD-TYPE
  R0          13           332
  R1           1             3
  R2           0            31
  RX           0            25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D748V12, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TOX MUTATED                                  0     0
  TOX WILD-TYPE                                1    11
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  TOX MUTATED                           0     6
  TOX WILD-TYPE                        22   220
D748V13, multiclass
                                  clus
vv                                 TOX MUTATED TOX WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      0            11
  BLACK OR AFRICAN AMERICAN                  0            22
  WHITE                                      6           220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(749) Variable = SNX2 MUTATION ANALYSIS
D749V1, survival
                sevent
clus2              0   1
  SNX2 MUTATED    11   2
  SNX2 WILD-TYPE 367  91
  SNX2 MUTATED SNX2 WILD-TYPE 
            13            458 
  SNX2 MUTATED SNX2 WILD-TYPE 
             2             91 
$`SNX2 MUTATED`
TCGA-A6-6781 TCGA-AA-3510 TCGA-AA-3811 TCGA-AA-3982 TCGA-AA-A010 TCGA-AA-A02H 
       19.66        63.98        10.06        27.02        34.98         2.01 
TCGA-CA-6717 TCGA-CM-6162 TCGA-D5-6540 TCGA-G4-6628 TCGA-AG-A002 TCGA-EF-5830 
       12.76        12.00        16.14        79.69        20.98         0.49 
TCGA-EI-6506 
       20.55 

$`SNX2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        19.04        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3986 
       34.06        26.01        25.02        24.00        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02J TCGA-AA-A02K 
       37.02        39.06        51.98        39.98         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07        12.20        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       17.03        15.02         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
        4.80        17.13        12.49        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       91.79        46.75        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
       51.48        32.61        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  SNX2 MUTATED SNX2 WILD-TYPE 
          0.49           0.00 
  SNX2 MUTATED SNX2 WILD-TYPE 
         79.69         148.01 
  SNX2 MUTATED SNX2 WILD-TYPE 
        19.660         20.235 
[1] "0.5 - 79.7 (19.7)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.2"
D749V2, continuous
D749V3, binary
                cls
clus               0   1
  SNX2 MUTATED    11   3
  SNX2 WILD-TYPE 355 116
[1] "tbl2"
                cls
clus             [,1] [,2]
  SNX2 MUTATED     11    3
  SNX2 WILD-TYPE  355  116
        clus
vv       SNX2 MUTATED SNX2 WILD-TYPE
  COLON            11            355
  RECTUM            3            116
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SNX2 MUTATED         3        0        1         2         3         0
  SNX2 WILD-TYPE      88        1       31       136         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SNX2 MUTATED           1          0          2          1        1         0
  SNX2 WILD-TYPE        23         11         57         41       47        18
                vv
clus             STAGE IVB
  SNX2 MUTATED           0
  SNX2 WILD-TYPE         1
D749V4, multiclass
            clus
vv           SNX2 MUTATED SNX2 WILD-TYPE
  STAGE I               3             88
  STAGE IA              0              1
  STAGE II              1             31
  STAGE IIA             2            136
  STAGE IIB             3              7
  STAGE IIC             0              1
  STAGE III             1             23
  STAGE IIIA            0             11
  STAGE IIIB            2             57
  STAGE IIIC            1             41
  STAGE IV              1             47
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  SNX2 MUTATED     0   3   7   4
  SNX2 WILD-TYPE  17  89 322  46
D749V5, multiclass
    clus
vv   SNX2 MUTATED SNX2 WILD-TYPE
  T1            0             17
  T2            3             89
  T3            7            322
  T4            4             46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  SNX2 MUTATED     9   3   2
  SNX2 WILD-TYPE 278 110  85
D749V6, multiclass
    clus
vv   SNX2 MUTATED SNX2 WILD-TYPE
  N0            9            278
  N1            3            110
  N2            2             85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D749V7, binary
                cls
clus               0   1
  SNX2 MUTATED    11   1
  SNX2 WILD-TYPE 364  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  SNX2 MUTATED     11    1
  SNX2 WILD-TYPE  364   64
   clus
vv  SNX2 MUTATED SNX2 WILD-TYPE
  0           11            364
  1            1             64
[1] 2 2
[1] FALSE
D749V8, binary
                cls
clus               0   1
  SNX2 MUTATED     6   8
  SNX2 WILD-TYPE 219 256
[1] "tbl2"
                cls
clus             [,1] [,2]
  SNX2 MUTATED      6    8
  SNX2 WILD-TYPE  219  256
        clus
vv       SNX2 MUTATED SNX2 WILD-TYPE
  FEMALE            6            219
  MALE              8            256
[1] 2 2
[1] FALSE
D749V9, binary
                cls
clus               0   1
  SNX2 MUTATED    11   0
  SNX2 WILD-TYPE 339  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  SNX2 MUTATED     11    0
  SNX2 WILD-TYPE  339   22
     clus
vv    SNX2 MUTATED SNX2 WILD-TYPE
  NO            11            339
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SNX2 MUTATED                      7                             4
  SNX2 WILD-TYPE                  308                            43
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SNX2 MUTATED                       3                              0
  SNX2 WILD-TYPE                   103                             10
D749V10, multiclass
                                clus
vv                               SNX2 MUTATED SNX2 WILD-TYPE
  COLON ADENOCARCINOMA                      7            308
  COLON MUCINOUS ADENOCARCINOMA             4             43
  RECTAL ADENOCARCINOMA                     3            103
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  SNX2 MUTATED    10   0   1   2
  SNX2 WILD-TYPE 335   4  30  23
D749V11, multiclass
    clus
vv   SNX2 MUTATED SNX2 WILD-TYPE
  R0           10            335
  R1            0              4
  R2            1             30
  RX            2             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D749V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SNX2 MUTATED                                  0     1
  SNX2 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  SNX2 MUTATED                           0     7
  SNX2 WILD-TYPE                        22   219
D749V13, multiclass
                                  clus
vv                                 SNX2 MUTATED SNX2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       7            219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(750) Variable = HDAC5 MUTATION ANALYSIS
D750V1, survival
                 sevent
clus2               0   1
  HDAC5 MUTATED     7   5
  HDAC5 WILD-TYPE 371  88
  HDAC5 MUTATED HDAC5 WILD-TYPE 
             12             459 
  HDAC5 MUTATED HDAC5 WILD-TYPE 
              5              88 
$`HDAC5 MUTATED`
TCGA-AA-3492 TCGA-AA-A01R TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6601 TCGA-CK-5916 
        3.02        35.01        62.79        49.41       100.01        21.14 
TCGA-CM-5860 TCGA-D5-6930 TCGA-F4-6703 TCGA-F4-6856 TCGA-G4-6315 TCGA-AG-A002 
       32.02         1.51        47.87        35.31        61.91        20.98 

$`HDAC5 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S 
       12.00        31.00        31.00        38.07         1.02         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 
      106.75        22.36        88.21         6.77        12.10        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       51.32         9.99        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       22.98        30.08        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
        9.44        11.64         4.80        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
        6.18         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
       13.25         0.53        47.41       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6317 
       53.62        44.68        55.04        85.48        63.62        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  HDAC5 MUTATED HDAC5 WILD-TYPE 
           1.51            0.00 
  HDAC5 MUTATED HDAC5 WILD-TYPE 
         100.01          148.01 
  HDAC5 MUTATED HDAC5 WILD-TYPE 
          35.16           20.02 
[1] "1.5 - 100.0 (35.2)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.4"
D750V2, continuous
D750V3, binary
                 cls
clus                0   1
  HDAC5 MUTATED    11   1
  HDAC5 WILD-TYPE 355 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HDAC5 MUTATED     11    1
  HDAC5 WILD-TYPE  355  118
        clus
vv       HDAC5 MUTATED HDAC5 WILD-TYPE
  COLON             11             355
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  HDAC5 MUTATED         3        0        4         3         0         0
  HDAC5 WILD-TYPE      88        1       28       135        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  HDAC5 MUTATED           1          0          0          0        1         0
  HDAC5 WILD-TYPE        23         11         59         42       47        18
                 vv
clus              STAGE IVB
  HDAC5 MUTATED           0
  HDAC5 WILD-TYPE         1
D750V4, multiclass
            clus
vv           HDAC5 MUTATED HDAC5 WILD-TYPE
  STAGE I                3              88
  STAGE IA               0               1
  STAGE II               4              28
  STAGE IIA              3             135
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             0              42
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  HDAC5 MUTATED     1   2   9   0
  HDAC5 WILD-TYPE  16  90 320  50
D750V5, multiclass
    clus
vv   HDAC5 MUTATED HDAC5 WILD-TYPE
  T1             1              16
  T2             2              90
  T3             9             320
  T4             0              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  HDAC5 MUTATED    10   1   1
  HDAC5 WILD-TYPE 277 112  86
D750V6, multiclass
    clus
vv   HDAC5 MUTATED HDAC5 WILD-TYPE
  N0            10             277
  N1             1             112
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D750V7, binary
                 cls
clus                0   1
  HDAC5 MUTATED     9   1
  HDAC5 WILD-TYPE 366  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HDAC5 MUTATED      9    1
  HDAC5 WILD-TYPE  366   64
   clus
vv  HDAC5 MUTATED HDAC5 WILD-TYPE
  0             9             366
  1             1              64
[1] 2 2
[1] FALSE
D750V8, binary
                 cls
clus                0   1
  HDAC5 MUTATED     3   9
  HDAC5 WILD-TYPE 222 255
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HDAC5 MUTATED      3    9
  HDAC5 WILD-TYPE  222  255
        clus
vv       HDAC5 MUTATED HDAC5 WILD-TYPE
  FEMALE             3             222
  MALE               9             255
[1] 2 2
[1] FALSE
D750V9, binary
                 cls
clus                0   1
  HDAC5 MUTATED    10   1
  HDAC5 WILD-TYPE 340  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HDAC5 MUTATED     10    1
  HDAC5 WILD-TYPE  340   21
     clus
vv    HDAC5 MUTATED HDAC5 WILD-TYPE
  NO             10             340
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  HDAC5 MUTATED                      8                             3
  HDAC5 WILD-TYPE                  307                            44
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  HDAC5 MUTATED                       1                              0
  HDAC5 WILD-TYPE                   105                             10
D750V10, multiclass
                                clus
vv                               HDAC5 MUTATED HDAC5 WILD-TYPE
  COLON ADENOCARCINOMA                       8             307
  COLON MUCINOUS ADENOCARCINOMA              3              44
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  HDAC5 MUTATED     8   0   0   1
  HDAC5 WILD-TYPE 337   4  31  24
D750V11, multiclass
    clus
vv   HDAC5 MUTATED HDAC5 WILD-TYPE
  R0             8             337
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D750V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HDAC5 MUTATED                                  0     0
  HDAC5 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  HDAC5 MUTATED                           0     9
  HDAC5 WILD-TYPE                        22   217
D750V13, multiclass
                                  clus
vv                                 HDAC5 MUTATED HDAC5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        9             217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(751) Variable = IVNS1ABP MUTATION ANALYSIS
D751V1, survival
                    sevent
clus2                  0   1
  IVNS1ABP MUTATED    10   3
  IVNS1ABP WILD-TYPE 368  90
  IVNS1ABP MUTATED IVNS1ABP WILD-TYPE 
                13                458 
  IVNS1ABP MUTATED IVNS1ABP WILD-TYPE 
                 3                 90 
$`IVNS1ABP MUTATED`
TCGA-A6-5660 TCGA-AA-3660 TCGA-AD-6895 TCGA-AD-6901 TCGA-CA-6717 TCGA-CM-5348 
       29.19        78.08         0.72        22.42        12.76        22.98 
TCGA-D5-6920 TCGA-DM-A1DB TCGA-DM-A28K TCGA-AG-A002 TCGA-AG-A026 TCGA-AH-6644 
        3.68        44.32        98.24        20.98         1.94         0.72 
TCGA-EI-6506 
       20.55 

$`IVNS1ABP WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 
       19.99        13.94        19.99        61.02         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
       56.55         0.79         5.79        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07        12.20        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.03        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
       15.58         1.48         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HA 
       49.91        13.32        12.59       140.38         7.50       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
       60.79       117.07         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
        1.45        17.49         0.69         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
       32.61         0.49        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  IVNS1ABP MUTATED IVNS1ABP WILD-TYPE 
              0.72               0.00 
  IVNS1ABP MUTATED IVNS1ABP WILD-TYPE 
             98.24             148.01 
  IVNS1ABP MUTATED IVNS1ABP WILD-TYPE 
            20.980             20.085 
[1] "0.7 - 98.2 (21.0)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.1"
D751V2, continuous
D751V3, binary
                    cls
clus                   0   1
  IVNS1ABP MUTATED    10   4
  IVNS1ABP WILD-TYPE 356 115
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  IVNS1ABP MUTATED     10    4
  IVNS1ABP WILD-TYPE  356  115
        clus
vv       IVNS1ABP MUTATED IVNS1ABP WILD-TYPE
  COLON                10                356
  RECTUM                4                115
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  IVNS1ABP MUTATED         1        0        2         6         0         0
  IVNS1ABP WILD-TYPE      90        1       30       132        10         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  IVNS1ABP MUTATED           0          0          1          1        0
  IVNS1ABP WILD-TYPE        24         11         58         41       48
                    vv
clus                 STAGE IVA STAGE IVB
  IVNS1ABP MUTATED           0         0
  IVNS1ABP WILD-TYPE        18         1
D751V4, multiclass
            clus
vv           IVNS1ABP MUTATED IVNS1ABP WILD-TYPE
  STAGE I                   1                 90
  STAGE IA                  0                  1
  STAGE II                  2                 30
  STAGE IIA                 6                132
  STAGE IIB                 0                 10
  STAGE IIC                 0                  1
  STAGE III                 0                 24
  STAGE IIIA                0                 11
  STAGE IIIB                1                 58
  STAGE IIIC                1                 41
  STAGE IV                  0                 48
  STAGE IVA                 0                 18
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  IVNS1ABP MUTATED     0   1  12   1
  IVNS1ABP WILD-TYPE  17  91 317  49
D751V5, multiclass
    clus
vv   IVNS1ABP MUTATED IVNS1ABP WILD-TYPE
  T1                0                 17
  T2                1                 91
  T3               12                317
  T4                1                 49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  IVNS1ABP MUTATED    10   2   1
  IVNS1ABP WILD-TYPE 277 111  86
D751V6, multiclass
    clus
vv   IVNS1ABP MUTATED IVNS1ABP WILD-TYPE
  N0               10                277
  N1                2                111
  N2                1                 86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D751V7, binary
                    cls
clus                   0   1
  IVNS1ABP MUTATED    11   0
  IVNS1ABP WILD-TYPE 364  65
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  IVNS1ABP MUTATED     11    0
  IVNS1ABP WILD-TYPE  364   65
   clus
vv  IVNS1ABP MUTATED IVNS1ABP WILD-TYPE
  0               11                364
  1                0                 65
[1] 2 2
[1] FALSE
D751V8, binary
                    cls
clus                   0   1
  IVNS1ABP MUTATED     4  10
  IVNS1ABP WILD-TYPE 221 254
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  IVNS1ABP MUTATED      4   10
  IVNS1ABP WILD-TYPE  221  254
        clus
vv       IVNS1ABP MUTATED IVNS1ABP WILD-TYPE
  FEMALE                4                221
  MALE                 10                254
[1] 2 2
[1] FALSE
D751V9, binary
                    cls
clus                   0   1
  IVNS1ABP MUTATED     7   0
  IVNS1ABP WILD-TYPE 343  22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  IVNS1ABP MUTATED      7    0
  IVNS1ABP WILD-TYPE  343   22
     clus
vv    IVNS1ABP MUTATED IVNS1ABP WILD-TYPE
  NO                 7                343
  YES                0                 22
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  IVNS1ABP MUTATED                      8                             2
  IVNS1ABP WILD-TYPE                  307                            45
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  IVNS1ABP MUTATED                       4                              0
  IVNS1ABP WILD-TYPE                   102                             10
D751V10, multiclass
                                clus
vv                               IVNS1ABP MUTATED IVNS1ABP WILD-TYPE
  COLON ADENOCARCINOMA                          8                307
  COLON MUCINOUS ADENOCARCINOMA                 2                 45
  RECTAL ADENOCARCINOMA                         4                102
  RECTAL MUCINOUS ADENOCARCINOMA                0                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  IVNS1ABP MUTATED     6   1   0   1
  IVNS1ABP WILD-TYPE 339   3  31  24
D751V11, multiclass
    clus
vv   IVNS1ABP MUTATED IVNS1ABP WILD-TYPE
  R0                6                339
  R1                1                  3
  R2                0                 31
  RX                1                 24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D751V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  IVNS1ABP MUTATED                                  0     1
  IVNS1ABP WILD-TYPE                                1    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  IVNS1ABP MUTATED                           1     8
  IVNS1ABP WILD-TYPE                        21   218
D751V13, multiclass
                                  clus
vv                                 IVNS1ABP MUTATED IVNS1ABP WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                 10
  BLACK OR AFRICAN AMERICAN                       1                 21
  WHITE                                           8                218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(752) Variable = SNRNP200 MUTATION ANALYSIS
D752V1, survival
                    sevent
clus2                  0   1
  SNRNP200 MUTATED    20   2
  SNRNP200 WILD-TYPE 358  91
  SNRNP200 MUTATED SNRNP200 WILD-TYPE 
                22                449 
  SNRNP200 MUTATED SNRNP200 WILD-TYPE 
                 2                 91 
$`SNRNP200 MUTATED`
TCGA-A6-6654 TCGA-A6-6780 TCGA-AA-3554 TCGA-AA-3685 TCGA-AA-3811 TCGA-AA-3821 
       23.87        20.12        17.95        37.05        10.06         1.02 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AY-5543 TCGA-CA-5796 TCGA-CA-6717 TCGA-CM-5348 
       38.04         4.01        33.01         3.25        12.76        22.98 
TCGA-CM-6674 TCGA-D5-6533 TCGA-D5-6536 TCGA-F4-6806 TCGA-G4-6304 TCGA-G4-6307 
       12.95         1.32        17.85        41.42        53.62        55.04 
TCGA-G4-6321 TCGA-AF-2687 TCGA-AG-A002 TCGA-AG-A02N 
       22.09        24.13        20.98        61.97 

$`SNRNP200 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       24.00        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
       11.01         5.98        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       26.99        19.04        19.04        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
       25.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       18.05        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
       12.69         3.06         3.29         0.07        12.20        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.03        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       14.04        11.01        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 
       55.92        20.19        18.25        43.27        15.12         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
       47.87         1.55        34.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 
       44.68        85.48        63.62        61.91        36.00        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2689 
       35.80        26.17        91.79        46.75        79.69        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
       49.97         1.94        38.96        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  SNRNP200 MUTATED SNRNP200 WILD-TYPE 
              1.02               0.00 
  SNRNP200 MUTATED SNRNP200 WILD-TYPE 
             61.97             148.01 
  SNRNP200 MUTATED SNRNP200 WILD-TYPE 
            21.535             20.050 
[1] "1.0 - 62.0 (21.5)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "2.1"
D752V2, continuous
D752V3, binary
                    cls
clus                   0   1
  SNRNP200 MUTATED    20   3
  SNRNP200 WILD-TYPE 346 116
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SNRNP200 MUTATED     20    3
  SNRNP200 WILD-TYPE  346  116
        clus
vv       SNRNP200 MUTATED SNRNP200 WILD-TYPE
  COLON                20                346
  RECTUM                3                116
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SNRNP200 MUTATED         3        0        2         8         2         0
  SNRNP200 WILD-TYPE      88        1       30       130         8         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SNRNP200 MUTATED           2          0          4          1        0
  SNRNP200 WILD-TYPE        22         11         55         41       48
                    vv
clus                 STAGE IVA STAGE IVB
  SNRNP200 MUTATED           1         0
  SNRNP200 WILD-TYPE        17         1
D752V4, multiclass
            clus
vv           SNRNP200 MUTATED SNRNP200 WILD-TYPE
  STAGE I                   3                 88
  STAGE IA                  0                  1
  STAGE II                  2                 30
  STAGE IIA                 8                130
  STAGE IIB                 2                  8
  STAGE IIC                 0                  1
  STAGE III                 2                 22
  STAGE IIIA                0                 11
  STAGE IIIB                4                 55
  STAGE IIIC                1                 41
  STAGE IV                  0                 48
  STAGE IVA                 1                 17
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  SNRNP200 MUTATED     0   4  16   3
  SNRNP200 WILD-TYPE  17  88 313  47
D752V5, multiclass
    clus
vv   SNRNP200 MUTATED SNRNP200 WILD-TYPE
  T1                0                 17
  T2                4                 88
  T3               16                313
  T4                3                 47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  SNRNP200 MUTATED    16   5   2
  SNRNP200 WILD-TYPE 271 108  85
D752V6, multiclass
    clus
vv   SNRNP200 MUTATED SNRNP200 WILD-TYPE
  N0               16                271
  N1                5                108
  N2                2                 85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D752V7, binary
                    cls
clus                   0   1
  SNRNP200 MUTATED    20   1
  SNRNP200 WILD-TYPE 355  64
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SNRNP200 MUTATED     20    1
  SNRNP200 WILD-TYPE  355   64
   clus
vv  SNRNP200 MUTATED SNRNP200 WILD-TYPE
  0               20                355
  1                1                 64
[1] 2 2
[1] FALSE
D752V8, binary
                    cls
clus                   0   1
  SNRNP200 MUTATED    12  11
  SNRNP200 WILD-TYPE 213 253
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SNRNP200 MUTATED     12   11
  SNRNP200 WILD-TYPE  213  253
        clus
vv       SNRNP200 MUTATED SNRNP200 WILD-TYPE
  FEMALE               12                213
  MALE                 11                253
[1] 2 2
[1] FALSE
D752V9, binary
                    cls
clus                   0   1
  SNRNP200 MUTATED    18   1
  SNRNP200 WILD-TYPE 332  21
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SNRNP200 MUTATED     18    1
  SNRNP200 WILD-TYPE  332   21
     clus
vv    SNRNP200 MUTATED SNRNP200 WILD-TYPE
  NO                18                332
  YES                1                 21
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SNRNP200 MUTATED                     15                             5
  SNRNP200 WILD-TYPE                  300                            42
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SNRNP200 MUTATED                       3                              0
  SNRNP200 WILD-TYPE                   103                             10
D752V10, multiclass
                                clus
vv                               SNRNP200 MUTATED SNRNP200 WILD-TYPE
  COLON ADENOCARCINOMA                         15                300
  COLON MUCINOUS ADENOCARCINOMA                 5                 42
  RECTAL ADENOCARCINOMA                         3                103
  RECTAL MUCINOUS ADENOCARCINOMA                0                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  SNRNP200 MUTATED    20   0   0   1
  SNRNP200 WILD-TYPE 325   4  31  24
D752V11, multiclass
    clus
vv   SNRNP200 MUTATED SNRNP200 WILD-TYPE
  R0               20                325
  R1                0                  4
  R2                0                 31
  RX                1                 24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D752V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SNRNP200 MUTATED                                  0     2
  SNRNP200 WILD-TYPE                                1     9
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  SNRNP200 MUTATED                           1    11
  SNRNP200 WILD-TYPE                        21   215
D752V13, multiclass
                                  clus
vv                                 SNRNP200 MUTATED SNRNP200 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           2                  9
  BLACK OR AFRICAN AMERICAN                       1                 21
  WHITE                                          11                215
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(753) Variable = RFXAP MUTATION ANALYSIS
D753V1, survival
                 sevent
clus2               0   1
  RFXAP MUTATED     4   2
  RFXAP WILD-TYPE 374  91
  RFXAP MUTATED RFXAP WILD-TYPE 
              6             465 
  RFXAP MUTATED RFXAP WILD-TYPE 
              2              91 
$`RFXAP MUTATED`
TCGA-A6-5660 TCGA-A6-6654 TCGA-AA-3529 TCGA-AZ-6600 TCGA-CA-6717 TCGA-D5-6927 
       29.19        23.87         0.00        12.10        12.76         9.44 

$`RFXAP WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 
       25.18        24.16        21.76        24.69        24.39        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 
       22.36        62.79        88.21        49.41         6.77       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07        12.20        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
       14.30         9.04        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  RFXAP MUTATED RFXAP WILD-TYPE 
              0               0 
  RFXAP MUTATED RFXAP WILD-TYPE 
          29.19          148.01 
  RFXAP MUTATED RFXAP WILD-TYPE 
          12.43           20.28 
[1] "0.0 - 29.2 (12.4)"  "0.0 - 148.0 (20.3)"
[1] "hr=" "3.1"
D753V2, continuous
D753V3, binary
                 cls
clus                0   1
  RFXAP MUTATED     6   0
  RFXAP WILD-TYPE 360 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RFXAP MUTATED      6    0
  RFXAP WILD-TYPE  360  119
        clus
vv       RFXAP MUTATED RFXAP WILD-TYPE
  COLON              6             360
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RFXAP MUTATED         0        0        0         2         0         0
  RFXAP WILD-TYPE      91        1       32       136        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RFXAP MUTATED           0          0          1          2        1         0
  RFXAP WILD-TYPE        24         11         58         40       47        18
                 vv
clus              STAGE IVB
  RFXAP MUTATED           0
  RFXAP WILD-TYPE         1
D753V4, multiclass
            clus
vv           RFXAP MUTATED RFXAP WILD-TYPE
  STAGE I                0              91
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              2             136
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             2              40
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  RFXAP MUTATED     0   0   5   1
  RFXAP WILD-TYPE  17  92 324  49
D753V5, multiclass
    clus
vv   RFXAP MUTATED RFXAP WILD-TYPE
  T1             0              17
  T2             0              92
  T3             5             324
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  RFXAP MUTATED     2   2   2
  RFXAP WILD-TYPE 285 111  85
D753V6, multiclass
    clus
vv   RFXAP MUTATED RFXAP WILD-TYPE
  N0             2             285
  N1             2             111
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D753V7, binary
                 cls
clus                0   1
  RFXAP MUTATED     5   1
  RFXAP WILD-TYPE 370  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RFXAP MUTATED      5    1
  RFXAP WILD-TYPE  370   64
   clus
vv  RFXAP MUTATED RFXAP WILD-TYPE
  0             5             370
  1             1              64
[1] 2 2
[1] FALSE
D753V8, binary
                 cls
clus                0   1
  RFXAP MUTATED     2   4
  RFXAP WILD-TYPE 223 260
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RFXAP MUTATED      2    4
  RFXAP WILD-TYPE  223  260
        clus
vv       RFXAP MUTATED RFXAP WILD-TYPE
  FEMALE             2             223
  MALE               4             260
[1] 2 2
[1] FALSE
D753V9, binary
                 cls
clus                0   1
  RFXAP MUTATED     4   0
  RFXAP WILD-TYPE 346  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RFXAP MUTATED      4    0
  RFXAP WILD-TYPE  346   22
     clus
vv    RFXAP MUTATED RFXAP WILD-TYPE
  NO              4             346
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  RFXAP MUTATED                      5                             1
  RFXAP WILD-TYPE                  310                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  RFXAP MUTATED                       0                              0
  RFXAP WILD-TYPE                   106                             10
D753V10, multiclass
                                clus
vv                               RFXAP MUTATED RFXAP WILD-TYPE
  COLON ADENOCARCINOMA                       5             310
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  RFXAP MUTATED     2   0   0   1
  RFXAP WILD-TYPE 343   4  31  24
D753V11, multiclass
    clus
vv   RFXAP MUTATED RFXAP WILD-TYPE
  R0             2             343
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D753V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RFXAP MUTATED                                  0     1
  RFXAP WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  RFXAP MUTATED                           2     2
  RFXAP WILD-TYPE                        20   224
D753V13, multiclass
                                  clus
vv                                 RFXAP MUTATED RFXAP WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    2              20
  WHITE                                        2             224
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(754) Variable = ABCF3 MUTATION ANALYSIS
D754V1, survival
                 sevent
clus2               0   1
  ABCF3 MUTATED    13   2
  ABCF3 WILD-TYPE 365  91
  ABCF3 MUTATED ABCF3 WILD-TYPE 
             15             456 
  ABCF3 MUTATED ABCF3 WILD-TYPE 
              2              91 
$`ABCF3 MUTATED`
TCGA-A6-6781 TCGA-AA-3815 TCGA-AA-3852 TCGA-AA-A00J TCGA-AD-6889 TCGA-AZ-4315 
       19.66        33.04         0.00        18.05        56.55        58.39 
TCGA-AZ-6601 TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-6161 TCGA-CM-6165 TCGA-D5-6535 
      100.01        23.05        37.02        15.02        16.04        15.12 
TCGA-G4-6293 TCGA-G4-6310 TCGA-AH-6547 
      133.18        63.62         1.45 

$`ABCF3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       10.06        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
       10.06         0.00        33.07        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 
       40.96         0.07        21.37        15.52         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       49.41         6.77        12.10        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4747 
       21.14        82.95         1.91       124.27        20.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6162 
       15.02         5.03        15.02        15.02        17.03        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
        2.96        29.03        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       43.27        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
       35.31        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       85.48        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
       38.04       117.11        38.56        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  ABCF3 MUTATED ABCF3 WILD-TYPE 
              0               0 
  ABCF3 MUTATED ABCF3 WILD-TYPE 
         133.18          148.01 
  ABCF3 MUTATED ABCF3 WILD-TYPE 
         23.050          20.155 
[1] "0.0 - 133.2 (23.1)" "0.0 - 148.0 (20.2)"
[1] "hr=" "2.2"
D754V2, continuous
D754V3, binary
                 cls
clus                0   1
  ABCF3 MUTATED    15   1
  ABCF3 WILD-TYPE 351 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCF3 MUTATED     15    1
  ABCF3 WILD-TYPE  351  118
        clus
vv       ABCF3 MUTATED ABCF3 WILD-TYPE
  COLON             15             351
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ABCF3 MUTATED         2        0        1         6         1         0
  ABCF3 WILD-TYPE      89        1       31       132         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ABCF3 MUTATED           1          0          3          1        0         0
  ABCF3 WILD-TYPE        23         11         56         41       48        18
                 vv
clus              STAGE IVB
  ABCF3 MUTATED           0
  ABCF3 WILD-TYPE         1
D754V4, multiclass
            clus
vv           ABCF3 MUTATED ABCF3 WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              6             132
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             3              56
  STAGE IIIC             1              41
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ABCF3 MUTATED     0   2  11   3
  ABCF3 WILD-TYPE  17  90 318  47
D754V5, multiclass
    clus
vv   ABCF3 MUTATED ABCF3 WILD-TYPE
  T1             0              17
  T2             2              90
  T3            11             318
  T4             3              47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  ABCF3 MUTATED    11   5   0
  ABCF3 WILD-TYPE 276 108  87
D754V6, multiclass
    clus
vv   ABCF3 MUTATED ABCF3 WILD-TYPE
  N0            11             276
  N1             5             108
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D754V7, binary
                 cls
clus                0   1
  ABCF3 MUTATED    12   0
  ABCF3 WILD-TYPE 363  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCF3 MUTATED     12    0
  ABCF3 WILD-TYPE  363   65
   clus
vv  ABCF3 MUTATED ABCF3 WILD-TYPE
  0            12             363
  1             0              65
[1] 2 2
[1] FALSE
D754V8, binary
                 cls
clus                0   1
  ABCF3 MUTATED     6  10
  ABCF3 WILD-TYPE 219 254
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCF3 MUTATED      6   10
  ABCF3 WILD-TYPE  219  254
        clus
vv       ABCF3 MUTATED ABCF3 WILD-TYPE
  FEMALE             6             219
  MALE              10             254
[1] 2 2
[1] FALSE
D754V9, binary
                 cls
clus                0   1
  ABCF3 MUTATED    11   1
  ABCF3 WILD-TYPE 339  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCF3 MUTATED     11    1
  ABCF3 WILD-TYPE  339   21
     clus
vv    ABCF3 MUTATED ABCF3 WILD-TYPE
  NO             11             339
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ABCF3 MUTATED                     12                             3
  ABCF3 WILD-TYPE                  303                            44
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ABCF3 MUTATED                       1                              0
  ABCF3 WILD-TYPE                   105                             10
D754V10, multiclass
                                clus
vv                               ABCF3 MUTATED ABCF3 WILD-TYPE
  COLON ADENOCARCINOMA                      12             303
  COLON MUCINOUS ADENOCARCINOMA              3              44
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  ABCF3 MUTATED    11   0   0   2
  ABCF3 WILD-TYPE 334   4  31  23
D754V11, multiclass
    clus
vv   ABCF3 MUTATED ABCF3 WILD-TYPE
  R0            11             334
  R1             0               4
  R2             0              31
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D754V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ABCF3 MUTATED                                  0     1
  ABCF3 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ABCF3 MUTATED                           1    11
  ABCF3 WILD-TYPE                        21   215
D754V13, multiclass
                                  clus
vv                                 ABCF3 MUTATED ABCF3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                       11             215
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(755) Variable = ZMYM4 MUTATION ANALYSIS
D755V1, survival
                 sevent
clus2               0   1
  ZMYM4 MUTATED    14   4
  ZMYM4 WILD-TYPE 364  89
  ZMYM4 MUTATED ZMYM4 WILD-TYPE 
             18             453 
  ZMYM4 MUTATED ZMYM4 WILD-TYPE 
              4              89 
$`ZMYM4 MUTATED`
TCGA-AA-3875 TCGA-AA-3949 TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A02J TCGA-AZ-5407 
       18.05        26.01        25.02         4.01         5.03        88.21 
TCGA-CA-6717 TCGA-CM-5344 TCGA-CM-5861 TCGA-CM-6172 TCGA-D5-5537 TCGA-D5-6928 
       12.76        22.03        15.02        11.01        45.40        11.64 
TCGA-F4-6855 TCGA-G4-6588 TCGA-AG-3599 TCGA-AG-A002 TCGA-DY-A1DG TCGA-EI-6510 
       47.41        26.17        12.03        20.98        51.48        18.28 

$`ZMYM4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3877 
       53.00        17.03        24.03        27.02        29.98        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-3952 
        2.01        12.99        24.00        33.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07        12.20        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5349 
       37.02        25.02        13.02        29.06        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       32.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 
       12.99        13.02        15.02        14.04        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5538 
       11.08        11.08        11.01        10.06        12.03        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
       14.30         9.04         9.44         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6856 
       41.42        16.24        33.67        13.25         0.53        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       35.80        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3600 
        1.02        46.03        34.03         2.01        50.04         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       24.13        32.61         0.49        20.55        19.96        20.91 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  ZMYM4 MUTATED ZMYM4 WILD-TYPE 
           4.01            0.00 
  ZMYM4 MUTATED ZMYM4 WILD-TYPE 
          88.21          148.01 
  ZMYM4 MUTATED ZMYM4 WILD-TYPE 
          19.63           20.19 
[1] "4.0 - 88.2 (19.6)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.1"
D755V2, continuous
D755V3, binary
                 cls
clus                0   1
  ZMYM4 MUTATED    15   4
  ZMYM4 WILD-TYPE 351 115
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZMYM4 MUTATED     15    4
  ZMYM4 WILD-TYPE  351  115
        clus
vv       ZMYM4 MUTATED ZMYM4 WILD-TYPE
  COLON             15             351
  RECTUM             4             115
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZMYM4 MUTATED         4        0        0         7         1         0
  ZMYM4 WILD-TYPE      87        1       32       131         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ZMYM4 MUTATED           0          0          3          0        1         2
  ZMYM4 WILD-TYPE        24         11         56         42       47        16
                 vv
clus              STAGE IVB
  ZMYM4 MUTATED           0
  ZMYM4 WILD-TYPE         1
D755V4, multiclass
            clus
vv           ZMYM4 MUTATED ZMYM4 WILD-TYPE
  STAGE I                4              87
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              7             131
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             3              56
  STAGE IIIC             0              42
  STAGE IV               1              47
  STAGE IVA              2              16
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ZMYM4 MUTATED     2   4  12   1
  ZMYM4 WILD-TYPE  15  88 317  49
D755V5, multiclass
    clus
vv   ZMYM4 MUTATED ZMYM4 WILD-TYPE
  T1             2              15
  T2             4              88
  T3            12             317
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  ZMYM4 MUTATED    14   4   1
  ZMYM4 WILD-TYPE 273 109  86
D755V6, multiclass
    clus
vv   ZMYM4 MUTATED ZMYM4 WILD-TYPE
  N0            14             273
  N1             4             109
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D755V7, binary
                 cls
clus                0   1
  ZMYM4 MUTATED    14   2
  ZMYM4 WILD-TYPE 361  63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZMYM4 MUTATED     14    2
  ZMYM4 WILD-TYPE  361   63
   clus
vv  ZMYM4 MUTATED ZMYM4 WILD-TYPE
  0            14             361
  1             2              63
[1] 2 2
[1] FALSE
D755V8, binary
                 cls
clus                0   1
  ZMYM4 MUTATED    11   8
  ZMYM4 WILD-TYPE 214 256
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZMYM4 MUTATED     11    8
  ZMYM4 WILD-TYPE  214  256
        clus
vv       ZMYM4 MUTATED ZMYM4 WILD-TYPE
  FEMALE            11             214
  MALE               8             256
[1] 2 2
[1] FALSE
D755V9, binary
                 cls
clus                0   1
  ZMYM4 MUTATED    15   0
  ZMYM4 WILD-TYPE 335  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZMYM4 MUTATED     15    0
  ZMYM4 WILD-TYPE  335   22
     clus
vv    ZMYM4 MUTATED ZMYM4 WILD-TYPE
  NO             15             335
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ZMYM4 MUTATED                     11                             4
  ZMYM4 WILD-TYPE                  304                            43
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ZMYM4 MUTATED                       3                              0
  ZMYM4 WILD-TYPE                   103                             10
D755V10, multiclass
                                clus
vv                               ZMYM4 MUTATED ZMYM4 WILD-TYPE
  COLON ADENOCARCINOMA                      11             304
  COLON MUCINOUS ADENOCARCINOMA              4              43
  RECTAL ADENOCARCINOMA                      3             103
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  ZMYM4 MUTATED    13   0   1   2
  ZMYM4 WILD-TYPE 332   4  30  23
D755V11, multiclass
    clus
vv   ZMYM4 MUTATED ZMYM4 WILD-TYPE
  R0            13             332
  R1             0               4
  R2             1              30
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D755V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZMYM4 MUTATED                                  0     1
  ZMYM4 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ZMYM4 MUTATED                           0    10
  ZMYM4 WILD-TYPE                        22   216
D755V13, multiclass
                                  clus
vv                                 ZMYM4 MUTATED ZMYM4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                       10             216
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(756) Variable = WWC3 MUTATION ANALYSIS
D756V1, survival
                sevent
clus2              0   1
  WWC3 MUTATED    20   6
  WWC3 WILD-TYPE 358  87
  WWC3 MUTATED WWC3 WILD-TYPE 
            26            445 
  WWC3 MUTATED WWC3 WILD-TYPE 
             6             87 
$`WWC3 MUTATED`
TCGA-AA-3510 TCGA-AA-3833 TCGA-AA-3864 TCGA-AA-3877 TCGA-AA-3950 TCGA-AA-A00N 
       63.98        15.95        53.00        31.00        24.00         4.01 
TCGA-AD-5900 TCGA-AZ-6608 TCGA-CA-5797 TCGA-CK-4947 TCGA-CK-5913 TCGA-CM-6171 
        0.07         1.61         3.29        17.56        51.32        14.04 
TCGA-DM-A1DA TCGA-DM-A1HB TCGA-F4-6570 TCGA-F4-6808 TCGA-G4-6304 TCGA-G4-6309 
        7.50       135.65         6.18        33.67        53.62        85.48 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6626 TCGA-AF-6655 TCGA-AG-3892 TCGA-AG-A002 
       35.80        26.17        46.75        20.02        13.02        20.98 
TCGA-AH-6643 TCGA-F5-6464 
        0.69         9.96 

$`WWC3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       17.98        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 
        0.99        31.07        31.07        30.05        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       27.02        29.98        18.05         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       33.01        26.01         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 
        0.92        41.00        39.98        18.05        40.96        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6716 
        3.19        12.69         3.06         3.25         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       12.76        10.06        14.30       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       49.08         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       15.02        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB 
       92.75        49.91        13.32        12.59       140.38        44.32 
TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      131.51       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6809 
       47.87         1.55        34.42        41.42        16.24        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       44.68        55.04        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6625 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       13.78        91.79        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       15.39        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 
        1.02        17.95        36.95        17.03        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
       17.49         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6465 
        0.49        20.55        19.96        20.91        18.28        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  WWC3 MUTATED WWC3 WILD-TYPE 
          0.07           0.00 
  WWC3 MUTATED WWC3 WILD-TYPE 
        135.65         148.01 
  WWC3 MUTATED WWC3 WILD-TYPE 
         20.50          20.19 
[1] "0.1 - 135.7 (20.5)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1"  
D756V2, continuous
D756V3, binary
                cls
clus               0   1
  WWC3 MUTATED    22   5
  WWC3 WILD-TYPE 344 114
[1] "tbl2"
                cls
clus             [,1] [,2]
  WWC3 MUTATED     22    5
  WWC3 WILD-TYPE  344  114
        clus
vv       WWC3 MUTATED WWC3 WILD-TYPE
  COLON            22            344
  RECTUM            5            114
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  WWC3 MUTATED         6        0        2         9         2         0
  WWC3 WILD-TYPE      85        1       30       129         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  WWC3 MUTATED           0          2          3          3        0         0
  WWC3 WILD-TYPE        24          9         56         39       48        18
                vv
clus             STAGE IVB
  WWC3 MUTATED           0
  WWC3 WILD-TYPE         1
D756V4, multiclass
            clus
vv           WWC3 MUTATED WWC3 WILD-TYPE
  STAGE I               6             85
  STAGE IA              0              1
  STAGE II              2             30
  STAGE IIA             9            129
  STAGE IIB             2              8
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            2              9
  STAGE IIIB            3             56
  STAGE IIIC            3             39
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  WWC3 MUTATED     3   5  15   4
  WWC3 WILD-TYPE  14  87 314  46
D756V5, multiclass
    clus
vv   WWC3 MUTATED WWC3 WILD-TYPE
  T1            3             14
  T2            5             87
  T3           15            314
  T4            4             46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  WWC3 MUTATED    19   5   3
  WWC3 WILD-TYPE 268 108  84
D756V6, multiclass
    clus
vv   WWC3 MUTATED WWC3 WILD-TYPE
  N0           19            268
  N1            5            108
  N2            3             84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D756V7, binary
                cls
clus               0   1
  WWC3 MUTATED    25   0
  WWC3 WILD-TYPE 350  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  WWC3 MUTATED     25    0
  WWC3 WILD-TYPE  350   65
   clus
vv  WWC3 MUTATED WWC3 WILD-TYPE
  0           25            350
  1            0             65
[1] 2 2
[1] FALSE
D756V8, binary
                cls
clus               0   1
  WWC3 MUTATED    17  10
  WWC3 WILD-TYPE 208 254
[1] "tbl2"
                cls
clus             [,1] [,2]
  WWC3 MUTATED     17   10
  WWC3 WILD-TYPE  208  254
        clus
vv       WWC3 MUTATED WWC3 WILD-TYPE
  FEMALE           17            208
  MALE             10            254
[1] 2 2
[1] FALSE
D756V9, binary
                cls
clus               0   1
  WWC3 MUTATED    21   0
  WWC3 WILD-TYPE 329  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  WWC3 MUTATED     21    0
  WWC3 WILD-TYPE  329   22
     clus
vv    WWC3 MUTATED WWC3 WILD-TYPE
  NO            21            329
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  WWC3 MUTATED                     17                             4
  WWC3 WILD-TYPE                  298                            43
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  WWC3 MUTATED                       5                              0
  WWC3 WILD-TYPE                   101                             10
D756V10, multiclass
                                clus
vv                               WWC3 MUTATED WWC3 WILD-TYPE
  COLON ADENOCARCINOMA                     17            298
  COLON MUCINOUS ADENOCARCINOMA             4             43
  RECTAL ADENOCARCINOMA                     5            101
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  WWC3 MUTATED    22   0   0   2
  WWC3 WILD-TYPE 323   4  31  23
D756V11, multiclass
    clus
vv   WWC3 MUTATED WWC3 WILD-TYPE
  R0           22            323
  R1            0              4
  R2            0             31
  RX            2             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D756V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  WWC3 MUTATED                                  0     1
  WWC3 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  WWC3 MUTATED                           1    16
  WWC3 WILD-TYPE                        21   210
D756V13, multiclass
                                  clus
vv                                 WWC3 MUTATED WWC3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                      16            210
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(757) Variable = OR7C1 MUTATION ANALYSIS
D757V1, survival
                 sevent
clus2               0   1
  OR7C1 MUTATED     7   4
  OR7C1 WILD-TYPE 371  89
  OR7C1 MUTATED OR7C1 WILD-TYPE 
             11             460 
  OR7C1 MUTATED OR7C1 WILD-TYPE 
              4              89 
$`OR7C1 MUTATED`
TCGA-AA-3492 TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3821 TCGA-AA-3864 TCGA-AA-3982 
        3.02        13.02         1.02         1.02        53.00        27.02 
TCGA-AD-5900 TCGA-AY-4071 TCGA-AZ-6603 TCGA-DT-5265 TCGA-F5-6702 
        0.07         0.95        29.56         5.29        28.57 

$`OR7C1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3519 
       35.01        63.98         6.97         1.02        38.99         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
       33.04         0.99        25.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       31.07        30.05        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       25.02        24.00        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 
        0.92        41.00        39.98        18.05        40.96        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
       12.10       100.01         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        5.95         4.01         5.03       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6811 
       20.91        18.28         9.96        49.51        31.30        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  OR7C1 MUTATED OR7C1 WILD-TYPE 
           0.07            0.00 
  OR7C1 MUTATED OR7C1 WILD-TYPE 
          53.00          148.01 
  OR7C1 MUTATED OR7C1 WILD-TYPE 
          5.290          20.415 
[1] "0.1 - 53.0 (5.3)"   "0.0 - 148.0 (20.4)"
[1] "hr=" "3.2"
D757V2, continuous
D757V3, binary
                 cls
clus                0   1
  OR7C1 MUTATED     8   2
  OR7C1 WILD-TYPE 358 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR7C1 MUTATED      8    2
  OR7C1 WILD-TYPE  358  117
        clus
vv       OR7C1 MUTATED OR7C1 WILD-TYPE
  COLON              8             358
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  OR7C1 MUTATED         3        0        3         1         0         0
  OR7C1 WILD-TYPE      88        1       29       137        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  OR7C1 MUTATED           1          0          1          0        0         1
  OR7C1 WILD-TYPE        23         11         58         42       48        17
                 vv
clus              STAGE IVB
  OR7C1 MUTATED           0
  OR7C1 WILD-TYPE         1
D757V4, multiclass
            clus
vv           OR7C1 MUTATED OR7C1 WILD-TYPE
  STAGE I                3              88
  STAGE IA               0               1
  STAGE II               3              29
  STAGE IIA              1             137
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  OR7C1 MUTATED     1   3   7   0
  OR7C1 WILD-TYPE  16  89 322  50
D757V5, multiclass
    clus
vv   OR7C1 MUTATED OR7C1 WILD-TYPE
  T1             1              16
  T2             3              89
  T3             7             322
  T4             0              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  OR7C1 MUTATED     7   3   1
  OR7C1 WILD-TYPE 280 110  86
D757V6, multiclass
    clus
vv   OR7C1 MUTATED OR7C1 WILD-TYPE
  N0             7             280
  N1             3             110
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D757V7, binary
                 cls
clus                0   1
  OR7C1 MUTATED     7   1
  OR7C1 WILD-TYPE 368  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR7C1 MUTATED      7    1
  OR7C1 WILD-TYPE  368   64
   clus
vv  OR7C1 MUTATED OR7C1 WILD-TYPE
  0             7             368
  1             1              64
[1] 2 2
[1] FALSE
D757V8, binary
                 cls
clus                0   1
  OR7C1 MUTATED     6   5
  OR7C1 WILD-TYPE 219 259
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR7C1 MUTATED      6    5
  OR7C1 WILD-TYPE  219  259
        clus
vv       OR7C1 MUTATED OR7C1 WILD-TYPE
  FEMALE             6             219
  MALE               5             259
[1] 2 2
[1] FALSE
D757V9, binary
                 cls
clus                0   1
  OR7C1 MUTATED     9   0
  OR7C1 WILD-TYPE 341  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR7C1 MUTATED      9    0
  OR7C1 WILD-TYPE  341   22
     clus
vv    OR7C1 MUTATED OR7C1 WILD-TYPE
  NO              9             341
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  OR7C1 MUTATED                      5                             3
  OR7C1 WILD-TYPE                  310                            44
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  OR7C1 MUTATED                       1                              1
  OR7C1 WILD-TYPE                   105                              9
D757V10, multiclass
                                clus
vv                               OR7C1 MUTATED OR7C1 WILD-TYPE
  COLON ADENOCARCINOMA                       5             310
  COLON MUCINOUS ADENOCARCINOMA              3              44
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             1               9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  OR7C1 MUTATED     7   0   0   1
  OR7C1 WILD-TYPE 338   4  31  24
D757V11, multiclass
    clus
vv   OR7C1 MUTATED OR7C1 WILD-TYPE
  R0             7             338
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D757V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OR7C1 MUTATED                                  0     1
  OR7C1 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  OR7C1 MUTATED                           0     4
  OR7C1 WILD-TYPE                        22   222
D757V13, multiclass
                                  clus
vv                                 OR7C1 MUTATED OR7C1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        4             222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(758) Variable = GRM7 MUTATION ANALYSIS
D758V1, survival
                sevent
clus2              0   1
  GRM7 MUTATED    22   5
  GRM7 WILD-TYPE 356  88
  GRM7 MUTATED GRM7 WILD-TYPE 
            27            444 
  GRM7 MUTATED GRM7 WILD-TYPE 
             5             88 
$`GRM7 MUTATED`
TCGA-A6-3809 TCGA-A6-5661 TCGA-A6-5665 TCGA-A6-6141 TCGA-A6-6652 TCGA-AA-3662 
       32.75        33.53        22.06         8.38        24.69         6.05 
TCGA-AA-3680 TCGA-AA-3697 TCGA-AA-3844 TCGA-AA-3947 TCGA-AA-A00N TCGA-AA-A02W 
       11.01        85.05        14.93        33.01         4.01        41.00 
TCGA-AU-6004 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-CA-6717 TCGA-CK-5913 TCGA-CM-6165 
       27.09         6.77       100.01        12.76        51.32        16.04 
TCGA-CM-6171 TCGA-F4-6807 TCGA-G4-6309 TCGA-G4-6628 TCGA-AG-3726 TCGA-AG-4007 
       14.04        16.24        85.48        79.69         7.99         1.02 
TCGA-AG-A002 TCGA-DC-6158 TCGA-F5-6702 
       20.98        10.98        28.57 

$`GRM7 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 
       31.63        30.44        29.19        23.61        22.09        32.71 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 
       27.09        22.52        25.08        25.18        24.16        21.76 
TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 
       24.39        23.87        20.12        19.66        20.28         7.04 
TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
        3.02         1.02        35.01        63.98         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
       13.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       36.03         8.05        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
       78.08         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       50.04        47.01        15.02         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       15.95        38.99        37.02         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
       14.01         0.92        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 
       22.42        27.42        10.88         0.20        14.50        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
       12.10        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       49.08         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       29.03        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 
       74.56        65.85        53.62        44.68        55.04        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       91.79        46.75        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3727 TCGA-AG-3731 
       15.95        19.99        13.94        19.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       14.04        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       31.30        32.19         0.66         0.69        55.76        26.43 

  GRM7 MUTATED GRM7 WILD-TYPE 
          1.02           0.00 
  GRM7 MUTATED GRM7 WILD-TYPE 
        100.01         148.01 
  GRM7 MUTATED GRM7 WILD-TYPE 
        20.980         20.155 
[1] "1.0 - 100.0 (21.0)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.2"
D758V2, continuous
D758V3, binary
                cls
clus               0   1
  GRM7 MUTATED    25   5
  GRM7 WILD-TYPE 341 114
[1] "tbl2"
                cls
clus             [,1] [,2]
  GRM7 MUTATED     25    5
  GRM7 WILD-TYPE  341  114
        clus
vv       GRM7 MUTATED GRM7 WILD-TYPE
  COLON            25            341
  RECTUM            5            114
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GRM7 MUTATED         9        0        1         8         3         0
  GRM7 WILD-TYPE      82        1       31       130         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  GRM7 MUTATED           1          0          1          2        3         2
  GRM7 WILD-TYPE        23         11         58         40       45        16
                vv
clus             STAGE IVB
  GRM7 MUTATED           0
  GRM7 WILD-TYPE         1
D758V4, multiclass
            clus
vv           GRM7 MUTATED GRM7 WILD-TYPE
  STAGE I               9             82
  STAGE IA              0              1
  STAGE II              1             31
  STAGE IIA             8            130
  STAGE IIB             3              7
  STAGE IIC             0              1
  STAGE III             1             23
  STAGE IIIA            0             11
  STAGE IIIB            1             58
  STAGE IIIC            2             40
  STAGE IV              3             45
  STAGE IVA             2             16
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  GRM7 MUTATED     0   9  15   6
  GRM7 WILD-TYPE  17  83 314  44
D758V5, multiclass
    clus
vv   GRM7 MUTATED GRM7 WILD-TYPE
  T1            0             17
  T2            9             83
  T3           15            314
  T4            6             44
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  GRM7 MUTATED    23   2   5
  GRM7 WILD-TYPE 264 111  82
D758V6, multiclass
    clus
vv   GRM7 MUTATED GRM7 WILD-TYPE
  N0           23            264
  N1            2            111
  N2            5             82
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D758V7, binary
                cls
clus               0   1
  GRM7 MUTATED    22   5
  GRM7 WILD-TYPE 353  60
[1] "tbl2"
                cls
clus             [,1] [,2]
  GRM7 MUTATED     22    5
  GRM7 WILD-TYPE  353   60
   clus
vv  GRM7 MUTATED GRM7 WILD-TYPE
  0           22            353
  1            5             60
[1] 2 2
[1] FALSE
D758V8, binary
                cls
clus               0   1
  GRM7 MUTATED    16  14
  GRM7 WILD-TYPE 209 250
[1] "tbl2"
                cls
clus             [,1] [,2]
  GRM7 MUTATED     16   14
  GRM7 WILD-TYPE  209  250
        clus
vv       GRM7 MUTATED GRM7 WILD-TYPE
  FEMALE           16            209
  MALE             14            250
[1] 2 2
[1] FALSE
D758V9, binary
                cls
clus               0   1
  GRM7 MUTATED    23   1
  GRM7 WILD-TYPE 327  21
[1] "tbl2"
                cls
clus             [,1] [,2]
  GRM7 MUTATED     23    1
  GRM7 WILD-TYPE  327   21
     clus
vv    GRM7 MUTATED GRM7 WILD-TYPE
  NO            23            327
  YES            1             21
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  GRM7 MUTATED                     21                             4
  GRM7 WILD-TYPE                  294                            43
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  GRM7 MUTATED                       5                              0
  GRM7 WILD-TYPE                   101                             10
D758V10, multiclass
                                clus
vv                               GRM7 MUTATED GRM7 WILD-TYPE
  COLON ADENOCARCINOMA                     21            294
  COLON MUCINOUS ADENOCARCINOMA             4             43
  RECTAL ADENOCARCINOMA                     5            101
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  GRM7 MUTATED    20   0   3   3
  GRM7 WILD-TYPE 325   4  28  22
D758V11, multiclass
    clus
vv   GRM7 MUTATED GRM7 WILD-TYPE
  R0           20            325
  R1            0              4
  R2            3             28
  RX            3             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D758V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GRM7 MUTATED                                  0     1
  GRM7 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  GRM7 MUTATED                           4    13
  GRM7 WILD-TYPE                        18   213
D758V13, multiclass
                                  clus
vv                                 GRM7 MUTATED GRM7 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   4             18
  WHITE                                      13            213
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(759) Variable = RANBP1 MUTATION ANALYSIS
D759V1, survival
                  sevent
clus2                0   1
  RANBP1 MUTATED     5   1
  RANBP1 WILD-TYPE 373  92
  RANBP1 MUTATED RANBP1 WILD-TYPE 
               6              465 
  RANBP1 MUTATED RANBP1 WILD-TYPE 
               1               92 
$`RANBP1 MUTATED`
TCGA-A6-5665 TCGA-AZ-4315 TCGA-CM-5860 TCGA-F4-6460 TCGA-F4-6856 TCGA-G4-6588 
       22.06        58.39        32.02        31.96        35.31        26.17 

$`RANBP1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        33.01        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
      117.07        98.24         8.61        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
        0.53        47.41       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       22.09        13.78        35.80        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  RANBP1 MUTATED RANBP1 WILD-TYPE 
           22.06             0.00 
  RANBP1 MUTATED RANBP1 WILD-TYPE 
           58.39           148.01 
  RANBP1 MUTATED RANBP1 WILD-TYPE 
           31.99            20.02 
[1] "22.1 - 58.4 (32.0)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.5"
D759V2, continuous
D759V3, binary
                  cls
clus                 0   1
  RANBP1 MUTATED     6   0
  RANBP1 WILD-TYPE 360 119
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RANBP1 MUTATED      6    0
  RANBP1 WILD-TYPE  360  119
        clus
vv       RANBP1 MUTATED RANBP1 WILD-TYPE
  COLON               6              360
  RECTUM              0              119
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RANBP1 MUTATED         1        0        0         4         0         0
  RANBP1 WILD-TYPE      90        1       32       134        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RANBP1 MUTATED           0          0          1          0        0
  RANBP1 WILD-TYPE        24         11         58         42       48
                  vv
clus               STAGE IVA STAGE IVB
  RANBP1 MUTATED           0         0
  RANBP1 WILD-TYPE        18         1
D759V4, multiclass
            clus
vv           RANBP1 MUTATED RANBP1 WILD-TYPE
  STAGE I                 1               90
  STAGE IA                0                1
  STAGE II                0               32
  STAGE IIA               4              134
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              1               58
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  RANBP1 MUTATED     0   1   5   0
  RANBP1 WILD-TYPE  17  91 324  50
D759V5, multiclass
    clus
vv   RANBP1 MUTATED RANBP1 WILD-TYPE
  T1              0               17
  T2              1               91
  T3              5              324
  T4              0               50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  RANBP1 MUTATED     5   1   0
  RANBP1 WILD-TYPE 282 112  87
D759V6, multiclass
    clus
vv   RANBP1 MUTATED RANBP1 WILD-TYPE
  N0              5              282
  N1              1              112
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D759V7, binary
                  cls
clus                 0   1
  RANBP1 MUTATED     6   0
  RANBP1 WILD-TYPE 369  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RANBP1 MUTATED      6    0
  RANBP1 WILD-TYPE  369   65
   clus
vv  RANBP1 MUTATED RANBP1 WILD-TYPE
  0              6              369
  1              0               65
[1] 2 2
[1] FALSE
D759V8, binary
                  cls
clus                 0   1
  RANBP1 MUTATED     3   3
  RANBP1 WILD-TYPE 222 261
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RANBP1 MUTATED      3    3
  RANBP1 WILD-TYPE  222  261
        clus
vv       RANBP1 MUTATED RANBP1 WILD-TYPE
  FEMALE              3              222
  MALE                3              261
[1] 2 2
[1] FALSE
D759V9, binary
                  cls
clus                 0   1
  RANBP1 MUTATED     6   0
  RANBP1 WILD-TYPE 344  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RANBP1 MUTATED      6    0
  RANBP1 WILD-TYPE  344   22
     clus
vv    RANBP1 MUTATED RANBP1 WILD-TYPE
  NO               6              344
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  RANBP1 MUTATED                      5                             1
  RANBP1 WILD-TYPE                  310                            46
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  RANBP1 MUTATED                       0                              0
  RANBP1 WILD-TYPE                   106                             10
D759V10, multiclass
                                clus
vv                               RANBP1 MUTATED RANBP1 WILD-TYPE
  COLON ADENOCARCINOMA                        5              310
  COLON MUCINOUS ADENOCARCINOMA               1               46
  RECTAL ADENOCARCINOMA                       0              106
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  RANBP1 MUTATED     6   0   0   0
  RANBP1 WILD-TYPE 339   4  31  25
D759V11, multiclass
    clus
vv   RANBP1 MUTATED RANBP1 WILD-TYPE
  R0              6              339
  R1              0                4
  R2              0               31
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D759V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RANBP1 MUTATED                                  0     0
  RANBP1 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  RANBP1 MUTATED                           0     6
  RANBP1 WILD-TYPE                        22   220
D759V13, multiclass
                                  clus
vv                                 RANBP1 MUTATED RANBP1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         6              220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(760) Variable = PAK7 MUTATION ANALYSIS
D760V1, survival
                sevent
clus2              0   1
  PAK7 MUTATED    18   8
  PAK7 WILD-TYPE 360  85
  PAK7 MUTATED PAK7 WILD-TYPE 
            26            445 
  PAK7 MUTATED PAK7 WILD-TYPE 
             8             85 
$`PAK7 MUTATED`
TCGA-A6-6141 TCGA-AA-3662 TCGA-AA-3815 TCGA-AA-3837 TCGA-AA-A00N TCGA-AA-A010 
        8.38         6.05        33.04        38.99         4.01        34.98 
TCGA-AA-A024 TCGA-AD-6889 TCGA-AZ-4315 TCGA-AZ-6603 TCGA-AZ-6607 TCGA-CA-5797 
       39.06        56.55        58.39        29.56         3.19         3.29 
TCGA-CK-5912 TCGA-D5-6540 TCGA-D5-6541 TCGA-DM-A285 TCGA-F4-6570 TCGA-F4-6703 
       49.08        16.14        15.58         6.12         6.18        47.87 
TCGA-G4-6307 TCGA-G4-6321 TCGA-AF-5654 TCGA-AG-3732 TCGA-AG-A002 TCGA-AG-A02N 
       55.04        22.09        16.83        32.98        20.98        61.97 
TCGA-EI-6508 TCGA-G5-6235 
       20.91        55.76 

$`PAK7 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 
       22.09        22.06        32.71        27.09        22.52        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       19.99        13.94        19.99        61.02        78.08         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       35.05         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       15.52         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       33.01        21.44        17.82         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
      100.01         5.23        11.74         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.25         0.07        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 
       17.56       148.01        85.45        15.62        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6898 TCGA-D5-6920 
       17.85         4.80        17.13        12.49         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
      139.17        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6704 TCGA-F4-6805 
       98.24         8.61        31.96        35.74         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6586 
       85.48        63.62        61.91        36.00        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
        0.99        37.02         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       38.96        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6510 TCGA-F5-6464 
       32.61         0.49        20.55        19.96        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6641 
       26.43 

  PAK7 MUTATED PAK7 WILD-TYPE 
          3.19           0.00 
  PAK7 MUTATED PAK7 WILD-TYPE 
         61.97         148.01 
  PAK7 MUTATED PAK7 WILD-TYPE 
        25.825         20.020 
[1] "3.2 - 62.0 (25.8)"  "0.0 - 148.0 (20.0)"
[1] "hr=" "1.4"
D760V2, continuous
D760V3, binary
                cls
clus               0   1
  PAK7 MUTATED    20   6
  PAK7 WILD-TYPE 346 113
[1] "tbl2"
                cls
clus             [,1] [,2]
  PAK7 MUTATED     20    6
  PAK7 WILD-TYPE  346  113
        clus
vv       PAK7 MUTATED PAK7 WILD-TYPE
  COLON            20            346
  RECTUM            6            113
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PAK7 MUTATED         5        0        2         9         2         0
  PAK7 WILD-TYPE      86        1       30       129         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PAK7 MUTATED           1          0          3          0        3         0
  PAK7 WILD-TYPE        23         11         56         42       45        18
                vv
clus             STAGE IVB
  PAK7 MUTATED           0
  PAK7 WILD-TYPE         1
D760V4, multiclass
            clus
vv           PAK7 MUTATED PAK7 WILD-TYPE
  STAGE I               5             86
  STAGE IA              0              1
  STAGE II              2             30
  STAGE IIA             9            129
  STAGE IIB             2              8
  STAGE IIC             0              1
  STAGE III             1             23
  STAGE IIIA            0             11
  STAGE IIIB            3             56
  STAGE IIIC            0             42
  STAGE IV              3             45
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  PAK7 MUTATED     0   7  15   4
  PAK7 WILD-TYPE  17  85 314  46
D760V5, multiclass
    clus
vv   PAK7 MUTATED PAK7 WILD-TYPE
  T1            0             17
  T2            7             85
  T3           15            314
  T4            4             46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  PAK7 MUTATED    18   5   3
  PAK7 WILD-TYPE 269 108  84
D760V6, multiclass
    clus
vv   PAK7 MUTATED PAK7 WILD-TYPE
  N0           18            269
  N1            5            108
  N2            3             84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D760V7, binary
                cls
clus               0   1
  PAK7 MUTATED    19   3
  PAK7 WILD-TYPE 356  62
[1] "tbl2"
                cls
clus             [,1] [,2]
  PAK7 MUTATED     19    3
  PAK7 WILD-TYPE  356   62
   clus
vv  PAK7 MUTATED PAK7 WILD-TYPE
  0           19            356
  1            3             62
[1] 2 2
[1] FALSE
D760V8, binary
                cls
clus               0   1
  PAK7 MUTATED    11  15
  PAK7 WILD-TYPE 214 249
[1] "tbl2"
                cls
clus             [,1] [,2]
  PAK7 MUTATED     11   15
  PAK7 WILD-TYPE  214  249
        clus
vv       PAK7 MUTATED PAK7 WILD-TYPE
  FEMALE           11            214
  MALE             15            249
[1] 2 2
[1] FALSE
D760V9, binary
                cls
clus               0   1
  PAK7 MUTATED    22   0
  PAK7 WILD-TYPE 328  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  PAK7 MUTATED     22    0
  PAK7 WILD-TYPE  328   22
     clus
vv    PAK7 MUTATED PAK7 WILD-TYPE
  NO            22            328
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PAK7 MUTATED                     15                             5
  PAK7 WILD-TYPE                  300                            42
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PAK7 MUTATED                       6                              0
  PAK7 WILD-TYPE                   100                             10
D760V10, multiclass
                                clus
vv                               PAK7 MUTATED PAK7 WILD-TYPE
  COLON ADENOCARCINOMA                     15            300
  COLON MUCINOUS ADENOCARCINOMA             5             42
  RECTAL ADENOCARCINOMA                     6            100
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  PAK7 MUTATED    18   1   1   1
  PAK7 WILD-TYPE 327   3  30  24
D760V11, multiclass
    clus
vv   PAK7 MUTATED PAK7 WILD-TYPE
  R0           18            327
  R1            1              3
  R2            1             30
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D760V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PAK7 MUTATED                                  0     2
  PAK7 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  PAK7 MUTATED                           1    14
  PAK7 WILD-TYPE                        21   212
D760V13, multiclass
                                  clus
vv                                 PAK7 MUTATED PAK7 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              9
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                      14            212
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(761) Variable = LUM MUTATION ANALYSIS
D761V1, survival
               sevent
clus2             0   1
  LUM MUTATED    10   3
  LUM WILD-TYPE 368  90
  LUM MUTATED LUM WILD-TYPE 
           13           458 
  LUM MUTATED LUM WILD-TYPE 
            3            90 
$`LUM MUTATED`
TCGA-AA-3510 TCGA-AA-3548 TCGA-AA-3845 TCGA-AA-A010 TCGA-AA-A01R TCGA-AZ-6600 
       63.98        33.99         0.00        34.98        35.01        12.10 
TCGA-CM-6161 TCGA-D5-6536 TCGA-D5-6538 TCGA-DM-A1HB TCGA-DM-A285 TCGA-AG-3731 
       15.02        17.85        17.13       135.65         6.12        37.02 
TCGA-AG-A002 
       20.98 

$`LUM WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3549 TCGA-AA-3552 
       26.01        12.99         0.99        14.01        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 
       15.95        38.99        37.02        14.93        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
       38.07         1.02         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       88.21        49.41         6.77       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       15.02        17.03        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6537 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
        4.80        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 
       12.59       140.38         7.50        44.32       131.51       139.17 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3732 
       19.99        13.94        19.99         7.99         0.99        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  LUM MUTATED LUM WILD-TYPE 
            0             0 
  LUM MUTATED LUM WILD-TYPE 
       135.65        148.01 
  LUM MUTATED LUM WILD-TYPE 
       20.980        20.155 
[1] "0.0 - 135.7 (21.0)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1"  
D761V2, continuous
D761V3, binary
               cls
clus              0   1
  LUM MUTATED    12   2
  LUM WILD-TYPE 354 117
[1] "tbl2"
               cls
clus            [,1] [,2]
  LUM MUTATED     12    2
  LUM WILD-TYPE  354  117
        clus
vv       LUM MUTATED LUM WILD-TYPE
  COLON           12           354
  RECTUM           2           117
[1] 2 2
[1] FALSE
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  LUM MUTATED         2        0        2         2         1         0
  LUM WILD-TYPE      89        1       30       136         9         1
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  LUM MUTATED           1          0          2          1        3         0
  LUM WILD-TYPE        23         11         57         41       45        18
               vv
clus            STAGE IVB
  LUM MUTATED           0
  LUM WILD-TYPE         1
D761V4, multiclass
            clus
vv           LUM MUTATED LUM WILD-TYPE
  STAGE I              2            89
  STAGE IA             0             1
  STAGE II             2            30
  STAGE IIA            2           136
  STAGE IIB            1             9
  STAGE IIC            0             1
  STAGE III            1            23
  STAGE IIIA           0            11
  STAGE IIIB           2            57
  STAGE IIIC           1            41
  STAGE IV             3            45
  STAGE IVA            0            18
  STAGE IVB            0             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  LUM MUTATED     0   2   9   3
  LUM WILD-TYPE  17  90 320  47
D761V5, multiclass
    clus
vv   LUM MUTATED LUM WILD-TYPE
  T1           0            17
  T2           2            90
  T3           9           320
  T4           3            47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2
  LUM MUTATED     7   3   4
  LUM WILD-TYPE 280 110  83
D761V6, multiclass
    clus
vv   LUM MUTATED LUM WILD-TYPE
  N0           7           280
  N1           3           110
  N2           4            83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D761V7, binary
               cls
clus              0   1
  LUM MUTATED    11   3
  LUM WILD-TYPE 364  62
[1] "tbl2"
               cls
clus            [,1] [,2]
  LUM MUTATED     11    3
  LUM WILD-TYPE  364   62
   clus
vv  LUM MUTATED LUM WILD-TYPE
  0          11           364
  1           3            62
[1] 2 2
[1] FALSE
D761V8, binary
               cls
clus              0   1
  LUM MUTATED     7   7
  LUM WILD-TYPE 218 257
[1] "tbl2"
               cls
clus            [,1] [,2]
  LUM MUTATED      7    7
  LUM WILD-TYPE  218  257
        clus
vv       LUM MUTATED LUM WILD-TYPE
  FEMALE           7           218
  MALE             7           257
[1] 2 2
[1] FALSE
D761V9, binary
               cls
clus              0   1
  LUM MUTATED     8   1
  LUM WILD-TYPE 342  21
[1] "tbl2"
               cls
clus            [,1] [,2]
  LUM MUTATED      8    1
  LUM WILD-TYPE  342   21
     clus
vv    LUM MUTATED LUM WILD-TYPE
  NO            8           342
  YES           1            21
[1] 2 2
[1] FALSE
               vv
clus            COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  LUM MUTATED                      9                             2
  LUM WILD-TYPE                  306                            45
               vv
clus            RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  LUM MUTATED                       2                              0
  LUM WILD-TYPE                   104                             10
D761V10, multiclass
                                clus
vv                               LUM MUTATED LUM WILD-TYPE
  COLON ADENOCARCINOMA                     9           306
  COLON MUCINOUS ADENOCARCINOMA            2            45
  RECTAL ADENOCARCINOMA                    2           104
  RECTAL MUCINOUS ADENOCARCINOMA           0            10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             R0  R1  R2  RX
  LUM MUTATED    10   0   1   0
  LUM WILD-TYPE 335   4  30  25
D761V11, multiclass
    clus
vv   LUM MUTATED LUM WILD-TYPE
  R0          10           335
  R1           0             4
  R2           1            30
  RX           0            25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D761V12, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  LUM MUTATED                                  0     0
  LUM WILD-TYPE                                1    11
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  LUM MUTATED                           1     5
  LUM WILD-TYPE                        21   221
D761V13, multiclass
                                  clus
vv                                 LUM MUTATED LUM WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      0            11
  BLACK OR AFRICAN AMERICAN                  1            21
  WHITE                                      5           221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(762) Variable = WDR66 MUTATION ANALYSIS
D762V1, survival
                 sevent
clus2               0   1
  WDR66 MUTATED    15   5
  WDR66 WILD-TYPE 363  88
  WDR66 MUTATED WDR66 WILD-TYPE 
             20             451 
  WDR66 MUTATED WDR66 WILD-TYPE 
              5              88 
$`WDR66 MUTATED`
TCGA-AA-3510 TCGA-AA-3663 TCGA-AA-3710 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3977 
       63.98         6.97        26.99        31.07        30.05        25.02 
TCGA-AA-A00N TCGA-AA-A010 TCGA-AD-6964 TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-6162 
        4.01        34.98        10.88        12.76        10.06        12.00 
TCGA-D5-6930 TCGA-DM-A282 TCGA-F4-6459 TCGA-F4-6808 TCGA-G4-6586 TCGA-AF-5654 
        1.51       139.17         8.61        33.67        35.80        16.83 
TCGA-AG-3885 TCGA-AG-A002 
       17.95        20.98 

$`WDR66 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       31.07        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 
       15.02        15.02        17.03        15.02         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 
        9.04         9.44        11.64         4.80        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      131.51       135.65         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
       60.79       117.07        98.24        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6809 
       47.87         1.55        34.42        41.42        16.24        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       34.49        10.39        14.50        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 
        0.99         0.99        19.04        19.99         1.02        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  WDR66 MUTATED WDR66 WILD-TYPE 
           1.51            0.00 
  WDR66 MUTATED WDR66 WILD-TYPE 
         139.17          148.01 
  WDR66 MUTATED WDR66 WILD-TYPE 
         19.465          20.190 
[1] "1.5 - 139.2 (19.5)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.4"
D762V2, continuous
D762V3, binary
                 cls
clus                0   1
  WDR66 MUTATED    19   3
  WDR66 WILD-TYPE 347 116
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WDR66 MUTATED     19    3
  WDR66 WILD-TYPE  347  116
        clus
vv       WDR66 MUTATED WDR66 WILD-TYPE
  COLON             19             347
  RECTUM             3             116
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  WDR66 MUTATED         3        0        2         8         2         0
  WDR66 WILD-TYPE      88        1       30       130         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  WDR66 MUTATED           0          0          4          1        0         0
  WDR66 WILD-TYPE        24         11         55         41       48        18
                 vv
clus              STAGE IVB
  WDR66 MUTATED           0
  WDR66 WILD-TYPE         1
D762V4, multiclass
            clus
vv           WDR66 MUTATED WDR66 WILD-TYPE
  STAGE I                3              88
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA              8             130
  STAGE IIB              2               8
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             4              55
  STAGE IIIC             1              41
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  WDR66 MUTATED     1   3  15   3
  WDR66 WILD-TYPE  16  89 314  47
D762V5, multiclass
    clus
vv   WDR66 MUTATED WDR66 WILD-TYPE
  T1             1              16
  T2             3              89
  T3            15             314
  T4             3              47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  WDR66 MUTATED    16   3   3
  WDR66 WILD-TYPE 271 110  84
D762V6, multiclass
    clus
vv   WDR66 MUTATED WDR66 WILD-TYPE
  N0            16             271
  N1             3             110
  N2             3              84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D762V7, binary
                 cls
clus                0   1
  WDR66 MUTATED    19   0
  WDR66 WILD-TYPE 356  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WDR66 MUTATED     19    0
  WDR66 WILD-TYPE  356   65
   clus
vv  WDR66 MUTATED WDR66 WILD-TYPE
  0            19             356
  1             0              65
[1] 2 2
[1] FALSE
D762V8, binary
                 cls
clus                0   1
  WDR66 MUTATED    11  11
  WDR66 WILD-TYPE 214 253
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WDR66 MUTATED     11   11
  WDR66 WILD-TYPE  214  253
        clus
vv       WDR66 MUTATED WDR66 WILD-TYPE
  FEMALE            11             214
  MALE              11             253
[1] 2 2
[1] FALSE
D762V9, binary
                 cls
clus                0   1
  WDR66 MUTATED    16   1
  WDR66 WILD-TYPE 334  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WDR66 MUTATED     16    1
  WDR66 WILD-TYPE  334   21
     clus
vv    WDR66 MUTATED WDR66 WILD-TYPE
  NO             16             334
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  WDR66 MUTATED                     14                             5
  WDR66 WILD-TYPE                  301                            42
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  WDR66 MUTATED                       3                              0
  WDR66 WILD-TYPE                   103                             10
D762V10, multiclass
                                clus
vv                               WDR66 MUTATED WDR66 WILD-TYPE
  COLON ADENOCARCINOMA                      14             301
  COLON MUCINOUS ADENOCARCINOMA              5              42
  RECTAL ADENOCARCINOMA                      3             103
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  WDR66 MUTATED    17   0   0   2
  WDR66 WILD-TYPE 328   4  31  23
D762V11, multiclass
    clus
vv   WDR66 MUTATED WDR66 WILD-TYPE
  R0            17             328
  R1             0               4
  R2             0              31
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D762V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  WDR66 MUTATED                                  0     2
  WDR66 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  WDR66 MUTATED                           0     9
  WDR66 WILD-TYPE                        22   217
D762V13, multiclass
                                  clus
vv                                 WDR66 MUTATED WDR66 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               9
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        9             217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(763) Variable = IRAK3 MUTATION ANALYSIS
D763V1, survival
                 sevent
clus2               0   1
  IRAK3 MUTATED     6   2
  IRAK3 WILD-TYPE 372  91
  IRAK3 MUTATED IRAK3 WILD-TYPE 
              8             463 
  IRAK3 MUTATED IRAK3 WILD-TYPE 
              2              91 
$`IRAK3 MUTATED`
TCGA-AA-3492 TCGA-AA-A00N TCGA-AZ-4315 TCGA-CA-6717 TCGA-D5-6535 TCGA-D5-6540 
        3.02         4.01        58.39        12.76        15.12        16.14 
TCGA-G4-6309 TCGA-AG-A002 
       85.48        20.98 

$`IRAK3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       33.01        21.44        17.82         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
        1.32        43.27        17.85         4.80        17.13        12.49 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       55.04        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  IRAK3 MUTATED IRAK3 WILD-TYPE 
           3.02            0.00 
  IRAK3 MUTATED IRAK3 WILD-TYPE 
          85.48          148.01 
  IRAK3 MUTATED IRAK3 WILD-TYPE 
          15.63           20.28 
[1] "3.0 - 85.5 (15.6)"  "0.0 - 148.0 (20.3)"
[1] "hr=" "1.2"
D763V2, continuous
D763V3, binary
                 cls
clus                0   1
  IRAK3 MUTATED     8   1
  IRAK3 WILD-TYPE 358 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IRAK3 MUTATED      8    1
  IRAK3 WILD-TYPE  358  118
        clus
vv       IRAK3 MUTATED IRAK3 WILD-TYPE
  COLON              8             358
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  IRAK3 MUTATED         3        0        1         2         1         0
  IRAK3 WILD-TYPE      88        1       31       136         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  IRAK3 MUTATED           0          0          2          0        0         0
  IRAK3 WILD-TYPE        24         11         57         42       48        18
                 vv
clus              STAGE IVB
  IRAK3 MUTATED           0
  IRAK3 WILD-TYPE         1
D763V4, multiclass
            clus
vv           IRAK3 MUTATED IRAK3 WILD-TYPE
  STAGE I                3              88
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              2             136
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             2              57
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  IRAK3 MUTATED     0   3   5   1
  IRAK3 WILD-TYPE  17  89 324  49
D763V5, multiclass
    clus
vv   IRAK3 MUTATED IRAK3 WILD-TYPE
  T1             0              17
  T2             3              89
  T3             5             324
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  IRAK3 MUTATED     7   2   0
  IRAK3 WILD-TYPE 280 111  87
D763V6, multiclass
    clus
vv   IRAK3 MUTATED IRAK3 WILD-TYPE
  N0             7             280
  N1             2             111
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D763V7, binary
                 cls
clus                0   1
  IRAK3 MUTATED     7   0
  IRAK3 WILD-TYPE 368  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IRAK3 MUTATED      7    0
  IRAK3 WILD-TYPE  368   65
   clus
vv  IRAK3 MUTATED IRAK3 WILD-TYPE
  0             7             368
  1             0              65
[1] 2 2
[1] FALSE
D763V8, binary
                 cls
clus                0   1
  IRAK3 MUTATED     3   6
  IRAK3 WILD-TYPE 222 258
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IRAK3 MUTATED      3    6
  IRAK3 WILD-TYPE  222  258
        clus
vv       IRAK3 MUTATED IRAK3 WILD-TYPE
  FEMALE             3             222
  MALE               6             258
[1] 2 2
[1] FALSE
D763V9, binary
                 cls
clus                0   1
  IRAK3 MUTATED     7   0
  IRAK3 WILD-TYPE 343  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IRAK3 MUTATED      7    0
  IRAK3 WILD-TYPE  343   22
     clus
vv    IRAK3 MUTATED IRAK3 WILD-TYPE
  NO              7             343
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  IRAK3 MUTATED                      5                             3
  IRAK3 WILD-TYPE                  310                            44
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  IRAK3 MUTATED                       1                              0
  IRAK3 WILD-TYPE                   105                             10
D763V10, multiclass
                                clus
vv                               IRAK3 MUTATED IRAK3 WILD-TYPE
  COLON ADENOCARCINOMA                       5             310
  COLON MUCINOUS ADENOCARCINOMA              3              44
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  IRAK3 MUTATED     6   0   0   3
  IRAK3 WILD-TYPE 339   4  31  22
D763V11, multiclass
    clus
vv   IRAK3 MUTATED IRAK3 WILD-TYPE
  R0             6             339
  R1             0               4
  R2             0              31
  RX             3              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D763V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  IRAK3 MUTATED                                  0     1
  IRAK3 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  IRAK3 MUTATED                           1     4
  IRAK3 WILD-TYPE                        21   222
D763V13, multiclass
                                  clus
vv                                 IRAK3 MUTATED IRAK3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        4             222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(764) Variable = SLC41A2 MUTATION ANALYSIS
D764V1, survival
                   sevent
clus2                 0   1
  SLC41A2 MUTATED     8   0
  SLC41A2 WILD-TYPE 370  93
  SLC41A2 MUTATED SLC41A2 WILD-TYPE 
                8               463 
  SLC41A2 MUTATED SLC41A2 WILD-TYPE 
                0                93 
$`SLC41A2 MUTATED`
TCGA-CA-6717 TCGA-CM-6164 TCGA-CM-6168 TCGA-D5-5540 TCGA-D5-6928 TCGA-DM-A1HB 
       12.76        29.03        12.99        56.09        11.64       135.65 
TCGA-G4-6315 TCGA-AG-A002 
       61.91        20.98 

$`SLC41A2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07        12.20        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6165 TCGA-CM-6166 
       17.03        15.02        12.00         2.96        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       14.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       45.40        12.26        19.59        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6930 
       12.43        14.30         9.04         9.44         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
        7.50        44.32       131.51       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       55.04        85.48        63.62        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  SLC41A2 MUTATED SLC41A2 WILD-TYPE 
            11.64              0.00 
  SLC41A2 MUTATED SLC41A2 WILD-TYPE 
           135.65            148.01 
  SLC41A2 MUTATED SLC41A2 WILD-TYPE 
           25.005            20.120 
[1] "11.6 - 135.7 (25.0)" "0.0 - 148.0 (20.1)" 
[1] "hr="     "9300000"
D764V2, continuous
D764V3, binary
                   cls
clus                  0   1
  SLC41A2 MUTATED     8   1
  SLC41A2 WILD-TYPE 358 118
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC41A2 MUTATED      8    1
  SLC41A2 WILD-TYPE  358  118
        clus
vv       SLC41A2 MUTATED SLC41A2 WILD-TYPE
  COLON                8               358
  RECTUM               1               118
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SLC41A2 MUTATED         1        0        0         6         0         0
  SLC41A2 WILD-TYPE      90        1       32       132        10         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC41A2 MUTATED           0          0          1          0        1
  SLC41A2 WILD-TYPE        24         11         58         42       47
                   vv
clus                STAGE IVA STAGE IVB
  SLC41A2 MUTATED           0         0
  SLC41A2 WILD-TYPE        18         1
D764V4, multiclass
            clus
vv           SLC41A2 MUTATED SLC41A2 WILD-TYPE
  STAGE I                  1                90
  STAGE IA                 0                 1
  STAGE II                 0                32
  STAGE IIA                6               132
  STAGE IIB                0                10
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               0                11
  STAGE IIIB               1                58
  STAGE IIIC               0                42
  STAGE IV                 1                47
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  SLC41A2 MUTATED     0   1   8   0
  SLC41A2 WILD-TYPE  17  91 321  50
D764V5, multiclass
    clus
vv   SLC41A2 MUTATED SLC41A2 WILD-TYPE
  T1               0                17
  T2               1                91
  T3               8               321
  T4               0                50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  SLC41A2 MUTATED     7   2   0
  SLC41A2 WILD-TYPE 280 111  87
D764V6, multiclass
    clus
vv   SLC41A2 MUTATED SLC41A2 WILD-TYPE
  N0               7               280
  N1               2               111
  N2               0                87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D764V7, binary
                   cls
clus                  0   1
  SLC41A2 MUTATED     8   1
  SLC41A2 WILD-TYPE 367  64
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC41A2 MUTATED      8    1
  SLC41A2 WILD-TYPE  367   64
   clus
vv  SLC41A2 MUTATED SLC41A2 WILD-TYPE
  0               8               367
  1               1                64
[1] 2 2
[1] FALSE
D764V8, binary
                   cls
clus                  0   1
  SLC41A2 MUTATED     3   6
  SLC41A2 WILD-TYPE 222 258
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC41A2 MUTATED      3    6
  SLC41A2 WILD-TYPE  222  258
        clus
vv       SLC41A2 MUTATED SLC41A2 WILD-TYPE
  FEMALE               3               222
  MALE                 6               258
[1] 2 2
[1] FALSE
D764V9, binary
                   cls
clus                  0   1
  SLC41A2 MUTATED     7   0
  SLC41A2 WILD-TYPE 343  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC41A2 MUTATED      7    0
  SLC41A2 WILD-TYPE  343   22
     clus
vv    SLC41A2 MUTATED SLC41A2 WILD-TYPE
  NO                7               343
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SLC41A2 MUTATED                      5                             2
  SLC41A2 WILD-TYPE                  310                            45
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SLC41A2 MUTATED                       1                              0
  SLC41A2 WILD-TYPE                   105                             10
D764V10, multiclass
                                clus
vv                               SLC41A2 MUTATED SLC41A2 WILD-TYPE
  COLON ADENOCARCINOMA                         5               310
  COLON MUCINOUS ADENOCARCINOMA                2                45
  RECTAL ADENOCARCINOMA                        1               105
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  SLC41A2 MUTATED     7   0   0   1
  SLC41A2 WILD-TYPE 338   4  31  24
D764V11, multiclass
    clus
vv   SLC41A2 MUTATED SLC41A2 WILD-TYPE
  R0               7               338
  R1               0                 4
  R2               0                31
  RX               1                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D764V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SLC41A2 MUTATED                                  0     1
  SLC41A2 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  SLC41A2 MUTATED                           1     5
  SLC41A2 WILD-TYPE                        21   221
D764V13, multiclass
                                  clus
vv                                 SLC41A2 MUTATED SLC41A2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                10
  BLACK OR AFRICAN AMERICAN                      1                21
  WHITE                                          5               221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(765) Variable = ING2 MUTATION ANALYSIS
D765V1, survival
                sevent
clus2              0   1
  ING2 MUTATED     7   0
  ING2 WILD-TYPE 371  93
  ING2 MUTATED ING2 WILD-TYPE 
             7            464 
  ING2 MUTATED ING2 WILD-TYPE 
             0             93 
$`ING2 MUTATED`
TCGA-AA-3663 TCGA-AD-5900 TCGA-AZ-4315 TCGA-AZ-5407 TCGA-F4-6703 TCGA-G4-6586 
        6.97         0.07        58.39        88.21        47.87        35.80 
TCGA-AG-A002 
       20.98 

$`ING2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.05        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 
       41.00        39.98        18.05        40.96        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       33.01        21.44        17.82         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6704 
       98.24         8.61        31.96        35.74         6.18         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       22.09        13.78        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  ING2 MUTATED ING2 WILD-TYPE 
          0.07           0.00 
  ING2 MUTATED ING2 WILD-TYPE 
         88.21         148.01 
  ING2 MUTATED ING2 WILD-TYPE 
        35.800         20.085 
[1] "0.1 - 88.2 (35.8)"  "0.0 - 148.0 (20.1)"
[1] "hr="     "9300000"
D765V2, continuous
D765V3, binary
                cls
clus               0   1
  ING2 MUTATED     6   1
  ING2 WILD-TYPE 360 118
[1] "tbl2"
                cls
clus             [,1] [,2]
  ING2 MUTATED      6    1
  ING2 WILD-TYPE  360  118
        clus
vv       ING2 MUTATED ING2 WILD-TYPE
  COLON             6            360
  RECTUM            1            118
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ING2 MUTATED         3        0        1         3         0         0
  ING2 WILD-TYPE      88        1       31       135        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ING2 MUTATED           0          0          0          0        0         0
  ING2 WILD-TYPE        24         11         59         42       48        18
                vv
clus             STAGE IVB
  ING2 MUTATED           0
  ING2 WILD-TYPE         1
D765V4, multiclass
            clus
vv           ING2 MUTATED ING2 WILD-TYPE
  STAGE I               3             88
  STAGE IA              0              1
  STAGE II              1             31
  STAGE IIA             3            135
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            0             59
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  ING2 MUTATED     1   2   4   0
  ING2 WILD-TYPE  16  90 325  50
D765V5, multiclass
    clus
vv   ING2 MUTATED ING2 WILD-TYPE
  T1            1             16
  T2            2             90
  T3            4            325
  T4            0             50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  ING2 MUTATED     7   0   0
  ING2 WILD-TYPE 280 113  87
D765V6, multiclass
    clus
vv   ING2 MUTATED ING2 WILD-TYPE
  N0            7            280
  N1            0            113
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D765V7, binary
                cls
clus               0   1
  ING2 MUTATED     6   0
  ING2 WILD-TYPE 369  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  ING2 MUTATED      6    0
  ING2 WILD-TYPE  369   65
   clus
vv  ING2 MUTATED ING2 WILD-TYPE
  0            6            369
  1            0             65
[1] 2 2
[1] FALSE
D765V8, binary
                cls
clus               0   1
  ING2 MUTATED     2   5
  ING2 WILD-TYPE 223 259
[1] "tbl2"
                cls
clus             [,1] [,2]
  ING2 MUTATED      2    5
  ING2 WILD-TYPE  223  259
        clus
vv       ING2 MUTATED ING2 WILD-TYPE
  FEMALE            2            223
  MALE              5            259
[1] 2 2
[1] FALSE
D765V9, binary
                cls
clus               0   1
  ING2 MUTATED     6   0
  ING2 WILD-TYPE 344  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  ING2 MUTATED      6    0
  ING2 WILD-TYPE  344   22
     clus
vv    ING2 MUTATED ING2 WILD-TYPE
  NO             6            344
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ING2 MUTATED                      5                             1
  ING2 WILD-TYPE                  310                            46
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ING2 MUTATED                       1                              0
  ING2 WILD-TYPE                   105                             10
D765V10, multiclass
                                clus
vv                               ING2 MUTATED ING2 WILD-TYPE
  COLON ADENOCARCINOMA                      5            310
  COLON MUCINOUS ADENOCARCINOMA             1             46
  RECTAL ADENOCARCINOMA                     1            105
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  ING2 MUTATED     6   0   0   0
  ING2 WILD-TYPE 339   4  31  25
D765V11, multiclass
    clus
vv   ING2 MUTATED ING2 WILD-TYPE
  R0            6            339
  R1            0              4
  R2            0             31
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D765V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ING2 MUTATED                                  0     0
  ING2 WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  ING2 MUTATED                           0     5
  ING2 WILD-TYPE                        22   221
D765V13, multiclass
                                  clus
vv                                 ING2 MUTATED ING2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       5            221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(766) Variable = DNAJC11 MUTATION ANALYSIS
D766V1, survival
                   sevent
clus2                 0   1
  DNAJC11 MUTATED    10   1
  DNAJC11 WILD-TYPE 368  92
  DNAJC11 MUTATED DNAJC11 WILD-TYPE 
               11               460 
  DNAJC11 MUTATED DNAJC11 WILD-TYPE 
                1                92 
$`DNAJC11 MUTATED`
TCGA-AA-3950 TCGA-AA-3966 TCGA-AA-A01R TCGA-AY-6197 TCGA-CM-6161 TCGA-D5-6929 
       24.00         2.01        35.01        21.44        15.02         4.80 
TCGA-F4-6570 TCGA-G4-6307 TCGA-AG-3600 TCGA-AG-A002 TCGA-AG-A02N 
        6.18        55.04         6.05        20.98        61.97 

$`DNAJC11 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
        2.01        20.98        34.03        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T 
       31.00        31.00        38.07         1.02         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6162 TCGA-CM-6163 
        5.03        15.02        15.02        17.03        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 
       14.30         9.04         9.44        11.64         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       31.96        35.74        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 
      133.18        74.56        65.85        53.62        44.68        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
        1.94        38.96        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  DNAJC11 MUTATED DNAJC11 WILD-TYPE 
             2.01              0.00 
  DNAJC11 MUTATED DNAJC11 WILD-TYPE 
            61.97            148.01 
  DNAJC11 MUTATED DNAJC11 WILD-TYPE 
           20.980            20.155 
[1] "2.0 - 62.0 (21.0)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "2"  
D766V2, continuous
D766V3, binary
                   cls
clus                  0   1
  DNAJC11 MUTATED     9   3
  DNAJC11 WILD-TYPE 357 116
[1] "tbl2"
                   cls
clus                [,1] [,2]
  DNAJC11 MUTATED      9    3
  DNAJC11 WILD-TYPE  357  116
        clus
vv       DNAJC11 MUTATED DNAJC11 WILD-TYPE
  COLON                9               357
  RECTUM               3               116
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DNAJC11 MUTATED         2        0        1         5         0         0
  DNAJC11 WILD-TYPE      89        1       31       133        10         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DNAJC11 MUTATED           1          0          1          1        1
  DNAJC11 WILD-TYPE        23         11         58         41       47
                   vv
clus                STAGE IVA STAGE IVB
  DNAJC11 MUTATED           0         0
  DNAJC11 WILD-TYPE        18         1
D766V4, multiclass
            clus
vv           DNAJC11 MUTATED DNAJC11 WILD-TYPE
  STAGE I                  2                89
  STAGE IA                 0                 1
  STAGE II                 1                31
  STAGE IIA                5               133
  STAGE IIB                0                10
  STAGE IIC                0                 1
  STAGE III                1                23
  STAGE IIIA               0                11
  STAGE IIIB               1                58
  STAGE IIIC               1                41
  STAGE IV                 1                47
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  DNAJC11 MUTATED     0   2  10   0
  DNAJC11 WILD-TYPE  17  90 319  50
D766V5, multiclass
    clus
vv   DNAJC11 MUTATED DNAJC11 WILD-TYPE
  T1               0                17
  T2               2                90
  T3              10               319
  T4               0                50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  DNAJC11 MUTATED     8   2   2
  DNAJC11 WILD-TYPE 279 111  85
D766V6, multiclass
    clus
vv   DNAJC11 MUTATED DNAJC11 WILD-TYPE
  N0               8               279
  N1               2               111
  N2               2                85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D766V7, binary
                   cls
clus                  0   1
  DNAJC11 MUTATED    10   1
  DNAJC11 WILD-TYPE 365  64
[1] "tbl2"
                   cls
clus                [,1] [,2]
  DNAJC11 MUTATED     10    1
  DNAJC11 WILD-TYPE  365   64
   clus
vv  DNAJC11 MUTATED DNAJC11 WILD-TYPE
  0              10               365
  1               1                64
[1] 2 2
[1] FALSE
D766V8, binary
                   cls
clus                  0   1
  DNAJC11 MUTATED     7   5
  DNAJC11 WILD-TYPE 218 259
[1] "tbl2"
                   cls
clus                [,1] [,2]
  DNAJC11 MUTATED      7    5
  DNAJC11 WILD-TYPE  218  259
        clus
vv       DNAJC11 MUTATED DNAJC11 WILD-TYPE
  FEMALE               7               218
  MALE                 5               259
[1] 2 2
[1] FALSE
D766V9, binary
                   cls
clus                  0   1
  DNAJC11 MUTATED     6   2
  DNAJC11 WILD-TYPE 344  20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  DNAJC11 MUTATED      6    2
  DNAJC11 WILD-TYPE  344   20
     clus
vv    DNAJC11 MUTATED DNAJC11 WILD-TYPE
  NO                6               344
  YES               2                20
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  DNAJC11 MUTATED                      6                             3
  DNAJC11 WILD-TYPE                  309                            44
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  DNAJC11 MUTATED                       3                              0
  DNAJC11 WILD-TYPE                   103                             10
D766V10, multiclass
                                clus
vv                               DNAJC11 MUTATED DNAJC11 WILD-TYPE
  COLON ADENOCARCINOMA                         6               309
  COLON MUCINOUS ADENOCARCINOMA                3                44
  RECTAL ADENOCARCINOMA                        3               103
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  DNAJC11 MUTATED    11   0   0   0
  DNAJC11 WILD-TYPE 334   4  31  25
D766V11, multiclass
    clus
vv   DNAJC11 MUTATED DNAJC11 WILD-TYPE
  R0              11               334
  R1               0                 4
  R2               0                31
  RX               0                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D766V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DNAJC11 MUTATED                                  0     0
  DNAJC11 WILD-TYPE                                1    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  DNAJC11 MUTATED                           0     5
  DNAJC11 WILD-TYPE                        22   221
D766V13, multiclass
                                  clus
vv                                 DNAJC11 MUTATED DNAJC11 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                      0                22
  WHITE                                          5               221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(767) Variable = CORO1C MUTATION ANALYSIS
D767V1, survival
                  sevent
clus2                0   1
  CORO1C MUTATED     8   0
  CORO1C WILD-TYPE 370  93
  CORO1C MUTATED CORO1C WILD-TYPE 
               8              463 
  CORO1C MUTATED CORO1C WILD-TYPE 
               0               93 
$`CORO1C MUTATED`
TCGA-AU-3779 TCGA-CA-6717 TCGA-CK-5913 TCGA-CM-5860 TCGA-D5-6540 TCGA-G4-6309 
       14.50        12.76        51.32        32.02        16.14        85.48 
TCGA-AG-3731 TCGA-CL-5917 
       37.02        78.12 

$`CORO1C WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        10.88         0.20        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07        12.20        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       85.45        15.62        49.08         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5861 
       13.02        29.06        22.03        22.98        30.08        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       12.49        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       44.68        55.04        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3732 TCGA-AG-3742 
       13.94        19.99         7.99         0.99        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  CORO1C MUTATED CORO1C WILD-TYPE 
           12.76             0.00 
  CORO1C MUTATED CORO1C WILD-TYPE 
           85.48           148.01 
  CORO1C MUTATED CORO1C WILD-TYPE 
           34.52            20.12 
[1] "12.8 - 85.5 (34.5)" "0.0 - 148.0 (20.1)"
[1] "hr="     "9400000"
D767V2, continuous
D767V3, binary
                  cls
clus                 0   1
  CORO1C MUTATED     6   2
  CORO1C WILD-TYPE 360 117
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CORO1C MUTATED      6    2
  CORO1C WILD-TYPE  360  117
        clus
vv       CORO1C MUTATED CORO1C WILD-TYPE
  COLON               6              360
  RECTUM              2              117
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CORO1C MUTATED         1        0        0         4         0         0
  CORO1C WILD-TYPE      90        1       32       134        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CORO1C MUTATED           0          0          1          1        1
  CORO1C WILD-TYPE        24         11         58         41       47
                  vv
clus               STAGE IVA STAGE IVB
  CORO1C MUTATED           0         0
  CORO1C WILD-TYPE        18         1
D767V4, multiclass
            clus
vv           CORO1C MUTATED CORO1C WILD-TYPE
  STAGE I                 1               90
  STAGE IA                0                1
  STAGE II                0               32
  STAGE IIA               4              134
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              1               58
  STAGE IIIC              1               41
  STAGE IV                1               47
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  CORO1C MUTATED     0   1   7   0
  CORO1C WILD-TYPE  17  91 322  50
D767V5, multiclass
    clus
vv   CORO1C MUTATED CORO1C WILD-TYPE
  T1              0               17
  T2              1               91
  T3              7              322
  T4              0               50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  CORO1C MUTATED     5   2   1
  CORO1C WILD-TYPE 282 111  86
D767V6, multiclass
    clus
vv   CORO1C MUTATED CORO1C WILD-TYPE
  N0              5              282
  N1              2              111
  N2              1               86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D767V7, binary
                  cls
clus                 0   1
  CORO1C MUTATED     5   1
  CORO1C WILD-TYPE 370  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CORO1C MUTATED      5    1
  CORO1C WILD-TYPE  370   64
   clus
vv  CORO1C MUTATED CORO1C WILD-TYPE
  0              5              370
  1              1               64
[1] 2 2
[1] FALSE
D767V8, binary
                  cls
clus                 0   1
  CORO1C MUTATED     4   4
  CORO1C WILD-TYPE 221 260
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CORO1C MUTATED      4    4
  CORO1C WILD-TYPE  221  260
        clus
vv       CORO1C MUTATED CORO1C WILD-TYPE
  FEMALE              4              221
  MALE                4              260
[1] 2 2
[1] FALSE
D767V9, binary
                  cls
clus                 0   1
  CORO1C MUTATED     8   0
  CORO1C WILD-TYPE 342  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CORO1C MUTATED      8    0
  CORO1C WILD-TYPE  342   22
     clus
vv    CORO1C MUTATED CORO1C WILD-TYPE
  NO               8              342
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CORO1C MUTATED                      4                             2
  CORO1C WILD-TYPE                  311                            45
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CORO1C MUTATED                       2                              0
  CORO1C WILD-TYPE                   104                             10
D767V10, multiclass
                                clus
vv                               CORO1C MUTATED CORO1C WILD-TYPE
  COLON ADENOCARCINOMA                        4              311
  COLON MUCINOUS ADENOCARCINOMA               2               45
  RECTAL ADENOCARCINOMA                       2              104
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  CORO1C MUTATED     4   0   1   3
  CORO1C WILD-TYPE 341   4  30  22
D767V11, multiclass
    clus
vv   CORO1C MUTATED CORO1C WILD-TYPE
  R0              4              341
  R1              0                4
  R2              1               30
  RX              3               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D767V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CORO1C MUTATED                                  0     1
  CORO1C WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  CORO1C MUTATED                           1     5
  CORO1C WILD-TYPE                        21   221
D767V13, multiclass
                                  clus
vv                                 CORO1C MUTATED CORO1C WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                         5              221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(768) Variable = ATP6V1D MUTATION ANALYSIS
D768V1, survival
                   sevent
clus2                 0   1
  ATP6V1D MUTATED     5   1
  ATP6V1D WILD-TYPE 373  92
  ATP6V1D MUTATED ATP6V1D WILD-TYPE 
                6               465 
  ATP6V1D MUTATED ATP6V1D WILD-TYPE 
                1                92 
$`ATP6V1D MUTATED`
TCGA-A6-5660 TCGA-AA-3713 TCGA-AZ-6600 TCGA-CK-5914 TCGA-CM-6164 TCGA-F4-6856 
       29.19        19.04        12.10         9.99        29.03        35.31 

$`ATP6V1D WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        49.08        51.32        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
        2.96        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       47.41       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  ATP6V1D MUTATED ATP6V1D WILD-TYPE 
             9.99              0.00 
  ATP6V1D MUTATED ATP6V1D WILD-TYPE 
            35.31            148.01 
  ATP6V1D MUTATED ATP6V1D WILD-TYPE 
           24.035            20.190 
[1] "10.0 - 35.3 (24.0)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.1"
D768V2, continuous
D768V3, binary
                   cls
clus                  0   1
  ATP6V1D MUTATED     6   0
  ATP6V1D WILD-TYPE 360 119
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ATP6V1D MUTATED      6    0
  ATP6V1D WILD-TYPE  360  119
        clus
vv       ATP6V1D MUTATED ATP6V1D WILD-TYPE
  COLON                6               360
  RECTUM               0               119
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ATP6V1D MUTATED         1        0        0         1         0         0
  ATP6V1D WILD-TYPE      90        1       32       137        10         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ATP6V1D MUTATED           0          0          1          1        2
  ATP6V1D WILD-TYPE        24         11         58         41       46
                   vv
clus                STAGE IVA STAGE IVB
  ATP6V1D MUTATED           0         0
  ATP6V1D WILD-TYPE        18         1
D768V4, multiclass
            clus
vv           ATP6V1D MUTATED ATP6V1D WILD-TYPE
  STAGE I                  1                90
  STAGE IA                 0                 1
  STAGE II                 0                32
  STAGE IIA                1               137
  STAGE IIB                0                10
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               0                11
  STAGE IIIB               1                58
  STAGE IIIC               1                41
  STAGE IV                 2                46
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  ATP6V1D MUTATED     0   1   4   1
  ATP6V1D WILD-TYPE  17  91 325  49
D768V5, multiclass
    clus
vv   ATP6V1D MUTATED ATP6V1D WILD-TYPE
  T1               0                17
  T2               1                91
  T3               4               325
  T4               1                49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  ATP6V1D MUTATED     3   2   1
  ATP6V1D WILD-TYPE 284 111  86
D768V6, multiclass
    clus
vv   ATP6V1D MUTATED ATP6V1D WILD-TYPE
  N0               3               284
  N1               2               111
  N2               1                86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D768V7, binary
                   cls
clus                  0   1
  ATP6V1D MUTATED     3   2
  ATP6V1D WILD-TYPE 372  63
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ATP6V1D MUTATED      3    2
  ATP6V1D WILD-TYPE  372   63
   clus
vv  ATP6V1D MUTATED ATP6V1D WILD-TYPE
  0               3               372
  1               2                63
[1] 2 2
[1] FALSE
D768V8, binary
                   cls
clus                  0   1
  ATP6V1D MUTATED     1   5
  ATP6V1D WILD-TYPE 224 259
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ATP6V1D MUTATED      1    5
  ATP6V1D WILD-TYPE  224  259
        clus
vv       ATP6V1D MUTATED ATP6V1D WILD-TYPE
  FEMALE               1               224
  MALE                 5               259
[1] 2 2
[1] FALSE
D768V9, binary
                   cls
clus                  0   1
  ATP6V1D MUTATED     3   1
  ATP6V1D WILD-TYPE 347  21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ATP6V1D MUTATED      3    1
  ATP6V1D WILD-TYPE  347   21
     clus
vv    ATP6V1D MUTATED ATP6V1D WILD-TYPE
  NO                3               347
  YES               1                21
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ATP6V1D MUTATED                      5                             1
  ATP6V1D WILD-TYPE                  310                            46
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ATP6V1D MUTATED                       0                              0
  ATP6V1D WILD-TYPE                   106                             10
D768V10, multiclass
                                clus
vv                               ATP6V1D MUTATED ATP6V1D WILD-TYPE
  COLON ADENOCARCINOMA                         5               310
  COLON MUCINOUS ADENOCARCINOMA                1                46
  RECTAL ADENOCARCINOMA                        0               106
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  ATP6V1D MUTATED     2   0   1   1
  ATP6V1D WILD-TYPE 343   4  30  24
D768V11, multiclass
    clus
vv   ATP6V1D MUTATED ATP6V1D WILD-TYPE
  R0               2               343
  R1               0                 4
  R2               1                30
  RX               1                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D768V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ATP6V1D MUTATED                                  0     0
  ATP6V1D WILD-TYPE                                1    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  ATP6V1D MUTATED                           2     3
  ATP6V1D WILD-TYPE                        20   223
D768V13, multiclass
                                  clus
vv                                 ATP6V1D MUTATED ATP6V1D WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                      2                20
  WHITE                                          3               223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(769) Variable = WNK3 MUTATION ANALYSIS
D769V1, survival
                sevent
clus2              0   1
  WNK3 MUTATED    27   3
  WNK3 WILD-TYPE 351  90
  WNK3 MUTATED WNK3 WILD-TYPE 
            30            441 
  WNK3 MUTATED WNK3 WILD-TYPE 
             3             90 
$`WNK3 MUTATED`
TCGA-A6-5657 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6781 TCGA-AA-3555 TCGA-AA-3660 
       31.63        22.06        32.71        19.66        29.95        78.08 
TCGA-AA-3663 TCGA-AA-3667 TCGA-AA-3710 TCGA-AA-3875 TCGA-AA-A00J TCGA-AA-A00N 
        6.97        14.01        26.99        18.05        18.05         4.01 
TCGA-AD-6895 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-CA-6717 TCGA-CM-6168 TCGA-D5-6928 
        0.72        58.39        49.41        12.76        12.99        11.64 
TCGA-F4-6807 TCGA-F4-6856 TCGA-G4-6309 TCGA-G4-6310 TCGA-AF-2689 TCGA-AG-3731 
       16.24        35.31        85.48        63.62        39.48        37.02 
TCGA-AG-3732 TCGA-AG-3892 TCGA-AG-A002 TCGA-AG-A00C TCGA-DC-6155 TCGA-F5-6813 
       32.98        13.02        20.98         6.02        13.97         0.69 

$`WNK3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       27.09        22.52         8.38        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 
       21.76        24.69        24.39        23.87        20.12        20.28 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
        7.04         3.02         1.02        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
        6.05        54.02         2.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       27.02        29.98        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       34.03        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       21.37        15.52        56.55         0.79         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        33.01        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 
      106.75        22.36        62.79        88.21         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6169 
        2.96        29.03        16.04        21.99        14.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
       14.30         9.04         9.44         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 
       41.42        33.67        13.25         0.53        47.41       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6315 
       74.56        65.85        53.62        44.68        55.04        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       46.75        79.69        24.13        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3742 
       19.99        13.94        19.99         7.99         0.99         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       17.03        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
       13.94        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
        5.03        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-G5-6235 TCGA-G5-6641 
        0.66        55.76        26.43 

  WNK3 MUTATED WNK3 WILD-TYPE 
          0.69           0.00 
  WNK3 MUTATED WNK3 WILD-TYPE 
         85.48         148.01 
  WNK3 MUTATED WNK3 WILD-TYPE 
         20.32          20.19 
[1] "0.7 - 85.5 (20.3)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "2.1"
D769V2, continuous
D769V3, binary
                cls
clus               0   1
  WNK3 MUTATED    24   8
  WNK3 WILD-TYPE 342 111
[1] "tbl2"
                cls
clus             [,1] [,2]
  WNK3 MUTATED     24    8
  WNK3 WILD-TYPE  342  111
        clus
vv       WNK3 MUTATED WNK3 WILD-TYPE
  COLON            24            342
  RECTUM            8            111
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  WNK3 MUTATED         6        0        3         8         1         1
  WNK3 WILD-TYPE      85        1       29       130         9         0
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  WNK3 MUTATED           0          1          5          3        3         0
  WNK3 WILD-TYPE        24         10         54         39       45        18
                vv
clus             STAGE IVB
  WNK3 MUTATED           0
  WNK3 WILD-TYPE         1
D769V4, multiclass
            clus
vv           WNK3 MUTATED WNK3 WILD-TYPE
  STAGE I               6             85
  STAGE IA              0              1
  STAGE II              3             29
  STAGE IIA             8            130
  STAGE IIB             1              9
  STAGE IIC             1              0
  STAGE III             0             24
  STAGE IIIA            1             10
  STAGE IIIB            5             54
  STAGE IIIC            3             39
  STAGE IV              3             45
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  WNK3 MUTATED     2   5  19   6
  WNK3 WILD-TYPE  15  87 310  44
D769V5, multiclass
    clus
vv   WNK3 MUTATED WNK3 WILD-TYPE
  T1            2             15
  T2            5             87
  T3           19            310
  T4            6             44
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  WNK3 MUTATED    19  10   3
  WNK3 WILD-TYPE 268 103  84
D769V6, multiclass
    clus
vv   WNK3 MUTATED WNK3 WILD-TYPE
  N0           19            268
  N1           10            103
  N2            3             84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D769V7, binary
                cls
clus               0   1
  WNK3 MUTATED    26   3
  WNK3 WILD-TYPE 349  62
[1] "tbl2"
                cls
clus             [,1] [,2]
  WNK3 MUTATED     26    3
  WNK3 WILD-TYPE  349   62
   clus
vv  WNK3 MUTATED WNK3 WILD-TYPE
  0           26            349
  1            3             62
[1] 2 2
[1] FALSE
D769V8, binary
                cls
clus               0   1
  WNK3 MUTATED    17  15
  WNK3 WILD-TYPE 208 249
[1] "tbl2"
                cls
clus             [,1] [,2]
  WNK3 MUTATED     17   15
  WNK3 WILD-TYPE  208  249
        clus
vv       WNK3 MUTATED WNK3 WILD-TYPE
  FEMALE           17            208
  MALE             15            249
[1] 2 2
[1] FALSE
D769V9, binary
                cls
clus               0   1
  WNK3 MUTATED    25   2
  WNK3 WILD-TYPE 325  20
[1] "tbl2"
                cls
clus             [,1] [,2]
  WNK3 MUTATED     25    2
  WNK3 WILD-TYPE  325   20
     clus
vv    WNK3 MUTATED WNK3 WILD-TYPE
  NO            25            325
  YES            2             20
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  WNK3 MUTATED                     17                             7
  WNK3 WILD-TYPE                  298                            40
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  WNK3 MUTATED                       8                              0
  WNK3 WILD-TYPE                    98                             10
D769V10, multiclass
                                clus
vv                               WNK3 MUTATED WNK3 WILD-TYPE
  COLON ADENOCARCINOMA                     17            298
  COLON MUCINOUS ADENOCARCINOMA             7             40
  RECTAL ADENOCARCINOMA                     8             98
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  WNK3 MUTATED    26   0   2   1
  WNK3 WILD-TYPE 319   4  29  24
D769V11, multiclass
    clus
vv   WNK3 MUTATED WNK3 WILD-TYPE
  R0           26            319
  R1            0              4
  R2            2             29
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D769V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  WNK3 MUTATED                                  0     1
  WNK3 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  WNK3 MUTATED                           3    13
  WNK3 WILD-TYPE                        19   213
D769V13, multiclass
                                  clus
vv                                 WNK3 MUTATED WNK3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   3             19
  WHITE                                      13            213
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(770) Variable = C1ORF168 MUTATION ANALYSIS
D770V1, survival
                    sevent
clus2                  0   1
  C1ORF168 MUTATED    12   4
  C1ORF168 WILD-TYPE 366  89
  C1ORF168 MUTATED C1ORF168 WILD-TYPE 
                16                455 
  C1ORF168 MUTATED C1ORF168 WILD-TYPE 
                 4                 89 
$`C1ORF168 MUTATED`
TCGA-A6-6137 TCGA-AA-3710 TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A010 TCGA-AZ-5407 
       27.09        26.99        25.02         4.01        34.98        88.21 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-5916 TCGA-CM-4746 TCGA-D5-6923 TCGA-DM-A28H 
       12.76        10.06        21.14        37.02        12.43       117.07 
TCGA-F4-6570 TCGA-G4-6304 TCGA-AF-2693 TCGA-AG-A002 
        6.18        53.62        19.10        20.98 

$`C1ORF168 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        22.06        32.71        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        85.05        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        3.29         0.07        12.20        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 
       85.45        15.62        49.08        51.32         9.99        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4752 
        1.91       124.27        23.05        20.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28K TCGA-F4-6459 
       81.37       119.93        35.97        60.79        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       31.96        35.74        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
      133.18        74.56        65.85        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       43.04        13.55        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  C1ORF168 MUTATED C1ORF168 WILD-TYPE 
              4.01               0.00 
  C1ORF168 MUTATED C1ORF168 WILD-TYPE 
            117.07             148.01 
  C1ORF168 MUTATED C1ORF168 WILD-TYPE 
             23.08              20.05 
[1] "4.0 - 117.1 (23.1)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.1"
D770V2, continuous
D770V3, binary
                    cls
clus                   0   1
  C1ORF168 MUTATED    14   1
  C1ORF168 WILD-TYPE 352 118
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C1ORF168 MUTATED     14    1
  C1ORF168 WILD-TYPE  352  118
        clus
vv       C1ORF168 MUTATED C1ORF168 WILD-TYPE
  COLON                14                352
  RECTUM                1                118
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  C1ORF168 MUTATED         6        0        0         4         3         0
  C1ORF168 WILD-TYPE      85        1       32       134         7         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C1ORF168 MUTATED           0          0          1          1        0
  C1ORF168 WILD-TYPE        24         11         58         41       48
                    vv
clus                 STAGE IVA STAGE IVB
  C1ORF168 MUTATED           0         0
  C1ORF168 WILD-TYPE        18         1
D770V4, multiclass
            clus
vv           C1ORF168 MUTATED C1ORF168 WILD-TYPE
  STAGE I                   6                 85
  STAGE IA                  0                  1
  STAGE II                  0                 32
  STAGE IIA                 4                134
  STAGE IIB                 3                  7
  STAGE IIC                 0                  1
  STAGE III                 0                 24
  STAGE IIIA                0                 11
  STAGE IIIB                1                 58
  STAGE IIIC                1                 41
  STAGE IV                  0                 48
  STAGE IVA                 0                 18
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  C1ORF168 MUTATED     2   5   6   3
  C1ORF168 WILD-TYPE  15  87 323  47
D770V5, multiclass
    clus
vv   C1ORF168 MUTATED C1ORF168 WILD-TYPE
  T1                2                 15
  T2                5                 87
  T3                6                323
  T4                3                 47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  C1ORF168 MUTATED    14   1   1
  C1ORF168 WILD-TYPE 273 112  86
D770V6, multiclass
    clus
vv   C1ORF168 MUTATED C1ORF168 WILD-TYPE
  N0               14                273
  N1                1                112
  N2                1                 86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D770V7, binary
                    cls
clus                   0   1
  C1ORF168 MUTATED    14   0
  C1ORF168 WILD-TYPE 361  65
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C1ORF168 MUTATED     14    0
  C1ORF168 WILD-TYPE  361   65
   clus
vv  C1ORF168 MUTATED C1ORF168 WILD-TYPE
  0               14                361
  1                0                 65
[1] 2 2
[1] FALSE
D770V8, binary
                    cls
clus                   0   1
  C1ORF168 MUTATED     6  10
  C1ORF168 WILD-TYPE 219 254
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C1ORF168 MUTATED      6   10
  C1ORF168 WILD-TYPE  219  254
        clus
vv       C1ORF168 MUTATED C1ORF168 WILD-TYPE
  FEMALE                6                219
  MALE                 10                254
[1] 2 2
[1] FALSE
D770V9, binary
                    cls
clus                   0   1
  C1ORF168 MUTATED    14   0
  C1ORF168 WILD-TYPE 336  22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C1ORF168 MUTATED     14    0
  C1ORF168 WILD-TYPE  336   22
     clus
vv    C1ORF168 MUTATED C1ORF168 WILD-TYPE
  NO                14                336
  YES                0                 22
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  C1ORF168 MUTATED                     12                             2
  C1ORF168 WILD-TYPE                  303                            45
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  C1ORF168 MUTATED                       1                              0
  C1ORF168 WILD-TYPE                   105                             10
D770V10, multiclass
                                clus
vv                               C1ORF168 MUTATED C1ORF168 WILD-TYPE
  COLON ADENOCARCINOMA                         12                303
  COLON MUCINOUS ADENOCARCINOMA                 2                 45
  RECTAL ADENOCARCINOMA                         1                105
  RECTAL MUCINOUS ADENOCARCINOMA                0                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  C1ORF168 MUTATED     8   0   0   3
  C1ORF168 WILD-TYPE 337   4  31  22
D770V11, multiclass
    clus
vv   C1ORF168 MUTATED C1ORF168 WILD-TYPE
  R0                8                337
  R1                0                  4
  R2                0                 31
  RX                3                 22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D770V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C1ORF168 MUTATED                                  0     2
  C1ORF168 WILD-TYPE                                1     9
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  C1ORF168 MUTATED                           1     8
  C1ORF168 WILD-TYPE                        21   218
D770V13, multiclass
                                  clus
vv                                 C1ORF168 MUTATED C1ORF168 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           2                  9
  BLACK OR AFRICAN AMERICAN                       1                 21
  WHITE                                           8                218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(771) Variable = VANGL1 MUTATION ANALYSIS
D771V1, survival
                  sevent
clus2                0   1
  VANGL1 MUTATED     8   4
  VANGL1 WILD-TYPE 370  89
  VANGL1 MUTATED VANGL1 WILD-TYPE 
              12              459 
  VANGL1 MUTATED VANGL1 WILD-TYPE 
               4               89 
$`VANGL1 MUTATED`
TCGA-AA-3715 TCGA-AA-A00J TCGA-AZ-6600 TCGA-AZ-6601 TCGA-CM-4746 TCGA-CM-4752 
       19.04        18.05        12.10       100.01        37.02        13.02 
TCGA-D5-6535 TCGA-DM-A28H TCGA-G4-6588 TCGA-AF-5654 TCGA-AG-3731 TCGA-F5-6465 
       15.12       117.07        26.17        16.83        37.02        49.51 

$`VANGL1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L 
       38.04        19.00        30.02        34.03        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-5341 TCGA-CM-5344 
      124.27        23.05        20.02        25.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       35.97        60.79        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-6136 
       13.55        19.10        34.49        10.39        14.50        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
       18.28         9.96        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  VANGL1 MUTATED VANGL1 WILD-TYPE 
            12.1              0.0 
  VANGL1 MUTATED VANGL1 WILD-TYPE 
          117.07           148.01 
  VANGL1 MUTATED VANGL1 WILD-TYPE 
          22.605           20.190 
[1] "12.1 - 117.1 (22.6)" "0.0 - 148.0 (20.2)" 
[1] "hr=" "1.2"
D771V2, continuous
D771V3, binary
                  cls
clus                 0   1
  VANGL1 MUTATED    10   3
  VANGL1 WILD-TYPE 356 116
[1] "tbl2"
                  cls
clus               [,1] [,2]
  VANGL1 MUTATED     10    3
  VANGL1 WILD-TYPE  356  116
        clus
vv       VANGL1 MUTATED VANGL1 WILD-TYPE
  COLON              10              356
  RECTUM              3              116
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  VANGL1 MUTATED         2        0        2         3         0         0
  VANGL1 WILD-TYPE      89        1       30       135        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  VANGL1 MUTATED           1          0          2          1        2
  VANGL1 WILD-TYPE        23         11         57         41       46
                  vv
clus               STAGE IVA STAGE IVB
  VANGL1 MUTATED           0         0
  VANGL1 WILD-TYPE        18         1
D771V4, multiclass
            clus
vv           VANGL1 MUTATED VANGL1 WILD-TYPE
  STAGE I                 2               89
  STAGE IA                0                1
  STAGE II                2               30
  STAGE IIA               3              135
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               1               23
  STAGE IIIA              0               11
  STAGE IIIB              2               57
  STAGE IIIC              1               41
  STAGE IV                2               46
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  VANGL1 MUTATED     0   2   9   2
  VANGL1 WILD-TYPE  17  90 320  48
D771V5, multiclass
    clus
vv   VANGL1 MUTATED VANGL1 WILD-TYPE
  T1              0               17
  T2              2               90
  T3              9              320
  T4              2               48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  VANGL1 MUTATED     7   4   2
  VANGL1 WILD-TYPE 280 109  85
D771V6, multiclass
    clus
vv   VANGL1 MUTATED VANGL1 WILD-TYPE
  N0              7              280
  N1              4              109
  N2              2               85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D771V7, binary
                  cls
clus                 0   1
  VANGL1 MUTATED    10   2
  VANGL1 WILD-TYPE 365  63
[1] "tbl2"
                  cls
clus               [,1] [,2]
  VANGL1 MUTATED     10    2
  VANGL1 WILD-TYPE  365   63
   clus
vv  VANGL1 MUTATED VANGL1 WILD-TYPE
  0             10              365
  1              2               63
[1] 2 2
[1] FALSE
D771V8, binary
                  cls
clus                 0   1
  VANGL1 MUTATED     4   9
  VANGL1 WILD-TYPE 221 255
[1] "tbl2"
                  cls
clus               [,1] [,2]
  VANGL1 MUTATED      4    9
  VANGL1 WILD-TYPE  221  255
        clus
vv       VANGL1 MUTATED VANGL1 WILD-TYPE
  FEMALE              4              221
  MALE                9              255
[1] 2 2
[1] FALSE
D771V9, binary
                  cls
clus                 0   1
  VANGL1 MUTATED    10   0
  VANGL1 WILD-TYPE 340  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  VANGL1 MUTATED     10    0
  VANGL1 WILD-TYPE  340   22
     clus
vv    VANGL1 MUTATED VANGL1 WILD-TYPE
  NO              10              340
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  VANGL1 MUTATED                      9                             1
  VANGL1 WILD-TYPE                  306                            46
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  VANGL1 MUTATED                       3                              0
  VANGL1 WILD-TYPE                   103                             10
D771V10, multiclass
                                clus
vv                               VANGL1 MUTATED VANGL1 WILD-TYPE
  COLON ADENOCARCINOMA                        9              306
  COLON MUCINOUS ADENOCARCINOMA               1               46
  RECTAL ADENOCARCINOMA                       3              103
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  VANGL1 MUTATED     8   0   1   1
  VANGL1 WILD-TYPE 337   4  30  24
D771V11, multiclass
    clus
vv   VANGL1 MUTATED VANGL1 WILD-TYPE
  R0              8              337
  R1              0                4
  R2              1               30
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D771V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  VANGL1 MUTATED                                  0     0
  VANGL1 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  VANGL1 MUTATED                           3     6
  VANGL1 WILD-TYPE                        19   220
D771V13, multiclass
                                  clus
vv                                 VANGL1 MUTATED VANGL1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     3               19
  WHITE                                         6              220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(772) Variable = SPANXC MUTATION ANALYSIS
D772V1, survival
                  sevent
clus2                0   1
  SPANXC MUTATED     3   0
  SPANXC WILD-TYPE 375  93
  SPANXC MUTATED SPANXC WILD-TYPE 
               3              468 
  SPANXC MUTATED SPANXC WILD-TYPE 
               0               93 
$`SPANXC MUTATED`
TCGA-A6-5661 TCGA-A6-6653 TCGA-CK-5913 
       33.53        24.39        51.32 

$`SPANXC WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 
       25.18        24.16        21.76        24.69        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       85.45        15.62        49.08         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  SPANXC MUTATED SPANXC WILD-TYPE 
           24.39             0.00 
  SPANXC MUTATED SPANXC WILD-TYPE 
           51.32           148.01 
  SPANXC MUTATED SPANXC WILD-TYPE 
          33.530           20.085 
[1] "24.4 - 51.3 (33.5)" "0.0 - 148.0 (20.1)"
[1] "hr="     "3300000"
D772V2, continuous
D772V3, binary
                  cls
clus                 0   1
  SPANXC MUTATED     4   0
  SPANXC WILD-TYPE 362 119
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SPANXC MUTATED      4    0
  SPANXC WILD-TYPE  362  119
        clus
vv       SPANXC MUTATED SPANXC WILD-TYPE
  COLON               4              362
  RECTUM              0              119
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SPANXC MUTATED         1        0        0         2         0         0
  SPANXC WILD-TYPE      90        1       32       136        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SPANXC MUTATED           0          0          0          0        1
  SPANXC WILD-TYPE        24         11         59         42       47
                  vv
clus               STAGE IVA STAGE IVB
  SPANXC MUTATED           0         0
  SPANXC WILD-TYPE        18         1
D772V4, multiclass
            clus
vv           SPANXC MUTATED SPANXC WILD-TYPE
  STAGE I                 1               90
  STAGE IA                0                1
  STAGE II                0               32
  STAGE IIA               2              136
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              0               59
  STAGE IIIC              0               42
  STAGE IV                1               47
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  SPANXC MUTATED     0   1   2   1
  SPANXC WILD-TYPE  17  91 327  49
D772V5, multiclass
    clus
vv   SPANXC MUTATED SPANXC WILD-TYPE
  T1              0               17
  T2              1               91
  T3              2              327
  T4              1               49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  SPANXC MUTATED     3   0   1
  SPANXC WILD-TYPE 284 113  86
D772V6, multiclass
    clus
vv   SPANXC MUTATED SPANXC WILD-TYPE
  N0              3              284
  N1              0              113
  N2              1               86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D772V7, binary
                  cls
clus                 0   1
  SPANXC MUTATED     2   1
  SPANXC WILD-TYPE 373  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SPANXC MUTATED      2    1
  SPANXC WILD-TYPE  373   64
   clus
vv  SPANXC MUTATED SPANXC WILD-TYPE
  0              2              373
  1              1               64
[1] 2 2
[1] FALSE
D772V8, binary
                  cls
clus                 0   1
  SPANXC MUTATED     2   2
  SPANXC WILD-TYPE 223 262
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SPANXC MUTATED      2    2
  SPANXC WILD-TYPE  223  262
        clus
vv       SPANXC MUTATED SPANXC WILD-TYPE
  FEMALE              2              223
  MALE                2              262
[1] 2 2
[1] FALSE
D772V9, binary
                  cls
clus                 0   1
  SPANXC MUTATED     3   0
  SPANXC WILD-TYPE 347  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SPANXC MUTATED      3    0
  SPANXC WILD-TYPE  347   22
     clus
vv    SPANXC MUTATED SPANXC WILD-TYPE
  NO               3              347
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SPANXC MUTATED                      4                             0
  SPANXC WILD-TYPE                  311                            47
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SPANXC MUTATED                       0                              0
  SPANXC WILD-TYPE                   106                             10
D772V10, multiclass
                                clus
vv                               SPANXC MUTATED SPANXC WILD-TYPE
  COLON ADENOCARCINOMA                        4              311
  COLON MUCINOUS ADENOCARCINOMA               0               47
  RECTAL ADENOCARCINOMA                       0              106
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  SPANXC MUTATED     1   0   1   1
  SPANXC WILD-TYPE 344   4  30  24
D772V11, multiclass
    clus
vv   SPANXC MUTATED SPANXC WILD-TYPE
  R0              1              344
  R1              0                4
  R2              1               30
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D772V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SPANXC MUTATED                                  0     0
  SPANXC WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  SPANXC MUTATED                           1     2
  SPANXC WILD-TYPE                        21   224
D772V13, multiclass
                                  clus
vv                                 SPANXC MUTATED SPANXC WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                         2              224
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(773) Variable = KLKB1 MUTATION ANALYSIS
D773V1, survival
                 sevent
clus2               0   1
  KLKB1 MUTATED    13   2
  KLKB1 WILD-TYPE 365  91
  KLKB1 MUTATED KLKB1 WILD-TYPE 
             15             456 
  KLKB1 MUTATED KLKB1 WILD-TYPE 
              2              91 
$`KLKB1 MUTATED`
TCGA-A6-2676 TCGA-A6-5661 TCGA-A6-5665 TCGA-AA-3525 TCGA-AA-3950 TCGA-AA-A00J 
       42.90        33.53        22.06         8.05        24.00        18.05 
TCGA-AA-A00N TCGA-AD-5900 TCGA-CA-6715 TCGA-CM-4743 TCGA-CM-6171 TCGA-D5-6927 
        4.01         0.07         0.07        23.05        14.04         9.44 
TCGA-G4-6588 TCGA-AG-A002 TCGA-DC-6682 
       26.17        20.98         4.01 

$`KLKB1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 
       31.63        30.44        29.19        23.61        22.09        32.71 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       27.09        22.52         8.38        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       24.03        37.05        36.03        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       33.01        26.01         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 
       41.00        39.98        18.05        40.96        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6716 
        1.61        12.69         3.06         3.25         3.29        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
        1.91       124.27        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       13.02        15.02        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
       14.30         9.04        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       13.78        35.80        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
       19.99         5.95         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  KLKB1 MUTATED KLKB1 WILD-TYPE 
           0.07            0.00 
  KLKB1 MUTATED KLKB1 WILD-TYPE 
          42.90          148.01 
  KLKB1 MUTATED KLKB1 WILD-TYPE 
         18.050          20.235 
[1] "0.1 - 42.9 (18.1)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.1"
D773V2, continuous
D773V3, binary
                 cls
clus                0   1
  KLKB1 MUTATED    13   2
  KLKB1 WILD-TYPE 353 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLKB1 MUTATED     13    2
  KLKB1 WILD-TYPE  353  117
        clus
vv       KLKB1 MUTATED KLKB1 WILD-TYPE
  COLON             13             353
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KLKB1 MUTATED         3        0        0         7         2         0
  KLKB1 WILD-TYPE      88        1       32       131         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  KLKB1 MUTATED           0          0          3          0        0         0
  KLKB1 WILD-TYPE        24         11         56         42       48        18
                 vv
clus              STAGE IVB
  KLKB1 MUTATED           0
  KLKB1 WILD-TYPE         1
D773V4, multiclass
            clus
vv           KLKB1 MUTATED KLKB1 WILD-TYPE
  STAGE I                3              88
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              7             131
  STAGE IIB              2               8
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             3              56
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  KLKB1 MUTATED     0   3   9   3
  KLKB1 WILD-TYPE  17  89 320  47
D773V5, multiclass
    clus
vv   KLKB1 MUTATED KLKB1 WILD-TYPE
  T1             0              17
  T2             3              89
  T3             9             320
  T4             3              47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  KLKB1 MUTATED    12   3   0
  KLKB1 WILD-TYPE 275 110  87
D773V6, multiclass
    clus
vv   KLKB1 MUTATED KLKB1 WILD-TYPE
  N0            12             275
  N1             3             110
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D773V7, binary
                 cls
clus                0   1
  KLKB1 MUTATED    14   0
  KLKB1 WILD-TYPE 361  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLKB1 MUTATED     14    0
  KLKB1 WILD-TYPE  361   65
   clus
vv  KLKB1 MUTATED KLKB1 WILD-TYPE
  0            14             361
  1             0              65
[1] 2 2
[1] FALSE
D773V8, binary
                 cls
clus                0   1
  KLKB1 MUTATED     6   9
  KLKB1 WILD-TYPE 219 255
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLKB1 MUTATED      6    9
  KLKB1 WILD-TYPE  219  255
        clus
vv       KLKB1 MUTATED KLKB1 WILD-TYPE
  FEMALE             6             219
  MALE               9             255
[1] 2 2
[1] FALSE
D773V9, binary
                 cls
clus                0   1
  KLKB1 MUTATED    11   0
  KLKB1 WILD-TYPE 339  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLKB1 MUTATED     11    0
  KLKB1 WILD-TYPE  339   22
     clus
vv    KLKB1 MUTATED KLKB1 WILD-TYPE
  NO             11             339
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  KLKB1 MUTATED                      9                             4
  KLKB1 WILD-TYPE                  306                            43
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  KLKB1 MUTATED                       2                              0
  KLKB1 WILD-TYPE                   104                             10
D773V10, multiclass
                                clus
vv                               KLKB1 MUTATED KLKB1 WILD-TYPE
  COLON ADENOCARCINOMA                       9             306
  COLON MUCINOUS ADENOCARCINOMA              4              43
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  KLKB1 MUTATED    14   0   0   1
  KLKB1 WILD-TYPE 331   4  31  24
D773V11, multiclass
    clus
vv   KLKB1 MUTATED KLKB1 WILD-TYPE
  R0            14             331
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D773V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KLKB1 MUTATED                                  0     1
  KLKB1 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  KLKB1 MUTATED                           1     8
  KLKB1 WILD-TYPE                        21   218
D773V13, multiclass
                                  clus
vv                                 KLKB1 MUTATED KLKB1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        8             218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(774) Variable = SV2A MUTATION ANALYSIS
D774V1, survival
                sevent
clus2              0   1
  SV2A MUTATED    20   3
  SV2A WILD-TYPE 358  90
  SV2A MUTATED SV2A WILD-TYPE 
            23            448 
  SV2A MUTATED SV2A WILD-TYPE 
             3             90 
$`SV2A MUTATED`
TCGA-A6-6781 TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3672 TCGA-AA-3864 TCGA-AA-3950 
       19.66         3.02        63.98         0.92        53.00        24.00 
TCGA-AA-3956 TCGA-AA-A010 TCGA-AU-6004 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-CA-6717 
       34.03        34.98        27.09        49.41        12.10        12.76 
TCGA-CK-4952 TCGA-CM-5349 TCGA-CM-6161 TCGA-CM-6163 TCGA-D5-6928 TCGA-D5-6930 
       15.62        30.08        15.02         2.96        11.64         1.51 
TCGA-DM-A28E TCGA-G4-6304 TCGA-G4-6321 TCGA-AG-A011 TCGA-G5-6235 
      119.93        53.62        22.09        37.02        55.76 

$`SV2A WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 
       23.87        20.12        20.28         7.04         1.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
        2.01        14.01        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       31.07        30.05        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01         2.01        20.98         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       10.88         0.20        14.50        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6603 
       22.36        62.79        88.21         6.77       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07        12.20        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
       17.56       148.01        85.45        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6162 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
       12.00        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6931 
       12.43        14.30         9.04         9.44         4.80        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
      133.18        74.56        65.85        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       63.62        61.91        36.00        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A014 TCGA-AG-A015 
       13.94         6.02        25.97        23.01        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6641 
       32.19         0.66         0.69        26.43 

  SV2A MUTATED SV2A WILD-TYPE 
          0.92           0.00 
  SV2A MUTATED SV2A WILD-TYPE 
        119.93         148.01 
  SV2A MUTATED SV2A WILD-TYPE 
        24.000         20.085 
[1] "0.9 - 119.9 (24.0)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.8"
D774V2, continuous
D774V3, binary
                cls
clus               0   1
  SV2A MUTATED    21   2
  SV2A WILD-TYPE 345 117
[1] "tbl2"
                cls
clus             [,1] [,2]
  SV2A MUTATED     21    2
  SV2A WILD-TYPE  345  117
        clus
vv       SV2A MUTATED SV2A WILD-TYPE
  COLON            21            345
  RECTUM            2            117
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SV2A MUTATED         3        0        4         8         2         0
  SV2A WILD-TYPE      88        1       28       130         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SV2A MUTATED           2          0          1          2        1         0
  SV2A WILD-TYPE        22         11         58         40       47        18
                vv
clus             STAGE IVB
  SV2A MUTATED           0
  SV2A WILD-TYPE         1
D774V4, multiclass
            clus
vv           SV2A MUTATED SV2A WILD-TYPE
  STAGE I               3             88
  STAGE IA              0              1
  STAGE II              4             28
  STAGE IIA             8            130
  STAGE IIB             2              8
  STAGE IIC             0              1
  STAGE III             2             22
  STAGE IIIA            0             11
  STAGE IIIB            1             58
  STAGE IIIC            2             40
  STAGE IV              1             47
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  SV2A MUTATED     1   3  14   5
  SV2A WILD-TYPE  16  89 315  45
D774V5, multiclass
    clus
vv   SV2A MUTATED SV2A WILD-TYPE
  T1            1             16
  T2            3             89
  T3           14            315
  T4            5             45
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  SV2A MUTATED    17   5   1
  SV2A WILD-TYPE 270 108  86
D774V6, multiclass
    clus
vv   SV2A MUTATED SV2A WILD-TYPE
  N0           17            270
  N1            5            108
  N2            1             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D774V7, binary
                cls
clus               0   1
  SV2A MUTATED    18   1
  SV2A WILD-TYPE 357  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  SV2A MUTATED     18    1
  SV2A WILD-TYPE  357   64
   clus
vv  SV2A MUTATED SV2A WILD-TYPE
  0           18            357
  1            1             64
[1] 2 2
[1] FALSE
D774V8, binary
                cls
clus               0   1
  SV2A MUTATED    12  11
  SV2A WILD-TYPE 213 253
[1] "tbl2"
                cls
clus             [,1] [,2]
  SV2A MUTATED     12   11
  SV2A WILD-TYPE  213  253
        clus
vv       SV2A MUTATED SV2A WILD-TYPE
  FEMALE           12            213
  MALE             11            253
[1] 2 2
[1] FALSE
D774V9, binary
                cls
clus               0   1
  SV2A MUTATED    18   0
  SV2A WILD-TYPE 332  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  SV2A MUTATED     18    0
  SV2A WILD-TYPE  332   22
     clus
vv    SV2A MUTATED SV2A WILD-TYPE
  NO            18            332
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SV2A MUTATED                     15                             6
  SV2A WILD-TYPE                  300                            41
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SV2A MUTATED                       2                              0
  SV2A WILD-TYPE                   104                             10
D774V10, multiclass
                                clus
vv                               SV2A MUTATED SV2A WILD-TYPE
  COLON ADENOCARCINOMA                     15            300
  COLON MUCINOUS ADENOCARCINOMA             6             41
  RECTAL ADENOCARCINOMA                     2            104
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  SV2A MUTATED    17   1   0   2
  SV2A WILD-TYPE 328   3  31  23
D774V11, multiclass
    clus
vv   SV2A MUTATED SV2A WILD-TYPE
  R0           17            328
  R1            1              3
  R2            0             31
  RX            2             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D774V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SV2A MUTATED                                  0     1
  SV2A WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  SV2A MUTATED                           1    13
  SV2A WILD-TYPE                        21   213
D774V13, multiclass
                                  clus
vv                                 SV2A MUTATED SV2A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                      13            213
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(775) Variable = POLA1 MUTATION ANALYSIS
D775V1, survival
                 sevent
clus2               0   1
  POLA1 MUTATED     9   3
  POLA1 WILD-TYPE 369  90
  POLA1 MUTATED POLA1 WILD-TYPE 
             12             459 
  POLA1 MUTATED POLA1 WILD-TYPE 
              3              90 
$`POLA1 MUTATED`
TCGA-AA-3848 TCGA-AA-3947 TCGA-AA-A010 TCGA-AY-5543 TCGA-CM-6161 TCGA-D5-6532 
       10.06        33.01        34.98        33.01        15.02        18.25 
TCGA-D5-6540 TCGA-AF-5654 TCGA-AG-3609 TCGA-AG-3892 TCGA-AG-3898 TCGA-DY-A1DC 
       16.14        16.83        19.99        13.02        48.03        41.36 

$`POLA1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
        0.00        17.03         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
        2.01        12.99        24.00        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6197 
        0.20        14.50        27.09        16.31         0.95        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6162 TCGA-CM-6163 
        5.03        15.02        15.02        17.03        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6534 
       19.59        56.09        55.92        20.19         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 
       15.12        17.85         4.80        17.13        12.49        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       14.50        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        6.05         0.99        15.95        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 
       19.99         1.02        17.95        36.95        17.03        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
       14.01         1.02        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.03         5.29       126.44        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  POLA1 MUTATED POLA1 WILD-TYPE 
          10.06            0.00 
  POLA1 MUTATED POLA1 WILD-TYPE 
          48.03          148.01 
  POLA1 MUTATED POLA1 WILD-TYPE 
          19.12           20.28 
[1] "10.1 - 48.0 (19.1)" "0.0 - 148.0 (20.3)"
[1] "hr=" "1.4"
D775V2, continuous
D775V3, binary
                 cls
clus                0   1
  POLA1 MUTATED     9   5
  POLA1 WILD-TYPE 357 114
[1] "tbl2"
                 cls
clus              [,1] [,2]
  POLA1 MUTATED      9    5
  POLA1 WILD-TYPE  357  114
        clus
vv       POLA1 MUTATED POLA1 WILD-TYPE
  COLON              9             357
  RECTUM             5             114
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  POLA1 MUTATED         4        0        0         4         3         0
  POLA1 WILD-TYPE      87        1       32       134         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  POLA1 MUTATED           0          0          0          2        0         1
  POLA1 WILD-TYPE        24         11         59         40       48        17
                 vv
clus              STAGE IVB
  POLA1 MUTATED           0
  POLA1 WILD-TYPE         1
D775V4, multiclass
            clus
vv           POLA1 MUTATED POLA1 WILD-TYPE
  STAGE I                4              87
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              4             134
  STAGE IIB              3               7
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             2              40
  STAGE IV               0              48
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  POLA1 MUTATED     1   3   7   3
  POLA1 WILD-TYPE  16  89 322  47
D775V5, multiclass
    clus
vv   POLA1 MUTATED POLA1 WILD-TYPE
  T1             1              16
  T2             3              89
  T3             7             322
  T4             3              47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  POLA1 MUTATED    11   1   2
  POLA1 WILD-TYPE 276 112  85
D775V6, multiclass
    clus
vv   POLA1 MUTATED POLA1 WILD-TYPE
  N0            11             276
  N1             1             112
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D775V7, binary
                 cls
clus                0   1
  POLA1 MUTATED    12   1
  POLA1 WILD-TYPE 363  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  POLA1 MUTATED     12    1
  POLA1 WILD-TYPE  363   64
   clus
vv  POLA1 MUTATED POLA1 WILD-TYPE
  0            12             363
  1             1              64
[1] 2 2
[1] FALSE
D775V8, binary
                 cls
clus                0   1
  POLA1 MUTATED    11   3
  POLA1 WILD-TYPE 214 261
[1] "tbl2"
                 cls
clus              [,1] [,2]
  POLA1 MUTATED     11    3
  POLA1 WILD-TYPE  214  261
        clus
vv       POLA1 MUTATED POLA1 WILD-TYPE
  FEMALE            11             214
  MALE               3             261
[1] 2 2
[1] FALSE
D775V9, binary
                 cls
clus                0   1
  POLA1 MUTATED    11   0
  POLA1 WILD-TYPE 339  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  POLA1 MUTATED     11    0
  POLA1 WILD-TYPE  339   22
     clus
vv    POLA1 MUTATED POLA1 WILD-TYPE
  NO             11             339
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  POLA1 MUTATED                      7                             2
  POLA1 WILD-TYPE                  308                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  POLA1 MUTATED                       5                              0
  POLA1 WILD-TYPE                   101                             10
D775V10, multiclass
                                clus
vv                               POLA1 MUTATED POLA1 WILD-TYPE
  COLON ADENOCARCINOMA                       7             308
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      5             101
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  POLA1 MUTATED    12   0   0   1
  POLA1 WILD-TYPE 333   4  31  24
D775V11, multiclass
    clus
vv   POLA1 MUTATED POLA1 WILD-TYPE
  R0            12             333
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D775V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  POLA1 MUTATED                                  0     0
  POLA1 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  POLA1 MUTATED                           1     6
  POLA1 WILD-TYPE                        21   220
D775V13, multiclass
                                  clus
vv                                 POLA1 MUTATED POLA1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        6             220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(776) Variable = RAB40C MUTATION ANALYSIS
D776V1, survival
                  sevent
clus2                0   1
  RAB40C MUTATED     5   2
  RAB40C WILD-TYPE 373  91
  RAB40C MUTATED RAB40C WILD-TYPE 
               7              464 
  RAB40C MUTATED RAB40C WILD-TYPE 
               2               91 
$`RAB40C MUTATED`
TCGA-A6-6781 TCGA-AA-3492 TCGA-AA-3815 TCGA-AU-6004 TCGA-AZ-6598 TCGA-CM-4746 
       19.66         3.02        33.04        27.09        49.41        37.02 
TCGA-F4-6856 
       35.31 

$`RAB40C WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 
       23.87        20.12        20.28         7.04         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       35.05         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
        0.20        14.50        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        88.21         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       23.05        20.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  RAB40C MUTATED RAB40C WILD-TYPE 
            3.02             0.00 
  RAB40C MUTATED RAB40C WILD-TYPE 
           49.41           148.01 
  RAB40C MUTATED RAB40C WILD-TYPE 
          33.040           20.085 
[1] "3.0 - 49.4 (33.0)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.4"
D776V2, continuous
D776V3, binary
                  cls
clus                 0   1
  RAB40C MUTATED     8   0
  RAB40C WILD-TYPE 358 119
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RAB40C MUTATED      8    0
  RAB40C WILD-TYPE  358  119
        clus
vv       RAB40C MUTATED RAB40C WILD-TYPE
  COLON               8              358
  RECTUM              0              119
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RAB40C MUTATED         3        0        2         1         1         0
  RAB40C WILD-TYPE      88        1       30       137         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RAB40C MUTATED           0          0          0          1        0
  RAB40C WILD-TYPE        24         11         59         41       48
                  vv
clus               STAGE IVA STAGE IVB
  RAB40C MUTATED           0         0
  RAB40C WILD-TYPE        18         1
D776V4, multiclass
            clus
vv           RAB40C MUTATED RAB40C WILD-TYPE
  STAGE I                 3               88
  STAGE IA                0                1
  STAGE II                2               30
  STAGE IIA               1              137
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              0               59
  STAGE IIIC              1               41
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  RAB40C MUTATED     0   3   3   2
  RAB40C WILD-TYPE  17  89 326  48
D776V5, multiclass
    clus
vv   RAB40C MUTATED RAB40C WILD-TYPE
  T1              0               17
  T2              3               89
  T3              3              326
  T4              2               48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  RAB40C MUTATED     7   1   0
  RAB40C WILD-TYPE 280 112  87
D776V6, multiclass
    clus
vv   RAB40C MUTATED RAB40C WILD-TYPE
  N0              7              280
  N1              1              112
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D776V7, binary
                  cls
clus                 0   1
  RAB40C MUTATED     5   0
  RAB40C WILD-TYPE 370  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RAB40C MUTATED      5    0
  RAB40C WILD-TYPE  370   65
   clus
vv  RAB40C MUTATED RAB40C WILD-TYPE
  0              5              370
  1              0               65
[1] 2 2
[1] FALSE
D776V8, binary
                  cls
clus                 0   1
  RAB40C MUTATED     5   3
  RAB40C WILD-TYPE 220 261
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RAB40C MUTATED      5    3
  RAB40C WILD-TYPE  220  261
        clus
vv       RAB40C MUTATED RAB40C WILD-TYPE
  FEMALE              5              220
  MALE                3              261
[1] 2 2
[1] FALSE
D776V9, binary
                  cls
clus                 0   1
  RAB40C MUTATED     6   0
  RAB40C WILD-TYPE 344  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RAB40C MUTATED      6    0
  RAB40C WILD-TYPE  344   22
     clus
vv    RAB40C MUTATED RAB40C WILD-TYPE
  NO               6              344
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  RAB40C MUTATED                      6                             2
  RAB40C WILD-TYPE                  309                            45
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  RAB40C MUTATED                       0                              0
  RAB40C WILD-TYPE                   106                             10
D776V10, multiclass
                                clus
vv                               RAB40C MUTATED RAB40C WILD-TYPE
  COLON ADENOCARCINOMA                        6              309
  COLON MUCINOUS ADENOCARCINOMA               2               45
  RECTAL ADENOCARCINOMA                       0              106
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  RAB40C MUTATED     6   0   0   1
  RAB40C WILD-TYPE 339   4  31  24
D776V11, multiclass
    clus
vv   RAB40C MUTATED RAB40C WILD-TYPE
  R0              6              339
  R1              0                4
  R2              0               31
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D776V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RAB40C MUTATED                                  0     0
  RAB40C WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  RAB40C MUTATED                           1     5
  RAB40C WILD-TYPE                        21   221
D776V13, multiclass
                                  clus
vv                                 RAB40C MUTATED RAB40C WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                         5              221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(777) Variable = DHX35 MUTATION ANALYSIS
D777V1, survival
                 sevent
clus2               0   1
  DHX35 MUTATED     9   3
  DHX35 WILD-TYPE 369  90
  DHX35 MUTATED DHX35 WILD-TYPE 
             12             459 
  DHX35 MUTATED DHX35 WILD-TYPE 
              3              90 
$`DHX35 MUTATED`
TCGA-A6-5661 TCGA-AA-3518 TCGA-AA-A010 TCGA-AA-A02K TCGA-AZ-4315 TCGA-AZ-6598 
       33.53         1.02        34.98        14.01        58.39        49.41 
TCGA-AZ-6600 TCGA-CM-5860 TCGA-CM-6171 TCGA-G4-6315 TCGA-AG-A002 TCGA-CL-5917 
       12.10        32.02        14.04        61.91        20.98        78.12 

$`DHX35 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        2.01         5.03         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       88.21         6.77       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       30.08        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 
       14.99        12.99        13.02        15.02        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        6.97         4.73         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  DHX35 MUTATED DHX35 WILD-TYPE 
           1.02            0.00 
  DHX35 MUTATED DHX35 WILD-TYPE 
          78.12          148.01 
  DHX35 MUTATED DHX35 WILD-TYPE 
         32.775          20.050 
[1] "1.0 - 78.1 (32.8)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.1"
D777V2, continuous
D777V3, binary
                 cls
clus                0   1
  DHX35 MUTATED    11   2
  DHX35 WILD-TYPE 355 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DHX35 MUTATED     11    2
  DHX35 WILD-TYPE  355  117
        clus
vv       DHX35 MUTATED DHX35 WILD-TYPE
  COLON             11             355
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DHX35 MUTATED         2        0        1         5         1         0
  DHX35 WILD-TYPE      89        1       31       133         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DHX35 MUTATED           0          0          0          1        3         0
  DHX35 WILD-TYPE        24         11         59         41       45        18
                 vv
clus              STAGE IVB
  DHX35 MUTATED           0
  DHX35 WILD-TYPE         1
D777V4, multiclass
            clus
vv           DHX35 MUTATED DHX35 WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              5             133
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             1              41
  STAGE IV               3              45
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  DHX35 MUTATED     0   2   8   3
  DHX35 WILD-TYPE  17  90 321  47
D777V5, multiclass
    clus
vv   DHX35 MUTATED DHX35 WILD-TYPE
  T1             0              17
  T2             2              90
  T3             8             321
  T4             3              47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  DHX35 MUTATED     9   2   2
  DHX35 WILD-TYPE 278 111  85
D777V6, multiclass
    clus
vv   DHX35 MUTATED DHX35 WILD-TYPE
  N0             9             278
  N1             2             111
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D777V7, binary
                 cls
clus                0   1
  DHX35 MUTATED     8   3
  DHX35 WILD-TYPE 367  62
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DHX35 MUTATED      8    3
  DHX35 WILD-TYPE  367   62
   clus
vv  DHX35 MUTATED DHX35 WILD-TYPE
  0             8             367
  1             3              62
[1] 2 2
[1] FALSE
D777V8, binary
                 cls
clus                0   1
  DHX35 MUTATED     7   6
  DHX35 WILD-TYPE 218 258
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DHX35 MUTATED      7    6
  DHX35 WILD-TYPE  218  258
        clus
vv       DHX35 MUTATED DHX35 WILD-TYPE
  FEMALE             7             218
  MALE               6             258
[1] 2 2
[1] FALSE
D777V9, binary
                 cls
clus                0   1
  DHX35 MUTATED    10   0
  DHX35 WILD-TYPE 340  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DHX35 MUTATED     10    0
  DHX35 WILD-TYPE  340   22
     clus
vv    DHX35 MUTATED DHX35 WILD-TYPE
  NO             10             340
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  DHX35 MUTATED                     11                             0
  DHX35 WILD-TYPE                  304                            47
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  DHX35 MUTATED                       2                              0
  DHX35 WILD-TYPE                   104                             10
D777V10, multiclass
                                clus
vv                               DHX35 MUTATED DHX35 WILD-TYPE
  COLON ADENOCARCINOMA                      11             304
  COLON MUCINOUS ADENOCARCINOMA              0              47
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  DHX35 MUTATED     9   0   1   1
  DHX35 WILD-TYPE 336   4  30  24
D777V11, multiclass
    clus
vv   DHX35 MUTATED DHX35 WILD-TYPE
  R0             9             336
  R1             0               4
  R2             1              30
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D777V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DHX35 MUTATED                                  0     0
  DHX35 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  DHX35 MUTATED                           2     6
  DHX35 WILD-TYPE                        20   220
D777V13, multiclass
                                  clus
vv                                 DHX35 MUTATED DHX35 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    2              20
  WHITE                                        6             220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(778) Variable = SLC25A13 MUTATION ANALYSIS
D778V1, survival
                    sevent
clus2                  0   1
  SLC25A13 MUTATED    14   3
  SLC25A13 WILD-TYPE 364  90
  SLC25A13 MUTATED SLC25A13 WILD-TYPE 
                17                454 
  SLC25A13 MUTATED SLC25A13 WILD-TYPE 
                 3                 90 
$`SLC25A13 MUTATED`
TCGA-A6-3810 TCGA-AA-3850 TCGA-AA-3955 TCGA-AA-A00N TCGA-AA-A010 TCGA-AY-6197 
       36.53         0.00        20.98         4.01        34.98        21.44 
TCGA-AZ-4315 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-CA-6719 TCGA-CK-5913 TCGA-CM-6169 
       58.39        88.21        49.41        14.30        51.32        13.02 
TCGA-D5-6923 TCGA-G4-6304 TCGA-AG-A002 TCGA-AG-A011 TCGA-DY-A0XA 
       12.43        53.62        20.98        37.02       126.44 

$`SLC25A13 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        32.75        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       17.03        10.06        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4323 
       27.09        16.31         0.95        33.01        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6599 TCGA-AZ-6600 
        5.13       106.75        22.36        62.79         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       12.76        10.06        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       49.08         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6170 
       29.03        16.04        21.99        14.99        12.99        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6924 TCGA-D5-6926 
       15.58         1.48         3.68         4.41        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
      133.18        74.56        65.85        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A014 TCGA-AG-A015 
       13.94         6.02        25.97        23.01        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        4.01         5.03         5.29        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  SLC25A13 MUTATED SLC25A13 WILD-TYPE 
                 0                  0 
  SLC25A13 MUTATED SLC25A13 WILD-TYPE 
            126.44             148.01 
  SLC25A13 MUTATED SLC25A13 WILD-TYPE 
             34.98              20.02 
[1] "0.0 - 126.4 (35.0)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.6"
D778V2, continuous
D778V3, binary
                    cls
clus                   0   1
  SLC25A13 MUTATED    14   3
  SLC25A13 WILD-TYPE 352 116
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SLC25A13 MUTATED     14    3
  SLC25A13 WILD-TYPE  352  116
        clus
vv       SLC25A13 MUTATED SLC25A13 WILD-TYPE
  COLON                14                352
  RECTUM                3                116
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SLC25A13 MUTATED         4        0        1         8         3         0
  SLC25A13 WILD-TYPE      87        1       31       130         7         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC25A13 MUTATED           0          0          1          0        0
  SLC25A13 WILD-TYPE        24         11         58         42       48
                    vv
clus                 STAGE IVA STAGE IVB
  SLC25A13 MUTATED           0         0
  SLC25A13 WILD-TYPE        18         1
D778V4, multiclass
            clus
vv           SLC25A13 MUTATED SLC25A13 WILD-TYPE
  STAGE I                   4                 87
  STAGE IA                  0                  1
  STAGE II                  1                 31
  STAGE IIA                 8                130
  STAGE IIB                 3                  7
  STAGE IIC                 0                  1
  STAGE III                 0                 24
  STAGE IIIA                0                 11
  STAGE IIIB                1                 58
  STAGE IIIC                0                 42
  STAGE IV                  0                 48
  STAGE IVA                 0                 18
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  SLC25A13 MUTATED     1   4   9   3
  SLC25A13 WILD-TYPE  16  88 320  47
D778V5, multiclass
    clus
vv   SLC25A13 MUTATED SLC25A13 WILD-TYPE
  T1                1                 16
  T2                4                 88
  T3                9                320
  T4                3                 47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  SLC25A13 MUTATED    16   0   1
  SLC25A13 WILD-TYPE 271 113  86
D778V6, multiclass
    clus
vv   SLC25A13 MUTATED SLC25A13 WILD-TYPE
  N0               16                271
  N1                0                113
  N2                1                 86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D778V7, binary
                    cls
clus                   0   1
  SLC25A13 MUTATED    14   0
  SLC25A13 WILD-TYPE 361  65
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SLC25A13 MUTATED     14    0
  SLC25A13 WILD-TYPE  361   65
   clus
vv  SLC25A13 MUTATED SLC25A13 WILD-TYPE
  0               14                361
  1                0                 65
[1] 2 2
[1] FALSE
D778V8, binary
                    cls
clus                   0   1
  SLC25A13 MUTATED     6  11
  SLC25A13 WILD-TYPE 219 253
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SLC25A13 MUTATED      6   11
  SLC25A13 WILD-TYPE  219  253
        clus
vv       SLC25A13 MUTATED SLC25A13 WILD-TYPE
  FEMALE                6                219
  MALE                 11                253
[1] 2 2
[1] FALSE
D778V9, binary
                    cls
clus                   0   1
  SLC25A13 MUTATED    14   0
  SLC25A13 WILD-TYPE 336  22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SLC25A13 MUTATED     14    0
  SLC25A13 WILD-TYPE  336   22
     clus
vv    SLC25A13 MUTATED SLC25A13 WILD-TYPE
  NO                14                336
  YES                0                 22
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SLC25A13 MUTATED                     13                             1
  SLC25A13 WILD-TYPE                  302                            46
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SLC25A13 MUTATED                       3                              0
  SLC25A13 WILD-TYPE                   103                             10
D778V10, multiclass
                                clus
vv                               SLC25A13 MUTATED SLC25A13 WILD-TYPE
  COLON ADENOCARCINOMA                         13                302
  COLON MUCINOUS ADENOCARCINOMA                 1                 46
  RECTAL ADENOCARCINOMA                         3                103
  RECTAL MUCINOUS ADENOCARCINOMA                0                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  SLC25A13 MUTATED    12   0   0   2
  SLC25A13 WILD-TYPE 333   4  31  23
D778V11, multiclass
    clus
vv   SLC25A13 MUTATED SLC25A13 WILD-TYPE
  R0               12                333
  R1                0                  4
  R2                0                 31
  RX                2                 23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D778V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SLC25A13 MUTATED                                  0     1
  SLC25A13 WILD-TYPE                                1    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  SLC25A13 MUTATED                           1     9
  SLC25A13 WILD-TYPE                        21   217
D778V13, multiclass
                                  clus
vv                                 SLC25A13 MUTATED SLC25A13 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                 10
  BLACK OR AFRICAN AMERICAN                       1                 21
  WHITE                                           9                217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(779) Variable = FAM26E MUTATION ANALYSIS
D779V1, survival
                  sevent
clus2                0   1
  FAM26E MUTATED     5   0
  FAM26E WILD-TYPE 373  93
  FAM26E MUTATED FAM26E WILD-TYPE 
               5              466 
  FAM26E MUTATED FAM26E WILD-TYPE 
               0               93 
$`FAM26E MUTATED`
TCGA-A6-5661 TCGA-AA-3977 TCGA-AD-6889 TCGA-D5-6540 TCGA-F4-6856 
       33.53        25.02        56.55        16.14        35.31 

$`FAM26E WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       17.13        12.49        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
        0.53        47.41       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  FAM26E MUTATED FAM26E WILD-TYPE 
           16.14             0.00 
  FAM26E MUTATED FAM26E WILD-TYPE 
           56.55           148.01 
  FAM26E MUTATED FAM26E WILD-TYPE 
          33.530           20.085 
[1] "16.1 - 56.5 (33.5)" "0.0 - 148.0 (20.1)"
[1] "hr="     "9100000"
D779V2, continuous
D779V3, binary
                  cls
clus                 0   1
  FAM26E MUTATED     5   0
  FAM26E WILD-TYPE 361 119
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM26E MUTATED      5    0
  FAM26E WILD-TYPE  361  119
        clus
vv       FAM26E MUTATED FAM26E WILD-TYPE
  COLON               5              361
  RECTUM              0              119
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FAM26E MUTATED         2        0        0         2         0         0
  FAM26E WILD-TYPE      89        1       32       136        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FAM26E MUTATED           0          0          0          0        0
  FAM26E WILD-TYPE        24         11         59         42       48
                  vv
clus               STAGE IVA STAGE IVB
  FAM26E MUTATED           0         0
  FAM26E WILD-TYPE        18         1
D779V4, multiclass
            clus
vv           FAM26E MUTATED FAM26E WILD-TYPE
  STAGE I                 2               89
  STAGE IA                0                1
  STAGE II                0               32
  STAGE IIA               2              136
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              0               59
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  FAM26E MUTATED     0   3   2   0
  FAM26E WILD-TYPE  17  89 327  50
D779V5, multiclass
    clus
vv   FAM26E MUTATED FAM26E WILD-TYPE
  T1              0               17
  T2              3               89
  T3              2              327
  T4              0               50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  FAM26E MUTATED     5   0   0
  FAM26E WILD-TYPE 282 113  87
D779V6, multiclass
    clus
vv   FAM26E MUTATED FAM26E WILD-TYPE
  N0              5              282
  N1              0              113
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D779V7, binary
                  cls
clus                 0   1
  FAM26E MUTATED     4   0
  FAM26E WILD-TYPE 371  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM26E MUTATED      4    0
  FAM26E WILD-TYPE  371   65
   clus
vv  FAM26E MUTATED FAM26E WILD-TYPE
  0              4              371
  1              0               65
[1] 2 2
[1] FALSE
D779V8, binary
                  cls
clus                 0   1
  FAM26E MUTATED     1   4
  FAM26E WILD-TYPE 224 260
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM26E MUTATED      1    4
  FAM26E WILD-TYPE  224  260
        clus
vv       FAM26E MUTATED FAM26E WILD-TYPE
  FEMALE              1              224
  MALE                4              260
[1] 2 2
[1] FALSE
D779V9, binary
                  cls
clus                 0   1
  FAM26E MUTATED     4   0
  FAM26E WILD-TYPE 346  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM26E MUTATED      4    0
  FAM26E WILD-TYPE  346   22
     clus
vv    FAM26E MUTATED FAM26E WILD-TYPE
  NO               4              346
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  FAM26E MUTATED                      3                             2
  FAM26E WILD-TYPE                  312                            45
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  FAM26E MUTATED                       0                              0
  FAM26E WILD-TYPE                   106                             10
D779V10, multiclass
                                clus
vv                               FAM26E MUTATED FAM26E WILD-TYPE
  COLON ADENOCARCINOMA                        3              312
  COLON MUCINOUS ADENOCARCINOMA               2               45
  RECTAL ADENOCARCINOMA                       0              106
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  FAM26E MUTATED     3   0   0   0
  FAM26E WILD-TYPE 342   4  31  25
D779V11, multiclass
    clus
vv   FAM26E MUTATED FAM26E WILD-TYPE
  R0              3              342
  R1              0                4
  R2              0               31
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D779V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FAM26E MUTATED                                  0     1
  FAM26E WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  FAM26E MUTATED                           1     2
  FAM26E WILD-TYPE                        21   224
D779V13, multiclass
                                  clus
vv                                 FAM26E MUTATED FAM26E WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                         2              224
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(780) Variable = SAFB MUTATION ANALYSIS
D780V1, survival
                sevent
clus2              0   1
  SAFB MUTATED    14   1
  SAFB WILD-TYPE 364  92
  SAFB MUTATED SAFB WILD-TYPE 
            15            456 
  SAFB MUTATED SAFB WILD-TYPE 
             1             92 
$`SAFB MUTATED`
TCGA-A6-5661 TCGA-A6-5665 TCGA-A6-6781 TCGA-AA-3663 TCGA-AA-3833 TCGA-AA-3950 
       33.53        22.06        19.66         6.97        15.95        24.00 
TCGA-AA-3973 TCGA-AZ-6608 TCGA-CA-6717 TCGA-CM-4743 TCGA-CM-6161 TCGA-D5-6930 
       13.05         1.61        12.76        23.05        15.02         1.51 
TCGA-G4-6293 TCGA-AH-6644 TCGA-EI-6510 
      133.18         0.72        18.28 

$`SAFB WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02        78.08         6.05        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3837 TCGA-AA-3842 
        0.99        25.02         1.02        17.98        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       26.01         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       16.08        50.99        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        3.19        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.20        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
        1.91       124.27        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6162 TCGA-CM-6163 
        5.03        15.02        15.02        17.03        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6931 
       14.30         9.04         9.44        11.64         4.80        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
       35.31        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.69         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       20.55        19.96        20.91         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  SAFB MUTATED SAFB WILD-TYPE 
          0.72           0.00 
  SAFB MUTATED SAFB WILD-TYPE 
        133.18         148.01 
  SAFB MUTATED SAFB WILD-TYPE 
         15.95          20.73 
[1] "0.7 - 133.2 (15.9)" "0.0 - 148.0 (20.7)"
[1] "hr=" "2.4"
D780V2, continuous
D780V3, binary
                cls
clus               0   1
  SAFB MUTATED    14   2
  SAFB WILD-TYPE 352 117
[1] "tbl2"
                cls
clus             [,1] [,2]
  SAFB MUTATED     14    2
  SAFB WILD-TYPE  352  117
        clus
vv       SAFB MUTATED SAFB WILD-TYPE
  COLON            14            352
  RECTUM            2            117
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SAFB MUTATED         1        0        1         8         0         0
  SAFB WILD-TYPE      90        1       31       130        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SAFB MUTATED           1          1          0          1        1         1
  SAFB WILD-TYPE        23         10         59         41       47        17
                vv
clus             STAGE IVB
  SAFB MUTATED           0
  SAFB WILD-TYPE         1
D780V4, multiclass
            clus
vv           SAFB MUTATED SAFB WILD-TYPE
  STAGE I               1             90
  STAGE IA              0              1
  STAGE II              1             31
  STAGE IIA             8            130
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             1             23
  STAGE IIIA            1             10
  STAGE IIIB            0             59
  STAGE IIIC            1             41
  STAGE IV              1             47
  STAGE IVA             1             17
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  SAFB MUTATED     0   3  11   2
  SAFB WILD-TYPE  17  89 318  48
D780V5, multiclass
    clus
vv   SAFB MUTATED SAFB WILD-TYPE
  T1            0             17
  T2            3             89
  T3           11            318
  T4            2             48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  SAFB MUTATED    11   4   0
  SAFB WILD-TYPE 276 109  87
D780V6, multiclass
    clus
vv   SAFB MUTATED SAFB WILD-TYPE
  N0           11            276
  N1            4            109
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D780V7, binary
                cls
clus               0   1
  SAFB MUTATED    12   1
  SAFB WILD-TYPE 363  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  SAFB MUTATED     12    1
  SAFB WILD-TYPE  363   64
   clus
vv  SAFB MUTATED SAFB WILD-TYPE
  0           12            363
  1            1             64
[1] 2 2
[1] FALSE
D780V8, binary
                cls
clus               0   1
  SAFB MUTATED     9   7
  SAFB WILD-TYPE 216 257
[1] "tbl2"
                cls
clus             [,1] [,2]
  SAFB MUTATED      9    7
  SAFB WILD-TYPE  216  257
        clus
vv       SAFB MUTATED SAFB WILD-TYPE
  FEMALE            9            216
  MALE              7            257
[1] 2 2
[1] FALSE
D780V9, binary
                cls
clus               0   1
  SAFB MUTATED    13   0
  SAFB WILD-TYPE 337  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  SAFB MUTATED     13    0
  SAFB WILD-TYPE  337   22
     clus
vv    SAFB MUTATED SAFB WILD-TYPE
  NO            13            337
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SAFB MUTATED                     10                             4
  SAFB WILD-TYPE                  305                            43
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SAFB MUTATED                       2                              0
  SAFB WILD-TYPE                   104                             10
D780V10, multiclass
                                clus
vv                               SAFB MUTATED SAFB WILD-TYPE
  COLON ADENOCARCINOMA                     10            305
  COLON MUCINOUS ADENOCARCINOMA             4             43
  RECTAL ADENOCARCINOMA                     2            104
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  SAFB MUTATED    12   0   1   1
  SAFB WILD-TYPE 333   4  30  24
D780V11, multiclass
    clus
vv   SAFB MUTATED SAFB WILD-TYPE
  R0           12            333
  R1            0              4
  R2            1             30
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D780V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SAFB MUTATED                                  0     1
  SAFB WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  SAFB MUTATED                           1     9
  SAFB WILD-TYPE                        21   217
D780V13, multiclass
                                  clus
vv                                 SAFB MUTATED SAFB WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                       9            217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(781) Variable = YES1 MUTATION ANALYSIS
D781V1, survival
                sevent
clus2              0   1
  YES1 MUTATED     6   4
  YES1 WILD-TYPE 372  89
  YES1 MUTATED YES1 WILD-TYPE 
            10            461 
  YES1 MUTATED YES1 WILD-TYPE 
             4             89 
$`YES1 MUTATED`
TCGA-AA-3663 TCGA-AA-3819 TCGA-AU-3779 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-CA-6718 
        6.97        25.02        14.50         6.77       100.01        10.06 
TCGA-D5-6928 TCGA-DM-A1HB TCGA-F4-6809 TCGA-F5-6571 
       11.64       135.65        13.25        31.30 

$`YES1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.05        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3821 TCGA-AA-3831 
       10.06        35.05        33.04         0.99         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       10.88         0.20        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6603 
       22.36        62.79        88.21        49.41        12.10        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 
        3.25         3.29         0.07        12.20        12.76        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.04         9.44         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      131.51       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       33.67         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6702 
       19.96        20.91        18.28         9.96        49.51        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  YES1 MUTATED YES1 WILD-TYPE 
          6.77           0.00 
  YES1 MUTATED YES1 WILD-TYPE 
        135.65         148.01 
  YES1 MUTATED YES1 WILD-TYPE 
        13.875         20.280 
[1] "6.8 - 135.7 (13.9)" "0.0 - 148.0 (20.3)"
[1] "hr=" "1.7"
D781V2, continuous
D781V3, binary
                cls
clus               0   1
  YES1 MUTATED     9   1
  YES1 WILD-TYPE 357 118
[1] "tbl2"
                cls
clus             [,1] [,2]
  YES1 MUTATED      9    1
  YES1 WILD-TYPE  357  118
        clus
vv       YES1 MUTATED YES1 WILD-TYPE
  COLON             9            357
  RECTUM            1            118
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  YES1 MUTATED         1        0        2         5         0         0
  YES1 WILD-TYPE      90        1       30       133        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  YES1 MUTATED           0          0          1          0        0         1
  YES1 WILD-TYPE        24         11         58         42       48        17
                vv
clus             STAGE IVB
  YES1 MUTATED           0
  YES1 WILD-TYPE         1
D781V4, multiclass
            clus
vv           YES1 MUTATED YES1 WILD-TYPE
  STAGE I               1             90
  STAGE IA              0              1
  STAGE II              2             30
  STAGE IIA             5            133
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            1             58
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             1             17
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  YES1 MUTATED     0   1   9   0
  YES1 WILD-TYPE  17  91 320  50
D781V5, multiclass
    clus
vv   YES1 MUTATED YES1 WILD-TYPE
  T1            0             17
  T2            1             91
  T3            9            320
  T4            0             50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  YES1 MUTATED     8   2   0
  YES1 WILD-TYPE 279 111  87
D781V6, multiclass
    clus
vv   YES1 MUTATED YES1 WILD-TYPE
  N0            8            279
  N1            2            111
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D781V7, binary
                cls
clus               0   1
  YES1 MUTATED     8   1
  YES1 WILD-TYPE 367  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  YES1 MUTATED      8    1
  YES1 WILD-TYPE  367   64
   clus
vv  YES1 MUTATED YES1 WILD-TYPE
  0            8            367
  1            1             64
[1] 2 2
[1] FALSE
D781V8, binary
                cls
clus               0   1
  YES1 MUTATED     4   6
  YES1 WILD-TYPE 221 258
[1] "tbl2"
                cls
clus             [,1] [,2]
  YES1 MUTATED      4    6
  YES1 WILD-TYPE  221  258
        clus
vv       YES1 MUTATED YES1 WILD-TYPE
  FEMALE            4            221
  MALE              6            258
[1] 2 2
[1] FALSE
D781V9, binary
                cls
clus               0   1
  YES1 MUTATED     9   0
  YES1 WILD-TYPE 341  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  YES1 MUTATED      9    0
  YES1 WILD-TYPE  341   22
     clus
vv    YES1 MUTATED YES1 WILD-TYPE
  NO             9            341
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  YES1 MUTATED                      7                             1
  YES1 WILD-TYPE                  308                            46
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  YES1 MUTATED                       1                              0
  YES1 WILD-TYPE                   105                             10
D781V10, multiclass
                                clus
vv                               YES1 MUTATED YES1 WILD-TYPE
  COLON ADENOCARCINOMA                      7            308
  COLON MUCINOUS ADENOCARCINOMA             1             46
  RECTAL ADENOCARCINOMA                     1            105
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  YES1 MUTATED     6   0   0   1
  YES1 WILD-TYPE 339   4  31  24
D781V11, multiclass
    clus
vv   YES1 MUTATED YES1 WILD-TYPE
  R0            6            339
  R1            0              4
  R2            0             31
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D781V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  YES1 MUTATED                                  0     1
  YES1 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  YES1 MUTATED                           0     7
  YES1 WILD-TYPE                        22   219
D781V13, multiclass
                                  clus
vv                                 YES1 MUTATED YES1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       7            219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(782) Variable = ACTL8 MUTATION ANALYSIS
D782V1, survival
                 sevent
clus2               0   1
  ACTL8 MUTATED     6   2
  ACTL8 WILD-TYPE 372  91
  ACTL8 MUTATED ACTL8 WILD-TYPE 
              8             463 
  ACTL8 MUTATED ACTL8 WILD-TYPE 
              2              91 
$`ACTL8 MUTATED`
TCGA-AA-3715 TCGA-AA-3870 TCGA-AD-6963 TCGA-AY-6197 TCGA-AZ-6600 TCGA-CK-4950 
       19.04        29.98        27.42        21.44        12.10        85.45 
TCGA-CM-6676 TCGA-G4-6323 
       11.08        13.78 

$`ACTL8 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       17.03        24.03        27.02        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6964 
       56.55         0.79         0.72         5.79        22.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        88.21        49.41         6.77       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       14.30        17.56       148.01        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6677 TCGA-CM-6678 
       14.04        11.01        12.95        13.05        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6586 
       85.48        63.62        61.91        36.00        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  ACTL8 MUTATED ACTL8 WILD-TYPE 
          11.08            0.00 
  ACTL8 MUTATED ACTL8 WILD-TYPE 
          85.45          148.01 
  ACTL8 MUTATED ACTL8 WILD-TYPE 
          20.24           20.19 
[1] "11.1 - 85.5 (20.2)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.2"
D782V2, continuous
D782V3, binary
                 cls
clus                0   1
  ACTL8 MUTATED     9   0
  ACTL8 WILD-TYPE 357 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ACTL8 MUTATED      9    0
  ACTL8 WILD-TYPE  357  119
        clus
vv       ACTL8 MUTATED ACTL8 WILD-TYPE
  COLON              9             357
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ACTL8 MUTATED         1        1        1         2         0         0
  ACTL8 WILD-TYPE      90        0       31       136        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ACTL8 MUTATED           0          0          1          0        2         0
  ACTL8 WILD-TYPE        24         11         58         42       46        18
                 vv
clus              STAGE IVB
  ACTL8 MUTATED           0
  ACTL8 WILD-TYPE         1
D782V4, multiclass
            clus
vv           ACTL8 MUTATED ACTL8 WILD-TYPE
  STAGE I                1              90
  STAGE IA               1               0
  STAGE II               1              31
  STAGE IIA              2             136
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             0              42
  STAGE IV               2              46
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ACTL8 MUTATED     0   1   6   1
  ACTL8 WILD-TYPE  17  91 323  49
D782V5, multiclass
    clus
vv   ACTL8 MUTATED ACTL8 WILD-TYPE
  T1             0              17
  T2             1              91
  T3             6             323
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  ACTL8 MUTATED     6   2   1
  ACTL8 WILD-TYPE 281 111  86
D782V6, multiclass
    clus
vv   ACTL8 MUTATED ACTL8 WILD-TYPE
  N0             6             281
  N1             2             111
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D782V7, binary
                 cls
clus                0   1
  ACTL8 MUTATED     4   2
  ACTL8 WILD-TYPE 371  63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ACTL8 MUTATED      4    2
  ACTL8 WILD-TYPE  371   63
   clus
vv  ACTL8 MUTATED ACTL8 WILD-TYPE
  0             4             371
  1             2              63
[1] 2 2
[1] FALSE
D782V8, binary
                 cls
clus                0   1
  ACTL8 MUTATED     3   6
  ACTL8 WILD-TYPE 222 258
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ACTL8 MUTATED      3    6
  ACTL8 WILD-TYPE  222  258
        clus
vv       ACTL8 MUTATED ACTL8 WILD-TYPE
  FEMALE             3             222
  MALE               6             258
[1] 2 2
[1] FALSE
D782V9, binary
                 cls
clus                0   1
  ACTL8 MUTATED     6   0
  ACTL8 WILD-TYPE 344  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ACTL8 MUTATED      6    0
  ACTL8 WILD-TYPE  344   22
     clus
vv    ACTL8 MUTATED ACTL8 WILD-TYPE
  NO              6             344
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ACTL8 MUTATED                      9                             0
  ACTL8 WILD-TYPE                  306                            47
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ACTL8 MUTATED                       0                              0
  ACTL8 WILD-TYPE                   106                             10
D782V10, multiclass
                                clus
vv                               ACTL8 MUTATED ACTL8 WILD-TYPE
  COLON ADENOCARCINOMA                       9             306
  COLON MUCINOUS ADENOCARCINOMA              0              47
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  ACTL8 MUTATED     6   1   0   0
  ACTL8 WILD-TYPE 339   3  31  25
D782V11, multiclass
    clus
vv   ACTL8 MUTATED ACTL8 WILD-TYPE
  R0             6             339
  R1             1               3
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D782V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ACTL8 MUTATED                                  0     0
  ACTL8 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ACTL8 MUTATED                           3     3
  ACTL8 WILD-TYPE                        19   223
D782V13, multiclass
                                  clus
vv                                 ACTL8 MUTATED ACTL8 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    3              19
  WHITE                                        3             223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(783) Variable = CNTFR MUTATION ANALYSIS
D783V1, survival
                 sevent
clus2               0   1
  CNTFR MUTATED     6   3
  CNTFR WILD-TYPE 372  90
  CNTFR MUTATED CNTFR WILD-TYPE 
              9             462 
  CNTFR MUTATED CNTFR WILD-TYPE 
              3              90 
$`CNTFR MUTATED`
TCGA-A6-6780 TCGA-AA-3673 TCGA-AZ-6598 TCGA-AZ-6601 TCGA-CA-6715 TCGA-CA-6717 
       20.12        50.04        49.41       100.01         0.07        12.76 
TCGA-CM-5862 TCGA-F4-6808 TCGA-G4-6586 
        5.03        33.67        35.80 

$`CNTFR WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3678 
        6.97        54.02         2.01        14.01         0.92        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 
      106.75        22.36        62.79        88.21         6.77        12.10 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.06         3.25         3.29        12.20        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5864 
       22.98        30.08        32.02        15.02        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       16.24        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 
       63.62        61.91        36.00        22.09        13.78        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  CNTFR MUTATED CNTFR WILD-TYPE 
           0.07            0.00 
  CNTFR MUTATED CNTFR WILD-TYPE 
         100.01          148.01 
  CNTFR MUTATED CNTFR WILD-TYPE 
          33.67           20.12 
[1] "0.1 - 100.0 (33.7)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.3"
D783V2, continuous
D783V3, binary
                 cls
clus                0   1
  CNTFR MUTATED    10   0
  CNTFR WILD-TYPE 356 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CNTFR MUTATED     10    0
  CNTFR WILD-TYPE  356  119
        clus
vv       CNTFR MUTATED CNTFR WILD-TYPE
  COLON             10             356
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CNTFR MUTATED         1        0        3         4         0         0
  CNTFR WILD-TYPE      90        1       29       134        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CNTFR MUTATED           0          0          1          0        0         1
  CNTFR WILD-TYPE        24         11         58         42       48        17
                 vv
clus              STAGE IVB
  CNTFR MUTATED           0
  CNTFR WILD-TYPE         1
D783V4, multiclass
            clus
vv           CNTFR MUTATED CNTFR WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               3              29
  STAGE IIA              4             134
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CNTFR MUTATED     1   0   9   0
  CNTFR WILD-TYPE  16  92 320  50
D783V5, multiclass
    clus
vv   CNTFR MUTATED CNTFR WILD-TYPE
  T1             1              16
  T2             0              92
  T3             9             320
  T4             0              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  CNTFR MUTATED     8   2   0
  CNTFR WILD-TYPE 279 111  87
D783V6, multiclass
    clus
vv   CNTFR MUTATED CNTFR WILD-TYPE
  N0             8             279
  N1             2             111
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D783V7, binary
                 cls
clus                0   1
  CNTFR MUTATED     7   1
  CNTFR WILD-TYPE 368  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CNTFR MUTATED      7    1
  CNTFR WILD-TYPE  368   64
   clus
vv  CNTFR MUTATED CNTFR WILD-TYPE
  0             7             368
  1             1              64
[1] 2 2
[1] FALSE
D783V8, binary
                 cls
clus                0   1
  CNTFR MUTATED     5   5
  CNTFR WILD-TYPE 220 259
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CNTFR MUTATED      5    5
  CNTFR WILD-TYPE  220  259
        clus
vv       CNTFR MUTATED CNTFR WILD-TYPE
  FEMALE             5             220
  MALE               5             259
[1] 2 2
[1] FALSE
D783V9, binary
                 cls
clus                0   1
  CNTFR MUTATED     8   0
  CNTFR WILD-TYPE 342  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CNTFR MUTATED      8    0
  CNTFR WILD-TYPE  342   22
     clus
vv    CNTFR MUTATED CNTFR WILD-TYPE
  NO              8             342
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CNTFR MUTATED                      8                             2
  CNTFR WILD-TYPE                  307                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CNTFR MUTATED                       0                              0
  CNTFR WILD-TYPE                   106                             10
D783V10, multiclass
                                clus
vv                               CNTFR MUTATED CNTFR WILD-TYPE
  COLON ADENOCARCINOMA                       8             307
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  CNTFR MUTATED     5   0   0   2
  CNTFR WILD-TYPE 340   4  31  23
D783V11, multiclass
    clus
vv   CNTFR MUTATED CNTFR WILD-TYPE
  R0             5             340
  R1             0               4
  R2             0              31
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D783V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CNTFR MUTATED                                  0     2
  CNTFR WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CNTFR MUTATED                           0     6
  CNTFR WILD-TYPE                        22   220
D783V13, multiclass
                                  clus
vv                                 CNTFR MUTATED CNTFR WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               9
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        6             220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(784) Variable = OR4E2 MUTATION ANALYSIS
D784V1, survival
                 sevent
clus2               0   1
  OR4E2 MUTATED     4   0
  OR4E2 WILD-TYPE 374  93
  OR4E2 MUTATED OR4E2 WILD-TYPE 
              4             467 
  OR4E2 MUTATED OR4E2 WILD-TYPE 
              0              93 
$`OR4E2 MUTATED`
TCGA-A6-5665 TCGA-AA-3510 TCGA-CM-6675 TCGA-G4-6586 
       22.06        63.98        13.05        35.80 

$`OR4E2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       12.95        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 
       61.91        36.00        22.09        13.78        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  OR4E2 MUTATED OR4E2 WILD-TYPE 
          13.05            0.00 
  OR4E2 MUTATED OR4E2 WILD-TYPE 
          63.98          148.01 
  OR4E2 MUTATED OR4E2 WILD-TYPE 
          28.93           20.12 
[1] "13.1 - 64.0 (28.9)" "0.0 - 148.0 (20.1)"
[1] "hr="     "9100000"
D784V2, continuous
D784V3, binary
                 cls
clus                0   1
  OR4E2 MUTATED     5   0
  OR4E2 WILD-TYPE 361 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR4E2 MUTATED      5    0
  OR4E2 WILD-TYPE  361  119
        clus
vv       OR4E2 MUTATED OR4E2 WILD-TYPE
  COLON              5             361
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  OR4E2 MUTATED         0        0        1         2         1         0
  OR4E2 WILD-TYPE      91        1       31       136         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  OR4E2 MUTATED           0          0          0          0        0         0
  OR4E2 WILD-TYPE        24         11         59         42       48        18
                 vv
clus              STAGE IVB
  OR4E2 MUTATED           1
  OR4E2 WILD-TYPE         0
D784V4, multiclass
            clus
vv           OR4E2 MUTATED OR4E2 WILD-TYPE
  STAGE I                0              91
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              2             136
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              1               0
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  OR4E2 MUTATED     0   0   4   1
  OR4E2 WILD-TYPE  17  92 325  49
D784V5, multiclass
    clus
vv   OR4E2 MUTATED OR4E2 WILD-TYPE
  T1             0              17
  T2             0              92
  T3             4             325
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  OR4E2 MUTATED     4   0   1
  OR4E2 WILD-TYPE 283 113  86
D784V6, multiclass
    clus
vv   OR4E2 MUTATED OR4E2 WILD-TYPE
  N0             4             283
  N1             0             113
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D784V7, binary
                 cls
clus                0   1
  OR4E2 MUTATED     3   1
  OR4E2 WILD-TYPE 372  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR4E2 MUTATED      3    1
  OR4E2 WILD-TYPE  372   64
   clus
vv  OR4E2 MUTATED OR4E2 WILD-TYPE
  0             3             372
  1             1              64
[1] 2 2
[1] FALSE
D784V8, binary
                 cls
clus                0   1
  OR4E2 MUTATED     3   2
  OR4E2 WILD-TYPE 222 262
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR4E2 MUTATED      3    2
  OR4E2 WILD-TYPE  222  262
        clus
vv       OR4E2 MUTATED OR4E2 WILD-TYPE
  FEMALE             3             222
  MALE               2             262
[1] 2 2
[1] FALSE
D784V9, binary
                 cls
clus                0   1
  OR4E2 MUTATED     4   0
  OR4E2 WILD-TYPE 346  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR4E2 MUTATED      4    0
  OR4E2 WILD-TYPE  346   22
     clus
vv    OR4E2 MUTATED OR4E2 WILD-TYPE
  NO              4             346
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  OR4E2 MUTATED                      5                             0
  OR4E2 WILD-TYPE                  310                            47
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  OR4E2 MUTATED                       0                              0
  OR4E2 WILD-TYPE                   106                             10
D784V10, multiclass
                                clus
vv                               OR4E2 MUTATED OR4E2 WILD-TYPE
  COLON ADENOCARCINOMA                       5             310
  COLON MUCINOUS ADENOCARCINOMA              0              47
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  OR4E2 MUTATED     4   0   0   1
  OR4E2 WILD-TYPE 341   4  31  24
D784V11, multiclass
    clus
vv   OR4E2 MUTATED OR4E2 WILD-TYPE
  R0             4             341
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D784V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OR4E2 MUTATED                                  0     0
  OR4E2 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  OR4E2 MUTATED                           1     3
  OR4E2 WILD-TYPE                        21   223
D784V13, multiclass
                                  clus
vv                                 OR4E2 MUTATED OR4E2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        3             223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(785) Variable = PPP1R12A MUTATION ANALYSIS
D785V1, survival
                    sevent
clus2                  0   1
  PPP1R12A MUTATED    11   5
  PPP1R12A WILD-TYPE 367  88
  PPP1R12A MUTATED PPP1R12A WILD-TYPE 
                16                455 
  PPP1R12A MUTATED PPP1R12A WILD-TYPE 
                 5                 88 
$`PPP1R12A MUTATED`
TCGA-A6-2671 TCGA-A6-6781 TCGA-AA-3502 TCGA-AA-3845 TCGA-AA-3864 TCGA-AZ-6608 
       43.76        19.66        35.01         0.00        53.00         1.61 
TCGA-CA-6718 TCGA-CK-5913 TCGA-CK-6751 TCGA-D5-5540 TCGA-D5-6539 TCGA-DM-A1HA 
       10.06        51.32       124.27        56.09        12.49       131.51 
TCGA-F4-6808 TCGA-AG-4007 TCGA-DY-A1DG TCGA-EI-6507 
       33.67         1.02        51.48        19.96 

$`PPP1R12A WILD-TYPE`
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       46.65        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3510 
       20.12        20.28         7.04         3.02         1.02        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       38.99        37.02        14.93        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       31.07        30.05        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07        12.20        12.76        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 
      148.01        85.45        15.62        49.08         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
       82.95         1.91        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       45.40        12.26        19.59        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
        7.50        44.32       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       41.42        16.24        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4008 
       32.02        19.99        28.04        36.03        14.04        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       41.36        57.24        24.13        32.61         0.49        20.55 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  PPP1R12A MUTATED PPP1R12A WILD-TYPE 
                 0                  0 
  PPP1R12A MUTATED PPP1R12A WILD-TYPE 
            131.51             148.01 
  PPP1R12A MUTATED PPP1R12A WILD-TYPE 
             34.34              20.12 
[1] "0.0 - 131.5 (34.3)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.1"
D785V2, continuous
D785V3, binary
                    cls
clus                   0   1
  PPP1R12A MUTATED    13   3
  PPP1R12A WILD-TYPE 353 116
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  PPP1R12A MUTATED     13    3
  PPP1R12A WILD-TYPE  353  116
        clus
vv       PPP1R12A MUTATED PPP1R12A WILD-TYPE
  COLON                13                353
  RECTUM                3                116
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PPP1R12A MUTATED         3        0        1         5         0         0
  PPP1R12A WILD-TYPE      88        1       31       133        10         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PPP1R12A MUTATED           0          2          0          2        2
  PPP1R12A WILD-TYPE        24          9         59         40       46
                    vv
clus                 STAGE IVA STAGE IVB
  PPP1R12A MUTATED           1         0
  PPP1R12A WILD-TYPE        17         1
D785V4, multiclass
            clus
vv           PPP1R12A MUTATED PPP1R12A WILD-TYPE
  STAGE I                   3                 88
  STAGE IA                  0                  1
  STAGE II                  1                 31
  STAGE IIA                 5                133
  STAGE IIB                 0                 10
  STAGE IIC                 0                  1
  STAGE III                 0                 24
  STAGE IIIA                2                  9
  STAGE IIIB                0                 59
  STAGE IIIC                2                 40
  STAGE IV                  2                 46
  STAGE IVA                 1                 17
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  PPP1R12A MUTATED     1   3  10   2
  PPP1R12A WILD-TYPE  16  89 319  48
D785V5, multiclass
    clus
vv   PPP1R12A MUTATED PPP1R12A WILD-TYPE
  T1                1                 16
  T2                3                 89
  T3               10                319
  T4                2                 48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  PPP1R12A MUTATED    10   3   3
  PPP1R12A WILD-TYPE 277 110  84
D785V6, multiclass
    clus
vv   PPP1R12A MUTATED PPP1R12A WILD-TYPE
  N0               10                277
  N1                3                110
  N2                3                 84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D785V7, binary
                    cls
clus                   0   1
  PPP1R12A MUTATED    10   3
  PPP1R12A WILD-TYPE 365  62
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  PPP1R12A MUTATED     10    3
  PPP1R12A WILD-TYPE  365   62
   clus
vv  PPP1R12A MUTATED PPP1R12A WILD-TYPE
  0               10                365
  1                3                 62
[1] 2 2
[1] FALSE
D785V8, binary
                    cls
clus                   0   1
  PPP1R12A MUTATED     6  10
  PPP1R12A WILD-TYPE 219 254
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  PPP1R12A MUTATED      6   10
  PPP1R12A WILD-TYPE  219  254
        clus
vv       PPP1R12A MUTATED PPP1R12A WILD-TYPE
  FEMALE                6                219
  MALE                 10                254
[1] 2 2
[1] FALSE
D785V9, binary
                    cls
clus                   0   1
  PPP1R12A MUTATED    12   0
  PPP1R12A WILD-TYPE 338  22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  PPP1R12A MUTATED     12    0
  PPP1R12A WILD-TYPE  338   22
     clus
vv    PPP1R12A MUTATED PPP1R12A WILD-TYPE
  NO                12                338
  YES                0                 22
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PPP1R12A MUTATED                     11                             2
  PPP1R12A WILD-TYPE                  304                            45
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PPP1R12A MUTATED                       3                              0
  PPP1R12A WILD-TYPE                   103                             10
D785V10, multiclass
                                clus
vv                               PPP1R12A MUTATED PPP1R12A WILD-TYPE
  COLON ADENOCARCINOMA                         11                304
  COLON MUCINOUS ADENOCARCINOMA                 2                 45
  RECTAL ADENOCARCINOMA                         3                103
  RECTAL MUCINOUS ADENOCARCINOMA                0                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  PPP1R12A MUTATED     9   0   1   3
  PPP1R12A WILD-TYPE 336   4  30  22
D785V11, multiclass
    clus
vv   PPP1R12A MUTATED PPP1R12A WILD-TYPE
  R0                9                336
  R1                0                  4
  R2                1                 30
  RX                3                 22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D785V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PPP1R12A MUTATED                                  0     1
  PPP1R12A WILD-TYPE                                1    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  PPP1R12A MUTATED                           0    11
  PPP1R12A WILD-TYPE                        22   215
D785V13, multiclass
                                  clus
vv                                 PPP1R12A MUTATED PPP1R12A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                 10
  BLACK OR AFRICAN AMERICAN                       0                 22
  WHITE                                          11                215
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(786) Variable = ZNF721 MUTATION ANALYSIS
D786V1, survival
                  sevent
clus2                0   1
  ZNF721 MUTATED    12   4
  ZNF721 WILD-TYPE 366  89
  ZNF721 MUTATED ZNF721 WILD-TYPE 
              16              455 
  ZNF721 MUTATED ZNF721 WILD-TYPE 
               4               89 
$`ZNF721 MUTATED`
TCGA-A6-6141 TCGA-A6-6653 TCGA-AA-3510 TCGA-AA-3710 TCGA-AA-3815 TCGA-AA-3977 
        8.38        24.39        63.98        26.99        33.04        25.02 
TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A03F TCGA-AU-6004 TCGA-AZ-4315 TCGA-CA-6717 
        4.01        34.98        18.05        27.09        58.39        12.76 
TCGA-CA-6718 TCGA-CM-5862 TCGA-AG-3892 TCGA-AG-A002 
       10.06         5.03        13.02        20.98 

$`ZNF721 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 
       22.09        22.06        32.71        27.09        22.52        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 
       25.18        24.16        21.76        24.69        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
       85.05        19.04        19.04        10.06        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       39.98        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
        0.20        14.50        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 
        3.25         3.29         0.07        12.20        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       30.08        32.02        15.02        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  ZNF721 MUTATED ZNF721 WILD-TYPE 
            4.01             0.00 
  ZNF721 MUTATED ZNF721 WILD-TYPE 
           63.98           148.01 
  ZNF721 MUTATED ZNF721 WILD-TYPE 
          22.685           20.120 
[1] "4.0 - 64.0 (22.7)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.4"
D786V2, continuous
D786V3, binary
                  cls
clus                 0   1
  ZNF721 MUTATED    15   2
  ZNF721 WILD-TYPE 351 117
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF721 MUTATED     15    2
  ZNF721 WILD-TYPE  351  117
        clus
vv       ZNF721 MUTATED ZNF721 WILD-TYPE
  COLON              15              351
  RECTUM              2              117
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZNF721 MUTATED         4        0        1         7         2         0
  ZNF721 WILD-TYPE      87        1       31       131         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF721 MUTATED           1          0          0          0        0
  ZNF721 WILD-TYPE        23         11         59         42       48
                  vv
clus               STAGE IVA STAGE IVB
  ZNF721 MUTATED           1         0
  ZNF721 WILD-TYPE        17         1
D786V4, multiclass
            clus
vv           ZNF721 MUTATED ZNF721 WILD-TYPE
  STAGE I                 4               87
  STAGE IA                0                1
  STAGE II                1               31
  STAGE IIA               7              131
  STAGE IIB               2                8
  STAGE IIC               0                1
  STAGE III               1               23
  STAGE IIIA              0               11
  STAGE IIIB              0               59
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               1               17
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZNF721 MUTATED     1   4  10   2
  ZNF721 WILD-TYPE  16  88 319  48
D786V5, multiclass
    clus
vv   ZNF721 MUTATED ZNF721 WILD-TYPE
  T1              1               16
  T2              4               88
  T3             10              319
  T4              2               48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  ZNF721 MUTATED    15   1   1
  ZNF721 WILD-TYPE 272 112  86
D786V6, multiclass
    clus
vv   ZNF721 MUTATED ZNF721 WILD-TYPE
  N0             15              272
  N1              1              112
  N2              1               86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D786V7, binary
                  cls
clus                 0   1
  ZNF721 MUTATED    15   1
  ZNF721 WILD-TYPE 360  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF721 MUTATED     15    1
  ZNF721 WILD-TYPE  360   64
   clus
vv  ZNF721 MUTATED ZNF721 WILD-TYPE
  0             15              360
  1              1               64
[1] 2 2
[1] FALSE
D786V8, binary
                  cls
clus                 0   1
  ZNF721 MUTATED     7  10
  ZNF721 WILD-TYPE 218 254
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF721 MUTATED      7   10
  ZNF721 WILD-TYPE  218  254
        clus
vv       ZNF721 MUTATED ZNF721 WILD-TYPE
  FEMALE              7              218
  MALE               10              254
[1] 2 2
[1] FALSE
D786V9, binary
                  cls
clus                 0   1
  ZNF721 MUTATED    13   0
  ZNF721 WILD-TYPE 337  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF721 MUTATED     13    0
  ZNF721 WILD-TYPE  337   22
     clus
vv    ZNF721 MUTATED ZNF721 WILD-TYPE
  NO              13              337
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ZNF721 MUTATED                     12                             3
  ZNF721 WILD-TYPE                  303                            44
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ZNF721 MUTATED                       2                              0
  ZNF721 WILD-TYPE                   104                             10
D786V10, multiclass
                                clus
vv                               ZNF721 MUTATED ZNF721 WILD-TYPE
  COLON ADENOCARCINOMA                       12              303
  COLON MUCINOUS ADENOCARCINOMA               3               44
  RECTAL ADENOCARCINOMA                       2              104
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ZNF721 MUTATED    12   0   0   2
  ZNF721 WILD-TYPE 333   4  31  23
D786V11, multiclass
    clus
vv   ZNF721 MUTATED ZNF721 WILD-TYPE
  R0             12              333
  R1              0                4
  R2              0               31
  RX              2               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D786V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF721 MUTATED                                  0     2
  ZNF721 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZNF721 MUTATED                           1     4
  ZNF721 WILD-TYPE                        21   222
D786V13, multiclass
                                  clus
vv                                 ZNF721 MUTATED ZNF721 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                9
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                         4              222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(787) Variable = KIFAP3 MUTATION ANALYSIS
D787V1, survival
                  sevent
clus2                0   1
  KIFAP3 MUTATED     8   0
  KIFAP3 WILD-TYPE 370  93
  KIFAP3 MUTATED KIFAP3 WILD-TYPE 
               8              463 
  KIFAP3 MUTATED KIFAP3 WILD-TYPE 
               0               93 
$`KIFAP3 MUTATED`
TCGA-AA-3663 TCGA-AA-3713 TCGA-AA-3815 TCGA-AA-A00A TCGA-AU-6004 TCGA-CA-6717 
        6.97        19.04        33.04        38.04        27.09        12.76 
TCGA-CM-4746 TCGA-D5-6540 
       37.02        16.14 

$`KIFAP3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.05        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       35.05         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00E 
       19.07         7.96        27.02        13.94        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       14.50        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07        12.20        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       20.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 
       17.85         4.80        17.13        12.49        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  KIFAP3 MUTATED KIFAP3 WILD-TYPE 
            6.97             0.00 
  KIFAP3 MUTATED KIFAP3 WILD-TYPE 
           38.04           148.01 
  KIFAP3 MUTATED KIFAP3 WILD-TYPE 
          23.065           20.190 
[1] "7.0 - 38.0 (23.1)"  "0.0 - 148.0 (20.2)"
[1] "hr="     "9200000"
D787V2, continuous
D787V3, binary
                  cls
clus                 0   1
  KIFAP3 MUTATED     9   0
  KIFAP3 WILD-TYPE 357 119
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KIFAP3 MUTATED      9    0
  KIFAP3 WILD-TYPE  357  119
        clus
vv       KIFAP3 MUTATED KIFAP3 WILD-TYPE
  COLON               9              357
  RECTUM              0              119
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KIFAP3 MUTATED         3        0        2         3         0         0
  KIFAP3 WILD-TYPE      88        1       30       135        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIFAP3 MUTATED           0          0          0          0        1
  KIFAP3 WILD-TYPE        24         11         59         42       47
                  vv
clus               STAGE IVA STAGE IVB
  KIFAP3 MUTATED           0         0
  KIFAP3 WILD-TYPE        18         1
D787V4, multiclass
            clus
vv           KIFAP3 MUTATED KIFAP3 WILD-TYPE
  STAGE I                 3               88
  STAGE IA                0                1
  STAGE II                2               30
  STAGE IIA               3              135
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              0               59
  STAGE IIIC              0               42
  STAGE IV                1               47
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  KIFAP3 MUTATED     0   3   5   1
  KIFAP3 WILD-TYPE  17  89 324  49
D787V5, multiclass
    clus
vv   KIFAP3 MUTATED KIFAP3 WILD-TYPE
  T1              0               17
  T2              3               89
  T3              5              324
  T4              1               49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  KIFAP3 MUTATED     9   0   0
  KIFAP3 WILD-TYPE 278 113  87
D787V6, multiclass
    clus
vv   KIFAP3 MUTATED KIFAP3 WILD-TYPE
  N0              9              278
  N1              0              113
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D787V7, binary
                  cls
clus                 0   1
  KIFAP3 MUTATED     8   1
  KIFAP3 WILD-TYPE 367  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KIFAP3 MUTATED      8    1
  KIFAP3 WILD-TYPE  367   64
   clus
vv  KIFAP3 MUTATED KIFAP3 WILD-TYPE
  0              8              367
  1              1               64
[1] 2 2
[1] FALSE
D787V8, binary
                  cls
clus                 0   1
  KIFAP3 MUTATED     3   6
  KIFAP3 WILD-TYPE 222 258
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KIFAP3 MUTATED      3    6
  KIFAP3 WILD-TYPE  222  258
        clus
vv       KIFAP3 MUTATED KIFAP3 WILD-TYPE
  FEMALE              3              222
  MALE                6              258
[1] 2 2
[1] FALSE
D787V9, binary
                  cls
clus                 0   1
  KIFAP3 MUTATED     6   1
  KIFAP3 WILD-TYPE 344  21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KIFAP3 MUTATED      6    1
  KIFAP3 WILD-TYPE  344   21
     clus
vv    KIFAP3 MUTATED KIFAP3 WILD-TYPE
  NO               6              344
  YES              1               21
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  KIFAP3 MUTATED                      7                             2
  KIFAP3 WILD-TYPE                  308                            45
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  KIFAP3 MUTATED                       0                              0
  KIFAP3 WILD-TYPE                   106                             10
D787V10, multiclass
                                clus
vv                               KIFAP3 MUTATED KIFAP3 WILD-TYPE
  COLON ADENOCARCINOMA                        7              308
  COLON MUCINOUS ADENOCARCINOMA               2               45
  RECTAL ADENOCARCINOMA                       0              106
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  KIFAP3 MUTATED     7   0   1   1
  KIFAP3 WILD-TYPE 338   4  30  24
D787V11, multiclass
    clus
vv   KIFAP3 MUTATED KIFAP3 WILD-TYPE
  R0              7              338
  R1              0                4
  R2              1               30
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D787V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KIFAP3 MUTATED                                  0     1
  KIFAP3 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  KIFAP3 MUTATED                           1     2
  KIFAP3 WILD-TYPE                        21   224
D787V13, multiclass
                                  clus
vv                                 KIFAP3 MUTATED KIFAP3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                         2              224
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(788) Variable = SLC22A9 MUTATION ANALYSIS
D788V1, survival
                   sevent
clus2                 0   1
  SLC22A9 MUTATED     8   0
  SLC22A9 WILD-TYPE 370  93
  SLC22A9 MUTATED SLC22A9 WILD-TYPE 
                8               463 
  SLC22A9 MUTATED SLC22A9 WILD-TYPE 
                0                93 
$`SLC22A9 MUTATED`
TCGA-A6-6142 TCGA-A6-6781 TCGA-AA-3511 TCGA-AA-3977 TCGA-CA-6717 TCGA-CK-5913 
       25.08        19.66         6.97        25.02        12.76        51.32 
TCGA-D5-6541 TCGA-EI-6507 
       15.58        19.96 

$`SLC22A9 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
       63.98         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07        12.20        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
        0.49        20.55        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  SLC22A9 MUTATED SLC22A9 WILD-TYPE 
             6.97              0.00 
  SLC22A9 MUTATED SLC22A9 WILD-TYPE 
            51.32            148.01 
  SLC22A9 MUTATED SLC22A9 WILD-TYPE 
            19.81             20.28 
[1] "7.0 - 51.3 (19.8)"  "0.0 - 148.0 (20.3)"
[1] "hr="     "9100000"
D788V2, continuous
D788V3, binary
                   cls
clus                  0   1
  SLC22A9 MUTATED     9   1
  SLC22A9 WILD-TYPE 357 118
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC22A9 MUTATED      9    1
  SLC22A9 WILD-TYPE  357  118
        clus
vv       SLC22A9 MUTATED SLC22A9 WILD-TYPE
  COLON                9               357
  RECTUM               1               118
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SLC22A9 MUTATED         0        0        1         5         0         0
  SLC22A9 WILD-TYPE      91        1       31       133        10         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC22A9 MUTATED           0          0          0          2        0
  SLC22A9 WILD-TYPE        24         11         59         40       48
                   vv
clus                STAGE IVA STAGE IVB
  SLC22A9 MUTATED           1         0
  SLC22A9 WILD-TYPE        17         1
D788V4, multiclass
            clus
vv           SLC22A9 MUTATED SLC22A9 WILD-TYPE
  STAGE I                  0                91
  STAGE IA                 0                 1
  STAGE II                 1                31
  STAGE IIA                5               133
  STAGE IIB                0                10
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               0                11
  STAGE IIIB               0                59
  STAGE IIIC               2                40
  STAGE IV                 0                48
  STAGE IVA                1                17
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  SLC22A9 MUTATED     0   1   7   2
  SLC22A9 WILD-TYPE  17  91 322  48
D788V5, multiclass
    clus
vv   SLC22A9 MUTATED SLC22A9 WILD-TYPE
  T1               0                17
  T2               1                91
  T3               7               322
  T4               2                48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  SLC22A9 MUTATED     7   2   1
  SLC22A9 WILD-TYPE 280 111  86
D788V6, multiclass
    clus
vv   SLC22A9 MUTATED SLC22A9 WILD-TYPE
  N0               7               280
  N1               2               111
  N2               1                86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D788V7, binary
                   cls
clus                  0   1
  SLC22A9 MUTATED     5   1
  SLC22A9 WILD-TYPE 370  64
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC22A9 MUTATED      5    1
  SLC22A9 WILD-TYPE  370   64
   clus
vv  SLC22A9 MUTATED SLC22A9 WILD-TYPE
  0               5               370
  1               1                64
[1] 2 2
[1] FALSE
D788V8, binary
                   cls
clus                  0   1
  SLC22A9 MUTATED     3   7
  SLC22A9 WILD-TYPE 222 257
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC22A9 MUTATED      3    7
  SLC22A9 WILD-TYPE  222  257
        clus
vv       SLC22A9 MUTATED SLC22A9 WILD-TYPE
  FEMALE               3               222
  MALE                 7               257
[1] 2 2
[1] FALSE
D788V9, binary
                   cls
clus                  0   1
  SLC22A9 MUTATED     8   0
  SLC22A9 WILD-TYPE 342  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC22A9 MUTATED      8    0
  SLC22A9 WILD-TYPE  342   22
     clus
vv    SLC22A9 MUTATED SLC22A9 WILD-TYPE
  NO                8               342
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SLC22A9 MUTATED                      6                             3
  SLC22A9 WILD-TYPE                  309                            44
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SLC22A9 MUTATED                       1                              0
  SLC22A9 WILD-TYPE                   105                             10
D788V10, multiclass
                                clus
vv                               SLC22A9 MUTATED SLC22A9 WILD-TYPE
  COLON ADENOCARCINOMA                         6               309
  COLON MUCINOUS ADENOCARCINOMA                3                44
  RECTAL ADENOCARCINOMA                        1               105
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  SLC22A9 MUTATED     6   0   0   2
  SLC22A9 WILD-TYPE 339   4  31  23
D788V11, multiclass
    clus
vv   SLC22A9 MUTATED SLC22A9 WILD-TYPE
  R0               6               339
  R1               0                 4
  R2               0                31
  RX               2                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D788V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SLC22A9 MUTATED                                  0     1
  SLC22A9 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  SLC22A9 MUTATED                           0     6
  SLC22A9 WILD-TYPE                        22   220
D788V13, multiclass
                                  clus
vv                                 SLC22A9 MUTATED SLC22A9 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                10
  BLACK OR AFRICAN AMERICAN                      0                22
  WHITE                                          6               220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(789) Variable = C5ORF22 MUTATION ANALYSIS
D789V1, survival
                   sevent
clus2                 0   1
  C5ORF22 MUTATED     7   3
  C5ORF22 WILD-TYPE 371  90
  C5ORF22 MUTATED C5ORF22 WILD-TYPE 
               10               461 
  C5ORF22 MUTATED C5ORF22 WILD-TYPE 
                3                90 
$`C5ORF22 MUTATED`
TCGA-A6-5661 TCGA-AA-3655 TCGA-AA-3672 TCGA-AA-3850 TCGA-CK-5912 TCGA-DM-A1D4 
       33.53        61.02         0.92         0.00        49.08        92.75 
TCGA-F4-6805 TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6588 
       34.42        85.48        61.91        26.17 

$`C5ORF22 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       19.99        13.94        19.99        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
       54.02         2.01        14.01        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
      130.65        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6806 
       31.96        35.74         6.18        47.87         1.55        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6310 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 
       63.62        36.00        22.09        13.78        35.80        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  C5ORF22 MUTATED C5ORF22 WILD-TYPE 
                0                 0 
  C5ORF22 MUTATED C5ORF22 WILD-TYPE 
            92.75            148.01 
  C5ORF22 MUTATED C5ORF22 WILD-TYPE 
            41.75             20.02 
[1] "0.0 - 92.8 (41.8)"  "0.0 - 148.0 (20.0)"
[1] "hr=" "1.1"
D789V2, continuous
D789V3, binary
                   cls
clus                  0   1
  C5ORF22 MUTATED    11   0
  C5ORF22 WILD-TYPE 355 119
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C5ORF22 MUTATED     11    0
  C5ORF22 WILD-TYPE  355  119
        clus
vv       C5ORF22 MUTATED C5ORF22 WILD-TYPE
  COLON               11               355
  RECTUM               0               119
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  C5ORF22 MUTATED         3        0        1         4         0         0
  C5ORF22 WILD-TYPE      88        1       31       134        10         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C5ORF22 MUTATED           1          0          1          0        1
  C5ORF22 WILD-TYPE        23         11         58         42       47
                   vv
clus                STAGE IVA STAGE IVB
  C5ORF22 MUTATED           0         0
  C5ORF22 WILD-TYPE        18         1
D789V4, multiclass
            clus
vv           C5ORF22 MUTATED C5ORF22 WILD-TYPE
  STAGE I                  3                88
  STAGE IA                 0                 1
  STAGE II                 1                31
  STAGE IIA                4               134
  STAGE IIB                0                10
  STAGE IIC                0                 1
  STAGE III                1                23
  STAGE IIIA               0                11
  STAGE IIIB               1                58
  STAGE IIIC               0                42
  STAGE IV                 1                47
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  C5ORF22 MUTATED     0   3   8   0
  C5ORF22 WILD-TYPE  17  89 321  50
D789V5, multiclass
    clus
vv   C5ORF22 MUTATED C5ORF22 WILD-TYPE
  T1               0                17
  T2               3                89
  T3               8               321
  T4               0                50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  C5ORF22 MUTATED     8   3   0
  C5ORF22 WILD-TYPE 279 110  87
D789V6, multiclass
    clus
vv   C5ORF22 MUTATED C5ORF22 WILD-TYPE
  N0               8               279
  N1               3               110
  N2               0                87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D789V7, binary
                   cls
clus                  0   1
  C5ORF22 MUTATED     8   1
  C5ORF22 WILD-TYPE 367  64
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C5ORF22 MUTATED      8    1
  C5ORF22 WILD-TYPE  367   64
   clus
vv  C5ORF22 MUTATED C5ORF22 WILD-TYPE
  0               8               367
  1               1                64
[1] 2 2
[1] FALSE
D789V8, binary
                   cls
clus                  0   1
  C5ORF22 MUTATED     5   6
  C5ORF22 WILD-TYPE 220 258
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C5ORF22 MUTATED      5    6
  C5ORF22 WILD-TYPE  220  258
        clus
vv       C5ORF22 MUTATED C5ORF22 WILD-TYPE
  FEMALE               5               220
  MALE                 6               258
[1] 2 2
[1] FALSE
D789V9, binary
                   cls
clus                  0   1
  C5ORF22 MUTATED     8   0
  C5ORF22 WILD-TYPE 342  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C5ORF22 MUTATED      8    0
  C5ORF22 WILD-TYPE  342   22
     clus
vv    C5ORF22 MUTATED C5ORF22 WILD-TYPE
  NO                8               342
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  C5ORF22 MUTATED                     11                             0
  C5ORF22 WILD-TYPE                  304                            47
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  C5ORF22 MUTATED                       0                              0
  C5ORF22 WILD-TYPE                   106                             10
D789V10, multiclass
                                clus
vv                               C5ORF22 MUTATED C5ORF22 WILD-TYPE
  COLON ADENOCARCINOMA                        11               304
  COLON MUCINOUS ADENOCARCINOMA                0                47
  RECTAL ADENOCARCINOMA                        0               106
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  C5ORF22 MUTATED     8   0   0   2
  C5ORF22 WILD-TYPE 337   4  31  23
D789V11, multiclass
    clus
vv   C5ORF22 MUTATED C5ORF22 WILD-TYPE
  R0               8               337
  R1               0                 4
  R2               0                31
  RX               2                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D789V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C5ORF22 MUTATED                                  0     0
  C5ORF22 WILD-TYPE                                1    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  C5ORF22 MUTATED                           2     6
  C5ORF22 WILD-TYPE                        20   220
D789V13, multiclass
                                  clus
vv                                 C5ORF22 MUTATED C5ORF22 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                      2                20
  WHITE                                          6               220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(790) Variable = FOXN3 MUTATION ANALYSIS
D790V1, survival
                 sevent
clus2               0   1
  FOXN3 MUTATED    11   0
  FOXN3 WILD-TYPE 367  93
  FOXN3 MUTATED FOXN3 WILD-TYPE 
             11             460 
  FOXN3 MUTATED FOXN3 WILD-TYPE 
              0              93 
$`FOXN3 MUTATED`
TCGA-A6-6653 TCGA-A6-6781 TCGA-AA-3663 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3821 
       24.39        19.66         6.97        26.99        19.04         1.02 
TCGA-AA-3864 TCGA-CA-6717 TCGA-CM-4743 TCGA-CM-5864 TCGA-CM-6169 
       53.00        12.76        23.05        15.02        13.02 

$`FOXN3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
       25.08        25.18        24.16        21.76        24.69        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       85.05        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
       25.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07        12.20        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
       82.95         1.91       124.27        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
       15.02         5.03        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  FOXN3 MUTATED FOXN3 WILD-TYPE 
           1.02            0.00 
  FOXN3 MUTATED FOXN3 WILD-TYPE 
          53.00          148.01 
  FOXN3 MUTATED FOXN3 WILD-TYPE 
         19.040          20.415 
[1] "1.0 - 53.0 (19.0)"  "0.0 - 148.0 (20.4)"
[1] "hr="     "9200000"
D790V2, continuous
D790V3, binary
                 cls
clus                0   1
  FOXN3 MUTATED    11   0
  FOXN3 WILD-TYPE 355 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FOXN3 MUTATED     11    0
  FOXN3 WILD-TYPE  355  119
        clus
vv       FOXN3 MUTATED FOXN3 WILD-TYPE
  COLON             11             355
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FOXN3 MUTATED         3        0        2         4         0         0
  FOXN3 WILD-TYPE      88        1       30       134        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  FOXN3 MUTATED           0          0          0          1        1         0
  FOXN3 WILD-TYPE        24         11         59         41       47        18
                 vv
clus              STAGE IVB
  FOXN3 MUTATED           0
  FOXN3 WILD-TYPE         1
D790V4, multiclass
            clus
vv           FOXN3 MUTATED FOXN3 WILD-TYPE
  STAGE I                3              88
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA              4             134
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             1              41
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  FOXN3 MUTATED     0   3   7   1
  FOXN3 WILD-TYPE  17  89 322  49
D790V5, multiclass
    clus
vv   FOXN3 MUTATED FOXN3 WILD-TYPE
  T1             0              17
  T2             3              89
  T3             7             322
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  FOXN3 MUTATED    10   1   0
  FOXN3 WILD-TYPE 277 112  87
D790V6, multiclass
    clus
vv   FOXN3 MUTATED FOXN3 WILD-TYPE
  N0            10             277
  N1             1             112
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D790V7, binary
                 cls
clus                0   1
  FOXN3 MUTATED     9   1
  FOXN3 WILD-TYPE 366  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FOXN3 MUTATED      9    1
  FOXN3 WILD-TYPE  366   64
   clus
vv  FOXN3 MUTATED FOXN3 WILD-TYPE
  0             9             366
  1             1              64
[1] 2 2
[1] FALSE
D790V8, binary
                 cls
clus                0   1
  FOXN3 MUTATED     2   9
  FOXN3 WILD-TYPE 223 255
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FOXN3 MUTATED      2    9
  FOXN3 WILD-TYPE  223  255
        clus
vv       FOXN3 MUTATED FOXN3 WILD-TYPE
  FEMALE             2             223
  MALE               9             255
[1] 2 2
[1] FALSE
D790V9, binary
                 cls
clus                0   1
  FOXN3 MUTATED    10   1
  FOXN3 WILD-TYPE 340  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FOXN3 MUTATED     10    1
  FOXN3 WILD-TYPE  340   21
     clus
vv    FOXN3 MUTATED FOXN3 WILD-TYPE
  NO             10             340
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  FOXN3 MUTATED                      8                             3
  FOXN3 WILD-TYPE                  307                            44
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  FOXN3 MUTATED                       0                              0
  FOXN3 WILD-TYPE                   106                             10
D790V10, multiclass
                                clus
vv                               FOXN3 MUTATED FOXN3 WILD-TYPE
  COLON ADENOCARCINOMA                       8             307
  COLON MUCINOUS ADENOCARCINOMA              3              44
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  FOXN3 MUTATED     8   0   1   1
  FOXN3 WILD-TYPE 337   4  30  24
D790V11, multiclass
    clus
vv   FOXN3 MUTATED FOXN3 WILD-TYPE
  R0             8             337
  R1             0               4
  R2             1              30
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D790V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FOXN3 MUTATED                                  0     1
  FOXN3 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  FOXN3 MUTATED                           1     4
  FOXN3 WILD-TYPE                        21   222
D790V13, multiclass
                                  clus
vv                                 FOXN3 MUTATED FOXN3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        4             222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(791) Variable = IL2RG MUTATION ANALYSIS
D791V1, survival
                 sevent
clus2               0   1
  IL2RG MUTATED     6   2
  IL2RG WILD-TYPE 372  91
  IL2RG MUTATED IL2RG WILD-TYPE 
              8             463 
  IL2RG MUTATED IL2RG WILD-TYPE 
              2              91 
$`IL2RG MUTATED`
TCGA-A6-6781 TCGA-AA-3492 TCGA-AY-6386 TCGA-CA-6717 TCGA-F4-6570 TCGA-G4-6309 
       19.66         3.02        17.82        12.76         6.18        85.48 
TCGA-G4-6586 TCGA-EI-6507 
       35.80        19.96 

$`IL2RG WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 
       23.87        20.12        20.28         7.04         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       33.01        21.44        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 
       98.24         8.61        31.96        35.74        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       44.68        55.04        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       13.78        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
        0.49        20.55        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  IL2RG MUTATED IL2RG WILD-TYPE 
           3.02            0.00 
  IL2RG MUTATED IL2RG WILD-TYPE 
          85.48          148.01 
  IL2RG MUTATED IL2RG WILD-TYPE 
          18.74           20.55 
[1] "3.0 - 85.5 (18.7)"  "0.0 - 148.0 (20.6)"
[1] "hr=" "1.4"
D791V2, continuous
D791V3, binary
                 cls
clus                0   1
  IL2RG MUTATED     7   1
  IL2RG WILD-TYPE 359 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IL2RG MUTATED      7    1
  IL2RG WILD-TYPE  359  118
        clus
vv       IL2RG MUTATED IL2RG WILD-TYPE
  COLON              7             359
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  IL2RG MUTATED         0        0        1         4         0         0
  IL2RG WILD-TYPE      91        1       31       134        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  IL2RG MUTATED           0          0          2          1        0         0
  IL2RG WILD-TYPE        24         11         57         41       48        18
                 vv
clus              STAGE IVB
  IL2RG MUTATED           0
  IL2RG WILD-TYPE         1
D791V4, multiclass
            clus
vv           IL2RG MUTATED IL2RG WILD-TYPE
  STAGE I                0              91
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              4             134
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             2              57
  STAGE IIIC             1              41
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  IL2RG MUTATED     0   0   7   1
  IL2RG WILD-TYPE  17  92 322  49
D791V5, multiclass
    clus
vv   IL2RG MUTATED IL2RG WILD-TYPE
  T1             0              17
  T2             0              92
  T3             7             322
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  IL2RG MUTATED     5   3   0
  IL2RG WILD-TYPE 282 110  87
D791V6, multiclass
    clus
vv   IL2RG MUTATED IL2RG WILD-TYPE
  N0             5             282
  N1             3             110
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D791V7, binary
                 cls
clus                0   1
  IL2RG MUTATED     7   0
  IL2RG WILD-TYPE 368  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IL2RG MUTATED      7    0
  IL2RG WILD-TYPE  368   65
   clus
vv  IL2RG MUTATED IL2RG WILD-TYPE
  0             7             368
  1             0              65
[1] 2 2
[1] FALSE
D791V8, binary
                 cls
clus                0   1
  IL2RG MUTATED     5   3
  IL2RG WILD-TYPE 220 261
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IL2RG MUTATED      5    3
  IL2RG WILD-TYPE  220  261
        clus
vv       IL2RG MUTATED IL2RG WILD-TYPE
  FEMALE             5             220
  MALE               3             261
[1] 2 2
[1] FALSE
D791V9, binary
                 cls
clus                0   1
  IL2RG MUTATED     8   0
  IL2RG WILD-TYPE 342  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IL2RG MUTATED      8    0
  IL2RG WILD-TYPE  342   22
     clus
vv    IL2RG MUTATED IL2RG WILD-TYPE
  NO              8             342
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  IL2RG MUTATED                      5                             2
  IL2RG WILD-TYPE                  310                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  IL2RG MUTATED                       1                              0
  IL2RG WILD-TYPE                   105                             10
D791V10, multiclass
                                clus
vv                               IL2RG MUTATED IL2RG WILD-TYPE
  COLON ADENOCARCINOMA                       5             310
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  IL2RG MUTATED     7   0   0   1
  IL2RG WILD-TYPE 338   4  31  24
D791V11, multiclass
    clus
vv   IL2RG MUTATED IL2RG WILD-TYPE
  R0             7             338
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D791V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  IL2RG MUTATED                                  0     1
  IL2RG WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  IL2RG MUTATED                           2     4
  IL2RG WILD-TYPE                        20   222
D791V13, multiclass
                                  clus
vv                                 IL2RG MUTATED IL2RG WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    2              20
  WHITE                                        4             222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(792) Variable = CARD6 MUTATION ANALYSIS
D792V1, survival
                 sevent
clus2               0   1
  CARD6 MUTATED    13   4
  CARD6 WILD-TYPE 365  89
  CARD6 MUTATED CARD6 WILD-TYPE 
             17             454 
  CARD6 MUTATED CARD6 WILD-TYPE 
              4              89 
$`CARD6 MUTATED`
TCGA-AA-3511 TCGA-AA-3518 TCGA-AA-3811 TCGA-AA-A010 TCGA-AA-A01P TCGA-AD-6889 
        6.97         1.02        10.06        34.98        38.07        56.55 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CM-5341 TCGA-D5-5540 TCGA-D5-6928 
       12.76        10.06        14.30        29.06        56.09        11.64 
TCGA-DM-A28F TCGA-G4-6588 TCGA-AG-3575 TCGA-AG-A002 TCGA-G5-6235 
       35.97        26.17        12.00        20.98        55.76 

$`CARD6 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01        63.98         1.02        13.02        38.99 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        19.04        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
        0.07        21.37        15.52         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        3.29         0.07        12.20        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       13.02        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       12.26        19.59        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
       14.30         9.04         9.44         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
      119.93        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       35.80        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3578 
       16.83        15.39        20.02        10.39        36.03        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6641 
       32.19         0.66         0.69        26.43 

  CARD6 MUTATED CARD6 WILD-TYPE 
           1.02            0.00 
  CARD6 MUTATED CARD6 WILD-TYPE 
          56.55          148.01 
  CARD6 MUTATED CARD6 WILD-TYPE 
         20.980          20.155 
[1] "1.0 - 56.5 (21.0)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.2"
D792V2, continuous
D792V3, binary
                 cls
clus                0   1
  CARD6 MUTATED    15   3
  CARD6 WILD-TYPE 351 116
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CARD6 MUTATED     15    3
  CARD6 WILD-TYPE  351  116
        clus
vv       CARD6 MUTATED CARD6 WILD-TYPE
  COLON             15             351
  RECTUM             3             116
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CARD6 MUTATED         1        0        2         8         1         0
  CARD6 WILD-TYPE      90        1       30       130         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CARD6 MUTATED           2          1          2          1        0         0
  CARD6 WILD-TYPE        22         10         57         41       48        18
                 vv
clus              STAGE IVB
  CARD6 MUTATED           0
  CARD6 WILD-TYPE         1
D792V4, multiclass
            clus
vv           CARD6 MUTATED CARD6 WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA              8             130
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              2              22
  STAGE IIIA             1              10
  STAGE IIIB             2              57
  STAGE IIIC             1              41
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CARD6 MUTATED     0   2  14   2
  CARD6 WILD-TYPE  17  90 315  48
D792V5, multiclass
    clus
vv   CARD6 MUTATED CARD6 WILD-TYPE
  T1             0              17
  T2             2              90
  T3            14             315
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  CARD6 MUTATED    12   4   2
  CARD6 WILD-TYPE 275 109  85
D792V6, multiclass
    clus
vv   CARD6 MUTATED CARD6 WILD-TYPE
  N0            12             275
  N1             4             109
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D792V7, binary
                 cls
clus                0   1
  CARD6 MUTATED    16   0
  CARD6 WILD-TYPE 359  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CARD6 MUTATED     16    0
  CARD6 WILD-TYPE  359   65
   clus
vv  CARD6 MUTATED CARD6 WILD-TYPE
  0            16             359
  1             0              65
[1] 2 2
[1] FALSE
D792V8, binary
                 cls
clus                0   1
  CARD6 MUTATED     6  12
  CARD6 WILD-TYPE 219 252
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CARD6 MUTATED      6   12
  CARD6 WILD-TYPE  219  252
        clus
vv       CARD6 MUTATED CARD6 WILD-TYPE
  FEMALE             6             219
  MALE              12             252
[1] 2 2
[1] FALSE
D792V9, binary
                 cls
clus                0   1
  CARD6 MUTATED    14   0
  CARD6 WILD-TYPE 336  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CARD6 MUTATED     14    0
  CARD6 WILD-TYPE  336   22
     clus
vv    CARD6 MUTATED CARD6 WILD-TYPE
  NO             14             336
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CARD6 MUTATED                     12                             3
  CARD6 WILD-TYPE                  303                            44
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CARD6 MUTATED                       3                              0
  CARD6 WILD-TYPE                   103                             10
D792V10, multiclass
                                clus
vv                               CARD6 MUTATED CARD6 WILD-TYPE
  COLON ADENOCARCINOMA                      12             303
  COLON MUCINOUS ADENOCARCINOMA              3              44
  RECTAL ADENOCARCINOMA                      3             103
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  CARD6 MUTATED    12   1   0   3
  CARD6 WILD-TYPE 333   3  31  22
D792V11, multiclass
    clus
vv   CARD6 MUTATED CARD6 WILD-TYPE
  R0            12             333
  R1             1               3
  R2             0              31
  RX             3              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D792V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CARD6 MUTATED                                  0     4
  CARD6 WILD-TYPE                                1     7
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CARD6 MUTATED                           0     7
  CARD6 WILD-TYPE                        22   219
D792V13, multiclass
                                  clus
vv                                 CARD6 MUTATED CARD6 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        4               7
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        7             219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(793) Variable = BAZ2B MUTATION ANALYSIS
D793V1, survival
                 sevent
clus2               0   1
  BAZ2B MUTATED    15   3
  BAZ2B WILD-TYPE 363  90
  BAZ2B MUTATED BAZ2B WILD-TYPE 
             18             453 
  BAZ2B MUTATED BAZ2B WILD-TYPE 
              3              90 
$`BAZ2B MUTATED`
TCGA-A6-5660 TCGA-AA-3496 TCGA-AA-3510 TCGA-AA-3715 TCGA-AA-3950 TCGA-AA-3966 
       29.19         1.02        63.98        19.04        24.00         2.01 
TCGA-AA-A010 TCGA-CA-5255 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-5912 TCGA-D5-6922 
       34.98         3.06        12.76        10.06        49.08         4.41 
TCGA-DM-A1HB TCGA-G4-6588 TCGA-AF-6136 TCGA-AG-A002 TCGA-EI-6510 TCGA-G5-6235 
      135.65        26.17        15.39        20.98        18.28        55.76 

$`BAZ2B WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 
       20.12        19.66        20.28         7.04         3.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       85.05        26.99        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 
       33.01        26.01         2.01        20.98        34.03        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        3.19         1.61        12.69         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       12.20        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6923 TCGA-D5-6924 
       16.14        15.58         1.48         3.68        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
       44.32       131.51       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       35.80        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       16.83        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       20.91         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6641 
        0.66         0.69        26.43 

  BAZ2B MUTATED BAZ2B WILD-TYPE 
           1.02            0.00 
  BAZ2B MUTATED BAZ2B WILD-TYPE 
         135.65          148.01 
  BAZ2B MUTATED BAZ2B WILD-TYPE 
          20.01           20.19 
[1] "1.0 - 135.7 (20.0)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.3"
D793V2, continuous
D793V3, binary
                 cls
clus                0   1
  BAZ2B MUTATED    15   4
  BAZ2B WILD-TYPE 351 115
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BAZ2B MUTATED     15    4
  BAZ2B WILD-TYPE  351  115
        clus
vv       BAZ2B MUTATED BAZ2B WILD-TYPE
  COLON             15             351
  RECTUM             4             115
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  BAZ2B MUTATED         2        0        3         6         2         0
  BAZ2B WILD-TYPE      89        1       29       132         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  BAZ2B MUTATED           0          1          3          1        0         1
  BAZ2B WILD-TYPE        24         10         56         41       48        17
                 vv
clus              STAGE IVB
  BAZ2B MUTATED           0
  BAZ2B WILD-TYPE         1
D793V4, multiclass
            clus
vv           BAZ2B MUTATED BAZ2B WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               3              29
  STAGE IIA              6             132
  STAGE IIB              2               8
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             1              10
  STAGE IIIB             3              56
  STAGE IIIC             1              41
  STAGE IV               0              48
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  BAZ2B MUTATED     0   3  14   2
  BAZ2B WILD-TYPE  17  89 315  48
D793V5, multiclass
    clus
vv   BAZ2B MUTATED BAZ2B WILD-TYPE
  T1             0              17
  T2             3              89
  T3            14             315
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  BAZ2B MUTATED    14   4   1
  BAZ2B WILD-TYPE 273 109  86
D793V6, multiclass
    clus
vv   BAZ2B MUTATED BAZ2B WILD-TYPE
  N0            14             273
  N1             4             109
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D793V7, binary
                 cls
clus                0   1
  BAZ2B MUTATED    14   0
  BAZ2B WILD-TYPE 361  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BAZ2B MUTATED     14    0
  BAZ2B WILD-TYPE  361   65
   clus
vv  BAZ2B MUTATED BAZ2B WILD-TYPE
  0            14             361
  1             0              65
[1] 2 2
[1] FALSE
D793V8, binary
                 cls
clus                0   1
  BAZ2B MUTATED     8  11
  BAZ2B WILD-TYPE 217 253
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BAZ2B MUTATED      8   11
  BAZ2B WILD-TYPE  217  253
        clus
vv       BAZ2B MUTATED BAZ2B WILD-TYPE
  FEMALE             8             217
  MALE              11             253
[1] 2 2
[1] FALSE
D793V9, binary
                 cls
clus                0   1
  BAZ2B MUTATED    12   2
  BAZ2B WILD-TYPE 338  20
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BAZ2B MUTATED     12    2
  BAZ2B WILD-TYPE  338   20
     clus
vv    BAZ2B MUTATED BAZ2B WILD-TYPE
  NO             12             338
  YES             2              20
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  BAZ2B MUTATED                     11                             3
  BAZ2B WILD-TYPE                  304                            44
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  BAZ2B MUTATED                       4                              0
  BAZ2B WILD-TYPE                   102                             10
D793V10, multiclass
                                clus
vv                               BAZ2B MUTATED BAZ2B WILD-TYPE
  COLON ADENOCARCINOMA                      11             304
  COLON MUCINOUS ADENOCARCINOMA              3              44
  RECTAL ADENOCARCINOMA                      4             102
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  BAZ2B MUTATED     9   1   0   5
  BAZ2B WILD-TYPE 336   3  31  20
D793V11, multiclass
    clus
vv   BAZ2B MUTATED BAZ2B WILD-TYPE
  R0             9             336
  R1             1               3
  R2             0              31
  RX             5              20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D793V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  BAZ2B MUTATED                                  0     3
  BAZ2B WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  BAZ2B MUTATED                           1     8
  BAZ2B WILD-TYPE                        21   218
D793V13, multiclass
                                  clus
vv                                 BAZ2B MUTATED BAZ2B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        3               8
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        8             218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(794) Variable = ZNF384 MUTATION ANALYSIS
D794V1, survival
                  sevent
clus2                0   1
  ZNF384 MUTATED     8   1
  ZNF384 WILD-TYPE 370  92
  ZNF384 MUTATED ZNF384 WILD-TYPE 
               9              462 
  ZNF384 MUTATED ZNF384 WILD-TYPE 
               1               92 
$`ZNF384 MUTATED`
TCGA-AA-3815 TCGA-AD-6889 TCGA-AZ-4315 TCGA-AZ-5403 TCGA-CM-5864 TCGA-CM-6674 
       33.04        56.55        58.39        62.79        15.02        12.95 
TCGA-D5-5539 TCGA-D5-6540 TCGA-DM-A1HB 
       19.59        16.14       135.65 

$`ZNF384 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       19.04        10.06        35.05         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       15.52         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       33.01        21.44        17.82         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
        5.03        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       15.02        14.04        11.01        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 
       11.01        10.06        12.03        45.40        12.26        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 
       17.85         4.80        17.13        12.49        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  ZNF384 MUTATED ZNF384 WILD-TYPE 
           12.95             0.00 
  ZNF384 MUTATED ZNF384 WILD-TYPE 
          135.65           148.01 
  ZNF384 MUTATED ZNF384 WILD-TYPE 
          33.040           20.155 
[1] "12.9 - 135.7 (33.0)" "0.0 - 148.0 (20.2)" 
[1] "hr=" "3"  
D794V2, continuous
D794V3, binary
                  cls
clus                 0   1
  ZNF384 MUTATED     9   0
  ZNF384 WILD-TYPE 357 119
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF384 MUTATED      9    0
  ZNF384 WILD-TYPE  357  119
        clus
vv       ZNF384 MUTATED ZNF384 WILD-TYPE
  COLON               9              357
  RECTUM              0              119
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZNF384 MUTATED         2        0        1         4         0         0
  ZNF384 WILD-TYPE      89        1       31       134        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF384 MUTATED           0          1          1          0        0
  ZNF384 WILD-TYPE        24         10         58         42       48
                  vv
clus               STAGE IVA STAGE IVB
  ZNF384 MUTATED           0         0
  ZNF384 WILD-TYPE        18         1
D794V4, multiclass
            clus
vv           ZNF384 MUTATED ZNF384 WILD-TYPE
  STAGE I                 2               89
  STAGE IA                0                1
  STAGE II                1               31
  STAGE IIA               4              134
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              1               10
  STAGE IIIB              1               58
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZNF384 MUTATED     0   2   7   0
  ZNF384 WILD-TYPE  17  90 322  50
D794V5, multiclass
    clus
vv   ZNF384 MUTATED ZNF384 WILD-TYPE
  T1              0               17
  T2              2               90
  T3              7              322
  T4              0               50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  ZNF384 MUTATED     7   2   0
  ZNF384 WILD-TYPE 280 111  87
D794V6, multiclass
    clus
vv   ZNF384 MUTATED ZNF384 WILD-TYPE
  N0              7              280
  N1              2              111
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D794V7, binary
                  cls
clus                 0   1
  ZNF384 MUTATED     8   0
  ZNF384 WILD-TYPE 367  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF384 MUTATED      8    0
  ZNF384 WILD-TYPE  367   65
   clus
vv  ZNF384 MUTATED ZNF384 WILD-TYPE
  0              8              367
  1              0               65
[1] 2 2
[1] FALSE
D794V8, binary
                  cls
clus                 0   1
  ZNF384 MUTATED     1   8
  ZNF384 WILD-TYPE 224 256
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF384 MUTATED      1    8
  ZNF384 WILD-TYPE  224  256
        clus
vv       ZNF384 MUTATED ZNF384 WILD-TYPE
  FEMALE              1              224
  MALE                8              256
[1] 2 2
[1] FALSE
D794V9, binary
                  cls
clus                 0   1
  ZNF384 MUTATED     7   0
  ZNF384 WILD-TYPE 343  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF384 MUTATED      7    0
  ZNF384 WILD-TYPE  343   22
     clus
vv    ZNF384 MUTATED ZNF384 WILD-TYPE
  NO               7              343
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ZNF384 MUTATED                      6                             2
  ZNF384 WILD-TYPE                  309                            45
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ZNF384 MUTATED                       0                              0
  ZNF384 WILD-TYPE                   106                             10
D794V10, multiclass
                                clus
vv                               ZNF384 MUTATED ZNF384 WILD-TYPE
  COLON ADENOCARCINOMA                        6              309
  COLON MUCINOUS ADENOCARCINOMA               2               45
  RECTAL ADENOCARCINOMA                       0              106
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ZNF384 MUTATED     6   0   0   0
  ZNF384 WILD-TYPE 339   4  31  25
D794V11, multiclass
    clus
vv   ZNF384 MUTATED ZNF384 WILD-TYPE
  R0              6              339
  R1              0                4
  R2              0               31
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D794V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF384 MUTATED                                  0     1
  ZNF384 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZNF384 MUTATED                           0     7
  ZNF384 WILD-TYPE                        22   219
D794V13, multiclass
                                  clus
vv                                 ZNF384 MUTATED ZNF384 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         7              219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(795) Variable = MORC2 MUTATION ANALYSIS
D795V1, survival
                 sevent
clus2               0   1
  MORC2 MUTATED     9   3
  MORC2 WILD-TYPE 369  90
  MORC2 MUTATED MORC2 WILD-TYPE 
             12             459 
  MORC2 MUTATED MORC2 WILD-TYPE 
              3              90 
$`MORC2 MUTATED`
TCGA-A6-6137 TCGA-AA-3510 TCGA-AA-3542 TCGA-AA-3811 TCGA-AA-A00R TCGA-AZ-4315 
       27.09        63.98        12.99        10.06         0.99        58.39 
TCGA-AZ-6598 TCGA-AZ-6601 TCGA-D5-6532 TCGA-D5-6927 TCGA-AG-3892 TCGA-AG-A002 
       49.41       100.01        18.25         9.44        13.02        20.98 

$`MORC2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        22.06        32.71        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3815 
       85.05        26.99        19.04        19.04        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
       42.02        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77        12.10        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       20.19         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6929 
        4.41        12.43        14.30         9.04        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 
        1.02        17.95        36.95        17.03        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  MORC2 MUTATED MORC2 WILD-TYPE 
           0.99            0.00 
  MORC2 MUTATED MORC2 WILD-TYPE 
         100.01          148.01 
  MORC2 MUTATED MORC2 WILD-TYPE 
         19.615          20.190 
[1] "1.0 - 100.0 (19.6)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1"  
D795V2, continuous
D795V3, binary
                 cls
clus                0   1
  MORC2 MUTATED    12   2
  MORC2 WILD-TYPE 354 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MORC2 MUTATED     12    2
  MORC2 WILD-TYPE  354  117
        clus
vv       MORC2 MUTATED MORC2 WILD-TYPE
  COLON             12             354
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MORC2 MUTATED         3        0        3         3         1         0
  MORC2 WILD-TYPE      88        1       29       135         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MORC2 MUTATED           1          0          1          2        0         0
  MORC2 WILD-TYPE        23         11         58         40       48        18
                 vv
clus              STAGE IVB
  MORC2 MUTATED           0
  MORC2 WILD-TYPE         1
D795V4, multiclass
            clus
vv           MORC2 MUTATED MORC2 WILD-TYPE
  STAGE I                3              88
  STAGE IA               0               1
  STAGE II               3              29
  STAGE IIA              3             135
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             2              40
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  MORC2 MUTATED     1   2  10   1
  MORC2 WILD-TYPE  16  90 319  49
D795V5, multiclass
    clus
vv   MORC2 MUTATED MORC2 WILD-TYPE
  T1             1              16
  T2             2              90
  T3            10             319
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  MORC2 MUTATED    10   1   3
  MORC2 WILD-TYPE 277 112  84
D795V6, multiclass
    clus
vv   MORC2 MUTATED MORC2 WILD-TYPE
  N0            10             277
  N1             1             112
  N2             3              84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D795V7, binary
                 cls
clus                0   1
  MORC2 MUTATED    11   0
  MORC2 WILD-TYPE 364  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MORC2 MUTATED     11    0
  MORC2 WILD-TYPE  364   65
   clus
vv  MORC2 MUTATED MORC2 WILD-TYPE
  0            11             364
  1             0              65
[1] 2 2
[1] FALSE
D795V8, binary
                 cls
clus                0   1
  MORC2 MUTATED     5   9
  MORC2 WILD-TYPE 220 255
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MORC2 MUTATED      5    9
  MORC2 WILD-TYPE  220  255
        clus
vv       MORC2 MUTATED MORC2 WILD-TYPE
  FEMALE             5             220
  MALE               9             255
[1] 2 2
[1] FALSE
D795V9, binary
                 cls
clus                0   1
  MORC2 MUTATED    11   0
  MORC2 WILD-TYPE 339  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MORC2 MUTATED     11    0
  MORC2 WILD-TYPE  339   22
     clus
vv    MORC2 MUTATED MORC2 WILD-TYPE
  NO             11             339
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MORC2 MUTATED                     11                             1
  MORC2 WILD-TYPE                  304                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MORC2 MUTATED                       2                              0
  MORC2 WILD-TYPE                   104                             10
D795V10, multiclass
                                clus
vv                               MORC2 MUTATED MORC2 WILD-TYPE
  COLON ADENOCARCINOMA                      11             304
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  MORC2 MUTATED    10   0   0   1
  MORC2 WILD-TYPE 335   4  31  24
D795V11, multiclass
    clus
vv   MORC2 MUTATED MORC2 WILD-TYPE
  R0            10             335
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D795V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MORC2 MUTATED                                  0     0
  MORC2 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  MORC2 MUTATED                           0     8
  MORC2 WILD-TYPE                        22   218
D795V13, multiclass
                                  clus
vv                                 MORC2 MUTATED MORC2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        8             218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(796) Variable = OTX2 MUTATION ANALYSIS
D796V1, survival
                sevent
clus2              0   1
  OTX2 MUTATED     6   1
  OTX2 WILD-TYPE 372  92
  OTX2 MUTATED OTX2 WILD-TYPE 
             7            464 
  OTX2 MUTATED OTX2 WILD-TYPE 
             1             92 
$`OTX2 MUTATED`
TCGA-A6-6780 TCGA-AA-3492 TCGA-AA-3697 TCGA-AD-6889 TCGA-D5-6540 TCGA-AF-6136 
       20.12         3.02        85.05        56.55        16.14        15.39 
TCGA-AG-3892 
       13.02 

$`OTX2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 
       23.87        19.66        20.28         7.04         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 
       18.05        40.96         0.07        21.37        15.52         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       12.49        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 
       34.49        10.39        14.50        16.83        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       36.95        17.03        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  OTX2 MUTATED OTX2 WILD-TYPE 
          3.02           0.00 
  OTX2 MUTATED OTX2 WILD-TYPE 
         85.05         148.01 
  OTX2 MUTATED OTX2 WILD-TYPE 
        16.140         20.415 
[1] "3.0 - 85.0 (16.1)"  "0.0 - 148.0 (20.4)"
[1] "hr=" "1.7"
D796V2, continuous
D796V3, binary
                cls
clus               0   1
  OTX2 MUTATED     6   2
  OTX2 WILD-TYPE 360 117
[1] "tbl2"
                cls
clus             [,1] [,2]
  OTX2 MUTATED      6    2
  OTX2 WILD-TYPE  360  117
        clus
vv       OTX2 MUTATED OTX2 WILD-TYPE
  COLON             6            360
  RECTUM            2            117
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  OTX2 MUTATED         2        0        1         3         0         0
  OTX2 WILD-TYPE      89        1       31       135        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  OTX2 MUTATED           1          0          1          0        0         0
  OTX2 WILD-TYPE        23         11         58         42       48        18
                vv
clus             STAGE IVB
  OTX2 MUTATED           0
  OTX2 WILD-TYPE         1
D796V4, multiclass
            clus
vv           OTX2 MUTATED OTX2 WILD-TYPE
  STAGE I               2             89
  STAGE IA              0              1
  STAGE II              1             31
  STAGE IIA             3            135
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             1             23
  STAGE IIIA            0             11
  STAGE IIIB            1             58
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  OTX2 MUTATED     1   1   6   0
  OTX2 WILD-TYPE  16  91 323  50
D796V5, multiclass
    clus
vv   OTX2 MUTATED OTX2 WILD-TYPE
  T1            1             16
  T2            1             91
  T3            6            323
  T4            0             50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  OTX2 MUTATED     7   1   0
  OTX2 WILD-TYPE 280 112  87
D796V6, multiclass
    clus
vv   OTX2 MUTATED OTX2 WILD-TYPE
  N0            7            280
  N1            1            112
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D796V7, binary
                cls
clus               0   1
  OTX2 MUTATED     6   0
  OTX2 WILD-TYPE 369  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  OTX2 MUTATED      6    0
  OTX2 WILD-TYPE  369   65
   clus
vv  OTX2 MUTATED OTX2 WILD-TYPE
  0            6            369
  1            0             65
[1] 2 2
[1] FALSE
D796V8, binary
                cls
clus               0   1
  OTX2 MUTATED     4   4
  OTX2 WILD-TYPE 221 260
[1] "tbl2"
                cls
clus             [,1] [,2]
  OTX2 MUTATED      4    4
  OTX2 WILD-TYPE  221  260
        clus
vv       OTX2 MUTATED OTX2 WILD-TYPE
  FEMALE            4            221
  MALE              4            260
[1] 2 2
[1] FALSE
D796V9, binary
                cls
clus               0   1
  OTX2 MUTATED     5   1
  OTX2 WILD-TYPE 345  21
[1] "tbl2"
                cls
clus             [,1] [,2]
  OTX2 MUTATED      5    1
  OTX2 WILD-TYPE  345   21
     clus
vv    OTX2 MUTATED OTX2 WILD-TYPE
  NO             5            345
  YES            1             21
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  OTX2 MUTATED                      4                             2
  OTX2 WILD-TYPE                  311                            45
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  OTX2 MUTATED                       2                              0
  OTX2 WILD-TYPE                   104                             10
D796V10, multiclass
                                clus
vv                               OTX2 MUTATED OTX2 WILD-TYPE
  COLON ADENOCARCINOMA                      4            311
  COLON MUCINOUS ADENOCARCINOMA             2             45
  RECTAL ADENOCARCINOMA                     2            104
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  OTX2 MUTATED     5   0   0   0
  OTX2 WILD-TYPE 340   4  31  25
D796V11, multiclass
    clus
vv   OTX2 MUTATED OTX2 WILD-TYPE
  R0            5            340
  R1            0              4
  R2            0             31
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D796V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OTX2 MUTATED                                  0     1
  OTX2 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  OTX2 MUTATED                           0     3
  OTX2 WILD-TYPE                        22   223
D796V13, multiclass
                                  clus
vv                                 OTX2 MUTATED OTX2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       3            223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(797) Variable = CYP4A22 MUTATION ANALYSIS
D797V1, survival
                   sevent
clus2                 0   1
  CYP4A22 MUTATED     8   4
  CYP4A22 WILD-TYPE 370  89
  CYP4A22 MUTATED CYP4A22 WILD-TYPE 
               12               459 
  CYP4A22 MUTATED CYP4A22 WILD-TYPE 
                4                89 
$`CYP4A22 MUTATED`
TCGA-AA-3821 TCGA-AD-6889 TCGA-AD-6895 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-6717 
        1.02        56.55         0.72        11.74         3.19        12.76 
TCGA-CM-5864 TCGA-CM-6163 TCGA-D5-6537 TCGA-D5-6924 TCGA-DM-A0XF TCGA-DM-A282 
       15.02         2.96         4.80        14.30        38.20       139.17 

$`CYP4A22 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
       15.52         0.79         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
      100.01        29.56         5.23         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07        12.20        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       17.03        15.02        12.00        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
        4.41        12.43         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A285 TCGA-DM-A28C 
        7.50        44.32       131.51       135.65         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  CYP4A22 MUTATED CYP4A22 WILD-TYPE 
             0.72              0.00 
  CYP4A22 MUTATED CYP4A22 WILD-TYPE 
           139.17            148.01 
  CYP4A22 MUTATED CYP4A22 WILD-TYPE 
            12.25             20.91 
[1] "0.7 - 139.2 (12.2)" "0.0 - 148.0 (20.9)"
[1] "hr=" "2"  
D797V2, continuous
D797V3, binary
                   cls
clus                  0   1
  CYP4A22 MUTATED    13   0
  CYP4A22 WILD-TYPE 353 119
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CYP4A22 MUTATED     13    0
  CYP4A22 WILD-TYPE  353  119
        clus
vv       CYP4A22 MUTATED CYP4A22 WILD-TYPE
  COLON               13               353
  RECTUM               0               119
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CYP4A22 MUTATED         3        0        0         5         0         0
  CYP4A22 WILD-TYPE      88        1       32       133        10         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CYP4A22 MUTATED           0          0          1          1        2
  CYP4A22 WILD-TYPE        24         11         58         41       46
                   vv
clus                STAGE IVA STAGE IVB
  CYP4A22 MUTATED           0         0
  CYP4A22 WILD-TYPE        18         1
D797V4, multiclass
            clus
vv           CYP4A22 MUTATED CYP4A22 WILD-TYPE
  STAGE I                  3                88
  STAGE IA                 0                 1
  STAGE II                 0                32
  STAGE IIA                5               133
  STAGE IIB                0                10
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               0                11
  STAGE IIIB               1                58
  STAGE IIIC               1                41
  STAGE IV                 2                46
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  CYP4A22 MUTATED     1   2   8   2
  CYP4A22 WILD-TYPE  16  90 321  48
D797V5, multiclass
    clus
vv   CYP4A22 MUTATED CYP4A22 WILD-TYPE
  T1               1                16
  T2               2                90
  T3               8               321
  T4               2                48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  CYP4A22 MUTATED     8   2   3
  CYP4A22 WILD-TYPE 279 111  84
D797V6, multiclass
    clus
vv   CYP4A22 MUTATED CYP4A22 WILD-TYPE
  N0               8               279
  N1               2               111
  N2               3                84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D797V7, binary
                   cls
clus                  0   1
  CYP4A22 MUTATED     9   2
  CYP4A22 WILD-TYPE 366  63
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CYP4A22 MUTATED      9    2
  CYP4A22 WILD-TYPE  366   63
   clus
vv  CYP4A22 MUTATED CYP4A22 WILD-TYPE
  0               9               366
  1               2                63
[1] 2 2
[1] FALSE
D797V8, binary
                   cls
clus                  0   1
  CYP4A22 MUTATED     4   9
  CYP4A22 WILD-TYPE 221 255
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CYP4A22 MUTATED      4    9
  CYP4A22 WILD-TYPE  221  255
        clus
vv       CYP4A22 MUTATED CYP4A22 WILD-TYPE
  FEMALE               4               221
  MALE                 9               255
[1] 2 2
[1] FALSE
D797V9, binary
                   cls
clus                  0   1
  CYP4A22 MUTATED     8   0
  CYP4A22 WILD-TYPE 342  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CYP4A22 MUTATED      8    0
  CYP4A22 WILD-TYPE  342   22
     clus
vv    CYP4A22 MUTATED CYP4A22 WILD-TYPE
  NO                8               342
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CYP4A22 MUTATED                     10                             2
  CYP4A22 WILD-TYPE                  305                            45
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CYP4A22 MUTATED                       0                              0
  CYP4A22 WILD-TYPE                   106                             10
D797V10, multiclass
                                clus
vv                               CYP4A22 MUTATED CYP4A22 WILD-TYPE
  COLON ADENOCARCINOMA                        10               305
  COLON MUCINOUS ADENOCARCINOMA                2                45
  RECTAL ADENOCARCINOMA                        0               106
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  CYP4A22 MUTATED     6   0   0   1
  CYP4A22 WILD-TYPE 339   4  31  24
D797V11, multiclass
    clus
vv   CYP4A22 MUTATED CYP4A22 WILD-TYPE
  R0               6               339
  R1               0                 4
  R2               0                31
  RX               1                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D797V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CYP4A22 MUTATED                                  0     2
  CYP4A22 WILD-TYPE                                1     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  CYP4A22 MUTATED                           0     9
  CYP4A22 WILD-TYPE                        22   217
D797V13, multiclass
                                  clus
vv                                 CYP4A22 MUTATED CYP4A22 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          2                 9
  BLACK OR AFRICAN AMERICAN                      0                22
  WHITE                                          9               217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(798) Variable = C14ORF102 MUTATION ANALYSIS
D798V1, survival
                     sevent
clus2                   0   1
  C14ORF102 MUTATED    14   5
  C14ORF102 WILD-TYPE 364  88
  C14ORF102 MUTATED C14ORF102 WILD-TYPE 
                 19                 452 
  C14ORF102 MUTATED C14ORF102 WILD-TYPE 
                  5                  88 
$`C14ORF102 MUTATED`
TCGA-A6-5661 TCGA-A6-5664 TCGA-AA-3516 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3815 
       33.53        22.09        13.02         6.97        54.02        33.04 
TCGA-AA-A00J TCGA-AA-A010 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-CA-6716 TCGA-CA-6717 
       18.05        34.98        58.39        49.41        12.20        12.76 
TCGA-CA-6718 TCGA-CM-6171 TCGA-D5-6537 TCGA-F4-6459 TCGA-G4-6310 TCGA-AG-3892 
       10.06        14.04         4.80         8.61        63.62        13.02 
TCGA-AG-A002 
       20.98 

$`C14ORF102 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5665 
       32.91        31.63        30.44        29.19        23.61        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
       63.98         6.97         1.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3666 TCGA-AA-3667 
       19.99        61.02        78.08         6.05         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
       19.04        19.04        10.06        35.05         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       33.01        21.44        17.82         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        88.21         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6719 TCGA-CK-4947 
        3.06         3.25         3.29         0.07        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 
       21.99        14.99        12.99        13.02        15.02        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
      117.07        98.24        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6317 
       53.62        44.68        55.04        85.48        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       17.95        36.95        17.03        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  C14ORF102 MUTATED C14ORF102 WILD-TYPE 
                4.8                 0.0 
  C14ORF102 MUTATED C14ORF102 WILD-TYPE 
              63.62              148.01 
  C14ORF102 MUTATED C14ORF102 WILD-TYPE 
             18.050              20.235 
[1] "4.8 - 63.6 (18.1)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.3"
D798V2, continuous
D798V3, binary
                     cls
clus                    0   1
  C14ORF102 MUTATED    17   2
  C14ORF102 WILD-TYPE 349 117
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  C14ORF102 MUTATED     17    2
  C14ORF102 WILD-TYPE  349  117
        clus
vv       C14ORF102 MUTATED C14ORF102 WILD-TYPE
  COLON                 17                 349
  RECTUM                 2                 117
[1] 2 2
[1] FALSE
                     vv
clus                  STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  C14ORF102 MUTATED         3        0        3         6         1         0
  C14ORF102 WILD-TYPE      88        1       29       132         9         1
                     vv
clus                  STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C14ORF102 MUTATED           1          0          4          1        0
  C14ORF102 WILD-TYPE        23         11         55         41       48
                     vv
clus                  STAGE IVA STAGE IVB
  C14ORF102 MUTATED           0         0
  C14ORF102 WILD-TYPE        18         1
D798V4, multiclass
            clus
vv           C14ORF102 MUTATED C14ORF102 WILD-TYPE
  STAGE I                    3                  88
  STAGE IA                   0                   1
  STAGE II                   3                  29
  STAGE IIA                  6                 132
  STAGE IIB                  1                   9
  STAGE IIC                  0                   1
  STAGE III                  1                  23
  STAGE IIIA                 0                  11
  STAGE IIIB                 4                  55
  STAGE IIIC                 1                  41
  STAGE IV                   0                  48
  STAGE IVA                  0                  18
  STAGE IVB                  0                   1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                   T1  T2  T3  T4
  C14ORF102 MUTATED     1   2  13   3
  C14ORF102 WILD-TYPE  16  90 316  47
D798V5, multiclass
    clus
vv   C14ORF102 MUTATED C14ORF102 WILD-TYPE
  T1                 1                  16
  T2                 2                  90
  T3                13                 316
  T4                 3                  47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                   N0  N1  N2
  C14ORF102 MUTATED    13   3   3
  C14ORF102 WILD-TYPE 274 110  84
D798V6, multiclass
    clus
vv   C14ORF102 MUTATED C14ORF102 WILD-TYPE
  N0                13                 274
  N1                 3                 110
  N2                 3                  84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D798V7, binary
                     cls
clus                    0   1
  C14ORF102 MUTATED    16   0
  C14ORF102 WILD-TYPE 359  65
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  C14ORF102 MUTATED     16    0
  C14ORF102 WILD-TYPE  359   65
   clus
vv  C14ORF102 MUTATED C14ORF102 WILD-TYPE
  0                16                 359
  1                 0                  65
[1] 2 2
[1] FALSE
D798V8, binary
                     cls
clus                    0   1
  C14ORF102 MUTATED     9  10
  C14ORF102 WILD-TYPE 216 254
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  C14ORF102 MUTATED      9   10
  C14ORF102 WILD-TYPE  216  254
        clus
vv       C14ORF102 MUTATED C14ORF102 WILD-TYPE
  FEMALE                 9                 216
  MALE                  10                 254
[1] 2 2
[1] FALSE
D798V9, binary
                     cls
clus                    0   1
  C14ORF102 MUTATED    18   1
  C14ORF102 WILD-TYPE 332  21
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  C14ORF102 MUTATED     18    1
  C14ORF102 WILD-TYPE  332   21
     clus
vv    C14ORF102 MUTATED C14ORF102 WILD-TYPE
  NO                 18                 332
  YES                 1                  21
[1] 2 2
[1] FALSE
                     vv
clus                  COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  C14ORF102 MUTATED                     14                             3
  C14ORF102 WILD-TYPE                  301                            44
                     vv
clus                  RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  C14ORF102 MUTATED                       2                              0
  C14ORF102 WILD-TYPE                   104                             10
D798V10, multiclass
                                clus
vv                               C14ORF102 MUTATED C14ORF102 WILD-TYPE
  COLON ADENOCARCINOMA                          14                 301
  COLON MUCINOUS ADENOCARCINOMA                  3                  44
  RECTAL ADENOCARCINOMA                          2                 104
  RECTAL MUCINOUS ADENOCARCINOMA                 0                  10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                   R0  R1  R2  RX
  C14ORF102 MUTATED    13   0   0   3
  C14ORF102 WILD-TYPE 332   4  31  22
D798V11, multiclass
    clus
vv   C14ORF102 MUTATED C14ORF102 WILD-TYPE
  R0                13                 332
  R1                 0                   4
  R2                 0                  31
  RX                 3                  22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D798V12, continuous
                     vv
clus                  AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C14ORF102 MUTATED                                  0     3
  C14ORF102 WILD-TYPE                                1     8
                     vv
clus                  BLACK OR AFRICAN AMERICAN WHITE
  C14ORF102 MUTATED                           2     6
  C14ORF102 WILD-TYPE                        20   220
D798V13, multiclass
                                  clus
vv                                 C14ORF102 MUTATED C14ORF102 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                 0                   1
  ASIAN                                            3                   8
  BLACK OR AFRICAN AMERICAN                        2                  20
  WHITE                                            6                 220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(799) Variable = LPGAT1 MUTATION ANALYSIS
D799V1, survival
                  sevent
clus2                0   1
  LPGAT1 MUTATED     4   0
  LPGAT1 WILD-TYPE 374  93
  LPGAT1 MUTATED LPGAT1 WILD-TYPE 
               4              467 
  LPGAT1 MUTATED LPGAT1 WILD-TYPE 
               0               93 
$`LPGAT1 MUTATED`
TCGA-D5-5540 TCGA-D5-6533 TCGA-G4-6628 TCGA-F5-6811 
       56.09         1.32        79.69        32.19 

$`LPGAT1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       55.92        20.19        18.25        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       26.17        91.79        46.75        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57         0.66         0.69        55.76        26.43 

  LPGAT1 MUTATED LPGAT1 WILD-TYPE 
            1.32             0.00 
  LPGAT1 MUTATED LPGAT1 WILD-TYPE 
           79.69           148.01 
  LPGAT1 MUTATED LPGAT1 WILD-TYPE 
           44.14            20.12 
[1] "1.3 - 79.7 (44.1)"  "0.0 - 148.0 (20.1)"
[1] "hr="     "9200000"
D799V2, continuous
D799V3, binary
                  cls
clus                 0   1
  LPGAT1 MUTATED     3   1
  LPGAT1 WILD-TYPE 363 118
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LPGAT1 MUTATED      3    1
  LPGAT1 WILD-TYPE  363  118
        clus
vv       LPGAT1 MUTATED LPGAT1 WILD-TYPE
  COLON               3              363
  RECTUM              1              118
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  LPGAT1 MUTATED         1        0        0         2         0         0
  LPGAT1 WILD-TYPE      90        1       32       136        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  LPGAT1 MUTATED           0          0          1          0        0
  LPGAT1 WILD-TYPE        24         11         58         42       48
                  vv
clus               STAGE IVA STAGE IVB
  LPGAT1 MUTATED           0         0
  LPGAT1 WILD-TYPE        18         1
D799V4, multiclass
            clus
vv           LPGAT1 MUTATED LPGAT1 WILD-TYPE
  STAGE I                 1               90
  STAGE IA                0                1
  STAGE II                0               32
  STAGE IIA               2              136
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              1               58
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  LPGAT1 MUTATED     0   1   2   1
  LPGAT1 WILD-TYPE  17  91 327  49
D799V5, multiclass
    clus
vv   LPGAT1 MUTATED LPGAT1 WILD-TYPE
  T1              0               17
  T2              1               91
  T3              2              327
  T4              1               49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  LPGAT1 MUTATED     4   0   0
  LPGAT1 WILD-TYPE 283 113  87
D799V6, multiclass
    clus
vv   LPGAT1 MUTATED LPGAT1 WILD-TYPE
  N0              4              283
  N1              0              113
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D799V7, binary
                  cls
clus                 0   1
  LPGAT1 MUTATED     4   0
  LPGAT1 WILD-TYPE 371  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LPGAT1 MUTATED      4    0
  LPGAT1 WILD-TYPE  371   65
   clus
vv  LPGAT1 MUTATED LPGAT1 WILD-TYPE
  0              4              371
  1              0               65
[1] 2 2
[1] FALSE
D799V8, binary
                  cls
clus                 0   1
  LPGAT1 MUTATED     2   2
  LPGAT1 WILD-TYPE 223 262
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LPGAT1 MUTATED      2    2
  LPGAT1 WILD-TYPE  223  262
        clus
vv       LPGAT1 MUTATED LPGAT1 WILD-TYPE
  FEMALE              2              223
  MALE                2              262
[1] 2 2
[1] FALSE
D799V9, binary
                  cls
clus                 0   1
  LPGAT1 MUTATED     3   0
  LPGAT1 WILD-TYPE 347  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LPGAT1 MUTATED      3    0
  LPGAT1 WILD-TYPE  347   22
     clus
vv    LPGAT1 MUTATED LPGAT1 WILD-TYPE
  NO               3              347
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  LPGAT1 MUTATED                      3                             0
  LPGAT1 WILD-TYPE                  312                            47
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  LPGAT1 MUTATED                       1                              0
  LPGAT1 WILD-TYPE                   105                             10
D799V10, multiclass
                                clus
vv                               LPGAT1 MUTATED LPGAT1 WILD-TYPE
  COLON ADENOCARCINOMA                        3              312
  COLON MUCINOUS ADENOCARCINOMA               0               47
  RECTAL ADENOCARCINOMA                       1              105
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  LPGAT1 MUTATED     3   0   0   0
  LPGAT1 WILD-TYPE 342   4  31  25
D799V11, multiclass
    clus
vv   LPGAT1 MUTATED LPGAT1 WILD-TYPE
  R0              3              342
  R1              0                4
  R2              0               31
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D799V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  LPGAT1 MUTATED                                  0     0
  LPGAT1 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  LPGAT1 MUTATED                           0     4
  LPGAT1 WILD-TYPE                        22   222
D799V13, multiclass
                                  clus
vv                                 LPGAT1 MUTATED LPGAT1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         4              222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(800) Variable = MAGEC1 MUTATION ANALYSIS
D800V1, survival
                  sevent
clus2                0   1
  MAGEC1 MUTATED    26   5
  MAGEC1 WILD-TYPE 352  88
  MAGEC1 MUTATED MAGEC1 WILD-TYPE 
              31              440 
  MAGEC1 MUTATED MAGEC1 WILD-TYPE 
               5               88 
$`MAGEC1 MUTATED`
TCGA-A6-2672 TCGA-A6-3809 TCGA-A6-5664 TCGA-A6-5666 TCGA-AA-3502 TCGA-AA-3662 
       46.65        32.75        22.09        32.71        35.01         6.05 
TCGA-AA-3955 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-A00N TCGA-AA-A010 
       20.98        34.06        25.02        27.02         4.01        34.98 
TCGA-AD-6889 TCGA-AD-6901 TCGA-CA-6717 TCGA-D5-5538 TCGA-D5-6538 TCGA-D5-6898 
       56.55        22.42        12.76        12.26        17.13         1.48 
TCGA-D5-6931 TCGA-D5-6932 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-F4-6808 TCGA-F4-6855 
       12.00        11.38        24.43        38.20        33.67        47.41 
TCGA-G4-6304 TCGA-G4-6586 TCGA-AF-5654 TCGA-AG-3892 TCGA-CI-6624 TCGA-F5-6465 
       53.62        35.80        16.83        13.02         4.73        49.51 
TCGA-G5-6641 
       26.43 

$`MAGEC1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5657 
       34.65        33.34        36.53        14.53        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5665 TCGA-A6-6137 
       30.44        29.19        33.53        23.61        22.06        27.09 
TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 
       22.52         8.38        25.08        25.18        24.16        21.76 
TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       24.69        24.39        23.87        20.12        19.66        20.28 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
        7.04         3.02         1.02        63.98         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
       13.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       36.03         8.05        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
       78.08         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       24.00         2.01        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 
       50.99        13.05        26.01        24.00        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6963 
       21.37        15.52         0.79         0.72         5.79        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.20        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       45.40        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6539 
        1.32        43.27        15.12        17.85         4.80        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       16.14        15.58         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-7000 
        9.04         9.44        11.64         4.80         1.51        10.26 
TCGA-DM-A0X9 TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
      119.70       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6854 
        1.55        34.42        41.42        16.24        13.25         0.53 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 
       35.31       133.18        74.56        65.85        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 
       19.99         1.02        17.95        36.95        17.03        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
       33.17         6.97        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
       18.28         9.96        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 
        0.69        55.76 

  MAGEC1 MUTATED MAGEC1 WILD-TYPE 
            1.48             0.00 
  MAGEC1 MUTATED MAGEC1 WILD-TYPE 
           56.55           148.01 
  MAGEC1 MUTATED MAGEC1 WILD-TYPE 
          25.020           20.005 
[1] "1.5 - 56.5 (25.0)"  "0.0 - 148.0 (20.0)"
[1] "hr=" "1.2"
D800V2, continuous
D800V3, binary
                  cls
clus                 0   1
  MAGEC1 MUTATED    28   5
  MAGEC1 WILD-TYPE 338 114
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAGEC1 MUTATED     28    5
  MAGEC1 WILD-TYPE  338  114
        clus
vv       MAGEC1 MUTATED MAGEC1 WILD-TYPE
  COLON              28              338
  RECTUM              5              114
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MAGEC1 MUTATED         8        0        0         8         4         1
  MAGEC1 WILD-TYPE      83        1       32       130         6         0
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MAGEC1 MUTATED           0          1          4          3        2
  MAGEC1 WILD-TYPE        24         10         55         39       46
                  vv
clus               STAGE IVA STAGE IVB
  MAGEC1 MUTATED           0         0
  MAGEC1 WILD-TYPE        18         1
D800V4, multiclass
            clus
vv           MAGEC1 MUTATED MAGEC1 WILD-TYPE
  STAGE I                 8               83
  STAGE IA                0                1
  STAGE II                0               32
  STAGE IIA               8              130
  STAGE IIB               4                6
  STAGE IIC               1                0
  STAGE III               0               24
  STAGE IIIA              1               10
  STAGE IIIB              4               55
  STAGE IIIC              3               39
  STAGE IV                2               46
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  MAGEC1 MUTATED     3   8  13   9
  MAGEC1 WILD-TYPE  14  84 316  41
D800V5, multiclass
    clus
vv   MAGEC1 MUTATED MAGEC1 WILD-TYPE
  T1              3               14
  T2              8               84
  T3             13              316
  T4              9               41
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  MAGEC1 MUTATED    23   4   6
  MAGEC1 WILD-TYPE 264 109  81
D800V6, multiclass
    clus
vv   MAGEC1 MUTATED MAGEC1 WILD-TYPE
  N0             23              264
  N1              4              109
  N2              6               81
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D800V7, binary
                  cls
clus                 0   1
  MAGEC1 MUTATED    27   2
  MAGEC1 WILD-TYPE 348  63
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAGEC1 MUTATED     27    2
  MAGEC1 WILD-TYPE  348   63
   clus
vv  MAGEC1 MUTATED MAGEC1 WILD-TYPE
  0             27              348
  1              2               63
[1] 2 2
[1] FALSE
D800V8, binary
                  cls
clus                 0   1
  MAGEC1 MUTATED    19  14
  MAGEC1 WILD-TYPE 206 250
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAGEC1 MUTATED     19   14
  MAGEC1 WILD-TYPE  206  250
        clus
vv       MAGEC1 MUTATED MAGEC1 WILD-TYPE
  FEMALE             19              206
  MALE               14              250
[1] 2 2
[1] FALSE
D800V9, binary
                  cls
clus                 0   1
  MAGEC1 MUTATED    25   0
  MAGEC1 WILD-TYPE 325  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAGEC1 MUTATED     25    0
  MAGEC1 WILD-TYPE  325   22
     clus
vv    MAGEC1 MUTATED MAGEC1 WILD-TYPE
  NO              25              325
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MAGEC1 MUTATED                     24                             3
  MAGEC1 WILD-TYPE                  291                            44
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MAGEC1 MUTATED                       4                              1
  MAGEC1 WILD-TYPE                   102                              9
D800V10, multiclass
                                clus
vv                               MAGEC1 MUTATED MAGEC1 WILD-TYPE
  COLON ADENOCARCINOMA                       24              291
  COLON MUCINOUS ADENOCARCINOMA               3               44
  RECTAL ADENOCARCINOMA                       4              102
  RECTAL MUCINOUS ADENOCARCINOMA              1                9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  MAGEC1 MUTATED    21   0   2   1
  MAGEC1 WILD-TYPE 324   4  29  24
D800V11, multiclass
    clus
vv   MAGEC1 MUTATED MAGEC1 WILD-TYPE
  R0             21              324
  R1              0                4
  R2              2               29
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D800V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MAGEC1 MUTATED                                  0     2
  MAGEC1 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  MAGEC1 MUTATED                           1    19
  MAGEC1 WILD-TYPE                        21   207
D800V13, multiclass
                                  clus
vv                                 MAGEC1 MUTATED MAGEC1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                9
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                        19              207
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(801) Variable = EEA1 MUTATION ANALYSIS
D801V1, survival
                sevent
clus2              0   1
  EEA1 MUTATED    13   3
  EEA1 WILD-TYPE 365  90
  EEA1 MUTATED EEA1 WILD-TYPE 
            16            455 
  EEA1 MUTATED EEA1 WILD-TYPE 
             3             90 
$`EEA1 MUTATED`
TCGA-A6-5665 TCGA-AA-3510 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3947 TCGA-AA-A010 
       22.06        63.98        19.04        19.04        33.01        34.98 
TCGA-AZ-4315 TCGA-CA-6717 TCGA-CM-4746 TCGA-D5-6927 TCGA-DM-A1DA TCGA-F4-6570 
       58.39        12.76        37.02         9.44         7.50         6.18 
TCGA-F4-6856 TCGA-AG-3578 TCGA-AG-A002 TCGA-AG-A032 
       35.31        32.02        20.98        38.04 

$`EEA1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
        5.03        85.05        26.99        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
       16.31         0.95        33.01        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07        12.20        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4747 
       82.95         1.91       124.27        23.05        20.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6929 
        4.41        12.43        14.30         9.04        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
      140.38        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
        8.61        31.96        35.74        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       12.00         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A036 
       49.97         1.94        38.96        61.97        41.00       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  EEA1 MUTATED EEA1 WILD-TYPE 
          6.18           0.00 
  EEA1 MUTATED EEA1 WILD-TYPE 
         63.98         148.01 
  EEA1 MUTATED EEA1 WILD-TYPE 
         27.04          20.05 
[1] "6.2 - 64.0 (27.0)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.1"
D801V2, continuous
D801V3, binary
                cls
clus               0   1
  EEA1 MUTATED    13   3
  EEA1 WILD-TYPE 353 116
[1] "tbl2"
                cls
clus             [,1] [,2]
  EEA1 MUTATED     13    3
  EEA1 WILD-TYPE  353  116
        clus
vv       EEA1 MUTATED EEA1 WILD-TYPE
  COLON            13            353
  RECTUM            3            116
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  EEA1 MUTATED         3        0        2         6         2         0
  EEA1 WILD-TYPE      88        1       30       132         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  EEA1 MUTATED           0          0          1          1        1         0
  EEA1 WILD-TYPE        24         11         58         41       47        18
                vv
clus             STAGE IVB
  EEA1 MUTATED           0
  EEA1 WILD-TYPE         1
D801V4, multiclass
            clus
vv           EEA1 MUTATED EEA1 WILD-TYPE
  STAGE I               3             88
  STAGE IA              0              1
  STAGE II              2             30
  STAGE IIA             6            132
  STAGE IIB             2              8
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            1             58
  STAGE IIIC            1             41
  STAGE IV              1             47
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  EEA1 MUTATED     0   3  11   2
  EEA1 WILD-TYPE  17  89 318  48
D801V5, multiclass
    clus
vv   EEA1 MUTATED EEA1 WILD-TYPE
  T1            0             17
  T2            3             89
  T3           11            318
  T4            2             48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  EEA1 MUTATED    14   1   1
  EEA1 WILD-TYPE 273 112  86
D801V6, multiclass
    clus
vv   EEA1 MUTATED EEA1 WILD-TYPE
  N0           14            273
  N1            1            112
  N2            1             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D801V7, binary
                cls
clus               0   1
  EEA1 MUTATED    15   1
  EEA1 WILD-TYPE 360  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  EEA1 MUTATED     15    1
  EEA1 WILD-TYPE  360   64
   clus
vv  EEA1 MUTATED EEA1 WILD-TYPE
  0           15            360
  1            1             64
[1] 2 2
[1] FALSE
D801V8, binary
                cls
clus               0   1
  EEA1 MUTATED     6  10
  EEA1 WILD-TYPE 219 254
[1] "tbl2"
                cls
clus             [,1] [,2]
  EEA1 MUTATED      6   10
  EEA1 WILD-TYPE  219  254
        clus
vv       EEA1 MUTATED EEA1 WILD-TYPE
  FEMALE            6            219
  MALE             10            254
[1] 2 2
[1] FALSE
D801V9, binary
                cls
clus               0   1
  EEA1 MUTATED    13   2
  EEA1 WILD-TYPE 337  20
[1] "tbl2"
                cls
clus             [,1] [,2]
  EEA1 MUTATED     13    2
  EEA1 WILD-TYPE  337   20
     clus
vv    EEA1 MUTATED EEA1 WILD-TYPE
  NO            13            337
  YES            2             20
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  EEA1 MUTATED                     10                             3
  EEA1 WILD-TYPE                  305                            44
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  EEA1 MUTATED                       2                              1
  EEA1 WILD-TYPE                   104                              9
D801V10, multiclass
                                clus
vv                               EEA1 MUTATED EEA1 WILD-TYPE
  COLON ADENOCARCINOMA                     10            305
  COLON MUCINOUS ADENOCARCINOMA             3             44
  RECTAL ADENOCARCINOMA                     2            104
  RECTAL MUCINOUS ADENOCARCINOMA            1              9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  EEA1 MUTATED    13   0   1   1
  EEA1 WILD-TYPE 332   4  30  24
D801V11, multiclass
    clus
vv   EEA1 MUTATED EEA1 WILD-TYPE
  R0           13            332
  R1            0              4
  R2            1             30
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D801V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  EEA1 MUTATED                                  0     1
  EEA1 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  EEA1 MUTATED                           1     6
  EEA1 WILD-TYPE                        21   220
D801V13, multiclass
                                  clus
vv                                 EEA1 MUTATED EEA1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                       6            220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(802) Variable = ADAM22 MUTATION ANALYSIS
D802V1, survival
                  sevent
clus2                0   1
  ADAM22 MUTATED     4   7
  ADAM22 WILD-TYPE 374  86
  ADAM22 MUTATED ADAM22 WILD-TYPE 
              11              460 
  ADAM22 MUTATED ADAM22 WILD-TYPE 
               7               86 
$`ADAM22 MUTATED`
TCGA-A6-6781 TCGA-AA-3848 TCGA-AA-3852 TCGA-AA-A00N TCGA-AZ-6598 TCGA-AZ-6600 
       19.66        10.06         0.00         4.01        49.41        12.10 
TCGA-AZ-6601 TCGA-D5-6536 TCGA-F4-6570 TCGA-AG-A002 TCGA-G5-6235 
      100.01        17.85         6.18        20.98        55.76 

$`ADAM22 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
       17.03         0.00        33.07        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       62.79        88.21         6.77        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6641 
       32.19         0.66         0.69        26.43 

  ADAM22 MUTATED ADAM22 WILD-TYPE 
               0                0 
  ADAM22 MUTATED ADAM22 WILD-TYPE 
          100.01           148.01 
  ADAM22 MUTATED ADAM22 WILD-TYPE 
          17.850           20.415 
[1] "0.0 - 100.0 (17.9)" "0.0 - 148.0 (20.4)"
[1] "hr=" "3.1"
D802V2, continuous
D802V3, binary
                  cls
clus                 0   1
  ADAM22 MUTATED     9   2
  ADAM22 WILD-TYPE 357 117
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ADAM22 MUTATED      9    2
  ADAM22 WILD-TYPE  357  117
        clus
vv       ADAM22 MUTATED ADAM22 WILD-TYPE
  COLON               9              357
  RECTUM              2              117
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ADAM22 MUTATED         1        0        2         3         1         0
  ADAM22 WILD-TYPE      90        1       30       135         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ADAM22 MUTATED           0          0          1          2        1
  ADAM22 WILD-TYPE        24         11         58         40       47
                  vv
clus               STAGE IVA STAGE IVB
  ADAM22 MUTATED           0         0
  ADAM22 WILD-TYPE        18         1
D802V4, multiclass
            clus
vv           ADAM22 MUTATED ADAM22 WILD-TYPE
  STAGE I                 1               90
  STAGE IA                0                1
  STAGE II                2               30
  STAGE IIA               3              135
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              1               58
  STAGE IIIC              2               40
  STAGE IV                1               47
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ADAM22 MUTATED     0   1   7   3
  ADAM22 WILD-TYPE  17  91 322  47
D802V5, multiclass
    clus
vv   ADAM22 MUTATED ADAM22 WILD-TYPE
  T1              0               17
  T2              1               91
  T3              7              322
  T4              3               47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  ADAM22 MUTATED     7   3   1
  ADAM22 WILD-TYPE 280 110  86
D802V6, multiclass
    clus
vv   ADAM22 MUTATED ADAM22 WILD-TYPE
  N0              7              280
  N1              3              110
  N2              1               86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D802V7, binary
                  cls
clus                 0   1
  ADAM22 MUTATED     7   1
  ADAM22 WILD-TYPE 368  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ADAM22 MUTATED      7    1
  ADAM22 WILD-TYPE  368   64
   clus
vv  ADAM22 MUTATED ADAM22 WILD-TYPE
  0              7              368
  1              1               64
[1] 2 2
[1] FALSE
D802V8, binary
                  cls
clus                 0   1
  ADAM22 MUTATED     3   8
  ADAM22 WILD-TYPE 222 256
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ADAM22 MUTATED      3    8
  ADAM22 WILD-TYPE  222  256
        clus
vv       ADAM22 MUTATED ADAM22 WILD-TYPE
  FEMALE              3              222
  MALE                8              256
[1] 2 2
[1] FALSE
D802V9, binary
                  cls
clus                 0   1
  ADAM22 MUTATED     8   0
  ADAM22 WILD-TYPE 342  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ADAM22 MUTATED      8    0
  ADAM22 WILD-TYPE  342   22
     clus
vv    ADAM22 MUTATED ADAM22 WILD-TYPE
  NO               8              342
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ADAM22 MUTATED                      6                             3
  ADAM22 WILD-TYPE                  309                            44
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ADAM22 MUTATED                       2                              0
  ADAM22 WILD-TYPE                   104                             10
D802V10, multiclass
                                clus
vv                               ADAM22 MUTATED ADAM22 WILD-TYPE
  COLON ADENOCARCINOMA                        6              309
  COLON MUCINOUS ADENOCARCINOMA               3               44
  RECTAL ADENOCARCINOMA                       2              104
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ADAM22 MUTATED     7   1   0   0
  ADAM22 WILD-TYPE 338   3  31  25
D802V11, multiclass
    clus
vv   ADAM22 MUTATED ADAM22 WILD-TYPE
  R0              7              338
  R1              1                3
  R2              0               31
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D802V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ADAM22 MUTATED                                  0     0
  ADAM22 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ADAM22 MUTATED                           1     6
  ADAM22 WILD-TYPE                        21   220
D802V13, multiclass
                                  clus
vv                                 ADAM22 MUTATED ADAM22 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                         6              220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(803) Variable = DDB1 MUTATION ANALYSIS
D803V1, survival
                sevent
clus2              0   1
  DDB1 MUTATED     9   6
  DDB1 WILD-TYPE 369  87
  DDB1 MUTATED DDB1 WILD-TYPE 
            15            456 
  DDB1 MUTATED DDB1 WILD-TYPE 
             6             87 
$`DDB1 MUTATED`
TCGA-A6-5661 TCGA-A6-6780 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3949 TCGA-AA-A01Q 
       33.53        20.12         1.02        13.02        26.01         1.02 
TCGA-AD-6964 TCGA-AZ-6599 TCGA-CM-5862 TCGA-D5-6537 TCGA-D5-7000 TCGA-DM-A1HB 
       10.88         6.77         5.03         4.80        10.26       135.65 
TCGA-F4-6460 TCGA-AG-A002 TCGA-AG-A02N 
       31.96        20.98        61.97 

$`DDB1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3510 
       19.66        20.28         7.04         3.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        6.97         1.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       33.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       32.02        15.02        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6538 
       18.25         1.32        43.27        15.12        17.85        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
        1.51        12.00        11.38       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
        7.50        44.32       131.51       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 
       10.98        49.97         1.94        38.96        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  DDB1 MUTATED DDB1 WILD-TYPE 
          1.02           0.00 
  DDB1 MUTATED DDB1 WILD-TYPE 
        135.65         148.01 
  DDB1 MUTATED DDB1 WILD-TYPE 
        13.020         20.415 
[1] "1.0 - 135.7 (13.0)" "0.0 - 148.0 (20.4)"
[1] "hr=" "2.4"
D803V2, continuous
D803V3, binary
                cls
clus               0   1
  DDB1 MUTATED    13   2
  DDB1 WILD-TYPE 353 117
[1] "tbl2"
                cls
clus             [,1] [,2]
  DDB1 MUTATED     13    2
  DDB1 WILD-TYPE  353  117
        clus
vv       DDB1 MUTATED DDB1 WILD-TYPE
  COLON            13            353
  RECTUM            2            117
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DDB1 MUTATED         3        0        3         2         0         0
  DDB1 WILD-TYPE      88        1       29       136        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DDB1 MUTATED           1          0          4          0        0         1
  DDB1 WILD-TYPE        23         11         55         42       48        17
                vv
clus             STAGE IVB
  DDB1 MUTATED           0
  DDB1 WILD-TYPE         1
D803V4, multiclass
            clus
vv           DDB1 MUTATED DDB1 WILD-TYPE
  STAGE I               3             88
  STAGE IA              0              1
  STAGE II              3             29
  STAGE IIA             2            136
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             1             23
  STAGE IIIA            0             11
  STAGE IIIB            4             55
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             1             17
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  DDB1 MUTATED     0   3  11   1
  DDB1 WILD-TYPE  17  89 318  49
D803V5, multiclass
    clus
vv   DDB1 MUTATED DDB1 WILD-TYPE
  T1            0             17
  T2            3             89
  T3           11            318
  T4            1             49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  DDB1 MUTATED     8   5   2
  DDB1 WILD-TYPE 279 108  85
D803V6, multiclass
    clus
vv   DDB1 MUTATED DDB1 WILD-TYPE
  N0            8            279
  N1            5            108
  N2            2             85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D803V7, binary
                cls
clus               0   1
  DDB1 MUTATED    10   1
  DDB1 WILD-TYPE 365  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  DDB1 MUTATED     10    1
  DDB1 WILD-TYPE  365   64
   clus
vv  DDB1 MUTATED DDB1 WILD-TYPE
  0           10            365
  1            1             64
[1] 2 2
[1] FALSE
D803V8, binary
                cls
clus               0   1
  DDB1 MUTATED     7   8
  DDB1 WILD-TYPE 218 256
[1] "tbl2"
                cls
clus             [,1] [,2]
  DDB1 MUTATED      7    8
  DDB1 WILD-TYPE  218  256
        clus
vv       DDB1 MUTATED DDB1 WILD-TYPE
  FEMALE            7            218
  MALE              8            256
[1] 2 2
[1] FALSE
D803V9, binary
                cls
clus               0   1
  DDB1 MUTATED    11   0
  DDB1 WILD-TYPE 339  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  DDB1 MUTATED     11    0
  DDB1 WILD-TYPE  339   22
     clus
vv    DDB1 MUTATED DDB1 WILD-TYPE
  NO            11            339
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  DDB1 MUTATED                      8                             4
  DDB1 WILD-TYPE                  307                            43
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  DDB1 MUTATED                       2                              0
  DDB1 WILD-TYPE                   104                             10
D803V10, multiclass
                                clus
vv                               DDB1 MUTATED DDB1 WILD-TYPE
  COLON ADENOCARCINOMA                      8            307
  COLON MUCINOUS ADENOCARCINOMA             4             43
  RECTAL ADENOCARCINOMA                     2            104
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  DDB1 MUTATED    10   0   0   0
  DDB1 WILD-TYPE 335   4  31  25
D803V11, multiclass
    clus
vv   DDB1 MUTATED DDB1 WILD-TYPE
  R0           10            335
  R1            0              4
  R2            0             31
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D803V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DDB1 MUTATED                                  0     0
  DDB1 WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  DDB1 MUTATED                           1     8
  DDB1 WILD-TYPE                        21   218
D803V13, multiclass
                                  clus
vv                                 DDB1 MUTATED DDB1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                       8            218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(804) Variable = GLI2 MUTATION ANALYSIS
D804V1, survival
                sevent
clus2              0   1
  GLI2 MUTATED    16   8
  GLI2 WILD-TYPE 362  85
  GLI2 MUTATED GLI2 WILD-TYPE 
            24            447 
  GLI2 MUTATED GLI2 WILD-TYPE 
             8             85 
$`GLI2 MUTATED`
TCGA-AA-3492 TCGA-AA-A01P TCGA-AY-5543 TCGA-CA-5255 TCGA-CA-6717 TCGA-CA-6718 
        3.02        38.07        33.01         3.06        12.76        10.06 
TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-6163 TCGA-CM-6171 TCGA-D5-6537 TCGA-D5-6539 
        5.03        15.02         2.96        14.04         4.80        12.49 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6928 TCGA-DM-A1DA TCGA-G4-6625 TCGA-G4-6628 
        4.41        12.43        11.64         7.50        91.79        79.69 
TCGA-AF-6655 TCGA-AG-3594 TCGA-AG-3732 TCGA-AG-3893 TCGA-CL-5917 TCGA-DY-A1DF 
       20.02         2.01        32.98        35.01        78.12        24.13 

$`GLI2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       12.00        31.00        31.00         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 
       12.69         3.25         3.29         0.07        12.20        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5868 
       22.98        30.08        32.02        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       15.02        12.00        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       12.99        13.02        15.02        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6540 
        1.32        43.27        15.12        17.85        17.13        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       15.58         1.48         3.68        14.30         9.04         9.44 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
       12.59       140.38        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6626 
       36.00        22.09        13.78        35.80        26.17        46.75 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6672 TCGA-AG-3574 
       10.39        14.50        16.83        15.39        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3598 TCGA-AG-3599 
       24.00         1.02        46.03        34.03        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        7.99         0.99        37.02         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
       33.17         6.97         4.73         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DG 
        5.03         5.29       126.44        41.36        57.24        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  GLI2 MUTATED GLI2 WILD-TYPE 
          2.01           0.00 
  GLI2 MUTATED GLI2 WILD-TYPE 
         91.79         148.01 
  GLI2 MUTATED GLI2 WILD-TYPE 
        12.625         20.980 
[1] "2.0 - 91.8 (12.6)"  "0.0 - 148.0 (21.0)"
[1] "hr=" "2.1"
D804V2, continuous
D804V3, binary
                cls
clus               0   1
  GLI2 MUTATED    20   6
  GLI2 WILD-TYPE 346 113
[1] "tbl2"
                cls
clus             [,1] [,2]
  GLI2 MUTATED     20    6
  GLI2 WILD-TYPE  346  113
        clus
vv       GLI2 MUTATED GLI2 WILD-TYPE
  COLON            20            346
  RECTUM            6            113
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GLI2 MUTATED         6        0        2         6         0         0
  GLI2 WILD-TYPE      85        1       30       132        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  GLI2 MUTATED           1          3          2          4        0         2
  GLI2 WILD-TYPE        23          8         57         38       48        16
                vv
clus             STAGE IVB
  GLI2 MUTATED           0
  GLI2 WILD-TYPE         1
D804V4, multiclass
            clus
vv           GLI2 MUTATED GLI2 WILD-TYPE
  STAGE I               6             85
  STAGE IA              0              1
  STAGE II              2             30
  STAGE IIA             6            132
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             1             23
  STAGE IIIA            3              8
  STAGE IIIB            2             57
  STAGE IIIC            4             38
  STAGE IV              0             48
  STAGE IVA             2             16
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  GLI2 MUTATED     1   6  18   1
  GLI2 WILD-TYPE  16  86 311  49
D804V5, multiclass
    clus
vv   GLI2 MUTATED GLI2 WILD-TYPE
  T1            1             16
  T2            6             86
  T3           18            311
  T4            1             49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  GLI2 MUTATED    15   7   4
  GLI2 WILD-TYPE 272 106  83
D804V6, multiclass
    clus
vv   GLI2 MUTATED GLI2 WILD-TYPE
  N0           15            272
  N1            7            106
  N2            4             83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D804V7, binary
                cls
clus               0   1
  GLI2 MUTATED    21   2
  GLI2 WILD-TYPE 354  63
[1] "tbl2"
                cls
clus             [,1] [,2]
  GLI2 MUTATED     21    2
  GLI2 WILD-TYPE  354   63
   clus
vv  GLI2 MUTATED GLI2 WILD-TYPE
  0           21            354
  1            2             63
[1] 2 2
[1] FALSE
D804V8, binary
                cls
clus               0   1
  GLI2 MUTATED    11  15
  GLI2 WILD-TYPE 214 249
[1] "tbl2"
                cls
clus             [,1] [,2]
  GLI2 MUTATED     11   15
  GLI2 WILD-TYPE  214  249
        clus
vv       GLI2 MUTATED GLI2 WILD-TYPE
  FEMALE           11            214
  MALE             15            249
[1] 2 2
[1] FALSE
D804V9, binary
                cls
clus               0   1
  GLI2 MUTATED    20   1
  GLI2 WILD-TYPE 330  21
[1] "tbl2"
                cls
clus             [,1] [,2]
  GLI2 MUTATED     20    1
  GLI2 WILD-TYPE  330   21
     clus
vv    GLI2 MUTATED GLI2 WILD-TYPE
  NO            20            330
  YES            1             21
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  GLI2 MUTATED                     17                             3
  GLI2 WILD-TYPE                  298                            44
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  GLI2 MUTATED                       5                              1
  GLI2 WILD-TYPE                   101                              9
D804V10, multiclass
                                clus
vv                               GLI2 MUTATED GLI2 WILD-TYPE
  COLON ADENOCARCINOMA                     17            298
  COLON MUCINOUS ADENOCARCINOMA             3             44
  RECTAL ADENOCARCINOMA                     5            101
  RECTAL MUCINOUS ADENOCARCINOMA            1              9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  GLI2 MUTATED    20   0   0   4
  GLI2 WILD-TYPE 325   4  31  21
D804V11, multiclass
    clus
vv   GLI2 MUTATED GLI2 WILD-TYPE
  R0           20            325
  R1            0              4
  R2            0             31
  RX            4             21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D804V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GLI2 MUTATED                                  0     3
  GLI2 WILD-TYPE                                1     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  GLI2 MUTATED                           1    16
  GLI2 WILD-TYPE                        21   210
D804V13, multiclass
                                  clus
vv                                 GLI2 MUTATED GLI2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       3              8
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                      16            210
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(805) Variable = ADAM30 MUTATION ANALYSIS
D805V1, survival
                  sevent
clus2                0   1
  ADAM30 MUTATED    12   1
  ADAM30 WILD-TYPE 366  92
  ADAM30 MUTATED ADAM30 WILD-TYPE 
              13              458 
  ADAM30 MUTATED ADAM30 WILD-TYPE 
               1               92 
$`ADAM30 MUTATED`
TCGA-A6-5661 TCGA-AA-3821 TCGA-AA-3877 TCGA-AA-3977 TCGA-CM-6674 TCGA-D5-6928 
       33.53         1.02        31.00        25.02        12.95        11.64 
TCGA-DM-A1D7 TCGA-F4-6856 TCGA-AG-3599 TCGA-AG-A002 TCGA-EI-6506 TCGA-EI-6507 
       13.32        35.31        12.03        20.98        20.55        19.96 
TCGA-F5-6465 
       49.51 

$`ADAM30 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 
       10.06        35.05        33.04         0.99        25.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 
       24.03        27.02        29.98        18.05         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6676 
       13.02        15.02        14.04        11.01        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
       14.30         9.04         9.44         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       92.75        49.91        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 
       16.24        33.67        13.25         0.53        47.41       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3600 
        1.02        46.03        34.03         2.01        50.04         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6508 TCGA-EI-6510 
       24.13        51.48        32.61         0.49        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
        9.96        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  ADAM30 MUTATED ADAM30 WILD-TYPE 
            1.02             0.00 
  ADAM30 MUTATED ADAM30 WILD-TYPE 
           49.51           148.01 
  ADAM30 MUTATED ADAM30 WILD-TYPE 
          20.550           20.155 
[1] "1.0 - 49.5 (20.6)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "2.2"
D805V2, continuous
D805V3, binary
                  cls
clus                 0   1
  ADAM30 MUTATED     8   5
  ADAM30 WILD-TYPE 358 114
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ADAM30 MUTATED      8    5
  ADAM30 WILD-TYPE  358  114
        clus
vv       ADAM30 MUTATED ADAM30 WILD-TYPE
  COLON               8              358
  RECTUM              5              114
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ADAM30 MUTATED         5        0        0         7         0         0
  ADAM30 WILD-TYPE      86        1       32       131        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ADAM30 MUTATED           0          0          0          0        0
  ADAM30 WILD-TYPE        24         11         59         42       48
                  vv
clus               STAGE IVA STAGE IVB
  ADAM30 MUTATED           0         0
  ADAM30 WILD-TYPE        18         1
D805V4, multiclass
            clus
vv           ADAM30 MUTATED ADAM30 WILD-TYPE
  STAGE I                 5               86
  STAGE IA                0                1
  STAGE II                0               32
  STAGE IIA               7              131
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              0               59
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ADAM30 MUTATED     1   5   7   0
  ADAM30 WILD-TYPE  16  87 322  50
D805V5, multiclass
    clus
vv   ADAM30 MUTATED ADAM30 WILD-TYPE
  T1              1               16
  T2              5               87
  T3              7              322
  T4              0               50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  ADAM30 MUTATED    13   0   0
  ADAM30 WILD-TYPE 274 113  87
D805V6, multiclass
    clus
vv   ADAM30 MUTATED ADAM30 WILD-TYPE
  N0             13              274
  N1              0              113
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D805V7, binary
                  cls
clus                 0   1
  ADAM30 MUTATED    12   0
  ADAM30 WILD-TYPE 363  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ADAM30 MUTATED     12    0
  ADAM30 WILD-TYPE  363   65
   clus
vv  ADAM30 MUTATED ADAM30 WILD-TYPE
  0             12              363
  1              0               65
[1] 2 2
[1] FALSE
D805V8, binary
                  cls
clus                 0   1
  ADAM30 MUTATED     5   8
  ADAM30 WILD-TYPE 220 256
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ADAM30 MUTATED      5    8
  ADAM30 WILD-TYPE  220  256
        clus
vv       ADAM30 MUTATED ADAM30 WILD-TYPE
  FEMALE              5              220
  MALE                8              256
[1] 2 2
[1] FALSE
D805V9, binary
                  cls
clus                 0   1
  ADAM30 MUTATED    12   0
  ADAM30 WILD-TYPE 338  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ADAM30 MUTATED     12    0
  ADAM30 WILD-TYPE  338   22
     clus
vv    ADAM30 MUTATED ADAM30 WILD-TYPE
  NO              12              338
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ADAM30 MUTATED                      3                             4
  ADAM30 WILD-TYPE                  312                            43
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ADAM30 MUTATED                       4                              0
  ADAM30 WILD-TYPE                   102                             10
D805V10, multiclass
                                clus
vv                               ADAM30 MUTATED ADAM30 WILD-TYPE
  COLON ADENOCARCINOMA                        3              312
  COLON MUCINOUS ADENOCARCINOMA               4               43
  RECTAL ADENOCARCINOMA                       4              102
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ADAM30 MUTATED    11   0   0   0
  ADAM30 WILD-TYPE 334   4  31  25
D805V11, multiclass
    clus
vv   ADAM30 MUTATED ADAM30 WILD-TYPE
  R0             11              334
  R1              0                4
  R2              0               31
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D805V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ADAM30 MUTATED                                  0     0
  ADAM30 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ADAM30 MUTATED                           1     7
  ADAM30 WILD-TYPE                        21   219
D805V13, multiclass
                                  clus
vv                                 ADAM30 MUTATED ADAM30 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                         7              219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(806) Variable = RGS22 MUTATION ANALYSIS
D806V1, survival
                 sevent
clus2               0   1
  RGS22 MUTATED    22   5
  RGS22 WILD-TYPE 356  88
  RGS22 MUTATED RGS22 WILD-TYPE 
             27             444 
  RGS22 MUTATED RGS22 WILD-TYPE 
              5              88 
$`RGS22 MUTATED`
TCGA-A6-5665 TCGA-AA-3510 TCGA-AA-3713 TCGA-AA-A00N TCGA-AA-A010 TCGA-AD-6895 
       22.06        63.98        19.04         4.01        34.98         0.72 
TCGA-AU-6004 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4952 
       27.09        58.39        49.41        12.76        10.06        15.62 
TCGA-CK-5913 TCGA-CM-5348 TCGA-CM-6172 TCGA-D5-6536 TCGA-D5-6930 TCGA-DM-A1D6 
       51.32        22.98        11.01        17.85         1.51        49.91 
TCGA-DM-A1HA TCGA-DM-A28G TCGA-F4-6569 TCGA-G4-6309 TCGA-G4-6586 TCGA-G4-6628 
      131.51        60.79        35.74        85.48        35.80        79.69 
TCGA-AG-3883 TCGA-AG-A002 TCGA-DC-6160 
        1.02        20.98        19.99 

$`RGS22 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 
        0.07        21.37        15.52        56.55         0.79         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 
       22.42        27.42        10.88         0.20        14.50        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        33.01        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 
      106.75        22.36        62.79        88.21         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5914 
       14.30        17.56       148.01        85.45        49.08         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5349 
       37.02        25.02        13.02        29.06        22.03        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6674 
       14.99        12.99        13.02        15.02        14.04        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 
       18.25         1.32        43.27        15.12         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
      130.65        92.75        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
       44.32       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6570 
       35.97       117.07        98.24         8.61        31.96         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 
       65.85        53.62        44.68        55.04        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        26.17        91.79        46.75 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3885 TCGA-AG-3887 
        0.99         0.99        19.04        19.99        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  RGS22 MUTATED RGS22 WILD-TYPE 
           0.72            0.00 
  RGS22 MUTATED RGS22 WILD-TYPE 
         131.51          148.01 
  RGS22 MUTATED RGS22 WILD-TYPE 
         22.980          20.035 
[1] "0.7 - 131.5 (23.0)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.4"
D806V2, continuous
D806V3, binary
                 cls
clus                0   1
  RGS22 MUTATED    24   3
  RGS22 WILD-TYPE 342 116
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RGS22 MUTATED     24    3
  RGS22 WILD-TYPE  342  116
        clus
vv       RGS22 MUTATED RGS22 WILD-TYPE
  COLON             24             342
  RECTUM             3             116
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RGS22 MUTATED         6        0        2        10         2         0
  RGS22 WILD-TYPE      85        1       30       128         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RGS22 MUTATED           0          0          3          2        1         0
  RGS22 WILD-TYPE        24         11         56         40       47        18
                 vv
clus              STAGE IVB
  RGS22 MUTATED           0
  RGS22 WILD-TYPE         1
D806V4, multiclass
            clus
vv           RGS22 MUTATED RGS22 WILD-TYPE
  STAGE I                6              85
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA             10             128
  STAGE IIB              2               8
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             3              56
  STAGE IIIC             2              40
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  RGS22 MUTATED     0   6  18   3
  RGS22 WILD-TYPE  17  86 311  47
D806V5, multiclass
    clus
vv   RGS22 MUTATED RGS22 WILD-TYPE
  T1             0              17
  T2             6              86
  T3            18             311
  T4             3              47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  RGS22 MUTATED    21   4   2
  RGS22 WILD-TYPE 266 109  85
D806V6, multiclass
    clus
vv   RGS22 MUTATED RGS22 WILD-TYPE
  N0            21             266
  N1             4             109
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D806V7, binary
                 cls
clus                0   1
  RGS22 MUTATED    23   1
  RGS22 WILD-TYPE 352  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RGS22 MUTATED     23    1
  RGS22 WILD-TYPE  352   64
   clus
vv  RGS22 MUTATED RGS22 WILD-TYPE
  0            23             352
  1             1              64
[1] 2 2
[1] FALSE
D806V8, binary
                 cls
clus                0   1
  RGS22 MUTATED     9  18
  RGS22 WILD-TYPE 216 246
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RGS22 MUTATED      9   18
  RGS22 WILD-TYPE  216  246
        clus
vv       RGS22 MUTATED RGS22 WILD-TYPE
  FEMALE             9             216
  MALE              18             246
[1] 2 2
[1] FALSE
D806V9, binary
                 cls
clus                0   1
  RGS22 MUTATED    16   1
  RGS22 WILD-TYPE 334  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RGS22 MUTATED     16    1
  RGS22 WILD-TYPE  334   21
     clus
vv    RGS22 MUTATED RGS22 WILD-TYPE
  NO             16             334
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  RGS22 MUTATED                     19                             5
  RGS22 WILD-TYPE                  296                            42
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  RGS22 MUTATED                       3                              0
  RGS22 WILD-TYPE                   103                             10
D806V10, multiclass
                                clus
vv                               RGS22 MUTATED RGS22 WILD-TYPE
  COLON ADENOCARCINOMA                      19             296
  COLON MUCINOUS ADENOCARCINOMA              5              42
  RECTAL ADENOCARCINOMA                      3             103
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  RGS22 MUTATED    17   0   1   4
  RGS22 WILD-TYPE 328   4  30  21
D806V11, multiclass
    clus
vv   RGS22 MUTATED RGS22 WILD-TYPE
  R0            17             328
  R1             0               4
  R2             1              30
  RX             4              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D806V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RGS22 MUTATED                                  0     2
  RGS22 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  RGS22 MUTATED                           1    18
  RGS22 WILD-TYPE                        21   208
D806V13, multiclass
                                  clus
vv                                 RGS22 MUTATED RGS22 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               9
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                       18             208
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(807) Variable = PPP1R3A MUTATION ANALYSIS
D807V1, survival
                   sevent
clus2                 0   1
  PPP1R3A MUTATED    26   9
  PPP1R3A WILD-TYPE 352  84
  PPP1R3A MUTATED PPP1R3A WILD-TYPE 
               35               436 
  PPP1R3A MUTATED PPP1R3A WILD-TYPE 
                9                84 
$`PPP1R3A MUTATED`
TCGA-A6-6648 TCGA-A6-6652 TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3655 TCGA-AA-3660 
       25.18        24.69         3.02        63.98        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3713 TCGA-AA-3848 TCGA-AA-3852 TCGA-AA-3977 
        6.05         0.92        19.04        10.06         0.00        25.02 
TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01Q TCGA-AD-6963 TCGA-AD-6964 TCGA-AZ-4315 
        4.01        34.98         1.02        27.42        10.88        58.39 
TCGA-AZ-6608 TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-5861 TCGA-CM-6163 TCGA-CM-6675 
        1.61        12.76        10.06        15.02         2.96        13.05 
TCGA-D5-5540 TCGA-D5-6538 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A28K TCGA-F4-6703 
       56.09        17.13        44.32       131.51        98.24        47.87 
TCGA-AF-2689 TCGA-AG-3892 TCGA-AG-A002 TCGA-CL-5917 TCGA-DC-5869 
       39.48        13.02        20.98        78.12         5.03 

$`PPP1R3A WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       25.08        24.16        21.76        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 
       19.66        20.28         7.04         1.02        35.01         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 
        6.97        54.02         2.01        14.01        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3850 
       38.99        37.02        14.93         0.00        17.03         0.00 
TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
       33.07        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        31.00        38.07        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6965 TCGA-AU-3779 
        0.79         0.72         5.79        22.42         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
       11.74         3.19        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.07        12.20        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6676 TCGA-CM-6677 
       15.02        14.04        11.01        12.95        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
       17.85         4.80        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HB TCGA-DM-A282 
       13.32        12.59       140.38         7.50       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6704 TCGA-F4-6805 
        8.61        31.96        35.74         6.18         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       24.13        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       17.03        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5918 TCGA-DC-5337 
        6.05        33.17         6.97         4.73         7.17        15.02 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  PPP1R3A MUTATED PPP1R3A WILD-TYPE 
                0                 0 
  PPP1R3A MUTATED PPP1R3A WILD-TYPE 
           131.51            148.01 
  PPP1R3A MUTATED PPP1R3A WILD-TYPE 
           19.040            20.235 
[1] "0.0 - 131.5 (19.0)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.1"
D807V2, continuous
D807V3, binary
                   cls
clus                  0   1
  PPP1R3A MUTATED    32   6
  PPP1R3A WILD-TYPE 334 113
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PPP1R3A MUTATED     32    6
  PPP1R3A WILD-TYPE  334  113
        clus
vv       PPP1R3A MUTATED PPP1R3A WILD-TYPE
  COLON               32               334
  RECTUM               6               113
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PPP1R3A MUTATED         3        0        5        10         3         0
  PPP1R3A WILD-TYPE      88        1       27       128         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PPP1R3A MUTATED           1          1          2          4        3
  PPP1R3A WILD-TYPE        23         10         57         38       45
                   vv
clus                STAGE IVA STAGE IVB
  PPP1R3A MUTATED           2         1
  PPP1R3A WILD-TYPE        16         0
D807V4, multiclass
            clus
vv           PPP1R3A MUTATED PPP1R3A WILD-TYPE
  STAGE I                  3                88
  STAGE IA                 0                 1
  STAGE II                 5                27
  STAGE IIA               10               128
  STAGE IIB                3                 7
  STAGE IIC                0                 1
  STAGE III                1                23
  STAGE IIIA               1                10
  STAGE IIIB               2                57
  STAGE IIIC               4                38
  STAGE IV                 3                45
  STAGE IVA                2                16
  STAGE IVB                1                 0
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  PPP1R3A MUTATED     2   3  28   5
  PPP1R3A WILD-TYPE  15  89 301  45
D807V5, multiclass
    clus
vv   PPP1R3A MUTATED PPP1R3A WILD-TYPE
  T1               2                15
  T2               3                89
  T3              28               301
  T4               5                45
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  PPP1R3A MUTATED    26   3   9
  PPP1R3A WILD-TYPE 261 110  78
D807V6, multiclass
    clus
vv   PPP1R3A MUTATED PPP1R3A WILD-TYPE
  N0              26               261
  N1               3               110
  N2               9                78
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D807V7, binary
                   cls
clus                  0   1
  PPP1R3A MUTATED    27   6
  PPP1R3A WILD-TYPE 348  59
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PPP1R3A MUTATED     27    6
  PPP1R3A WILD-TYPE  348   59
   clus
vv  PPP1R3A MUTATED PPP1R3A WILD-TYPE
  0              27               348
  1               6                59
[1] 2 2
[1] FALSE
D807V8, binary
                   cls
clus                  0   1
  PPP1R3A MUTATED    17  21
  PPP1R3A WILD-TYPE 208 243
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PPP1R3A MUTATED     17   21
  PPP1R3A WILD-TYPE  208  243
        clus
vv       PPP1R3A MUTATED PPP1R3A WILD-TYPE
  FEMALE              17               208
  MALE                21               243
[1] 2 2
[1] FALSE
D807V9, binary
                   cls
clus                  0   1
  PPP1R3A MUTATED    27   1
  PPP1R3A WILD-TYPE 323  21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PPP1R3A MUTATED     27    1
  PPP1R3A WILD-TYPE  323   21
     clus
vv    PPP1R3A MUTATED PPP1R3A WILD-TYPE
  NO               27               323
  YES               1                21
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PPP1R3A MUTATED                     28                             4
  PPP1R3A WILD-TYPE                  287                            43
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PPP1R3A MUTATED                       6                              0
  PPP1R3A WILD-TYPE                   100                             10
D807V10, multiclass
                                clus
vv                               PPP1R3A MUTATED PPP1R3A WILD-TYPE
  COLON ADENOCARCINOMA                        28               287
  COLON MUCINOUS ADENOCARCINOMA                4                43
  RECTAL ADENOCARCINOMA                        6               100
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  PPP1R3A MUTATED    23   0   2   4
  PPP1R3A WILD-TYPE 322   4  29  21
D807V11, multiclass
    clus
vv   PPP1R3A MUTATED PPP1R3A WILD-TYPE
  R0              23               322
  R1               0                 4
  R2               2                29
  RX               4                21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D807V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PPP1R3A MUTATED                                  0     2
  PPP1R3A WILD-TYPE                                1     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  PPP1R3A MUTATED                           3    16
  PPP1R3A WILD-TYPE                        19   210
D807V13, multiclass
                                  clus
vv                                 PPP1R3A MUTATED PPP1R3A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          2                 9
  BLACK OR AFRICAN AMERICAN                      3                19
  WHITE                                         16               210
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(808) Variable = CCR2 MUTATION ANALYSIS
D808V1, survival
                sevent
clus2              0   1
  CCR2 MUTATED     7   0
  CCR2 WILD-TYPE 371  93
  CCR2 MUTATED CCR2 WILD-TYPE 
             7            464 
  CCR2 MUTATED CCR2 WILD-TYPE 
             0             93 
$`CCR2 MUTATED`
TCGA-A6-5666 TCGA-A6-6781 TCGA-AD-6548 TCGA-CA-6717 TCGA-CK-4950 TCGA-D5-5541 
       32.71        19.66        21.37        12.76        85.45        55.92 
TCGA-D5-6540 
       16.14 

$`CCR2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        22.06        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6888 TCGA-AD-6889 
       39.98        18.05        40.96         0.07        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5912 
       10.06        14.30        17.56       148.01        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       19.59        56.09        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 
       15.12        17.85         4.80        17.13        12.49        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  CCR2 MUTATED CCR2 WILD-TYPE 
         12.76           0.00 
  CCR2 MUTATED CCR2 WILD-TYPE 
         85.45         148.01 
  CCR2 MUTATED CCR2 WILD-TYPE 
        21.370         20.155 
[1] "12.8 - 85.5 (21.4)" "0.0 - 148.0 (20.2)"
[1] "hr="     "9200000"
D808V2, continuous
D808V3, binary
                cls
clus               0   1
  CCR2 MUTATED     7   0
  CCR2 WILD-TYPE 359 119
[1] "tbl2"
                cls
clus             [,1] [,2]
  CCR2 MUTATED      7    0
  CCR2 WILD-TYPE  359  119
        clus
vv       CCR2 MUTATED CCR2 WILD-TYPE
  COLON             7            359
  RECTUM            0            119
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CCR2 MUTATED         2        0        0         1         0         1
  CCR2 WILD-TYPE      89        1       32       137        10         0
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CCR2 MUTATED           0          0          2          1        0         0
  CCR2 WILD-TYPE        24         11         57         41       48        18
                vv
clus             STAGE IVB
  CCR2 MUTATED           0
  CCR2 WILD-TYPE         1
D808V4, multiclass
            clus
vv           CCR2 MUTATED CCR2 WILD-TYPE
  STAGE I               2             89
  STAGE IA              0              1
  STAGE II              0             32
  STAGE IIA             1            137
  STAGE IIB             0             10
  STAGE IIC             1              0
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            2             57
  STAGE IIIC            1             41
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  CCR2 MUTATED     0   2   3   2
  CCR2 WILD-TYPE  17  90 326  48
D808V5, multiclass
    clus
vv   CCR2 MUTATED CCR2 WILD-TYPE
  T1            0             17
  T2            2             90
  T3            3            326
  T4            2             48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  CCR2 MUTATED     4   3   0
  CCR2 WILD-TYPE 283 110  87
D808V6, multiclass
    clus
vv   CCR2 MUTATED CCR2 WILD-TYPE
  N0            4            283
  N1            3            110
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D808V7, binary
                cls
clus               0   1
  CCR2 MUTATED     6   0
  CCR2 WILD-TYPE 369  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  CCR2 MUTATED      6    0
  CCR2 WILD-TYPE  369   65
   clus
vv  CCR2 MUTATED CCR2 WILD-TYPE
  0            6            369
  1            0             65
[1] 2 2
[1] FALSE
D808V8, binary
                cls
clus               0   1
  CCR2 MUTATED     2   5
  CCR2 WILD-TYPE 223 259
[1] "tbl2"
                cls
clus             [,1] [,2]
  CCR2 MUTATED      2    5
  CCR2 WILD-TYPE  223  259
        clus
vv       CCR2 MUTATED CCR2 WILD-TYPE
  FEMALE            2            223
  MALE              5            259
[1] 2 2
[1] FALSE
D808V9, binary
                cls
clus               0   1
  CCR2 MUTATED     7   0
  CCR2 WILD-TYPE 343  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  CCR2 MUTATED      7    0
  CCR2 WILD-TYPE  343   22
     clus
vv    CCR2 MUTATED CCR2 WILD-TYPE
  NO             7            343
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CCR2 MUTATED                      4                             3
  CCR2 WILD-TYPE                  311                            44
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CCR2 MUTATED                       0                              0
  CCR2 WILD-TYPE                   106                             10
D808V10, multiclass
                                clus
vv                               CCR2 MUTATED CCR2 WILD-TYPE
  COLON ADENOCARCINOMA                      4            311
  COLON MUCINOUS ADENOCARCINOMA             3             44
  RECTAL ADENOCARCINOMA                     0            106
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  CCR2 MUTATED     4   1   0   1
  CCR2 WILD-TYPE 341   3  31  24
D808V11, multiclass
    clus
vv   CCR2 MUTATED CCR2 WILD-TYPE
  R0            4            341
  R1            1              3
  R2            0             31
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D808V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CCR2 MUTATED                                  0     1
  CCR2 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  CCR2 MUTATED                           1     5
  CCR2 WILD-TYPE                        21   221
D808V13, multiclass
                                  clus
vv                                 CCR2 MUTATED CCR2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                       5            221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(809) Variable = OR4D2 MUTATION ANALYSIS
D809V1, survival
                 sevent
clus2               0   1
  OR4D2 MUTATED     3   1
  OR4D2 WILD-TYPE 375  92
  OR4D2 MUTATED OR4D2 WILD-TYPE 
              4             467 
  OR4D2 MUTATED OR4D2 WILD-TYPE 
              1              92 
$`OR4D2 MUTATED`
TCGA-A6-6653 TCGA-AA-3496 TCGA-AZ-6601 TCGA-G4-6588 
       24.39         1.02       100.01        26.17 

$`OR4D2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
       25.08        25.18        24.16        21.76        24.69        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 
       20.12        19.66        20.28         7.04         3.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
       12.10        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 
       61.91        36.00        22.09        13.78        35.80        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  OR4D2 MUTATED OR4D2 WILD-TYPE 
           1.02            0.00 
  OR4D2 MUTATED OR4D2 WILD-TYPE 
         100.01          148.01 
  OR4D2 MUTATED OR4D2 WILD-TYPE 
          25.28           20.12 
[1] "1.0 - 100.0 (25.3)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.1"
D809V2, continuous
D809V3, binary
                 cls
clus                0   1
  OR4D2 MUTATED     4   0
  OR4D2 WILD-TYPE 362 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR4D2 MUTATED      4    0
  OR4D2 WILD-TYPE  362  119
        clus
vv       OR4D2 MUTATED OR4D2 WILD-TYPE
  COLON              4             362
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  OR4D2 MUTATED         1        0        2         1         0         0
  OR4D2 WILD-TYPE      90        1       30       137        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  OR4D2 MUTATED           0          0          0          0        0         0
  OR4D2 WILD-TYPE        24         11         59         42       48        18
                 vv
clus              STAGE IVB
  OR4D2 MUTATED           0
  OR4D2 WILD-TYPE         1
D809V4, multiclass
            clus
vv           OR4D2 MUTATED OR4D2 WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA              1             137
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  OR4D2 MUTATED     0   1   3   0
  OR4D2 WILD-TYPE  17  91 326  50
D809V5, multiclass
    clus
vv   OR4D2 MUTATED OR4D2 WILD-TYPE
  T1             0              17
  T2             1              91
  T3             3             326
  T4             0              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  OR4D2 MUTATED     4   0   0
  OR4D2 WILD-TYPE 283 113  87
D809V6, multiclass
    clus
vv   OR4D2 MUTATED OR4D2 WILD-TYPE
  N0             4             283
  N1             0             113
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D809V7, binary
                 cls
clus                0   1
  OR4D2 MUTATED     4   0
  OR4D2 WILD-TYPE 371  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR4D2 MUTATED      4    0
  OR4D2 WILD-TYPE  371   65
   clus
vv  OR4D2 MUTATED OR4D2 WILD-TYPE
  0             4             371
  1             0              65
[1] 2 2
[1] FALSE
D809V8, binary
                 cls
clus                0   1
  OR4D2 MUTATED     2   2
  OR4D2 WILD-TYPE 223 262
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR4D2 MUTATED      2    2
  OR4D2 WILD-TYPE  223  262
        clus
vv       OR4D2 MUTATED OR4D2 WILD-TYPE
  FEMALE             2             223
  MALE               2             262
[1] 2 2
[1] FALSE
D809V9, binary
                 cls
clus                0   1
  OR4D2 MUTATED     3   0
  OR4D2 WILD-TYPE 347  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR4D2 MUTATED      3    0
  OR4D2 WILD-TYPE  347   22
     clus
vv    OR4D2 MUTATED OR4D2 WILD-TYPE
  NO              3             347
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  OR4D2 MUTATED                      4                             0
  OR4D2 WILD-TYPE                  311                            47
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  OR4D2 MUTATED                       0                              0
  OR4D2 WILD-TYPE                   106                             10
D809V10, multiclass
                                clus
vv                               OR4D2 MUTATED OR4D2 WILD-TYPE
  COLON ADENOCARCINOMA                       4             311
  COLON MUCINOUS ADENOCARCINOMA              0              47
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  OR4D2 MUTATED     2   0   0   0
  OR4D2 WILD-TYPE 343   4  31  25
D809V11, multiclass
[1] "Remove cluster labels:" "OR4D2 MUTATED"         
clus
  OR4D2 MUTATED OR4D2 WILD-TYPE 
              2             403 
     TCGA-A6-2671      TCGA-A6-2672      TCGA-A6-2674      TCGA-A6-2676 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-A6-2677      TCGA-A6-2678      TCGA-A6-2683      TCGA-A6-3807 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-A6-3808      TCGA-A6-3809      TCGA-A6-3810      TCGA-A6-5657 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-A6-5659      TCGA-A6-5661      TCGA-A6-5665      TCGA-A6-6781 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AA-3489      TCGA-AA-3492      TCGA-AA-3502      TCGA-AA-3510 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AA-3511      TCGA-AA-3514      TCGA-AA-3517      TCGA-AA-3518 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AA-3519      TCGA-AA-3520      TCGA-AA-3521      TCGA-AA-3522 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AA-3524      TCGA-AA-3525      TCGA-AA-3526      TCGA-AA-3527 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AA-3529      TCGA-AA-3530      TCGA-AA-3531      TCGA-AA-3532 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AA-3534      TCGA-AA-3538      TCGA-AA-3542      TCGA-AA-3543 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AA-3544      TCGA-AA-3548      TCGA-AA-3549      TCGA-AA-3552 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AA-3553      TCGA-AA-3554      TCGA-AA-3555      TCGA-AA-3556 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AA-3558      TCGA-AA-3560      TCGA-AA-3561      TCGA-AA-3562 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AA-3655      TCGA-AA-3660      TCGA-AA-3662      TCGA-AA-3663 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AA-3664      TCGA-AA-3666      TCGA-AA-3667      TCGA-AA-3672 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AA-3673      TCGA-AA-3678      TCGA-AA-3679      TCGA-AA-3680 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AA-3681      TCGA-AA-3684      TCGA-AA-3685      TCGA-AA-3688 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AA-3692      TCGA-AA-3693      TCGA-AA-3695      TCGA-AA-3696 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AA-3697      TCGA-AA-3710      TCGA-AA-3712      TCGA-AA-3713 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AA-3715      TCGA-AA-3811      TCGA-AA-3812      TCGA-AA-3814 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AA-3815      TCGA-AA-3818      TCGA-AA-3819      TCGA-AA-3821 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AA-3831      TCGA-AA-3833      TCGA-AA-3837      TCGA-AA-3842 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AA-3844      TCGA-AA-3845      TCGA-AA-3846      TCGA-AA-3848 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AA-3850      TCGA-AA-3851      TCGA-AA-3852      TCGA-AA-3854 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AA-3855      TCGA-AA-3856      TCGA-AA-3858      TCGA-AA-3860 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AA-3861      TCGA-AA-3864      TCGA-AA-3866      TCGA-AA-3867 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AA-3869      TCGA-AA-3870      TCGA-AA-3872      TCGA-AA-3875 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AA-3877      TCGA-AA-3930      TCGA-AA-3939      TCGA-AA-3941 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AA-3947      TCGA-AA-3949      TCGA-AA-3950      TCGA-AA-3952 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AA-3955      TCGA-AA-3956      TCGA-AA-3968      TCGA-AA-3971 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AA-3972      TCGA-AA-3973      TCGA-AA-3975      TCGA-AA-3976 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AA-3979      TCGA-AA-3984      TCGA-AA-3986      TCGA-AA-3989 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AA-3994      TCGA-AA-A004      TCGA-AA-A00A      TCGA-AA-A00D 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AA-A00E      TCGA-AA-A00F      TCGA-AA-A00J      TCGA-AA-A00K 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AA-A00L      TCGA-AA-A00N      TCGA-AA-A00O      TCGA-AA-A00Q 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AA-A00R      TCGA-AA-A00U      TCGA-AA-A00W      TCGA-AA-A00Z 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AA-A010      TCGA-AA-A017      TCGA-AA-A01D      TCGA-AA-A01F 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AA-A01G      TCGA-AA-A01I      TCGA-AA-A01K      TCGA-AA-A01P 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AA-A01Q      TCGA-AA-A01R      TCGA-AA-A01S      TCGA-AA-A01T 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AA-A01V      TCGA-AA-A01X      TCGA-AA-A01Z      TCGA-AA-A022 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AA-A024      TCGA-AA-A029      TCGA-AA-A02F      TCGA-AA-A02H 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AA-A02J      TCGA-AA-A02K      TCGA-AA-A02O      TCGA-AA-A02W 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AA-A02Y      TCGA-AA-A03F      TCGA-AA-A03J      TCGA-AD-5900 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AD-6548      TCGA-AD-6888      TCGA-AU-3779      TCGA-AU-6004 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AY-4070      TCGA-AY-4071      TCGA-AY-5543      TCGA-AY-6196 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AY-6197      TCGA-AY-6386      TCGA-AZ-4315      TCGA-AZ-4681 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AZ-4682      TCGA-CA-5254      TCGA-CA-5255      TCGA-CA-5796 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-CA-5797      TCGA-CA-6715      TCGA-CA-6716      TCGA-CA-6717 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-CA-6718      TCGA-CA-6719      TCGA-CK-4947      TCGA-CK-4948 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-CK-4950      TCGA-CK-4952      TCGA-CK-5912      TCGA-CK-5913 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-CK-5914      TCGA-CK-5915      TCGA-CK-5916      TCGA-CK-6746 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-CK-6747      TCGA-CK-6748      TCGA-CK-6751      TCGA-CM-4743 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-CM-4744      TCGA-CM-4746      TCGA-CM-4747      TCGA-CM-4752 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-CM-5341      TCGA-CM-5344      TCGA-CM-5348      TCGA-CM-5349 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-CM-5860      TCGA-CM-5861      TCGA-CM-5862      TCGA-CM-5863 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-CM-5864      TCGA-CM-5868      TCGA-CM-6161      TCGA-CM-6162 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-CM-6163      TCGA-CM-6164      TCGA-CM-6165      TCGA-CM-6166 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-CM-6167      TCGA-CM-6168      TCGA-CM-6169      TCGA-CM-6170 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-CM-6171      TCGA-CM-6172      TCGA-CM-6674      TCGA-CM-6675 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-CM-6676      TCGA-CM-6677      TCGA-CM-6678      TCGA-CM-6679 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-CM-6680      TCGA-D5-5537      TCGA-D5-5538      TCGA-D5-5539 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-D5-5540      TCGA-D5-5541      TCGA-D5-6529      TCGA-D5-6532 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-D5-6533      TCGA-D5-6534      TCGA-D5-6535      TCGA-D5-6536 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-D5-6537      TCGA-D5-6538      TCGA-D5-6539      TCGA-D5-6540 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-D5-6541      TCGA-D5-6898      TCGA-D5-6920      TCGA-D5-6922 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-D5-6923      TCGA-D5-6924      TCGA-D5-6926      TCGA-D5-6927 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-D5-6928      TCGA-D5-6929      TCGA-D5-6930      TCGA-D5-6931 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-D5-6932      TCGA-D5-7000      TCGA-F4-6459      TCGA-F4-6460 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-F4-6569      TCGA-F4-6570      TCGA-F4-6703      TCGA-F4-6704 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-F4-6805      TCGA-F4-6806      TCGA-F4-6807      TCGA-F4-6808 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-F4-6809      TCGA-F4-6854      TCGA-F4-6855      TCGA-F4-6856 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-G4-6293      TCGA-G4-6299      TCGA-G4-6303      TCGA-G4-6304 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-G4-6306      TCGA-G4-6307      TCGA-G4-6309      TCGA-G4-6310 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-G4-6315      TCGA-G4-6317      TCGA-G4-6321      TCGA-G4-6323 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-G4-6586      TCGA-G4-6625      TCGA-G4-6626      TCGA-G4-6628 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AF-2687      TCGA-AF-2689      TCGA-AF-2691      TCGA-AF-2692 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AF-3400      TCGA-AF-3913      TCGA-AF-4110      TCGA-AF-5654 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AF-6655      TCGA-AG-3574      TCGA-AG-3575      TCGA-AG-3578 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AG-3580      TCGA-AG-3581      TCGA-AG-3582      TCGA-AG-3583 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AG-3584      TCGA-AG-3586      TCGA-AG-3587      TCGA-AG-3593 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AG-3594      TCGA-AG-3598      TCGA-AG-3599      TCGA-AG-3600 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AG-3601      TCGA-AG-3602      TCGA-AG-3605      TCGA-AG-3608 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AG-3609      TCGA-AG-3611      TCGA-AG-3612      TCGA-AG-3726 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AG-3727      TCGA-AG-3731      TCGA-AG-3732      TCGA-AG-3742 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AG-3878      TCGA-AG-3882      TCGA-AG-3883      TCGA-AG-3885 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AG-3887      TCGA-AG-3890      TCGA-AG-3892      TCGA-AG-3893 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AG-3894      TCGA-AG-3896      TCGA-AG-3898      TCGA-AG-3901 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AG-3902      TCGA-AG-3909      TCGA-AG-3999      TCGA-AG-4001 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AG-4005      TCGA-AG-4007      TCGA-AG-4008      TCGA-AG-4015 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AG-A002      TCGA-AG-A008      TCGA-AG-A00C      TCGA-AG-A00H 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AG-A00Y      TCGA-AG-A011      TCGA-AG-A014      TCGA-AG-A015 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AG-A016      TCGA-AG-A01L      TCGA-AG-A01W      TCGA-AG-A01Y 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AG-A020      TCGA-AG-A025      TCGA-AG-A026      TCGA-AG-A02G 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AG-A02N      TCGA-AG-A02X      TCGA-AG-A032      TCGA-AG-A036 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-AH-6549      TCGA-AH-6643      TCGA-CL-5917      TCGA-CL-5918 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-DC-5337      TCGA-DC-5869      TCGA-DC-6155      TCGA-DC-6157 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-DC-6158      TCGA-DC-6160      TCGA-DC-6681      TCGA-DC-6682 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-DC-6683      TCGA-DT-5265      TCGA-EF-5830      TCGA-EI-6506 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-EI-6507      TCGA-EI-6508      TCGA-EI-6510      TCGA-F5-6464 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-F5-6465      TCGA-F5-6571      TCGA-F5-6702      TCGA-F5-6812 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
     TCGA-F5-6813      TCGA-G5-6235      TCGA-G5-6641 
"OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" "OR4D2 WILD-TYPE" 
D809V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OR4D2 MUTATED                                  0     0
  OR4D2 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  OR4D2 MUTATED                           0     3
  OR4D2 WILD-TYPE                        22   223
D809V13, multiclass
                                  clus
vv                                 OR4D2 MUTATED OR4D2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        3             223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(810) Variable = OR4M2 MUTATION ANALYSIS
D810V1, survival
                 sevent
clus2               0   1
  OR4M2 MUTATED    11   4
  OR4M2 WILD-TYPE 367  89
  OR4M2 MUTATED OR4M2 WILD-TYPE 
             15             456 
  OR4M2 MUTATED OR4M2 WILD-TYPE 
              4              89 
$`OR4M2 MUTATED`
TCGA-A6-5665 TCGA-A6-6653 TCGA-AA-3715 TCGA-AA-3864 TCGA-AA-A010 TCGA-AU-6004 
       22.06        24.39        19.04        53.00        34.98        27.09 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-5913 TCGA-D5-6927 
       49.41         6.77        12.76        10.06        51.32         9.44 
TCGA-D5-6930 TCGA-AG-3892 TCGA-AG-A002 
        1.51        13.02        20.98 

$`OR4M2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 
       25.18        24.16        21.76        24.69        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        31.07        30.05        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       12.20        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       49.08         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 
       14.30         9.04        11.64         4.80        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       17.03        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  OR4M2 MUTATED OR4M2 WILD-TYPE 
           1.51            0.00 
  OR4M2 MUTATED OR4M2 WILD-TYPE 
          53.00          148.01 
  OR4M2 MUTATED OR4M2 WILD-TYPE 
         20.980          20.155 
[1] "1.5 - 53.0 (21.0)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.4"
D810V2, continuous
D810V3, binary
                 cls
clus                0   1
  OR4M2 MUTATED    14   2
  OR4M2 WILD-TYPE 352 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR4M2 MUTATED     14    2
  OR4M2 WILD-TYPE  352  117
        clus
vv       OR4M2 MUTATED OR4M2 WILD-TYPE
  COLON             14             352
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  OR4M2 MUTATED         5        0        3         6         2         0
  OR4M2 WILD-TYPE      86        1       29       132         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  OR4M2 MUTATED           0          0          0          0        0         0
  OR4M2 WILD-TYPE        24         11         59         42       48        18
                 vv
clus              STAGE IVB
  OR4M2 MUTATED           0
  OR4M2 WILD-TYPE         1
D810V4, multiclass
            clus
vv           OR4M2 MUTATED OR4M2 WILD-TYPE
  STAGE I                5              86
  STAGE IA               0               1
  STAGE II               3              29
  STAGE IIA              6             132
  STAGE IIB              2               8
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  OR4M2 MUTATED     1   4   9   2
  OR4M2 WILD-TYPE  16  88 320  48
D810V5, multiclass
    clus
vv   OR4M2 MUTATED OR4M2 WILD-TYPE
  T1             1              16
  T2             4              88
  T3             9             320
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  OR4M2 MUTATED    16   0   0
  OR4M2 WILD-TYPE 271 113  87
D810V6, multiclass
    clus
vv   OR4M2 MUTATED OR4M2 WILD-TYPE
  N0            16             271
  N1             0             113
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D810V7, binary
                 cls
clus                0   1
  OR4M2 MUTATED    12   0
  OR4M2 WILD-TYPE 363  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR4M2 MUTATED     12    0
  OR4M2 WILD-TYPE  363   65
   clus
vv  OR4M2 MUTATED OR4M2 WILD-TYPE
  0            12             363
  1             0              65
[1] 2 2
[1] FALSE
D810V8, binary
                 cls
clus                0   1
  OR4M2 MUTATED     7   9
  OR4M2 WILD-TYPE 218 255
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR4M2 MUTATED      7    9
  OR4M2 WILD-TYPE  218  255
        clus
vv       OR4M2 MUTATED OR4M2 WILD-TYPE
  FEMALE             7             218
  MALE               9             255
[1] 2 2
[1] FALSE
D810V9, binary
                 cls
clus                0   1
  OR4M2 MUTATED    13   0
  OR4M2 WILD-TYPE 337  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR4M2 MUTATED     13    0
  OR4M2 WILD-TYPE  337   22
     clus
vv    OR4M2 MUTATED OR4M2 WILD-TYPE
  NO             13             337
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  OR4M2 MUTATED                     12                             2
  OR4M2 WILD-TYPE                  303                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  OR4M2 MUTATED                       2                              0
  OR4M2 WILD-TYPE                   104                             10
D810V10, multiclass
                                clus
vv                               OR4M2 MUTATED OR4M2 WILD-TYPE
  COLON ADENOCARCINOMA                      12             303
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  OR4M2 MUTATED     9   0   0   4
  OR4M2 WILD-TYPE 336   4  31  21
D810V11, multiclass
    clus
vv   OR4M2 MUTATED OR4M2 WILD-TYPE
  R0             9             336
  R1             0               4
  R2             0              31
  RX             4              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D810V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OR4M2 MUTATED                                  0     2
  OR4M2 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  OR4M2 MUTATED                           0     9
  OR4M2 WILD-TYPE                        22   217
D810V13, multiclass
                                  clus
vv                                 OR4M2 MUTATED OR4M2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               9
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        9             217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(811) Variable = EYS MUTATION ANALYSIS
D811V1, survival
               sevent
clus2             0   1
  EYS MUTATED    33   8
  EYS WILD-TYPE 345  85
  EYS MUTATED EYS WILD-TYPE 
           41           430 
  EYS MUTATED EYS WILD-TYPE 
            8            85 
$`EYS MUTATED`
TCGA-A6-3809 TCGA-A6-6141 TCGA-A6-6782 TCGA-AA-3496 TCGA-AA-3511 TCGA-AA-3516 
       32.75         8.38        20.28         1.02         6.97        13.02 
TCGA-AA-3815 TCGA-AA-3831 TCGA-AA-3861 TCGA-AA-3930 TCGA-AA-3977 TCGA-AA-3994 
       33.04        17.98        30.05         2.01        25.02        27.02 
TCGA-AA-A00J TCGA-AA-A00N TCGA-AA-A01Q TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6964 
       18.05         4.01         1.02         5.79        27.42        10.88 
TCGA-AY-6197 TCGA-AZ-4315 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-5913 TCGA-CM-4743 
       21.44        58.39        12.76        10.06        51.32        23.05 
TCGA-CM-5348 TCGA-CM-5861 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6678 TCGA-D5-6533 
       22.98        15.02        13.05        11.08        11.01         1.32 
TCGA-D5-6540 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6931 TCGA-DM-A1DA TCGA-DM-A28E 
       16.14         9.44        11.64        12.00         7.50       119.93 
TCGA-F4-6570 TCGA-G4-6628 TCGA-AG-A002 TCGA-EF-5830 TCGA-EI-6510 
        6.18        79.69        20.98         0.49        18.28 

$`EYS WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 
       22.06        32.71        27.09        22.52        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3514 
       19.66         7.04         3.02        35.01        63.98         1.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       19.04        10.06        35.05         0.99        25.02         1.02 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
        0.99        31.07        31.07        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3939 TCGA-AA-3941 
       27.02        29.98        18.05        31.00        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        31.00        38.07        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6901 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        0.79         0.72        22.42         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
       16.31         0.95        33.01        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       12.20        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       49.08         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       30.08        32.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6677 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       12.95        11.08        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6534 
       19.59        56.09        55.92        20.19        18.25        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 
       15.12        17.85         4.80        17.13        12.49        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        4.80         1.51        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
      140.38        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
       81.37        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       31.96        35.74        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 
       35.80        26.17        91.79        46.75        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EI-6506 TCGA-EI-6507 
       57.24        24.13        51.48        32.61        20.55        19.96 
TCGA-EI-6508 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       20.91         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  EYS MUTATED EYS WILD-TYPE 
         0.49          0.00 
  EYS MUTATED EYS WILD-TYPE 
       119.93        148.01 
  EYS MUTATED EYS WILD-TYPE 
       13.050        21.075 
[1] "0.5 - 119.9 (13.1)" "0.0 - 148.0 (21.1)"
[1] "hr=" "1.3"
D811V2, continuous
D811V3, binary
               cls
clus              0   1
  EYS MUTATED    38   3
  EYS WILD-TYPE 328 116
[1] "tbl2"
               cls
clus            [,1] [,2]
  EYS MUTATED     38    3
  EYS WILD-TYPE  328  116
        clus
vv       EYS MUTATED EYS WILD-TYPE
  COLON           38           328
  RECTUM           3           116
[1] 2 2
[1] FALSE
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  EYS MUTATED         4        0        3        15         4         0
  EYS WILD-TYPE      87        1       29       123         6         1
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  EYS MUTATED           1          0          4          3        1         2
  EYS WILD-TYPE        23         11         55         39       47        16
               vv
clus            STAGE IVB
  EYS MUTATED           1
  EYS WILD-TYPE         0
D811V4, multiclass
            clus
vv           EYS MUTATED EYS WILD-TYPE
  STAGE I              4            87
  STAGE IA             0             1
  STAGE II             3            29
  STAGE IIA           15           123
  STAGE IIB            4             6
  STAGE IIC            0             1
  STAGE III            1            23
  STAGE IIIA           0            11
  STAGE IIIB           4            55
  STAGE IIIC           3            39
  STAGE IV             1            47
  STAGE IVA            2            16
  STAGE IVB            1             0
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  EYS MUTATED     0   6  24  11
  EYS WILD-TYPE  17  86 305  39
D811V5, multiclass
    clus
vv   EYS MUTATED EYS WILD-TYPE
  T1           0            17
  T2           6            86
  T3          24           305
  T4          11            39
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2
  EYS MUTATED    30   4   7
  EYS WILD-TYPE 257 109  80
D811V6, multiclass
    clus
vv   EYS MUTATED EYS WILD-TYPE
  N0          30           257
  N1           4           109
  N2           7            80
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D811V7, binary
               cls
clus              0   1
  EYS MUTATED    30   3
  EYS WILD-TYPE 345  62
[1] "tbl2"
               cls
clus            [,1] [,2]
  EYS MUTATED     30    3
  EYS WILD-TYPE  345   62
   clus
vv  EYS MUTATED EYS WILD-TYPE
  0          30           345
  1           3            62
[1] 2 2
[1] FALSE
D811V8, binary
               cls
clus              0   1
  EYS MUTATED    13  28
  EYS WILD-TYPE 212 236
[1] "tbl2"
               cls
clus            [,1] [,2]
  EYS MUTATED     13   28
  EYS WILD-TYPE  212  236
        clus
vv       EYS MUTATED EYS WILD-TYPE
  FEMALE          13           212
  MALE            28           236
[1] 2 2
[1] FALSE
D811V9, binary
               cls
clus              0   1
  EYS MUTATED    34   0
  EYS WILD-TYPE 316  22
[1] "tbl2"
               cls
clus            [,1] [,2]
  EYS MUTATED     34    0
  EYS WILD-TYPE  316   22
     clus
vv    EYS MUTATED EYS WILD-TYPE
  NO           34           316
  YES           0            22
[1] 2 2
[1] FALSE
               vv
clus            COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  EYS MUTATED                     29                             9
  EYS WILD-TYPE                  286                            38
               vv
clus            RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  EYS MUTATED                       3                              0
  EYS WILD-TYPE                   103                             10
D811V10, multiclass
                                clus
vv                               EYS MUTATED EYS WILD-TYPE
  COLON ADENOCARCINOMA                    29           286
  COLON MUCINOUS ADENOCARCINOMA            9            38
  RECTAL ADENOCARCINOMA                    3           103
  RECTAL MUCINOUS ADENOCARCINOMA           0            10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             R0  R1  R2  RX
  EYS MUTATED    28   0   1   3
  EYS WILD-TYPE 317   4  30  22
D811V11, multiclass
    clus
vv   EYS MUTATED EYS WILD-TYPE
  R0          28           317
  R1           0             4
  R2           1            30
  RX           3            22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D811V12, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  EYS MUTATED                                  0     2
  EYS WILD-TYPE                                1     9
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  EYS MUTATED                           2    24
  EYS WILD-TYPE                        20   202
D811V13, multiclass
                                  clus
vv                                 EYS MUTATED EYS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      2             9
  BLACK OR AFRICAN AMERICAN                  2            20
  WHITE                                     24           202
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(812) Variable = ARNT2 MUTATION ANALYSIS
D812V1, survival
                 sevent
clus2               0   1
  ARNT2 MUTATED     9   4
  ARNT2 WILD-TYPE 369  89
  ARNT2 MUTATED ARNT2 WILD-TYPE 
             13             458 
  ARNT2 MUTATED ARNT2 WILD-TYPE 
              4              89 
$`ARNT2 MUTATED`
TCGA-AA-3663 TCGA-AA-3811 TCGA-AA-A00E TCGA-AA-A00J TCGA-AZ-5407 TCGA-AZ-6601 
        6.97        10.06        30.02        18.05        88.21       100.01 
TCGA-CA-6717 TCGA-D5-6928 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6588 TCGA-AG-A002 
       12.76        11.64        74.56        65.85        26.17        20.98 
TCGA-DY-A1DC 
       41.36 

$`ARNT2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.05        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       19.00        34.03        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 
       62.79        49.41         6.77        12.10        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07        12.20        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
        9.44         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        35.80        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
        5.29       126.44        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  ARNT2 MUTATED ARNT2 WILD-TYPE 
           6.97            0.00 
  ARNT2 MUTATED ARNT2 WILD-TYPE 
         100.01          148.01 
  ARNT2 MUTATED ARNT2 WILD-TYPE 
         26.170          20.085 
[1] "7.0 - 100.0 (26.2)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1"  
D812V2, continuous
D812V3, binary
                 cls
clus                0   1
  ARNT2 MUTATED    12   2
  ARNT2 WILD-TYPE 354 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ARNT2 MUTATED     12    2
  ARNT2 WILD-TYPE  354  117
        clus
vv       ARNT2 MUTATED ARNT2 WILD-TYPE
  COLON             12             354
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ARNT2 MUTATED         2        0        2         6         0         0
  ARNT2 WILD-TYPE      89        1       30       132        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ARNT2 MUTATED           1          0          1          1        1         0
  ARNT2 WILD-TYPE        23         11         58         41       47        18
                 vv
clus              STAGE IVB
  ARNT2 MUTATED           0
  ARNT2 WILD-TYPE         1
D812V4, multiclass
            clus
vv           ARNT2 MUTATED ARNT2 WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA              6             132
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             1              41
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ARNT2 MUTATED     1   1  11   1
  ARNT2 WILD-TYPE  16  91 318  49
D812V5, multiclass
    clus
vv   ARNT2 MUTATED ARNT2 WILD-TYPE
  T1             1              16
  T2             1              91
  T3            11             318
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  ARNT2 MUTATED    10   2   2
  ARNT2 WILD-TYPE 277 111  85
D812V6, multiclass
    clus
vv   ARNT2 MUTATED ARNT2 WILD-TYPE
  N0            10             277
  N1             2             111
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D812V7, binary
                 cls
clus                0   1
  ARNT2 MUTATED    13   1
  ARNT2 WILD-TYPE 362  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ARNT2 MUTATED     13    1
  ARNT2 WILD-TYPE  362   64
   clus
vv  ARNT2 MUTATED ARNT2 WILD-TYPE
  0            13             362
  1             1              64
[1] 2 2
[1] FALSE
D812V8, binary
                 cls
clus                0   1
  ARNT2 MUTATED     6   8
  ARNT2 WILD-TYPE 219 256
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ARNT2 MUTATED      6    8
  ARNT2 WILD-TYPE  219  256
        clus
vv       ARNT2 MUTATED ARNT2 WILD-TYPE
  FEMALE             6             219
  MALE               8             256
[1] 2 2
[1] FALSE
D812V9, binary
                 cls
clus                0   1
  ARNT2 MUTATED    12   0
  ARNT2 WILD-TYPE 338  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ARNT2 MUTATED     12    0
  ARNT2 WILD-TYPE  338   22
     clus
vv    ARNT2 MUTATED ARNT2 WILD-TYPE
  NO             12             338
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ARNT2 MUTATED                      9                             3
  ARNT2 WILD-TYPE                  306                            44
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ARNT2 MUTATED                       2                              0
  ARNT2 WILD-TYPE                   104                             10
D812V10, multiclass
                                clus
vv                               ARNT2 MUTATED ARNT2 WILD-TYPE
  COLON ADENOCARCINOMA                       9             306
  COLON MUCINOUS ADENOCARCINOMA              3              44
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  ARNT2 MUTATED    10   0   0   1
  ARNT2 WILD-TYPE 335   4  31  24
D812V11, multiclass
    clus
vv   ARNT2 MUTATED ARNT2 WILD-TYPE
  R0            10             335
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D812V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ARNT2 MUTATED                                  0     1
  ARNT2 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ARNT2 MUTATED                           0     7
  ARNT2 WILD-TYPE                        22   219
D812V13, multiclass
                                  clus
vv                                 ARNT2 MUTATED ARNT2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        7             219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(813) Variable = NIPBL MUTATION ANALYSIS
D813V1, survival
                 sevent
clus2               0   1
  NIPBL MUTATED    28   7
  NIPBL WILD-TYPE 350  86
  NIPBL MUTATED NIPBL WILD-TYPE 
             35             436 
  NIPBL MUTATED NIPBL WILD-TYPE 
              7              86 
$`NIPBL MUTATED`
TCGA-A6-2672 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5665 TCGA-A6-6780 TCGA-A6-6781 
       46.65        30.44        29.19        22.06        20.12        19.66 
TCGA-AA-3510 TCGA-AA-3663 TCGA-AA-3672 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 
       63.98         6.97         0.92        26.99        19.04        10.06 
TCGA-AA-3877 TCGA-AA-3947 TCGA-AA-A010 TCGA-AA-A01R TCGA-AD-6895 TCGA-AZ-4315 
       31.00        33.01        34.98        35.01         0.72        58.39 
TCGA-AZ-4616 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-5868 
        5.13        12.10       100.01        12.76        10.06        17.03 
TCGA-CM-6162 TCGA-D5-6539 TCGA-D5-6920 TCGA-DM-A28F TCGA-G4-6304 TCGA-G4-6309 
       12.00        12.49         3.68        35.97        53.62        85.48 
TCGA-G4-6315 TCGA-AG-3587 TCGA-AG-3892 TCGA-AG-A002 TCGA-EI-6507 
       61.91        46.03        13.02        20.98        19.96 

$`NIPBL WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 
       31.63        33.53        23.61        22.09        32.71        27.09 
TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 
       22.52         8.38        25.08        25.18        24.16        21.76 
TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       24.69        24.39        23.87        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
       54.02         2.01        14.01        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       85.05        19.04        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
        2.01        12.99        24.00        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       31.00        38.07         1.02         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        1.41       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
        6.77        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       15.02        15.02        15.02         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
       17.85         4.80        17.13        16.14        15.58         1.48 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H 
      139.17         6.12        81.37       119.93        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       44.68        55.04        63.62        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
       24.00         1.02        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6508 
       24.13        51.48        32.61         0.49        20.55        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  NIPBL MUTATED NIPBL WILD-TYPE 
           0.72            0.00 
  NIPBL MUTATED NIPBL WILD-TYPE 
         100.01          148.01 
  NIPBL MUTATED NIPBL WILD-TYPE 
          20.98           20.12 
[1] "0.7 - 100.0 (21.0)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.1"
D813V2, continuous
D813V3, binary
                 cls
clus                0   1
  NIPBL MUTATED    32   5
  NIPBL WILD-TYPE 334 114
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NIPBL MUTATED     32    5
  NIPBL WILD-TYPE  334  114
        clus
vv       NIPBL MUTATED NIPBL WILD-TYPE
  COLON             32             334
  RECTUM             5             114
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NIPBL MUTATED         5        0        4         9         3         0
  NIPBL WILD-TYPE      86        1       28       129         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NIPBL MUTATED           3          1          5          2        3         1
  NIPBL WILD-TYPE        21         10         54         40       45        17
                 vv
clus              STAGE IVB
  NIPBL MUTATED           0
  NIPBL WILD-TYPE         1
D813V4, multiclass
            clus
vv           NIPBL MUTATED NIPBL WILD-TYPE
  STAGE I                5              86
  STAGE IA               0               1
  STAGE II               4              28
  STAGE IIA              9             129
  STAGE IIB              3               7
  STAGE IIC              0               1
  STAGE III              3              21
  STAGE IIIA             1              10
  STAGE IIIB             5              54
  STAGE IIIC             2              40
  STAGE IV               3              45
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  NIPBL MUTATED     2   3  26   6
  NIPBL WILD-TYPE  15  89 303  44
D813V5, multiclass
    clus
vv   NIPBL MUTATED NIPBL WILD-TYPE
  T1             2              15
  T2             3              89
  T3            26             303
  T4             6              44
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  NIPBL MUTATED    22  11   4
  NIPBL WILD-TYPE 265 102  83
D813V6, multiclass
    clus
vv   NIPBL MUTATED NIPBL WILD-TYPE
  N0            22             265
  N1            11             102
  N2             4              83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D813V7, binary
                 cls
clus                0   1
  NIPBL MUTATED    30   4
  NIPBL WILD-TYPE 345  61
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NIPBL MUTATED     30    4
  NIPBL WILD-TYPE  345   61
   clus
vv  NIPBL MUTATED NIPBL WILD-TYPE
  0            30             345
  1             4              61
[1] 2 2
[1] FALSE
D813V8, binary
                 cls
clus                0   1
  NIPBL MUTATED    18  19
  NIPBL WILD-TYPE 207 245
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NIPBL MUTATED     18   19
  NIPBL WILD-TYPE  207  245
        clus
vv       NIPBL MUTATED NIPBL WILD-TYPE
  FEMALE            18             207
  MALE              19             245
[1] 2 2
[1] FALSE
D813V9, binary
                 cls
clus                0   1
  NIPBL MUTATED    29   2
  NIPBL WILD-TYPE 321  20
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NIPBL MUTATED     29    2
  NIPBL WILD-TYPE  321   20
     clus
vv    NIPBL MUTATED NIPBL WILD-TYPE
  NO             29             321
  YES             2              20
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  NIPBL MUTATED                     25                             7
  NIPBL WILD-TYPE                  290                            40
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  NIPBL MUTATED                       4                              1
  NIPBL WILD-TYPE                   102                              9
D813V10, multiclass
                                clus
vv                               NIPBL MUTATED NIPBL WILD-TYPE
  COLON ADENOCARCINOMA                      25             290
  COLON MUCINOUS ADENOCARCINOMA              7              40
  RECTAL ADENOCARCINOMA                      4             102
  RECTAL MUCINOUS ADENOCARCINOMA             1               9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  NIPBL MUTATED    28   0   0   2
  NIPBL WILD-TYPE 317   4  31  23
D813V11, multiclass
    clus
vv   NIPBL MUTATED NIPBL WILD-TYPE
  R0            28             317
  R1             0               4
  R2             0              31
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D813V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NIPBL MUTATED                                  0     2
  NIPBL WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  NIPBL MUTATED                           3    17
  NIPBL WILD-TYPE                        19   209
D813V13, multiclass
                                  clus
vv                                 NIPBL MUTATED NIPBL WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               9
  BLACK OR AFRICAN AMERICAN                    3              19
  WHITE                                       17             209
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(814) Variable = G2E3 MUTATION ANALYSIS
D814V1, survival
                sevent
clus2              0   1
  G2E3 MUTATED    13   2
  G2E3 WILD-TYPE 365  91
  G2E3 MUTATED G2E3 WILD-TYPE 
            15            456 
  G2E3 MUTATED G2E3 WILD-TYPE 
             2             91 
$`G2E3 MUTATED`
TCGA-A6-2672 TCGA-AA-3510 TCGA-AA-3663 TCGA-AA-A00N TCGA-AZ-4315 TCGA-CA-6717 
       46.65        63.98         6.97         4.01        58.39        12.76 
TCGA-CM-6171 TCGA-CM-6676 TCGA-CM-6678 TCGA-D5-6928 TCGA-DM-A1D6 TCGA-G4-6304 
       14.04        11.08        11.01        11.64        49.91        53.62 
TCGA-AF-6136 TCGA-AG-3598 TCGA-AG-A002 
       15.39        50.04        20.98 

$`G2E3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07        12.20        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6677 TCGA-CM-6679 TCGA-CM-6680 
       11.01        12.95        13.05        11.08        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 
        4.41        12.43        14.30         9.04         9.44         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
       38.20       130.65        92.75        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 
       47.41        35.31       133.18        74.56        65.85        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       10.39        14.50        16.83        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3599 
       24.00         1.02        46.03        34.03         2.01        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  G2E3 MUTATED G2E3 WILD-TYPE 
          4.01           0.00 
  G2E3 MUTATED G2E3 WILD-TYPE 
         63.98         148.01 
  G2E3 MUTATED G2E3 WILD-TYPE 
        15.390         20.235 
[1] "4.0 - 64.0 (15.4)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.9"
D814V2, continuous
D814V3, binary
                cls
clus               0   1
  G2E3 MUTATED    12   3
  G2E3 WILD-TYPE 354 116
[1] "tbl2"
                cls
clus             [,1] [,2]
  G2E3 MUTATED     12    3
  G2E3 WILD-TYPE  354  116
        clus
vv       G2E3 MUTATED G2E3 WILD-TYPE
  COLON            12            354
  RECTUM            3            116
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  G2E3 MUTATED         3        0        2         5         2         0
  G2E3 WILD-TYPE      88        1       30       133         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  G2E3 MUTATED           0          0          2          0        0         1
  G2E3 WILD-TYPE        24         11         57         42       48        17
                vv
clus             STAGE IVB
  G2E3 MUTATED           0
  G2E3 WILD-TYPE         1
D814V4, multiclass
            clus
vv           G2E3 MUTATED G2E3 WILD-TYPE
  STAGE I               3             88
  STAGE IA              0              1
  STAGE II              2             30
  STAGE IIA             5            133
  STAGE IIB             2              8
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            2             57
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             1             17
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  G2E3 MUTATED     0   3   9   3
  G2E3 WILD-TYPE  17  89 320  47
D814V5, multiclass
    clus
vv   G2E3 MUTATED G2E3 WILD-TYPE
  T1            0             17
  T2            3             89
  T3            9            320
  T4            3             47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  G2E3 MUTATED    12   3   0
  G2E3 WILD-TYPE 275 110  87
D814V6, multiclass
    clus
vv   G2E3 MUTATED G2E3 WILD-TYPE
  N0           12            275
  N1            3            110
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D814V7, binary
                cls
clus               0   1
  G2E3 MUTATED    13   1
  G2E3 WILD-TYPE 362  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  G2E3 MUTATED     13    1
  G2E3 WILD-TYPE  362   64
   clus
vv  G2E3 MUTATED G2E3 WILD-TYPE
  0           13            362
  1            1             64
[1] 2 2
[1] FALSE
D814V8, binary
                cls
clus               0   1
  G2E3 MUTATED     5  10
  G2E3 WILD-TYPE 220 254
[1] "tbl2"
                cls
clus             [,1] [,2]
  G2E3 MUTATED      5   10
  G2E3 WILD-TYPE  220  254
        clus
vv       G2E3 MUTATED G2E3 WILD-TYPE
  FEMALE            5            220
  MALE             10            254
[1] 2 2
[1] FALSE
D814V9, binary
                cls
clus               0   1
  G2E3 MUTATED    12   1
  G2E3 WILD-TYPE 338  21
[1] "tbl2"
                cls
clus             [,1] [,2]
  G2E3 MUTATED     12    1
  G2E3 WILD-TYPE  338   21
     clus
vv    G2E3 MUTATED G2E3 WILD-TYPE
  NO            12            338
  YES            1             21
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  G2E3 MUTATED                      8                             4
  G2E3 WILD-TYPE                  307                            43
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  G2E3 MUTATED                       3                              0
  G2E3 WILD-TYPE                   103                             10
D814V10, multiclass
                                clus
vv                               G2E3 MUTATED G2E3 WILD-TYPE
  COLON ADENOCARCINOMA                      8            307
  COLON MUCINOUS ADENOCARCINOMA             4             43
  RECTAL ADENOCARCINOMA                     3            103
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  G2E3 MUTATED    12   0   0   1
  G2E3 WILD-TYPE 333   4  31  24
D814V11, multiclass
    clus
vv   G2E3 MUTATED G2E3 WILD-TYPE
  R0           12            333
  R1            0              4
  R2            0             31
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D814V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  G2E3 MUTATED                                  0     1
  G2E3 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  G2E3 MUTATED                           0     9
  G2E3 WILD-TYPE                        22   217
D814V13, multiclass
                                  clus
vv                                 G2E3 MUTATED G2E3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       9            217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(815) Variable = NOS3 MUTATION ANALYSIS
D815V1, survival
                sevent
clus2              0   1
  NOS3 MUTATED    16   4
  NOS3 WILD-TYPE 362  89
  NOS3 MUTATED NOS3 WILD-TYPE 
            20            451 
  NOS3 MUTATED NOS3 WILD-TYPE 
             4             89 
$`NOS3 MUTATED`
TCGA-A6-6781 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3976 TCGA-AA-3977 TCGA-AD-6889 
       19.66         6.05         6.97        26.01        25.02        56.55 
TCGA-AY-6197 TCGA-AZ-6598 TCGA-CA-5254 TCGA-CA-6717 TCGA-CK-5916 TCGA-CM-4746 
       21.44        49.41        12.69        12.76        21.14        37.02 
TCGA-CM-5861 TCGA-CM-6674 TCGA-D5-6535 TCGA-F4-6570 TCGA-F4-6856 TCGA-G4-6307 
       15.02        12.95        15.12         6.18        35.31        55.04 
TCGA-DY-A1DG TCGA-EI-6508 
       51.48        20.91 

$`NOS3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 
       19.99        13.94        19.99        61.02        78.08        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       34.06        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
        0.07        21.37        15.52         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       16.31         0.95        33.01        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 
        5.13       106.75        22.36        62.79        88.21         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        1.61         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       49.08        51.32         9.99        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       23.05        20.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       22.98        30.08        32.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       11.01        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 
       20.19        18.25         1.32        43.27        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 
      117.07        98.24         8.61        31.96        35.74        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
        0.53        47.41       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       44.68        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1H8 
        5.29       126.44        41.36        57.24        24.13        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
        0.49        20.55        19.96        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  NOS3 MUTATED NOS3 WILD-TYPE 
          6.05           0.00 
  NOS3 MUTATED NOS3 WILD-TYPE 
         56.55         148.01 
  NOS3 MUTATED NOS3 WILD-TYPE 
        21.025         20.120 
[1] "6.0 - 56.5 (21.0)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1"  
D815V2, continuous
D815V3, binary
                cls
clus               0   1
  NOS3 MUTATED    18   2
  NOS3 WILD-TYPE 348 117
[1] "tbl2"
                cls
clus             [,1] [,2]
  NOS3 MUTATED     18    2
  NOS3 WILD-TYPE  348  117
        clus
vv       NOS3 MUTATED NOS3 WILD-TYPE
  COLON            18            348
  RECTUM            2            117
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NOS3 MUTATED         3        0        2         7         0         0
  NOS3 WILD-TYPE      88        1       30       131        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NOS3 MUTATED           0          1          3          1        1         1
  NOS3 WILD-TYPE        24         10         56         41       47        17
                vv
clus             STAGE IVB
  NOS3 MUTATED           0
  NOS3 WILD-TYPE         1
D815V4, multiclass
            clus
vv           NOS3 MUTATED NOS3 WILD-TYPE
  STAGE I               3             88
  STAGE IA              0              1
  STAGE II              2             30
  STAGE IIA             7            131
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            1             10
  STAGE IIIB            3             56
  STAGE IIIC            1             41
  STAGE IV              1             47
  STAGE IVA             1             17
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  NOS3 MUTATED     1   4  13   2
  NOS3 WILD-TYPE  16  88 316  48
D815V5, multiclass
    clus
vv   NOS3 MUTATED NOS3 WILD-TYPE
  T1            1             16
  T2            4             88
  T3           13            316
  T4            2             48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  NOS3 MUTATED    13   6   1
  NOS3 WILD-TYPE 274 107  86
D815V6, multiclass
    clus
vv   NOS3 MUTATED NOS3 WILD-TYPE
  N0           13            274
  N1            6            107
  N2            1             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D815V7, binary
                cls
clus               0   1
  NOS3 MUTATED    13   2
  NOS3 WILD-TYPE 362  63
[1] "tbl2"
                cls
clus             [,1] [,2]
  NOS3 MUTATED     13    2
  NOS3 WILD-TYPE  362   63
   clus
vv  NOS3 MUTATED NOS3 WILD-TYPE
  0           13            362
  1            2             63
[1] 2 2
[1] FALSE
D815V8, binary
                cls
clus               0   1
  NOS3 MUTATED     9  11
  NOS3 WILD-TYPE 216 253
[1] "tbl2"
                cls
clus             [,1] [,2]
  NOS3 MUTATED      9   11
  NOS3 WILD-TYPE  216  253
        clus
vv       NOS3 MUTATED NOS3 WILD-TYPE
  FEMALE            9            216
  MALE             11            253
[1] 2 2
[1] FALSE
D815V9, binary
                cls
clus               0   1
  NOS3 MUTATED    18   0
  NOS3 WILD-TYPE 332  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  NOS3 MUTATED     18    0
  NOS3 WILD-TYPE  332   22
     clus
vv    NOS3 MUTATED NOS3 WILD-TYPE
  NO            18            332
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  NOS3 MUTATED                     15                             3
  NOS3 WILD-TYPE                  300                            44
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  NOS3 MUTATED                       2                              0
  NOS3 WILD-TYPE                   104                             10
D815V10, multiclass
                                clus
vv                               NOS3 MUTATED NOS3 WILD-TYPE
  COLON ADENOCARCINOMA                     15            300
  COLON MUCINOUS ADENOCARCINOMA             3             44
  RECTAL ADENOCARCINOMA                     2            104
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  NOS3 MUTATED    11   0   1   4
  NOS3 WILD-TYPE 334   4  30  21
D815V11, multiclass
    clus
vv   NOS3 MUTATED NOS3 WILD-TYPE
  R0           11            334
  R1            0              4
  R2            1             30
  RX            4             21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D815V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NOS3 MUTATED                                  0     3
  NOS3 WILD-TYPE                                1     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  NOS3 MUTATED                           1    12
  NOS3 WILD-TYPE                        21   214
D815V13, multiclass
                                  clus
vv                                 NOS3 MUTATED NOS3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       3              8
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                      12            214
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(816) Variable = EFEMP1 MUTATION ANALYSIS
D816V1, survival
                  sevent
clus2                0   1
  EFEMP1 MUTATED    16   4
  EFEMP1 WILD-TYPE 362  89
  EFEMP1 MUTATED EFEMP1 WILD-TYPE 
              20              451 
  EFEMP1 MUTATED EFEMP1 WILD-TYPE 
               4               89 
$`EFEMP1 MUTATED`
TCGA-AA-3672 TCGA-AA-3844 TCGA-AA-3950 TCGA-AD-6965 TCGA-AZ-6601 TCGA-CA-6718 
        0.92        14.93        24.00         0.20       100.01        10.06 
TCGA-CK-5916 TCGA-CM-4752 TCGA-CM-5860 TCGA-CM-5863 TCGA-CM-6168 TCGA-CM-6172 
       21.14        13.02        32.02        15.02        12.99        11.01 
TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-6529 TCGA-DM-A1D9 TCGA-DM-A1HB TCGA-DM-A28C 
       12.26        56.09        20.19       140.38       135.65        81.37 
TCGA-F4-6569 TCGA-F4-6807 
       35.74        16.24 

$`EFEMP1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
        6.05         6.97        54.02         2.01        14.01        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3846 
       17.98        15.95        38.99        37.02         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 
       12.99        24.00        33.01        26.01         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 
       62.79        88.21        49.41         6.77        12.10        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 
        3.25         3.29         0.07        12.20        12.76        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
        9.99        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       37.02        25.02        29.06        22.03        22.98        30.08 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
       15.02         5.03        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6169 
        2.96        29.03        16.04        21.99        14.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       15.02        14.04        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5539 TCGA-D5-5541 
       11.01        10.06        12.03        45.40        19.59        55.92 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 
       12.59         7.50        44.32       131.51       139.17         6.12 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       31.96         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  EFEMP1 MUTATED EFEMP1 WILD-TYPE 
             0.2              0.0 
  EFEMP1 MUTATED EFEMP1 WILD-TYPE 
          140.38           148.01 
  EFEMP1 MUTATED EFEMP1 WILD-TYPE 
          18.215           20.280 
[1] "0.2 - 140.4 (18.2)" "0.0 - 148.0 (20.3)"
[1] "hr=" "1.3"
D816V2, continuous
D816V3, binary
                  cls
clus                 0   1
  EFEMP1 MUTATED    20   0
  EFEMP1 WILD-TYPE 346 119
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EFEMP1 MUTATED     20    0
  EFEMP1 WILD-TYPE  346  119
        clus
vv       EFEMP1 MUTATED EFEMP1 WILD-TYPE
  COLON              20              346
  RECTUM              0              119
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  EFEMP1 MUTATED         2        0        1         9         0         0
  EFEMP1 WILD-TYPE      89        1       31       129        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  EFEMP1 MUTATED           1          0          4          2        0
  EFEMP1 WILD-TYPE        23         11         55         40       48
                  vv
clus               STAGE IVA STAGE IVB
  EFEMP1 MUTATED           0         0
  EFEMP1 WILD-TYPE        18         1
D816V4, multiclass
            clus
vv           EFEMP1 MUTATED EFEMP1 WILD-TYPE
  STAGE I                 2               89
  STAGE IA                0                1
  STAGE II                1               31
  STAGE IIA               9              129
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               1               23
  STAGE IIIA              0               11
  STAGE IIIB              4               55
  STAGE IIIC              2               40
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  EFEMP1 MUTATED     1   1  17   1
  EFEMP1 WILD-TYPE  16  91 312  49
D816V5, multiclass
    clus
vv   EFEMP1 MUTATED EFEMP1 WILD-TYPE
  T1              1               16
  T2              1               91
  T3             17              312
  T4              1               49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  EFEMP1 MUTATED    12   5   3
  EFEMP1 WILD-TYPE 275 108  84
D816V6, multiclass
    clus
vv   EFEMP1 MUTATED EFEMP1 WILD-TYPE
  N0             12              275
  N1              5              108
  N2              3               84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D816V7, binary
                  cls
clus                 0   1
  EFEMP1 MUTATED    19   0
  EFEMP1 WILD-TYPE 356  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EFEMP1 MUTATED     19    0
  EFEMP1 WILD-TYPE  356   65
   clus
vv  EFEMP1 MUTATED EFEMP1 WILD-TYPE
  0             19              356
  1              0               65
[1] 2 2
[1] FALSE
D816V8, binary
                  cls
clus                 0   1
  EFEMP1 MUTATED    10  10
  EFEMP1 WILD-TYPE 215 254
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EFEMP1 MUTATED     10   10
  EFEMP1 WILD-TYPE  215  254
        clus
vv       EFEMP1 MUTATED EFEMP1 WILD-TYPE
  FEMALE             10              215
  MALE               10              254
[1] 2 2
[1] FALSE
D816V9, binary
                  cls
clus                 0   1
  EFEMP1 MUTATED    15   1
  EFEMP1 WILD-TYPE 335  21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EFEMP1 MUTATED     15    1
  EFEMP1 WILD-TYPE  335   21
     clus
vv    EFEMP1 MUTATED EFEMP1 WILD-TYPE
  NO              15              335
  YES              1               21
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  EFEMP1 MUTATED                     17                             2
  EFEMP1 WILD-TYPE                  298                            45
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  EFEMP1 MUTATED                       0                              0
  EFEMP1 WILD-TYPE                   106                             10
D816V10, multiclass
                                clus
vv                               EFEMP1 MUTATED EFEMP1 WILD-TYPE
  COLON ADENOCARCINOMA                       17              298
  COLON MUCINOUS ADENOCARCINOMA               2               45
  RECTAL ADENOCARCINOMA                       0              106
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  EFEMP1 MUTATED    13   0   0   2
  EFEMP1 WILD-TYPE 332   4  31  23
D816V11, multiclass
    clus
vv   EFEMP1 MUTATED EFEMP1 WILD-TYPE
  R0             13              332
  R1              0                4
  R2              0               31
  RX              2               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D816V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  EFEMP1 MUTATED                                  0     1
  EFEMP1 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  EFEMP1 MUTATED                           2    14
  EFEMP1 WILD-TYPE                        20   212
D816V13, multiclass
                                  clus
vv                                 EFEMP1 MUTATED EFEMP1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     2               20
  WHITE                                        14              212
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(817) Variable = SPANXN2 MUTATION ANALYSIS
D817V1, survival
                   sevent
clus2                 0   1
  SPANXN2 MUTATED     8   0
  SPANXN2 WILD-TYPE 370  93
  SPANXN2 MUTATED SPANXN2 WILD-TYPE 
                8               463 
  SPANXN2 MUTATED SPANXN2 WILD-TYPE 
                0                93 
$`SPANXN2 MUTATED`
TCGA-A6-6781 TCGA-AA-3815 TCGA-AA-3950 TCGA-AA-3977 TCGA-AZ-4315 TCGA-D5-6535 
       19.66        33.04        24.00        25.02        58.39        15.12 
TCGA-G4-6307 TCGA-G4-6309 
       55.04        85.48 

$`SPANXN2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       10.06        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 
       12.99        24.00        33.01        26.01         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       43.27        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  SPANXN2 MUTATED SPANXN2 WILD-TYPE 
            15.12              0.00 
  SPANXN2 MUTATED SPANXN2 WILD-TYPE 
            85.48            148.01 
  SPANXN2 MUTATED SPANXN2 WILD-TYPE 
            29.03             20.05 
[1] "15.1 - 85.5 (29.0)" "0.0 - 148.0 (20.1)"
[1] "hr="     "9300000"
D817V2, continuous
D817V3, binary
                   cls
clus                  0   1
  SPANXN2 MUTATED     8   0
  SPANXN2 WILD-TYPE 358 119
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SPANXN2 MUTATED      8    0
  SPANXN2 WILD-TYPE  358  119
        clus
vv       SPANXN2 MUTATED SPANXN2 WILD-TYPE
  COLON                8               358
  RECTUM               0               119
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SPANXN2 MUTATED         0        0        0         3         0         0
  SPANXN2 WILD-TYPE      91        1       32       135        10         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SPANXN2 MUTATED           0          0          3          1        0
  SPANXN2 WILD-TYPE        24         11         56         41       48
                   vv
clus                STAGE IVA STAGE IVB
  SPANXN2 MUTATED           0         0
  SPANXN2 WILD-TYPE        18         1
D817V4, multiclass
            clus
vv           SPANXN2 MUTATED SPANXN2 WILD-TYPE
  STAGE I                  0                91
  STAGE IA                 0                 1
  STAGE II                 0                32
  STAGE IIA                3               135
  STAGE IIB                0                10
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               0                11
  STAGE IIIB               3                56
  STAGE IIIC               1                41
  STAGE IV                 0                48
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  SPANXN2 MUTATED     0   1   6   1
  SPANXN2 WILD-TYPE  17  91 323  49
D817V5, multiclass
    clus
vv   SPANXN2 MUTATED SPANXN2 WILD-TYPE
  T1               0                17
  T2               1                91
  T3               6               323
  T4               1                49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  SPANXN2 MUTATED     4   4   0
  SPANXN2 WILD-TYPE 283 109  87
D817V6, multiclass
    clus
vv   SPANXN2 MUTATED SPANXN2 WILD-TYPE
  N0               4               283
  N1               4               109
  N2               0                87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D817V7, binary
                   cls
clus                  0   1
  SPANXN2 MUTATED     5   0
  SPANXN2 WILD-TYPE 370  65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SPANXN2 MUTATED      5    0
  SPANXN2 WILD-TYPE  370   65
   clus
vv  SPANXN2 MUTATED SPANXN2 WILD-TYPE
  0               5               370
  1               0                65
[1] 2 2
[1] FALSE
D817V8, binary
                   cls
clus                  0   1
  SPANXN2 MUTATED     5   3
  SPANXN2 WILD-TYPE 220 261
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SPANXN2 MUTATED      5    3
  SPANXN2 WILD-TYPE  220  261
        clus
vv       SPANXN2 MUTATED SPANXN2 WILD-TYPE
  FEMALE               5               220
  MALE                 3               261
[1] 2 2
[1] FALSE
D817V9, binary
                   cls
clus                  0   1
  SPANXN2 MUTATED     8   0
  SPANXN2 WILD-TYPE 342  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SPANXN2 MUTATED      8    0
  SPANXN2 WILD-TYPE  342   22
     clus
vv    SPANXN2 MUTATED SPANXN2 WILD-TYPE
  NO                8               342
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SPANXN2 MUTATED                      6                             2
  SPANXN2 WILD-TYPE                  309                            45
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SPANXN2 MUTATED                       0                              0
  SPANXN2 WILD-TYPE                   106                             10
D817V10, multiclass
                                clus
vv                               SPANXN2 MUTATED SPANXN2 WILD-TYPE
  COLON ADENOCARCINOMA                         6               309
  COLON MUCINOUS ADENOCARCINOMA                2                45
  RECTAL ADENOCARCINOMA                        0               106
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  SPANXN2 MUTATED     6   0   0   1
  SPANXN2 WILD-TYPE 339   4  31  24
D817V11, multiclass
    clus
vv   SPANXN2 MUTATED SPANXN2 WILD-TYPE
  R0               6               339
  R1               0                 4
  R2               0                31
  RX               1                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D817V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SPANXN2 MUTATED                                  0     0
  SPANXN2 WILD-TYPE                                1    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  SPANXN2 MUTATED                           1     4
  SPANXN2 WILD-TYPE                        21   222
D817V13, multiclass
                                  clus
vv                                 SPANXN2 MUTATED SPANXN2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                      1                21
  WHITE                                          4               222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(818) Variable = RPS6KA3 MUTATION ANALYSIS
D818V1, survival
                   sevent
clus2                 0   1
  RPS6KA3 MUTATED    14   2
  RPS6KA3 WILD-TYPE 364  91
  RPS6KA3 MUTATED RPS6KA3 WILD-TYPE 
               16               455 
  RPS6KA3 MUTATED RPS6KA3 WILD-TYPE 
                2                91 
$`RPS6KA3 MUTATED`
TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3662 TCGA-AA-3854 TCGA-AA-3877 TCGA-AA-3950 
        3.02        63.98         6.05        36.03        31.00        24.00 
TCGA-AA-A010 TCGA-AZ-6598 TCGA-CK-4952 TCGA-CM-6680 TCGA-D5-6539 TCGA-D5-7000 
       34.98        49.41        15.62        12.03        12.49        10.26 
TCGA-DM-A28E TCGA-AG-3892 TCGA-AG-A002 TCGA-DT-5265 
      119.93        13.02        20.98         5.29 

$`RPS6KA3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
        0.00        33.07         0.00        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       29.98        18.05         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       26.01         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 
        5.13       106.75        22.36        62.79        88.21         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       85.45        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-D5-5537 
       13.05        11.08        11.08        11.01        10.06        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       12.00        11.38       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       17.03        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        5.95         4.01         5.03       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  RPS6KA3 MUTATED RPS6KA3 WILD-TYPE 
             3.02              0.00 
  RPS6KA3 MUTATED RPS6KA3 WILD-TYPE 
           119.93            148.01 
  RPS6KA3 MUTATED RPS6KA3 WILD-TYPE 
            18.30             20.19 
[1] "3.0 - 119.9 (18.3)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.7"
D818V2, continuous
D818V3, binary
                   cls
clus                  0   1
  RPS6KA3 MUTATED    13   3
  RPS6KA3 WILD-TYPE 353 116
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RPS6KA3 MUTATED     13    3
  RPS6KA3 WILD-TYPE  353  116
        clus
vv       RPS6KA3 MUTATED RPS6KA3 WILD-TYPE
  COLON               13               353
  RECTUM               3               116
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RPS6KA3 MUTATED         5        0        4         2         1         0
  RPS6KA3 WILD-TYPE      86        1       28       136         9         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RPS6KA3 MUTATED           0          1          1          1        1
  RPS6KA3 WILD-TYPE        24         10         58         41       47
                   vv
clus                STAGE IVA STAGE IVB
  RPS6KA3 MUTATED           0         0
  RPS6KA3 WILD-TYPE        18         1
D818V4, multiclass
            clus
vv           RPS6KA3 MUTATED RPS6KA3 WILD-TYPE
  STAGE I                  5                86
  STAGE IA                 0                 1
  STAGE II                 4                28
  STAGE IIA                2               136
  STAGE IIB                1                 9
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               1                10
  STAGE IIIB               1                58
  STAGE IIIC               1                41
  STAGE IV                 1                47
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  RPS6KA3 MUTATED     2   3   8   3
  RPS6KA3 WILD-TYPE  15  89 321  47
D818V5, multiclass
    clus
vv   RPS6KA3 MUTATED RPS6KA3 WILD-TYPE
  T1               2                15
  T2               3                89
  T3               8               321
  T4               3                47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  RPS6KA3 MUTATED    13   0   3
  RPS6KA3 WILD-TYPE 274 113  84
D818V6, multiclass
    clus
vv   RPS6KA3 MUTATED RPS6KA3 WILD-TYPE
  N0              13               274
  N1               0               113
  N2               3                84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D818V7, binary
                   cls
clus                  0   1
  RPS6KA3 MUTATED    14   1
  RPS6KA3 WILD-TYPE 361  64
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RPS6KA3 MUTATED     14    1
  RPS6KA3 WILD-TYPE  361   64
   clus
vv  RPS6KA3 MUTATED RPS6KA3 WILD-TYPE
  0              14               361
  1               1                64
[1] 2 2
[1] FALSE
D818V8, binary
                   cls
clus                  0   1
  RPS6KA3 MUTATED    13   3
  RPS6KA3 WILD-TYPE 212 261
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RPS6KA3 MUTATED     13    3
  RPS6KA3 WILD-TYPE  212  261
        clus
vv       RPS6KA3 MUTATED RPS6KA3 WILD-TYPE
  FEMALE              13               212
  MALE                 3               261
[1] 2 2
[1] FALSE
D818V9, binary
                   cls
clus                  0   1
  RPS6KA3 MUTATED    14   0
  RPS6KA3 WILD-TYPE 336  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RPS6KA3 MUTATED     14    0
  RPS6KA3 WILD-TYPE  336   22
     clus
vv    RPS6KA3 MUTATED RPS6KA3 WILD-TYPE
  NO               14               336
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  RPS6KA3 MUTATED                      8                             5
  RPS6KA3 WILD-TYPE                  307                            42
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  RPS6KA3 MUTATED                       2                              1
  RPS6KA3 WILD-TYPE                   104                              9
D818V10, multiclass
                                clus
vv                               RPS6KA3 MUTATED RPS6KA3 WILD-TYPE
  COLON ADENOCARCINOMA                         8               307
  COLON MUCINOUS ADENOCARCINOMA                5                42
  RECTAL ADENOCARCINOMA                        2               104
  RECTAL MUCINOUS ADENOCARCINOMA               1                 9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  RPS6KA3 MUTATED    11   0   1   2
  RPS6KA3 WILD-TYPE 334   4  30  23
D818V11, multiclass
    clus
vv   RPS6KA3 MUTATED RPS6KA3 WILD-TYPE
  R0              11               334
  R1               0                 4
  R2               1                30
  RX               2                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D818V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RPS6KA3 MUTATED                                  0     1
  RPS6KA3 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  RPS6KA3 MUTATED                           0     6
  RPS6KA3 WILD-TYPE                        22   220
D818V13, multiclass
                                  clus
vv                                 RPS6KA3 MUTATED RPS6KA3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                10
  BLACK OR AFRICAN AMERICAN                      0                22
  WHITE                                          6               220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(819) Variable = ICOSLG MUTATION ANALYSIS
D819V1, survival
                  sevent
clus2                0   1
  ICOSLG MUTATED     4   1
  ICOSLG WILD-TYPE 374  92
  ICOSLG MUTATED ICOSLG WILD-TYPE 
               5              466 
  ICOSLG MUTATED ICOSLG WILD-TYPE 
               1               92 
$`ICOSLG MUTATED`
TCGA-AD-6889 TCGA-AZ-4315 TCGA-CK-5916 TCGA-CM-6674 TCGA-AF-6136 
       56.55        58.39        21.14        12.95        15.39 

$`ICOSLG WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       21.37        15.52         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        33.01        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 
       85.45        15.62        49.08        51.32         9.99        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6675 
       12.99        13.02        15.02        14.04        11.01        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6655 
       19.10        34.49        10.39        14.50        16.83        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  ICOSLG MUTATED ICOSLG WILD-TYPE 
           12.95             0.00 
  ICOSLG MUTATED ICOSLG WILD-TYPE 
           58.39           148.01 
  ICOSLG MUTATED ICOSLG WILD-TYPE 
          21.140           20.155 
[1] "12.9 - 58.4 (21.1)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.3"
D819V2, continuous
D819V3, binary
                  cls
clus                 0   1
  ICOSLG MUTATED     4   1
  ICOSLG WILD-TYPE 362 118
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ICOSLG MUTATED      4    1
  ICOSLG WILD-TYPE  362  118
        clus
vv       ICOSLG MUTATED ICOSLG WILD-TYPE
  COLON               4              362
  RECTUM              1              118
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ICOSLG MUTATED         1        0        0         3         0         0
  ICOSLG WILD-TYPE      90        1       32       135        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ICOSLG MUTATED           0          0          1          0        0
  ICOSLG WILD-TYPE        24         11         58         42       48
                  vv
clus               STAGE IVA STAGE IVB
  ICOSLG MUTATED           0         0
  ICOSLG WILD-TYPE        18         1
D819V4, multiclass
            clus
vv           ICOSLG MUTATED ICOSLG WILD-TYPE
  STAGE I                 1               90
  STAGE IA                0                1
  STAGE II                0               32
  STAGE IIA               3              135
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              1               58
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ICOSLG MUTATED     1   0   4   0
  ICOSLG WILD-TYPE  16  92 325  50
D819V5, multiclass
    clus
vv   ICOSLG MUTATED ICOSLG WILD-TYPE
  T1              1               16
  T2              0               92
  T3              4              325
  T4              0               50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  ICOSLG MUTATED     4   1   0
  ICOSLG WILD-TYPE 283 112  87
D819V6, multiclass
    clus
vv   ICOSLG MUTATED ICOSLG WILD-TYPE
  N0              4              283
  N1              1              112
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D819V7, binary
                  cls
clus                 0   1
  ICOSLG MUTATED     4   0
  ICOSLG WILD-TYPE 371  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ICOSLG MUTATED      4    0
  ICOSLG WILD-TYPE  371   65
   clus
vv  ICOSLG MUTATED ICOSLG WILD-TYPE
  0              4              371
  1              0               65
[1] 2 2
[1] FALSE
D819V8, binary
                  cls
clus                 0   1
  ICOSLG MUTATED     2   3
  ICOSLG WILD-TYPE 223 261
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ICOSLG MUTATED      2    3
  ICOSLG WILD-TYPE  223  261
        clus
vv       ICOSLG MUTATED ICOSLG WILD-TYPE
  FEMALE              2              223
  MALE                3              261
[1] 2 2
[1] FALSE
D819V9, binary
                  cls
clus                 0   1
  ICOSLG MUTATED     3   1
  ICOSLG WILD-TYPE 347  21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ICOSLG MUTATED      3    1
  ICOSLG WILD-TYPE  347   21
     clus
vv    ICOSLG MUTATED ICOSLG WILD-TYPE
  NO               3              347
  YES              1               21
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ICOSLG MUTATED                      4                             0
  ICOSLG WILD-TYPE                  311                            47
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ICOSLG MUTATED                       1                              0
  ICOSLG WILD-TYPE                   105                             10
D819V10, multiclass
                                clus
vv                               ICOSLG MUTATED ICOSLG WILD-TYPE
  COLON ADENOCARCINOMA                        4              311
  COLON MUCINOUS ADENOCARCINOMA               0               47
  RECTAL ADENOCARCINOMA                       1              105
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ICOSLG MUTATED     2   0   0   1
  ICOSLG WILD-TYPE 343   4  31  24
D819V11, multiclass
    clus
vv   ICOSLG MUTATED ICOSLG WILD-TYPE
  R0              2              343
  R1              0                4
  R2              0               31
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D819V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ICOSLG MUTATED                                  0     1
  ICOSLG WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ICOSLG MUTATED                           0     4
  ICOSLG WILD-TYPE                        22   222
D819V13, multiclass
                                  clus
vv                                 ICOSLG MUTATED ICOSLG WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         4              222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(820) Variable = PPIG MUTATION ANALYSIS
D820V1, survival
                sevent
clus2              0   1
  PPIG MUTATED    13   2
  PPIG WILD-TYPE 365  91
  PPIG MUTATED PPIG WILD-TYPE 
            15            456 
  PPIG MUTATED PPIG WILD-TYPE 
             2             91 
$`PPIG MUTATED`
TCGA-A6-6137 TCGA-AA-3525 TCGA-AA-3949 TCGA-AA-A00E TCGA-AA-A00N TCGA-AA-A010 
       27.09         8.05        26.01        30.02         4.01        34.98 
TCGA-AZ-4315 TCGA-AZ-6601 TCGA-D5-6540 TCGA-DM-A282 TCGA-G4-6309 TCGA-G4-6586 
       58.39       100.01        16.14       139.17        85.48        35.80 
TCGA-AF-2691 TCGA-AF-2693 TCGA-EF-5830 
       43.04        19.10         0.49 

$`PPIG WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        22.06        32.71        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3526 
        1.02         9.07        24.03        37.05        36.03        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       12.99        24.00        33.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
       16.31         0.95        33.01        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77        12.10        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
        4.80        17.13        12.49        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       53.62        44.68        55.04        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       22.09        13.78        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       24.13        39.48        13.55        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EI-6506 
       41.36        57.24        24.13        51.48        32.61        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  PPIG MUTATED PPIG WILD-TYPE 
          0.49           0.00 
  PPIG MUTATED PPIG WILD-TYPE 
        139.17         148.01 
  PPIG MUTATED PPIG WILD-TYPE 
        30.020         20.035 
[1] "0.5 - 139.2 (30.0)" "0.0 - 148.0 (20.0)"
[1] "hr=" "2.2"
D820V2, continuous
D820V3, binary
                cls
clus               0   1
  PPIG MUTATED    12   2
  PPIG WILD-TYPE 354 117
[1] "tbl2"
                cls
clus             [,1] [,2]
  PPIG MUTATED     12    2
  PPIG WILD-TYPE  354  117
        clus
vv       PPIG MUTATED PPIG WILD-TYPE
  COLON            12            354
  RECTUM            2            117
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PPIG MUTATED         3        0        1         4         3         0
  PPIG WILD-TYPE      88        1       31       134         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PPIG MUTATED           0          0          4          0        0         0
  PPIG WILD-TYPE        24         11         55         42       48        18
                vv
clus             STAGE IVB
  PPIG MUTATED           0
  PPIG WILD-TYPE         1
D820V4, multiclass
            clus
vv           PPIG MUTATED PPIG WILD-TYPE
  STAGE I               3             88
  STAGE IA              0              1
  STAGE II              1             31
  STAGE IIA             4            134
  STAGE IIB             3              7
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            4             55
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  PPIG MUTATED     1   2   9   3
  PPIG WILD-TYPE  16  90 320  47
D820V5, multiclass
    clus
vv   PPIG MUTATED PPIG WILD-TYPE
  T1            1             16
  T2            2             90
  T3            9            320
  T4            3             47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  PPIG MUTATED    11   4   0
  PPIG WILD-TYPE 276 109  87
D820V6, multiclass
    clus
vv   PPIG MUTATED PPIG WILD-TYPE
  N0           11            276
  N1            4            109
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D820V7, binary
                cls
clus               0   1
  PPIG MUTATED    14   0
  PPIG WILD-TYPE 361  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  PPIG MUTATED     14    0
  PPIG WILD-TYPE  361   65
   clus
vv  PPIG MUTATED PPIG WILD-TYPE
  0           14            361
  1            0             65
[1] 2 2
[1] FALSE
D820V8, binary
                cls
clus               0   1
  PPIG MUTATED     6   9
  PPIG WILD-TYPE 219 255
[1] "tbl2"
                cls
clus             [,1] [,2]
  PPIG MUTATED      6    9
  PPIG WILD-TYPE  219  255
        clus
vv       PPIG MUTATED PPIG WILD-TYPE
  FEMALE            6            219
  MALE              9            255
[1] 2 2
[1] FALSE
D820V9, binary
                cls
clus               0   1
  PPIG MUTATED    12   0
  PPIG WILD-TYPE 338  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  PPIG MUTATED     12    0
  PPIG WILD-TYPE  338   22
     clus
vv    PPIG MUTATED PPIG WILD-TYPE
  NO            12            338
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PPIG MUTATED                      9                             3
  PPIG WILD-TYPE                  306                            44
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PPIG MUTATED                       2                              0
  PPIG WILD-TYPE                   104                             10
D820V10, multiclass
                                clus
vv                               PPIG MUTATED PPIG WILD-TYPE
  COLON ADENOCARCINOMA                      9            306
  COLON MUCINOUS ADENOCARCINOMA             3             44
  RECTAL ADENOCARCINOMA                     2            104
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  PPIG MUTATED    11   0   0   0
  PPIG WILD-TYPE 334   4  31  25
D820V11, multiclass
    clus
vv   PPIG MUTATED PPIG WILD-TYPE
  R0           11            334
  R1            0              4
  R2            0             31
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D820V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PPIG MUTATED                                  0     0
  PPIG WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  PPIG MUTATED                           1     9
  PPIG WILD-TYPE                        21   217
D820V13, multiclass
                                  clus
vv                                 PPIG MUTATED PPIG WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                       9            217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(821) Variable = PTPRN MUTATION ANALYSIS
D821V1, survival
                 sevent
clus2               0   1
  PTPRN MUTATED    14   2
  PTPRN WILD-TYPE 364  91
  PTPRN MUTATED PTPRN WILD-TYPE 
             16             455 
  PTPRN MUTATED PTPRN WILD-TYPE 
              2              91 
$`PTPRN MUTATED`
TCGA-A6-6781 TCGA-AA-3510 TCGA-AA-3555 TCGA-AA-3821 TCGA-AA-3977 TCGA-AA-A010 
       19.66        63.98        29.95         1.02        25.02        34.98 
TCGA-AA-A01R TCGA-AZ-4315 TCGA-AZ-6598 TCGA-CA-6717 TCGA-CM-4743 TCGA-CM-6680 
       35.01        58.39        49.41        12.76        23.05        12.03 
TCGA-F4-6570 TCGA-AG-3894 TCGA-DY-A0XA TCGA-F5-6813 
        6.18        14.01       126.44         0.69 

$`PTPRN WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       24.00        17.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
       33.04         0.99        25.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        33.01        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 
      106.75        22.36        62.79        88.21         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
      124.27        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.08        11.01        10.06        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       31.96        35.74        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       17.03        13.02        35.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC 
       19.99         5.95         4.01         5.03         5.29        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66        55.76        26.43 

  PTPRN MUTATED PTPRN WILD-TYPE 
           0.69            0.00 
  PTPRN MUTATED PTPRN WILD-TYPE 
         126.44          148.01 
  PTPRN MUTATED PTPRN WILD-TYPE 
         24.035          20.120 
[1] "0.7 - 126.4 (24.0)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.9"
D821V2, continuous
D821V3, binary
                 cls
clus                0   1
  PTPRN MUTATED    14   3
  PTPRN WILD-TYPE 352 116
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPRN MUTATED     14    3
  PTPRN WILD-TYPE  352  116
        clus
vv       PTPRN MUTATED PTPRN WILD-TYPE
  COLON             14             352
  RECTUM             3             116
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PTPRN MUTATED         1        0        2         7         2         0
  PTPRN WILD-TYPE      90        1       30       131         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PTPRN MUTATED           1          0          1          2        0         0
  PTPRN WILD-TYPE        23         11         58         40       48        18
                 vv
clus              STAGE IVB
  PTPRN MUTATED           0
  PTPRN WILD-TYPE         1
D821V4, multiclass
            clus
vv           PTPRN MUTATED PTPRN WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA              7             131
  STAGE IIB              2               8
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             2              40
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PTPRN MUTATED     0   2  11   4
  PTPRN WILD-TYPE  17  90 318  46
D821V5, multiclass
    clus
vv   PTPRN MUTATED PTPRN WILD-TYPE
  T1             0              17
  T2             2              90
  T3            11             318
  T4             4              46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  PTPRN MUTATED    13   1   3
  PTPRN WILD-TYPE 274 112  84
D821V6, multiclass
    clus
vv   PTPRN MUTATED PTPRN WILD-TYPE
  N0            13             274
  N1             1             112
  N2             3              84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D821V7, binary
                 cls
clus                0   1
  PTPRN MUTATED    13   0
  PTPRN WILD-TYPE 362  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPRN MUTATED     13    0
  PTPRN WILD-TYPE  362   65
   clus
vv  PTPRN MUTATED PTPRN WILD-TYPE
  0            13             362
  1             0              65
[1] 2 2
[1] FALSE
D821V8, binary
                 cls
clus                0   1
  PTPRN MUTATED     8   9
  PTPRN WILD-TYPE 217 255
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPRN MUTATED      8    9
  PTPRN WILD-TYPE  217  255
        clus
vv       PTPRN MUTATED PTPRN WILD-TYPE
  FEMALE             8             217
  MALE               9             255
[1] 2 2
[1] FALSE
D821V9, binary
                 cls
clus                0   1
  PTPRN MUTATED    12   2
  PTPRN WILD-TYPE 338  20
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPRN MUTATED     12    2
  PTPRN WILD-TYPE  338   20
     clus
vv    PTPRN MUTATED PTPRN WILD-TYPE
  NO             12             338
  YES             2              20
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PTPRN MUTATED                      9                             5
  PTPRN WILD-TYPE                  306                            42
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PTPRN MUTATED                       3                              0
  PTPRN WILD-TYPE                   103                             10
D821V10, multiclass
                                clus
vv                               PTPRN MUTATED PTPRN WILD-TYPE
  COLON ADENOCARCINOMA                       9             306
  COLON MUCINOUS ADENOCARCINOMA              5              42
  RECTAL ADENOCARCINOMA                      3             103
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  PTPRN MUTATED    12   0   0   2
  PTPRN WILD-TYPE 333   4  31  23
D821V11, multiclass
    clus
vv   PTPRN MUTATED PTPRN WILD-TYPE
  R0            12             333
  R1             0               4
  R2             0              31
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D821V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PTPRN MUTATED                                  0     1
  PTPRN WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PTPRN MUTATED                           0     9
  PTPRN WILD-TYPE                        22   217
D821V13, multiclass
                                  clus
vv                                 PTPRN MUTATED PTPRN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        9             217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(822) Variable = THOC6 MUTATION ANALYSIS
D822V1, survival
                 sevent
clus2               0   1
  THOC6 MUTATED     5   2
  THOC6 WILD-TYPE 373  91
  THOC6 MUTATED THOC6 WILD-TYPE 
              7             464 
  THOC6 MUTATED THOC6 WILD-TYPE 
              2              91 
$`THOC6 MUTATED`
TCGA-AA-3516 TCGA-AA-3713 TCGA-AA-A010 TCGA-AZ-6600 TCGA-CM-5349 TCGA-G4-6293 
       13.02        19.04        34.98        12.10        30.08       133.18 
TCGA-G4-6299 
       74.56 

$`THOC6 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        1.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 
       22.36        62.79        88.21        49.41         6.77       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       29.06        22.03        22.98        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
       47.41        35.31        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  THOC6 MUTATED THOC6 WILD-TYPE 
           12.1             0.0 
  THOC6 MUTATED THOC6 WILD-TYPE 
         133.18          148.01 
  THOC6 MUTATED THOC6 WILD-TYPE 
         30.080          20.155 
[1] "12.1 - 133.2 (30.1)" "0.0 - 148.0 (20.2)" 
[1] "hr=" "1"  
D822V2, continuous
D822V3, binary
                 cls
clus                0   1
  THOC6 MUTATED     8   0
  THOC6 WILD-TYPE 358 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  THOC6 MUTATED      8    0
  THOC6 WILD-TYPE  358  119
        clus
vv       THOC6 MUTATED THOC6 WILD-TYPE
  COLON              8             358
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  THOC6 MUTATED         0        0        0         1         1         0
  THOC6 WILD-TYPE      91        1       32       137         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  THOC6 MUTATED           3          0          0          1        2         0
  THOC6 WILD-TYPE        21         11         59         41       46        18
                 vv
clus              STAGE IVB
  THOC6 MUTATED           0
  THOC6 WILD-TYPE         1
D822V4, multiclass
            clus
vv           THOC6 MUTATED THOC6 WILD-TYPE
  STAGE I                0              91
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              1             137
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              3              21
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             1              41
  STAGE IV               2              46
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  THOC6 MUTATED     0   0   6   2
  THOC6 WILD-TYPE  17  92 323  48
D822V5, multiclass
    clus
vv   THOC6 MUTATED THOC6 WILD-TYPE
  T1             0              17
  T2             0              92
  T3             6             323
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  THOC6 MUTATED     3   2   3
  THOC6 WILD-TYPE 284 111  84
D822V6, multiclass
    clus
vv   THOC6 MUTATED THOC6 WILD-TYPE
  N0             3             284
  N1             2             111
  N2             3              84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D822V7, binary
                 cls
clus                0   1
  THOC6 MUTATED     6   2
  THOC6 WILD-TYPE 369  63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  THOC6 MUTATED      6    2
  THOC6 WILD-TYPE  369   63
   clus
vv  THOC6 MUTATED THOC6 WILD-TYPE
  0             6             369
  1             2              63
[1] 2 2
[1] FALSE
D822V8, binary
                 cls
clus                0   1
  THOC6 MUTATED     4   4
  THOC6 WILD-TYPE 221 260
[1] "tbl2"
                 cls
clus              [,1] [,2]
  THOC6 MUTATED      4    4
  THOC6 WILD-TYPE  221  260
        clus
vv       THOC6 MUTATED THOC6 WILD-TYPE
  FEMALE             4             221
  MALE               4             260
[1] 2 2
[1] FALSE
D822V9, binary
                 cls
clus                0   1
  THOC6 MUTATED     5   1
  THOC6 WILD-TYPE 345  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  THOC6 MUTATED      5    1
  THOC6 WILD-TYPE  345   21
     clus
vv    THOC6 MUTATED THOC6 WILD-TYPE
  NO              5             345
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  THOC6 MUTATED                      7                             1
  THOC6 WILD-TYPE                  308                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  THOC6 MUTATED                       0                              0
  THOC6 WILD-TYPE                   106                             10
D822V10, multiclass
                                clus
vv                               THOC6 MUTATED THOC6 WILD-TYPE
  COLON ADENOCARCINOMA                       7             308
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  THOC6 MUTATED     5   0   1   0
  THOC6 WILD-TYPE 340   4  30  25
D822V11, multiclass
    clus
vv   THOC6 MUTATED THOC6 WILD-TYPE
  R0             5             340
  R1             0               4
  R2             1              30
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D822V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  THOC6 MUTATED                                  0     0
  THOC6 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  THOC6 MUTATED                           1     3
  THOC6 WILD-TYPE                        21   223
D822V13, multiclass
                                  clus
vv                                 THOC6 MUTATED THOC6 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        3             223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(823) Variable = HNRNPH3 MUTATION ANALYSIS
D823V1, survival
                   sevent
clus2                 0   1
  HNRNPH3 MUTATED     3   1
  HNRNPH3 WILD-TYPE 375  92
  HNRNPH3 MUTATED HNRNPH3 WILD-TYPE 
                4               467 
  HNRNPH3 MUTATED HNRNPH3 WILD-TYPE 
                1                92 
$`HNRNPH3 MUTATED`
TCGA-AA-3956 TCGA-AZ-6598 TCGA-CM-5861 TCGA-CM-6171 
       34.03        49.41        15.02        14.04 

$`HNRNPH3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       24.00         2.01        20.98         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 
        5.13       106.75        22.36        62.79        88.21         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       32.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       12.99        13.02        15.02        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  HNRNPH3 MUTATED HNRNPH3 WILD-TYPE 
            14.04              0.00 
  HNRNPH3 MUTATED HNRNPH3 WILD-TYPE 
            49.41            148.01 
  HNRNPH3 MUTATED HNRNPH3 WILD-TYPE 
           24.525            20.190 
[1] "14.0 - 49.4 (24.5)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.1"
D823V2, continuous
D823V3, binary
                   cls
clus                  0   1
  HNRNPH3 MUTATED     4   0
  HNRNPH3 WILD-TYPE 362 119
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HNRNPH3 MUTATED      4    0
  HNRNPH3 WILD-TYPE  362  119
        clus
vv       HNRNPH3 MUTATED HNRNPH3 WILD-TYPE
  COLON                4               362
  RECTUM               0               119
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  HNRNPH3 MUTATED         1        0        1         2         0         0
  HNRNPH3 WILD-TYPE      90        1       31       136        10         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HNRNPH3 MUTATED           0          0          0          0        0
  HNRNPH3 WILD-TYPE        24         11         59         42       48
                   vv
clus                STAGE IVA STAGE IVB
  HNRNPH3 MUTATED           0         0
  HNRNPH3 WILD-TYPE        18         1
D823V4, multiclass
            clus
vv           HNRNPH3 MUTATED HNRNPH3 WILD-TYPE
  STAGE I                  1                90
  STAGE IA                 0                 1
  STAGE II                 1                31
  STAGE IIA                2               136
  STAGE IIB                0                10
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               0                11
  STAGE IIIB               0                59
  STAGE IIIC               0                42
  STAGE IV                 0                48
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  HNRNPH3 MUTATED     0   1   3   0
  HNRNPH3 WILD-TYPE  17  91 326  50
D823V5, multiclass
    clus
vv   HNRNPH3 MUTATED HNRNPH3 WILD-TYPE
  T1               0                17
  T2               1                91
  T3               3               326
  T4               0                50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  HNRNPH3 MUTATED     4   0   0
  HNRNPH3 WILD-TYPE 283 113  87
D823V6, multiclass
    clus
vv   HNRNPH3 MUTATED HNRNPH3 WILD-TYPE
  N0               4               283
  N1               0               113
  N2               0                87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D823V7, binary
                   cls
clus                  0   1
  HNRNPH3 MUTATED     3   0
  HNRNPH3 WILD-TYPE 372  65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HNRNPH3 MUTATED      3    0
  HNRNPH3 WILD-TYPE  372   65
   clus
vv  HNRNPH3 MUTATED HNRNPH3 WILD-TYPE
  0               3               372
  1               0                65
[1] 2 2
[1] FALSE
D823V8, binary
                   cls
clus                  0   1
  HNRNPH3 MUTATED     3   1
  HNRNPH3 WILD-TYPE 222 263
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HNRNPH3 MUTATED      3    1
  HNRNPH3 WILD-TYPE  222  263
        clus
vv       HNRNPH3 MUTATED HNRNPH3 WILD-TYPE
  FEMALE               3               222
  MALE                 1               263
[1] 2 2
[1] FALSE
D823V9, binary
                   cls
clus                  0   1
  HNRNPH3 MUTATED     4   0
  HNRNPH3 WILD-TYPE 346  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HNRNPH3 MUTATED      4    0
  HNRNPH3 WILD-TYPE  346   22
     clus
vv    HNRNPH3 MUTATED HNRNPH3 WILD-TYPE
  NO                4               346
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  HNRNPH3 MUTATED                      4                             0
  HNRNPH3 WILD-TYPE                  311                            47
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  HNRNPH3 MUTATED                       0                              0
  HNRNPH3 WILD-TYPE                   106                             10
D823V10, multiclass
                                clus
vv                               HNRNPH3 MUTATED HNRNPH3 WILD-TYPE
  COLON ADENOCARCINOMA                         4               311
  COLON MUCINOUS ADENOCARCINOMA                0                47
  RECTAL ADENOCARCINOMA                        0               106
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  HNRNPH3 MUTATED     3   0   0   0
  HNRNPH3 WILD-TYPE 342   4  31  25
D823V11, multiclass
    clus
vv   HNRNPH3 MUTATED HNRNPH3 WILD-TYPE
  R0               3               342
  R1               0                 4
  R2               0                31
  RX               0                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D823V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HNRNPH3 MUTATED                                  0     0
  HNRNPH3 WILD-TYPE                                1    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  HNRNPH3 MUTATED                           0     3
  HNRNPH3 WILD-TYPE                        22   223
D823V13, multiclass
                                  clus
vv                                 HNRNPH3 MUTATED HNRNPH3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                      0                22
  WHITE                                          3               223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(824) Variable = FSHR MUTATION ANALYSIS
D824V1, survival
                sevent
clus2              0   1
  FSHR MUTATED    15   3
  FSHR WILD-TYPE 363  90
  FSHR MUTATED FSHR WILD-TYPE 
            18            453 
  FSHR MUTATED FSHR WILD-TYPE 
             3             90 
$`FSHR MUTATED`
TCGA-A6-5657 TCGA-A6-5666 TCGA-A6-6649 TCGA-AA-3662 TCGA-AA-3710 TCGA-AA-A00J 
       31.63        32.71        24.16         6.05        26.99        18.05 
TCGA-AA-A00N TCGA-AA-A010 TCGA-AY-4071 TCGA-AZ-4323 TCGA-CA-6717 TCGA-CM-6164 
        4.01        34.98         0.95         1.41        12.76        29.03 
TCGA-CM-6171 TCGA-CM-6172 TCGA-AF-6655 TCGA-AG-A002 TCGA-AG-A02X TCGA-DC-6681 
       14.04        11.01        20.02        20.98        41.00         5.95 

$`FSHR WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       22.06        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02        78.08         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-5543 
       10.88         0.20        14.50        27.09        16.31        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82        58.39         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07        12.20        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       16.83        15.39        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
        1.94        38.96        61.97        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6682 TCGA-DC-6683 
       13.97        27.95        10.98        19.99         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  FSHR MUTATED FSHR WILD-TYPE 
          0.95           0.00 
  FSHR MUTATED FSHR WILD-TYPE 
         41.00         148.01 
  FSHR MUTATED FSHR WILD-TYPE 
        19.035         20.280 
[1] "0.9 - 41.0 (19.0)"  "0.0 - 148.0 (20.3)"
[1] "hr=" "1.2"
D824V2, continuous
D824V3, binary
                cls
clus               0   1
  FSHR MUTATED    14   4
  FSHR WILD-TYPE 352 115
[1] "tbl2"
                cls
clus             [,1] [,2]
  FSHR MUTATED     14    4
  FSHR WILD-TYPE  352  115
        clus
vv       FSHR MUTATED FSHR WILD-TYPE
  COLON            14            352
  RECTUM            4            115
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FSHR MUTATED         4        0        0         4         2         1
  FSHR WILD-TYPE      87        1       32       134         8         0
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  FSHR MUTATED           0          1          4          0        2         1
  FSHR WILD-TYPE        24         10         55         42       46        17
                vv
clus             STAGE IVB
  FSHR MUTATED           0
  FSHR WILD-TYPE         1
D824V4, multiclass
            clus
vv           FSHR MUTATED FSHR WILD-TYPE
  STAGE I               4             87
  STAGE IA              0              1
  STAGE II              0             32
  STAGE IIA             4            134
  STAGE IIB             2              8
  STAGE IIC             1              0
  STAGE III             0             24
  STAGE IIIA            1             10
  STAGE IIIB            4             55
  STAGE IIIC            0             42
  STAGE IV              2             46
  STAGE IVA             1             17
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  FSHR MUTATED     1   4   8   6
  FSHR WILD-TYPE  16  88 321  44
D824V5, multiclass
    clus
vv   FSHR MUTATED FSHR WILD-TYPE
  T1            1             16
  T2            4             88
  T3            8            321
  T4            6             44
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  FSHR MUTATED    11   5   3
  FSHR WILD-TYPE 276 108  84
D824V6, multiclass
    clus
vv   FSHR MUTATED FSHR WILD-TYPE
  N0           11            276
  N1            5            108
  N2            3             84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D824V7, binary
                cls
clus               0   1
  FSHR MUTATED    15   3
  FSHR WILD-TYPE 360  62
[1] "tbl2"
                cls
clus             [,1] [,2]
  FSHR MUTATED     15    3
  FSHR WILD-TYPE  360   62
   clus
vv  FSHR MUTATED FSHR WILD-TYPE
  0           15            360
  1            3             62
[1] 2 2
[1] FALSE
D824V8, binary
                cls
clus               0   1
  FSHR MUTATED     9  10
  FSHR WILD-TYPE 216 254
[1] "tbl2"
                cls
clus             [,1] [,2]
  FSHR MUTATED      9   10
  FSHR WILD-TYPE  216  254
        clus
vv       FSHR MUTATED FSHR WILD-TYPE
  FEMALE            9            216
  MALE             10            254
[1] 2 2
[1] FALSE
D824V9, binary
                cls
clus               0   1
  FSHR MUTATED    15   0
  FSHR WILD-TYPE 335  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  FSHR MUTATED     15    0
  FSHR WILD-TYPE  335   22
     clus
vv    FSHR MUTATED FSHR WILD-TYPE
  NO            15            335
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  FSHR MUTATED                     11                             3
  FSHR WILD-TYPE                  304                            44
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  FSHR MUTATED                       4                              0
  FSHR WILD-TYPE                   102                             10
D824V10, multiclass
                                clus
vv                               FSHR MUTATED FSHR WILD-TYPE
  COLON ADENOCARCINOMA                     11            304
  COLON MUCINOUS ADENOCARCINOMA             3             44
  RECTAL ADENOCARCINOMA                     4            102
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  FSHR MUTATED    14   0   1   1
  FSHR WILD-TYPE 331   4  30  24
D824V11, multiclass
    clus
vv   FSHR MUTATED FSHR WILD-TYPE
  R0           14            331
  R1            0              4
  R2            1             30
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D824V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FSHR MUTATED                                  0     1
  FSHR WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  FSHR MUTATED                           1     9
  FSHR WILD-TYPE                        21   217
D824V13, multiclass
                                  clus
vv                                 FSHR MUTATED FSHR WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                       9            217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(825) Variable = HUWE1 MUTATION ANALYSIS
D825V1, survival
                 sevent
clus2               0   1
  HUWE1 MUTATED    35  11
  HUWE1 WILD-TYPE 343  82
  HUWE1 MUTATED HUWE1 WILD-TYPE 
             46             425 
  HUWE1 MUTATED HUWE1 WILD-TYPE 
             11              82 
$`HUWE1 MUTATED`
TCGA-A6-5665 TCGA-A6-6780 TCGA-AA-3555 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       22.06        20.12        29.95        78.08         6.05         6.97 
TCGA-AA-3713 TCGA-AA-3818 TCGA-AA-3837 TCGA-AA-3854 TCGA-AA-3864 TCGA-AA-3941 
       19.04         0.99        38.99        36.03        53.00        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3966 TCGA-AA-A010 TCGA-AA-A01P 
       33.01        26.01        24.00         2.01        34.98        38.07 
TCGA-AA-A01Q TCGA-AA-A02F TCGA-AD-6895 TCGA-AD-6964 TCGA-AU-3779 TCGA-AU-6004 
        1.02        39.98         0.72        10.88        14.50        27.09 
TCGA-AZ-4315 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6603 TCGA-CM-4752 TCGA-CM-6162 
       58.39        62.79        49.41        29.56        13.02        12.00 
TCGA-CM-6164 TCGA-CM-6167 TCGA-CM-6169 TCGA-CM-6674 TCGA-D5-6540 TCGA-D5-6541 
       29.03        14.99        13.02        12.95        16.14        15.58 
TCGA-DM-A1DA TCGA-DM-A1HB TCGA-F4-6459 TCGA-F4-6570 TCGA-F4-6703 TCGA-AF-2689 
        7.50       135.65         8.61         6.18        47.87        39.48 
TCGA-AG-A002 TCGA-AG-A020 TCGA-DC-5869 TCGA-DY-A1DF 
       20.98        10.98         5.03        24.13 

$`HUWE1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       24.00        17.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
       19.99        61.02        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       10.06        35.05        33.04        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       15.95        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
        0.00        33.07         0.00        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       31.07        30.05        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3955 
       18.05        31.00         2.01        12.99         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
       34.03        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01R 
       10.98        32.02        12.00        31.00        31.00        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       51.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       56.55         0.79         5.79        22.42        27.42         0.20 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
       16.31         0.95        33.01        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 
        5.13       106.75        22.36        88.21         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
      100.01         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-5341 
      124.27        23.05        20.02        37.02        25.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6165 
       15.02        15.02        17.03        15.02         2.96        16.04 
TCGA-CM-6166 TCGA-CM-6168 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6675 
       21.99        12.99        15.02        14.04        11.01        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       12.49         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB 
       92.75        49.91        13.32        12.59       140.38        44.32 
TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      131.51       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6704 
       60.79       117.07        98.24        31.96        35.74         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       79.69        24.13        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       64.01        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
        7.17        15.02        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       57.24        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  HUWE1 MUTATED HUWE1 WILD-TYPE 
           0.72            0.00 
  HUWE1 MUTATED HUWE1 WILD-TYPE 
         135.65          148.01 
  HUWE1 MUTATED HUWE1 WILD-TYPE 
          21.52           20.05 
[1] "0.7 - 135.7 (21.5)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.2"
D825V2, continuous
D825V3, binary
                 cls
clus                0   1
  HUWE1 MUTATED    42   5
  HUWE1 WILD-TYPE 324 114
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HUWE1 MUTATED     42    5
  HUWE1 WILD-TYPE  324  114
        clus
vv       HUWE1 MUTATED HUWE1 WILD-TYPE
  COLON             42             324
  RECTUM             5             114
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  HUWE1 MUTATED         4        0        6        16         3         0
  HUWE1 WILD-TYPE      87        1       26       122         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  HUWE1 MUTATED           2          0          5          3        4         1
  HUWE1 WILD-TYPE        22         11         54         39       44        17
                 vv
clus              STAGE IVB
  HUWE1 MUTATED           0
  HUWE1 WILD-TYPE         1
D825V4, multiclass
            clus
vv           HUWE1 MUTATED HUWE1 WILD-TYPE
  STAGE I                4              87
  STAGE IA               0               1
  STAGE II               6              26
  STAGE IIA             16             122
  STAGE IIB              3               7
  STAGE IIC              0               1
  STAGE III              2              22
  STAGE IIIA             0              11
  STAGE IIIB             5              54
  STAGE IIIC             3              39
  STAGE IV               4              44
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  HUWE1 MUTATED     0   5  36   6
  HUWE1 WILD-TYPE  17  87 293  44
D825V5, multiclass
    clus
vv   HUWE1 MUTATED HUWE1 WILD-TYPE
  T1             0              17
  T2             5              87
  T3            36             293
  T4             6              44
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  HUWE1 MUTATED    30  10   7
  HUWE1 WILD-TYPE 257 103  80
D825V6, multiclass
    clus
vv   HUWE1 MUTATED HUWE1 WILD-TYPE
  N0            30             257
  N1            10             103
  N2             7              80
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D825V7, binary
                 cls
clus                0   1
  HUWE1 MUTATED    35   5
  HUWE1 WILD-TYPE 340  60
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HUWE1 MUTATED     35    5
  HUWE1 WILD-TYPE  340   60
   clus
vv  HUWE1 MUTATED HUWE1 WILD-TYPE
  0            35             340
  1             5              60
[1] 2 2
[1] FALSE
D825V8, binary
                 cls
clus                0   1
  HUWE1 MUTATED    30  17
  HUWE1 WILD-TYPE 195 247
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HUWE1 MUTATED     30   17
  HUWE1 WILD-TYPE  195  247
        clus
vv       HUWE1 MUTATED HUWE1 WILD-TYPE
  FEMALE            30             195
  MALE              17             247
[1] 2 2
[1] FALSE
D825V9, binary
                 cls
clus                0   1
  HUWE1 MUTATED    35   1
  HUWE1 WILD-TYPE 315  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HUWE1 MUTATED     35    1
  HUWE1 WILD-TYPE  315   21
     clus
vv    HUWE1 MUTATED HUWE1 WILD-TYPE
  NO             35             315
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  HUWE1 MUTATED                     31                            10
  HUWE1 WILD-TYPE                  284                            37
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  HUWE1 MUTATED                       4                              1
  HUWE1 WILD-TYPE                   102                              9
D825V10, multiclass
                                clus
vv                               HUWE1 MUTATED HUWE1 WILD-TYPE
  COLON ADENOCARCINOMA                      31             284
  COLON MUCINOUS ADENOCARCINOMA             10              37
  RECTAL ADENOCARCINOMA                      4             102
  RECTAL MUCINOUS ADENOCARCINOMA             1               9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  HUWE1 MUTATED    33   0   3   1
  HUWE1 WILD-TYPE 312   4  28  24
D825V11, multiclass
    clus
vv   HUWE1 MUTATED HUWE1 WILD-TYPE
  R0            33             312
  R1             0               4
  R2             3              28
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D825V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HUWE1 MUTATED                                  0     0
  HUWE1 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  HUWE1 MUTATED                           4    23
  HUWE1 WILD-TYPE                        18   203
D825V13, multiclass
                                  clus
vv                                 HUWE1 MUTATED HUWE1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    4              18
  WHITE                                       23             203
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(826) Variable = EIF2B5 MUTATION ANALYSIS
D826V1, survival
                  sevent
clus2                0   1
  EIF2B5 MUTATED    13   3
  EIF2B5 WILD-TYPE 365  90
  EIF2B5 MUTATED EIF2B5 WILD-TYPE 
              16              455 
  EIF2B5 MUTATED EIF2B5 WILD-TYPE 
               3               90 
$`EIF2B5 MUTATED`
TCGA-AA-3525 TCGA-AA-3542 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-A00J TCGA-AA-A010 
        8.05        12.99        19.04        10.06        18.05        34.98 
TCGA-AY-5543 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-CM-6170 TCGA-CM-6675 
       33.01        58.39        49.41        12.10        15.02        13.05 
TCGA-D5-6536 TCGA-G4-6307 TCGA-G4-6321 TCGA-DY-A0XA 
       17.85        55.04        22.09       126.44 

$`EIF2B5 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       26.01         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3815 
        5.03        85.05        26.99        19.04        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
       16.31         0.95        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6601 
      106.75        22.36        62.79        88.21         6.77       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6676 TCGA-CM-6677 
       13.02        14.04        11.01        12.95        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       15.12         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 
      133.18        74.56        65.85        53.62        44.68        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       63.62        61.91        36.00        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD 
        5.95         4.01         5.03         5.29        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  EIF2B5 MUTATED EIF2B5 WILD-TYPE 
            8.05             0.00 
  EIF2B5 MUTATED EIF2B5 WILD-TYPE 
          126.44           148.01 
  EIF2B5 MUTATED EIF2B5 WILD-TYPE 
          18.545           20.280 
[1] "8.1 - 126.4 (18.5)" "0.0 - 148.0 (20.3)"
[1] "hr=" "1.3"
D826V2, continuous
D826V3, binary
                  cls
clus                 0   1
  EIF2B5 MUTATED    15   1
  EIF2B5 WILD-TYPE 351 118
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EIF2B5 MUTATED     15    1
  EIF2B5 WILD-TYPE  351  118
        clus
vv       EIF2B5 MUTATED EIF2B5 WILD-TYPE
  COLON              15              351
  RECTUM              1              118
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  EIF2B5 MUTATED         1        0        1         3         1         0
  EIF2B5 WILD-TYPE      90        1       31       135         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  EIF2B5 MUTATED           2          0          3          1        2
  EIF2B5 WILD-TYPE        22         11         56         41       46
                  vv
clus               STAGE IVA STAGE IVB
  EIF2B5 MUTATED           1         1
  EIF2B5 WILD-TYPE        17         0
D826V4, multiclass
            clus
vv           EIF2B5 MUTATED EIF2B5 WILD-TYPE
  STAGE I                 1               90
  STAGE IA                0                1
  STAGE II                1               31
  STAGE IIA               3              135
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               2               22
  STAGE IIIA              0               11
  STAGE IIIB              3               56
  STAGE IIIC              1               41
  STAGE IV                2               46
  STAGE IVA               1               17
  STAGE IVB               1                0
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  EIF2B5 MUTATED     0   2  11   3
  EIF2B5 WILD-TYPE  17  90 318  47
D826V5, multiclass
    clus
vv   EIF2B5 MUTATED EIF2B5 WILD-TYPE
  T1              0               17
  T2              2               90
  T3             11              318
  T4              3               47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  EIF2B5 MUTATED     7   6   3
  EIF2B5 WILD-TYPE 280 107  84
D826V6, multiclass
    clus
vv   EIF2B5 MUTATED EIF2B5 WILD-TYPE
  N0              7              280
  N1              6              107
  N2              3               84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D826V7, binary
                  cls
clus                 0   1
  EIF2B5 MUTATED    10   4
  EIF2B5 WILD-TYPE 365  61
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EIF2B5 MUTATED     10    4
  EIF2B5 WILD-TYPE  365   61
   clus
vv  EIF2B5 MUTATED EIF2B5 WILD-TYPE
  0             10              365
  1              4               61
[1] 2 2
[1] FALSE
D826V8, binary
                  cls
clus                 0   1
  EIF2B5 MUTATED     8   8
  EIF2B5 WILD-TYPE 217 256
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EIF2B5 MUTATED      8    8
  EIF2B5 WILD-TYPE  217  256
        clus
vv       EIF2B5 MUTATED EIF2B5 WILD-TYPE
  FEMALE              8              217
  MALE                8              256
[1] 2 2
[1] FALSE
D826V9, binary
                  cls
clus                 0   1
  EIF2B5 MUTATED    13   1
  EIF2B5 WILD-TYPE 337  21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EIF2B5 MUTATED     13    1
  EIF2B5 WILD-TYPE  337   21
     clus
vv    EIF2B5 MUTATED EIF2B5 WILD-TYPE
  NO              13              337
  YES              1               21
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  EIF2B5 MUTATED                     14                             1
  EIF2B5 WILD-TYPE                  301                            46
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  EIF2B5 MUTATED                       1                              0
  EIF2B5 WILD-TYPE                   105                             10
D826V10, multiclass
                                clus
vv                               EIF2B5 MUTATED EIF2B5 WILD-TYPE
  COLON ADENOCARCINOMA                       14              301
  COLON MUCINOUS ADENOCARCINOMA               1               46
  RECTAL ADENOCARCINOMA                       1              105
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  EIF2B5 MUTATED    12   0   1   0
  EIF2B5 WILD-TYPE 333   4  30  25
D826V11, multiclass
    clus
vv   EIF2B5 MUTATED EIF2B5 WILD-TYPE
  R0             12              333
  R1              0                4
  R2              1               30
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D826V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  EIF2B5 MUTATED                                  0     0
  EIF2B5 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  EIF2B5 MUTATED                           3     7
  EIF2B5 WILD-TYPE                        19   219
D826V13, multiclass
                                  clus
vv                                 EIF2B5 MUTATED EIF2B5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     3               19
  WHITE                                         7              219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(827) Variable = C14ORF118 MUTATION ANALYSIS
D827V1, survival
                     sevent
clus2                   0   1
  C14ORF118 MUTATED     8   1
  C14ORF118 WILD-TYPE 370  92
  C14ORF118 MUTATED C14ORF118 WILD-TYPE 
                  9                 462 
  C14ORF118 MUTATED C14ORF118 WILD-TYPE 
                  1                  92 
$`C14ORF118 MUTATED`
TCGA-AA-A010 TCGA-AA-A01K TCGA-CM-6163 TCGA-D5-6529 TCGA-D5-6535 TCGA-DM-A28F 
       34.98        31.00         2.96        20.19        15.12        35.97 
TCGA-G4-6310 TCGA-G4-6586 TCGA-AG-A002 
       63.62        35.80        20.98 

$`C14ORF118 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       12.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       15.02        12.00        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6532 
       45.40        12.26        19.59        56.09        55.92        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
        1.32        43.27        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
       81.37       119.93        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       55.04        85.48        61.91        36.00        22.09        13.78 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  C14ORF118 MUTATED C14ORF118 WILD-TYPE 
               2.96                0.00 
  C14ORF118 MUTATED C14ORF118 WILD-TYPE 
              63.62              148.01 
  C14ORF118 MUTATED C14ORF118 WILD-TYPE 
             31.000              20.035 
[1] "3.0 - 63.6 (31.0)"  "0.0 - 148.0 (20.0)"
[1] "hr=" "1.9"
D827V2, continuous
D827V3, binary
                     cls
clus                    0   1
  C14ORF118 MUTATED     9   1
  C14ORF118 WILD-TYPE 357 118
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  C14ORF118 MUTATED      9    1
  C14ORF118 WILD-TYPE  357  118
        clus
vv       C14ORF118 MUTATED C14ORF118 WILD-TYPE
  COLON                  9                 357
  RECTUM                 1                 118
[1] 2 2
[1] FALSE
                     vv
clus                  STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  C14ORF118 MUTATED         2        0        0         3         1         0
  C14ORF118 WILD-TYPE      89        1       32       135         9         1
                     vv
clus                  STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C14ORF118 MUTATED           0          0          3          1        0
  C14ORF118 WILD-TYPE        24         11         56         41       48
                     vv
clus                  STAGE IVA STAGE IVB
  C14ORF118 MUTATED           0         0
  C14ORF118 WILD-TYPE        18         1
D827V4, multiclass
            clus
vv           C14ORF118 MUTATED C14ORF118 WILD-TYPE
  STAGE I                    2                  89
  STAGE IA                   0                   1
  STAGE II                   0                  32
  STAGE IIA                  3                 135
  STAGE IIB                  1                   9
  STAGE IIC                  0                   1
  STAGE III                  0                  24
  STAGE IIIA                 0                  11
  STAGE IIIB                 3                  56
  STAGE IIIC                 1                  41
  STAGE IV                   0                  48
  STAGE IVA                  0                  18
  STAGE IVB                  0                   1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                   T1  T2  T3  T4
  C14ORF118 MUTATED     1   1   7   1
  C14ORF118 WILD-TYPE  16  91 322  49
D827V5, multiclass
    clus
vv   C14ORF118 MUTATED C14ORF118 WILD-TYPE
  T1                 1                  16
  T2                 1                  91
  T3                 7                 322
  T4                 1                  49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                   N0  N1  N2
  C14ORF118 MUTATED     6   3   1
  C14ORF118 WILD-TYPE 281 110  86
D827V6, multiclass
    clus
vv   C14ORF118 MUTATED C14ORF118 WILD-TYPE
  N0                 6                 281
  N1                 3                 110
  N2                 1                  86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D827V7, binary
                     cls
clus                    0   1
  C14ORF118 MUTATED     9   0
  C14ORF118 WILD-TYPE 366  65
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  C14ORF118 MUTATED      9    0
  C14ORF118 WILD-TYPE  366   65
   clus
vv  C14ORF118 MUTATED C14ORF118 WILD-TYPE
  0                 9                 366
  1                 0                  65
[1] 2 2
[1] FALSE
D827V8, binary
                     cls
clus                    0   1
  C14ORF118 MUTATED     5   5
  C14ORF118 WILD-TYPE 220 259
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  C14ORF118 MUTATED      5    5
  C14ORF118 WILD-TYPE  220  259
        clus
vv       C14ORF118 MUTATED C14ORF118 WILD-TYPE
  FEMALE                 5                 220
  MALE                   5                 259
[1] 2 2
[1] FALSE
D827V9, binary
                     cls
clus                    0   1
  C14ORF118 MUTATED     7   1
  C14ORF118 WILD-TYPE 343  21
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  C14ORF118 MUTATED      7    1
  C14ORF118 WILD-TYPE  343   21
     clus
vv    C14ORF118 MUTATED C14ORF118 WILD-TYPE
  NO                  7                 343
  YES                 1                  21
[1] 2 2
[1] FALSE
                     vv
clus                  COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  C14ORF118 MUTATED                      9                             0
  C14ORF118 WILD-TYPE                  306                            47
                     vv
clus                  RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  C14ORF118 MUTATED                       1                              0
  C14ORF118 WILD-TYPE                   105                             10
D827V10, multiclass
                                clus
vv                               C14ORF118 MUTATED C14ORF118 WILD-TYPE
  COLON ADENOCARCINOMA                           9                 306
  COLON MUCINOUS ADENOCARCINOMA                  0                  47
  RECTAL ADENOCARCINOMA                          1                 105
  RECTAL MUCINOUS ADENOCARCINOMA                 0                  10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                   R0  R1  R2  RX
  C14ORF118 MUTATED     8   0   0   1
  C14ORF118 WILD-TYPE 337   4  31  24
D827V11, multiclass
    clus
vv   C14ORF118 MUTATED C14ORF118 WILD-TYPE
  R0                 8                 337
  R1                 0                   4
  R2                 0                  31
  RX                 1                  24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D827V12, continuous
                     vv
clus                  AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C14ORF118 MUTATED                                  0     0
  C14ORF118 WILD-TYPE                                1    11
                     vv
clus                  BLACK OR AFRICAN AMERICAN WHITE
  C14ORF118 MUTATED                           0     6
  C14ORF118 WILD-TYPE                        22   220
D827V13, multiclass
                                  clus
vv                                 C14ORF118 MUTATED C14ORF118 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                 0                   1
  ASIAN                                            0                  11
  BLACK OR AFRICAN AMERICAN                        0                  22
  WHITE                                            6                 220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(828) Variable = USP9X MUTATION ANALYSIS
D828V1, survival
                 sevent
clus2               0   1
  USP9X MUTATED    21  11
  USP9X WILD-TYPE 357  82
  USP9X MUTATED USP9X WILD-TYPE 
             32             439 
  USP9X MUTATED USP9X WILD-TYPE 
             11              82 
$`USP9X MUTATED`
TCGA-A6-5660 TCGA-A6-5665 TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3663 TCGA-AA-3713 
       29.19        22.06         3.02        63.98         6.97        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3815 TCGA-AA-3864 TCGA-AA-A00N TCGA-AZ-4315 
       19.04        10.06        33.04        53.00         4.01        58.39 
TCGA-AZ-4682 TCGA-AZ-6598 TCGA-CA-6718 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 
       22.36        49.41        10.06        85.45        49.08        51.32 
TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6680 TCGA-D5-6537 
        5.03        15.02        12.00        16.04        12.03         4.80 
TCGA-D5-6538 TCGA-D5-6898 TCGA-F4-6570 TCGA-F4-6856 TCGA-G4-6588 TCGA-G4-6628 
       17.13         1.48         6.18        35.31        26.17        79.69 
TCGA-AG-3892 TCGA-AG-A002 
       13.02        20.98 

$`USP9X WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        33.53        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 
       19.66        20.28         7.04         1.02        35.01         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       61.02        78.08         6.05        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       35.05         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        31.07        30.05        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 
        1.41         5.13       106.75        62.79        88.21         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 
       12.20        12.76        14.30        17.56       148.01        15.62 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5868 
       22.98        30.08        32.02        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
       15.02         2.96        29.03        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.08        11.01        10.06        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       43.27        15.12        17.85        12.49        16.14        15.58 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
       13.25         0.53        47.41       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        35.80        91.79        46.75 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       36.95        17.03        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  USP9X MUTATED USP9X WILD-TYPE 
           1.48            0.00 
  USP9X MUTATED USP9X WILD-TYPE 
          85.45          148.01 
  USP9X MUTATED USP9X WILD-TYPE 
          19.04           20.28 
[1] "1.5 - 85.5 (19.0)"  "0.0 - 148.0 (20.3)"
[1] "hr=" "1.7"
D828V2, continuous
D828V3, binary
                 cls
clus                0   1
  USP9X MUTATED    31   2
  USP9X WILD-TYPE 335 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP9X MUTATED     31    2
  USP9X WILD-TYPE  335  117
        clus
vv       USP9X MUTATED USP9X WILD-TYPE
  COLON             31             335
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  USP9X MUTATED         7        0        6         9         1         0
  USP9X WILD-TYPE      84        1       26       129         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  USP9X MUTATED           1          0          5          1        1         2
  USP9X WILD-TYPE        23         11         54         41       47        16
                 vv
clus              STAGE IVB
  USP9X MUTATED           0
  USP9X WILD-TYPE         1
D828V4, multiclass
            clus
vv           USP9X MUTATED USP9X WILD-TYPE
  STAGE I                7              84
  STAGE IA               0               1
  STAGE II               6              26
  STAGE IIA              9             129
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             5              54
  STAGE IIIC             1              41
  STAGE IV               1              47
  STAGE IVA              2              16
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  USP9X MUTATED     1   6  25   1
  USP9X WILD-TYPE  16  86 304  49
D828V5, multiclass
    clus
vv   USP9X MUTATED USP9X WILD-TYPE
  T1             1              16
  T2             6              86
  T3            25             304
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  USP9X MUTATED    25   4   4
  USP9X WILD-TYPE 262 109  83
D828V6, multiclass
    clus
vv   USP9X MUTATED USP9X WILD-TYPE
  N0            25             262
  N1             4             109
  N2             4              83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D828V7, binary
                 cls
clus                0   1
  USP9X MUTATED    26   3
  USP9X WILD-TYPE 349  62
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP9X MUTATED     26    3
  USP9X WILD-TYPE  349   62
   clus
vv  USP9X MUTATED USP9X WILD-TYPE
  0            26             349
  1             3              62
[1] 2 2
[1] FALSE
D828V8, binary
                 cls
clus                0   1
  USP9X MUTATED    15  18
  USP9X WILD-TYPE 210 246
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP9X MUTATED     15   18
  USP9X WILD-TYPE  210  246
        clus
vv       USP9X MUTATED USP9X WILD-TYPE
  FEMALE            15             210
  MALE              18             246
[1] 2 2
[1] FALSE
D828V9, binary
                 cls
clus                0   1
  USP9X MUTATED    29   1
  USP9X WILD-TYPE 321  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP9X MUTATED     29    1
  USP9X WILD-TYPE  321   21
     clus
vv    USP9X MUTATED USP9X WILD-TYPE
  NO             29             321
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  USP9X MUTATED                     28                             3
  USP9X WILD-TYPE                  287                            44
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  USP9X MUTATED                       2                              0
  USP9X WILD-TYPE                   104                             10
D828V10, multiclass
                                clus
vv                               USP9X MUTATED USP9X WILD-TYPE
  COLON ADENOCARCINOMA                      28             287
  COLON MUCINOUS ADENOCARCINOMA              3              44
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  USP9X MUTATED    26   1   1   3
  USP9X WILD-TYPE 319   3  30  22
D828V11, multiclass
    clus
vv   USP9X MUTATED USP9X WILD-TYPE
  R0            26             319
  R1             1               3
  R2             1              30
  RX             3              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D828V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  USP9X MUTATED                                  0     1
  USP9X WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  USP9X MUTATED                           2    18
  USP9X WILD-TYPE                        20   208
D828V13, multiclass
                                  clus
vv                                 USP9X MUTATED USP9X WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    2              20
  WHITE                                       18             208
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(829) Variable = SLC35A5 MUTATION ANALYSIS
D829V1, survival
                   sevent
clus2                 0   1
  SLC35A5 MUTATED     6   2
  SLC35A5 WILD-TYPE 372  91
  SLC35A5 MUTATED SLC35A5 WILD-TYPE 
                8               463 
  SLC35A5 MUTATED SLC35A5 WILD-TYPE 
                2                91 
$`SLC35A5 MUTATED`
TCGA-AA-3510 TCGA-AA-3663 TCGA-AZ-4682 TCGA-CM-6163 TCGA-CM-6164 TCGA-G4-6303 
       63.98         6.97        22.36         2.96        29.03        65.85 
TCGA-G4-6628 TCGA-AG-A002 
       79.69        20.98 

$`SLC35A5 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
      106.75        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       12.00        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6304 TCGA-G4-6306 
       47.41        35.31       133.18        74.56        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 
       13.78        35.80        26.17        91.79        46.75        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  SLC35A5 MUTATED SLC35A5 WILD-TYPE 
             2.96              0.00 
  SLC35A5 MUTATED SLC35A5 WILD-TYPE 
            79.69            148.01 
  SLC35A5 MUTATED SLC35A5 WILD-TYPE 
           25.695            20.050 
[1] "3.0 - 79.7 (25.7)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.2"
D829V2, continuous
D829V3, binary
                   cls
clus                  0   1
  SLC35A5 MUTATED     7   1
  SLC35A5 WILD-TYPE 359 118
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC35A5 MUTATED      7    1
  SLC35A5 WILD-TYPE  359  118
        clus
vv       SLC35A5 MUTATED SLC35A5 WILD-TYPE
  COLON                7               359
  RECTUM               1               118
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SLC35A5 MUTATED         3        0        2         1         0         0
  SLC35A5 WILD-TYPE      88        1       30       137        10         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC35A5 MUTATED           0          0          0          0        1
  SLC35A5 WILD-TYPE        24         11         59         42       47
                   vv
clus                STAGE IVA STAGE IVB
  SLC35A5 MUTATED           1         0
  SLC35A5 WILD-TYPE        17         1
D829V4, multiclass
            clus
vv           SLC35A5 MUTATED SLC35A5 WILD-TYPE
  STAGE I                  3                88
  STAGE IA                 0                 1
  STAGE II                 2                30
  STAGE IIA                1               137
  STAGE IIB                0                10
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               0                11
  STAGE IIIB               0                59
  STAGE IIIC               0                42
  STAGE IV                 1                47
  STAGE IVA                1                17
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  SLC35A5 MUTATED     1   2   5   0
  SLC35A5 WILD-TYPE  16  90 324  50
D829V5, multiclass
    clus
vv   SLC35A5 MUTATED SLC35A5 WILD-TYPE
  T1               1                16
  T2               2                90
  T3               5               324
  T4               0                50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  SLC35A5 MUTATED     7   1   0
  SLC35A5 WILD-TYPE 280 112  87
D829V6, multiclass
    clus
vv   SLC35A5 MUTATED SLC35A5 WILD-TYPE
  N0               7               280
  N1               1               112
  N2               0                87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D829V7, binary
                   cls
clus                  0   1
  SLC35A5 MUTATED     6   2
  SLC35A5 WILD-TYPE 369  63
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC35A5 MUTATED      6    2
  SLC35A5 WILD-TYPE  369   63
   clus
vv  SLC35A5 MUTATED SLC35A5 WILD-TYPE
  0               6               369
  1               2                63
[1] 2 2
[1] FALSE
D829V8, binary
                   cls
clus                  0   1
  SLC35A5 MUTATED     2   6
  SLC35A5 WILD-TYPE 223 258
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC35A5 MUTATED      2    6
  SLC35A5 WILD-TYPE  223  258
        clus
vv       SLC35A5 MUTATED SLC35A5 WILD-TYPE
  FEMALE               2               223
  MALE                 6               258
[1] 2 2
[1] FALSE
D829V9, binary
                   cls
clus                  0   1
  SLC35A5 MUTATED     8   0
  SLC35A5 WILD-TYPE 342  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC35A5 MUTATED      8    0
  SLC35A5 WILD-TYPE  342   22
     clus
vv    SLC35A5 MUTATED SLC35A5 WILD-TYPE
  NO                8               342
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SLC35A5 MUTATED                      7                             0
  SLC35A5 WILD-TYPE                  308                            47
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SLC35A5 MUTATED                       1                              0
  SLC35A5 WILD-TYPE                   105                             10
D829V10, multiclass
                                clus
vv                               SLC35A5 MUTATED SLC35A5 WILD-TYPE
  COLON ADENOCARCINOMA                         7               308
  COLON MUCINOUS ADENOCARCINOMA                0                47
  RECTAL ADENOCARCINOMA                        1               105
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  SLC35A5 MUTATED     8   0   0   0
  SLC35A5 WILD-TYPE 337   4  31  25
D829V11, multiclass
    clus
vv   SLC35A5 MUTATED SLC35A5 WILD-TYPE
  R0               8               337
  R1               0                 4
  R2               0                31
  RX               0                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D829V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SLC35A5 MUTATED                                  0     0
  SLC35A5 WILD-TYPE                                1    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  SLC35A5 MUTATED                           0     5
  SLC35A5 WILD-TYPE                        22   221
D829V13, multiclass
                                  clus
vv                                 SLC35A5 MUTATED SLC35A5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                      0                22
  WHITE                                          5               221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(830) Variable = FAS MUTATION ANALYSIS
D830V1, survival
               sevent
clus2             0   1
  FAS MUTATED     8   1
  FAS WILD-TYPE 370  92
  FAS MUTATED FAS WILD-TYPE 
            9           462 
  FAS MUTATED FAS WILD-TYPE 
            1            92 
$`FAS MUTATED`
TCGA-A6-6780 TCGA-AD-6889 TCGA-AZ-4315 TCGA-CA-6717 TCGA-CK-4947 TCGA-CM-5862 
       20.12        56.55        58.39        12.76        17.56         5.03 
TCGA-D5-6927 TCGA-AG-3598 TCGA-AG-3892 
        9.44        50.04        13.02 

$`FAS WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       15.52         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       33.01        21.44        17.82         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       10.06        14.30       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 
       22.03        22.98        30.08        32.02        15.02        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.04        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3599 
       24.00         1.02        46.03        34.03         2.01        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  FAS MUTATED FAS WILD-TYPE 
         5.03          0.00 
  FAS MUTATED FAS WILD-TYPE 
        58.39        148.01 
  FAS MUTATED FAS WILD-TYPE 
       17.560        20.415 
[1] "5.0 - 58.4 (17.6)"  "0.0 - 148.0 (20.4)"
[1] "hr=" "2.1"
D830V2, continuous
D830V3, binary
               cls
clus              0   1
  FAS MUTATED     7   2
  FAS WILD-TYPE 359 117
[1] "tbl2"
               cls
clus            [,1] [,2]
  FAS MUTATED      7    2
  FAS WILD-TYPE  359  117
        clus
vv       FAS MUTATED FAS WILD-TYPE
  COLON            7           359
  RECTUM           2           117
[1] 2 2
[1] FALSE
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FAS MUTATED         1        0        0         6         0         0
  FAS WILD-TYPE      90        1       32       132        10         1
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  FAS MUTATED           0          0          1          0        0         1
  FAS WILD-TYPE        24         11         58         42       48        17
               vv
clus            STAGE IVB
  FAS MUTATED           0
  FAS WILD-TYPE         1
D830V4, multiclass
            clus
vv           FAS MUTATED FAS WILD-TYPE
  STAGE I              1            90
  STAGE IA             0             1
  STAGE II             0            32
  STAGE IIA            6           132
  STAGE IIB            0            10
  STAGE IIC            0             1
  STAGE III            0            24
  STAGE IIIA           0            11
  STAGE IIIB           1            58
  STAGE IIIC           0            42
  STAGE IV             0            48
  STAGE IVA            1            17
  STAGE IVB            0             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  FAS MUTATED     1   0   7   1
  FAS WILD-TYPE  16  92 322  49
D830V5, multiclass
    clus
vv   FAS MUTATED FAS WILD-TYPE
  T1           1            16
  T2           0            92
  T3           7           322
  T4           1            49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2
  FAS MUTATED     7   2   0
  FAS WILD-TYPE 280 111  87
D830V6, multiclass
    clus
vv   FAS MUTATED FAS WILD-TYPE
  N0           7           280
  N1           2           111
  N2           0            87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D830V7, binary
               cls
clus              0   1
  FAS MUTATED     7   1
  FAS WILD-TYPE 368  64
[1] "tbl2"
               cls
clus            [,1] [,2]
  FAS MUTATED      7    1
  FAS WILD-TYPE  368   64
   clus
vv  FAS MUTATED FAS WILD-TYPE
  0           7           368
  1           1            64
[1] 2 2
[1] FALSE
D830V8, binary
               cls
clus              0   1
  FAS MUTATED     2   7
  FAS WILD-TYPE 223 257
[1] "tbl2"
               cls
clus            [,1] [,2]
  FAS MUTATED      2    7
  FAS WILD-TYPE  223  257
        clus
vv       FAS MUTATED FAS WILD-TYPE
  FEMALE           2           223
  MALE             7           257
[1] 2 2
[1] FALSE
D830V9, binary
               cls
clus              0   1
  FAS MUTATED     8   0
  FAS WILD-TYPE 342  22
[1] "tbl2"
               cls
clus            [,1] [,2]
  FAS MUTATED      8    0
  FAS WILD-TYPE  342   22
     clus
vv    FAS MUTATED FAS WILD-TYPE
  NO            8           342
  YES           0            22
[1] 2 2
[1] FALSE
               vv
clus            COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  FAS MUTATED                      5                             2
  FAS WILD-TYPE                  310                            45
               vv
clus            RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  FAS MUTATED                       2                              0
  FAS WILD-TYPE                   104                             10
D830V10, multiclass
                                clus
vv                               FAS MUTATED FAS WILD-TYPE
  COLON ADENOCARCINOMA                     5           310
  COLON MUCINOUS ADENOCARCINOMA            2            45
  RECTAL ADENOCARCINOMA                    2           104
  RECTAL MUCINOUS ADENOCARCINOMA           0            10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             R0  R1  R2  RX
  FAS MUTATED     5   0   0   2
  FAS WILD-TYPE 340   4  31  23
D830V11, multiclass
    clus
vv   FAS MUTATED FAS WILD-TYPE
  R0           5           340
  R1           0             4
  R2           0            31
  RX           2            23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D830V12, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FAS MUTATED                                  0     2
  FAS WILD-TYPE                                1     9
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  FAS MUTATED                           0     5
  FAS WILD-TYPE                        22   221
D830V13, multiclass
                                  clus
vv                                 FAS MUTATED FAS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      2             9
  BLACK OR AFRICAN AMERICAN                  0            22
  WHITE                                      5           221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(831) Variable = PGM2 MUTATION ANALYSIS
D831V1, survival
                sevent
clus2              0   1
  PGM2 MUTATED     3   1
  PGM2 WILD-TYPE 375  92
  PGM2 MUTATED PGM2 WILD-TYPE 
             4            467 
  PGM2 MUTATED PGM2 WILD-TYPE 
             1             92 
$`PGM2 MUTATED`
TCGA-A6-6653 TCGA-CM-5344 TCGA-CM-5860 TCGA-DY-A1DF 
       24.39        22.03        32.02        24.13 

$`PGM2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
       25.08        25.18        24.16        21.76        24.69        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5349 
       37.02        25.02        13.02        29.06        22.98        30.08 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       57.24        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  PGM2 MUTATED PGM2 WILD-TYPE 
         22.03           0.00 
  PGM2 MUTATED PGM2 WILD-TYPE 
         32.02         148.01 
  PGM2 MUTATED PGM2 WILD-TYPE 
         24.26          20.05 
[1] "22.0 - 32.0 (24.3)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.4"
D831V2, continuous
D831V3, binary
                cls
clus               0   1
  PGM2 MUTATED     3   1
  PGM2 WILD-TYPE 363 118
[1] "tbl2"
                cls
clus             [,1] [,2]
  PGM2 MUTATED      3    1
  PGM2 WILD-TYPE  363  118
        clus
vv       PGM2 MUTATED PGM2 WILD-TYPE
  COLON             3            363
  RECTUM            1            118
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PGM2 MUTATED         1        0        0         1         0         0
  PGM2 WILD-TYPE      90        1       32       137        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PGM2 MUTATED           0          0          1          1        0         0
  PGM2 WILD-TYPE        24         11         58         41       48        18
                vv
clus             STAGE IVB
  PGM2 MUTATED           0
  PGM2 WILD-TYPE         1
D831V4, multiclass
            clus
vv           PGM2 MUTATED PGM2 WILD-TYPE
  STAGE I               1             90
  STAGE IA              0              1
  STAGE II              0             32
  STAGE IIA             1            137
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            1             58
  STAGE IIIC            1             41
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  PGM2 MUTATED     0   1   3   0
  PGM2 WILD-TYPE  17  91 326  50
D831V5, multiclass
    clus
vv   PGM2 MUTATED PGM2 WILD-TYPE
  T1            0             17
  T2            1             91
  T3            3            326
  T4            0             50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  PGM2 MUTATED     2   1   1
  PGM2 WILD-TYPE 285 112  86
D831V6, multiclass
    clus
vv   PGM2 MUTATED PGM2 WILD-TYPE
  N0            2            285
  N1            1            112
  N2            1             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D831V7, binary
                cls
clus               0   1
  PGM2 MUTATED     4   0
  PGM2 WILD-TYPE 371  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  PGM2 MUTATED      4    0
  PGM2 WILD-TYPE  371   65
   clus
vv  PGM2 MUTATED PGM2 WILD-TYPE
  0            4            371
  1            0             65
[1] 2 2
[1] FALSE
D831V8, binary
                cls
clus               0   1
  PGM2 MUTATED     2   2
  PGM2 WILD-TYPE 223 262
[1] "tbl2"
                cls
clus             [,1] [,2]
  PGM2 MUTATED      2    2
  PGM2 WILD-TYPE  223  262
        clus
vv       PGM2 MUTATED PGM2 WILD-TYPE
  FEMALE            2            223
  MALE              2            262
[1] 2 2
[1] FALSE
D831V9, binary
                cls
clus               0   1
  PGM2 MUTATED     3   0
  PGM2 WILD-TYPE 347  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  PGM2 MUTATED      3    0
  PGM2 WILD-TYPE  347   22
     clus
vv    PGM2 MUTATED PGM2 WILD-TYPE
  NO             3            347
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PGM2 MUTATED                      3                             0
  PGM2 WILD-TYPE                  312                            47
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PGM2 MUTATED                       1                              0
  PGM2 WILD-TYPE                   105                             10
D831V10, multiclass
                                clus
vv                               PGM2 MUTATED PGM2 WILD-TYPE
  COLON ADENOCARCINOMA                      3            312
  COLON MUCINOUS ADENOCARCINOMA             0             47
  RECTAL ADENOCARCINOMA                     1            105
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  PGM2 MUTATED     2   0   0   0
  PGM2 WILD-TYPE 343   4  31  25
D831V11, multiclass
[1] "Remove cluster labels:" "PGM2 MUTATED"          
clus
  PGM2 MUTATED PGM2 WILD-TYPE 
             2            403 
    TCGA-A6-2671     TCGA-A6-2672     TCGA-A6-2674     TCGA-A6-2676 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-A6-2677     TCGA-A6-2678     TCGA-A6-2683     TCGA-A6-3807 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-A6-3808     TCGA-A6-3809     TCGA-A6-3810     TCGA-A6-5657 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-A6-5659     TCGA-A6-5661     TCGA-A6-5665     TCGA-A6-6781 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-AA-3489     TCGA-AA-3492     TCGA-AA-3496     TCGA-AA-3502 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-AA-3510     TCGA-AA-3511     TCGA-AA-3514     TCGA-AA-3517 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-AA-3518     TCGA-AA-3519     TCGA-AA-3520     TCGA-AA-3521 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-AA-3522     TCGA-AA-3524     TCGA-AA-3525     TCGA-AA-3526 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-AA-3527     TCGA-AA-3529     TCGA-AA-3530     TCGA-AA-3531 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-AA-3532     TCGA-AA-3534     TCGA-AA-3538     TCGA-AA-3542 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-AA-3543     TCGA-AA-3544     TCGA-AA-3548     TCGA-AA-3549 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-AA-3552     TCGA-AA-3553     TCGA-AA-3554     TCGA-AA-3555 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-AA-3556     TCGA-AA-3558     TCGA-AA-3560     TCGA-AA-3561 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-AA-3562     TCGA-AA-3655     TCGA-AA-3660     TCGA-AA-3662 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-AA-3663     TCGA-AA-3664     TCGA-AA-3666     TCGA-AA-3667 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-AA-3672     TCGA-AA-3673     TCGA-AA-3678     TCGA-AA-3679 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-AA-3680     TCGA-AA-3681     TCGA-AA-3684     TCGA-AA-3685 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-AA-3688     TCGA-AA-3692     TCGA-AA-3693     TCGA-AA-3695 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-AA-3696     TCGA-AA-3697     TCGA-AA-3710     TCGA-AA-3712 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-AA-3713     TCGA-AA-3715     TCGA-AA-3811     TCGA-AA-3812 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-AA-3814     TCGA-AA-3815     TCGA-AA-3818     TCGA-AA-3819 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-AA-3821     TCGA-AA-3831     TCGA-AA-3833     TCGA-AA-3837 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-AA-3842     TCGA-AA-3844     TCGA-AA-3845     TCGA-AA-3846 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-AA-3848     TCGA-AA-3850     TCGA-AA-3851     TCGA-AA-3852 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-AA-3854     TCGA-AA-3855     TCGA-AA-3856     TCGA-AA-3858 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-AA-3860     TCGA-AA-3861     TCGA-AA-3864     TCGA-AA-3866 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-AA-3867     TCGA-AA-3869     TCGA-AA-3870     TCGA-AA-3872 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-AA-3875     TCGA-AA-3877     TCGA-AA-3930     TCGA-AA-3939 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-AA-3941     TCGA-AA-3947     TCGA-AA-3949     TCGA-AA-3950 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-AA-3952     TCGA-AA-3955     TCGA-AA-3956     TCGA-AA-3968 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-AA-3971     TCGA-AA-3972     TCGA-AA-3973     TCGA-AA-3975 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-AA-3976     TCGA-AA-3979     TCGA-AA-3984     TCGA-AA-3986 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-AA-3989     TCGA-AA-3994     TCGA-AA-A004     TCGA-AA-A00A 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-AA-A00D     TCGA-AA-A00E     TCGA-AA-A00F     TCGA-AA-A00J 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-AA-A00K     TCGA-AA-A00L     TCGA-AA-A00N     TCGA-AA-A00O 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-AA-A00Q     TCGA-AA-A00R     TCGA-AA-A00U     TCGA-AA-A00W 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-AA-A00Z     TCGA-AA-A010     TCGA-AA-A017     TCGA-AA-A01D 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-AA-A01F     TCGA-AA-A01G     TCGA-AA-A01I     TCGA-AA-A01K 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-AA-A01P     TCGA-AA-A01Q     TCGA-AA-A01R     TCGA-AA-A01S 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-AA-A01T     TCGA-AA-A01V     TCGA-AA-A01X     TCGA-AA-A01Z 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-AA-A022     TCGA-AA-A024     TCGA-AA-A029     TCGA-AA-A02F 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-AA-A02H     TCGA-AA-A02J     TCGA-AA-A02K     TCGA-AA-A02O 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-AA-A02W     TCGA-AA-A02Y     TCGA-AA-A03F     TCGA-AA-A03J 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-AD-5900     TCGA-AD-6548     TCGA-AD-6888     TCGA-AU-3779 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-AU-6004     TCGA-AY-4070     TCGA-AY-4071     TCGA-AY-5543 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-AY-6196     TCGA-AY-6197     TCGA-AY-6386     TCGA-AZ-4315 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-AZ-4681     TCGA-AZ-4682     TCGA-CA-5254     TCGA-CA-5255 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-CA-5796     TCGA-CA-5797     TCGA-CA-6715     TCGA-CA-6716 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-CA-6717     TCGA-CA-6718     TCGA-CA-6719     TCGA-CK-4947 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-CK-4948     TCGA-CK-4950     TCGA-CK-4952     TCGA-CK-5912 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-CK-5913     TCGA-CK-5914     TCGA-CK-5915     TCGA-CK-5916 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-CK-6746     TCGA-CK-6747     TCGA-CK-6748     TCGA-CK-6751 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-CM-4743     TCGA-CM-4744     TCGA-CM-4746     TCGA-CM-4747 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-CM-4752     TCGA-CM-5341     TCGA-CM-5348     TCGA-CM-5349 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-CM-5861     TCGA-CM-5862     TCGA-CM-5863     TCGA-CM-5864 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-CM-5868     TCGA-CM-6161     TCGA-CM-6162     TCGA-CM-6163 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-CM-6164     TCGA-CM-6165     TCGA-CM-6166     TCGA-CM-6167 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-CM-6168     TCGA-CM-6169     TCGA-CM-6170     TCGA-CM-6171 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-CM-6172     TCGA-CM-6674     TCGA-CM-6675     TCGA-CM-6676 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-CM-6677     TCGA-CM-6678     TCGA-CM-6679     TCGA-CM-6680 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-D5-5537     TCGA-D5-5538     TCGA-D5-5539     TCGA-D5-5540 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-D5-5541     TCGA-D5-6529     TCGA-D5-6532     TCGA-D5-6533 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-D5-6534     TCGA-D5-6535     TCGA-D5-6536     TCGA-D5-6537 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-D5-6538     TCGA-D5-6539     TCGA-D5-6540     TCGA-D5-6541 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-D5-6898     TCGA-D5-6920     TCGA-D5-6922     TCGA-D5-6923 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-D5-6924     TCGA-D5-6926     TCGA-D5-6927     TCGA-D5-6928 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-D5-6929     TCGA-D5-6930     TCGA-D5-6931     TCGA-D5-6932 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-D5-7000     TCGA-F4-6459     TCGA-F4-6460     TCGA-F4-6569 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-F4-6570     TCGA-F4-6703     TCGA-F4-6704     TCGA-F4-6805 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-F4-6806     TCGA-F4-6807     TCGA-F4-6808     TCGA-F4-6809 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-F4-6854     TCGA-F4-6855     TCGA-F4-6856     TCGA-G4-6293 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-G4-6299     TCGA-G4-6303     TCGA-G4-6304     TCGA-G4-6306 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-G4-6307     TCGA-G4-6309     TCGA-G4-6310     TCGA-G4-6315 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-G4-6317     TCGA-G4-6321     TCGA-G4-6323     TCGA-G4-6586 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-G4-6588     TCGA-G4-6625     TCGA-G4-6626     TCGA-G4-6628 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-AF-2687     TCGA-AF-2689     TCGA-AF-2691     TCGA-AF-2692 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-AF-3400     TCGA-AF-3913     TCGA-AF-4110     TCGA-AF-5654 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-AF-6655     TCGA-AG-3574     TCGA-AG-3575     TCGA-AG-3578 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-AG-3580     TCGA-AG-3581     TCGA-AG-3582     TCGA-AG-3583 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-AG-3584     TCGA-AG-3586     TCGA-AG-3587     TCGA-AG-3593 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-AG-3594     TCGA-AG-3598     TCGA-AG-3599     TCGA-AG-3600 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-AG-3601     TCGA-AG-3602     TCGA-AG-3605     TCGA-AG-3608 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-AG-3609     TCGA-AG-3611     TCGA-AG-3612     TCGA-AG-3726 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-AG-3727     TCGA-AG-3731     TCGA-AG-3732     TCGA-AG-3742 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-AG-3878     TCGA-AG-3882     TCGA-AG-3883     TCGA-AG-3885 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-AG-3887     TCGA-AG-3890     TCGA-AG-3892     TCGA-AG-3893 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-AG-3894     TCGA-AG-3896     TCGA-AG-3898     TCGA-AG-3901 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-AG-3902     TCGA-AG-3909     TCGA-AG-3999     TCGA-AG-4001 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-AG-4005     TCGA-AG-4007     TCGA-AG-4008     TCGA-AG-4015 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-AG-A002     TCGA-AG-A008     TCGA-AG-A00C     TCGA-AG-A00H 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-AG-A00Y     TCGA-AG-A011     TCGA-AG-A014     TCGA-AG-A015 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-AG-A016     TCGA-AG-A01L     TCGA-AG-A01W     TCGA-AG-A01Y 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-AG-A020     TCGA-AG-A025     TCGA-AG-A026     TCGA-AG-A02G 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-AG-A02N     TCGA-AG-A02X     TCGA-AG-A032     TCGA-AG-A036 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-AH-6549     TCGA-AH-6643     TCGA-CL-5917     TCGA-CL-5918 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-DC-5337     TCGA-DC-5869     TCGA-DC-6155     TCGA-DC-6157 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-DC-6158     TCGA-DC-6160     TCGA-DC-6681     TCGA-DC-6682 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-DC-6683     TCGA-DT-5265     TCGA-EF-5830     TCGA-EI-6506 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-EI-6507     TCGA-EI-6508     TCGA-EI-6510     TCGA-F5-6464 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-F5-6465     TCGA-F5-6571     TCGA-F5-6702     TCGA-F5-6812 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
    TCGA-F5-6813     TCGA-G5-6235     TCGA-G5-6641 
"PGM2 WILD-TYPE" "PGM2 WILD-TYPE" "PGM2 WILD-TYPE" 
D831V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PGM2 MUTATED                                  0     0
  PGM2 WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  PGM2 MUTATED                           0     4
  PGM2 WILD-TYPE                        22   222
D831V13, multiclass
                                  clus
vv                                 PGM2 MUTATED PGM2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       4            222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(832) Variable = STX16 MUTATION ANALYSIS
D832V1, survival
                 sevent
clus2               0   1
  STX16 MUTATED     5   2
  STX16 WILD-TYPE 373  91
  STX16 MUTATED STX16 WILD-TYPE 
              7             464 
  STX16 MUTATED STX16 WILD-TYPE 
              2              91 
$`STX16 MUTATED`
TCGA-A6-2676 TCGA-A6-5657 TCGA-AA-3679 TCGA-AA-3947 TCGA-CM-6162 TCGA-F4-6809 
       42.90        31.63        15.02        33.01        12.00        13.25 
TCGA-G4-6317 
       36.00 

$`STX16 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       30.44        29.19        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 
        5.03        15.02        15.02        17.03        15.02         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6854 TCGA-F4-6855 
       34.42        41.42        16.24        33.67         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6321 TCGA-G4-6323 
       55.04        85.48        63.62        61.91        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  STX16 MUTATED STX16 WILD-TYPE 
             12               0 
  STX16 MUTATED STX16 WILD-TYPE 
          42.90          148.01 
  STX16 MUTATED STX16 WILD-TYPE 
         31.630          20.155 
[1] "12.0 - 42.9 (31.6)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.5"
D832V2, continuous
D832V3, binary
                 cls
clus                0   1
  STX16 MUTATED     7   0
  STX16 WILD-TYPE 359 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STX16 MUTATED      7    0
  STX16 WILD-TYPE  359  119
        clus
vv       STX16 MUTATED STX16 WILD-TYPE
  COLON              7             359
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  STX16 MUTATED         0        0        0         0         2         0
  STX16 WILD-TYPE      91        1       32       138         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  STX16 MUTATED           0          0          2          1        1         1
  STX16 WILD-TYPE        24         11         57         41       47        17
                 vv
clus              STAGE IVB
  STX16 MUTATED           0
  STX16 WILD-TYPE         1
D832V4, multiclass
            clus
vv           STX16 MUTATED STX16 WILD-TYPE
  STAGE I                0              91
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              0             138
  STAGE IIB              2               8
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             2              57
  STAGE IIIC             1              41
  STAGE IV               1              47
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  STX16 MUTATED     0   0   5   2
  STX16 WILD-TYPE  17  92 324  48
D832V5, multiclass
    clus
vv   STX16 MUTATED STX16 WILD-TYPE
  T1             0              17
  T2             0              92
  T3             5             324
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  STX16 MUTATED     2   3   2
  STX16 WILD-TYPE 285 110  85
D832V6, multiclass
    clus
vv   STX16 MUTATED STX16 WILD-TYPE
  N0             2             285
  N1             3             110
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D832V7, binary
                 cls
clus                0   1
  STX16 MUTATED     4   2
  STX16 WILD-TYPE 371  63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STX16 MUTATED      4    2
  STX16 WILD-TYPE  371   63
   clus
vv  STX16 MUTATED STX16 WILD-TYPE
  0             4             371
  1             2              63
[1] 2 2
[1] FALSE
D832V8, binary
                 cls
clus                0   1
  STX16 MUTATED     5   2
  STX16 WILD-TYPE 220 262
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STX16 MUTATED      5    2
  STX16 WILD-TYPE  220  262
        clus
vv       STX16 MUTATED STX16 WILD-TYPE
  FEMALE             5             220
  MALE               2             262
[1] 2 2
[1] FALSE
D832V9, binary
                 cls
clus                0   1
  STX16 MUTATED     7   0
  STX16 WILD-TYPE 343  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STX16 MUTATED      7    0
  STX16 WILD-TYPE  343   22
     clus
vv    STX16 MUTATED STX16 WILD-TYPE
  NO              7             343
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  STX16 MUTATED                      5                             2
  STX16 WILD-TYPE                  310                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  STX16 MUTATED                       0                              0
  STX16 WILD-TYPE                   106                             10
D832V10, multiclass
                                clus
vv                               STX16 MUTATED STX16 WILD-TYPE
  COLON ADENOCARCINOMA                       5             310
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  STX16 MUTATED     6   0   1   0
  STX16 WILD-TYPE 339   4  30  25
D832V11, multiclass
    clus
vv   STX16 MUTATED STX16 WILD-TYPE
  R0             6             339
  R1             0               4
  R2             1              30
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D832V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  STX16 MUTATED                                  0     0
  STX16 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  STX16 MUTATED                           1     4
  STX16 WILD-TYPE                        21   222
D832V13, multiclass
                                  clus
vv                                 STX16 MUTATED STX16 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        4             222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(833) Variable = TJP1 MUTATION ANALYSIS
D833V1, survival
                sevent
clus2              0   1
  TJP1 MUTATED    15   6
  TJP1 WILD-TYPE 363  87
  TJP1 MUTATED TJP1 WILD-TYPE 
            21            450 
  TJP1 MUTATED TJP1 WILD-TYPE 
             6             87 
$`TJP1 MUTATED`
TCGA-A6-5666 TCGA-AA-3492 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3715 TCGA-AA-3864 
       32.71         3.02        78.08         6.97        19.04        53.00 
TCGA-AA-3977 TCGA-AA-A00N TCGA-AD-6895 TCGA-AZ-5403 TCGA-CA-6718 TCGA-D5-5539 
       25.02         4.01         0.72        62.79        10.06        19.59 
TCGA-D5-6538 TCGA-D5-6928 TCGA-DM-A1D6 TCGA-DM-A1HB TCGA-G4-6588 TCGA-AG-3892 
       17.13        11.64        49.91       135.65        26.17        13.02 
TCGA-AG-A002 TCGA-EI-6506 TCGA-F5-6813 
       20.98        20.55         0.69 

$`TJP1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        22.06        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 
       20.12        19.66        20.28         7.04         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 
       13.94        19.99        61.02         6.05        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       26.99        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       30.05        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
       56.55         0.79         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       15.12        17.85         4.80        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
        9.44         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D7 
      119.70        24.43        38.20       130.65        92.75        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 
       12.59       140.38         7.50        44.32       131.51       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        35.80        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       17.95        36.95        17.03        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
        0.49        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-G5-6235 TCGA-G5-6641 
       31.30        28.57        32.19         0.66        55.76        26.43 

  TJP1 MUTATED TJP1 WILD-TYPE 
          0.69           0.00 
  TJP1 MUTATED TJP1 WILD-TYPE 
        135.65         148.01 
  TJP1 MUTATED TJP1 WILD-TYPE 
        19.590         20.235 
[1] "0.7 - 135.7 (19.6)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.3"
D833V2, continuous
D833V3, binary
                cls
clus               0   1
  TJP1 MUTATED    18   4
  TJP1 WILD-TYPE 348 115
[1] "tbl2"
                cls
clus             [,1] [,2]
  TJP1 MUTATED     18    4
  TJP1 WILD-TYPE  348  115
        clus
vv       TJP1 MUTATED TJP1 WILD-TYPE
  COLON            18            348
  RECTUM            4            115
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TJP1 MUTATED         2        0        6         5         1         1
  TJP1 WILD-TYPE      89        1       26       133         9         0
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TJP1 MUTATED           0          1          2          2        0         0
  TJP1 WILD-TYPE        24         10         57         40       48        18
                vv
clus             STAGE IVB
  TJP1 MUTATED           0
  TJP1 WILD-TYPE         1
D833V4, multiclass
            clus
vv           TJP1 MUTATED TJP1 WILD-TYPE
  STAGE I               2             89
  STAGE IA              0              1
  STAGE II              6             26
  STAGE IIA             5            133
  STAGE IIB             1              9
  STAGE IIC             1              0
  STAGE III             0             24
  STAGE IIIA            1             10
  STAGE IIIB            2             57
  STAGE IIIC            2             40
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  TJP1 MUTATED     1   2  16   3
  TJP1 WILD-TYPE  16  90 313  47
D833V5, multiclass
    clus
vv   TJP1 MUTATED TJP1 WILD-TYPE
  T1            1             16
  T2            2             90
  T3           16            313
  T4            3             47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  TJP1 MUTATED    16   3   3
  TJP1 WILD-TYPE 271 110  84
D833V6, multiclass
    clus
vv   TJP1 MUTATED TJP1 WILD-TYPE
  N0           16            271
  N1            3            110
  N2            3             84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D833V7, binary
                cls
clus               0   1
  TJP1 MUTATED    18   0
  TJP1 WILD-TYPE 357  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  TJP1 MUTATED     18    0
  TJP1 WILD-TYPE  357   65
   clus
vv  TJP1 MUTATED TJP1 WILD-TYPE
  0           18            357
  1            0             65
[1] 2 2
[1] FALSE
D833V8, binary
                cls
clus               0   1
  TJP1 MUTATED     6  16
  TJP1 WILD-TYPE 219 248
[1] "tbl2"
                cls
clus             [,1] [,2]
  TJP1 MUTATED      6   16
  TJP1 WILD-TYPE  219  248
        clus
vv       TJP1 MUTATED TJP1 WILD-TYPE
  FEMALE            6            219
  MALE             16            248
[1] 2 2
[1] FALSE
D833V9, binary
                cls
clus               0   1
  TJP1 MUTATED    16   0
  TJP1 WILD-TYPE 334  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  TJP1 MUTATED     16    0
  TJP1 WILD-TYPE  334   22
     clus
vv    TJP1 MUTATED TJP1 WILD-TYPE
  NO            16            334
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  TJP1 MUTATED                     12                             5
  TJP1 WILD-TYPE                  303                            42
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  TJP1 MUTATED                       4                              0
  TJP1 WILD-TYPE                   102                             10
D833V10, multiclass
                                clus
vv                               TJP1 MUTATED TJP1 WILD-TYPE
  COLON ADENOCARCINOMA                     12            303
  COLON MUCINOUS ADENOCARCINOMA             5             42
  RECTAL ADENOCARCINOMA                     4            102
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  TJP1 MUTATED    15   0   0   1
  TJP1 WILD-TYPE 330   4  31  24
D833V11, multiclass
    clus
vv   TJP1 MUTATED TJP1 WILD-TYPE
  R0           15            330
  R1            0              4
  R2            0             31
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D833V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TJP1 MUTATED                                  0     1
  TJP1 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  TJP1 MUTATED                           0    12
  TJP1 WILD-TYPE                        22   214
D833V13, multiclass
                                  clus
vv                                 TJP1 MUTATED TJP1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                      12            214
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(834) Variable = INTS3 MUTATION ANALYSIS
D834V1, survival
                 sevent
clus2               0   1
  INTS3 MUTATED     7   0
  INTS3 WILD-TYPE 371  93
  INTS3 MUTATED INTS3 WILD-TYPE 
              7             464 
  INTS3 MUTATED INTS3 WILD-TYPE 
              0              93 
$`INTS3 MUTATED`
TCGA-AA-3525 TCGA-AA-3947 TCGA-AA-A00J TCGA-CM-5864 TCGA-CM-6171 TCGA-G4-6317 
        8.05        33.01        18.05        15.02        14.04        36.00 
TCGA-AH-6547 
        1.45 

$`INTS3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
        2.01        12.99        24.00        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       19.00        30.02        34.03        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
       15.02         5.03        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       13.02        15.02        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6321 
       44.68        55.04        85.48        63.62        61.91        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6549 
       61.97        41.00        38.04       117.11        38.56        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  INTS3 MUTATED INTS3 WILD-TYPE 
           1.45            0.00 
  INTS3 MUTATED INTS3 WILD-TYPE 
          36.00          148.01 
  INTS3 MUTATED INTS3 WILD-TYPE 
         15.020          20.415 
[1] "1.4 - 36.0 (15.0)"  "0.0 - 148.0 (20.4)"
[1] "hr="     "3300000"
D834V2, continuous
D834V3, binary
                 cls
clus                0   1
  INTS3 MUTATED     7   1
  INTS3 WILD-TYPE 359 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  INTS3 MUTATED      7    1
  INTS3 WILD-TYPE  359  118
        clus
vv       INTS3 MUTATED INTS3 WILD-TYPE
  COLON              7             359
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  INTS3 MUTATED         3        0        0         0         1         0
  INTS3 WILD-TYPE      88        1       32       138         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  INTS3 MUTATED           0          0          2          1        0         0
  INTS3 WILD-TYPE        24         11         57         41       48        18
                 vv
clus              STAGE IVB
  INTS3 MUTATED           0
  INTS3 WILD-TYPE         1
D834V4, multiclass
            clus
vv           INTS3 MUTATED INTS3 WILD-TYPE
  STAGE I                3              88
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              0             138
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             2              57
  STAGE IIIC             1              41
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  INTS3 MUTATED     0   3   3   2
  INTS3 WILD-TYPE  17  89 326  48
D834V5, multiclass
    clus
vv   INTS3 MUTATED INTS3 WILD-TYPE
  T1             0              17
  T2             3              89
  T3             3             326
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  INTS3 MUTATED     5   2   1
  INTS3 WILD-TYPE 282 111  86
D834V6, multiclass
    clus
vv   INTS3 MUTATED INTS3 WILD-TYPE
  N0             5             282
  N1             2             111
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D834V7, binary
                 cls
clus                0   1
  INTS3 MUTATED     5   0
  INTS3 WILD-TYPE 370  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  INTS3 MUTATED      5    0
  INTS3 WILD-TYPE  370   65
   clus
vv  INTS3 MUTATED INTS3 WILD-TYPE
  0             5             370
  1             0              65
[1] 2 2
[1] FALSE
D834V8, binary
                 cls
clus                0   1
  INTS3 MUTATED     4   4
  INTS3 WILD-TYPE 221 260
[1] "tbl2"
                 cls
clus              [,1] [,2]
  INTS3 MUTATED      4    4
  INTS3 WILD-TYPE  221  260
        clus
vv       INTS3 MUTATED INTS3 WILD-TYPE
  FEMALE             4             221
  MALE               4             260
[1] 2 2
[1] FALSE
D834V9, binary
                 cls
clus                0   1
  INTS3 MUTATED     6   0
  INTS3 WILD-TYPE 344  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  INTS3 MUTATED      6    0
  INTS3 WILD-TYPE  344   22
     clus
vv    INTS3 MUTATED INTS3 WILD-TYPE
  NO              6             344
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  INTS3 MUTATED                      5                             2
  INTS3 WILD-TYPE                  310                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  INTS3 MUTATED                       1                              0
  INTS3 WILD-TYPE                   105                             10
D834V10, multiclass
                                clus
vv                               INTS3 MUTATED INTS3 WILD-TYPE
  COLON ADENOCARCINOMA                       5             310
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  INTS3 MUTATED     6   0   0   1
  INTS3 WILD-TYPE 339   4  31  24
D834V11, multiclass
    clus
vv   INTS3 MUTATED INTS3 WILD-TYPE
  R0             6             339
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D834V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  INTS3 MUTATED                                  0     0
  INTS3 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  INTS3 MUTATED                           0     5
  INTS3 WILD-TYPE                        22   221
D834V13, multiclass
                                  clus
vv                                 INTS3 MUTATED INTS3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        5             221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(835) Variable = DBN1 MUTATION ANALYSIS
D835V1, survival
                sevent
clus2              0   1
  DBN1 MUTATED    11   2
  DBN1 WILD-TYPE 367  91
  DBN1 MUTATED DBN1 WILD-TYPE 
            13            458 
  DBN1 MUTATED DBN1 WILD-TYPE 
             2             91 
$`DBN1 MUTATED`
TCGA-A6-5662 TCGA-AA-3713 TCGA-AA-3950 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-D5-6533 
       23.61        19.04        24.00        49.41        12.10         1.32 
TCGA-D5-6540 TCGA-D5-6924 TCGA-D5-7000 TCGA-AG-A002 TCGA-EI-6507 TCGA-EI-6510 
       16.14        14.30        10.26        20.98        19.96        18.28 
TCGA-G5-6235 
       55.76 

$`DBN1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        33.53        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 
       12.99        24.00        33.01        26.01         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6603 
       22.36        62.79        88.21         6.77       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6534 
       19.59        56.09        55.92        20.19        18.25        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 
       15.12        17.85         4.80        17.13        12.49        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 TCGA-D5-6927 
        1.48         3.68         4.41        12.43         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-DM-A0X9 
       11.64         4.80         1.51        12.00        11.38       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6508 
       24.13        51.48        32.61         0.49        20.55        20.91 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6641 
        0.69        26.43 

  DBN1 MUTATED DBN1 WILD-TYPE 
          1.32           0.00 
  DBN1 MUTATED DBN1 WILD-TYPE 
         55.76         148.01 
  DBN1 MUTATED DBN1 WILD-TYPE 
        19.040         20.415 
[1] "1.3 - 55.8 (19.0)"  "0.0 - 148.0 (20.4)"
[1] "hr=" "1.1"
D835V2, continuous
D835V3, binary
                cls
clus               0   1
  DBN1 MUTATED     9   4
  DBN1 WILD-TYPE 357 115
[1] "tbl2"
                cls
clus             [,1] [,2]
  DBN1 MUTATED      9    4
  DBN1 WILD-TYPE  357  115
        clus
vv       DBN1 MUTATED DBN1 WILD-TYPE
  COLON             9            357
  RECTUM            4            115
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DBN1 MUTATED         3        0        1         3         0         0
  DBN1 WILD-TYPE      88        1       31       135        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DBN1 MUTATED           0          0          2          0        2         2
  DBN1 WILD-TYPE        24         11         57         42       46        16
                vv
clus             STAGE IVB
  DBN1 MUTATED           0
  DBN1 WILD-TYPE         1
D835V4, multiclass
            clus
vv           DBN1 MUTATED DBN1 WILD-TYPE
  STAGE I               3             88
  STAGE IA              0              1
  STAGE II              1             31
  STAGE IIA             3            135
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            2             57
  STAGE IIIC            0             42
  STAGE IV              2             46
  STAGE IVA             2             16
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  DBN1 MUTATED     0   4   7   2
  DBN1 WILD-TYPE  17  88 322  48
D835V5, multiclass
    clus
vv   DBN1 MUTATED DBN1 WILD-TYPE
  T1            0             17
  T2            4             88
  T3            7            322
  T4            2             48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  DBN1 MUTATED    10   2   1
  DBN1 WILD-TYPE 277 111  86
D835V6, multiclass
    clus
vv   DBN1 MUTATED DBN1 WILD-TYPE
  N0           10            277
  N1            2            111
  N2            1             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D835V7, binary
                cls
clus               0   1
  DBN1 MUTATED     7   3
  DBN1 WILD-TYPE 368  62
[1] "tbl2"
                cls
clus             [,1] [,2]
  DBN1 MUTATED      7    3
  DBN1 WILD-TYPE  368   62
   clus
vv  DBN1 MUTATED DBN1 WILD-TYPE
  0            7            368
  1            3             62
[1] 2 2
[1] FALSE
D835V8, binary
                cls
clus               0   1
  DBN1 MUTATED     5   8
  DBN1 WILD-TYPE 220 256
[1] "tbl2"
                cls
clus             [,1] [,2]
  DBN1 MUTATED      5    8
  DBN1 WILD-TYPE  220  256
        clus
vv       DBN1 MUTATED DBN1 WILD-TYPE
  FEMALE            5            220
  MALE              8            256
[1] 2 2
[1] FALSE
D835V9, binary
                cls
clus               0   1
  DBN1 MUTATED    10   1
  DBN1 WILD-TYPE 340  21
[1] "tbl2"
                cls
clus             [,1] [,2]
  DBN1 MUTATED     10    1
  DBN1 WILD-TYPE  340   21
     clus
vv    DBN1 MUTATED DBN1 WILD-TYPE
  NO            10            340
  YES            1             21
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  DBN1 MUTATED                      6                             3
  DBN1 WILD-TYPE                  309                            44
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  DBN1 MUTATED                       4                              0
  DBN1 WILD-TYPE                   102                             10
D835V10, multiclass
                                clus
vv                               DBN1 MUTATED DBN1 WILD-TYPE
  COLON ADENOCARCINOMA                      6            309
  COLON MUCINOUS ADENOCARCINOMA             3             44
  RECTAL ADENOCARCINOMA                     4            102
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  DBN1 MUTATED     8   1   1   0
  DBN1 WILD-TYPE 337   3  30  25
D835V11, multiclass
    clus
vv   DBN1 MUTATED DBN1 WILD-TYPE
  R0            8            337
  R1            1              3
  R2            1             30
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D835V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DBN1 MUTATED                                  0     0
  DBN1 WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  DBN1 MUTATED                           1     9
  DBN1 WILD-TYPE                        21   217
D835V13, multiclass
                                  clus
vv                                 DBN1 MUTATED DBN1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                       9            217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(836) Variable = MCCC1 MUTATION ANALYSIS
D836V1, survival
                 sevent
clus2               0   1
  MCCC1 MUTATED    15   3
  MCCC1 WILD-TYPE 363  90
  MCCC1 MUTATED MCCC1 WILD-TYPE 
             18             453 
  MCCC1 MUTATED MCCC1 WILD-TYPE 
              3              90 
$`MCCC1 MUTATED`
TCGA-A6-2676 TCGA-A6-6652 TCGA-AA-3555 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3877 
       42.90        24.69        29.95        78.08        54.02        31.00 
TCGA-AA-A00E TCGA-AA-A010 TCGA-AD-6890 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-AZ-6608 
       30.02        34.98         0.79        58.39        49.41         1.61 
TCGA-CM-4743 TCGA-G4-6293 TCGA-G4-6304 TCGA-G4-6307 TCGA-AG-A002 TCGA-DY-A0XA 
       23.05       133.18        53.62        55.04        20.98       126.44 

$`MCCC1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       25.18        24.16        21.76        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       24.00        17.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3666 TCGA-AA-3667 
       19.99        61.02         6.05         6.97         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       18.05         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       13.94        38.04        19.00        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
       56.55         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        88.21         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 
        9.99        21.14        82.95         1.91       124.27        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       74.56        65.85        44.68        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.03         5.29        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  MCCC1 MUTATED MCCC1 WILD-TYPE 
           0.79            0.00 
  MCCC1 MUTATED MCCC1 WILD-TYPE 
         133.18          148.01 
  MCCC1 MUTATED MCCC1 WILD-TYPE 
          38.94           19.99 
[1] "0.8 - 133.2 (38.9)" "0.0 - 148.0 (20.0)"
[1] "hr=" "2.1"
D836V2, continuous
D836V3, binary
                 cls
clus                0   1
  MCCC1 MUTATED    17   2
  MCCC1 WILD-TYPE 349 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MCCC1 MUTATED     17    2
  MCCC1 WILD-TYPE  349  117
        clus
vv       MCCC1 MUTATED MCCC1 WILD-TYPE
  COLON             17             349
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MCCC1 MUTATED         2        0        4         5         3         0
  MCCC1 WILD-TYPE      89        1       28       133         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MCCC1 MUTATED           1          1          1          0        0         1
  MCCC1 WILD-TYPE        23         10         58         42       48        17
                 vv
clus              STAGE IVB
  MCCC1 MUTATED           0
  MCCC1 WILD-TYPE         1
D836V4, multiclass
            clus
vv           MCCC1 MUTATED MCCC1 WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               4              28
  STAGE IIA              5             133
  STAGE IIB              3               7
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             1              10
  STAGE IIIB             1              58
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  MCCC1 MUTATED     2   2  11   4
  MCCC1 WILD-TYPE  15  90 318  46
D836V5, multiclass
    clus
vv   MCCC1 MUTATED MCCC1 WILD-TYPE
  T1             2              15
  T2             2              90
  T3            11             318
  T4             4              46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  MCCC1 MUTATED    16   3   0
  MCCC1 WILD-TYPE 271 110  87
D836V6, multiclass
    clus
vv   MCCC1 MUTATED MCCC1 WILD-TYPE
  N0            16             271
  N1             3             110
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D836V7, binary
                 cls
clus                0   1
  MCCC1 MUTATED    16   1
  MCCC1 WILD-TYPE 359  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MCCC1 MUTATED     16    1
  MCCC1 WILD-TYPE  359   64
   clus
vv  MCCC1 MUTATED MCCC1 WILD-TYPE
  0            16             359
  1             1              64
[1] 2 2
[1] FALSE
D836V8, binary
                 cls
clus                0   1
  MCCC1 MUTATED    13   6
  MCCC1 WILD-TYPE 212 258
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MCCC1 MUTATED     13    6
  MCCC1 WILD-TYPE  212  258
        clus
vv       MCCC1 MUTATED MCCC1 WILD-TYPE
  FEMALE            13             212
  MALE               6             258
[1] 2 2
[1] FALSE
D836V9, binary
                 cls
clus                0   1
  MCCC1 MUTATED    16   0
  MCCC1 WILD-TYPE 334  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MCCC1 MUTATED     16    0
  MCCC1 WILD-TYPE  334   22
     clus
vv    MCCC1 MUTATED MCCC1 WILD-TYPE
  NO             16             334
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MCCC1 MUTATED                     15                             2
  MCCC1 WILD-TYPE                  300                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MCCC1 MUTATED                       2                              0
  MCCC1 WILD-TYPE                   104                             10
D836V10, multiclass
                                clus
vv                               MCCC1 MUTATED MCCC1 WILD-TYPE
  COLON ADENOCARCINOMA                      15             300
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  MCCC1 MUTATED    14   0   0   0
  MCCC1 WILD-TYPE 331   4  31  25
D836V11, multiclass
    clus
vv   MCCC1 MUTATED MCCC1 WILD-TYPE
  R0            14             331
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D836V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MCCC1 MUTATED                                  0     0
  MCCC1 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  MCCC1 MUTATED                           1    10
  MCCC1 WILD-TYPE                        21   216
D836V13, multiclass
                                  clus
vv                                 MCCC1 MUTATED MCCC1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                       10             216
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(837) Variable = ETF1 MUTATION ANALYSIS
D837V1, survival
                sevent
clus2              0   1
  ETF1 MUTATED    11   1
  ETF1 WILD-TYPE 367  92
  ETF1 MUTATED ETF1 WILD-TYPE 
            12            459 
  ETF1 MUTATED ETF1 WILD-TYPE 
             1             92 
$`ETF1 MUTATED`
TCGA-A6-5665 TCGA-A6-6654 TCGA-AA-3663 TCGA-AA-3672 TCGA-AA-3966 TCGA-CA-5797 
       22.06        23.87         6.97         0.92         2.01         3.29 
TCGA-CA-6716 TCGA-CM-6168 TCGA-F4-6809 TCGA-G4-6586 TCGA-AG-3892 TCGA-AG-A002 
       12.20        12.99        13.25        35.80        13.02        20.98 

$`ETF1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 
       25.18        24.16        21.76        24.69        24.39        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
        2.01        14.01        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.25         0.07        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       21.99        14.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       33.67         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 
       61.91        36.00        22.09        13.78        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 
        1.02        17.95        36.95        17.03        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  ETF1 MUTATED ETF1 WILD-TYPE 
          0.92           0.00 
  ETF1 MUTATED ETF1 WILD-TYPE 
         35.80         148.01 
  ETF1 MUTATED ETF1 WILD-TYPE 
        13.005         20.550 
[1] "0.9 - 35.8 (13.0)"  "0.0 - 148.0 (20.6)"
[1] "hr=" "1.3"
D837V2, continuous
D837V3, binary
                cls
clus               0   1
  ETF1 MUTATED    10   2
  ETF1 WILD-TYPE 356 117
[1] "tbl2"
                cls
clus             [,1] [,2]
  ETF1 MUTATED     10    2
  ETF1 WILD-TYPE  356  117
        clus
vv       ETF1 MUTATED ETF1 WILD-TYPE
  COLON            10            356
  RECTUM            2            117
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ETF1 MUTATED         2        0        1         6         0         0
  ETF1 WILD-TYPE      89        1       31       132        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ETF1 MUTATED           1          0          1          0        0         1
  ETF1 WILD-TYPE        23         11         58         42       48        17
                vv
clus             STAGE IVB
  ETF1 MUTATED           0
  ETF1 WILD-TYPE         1
D837V4, multiclass
            clus
vv           ETF1 MUTATED ETF1 WILD-TYPE
  STAGE I               2             89
  STAGE IA              0              1
  STAGE II              1             31
  STAGE IIA             6            132
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             1             23
  STAGE IIIA            0             11
  STAGE IIIB            1             58
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             1             17
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  ETF1 MUTATED     1   1  10   0
  ETF1 WILD-TYPE  16  91 319  50
D837V5, multiclass
    clus
vv   ETF1 MUTATED ETF1 WILD-TYPE
  T1            1             16
  T2            1             91
  T3           10            319
  T4            0             50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  ETF1 MUTATED     9   3   0
  ETF1 WILD-TYPE 278 110  87
D837V6, multiclass
    clus
vv   ETF1 MUTATED ETF1 WILD-TYPE
  N0            9            278
  N1            3            110
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D837V7, binary
                cls
clus               0   1
  ETF1 MUTATED    11   1
  ETF1 WILD-TYPE 364  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  ETF1 MUTATED     11    1
  ETF1 WILD-TYPE  364   64
   clus
vv  ETF1 MUTATED ETF1 WILD-TYPE
  0           11            364
  1            1             64
[1] 2 2
[1] FALSE
D837V8, binary
                cls
clus               0   1
  ETF1 MUTATED     8   4
  ETF1 WILD-TYPE 217 260
[1] "tbl2"
                cls
clus             [,1] [,2]
  ETF1 MUTATED      8    4
  ETF1 WILD-TYPE  217  260
        clus
vv       ETF1 MUTATED ETF1 WILD-TYPE
  FEMALE            8            217
  MALE              4            260
[1] 2 2
[1] FALSE
D837V9, binary
                cls
clus               0   1
  ETF1 MUTATED    11   0
  ETF1 WILD-TYPE 339  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  ETF1 MUTATED     11    0
  ETF1 WILD-TYPE  339   22
     clus
vv    ETF1 MUTATED ETF1 WILD-TYPE
  NO            11            339
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ETF1 MUTATED                      9                             1
  ETF1 WILD-TYPE                  306                            46
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ETF1 MUTATED                       2                              0
  ETF1 WILD-TYPE                   104                             10
D837V10, multiclass
                                clus
vv                               ETF1 MUTATED ETF1 WILD-TYPE
  COLON ADENOCARCINOMA                      9            306
  COLON MUCINOUS ADENOCARCINOMA             1             46
  RECTAL ADENOCARCINOMA                     2            104
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  ETF1 MUTATED     9   0   0   1
  ETF1 WILD-TYPE 336   4  31  24
D837V11, multiclass
    clus
vv   ETF1 MUTATED ETF1 WILD-TYPE
  R0            9            336
  R1            0              4
  R2            0             31
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D837V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ETF1 MUTATED                                  0     2
  ETF1 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  ETF1 MUTATED                           1     4
  ETF1 WILD-TYPE                        21   222
D837V13, multiclass
                                  clus
vv                                 ETF1 MUTATED ETF1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              9
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                       4            222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(838) Variable = ALDOB MUTATION ANALYSIS
D838V1, survival
                 sevent
clus2               0   1
  ALDOB MUTATED    12   3
  ALDOB WILD-TYPE 366  90
  ALDOB MUTATED ALDOB WILD-TYPE 
             15             456 
  ALDOB MUTATED ALDOB WILD-TYPE 
              3              90 
$`ALDOB MUTATED`
TCGA-A6-2676 TCGA-A6-6141 TCGA-AA-3821 TCGA-AA-3845 TCGA-AA-3949 TCGA-AA-A01Q 
       42.90         8.38         1.02         0.00        26.01         1.02 
TCGA-AD-6895 TCGA-AZ-6599 TCGA-CK-4948 TCGA-CK-6747 TCGA-D5-6534 TCGA-D5-6540 
        0.72         6.77       148.01        82.95        43.27        16.14 
TCGA-D5-6928 TCGA-G4-6586 TCGA-G4-6628 
       11.64        35.80        79.69 

$`ALDOB WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 
       22.06        32.71        27.09        22.52        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 
       35.05        33.04         0.99        25.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       38.99        37.02        14.93        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       33.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       21.37        15.52        56.55         0.79         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 
       12.20        12.76        10.06        14.30        17.56        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6748 
       15.62        49.08        51.32         9.99        21.14         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
        1.32        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.04         9.44         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       26.17        91.79        46.75        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  ALDOB MUTATED ALDOB WILD-TYPE 
              0               0 
  ALDOB MUTATED ALDOB WILD-TYPE 
         148.01          140.38 
  ALDOB MUTATED ALDOB WILD-TYPE 
         16.140          20.235 
[1] "0.0 - 148.0 (16.1)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.1"
D838V2, continuous
D838V3, binary
                 cls
clus                0   1
  ALDOB MUTATED    15   0
  ALDOB WILD-TYPE 351 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ALDOB MUTATED     15    0
  ALDOB WILD-TYPE  351  119
        clus
vv       ALDOB MUTATED ALDOB WILD-TYPE
  COLON             15             351
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ALDOB MUTATED         4        0        1         6         1         0
  ALDOB WILD-TYPE      87        1       31       132         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ALDOB MUTATED           1          0          1          0        0         0
  ALDOB WILD-TYPE        23         11         58         42       48        18
                 vv
clus              STAGE IVB
  ALDOB MUTATED           0
  ALDOB WILD-TYPE         1
D838V4, multiclass
            clus
vv           ALDOB MUTATED ALDOB WILD-TYPE
  STAGE I                4              87
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              6             132
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ALDOB MUTATED     0   4  10   1
  ALDOB WILD-TYPE  17  88 319  49
D838V5, multiclass
    clus
vv   ALDOB MUTATED ALDOB WILD-TYPE
  T1             0              17
  T2             4              88
  T3            10             319
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  ALDOB MUTATED    12   3   0
  ALDOB WILD-TYPE 275 110  87
D838V6, multiclass
    clus
vv   ALDOB MUTATED ALDOB WILD-TYPE
  N0            12             275
  N1             3             110
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D838V7, binary
                 cls
clus                0   1
  ALDOB MUTATED    12   0
  ALDOB WILD-TYPE 363  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ALDOB MUTATED     12    0
  ALDOB WILD-TYPE  363   65
   clus
vv  ALDOB MUTATED ALDOB WILD-TYPE
  0            12             363
  1             0              65
[1] 2 2
[1] FALSE
D838V8, binary
                 cls
clus                0   1
  ALDOB MUTATED     9   6
  ALDOB WILD-TYPE 216 258
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ALDOB MUTATED      9    6
  ALDOB WILD-TYPE  216  258
        clus
vv       ALDOB MUTATED ALDOB WILD-TYPE
  FEMALE             9             216
  MALE               6             258
[1] 2 2
[1] FALSE
D838V9, binary
                 cls
clus                0   1
  ALDOB MUTATED    12   0
  ALDOB WILD-TYPE 338  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ALDOB MUTATED     12    0
  ALDOB WILD-TYPE  338   22
     clus
vv    ALDOB MUTATED ALDOB WILD-TYPE
  NO             12             338
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ALDOB MUTATED                     10                             5
  ALDOB WILD-TYPE                  305                            42
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ALDOB MUTATED                       0                              0
  ALDOB WILD-TYPE                   106                             10
D838V10, multiclass
                                clus
vv                               ALDOB MUTATED ALDOB WILD-TYPE
  COLON ADENOCARCINOMA                      10             305
  COLON MUCINOUS ADENOCARCINOMA              5              42
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  ALDOB MUTATED    11   0   0   1
  ALDOB WILD-TYPE 334   4  31  24
D838V11, multiclass
    clus
vv   ALDOB MUTATED ALDOB WILD-TYPE
  R0            11             334
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D838V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ALDOB MUTATED                                  0     0
  ALDOB WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ALDOB MUTATED                           1    10
  ALDOB WILD-TYPE                        21   216
D838V13, multiclass
                                  clus
vv                                 ALDOB MUTATED ALDOB WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                       10             216
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(839) Variable = TFEC MUTATION ANALYSIS
D839V1, survival
                sevent
clus2              0   1
  TFEC MUTATED    11   1
  TFEC WILD-TYPE 367  92
  TFEC MUTATED TFEC WILD-TYPE 
            12            459 
  TFEC MUTATED TFEC WILD-TYPE 
             1             92 
$`TFEC MUTATED`
TCGA-A6-6137 TCGA-AA-3510 TCGA-AA-3977 TCGA-AA-A01K TCGA-AZ-4315 TCGA-CA-5796 
       27.09        63.98        25.02        31.00        58.39         3.25 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-6171 TCGA-D5-6535 TCGA-AG-A02N TCGA-EI-6506 
       12.76        10.06        14.04        15.12        61.97        20.55 

$`TFEC WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        22.06        32.71        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        3.29         0.07        12.20        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 
       14.99        12.99        13.02        15.02        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       18.25         1.32        43.27        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
        1.94        38.96        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       51.48        32.61         0.49        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  TFEC MUTATED TFEC WILD-TYPE 
          3.25           0.00 
  TFEC MUTATED TFEC WILD-TYPE 
         63.98         148.01 
  TFEC MUTATED TFEC WILD-TYPE 
        22.785         20.120 
[1] "3.2 - 64.0 (22.8)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "2.8"
D839V2, continuous
D839V3, binary
                cls
clus               0   1
  TFEC MUTATED    10   2
  TFEC WILD-TYPE 356 117
[1] "tbl2"
                cls
clus             [,1] [,2]
  TFEC MUTATED     10    2
  TFEC WILD-TYPE  356  117
        clus
vv       TFEC MUTATED TFEC WILD-TYPE
  COLON            10            356
  RECTUM            2            117
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TFEC MUTATED         1        0        2         5         0         0
  TFEC WILD-TYPE      90        1       30       133        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TFEC MUTATED           0          0          2          1        0         0
  TFEC WILD-TYPE        24         11         57         41       48        18
                vv
clus             STAGE IVB
  TFEC MUTATED           0
  TFEC WILD-TYPE         1
D839V4, multiclass
            clus
vv           TFEC MUTATED TFEC WILD-TYPE
  STAGE I               1             90
  STAGE IA              0              1
  STAGE II              2             30
  STAGE IIA             5            133
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            2             57
  STAGE IIIC            1             41
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  TFEC MUTATED     0   2  10   0
  TFEC WILD-TYPE  17  90 319  50
D839V5, multiclass
    clus
vv   TFEC MUTATED TFEC WILD-TYPE
  T1            0             17
  T2            2             90
  T3           10            319
  T4            0             50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  TFEC MUTATED     9   2   1
  TFEC WILD-TYPE 278 111  86
D839V6, multiclass
    clus
vv   TFEC MUTATED TFEC WILD-TYPE
  N0            9            278
  N1            2            111
  N2            1             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D839V7, binary
                cls
clus               0   1
  TFEC MUTATED    10   0
  TFEC WILD-TYPE 365  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  TFEC MUTATED     10    0
  TFEC WILD-TYPE  365   65
   clus
vv  TFEC MUTATED TFEC WILD-TYPE
  0           10            365
  1            0             65
[1] 2 2
[1] FALSE
D839V8, binary
                cls
clus               0   1
  TFEC MUTATED     5   7
  TFEC WILD-TYPE 220 257
[1] "tbl2"
                cls
clus             [,1] [,2]
  TFEC MUTATED      5    7
  TFEC WILD-TYPE  220  257
        clus
vv       TFEC MUTATED TFEC WILD-TYPE
  FEMALE            5            220
  MALE              7            257
[1] 2 2
[1] FALSE
D839V9, binary
                cls
clus               0   1
  TFEC MUTATED    11   0
  TFEC WILD-TYPE 339  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  TFEC MUTATED     11    0
  TFEC WILD-TYPE  339   22
     clus
vv    TFEC MUTATED TFEC WILD-TYPE
  NO            11            339
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  TFEC MUTATED                      8                             2
  TFEC WILD-TYPE                  307                            45
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  TFEC MUTATED                       2                              0
  TFEC WILD-TYPE                   104                             10
D839V10, multiclass
                                clus
vv                               TFEC MUTATED TFEC WILD-TYPE
  COLON ADENOCARCINOMA                      8            307
  COLON MUCINOUS ADENOCARCINOMA             2             45
  RECTAL ADENOCARCINOMA                     2            104
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  TFEC MUTATED     7   0   0   3
  TFEC WILD-TYPE 338   4  31  22
D839V11, multiclass
    clus
vv   TFEC MUTATED TFEC WILD-TYPE
  R0            7            338
  R1            0              4
  R2            0             31
  RX            3             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D839V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TFEC MUTATED                                  0     3
  TFEC WILD-TYPE                                1     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  TFEC MUTATED                           0     5
  TFEC WILD-TYPE                        22   221
D839V13, multiclass
                                  clus
vv                                 TFEC MUTATED TFEC WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       3              8
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       5            221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(840) Variable = NFATC3 MUTATION ANALYSIS
D840V1, survival
                  sevent
clus2                0   1
  NFATC3 MUTATED    11   1
  NFATC3 WILD-TYPE 367  92
  NFATC3 MUTATED NFATC3 WILD-TYPE 
              12              459 
  NFATC3 MUTATED NFATC3 WILD-TYPE 
               1               92 
$`NFATC3 MUTATED`
TCGA-A6-6653 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-A010 TCGA-CA-6716 TCGA-CA-6717 
       24.39        35.01        63.98        34.98        12.20        12.76 
TCGA-CM-5868 TCGA-D5-6532 TCGA-D5-6540 TCGA-G4-6303 TCGA-AG-A011 TCGA-DC-6157 
       17.03        18.25        16.14        65.85        37.02        27.95 

$`NFATC3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
       25.08        25.18        24.16        21.76        24.69        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6718 TCGA-CA-6719 
        3.06         3.25         3.29         0.07        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       15.02        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       55.92        20.19         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
        4.80        17.13        12.49        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
        6.02        25.97        23.01        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       13.97        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  NFATC3 MUTATED NFATC3 WILD-TYPE 
            12.2              0.0 
  NFATC3 MUTATED NFATC3 WILD-TYPE 
           65.85           148.01 
  NFATC3 MUTATED NFATC3 WILD-TYPE 
           26.17            20.12 
[1] "12.2 - 65.8 (26.2)" "0.0 - 148.0 (20.1)"
[1] "hr=" "2.8"
D840V2, continuous
D840V3, binary
                  cls
clus                 0   1
  NFATC3 MUTATED    12   2
  NFATC3 WILD-TYPE 354 117
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NFATC3 MUTATED     12    2
  NFATC3 WILD-TYPE  354  117
        clus
vv       NFATC3 MUTATED NFATC3 WILD-TYPE
  COLON              12              354
  RECTUM              2              117
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NFATC3 MUTATED         4        0        2         4         1         0
  NFATC3 WILD-TYPE      87        1       30       134         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NFATC3 MUTATED           0          0          0          0        2
  NFATC3 WILD-TYPE        24         11         59         42       46
                  vv
clus               STAGE IVA STAGE IVB
  NFATC3 MUTATED           1         0
  NFATC3 WILD-TYPE        17         1
D840V4, multiclass
            clus
vv           NFATC3 MUTATED NFATC3 WILD-TYPE
  STAGE I                 4               87
  STAGE IA                0                1
  STAGE II                2               30
  STAGE IIA               4              134
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              0               59
  STAGE IIIC              0               42
  STAGE IV                2               46
  STAGE IVA               1               17
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  NFATC3 MUTATED     0   4   6   4
  NFATC3 WILD-TYPE  17  88 323  46
D840V5, multiclass
    clus
vv   NFATC3 MUTATED NFATC3 WILD-TYPE
  T1              0               17
  T2              4               88
  T3              6              323
  T4              4               46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  NFATC3 MUTATED    11   3   0
  NFATC3 WILD-TYPE 276 110  87
D840V6, multiclass
    clus
vv   NFATC3 MUTATED NFATC3 WILD-TYPE
  N0             11              276
  N1              3              110
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D840V7, binary
                  cls
clus                 0   1
  NFATC3 MUTATED    11   3
  NFATC3 WILD-TYPE 364  62
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NFATC3 MUTATED     11    3
  NFATC3 WILD-TYPE  364   62
   clus
vv  NFATC3 MUTATED NFATC3 WILD-TYPE
  0             11              364
  1              3               62
[1] 2 2
[1] FALSE
D840V8, binary
                  cls
clus                 0   1
  NFATC3 MUTATED     5   9
  NFATC3 WILD-TYPE 220 255
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NFATC3 MUTATED      5    9
  NFATC3 WILD-TYPE  220  255
        clus
vv       NFATC3 MUTATED NFATC3 WILD-TYPE
  FEMALE              5              220
  MALE                9              255
[1] 2 2
[1] FALSE
D840V9, binary
                  cls
clus                 0   1
  NFATC3 MUTATED    11   0
  NFATC3 WILD-TYPE 339  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NFATC3 MUTATED     11    0
  NFATC3 WILD-TYPE  339   22
     clus
vv    NFATC3 MUTATED NFATC3 WILD-TYPE
  NO              11              339
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  NFATC3 MUTATED                     10                             2
  NFATC3 WILD-TYPE                  305                            45
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  NFATC3 MUTATED                       2                              0
  NFATC3 WILD-TYPE                   104                             10
D840V10, multiclass
                                clus
vv                               NFATC3 MUTATED NFATC3 WILD-TYPE
  COLON ADENOCARCINOMA                       10              305
  COLON MUCINOUS ADENOCARCINOMA               2               45
  RECTAL ADENOCARCINOMA                       2              104
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  NFATC3 MUTATED    10   0   1   2
  NFATC3 WILD-TYPE 335   4  30  23
D840V11, multiclass
    clus
vv   NFATC3 MUTATED NFATC3 WILD-TYPE
  R0             10              335
  R1              0                4
  R2              1               30
  RX              2               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D840V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NFATC3 MUTATED                                  0     2
  NFATC3 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  NFATC3 MUTATED                           1     5
  NFATC3 WILD-TYPE                        21   221
D840V13, multiclass
                                  clus
vv                                 NFATC3 MUTATED NFATC3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                9
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                         5              221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(841) Variable = ZNF83 MUTATION ANALYSIS
D841V1, survival
                 sevent
clus2               0   1
  ZNF83 MUTATED    15   4
  ZNF83 WILD-TYPE 363  89
  ZNF83 MUTATED ZNF83 WILD-TYPE 
             19             452 
  ZNF83 MUTATED ZNF83 WILD-TYPE 
              4              89 
$`ZNF83 MUTATED`
TCGA-A6-3809 TCGA-A6-6781 TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3525 TCGA-AA-3864 
       32.75        19.66         3.02        63.98         8.05        53.00 
TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A02K TCGA-AZ-4315 TCGA-AZ-6601 TCGA-CM-4752 
        4.01        34.98        14.01        58.39       100.01        13.02 
TCGA-CM-6674 TCGA-D5-6923 TCGA-DM-A28K TCGA-G4-6586 TCGA-AG-3726 TCGA-AG-3885 
       12.95        12.43        98.24        35.80         7.99        17.95 
TCGA-AG-A002 
       20.98 

$`ZNF83 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 
       20.12        20.28         7.04         1.02        35.01         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       37.05        36.03        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       78.08         6.05         6.97        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       30.05        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
       39.98         2.01         5.03         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 
       62.79        88.21        49.41         6.77        12.10        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-5341 TCGA-CM-5344 
       23.05        20.02        37.02        25.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       14.04        11.01        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        1.48         3.68         4.41        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
       60.79       117.07         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 
       61.91        36.00        22.09        13.78        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3727 TCGA-AG-3731 
       15.95        19.99        13.94        19.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  ZNF83 MUTATED ZNF83 WILD-TYPE 
           3.02            0.00 
  ZNF83 MUTATED ZNF83 WILD-TYPE 
         100.01          148.01 
  ZNF83 MUTATED ZNF83 WILD-TYPE 
         19.660          20.235 
[1] "3.0 - 100.0 (19.7)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.2"
D841V2, continuous
D841V3, binary
                 cls
clus                0   1
  ZNF83 MUTATED    17   3
  ZNF83 WILD-TYPE 349 116
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZNF83 MUTATED     17    3
  ZNF83 WILD-TYPE  349  116
        clus
vv       ZNF83 MUTATED ZNF83 WILD-TYPE
  COLON             17             349
  RECTUM             3             116
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZNF83 MUTATED         3        0        4         6         3         0
  ZNF83 WILD-TYPE      88        1       28       132         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ZNF83 MUTATED           0          0          2          1        1         0
  ZNF83 WILD-TYPE        24         11         57         41       47        18
                 vv
clus              STAGE IVB
  ZNF83 MUTATED           0
  ZNF83 WILD-TYPE         1
D841V4, multiclass
            clus
vv           ZNF83 MUTATED ZNF83 WILD-TYPE
  STAGE I                3              88
  STAGE IA               0               1
  STAGE II               4              28
  STAGE IIA              6             132
  STAGE IIB              3               7
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             2              57
  STAGE IIIC             1              41
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ZNF83 MUTATED     0   3  12   5
  ZNF83 WILD-TYPE  17  89 317  45
D841V5, multiclass
    clus
vv   ZNF83 MUTATED ZNF83 WILD-TYPE
  T1             0              17
  T2             3              89
  T3            12             317
  T4             5              45
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  ZNF83 MUTATED    16   3   1
  ZNF83 WILD-TYPE 271 110  86
D841V6, multiclass
    clus
vv   ZNF83 MUTATED ZNF83 WILD-TYPE
  N0            16             271
  N1             3             110
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D841V7, binary
                 cls
clus                0   1
  ZNF83 MUTATED    18   1
  ZNF83 WILD-TYPE 357  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZNF83 MUTATED     18    1
  ZNF83 WILD-TYPE  357   64
   clus
vv  ZNF83 MUTATED ZNF83 WILD-TYPE
  0            18             357
  1             1              64
[1] 2 2
[1] FALSE
D841V8, binary
                 cls
clus                0   1
  ZNF83 MUTATED     7  13
  ZNF83 WILD-TYPE 218 251
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZNF83 MUTATED      7   13
  ZNF83 WILD-TYPE  218  251
        clus
vv       ZNF83 MUTATED ZNF83 WILD-TYPE
  FEMALE             7             218
  MALE              13             251
[1] 2 2
[1] FALSE
D841V9, binary
                 cls
clus                0   1
  ZNF83 MUTATED    16   1
  ZNF83 WILD-TYPE 334  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZNF83 MUTATED     16    1
  ZNF83 WILD-TYPE  334   21
     clus
vv    ZNF83 MUTATED ZNF83 WILD-TYPE
  NO             16             334
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ZNF83 MUTATED                     13                             4
  ZNF83 WILD-TYPE                  302                            43
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ZNF83 MUTATED                       3                              0
  ZNF83 WILD-TYPE                   103                             10
D841V10, multiclass
                                clus
vv                               ZNF83 MUTATED ZNF83 WILD-TYPE
  COLON ADENOCARCINOMA                      13             302
  COLON MUCINOUS ADENOCARCINOMA              4              43
  RECTAL ADENOCARCINOMA                      3             103
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  ZNF83 MUTATED    17   0   1   0
  ZNF83 WILD-TYPE 328   4  30  25
D841V11, multiclass
    clus
vv   ZNF83 MUTATED ZNF83 WILD-TYPE
  R0            17             328
  R1             0               4
  R2             1              30
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D841V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF83 MUTATED                                  0     0
  ZNF83 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ZNF83 MUTATED                           1     8
  ZNF83 WILD-TYPE                        21   218
D841V13, multiclass
                                  clus
vv                                 ZNF83 MUTATED ZNF83 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        8             218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(842) Variable = CDC27 MUTATION ANALYSIS
D842V1, survival
                 sevent
clus2               0   1
  CDC27 MUTATED    12   3
  CDC27 WILD-TYPE 366  90
  CDC27 MUTATED CDC27 WILD-TYPE 
             15             456 
  CDC27 MUTATED CDC27 WILD-TYPE 
              3              90 
$`CDC27 MUTATED`
TCGA-AA-3555 TCGA-AA-3811 TCGA-AA-3861 TCGA-AA-A010 TCGA-AA-A01P TCGA-AA-A01Q 
       29.95        10.06        30.05        34.98        38.07         1.02 
TCGA-AD-6965 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-CA-6717 TCGA-DM-A1D4 
        0.20        21.44        17.82        58.39        12.76        92.75 
TCGA-G4-6628 TCGA-AG-3892 TCGA-AG-A002 
       79.69        13.02        20.98 

$`CDC27 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 
       21.01        13.02        24.00        17.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
        0.99        31.07        31.07        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        10.88        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
        0.95        33.01         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07        12.20        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
      130.65        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 
       13.78        35.80        26.17        91.79        46.75        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       17.03        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  CDC27 MUTATED CDC27 WILD-TYPE 
            0.2             0.0 
  CDC27 MUTATED CDC27 WILD-TYPE 
          92.75          148.01 
  CDC27 MUTATED CDC27 WILD-TYPE 
         21.440          20.085 
[1] "0.2 - 92.8 (21.4)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.1"
D842V2, continuous
D842V3, binary
                 cls
clus                0   1
  CDC27 MUTATED    14   2
  CDC27 WILD-TYPE 352 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDC27 MUTATED     14    2
  CDC27 WILD-TYPE  352  117
        clus
vv       CDC27 MUTATED CDC27 WILD-TYPE
  COLON             14             352
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CDC27 MUTATED         3        0        1         7         1         0
  CDC27 WILD-TYPE      88        1       31       131         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CDC27 MUTATED           2          0          1          0        0         0
  CDC27 WILD-TYPE        22         11         58         42       48        18
                 vv
clus              STAGE IVB
  CDC27 MUTATED           0
  CDC27 WILD-TYPE         1
D842V4, multiclass
            clus
vv           CDC27 MUTATED CDC27 WILD-TYPE
  STAGE I                3              88
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              7             131
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              2              22
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CDC27 MUTATED     1   2  11   2
  CDC27 WILD-TYPE  16  90 318  48
D842V5, multiclass
    clus
vv   CDC27 MUTATED CDC27 WILD-TYPE
  T1             1              16
  T2             2              90
  T3            11             318
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  CDC27 MUTATED    12   2   2
  CDC27 WILD-TYPE 275 111  85
D842V6, multiclass
    clus
vv   CDC27 MUTATED CDC27 WILD-TYPE
  N0            12             275
  N1             2             111
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D842V7, binary
                 cls
clus                0   1
  CDC27 MUTATED    14   0
  CDC27 WILD-TYPE 361  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDC27 MUTATED     14    0
  CDC27 WILD-TYPE  361   65
   clus
vv  CDC27 MUTATED CDC27 WILD-TYPE
  0            14             361
  1             0              65
[1] 2 2
[1] FALSE
D842V8, binary
                 cls
clus                0   1
  CDC27 MUTATED     8   8
  CDC27 WILD-TYPE 217 256
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDC27 MUTATED      8    8
  CDC27 WILD-TYPE  217  256
        clus
vv       CDC27 MUTATED CDC27 WILD-TYPE
  FEMALE             8             217
  MALE               8             256
[1] 2 2
[1] FALSE
D842V9, binary
                 cls
clus                0   1
  CDC27 MUTATED    12   0
  CDC27 WILD-TYPE 338  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDC27 MUTATED     12    0
  CDC27 WILD-TYPE  338   22
     clus
vv    CDC27 MUTATED CDC27 WILD-TYPE
  NO             12             338
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CDC27 MUTATED                     12                             2
  CDC27 WILD-TYPE                  303                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CDC27 MUTATED                       2                              0
  CDC27 WILD-TYPE                   104                             10
D842V10, multiclass
                                clus
vv                               CDC27 MUTATED CDC27 WILD-TYPE
  COLON ADENOCARCINOMA                      12             303
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  CDC27 MUTATED    13   0   0   1
  CDC27 WILD-TYPE 332   4  31  24
D842V11, multiclass
    clus
vv   CDC27 MUTATED CDC27 WILD-TYPE
  R0            13             332
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D842V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CDC27 MUTATED                                  0     1
  CDC27 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CDC27 MUTATED                           1     5
  CDC27 WILD-TYPE                        21   221
D842V13, multiclass
                                  clus
vv                                 CDC27 MUTATED CDC27 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        5             221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(843) Variable = PAAF1 MUTATION ANALYSIS
D843V1, survival
                 sevent
clus2               0   1
  PAAF1 MUTATED     5   1
  PAAF1 WILD-TYPE 373  92
  PAAF1 MUTATED PAAF1 WILD-TYPE 
              6             465 
  PAAF1 MUTATED PAAF1 WILD-TYPE 
              1              92 
$`PAAF1 MUTATED`
TCGA-A6-5661 TCGA-AZ-4315 TCGA-AZ-6603 TCGA-DM-A282 TCGA-G4-6315 TCGA-AG-A020 
       33.53        58.39        29.56       139.17        61.91        10.98 

$`PAAF1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        33.01        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
       12.10       100.01         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6317 
       53.62        44.68        55.04        85.48        63.62        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       12.00        70.03        64.01        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  PAAF1 MUTATED PAAF1 WILD-TYPE 
          10.98            0.00 
  PAAF1 MUTATED PAAF1 WILD-TYPE 
         139.17          148.01 
  PAAF1 MUTATED PAAF1 WILD-TYPE 
          45.96           20.05 
[1] "11.0 - 139.2 (46.0)" "0.0 - 148.0 (20.1)" 
[1] "hr=" "2.3"
D843V2, continuous
D843V3, binary
                 cls
clus                0   1
  PAAF1 MUTATED     5   1
  PAAF1 WILD-TYPE 361 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PAAF1 MUTATED      5    1
  PAAF1 WILD-TYPE  361  118
        clus
vv       PAAF1 MUTATED PAAF1 WILD-TYPE
  COLON              5             361
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PAAF1 MUTATED         0        0        0         3         0         0
  PAAF1 WILD-TYPE      91        1       32       135        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PAAF1 MUTATED           1          0          0          0        1         0
  PAAF1 WILD-TYPE        23         11         59         42       47        18
                 vv
clus              STAGE IVB
  PAAF1 MUTATED           0
  PAAF1 WILD-TYPE         1
D843V4, multiclass
            clus
vv           PAAF1 MUTATED PAAF1 WILD-TYPE
  STAGE I                0              91
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              3             135
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             0              42
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PAAF1 MUTATED     0   1   5   0
  PAAF1 WILD-TYPE  17  91 324  50
D843V5, multiclass
    clus
vv   PAAF1 MUTATED PAAF1 WILD-TYPE
  T1             0              17
  T2             1              91
  T3             5             324
  T4             0              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  PAAF1 MUTATED     3   3   0
  PAAF1 WILD-TYPE 284 110  87
D843V6, multiclass
    clus
vv   PAAF1 MUTATED PAAF1 WILD-TYPE
  N0             3             284
  N1             3             110
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D843V7, binary
                 cls
clus                0   1
  PAAF1 MUTATED     4   1
  PAAF1 WILD-TYPE 371  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PAAF1 MUTATED      4    1
  PAAF1 WILD-TYPE  371   64
   clus
vv  PAAF1 MUTATED PAAF1 WILD-TYPE
  0             4             371
  1             1              64
[1] 2 2
[1] FALSE
D843V8, binary
                 cls
clus                0   1
  PAAF1 MUTATED     4   2
  PAAF1 WILD-TYPE 221 262
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PAAF1 MUTATED      4    2
  PAAF1 WILD-TYPE  221  262
        clus
vv       PAAF1 MUTATED PAAF1 WILD-TYPE
  FEMALE             4             221
  MALE               2             262
[1] 2 2
[1] FALSE
D843V9, binary
                 cls
clus                0   1
  PAAF1 MUTATED     4   0
  PAAF1 WILD-TYPE 346  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PAAF1 MUTATED      4    0
  PAAF1 WILD-TYPE  346   22
     clus
vv    PAAF1 MUTATED PAAF1 WILD-TYPE
  NO              4             346
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PAAF1 MUTATED                      5                             0
  PAAF1 WILD-TYPE                  310                            47
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PAAF1 MUTATED                       0                              1
  PAAF1 WILD-TYPE                   106                              9
D843V10, multiclass
                                clus
vv                               PAAF1 MUTATED PAAF1 WILD-TYPE
  COLON ADENOCARCINOMA                       5             310
  COLON MUCINOUS ADENOCARCINOMA              0              47
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             1               9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  PAAF1 MUTATED     4   0   0   0
  PAAF1 WILD-TYPE 341   4  31  25
D843V11, multiclass
    clus
vv   PAAF1 MUTATED PAAF1 WILD-TYPE
  R0             4             341
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D843V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PAAF1 MUTATED                                  0     0
  PAAF1 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PAAF1 MUTATED                           1     4
  PAAF1 WILD-TYPE                        21   222
D843V13, multiclass
                                  clus
vv                                 PAAF1 MUTATED PAAF1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        4             222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(844) Variable = CD244 MUTATION ANALYSIS
D844V1, survival
                 sevent
clus2               0   1
  CD244 MUTATED     5   2
  CD244 WILD-TYPE 373  91
  CD244 MUTATED CD244 WILD-TYPE 
              7             464 
  CD244 MUTATED CD244 WILD-TYPE 
              2              91 
$`CD244 MUTATED`
TCGA-A6-5657 TCGA-AA-3510 TCGA-AA-3864 TCGA-AA-A00N TCGA-AA-A010 TCGA-F4-6460 
       31.63        63.98        53.00         4.01        34.98        31.96 
TCGA-G4-6306 
       44.68 

$`CD244 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 
        0.99        31.07        31.07        30.05        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
        8.61        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6307 
       35.31       133.18        74.56        65.85        53.62        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  CD244 MUTATED CD244 WILD-TYPE 
           4.01            0.00 
  CD244 MUTATED CD244 WILD-TYPE 
          63.98          148.01 
  CD244 MUTATED CD244 WILD-TYPE 
         34.980          20.035 
[1] "4.0 - 64.0 (35.0)"  "0.0 - 148.0 (20.0)"
[1] "hr=" "1"  
D844V2, continuous
D844V3, binary
                 cls
clus                0   1
  CD244 MUTATED     7   0
  CD244 WILD-TYPE 359 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CD244 MUTATED      7    0
  CD244 WILD-TYPE  359  119
        clus
vv       CD244 MUTATED CD244 WILD-TYPE
  COLON              7             359
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CD244 MUTATED         0        0        2         1         2         0
  CD244 WILD-TYPE      91        1       30       137         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CD244 MUTATED           0          0          2          0        0         0
  CD244 WILD-TYPE        24         11         57         42       48        18
                 vv
clus              STAGE IVB
  CD244 MUTATED           0
  CD244 WILD-TYPE         1
D844V4, multiclass
            clus
vv           CD244 MUTATED CD244 WILD-TYPE
  STAGE I                0              91
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA              1             137
  STAGE IIB              2               8
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             2              57
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CD244 MUTATED     0   1   4   2
  CD244 WILD-TYPE  17  91 325  48
D844V5, multiclass
    clus
vv   CD244 MUTATED CD244 WILD-TYPE
  T1             0              17
  T2             1              91
  T3             4             325
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  CD244 MUTATED     5   2   0
  CD244 WILD-TYPE 282 111  87
D844V6, multiclass
    clus
vv   CD244 MUTATED CD244 WILD-TYPE
  N0             5             282
  N1             2             111
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D844V7, binary
                 cls
clus                0   1
  CD244 MUTATED     7   0
  CD244 WILD-TYPE 368  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CD244 MUTATED      7    0
  CD244 WILD-TYPE  368   65
   clus
vv  CD244 MUTATED CD244 WILD-TYPE
  0             7             368
  1             0              65
[1] 2 2
[1] FALSE
D844V8, binary
                 cls
clus                0   1
  CD244 MUTATED     2   5
  CD244 WILD-TYPE 223 259
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CD244 MUTATED      2    5
  CD244 WILD-TYPE  223  259
        clus
vv       CD244 MUTATED CD244 WILD-TYPE
  FEMALE             2             223
  MALE               5             259
[1] 2 2
[1] FALSE
D844V9, binary
                 cls
clus                0   1
  CD244 MUTATED     6   0
  CD244 WILD-TYPE 344  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CD244 MUTATED      6    0
  CD244 WILD-TYPE  344   22
     clus
vv    CD244 MUTATED CD244 WILD-TYPE
  NO              6             344
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CD244 MUTATED                      6                             1
  CD244 WILD-TYPE                  309                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CD244 MUTATED                       0                              0
  CD244 WILD-TYPE                   106                             10
D844V10, multiclass
                                clus
vv                               CD244 MUTATED CD244 WILD-TYPE
  COLON ADENOCARCINOMA                       6             309
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  CD244 MUTATED     7   0   0   0
  CD244 WILD-TYPE 338   4  31  25
D844V11, multiclass
    clus
vv   CD244 MUTATED CD244 WILD-TYPE
  R0             7             338
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D844V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CD244 MUTATED                                  0     0
  CD244 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CD244 MUTATED                           1     2
  CD244 WILD-TYPE                        21   224
D844V13, multiclass
                                  clus
vv                                 CD244 MUTATED CD244 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        2             224
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(845) Variable = UAP1L1 MUTATION ANALYSIS
D845V1, survival
                  sevent
clus2                0   1
  UAP1L1 MUTATED     5   2
  UAP1L1 WILD-TYPE 373  91
  UAP1L1 MUTATED UAP1L1 WILD-TYPE 
               7              464 
  UAP1L1 MUTATED UAP1L1 WILD-TYPE 
               2               91 
$`UAP1L1 MUTATED`
TCGA-AA-3662 TCGA-AA-3930 TCGA-AA-3977 TCGA-AD-5900 TCGA-AD-6895 TCGA-DM-A28F 
        6.05         2.01        25.02         0.07         0.72        35.97 
TCGA-G4-6299 
       74.56 

$`UAP1L1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       18.05        40.96        21.37        15.52        56.55         0.79 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
       81.37       119.93        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
       35.31       133.18        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  UAP1L1 MUTATED UAP1L1 WILD-TYPE 
            0.07             0.00 
  UAP1L1 MUTATED UAP1L1 WILD-TYPE 
           74.56           148.01 
  UAP1L1 MUTATED UAP1L1 WILD-TYPE 
           6.050           20.235 
[1] "0.1 - 74.6 (6.0)"   "0.0 - 148.0 (20.2)"
[1] "hr=" "1.9"
D845V2, continuous
D845V3, binary
                  cls
clus                 0   1
  UAP1L1 MUTATED     7   0
  UAP1L1 WILD-TYPE 359 119
[1] "tbl2"
                  cls
clus               [,1] [,2]
  UAP1L1 MUTATED      7    0
  UAP1L1 WILD-TYPE  359  119
        clus
vv       UAP1L1 MUTATED UAP1L1 WILD-TYPE
  COLON               7              359
  RECTUM              0              119
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  UAP1L1 MUTATED         1        0        0         0         0         0
  UAP1L1 WILD-TYPE      90        1       32       138        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  UAP1L1 MUTATED           0          0          1          1        2
  UAP1L1 WILD-TYPE        24         11         58         41       46
                  vv
clus               STAGE IVA STAGE IVB
  UAP1L1 MUTATED           0         0
  UAP1L1 WILD-TYPE        18         1
D845V4, multiclass
            clus
vv           UAP1L1 MUTATED UAP1L1 WILD-TYPE
  STAGE I                 1               90
  STAGE IA                0                1
  STAGE II                0               32
  STAGE IIA               0              138
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              1               58
  STAGE IIIC              1               41
  STAGE IV                2               46
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  UAP1L1 MUTATED     0   2   4   1
  UAP1L1 WILD-TYPE  17  90 325  49
D845V5, multiclass
    clus
vv   UAP1L1 MUTATED UAP1L1 WILD-TYPE
  T1              0               17
  T2              2               90
  T3              4              325
  T4              1               49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  UAP1L1 MUTATED     2   2   3
  UAP1L1 WILD-TYPE 285 111  84
D845V6, multiclass
    clus
vv   UAP1L1 MUTATED UAP1L1 WILD-TYPE
  N0              2              285
  N1              2              111
  N2              3               84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D845V7, binary
                  cls
clus                 0   1
  UAP1L1 MUTATED     2   2
  UAP1L1 WILD-TYPE 373  63
[1] "tbl2"
                  cls
clus               [,1] [,2]
  UAP1L1 MUTATED      2    2
  UAP1L1 WILD-TYPE  373   63
   clus
vv  UAP1L1 MUTATED UAP1L1 WILD-TYPE
  0              2              373
  1              2               63
[1] 2 2
[1] FALSE
D845V8, binary
                  cls
clus                 0   1
  UAP1L1 MUTATED     1   6
  UAP1L1 WILD-TYPE 224 258
[1] "tbl2"
                  cls
clus               [,1] [,2]
  UAP1L1 MUTATED      1    6
  UAP1L1 WILD-TYPE  224  258
        clus
vv       UAP1L1 MUTATED UAP1L1 WILD-TYPE
  FEMALE              1              224
  MALE                6              258
[1] 2 2
[1] FALSE
D845V9, binary
                  cls
clus                 0   1
  UAP1L1 MUTATED     4   0
  UAP1L1 WILD-TYPE 346  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  UAP1L1 MUTATED      4    0
  UAP1L1 WILD-TYPE  346   22
     clus
vv    UAP1L1 MUTATED UAP1L1 WILD-TYPE
  NO               4              346
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  UAP1L1 MUTATED                      6                             1
  UAP1L1 WILD-TYPE                  309                            46
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  UAP1L1 MUTATED                       0                              0
  UAP1L1 WILD-TYPE                   106                             10
D845V10, multiclass
                                clus
vv                               UAP1L1 MUTATED UAP1L1 WILD-TYPE
  COLON ADENOCARCINOMA                        6              309
  COLON MUCINOUS ADENOCARCINOMA               1               46
  RECTAL ADENOCARCINOMA                       0              106
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  UAP1L1 MUTATED     2   0   2   0
  UAP1L1 WILD-TYPE 343   4  29  25
D845V11, multiclass
    clus
vv   UAP1L1 MUTATED UAP1L1 WILD-TYPE
  R0              2              343
  R1              0                4
  R2              2               29
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D845V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  UAP1L1 MUTATED                                  0     0
  UAP1L1 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  UAP1L1 MUTATED                           0     4
  UAP1L1 WILD-TYPE                        22   222
D845V13, multiclass
                                  clus
vv                                 UAP1L1 MUTATED UAP1L1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         4              222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(846) Variable = FAM189B MUTATION ANALYSIS
D846V1, survival
                   sevent
clus2                 0   1
  FAM189B MUTATED    11   1
  FAM189B WILD-TYPE 367  92
  FAM189B MUTATED FAM189B WILD-TYPE 
               12               459 
  FAM189B MUTATED FAM189B WILD-TYPE 
                1                92 
$`FAM189B MUTATED`
TCGA-A6-5657 TCGA-AA-3663 TCGA-AA-3672 TCGA-AA-A00E TCGA-AA-A00J TCGA-AD-6895 
       31.63         6.97         0.92        30.02        18.05         0.72 
TCGA-AZ-6598 TCGA-D5-6540 TCGA-D5-6930 TCGA-DM-A1HB TCGA-AG-A02N TCGA-DY-A0XA 
       49.41        16.14         1.51       135.65        61.97       126.44 

$`FAM189B WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
       54.02         2.01        14.01        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 
        0.07        21.37        15.52        56.55         0.79         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 
       17.85         4.80        17.13        12.49        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       11.64         4.80        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 
       12.59       140.38         7.50        44.32       131.51       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
        1.94        38.96        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.03         5.29        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  FAM189B MUTATED FAM189B WILD-TYPE 
             0.72              0.00 
  FAM189B MUTATED FAM189B WILD-TYPE 
           135.65            148.01 
  FAM189B MUTATED FAM189B WILD-TYPE 
           24.035            20.190 
[1] "0.7 - 135.7 (24.0)" "0.0 - 148.0 (20.2)"
[1] "hr=" "3.3"
D846V2, continuous
D846V3, binary
                   cls
clus                  0   1
  FAM189B MUTATED    11   2
  FAM189B WILD-TYPE 355 117
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM189B MUTATED     11    2
  FAM189B WILD-TYPE  355  117
        clus
vv       FAM189B MUTATED FAM189B WILD-TYPE
  COLON               11               355
  RECTUM               2               117
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FAM189B MUTATED         1        0        3         3         0         0
  FAM189B WILD-TYPE      90        1       29       135        10         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FAM189B MUTATED           1          0          3          1        0
  FAM189B WILD-TYPE        23         11         56         41       48
                   vv
clus                STAGE IVA STAGE IVB
  FAM189B MUTATED           0         0
  FAM189B WILD-TYPE        18         1
D846V4, multiclass
            clus
vv           FAM189B MUTATED FAM189B WILD-TYPE
  STAGE I                  1                90
  STAGE IA                 0                 1
  STAGE II                 3                29
  STAGE IIA                3               135
  STAGE IIB                0                10
  STAGE IIC                0                 1
  STAGE III                1                23
  STAGE IIIA               0                11
  STAGE IIIB               3                56
  STAGE IIIC               1                41
  STAGE IV                 0                48
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  FAM189B MUTATED     0   1  11   1
  FAM189B WILD-TYPE  17  91 318  49
D846V5, multiclass
    clus
vv   FAM189B MUTATED FAM189B WILD-TYPE
  T1               0                17
  T2               1                91
  T3              11               318
  T4               1                49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  FAM189B MUTATED     7   5   1
  FAM189B WILD-TYPE 280 108  86
D846V6, multiclass
    clus
vv   FAM189B MUTATED FAM189B WILD-TYPE
  N0               7               280
  N1               5               108
  N2               1                86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D846V7, binary
                   cls
clus                  0   1
  FAM189B MUTATED    10   0
  FAM189B WILD-TYPE 365  65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM189B MUTATED     10    0
  FAM189B WILD-TYPE  365   65
   clus
vv  FAM189B MUTATED FAM189B WILD-TYPE
  0              10               365
  1               0                65
[1] 2 2
[1] FALSE
D846V8, binary
                   cls
clus                  0   1
  FAM189B MUTATED     3  10
  FAM189B WILD-TYPE 222 254
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM189B MUTATED      3   10
  FAM189B WILD-TYPE  222  254
        clus
vv       FAM189B MUTATED FAM189B WILD-TYPE
  FEMALE               3               222
  MALE                10               254
[1] 2 2
[1] FALSE
D846V9, binary
                   cls
clus                  0   1
  FAM189B MUTATED     7   0
  FAM189B WILD-TYPE 343  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM189B MUTATED      7    0
  FAM189B WILD-TYPE  343   22
     clus
vv    FAM189B MUTATED FAM189B WILD-TYPE
  NO                7               343
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  FAM189B MUTATED                      6                             4
  FAM189B WILD-TYPE                  309                            43
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  FAM189B MUTATED                       2                              0
  FAM189B WILD-TYPE                   104                             10
D846V10, multiclass
                                clus
vv                               FAM189B MUTATED FAM189B WILD-TYPE
  COLON ADENOCARCINOMA                         6               309
  COLON MUCINOUS ADENOCARCINOMA                4                43
  RECTAL ADENOCARCINOMA                        2               104
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  FAM189B MUTATED     9   0   0   0
  FAM189B WILD-TYPE 336   4  31  25
D846V11, multiclass
    clus
vv   FAM189B MUTATED FAM189B WILD-TYPE
  R0               9               336
  R1               0                 4
  R2               0                31
  RX               0                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D846V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FAM189B MUTATED                                  0     0
  FAM189B WILD-TYPE                                1    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  FAM189B MUTATED                           1     7
  FAM189B WILD-TYPE                        21   219
D846V13, multiclass
                                  clus
vv                                 FAM189B MUTATED FAM189B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                      1                21
  WHITE                                          7               219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(847) Variable = MIA3 MUTATION ANALYSIS
D847V1, survival
                sevent
clus2              0   1
  MIA3 MUTATED    15   4
  MIA3 WILD-TYPE 363  89
  MIA3 MUTATED MIA3 WILD-TYPE 
            19            452 
  MIA3 MUTATED MIA3 WILD-TYPE 
             4             89 
$`MIA3 MUTATED`
TCGA-A6-6653 TCGA-AA-3510 TCGA-AA-3855 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3977 
       24.39        63.98        32.05         2.01        21.99        25.02 
TCGA-AA-A00N TCGA-AA-A010 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-CA-6717 TCGA-CA-6718 
        4.01        34.98        58.39        49.41        12.76        10.06 
TCGA-CK-5916 TCGA-CM-5861 TCGA-DM-A0X9 TCGA-G4-6309 TCGA-G4-6586 TCGA-AG-3892 
       21.14        15.02       119.70        85.48        35.80        13.02 
TCGA-AG-A002 
       20.98 

$`MIA3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
       25.08        25.18        24.16        21.76        24.69        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3856 
       10.06         0.00        33.07         0.00        36.03         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       34.03        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       33.01        21.44        17.82         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        88.21         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 
        3.06         3.25         3.29         0.07        12.20        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
        9.99        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       30.08        32.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 
       65.85        53.62        44.68        55.04        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       17.95        36.95        17.03        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  MIA3 MUTATED MIA3 WILD-TYPE 
          2.01           0.00 
  MIA3 MUTATED MIA3 WILD-TYPE 
        119.70         148.01 
  MIA3 MUTATED MIA3 WILD-TYPE 
         24.39          20.02 
[1] "2.0 - 119.7 (24.4)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.2"
D847V2, continuous
D847V3, binary
                cls
clus               0   1
  MIA3 MUTATED    19   2
  MIA3 WILD-TYPE 347 117
[1] "tbl2"
                cls
clus             [,1] [,2]
  MIA3 MUTATED     19    2
  MIA3 WILD-TYPE  347  117
        clus
vv       MIA3 MUTATED MIA3 WILD-TYPE
  COLON            19            347
  RECTUM            2            117
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MIA3 MUTATED         7        0        2         8         2         0
  MIA3 WILD-TYPE      84        1       30       130         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MIA3 MUTATED           0          0          1          0        0         0
  MIA3 WILD-TYPE        24         11         58         42       48        18
                vv
clus             STAGE IVB
  MIA3 MUTATED           0
  MIA3 WILD-TYPE         1
D847V4, multiclass
            clus
vv           MIA3 MUTATED MIA3 WILD-TYPE
  STAGE I               7             84
  STAGE IA              0              1
  STAGE II              2             30
  STAGE IIA             8            130
  STAGE IIB             2              8
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            1             58
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  MIA3 MUTATED     2   6  11   2
  MIA3 WILD-TYPE  15  86 318  48
D847V5, multiclass
    clus
vv   MIA3 MUTATED MIA3 WILD-TYPE
  T1            2             15
  T2            6             86
  T3           11            318
  T4            2             48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  MIA3 MUTATED    20   1   0
  MIA3 WILD-TYPE 267 112  87
D847V6, multiclass
    clus
vv   MIA3 MUTATED MIA3 WILD-TYPE
  N0           20            267
  N1            1            112
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D847V7, binary
                cls
clus               0   1
  MIA3 MUTATED    18   0
  MIA3 WILD-TYPE 357  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  MIA3 MUTATED     18    0
  MIA3 WILD-TYPE  357   65
   clus
vv  MIA3 MUTATED MIA3 WILD-TYPE
  0           18            357
  1            0             65
[1] 2 2
[1] FALSE
D847V8, binary
                cls
clus               0   1
  MIA3 MUTATED    11  10
  MIA3 WILD-TYPE 214 254
[1] "tbl2"
                cls
clus             [,1] [,2]
  MIA3 MUTATED     11   10
  MIA3 WILD-TYPE  214  254
        clus
vv       MIA3 MUTATED MIA3 WILD-TYPE
  FEMALE           11            214
  MALE             10            254
[1] 2 2
[1] FALSE
D847V9, binary
                cls
clus               0   1
  MIA3 MUTATED    16   0
  MIA3 WILD-TYPE 334  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  MIA3 MUTATED     16    0
  MIA3 WILD-TYPE  334   22
     clus
vv    MIA3 MUTATED MIA3 WILD-TYPE
  NO            16            334
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MIA3 MUTATED                     16                             3
  MIA3 WILD-TYPE                  299                            44
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MIA3 MUTATED                       2                              0
  MIA3 WILD-TYPE                   104                             10
D847V10, multiclass
                                clus
vv                               MIA3 MUTATED MIA3 WILD-TYPE
  COLON ADENOCARCINOMA                     16            299
  COLON MUCINOUS ADENOCARCINOMA             3             44
  RECTAL ADENOCARCINOMA                     2            104
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  MIA3 MUTATED    12   0   0   4
  MIA3 WILD-TYPE 333   4  31  21
D847V11, multiclass
    clus
vv   MIA3 MUTATED MIA3 WILD-TYPE
  R0           12            333
  R1            0              4
  R2            0             31
  RX            4             21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D847V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MIA3 MUTATED                                  0     2
  MIA3 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  MIA3 MUTATED                           1     8
  MIA3 WILD-TYPE                        21   218
D847V13, multiclass
                                  clus
vv                                 MIA3 MUTATED MIA3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              9
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                       8            218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(848) Variable = EFHC2 MUTATION ANALYSIS
D848V1, survival
                 sevent
clus2               0   1
  EFHC2 MUTATED    13   4
  EFHC2 WILD-TYPE 365  89
  EFHC2 MUTATED EFHC2 WILD-TYPE 
             17             454 
  EFHC2 MUTATED EFHC2 WILD-TYPE 
              4              89 
$`EFHC2 MUTATED`
TCGA-AA-3492 TCGA-AA-3877 TCGA-AA-3977 TCGA-AA-A00N TCGA-AD-5900 TCGA-AZ-4315 
        3.02        31.00        25.02         4.01         0.07        58.39 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4952 TCGA-CM-5860 TCGA-CM-6161 TCGA-CM-6170 
       12.76        10.06        15.62        32.02        15.02        15.02 
TCGA-D5-6535 TCGA-DM-A1DB TCGA-F4-6856 TCGA-AG-3892 TCGA-AG-A002 
       15.12        44.32        35.31        13.02        20.98 

$`EFHC2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 
       17.03        24.03        27.02        29.98        18.05         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
       40.96        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        3.29         0.07        12.20        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       85.45        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5861 
       13.02        29.06        22.03        22.98        30.08        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6162 TCGA-CM-6163 
        5.03        15.02        15.02        17.03        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HA 
       49.91        13.32        12.59       140.38         7.50       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 
       33.67        13.25         0.53        47.41       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 
       19.99         1.02        17.95        36.95        17.03        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  EFHC2 MUTATED EFHC2 WILD-TYPE 
           0.07            0.00 
  EFHC2 MUTATED EFHC2 WILD-TYPE 
          58.39          148.01 
  EFHC2 MUTATED EFHC2 WILD-TYPE 
         15.120          20.415 
[1] "0.1 - 58.4 (15.1)"  "0.0 - 148.0 (20.4)"
[1] "hr=" "1.5"
D848V2, continuous
D848V3, binary
                 cls
clus                0   1
  EFHC2 MUTATED    15   2
  EFHC2 WILD-TYPE 351 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EFHC2 MUTATED     15    2
  EFHC2 WILD-TYPE  351  117
        clus
vv       EFHC2 MUTATED EFHC2 WILD-TYPE
  COLON             15             351
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  EFHC2 MUTATED         7        0        1         5         1         0
  EFHC2 WILD-TYPE      84        1       31       133         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  EFHC2 MUTATED           0          0          1          1        0         0
  EFHC2 WILD-TYPE        24         11         58         41       48        18
                 vv
clus              STAGE IVB
  EFHC2 MUTATED           0
  EFHC2 WILD-TYPE         1
D848V4, multiclass
            clus
vv           EFHC2 MUTATED EFHC2 WILD-TYPE
  STAGE I                7              84
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              5             133
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             1              41
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  EFHC2 MUTATED     2   6   7   2
  EFHC2 WILD-TYPE  15  86 322  48
D848V5, multiclass
    clus
vv   EFHC2 MUTATED EFHC2 WILD-TYPE
  T1             2              15
  T2             6              86
  T3             7             322
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  EFHC2 MUTATED    15   1   1
  EFHC2 WILD-TYPE 272 112  86
D848V6, multiclass
    clus
vv   EFHC2 MUTATED EFHC2 WILD-TYPE
  N0            15             272
  N1             1             112
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D848V7, binary
                 cls
clus                0   1
  EFHC2 MUTATED    14   0
  EFHC2 WILD-TYPE 361  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EFHC2 MUTATED     14    0
  EFHC2 WILD-TYPE  361   65
   clus
vv  EFHC2 MUTATED EFHC2 WILD-TYPE
  0            14             361
  1             0              65
[1] 2 2
[1] FALSE
D848V8, binary
                 cls
clus                0   1
  EFHC2 MUTATED     7  10
  EFHC2 WILD-TYPE 218 254
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EFHC2 MUTATED      7   10
  EFHC2 WILD-TYPE  218  254
        clus
vv       EFHC2 MUTATED EFHC2 WILD-TYPE
  FEMALE             7             218
  MALE              10             254
[1] 2 2
[1] FALSE
D848V9, binary
                 cls
clus                0   1
  EFHC2 MUTATED    13   0
  EFHC2 WILD-TYPE 337  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EFHC2 MUTATED     13    0
  EFHC2 WILD-TYPE  337   22
     clus
vv    EFHC2 MUTATED EFHC2 WILD-TYPE
  NO             13             337
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  EFHC2 MUTATED                      9                             6
  EFHC2 WILD-TYPE                  306                            41
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  EFHC2 MUTATED                       2                              0
  EFHC2 WILD-TYPE                   104                             10
D848V10, multiclass
                                clus
vv                               EFHC2 MUTATED EFHC2 WILD-TYPE
  COLON ADENOCARCINOMA                       9             306
  COLON MUCINOUS ADENOCARCINOMA              6              41
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  EFHC2 MUTATED    11   0   0   4
  EFHC2 WILD-TYPE 334   4  31  21
D848V11, multiclass
    clus
vv   EFHC2 MUTATED EFHC2 WILD-TYPE
  R0            11             334
  R1             0               4
  R2             0              31
  RX             4              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D848V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  EFHC2 MUTATED                                  0     2
  EFHC2 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  EFHC2 MUTATED                           0     9
  EFHC2 WILD-TYPE                        22   217
D848V13, multiclass
                                  clus
vv                                 EFHC2 MUTATED EFHC2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               9
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        9             217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(849) Variable = PALLD MUTATION ANALYSIS
D849V1, survival
                 sevent
clus2               0   1
  PALLD MUTATED    10   2
  PALLD WILD-TYPE 368  91
  PALLD MUTATED PALLD WILD-TYPE 
             12             459 
  PALLD MUTATED PALLD WILD-TYPE 
              2              91 
$`PALLD MUTATED`
TCGA-AA-3660 TCGA-AA-3680 TCGA-AA-3966 TCGA-AU-6004 TCGA-AZ-6601 TCGA-CM-4747 
       78.08        11.01         2.01        27.09       100.01        25.02 
TCGA-D5-6533 TCGA-DM-A1HB TCGA-G4-6588 TCGA-AG-3892 TCGA-AG-A002 TCGA-EI-6507 
        1.32       135.65        26.17        13.02        20.98        19.96 

$`PALLD WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 
       20.98        19.99        13.94        19.99        61.02         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       47.01        15.02         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       20.98        34.03        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
        0.20        14.50        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 
       62.79        88.21        49.41         6.77        12.10        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       23.05        20.02        37.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 
       56.09        55.92        20.19        18.25        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      131.51       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 
       19.99         1.02        17.95        36.95        17.03        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6510 
       51.48        32.61         0.49        20.55        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  PALLD MUTATED PALLD WILD-TYPE 
           1.32            0.00 
  PALLD MUTATED PALLD WILD-TYPE 
         135.65          148.01 
  PALLD MUTATED PALLD WILD-TYPE 
          23.00           20.12 
[1] "1.3 - 135.7 (23.0)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.6"
D849V2, continuous
D849V3, binary
                 cls
clus                0   1
  PALLD MUTATED     9   3
  PALLD WILD-TYPE 357 116
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PALLD MUTATED      9    3
  PALLD WILD-TYPE  357  116
        clus
vv       PALLD MUTATED PALLD WILD-TYPE
  COLON              9             357
  RECTUM             3             116
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PALLD MUTATED         3        0        2         3         0         0
  PALLD WILD-TYPE      88        1       30       135        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PALLD MUTATED           0          0          2          0        1         1
  PALLD WILD-TYPE        24         11         57         42       47        17
                 vv
clus              STAGE IVB
  PALLD MUTATED           0
  PALLD WILD-TYPE         1
D849V4, multiclass
            clus
vv           PALLD MUTATED PALLD WILD-TYPE
  STAGE I                3              88
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA              3             135
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             2              57
  STAGE IIIC             0              42
  STAGE IV               1              47
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PALLD MUTATED     1   2   6   3
  PALLD WILD-TYPE  16  90 323  47
D849V5, multiclass
    clus
vv   PALLD MUTATED PALLD WILD-TYPE
  T1             1              16
  T2             2              90
  T3             6             323
  T4             3              47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  PALLD MUTATED     9   2   1
  PALLD WILD-TYPE 278 111  86
D849V6, multiclass
    clus
vv   PALLD MUTATED PALLD WILD-TYPE
  N0             9             278
  N1             2             111
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D849V7, binary
                 cls
clus                0   1
  PALLD MUTATED    10   2
  PALLD WILD-TYPE 365  63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PALLD MUTATED     10    2
  PALLD WILD-TYPE  365   63
   clus
vv  PALLD MUTATED PALLD WILD-TYPE
  0            10             365
  1             2              63
[1] 2 2
[1] FALSE
D849V8, binary
                 cls
clus                0   1
  PALLD MUTATED     7   5
  PALLD WILD-TYPE 218 259
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PALLD MUTATED      7    5
  PALLD WILD-TYPE  218  259
        clus
vv       PALLD MUTATED PALLD WILD-TYPE
  FEMALE             7             218
  MALE               5             259
[1] 2 2
[1] FALSE
D849V9, binary
                 cls
clus                0   1
  PALLD MUTATED     8   0
  PALLD WILD-TYPE 342  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PALLD MUTATED      8    0
  PALLD WILD-TYPE  342   22
     clus
vv    PALLD MUTATED PALLD WILD-TYPE
  NO              8             342
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PALLD MUTATED                      7                             1
  PALLD WILD-TYPE                  308                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PALLD MUTATED                       3                              0
  PALLD WILD-TYPE                   103                             10
D849V10, multiclass
                                clus
vv                               PALLD MUTATED PALLD WILD-TYPE
  COLON ADENOCARCINOMA                       7             308
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      3             103
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  PALLD MUTATED     8   0   1   0
  PALLD WILD-TYPE 337   4  30  25
D849V11, multiclass
    clus
vv   PALLD MUTATED PALLD WILD-TYPE
  R0             8             337
  R1             0               4
  R2             1              30
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D849V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PALLD MUTATED                                  0     0
  PALLD WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PALLD MUTATED                           0     7
  PALLD WILD-TYPE                        22   219
D849V13, multiclass
                                  clus
vv                                 PALLD MUTATED PALLD WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        7             219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(850) Variable = C1QL3 MUTATION ANALYSIS
D850V1, survival
                 sevent
clus2               0   1
  C1QL3 MUTATED     4   0
  C1QL3 WILD-TYPE 374  93
  C1QL3 MUTATED C1QL3 WILD-TYPE 
              4             467 
  C1QL3 MUTATED C1QL3 WILD-TYPE 
              0              93 
$`C1QL3 MUTATED`
TCGA-A6-5665 TCGA-A6-6138 TCGA-CM-6166 TCGA-D5-6533 
       22.06        22.52        21.99         1.32 

$`C1QL3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       22.09        32.71        27.09         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6167 
       15.02        12.00         2.96        29.03        16.04        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       18.25        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  C1QL3 MUTATED C1QL3 WILD-TYPE 
           1.32            0.00 
  C1QL3 MUTATED C1QL3 WILD-TYPE 
          22.52          148.01 
  C1QL3 MUTATED C1QL3 WILD-TYPE 
         22.025          20.120 
[1] "1.3 - 22.5 (22.0)"  "0.0 - 148.0 (20.1)"
[1] "hr="     "3300000"
D850V2, continuous
D850V3, binary
                 cls
clus                0   1
  C1QL3 MUTATED     4   0
  C1QL3 WILD-TYPE 362 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  C1QL3 MUTATED      4    0
  C1QL3 WILD-TYPE  362  119
        clus
vv       C1QL3 MUTATED C1QL3 WILD-TYPE
  COLON              4             362
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  C1QL3 MUTATED         2        0        0         1         0         0
  C1QL3 WILD-TYPE      89        1       32       137        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  C1QL3 MUTATED           0          0          1          0        0         0
  C1QL3 WILD-TYPE        24         11         58         42       48        18
                 vv
clus              STAGE IVB
  C1QL3 MUTATED           0
  C1QL3 WILD-TYPE         1
D850V4, multiclass
            clus
vv           C1QL3 MUTATED C1QL3 WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              1             137
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  C1QL3 MUTATED     0   2   1   1
  C1QL3 WILD-TYPE  17  90 328  49
D850V5, multiclass
    clus
vv   C1QL3 MUTATED C1QL3 WILD-TYPE
  T1             0              17
  T2             2              90
  T3             1             328
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  C1QL3 MUTATED     4   0   0
  C1QL3 WILD-TYPE 283 113  87
D850V6, multiclass
    clus
vv   C1QL3 MUTATED C1QL3 WILD-TYPE
  N0             4             283
  N1             0             113
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D850V7, binary
                 cls
clus                0   1
  C1QL3 MUTATED     4   0
  C1QL3 WILD-TYPE 371  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  C1QL3 MUTATED      4    0
  C1QL3 WILD-TYPE  371   65
   clus
vv  C1QL3 MUTATED C1QL3 WILD-TYPE
  0             4             371
  1             0              65
[1] 2 2
[1] FALSE
D850V8, binary
                 cls
clus                0   1
  C1QL3 MUTATED     3   1
  C1QL3 WILD-TYPE 222 263
[1] "tbl2"
                 cls
clus              [,1] [,2]
  C1QL3 MUTATED      3    1
  C1QL3 WILD-TYPE  222  263
        clus
vv       C1QL3 MUTATED C1QL3 WILD-TYPE
  FEMALE             3             222
  MALE               1             263
[1] 2 2
[1] FALSE
D850V9, binary
                 cls
clus                0   1
  C1QL3 MUTATED     3   0
  C1QL3 WILD-TYPE 347  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  C1QL3 MUTATED      3    0
  C1QL3 WILD-TYPE  347   22
     clus
vv    C1QL3 MUTATED C1QL3 WILD-TYPE
  NO              3             347
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  C1QL3 MUTATED                      4                             0
  C1QL3 WILD-TYPE                  311                            47
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  C1QL3 MUTATED                       0                              0
  C1QL3 WILD-TYPE                   106                             10
D850V10, multiclass
                                clus
vv                               C1QL3 MUTATED C1QL3 WILD-TYPE
  COLON ADENOCARCINOMA                       4             311
  COLON MUCINOUS ADENOCARCINOMA              0              47
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  C1QL3 MUTATED     3   0   0   0
  C1QL3 WILD-TYPE 342   4  31  25
D850V11, multiclass
    clus
vv   C1QL3 MUTATED C1QL3 WILD-TYPE
  R0             3             342
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D850V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C1QL3 MUTATED                                  0     0
  C1QL3 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  C1QL3 MUTATED                           0     4
  C1QL3 WILD-TYPE                        22   222
D850V13, multiclass
                                  clus
vv                                 C1QL3 MUTATED C1QL3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        4             222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(851) Variable = SFRS18 MUTATION ANALYSIS
D851V1, survival
                  sevent
clus2                0   1
  SFRS18 MUTATED    11   1
  SFRS18 WILD-TYPE 367  92
  SFRS18 MUTATED SFRS18 WILD-TYPE 
              12              459 
  SFRS18 MUTATED SFRS18 WILD-TYPE 
               1               92 
$`SFRS18 MUTATED`
TCGA-A6-5661 TCGA-AA-3947 TCGA-AA-A00E TCGA-AA-A010 TCGA-AD-5900 TCGA-AD-6889 
       33.53        33.01        30.02        34.98         0.07        56.55 
TCGA-AD-6895 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-CA-6717 TCGA-CK-5913 TCGA-AG-A002 
        0.72        58.39        49.41        12.76        51.32        20.98 

$`SFRS18 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
        2.01        12.99        24.00        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       19.00        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        21.37        15.52         0.79         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        33.01        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 
      106.75        22.36        62.79        88.21         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       49.08         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  SFRS18 MUTATED SFRS18 WILD-TYPE 
            0.07             0.00 
  SFRS18 MUTATED SFRS18 WILD-TYPE 
           58.39           148.01 
  SFRS18 MUTATED SFRS18 WILD-TYPE 
           33.27            20.02 
[1] "0.1 - 58.4 (33.3)"  "0.0 - 148.0 (20.0)"
[1] "hr=" "3"  
D851V2, continuous
D851V3, binary
                  cls
clus                 0   1
  SFRS18 MUTATED    12   1
  SFRS18 WILD-TYPE 354 118
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SFRS18 MUTATED     12    1
  SFRS18 WILD-TYPE  354  118
        clus
vv       SFRS18 MUTATED SFRS18 WILD-TYPE
  COLON              12              354
  RECTUM              1              118
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SFRS18 MUTATED         2        0        1         7         2         0
  SFRS18 WILD-TYPE      89        1       31       131         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SFRS18 MUTATED           0          0          0          0        0
  SFRS18 WILD-TYPE        24         11         59         42       48
                  vv
clus               STAGE IVA STAGE IVB
  SFRS18 MUTATED           0         0
  SFRS18 WILD-TYPE        18         1
D851V4, multiclass
            clus
vv           SFRS18 MUTATED SFRS18 WILD-TYPE
  STAGE I                 2               89
  STAGE IA                0                1
  STAGE II                1               31
  STAGE IIA               7              131
  STAGE IIB               2                8
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              0               59
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  SFRS18 MUTATED     0   2   9   2
  SFRS18 WILD-TYPE  17  90 320  48
D851V5, multiclass
    clus
vv   SFRS18 MUTATED SFRS18 WILD-TYPE
  T1              0               17
  T2              2               90
  T3              9              320
  T4              2               48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  SFRS18 MUTATED    12   1   0
  SFRS18 WILD-TYPE 275 112  87
D851V6, multiclass
    clus
vv   SFRS18 MUTATED SFRS18 WILD-TYPE
  N0             12              275
  N1              1              112
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D851V7, binary
                  cls
clus                 0   1
  SFRS18 MUTATED     9   0
  SFRS18 WILD-TYPE 366  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SFRS18 MUTATED      9    0
  SFRS18 WILD-TYPE  366   65
   clus
vv  SFRS18 MUTATED SFRS18 WILD-TYPE
  0              9              366
  1              0               65
[1] 2 2
[1] FALSE
D851V8, binary
                  cls
clus                 0   1
  SFRS18 MUTATED     6   7
  SFRS18 WILD-TYPE 219 257
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SFRS18 MUTATED      6    7
  SFRS18 WILD-TYPE  219  257
        clus
vv       SFRS18 MUTATED SFRS18 WILD-TYPE
  FEMALE              6              219
  MALE                7              257
[1] 2 2
[1] FALSE
D851V9, binary
                  cls
clus                 0   1
  SFRS18 MUTATED     9   0
  SFRS18 WILD-TYPE 341  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SFRS18 MUTATED      9    0
  SFRS18 WILD-TYPE  341   22
     clus
vv    SFRS18 MUTATED SFRS18 WILD-TYPE
  NO               9              341
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SFRS18 MUTATED                      9                             3
  SFRS18 WILD-TYPE                  306                            44
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SFRS18 MUTATED                       1                              0
  SFRS18 WILD-TYPE                   105                             10
D851V10, multiclass
                                clus
vv                               SFRS18 MUTATED SFRS18 WILD-TYPE
  COLON ADENOCARCINOMA                        9              306
  COLON MUCINOUS ADENOCARCINOMA               3               44
  RECTAL ADENOCARCINOMA                       1              105
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  SFRS18 MUTATED     8   0   0   2
  SFRS18 WILD-TYPE 337   4  31  23
D851V11, multiclass
    clus
vv   SFRS18 MUTATED SFRS18 WILD-TYPE
  R0              8              337
  R1              0                4
  R2              0               31
  RX              2               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D851V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SFRS18 MUTATED                                  0     2
  SFRS18 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  SFRS18 MUTATED                           1     5
  SFRS18 WILD-TYPE                        21   221
D851V13, multiclass
                                  clus
vv                                 SFRS18 MUTATED SFRS18 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                9
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                         5              221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(852) Variable = TAT MUTATION ANALYSIS
D852V1, survival
               sevent
clus2             0   1
  TAT MUTATED    11   3
  TAT WILD-TYPE 367  90
  TAT MUTATED TAT WILD-TYPE 
           14           457 
  TAT MUTATED TAT WILD-TYPE 
            3            90 
$`TAT MUTATED`
TCGA-AA-3713 TCGA-AA-3950 TCGA-AA-3977 TCGA-AA-A00R TCGA-AZ-6598 TCGA-AZ-6601 
       19.04        24.00        25.02         0.99        49.41       100.01 
TCGA-CA-6718 TCGA-CK-4950 TCGA-CM-5348 TCGA-CM-6161 TCGA-D5-7000 TCGA-G4-6304 
       10.06        85.45        22.98        15.02        10.26        53.62 
TCGA-G4-6588 TCGA-AG-A002 
       26.17        20.98 

$`TAT WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 
        2.01        12.99        24.00        33.01        26.01         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       27.02        42.02        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 
       62.79        88.21         6.77        12.10        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07        12.20        12.76        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
      148.01        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5860 
       25.02        13.02        29.06        22.03        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6162 
       15.02         5.03        15.02        15.02        17.03        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
        1.51        12.00        11.38       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 
       47.41        35.31       133.18        74.56        65.85        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       13.78        35.80        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  TAT MUTATED TAT WILD-TYPE 
         0.99          0.00 
  TAT MUTATED TAT WILD-TYPE 
       100.01        148.01 
  TAT MUTATED TAT WILD-TYPE 
        23.49         20.05 
[1] "1.0 - 100.0 (23.5)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.2"
D852V2, continuous
D852V3, binary
               cls
clus              0   1
  TAT MUTATED    14   1
  TAT WILD-TYPE 352 118
[1] "tbl2"
               cls
clus            [,1] [,2]
  TAT MUTATED     14    1
  TAT WILD-TYPE  352  118
        clus
vv       TAT MUTATED TAT WILD-TYPE
  COLON           14           352
  RECTUM           1           118
[1] 2 2
[1] FALSE
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TAT MUTATED         4        0        2         4         1         0
  TAT WILD-TYPE      87        1       30       134         9         1
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TAT MUTATED           0          0          2          0        1         0
  TAT WILD-TYPE        24         11         57         42       47        18
               vv
clus            STAGE IVB
  TAT MUTATED           0
  TAT WILD-TYPE         1
D852V4, multiclass
            clus
vv           TAT MUTATED TAT WILD-TYPE
  STAGE I              4            87
  STAGE IA             0             1
  STAGE II             2            30
  STAGE IIA            4           134
  STAGE IIB            1             9
  STAGE IIC            0             1
  STAGE III            0            24
  STAGE IIIA           0            11
  STAGE IIIB           2            57
  STAGE IIIC           0            42
  STAGE IV             1            47
  STAGE IVA            0            18
  STAGE IVB            0             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  TAT MUTATED     0   5   9   1
  TAT WILD-TYPE  17  87 320  49
D852V5, multiclass
    clus
vv   TAT MUTATED TAT WILD-TYPE
  T1           0            17
  T2           5            87
  T3           9           320
  T4           1            49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2
  TAT MUTATED    13   2   0
  TAT WILD-TYPE 274 111  87
D852V6, multiclass
    clus
vv   TAT MUTATED TAT WILD-TYPE
  N0          13           274
  N1           2           111
  N2           0            87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D852V7, binary
               cls
clus              0   1
  TAT MUTATED    12   1
  TAT WILD-TYPE 363  64
[1] "tbl2"
               cls
clus            [,1] [,2]
  TAT MUTATED     12    1
  TAT WILD-TYPE  363   64
   clus
vv  TAT MUTATED TAT WILD-TYPE
  0          12           363
  1           1            64
[1] 2 2
[1] FALSE
D852V8, binary
               cls
clus              0   1
  TAT MUTATED     9   6
  TAT WILD-TYPE 216 258
[1] "tbl2"
               cls
clus            [,1] [,2]
  TAT MUTATED      9    6
  TAT WILD-TYPE  216  258
        clus
vv       TAT MUTATED TAT WILD-TYPE
  FEMALE           9           216
  MALE             6           258
[1] 2 2
[1] FALSE
D852V9, binary
               cls
clus              0   1
  TAT MUTATED    12   1
  TAT WILD-TYPE 338  21
[1] "tbl2"
               cls
clus            [,1] [,2]
  TAT MUTATED     12    1
  TAT WILD-TYPE  338   21
     clus
vv    TAT MUTATED TAT WILD-TYPE
  NO           12           338
  YES           1            21
[1] 2 2
[1] FALSE
               vv
clus            COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  TAT MUTATED                     12                             2
  TAT WILD-TYPE                  303                            45
               vv
clus            RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  TAT MUTATED                       1                              0
  TAT WILD-TYPE                   105                             10
D852V10, multiclass
                                clus
vv                               TAT MUTATED TAT WILD-TYPE
  COLON ADENOCARCINOMA                    12           303
  COLON MUCINOUS ADENOCARCINOMA            2            45
  RECTAL ADENOCARCINOMA                    1           105
  RECTAL MUCINOUS ADENOCARCINOMA           0            10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             R0  R1  R2  RX
  TAT MUTATED     9   1   1   1
  TAT WILD-TYPE 336   3  30  24
D852V11, multiclass
    clus
vv   TAT MUTATED TAT WILD-TYPE
  R0           9           336
  R1           1             3
  R2           1            30
  RX           1            24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D852V12, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TAT MUTATED                                  0     1
  TAT WILD-TYPE                                1    10
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  TAT MUTATED                           1     7
  TAT WILD-TYPE                        21   219
D852V13, multiclass
                                  clus
vv                                 TAT MUTATED TAT WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      1            10
  BLACK OR AFRICAN AMERICAN                  1            21
  WHITE                                      7           219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(853) Variable = LRRC6 MUTATION ANALYSIS
D853V1, survival
                 sevent
clus2               0   1
  LRRC6 MUTATED     3   1
  LRRC6 WILD-TYPE 375  92
  LRRC6 MUTATED LRRC6 WILD-TYPE 
              4             467 
  LRRC6 MUTATED LRRC6 WILD-TYPE 
              1              92 
$`LRRC6 MUTATED`
TCGA-A6-6142 TCGA-AZ-6607 TCGA-F4-6808 TCGA-AG-3892 
       25.08         3.19        33.67        13.02 

$`LRRC6 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 
       19.99         1.02        17.95        36.95        17.03        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  LRRC6 MUTATED LRRC6 WILD-TYPE 
           3.19            0.00 
  LRRC6 MUTATED LRRC6 WILD-TYPE 
          33.67          148.01 
  LRRC6 MUTATED LRRC6 WILD-TYPE 
          19.05           20.19 
[1] "3.2 - 33.7 (19.0)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.8"
D853V2, continuous
D853V3, binary
                 cls
clus                0   1
  LRRC6 MUTATED     3   1
  LRRC6 WILD-TYPE 363 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LRRC6 MUTATED      3    1
  LRRC6 WILD-TYPE  363  118
        clus
vv       LRRC6 MUTATED LRRC6 WILD-TYPE
  COLON              3             363
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  LRRC6 MUTATED         2        0        0         0         0         0
  LRRC6 WILD-TYPE      89        1       32       138        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  LRRC6 MUTATED           0          0          0          0        1         1
  LRRC6 WILD-TYPE        24         11         59         42       47        17
                 vv
clus              STAGE IVB
  LRRC6 MUTATED           0
  LRRC6 WILD-TYPE         1
D853V4, multiclass
            clus
vv           LRRC6 MUTATED LRRC6 WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              0             138
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             0              42
  STAGE IV               1              47
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  LRRC6 MUTATED     2   0   1   1
  LRRC6 WILD-TYPE  15  92 328  49
D853V5, multiclass
    clus
vv   LRRC6 MUTATED LRRC6 WILD-TYPE
  T1             2              15
  T2             0              92
  T3             1             328
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  LRRC6 MUTATED     2   1   1
  LRRC6 WILD-TYPE 285 112  86
D853V6, multiclass
    clus
vv   LRRC6 MUTATED LRRC6 WILD-TYPE
  N0             2             285
  N1             1             112
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D853V7, binary
                 cls
clus                0   1
  LRRC6 MUTATED     2   2
  LRRC6 WILD-TYPE 373  63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LRRC6 MUTATED      2    2
  LRRC6 WILD-TYPE  373   63
   clus
vv  LRRC6 MUTATED LRRC6 WILD-TYPE
  0             2             373
  1             2              63
[1] 2 2
[1] FALSE
D853V8, binary
                 cls
clus                0   1
  LRRC6 MUTATED     3   1
  LRRC6 WILD-TYPE 222 263
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LRRC6 MUTATED      3    1
  LRRC6 WILD-TYPE  222  263
        clus
vv       LRRC6 MUTATED LRRC6 WILD-TYPE
  FEMALE             3             222
  MALE               1             263
[1] 2 2
[1] FALSE
D853V9, binary
                 cls
clus                0   1
  LRRC6 MUTATED     4   0
  LRRC6 WILD-TYPE 346  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LRRC6 MUTATED      4    0
  LRRC6 WILD-TYPE  346   22
     clus
vv    LRRC6 MUTATED LRRC6 WILD-TYPE
  NO              4             346
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  LRRC6 MUTATED                      3                             0
  LRRC6 WILD-TYPE                  312                            47
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  LRRC6 MUTATED                       1                              0
  LRRC6 WILD-TYPE                   105                             10
D853V10, multiclass
                                clus
vv                               LRRC6 MUTATED LRRC6 WILD-TYPE
  COLON ADENOCARCINOMA                       3             312
  COLON MUCINOUS ADENOCARCINOMA              0              47
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  LRRC6 MUTATED     2   0   0   0
  LRRC6 WILD-TYPE 343   4  31  25
D853V11, multiclass
[1] "Remove cluster labels:" "LRRC6 MUTATED"         
clus
  LRRC6 MUTATED LRRC6 WILD-TYPE 
              2             403 
     TCGA-A6-2671      TCGA-A6-2672      TCGA-A6-2674      TCGA-A6-2676 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-A6-2677      TCGA-A6-2678      TCGA-A6-2683      TCGA-A6-3807 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-A6-3808      TCGA-A6-3809      TCGA-A6-3810      TCGA-A6-5657 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-A6-5659      TCGA-A6-5661      TCGA-A6-5665      TCGA-A6-6781 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-AA-3489      TCGA-AA-3492      TCGA-AA-3496      TCGA-AA-3502 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-AA-3510      TCGA-AA-3511      TCGA-AA-3514      TCGA-AA-3517 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-AA-3518      TCGA-AA-3519      TCGA-AA-3520      TCGA-AA-3521 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-AA-3522      TCGA-AA-3524      TCGA-AA-3525      TCGA-AA-3526 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-AA-3527      TCGA-AA-3529      TCGA-AA-3530      TCGA-AA-3531 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-AA-3532      TCGA-AA-3534      TCGA-AA-3538      TCGA-AA-3542 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-AA-3543      TCGA-AA-3544      TCGA-AA-3548      TCGA-AA-3549 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-AA-3552      TCGA-AA-3553      TCGA-AA-3554      TCGA-AA-3555 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-AA-3556      TCGA-AA-3558      TCGA-AA-3560      TCGA-AA-3561 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-AA-3562      TCGA-AA-3655      TCGA-AA-3660      TCGA-AA-3662 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-AA-3663      TCGA-AA-3664      TCGA-AA-3666      TCGA-AA-3667 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-AA-3672      TCGA-AA-3673      TCGA-AA-3678      TCGA-AA-3679 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-AA-3680      TCGA-AA-3681      TCGA-AA-3684      TCGA-AA-3685 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-AA-3688      TCGA-AA-3692      TCGA-AA-3693      TCGA-AA-3695 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-AA-3696      TCGA-AA-3697      TCGA-AA-3710      TCGA-AA-3712 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-AA-3713      TCGA-AA-3715      TCGA-AA-3811      TCGA-AA-3812 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-AA-3814      TCGA-AA-3815      TCGA-AA-3818      TCGA-AA-3819 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-AA-3821      TCGA-AA-3831      TCGA-AA-3833      TCGA-AA-3837 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-AA-3842      TCGA-AA-3844      TCGA-AA-3845      TCGA-AA-3846 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-AA-3848      TCGA-AA-3850      TCGA-AA-3851      TCGA-AA-3852 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-AA-3854      TCGA-AA-3855      TCGA-AA-3856      TCGA-AA-3858 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-AA-3860      TCGA-AA-3861      TCGA-AA-3864      TCGA-AA-3866 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-AA-3867      TCGA-AA-3869      TCGA-AA-3870      TCGA-AA-3872 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-AA-3875      TCGA-AA-3877      TCGA-AA-3930      TCGA-AA-3939 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-AA-3941      TCGA-AA-3947      TCGA-AA-3949      TCGA-AA-3950 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-AA-3952      TCGA-AA-3955      TCGA-AA-3956      TCGA-AA-3968 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-AA-3971      TCGA-AA-3972      TCGA-AA-3973      TCGA-AA-3975 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-AA-3976      TCGA-AA-3979      TCGA-AA-3984      TCGA-AA-3986 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-AA-3989      TCGA-AA-3994      TCGA-AA-A004      TCGA-AA-A00A 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-AA-A00D      TCGA-AA-A00E      TCGA-AA-A00F      TCGA-AA-A00J 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-AA-A00K      TCGA-AA-A00L      TCGA-AA-A00N      TCGA-AA-A00O 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-AA-A00Q      TCGA-AA-A00R      TCGA-AA-A00U      TCGA-AA-A00W 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-AA-A00Z      TCGA-AA-A010      TCGA-AA-A017      TCGA-AA-A01D 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-AA-A01F      TCGA-AA-A01G      TCGA-AA-A01I      TCGA-AA-A01K 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-AA-A01P      TCGA-AA-A01Q      TCGA-AA-A01R      TCGA-AA-A01S 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-AA-A01T      TCGA-AA-A01V      TCGA-AA-A01X      TCGA-AA-A01Z 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-AA-A022      TCGA-AA-A024      TCGA-AA-A029      TCGA-AA-A02F 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-AA-A02H      TCGA-AA-A02J      TCGA-AA-A02K      TCGA-AA-A02O 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-AA-A02W      TCGA-AA-A02Y      TCGA-AA-A03F      TCGA-AA-A03J 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-AD-5900      TCGA-AD-6548      TCGA-AD-6888      TCGA-AU-3779 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-AU-6004      TCGA-AY-4070      TCGA-AY-4071      TCGA-AY-5543 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-AY-6196      TCGA-AY-6197      TCGA-AY-6386      TCGA-AZ-4315 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-AZ-4681      TCGA-AZ-4682      TCGA-CA-5254      TCGA-CA-5255 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-CA-5796      TCGA-CA-5797      TCGA-CA-6715      TCGA-CA-6716 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-CA-6717      TCGA-CA-6718      TCGA-CA-6719      TCGA-CK-4947 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-CK-4948      TCGA-CK-4950      TCGA-CK-4952      TCGA-CK-5912 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-CK-5913      TCGA-CK-5914      TCGA-CK-5915      TCGA-CK-5916 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-CK-6746      TCGA-CK-6747      TCGA-CK-6748      TCGA-CK-6751 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-CM-4743      TCGA-CM-4744      TCGA-CM-4746      TCGA-CM-4747 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-CM-4752      TCGA-CM-5341      TCGA-CM-5344      TCGA-CM-5348 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-CM-5349      TCGA-CM-5860      TCGA-CM-5861      TCGA-CM-5862 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-CM-5863      TCGA-CM-5864      TCGA-CM-5868      TCGA-CM-6161 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-CM-6162      TCGA-CM-6163      TCGA-CM-6164      TCGA-CM-6165 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-CM-6166      TCGA-CM-6167      TCGA-CM-6168      TCGA-CM-6169 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-CM-6170      TCGA-CM-6171      TCGA-CM-6172      TCGA-CM-6674 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-CM-6675      TCGA-CM-6676      TCGA-CM-6677      TCGA-CM-6678 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-CM-6679      TCGA-CM-6680      TCGA-D5-5537      TCGA-D5-5538 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-D5-5539      TCGA-D5-5540      TCGA-D5-5541      TCGA-D5-6529 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-D5-6532      TCGA-D5-6533      TCGA-D5-6534      TCGA-D5-6535 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-D5-6536      TCGA-D5-6537      TCGA-D5-6538      TCGA-D5-6539 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-D5-6540      TCGA-D5-6541      TCGA-D5-6898      TCGA-D5-6920 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-D5-6922      TCGA-D5-6923      TCGA-D5-6924      TCGA-D5-6926 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-D5-6927      TCGA-D5-6928      TCGA-D5-6929      TCGA-D5-6930 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-D5-6931      TCGA-D5-6932      TCGA-D5-7000      TCGA-F4-6459 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-F4-6460      TCGA-F4-6569      TCGA-F4-6570      TCGA-F4-6703 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-F4-6704      TCGA-F4-6805      TCGA-F4-6806      TCGA-F4-6807 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-F4-6809      TCGA-F4-6854      TCGA-F4-6855      TCGA-F4-6856 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-G4-6293      TCGA-G4-6299      TCGA-G4-6303      TCGA-G4-6304 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-G4-6306      TCGA-G4-6307      TCGA-G4-6309      TCGA-G4-6310 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-G4-6315      TCGA-G4-6317      TCGA-G4-6321      TCGA-G4-6323 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-G4-6586      TCGA-G4-6588      TCGA-G4-6625      TCGA-G4-6626 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-G4-6628      TCGA-AF-2687      TCGA-AF-2689      TCGA-AF-2691 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-AF-2692      TCGA-AF-3400      TCGA-AF-3913      TCGA-AF-4110 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-AF-5654      TCGA-AF-6655      TCGA-AG-3574      TCGA-AG-3575 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-AG-3578      TCGA-AG-3580      TCGA-AG-3581      TCGA-AG-3582 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-AG-3583      TCGA-AG-3584      TCGA-AG-3586      TCGA-AG-3587 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-AG-3593      TCGA-AG-3594      TCGA-AG-3598      TCGA-AG-3599 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-AG-3600      TCGA-AG-3601      TCGA-AG-3602      TCGA-AG-3605 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-AG-3608      TCGA-AG-3609      TCGA-AG-3611      TCGA-AG-3612 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-AG-3726      TCGA-AG-3727      TCGA-AG-3731      TCGA-AG-3732 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-AG-3742      TCGA-AG-3878      TCGA-AG-3882      TCGA-AG-3883 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-AG-3885      TCGA-AG-3887      TCGA-AG-3890      TCGA-AG-3893 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-AG-3894      TCGA-AG-3896      TCGA-AG-3898      TCGA-AG-3901 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-AG-3902      TCGA-AG-3909      TCGA-AG-3999      TCGA-AG-4001 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-AG-4005      TCGA-AG-4007      TCGA-AG-4008      TCGA-AG-4015 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-AG-A002      TCGA-AG-A008      TCGA-AG-A00C      TCGA-AG-A00H 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-AG-A00Y      TCGA-AG-A011      TCGA-AG-A014      TCGA-AG-A015 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-AG-A016      TCGA-AG-A01L      TCGA-AG-A01W      TCGA-AG-A01Y 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-AG-A020      TCGA-AG-A025      TCGA-AG-A026      TCGA-AG-A02G 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-AG-A02N      TCGA-AG-A02X      TCGA-AG-A032      TCGA-AG-A036 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-AH-6549      TCGA-AH-6643      TCGA-CL-5917      TCGA-CL-5918 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-DC-5337      TCGA-DC-5869      TCGA-DC-6155      TCGA-DC-6157 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-DC-6158      TCGA-DC-6160      TCGA-DC-6681      TCGA-DC-6682 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-DC-6683      TCGA-DT-5265      TCGA-EF-5830      TCGA-EI-6506 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-EI-6507      TCGA-EI-6508      TCGA-EI-6510      TCGA-F5-6464 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-F5-6465      TCGA-F5-6571      TCGA-F5-6702      TCGA-F5-6812 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
     TCGA-F5-6813      TCGA-G5-6235      TCGA-G5-6641 
"LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" "LRRC6 WILD-TYPE" 
D853V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  LRRC6 MUTATED                                  0     0
  LRRC6 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  LRRC6 MUTATED                           0     3
  LRRC6 WILD-TYPE                        22   223
D853V13, multiclass
                                  clus
vv                                 LRRC6 MUTATED LRRC6 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        3             223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(854) Variable = ADAM18 MUTATION ANALYSIS
D854V1, survival
                  sevent
clus2                0   1
  ADAM18 MUTATED    19   4
  ADAM18 WILD-TYPE 359  89
  ADAM18 MUTATED ADAM18 WILD-TYPE 
              23              448 
  ADAM18 MUTATED ADAM18 WILD-TYPE 
               4               89 
$`ADAM18 MUTATED`
TCGA-A6-5661 TCGA-A6-6137 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3815 
       33.53        27.09        19.04        19.04        35.05        33.04 
TCGA-AA-3845 TCGA-AA-A010 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-CA-6717 TCGA-CK-5913 
        0.00        34.98        58.39        49.41        12.76        51.32 
TCGA-CM-6168 TCGA-CM-6172 TCGA-D5-5541 TCGA-D5-6540 TCGA-DM-A1DB TCGA-G4-6307 
       12.99        11.01        55.92        16.14        44.32        55.04 
TCGA-AG-3609 TCGA-AG-A002 TCGA-AG-A02N TCGA-DY-A0XA TCGA-F5-6813 
       19.99        20.98        61.97       126.44         0.69 

$`ADAM18 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       22.06        32.71        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3818 TCGA-AA-3819 
        5.03        85.05        26.99        10.06         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       33.01        21.44        17.82         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        88.21         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07        12.20        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       16.04        21.99        14.99        13.02        15.02        14.04 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-6529 
       12.03        45.40        12.26        19.59        56.09        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       17.13        12.49        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
      140.38         7.50       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       44.68        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3611 
       50.04        12.03         6.05         0.99        15.95        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 
       10.98        49.97         1.94        38.96        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD 
        5.95         4.01         5.03         5.29        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66        55.76        26.43 

  ADAM18 MUTATED ADAM18 WILD-TYPE 
               0                0 
  ADAM18 MUTATED ADAM18 WILD-TYPE 
          126.44           148.01 
  ADAM18 MUTATED ADAM18 WILD-TYPE 
          33.040           20.035 
[1] "0.0 - 126.4 (33.0)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.5"
D854V2, continuous
D854V3, binary
                  cls
clus                 0   1
  ADAM18 MUTATED    18   5
  ADAM18 WILD-TYPE 348 114
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ADAM18 MUTATED     18    5
  ADAM18 WILD-TYPE  348  114
        clus
vv       ADAM18 MUTATED ADAM18 WILD-TYPE
  COLON              18              348
  RECTUM              5              114
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ADAM18 MUTATED         2        0        3        10         1         0
  ADAM18 WILD-TYPE      89        1       29       128         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ADAM18 MUTATED           0          0          4          2        1
  ADAM18 WILD-TYPE        24         11         55         40       47
                  vv
clus               STAGE IVA STAGE IVB
  ADAM18 MUTATED           0         0
  ADAM18 WILD-TYPE        18         1
D854V4, multiclass
            clus
vv           ADAM18 MUTATED ADAM18 WILD-TYPE
  STAGE I                 2               89
  STAGE IA                0                1
  STAGE II                3               29
  STAGE IIA              10              128
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              4               55
  STAGE IIIC              2               40
  STAGE IV                1               47
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ADAM18 MUTATED     0   2  19   2
  ADAM18 WILD-TYPE  17  90 310  48
D854V5, multiclass
    clus
vv   ADAM18 MUTATED ADAM18 WILD-TYPE
  T1              0               17
  T2              2               90
  T3             19              310
  T4              2               48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  ADAM18 MUTATED    17   4   2
  ADAM18 WILD-TYPE 270 109  85
D854V6, multiclass
    clus
vv   ADAM18 MUTATED ADAM18 WILD-TYPE
  N0             17              270
  N1              4              109
  N2              2               85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D854V7, binary
                  cls
clus                 0   1
  ADAM18 MUTATED    20   1
  ADAM18 WILD-TYPE 355  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ADAM18 MUTATED     20    1
  ADAM18 WILD-TYPE  355   64
   clus
vv  ADAM18 MUTATED ADAM18 WILD-TYPE
  0             20              355
  1              1               64
[1] 2 2
[1] FALSE
D854V8, binary
                  cls
clus                 0   1
  ADAM18 MUTATED    12  11
  ADAM18 WILD-TYPE 213 253
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ADAM18 MUTATED     12   11
  ADAM18 WILD-TYPE  213  253
        clus
vv       ADAM18 MUTATED ADAM18 WILD-TYPE
  FEMALE             12              213
  MALE               11              253
[1] 2 2
[1] FALSE
D854V9, binary
                  cls
clus                 0   1
  ADAM18 MUTATED    17   1
  ADAM18 WILD-TYPE 333  21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ADAM18 MUTATED     17    1
  ADAM18 WILD-TYPE  333   21
     clus
vv    ADAM18 MUTATED ADAM18 WILD-TYPE
  NO              17              333
  YES              1               21
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ADAM18 MUTATED                     16                             2
  ADAM18 WILD-TYPE                  299                            45
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ADAM18 MUTATED                       5                              0
  ADAM18 WILD-TYPE                   101                             10
D854V10, multiclass
                                clus
vv                               ADAM18 MUTATED ADAM18 WILD-TYPE
  COLON ADENOCARCINOMA                       16              299
  COLON MUCINOUS ADENOCARCINOMA               2               45
  RECTAL ADENOCARCINOMA                       5              101
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ADAM18 MUTATED    16   0   1   2
  ADAM18 WILD-TYPE 329   4  30  23
D854V11, multiclass
    clus
vv   ADAM18 MUTATED ADAM18 WILD-TYPE
  R0             16              329
  R1              0                4
  R2              1               30
  RX              2               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D854V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ADAM18 MUTATED                                  0     1
  ADAM18 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ADAM18 MUTATED                           2    11
  ADAM18 WILD-TYPE                        20   215
D854V13, multiclass
                                  clus
vv                                 ADAM18 MUTATED ADAM18 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     2               20
  WHITE                                        11              215
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(855) Variable = MRAS MUTATION ANALYSIS
D855V1, survival
                sevent
clus2              0   1
  MRAS MUTATED     3   1
  MRAS WILD-TYPE 375  92
  MRAS MUTATED MRAS WILD-TYPE 
             4            467 
  MRAS MUTATED MRAS WILD-TYPE 
             1             92 
$`MRAS MUTATED`
TCGA-A6-2676 TCGA-CM-5344 TCGA-CM-6161 TCGA-DM-A1HB 
       42.90        22.03        15.02       135.65 

$`MRAS WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5349 
       37.02        25.02        13.02        29.06        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 
       12.59       140.38         7.50        44.32       131.51       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  MRAS MUTATED MRAS WILD-TYPE 
         15.02           0.00 
  MRAS MUTATED MRAS WILD-TYPE 
        135.65         148.01 
  MRAS MUTATED MRAS WILD-TYPE 
        32.465         20.120 
[1] "15.0 - 135.7 (32.5)" "0.0 - 148.0 (20.1)" 
[1] "hr=" "1.4"
D855V2, continuous
D855V3, binary
                cls
clus               0   1
  MRAS MUTATED     4   0
  MRAS WILD-TYPE 362 119
[1] "tbl2"
                cls
clus             [,1] [,2]
  MRAS MUTATED      4    0
  MRAS WILD-TYPE  362  119
        clus
vv       MRAS MUTATED MRAS WILD-TYPE
  COLON             4            362
  RECTUM            0            119
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MRAS MUTATED         1        0        0         0         1         0
  MRAS WILD-TYPE      90        1       32       138         9         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MRAS MUTATED           0          0          2          0        0         0
  MRAS WILD-TYPE        24         11         57         42       48        18
                vv
clus             STAGE IVB
  MRAS MUTATED           0
  MRAS WILD-TYPE         1
D855V4, multiclass
            clus
vv           MRAS MUTATED MRAS WILD-TYPE
  STAGE I               1             90
  STAGE IA              0              1
  STAGE II              0             32
  STAGE IIA             0            138
  STAGE IIB             1              9
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            2             57
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  MRAS MUTATED     0   1   2   1
  MRAS WILD-TYPE  17  91 327  49
D855V5, multiclass
    clus
vv   MRAS MUTATED MRAS WILD-TYPE
  T1            0             17
  T2            1             91
  T3            2            327
  T4            1             49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  MRAS MUTATED     2   2   0
  MRAS WILD-TYPE 285 111  87
D855V6, multiclass
    clus
vv   MRAS MUTATED MRAS WILD-TYPE
  N0            2            285
  N1            2            111
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D855V7, binary
                cls
clus               0   1
  MRAS MUTATED     4   0
  MRAS WILD-TYPE 371  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  MRAS MUTATED      4    0
  MRAS WILD-TYPE  371   65
   clus
vv  MRAS MUTATED MRAS WILD-TYPE
  0            4            371
  1            0             65
[1] 2 2
[1] FALSE
D855V8, binary
                cls
clus               0   1
  MRAS MUTATED     3   1
  MRAS WILD-TYPE 222 263
[1] "tbl2"
                cls
clus             [,1] [,2]
  MRAS MUTATED      3    1
  MRAS WILD-TYPE  222  263
        clus
vv       MRAS MUTATED MRAS WILD-TYPE
  FEMALE            3            222
  MALE              1            263
[1] 2 2
[1] FALSE
D855V9, binary
                cls
clus               0   1
  MRAS MUTATED     3   0
  MRAS WILD-TYPE 347  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  MRAS MUTATED      3    0
  MRAS WILD-TYPE  347   22
     clus
vv    MRAS MUTATED MRAS WILD-TYPE
  NO             3            347
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MRAS MUTATED                      3                             0
  MRAS WILD-TYPE                  312                            47
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MRAS MUTATED                       0                              0
  MRAS WILD-TYPE                   106                             10
D855V10, multiclass
                                clus
vv                               MRAS MUTATED MRAS WILD-TYPE
  COLON ADENOCARCINOMA                      3            312
  COLON MUCINOUS ADENOCARCINOMA             0             47
  RECTAL ADENOCARCINOMA                     0            106
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  MRAS MUTATED     3   0   0   0
  MRAS WILD-TYPE 342   4  31  25
D855V11, multiclass
    clus
vv   MRAS MUTATED MRAS WILD-TYPE
  R0            3            342
  R1            0              4
  R2            0             31
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D855V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MRAS MUTATED                                  0     0
  MRAS WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  MRAS MUTATED                           0     4
  MRAS WILD-TYPE                        22   222
D855V13, multiclass
                                  clus
vv                                 MRAS MUTATED MRAS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       4            222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(856) Variable = ADNP2 MUTATION ANALYSIS
D856V1, survival
                 sevent
clus2               0   1
  ADNP2 MUTATED    14   3
  ADNP2 WILD-TYPE 364  90
  ADNP2 MUTATED ADNP2 WILD-TYPE 
             17             454 
  ADNP2 MUTATED ADNP2 WILD-TYPE 
              3              90 
$`ADNP2 MUTATED`
TCGA-A6-5665 TCGA-A6-6141 TCGA-AA-3510 TCGA-AA-3710 TCGA-AA-A01Q TCGA-AA-A02O 
       22.06         8.38        63.98        26.99         1.02         0.92 
TCGA-AY-6197 TCGA-CK-4947 TCGA-D5-6535 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1HB 
       21.44        17.56        15.12        92.75        49.91       135.65 
TCGA-F4-6570 TCGA-G4-6293 TCGA-G4-6628 TCGA-AG-3892 TCGA-AG-A002 
        6.18       133.18        79.69        13.02        20.98 

$`ADNP2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 
       22.09        32.71        27.09        22.52        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       85.05        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
       38.07        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
       14.01        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       16.31         0.95        33.01        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4948 
        0.07        12.20        12.76        10.06        14.30       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 
       20.19        18.25         1.32        43.27        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
       24.43        38.20       130.65        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
        7.50        44.32       131.51       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       31.96        35.74        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       26.17        91.79        46.75        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 
       19.99         1.02        17.95        36.95        17.03        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  ADNP2 MUTATED ADNP2 WILD-TYPE 
           0.92            0.00 
  ADNP2 MUTATED ADNP2 WILD-TYPE 
         135.65          148.01 
  ADNP2 MUTATED ADNP2 WILD-TYPE 
         21.440          20.085 
[1] "0.9 - 135.7 (21.4)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.7"
D856V2, continuous
D856V3, binary
                 cls
clus                0   1
  ADNP2 MUTATED    15   2
  ADNP2 WILD-TYPE 351 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ADNP2 MUTATED     15    2
  ADNP2 WILD-TYPE  351  117
        clus
vv       ADNP2 MUTATED ADNP2 WILD-TYPE
  COLON             15             351
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ADNP2 MUTATED         3        0        3         7         0         0
  ADNP2 WILD-TYPE      88        1       29       131        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ADNP2 MUTATED           1          0          3          0        0         0
  ADNP2 WILD-TYPE        23         11         56         42       48        18
                 vv
clus              STAGE IVB
  ADNP2 MUTATED           0
  ADNP2 WILD-TYPE         1
D856V4, multiclass
            clus
vv           ADNP2 MUTATED ADNP2 WILD-TYPE
  STAGE I                3              88
  STAGE IA               0               1
  STAGE II               3              29
  STAGE IIA              7             131
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             3              56
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ADNP2 MUTATED     1   2  13   1
  ADNP2 WILD-TYPE  16  90 316  49
D856V5, multiclass
    clus
vv   ADNP2 MUTATED ADNP2 WILD-TYPE
  T1             1              16
  T2             2              90
  T3            13             316
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  ADNP2 MUTATED    13   4   0
  ADNP2 WILD-TYPE 274 109  87
D856V6, multiclass
    clus
vv   ADNP2 MUTATED ADNP2 WILD-TYPE
  N0            13             274
  N1             4             109
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D856V7, binary
                 cls
clus                0   1
  ADNP2 MUTATED    15   0
  ADNP2 WILD-TYPE 360  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ADNP2 MUTATED     15    0
  ADNP2 WILD-TYPE  360   65
   clus
vv  ADNP2 MUTATED ADNP2 WILD-TYPE
  0            15             360
  1             0              65
[1] 2 2
[1] FALSE
D856V8, binary
                 cls
clus                0   1
  ADNP2 MUTATED     8   9
  ADNP2 WILD-TYPE 217 255
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ADNP2 MUTATED      8    9
  ADNP2 WILD-TYPE  217  255
        clus
vv       ADNP2 MUTATED ADNP2 WILD-TYPE
  FEMALE             8             217
  MALE               9             255
[1] 2 2
[1] FALSE
D856V9, binary
                 cls
clus                0   1
  ADNP2 MUTATED    12   0
  ADNP2 WILD-TYPE 338  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ADNP2 MUTATED     12    0
  ADNP2 WILD-TYPE  338   22
     clus
vv    ADNP2 MUTATED ADNP2 WILD-TYPE
  NO             12             338
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ADNP2 MUTATED                     13                             1
  ADNP2 WILD-TYPE                  302                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ADNP2 MUTATED                       2                              0
  ADNP2 WILD-TYPE                   104                             10
D856V10, multiclass
                                clus
vv                               ADNP2 MUTATED ADNP2 WILD-TYPE
  COLON ADENOCARCINOMA                      13             302
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  ADNP2 MUTATED    11   0   0   2
  ADNP2 WILD-TYPE 334   4  31  23
D856V11, multiclass
    clus
vv   ADNP2 MUTATED ADNP2 WILD-TYPE
  R0            11             334
  R1             0               4
  R2             0              31
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D856V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ADNP2 MUTATED                                  0     0
  ADNP2 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ADNP2 MUTATED                           1    10
  ADNP2 WILD-TYPE                        21   216
D856V13, multiclass
                                  clus
vv                                 ADNP2 MUTATED ADNP2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                       10             216
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(857) Variable = SLC22A16 MUTATION ANALYSIS
D857V1, survival
                    sevent
clus2                  0   1
  SLC22A16 MUTATED    11   3
  SLC22A16 WILD-TYPE 367  90
  SLC22A16 MUTATED SLC22A16 WILD-TYPE 
                14                457 
  SLC22A16 MUTATED SLC22A16 WILD-TYPE 
                 3                 90 
$`SLC22A16 MUTATED`
TCGA-A6-5665 TCGA-A6-6781 TCGA-AA-3492 TCGA-AA-A00R TCGA-AA-A01T TCGA-AD-6964 
       22.06        19.66         3.02         0.99        33.04        10.88 
TCGA-AU-6004 TCGA-CA-6718 TCGA-CK-5913 TCGA-CM-4746 TCGA-CM-6171 TCGA-G4-6588 
       27.09        10.06        51.32        37.02        14.04        26.17 
TCGA-AG-3892 TCGA-AG-A002 
       13.02        20.98 

$`SLC22A16 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.12        20.28         7.04         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       27.02        42.02        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01X 
       38.07         1.02        35.01         1.02        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 
        5.79        22.42        27.42         0.20        14.50        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07        12.20        12.76        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       85.45        15.62        49.08         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4752 
        1.91       124.27        23.05        20.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       13.02        15.02        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       22.09        13.78        35.80        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       36.95        17.03        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  SLC22A16 MUTATED SLC22A16 WILD-TYPE 
              0.99               0.00 
  SLC22A16 MUTATED SLC22A16 WILD-TYPE 
             51.32             148.01 
  SLC22A16 MUTATED SLC22A16 WILD-TYPE 
             20.32              20.19 
[1] "1.0 - 51.3 (20.3)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.4"
D857V2, continuous
D857V3, binary
                    cls
clus                   0   1
  SLC22A16 MUTATED    13   2
  SLC22A16 WILD-TYPE 353 117
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SLC22A16 MUTATED     13    2
  SLC22A16 WILD-TYPE  353  117
        clus
vv       SLC22A16 MUTATED SLC22A16 WILD-TYPE
  COLON                13                353
  RECTUM                2                117
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SLC22A16 MUTATED         6        0        1         5         0         0
  SLC22A16 WILD-TYPE      85        1       31       133        10         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC22A16 MUTATED           1          0          0          1        0
  SLC22A16 WILD-TYPE        23         11         59         41       48
                    vv
clus                 STAGE IVA STAGE IVB
  SLC22A16 MUTATED           0         0
  SLC22A16 WILD-TYPE        18         1
D857V4, multiclass
            clus
vv           SLC22A16 MUTATED SLC22A16 WILD-TYPE
  STAGE I                   6                 85
  STAGE IA                  0                  1
  STAGE II                  1                 31
  STAGE IIA                 5                133
  STAGE IIB                 0                 10
  STAGE IIC                 0                  1
  STAGE III                 1                 23
  STAGE IIIA                0                 11
  STAGE IIIB                0                 59
  STAGE IIIC                1                 41
  STAGE IV                  0                 48
  STAGE IVA                 0                 18
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  SLC22A16 MUTATED     1   5   7   2
  SLC22A16 WILD-TYPE  16  87 322  48
D857V5, multiclass
    clus
vv   SLC22A16 MUTATED SLC22A16 WILD-TYPE
  T1                1                 16
  T2                5                 87
  T3                7                322
  T4                2                 48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  SLC22A16 MUTATED    12   2   1
  SLC22A16 WILD-TYPE 275 111  86
D857V6, multiclass
    clus
vv   SLC22A16 MUTATED SLC22A16 WILD-TYPE
  N0               12                275
  N1                2                111
  N2                1                 86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D857V7, binary
                    cls
clus                   0   1
  SLC22A16 MUTATED    12   0
  SLC22A16 WILD-TYPE 363  65
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SLC22A16 MUTATED     12    0
  SLC22A16 WILD-TYPE  363   65
   clus
vv  SLC22A16 MUTATED SLC22A16 WILD-TYPE
  0               12                363
  1                0                 65
[1] 2 2
[1] FALSE
D857V8, binary
                    cls
clus                   0   1
  SLC22A16 MUTATED    10   5
  SLC22A16 WILD-TYPE 215 259
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SLC22A16 MUTATED     10    5
  SLC22A16 WILD-TYPE  215  259
        clus
vv       SLC22A16 MUTATED SLC22A16 WILD-TYPE
  FEMALE               10                215
  MALE                  5                259
[1] 2 2
[1] FALSE
D857V9, binary
                    cls
clus                   0   1
  SLC22A16 MUTATED    12   0
  SLC22A16 WILD-TYPE 338  22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SLC22A16 MUTATED     12    0
  SLC22A16 WILD-TYPE  338   22
     clus
vv    SLC22A16 MUTATED SLC22A16 WILD-TYPE
  NO                12                338
  YES                0                 22
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SLC22A16 MUTATED                     12                             1
  SLC22A16 WILD-TYPE                  303                            46
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SLC22A16 MUTATED                       2                              0
  SLC22A16 WILD-TYPE                   104                             10
D857V10, multiclass
                                clus
vv                               SLC22A16 MUTATED SLC22A16 WILD-TYPE
  COLON ADENOCARCINOMA                         12                303
  COLON MUCINOUS ADENOCARCINOMA                 1                 46
  RECTAL ADENOCARCINOMA                         2                104
  RECTAL MUCINOUS ADENOCARCINOMA                0                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  SLC22A16 MUTATED    12   0   0   2
  SLC22A16 WILD-TYPE 333   4  31  23
D857V11, multiclass
    clus
vv   SLC22A16 MUTATED SLC22A16 WILD-TYPE
  R0               12                333
  R1                0                  4
  R2                0                 31
  RX                2                 23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D857V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SLC22A16 MUTATED                                  0     1
  SLC22A16 WILD-TYPE                                1    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  SLC22A16 MUTATED                           1     7
  SLC22A16 WILD-TYPE                        21   219
D857V13, multiclass
                                  clus
vv                                 SLC22A16 MUTATED SLC22A16 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                 10
  BLACK OR AFRICAN AMERICAN                       1                 21
  WHITE                                           7                219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(858) Variable = GSS MUTATION ANALYSIS
D858V1, survival
               sevent
clus2             0   1
  GSS MUTATED     6   2
  GSS WILD-TYPE 372  91
  GSS MUTATED GSS WILD-TYPE 
            8           463 
  GSS MUTATED GSS WILD-TYPE 
            2            91 
$`GSS MUTATED`
TCGA-A6-5665 TCGA-AA-A00A TCGA-AA-A00N TCGA-AA-A010 TCGA-AZ-6605 TCGA-CM-6171 
       22.06        38.04         4.01        34.98         5.23        14.04 
TCGA-D5-6929 TCGA-CI-6619 
        4.80         6.05 

$`GSS WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
       29.56        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       15.02        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.04         9.44        11.64         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.69         0.72        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  GSS MUTATED GSS WILD-TYPE 
         4.01          0.00 
  GSS MUTATED GSS WILD-TYPE 
        38.04        148.01 
  GSS MUTATED GSS WILD-TYPE 
       10.045        20.280 
[1] "4.0 - 38.0 (10.0)"  "0.0 - 148.0 (20.3)"
[1] "hr=" "2.2"
D858V2, continuous
D858V3, binary
               cls
clus              0   1
  GSS MUTATED     8   1
  GSS WILD-TYPE 358 118
[1] "tbl2"
               cls
clus            [,1] [,2]
  GSS MUTATED      8    1
  GSS WILD-TYPE  358  118
        clus
vv       GSS MUTATED GSS WILD-TYPE
  COLON            8           358
  RECTUM           1           118
[1] 2 2
[1] FALSE
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GSS MUTATED         1        0        1         2         2         0
  GSS WILD-TYPE      90        1       31       136         8         1
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  GSS MUTATED           0          0          1          0        2         0
  GSS WILD-TYPE        24         11         58         42       46        18
               vv
clus            STAGE IVB
  GSS MUTATED           0
  GSS WILD-TYPE         1
D858V4, multiclass
            clus
vv           GSS MUTATED GSS WILD-TYPE
  STAGE I              1            90
  STAGE IA             0             1
  STAGE II             1            31
  STAGE IIA            2           136
  STAGE IIB            2             8
  STAGE IIC            0             1
  STAGE III            0            24
  STAGE IIIA           0            11
  STAGE IIIB           1            58
  STAGE IIIC           0            42
  STAGE IV             2            46
  STAGE IVA            0            18
  STAGE IVB            0             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  GSS MUTATED     0   1   4   4
  GSS WILD-TYPE  17  91 325  46
D858V5, multiclass
    clus
vv   GSS MUTATED GSS WILD-TYPE
  T1           0            17
  T2           1            91
  T3           4           325
  T4           4            46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2
  GSS MUTATED     6   3   0
  GSS WILD-TYPE 281 110  87
D858V6, multiclass
    clus
vv   GSS MUTATED GSS WILD-TYPE
  N0           6           281
  N1           3           110
  N2           0            87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D858V7, binary
               cls
clus              0   1
  GSS MUTATED     7   2
  GSS WILD-TYPE 368  63
[1] "tbl2"
               cls
clus            [,1] [,2]
  GSS MUTATED      7    2
  GSS WILD-TYPE  368   63
   clus
vv  GSS MUTATED GSS WILD-TYPE
  0           7           368
  1           2            63
[1] 2 2
[1] FALSE
D858V8, binary
               cls
clus              0   1
  GSS MUTATED     5   4
  GSS WILD-TYPE 220 260
[1] "tbl2"
               cls
clus            [,1] [,2]
  GSS MUTATED      5    4
  GSS WILD-TYPE  220  260
        clus
vv       GSS MUTATED GSS WILD-TYPE
  FEMALE           5           220
  MALE             4           260
[1] 2 2
[1] FALSE
D858V9, binary
               cls
clus              0   1
  GSS MUTATED     5   0
  GSS WILD-TYPE 345  22
[1] "tbl2"
               cls
clus            [,1] [,2]
  GSS MUTATED      5    0
  GSS WILD-TYPE  345   22
     clus
vv    GSS MUTATED GSS WILD-TYPE
  NO            5           345
  YES           0            22
[1] 2 2
[1] FALSE
               vv
clus            COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  GSS MUTATED                      7                             1
  GSS WILD-TYPE                  308                            46
               vv
clus            RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  GSS MUTATED                       1                              0
  GSS WILD-TYPE                   105                             10
D858V10, multiclass
                                clus
vv                               GSS MUTATED GSS WILD-TYPE
  COLON ADENOCARCINOMA                     7           308
  COLON MUCINOUS ADENOCARCINOMA            1            46
  RECTAL ADENOCARCINOMA                    1           105
  RECTAL MUCINOUS ADENOCARCINOMA           0            10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             R0  R1  R2  RX
  GSS MUTATED     7   0   0   0
  GSS WILD-TYPE 338   4  31  25
D858V11, multiclass
    clus
vv   GSS MUTATED GSS WILD-TYPE
  R0           7           338
  R1           0             4
  R2           0            31
  RX           0            25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D858V12, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GSS MUTATED                                  0     0
  GSS WILD-TYPE                                1    11
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  GSS MUTATED                           0     5
  GSS WILD-TYPE                        22   221
D858V13, multiclass
                                  clus
vv                                 GSS MUTATED GSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      0            11
  BLACK OR AFRICAN AMERICAN                  0            22
  WHITE                                      5           221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(859) Variable = IGF2R MUTATION ANALYSIS
D859V1, survival
                 sevent
clus2               0   1
  IGF2R MUTATED    33   6
  IGF2R WILD-TYPE 345  87
  IGF2R MUTATED IGF2R WILD-TYPE 
             39             432 
  IGF2R MUTATED IGF2R WILD-TYPE 
              6              87 
$`IGF2R MUTATED`
TCGA-A6-3809 TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3492 TCGA-AA-3516 TCGA-AA-3525 
       32.75        20.12        19.66         3.02        13.02         8.05 
TCGA-AA-3543 TCGA-AA-3663 TCGA-AA-3672 TCGA-AA-3679 TCGA-AA-3864 TCGA-AA-3947 
        0.99         6.97         0.92        15.02        53.00        33.01 
TCGA-AA-A00A TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01R TCGA-AD-6889 TCGA-AD-6895 
       38.04         4.01        34.98        35.01        56.55         0.72 
TCGA-AZ-4315 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6601 TCGA-CA-6717 TCGA-CA-6718 
       58.39        88.21        49.41       100.01        12.76        10.06 
TCGA-CK-4952 TCGA-CM-4746 TCGA-D5-6540 TCGA-D5-6928 TCGA-D5-6930 TCGA-DM-A28H 
       15.62        37.02        16.14        11.64         1.51       117.07 
TCGA-DM-A28K TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6317 TCGA-G4-6588 TCGA-AG-3731 
       98.24        44.68        55.04        36.00        26.17        37.02 
TCGA-AG-3892 TCGA-AG-A002 TCGA-AG-A02N 
       13.02        20.98        61.97 

$`IGF2R WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
       20.28         7.04         1.02        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
        1.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
       36.03        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       29.00        26.01        12.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3680 
       54.02         2.01        14.01        50.04        47.01        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       31.07        30.05        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 
       18.05        31.00         2.01        12.99        24.00        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       13.94        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       31.00        38.07         1.02         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6899 
       40.96         0.07        21.37        15.52         0.79         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
       16.31         0.95        33.01        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6599 TCGA-AZ-6600 
        5.13       106.75        22.36        62.79         6.77        12.10 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 
        3.06         3.25         3.29         0.07        12.20        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
       17.56       148.01        85.45        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
        4.80        17.13        12.49        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 
        4.41        12.43        14.30         9.04         9.44         4.80 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-F4-6459 TCGA-F4-6460 
       81.37       119.93        35.97        60.79         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6309 TCGA-G4-6310 
      133.18        74.56        65.85        53.62        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 
       61.91        22.09        13.78        35.80        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3732 
       19.99        13.94        19.99         7.99         0.99        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       36.95        17.03        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 
       10.98        49.97         1.94        38.96        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  IGF2R MUTATED IGF2R WILD-TYPE 
           0.72            0.00 
  IGF2R MUTATED IGF2R WILD-TYPE 
         117.07          148.01 
  IGF2R MUTATED IGF2R WILD-TYPE 
         26.170          20.035 
[1] "0.7 - 117.1 (26.2)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.7"
D859V2, continuous
D859V3, binary
                 cls
clus                0   1
  IGF2R MUTATED    37   4
  IGF2R WILD-TYPE 329 115
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IGF2R MUTATED     37    4
  IGF2R WILD-TYPE  329  115
        clus
vv       IGF2R MUTATED IGF2R WILD-TYPE
  COLON             37             329
  RECTUM             4             115
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  IGF2R MUTATED         6        0        6        12         5         0
  IGF2R WILD-TYPE      85        1       26       126         5         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  IGF2R MUTATED           3          0          2          4        2         0
  IGF2R WILD-TYPE        21         11         57         38       46        18
                 vv
clus              STAGE IVB
  IGF2R MUTATED           0
  IGF2R WILD-TYPE         1
D859V4, multiclass
            clus
vv           IGF2R MUTATED IGF2R WILD-TYPE
  STAGE I                6              85
  STAGE IA               0               1
  STAGE II               6              26
  STAGE IIA             12             126
  STAGE IIB              5               5
  STAGE IIC              0               1
  STAGE III              3              21
  STAGE IIIA             0              11
  STAGE IIIB             2              57
  STAGE IIIC             4              38
  STAGE IV               2              46
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  IGF2R MUTATED     2   5  27   7
  IGF2R WILD-TYPE  15  87 302  43
D859V5, multiclass
    clus
vv   IGF2R MUTATED IGF2R WILD-TYPE
  T1             2              15
  T2             5              87
  T3            27             302
  T4             7              43
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  IGF2R MUTATED    29   6   6
  IGF2R WILD-TYPE 258 107  81
D859V6, multiclass
    clus
vv   IGF2R MUTATED IGF2R WILD-TYPE
  N0            29             258
  N1             6             107
  N2             6              81
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D859V7, binary
                 cls
clus                0   1
  IGF2R MUTATED    33   2
  IGF2R WILD-TYPE 342  63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IGF2R MUTATED     33    2
  IGF2R WILD-TYPE  342   63
   clus
vv  IGF2R MUTATED IGF2R WILD-TYPE
  0            33             342
  1             2              63
[1] 2 2
[1] FALSE
D859V8, binary
                 cls
clus                0   1
  IGF2R MUTATED    15  26
  IGF2R WILD-TYPE 210 238
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IGF2R MUTATED     15   26
  IGF2R WILD-TYPE  210  238
        clus
vv       IGF2R MUTATED IGF2R WILD-TYPE
  FEMALE            15             210
  MALE              26             238
[1] 2 2
[1] FALSE
D859V9, binary
                 cls
clus                0   1
  IGF2R MUTATED    30   1
  IGF2R WILD-TYPE 320  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IGF2R MUTATED     30    1
  IGF2R WILD-TYPE  320   21
     clus
vv    IGF2R MUTATED IGF2R WILD-TYPE
  NO             30             320
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  IGF2R MUTATED                     23                            14
  IGF2R WILD-TYPE                  292                            33
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  IGF2R MUTATED                       4                              0
  IGF2R WILD-TYPE                   102                             10
D859V10, multiclass
                                clus
vv                               IGF2R MUTATED IGF2R WILD-TYPE
  COLON ADENOCARCINOMA                      23             292
  COLON MUCINOUS ADENOCARCINOMA             14              33
  RECTAL ADENOCARCINOMA                      4             102
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  IGF2R MUTATED    26   0   2   4
  IGF2R WILD-TYPE 319   4  29  21
D859V11, multiclass
    clus
vv   IGF2R MUTATED IGF2R WILD-TYPE
  R0            26             319
  R1             0               4
  R2             2              29
  RX             4              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D859V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  IGF2R MUTATED                                  0     3
  IGF2R WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  IGF2R MUTATED                           1    19
  IGF2R WILD-TYPE                        21   207
D859V13, multiclass
                                  clus
vv                                 IGF2R MUTATED IGF2R WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        3               8
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                       19             207
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(860) Variable = OR51A4 MUTATION ANALYSIS
D860V1, survival
                  sevent
clus2                0   1
  OR51A4 MUTATED     5   1
  OR51A4 WILD-TYPE 373  92
  OR51A4 MUTATED OR51A4 WILD-TYPE 
               6              465 
  OR51A4 MUTATED OR51A4 WILD-TYPE 
               1               92 
$`OR51A4 MUTATED`
TCGA-A6-6781 TCGA-AA-3821 TCGA-AA-3864 TCGA-AD-6899 TCGA-D5-6535 TCGA-D5-6540 
       19.66         1.02        53.00         5.79        15.12        16.14 

$`OR51A4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 
       10.06        35.05        33.04         0.99        25.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 
        0.99        31.07        31.07        30.05        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.79         0.72        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
        1.32        43.27        17.85         4.80        17.13        12.49 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  OR51A4 MUTATED OR51A4 WILD-TYPE 
            1.02             0.00 
  OR51A4 MUTATED OR51A4 WILD-TYPE 
           53.00           148.01 
  OR51A4 MUTATED OR51A4 WILD-TYPE 
           15.63            20.55 
[1] "1.0 - 53.0 (15.6)"  "0.0 - 148.0 (20.6)"
[1] "hr=" "1.1"
D860V2, continuous
D860V3, binary
                  cls
clus                 0   1
  OR51A4 MUTATED     8   0
  OR51A4 WILD-TYPE 358 119
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR51A4 MUTATED      8    0
  OR51A4 WILD-TYPE  358  119
        clus
vv       OR51A4 MUTATED OR51A4 WILD-TYPE
  COLON               8              358
  RECTUM              0              119
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  OR51A4 MUTATED         2        0        1         1         1         0
  OR51A4 WILD-TYPE      89        1       31       137         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  OR51A4 MUTATED           0          0          1          2        0
  OR51A4 WILD-TYPE        24         11         58         40       48
                  vv
clus               STAGE IVA STAGE IVB
  OR51A4 MUTATED           0         0
  OR51A4 WILD-TYPE        18         1
D860V4, multiclass
            clus
vv           OR51A4 MUTATED OR51A4 WILD-TYPE
  STAGE I                 2               89
  STAGE IA                0                1
  STAGE II                1               31
  STAGE IIA               1              137
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              1               58
  STAGE IIIC              2               40
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  OR51A4 MUTATED     0   2   3   3
  OR51A4 WILD-TYPE  17  90 326  47
D860V5, multiclass
    clus
vv   OR51A4 MUTATED OR51A4 WILD-TYPE
  T1              0               17
  T2              2               90
  T3              3              326
  T4              3               47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  OR51A4 MUTATED     5   2   1
  OR51A4 WILD-TYPE 282 111  86
D860V6, multiclass
    clus
vv   OR51A4 MUTATED OR51A4 WILD-TYPE
  N0              5              282
  N1              2              111
  N2              1               86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D860V7, binary
                  cls
clus                 0   1
  OR51A4 MUTATED     4   0
  OR51A4 WILD-TYPE 371  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR51A4 MUTATED      4    0
  OR51A4 WILD-TYPE  371   65
   clus
vv  OR51A4 MUTATED OR51A4 WILD-TYPE
  0              4              371
  1              0               65
[1] 2 2
[1] FALSE
D860V8, binary
                  cls
clus                 0   1
  OR51A4 MUTATED     4   4
  OR51A4 WILD-TYPE 221 260
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR51A4 MUTATED      4    4
  OR51A4 WILD-TYPE  221  260
        clus
vv       OR51A4 MUTATED OR51A4 WILD-TYPE
  FEMALE              4              221
  MALE                4              260
[1] 2 2
[1] FALSE
D860V9, binary
                  cls
clus                 0   1
  OR51A4 MUTATED     6   0
  OR51A4 WILD-TYPE 344  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR51A4 MUTATED      6    0
  OR51A4 WILD-TYPE  344   22
     clus
vv    OR51A4 MUTATED OR51A4 WILD-TYPE
  NO               6              344
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  OR51A4 MUTATED                      4                             4
  OR51A4 WILD-TYPE                  311                            43
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  OR51A4 MUTATED                       0                              0
  OR51A4 WILD-TYPE                   106                             10
D860V10, multiclass
                                clus
vv                               OR51A4 MUTATED OR51A4 WILD-TYPE
  COLON ADENOCARCINOMA                        4              311
  COLON MUCINOUS ADENOCARCINOMA               4               43
  RECTAL ADENOCARCINOMA                       0              106
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  OR51A4 MUTATED     5   0   0   2
  OR51A4 WILD-TYPE 340   4  31  23
D860V11, multiclass
    clus
vv   OR51A4 MUTATED OR51A4 WILD-TYPE
  R0              5              340
  R1              0                4
  R2              0               31
  RX              2               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D860V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OR51A4 MUTATED                                  0     0
  OR51A4 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  OR51A4 MUTATED                           0     5
  OR51A4 WILD-TYPE                        22   221
D860V13, multiclass
                                  clus
vv                                 OR51A4 MUTATED OR51A4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         5              221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(861) Variable = CRYGA MUTATION ANALYSIS
D861V1, survival
                 sevent
clus2               0   1
  CRYGA MUTATED     4   1
  CRYGA WILD-TYPE 374  92
  CRYGA MUTATED CRYGA WILD-TYPE 
              5             466 
  CRYGA MUTATED CRYGA WILD-TYPE 
              1              92 
$`CRYGA MUTATED`
TCGA-A6-6653 TCGA-A6-6780 TCGA-AZ-6598 TCGA-G4-6586 TCGA-G4-6588 
       24.39        20.12        49.41        35.80        26.17 

$`CRYGA WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
       25.08        25.18        24.16        21.76        24.69        23.87 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 
      106.75        22.36        62.79        88.21         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6625 TCGA-G4-6626 
       61.91        36.00        22.09        13.78        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  CRYGA MUTATED CRYGA WILD-TYPE 
          20.12            0.00 
  CRYGA MUTATED CRYGA WILD-TYPE 
          49.41          148.01 
  CRYGA MUTATED CRYGA WILD-TYPE 
         26.170          20.035 
[1] "20.1 - 49.4 (26.2)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.2"
D861V2, continuous
D861V3, binary
                 cls
clus                0   1
  CRYGA MUTATED     5   0
  CRYGA WILD-TYPE 361 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CRYGA MUTATED      5    0
  CRYGA WILD-TYPE  361  119
        clus
vv       CRYGA MUTATED CRYGA WILD-TYPE
  COLON              5             361
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CRYGA MUTATED         1        0        1         3         0         0
  CRYGA WILD-TYPE      90        1       31       135        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CRYGA MUTATED           0          0          0          0        0         0
  CRYGA WILD-TYPE        24         11         59         42       48        18
                 vv
clus              STAGE IVB
  CRYGA MUTATED           0
  CRYGA WILD-TYPE         1
D861V4, multiclass
            clus
vv           CRYGA MUTATED CRYGA WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              3             135
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CRYGA MUTATED     0   1   4   0
  CRYGA WILD-TYPE  17  91 325  50
D861V5, multiclass
    clus
vv   CRYGA MUTATED CRYGA WILD-TYPE
  T1             0              17
  T2             1              91
  T3             4             325
  T4             0              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  CRYGA MUTATED     5   0   0
  CRYGA WILD-TYPE 282 113  87
D861V6, multiclass
    clus
vv   CRYGA MUTATED CRYGA WILD-TYPE
  N0             5             282
  N1             0             113
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D861V7, binary
                 cls
clus                0   1
  CRYGA MUTATED     3   0
  CRYGA WILD-TYPE 372  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CRYGA MUTATED      3    0
  CRYGA WILD-TYPE  372   65
   clus
vv  CRYGA MUTATED CRYGA WILD-TYPE
  0             3             372
  1             0              65
[1] 2 2
[1] FALSE
D861V8, binary
                 cls
clus                0   1
  CRYGA MUTATED     3   2
  CRYGA WILD-TYPE 222 262
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CRYGA MUTATED      3    2
  CRYGA WILD-TYPE  222  262
        clus
vv       CRYGA MUTATED CRYGA WILD-TYPE
  FEMALE             3             222
  MALE               2             262
[1] 2 2
[1] FALSE
D861V9, binary
                 cls
clus                0   1
  CRYGA MUTATED     5   0
  CRYGA WILD-TYPE 345  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CRYGA MUTATED      5    0
  CRYGA WILD-TYPE  345   22
     clus
vv    CRYGA MUTATED CRYGA WILD-TYPE
  NO              5             345
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CRYGA MUTATED                      4                             1
  CRYGA WILD-TYPE                  311                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CRYGA MUTATED                       0                              0
  CRYGA WILD-TYPE                   106                             10
D861V10, multiclass
                                clus
vv                               CRYGA MUTATED CRYGA WILD-TYPE
  COLON ADENOCARCINOMA                       4             311
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  CRYGA MUTATED     2   0   0   0
  CRYGA WILD-TYPE 343   4  31  25
D861V11, multiclass
[1] "Remove cluster labels:" "CRYGA MUTATED"         
clus
  CRYGA MUTATED CRYGA WILD-TYPE 
              2             403 
     TCGA-A6-2671      TCGA-A6-2672      TCGA-A6-2674      TCGA-A6-2676 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-A6-2677      TCGA-A6-2678      TCGA-A6-2683      TCGA-A6-3807 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-A6-3808      TCGA-A6-3809      TCGA-A6-3810      TCGA-A6-5657 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-A6-5659      TCGA-A6-5661      TCGA-A6-5665      TCGA-A6-6781 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AA-3489      TCGA-AA-3492      TCGA-AA-3496      TCGA-AA-3502 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AA-3510      TCGA-AA-3511      TCGA-AA-3514      TCGA-AA-3517 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AA-3518      TCGA-AA-3519      TCGA-AA-3520      TCGA-AA-3521 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AA-3522      TCGA-AA-3524      TCGA-AA-3525      TCGA-AA-3526 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AA-3527      TCGA-AA-3529      TCGA-AA-3530      TCGA-AA-3531 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AA-3532      TCGA-AA-3534      TCGA-AA-3538      TCGA-AA-3542 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AA-3543      TCGA-AA-3544      TCGA-AA-3548      TCGA-AA-3549 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AA-3552      TCGA-AA-3553      TCGA-AA-3554      TCGA-AA-3555 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AA-3556      TCGA-AA-3558      TCGA-AA-3560      TCGA-AA-3561 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AA-3562      TCGA-AA-3655      TCGA-AA-3660      TCGA-AA-3662 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AA-3663      TCGA-AA-3664      TCGA-AA-3666      TCGA-AA-3667 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AA-3672      TCGA-AA-3673      TCGA-AA-3678      TCGA-AA-3679 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AA-3680      TCGA-AA-3681      TCGA-AA-3684      TCGA-AA-3685 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AA-3688      TCGA-AA-3692      TCGA-AA-3693      TCGA-AA-3695 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AA-3696      TCGA-AA-3697      TCGA-AA-3710      TCGA-AA-3712 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AA-3713      TCGA-AA-3715      TCGA-AA-3811      TCGA-AA-3812 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AA-3814      TCGA-AA-3815      TCGA-AA-3818      TCGA-AA-3819 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AA-3821      TCGA-AA-3831      TCGA-AA-3833      TCGA-AA-3837 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AA-3842      TCGA-AA-3844      TCGA-AA-3845      TCGA-AA-3846 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AA-3848      TCGA-AA-3850      TCGA-AA-3851      TCGA-AA-3852 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AA-3854      TCGA-AA-3855      TCGA-AA-3856      TCGA-AA-3858 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AA-3860      TCGA-AA-3861      TCGA-AA-3864      TCGA-AA-3866 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AA-3867      TCGA-AA-3869      TCGA-AA-3870      TCGA-AA-3872 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AA-3875      TCGA-AA-3877      TCGA-AA-3930      TCGA-AA-3939 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AA-3941      TCGA-AA-3947      TCGA-AA-3949      TCGA-AA-3950 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AA-3952      TCGA-AA-3955      TCGA-AA-3956      TCGA-AA-3968 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AA-3971      TCGA-AA-3972      TCGA-AA-3973      TCGA-AA-3975 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AA-3976      TCGA-AA-3979      TCGA-AA-3984      TCGA-AA-3986 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AA-3989      TCGA-AA-3994      TCGA-AA-A004      TCGA-AA-A00A 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AA-A00D      TCGA-AA-A00E      TCGA-AA-A00F      TCGA-AA-A00J 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AA-A00K      TCGA-AA-A00L      TCGA-AA-A00N      TCGA-AA-A00O 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AA-A00Q      TCGA-AA-A00R      TCGA-AA-A00U      TCGA-AA-A00W 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AA-A00Z      TCGA-AA-A010      TCGA-AA-A017      TCGA-AA-A01D 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AA-A01F      TCGA-AA-A01G      TCGA-AA-A01I      TCGA-AA-A01K 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AA-A01P      TCGA-AA-A01Q      TCGA-AA-A01R      TCGA-AA-A01S 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AA-A01T      TCGA-AA-A01V      TCGA-AA-A01X      TCGA-AA-A01Z 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AA-A022      TCGA-AA-A024      TCGA-AA-A029      TCGA-AA-A02F 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AA-A02H      TCGA-AA-A02J      TCGA-AA-A02K      TCGA-AA-A02O 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AA-A02W      TCGA-AA-A02Y      TCGA-AA-A03F      TCGA-AA-A03J 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AD-5900      TCGA-AD-6548      TCGA-AD-6888      TCGA-AU-3779 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AU-6004      TCGA-AY-4070      TCGA-AY-4071      TCGA-AY-5543 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AY-6196      TCGA-AY-6197      TCGA-AY-6386      TCGA-AZ-4315 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AZ-4681      TCGA-AZ-4682      TCGA-CA-5254      TCGA-CA-5255 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-CA-5796      TCGA-CA-5797      TCGA-CA-6715      TCGA-CA-6716 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-CA-6717      TCGA-CA-6718      TCGA-CA-6719      TCGA-CK-4947 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-CK-4948      TCGA-CK-4950      TCGA-CK-4952      TCGA-CK-5912 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-CK-5913      TCGA-CK-5914      TCGA-CK-5915      TCGA-CK-5916 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-CK-6746      TCGA-CK-6747      TCGA-CK-6748      TCGA-CK-6751 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-CM-4743      TCGA-CM-4744      TCGA-CM-4746      TCGA-CM-4747 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-CM-4752      TCGA-CM-5341      TCGA-CM-5344      TCGA-CM-5348 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-CM-5349      TCGA-CM-5860      TCGA-CM-5861      TCGA-CM-5862 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-CM-5863      TCGA-CM-5864      TCGA-CM-5868      TCGA-CM-6161 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-CM-6162      TCGA-CM-6163      TCGA-CM-6164      TCGA-CM-6165 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-CM-6166      TCGA-CM-6167      TCGA-CM-6168      TCGA-CM-6169 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-CM-6170      TCGA-CM-6171      TCGA-CM-6172      TCGA-CM-6674 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-CM-6675      TCGA-CM-6676      TCGA-CM-6677      TCGA-CM-6678 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-CM-6679      TCGA-CM-6680      TCGA-D5-5537      TCGA-D5-5538 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-D5-5539      TCGA-D5-5540      TCGA-D5-5541      TCGA-D5-6529 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-D5-6532      TCGA-D5-6533      TCGA-D5-6534      TCGA-D5-6535 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-D5-6536      TCGA-D5-6537      TCGA-D5-6538      TCGA-D5-6539 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-D5-6540      TCGA-D5-6541      TCGA-D5-6898      TCGA-D5-6920 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-D5-6922      TCGA-D5-6923      TCGA-D5-6924      TCGA-D5-6926 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-D5-6927      TCGA-D5-6928      TCGA-D5-6929      TCGA-D5-6930 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-D5-6931      TCGA-D5-6932      TCGA-D5-7000      TCGA-F4-6459 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-F4-6460      TCGA-F4-6569      TCGA-F4-6570      TCGA-F4-6703 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-F4-6704      TCGA-F4-6805      TCGA-F4-6806      TCGA-F4-6807 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-F4-6808      TCGA-F4-6809      TCGA-F4-6854      TCGA-F4-6855 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-F4-6856      TCGA-G4-6293      TCGA-G4-6299      TCGA-G4-6303 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-G4-6304      TCGA-G4-6306      TCGA-G4-6307      TCGA-G4-6309 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-G4-6310      TCGA-G4-6315      TCGA-G4-6317      TCGA-G4-6321 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-G4-6323      TCGA-G4-6625      TCGA-G4-6626      TCGA-G4-6628 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AF-2687      TCGA-AF-2689      TCGA-AF-2691      TCGA-AF-2692 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AF-3400      TCGA-AF-3913      TCGA-AF-4110      TCGA-AF-5654 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AF-6655      TCGA-AG-3574      TCGA-AG-3575      TCGA-AG-3578 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AG-3580      TCGA-AG-3581      TCGA-AG-3582      TCGA-AG-3583 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AG-3584      TCGA-AG-3586      TCGA-AG-3587      TCGA-AG-3593 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AG-3594      TCGA-AG-3598      TCGA-AG-3599      TCGA-AG-3600 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AG-3601      TCGA-AG-3602      TCGA-AG-3605      TCGA-AG-3608 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AG-3609      TCGA-AG-3611      TCGA-AG-3612      TCGA-AG-3726 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AG-3727      TCGA-AG-3731      TCGA-AG-3732      TCGA-AG-3742 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AG-3878      TCGA-AG-3882      TCGA-AG-3883      TCGA-AG-3885 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AG-3887      TCGA-AG-3890      TCGA-AG-3892      TCGA-AG-3893 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AG-3894      TCGA-AG-3896      TCGA-AG-3898      TCGA-AG-3901 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AG-3902      TCGA-AG-3909      TCGA-AG-3999      TCGA-AG-4001 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AG-4005      TCGA-AG-4007      TCGA-AG-4008      TCGA-AG-4015 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AG-A002      TCGA-AG-A008      TCGA-AG-A00C      TCGA-AG-A00H 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AG-A00Y      TCGA-AG-A011      TCGA-AG-A014      TCGA-AG-A015 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AG-A016      TCGA-AG-A01L      TCGA-AG-A01W      TCGA-AG-A01Y 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AG-A020      TCGA-AG-A025      TCGA-AG-A026      TCGA-AG-A02G 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AG-A02N      TCGA-AG-A02X      TCGA-AG-A032      TCGA-AG-A036 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-AH-6549      TCGA-AH-6643      TCGA-CL-5917      TCGA-CL-5918 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-DC-5337      TCGA-DC-5869      TCGA-DC-6155      TCGA-DC-6157 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-DC-6158      TCGA-DC-6160      TCGA-DC-6681      TCGA-DC-6682 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-DC-6683      TCGA-DT-5265      TCGA-EF-5830      TCGA-EI-6506 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-EI-6507      TCGA-EI-6508      TCGA-EI-6510      TCGA-F5-6464 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-F5-6465      TCGA-F5-6571      TCGA-F5-6702      TCGA-F5-6812 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
     TCGA-F5-6813      TCGA-G5-6235      TCGA-G5-6641 
"CRYGA WILD-TYPE" "CRYGA WILD-TYPE" "CRYGA WILD-TYPE" 
D861V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CRYGA MUTATED                                  0     0
  CRYGA WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CRYGA MUTATED                           0     5
  CRYGA WILD-TYPE                        22   221
D861V13, multiclass
                                  clus
vv                                 CRYGA MUTATED CRYGA WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        5             221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(862) Variable = RNF10 MUTATION ANALYSIS
D862V1, survival
                 sevent
clus2               0   1
  RNF10 MUTATED    14   1
  RNF10 WILD-TYPE 364  92
  RNF10 MUTATED RNF10 WILD-TYPE 
             15             456 
  RNF10 MUTATED RNF10 WILD-TYPE 
              1              92 
$`RNF10 MUTATED`
TCGA-AA-3510 TCGA-AA-3554 TCGA-AA-3815 TCGA-AA-3864 TCGA-AA-3950 TCGA-AA-A00U 
       63.98        17.95        33.04        53.00        24.00        17.03 
TCGA-AZ-4315 TCGA-CA-6717 TCGA-CM-4744 TCGA-CM-5348 TCGA-DM-A0XD TCGA-DM-A1D9 
       58.39        12.76        20.02        22.98        24.43       140.38 
TCGA-G4-6321 TCGA-AG-A002 TCGA-DC-5337 
       22.09        20.98        15.02 

$`RNF10 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       13.02        24.00        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       35.05         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        31.07        30.05        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       33.01        26.01         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
       16.31         0.95        33.01        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07        12.20        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-4747 
       82.95         1.91       124.27        23.05        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       13.02        29.06        22.03        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XF 
        1.51        12.00        11.38        10.26       119.70        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1DA 
      130.65        92.75        49.91        13.32        12.59         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 
       55.04        85.48        63.62        61.91        36.00        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
        7.17         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  RNF10 MUTATED RNF10 WILD-TYPE 
          12.76            0.00 
  RNF10 MUTATED RNF10 WILD-TYPE 
         140.38          148.01 
  RNF10 MUTATED RNF10 WILD-TYPE 
         22.980          20.035 
[1] "12.8 - 140.4 (23.0)" "0.0 - 148.0 (20.0)" 
[1] "hr=" "4.1"
D862V2, continuous
D862V3, binary
                 cls
clus                0   1
  RNF10 MUTATED    13   2
  RNF10 WILD-TYPE 353 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RNF10 MUTATED     13    2
  RNF10 WILD-TYPE  353  117
        clus
vv       RNF10 MUTATED RNF10 WILD-TYPE
  COLON             13             353
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RNF10 MUTATED         3        0        2         7         0         0
  RNF10 WILD-TYPE      88        1       30       131        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RNF10 MUTATED           1          0          2          0        0         0
  RNF10 WILD-TYPE        23         11         57         42       48        18
                 vv
clus              STAGE IVB
  RNF10 MUTATED           0
  RNF10 WILD-TYPE         1
D862V4, multiclass
            clus
vv           RNF10 MUTATED RNF10 WILD-TYPE
  STAGE I                3              88
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA              7             131
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             2              57
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  RNF10 MUTATED     1   3  11   0
  RNF10 WILD-TYPE  16  89 318  50
D862V5, multiclass
    clus
vv   RNF10 MUTATED RNF10 WILD-TYPE
  T1             1              16
  T2             3              89
  T3            11             318
  T4             0              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  RNF10 MUTATED    12   3   0
  RNF10 WILD-TYPE 275 110  87
D862V6, multiclass
    clus
vv   RNF10 MUTATED RNF10 WILD-TYPE
  N0            12             275
  N1             3             110
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D862V7, binary
                 cls
clus                0   1
  RNF10 MUTATED    14   0
  RNF10 WILD-TYPE 361  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RNF10 MUTATED     14    0
  RNF10 WILD-TYPE  361   65
   clus
vv  RNF10 MUTATED RNF10 WILD-TYPE
  0            14             361
  1             0              65
[1] 2 2
[1] FALSE
D862V8, binary
                 cls
clus                0   1
  RNF10 MUTATED     5  10
  RNF10 WILD-TYPE 220 254
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RNF10 MUTATED      5   10
  RNF10 WILD-TYPE  220  254
        clus
vv       RNF10 MUTATED RNF10 WILD-TYPE
  FEMALE             5             220
  MALE              10             254
[1] 2 2
[1] FALSE
D862V9, binary
                 cls
clus                0   1
  RNF10 MUTATED    13   0
  RNF10 WILD-TYPE 337  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RNF10 MUTATED     13    0
  RNF10 WILD-TYPE  337   22
     clus
vv    RNF10 MUTATED RNF10 WILD-TYPE
  NO             13             337
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  RNF10 MUTATED                     11                             2
  RNF10 WILD-TYPE                  304                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  RNF10 MUTATED                       2                              0
  RNF10 WILD-TYPE                   104                             10
D862V10, multiclass
                                clus
vv                               RNF10 MUTATED RNF10 WILD-TYPE
  COLON ADENOCARCINOMA                      11             304
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  RNF10 MUTATED    12   0   0   1
  RNF10 WILD-TYPE 333   4  31  24
D862V11, multiclass
    clus
vv   RNF10 MUTATED RNF10 WILD-TYPE
  R0            12             333
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D862V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RNF10 MUTATED                                  0     1
  RNF10 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  RNF10 MUTATED                           0     7
  RNF10 WILD-TYPE                        22   219
D862V13, multiclass
                                  clus
vv                                 RNF10 MUTATED RNF10 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        7             219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(863) Variable = NCAPD3 MUTATION ANALYSIS
D863V1, survival
                  sevent
clus2                0   1
  NCAPD3 MUTATED    23   3
  NCAPD3 WILD-TYPE 355  90
  NCAPD3 MUTATED NCAPD3 WILD-TYPE 
              26              445 
  NCAPD3 MUTATED NCAPD3 WILD-TYPE 
               3               90 
$`NCAPD3 MUTATED`
TCGA-A6-3809 TCGA-A6-5665 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3518 TCGA-AA-3655 
       32.75        22.06        63.98         1.02         1.02        61.02 
TCGA-AA-3713 TCGA-AA-3869 TCGA-AA-A010 TCGA-AD-6889 TCGA-AD-6963 TCGA-AD-6965 
       19.04        27.02        34.98        56.55        27.42         0.20 
TCGA-AZ-4315 TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-4743 TCGA-CM-5861 TCGA-CM-6162 
       58.39        12.76        10.06        23.05        15.02        12.00 
TCGA-CM-6166 TCGA-CM-6170 TCGA-CM-6171 TCGA-D5-5541 TCGA-DM-A1D9 TCGA-F4-6570 
       21.99        15.02        14.04        55.92       140.38         6.18 
TCGA-G4-6586 TCGA-AG-3881 
       35.80        19.04 

$`NCAPD3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3511 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
        6.97        13.02        38.99         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       36.03         8.05        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3660 
       23.01        20.98        19.99        13.94        19.99        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       17.03        24.03        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 
       18.05        40.96         0.07        21.37        15.52         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6964 TCGA-AU-3779 TCGA-AU-6004 
        0.72         5.79        22.42        10.88        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
       16.31         0.95        33.01        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.07        12.20        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
        1.91       124.27        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 
       29.06        22.03        22.98        30.08        32.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 
       15.02        15.02        17.03        15.02         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6172 TCGA-CM-6674 
       16.04        14.99        12.99        13.02        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-6529 TCGA-D5-6532 
       45.40        12.26        19.59        56.09        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
        8.61        31.96        35.74        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       13.78        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
        0.99        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  NCAPD3 MUTATED NCAPD3 WILD-TYPE 
             0.2              0.0 
  NCAPD3 MUTATED NCAPD3 WILD-TYPE 
          140.38           148.01 
  NCAPD3 MUTATED NCAPD3 WILD-TYPE 
          22.025           20.120 
[1] "0.2 - 140.4 (22.0)" "0.0 - 148.0 (20.1)"
[1] "hr=" "2"  
D863V2, continuous
D863V3, binary
                  cls
clus                 0   1
  NCAPD3 MUTATED    25   1
  NCAPD3 WILD-TYPE 341 118
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NCAPD3 MUTATED     25    1
  NCAPD3 WILD-TYPE  341  118
        clus
vv       NCAPD3 MUTATED NCAPD3 WILD-TYPE
  COLON              25              341
  RECTUM              1              118
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NCAPD3 MUTATED         4        0        2        12         2         0
  NCAPD3 WILD-TYPE      87        1       30       126         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NCAPD3 MUTATED           0          0          2          0        2
  NCAPD3 WILD-TYPE        24         11         57         42       46
                  vv
clus               STAGE IVA STAGE IVB
  NCAPD3 MUTATED           0         0
  NCAPD3 WILD-TYPE        18         1
D863V4, multiclass
            clus
vv           NCAPD3 MUTATED NCAPD3 WILD-TYPE
  STAGE I                 4               87
  STAGE IA                0                1
  STAGE II                2               30
  STAGE IIA              12              126
  STAGE IIB               2                8
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              2               57
  STAGE IIIC              0               42
  STAGE IV                2               46
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  NCAPD3 MUTATED     0   4  18   4
  NCAPD3 WILD-TYPE  17  88 311  46
D863V5, multiclass
    clus
vv   NCAPD3 MUTATED NCAPD3 WILD-TYPE
  T1              0               17
  T2              4               88
  T3             18              311
  T4              4               46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  NCAPD3 MUTATED    22   2   2
  NCAPD3 WILD-TYPE 265 111  85
D863V6, multiclass
    clus
vv   NCAPD3 MUTATED NCAPD3 WILD-TYPE
  N0             22              265
  N1              2              111
  N2              2               85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D863V7, binary
                  cls
clus                 0   1
  NCAPD3 MUTATED    22   2
  NCAPD3 WILD-TYPE 353  63
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NCAPD3 MUTATED     22    2
  NCAPD3 WILD-TYPE  353   63
   clus
vv  NCAPD3 MUTATED NCAPD3 WILD-TYPE
  0             22              353
  1              2               63
[1] 2 2
[1] FALSE
D863V8, binary
                  cls
clus                 0   1
  NCAPD3 MUTATED    14  12
  NCAPD3 WILD-TYPE 211 252
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NCAPD3 MUTATED     14   12
  NCAPD3 WILD-TYPE  211  252
        clus
vv       NCAPD3 MUTATED NCAPD3 WILD-TYPE
  FEMALE             14              211
  MALE               12              252
[1] 2 2
[1] FALSE
D863V9, binary
                  cls
clus                 0   1
  NCAPD3 MUTATED    21   1
  NCAPD3 WILD-TYPE 329  21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NCAPD3 MUTATED     21    1
  NCAPD3 WILD-TYPE  329   21
     clus
vv    NCAPD3 MUTATED NCAPD3 WILD-TYPE
  NO              21              329
  YES              1               21
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  NCAPD3 MUTATED                     22                             3
  NCAPD3 WILD-TYPE                  293                            44
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  NCAPD3 MUTATED                       0                              0
  NCAPD3 WILD-TYPE                   106                             10
D863V10, multiclass
                                clus
vv                               NCAPD3 MUTATED NCAPD3 WILD-TYPE
  COLON ADENOCARCINOMA                       22              293
  COLON MUCINOUS ADENOCARCINOMA               3               44
  RECTAL ADENOCARCINOMA                       0              106
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  NCAPD3 MUTATED    17   0   2   2
  NCAPD3 WILD-TYPE 328   4  29  23
D863V11, multiclass
    clus
vv   NCAPD3 MUTATED NCAPD3 WILD-TYPE
  R0             17              328
  R1              0                4
  R2              2               29
  RX              2               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D863V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NCAPD3 MUTATED                                  0     3
  NCAPD3 WILD-TYPE                                1     8
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  NCAPD3 MUTATED                           0    15
  NCAPD3 WILD-TYPE                        22   211
D863V13, multiclass
                                  clus
vv                                 NCAPD3 MUTATED NCAPD3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         3                8
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                        15              211
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(864) Variable = MTTP MUTATION ANALYSIS
D864V1, survival
                sevent
clus2              0   1
  MTTP MUTATED    17  10
  MTTP WILD-TYPE 361  83
  MTTP MUTATED MTTP WILD-TYPE 
            27            444 
  MTTP MUTATED MTTP WILD-TYPE 
            10             83 
$`MTTP MUTATED`
TCGA-A6-2676 TCGA-A6-5661 TCGA-A6-5665 TCGA-A6-6653 TCGA-AA-3492 TCGA-AA-3811 
       42.90        33.53        22.06        24.39         3.02        10.06 
TCGA-AA-3966 TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A02K TCGA-AD-6888 TCGA-AZ-6600 
        2.01        25.02         4.01        14.01        15.52        12.10 
TCGA-CA-6717 TCGA-CK-5916 TCGA-CM-4752 TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6674 
       12.76        21.14        13.02        16.04        14.99        12.95 
TCGA-D5-6534 TCGA-F4-6459 TCGA-G4-6586 TCGA-G4-6588 TCGA-AF-2692 TCGA-AG-A002 
       43.27         8.61        35.80        26.17        13.55        20.98 
TCGA-AG-A02N TCGA-AG-A032 TCGA-DY-A1DC 
       61.97        38.04        41.36 

$`MTTP WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 
       31.63        30.44        29.19        23.61        22.09        32.71 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       27.09        22.52         8.38        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       21.76        24.69        23.87        20.12        19.66        20.28 
TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
        7.04         1.02        35.01        63.98         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
       13.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       36.03         8.05        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       78.08         6.05         6.97        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        19.04        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 
       24.00         2.01        20.98        34.03        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        2.01         5.03         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
       40.96         0.07        21.37        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       88.21        49.41         6.77       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07        12.20        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       25.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6166 TCGA-CM-6168 TCGA-CM-6169 
       12.00         2.96        29.03        21.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       15.02        14.04        11.01        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6535 
       56.09        55.92        20.19        18.25         1.32        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6460 TCGA-F4-6569 
       35.97        60.79       117.07        98.24        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6625 
       63.62        61.91        36.00        22.09        13.78        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2693 
       46.75        79.69        24.13        39.48        43.04        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02X TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       41.00       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  MTTP MUTATED MTTP WILD-TYPE 
          2.01           0.00 
  MTTP MUTATED MTTP WILD-TYPE 
         61.97         148.01 
  MTTP MUTATED MTTP WILD-TYPE 
        16.040         20.235 
[1] "2.0 - 62.0 (16.0)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "2.4"
D864V2, continuous
D864V3, binary
                cls
clus               0   1
  MTTP MUTATED    23   4
  MTTP WILD-TYPE 343 115
[1] "tbl2"
                cls
clus             [,1] [,2]
  MTTP MUTATED     23    4
  MTTP WILD-TYPE  343  115
        clus
vv       MTTP MUTATED MTTP WILD-TYPE
  COLON            23            343
  RECTUM            4            115
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MTTP MUTATED         3        0        2        13         2         0
  MTTP WILD-TYPE      88        1       30       125         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MTTP MUTATED           1          0          3          1        2         0
  MTTP WILD-TYPE        23         11         56         41       46        18
                vv
clus             STAGE IVB
  MTTP MUTATED           0
  MTTP WILD-TYPE         1
D864V4, multiclass
            clus
vv           MTTP MUTATED MTTP WILD-TYPE
  STAGE I               3             88
  STAGE IA              0              1
  STAGE II              2             30
  STAGE IIA            13            125
  STAGE IIB             2              8
  STAGE IIC             0              1
  STAGE III             1             23
  STAGE IIIA            0             11
  STAGE IIIB            3             56
  STAGE IIIC            1             41
  STAGE IV              2             46
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  MTTP MUTATED     1   3  20   4
  MTTP WILD-TYPE  16  89 309  46
D864V5, multiclass
    clus
vv   MTTP MUTATED MTTP WILD-TYPE
  T1            1             16
  T2            3             89
  T3           20            309
  T4            4             46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  MTTP MUTATED    21   3   4
  MTTP WILD-TYPE 266 110  83
D864V6, multiclass
    clus
vv   MTTP MUTATED MTTP WILD-TYPE
  N0           21            266
  N1            3            110
  N2            4             83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D864V7, binary
                cls
clus               0   1
  MTTP MUTATED    25   2
  MTTP WILD-TYPE 350  63
[1] "tbl2"
                cls
clus             [,1] [,2]
  MTTP MUTATED     25    2
  MTTP WILD-TYPE  350   63
   clus
vv  MTTP MUTATED MTTP WILD-TYPE
  0           25            350
  1            2             63
[1] 2 2
[1] FALSE
D864V8, binary
                cls
clus               0   1
  MTTP MUTATED    15  13
  MTTP WILD-TYPE 210 251
[1] "tbl2"
                cls
clus             [,1] [,2]
  MTTP MUTATED     15   13
  MTTP WILD-TYPE  210  251
        clus
vv       MTTP MUTATED MTTP WILD-TYPE
  FEMALE           15            210
  MALE             13            251
[1] 2 2
[1] FALSE
D864V9, binary
                cls
clus               0   1
  MTTP MUTATED    21   1
  MTTP WILD-TYPE 329  21
[1] "tbl2"
                cls
clus             [,1] [,2]
  MTTP MUTATED     21    1
  MTTP WILD-TYPE  329   21
     clus
vv    MTTP MUTATED MTTP WILD-TYPE
  NO            21            329
  YES            1             21
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MTTP MUTATED                     19                             4
  MTTP WILD-TYPE                  296                            43
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MTTP MUTATED                       4                              0
  MTTP WILD-TYPE                   102                             10
D864V10, multiclass
                                clus
vv                               MTTP MUTATED MTTP WILD-TYPE
  COLON ADENOCARCINOMA                     19            296
  COLON MUCINOUS ADENOCARCINOMA             4             43
  RECTAL ADENOCARCINOMA                     4            102
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  MTTP MUTATED    20   0   1   2
  MTTP WILD-TYPE 325   4  30  23
D864V11, multiclass
    clus
vv   MTTP MUTATED MTTP WILD-TYPE
  R0           20            325
  R1            0              4
  R2            1             30
  RX            2             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D864V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MTTP MUTATED                                  0     1
  MTTP WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  MTTP MUTATED                           4    13
  MTTP WILD-TYPE                        18   213
D864V13, multiclass
                                  clus
vv                                 MTTP MUTATED MTTP WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   4             18
  WHITE                                      13            213
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(865) Variable = HEPH MUTATION ANALYSIS
D865V1, survival
                sevent
clus2              0   1
  HEPH MUTATED    17   2
  HEPH WILD-TYPE 361  91
  HEPH MUTATED HEPH WILD-TYPE 
            19            452 
  HEPH MUTATED HEPH WILD-TYPE 
             2             91 
$`HEPH MUTATED`
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-AA-3655 TCGA-AA-A00N TCGA-AZ-4315 
       31.63        30.44        33.53        61.02         4.01        58.39 
TCGA-CK-4952 TCGA-CM-4743 TCGA-CM-5861 TCGA-D5-5538 TCGA-D5-5541 TCGA-DM-A1D8 
       15.62        23.05        15.02        12.26        55.92        12.59 
TCGA-DM-A28H TCGA-F4-6856 TCGA-G4-6321 TCGA-AG-3892 TCGA-AG-A002 TCGA-CI-6620 
      117.07        35.31        22.09        13.02        20.98        33.17 
TCGA-DY-A0XA 
      126.44 

$`HEPH WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 
       32.91        29.19        23.61        22.09        22.06        32.71 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       27.09        22.52         8.38        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       19.99        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
       17.56       148.01        85.45        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 
       21.14        82.95         1.91       124.27        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       32.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       45.40        19.59        56.09        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A1DA 
      130.65        92.75        49.91        13.32       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
      119.93        35.97        60.79        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 
       16.24        33.67        13.25         0.53        47.41       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       63.62        61.91        36.00        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 
       19.99         1.02        17.95        36.95        17.03        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6622 
        1.45        17.49         0.69         0.72         6.05         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
        5.29        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  HEPH MUTATED HEPH WILD-TYPE 
          4.01           0.00 
  HEPH MUTATED HEPH WILD-TYPE 
        126.44         148.01 
  HEPH MUTATED HEPH WILD-TYPE 
         30.44          20.02 
[1] "4.0 - 126.4 (30.4)" "0.0 - 148.0 (20.0)"
[1] "hr=" "2.6"
D865V2, continuous
D865V3, binary
                cls
clus               0   1
  HEPH MUTATED    15   4
  HEPH WILD-TYPE 351 115
[1] "tbl2"
                cls
clus             [,1] [,2]
  HEPH MUTATED     15    4
  HEPH WILD-TYPE  351  115
        clus
vv       HEPH MUTATED HEPH WILD-TYPE
  COLON            15            351
  RECTUM            4            115
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  HEPH MUTATED         4        0        1         5         1         0
  HEPH WILD-TYPE      87        1       31       133         9         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  HEPH MUTATED           1          0          3          2        0         1
  HEPH WILD-TYPE        23         11         56         40       48        17
                vv
clus             STAGE IVB
  HEPH MUTATED           0
  HEPH WILD-TYPE         1
D865V4, multiclass
            clus
vv           HEPH MUTATED HEPH WILD-TYPE
  STAGE I               4             87
  STAGE IA              0              1
  STAGE II              1             31
  STAGE IIA             5            133
  STAGE IIB             1              9
  STAGE IIC             0              1
  STAGE III             1             23
  STAGE IIIA            0             11
  STAGE IIIB            3             56
  STAGE IIIC            2             40
  STAGE IV              0             48
  STAGE IVA             1             17
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  HEPH MUTATED     1   4  12   2
  HEPH WILD-TYPE  16  88 317  48
D865V5, multiclass
    clus
vv   HEPH MUTATED HEPH WILD-TYPE
  T1            1             16
  T2            4             88
  T3           12            317
  T4            2             48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  HEPH MUTATED    11   6   2
  HEPH WILD-TYPE 276 107  85
D865V6, multiclass
    clus
vv   HEPH MUTATED HEPH WILD-TYPE
  N0           11            276
  N1            6            107
  N2            2             85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D865V7, binary
                cls
clus               0   1
  HEPH MUTATED    16   1
  HEPH WILD-TYPE 359  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  HEPH MUTATED     16    1
  HEPH WILD-TYPE  359   64
   clus
vv  HEPH MUTATED HEPH WILD-TYPE
  0           16            359
  1            1             64
[1] 2 2
[1] FALSE
D865V8, binary
                cls
clus               0   1
  HEPH MUTATED     9  10
  HEPH WILD-TYPE 216 254
[1] "tbl2"
                cls
clus             [,1] [,2]
  HEPH MUTATED      9   10
  HEPH WILD-TYPE  216  254
        clus
vv       HEPH MUTATED HEPH WILD-TYPE
  FEMALE            9            216
  MALE             10            254
[1] 2 2
[1] FALSE
D865V9, binary
                cls
clus               0   1
  HEPH MUTATED    14   0
  HEPH WILD-TYPE 336  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  HEPH MUTATED     14    0
  HEPH WILD-TYPE  336   22
     clus
vv    HEPH MUTATED HEPH WILD-TYPE
  NO            14            336
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  HEPH MUTATED                     12                             3
  HEPH WILD-TYPE                  303                            44
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  HEPH MUTATED                       4                              0
  HEPH WILD-TYPE                   102                             10
D865V10, multiclass
                                clus
vv                               HEPH MUTATED HEPH WILD-TYPE
  COLON ADENOCARCINOMA                     12            303
  COLON MUCINOUS ADENOCARCINOMA             3             44
  RECTAL ADENOCARCINOMA                     4            102
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  HEPH MUTATED    14   0   0   1
  HEPH WILD-TYPE 331   4  31  24
D865V11, multiclass
    clus
vv   HEPH MUTATED HEPH WILD-TYPE
  R0           14            331
  R1            0              4
  R2            0             31
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D865V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HEPH MUTATED                                  0     0
  HEPH WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  HEPH MUTATED                           2    13
  HEPH WILD-TYPE                        20   213
D865V13, multiclass
                                  clus
vv                                 HEPH MUTATED HEPH WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   2             20
  WHITE                                      13            213
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(866) Variable = MAP2 MUTATION ANALYSIS
D866V1, survival
                sevent
clus2              0   1
  MAP2 MUTATED    31  11
  MAP2 WILD-TYPE 347  82
  MAP2 MUTATED MAP2 WILD-TYPE 
            42            429 
  MAP2 MUTATED MAP2 WILD-TYPE 
            11             82 
$`MAP2 MUTATED`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-5660 TCGA-A6-5665 TCGA-A6-6781 TCGA-AA-3492 
       43.76        46.65        29.19        22.06        19.66         3.02 
TCGA-AA-3510 TCGA-AA-3518 TCGA-AA-3525 TCGA-AA-3663 TCGA-AA-3818 TCGA-AA-3819 
       63.98         1.02         8.05         6.97         0.99        25.02 
TCGA-AA-3852 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3980 TCGA-AA-A00J TCGA-AA-A00N 
        0.00        26.01        24.00        27.02        18.05         4.01 
TCGA-AA-A010 TCGA-AA-A01Z TCGA-AD-5900 TCGA-AD-6964 TCGA-AD-6965 TCGA-AZ-4315 
       34.98        37.02         0.07        10.88         0.20        58.39 
TCGA-AZ-6601 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4950 TCGA-CM-6167 TCGA-CM-6171 
      100.01        12.76        10.06        85.45        14.99        14.04 
TCGA-CM-6676 TCGA-D5-5540 TCGA-F4-6570 TCGA-F4-6856 TCGA-G4-6323 TCGA-AG-3612 
       11.08        56.09         6.18        35.31        13.78        19.99 
TCGA-AG-3892 TCGA-AH-6544 TCGA-AH-6643 TCGA-DY-A1DD TCGA-F5-6464 TCGA-G5-6235 
       13.02        38.56         0.69        57.24         9.96        55.76 

$`MAP2 WILD-TYPE`
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       43.76        42.90        24.33        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5657 
       33.34        32.75        36.53        14.53        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 
       30.44        33.53        23.61        22.09        32.71        27.09 
TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 
       22.52         8.38        25.08        25.18        24.16        21.76 
TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 
       24.69        24.39        23.87        20.12        20.28         7.04 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3529 
        9.07        24.03        37.05        36.03        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02        78.08         6.05        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3854 
        0.00        17.03        10.06         0.00        33.07        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3952 TCGA-AA-3955 
        2.01        12.99        24.00        33.01         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        25.02        24.00        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       34.03        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A024 TCGA-AA-A029 
        1.02        33.04        35.01        26.01        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       39.98        18.05        40.96        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AU-3779 
        0.79         0.72         5.79        22.42        27.42        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       49.41         6.77        12.10        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 
        0.07        12.20        14.30        17.56       148.01        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6168 TCGA-CM-6169 
        2.96        29.03        16.04        21.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6677 TCGA-CM-6678 
       15.02        11.01        12.95        13.05        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5541 
       10.06        12.03        45.40        12.26        19.59        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
       13.25         0.53        47.41       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       19.99        13.94         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       36.95        17.03        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6644 
       41.00        38.04       117.11         1.45        17.49         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       20.91        18.28        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6641 
        0.66         0.69        26.43 

  MAP2 MUTATED MAP2 WILD-TYPE 
             0              0 
  MAP2 MUTATED MAP2 WILD-TYPE 
        100.01         148.01 
  MAP2 MUTATED MAP2 WILD-TYPE 
        18.855         20.550 
[1] "0.0 - 100.0 (18.9)" "0.0 - 148.0 (20.6)"
[1] "hr=" "1.4"
D866V2, continuous
D866V3, binary
                cls
clus               0   1
  MAP2 MUTATED    36   7
  MAP2 WILD-TYPE 330 112
[1] "tbl2"
                cls
clus             [,1] [,2]
  MAP2 MUTATED     36    7
  MAP2 WILD-TYPE  330  112
        clus
vv       MAP2 MUTATED MAP2 WILD-TYPE
  COLON            36            330
  RECTUM            7            112
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MAP2 MUTATED         6        1        5        12         2         0
  MAP2 WILD-TYPE      85        0       27       126         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MAP2 MUTATED           0          0          8          5        1         0
  MAP2 WILD-TYPE        24         11         51         37       47        18
                vv
clus             STAGE IVB
  MAP2 MUTATED           0
  MAP2 WILD-TYPE         1
D866V4, multiclass
            clus
vv           MAP2 MUTATED MAP2 WILD-TYPE
  STAGE I               6             85
  STAGE IA              1              0
  STAGE II              5             27
  STAGE IIA            12            126
  STAGE IIB             2              8
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            8             51
  STAGE IIIC            5             37
  STAGE IV              1             47
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  MAP2 MUTATED     1   5  29   7
  MAP2 WILD-TYPE  16  87 300  43
D866V5, multiclass
    clus
vv   MAP2 MUTATED MAP2 WILD-TYPE
  T1            1             16
  T2            5             87
  T3           29            300
  T4            7             43
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  MAP2 MUTATED    26  10   7
  MAP2 WILD-TYPE 261 103  80
D866V6, multiclass
    clus
vv   MAP2 MUTATED MAP2 WILD-TYPE
  N0           26            261
  N1           10            103
  N2            7             80
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D866V7, binary
                cls
clus               0   1
  MAP2 MUTATED    35   2
  MAP2 WILD-TYPE 340  63
[1] "tbl2"
                cls
clus             [,1] [,2]
  MAP2 MUTATED     35    2
  MAP2 WILD-TYPE  340   63
   clus
vv  MAP2 MUTATED MAP2 WILD-TYPE
  0           35            340
  1            2             63
[1] 2 2
[1] FALSE
D866V8, binary
                cls
clus               0   1
  MAP2 MUTATED    19  24
  MAP2 WILD-TYPE 206 240
[1] "tbl2"
                cls
clus             [,1] [,2]
  MAP2 MUTATED     19   24
  MAP2 WILD-TYPE  206  240
        clus
vv       MAP2 MUTATED MAP2 WILD-TYPE
  FEMALE           19            206
  MALE             24            240
[1] 2 2
[1] FALSE
D866V9, binary
                cls
clus               0   1
  MAP2 MUTATED    34   0
  MAP2 WILD-TYPE 316  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  MAP2 MUTATED     34    0
  MAP2 WILD-TYPE  316   22
     clus
vv    MAP2 MUTATED MAP2 WILD-TYPE
  NO            34            316
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MAP2 MUTATED                     27                             9
  MAP2 WILD-TYPE                  288                            38
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MAP2 MUTATED                       7                              0
  MAP2 WILD-TYPE                    99                             10
D866V10, multiclass
                                clus
vv                               MAP2 MUTATED MAP2 WILD-TYPE
  COLON ADENOCARCINOMA                     27            288
  COLON MUCINOUS ADENOCARCINOMA             9             38
  RECTAL ADENOCARCINOMA                     7             99
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  MAP2 MUTATED    32   2   0   2
  MAP2 WILD-TYPE 313   2  31  23
D866V11, multiclass
    clus
vv   MAP2 MUTATED MAP2 WILD-TYPE
  R0           32            313
  R1            2              2
  R2            0             31
  RX            2             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D866V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MAP2 MUTATED                                  0     2
  MAP2 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  MAP2 MUTATED                           4    19
  MAP2 WILD-TYPE                        18   207
D866V13, multiclass
                                  clus
vv                                 MAP2 MUTATED MAP2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              9
  BLACK OR AFRICAN AMERICAN                   4             18
  WHITE                                      19            207
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(867) Variable = NOD2 MUTATION ANALYSIS
D867V1, survival
                sevent
clus2              0   1
  NOD2 MUTATED    18   2
  NOD2 WILD-TYPE 360  91
  NOD2 MUTATED NOD2 WILD-TYPE 
            20            451 
  NOD2 MUTATED NOD2 WILD-TYPE 
             2             91 
$`NOD2 MUTATED`
TCGA-A6-5665 TCGA-AA-3977 TCGA-AA-A01R TCGA-AD-6901 TCGA-AD-6964 TCGA-CM-4743 
       22.06        25.02        35.01        22.42        10.88        23.05 
TCGA-CM-4744 TCGA-CM-5861 TCGA-CM-6162 TCGA-CM-6165 TCGA-D5-6538 TCGA-F4-6855 
       20.02        15.02        12.00        16.04        17.13        47.41 
TCGA-F4-6856 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-AF-2687 TCGA-AG-3892 
       35.31        22.09        35.80        26.17        24.13        13.02 
TCGA-AG-A002 TCGA-CL-5917 
       20.98        78.12 

$`NOD2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T 
       31.00        31.00        38.07         1.02         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
        0.79         0.72         5.79        27.42         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       30.08        32.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
       15.02         2.96        29.03        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6539 
        1.32        43.27        15.12        17.85         4.80        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6625 
       85.48        63.62        61.91        36.00        13.78        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       46.75        79.69        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       17.95        36.95        17.03        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  NOD2 MUTATED NOD2 WILD-TYPE 
         10.88           0.00 
  NOD2 MUTATED NOD2 WILD-TYPE 
         78.12         148.01 
  NOD2 MUTATED NOD2 WILD-TYPE 
        22.255         20.020 
[1] "10.9 - 78.1 (22.3)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.9"
D867V2, continuous
D867V3, binary
                cls
clus               0   1
  NOD2 MUTATED    16   4
  NOD2 WILD-TYPE 350 115
[1] "tbl2"
                cls
clus             [,1] [,2]
  NOD2 MUTATED     16    4
  NOD2 WILD-TYPE  350  115
        clus
vv       NOD2 MUTATED NOD2 WILD-TYPE
  COLON            16            350
  RECTUM            4            115
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NOD2 MUTATED         4        0        0         7         0         0
  NOD2 WILD-TYPE      87        1       32       131        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NOD2 MUTATED           2          0          2          2        0         0
  NOD2 WILD-TYPE        22         11         57         40       48        18
                vv
clus             STAGE IVB
  NOD2 MUTATED           0
  NOD2 WILD-TYPE         1
D867V4, multiclass
            clus
vv           NOD2 MUTATED NOD2 WILD-TYPE
  STAGE I               4             87
  STAGE IA              0              1
  STAGE II              0             32
  STAGE IIA             7            131
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             2             22
  STAGE IIIA            0             11
  STAGE IIIB            2             57
  STAGE IIIC            2             40
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  NOD2 MUTATED     1   5  13   1
  NOD2 WILD-TYPE  16  87 316  49
D867V5, multiclass
    clus
vv   NOD2 MUTATED NOD2 WILD-TYPE
  T1            1             16
  T2            5             87
  T3           13            316
  T4            1             49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  NOD2 MUTATED    13   2   5
  NOD2 WILD-TYPE 274 111  82
D867V6, multiclass
    clus
vv   NOD2 MUTATED NOD2 WILD-TYPE
  N0           13            274
  N1            2            111
  N2            5             82
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D867V7, binary
                cls
clus               0   1
  NOD2 MUTATED    15   0
  NOD2 WILD-TYPE 360  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  NOD2 MUTATED     15    0
  NOD2 WILD-TYPE  360   65
   clus
vv  NOD2 MUTATED NOD2 WILD-TYPE
  0           15            360
  1            0             65
[1] 2 2
[1] FALSE
D867V8, binary
                cls
clus               0   1
  NOD2 MUTATED    10  10
  NOD2 WILD-TYPE 215 254
[1] "tbl2"
                cls
clus             [,1] [,2]
  NOD2 MUTATED     10   10
  NOD2 WILD-TYPE  215  254
        clus
vv       NOD2 MUTATED NOD2 WILD-TYPE
  FEMALE           10            215
  MALE             10            254
[1] 2 2
[1] FALSE
D867V9, binary
                cls
clus               0   1
  NOD2 MUTATED    18   2
  NOD2 WILD-TYPE 332  20
[1] "tbl2"
                cls
clus             [,1] [,2]
  NOD2 MUTATED     18    2
  NOD2 WILD-TYPE  332   20
     clus
vv    NOD2 MUTATED NOD2 WILD-TYPE
  NO            18            332
  YES            2             20
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  NOD2 MUTATED                     13                             3
  NOD2 WILD-TYPE                  302                            44
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  NOD2 MUTATED                       4                              0
  NOD2 WILD-TYPE                   102                             10
D867V10, multiclass
                                clus
vv                               NOD2 MUTATED NOD2 WILD-TYPE
  COLON ADENOCARCINOMA                     13            302
  COLON MUCINOUS ADENOCARCINOMA             3             44
  RECTAL ADENOCARCINOMA                     4            102
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  NOD2 MUTATED    16   0   0   1
  NOD2 WILD-TYPE 329   4  31  24
D867V11, multiclass
    clus
vv   NOD2 MUTATED NOD2 WILD-TYPE
  R0           16            329
  R1            0              4
  R2            0             31
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D867V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NOD2 MUTATED                                  0     0
  NOD2 WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  NOD2 MUTATED                           0    16
  NOD2 WILD-TYPE                        22   210
D867V13, multiclass
                                  clus
vv                                 NOD2 MUTATED NOD2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                      16            210
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(868) Variable = RSPO2 MUTATION ANALYSIS
D868V1, survival
                 sevent
clus2               0   1
  RSPO2 MUTATED    15   5
  RSPO2 WILD-TYPE 363  88
  RSPO2 MUTATED RSPO2 WILD-TYPE 
             20             451 
  RSPO2 MUTATED RSPO2 WILD-TYPE 
              5              88 
$`RSPO2 MUTATED`
TCGA-A6-5659 TCGA-A6-6651 TCGA-A6-6654 TCGA-AA-3855 TCGA-AA-3947 TCGA-AA-A010 
       30.44        21.76        23.87        32.05        33.01        34.98 
TCGA-AZ-6605 TCGA-CA-5796 TCGA-CA-6718 TCGA-CM-5349 TCGA-CM-6680 TCGA-D5-6929 
        5.23         3.25        10.06        30.08        12.03         4.80 
TCGA-DM-A1D4 TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6570 TCGA-AF-6655 TCGA-AG-3896 
       92.75       117.07        98.24         6.18        20.02         1.02 
TCGA-AG-A026 TCGA-CI-6622 
        1.94         6.97 

$`RSPO2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 
       25.18        24.16        24.69        24.39        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3858 
        0.00        33.07         0.00        36.03         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6606 
       49.41         6.77        12.10       100.01        29.56        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5797 TCGA-CA-6715 
        3.19         1.61        12.69         3.06         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.20        12.76        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5861 
       13.02        29.06        22.03        22.98        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.08        11.01        10.06        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 
       14.30         9.04         9.44        11.64         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 
       35.97        60.79         8.61        31.96        35.74        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A02G TCGA-AG-A02N 
       70.03        64.01        10.98        49.97        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6624 TCGA-CL-5917 
        0.69         0.72         6.05        33.17         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  RSPO2 MUTATED RSPO2 WILD-TYPE 
           1.02            0.00 
  RSPO2 MUTATED RSPO2 WILD-TYPE 
         117.07          148.01 
  RSPO2 MUTATED RSPO2 WILD-TYPE 
          20.89           20.19 
[1] "1.0 - 117.1 (20.9)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.2"
D868V2, continuous
D868V3, binary
                 cls
clus                0   1
  RSPO2 MUTATED    17   4
  RSPO2 WILD-TYPE 349 115
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RSPO2 MUTATED     17    4
  RSPO2 WILD-TYPE  349  115
        clus
vv       RSPO2 MUTATED RSPO2 WILD-TYPE
  COLON             17             349
  RECTUM             4             115
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RSPO2 MUTATED         3        0        1         7         3         0
  RSPO2 WILD-TYPE      88        1       31       131         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RSPO2 MUTATED           0          1          4          1        1         0
  RSPO2 WILD-TYPE        24         10         55         41       47        18
                 vv
clus              STAGE IVB
  RSPO2 MUTATED           0
  RSPO2 WILD-TYPE         1
D868V4, multiclass
            clus
vv           RSPO2 MUTATED RSPO2 WILD-TYPE
  STAGE I                3              88
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              7             131
  STAGE IIB              3               7
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             1              10
  STAGE IIIB             4              55
  STAGE IIIC             1              41
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  RSPO2 MUTATED     0   4  12   5
  RSPO2 WILD-TYPE  17  88 317  45
D868V5, multiclass
    clus
vv   RSPO2 MUTATED RSPO2 WILD-TYPE
  T1             0              17
  T2             4              88
  T3            12             317
  T4             5              45
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  RSPO2 MUTATED    14   5   2
  RSPO2 WILD-TYPE 273 108  85
D868V6, multiclass
    clus
vv   RSPO2 MUTATED RSPO2 WILD-TYPE
  N0            14             273
  N1             5             108
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D868V7, binary
                 cls
clus                0   1
  RSPO2 MUTATED    19   1
  RSPO2 WILD-TYPE 356  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RSPO2 MUTATED     19    1
  RSPO2 WILD-TYPE  356   64
   clus
vv  RSPO2 MUTATED RSPO2 WILD-TYPE
  0            19             356
  1             1              64
[1] 2 2
[1] FALSE
D868V8, binary
                 cls
clus                0   1
  RSPO2 MUTATED    11  10
  RSPO2 WILD-TYPE 214 254
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RSPO2 MUTATED     11   10
  RSPO2 WILD-TYPE  214  254
        clus
vv       RSPO2 MUTATED RSPO2 WILD-TYPE
  FEMALE            11             214
  MALE              10             254
[1] 2 2
[1] FALSE
D868V9, binary
                 cls
clus                0   1
  RSPO2 MUTATED    13   0
  RSPO2 WILD-TYPE 337  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RSPO2 MUTATED     13    0
  RSPO2 WILD-TYPE  337   22
     clus
vv    RSPO2 MUTATED RSPO2 WILD-TYPE
  NO             13             337
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  RSPO2 MUTATED                     14                             3
  RSPO2 WILD-TYPE                  301                            44
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  RSPO2 MUTATED                       4                              0
  RSPO2 WILD-TYPE                   102                             10
D868V10, multiclass
                                clus
vv                               RSPO2 MUTATED RSPO2 WILD-TYPE
  COLON ADENOCARCINOMA                      14             301
  COLON MUCINOUS ADENOCARCINOMA              3              44
  RECTAL ADENOCARCINOMA                      4             102
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  RSPO2 MUTATED    12   1   0   1
  RSPO2 WILD-TYPE 333   3  31  24
D868V11, multiclass
    clus
vv   RSPO2 MUTATED RSPO2 WILD-TYPE
  R0            12             333
  R1             1               3
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D868V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RSPO2 MUTATED                                  0     2
  RSPO2 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  RSPO2 MUTATED                           0    13
  RSPO2 WILD-TYPE                        22   213
D868V13, multiclass
                                  clus
vv                                 RSPO2 MUTATED RSPO2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               9
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                       13             213
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(869) Variable = PCDH20 MUTATION ANALYSIS
D869V1, survival
                  sevent
clus2                0   1
  PCDH20 MUTATED    15   8
  PCDH20 WILD-TYPE 363  85
  PCDH20 MUTATED PCDH20 WILD-TYPE 
              23              448 
  PCDH20 MUTATED PCDH20 WILD-TYPE 
               8               85 
$`PCDH20 MUTATED`
TCGA-A6-6649 TCGA-A6-6782 TCGA-AA-3492 TCGA-AA-3672 TCGA-AA-3850 TCGA-AA-3947 
       24.16        20.28         3.02         0.92         0.00        33.01 
TCGA-AA-3977 TCGA-AA-A010 TCGA-AU-6004 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-CA-6718 
       25.02        34.98        27.09        58.39        49.41        10.06 
TCGA-CK-5913 TCGA-CM-5864 TCGA-D5-5537 TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-G4-6293 
       51.32        15.02        45.40        12.59         7.50       133.18 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AG-A02N TCGA-AG-A02X TCGA-G5-6235 
       46.75        79.69        61.97        41.00        55.76 

$`PCDH20 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.08        25.18        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.12        19.66         7.04         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
        2.01        14.01        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 
       37.02        14.93         0.00        17.03        10.06        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 
       18.05        31.00         2.01        12.99        24.00        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       10.88         0.20        14.50        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        88.21         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 
        3.25         3.29         0.07        12.20        12.76        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 
       17.56       148.01        85.45        15.62        49.08         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5868 
       30.08        32.02        15.02         5.03        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       12.03        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
      140.38        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       47.41        35.31        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-AF-2687 TCGA-AF-2689 
       13.78        35.80        26.17        91.79        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A032 TCGA-AG-A036 
       10.98        49.97         1.94        38.96        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6641 
       32.19         0.66         0.69        26.43 

  PCDH20 MUTATED PCDH20 WILD-TYPE 
               0                0 
  PCDH20 MUTATED PCDH20 WILD-TYPE 
          133.18           148.01 
  PCDH20 MUTATED PCDH20 WILD-TYPE 
          33.010           20.005 
[1] "0.0 - 133.2 (33.0)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.3"
D869V2, continuous
D869V3, binary
                  cls
clus                 0   1
  PCDH20 MUTATED    21   3
  PCDH20 WILD-TYPE 345 116
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PCDH20 MUTATED     21    3
  PCDH20 WILD-TYPE  345  116
        clus
vv       PCDH20 MUTATED PCDH20 WILD-TYPE
  COLON              21              345
  RECTUM              3              116
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PCDH20 MUTATED         5        0        4         5         3         0
  PCDH20 WILD-TYPE      86        1       28       133         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PCDH20 MUTATED           2          0          2          1        0
  PCDH20 WILD-TYPE        22         11         57         41       48
                  vv
clus               STAGE IVA STAGE IVB
  PCDH20 MUTATED           0         0
  PCDH20 WILD-TYPE        18         1
D869V4, multiclass
            clus
vv           PCDH20 MUTATED PCDH20 WILD-TYPE
  STAGE I                 5               86
  STAGE IA                0                1
  STAGE II                4               28
  STAGE IIA               5              133
  STAGE IIB               3                7
  STAGE IIC               0                1
  STAGE III               2               22
  STAGE IIIA              0               11
  STAGE IIIB              2               57
  STAGE IIIC              1               41
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  PCDH20 MUTATED     0   6  15   3
  PCDH20 WILD-TYPE  17  86 314  47
D869V5, multiclass
    clus
vv   PCDH20 MUTATED PCDH20 WILD-TYPE
  T1              0               17
  T2              6               86
  T3             15              314
  T4              3               47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  PCDH20 MUTATED    17   5   2
  PCDH20 WILD-TYPE 270 108  85
D869V6, multiclass
    clus
vv   PCDH20 MUTATED PCDH20 WILD-TYPE
  N0             17              270
  N1              5              108
  N2              2               85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D869V7, binary
                  cls
clus                 0   1
  PCDH20 MUTATED    17   0
  PCDH20 WILD-TYPE 358  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PCDH20 MUTATED     17    0
  PCDH20 WILD-TYPE  358   65
   clus
vv  PCDH20 MUTATED PCDH20 WILD-TYPE
  0             17              358
  1              0               65
[1] 2 2
[1] FALSE
D869V8, binary
                  cls
clus                 0   1
  PCDH20 MUTATED    10  14
  PCDH20 WILD-TYPE 215 250
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PCDH20 MUTATED     10   14
  PCDH20 WILD-TYPE  215  250
        clus
vv       PCDH20 MUTATED PCDH20 WILD-TYPE
  FEMALE             10              215
  MALE               14              250
[1] 2 2
[1] FALSE
D869V9, binary
                  cls
clus                 0   1
  PCDH20 MUTATED    17   0
  PCDH20 WILD-TYPE 333  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PCDH20 MUTATED     17    0
  PCDH20 WILD-TYPE  333   22
     clus
vv    PCDH20 MUTATED PCDH20 WILD-TYPE
  NO              17              333
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PCDH20 MUTATED                     20                             1
  PCDH20 WILD-TYPE                  295                            46
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PCDH20 MUTATED                       3                              0
  PCDH20 WILD-TYPE                   103                             10
D869V10, multiclass
                                clus
vv                               PCDH20 MUTATED PCDH20 WILD-TYPE
  COLON ADENOCARCINOMA                       20              295
  COLON MUCINOUS ADENOCARCINOMA               1               46
  RECTAL ADENOCARCINOMA                       3              103
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  PCDH20 MUTATED    14   1   0   3
  PCDH20 WILD-TYPE 331   3  31  22
D869V11, multiclass
    clus
vv   PCDH20 MUTATED PCDH20 WILD-TYPE
  R0             14              331
  R1              1                3
  R2              0               31
  RX              3               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D869V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PCDH20 MUTATED                                  0     1
  PCDH20 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  PCDH20 MUTATED                           0    14
  PCDH20 WILD-TYPE                        22   212
D869V13, multiclass
                                  clus
vv                                 PCDH20 MUTATED PCDH20 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                        14              212
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(870) Variable = OR5H15 MUTATION ANALYSIS
D870V1, survival
                  sevent
clus2                0   1
  OR5H15 MUTATED     7   0
  OR5H15 WILD-TYPE 371  93
  OR5H15 MUTATED OR5H15 WILD-TYPE 
               7              464 
  OR5H15 MUTATED OR5H15 WILD-TYPE 
               0               93 
$`OR5H15 MUTATED`
TCGA-A6-5659 TCGA-CM-4744 TCGA-CM-5349 TCGA-CM-5861 TCGA-F4-6569 TCGA-AG-A002 
       30.44        20.02        30.08        15.02        35.74        20.98 
TCGA-F5-6571 
       31.30 

$`OR5H15 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4746 
       21.14        82.95         1.91       124.27        23.05        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5860 
       25.02        13.02        29.06        22.03        22.98        32.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
       98.24         8.61        31.96         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
        9.96        49.51        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  OR5H15 MUTATED OR5H15 WILD-TYPE 
           15.02             0.00 
  OR5H15 MUTATED OR5H15 WILD-TYPE 
           35.74           148.01 
  OR5H15 MUTATED OR5H15 WILD-TYPE 
          30.080           20.085 
[1] "15.0 - 35.7 (30.1)" "0.0 - 148.0 (20.1)"
[1] "hr="     "9200000"
D870V2, continuous
D870V3, binary
                  cls
clus                 0   1
  OR5H15 MUTATED     5   2
  OR5H15 WILD-TYPE 361 117
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR5H15 MUTATED      5    2
  OR5H15 WILD-TYPE  361  117
        clus
vv       OR5H15 MUTATED OR5H15 WILD-TYPE
  COLON               5              361
  RECTUM              2              117
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  OR5H15 MUTATED         4        0        0         3         0         0
  OR5H15 WILD-TYPE      87        1       32       135        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  OR5H15 MUTATED           0          0          0          0        0
  OR5H15 WILD-TYPE        24         11         59         42       48
                  vv
clus               STAGE IVA STAGE IVB
  OR5H15 MUTATED           0         0
  OR5H15 WILD-TYPE        18         1
D870V4, multiclass
            clus
vv           OR5H15 MUTATED OR5H15 WILD-TYPE
  STAGE I                 4               87
  STAGE IA                0                1
  STAGE II                0               32
  STAGE IIA               3              135
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              0               59
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  OR5H15 MUTATED     0   4   3   0
  OR5H15 WILD-TYPE  17  88 326  50
D870V5, multiclass
    clus
vv   OR5H15 MUTATED OR5H15 WILD-TYPE
  T1              0               17
  T2              4               88
  T3              3              326
  T4              0               50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  OR5H15 MUTATED     7   0   0
  OR5H15 WILD-TYPE 280 113  87
D870V6, multiclass
    clus
vv   OR5H15 MUTATED OR5H15 WILD-TYPE
  N0              7              280
  N1              0              113
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D870V7, binary
                  cls
clus                 0   1
  OR5H15 MUTATED     7   0
  OR5H15 WILD-TYPE 368  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR5H15 MUTATED      7    0
  OR5H15 WILD-TYPE  368   65
   clus
vv  OR5H15 MUTATED OR5H15 WILD-TYPE
  0              7              368
  1              0               65
[1] 2 2
[1] FALSE
D870V8, binary
                  cls
clus                 0   1
  OR5H15 MUTATED     3   4
  OR5H15 WILD-TYPE 222 260
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR5H15 MUTATED      3    4
  OR5H15 WILD-TYPE  222  260
        clus
vv       OR5H15 MUTATED OR5H15 WILD-TYPE
  FEMALE              3              222
  MALE                4              260
[1] 2 2
[1] FALSE
D870V9, binary
                  cls
clus                 0   1
  OR5H15 MUTATED     7   0
  OR5H15 WILD-TYPE 343  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR5H15 MUTATED      7    0
  OR5H15 WILD-TYPE  343   22
     clus
vv    OR5H15 MUTATED OR5H15 WILD-TYPE
  NO               7              343
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  OR5H15 MUTATED                      5                             0
  OR5H15 WILD-TYPE                  310                            47
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  OR5H15 MUTATED                       2                              0
  OR5H15 WILD-TYPE                   104                             10
D870V10, multiclass
                                clus
vv                               OR5H15 MUTATED OR5H15 WILD-TYPE
  COLON ADENOCARCINOMA                        5              310
  COLON MUCINOUS ADENOCARCINOMA               0               47
  RECTAL ADENOCARCINOMA                       2              104
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  OR5H15 MUTATED     7   0   0   0
  OR5H15 WILD-TYPE 338   4  31  25
D870V11, multiclass
    clus
vv   OR5H15 MUTATED OR5H15 WILD-TYPE
  R0              7              338
  R1              0                4
  R2              0               31
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D870V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OR5H15 MUTATED                                  0     0
  OR5H15 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  OR5H15 MUTATED                           0     6
  OR5H15 WILD-TYPE                        22   220
D870V13, multiclass
                                  clus
vv                                 OR5H15 MUTATED OR5H15 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         6              220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(871) Variable = ACTL6B MUTATION ANALYSIS
D871V1, survival
                  sevent
clus2                0   1
  ACTL6B MUTATED     8   1
  ACTL6B WILD-TYPE 370  92
  ACTL6B MUTATED ACTL6B WILD-TYPE 
               9              462 
  ACTL6B MUTATED ACTL6B WILD-TYPE 
               1               92 
$`ACTL6B MUTATED`
TCGA-A6-4105 TCGA-A6-5665 TCGA-AA-3877 TCGA-AA-A02O TCGA-CM-5860 TCGA-CM-6170 
       14.53        22.06        31.00         0.92        32.02        15.02 
TCGA-D5-5539 TCGA-D5-6533 TCGA-G4-6321 
       19.59         1.32        22.09 

$`ACTL6B WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 
       16.57        34.65        33.34        32.75        36.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 
       24.03        27.02        29.98        18.05         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        2.01         5.03        14.01        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-5862 
       29.06        22.03        22.98        30.08        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 
       11.01        10.06        12.03        45.40        12.26        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       55.92        20.19        18.25        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       63.62        61.91        36.00        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  ACTL6B MUTATED ACTL6B WILD-TYPE 
            0.92             0.00 
  ACTL6B MUTATED ACTL6B WILD-TYPE 
           32.02           148.01 
  ACTL6B MUTATED ACTL6B WILD-TYPE 
          19.590           20.235 
[1] "0.9 - 32.0 (19.6)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.1"
D871V2, continuous
D871V3, binary
                  cls
clus                 0   1
  ACTL6B MUTATED     9   0
  ACTL6B WILD-TYPE 357 119
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ACTL6B MUTATED      9    0
  ACTL6B WILD-TYPE  357  119
        clus
vv       ACTL6B MUTATED ACTL6B WILD-TYPE
  COLON               9              357
  RECTUM              0              119
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ACTL6B MUTATED         2        0        1         3         0         0
  ACTL6B WILD-TYPE      89        1       31       135        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ACTL6B MUTATED           1          1          1          0        0
  ACTL6B WILD-TYPE        23         10         58         42       48
                  vv
clus               STAGE IVA STAGE IVB
  ACTL6B MUTATED           0         0
  ACTL6B WILD-TYPE        18         1
D871V4, multiclass
            clus
vv           ACTL6B MUTATED ACTL6B WILD-TYPE
  STAGE I                 2               89
  STAGE IA                0                1
  STAGE II                1               31
  STAGE IIA               3              135
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               1               23
  STAGE IIIA              1               10
  STAGE IIIB              1               58
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ACTL6B MUTATED     1   2   5   1
  ACTL6B WILD-TYPE  16  90 324  49
D871V5, multiclass
    clus
vv   ACTL6B MUTATED ACTL6B WILD-TYPE
  T1              1               16
  T2              2               90
  T3              5              324
  T4              1               49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  ACTL6B MUTATED     7   2   0
  ACTL6B WILD-TYPE 280 111  87
D871V6, multiclass
    clus
vv   ACTL6B MUTATED ACTL6B WILD-TYPE
  N0              7              280
  N1              2              111
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D871V7, binary
                  cls
clus                 0   1
  ACTL6B MUTATED     8   0
  ACTL6B WILD-TYPE 367  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ACTL6B MUTATED      8    0
  ACTL6B WILD-TYPE  367   65
   clus
vv  ACTL6B MUTATED ACTL6B WILD-TYPE
  0              8              367
  1              0               65
[1] 2 2
[1] FALSE
D871V8, binary
                  cls
clus                 0   1
  ACTL6B MUTATED     5   4
  ACTL6B WILD-TYPE 220 260
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ACTL6B MUTATED      5    4
  ACTL6B WILD-TYPE  220  260
        clus
vv       ACTL6B MUTATED ACTL6B WILD-TYPE
  FEMALE              5              220
  MALE                4              260
[1] 2 2
[1] FALSE
D871V9, binary
                  cls
clus                 0   1
  ACTL6B MUTATED     7   0
  ACTL6B WILD-TYPE 343  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ACTL6B MUTATED      7    0
  ACTL6B WILD-TYPE  343   22
     clus
vv    ACTL6B MUTATED ACTL6B WILD-TYPE
  NO               7              343
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ACTL6B MUTATED                      7                             2
  ACTL6B WILD-TYPE                  308                            45
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ACTL6B MUTATED                       0                              0
  ACTL6B WILD-TYPE                   106                             10
D871V10, multiclass
                                clus
vv                               ACTL6B MUTATED ACTL6B WILD-TYPE
  COLON ADENOCARCINOMA                        7              308
  COLON MUCINOUS ADENOCARCINOMA               2               45
  RECTAL ADENOCARCINOMA                       0              106
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ACTL6B MUTATED     8   0   0   0
  ACTL6B WILD-TYPE 337   4  31  25
D871V11, multiclass
    clus
vv   ACTL6B MUTATED ACTL6B WILD-TYPE
  R0              8              337
  R1              0                4
  R2              0               31
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D871V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ACTL6B MUTATED                                  0     0
  ACTL6B WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ACTL6B MUTATED                           0     7
  ACTL6B WILD-TYPE                        22   219
D871V13, multiclass
                                  clus
vv                                 ACTL6B MUTATED ACTL6B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         7              219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(872) Variable = ZNF167 MUTATION ANALYSIS
D872V1, survival
                  sevent
clus2                0   1
  ZNF167 MUTATED    11   6
  ZNF167 WILD-TYPE 367  87
  ZNF167 MUTATED ZNF167 WILD-TYPE 
              17              454 
  ZNF167 MUTATED ZNF167 WILD-TYPE 
               6               87 
$`ZNF167 MUTATED`
TCGA-A6-6141 TCGA-AA-3510 TCGA-AA-3696 TCGA-AA-3715 TCGA-AA-3979 TCGA-AA-A00N 
        8.38        63.98         5.03        19.04        24.00         4.01 
TCGA-AA-A010 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-CA-6717 TCGA-CA-6718 
       34.98        10.88       106.75       100.01        12.76        10.06 
TCGA-CM-6171 TCGA-D5-6923 TCGA-D5-6929 TCGA-G4-6586 TCGA-AG-A002 
       14.04        12.43         4.80        35.80        20.98 

$`ZNF167 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 
       22.09        22.06        32.71        27.09        22.52        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       85.05        26.99        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        25.02        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 
        3.06         3.25         3.29         0.07        12.20        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        1.48         3.68         4.41        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       11.64         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 
       61.91        36.00        22.09        13.78        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  ZNF167 MUTATED ZNF167 WILD-TYPE 
            4.01             0.00 
  ZNF167 MUTATED ZNF167 WILD-TYPE 
          106.75           148.01 
  ZNF167 MUTATED ZNF167 WILD-TYPE 
          14.040           20.415 
[1] "4.0 - 106.8 (14.0)" "0.0 - 148.0 (20.4)"
[1] "hr=" "1.7"
D872V2, continuous
D872V3, binary
                  cls
clus                 0   1
  ZNF167 MUTATED    17   1
  ZNF167 WILD-TYPE 349 118
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF167 MUTATED     17    1
  ZNF167 WILD-TYPE  349  118
        clus
vv       ZNF167 MUTATED ZNF167 WILD-TYPE
  COLON              17              349
  RECTUM              1              118
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZNF167 MUTATED         3        0        3         7         2         0
  ZNF167 WILD-TYPE      88        1       29       131         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF167 MUTATED           0          0          0          0        2
  ZNF167 WILD-TYPE        24         11         59         42       46
                  vv
clus               STAGE IVA STAGE IVB
  ZNF167 MUTATED           0         0
  ZNF167 WILD-TYPE        18         1
D872V4, multiclass
            clus
vv           ZNF167 MUTATED ZNF167 WILD-TYPE
  STAGE I                 3               88
  STAGE IA                0                1
  STAGE II                3               29
  STAGE IIA               7              131
  STAGE IIB               2                8
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              0               59
  STAGE IIIC              0               42
  STAGE IV                2               46
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZNF167 MUTATED     0   3  12   3
  ZNF167 WILD-TYPE  17  89 317  47
D872V5, multiclass
    clus
vv   ZNF167 MUTATED ZNF167 WILD-TYPE
  T1              0               17
  T2              3               89
  T3             12              317
  T4              3               47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  ZNF167 MUTATED    15   2   1
  ZNF167 WILD-TYPE 272 111  86
D872V6, multiclass
    clus
vv   ZNF167 MUTATED ZNF167 WILD-TYPE
  N0             15              272
  N1              2              111
  N2              1               86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D872V7, binary
                  cls
clus                 0   1
  ZNF167 MUTATED    15   2
  ZNF167 WILD-TYPE 360  63
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF167 MUTATED     15    2
  ZNF167 WILD-TYPE  360   63
   clus
vv  ZNF167 MUTATED ZNF167 WILD-TYPE
  0             15              360
  1              2               63
[1] 2 2
[1] FALSE
D872V8, binary
                  cls
clus                 0   1
  ZNF167 MUTATED     7  11
  ZNF167 WILD-TYPE 218 253
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF167 MUTATED      7   11
  ZNF167 WILD-TYPE  218  253
        clus
vv       ZNF167 MUTATED ZNF167 WILD-TYPE
  FEMALE              7              218
  MALE               11              253
[1] 2 2
[1] FALSE
D872V9, binary
                  cls
clus                 0   1
  ZNF167 MUTATED    15   0
  ZNF167 WILD-TYPE 335  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF167 MUTATED     15    0
  ZNF167 WILD-TYPE  335   22
     clus
vv    ZNF167 MUTATED ZNF167 WILD-TYPE
  NO              15              335
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ZNF167 MUTATED                     15                             2
  ZNF167 WILD-TYPE                  300                            45
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ZNF167 MUTATED                       1                              0
  ZNF167 WILD-TYPE                   105                             10
D872V10, multiclass
                                clus
vv                               ZNF167 MUTATED ZNF167 WILD-TYPE
  COLON ADENOCARCINOMA                       15              300
  COLON MUCINOUS ADENOCARCINOMA               2               45
  RECTAL ADENOCARCINOMA                       1              105
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ZNF167 MUTATED    12   0   1   2
  ZNF167 WILD-TYPE 333   4  30  23
D872V11, multiclass
    clus
vv   ZNF167 MUTATED ZNF167 WILD-TYPE
  R0             12              333
  R1              0                4
  R2              1               30
  RX              2               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D872V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF167 MUTATED                                  0     2
  ZNF167 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZNF167 MUTATED                           1     7
  ZNF167 WILD-TYPE                        21   219
D872V13, multiclass
                                  clus
vv                                 ZNF167 MUTATED ZNF167 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                9
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                         7              219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(873) Variable = LPAR6 MUTATION ANALYSIS
D873V1, survival
                 sevent
clus2               0   1
  LPAR6 MUTATED     5   2
  LPAR6 WILD-TYPE 373  91
  LPAR6 MUTATED LPAR6 WILD-TYPE 
              7             464 
  LPAR6 MUTATED LPAR6 WILD-TYPE 
              2              91 
$`LPAR6 MUTATED`
TCGA-AA-A00N TCGA-AD-6963 TCGA-AY-6197 TCGA-AZ-4315 TCGA-CA-6718 TCGA-CM-6169 
        4.01        27.42        21.44        58.39        10.06        13.02 
TCGA-AG-A002 
       20.98 

$`LPAR6 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       33.01        17.82         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6170 
       29.03        16.04        21.99        14.99        12.99        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  LPAR6 MUTATED LPAR6 WILD-TYPE 
           4.01            0.00 
  LPAR6 MUTATED LPAR6 WILD-TYPE 
          58.39          148.01 
  LPAR6 MUTATED LPAR6 WILD-TYPE 
         20.980          20.155 
[1] "4.0 - 58.4 (21.0)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.6"
D873V2, continuous
D873V3, binary
                 cls
clus                0   1
  LPAR6 MUTATED     7   1
  LPAR6 WILD-TYPE 359 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LPAR6 MUTATED      7    1
  LPAR6 WILD-TYPE  359  118
        clus
vv       LPAR6 MUTATED LPAR6 WILD-TYPE
  COLON              7             359
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  LPAR6 MUTATED         2        0        0         4         1         0
  LPAR6 WILD-TYPE      89        1       32       134         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  LPAR6 MUTATED           0          0          0          0        0         0
  LPAR6 WILD-TYPE        24         11         59         42       48        18
                 vv
clus              STAGE IVB
  LPAR6 MUTATED           0
  LPAR6 WILD-TYPE         1
D873V4, multiclass
            clus
vv           LPAR6 MUTATED LPAR6 WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              4             134
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  LPAR6 MUTATED     0   2   5   1
  LPAR6 WILD-TYPE  17  90 324  49
D873V5, multiclass
    clus
vv   LPAR6 MUTATED LPAR6 WILD-TYPE
  T1             0              17
  T2             2              90
  T3             5             324
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  LPAR6 MUTATED     8   0   0
  LPAR6 WILD-TYPE 279 113  87
D873V6, multiclass
    clus
vv   LPAR6 MUTATED LPAR6 WILD-TYPE
  N0             8             279
  N1             0             113
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D873V7, binary
                 cls
clus                0   1
  LPAR6 MUTATED     5   0
  LPAR6 WILD-TYPE 370  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LPAR6 MUTATED      5    0
  LPAR6 WILD-TYPE  370   65
   clus
vv  LPAR6 MUTATED LPAR6 WILD-TYPE
  0             5             370
  1             0              65
[1] 2 2
[1] FALSE
D873V8, binary
                 cls
clus                0   1
  LPAR6 MUTATED     0   8
  LPAR6 WILD-TYPE 225 256
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LPAR6 MUTATED      0    8
  LPAR6 WILD-TYPE  225  256
        clus
vv       LPAR6 MUTATED LPAR6 WILD-TYPE
  FEMALE             0             225
  MALE               8             256
[1] 2 2
[1] FALSE
D873V9, binary
                 cls
clus                0   1
  LPAR6 MUTATED     6   0
  LPAR6 WILD-TYPE 344  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LPAR6 MUTATED      6    0
  LPAR6 WILD-TYPE  344   22
     clus
vv    LPAR6 MUTATED LPAR6 WILD-TYPE
  NO              6             344
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  LPAR6 MUTATED                      6                             1
  LPAR6 WILD-TYPE                  309                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  LPAR6 MUTATED                       1                              0
  LPAR6 WILD-TYPE                   105                             10
D873V10, multiclass
                                clus
vv                               LPAR6 MUTATED LPAR6 WILD-TYPE
  COLON ADENOCARCINOMA                       6             309
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  LPAR6 MUTATED     5   0   0   2
  LPAR6 WILD-TYPE 340   4  31  23
D873V11, multiclass
    clus
vv   LPAR6 MUTATED LPAR6 WILD-TYPE
  R0             5             340
  R1             0               4
  R2             0              31
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D873V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  LPAR6 MUTATED                                  0     1
  LPAR6 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  LPAR6 MUTATED                           1     4
  LPAR6 WILD-TYPE                        21   222
D873V13, multiclass
                                  clus
vv                                 LPAR6 MUTATED LPAR6 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        4             222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(874) Variable = EIF4G2 MUTATION ANALYSIS
D874V1, survival
                  sevent
clus2                0   1
  EIF4G2 MUTATED     8   5
  EIF4G2 WILD-TYPE 370  88
  EIF4G2 MUTATED EIF4G2 WILD-TYPE 
              13              458 
  EIF4G2 MUTATED EIF4G2 WILD-TYPE 
               5               88 
$`EIF4G2 MUTATED`
TCGA-A6-5657 TCGA-AA-3811 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-A00N TCGA-AA-A010 
       31.63        10.06        33.01        26.01         4.01        34.98 
TCGA-AZ-4315 TCGA-CA-5797 TCGA-CK-5916 TCGA-CM-5862 TCGA-DM-A1D8 TCGA-DM-A28K 
       58.39         3.29        21.14         5.03        12.59        98.24 
TCGA-G4-6588 
       26.17 

$`EIF4G2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       12.99        24.00        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
       16.31         0.95        33.01        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-6715 
        3.19         1.61        12.69         3.06         3.25         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 
       85.45        15.62        49.08        51.32         9.99        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
       15.02        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D9 
       38.20       130.65        92.75        49.91        13.32       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-F4-6459 
       81.37       119.93        35.97        60.79       117.07         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       13.78        35.80        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  EIF4G2 MUTATED EIF4G2 WILD-TYPE 
            3.29             0.00 
  EIF4G2 MUTATED EIF4G2 WILD-TYPE 
           98.24           148.01 
  EIF4G2 MUTATED EIF4G2 WILD-TYPE 
          26.010           20.085 
[1] "3.3 - 98.2 (26.0)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "2"  
D874V2, continuous
D874V3, binary
                  cls
clus                 0   1
  EIF4G2 MUTATED    15   0
  EIF4G2 WILD-TYPE 351 119
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EIF4G2 MUTATED     15    0
  EIF4G2 WILD-TYPE  351  119
        clus
vv       EIF4G2 MUTATED EIF4G2 WILD-TYPE
  COLON              15              351
  RECTUM              0              119
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  EIF4G2 MUTATED         1        0        0         5         4         0
  EIF4G2 WILD-TYPE      90        1       32       133         6         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  EIF4G2 MUTATED           1          0          2          0        0
  EIF4G2 WILD-TYPE        23         11         57         42       48
                  vv
clus               STAGE IVA STAGE IVB
  EIF4G2 MUTATED           1         0
  EIF4G2 WILD-TYPE        17         1
D874V4, multiclass
            clus
vv           EIF4G2 MUTATED EIF4G2 WILD-TYPE
  STAGE I                 1               90
  STAGE IA                0                1
  STAGE II                0               32
  STAGE IIA               5              133
  STAGE IIB               4                6
  STAGE IIC               0                1
  STAGE III               1               23
  STAGE IIIA              0               11
  STAGE IIIB              2               57
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               1               17
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  EIF4G2 MUTATED     1   0  10   4
  EIF4G2 WILD-TYPE  16  92 319  46
D874V5, multiclass
    clus
vv   EIF4G2 MUTATED EIF4G2 WILD-TYPE
  T1              1               16
  T2              0               92
  T3             10              319
  T4              4               46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  EIF4G2 MUTATED    10   4   1
  EIF4G2 WILD-TYPE 277 109  86
D874V6, multiclass
    clus
vv   EIF4G2 MUTATED EIF4G2 WILD-TYPE
  N0             10              277
  N1              4              109
  N2              1               86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D874V7, binary
                  cls
clus                 0   1
  EIF4G2 MUTATED    12   1
  EIF4G2 WILD-TYPE 363  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EIF4G2 MUTATED     12    1
  EIF4G2 WILD-TYPE  363   64
   clus
vv  EIF4G2 MUTATED EIF4G2 WILD-TYPE
  0             12              363
  1              1               64
[1] 2 2
[1] FALSE
D874V8, binary
                  cls
clus                 0   1
  EIF4G2 MUTATED     9   6
  EIF4G2 WILD-TYPE 216 258
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EIF4G2 MUTATED      9    6
  EIF4G2 WILD-TYPE  216  258
        clus
vv       EIF4G2 MUTATED EIF4G2 WILD-TYPE
  FEMALE              9              216
  MALE                6              258
[1] 2 2
[1] FALSE
D874V9, binary
                  cls
clus                 0   1
  EIF4G2 MUTATED    10   0
  EIF4G2 WILD-TYPE 340  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EIF4G2 MUTATED     10    0
  EIF4G2 WILD-TYPE  340   22
     clus
vv    EIF4G2 MUTATED EIF4G2 WILD-TYPE
  NO              10              340
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  EIF4G2 MUTATED                     11                             4
  EIF4G2 WILD-TYPE                  304                            43
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  EIF4G2 MUTATED                       0                              0
  EIF4G2 WILD-TYPE                   106                             10
D874V10, multiclass
                                clus
vv                               EIF4G2 MUTATED EIF4G2 WILD-TYPE
  COLON ADENOCARCINOMA                       11              304
  COLON MUCINOUS ADENOCARCINOMA               4               43
  RECTAL ADENOCARCINOMA                       0              106
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  EIF4G2 MUTATED    11   0   0   2
  EIF4G2 WILD-TYPE 334   4  31  23
D874V11, multiclass
    clus
vv   EIF4G2 MUTATED EIF4G2 WILD-TYPE
  R0             11              334
  R1              0                4
  R2              0               31
  RX              2               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D874V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  EIF4G2 MUTATED                                  0     1
  EIF4G2 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  EIF4G2 MUTATED                           1     7
  EIF4G2 WILD-TYPE                        21   219
D874V13, multiclass
                                  clus
vv                                 EIF4G2 MUTATED EIF4G2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                         7              219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(875) Variable = PDP2 MUTATION ANALYSIS
D875V1, survival
                sevent
clus2              0   1
  PDP2 MUTATED     6   0
  PDP2 WILD-TYPE 372  93
  PDP2 MUTATED PDP2 WILD-TYPE 
             6            465 
  PDP2 MUTATED PDP2 WILD-TYPE 
             0             93 
$`PDP2 MUTATED`
TCGA-AA-3713 TCGA-AD-6889 TCGA-AD-6895 TCGA-CA-6717 TCGA-CM-6165 TCGA-AG-A002 
       19.04        56.55         0.72        12.76        16.04        20.98 

$`PDP2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
       15.52         0.79         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
        2.96        29.03        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  PDP2 MUTATED PDP2 WILD-TYPE 
          0.72           0.00 
  PDP2 MUTATED PDP2 WILD-TYPE 
         56.55         148.01 
  PDP2 MUTATED PDP2 WILD-TYPE 
         17.54          20.28 
[1] "0.7 - 56.5 (17.5)"  "0.0 - 148.0 (20.3)"
[1] "hr="     "9100000"
D875V2, continuous
D875V3, binary
                cls
clus               0   1
  PDP2 MUTATED     5   1
  PDP2 WILD-TYPE 361 118
[1] "tbl2"
                cls
clus             [,1] [,2]
  PDP2 MUTATED      5    1
  PDP2 WILD-TYPE  361  118
        clus
vv       PDP2 MUTATED PDP2 WILD-TYPE
  COLON             5            361
  RECTUM            1            118
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PDP2 MUTATED         1        0        0         3         0         0
  PDP2 WILD-TYPE      90        1       32       135        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PDP2 MUTATED           0          0          0          0        1         0
  PDP2 WILD-TYPE        24         11         59         42       47        18
                vv
clus             STAGE IVB
  PDP2 MUTATED           0
  PDP2 WILD-TYPE         1
D875V4, multiclass
            clus
vv           PDP2 MUTATED PDP2 WILD-TYPE
  STAGE I               1             90
  STAGE IA              0              1
  STAGE II              0             32
  STAGE IIA             3            135
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            0             59
  STAGE IIIC            0             42
  STAGE IV              1             47
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  PDP2 MUTATED     0   1   5   0
  PDP2 WILD-TYPE  17  91 324  50
D875V5, multiclass
    clus
vv   PDP2 MUTATED PDP2 WILD-TYPE
  T1            0             17
  T2            1             91
  T3            5            324
  T4            0             50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  PDP2 MUTATED     5   1   0
  PDP2 WILD-TYPE 282 112  87
D875V6, multiclass
    clus
vv   PDP2 MUTATED PDP2 WILD-TYPE
  N0            5            282
  N1            1            112
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D875V7, binary
                cls
clus               0   1
  PDP2 MUTATED     4   1
  PDP2 WILD-TYPE 371  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  PDP2 MUTATED      4    1
  PDP2 WILD-TYPE  371   64
   clus
vv  PDP2 MUTATED PDP2 WILD-TYPE
  0            4            371
  1            1             64
[1] 2 2
[1] FALSE
D875V8, binary
                cls
clus               0   1
  PDP2 MUTATED     0   6
  PDP2 WILD-TYPE 225 258
[1] "tbl2"
                cls
clus             [,1] [,2]
  PDP2 MUTATED      0    6
  PDP2 WILD-TYPE  225  258
        clus
vv       PDP2 MUTATED PDP2 WILD-TYPE
  FEMALE            0            225
  MALE              6            258
[1] 2 2
[1] FALSE
D875V9, binary
                cls
clus               0   1
  PDP2 MUTATED     3   1
  PDP2 WILD-TYPE 347  21
[1] "tbl2"
                cls
clus             [,1] [,2]
  PDP2 MUTATED      3    1
  PDP2 WILD-TYPE  347   21
     clus
vv    PDP2 MUTATED PDP2 WILD-TYPE
  NO             3            347
  YES            1             21
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PDP2 MUTATED                      4                             1
  PDP2 WILD-TYPE                  311                            46
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PDP2 MUTATED                       1                              0
  PDP2 WILD-TYPE                   105                             10
D875V10, multiclass
                                clus
vv                               PDP2 MUTATED PDP2 WILD-TYPE
  COLON ADENOCARCINOMA                      4            311
  COLON MUCINOUS ADENOCARCINOMA             1             46
  RECTAL ADENOCARCINOMA                     1            105
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  PDP2 MUTATED     2   0   1   1
  PDP2 WILD-TYPE 343   4  30  24
D875V11, multiclass
    clus
vv   PDP2 MUTATED PDP2 WILD-TYPE
  R0            2            343
  R1            0              4
  R2            1             30
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D875V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PDP2 MUTATED                                  0     2
  PDP2 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  PDP2 MUTATED                           0     2
  PDP2 WILD-TYPE                        22   224
D875V13, multiclass
                                  clus
vv                                 PDP2 MUTATED PDP2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              9
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       2            224
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(876) Variable = C4ORF49 MUTATION ANALYSIS
D876V1, survival
                   sevent
clus2                 0   1
  C4ORF49 MUTATED     5   0
  C4ORF49 WILD-TYPE 373  93
  C4ORF49 MUTATED C4ORF49 WILD-TYPE 
                5               466 
  C4ORF49 MUTATED C4ORF49 WILD-TYPE 
                0                93 
$`C4ORF49 MUTATED`
TCGA-AA-3510 TCGA-CK-5914 TCGA-D5-5539 TCGA-DM-A1HB TCGA-G4-6293 
       63.98         9.99        19.59       135.65       133.18 

$`C4ORF49 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5916 
      148.01        85.45        15.62        49.08        51.32        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       12.03        45.40        12.26        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 
       12.59       140.38         7.50        44.32       131.51       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
        0.53        47.41        35.31        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  C4ORF49 MUTATED C4ORF49 WILD-TYPE 
             9.99              0.00 
  C4ORF49 MUTATED C4ORF49 WILD-TYPE 
           135.65            148.01 
  C4ORF49 MUTATED C4ORF49 WILD-TYPE 
           63.980            20.155 
[1] "10.0 - 135.7 (64.0)" "0.0 - 148.0 (20.2)" 
[1] "hr="     "9600000"
D876V2, continuous
D876V3, binary
                   cls
clus                  0   1
  C4ORF49 MUTATED     5   0
  C4ORF49 WILD-TYPE 361 119
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C4ORF49 MUTATED      5    0
  C4ORF49 WILD-TYPE  361  119
        clus
vv       C4ORF49 MUTATED C4ORF49 WILD-TYPE
  COLON                5               361
  RECTUM               0               119
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  C4ORF49 MUTATED         0        0        1         0         0         0
  C4ORF49 WILD-TYPE      91        1       31       138        10         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C4ORF49 MUTATED           1          1          2          0        0
  C4ORF49 WILD-TYPE        23         10         57         42       48
                   vv
clus                STAGE IVA STAGE IVB
  C4ORF49 MUTATED           0         0
  C4ORF49 WILD-TYPE        18         1
D876V4, multiclass
            clus
vv           C4ORF49 MUTATED C4ORF49 WILD-TYPE
  STAGE I                  0                91
  STAGE IA                 0                 1
  STAGE II                 1                31
  STAGE IIA                0               138
  STAGE IIB                0                10
  STAGE IIC                0                 1
  STAGE III                1                23
  STAGE IIIA               1                10
  STAGE IIIB               2                57
  STAGE IIIC               0                42
  STAGE IV                 0                48
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  C4ORF49 MUTATED     0   0   5   0
  C4ORF49 WILD-TYPE  17  92 324  50
D876V5, multiclass
    clus
vv   C4ORF49 MUTATED C4ORF49 WILD-TYPE
  T1               0                17
  T2               0                92
  T3               5               324
  T4               0                50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  C4ORF49 MUTATED     1   4   0
  C4ORF49 WILD-TYPE 286 109  87
D876V6, multiclass
    clus
vv   C4ORF49 MUTATED C4ORF49 WILD-TYPE
  N0               1               286
  N1               4               109
  N2               0                87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D876V7, binary
                   cls
clus                  0   1
  C4ORF49 MUTATED     4   0
  C4ORF49 WILD-TYPE 371  65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C4ORF49 MUTATED      4    0
  C4ORF49 WILD-TYPE  371   65
   clus
vv  C4ORF49 MUTATED C4ORF49 WILD-TYPE
  0               4               371
  1               0                65
[1] 2 2
[1] FALSE
D876V8, binary
                   cls
clus                  0   1
  C4ORF49 MUTATED     1   4
  C4ORF49 WILD-TYPE 224 260
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C4ORF49 MUTATED      1    4
  C4ORF49 WILD-TYPE  224  260
        clus
vv       C4ORF49 MUTATED C4ORF49 WILD-TYPE
  FEMALE               1               224
  MALE                 4               260
[1] 2 2
[1] FALSE
D876V9, binary
                   cls
clus                  0   1
  C4ORF49 MUTATED     3   0
  C4ORF49 WILD-TYPE 347  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C4ORF49 MUTATED      3    0
  C4ORF49 WILD-TYPE  347   22
     clus
vv    C4ORF49 MUTATED C4ORF49 WILD-TYPE
  NO                3               347
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  C4ORF49 MUTATED                      3                             1
  C4ORF49 WILD-TYPE                  312                            46
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  C4ORF49 MUTATED                       0                              0
  C4ORF49 WILD-TYPE                   106                             10
D876V10, multiclass
                                clus
vv                               C4ORF49 MUTATED C4ORF49 WILD-TYPE
  COLON ADENOCARCINOMA                         3               312
  COLON MUCINOUS ADENOCARCINOMA                1                46
  RECTAL ADENOCARCINOMA                        0               106
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  C4ORF49 MUTATED     3   0   0   1
  C4ORF49 WILD-TYPE 342   4  31  24
D876V11, multiclass
    clus
vv   C4ORF49 MUTATED C4ORF49 WILD-TYPE
  R0               3               342
  R1               0                 4
  R2               0                31
  RX               1                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D876V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C4ORF49 MUTATED                                  0     0
  C4ORF49 WILD-TYPE                                1    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  C4ORF49 MUTATED                           0     4
  C4ORF49 WILD-TYPE                        22   222
D876V13, multiclass
                                  clus
vv                                 C4ORF49 MUTATED C4ORF49 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                      0                22
  WHITE                                          4               222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(877) Variable = KLRC3 MUTATION ANALYSIS
D877V1, survival
                 sevent
clus2               0   1
  KLRC3 MUTATED     5   1
  KLRC3 WILD-TYPE 373  92
  KLRC3 MUTATED KLRC3 WILD-TYPE 
              6             465 
  KLRC3 MUTATED KLRC3 WILD-TYPE 
              1              92 
$`KLRC3 MUTATED`
TCGA-AA-3845 TCGA-D5-6931 TCGA-DM-A28K TCGA-F4-6704 TCGA-G4-6309 TCGA-AG-A002 
        0.00        12.00        98.24         1.55        85.48        20.98 

$`KLRC3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6932 TCGA-D5-7000 
        9.44        11.64         4.80         1.51        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
       60.79       117.07         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
       47.87        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       53.62        44.68        55.04        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  KLRC3 MUTATED KLRC3 WILD-TYPE 
              0               0 
  KLRC3 MUTATED KLRC3 WILD-TYPE 
          98.24          148.01 
  KLRC3 MUTATED KLRC3 WILD-TYPE 
          16.49           20.19 
[1] "0.0 - 98.2 (16.5)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.6"
D877V2, continuous
D877V3, binary
                 cls
clus                0   1
  KLRC3 MUTATED     5   1
  KLRC3 WILD-TYPE 361 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLRC3 MUTATED      5    1
  KLRC3 WILD-TYPE  361  118
        clus
vv       KLRC3 MUTATED KLRC3 WILD-TYPE
  COLON              5             361
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KLRC3 MUTATED         1        0        0         2         0         0
  KLRC3 WILD-TYPE      90        1       32       136        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  KLRC3 MUTATED           0          0          1          2        0         0
  KLRC3 WILD-TYPE        24         11         58         40       48        18
                 vv
clus              STAGE IVB
  KLRC3 MUTATED           0
  KLRC3 WILD-TYPE         1
D877V4, multiclass
            clus
vv           KLRC3 MUTATED KLRC3 WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              2             136
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             2              40
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  KLRC3 MUTATED     0   1   4   1
  KLRC3 WILD-TYPE  17  91 325  49
D877V5, multiclass
    clus
vv   KLRC3 MUTATED KLRC3 WILD-TYPE
  T1             0              17
  T2             1              91
  T3             4             325
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  KLRC3 MUTATED     3   1   2
  KLRC3 WILD-TYPE 284 112  85
D877V6, multiclass
    clus
vv   KLRC3 MUTATED KLRC3 WILD-TYPE
  N0             3             284
  N1             1             112
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D877V7, binary
                 cls
clus                0   1
  KLRC3 MUTATED     5   0
  KLRC3 WILD-TYPE 370  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLRC3 MUTATED      5    0
  KLRC3 WILD-TYPE  370   65
   clus
vv  KLRC3 MUTATED KLRC3 WILD-TYPE
  0             5             370
  1             0              65
[1] 2 2
[1] FALSE
D877V8, binary
                 cls
clus                0   1
  KLRC3 MUTATED     2   4
  KLRC3 WILD-TYPE 223 260
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLRC3 MUTATED      2    4
  KLRC3 WILD-TYPE  223  260
        clus
vv       KLRC3 MUTATED KLRC3 WILD-TYPE
  FEMALE             2             223
  MALE               4             260
[1] 2 2
[1] FALSE
D877V9, binary
                 cls
clus                0   1
  KLRC3 MUTATED     3   0
  KLRC3 WILD-TYPE 347  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLRC3 MUTATED      3    0
  KLRC3 WILD-TYPE  347   22
     clus
vv    KLRC3 MUTATED KLRC3 WILD-TYPE
  NO              3             347
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  KLRC3 MUTATED                      3                             2
  KLRC3 WILD-TYPE                  312                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  KLRC3 MUTATED                       1                              0
  KLRC3 WILD-TYPE                   105                             10
D877V10, multiclass
                                clus
vv                               KLRC3 MUTATED KLRC3 WILD-TYPE
  COLON ADENOCARCINOMA                       3             312
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  KLRC3 MUTATED     5   0   0   0
  KLRC3 WILD-TYPE 340   4  31  25
D877V11, multiclass
    clus
vv   KLRC3 MUTATED KLRC3 WILD-TYPE
  R0             5             340
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D877V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KLRC3 MUTATED                                  1     0
  KLRC3 WILD-TYPE                                0    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  KLRC3 MUTATED                           1     2
  KLRC3 WILD-TYPE                        21   224
D877V13, multiclass
                                  clus
vv                                 KLRC3 MUTATED KLRC3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             1               0
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        2             224
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(878) Variable = RARS2 MUTATION ANALYSIS
D878V1, survival
                 sevent
clus2               0   1
  RARS2 MUTATED     7   2
  RARS2 WILD-TYPE 371  91
  RARS2 MUTATED RARS2 WILD-TYPE 
              9             462 
  RARS2 MUTATED RARS2 WILD-TYPE 
              2              91 
$`RARS2 MUTATED`
TCGA-AA-3715 TCGA-AA-A00N TCGA-AZ-4315 TCGA-CA-6717 TCGA-CK-4948 TCGA-CK-4950 
       19.04         4.01        58.39        12.76       148.01        85.45 
TCGA-AG-3892 TCGA-AG-A002 TCGA-CI-6619 
       13.02        20.98         6.05 

$`RARS2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       33.01        21.44        17.82         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       10.06        14.30        17.56        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       36.95        17.03        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        0.72        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  RARS2 MUTATED RARS2 WILD-TYPE 
           4.01            0.00 
  RARS2 MUTATED RARS2 WILD-TYPE 
         148.01          140.38 
  RARS2 MUTATED RARS2 WILD-TYPE 
         19.040          20.235 
[1] "4.0 - 148.0 (19.0)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.2"
D878V2, continuous
D878V3, binary
                 cls
clus                0   1
  RARS2 MUTATED     7   3
  RARS2 WILD-TYPE 359 116
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RARS2 MUTATED      7    3
  RARS2 WILD-TYPE  359  116
        clus
vv       RARS2 MUTATED RARS2 WILD-TYPE
  COLON              7             359
  RECTUM             3             116
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RARS2 MUTATED         2        0        1         3         1         0
  RARS2 WILD-TYPE      89        1       31       135         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RARS2 MUTATED           1          0          1          0        1         0
  RARS2 WILD-TYPE        23         11         58         42       47        18
                 vv
clus              STAGE IVB
  RARS2 MUTATED           0
  RARS2 WILD-TYPE         1
D878V4, multiclass
            clus
vv           RARS2 MUTATED RARS2 WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              3             135
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             0              42
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  RARS2 MUTATED     1   1   7   1
  RARS2 WILD-TYPE  16  91 322  49
D878V5, multiclass
    clus
vv   RARS2 MUTATED RARS2 WILD-TYPE
  T1             1              16
  T2             1              91
  T3             7             322
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  RARS2 MUTATED     7   3   0
  RARS2 WILD-TYPE 280 110  87
D878V6, multiclass
    clus
vv   RARS2 MUTATED RARS2 WILD-TYPE
  N0             7             280
  N1             3             110
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D878V7, binary
                 cls
clus                0   1
  RARS2 MUTATED     9   1
  RARS2 WILD-TYPE 366  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RARS2 MUTATED      9    1
  RARS2 WILD-TYPE  366   64
   clus
vv  RARS2 MUTATED RARS2 WILD-TYPE
  0             9             366
  1             1              64
[1] 2 2
[1] FALSE
D878V8, binary
                 cls
clus                0   1
  RARS2 MUTATED     4   6
  RARS2 WILD-TYPE 221 258
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RARS2 MUTATED      4    6
  RARS2 WILD-TYPE  221  258
        clus
vv       RARS2 MUTATED RARS2 WILD-TYPE
  FEMALE             4             221
  MALE               6             258
[1] 2 2
[1] FALSE
D878V9, binary
                 cls
clus                0   1
  RARS2 MUTATED     7   0
  RARS2 WILD-TYPE 343  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RARS2 MUTATED      7    0
  RARS2 WILD-TYPE  343   22
     clus
vv    RARS2 MUTATED RARS2 WILD-TYPE
  NO              7             343
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  RARS2 MUTATED                      5                             2
  RARS2 WILD-TYPE                  310                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  RARS2 MUTATED                       3                              0
  RARS2 WILD-TYPE                   103                             10
D878V10, multiclass
                                clus
vv                               RARS2 MUTATED RARS2 WILD-TYPE
  COLON ADENOCARCINOMA                       5             310
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      3             103
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  RARS2 MUTATED     7   1   0   1
  RARS2 WILD-TYPE 338   3  31  24
D878V11, multiclass
    clus
vv   RARS2 MUTATED RARS2 WILD-TYPE
  R0             7             338
  R1             1               3
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D878V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RARS2 MUTATED                                  0     1
  RARS2 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  RARS2 MUTATED                           1     3
  RARS2 WILD-TYPE                        21   223
D878V13, multiclass
                                  clus
vv                                 RARS2 MUTATED RARS2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        3             223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(879) Variable = OR5K2 MUTATION ANALYSIS
D879V1, survival
                 sevent
clus2               0   1
  OR5K2 MUTATED    11   0
  OR5K2 WILD-TYPE 367  93
  OR5K2 MUTATED OR5K2 WILD-TYPE 
             11             460 
  OR5K2 MUTATED OR5K2 WILD-TYPE 
              0              93 
$`OR5K2 MUTATED`
TCGA-A6-5665 TCGA-A6-6649 TCGA-AA-3510 TCGA-AA-3713 TCGA-AD-5900 TCGA-AD-6889 
       22.06        24.16        63.98        19.04         0.07        56.55 
TCGA-AU-6004 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AG-A025 TCGA-G5-6235 
       27.09        17.82        58.39        49.97        55.76 

$`OR5K2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       25.18        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       85.05        26.99        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       40.96        21.37        15.52         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 
       22.42        27.42        10.88         0.20        14.50        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
        0.95        33.01        21.44         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6641 
       32.19         0.66         0.69        26.43 

  OR5K2 MUTATED OR5K2 WILD-TYPE 
           0.07            0.00 
  OR5K2 MUTATED OR5K2 WILD-TYPE 
          63.98          148.01 
  OR5K2 MUTATED OR5K2 WILD-TYPE 
         27.090          20.035 
[1] "0.1 - 64.0 (27.1)"  "0.0 - 148.0 (20.0)"
[1] "hr="     "2.6e+07"
D879V2, continuous
D879V3, binary
                 cls
clus                0   1
  OR5K2 MUTATED     9   2
  OR5K2 WILD-TYPE 357 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR5K2 MUTATED      9    2
  OR5K2 WILD-TYPE  357  117
        clus
vv       OR5K2 MUTATED OR5K2 WILD-TYPE
  COLON              9             357
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  OR5K2 MUTATED         3        0        1         3         0         0
  OR5K2 WILD-TYPE      88        1       31       135        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  OR5K2 MUTATED           0          0          3          0        1         0
  OR5K2 WILD-TYPE        24         11         56         42       47        18
                 vv
clus              STAGE IVB
  OR5K2 MUTATED           0
  OR5K2 WILD-TYPE         1
D879V4, multiclass
            clus
vv           OR5K2 MUTATED OR5K2 WILD-TYPE
  STAGE I                3              88
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              3             135
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             3              56
  STAGE IIIC             0              42
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  OR5K2 MUTATED     1   2   8   0
  OR5K2 WILD-TYPE  16  90 321  50
D879V5, multiclass
    clus
vv   OR5K2 MUTATED OR5K2 WILD-TYPE
  T1             1              16
  T2             2              90
  T3             8             321
  T4             0              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  OR5K2 MUTATED     8   3   0
  OR5K2 WILD-TYPE 279 110  87
D879V6, multiclass
    clus
vv   OR5K2 MUTATED OR5K2 WILD-TYPE
  N0             8             279
  N1             3             110
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D879V7, binary
                 cls
clus                0   1
  OR5K2 MUTATED     8   1
  OR5K2 WILD-TYPE 367  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR5K2 MUTATED      8    1
  OR5K2 WILD-TYPE  367   64
   clus
vv  OR5K2 MUTATED OR5K2 WILD-TYPE
  0             8             367
  1             1              64
[1] 2 2
[1] FALSE
D879V8, binary
                 cls
clus                0   1
  OR5K2 MUTATED     4   7
  OR5K2 WILD-TYPE 221 257
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR5K2 MUTATED      4    7
  OR5K2 WILD-TYPE  221  257
        clus
vv       OR5K2 MUTATED OR5K2 WILD-TYPE
  FEMALE             4             221
  MALE               7             257
[1] 2 2
[1] FALSE
D879V9, binary
                 cls
clus                0   1
  OR5K2 MUTATED     6   1
  OR5K2 WILD-TYPE 344  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR5K2 MUTATED      6    1
  OR5K2 WILD-TYPE  344   21
     clus
vv    OR5K2 MUTATED OR5K2 WILD-TYPE
  NO              6             344
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  OR5K2 MUTATED                      8                             1
  OR5K2 WILD-TYPE                  307                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  OR5K2 MUTATED                       2                              0
  OR5K2 WILD-TYPE                   104                             10
D879V10, multiclass
                                clus
vv                               OR5K2 MUTATED OR5K2 WILD-TYPE
  COLON ADENOCARCINOMA                       8             307
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  OR5K2 MUTATED     7   1   1   0
  OR5K2 WILD-TYPE 338   3  30  25
D879V11, multiclass
    clus
vv   OR5K2 MUTATED OR5K2 WILD-TYPE
  R0             7             338
  R1             1               3
  R2             1              30
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D879V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OR5K2 MUTATED                                  0     1
  OR5K2 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  OR5K2 MUTATED                           1     6
  OR5K2 WILD-TYPE                        21   220
D879V13, multiclass
                                  clus
vv                                 OR5K2 MUTATED OR5K2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        6             220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(880) Variable = GABRP MUTATION ANALYSIS
D880V1, survival
                 sevent
clus2               0   1
  GABRP MUTATED    11   1
  GABRP WILD-TYPE 367  92
  GABRP MUTATED GABRP WILD-TYPE 
             12             459 
  GABRP MUTATED GABRP WILD-TYPE 
              1              92 
$`GABRP MUTATED`
TCGA-A6-6141 TCGA-AA-3663 TCGA-AA-A010 TCGA-CK-4952 TCGA-D5-5539 TCGA-F4-6460 
        8.38         6.97        34.98        15.62        19.59        31.96 
TCGA-F4-6856 TCGA-G4-6317 TCGA-AG-3732 TCGA-AG-3892 TCGA-AG-A02N TCGA-EF-5830 
       35.31        36.00        32.98        13.02        61.97         0.49 

$`GABRP WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 
       22.09        22.06        32.71        27.09        22.52        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       12.26        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
        8.61        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       85.48        63.62        61.91        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        7.99         0.99        37.02         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 
       19.99         1.02        17.95        36.95        17.03        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
        1.94        38.96        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       51.48        32.61        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  GABRP MUTATED GABRP WILD-TYPE 
           0.49            0.00 
  GABRP MUTATED GABRP WILD-TYPE 
          61.97          148.01 
  GABRP MUTATED GABRP WILD-TYPE 
         25.775          20.190 
[1] "0.5 - 62.0 (25.8)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "2.1"
D880V2, continuous
D880V3, binary
                 cls
clus                0   1
  GABRP MUTATED     9   4
  GABRP WILD-TYPE 357 115
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GABRP MUTATED      9    4
  GABRP WILD-TYPE  357  115
        clus
vv       GABRP MUTATED GABRP WILD-TYPE
  COLON              9             357
  RECTUM             4             115
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GABRP MUTATED         3        0        2         2         2         0
  GABRP WILD-TYPE      88        1       30       136         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  GABRP MUTATED           0          1          1          2        0         0
  GABRP WILD-TYPE        24         10         58         40       48        18
                 vv
clus              STAGE IVB
  GABRP MUTATED           0
  GABRP WILD-TYPE         1
D880V4, multiclass
            clus
vv           GABRP MUTATED GABRP WILD-TYPE
  STAGE I                3              88
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA              2             136
  STAGE IIB              2               8
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             1              10
  STAGE IIIB             1              58
  STAGE IIIC             2              40
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  GABRP MUTATED     1   2   7   3
  GABRP WILD-TYPE  16  90 322  47
D880V5, multiclass
    clus
vv   GABRP MUTATED GABRP WILD-TYPE
  T1             1              16
  T2             2              90
  T3             7             322
  T4             3              47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  GABRP MUTATED     9   2   2
  GABRP WILD-TYPE 278 111  85
D880V6, multiclass
    clus
vv   GABRP MUTATED GABRP WILD-TYPE
  N0             9             278
  N1             2             111
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D880V7, binary
                 cls
clus                0   1
  GABRP MUTATED    12   0
  GABRP WILD-TYPE 363  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GABRP MUTATED     12    0
  GABRP WILD-TYPE  363   65
   clus
vv  GABRP MUTATED GABRP WILD-TYPE
  0            12             363
  1             0              65
[1] 2 2
[1] FALSE
D880V8, binary
                 cls
clus                0   1
  GABRP MUTATED     7   6
  GABRP WILD-TYPE 218 258
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GABRP MUTATED      7    6
  GABRP WILD-TYPE  218  258
        clus
vv       GABRP MUTATED GABRP WILD-TYPE
  FEMALE             7             218
  MALE               6             258
[1] 2 2
[1] FALSE
D880V9, binary
                 cls
clus                0   1
  GABRP MUTATED     9   0
  GABRP WILD-TYPE 341  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GABRP MUTATED      9    0
  GABRP WILD-TYPE  341   22
     clus
vv    GABRP MUTATED GABRP WILD-TYPE
  NO              9             341
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  GABRP MUTATED                      6                             3
  GABRP WILD-TYPE                  309                            44
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  GABRP MUTATED                       4                              0
  GABRP WILD-TYPE                   102                             10
D880V10, multiclass
                                clus
vv                               GABRP MUTATED GABRP WILD-TYPE
  COLON ADENOCARCINOMA                       6             309
  COLON MUCINOUS ADENOCARCINOMA              3              44
  RECTAL ADENOCARCINOMA                      4             102
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  GABRP MUTATED    11   0   0   1
  GABRP WILD-TYPE 334   4  31  24
D880V11, multiclass
    clus
vv   GABRP MUTATED GABRP WILD-TYPE
  R0            11             334
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D880V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GABRP MUTATED                                  0     0
  GABRP WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  GABRP MUTATED                           1     6
  GABRP WILD-TYPE                        21   220
D880V13, multiclass
                                  clus
vv                                 GABRP MUTATED GABRP WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        6             220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(881) Variable = CCT5 MUTATION ANALYSIS
D881V1, survival
                sevent
clus2              0   1
  CCT5 MUTATED     7   0
  CCT5 WILD-TYPE 371  93
  CCT5 MUTATED CCT5 WILD-TYPE 
             7            464 
  CCT5 MUTATED CCT5 WILD-TYPE 
             0             93 
$`CCT5 MUTATED`
TCGA-A6-5661 TCGA-AA-3544 TCGA-AA-3949 TCGA-AA-A010 TCGA-CM-5861 TCGA-D5-6928 
       33.53        14.01        26.01        34.98        15.02        11.64 
TCGA-G4-6321 
       22.09 

$`CCT5 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       26.01        12.99         0.99        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       12.99        24.00        33.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 
       29.06        22.03        22.98        30.08        32.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
       14.30         9.04         9.44         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 
       55.04        85.48        63.62        61.91        36.00        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  CCT5 MUTATED CCT5 WILD-TYPE 
         11.64           0.00 
  CCT5 MUTATED CCT5 WILD-TYPE 
         34.98         148.01 
  CCT5 MUTATED CCT5 WILD-TYPE 
        22.090         20.155 
[1] "11.6 - 35.0 (22.1)" "0.0 - 148.0 (20.2)"
[1] "hr="     "9100000"
D881V2, continuous
D881V3, binary
                cls
clus               0   1
  CCT5 MUTATED     8   0
  CCT5 WILD-TYPE 358 119
[1] "tbl2"
                cls
clus             [,1] [,2]
  CCT5 MUTATED      8    0
  CCT5 WILD-TYPE  358  119
        clus
vv       CCT5 MUTATED CCT5 WILD-TYPE
  COLON             8            358
  RECTUM            0            119
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CCT5 MUTATED         1        0        0         3         1         0
  CCT5 WILD-TYPE      90        1       32       135         9         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CCT5 MUTATED           2          0          1          0        0         0
  CCT5 WILD-TYPE        22         11         58         42       48        18
                vv
clus             STAGE IVB
  CCT5 MUTATED           0
  CCT5 WILD-TYPE         1
D881V4, multiclass
            clus
vv           CCT5 MUTATED CCT5 WILD-TYPE
  STAGE I               1             90
  STAGE IA              0              1
  STAGE II              0             32
  STAGE IIA             3            135
  STAGE IIB             1              9
  STAGE IIC             0              1
  STAGE III             2             22
  STAGE IIIA            0             11
  STAGE IIIB            1             58
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  CCT5 MUTATED     0   2   5   1
  CCT5 WILD-TYPE  17  90 324  49
D881V5, multiclass
    clus
vv   CCT5 MUTATED CCT5 WILD-TYPE
  T1            0             17
  T2            2             90
  T3            5            324
  T4            1             49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  CCT5 MUTATED     5   2   1
  CCT5 WILD-TYPE 282 111  86
D881V6, multiclass
    clus
vv   CCT5 MUTATED CCT5 WILD-TYPE
  N0            5            282
  N1            2            111
  N2            1             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D881V7, binary
                cls
clus               0   1
  CCT5 MUTATED     7   0
  CCT5 WILD-TYPE 368  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  CCT5 MUTATED      7    0
  CCT5 WILD-TYPE  368   65
   clus
vv  CCT5 MUTATED CCT5 WILD-TYPE
  0            7            368
  1            0             65
[1] 2 2
[1] FALSE
D881V8, binary
                cls
clus               0   1
  CCT5 MUTATED     5   3
  CCT5 WILD-TYPE 220 261
[1] "tbl2"
                cls
clus             [,1] [,2]
  CCT5 MUTATED      5    3
  CCT5 WILD-TYPE  220  261
        clus
vv       CCT5 MUTATED CCT5 WILD-TYPE
  FEMALE            5            220
  MALE              3            261
[1] 2 2
[1] FALSE
D881V9, binary
                cls
clus               0   1
  CCT5 MUTATED     7   0
  CCT5 WILD-TYPE 343  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  CCT5 MUTATED      7    0
  CCT5 WILD-TYPE  343   22
     clus
vv    CCT5 MUTATED CCT5 WILD-TYPE
  NO             7            343
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CCT5 MUTATED                      6                             2
  CCT5 WILD-TYPE                  309                            45
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CCT5 MUTATED                       0                              0
  CCT5 WILD-TYPE                   106                             10
D881V10, multiclass
                                clus
vv                               CCT5 MUTATED CCT5 WILD-TYPE
  COLON ADENOCARCINOMA                      6            309
  COLON MUCINOUS ADENOCARCINOMA             2             45
  RECTAL ADENOCARCINOMA                     0            106
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  CCT5 MUTATED     8   0   0   0
  CCT5 WILD-TYPE 337   4  31  25
D881V11, multiclass
    clus
vv   CCT5 MUTATED CCT5 WILD-TYPE
  R0            8            337
  R1            0              4
  R2            0             31
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D881V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CCT5 MUTATED                                  0     0
  CCT5 WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  CCT5 MUTATED                           1     3
  CCT5 WILD-TYPE                        21   223
D881V13, multiclass
                                  clus
vv                                 CCT5 MUTATED CCT5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                       3            223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(882) Variable = MRPS18B MUTATION ANALYSIS
D882V1, survival
                   sevent
clus2                 0   1
  MRPS18B MUTATED     5   0
  MRPS18B WILD-TYPE 373  93
  MRPS18B MUTATED MRPS18B WILD-TYPE 
                5               466 
  MRPS18B MUTATED MRPS18B WILD-TYPE 
                0                93 
$`MRPS18B MUTATED`
TCGA-A6-2672 TCGA-AA-3662 TCGA-DM-A28K TCGA-G4-6315 TCGA-G5-6641 
       46.65         6.05        98.24        61.91        26.43 

$`MRPS18B WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       19.99        13.94        19.99        61.02        78.08         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
       60.79       117.07         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       32.19         0.66         0.69        55.76 

  MRPS18B MUTATED MRPS18B WILD-TYPE 
             6.05              0.00 
  MRPS18B MUTATED MRPS18B WILD-TYPE 
            98.24            148.01 
  MRPS18B MUTATED MRPS18B WILD-TYPE 
           46.650            20.085 
[1] "6.0 - 98.2 (46.6)"  "0.0 - 148.0 (20.1)"
[1] "hr="     "9300000"
D882V2, continuous
D882V3, binary
                   cls
clus                  0   1
  MRPS18B MUTATED     4   1
  MRPS18B WILD-TYPE 362 118
[1] "tbl2"
                   cls
clus                [,1] [,2]
  MRPS18B MUTATED      4    1
  MRPS18B WILD-TYPE  362  118
        clus
vv       MRPS18B MUTATED MRPS18B WILD-TYPE
  COLON                4               362
  RECTUM               1               118
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MRPS18B MUTATED         0        0        0         1         0         0
  MRPS18B WILD-TYPE      91        1       32       137        10         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MRPS18B MUTATED           0          1          1          0        2
  MRPS18B WILD-TYPE        24         10         58         42       46
                   vv
clus                STAGE IVA STAGE IVB
  MRPS18B MUTATED           0         0
  MRPS18B WILD-TYPE        18         1
D882V4, multiclass
            clus
vv           MRPS18B MUTATED MRPS18B WILD-TYPE
  STAGE I                  0                91
  STAGE IA                 0                 1
  STAGE II                 0                32
  STAGE IIA                1               137
  STAGE IIB                0                10
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               1                10
  STAGE IIIB               1                58
  STAGE IIIC               0                42
  STAGE IV                 2                46
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  MRPS18B MUTATED     1   0   3   1
  MRPS18B WILD-TYPE  16  92 326  49
D882V5, multiclass
    clus
vv   MRPS18B MUTATED MRPS18B WILD-TYPE
  T1               1                16
  T2               0                92
  T3               3               326
  T4               1                49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  MRPS18B MUTATED     1   3   1
  MRPS18B WILD-TYPE 286 110  86
D882V6, multiclass
    clus
vv   MRPS18B MUTATED MRPS18B WILD-TYPE
  N0               1               286
  N1               3               110
  N2               1                86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D882V7, binary
                   cls
clus                  0   1
  MRPS18B MUTATED     2   2
  MRPS18B WILD-TYPE 373  63
[1] "tbl2"
                   cls
clus                [,1] [,2]
  MRPS18B MUTATED      2    2
  MRPS18B WILD-TYPE  373   63
   clus
vv  MRPS18B MUTATED MRPS18B WILD-TYPE
  0               2               373
  1               2                63
[1] 2 2
[1] FALSE
D882V8, binary
                   cls
clus                  0   1
  MRPS18B MUTATED     2   3
  MRPS18B WILD-TYPE 223 261
[1] "tbl2"
                   cls
clus                [,1] [,2]
  MRPS18B MUTATED      2    3
  MRPS18B WILD-TYPE  223  261
        clus
vv       MRPS18B MUTATED MRPS18B WILD-TYPE
  FEMALE               2               223
  MALE                 3               261
[1] 2 2
[1] FALSE
D882V9, binary
                   cls
clus                  0   1
  MRPS18B MUTATED     4   0
  MRPS18B WILD-TYPE 346  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  MRPS18B MUTATED      4    0
  MRPS18B WILD-TYPE  346   22
     clus
vv    MRPS18B MUTATED MRPS18B WILD-TYPE
  NO                4               346
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MRPS18B MUTATED                      3                             1
  MRPS18B WILD-TYPE                  312                            46
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MRPS18B MUTATED                       0                              1
  MRPS18B WILD-TYPE                   106                              9
D882V10, multiclass
                                clus
vv                               MRPS18B MUTATED MRPS18B WILD-TYPE
  COLON ADENOCARCINOMA                         3               312
  COLON MUCINOUS ADENOCARCINOMA                1                46
  RECTAL ADENOCARCINOMA                        0               106
  RECTAL MUCINOUS ADENOCARCINOMA               1                 9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  MRPS18B MUTATED     3   0   1   0
  MRPS18B WILD-TYPE 342   4  30  25
D882V11, multiclass
    clus
vv   MRPS18B MUTATED MRPS18B WILD-TYPE
  R0               3               342
  R1               0                 4
  R2               1                30
  RX               0                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D882V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MRPS18B MUTATED                                  0     0
  MRPS18B WILD-TYPE                                1    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  MRPS18B MUTATED                           0     4
  MRPS18B WILD-TYPE                        22   222
D882V13, multiclass
                                  clus
vv                                 MRPS18B MUTATED MRPS18B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                      0                22
  WHITE                                          4               222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(883) Variable = LEF1 MUTATION ANALYSIS
D883V1, survival
                sevent
clus2              0   1
  LEF1 MUTATED     7   1
  LEF1 WILD-TYPE 371  92
  LEF1 MUTATED LEF1 WILD-TYPE 
             8            463 
  LEF1 MUTATED LEF1 WILD-TYPE 
             1             92 
$`LEF1 MUTATED`
TCGA-AA-3510 TCGA-AA-3553 TCGA-AA-3811 TCGA-AA-3815 TCGA-AA-3994 TCGA-AD-5900 
       63.98        24.00        10.06        33.04        27.02         0.07 
TCGA-CA-6717 TCGA-G4-6586 
       12.76        35.80 

$`LEF1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       13.02        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        19.04        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
        7.96        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07        12.20        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  LEF1 MUTATED LEF1 WILD-TYPE 
          0.07           0.00 
  LEF1 MUTATED LEF1 WILD-TYPE 
         63.98         148.01 
  LEF1 MUTATED LEF1 WILD-TYPE 
         25.51          20.12 
[1] "0.1 - 64.0 (25.5)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.5"
D883V2, continuous
D883V3, binary
                cls
clus               0   1
  LEF1 MUTATED     9   0
  LEF1 WILD-TYPE 357 119
[1] "tbl2"
                cls
clus             [,1] [,2]
  LEF1 MUTATED      9    0
  LEF1 WILD-TYPE  357  119
        clus
vv       LEF1 MUTATED LEF1 WILD-TYPE
  COLON             9            357
  RECTUM            0            119
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  LEF1 MUTATED         2        0        1         4         0         0
  LEF1 WILD-TYPE      89        1       31       134        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  LEF1 MUTATED           1          0          1          0        0         0
  LEF1 WILD-TYPE        23         11         58         42       48        18
                vv
clus             STAGE IVB
  LEF1 MUTATED           0
  LEF1 WILD-TYPE         1
D883V4, multiclass
            clus
vv           LEF1 MUTATED LEF1 WILD-TYPE
  STAGE I               2             89
  STAGE IA              0              1
  STAGE II              1             31
  STAGE IIA             4            134
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             1             23
  STAGE IIIA            0             11
  STAGE IIIB            1             58
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  LEF1 MUTATED     0   2   7   0
  LEF1 WILD-TYPE  17  90 322  50
D883V5, multiclass
    clus
vv   LEF1 MUTATED LEF1 WILD-TYPE
  T1            0             17
  T2            2             90
  T3            7            322
  T4            0             50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  LEF1 MUTATED     7   1   1
  LEF1 WILD-TYPE 280 112  86
D883V6, multiclass
    clus
vv   LEF1 MUTATED LEF1 WILD-TYPE
  N0            7            280
  N1            1            112
  N2            1             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D883V7, binary
                cls
clus               0   1
  LEF1 MUTATED     8   0
  LEF1 WILD-TYPE 367  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  LEF1 MUTATED      8    0
  LEF1 WILD-TYPE  367   65
   clus
vv  LEF1 MUTATED LEF1 WILD-TYPE
  0            8            367
  1            0             65
[1] 2 2
[1] FALSE
D883V8, binary
                cls
clus               0   1
  LEF1 MUTATED     5   4
  LEF1 WILD-TYPE 220 260
[1] "tbl2"
                cls
clus             [,1] [,2]
  LEF1 MUTATED      5    4
  LEF1 WILD-TYPE  220  260
        clus
vv       LEF1 MUTATED LEF1 WILD-TYPE
  FEMALE            5            220
  MALE              4            260
[1] 2 2
[1] FALSE
D883V9, binary
                cls
clus               0   1
  LEF1 MUTATED     7   0
  LEF1 WILD-TYPE 343  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  LEF1 MUTATED      7    0
  LEF1 WILD-TYPE  343   22
     clus
vv    LEF1 MUTATED LEF1 WILD-TYPE
  NO             7            343
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  LEF1 MUTATED                      6                             3
  LEF1 WILD-TYPE                  309                            44
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  LEF1 MUTATED                       0                              0
  LEF1 WILD-TYPE                   106                             10
D883V10, multiclass
                                clus
vv                               LEF1 MUTATED LEF1 WILD-TYPE
  COLON ADENOCARCINOMA                      6            309
  COLON MUCINOUS ADENOCARCINOMA             3             44
  RECTAL ADENOCARCINOMA                     0            106
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  LEF1 MUTATED     8   0   0   1
  LEF1 WILD-TYPE 337   4  31  24
D883V11, multiclass
    clus
vv   LEF1 MUTATED LEF1 WILD-TYPE
  R0            8            337
  R1            0              4
  R2            0             31
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D883V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  LEF1 MUTATED                                  0     1
  LEF1 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  LEF1 MUTATED                           0     2
  LEF1 WILD-TYPE                        22   224
D883V13, multiclass
                                  clus
vv                                 LEF1 MUTATED LEF1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       2            224
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(884) Variable = CD55 MUTATION ANALYSIS
D884V1, survival
                sevent
clus2              0   1
  CD55 MUTATED     8   0
  CD55 WILD-TYPE 370  93
  CD55 MUTATED CD55 WILD-TYPE 
             8            463 
  CD55 MUTATED CD55 WILD-TYPE 
             0             93 
$`CD55 MUTATED`
TCGA-AA-3518 TCGA-AA-3672 TCGA-AA-3713 TCGA-AA-3877 TCGA-AZ-5407 TCGA-CA-5255 
        1.02         0.92        19.04        31.00        88.21         3.06 
TCGA-CM-6674 TCGA-AF-2691 
       12.95        43.04 

$`CD55 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
       38.99         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 
        6.97        54.02         2.01        14.01        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       27.02        29.98        18.05         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5796 
        5.23        11.74         3.19         1.61        12.69         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       14.04        11.01        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       39.48        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  CD55 MUTATED CD55 WILD-TYPE 
          0.92           0.00 
  CD55 MUTATED CD55 WILD-TYPE 
         88.21         148.01 
  CD55 MUTATED CD55 WILD-TYPE 
        15.995         20.280 
[1] "0.9 - 88.2 (16.0)"  "0.0 - 148.0 (20.3)"
[1] "hr="     "9100000"
D884V2, continuous
D884V3, binary
                cls
clus               0   1
  CD55 MUTATED     7   1
  CD55 WILD-TYPE 359 118
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD55 MUTATED      7    1
  CD55 WILD-TYPE  359  118
        clus
vv       CD55 MUTATED CD55 WILD-TYPE
  COLON             7            359
  RECTUM            1            118
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CD55 MUTATED         3        0        0         3         0         0
  CD55 WILD-TYPE      88        1       32       135        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CD55 MUTATED           1          0          0          0        1         0
  CD55 WILD-TYPE        23         11         59         42       47        18
                vv
clus             STAGE IVB
  CD55 MUTATED           0
  CD55 WILD-TYPE         1
D884V4, multiclass
            clus
vv           CD55 MUTATED CD55 WILD-TYPE
  STAGE I               3             88
  STAGE IA              0              1
  STAGE II              0             32
  STAGE IIA             3            135
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             1             23
  STAGE IIIA            0             11
  STAGE IIIB            0             59
  STAGE IIIC            0             42
  STAGE IV              1             47
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  CD55 MUTATED     3   0   5   0
  CD55 WILD-TYPE  14  92 324  50
D884V5, multiclass
    clus
vv   CD55 MUTATED CD55 WILD-TYPE
  T1            3             14
  T2            0             92
  T3            5            324
  T4            0             50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  CD55 MUTATED     7   1   0
  CD55 WILD-TYPE 280 112  87
D884V6, multiclass
    clus
vv   CD55 MUTATED CD55 WILD-TYPE
  N0            7            280
  N1            1            112
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D884V7, binary
                cls
clus               0   1
  CD55 MUTATED     7   1
  CD55 WILD-TYPE 368  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD55 MUTATED      7    1
  CD55 WILD-TYPE  368   64
   clus
vv  CD55 MUTATED CD55 WILD-TYPE
  0            7            368
  1            1             64
[1] 2 2
[1] FALSE
D884V8, binary
                cls
clus               0   1
  CD55 MUTATED     5   3
  CD55 WILD-TYPE 220 261
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD55 MUTATED      5    3
  CD55 WILD-TYPE  220  261
        clus
vv       CD55 MUTATED CD55 WILD-TYPE
  FEMALE            5            220
  MALE              3            261
[1] 2 2
[1] FALSE
D884V9, binary
                cls
clus               0   1
  CD55 MUTATED     5   2
  CD55 WILD-TYPE 345  20
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD55 MUTATED      5    2
  CD55 WILD-TYPE  345   20
     clus
vv    CD55 MUTATED CD55 WILD-TYPE
  NO             5            345
  YES            2             20
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CD55 MUTATED                      6                             1
  CD55 WILD-TYPE                  309                            46
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CD55 MUTATED                       1                              0
  CD55 WILD-TYPE                   105                             10
D884V10, multiclass
                                clus
vv                               CD55 MUTATED CD55 WILD-TYPE
  COLON ADENOCARCINOMA                      6            309
  COLON MUCINOUS ADENOCARCINOMA             1             46
  RECTAL ADENOCARCINOMA                     1            105
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  CD55 MUTATED     5   0   1   1
  CD55 WILD-TYPE 340   4  30  24
D884V11, multiclass
    clus
vv   CD55 MUTATED CD55 WILD-TYPE
  R0            5            340
  R1            0              4
  R2            1             30
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D884V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CD55 MUTATED                                  0     1
  CD55 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  CD55 MUTATED                           0     3
  CD55 WILD-TYPE                        22   223
D884V13, multiclass
                                  clus
vv                                 CD55 MUTATED CD55 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       3            223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(885) Variable = CIC MUTATION ANALYSIS
D885V1, survival
               sevent
clus2             0   1
  CIC MUTATED    19   4
  CIC WILD-TYPE 359  89
  CIC MUTATED CIC WILD-TYPE 
           23           448 
  CIC MUTATED CIC WILD-TYPE 
            4            89 
$`CIC MUTATED`
TCGA-A6-5665 TCGA-AA-3715 TCGA-AA-3877 TCGA-AA-3966 TCGA-AA-A01R TCGA-AD-6889 
       22.06        19.04        31.00         2.01        35.01        56.55 
TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-6601 TCGA-CA-6718 TCGA-CK-5913 TCGA-CK-5914 
       21.44        58.39       100.01        10.06        51.32         9.99 
TCGA-CM-4743 TCGA-CM-6163 TCGA-CM-6171 TCGA-CM-6674 TCGA-D5-6928 TCGA-DM-A1HB 
       23.05         2.96        14.04        12.95        11.64       135.65 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 
       65.85        53.62        35.80        26.17        79.69 

$`CIC WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 
       36.00         5.03        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 
       24.03        27.02        29.98        18.05         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
       34.03        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
       38.07         1.02         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
        0.07        21.37        15.52         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
       16.31         0.95        33.01        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
       12.10        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       12.76        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 
       49.08        21.14        82.95         1.91       124.27        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       17.03        15.02        12.00        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6675 
       14.99        12.99        13.02        15.02        11.01        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6930 
       12.43        14.30         9.04         9.44         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
        7.50        44.32       131.51       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       35.31       133.18        74.56        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6625 
       63.62        61.91        36.00        22.09        13.78        91.79 
TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       46.75        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  CIC MUTATED CIC WILD-TYPE 
         2.01          0.00 
  CIC MUTATED CIC WILD-TYPE 
       135.65        148.01 
  CIC MUTATED CIC WILD-TYPE 
        26.17         20.02 
[1] "2.0 - 135.7 (26.2)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.7"
D885V2, continuous
D885V3, binary
               cls
clus              0   1
  CIC MUTATED    23   0
  CIC WILD-TYPE 343 119
[1] "tbl2"
               cls
clus            [,1] [,2]
  CIC MUTATED     23    0
  CIC WILD-TYPE  343  119
        clus
vv       CIC MUTATED CIC WILD-TYPE
  COLON           23           343
  RECTUM           0           119
[1] 2 2
[1] FALSE
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CIC MUTATED         4        0        2        12         1         0
  CIC WILD-TYPE      87        1       30       126         9         1
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CIC MUTATED           1          0          2          0        1         0
  CIC WILD-TYPE        23         11         57         42       47        18
               vv
clus            STAGE IVB
  CIC MUTATED           0
  CIC WILD-TYPE         1
D885V4, multiclass
            clus
vv           CIC MUTATED CIC WILD-TYPE
  STAGE I              4            87
  STAGE IA             0             1
  STAGE II             2            30
  STAGE IIA           12           126
  STAGE IIB            1             9
  STAGE IIC            0             1
  STAGE III            1            23
  STAGE IIIA           0            11
  STAGE IIIB           2            57
  STAGE IIIC           0            42
  STAGE IV             1            47
  STAGE IVA            0            18
  STAGE IVB            0             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  CIC MUTATED     2   2  18   1
  CIC WILD-TYPE  15  90 311  49
D885V5, multiclass
    clus
vv   CIC MUTATED CIC WILD-TYPE
  T1           2            15
  T2           2            90
  T3          18           311
  T4           1            49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2
  CIC MUTATED    19   3   1
  CIC WILD-TYPE 268 110  86
D885V6, multiclass
    clus
vv   CIC MUTATED CIC WILD-TYPE
  N0          19           268
  N1           3           110
  N2           1            86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D885V7, binary
               cls
clus              0   1
  CIC MUTATED    19   1
  CIC WILD-TYPE 356  64
[1] "tbl2"
               cls
clus            [,1] [,2]
  CIC MUTATED     19    1
  CIC WILD-TYPE  356   64
   clus
vv  CIC MUTATED CIC WILD-TYPE
  0          19           356
  1           1            64
[1] 2 2
[1] FALSE
D885V8, binary
               cls
clus              0   1
  CIC MUTATED     9  14
  CIC WILD-TYPE 216 250
[1] "tbl2"
               cls
clus            [,1] [,2]
  CIC MUTATED      9   14
  CIC WILD-TYPE  216  250
        clus
vv       CIC MUTATED CIC WILD-TYPE
  FEMALE           9           216
  MALE            14           250
[1] 2 2
[1] FALSE
D885V9, binary
               cls
clus              0   1
  CIC MUTATED    18   1
  CIC WILD-TYPE 332  21
[1] "tbl2"
               cls
clus            [,1] [,2]
  CIC MUTATED     18    1
  CIC WILD-TYPE  332   21
     clus
vv    CIC MUTATED CIC WILD-TYPE
  NO           18           332
  YES           1            21
[1] 2 2
[1] FALSE
               vv
clus            COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CIC MUTATED                     18                             4
  CIC WILD-TYPE                  297                            43
               vv
clus            RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CIC MUTATED                       0                              0
  CIC WILD-TYPE                   106                             10
D885V10, multiclass
                                clus
vv                               CIC MUTATED CIC WILD-TYPE
  COLON ADENOCARCINOMA                    18           297
  COLON MUCINOUS ADENOCARCINOMA            4            43
  RECTAL ADENOCARCINOMA                    0           106
  RECTAL MUCINOUS ADENOCARCINOMA           0            10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             R0  R1  R2  RX
  CIC MUTATED    16   0   0   3
  CIC WILD-TYPE 329   4  31  22
D885V11, multiclass
    clus
vv   CIC MUTATED CIC WILD-TYPE
  R0          16           329
  R1           0             4
  R2           0            31
  RX           3            22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D885V12, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CIC MUTATED                                  0     2
  CIC WILD-TYPE                                1     9
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  CIC MUTATED                           0    17
  CIC WILD-TYPE                        22   209
D885V13, multiclass
                                  clus
vv                                 CIC MUTATED CIC WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      2             9
  BLACK OR AFRICAN AMERICAN                  0            22
  WHITE                                     17           209
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(886) Variable = TXNDC6 MUTATION ANALYSIS
D886V1, survival
                  sevent
clus2                0   1
  TXNDC6 MUTATED     7   2
  TXNDC6 WILD-TYPE 371  91
  TXNDC6 MUTATED TXNDC6 WILD-TYPE 
               9              462 
  TXNDC6 MUTATED TXNDC6 WILD-TYPE 
               2               91 
$`TXNDC6 MUTATED`
TCGA-A6-2677 TCGA-AA-3510 TCGA-AA-3821 TCGA-AZ-5407 TCGA-CM-4752 TCGA-D5-6536 
       24.33        63.98         1.02        88.21        13.02        17.85 
TCGA-DM-A1DA TCGA-DM-A1HB TCGA-AG-A002 
        7.50       135.65        20.98 

$`TXNDC6 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        42.90        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 
       35.05        33.04         0.99        25.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-5341 
      124.27        23.05        20.02        37.02        25.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       43.27        15.12         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB 
       92.75        49.91        13.32        12.59       140.38        44.32 
TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      131.51       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  TXNDC6 MUTATED TXNDC6 WILD-TYPE 
            1.02             0.00 
  TXNDC6 MUTATED TXNDC6 WILD-TYPE 
          135.65           148.01 
  TXNDC6 MUTATED TXNDC6 WILD-TYPE 
          20.980           20.155 
[1] "1.0 - 135.7 (21.0)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.3"
D886V2, continuous
D886V3, binary
                  cls
clus                 0   1
  TXNDC6 MUTATED     8   1
  TXNDC6 WILD-TYPE 358 118
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TXNDC6 MUTATED      8    1
  TXNDC6 WILD-TYPE  358  118
        clus
vv       TXNDC6 MUTATED TXNDC6 WILD-TYPE
  COLON               8              358
  RECTUM              1              118
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TXNDC6 MUTATED         3        0        1         2         0         0
  TXNDC6 WILD-TYPE      88        1       31       136        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TXNDC6 MUTATED           0          0          1          2        0
  TXNDC6 WILD-TYPE        24         11         58         40       48
                  vv
clus               STAGE IVA STAGE IVB
  TXNDC6 MUTATED           0         0
  TXNDC6 WILD-TYPE        18         1
D886V4, multiclass
            clus
vv           TXNDC6 MUTATED TXNDC6 WILD-TYPE
  STAGE I                 3               88
  STAGE IA                0                1
  STAGE II                1               31
  STAGE IIA               2              136
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              1               58
  STAGE IIIC              2               40
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  TXNDC6 MUTATED     1   2   6   0
  TXNDC6 WILD-TYPE  16  90 323  50
D886V5, multiclass
    clus
vv   TXNDC6 MUTATED TXNDC6 WILD-TYPE
  T1              1               16
  T2              2               90
  T3              6              323
  T4              0               50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  TXNDC6 MUTATED     6   1   2
  TXNDC6 WILD-TYPE 281 112  85
D886V6, multiclass
    clus
vv   TXNDC6 MUTATED TXNDC6 WILD-TYPE
  N0              6              281
  N1              1              112
  N2              2               85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D886V7, binary
                  cls
clus                 0   1
  TXNDC6 MUTATED     9   0
  TXNDC6 WILD-TYPE 366  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TXNDC6 MUTATED      9    0
  TXNDC6 WILD-TYPE  366   65
   clus
vv  TXNDC6 MUTATED TXNDC6 WILD-TYPE
  0              9              366
  1              0               65
[1] 2 2
[1] FALSE
D886V8, binary
                  cls
clus                 0   1
  TXNDC6 MUTATED     4   5
  TXNDC6 WILD-TYPE 221 259
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TXNDC6 MUTATED      4    5
  TXNDC6 WILD-TYPE  221  259
        clus
vv       TXNDC6 MUTATED TXNDC6 WILD-TYPE
  FEMALE              4              221
  MALE                5              259
[1] 2 2
[1] FALSE
D886V9, binary
                  cls
clus                 0   1
  TXNDC6 MUTATED     7   0
  TXNDC6 WILD-TYPE 343  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TXNDC6 MUTATED      7    0
  TXNDC6 WILD-TYPE  343   22
     clus
vv    TXNDC6 MUTATED TXNDC6 WILD-TYPE
  NO               7              343
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  TXNDC6 MUTATED                      6                             1
  TXNDC6 WILD-TYPE                  309                            46
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  TXNDC6 MUTATED                       1                              0
  TXNDC6 WILD-TYPE                   105                             10
D886V10, multiclass
                                clus
vv                               TXNDC6 MUTATED TXNDC6 WILD-TYPE
  COLON ADENOCARCINOMA                        6              309
  COLON MUCINOUS ADENOCARCINOMA               1               46
  RECTAL ADENOCARCINOMA                       1              105
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  TXNDC6 MUTATED     6   0   0   0
  TXNDC6 WILD-TYPE 339   4  31  25
D886V11, multiclass
    clus
vv   TXNDC6 MUTATED TXNDC6 WILD-TYPE
  R0              6              339
  R1              0                4
  R2              0               31
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D886V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TXNDC6 MUTATED                                  0     0
  TXNDC6 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  TXNDC6 MUTATED                           1     5
  TXNDC6 WILD-TYPE                        21   221
D886V13, multiclass
                                  clus
vv                                 TXNDC6 MUTATED TXNDC6 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                         5              221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(887) Variable = HERC5 MUTATION ANALYSIS
D887V1, survival
                 sevent
clus2               0   1
  HERC5 MUTATED    18   3
  HERC5 WILD-TYPE 360  90
  HERC5 MUTATED HERC5 WILD-TYPE 
             21             450 
  HERC5 MUTATED HERC5 WILD-TYPE 
              3              90 
$`HERC5 MUTATED`
TCGA-A6-5659 TCGA-A6-6649 TCGA-AA-3510 TCGA-AA-3555 TCGA-AA-3713 TCGA-AA-3715 
       30.44        24.16        63.98        29.95        19.04        19.04 
TCGA-AA-3848 TCGA-AA-3982 TCGA-AA-A010 TCGA-AD-6965 TCGA-AZ-4315 TCGA-CK-5914 
       10.06        27.02        34.98         0.20        58.39         9.99 
TCGA-CM-6675 TCGA-D5-6926 TCGA-DM-A1D4 TCGA-F4-6854 TCGA-G4-6307 TCGA-G4-6586 
       13.05         9.04        92.75         0.53        55.04        35.80 
TCGA-AG-A002 TCGA-EI-6510 TCGA-G5-6235 
       20.98        18.28        55.76 

$`HERC5 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       25.18        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       17.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       26.99        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
        0.00        17.03         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       51.32        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       14.04        11.01        12.95        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6927 
        1.48         3.68         4.41        12.43        14.30         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-DM-A1D7 
      119.70        24.43        38.20       130.65        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
       13.25        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       53.62        44.68        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       22.09        13.78        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-F5-6464 TCGA-F5-6465 
        0.49        20.55        19.96        20.91         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6641 
       31.30        28.57        32.19         0.66         0.69        26.43 

  HERC5 MUTATED HERC5 WILD-TYPE 
            0.2             0.0 
  HERC5 MUTATED HERC5 WILD-TYPE 
          92.75          148.01 
  HERC5 MUTATED HERC5 WILD-TYPE 
         24.160          20.085 
[1] "0.2 - 92.8 (24.2)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.6"
D887V2, continuous
D887V3, binary
                 cls
clus                0   1
  HERC5 MUTATED    18   3
  HERC5 WILD-TYPE 348 116
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HERC5 MUTATED     18    3
  HERC5 WILD-TYPE  348  116
        clus
vv       HERC5 MUTATED HERC5 WILD-TYPE
  COLON             18             348
  RECTUM             3             116
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  HERC5 MUTATED         2        0        2         5         1         0
  HERC5 WILD-TYPE      89        1       30       133         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  HERC5 MUTATED           0          0          6          1        1         1
  HERC5 WILD-TYPE        24         11         53         41       47        17
                 vv
clus              STAGE IVB
  HERC5 MUTATED           1
  HERC5 WILD-TYPE         0
D887V4, multiclass
            clus
vv           HERC5 MUTATED HERC5 WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA              5             133
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             6              53
  STAGE IIIC             1              41
  STAGE IV               1              47
  STAGE IVA              1              17
  STAGE IVB              1               0
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  HERC5 MUTATED     0   3  15   3
  HERC5 WILD-TYPE  17  89 314  47
D887V5, multiclass
    clus
vv   HERC5 MUTATED HERC5 WILD-TYPE
  T1             0              17
  T2             3              89
  T3            15             314
  T4             3              47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  HERC5 MUTATED    12   6   3
  HERC5 WILD-TYPE 275 107  84
D887V6, multiclass
    clus
vv   HERC5 MUTATED HERC5 WILD-TYPE
  N0            12             275
  N1             6             107
  N2             3              84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D887V7, binary
                 cls
clus                0   1
  HERC5 MUTATED    15   2
  HERC5 WILD-TYPE 360  63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HERC5 MUTATED     15    2
  HERC5 WILD-TYPE  360   63
   clus
vv  HERC5 MUTATED HERC5 WILD-TYPE
  0            15             360
  1             2              63
[1] 2 2
[1] FALSE
D887V8, binary
                 cls
clus                0   1
  HERC5 MUTATED     7  14
  HERC5 WILD-TYPE 218 250
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HERC5 MUTATED      7   14
  HERC5 WILD-TYPE  218  250
        clus
vv       HERC5 MUTATED HERC5 WILD-TYPE
  FEMALE             7             218
  MALE              14             250
[1] 2 2
[1] FALSE
D887V9, binary
                 cls
clus                0   1
  HERC5 MUTATED    16   2
  HERC5 WILD-TYPE 334  20
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HERC5 MUTATED     16    2
  HERC5 WILD-TYPE  334   20
     clus
vv    HERC5 MUTATED HERC5 WILD-TYPE
  NO             16             334
  YES             2              20
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  HERC5 MUTATED                     17                             1
  HERC5 WILD-TYPE                  298                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  HERC5 MUTATED                       3                              0
  HERC5 WILD-TYPE                   103                             10
D887V10, multiclass
                                clus
vv                               HERC5 MUTATED HERC5 WILD-TYPE
  COLON ADENOCARCINOMA                      17             298
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      3             103
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  HERC5 MUTATED    14   1   1   1
  HERC5 WILD-TYPE 331   3  30  24
D887V11, multiclass
    clus
vv   HERC5 MUTATED HERC5 WILD-TYPE
  R0            14             331
  R1             1               3
  R2             1              30
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D887V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HERC5 MUTATED                                  0     0
  HERC5 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  HERC5 MUTATED                           1    12
  HERC5 WILD-TYPE                        21   214
D887V13, multiclass
                                  clus
vv                                 HERC5 MUTATED HERC5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                       12             214
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(888) Variable = ENSA MUTATION ANALYSIS
D888V1, survival
                sevent
clus2              0   1
  ENSA MUTATED     3   3
  ENSA WILD-TYPE 375  90
  ENSA MUTATED ENSA WILD-TYPE 
             6            465 
  ENSA MUTATED ENSA WILD-TYPE 
             3             90 
$`ENSA MUTATED`
TCGA-AA-3492 TCGA-CA-6718 TCGA-D5-5537 TCGA-D5-6532 TCGA-G4-6309 TCGA-AG-A002 
        3.02        10.06        45.40        18.25        85.48        20.98 

$`ENSA WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07        12.20        12.76        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       12.03        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       53.62        44.68        55.04        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  ENSA MUTATED ENSA WILD-TYPE 
          3.02           0.00 
  ENSA MUTATED ENSA WILD-TYPE 
         85.48         148.01 
  ENSA MUTATED ENSA WILD-TYPE 
        19.615         20.190 
[1] "3.0 - 85.5 (19.6)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "2.2"
D888V2, continuous
D888V3, binary
                cls
clus               0   1
  ENSA MUTATED     5   1
  ENSA WILD-TYPE 361 118
[1] "tbl2"
                cls
clus             [,1] [,2]
  ENSA MUTATED      5    1
  ENSA WILD-TYPE  361  118
        clus
vv       ENSA MUTATED ENSA WILD-TYPE
  COLON             5            361
  RECTUM            1            118
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ENSA MUTATED         1        0        1         3         0         0
  ENSA WILD-TYPE      90        1       31       135        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ENSA MUTATED           0          0          1          0        0         0
  ENSA WILD-TYPE        24         11         58         42       48        18
                vv
clus             STAGE IVB
  ENSA MUTATED           0
  ENSA WILD-TYPE         1
D888V4, multiclass
            clus
vv           ENSA MUTATED ENSA WILD-TYPE
  STAGE I               1             90
  STAGE IA              0              1
  STAGE II              1             31
  STAGE IIA             3            135
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            1             58
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  ENSA MUTATED     0   1   5   0
  ENSA WILD-TYPE  17  91 324  50
D888V5, multiclass
    clus
vv   ENSA MUTATED ENSA WILD-TYPE
  T1            0             17
  T2            1             91
  T3            5            324
  T4            0             50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  ENSA MUTATED     4   1   1
  ENSA WILD-TYPE 283 112  86
D888V6, multiclass
    clus
vv   ENSA MUTATED ENSA WILD-TYPE
  N0            4            283
  N1            1            112
  N2            1             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D888V7, binary
                cls
clus               0   1
  ENSA MUTATED     5   0
  ENSA WILD-TYPE 370  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  ENSA MUTATED      5    0
  ENSA WILD-TYPE  370   65
   clus
vv  ENSA MUTATED ENSA WILD-TYPE
  0            5            370
  1            0             65
[1] 2 2
[1] FALSE
D888V8, binary
                cls
clus               0   1
  ENSA MUTATED     2   4
  ENSA WILD-TYPE 223 260
[1] "tbl2"
                cls
clus             [,1] [,2]
  ENSA MUTATED      2    4
  ENSA WILD-TYPE  223  260
        clus
vv       ENSA MUTATED ENSA WILD-TYPE
  FEMALE            2            223
  MALE              4            260
[1] 2 2
[1] FALSE
D888V9, binary
                cls
clus               0   1
  ENSA MUTATED     6   0
  ENSA WILD-TYPE 344  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  ENSA MUTATED      6    0
  ENSA WILD-TYPE  344   22
     clus
vv    ENSA MUTATED ENSA WILD-TYPE
  NO             6            344
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ENSA MUTATED                      5                             0
  ENSA WILD-TYPE                  310                            47
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ENSA MUTATED                       1                              0
  ENSA WILD-TYPE                   105                             10
D888V10, multiclass
                                clus
vv                               ENSA MUTATED ENSA WILD-TYPE
  COLON ADENOCARCINOMA                      5            310
  COLON MUCINOUS ADENOCARCINOMA             0             47
  RECTAL ADENOCARCINOMA                     1            105
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  ENSA MUTATED     4   0   0   2
  ENSA WILD-TYPE 341   4  31  23
D888V11, multiclass
    clus
vv   ENSA MUTATED ENSA WILD-TYPE
  R0            4            341
  R1            0              4
  R2            0             31
  RX            2             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D888V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ENSA MUTATED                                  0     1
  ENSA WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  ENSA MUTATED                           1     2
  ENSA WILD-TYPE                        21   224
D888V13, multiclass
                                  clus
vv                                 ENSA MUTATED ENSA WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                       2            224
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(889) Variable = TMEM45A MUTATION ANALYSIS
D889V1, survival
                   sevent
clus2                 0   1
  TMEM45A MUTATED     3   1
  TMEM45A WILD-TYPE 375  92
  TMEM45A MUTATED TMEM45A WILD-TYPE 
                4               467 
  TMEM45A MUTATED TMEM45A WILD-TYPE 
                1                92 
$`TMEM45A MUTATED`
TCGA-A6-6138 TCGA-AZ-6598 TCGA-G4-6323 TCGA-G4-6628 
       22.52        49.41        13.78        79.69 

$`TMEM45A WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6141 TCGA-A6-6142 
       22.09        22.06        32.71        27.09         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 
        5.13       106.75        22.36        62.79        88.21         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
       63.62        61.91        36.00        22.09        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       91.79        46.75        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  TMEM45A MUTATED TMEM45A WILD-TYPE 
            13.78              0.00 
  TMEM45A MUTATED TMEM45A WILD-TYPE 
            79.69            148.01 
  TMEM45A MUTATED TMEM45A WILD-TYPE 
           35.965            20.120 
[1] "13.8 - 79.7 (36.0)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.3"
D889V2, continuous
D889V3, binary
                   cls
clus                  0   1
  TMEM45A MUTATED     4   0
  TMEM45A WILD-TYPE 362 119
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM45A MUTATED      4    0
  TMEM45A WILD-TYPE  362  119
        clus
vv       TMEM45A MUTATED TMEM45A WILD-TYPE
  COLON                4               362
  RECTUM               0               119
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TMEM45A MUTATED         2        1        1         0         0         0
  TMEM45A WILD-TYPE      89        0       31       138        10         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TMEM45A MUTATED           0          0          0          0        0
  TMEM45A WILD-TYPE        24         11         59         42       48
                   vv
clus                STAGE IVA STAGE IVB
  TMEM45A MUTATED           0         0
  TMEM45A WILD-TYPE        18         1
D889V4, multiclass
            clus
vv           TMEM45A MUTATED TMEM45A WILD-TYPE
  STAGE I                  2                89
  STAGE IA                 1                 0
  STAGE II                 1                31
  STAGE IIA                0               138
  STAGE IIB                0                10
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               0                11
  STAGE IIIB               0                59
  STAGE IIIC               0                42
  STAGE IV                 0                48
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  TMEM45A MUTATED     0   2   1   0
  TMEM45A WILD-TYPE  17  90 328  50
D889V5, multiclass
    clus
vv   TMEM45A MUTATED TMEM45A WILD-TYPE
  T1               0                17
  T2               2                90
  T3               1               328
  T4               0                50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  TMEM45A MUTATED     4   0   0
  TMEM45A WILD-TYPE 283 113  87
D889V6, multiclass
    clus
vv   TMEM45A MUTATED TMEM45A WILD-TYPE
  N0               4               283
  N1               0               113
  N2               0                87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D889V7, binary
                   cls
clus                  0   1
  TMEM45A MUTATED     2   0
  TMEM45A WILD-TYPE 373  65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM45A MUTATED      2    0
  TMEM45A WILD-TYPE  373   65
   clus
vv  TMEM45A MUTATED TMEM45A WILD-TYPE
  0               2               373
  1               0                65
[1] 2 2
[1] FALSE
D889V8, binary
                   cls
clus                  0   1
  TMEM45A MUTATED     1   3
  TMEM45A WILD-TYPE 224 261
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM45A MUTATED      1    3
  TMEM45A WILD-TYPE  224  261
        clus
vv       TMEM45A MUTATED TMEM45A WILD-TYPE
  FEMALE               1               224
  MALE                 3               261
[1] 2 2
[1] FALSE
D889V9, binary
                   cls
clus                  0   1
  TMEM45A MUTATED     4   0
  TMEM45A WILD-TYPE 346  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM45A MUTATED      4    0
  TMEM45A WILD-TYPE  346   22
     clus
vv    TMEM45A MUTATED TMEM45A WILD-TYPE
  NO                4               346
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  TMEM45A MUTATED                      4                             0
  TMEM45A WILD-TYPE                  311                            47
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  TMEM45A MUTATED                       0                              0
  TMEM45A WILD-TYPE                   106                             10
D889V10, multiclass
                                clus
vv                               TMEM45A MUTATED TMEM45A WILD-TYPE
  COLON ADENOCARCINOMA                         4               311
  COLON MUCINOUS ADENOCARCINOMA                0                47
  RECTAL ADENOCARCINOMA                        0               106
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  TMEM45A MUTATED     2   0   0   0
  TMEM45A WILD-TYPE 343   4  31  25
D889V11, multiclass
[1] "Remove cluster labels:" "TMEM45A MUTATED"       
clus
  TMEM45A MUTATED TMEM45A WILD-TYPE 
                2               403 
       TCGA-A6-2671        TCGA-A6-2672        TCGA-A6-2674        TCGA-A6-2676 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-A6-2677        TCGA-A6-2678        TCGA-A6-2683        TCGA-A6-3807 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-A6-3808        TCGA-A6-3809        TCGA-A6-3810        TCGA-A6-5657 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-A6-5659        TCGA-A6-5661        TCGA-A6-5665        TCGA-A6-6781 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AA-3489        TCGA-AA-3492        TCGA-AA-3496        TCGA-AA-3502 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AA-3510        TCGA-AA-3511        TCGA-AA-3514        TCGA-AA-3517 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AA-3518        TCGA-AA-3519        TCGA-AA-3520        TCGA-AA-3521 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AA-3522        TCGA-AA-3524        TCGA-AA-3525        TCGA-AA-3526 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AA-3527        TCGA-AA-3529        TCGA-AA-3530        TCGA-AA-3531 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AA-3532        TCGA-AA-3534        TCGA-AA-3538        TCGA-AA-3542 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AA-3543        TCGA-AA-3544        TCGA-AA-3548        TCGA-AA-3549 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AA-3552        TCGA-AA-3553        TCGA-AA-3554        TCGA-AA-3555 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AA-3556        TCGA-AA-3558        TCGA-AA-3560        TCGA-AA-3561 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AA-3562        TCGA-AA-3655        TCGA-AA-3660        TCGA-AA-3662 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AA-3663        TCGA-AA-3664        TCGA-AA-3666        TCGA-AA-3667 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AA-3672        TCGA-AA-3673        TCGA-AA-3678        TCGA-AA-3679 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AA-3680        TCGA-AA-3681        TCGA-AA-3684        TCGA-AA-3685 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AA-3688        TCGA-AA-3692        TCGA-AA-3693        TCGA-AA-3695 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AA-3696        TCGA-AA-3697        TCGA-AA-3710        TCGA-AA-3712 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AA-3713        TCGA-AA-3715        TCGA-AA-3811        TCGA-AA-3812 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AA-3814        TCGA-AA-3815        TCGA-AA-3818        TCGA-AA-3819 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AA-3821        TCGA-AA-3831        TCGA-AA-3833        TCGA-AA-3837 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AA-3842        TCGA-AA-3844        TCGA-AA-3845        TCGA-AA-3846 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AA-3848        TCGA-AA-3850        TCGA-AA-3851        TCGA-AA-3852 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AA-3854        TCGA-AA-3855        TCGA-AA-3856        TCGA-AA-3858 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AA-3860        TCGA-AA-3861        TCGA-AA-3864        TCGA-AA-3866 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AA-3867        TCGA-AA-3869        TCGA-AA-3870        TCGA-AA-3872 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AA-3875        TCGA-AA-3877        TCGA-AA-3930        TCGA-AA-3939 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AA-3941        TCGA-AA-3947        TCGA-AA-3949        TCGA-AA-3950 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AA-3952        TCGA-AA-3955        TCGA-AA-3956        TCGA-AA-3968 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AA-3971        TCGA-AA-3972        TCGA-AA-3973        TCGA-AA-3975 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AA-3976        TCGA-AA-3979        TCGA-AA-3984        TCGA-AA-3986 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AA-3989        TCGA-AA-3994        TCGA-AA-A004        TCGA-AA-A00A 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AA-A00D        TCGA-AA-A00E        TCGA-AA-A00F        TCGA-AA-A00J 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AA-A00K        TCGA-AA-A00L        TCGA-AA-A00N        TCGA-AA-A00O 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AA-A00Q        TCGA-AA-A00R        TCGA-AA-A00U        TCGA-AA-A00W 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AA-A00Z        TCGA-AA-A010        TCGA-AA-A017        TCGA-AA-A01D 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AA-A01F        TCGA-AA-A01G        TCGA-AA-A01I        TCGA-AA-A01K 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AA-A01P        TCGA-AA-A01Q        TCGA-AA-A01R        TCGA-AA-A01S 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AA-A01T        TCGA-AA-A01V        TCGA-AA-A01X        TCGA-AA-A01Z 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AA-A022        TCGA-AA-A024        TCGA-AA-A029        TCGA-AA-A02F 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AA-A02H        TCGA-AA-A02J        TCGA-AA-A02K        TCGA-AA-A02O 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AA-A02W        TCGA-AA-A02Y        TCGA-AA-A03F        TCGA-AA-A03J 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AD-5900        TCGA-AD-6548        TCGA-AD-6888        TCGA-AU-3779 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AU-6004        TCGA-AY-4070        TCGA-AY-4071        TCGA-AY-5543 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AY-6196        TCGA-AY-6197        TCGA-AY-6386        TCGA-AZ-4315 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AZ-4681        TCGA-AZ-4682        TCGA-CA-5254        TCGA-CA-5255 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-CA-5796        TCGA-CA-5797        TCGA-CA-6715        TCGA-CA-6716 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-CA-6717        TCGA-CA-6718        TCGA-CA-6719        TCGA-CK-4947 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-CK-4948        TCGA-CK-4950        TCGA-CK-4952        TCGA-CK-5912 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-CK-5913        TCGA-CK-5914        TCGA-CK-5915        TCGA-CK-5916 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-CK-6746        TCGA-CK-6747        TCGA-CK-6748        TCGA-CK-6751 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-CM-4743        TCGA-CM-4744        TCGA-CM-4746        TCGA-CM-4747 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-CM-4752        TCGA-CM-5341        TCGA-CM-5344        TCGA-CM-5348 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-CM-5349        TCGA-CM-5860        TCGA-CM-5861        TCGA-CM-5862 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-CM-5863        TCGA-CM-5864        TCGA-CM-5868        TCGA-CM-6161 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-CM-6162        TCGA-CM-6163        TCGA-CM-6164        TCGA-CM-6165 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-CM-6166        TCGA-CM-6167        TCGA-CM-6168        TCGA-CM-6169 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-CM-6170        TCGA-CM-6171        TCGA-CM-6172        TCGA-CM-6674 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-CM-6675        TCGA-CM-6676        TCGA-CM-6677        TCGA-CM-6678 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-CM-6679        TCGA-CM-6680        TCGA-D5-5537        TCGA-D5-5538 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-D5-5539        TCGA-D5-5540        TCGA-D5-5541        TCGA-D5-6529 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-D5-6532        TCGA-D5-6533        TCGA-D5-6534        TCGA-D5-6535 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-D5-6536        TCGA-D5-6537        TCGA-D5-6538        TCGA-D5-6539 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-D5-6540        TCGA-D5-6541        TCGA-D5-6898        TCGA-D5-6920 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-D5-6922        TCGA-D5-6923        TCGA-D5-6924        TCGA-D5-6926 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-D5-6927        TCGA-D5-6928        TCGA-D5-6929        TCGA-D5-6930 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-D5-6931        TCGA-D5-6932        TCGA-D5-7000        TCGA-F4-6459 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-F4-6460        TCGA-F4-6569        TCGA-F4-6570        TCGA-F4-6703 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-F4-6704        TCGA-F4-6805        TCGA-F4-6806        TCGA-F4-6807 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-F4-6808        TCGA-F4-6809        TCGA-F4-6854        TCGA-F4-6855 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-F4-6856        TCGA-G4-6293        TCGA-G4-6299        TCGA-G4-6303 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-G4-6304        TCGA-G4-6306        TCGA-G4-6307        TCGA-G4-6309 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-G4-6310        TCGA-G4-6315        TCGA-G4-6317        TCGA-G4-6321 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-G4-6586        TCGA-G4-6588        TCGA-G4-6625        TCGA-G4-6626 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2691        TCGA-AF-2692 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AF-3400        TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AF-6655        TCGA-AG-3574        TCGA-AG-3575        TCGA-AG-3578 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AG-3580        TCGA-AG-3581        TCGA-AG-3582        TCGA-AG-3583 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AG-3584        TCGA-AG-3586        TCGA-AG-3587        TCGA-AG-3593 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AG-3594        TCGA-AG-3598        TCGA-AG-3599        TCGA-AG-3600 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AG-3601        TCGA-AG-3602        TCGA-AG-3605        TCGA-AG-3608 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AG-3609        TCGA-AG-3611        TCGA-AG-3612        TCGA-AG-3726 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AG-3727        TCGA-AG-3731        TCGA-AG-3732        TCGA-AG-3742 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AG-3878        TCGA-AG-3882        TCGA-AG-3883        TCGA-AG-3885 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3890        TCGA-AG-3892        TCGA-AG-3893 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AG-3894        TCGA-AG-3896        TCGA-AG-3898        TCGA-AG-3901 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AG-3902        TCGA-AG-3909        TCGA-AG-3999        TCGA-AG-4001 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AG-4005        TCGA-AG-4007        TCGA-AG-4008        TCGA-AG-4015 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AG-A002        TCGA-AG-A008        TCGA-AG-A00C        TCGA-AG-A00H 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AG-A00Y        TCGA-AG-A011        TCGA-AG-A014        TCGA-AG-A015 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AG-A016        TCGA-AG-A01L        TCGA-AG-A01W        TCGA-AG-A01Y 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A025        TCGA-AG-A026        TCGA-AG-A02G 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032        TCGA-AG-A036 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-AH-6549        TCGA-AH-6643        TCGA-CL-5917        TCGA-CL-5918 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6155        TCGA-DC-6157 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-DC-6158        TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-DC-6683        TCGA-DT-5265        TCGA-EF-5830        TCGA-EI-6506 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-EI-6507        TCGA-EI-6508        TCGA-EI-6510        TCGA-F5-6464 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-F5-6465        TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6812 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
       TCGA-F5-6813        TCGA-G5-6235        TCGA-G5-6641 
"TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" "TMEM45A WILD-TYPE" 
D889V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TMEM45A MUTATED                                  0     0
  TMEM45A WILD-TYPE                                1    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  TMEM45A MUTATED                           1     3
  TMEM45A WILD-TYPE                        21   223
D889V13, multiclass
                                  clus
vv                                 TMEM45A MUTATED TMEM45A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                      1                21
  WHITE                                          3               223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(890) Variable = TNNI3K MUTATION ANALYSIS
D890V1, survival
                  sevent
clus2                0   1
  TNNI3K MUTATED    21   3
  TNNI3K WILD-TYPE 357  90
  TNNI3K MUTATED TNNI3K WILD-TYPE 
              24              447 
  TNNI3K MUTATED TNNI3K WILD-TYPE 
               3               90 
$`TNNI3K MUTATED`
TCGA-A6-2672 TCGA-A6-3809 TCGA-A6-5660 TCGA-A6-5665 TCGA-A6-6137 TCGA-AA-3510 
       46.65        32.75        29.19        22.06        27.09        63.98 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3696 TCGA-AA-3833 TCGA-AA-3950 TCGA-AA-A00N 
       14.01         0.92         5.03        15.95        24.00         4.01 
TCGA-AA-A00R TCGA-AZ-4315 TCGA-CK-5914 TCGA-CM-4743 TCGA-CM-6168 TCGA-D5-6533 
        0.99        58.39         9.99        23.05        12.99         1.32 
TCGA-D5-6541 TCGA-DM-A0X9 TCGA-DM-A28F TCGA-DM-A28H TCGA-AG-3892 TCGA-AG-A002 
       15.58       119.70        35.97       117.07        13.02        20.98 

$`TNNI3K WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5657 
       34.65        33.34        36.53        14.53        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6138 
       30.44        33.53        23.61        22.09        32.71        22.52 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 
        8.38        25.08        25.18        24.16        21.76        24.69 
TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 
       24.39        23.87        20.12        19.66        20.28         7.04 
TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        3.02         1.02        35.01         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3673 TCGA-AA-3678 
        6.05         6.97        54.02         2.01        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3837 
       33.04         0.99        25.02         1.02        17.98        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       33.01        26.01         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00U 
       18.05        18.05        38.04        27.02        42.02        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        33.01        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 
       85.45        15.62        49.08        51.32        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
        1.91       124.27        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6169 
        2.96        29.03        16.04        21.99        14.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6534 
       19.59        56.09        55.92        20.19        18.25        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
       10.26        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G 
      135.65       139.17         6.12        81.37       119.93        60.79 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 
        1.02        17.95        36.95        17.03        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  TNNI3K MUTATED TNNI3K WILD-TYPE 
            0.92             0.00 
  TNNI3K MUTATED TNNI3K WILD-TYPE 
          119.70           148.01 
  TNNI3K MUTATED TNNI3K WILD-TYPE 
           21.52            20.12 
[1] "0.9 - 119.7 (21.5)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.8"
D890V2, continuous
D890V3, binary
                  cls
clus                 0   1
  TNNI3K MUTATED    24   2
  TNNI3K WILD-TYPE 342 117
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TNNI3K MUTATED     24    2
  TNNI3K WILD-TYPE  342  117
        clus
vv       TNNI3K MUTATED TNNI3K WILD-TYPE
  COLON              24              342
  RECTUM              2              117
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TNNI3K MUTATED         4        0        1         8         2         0
  TNNI3K WILD-TYPE      87        1       31       130         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TNNI3K MUTATED           1          0          5          3        2
  TNNI3K WILD-TYPE        23         11         54         39       46
                  vv
clus               STAGE IVA STAGE IVB
  TNNI3K MUTATED           0         0
  TNNI3K WILD-TYPE        18         1
D890V4, multiclass
            clus
vv           TNNI3K MUTATED TNNI3K WILD-TYPE
  STAGE I                 4               87
  STAGE IA                0                1
  STAGE II                1               31
  STAGE IIA               8              130
  STAGE IIB               2                8
  STAGE IIC               0                1
  STAGE III               1               23
  STAGE IIIA              0               11
  STAGE IIIB              5               54
  STAGE IIIC              3               39
  STAGE IV                2               46
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  TNNI3K MUTATED     1   3  19   3
  TNNI3K WILD-TYPE  16  89 310  47
D890V5, multiclass
    clus
vv   TNNI3K MUTATED TNNI3K WILD-TYPE
  T1              1               16
  T2              3               89
  T3             19              310
  T4              3               47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  TNNI3K MUTATED    16   6   4
  TNNI3K WILD-TYPE 271 107  83
D890V6, multiclass
    clus
vv   TNNI3K MUTATED TNNI3K WILD-TYPE
  N0             16              271
  N1              6              107
  N2              4               83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D890V7, binary
                  cls
clus                 0   1
  TNNI3K MUTATED    22   2
  TNNI3K WILD-TYPE 353  63
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TNNI3K MUTATED     22    2
  TNNI3K WILD-TYPE  353   63
   clus
vv  TNNI3K MUTATED TNNI3K WILD-TYPE
  0             22              353
  1              2               63
[1] 2 2
[1] FALSE
D890V8, binary
                  cls
clus                 0   1
  TNNI3K MUTATED    14  12
  TNNI3K WILD-TYPE 211 252
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TNNI3K MUTATED     14   12
  TNNI3K WILD-TYPE  211  252
        clus
vv       TNNI3K MUTATED TNNI3K WILD-TYPE
  FEMALE             14              211
  MALE               12              252
[1] 2 2
[1] FALSE
D890V9, binary
                  cls
clus                 0   1
  TNNI3K MUTATED    17   0
  TNNI3K WILD-TYPE 333  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TNNI3K MUTATED     17    0
  TNNI3K WILD-TYPE  333   22
     clus
vv    TNNI3K MUTATED TNNI3K WILD-TYPE
  NO              17              333
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  TNNI3K MUTATED                     20                             4
  TNNI3K WILD-TYPE                  295                            43
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  TNNI3K MUTATED                       2                              0
  TNNI3K WILD-TYPE                   104                             10
D890V10, multiclass
                                clus
vv                               TNNI3K MUTATED TNNI3K WILD-TYPE
  COLON ADENOCARCINOMA                       20              295
  COLON MUCINOUS ADENOCARCINOMA               4               43
  RECTAL ADENOCARCINOMA                       2              104
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  TNNI3K MUTATED    18   0   2   1
  TNNI3K WILD-TYPE 327   4  29  24
D890V11, multiclass
    clus
vv   TNNI3K MUTATED TNNI3K WILD-TYPE
  R0             18              327
  R1              0                4
  R2              2               29
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D890V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TNNI3K MUTATED                                  0     0
  TNNI3K WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  TNNI3K MUTATED                           2    13
  TNNI3K WILD-TYPE                        20   213
D890V13, multiclass
                                  clus
vv                                 TNNI3K MUTATED TNNI3K WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     2               20
  WHITE                                        13              213
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(891) Variable = PFN4 MUTATION ANALYSIS
D891V1, survival
                sevent
clus2              0   1
  PFN4 MUTATED     5   1
  PFN4 WILD-TYPE 373  92
  PFN4 MUTATED PFN4 WILD-TYPE 
             6            465 
  PFN4 MUTATED PFN4 WILD-TYPE 
             1             92 
$`PFN4 MUTATED`
TCGA-AA-3492 TCGA-AA-3663 TCGA-AA-3977 TCGA-AY-6197 TCGA-CM-5349 TCGA-CM-5861 
        3.02         6.97        25.02        21.44        30.08        15.02 

$`PFN4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 
       29.06        22.03        22.98        32.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  PFN4 MUTATED PFN4 WILD-TYPE 
          3.02           0.00 
  PFN4 MUTATED PFN4 WILD-TYPE 
         30.08         148.01 
  PFN4 MUTATED PFN4 WILD-TYPE 
         18.23          20.19 
[1] "3.0 - 30.1 (18.2)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.3"
D891V2, continuous
D891V3, binary
                cls
clus               0   1
  PFN4 MUTATED     6   0
  PFN4 WILD-TYPE 360 119
[1] "tbl2"
                cls
clus             [,1] [,2]
  PFN4 MUTATED      6    0
  PFN4 WILD-TYPE  360  119
        clus
vv       PFN4 MUTATED PFN4 WILD-TYPE
  COLON             6            360
  RECTUM            0            119
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PFN4 MUTATED         0        0        2         3         0         0
  PFN4 WILD-TYPE      91        1       30       135        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PFN4 MUTATED           0          0          0          0        0         0
  PFN4 WILD-TYPE        24         11         59         42       48        18
                vv
clus             STAGE IVB
  PFN4 MUTATED           0
  PFN4 WILD-TYPE         1
D891V4, multiclass
            clus
vv           PFN4 MUTATED PFN4 WILD-TYPE
  STAGE I               0             91
  STAGE IA              0              1
  STAGE II              2             30
  STAGE IIA             3            135
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            0             59
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  PFN4 MUTATED     0   1   5   0
  PFN4 WILD-TYPE  17  91 324  50
D891V5, multiclass
    clus
vv   PFN4 MUTATED PFN4 WILD-TYPE
  T1            0             17
  T2            1             91
  T3            5            324
  T4            0             50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  PFN4 MUTATED     6   0   0
  PFN4 WILD-TYPE 281 113  87
D891V6, multiclass
    clus
vv   PFN4 MUTATED PFN4 WILD-TYPE
  N0            6            281
  N1            0            113
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D891V7, binary
                cls
clus               0   1
  PFN4 MUTATED     4   0
  PFN4 WILD-TYPE 371  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  PFN4 MUTATED      4    0
  PFN4 WILD-TYPE  371   65
   clus
vv  PFN4 MUTATED PFN4 WILD-TYPE
  0            4            371
  1            0             65
[1] 2 2
[1] FALSE
D891V8, binary
                cls
clus               0   1
  PFN4 MUTATED     3   3
  PFN4 WILD-TYPE 222 261
[1] "tbl2"
                cls
clus             [,1] [,2]
  PFN4 MUTATED      3    3
  PFN4 WILD-TYPE  222  261
        clus
vv       PFN4 MUTATED PFN4 WILD-TYPE
  FEMALE            3            222
  MALE              3            261
[1] 2 2
[1] FALSE
D891V9, binary
                cls
clus               0   1
  PFN4 MUTATED     6   0
  PFN4 WILD-TYPE 344  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  PFN4 MUTATED      6    0
  PFN4 WILD-TYPE  344   22
     clus
vv    PFN4 MUTATED PFN4 WILD-TYPE
  NO             6            344
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PFN4 MUTATED                      6                             0
  PFN4 WILD-TYPE                  309                            47
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PFN4 MUTATED                       0                              0
  PFN4 WILD-TYPE                   106                             10
D891V10, multiclass
                                clus
vv                               PFN4 MUTATED PFN4 WILD-TYPE
  COLON ADENOCARCINOMA                      6            309
  COLON MUCINOUS ADENOCARCINOMA             0             47
  RECTAL ADENOCARCINOMA                     0            106
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  PFN4 MUTATED     5   0   0   0
  PFN4 WILD-TYPE 340   4  31  25
D891V11, multiclass
    clus
vv   PFN4 MUTATED PFN4 WILD-TYPE
  R0            5            340
  R1            0              4
  R2            0             31
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D891V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PFN4 MUTATED                                  0     0
  PFN4 WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  PFN4 MUTATED                           0     3
  PFN4 WILD-TYPE                        22   223
D891V13, multiclass
                                  clus
vv                                 PFN4 MUTATED PFN4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       3            223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(892) Variable = GPR75 MUTATION ANALYSIS
D892V1, survival
                 sevent
clus2               0   1
  GPR75 MUTATED     7   2
  GPR75 WILD-TYPE 371  91
  GPR75 MUTATED GPR75 WILD-TYPE 
              9             462 
  GPR75 MUTATED GPR75 WILD-TYPE 
              2              91 
$`GPR75 MUTATED`
TCGA-AA-3811 TCGA-AZ-6598 TCGA-CA-6717 TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-6162 
       10.06        49.41        12.76        30.08        15.02        12.00 
TCGA-G4-6306 TCGA-G4-6588 TCGA-AG-A025 
       44.68        26.17        49.97 

$`GPR75 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       19.04        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 
        5.13       106.75        22.36        62.79        88.21         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.20        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5862 
       13.02        29.06        22.03        22.98        32.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 
       15.02        15.02        17.03        15.02         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6307 
       35.31       133.18        74.56        65.85        53.62        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       35.80        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       10.98         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  GPR75 MUTATED GPR75 WILD-TYPE 
          10.06            0.00 
  GPR75 MUTATED GPR75 WILD-TYPE 
          49.97          148.01 
  GPR75 MUTATED GPR75 WILD-TYPE 
         26.170          20.155 
[1] "10.1 - 50.0 (26.2)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1"  
D892V2, continuous
D892V3, binary
                 cls
clus                0   1
  GPR75 MUTATED     8   1
  GPR75 WILD-TYPE 358 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPR75 MUTATED      8    1
  GPR75 WILD-TYPE  358  118
        clus
vv       GPR75 MUTATED GPR75 WILD-TYPE
  COLON              8             358
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GPR75 MUTATED         1        0        1         5         0         0
  GPR75 WILD-TYPE      90        1       31       133        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  GPR75 MUTATED           1          0          1          0        0         0
  GPR75 WILD-TYPE        23         11         58         42       48        18
                 vv
clus              STAGE IVB
  GPR75 MUTATED           0
  GPR75 WILD-TYPE         1
D892V4, multiclass
            clus
vv           GPR75 MUTATED GPR75 WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              5             133
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  GPR75 MUTATED     1   1   7   0
  GPR75 WILD-TYPE  16  91 322  50
D892V5, multiclass
    clus
vv   GPR75 MUTATED GPR75 WILD-TYPE
  T1             1              16
  T2             1              91
  T3             7             322
  T4             0              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  GPR75 MUTATED     7   1   1
  GPR75 WILD-TYPE 280 112  86
D892V6, multiclass
    clus
vv   GPR75 MUTATED GPR75 WILD-TYPE
  N0             7             280
  N1             1             112
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D892V7, binary
                 cls
clus                0   1
  GPR75 MUTATED     8   0
  GPR75 WILD-TYPE 367  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPR75 MUTATED      8    0
  GPR75 WILD-TYPE  367   65
   clus
vv  GPR75 MUTATED GPR75 WILD-TYPE
  0             8             367
  1             0              65
[1] 2 2
[1] FALSE
D892V8, binary
                 cls
clus                0   1
  GPR75 MUTATED     7   2
  GPR75 WILD-TYPE 218 262
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPR75 MUTATED      7    2
  GPR75 WILD-TYPE  218  262
        clus
vv       GPR75 MUTATED GPR75 WILD-TYPE
  FEMALE             7             218
  MALE               2             262
[1] 2 2
[1] FALSE
D892V9, binary
                 cls
clus                0   1
  GPR75 MUTATED     8   0
  GPR75 WILD-TYPE 342  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPR75 MUTATED      8    0
  GPR75 WILD-TYPE  342   22
     clus
vv    GPR75 MUTATED GPR75 WILD-TYPE
  NO              8             342
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  GPR75 MUTATED                      6                             2
  GPR75 WILD-TYPE                  309                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  GPR75 MUTATED                       1                              0
  GPR75 WILD-TYPE                   105                             10
D892V10, multiclass
                                clus
vv                               GPR75 MUTATED GPR75 WILD-TYPE
  COLON ADENOCARCINOMA                       6             309
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  GPR75 MUTATED     7   0   0   1
  GPR75 WILD-TYPE 338   4  31  24
D892V11, multiclass
    clus
vv   GPR75 MUTATED GPR75 WILD-TYPE
  R0             7             338
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D892V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GPR75 MUTATED                                  0     1
  GPR75 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  GPR75 MUTATED                           0     6
  GPR75 WILD-TYPE                        22   220
D892V13, multiclass
                                  clus
vv                                 GPR75 MUTATED GPR75 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        6             220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(893) Variable = LAX1 MUTATION ANALYSIS
D893V1, survival
                sevent
clus2              0   1
  LAX1 MUTATED     4   1
  LAX1 WILD-TYPE 374  92
  LAX1 MUTATED LAX1 WILD-TYPE 
             5            466 
  LAX1 MUTATED LAX1 WILD-TYPE 
             1             92 
$`LAX1 MUTATED`
TCGA-CK-5916 TCGA-CM-4743 TCGA-G4-6588 TCGA-AG-A002 TCGA-EI-6507 
       21.14        23.05        26.17        20.98        19.96 

$`LAX1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 
        9.99        82.95         1.91       124.27        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6508 
       24.13        51.48        32.61         0.49        20.55        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  LAX1 MUTATED LAX1 WILD-TYPE 
         19.96           0.00 
  LAX1 MUTATED LAX1 WILD-TYPE 
         26.17         148.01 
  LAX1 MUTATED LAX1 WILD-TYPE 
        21.140         20.085 
[1] "20.0 - 26.2 (21.1)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.2"
D893V2, continuous
D893V3, binary
                cls
clus               0   1
  LAX1 MUTATED     3   2
  LAX1 WILD-TYPE 363 117
[1] "tbl2"
                cls
clus             [,1] [,2]
  LAX1 MUTATED      3    2
  LAX1 WILD-TYPE  363  117
        clus
vv       LAX1 MUTATED LAX1 WILD-TYPE
  COLON             3            363
  RECTUM            2            117
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  LAX1 MUTATED         2        0        0         3         0         0
  LAX1 WILD-TYPE      89        1       32       135        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  LAX1 MUTATED           0          0          0          0        0         0
  LAX1 WILD-TYPE        24         11         59         42       48        18
                vv
clus             STAGE IVB
  LAX1 MUTATED           0
  LAX1 WILD-TYPE         1
D893V4, multiclass
            clus
vv           LAX1 MUTATED LAX1 WILD-TYPE
  STAGE I               2             89
  STAGE IA              0              1
  STAGE II              0             32
  STAGE IIA             3            135
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            0             59
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  LAX1 MUTATED     1   1   3   0
  LAX1 WILD-TYPE  16  91 326  50
D893V5, multiclass
    clus
vv   LAX1 MUTATED LAX1 WILD-TYPE
  T1            1             16
  T2            1             91
  T3            3            326
  T4            0             50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  LAX1 MUTATED     5   0   0
  LAX1 WILD-TYPE 282 113  87
D893V6, multiclass
    clus
vv   LAX1 MUTATED LAX1 WILD-TYPE
  N0            5            282
  N1            0            113
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D893V7, binary
                cls
clus               0   1
  LAX1 MUTATED     5   0
  LAX1 WILD-TYPE 370  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  LAX1 MUTATED      5    0
  LAX1 WILD-TYPE  370   65
   clus
vv  LAX1 MUTATED LAX1 WILD-TYPE
  0            5            370
  1            0             65
[1] 2 2
[1] FALSE
D893V8, binary
                cls
clus               0   1
  LAX1 MUTATED     2   3
  LAX1 WILD-TYPE 223 261
[1] "tbl2"
                cls
clus             [,1] [,2]
  LAX1 MUTATED      2    3
  LAX1 WILD-TYPE  223  261
        clus
vv       LAX1 MUTATED LAX1 WILD-TYPE
  FEMALE            2            223
  MALE              3            261
[1] 2 2
[1] FALSE
D893V9, binary
                cls
clus               0   1
  LAX1 MUTATED     5   0
  LAX1 WILD-TYPE 345  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  LAX1 MUTATED      5    0
  LAX1 WILD-TYPE  345   22
     clus
vv    LAX1 MUTATED LAX1 WILD-TYPE
  NO             5            345
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  LAX1 MUTATED                      3                             0
  LAX1 WILD-TYPE                  312                            47
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  LAX1 MUTATED                       2                              0
  LAX1 WILD-TYPE                   104                             10
D893V10, multiclass
                                clus
vv                               LAX1 MUTATED LAX1 WILD-TYPE
  COLON ADENOCARCINOMA                      3            312
  COLON MUCINOUS ADENOCARCINOMA             0             47
  RECTAL ADENOCARCINOMA                     2            104
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  LAX1 MUTATED     4   0   0   1
  LAX1 WILD-TYPE 341   4  31  24
D893V11, multiclass
    clus
vv   LAX1 MUTATED LAX1 WILD-TYPE
  R0            4            341
  R1            0              4
  R2            0             31
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D893V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  LAX1 MUTATED                                  0     0
  LAX1 WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  LAX1 MUTATED                           0     4
  LAX1 WILD-TYPE                        22   222
D893V13, multiclass
                                  clus
vv                                 LAX1 MUTATED LAX1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       4            222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(894) Variable = DHX36 MUTATION ANALYSIS
D894V1, survival
                 sevent
clus2               0   1
  DHX36 MUTATED    12   5
  DHX36 WILD-TYPE 366  88
  DHX36 MUTATED DHX36 WILD-TYPE 
             17             454 
  DHX36 MUTATED DHX36 WILD-TYPE 
              5              88 
$`DHX36 MUTATED`
TCGA-AA-3516 TCGA-AA-3663 TCGA-AD-6964 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-CM-6674 
       13.02         6.97        10.88        58.39        49.41        12.95 
TCGA-D5-6540 TCGA-D5-6928 TCGA-DM-A0XF TCGA-G4-6307 TCGA-G4-6625 TCGA-G4-6628 
       16.14        11.64        38.20        55.04        91.79        79.69 
TCGA-AG-A002 TCGA-AG-A02N TCGA-DY-A1H8 TCGA-EI-6507 TCGA-G5-6641 
       20.98        61.97        32.61        19.96        26.43 

$`DHX36 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        1.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        88.21         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       15.02        14.04        11.01        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 
       15.12        17.85         4.80        17.13        12.49        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
        9.44         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
      119.70        24.43       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       65.85        53.62        44.68        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6626 
       36.00        22.09        13.78        35.80        26.17        46.75 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X 
       64.01        10.98        49.97         1.94        38.96        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EF-5830 TCGA-EI-6506 
       41.36        57.24        24.13        51.48         0.49        20.55 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       32.19         0.66         0.69        55.76 

  DHX36 MUTATED DHX36 WILD-TYPE 
           6.97            0.00 
  DHX36 MUTATED DHX36 WILD-TYPE 
          91.79          148.01 
  DHX36 MUTATED DHX36 WILD-TYPE 
         26.430          20.085 
[1] "7.0 - 91.8 (26.4)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.1"
D894V2, continuous
D894V3, binary
                 cls
clus                0   1
  DHX36 MUTATED    12   5
  DHX36 WILD-TYPE 354 114
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DHX36 MUTATED     12    5
  DHX36 WILD-TYPE  354  114
        clus
vv       DHX36 MUTATED DHX36 WILD-TYPE
  COLON             12             354
  RECTUM             5             114
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DHX36 MUTATED         3        0        3         5         0         0
  DHX36 WILD-TYPE      88        1       29       133        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DHX36 MUTATED           1          2          1          1        0         0
  DHX36 WILD-TYPE        23          9         58         41       48        18
                 vv
clus              STAGE IVB
  DHX36 MUTATED           0
  DHX36 WILD-TYPE         1
D894V4, multiclass
            clus
vv           DHX36 MUTATED DHX36 WILD-TYPE
  STAGE I                3              88
  STAGE IA               0               1
  STAGE II               3              29
  STAGE IIA              5             133
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             2               9
  STAGE IIIB             1              58
  STAGE IIIC             1              41
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  DHX36 MUTATED     1   4  11   1
  DHX36 WILD-TYPE  16  88 318  49
D894V5, multiclass
    clus
vv   DHX36 MUTATED DHX36 WILD-TYPE
  T1             1              16
  T2             4              88
  T3            11             318
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  DHX36 MUTATED    11   3   3
  DHX36 WILD-TYPE 276 110  84
D894V6, multiclass
    clus
vv   DHX36 MUTATED DHX36 WILD-TYPE
  N0            11             276
  N1             3             110
  N2             3              84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D894V7, binary
                 cls
clus                0   1
  DHX36 MUTATED    14   0
  DHX36 WILD-TYPE 361  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DHX36 MUTATED     14    0
  DHX36 WILD-TYPE  361   65
   clus
vv  DHX36 MUTATED DHX36 WILD-TYPE
  0            14             361
  1             0              65
[1] 2 2
[1] FALSE
D894V8, binary
                 cls
clus                0   1
  DHX36 MUTATED     6  11
  DHX36 WILD-TYPE 219 253
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DHX36 MUTATED      6   11
  DHX36 WILD-TYPE  219  253
        clus
vv       DHX36 MUTATED DHX36 WILD-TYPE
  FEMALE             6             219
  MALE              11             253
[1] 2 2
[1] FALSE
D894V9, binary
                 cls
clus                0   1
  DHX36 MUTATED    14   0
  DHX36 WILD-TYPE 336  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DHX36 MUTATED     14    0
  DHX36 WILD-TYPE  336   22
     clus
vv    DHX36 MUTATED DHX36 WILD-TYPE
  NO             14             336
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  DHX36 MUTATED                      8                             3
  DHX36 WILD-TYPE                  307                            44
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  DHX36 MUTATED                       4                              1
  DHX36 WILD-TYPE                   102                              9
D894V10, multiclass
                                clus
vv                               DHX36 MUTATED DHX36 WILD-TYPE
  COLON ADENOCARCINOMA                       8             307
  COLON MUCINOUS ADENOCARCINOMA              3              44
  RECTAL ADENOCARCINOMA                      4             102
  RECTAL MUCINOUS ADENOCARCINOMA             1               9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  DHX36 MUTATED    12   0   0   0
  DHX36 WILD-TYPE 333   4  31  25
D894V11, multiclass
    clus
vv   DHX36 MUTATED DHX36 WILD-TYPE
  R0            12             333
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D894V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DHX36 MUTATED                                  0     0
  DHX36 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  DHX36 MUTATED                           0    13
  DHX36 WILD-TYPE                        22   213
D894V13, multiclass
                                  clus
vv                                 DHX36 MUTATED DHX36 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                       13             213
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(895) Variable = C13ORF23 MUTATION ANALYSIS
D895V1, survival
                    sevent
clus2                  0   1
  C13ORF23 MUTATED    11   2
  C13ORF23 WILD-TYPE 367  91
  C13ORF23 MUTATED C13ORF23 WILD-TYPE 
                13                458 
  C13ORF23 MUTATED C13ORF23 WILD-TYPE 
                 2                 91 
$`C13ORF23 MUTATED`
TCGA-AA-3543 TCGA-AA-A00J TCGA-AA-A010 TCGA-AD-6889 TCGA-AD-6963 TCGA-AZ-6598 
        0.99        18.05        34.98        56.55        27.42        49.41 
TCGA-CA-6717 TCGA-D5-6928 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-G4-6293 TCGA-G4-6628 
       12.76        11.64       140.38        44.32       133.18        79.69 
TCGA-F5-6812 
        0.66 

$`C13ORF23 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       29.00        26.01        12.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L 
       38.04        19.00        30.02        34.03        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 
       18.05        40.96         0.07        21.37        15.52         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        0.72         5.79        22.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       88.21         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07        12.20        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
        9.44         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
       13.32        12.59         7.50       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
        0.53        47.41        35.31        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6813 
        9.96        49.51        31.30        28.57        32.19         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  C13ORF23 MUTATED C13ORF23 WILD-TYPE 
              0.66               0.00 
  C13ORF23 MUTATED C13ORF23 WILD-TYPE 
            140.38             148.01 
  C13ORF23 MUTATED C13ORF23 WILD-TYPE 
            34.980             20.085 
[1] "0.7 - 140.4 (35.0)" "0.0 - 148.0 (20.1)"
[1] "hr=" "2.1"
D895V2, continuous
D895V3, binary
                    cls
clus                   0   1
  C13ORF23 MUTATED    12   1
  C13ORF23 WILD-TYPE 354 118
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C13ORF23 MUTATED     12    1
  C13ORF23 WILD-TYPE  354  118
        clus
vv       C13ORF23 MUTATED C13ORF23 WILD-TYPE
  COLON                12                354
  RECTUM                1                118
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  C13ORF23 MUTATED         2        0        1         6         1         0
  C13ORF23 WILD-TYPE      89        1       31       132         9         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C13ORF23 MUTATED           1          0          1          0        0
  C13ORF23 WILD-TYPE        23         11         58         42       48
                    vv
clus                 STAGE IVA STAGE IVB
  C13ORF23 MUTATED           0         0
  C13ORF23 WILD-TYPE        18         1
D895V4, multiclass
            clus
vv           C13ORF23 MUTATED C13ORF23 WILD-TYPE
  STAGE I                   2                 89
  STAGE IA                  0                  1
  STAGE II                  1                 31
  STAGE IIA                 6                132
  STAGE IIB                 1                  9
  STAGE IIC                 0                  1
  STAGE III                 1                 23
  STAGE IIIA                0                 11
  STAGE IIIB                1                 58
  STAGE IIIC                0                 42
  STAGE IV                  0                 48
  STAGE IVA                 0                 18
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  C13ORF23 MUTATED     0   2   9   2
  C13ORF23 WILD-TYPE  17  90 320  48
D895V5, multiclass
    clus
vv   C13ORF23 MUTATED C13ORF23 WILD-TYPE
  T1                0                 17
  T2                2                 90
  T3                9                320
  T4                2                 48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  C13ORF23 MUTATED    11   2   0
  C13ORF23 WILD-TYPE 276 111  87
D895V6, multiclass
    clus
vv   C13ORF23 MUTATED C13ORF23 WILD-TYPE
  N0               11                276
  N1                2                111
  N2                0                 87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D895V7, binary
                    cls
clus                   0   1
  C13ORF23 MUTATED    11   0
  C13ORF23 WILD-TYPE 364  65
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C13ORF23 MUTATED     11    0
  C13ORF23 WILD-TYPE  364   65
   clus
vv  C13ORF23 MUTATED C13ORF23 WILD-TYPE
  0               11                364
  1                0                 65
[1] 2 2
[1] FALSE
D895V8, binary
                    cls
clus                   0   1
  C13ORF23 MUTATED     4   9
  C13ORF23 WILD-TYPE 221 255
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C13ORF23 MUTATED      4    9
  C13ORF23 WILD-TYPE  221  255
        clus
vv       C13ORF23 MUTATED C13ORF23 WILD-TYPE
  FEMALE                4                221
  MALE                  9                255
[1] 2 2
[1] FALSE
D895V9, binary
                    cls
clus                   0   1
  C13ORF23 MUTATED     9   0
  C13ORF23 WILD-TYPE 341  22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C13ORF23 MUTATED      9    0
  C13ORF23 WILD-TYPE  341   22
     clus
vv    C13ORF23 MUTATED C13ORF23 WILD-TYPE
  NO                 9                341
  YES                0                 22
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  C13ORF23 MUTATED                      8                             4
  C13ORF23 WILD-TYPE                  307                            43
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  C13ORF23 MUTATED                       1                              0
  C13ORF23 WILD-TYPE                   105                             10
D895V10, multiclass
                                clus
vv                               C13ORF23 MUTATED C13ORF23 WILD-TYPE
  COLON ADENOCARCINOMA                          8                307
  COLON MUCINOUS ADENOCARCINOMA                 4                 43
  RECTAL ADENOCARCINOMA                         1                105
  RECTAL MUCINOUS ADENOCARCINOMA                0                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  C13ORF23 MUTATED     7   0   0   1
  C13ORF23 WILD-TYPE 338   4  31  24
D895V11, multiclass
    clus
vv   C13ORF23 MUTATED C13ORF23 WILD-TYPE
  R0                7                338
  R1                0                  4
  R2                0                 31
  RX                1                 24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D895V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C13ORF23 MUTATED                                  0     2
  C13ORF23 WILD-TYPE                                1     9
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  C13ORF23 MUTATED                           0     8
  C13ORF23 WILD-TYPE                        22   218
D895V13, multiclass
                                  clus
vv                                 C13ORF23 MUTATED C13ORF23 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           2                  9
  BLACK OR AFRICAN AMERICAN                       0                 22
  WHITE                                           8                218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(896) Variable = BAG5 MUTATION ANALYSIS
D896V1, survival
                sevent
clus2              0   1
  BAG5 MUTATED     3   0
  BAG5 WILD-TYPE 375  93
  BAG5 MUTATED BAG5 WILD-TYPE 
             3            468 
  BAG5 MUTATED BAG5 WILD-TYPE 
             0             93 
$`BAG5 MUTATED`
TCGA-G4-6588 TCGA-AG-3892 TCGA-AG-A002 
       26.17        13.02        20.98 

$`BAG5 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       13.78        35.80        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       17.03        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  BAG5 MUTATED BAG5 WILD-TYPE 
         13.02           0.00 
  BAG5 MUTATED BAG5 WILD-TYPE 
         26.17         148.01 
  BAG5 MUTATED BAG5 WILD-TYPE 
        20.980         20.155 
[1] "13.0 - 26.2 (21.0)" "0.0 - 148.0 (20.2)"
[1] "hr="     "3300000"
D896V2, continuous
D896V3, binary
                cls
clus               0   1
  BAG5 MUTATED     1   2
  BAG5 WILD-TYPE 365 117
[1] "tbl2"
                cls
clus             [,1] [,2]
  BAG5 MUTATED      1    2
  BAG5 WILD-TYPE  365  117
        clus
vv       BAG5 MUTATED BAG5 WILD-TYPE
  COLON             1            365
  RECTUM            2            117
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  BAG5 MUTATED         2        0        0         1         0         0
  BAG5 WILD-TYPE      89        1       32       137        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  BAG5 MUTATED           0          0          0          0        0         0
  BAG5 WILD-TYPE        24         11         59         42       48        18
                vv
clus             STAGE IVB
  BAG5 MUTATED           0
  BAG5 WILD-TYPE         1
D896V4, multiclass
            clus
vv           BAG5 MUTATED BAG5 WILD-TYPE
  STAGE I               2             89
  STAGE IA              0              1
  STAGE II              0             32
  STAGE IIA             1            137
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            0             59
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  BAG5 MUTATED     1   1   1   0
  BAG5 WILD-TYPE  16  91 328  50
D896V5, multiclass
    clus
vv   BAG5 MUTATED BAG5 WILD-TYPE
  T1            1             16
  T2            1             91
  T3            1            328
  T4            0             50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  BAG5 MUTATED     3   0   0
  BAG5 WILD-TYPE 284 113  87
D896V6, multiclass
    clus
vv   BAG5 MUTATED BAG5 WILD-TYPE
  N0            3            284
  N1            0            113
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D896V7, binary
                cls
clus               0   1
  BAG5 MUTATED     3   0
  BAG5 WILD-TYPE 372  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  BAG5 MUTATED      3    0
  BAG5 WILD-TYPE  372   65
   clus
vv  BAG5 MUTATED BAG5 WILD-TYPE
  0            3            372
  1            0             65
[1] 2 2
[1] FALSE
D896V8, binary
                cls
clus               0   1
  BAG5 MUTATED     2   1
  BAG5 WILD-TYPE 223 263
[1] "tbl2"
                cls
clus             [,1] [,2]
  BAG5 MUTATED      2    1
  BAG5 WILD-TYPE  223  263
        clus
vv       BAG5 MUTATED BAG5 WILD-TYPE
  FEMALE            2            223
  MALE              1            263
[1] 2 2
[1] FALSE
D896V9, binary
                cls
clus               0   1
  BAG5 MUTATED     3   0
  BAG5 WILD-TYPE 347  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  BAG5 MUTATED      3    0
  BAG5 WILD-TYPE  347   22
     clus
vv    BAG5 MUTATED BAG5 WILD-TYPE
  NO             3            347
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  BAG5 MUTATED                      1                             0
  BAG5 WILD-TYPE                  314                            47
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  BAG5 MUTATED                       2                              0
  BAG5 WILD-TYPE                   104                             10
D896V10, multiclass
                                clus
vv                               BAG5 MUTATED BAG5 WILD-TYPE
  COLON ADENOCARCINOMA                      1            314
  COLON MUCINOUS ADENOCARCINOMA             0             47
  RECTAL ADENOCARCINOMA                     2            104
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  BAG5 MUTATED     3   0   0   0
  BAG5 WILD-TYPE 342   4  31  25
D896V11, multiclass
    clus
vv   BAG5 MUTATED BAG5 WILD-TYPE
  R0            3            342
  R1            0              4
  R2            0             31
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D896V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  BAG5 MUTATED                                  0     0
  BAG5 WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  BAG5 MUTATED                           0     1
  BAG5 WILD-TYPE                        22   225
D896V13, multiclass
[1] "Remove cluster labels:" "BAG5 MUTATED"          
clus
  BAG5 MUTATED BAG5 WILD-TYPE 
             1            259 
    TCGA-A6-2671     TCGA-A6-2672     TCGA-A6-2674     TCGA-A6-2676 
"BAG5 WILD-TYPE" "BAG5 WILD-TYPE" "BAG5 WILD-TYPE" "BAG5 WILD-TYPE" 
    TCGA-A6-2677     TCGA-A6-2678     TCGA-A6-2683     TCGA-A6-3807 
"BAG5 WILD-TYPE" "BAG5 WILD-TYPE" "BAG5 WILD-TYPE" "BAG5 WILD-TYPE" 
    TCGA-A6-3808     TCGA-A6-3809     TCGA-A6-3810     TCGA-A6-4105 
"BAG5 WILD-TYPE" "BAG5 WILD-TYPE" "BAG5 WILD-TYPE" "BAG5 WILD-TYPE" 
    TCGA-A6-5656     TCGA-A6-5657     TCGA-A6-5659     TCGA-A6-5660 
"BAG5 WILD-TYPE" "BAG5 WILD-TYPE" "BAG5 WILD-TYPE" "BAG5 WILD-TYPE" 
    TCGA-A6-5661     TCGA-A6-5662     TCGA-A6-5664     TCGA-A6-5665 
"BAG5 WILD-TYPE" "BAG5 WILD-TYPE" "BAG5 WILD-TYPE" "BAG5 WILD-TYPE" 
    TCGA-A6-5666     TCGA-A6-6137     TCGA-A6-6138     TCGA-A6-6141 
"BAG5 WILD-TYPE" "BAG5 WILD-TYPE" "BAG5 WILD-TYPE" "BAG5 WILD-TYPE" 
    TCGA-A6-6142     TCGA-A6-6648     TCGA-A6-6649     TCGA-A6-6651 
"BAG5 WILD-TYPE" "BAG5 WILD-TYPE" "BAG5 WILD-TYPE" "BAG5 WILD-TYPE" 
    TCGA-A6-6652     TCGA-A6-6653     TCGA-A6-6654     TCGA-A6-6780 
"BAG5 WILD-TYPE" "BAG5 WILD-TYPE" "BAG5 WILD-TYPE" "BAG5 WILD-TYPE" 
    TCGA-A6-6781     TCGA-A6-6782     TCGA-AD-5900     TCGA-AD-6548 
"BAG5 WILD-TYPE" "BAG5 WILD-TYPE" "BAG5 WILD-TYPE" "BAG5 WILD-TYPE" 
    TCGA-AD-6888     TCGA-AD-6889     TCGA-AD-6890     TCGA-AD-6895 
"BAG5 WILD-TYPE" "BAG5 WILD-TYPE" "BAG5 WILD-TYPE" "BAG5 WILD-TYPE" 
    TCGA-AD-6899     TCGA-AD-6901     TCGA-AD-6963     TCGA-AD-6964 
"BAG5 WILD-TYPE" "BAG5 WILD-TYPE" "BAG5 WILD-TYPE" "BAG5 WILD-TYPE" 
    TCGA-AD-6965     TCGA-AU-3779     TCGA-AU-6004     TCGA-AY-4070 
"BAG5 WILD-TYPE" "BAG5 WILD-TYPE" "BAG5 WILD-TYPE" "BAG5 WILD-TYPE" 
    TCGA-AY-4071     TCGA-AY-5543     TCGA-AY-6196     TCGA-AY-6197 
"BAG5 WILD-TYPE" "BAG5 WILD-TYPE" "BAG5 WILD-TYPE" "BAG5 WILD-TYPE" 
    TCGA-AY-6386     TCGA-AZ-4315     TCGA-AZ-4323     TCGA-AZ-4616 
"BAG5 WILD-TYPE" "BAG5 WILD-TYPE" "BAG5 WILD-TYPE" "BAG5 WILD-TYPE" 
    TCGA-AZ-4681     TCGA-AZ-4682     TCGA-AZ-5403     TCGA-AZ-5407 
"BAG5 WILD-TYPE" "BAG5 WILD-TYPE" "BAG5 WILD-TYPE" "BAG5 WILD-TYPE" 
    TCGA-AZ-6598     TCGA-AZ-6599     TCGA-AZ-6600     TCGA-AZ-6601 
"BAG5 WILD-TYPE" "BAG5 WILD-TYPE" "BAG5 WILD-TYPE" "BAG5 WILD-TYPE" 
    TCGA-AZ-6603     TCGA-AZ-6605     TCGA-AZ-6606     TCGA-AZ-6607 
"BAG5 WILD-TYPE" "BAG5 WILD-TYPE" "BAG5 WILD-TYPE" "BAG5 WILD-TYPE" 
    TCGA-AZ-6608     TCGA-CA-5254     TCGA-CA-5255     TCGA-CA-5796 
"BAG5 WILD-TYPE" "BAG5 WILD-TYPE" "BAG5 WILD-TYPE" "BAG5 WILD-TYPE" 
    TCGA-CA-5797     TCGA-CA-6715     TCGA-CA-6716     TCGA-CA-6717 
"BAG5 WILD-TYPE" "BAG5 WILD-TYPE" "BAG5 WILD-TYPE" "BAG5 WILD-TYPE" 
    TCGA-CA-6718     TCGA-CA-6719     TCGA-CK-4947     TCGA-CK-4948 
"BAG5 WILD-TYPE" "BAG5 WILD-TYPE" "BAG5 WILD-TYPE" "BAG5 WILD-TYPE" 
    TCGA-CK-4950     TCGA-CK-4952     TCGA-CK-5912     TCGA-CK-5913 
"BAG5 WILD-TYPE" "BAG5 WILD-TYPE" "BAG5 WILD-TYPE" "BAG5 WILD-TYPE" 
    TCGA-CK-5914     TCGA-CK-5915     TCGA-CK-5916     TCGA-CK-6746 
"BAG5 WILD-TYPE" "BAG5 WILD-TYPE" "BAG5 WILD-TYPE" "BAG5 WILD-TYPE" 
    TCGA-CK-6747     TCGA-CK-6748     TCGA-CK-6751     TCGA-CM-4743 
"BAG5 WILD-TYPE" "BAG5 WILD-TYPE" "BAG5 WILD-TYPE" "BAG5 WILD-TYPE" 
    TCGA-CM-4744     TCGA-CM-4746     TCGA-CM-4747     TCGA-CM-4752 
"BAG5 WILD-TYPE" "BAG5 WILD-TYPE" "BAG5 WILD-TYPE" "BAG5 WILD-TYPE" 
    TCGA-CM-5341     TCGA-CM-5344     TCGA-CM-5348     TCGA-CM-5349 
"BAG5 WILD-TYPE" "BAG5 WILD-TYPE" "BAG5 WILD-TYPE" "BAG5 WILD-TYPE" 
    TCGA-CM-5860     TCGA-CM-5861     TCGA-CM-5862     TCGA-CM-5863 
"BAG5 WILD-TYPE" "BAG5 WILD-TYPE" "BAG5 WILD-TYPE" "BAG5 WILD-TYPE" 
    TCGA-CM-5864     TCGA-CM-5868     TCGA-CM-6161     TCGA-CM-6162 
"BAG5 WILD-TYPE" "BAG5 WILD-TYPE" "BAG5 WILD-TYPE" "BAG5 WILD-TYPE" 
    TCGA-CM-6163     TCGA-CM-6164     TCGA-CM-6165     TCGA-CM-6166 
"BAG5 WILD-TYPE" "BAG5 WILD-TYPE" "BAG5 WILD-TYPE" "BAG5 WILD-TYPE" 
    TCGA-CM-6167     TCGA-CM-6168     TCGA-CM-6169     TCGA-CM-6170 
"BAG5 WILD-TYPE" "BAG5 WILD-TYPE" "BAG5 WILD-TYPE" "BAG5 WILD-TYPE" 
    TCGA-CM-6171     TCGA-CM-6172     TCGA-CM-6674     TCGA-CM-6675 
"BAG5 WILD-TYPE" "BAG5 WILD-TYPE" "BAG5 WILD-TYPE" "BAG5 WILD-TYPE" 
    TCGA-CM-6676     TCGA-CM-6677     TCGA-CM-6678     TCGA-CM-6679 
"BAG5 WILD-TYPE" "BAG5 WILD-TYPE" "BAG5 WILD-TYPE" "BAG5 WILD-TYPE" 
    TCGA-CM-6680     TCGA-D5-5537     TCGA-D5-5538     TCGA-D5-5539 
"BAG5 WILD-TYPE" "BAG5 WILD-TYPE" "BAG5 WILD-TYPE" "BAG5 WILD-TYPE" 
    TCGA-D5-5540     TCGA-D5-5541     TCGA-D5-6529     TCGA-D5-6532 
"BAG5 WILD-TYPE" "BAG5 WILD-TYPE" "BAG5 WILD-TYPE" "BAG5 WILD-TYPE" 
    TCGA-D5-6533     TCGA-D5-6534     TCGA-D5-6535     TCGA-D5-6536 
"BAG5 WILD-TYPE" "BAG5 WILD-TYPE" "BAG5 WILD-TYPE" "BAG5 WILD-TYPE" 
    TCGA-D5-6537     TCGA-D5-6538     TCGA-D5-6539     TCGA-D5-6540 
"BAG5 WILD-TYPE" "BAG5 WILD-TYPE" "BAG5 WILD-TYPE" "BAG5 WILD-TYPE" 
    TCGA-D5-6541     TCGA-D5-6898     TCGA-D5-6920     TCGA-D5-6922 
"BAG5 WILD-TYPE" "BAG5 WILD-TYPE" "BAG5 WILD-TYPE" "BAG5 WILD-TYPE" 
    TCGA-D5-6923     TCGA-D5-6924     TCGA-D5-6926     TCGA-D5-6927 
"BAG5 WILD-TYPE" "BAG5 WILD-TYPE" "BAG5 WILD-TYPE" "BAG5 WILD-TYPE" 
    TCGA-D5-6928     TCGA-D5-6929     TCGA-D5-6930     TCGA-D5-6931 
"BAG5 WILD-TYPE" "BAG5 WILD-TYPE" "BAG5 WILD-TYPE" "BAG5 WILD-TYPE" 
    TCGA-D5-6932     TCGA-D5-7000     TCGA-DM-A0X9     TCGA-DM-A0XD 
"BAG5 WILD-TYPE" "BAG5 WILD-TYPE" "BAG5 WILD-TYPE" "BAG5 WILD-TYPE" 
    TCGA-DM-A0XF     TCGA-DM-A1D0     TCGA-DM-A1D4     TCGA-DM-A1D6 
"BAG5 WILD-TYPE" "BAG5 WILD-TYPE" "BAG5 WILD-TYPE" "BAG5 WILD-TYPE" 
    TCGA-DM-A1D7     TCGA-DM-A1D8     TCGA-DM-A1D9     TCGA-DM-A1DA 
"BAG5 WILD-TYPE" "BAG5 WILD-TYPE" "BAG5 WILD-TYPE" "BAG5 WILD-TYPE" 
    TCGA-DM-A1DB     TCGA-DM-A1HA     TCGA-DM-A1HB     TCGA-DM-A282 
"BAG5 WILD-TYPE" "BAG5 WILD-TYPE" "BAG5 WILD-TYPE" "BAG5 WILD-TYPE" 
    TCGA-DM-A285     TCGA-DM-A28C     TCGA-DM-A28E     TCGA-DM-A28F 
"BAG5 WILD-TYPE" "BAG5 WILD-TYPE" "BAG5 WILD-TYPE" "BAG5 WILD-TYPE" 
    TCGA-DM-A28G     TCGA-DM-A28H     TCGA-DM-A28K     TCGA-F4-6459 
"BAG5 WILD-TYPE" "BAG5 WILD-TYPE" "BAG5 WILD-TYPE" "BAG5 WILD-TYPE" 
    TCGA-F4-6460     TCGA-F4-6569     TCGA-F4-6570     TCGA-F4-6703 
"BAG5 WILD-TYPE" "BAG5 WILD-TYPE" "BAG5 WILD-TYPE" "BAG5 WILD-TYPE" 
    TCGA-F4-6704     TCGA-F4-6805     TCGA-F4-6806     TCGA-F4-6807 
"BAG5 WILD-TYPE" "BAG5 WILD-TYPE" "BAG5 WILD-TYPE" "BAG5 WILD-TYPE" 
    TCGA-F4-6808     TCGA-F4-6809     TCGA-F4-6854     TCGA-F4-6855 
"BAG5 WILD-TYPE" "BAG5 WILD-TYPE" "BAG5 WILD-TYPE" "BAG5 WILD-TYPE" 
    TCGA-F4-6856     TCGA-G4-6293     TCGA-G4-6299     TCGA-G4-6303 
"BAG5 WILD-TYPE" "BAG5 WILD-TYPE" "BAG5 WILD-TYPE" "BAG5 WILD-TYPE" 
    TCGA-G4-6304     TCGA-G4-6306     TCGA-G4-6307     TCGA-G4-6309 
"BAG5 WILD-TYPE" "BAG5 WILD-TYPE" "BAG5 WILD-TYPE" "BAG5 WILD-TYPE" 
    TCGA-G4-6310     TCGA-G4-6315     TCGA-G4-6317     TCGA-G4-6321 
"BAG5 WILD-TYPE" "BAG5 WILD-TYPE" "BAG5 WILD-TYPE" "BAG5 WILD-TYPE" 
    TCGA-G4-6323     TCGA-G4-6586     TCGA-G4-6625     TCGA-G4-6626 
"BAG5 WILD-TYPE" "BAG5 WILD-TYPE" "BAG5 WILD-TYPE" "BAG5 WILD-TYPE" 
    TCGA-G4-6628     TCGA-AF-2687     TCGA-AF-2689     TCGA-AF-2691 
"BAG5 WILD-TYPE" "BAG5 WILD-TYPE" "BAG5 WILD-TYPE" "BAG5 WILD-TYPE" 
    TCGA-AF-2692     TCGA-AF-2693     TCGA-AF-3400     TCGA-AF-3913 
"BAG5 WILD-TYPE" "BAG5 WILD-TYPE" "BAG5 WILD-TYPE" "BAG5 WILD-TYPE" 
    TCGA-AF-4110     TCGA-AF-5654     TCGA-AF-6136     TCGA-AF-6655 
"BAG5 WILD-TYPE" "BAG5 WILD-TYPE" "BAG5 WILD-TYPE" "BAG5 WILD-TYPE" 
    TCGA-AF-6672     TCGA-AH-6544     TCGA-AH-6547     TCGA-AH-6549 
"BAG5 WILD-TYPE" "BAG5 WILD-TYPE" "BAG5 WILD-TYPE" "BAG5 WILD-TYPE" 
    TCGA-AH-6643     TCGA-AH-6644     TCGA-CI-6619     TCGA-CI-6620 
"BAG5 WILD-TYPE" "BAG5 WILD-TYPE" "BAG5 WILD-TYPE" "BAG5 WILD-TYPE" 
    TCGA-CI-6621     TCGA-CI-6622     TCGA-CI-6624     TCGA-CL-5917 
"BAG5 WILD-TYPE" "BAG5 WILD-TYPE" "BAG5 WILD-TYPE" "BAG5 WILD-TYPE" 
    TCGA-CL-5918     TCGA-DC-5337     TCGA-DC-5869     TCGA-DC-6155 
"BAG5 WILD-TYPE" "BAG5 WILD-TYPE" "BAG5 WILD-TYPE" "BAG5 WILD-TYPE" 
    TCGA-DC-6157     TCGA-DC-6158     TCGA-DC-6160     TCGA-DC-6681 
"BAG5 WILD-TYPE" "BAG5 WILD-TYPE" "BAG5 WILD-TYPE" "BAG5 WILD-TYPE" 
    TCGA-DC-6682     TCGA-DC-6683     TCGA-DT-5265     TCGA-DY-A0XA 
"BAG5 WILD-TYPE" "BAG5 WILD-TYPE" "BAG5 WILD-TYPE" "BAG5 WILD-TYPE" 
    TCGA-DY-A1DC     TCGA-DY-A1DD     TCGA-DY-A1DF     TCGA-DY-A1DG 
"BAG5 WILD-TYPE" "BAG5 WILD-TYPE" "BAG5 WILD-TYPE" "BAG5 WILD-TYPE" 
    TCGA-DY-A1H8     TCGA-EF-5830     TCGA-EI-6506     TCGA-EI-6507 
"BAG5 WILD-TYPE" "BAG5 WILD-TYPE" "BAG5 WILD-TYPE" "BAG5 WILD-TYPE" 
    TCGA-EI-6508     TCGA-EI-6510     TCGA-F5-6464     TCGA-F5-6465 
"BAG5 WILD-TYPE" "BAG5 WILD-TYPE" "BAG5 WILD-TYPE" "BAG5 WILD-TYPE" 
    TCGA-F5-6571     TCGA-F5-6702     TCGA-F5-6811     TCGA-F5-6812 
"BAG5 WILD-TYPE" "BAG5 WILD-TYPE" "BAG5 WILD-TYPE" "BAG5 WILD-TYPE" 
    TCGA-F5-6813     TCGA-G5-6235     TCGA-G5-6641 
"BAG5 WILD-TYPE" "BAG5 WILD-TYPE" "BAG5 WILD-TYPE" 

Clustering(897) Variable = MIPOL1 MUTATION ANALYSIS
D897V1, survival
                  sevent
clus2                0   1
  MIPOL1 MUTATED     3   1
  MIPOL1 WILD-TYPE 375  92
  MIPOL1 MUTATED MIPOL1 WILD-TYPE 
               4              467 
  MIPOL1 MUTATED MIPOL1 WILD-TYPE 
               1               92 
$`MIPOL1 MUTATED`
TCGA-AA-3855 TCGA-CA-6716 TCGA-DM-A1D6 TCGA-EI-6507 
       32.05        12.20        49.91        19.96 

$`MIPOL1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       36.03         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D7 
      119.70        24.43        38.20       130.65        92.75        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  MIPOL1 MUTATED MIPOL1 WILD-TYPE 
            12.2              0.0 
  MIPOL1 MUTATED MIPOL1 WILD-TYPE 
           49.91           148.01 
  MIPOL1 MUTATED MIPOL1 WILD-TYPE 
          26.005           20.190 
[1] "12.2 - 49.9 (26.0)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.1"
D897V2, continuous
D897V3, binary
                  cls
clus                 0   1
  MIPOL1 MUTATED     4   1
  MIPOL1 WILD-TYPE 362 118
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MIPOL1 MUTATED      4    1
  MIPOL1 WILD-TYPE  362  118
        clus
vv       MIPOL1 MUTATED MIPOL1 WILD-TYPE
  COLON               4              362
  RECTUM              1              118
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MIPOL1 MUTATED         1        0        0         3         0         0
  MIPOL1 WILD-TYPE      90        1       32       135        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MIPOL1 MUTATED           0          0          0          1        0
  MIPOL1 WILD-TYPE        24         11         59         41       48
                  vv
clus               STAGE IVA STAGE IVB
  MIPOL1 MUTATED           0         0
  MIPOL1 WILD-TYPE        18         1
D897V4, multiclass
            clus
vv           MIPOL1 MUTATED MIPOL1 WILD-TYPE
  STAGE I                 1               90
  STAGE IA                0                1
  STAGE II                0               32
  STAGE IIA               3              135
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              0               59
  STAGE IIIC              1               41
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  MIPOL1 MUTATED     0   1   4   0
  MIPOL1 WILD-TYPE  17  91 325  50
D897V5, multiclass
    clus
vv   MIPOL1 MUTATED MIPOL1 WILD-TYPE
  T1              0               17
  T2              1               91
  T3              4              325
  T4              0               50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  MIPOL1 MUTATED     4   0   1
  MIPOL1 WILD-TYPE 283 113  86
D897V6, multiclass
    clus
vv   MIPOL1 MUTATED MIPOL1 WILD-TYPE
  N0              4              283
  N1              0              113
  N2              1               86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D897V7, binary
                  cls
clus                 0   1
  MIPOL1 MUTATED     4   0
  MIPOL1 WILD-TYPE 371  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MIPOL1 MUTATED      4    0
  MIPOL1 WILD-TYPE  371   65
   clus
vv  MIPOL1 MUTATED MIPOL1 WILD-TYPE
  0              4              371
  1              0               65
[1] 2 2
[1] FALSE
D897V8, binary
                  cls
clus                 0   1
  MIPOL1 MUTATED     0   5
  MIPOL1 WILD-TYPE 225 259
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MIPOL1 MUTATED      0    5
  MIPOL1 WILD-TYPE  225  259
        clus
vv       MIPOL1 MUTATED MIPOL1 WILD-TYPE
  FEMALE              0              225
  MALE                5              259
[1] 2 2
[1] FALSE
D897V9, binary
                  cls
clus                 0   1
  MIPOL1 MUTATED     3   0
  MIPOL1 WILD-TYPE 347  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MIPOL1 MUTATED      3    0
  MIPOL1 WILD-TYPE  347   22
     clus
vv    MIPOL1 MUTATED MIPOL1 WILD-TYPE
  NO               3              347
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MIPOL1 MUTATED                      2                             2
  MIPOL1 WILD-TYPE                  313                            45
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MIPOL1 MUTATED                       1                              0
  MIPOL1 WILD-TYPE                   105                             10
D897V10, multiclass
                                clus
vv                               MIPOL1 MUTATED MIPOL1 WILD-TYPE
  COLON ADENOCARCINOMA                        2              313
  COLON MUCINOUS ADENOCARCINOMA               2               45
  RECTAL ADENOCARCINOMA                       1              105
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  MIPOL1 MUTATED     3   0   0   1
  MIPOL1 WILD-TYPE 342   4  31  24
D897V11, multiclass
    clus
vv   MIPOL1 MUTATED MIPOL1 WILD-TYPE
  R0              3              342
  R1              0                4
  R2              0               31
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D897V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MIPOL1 MUTATED                                  0     1
  MIPOL1 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  MIPOL1 MUTATED                           0     3
  MIPOL1 WILD-TYPE                        22   223
D897V13, multiclass
                                  clus
vv                                 MIPOL1 MUTATED MIPOL1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         3              223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(898) Variable = CDH22 MUTATION ANALYSIS
D898V1, survival
                 sevent
clus2               0   1
  CDH22 MUTATED    13   5
  CDH22 WILD-TYPE 365  88
  CDH22 MUTATED CDH22 WILD-TYPE 
             18             453 
  CDH22 MUTATED CDH22 WILD-TYPE 
              5              88 
$`CDH22 MUTATED`
TCGA-A6-5665 TCGA-AA-3516 TCGA-AA-3681 TCGA-AA-3837 TCGA-AA-3950 TCGA-AZ-6599 
       22.06        13.02         5.98        38.99        24.00         6.77 
TCGA-AZ-6606 TCGA-CM-6677 TCGA-D5-6540 TCGA-DM-A1HA TCGA-G4-6303 TCGA-G4-6306 
       11.74        11.08        16.14       131.51        65.85        44.68 
TCGA-G4-6315 TCGA-G4-6586 TCGA-AG-3611 TCGA-AG-4008 TCGA-AG-A02X TCGA-DY-A1DD 
       61.91        35.80        13.94        17.03        41.00        57.24 

$`CDH22 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       15.02        11.01        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       33.01        26.01         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       88.21        49.41        12.10       100.01        29.56         5.23 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6678 TCGA-CM-6679 
       11.01        12.95        13.05        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
        4.80        17.13        12.49        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A282 
       12.59       140.38         7.50        44.32       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6304 
        0.53        47.41        35.31       133.18        74.56        53.62 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       55.04        85.48        63.62        36.00        22.09        13.78 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 
        6.05         0.99        15.95        19.99        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-A002 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
        1.94        38.96        61.97        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DF TCGA-DY-A1DG 
        5.03         5.29       126.44        41.36        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  CDH22 MUTATED CDH22 WILD-TYPE 
           5.98            0.00 
  CDH22 MUTATED CDH22 WILD-TYPE 
         131.51          148.01 
  CDH22 MUTATED CDH22 WILD-TYPE 
          23.03           20.12 
[1] "6.0 - 131.5 (23.0)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.1"
D898V2, continuous
D898V3, binary
                 cls
clus                0   1
  CDH22 MUTATED    16   4
  CDH22 WILD-TYPE 350 115
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDH22 MUTATED     16    4
  CDH22 WILD-TYPE  350  115
        clus
vv       CDH22 MUTATED CDH22 WILD-TYPE
  COLON             16             350
  RECTUM             4             115
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CDH22 MUTATED         3        0        0         9         0         0
  CDH22 WILD-TYPE      88        1       32       129        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CDH22 MUTATED           2          0          1          2        3         0
  CDH22 WILD-TYPE        22         11         58         40       45        18
                 vv
clus              STAGE IVB
  CDH22 MUTATED           0
  CDH22 WILD-TYPE         1
D898V4, multiclass
            clus
vv           CDH22 MUTATED CDH22 WILD-TYPE
  STAGE I                3              88
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              9             129
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              2              22
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             2              40
  STAGE IV               3              45
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CDH22 MUTATED     0   4  15   1
  CDH22 WILD-TYPE  17  88 314  49
D898V5, multiclass
    clus
vv   CDH22 MUTATED CDH22 WILD-TYPE
  T1             0              17
  T2             4              88
  T3            15             314
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  CDH22 MUTATED    12   4   4
  CDH22 WILD-TYPE 275 109  83
D898V6, multiclass
    clus
vv   CDH22 MUTATED CDH22 WILD-TYPE
  N0            12             275
  N1             4             109
  N2             4              83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D898V7, binary
                 cls
clus                0   1
  CDH22 MUTATED    15   3
  CDH22 WILD-TYPE 360  62
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDH22 MUTATED     15    3
  CDH22 WILD-TYPE  360   62
   clus
vv  CDH22 MUTATED CDH22 WILD-TYPE
  0            15             360
  1             3              62
[1] 2 2
[1] FALSE
D898V8, binary
                 cls
clus                0   1
  CDH22 MUTATED     9  11
  CDH22 WILD-TYPE 216 253
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDH22 MUTATED      9   11
  CDH22 WILD-TYPE  216  253
        clus
vv       CDH22 MUTATED CDH22 WILD-TYPE
  FEMALE             9             216
  MALE              11             253
[1] 2 2
[1] FALSE
D898V9, binary
                 cls
clus                0   1
  CDH22 MUTATED    15   0
  CDH22 WILD-TYPE 335  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDH22 MUTATED     15    0
  CDH22 WILD-TYPE  335   22
     clus
vv    CDH22 MUTATED CDH22 WILD-TYPE
  NO             15             335
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CDH22 MUTATED                     11                             5
  CDH22 WILD-TYPE                  304                            42
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CDH22 MUTATED                       4                              0
  CDH22 WILD-TYPE                   102                             10
D898V10, multiclass
                                clus
vv                               CDH22 MUTATED CDH22 WILD-TYPE
  COLON ADENOCARCINOMA                      11             304
  COLON MUCINOUS ADENOCARCINOMA              5              42
  RECTAL ADENOCARCINOMA                      4             102
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  CDH22 MUTATED    15   0   0   0
  CDH22 WILD-TYPE 330   4  31  25
D898V11, multiclass
    clus
vv   CDH22 MUTATED CDH22 WILD-TYPE
  R0            15             330
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D898V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CDH22 MUTATED                                  0     0
  CDH22 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CDH22 MUTATED                           0    12
  CDH22 WILD-TYPE                        22   214
D898V13, multiclass
                                  clus
vv                                 CDH22 MUTATED CDH22 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                       12             214
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(899) Variable = MAPK9 MUTATION ANALYSIS
D899V1, survival
                 sevent
clus2               0   1
  MAPK9 MUTATED     8   3
  MAPK9 WILD-TYPE 370  90
  MAPK9 MUTATED MAPK9 WILD-TYPE 
             11             460 
  MAPK9 MUTATED MAPK9 WILD-TYPE 
              3              90 
$`MAPK9 MUTATED`
TCGA-AA-A010 TCGA-AA-A02F TCGA-AY-6386 TCGA-AZ-6598 TCGA-CA-6718 TCGA-CM-6168 
       34.98        39.98        17.82        49.41        10.06        12.99 
TCGA-D5-6929 TCGA-F4-6570 TCGA-G4-6306 TCGA-AG-A002 TCGA-CL-5918 
        4.80         6.18        44.68        20.98         7.17 

$`MAPK9 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       51.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       33.01        21.44        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        88.21         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6169 TCGA-CM-6170 
       29.03        16.04        21.99        14.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.04         9.44        11.64         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       35.74        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       74.56        65.85        53.62        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-DC-5337 TCGA-DC-5869 
       33.17         6.97         4.73        78.12        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  MAPK9 MUTATED MAPK9 WILD-TYPE 
            4.8             0.0 
  MAPK9 MUTATED MAPK9 WILD-TYPE 
          49.41          148.01 
  MAPK9 MUTATED MAPK9 WILD-TYPE 
         17.820          20.235 
[1] "4.8 - 49.4 (17.8)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.6"
D899V2, continuous
D899V3, binary
                 cls
clus                0   1
  MAPK9 MUTATED    10   2
  MAPK9 WILD-TYPE 356 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MAPK9 MUTATED     10    2
  MAPK9 WILD-TYPE  356  117
        clus
vv       MAPK9 MUTATED MAPK9 WILD-TYPE
  COLON             10             356
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MAPK9 MUTATED         1        0        1         6         1         0
  MAPK9 WILD-TYPE      90        1       31       132         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MAPK9 MUTATED           0          0          1          0        2         0
  MAPK9 WILD-TYPE        24         11         58         42       46        18
                 vv
clus              STAGE IVB
  MAPK9 MUTATED           0
  MAPK9 WILD-TYPE         1
D899V4, multiclass
            clus
vv           MAPK9 MUTATED MAPK9 WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              6             132
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             0              42
  STAGE IV               2              46
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  MAPK9 MUTATED     0   2   9   1
  MAPK9 WILD-TYPE  17  90 320  49
D899V5, multiclass
    clus
vv   MAPK9 MUTATED MAPK9 WILD-TYPE
  T1             0              17
  T2             2              90
  T3             9             320
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  MAPK9 MUTATED     9   3   0
  MAPK9 WILD-TYPE 278 110  87
D899V6, multiclass
    clus
vv   MAPK9 MUTATED MAPK9 WILD-TYPE
  N0             9             278
  N1             3             110
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D899V7, binary
                 cls
clus                0   1
  MAPK9 MUTATED     8   2
  MAPK9 WILD-TYPE 367  63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MAPK9 MUTATED      8    2
  MAPK9 WILD-TYPE  367   63
   clus
vv  MAPK9 MUTATED MAPK9 WILD-TYPE
  0             8             367
  1             2              63
[1] 2 2
[1] FALSE
D899V8, binary
                 cls
clus                0   1
  MAPK9 MUTATED     9   3
  MAPK9 WILD-TYPE 216 261
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MAPK9 MUTATED      9    3
  MAPK9 WILD-TYPE  216  261
        clus
vv       MAPK9 MUTATED MAPK9 WILD-TYPE
  FEMALE             9             216
  MALE               3             261
[1] 2 2
[1] FALSE
D899V9, binary
                 cls
clus                0   1
  MAPK9 MUTATED    10   0
  MAPK9 WILD-TYPE 340  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MAPK9 MUTATED     10    0
  MAPK9 WILD-TYPE  340   22
     clus
vv    MAPK9 MUTATED MAPK9 WILD-TYPE
  NO             10             340
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MAPK9 MUTATED                     10                             0
  MAPK9 WILD-TYPE                  305                            47
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MAPK9 MUTATED                       2                              0
  MAPK9 WILD-TYPE                   104                             10
D899V10, multiclass
                                clus
vv                               MAPK9 MUTATED MAPK9 WILD-TYPE
  COLON ADENOCARCINOMA                      10             305
  COLON MUCINOUS ADENOCARCINOMA              0              47
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  MAPK9 MUTATED     8   0   1   2
  MAPK9 WILD-TYPE 337   4  30  23
D899V11, multiclass
    clus
vv   MAPK9 MUTATED MAPK9 WILD-TYPE
  R0             8             337
  R1             0               4
  R2             1              30
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D899V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MAPK9 MUTATED                                  0     1
  MAPK9 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  MAPK9 MUTATED                           2     5
  MAPK9 WILD-TYPE                        20   221
D899V13, multiclass
                                  clus
vv                                 MAPK9 MUTATED MAPK9 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    2              20
  WHITE                                        5             221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(900) Variable = NRK MUTATION ANALYSIS
D900V1, survival
               sevent
clus2             0   1
  NRK MUTATED    24   3
  NRK WILD-TYPE 354  90
  NRK MUTATED NRK WILD-TYPE 
           27           444 
  NRK MUTATED NRK WILD-TYPE 
            3            90 
$`NRK MUTATED`
TCGA-A6-5661 TCGA-A6-5666 TCGA-A6-6654 TCGA-AA-3496 TCGA-AA-3511 TCGA-AA-3663 
       33.53        32.71        23.87         1.02         6.97         6.97 
TCGA-AA-3672 TCGA-AA-3696 TCGA-AA-3811 TCGA-AA-3966 TCGA-AA-3977 TCGA-AA-A010 
        0.92         5.03        10.06         2.01        25.02        34.98 
TCGA-AU-6004 TCGA-AZ-6600 TCGA-CA-6717 TCGA-CK-4950 TCGA-CK-5913 TCGA-CM-5860 
       27.09        12.10        12.76        85.45        51.32        32.02 
TCGA-CM-5861 TCGA-CM-6171 TCGA-D5-6931 TCGA-AF-6655 TCGA-AG-3742 TCGA-AG-3892 
       15.02        14.04        12.00        20.02         0.99        13.02 
TCGA-AG-A002 TCGA-CI-6624 TCGA-EI-6508 
       20.98         4.73        20.91 

$`NRK WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       22.06        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 
       24.16        21.76        24.69        24.39        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3514 
       20.28         7.04         3.02        35.01        63.98         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
       13.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       36.03         8.05        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
       78.08         6.05        54.02         2.01        14.01        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 
       36.00        85.05        26.99        19.04        19.04        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
       34.03        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 
       22.42        27.42        10.88         0.20        14.50        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 
       12.20        10.06        14.30        17.56       148.01        15.62 
TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       49.08         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       22.03        22.98        30.08         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 
       21.99        14.99        12.99        13.02        15.02        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       11.64         4.80         1.51        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       15.39        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       37.02        32.98         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       17.95        36.95        17.03        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CL-5917 
        0.69         0.72         6.05        33.17         6.97        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       20.55        19.96        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  NRK MUTATED NRK WILD-TYPE 
         0.92          0.00 
  NRK MUTATED NRK WILD-TYPE 
        85.45        148.01 
  NRK MUTATED NRK WILD-TYPE 
       14.040        20.765 
[1] "0.9 - 85.5 (14.0)"  "0.0 - 148.0 (20.8)"
[1] "hr=" "1.3"
D900V2, continuous
D900V3, binary
               cls
clus              0   1
  NRK MUTATED    23   6
  NRK WILD-TYPE 343 113
[1] "tbl2"
               cls
clus            [,1] [,2]
  NRK MUTATED     23    6
  NRK WILD-TYPE  343  113
        clus
vv       NRK MUTATED NRK WILD-TYPE
  COLON           23           343
  RECTUM           6           113
[1] 2 2
[1] FALSE
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NRK MUTATED         7        0        3         7         1         1
  NRK WILD-TYPE      84        1       29       131         9         0
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NRK MUTATED           2          1          3          1        2         0
  NRK WILD-TYPE        22         10         56         41       46        18
               vv
clus            STAGE IVB
  NRK MUTATED           0
  NRK WILD-TYPE         1
D900V4, multiclass
            clus
vv           NRK MUTATED NRK WILD-TYPE
  STAGE I              7            84
  STAGE IA             0             1
  STAGE II             3            29
  STAGE IIA            7           131
  STAGE IIB            1             9
  STAGE IIC            1             0
  STAGE III            2            22
  STAGE IIIA           1            10
  STAGE IIIB           3            56
  STAGE IIIC           1            41
  STAGE IV             2            46
  STAGE IVA            0            18
  STAGE IVB            0             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  NRK MUTATED     2   7  15   5
  NRK WILD-TYPE  15  85 314  45
D900V5, multiclass
    clus
vv   NRK MUTATED NRK WILD-TYPE
  T1           2            15
  T2           7            85
  T3          15           314
  T4           5            45
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2
  NRK MUTATED    20   7   2
  NRK WILD-TYPE 267 106  85
D900V6, multiclass
    clus
vv   NRK MUTATED NRK WILD-TYPE
  N0          20           267
  N1           7           106
  N2           2            85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D900V7, binary
               cls
clus              0   1
  NRK MUTATED    24   2
  NRK WILD-TYPE 351  63
[1] "tbl2"
               cls
clus            [,1] [,2]
  NRK MUTATED     24    2
  NRK WILD-TYPE  351   63
   clus
vv  NRK MUTATED NRK WILD-TYPE
  0          24           351
  1           2            63
[1] 2 2
[1] FALSE
D900V8, binary
               cls
clus              0   1
  NRK MUTATED    18  11
  NRK WILD-TYPE 207 253
[1] "tbl2"
               cls
clus            [,1] [,2]
  NRK MUTATED     18   11
  NRK WILD-TYPE  207  253
        clus
vv       NRK MUTATED NRK WILD-TYPE
  FEMALE          18           207
  MALE            11           253
[1] 2 2
[1] FALSE
D900V9, binary
               cls
clus              0   1
  NRK MUTATED    21   0
  NRK WILD-TYPE 329  22
[1] "tbl2"
               cls
clus            [,1] [,2]
  NRK MUTATED     21    0
  NRK WILD-TYPE  329   22
     clus
vv    NRK MUTATED NRK WILD-TYPE
  NO           21           329
  YES           0            22
[1] 2 2
[1] FALSE
               vv
clus            COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  NRK MUTATED                     21                             2
  NRK WILD-TYPE                  294                            45
               vv
clus            RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  NRK MUTATED                       6                              0
  NRK WILD-TYPE                   100                             10
D900V10, multiclass
                                clus
vv                               NRK MUTATED NRK WILD-TYPE
  COLON ADENOCARCINOMA                    21           294
  COLON MUCINOUS ADENOCARCINOMA            2            45
  RECTAL ADENOCARCINOMA                    6           100
  RECTAL MUCINOUS ADENOCARCINOMA           0            10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             R0  R1  R2  RX
  NRK MUTATED    18   1   1   3
  NRK WILD-TYPE 327   3  30  22
D900V11, multiclass
    clus
vv   NRK MUTATED NRK WILD-TYPE
  R0          18           327
  R1           1             3
  R2           1            30
  RX           3            22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D900V12, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NRK MUTATED                                  0     1
  NRK WILD-TYPE                                1    10
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  NRK MUTATED                           3    12
  NRK WILD-TYPE                        19   214
D900V13, multiclass
                                  clus
vv                                 NRK MUTATED NRK WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      1            10
  BLACK OR AFRICAN AMERICAN                  3            19
  WHITE                                     12           214
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(901) Variable = TMEM131 MUTATION ANALYSIS
D901V1, survival
                   sevent
clus2                 0   1
  TMEM131 MUTATED    17   4
  TMEM131 WILD-TYPE 361  89
  TMEM131 MUTATED TMEM131 WILD-TYPE 
               21               450 
  TMEM131 MUTATED TMEM131 WILD-TYPE 
                4                89 
$`TMEM131 MUTATED`
TCGA-A6-5666 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3672 TCGA-AA-3845 
       32.71         1.02        35.01        63.98         0.92         0.00 
TCGA-AA-3861 TCGA-AY-6197 TCGA-AZ-4682 TCGA-CA-6717 TCGA-CK-4952 TCGA-CM-4743 
       30.05        21.44        22.36        12.76        15.62        23.05 
TCGA-D5-6535 TCGA-D5-6540 TCGA-DM-A0XF TCGA-DM-A28E TCGA-F4-6570 TCGA-F4-6855 
       15.12        16.14        38.20       119.93         6.18        47.41 
TCGA-F4-6856 TCGA-G4-6309 TCGA-AG-3999 
       35.31        85.48        28.04 

$`TMEM131 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        22.06        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3511 
       20.12        19.66        20.28         7.04         3.02         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
       14.01        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
       14.93        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        31.07        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        33.01        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
      106.75        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 
       10.06        14.30        17.56       148.01        85.45        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 
       17.85         4.80        17.13        12.49        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
      119.70        24.43       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
      139.17         6.12        81.37        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 
       98.24         8.61        31.96        35.74        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       19.99        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  TMEM131 MUTATED TMEM131 WILD-TYPE 
                0                 0 
  TMEM131 MUTATED TMEM131 WILD-TYPE 
           119.93            148.01 
  TMEM131 MUTATED TMEM131 WILD-TYPE 
           23.050            20.035 
[1] "0.0 - 119.9 (23.1)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.2"
D901V2, continuous
D901V3, binary
                   cls
clus                  0   1
  TMEM131 MUTATED    21   1
  TMEM131 WILD-TYPE 345 118
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM131 MUTATED     21    1
  TMEM131 WILD-TYPE  345  118
        clus
vv       TMEM131 MUTATED TMEM131 WILD-TYPE
  COLON               21               345
  RECTUM               1               118
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TMEM131 MUTATED         3        0        2         9         0         1
  TMEM131 WILD-TYPE      88        1       30       129        10         0
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TMEM131 MUTATED           1          0          2          3        0
  TMEM131 WILD-TYPE        23         11         57         39       48
                   vv
clus                STAGE IVA STAGE IVB
  TMEM131 MUTATED           1         0
  TMEM131 WILD-TYPE        17         1
D901V4, multiclass
            clus
vv           TMEM131 MUTATED TMEM131 WILD-TYPE
  STAGE I                  3                88
  STAGE IA                 0                 1
  STAGE II                 2                30
  STAGE IIA                9               129
  STAGE IIB                0                10
  STAGE IIC                1                 0
  STAGE III                1                23
  STAGE IIIA               0                11
  STAGE IIIB               2                57
  STAGE IIIC               3                39
  STAGE IV                 0                48
  STAGE IVA                1                17
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  TMEM131 MUTATED     0   3  17   2
  TMEM131 WILD-TYPE  17  89 312  48
D901V5, multiclass
    clus
vv   TMEM131 MUTATED TMEM131 WILD-TYPE
  T1               0                17
  T2               3                89
  T3              17               312
  T4               2                48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  TMEM131 MUTATED    16   3   3
  TMEM131 WILD-TYPE 271 110  84
D901V6, multiclass
    clus
vv   TMEM131 MUTATED TMEM131 WILD-TYPE
  N0              16               271
  N1               3               110
  N2               3                84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D901V7, binary
                   cls
clus                  0   1
  TMEM131 MUTATED    19   1
  TMEM131 WILD-TYPE 356  64
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM131 MUTATED     19    1
  TMEM131 WILD-TYPE  356   64
   clus
vv  TMEM131 MUTATED TMEM131 WILD-TYPE
  0              19               356
  1               1                64
[1] 2 2
[1] FALSE
D901V8, binary
                   cls
clus                  0   1
  TMEM131 MUTATED    12  10
  TMEM131 WILD-TYPE 213 254
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM131 MUTATED     12   10
  TMEM131 WILD-TYPE  213  254
        clus
vv       TMEM131 MUTATED TMEM131 WILD-TYPE
  FEMALE              12               213
  MALE                10               254
[1] 2 2
[1] FALSE
D901V9, binary
                   cls
clus                  0   1
  TMEM131 MUTATED    16   0
  TMEM131 WILD-TYPE 334  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM131 MUTATED     16    0
  TMEM131 WILD-TYPE  334   22
     clus
vv    TMEM131 MUTATED TMEM131 WILD-TYPE
  NO               16               334
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  TMEM131 MUTATED                     16                             4
  TMEM131 WILD-TYPE                  299                            43
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  TMEM131 MUTATED                       1                              0
  TMEM131 WILD-TYPE                   105                             10
D901V10, multiclass
                                clus
vv                               TMEM131 MUTATED TMEM131 WILD-TYPE
  COLON ADENOCARCINOMA                        16               299
  COLON MUCINOUS ADENOCARCINOMA                4                43
  RECTAL ADENOCARCINOMA                        1               105
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  TMEM131 MUTATED    16   0   0   3
  TMEM131 WILD-TYPE 329   4  31  22
D901V11, multiclass
    clus
vv   TMEM131 MUTATED TMEM131 WILD-TYPE
  R0              16               329
  R1               0                 4
  R2               0                31
  RX               3                22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D901V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TMEM131 MUTATED                                  0     1
  TMEM131 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  TMEM131 MUTATED                           1    12
  TMEM131 WILD-TYPE                        21   214
D901V13, multiclass
                                  clus
vv                                 TMEM131 MUTATED TMEM131 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                10
  BLACK OR AFRICAN AMERICAN                      1                21
  WHITE                                         12               214
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(902) Variable = DOCK8 MUTATION ANALYSIS
D902V1, survival
                 sevent
clus2               0   1
  DOCK8 MUTATED    16   4
  DOCK8 WILD-TYPE 362  89
  DOCK8 MUTATED DOCK8 WILD-TYPE 
             20             451 
  DOCK8 MUTATED DOCK8 WILD-TYPE 
              4              89 
$`DOCK8 MUTATED`
TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3815 TCGA-AA-3842 TCGA-AA-3979 TCGA-AA-A010 
       78.08         6.97        33.04        37.02        24.00        34.98 
TCGA-AD-6890 TCGA-AU-6004 TCGA-AY-6197 TCGA-AZ-6598 TCGA-CA-6717 TCGA-CA-6718 
        0.79        27.09        21.44        49.41        12.76        10.06 
TCGA-CM-6167 TCGA-CM-6171 TCGA-D5-5537 TCGA-F4-6570 TCGA-G4-6309 TCGA-G4-6628 
       14.99        14.04        45.40         6.18        85.48        79.69 
TCGA-AG-3893 TCGA-AG-A002 
       35.01        20.98 

$`DOCK8 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 
       20.98        19.99        13.94        19.99        61.02         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       35.05         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       38.99        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        25.02        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       21.37        15.52        56.55         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 
       27.42        10.88         0.20        14.50        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       33.01        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        88.21         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 
        3.06         3.25         3.29         0.07        12.20        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 
       16.04        21.99        12.99        13.02        15.02        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       12.03        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 
      117.07        98.24         8.61        31.96        35.74        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       53.62        44.68        55.04        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       36.95        17.03        13.02        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  DOCK8 MUTATED DOCK8 WILD-TYPE 
           0.79            0.00 
  DOCK8 MUTATED DOCK8 WILD-TYPE 
          85.48          148.01 
  DOCK8 MUTATED DOCK8 WILD-TYPE 
         25.545          20.020 
[1] "0.8 - 85.5 (25.5)"  "0.0 - 148.0 (20.0)"
[1] "hr=" "1.2"
D902V2, continuous
D902V3, binary
                 cls
clus                0   1
  DOCK8 MUTATED    20   2
  DOCK8 WILD-TYPE 346 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DOCK8 MUTATED     20    2
  DOCK8 WILD-TYPE  346  117
        clus
vv       DOCK8 MUTATED DOCK8 WILD-TYPE
  COLON             20             346
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DOCK8 MUTATED         4        0        3         8         1         0
  DOCK8 WILD-TYPE      87        1       29       130         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DOCK8 MUTATED           0          1          2          2        0         0
  DOCK8 WILD-TYPE        24         10         57         40       48        18
                 vv
clus              STAGE IVB
  DOCK8 MUTATED           0
  DOCK8 WILD-TYPE         1
D902V4, multiclass
            clus
vv           DOCK8 MUTATED DOCK8 WILD-TYPE
  STAGE I                4              87
  STAGE IA               0               1
  STAGE II               3              29
  STAGE IIA              8             130
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             1              10
  STAGE IIIB             2              57
  STAGE IIIC             2              40
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  DOCK8 MUTATED     1   5  15   1
  DOCK8 WILD-TYPE  16  87 314  49
D902V5, multiclass
    clus
vv   DOCK8 MUTATED DOCK8 WILD-TYPE
  T1             1              16
  T2             5              87
  T3            15             314
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  DOCK8 MUTATED    16   3   3
  DOCK8 WILD-TYPE 271 110  84
D902V6, multiclass
    clus
vv   DOCK8 MUTATED DOCK8 WILD-TYPE
  N0            16             271
  N1             3             110
  N2             3              84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D902V7, binary
                 cls
clus                0   1
  DOCK8 MUTATED    17   0
  DOCK8 WILD-TYPE 358  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DOCK8 MUTATED     17    0
  DOCK8 WILD-TYPE  358   65
   clus
vv  DOCK8 MUTATED DOCK8 WILD-TYPE
  0            17             358
  1             0              65
[1] 2 2
[1] FALSE
D902V8, binary
                 cls
clus                0   1
  DOCK8 MUTATED    10  12
  DOCK8 WILD-TYPE 215 252
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DOCK8 MUTATED     10   12
  DOCK8 WILD-TYPE  215  252
        clus
vv       DOCK8 MUTATED DOCK8 WILD-TYPE
  FEMALE            10             215
  MALE              12             252
[1] 2 2
[1] FALSE
D902V9, binary
                 cls
clus                0   1
  DOCK8 MUTATED    18   0
  DOCK8 WILD-TYPE 332  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DOCK8 MUTATED     18    0
  DOCK8 WILD-TYPE  332   22
     clus
vv    DOCK8 MUTATED DOCK8 WILD-TYPE
  NO             18             332
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  DOCK8 MUTATED                     18                             2
  DOCK8 WILD-TYPE                  297                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  DOCK8 MUTATED                       2                              0
  DOCK8 WILD-TYPE                   104                             10
D902V10, multiclass
                                clus
vv                               DOCK8 MUTATED DOCK8 WILD-TYPE
  COLON ADENOCARCINOMA                      18             297
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  DOCK8 MUTATED    17   0   0   3
  DOCK8 WILD-TYPE 328   4  31  22
D902V11, multiclass
    clus
vv   DOCK8 MUTATED DOCK8 WILD-TYPE
  R0            17             328
  R1             0               4
  R2             0              31
  RX             3              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D902V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DOCK8 MUTATED                                  0     2
  DOCK8 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  DOCK8 MUTATED                           2     9
  DOCK8 WILD-TYPE                        20   217
D902V13, multiclass
                                  clus
vv                                 DOCK8 MUTATED DOCK8 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               9
  BLACK OR AFRICAN AMERICAN                    2              20
  WHITE                                        9             217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(903) Variable = FLNB MUTATION ANALYSIS
D903V1, survival
                sevent
clus2              0   1
  FLNB MUTATED    25   5
  FLNB WILD-TYPE 353  88
  FLNB MUTATED FLNB WILD-TYPE 
            30            441 
  FLNB MUTATED FLNB WILD-TYPE 
             5             88 
$`FLNB MUTATED`
TCGA-A6-5661 TCGA-A6-6138 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3492 
       33.53        22.52        24.39        20.12        19.66         3.02 
TCGA-AA-3516 TCGA-AA-3663 TCGA-AA-3713 TCGA-AA-3864 TCGA-AA-3877 TCGA-AA-A00A 
       13.02         6.97        19.04        53.00        31.00        38.04 
TCGA-AA-A00J TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01T 
       18.05         4.01        34.98         1.02        35.01        33.04 
TCGA-AD-6889 TCGA-AU-6004 TCGA-AY-6197 TCGA-CA-6717 TCGA-CK-5916 TCGA-CM-4746 
       56.55        27.09        21.44        12.76        21.14        37.02 
TCGA-D5-6920 TCGA-DM-A1D4 TCGA-G4-6588 TCGA-AG-A002 TCGA-EF-5830 TCGA-G5-6641 
        3.68        92.75        26.17        20.98         0.49        26.43 

$`FLNB WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       22.06        32.71        27.09         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6782 TCGA-AA-3489 
       24.16        21.76        24.69        23.87        20.28         7.04 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        1.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        31.07        30.05        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       29.98        18.05         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K 
       27.02        13.94        19.00        30.02        34.03        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       31.00        38.07         1.02        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       21.37        15.52         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 
       27.42        10.88         0.20        14.50        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       33.01        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       49.08        51.32         9.99        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       23.05        20.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
       15.58         1.48         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D6 
       10.26       119.70        24.43        38.20       130.65        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       24.13        51.48        32.61        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
        0.66         0.69        55.76 

  FLNB MUTATED FLNB WILD-TYPE 
          0.49           0.00 
  FLNB MUTATED FLNB WILD-TYPE 
         92.75         148.01 
  FLNB MUTATED FLNB WILD-TYPE 
         21.98          20.02 
[1] "0.5 - 92.8 (22.0)"  "0.0 - 148.0 (20.0)"
[1] "hr=" "1.1"
D903V2, continuous
D903V3, binary
                cls
clus               0   1
  FLNB MUTATED    28   3
  FLNB WILD-TYPE 338 116
[1] "tbl2"
                cls
clus             [,1] [,2]
  FLNB MUTATED     28    3
  FLNB WILD-TYPE  338  116
        clus
vv       FLNB MUTATED FLNB WILD-TYPE
  COLON            28            338
  RECTUM            3            116
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FLNB MUTATED         7        0        5         9         3         0
  FLNB WILD-TYPE      84        1       27       129         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  FLNB MUTATED           3          1          1          1        1         0
  FLNB WILD-TYPE        21         10         58         41       47        18
                vv
clus             STAGE IVB
  FLNB MUTATED           0
  FLNB WILD-TYPE         1
D903V4, multiclass
            clus
vv           FLNB MUTATED FLNB WILD-TYPE
  STAGE I               7             84
  STAGE IA              0              1
  STAGE II              5             27
  STAGE IIA             9            129
  STAGE IIB             3              7
  STAGE IIC             0              1
  STAGE III             3             21
  STAGE IIIA            1             10
  STAGE IIIB            1             58
  STAGE IIIC            1             41
  STAGE IV              1             47
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  FLNB MUTATED     3   5  17   6
  FLNB WILD-TYPE  14  87 312  44
D903V5, multiclass
    clus
vv   FLNB MUTATED FLNB WILD-TYPE
  T1            3             14
  T2            5             87
  T3           17            312
  T4            6             44
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  FLNB MUTATED    25   4   2
  FLNB WILD-TYPE 262 109  85
D903V6, multiclass
    clus
vv   FLNB MUTATED FLNB WILD-TYPE
  N0           25            262
  N1            4            109
  N2            2             85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D903V7, binary
                cls
clus               0   1
  FLNB MUTATED    26   1
  FLNB WILD-TYPE 349  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  FLNB MUTATED     26    1
  FLNB WILD-TYPE  349   64
   clus
vv  FLNB MUTATED FLNB WILD-TYPE
  0           26            349
  1            1             64
[1] 2 2
[1] FALSE
D903V8, binary
                cls
clus               0   1
  FLNB MUTATED    12  19
  FLNB WILD-TYPE 213 245
[1] "tbl2"
                cls
clus             [,1] [,2]
  FLNB MUTATED     12   19
  FLNB WILD-TYPE  213  245
        clus
vv       FLNB MUTATED FLNB WILD-TYPE
  FEMALE           12            213
  MALE             19            245
[1] 2 2
[1] FALSE
D903V9, binary
                cls
clus               0   1
  FLNB MUTATED    21   2
  FLNB WILD-TYPE 329  20
[1] "tbl2"
                cls
clus             [,1] [,2]
  FLNB MUTATED     21    2
  FLNB WILD-TYPE  329   20
     clus
vv    FLNB MUTATED FLNB WILD-TYPE
  NO            21            329
  YES            2             20
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  FLNB MUTATED                     20                             8
  FLNB WILD-TYPE                  295                            39
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  FLNB MUTATED                       2                              1
  FLNB WILD-TYPE                   104                              9
D903V10, multiclass
                                clus
vv                               FLNB MUTATED FLNB WILD-TYPE
  COLON ADENOCARCINOMA                     20            295
  COLON MUCINOUS ADENOCARCINOMA             8             39
  RECTAL ADENOCARCINOMA                     2            104
  RECTAL MUCINOUS ADENOCARCINOMA            1              9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  FLNB MUTATED    22   0   1   2
  FLNB WILD-TYPE 323   4  30  23
D903V11, multiclass
    clus
vv   FLNB MUTATED FLNB WILD-TYPE
  R0           22            323
  R1            0              4
  R2            1             30
  RX            2             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D903V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FLNB MUTATED                                  0     2
  FLNB WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  FLNB MUTATED                           2    12
  FLNB WILD-TYPE                        20   214
D903V13, multiclass
                                  clus
vv                                 FLNB MUTATED FLNB WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              9
  BLACK OR AFRICAN AMERICAN                   2             20
  WHITE                                      12            214
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(904) Variable = PTTG1IP MUTATION ANALYSIS
D904V1, survival
                   sevent
clus2                 0   1
  PTTG1IP MUTATED     6   1
  PTTG1IP WILD-TYPE 372  92
  PTTG1IP MUTATED PTTG1IP WILD-TYPE 
                7               464 
  PTTG1IP MUTATED PTTG1IP WILD-TYPE 
                1                92 
$`PTTG1IP MUTATED`
TCGA-AA-3510 TCGA-CA-5255 TCGA-D5-6539 TCGA-DM-A1DB TCGA-G4-6304 TCGA-G4-6588 
       63.98         3.06        12.49        44.32        53.62        26.17 
TCGA-G4-6628 
       79.69 

$`PTTG1IP WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        3.19         1.61        12.69         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
        4.80        17.13        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
       12.59       140.38         7.50       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 
       22.09        13.78        35.80        91.79        46.75        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  PTTG1IP MUTATED PTTG1IP WILD-TYPE 
             3.06              0.00 
  PTTG1IP MUTATED PTTG1IP WILD-TYPE 
            79.69            148.01 
  PTTG1IP MUTATED PTTG1IP WILD-TYPE 
           44.320            20.085 
[1] "3.1 - 79.7 (44.3)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "2.3"
D904V2, continuous
D904V3, binary
                   cls
clus                  0   1
  PTTG1IP MUTATED     7   0
  PTTG1IP WILD-TYPE 359 119
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PTTG1IP MUTATED      7    0
  PTTG1IP WILD-TYPE  359  119
        clus
vv       PTTG1IP MUTATED PTTG1IP WILD-TYPE
  COLON                7               359
  RECTUM               0               119
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PTTG1IP MUTATED         1        0        1         3         1         0
  PTTG1IP WILD-TYPE      90        1       31       135         9         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PTTG1IP MUTATED           0          1          0          0        0
  PTTG1IP WILD-TYPE        24         10         59         42       48
                   vv
clus                STAGE IVA STAGE IVB
  PTTG1IP MUTATED           0         0
  PTTG1IP WILD-TYPE        18         1
D904V4, multiclass
            clus
vv           PTTG1IP MUTATED PTTG1IP WILD-TYPE
  STAGE I                  1                90
  STAGE IA                 0                 1
  STAGE II                 1                31
  STAGE IIA                3               135
  STAGE IIB                1                 9
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               1                10
  STAGE IIIB               0                59
  STAGE IIIC               0                42
  STAGE IV                 0                48
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  PTTG1IP MUTATED     0   1   5   1
  PTTG1IP WILD-TYPE  17  91 324  49
D904V5, multiclass
    clus
vv   PTTG1IP MUTATED PTTG1IP WILD-TYPE
  T1               0                17
  T2               1                91
  T3               5               324
  T4               1                49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  PTTG1IP MUTATED     7   0   0
  PTTG1IP WILD-TYPE 280 113  87
D904V6, multiclass
    clus
vv   PTTG1IP MUTATED PTTG1IP WILD-TYPE
  N0               7               280
  N1               0               113
  N2               0                87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D904V7, binary
                   cls
clus                  0   1
  PTTG1IP MUTATED     7   0
  PTTG1IP WILD-TYPE 368  65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PTTG1IP MUTATED      7    0
  PTTG1IP WILD-TYPE  368   65
   clus
vv  PTTG1IP MUTATED PTTG1IP WILD-TYPE
  0               7               368
  1               0                65
[1] 2 2
[1] FALSE
D904V8, binary
                   cls
clus                  0   1
  PTTG1IP MUTATED     3   4
  PTTG1IP WILD-TYPE 222 260
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PTTG1IP MUTATED      3    4
  PTTG1IP WILD-TYPE  222  260
        clus
vv       PTTG1IP MUTATED PTTG1IP WILD-TYPE
  FEMALE               3               222
  MALE                 4               260
[1] 2 2
[1] FALSE
D904V9, binary
                   cls
clus                  0   1
  PTTG1IP MUTATED     5   1
  PTTG1IP WILD-TYPE 345  21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PTTG1IP MUTATED      5    1
  PTTG1IP WILD-TYPE  345   21
     clus
vv    PTTG1IP MUTATED PTTG1IP WILD-TYPE
  NO                5               345
  YES               1                21
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PTTG1IP MUTATED                      7                             0
  PTTG1IP WILD-TYPE                  308                            47
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PTTG1IP MUTATED                       0                              0
  PTTG1IP WILD-TYPE                   106                             10
D904V10, multiclass
                                clus
vv                               PTTG1IP MUTATED PTTG1IP WILD-TYPE
  COLON ADENOCARCINOMA                         7               308
  COLON MUCINOUS ADENOCARCINOMA                0                47
  RECTAL ADENOCARCINOMA                        0               106
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  PTTG1IP MUTATED     5   0   0   1
  PTTG1IP WILD-TYPE 340   4  31  24
D904V11, multiclass
    clus
vv   PTTG1IP MUTATED PTTG1IP WILD-TYPE
  R0               5               340
  R1               0                 4
  R2               0                31
  RX               1                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D904V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PTTG1IP MUTATED                                  0     1
  PTTG1IP WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  PTTG1IP MUTATED                           0     5
  PTTG1IP WILD-TYPE                        22   221
D904V13, multiclass
                                  clus
vv                                 PTTG1IP MUTATED PTTG1IP WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                10
  BLACK OR AFRICAN AMERICAN                      0                22
  WHITE                                          5               221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(905) Variable = FUCA2 MUTATION ANALYSIS
D905V1, survival
                 sevent
clus2               0   1
  FUCA2 MUTATED     3   2
  FUCA2 WILD-TYPE 375  91
  FUCA2 MUTATED FUCA2 WILD-TYPE 
              5             466 
  FUCA2 MUTATED FUCA2 WILD-TYPE 
              2              91 
$`FUCA2 MUTATED`
TCGA-AZ-6608 TCGA-CA-6718 TCGA-CK-4948 TCGA-D5-6539 TCGA-DY-A0XA 
        1.61        10.06       148.01        12.49       126.44 

$`FUCA2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
       11.74         3.19        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 
        0.07        12.20        12.76        14.30        17.56        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       17.13        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        4.01         5.03         5.29        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  FUCA2 MUTATED FUCA2 WILD-TYPE 
           1.61            0.00 
  FUCA2 MUTATED FUCA2 WILD-TYPE 
         148.01          140.38 
  FUCA2 MUTATED FUCA2 WILD-TYPE 
         12.490          20.235 
[1] "1.6 - 148.0 (12.5)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.2"
D905V2, continuous
D905V3, binary
                 cls
clus                0   1
  FUCA2 MUTATED     4   1
  FUCA2 WILD-TYPE 362 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FUCA2 MUTATED      4    1
  FUCA2 WILD-TYPE  362  118
        clus
vv       FUCA2 MUTATED FUCA2 WILD-TYPE
  COLON              4             362
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FUCA2 MUTATED         0        0        0         2         0         0
  FUCA2 WILD-TYPE      91        1       32       136        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  FUCA2 MUTATED           1          2          0          0        0         0
  FUCA2 WILD-TYPE        23          9         59         42       48        18
                 vv
clus              STAGE IVB
  FUCA2 MUTATED           0
  FUCA2 WILD-TYPE         1
D905V4, multiclass
            clus
vv           FUCA2 MUTATED FUCA2 WILD-TYPE
  STAGE I                0              91
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              2             136
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             2               9
  STAGE IIIB             0              59
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  FUCA2 MUTATED     0   1   4   0
  FUCA2 WILD-TYPE  17  91 325  50
D905V5, multiclass
    clus
vv   FUCA2 MUTATED FUCA2 WILD-TYPE
  T1             0              17
  T2             1              91
  T3             4             325
  T4             0              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  FUCA2 MUTATED     3   2   0
  FUCA2 WILD-TYPE 284 111  87
D905V6, multiclass
    clus
vv   FUCA2 MUTATED FUCA2 WILD-TYPE
  N0             3             284
  N1             2             111
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D905V7, binary
                 cls
clus                0   1
  FUCA2 MUTATED     5   0
  FUCA2 WILD-TYPE 370  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FUCA2 MUTATED      5    0
  FUCA2 WILD-TYPE  370   65
   clus
vv  FUCA2 MUTATED FUCA2 WILD-TYPE
  0             5             370
  1             0              65
[1] 2 2
[1] FALSE
D905V8, binary
                 cls
clus                0   1
  FUCA2 MUTATED     4   1
  FUCA2 WILD-TYPE 221 263
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FUCA2 MUTATED      4    1
  FUCA2 WILD-TYPE  221  263
        clus
vv       FUCA2 MUTATED FUCA2 WILD-TYPE
  FEMALE             4             221
  MALE               1             263
[1] 2 2
[1] FALSE
D905V9, binary
                 cls
clus                0   1
  FUCA2 MUTATED     4   0
  FUCA2 WILD-TYPE 346  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FUCA2 MUTATED      4    0
  FUCA2 WILD-TYPE  346   22
     clus
vv    FUCA2 MUTATED FUCA2 WILD-TYPE
  NO              4             346
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  FUCA2 MUTATED                      4                             0
  FUCA2 WILD-TYPE                  311                            47
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  FUCA2 MUTATED                       1                              0
  FUCA2 WILD-TYPE                   105                             10
D905V10, multiclass
                                clus
vv                               FUCA2 MUTATED FUCA2 WILD-TYPE
  COLON ADENOCARCINOMA                       4             311
  COLON MUCINOUS ADENOCARCINOMA              0              47
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  FUCA2 MUTATED     2   0   0   1
  FUCA2 WILD-TYPE 343   4  31  24
D905V11, multiclass
    clus
vv   FUCA2 MUTATED FUCA2 WILD-TYPE
  R0             2             343
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D905V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FUCA2 MUTATED                                  0     1
  FUCA2 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  FUCA2 MUTATED                           0     4
  FUCA2 WILD-TYPE                        22   222
D905V13, multiclass
                                  clus
vv                                 FUCA2 MUTATED FUCA2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        4             222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(906) Variable = VN1R4 MUTATION ANALYSIS
D906V1, survival
                 sevent
clus2               0   1
  VN1R4 MUTATED     7   1
  VN1R4 WILD-TYPE 371  92
  VN1R4 MUTATED VN1R4 WILD-TYPE 
              8             463 
  VN1R4 MUTATED VN1R4 WILD-TYPE 
              1              92 
$`VN1R4 MUTATED`
TCGA-AA-3815 TCGA-AA-A010 TCGA-AZ-6601 TCGA-CA-6717 TCGA-CK-4952 TCGA-CM-5348 
       33.04        34.98       100.01        12.76        15.62        22.98 
TCGA-DT-5265 TCGA-F5-6811 
        5.29        32.19 

$`VN1R4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       19.04        10.06        35.05         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
       12.10        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 
       10.06        14.30        17.56       148.01        85.45        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.03        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       49.51        31.30        28.57         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  VN1R4 MUTATED VN1R4 WILD-TYPE 
           5.29            0.00 
  VN1R4 MUTATED VN1R4 WILD-TYPE 
         100.01          148.01 
  VN1R4 MUTATED VN1R4 WILD-TYPE 
         27.585          20.120 
[1] "5.3 - 100.0 (27.6)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.8"
D906V2, continuous
D906V3, binary
                 cls
clus                0   1
  VN1R4 MUTATED     6   2
  VN1R4 WILD-TYPE 360 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VN1R4 MUTATED      6    2
  VN1R4 WILD-TYPE  360  117
        clus
vv       VN1R4 MUTATED VN1R4 WILD-TYPE
  COLON              6             360
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  VN1R4 MUTATED         0        0        2         3         1         0
  VN1R4 WILD-TYPE      91        1       30       135         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  VN1R4 MUTATED           0          0          1          1        0         0
  VN1R4 WILD-TYPE        24         11         58         41       48        18
                 vv
clus              STAGE IVB
  VN1R4 MUTATED           0
  VN1R4 WILD-TYPE         1
D906V4, multiclass
            clus
vv           VN1R4 MUTATED VN1R4 WILD-TYPE
  STAGE I                0              91
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA              3             135
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             1              41
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  VN1R4 MUTATED     0   0   6   2
  VN1R4 WILD-TYPE  17  92 323  48
D906V5, multiclass
    clus
vv   VN1R4 MUTATED VN1R4 WILD-TYPE
  T1             0              17
  T2             0              92
  T3             6             323
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  VN1R4 MUTATED     6   1   1
  VN1R4 WILD-TYPE 281 112  86
D906V6, multiclass
    clus
vv   VN1R4 MUTATED VN1R4 WILD-TYPE
  N0             6             281
  N1             1             112
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D906V7, binary
                 cls
clus                0   1
  VN1R4 MUTATED     8   0
  VN1R4 WILD-TYPE 367  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VN1R4 MUTATED      8    0
  VN1R4 WILD-TYPE  367   65
   clus
vv  VN1R4 MUTATED VN1R4 WILD-TYPE
  0             8             367
  1             0              65
[1] 2 2
[1] FALSE
D906V8, binary
                 cls
clus                0   1
  VN1R4 MUTATED     4   4
  VN1R4 WILD-TYPE 221 260
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VN1R4 MUTATED      4    4
  VN1R4 WILD-TYPE  221  260
        clus
vv       VN1R4 MUTATED VN1R4 WILD-TYPE
  FEMALE             4             221
  MALE               4             260
[1] 2 2
[1] FALSE
D906V9, binary
                 cls
clus                0   1
  VN1R4 MUTATED     7   0
  VN1R4 WILD-TYPE 343  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VN1R4 MUTATED      7    0
  VN1R4 WILD-TYPE  343   22
     clus
vv    VN1R4 MUTATED VN1R4 WILD-TYPE
  NO              7             343
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  VN1R4 MUTATED                      4                             2
  VN1R4 WILD-TYPE                  311                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  VN1R4 MUTATED                       1                              1
  VN1R4 WILD-TYPE                   105                              9
D906V10, multiclass
                                clus
vv                               VN1R4 MUTATED VN1R4 WILD-TYPE
  COLON ADENOCARCINOMA                       4             311
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             1               9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  VN1R4 MUTATED     3   0   0   3
  VN1R4 WILD-TYPE 342   4  31  22
D906V11, multiclass
    clus
vv   VN1R4 MUTATED VN1R4 WILD-TYPE
  R0             3             342
  R1             0               4
  R2             0              31
  RX             3              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D906V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  VN1R4 MUTATED                                  0     2
  VN1R4 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  VN1R4 MUTATED                           0     4
  VN1R4 WILD-TYPE                        22   222
D906V13, multiclass
                                  clus
vv                                 VN1R4 MUTATED VN1R4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               9
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        4             222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(907) Variable = ARFIP1 MUTATION ANALYSIS
D907V1, survival
                  sevent
clus2                0   1
  ARFIP1 MUTATED     9   3
  ARFIP1 WILD-TYPE 369  90
  ARFIP1 MUTATED ARFIP1 WILD-TYPE 
              12              459 
  ARFIP1 MUTATED ARFIP1 WILD-TYPE 
               3               90 
$`ARFIP1 MUTATED`
TCGA-A6-5657 TCGA-AA-3518 TCGA-AA-3558 TCGA-AA-3975 TCGA-AA-A00N TCGA-AA-A01P 
       31.63         1.02        20.98        34.06         4.01        38.07 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-4743 TCGA-G4-6588 
       17.82        58.39        12.76        10.06        23.05        26.17 

$`ARFIP1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3561 
       24.00        17.95        29.95        23.01        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01Q 
       10.98        32.02        12.00        31.00        31.00         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AZ-4323 TCGA-AZ-4616 
       16.31         0.95        33.01        21.44         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       12.20        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
      124.27        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       22.09        13.78        35.80        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  ARFIP1 MUTATED ARFIP1 WILD-TYPE 
            1.02             0.00 
  ARFIP1 MUTATED ARFIP1 WILD-TYPE 
           58.39           148.01 
  ARFIP1 MUTATED ARFIP1 WILD-TYPE 
          22.015           20.120 
[1] "1.0 - 58.4 (22.0)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.5"
D907V2, continuous
D907V3, binary
                  cls
clus                 0   1
  ARFIP1 MUTATED    12   0
  ARFIP1 WILD-TYPE 354 119
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARFIP1 MUTATED     12    0
  ARFIP1 WILD-TYPE  354  119
        clus
vv       ARFIP1 MUTATED ARFIP1 WILD-TYPE
  COLON              12              354
  RECTUM              0              119
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ARFIP1 MUTATED         2        0        0         6         1         0
  ARFIP1 WILD-TYPE      89        1       32       132         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ARFIP1 MUTATED           1          0          2          0        0
  ARFIP1 WILD-TYPE        23         11         57         42       48
                  vv
clus               STAGE IVA STAGE IVB
  ARFIP1 MUTATED           0         0
  ARFIP1 WILD-TYPE        18         1
D907V4, multiclass
            clus
vv           ARFIP1 MUTATED ARFIP1 WILD-TYPE
  STAGE I                 2               89
  STAGE IA                0                1
  STAGE II                0               32
  STAGE IIA               6              132
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               1               23
  STAGE IIIA              0               11
  STAGE IIIB              2               57
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ARFIP1 MUTATED     0   2   9   1
  ARFIP1 WILD-TYPE  17  90 320  49
D907V5, multiclass
    clus
vv   ARFIP1 MUTATED ARFIP1 WILD-TYPE
  T1              0               17
  T2              2               90
  T3              9              320
  T4              1               49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  ARFIP1 MUTATED     9   3   0
  ARFIP1 WILD-TYPE 278 110  87
D907V6, multiclass
    clus
vv   ARFIP1 MUTATED ARFIP1 WILD-TYPE
  N0              9              278
  N1              3              110
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D907V7, binary
                  cls
clus                 0   1
  ARFIP1 MUTATED    12   0
  ARFIP1 WILD-TYPE 363  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARFIP1 MUTATED     12    0
  ARFIP1 WILD-TYPE  363   65
   clus
vv  ARFIP1 MUTATED ARFIP1 WILD-TYPE
  0             12              363
  1              0               65
[1] 2 2
[1] FALSE
D907V8, binary
                  cls
clus                 0   1
  ARFIP1 MUTATED     4   8
  ARFIP1 WILD-TYPE 221 256
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARFIP1 MUTATED      4    8
  ARFIP1 WILD-TYPE  221  256
        clus
vv       ARFIP1 MUTATED ARFIP1 WILD-TYPE
  FEMALE              4              221
  MALE                8              256
[1] 2 2
[1] FALSE
D907V9, binary
                  cls
clus                 0   1
  ARFIP1 MUTATED    10   0
  ARFIP1 WILD-TYPE 340  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARFIP1 MUTATED     10    0
  ARFIP1 WILD-TYPE  340   22
     clus
vv    ARFIP1 MUTATED ARFIP1 WILD-TYPE
  NO              10              340
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ARFIP1 MUTATED                     10                             2
  ARFIP1 WILD-TYPE                  305                            45
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ARFIP1 MUTATED                       0                              0
  ARFIP1 WILD-TYPE                   106                             10
D907V10, multiclass
                                clus
vv                               ARFIP1 MUTATED ARFIP1 WILD-TYPE
  COLON ADENOCARCINOMA                       10              305
  COLON MUCINOUS ADENOCARCINOMA               2               45
  RECTAL ADENOCARCINOMA                       0              106
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ARFIP1 MUTATED     9   0   1   2
  ARFIP1 WILD-TYPE 336   4  30  23
D907V11, multiclass
    clus
vv   ARFIP1 MUTATED ARFIP1 WILD-TYPE
  R0              9              336
  R1              0                4
  R2              1               30
  RX              2               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D907V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ARFIP1 MUTATED                                  0     2
  ARFIP1 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ARFIP1 MUTATED                           2     3
  ARFIP1 WILD-TYPE                        20   223
D907V13, multiclass
                                  clus
vv                                 ARFIP1 MUTATED ARFIP1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                9
  BLACK OR AFRICAN AMERICAN                     2               20
  WHITE                                         3              223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(908) Variable = UPF2 MUTATION ANALYSIS
D908V1, survival
                sevent
clus2              0   1
  UPF2 MUTATED    13   5
  UPF2 WILD-TYPE 365  88
  UPF2 MUTATED UPF2 WILD-TYPE 
            18            453 
  UPF2 MUTATED UPF2 WILD-TYPE 
             5             88 
$`UPF2 MUTATED`
TCGA-A6-2676 TCGA-A6-5661 TCGA-A6-5665 TCGA-AA-3525 TCGA-AA-3662 TCGA-AA-3713 
       42.90        33.53        22.06         8.05         6.05        19.04 
TCGA-AA-3818 TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A02Y TCGA-AZ-4315 TCGA-AZ-6601 
        0.99        25.02         4.01        39.98        58.39       100.01 
TCGA-CA-6717 TCGA-CK-5916 TCGA-CM-6162 TCGA-AG-3892 TCGA-AG-A002 TCGA-F5-6812 
       12.76        21.14        12.00        13.02        20.98         0.66 

$`UPF2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 
       31.63        30.44        29.19        23.61        22.09        32.71 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       27.09        22.52         8.38        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       24.03        37.05        36.03        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       61.02        78.08         6.97        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3819 TCGA-AA-3821 
       19.04        10.06        35.05        33.04        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A03F 
        2.01         5.03        14.01         0.92        41.00        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 
       88.21        49.41         6.77        12.10        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07        12.20        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       15.02         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 
       19.99         1.02        17.95        36.95        17.03        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  UPF2 MUTATED UPF2 WILD-TYPE 
          0.66           0.00 
  UPF2 MUTATED UPF2 WILD-TYPE 
        100.01         148.01 
  UPF2 MUTATED UPF2 WILD-TYPE 
         20.01          20.19 
[1] "0.7 - 100.0 (20.0)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.5"
D908V2, continuous
D908V3, binary
                cls
clus               0   1
  UPF2 MUTATED    16   3
  UPF2 WILD-TYPE 350 116
[1] "tbl2"
                cls
clus             [,1] [,2]
  UPF2 MUTATED     16    3
  UPF2 WILD-TYPE  350  116
        clus
vv       UPF2 MUTATED UPF2 WILD-TYPE
  COLON            16            350
  RECTUM            3            116
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  UPF2 MUTATED         4        0        1         6         3         0
  UPF2 WILD-TYPE      87        1       31       132         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  UPF2 MUTATED           0          0          2          0        2         0
  UPF2 WILD-TYPE        24         11         57         42       46        18
                vv
clus             STAGE IVB
  UPF2 MUTATED           0
  UPF2 WILD-TYPE         1
D908V4, multiclass
            clus
vv           UPF2 MUTATED UPF2 WILD-TYPE
  STAGE I               4             87
  STAGE IA              0              1
  STAGE II              1             31
  STAGE IIA             6            132
  STAGE IIB             3              7
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            2             57
  STAGE IIIC            0             42
  STAGE IV              2             46
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  UPF2 MUTATED     2   3  10   4
  UPF2 WILD-TYPE  15  89 319  46
D908V5, multiclass
    clus
vv   UPF2 MUTATED UPF2 WILD-TYPE
  T1            2             15
  T2            3             89
  T3           10            319
  T4            4             46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  UPF2 MUTATED    16   2   1
  UPF2 WILD-TYPE 271 111  86
D908V6, multiclass
    clus
vv   UPF2 MUTATED UPF2 WILD-TYPE
  N0           16            271
  N1            2            111
  N2            1             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D908V7, binary
                cls
clus               0   1
  UPF2 MUTATED    15   2
  UPF2 WILD-TYPE 360  63
[1] "tbl2"
                cls
clus             [,1] [,2]
  UPF2 MUTATED     15    2
  UPF2 WILD-TYPE  360   63
   clus
vv  UPF2 MUTATED UPF2 WILD-TYPE
  0           15            360
  1            2             63
[1] 2 2
[1] FALSE
D908V8, binary
                cls
clus               0   1
  UPF2 MUTATED     9  10
  UPF2 WILD-TYPE 216 254
[1] "tbl2"
                cls
clus             [,1] [,2]
  UPF2 MUTATED      9   10
  UPF2 WILD-TYPE  216  254
        clus
vv       UPF2 MUTATED UPF2 WILD-TYPE
  FEMALE            9            216
  MALE             10            254
[1] 2 2
[1] FALSE
D908V9, binary
                cls
clus               0   1
  UPF2 MUTATED    14   1
  UPF2 WILD-TYPE 336  21
[1] "tbl2"
                cls
clus             [,1] [,2]
  UPF2 MUTATED     14    1
  UPF2 WILD-TYPE  336   21
     clus
vv    UPF2 MUTATED UPF2 WILD-TYPE
  NO            14            336
  YES            1             21
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  UPF2 MUTATED                     13                             3
  UPF2 WILD-TYPE                  302                            44
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  UPF2 MUTATED                       3                              0
  UPF2 WILD-TYPE                   103                             10
D908V10, multiclass
                                clus
vv                               UPF2 MUTATED UPF2 WILD-TYPE
  COLON ADENOCARCINOMA                     13            302
  COLON MUCINOUS ADENOCARCINOMA             3             44
  RECTAL ADENOCARCINOMA                     3            103
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  UPF2 MUTATED    12   0   2   3
  UPF2 WILD-TYPE 333   4  29  22
D908V11, multiclass
    clus
vv   UPF2 MUTATED UPF2 WILD-TYPE
  R0           12            333
  R1            0              4
  R2            2             29
  RX            3             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D908V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  UPF2 MUTATED                                  0     1
  UPF2 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  UPF2 MUTATED                           1     8
  UPF2 WILD-TYPE                        21   218
D908V13, multiclass
                                  clus
vv                                 UPF2 MUTATED UPF2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                       8            218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(909) Variable = DCUN1D3 MUTATION ANALYSIS
D909V1, survival
                   sevent
clus2                 0   1
  DCUN1D3 MUTATED     6   1
  DCUN1D3 WILD-TYPE 372  92
  DCUN1D3 MUTATED DCUN1D3 WILD-TYPE 
                7               464 
  DCUN1D3 MUTATED DCUN1D3 WILD-TYPE 
                1                92 
$`DCUN1D3 MUTATED`
TCGA-A6-6649 TCGA-AA-3554 TCGA-AA-A00A TCGA-CM-5864 TCGA-CM-6171 TCGA-DM-A1DB 
       24.16        17.95        38.04        15.02        14.04        44.32 
TCGA-F5-6811 
       32.19 

$`DCUN1D3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.08        25.18        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       13.02        24.00        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00D 
       27.02        19.07         7.96        27.02        13.94        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
       15.02         5.03        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       13.02        15.02        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
        7.50       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6812 TCGA-F5-6813 
        9.96        49.51        31.30        28.57         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  DCUN1D3 MUTATED DCUN1D3 WILD-TYPE 
            14.04              0.00 
  DCUN1D3 MUTATED DCUN1D3 WILD-TYPE 
            44.32            148.01 
  DCUN1D3 MUTATED DCUN1D3 WILD-TYPE 
           24.160            20.155 
[1] "14.0 - 44.3 (24.2)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.4"
D909V2, continuous
D909V3, binary
                   cls
clus                  0   1
  DCUN1D3 MUTATED     6   1
  DCUN1D3 WILD-TYPE 360 118
[1] "tbl2"
                   cls
clus                [,1] [,2]
  DCUN1D3 MUTATED      6    1
  DCUN1D3 WILD-TYPE  360  118
        clus
vv       DCUN1D3 MUTATED DCUN1D3 WILD-TYPE
  COLON                6               360
  RECTUM               1               118
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DCUN1D3 MUTATED         2        0        0         4         0         0
  DCUN1D3 WILD-TYPE      89        1       32       134        10         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DCUN1D3 MUTATED           0          0          1          0        0
  DCUN1D3 WILD-TYPE        24         11         58         42       48
                   vv
clus                STAGE IVA STAGE IVB
  DCUN1D3 MUTATED           0         0
  DCUN1D3 WILD-TYPE        18         1
D909V4, multiclass
            clus
vv           DCUN1D3 MUTATED DCUN1D3 WILD-TYPE
  STAGE I                  2                89
  STAGE IA                 0                 1
  STAGE II                 0                32
  STAGE IIA                4               134
  STAGE IIB                0                10
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               0                11
  STAGE IIIB               1                58
  STAGE IIIC               0                42
  STAGE IV                 0                48
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  DCUN1D3 MUTATED     0   2   5   0
  DCUN1D3 WILD-TYPE  17  90 324  50
D909V5, multiclass
    clus
vv   DCUN1D3 MUTATED DCUN1D3 WILD-TYPE
  T1               0                17
  T2               2                90
  T3               5               324
  T4               0                50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  DCUN1D3 MUTATED     6   1   0
  DCUN1D3 WILD-TYPE 281 112  87
D909V6, multiclass
    clus
vv   DCUN1D3 MUTATED DCUN1D3 WILD-TYPE
  N0               6               281
  N1               1               112
  N2               0                87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D909V7, binary
                   cls
clus                  0   1
  DCUN1D3 MUTATED     7   0
  DCUN1D3 WILD-TYPE 368  65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  DCUN1D3 MUTATED      7    0
  DCUN1D3 WILD-TYPE  368   65
   clus
vv  DCUN1D3 MUTATED DCUN1D3 WILD-TYPE
  0               7               368
  1               0                65
[1] 2 2
[1] FALSE
D909V8, binary
                   cls
clus                  0   1
  DCUN1D3 MUTATED     3   4
  DCUN1D3 WILD-TYPE 222 260
[1] "tbl2"
                   cls
clus                [,1] [,2]
  DCUN1D3 MUTATED      3    4
  DCUN1D3 WILD-TYPE  222  260
        clus
vv       DCUN1D3 MUTATED DCUN1D3 WILD-TYPE
  FEMALE               3               222
  MALE                 4               260
[1] 2 2
[1] FALSE
D909V9, binary
                   cls
clus                  0   1
  DCUN1D3 MUTATED     6   0
  DCUN1D3 WILD-TYPE 344  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  DCUN1D3 MUTATED      6    0
  DCUN1D3 WILD-TYPE  344   22
     clus
vv    DCUN1D3 MUTATED DCUN1D3 WILD-TYPE
  NO                6               344
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  DCUN1D3 MUTATED                      6                             0
  DCUN1D3 WILD-TYPE                  309                            47
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  DCUN1D3 MUTATED                       1                              0
  DCUN1D3 WILD-TYPE                   105                             10
D909V10, multiclass
                                clus
vv                               DCUN1D3 MUTATED DCUN1D3 WILD-TYPE
  COLON ADENOCARCINOMA                         6               309
  COLON MUCINOUS ADENOCARCINOMA                0                47
  RECTAL ADENOCARCINOMA                        1               105
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  DCUN1D3 MUTATED     4   0   0   0
  DCUN1D3 WILD-TYPE 341   4  31  25
D909V11, multiclass
    clus
vv   DCUN1D3 MUTATED DCUN1D3 WILD-TYPE
  R0               4               341
  R1               0                 4
  R2               0                31
  RX               0                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D909V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DCUN1D3 MUTATED                                  0     0
  DCUN1D3 WILD-TYPE                                1    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  DCUN1D3 MUTATED                           0     5
  DCUN1D3 WILD-TYPE                        22   221
D909V13, multiclass
                                  clus
vv                                 DCUN1D3 MUTATED DCUN1D3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                      0                22
  WHITE                                          5               221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(910) Variable = GPR115 MUTATION ANALYSIS
D910V1, survival
                  sevent
clus2                0   1
  GPR115 MUTATED    16   6
  GPR115 WILD-TYPE 362  87
  GPR115 MUTATED GPR115 WILD-TYPE 
              22              449 
  GPR115 MUTATED GPR115 WILD-TYPE 
               6               87 
$`GPR115 MUTATED`
TCGA-A6-5661 TCGA-A6-5665 TCGA-A6-5666 TCGA-AA-3510 TCGA-AA-3713 TCGA-AA-3715 
       33.53        22.06        32.71        63.98        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3815 TCGA-AD-6964 TCGA-AZ-4315 TCGA-AZ-6603 TCGA-CA-6717 
       10.06        33.04        10.88        58.39        29.56        12.76 
TCGA-CK-5916 TCGA-CM-5341 TCGA-DM-A1DA TCGA-DM-A28H TCGA-G4-6306 TCGA-G4-6321 
       21.14        29.06         7.50       117.07        44.68        22.09 
TCGA-AF-2687 TCGA-AG-3587 TCGA-AG-3999 TCGA-AG-A002 
       24.13        46.03        28.04        20.98 

$`GPR115 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       27.09        22.52         8.38        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 
       20.28         7.04         3.02         1.02        35.01         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       26.99        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07        12.20        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
        9.99        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       37.02        25.02        13.02        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       13.32        12.59       140.38        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       53.62        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
       24.00         1.02        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       19.99        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  GPR115 MUTATED GPR115 WILD-TYPE 
             7.5              0.0 
  GPR115 MUTATED GPR115 WILD-TYPE 
          117.07           148.01 
  GPR115 MUTATED GPR115 WILD-TYPE 
          26.085           19.990 
[1] "7.5 - 117.1 (26.1)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.2"
D910V2, continuous
D910V3, binary
                  cls
clus                 0   1
  GPR115 MUTATED    18   4
  GPR115 WILD-TYPE 348 115
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR115 MUTATED     18    4
  GPR115 WILD-TYPE  348  115
        clus
vv       GPR115 MUTATED GPR115 WILD-TYPE
  COLON              18              348
  RECTUM              4              115
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GPR115 MUTATED         3        0        2         6         0         1
  GPR115 WILD-TYPE      88        1       30       132        10         0
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GPR115 MUTATED           2          1          0          4        1
  GPR115 WILD-TYPE        22         10         59         38       47
                  vv
clus               STAGE IVA STAGE IVB
  GPR115 MUTATED           0         0
  GPR115 WILD-TYPE        18         1
D910V4, multiclass
            clus
vv           GPR115 MUTATED GPR115 WILD-TYPE
  STAGE I                 3               88
  STAGE IA                0                1
  STAGE II                2               30
  STAGE IIA               6              132
  STAGE IIB               0               10
  STAGE IIC               1                0
  STAGE III               2               22
  STAGE IIIA              1               10
  STAGE IIIB              0               59
  STAGE IIIC              4               38
  STAGE IV                1               47
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  GPR115 MUTATED     1   6  13   2
  GPR115 WILD-TYPE  16  86 316  48
D910V5, multiclass
    clus
vv   GPR115 MUTATED GPR115 WILD-TYPE
  T1              1               16
  T2              6               86
  T3             13              316
  T4              2               48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  GPR115 MUTATED    13   3   6
  GPR115 WILD-TYPE 274 110  81
D910V6, multiclass
    clus
vv   GPR115 MUTATED GPR115 WILD-TYPE
  N0             13              274
  N1              3              110
  N2              6               81
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D910V7, binary
                  cls
clus                 0   1
  GPR115 MUTATED    18   1
  GPR115 WILD-TYPE 357  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR115 MUTATED     18    1
  GPR115 WILD-TYPE  357   64
   clus
vv  GPR115 MUTATED GPR115 WILD-TYPE
  0             18              357
  1              1               64
[1] 2 2
[1] FALSE
D910V8, binary
                  cls
clus                 0   1
  GPR115 MUTATED    10  12
  GPR115 WILD-TYPE 215 252
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR115 MUTATED     10   12
  GPR115 WILD-TYPE  215  252
        clus
vv       GPR115 MUTATED GPR115 WILD-TYPE
  FEMALE             10              215
  MALE               12              252
[1] 2 2
[1] FALSE
D910V9, binary
                  cls
clus                 0   1
  GPR115 MUTATED    17   3
  GPR115 WILD-TYPE 333  19
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR115 MUTATED     17    3
  GPR115 WILD-TYPE  333   19
     clus
vv    GPR115 MUTATED GPR115 WILD-TYPE
  NO              17              333
  YES              3               19
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  GPR115 MUTATED                     17                             1
  GPR115 WILD-TYPE                  298                            46
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  GPR115 MUTATED                       4                              0
  GPR115 WILD-TYPE                   102                             10
D910V10, multiclass
                                clus
vv                               GPR115 MUTATED GPR115 WILD-TYPE
  COLON ADENOCARCINOMA                       17              298
  COLON MUCINOUS ADENOCARCINOMA               1               46
  RECTAL ADENOCARCINOMA                       4              102
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  GPR115 MUTATED    14   0   1   2
  GPR115 WILD-TYPE 331   4  30  23
D910V11, multiclass
    clus
vv   GPR115 MUTATED GPR115 WILD-TYPE
  R0             14              331
  R1              0                4
  R2              1               30
  RX              2               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D910V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GPR115 MUTATED                                  0     1
  GPR115 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  GPR115 MUTATED                           1    12
  GPR115 WILD-TYPE                        21   214
D910V13, multiclass
                                  clus
vv                                 GPR115 MUTATED GPR115 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                        12              214
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(911) Variable = NLK MUTATION ANALYSIS
D911V1, survival
               sevent
clus2             0   1
  NLK MUTATED    11   0
  NLK WILD-TYPE 367  93
  NLK MUTATED NLK WILD-TYPE 
           11           460 
  NLK MUTATED NLK WILD-TYPE 
            0            93 
$`NLK MUTATED`
TCGA-A6-3807 TCGA-A6-5661 TCGA-AA-3662 TCGA-AA-3663 TCGA-AU-6004 TCGA-CK-6747 
       34.65        33.53         6.05         6.97        27.09        82.95 
TCGA-CM-5349 TCGA-D5-5539 TCGA-F4-6805 TCGA-G4-6307 TCGA-G4-6309 
       30.08        19.59        34.42        55.04        85.48 

$`NLK WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       31.63        30.44        29.19        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 
       13.94        19.99        61.02        78.08        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       14.50        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       51.32         9.99        21.14         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       22.98        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-5541 
       10.06        12.03        45.40        12.26        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
        6.18        47.87         1.55        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       65.85        53.62        44.68        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  NLK MUTATED NLK WILD-TYPE 
         6.05          0.00 
  NLK MUTATED NLK WILD-TYPE 
        85.48        148.01 
  NLK MUTATED NLK WILD-TYPE 
       33.530        20.035 
[1] "6.0 - 85.5 (33.5)"  "0.0 - 148.0 (20.0)"
[1] "hr="     "2.6e+07"
D911V2, continuous
D911V3, binary
               cls
clus              0   1
  NLK MUTATED    11   0
  NLK WILD-TYPE 355 119
[1] "tbl2"
               cls
clus            [,1] [,2]
  NLK MUTATED     11    0
  NLK WILD-TYPE  355  119
        clus
vv       NLK MUTATED NLK WILD-TYPE
  COLON           11           355
  RECTUM           0           119
[1] 2 2
[1] FALSE
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NLK MUTATED         1        0        1         4         0         0
  NLK WILD-TYPE      90        1       31       134        10         1
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NLK MUTATED           0          1          2          1        1         0
  NLK WILD-TYPE        24         10         57         41       47        18
               vv
clus            STAGE IVB
  NLK MUTATED           0
  NLK WILD-TYPE         1
D911V4, multiclass
            clus
vv           NLK MUTATED NLK WILD-TYPE
  STAGE I              1            90
  STAGE IA             0             1
  STAGE II             1            31
  STAGE IIA            4           134
  STAGE IIB            0            10
  STAGE IIC            0             1
  STAGE III            0            24
  STAGE IIIA           1            10
  STAGE IIIB           2            57
  STAGE IIIC           1            41
  STAGE IV             1            47
  STAGE IVA            0            18
  STAGE IVB            0             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  NLK MUTATED     0   1   9   1
  NLK WILD-TYPE  17  91 320  49
D911V5, multiclass
    clus
vv   NLK MUTATED NLK WILD-TYPE
  T1           0            17
  T2           1            91
  T3           9           320
  T4           1            49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2
  NLK MUTATED     6   3   2
  NLK WILD-TYPE 281 110  85
D911V6, multiclass
    clus
vv   NLK MUTATED NLK WILD-TYPE
  N0           6           281
  N1           3           110
  N2           2            85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D911V7, binary
               cls
clus              0   1
  NLK MUTATED     9   1
  NLK WILD-TYPE 366  64
[1] "tbl2"
               cls
clus            [,1] [,2]
  NLK MUTATED      9    1
  NLK WILD-TYPE  366   64
   clus
vv  NLK MUTATED NLK WILD-TYPE
  0           9           366
  1           1            64
[1] 2 2
[1] FALSE
D911V8, binary
               cls
clus              0   1
  NLK MUTATED     9   2
  NLK WILD-TYPE 216 262
[1] "tbl2"
               cls
clus            [,1] [,2]
  NLK MUTATED      9    2
  NLK WILD-TYPE  216  262
        clus
vv       NLK MUTATED NLK WILD-TYPE
  FEMALE           9           216
  MALE             2           262
[1] 2 2
[1] FALSE
D911V9, binary
               cls
clus              0   1
  NLK MUTATED    10   0
  NLK WILD-TYPE 340  22
[1] "tbl2"
               cls
clus            [,1] [,2]
  NLK MUTATED     10    0
  NLK WILD-TYPE  340   22
     clus
vv    NLK MUTATED NLK WILD-TYPE
  NO           10           340
  YES           0            22
[1] 2 2
[1] FALSE
               vv
clus            COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  NLK MUTATED                     10                             1
  NLK WILD-TYPE                  305                            46
               vv
clus            RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  NLK MUTATED                       0                              0
  NLK WILD-TYPE                   106                             10
D911V10, multiclass
                                clus
vv                               NLK MUTATED NLK WILD-TYPE
  COLON ADENOCARCINOMA                    10           305
  COLON MUCINOUS ADENOCARCINOMA            1            46
  RECTAL ADENOCARCINOMA                    0           106
  RECTAL MUCINOUS ADENOCARCINOMA           0            10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             R0  R1  R2  RX
  NLK MUTATED     9   0   1   1
  NLK WILD-TYPE 336   4  30  24
D911V11, multiclass
    clus
vv   NLK MUTATED NLK WILD-TYPE
  R0           9           336
  R1           0             4
  R2           1            30
  RX           1            24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D911V12, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NLK MUTATED                                  0     0
  NLK WILD-TYPE                                1    11
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  NLK MUTATED                           2     7
  NLK WILD-TYPE                        20   219
D911V13, multiclass
                                  clus
vv                                 NLK MUTATED NLK WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      0            11
  BLACK OR AFRICAN AMERICAN                  2            20
  WHITE                                      7           219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(912) Variable = ARHGAP32 MUTATION ANALYSIS
D912V1, survival
                    sevent
clus2                  0   1
  ARHGAP32 MUTATED    22   3
  ARHGAP32 WILD-TYPE 356  90
  ARHGAP32 MUTATED ARHGAP32 WILD-TYPE 
                25                446 
  ARHGAP32 MUTATED ARHGAP32 WILD-TYPE 
                 3                 90 
$`ARHGAP32 MUTATED`
TCGA-A6-3809 TCGA-A6-5661 TCGA-A6-5665 TCGA-AA-3492 TCGA-AA-3555 TCGA-AA-3697 
       32.75        33.53        22.06         3.02        29.95        85.05 
TCGA-AA-3713 TCGA-AA-3815 TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01Q TCGA-AZ-4682 
       19.04        33.04         4.01        34.98         1.02        22.36 
TCGA-CK-6751 TCGA-CM-5341 TCGA-CM-6674 TCGA-D5-5539 TCGA-D5-6532 TCGA-D5-6541 
      124.27        29.06        12.95        19.59        18.25        15.58 
TCGA-D5-6923 TCGA-DM-A0X9 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6588 TCGA-AG-A002 
       12.43       119.70        36.00        13.78        26.17        20.98 
TCGA-AG-A02N 
       61.97 

$`ARHGAP32 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 
       31.63        30.44        29.19        23.61        22.09        32.71 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       27.09        22.52         8.38        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
       20.28         7.04         1.02        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       78.08         6.05         6.97        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3715 
       37.05        19.00        36.00         5.03        26.99        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       10.06        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
       38.07        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-5403 TCGA-AZ-5407 
       58.39         1.41         5.13       106.75        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CM-4743 TCGA-CM-4744 
        9.99        21.14        82.95         1.91        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       37.02        25.02        13.02        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6533 
       45.40        12.26        56.09        55.92        20.19         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6924 TCGA-D5-6926 
       16.14         1.48         3.68         4.41        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
       10.26        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 
       63.62        61.91        22.09        35.80        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  ARHGAP32 MUTATED ARHGAP32 WILD-TYPE 
              1.02               0.00 
  ARHGAP32 MUTATED ARHGAP32 WILD-TYPE 
            124.27             148.01 
  ARHGAP32 MUTATED ARHGAP32 WILD-TYPE 
            22.360             20.035 
[1] "1.0 - 124.3 (22.4)" "0.0 - 148.0 (20.0)"
[1] "hr=" "2"  
D912V2, continuous
D912V3, binary
                    cls
clus                   0   1
  ARHGAP32 MUTATED    24   2
  ARHGAP32 WILD-TYPE 342 117
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ARHGAP32 MUTATED     24    2
  ARHGAP32 WILD-TYPE  342  117
        clus
vv       ARHGAP32 MUTATED ARHGAP32 WILD-TYPE
  COLON                24                342
  RECTUM                2                117
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ARHGAP32 MUTATED         3        1        4         9         3         0
  ARHGAP32 WILD-TYPE      88        0       28       129         7         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ARHGAP32 MUTATED           1          2          0          1        1
  ARHGAP32 WILD-TYPE        23          9         59         41       47
                    vv
clus                 STAGE IVA STAGE IVB
  ARHGAP32 MUTATED           1         0
  ARHGAP32 WILD-TYPE        17         1
D912V4, multiclass
            clus
vv           ARHGAP32 MUTATED ARHGAP32 WILD-TYPE
  STAGE I                   3                 88
  STAGE IA                  1                  0
  STAGE II                  4                 28
  STAGE IIA                 9                129
  STAGE IIB                 3                  7
  STAGE IIC                 0                  1
  STAGE III                 1                 23
  STAGE IIIA                2                  9
  STAGE IIIB                0                 59
  STAGE IIIC                1                 41
  STAGE IV                  1                 47
  STAGE IVA                 1                 17
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  ARHGAP32 MUTATED     0   4  17   4
  ARHGAP32 WILD-TYPE  17  88 312  46
D912V5, multiclass
    clus
vv   ARHGAP32 MUTATED ARHGAP32 WILD-TYPE
  T1                0                 17
  T2                4                 88
  T3               17                312
  T4                4                 46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  ARHGAP32 MUTATED    23   2   1
  ARHGAP32 WILD-TYPE 264 111  86
D912V6, multiclass
    clus
vv   ARHGAP32 MUTATED ARHGAP32 WILD-TYPE
  N0               23                264
  N1                2                111
  N2                1                 86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D912V7, binary
                    cls
clus                   0   1
  ARHGAP32 MUTATED    21   2
  ARHGAP32 WILD-TYPE 354  63
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ARHGAP32 MUTATED     21    2
  ARHGAP32 WILD-TYPE  354   63
   clus
vv  ARHGAP32 MUTATED ARHGAP32 WILD-TYPE
  0               21                354
  1                2                 63
[1] 2 2
[1] FALSE
D912V8, binary
                    cls
clus                   0   1
  ARHGAP32 MUTATED    14  12
  ARHGAP32 WILD-TYPE 211 252
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ARHGAP32 MUTATED     14   12
  ARHGAP32 WILD-TYPE  211  252
        clus
vv       ARHGAP32 MUTATED ARHGAP32 WILD-TYPE
  FEMALE               14                211
  MALE                 12                252
[1] 2 2
[1] FALSE
D912V9, binary
                    cls
clus                   0   1
  ARHGAP32 MUTATED    20   1
  ARHGAP32 WILD-TYPE 330  21
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ARHGAP32 MUTATED     20    1
  ARHGAP32 WILD-TYPE  330   21
     clus
vv    ARHGAP32 MUTATED ARHGAP32 WILD-TYPE
  NO                20                330
  YES                1                 21
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ARHGAP32 MUTATED                     19                             5
  ARHGAP32 WILD-TYPE                  296                            42
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ARHGAP32 MUTATED                       2                              0
  ARHGAP32 WILD-TYPE                   104                             10
D912V10, multiclass
                                clus
vv                               ARHGAP32 MUTATED ARHGAP32 WILD-TYPE
  COLON ADENOCARCINOMA                         19                296
  COLON MUCINOUS ADENOCARCINOMA                 5                 42
  RECTAL ADENOCARCINOMA                         2                104
  RECTAL MUCINOUS ADENOCARCINOMA                0                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  ARHGAP32 MUTATED    23   0   1   1
  ARHGAP32 WILD-TYPE 322   4  30  24
D912V11, multiclass
    clus
vv   ARHGAP32 MUTATED ARHGAP32 WILD-TYPE
  R0               23                322
  R1                0                  4
  R2                1                 30
  RX                1                 24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D912V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ARHGAP32 MUTATED                                  0     0
  ARHGAP32 WILD-TYPE                                1    11
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  ARHGAP32 MUTATED                           2    13
  ARHGAP32 WILD-TYPE                        20   213
D912V13, multiclass
                                  clus
vv                                 ARHGAP32 MUTATED ARHGAP32 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 11
  BLACK OR AFRICAN AMERICAN                       2                 20
  WHITE                                          13                213
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(913) Variable = PIK3R4 MUTATION ANALYSIS
D913V1, survival
                  sevent
clus2                0   1
  PIK3R4 MUTATED    12   4
  PIK3R4 WILD-TYPE 366  89
  PIK3R4 MUTATED PIK3R4 WILD-TYPE 
              16              455 
  PIK3R4 MUTATED PIK3R4 WILD-TYPE 
               4               89 
$`PIK3R4 MUTATED`
TCGA-A6-2676 TCGA-A6-5660 TCGA-AA-3555 TCGA-AA-3713 TCGA-AA-3851 TCGA-AA-A00A 
       42.90        29.19        29.95        19.04        33.07        38.04 
TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01Q TCGA-AD-6965 TCGA-AZ-6598 TCGA-CA-5255 
        4.01        34.98         1.02         0.20        49.41         3.06 
TCGA-CM-5861 TCGA-F4-6459 TCGA-G4-6588 TCGA-CI-6624 
       15.02         8.61        26.17         4.73 

$`PIK3R4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       31.63        30.44        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       24.00        17.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       85.05        26.99        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       27.02        13.94        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        31.00        38.07        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        88.21         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5796 
        5.23        11.74         3.19         1.61        12.69         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       22.98        30.08        32.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6460 TCGA-F4-6569 
       35.97        60.79       117.07        98.24        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
        6.05        33.17         6.97        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  PIK3R4 MUTATED PIK3R4 WILD-TYPE 
             0.2              0.0 
  PIK3R4 MUTATED PIK3R4 WILD-TYPE 
           49.41           148.01 
  PIK3R4 MUTATED PIK3R4 WILD-TYPE 
          22.605           20.190 
[1] "0.2 - 49.4 (22.6)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.6"
D913V2, continuous
D913V3, binary
                  cls
clus                 0   1
  PIK3R4 MUTATED    16   1
  PIK3R4 WILD-TYPE 350 118
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3R4 MUTATED     16    1
  PIK3R4 WILD-TYPE  350  118
        clus
vv       PIK3R4 MUTATED PIK3R4 WILD-TYPE
  COLON              16              350
  RECTUM              1              118
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PIK3R4 MUTATED         1        0        2         7         3         0
  PIK3R4 WILD-TYPE      90        1       30       131         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PIK3R4 MUTATED           0          0          1          1        1
  PIK3R4 WILD-TYPE        24         11         58         41       47
                  vv
clus               STAGE IVA STAGE IVB
  PIK3R4 MUTATED           0         0
  PIK3R4 WILD-TYPE        18         1
D913V4, multiclass
            clus
vv           PIK3R4 MUTATED PIK3R4 WILD-TYPE
  STAGE I                 1               90
  STAGE IA                0                1
  STAGE II                2               30
  STAGE IIA               7              131
  STAGE IIB               3                7
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              1               58
  STAGE IIIC              1               41
  STAGE IV                1               47
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  PIK3R4 MUTATED     0   1  12   4
  PIK3R4 WILD-TYPE  17  91 317  46
D913V5, multiclass
    clus
vv   PIK3R4 MUTATED PIK3R4 WILD-TYPE
  T1              0               17
  T2              1               91
  T3             12              317
  T4              4               46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  PIK3R4 MUTATED    14   0   3
  PIK3R4 WILD-TYPE 273 113  84
D913V6, multiclass
    clus
vv   PIK3R4 MUTATED PIK3R4 WILD-TYPE
  N0             14              273
  N1              0              113
  N2              3               84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D913V7, binary
                  cls
clus                 0   1
  PIK3R4 MUTATED    14   1
  PIK3R4 WILD-TYPE 361  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3R4 MUTATED     14    1
  PIK3R4 WILD-TYPE  361   64
   clus
vv  PIK3R4 MUTATED PIK3R4 WILD-TYPE
  0             14              361
  1              1               64
[1] 2 2
[1] FALSE
D913V8, binary
                  cls
clus                 0   1
  PIK3R4 MUTATED    10   7
  PIK3R4 WILD-TYPE 215 257
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3R4 MUTATED     10    7
  PIK3R4 WILD-TYPE  215  257
        clus
vv       PIK3R4 MUTATED PIK3R4 WILD-TYPE
  FEMALE             10              215
  MALE                7              257
[1] 2 2
[1] FALSE
D913V9, binary
                  cls
clus                 0   1
  PIK3R4 MUTATED    10   2
  PIK3R4 WILD-TYPE 340  20
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3R4 MUTATED     10    2
  PIK3R4 WILD-TYPE  340   20
     clus
vv    PIK3R4 MUTATED PIK3R4 WILD-TYPE
  NO              10              340
  YES              2               20
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PIK3R4 MUTATED                     14                             2
  PIK3R4 WILD-TYPE                  301                            45
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PIK3R4 MUTATED                       1                              0
  PIK3R4 WILD-TYPE                   105                             10
D913V10, multiclass
                                clus
vv                               PIK3R4 MUTATED PIK3R4 WILD-TYPE
  COLON ADENOCARCINOMA                       14              301
  COLON MUCINOUS ADENOCARCINOMA               2               45
  RECTAL ADENOCARCINOMA                       1              105
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  PIK3R4 MUTATED    11   0   1   1
  PIK3R4 WILD-TYPE 334   4  30  24
D913V11, multiclass
    clus
vv   PIK3R4 MUTATED PIK3R4 WILD-TYPE
  R0             11              334
  R1              0                4
  R2              1               30
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D913V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PIK3R4 MUTATED                                  0     1
  PIK3R4 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  PIK3R4 MUTATED                           1     7
  PIK3R4 WILD-TYPE                        21   219
D913V13, multiclass
                                  clus
vv                                 PIK3R4 MUTATED PIK3R4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                         7              219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(914) Variable = GNAS MUTATION ANALYSIS
D914V1, survival
                sevent
clus2              0   1
  GNAS MUTATED    28   8
  GNAS WILD-TYPE 350  85
  GNAS MUTATED GNAS WILD-TYPE 
            36            435 
  GNAS MUTATED GNAS WILD-TYPE 
             8             85 
$`GNAS MUTATED`
TCGA-A6-2678 TCGA-A6-6141 TCGA-AA-3489 TCGA-AA-3502 TCGA-AA-3518 TCGA-AA-3660 
       42.28         8.38         7.04        35.01         1.02        78.08 
TCGA-AA-3663 TCGA-AA-3679 TCGA-AA-3681 TCGA-AA-3815 TCGA-AA-3861 TCGA-AA-3869 
        6.97        15.02         5.98        33.04        30.05        27.02 
TCGA-AA-3989 TCGA-AD-5900 TCGA-AD-6889 TCGA-AU-6004 TCGA-AZ-6598 TCGA-AZ-6599 
        7.96         0.07        56.55        27.09        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-CA-6718 TCGA-CK-4952 TCGA-CM-4743 TCGA-CM-6675 
       12.10        29.56        10.06        15.62        23.05        13.05 
TCGA-D5-6928 TCGA-DM-A1HA TCGA-G4-6306 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       11.64       131.51        44.68        61.91        36.00        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-AG-3732 TCGA-DC-6155 TCGA-DC-6157 TCGA-EI-6507 
       35.80        26.17        32.98        13.97        27.95        19.96 

$`GNAS WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2683 
       43.76        46.65        43.76        42.90        24.33        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 
       22.06        32.71        27.09        22.52        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3510 TCGA-AA-3511 
       19.66        20.28         3.02         1.02        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
        1.02        13.02        38.99         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       36.03         8.05        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.05        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3680 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       47.01        11.01        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3875 
       31.07        53.00        17.03        24.03        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3994 TCGA-AA-A004 
       24.00        27.02        27.02        19.07        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 
       41.00        39.98        18.05        40.96        21.37        15.52 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
        0.20        14.50        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       62.79        88.21       100.01         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.20        12.76        14.30        17.56       148.01        85.45 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
      124.27        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6676 TCGA-CM-6677 
       15.02        14.04        11.01        12.95        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.04         9.44         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       74.56        65.85        53.62        55.04        85.48        63.62 
TCGA-G4-6323 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       13.78        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        7.99         0.99        37.02         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       15.02         5.03        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6510 
       51.48        32.61         0.49        20.55        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  GNAS MUTATED GNAS WILD-TYPE 
          0.07           0.00 
  GNAS MUTATED GNAS WILD-TYPE 
        131.51         148.01 
  GNAS MUTATED GNAS WILD-TYPE 
         24.61          20.05 
[1] "0.1 - 131.5 (24.6)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.1"
D914V2, continuous
D914V3, binary
                cls
clus               0   1
  GNAS MUTATED    32   4
  GNAS WILD-TYPE 334 115
[1] "tbl2"
                cls
clus             [,1] [,2]
  GNAS MUTATED     32    4
  GNAS WILD-TYPE  334  115
        clus
vv       GNAS MUTATED GNAS WILD-TYPE
  COLON            32            334
  RECTUM            4            115
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GNAS MUTATED         6        0        4        12         0         0
  GNAS WILD-TYPE      85        1       28       126        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  GNAS MUTATED           2          1          1          3        5         0
  GNAS WILD-TYPE        22         10         58         39       43        18
                vv
clus             STAGE IVB
  GNAS MUTATED           1
  GNAS WILD-TYPE         0
D914V4, multiclass
            clus
vv           GNAS MUTATED GNAS WILD-TYPE
  STAGE I               6             85
  STAGE IA              0              1
  STAGE II              4             28
  STAGE IIA            12            126
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             2             22
  STAGE IIIA            1             10
  STAGE IIIB            1             58
  STAGE IIIC            3             39
  STAGE IV              5             43
  STAGE IVA             0             18
  STAGE IVB             1              0
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  GNAS MUTATED     0  10  23   3
  GNAS WILD-TYPE  17  82 306  47
D914V5, multiclass
    clus
vv   GNAS MUTATED GNAS WILD-TYPE
  T1            0             17
  T2           10             82
  T3           23            306
  T4            3             47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  GNAS MUTATED    22   7   7
  GNAS WILD-TYPE 265 106  80
D914V6, multiclass
    clus
vv   GNAS MUTATED GNAS WILD-TYPE
  N0           22            265
  N1            7            106
  N2            7             80
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D914V7, binary
                cls
clus               0   1
  GNAS MUTATED    24   6
  GNAS WILD-TYPE 351  59
[1] "tbl2"
                cls
clus             [,1] [,2]
  GNAS MUTATED     24    6
  GNAS WILD-TYPE  351   59
   clus
vv  GNAS MUTATED GNAS WILD-TYPE
  0           24            351
  1            6             59
[1] 2 2
[1] FALSE
D914V8, binary
                cls
clus               0   1
  GNAS MUTATED    15  21
  GNAS WILD-TYPE 210 243
[1] "tbl2"
                cls
clus             [,1] [,2]
  GNAS MUTATED     15   21
  GNAS WILD-TYPE  210  243
        clus
vv       GNAS MUTATED GNAS WILD-TYPE
  FEMALE           15            210
  MALE             21            243
[1] 2 2
[1] FALSE
D914V9, binary
                cls
clus               0   1
  GNAS MUTATED    28   0
  GNAS WILD-TYPE 322  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  GNAS MUTATED     28    0
  GNAS WILD-TYPE  322   22
     clus
vv    GNAS MUTATED GNAS WILD-TYPE
  NO            28            322
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  GNAS MUTATED                     29                             3
  GNAS WILD-TYPE                  286                            44
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  GNAS MUTATED                       4                              0
  GNAS WILD-TYPE                   102                             10
D914V10, multiclass
                                clus
vv                               GNAS MUTATED GNAS WILD-TYPE
  COLON ADENOCARCINOMA                     29            286
  COLON MUCINOUS ADENOCARCINOMA             3             44
  RECTAL ADENOCARCINOMA                     4            102
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  GNAS MUTATED    24   0   3   2
  GNAS WILD-TYPE 321   4  28  23
D914V11, multiclass
    clus
vv   GNAS MUTATED GNAS WILD-TYPE
  R0           24            321
  R1            0              4
  R2            3             28
  RX            2             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D914V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GNAS MUTATED                                  0     2
  GNAS WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  GNAS MUTATED                           4    18
  GNAS WILD-TYPE                        18   208
D914V13, multiclass
                                  clus
vv                                 GNAS MUTATED GNAS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              9
  BLACK OR AFRICAN AMERICAN                   4             18
  WHITE                                      18            208
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(915) Variable = TRIB1 MUTATION ANALYSIS
D915V1, survival
                 sevent
clus2               0   1
  TRIB1 MUTATED     7   2
  TRIB1 WILD-TYPE 371  91
  TRIB1 MUTATED TRIB1 WILD-TYPE 
              9             462 
  TRIB1 MUTATED TRIB1 WILD-TYPE 
              2              91 
$`TRIB1 MUTATED`
TCGA-A6-6781 TCGA-AA-3715 TCGA-AD-6964 TCGA-AY-6197 TCGA-CK-4950 TCGA-CK-4952 
       19.66        19.04        10.88        21.44        85.45        15.62 
TCGA-D5-6533 TCGA-AG-A002 TCGA-CI-6624 
        1.32        20.98         4.73 

$`TRIB1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 
       36.00         5.03        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-5912 TCGA-CK-5913 
       10.06        14.30        17.56       148.01        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 
       56.09        55.92        20.19        18.25        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CL-5917 TCGA-CL-5918 
        0.72         6.05        33.17         6.97        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  TRIB1 MUTATED TRIB1 WILD-TYPE 
           1.32            0.00 
  TRIB1 MUTATED TRIB1 WILD-TYPE 
          85.45          148.01 
  TRIB1 MUTATED TRIB1 WILD-TYPE 
         19.040          20.415 
[1] "1.3 - 85.5 (19.0)"  "0.0 - 148.0 (20.4)"
[1] "hr=" "1.3"
D915V2, continuous
D915V3, binary
                 cls
clus                0   1
  TRIB1 MUTATED     7   2
  TRIB1 WILD-TYPE 359 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRIB1 MUTATED      7    2
  TRIB1 WILD-TYPE  359  117
        clus
vv       TRIB1 MUTATED TRIB1 WILD-TYPE
  COLON              7             359
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TRIB1 MUTATED         2        0        1         1         0         0
  TRIB1 WILD-TYPE      89        1       31       137        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TRIB1 MUTATED           0          0          2          2        0         0
  TRIB1 WILD-TYPE        24         11         57         40       48        18
                 vv
clus              STAGE IVB
  TRIB1 MUTATED           0
  TRIB1 WILD-TYPE         1
D915V4, multiclass
            clus
vv           TRIB1 MUTATED TRIB1 WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              1             137
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             2              57
  STAGE IIIC             2              40
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  TRIB1 MUTATED     0   2   3   4
  TRIB1 WILD-TYPE  17  90 326  46
D915V5, multiclass
    clus
vv   TRIB1 MUTATED TRIB1 WILD-TYPE
  T1             0              17
  T2             2              90
  T3             3             326
  T4             4              46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  TRIB1 MUTATED     5   2   2
  TRIB1 WILD-TYPE 282 111  85
D915V6, multiclass
    clus
vv   TRIB1 MUTATED TRIB1 WILD-TYPE
  N0             5             282
  N1             2             111
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D915V7, binary
                 cls
clus                0   1
  TRIB1 MUTATED     6   0
  TRIB1 WILD-TYPE 369  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRIB1 MUTATED      6    0
  TRIB1 WILD-TYPE  369   65
   clus
vv  TRIB1 MUTATED TRIB1 WILD-TYPE
  0             6             369
  1             0              65
[1] 2 2
[1] FALSE
D915V8, binary
                 cls
clus                0   1
  TRIB1 MUTATED     4   5
  TRIB1 WILD-TYPE 221 259
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRIB1 MUTATED      4    5
  TRIB1 WILD-TYPE  221  259
        clus
vv       TRIB1 MUTATED TRIB1 WILD-TYPE
  FEMALE             4             221
  MALE               5             259
[1] 2 2
[1] FALSE
D915V9, binary
                 cls
clus                0   1
  TRIB1 MUTATED     6   0
  TRIB1 WILD-TYPE 344  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRIB1 MUTATED      6    0
  TRIB1 WILD-TYPE  344   22
     clus
vv    TRIB1 MUTATED TRIB1 WILD-TYPE
  NO              6             344
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  TRIB1 MUTATED                      5                             2
  TRIB1 WILD-TYPE                  310                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  TRIB1 MUTATED                       2                              0
  TRIB1 WILD-TYPE                   104                             10
D915V10, multiclass
                                clus
vv                               TRIB1 MUTATED TRIB1 WILD-TYPE
  COLON ADENOCARCINOMA                       5             310
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  TRIB1 MUTATED     5   1   0   1
  TRIB1 WILD-TYPE 340   3  31  24
D915V11, multiclass
    clus
vv   TRIB1 MUTATED TRIB1 WILD-TYPE
  R0             5             340
  R1             1               3
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D915V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TRIB1 MUTATED                                  0     0
  TRIB1 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  TRIB1 MUTATED                           1     6
  TRIB1 WILD-TYPE                        21   220
D915V13, multiclass
                                  clus
vv                                 TRIB1 MUTATED TRIB1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        6             220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(916) Variable = VWCE MUTATION ANALYSIS
D916V1, survival
                sevent
clus2              0   1
  VWCE MUTATED    13   1
  VWCE WILD-TYPE 365  92
  VWCE MUTATED VWCE WILD-TYPE 
            14            457 
  VWCE MUTATED VWCE WILD-TYPE 
             1             92 
$`VWCE MUTATED`
TCGA-A6-5661 TCGA-AA-3864 TCGA-AD-6895 TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-5543 
       33.53        53.00         0.72         0.20        27.09        33.01 
TCGA-AZ-6598 TCGA-CM-5861 TCGA-CM-6166 TCGA-F4-6854 TCGA-G4-6588 TCGA-AG-A02X 
       49.41        15.02        21.99         0.53        26.17        41.00 
TCGA-DC-5337 TCGA-EI-6506 
       15.02        20.55 

$`VWCE WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 
       32.05         0.99        31.07        31.07        30.05        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
       56.55         0.79         5.79        22.42        27.42        10.88 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       14.50        16.31         0.95        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       30.08        32.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6167 
       15.02        12.00         2.96        29.03        16.04        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
       13.25        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        35.80        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       38.96        61.97        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
        4.73        78.12         7.17         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
        0.49        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  VWCE MUTATED VWCE WILD-TYPE 
           0.2            0.0 
  VWCE MUTATED VWCE WILD-TYPE 
         53.00         148.01 
  VWCE MUTATED VWCE WILD-TYPE 
         24.08          20.05 
[1] "0.2 - 53.0 (24.1)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "2.6"
D916V2, continuous
D916V3, binary
                cls
clus               0   1
  VWCE MUTATED    12   3
  VWCE WILD-TYPE 354 116
[1] "tbl2"
                cls
clus             [,1] [,2]
  VWCE MUTATED     12    3
  VWCE WILD-TYPE  354  116
        clus
vv       VWCE MUTATED VWCE WILD-TYPE
  COLON            12            354
  RECTUM            3            116
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  VWCE MUTATED         4        0        2         6         0         0
  VWCE WILD-TYPE      87        1       30       132        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  VWCE MUTATED           0          0          0          0        0         1
  VWCE WILD-TYPE        24         11         59         42       48        17
                vv
clus             STAGE IVB
  VWCE MUTATED           0
  VWCE WILD-TYPE         1
D916V4, multiclass
            clus
vv           VWCE MUTATED VWCE WILD-TYPE
  STAGE I               4             87
  STAGE IA              0              1
  STAGE II              2             30
  STAGE IIA             6            132
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            0             59
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             1             17
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  VWCE MUTATED     1   3  10   1
  VWCE WILD-TYPE  16  89 319  49
D916V5, multiclass
    clus
vv   VWCE MUTATED VWCE WILD-TYPE
  T1            1             16
  T2            3             89
  T3           10            319
  T4            1             49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  VWCE MUTATED    12   2   1
  VWCE WILD-TYPE 275 111  86
D916V6, multiclass
    clus
vv   VWCE MUTATED VWCE WILD-TYPE
  N0           12            275
  N1            2            111
  N2            1             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D916V7, binary
                cls
clus               0   1
  VWCE MUTATED    11   1
  VWCE WILD-TYPE 364  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  VWCE MUTATED     11    1
  VWCE WILD-TYPE  364   64
   clus
vv  VWCE MUTATED VWCE WILD-TYPE
  0           11            364
  1            1             64
[1] 2 2
[1] FALSE
D916V8, binary
                cls
clus               0   1
  VWCE MUTATED    10   5
  VWCE WILD-TYPE 215 259
[1] "tbl2"
                cls
clus             [,1] [,2]
  VWCE MUTATED     10    5
  VWCE WILD-TYPE  215  259
        clus
vv       VWCE MUTATED VWCE WILD-TYPE
  FEMALE           10            215
  MALE              5            259
[1] 2 2
[1] FALSE
D916V9, binary
                cls
clus               0   1
  VWCE MUTATED    10   0
  VWCE WILD-TYPE 340  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  VWCE MUTATED     10    0
  VWCE WILD-TYPE  340   22
     clus
vv    VWCE MUTATED VWCE WILD-TYPE
  NO            10            340
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  VWCE MUTATED                     12                             0
  VWCE WILD-TYPE                  303                            47
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  VWCE MUTATED                       3                              0
  VWCE WILD-TYPE                   103                             10
D916V10, multiclass
                                clus
vv                               VWCE MUTATED VWCE WILD-TYPE
  COLON ADENOCARCINOMA                     12            303
  COLON MUCINOUS ADENOCARCINOMA             0             47
  RECTAL ADENOCARCINOMA                     3            103
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  VWCE MUTATED    12   0   0   0
  VWCE WILD-TYPE 333   4  31  25
D916V11, multiclass
    clus
vv   VWCE MUTATED VWCE WILD-TYPE
  R0           12            333
  R1            0              4
  R2            0             31
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D916V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  VWCE MUTATED                                  0     0
  VWCE WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  VWCE MUTATED                           2    10
  VWCE WILD-TYPE                        20   216
D916V13, multiclass
                                  clus
vv                                 VWCE MUTATED VWCE WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   2             20
  WHITE                                      10            216
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(917) Variable = JMJD6 MUTATION ANALYSIS
D917V1, survival
                 sevent
clus2               0   1
  JMJD6 MUTATED     9   0
  JMJD6 WILD-TYPE 369  93
  JMJD6 MUTATED JMJD6 WILD-TYPE 
              9             462 
  JMJD6 MUTATED JMJD6 WILD-TYPE 
              0              93 
$`JMJD6 MUTATED`
TCGA-A6-6142 TCGA-AA-3663 TCGA-AA-A010 TCGA-AA-A01R TCGA-AD-5900 TCGA-CM-5348 
       25.08         6.97        34.98        35.01         0.07        22.98 
TCGA-D5-6540 TCGA-G4-6293 TCGA-DC-5869 
       16.14       133.18         5.03 

$`JMJD6 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       31.00        38.07         1.02         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
       40.96        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.03        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 
       15.12        17.85         4.80        17.13        12.49        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
        7.17        15.02        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  JMJD6 MUTATED JMJD6 WILD-TYPE 
           0.07            0.00 
  JMJD6 MUTATED JMJD6 WILD-TYPE 
         133.18          148.01 
  JMJD6 MUTATED JMJD6 WILD-TYPE 
         22.980          20.155 
[1] "0.1 - 133.2 (23.0)" "0.0 - 148.0 (20.2)"
[1] "hr="     "9200000"
D917V2, continuous
D917V3, binary
                 cls
clus                0   1
  JMJD6 MUTATED     8   1
  JMJD6 WILD-TYPE 358 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  JMJD6 MUTATED      8    1
  JMJD6 WILD-TYPE  358  118
        clus
vv       JMJD6 MUTATED JMJD6 WILD-TYPE
  COLON              8             358
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  JMJD6 MUTATED         2        0        1         0         1         0
  JMJD6 WILD-TYPE      89        1       31       138         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  JMJD6 MUTATED           2          0          2          0        0         1
  JMJD6 WILD-TYPE        22         11         57         42       48        17
                 vv
clus              STAGE IVB
  JMJD6 MUTATED           0
  JMJD6 WILD-TYPE         1
D917V4, multiclass
            clus
vv           JMJD6 MUTATED JMJD6 WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              0             138
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              2              22
  STAGE IIIA             0              11
  STAGE IIIB             2              57
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  JMJD6 MUTATED     0   2   6   1
  JMJD6 WILD-TYPE  17  90 323  49
D917V5, multiclass
    clus
vv   JMJD6 MUTATED JMJD6 WILD-TYPE
  T1             0              17
  T2             2              90
  T3             6             323
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  JMJD6 MUTATED     4   4   1
  JMJD6 WILD-TYPE 283 109  86
D917V6, multiclass
    clus
vv   JMJD6 MUTATED JMJD6 WILD-TYPE
  N0             4             283
  N1             4             109
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D917V7, binary
                 cls
clus                0   1
  JMJD6 MUTATED     7   1
  JMJD6 WILD-TYPE 368  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  JMJD6 MUTATED      7    1
  JMJD6 WILD-TYPE  368   64
   clus
vv  JMJD6 MUTATED JMJD6 WILD-TYPE
  0             7             368
  1             1              64
[1] 2 2
[1] FALSE
D917V8, binary
                 cls
clus                0   1
  JMJD6 MUTATED     4   5
  JMJD6 WILD-TYPE 221 259
[1] "tbl2"
                 cls
clus              [,1] [,2]
  JMJD6 MUTATED      4    5
  JMJD6 WILD-TYPE  221  259
        clus
vv       JMJD6 MUTATED JMJD6 WILD-TYPE
  FEMALE             4             221
  MALE               5             259
[1] 2 2
[1] FALSE
D917V9, binary
                 cls
clus                0   1
  JMJD6 MUTATED     6   1
  JMJD6 WILD-TYPE 344  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  JMJD6 MUTATED      6    1
  JMJD6 WILD-TYPE  344   21
     clus
vv    JMJD6 MUTATED JMJD6 WILD-TYPE
  NO              6             344
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  JMJD6 MUTATED                      5                             3
  JMJD6 WILD-TYPE                  310                            44
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  JMJD6 MUTATED                       1                              0
  JMJD6 WILD-TYPE                   105                             10
D917V10, multiclass
                                clus
vv                               JMJD6 MUTATED JMJD6 WILD-TYPE
  COLON ADENOCARCINOMA                       5             310
  COLON MUCINOUS ADENOCARCINOMA              3              44
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  JMJD6 MUTATED     8   0   0   0
  JMJD6 WILD-TYPE 337   4  31  25
D917V11, multiclass
    clus
vv   JMJD6 MUTATED JMJD6 WILD-TYPE
  R0             8             337
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D917V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  JMJD6 MUTATED                                  0     0
  JMJD6 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  JMJD6 MUTATED                           1     5
  JMJD6 WILD-TYPE                        21   221
D917V13, multiclass
                                  clus
vv                                 JMJD6 MUTATED JMJD6 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        5             221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(918) Variable = AGFG2 MUTATION ANALYSIS
D918V1, survival
                 sevent
clus2               0   1
  AGFG2 MUTATED     9   3
  AGFG2 WILD-TYPE 369  90
  AGFG2 MUTATED AGFG2 WILD-TYPE 
             12             459 
  AGFG2 MUTATED AGFG2 WILD-TYPE 
              3              90 
$`AGFG2 MUTATED`
TCGA-AA-3492 TCGA-AA-3518 TCGA-AA-3663 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3947 
        3.02         1.02         6.97        19.04        19.04        33.01 
TCGA-AZ-6601 TCGA-CA-6717 TCGA-G4-6586 TCGA-AG-A002 TCGA-DC-5869 TCGA-F5-6811 
      100.01        12.76        35.80        20.98         5.03        32.19 

$`AGFG2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       85.05        26.99        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 
       18.05        31.00         2.01        12.99        24.00        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       49.41         6.77        12.10        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07        12.20        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 
       63.62        61.91        36.00        22.09        13.78        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6812 
       18.28         9.96        49.51        31.30        28.57         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  AGFG2 MUTATED AGFG2 WILD-TYPE 
           1.02            0.00 
  AGFG2 MUTATED AGFG2 WILD-TYPE 
         100.01          148.01 
  AGFG2 MUTATED AGFG2 WILD-TYPE 
          19.04           20.28 
[1] "1.0 - 100.0 (19.0)" "0.0 - 148.0 (20.3)"
[1] "hr=" "1.5"
D918V2, continuous
D918V3, binary
                 cls
clus                0   1
  AGFG2 MUTATED     9   3
  AGFG2 WILD-TYPE 357 116
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AGFG2 MUTATED      9    3
  AGFG2 WILD-TYPE  357  116
        clus
vv       AGFG2 MUTATED AGFG2 WILD-TYPE
  COLON              9             357
  RECTUM             3             116
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  AGFG2 MUTATED         1        0        4         4         1         0
  AGFG2 WILD-TYPE      90        1       28       134         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AGFG2 MUTATED           0          0          1          0        1         0
  AGFG2 WILD-TYPE        24         11         58         42       47        18
                 vv
clus              STAGE IVB
  AGFG2 MUTATED           0
  AGFG2 WILD-TYPE         1
D918V4, multiclass
            clus
vv           AGFG2 MUTATED AGFG2 WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               4              28
  STAGE IIA              4             134
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             0              42
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  AGFG2 MUTATED     0   1  10   1
  AGFG2 WILD-TYPE  17  91 319  49
D918V5, multiclass
    clus
vv   AGFG2 MUTATED AGFG2 WILD-TYPE
  T1             0              17
  T2             1              91
  T3            10             319
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  AGFG2 MUTATED    11   1   0
  AGFG2 WILD-TYPE 276 112  87
D918V6, multiclass
    clus
vv   AGFG2 MUTATED AGFG2 WILD-TYPE
  N0            11             276
  N1             1             112
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D918V7, binary
                 cls
clus                0   1
  AGFG2 MUTATED    11   1
  AGFG2 WILD-TYPE 364  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AGFG2 MUTATED     11    1
  AGFG2 WILD-TYPE  364   64
   clus
vv  AGFG2 MUTATED AGFG2 WILD-TYPE
  0            11             364
  1             1              64
[1] 2 2
[1] FALSE
D918V8, binary
                 cls
clus                0   1
  AGFG2 MUTATED     6   6
  AGFG2 WILD-TYPE 219 258
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AGFG2 MUTATED      6    6
  AGFG2 WILD-TYPE  219  258
        clus
vv       AGFG2 MUTATED AGFG2 WILD-TYPE
  FEMALE             6             219
  MALE               6             258
[1] 2 2
[1] FALSE
D918V9, binary
                 cls
clus                0   1
  AGFG2 MUTATED     9   1
  AGFG2 WILD-TYPE 341  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AGFG2 MUTATED      9    1
  AGFG2 WILD-TYPE  341   21
     clus
vv    AGFG2 MUTATED AGFG2 WILD-TYPE
  NO              9             341
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  AGFG2 MUTATED                      7                             2
  AGFG2 WILD-TYPE                  308                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  AGFG2 MUTATED                       3                              0
  AGFG2 WILD-TYPE                   103                             10
D918V10, multiclass
                                clus
vv                               AGFG2 MUTATED AGFG2 WILD-TYPE
  COLON ADENOCARCINOMA                       7             308
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      3             103
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  AGFG2 MUTATED     8   0   1   1
  AGFG2 WILD-TYPE 337   4  30  24
D918V11, multiclass
    clus
vv   AGFG2 MUTATED AGFG2 WILD-TYPE
  R0             8             337
  R1             0               4
  R2             1              30
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D918V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AGFG2 MUTATED                                  0     1
  AGFG2 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  AGFG2 MUTATED                           1     3
  AGFG2 WILD-TYPE                        21   223
D918V13, multiclass
                                  clus
vv                                 AGFG2 MUTATED AGFG2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        3             223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(919) Variable = VWA5A MUTATION ANALYSIS
D919V1, survival
                 sevent
clus2               0   1
  VWA5A MUTATED    11   3
  VWA5A WILD-TYPE 367  90
  VWA5A MUTATED VWA5A WILD-TYPE 
             14             457 
  VWA5A MUTATED VWA5A WILD-TYPE 
              3              90 
$`VWA5A MUTATED`
TCGA-A6-2683 TCGA-A6-6653 TCGA-AA-3522 TCGA-AA-3672 TCGA-AA-3821 TCGA-AA-3966 
       16.57        24.39        37.05         0.92         1.02         2.01 
TCGA-AA-A010 TCGA-AZ-6598 TCGA-CM-6168 TCGA-G4-6303 TCGA-G4-6307 TCGA-AG-A002 
       34.98        49.41        12.99        65.85        55.04        20.98 
TCGA-AG-A02N TCGA-EI-6508 
       61.97        20.91 

$`VWA5A WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 
       25.18        24.16        21.76        24.69        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
        9.07        24.03        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
        2.01        14.01        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
        0.99        25.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 
       26.01        24.00         2.01        20.98        34.03        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 
        5.13       106.75        22.36        62.79        88.21         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       14.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       53.62        44.68        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
        0.49        20.55        19.96        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  VWA5A MUTATED VWA5A WILD-TYPE 
           0.92            0.00 
  VWA5A MUTATED VWA5A WILD-TYPE 
          65.85          148.01 
  VWA5A MUTATED VWA5A WILD-TYPE 
         22.685          20.050 
[1] "0.9 - 65.8 (22.7)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.1"
D919V2, continuous
D919V3, binary
                 cls
clus                0   1
  VWA5A MUTATED    12   3
  VWA5A WILD-TYPE 354 116
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VWA5A MUTATED     12    3
  VWA5A WILD-TYPE  354  116
        clus
vv       VWA5A MUTATED VWA5A WILD-TYPE
  COLON             12             354
  RECTUM             3             116
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  VWA5A MUTATED         3        0        2         3         2         0
  VWA5A WILD-TYPE      88        1       30       135         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  VWA5A MUTATED           1          0          2          0        2         0
  VWA5A WILD-TYPE        23         11         57         42       46        18
                 vv
clus              STAGE IVB
  VWA5A MUTATED           0
  VWA5A WILD-TYPE         1
D919V4, multiclass
            clus
vv           VWA5A MUTATED VWA5A WILD-TYPE
  STAGE I                3              88
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA              3             135
  STAGE IIB              2               8
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             2              57
  STAGE IIIC             0              42
  STAGE IV               2              46
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  VWA5A MUTATED     0   3   9   3
  VWA5A WILD-TYPE  17  89 320  47
D919V5, multiclass
    clus
vv   VWA5A MUTATED VWA5A WILD-TYPE
  T1             0              17
  T2             3              89
  T3             9             320
  T4             3              47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  VWA5A MUTATED    11   4   0
  VWA5A WILD-TYPE 276 109  87
D919V6, multiclass
    clus
vv   VWA5A MUTATED VWA5A WILD-TYPE
  N0            11             276
  N1             4             109
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D919V7, binary
                 cls
clus                0   1
  VWA5A MUTATED    11   2
  VWA5A WILD-TYPE 364  63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VWA5A MUTATED     11    2
  VWA5A WILD-TYPE  364   63
   clus
vv  VWA5A MUTATED VWA5A WILD-TYPE
  0            11             364
  1             2              63
[1] 2 2
[1] FALSE
D919V8, binary
                 cls
clus                0   1
  VWA5A MUTATED    11   4
  VWA5A WILD-TYPE 214 260
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VWA5A MUTATED     11    4
  VWA5A WILD-TYPE  214  260
        clus
vv       VWA5A MUTATED VWA5A WILD-TYPE
  FEMALE            11             214
  MALE               4             260
[1] 2 2
[1] FALSE
D919V9, binary
                 cls
clus                0   1
  VWA5A MUTATED    12   0
  VWA5A WILD-TYPE 338  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VWA5A MUTATED     12    0
  VWA5A WILD-TYPE  338   22
     clus
vv    VWA5A MUTATED VWA5A WILD-TYPE
  NO             12             338
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  VWA5A MUTATED                     10                             2
  VWA5A WILD-TYPE                  305                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  VWA5A MUTATED                       3                              0
  VWA5A WILD-TYPE                   103                             10
D919V10, multiclass
                                clus
vv                               VWA5A MUTATED VWA5A WILD-TYPE
  COLON ADENOCARCINOMA                      10             305
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      3             103
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  VWA5A MUTATED    11   0   0   1
  VWA5A WILD-TYPE 334   4  31  24
D919V11, multiclass
    clus
vv   VWA5A MUTATED VWA5A WILD-TYPE
  R0            11             334
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D919V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  VWA5A MUTATED                                  0     0
  VWA5A WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  VWA5A MUTATED                           1     7
  VWA5A WILD-TYPE                        21   219
D919V13, multiclass
                                  clus
vv                                 VWA5A MUTATED VWA5A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        7             219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(920) Variable = BAIAP2L1 MUTATION ANALYSIS
D920V1, survival
                    sevent
clus2                  0   1
  BAIAP2L1 MUTATED    10   3
  BAIAP2L1 WILD-TYPE 368  90
  BAIAP2L1 MUTATED BAIAP2L1 WILD-TYPE 
                13                458 
  BAIAP2L1 MUTATED BAIAP2L1 WILD-TYPE 
                 3                 90 
$`BAIAP2L1 MUTATED`
TCGA-AA-3663 TCGA-AA-3966 TCGA-AA-3977 TCGA-AA-A01R TCGA-AD-5900 TCGA-AD-6964 
        6.97         2.01        25.02        35.01         0.07        10.88 
TCGA-AZ-4315 TCGA-D5-6927 TCGA-DM-A1DA TCGA-F4-6570 TCGA-G4-6586 TCGA-G4-6588 
       58.39         9.44         7.50         6.18        35.80        26.17 
TCGA-EI-6510 
       18.28 

$`BAIAP2L1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.05        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
        2.01        20.98        34.03        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       31.00        38.07         1.02         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
       40.96        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
       16.31         0.95        33.01        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       13.32        12.59       140.38        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 
      117.07        98.24         8.61        31.96        35.74        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       36.00        22.09        13.78        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-F5-6464 
       32.61         0.49        20.55        19.96        20.91         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  BAIAP2L1 MUTATED BAIAP2L1 WILD-TYPE 
              0.07               0.00 
  BAIAP2L1 MUTATED BAIAP2L1 WILD-TYPE 
             58.39             148.01 
  BAIAP2L1 MUTATED BAIAP2L1 WILD-TYPE 
            10.880             20.415 
[1] "0.1 - 58.4 (10.9)"  "0.0 - 148.0 (20.4)"
[1] "hr=" "1.7"
D920V2, continuous
D920V3, binary
                    cls
clus                   0   1
  BAIAP2L1 MUTATED    12   1
  BAIAP2L1 WILD-TYPE 354 118
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  BAIAP2L1 MUTATED     12    1
  BAIAP2L1 WILD-TYPE  354  118
        clus
vv       BAIAP2L1 MUTATED BAIAP2L1 WILD-TYPE
  COLON                12                354
  RECTUM                1                118
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  BAIAP2L1 MUTATED         1        0        1         6         0         0
  BAIAP2L1 WILD-TYPE      90        1       31       132        10         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  BAIAP2L1 MUTATED           1          0          0          1        0
  BAIAP2L1 WILD-TYPE        23         11         59         41       48
                    vv
clus                 STAGE IVA STAGE IVB
  BAIAP2L1 MUTATED           1         0
  BAIAP2L1 WILD-TYPE        17         1
D920V4, multiclass
            clus
vv           BAIAP2L1 MUTATED BAIAP2L1 WILD-TYPE
  STAGE I                   1                 90
  STAGE IA                  0                  1
  STAGE II                  1                 31
  STAGE IIA                 6                132
  STAGE IIB                 0                 10
  STAGE IIC                 0                  1
  STAGE III                 1                 23
  STAGE IIIA                0                 11
  STAGE IIIB                0                 59
  STAGE IIIC                1                 41
  STAGE IV                  0                 48
  STAGE IVA                 1                 17
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  BAIAP2L1 MUTATED     0   3   9   1
  BAIAP2L1 WILD-TYPE  17  89 320  49
D920V5, multiclass
    clus
vv   BAIAP2L1 MUTATED BAIAP2L1 WILD-TYPE
  T1                0                 17
  T2                3                 89
  T3                9                320
  T4                1                 49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  BAIAP2L1 MUTATED    10   0   3
  BAIAP2L1 WILD-TYPE 277 113  84
D920V6, multiclass
    clus
vv   BAIAP2L1 MUTATED BAIAP2L1 WILD-TYPE
  N0               10                277
  N1                0                113
  N2                3                 84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D920V7, binary
                    cls
clus                   0   1
  BAIAP2L1 MUTATED     9   0
  BAIAP2L1 WILD-TYPE 366  65
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  BAIAP2L1 MUTATED      9    0
  BAIAP2L1 WILD-TYPE  366   65
   clus
vv  BAIAP2L1 MUTATED BAIAP2L1 WILD-TYPE
  0                9                366
  1                0                 65
[1] 2 2
[1] FALSE
D920V8, binary
                    cls
clus                   0   1
  BAIAP2L1 MUTATED     6   7
  BAIAP2L1 WILD-TYPE 219 257
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  BAIAP2L1 MUTATED      6    7
  BAIAP2L1 WILD-TYPE  219  257
        clus
vv       BAIAP2L1 MUTATED BAIAP2L1 WILD-TYPE
  FEMALE                6                219
  MALE                  7                257
[1] 2 2
[1] FALSE
D920V9, binary
                    cls
clus                   0   1
  BAIAP2L1 MUTATED     9   1
  BAIAP2L1 WILD-TYPE 341  21
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  BAIAP2L1 MUTATED      9    1
  BAIAP2L1 WILD-TYPE  341   21
     clus
vv    BAIAP2L1 MUTATED BAIAP2L1 WILD-TYPE
  NO                 9                341
  YES                1                 21
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  BAIAP2L1 MUTATED                      9                             3
  BAIAP2L1 WILD-TYPE                  306                            44
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  BAIAP2L1 MUTATED                       1                              0
  BAIAP2L1 WILD-TYPE                   105                             10
D920V10, multiclass
                                clus
vv                               BAIAP2L1 MUTATED BAIAP2L1 WILD-TYPE
  COLON ADENOCARCINOMA                          9                306
  COLON MUCINOUS ADENOCARCINOMA                 3                 44
  RECTAL ADENOCARCINOMA                         1                105
  RECTAL MUCINOUS ADENOCARCINOMA                0                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  BAIAP2L1 MUTATED     9   0   0   0
  BAIAP2L1 WILD-TYPE 336   4  31  25
D920V11, multiclass
    clus
vv   BAIAP2L1 MUTATED BAIAP2L1 WILD-TYPE
  R0                9                336
  R1                0                  4
  R2                0                 31
  RX                0                 25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D920V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  BAIAP2L1 MUTATED                                  0     0
  BAIAP2L1 WILD-TYPE                                1    11
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  BAIAP2L1 MUTATED                           0     9
  BAIAP2L1 WILD-TYPE                        22   217
D920V13, multiclass
                                  clus
vv                                 BAIAP2L1 MUTATED BAIAP2L1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 11
  BLACK OR AFRICAN AMERICAN                       0                 22
  WHITE                                           9                217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(921) Variable = BRD4 MUTATION ANALYSIS
D921V1, survival
                sevent
clus2              0   1
  BRD4 MUTATED    19   1
  BRD4 WILD-TYPE 359  92
  BRD4 MUTATED BRD4 WILD-TYPE 
            20            451 
  BRD4 MUTATED BRD4 WILD-TYPE 
             1             92 
$`BRD4 MUTATED`
TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3510 TCGA-AA-3710 TCGA-AA-3812 TCGA-AA-3815 
       20.12        19.66        63.98        26.99        35.05        33.04 
TCGA-AA-3864 TCGA-AA-3949 TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6895 TCGA-CM-4752 
       53.00        26.01         0.07        56.55         0.72        13.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-6171 TCGA-D5-6539 TCGA-D5-6928 TCGA-DM-A1D9 
       15.02         5.03        14.04        12.49        11.64       140.38 
TCGA-G4-6628 TCGA-CI-6619 
       79.69         6.05 

$`BRD4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       23.87        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3818 TCGA-AA-3819 
       85.05        19.04        19.04        10.06         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-3952 
        2.01        12.99        24.00        33.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 
       39.98        18.05        40.96        21.37        15.52         0.79 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-5341 TCGA-CM-5344 
       23.05        20.02        37.02        25.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       22.98        30.08        32.02        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 
       14.99        12.99        13.02        15.02        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       17.13        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6930 
       12.43        14.30         9.04         9.44         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1DA 
      130.65        92.75        49.91        13.32        12.59         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 
       13.78        35.80        26.17        91.79        46.75        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.69         0.72        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  BRD4 MUTATED BRD4 WILD-TYPE 
          0.07           0.00 
  BRD4 MUTATED BRD4 WILD-TYPE 
        140.38         148.01 
  BRD4 MUTATED BRD4 WILD-TYPE 
         19.89          20.28 
[1] "0.1 - 140.4 (19.9)" "0.0 - 148.0 (20.3)"
[1] "hr=" "4.8"
D921V2, continuous
D921V3, binary
                cls
clus               0   1
  BRD4 MUTATED    20   1
  BRD4 WILD-TYPE 346 118
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRD4 MUTATED     20    1
  BRD4 WILD-TYPE  346  118
        clus
vv       BRD4 MUTATED BRD4 WILD-TYPE
  COLON            20            346
  RECTUM            1            118
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  BRD4 MUTATED         3        0        2         9         0         0
  BRD4 WILD-TYPE      88        1       30       129        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  BRD4 MUTATED           1          1          1          1        1         1
  BRD4 WILD-TYPE        23         10         58         41       47        17
                vv
clus             STAGE IVB
  BRD4 MUTATED           0
  BRD4 WILD-TYPE         1
D921V4, multiclass
            clus
vv           BRD4 MUTATED BRD4 WILD-TYPE
  STAGE I               3             88
  STAGE IA              0              1
  STAGE II              2             30
  STAGE IIA             9            129
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             1             23
  STAGE IIIA            1             10
  STAGE IIIB            1             58
  STAGE IIIC            1             41
  STAGE IV              1             47
  STAGE IVA             1             17
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  BRD4 MUTATED     0   3  17   1
  BRD4 WILD-TYPE  17  89 312  49
D921V5, multiclass
    clus
vv   BRD4 MUTATED BRD4 WILD-TYPE
  T1            0             17
  T2            3             89
  T3           17            312
  T4            1             49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  BRD4 MUTATED    15   5   1
  BRD4 WILD-TYPE 272 108  86
D921V6, multiclass
    clus
vv   BRD4 MUTATED BRD4 WILD-TYPE
  N0           15            272
  N1            5            108
  N2            1             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D921V7, binary
                cls
clus               0   1
  BRD4 MUTATED    15   2
  BRD4 WILD-TYPE 360  63
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRD4 MUTATED     15    2
  BRD4 WILD-TYPE  360   63
   clus
vv  BRD4 MUTATED BRD4 WILD-TYPE
  0           15            360
  1            2             63
[1] 2 2
[1] FALSE
D921V8, binary
                cls
clus               0   1
  BRD4 MUTATED     8  13
  BRD4 WILD-TYPE 217 251
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRD4 MUTATED      8   13
  BRD4 WILD-TYPE  217  251
        clus
vv       BRD4 MUTATED BRD4 WILD-TYPE
  FEMALE            8            217
  MALE             13            251
[1] 2 2
[1] FALSE
D921V9, binary
                cls
clus               0   1
  BRD4 MUTATED    15   0
  BRD4 WILD-TYPE 335  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRD4 MUTATED     15    0
  BRD4 WILD-TYPE  335   22
     clus
vv    BRD4 MUTATED BRD4 WILD-TYPE
  NO            15            335
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  BRD4 MUTATED                     15                             5
  BRD4 WILD-TYPE                  300                            42
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  BRD4 MUTATED                       1                              0
  BRD4 WILD-TYPE                   105                             10
D921V10, multiclass
                                clus
vv                               BRD4 MUTATED BRD4 WILD-TYPE
  COLON ADENOCARCINOMA                     15            300
  COLON MUCINOUS ADENOCARCINOMA             5             42
  RECTAL ADENOCARCINOMA                     1            105
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  BRD4 MUTATED    16   0   0   0
  BRD4 WILD-TYPE 329   4  31  25
D921V11, multiclass
    clus
vv   BRD4 MUTATED BRD4 WILD-TYPE
  R0           16            329
  R1            0              4
  R2            0             31
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D921V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  BRD4 MUTATED                                  0     1
  BRD4 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  BRD4 MUTATED                           1    12
  BRD4 WILD-TYPE                        21   214
D921V13, multiclass
                                  clus
vv                                 BRD4 MUTATED BRD4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                      12            214
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(922) Variable = GUCY1A3 MUTATION ANALYSIS
D922V1, survival
                   sevent
clus2                 0   1
  GUCY1A3 MUTATED    20   6
  GUCY1A3 WILD-TYPE 358  87
  GUCY1A3 MUTATED GUCY1A3 WILD-TYPE 
               26               445 
  GUCY1A3 MUTATED GUCY1A3 WILD-TYPE 
                6                87 
$`GUCY1A3 MUTATED`
TCGA-A6-5661 TCGA-A6-5666 TCGA-A6-6141 TCGA-A6-6651 TCGA-AA-3663 TCGA-AA-3666 
       33.53        32.71         8.38        21.76         6.97         2.01 
TCGA-AA-3673 TCGA-AA-3811 TCGA-AA-3851 TCGA-AA-3947 TCGA-AA-3977 TCGA-AA-A00N 
       50.04        10.06        33.07        33.01        25.02         4.01 
TCGA-AA-A010 TCGA-AA-A01D TCGA-AA-A01R TCGA-AD-6889 TCGA-CA-6717 TCGA-CM-5861 
       34.98        10.98        35.01        56.55        12.76        15.02 
TCGA-D5-6533 TCGA-DM-A0X9 TCGA-DM-A1DA TCGA-G4-6315 TCGA-AG-3885 TCGA-AG-A002 
        1.32       119.70         7.50        61.91        17.95        20.98 
TCGA-DC-6157 TCGA-DY-A1DD 
       27.95        57.24 

$`GUCY1A3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       22.06        27.09        22.52        25.08        25.18        24.16 
TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       24.69        24.39        23.87        20.12        19.66        20.28 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
        7.04         3.02         1.02        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3672 
       61.02        78.08         6.05        54.02        14.01         0.92 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
       10.06         0.00         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01F TCGA-AA-A01G 
       17.03        14.99        21.99         1.02        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T 
       31.00        31.00        38.07         1.02         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 
       18.05        40.96         0.07        21.37        15.52         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07        12.20        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 
       22.03        22.98        30.08        32.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 
       56.09        55.92        20.19        18.25        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
       10.26        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       13.32        12.59       140.38        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
        1.02        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
      126.44        41.36        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  GUCY1A3 MUTATED GUCY1A3 WILD-TYPE 
             1.32              0.00 
  GUCY1A3 MUTATED GUCY1A3 WILD-TYPE 
           119.70            148.01 
  GUCY1A3 MUTATED GUCY1A3 WILD-TYPE 
            23.39             20.05 
[1] "1.3 - 119.7 (23.4)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.1"
D922V2, continuous
D922V3, binary
                   cls
clus                  0   1
  GUCY1A3 MUTATED    22   4
  GUCY1A3 WILD-TYPE 344 115
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GUCY1A3 MUTATED     22    4
  GUCY1A3 WILD-TYPE  344  115
        clus
vv       GUCY1A3 MUTATED GUCY1A3 WILD-TYPE
  COLON               22               344
  RECTUM               4               115
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GUCY1A3 MUTATED         2        0        2         7         3         1
  GUCY1A3 WILD-TYPE      89        1       30       131         7         0
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GUCY1A3 MUTATED           3          0          4          2        1
  GUCY1A3 WILD-TYPE        21         11         55         40       47
                   vv
clus                STAGE IVA STAGE IVB
  GUCY1A3 MUTATED           0         0
  GUCY1A3 WILD-TYPE        18         1
D922V4, multiclass
            clus
vv           GUCY1A3 MUTATED GUCY1A3 WILD-TYPE
  STAGE I                  2                89
  STAGE IA                 0                 1
  STAGE II                 2                30
  STAGE IIA                7               131
  STAGE IIB                3                 7
  STAGE IIC                1                 0
  STAGE III                3                21
  STAGE IIIA               0                11
  STAGE IIIB               4                55
  STAGE IIIC               2                40
  STAGE IV                 1                47
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  GUCY1A3 MUTATED     0   3  18   5
  GUCY1A3 WILD-TYPE  17  89 311  45
D922V5, multiclass
    clus
vv   GUCY1A3 MUTATED GUCY1A3 WILD-TYPE
  T1               0                17
  T2               3                89
  T3              18               311
  T4               5                45
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  GUCY1A3 MUTATED    17   5   4
  GUCY1A3 WILD-TYPE 270 108  83
D922V6, multiclass
    clus
vv   GUCY1A3 MUTATED GUCY1A3 WILD-TYPE
  N0              17               270
  N1               5               108
  N2               4                83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D922V7, binary
                   cls
clus                  0   1
  GUCY1A3 MUTATED    23   1
  GUCY1A3 WILD-TYPE 352  64
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GUCY1A3 MUTATED     23    1
  GUCY1A3 WILD-TYPE  352   64
   clus
vv  GUCY1A3 MUTATED GUCY1A3 WILD-TYPE
  0              23               352
  1               1                64
[1] 2 2
[1] FALSE
D922V8, binary
                   cls
clus                  0   1
  GUCY1A3 MUTATED    13  13
  GUCY1A3 WILD-TYPE 212 251
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GUCY1A3 MUTATED     13   13
  GUCY1A3 WILD-TYPE  212  251
        clus
vv       GUCY1A3 MUTATED GUCY1A3 WILD-TYPE
  FEMALE              13               212
  MALE                13               251
[1] 2 2
[1] FALSE
D922V9, binary
                   cls
clus                  0   1
  GUCY1A3 MUTATED    16   2
  GUCY1A3 WILD-TYPE 334  20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GUCY1A3 MUTATED     16    2
  GUCY1A3 WILD-TYPE  334   20
     clus
vv    GUCY1A3 MUTATED GUCY1A3 WILD-TYPE
  NO               16               334
  YES               2                20
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  GUCY1A3 MUTATED                     17                             5
  GUCY1A3 WILD-TYPE                  298                            42
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  GUCY1A3 MUTATED                       4                              0
  GUCY1A3 WILD-TYPE                   102                             10
D922V10, multiclass
                                clus
vv                               GUCY1A3 MUTATED GUCY1A3 WILD-TYPE
  COLON ADENOCARCINOMA                        17               298
  COLON MUCINOUS ADENOCARCINOMA                5                42
  RECTAL ADENOCARCINOMA                        4               102
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  GUCY1A3 MUTATED    17   0   0   1
  GUCY1A3 WILD-TYPE 328   4  31  24
D922V11, multiclass
    clus
vv   GUCY1A3 MUTATED GUCY1A3 WILD-TYPE
  R0              17               328
  R1               0                 4
  R2               0                31
  RX               1                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D922V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GUCY1A3 MUTATED                                  0     2
  GUCY1A3 WILD-TYPE                                1     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  GUCY1A3 MUTATED                           3     8
  GUCY1A3 WILD-TYPE                        19   218
D922V13, multiclass
                                  clus
vv                                 GUCY1A3 MUTATED GUCY1A3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          2                 9
  BLACK OR AFRICAN AMERICAN                      3                19
  WHITE                                          8               218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(923) Variable = MCF2L2 MUTATION ANALYSIS
D923V1, survival
                  sevent
clus2                0   1
  MCF2L2 MUTATED    17   4
  MCF2L2 WILD-TYPE 361  89
  MCF2L2 MUTATED MCF2L2 WILD-TYPE 
              21              450 
  MCF2L2 MUTATED MCF2L2 WILD-TYPE 
               4               89 
$`MCF2L2 MUTATED`
TCGA-AA-3510 TCGA-AA-3952 TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A01R TCGA-AA-A02Y 
       63.98         2.01        25.02         4.01        35.01        39.98 
TCGA-AD-6964 TCGA-AU-6004 TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-6164 TCGA-D5-6535 
       10.88        27.09        12.76        10.06        29.03        15.12 
TCGA-D5-6536 TCGA-D5-6540 TCGA-D5-6929 TCGA-G4-6309 TCGA-G4-6588 TCGA-AG-3892 
       17.85        16.14         4.80        85.48        26.17        13.02 
TCGA-AG-3909 TCGA-AG-A002 TCGA-AG-A02N 
       19.99        20.98        61.97 

$`MCF2L2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
       38.07         1.02         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
       14.01         0.92        41.00        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 
       22.42        27.42         0.20        14.50        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       12.20        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
        2.96        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 
       43.27         4.80        17.13        12.49        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       11.64         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 
       65.85        53.62        44.68        55.04        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        35.80        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       17.95        36.95        17.03        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       48.03        32.02        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 
       10.98        49.97         1.94        38.96        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  MCF2L2 MUTATED MCF2L2 WILD-TYPE 
            2.01             0.00 
  MCF2L2 MUTATED MCF2L2 WILD-TYPE 
           85.48           148.01 
  MCF2L2 MUTATED MCF2L2 WILD-TYPE 
          19.990           20.235 
[1] "2.0 - 85.5 (20.0)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1"  
D923V2, continuous
D923V3, binary
                  cls
clus                 0   1
  MCF2L2 MUTATED    19   4
  MCF2L2 WILD-TYPE 347 115
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MCF2L2 MUTATED     19    4
  MCF2L2 WILD-TYPE  347  115
        clus
vv       MCF2L2 MUTATED MCF2L2 WILD-TYPE
  COLON              19              347
  RECTUM              4              115
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MCF2L2 MUTATED         5        0        2         6         2         0
  MCF2L2 WILD-TYPE      86        1       30       132         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MCF2L2 MUTATED           1          0          3          1        1
  MCF2L2 WILD-TYPE        23         11         56         41       47
                  vv
clus               STAGE IVA STAGE IVB
  MCF2L2 MUTATED           0         0
  MCF2L2 WILD-TYPE        18         1
D923V4, multiclass
            clus
vv           MCF2L2 MUTATED MCF2L2 WILD-TYPE
  STAGE I                 5               86
  STAGE IA                0                1
  STAGE II                2               30
  STAGE IIA               6              132
  STAGE IIB               2                8
  STAGE IIC               0                1
  STAGE III               1               23
  STAGE IIIA              0               11
  STAGE IIIB              3               56
  STAGE IIIC              1               41
  STAGE IV                1               47
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  MCF2L2 MUTATED     1   5  14   3
  MCF2L2 WILD-TYPE  16  87 315  47
D923V5, multiclass
    clus
vv   MCF2L2 MUTATED MCF2L2 WILD-TYPE
  T1              1               16
  T2              5               87
  T3             14              315
  T4              3               47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  MCF2L2 MUTATED    16   4   3
  MCF2L2 WILD-TYPE 271 109  84
D923V6, multiclass
    clus
vv   MCF2L2 MUTATED MCF2L2 WILD-TYPE
  N0             16              271
  N1              4              109
  N2              3               84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D923V7, binary
                  cls
clus                 0   1
  MCF2L2 MUTATED    18   1
  MCF2L2 WILD-TYPE 357  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MCF2L2 MUTATED     18    1
  MCF2L2 WILD-TYPE  357   64
   clus
vv  MCF2L2 MUTATED MCF2L2 WILD-TYPE
  0             18              357
  1              1               64
[1] 2 2
[1] FALSE
D923V8, binary
                  cls
clus                 0   1
  MCF2L2 MUTATED    10  13
  MCF2L2 WILD-TYPE 215 251
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MCF2L2 MUTATED     10   13
  MCF2L2 WILD-TYPE  215  251
        clus
vv       MCF2L2 MUTATED MCF2L2 WILD-TYPE
  FEMALE             10              215
  MALE               13              251
[1] 2 2
[1] FALSE
D923V9, binary
                  cls
clus                 0   1
  MCF2L2 MUTATED    15   1
  MCF2L2 WILD-TYPE 335  21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MCF2L2 MUTATED     15    1
  MCF2L2 WILD-TYPE  335   21
     clus
vv    MCF2L2 MUTATED MCF2L2 WILD-TYPE
  NO              15              335
  YES              1               21
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MCF2L2 MUTATED                     15                             4
  MCF2L2 WILD-TYPE                  300                            43
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MCF2L2 MUTATED                       4                              0
  MCF2L2 WILD-TYPE                   102                             10
D923V10, multiclass
                                clus
vv                               MCF2L2 MUTATED MCF2L2 WILD-TYPE
  COLON ADENOCARCINOMA                       15              300
  COLON MUCINOUS ADENOCARCINOMA               4               43
  RECTAL ADENOCARCINOMA                       4              102
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  MCF2L2 MUTATED    17   0   0   4
  MCF2L2 WILD-TYPE 328   4  31  21
D923V11, multiclass
    clus
vv   MCF2L2 MUTATED MCF2L2 WILD-TYPE
  R0             17              328
  R1              0                4
  R2              0               31
  RX              4               21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D923V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MCF2L2 MUTATED                                  0     2
  MCF2L2 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  MCF2L2 MUTATED                           1     9
  MCF2L2 WILD-TYPE                        21   217
D923V13, multiclass
                                  clus
vv                                 MCF2L2 MUTATED MCF2L2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                9
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                         9              217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(924) Variable = DNAH17 MUTATION ANALYSIS
D924V1, survival
                  sevent
clus2                0   1
  DNAH17 MUTATED    26   6
  DNAH17 WILD-TYPE 352  87
  DNAH17 MUTATED DNAH17 WILD-TYPE 
              32              439 
  DNAH17 MUTATED DNAH17 WILD-TYPE 
               6               87 
$`DNAH17 MUTATED`
TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-6141 TCGA-A6-6780 TCGA-AA-3492 TCGA-AA-3510 
       29.19        23.61         8.38        20.12         3.02        63.98 
TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3713 TCGA-AA-3968 TCGA-AD-5900 TCGA-AD-6889 
       78.08         6.97        19.04        21.99         0.07        56.55 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-6601 TCGA-CA-6716 TCGA-CA-6717 
       17.82        58.39         1.41       100.01        12.20        12.76 
TCGA-CA-6718 TCGA-CK-5912 TCGA-CM-4752 TCGA-CM-5861 TCGA-CM-5868 TCGA-CM-6168 
       10.06        49.08        13.02        15.02        17.03        12.99 
TCGA-D5-5537 TCGA-D5-6540 TCGA-D5-6541 TCGA-DM-A1HB TCGA-G4-6293 TCGA-G4-6628 
       45.40        16.14        15.58       135.65       133.18        79.69 
TCGA-EI-6507 TCGA-F5-6812 
       19.96         0.66 

$`DNAH17 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5664 TCGA-A6-5665 
       32.91        31.63        30.44        33.53        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       32.71        27.09        22.52        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 
       21.76        24.69        24.39        23.87        19.66        20.28 
TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        7.04         1.02        35.01         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 
       20.98        19.99        13.94        19.99        61.02         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       40.96        21.37        15.52         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AZ-4616 TCGA-AZ-4681 
       16.31         0.95        33.01        21.44         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6719 TCGA-CK-4947 
        3.06         3.25         3.29         0.07        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
      148.01        85.45        15.62        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       25.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
        5.03        15.02        15.02        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6169 TCGA-CM-6170 
       29.03        16.04        21.99        14.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       11.01        10.06        12.03        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6898 TCGA-D5-6920 
       17.85         4.80        17.13        12.49         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 
       12.59       140.38         7.50        44.32       131.51       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
        0.53        47.41        35.31        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
       32.61         0.49        20.55        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6813 TCGA-G5-6235 
       49.51        31.30        28.57        32.19         0.69        55.76 
TCGA-G5-6641 
       26.43 

  DNAH17 MUTATED DNAH17 WILD-TYPE 
            0.07             0.00 
  DNAH17 MUTATED DNAH17 WILD-TYPE 
          135.65           148.01 
  DNAH17 MUTATED DNAH17 WILD-TYPE 
           18.43            20.91 
[1] "0.1 - 135.7 (18.4)" "0.0 - 148.0 (20.9)"
[1] "hr=" "1.4"
D924V2, continuous
D924V3, binary
                  cls
clus                 0   1
  DNAH17 MUTATED    30   2
  DNAH17 WILD-TYPE 336 117
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DNAH17 MUTATED     30    2
  DNAH17 WILD-TYPE  336  117
        clus
vv       DNAH17 MUTATED DNAH17 WILD-TYPE
  COLON              30              336
  RECTUM              2              117
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DNAH17 MUTATED         5        0        5        14         0         0
  DNAH17 WILD-TYPE      86        1       27       124        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DNAH17 MUTATED           1          0          2          1        2
  DNAH17 WILD-TYPE        23         11         57         41       46
                  vv
clus               STAGE IVA STAGE IVB
  DNAH17 MUTATED           2         0
  DNAH17 WILD-TYPE        16         1
D924V4, multiclass
            clus
vv           DNAH17 MUTATED DNAH17 WILD-TYPE
  STAGE I                 5               86
  STAGE IA                0                1
  STAGE II                5               27
  STAGE IIA              14              124
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               1               23
  STAGE IIIA              0               11
  STAGE IIIB              2               57
  STAGE IIIC              1               41
  STAGE IV                2               46
  STAGE IVA               2               16
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  DNAH17 MUTATED     0   5  25   2
  DNAH17 WILD-TYPE  17  87 304  48
D924V5, multiclass
    clus
vv   DNAH17 MUTATED DNAH17 WILD-TYPE
  T1              0               17
  T2              5               87
  T3             25              304
  T4              2               48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  DNAH17 MUTATED    24   4   4
  DNAH17 WILD-TYPE 263 109  83
D924V6, multiclass
    clus
vv   DNAH17 MUTATED DNAH17 WILD-TYPE
  N0             24              263
  N1              4              109
  N2              4               83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D924V7, binary
                  cls
clus                 0   1
  DNAH17 MUTATED    24   4
  DNAH17 WILD-TYPE 351  61
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DNAH17 MUTATED     24    4
  DNAH17 WILD-TYPE  351   61
   clus
vv  DNAH17 MUTATED DNAH17 WILD-TYPE
  0             24              351
  1              4               61
[1] 2 2
[1] FALSE
D924V8, binary
                  cls
clus                 0   1
  DNAH17 MUTATED     8  24
  DNAH17 WILD-TYPE 217 240
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DNAH17 MUTATED      8   24
  DNAH17 WILD-TYPE  217  240
        clus
vv       DNAH17 MUTATED DNAH17 WILD-TYPE
  FEMALE              8              217
  MALE               24              240
[1] 2 2
[1] FALSE
D924V9, binary
                  cls
clus                 0   1
  DNAH17 MUTATED    27   1
  DNAH17 WILD-TYPE 323  21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DNAH17 MUTATED     27    1
  DNAH17 WILD-TYPE  323   21
     clus
vv    DNAH17 MUTATED DNAH17 WILD-TYPE
  NO              27              323
  YES              1               21
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  DNAH17 MUTATED                     25                             4
  DNAH17 WILD-TYPE                  290                            43
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  DNAH17 MUTATED                       2                              0
  DNAH17 WILD-TYPE                   104                             10
D924V10, multiclass
                                clus
vv                               DNAH17 MUTATED DNAH17 WILD-TYPE
  COLON ADENOCARCINOMA                       25              290
  COLON MUCINOUS ADENOCARCINOMA               4               43
  RECTAL ADENOCARCINOMA                       2              104
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  DNAH17 MUTATED    18   0   1   5
  DNAH17 WILD-TYPE 327   4  30  20
D924V11, multiclass
    clus
vv   DNAH17 MUTATED DNAH17 WILD-TYPE
  R0             18              327
  R1              0                4
  R2              1               30
  RX              5               20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D924V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DNAH17 MUTATED                                  0     4
  DNAH17 WILD-TYPE                                1     7
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  DNAH17 MUTATED                           5    17
  DNAH17 WILD-TYPE                        17   209
D924V13, multiclass
                                  clus
vv                                 DNAH17 MUTATED DNAH17 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         4                7
  BLACK OR AFRICAN AMERICAN                     5               17
  WHITE                                        17              209
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(925) Variable = ANKRD17 MUTATION ANALYSIS
D925V1, survival
                   sevent
clus2                 0   1
  ANKRD17 MUTATED    25   4
  ANKRD17 WILD-TYPE 353  89
  ANKRD17 MUTATED ANKRD17 WILD-TYPE 
               29               442 
  ANKRD17 MUTATED ANKRD17 WILD-TYPE 
                4                89 
$`ANKRD17 MUTATED`
TCGA-A6-5661 TCGA-A6-5666 TCGA-A6-6653 TCGA-AA-3510 TCGA-AA-3525 TCGA-AA-3715 
       33.53        32.71        24.39        63.98         8.05        19.04 
TCGA-AA-3833 TCGA-AA-3977 TCGA-AA-A00J TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A02W 
       15.95        25.02        18.05         4.01        34.98        41.00 
TCGA-AD-5900 TCGA-AZ-4315 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4952 TCGA-CK-6748 
        0.07        58.39        12.76        10.06        15.62         1.91 
TCGA-CM-4746 TCGA-CM-5860 TCGA-CM-5861 TCGA-D5-5539 TCGA-D5-6540 TCGA-F4-6856 
       37.02        32.02        15.02        19.59        16.14        35.31 
TCGA-G4-6309 TCGA-AF-5654 TCGA-AG-A002 TCGA-AG-A015 TCGA-EI-6507 
       85.48        16.83        20.98        36.03        19.96 

$`ANKRD17 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       22.06        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       24.16        21.76        24.69        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 
       20.28         7.04         3.02         1.02        35.01         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       37.05        36.03        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       78.08         6.05         6.97        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
        1.02        17.98        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       19.00        30.02        34.03        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 
       14.01         0.92        39.98        18.05        40.96        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        33.01        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 
       12.20        14.30        17.56       148.01        85.45        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 
       51.32         9.99        21.14        82.95       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       20.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       30.08         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       45.40        12.26        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       12.49        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       47.41       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       55.04        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       14.50        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6508 
       24.13        51.48        32.61         0.49        20.55        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  ANKRD17 MUTATED ANKRD17 WILD-TYPE 
             0.07              0.00 
  ANKRD17 MUTATED ANKRD17 WILD-TYPE 
            85.48            148.01 
  ANKRD17 MUTATED ANKRD17 WILD-TYPE 
           19.960            20.235 
[1] "0.1 - 85.5 (20.0)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.4"
D925V2, continuous
D925V3, binary
                   cls
clus                  0   1
  ANKRD17 MUTATED    26   4
  ANKRD17 WILD-TYPE 340 115
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD17 MUTATED     26    4
  ANKRD17 WILD-TYPE  340  115
        clus
vv       ANKRD17 MUTATED ANKRD17 WILD-TYPE
  COLON               26               340
  RECTUM               4               115
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ANKRD17 MUTATED         9        0        2         8         3         1
  ANKRD17 WILD-TYPE      82        1       30       130         7         0
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ANKRD17 MUTATED           0          1          3          1        1
  ANKRD17 WILD-TYPE        24         10         56         41       47
                   vv
clus                STAGE IVA STAGE IVB
  ANKRD17 MUTATED           0         0
  ANKRD17 WILD-TYPE        18         1
D925V4, multiclass
            clus
vv           ANKRD17 MUTATED ANKRD17 WILD-TYPE
  STAGE I                  9                82
  STAGE IA                 0                 1
  STAGE II                 2                30
  STAGE IIA                8               130
  STAGE IIB                3                 7
  STAGE IIC                1                 0
  STAGE III                0                24
  STAGE IIIA               1                10
  STAGE IIIB               3                56
  STAGE IIIC               1                41
  STAGE IV                 1                47
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  ANKRD17 MUTATED     1   9  14   6
  ANKRD17 WILD-TYPE  16  83 315  44
D925V5, multiclass
    clus
vv   ANKRD17 MUTATED ANKRD17 WILD-TYPE
  T1               1                16
  T2               9                83
  T3              14               315
  T4               6                44
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  ANKRD17 MUTATED    24   5   1
  ANKRD17 WILD-TYPE 263 108  86
D925V6, multiclass
    clus
vv   ANKRD17 MUTATED ANKRD17 WILD-TYPE
  N0              24               263
  N1               5               108
  N2               1                86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D925V7, binary
                   cls
clus                  0   1
  ANKRD17 MUTATED    26   1
  ANKRD17 WILD-TYPE 349  64
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD17 MUTATED     26    1
  ANKRD17 WILD-TYPE  349   64
   clus
vv  ANKRD17 MUTATED ANKRD17 WILD-TYPE
  0              26               349
  1               1                64
[1] 2 2
[1] FALSE
D925V8, binary
                   cls
clus                  0   1
  ANKRD17 MUTATED    11  19
  ANKRD17 WILD-TYPE 214 245
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD17 MUTATED     11   19
  ANKRD17 WILD-TYPE  214  245
        clus
vv       ANKRD17 MUTATED ANKRD17 WILD-TYPE
  FEMALE              11               214
  MALE                19               245
[1] 2 2
[1] FALSE
D925V9, binary
                   cls
clus                  0   1
  ANKRD17 MUTATED    26   0
  ANKRD17 WILD-TYPE 324  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD17 MUTATED     26    0
  ANKRD17 WILD-TYPE  324   22
     clus
vv    ANKRD17 MUTATED ANKRD17 WILD-TYPE
  NO               26               324
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ANKRD17 MUTATED                     17                             9
  ANKRD17 WILD-TYPE                  298                            38
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ANKRD17 MUTATED                       4                              0
  ANKRD17 WILD-TYPE                   102                             10
D925V10, multiclass
                                clus
vv                               ANKRD17 MUTATED ANKRD17 WILD-TYPE
  COLON ADENOCARCINOMA                        17               298
  COLON MUCINOUS ADENOCARCINOMA                9                38
  RECTAL ADENOCARCINOMA                        4               102
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  ANKRD17 MUTATED    22   0   0   5
  ANKRD17 WILD-TYPE 323   4  31  20
D925V11, multiclass
    clus
vv   ANKRD17 MUTATED ANKRD17 WILD-TYPE
  R0              22               323
  R1               0                 4
  R2               0                31
  RX               5                20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D925V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ANKRD17 MUTATED                                  0     2
  ANKRD17 WILD-TYPE                                1     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  ANKRD17 MUTATED                           3    14
  ANKRD17 WILD-TYPE                        19   212
D925V13, multiclass
                                  clus
vv                                 ANKRD17 MUTATED ANKRD17 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          2                 9
  BLACK OR AFRICAN AMERICAN                      3                19
  WHITE                                         14               212
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(926) Variable = RAB42 MUTATION ANALYSIS
D926V1, survival
                 sevent
clus2               0   1
  RAB42 MUTATED     3   0
  RAB42 WILD-TYPE 375  93
  RAB42 MUTATED RAB42 WILD-TYPE 
              3             468 
  RAB42 MUTATED RAB42 WILD-TYPE 
              0              93 
$`RAB42 MUTATED`
TCGA-A6-6781 TCGA-AA-3663 TCGA-G4-6304 
       19.66         6.97        53.62 

$`RAB42 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       74.56        65.85        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  RAB42 MUTATED RAB42 WILD-TYPE 
           6.97            0.00 
  RAB42 MUTATED RAB42 WILD-TYPE 
          53.62          148.01 
  RAB42 MUTATED RAB42 WILD-TYPE 
         19.660          20.235 
[1] "7.0 - 53.6 (19.7)"  "0.0 - 148.0 (20.2)"
[1] "hr="     "3300000"
D926V2, continuous
D926V3, binary
                 cls
clus                0   1
  RAB42 MUTATED     4   0
  RAB42 WILD-TYPE 362 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RAB42 MUTATED      4    0
  RAB42 WILD-TYPE  362  119
        clus
vv       RAB42 MUTATED RAB42 WILD-TYPE
  COLON              4             362
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RAB42 MUTATED         0        0        2         0         1         0
  RAB42 WILD-TYPE      91        1       30       138         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RAB42 MUTATED           0          0          0          1        0         0
  RAB42 WILD-TYPE        24         11         59         41       48        18
                 vv
clus              STAGE IVB
  RAB42 MUTATED           0
  RAB42 WILD-TYPE         1
D926V4, multiclass
            clus
vv           RAB42 MUTATED RAB42 WILD-TYPE
  STAGE I                0              91
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA              0             138
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             1              41
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  RAB42 MUTATED     0   0   1   3
  RAB42 WILD-TYPE  17  92 328  47
D926V5, multiclass
    clus
vv   RAB42 MUTATED RAB42 WILD-TYPE
  T1             0              17
  T2             0              92
  T3             1             328
  T4             3              47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  RAB42 MUTATED     3   1   0
  RAB42 WILD-TYPE 284 112  87
D926V6, multiclass
    clus
vv   RAB42 MUTATED RAB42 WILD-TYPE
  N0             3             284
  N1             1             112
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D926V7, binary
                 cls
clus                0   1
  RAB42 MUTATED     3   0
  RAB42 WILD-TYPE 372  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RAB42 MUTATED      3    0
  RAB42 WILD-TYPE  372   65
   clus
vv  RAB42 MUTATED RAB42 WILD-TYPE
  0             3             372
  1             0              65
[1] 2 2
[1] FALSE
D926V8, binary
                 cls
clus                0   1
  RAB42 MUTATED     2   2
  RAB42 WILD-TYPE 223 262
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RAB42 MUTATED      2    2
  RAB42 WILD-TYPE  223  262
        clus
vv       RAB42 MUTATED RAB42 WILD-TYPE
  FEMALE             2             223
  MALE               2             262
[1] 2 2
[1] FALSE
D926V9, binary
                 cls
clus                0   1
  RAB42 MUTATED     3   0
  RAB42 WILD-TYPE 347  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RAB42 MUTATED      3    0
  RAB42 WILD-TYPE  347   22
     clus
vv    RAB42 MUTATED RAB42 WILD-TYPE
  NO              3             347
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  RAB42 MUTATED                      3                             1
  RAB42 WILD-TYPE                  312                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  RAB42 MUTATED                       0                              0
  RAB42 WILD-TYPE                   106                             10
D926V10, multiclass
                                clus
vv                               RAB42 MUTATED RAB42 WILD-TYPE
  COLON ADENOCARCINOMA                       3             312
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  RAB42 MUTATED     4   0   0   0
  RAB42 WILD-TYPE 341   4  31  25
D926V11, multiclass
    clus
vv   RAB42 MUTATED RAB42 WILD-TYPE
  R0             4             341
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D926V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RAB42 MUTATED                                  0     0
  RAB42 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  RAB42 MUTATED                           0     2
  RAB42 WILD-TYPE                        22   224
D926V13, multiclass
[1] "Remove cluster labels:" "RAB42 MUTATED"         
clus
  RAB42 MUTATED RAB42 WILD-TYPE 
              2             258 
     TCGA-A6-2671      TCGA-A6-2672      TCGA-A6-2674      TCGA-A6-2676 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-A6-2677      TCGA-A6-2678      TCGA-A6-2683      TCGA-A6-3807 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-A6-3808      TCGA-A6-3809      TCGA-A6-3810      TCGA-A6-4105 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-A6-5656      TCGA-A6-5657      TCGA-A6-5659      TCGA-A6-5660 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-A6-5661      TCGA-A6-5662      TCGA-A6-5664      TCGA-A6-5665 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-A6-5666      TCGA-A6-6137      TCGA-A6-6138      TCGA-A6-6141 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-A6-6142      TCGA-A6-6648      TCGA-A6-6649      TCGA-A6-6651 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-A6-6652      TCGA-A6-6653      TCGA-A6-6654      TCGA-A6-6780 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-A6-6782      TCGA-AD-5900      TCGA-AD-6548      TCGA-AD-6888 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-AD-6889      TCGA-AD-6890      TCGA-AD-6895      TCGA-AD-6899 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-AD-6901      TCGA-AD-6963      TCGA-AD-6964      TCGA-AD-6965 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-AU-3779      TCGA-AU-6004      TCGA-AY-4070      TCGA-AY-4071 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-AY-5543      TCGA-AY-6196      TCGA-AY-6197      TCGA-AY-6386 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-AZ-4315      TCGA-AZ-4323      TCGA-AZ-4616      TCGA-AZ-4681 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-AZ-4682      TCGA-AZ-5403      TCGA-AZ-5407      TCGA-AZ-6598 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-AZ-6599      TCGA-AZ-6600      TCGA-AZ-6601      TCGA-AZ-6603 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-AZ-6605      TCGA-AZ-6606      TCGA-AZ-6607      TCGA-AZ-6608 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-CA-5254      TCGA-CA-5255      TCGA-CA-5796      TCGA-CA-5797 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-CA-6715      TCGA-CA-6716      TCGA-CA-6717      TCGA-CA-6718 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-CA-6719      TCGA-CK-4947      TCGA-CK-4948      TCGA-CK-4950 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-CK-4952      TCGA-CK-5912      TCGA-CK-5913      TCGA-CK-5914 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-CK-5915      TCGA-CK-5916      TCGA-CK-6746      TCGA-CK-6747 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-CK-6748      TCGA-CK-6751      TCGA-CM-4743      TCGA-CM-4744 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-CM-4746      TCGA-CM-4747      TCGA-CM-4752      TCGA-CM-5341 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-CM-5344      TCGA-CM-5348      TCGA-CM-5349      TCGA-CM-5860 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-CM-5861      TCGA-CM-5862      TCGA-CM-5863      TCGA-CM-5864 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-CM-5868      TCGA-CM-6161      TCGA-CM-6162      TCGA-CM-6163 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-CM-6164      TCGA-CM-6165      TCGA-CM-6166      TCGA-CM-6167 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-CM-6168      TCGA-CM-6169      TCGA-CM-6170      TCGA-CM-6171 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-CM-6172      TCGA-CM-6674      TCGA-CM-6675      TCGA-CM-6676 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-CM-6677      TCGA-CM-6678      TCGA-CM-6679      TCGA-CM-6680 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-D5-5537      TCGA-D5-5538      TCGA-D5-5539      TCGA-D5-5540 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-D5-5541      TCGA-D5-6529      TCGA-D5-6532      TCGA-D5-6533 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-D5-6534      TCGA-D5-6535      TCGA-D5-6536      TCGA-D5-6537 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-D5-6538      TCGA-D5-6539      TCGA-D5-6540      TCGA-D5-6541 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-D5-6898      TCGA-D5-6920      TCGA-D5-6922      TCGA-D5-6923 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-D5-6924      TCGA-D5-6926      TCGA-D5-6927      TCGA-D5-6928 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-D5-6929      TCGA-D5-6930      TCGA-D5-6931      TCGA-D5-6932 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-D5-7000      TCGA-DM-A0X9      TCGA-DM-A0XD      TCGA-DM-A0XF 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-DM-A1D0      TCGA-DM-A1D4      TCGA-DM-A1D6      TCGA-DM-A1D7 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-DM-A1D8      TCGA-DM-A1D9      TCGA-DM-A1DA      TCGA-DM-A1DB 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-DM-A1HA      TCGA-DM-A1HB      TCGA-DM-A282      TCGA-DM-A285 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-DM-A28C      TCGA-DM-A28E      TCGA-DM-A28F      TCGA-DM-A28G 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-DM-A28H      TCGA-DM-A28K      TCGA-F4-6459      TCGA-F4-6460 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-F4-6569      TCGA-F4-6570      TCGA-F4-6703      TCGA-F4-6704 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-F4-6805      TCGA-F4-6806      TCGA-F4-6807      TCGA-F4-6808 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-F4-6809      TCGA-F4-6854      TCGA-F4-6855      TCGA-F4-6856 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-G4-6293      TCGA-G4-6299      TCGA-G4-6303      TCGA-G4-6306 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-G4-6307      TCGA-G4-6309      TCGA-G4-6310      TCGA-G4-6315 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-G4-6317      TCGA-G4-6321      TCGA-G4-6323      TCGA-G4-6586 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-G4-6588      TCGA-G4-6625      TCGA-G4-6626      TCGA-G4-6628 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-AF-2687      TCGA-AF-2689      TCGA-AF-2691      TCGA-AF-2692 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-AF-2693      TCGA-AF-3400      TCGA-AF-3913      TCGA-AF-4110 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-AF-5654      TCGA-AF-6136      TCGA-AF-6655      TCGA-AF-6672 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-AH-6544      TCGA-AH-6547      TCGA-AH-6549      TCGA-AH-6643 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-AH-6644      TCGA-CI-6619      TCGA-CI-6620      TCGA-CI-6621 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-CI-6622      TCGA-CI-6624      TCGA-CL-5917      TCGA-CL-5918 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-DC-5337      TCGA-DC-5869      TCGA-DC-6155      TCGA-DC-6157 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-DC-6158      TCGA-DC-6160      TCGA-DC-6681      TCGA-DC-6682 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-DC-6683      TCGA-DT-5265      TCGA-DY-A0XA      TCGA-DY-A1DC 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-DY-A1DD      TCGA-DY-A1DF      TCGA-DY-A1DG      TCGA-DY-A1H8 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-EF-5830      TCGA-EI-6506      TCGA-EI-6507      TCGA-EI-6508 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-EI-6510      TCGA-F5-6464      TCGA-F5-6465      TCGA-F5-6571 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-F5-6702      TCGA-F5-6811      TCGA-F5-6812      TCGA-F5-6813 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 
     TCGA-G5-6235      TCGA-G5-6641 
"RAB42 WILD-TYPE" "RAB42 WILD-TYPE" 

Clustering(927) Variable = PSMA2 MUTATION ANALYSIS
D927V1, survival
                 sevent
clus2               0   1
  PSMA2 MUTATED     4   2
  PSMA2 WILD-TYPE 374  91
  PSMA2 MUTATED PSMA2 WILD-TYPE 
              6             465 
  PSMA2 MUTATED PSMA2 WILD-TYPE 
              2              91 
$`PSMA2 MUTATED`
TCGA-AA-3492 TCGA-AA-A00A TCGA-AD-6895 TCGA-CK-4950 TCGA-F4-6570 TCGA-G4-6321 
        3.02        38.04         0.72        85.45         6.18        22.09 

$`PSMA2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
       56.55         0.79         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 
       12.76        10.06        14.30        17.56       148.01        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 
       98.24         8.61        31.96        35.74        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  PSMA2 MUTATED PSMA2 WILD-TYPE 
           0.72            0.00 
  PSMA2 MUTATED PSMA2 WILD-TYPE 
          85.45          148.01 
  PSMA2 MUTATED PSMA2 WILD-TYPE 
         14.135          20.190 
[1] "0.7 - 85.5 (14.1)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.8"
D927V2, continuous
D927V3, binary
                 cls
clus                0   1
  PSMA2 MUTATED     6   0
  PSMA2 WILD-TYPE 360 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PSMA2 MUTATED      6    0
  PSMA2 WILD-TYPE  360  119
        clus
vv       PSMA2 MUTATED PSMA2 WILD-TYPE
  COLON              6             360
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PSMA2 MUTATED         0        0        1         2         0         0
  PSMA2 WILD-TYPE      91        1       31       136        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PSMA2 MUTATED           1          0          1          0        0         0
  PSMA2 WILD-TYPE        23         11         58         42       48        18
                 vv
clus              STAGE IVB
  PSMA2 MUTATED           0
  PSMA2 WILD-TYPE         1
D927V4, multiclass
            clus
vv           PSMA2 MUTATED PSMA2 WILD-TYPE
  STAGE I                0              91
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              2             136
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PSMA2 MUTATED     0   1   5   0
  PSMA2 WILD-TYPE  17  91 324  50
D927V5, multiclass
    clus
vv   PSMA2 MUTATED PSMA2 WILD-TYPE
  T1             0              17
  T2             1              91
  T3             5             324
  T4             0              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  PSMA2 MUTATED     3   3   0
  PSMA2 WILD-TYPE 284 110  87
D927V6, multiclass
    clus
vv   PSMA2 MUTATED PSMA2 WILD-TYPE
  N0             3             284
  N1             3             110
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D927V7, binary
                 cls
clus                0   1
  PSMA2 MUTATED     4   0
  PSMA2 WILD-TYPE 371  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PSMA2 MUTATED      4    0
  PSMA2 WILD-TYPE  371   65
   clus
vv  PSMA2 MUTATED PSMA2 WILD-TYPE
  0             4             371
  1             0              65
[1] 2 2
[1] FALSE
D927V8, binary
                 cls
clus                0   1
  PSMA2 MUTATED     4   2
  PSMA2 WILD-TYPE 221 262
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PSMA2 MUTATED      4    2
  PSMA2 WILD-TYPE  221  262
        clus
vv       PSMA2 MUTATED PSMA2 WILD-TYPE
  FEMALE             4             221
  MALE               2             262
[1] 2 2
[1] FALSE
D927V9, binary
                 cls
clus                0   1
  PSMA2 MUTATED     5   0
  PSMA2 WILD-TYPE 345  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PSMA2 MUTATED      5    0
  PSMA2 WILD-TYPE  345   22
     clus
vv    PSMA2 MUTATED PSMA2 WILD-TYPE
  NO              5             345
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PSMA2 MUTATED                      6                             0
  PSMA2 WILD-TYPE                  309                            47
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PSMA2 MUTATED                       0                              0
  PSMA2 WILD-TYPE                   106                             10
D927V10, multiclass
                                clus
vv                               PSMA2 MUTATED PSMA2 WILD-TYPE
  COLON ADENOCARCINOMA                       6             309
  COLON MUCINOUS ADENOCARCINOMA              0              47
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  PSMA2 MUTATED     4   1   0   0
  PSMA2 WILD-TYPE 341   3  31  25
D927V11, multiclass
    clus
vv   PSMA2 MUTATED PSMA2 WILD-TYPE
  R0             4             341
  R1             1               3
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D927V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PSMA2 MUTATED                                  0     0
  PSMA2 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PSMA2 MUTATED                           1     3
  PSMA2 WILD-TYPE                        21   223
D927V13, multiclass
                                  clus
vv                                 PSMA2 MUTATED PSMA2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        3             223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(928) Variable = ZKSCAN1 MUTATION ANALYSIS
D928V1, survival
                   sevent
clus2                 0   1
  ZKSCAN1 MUTATED     6   2
  ZKSCAN1 WILD-TYPE 372  91
  ZKSCAN1 MUTATED ZKSCAN1 WILD-TYPE 
                8               463 
  ZKSCAN1 MUTATED ZKSCAN1 WILD-TYPE 
                2                91 
$`ZKSCAN1 MUTATED`
TCGA-AA-3492 TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3864 TCGA-AA-A00J TCGA-AD-5900 
        3.02        13.02         1.02        53.00        18.05         0.07 
TCGA-G4-6293 TCGA-AG-3878 
      133.18         0.99 

$`ZKSCAN1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3519 
       35.01        63.98         6.97         1.02        38.99         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        31.07        30.05        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
       35.31        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  ZKSCAN1 MUTATED ZKSCAN1 WILD-TYPE 
             0.07              0.00 
  ZKSCAN1 MUTATED ZKSCAN1 WILD-TYPE 
           133.18            148.01 
  ZKSCAN1 MUTATED ZKSCAN1 WILD-TYPE 
             8.02             20.55 
[1] "0.1 - 133.2 (8.0)"  "0.0 - 148.0 (20.6)"
[1] "hr=" "1.3"
D928V2, continuous
D928V3, binary
                   cls
clus                  0   1
  ZKSCAN1 MUTATED     7   1
  ZKSCAN1 WILD-TYPE 359 118
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZKSCAN1 MUTATED      7    1
  ZKSCAN1 WILD-TYPE  359  118
        clus
vv       ZKSCAN1 MUTATED ZKSCAN1 WILD-TYPE
  COLON                7               359
  RECTUM               1               118
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZKSCAN1 MUTATED         2        0        2         1         0         0
  ZKSCAN1 WILD-TYPE      89        1       30       137        10         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZKSCAN1 MUTATED           2          0          1          0        0
  ZKSCAN1 WILD-TYPE        22         11         58         42       48
                   vv
clus                STAGE IVA STAGE IVB
  ZKSCAN1 MUTATED           0         0
  ZKSCAN1 WILD-TYPE        18         1
D928V4, multiclass
            clus
vv           ZKSCAN1 MUTATED ZKSCAN1 WILD-TYPE
  STAGE I                  2                89
  STAGE IA                 0                 1
  STAGE II                 2                30
  STAGE IIA                1               137
  STAGE IIB                0                10
  STAGE IIC                0                 1
  STAGE III                2                22
  STAGE IIIA               0                11
  STAGE IIIB               1                58
  STAGE IIIC               0                42
  STAGE IV                 0                48
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  ZKSCAN1 MUTATED     0   2   5   1
  ZKSCAN1 WILD-TYPE  17  90 324  49
D928V5, multiclass
    clus
vv   ZKSCAN1 MUTATED ZKSCAN1 WILD-TYPE
  T1               0                17
  T2               2                90
  T3               5               324
  T4               1                49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  ZKSCAN1 MUTATED     5   2   1
  ZKSCAN1 WILD-TYPE 282 111  86
D928V6, multiclass
    clus
vv   ZKSCAN1 MUTATED ZKSCAN1 WILD-TYPE
  N0               5               282
  N1               2               111
  N2               1                86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D928V7, binary
                   cls
clus                  0   1
  ZKSCAN1 MUTATED     7   0
  ZKSCAN1 WILD-TYPE 368  65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZKSCAN1 MUTATED      7    0
  ZKSCAN1 WILD-TYPE  368   65
   clus
vv  ZKSCAN1 MUTATED ZKSCAN1 WILD-TYPE
  0               7               368
  1               0                65
[1] 2 2
[1] FALSE
D928V8, binary
                   cls
clus                  0   1
  ZKSCAN1 MUTATED     4   4
  ZKSCAN1 WILD-TYPE 221 260
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZKSCAN1 MUTATED      4    4
  ZKSCAN1 WILD-TYPE  221  260
        clus
vv       ZKSCAN1 MUTATED ZKSCAN1 WILD-TYPE
  FEMALE               4               221
  MALE                 4               260
[1] 2 2
[1] FALSE
D928V9, binary
                   cls
clus                  0   1
  ZKSCAN1 MUTATED     5   0
  ZKSCAN1 WILD-TYPE 345  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZKSCAN1 MUTATED      5    0
  ZKSCAN1 WILD-TYPE  345   22
     clus
vv    ZKSCAN1 MUTATED ZKSCAN1 WILD-TYPE
  NO                5               345
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ZKSCAN1 MUTATED                      4                             3
  ZKSCAN1 WILD-TYPE                  311                            44
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ZKSCAN1 MUTATED                       1                              0
  ZKSCAN1 WILD-TYPE                   105                             10
D928V10, multiclass
                                clus
vv                               ZKSCAN1 MUTATED ZKSCAN1 WILD-TYPE
  COLON ADENOCARCINOMA                         4               311
  COLON MUCINOUS ADENOCARCINOMA                3                44
  RECTAL ADENOCARCINOMA                        1               105
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  ZKSCAN1 MUTATED     7   0   0   0
  ZKSCAN1 WILD-TYPE 338   4  31  25
D928V11, multiclass
    clus
vv   ZKSCAN1 MUTATED ZKSCAN1 WILD-TYPE
  R0               7               338
  R1               0                 4
  R2               0                31
  RX               0                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D928V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZKSCAN1 MUTATED                                  0     0
  ZKSCAN1 WILD-TYPE                                1    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  ZKSCAN1 MUTATED                           0     2
  ZKSCAN1 WILD-TYPE                        22   224
D928V13, multiclass
[1] "Remove cluster labels:" "ZKSCAN1 MUTATED"       
clus
  ZKSCAN1 MUTATED ZKSCAN1 WILD-TYPE 
                2               258 
       TCGA-A6-2671        TCGA-A6-2672        TCGA-A6-2674        TCGA-A6-2676 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-A6-2677        TCGA-A6-2678        TCGA-A6-2683        TCGA-A6-3807 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-A6-3808        TCGA-A6-3809        TCGA-A6-3810        TCGA-A6-4105 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-A6-5656        TCGA-A6-5657        TCGA-A6-5659        TCGA-A6-5660 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-A6-5661        TCGA-A6-5662        TCGA-A6-5664        TCGA-A6-5665 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-A6-5666        TCGA-A6-6137        TCGA-A6-6138        TCGA-A6-6141 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-A6-6142        TCGA-A6-6648        TCGA-A6-6649        TCGA-A6-6651 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-A6-6652        TCGA-A6-6653        TCGA-A6-6654        TCGA-A6-6780 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-A6-6781        TCGA-A6-6782        TCGA-AD-6548        TCGA-AD-6888 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-AD-6889        TCGA-AD-6890        TCGA-AD-6895        TCGA-AD-6899 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-AD-6901        TCGA-AD-6963        TCGA-AD-6964        TCGA-AD-6965 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-AU-3779        TCGA-AU-6004        TCGA-AY-4070        TCGA-AY-4071 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-AY-5543        TCGA-AY-6196        TCGA-AY-6197        TCGA-AY-6386 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-AZ-4315        TCGA-AZ-4323        TCGA-AZ-4616        TCGA-AZ-4681 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-AZ-4682        TCGA-AZ-5403        TCGA-AZ-5407        TCGA-AZ-6598 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-AZ-6599        TCGA-AZ-6600        TCGA-AZ-6601        TCGA-AZ-6603 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-AZ-6605        TCGA-AZ-6606        TCGA-AZ-6607        TCGA-AZ-6608 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-CA-5254        TCGA-CA-5255        TCGA-CA-5796        TCGA-CA-5797 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-CA-6715        TCGA-CA-6716        TCGA-CA-6717        TCGA-CA-6718 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-CA-6719        TCGA-CK-4947        TCGA-CK-4948        TCGA-CK-4950 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-CK-4952        TCGA-CK-5912        TCGA-CK-5913        TCGA-CK-5914 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-CK-5915        TCGA-CK-5916        TCGA-CK-6746        TCGA-CK-6747 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-CK-6748        TCGA-CK-6751        TCGA-CM-4743        TCGA-CM-4744 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-CM-4746        TCGA-CM-4747        TCGA-CM-4752        TCGA-CM-5341 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-CM-5344        TCGA-CM-5348        TCGA-CM-5349        TCGA-CM-5860 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-CM-5861        TCGA-CM-5862        TCGA-CM-5863        TCGA-CM-5864 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-CM-5868        TCGA-CM-6161        TCGA-CM-6162        TCGA-CM-6163 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-CM-6164        TCGA-CM-6165        TCGA-CM-6166        TCGA-CM-6167 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-CM-6168        TCGA-CM-6169        TCGA-CM-6170        TCGA-CM-6171 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-CM-6172        TCGA-CM-6674        TCGA-CM-6675        TCGA-CM-6676 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-CM-6677        TCGA-CM-6678        TCGA-CM-6679        TCGA-CM-6680 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-D5-5537        TCGA-D5-5538        TCGA-D5-5539        TCGA-D5-5540 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-D5-5541        TCGA-D5-6529        TCGA-D5-6532        TCGA-D5-6533 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-D5-6534        TCGA-D5-6535        TCGA-D5-6536        TCGA-D5-6537 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-D5-6538        TCGA-D5-6539        TCGA-D5-6540        TCGA-D5-6541 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-D5-6898        TCGA-D5-6920        TCGA-D5-6922        TCGA-D5-6923 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-D5-6924        TCGA-D5-6926        TCGA-D5-6927        TCGA-D5-6928 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-D5-6929        TCGA-D5-6930        TCGA-D5-6931        TCGA-D5-6932 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-D5-7000        TCGA-DM-A0X9        TCGA-DM-A0XD        TCGA-DM-A0XF 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-DM-A1D0        TCGA-DM-A1D4        TCGA-DM-A1D6        TCGA-DM-A1D7 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-DM-A1D8        TCGA-DM-A1D9        TCGA-DM-A1DA        TCGA-DM-A1DB 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-DM-A1HA        TCGA-DM-A1HB        TCGA-DM-A282        TCGA-DM-A285 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-DM-A28C        TCGA-DM-A28E        TCGA-DM-A28F        TCGA-DM-A28G 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-DM-A28H        TCGA-DM-A28K        TCGA-F4-6459        TCGA-F4-6460 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-F4-6569        TCGA-F4-6570        TCGA-F4-6703        TCGA-F4-6704 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-F4-6805        TCGA-F4-6806        TCGA-F4-6807        TCGA-F4-6808 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-F4-6809        TCGA-F4-6854        TCGA-F4-6855        TCGA-F4-6856 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-G4-6299        TCGA-G4-6303        TCGA-G4-6304        TCGA-G4-6306 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-G4-6307        TCGA-G4-6309        TCGA-G4-6310        TCGA-G4-6315 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-G4-6317        TCGA-G4-6321        TCGA-G4-6323        TCGA-G4-6586 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-G4-6588        TCGA-G4-6625        TCGA-G4-6626        TCGA-G4-6628 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2691        TCGA-AF-2692 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3913        TCGA-AF-4110 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-AF-5654        TCGA-AF-6136        TCGA-AF-6655        TCGA-AF-6672 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6549        TCGA-AH-6643 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-AH-6644        TCGA-CI-6619        TCGA-CI-6620        TCGA-CI-6621 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-CI-6622        TCGA-CI-6624        TCGA-CL-5917        TCGA-CL-5918 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6155        TCGA-DC-6157 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-DC-6158        TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-DC-6683        TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-DY-A1DD        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-EF-5830        TCGA-EI-6506        TCGA-EI-6507        TCGA-EI-6508 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-EI-6510        TCGA-F5-6464        TCGA-F5-6465        TCGA-F5-6571 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-F5-6702        TCGA-F5-6811        TCGA-F5-6812        TCGA-F5-6813 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 
       TCGA-G5-6235        TCGA-G5-6641 
"ZKSCAN1 WILD-TYPE" "ZKSCAN1 WILD-TYPE" 

Clustering(929) Variable = SLC27A2 MUTATION ANALYSIS
D929V1, survival
                   sevent
clus2                 0   1
  SLC27A2 MUTATED     5   1
  SLC27A2 WILD-TYPE 373  92
  SLC27A2 MUTATED SLC27A2 WILD-TYPE 
                6               465 
  SLC27A2 MUTATED SLC27A2 WILD-TYPE 
                1                92 
$`SLC27A2 MUTATED`
TCGA-A6-5657 TCGA-AA-3510 TCGA-AA-A01D TCGA-D5-6533 TCGA-F4-6856 TCGA-AG-3892 
       31.63        63.98        10.98         1.32        35.31        13.02 

$`SLC27A2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99        34.98         1.02        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       18.25        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
        0.53        47.41       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       17.95        36.95        17.03        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  SLC27A2 MUTATED SLC27A2 WILD-TYPE 
             1.32              0.00 
  SLC27A2 MUTATED SLC27A2 WILD-TYPE 
            63.98            148.01 
  SLC27A2 MUTATED SLC27A2 WILD-TYPE 
           22.325            20.190 
[1] "1.3 - 64.0 (22.3)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.2"
D929V2, continuous
D929V3, binary
                   cls
clus                  0   1
  SLC27A2 MUTATED     6   1
  SLC27A2 WILD-TYPE 360 118
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC27A2 MUTATED      6    1
  SLC27A2 WILD-TYPE  360  118
        clus
vv       SLC27A2 MUTATED SLC27A2 WILD-TYPE
  COLON                6               360
  RECTUM               1               118
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SLC27A2 MUTATED         2        0        1         1         0         0
  SLC27A2 WILD-TYPE      89        1       31       137        10         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC27A2 MUTATED           0          0          2          1        0
  SLC27A2 WILD-TYPE        24         11         57         41       48
                   vv
clus                STAGE IVA STAGE IVB
  SLC27A2 MUTATED           0         0
  SLC27A2 WILD-TYPE        18         1
D929V4, multiclass
            clus
vv           SLC27A2 MUTATED SLC27A2 WILD-TYPE
  STAGE I                  2                89
  STAGE IA                 0                 1
  STAGE II                 1                31
  STAGE IIA                1               137
  STAGE IIB                0                10
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               0                11
  STAGE IIIB               2                57
  STAGE IIIC               1                41
  STAGE IV                 0                48
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  SLC27A2 MUTATED     1   1   4   1
  SLC27A2 WILD-TYPE  16  91 325  49
D929V5, multiclass
    clus
vv   SLC27A2 MUTATED SLC27A2 WILD-TYPE
  T1               1                16
  T2               1                91
  T3               4               325
  T4               1                49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  SLC27A2 MUTATED     5   1   1
  SLC27A2 WILD-TYPE 282 112  86
D929V6, multiclass
    clus
vv   SLC27A2 MUTATED SLC27A2 WILD-TYPE
  N0               5               282
  N1               1               112
  N2               1                86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D929V7, binary
                   cls
clus                  0   1
  SLC27A2 MUTATED     7   0
  SLC27A2 WILD-TYPE 368  65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC27A2 MUTATED      7    0
  SLC27A2 WILD-TYPE  368   65
   clus
vv  SLC27A2 MUTATED SLC27A2 WILD-TYPE
  0               7               368
  1               0                65
[1] 2 2
[1] FALSE
D929V8, binary
                   cls
clus                  0   1
  SLC27A2 MUTATED     4   3
  SLC27A2 WILD-TYPE 221 261
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC27A2 MUTATED      4    3
  SLC27A2 WILD-TYPE  221  261
        clus
vv       SLC27A2 MUTATED SLC27A2 WILD-TYPE
  FEMALE               4               221
  MALE                 3               261
[1] 2 2
[1] FALSE
D929V9, binary
                   cls
clus                  0   1
  SLC27A2 MUTATED     5   0
  SLC27A2 WILD-TYPE 345  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC27A2 MUTATED      5    0
  SLC27A2 WILD-TYPE  345   22
     clus
vv    SLC27A2 MUTATED SLC27A2 WILD-TYPE
  NO                5               345
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SLC27A2 MUTATED                      4                             2
  SLC27A2 WILD-TYPE                  311                            45
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SLC27A2 MUTATED                       1                              0
  SLC27A2 WILD-TYPE                   105                             10
D929V10, multiclass
                                clus
vv                               SLC27A2 MUTATED SLC27A2 WILD-TYPE
  COLON ADENOCARCINOMA                         4               311
  COLON MUCINOUS ADENOCARCINOMA                2                45
  RECTAL ADENOCARCINOMA                        1               105
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  SLC27A2 MUTATED     7   0   0   0
  SLC27A2 WILD-TYPE 338   4  31  25
D929V11, multiclass
    clus
vv   SLC27A2 MUTATED SLC27A2 WILD-TYPE
  R0               7               338
  R1               0                 4
  R2               0                31
  RX               0                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D929V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SLC27A2 MUTATED                                  0     0
  SLC27A2 WILD-TYPE                                1    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  SLC27A2 MUTATED                           1     2
  SLC27A2 WILD-TYPE                        21   224
D929V13, multiclass
                                  clus
vv                                 SLC27A2 MUTATED SLC27A2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                      1                21
  WHITE                                          2               224
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(930) Variable = OR6C75 MUTATION ANALYSIS
D930V1, survival
                  sevent
clus2                0   1
  OR6C75 MUTATED     7   1
  OR6C75 WILD-TYPE 371  92
  OR6C75 MUTATED OR6C75 WILD-TYPE 
               8              463 
  OR6C75 MUTATED OR6C75 WILD-TYPE 
               1               92 
$`OR6C75 MUTATED`
TCGA-AA-3710 TCGA-AA-3977 TCGA-AZ-4315 TCGA-AZ-6601 TCGA-CA-5255 TCGA-CM-6170 
       26.99        25.02        58.39       100.01         3.06        15.02 
TCGA-D5-6932 TCGA-EI-6510 
       11.38        18.28 

$`OR6C75 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
       19.00        36.00         5.03        85.05        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       33.01        21.44        17.82         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-F5-6464 TCGA-F5-6465 
        0.49        20.55        19.96        20.91         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  OR6C75 MUTATED OR6C75 WILD-TYPE 
            3.06             0.00 
  OR6C75 MUTATED OR6C75 WILD-TYPE 
          100.01           148.01 
  OR6C75 MUTATED OR6C75 WILD-TYPE 
           21.65            20.19 
[1] "3.1 - 100.0 (21.6)" "0.0 - 148.0 (20.2)"
[1] "hr=" "2"  
D930V2, continuous
D930V3, binary
                  cls
clus                 0   1
  OR6C75 MUTATED     7   1
  OR6C75 WILD-TYPE 359 118
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR6C75 MUTATED      7    1
  OR6C75 WILD-TYPE  359  118
        clus
vv       OR6C75 MUTATED OR6C75 WILD-TYPE
  COLON               7              359
  RECTUM              1              118
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  OR6C75 MUTATED         1        0        1         4         0         0
  OR6C75 WILD-TYPE      90        1       31       134        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  OR6C75 MUTATED           0          0          0          0        0
  OR6C75 WILD-TYPE        24         11         59         42       48
                  vv
clus               STAGE IVA STAGE IVB
  OR6C75 MUTATED           1         0
  OR6C75 WILD-TYPE        17         1
D930V4, multiclass
            clus
vv           OR6C75 MUTATED OR6C75 WILD-TYPE
  STAGE I                 1               90
  STAGE IA                0                1
  STAGE II                1               31
  STAGE IIA               4              134
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              0               59
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               1               17
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  OR6C75 MUTATED     0   3   5   0
  OR6C75 WILD-TYPE  17  89 324  50
D930V5, multiclass
    clus
vv   OR6C75 MUTATED OR6C75 WILD-TYPE
  T1              0               17
  T2              3               89
  T3              5              324
  T4              0               50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  OR6C75 MUTATED     8   0   0
  OR6C75 WILD-TYPE 279 113  87
D930V6, multiclass
    clus
vv   OR6C75 MUTATED OR6C75 WILD-TYPE
  N0              8              279
  N1              0              113
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D930V7, binary
                  cls
clus                 0   1
  OR6C75 MUTATED     6   0
  OR6C75 WILD-TYPE 369  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR6C75 MUTATED      6    0
  OR6C75 WILD-TYPE  369   65
   clus
vv  OR6C75 MUTATED OR6C75 WILD-TYPE
  0              6              369
  1              0               65
[1] 2 2
[1] FALSE
D930V8, binary
                  cls
clus                 0   1
  OR6C75 MUTATED     3   5
  OR6C75 WILD-TYPE 222 259
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR6C75 MUTATED      3    5
  OR6C75 WILD-TYPE  222  259
        clus
vv       OR6C75 MUTATED OR6C75 WILD-TYPE
  FEMALE              3              222
  MALE                5              259
[1] 2 2
[1] FALSE
D930V9, binary
                  cls
clus                 0   1
  OR6C75 MUTATED     7   1
  OR6C75 WILD-TYPE 343  21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR6C75 MUTATED      7    1
  OR6C75 WILD-TYPE  343   21
     clus
vv    OR6C75 MUTATED OR6C75 WILD-TYPE
  NO               7              343
  YES              1               21
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  OR6C75 MUTATED                      7                             0
  OR6C75 WILD-TYPE                  308                            47
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  OR6C75 MUTATED                       1                              0
  OR6C75 WILD-TYPE                   105                             10
D930V10, multiclass
                                clus
vv                               OR6C75 MUTATED OR6C75 WILD-TYPE
  COLON ADENOCARCINOMA                        7              308
  COLON MUCINOUS ADENOCARCINOMA               0               47
  RECTAL ADENOCARCINOMA                       1              105
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  OR6C75 MUTATED     5   0   0   1
  OR6C75 WILD-TYPE 340   4  31  24
D930V11, multiclass
    clus
vv   OR6C75 MUTATED OR6C75 WILD-TYPE
  R0              5              340
  R1              0                4
  R2              0               31
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D930V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OR6C75 MUTATED                                  0     1
  OR6C75 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  OR6C75 MUTATED                           0     5
  OR6C75 WILD-TYPE                        22   221
D930V13, multiclass
                                  clus
vv                                 OR6C75 MUTATED OR6C75 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         5              221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(931) Variable = TRIM54 MUTATION ANALYSIS
D931V1, survival
                  sevent
clus2                0   1
  TRIM54 MUTATED     5   3
  TRIM54 WILD-TYPE 373  90
  TRIM54 MUTATED TRIM54 WILD-TYPE 
               8              463 
  TRIM54 MUTATED TRIM54 WILD-TYPE 
               3               90 
$`TRIM54 MUTATED`
TCGA-A6-5666 TCGA-AA-A00E TCGA-AZ-6598 TCGA-CA-6716 TCGA-CM-6163 TCGA-D5-6533 
       32.71        30.02        49.41        12.20         2.96         1.32 
TCGA-DM-A1D4 TCGA-F4-6460 
       92.75        31.96 

$`TRIM54 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        22.06        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       38.04        19.00        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 
      106.75        22.36        62.79        88.21         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6717 
       12.69         3.06         3.25         3.29         0.07        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6534 
       19.59        56.09        55.92        20.19        18.25        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6569 
       35.97        60.79       117.07        98.24         8.61        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  TRIM54 MUTATED TRIM54 WILD-TYPE 
            1.32             0.00 
  TRIM54 MUTATED TRIM54 WILD-TYPE 
           92.75           148.01 
  TRIM54 MUTATED TRIM54 WILD-TYPE 
           30.99            20.12 
[1] "1.3 - 92.8 (31.0)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.6"
D931V2, continuous
D931V3, binary
                  cls
clus                 0   1
  TRIM54 MUTATED     9   0
  TRIM54 WILD-TYPE 357 119
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIM54 MUTATED      9    0
  TRIM54 WILD-TYPE  357  119
        clus
vv       TRIM54 MUTATED TRIM54 WILD-TYPE
  COLON               9              357
  RECTUM              0              119
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TRIM54 MUTATED         1        0        1         4         0         1
  TRIM54 WILD-TYPE      90        1       31       134        10         0
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TRIM54 MUTATED           0          0          2          0        0
  TRIM54 WILD-TYPE        24         11         57         42       48
                  vv
clus               STAGE IVA STAGE IVB
  TRIM54 MUTATED           0         0
  TRIM54 WILD-TYPE        18         1
D931V4, multiclass
            clus
vv           TRIM54 MUTATED TRIM54 WILD-TYPE
  STAGE I                 1               90
  STAGE IA                0                1
  STAGE II                1               31
  STAGE IIA               4              134
  STAGE IIB               0               10
  STAGE IIC               1                0
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              2               57
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  TRIM54 MUTATED     1   0   6   2
  TRIM54 WILD-TYPE  16  92 323  48
D931V5, multiclass
    clus
vv   TRIM54 MUTATED TRIM54 WILD-TYPE
  T1              1               16
  T2              0               92
  T3              6              323
  T4              2               48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  TRIM54 MUTATED     8   1   0
  TRIM54 WILD-TYPE 279 112  87
D931V6, multiclass
    clus
vv   TRIM54 MUTATED TRIM54 WILD-TYPE
  N0              8              279
  N1              1              112
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D931V7, binary
                  cls
clus                 0   1
  TRIM54 MUTATED     8   0
  TRIM54 WILD-TYPE 367  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIM54 MUTATED      8    0
  TRIM54 WILD-TYPE  367   65
   clus
vv  TRIM54 MUTATED TRIM54 WILD-TYPE
  0              8              367
  1              0               65
[1] 2 2
[1] FALSE
D931V8, binary
                  cls
clus                 0   1
  TRIM54 MUTATED     4   5
  TRIM54 WILD-TYPE 221 259
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIM54 MUTATED      4    5
  TRIM54 WILD-TYPE  221  259
        clus
vv       TRIM54 MUTATED TRIM54 WILD-TYPE
  FEMALE              4              221
  MALE                5              259
[1] 2 2
[1] FALSE
D931V9, binary
                  cls
clus                 0   1
  TRIM54 MUTATED     6   0
  TRIM54 WILD-TYPE 344  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIM54 MUTATED      6    0
  TRIM54 WILD-TYPE  344   22
     clus
vv    TRIM54 MUTATED TRIM54 WILD-TYPE
  NO               6              344
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  TRIM54 MUTATED                      9                             0
  TRIM54 WILD-TYPE                  306                            47
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  TRIM54 MUTATED                       0                              0
  TRIM54 WILD-TYPE                   106                             10
D931V10, multiclass
                                clus
vv                               TRIM54 MUTATED TRIM54 WILD-TYPE
  COLON ADENOCARCINOMA                        9              306
  COLON MUCINOUS ADENOCARCINOMA               0               47
  RECTAL ADENOCARCINOMA                       0              106
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  TRIM54 MUTATED     5   0   0   1
  TRIM54 WILD-TYPE 340   4  31  24
D931V11, multiclass
    clus
vv   TRIM54 MUTATED TRIM54 WILD-TYPE
  R0              5              340
  R1              0                4
  R2              0               31
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D931V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TRIM54 MUTATED                                  0     1
  TRIM54 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  TRIM54 MUTATED                           0     6
  TRIM54 WILD-TYPE                        22   220
D931V13, multiclass
                                  clus
vv                                 TRIM54 MUTATED TRIM54 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         6              220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(932) Variable = ERCC6L MUTATION ANALYSIS
D932V1, survival
                  sevent
clus2                0   1
  ERCC6L MUTATED    13   2
  ERCC6L WILD-TYPE 365  91
  ERCC6L MUTATED ERCC6L WILD-TYPE 
              15              456 
  ERCC6L MUTATED ERCC6L WILD-TYPE 
               2               91 
$`ERCC6L MUTATED`
TCGA-A6-2672 TCGA-A6-5661 TCGA-A6-5665 TCGA-A6-6141 TCGA-AA-3660 TCGA-AA-3860 
       46.65        33.53        22.06         8.38        78.08        31.07 
TCGA-AA-3950 TCGA-AA-A01D TCGA-AD-6895 TCGA-AZ-6601 TCGA-G4-6586 TCGA-AG-3892 
       24.00        10.98         0.72       100.01        35.80        13.02 
TCGA-AG-A002 TCGA-DT-5265 TCGA-EI-6507 
       20.98         5.29        19.96 

$`ERCC6L WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 
       31.63        30.44        29.19        23.61        22.09        32.71 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 
       27.09        22.52        25.08        25.18        24.16        21.76 
TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       24.69        24.39        23.87        20.12        19.66        20.28 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
        7.04         3.02         1.02        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       61.02         6.05         6.97        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 
        0.00        36.03        32.05         0.99        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        34.98         1.02        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
       56.55         0.79         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       17.95        36.95        17.03        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A0XA 
       10.98        19.99         5.95         4.01         5.03       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       20.55        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  ERCC6L MUTATED ERCC6L WILD-TYPE 
            0.72             0.00 
  ERCC6L MUTATED ERCC6L WILD-TYPE 
          100.01           148.01 
  ERCC6L MUTATED ERCC6L WILD-TYPE 
          22.060           20.085 
[1] "0.7 - 100.0 (22.1)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.7"
D932V2, continuous
D932V3, binary
                  cls
clus                 0   1
  ERCC6L MUTATED    12   4
  ERCC6L WILD-TYPE 354 115
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ERCC6L MUTATED     12    4
  ERCC6L WILD-TYPE  354  115
        clus
vv       ERCC6L MUTATED ERCC6L WILD-TYPE
  COLON              12              354
  RECTUM              4              115
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ERCC6L MUTATED         2        0        3         7         0         0
  ERCC6L WILD-TYPE      89        1       29       131        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ERCC6L MUTATED           0          0          2          1        0
  ERCC6L WILD-TYPE        24         11         57         41       48
                  vv
clus               STAGE IVA STAGE IVB
  ERCC6L MUTATED           0         0
  ERCC6L WILD-TYPE        18         1
D932V4, multiclass
            clus
vv           ERCC6L MUTATED ERCC6L WILD-TYPE
  STAGE I                 2               89
  STAGE IA                0                1
  STAGE II                3               29
  STAGE IIA               7              131
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              2               57
  STAGE IIIC              1               41
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ERCC6L MUTATED     1   1  14   0
  ERCC6L WILD-TYPE  16  91 315  50
D932V5, multiclass
    clus
vv   ERCC6L MUTATED ERCC6L WILD-TYPE
  T1              1               16
  T2              1               91
  T3             14              315
  T4              0               50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  ERCC6L MUTATED    12   3   1
  ERCC6L WILD-TYPE 275 110  86
D932V6, multiclass
    clus
vv   ERCC6L MUTATED ERCC6L WILD-TYPE
  N0             12              275
  N1              3              110
  N2              1               86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D932V7, binary
                  cls
clus                 0   1
  ERCC6L MUTATED    15   0
  ERCC6L WILD-TYPE 360  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ERCC6L MUTATED     15    0
  ERCC6L WILD-TYPE  360   65
   clus
vv  ERCC6L MUTATED ERCC6L WILD-TYPE
  0             15              360
  1              0               65
[1] 2 2
[1] FALSE
D932V8, binary
                  cls
clus                 0   1
  ERCC6L MUTATED    10   6
  ERCC6L WILD-TYPE 215 258
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ERCC6L MUTATED     10    6
  ERCC6L WILD-TYPE  215  258
        clus
vv       ERCC6L MUTATED ERCC6L WILD-TYPE
  FEMALE             10              215
  MALE                6              258
[1] 2 2
[1] FALSE
D932V9, binary
                  cls
clus                 0   1
  ERCC6L MUTATED    14   0
  ERCC6L WILD-TYPE 336  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ERCC6L MUTATED     14    0
  ERCC6L WILD-TYPE  336   22
     clus
vv    ERCC6L MUTATED ERCC6L WILD-TYPE
  NO              14              336
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ERCC6L MUTATED                     10                             2
  ERCC6L WILD-TYPE                  305                            45
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ERCC6L MUTATED                       3                              1
  ERCC6L WILD-TYPE                   103                              9
D932V10, multiclass
                                clus
vv                               ERCC6L MUTATED ERCC6L WILD-TYPE
  COLON ADENOCARCINOMA                       10              305
  COLON MUCINOUS ADENOCARCINOMA               2               45
  RECTAL ADENOCARCINOMA                       3              103
  RECTAL MUCINOUS ADENOCARCINOMA              1                9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ERCC6L MUTATED    12   0   0   1
  ERCC6L WILD-TYPE 333   4  31  24
D932V11, multiclass
    clus
vv   ERCC6L MUTATED ERCC6L WILD-TYPE
  R0             12              333
  R1              0                4
  R2              0               31
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D932V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ERCC6L MUTATED                                  0     1
  ERCC6L WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ERCC6L MUTATED                           2     6
  ERCC6L WILD-TYPE                        20   220
D932V13, multiclass
                                  clus
vv                                 ERCC6L MUTATED ERCC6L WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     2               20
  WHITE                                         6              220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(933) Variable = CXORF38 MUTATION ANALYSIS
D933V1, survival
                   sevent
clus2                 0   1
  CXORF38 MUTATED     6   0
  CXORF38 WILD-TYPE 372  93
  CXORF38 MUTATED CXORF38 WILD-TYPE 
                6               465 
  CXORF38 MUTATED CXORF38 WILD-TYPE 
                0                93 
$`CXORF38 MUTATED`
TCGA-AY-6197 TCGA-AZ-4315 TCGA-CM-5349 TCGA-G4-6309 TCGA-G4-6588 TCGA-F5-6702 
       21.44        58.39        30.08        85.48        26.17        28.57 

$`CXORF38 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
       16.31         0.95        33.01        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5860 
       25.02        13.02        29.06        22.03        22.98        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 
       65.85        53.62        44.68        55.04        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        35.80        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6811 TCGA-F5-6812 
       18.28         9.96        49.51        31.30        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  CXORF38 MUTATED CXORF38 WILD-TYPE 
            21.44              0.00 
  CXORF38 MUTATED CXORF38 WILD-TYPE 
            85.48            148.01 
  CXORF38 MUTATED CXORF38 WILD-TYPE 
           29.325            20.020 
[1] "21.4 - 85.5 (29.3)" "0.0 - 148.0 (20.0)"
[1] "hr="     "9200000"
D933V2, continuous
D933V3, binary
                   cls
clus                  0   1
  CXORF38 MUTATED     5   1
  CXORF38 WILD-TYPE 361 118
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CXORF38 MUTATED      5    1
  CXORF38 WILD-TYPE  361  118
        clus
vv       CXORF38 MUTATED CXORF38 WILD-TYPE
  COLON                5               361
  RECTUM               1               118
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CXORF38 MUTATED         0        0        0         4         0         0
  CXORF38 WILD-TYPE      91        1       32       134        10         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CXORF38 MUTATED           0          0          1          0        0
  CXORF38 WILD-TYPE        24         11         58         42       48
                   vv
clus                STAGE IVA STAGE IVB
  CXORF38 MUTATED           1         0
  CXORF38 WILD-TYPE        17         1
D933V4, multiclass
            clus
vv           CXORF38 MUTATED CXORF38 WILD-TYPE
  STAGE I                  0                91
  STAGE IA                 0                 1
  STAGE II                 0                32
  STAGE IIA                4               134
  STAGE IIB                0                10
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               0                11
  STAGE IIIB               1                58
  STAGE IIIC               0                42
  STAGE IV                 0                48
  STAGE IVA                1                17
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  CXORF38 MUTATED     0   0   6   0
  CXORF38 WILD-TYPE  17  92 323  50
D933V5, multiclass
    clus
vv   CXORF38 MUTATED CXORF38 WILD-TYPE
  T1               0                17
  T2               0                92
  T3               6               323
  T4               0                50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  CXORF38 MUTATED     4   2   0
  CXORF38 WILD-TYPE 283 111  87
D933V6, multiclass
    clus
vv   CXORF38 MUTATED CXORF38 WILD-TYPE
  N0               4               283
  N1               2               111
  N2               0                87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D933V7, binary
                   cls
clus                  0   1
  CXORF38 MUTATED     4   1
  CXORF38 WILD-TYPE 371  64
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CXORF38 MUTATED      4    1
  CXORF38 WILD-TYPE  371   64
   clus
vv  CXORF38 MUTATED CXORF38 WILD-TYPE
  0               4               371
  1               1                64
[1] 2 2
[1] FALSE
D933V8, binary
                   cls
clus                  0   1
  CXORF38 MUTATED     3   3
  CXORF38 WILD-TYPE 222 261
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CXORF38 MUTATED      3    3
  CXORF38 WILD-TYPE  222  261
        clus
vv       CXORF38 MUTATED CXORF38 WILD-TYPE
  FEMALE               3               222
  MALE                 3               261
[1] 2 2
[1] FALSE
D933V9, binary
                   cls
clus                  0   1
  CXORF38 MUTATED     6   0
  CXORF38 WILD-TYPE 344  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CXORF38 MUTATED      6    0
  CXORF38 WILD-TYPE  344   22
     clus
vv    CXORF38 MUTATED CXORF38 WILD-TYPE
  NO                6               344
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CXORF38 MUTATED                      5                             0
  CXORF38 WILD-TYPE                  310                            47
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CXORF38 MUTATED                       1                              0
  CXORF38 WILD-TYPE                   105                             10
D933V10, multiclass
                                clus
vv                               CXORF38 MUTATED CXORF38 WILD-TYPE
  COLON ADENOCARCINOMA                         5               310
  COLON MUCINOUS ADENOCARCINOMA                0                47
  RECTAL ADENOCARCINOMA                        1               105
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  CXORF38 MUTATED     6   0   0   0
  CXORF38 WILD-TYPE 339   4  31  25
D933V11, multiclass
    clus
vv   CXORF38 MUTATED CXORF38 WILD-TYPE
  R0               6               339
  R1               0                 4
  R2               0                31
  RX               0                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D933V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CXORF38 MUTATED                                  0     0
  CXORF38 WILD-TYPE                                1    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  CXORF38 MUTATED                           1     5
  CXORF38 WILD-TYPE                        21   221
D933V13, multiclass
                                  clus
vv                                 CXORF38 MUTATED CXORF38 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                      1                21
  WHITE                                          5               221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(934) Variable = C12ORF49 MUTATION ANALYSIS
D934V1, survival
                    sevent
clus2                  0   1
  C12ORF49 MUTATED     1   3
  C12ORF49 WILD-TYPE 377  90
  C12ORF49 MUTATED C12ORF49 WILD-TYPE 
                 4                467 
  C12ORF49 MUTATED C12ORF49 WILD-TYPE 
                 3                 90 
$`C12ORF49 MUTATED`
TCGA-AA-3663 TCGA-AZ-6598 TCGA-DM-A1DA TCGA-G4-6626 
        6.97        49.41         7.50        46.75 

$`C12ORF49 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.05        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 
        5.13       106.75        22.36        62.79        88.21         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       13.32        12.59       140.38        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       91.79        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  C12ORF49 MUTATED C12ORF49 WILD-TYPE 
              6.97               0.00 
  C12ORF49 MUTATED C12ORF49 WILD-TYPE 
             49.41             148.01 
  C12ORF49 MUTATED C12ORF49 WILD-TYPE 
            27.125             20.190 
[1] "7.0 - 49.4 (27.1)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "3.3"
D934V2, continuous
D934V3, binary
                    cls
clus                   0   1
  C12ORF49 MUTATED     4   0
  C12ORF49 WILD-TYPE 362 119
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C12ORF49 MUTATED      4    0
  C12ORF49 WILD-TYPE  362  119
        clus
vv       C12ORF49 MUTATED C12ORF49 WILD-TYPE
  COLON                 4                362
  RECTUM                0                119
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  C12ORF49 MUTATED         0        0        2         1         0         0
  C12ORF49 WILD-TYPE      91        1       30       137        10         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C12ORF49 MUTATED           0          0          0          1        0
  C12ORF49 WILD-TYPE        24         11         59         41       48
                    vv
clus                 STAGE IVA STAGE IVB
  C12ORF49 MUTATED           0         0
  C12ORF49 WILD-TYPE        18         1
D934V4, multiclass
            clus
vv           C12ORF49 MUTATED C12ORF49 WILD-TYPE
  STAGE I                   0                 91
  STAGE IA                  0                  1
  STAGE II                  2                 30
  STAGE IIA                 1                137
  STAGE IIB                 0                 10
  STAGE IIC                 0                  1
  STAGE III                 0                 24
  STAGE IIIA                0                 11
  STAGE IIIB                0                 59
  STAGE IIIC                1                 41
  STAGE IV                  0                 48
  STAGE IVA                 0                 18
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  C12ORF49 MUTATED     0   0   4   0
  C12ORF49 WILD-TYPE  17  92 325  50
D934V5, multiclass
    clus
vv   C12ORF49 MUTATED C12ORF49 WILD-TYPE
  T1                0                 17
  T2                0                 92
  T3                4                325
  T4                0                 50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  C12ORF49 MUTATED     3   0   1
  C12ORF49 WILD-TYPE 284 113  86
D934V6, multiclass
    clus
vv   C12ORF49 MUTATED C12ORF49 WILD-TYPE
  N0                3                284
  N1                0                113
  N2                1                 86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D934V7, binary
                    cls
clus                   0   1
  C12ORF49 MUTATED     3   0
  C12ORF49 WILD-TYPE 372  65
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C12ORF49 MUTATED      3    0
  C12ORF49 WILD-TYPE  372   65
   clus
vv  C12ORF49 MUTATED C12ORF49 WILD-TYPE
  0                3                372
  1                0                 65
[1] 2 2
[1] FALSE
D934V8, binary
                    cls
clus                   0   1
  C12ORF49 MUTATED     2   2
  C12ORF49 WILD-TYPE 223 262
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C12ORF49 MUTATED      2    2
  C12ORF49 WILD-TYPE  223  262
        clus
vv       C12ORF49 MUTATED C12ORF49 WILD-TYPE
  FEMALE                2                223
  MALE                  2                262
[1] 2 2
[1] FALSE
D934V9, binary
                    cls
clus                   0   1
  C12ORF49 MUTATED     3   0
  C12ORF49 WILD-TYPE 347  22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C12ORF49 MUTATED      3    0
  C12ORF49 WILD-TYPE  347   22
     clus
vv    C12ORF49 MUTATED C12ORF49 WILD-TYPE
  NO                 3                347
  YES                0                 22
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  C12ORF49 MUTATED                      4                             0
  C12ORF49 WILD-TYPE                  311                            47
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  C12ORF49 MUTATED                       0                              0
  C12ORF49 WILD-TYPE                   106                             10
D934V10, multiclass
                                clus
vv                               C12ORF49 MUTATED C12ORF49 WILD-TYPE
  COLON ADENOCARCINOMA                          4                311
  COLON MUCINOUS ADENOCARCINOMA                 0                 47
  RECTAL ADENOCARCINOMA                         0                106
  RECTAL MUCINOUS ADENOCARCINOMA                0                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  C12ORF49 MUTATED     2   0   0   0
  C12ORF49 WILD-TYPE 343   4  31  25
D934V11, multiclass
[1] "Remove cluster labels:" "C12ORF49 MUTATED"      
clus
  C12ORF49 MUTATED C12ORF49 WILD-TYPE 
                 2                403 
        TCGA-A6-2671         TCGA-A6-2672         TCGA-A6-2674 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-A6-2676         TCGA-A6-2677         TCGA-A6-2678 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-A6-2683         TCGA-A6-3807         TCGA-A6-3808 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-A6-3809         TCGA-A6-3810         TCGA-A6-5657 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-A6-5659         TCGA-A6-5661         TCGA-A6-5665 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-A6-6781         TCGA-AA-3489         TCGA-AA-3492 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AA-3496         TCGA-AA-3502         TCGA-AA-3510 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AA-3511         TCGA-AA-3514         TCGA-AA-3517 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AA-3518         TCGA-AA-3519         TCGA-AA-3520 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AA-3521         TCGA-AA-3522         TCGA-AA-3524 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AA-3525         TCGA-AA-3526         TCGA-AA-3527 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AA-3529         TCGA-AA-3530         TCGA-AA-3531 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AA-3532         TCGA-AA-3534         TCGA-AA-3538 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AA-3542         TCGA-AA-3543         TCGA-AA-3544 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AA-3548         TCGA-AA-3549         TCGA-AA-3552 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AA-3553         TCGA-AA-3554         TCGA-AA-3555 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AA-3556         TCGA-AA-3558         TCGA-AA-3560 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AA-3561         TCGA-AA-3562         TCGA-AA-3655 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AA-3660         TCGA-AA-3662         TCGA-AA-3664 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AA-3666         TCGA-AA-3667         TCGA-AA-3672 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AA-3673         TCGA-AA-3678         TCGA-AA-3679 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AA-3680         TCGA-AA-3681         TCGA-AA-3684 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AA-3685         TCGA-AA-3688         TCGA-AA-3692 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AA-3693         TCGA-AA-3695         TCGA-AA-3696 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AA-3697         TCGA-AA-3710         TCGA-AA-3712 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AA-3713         TCGA-AA-3715         TCGA-AA-3811 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AA-3812         TCGA-AA-3814         TCGA-AA-3815 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AA-3818         TCGA-AA-3819         TCGA-AA-3821 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AA-3831         TCGA-AA-3833         TCGA-AA-3837 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AA-3842         TCGA-AA-3844         TCGA-AA-3845 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AA-3846         TCGA-AA-3848         TCGA-AA-3850 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AA-3851         TCGA-AA-3852         TCGA-AA-3854 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AA-3855         TCGA-AA-3856         TCGA-AA-3858 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AA-3860         TCGA-AA-3861         TCGA-AA-3864 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AA-3866         TCGA-AA-3867         TCGA-AA-3869 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AA-3870         TCGA-AA-3872         TCGA-AA-3875 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AA-3877         TCGA-AA-3930         TCGA-AA-3939 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AA-3941         TCGA-AA-3947         TCGA-AA-3949 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AA-3950         TCGA-AA-3952         TCGA-AA-3955 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AA-3956         TCGA-AA-3968         TCGA-AA-3971 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AA-3972         TCGA-AA-3973         TCGA-AA-3975 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AA-3976         TCGA-AA-3979         TCGA-AA-3984 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AA-3986         TCGA-AA-3989         TCGA-AA-3994 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AA-A004         TCGA-AA-A00A         TCGA-AA-A00D 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AA-A00E         TCGA-AA-A00F         TCGA-AA-A00J 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AA-A00K         TCGA-AA-A00L         TCGA-AA-A00N 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AA-A00O         TCGA-AA-A00Q         TCGA-AA-A00R 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AA-A00U         TCGA-AA-A00W         TCGA-AA-A00Z 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AA-A010         TCGA-AA-A017         TCGA-AA-A01D 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AA-A01F         TCGA-AA-A01G         TCGA-AA-A01I 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AA-A01K         TCGA-AA-A01P         TCGA-AA-A01Q 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AA-A01R         TCGA-AA-A01S         TCGA-AA-A01T 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AA-A01V         TCGA-AA-A01X         TCGA-AA-A01Z 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AA-A022         TCGA-AA-A024         TCGA-AA-A029 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AA-A02F         TCGA-AA-A02H         TCGA-AA-A02J 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AA-A02K         TCGA-AA-A02O         TCGA-AA-A02W 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AA-A02Y         TCGA-AA-A03F         TCGA-AA-A03J 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AD-5900         TCGA-AD-6548         TCGA-AD-6888 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AU-3779         TCGA-AU-6004         TCGA-AY-4070 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AY-4071         TCGA-AY-5543         TCGA-AY-6196 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AY-6197         TCGA-AY-6386         TCGA-AZ-4315 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AZ-4681         TCGA-AZ-4682         TCGA-CA-5254 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-CA-5255         TCGA-CA-5796         TCGA-CA-5797 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-CA-6715         TCGA-CA-6716         TCGA-CA-6717 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-CA-6718         TCGA-CA-6719         TCGA-CK-4947 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-CK-4948         TCGA-CK-4950         TCGA-CK-4952 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-CK-5912         TCGA-CK-5913         TCGA-CK-5914 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-CK-5915         TCGA-CK-5916         TCGA-CK-6746 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-CK-6747         TCGA-CK-6748         TCGA-CK-6751 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-CM-4743         TCGA-CM-4744         TCGA-CM-4746 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-CM-4747         TCGA-CM-4752         TCGA-CM-5341 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-CM-5344         TCGA-CM-5348         TCGA-CM-5349 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-CM-5860         TCGA-CM-5861         TCGA-CM-5862 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-CM-5863         TCGA-CM-5864         TCGA-CM-5868 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-CM-6161         TCGA-CM-6162         TCGA-CM-6163 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-CM-6164         TCGA-CM-6165         TCGA-CM-6166 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-CM-6167         TCGA-CM-6168         TCGA-CM-6169 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-CM-6170         TCGA-CM-6171         TCGA-CM-6172 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-CM-6674         TCGA-CM-6675         TCGA-CM-6676 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-CM-6677         TCGA-CM-6678         TCGA-CM-6679 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-CM-6680         TCGA-D5-5537         TCGA-D5-5538 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-D5-5539         TCGA-D5-5540         TCGA-D5-5541 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-D5-6529         TCGA-D5-6532         TCGA-D5-6533 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-D5-6534         TCGA-D5-6535         TCGA-D5-6536 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-D5-6537         TCGA-D5-6538         TCGA-D5-6539 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-D5-6540         TCGA-D5-6541         TCGA-D5-6898 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-D5-6920         TCGA-D5-6922         TCGA-D5-6923 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-D5-6924         TCGA-D5-6926         TCGA-D5-6927 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-D5-6928         TCGA-D5-6929         TCGA-D5-6930 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-D5-6931         TCGA-D5-6932         TCGA-D5-7000 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-F4-6459         TCGA-F4-6460         TCGA-F4-6569 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-F4-6570         TCGA-F4-6703         TCGA-F4-6704 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-F4-6805         TCGA-F4-6806         TCGA-F4-6807 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-F4-6808         TCGA-F4-6809         TCGA-F4-6854 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-F4-6855         TCGA-F4-6856         TCGA-G4-6293 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-G4-6299         TCGA-G4-6303         TCGA-G4-6304 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-G4-6306         TCGA-G4-6307         TCGA-G4-6309 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-G4-6310         TCGA-G4-6315         TCGA-G4-6317 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-G4-6321         TCGA-G4-6323         TCGA-G4-6586 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-G4-6588         TCGA-G4-6625         TCGA-G4-6628 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2691 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AF-2692         TCGA-AF-3400         TCGA-AF-3913 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6655 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AG-3574         TCGA-AG-3575         TCGA-AG-3578 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AG-3580         TCGA-AG-3581         TCGA-AG-3582 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AG-3583         TCGA-AG-3584         TCGA-AG-3586 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AG-3587         TCGA-AG-3593         TCGA-AG-3594 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AG-3598         TCGA-AG-3599         TCGA-AG-3600 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AG-3601         TCGA-AG-3602         TCGA-AG-3605 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AG-3608         TCGA-AG-3609         TCGA-AG-3611 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AG-3612         TCGA-AG-3726         TCGA-AG-3727 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3732         TCGA-AG-3742 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AG-3878         TCGA-AG-3882         TCGA-AG-3883 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AG-3885         TCGA-AG-3887         TCGA-AG-3890 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AG-3892         TCGA-AG-3893         TCGA-AG-3894 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AG-3896         TCGA-AG-3898         TCGA-AG-3901 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AG-3902         TCGA-AG-3909         TCGA-AG-3999 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AG-4001         TCGA-AG-4005         TCGA-AG-4007 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4015         TCGA-AG-A002 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01L 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AG-A01W         TCGA-AG-A01Y         TCGA-AG-A020 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-AG-A036         TCGA-AH-6549         TCGA-AH-6643 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-CL-5917         TCGA-CL-5918         TCGA-DC-5337 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6155         TCGA-DC-6157 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-DC-6158         TCGA-DC-6160         TCGA-DC-6681 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-DC-6682         TCGA-DC-6683         TCGA-DT-5265 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-EF-5830         TCGA-EI-6506         TCGA-EI-6507 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-EI-6508         TCGA-EI-6510         TCGA-F5-6464 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-F5-6465         TCGA-F5-6571         TCGA-F5-6702 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-G5-6235 
"C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" "C12ORF49 WILD-TYPE" 
        TCGA-G5-6641 
"C12ORF49 WILD-TYPE" 
D934V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C12ORF49 MUTATED                                  0     0
  C12ORF49 WILD-TYPE                                1    11
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  C12ORF49 MUTATED                           0     3
  C12ORF49 WILD-TYPE                        22   223
D934V13, multiclass
                                  clus
vv                                 C12ORF49 MUTATED C12ORF49 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 11
  BLACK OR AFRICAN AMERICAN                       0                 22
  WHITE                                           3                223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(935) Variable = VEZF1 MUTATION ANALYSIS
D935V1, survival
                 sevent
clus2               0   1
  VEZF1 MUTATED     7   0
  VEZF1 WILD-TYPE 371  93
  VEZF1 MUTATED VEZF1 WILD-TYPE 
              7             464 
  VEZF1 MUTATED VEZF1 WILD-TYPE 
              0              93 
$`VEZF1 MUTATED`
TCGA-AD-6895 TCGA-CM-6171 TCGA-D5-6928 TCGA-D5-6930 TCGA-F4-6856 TCGA-G4-6588 
        0.72        14.04        11.64         1.51        35.31        26.17 
TCGA-DC-6682 
        4.01 

$`VEZF1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       21.37        15.52        56.55         0.79         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 
       21.99        14.99        12.99        13.02        15.02        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        4.80        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
        0.53        47.41       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       22.09        13.78        35.80        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 
       27.95        10.98        19.99         5.95         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  VEZF1 MUTATED VEZF1 WILD-TYPE 
           0.72            0.00 
  VEZF1 MUTATED VEZF1 WILD-TYPE 
          35.31          148.01 
  VEZF1 MUTATED VEZF1 WILD-TYPE 
         11.640          20.415 
[1] "0.7 - 35.3 (11.6)"  "0.0 - 148.0 (20.4)"
[1] "hr="     "3300000"
D935V2, continuous
D935V3, binary
                 cls
clus                0   1
  VEZF1 MUTATED     6   1
  VEZF1 WILD-TYPE 360 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VEZF1 MUTATED      6    1
  VEZF1 WILD-TYPE  360  118
        clus
vv       VEZF1 MUTATED VEZF1 WILD-TYPE
  COLON              6             360
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  VEZF1 MUTATED         2        0        0         4         0         0
  VEZF1 WILD-TYPE      89        1       32       134        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  VEZF1 MUTATED           0          0          0          0        0         0
  VEZF1 WILD-TYPE        24         11         59         42       48        18
                 vv
clus              STAGE IVB
  VEZF1 MUTATED           0
  VEZF1 WILD-TYPE         1
D935V4, multiclass
            clus
vv           VEZF1 MUTATED VEZF1 WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              4             134
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  VEZF1 MUTATED     0   2   5   0
  VEZF1 WILD-TYPE  17  90 324  50
D935V5, multiclass
    clus
vv   VEZF1 MUTATED VEZF1 WILD-TYPE
  T1             0              17
  T2             2              90
  T3             5             324
  T4             0              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  VEZF1 MUTATED     6   1   0
  VEZF1 WILD-TYPE 281 112  87
D935V6, multiclass
    clus
vv   VEZF1 MUTATED VEZF1 WILD-TYPE
  N0             6             281
  N1             1             112
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D935V7, binary
                 cls
clus                0   1
  VEZF1 MUTATED     6   0
  VEZF1 WILD-TYPE 369  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VEZF1 MUTATED      6    0
  VEZF1 WILD-TYPE  369   65
   clus
vv  VEZF1 MUTATED VEZF1 WILD-TYPE
  0             6             369
  1             0              65
[1] 2 2
[1] FALSE
D935V8, binary
                 cls
clus                0   1
  VEZF1 MUTATED     2   5
  VEZF1 WILD-TYPE 223 259
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VEZF1 MUTATED      2    5
  VEZF1 WILD-TYPE  223  259
        clus
vv       VEZF1 MUTATED VEZF1 WILD-TYPE
  FEMALE             2             223
  MALE               5             259
[1] 2 2
[1] FALSE
D935V9, binary
                 cls
clus                0   1
  VEZF1 MUTATED     4   0
  VEZF1 WILD-TYPE 346  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VEZF1 MUTATED      4    0
  VEZF1 WILD-TYPE  346   22
     clus
vv    VEZF1 MUTATED VEZF1 WILD-TYPE
  NO              4             346
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  VEZF1 MUTATED                      3                             3
  VEZF1 WILD-TYPE                  312                            44
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  VEZF1 MUTATED                       1                              0
  VEZF1 WILD-TYPE                   105                             10
D935V10, multiclass
                                clus
vv                               VEZF1 MUTATED VEZF1 WILD-TYPE
  COLON ADENOCARCINOMA                       3             312
  COLON MUCINOUS ADENOCARCINOMA              3              44
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  VEZF1 MUTATED     6   0   0   0
  VEZF1 WILD-TYPE 339   4  31  25
D935V11, multiclass
    clus
vv   VEZF1 MUTATED VEZF1 WILD-TYPE
  R0             6             339
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D935V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  VEZF1 MUTATED                                  0     0
  VEZF1 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  VEZF1 MUTATED                           0     7
  VEZF1 WILD-TYPE                        22   219
D935V13, multiclass
                                  clus
vv                                 VEZF1 MUTATED VEZF1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        7             219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(936) Variable = DNAH6 MUTATION ANALYSIS
D936V1, survival
                 sevent
clus2               0   1
  DNAH6 MUTATED    21   3
  DNAH6 WILD-TYPE 357  90
  DNAH6 MUTATED DNAH6 WILD-TYPE 
             24             447 
  DNAH6 MUTATED DNAH6 WILD-TYPE 
              3              90 
$`DNAH6 MUTATED`
TCGA-A6-5659 TCGA-A6-6141 TCGA-A6-6781 TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3663 
       30.44         8.38        19.66         3.02        63.98         6.97 
TCGA-AA-3977 TCGA-AD-5900 TCGA-AD-6889 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-CA-6717 
       25.02         0.07        56.55        58.39        49.41        12.76 
TCGA-CA-6718 TCGA-CM-4747 TCGA-CM-6162 TCGA-CM-6171 TCGA-CM-6674 TCGA-D5-6928 
       10.06        25.02        12.00        14.04        12.95        11.64 
TCGA-F4-6703 TCGA-G4-6588 TCGA-AG-3892 TCGA-AG-A002 TCGA-DC-6160 TCGA-DC-6682 
       47.87        26.17        13.02        20.98        19.99         4.01 

$`DNAH6 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 
       22.06        32.71        27.09        22.52        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 
       20.28         7.04         1.02        35.01         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
       13.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       36.03         8.05        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
       78.08         6.05        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 
       41.00        39.98        18.05        40.96        21.37        15.52 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        88.21         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 
        3.25         3.29         0.07        12.20        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       37.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       15.02         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6676 
       12.99        13.02        15.02        11.01        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
       14.30         9.04         9.44         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       31.96        35.74         6.18         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       35.80        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6681 TCGA-DC-6683 
        5.03        13.97        27.95        10.98         5.95         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  DNAH6 MUTATED DNAH6 WILD-TYPE 
           0.07            0.00 
  DNAH6 MUTATED DNAH6 WILD-TYPE 
          63.98          148.01 
  DNAH6 MUTATED DNAH6 WILD-TYPE 
          16.85           20.55 
[1] "0.1 - 64.0 (16.9)"  "0.0 - 148.0 (20.6)"
[1] "hr=" "1.5"
D936V2, continuous
D936V3, binary
                 cls
clus                0   1
  DNAH6 MUTATED    20   4
  DNAH6 WILD-TYPE 346 115
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DNAH6 MUTATED     20    4
  DNAH6 WILD-TYPE  346  115
        clus
vv       DNAH6 MUTATED DNAH6 WILD-TYPE
  COLON             20             346
  RECTUM             4             115
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DNAH6 MUTATED         6        0        4        10         0         0
  DNAH6 WILD-TYPE      85        1       28       128        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DNAH6 MUTATED           0          0          1          1        0         1
  DNAH6 WILD-TYPE        24         11         58         41       48        17
                 vv
clus              STAGE IVB
  DNAH6 MUTATED           0
  DNAH6 WILD-TYPE         1
D936V4, multiclass
            clus
vv           DNAH6 MUTATED DNAH6 WILD-TYPE
  STAGE I                6              85
  STAGE IA               0               1
  STAGE II               4              28
  STAGE IIA             10             128
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             1              41
  STAGE IV               0              48
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  DNAH6 MUTATED     1   6  15   2
  DNAH6 WILD-TYPE  16  86 314  48
D936V5, multiclass
    clus
vv   DNAH6 MUTATED DNAH6 WILD-TYPE
  T1             1              16
  T2             6              86
  T3            15             314
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  DNAH6 MUTATED    21   3   0
  DNAH6 WILD-TYPE 266 110  87
D936V6, multiclass
    clus
vv   DNAH6 MUTATED DNAH6 WILD-TYPE
  N0            21             266
  N1             3             110
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D936V7, binary
                 cls
clus                0   1
  DNAH6 MUTATED    19   1
  DNAH6 WILD-TYPE 356  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DNAH6 MUTATED     19    1
  DNAH6 WILD-TYPE  356   64
   clus
vv  DNAH6 MUTATED DNAH6 WILD-TYPE
  0            19             356
  1             1              64
[1] 2 2
[1] FALSE
D936V8, binary
                 cls
clus                0   1
  DNAH6 MUTATED     6  18
  DNAH6 WILD-TYPE 219 246
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DNAH6 MUTATED      6   18
  DNAH6 WILD-TYPE  219  246
        clus
vv       DNAH6 MUTATED DNAH6 WILD-TYPE
  FEMALE             6             219
  MALE              18             246
[1] 2 2
[1] FALSE
D936V9, binary
                 cls
clus                0   1
  DNAH6 MUTATED    20   0
  DNAH6 WILD-TYPE 330  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DNAH6 MUTATED     20    0
  DNAH6 WILD-TYPE  330   22
     clus
vv    DNAH6 MUTATED DNAH6 WILD-TYPE
  NO             20             330
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  DNAH6 MUTATED                     15                             5
  DNAH6 WILD-TYPE                  300                            42
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  DNAH6 MUTATED                       4                              0
  DNAH6 WILD-TYPE                   102                             10
D936V10, multiclass
                                clus
vv                               DNAH6 MUTATED DNAH6 WILD-TYPE
  COLON ADENOCARCINOMA                      15             300
  COLON MUCINOUS ADENOCARCINOMA              5              42
  RECTAL ADENOCARCINOMA                      4             102
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  DNAH6 MUTATED    18   0   0   2
  DNAH6 WILD-TYPE 327   4  31  23
D936V11, multiclass
    clus
vv   DNAH6 MUTATED DNAH6 WILD-TYPE
  R0            18             327
  R1             0               4
  R2             0              31
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D936V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DNAH6 MUTATED                                  0     3
  DNAH6 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  DNAH6 MUTATED                           1    14
  DNAH6 WILD-TYPE                        21   212
D936V13, multiclass
                                  clus
vv                                 DNAH6 MUTATED DNAH6 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        3               8
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                       14             212
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(937) Variable = ATP12A MUTATION ANALYSIS
D937V1, survival
                  sevent
clus2                0   1
  ATP12A MUTATED    21   7
  ATP12A WILD-TYPE 357  86
  ATP12A MUTATED ATP12A WILD-TYPE 
              28              443 
  ATP12A MUTATED ATP12A WILD-TYPE 
               7               86 
$`ATP12A MUTATED`
TCGA-A6-5656 TCGA-A6-5661 TCGA-A6-6781 TCGA-AA-3492 TCGA-AA-3530 TCGA-AA-3543 
       32.91        33.53        19.66         3.02        19.07         0.99 
TCGA-AA-3672 TCGA-AA-3864 TCGA-AA-3947 TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A010 
        0.92        53.00        33.01        25.02         4.01        34.98 
TCGA-AD-6963 TCGA-AY-4071 TCGA-CK-4952 TCGA-CM-4743 TCGA-CM-6161 TCGA-CM-6675 
       27.42         0.95        15.62        23.05        15.02        13.05 
TCGA-D5-6529 TCGA-DM-A1D6 TCGA-DM-A1DA TCGA-F4-6704 TCGA-G4-6307 TCGA-G4-6628 
       20.19        49.91         7.50         1.55        55.04        79.69 
TCGA-AG-3892 TCGA-AG-A002 TCGA-DY-A1DF TCGA-DY-A1DG 
       13.02        20.98        24.13        51.48 

$`ATP12A WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       31.63        30.44        29.19        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
       20.28         7.04         1.02        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3531 
       37.05        36.03         8.05        19.07         0.00        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 
       29.00        29.00        26.01        12.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
        6.05         6.97        54.02         2.01        14.01        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 
       32.05         0.99        31.07        31.07        30.05        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       12.99        24.00        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       85.45        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
        1.91       124.27        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6162 TCGA-CM-6163 
        5.03        15.02        15.02        17.03        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6676 TCGA-CM-6677 
       15.02        14.04        11.01        12.95        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       56.09        55.92        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       13.32        12.59       140.38        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
       47.87        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       53.62        44.68        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       36.95        17.03        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       41.36        57.24        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  ATP12A MUTATED ATP12A WILD-TYPE 
            0.92             0.00 
  ATP12A MUTATED ATP12A WILD-TYPE 
           79.69           148.01 
  ATP12A MUTATED ATP12A WILD-TYPE 
          20.585           20.120 
[1] "0.9 - 79.7 (20.6)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.4"
D937V2, continuous
D937V3, binary
                  cls
clus                 0   1
  ATP12A MUTATED    25   4
  ATP12A WILD-TYPE 341 115
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP12A MUTATED     25    4
  ATP12A WILD-TYPE  341  115
        clus
vv       ATP12A MUTATED ATP12A WILD-TYPE
  COLON              25              341
  RECTUM              4              115
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ATP12A MUTATED         9        0        3         4         3         0
  ATP12A WILD-TYPE      82        1       29       134         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ATP12A MUTATED           1          0          1          5        0
  ATP12A WILD-TYPE        23         11         58         37       48
                  vv
clus               STAGE IVA STAGE IVB
  ATP12A MUTATED           1         1
  ATP12A WILD-TYPE        17         0
D937V4, multiclass
            clus
vv           ATP12A MUTATED ATP12A WILD-TYPE
  STAGE I                 9               82
  STAGE IA                0                1
  STAGE II                3               29
  STAGE IIA               4              134
  STAGE IIB               3                7
  STAGE IIC               0                1
  STAGE III               1               23
  STAGE IIIA              0               11
  STAGE IIIB              1               58
  STAGE IIIC              5               37
  STAGE IV                0               48
  STAGE IVA               1               17
  STAGE IVB               1                0
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ATP12A MUTATED     2   8  14   6
  ATP12A WILD-TYPE  15  84 315  44
D937V5, multiclass
    clus
vv   ATP12A MUTATED ATP12A WILD-TYPE
  T1              2               15
  T2              8               84
  T3             14              315
  T4              6               44
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  ATP12A MUTATED    21   4   5
  ATP12A WILD-TYPE 266 109  82
D937V6, multiclass
    clus
vv   ATP12A MUTATED ATP12A WILD-TYPE
  N0             21              266
  N1              4              109
  N2              5               82
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D937V7, binary
                  cls
clus                 0   1
  ATP12A MUTATED    22   2
  ATP12A WILD-TYPE 353  63
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP12A MUTATED     22    2
  ATP12A WILD-TYPE  353   63
   clus
vv  ATP12A MUTATED ATP12A WILD-TYPE
  0             22              353
  1              2               63
[1] 2 2
[1] FALSE
D937V8, binary
                  cls
clus                 0   1
  ATP12A MUTATED    13  17
  ATP12A WILD-TYPE 212 247
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP12A MUTATED     13   17
  ATP12A WILD-TYPE  212  247
        clus
vv       ATP12A MUTATED ATP12A WILD-TYPE
  FEMALE             13              212
  MALE               17              247
[1] 2 2
[1] FALSE
D937V9, binary
                  cls
clus                 0   1
  ATP12A MUTATED    21   0
  ATP12A WILD-TYPE 329  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP12A MUTATED     21    0
  ATP12A WILD-TYPE  329   22
     clus
vv    ATP12A MUTATED ATP12A WILD-TYPE
  NO              21              329
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ATP12A MUTATED                     18                             7
  ATP12A WILD-TYPE                  297                            40
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ATP12A MUTATED                       4                              0
  ATP12A WILD-TYPE                   102                             10
D937V10, multiclass
                                clus
vv                               ATP12A MUTATED ATP12A WILD-TYPE
  COLON ADENOCARCINOMA                       18              297
  COLON MUCINOUS ADENOCARCINOMA               7               40
  RECTAL ADENOCARCINOMA                       4              102
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ATP12A MUTATED    21   0   0   2
  ATP12A WILD-TYPE 324   4  31  23
D937V11, multiclass
    clus
vv   ATP12A MUTATED ATP12A WILD-TYPE
  R0             21              324
  R1              0                4
  R2              0               31
  RX              2               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D937V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ATP12A MUTATED                                  1     0
  ATP12A WILD-TYPE                                0    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ATP12A MUTATED                           2    15
  ATP12A WILD-TYPE                        20   211
D937V13, multiclass
                                  clus
vv                                 ATP12A MUTATED ATP12A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              1                0
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     2               20
  WHITE                                        15              211
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(938) Variable = SGK3 MUTATION ANALYSIS
D938V1, survival
                sevent
clus2              0   1
  SGK3 MUTATED     6   4
  SGK3 WILD-TYPE 372  89
  SGK3 MUTATED SGK3 WILD-TYPE 
            10            461 
  SGK3 MUTATED SGK3 WILD-TYPE 
             4             89 
$`SGK3 MUTATED`
TCGA-AA-3510 TCGA-AD-6899 TCGA-AD-6901 TCGA-AZ-4315 TCGA-AZ-6607 TCGA-D5-6532 
       63.98         5.79        22.42        58.39         3.19        18.25 
TCGA-D5-6930 TCGA-DM-A28G TCGA-AG-3902 TCGA-AG-A002 
        1.51        60.79        32.02        20.98 

$`SGK3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6963 TCGA-AD-6964 
       15.52        56.55         0.79         0.72        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6534 
       19.59        56.09        55.92        20.19         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 
        9.04         9.44        11.64         4.80        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       35.97       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3909 
       13.02        35.01        14.01         1.02        48.03        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  SGK3 MUTATED SGK3 WILD-TYPE 
          1.51           0.00 
  SGK3 MUTATED SGK3 WILD-TYPE 
         63.98         148.01 
  SGK3 MUTATED SGK3 WILD-TYPE 
         21.70          20.12 
[1] "1.5 - 64.0 (21.7)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.8"
D938V2, continuous
D938V3, binary
                cls
clus               0   1
  SGK3 MUTATED     8   2
  SGK3 WILD-TYPE 358 117
[1] "tbl2"
                cls
clus             [,1] [,2]
  SGK3 MUTATED      8    2
  SGK3 WILD-TYPE  358  117
        clus
vv       SGK3 MUTATED SGK3 WILD-TYPE
  COLON             8            358
  RECTUM            2            117
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SGK3 MUTATED         1        0        1         5         0         0
  SGK3 WILD-TYPE      90        1       31       133        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SGK3 MUTATED           0          0          0          1        1         0
  SGK3 WILD-TYPE        24         11         59         41       47        18
                vv
clus             STAGE IVB
  SGK3 MUTATED           0
  SGK3 WILD-TYPE         1
D938V4, multiclass
            clus
vv           SGK3 MUTATED SGK3 WILD-TYPE
  STAGE I               1             90
  STAGE IA              0              1
  STAGE II              1             31
  STAGE IIA             5            133
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            0             59
  STAGE IIIC            1             41
  STAGE IV              1             47
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  SGK3 MUTATED     0   1   7   2
  SGK3 WILD-TYPE  17  91 322  48
D938V5, multiclass
    clus
vv   SGK3 MUTATED SGK3 WILD-TYPE
  T1            0             17
  T2            1             91
  T3            7            322
  T4            2             48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  SGK3 MUTATED     8   0   2
  SGK3 WILD-TYPE 279 113  85
D938V6, multiclass
    clus
vv   SGK3 MUTATED SGK3 WILD-TYPE
  N0            8            279
  N1            0            113
  N2            2             85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D938V7, binary
                cls
clus               0   1
  SGK3 MUTATED     7   1
  SGK3 WILD-TYPE 368  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  SGK3 MUTATED      7    1
  SGK3 WILD-TYPE  368   64
   clus
vv  SGK3 MUTATED SGK3 WILD-TYPE
  0            7            368
  1            1             64
[1] 2 2
[1] FALSE
D938V8, binary
                cls
clus               0   1
  SGK3 MUTATED     0  10
  SGK3 WILD-TYPE 225 254
[1] "tbl2"
                cls
clus             [,1] [,2]
  SGK3 MUTATED      0   10
  SGK3 WILD-TYPE  225  254
        clus
vv       SGK3 MUTATED SGK3 WILD-TYPE
  FEMALE            0            225
  MALE             10            254
[1] 2 2
[1] FALSE
D938V9, binary
                cls
clus               0   1
  SGK3 MUTATED     8   0
  SGK3 WILD-TYPE 342  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  SGK3 MUTATED      8    0
  SGK3 WILD-TYPE  342   22
     clus
vv    SGK3 MUTATED SGK3 WILD-TYPE
  NO             8            342
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SGK3 MUTATED                      6                             2
  SGK3 WILD-TYPE                  309                            45
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SGK3 MUTATED                       2                              0
  SGK3 WILD-TYPE                   104                             10
D938V10, multiclass
                                clus
vv                               SGK3 MUTATED SGK3 WILD-TYPE
  COLON ADENOCARCINOMA                      6            309
  COLON MUCINOUS ADENOCARCINOMA             2             45
  RECTAL ADENOCARCINOMA                     2            104
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  SGK3 MUTATED     6   0   0   0
  SGK3 WILD-TYPE 339   4  31  25
D938V11, multiclass
    clus
vv   SGK3 MUTATED SGK3 WILD-TYPE
  R0            6            339
  R1            0              4
  R2            0             31
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D938V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SGK3 MUTATED                                  0     0
  SGK3 WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  SGK3 MUTATED                           0     7
  SGK3 WILD-TYPE                        22   219
D938V13, multiclass
                                  clus
vv                                 SGK3 MUTATED SGK3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       7            219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(939) Variable = ODAM MUTATION ANALYSIS
D939V1, survival
                sevent
clus2              0   1
  ODAM MUTATED     4   2
  ODAM WILD-TYPE 374  91
  ODAM MUTATED ODAM WILD-TYPE 
             6            465 
  ODAM MUTATED ODAM WILD-TYPE 
             2             91 
$`ODAM MUTATED`
TCGA-AA-3977 TCGA-CM-5348 TCGA-DM-A1D4 TCGA-DM-A28H TCGA-G4-6306 TCGA-DY-A1DG 
       25.02        22.98        92.75       117.07        44.68        51.48 

$`ODAM WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5349 
       37.02        25.02        13.02        29.06        22.03        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-DM-A1D7 
      119.70        24.43        38.20       130.65        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       53.62        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  ODAM MUTATED ODAM WILD-TYPE 
         22.98           0.00 
  ODAM MUTATED ODAM WILD-TYPE 
        117.07         148.01 
  ODAM MUTATED ODAM WILD-TYPE 
         48.08          20.02 
[1] "23.0 - 117.1 (48.1)" "0.0 - 148.0 (20.0)" 
[1] "hr=" "1.3"
D939V2, continuous
D939V3, binary
                cls
clus               0   1
  ODAM MUTATED     5   1
  ODAM WILD-TYPE 361 118
[1] "tbl2"
                cls
clus             [,1] [,2]
  ODAM MUTATED      5    1
  ODAM WILD-TYPE  361  118
        clus
vv       ODAM MUTATED ODAM WILD-TYPE
  COLON             5            361
  RECTUM            1            118
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ODAM MUTATED         0        0        0         2         0         0
  ODAM WILD-TYPE      91        1       32       136        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ODAM MUTATED           0          0          1          1        0         1
  ODAM WILD-TYPE        24         11         58         41       48        17
                vv
clus             STAGE IVB
  ODAM MUTATED           0
  ODAM WILD-TYPE         1
D939V4, multiclass
            clus
vv           ODAM MUTATED ODAM WILD-TYPE
  STAGE I               0             91
  STAGE IA              0              1
  STAGE II              0             32
  STAGE IIA             2            136
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            1             58
  STAGE IIIC            1             41
  STAGE IV              0             48
  STAGE IVA             1             17
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  ODAM MUTATED     0   2   4   0
  ODAM WILD-TYPE  17  90 325  50
D939V5, multiclass
    clus
vv   ODAM MUTATED ODAM WILD-TYPE
  T1            0             17
  T2            2             90
  T3            4            325
  T4            0             50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  ODAM MUTATED     3   2   1
  ODAM WILD-TYPE 284 111  86
D939V6, multiclass
    clus
vv   ODAM MUTATED ODAM WILD-TYPE
  N0            3            284
  N1            2            111
  N2            1             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D939V7, binary
                cls
clus               0   1
  ODAM MUTATED     4   1
  ODAM WILD-TYPE 371  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  ODAM MUTATED      4    1
  ODAM WILD-TYPE  371   64
   clus
vv  ODAM MUTATED ODAM WILD-TYPE
  0            4            371
  1            1             64
[1] 2 2
[1] FALSE
D939V8, binary
                cls
clus               0   1
  ODAM MUTATED     0   6
  ODAM WILD-TYPE 225 258
[1] "tbl2"
                cls
clus             [,1] [,2]
  ODAM MUTATED      0    6
  ODAM WILD-TYPE  225  258
        clus
vv       ODAM MUTATED ODAM WILD-TYPE
  FEMALE            0            225
  MALE              6            258
[1] 2 2
[1] FALSE
D939V9, binary
                cls
clus               0   1
  ODAM MUTATED     3   0
  ODAM WILD-TYPE 347  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  ODAM MUTATED      3    0
  ODAM WILD-TYPE  347   22
     clus
vv    ODAM MUTATED ODAM WILD-TYPE
  NO             3            347
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ODAM MUTATED                      5                             0
  ODAM WILD-TYPE                  310                            47
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ODAM MUTATED                       1                              0
  ODAM WILD-TYPE                   105                             10
D939V10, multiclass
                                clus
vv                               ODAM MUTATED ODAM WILD-TYPE
  COLON ADENOCARCINOMA                      5            310
  COLON MUCINOUS ADENOCARCINOMA             0             47
  RECTAL ADENOCARCINOMA                     1            105
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  ODAM MUTATED     2   0   0   0
  ODAM WILD-TYPE 343   4  31  25
D939V11, multiclass
[1] "Remove cluster labels:" "ODAM MUTATED"          
clus
  ODAM MUTATED ODAM WILD-TYPE 
             2            403 
    TCGA-A6-2671     TCGA-A6-2672     TCGA-A6-2674     TCGA-A6-2676 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-A6-2677     TCGA-A6-2678     TCGA-A6-2683     TCGA-A6-3807 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-A6-3808     TCGA-A6-3809     TCGA-A6-3810     TCGA-A6-5657 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-A6-5659     TCGA-A6-5661     TCGA-A6-5665     TCGA-A6-6781 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-AA-3489     TCGA-AA-3492     TCGA-AA-3496     TCGA-AA-3502 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-AA-3510     TCGA-AA-3511     TCGA-AA-3514     TCGA-AA-3517 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-AA-3518     TCGA-AA-3519     TCGA-AA-3520     TCGA-AA-3521 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-AA-3522     TCGA-AA-3524     TCGA-AA-3525     TCGA-AA-3526 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-AA-3527     TCGA-AA-3529     TCGA-AA-3530     TCGA-AA-3531 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-AA-3532     TCGA-AA-3534     TCGA-AA-3538     TCGA-AA-3542 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-AA-3543     TCGA-AA-3544     TCGA-AA-3548     TCGA-AA-3549 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-AA-3552     TCGA-AA-3553     TCGA-AA-3554     TCGA-AA-3555 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-AA-3556     TCGA-AA-3558     TCGA-AA-3560     TCGA-AA-3561 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-AA-3562     TCGA-AA-3655     TCGA-AA-3660     TCGA-AA-3662 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-AA-3663     TCGA-AA-3664     TCGA-AA-3666     TCGA-AA-3667 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-AA-3672     TCGA-AA-3673     TCGA-AA-3678     TCGA-AA-3679 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-AA-3680     TCGA-AA-3681     TCGA-AA-3684     TCGA-AA-3685 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-AA-3688     TCGA-AA-3692     TCGA-AA-3693     TCGA-AA-3695 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-AA-3696     TCGA-AA-3697     TCGA-AA-3710     TCGA-AA-3712 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-AA-3713     TCGA-AA-3715     TCGA-AA-3811     TCGA-AA-3812 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-AA-3814     TCGA-AA-3815     TCGA-AA-3818     TCGA-AA-3819 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-AA-3821     TCGA-AA-3831     TCGA-AA-3833     TCGA-AA-3837 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-AA-3842     TCGA-AA-3844     TCGA-AA-3845     TCGA-AA-3846 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-AA-3848     TCGA-AA-3850     TCGA-AA-3851     TCGA-AA-3852 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-AA-3854     TCGA-AA-3855     TCGA-AA-3856     TCGA-AA-3858 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-AA-3860     TCGA-AA-3861     TCGA-AA-3864     TCGA-AA-3866 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-AA-3867     TCGA-AA-3869     TCGA-AA-3870     TCGA-AA-3872 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-AA-3875     TCGA-AA-3877     TCGA-AA-3930     TCGA-AA-3939 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-AA-3941     TCGA-AA-3947     TCGA-AA-3949     TCGA-AA-3950 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-AA-3952     TCGA-AA-3955     TCGA-AA-3956     TCGA-AA-3968 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-AA-3971     TCGA-AA-3972     TCGA-AA-3973     TCGA-AA-3975 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-AA-3976     TCGA-AA-3979     TCGA-AA-3984     TCGA-AA-3986 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-AA-3989     TCGA-AA-3994     TCGA-AA-A004     TCGA-AA-A00A 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-AA-A00D     TCGA-AA-A00E     TCGA-AA-A00F     TCGA-AA-A00J 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-AA-A00K     TCGA-AA-A00L     TCGA-AA-A00N     TCGA-AA-A00O 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-AA-A00Q     TCGA-AA-A00R     TCGA-AA-A00U     TCGA-AA-A00W 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-AA-A00Z     TCGA-AA-A010     TCGA-AA-A017     TCGA-AA-A01D 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-AA-A01F     TCGA-AA-A01G     TCGA-AA-A01I     TCGA-AA-A01K 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-AA-A01P     TCGA-AA-A01Q     TCGA-AA-A01R     TCGA-AA-A01S 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-AA-A01T     TCGA-AA-A01V     TCGA-AA-A01X     TCGA-AA-A01Z 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-AA-A022     TCGA-AA-A024     TCGA-AA-A029     TCGA-AA-A02F 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-AA-A02H     TCGA-AA-A02J     TCGA-AA-A02K     TCGA-AA-A02O 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-AA-A02W     TCGA-AA-A02Y     TCGA-AA-A03F     TCGA-AA-A03J 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-AD-5900     TCGA-AD-6548     TCGA-AD-6888     TCGA-AU-3779 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-AU-6004     TCGA-AY-4070     TCGA-AY-4071     TCGA-AY-5543 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-AY-6196     TCGA-AY-6197     TCGA-AY-6386     TCGA-AZ-4315 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-AZ-4681     TCGA-AZ-4682     TCGA-CA-5254     TCGA-CA-5255 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-CA-5796     TCGA-CA-5797     TCGA-CA-6715     TCGA-CA-6716 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-CA-6717     TCGA-CA-6718     TCGA-CA-6719     TCGA-CK-4947 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-CK-4948     TCGA-CK-4950     TCGA-CK-4952     TCGA-CK-5912 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-CK-5913     TCGA-CK-5914     TCGA-CK-5915     TCGA-CK-5916 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-CK-6746     TCGA-CK-6747     TCGA-CK-6748     TCGA-CK-6751 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-CM-4743     TCGA-CM-4744     TCGA-CM-4746     TCGA-CM-4747 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-CM-4752     TCGA-CM-5341     TCGA-CM-5344     TCGA-CM-5349 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-CM-5860     TCGA-CM-5861     TCGA-CM-5862     TCGA-CM-5863 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-CM-5864     TCGA-CM-5868     TCGA-CM-6161     TCGA-CM-6162 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-CM-6163     TCGA-CM-6164     TCGA-CM-6165     TCGA-CM-6166 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-CM-6167     TCGA-CM-6168     TCGA-CM-6169     TCGA-CM-6170 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-CM-6171     TCGA-CM-6172     TCGA-CM-6674     TCGA-CM-6675 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-CM-6676     TCGA-CM-6677     TCGA-CM-6678     TCGA-CM-6679 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-CM-6680     TCGA-D5-5537     TCGA-D5-5538     TCGA-D5-5539 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-D5-5540     TCGA-D5-5541     TCGA-D5-6529     TCGA-D5-6532 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-D5-6533     TCGA-D5-6534     TCGA-D5-6535     TCGA-D5-6536 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-D5-6537     TCGA-D5-6538     TCGA-D5-6539     TCGA-D5-6540 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-D5-6541     TCGA-D5-6898     TCGA-D5-6920     TCGA-D5-6922 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-D5-6923     TCGA-D5-6924     TCGA-D5-6926     TCGA-D5-6927 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-D5-6928     TCGA-D5-6929     TCGA-D5-6930     TCGA-D5-6931 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-D5-6932     TCGA-D5-7000     TCGA-F4-6459     TCGA-F4-6460 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-F4-6569     TCGA-F4-6570     TCGA-F4-6703     TCGA-F4-6704 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-F4-6805     TCGA-F4-6806     TCGA-F4-6807     TCGA-F4-6808 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-F4-6809     TCGA-F4-6854     TCGA-F4-6855     TCGA-F4-6856 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-G4-6293     TCGA-G4-6299     TCGA-G4-6303     TCGA-G4-6304 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-G4-6307     TCGA-G4-6309     TCGA-G4-6310     TCGA-G4-6315 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-G4-6317     TCGA-G4-6321     TCGA-G4-6323     TCGA-G4-6586 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-G4-6588     TCGA-G4-6625     TCGA-G4-6626     TCGA-G4-6628 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-AF-2687     TCGA-AF-2689     TCGA-AF-2691     TCGA-AF-2692 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-AF-3400     TCGA-AF-3913     TCGA-AF-4110     TCGA-AF-5654 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-AF-6655     TCGA-AG-3574     TCGA-AG-3575     TCGA-AG-3578 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-AG-3580     TCGA-AG-3581     TCGA-AG-3582     TCGA-AG-3583 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-AG-3584     TCGA-AG-3586     TCGA-AG-3587     TCGA-AG-3593 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-AG-3594     TCGA-AG-3598     TCGA-AG-3599     TCGA-AG-3600 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-AG-3601     TCGA-AG-3602     TCGA-AG-3605     TCGA-AG-3608 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-AG-3609     TCGA-AG-3611     TCGA-AG-3612     TCGA-AG-3726 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-AG-3727     TCGA-AG-3731     TCGA-AG-3732     TCGA-AG-3742 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-AG-3878     TCGA-AG-3882     TCGA-AG-3883     TCGA-AG-3885 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-AG-3887     TCGA-AG-3890     TCGA-AG-3892     TCGA-AG-3893 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-AG-3894     TCGA-AG-3896     TCGA-AG-3898     TCGA-AG-3901 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-AG-3902     TCGA-AG-3909     TCGA-AG-3999     TCGA-AG-4001 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-AG-4005     TCGA-AG-4007     TCGA-AG-4008     TCGA-AG-4015 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-AG-A002     TCGA-AG-A008     TCGA-AG-A00C     TCGA-AG-A00H 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-AG-A00Y     TCGA-AG-A011     TCGA-AG-A014     TCGA-AG-A015 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-AG-A016     TCGA-AG-A01L     TCGA-AG-A01W     TCGA-AG-A01Y 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-AG-A020     TCGA-AG-A025     TCGA-AG-A026     TCGA-AG-A02G 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-AG-A02N     TCGA-AG-A02X     TCGA-AG-A032     TCGA-AG-A036 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-AH-6549     TCGA-AH-6643     TCGA-CL-5917     TCGA-CL-5918 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-DC-5337     TCGA-DC-5869     TCGA-DC-6155     TCGA-DC-6157 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-DC-6158     TCGA-DC-6160     TCGA-DC-6681     TCGA-DC-6682 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-DC-6683     TCGA-DT-5265     TCGA-EF-5830     TCGA-EI-6506 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-EI-6507     TCGA-EI-6508     TCGA-EI-6510     TCGA-F5-6464 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-F5-6465     TCGA-F5-6571     TCGA-F5-6702     TCGA-F5-6812 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
    TCGA-F5-6813     TCGA-G5-6235     TCGA-G5-6641 
"ODAM WILD-TYPE" "ODAM WILD-TYPE" "ODAM WILD-TYPE" 
D939V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ODAM MUTATED                                  0     0
  ODAM WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  ODAM MUTATED                           0     5
  ODAM WILD-TYPE                        22   221
D939V13, multiclass
                                  clus
vv                                 ODAM MUTATED ODAM WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       5            221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(940) Variable = CYSLTR2 MUTATION ANALYSIS
D940V1, survival
                   sevent
clus2                 0   1
  CYSLTR2 MUTATED    15   2
  CYSLTR2 WILD-TYPE 363  91
  CYSLTR2 MUTATED CYSLTR2 WILD-TYPE 
               17               454 
  CYSLTR2 MUTATED CYSLTR2 WILD-TYPE 
                2                91 
$`CYSLTR2 MUTATED`
TCGA-A6-2671 TCGA-A6-6781 TCGA-AA-3496 TCGA-AA-3525 TCGA-AA-A00J TCGA-AA-A00O 
       43.76        19.66         1.02         8.05        18.05        27.02 
TCGA-AD-6548 TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-4752 TCGA-CM-6676 TCGA-CM-6680 
       21.37        12.76        10.06        13.02        11.08        12.03 
TCGA-D5-5539 TCGA-DM-A28K TCGA-G4-6310 TCGA-AG-3892 TCGA-CI-6619 
       19.59        98.24        63.62        13.02         6.05 

$`CYSLTR2 WILD-TYPE`
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       46.65        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3510 
       20.12        20.28         7.04         3.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       24.03        37.05        36.03        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00Q TCGA-AA-A00R 
       34.03        18.05        38.04         4.01        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.07        12.20        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 
       11.08        11.01        10.06        45.40        12.26        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       35.97        60.79       117.07         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 
       19.99         1.02        17.95        36.95        17.03        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6620 
       38.56         1.45        17.49         0.69         0.72        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  CYSLTR2 MUTATED CYSLTR2 WILD-TYPE 
             1.02              0.00 
  CYSLTR2 MUTATED CYSLTR2 WILD-TYPE 
            98.24            148.01 
  CYSLTR2 MUTATED CYSLTR2 WILD-TYPE 
           13.020            20.945 
[1] "1.0 - 98.2 (13.0)"  "0.0 - 148.0 (20.9)"
[1] "hr=" "1.6"
D940V2, continuous
D940V3, binary
                   cls
clus                  0   1
  CYSLTR2 MUTATED    15   2
  CYSLTR2 WILD-TYPE 351 117
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CYSLTR2 MUTATED     15    2
  CYSLTR2 WILD-TYPE  351  117
        clus
vv       CYSLTR2 MUTATED CYSLTR2 WILD-TYPE
  COLON               15               351
  RECTUM               2               117
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CYSLTR2 MUTATED         3        0        1         4         0         0
  CYSLTR2 WILD-TYPE      88        1       31       134        10         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CYSLTR2 MUTATED           0          1          4          2        2
  CYSLTR2 WILD-TYPE        24         10         55         40       46
                   vv
clus                STAGE IVA STAGE IVB
  CYSLTR2 MUTATED           0         0
  CYSLTR2 WILD-TYPE        18         1
D940V4, multiclass
            clus
vv           CYSLTR2 MUTATED CYSLTR2 WILD-TYPE
  STAGE I                  3                88
  STAGE IA                 0                 1
  STAGE II                 1                31
  STAGE IIA                4               134
  STAGE IIB                0                10
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               1                10
  STAGE IIIB               4                55
  STAGE IIIC               2                40
  STAGE IV                 2                46
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  CYSLTR2 MUTATED     1   2  12   2
  CYSLTR2 WILD-TYPE  16  90 317  48
D940V5, multiclass
    clus
vv   CYSLTR2 MUTATED CYSLTR2 WILD-TYPE
  T1               1                16
  T2               2                90
  T3              12               317
  T4               2                48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  CYSLTR2 MUTATED     8   6   3
  CYSLTR2 WILD-TYPE 279 107  84
D940V6, multiclass
    clus
vv   CYSLTR2 MUTATED CYSLTR2 WILD-TYPE
  N0               8               279
  N1               6               107
  N2               3                84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D940V7, binary
                   cls
clus                  0   1
  CYSLTR2 MUTATED    14   2
  CYSLTR2 WILD-TYPE 361  63
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CYSLTR2 MUTATED     14    2
  CYSLTR2 WILD-TYPE  361   63
   clus
vv  CYSLTR2 MUTATED CYSLTR2 WILD-TYPE
  0              14               361
  1               2                63
[1] 2 2
[1] FALSE
D940V8, binary
                   cls
clus                  0   1
  CYSLTR2 MUTATED     5  12
  CYSLTR2 WILD-TYPE 220 252
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CYSLTR2 MUTATED      5   12
  CYSLTR2 WILD-TYPE  220  252
        clus
vv       CYSLTR2 MUTATED CYSLTR2 WILD-TYPE
  FEMALE               5               220
  MALE                12               252
[1] 2 2
[1] FALSE
D940V9, binary
                   cls
clus                  0   1
  CYSLTR2 MUTATED    13   1
  CYSLTR2 WILD-TYPE 337  21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CYSLTR2 MUTATED     13    1
  CYSLTR2 WILD-TYPE  337   21
     clus
vv    CYSLTR2 MUTATED CYSLTR2 WILD-TYPE
  NO               13               337
  YES               1                21
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CYSLTR2 MUTATED                     10                             5
  CYSLTR2 WILD-TYPE                  305                            42
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CYSLTR2 MUTATED                       2                              0
  CYSLTR2 WILD-TYPE                   104                             10
D940V10, multiclass
                                clus
vv                               CYSLTR2 MUTATED CYSLTR2 WILD-TYPE
  COLON ADENOCARCINOMA                        10               305
  COLON MUCINOUS ADENOCARCINOMA                5                42
  RECTAL ADENOCARCINOMA                        2               104
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  CYSLTR2 MUTATED    13   0   0   2
  CYSLTR2 WILD-TYPE 332   4  31  23
D940V11, multiclass
    clus
vv   CYSLTR2 MUTATED CYSLTR2 WILD-TYPE
  R0              13               332
  R1               0                 4
  R2               0                31
  RX               2                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D940V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CYSLTR2 MUTATED                                  0     2
  CYSLTR2 WILD-TYPE                                1     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  CYSLTR2 MUTATED                           1     9
  CYSLTR2 WILD-TYPE                        21   217
D940V13, multiclass
                                  clus
vv                                 CYSLTR2 MUTATED CYSLTR2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          2                 9
  BLACK OR AFRICAN AMERICAN                      1                21
  WHITE                                          9               217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(941) Variable = RAB6C MUTATION ANALYSIS
D941V1, survival
                 sevent
clus2               0   1
  RAB6C MUTATED     3   2
  RAB6C WILD-TYPE 375  91
  RAB6C MUTATED RAB6C WILD-TYPE 
              5             466 
  RAB6C MUTATED RAB6C WILD-TYPE 
              2              91 
$`RAB6C MUTATED`
TCGA-AA-3660 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4952 TCGA-D5-5537 
       78.08        12.76        10.06        15.62        45.40 

$`RAB6C WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 
       20.98        19.99        13.94        19.99        61.02         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.07        12.20        14.30        17.56       148.01        85.45 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5538 
       11.08        11.08        11.01        10.06        12.03        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  RAB6C MUTATED RAB6C WILD-TYPE 
          10.06            0.00 
  RAB6C MUTATED RAB6C WILD-TYPE 
          78.08          148.01 
  RAB6C MUTATED RAB6C WILD-TYPE 
         15.620          20.235 
[1] "10.1 - 78.1 (15.6)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.6"
D941V2, continuous
D941V3, binary
                 cls
clus                0   1
  RAB6C MUTATED     5   0
  RAB6C WILD-TYPE 361 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RAB6C MUTATED      5    0
  RAB6C WILD-TYPE  361  119
        clus
vv       RAB6C MUTATED RAB6C WILD-TYPE
  COLON              5             361
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RAB6C MUTATED         0        0        1         3         0         0
  RAB6C WILD-TYPE      91        1       31       135        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RAB6C MUTATED           0          0          0          1        0         0
  RAB6C WILD-TYPE        24         11         59         41       48        18
                 vv
clus              STAGE IVB
  RAB6C MUTATED           0
  RAB6C WILD-TYPE         1
D941V4, multiclass
            clus
vv           RAB6C MUTATED RAB6C WILD-TYPE
  STAGE I                0              91
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              3             135
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             1              41
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  RAB6C MUTATED     0   0   4   1
  RAB6C WILD-TYPE  17  92 325  49
D941V5, multiclass
    clus
vv   RAB6C MUTATED RAB6C WILD-TYPE
  T1             0              17
  T2             0              92
  T3             4             325
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  RAB6C MUTATED     3   0   2
  RAB6C WILD-TYPE 284 113  85
D941V6, multiclass
    clus
vv   RAB6C MUTATED RAB6C WILD-TYPE
  N0             3             284
  N1             0             113
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D941V7, binary
                 cls
clus                0   1
  RAB6C MUTATED     4   0
  RAB6C WILD-TYPE 371  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RAB6C MUTATED      4    0
  RAB6C WILD-TYPE  371   65
   clus
vv  RAB6C MUTATED RAB6C WILD-TYPE
  0             4             371
  1             0              65
[1] 2 2
[1] FALSE
D941V8, binary
                 cls
clus                0   1
  RAB6C MUTATED     2   3
  RAB6C WILD-TYPE 223 261
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RAB6C MUTATED      2    3
  RAB6C WILD-TYPE  223  261
        clus
vv       RAB6C MUTATED RAB6C WILD-TYPE
  FEMALE             2             223
  MALE               3             261
[1] 2 2
[1] FALSE
D941V9, binary
                 cls
clus                0   1
  RAB6C MUTATED     4   0
  RAB6C WILD-TYPE 346  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RAB6C MUTATED      4    0
  RAB6C WILD-TYPE  346   22
     clus
vv    RAB6C MUTATED RAB6C WILD-TYPE
  NO              4             346
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  RAB6C MUTATED                      3                             2
  RAB6C WILD-TYPE                  312                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  RAB6C MUTATED                       0                              0
  RAB6C WILD-TYPE                   106                             10
D941V10, multiclass
                                clus
vv                               RAB6C MUTATED RAB6C WILD-TYPE
  COLON ADENOCARCINOMA                       3             312
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  RAB6C MUTATED     1   0   0   4
  RAB6C WILD-TYPE 344   4  31  21
D941V11, multiclass
    clus
vv   RAB6C MUTATED RAB6C WILD-TYPE
  R0             1             344
  R1             0               4
  R2             0              31
  RX             4              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D941V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RAB6C MUTATED                                  0     2
  RAB6C WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  RAB6C MUTATED                           0     2
  RAB6C WILD-TYPE                        22   224
D941V13, multiclass
                                  clus
vv                                 RAB6C MUTATED RAB6C WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               9
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        2             224
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(942) Variable = ZC3H6 MUTATION ANALYSIS
D942V1, survival
                 sevent
clus2               0   1
  ZC3H6 MUTATED    14   3
  ZC3H6 WILD-TYPE 364  90
  ZC3H6 MUTATED ZC3H6 WILD-TYPE 
             17             454 
  ZC3H6 MUTATED ZC3H6 WILD-TYPE 
              3              90 
$`ZC3H6 MUTATED`
TCGA-A6-5661 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-A00N TCGA-AA-A010 TCGA-AY-6386 
       33.53        25.02        24.00         4.01        34.98        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-CA-6717 TCGA-CK-4950 TCGA-CM-6162 TCGA-DM-A1D7 
       58.39         1.41        12.76        85.45        12.00        13.32 
TCGA-G4-6586 TCGA-G4-6628 TCGA-AG-A002 TCGA-AH-6547 TCGA-F5-6811 
       35.80        79.69        20.98         1.45        32.19 

$`ZC3H6 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3980 TCGA-AA-3982 
       50.99        13.05        34.06        26.01        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AZ-4616 
       27.09        16.31         0.95        33.01        21.44         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 
       12.20        10.06        14.30        17.56       148.01        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 
        5.03        15.02        15.02        17.03        15.02         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
      130.65        92.75        49.91        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 
       13.78        26.17        91.79        46.75        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
      117.11        38.56        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  ZC3H6 MUTATED ZC3H6 WILD-TYPE 
           1.41            0.00 
  ZC3H6 MUTATED ZC3H6 WILD-TYPE 
          85.45          148.01 
  ZC3H6 MUTATED ZC3H6 WILD-TYPE 
         24.000          20.085 
[1] "1.4 - 85.5 (24.0)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.2"
D942V2, continuous
D942V3, binary
                 cls
clus                0   1
  ZC3H6 MUTATED    15   3
  ZC3H6 WILD-TYPE 351 116
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZC3H6 MUTATED     15    3
  ZC3H6 WILD-TYPE  351  116
        clus
vv       ZC3H6 MUTATED ZC3H6 WILD-TYPE
  COLON             15             351
  RECTUM             3             116
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZC3H6 MUTATED         2        0        0         8         2         0
  ZC3H6 WILD-TYPE      89        1       32       130         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ZC3H6 MUTATED           0          0          3          0        1         0
  ZC3H6 WILD-TYPE        24         11         56         42       47        18
                 vv
clus              STAGE IVB
  ZC3H6 MUTATED           0
  ZC3H6 WILD-TYPE         1
D942V4, multiclass
            clus
vv           ZC3H6 MUTATED ZC3H6 WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              8             130
  STAGE IIB              2               8
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             3              56
  STAGE IIIC             0              42
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ZC3H6 MUTATED     0   3  12   3
  ZC3H6 WILD-TYPE  17  89 317  47
D942V5, multiclass
    clus
vv   ZC3H6 MUTATED ZC3H6 WILD-TYPE
  T1             0              17
  T2             3              89
  T3            12             317
  T4             3              47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  ZC3H6 MUTATED    14   3   1
  ZC3H6 WILD-TYPE 273 110  86
D942V6, multiclass
    clus
vv   ZC3H6 MUTATED ZC3H6 WILD-TYPE
  N0            14             273
  N1             3             110
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D942V7, binary
                 cls
clus                0   1
  ZC3H6 MUTATED    15   1
  ZC3H6 WILD-TYPE 360  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZC3H6 MUTATED     15    1
  ZC3H6 WILD-TYPE  360   64
   clus
vv  ZC3H6 MUTATED ZC3H6 WILD-TYPE
  0            15             360
  1             1              64
[1] 2 2
[1] FALSE
D942V8, binary
                 cls
clus                0   1
  ZC3H6 MUTATED     9   9
  ZC3H6 WILD-TYPE 216 255
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZC3H6 MUTATED      9    9
  ZC3H6 WILD-TYPE  216  255
        clus
vv       ZC3H6 MUTATED ZC3H6 WILD-TYPE
  FEMALE             9             216
  MALE               9             255
[1] 2 2
[1] FALSE
D942V9, binary
                 cls
clus                0   1
  ZC3H6 MUTATED    14   0
  ZC3H6 WILD-TYPE 336  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZC3H6 MUTATED     14    0
  ZC3H6 WILD-TYPE  336   22
     clus
vv    ZC3H6 MUTATED ZC3H6 WILD-TYPE
  NO             14             336
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ZC3H6 MUTATED                     11                             3
  ZC3H6 WILD-TYPE                  304                            44
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ZC3H6 MUTATED                       3                              0
  ZC3H6 WILD-TYPE                   103                             10
D942V10, multiclass
                                clus
vv                               ZC3H6 MUTATED ZC3H6 WILD-TYPE
  COLON ADENOCARCINOMA                      11             304
  COLON MUCINOUS ADENOCARCINOMA              3              44
  RECTAL ADENOCARCINOMA                      3             103
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  ZC3H6 MUTATED    11   1   0   1
  ZC3H6 WILD-TYPE 334   3  31  24
D942V11, multiclass
    clus
vv   ZC3H6 MUTATED ZC3H6 WILD-TYPE
  R0            11             334
  R1             1               3
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D942V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZC3H6 MUTATED                                  0     1
  ZC3H6 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ZC3H6 MUTATED                           3     8
  ZC3H6 WILD-TYPE                        19   218
D942V13, multiclass
                                  clus
vv                                 ZC3H6 MUTATED ZC3H6 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    3              19
  WHITE                                        8             218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(943) Variable = TMEM48 MUTATION ANALYSIS
D943V1, survival
                  sevent
clus2                0   1
  TMEM48 MUTATED     7   3
  TMEM48 WILD-TYPE 371  90
  TMEM48 MUTATED TMEM48 WILD-TYPE 
              10              461 
  TMEM48 MUTATED TMEM48 WILD-TYPE 
               3               90 
$`TMEM48 MUTATED`
TCGA-A6-5661 TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3525 TCGA-AZ-4315 TCGA-AZ-6598 
       33.53         3.02        63.98         8.05        58.39        49.41 
TCGA-CA-6717 TCGA-CA-6718 TCGA-G4-6317 TCGA-AG-A002 
       12.76        10.06        36.00        20.98 

$`TMEM48 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 
       20.12        19.66        20.28         7.04         1.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       24.03        37.05        36.03        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       88.21         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        3.29         0.07        12.20        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       63.62        61.91        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  TMEM48 MUTATED TMEM48 WILD-TYPE 
            3.02             0.00 
  TMEM48 MUTATED TMEM48 WILD-TYPE 
           63.98           148.01 
  TMEM48 MUTATED TMEM48 WILD-TYPE 
          27.255           20.120 
[1] "3.0 - 64.0 (27.3)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.3"
D943V2, continuous
D943V3, binary
                  cls
clus                 0   1
  TMEM48 MUTATED    10   1
  TMEM48 WILD-TYPE 356 118
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TMEM48 MUTATED     10    1
  TMEM48 WILD-TYPE  356  118
        clus
vv       TMEM48 MUTATED TMEM48 WILD-TYPE
  COLON              10              356
  RECTUM              1              118
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TMEM48 MUTATED         1        0        3         5         0         0
  TMEM48 WILD-TYPE      90        1       29       133        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TMEM48 MUTATED           0          0          1          1        0
  TMEM48 WILD-TYPE        24         11         58         41       48
                  vv
clus               STAGE IVA STAGE IVB
  TMEM48 MUTATED           0         0
  TMEM48 WILD-TYPE        18         1
D943V4, multiclass
            clus
vv           TMEM48 MUTATED TMEM48 WILD-TYPE
  STAGE I                 1               90
  STAGE IA                0                1
  STAGE II                3               29
  STAGE IIA               5              133
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              1               58
  STAGE IIIC              1               41
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  TMEM48 MUTATED     0   1  10   0
  TMEM48 WILD-TYPE  17  91 319  50
D943V5, multiclass
    clus
vv   TMEM48 MUTATED TMEM48 WILD-TYPE
  T1              0               17
  T2              1               91
  T3             10              319
  T4              0               50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  TMEM48 MUTATED     9   1   1
  TMEM48 WILD-TYPE 278 112  86
D943V6, multiclass
    clus
vv   TMEM48 MUTATED TMEM48 WILD-TYPE
  N0              9              278
  N1              1              112
  N2              1               86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D943V7, binary
                  cls
clus                 0   1
  TMEM48 MUTATED     9   0
  TMEM48 WILD-TYPE 366  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TMEM48 MUTATED      9    0
  TMEM48 WILD-TYPE  366   65
   clus
vv  TMEM48 MUTATED TMEM48 WILD-TYPE
  0              9              366
  1              0               65
[1] 2 2
[1] FALSE
D943V8, binary
                  cls
clus                 0   1
  TMEM48 MUTATED     5   6
  TMEM48 WILD-TYPE 220 258
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TMEM48 MUTATED      5    6
  TMEM48 WILD-TYPE  220  258
        clus
vv       TMEM48 MUTATED TMEM48 WILD-TYPE
  FEMALE              5              220
  MALE                6              258
[1] 2 2
[1] FALSE
D943V9, binary
                  cls
clus                 0   1
  TMEM48 MUTATED    10   0
  TMEM48 WILD-TYPE 340  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TMEM48 MUTATED     10    0
  TMEM48 WILD-TYPE  340   22
     clus
vv    TMEM48 MUTATED TMEM48 WILD-TYPE
  NO              10              340
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  TMEM48 MUTATED                      9                             1
  TMEM48 WILD-TYPE                  306                            46
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  TMEM48 MUTATED                       1                              0
  TMEM48 WILD-TYPE                   105                             10
D943V10, multiclass
                                clus
vv                               TMEM48 MUTATED TMEM48 WILD-TYPE
  COLON ADENOCARCINOMA                        9              306
  COLON MUCINOUS ADENOCARCINOMA               1               46
  RECTAL ADENOCARCINOMA                       1              105
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  TMEM48 MUTATED     8   0   0   2
  TMEM48 WILD-TYPE 337   4  31  23
D943V11, multiclass
    clus
vv   TMEM48 MUTATED TMEM48 WILD-TYPE
  R0              8              337
  R1              0                4
  R2              0               31
  RX              2               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D943V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TMEM48 MUTATED                                  0     2
  TMEM48 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  TMEM48 MUTATED                           1     3
  TMEM48 WILD-TYPE                        21   223
D943V13, multiclass
                                  clus
vv                                 TMEM48 MUTATED TMEM48 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                9
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                         3              223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(944) Variable = C12ORF10 MUTATION ANALYSIS
D944V1, survival
                    sevent
clus2                  0   1
  C12ORF10 MUTATED     2   2
  C12ORF10 WILD-TYPE 376  91
  C12ORF10 MUTATED C12ORF10 WILD-TYPE 
                 4                467 
  C12ORF10 MUTATED C12ORF10 WILD-TYPE 
                 2                 91 
$`C12ORF10 MUTATED`
TCGA-A6-4105 TCGA-CM-5861 TCGA-F4-6570 TCGA-G4-6293 
       14.53        15.02         6.18       133.18 

$`C12ORF10 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 
       16.57        34.65        33.34        32.75        36.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       30.08        32.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6303 
       13.25         0.53        47.41        35.31        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  C12ORF10 MUTATED C12ORF10 WILD-TYPE 
              6.18               0.00 
  C12ORF10 MUTATED C12ORF10 WILD-TYPE 
            133.18             148.01 
  C12ORF10 MUTATED C12ORF10 WILD-TYPE 
            14.775             20.280 
[1] "6.2 - 133.2 (14.8)" "0.0 - 148.0 (20.3)"
[1] "hr=" "1.9"
D944V2, continuous
D944V3, binary
                    cls
clus                   0   1
  C12ORF10 MUTATED     4   0
  C12ORF10 WILD-TYPE 362 119
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C12ORF10 MUTATED      4    0
  C12ORF10 WILD-TYPE  362  119
        clus
vv       C12ORF10 MUTATED C12ORF10 WILD-TYPE
  COLON                 4                362
  RECTUM                0                119
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  C12ORF10 MUTATED         0        0        0         3         0         0
  C12ORF10 WILD-TYPE      91        1       32       135        10         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C12ORF10 MUTATED           1          0          0          0        0
  C12ORF10 WILD-TYPE        23         11         59         42       48
                    vv
clus                 STAGE IVA STAGE IVB
  C12ORF10 MUTATED           0         0
  C12ORF10 WILD-TYPE        18         1
D944V4, multiclass
            clus
vv           C12ORF10 MUTATED C12ORF10 WILD-TYPE
  STAGE I                   0                 91
  STAGE IA                  0                  1
  STAGE II                  0                 32
  STAGE IIA                 3                135
  STAGE IIB                 0                 10
  STAGE IIC                 0                  1
  STAGE III                 1                 23
  STAGE IIIA                0                 11
  STAGE IIIB                0                 59
  STAGE IIIC                0                 42
  STAGE IV                  0                 48
  STAGE IVA                 0                 18
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  C12ORF10 MUTATED     0   0   4   0
  C12ORF10 WILD-TYPE  17  92 325  50
D944V5, multiclass
    clus
vv   C12ORF10 MUTATED C12ORF10 WILD-TYPE
  T1                0                 17
  T2                0                 92
  T3                4                325
  T4                0                 50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  C12ORF10 MUTATED     3   1   0
  C12ORF10 WILD-TYPE 284 112  87
D944V6, multiclass
    clus
vv   C12ORF10 MUTATED C12ORF10 WILD-TYPE
  N0                3                284
  N1                1                112
  N2                0                 87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D944V7, binary
                    cls
clus                   0   1
  C12ORF10 MUTATED     4   0
  C12ORF10 WILD-TYPE 371  65
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C12ORF10 MUTATED      4    0
  C12ORF10 WILD-TYPE  371   65
   clus
vv  C12ORF10 MUTATED C12ORF10 WILD-TYPE
  0                4                371
  1                0                 65
[1] 2 2
[1] FALSE
D944V8, binary
                    cls
clus                   0   1
  C12ORF10 MUTATED     3   1
  C12ORF10 WILD-TYPE 222 263
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C12ORF10 MUTATED      3    1
  C12ORF10 WILD-TYPE  222  263
        clus
vv       C12ORF10 MUTATED C12ORF10 WILD-TYPE
  FEMALE                3                222
  MALE                  1                263
[1] 2 2
[1] FALSE
D944V9, binary
                    cls
clus                   0   1
  C12ORF10 MUTATED     4   0
  C12ORF10 WILD-TYPE 346  22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C12ORF10 MUTATED      4    0
  C12ORF10 WILD-TYPE  346   22
     clus
vv    C12ORF10 MUTATED C12ORF10 WILD-TYPE
  NO                 4                346
  YES                0                 22
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  C12ORF10 MUTATED                      4                             0
  C12ORF10 WILD-TYPE                  311                            47
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  C12ORF10 MUTATED                       0                              0
  C12ORF10 WILD-TYPE                   106                             10
D944V10, multiclass
                                clus
vv                               C12ORF10 MUTATED C12ORF10 WILD-TYPE
  COLON ADENOCARCINOMA                          4                311
  COLON MUCINOUS ADENOCARCINOMA                 0                 47
  RECTAL ADENOCARCINOMA                         0                106
  RECTAL MUCINOUS ADENOCARCINOMA                0                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  C12ORF10 MUTATED     3   0   0   0
  C12ORF10 WILD-TYPE 342   4  31  25
D944V11, multiclass
    clus
vv   C12ORF10 MUTATED C12ORF10 WILD-TYPE
  R0                3                342
  R1                0                  4
  R2                0                 31
  RX                0                 25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D944V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C12ORF10 MUTATED                                  0     0
  C12ORF10 WILD-TYPE                                1    11
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  C12ORF10 MUTATED                           0     4
  C12ORF10 WILD-TYPE                        22   222
D944V13, multiclass
                                  clus
vv                                 C12ORF10 MUTATED C12ORF10 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 11
  BLACK OR AFRICAN AMERICAN                       0                 22
  WHITE                                           4                222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(945) Variable = OSTM1 MUTATION ANALYSIS
D945V1, survival
                 sevent
clus2               0   1
  OSTM1 MUTATED     4   1
  OSTM1 WILD-TYPE 374  92
  OSTM1 MUTATED OSTM1 WILD-TYPE 
              5             466 
  OSTM1 MUTATED OSTM1 WILD-TYPE 
              1              92 
$`OSTM1 MUTATED`
TCGA-AA-3496 TCGA-AA-3511 TCGA-AD-6889 TCGA-AZ-6598 TCGA-CM-6171 
        1.02         6.97        56.55        49.41        14.04 

$`OSTM1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01        63.98         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        88.21         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       13.02        15.02        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  OSTM1 MUTATED OSTM1 WILD-TYPE 
           1.02            0.00 
  OSTM1 MUTATED OSTM1 WILD-TYPE 
          56.55          148.01 
  OSTM1 MUTATED OSTM1 WILD-TYPE 
         14.040          20.235 
[1] "1.0 - 56.5 (14.0)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.1"
D945V2, continuous
D945V3, binary
                 cls
clus                0   1
  OSTM1 MUTATED     5   0
  OSTM1 WILD-TYPE 361 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OSTM1 MUTATED      5    0
  OSTM1 WILD-TYPE  361  119
        clus
vv       OSTM1 MUTATED OSTM1 WILD-TYPE
  COLON              5             361
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  OSTM1 MUTATED         1        0        3         1         0         0
  OSTM1 WILD-TYPE      90        1       29       137        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  OSTM1 MUTATED           0          0          0          0        0         0
  OSTM1 WILD-TYPE        24         11         59         42       48        18
                 vv
clus              STAGE IVB
  OSTM1 MUTATED           0
  OSTM1 WILD-TYPE         1
D945V4, multiclass
            clus
vv           OSTM1 MUTATED OSTM1 WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               3              29
  STAGE IIA              1             137
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  OSTM1 MUTATED     0   1   3   1
  OSTM1 WILD-TYPE  17  91 326  49
D945V5, multiclass
    clus
vv   OSTM1 MUTATED OSTM1 WILD-TYPE
  T1             0              17
  T2             1              91
  T3             3             326
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  OSTM1 MUTATED     5   0   0
  OSTM1 WILD-TYPE 282 113  87
D945V6, multiclass
    clus
vv   OSTM1 MUTATED OSTM1 WILD-TYPE
  N0             5             282
  N1             0             113
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D945V7, binary
                 cls
clus                0   1
  OSTM1 MUTATED     4   0
  OSTM1 WILD-TYPE 371  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OSTM1 MUTATED      4    0
  OSTM1 WILD-TYPE  371   65
   clus
vv  OSTM1 MUTATED OSTM1 WILD-TYPE
  0             4             371
  1             0              65
[1] 2 2
[1] FALSE
D945V8, binary
                 cls
clus                0   1
  OSTM1 MUTATED     3   2
  OSTM1 WILD-TYPE 222 262
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OSTM1 MUTATED      3    2
  OSTM1 WILD-TYPE  222  262
        clus
vv       OSTM1 MUTATED OSTM1 WILD-TYPE
  FEMALE             3             222
  MALE               2             262
[1] 2 2
[1] FALSE
D945V9, binary
                 cls
clus                0   1
  OSTM1 MUTATED     3   0
  OSTM1 WILD-TYPE 347  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OSTM1 MUTATED      3    0
  OSTM1 WILD-TYPE  347   22
     clus
vv    OSTM1 MUTATED OSTM1 WILD-TYPE
  NO              3             347
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  OSTM1 MUTATED                      5                             0
  OSTM1 WILD-TYPE                  310                            47
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  OSTM1 MUTATED                       0                              0
  OSTM1 WILD-TYPE                   106                             10
D945V10, multiclass
                                clus
vv                               OSTM1 MUTATED OSTM1 WILD-TYPE
  COLON ADENOCARCINOMA                       5             310
  COLON MUCINOUS ADENOCARCINOMA              0              47
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  OSTM1 MUTATED     3   0   0   0
  OSTM1 WILD-TYPE 342   4  31  25
D945V11, multiclass
    clus
vv   OSTM1 MUTATED OSTM1 WILD-TYPE
  R0             3             342
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D945V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OSTM1 MUTATED                                  0     1
  OSTM1 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  OSTM1 MUTATED                           0     2
  OSTM1 WILD-TYPE                        22   224
D945V13, multiclass
                                  clus
vv                                 OSTM1 MUTATED OSTM1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        2             224
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(946) Variable = PLEKHB2 MUTATION ANALYSIS
D946V1, survival
                   sevent
clus2                 0   1
  PLEKHB2 MUTATED     3   2
  PLEKHB2 WILD-TYPE 375  91
  PLEKHB2 MUTATED PLEKHB2 WILD-TYPE 
                5               466 
  PLEKHB2 MUTATED PLEKHB2 WILD-TYPE 
                2                91 
$`PLEKHB2 MUTATED`
TCGA-A6-5666 TCGA-AA-3662 TCGA-AA-3977 TCGA-AD-6964 TCGA-AZ-6601 
       32.71         6.05        25.02        10.88       100.01 

$`PLEKHB2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        22.06        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       19.99        13.94        19.99        61.02        78.08         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
        0.79         0.72         5.79        22.42        27.42         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 
       62.79        88.21        49.41         6.77        12.10        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  PLEKHB2 MUTATED PLEKHB2 WILD-TYPE 
             6.05              0.00 
  PLEKHB2 MUTATED PLEKHB2 WILD-TYPE 
           100.01            148.01 
  PLEKHB2 MUTATED PLEKHB2 WILD-TYPE 
           25.020            20.155 
[1] "6.0 - 100.0 (25.0)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.6"
D946V2, continuous
D946V3, binary
                   cls
clus                  0   1
  PLEKHB2 MUTATED     6   0
  PLEKHB2 WILD-TYPE 360 119
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLEKHB2 MUTATED      6    0
  PLEKHB2 WILD-TYPE  360  119
        clus
vv       PLEKHB2 MUTATED PLEKHB2 WILD-TYPE
  COLON                6               360
  RECTUM               0               119
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PLEKHB2 MUTATED         0        0        1         0         0         1
  PLEKHB2 WILD-TYPE      91        1       31       138        10         0
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PLEKHB2 MUTATED           1          0          0          0        1
  PLEKHB2 WILD-TYPE        23         11         59         42       47
                   vv
clus                STAGE IVA STAGE IVB
  PLEKHB2 MUTATED           0         0
  PLEKHB2 WILD-TYPE        18         1
D946V4, multiclass
            clus
vv           PLEKHB2 MUTATED PLEKHB2 WILD-TYPE
  STAGE I                  0                91
  STAGE IA                 0                 1
  STAGE II                 1                31
  STAGE IIA                0               138
  STAGE IIB                0                10
  STAGE IIC                1                 0
  STAGE III                1                23
  STAGE IIIA               0                11
  STAGE IIIB               0                59
  STAGE IIIC               0                42
  STAGE IV                 1                47
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  PLEKHB2 MUTATED     0   1   2   3
  PLEKHB2 WILD-TYPE  17  91 327  47
D946V5, multiclass
    clus
vv   PLEKHB2 MUTATED PLEKHB2 WILD-TYPE
  T1               0                17
  T2               1                91
  T3               2               327
  T4               3                47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  PLEKHB2 MUTATED     3   0   3
  PLEKHB2 WILD-TYPE 284 113  84
D946V6, multiclass
    clus
vv   PLEKHB2 MUTATED PLEKHB2 WILD-TYPE
  N0               3               284
  N1               0               113
  N2               3                84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D946V7, binary
                   cls
clus                  0   1
  PLEKHB2 MUTATED     3   1
  PLEKHB2 WILD-TYPE 372  64
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLEKHB2 MUTATED      3    1
  PLEKHB2 WILD-TYPE  372   64
   clus
vv  PLEKHB2 MUTATED PLEKHB2 WILD-TYPE
  0               3               372
  1               1                64
[1] 2 2
[1] FALSE
D946V8, binary
                   cls
clus                  0   1
  PLEKHB2 MUTATED     1   5
  PLEKHB2 WILD-TYPE 224 259
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLEKHB2 MUTATED      1    5
  PLEKHB2 WILD-TYPE  224  259
        clus
vv       PLEKHB2 MUTATED PLEKHB2 WILD-TYPE
  FEMALE               1               224
  MALE                 5               259
[1] 2 2
[1] FALSE
D946V9, binary
                   cls
clus                  0   1
  PLEKHB2 MUTATED     5   0
  PLEKHB2 WILD-TYPE 345  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLEKHB2 MUTATED      5    0
  PLEKHB2 WILD-TYPE  345   22
     clus
vv    PLEKHB2 MUTATED PLEKHB2 WILD-TYPE
  NO                5               345
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PLEKHB2 MUTATED                      6                             0
  PLEKHB2 WILD-TYPE                  309                            47
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PLEKHB2 MUTATED                       0                              0
  PLEKHB2 WILD-TYPE                   106                             10
D946V10, multiclass
                                clus
vv                               PLEKHB2 MUTATED PLEKHB2 WILD-TYPE
  COLON ADENOCARCINOMA                         6               309
  COLON MUCINOUS ADENOCARCINOMA                0                47
  RECTAL ADENOCARCINOMA                        0               106
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  PLEKHB2 MUTATED     1   0   1   0
  PLEKHB2 WILD-TYPE 344   4  30  25
D946V11, multiclass
[1] "Remove cluster labels:" "PLEKHB2 MUTATED"       
clus
  PLEKHB2 MUTATED PLEKHB2 WILD-TYPE 
                2               403 
       TCGA-A6-2671        TCGA-A6-2672        TCGA-A6-2674        TCGA-A6-2676 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-A6-2677        TCGA-A6-2678        TCGA-A6-2683        TCGA-A6-3807 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-A6-3808        TCGA-A6-3809        TCGA-A6-3810        TCGA-A6-5657 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-A6-5659        TCGA-A6-5661        TCGA-A6-5665        TCGA-A6-6781 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-AA-3489        TCGA-AA-3492        TCGA-AA-3496        TCGA-AA-3502 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-AA-3510        TCGA-AA-3511        TCGA-AA-3514        TCGA-AA-3517 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-AA-3518        TCGA-AA-3519        TCGA-AA-3520        TCGA-AA-3521 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-AA-3522        TCGA-AA-3524        TCGA-AA-3525        TCGA-AA-3526 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-AA-3527        TCGA-AA-3529        TCGA-AA-3530        TCGA-AA-3531 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-AA-3532        TCGA-AA-3534        TCGA-AA-3538        TCGA-AA-3542 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-AA-3543        TCGA-AA-3544        TCGA-AA-3548        TCGA-AA-3549 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-AA-3552        TCGA-AA-3553        TCGA-AA-3554        TCGA-AA-3555 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-AA-3556        TCGA-AA-3558        TCGA-AA-3560        TCGA-AA-3561 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-AA-3562        TCGA-AA-3655        TCGA-AA-3660        TCGA-AA-3663 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-AA-3664        TCGA-AA-3666        TCGA-AA-3667        TCGA-AA-3672 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-AA-3673        TCGA-AA-3678        TCGA-AA-3679        TCGA-AA-3680 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-AA-3681        TCGA-AA-3684        TCGA-AA-3685        TCGA-AA-3688 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-AA-3692        TCGA-AA-3693        TCGA-AA-3695        TCGA-AA-3696 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-AA-3697        TCGA-AA-3710        TCGA-AA-3713        TCGA-AA-3715 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-AA-3811        TCGA-AA-3812        TCGA-AA-3814        TCGA-AA-3815 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-AA-3818        TCGA-AA-3819        TCGA-AA-3821        TCGA-AA-3831 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-AA-3833        TCGA-AA-3837        TCGA-AA-3842        TCGA-AA-3844 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-AA-3845        TCGA-AA-3846        TCGA-AA-3848        TCGA-AA-3850 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-AA-3851        TCGA-AA-3852        TCGA-AA-3854        TCGA-AA-3855 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-AA-3856        TCGA-AA-3858        TCGA-AA-3860        TCGA-AA-3861 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-AA-3864        TCGA-AA-3866        TCGA-AA-3867        TCGA-AA-3869 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-AA-3870        TCGA-AA-3872        TCGA-AA-3875        TCGA-AA-3877 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-AA-3930        TCGA-AA-3939        TCGA-AA-3941        TCGA-AA-3947 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-AA-3949        TCGA-AA-3950        TCGA-AA-3952        TCGA-AA-3955 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-AA-3956        TCGA-AA-3968        TCGA-AA-3971        TCGA-AA-3972 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-AA-3973        TCGA-AA-3975        TCGA-AA-3976        TCGA-AA-3979 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-AA-3984        TCGA-AA-3986        TCGA-AA-3989        TCGA-AA-3994 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-AA-A004        TCGA-AA-A00A        TCGA-AA-A00D        TCGA-AA-A00E 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-AA-A00F        TCGA-AA-A00J        TCGA-AA-A00K        TCGA-AA-A00L 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-AA-A00N        TCGA-AA-A00O        TCGA-AA-A00Q        TCGA-AA-A00R 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-AA-A00U        TCGA-AA-A00W        TCGA-AA-A00Z        TCGA-AA-A010 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-AA-A017        TCGA-AA-A01D        TCGA-AA-A01F        TCGA-AA-A01G 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-AA-A01I        TCGA-AA-A01K        TCGA-AA-A01P        TCGA-AA-A01Q 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-AA-A01R        TCGA-AA-A01S        TCGA-AA-A01T        TCGA-AA-A01V 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-AA-A01X        TCGA-AA-A01Z        TCGA-AA-A022        TCGA-AA-A024 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-AA-A029        TCGA-AA-A02F        TCGA-AA-A02H        TCGA-AA-A02J 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-AA-A02K        TCGA-AA-A02O        TCGA-AA-A02W        TCGA-AA-A02Y 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-AA-A03F        TCGA-AA-A03J        TCGA-AD-5900        TCGA-AD-6548 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-AD-6888        TCGA-AU-3779        TCGA-AU-6004        TCGA-AY-4070 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-AY-4071        TCGA-AY-5543        TCGA-AY-6196        TCGA-AY-6197 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-AY-6386        TCGA-AZ-4315        TCGA-AZ-4681        TCGA-AZ-4682 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-CA-5254        TCGA-CA-5255        TCGA-CA-5796        TCGA-CA-5797 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-CA-6715        TCGA-CA-6716        TCGA-CA-6717        TCGA-CA-6718 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-CA-6719        TCGA-CK-4947        TCGA-CK-4948        TCGA-CK-4950 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-CK-4952        TCGA-CK-5912        TCGA-CK-5913        TCGA-CK-5914 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-CK-5915        TCGA-CK-5916        TCGA-CK-6746        TCGA-CK-6747 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-CK-6748        TCGA-CK-6751        TCGA-CM-4743        TCGA-CM-4744 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-CM-4746        TCGA-CM-4747        TCGA-CM-4752        TCGA-CM-5341 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-CM-5344        TCGA-CM-5348        TCGA-CM-5349        TCGA-CM-5860 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-CM-5861        TCGA-CM-5862        TCGA-CM-5863        TCGA-CM-5864 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-CM-5868        TCGA-CM-6161        TCGA-CM-6162        TCGA-CM-6163 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-CM-6164        TCGA-CM-6165        TCGA-CM-6166        TCGA-CM-6167 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-CM-6168        TCGA-CM-6169        TCGA-CM-6170        TCGA-CM-6171 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-CM-6172        TCGA-CM-6674        TCGA-CM-6675        TCGA-CM-6676 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-CM-6677        TCGA-CM-6678        TCGA-CM-6679        TCGA-CM-6680 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-D5-5537        TCGA-D5-5538        TCGA-D5-5539        TCGA-D5-5540 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-D5-5541        TCGA-D5-6529        TCGA-D5-6532        TCGA-D5-6533 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-D5-6534        TCGA-D5-6535        TCGA-D5-6536        TCGA-D5-6537 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-D5-6538        TCGA-D5-6539        TCGA-D5-6540        TCGA-D5-6541 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-D5-6898        TCGA-D5-6920        TCGA-D5-6922        TCGA-D5-6923 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-D5-6924        TCGA-D5-6926        TCGA-D5-6927        TCGA-D5-6928 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-D5-6929        TCGA-D5-6930        TCGA-D5-6931        TCGA-D5-6932 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-D5-7000        TCGA-F4-6459        TCGA-F4-6460        TCGA-F4-6569 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-F4-6570        TCGA-F4-6703        TCGA-F4-6704        TCGA-F4-6805 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-F4-6806        TCGA-F4-6807        TCGA-F4-6808        TCGA-F4-6809 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-F4-6854        TCGA-F4-6855        TCGA-F4-6856        TCGA-G4-6293 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-G4-6299        TCGA-G4-6303        TCGA-G4-6304        TCGA-G4-6306 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-G4-6307        TCGA-G4-6309        TCGA-G4-6310        TCGA-G4-6315 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-G4-6317        TCGA-G4-6321        TCGA-G4-6323        TCGA-G4-6586 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-G4-6588        TCGA-G4-6625        TCGA-G4-6626        TCGA-G4-6628 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2691        TCGA-AF-2692 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-AF-3400        TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-AF-6655        TCGA-AG-3574        TCGA-AG-3575        TCGA-AG-3578 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-AG-3580        TCGA-AG-3581        TCGA-AG-3582        TCGA-AG-3583 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-AG-3584        TCGA-AG-3586        TCGA-AG-3587        TCGA-AG-3593 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-AG-3594        TCGA-AG-3598        TCGA-AG-3599        TCGA-AG-3600 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-AG-3601        TCGA-AG-3602        TCGA-AG-3605        TCGA-AG-3608 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-AG-3609        TCGA-AG-3611        TCGA-AG-3612        TCGA-AG-3726 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-AG-3727        TCGA-AG-3731        TCGA-AG-3732        TCGA-AG-3742 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-AG-3878        TCGA-AG-3882        TCGA-AG-3883        TCGA-AG-3885 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3890        TCGA-AG-3892        TCGA-AG-3893 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-AG-3894        TCGA-AG-3896        TCGA-AG-3898        TCGA-AG-3901 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-AG-3902        TCGA-AG-3909        TCGA-AG-3999        TCGA-AG-4001 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-AG-4005        TCGA-AG-4007        TCGA-AG-4008        TCGA-AG-4015 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-AG-A002        TCGA-AG-A008        TCGA-AG-A00C        TCGA-AG-A00H 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-AG-A00Y        TCGA-AG-A011        TCGA-AG-A014        TCGA-AG-A015 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-AG-A016        TCGA-AG-A01L        TCGA-AG-A01W        TCGA-AG-A01Y 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A025        TCGA-AG-A026        TCGA-AG-A02G 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032        TCGA-AG-A036 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-AH-6549        TCGA-AH-6643        TCGA-CL-5917        TCGA-CL-5918 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6155        TCGA-DC-6157 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-DC-6158        TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-DC-6683        TCGA-DT-5265        TCGA-EF-5830        TCGA-EI-6506 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-EI-6507        TCGA-EI-6508        TCGA-EI-6510        TCGA-F5-6464 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-F5-6465        TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6812 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
       TCGA-F5-6813        TCGA-G5-6235        TCGA-G5-6641 
"PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" "PLEKHB2 WILD-TYPE" 
D946V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PLEKHB2 MUTATED                                  0     0
  PLEKHB2 WILD-TYPE                                1    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  PLEKHB2 MUTATED                           0     3
  PLEKHB2 WILD-TYPE                        22   223
D946V13, multiclass
                                  clus
vv                                 PLEKHB2 MUTATED PLEKHB2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                      0                22
  WHITE                                          3               223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(947) Variable = RALA MUTATION ANALYSIS
D947V1, survival
                sevent
clus2              0   1
  RALA MUTATED     7   1
  RALA WILD-TYPE 371  92
  RALA MUTATED RALA WILD-TYPE 
             8            463 
  RALA MUTATED RALA WILD-TYPE 
             1             92 
$`RALA MUTATED`
TCGA-AA-3510 TCGA-AA-3697 TCGA-AU-6004 TCGA-CA-6718 TCGA-CK-5913 TCGA-CM-4752 
       63.98        85.05        27.09        10.06        51.32        13.02 
TCGA-CM-6163 TCGA-AG-A002 
        2.96        20.98 

$`RALA WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       10.88         0.20        14.50        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       12.76        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       49.08         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-5341 TCGA-CM-5344 
       23.05        20.02        37.02        25.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6164 TCGA-CM-6165 
       15.02        17.03        15.02        12.00        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  RALA MUTATED RALA WILD-TYPE 
          2.96           0.00 
  RALA MUTATED RALA WILD-TYPE 
         85.05         148.01 
  RALA MUTATED RALA WILD-TYPE 
        24.035         20.120 
[1] "3.0 - 85.0 (24.0)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "2.2"
D947V2, continuous
D947V3, binary
                cls
clus               0   1
  RALA MUTATED     7   1
  RALA WILD-TYPE 359 118
[1] "tbl2"
                cls
clus             [,1] [,2]
  RALA MUTATED      7    1
  RALA WILD-TYPE  359  118
        clus
vv       RALA MUTATED RALA WILD-TYPE
  COLON             7            359
  RECTUM            1            118
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RALA MUTATED         3        0        1         3         0         0
  RALA WILD-TYPE      88        1       31       135        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RALA MUTATED           1          0          0          0        0         0
  RALA WILD-TYPE        23         11         59         42       48        18
                vv
clus             STAGE IVB
  RALA MUTATED           0
  RALA WILD-TYPE         1
D947V4, multiclass
            clus
vv           RALA MUTATED RALA WILD-TYPE
  STAGE I               3             88
  STAGE IA              0              1
  STAGE II              1             31
  STAGE IIA             3            135
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             1             23
  STAGE IIIA            0             11
  STAGE IIIB            0             59
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  RALA MUTATED     1   2   5   0
  RALA WILD-TYPE  16  90 324  50
D947V5, multiclass
    clus
vv   RALA MUTATED RALA WILD-TYPE
  T1            1             16
  T2            2             90
  T3            5            324
  T4            0             50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  RALA MUTATED     8   0   0
  RALA WILD-TYPE 279 113  87
D947V6, multiclass
    clus
vv   RALA MUTATED RALA WILD-TYPE
  N0            8            279
  N1            0            113
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D947V7, binary
                cls
clus               0   1
  RALA MUTATED     7   0
  RALA WILD-TYPE 368  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  RALA MUTATED      7    0
  RALA WILD-TYPE  368   65
   clus
vv  RALA MUTATED RALA WILD-TYPE
  0            7            368
  1            0             65
[1] 2 2
[1] FALSE
D947V8, binary
                cls
clus               0   1
  RALA MUTATED     2   6
  RALA WILD-TYPE 223 258
[1] "tbl2"
                cls
clus             [,1] [,2]
  RALA MUTATED      2    6
  RALA WILD-TYPE  223  258
        clus
vv       RALA MUTATED RALA WILD-TYPE
  FEMALE            2            223
  MALE              6            258
[1] 2 2
[1] FALSE
D947V9, binary
                cls
clus               0   1
  RALA MUTATED     7   0
  RALA WILD-TYPE 343  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  RALA MUTATED      7    0
  RALA WILD-TYPE  343   22
     clus
vv    RALA MUTATED RALA WILD-TYPE
  NO             7            343
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  RALA MUTATED                      7                             0
  RALA WILD-TYPE                  308                            47
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  RALA MUTATED                       1                              0
  RALA WILD-TYPE                   105                             10
D947V10, multiclass
                                clus
vv                               RALA MUTATED RALA WILD-TYPE
  COLON ADENOCARCINOMA                      7            308
  COLON MUCINOUS ADENOCARCINOMA             0             47
  RECTAL ADENOCARCINOMA                     1            105
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  RALA MUTATED     6   0   0   2
  RALA WILD-TYPE 339   4  31  23
D947V11, multiclass
    clus
vv   RALA MUTATED RALA WILD-TYPE
  R0            6            339
  R1            0              4
  R2            0             31
  RX            2             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D947V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RALA MUTATED                                  0     1
  RALA WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  RALA MUTATED                           1     3
  RALA WILD-TYPE                        21   223
D947V13, multiclass
                                  clus
vv                                 RALA MUTATED RALA WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                       3            223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(948) Variable = BRD8 MUTATION ANALYSIS
D948V1, survival
                sevent
clus2              0   1
  BRD8 MUTATED    15   3
  BRD8 WILD-TYPE 363  90
  BRD8 MUTATED BRD8 WILD-TYPE 
            18            453 
  BRD8 MUTATED BRD8 WILD-TYPE 
             3             90 
$`BRD8 MUTATED`
TCGA-A6-5665 TCGA-A6-6653 TCGA-AA-3555 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3994 
       22.06        24.39        29.95        19.04        19.04        27.02 
TCGA-AA-A00N TCGA-AD-5900 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-CK-5913 TCGA-CM-5860 
        4.01         0.07        58.39        49.41        51.32        32.02 
TCGA-CM-6171 TCGA-CM-6674 TCGA-DM-A28K TCGA-AG-3892 TCGA-AG-A002 TCGA-DC-6157 
       14.04        12.95        98.24        13.02        20.98        27.95 

$`BRD8 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 
       25.18        24.16        21.76        24.69        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       24.00        17.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       85.05        26.99        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 
       41.00        39.98        18.05        40.96        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       33.01        21.44        17.82         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        88.21         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       49.08         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.03        22.98        30.08        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       11.01        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
       60.79       117.07         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 
       19.99         1.02        17.95        36.95        17.03        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       13.97        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  BRD8 MUTATED BRD8 WILD-TYPE 
          0.07           0.00 
  BRD8 MUTATED BRD8 WILD-TYPE 
         98.24         148.01 
  BRD8 MUTATED BRD8 WILD-TYPE 
        23.225         20.050 
[1] "0.1 - 98.2 (23.2)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.3"
D948V2, continuous
D948V3, binary
                cls
clus               0   1
  BRD8 MUTATED    15   3
  BRD8 WILD-TYPE 351 116
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRD8 MUTATED     15    3
  BRD8 WILD-TYPE  351  116
        clus
vv       BRD8 MUTATED BRD8 WILD-TYPE
  COLON            15            351
  RECTUM            3            116
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  BRD8 MUTATED         6        0        2         7         1         0
  BRD8 WILD-TYPE      85        1       30       131         9         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  BRD8 MUTATED           0          0          1          0        1         0
  BRD8 WILD-TYPE        24         11         58         42       47        18
                vv
clus             STAGE IVB
  BRD8 MUTATED           0
  BRD8 WILD-TYPE         1
D948V4, multiclass
            clus
vv           BRD8 MUTATED BRD8 WILD-TYPE
  STAGE I               6             85
  STAGE IA              0              1
  STAGE II              2             30
  STAGE IIA             7            131
  STAGE IIB             1              9
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            1             58
  STAGE IIIC            0             42
  STAGE IV              1             47
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  BRD8 MUTATED     1   5  11   1
  BRD8 WILD-TYPE  16  87 318  49
D948V5, multiclass
    clus
vv   BRD8 MUTATED BRD8 WILD-TYPE
  T1            1             16
  T2            5             87
  T3           11            318
  T4            1             49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  BRD8 MUTATED    17   1   0
  BRD8 WILD-TYPE 270 112  87
D948V6, multiclass
    clus
vv   BRD8 MUTATED BRD8 WILD-TYPE
  N0           17            270
  N1            1            112
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D948V7, binary
                cls
clus               0   1
  BRD8 MUTATED    14   1
  BRD8 WILD-TYPE 361  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRD8 MUTATED     14    1
  BRD8 WILD-TYPE  361   64
   clus
vv  BRD8 MUTATED BRD8 WILD-TYPE
  0           14            361
  1            1             64
[1] 2 2
[1] FALSE
D948V8, binary
                cls
clus               0   1
  BRD8 MUTATED     6  12
  BRD8 WILD-TYPE 219 252
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRD8 MUTATED      6   12
  BRD8 WILD-TYPE  219  252
        clus
vv       BRD8 MUTATED BRD8 WILD-TYPE
  FEMALE            6            219
  MALE             12            252
[1] 2 2
[1] FALSE
D948V9, binary
                cls
clus               0   1
  BRD8 MUTATED    13   1
  BRD8 WILD-TYPE 337  21
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRD8 MUTATED     13    1
  BRD8 WILD-TYPE  337   21
     clus
vv    BRD8 MUTATED BRD8 WILD-TYPE
  NO            13            337
  YES            1             21
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  BRD8 MUTATED                     10                             5
  BRD8 WILD-TYPE                  305                            42
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  BRD8 MUTATED                       3                              0
  BRD8 WILD-TYPE                   103                             10
D948V10, multiclass
                                clus
vv                               BRD8 MUTATED BRD8 WILD-TYPE
  COLON ADENOCARCINOMA                     10            305
  COLON MUCINOUS ADENOCARCINOMA             5             42
  RECTAL ADENOCARCINOMA                     3            103
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  BRD8 MUTATED    13   0   1   1
  BRD8 WILD-TYPE 332   4  30  24
D948V11, multiclass
    clus
vv   BRD8 MUTATED BRD8 WILD-TYPE
  R0           13            332
  R1            0              4
  R2            1             30
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D948V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  BRD8 MUTATED                                  0     0
  BRD8 WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  BRD8 MUTATED                           1    10
  BRD8 WILD-TYPE                        21   216
D948V13, multiclass
                                  clus
vv                                 BRD8 MUTATED BRD8 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                      10            216
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(949) Variable = PER3 MUTATION ANALYSIS
D949V1, survival
                sevent
clus2              0   1
  PER3 MUTATED    13   4
  PER3 WILD-TYPE 365  89
  PER3 MUTATED PER3 WILD-TYPE 
            17            454 
  PER3 MUTATED PER3 WILD-TYPE 
             4             89 
$`PER3 MUTATED`
TCGA-A6-5665 TCGA-A6-5666 TCGA-AA-3663 TCGA-AA-3673 TCGA-AA-3680 TCGA-AA-3818 
       22.06        32.71         6.97        50.04        11.01         0.99 
TCGA-AA-3949 TCGA-AA-A00E TCGA-AA-A00N TCGA-AD-6889 TCGA-AZ-4315 TCGA-AZ-6601 
       26.01        30.02         4.01        56.55        58.39       100.01 
TCGA-CK-4947 TCGA-CM-4746 TCGA-CM-5860 TCGA-CM-6162 TCGA-AG-3892 
       17.56        37.02        32.02        12.00        13.02 

$`PER3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       22.09        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3681 
        2.01        14.01         0.92        47.01        15.02         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3819 
       19.04        19.04        10.06        35.05        33.04        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3950 
       31.00         2.01        12.99        24.00        33.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       38.04        19.00        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 
       18.05        40.96         0.07        21.37        15.52         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 
       88.21        49.41         6.77        12.10        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07        12.20        12.76        10.06        14.30 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 
        1.02        17.95        36.95        17.03        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  PER3 MUTATED PER3 WILD-TYPE 
          0.99           0.00 
  PER3 MUTATED PER3 WILD-TYPE 
        100.01         148.01 
  PER3 MUTATED PER3 WILD-TYPE 
        26.010         20.085 
[1] "1.0 - 100.0 (26.0)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1"  
D949V2, continuous
D949V3, binary
                cls
clus               0   1
  PER3 MUTATED    17   1
  PER3 WILD-TYPE 349 118
[1] "tbl2"
                cls
clus             [,1] [,2]
  PER3 MUTATED     17    1
  PER3 WILD-TYPE  349  118
        clus
vv       PER3 MUTATED PER3 WILD-TYPE
  COLON            17            349
  RECTUM            1            118
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PER3 MUTATED         2        0        3         7         1         1
  PER3 WILD-TYPE      89        1       29       131         9         0
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PER3 MUTATED           0          0          3          0        1         0
  PER3 WILD-TYPE        24         11         56         42       47        18
                vv
clus             STAGE IVB
  PER3 MUTATED           0
  PER3 WILD-TYPE         1
D949V4, multiclass
            clus
vv           PER3 MUTATED PER3 WILD-TYPE
  STAGE I               2             89
  STAGE IA              0              1
  STAGE II              3             29
  STAGE IIA             7            131
  STAGE IIB             1              9
  STAGE IIC             1              0
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            3             56
  STAGE IIIC            0             42
  STAGE IV              1             47
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  PER3 MUTATED     1   1  12   4
  PER3 WILD-TYPE  16  91 317  46
D949V5, multiclass
    clus
vv   PER3 MUTATED PER3 WILD-TYPE
  T1            1             16
  T2            1             91
  T3           12            317
  T4            4             46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  PER3 MUTATED    14   3   1
  PER3 WILD-TYPE 273 110  86
D949V6, multiclass
    clus
vv   PER3 MUTATED PER3 WILD-TYPE
  N0           14            273
  N1            3            110
  N2            1             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D949V7, binary
                cls
clus               0   1
  PER3 MUTATED    17   1
  PER3 WILD-TYPE 358  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  PER3 MUTATED     17    1
  PER3 WILD-TYPE  358   64
   clus
vv  PER3 MUTATED PER3 WILD-TYPE
  0           17            358
  1            1             64
[1] 2 2
[1] FALSE
D949V8, binary
                cls
clus               0   1
  PER3 MUTATED     9   9
  PER3 WILD-TYPE 216 255
[1] "tbl2"
                cls
clus             [,1] [,2]
  PER3 MUTATED      9    9
  PER3 WILD-TYPE  216  255
        clus
vv       PER3 MUTATED PER3 WILD-TYPE
  FEMALE            9            216
  MALE              9            255
[1] 2 2
[1] FALSE
D949V9, binary
                cls
clus               0   1
  PER3 MUTATED    14   0
  PER3 WILD-TYPE 336  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  PER3 MUTATED     14    0
  PER3 WILD-TYPE  336   22
     clus
vv    PER3 MUTATED PER3 WILD-TYPE
  NO            14            336
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PER3 MUTATED                     14                             3
  PER3 WILD-TYPE                  301                            44
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PER3 MUTATED                       1                              0
  PER3 WILD-TYPE                   105                             10
D949V10, multiclass
                                clus
vv                               PER3 MUTATED PER3 WILD-TYPE
  COLON ADENOCARCINOMA                     14            301
  COLON MUCINOUS ADENOCARCINOMA             3             44
  RECTAL ADENOCARCINOMA                     1            105
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  PER3 MUTATED    13   0   1   1
  PER3 WILD-TYPE 332   4  30  24
D949V11, multiclass
    clus
vv   PER3 MUTATED PER3 WILD-TYPE
  R0           13            332
  R1            0              4
  R2            1             30
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D949V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PER3 MUTATED                                  0     1
  PER3 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  PER3 MUTATED                           1     7
  PER3 WILD-TYPE                        21   219
D949V13, multiclass
                                  clus
vv                                 PER3 MUTATED PER3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                       7            219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(950) Variable = WT1 MUTATION ANALYSIS
D950V1, survival
               sevent
clus2             0   1
  WT1 MUTATED    25   5
  WT1 WILD-TYPE 353  88
  WT1 MUTATED WT1 WILD-TYPE 
           30           441 
  WT1 MUTATED WT1 WILD-TYPE 
            5            88 
$`WT1 MUTATED`
TCGA-A6-2672 TCGA-A6-5657 TCGA-A6-5662 TCGA-AA-3544 TCGA-AA-3662 TCGA-AA-3715 
       46.65        31.63        23.61        14.01         6.05        19.04 
TCGA-AA-3930 TCGA-AD-6895 TCGA-AY-6197 TCGA-AZ-4323 TCGA-AZ-6600 TCGA-AZ-6601 
        2.01         0.72        21.44         1.41        12.10       100.01 
TCGA-CA-6717 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5914 TCGA-CM-4743 
       12.76        17.56       148.01        15.62         9.99        23.05 
TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6675 TCGA-D5-5538 TCGA-D5-6532 TCGA-D5-6923 
       15.02        15.02        13.05        12.26        18.25        12.43 
TCGA-F4-6806 TCGA-G4-6306 TCGA-AF-6672 TCGA-AG-A002 TCGA-AG-A02N TCGA-CL-5917 
       41.42        44.68        10.39        20.98        61.97        78.12 

$`WT1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 
       30.44        29.19        33.53        22.09        22.06        32.71 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       27.09        22.52         8.38        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
        0.99        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       61.02        78.08         6.97        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
       31.00        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       15.52        56.55         0.79         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       33.01        17.82        58.39         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6603 TCGA-AZ-6605 
       62.79        88.21        49.41         6.77        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4950 
        3.29         0.07        12.20        10.06        14.30        85.45 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       49.08        51.32        21.14        82.95         1.91       124.27 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5868 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       17.03        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       12.95        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6533 
       45.40        19.59        56.09        55.92        20.19         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6924 
       16.14        15.58         1.48         3.68         4.41        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 
      133.18        74.56        65.85        53.62        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       16.83        15.39        20.02        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
        1.94        38.96        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        6.97         4.73         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  WT1 MUTATED WT1 WILD-TYPE 
         0.72          0.00 
  WT1 MUTATED WT1 WILD-TYPE 
       148.01        140.38 
  WT1 MUTATED WT1 WILD-TYPE 
        16.59         20.91 
[1] "0.7 - 148.0 (16.6)" "0.0 - 140.4 (20.9)"
[1] "hr=" "1.3"
D950V2, continuous
D950V3, binary
               cls
clus              0   1
  WT1 MUTATED    26   4
  WT1 WILD-TYPE 340 115
[1] "tbl2"
               cls
clus            [,1] [,2]
  WT1 MUTATED     26    4
  WT1 WILD-TYPE  340  115
        clus
vv       WT1 MUTATED WT1 WILD-TYPE
  COLON           26           340
  RECTUM           4           115
[1] 2 2
[1] FALSE
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  WT1 MUTATED         6        0        3         5         0         0
  WT1 WILD-TYPE      85        1       29       133        10         1
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  WT1 MUTATED           1          0          5          2        5         1
  WT1 WILD-TYPE        23         11         54         40       43        17
               vv
clus            STAGE IVB
  WT1 MUTATED           1
  WT1 WILD-TYPE         0
D950V4, multiclass
            clus
vv           WT1 MUTATED WT1 WILD-TYPE
  STAGE I              6            85
  STAGE IA             0             1
  STAGE II             3            29
  STAGE IIA            5           133
  STAGE IIB            0            10
  STAGE IIC            0             1
  STAGE III            1            23
  STAGE IIIA           0            11
  STAGE IIIB           5            54
  STAGE IIIC           2            40
  STAGE IV             5            43
  STAGE IVA            1            17
  STAGE IVB            1             0
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  WT1 MUTATED     0   7  17   6
  WT1 WILD-TYPE  17  85 312  44
D950V5, multiclass
    clus
vv   WT1 MUTATED WT1 WILD-TYPE
  T1           0            17
  T2           7            85
  T3          17           312
  T4           6            44
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2
  WT1 MUTATED    14   8   8
  WT1 WILD-TYPE 273 105  79
D950V6, multiclass
    clus
vv   WT1 MUTATED WT1 WILD-TYPE
  N0          14           273
  N1           8           105
  N2           8            79
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D950V7, binary
               cls
clus              0   1
  WT1 MUTATED    19   6
  WT1 WILD-TYPE 356  59
[1] "tbl2"
               cls
clus            [,1] [,2]
  WT1 MUTATED     19    6
  WT1 WILD-TYPE  356   59
   clus
vv  WT1 MUTATED WT1 WILD-TYPE
  0          19           356
  1           6            59
[1] 2 2
[1] FALSE
D950V8, binary
               cls
clus              0   1
  WT1 MUTATED     9  21
  WT1 WILD-TYPE 216 243
[1] "tbl2"
               cls
clus            [,1] [,2]
  WT1 MUTATED      9   21
  WT1 WILD-TYPE  216  243
        clus
vv       WT1 MUTATED WT1 WILD-TYPE
  FEMALE           9           216
  MALE            21           243
[1] 2 2
[1] FALSE
D950V9, binary
               cls
clus              0   1
  WT1 MUTATED    24   1
  WT1 WILD-TYPE 326  21
[1] "tbl2"
               cls
clus            [,1] [,2]
  WT1 MUTATED     24    1
  WT1 WILD-TYPE  326   21
     clus
vv    WT1 MUTATED WT1 WILD-TYPE
  NO           24           326
  YES           1            21
[1] 2 2
[1] FALSE
               vv
clus            COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  WT1 MUTATED                     24                             2
  WT1 WILD-TYPE                  291                            45
               vv
clus            RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  WT1 MUTATED                       4                              0
  WT1 WILD-TYPE                   102                             10
D950V10, multiclass
                                clus
vv                               WT1 MUTATED WT1 WILD-TYPE
  COLON ADENOCARCINOMA                    24           291
  COLON MUCINOUS ADENOCARCINOMA            2            45
  RECTAL ADENOCARCINOMA                    4           102
  RECTAL MUCINOUS ADENOCARCINOMA           0            10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             R0  R1  R2  RX
  WT1 MUTATED    17   0   2   5
  WT1 WILD-TYPE 328   4  29  20
D950V11, multiclass
    clus
vv   WT1 MUTATED WT1 WILD-TYPE
  R0          17           328
  R1           0             4
  R2           2            29
  RX           5            20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D950V12, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  WT1 MUTATED                                  0     1
  WT1 WILD-TYPE                                1    10
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  WT1 MUTATED                           3    20
  WT1 WILD-TYPE                        19   206
D950V13, multiclass
                                  clus
vv                                 WT1 MUTATED WT1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      1            10
  BLACK OR AFRICAN AMERICAN                  3            19
  WHITE                                     20           206
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(951) Variable = METTL9 MUTATION ANALYSIS
D951V1, survival
                  sevent
clus2                0   1
  METTL9 MUTATED     4   0
  METTL9 WILD-TYPE 374  93
  METTL9 MUTATED METTL9 WILD-TYPE 
               4              467 
  METTL9 MUTATED METTL9 WILD-TYPE 
               0               93 
$`METTL9 MUTATED`
TCGA-AD-6963 TCGA-AU-6004 TCGA-CA-6717 TCGA-CM-5861 
       27.42        27.09        12.76        15.02 

$`METTL9 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 
       22.42        10.88         0.20        14.50        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.20        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  METTL9 MUTATED METTL9 WILD-TYPE 
           12.76             0.00 
  METTL9 MUTATED METTL9 WILD-TYPE 
           27.42           148.01 
  METTL9 MUTATED METTL9 WILD-TYPE 
          21.055           20.190 
[1] "12.8 - 27.4 (21.1)" "0.0 - 148.0 (20.2)"
[1] "hr="     "3300000"
D951V2, continuous
D951V3, binary
                  cls
clus                 0   1
  METTL9 MUTATED     4   0
  METTL9 WILD-TYPE 362 119
[1] "tbl2"
                  cls
clus               [,1] [,2]
  METTL9 MUTATED      4    0
  METTL9 WILD-TYPE  362  119
        clus
vv       METTL9 MUTATED METTL9 WILD-TYPE
  COLON               4              362
  RECTUM              0              119
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  METTL9 MUTATED         1        0        0         2         0         0
  METTL9 WILD-TYPE      90        1       32       136        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  METTL9 MUTATED           0          0          0          0        0
  METTL9 WILD-TYPE        24         11         59         42       48
                  vv
clus               STAGE IVA STAGE IVB
  METTL9 MUTATED           0         0
  METTL9 WILD-TYPE        18         1
D951V4, multiclass
            clus
vv           METTL9 MUTATED METTL9 WILD-TYPE
  STAGE I                 1               90
  STAGE IA                0                1
  STAGE II                0               32
  STAGE IIA               2              136
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              0               59
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  METTL9 MUTATED     0   1   3   0
  METTL9 WILD-TYPE  17  91 326  50
D951V5, multiclass
    clus
vv   METTL9 MUTATED METTL9 WILD-TYPE
  T1              0               17
  T2              1               91
  T3              3              326
  T4              0               50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  METTL9 MUTATED     4   0   0
  METTL9 WILD-TYPE 283 113  87
D951V6, multiclass
    clus
vv   METTL9 MUTATED METTL9 WILD-TYPE
  N0              4              283
  N1              0              113
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D951V7, binary
                  cls
clus                 0   1
  METTL9 MUTATED     3   0
  METTL9 WILD-TYPE 372  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  METTL9 MUTATED      3    0
  METTL9 WILD-TYPE  372   65
   clus
vv  METTL9 MUTATED METTL9 WILD-TYPE
  0              3              372
  1              0               65
[1] 2 2
[1] FALSE
D951V8, binary
                  cls
clus                 0   1
  METTL9 MUTATED     2   2
  METTL9 WILD-TYPE 223 262
[1] "tbl2"
                  cls
clus               [,1] [,2]
  METTL9 MUTATED      2    2
  METTL9 WILD-TYPE  223  262
        clus
vv       METTL9 MUTATED METTL9 WILD-TYPE
  FEMALE              2              223
  MALE                2              262
[1] 2 2
[1] FALSE
D951V9, binary
                  cls
clus                 0   1
  METTL9 MUTATED     3   0
  METTL9 WILD-TYPE 347  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  METTL9 MUTATED      3    0
  METTL9 WILD-TYPE  347   22
     clus
vv    METTL9 MUTATED METTL9 WILD-TYPE
  NO               3              347
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  METTL9 MUTATED                      3                             1
  METTL9 WILD-TYPE                  312                            46
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  METTL9 MUTATED                       0                              0
  METTL9 WILD-TYPE                   106                             10
D951V10, multiclass
                                clus
vv                               METTL9 MUTATED METTL9 WILD-TYPE
  COLON ADENOCARCINOMA                        3              312
  COLON MUCINOUS ADENOCARCINOMA               1               46
  RECTAL ADENOCARCINOMA                       0              106
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  METTL9 MUTATED     2   0   0   1
  METTL9 WILD-TYPE 343   4  31  24
D951V11, multiclass
    clus
vv   METTL9 MUTATED METTL9 WILD-TYPE
  R0              2              343
  R1              0                4
  R2              0               31
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D951V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  METTL9 MUTATED                                  0     1
  METTL9 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  METTL9 MUTATED                           0     3
  METTL9 WILD-TYPE                        22   223
D951V13, multiclass
                                  clus
vv                                 METTL9 MUTATED METTL9 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         3              223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(952) Variable = FH MUTATION ANALYSIS
D952V1, survival
              sevent
clus2            0   1
  FH MUTATED     7   3
  FH WILD-TYPE 371  90
  FH MUTATED FH WILD-TYPE 
          10          461 
  FH MUTATED FH WILD-TYPE 
           3           90 
$`FH MUTATED`
TCGA-A6-3809 TCGA-AA-A01R TCGA-AD-6895 TCGA-CK-5916 TCGA-CM-4746 TCGA-CM-4752 
       32.75        35.01         0.72        21.14        37.02        13.02 
TCGA-CM-6171 TCGA-DM-A1D6 TCGA-DM-A1D8 TCGA-AG-3732 
       14.04        49.91        12.59        32.98 

$`FH WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S 
       12.00        31.00        31.00        38.07         1.02         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
       56.55         0.79         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 
       15.62        49.08        51.32         9.99        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-5341 TCGA-CM-5344 
      124.27        23.05        20.02        25.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       13.32       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
        0.99        37.02         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  FH MUTATED FH WILD-TYPE 
        0.72         0.00 
  FH MUTATED FH WILD-TYPE 
       49.91       148.01 
  FH MUTATED FH WILD-TYPE 
      26.945       20.120 
[1] "0.7 - 49.9 (26.9)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.7"
D952V2, continuous
D952V3, binary
              cls
clus             0   1
  FH MUTATED     9   1
  FH WILD-TYPE 357 118
[1] "tbl2"
              cls
clus           [,1] [,2]
  FH MUTATED      9    1
  FH WILD-TYPE  357  118
        clus
vv       FH MUTATED FH WILD-TYPE
  COLON           9          357
  RECTUM          1          118
[1] 2 2
[1] FALSE
              vv
clus           STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FH MUTATED         4        0        0         2         1         0
  FH WILD-TYPE      87        1       32       136         9         1
              vv
clus           STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  FH MUTATED           1          0          0          0        0         0
  FH WILD-TYPE        23         11         59         42       48        18
              vv
clus           STAGE IVB
  FH MUTATED           0
  FH WILD-TYPE         1
D952V4, multiclass
            clus
vv           FH MUTATED FH WILD-TYPE
  STAGE I             4           87
  STAGE IA            0            1
  STAGE II            0           32
  STAGE IIA           2          136
  STAGE IIB           1            9
  STAGE IIC           0            1
  STAGE III           1           23
  STAGE IIIA          0           11
  STAGE IIIB          0           59
  STAGE IIIC          0           42
  STAGE IV            0           48
  STAGE IVA           0           18
  STAGE IVB           0            1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
              vv
clus            T1  T2  T3  T4
  FH MUTATED     1   3   5   1
  FH WILD-TYPE  16  89 324  49
D952V5, multiclass
    clus
vv   FH MUTATED FH WILD-TYPE
  T1          1           16
  T2          3           89
  T3          5          324
  T4          1           49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
              vv
clus            N0  N1  N2
  FH MUTATED     7   2   1
  FH WILD-TYPE 280 111  86
D952V6, multiclass
    clus
vv   FH MUTATED FH WILD-TYPE
  N0          7          280
  N1          2          111
  N2          1           86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D952V7, binary
              cls
clus             0   1
  FH MUTATED     8   0
  FH WILD-TYPE 367  65
[1] "tbl2"
              cls
clus           [,1] [,2]
  FH MUTATED      8    0
  FH WILD-TYPE  367   65
   clus
vv  FH MUTATED FH WILD-TYPE
  0          8          367
  1          0           65
[1] 2 2
[1] FALSE
D952V8, binary
              cls
clus             0   1
  FH MUTATED     5   5
  FH WILD-TYPE 220 259
[1] "tbl2"
              cls
clus           [,1] [,2]
  FH MUTATED      5    5
  FH WILD-TYPE  220  259
        clus
vv       FH MUTATED FH WILD-TYPE
  FEMALE          5          220
  MALE            5          259
[1] 2 2
[1] FALSE
D952V9, binary
              cls
clus             0   1
  FH MUTATED     6   1
  FH WILD-TYPE 344  21
[1] "tbl2"
              cls
clus           [,1] [,2]
  FH MUTATED      6    1
  FH WILD-TYPE  344   21
     clus
vv    FH MUTATED FH WILD-TYPE
  NO           6          344
  YES          1           21
[1] 2 2
[1] FALSE
              vv
clus           COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  FH MUTATED                      6                             3
  FH WILD-TYPE                  309                            44
              vv
clus           RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  FH MUTATED                       1                              0
  FH WILD-TYPE                   105                             10
D952V10, multiclass
                                clus
vv                               FH MUTATED FH WILD-TYPE
  COLON ADENOCARCINOMA                    6          309
  COLON MUCINOUS ADENOCARCINOMA           3           44
  RECTAL ADENOCARCINOMA                   1          105
  RECTAL MUCINOUS ADENOCARCINOMA          0           10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
              vv
clus            R0  R1  R2  RX
  FH MUTATED     6   0   0   1
  FH WILD-TYPE 339   4  31  24
D952V11, multiclass
    clus
vv   FH MUTATED FH WILD-TYPE
  R0          6          339
  R1          0            4
  R2          0           31
  RX          1           24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D952V12, continuous
              vv
clus           AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  FH MUTATED                                  0     0                         2
  FH WILD-TYPE                                1    11                        20
              vv
clus           WHITE
  FH MUTATED       6
  FH WILD-TYPE   220
D952V13, multiclass
                                  clus
vv                                 FH MUTATED FH WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE          0            1
  ASIAN                                     0           11
  BLACK OR AFRICAN AMERICAN                 2           20
  WHITE                                     6          220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(953) Variable = H2AFJ MUTATION ANALYSIS
D953V1, survival
                 sevent
clus2               0   1
  H2AFJ MUTATED     3   0
  H2AFJ WILD-TYPE 375  93
  H2AFJ MUTATED H2AFJ WILD-TYPE 
              3             468 
  H2AFJ MUTATED H2AFJ WILD-TYPE 
              0              93 
$`H2AFJ MUTATED`
TCGA-AA-3663 TCGA-AA-3713 TCGA-CM-5348 
        6.97        19.04        22.98 

$`H2AFJ WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.05        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5860 
       25.02        13.02        29.06        22.03        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  H2AFJ MUTATED H2AFJ WILD-TYPE 
           6.97            0.00 
  H2AFJ MUTATED H2AFJ WILD-TYPE 
          22.98          148.01 
  H2AFJ MUTATED H2AFJ WILD-TYPE 
         19.040          20.235 
[1] "7.0 - 23.0 (19.0)"  "0.0 - 148.0 (20.2)"
[1] "hr="     "3300000"
D953V2, continuous
D953V3, binary
                 cls
clus                0   1
  H2AFJ MUTATED     3   0
  H2AFJ WILD-TYPE 363 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  H2AFJ MUTATED      3    0
  H2AFJ WILD-TYPE  363  119
        clus
vv       H2AFJ MUTATED H2AFJ WILD-TYPE
  COLON              3             363
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  H2AFJ MUTATED         0        0        1         0         0         0
  H2AFJ WILD-TYPE      91        1       31       138        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  H2AFJ MUTATED           0          0          1          0        1         0
  H2AFJ WILD-TYPE        24         11         58         42       47        18
                 vv
clus              STAGE IVB
  H2AFJ MUTATED           0
  H2AFJ WILD-TYPE         1
D953V4, multiclass
            clus
vv           H2AFJ MUTATED H2AFJ WILD-TYPE
  STAGE I                0              91
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              0             138
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             0              42
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  H2AFJ MUTATED     0   0   3   0
  H2AFJ WILD-TYPE  17  92 326  50
D953V5, multiclass
    clus
vv   H2AFJ MUTATED H2AFJ WILD-TYPE
  T1             0              17
  T2             0              92
  T3             3             326
  T4             0              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  H2AFJ MUTATED     2   1   0
  H2AFJ WILD-TYPE 285 112  87
D953V6, multiclass
    clus
vv   H2AFJ MUTATED H2AFJ WILD-TYPE
  N0             2             285
  N1             1             112
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D953V7, binary
                 cls
clus                0   1
  H2AFJ MUTATED     2   1
  H2AFJ WILD-TYPE 373  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  H2AFJ MUTATED      2    1
  H2AFJ WILD-TYPE  373   64
   clus
vv  H2AFJ MUTATED H2AFJ WILD-TYPE
  0             2             373
  1             1              64
[1] 2 2
[1] FALSE
D953V8, binary
                 cls
clus                0   1
  H2AFJ MUTATED     0   3
  H2AFJ WILD-TYPE 225 261
[1] "tbl2"
                 cls
clus              [,1] [,2]
  H2AFJ MUTATED      0    3
  H2AFJ WILD-TYPE  225  261
        clus
vv       H2AFJ MUTATED H2AFJ WILD-TYPE
  FEMALE             0             225
  MALE               3             261
[1] 2 2
[1] FALSE
D953V9, binary
                 cls
clus                0   1
  H2AFJ MUTATED     2   1
  H2AFJ WILD-TYPE 348  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  H2AFJ MUTATED      2    1
  H2AFJ WILD-TYPE  348   21
     clus
vv    H2AFJ MUTATED H2AFJ WILD-TYPE
  NO              2             348
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  H2AFJ MUTATED                      3                             0
  H2AFJ WILD-TYPE                  312                            47
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  H2AFJ MUTATED                       0                              0
  H2AFJ WILD-TYPE                   106                             10
D953V10, multiclass
                                clus
vv                               H2AFJ MUTATED H2AFJ WILD-TYPE
  COLON ADENOCARCINOMA                       3             312
  COLON MUCINOUS ADENOCARCINOMA              0              47
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  H2AFJ MUTATED     2   0   1   0
  H2AFJ WILD-TYPE 343   4  30  25
D953V11, multiclass
    clus
vv   H2AFJ MUTATED H2AFJ WILD-TYPE
  R0             2             343
  R1             0               4
  R2             1              30
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D953V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  H2AFJ MUTATED                                  0     0
  H2AFJ WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  H2AFJ MUTATED                           0     1
  H2AFJ WILD-TYPE                        22   225
D953V13, multiclass
[1] "Remove cluster labels:" "H2AFJ MUTATED"         
clus
  H2AFJ MUTATED H2AFJ WILD-TYPE 
              1             259 
     TCGA-A6-2671      TCGA-A6-2672      TCGA-A6-2674      TCGA-A6-2676 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-A6-2677      TCGA-A6-2678      TCGA-A6-2683      TCGA-A6-3807 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-A6-3808      TCGA-A6-3809      TCGA-A6-3810      TCGA-A6-4105 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-A6-5656      TCGA-A6-5657      TCGA-A6-5659      TCGA-A6-5660 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-A6-5661      TCGA-A6-5662      TCGA-A6-5664      TCGA-A6-5665 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-A6-5666      TCGA-A6-6137      TCGA-A6-6138      TCGA-A6-6141 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-A6-6142      TCGA-A6-6648      TCGA-A6-6649      TCGA-A6-6651 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-A6-6652      TCGA-A6-6653      TCGA-A6-6654      TCGA-A6-6780 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-A6-6781      TCGA-A6-6782      TCGA-AD-5900      TCGA-AD-6548 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-AD-6888      TCGA-AD-6889      TCGA-AD-6890      TCGA-AD-6895 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-AD-6899      TCGA-AD-6901      TCGA-AD-6963      TCGA-AD-6964 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-AD-6965      TCGA-AU-3779      TCGA-AU-6004      TCGA-AY-4070 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-AY-4071      TCGA-AY-5543      TCGA-AY-6196      TCGA-AY-6197 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-AY-6386      TCGA-AZ-4315      TCGA-AZ-4323      TCGA-AZ-4616 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-AZ-4681      TCGA-AZ-4682      TCGA-AZ-5403      TCGA-AZ-5407 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-AZ-6598      TCGA-AZ-6599      TCGA-AZ-6600      TCGA-AZ-6601 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-AZ-6603      TCGA-AZ-6605      TCGA-AZ-6606      TCGA-AZ-6607 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-AZ-6608      TCGA-CA-5254      TCGA-CA-5255      TCGA-CA-5796 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-CA-5797      TCGA-CA-6715      TCGA-CA-6716      TCGA-CA-6717 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-CA-6718      TCGA-CA-6719      TCGA-CK-4947      TCGA-CK-4948 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-CK-4950      TCGA-CK-4952      TCGA-CK-5912      TCGA-CK-5913 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-CK-5914      TCGA-CK-5915      TCGA-CK-5916      TCGA-CK-6746 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-CK-6747      TCGA-CK-6748      TCGA-CK-6751      TCGA-CM-4743 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-CM-4744      TCGA-CM-4746      TCGA-CM-4747      TCGA-CM-4752 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-CM-5341      TCGA-CM-5344      TCGA-CM-5349      TCGA-CM-5860 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-CM-5861      TCGA-CM-5862      TCGA-CM-5863      TCGA-CM-5864 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-CM-5868      TCGA-CM-6161      TCGA-CM-6162      TCGA-CM-6163 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-CM-6164      TCGA-CM-6165      TCGA-CM-6166      TCGA-CM-6167 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-CM-6168      TCGA-CM-6169      TCGA-CM-6170      TCGA-CM-6171 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-CM-6172      TCGA-CM-6674      TCGA-CM-6675      TCGA-CM-6676 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-CM-6677      TCGA-CM-6678      TCGA-CM-6679      TCGA-CM-6680 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-D5-5537      TCGA-D5-5538      TCGA-D5-5539      TCGA-D5-5540 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-D5-5541      TCGA-D5-6529      TCGA-D5-6532      TCGA-D5-6533 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-D5-6534      TCGA-D5-6535      TCGA-D5-6536      TCGA-D5-6537 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-D5-6538      TCGA-D5-6539      TCGA-D5-6540      TCGA-D5-6541 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-D5-6898      TCGA-D5-6920      TCGA-D5-6922      TCGA-D5-6923 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-D5-6924      TCGA-D5-6926      TCGA-D5-6927      TCGA-D5-6928 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-D5-6929      TCGA-D5-6930      TCGA-D5-6931      TCGA-D5-6932 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-D5-7000      TCGA-DM-A0X9      TCGA-DM-A0XD      TCGA-DM-A0XF 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-DM-A1D0      TCGA-DM-A1D4      TCGA-DM-A1D6      TCGA-DM-A1D7 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-DM-A1D8      TCGA-DM-A1D9      TCGA-DM-A1DA      TCGA-DM-A1DB 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-DM-A1HA      TCGA-DM-A1HB      TCGA-DM-A282      TCGA-DM-A285 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-DM-A28C      TCGA-DM-A28E      TCGA-DM-A28F      TCGA-DM-A28G 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-DM-A28H      TCGA-DM-A28K      TCGA-F4-6459      TCGA-F4-6460 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-F4-6569      TCGA-F4-6570      TCGA-F4-6703      TCGA-F4-6704 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-F4-6805      TCGA-F4-6806      TCGA-F4-6807      TCGA-F4-6808 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-F4-6809      TCGA-F4-6854      TCGA-F4-6855      TCGA-F4-6856 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-G4-6293      TCGA-G4-6299      TCGA-G4-6303      TCGA-G4-6304 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-G4-6306      TCGA-G4-6307      TCGA-G4-6309      TCGA-G4-6310 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-G4-6315      TCGA-G4-6317      TCGA-G4-6321      TCGA-G4-6323 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-G4-6586      TCGA-G4-6588      TCGA-G4-6625      TCGA-G4-6626 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-G4-6628      TCGA-AF-2687      TCGA-AF-2689      TCGA-AF-2691 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-AF-2692      TCGA-AF-2693      TCGA-AF-3400      TCGA-AF-3913 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-AF-4110      TCGA-AF-5654      TCGA-AF-6136      TCGA-AF-6655 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-AF-6672      TCGA-AH-6544      TCGA-AH-6547      TCGA-AH-6549 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-AH-6643      TCGA-AH-6644      TCGA-CI-6619      TCGA-CI-6620 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-CI-6621      TCGA-CI-6622      TCGA-CI-6624      TCGA-CL-5917 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-CL-5918      TCGA-DC-5337      TCGA-DC-5869      TCGA-DC-6155 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-DC-6157      TCGA-DC-6158      TCGA-DC-6160      TCGA-DC-6681 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-DC-6682      TCGA-DC-6683      TCGA-DT-5265      TCGA-DY-A0XA 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-DY-A1DC      TCGA-DY-A1DD      TCGA-DY-A1DF      TCGA-DY-A1DG 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-DY-A1H8      TCGA-EF-5830      TCGA-EI-6506      TCGA-EI-6507 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-EI-6508      TCGA-EI-6510      TCGA-F5-6464      TCGA-F5-6465 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-F5-6571      TCGA-F5-6702      TCGA-F5-6811      TCGA-F5-6812 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 
     TCGA-F5-6813      TCGA-G5-6235      TCGA-G5-6641 
"H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" "H2AFJ WILD-TYPE" 

Clustering(954) Variable = CDH10 MUTATION ANALYSIS
D954V1, survival
                 sevent
clus2               0   1
  CDH10 MUTATED    33   7
  CDH10 WILD-TYPE 345  86
  CDH10 MUTATED CDH10 WILD-TYPE 
             40             431 
  CDH10 MUTATED CDH10 WILD-TYPE 
              7              86 
$`CDH10 MUTATED`
TCGA-A6-5662 TCGA-A6-5665 TCGA-AA-3525 TCGA-AA-3555 TCGA-AA-3660 TCGA-AA-3672 
       23.61        22.06         8.05        29.95        78.08         0.92 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3815 TCGA-AA-3821 TCGA-AA-3864 TCGA-AA-3977 
       26.99        19.04        33.04         1.02        53.00        25.02 
TCGA-AA-3989 TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01I TCGA-AA-A01Z TCGA-AZ-4315 
        7.96         4.01        34.98        31.00        37.02        58.39 
TCGA-AZ-6598 TCGA-AZ-6603 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-6747 TCGA-CM-4743 
       49.41        29.56        12.76        10.06        82.95        23.05 
TCGA-CM-5861 TCGA-CM-6162 TCGA-CM-6164 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6680 
       15.02        12.00        29.03        14.04        12.95        12.03 
TCGA-D5-6536 TCGA-DM-A282 TCGA-F4-6570 TCGA-G4-6299 TCGA-G4-6317 TCGA-G4-6323 
       17.85       139.17         6.18        74.56        36.00        13.78 
TCGA-G4-6628 TCGA-AG-3575 TCGA-AG-A002 TCGA-F5-6464 
       79.69        12.00        20.98         9.96 

$`CDH10 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        33.53        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3529 
        9.07        24.03        37.05        36.03        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       17.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       61.02         6.05         6.97        54.02         2.01        14.01 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3811 
       19.00        36.00         5.03        85.05        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
       35.05         0.99        25.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       31.07        30.05        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3994 TCGA-AA-A004 
       24.00        27.02        27.02        19.07        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01K 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       26.01        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77        12.10       100.01         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       12.20        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6748 TCGA-CK-6751 
       49.08        51.32         9.99        21.14         1.91       124.27 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       22.98        30.08        32.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       17.03        15.02         2.96        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6676 
       12.99        13.02        15.02        11.01        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.08        11.01        10.06        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       15.12         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      131.51       135.65         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6303 
       13.25         0.53        47.41        35.31       133.18        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 
       22.09        35.80        26.17        91.79        46.75        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       19.96        20.91        18.28        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  CDH10 MUTATED CDH10 WILD-TYPE 
           0.92            0.00 
  CDH10 MUTATED CDH10 WILD-TYPE 
         139.17          148.01 
  CDH10 MUTATED CDH10 WILD-TYPE 
         22.555          20.050 
[1] "0.9 - 139.2 (22.6)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.3"
D954V2, continuous
D954V3, binary
                 cls
clus                0   1
  CDH10 MUTATED    39   3
  CDH10 WILD-TYPE 327 116
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDH10 MUTATED     39    3
  CDH10 WILD-TYPE  327  116
        clus
vv       CDH10 MUTATED CDH10 WILD-TYPE
  COLON             39             327
  RECTUM             3             116
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CDH10 MUTATED         5        1        5        15         2         0
  CDH10 WILD-TYPE      86        0       27       123         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CDH10 MUTATED           2          0          3          4        2         1
  CDH10 WILD-TYPE        22         11         56         38       46        17
                 vv
clus              STAGE IVB
  CDH10 MUTATED           0
  CDH10 WILD-TYPE         1
D954V4, multiclass
            clus
vv           CDH10 MUTATED CDH10 WILD-TYPE
  STAGE I                5              86
  STAGE IA               1               0
  STAGE II               5              27
  STAGE IIA             15             123
  STAGE IIB              2               8
  STAGE IIC              0               1
  STAGE III              2              22
  STAGE IIIA             0              11
  STAGE IIIB             3              56
  STAGE IIIC             4              38
  STAGE IV               2              46
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CDH10 MUTATED     0   7  31   3
  CDH10 WILD-TYPE  17  85 298  47
D954V5, multiclass
    clus
vv   CDH10 MUTATED CDH10 WILD-TYPE
  T1             0              17
  T2             7              85
  T3            31             298
  T4             3              47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  CDH10 MUTATED    30   4   8
  CDH10 WILD-TYPE 257 109  79
D954V6, multiclass
    clus
vv   CDH10 MUTATED CDH10 WILD-TYPE
  N0            30             257
  N1             4             109
  N2             8              79
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D954V7, binary
                 cls
clus                0   1
  CDH10 MUTATED    32   3
  CDH10 WILD-TYPE 343  62
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDH10 MUTATED     32    3
  CDH10 WILD-TYPE  343   62
   clus
vv  CDH10 MUTATED CDH10 WILD-TYPE
  0            32             343
  1             3              62
[1] 2 2
[1] FALSE
D954V8, binary
                 cls
clus                0   1
  CDH10 MUTATED    20  22
  CDH10 WILD-TYPE 205 242
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDH10 MUTATED     20   22
  CDH10 WILD-TYPE  205  242
        clus
vv       CDH10 MUTATED CDH10 WILD-TYPE
  FEMALE            20             205
  MALE              22             242
[1] 2 2
[1] FALSE
D954V9, binary
                 cls
clus                0   1
  CDH10 MUTATED    37   1
  CDH10 WILD-TYPE 313  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDH10 MUTATED     37    1
  CDH10 WILD-TYPE  313   21
     clus
vv    CDH10 MUTATED CDH10 WILD-TYPE
  NO             37             313
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CDH10 MUTATED                     33                             6
  CDH10 WILD-TYPE                  282                            41
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CDH10 MUTATED                       3                              0
  CDH10 WILD-TYPE                   103                             10
D954V10, multiclass
                                clus
vv                               CDH10 MUTATED CDH10 WILD-TYPE
  COLON ADENOCARCINOMA                      33             282
  COLON MUCINOUS ADENOCARCINOMA              6              41
  RECTAL ADENOCARCINOMA                      3             103
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  CDH10 MUTATED    32   0   2   3
  CDH10 WILD-TYPE 313   4  29  22
D954V11, multiclass
    clus
vv   CDH10 MUTATED CDH10 WILD-TYPE
  R0            32             313
  R1             0               4
  R2             2              29
  RX             3              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D954V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CDH10 MUTATED                                  0     2
  CDH10 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CDH10 MUTATED                           1    21
  CDH10 WILD-TYPE                        21   205
D954V13, multiclass
                                  clus
vv                                 CDH10 MUTATED CDH10 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               9
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                       21             205
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(955) Variable = HCRTR2 MUTATION ANALYSIS
D955V1, survival
                  sevent
clus2                0   1
  HCRTR2 MUTATED     6   1
  HCRTR2 WILD-TYPE 372  92
  HCRTR2 MUTATED HCRTR2 WILD-TYPE 
               7              464 
  HCRTR2 MUTATED HCRTR2 WILD-TYPE 
               1               92 
$`HCRTR2 MUTATED`
TCGA-AA-3815 TCGA-AA-3861 TCGA-AA-3977 TCGA-AZ-5407 TCGA-CM-4746 TCGA-CM-5861 
       33.04        30.05        25.02        88.21        37.02        15.02 
TCGA-DM-A1DA 
        7.50 

$`HCRTR2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       19.04        10.06        35.05         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 
       32.05         0.99        31.07        31.07        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
      124.27        23.05        20.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 
       22.03        22.98        30.08        32.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB 
       92.75        49.91        13.32        12.59       140.38        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  HCRTR2 MUTATED HCRTR2 WILD-TYPE 
             7.5              0.0 
  HCRTR2 MUTATED HCRTR2 WILD-TYPE 
           88.21           148.01 
  HCRTR2 MUTATED HCRTR2 WILD-TYPE 
          30.050           20.085 
[1] "7.5 - 88.2 (30.1)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.7"
D955V2, continuous
D955V3, binary
                  cls
clus                 0   1
  HCRTR2 MUTATED     7   0
  HCRTR2 WILD-TYPE 359 119
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HCRTR2 MUTATED      7    0
  HCRTR2 WILD-TYPE  359  119
        clus
vv       HCRTR2 MUTATED HCRTR2 WILD-TYPE
  COLON               7              359
  RECTUM              0              119
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  HCRTR2 MUTATED         2        0        0         3         0         0
  HCRTR2 WILD-TYPE      89        1       32       135        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HCRTR2 MUTATED           0          0          0          1        0
  HCRTR2 WILD-TYPE        24         11         59         41       48
                  vv
clus               STAGE IVA STAGE IVB
  HCRTR2 MUTATED           0         0
  HCRTR2 WILD-TYPE        18         1
D955V4, multiclass
            clus
vv           HCRTR2 MUTATED HCRTR2 WILD-TYPE
  STAGE I                 2               89
  STAGE IA                0                1
  STAGE II                0               32
  STAGE IIA               3              135
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              0               59
  STAGE IIIC              1               41
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  HCRTR2 MUTATED     1   2   4   0
  HCRTR2 WILD-TYPE  16  90 325  50
D955V5, multiclass
    clus
vv   HCRTR2 MUTATED HCRTR2 WILD-TYPE
  T1              1               16
  T2              2               90
  T3              4              325
  T4              0               50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  HCRTR2 MUTATED     6   0   1
  HCRTR2 WILD-TYPE 281 113  86
D955V6, multiclass
    clus
vv   HCRTR2 MUTATED HCRTR2 WILD-TYPE
  N0              6              281
  N1              0              113
  N2              1               86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D955V7, binary
                  cls
clus                 0   1
  HCRTR2 MUTATED     6   0
  HCRTR2 WILD-TYPE 369  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HCRTR2 MUTATED      6    0
  HCRTR2 WILD-TYPE  369   65
   clus
vv  HCRTR2 MUTATED HCRTR2 WILD-TYPE
  0              6              369
  1              0               65
[1] 2 2
[1] FALSE
D955V8, binary
                  cls
clus                 0   1
  HCRTR2 MUTATED     4   3
  HCRTR2 WILD-TYPE 221 261
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HCRTR2 MUTATED      4    3
  HCRTR2 WILD-TYPE  221  261
        clus
vv       HCRTR2 MUTATED HCRTR2 WILD-TYPE
  FEMALE              4              221
  MALE                3              261
[1] 2 2
[1] FALSE
D955V9, binary
                  cls
clus                 0   1
  HCRTR2 MUTATED     6   0
  HCRTR2 WILD-TYPE 344  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HCRTR2 MUTATED      6    0
  HCRTR2 WILD-TYPE  344   22
     clus
vv    HCRTR2 MUTATED HCRTR2 WILD-TYPE
  NO               6              344
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  HCRTR2 MUTATED                      7                             0
  HCRTR2 WILD-TYPE                  308                            47
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  HCRTR2 MUTATED                       0                              0
  HCRTR2 WILD-TYPE                   106                             10
D955V10, multiclass
                                clus
vv                               HCRTR2 MUTATED HCRTR2 WILD-TYPE
  COLON ADENOCARCINOMA                        7              308
  COLON MUCINOUS ADENOCARCINOMA               0               47
  RECTAL ADENOCARCINOMA                       0              106
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  HCRTR2 MUTATED     4   0   0   0
  HCRTR2 WILD-TYPE 341   4  31  25
D955V11, multiclass
    clus
vv   HCRTR2 MUTATED HCRTR2 WILD-TYPE
  R0              4              341
  R1              0                4
  R2              0               31
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D955V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HCRTR2 MUTATED                                  0     0
  HCRTR2 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  HCRTR2 MUTATED                           1     3
  HCRTR2 WILD-TYPE                        21   223
D955V13, multiclass
                                  clus
vv                                 HCRTR2 MUTATED HCRTR2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                         3              223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(956) Variable = MTF1 MUTATION ANALYSIS
D956V1, survival
                sevent
clus2              0   1
  MTF1 MUTATED     9   0
  MTF1 WILD-TYPE 369  93
  MTF1 MUTATED MTF1 WILD-TYPE 
             9            462 
  MTF1 MUTATED MTF1 WILD-TYPE 
             0             93 
$`MTF1 MUTATED`
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-A00J TCGA-AD-6895 TCGA-CA-6717 TCGA-CM-5861 
       24.00        33.01        18.05         0.72        12.76        15.02 
TCGA-D5-6536 TCGA-D5-6541 TCGA-AG-A002 
       17.85        15.58        20.98 

$`MTF1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       31.00         2.01        12.99        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       19.00        30.02        34.03        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.79         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07        12.20        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 
       22.03        22.98        30.08        32.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6898 
       15.12         4.80        17.13        12.49        16.14         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  MTF1 MUTATED MTF1 WILD-TYPE 
          0.72           0.00 
  MTF1 MUTATED MTF1 WILD-TYPE 
         33.01         148.01 
  MTF1 MUTATED MTF1 WILD-TYPE 
        17.850         20.415 
[1] "0.7 - 33.0 (17.9)"  "0.0 - 148.0 (20.4)"
[1] "hr="     "9200000"
D956V2, continuous
D956V3, binary
                cls
clus               0   1
  MTF1 MUTATED     9   1
  MTF1 WILD-TYPE 357 118
[1] "tbl2"
                cls
clus             [,1] [,2]
  MTF1 MUTATED      9    1
  MTF1 WILD-TYPE  357  118
        clus
vv       MTF1 MUTATED MTF1 WILD-TYPE
  COLON             9            357
  RECTUM            1            118
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MTF1 MUTATED         1        0        0         5         1         0
  MTF1 WILD-TYPE      90        1       32       133         9         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MTF1 MUTATED           0          0          1          0        0         1
  MTF1 WILD-TYPE        24         11         58         42       48        17
                vv
clus             STAGE IVB
  MTF1 MUTATED           0
  MTF1 WILD-TYPE         1
D956V4, multiclass
            clus
vv           MTF1 MUTATED MTF1 WILD-TYPE
  STAGE I               1             90
  STAGE IA              0              1
  STAGE II              0             32
  STAGE IIA             5            133
  STAGE IIB             1              9
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            1             58
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             1             17
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  MTF1 MUTATED     0   1   6   3
  MTF1 WILD-TYPE  17  91 323  47
D956V5, multiclass
    clus
vv   MTF1 MUTATED MTF1 WILD-TYPE
  T1            0             17
  T2            1             91
  T3            6            323
  T4            3             47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  MTF1 MUTATED     7   3   0
  MTF1 WILD-TYPE 280 110  87
D956V6, multiclass
    clus
vv   MTF1 MUTATED MTF1 WILD-TYPE
  N0            7            280
  N1            3            110
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D956V7, binary
                cls
clus               0   1
  MTF1 MUTATED     8   1
  MTF1 WILD-TYPE 367  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  MTF1 MUTATED      8    1
  MTF1 WILD-TYPE  367   64
   clus
vv  MTF1 MUTATED MTF1 WILD-TYPE
  0            8            367
  1            1             64
[1] 2 2
[1] FALSE
D956V8, binary
                cls
clus               0   1
  MTF1 MUTATED     4   6
  MTF1 WILD-TYPE 221 258
[1] "tbl2"
                cls
clus             [,1] [,2]
  MTF1 MUTATED      4    6
  MTF1 WILD-TYPE  221  258
        clus
vv       MTF1 MUTATED MTF1 WILD-TYPE
  FEMALE            4            221
  MALE              6            258
[1] 2 2
[1] FALSE
D956V9, binary
                cls
clus               0   1
  MTF1 MUTATED     8   0
  MTF1 WILD-TYPE 342  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  MTF1 MUTATED      8    0
  MTF1 WILD-TYPE  342   22
     clus
vv    MTF1 MUTATED MTF1 WILD-TYPE
  NO             8            342
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MTF1 MUTATED                      6                             3
  MTF1 WILD-TYPE                  309                            44
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MTF1 MUTATED                       1                              0
  MTF1 WILD-TYPE                   105                             10
D956V10, multiclass
                                clus
vv                               MTF1 MUTATED MTF1 WILD-TYPE
  COLON ADENOCARCINOMA                      6            309
  COLON MUCINOUS ADENOCARCINOMA             3             44
  RECTAL ADENOCARCINOMA                     1            105
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  MTF1 MUTATED     8   0   0   1
  MTF1 WILD-TYPE 337   4  31  24
D956V11, multiclass
    clus
vv   MTF1 MUTATED MTF1 WILD-TYPE
  R0            8            337
  R1            0              4
  R2            0             31
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D956V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MTF1 MUTATED                                  0     1
  MTF1 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  MTF1 MUTATED                           0     4
  MTF1 WILD-TYPE                        22   222
D956V13, multiclass
                                  clus
vv                                 MTF1 MUTATED MTF1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       4            222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(957) Variable = ZNF518B MUTATION ANALYSIS
D957V1, survival
                   sevent
clus2                 0   1
  ZNF518B MUTATED     9   3
  ZNF518B WILD-TYPE 369  90
  ZNF518B MUTATED ZNF518B WILD-TYPE 
               12               459 
  ZNF518B MUTATED ZNF518B WILD-TYPE 
                3                90 
$`ZNF518B MUTATED`
TCGA-A6-6781 TCGA-AD-6889 TCGA-AD-6901 TCGA-CA-6717 TCGA-CM-6163 TCGA-CM-6171 
       19.66        56.55        22.42        12.76         2.96        14.04 
TCGA-CM-6172 TCGA-D5-6929 TCGA-G4-6306 TCGA-AG-3582 TCGA-AG-A002 TCGA-DY-A1DD 
       11.01         4.80        44.68        36.03        20.98        57.24 

$`ZNF518B WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6964 
       15.52         0.79         0.72         5.79        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       15.02        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
        9.44        11.64         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       74.56        65.85        53.62        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        8.02         7.07        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DF TCGA-DY-A1DG 
        5.03         5.29       126.44        41.36        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  ZNF518B MUTATED ZNF518B WILD-TYPE 
             2.96              0.00 
  ZNF518B MUTATED ZNF518B WILD-TYPE 
            57.24            148.01 
  ZNF518B MUTATED ZNF518B WILD-TYPE 
            20.32             20.19 
[1] "3.0 - 57.2 (20.3)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.2"
D957V2, continuous
D957V3, binary
                   cls
clus                  0   1
  ZNF518B MUTATED    10   4
  ZNF518B WILD-TYPE 356 115
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZNF518B MUTATED     10    4
  ZNF518B WILD-TYPE  356  115
        clus
vv       ZNF518B MUTATED ZNF518B WILD-TYPE
  COLON               10               356
  RECTUM               4               115
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZNF518B MUTATED         4        0        0         3         0         0
  ZNF518B WILD-TYPE      87        1       32       135        10         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF518B MUTATED           0          0          3          1        2
  ZNF518B WILD-TYPE        24         11         56         41       46
                   vv
clus                STAGE IVA STAGE IVB
  ZNF518B MUTATED           0         0
  ZNF518B WILD-TYPE        18         1
D957V4, multiclass
            clus
vv           ZNF518B MUTATED ZNF518B WILD-TYPE
  STAGE I                  4                87
  STAGE IA                 0                 1
  STAGE II                 0                32
  STAGE IIA                3               135
  STAGE IIB                0                10
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               0                11
  STAGE IIIB               3                56
  STAGE IIIC               1                41
  STAGE IV                 2                46
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  ZNF518B MUTATED     1   4   7   2
  ZNF518B WILD-TYPE  16  88 322  48
D957V5, multiclass
    clus
vv   ZNF518B MUTATED ZNF518B WILD-TYPE
  T1               1                16
  T2               4                88
  T3               7               322
  T4               2                48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  ZNF518B MUTATED     8   6   0
  ZNF518B WILD-TYPE 279 107  87
D957V6, multiclass
    clus
vv   ZNF518B MUTATED ZNF518B WILD-TYPE
  N0               8               279
  N1               6               107
  N2               0                87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D957V7, binary
                   cls
clus                  0   1
  ZNF518B MUTATED     9   2
  ZNF518B WILD-TYPE 366  63
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZNF518B MUTATED      9    2
  ZNF518B WILD-TYPE  366   63
   clus
vv  ZNF518B MUTATED ZNF518B WILD-TYPE
  0               9               366
  1               2                63
[1] 2 2
[1] FALSE
D957V8, binary
                   cls
clus                  0   1
  ZNF518B MUTATED     4  10
  ZNF518B WILD-TYPE 221 254
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZNF518B MUTATED      4   10
  ZNF518B WILD-TYPE  221  254
        clus
vv       ZNF518B MUTATED ZNF518B WILD-TYPE
  FEMALE               4               221
  MALE                10               254
[1] 2 2
[1] FALSE
D957V9, binary
                   cls
clus                  0   1
  ZNF518B MUTATED     9   0
  ZNF518B WILD-TYPE 341  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZNF518B MUTATED      9    0
  ZNF518B WILD-TYPE  341   22
     clus
vv    ZNF518B MUTATED ZNF518B WILD-TYPE
  NO                9               341
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ZNF518B MUTATED                      8                             2
  ZNF518B WILD-TYPE                  307                            45
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ZNF518B MUTATED                       4                              0
  ZNF518B WILD-TYPE                   102                             10
D957V10, multiclass
                                clus
vv                               ZNF518B MUTATED ZNF518B WILD-TYPE
  COLON ADENOCARCINOMA                         8               307
  COLON MUCINOUS ADENOCARCINOMA                2                45
  RECTAL ADENOCARCINOMA                        4               102
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  ZNF518B MUTATED     7   0   2   2
  ZNF518B WILD-TYPE 338   4  29  23
D957V11, multiclass
    clus
vv   ZNF518B MUTATED ZNF518B WILD-TYPE
  R0               7               338
  R1               0                 4
  R2               2                29
  RX               2                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D957V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF518B MUTATED                                  0     2
  ZNF518B WILD-TYPE                                1     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  ZNF518B MUTATED                           0     9
  ZNF518B WILD-TYPE                        22   217
D957V13, multiclass
                                  clus
vv                                 ZNF518B MUTATED ZNF518B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          2                 9
  BLACK OR AFRICAN AMERICAN                      0                22
  WHITE                                          9               217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(958) Variable = KIAA0195 MUTATION ANALYSIS
D958V1, survival
                    sevent
clus2                  0   1
  KIAA0195 MUTATED    15   2
  KIAA0195 WILD-TYPE 363  91
  KIAA0195 MUTATED KIAA0195 WILD-TYPE 
                17                454 
  KIAA0195 MUTATED KIAA0195 WILD-TYPE 
                 2                 91 
$`KIAA0195 MUTATED`
TCGA-AA-3672 TCGA-AA-A00W TCGA-AA-A01K TCGA-AD-5900 TCGA-AD-6895 TCGA-AD-6964 
        0.92        14.99        31.00         0.07         0.72        10.88 
TCGA-AY-6197 TCGA-CK-5916 TCGA-CM-4743 TCGA-CM-5861 TCGA-CM-6674 TCGA-D5-6540 
       21.44        21.14        23.05        15.02        12.95        16.14 
TCGA-DM-A1HB TCGA-F4-6808 TCGA-G4-6304 TCGA-G4-6588 TCGA-AG-3580 
      135.65        33.67        53.62        26.17         8.02 

$`KIAA0195 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
        6.05         6.97        54.02         2.01        14.01        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       18.05        40.96        21.37        15.52        56.55         0.79 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       16.31         0.95        33.01        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
       82.95         1.91       124.27        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6676 
       13.02        15.02        14.04        11.01        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
       44.32       131.51       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       16.24        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       74.56        65.85        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 
       61.91        36.00        22.09        13.78        35.80        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3581 
       20.02        10.39        36.03        12.00        32.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  KIAA0195 MUTATED KIAA0195 WILD-TYPE 
              0.07               0.00 
  KIAA0195 MUTATED KIAA0195 WILD-TYPE 
            135.65             148.01 
  KIAA0195 MUTATED KIAA0195 WILD-TYPE 
            16.140             20.235 
[1] "0.1 - 135.7 (16.1)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.5"
D958V2, continuous
D958V3, binary
                    cls
clus                   0   1
  KIAA0195 MUTATED    17   1
  KIAA0195 WILD-TYPE 349 118
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0195 MUTATED     17    1
  KIAA0195 WILD-TYPE  349  118
        clus
vv       KIAA0195 MUTATED KIAA0195 WILD-TYPE
  COLON                17                349
  RECTUM                1                118
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KIAA0195 MUTATED         6        0        1         5         1         0
  KIAA0195 WILD-TYPE      85        1       31       133         9         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIAA0195 MUTATED           1          0          1          1        0
  KIAA0195 WILD-TYPE        23         11         58         41       48
                    vv
clus                 STAGE IVA STAGE IVB
  KIAA0195 MUTATED           0         0
  KIAA0195 WILD-TYPE        18         1
D958V4, multiclass
            clus
vv           KIAA0195 MUTATED KIAA0195 WILD-TYPE
  STAGE I                   6                 85
  STAGE IA                  0                  1
  STAGE II                  1                 31
  STAGE IIA                 5                133
  STAGE IIB                 1                  9
  STAGE IIC                 0                  1
  STAGE III                 1                 23
  STAGE IIIA                0                 11
  STAGE IIIB                1                 58
  STAGE IIIC                1                 41
  STAGE IV                  0                 48
  STAGE IVA                 0                 18
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  KIAA0195 MUTATED     4   2   9   3
  KIAA0195 WILD-TYPE  13  90 320  47
D958V5, multiclass
    clus
vv   KIAA0195 MUTATED KIAA0195 WILD-TYPE
  T1                4                 13
  T2                2                 90
  T3                9                320
  T4                3                 47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  KIAA0195 MUTATED    13   3   2
  KIAA0195 WILD-TYPE 274 110  85
D958V6, multiclass
    clus
vv   KIAA0195 MUTATED KIAA0195 WILD-TYPE
  N0               13                274
  N1                3                110
  N2                2                 85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D958V7, binary
                    cls
clus                   0   1
  KIAA0195 MUTATED    14   0
  KIAA0195 WILD-TYPE 361  65
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0195 MUTATED     14    0
  KIAA0195 WILD-TYPE  361   65
   clus
vv  KIAA0195 MUTATED KIAA0195 WILD-TYPE
  0               14                361
  1                0                 65
[1] 2 2
[1] FALSE
D958V8, binary
                    cls
clus                   0   1
  KIAA0195 MUTATED     8  10
  KIAA0195 WILD-TYPE 217 254
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0195 MUTATED      8   10
  KIAA0195 WILD-TYPE  217  254
        clus
vv       KIAA0195 MUTATED KIAA0195 WILD-TYPE
  FEMALE                8                217
  MALE                 10                254
[1] 2 2
[1] FALSE
D958V9, binary
                    cls
clus                   0   1
  KIAA0195 MUTATED    14   0
  KIAA0195 WILD-TYPE 336  22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0195 MUTATED     14    0
  KIAA0195 WILD-TYPE  336   22
     clus
vv    KIAA0195 MUTATED KIAA0195 WILD-TYPE
  NO                14                336
  YES                0                 22
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  KIAA0195 MUTATED                     14                             2
  KIAA0195 WILD-TYPE                  301                            45
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  KIAA0195 MUTATED                       1                              0
  KIAA0195 WILD-TYPE                   105                             10
D958V10, multiclass
                                clus
vv                               KIAA0195 MUTATED KIAA0195 WILD-TYPE
  COLON ADENOCARCINOMA                         14                301
  COLON MUCINOUS ADENOCARCINOMA                 2                 45
  RECTAL ADENOCARCINOMA                         1                105
  RECTAL MUCINOUS ADENOCARCINOMA                0                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  KIAA0195 MUTATED    14   0   0   1
  KIAA0195 WILD-TYPE 331   4  31  24
D958V11, multiclass
    clus
vv   KIAA0195 MUTATED KIAA0195 WILD-TYPE
  R0               14                331
  R1                0                  4
  R2                0                 31
  RX                1                 24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D958V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KIAA0195 MUTATED                                  0     0
  KIAA0195 WILD-TYPE                                1    11
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  KIAA0195 MUTATED                           0    13
  KIAA0195 WILD-TYPE                        22   213
D958V13, multiclass
                                  clus
vv                                 KIAA0195 MUTATED KIAA0195 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 11
  BLACK OR AFRICAN AMERICAN                       0                 22
  WHITE                                          13                213
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(959) Variable = FAM20B MUTATION ANALYSIS
D959V1, survival
                  sevent
clus2                0   1
  FAM20B MUTATED     9   1
  FAM20B WILD-TYPE 369  92
  FAM20B MUTATED FAM20B WILD-TYPE 
              10              461 
  FAM20B MUTATED FAM20B WILD-TYPE 
               1               92 
$`FAM20B MUTATED`
TCGA-A6-5665 TCGA-A6-6781 TCGA-AA-3510 TCGA-AA-3966 TCGA-AA-A00N TCGA-AD-6889 
       22.06        19.66        63.98         2.01         4.01        56.55 
TCGA-CM-5344 TCGA-D5-6536 TCGA-D5-6929 TCGA-G4-6309 
       22.03        17.85         4.80        85.48 

$`FAM20B WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
       34.03        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
        0.07        21.37        15.52         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5348 
       20.02        37.02        25.02        13.02        29.06        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       11.64         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 
       65.85        53.62        44.68        55.04        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  FAM20B MUTATED FAM20B WILD-TYPE 
            2.01             0.00 
  FAM20B MUTATED FAM20B WILD-TYPE 
           85.48           148.01 
  FAM20B MUTATED FAM20B WILD-TYPE 
          20.845           20.190 
[1] "2.0 - 85.5 (20.8)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "2.4"
D959V2, continuous
D959V3, binary
                  cls
clus                 0   1
  FAM20B MUTATED    10   0
  FAM20B WILD-TYPE 356 119
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM20B MUTATED     10    0
  FAM20B WILD-TYPE  356  119
        clus
vv       FAM20B MUTATED FAM20B WILD-TYPE
  COLON              10              356
  RECTUM              0              119
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FAM20B MUTATED         0        0        1         4         1         0
  FAM20B WILD-TYPE      91        1       31       134         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FAM20B MUTATED           0          0          2          1        1
  FAM20B WILD-TYPE        24         11         57         41       47
                  vv
clus               STAGE IVA STAGE IVB
  FAM20B MUTATED           0         0
  FAM20B WILD-TYPE        18         1
D959V4, multiclass
            clus
vv           FAM20B MUTATED FAM20B WILD-TYPE
  STAGE I                 0               91
  STAGE IA                0                1
  STAGE II                1               31
  STAGE IIA               4              134
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              2               57
  STAGE IIIC              1               41
  STAGE IV                1               47
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  FAM20B MUTATED     0   0   8   2
  FAM20B WILD-TYPE  17  92 321  48
D959V5, multiclass
    clus
vv   FAM20B MUTATED FAM20B WILD-TYPE
  T1              0               17
  T2              0               92
  T3              8              321
  T4              2               48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  FAM20B MUTATED     6   4   0
  FAM20B WILD-TYPE 281 109  87
D959V6, multiclass
    clus
vv   FAM20B MUTATED FAM20B WILD-TYPE
  N0              6              281
  N1              4              109
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D959V7, binary
                  cls
clus                 0   1
  FAM20B MUTATED     8   1
  FAM20B WILD-TYPE 367  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM20B MUTATED      8    1
  FAM20B WILD-TYPE  367   64
   clus
vv  FAM20B MUTATED FAM20B WILD-TYPE
  0              8              367
  1              1               64
[1] 2 2
[1] FALSE
D959V8, binary
                  cls
clus                 0   1
  FAM20B MUTATED     5   5
  FAM20B WILD-TYPE 220 259
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM20B MUTATED      5    5
  FAM20B WILD-TYPE  220  259
        clus
vv       FAM20B MUTATED FAM20B WILD-TYPE
  FEMALE              5              220
  MALE                5              259
[1] 2 2
[1] FALSE
D959V9, binary
                  cls
clus                 0   1
  FAM20B MUTATED     6   0
  FAM20B WILD-TYPE 344  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM20B MUTATED      6    0
  FAM20B WILD-TYPE  344   22
     clus
vv    FAM20B MUTATED FAM20B WILD-TYPE
  NO               6              344
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  FAM20B MUTATED                      7                             3
  FAM20B WILD-TYPE                  308                            44
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  FAM20B MUTATED                       0                              0
  FAM20B WILD-TYPE                   106                             10
D959V10, multiclass
                                clus
vv                               FAM20B MUTATED FAM20B WILD-TYPE
  COLON ADENOCARCINOMA                        7              308
  COLON MUCINOUS ADENOCARCINOMA               3               44
  RECTAL ADENOCARCINOMA                       0              106
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  FAM20B MUTATED     8   0   0   0
  FAM20B WILD-TYPE 337   4  31  25
D959V11, multiclass
    clus
vv   FAM20B MUTATED FAM20B WILD-TYPE
  R0              8              337
  R1              0                4
  R2              0               31
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D959V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FAM20B MUTATED                                  0     1
  FAM20B WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  FAM20B MUTATED                           1     5
  FAM20B WILD-TYPE                        21   221
D959V13, multiclass
                                  clus
vv                                 FAM20B MUTATED FAM20B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                         5              221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(960) Variable = EPHB1 MUTATION ANALYSIS
D960V1, survival
                 sevent
clus2               0   1
  EPHB1 MUTATED    31  10
  EPHB1 WILD-TYPE 347  83
  EPHB1 MUTATED EPHB1 WILD-TYPE 
             41             430 
  EPHB1 MUTATED EPHB1 WILD-TYPE 
             10              83 
$`EPHB1 MUTATED`
TCGA-A6-4105 TCGA-A6-5660 TCGA-A6-6141 TCGA-A6-6653 TCGA-AA-3662 TCGA-AA-3680 
       14.53        29.19         8.38        24.39         6.05        11.01 
TCGA-AA-3685 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3864 TCGA-AA-3950 TCGA-AA-A01P 
       37.05        85.05        19.04        53.00        24.00        38.07 
TCGA-AA-A01R TCGA-AD-6901 TCGA-AZ-4315 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6607 
       35.01        22.42        58.39         6.77        12.10         3.19 
TCGA-CA-6718 TCGA-CM-5348 TCGA-CM-5862 TCGA-CM-6161 TCGA-CM-6162 TCGA-D5-5538 
       10.06        22.98         5.03        15.02        12.00        12.26 
TCGA-D5-5539 TCGA-D5-6533 TCGA-D5-6540 TCGA-D5-6920 TCGA-DM-A0X9 TCGA-F4-6808 
       19.59         1.32        16.14         3.68       119.70        33.67 
TCGA-G4-6303 TCGA-G4-6307 TCGA-G4-6317 TCGA-G4-6628 TCGA-AF-6672 TCGA-AG-3892 
       65.85        55.04        36.00        79.69        10.39        13.02 
TCGA-AG-A002 TCGA-DC-6157 TCGA-DC-6160 TCGA-DC-6681 TCGA-EI-6507 
       20.98        27.95        19.99         5.95        19.96 

$`EPHB1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 
       16.57        34.65        33.34        32.75        36.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       31.63        30.44        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       32.71        27.09        22.52        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       21.76        24.69        23.87        20.12        19.66        20.28 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
        7.04         3.02         1.02        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       61.02        78.08         6.97        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3681 TCGA-AA-3688 
        0.92        50.04        47.01        15.02         5.98        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       36.00         5.03        26.99        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        31.07        30.05        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       33.01        26.01         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01Q 
       10.98        32.02        12.00        31.00        31.00         1.02 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6963 
       15.52        56.55         0.79         0.72         5.79        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       33.01        21.44        17.82         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6601 TCGA-AZ-6603 
       22.36        62.79        88.21        49.41       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07        12.20        12.76        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5349 
       37.02        25.02        13.02        29.06        22.03        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6163 
       32.02        15.02        15.02        15.02        17.03         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5540 
       11.08        11.01        10.06        12.03        45.40        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       55.92        20.19        18.25        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6922 
        4.80        17.13        12.49        15.58         1.48         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0XD TCGA-DM-A0XF 
        1.51        12.00        11.38        10.26        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       34.42        41.42        16.24        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 
       35.31       133.18        74.56        53.62        44.68        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       63.62        61.91        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       91.79        46.75        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       20.02        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       17.95        36.95        17.03        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6158 
       78.12         7.17        15.02         5.03        13.97        10.98 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6508 
       24.13        51.48        32.61         0.49        20.55        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  EPHB1 MUTATED EPHB1 WILD-TYPE 
           1.32            0.00 
  EPHB1 MUTATED EPHB1 WILD-TYPE 
         119.70          148.01 
  EPHB1 MUTATED EPHB1 WILD-TYPE 
         19.960          20.415 
[1] "1.3 - 119.7 (20.0)" "0.0 - 148.0 (20.4)"
[1] "hr=" "1.2"
D960V2, continuous
D960V3, binary
                 cls
clus                0   1
  EPHB1 MUTATED    36   7
  EPHB1 WILD-TYPE 330 112
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPHB1 MUTATED     36    7
  EPHB1 WILD-TYPE  330  112
        clus
vv       EPHB1 MUTATED EPHB1 WILD-TYPE
  COLON             36             330
  RECTUM             7             112
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  EPHB1 MUTATED        10        0        2         8         0         0
  EPHB1 WILD-TYPE      81        1       30       130        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  EPHB1 MUTATED           3          1          5          3        8         2
  EPHB1 WILD-TYPE        21         10         54         39       40        16
                 vv
clus              STAGE IVB
  EPHB1 MUTATED           0
  EPHB1 WILD-TYPE         1
D960V4, multiclass
            clus
vv           EPHB1 MUTATED EPHB1 WILD-TYPE
  STAGE I               10              81
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA              8             130
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              3              21
  STAGE IIIA             1              10
  STAGE IIIB             5              54
  STAGE IIIC             3              39
  STAGE IV               8              40
  STAGE IVA              2              16
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  EPHB1 MUTATED     2   8  27   6
  EPHB1 WILD-TYPE  15  84 302  44
D960V5, multiclass
    clus
vv   EPHB1 MUTATED EPHB1 WILD-TYPE
  T1             2              15
  T2             8              84
  T3            27             302
  T4             6              44
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  EPHB1 MUTATED    24   9  10
  EPHB1 WILD-TYPE 263 104  77
D960V6, multiclass
    clus
vv   EPHB1 MUTATED EPHB1 WILD-TYPE
  N0            24             263
  N1             9             104
  N2            10              77
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D960V7, binary
                 cls
clus                0   1
  EPHB1 MUTATED    29   9
  EPHB1 WILD-TYPE 346  56
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPHB1 MUTATED     29    9
  EPHB1 WILD-TYPE  346   56
   clus
vv  EPHB1 MUTATED EPHB1 WILD-TYPE
  0            29             346
  1             9              56
[1] 2 2
[1] FALSE
D960V8, binary
                 cls
clus                0   1
  EPHB1 MUTATED    17  26
  EPHB1 WILD-TYPE 208 238
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPHB1 MUTATED     17   26
  EPHB1 WILD-TYPE  208  238
        clus
vv       EPHB1 MUTATED EPHB1 WILD-TYPE
  FEMALE            17             208
  MALE              26             238
[1] 2 2
[1] FALSE
D960V9, binary
                 cls
clus                0   1
  EPHB1 MUTATED    31   3
  EPHB1 WILD-TYPE 319  19
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPHB1 MUTATED     31    3
  EPHB1 WILD-TYPE  319   19
     clus
vv    EPHB1 MUTATED EPHB1 WILD-TYPE
  NO             31             319
  YES             3              19
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  EPHB1 MUTATED                     30                             6
  EPHB1 WILD-TYPE                  285                            41
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  EPHB1 MUTATED                       7                              0
  EPHB1 WILD-TYPE                    99                             10
D960V10, multiclass
                                clus
vv                               EPHB1 MUTATED EPHB1 WILD-TYPE
  COLON ADENOCARCINOMA                      30             285
  COLON MUCINOUS ADENOCARCINOMA              6              41
  RECTAL ADENOCARCINOMA                      7              99
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  EPHB1 MUTATED    28   0   4   1
  EPHB1 WILD-TYPE 317   4  27  24
D960V11, multiclass
    clus
vv   EPHB1 MUTATED EPHB1 WILD-TYPE
  R0            28             317
  R1             0               4
  R2             4              27
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D960V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  EPHB1 MUTATED                                  0     1
  EPHB1 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  EPHB1 MUTATED                           4    26
  EPHB1 WILD-TYPE                        18   200
D960V13, multiclass
                                  clus
vv                                 EPHB1 MUTATED EPHB1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    4              18
  WHITE                                       26             200
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(961) Variable = APBB1IP MUTATION ANALYSIS
D961V1, survival
                   sevent
clus2                 0   1
  APBB1IP MUTATED    13   5
  APBB1IP WILD-TYPE 365  88
  APBB1IP MUTATED APBB1IP WILD-TYPE 
               18               453 
  APBB1IP MUTATED APBB1IP WILD-TYPE 
                5                88 
$`APBB1IP MUTATED`
TCGA-A6-4105 TCGA-AA-3510 TCGA-AA-3697 TCGA-AA-3877 TCGA-AA-3994 TCGA-AA-A00N 
       14.53        63.98        85.05        31.00        27.02         4.01 
TCGA-AD-6895 TCGA-AD-6964 TCGA-AD-6965 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-CM-5344 
        0.72        10.88         0.20        88.21         6.77        22.03 
TCGA-D5-6534 TCGA-DM-A28E TCGA-F4-6570 TCGA-F4-6807 TCGA-G4-6628 TCGA-AG-3598 
       43.27       119.93         6.18        16.24        79.69        50.04 

$`APBB1IP WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 
       16.57        34.65        33.34        32.75        36.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       27.02        29.98        18.05         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
        7.96        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       21.37        15.52        56.55         0.79         5.79        22.42 
TCGA-AD-6963 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       27.42        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       22.36        62.79        49.41        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6535 
       56.09        55.92        20.19        18.25         1.32        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28F 
      131.51       135.65       139.17         6.12        81.37        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6808 TCGA-F4-6809 
       47.87         1.55        34.42        41.42        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       46.75        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
        2.01        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  APBB1IP MUTATED APBB1IP WILD-TYPE 
              0.2               0.0 
  APBB1IP MUTATED APBB1IP WILD-TYPE 
           119.93            148.01 
  APBB1IP MUTATED APBB1IP WILD-TYPE 
           24.525            20.120 
[1] "0.2 - 119.9 (24.5)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1"  
D961V2, continuous
D961V3, binary
                   cls
clus                  0   1
  APBB1IP MUTATED    18   1
  APBB1IP WILD-TYPE 348 118
[1] "tbl2"
                   cls
clus                [,1] [,2]
  APBB1IP MUTATED     18    1
  APBB1IP WILD-TYPE  348  118
        clus
vv       APBB1IP MUTATED APBB1IP WILD-TYPE
  COLON               18               348
  RECTUM               1               118
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  APBB1IP MUTATED         4        0        1         6         1         0
  APBB1IP WILD-TYPE      87        1       31       132         9         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  APBB1IP MUTATED           1          0          2          1        0
  APBB1IP WILD-TYPE        23         11         57         41       48
                   vv
clus                STAGE IVA STAGE IVB
  APBB1IP MUTATED           0         0
  APBB1IP WILD-TYPE        18         1
D961V4, multiclass
            clus
vv           APBB1IP MUTATED APBB1IP WILD-TYPE
  STAGE I                  4                87
  STAGE IA                 0                 1
  STAGE II                 1                31
  STAGE IIA                6               132
  STAGE IIB                1                 9
  STAGE IIC                0                 1
  STAGE III                1                23
  STAGE IIIA               0                11
  STAGE IIIB               2                57
  STAGE IIIC               1                41
  STAGE IV                 0                48
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  APBB1IP MUTATED     2   2  12   3
  APBB1IP WILD-TYPE  15  90 317  47
D961V5, multiclass
    clus
vv   APBB1IP MUTATED APBB1IP WILD-TYPE
  T1               2                15
  T2               2                90
  T3              12               317
  T4               3                47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  APBB1IP MUTATED    13   3   3
  APBB1IP WILD-TYPE 274 110  84
D961V6, multiclass
    clus
vv   APBB1IP MUTATED APBB1IP WILD-TYPE
  N0              13               274
  N1               3               110
  N2               3                84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D961V7, binary
                   cls
clus                  0   1
  APBB1IP MUTATED    15   0
  APBB1IP WILD-TYPE 360  65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  APBB1IP MUTATED     15    0
  APBB1IP WILD-TYPE  360   65
   clus
vv  APBB1IP MUTATED APBB1IP WILD-TYPE
  0              15               360
  1               0                65
[1] 2 2
[1] FALSE
D961V8, binary
                   cls
clus                  0   1
  APBB1IP MUTATED     8  11
  APBB1IP WILD-TYPE 217 253
[1] "tbl2"
                   cls
clus                [,1] [,2]
  APBB1IP MUTATED      8   11
  APBB1IP WILD-TYPE  217  253
        clus
vv       APBB1IP MUTATED APBB1IP WILD-TYPE
  FEMALE               8               217
  MALE                11               253
[1] 2 2
[1] FALSE
D961V9, binary
                   cls
clus                  0   1
  APBB1IP MUTATED    14   0
  APBB1IP WILD-TYPE 336  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  APBB1IP MUTATED     14    0
  APBB1IP WILD-TYPE  336   22
     clus
vv    APBB1IP MUTATED APBB1IP WILD-TYPE
  NO               14               336
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  APBB1IP MUTATED                     14                             4
  APBB1IP WILD-TYPE                  301                            43
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  APBB1IP MUTATED                       1                              0
  APBB1IP WILD-TYPE                   105                             10
D961V10, multiclass
                                clus
vv                               APBB1IP MUTATED APBB1IP WILD-TYPE
  COLON ADENOCARCINOMA                        14               301
  COLON MUCINOUS ADENOCARCINOMA                4                43
  RECTAL ADENOCARCINOMA                        1               105
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  APBB1IP MUTATED    12   0   0   0
  APBB1IP WILD-TYPE 333   4  31  25
D961V11, multiclass
    clus
vv   APBB1IP MUTATED APBB1IP WILD-TYPE
  R0              12               333
  R1               0                 4
  R2               0                31
  RX               0                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D961V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  APBB1IP MUTATED                                  0     0
  APBB1IP WILD-TYPE                                1    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  APBB1IP MUTATED                           0    12
  APBB1IP WILD-TYPE                        22   214
D961V13, multiclass
                                  clus
vv                                 APBB1IP MUTATED APBB1IP WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                      0                22
  WHITE                                         12               214
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(962) Variable = TXNDC17 MUTATION ANALYSIS
D962V1, survival
                   sevent
clus2                 0   1
  TXNDC17 MUTATED     5   0
  TXNDC17 WILD-TYPE 373  93
  TXNDC17 MUTATED TXNDC17 WILD-TYPE 
                5               466 
  TXNDC17 MUTATED TXNDC17 WILD-TYPE 
                0                93 
$`TXNDC17 MUTATED`
TCGA-A6-5665 TCGA-AA-3663 TCGA-CM-5861 TCGA-D5-6533 TCGA-D5-6923 
       22.06         6.97        15.02         1.32        12.43 

$`TXNDC17 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       32.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       18.25        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  TXNDC17 MUTATED TXNDC17 WILD-TYPE 
             1.32              0.00 
  TXNDC17 MUTATED TXNDC17 WILD-TYPE 
            22.06            148.01 
  TXNDC17 MUTATED TXNDC17 WILD-TYPE 
           12.430            20.415 
[1] "1.3 - 22.1 (12.4)"  "0.0 - 148.0 (20.4)"
[1] "hr="     "3300000"
D962V2, continuous
D962V3, binary
                   cls
clus                  0   1
  TXNDC17 MUTATED     5   0
  TXNDC17 WILD-TYPE 361 119
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TXNDC17 MUTATED      5    0
  TXNDC17 WILD-TYPE  361  119
        clus
vv       TXNDC17 MUTATED TXNDC17 WILD-TYPE
  COLON                5               361
  RECTUM               0               119
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TXNDC17 MUTATED         1        0        1         2         0         0
  TXNDC17 WILD-TYPE      90        1       31       136        10         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TXNDC17 MUTATED           0          0          1          0        0
  TXNDC17 WILD-TYPE        24         11         58         42       48
                   vv
clus                STAGE IVA STAGE IVB
  TXNDC17 MUTATED           0         0
  TXNDC17 WILD-TYPE        18         1
D962V4, multiclass
            clus
vv           TXNDC17 MUTATED TXNDC17 WILD-TYPE
  STAGE I                  1                90
  STAGE IA                 0                 1
  STAGE II                 1                31
  STAGE IIA                2               136
  STAGE IIB                0                10
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               0                11
  STAGE IIIB               1                58
  STAGE IIIC               0                42
  STAGE IV                 0                48
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  TXNDC17 MUTATED     0   1   3   1
  TXNDC17 WILD-TYPE  17  91 326  49
D962V5, multiclass
    clus
vv   TXNDC17 MUTATED TXNDC17 WILD-TYPE
  T1               0                17
  T2               1                91
  T3               3               326
  T4               1                49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  TXNDC17 MUTATED     5   0   0
  TXNDC17 WILD-TYPE 282 113  87
D962V6, multiclass
    clus
vv   TXNDC17 MUTATED TXNDC17 WILD-TYPE
  N0               5               282
  N1               0               113
  N2               0                87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D962V7, binary
                   cls
clus                  0   1
  TXNDC17 MUTATED     5   0
  TXNDC17 WILD-TYPE 370  65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TXNDC17 MUTATED      5    0
  TXNDC17 WILD-TYPE  370   65
   clus
vv  TXNDC17 MUTATED TXNDC17 WILD-TYPE
  0               5               370
  1               0                65
[1] 2 2
[1] FALSE
D962V8, binary
                   cls
clus                  0   1
  TXNDC17 MUTATED     3   2
  TXNDC17 WILD-TYPE 222 262
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TXNDC17 MUTATED      3    2
  TXNDC17 WILD-TYPE  222  262
        clus
vv       TXNDC17 MUTATED TXNDC17 WILD-TYPE
  FEMALE               3               222
  MALE                 2               262
[1] 2 2
[1] FALSE
D962V9, binary
                   cls
clus                  0   1
  TXNDC17 MUTATED     4   0
  TXNDC17 WILD-TYPE 346  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TXNDC17 MUTATED      4    0
  TXNDC17 WILD-TYPE  346   22
     clus
vv    TXNDC17 MUTATED TXNDC17 WILD-TYPE
  NO                4               346
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  TXNDC17 MUTATED                      5                             0
  TXNDC17 WILD-TYPE                  310                            47
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  TXNDC17 MUTATED                       0                              0
  TXNDC17 WILD-TYPE                   106                             10
D962V10, multiclass
                                clus
vv                               TXNDC17 MUTATED TXNDC17 WILD-TYPE
  COLON ADENOCARCINOMA                         5               310
  COLON MUCINOUS ADENOCARCINOMA                0                47
  RECTAL ADENOCARCINOMA                        0               106
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  TXNDC17 MUTATED     5   0   0   0
  TXNDC17 WILD-TYPE 340   4  31  25
D962V11, multiclass
    clus
vv   TXNDC17 MUTATED TXNDC17 WILD-TYPE
  R0               5               340
  R1               0                 4
  R2               0                31
  RX               0                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D962V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TXNDC17 MUTATED                                  0     0
  TXNDC17 WILD-TYPE                                1    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  TXNDC17 MUTATED                           0     4
  TXNDC17 WILD-TYPE                        22   222
D962V13, multiclass
                                  clus
vv                                 TXNDC17 MUTATED TXNDC17 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                      0                22
  WHITE                                          4               222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(963) Variable = HPSE MUTATION ANALYSIS
D963V1, survival
                sevent
clus2              0   1
  HPSE MUTATED    10   1
  HPSE WILD-TYPE 368  92
  HPSE MUTATED HPSE WILD-TYPE 
            11            460 
  HPSE MUTATED HPSE WILD-TYPE 
             1             92 
$`HPSE MUTATED`
TCGA-AA-3864 TCGA-AA-A010 TCGA-AD-6889 TCGA-AY-6197 TCGA-AZ-4315 TCGA-CA-6717 
       53.00        34.98        56.55        21.44        58.39        12.76 
TCGA-CK-6747 TCGA-DM-A0XD TCGA-G4-6304 TCGA-AG-3732 TCGA-CI-6624 
       82.95        24.43        53.62        32.98         4.73 

$`HPSE WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07        12.20        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
        9.99        21.14         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
       10.26       119.70        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       74.56        65.85        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
        0.99        37.02         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
       33.17         6.97        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  HPSE MUTATED HPSE WILD-TYPE 
          4.73           0.00 
  HPSE MUTATED HPSE WILD-TYPE 
         82.95         148.01 
  HPSE MUTATED HPSE WILD-TYPE 
         34.98          20.02 
[1] "4.7 - 83.0 (35.0)"  "0.0 - 148.0 (20.0)"
[1] "hr=" "3.5"
D963V2, continuous
D963V3, binary
                cls
clus               0   1
  HPSE MUTATED     9   2
  HPSE WILD-TYPE 357 117
[1] "tbl2"
                cls
clus             [,1] [,2]
  HPSE MUTATED      9    2
  HPSE WILD-TYPE  357  117
        clus
vv       HPSE MUTATED HPSE WILD-TYPE
  COLON             9            357
  RECTUM            2            117
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  HPSE MUTATED         2        0        1         6         2         0
  HPSE WILD-TYPE      89        1       31       132         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  HPSE MUTATED           0          0          0          0        0         0
  HPSE WILD-TYPE        24         11         59         42       48        18
                vv
clus             STAGE IVB
  HPSE MUTATED           0
  HPSE WILD-TYPE         1
D963V4, multiclass
            clus
vv           HPSE MUTATED HPSE WILD-TYPE
  STAGE I               2             89
  STAGE IA              0              1
  STAGE II              1             31
  STAGE IIA             6            132
  STAGE IIB             2              8
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            0             59
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  HPSE MUTATED     0   2   7   2
  HPSE WILD-TYPE  17  90 322  48
D963V5, multiclass
    clus
vv   HPSE MUTATED HPSE WILD-TYPE
  T1            0             17
  T2            2             90
  T3            7            322
  T4            2             48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  HPSE MUTATED    11   0   0
  HPSE WILD-TYPE 276 113  87
D963V6, multiclass
    clus
vv   HPSE MUTATED HPSE WILD-TYPE
  N0           11            276
  N1            0            113
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D963V7, binary
                cls
clus               0   1
  HPSE MUTATED     9   0
  HPSE WILD-TYPE 366  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  HPSE MUTATED      9    0
  HPSE WILD-TYPE  366   65
   clus
vv  HPSE MUTATED HPSE WILD-TYPE
  0            9            366
  1            0             65
[1] 2 2
[1] FALSE
D963V8, binary
                cls
clus               0   1
  HPSE MUTATED     5   6
  HPSE WILD-TYPE 220 258
[1] "tbl2"
                cls
clus             [,1] [,2]
  HPSE MUTATED      5    6
  HPSE WILD-TYPE  220  258
        clus
vv       HPSE MUTATED HPSE WILD-TYPE
  FEMALE            5            220
  MALE              6            258
[1] 2 2
[1] FALSE
D963V9, binary
                cls
clus               0   1
  HPSE MUTATED     8   0
  HPSE WILD-TYPE 342  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  HPSE MUTATED      8    0
  HPSE WILD-TYPE  342   22
     clus
vv    HPSE MUTATED HPSE WILD-TYPE
  NO             8            342
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  HPSE MUTATED                      8                             1
  HPSE WILD-TYPE                  307                            46
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  HPSE MUTATED                       2                              0
  HPSE WILD-TYPE                   104                             10
D963V10, multiclass
                                clus
vv                               HPSE MUTATED HPSE WILD-TYPE
  COLON ADENOCARCINOMA                      8            307
  COLON MUCINOUS ADENOCARCINOMA             1             46
  RECTAL ADENOCARCINOMA                     2            104
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  HPSE MUTATED     6   0   0   2
  HPSE WILD-TYPE 339   4  31  23
D963V11, multiclass
    clus
vv   HPSE MUTATED HPSE WILD-TYPE
  R0            6            339
  R1            0              4
  R2            0             31
  RX            2             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D963V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HPSE MUTATED                                  0     2
  HPSE WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  HPSE MUTATED                           0     6
  HPSE WILD-TYPE                        22   220
D963V13, multiclass
                                  clus
vv                                 HPSE MUTATED HPSE WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              9
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       6            220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(964) Variable = SLC39A2 MUTATION ANALYSIS
D964V1, survival
                   sevent
clus2                 0   1
  SLC39A2 MUTATED     9   1
  SLC39A2 WILD-TYPE 369  92
  SLC39A2 MUTATED SLC39A2 WILD-TYPE 
               10               461 
  SLC39A2 MUTATED SLC39A2 WILD-TYPE 
                1                92 
$`SLC39A2 MUTATED`
TCGA-A6-6649 TCGA-AA-3977 TCGA-AA-A01Q TCGA-CM-6162 TCGA-D5-6927 TCGA-G4-6626 
       24.16        25.02         1.02        12.00         9.44        46.75 
TCGA-AG-A002 TCGA-AG-A016 TCGA-CI-6619 TCGA-DY-A0XA 
       20.98         9.07         6.05       126.44 

$`SLC39A2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.08        25.18        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        31.00        38.07        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       12.43        14.30         9.04        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 
       22.09        13.78        35.80        26.17        91.79        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       37.02        15.95        36.03        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        0.72        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD 
        5.95         4.01         5.03         5.29        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  SLC39A2 MUTATED SLC39A2 WILD-TYPE 
             1.02              0.00 
  SLC39A2 MUTATED SLC39A2 WILD-TYPE 
           126.44            148.01 
  SLC39A2 MUTATED SLC39A2 WILD-TYPE 
            16.49             20.19 
[1] "1.0 - 126.4 (16.5)" "0.0 - 148.0 (20.2)"
[1] "hr=" "2"  
D964V2, continuous
D964V3, binary
                   cls
clus                  0   1
  SLC39A2 MUTATED     6   4
  SLC39A2 WILD-TYPE 360 115
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC39A2 MUTATED      6    4
  SLC39A2 WILD-TYPE  360  115
        clus
vv       SLC39A2 MUTATED SLC39A2 WILD-TYPE
  COLON                6               360
  RECTUM               4               115
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SLC39A2 MUTATED         1        0        1         3         0         0
  SLC39A2 WILD-TYPE      90        1       31       135        10         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC39A2 MUTATED           0          0          2          0        2
  SLC39A2 WILD-TYPE        24         11         57         42       46
                   vv
clus                STAGE IVA STAGE IVB
  SLC39A2 MUTATED           0         0
  SLC39A2 WILD-TYPE        18         1
D964V4, multiclass
            clus
vv           SLC39A2 MUTATED SLC39A2 WILD-TYPE
  STAGE I                  1                90
  STAGE IA                 0                 1
  STAGE II                 1                31
  STAGE IIA                3               135
  STAGE IIB                0                10
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               0                11
  STAGE IIIB               2                57
  STAGE IIIC               0                42
  STAGE IV                 2                46
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  SLC39A2 MUTATED     0   2   8   0
  SLC39A2 WILD-TYPE  17  90 321  50
D964V5, multiclass
    clus
vv   SLC39A2 MUTATED SLC39A2 WILD-TYPE
  T1               0                17
  T2               2                90
  T3               8               321
  T4               0                50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  SLC39A2 MUTATED     6   3   1
  SLC39A2 WILD-TYPE 281 110  86
D964V6, multiclass
    clus
vv   SLC39A2 MUTATED SLC39A2 WILD-TYPE
  N0               6               281
  N1               3               110
  N2               1                86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D964V7, binary
                   cls
clus                  0   1
  SLC39A2 MUTATED     7   2
  SLC39A2 WILD-TYPE 368  63
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC39A2 MUTATED      7    2
  SLC39A2 WILD-TYPE  368   63
   clus
vv  SLC39A2 MUTATED SLC39A2 WILD-TYPE
  0               7               368
  1               2                63
[1] 2 2
[1] FALSE
D964V8, binary
                   cls
clus                  0   1
  SLC39A2 MUTATED     3   7
  SLC39A2 WILD-TYPE 222 257
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC39A2 MUTATED      3    7
  SLC39A2 WILD-TYPE  222  257
        clus
vv       SLC39A2 MUTATED SLC39A2 WILD-TYPE
  FEMALE               3               222
  MALE                 7               257
[1] 2 2
[1] FALSE
D964V9, binary
                   cls
clus                  0   1
  SLC39A2 MUTATED     7   0
  SLC39A2 WILD-TYPE 343  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC39A2 MUTATED      7    0
  SLC39A2 WILD-TYPE  343   22
     clus
vv    SLC39A2 MUTATED SLC39A2 WILD-TYPE
  NO                7               343
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SLC39A2 MUTATED                      5                             1
  SLC39A2 WILD-TYPE                  310                            46
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SLC39A2 MUTATED                       4                              0
  SLC39A2 WILD-TYPE                   102                             10
D964V10, multiclass
                                clus
vv                               SLC39A2 MUTATED SLC39A2 WILD-TYPE
  COLON ADENOCARCINOMA                         5               310
  COLON MUCINOUS ADENOCARCINOMA                1                46
  RECTAL ADENOCARCINOMA                        4               102
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  SLC39A2 MUTATED     5   0   1   0
  SLC39A2 WILD-TYPE 340   4  30  25
D964V11, multiclass
    clus
vv   SLC39A2 MUTATED SLC39A2 WILD-TYPE
  R0               5               340
  R1               0                 4
  R2               1                30
  RX               0                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D964V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SLC39A2 MUTATED                                  0     0
  SLC39A2 WILD-TYPE                                1    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  SLC39A2 MUTATED                           0     6
  SLC39A2 WILD-TYPE                        22   220
D964V13, multiclass
                                  clus
vv                                 SLC39A2 MUTATED SLC39A2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                      0                22
  WHITE                                          6               220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(965) Variable = C9ORF71 MUTATION ANALYSIS
D965V1, survival
                   sevent
clus2                 0   1
  C9ORF71 MUTATED     4   0
  C9ORF71 WILD-TYPE 374  93
  C9ORF71 MUTATED C9ORF71 WILD-TYPE 
                4               467 
  C9ORF71 MUTATED C9ORF71 WILD-TYPE 
                0                93 
$`C9ORF71 MUTATED`
TCGA-CA-6717 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 
       12.76        35.80        26.17        79.69 

$`C9ORF71 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07        12.20        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       91.79        46.75        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  C9ORF71 MUTATED C9ORF71 WILD-TYPE 
            12.76              0.00 
  C9ORF71 MUTATED C9ORF71 WILD-TYPE 
            79.69            148.01 
  C9ORF71 MUTATED C9ORF71 WILD-TYPE 
           30.985            20.120 
[1] "12.8 - 79.7 (31.0)" "0.0 - 148.0 (20.1)"
[1] "hr="     "9100000"
D965V2, continuous
D965V3, binary
                   cls
clus                  0   1
  C9ORF71 MUTATED     4   0
  C9ORF71 WILD-TYPE 362 119
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C9ORF71 MUTATED      4    0
  C9ORF71 WILD-TYPE  362  119
        clus
vv       C9ORF71 MUTATED C9ORF71 WILD-TYPE
  COLON                4               362
  RECTUM               0               119
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  C9ORF71 MUTATED         1        0        0         3         0         0
  C9ORF71 WILD-TYPE      90        1       32       135        10         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C9ORF71 MUTATED           0          0          0          0        0
  C9ORF71 WILD-TYPE        24         11         59         42       48
                   vv
clus                STAGE IVA STAGE IVB
  C9ORF71 MUTATED           0         0
  C9ORF71 WILD-TYPE        18         1
D965V4, multiclass
            clus
vv           C9ORF71 MUTATED C9ORF71 WILD-TYPE
  STAGE I                  1                90
  STAGE IA                 0                 1
  STAGE II                 0                32
  STAGE IIA                3               135
  STAGE IIB                0                10
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               0                11
  STAGE IIIB               0                59
  STAGE IIIC               0                42
  STAGE IV                 0                48
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  C9ORF71 MUTATED     0   1   3   0
  C9ORF71 WILD-TYPE  17  91 326  50
D965V5, multiclass
    clus
vv   C9ORF71 MUTATED C9ORF71 WILD-TYPE
  T1               0                17
  T2               1                91
  T3               3               326
  T4               0                50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  C9ORF71 MUTATED     4   0   0
  C9ORF71 WILD-TYPE 283 113  87
D965V6, multiclass
    clus
vv   C9ORF71 MUTATED C9ORF71 WILD-TYPE
  N0               4               283
  N1               0               113
  N2               0                87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D965V7, binary
                   cls
clus                  0   1
  C9ORF71 MUTATED     4   0
  C9ORF71 WILD-TYPE 371  65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C9ORF71 MUTATED      4    0
  C9ORF71 WILD-TYPE  371   65
   clus
vv  C9ORF71 MUTATED C9ORF71 WILD-TYPE
  0               4               371
  1               0                65
[1] 2 2
[1] FALSE
D965V8, binary
                   cls
clus                  0   1
  C9ORF71 MUTATED     2   2
  C9ORF71 WILD-TYPE 223 262
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C9ORF71 MUTATED      2    2
  C9ORF71 WILD-TYPE  223  262
        clus
vv       C9ORF71 MUTATED C9ORF71 WILD-TYPE
  FEMALE               2               223
  MALE                 2               262
[1] 2 2
[1] FALSE
D965V9, binary
                   cls
clus                  0   1
  C9ORF71 MUTATED     4   0
  C9ORF71 WILD-TYPE 346  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C9ORF71 MUTATED      4    0
  C9ORF71 WILD-TYPE  346   22
     clus
vv    C9ORF71 MUTATED C9ORF71 WILD-TYPE
  NO                4               346
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  C9ORF71 MUTATED                      3                             1
  C9ORF71 WILD-TYPE                  312                            46
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  C9ORF71 MUTATED                       0                              0
  C9ORF71 WILD-TYPE                   106                             10
D965V10, multiclass
                                clus
vv                               C9ORF71 MUTATED C9ORF71 WILD-TYPE
  COLON ADENOCARCINOMA                         3               312
  COLON MUCINOUS ADENOCARCINOMA                1                46
  RECTAL ADENOCARCINOMA                        0               106
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  C9ORF71 MUTATED     3   0   0   1
  C9ORF71 WILD-TYPE 342   4  31  24
D965V11, multiclass
    clus
vv   C9ORF71 MUTATED C9ORF71 WILD-TYPE
  R0               3               342
  R1               0                 4
  R2               0                31
  RX               1                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D965V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C9ORF71 MUTATED                                  0     1
  C9ORF71 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  C9ORF71 MUTATED                           0     3
  C9ORF71 WILD-TYPE                        22   223
D965V13, multiclass
                                  clus
vv                                 C9ORF71 MUTATED C9ORF71 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                10
  BLACK OR AFRICAN AMERICAN                      0                22
  WHITE                                          3               223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(966) Variable = STYK1 MUTATION ANALYSIS
D966V1, survival
                 sevent
clus2               0   1
  STYK1 MUTATED     4   3
  STYK1 WILD-TYPE 374  90
  STYK1 MUTATED STYK1 WILD-TYPE 
              7             464 
  STYK1 MUTATED STYK1 WILD-TYPE 
              3              90 
$`STYK1 MUTATED`
TCGA-AA-A01R TCGA-AD-6964 TCGA-AZ-6608 TCGA-D5-6537 TCGA-D5-6538 TCGA-G4-6307 
       35.01        10.88         1.61         4.80        17.13        55.04 
TCGA-G4-6588 
       26.17 

$`STYK1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6539 
       18.25         1.32        43.27        15.12        17.85        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       44.68        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       13.78        35.80        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  STYK1 MUTATED STYK1 WILD-TYPE 
           1.61            0.00 
  STYK1 MUTATED STYK1 WILD-TYPE 
          55.04          148.01 
  STYK1 MUTATED STYK1 WILD-TYPE 
         17.130          20.235 
[1] "1.6 - 55.0 (17.1)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "2.7"
D966V2, continuous
D966V3, binary
                 cls
clus                0   1
  STYK1 MUTATED     7   0
  STYK1 WILD-TYPE 359 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STYK1 MUTATED      7    0
  STYK1 WILD-TYPE  359  119
        clus
vv       STYK1 MUTATED STYK1 WILD-TYPE
  COLON              7             359
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  STYK1 MUTATED         0        0        0         1         0         0
  STYK1 WILD-TYPE      91        1       32       137        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  STYK1 MUTATED           1          1          3          0        0         0
  STYK1 WILD-TYPE        23         10         56         42       48        18
                 vv
clus              STAGE IVB
  STYK1 MUTATED           0
  STYK1 WILD-TYPE         1
D966V4, multiclass
            clus
vv           STYK1 MUTATED STYK1 WILD-TYPE
  STAGE I                0              91
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              1             137
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             1              10
  STAGE IIIB             3              56
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  STYK1 MUTATED     0   1   5   1
  STYK1 WILD-TYPE  17  91 324  49
D966V5, multiclass
    clus
vv   STYK1 MUTATED STYK1 WILD-TYPE
  T1             0              17
  T2             1              91
  T3             5             324
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  STYK1 MUTATED     1   3   3
  STYK1 WILD-TYPE 286 110  84
D966V6, multiclass
    clus
vv   STYK1 MUTATED STYK1 WILD-TYPE
  N0             1             286
  N1             3             110
  N2             3              84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D966V7, binary
                 cls
clus                0   1
  STYK1 MUTATED     5   0
  STYK1 WILD-TYPE 370  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STYK1 MUTATED      5    0
  STYK1 WILD-TYPE  370   65
   clus
vv  STYK1 MUTATED STYK1 WILD-TYPE
  0             5             370
  1             0              65
[1] 2 2
[1] FALSE
D966V8, binary
                 cls
clus                0   1
  STYK1 MUTATED     4   3
  STYK1 WILD-TYPE 221 261
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STYK1 MUTATED      4    3
  STYK1 WILD-TYPE  221  261
        clus
vv       STYK1 MUTATED STYK1 WILD-TYPE
  FEMALE             4             221
  MALE               3             261
[1] 2 2
[1] FALSE
D966V9, binary
                 cls
clus                0   1
  STYK1 MUTATED     6   1
  STYK1 WILD-TYPE 344  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STYK1 MUTATED      6    1
  STYK1 WILD-TYPE  344   21
     clus
vv    STYK1 MUTATED STYK1 WILD-TYPE
  NO              6             344
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  STYK1 MUTATED                      6                             1
  STYK1 WILD-TYPE                  309                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  STYK1 MUTATED                       0                              0
  STYK1 WILD-TYPE                   106                             10
D966V10, multiclass
                                clus
vv                               STYK1 MUTATED STYK1 WILD-TYPE
  COLON ADENOCARCINOMA                       6             309
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  STYK1 MUTATED     5   0   0   0
  STYK1 WILD-TYPE 340   4  31  25
D966V11, multiclass
    clus
vv   STYK1 MUTATED STYK1 WILD-TYPE
  R0             5             340
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D966V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  STYK1 MUTATED                                  0     0
  STYK1 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  STYK1 MUTATED                           0     6
  STYK1 WILD-TYPE                        22   220
D966V13, multiclass
                                  clus
vv                                 STYK1 MUTATED STYK1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        6             220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(967) Variable = LGR4 MUTATION ANALYSIS
D967V1, survival
                sevent
clus2              0   1
  LGR4 MUTATED    15   1
  LGR4 WILD-TYPE 363  92
  LGR4 MUTATED LGR4 WILD-TYPE 
            16            455 
  LGR4 MUTATED LGR4 WILD-TYPE 
             1             92 
$`LGR4 MUTATED`
TCGA-A6-5661 TCGA-A6-5665 TCGA-AA-3510 TCGA-AA-3713 TCGA-AA-3837 TCGA-AA-3977 
       33.53        22.06        63.98        19.04        38.99        25.02 
TCGA-AA-A01R TCGA-AY-6197 TCGA-AZ-4315 TCGA-CM-6162 TCGA-CM-6171 TCGA-F4-6570 
       35.01        21.44        58.39        12.00        14.04         6.18 
TCGA-G4-6628 TCGA-AG-3892 TCGA-AG-A002 TCGA-EI-6510 
       79.69        13.02        20.98        18.28 

$`LGR4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       85.05        26.99        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3842 
        0.99        25.02         1.02        17.98        15.95        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
        0.95        33.01        17.82         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       13.02        15.02        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
        8.61        31.96        35.74        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 
       13.78        35.80        26.17        91.79        46.75        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       17.03        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       19.96        20.91         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  LGR4 MUTATED LGR4 WILD-TYPE 
          6.18           0.00 
  LGR4 MUTATED LGR4 WILD-TYPE 
         79.69         148.01 
  LGR4 MUTATED LGR4 WILD-TYPE 
         21.75          20.05 
[1] "6.2 - 79.7 (21.8)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "3.8"
D967V2, continuous
D967V3, binary
                cls
clus               0   1
  LGR4 MUTATED    14   3
  LGR4 WILD-TYPE 352 116
[1] "tbl2"
                cls
clus             [,1] [,2]
  LGR4 MUTATED     14    3
  LGR4 WILD-TYPE  352  116
        clus
vv       LGR4 MUTATED LGR4 WILD-TYPE
  COLON            14            352
  RECTUM            3            116
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  LGR4 MUTATED         4        0        1         7         0         0
  LGR4 WILD-TYPE      87        1       31       131        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  LGR4 MUTATED           1          0          1          0        1         1
  LGR4 WILD-TYPE        23         11         58         42       47        17
                vv
clus             STAGE IVB
  LGR4 MUTATED           0
  LGR4 WILD-TYPE         1
D967V4, multiclass
            clus
vv           LGR4 MUTATED LGR4 WILD-TYPE
  STAGE I               4             87
  STAGE IA              0              1
  STAGE II              1             31
  STAGE IIA             7            131
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             1             23
  STAGE IIIA            0             11
  STAGE IIIB            1             58
  STAGE IIIC            0             42
  STAGE IV              1             47
  STAGE IVA             1             17
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  LGR4 MUTATED     1   5  11   0
  LGR4 WILD-TYPE  16  87 318  50
D967V5, multiclass
    clus
vv   LGR4 MUTATED LGR4 WILD-TYPE
  T1            1             16
  T2            5             87
  T3           11            318
  T4            0             50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  LGR4 MUTATED    15   1   1
  LGR4 WILD-TYPE 272 112  86
D967V6, multiclass
    clus
vv   LGR4 MUTATED LGR4 WILD-TYPE
  N0           15            272
  N1            1            112
  N2            1             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D967V7, binary
                cls
clus               0   1
  LGR4 MUTATED    13   1
  LGR4 WILD-TYPE 362  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  LGR4 MUTATED     13    1
  LGR4 WILD-TYPE  362   64
   clus
vv  LGR4 MUTATED LGR4 WILD-TYPE
  0           13            362
  1            1             64
[1] 2 2
[1] FALSE
D967V8, binary
                cls
clus               0   1
  LGR4 MUTATED     8   9
  LGR4 WILD-TYPE 217 255
[1] "tbl2"
                cls
clus             [,1] [,2]
  LGR4 MUTATED      8    9
  LGR4 WILD-TYPE  217  255
        clus
vv       LGR4 MUTATED LGR4 WILD-TYPE
  FEMALE            8            217
  MALE              9            255
[1] 2 2
[1] FALSE
D967V9, binary
                cls
clus               0   1
  LGR4 MUTATED    14   2
  LGR4 WILD-TYPE 336  20
[1] "tbl2"
                cls
clus             [,1] [,2]
  LGR4 MUTATED     14    2
  LGR4 WILD-TYPE  336   20
     clus
vv    LGR4 MUTATED LGR4 WILD-TYPE
  NO            14            336
  YES            2             20
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  LGR4 MUTATED                     11                             3
  LGR4 WILD-TYPE                  304                            44
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  LGR4 MUTATED                       3                              0
  LGR4 WILD-TYPE                   103                             10
D967V10, multiclass
                                clus
vv                               LGR4 MUTATED LGR4 WILD-TYPE
  COLON ADENOCARCINOMA                     11            304
  COLON MUCINOUS ADENOCARCINOMA             3             44
  RECTAL ADENOCARCINOMA                     3            103
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  LGR4 MUTATED    15   0   1   0
  LGR4 WILD-TYPE 330   4  30  25
D967V11, multiclass
    clus
vv   LGR4 MUTATED LGR4 WILD-TYPE
  R0           15            330
  R1            0              4
  R2            1             30
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D967V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  LGR4 MUTATED                                  0     0
  LGR4 WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  LGR4 MUTATED                           1     8
  LGR4 WILD-TYPE                        21   218
D967V13, multiclass
                                  clus
vv                                 LGR4 MUTATED LGR4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                       8            218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(968) Variable = C14ORF28 MUTATION ANALYSIS
D968V1, survival
                    sevent
clus2                  0   1
  C14ORF28 MUTATED     3   2
  C14ORF28 WILD-TYPE 375  91
  C14ORF28 MUTATED C14ORF28 WILD-TYPE 
                 5                466 
  C14ORF28 MUTATED C14ORF28 WILD-TYPE 
                 2                 91 
$`C14ORF28 MUTATED`
TCGA-AA-A00N TCGA-CA-6717 TCGA-G4-6586 TCGA-AG-A002 TCGA-F5-6464 
        4.01        12.76        35.80        20.98         9.96 

$`C14ORF28 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07        12.20        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 
       63.62        61.91        36.00        22.09        13.78        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       20.91        18.28        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  C14ORF28 MUTATED C14ORF28 WILD-TYPE 
              4.01               0.00 
  C14ORF28 MUTATED C14ORF28 WILD-TYPE 
             35.80             148.01 
  C14ORF28 MUTATED C14ORF28 WILD-TYPE 
            12.760             20.235 
[1] "4.0 - 35.8 (12.8)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "3.5"
D968V2, continuous
D968V3, binary
                    cls
clus                   0   1
  C14ORF28 MUTATED     3   2
  C14ORF28 WILD-TYPE 363 117
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C14ORF28 MUTATED      3    2
  C14ORF28 WILD-TYPE  363  117
        clus
vv       C14ORF28 MUTATED C14ORF28 WILD-TYPE
  COLON                 3                363
  RECTUM                2                117
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  C14ORF28 MUTATED         1        0        0         2         1         0
  C14ORF28 WILD-TYPE      90        1       32       136         9         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C14ORF28 MUTATED           0          0          0          1        0
  C14ORF28 WILD-TYPE        24         11         59         41       48
                    vv
clus                 STAGE IVA STAGE IVB
  C14ORF28 MUTATED           0         0
  C14ORF28 WILD-TYPE        18         1
D968V4, multiclass
            clus
vv           C14ORF28 MUTATED C14ORF28 WILD-TYPE
  STAGE I                   1                 90
  STAGE IA                  0                  1
  STAGE II                  0                 32
  STAGE IIA                 2                136
  STAGE IIB                 1                  9
  STAGE IIC                 0                  1
  STAGE III                 0                 24
  STAGE IIIA                0                 11
  STAGE IIIB                0                 59
  STAGE IIIC                1                 41
  STAGE IV                  0                 48
  STAGE IVA                 0                 18
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  C14ORF28 MUTATED     0   1   2   2
  C14ORF28 WILD-TYPE  17  91 327  48
D968V5, multiclass
    clus
vv   C14ORF28 MUTATED C14ORF28 WILD-TYPE
  T1                0                 17
  T2                1                 91
  T3                2                327
  T4                2                 48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  C14ORF28 MUTATED     4   0   1
  C14ORF28 WILD-TYPE 283 113  86
D968V6, multiclass
    clus
vv   C14ORF28 MUTATED C14ORF28 WILD-TYPE
  N0                4                283
  N1                0                113
  N2                1                 86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D968V7, binary
                    cls
clus                   0   1
  C14ORF28 MUTATED     5   0
  C14ORF28 WILD-TYPE 370  65
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C14ORF28 MUTATED      5    0
  C14ORF28 WILD-TYPE  370   65
   clus
vv  C14ORF28 MUTATED C14ORF28 WILD-TYPE
  0                5                370
  1                0                 65
[1] 2 2
[1] FALSE
D968V8, binary
                    cls
clus                   0   1
  C14ORF28 MUTATED     2   3
  C14ORF28 WILD-TYPE 223 261
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C14ORF28 MUTATED      2    3
  C14ORF28 WILD-TYPE  223  261
        clus
vv       C14ORF28 MUTATED C14ORF28 WILD-TYPE
  FEMALE                2                223
  MALE                  3                261
[1] 2 2
[1] FALSE
D968V9, binary
                    cls
clus                   0   1
  C14ORF28 MUTATED     4   0
  C14ORF28 WILD-TYPE 346  22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C14ORF28 MUTATED      4    0
  C14ORF28 WILD-TYPE  346   22
     clus
vv    C14ORF28 MUTATED C14ORF28 WILD-TYPE
  NO                 4                346
  YES                0                 22
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  C14ORF28 MUTATED                      1                             2
  C14ORF28 WILD-TYPE                  314                            45
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  C14ORF28 MUTATED                       2                              0
  C14ORF28 WILD-TYPE                   104                             10
D968V10, multiclass
                                clus
vv                               C14ORF28 MUTATED C14ORF28 WILD-TYPE
  COLON ADENOCARCINOMA                          1                314
  COLON MUCINOUS ADENOCARCINOMA                 2                 45
  RECTAL ADENOCARCINOMA                         2                104
  RECTAL MUCINOUS ADENOCARCINOMA                0                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  C14ORF28 MUTATED     4   0   0   1
  C14ORF28 WILD-TYPE 341   4  31  24
D968V11, multiclass
    clus
vv   C14ORF28 MUTATED C14ORF28 WILD-TYPE
  R0                4                341
  R1                0                  4
  R2                0                 31
  RX                1                 24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D968V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C14ORF28 MUTATED                                  0     1
  C14ORF28 WILD-TYPE                                1    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  C14ORF28 MUTATED                           0     2
  C14ORF28 WILD-TYPE                        22   224
D968V13, multiclass
                                  clus
vv                                 C14ORF28 MUTATED C14ORF28 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                 10
  BLACK OR AFRICAN AMERICAN                       0                 22
  WHITE                                           2                224
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(969) Variable = ACTL6A MUTATION ANALYSIS
D969V1, survival
                  sevent
clus2                0   1
  ACTL6A MUTATED     5   2
  ACTL6A WILD-TYPE 373  91
  ACTL6A MUTATED ACTL6A WILD-TYPE 
               7              464 
  ACTL6A MUTATED ACTL6A WILD-TYPE 
               2               91 
$`ACTL6A MUTATED`
TCGA-A6-2672 TCGA-A6-6781 TCGA-AA-3815 TCGA-AA-3947 TCGA-AA-A00N TCGA-CK-5916 
       46.65        19.66        33.04        33.01         4.01        21.14 
TCGA-AG-A002 
       20.98 

$`ACTL6A WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       35.05         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       51.32         9.99        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  ACTL6A MUTATED ACTL6A WILD-TYPE 
            4.01             0.00 
  ACTL6A MUTATED ACTL6A WILD-TYPE 
           46.65           148.01 
  ACTL6A MUTATED ACTL6A WILD-TYPE 
          21.140           20.085 
[1] "4.0 - 46.6 (21.1)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.6"
D969V2, continuous
D969V3, binary
                  cls
clus                 0   1
  ACTL6A MUTATED     6   1
  ACTL6A WILD-TYPE 360 118
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ACTL6A MUTATED      6    1
  ACTL6A WILD-TYPE  360  118
        clus
vv       ACTL6A MUTATED ACTL6A WILD-TYPE
  COLON               6              360
  RECTUM              1              118
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ACTL6A MUTATED         2        0        0         1         2         0
  ACTL6A WILD-TYPE      89        1       32       137         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ACTL6A MUTATED           0          0          1          1        0
  ACTL6A WILD-TYPE        24         11         58         41       48
                  vv
clus               STAGE IVA STAGE IVB
  ACTL6A MUTATED           0         0
  ACTL6A WILD-TYPE        18         1
D969V4, multiclass
            clus
vv           ACTL6A MUTATED ACTL6A WILD-TYPE
  STAGE I                 2               89
  STAGE IA                0                1
  STAGE II                0               32
  STAGE IIA               1              137
  STAGE IIB               2                8
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              1               58
  STAGE IIIC              1               41
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ACTL6A MUTATED     1   1   2   3
  ACTL6A WILD-TYPE  16  91 327  47
D969V5, multiclass
    clus
vv   ACTL6A MUTATED ACTL6A WILD-TYPE
  T1              1               16
  T2              1               91
  T3              2              327
  T4              3               47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  ACTL6A MUTATED     5   2   0
  ACTL6A WILD-TYPE 282 111  87
D969V6, multiclass
    clus
vv   ACTL6A MUTATED ACTL6A WILD-TYPE
  N0              5              282
  N1              2              111
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D969V7, binary
                  cls
clus                 0   1
  ACTL6A MUTATED     6   0
  ACTL6A WILD-TYPE 369  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ACTL6A MUTATED      6    0
  ACTL6A WILD-TYPE  369   65
   clus
vv  ACTL6A MUTATED ACTL6A WILD-TYPE
  0              6              369
  1              0               65
[1] 2 2
[1] FALSE
D969V8, binary
                  cls
clus                 0   1
  ACTL6A MUTATED     4   3
  ACTL6A WILD-TYPE 221 261
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ACTL6A MUTATED      4    3
  ACTL6A WILD-TYPE  221  261
        clus
vv       ACTL6A MUTATED ACTL6A WILD-TYPE
  FEMALE              4              221
  MALE                3              261
[1] 2 2
[1] FALSE
D969V9, binary
                  cls
clus                 0   1
  ACTL6A MUTATED     6   0
  ACTL6A WILD-TYPE 344  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ACTL6A MUTATED      6    0
  ACTL6A WILD-TYPE  344   22
     clus
vv    ACTL6A MUTATED ACTL6A WILD-TYPE
  NO               6              344
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ACTL6A MUTATED                      3                             3
  ACTL6A WILD-TYPE                  312                            44
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ACTL6A MUTATED                       1                              0
  ACTL6A WILD-TYPE                   105                             10
D969V10, multiclass
                                clus
vv                               ACTL6A MUTATED ACTL6A WILD-TYPE
  COLON ADENOCARCINOMA                        3              312
  COLON MUCINOUS ADENOCARCINOMA               3               44
  RECTAL ADENOCARCINOMA                       1              105
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ACTL6A MUTATED     6   0   0   1
  ACTL6A WILD-TYPE 339   4  31  24
D969V11, multiclass
    clus
vv   ACTL6A MUTATED ACTL6A WILD-TYPE
  R0              6              339
  R1              0                4
  R2              0               31
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D969V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ACTL6A MUTATED                                  0     0
  ACTL6A WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ACTL6A MUTATED                           0     3
  ACTL6A WILD-TYPE                        22   223
D969V13, multiclass
                                  clus
vv                                 ACTL6A MUTATED ACTL6A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         3              223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(970) Variable = UPF3A MUTATION ANALYSIS
D970V1, survival
                 sevent
clus2               0   1
  UPF3A MUTATED     7   2
  UPF3A WILD-TYPE 371  91
  UPF3A MUTATED UPF3A WILD-TYPE 
              9             462 
  UPF3A MUTATED UPF3A WILD-TYPE 
              2              91 
$`UPF3A MUTATED`
TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3555 TCGA-AA-3663 TCGA-AA-3977 TCGA-AD-6889 
        3.02        63.98        29.95         6.97        25.02        56.55 
TCGA-AZ-4681 TCGA-CA-6718 TCGA-CK-5913 
      106.75        10.06        51.32 

$`UPF3A WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       24.00        17.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02        78.08         6.05        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
        0.07        21.37        15.52         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        1.41         5.13        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07        12.20        12.76        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       85.45        15.62        49.08         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  UPF3A MUTATED UPF3A WILD-TYPE 
           3.02            0.00 
  UPF3A MUTATED UPF3A WILD-TYPE 
         106.75          148.01 
  UPF3A MUTATED UPF3A WILD-TYPE 
         29.950          20.085 
[1] "3.0 - 106.8 (29.9)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.4"
D970V2, continuous
D970V3, binary
                 cls
clus                0   1
  UPF3A MUTATED     9   0
  UPF3A WILD-TYPE 357 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UPF3A MUTATED      9    0
  UPF3A WILD-TYPE  357  119
        clus
vv       UPF3A MUTATED UPF3A WILD-TYPE
  COLON              9             357
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  UPF3A MUTATED         0        0        3         5         0         0
  UPF3A WILD-TYPE      91        1       29       133        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  UPF3A MUTATED           0          0          0          0        0         0
  UPF3A WILD-TYPE        24         11         59         42       48        18
                 vv
clus              STAGE IVB
  UPF3A MUTATED           0
  UPF3A WILD-TYPE         1
D970V4, multiclass
            clus
vv           UPF3A MUTATED UPF3A WILD-TYPE
  STAGE I                0              91
  STAGE IA               0               1
  STAGE II               3              29
  STAGE IIA              5             133
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  UPF3A MUTATED     0   1   8   0
  UPF3A WILD-TYPE  17  91 321  50
D970V5, multiclass
    clus
vv   UPF3A MUTATED UPF3A WILD-TYPE
  T1             0              17
  T2             1              91
  T3             8             321
  T4             0              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  UPF3A MUTATED     9   0   0
  UPF3A WILD-TYPE 278 113  87
D970V6, multiclass
    clus
vv   UPF3A MUTATED UPF3A WILD-TYPE
  N0             9             278
  N1             0             113
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D970V7, binary
                 cls
clus                0   1
  UPF3A MUTATED     7   0
  UPF3A WILD-TYPE 368  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UPF3A MUTATED      7    0
  UPF3A WILD-TYPE  368   65
   clus
vv  UPF3A MUTATED UPF3A WILD-TYPE
  0             7             368
  1             0              65
[1] 2 2
[1] FALSE
D970V8, binary
                 cls
clus                0   1
  UPF3A MUTATED     4   5
  UPF3A WILD-TYPE 221 259
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UPF3A MUTATED      4    5
  UPF3A WILD-TYPE  221  259
        clus
vv       UPF3A MUTATED UPF3A WILD-TYPE
  FEMALE             4             221
  MALE               5             259
[1] 2 2
[1] FALSE
D970V9, binary
                 cls
clus                0   1
  UPF3A MUTATED     8   0
  UPF3A WILD-TYPE 342  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UPF3A MUTATED      8    0
  UPF3A WILD-TYPE  342   22
     clus
vv    UPF3A MUTATED UPF3A WILD-TYPE
  NO              8             342
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  UPF3A MUTATED                      8                             1
  UPF3A WILD-TYPE                  307                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  UPF3A MUTATED                       0                              0
  UPF3A WILD-TYPE                   106                             10
D970V10, multiclass
                                clus
vv                               UPF3A MUTATED UPF3A WILD-TYPE
  COLON ADENOCARCINOMA                       8             307
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  UPF3A MUTATED     5   0   0   2
  UPF3A WILD-TYPE 340   4  31  23
D970V11, multiclass
    clus
vv   UPF3A MUTATED UPF3A WILD-TYPE
  R0             5             340
  R1             0               4
  R2             0              31
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D970V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  UPF3A MUTATED                                  0     2
  UPF3A WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  UPF3A MUTATED                           0     2
  UPF3A WILD-TYPE                        22   224
D970V13, multiclass
                                  clus
vv                                 UPF3A MUTATED UPF3A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               9
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        2             224
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(971) Variable = MDH1 MUTATION ANALYSIS
D971V1, survival
                sevent
clus2              0   1
  MDH1 MUTATED     6   2
  MDH1 WILD-TYPE 372  91
  MDH1 MUTATED MDH1 WILD-TYPE 
             8            463 
  MDH1 MUTATED MDH1 WILD-TYPE 
             2             91 
$`MDH1 MUTATED`
TCGA-AA-3845 TCGA-AY-5543 TCGA-AZ-4315 TCGA-AZ-4616 TCGA-CA-6717 TCGA-CM-5860 
        0.00        33.01        58.39         5.13        12.76        32.02 
TCGA-CM-6676 TCGA-D5-6532 
       11.08        18.25 

$`MDH1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4681 TCGA-AZ-4682 
        0.95        21.44        17.82         1.41       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07        12.20        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.03        22.98        30.08        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6677 TCGA-CM-6678 
       14.04        11.01        12.95        13.05        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       55.92        20.19         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  MDH1 MUTATED MDH1 WILD-TYPE 
             0              0 
  MDH1 MUTATED MDH1 WILD-TYPE 
         58.39         148.01 
  MDH1 MUTATED MDH1 WILD-TYPE 
        15.505         20.280 
[1] "0.0 - 58.4 (15.5)"  "0.0 - 148.0 (20.3)"
[1] "hr=" "1.5"
D971V2, continuous
D971V3, binary
                cls
clus               0   1
  MDH1 MUTATED     8   0
  MDH1 WILD-TYPE 358 119
[1] "tbl2"
                cls
clus             [,1] [,2]
  MDH1 MUTATED      8    0
  MDH1 WILD-TYPE  358  119
        clus
vv       MDH1 MUTATED MDH1 WILD-TYPE
  COLON             8            358
  RECTUM            0            119
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MDH1 MUTATED         1        0        0         5         0         0
  MDH1 WILD-TYPE      90        1       32       133        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MDH1 MUTATED           0          0          0          0        1         1
  MDH1 WILD-TYPE        24         11         59         42       47        17
                vv
clus             STAGE IVB
  MDH1 MUTATED           0
  MDH1 WILD-TYPE         1
D971V4, multiclass
            clus
vv           MDH1 MUTATED MDH1 WILD-TYPE
  STAGE I               1             90
  STAGE IA              0              1
  STAGE II              0             32
  STAGE IIA             5            133
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            0             59
  STAGE IIIC            0             42
  STAGE IV              1             47
  STAGE IVA             1             17
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  MDH1 MUTATED     0   1   7   0
  MDH1 WILD-TYPE  17  91 322  50
D971V5, multiclass
    clus
vv   MDH1 MUTATED MDH1 WILD-TYPE
  T1            0             17
  T2            1             91
  T3            7            322
  T4            0             50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  MDH1 MUTATED     6   1   1
  MDH1 WILD-TYPE 281 112  86
D971V6, multiclass
    clus
vv   MDH1 MUTATED MDH1 WILD-TYPE
  N0            6            281
  N1            1            112
  N2            1             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D971V7, binary
                cls
clus               0   1
  MDH1 MUTATED     6   2
  MDH1 WILD-TYPE 369  63
[1] "tbl2"
                cls
clus             [,1] [,2]
  MDH1 MUTATED      6    2
  MDH1 WILD-TYPE  369   63
   clus
vv  MDH1 MUTATED MDH1 WILD-TYPE
  0            6            369
  1            2             63
[1] 2 2
[1] FALSE
D971V8, binary
                cls
clus               0   1
  MDH1 MUTATED     3   5
  MDH1 WILD-TYPE 222 259
[1] "tbl2"
                cls
clus             [,1] [,2]
  MDH1 MUTATED      3    5
  MDH1 WILD-TYPE  222  259
        clus
vv       MDH1 MUTATED MDH1 WILD-TYPE
  FEMALE            3            222
  MALE              5            259
[1] 2 2
[1] FALSE
D971V9, binary
                cls
clus               0   1
  MDH1 MUTATED     7   0
  MDH1 WILD-TYPE 343  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  MDH1 MUTATED      7    0
  MDH1 WILD-TYPE  343   22
     clus
vv    MDH1 MUTATED MDH1 WILD-TYPE
  NO             7            343
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MDH1 MUTATED                      7                             1
  MDH1 WILD-TYPE                  308                            46
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MDH1 MUTATED                       0                              0
  MDH1 WILD-TYPE                   106                             10
D971V10, multiclass
                                clus
vv                               MDH1 MUTATED MDH1 WILD-TYPE
  COLON ADENOCARCINOMA                      7            308
  COLON MUCINOUS ADENOCARCINOMA             1             46
  RECTAL ADENOCARCINOMA                     0            106
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  MDH1 MUTATED     6   0   0   1
  MDH1 WILD-TYPE 339   4  31  24
D971V11, multiclass
    clus
vv   MDH1 MUTATED MDH1 WILD-TYPE
  R0            6            339
  R1            0              4
  R2            0             31
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D971V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MDH1 MUTATED                                  0     1
  MDH1 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  MDH1 MUTATED                           1     5
  MDH1 WILD-TYPE                        21   221
D971V13, multiclass
                                  clus
vv                                 MDH1 MUTATED MDH1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                       5            221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(972) Variable = MYH11 MUTATION ANALYSIS
D972V1, survival
                 sevent
clus2               0   1
  MYH11 MUTATED    28   6
  MYH11 WILD-TYPE 350  87
  MYH11 MUTATED MYH11 WILD-TYPE 
             34             437 
  MYH11 MUTATED MYH11 WILD-TYPE 
              6              87 
$`MYH11 MUTATED`
TCGA-A6-5665 TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3554 TCGA-AA-3715 TCGA-AA-3821 
       22.06        13.02         1.02        17.95        19.04         1.02 
TCGA-AA-3845 TCGA-AA-3864 TCGA-AA-3947 TCGA-AA-3966 TCGA-AA-3977 TCGA-AA-A00J 
        0.00        53.00        33.01         2.01        25.02        18.05 
TCGA-AA-A00R TCGA-AA-A01R TCGA-AA-A029 TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6901 
        0.99        35.01        51.98        40.96         0.07        22.42 
TCGA-AD-6964 TCGA-CK-5916 TCGA-CM-5860 TCGA-CM-6162 TCGA-CM-6171 TCGA-D5-6532 
       10.88        21.14        32.02        12.00        14.04        18.25 
TCGA-D5-6930 TCGA-G4-6307 TCGA-G4-6628 TCGA-AG-3892 TCGA-AG-4007 TCGA-AG-A002 
        1.51        55.04        79.69        13.02         1.02        20.98 
TCGA-AG-A02X TCGA-EI-6507 TCGA-EI-6508 TCGA-F5-6813 
       41.00        19.96        20.91         0.69 

$`MYH11 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3519 
       35.01        63.98         6.97         1.02        38.99         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       26.99        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
       25.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 
       32.05         0.99        31.07        31.07        30.05        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       12.99        24.00        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
       34.03        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00U 
       18.05        38.04         4.01        27.02        42.02        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S 
       12.00        31.00        31.00        38.07         1.02         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A02F 
       33.04        35.01        26.01        37.02        39.06        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
       18.05        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
        5.79        27.42         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       13.02        15.02        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6534 
       19.59        56.09        55.92        20.19         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 
        9.04         9.44        11.64         4.80        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 
      133.18        74.56        65.85        53.62        44.68        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       26.17        91.79        46.75        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 
       19.99         1.02        17.95        36.95        17.03        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       36.03        14.04        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       61.97        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
        0.49        20.55        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66        55.76        26.43 

  MYH11 MUTATED MYH11 WILD-TYPE 
              0               0 
  MYH11 MUTATED MYH11 WILD-TYPE 
          79.69          148.01 
  MYH11 MUTATED MYH11 WILD-TYPE 
         18.645          20.550 
[1] "0.0 - 79.7 (18.6)"  "0.0 - 148.0 (20.6)"
[1] "hr=" "1.1"
D972V2, continuous
D972V3, binary
                 cls
clus                0   1
  MYH11 MUTATED    28   7
  MYH11 WILD-TYPE 338 112
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYH11 MUTATED     28    7
  MYH11 WILD-TYPE  338  112
        clus
vv       MYH11 MUTATED MYH11 WILD-TYPE
  COLON             28             338
  RECTUM             7             112
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MYH11 MUTATED        10        0        3        10         1         0
  MYH11 WILD-TYPE      81        1       29       128         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MYH11 MUTATED           2          0          4          1        1         0
  MYH11 WILD-TYPE        22         11         55         41       47        18
                 vv
clus              STAGE IVB
  MYH11 MUTATED           0
  MYH11 WILD-TYPE         1
D972V4, multiclass
            clus
vv           MYH11 MUTATED MYH11 WILD-TYPE
  STAGE I               10              81
  STAGE IA               0               1
  STAGE II               3              29
  STAGE IIA             10             128
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              2              22
  STAGE IIIA             0              11
  STAGE IIIB             4              55
  STAGE IIIC             1              41
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  MYH11 MUTATED     2   9  19   5
  MYH11 WILD-TYPE  15  83 310  45
D972V5, multiclass
    clus
vv   MYH11 MUTATED MYH11 WILD-TYPE
  T1             2              15
  T2             9              83
  T3            19             310
  T4             5              45
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  MYH11 MUTATED    26   4   5
  MYH11 WILD-TYPE 261 109  82
D972V6, multiclass
    clus
vv   MYH11 MUTATED MYH11 WILD-TYPE
  N0            26             261
  N1             4             109
  N2             5              82
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D972V7, binary
                 cls
clus                0   1
  MYH11 MUTATED    30   1
  MYH11 WILD-TYPE 345  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYH11 MUTATED     30    1
  MYH11 WILD-TYPE  345   64
   clus
vv  MYH11 MUTATED MYH11 WILD-TYPE
  0            30             345
  1             1              64
[1] 2 2
[1] FALSE
D972V8, binary
                 cls
clus                0   1
  MYH11 MUTATED    17  18
  MYH11 WILD-TYPE 208 246
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYH11 MUTATED     17   18
  MYH11 WILD-TYPE  208  246
        clus
vv       MYH11 MUTATED MYH11 WILD-TYPE
  FEMALE            17             208
  MALE              18             246
[1] 2 2
[1] FALSE
D972V9, binary
                 cls
clus                0   1
  MYH11 MUTATED    24   1
  MYH11 WILD-TYPE 326  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYH11 MUTATED     24    1
  MYH11 WILD-TYPE  326   21
     clus
vv    MYH11 MUTATED MYH11 WILD-TYPE
  NO             24             326
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MYH11 MUTATED                     19                             9
  MYH11 WILD-TYPE                  296                            38
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MYH11 MUTATED                       7                              0
  MYH11 WILD-TYPE                    99                             10
D972V10, multiclass
                                clus
vv                               MYH11 MUTATED MYH11 WILD-TYPE
  COLON ADENOCARCINOMA                      19             296
  COLON MUCINOUS ADENOCARCINOMA              9              38
  RECTAL ADENOCARCINOMA                      7              99
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  MYH11 MUTATED    28   0   1   1
  MYH11 WILD-TYPE 317   4  30  24
D972V11, multiclass
    clus
vv   MYH11 MUTATED MYH11 WILD-TYPE
  R0            28             317
  R1             0               4
  R2             1              30
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D972V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MYH11 MUTATED                                  0     0
  MYH11 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  MYH11 MUTATED                           0    15
  MYH11 WILD-TYPE                        22   211
D972V13, multiclass
                                  clus
vv                                 MYH11 MUTATED MYH11 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                       15             211
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(973) Variable = KLF11 MUTATION ANALYSIS
D973V1, survival
                 sevent
clus2               0   1
  KLF11 MUTATED     6   1
  KLF11 WILD-TYPE 372  92
  KLF11 MUTATED KLF11 WILD-TYPE 
              7             464 
  KLF11 MUTATED KLF11 WILD-TYPE 
              1              92 
$`KLF11 MUTATED`
TCGA-AA-3662 TCGA-AA-3877 TCGA-AZ-5403 TCGA-CA-6717 TCGA-CM-5861 TCGA-D5-5539 
        6.05        31.00        62.79        12.76        15.02        19.59 
TCGA-AG-A00Y 
       23.01 

$`KLF11 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 
       17.03        24.03        27.02        29.98        18.05         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
      106.75        22.36        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 
       29.06        22.03        22.98        30.08        32.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  KLF11 MUTATED KLF11 WILD-TYPE 
           6.05            0.00 
  KLF11 MUTATED KLF11 WILD-TYPE 
          62.79          148.01 
  KLF11 MUTATED KLF11 WILD-TYPE 
         19.590          20.235 
[1] "6.0 - 62.8 (19.6)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.4"
D973V2, continuous
D973V3, binary
                 cls
clus                0   1
  KLF11 MUTATED     7   1
  KLF11 WILD-TYPE 359 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLF11 MUTATED      7    1
  KLF11 WILD-TYPE  359  118
        clus
vv       KLF11 MUTATED KLF11 WILD-TYPE
  COLON              7             359
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KLF11 MUTATED         1        0        1         3         1         0
  KLF11 WILD-TYPE      90        1       31       135         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  KLF11 MUTATED           0          1          0          0        1         0
  KLF11 WILD-TYPE        24         10         59         42       47        18
                 vv
clus              STAGE IVB
  KLF11 MUTATED           0
  KLF11 WILD-TYPE         1
D973V4, multiclass
            clus
vv           KLF11 MUTATED KLF11 WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              3             135
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             1              10
  STAGE IIIB             0              59
  STAGE IIIC             0              42
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  KLF11 MUTATED     1   0   5   2
  KLF11 WILD-TYPE  16  92 324  48
D973V5, multiclass
    clus
vv   KLF11 MUTATED KLF11 WILD-TYPE
  T1             1              16
  T2             0              92
  T3             5             324
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  KLF11 MUTATED     6   1   1
  KLF11 WILD-TYPE 281 112  86
D973V6, multiclass
    clus
vv   KLF11 MUTATED KLF11 WILD-TYPE
  N0             6             281
  N1             1             112
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D973V7, binary
                 cls
clus                0   1
  KLF11 MUTATED     5   1
  KLF11 WILD-TYPE 370  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLF11 MUTATED      5    1
  KLF11 WILD-TYPE  370   64
   clus
vv  KLF11 MUTATED KLF11 WILD-TYPE
  0             5             370
  1             1              64
[1] 2 2
[1] FALSE
D973V8, binary
                 cls
clus                0   1
  KLF11 MUTATED     4   4
  KLF11 WILD-TYPE 221 260
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLF11 MUTATED      4    4
  KLF11 WILD-TYPE  221  260
        clus
vv       KLF11 MUTATED KLF11 WILD-TYPE
  FEMALE             4             221
  MALE               4             260
[1] 2 2
[1] FALSE
D973V9, binary
                 cls
clus                0   1
  KLF11 MUTATED     7   0
  KLF11 WILD-TYPE 343  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLF11 MUTATED      7    0
  KLF11 WILD-TYPE  343   22
     clus
vv    KLF11 MUTATED KLF11 WILD-TYPE
  NO              7             343
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  KLF11 MUTATED                      4                             3
  KLF11 WILD-TYPE                  311                            44
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  KLF11 MUTATED                       1                              0
  KLF11 WILD-TYPE                   105                             10
D973V10, multiclass
                                clus
vv                               KLF11 MUTATED KLF11 WILD-TYPE
  COLON ADENOCARCINOMA                       4             311
  COLON MUCINOUS ADENOCARCINOMA              3              44
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  KLF11 MUTATED     4   0   1   2
  KLF11 WILD-TYPE 341   4  30  23
D973V11, multiclass
    clus
vv   KLF11 MUTATED KLF11 WILD-TYPE
  R0             4             341
  R1             0               4
  R2             1              30
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D973V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KLF11 MUTATED                                  0     1
  KLF11 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  KLF11 MUTATED                           0     4
  KLF11 WILD-TYPE                        22   222
D973V13, multiclass
                                  clus
vv                                 KLF11 MUTATED KLF11 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        4             222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(974) Variable = MED12L MUTATION ANALYSIS
D974V1, survival
                  sevent
clus2                0   1
  MED12L MUTATED    27   3
  MED12L WILD-TYPE 351  90
  MED12L MUTATED MED12L WILD-TYPE 
              30              441 
  MED12L MUTATED MED12L WILD-TYPE 
               3               90 
$`MED12L MUTATED`
TCGA-A6-4105 TCGA-A6-5659 TCGA-AA-3496 TCGA-AA-3510 TCGA-AA-3531 TCGA-AA-3543 
       14.53        30.44         1.02        63.98        34.03         0.99 
TCGA-AA-3555 TCGA-AA-3713 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3977 TCGA-AA-3986 
       29.95        19.04        26.01        24.00        25.02        19.07 
TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01Q TCGA-AD-5900 TCGA-AD-6895 TCGA-AY-5543 
        4.01        34.98         1.02         0.07         0.72        33.01 
TCGA-AZ-4315 TCGA-AZ-4681 TCGA-AZ-6598 TCGA-CA-6717 TCGA-CK-5913 TCGA-D5-6920 
       58.39       106.75        49.41        12.76        51.32         3.68 
TCGA-D5-6928 TCGA-F4-6807 TCGA-G4-6586 TCGA-AF-2687 TCGA-AG-A002 TCGA-EF-5830 
       11.64        16.24        35.80        24.13        20.98         0.49 

$`MED12L WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 
       16.57        34.65        33.34        32.75        36.53        32.91 
TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       31.63        29.19        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3511 
       19.66        20.28         7.04         3.02        35.01         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 
       29.00        29.00        26.01        12.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 
       21.01        13.02        24.00        17.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       12.99        24.00        33.01         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       26.01        24.00        27.02        27.02         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        31.00        38.07        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       18.05        40.96        21.37        15.52        56.55         0.79 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
       27.09        16.31         0.95        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 
        5.13        22.36        62.79        88.21         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       49.08         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       16.14        15.58         1.48         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.04         9.44         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 
       63.62        61.91        36.00        22.09        13.78        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       91.79        46.75        79.69        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       51.48        32.61        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  MED12L MUTATED MED12L WILD-TYPE 
            0.07             0.00 
  MED12L MUTATED MED12L WILD-TYPE 
          106.75           148.01 
  MED12L MUTATED MED12L WILD-TYPE 
           22.49            20.12 
[1] "0.1 - 106.8 (22.5)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.9"
D974V2, continuous
D974V3, binary
                  cls
clus                 0   1
  MED12L MUTATED    28   3
  MED12L WILD-TYPE 338 116
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MED12L MUTATED     28    3
  MED12L WILD-TYPE  338  116
        clus
vv       MED12L MUTATED MED12L WILD-TYPE
  COLON              28              338
  RECTUM              3              116
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MED12L MUTATED         5        0        4        12         3         0
  MED12L WILD-TYPE      86        1       28       126         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MED12L MUTATED           0          0          1          2        1
  MED12L WILD-TYPE        24         11         58         40       47
                  vv
clus               STAGE IVA STAGE IVB
  MED12L MUTATED           1         0
  MED12L WILD-TYPE        17         1
D974V4, multiclass
            clus
vv           MED12L MUTATED MED12L WILD-TYPE
  STAGE I                 5               86
  STAGE IA                0                1
  STAGE II                4               28
  STAGE IIA              12              126
  STAGE IIB               3                7
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              1               58
  STAGE IIIC              2               40
  STAGE IV                1               47
  STAGE IVA               1               17
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  MED12L MUTATED     0   6  22   3
  MED12L WILD-TYPE  17  86 307  47
D974V5, multiclass
    clus
vv   MED12L MUTATED MED12L WILD-TYPE
  T1              0               17
  T2              6               86
  T3             22              307
  T4              3               47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  MED12L MUTATED    26   3   2
  MED12L WILD-TYPE 261 110  85
D974V6, multiclass
    clus
vv   MED12L MUTATED MED12L WILD-TYPE
  N0             26              261
  N1              3              110
  N2              2               85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D974V7, binary
                  cls
clus                 0   1
  MED12L MUTATED    24   2
  MED12L WILD-TYPE 351  63
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MED12L MUTATED     24    2
  MED12L WILD-TYPE  351   63
   clus
vv  MED12L MUTATED MED12L WILD-TYPE
  0             24              351
  1              2               63
[1] 2 2
[1] FALSE
D974V8, binary
                  cls
clus                 0   1
  MED12L MUTATED    15  16
  MED12L WILD-TYPE 210 248
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MED12L MUTATED     15   16
  MED12L WILD-TYPE  210  248
        clus
vv       MED12L MUTATED MED12L WILD-TYPE
  FEMALE             15              210
  MALE               16              248
[1] 2 2
[1] FALSE
D974V9, binary
                  cls
clus                 0   1
  MED12L MUTATED    21   2
  MED12L WILD-TYPE 329  20
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MED12L MUTATED     21    2
  MED12L WILD-TYPE  329   20
     clus
vv    MED12L MUTATED MED12L WILD-TYPE
  NO              21              329
  YES              2               20
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MED12L MUTATED                     20                             8
  MED12L WILD-TYPE                  295                            39
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MED12L MUTATED                       3                              0
  MED12L WILD-TYPE                   103                             10
D974V10, multiclass
                                clus
vv                               MED12L MUTATED MED12L WILD-TYPE
  COLON ADENOCARCINOMA                       20              295
  COLON MUCINOUS ADENOCARCINOMA               8               39
  RECTAL ADENOCARCINOMA                       3              103
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  MED12L MUTATED    24   0   1   2
  MED12L WILD-TYPE 321   4  30  23
D974V11, multiclass
    clus
vv   MED12L MUTATED MED12L WILD-TYPE
  R0             24              321
  R1              0                4
  R2              1               30
  RX              2               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D974V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MED12L MUTATED                                  0     1
  MED12L WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  MED12L MUTATED                           1    14
  MED12L WILD-TYPE                        21   212
D974V13, multiclass
                                  clus
vv                                 MED12L MUTATED MED12L WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                        14              212
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(975) Variable = ZNF620 MUTATION ANALYSIS
D975V1, survival
                  sevent
clus2                0   1
  ZNF620 MUTATED     8   1
  ZNF620 WILD-TYPE 370  92
  ZNF620 MUTATED ZNF620 WILD-TYPE 
               9              462 
  ZNF620 MUTATED ZNF620 WILD-TYPE 
               1               92 
$`ZNF620 MUTATED`
TCGA-AA-3554 TCGA-AA-3655 TCGA-AA-A00J TCGA-AA-A02Y TCGA-AY-6197 TCGA-AZ-6600 
       17.95        61.02        18.05        39.98        21.44        12.10 
TCGA-CA-6717 TCGA-DM-A1HB TCGA-AG-3892 
       12.76       135.65        13.02 

$`ZNF620 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       21.01        13.02        24.00        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       19.99        13.94        19.99        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       19.00        30.02        34.03        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A03F 
        2.01         5.03        14.01         0.92        41.00        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 
       14.50        27.09        16.31         0.95        33.01        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       88.21        49.41         6.77       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07        12.20        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      131.51       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  ZNF620 MUTATED ZNF620 WILD-TYPE 
            12.1              0.0 
  ZNF620 MUTATED ZNF620 WILD-TYPE 
          135.65           148.01 
  ZNF620 MUTATED ZNF620 WILD-TYPE 
          18.050           20.235 
[1] "12.1 - 135.7 (18.1)" "0.0 - 148.0 (20.2)" 
[1] "hr=" "2.4"
D975V2, continuous
D975V3, binary
                  cls
clus                 0   1
  ZNF620 MUTATED     8   1
  ZNF620 WILD-TYPE 358 118
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF620 MUTATED      8    1
  ZNF620 WILD-TYPE  358  118
        clus
vv       ZNF620 MUTATED ZNF620 WILD-TYPE
  COLON               8              358
  RECTUM              1              118
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZNF620 MUTATED         2        0        1         3         0         0
  ZNF620 WILD-TYPE      89        1       31       135        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF620 MUTATED           0          0          2          0        1
  ZNF620 WILD-TYPE        24         11         57         42       47
                  vv
clus               STAGE IVA STAGE IVB
  ZNF620 MUTATED           0         0
  ZNF620 WILD-TYPE        18         1
D975V4, multiclass
            clus
vv           ZNF620 MUTATED ZNF620 WILD-TYPE
  STAGE I                 2               89
  STAGE IA                0                1
  STAGE II                1               31
  STAGE IIA               3              135
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              2               57
  STAGE IIIC              0               42
  STAGE IV                1               47
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZNF620 MUTATED     1   1   5   2
  ZNF620 WILD-TYPE  16  91 324  48
D975V5, multiclass
    clus
vv   ZNF620 MUTATED ZNF620 WILD-TYPE
  T1              1               16
  T2              1               91
  T3              5              324
  T4              2               48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  ZNF620 MUTATED     6   3   0
  ZNF620 WILD-TYPE 281 110  87
D975V6, multiclass
    clus
vv   ZNF620 MUTATED ZNF620 WILD-TYPE
  N0              6              281
  N1              3              110
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D975V7, binary
                  cls
clus                 0   1
  ZNF620 MUTATED     7   1
  ZNF620 WILD-TYPE 368  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF620 MUTATED      7    1
  ZNF620 WILD-TYPE  368   64
   clus
vv  ZNF620 MUTATED ZNF620 WILD-TYPE
  0              7              368
  1              1               64
[1] 2 2
[1] FALSE
D975V8, binary
                  cls
clus                 0   1
  ZNF620 MUTATED     2   7
  ZNF620 WILD-TYPE 223 257
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF620 MUTATED      2    7
  ZNF620 WILD-TYPE  223  257
        clus
vv       ZNF620 MUTATED ZNF620 WILD-TYPE
  FEMALE              2              223
  MALE                7              257
[1] 2 2
[1] FALSE
D975V9, binary
                  cls
clus                 0   1
  ZNF620 MUTATED     7   0
  ZNF620 WILD-TYPE 343  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF620 MUTATED      7    0
  ZNF620 WILD-TYPE  343   22
     clus
vv    ZNF620 MUTATED ZNF620 WILD-TYPE
  NO               7              343
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ZNF620 MUTATED                      5                             2
  ZNF620 WILD-TYPE                  310                            45
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ZNF620 MUTATED                       1                              0
  ZNF620 WILD-TYPE                   105                             10
D975V10, multiclass
                                clus
vv                               ZNF620 MUTATED ZNF620 WILD-TYPE
  COLON ADENOCARCINOMA                        5              310
  COLON MUCINOUS ADENOCARCINOMA               2               45
  RECTAL ADENOCARCINOMA                       1              105
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ZNF620 MUTATED     6   0   0   1
  ZNF620 WILD-TYPE 339   4  31  24
D975V11, multiclass
    clus
vv   ZNF620 MUTATED ZNF620 WILD-TYPE
  R0              6              339
  R1              0                4
  R2              0               31
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D975V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF620 MUTATED                                  0     1
  ZNF620 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZNF620 MUTATED                           1     2
  ZNF620 WILD-TYPE                        21   224
D975V13, multiclass
                                  clus
vv                                 ZNF620 MUTATED ZNF620 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                         2              224
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(976) Variable = UGT1A7 MUTATION ANALYSIS
D976V1, survival
                  sevent
clus2                0   1
  UGT1A7 MUTATED     6   2
  UGT1A7 WILD-TYPE 372  91
  UGT1A7 MUTATED UGT1A7 WILD-TYPE 
               8              463 
  UGT1A7 MUTATED UGT1A7 WILD-TYPE 
               2               91 
$`UGT1A7 MUTATED`
TCGA-AA-A00N TCGA-AA-A010 TCGA-AZ-4315 TCGA-AZ-5407 TCGA-CA-6715 TCGA-D5-6540 
        4.01        34.98        58.39        88.21         0.07        16.14 
TCGA-D5-6930 TCGA-DM-A1D8 
        1.51        12.59 

$`UGT1A7 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       33.01        21.44        17.82         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.06         3.25         3.29        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 
        9.04         9.44        11.64         4.80        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       49.91        13.32       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  UGT1A7 MUTATED UGT1A7 WILD-TYPE 
            0.07             0.00 
  UGT1A7 MUTATED UGT1A7 WILD-TYPE 
           88.21           148.01 
  UGT1A7 MUTATED UGT1A7 WILD-TYPE 
          14.365           20.280 
[1] "0.1 - 88.2 (14.4)"  "0.0 - 148.0 (20.3)"
[1] "hr=" "1.2"
D976V2, continuous
D976V3, binary
                  cls
clus                 0   1
  UGT1A7 MUTATED     8   0
  UGT1A7 WILD-TYPE 358 119
[1] "tbl2"
                  cls
clus               [,1] [,2]
  UGT1A7 MUTATED      8    0
  UGT1A7 WILD-TYPE  358  119
        clus
vv       UGT1A7 MUTATED UGT1A7 WILD-TYPE
  COLON               8              358
  RECTUM              0              119
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  UGT1A7 MUTATED         2        0        0         2         2         0
  UGT1A7 WILD-TYPE      89        1       32       136         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  UGT1A7 MUTATED           0          0          1          0        0
  UGT1A7 WILD-TYPE        24         11         58         42       48
                  vv
clus               STAGE IVA STAGE IVB
  UGT1A7 MUTATED           0         0
  UGT1A7 WILD-TYPE        18         1
D976V4, multiclass
            clus
vv           UGT1A7 MUTATED UGT1A7 WILD-TYPE
  STAGE I                 2               89
  STAGE IA                0                1
  STAGE II                0               32
  STAGE IIA               2              136
  STAGE IIB               2                8
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              1               58
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  UGT1A7 MUTATED     1   1   4   2
  UGT1A7 WILD-TYPE  16  91 325  48
D976V5, multiclass
    clus
vv   UGT1A7 MUTATED UGT1A7 WILD-TYPE
  T1              1               16
  T2              1               91
  T3              4              325
  T4              2               48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  UGT1A7 MUTATED     6   2   0
  UGT1A7 WILD-TYPE 281 111  87
D976V6, multiclass
    clus
vv   UGT1A7 MUTATED UGT1A7 WILD-TYPE
  N0              6              281
  N1              2              111
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D976V7, binary
                  cls
clus                 0   1
  UGT1A7 MUTATED     7   0
  UGT1A7 WILD-TYPE 368  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  UGT1A7 MUTATED      7    0
  UGT1A7 WILD-TYPE  368   65
   clus
vv  UGT1A7 MUTATED UGT1A7 WILD-TYPE
  0              7              368
  1              0               65
[1] 2 2
[1] FALSE
D976V8, binary
                  cls
clus                 0   1
  UGT1A7 MUTATED     3   5
  UGT1A7 WILD-TYPE 222 259
[1] "tbl2"
                  cls
clus               [,1] [,2]
  UGT1A7 MUTATED      3    5
  UGT1A7 WILD-TYPE  222  259
        clus
vv       UGT1A7 MUTATED UGT1A7 WILD-TYPE
  FEMALE              3              222
  MALE                5              259
[1] 2 2
[1] FALSE
D976V9, binary
                  cls
clus                 0   1
  UGT1A7 MUTATED     4   0
  UGT1A7 WILD-TYPE 346  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  UGT1A7 MUTATED      4    0
  UGT1A7 WILD-TYPE  346   22
     clus
vv    UGT1A7 MUTATED UGT1A7 WILD-TYPE
  NO               4              346
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  UGT1A7 MUTATED                      5                             3
  UGT1A7 WILD-TYPE                  310                            44
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  UGT1A7 MUTATED                       0                              0
  UGT1A7 WILD-TYPE                   106                             10
D976V10, multiclass
                                clus
vv                               UGT1A7 MUTATED UGT1A7 WILD-TYPE
  COLON ADENOCARCINOMA                        5              310
  COLON MUCINOUS ADENOCARCINOMA               3               44
  RECTAL ADENOCARCINOMA                       0              106
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  UGT1A7 MUTATED     5   0   0   1
  UGT1A7 WILD-TYPE 340   4  31  24
D976V11, multiclass
    clus
vv   UGT1A7 MUTATED UGT1A7 WILD-TYPE
  R0              5              340
  R1              0                4
  R2              0               31
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D976V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  UGT1A7 MUTATED                                  0     1
  UGT1A7 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  UGT1A7 MUTATED                           0     5
  UGT1A7 WILD-TYPE                        22   221
D976V13, multiclass
                                  clus
vv                                 UGT1A7 MUTATED UGT1A7 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         5              221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(977) Variable = UST MUTATION ANALYSIS
D977V1, survival
               sevent
clus2             0   1
  UST MUTATED    10   1
  UST WILD-TYPE 368  92
  UST MUTATED UST WILD-TYPE 
           11           460 
  UST MUTATED UST WILD-TYPE 
            1            92 
$`UST MUTATED`
TCGA-A6-6141 TCGA-AA-3510 TCGA-AA-3955 TCGA-AD-5900 TCGA-AZ-6600 TCGA-D5-5539 
        8.38        63.98        20.98         0.07        12.10        19.59 
TCGA-D5-6535 TCGA-DM-A1HB TCGA-G4-6317 TCGA-F5-6465 TCGA-F5-6571 
       15.12       135.65        36.00        49.51        31.30 

$`UST WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 
       22.09        22.06        32.71        27.09        22.52        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       18.05        40.96        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        88.21        49.41         6.77       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      131.51       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       63.62        61.91        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6702 TCGA-F5-6811 
       19.96        20.91        18.28         9.96        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  UST MUTATED UST WILD-TYPE 
         0.07          0.00 
  UST MUTATED UST WILD-TYPE 
       135.65        148.01 
  UST MUTATED UST WILD-TYPE 
       20.980        20.155 
[1] "0.1 - 135.7 (21.0)" "0.0 - 148.0 (20.2)"
[1] "hr=" "2.8"
D977V2, continuous
D977V3, binary
               cls
clus              0   1
  UST MUTATED     9   2
  UST WILD-TYPE 357 117
[1] "tbl2"
               cls
clus            [,1] [,2]
  UST MUTATED      9    2
  UST WILD-TYPE  357  117
        clus
vv       UST MUTATED UST WILD-TYPE
  COLON            9           357
  RECTUM           2           117
[1] 2 2
[1] FALSE
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  UST MUTATED         1        0        1         3         0         0
  UST WILD-TYPE      90        1       31       135        10         1
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  UST MUTATED           0          1          3          1        1         0
  UST WILD-TYPE        24         10         56         41       47        18
               vv
clus            STAGE IVB
  UST MUTATED           0
  UST WILD-TYPE         1
D977V4, multiclass
            clus
vv           UST MUTATED UST WILD-TYPE
  STAGE I              1            90
  STAGE IA             0             1
  STAGE II             1            31
  STAGE IIA            3           135
  STAGE IIB            0            10
  STAGE IIC            0             1
  STAGE III            0            24
  STAGE IIIA           1            10
  STAGE IIIB           3            56
  STAGE IIIC           1            41
  STAGE IV             1            47
  STAGE IVA            0            18
  STAGE IVB            0             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  UST MUTATED     0   2   8   1
  UST WILD-TYPE  17  90 321  49
D977V5, multiclass
    clus
vv   UST MUTATED UST WILD-TYPE
  T1           0            17
  T2           2            90
  T3           8           321
  T4           1            49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2
  UST MUTATED     5   4   2
  UST WILD-TYPE 282 109  85
D977V6, multiclass
    clus
vv   UST MUTATED UST WILD-TYPE
  N0           5           282
  N1           4           109
  N2           2            85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D977V7, binary
               cls
clus              0   1
  UST MUTATED     7   1
  UST WILD-TYPE 368  64
[1] "tbl2"
               cls
clus            [,1] [,2]
  UST MUTATED      7    1
  UST WILD-TYPE  368   64
   clus
vv  UST MUTATED UST WILD-TYPE
  0           7           368
  1           1            64
[1] 2 2
[1] FALSE
D977V8, binary
               cls
clus              0   1
  UST MUTATED     4   7
  UST WILD-TYPE 221 257
[1] "tbl2"
               cls
clus            [,1] [,2]
  UST MUTATED      4    7
  UST WILD-TYPE  221  257
        clus
vv       UST MUTATED UST WILD-TYPE
  FEMALE           4           221
  MALE             7           257
[1] 2 2
[1] FALSE
D977V9, binary
               cls
clus              0   1
  UST MUTATED     8   0
  UST WILD-TYPE 342  22
[1] "tbl2"
               cls
clus            [,1] [,2]
  UST MUTATED      8    0
  UST WILD-TYPE  342   22
     clus
vv    UST MUTATED UST WILD-TYPE
  NO            8           342
  YES           0            22
[1] 2 2
[1] FALSE
               vv
clus            COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  UST MUTATED                      6                             2
  UST WILD-TYPE                  309                            45
               vv
clus            RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  UST MUTATED                       2                              0
  UST WILD-TYPE                   104                             10
D977V10, multiclass
                                clus
vv                               UST MUTATED UST WILD-TYPE
  COLON ADENOCARCINOMA                     6           309
  COLON MUCINOUS ADENOCARCINOMA            2            45
  RECTAL ADENOCARCINOMA                    2           104
  RECTAL MUCINOUS ADENOCARCINOMA           0            10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             R0  R1  R2  RX
  UST MUTATED     7   0   0   1
  UST WILD-TYPE 338   4  31  24
D977V11, multiclass
    clus
vv   UST MUTATED UST WILD-TYPE
  R0           7           338
  R1           0             4
  R2           0            31
  RX           1            24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D977V12, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  UST MUTATED                                  0     0
  UST WILD-TYPE                                1    11
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  UST MUTATED                           2     7
  UST WILD-TYPE                        20   219
D977V13, multiclass
                                  clus
vv                                 UST MUTATED UST WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      0            11
  BLACK OR AFRICAN AMERICAN                  2            20
  WHITE                                      7           219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(978) Variable = NDUFAF1 MUTATION ANALYSIS
D978V1, survival
                   sevent
clus2                 0   1
  NDUFAF1 MUTATED     6   1
  NDUFAF1 WILD-TYPE 372  92
  NDUFAF1 MUTATED NDUFAF1 WILD-TYPE 
                7               464 
  NDUFAF1 MUTATED NDUFAF1 WILD-TYPE 
                1                92 
$`NDUFAF1 MUTATED`
TCGA-A6-6781 TCGA-AA-3713 TCGA-AY-6386 TCGA-D5-6537 TCGA-DM-A28H TCGA-G4-6310 
       19.66        19.04        17.82         4.80       117.07        63.62 
TCGA-G4-6588 
       26.17 

$`NDUFAF1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       33.01        21.44        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6538 
       18.25         1.32        43.27        15.12        17.85        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28K 
        6.12        81.37       119.93        35.97        60.79        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       44.68        55.04        85.48        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       13.78        35.80        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  NDUFAF1 MUTATED NDUFAF1 WILD-TYPE 
              4.8               0.0 
  NDUFAF1 MUTATED NDUFAF1 WILD-TYPE 
           117.07            148.01 
  NDUFAF1 MUTATED NDUFAF1 WILD-TYPE 
           19.660            20.235 
[1] "4.8 - 117.1 (19.7)" "0.0 - 148.0 (20.2)"
[1] "hr=" "2"  
D978V2, continuous
D978V3, binary
                   cls
clus                  0   1
  NDUFAF1 MUTATED     7   0
  NDUFAF1 WILD-TYPE 359 119
[1] "tbl2"
                   cls
clus                [,1] [,2]
  NDUFAF1 MUTATED      7    0
  NDUFAF1 WILD-TYPE  359  119
        clus
vv       NDUFAF1 MUTATED NDUFAF1 WILD-TYPE
  COLON                7               359
  RECTUM               0               119
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NDUFAF1 MUTATED         0        0        0         1         0         0
  NDUFAF1 WILD-TYPE      91        1       32       137        10         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NDUFAF1 MUTATED           0          0          3          2        1
  NDUFAF1 WILD-TYPE        24         11         56         40       47
                   vv
clus                STAGE IVA STAGE IVB
  NDUFAF1 MUTATED           0         0
  NDUFAF1 WILD-TYPE        18         1
D978V4, multiclass
            clus
vv           NDUFAF1 MUTATED NDUFAF1 WILD-TYPE
  STAGE I                  0                91
  STAGE IA                 0                 1
  STAGE II                 0                32
  STAGE IIA                1               137
  STAGE IIB                0                10
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               0                11
  STAGE IIIB               3                56
  STAGE IIIC               2                40
  STAGE IV                 1                47
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  NDUFAF1 MUTATED     0   0   6   1
  NDUFAF1 WILD-TYPE  17  92 323  49
D978V5, multiclass
    clus
vv   NDUFAF1 MUTATED NDUFAF1 WILD-TYPE
  T1               0                17
  T2               0                92
  T3               6               323
  T4               1                49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  NDUFAF1 MUTATED     2   4   1
  NDUFAF1 WILD-TYPE 285 109  86
D978V6, multiclass
    clus
vv   NDUFAF1 MUTATED NDUFAF1 WILD-TYPE
  N0               2               285
  N1               4               109
  N2               1                86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D978V7, binary
                   cls
clus                  0   1
  NDUFAF1 MUTATED     4   1
  NDUFAF1 WILD-TYPE 371  64
[1] "tbl2"
                   cls
clus                [,1] [,2]
  NDUFAF1 MUTATED      4    1
  NDUFAF1 WILD-TYPE  371   64
   clus
vv  NDUFAF1 MUTATED NDUFAF1 WILD-TYPE
  0               4               371
  1               1                64
[1] 2 2
[1] FALSE
D978V8, binary
                   cls
clus                  0   1
  NDUFAF1 MUTATED     2   5
  NDUFAF1 WILD-TYPE 223 259
[1] "tbl2"
                   cls
clus                [,1] [,2]
  NDUFAF1 MUTATED      2    5
  NDUFAF1 WILD-TYPE  223  259
        clus
vv       NDUFAF1 MUTATED NDUFAF1 WILD-TYPE
  FEMALE               2               223
  MALE                 5               259
[1] 2 2
[1] FALSE
D978V9, binary
                   cls
clus                  0   1
  NDUFAF1 MUTATED     4   2
  NDUFAF1 WILD-TYPE 346  20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  NDUFAF1 MUTATED      4    2
  NDUFAF1 WILD-TYPE  346   20
     clus
vv    NDUFAF1 MUTATED NDUFAF1 WILD-TYPE
  NO                4               346
  YES               2                20
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  NDUFAF1 MUTATED                      6                             1
  NDUFAF1 WILD-TYPE                  309                            46
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  NDUFAF1 MUTATED                       0                              0
  NDUFAF1 WILD-TYPE                   106                             10
D978V10, multiclass
                                clus
vv                               NDUFAF1 MUTATED NDUFAF1 WILD-TYPE
  COLON ADENOCARCINOMA                         6               309
  COLON MUCINOUS ADENOCARCINOMA                1                46
  RECTAL ADENOCARCINOMA                        0               106
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  NDUFAF1 MUTATED     5   0   1   0
  NDUFAF1 WILD-TYPE 340   4  30  25
D978V11, multiclass
    clus
vv   NDUFAF1 MUTATED NDUFAF1 WILD-TYPE
  R0               5               340
  R1               0                 4
  R2               1                30
  RX               0                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D978V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NDUFAF1 MUTATED                                  0     0
  NDUFAF1 WILD-TYPE                                1    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  NDUFAF1 MUTATED                           1     5
  NDUFAF1 WILD-TYPE                        21   221
D978V13, multiclass
                                  clus
vv                                 NDUFAF1 MUTATED NDUFAF1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                      1                21
  WHITE                                          5               221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(979) Variable = ENPP1 MUTATION ANALYSIS
D979V1, survival
                 sevent
clus2               0   1
  ENPP1 MUTATED    10   4
  ENPP1 WILD-TYPE 368  89
  ENPP1 MUTATED ENPP1 WILD-TYPE 
             14             457 
  ENPP1 MUTATED ENPP1 WILD-TYPE 
              4              89 
$`ENPP1 MUTATED`
TCGA-AA-3848 TCGA-AA-A00N TCGA-AZ-4315 TCGA-AZ-6601 TCGA-CA-5254 TCGA-CA-6717 
       10.06         4.01        58.39       100.01        12.69        12.76 
TCGA-CM-5861 TCGA-CM-6172 TCGA-D5-5541 TCGA-D5-6538 TCGA-F4-6570 TCGA-G4-6306 
       15.02        11.01        55.92        17.13         6.18        44.68 
TCGA-G4-6588 TCGA-AG-A002 
       26.17        20.98 

$`ENPP1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
        0.00        17.03         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       33.01        21.44        17.82         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5255 
       29.56         5.23        11.74         3.19         1.61         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07        12.20        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       22.98        30.08        32.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-6529 
       12.03        45.40        12.26        19.59        56.09        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 
       98.24         8.61        31.96        35.74        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       13.78        35.80        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  ENPP1 MUTATED ENPP1 WILD-TYPE 
           4.01            0.00 
  ENPP1 MUTATED ENPP1 WILD-TYPE 
         100.01          148.01 
  ENPP1 MUTATED ENPP1 WILD-TYPE 
         16.075          20.280 
[1] "4.0 - 100.0 (16.1)" "0.0 - 148.0 (20.3)"
[1] "hr=" "1.3"
D979V2, continuous
D979V3, binary
                 cls
clus                0   1
  ENPP1 MUTATED    14   1
  ENPP1 WILD-TYPE 352 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ENPP1 MUTATED     14    1
  ENPP1 WILD-TYPE  352  118
        clus
vv       ENPP1 MUTATED ENPP1 WILD-TYPE
  COLON             14             352
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ENPP1 MUTATED         1        0        1         8         1         0
  ENPP1 WILD-TYPE      90        1       31       130         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ENPP1 MUTATED           0          0          3          1        0         0
  ENPP1 WILD-TYPE        24         11         56         41       48        18
                 vv
clus              STAGE IVB
  ENPP1 MUTATED           0
  ENPP1 WILD-TYPE         1
D979V4, multiclass
            clus
vv           ENPP1 MUTATED ENPP1 WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              8             130
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             3              56
  STAGE IIIC             1              41
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ENPP1 MUTATED     0   2  12   1
  ENPP1 WILD-TYPE  17  90 317  49
D979V5, multiclass
    clus
vv   ENPP1 MUTATED ENPP1 WILD-TYPE
  T1             0              17
  T2             2              90
  T3            12             317
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  ENPP1 MUTATED    11   2   2
  ENPP1 WILD-TYPE 276 111  85
D979V6, multiclass
    clus
vv   ENPP1 MUTATED ENPP1 WILD-TYPE
  N0            11             276
  N1             2             111
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D979V7, binary
                 cls
clus                0   1
  ENPP1 MUTATED    15   0
  ENPP1 WILD-TYPE 360  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ENPP1 MUTATED     15    0
  ENPP1 WILD-TYPE  360   65
   clus
vv  ENPP1 MUTATED ENPP1 WILD-TYPE
  0            15             360
  1             0              65
[1] 2 2
[1] FALSE
D979V8, binary
                 cls
clus                0   1
  ENPP1 MUTATED     8   7
  ENPP1 WILD-TYPE 217 257
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ENPP1 MUTATED      8    7
  ENPP1 WILD-TYPE  217  257
        clus
vv       ENPP1 MUTATED ENPP1 WILD-TYPE
  FEMALE             8             217
  MALE               7             257
[1] 2 2
[1] FALSE
D979V9, binary
                 cls
clus                0   1
  ENPP1 MUTATED    13   0
  ENPP1 WILD-TYPE 337  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ENPP1 MUTATED     13    0
  ENPP1 WILD-TYPE  337   22
     clus
vv    ENPP1 MUTATED ENPP1 WILD-TYPE
  NO             13             337
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ENPP1 MUTATED                     12                             2
  ENPP1 WILD-TYPE                  303                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ENPP1 MUTATED                       1                              0
  ENPP1 WILD-TYPE                   105                             10
D979V10, multiclass
                                clus
vv                               ENPP1 MUTATED ENPP1 WILD-TYPE
  COLON ADENOCARCINOMA                      12             303
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  ENPP1 MUTATED    12   0   0   2
  ENPP1 WILD-TYPE 333   4  31  23
D979V11, multiclass
    clus
vv   ENPP1 MUTATED ENPP1 WILD-TYPE
  R0            12             333
  R1             0               4
  R2             0              31
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D979V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ENPP1 MUTATED                                  0     2
  ENPP1 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ENPP1 MUTATED                           0     9
  ENPP1 WILD-TYPE                        22   217
D979V13, multiclass
                                  clus
vv                                 ENPP1 MUTATED ENPP1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               9
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        9             217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(980) Variable = CASP4 MUTATION ANALYSIS
D980V1, survival
                 sevent
clus2               0   1
  CASP4 MUTATED     8   2
  CASP4 WILD-TYPE 370  91
  CASP4 MUTATED CASP4 WILD-TYPE 
             10             461 
  CASP4 MUTATED CASP4 WILD-TYPE 
              2              91 
$`CASP4 MUTATED`
TCGA-AA-3972 TCGA-AY-6197 TCGA-AZ-6603 TCGA-CA-6717 TCGA-CK-4952 TCGA-CM-6675 
       50.99        21.44        29.56        12.76        15.62        13.05 
TCGA-D5-5538 TCGA-D5-6529 TCGA-AG-A002 TCGA-DY-A1H8 
       12.26        20.19        20.98        32.61 

$`CASP4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       16.08        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        33.01        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
       12.10       100.01         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 
       10.06        14.30        17.56       148.01        85.45        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6676 TCGA-CM-6677 
       15.02        14.04        11.01        12.95        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5539 TCGA-D5-5540 
       11.01        10.06        12.03        45.40        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       55.92        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       57.24        24.13        51.48         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  CASP4 MUTATED CASP4 WILD-TYPE 
          12.26            0.00 
  CASP4 MUTATED CASP4 WILD-TYPE 
          50.99          148.01 
  CASP4 MUTATED CASP4 WILD-TYPE 
         20.585          20.120 
[1] "12.3 - 51.0 (20.6)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.1"
D980V2, continuous
D980V3, binary
                 cls
clus                0   1
  CASP4 MUTATED     8   2
  CASP4 WILD-TYPE 358 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASP4 MUTATED      8    2
  CASP4 WILD-TYPE  358  117
        clus
vv       CASP4 MUTATED CASP4 WILD-TYPE
  COLON              8             358
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CASP4 MUTATED         1        0        0         3         0         0
  CASP4 WILD-TYPE      90        1       32       135        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CASP4 MUTATED           0          1          1          1        1         0
  CASP4 WILD-TYPE        24         10         58         41       47        18
                 vv
clus              STAGE IVB
  CASP4 MUTATED           1
  CASP4 WILD-TYPE         0
D980V4, multiclass
            clus
vv           CASP4 MUTATED CASP4 WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              3             135
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             1              10
  STAGE IIIB             1              58
  STAGE IIIC             1              41
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              1               0
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CASP4 MUTATED     0   3   6   1
  CASP4 WILD-TYPE  17  89 323  49
D980V5, multiclass
    clus
vv   CASP4 MUTATED CASP4 WILD-TYPE
  T1             0              17
  T2             3              89
  T3             6             323
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  CASP4 MUTATED     4   4   2
  CASP4 WILD-TYPE 283 109  85
D980V6, multiclass
    clus
vv   CASP4 MUTATED CASP4 WILD-TYPE
  N0             4             283
  N1             4             109
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D980V7, binary
                 cls
clus                0   1
  CASP4 MUTATED     6   2
  CASP4 WILD-TYPE 369  63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASP4 MUTATED      6    2
  CASP4 WILD-TYPE  369   63
   clus
vv  CASP4 MUTATED CASP4 WILD-TYPE
  0             6             369
  1             2              63
[1] 2 2
[1] FALSE
D980V8, binary
                 cls
clus                0   1
  CASP4 MUTATED     4   6
  CASP4 WILD-TYPE 221 258
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASP4 MUTATED      4    6
  CASP4 WILD-TYPE  221  258
        clus
vv       CASP4 MUTATED CASP4 WILD-TYPE
  FEMALE             4             221
  MALE               6             258
[1] 2 2
[1] FALSE
D980V9, binary
                 cls
clus                0   1
  CASP4 MUTATED     8   0
  CASP4 WILD-TYPE 342  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASP4 MUTATED      8    0
  CASP4 WILD-TYPE  342   22
     clus
vv    CASP4 MUTATED CASP4 WILD-TYPE
  NO              8             342
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CASP4 MUTATED                      6                             2
  CASP4 WILD-TYPE                  309                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CASP4 MUTATED                       2                              0
  CASP4 WILD-TYPE                   104                             10
D980V10, multiclass
                                clus
vv                               CASP4 MUTATED CASP4 WILD-TYPE
  COLON ADENOCARCINOMA                       6             309
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  CASP4 MUTATED     5   0   1   2
  CASP4 WILD-TYPE 340   4  30  23
D980V11, multiclass
    clus
vv   CASP4 MUTATED CASP4 WILD-TYPE
  R0             5             340
  R1             0               4
  R2             1              30
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D980V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CASP4 MUTATED                                  0     1
  CASP4 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CASP4 MUTATED                           1     6
  CASP4 WILD-TYPE                        21   220
D980V13, multiclass
                                  clus
vv                                 CASP4 MUTATED CASP4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        6             220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(981) Variable = STK36 MUTATION ANALYSIS
D981V1, survival
                 sevent
clus2               0   1
  STK36 MUTATED    15   2
  STK36 WILD-TYPE 363  91
  STK36 MUTATED STK36 WILD-TYPE 
             17             454 
  STK36 MUTATED STK36 WILD-TYPE 
              2              91 
$`STK36 MUTATED`
TCGA-A6-5657 TCGA-AA-3966 TCGA-AA-A00E TCGA-AD-5900 TCGA-AY-6386 TCGA-AZ-4315 
       31.63         2.01        30.02         0.07        17.82        58.39 
TCGA-AZ-6600 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-5913 TCGA-CM-5348 TCGA-CM-5349 
       12.10        12.76        10.06        51.32        22.98        30.08 
TCGA-DM-A1HB TCGA-G4-6323 TCGA-DC-6157 TCGA-DC-6681 TCGA-F5-6811 
      135.65        13.78        27.95         5.95        32.19 

$`STK36 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
        2.01        20.98        34.03        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       19.00        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       18.05        40.96        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       49.41         6.77       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.07        12.20        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        49.08         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       29.06        22.03        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
       44.32       131.51       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6586 
       85.48        63.62        61.91        36.00        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6158 TCGA-DC-6160 
        7.17        15.02         5.03        13.97        10.98        19.99 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  STK36 MUTATED STK36 WILD-TYPE 
           0.07            0.00 
  STK36 MUTATED STK36 WILD-TYPE 
         135.65          148.01 
  STK36 MUTATED STK36 WILD-TYPE 
         22.980          20.155 
[1] "0.1 - 135.7 (23.0)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.8"
D981V2, continuous
D981V3, binary
                 cls
clus                0   1
  STK36 MUTATED    14   4
  STK36 WILD-TYPE 352 115
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STK36 MUTATED     14    4
  STK36 WILD-TYPE  352  115
        clus
vv       STK36 MUTATED STK36 WILD-TYPE
  COLON             14             352
  RECTUM             4             115
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  STK36 MUTATED         2        1        0         8         0         0
  STK36 WILD-TYPE      89        0       32       130        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  STK36 MUTATED           0          0          4          1        1         1
  STK36 WILD-TYPE        24         11         55         41       47        17
                 vv
clus              STAGE IVB
  STK36 MUTATED           0
  STK36 WILD-TYPE         1
D981V4, multiclass
            clus
vv           STK36 MUTATED STK36 WILD-TYPE
  STAGE I                2              89
  STAGE IA               1               0
  STAGE II               0              32
  STAGE IIA              8             130
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             4              55
  STAGE IIIC             1              41
  STAGE IV               1              47
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  STK36 MUTATED     0   2  14   1
  STK36 WILD-TYPE  17  90 315  49
D981V5, multiclass
    clus
vv   STK36 MUTATED STK36 WILD-TYPE
  T1             0              17
  T2             2              90
  T3            14             315
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  STK36 MUTATED    11   5   2
  STK36 WILD-TYPE 276 108  85
D981V6, multiclass
    clus
vv   STK36 MUTATED STK36 WILD-TYPE
  N0            11             276
  N1             5             108
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D981V7, binary
                 cls
clus                0   1
  STK36 MUTATED    13   2
  STK36 WILD-TYPE 362  63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STK36 MUTATED     13    2
  STK36 WILD-TYPE  362   63
   clus
vv  STK36 MUTATED STK36 WILD-TYPE
  0            13             362
  1             2              63
[1] 2 2
[1] FALSE
D981V8, binary
                 cls
clus                0   1
  STK36 MUTATED     7  11
  STK36 WILD-TYPE 218 253
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STK36 MUTATED      7   11
  STK36 WILD-TYPE  218  253
        clus
vv       STK36 MUTATED STK36 WILD-TYPE
  FEMALE             7             218
  MALE              11             253
[1] 2 2
[1] FALSE
D981V9, binary
                 cls
clus                0   1
  STK36 MUTATED    11   0
  STK36 WILD-TYPE 339  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STK36 MUTATED     11    0
  STK36 WILD-TYPE  339   22
     clus
vv    STK36 MUTATED STK36 WILD-TYPE
  NO             11             339
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  STK36 MUTATED                     10                             3
  STK36 WILD-TYPE                  305                            44
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  STK36 MUTATED                       4                              0
  STK36 WILD-TYPE                   102                             10
D981V10, multiclass
                                clus
vv                               STK36 MUTATED STK36 WILD-TYPE
  COLON ADENOCARCINOMA                      10             305
  COLON MUCINOUS ADENOCARCINOMA              3              44
  RECTAL ADENOCARCINOMA                      4             102
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  STK36 MUTATED    11   0   0   3
  STK36 WILD-TYPE 334   4  31  22
D981V11, multiclass
    clus
vv   STK36 MUTATED STK36 WILD-TYPE
  R0            11             334
  R1             0               4
  R2             0              31
  RX             3              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D981V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  STK36 MUTATED                                  0     2
  STK36 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  STK36 MUTATED                           5     8
  STK36 WILD-TYPE                        17   218
D981V13, multiclass
                                  clus
vv                                 STK36 MUTATED STK36 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               9
  BLACK OR AFRICAN AMERICAN                    5              17
  WHITE                                        8             218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(982) Variable = KRT19 MUTATION ANALYSIS
D982V1, survival
                 sevent
clus2               0   1
  KRT19 MUTATED     3   1
  KRT19 WILD-TYPE 375  92
  KRT19 MUTATED KRT19 WILD-TYPE 
              4             467 
  KRT19 MUTATED KRT19 WILD-TYPE 
              1              92 
$`KRT19 MUTATED`
TCGA-AA-3672 TCGA-AA-A010 TCGA-AZ-6598 TCGA-CM-4743 
        0.92        34.98        49.41        23.05 

$`KRT19 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
        6.05         6.97        54.02         2.01        14.01        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 
      106.75        22.36        62.79        88.21         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
        1.91       124.27        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  KRT19 MUTATED KRT19 WILD-TYPE 
           0.92            0.00 
  KRT19 MUTATED KRT19 WILD-TYPE 
          49.41          148.01 
  KRT19 MUTATED KRT19 WILD-TYPE 
         29.015          20.120 
[1] "0.9 - 49.4 (29.0)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.2"
D982V2, continuous
D982V3, binary
                 cls
clus                0   1
  KRT19 MUTATED     4   0
  KRT19 WILD-TYPE 362 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KRT19 MUTATED      4    0
  KRT19 WILD-TYPE  362  119
        clus
vv       KRT19 MUTATED KRT19 WILD-TYPE
  COLON              4             362
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KRT19 MUTATED         0        0        1         1         1         0
  KRT19 WILD-TYPE      91        1       31       137         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  KRT19 MUTATED           1          0          0          0        0         0
  KRT19 WILD-TYPE        23         11         59         42       48        18
                 vv
clus              STAGE IVB
  KRT19 MUTATED           0
  KRT19 WILD-TYPE         1
D982V4, multiclass
            clus
vv           KRT19 MUTATED KRT19 WILD-TYPE
  STAGE I                0              91
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              1             137
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  KRT19 MUTATED     0   0   3   1
  KRT19 WILD-TYPE  17  92 326  49
D982V5, multiclass
    clus
vv   KRT19 MUTATED KRT19 WILD-TYPE
  T1             0              17
  T2             0              92
  T3             3             326
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  KRT19 MUTATED     3   1   0
  KRT19 WILD-TYPE 284 112  87
D982V6, multiclass
    clus
vv   KRT19 MUTATED KRT19 WILD-TYPE
  N0             3             284
  N1             1             112
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D982V7, binary
                 cls
clus                0   1
  KRT19 MUTATED     3   0
  KRT19 WILD-TYPE 372  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KRT19 MUTATED      3    0
  KRT19 WILD-TYPE  372   65
   clus
vv  KRT19 MUTATED KRT19 WILD-TYPE
  0             3             372
  1             0              65
[1] 2 2
[1] FALSE
D982V8, binary
                 cls
clus                0   1
  KRT19 MUTATED     3   1
  KRT19 WILD-TYPE 222 263
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KRT19 MUTATED      3    1
  KRT19 WILD-TYPE  222  263
        clus
vv       KRT19 MUTATED KRT19 WILD-TYPE
  FEMALE             3             222
  MALE               1             263
[1] 2 2
[1] FALSE
D982V9, binary
                 cls
clus                0   1
  KRT19 MUTATED     4   0
  KRT19 WILD-TYPE 346  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KRT19 MUTATED      4    0
  KRT19 WILD-TYPE  346   22
     clus
vv    KRT19 MUTATED KRT19 WILD-TYPE
  NO              4             346
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  KRT19 MUTATED                      4                             0
  KRT19 WILD-TYPE                  311                            47
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  KRT19 MUTATED                       0                              0
  KRT19 WILD-TYPE                   106                             10
D982V10, multiclass
                                clus
vv                               KRT19 MUTATED KRT19 WILD-TYPE
  COLON ADENOCARCINOMA                       4             311
  COLON MUCINOUS ADENOCARCINOMA              0              47
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  KRT19 MUTATED     3   0   0   0
  KRT19 WILD-TYPE 342   4  31  25
D982V11, multiclass
    clus
vv   KRT19 MUTATED KRT19 WILD-TYPE
  R0             3             342
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D982V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KRT19 MUTATED                                  0     0
  KRT19 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  KRT19 MUTATED                           0     2
  KRT19 WILD-TYPE                        22   224
D982V13, multiclass
[1] "Remove cluster labels:" "KRT19 MUTATED"         
clus
  KRT19 MUTATED KRT19 WILD-TYPE 
              2             258 
     TCGA-A6-2671      TCGA-A6-2672      TCGA-A6-2674      TCGA-A6-2676 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-A6-2677      TCGA-A6-2678      TCGA-A6-2683      TCGA-A6-3807 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-A6-3808      TCGA-A6-3809      TCGA-A6-3810      TCGA-A6-4105 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-A6-5656      TCGA-A6-5657      TCGA-A6-5659      TCGA-A6-5660 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-A6-5661      TCGA-A6-5662      TCGA-A6-5664      TCGA-A6-5665 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-A6-5666      TCGA-A6-6137      TCGA-A6-6138      TCGA-A6-6141 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-A6-6142      TCGA-A6-6648      TCGA-A6-6649      TCGA-A6-6651 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-A6-6652      TCGA-A6-6653      TCGA-A6-6654      TCGA-A6-6780 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-A6-6781      TCGA-A6-6782      TCGA-AD-5900      TCGA-AD-6548 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-AD-6888      TCGA-AD-6889      TCGA-AD-6890      TCGA-AD-6895 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-AD-6899      TCGA-AD-6901      TCGA-AD-6963      TCGA-AD-6964 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-AD-6965      TCGA-AU-3779      TCGA-AU-6004      TCGA-AY-4070 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-AY-4071      TCGA-AY-5543      TCGA-AY-6196      TCGA-AY-6197 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-AY-6386      TCGA-AZ-4315      TCGA-AZ-4323      TCGA-AZ-4616 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-AZ-4681      TCGA-AZ-4682      TCGA-AZ-5403      TCGA-AZ-5407 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-AZ-6599      TCGA-AZ-6600      TCGA-AZ-6601      TCGA-AZ-6603 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-AZ-6605      TCGA-AZ-6606      TCGA-AZ-6607      TCGA-AZ-6608 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-CA-5254      TCGA-CA-5255      TCGA-CA-5796      TCGA-CA-5797 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-CA-6715      TCGA-CA-6716      TCGA-CA-6717      TCGA-CA-6718 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-CA-6719      TCGA-CK-4947      TCGA-CK-4948      TCGA-CK-4950 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-CK-4952      TCGA-CK-5912      TCGA-CK-5913      TCGA-CK-5914 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-CK-5915      TCGA-CK-5916      TCGA-CK-6746      TCGA-CK-6747 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-CK-6748      TCGA-CK-6751      TCGA-CM-4744      TCGA-CM-4746 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-CM-4747      TCGA-CM-4752      TCGA-CM-5341      TCGA-CM-5344 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-CM-5348      TCGA-CM-5349      TCGA-CM-5860      TCGA-CM-5861 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-CM-5862      TCGA-CM-5863      TCGA-CM-5864      TCGA-CM-5868 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-CM-6161      TCGA-CM-6162      TCGA-CM-6163      TCGA-CM-6164 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-CM-6165      TCGA-CM-6166      TCGA-CM-6167      TCGA-CM-6168 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-CM-6169      TCGA-CM-6170      TCGA-CM-6171      TCGA-CM-6172 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-CM-6674      TCGA-CM-6675      TCGA-CM-6676      TCGA-CM-6677 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-CM-6678      TCGA-CM-6679      TCGA-CM-6680      TCGA-D5-5537 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-D5-5538      TCGA-D5-5539      TCGA-D5-5540      TCGA-D5-5541 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-D5-6529      TCGA-D5-6532      TCGA-D5-6533      TCGA-D5-6534 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-D5-6535      TCGA-D5-6536      TCGA-D5-6537      TCGA-D5-6538 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-D5-6539      TCGA-D5-6540      TCGA-D5-6541      TCGA-D5-6898 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-D5-6920      TCGA-D5-6922      TCGA-D5-6923      TCGA-D5-6924 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-D5-6926      TCGA-D5-6927      TCGA-D5-6928      TCGA-D5-6929 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-D5-6930      TCGA-D5-6931      TCGA-D5-6932      TCGA-D5-7000 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-DM-A0X9      TCGA-DM-A0XD      TCGA-DM-A0XF      TCGA-DM-A1D0 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-DM-A1D4      TCGA-DM-A1D6      TCGA-DM-A1D7      TCGA-DM-A1D8 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-DM-A1D9      TCGA-DM-A1DA      TCGA-DM-A1DB      TCGA-DM-A1HA 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-DM-A1HB      TCGA-DM-A282      TCGA-DM-A285      TCGA-DM-A28C 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-DM-A28E      TCGA-DM-A28F      TCGA-DM-A28G      TCGA-DM-A28H 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-DM-A28K      TCGA-F4-6459      TCGA-F4-6460      TCGA-F4-6569 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-F4-6570      TCGA-F4-6703      TCGA-F4-6704      TCGA-F4-6805 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-F4-6806      TCGA-F4-6807      TCGA-F4-6808      TCGA-F4-6809 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-F4-6854      TCGA-F4-6855      TCGA-F4-6856      TCGA-G4-6293 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-G4-6299      TCGA-G4-6303      TCGA-G4-6304      TCGA-G4-6306 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-G4-6307      TCGA-G4-6309      TCGA-G4-6310      TCGA-G4-6315 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-G4-6317      TCGA-G4-6321      TCGA-G4-6323      TCGA-G4-6586 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-G4-6588      TCGA-G4-6625      TCGA-G4-6626      TCGA-G4-6628 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-AF-2687      TCGA-AF-2689      TCGA-AF-2691      TCGA-AF-2692 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-AF-2693      TCGA-AF-3400      TCGA-AF-3913      TCGA-AF-4110 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-AF-5654      TCGA-AF-6136      TCGA-AF-6655      TCGA-AF-6672 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-AH-6544      TCGA-AH-6547      TCGA-AH-6549      TCGA-AH-6643 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-AH-6644      TCGA-CI-6619      TCGA-CI-6620      TCGA-CI-6621 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-CI-6622      TCGA-CI-6624      TCGA-CL-5917      TCGA-CL-5918 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-DC-5337      TCGA-DC-5869      TCGA-DC-6155      TCGA-DC-6157 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-DC-6158      TCGA-DC-6160      TCGA-DC-6681      TCGA-DC-6682 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-DC-6683      TCGA-DT-5265      TCGA-DY-A0XA      TCGA-DY-A1DC 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-DY-A1DD      TCGA-DY-A1DF      TCGA-DY-A1DG      TCGA-DY-A1H8 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-EF-5830      TCGA-EI-6506      TCGA-EI-6507      TCGA-EI-6508 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-EI-6510      TCGA-F5-6464      TCGA-F5-6465      TCGA-F5-6571 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-F5-6702      TCGA-F5-6811      TCGA-F5-6812      TCGA-F5-6813 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 
     TCGA-G5-6235      TCGA-G5-6641 
"KRT19 WILD-TYPE" "KRT19 WILD-TYPE" 

Clustering(983) Variable = KIF16B MUTATION ANALYSIS
D983V1, survival
                  sevent
clus2                0   1
  KIF16B MUTATED    24   4
  KIF16B WILD-TYPE 354  89
  KIF16B MUTATED KIF16B WILD-TYPE 
              28              443 
  KIF16B MUTATED KIF16B WILD-TYPE 
               4               89 
$`KIF16B MUTATED`
TCGA-A6-6653 TCGA-AA-3663 TCGA-AA-3815 TCGA-AA-3864 TCGA-AA-3949 TCGA-AA-3950 
       24.39         6.97        33.04        53.00        26.01        24.00 
TCGA-AA-3966 TCGA-AA-3977 TCGA-AA-A00E TCGA-AA-A00N TCGA-AD-6548 TCGA-AY-6386 
        2.01        25.02        30.02         4.01        21.37        17.82 
TCGA-AZ-4315 TCGA-CA-5797 TCGA-CA-6717 TCGA-CK-5913 TCGA-CK-5914 TCGA-CM-5861 
       58.39         3.29        12.76        51.32         9.99        15.02 
TCGA-CM-5864 TCGA-D5-6537 TCGA-D5-6923 TCGA-D5-6930 TCGA-F4-6570 TCGA-AF-6672 
       15.02         4.80        12.43         1.51         6.18        10.39 
TCGA-AG-3892 TCGA-AG-A002 TCGA-AG-A02N TCGA-DY-A1DD 
       13.02        20.98        61.97        57.24 

$`KIF16B WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
       25.08        25.18        24.16        21.76        24.69        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       35.05         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        31.07        30.05        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 
       33.01         2.01        20.98        34.03        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       19.00        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
       40.96         0.07        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AZ-4323 
       27.09        16.31         0.95        33.01        21.44         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-6715 
        3.19         1.61        12.69         3.06         3.25         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.20        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       15.62        49.08        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 
       22.03        22.98        30.08        32.02         5.03        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
       17.85        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        3.68         4.41        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        4.80        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 
       98.24         8.61        31.96        35.74        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       36.95        17.03        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 
       10.98        49.97         1.94        38.96        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  KIF16B MUTATED KIF16B WILD-TYPE 
            1.51             0.00 
  KIF16B MUTATED KIF16B WILD-TYPE 
           61.97           148.01 
  KIF16B MUTATED KIF16B WILD-TYPE 
           16.42            20.28 
[1] "1.5 - 62.0 (16.4)"  "0.0 - 148.0 (20.3)"
[1] "hr=" "1.3"
D983V2, continuous
D983V3, binary
                  cls
clus                 0   1
  KIF16B MUTATED    26   5
  KIF16B WILD-TYPE 340 114
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KIF16B MUTATED     26    5
  KIF16B WILD-TYPE  340  114
        clus
vv       KIF16B MUTATED KIF16B WILD-TYPE
  COLON              26              340
  RECTUM              5              114
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KIF16B MUTATED         7        0        4        11         1         0
  KIF16B WILD-TYPE      84        1       28       127         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIF16B MUTATED           0          0          5          1        1
  KIF16B WILD-TYPE        24         11         54         41       47
                  vv
clus               STAGE IVA STAGE IVB
  KIF16B MUTATED           0         0
  KIF16B WILD-TYPE        18         1
D983V4, multiclass
            clus
vv           KIF16B MUTATED KIF16B WILD-TYPE
  STAGE I                 7               84
  STAGE IA                0                1
  STAGE II                4               28
  STAGE IIA              11              127
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              5               54
  STAGE IIIC              1               41
  STAGE IV                1               47
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  KIF16B MUTATED     1   7  20   3
  KIF16B WILD-TYPE  16  85 309  47
D983V5, multiclass
    clus
vv   KIF16B MUTATED KIF16B WILD-TYPE
  T1              1               16
  T2              7               85
  T3             20              309
  T4              3               47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  KIF16B MUTATED    24   5   2
  KIF16B WILD-TYPE 263 108  85
D983V6, multiclass
    clus
vv   KIF16B MUTATED KIF16B WILD-TYPE
  N0             24              263
  N1              5              108
  N2              2               85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D983V7, binary
                  cls
clus                 0   1
  KIF16B MUTATED    24   0
  KIF16B WILD-TYPE 351  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KIF16B MUTATED     24    0
  KIF16B WILD-TYPE  351   65
   clus
vv  KIF16B MUTATED KIF16B WILD-TYPE
  0             24              351
  1              0               65
[1] 2 2
[1] FALSE
D983V8, binary
                  cls
clus                 0   1
  KIF16B MUTATED    12  19
  KIF16B WILD-TYPE 213 245
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KIF16B MUTATED     12   19
  KIF16B WILD-TYPE  213  245
        clus
vv       KIF16B MUTATED KIF16B WILD-TYPE
  FEMALE             12              213
  MALE               19              245
[1] 2 2
[1] FALSE
D983V9, binary
                  cls
clus                 0   1
  KIF16B MUTATED    21   1
  KIF16B WILD-TYPE 329  21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KIF16B MUTATED     21    1
  KIF16B WILD-TYPE  329   21
     clus
vv    KIF16B MUTATED KIF16B WILD-TYPE
  NO              21              329
  YES              1               21
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  KIF16B MUTATED                     19                             7
  KIF16B WILD-TYPE                  296                            40
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  KIF16B MUTATED                       5                              0
  KIF16B WILD-TYPE                   101                             10
D983V10, multiclass
                                clus
vv                               KIF16B MUTATED KIF16B WILD-TYPE
  COLON ADENOCARCINOMA                       19              296
  COLON MUCINOUS ADENOCARCINOMA               7               40
  RECTAL ADENOCARCINOMA                       5              101
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  KIF16B MUTATED    22   0   0   4
  KIF16B WILD-TYPE 323   4  31  21
D983V11, multiclass
    clus
vv   KIF16B MUTATED KIF16B WILD-TYPE
  R0             22              323
  R1              0                4
  R2              0               31
  RX              4               21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D983V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KIF16B MUTATED                                  0     2
  KIF16B WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  KIF16B MUTATED                           1    15
  KIF16B WILD-TYPE                        21   211
D983V13, multiclass
                                  clus
vv                                 KIF16B MUTATED KIF16B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                9
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                        15              211
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(984) Variable = ZHX1 MUTATION ANALYSIS
D984V1, survival
                sevent
clus2              0   1
  ZHX1 MUTATED     7   4
  ZHX1 WILD-TYPE 371  89
  ZHX1 MUTATED ZHX1 WILD-TYPE 
            11            460 
  ZHX1 MUTATED ZHX1 WILD-TYPE 
             4             89 
$`ZHX1 MUTATED`
TCGA-AA-3510 TCGA-AA-A010 TCGA-AD-5900 TCGA-AZ-6598 TCGA-CA-6717 TCGA-CM-6678 
       63.98        34.98         0.07        49.41        12.76        11.01 
TCGA-D5-6929 TCGA-F4-6460 TCGA-G4-6626 TCGA-AG-A002 TCGA-DY-A1DF 
        4.80        31.96        46.75        20.98        24.13 

$`ZHX1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       39.98        18.05        40.96        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        88.21         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07        12.20        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.08        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.04         9.44        11.64         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6569 
       35.97        60.79       117.07        98.24         8.61        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       26.17        91.79        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  ZHX1 MUTATED ZHX1 WILD-TYPE 
          0.07           0.00 
  ZHX1 MUTATED ZHX1 WILD-TYPE 
         63.98         148.01 
  ZHX1 MUTATED ZHX1 WILD-TYPE 
        24.130         20.085 
[1] "0.1 - 64.0 (24.1)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.7"
D984V2, continuous
D984V3, binary
                cls
clus               0   1
  ZHX1 MUTATED     9   2
  ZHX1 WILD-TYPE 357 117
[1] "tbl2"
                cls
clus             [,1] [,2]
  ZHX1 MUTATED      9    2
  ZHX1 WILD-TYPE  357  117
        clus
vv       ZHX1 MUTATED ZHX1 WILD-TYPE
  COLON             9            357
  RECTUM            2            117
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZHX1 MUTATED         2        0        2         2         1         0
  ZHX1 WILD-TYPE      89        1       30       136         9         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ZHX1 MUTATED           0          0          1          1        1         1
  ZHX1 WILD-TYPE        24         11         58         41       47        17
                vv
clus             STAGE IVB
  ZHX1 MUTATED           0
  ZHX1 WILD-TYPE         1
D984V4, multiclass
            clus
vv           ZHX1 MUTATED ZHX1 WILD-TYPE
  STAGE I               2             89
  STAGE IA              0              1
  STAGE II              2             30
  STAGE IIA             2            136
  STAGE IIB             1              9
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            1             58
  STAGE IIIC            1             41
  STAGE IV              1             47
  STAGE IVA             1             17
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  ZHX1 MUTATED     0   2   7   2
  ZHX1 WILD-TYPE  17  90 322  48
D984V5, multiclass
    clus
vv   ZHX1 MUTATED ZHX1 WILD-TYPE
  T1            0             17
  T2            2             90
  T3            7            322
  T4            2             48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  ZHX1 MUTATED     7   3   1
  ZHX1 WILD-TYPE 280 110  86
D984V6, multiclass
    clus
vv   ZHX1 MUTATED ZHX1 WILD-TYPE
  N0            7            280
  N1            3            110
  N2            1             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D984V7, binary
                cls
clus               0   1
  ZHX1 MUTATED     7   2
  ZHX1 WILD-TYPE 368  63
[1] "tbl2"
                cls
clus             [,1] [,2]
  ZHX1 MUTATED      7    2
  ZHX1 WILD-TYPE  368   63
   clus
vv  ZHX1 MUTATED ZHX1 WILD-TYPE
  0            7            368
  1            2             63
[1] 2 2
[1] FALSE
D984V8, binary
                cls
clus               0   1
  ZHX1 MUTATED     6   5
  ZHX1 WILD-TYPE 219 259
[1] "tbl2"
                cls
clus             [,1] [,2]
  ZHX1 MUTATED      6    5
  ZHX1 WILD-TYPE  219  259
        clus
vv       ZHX1 MUTATED ZHX1 WILD-TYPE
  FEMALE            6            219
  MALE              5            259
[1] 2 2
[1] FALSE
D984V9, binary
                cls
clus               0   1
  ZHX1 MUTATED     8   0
  ZHX1 WILD-TYPE 342  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  ZHX1 MUTATED      8    0
  ZHX1 WILD-TYPE  342   22
     clus
vv    ZHX1 MUTATED ZHX1 WILD-TYPE
  NO             8            342
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ZHX1 MUTATED                      7                             2
  ZHX1 WILD-TYPE                  308                            45
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ZHX1 MUTATED                       2                              0
  ZHX1 WILD-TYPE                   104                             10
D984V10, multiclass
                                clus
vv                               ZHX1 MUTATED ZHX1 WILD-TYPE
  COLON ADENOCARCINOMA                      7            308
  COLON MUCINOUS ADENOCARCINOMA             2             45
  RECTAL ADENOCARCINOMA                     2            104
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  ZHX1 MUTATED     8   0   0   1
  ZHX1 WILD-TYPE 337   4  31  24
D984V11, multiclass
    clus
vv   ZHX1 MUTATED ZHX1 WILD-TYPE
  R0            8            337
  R1            0              4
  R2            0             31
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D984V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZHX1 MUTATED                                  0     1
  ZHX1 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  ZHX1 MUTATED                           0     7
  ZHX1 WILD-TYPE                        22   219
D984V13, multiclass
                                  clus
vv                                 ZHX1 MUTATED ZHX1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       7            219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(985) Variable = ZNF658 MUTATION ANALYSIS
D985V1, survival
                  sevent
clus2                0   1
  ZNF658 MUTATED     6   7
  ZNF658 WILD-TYPE 372  86
  ZNF658 MUTATED ZNF658 WILD-TYPE 
              13              458 
  ZNF658 MUTATED ZNF658 WILD-TYPE 
               7               86 
$`ZNF658 MUTATED`
TCGA-A6-2677 TCGA-AA-3662 TCGA-AA-3715 TCGA-AA-3977 TCGA-AA-A00N TCGA-AZ-6598 
       24.33         6.05        19.04        25.02         4.01        49.41 
TCGA-CK-5912 TCGA-CM-5860 TCGA-D5-6928 TCGA-AF-3913 TCGA-AG-3892 TCGA-AG-A002 
       49.08        32.02        11.64        10.39        13.02        20.98 
TCGA-DY-A1DG 
       51.48 

$`ZNF658 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        42.90        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       19.99        13.94        19.99        61.02        78.08         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       88.21         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 
       17.56       148.01        85.45        15.62        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       30.08        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       13.55        19.10        34.49        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 
        1.02        17.95        36.95        17.03        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1H8 
        5.29       126.44        41.36        57.24        24.13        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  ZNF658 MUTATED ZNF658 WILD-TYPE 
            4.01             0.00 
  ZNF658 MUTATED ZNF658 WILD-TYPE 
           51.48           148.01 
  ZNF658 MUTATED ZNF658 WILD-TYPE 
          20.980           20.155 
[1] "4.0 - 51.5 (21.0)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "2.9"
D985V2, continuous
D985V3, binary
                  cls
clus                 0   1
  ZNF658 MUTATED    10   4
  ZNF658 WILD-TYPE 356 115
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF658 MUTATED     10    4
  ZNF658 WILD-TYPE  356  115
        clus
vv       ZNF658 MUTATED ZNF658 WILD-TYPE
  COLON              10              356
  RECTUM              4              115
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZNF658 MUTATED         3        0        2         3         1         0
  ZNF658 WILD-TYPE      88        1       30       135         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF658 MUTATED           0          0          0          1        2
  ZNF658 WILD-TYPE        24         11         59         41       46
                  vv
clus               STAGE IVA STAGE IVB
  ZNF658 MUTATED           1         0
  ZNF658 WILD-TYPE        17         1
D985V4, multiclass
            clus
vv           ZNF658 MUTATED ZNF658 WILD-TYPE
  STAGE I                 3               88
  STAGE IA                0                1
  STAGE II                2               30
  STAGE IIA               3              135
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              0               59
  STAGE IIIC              1               41
  STAGE IV                2               46
  STAGE IVA               1               17
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZNF658 MUTATED     1   3   8   2
  ZNF658 WILD-TYPE  16  89 321  48
D985V5, multiclass
    clus
vv   ZNF658 MUTATED ZNF658 WILD-TYPE
  T1              1               16
  T2              3               89
  T3              8              321
  T4              2               48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  ZNF658 MUTATED    10   2   2
  ZNF658 WILD-TYPE 277 111  85
D985V6, multiclass
    clus
vv   ZNF658 MUTATED ZNF658 WILD-TYPE
  N0             10              277
  N1              2              111
  N2              2               85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D985V7, binary
                  cls
clus                 0   1
  ZNF658 MUTATED     8   3
  ZNF658 WILD-TYPE 367  62
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF658 MUTATED      8    3
  ZNF658 WILD-TYPE  367   62
   clus
vv  ZNF658 MUTATED ZNF658 WILD-TYPE
  0              8              367
  1              3               62
[1] 2 2
[1] FALSE
D985V8, binary
                  cls
clus                 0   1
  ZNF658 MUTATED     5   9
  ZNF658 WILD-TYPE 220 255
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF658 MUTATED      5    9
  ZNF658 WILD-TYPE  220  255
        clus
vv       ZNF658 MUTATED ZNF658 WILD-TYPE
  FEMALE              5              220
  MALE                9              255
[1] 2 2
[1] FALSE
D985V9, binary
                  cls
clus                 0   1
  ZNF658 MUTATED    11   0
  ZNF658 WILD-TYPE 339  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF658 MUTATED     11    0
  ZNF658 WILD-TYPE  339   22
     clus
vv    ZNF658 MUTATED ZNF658 WILD-TYPE
  NO              11              339
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ZNF658 MUTATED                      8                             2
  ZNF658 WILD-TYPE                  307                            45
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ZNF658 MUTATED                       4                              0
  ZNF658 WILD-TYPE                   102                             10
D985V10, multiclass
                                clus
vv                               ZNF658 MUTATED ZNF658 WILD-TYPE
  COLON ADENOCARCINOMA                        8              307
  COLON MUCINOUS ADENOCARCINOMA               2               45
  RECTAL ADENOCARCINOMA                       4              102
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ZNF658 MUTATED     9   0   1   1
  ZNF658 WILD-TYPE 336   4  30  24
D985V11, multiclass
    clus
vv   ZNF658 MUTATED ZNF658 WILD-TYPE
  R0              9              336
  R1              0                4
  R2              1               30
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D985V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF658 MUTATED                                  0     0
  ZNF658 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZNF658 MUTATED                           1     6
  ZNF658 WILD-TYPE                        21   220
D985V13, multiclass
                                  clus
vv                                 ZNF658 MUTATED ZNF658 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                         6              220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(986) Variable = GPR141 MUTATION ANALYSIS
D986V1, survival
                  sevent
clus2                0   1
  GPR141 MUTATED     8   3
  GPR141 WILD-TYPE 370  90
  GPR141 MUTATED GPR141 WILD-TYPE 
              11              460 
  GPR141 MUTATED GPR141 WILD-TYPE 
               3               90 
$`GPR141 MUTATED`
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3877 TCGA-AA-3947 TCGA-AZ-6601 TCGA-CA-6718 
       19.04        19.04        31.00        33.01       100.01        10.06 
TCGA-D5-5539 TCGA-D5-6930 TCGA-DM-A1HB TCGA-DM-A28E TCGA-G4-6306 
       19.59         1.51       135.65       119.93        44.68 

$`GPR141 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3811 
       19.00        36.00         5.03        85.05        26.99        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 
       24.03        27.02        29.98        18.05         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 
       62.79        88.21        49.41         6.77        12.10        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 
        3.25         3.29         0.07        12.20        12.76        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 
       11.01        10.06        12.03        45.40        12.26        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
        9.44        11.64         4.80        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
      139.17         6.12        81.37        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       53.62        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  GPR141 MUTATED GPR141 WILD-TYPE 
            1.51             0.00 
  GPR141 MUTATED GPR141 WILD-TYPE 
          135.65           148.01 
  GPR141 MUTATED GPR141 WILD-TYPE 
          31.000           20.155 
[1] "1.5 - 135.7 (31.0)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.2"
D986V2, continuous
D986V3, binary
                  cls
clus                 0   1
  GPR141 MUTATED    11   0
  GPR141 WILD-TYPE 355 119
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR141 MUTATED     11    0
  GPR141 WILD-TYPE  355  119
        clus
vv       GPR141 MUTATED GPR141 WILD-TYPE
  COLON              11              355
  RECTUM              0              119
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GPR141 MUTATED         1        0        2         4         1         0
  GPR141 WILD-TYPE      90        1       30       134         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GPR141 MUTATED           0          1          1          0        1
  GPR141 WILD-TYPE        24         10         58         42       47
                  vv
clus               STAGE IVA STAGE IVB
  GPR141 MUTATED           0         0
  GPR141 WILD-TYPE        18         1
D986V4, multiclass
            clus
vv           GPR141 MUTATED GPR141 WILD-TYPE
  STAGE I                 1               90
  STAGE IA                0                1
  STAGE II                2               30
  STAGE IIA               4              134
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              1               10
  STAGE IIIB              1               58
  STAGE IIIC              0               42
  STAGE IV                1               47
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  GPR141 MUTATED     1   1   8   1
  GPR141 WILD-TYPE  16  91 321  49
D986V5, multiclass
    clus
vv   GPR141 MUTATED GPR141 WILD-TYPE
  T1              1               16
  T2              1               91
  T3              8              321
  T4              1               49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  GPR141 MUTATED     9   2   0
  GPR141 WILD-TYPE 278 111  87
D986V6, multiclass
    clus
vv   GPR141 MUTATED GPR141 WILD-TYPE
  N0              9              278
  N1              2              111
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D986V7, binary
                  cls
clus                 0   1
  GPR141 MUTATED    10   1
  GPR141 WILD-TYPE 365  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR141 MUTATED     10    1
  GPR141 WILD-TYPE  365   64
   clus
vv  GPR141 MUTATED GPR141 WILD-TYPE
  0             10              365
  1              1               64
[1] 2 2
[1] FALSE
D986V8, binary
                  cls
clus                 0   1
  GPR141 MUTATED     3   8
  GPR141 WILD-TYPE 222 256
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR141 MUTATED      3    8
  GPR141 WILD-TYPE  222  256
        clus
vv       GPR141 MUTATED GPR141 WILD-TYPE
  FEMALE              3              222
  MALE                8              256
[1] 2 2
[1] FALSE
D986V9, binary
                  cls
clus                 0   1
  GPR141 MUTATED     7   1
  GPR141 WILD-TYPE 343  21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR141 MUTATED      7    1
  GPR141 WILD-TYPE  343   21
     clus
vv    GPR141 MUTATED GPR141 WILD-TYPE
  NO               7              343
  YES              1               21
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  GPR141 MUTATED                      6                             4
  GPR141 WILD-TYPE                  309                            43
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  GPR141 MUTATED                       0                              0
  GPR141 WILD-TYPE                   106                             10
D986V10, multiclass
                                clus
vv                               GPR141 MUTATED GPR141 WILD-TYPE
  COLON ADENOCARCINOMA                        6              309
  COLON MUCINOUS ADENOCARCINOMA               4               43
  RECTAL ADENOCARCINOMA                       0              106
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  GPR141 MUTATED     6   0   1   1
  GPR141 WILD-TYPE 339   4  30  24
D986V11, multiclass
    clus
vv   GPR141 MUTATED GPR141 WILD-TYPE
  R0              6              339
  R1              0                4
  R2              1               30
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D986V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GPR141 MUTATED                                  0     1
  GPR141 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  GPR141 MUTATED                           0     6
  GPR141 WILD-TYPE                        22   220
D986V13, multiclass
                                  clus
vv                                 GPR141 MUTATED GPR141 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         6              220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(987) Variable = ZNF585A MUTATION ANALYSIS
D987V1, survival
                   sevent
clus2                 0   1
  ZNF585A MUTATED    13   5
  ZNF585A WILD-TYPE 365  88
  ZNF585A MUTATED ZNF585A WILD-TYPE 
               18               453 
  ZNF585A MUTATED ZNF585A WILD-TYPE 
                5                88 
$`ZNF585A MUTATED`
TCGA-AA-3496 TCGA-AA-3510 TCGA-AA-3516 TCGA-AA-3525 TCGA-AA-3663 TCGA-AA-3713 
        1.02        63.98        13.02         8.05         6.97        19.04 
TCGA-AA-3715 TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A010 TCGA-AD-6895 TCGA-CA-6718 
       19.04        25.02         4.01        34.98         0.72        10.06 
TCGA-D5-6534 TCGA-G4-6293 TCGA-G4-6626 TCGA-AG-3578 TCGA-AG-3892 TCGA-AG-A002 
       43.27       133.18        46.75        32.02        13.02        20.98 

$`ZNF585A WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
       35.01         6.97         1.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       24.03        37.05        36.03        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       61.02        78.08         6.05        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 
        3.25         3.29         0.07        12.20        12.76        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6535 
       56.09        55.92        20.19        18.25         1.32        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       26.17        91.79        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3580 
       15.39        20.02        10.39        36.03        12.00         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 
        1.02        17.95        36.95        17.03        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  ZNF585A MUTATED ZNF585A WILD-TYPE 
             0.72              0.00 
  ZNF585A MUTATED ZNF585A WILD-TYPE 
           133.18            148.01 
  ZNF585A MUTATED ZNF585A WILD-TYPE 
            19.04             20.28 
[1] "0.7 - 133.2 (19.0)" "0.0 - 148.0 (20.3)"
[1] "hr=" "1.4"
D987V2, continuous
D987V3, binary
                   cls
clus                  0   1
  ZNF585A MUTATED    16   3
  ZNF585A WILD-TYPE 350 116
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZNF585A MUTATED     16    3
  ZNF585A WILD-TYPE  350  116
        clus
vv       ZNF585A MUTATED ZNF585A WILD-TYPE
  COLON               16               350
  RECTUM               3               116
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZNF585A MUTATED         2        0        4         5         2         0
  ZNF585A WILD-TYPE      89        1       28       133         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF585A MUTATED           2          0          1          0        1
  ZNF585A WILD-TYPE        22         11         58         42       47
                   vv
clus                STAGE IVA STAGE IVB
  ZNF585A MUTATED           0         0
  ZNF585A WILD-TYPE        18         1
D987V4, multiclass
            clus
vv           ZNF585A MUTATED ZNF585A WILD-TYPE
  STAGE I                  2                89
  STAGE IA                 0                 1
  STAGE II                 4                28
  STAGE IIA                5               133
  STAGE IIB                2                 8
  STAGE IIC                0                 1
  STAGE III                2                22
  STAGE IIIA               0                11
  STAGE IIIB               1                58
  STAGE IIIC               0                42
  STAGE IV                 1                47
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  ZNF585A MUTATED     1   2  14   2
  ZNF585A WILD-TYPE  16  90 315  48
D987V5, multiclass
    clus
vv   ZNF585A MUTATED ZNF585A WILD-TYPE
  T1               1                16
  T2               2                90
  T3              14               315
  T4               2                48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  ZNF585A MUTATED    15   3   1
  ZNF585A WILD-TYPE 272 110  86
D987V6, multiclass
    clus
vv   ZNF585A MUTATED ZNF585A WILD-TYPE
  N0              15               272
  N1               3               110
  N2               1                86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D987V7, binary
                   cls
clus                  0   1
  ZNF585A MUTATED    16   1
  ZNF585A WILD-TYPE 359  64
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZNF585A MUTATED     16    1
  ZNF585A WILD-TYPE  359   64
   clus
vv  ZNF585A MUTATED ZNF585A WILD-TYPE
  0              16               359
  1               1                64
[1] 2 2
[1] FALSE
D987V8, binary
                   cls
clus                  0   1
  ZNF585A MUTATED     8  11
  ZNF585A WILD-TYPE 217 253
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZNF585A MUTATED      8   11
  ZNF585A WILD-TYPE  217  253
        clus
vv       ZNF585A MUTATED ZNF585A WILD-TYPE
  FEMALE               8               217
  MALE                11               253
[1] 2 2
[1] FALSE
D987V9, binary
                   cls
clus                  0   1
  ZNF585A MUTATED    14   1
  ZNF585A WILD-TYPE 336  21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZNF585A MUTATED     14    1
  ZNF585A WILD-TYPE  336   21
     clus
vv    ZNF585A MUTATED ZNF585A WILD-TYPE
  NO               14               336
  YES               1                21
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ZNF585A MUTATED                     13                             3
  ZNF585A WILD-TYPE                  302                            44
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ZNF585A MUTATED                       2                              1
  ZNF585A WILD-TYPE                   104                              9
D987V10, multiclass
                                clus
vv                               ZNF585A MUTATED ZNF585A WILD-TYPE
  COLON ADENOCARCINOMA                        13               302
  COLON MUCINOUS ADENOCARCINOMA                3                44
  RECTAL ADENOCARCINOMA                        2               104
  RECTAL MUCINOUS ADENOCARCINOMA               1                 9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  ZNF585A MUTATED    14   0   1   1
  ZNF585A WILD-TYPE 331   4  30  24
D987V11, multiclass
    clus
vv   ZNF585A MUTATED ZNF585A WILD-TYPE
  R0              14               331
  R1               0                 4
  R2               1                30
  RX               1                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D987V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF585A MUTATED                                  0     1
  ZNF585A WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  ZNF585A MUTATED                           0     4
  ZNF585A WILD-TYPE                        22   222
D987V13, multiclass
                                  clus
vv                                 ZNF585A MUTATED ZNF585A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                10
  BLACK OR AFRICAN AMERICAN                      0                22
  WHITE                                          4               222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(988) Variable = DIAPH2 MUTATION ANALYSIS
D988V1, survival
                  sevent
clus2                0   1
  DIAPH2 MUTATED    17   6
  DIAPH2 WILD-TYPE 361  87
  DIAPH2 MUTATED DIAPH2 WILD-TYPE 
              23              448 
  DIAPH2 MUTATED DIAPH2 WILD-TYPE 
               6               87 
$`DIAPH2 MUTATED`
TCGA-A6-6782 TCGA-AA-3552 TCGA-AA-3555 TCGA-AA-3692 TCGA-AA-3815 TCGA-AA-3977 
       20.28        13.02        29.95        36.00        33.04        25.02 
TCGA-AA-A00N TCGA-AD-6548 TCGA-AD-6899 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        4.01        21.37         5.79        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CM-5860 TCGA-CM-6675 TCGA-DM-A28H TCGA-F4-6460 TCGA-G4-6306 
       14.30        32.02        13.05       117.07        31.96        44.68 
TCGA-G4-6323 TCGA-AF-2692 TCGA-AG-3892 TCGA-AG-A002 TCGA-DC-6683 
       13.78        13.55        13.02        20.98         5.03 

$`DIAPH2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        19.66         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       24.00        17.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3696 TCGA-AA-3697 
       11.01         5.98        37.05        19.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
       26.99        19.04        19.04        10.06        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6888 
       41.00        39.98        18.05        40.96         0.07        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
       56.55         0.79         0.72        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CK-4947 
       12.69         3.06         3.25         3.29         0.07        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       30.08        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       12.95        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
       98.24         8.61        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       39.48        43.04        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        4.01         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  DIAPH2 MUTATED DIAPH2 WILD-TYPE 
            4.01             0.00 
  DIAPH2 MUTATED DIAPH2 WILD-TYPE 
          117.07           148.01 
  DIAPH2 MUTATED DIAPH2 WILD-TYPE 
           14.30            20.37 
[1] "4.0 - 117.1 (14.3)" "0.0 - 148.0 (20.4)"
[1] "hr=" "1.6"
D988V2, continuous
D988V3, binary
                  cls
clus                 0   1
  DIAPH2 MUTATED    21   3
  DIAPH2 WILD-TYPE 345 116
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DIAPH2 MUTATED     21    3
  DIAPH2 WILD-TYPE  345  116
        clus
vv       DIAPH2 MUTATED DIAPH2 WILD-TYPE
  COLON              21              345
  RECTUM              3              116
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DIAPH2 MUTATED         3        1        1        10         2         0
  DIAPH2 WILD-TYPE      88        0       31       128         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DIAPH2 MUTATED           0          0          2          3        1
  DIAPH2 WILD-TYPE        24         11         57         39       47
                  vv
clus               STAGE IVA STAGE IVB
  DIAPH2 MUTATED           0         1
  DIAPH2 WILD-TYPE        18         0
D988V4, multiclass
            clus
vv           DIAPH2 MUTATED DIAPH2 WILD-TYPE
  STAGE I                 3               88
  STAGE IA                1                0
  STAGE II                1               31
  STAGE IIA              10              128
  STAGE IIB               2                8
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              2               57
  STAGE IIIC              3               39
  STAGE IV                1               47
  STAGE IVA               0               18
  STAGE IVB               1                0
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  DIAPH2 MUTATED     1   4  15   4
  DIAPH2 WILD-TYPE  16  88 314  46
D988V5, multiclass
    clus
vv   DIAPH2 MUTATED DIAPH2 WILD-TYPE
  T1              1               16
  T2              4               88
  T3             15              314
  T4              4               46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  DIAPH2 MUTATED    18   2   5
  DIAPH2 WILD-TYPE 269 111  82
D988V6, multiclass
    clus
vv   DIAPH2 MUTATED DIAPH2 WILD-TYPE
  N0             18              269
  N1              2              111
  N2              5               82
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D988V7, binary
                  cls
clus                 0   1
  DIAPH2 MUTATED    19   2
  DIAPH2 WILD-TYPE 356  63
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DIAPH2 MUTATED     19    2
  DIAPH2 WILD-TYPE  356   63
   clus
vv  DIAPH2 MUTATED DIAPH2 WILD-TYPE
  0             19              356
  1              2               63
[1] 2 2
[1] FALSE
D988V8, binary
                  cls
clus                 0   1
  DIAPH2 MUTATED     9  16
  DIAPH2 WILD-TYPE 216 248
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DIAPH2 MUTATED      9   16
  DIAPH2 WILD-TYPE  216  248
        clus
vv       DIAPH2 MUTATED DIAPH2 WILD-TYPE
  FEMALE              9              216
  MALE               16              248
[1] 2 2
[1] FALSE
D988V9, binary
                  cls
clus                 0   1
  DIAPH2 MUTATED    19   1
  DIAPH2 WILD-TYPE 331  21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DIAPH2 MUTATED     19    1
  DIAPH2 WILD-TYPE  331   21
     clus
vv    DIAPH2 MUTATED DIAPH2 WILD-TYPE
  NO              19              331
  YES              1               21
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  DIAPH2 MUTATED                     16                             5
  DIAPH2 WILD-TYPE                  299                            42
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  DIAPH2 MUTATED                       3                              0
  DIAPH2 WILD-TYPE                   103                             10
D988V10, multiclass
                                clus
vv                               DIAPH2 MUTATED DIAPH2 WILD-TYPE
  COLON ADENOCARCINOMA                       16              299
  COLON MUCINOUS ADENOCARCINOMA               5               42
  RECTAL ADENOCARCINOMA                       3              103
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  DIAPH2 MUTATED    16   0   1   4
  DIAPH2 WILD-TYPE 329   4  30  21
D988V11, multiclass
    clus
vv   DIAPH2 MUTATED DIAPH2 WILD-TYPE
  R0             16              329
  R1              0                4
  R2              1               30
  RX              4               21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D988V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DIAPH2 MUTATED                                  0     4
  DIAPH2 WILD-TYPE                                1     7
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  DIAPH2 MUTATED                           2     9
  DIAPH2 WILD-TYPE                        20   217
D988V13, multiclass
                                  clus
vv                                 DIAPH2 MUTATED DIAPH2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         4                7
  BLACK OR AFRICAN AMERICAN                     2               20
  WHITE                                         9              217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(989) Variable = ANKRD10 MUTATION ANALYSIS
D989V1, survival
                   sevent
clus2                 0   1
  ANKRD10 MUTATED     7   0
  ANKRD10 WILD-TYPE 371  93
  ANKRD10 MUTATED ANKRD10 WILD-TYPE 
                7               464 
  ANKRD10 MUTATED ANKRD10 WILD-TYPE 
                0                93 
$`ANKRD10 MUTATED`
TCGA-AA-3525 TCGA-AD-6895 TCGA-AZ-4315 TCGA-D5-6898 TCGA-AG-A02N TCGA-EI-6507 
        8.05         0.72        58.39         1.48        61.97        19.96 
TCGA-F5-6813 
        0.69 

$`ANKRD10 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       15.52        56.55         0.79         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       33.01        21.44        17.82         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6922 
       17.13        12.49        16.14        15.58         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
        1.94        38.96        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6510 
       51.48        32.61         0.49        20.55        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  ANKRD10 MUTATED ANKRD10 WILD-TYPE 
             0.69              0.00 
  ANKRD10 MUTATED ANKRD10 WILD-TYPE 
            61.97            148.01 
  ANKRD10 MUTATED ANKRD10 WILD-TYPE 
            8.050            20.415 
[1] "0.7 - 62.0 (8.1)"   "0.0 - 148.0 (20.4)"
[1] "hr="     "9200000"
D989V2, continuous
D989V3, binary
                   cls
clus                  0   1
  ANKRD10 MUTATED     6   3
  ANKRD10 WILD-TYPE 360 116
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD10 MUTATED      6    3
  ANKRD10 WILD-TYPE  360  116
        clus
vv       ANKRD10 MUTATED ANKRD10 WILD-TYPE
  COLON                6               360
  RECTUM               3               116
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ANKRD10 MUTATED         1        0        2         2         1         0
  ANKRD10 WILD-TYPE      90        1       30       136         9         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ANKRD10 MUTATED           0          0          1          1        0
  ANKRD10 WILD-TYPE        24         11         58         41       48
                   vv
clus                STAGE IVA STAGE IVB
  ANKRD10 MUTATED           0         0
  ANKRD10 WILD-TYPE        18         1
D989V4, multiclass
            clus
vv           ANKRD10 MUTATED ANKRD10 WILD-TYPE
  STAGE I                  1                90
  STAGE IA                 0                 1
  STAGE II                 2                30
  STAGE IIA                2               136
  STAGE IIB                1                 9
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               0                11
  STAGE IIIB               1                58
  STAGE IIIC               1                41
  STAGE IV                 0                48
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  ANKRD10 MUTATED     0   1   5   3
  ANKRD10 WILD-TYPE  17  91 324  47
D989V5, multiclass
    clus
vv   ANKRD10 MUTATED ANKRD10 WILD-TYPE
  T1               0                17
  T2               1                91
  T3               5               324
  T4               3                47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  ANKRD10 MUTATED     6   2   1
  ANKRD10 WILD-TYPE 281 111  86
D989V6, multiclass
    clus
vv   ANKRD10 MUTATED ANKRD10 WILD-TYPE
  N0               6               281
  N1               2               111
  N2               1                86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D989V7, binary
                   cls
clus                  0   1
  ANKRD10 MUTATED     7   0
  ANKRD10 WILD-TYPE 368  65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD10 MUTATED      7    0
  ANKRD10 WILD-TYPE  368   65
   clus
vv  ANKRD10 MUTATED ANKRD10 WILD-TYPE
  0               7               368
  1               0                65
[1] 2 2
[1] FALSE
D989V8, binary
                   cls
clus                  0   1
  ANKRD10 MUTATED     3   6
  ANKRD10 WILD-TYPE 222 258
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD10 MUTATED      3    6
  ANKRD10 WILD-TYPE  222  258
        clus
vv       ANKRD10 MUTATED ANKRD10 WILD-TYPE
  FEMALE               3               222
  MALE                 6               258
[1] 2 2
[1] FALSE
D989V9, binary
                   cls
clus                  0   1
  ANKRD10 MUTATED     3   0
  ANKRD10 WILD-TYPE 347  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD10 MUTATED      3    0
  ANKRD10 WILD-TYPE  347   22
     clus
vv    ANKRD10 MUTATED ANKRD10 WILD-TYPE
  NO                3               347
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ANKRD10 MUTATED                      6                             0
  ANKRD10 WILD-TYPE                  309                            47
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ANKRD10 MUTATED                       3                              0
  ANKRD10 WILD-TYPE                   103                             10
D989V10, multiclass
                                clus
vv                               ANKRD10 MUTATED ANKRD10 WILD-TYPE
  COLON ADENOCARCINOMA                         6               309
  COLON MUCINOUS ADENOCARCINOMA                0                47
  RECTAL ADENOCARCINOMA                        3               103
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  ANKRD10 MUTATED     7   0   0   1
  ANKRD10 WILD-TYPE 338   4  31  24
D989V11, multiclass
    clus
vv   ANKRD10 MUTATED ANKRD10 WILD-TYPE
  R0               7               338
  R1               0                 4
  R2               0                31
  RX               1                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D989V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ANKRD10 MUTATED                                  0     0
  ANKRD10 WILD-TYPE                                1    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  ANKRD10 MUTATED                           0     6
  ANKRD10 WILD-TYPE                        22   220
D989V13, multiclass
                                  clus
vv                                 ANKRD10 MUTATED ANKRD10 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                      0                22
  WHITE                                          6               220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(990) Variable = ASPG MUTATION ANALYSIS
D990V1, survival
                sevent
clus2              0   1
  ASPG MUTATED     6   1
  ASPG WILD-TYPE 372  92
  ASPG MUTATED ASPG WILD-TYPE 
             7            464 
  ASPG MUTATED ASPG WILD-TYPE 
             1             92 
$`ASPG MUTATED`
TCGA-A6-5661 TCGA-AA-3877 TCGA-AU-3779 TCGA-AZ-4315 TCGA-AZ-6601 TCGA-CM-5861 
       33.53        31.00        14.50        58.39       100.01        15.02 
TCGA-CM-6674 
       12.95 

$`ASPG WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 
       17.03        24.03        27.02        29.98        18.05         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       10.88         0.20        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 
       62.79        88.21        49.41         6.77        12.10        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 
       22.03        22.98        30.08        32.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       14.04        11.01        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  ASPG MUTATED ASPG WILD-TYPE 
         12.95           0.00 
  ASPG MUTATED ASPG WILD-TYPE 
        100.01         148.01 
  ASPG MUTATED ASPG WILD-TYPE 
        31.000         20.155 
[1] "12.9 - 100.0 (31.0)" "0.0 - 148.0 (20.2)" 
[1] "hr=" "2"  
D990V2, continuous
D990V3, binary
                cls
clus               0   1
  ASPG MUTATED     7   0
  ASPG WILD-TYPE 359 119
[1] "tbl2"
                cls
clus             [,1] [,2]
  ASPG MUTATED      7    0
  ASPG WILD-TYPE  359  119
        clus
vv       ASPG MUTATED ASPG WILD-TYPE
  COLON             7            359
  RECTUM            0            119
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ASPG MUTATED         1        0        1         5         0         0
  ASPG WILD-TYPE      90        1       31       133        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ASPG MUTATED           0          0          0          0        0         0
  ASPG WILD-TYPE        24         11         59         42       48        18
                vv
clus             STAGE IVB
  ASPG MUTATED           0
  ASPG WILD-TYPE         1
D990V4, multiclass
            clus
vv           ASPG MUTATED ASPG WILD-TYPE
  STAGE I               1             90
  STAGE IA              0              1
  STAGE II              1             31
  STAGE IIA             5            133
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            0             59
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  ASPG MUTATED     1   0   6   0
  ASPG WILD-TYPE  16  92 323  50
D990V5, multiclass
    clus
vv   ASPG MUTATED ASPG WILD-TYPE
  T1            1             16
  T2            0             92
  T3            6            323
  T4            0             50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  ASPG MUTATED     7   0   0
  ASPG WILD-TYPE 280 113  87
D990V6, multiclass
    clus
vv   ASPG MUTATED ASPG WILD-TYPE
  N0            7            280
  N1            0            113
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D990V7, binary
                cls
clus               0   1
  ASPG MUTATED     7   0
  ASPG WILD-TYPE 368  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  ASPG MUTATED      7    0
  ASPG WILD-TYPE  368   65
   clus
vv  ASPG MUTATED ASPG WILD-TYPE
  0            7            368
  1            0             65
[1] 2 2
[1] FALSE
D990V8, binary
                cls
clus               0   1
  ASPG MUTATED     4   3
  ASPG WILD-TYPE 221 261
[1] "tbl2"
                cls
clus             [,1] [,2]
  ASPG MUTATED      4    3
  ASPG WILD-TYPE  221  261
        clus
vv       ASPG MUTATED ASPG WILD-TYPE
  FEMALE            4            221
  MALE              3            261
[1] 2 2
[1] FALSE
D990V9, binary
                cls
clus               0   1
  ASPG MUTATED     7   0
  ASPG WILD-TYPE 343  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  ASPG MUTATED      7    0
  ASPG WILD-TYPE  343   22
     clus
vv    ASPG MUTATED ASPG WILD-TYPE
  NO             7            343
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ASPG MUTATED                      6                             1
  ASPG WILD-TYPE                  309                            46
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ASPG MUTATED                       0                              0
  ASPG WILD-TYPE                   106                             10
D990V10, multiclass
                                clus
vv                               ASPG MUTATED ASPG WILD-TYPE
  COLON ADENOCARCINOMA                      6            309
  COLON MUCINOUS ADENOCARCINOMA             1             46
  RECTAL ADENOCARCINOMA                     0            106
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  ASPG MUTATED     6   0   0   0
  ASPG WILD-TYPE 339   4  31  25
D990V11, multiclass
    clus
vv   ASPG MUTATED ASPG WILD-TYPE
  R0            6            339
  R1            0              4
  R2            0             31
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D990V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ASPG MUTATED                                  0     0
  ASPG WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  ASPG MUTATED                           1     5
  ASPG WILD-TYPE                        21   221
D990V13, multiclass
                                  clus
vv                                 ASPG MUTATED ASPG WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                       5            221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(991) Variable = CDK14 MUTATION ANALYSIS
D991V1, survival
                 sevent
clus2               0   1
  CDK14 MUTATED    12   5
  CDK14 WILD-TYPE 366  88
  CDK14 MUTATED CDK14 WILD-TYPE 
             17             454 
  CDK14 MUTATED CDK14 WILD-TYPE 
              5              88 
$`CDK14 MUTATED`
TCGA-A6-2676 TCGA-A6-3807 TCGA-A6-5665 TCGA-AA-3667 TCGA-AA-3855 TCGA-AA-A00N 
       42.90        34.65        22.06        14.01        32.05         4.01 
TCGA-AA-A02H TCGA-AZ-5407 TCGA-CA-6718 TCGA-CK-4952 TCGA-CM-4743 TCGA-D5-6532 
        2.01        88.21        10.06        15.62        23.05        18.25 
TCGA-D5-6539 TCGA-G4-6303 TCGA-G4-6588 TCGA-AG-3732 TCGA-F5-6811 
       12.49        65.85        26.17        32.98        32.19 

$`CDK14 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5657 
       33.34        32.75        36.53        14.53        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 
       30.44        29.19        33.53        23.61        22.09        32.71 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       27.09        22.52         8.38        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
        2.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
       33.07         0.00        36.03         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       39.06        51.98        39.98         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 
        5.13       106.75        22.36        62.79        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.20        12.76        14.30        17.56       148.01        85.45 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
      124.27        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6534 
       19.59        56.09        55.92        20.19         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 
       15.12        17.85         4.80        17.13        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
      133.18        74.56        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
        0.99        37.02         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  CDK14 MUTATED CDK14 WILD-TYPE 
           2.01            0.00 
  CDK14 MUTATED CDK14 WILD-TYPE 
          88.21          148.01 
  CDK14 MUTATED CDK14 WILD-TYPE 
         23.050          20.085 
[1] "2.0 - 88.2 (23.1)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.4"
D991V2, continuous
D991V3, binary
                 cls
clus                0   1
  CDK14 MUTATED    15   2
  CDK14 WILD-TYPE 351 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDK14 MUTATED     15    2
  CDK14 WILD-TYPE  351  117
        clus
vv       CDK14 MUTATED CDK14 WILD-TYPE
  COLON             15             351
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CDK14 MUTATED         4        0        0         6         2         0
  CDK14 WILD-TYPE      87        1       32       132         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CDK14 MUTATED           0          1          0          2        2         0
  CDK14 WILD-TYPE        24         10         59         40       46        18
                 vv
clus              STAGE IVB
  CDK14 MUTATED           0
  CDK14 WILD-TYPE         1
D991V4, multiclass
            clus
vv           CDK14 MUTATED CDK14 WILD-TYPE
  STAGE I                4              87
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              6             132
  STAGE IIB              2               8
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             1              10
  STAGE IIIB             0              59
  STAGE IIIC             2              40
  STAGE IV               2              46
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CDK14 MUTATED     1   3  10   3
  CDK14 WILD-TYPE  16  89 319  47
D991V5, multiclass
    clus
vv   CDK14 MUTATED CDK14 WILD-TYPE
  T1             1              16
  T2             3              89
  T3            10             319
  T4             3              47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  CDK14 MUTATED    13   1   3
  CDK14 WILD-TYPE 274 112  84
D991V6, multiclass
    clus
vv   CDK14 MUTATED CDK14 WILD-TYPE
  N0            13             274
  N1             1             112
  N2             3              84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D991V7, binary
                 cls
clus                0   1
  CDK14 MUTATED    15   2
  CDK14 WILD-TYPE 360  63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDK14 MUTATED     15    2
  CDK14 WILD-TYPE  360   63
   clus
vv  CDK14 MUTATED CDK14 WILD-TYPE
  0            15             360
  1             2              63
[1] 2 2
[1] FALSE
D991V8, binary
                 cls
clus                0   1
  CDK14 MUTATED    12   5
  CDK14 WILD-TYPE 213 259
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDK14 MUTATED     12    5
  CDK14 WILD-TYPE  213  259
        clus
vv       CDK14 MUTATED CDK14 WILD-TYPE
  FEMALE            12             213
  MALE               5             259
[1] 2 2
[1] FALSE
D991V9, binary
                 cls
clus                0   1
  CDK14 MUTATED    14   0
  CDK14 WILD-TYPE 336  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDK14 MUTATED     14    0
  CDK14 WILD-TYPE  336   22
     clus
vv    CDK14 MUTATED CDK14 WILD-TYPE
  NO             14             336
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CDK14 MUTATED                     13                             2
  CDK14 WILD-TYPE                  302                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CDK14 MUTATED                       2                              0
  CDK14 WILD-TYPE                   104                             10
D991V10, multiclass
                                clus
vv                               CDK14 MUTATED CDK14 WILD-TYPE
  COLON ADENOCARCINOMA                      13             302
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  CDK14 MUTATED    12   0   1   2
  CDK14 WILD-TYPE 333   4  30  23
D991V11, multiclass
    clus
vv   CDK14 MUTATED CDK14 WILD-TYPE
  R0            12             333
  R1             0               4
  R2             1              30
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D991V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CDK14 MUTATED                                  0     1
  CDK14 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CDK14 MUTATED                           0    11
  CDK14 WILD-TYPE                        22   215
D991V13, multiclass
                                  clus
vv                                 CDK14 MUTATED CDK14 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                       11             215
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(992) Variable = OR8A1 MUTATION ANALYSIS
D992V1, survival
                 sevent
clus2               0   1
  OR8A1 MUTATED     5   0
  OR8A1 WILD-TYPE 373  93
  OR8A1 MUTATED OR8A1 WILD-TYPE 
              5             466 
  OR8A1 MUTATED OR8A1 WILD-TYPE 
              0              93 
$`OR8A1 MUTATED`
TCGA-D5-6534 TCGA-D5-6539 TCGA-DM-A1HB TCGA-G4-6315 TCGA-AF-2693 
       43.27        12.49       135.65        61.91        19.10 

$`OR8A1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6535 
       56.09        55.92        20.19        18.25         1.32        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
       17.85         4.80        17.13        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  OR8A1 MUTATED OR8A1 WILD-TYPE 
          12.49            0.00 
  OR8A1 MUTATED OR8A1 WILD-TYPE 
         135.65          148.01 
  OR8A1 MUTATED OR8A1 WILD-TYPE 
         43.270          20.155 
[1] "12.5 - 135.7 (43.3)" "0.0 - 148.0 (20.2)" 
[1] "hr="     "9300000"
D992V2, continuous
D992V3, binary
                 cls
clus                0   1
  OR8A1 MUTATED     4   0
  OR8A1 WILD-TYPE 362 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR8A1 MUTATED      4    0
  OR8A1 WILD-TYPE  362  119
        clus
vv       OR8A1 MUTATED OR8A1 WILD-TYPE
  COLON              4             362
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  OR8A1 MUTATED         1        0        0         1         0         0
  OR8A1 WILD-TYPE      90        1       32       137        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  OR8A1 MUTATED           0          1          1          0        1         0
  OR8A1 WILD-TYPE        24         10         58         42       47        18
                 vv
clus              STAGE IVB
  OR8A1 MUTATED           0
  OR8A1 WILD-TYPE         1
D992V4, multiclass
            clus
vv           OR8A1 MUTATED OR8A1 WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              1             137
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             1              10
  STAGE IIIB             1              58
  STAGE IIIC             0              42
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  OR8A1 MUTATED     0   1   4   0
  OR8A1 WILD-TYPE  17  91 325  50
D992V5, multiclass
    clus
vv   OR8A1 MUTATED OR8A1 WILD-TYPE
  T1             0              17
  T2             1              91
  T3             4             325
  T4             0              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  OR8A1 MUTATED     3   2   0
  OR8A1 WILD-TYPE 284 111  87
D992V6, multiclass
    clus
vv   OR8A1 MUTATED OR8A1 WILD-TYPE
  N0             3             284
  N1             2             111
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D992V7, binary
                 cls
clus                0   1
  OR8A1 MUTATED     3   1
  OR8A1 WILD-TYPE 372  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR8A1 MUTATED      3    1
  OR8A1 WILD-TYPE  372   64
   clus
vv  OR8A1 MUTATED OR8A1 WILD-TYPE
  0             3             372
  1             1              64
[1] 2 2
[1] FALSE
D992V8, binary
                 cls
clus                0   1
  OR8A1 MUTATED     2   3
  OR8A1 WILD-TYPE 223 261
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR8A1 MUTATED      2    3
  OR8A1 WILD-TYPE  223  261
        clus
vv       OR8A1 MUTATED OR8A1 WILD-TYPE
  FEMALE             2             223
  MALE               3             261
[1] 2 2
[1] FALSE
D992V9, binary
                 cls
clus                0   1
  OR8A1 MUTATED     4   0
  OR8A1 WILD-TYPE 346  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR8A1 MUTATED      4    0
  OR8A1 WILD-TYPE  346   22
     clus
vv    OR8A1 MUTATED OR8A1 WILD-TYPE
  NO              4             346
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  OR8A1 MUTATED                      2                             1
  OR8A1 WILD-TYPE                  313                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  OR8A1 MUTATED                       0                              0
  OR8A1 WILD-TYPE                   106                             10
D992V10, multiclass
                                clus
vv                               OR8A1 MUTATED OR8A1 WILD-TYPE
  COLON ADENOCARCINOMA                       2             313
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  OR8A1 MUTATED     3   0   0   0
  OR8A1 WILD-TYPE 342   4  31  25
D992V11, multiclass
    clus
vv   OR8A1 MUTATED OR8A1 WILD-TYPE
  R0             3             342
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D992V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OR8A1 MUTATED                                  0     0
  OR8A1 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  OR8A1 MUTATED                           0     5
  OR8A1 WILD-TYPE                        22   221
D992V13, multiclass
                                  clus
vv                                 OR8A1 MUTATED OR8A1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        5             221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(993) Variable = SPINT4 MUTATION ANALYSIS
D993V1, survival
                  sevent
clus2                0   1
  SPINT4 MUTATED     3   1
  SPINT4 WILD-TYPE 375  92
  SPINT4 MUTATED SPINT4 WILD-TYPE 
               4              467 
  SPINT4 MUTATED SPINT4 WILD-TYPE 
               1               92 
$`SPINT4 MUTATED`
TCGA-AZ-6599 TCGA-CM-5861 TCGA-CM-6674 TCGA-DY-A0XA 
        6.77        15.02        12.95       126.44 

$`SPINT4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       49.41        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       30.08        32.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD 
        5.95         4.01         5.03         5.29        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  SPINT4 MUTATED SPINT4 WILD-TYPE 
            6.77             0.00 
  SPINT4 MUTATED SPINT4 WILD-TYPE 
          126.44           148.01 
  SPINT4 MUTATED SPINT4 WILD-TYPE 
          13.985           20.280 
[1] "6.8 - 126.4 (14.0)" "0.0 - 148.0 (20.3)"
[1] "hr=" "1"  
D993V2, continuous
D993V3, binary
                  cls
clus                 0   1
  SPINT4 MUTATED     3   1
  SPINT4 WILD-TYPE 363 118
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SPINT4 MUTATED      3    1
  SPINT4 WILD-TYPE  363  118
        clus
vv       SPINT4 MUTATED SPINT4 WILD-TYPE
  COLON               3              363
  RECTUM              1              118
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SPINT4 MUTATED         1        0        0         3         0         0
  SPINT4 WILD-TYPE      90        1       32       135        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SPINT4 MUTATED           0          0          0          0        0
  SPINT4 WILD-TYPE        24         11         59         42       48
                  vv
clus               STAGE IVA STAGE IVB
  SPINT4 MUTATED           0         0
  SPINT4 WILD-TYPE        18         1
D993V4, multiclass
            clus
vv           SPINT4 MUTATED SPINT4 WILD-TYPE
  STAGE I                 1               90
  STAGE IA                0                1
  STAGE II                0               32
  STAGE IIA               3              135
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              0               59
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  SPINT4 MUTATED     0   1   3   0
  SPINT4 WILD-TYPE  17  91 326  50
D993V5, multiclass
    clus
vv   SPINT4 MUTATED SPINT4 WILD-TYPE
  T1              0               17
  T2              1               91
  T3              3              326
  T4              0               50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  SPINT4 MUTATED     4   0   0
  SPINT4 WILD-TYPE 283 113  87
D993V6, multiclass
    clus
vv   SPINT4 MUTATED SPINT4 WILD-TYPE
  N0              4              283
  N1              0              113
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D993V7, binary
                  cls
clus                 0   1
  SPINT4 MUTATED     3   0
  SPINT4 WILD-TYPE 372  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SPINT4 MUTATED      3    0
  SPINT4 WILD-TYPE  372   65
   clus
vv  SPINT4 MUTATED SPINT4 WILD-TYPE
  0              3              372
  1              0               65
[1] 2 2
[1] FALSE
D993V8, binary
                  cls
clus                 0   1
  SPINT4 MUTATED     2   2
  SPINT4 WILD-TYPE 223 262
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SPINT4 MUTATED      2    2
  SPINT4 WILD-TYPE  223  262
        clus
vv       SPINT4 MUTATED SPINT4 WILD-TYPE
  FEMALE              2              223
  MALE                2              262
[1] 2 2
[1] FALSE
D993V9, binary
                  cls
clus                 0   1
  SPINT4 MUTATED     3   0
  SPINT4 WILD-TYPE 347  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SPINT4 MUTATED      3    0
  SPINT4 WILD-TYPE  347   22
     clus
vv    SPINT4 MUTATED SPINT4 WILD-TYPE
  NO               3              347
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SPINT4 MUTATED                      3                             0
  SPINT4 WILD-TYPE                  312                            47
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SPINT4 MUTATED                       1                              0
  SPINT4 WILD-TYPE                   105                             10
D993V10, multiclass
                                clus
vv                               SPINT4 MUTATED SPINT4 WILD-TYPE
  COLON ADENOCARCINOMA                        3              312
  COLON MUCINOUS ADENOCARCINOMA               0               47
  RECTAL ADENOCARCINOMA                       1              105
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  SPINT4 MUTATED     2   0   0   0
  SPINT4 WILD-TYPE 343   4  31  25
D993V11, multiclass
[1] "Remove cluster labels:" "SPINT4 MUTATED"        
clus
  SPINT4 MUTATED SPINT4 WILD-TYPE 
               2              403 
      TCGA-A6-2671       TCGA-A6-2672       TCGA-A6-2674       TCGA-A6-2676 
"SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" 
      TCGA-A6-2677       TCGA-A6-2678       TCGA-A6-2683       TCGA-A6-3807 
"SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" 
      TCGA-A6-3808       TCGA-A6-3809       TCGA-A6-3810       TCGA-A6-5657 
"SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" 
      TCGA-A6-5659       TCGA-A6-5661       TCGA-A6-5665       TCGA-A6-6781 
"SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" 
      TCGA-AA-3489       TCGA-AA-3492       TCGA-AA-3496       TCGA-AA-3502 
"SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" 
      TCGA-AA-3510       TCGA-AA-3511       TCGA-AA-3514       TCGA-AA-3517 
"SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" 
      TCGA-AA-3518       TCGA-AA-3519       TCGA-AA-3520       TCGA-AA-3521 
"SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" 
      TCGA-AA-3522       TCGA-AA-3524       TCGA-AA-3525       TCGA-AA-3526 
"SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" 
      TCGA-AA-3527       TCGA-AA-3529       TCGA-AA-3530       TCGA-AA-3531 
"SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" 
      TCGA-AA-3532       TCGA-AA-3534       TCGA-AA-3538       TCGA-AA-3542 
"SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" 
      TCGA-AA-3543       TCGA-AA-3544       TCGA-AA-3548       TCGA-AA-3549 
"SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" 
      TCGA-AA-3552       TCGA-AA-3553       TCGA-AA-3554       TCGA-AA-3555 
"SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" 
      TCGA-AA-3556       TCGA-AA-3558       TCGA-AA-3560       TCGA-AA-3561 
"SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" 
      TCGA-AA-3562       TCGA-AA-3655       TCGA-AA-3660       TCGA-AA-3662 
"SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" 
      TCGA-AA-3663       TCGA-AA-3664       TCGA-AA-3666       TCGA-AA-3667 
"SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" 
      TCGA-AA-3672       TCGA-AA-3673       TCGA-AA-3678       TCGA-AA-3679 
"SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" 
      TCGA-AA-3680       TCGA-AA-3681       TCGA-AA-3684       TCGA-AA-3685 
"SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" 
      TCGA-AA-3688       TCGA-AA-3692       TCGA-AA-3693       TCGA-AA-3695 
"SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" 
      TCGA-AA-3696       TCGA-AA-3697       TCGA-AA-3710       TCGA-AA-3712 
"SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" 
      TCGA-AA-3713       TCGA-AA-3715       TCGA-AA-3811       TCGA-AA-3812 
"SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" 
      TCGA-AA-3814       TCGA-AA-3815       TCGA-AA-3818       TCGA-AA-3819 
"SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" 
      TCGA-AA-3821       TCGA-AA-3831       TCGA-AA-3833       TCGA-AA-3837 
"SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" 
      TCGA-AA-3842       TCGA-AA-3844       TCGA-AA-3845       TCGA-AA-3846 
"SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" 
      TCGA-AA-3848       TCGA-AA-3850       TCGA-AA-3851       TCGA-AA-3852 
"SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" 
      TCGA-AA-3854       TCGA-AA-3855       TCGA-AA-3856       TCGA-AA-3858 
"SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" 
      TCGA-AA-3860       TCGA-AA-3861       TCGA-AA-3864       TCGA-AA-3866 
"SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" 
      TCGA-AA-3867       TCGA-AA-3869       TCGA-AA-3870       TCGA-AA-3872 
"SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" 
      TCGA-AA-3875       TCGA-AA-3877       TCGA-AA-3930       TCGA-AA-3939 
"SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" 
      TCGA-AA-3941       TCGA-AA-3947       TCGA-AA-3949       TCGA-AA-3950 
"SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" 
      TCGA-AA-3952       TCGA-AA-3955       TCGA-AA-3956       TCGA-AA-3968 
"SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" 
      TCGA-AA-3971       TCGA-AA-3972       TCGA-AA-3973       TCGA-AA-3975 
"SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" 
      TCGA-AA-3976       TCGA-AA-3979       TCGA-AA-3984       TCGA-AA-3986 
"SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" 
      TCGA-AA-3989       TCGA-AA-3994       TCGA-AA-A004       TCGA-AA-A00A 
"SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" 
      TCGA-AA-A00D       TCGA-AA-A00E       TCGA-AA-A00F       TCGA-AA-A00J 
"SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" 
      TCGA-AA-A00K       TCGA-AA-A00L       TCGA-AA-A00N       TCGA-AA-A00O 
"SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" 
      TCGA-AA-A00Q       TCGA-AA-A00R       TCGA-AA-A00U       TCGA-AA-A00W 
"SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" 
      TCGA-AA-A00Z       TCGA-AA-A010       TCGA-AA-A017       TCGA-AA-A01D 
"SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" 
      TCGA-AA-A01F       TCGA-AA-A01G       TCGA-AA-A01I       TCGA-AA-A01K 
"SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" 
      TCGA-AA-A01P       TCGA-AA-A01Q       TCGA-AA-A01R       TCGA-AA-A01S 
"SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" 
      TCGA-AA-A01T       TCGA-AA-A01V       TCGA-AA-A01X       TCGA-AA-A01Z 
"SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" 
      TCGA-AA-A022       TCGA-AA-A024       TCGA-AA-A029       TCGA-AA-A02F 
"SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" 
      TCGA-AA-A02H       TCGA-AA-A02J       TCGA-AA-A02K       TCGA-AA-A02O 
"SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" 
      TCGA-AA-A02W       TCGA-AA-A02Y       TCGA-AA-A03F       TCGA-AA-A03J 
"SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" 
      TCGA-AD-5900       TCGA-AD-6548       TCGA-AD-6888       TCGA-AU-3779 
"SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" 
      TCGA-AU-6004       TCGA-AY-4070       TCGA-AY-4071       TCGA-AY-5543 
"SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" 
      TCGA-AY-6196       TCGA-AY-6197       TCGA-AY-6386       TCGA-AZ-4315 
"SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" 
      TCGA-AZ-4681       TCGA-AZ-4682       TCGA-CA-5254       TCGA-CA-5255 
"SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" 
      TCGA-CA-5796       TCGA-CA-5797       TCGA-CA-6715       TCGA-CA-6716 
"SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" 
      TCGA-CA-6717       TCGA-CA-6718       TCGA-CA-6719       TCGA-CK-4947 
"SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" 
      TCGA-CK-4948       TCGA-CK-4950       TCGA-CK-4952       TCGA-CK-5912 
"SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" 
      TCGA-CK-5913       TCGA-CK-5914       TCGA-CK-5915       TCGA-CK-5916 
"SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" 
      TCGA-CK-6746       TCGA-CK-6747       TCGA-CK-6748       TCGA-CK-6751 
"SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" 
      TCGA-CM-4743       TCGA-CM-4744       TCGA-CM-4746       TCGA-CM-4747 
"SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" 
      TCGA-CM-4752       TCGA-CM-5341       TCGA-CM-5344       TCGA-CM-5348 
"SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" 
      TCGA-CM-5349       TCGA-CM-5860       TCGA-CM-5862       TCGA-CM-5863 
"SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" 
      TCGA-CM-5864       TCGA-CM-5868       TCGA-CM-6161       TCGA-CM-6162 
"SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" 
      TCGA-CM-6163       TCGA-CM-6164       TCGA-CM-6165       TCGA-CM-6166 
"SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" 
      TCGA-CM-6167       TCGA-CM-6168       TCGA-CM-6169       TCGA-CM-6170 
"SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" 
      TCGA-CM-6171       TCGA-CM-6172       TCGA-CM-6675       TCGA-CM-6676 
"SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" 
      TCGA-CM-6677       TCGA-CM-6678       TCGA-CM-6679       TCGA-CM-6680 
"SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" 
      TCGA-D5-5537       TCGA-D5-5538       TCGA-D5-5539       TCGA-D5-5540 
"SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" 
      TCGA-D5-5541       TCGA-D5-6529       TCGA-D5-6532       TCGA-D5-6533 
"SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" 
      TCGA-D5-6534       TCGA-D5-6535       TCGA-D5-6536       TCGA-D5-6537 
"SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" 
      TCGA-D5-6538       TCGA-D5-6539       TCGA-D5-6540       TCGA-D5-6541 
"SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" 
      TCGA-D5-6898       TCGA-D5-6920       TCGA-D5-6922       TCGA-D5-6923 
"SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" 
      TCGA-D5-6924       TCGA-D5-6926       TCGA-D5-6927       TCGA-D5-6928 
"SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" 
      TCGA-D5-6929       TCGA-D5-6930       TCGA-D5-6931       TCGA-D5-6932 
"SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" 
      TCGA-D5-7000       TCGA-F4-6459       TCGA-F4-6460       TCGA-F4-6569 
"SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" 
      TCGA-F4-6570       TCGA-F4-6703       TCGA-F4-6704       TCGA-F4-6805 
"SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" 
      TCGA-F4-6806       TCGA-F4-6807       TCGA-F4-6808       TCGA-F4-6809 
"SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" 
      TCGA-F4-6854       TCGA-F4-6855       TCGA-F4-6856       TCGA-G4-6293 
"SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" 
      TCGA-G4-6299       TCGA-G4-6303       TCGA-G4-6304       TCGA-G4-6306 
"SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" 
      TCGA-G4-6307       TCGA-G4-6309       TCGA-G4-6310       TCGA-G4-6315 
"SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" 
      TCGA-G4-6317       TCGA-G4-6321       TCGA-G4-6323       TCGA-G4-6586 
"SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" 
      TCGA-G4-6588       TCGA-G4-6625       TCGA-G4-6626       TCGA-G4-6628 
"SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" 
      TCGA-AF-2687       TCGA-AF-2689       TCGA-AF-2691       TCGA-AF-2692 
"SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" 
      TCGA-AF-3400       TCGA-AF-3913       TCGA-AF-4110       TCGA-AF-5654 
"SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" 
      TCGA-AF-6655       TCGA-AG-3574       TCGA-AG-3575       TCGA-AG-3578 
"SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" 
      TCGA-AG-3580       TCGA-AG-3581       TCGA-AG-3582       TCGA-AG-3583 
"SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" 
      TCGA-AG-3584       TCGA-AG-3586       TCGA-AG-3587       TCGA-AG-3593 
"SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" 
      TCGA-AG-3594       TCGA-AG-3598       TCGA-AG-3599       TCGA-AG-3600 
"SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" 
      TCGA-AG-3601       TCGA-AG-3602       TCGA-AG-3605       TCGA-AG-3608 
"SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" 
      TCGA-AG-3609       TCGA-AG-3611       TCGA-AG-3612       TCGA-AG-3726 
"SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" 
      TCGA-AG-3727       TCGA-AG-3731       TCGA-AG-3732       TCGA-AG-3742 
"SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" 
      TCGA-AG-3878       TCGA-AG-3882       TCGA-AG-3883       TCGA-AG-3885 
"SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" 
      TCGA-AG-3887       TCGA-AG-3890       TCGA-AG-3892       TCGA-AG-3893 
"SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" 
      TCGA-AG-3894       TCGA-AG-3896       TCGA-AG-3898       TCGA-AG-3901 
"SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" 
      TCGA-AG-3902       TCGA-AG-3909       TCGA-AG-3999       TCGA-AG-4001 
"SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" 
      TCGA-AG-4005       TCGA-AG-4007       TCGA-AG-4008       TCGA-AG-4015 
"SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" 
      TCGA-AG-A002       TCGA-AG-A008       TCGA-AG-A00C       TCGA-AG-A00H 
"SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" 
      TCGA-AG-A00Y       TCGA-AG-A011       TCGA-AG-A014       TCGA-AG-A015 
"SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" 
      TCGA-AG-A016       TCGA-AG-A01L       TCGA-AG-A01W       TCGA-AG-A01Y 
"SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" 
      TCGA-AG-A020       TCGA-AG-A025       TCGA-AG-A026       TCGA-AG-A02G 
"SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" 
      TCGA-AG-A02N       TCGA-AG-A02X       TCGA-AG-A032       TCGA-AG-A036 
"SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" 
      TCGA-AH-6549       TCGA-AH-6643       TCGA-CL-5917       TCGA-CL-5918 
"SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" 
      TCGA-DC-5337       TCGA-DC-5869       TCGA-DC-6155       TCGA-DC-6157 
"SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" 
      TCGA-DC-6158       TCGA-DC-6160       TCGA-DC-6681       TCGA-DC-6682 
"SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" 
      TCGA-DC-6683       TCGA-DT-5265       TCGA-EF-5830       TCGA-EI-6506 
"SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" 
      TCGA-EI-6507       TCGA-EI-6508       TCGA-EI-6510       TCGA-F5-6464 
"SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" 
      TCGA-F5-6465       TCGA-F5-6571       TCGA-F5-6702       TCGA-F5-6812 
"SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" 
      TCGA-F5-6813       TCGA-G5-6235       TCGA-G5-6641 
"SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" "SPINT4 WILD-TYPE" 
D993V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SPINT4 MUTATED                                  0     0
  SPINT4 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  SPINT4 MUTATED                           0     4
  SPINT4 WILD-TYPE                        22   222
D993V13, multiclass
                                  clus
vv                                 SPINT4 MUTATED SPINT4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         4              222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(994) Variable = E2F5 MUTATION ANALYSIS
D994V1, survival
                sevent
clus2              0   1
  E2F5 MUTATED     6   0
  E2F5 WILD-TYPE 372  93
  E2F5 MUTATED E2F5 WILD-TYPE 
             6            465 
  E2F5 MUTATED E2F5 WILD-TYPE 
             0             93 
$`E2F5 MUTATED`
TCGA-AA-3947 TCGA-AZ-4315 TCGA-CA-6716 TCGA-CA-6717 TCGA-D5-6536 TCGA-F4-6856 
       33.01        58.39        12.20        12.76        17.85        35.31 

$`E2F5 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 
       31.00         2.01        12.99        24.00        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        33.01        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
        1.32        43.27        15.12         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       47.41       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  E2F5 MUTATED E2F5 WILD-TYPE 
          12.2            0.0 
  E2F5 MUTATED E2F5 WILD-TYPE 
         58.39         148.01 
  E2F5 MUTATED E2F5 WILD-TYPE 
         25.43          20.19 
[1] "12.2 - 58.4 (25.4)" "0.0 - 148.0 (20.2)"
[1] "hr="     "9100000"
D994V2, continuous
D994V3, binary
                cls
clus               0   1
  E2F5 MUTATED     7   0
  E2F5 WILD-TYPE 359 119
[1] "tbl2"
                cls
clus             [,1] [,2]
  E2F5 MUTATED      7    0
  E2F5 WILD-TYPE  359  119
        clus
vv       E2F5 MUTATED E2F5 WILD-TYPE
  COLON             7            359
  RECTUM            0            119
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  E2F5 MUTATED         1        0        0         4         1         0
  E2F5 WILD-TYPE      90        1       32       134         9         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  E2F5 MUTATED           0          0          0          0        1         0
  E2F5 WILD-TYPE        24         11         59         42       47        18
                vv
clus             STAGE IVB
  E2F5 MUTATED           0
  E2F5 WILD-TYPE         1
D994V4, multiclass
            clus
vv           E2F5 MUTATED E2F5 WILD-TYPE
  STAGE I               1             90
  STAGE IA              0              1
  STAGE II              0             32
  STAGE IIA             4            134
  STAGE IIB             1              9
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            0             59
  STAGE IIIC            0             42
  STAGE IV              1             47
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  E2F5 MUTATED     0   1   4   2
  E2F5 WILD-TYPE  17  91 325  48
D994V5, multiclass
    clus
vv   E2F5 MUTATED E2F5 WILD-TYPE
  T1            0             17
  T2            1             91
  T3            4            325
  T4            2             48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  E2F5 MUTATED     6   1   0
  E2F5 WILD-TYPE 281 112  87
D994V6, multiclass
    clus
vv   E2F5 MUTATED E2F5 WILD-TYPE
  N0            6            281
  N1            1            112
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D994V7, binary
                cls
clus               0   1
  E2F5 MUTATED     6   1
  E2F5 WILD-TYPE 369  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  E2F5 MUTATED      6    1
  E2F5 WILD-TYPE  369   64
   clus
vv  E2F5 MUTATED E2F5 WILD-TYPE
  0            6            369
  1            1             64
[1] 2 2
[1] FALSE
D994V8, binary
                cls
clus               0   1
  E2F5 MUTATED     2   5
  E2F5 WILD-TYPE 223 259
[1] "tbl2"
                cls
clus             [,1] [,2]
  E2F5 MUTATED      2    5
  E2F5 WILD-TYPE  223  259
        clus
vv       E2F5 MUTATED E2F5 WILD-TYPE
  FEMALE            2            223
  MALE              5            259
[1] 2 2
[1] FALSE
D994V9, binary
                cls
clus               0   1
  E2F5 MUTATED     6   0
  E2F5 WILD-TYPE 344  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  E2F5 MUTATED      6    0
  E2F5 WILD-TYPE  344   22
     clus
vv    E2F5 MUTATED E2F5 WILD-TYPE
  NO             6            344
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  E2F5 MUTATED                      4                             3
  E2F5 WILD-TYPE                  311                            44
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  E2F5 MUTATED                       0                              0
  E2F5 WILD-TYPE                   106                             10
D994V10, multiclass
                                clus
vv                               E2F5 MUTATED E2F5 WILD-TYPE
  COLON ADENOCARCINOMA                      4            311
  COLON MUCINOUS ADENOCARCINOMA             3             44
  RECTAL ADENOCARCINOMA                     0            106
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  E2F5 MUTATED     4   0   1   2
  E2F5 WILD-TYPE 341   4  30  23
D994V11, multiclass
    clus
vv   E2F5 MUTATED E2F5 WILD-TYPE
  R0            4            341
  R1            0              4
  R2            1             30
  RX            2             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D994V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  E2F5 MUTATED                                  0     2
  E2F5 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  E2F5 MUTATED                           0     3
  E2F5 WILD-TYPE                        22   223
D994V13, multiclass
                                  clus
vv                                 E2F5 MUTATED E2F5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              9
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       3            223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(995) Variable = STRADB MUTATION ANALYSIS
D995V1, survival
                  sevent
clus2                0   1
  STRADB MUTATED     4   2
  STRADB WILD-TYPE 374  91
  STRADB MUTATED STRADB WILD-TYPE 
               6              465 
  STRADB MUTATED STRADB WILD-TYPE 
               2               91 
$`STRADB MUTATED`
TCGA-AA-3492 TCGA-AA-3713 TCGA-AD-6964 TCGA-DM-A28H TCGA-AG-A002 TCGA-AG-A01W 
        3.02        19.04        10.88       117.07        20.98        70.03 

$`STRADB WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       12.00        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  STRADB MUTATED STRADB WILD-TYPE 
            3.02             0.00 
  STRADB MUTATED STRADB WILD-TYPE 
          117.07           148.01 
  STRADB MUTATED STRADB WILD-TYPE 
           20.01            20.19 
[1] "3.0 - 117.1 (20.0)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.2"
D995V2, continuous
D995V3, binary
                  cls
clus                 0   1
  STRADB MUTATED     5   2
  STRADB WILD-TYPE 361 117
[1] "tbl2"
                  cls
clus               [,1] [,2]
  STRADB MUTATED      5    2
  STRADB WILD-TYPE  361  117
        clus
vv       STRADB MUTATED STRADB WILD-TYPE
  COLON               5              361
  RECTUM              2              117
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  STRADB MUTATED         1        0        2         0         0         0
  STRADB WILD-TYPE      90        1       30       138        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  STRADB MUTATED           0          0          0          2        1
  STRADB WILD-TYPE        24         11         59         40       47
                  vv
clus               STAGE IVA STAGE IVB
  STRADB MUTATED           0         0
  STRADB WILD-TYPE        18         1
D995V4, multiclass
            clus
vv           STRADB MUTATED STRADB WILD-TYPE
  STAGE I                 1               90
  STAGE IA                0                1
  STAGE II                2               30
  STAGE IIA               0              138
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              0               59
  STAGE IIIC              2               40
  STAGE IV                1               47
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  STRADB MUTATED     0   1   5   1
  STRADB WILD-TYPE  17  91 324  49
D995V5, multiclass
    clus
vv   STRADB MUTATED STRADB WILD-TYPE
  T1              0               17
  T2              1               91
  T3              5              324
  T4              1               49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  STRADB MUTATED     4   0   3
  STRADB WILD-TYPE 283 113  84
D995V6, multiclass
    clus
vv   STRADB MUTATED STRADB WILD-TYPE
  N0              4              283
  N1              0              113
  N2              3               84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D995V7, binary
                  cls
clus                 0   1
  STRADB MUTATED     4   1
  STRADB WILD-TYPE 371  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  STRADB MUTATED      4    1
  STRADB WILD-TYPE  371   64
   clus
vv  STRADB MUTATED STRADB WILD-TYPE
  0              4              371
  1              1               64
[1] 2 2
[1] FALSE
D995V8, binary
                  cls
clus                 0   1
  STRADB MUTATED     2   5
  STRADB WILD-TYPE 223 259
[1] "tbl2"
                  cls
clus               [,1] [,2]
  STRADB MUTATED      2    5
  STRADB WILD-TYPE  223  259
        clus
vv       STRADB MUTATED STRADB WILD-TYPE
  FEMALE              2              223
  MALE                5              259
[1] 2 2
[1] FALSE
D995V9, binary
                  cls
clus                 0   1
  STRADB MUTATED     3   1
  STRADB WILD-TYPE 347  21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  STRADB MUTATED      3    1
  STRADB WILD-TYPE  347   21
     clus
vv    STRADB MUTATED STRADB WILD-TYPE
  NO               3              347
  YES              1               21
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  STRADB MUTATED                      4                             1
  STRADB WILD-TYPE                  311                            46
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  STRADB MUTATED                       2                              0
  STRADB WILD-TYPE                   104                             10
D995V10, multiclass
                                clus
vv                               STRADB MUTATED STRADB WILD-TYPE
  COLON ADENOCARCINOMA                        4              311
  COLON MUCINOUS ADENOCARCINOMA               1               46
  RECTAL ADENOCARCINOMA                       2              104
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  STRADB MUTATED     4   0   1   0
  STRADB WILD-TYPE 341   4  30  25
D995V11, multiclass
    clus
vv   STRADB MUTATED STRADB WILD-TYPE
  R0              4              341
  R1              0                4
  R2              1               30
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D995V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  STRADB MUTATED                                  0     0
  STRADB WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  STRADB MUTATED                           0     3
  STRADB WILD-TYPE                        22   223
D995V13, multiclass
                                  clus
vv                                 STRADB MUTATED STRADB WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         3              223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(996) Variable = RANBP17 MUTATION ANALYSIS
D996V1, survival
                   sevent
clus2                 0   1
  RANBP17 MUTATED     9   3
  RANBP17 WILD-TYPE 369  90
  RANBP17 MUTATED RANBP17 WILD-TYPE 
               12               459 
  RANBP17 MUTATED RANBP17 WILD-TYPE 
                3                90 
$`RANBP17 MUTATED`
TCGA-AA-3696 TCGA-AA-3713 TCGA-AA-A01Q TCGA-AD-6889 TCGA-CA-6717 TCGA-CA-6718 
        5.03        19.04         1.02        56.55        12.76        10.06 
TCGA-CK-5916 TCGA-CM-6163 TCGA-D5-6924 TCGA-G4-6588 TCGA-AG-A002 TCGA-AH-6544 
       21.14         2.96        14.30        26.17        20.98        38.56 

$`RANBP17 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 
       19.00        36.00        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        31.00        38.07        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 
       18.05        40.96         0.07        21.37        15.52         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 
        3.06         3.25         3.29         0.07        12.20        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
        9.99        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       17.03        15.02        12.00        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        3.68         4.41        12.43         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 
       61.91        36.00        22.09        13.78        35.80        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6547 
       38.96        61.97        41.00        38.04       117.11         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  RANBP17 MUTATED RANBP17 WILD-TYPE 
             1.02              0.00 
  RANBP17 MUTATED RANBP17 WILD-TYPE 
            56.55            148.01 
  RANBP17 MUTATED RANBP17 WILD-TYPE 
            16.67             20.28 
[1] "1.0 - 56.5 (16.7)"  "0.0 - 148.0 (20.3)"
[1] "hr=" "1.7"
D996V2, continuous
D996V3, binary
                   cls
clus                  0   1
  RANBP17 MUTATED    10   2
  RANBP17 WILD-TYPE 356 117
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RANBP17 MUTATED     10    2
  RANBP17 WILD-TYPE  356  117
        clus
vv       RANBP17 MUTATED RANBP17 WILD-TYPE
  COLON               10               356
  RECTUM               2               117
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RANBP17 MUTATED         3        0        1         5         0         0
  RANBP17 WILD-TYPE      88        1       31       133        10         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RANBP17 MUTATED           0          0          0          0        2
  RANBP17 WILD-TYPE        24         11         59         42       46
                   vv
clus                STAGE IVA STAGE IVB
  RANBP17 MUTATED           0         0
  RANBP17 WILD-TYPE        18         1
D996V4, multiclass
            clus
vv           RANBP17 MUTATED RANBP17 WILD-TYPE
  STAGE I                  3                88
  STAGE IA                 0                 1
  STAGE II                 1                31
  STAGE IIA                5               133
  STAGE IIB                0                10
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               0                11
  STAGE IIIB               0                59
  STAGE IIIC               0                42
  STAGE IV                 2                46
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  RANBP17 MUTATED     2   1   9   0
  RANBP17 WILD-TYPE  15  91 320  50
D996V5, multiclass
    clus
vv   RANBP17 MUTATED RANBP17 WILD-TYPE
  T1               2                15
  T2               1                91
  T3               9               320
  T4               0                50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  RANBP17 MUTATED    10   2   0
  RANBP17 WILD-TYPE 277 111  87
D996V6, multiclass
    clus
vv   RANBP17 MUTATED RANBP17 WILD-TYPE
  N0              10               277
  N1               2               111
  N2               0                87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D996V7, binary
                   cls
clus                  0   1
  RANBP17 MUTATED     9   3
  RANBP17 WILD-TYPE 366  62
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RANBP17 MUTATED      9    3
  RANBP17 WILD-TYPE  366   62
   clus
vv  RANBP17 MUTATED RANBP17 WILD-TYPE
  0               9               366
  1               3                62
[1] 2 2
[1] FALSE
D996V8, binary
                   cls
clus                  0   1
  RANBP17 MUTATED     4   8
  RANBP17 WILD-TYPE 221 256
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RANBP17 MUTATED      4    8
  RANBP17 WILD-TYPE  221  256
        clus
vv       RANBP17 MUTATED RANBP17 WILD-TYPE
  FEMALE               4               221
  MALE                 8               256
[1] 2 2
[1] FALSE
D996V9, binary
                   cls
clus                  0   1
  RANBP17 MUTATED     9   1
  RANBP17 WILD-TYPE 341  21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RANBP17 MUTATED      9    1
  RANBP17 WILD-TYPE  341   21
     clus
vv    RANBP17 MUTATED RANBP17 WILD-TYPE
  NO                9               341
  YES               1                21
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  RANBP17 MUTATED                      9                             1
  RANBP17 WILD-TYPE                  306                            46
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  RANBP17 MUTATED                       2                              0
  RANBP17 WILD-TYPE                   104                             10
D996V10, multiclass
                                clus
vv                               RANBP17 MUTATED RANBP17 WILD-TYPE
  COLON ADENOCARCINOMA                         9               306
  COLON MUCINOUS ADENOCARCINOMA                1                46
  RECTAL ADENOCARCINOMA                        2               104
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  RANBP17 MUTATED     5   0   2   3
  RANBP17 WILD-TYPE 340   4  29  22
D996V11, multiclass
    clus
vv   RANBP17 MUTATED RANBP17 WILD-TYPE
  R0               5               340
  R1               0                 4
  R2               2                29
  RX               3                22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D996V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RANBP17 MUTATED                                  0     3
  RANBP17 WILD-TYPE                                1     8
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  RANBP17 MUTATED                           0     5
  RANBP17 WILD-TYPE                        22   221
D996V13, multiclass
                                  clus
vv                                 RANBP17 MUTATED RANBP17 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          3                 8
  BLACK OR AFRICAN AMERICAN                      0                22
  WHITE                                          5               221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(997) Variable = AHCTF1 MUTATION ANALYSIS
D997V1, survival
                  sevent
clus2                0   1
  AHCTF1 MUTATED    18   5
  AHCTF1 WILD-TYPE 360  88
  AHCTF1 MUTATED AHCTF1 WILD-TYPE 
              23              448 
  AHCTF1 MUTATED AHCTF1 WILD-TYPE 
               5               88 
$`AHCTF1 MUTATED`
TCGA-A6-6138 TCGA-A6-6653 TCGA-AA-3496 TCGA-AA-3518 TCGA-AA-3947 TCGA-AA-3956 
       22.52        24.39         1.02         1.02        33.01        34.03 
TCGA-AA-3966 TCGA-AA-3977 TCGA-AA-A010 TCGA-AA-A01I TCGA-AZ-4315 TCGA-AZ-5407 
        2.01        25.02        34.98        31.00        58.39        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-CA-6715 TCGA-CA-6717 TCGA-CK-6751 
       49.41         6.77        12.10         0.07        12.76       124.27 
TCGA-DM-A0XF TCGA-F4-6570 TCGA-G4-6628 TCGA-AG-3902 TCGA-DC-6681 
       38.20         6.18        79.69        32.02         5.95 

$`AHCTF1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6141 TCGA-A6-6142 
       22.09        22.06        32.71        27.09         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 
       25.18        24.16        21.76        24.69        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3510 
       19.66        20.28         7.04         3.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3520 
        6.97         1.02        13.02        38.99         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3968 TCGA-AA-3971 
       26.01        24.00         2.01        20.98        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01K 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6716 TCGA-CA-6718 
       12.69         3.06         3.25         3.29        12.20        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CM-4743 
       51.32         9.99        21.14        82.95         1.91        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A1D0 TCGA-DM-A1D4 
       11.38        10.26       119.70        24.43       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       35.74        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       26.17        91.79        46.75        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3909 TCGA-AG-3999 
       35.01        14.01         1.02        48.03        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6682 
        5.03        13.97        27.95        10.98        19.99         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  AHCTF1 MUTATED AHCTF1 WILD-TYPE 
            0.07             0.00 
  AHCTF1 MUTATED AHCTF1 WILD-TYPE 
          124.27           148.01 
  AHCTF1 MUTATED AHCTF1 WILD-TYPE 
          25.020           20.035 
[1] "0.1 - 124.3 (25.0)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1"  
D997V2, continuous
D997V3, binary
                  cls
clus                 0   1
  AHCTF1 MUTATED    21   2
  AHCTF1 WILD-TYPE 345 117
[1] "tbl2"
                  cls
clus               [,1] [,2]
  AHCTF1 MUTATED     21    2
  AHCTF1 WILD-TYPE  345  117
        clus
vv       AHCTF1 MUTATED AHCTF1 WILD-TYPE
  COLON              21              345
  RECTUM              2              117
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  AHCTF1 MUTATED         7        0        2         7         2         0
  AHCTF1 WILD-TYPE      84        1       30       131         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  AHCTF1 MUTATED           0          0          1          1        1
  AHCTF1 WILD-TYPE        24         11         58         41       47
                  vv
clus               STAGE IVA STAGE IVB
  AHCTF1 MUTATED           1         0
  AHCTF1 WILD-TYPE        17         1
D997V4, multiclass
            clus
vv           AHCTF1 MUTATED AHCTF1 WILD-TYPE
  STAGE I                 7               84
  STAGE IA                0                1
  STAGE II                2               30
  STAGE IIA               7              131
  STAGE IIB               2                8
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              1               58
  STAGE IIIC              1               41
  STAGE IV                1               47
  STAGE IVA               1               17
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  AHCTF1 MUTATED     1   7  12   3
  AHCTF1 WILD-TYPE  16  85 317  47
D997V5, multiclass
    clus
vv   AHCTF1 MUTATED AHCTF1 WILD-TYPE
  T1              1               16
  T2              7               85
  T3             12              317
  T4              3               47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  AHCTF1 MUTATED    19   2   2
  AHCTF1 WILD-TYPE 268 111  85
D997V6, multiclass
    clus
vv   AHCTF1 MUTATED AHCTF1 WILD-TYPE
  N0             19              268
  N1              2              111
  N2              2               85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D997V7, binary
                  cls
clus                 0   1
  AHCTF1 MUTATED    17   2
  AHCTF1 WILD-TYPE 358  63
[1] "tbl2"
                  cls
clus               [,1] [,2]
  AHCTF1 MUTATED     17    2
  AHCTF1 WILD-TYPE  358   63
   clus
vv  AHCTF1 MUTATED AHCTF1 WILD-TYPE
  0             17              358
  1              2               63
[1] 2 2
[1] FALSE
D997V8, binary
                  cls
clus                 0   1
  AHCTF1 MUTATED    11  12
  AHCTF1 WILD-TYPE 214 252
[1] "tbl2"
                  cls
clus               [,1] [,2]
  AHCTF1 MUTATED     11   12
  AHCTF1 WILD-TYPE  214  252
        clus
vv       AHCTF1 MUTATED AHCTF1 WILD-TYPE
  FEMALE             11              214
  MALE               12              252
[1] 2 2
[1] FALSE
D997V9, binary
                  cls
clus                 0   1
  AHCTF1 MUTATED    16   0
  AHCTF1 WILD-TYPE 334  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  AHCTF1 MUTATED     16    0
  AHCTF1 WILD-TYPE  334   22
     clus
vv    AHCTF1 MUTATED AHCTF1 WILD-TYPE
  NO              16              334
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  AHCTF1 MUTATED                     16                             4
  AHCTF1 WILD-TYPE                  299                            43
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  AHCTF1 MUTATED                       2                              0
  AHCTF1 WILD-TYPE                   104                             10
D997V10, multiclass
                                clus
vv                               AHCTF1 MUTATED AHCTF1 WILD-TYPE
  COLON ADENOCARCINOMA                       16              299
  COLON MUCINOUS ADENOCARCINOMA               4               43
  RECTAL ADENOCARCINOMA                       2              104
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  AHCTF1 MUTATED    11   0   0   3
  AHCTF1 WILD-TYPE 334   4  31  22
D997V11, multiclass
    clus
vv   AHCTF1 MUTATED AHCTF1 WILD-TYPE
  R0             11              334
  R1              0                4
  R2              0               31
  RX              3               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D997V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AHCTF1 MUTATED                                  0     2
  AHCTF1 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  AHCTF1 MUTATED                           1    11
  AHCTF1 WILD-TYPE                        21   215
D997V13, multiclass
                                  clus
vv                                 AHCTF1 MUTATED AHCTF1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                9
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                        11              215
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(998) Variable = OR10J1 MUTATION ANALYSIS
D998V1, survival
                  sevent
clus2                0   1
  OR10J1 MUTATED     8   4
  OR10J1 WILD-TYPE 370  89
  OR10J1 MUTATED OR10J1 WILD-TYPE 
              12              459 
  OR10J1 MUTATED OR10J1 WILD-TYPE 
               4               89 
$`OR10J1 MUTATED`
TCGA-AA-3877 TCGA-AA-3941 TCGA-AA-A00N TCGA-AZ-6606 TCGA-CA-6718 TCGA-CK-4947 
       31.00        24.00         4.01        11.74        10.06        17.56 
TCGA-CM-5861 TCGA-CM-6172 TCGA-D5-6533 TCGA-F4-6569 TCGA-F4-6570 TCGA-G4-6306 
       15.02        11.01         1.32        35.74         6.18        44.68 

$`OR10J1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
        2.01        12.99        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
      100.01        29.56         5.23         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       14.30       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       22.98        30.08        32.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       20.19        18.25        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6703 TCGA-F4-6704 
      117.07        98.24         8.61        31.96        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  OR10J1 MUTATED OR10J1 WILD-TYPE 
            1.32             0.00 
  OR10J1 MUTATED OR10J1 WILD-TYPE 
           44.68           148.01 
  OR10J1 MUTATED OR10J1 WILD-TYPE 
           13.38            20.55 
[1] "1.3 - 44.7 (13.4)"  "0.0 - 148.0 (20.6)"
[1] "hr=" "2.6"
D998V2, continuous
D998V3, binary
                  cls
clus                 0   1
  OR10J1 MUTATED    13   0
  OR10J1 WILD-TYPE 353 119
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR10J1 MUTATED     13    0
  OR10J1 WILD-TYPE  353  119
        clus
vv       OR10J1 MUTATED OR10J1 WILD-TYPE
  COLON              13              353
  RECTUM              0              119
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  OR10J1 MUTATED         2        0        0         5         1         0
  OR10J1 WILD-TYPE      89        1       32       133         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  OR10J1 MUTATED           0          0          3          0        1
  OR10J1 WILD-TYPE        24         11         56         42       47
                  vv
clus               STAGE IVA STAGE IVB
  OR10J1 MUTATED           1         0
  OR10J1 WILD-TYPE        17         1
D998V4, multiclass
            clus
vv           OR10J1 MUTATED OR10J1 WILD-TYPE
  STAGE I                 2               89
  STAGE IA                0                1
  STAGE II                0               32
  STAGE IIA               5              133
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              3               56
  STAGE IIIC              0               42
  STAGE IV                1               47
  STAGE IVA               1               17
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  OR10J1 MUTATED     1   2   5   5
  OR10J1 WILD-TYPE  16  90 324  45
D998V5, multiclass
    clus
vv   OR10J1 MUTATED OR10J1 WILD-TYPE
  T1              1               16
  T2              2               90
  T3              5              324
  T4              5               45
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  OR10J1 MUTATED     9   3   1
  OR10J1 WILD-TYPE 278 110  86
D998V6, multiclass
    clus
vv   OR10J1 MUTATED OR10J1 WILD-TYPE
  N0              9              278
  N1              3              110
  N2              1               86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D998V7, binary
                  cls
clus                 0   1
  OR10J1 MUTATED    11   2
  OR10J1 WILD-TYPE 364  63
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR10J1 MUTATED     11    2
  OR10J1 WILD-TYPE  364   63
   clus
vv  OR10J1 MUTATED OR10J1 WILD-TYPE
  0             11              364
  1              2               63
[1] 2 2
[1] FALSE
D998V8, binary
                  cls
clus                 0   1
  OR10J1 MUTATED     8   5
  OR10J1 WILD-TYPE 217 259
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR10J1 MUTATED      8    5
  OR10J1 WILD-TYPE  217  259
        clus
vv       OR10J1 MUTATED OR10J1 WILD-TYPE
  FEMALE              8              217
  MALE                5              259
[1] 2 2
[1] FALSE
D998V9, binary
                  cls
clus                 0   1
  OR10J1 MUTATED    10   0
  OR10J1 WILD-TYPE 340  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR10J1 MUTATED     10    0
  OR10J1 WILD-TYPE  340   22
     clus
vv    OR10J1 MUTATED OR10J1 WILD-TYPE
  NO              10              340
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  OR10J1 MUTATED                     11                             2
  OR10J1 WILD-TYPE                  304                            45
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  OR10J1 MUTATED                       0                              0
  OR10J1 WILD-TYPE                   106                             10
D998V10, multiclass
                                clus
vv                               OR10J1 MUTATED OR10J1 WILD-TYPE
  COLON ADENOCARCINOMA                       11              304
  COLON MUCINOUS ADENOCARCINOMA               2               45
  RECTAL ADENOCARCINOMA                       0              106
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  OR10J1 MUTATED    10   0   0   2
  OR10J1 WILD-TYPE 335   4  31  23
D998V11, multiclass
    clus
vv   OR10J1 MUTATED OR10J1 WILD-TYPE
  R0             10              335
  R1              0                4
  R2              0               31
  RX              2               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D998V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OR10J1 MUTATED                                  0     1
  OR10J1 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  OR10J1 MUTATED                           0     8
  OR10J1 WILD-TYPE                        22   218
D998V13, multiclass
                                  clus
vv                                 OR10J1 MUTATED OR10J1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         8              218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(999) Variable = MATN3 MUTATION ANALYSIS
D999V1, survival
                 sevent
clus2               0   1
  MATN3 MUTATED     4   2
  MATN3 WILD-TYPE 374  91
  MATN3 MUTATED MATN3 WILD-TYPE 
              6             465 
  MATN3 MUTATED MATN3 WILD-TYPE 
              2              91 
$`MATN3 MUTATED`
TCGA-A6-5665 TCGA-A6-6781 TCGA-AA-3672 TCGA-AA-3715 TCGA-AA-3950 TCGA-AA-A00N 
       22.06        19.66         0.92        19.04        24.00         4.01 

$`MATN3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
       54.02         2.01        14.01        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       85.05        26.99        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       33.01        26.01         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  MATN3 MUTATED MATN3 WILD-TYPE 
           0.92            0.00 
  MATN3 MUTATED MATN3 WILD-TYPE 
          24.00          148.01 
  MATN3 MUTATED MATN3 WILD-TYPE 
          19.35           20.28 
[1] "0.9 - 24.0 (19.4)"  "0.0 - 148.0 (20.3)"
[1] "hr=" "3"  
D999V2, continuous
D999V3, binary
                 cls
clus                0   1
  MATN3 MUTATED     6   0
  MATN3 WILD-TYPE 360 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MATN3 MUTATED      6    0
  MATN3 WILD-TYPE  360  119
        clus
vv       MATN3 MUTATED MATN3 WILD-TYPE
  COLON              6             360
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MATN3 MUTATED         0        0        1         2         1         0
  MATN3 WILD-TYPE      91        1       31       136         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MATN3 MUTATED           1          0          0          1        0         0
  MATN3 WILD-TYPE        23         11         59         41       48        18
                 vv
clus              STAGE IVB
  MATN3 MUTATED           0
  MATN3 WILD-TYPE         1
D999V4, multiclass
            clus
vv           MATN3 MUTATED MATN3 WILD-TYPE
  STAGE I                0              91
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              2             136
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             1              41
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  MATN3 MUTATED     0   0   4   2
  MATN3 WILD-TYPE  17  92 325  48
D999V5, multiclass
    clus
vv   MATN3 MUTATED MATN3 WILD-TYPE
  T1             0              17
  T2             0              92
  T3             4             325
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  MATN3 MUTATED     4   2   0
  MATN3 WILD-TYPE 283 111  87
D999V6, multiclass
    clus
vv   MATN3 MUTATED MATN3 WILD-TYPE
  N0             4             283
  N1             2             111
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D999V7, binary
                 cls
clus                0   1
  MATN3 MUTATED     5   0
  MATN3 WILD-TYPE 370  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MATN3 MUTATED      5    0
  MATN3 WILD-TYPE  370   65
   clus
vv  MATN3 MUTATED MATN3 WILD-TYPE
  0             5             370
  1             0              65
[1] 2 2
[1] FALSE
D999V8, binary
                 cls
clus                0   1
  MATN3 MUTATED     3   3
  MATN3 WILD-TYPE 222 261
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MATN3 MUTATED      3    3
  MATN3 WILD-TYPE  222  261
        clus
vv       MATN3 MUTATED MATN3 WILD-TYPE
  FEMALE             3             222
  MALE               3             261
[1] 2 2
[1] FALSE
D999V9, binary
                 cls
clus                0   1
  MATN3 MUTATED     5   0
  MATN3 WILD-TYPE 345  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MATN3 MUTATED      5    0
  MATN3 WILD-TYPE  345   22
     clus
vv    MATN3 MUTATED MATN3 WILD-TYPE
  NO              5             345
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MATN3 MUTATED                      3                             3
  MATN3 WILD-TYPE                  312                            44
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MATN3 MUTATED                       0                              0
  MATN3 WILD-TYPE                   106                             10
D999V10, multiclass
                                clus
vv                               MATN3 MUTATED MATN3 WILD-TYPE
  COLON ADENOCARCINOMA                       3             312
  COLON MUCINOUS ADENOCARCINOMA              3              44
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  MATN3 MUTATED     6   0   0   0
  MATN3 WILD-TYPE 339   4  31  25
D999V11, multiclass
    clus
vv   MATN3 MUTATED MATN3 WILD-TYPE
  R0             6             339
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D999V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MATN3 MUTATED                                  0     0
  MATN3 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  MATN3 MUTATED                           0     2
  MATN3 WILD-TYPE                        22   224
D999V13, multiclass
[1] "Remove cluster labels:" "MATN3 MUTATED"         
clus
  MATN3 MUTATED MATN3 WILD-TYPE 
              2             258 
     TCGA-A6-2671      TCGA-A6-2672      TCGA-A6-2674      TCGA-A6-2676 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-A6-2677      TCGA-A6-2678      TCGA-A6-2683      TCGA-A6-3807 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-A6-3808      TCGA-A6-3809      TCGA-A6-3810      TCGA-A6-4105 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-A6-5656      TCGA-A6-5657      TCGA-A6-5659      TCGA-A6-5660 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-A6-5661      TCGA-A6-5662      TCGA-A6-5664      TCGA-A6-5666 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-A6-6137      TCGA-A6-6138      TCGA-A6-6141      TCGA-A6-6142 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-A6-6648      TCGA-A6-6649      TCGA-A6-6651      TCGA-A6-6652 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-A6-6653      TCGA-A6-6654      TCGA-A6-6780      TCGA-A6-6782 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-AD-5900      TCGA-AD-6548      TCGA-AD-6888      TCGA-AD-6889 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-AD-6890      TCGA-AD-6895      TCGA-AD-6899      TCGA-AD-6901 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-AD-6963      TCGA-AD-6964      TCGA-AD-6965      TCGA-AU-3779 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-AU-6004      TCGA-AY-4070      TCGA-AY-4071      TCGA-AY-5543 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-AY-6196      TCGA-AY-6197      TCGA-AY-6386      TCGA-AZ-4315 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-AZ-4323      TCGA-AZ-4616      TCGA-AZ-4681      TCGA-AZ-4682 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-AZ-5403      TCGA-AZ-5407      TCGA-AZ-6598      TCGA-AZ-6599 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-AZ-6600      TCGA-AZ-6601      TCGA-AZ-6603      TCGA-AZ-6605 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-AZ-6606      TCGA-AZ-6607      TCGA-AZ-6608      TCGA-CA-5254 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-CA-5255      TCGA-CA-5796      TCGA-CA-5797      TCGA-CA-6715 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-CA-6716      TCGA-CA-6717      TCGA-CA-6718      TCGA-CA-6719 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-CK-4947      TCGA-CK-4948      TCGA-CK-4950      TCGA-CK-4952 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-CK-5912      TCGA-CK-5913      TCGA-CK-5914      TCGA-CK-5915 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-CK-5916      TCGA-CK-6746      TCGA-CK-6747      TCGA-CK-6748 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-CK-6751      TCGA-CM-4743      TCGA-CM-4744      TCGA-CM-4746 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-CM-4747      TCGA-CM-4752      TCGA-CM-5341      TCGA-CM-5344 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-CM-5348      TCGA-CM-5349      TCGA-CM-5860      TCGA-CM-5861 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-CM-5862      TCGA-CM-5863      TCGA-CM-5864      TCGA-CM-5868 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-CM-6161      TCGA-CM-6162      TCGA-CM-6163      TCGA-CM-6164 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-CM-6165      TCGA-CM-6166      TCGA-CM-6167      TCGA-CM-6168 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-CM-6169      TCGA-CM-6170      TCGA-CM-6171      TCGA-CM-6172 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-CM-6674      TCGA-CM-6675      TCGA-CM-6676      TCGA-CM-6677 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-CM-6678      TCGA-CM-6679      TCGA-CM-6680      TCGA-D5-5537 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-D5-5538      TCGA-D5-5539      TCGA-D5-5540      TCGA-D5-5541 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-D5-6529      TCGA-D5-6532      TCGA-D5-6533      TCGA-D5-6534 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-D5-6535      TCGA-D5-6536      TCGA-D5-6537      TCGA-D5-6538 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-D5-6539      TCGA-D5-6540      TCGA-D5-6541      TCGA-D5-6898 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-D5-6920      TCGA-D5-6922      TCGA-D5-6923      TCGA-D5-6924 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-D5-6926      TCGA-D5-6927      TCGA-D5-6928      TCGA-D5-6929 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-D5-6930      TCGA-D5-6931      TCGA-D5-6932      TCGA-D5-7000 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-DM-A0X9      TCGA-DM-A0XD      TCGA-DM-A0XF      TCGA-DM-A1D0 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-DM-A1D4      TCGA-DM-A1D6      TCGA-DM-A1D7      TCGA-DM-A1D8 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-DM-A1D9      TCGA-DM-A1DA      TCGA-DM-A1DB      TCGA-DM-A1HA 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-DM-A1HB      TCGA-DM-A282      TCGA-DM-A285      TCGA-DM-A28C 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-DM-A28E      TCGA-DM-A28F      TCGA-DM-A28G      TCGA-DM-A28H 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-DM-A28K      TCGA-F4-6459      TCGA-F4-6460      TCGA-F4-6569 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-F4-6570      TCGA-F4-6703      TCGA-F4-6704      TCGA-F4-6805 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-F4-6806      TCGA-F4-6807      TCGA-F4-6808      TCGA-F4-6809 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-F4-6854      TCGA-F4-6855      TCGA-F4-6856      TCGA-G4-6293 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-G4-6299      TCGA-G4-6303      TCGA-G4-6304      TCGA-G4-6306 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-G4-6307      TCGA-G4-6309      TCGA-G4-6310      TCGA-G4-6315 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-G4-6317      TCGA-G4-6321      TCGA-G4-6323      TCGA-G4-6586 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-G4-6588      TCGA-G4-6625      TCGA-G4-6626      TCGA-G4-6628 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-AF-2687      TCGA-AF-2689      TCGA-AF-2691      TCGA-AF-2692 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-AF-2693      TCGA-AF-3400      TCGA-AF-3913      TCGA-AF-4110 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-AF-5654      TCGA-AF-6136      TCGA-AF-6655      TCGA-AF-6672 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-AH-6544      TCGA-AH-6547      TCGA-AH-6549      TCGA-AH-6643 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-AH-6644      TCGA-CI-6619      TCGA-CI-6620      TCGA-CI-6621 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-CI-6622      TCGA-CI-6624      TCGA-CL-5917      TCGA-CL-5918 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-DC-5337      TCGA-DC-5869      TCGA-DC-6155      TCGA-DC-6157 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-DC-6158      TCGA-DC-6160      TCGA-DC-6681      TCGA-DC-6682 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-DC-6683      TCGA-DT-5265      TCGA-DY-A0XA      TCGA-DY-A1DC 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-DY-A1DD      TCGA-DY-A1DF      TCGA-DY-A1DG      TCGA-DY-A1H8 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-EF-5830      TCGA-EI-6506      TCGA-EI-6507      TCGA-EI-6508 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-EI-6510      TCGA-F5-6464      TCGA-F5-6465      TCGA-F5-6571 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-F5-6702      TCGA-F5-6811      TCGA-F5-6812      TCGA-F5-6813 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 
     TCGA-G5-6235      TCGA-G5-6641 
"MATN3 WILD-TYPE" "MATN3 WILD-TYPE" 

Clustering(1000) Variable = HNMT MUTATION ANALYSIS
D1000V1, survival
                sevent
clus2              0   1
  HNMT MUTATED     6   1
  HNMT WILD-TYPE 372  92
  HNMT MUTATED HNMT WILD-TYPE 
             7            464 
  HNMT MUTATED HNMT WILD-TYPE 
             1             92 
$`HNMT MUTATED`
TCGA-A6-6653 TCGA-AA-A010 TCGA-AD-6964 TCGA-CK-4948 TCGA-D5-5538 TCGA-D5-6536 
       24.39        34.98        10.88       148.01        12.26        17.85 
TCGA-DM-A1HB 
      135.65 

$`HNMT WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
       25.08        25.18        24.16        21.76        24.69        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4952 
       12.76        10.06        14.30        17.56        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       43.27        15.12         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
       44.32       131.51       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  HNMT MUTATED HNMT WILD-TYPE 
         10.88           0.00 
  HNMT MUTATED HNMT WILD-TYPE 
        148.01         140.38 
  HNMT MUTATED HNMT WILD-TYPE 
        24.390         20.155 
[1] "10.9 - 148.0 (24.4)" "0.0 - 140.4 (20.2)" 
[1] "hr=" "2.3"
D1000V2, continuous
D1000V3, binary
                cls
clus               0   1
  HNMT MUTATED     8   0
  HNMT WILD-TYPE 358 119
[1] "tbl2"
                cls
clus             [,1] [,2]
  HNMT MUTATED      8    0
  HNMT WILD-TYPE  358  119
        clus
vv       HNMT MUTATED HNMT WILD-TYPE
  COLON             8            358
  RECTUM            0            119
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  HNMT MUTATED         1        0        0         2         1         0
  HNMT WILD-TYPE      90        1       32       136         9         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  HNMT MUTATED           1          0          2          0        0         0
  HNMT WILD-TYPE        23         11         57         42       48        18
                vv
clus             STAGE IVB
  HNMT MUTATED           0
  HNMT WILD-TYPE         1
D1000V4, multiclass
            clus
vv           HNMT MUTATED HNMT WILD-TYPE
  STAGE I               1             90
  STAGE IA              0              1
  STAGE II              0             32
  STAGE IIA             2            136
  STAGE IIB             1              9
  STAGE IIC             0              1
  STAGE III             1             23
  STAGE IIIA            0             11
  STAGE IIIB            2             57
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  HNMT MUTATED     0   1   5   2
  HNMT WILD-TYPE  17  91 324  48
D1000V5, multiclass
    clus
vv   HNMT MUTATED HNMT WILD-TYPE
  T1            0             17
  T2            1             91
  T3            5            324
  T4            2             48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  HNMT MUTATED     4   3   1
  HNMT WILD-TYPE 283 110  86
D1000V6, multiclass
    clus
vv   HNMT MUTATED HNMT WILD-TYPE
  N0            4            283
  N1            3            110
  N2            1             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1000V7, binary
                cls
clus               0   1
  HNMT MUTATED     7   0
  HNMT WILD-TYPE 368  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  HNMT MUTATED      7    0
  HNMT WILD-TYPE  368   65
   clus
vv  HNMT MUTATED HNMT WILD-TYPE
  0            7            368
  1            0             65
[1] 2 2
[1] FALSE
D1000V8, binary
                cls
clus               0   1
  HNMT MUTATED     4   4
  HNMT WILD-TYPE 221 260
[1] "tbl2"
                cls
clus             [,1] [,2]
  HNMT MUTATED      4    4
  HNMT WILD-TYPE  221  260
        clus
vv       HNMT MUTATED HNMT WILD-TYPE
  FEMALE            4            221
  MALE              4            260
[1] 2 2
[1] FALSE
D1000V9, binary
                cls
clus               0   1
  HNMT MUTATED     6   0
  HNMT WILD-TYPE 344  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  HNMT MUTATED      6    0
  HNMT WILD-TYPE  344   22
     clus
vv    HNMT MUTATED HNMT WILD-TYPE
  NO             6            344
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  HNMT MUTATED                      7                             0
  HNMT WILD-TYPE                  308                            47
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  HNMT MUTATED                       0                              0
  HNMT WILD-TYPE                   106                             10
D1000V10, multiclass
                                clus
vv                               HNMT MUTATED HNMT WILD-TYPE
  COLON ADENOCARCINOMA                      7            308
  COLON MUCINOUS ADENOCARCINOMA             0             47
  RECTAL ADENOCARCINOMA                     0            106
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  HNMT MUTATED     5   0   0   0
  HNMT WILD-TYPE 340   4  31  25
D1000V11, multiclass
    clus
vv   HNMT MUTATED HNMT WILD-TYPE
  R0            5            340
  R1            0              4
  R2            0             31
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1000V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HNMT MUTATED                                  0     0
  HNMT WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  HNMT MUTATED                           0     6
  HNMT WILD-TYPE                        22   220
D1000V13, multiclass
                                  clus
vv                                 HNMT MUTATED HNMT WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       6            220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1001) Variable = PAGE2 MUTATION ANALYSIS
D1001V1, survival
                 sevent
clus2               0   1
  PAGE2 MUTATED     7   0
  PAGE2 WILD-TYPE 371  93
  PAGE2 MUTATED PAGE2 WILD-TYPE 
              7             464 
  PAGE2 MUTATED PAGE2 WILD-TYPE 
              0              93 
$`PAGE2 MUTATED`
TCGA-AA-3861 TCGA-CM-6162 TCGA-D5-5539 TCGA-DM-A282 TCGA-G4-6299 TCGA-G4-6625 
       30.05        12.00        19.59       139.17        74.56        91.79 
TCGA-AH-6549 
       17.49 

$`PAGE2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        31.07        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       17.03        15.02         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       12.03        45.40        12.26        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6303 TCGA-G4-6304 
        0.53        47.41        35.31       133.18        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6626 TCGA-G4-6628 
       22.09        13.78        35.80        26.17        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  PAGE2 MUTATED PAGE2 WILD-TYPE 
             12               0 
  PAGE2 MUTATED PAGE2 WILD-TYPE 
         139.17          148.01 
  PAGE2 MUTATED PAGE2 WILD-TYPE 
         30.050          20.155 
[1] "12.0 - 139.2 (30.1)" "0.0 - 148.0 (20.2)" 
[1] "hr="     "9500000"
D1001V2, continuous
D1001V3, binary
                 cls
clus                0   1
  PAGE2 MUTATED     8   1
  PAGE2 WILD-TYPE 358 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PAGE2 MUTATED      8    1
  PAGE2 WILD-TYPE  358  118
        clus
vv       PAGE2 MUTATED PAGE2 WILD-TYPE
  COLON              8             358
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PAGE2 MUTATED         0        0        0         4         0         0
  PAGE2 WILD-TYPE      91        1       32       134        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PAGE2 MUTATED           0          1          1          1        1         0
  PAGE2 WILD-TYPE        24         10         58         41       47        18
                 vv
clus              STAGE IVB
  PAGE2 MUTATED           0
  PAGE2 WILD-TYPE         1
D1001V4, multiclass
            clus
vv           PAGE2 MUTATED PAGE2 WILD-TYPE
  STAGE I                0              91
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              4             134
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             1              10
  STAGE IIIB             1              58
  STAGE IIIC             1              41
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PAGE2 MUTATED     0   0   8   1
  PAGE2 WILD-TYPE  17  92 321  49
D1001V5, multiclass
    clus
vv   PAGE2 MUTATED PAGE2 WILD-TYPE
  T1             0              17
  T2             0              92
  T3             8             321
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  PAGE2 MUTATED     4   2   2
  PAGE2 WILD-TYPE 283 111  85
D1001V6, multiclass
    clus
vv   PAGE2 MUTATED PAGE2 WILD-TYPE
  N0             4             283
  N1             2             111
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1001V7, binary
                 cls
clus                0   1
  PAGE2 MUTATED     7   1
  PAGE2 WILD-TYPE 368  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PAGE2 MUTATED      7    1
  PAGE2 WILD-TYPE  368   64
   clus
vv  PAGE2 MUTATED PAGE2 WILD-TYPE
  0             7             368
  1             1              64
[1] 2 2
[1] FALSE
D1001V8, binary
                 cls
clus                0   1
  PAGE2 MUTATED     5   4
  PAGE2 WILD-TYPE 220 260
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PAGE2 MUTATED      5    4
  PAGE2 WILD-TYPE  220  260
        clus
vv       PAGE2 MUTATED PAGE2 WILD-TYPE
  FEMALE             5             220
  MALE               4             260
[1] 2 2
[1] FALSE
D1001V9, binary
                 cls
clus                0   1
  PAGE2 MUTATED     6   0
  PAGE2 WILD-TYPE 344  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PAGE2 MUTATED      6    0
  PAGE2 WILD-TYPE  344   22
     clus
vv    PAGE2 MUTATED PAGE2 WILD-TYPE
  NO              6             344
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PAGE2 MUTATED                      5                             3
  PAGE2 WILD-TYPE                  310                            44
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PAGE2 MUTATED                       1                              0
  PAGE2 WILD-TYPE                   105                             10
D1001V10, multiclass
                                clus
vv                               PAGE2 MUTATED PAGE2 WILD-TYPE
  COLON ADENOCARCINOMA                       5             310
  COLON MUCINOUS ADENOCARCINOMA              3              44
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  PAGE2 MUTATED     6   0   1   1
  PAGE2 WILD-TYPE 339   4  30  24
D1001V11, multiclass
    clus
vv   PAGE2 MUTATED PAGE2 WILD-TYPE
  R0             6             339
  R1             0               4
  R2             1              30
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1001V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PAGE2 MUTATED                                  0     0
  PAGE2 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PAGE2 MUTATED                           0     6
  PAGE2 WILD-TYPE                        22   220
D1001V13, multiclass
                                  clus
vv                                 PAGE2 MUTATED PAGE2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        6             220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1002) Variable = MYH3 MUTATION ANALYSIS
D1002V1, survival
                sevent
clus2              0   1
  MYH3 MUTATED    26   8
  MYH3 WILD-TYPE 352  85
  MYH3 MUTATED MYH3 WILD-TYPE 
            34            437 
  MYH3 MUTATED MYH3 WILD-TYPE 
             8             85 
$`MYH3 MUTATED`
TCGA-A6-3809 TCGA-AA-3516 TCGA-AA-3555 TCGA-AA-3662 TCGA-AA-3950 TCGA-AA-A00N 
       32.75        13.02        29.95         6.05        24.00         4.01 
TCGA-AD-6889 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4315 TCGA-AZ-4616 TCGA-AZ-6600 
       56.55         0.72        10.88        58.39         5.13        12.10 
TCGA-AZ-6601 TCGA-AZ-6606 TCGA-CA-6717 TCGA-CK-4947 TCGA-CK-6751 TCGA-CM-4747 
      100.01        11.74        12.76        17.56       124.27        25.02 
TCGA-CM-6169 TCGA-CM-6172 TCGA-CM-6674 TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6535 
       13.02        11.01        12.95        20.19         1.32        15.12 
TCGA-D5-6539 TCGA-DM-A28G TCGA-F4-6808 TCGA-G4-6306 TCGA-G4-6321 TCGA-G4-6586 
       12.49        60.79        33.67        44.68        22.09        35.80 
TCGA-AF-2693 TCGA-AG-3881 TCGA-AG-A002 TCGA-DY-A0XA 
       19.10        19.04        20.98       126.44 

$`MYH3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       24.00        17.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02        78.08         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       33.01        26.01         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       21.37        15.52         0.79         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       21.44        17.82         1.41       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 
       88.21        49.41         6.77        29.56         5.23         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       12.20        10.06        14.30       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       23.05        20.02        37.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6170 TCGA-CM-6171 
       16.04        21.99        14.99        12.99        15.02        14.04 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6532 
       45.40        12.26        19.59        56.09        55.92        18.25 
TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 
       43.27        17.85         4.80        17.13        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       35.97       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       65.85        53.62        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       36.00        13.78        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3913 
       24.13        39.48        43.04        13.55        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
        0.99        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD 
        5.95         4.01         5.03         5.29        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  MYH3 MUTATED MYH3 WILD-TYPE 
          0.72           0.00 
  MYH3 MUTATED MYH3 WILD-TYPE 
        126.44         148.01 
  MYH3 MUTATED MYH3 WILD-TYPE 
         19.07          20.55 
[1] "0.7 - 126.4 (19.1)" "0.0 - 148.0 (20.6)"
[1] "hr=" "1.1"
D1002V2, continuous
D1002V3, binary
                cls
clus               0   1
  MYH3 MUTATED    33   3
  MYH3 WILD-TYPE 333 116
[1] "tbl2"
                cls
clus             [,1] [,2]
  MYH3 MUTATED     33    3
  MYH3 WILD-TYPE  333  116
        clus
vv       MYH3 MUTATED MYH3 WILD-TYPE
  COLON            33            333
  RECTUM            3            116
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MYH3 MUTATED         5        0        2        14         2         0
  MYH3 WILD-TYPE      86        1       30       124         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MYH3 MUTATED           2          1          4          0        4         1
  MYH3 WILD-TYPE        22         10         55         42       44        17
                vv
clus             STAGE IVB
  MYH3 MUTATED           0
  MYH3 WILD-TYPE         1
D1002V4, multiclass
            clus
vv           MYH3 MUTATED MYH3 WILD-TYPE
  STAGE I               5             86
  STAGE IA              0              1
  STAGE II              2             30
  STAGE IIA            14            124
  STAGE IIB             2              8
  STAGE IIC             0              1
  STAGE III             2             22
  STAGE IIIA            1             10
  STAGE IIIB            4             55
  STAGE IIIC            0             42
  STAGE IV              4             44
  STAGE IVA             1             17
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  MYH3 MUTATED     1   6  20  10
  MYH3 WILD-TYPE  16  86 309  40
D1002V5, multiclass
    clus
vv   MYH3 MUTATED MYH3 WILD-TYPE
  T1            1             16
  T2            6             86
  T3           20            309
  T4           10             40
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  MYH3 MUTATED    25   7   5
  MYH3 WILD-TYPE 262 106  82
D1002V6, multiclass
    clus
vv   MYH3 MUTATED MYH3 WILD-TYPE
  N0           25            262
  N1            7            106
  N2            5             82
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1002V7, binary
                cls
clus               0   1
  MYH3 MUTATED    25   5
  MYH3 WILD-TYPE 350  60
[1] "tbl2"
                cls
clus             [,1] [,2]
  MYH3 MUTATED     25    5
  MYH3 WILD-TYPE  350   60
   clus
vv  MYH3 MUTATED MYH3 WILD-TYPE
  0           25            350
  1            5             60
[1] 2 2
[1] FALSE
D1002V8, binary
                cls
clus               0   1
  MYH3 MUTATED    19  18
  MYH3 WILD-TYPE 206 246
[1] "tbl2"
                cls
clus             [,1] [,2]
  MYH3 MUTATED     19   18
  MYH3 WILD-TYPE  206  246
        clus
vv       MYH3 MUTATED MYH3 WILD-TYPE
  FEMALE           19            206
  MALE             18            246
[1] 2 2
[1] FALSE
D1002V9, binary
                cls
clus               0   1
  MYH3 MUTATED    27   0
  MYH3 WILD-TYPE 323  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  MYH3 MUTATED     27    0
  MYH3 WILD-TYPE  323   22
     clus
vv    MYH3 MUTATED MYH3 WILD-TYPE
  NO            27            323
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MYH3 MUTATED                     26                             7
  MYH3 WILD-TYPE                  289                            40
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MYH3 MUTATED                       2                              0
  MYH3 WILD-TYPE                   104                             10
D1002V10, multiclass
                                clus
vv                               MYH3 MUTATED MYH3 WILD-TYPE
  COLON ADENOCARCINOMA                     26            289
  COLON MUCINOUS ADENOCARCINOMA             7             40
  RECTAL ADENOCARCINOMA                     2            104
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  MYH3 MUTATED    19   0   1   5
  MYH3 WILD-TYPE 326   4  30  20
D1002V11, multiclass
    clus
vv   MYH3 MUTATED MYH3 WILD-TYPE
  R0           19            326
  R1            0              4
  R2            1             30
  RX            5             20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1002V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MYH3 MUTATED                                  0     2
  MYH3 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  MYH3 MUTATED                           2    24
  MYH3 WILD-TYPE                        20   202
D1002V13, multiclass
                                  clus
vv                                 MYH3 MUTATED MYH3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              9
  BLACK OR AFRICAN AMERICAN                   2             20
  WHITE                                      24            202
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1003) Variable = OR6C1 MUTATION ANALYSIS
D1003V1, survival
                 sevent
clus2               0   1
  OR6C1 MUTATED     6   2
  OR6C1 WILD-TYPE 372  91
  OR6C1 MUTATED OR6C1 WILD-TYPE 
              8             463 
  OR6C1 MUTATED OR6C1 WILD-TYPE 
              2              91 
$`OR6C1 MUTATED`
TCGA-A6-6651 TCGA-A6-6782 TCGA-AZ-4315 TCGA-CA-6717 TCGA-CA-6718 TCGA-DM-A285 
       21.76        20.28        58.39        12.76        10.06         6.12 
TCGA-DM-A28E TCGA-AG-3742 
      119.93         0.99 

$`OR6C1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.08        25.18        24.16        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        19.66         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       33.01        21.44        17.82         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A28C 
        7.50        44.32       131.51       135.65       139.17        81.37 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3878 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  OR6C1 MUTATED OR6C1 WILD-TYPE 
           0.99            0.00 
  OR6C1 MUTATED OR6C1 WILD-TYPE 
         119.93          148.01 
  OR6C1 MUTATED OR6C1 WILD-TYPE 
          16.52           20.19 
[1] "1.0 - 119.9 (16.5)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.1"
D1003V2, continuous
D1003V3, binary
                 cls
clus                0   1
  OR6C1 MUTATED     7   1
  OR6C1 WILD-TYPE 359 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR6C1 MUTATED      7    1
  OR6C1 WILD-TYPE  359  118
        clus
vv       OR6C1 MUTATED OR6C1 WILD-TYPE
  COLON              7             359
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  OR6C1 MUTATED         1        0        0         4         1         0
  OR6C1 WILD-TYPE      90        1       32       134         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  OR6C1 MUTATED           0          0          1          0        1         0
  OR6C1 WILD-TYPE        24         11         58         42       47        18
                 vv
clus              STAGE IVB
  OR6C1 MUTATED           0
  OR6C1 WILD-TYPE         1
D1003V4, multiclass
            clus
vv           OR6C1 MUTATED OR6C1 WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              4             134
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             0              42
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  OR6C1 MUTATED     1   0   6   1
  OR6C1 WILD-TYPE  16  92 323  49
D1003V5, multiclass
    clus
vv   OR6C1 MUTATED OR6C1 WILD-TYPE
  T1             1              16
  T2             0              92
  T3             6             323
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  OR6C1 MUTATED     6   1   1
  OR6C1 WILD-TYPE 281 112  86
D1003V6, multiclass
    clus
vv   OR6C1 MUTATED OR6C1 WILD-TYPE
  N0             6             281
  N1             1             112
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1003V7, binary
                 cls
clus                0   1
  OR6C1 MUTATED     5   1
  OR6C1 WILD-TYPE 370  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR6C1 MUTATED      5    1
  OR6C1 WILD-TYPE  370   64
   clus
vv  OR6C1 MUTATED OR6C1 WILD-TYPE
  0             5             370
  1             1              64
[1] 2 2
[1] FALSE
D1003V8, binary
                 cls
clus                0   1
  OR6C1 MUTATED     4   4
  OR6C1 WILD-TYPE 221 260
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR6C1 MUTATED      4    4
  OR6C1 WILD-TYPE  221  260
        clus
vv       OR6C1 MUTATED OR6C1 WILD-TYPE
  FEMALE             4             221
  MALE               4             260
[1] 2 2
[1] FALSE
D1003V9, binary
                 cls
clus                0   1
  OR6C1 MUTATED     5   0
  OR6C1 WILD-TYPE 345  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR6C1 MUTATED      5    0
  OR6C1 WILD-TYPE  345   22
     clus
vv    OR6C1 MUTATED OR6C1 WILD-TYPE
  NO              5             345
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  OR6C1 MUTATED                      5                             2
  OR6C1 WILD-TYPE                  310                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  OR6C1 MUTATED                       1                              0
  OR6C1 WILD-TYPE                   105                             10
D1003V10, multiclass
                                clus
vv                               OR6C1 MUTATED OR6C1 WILD-TYPE
  COLON ADENOCARCINOMA                       5             310
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  OR6C1 MUTATED     2   0   0   2
  OR6C1 WILD-TYPE 343   4  31  23
D1003V11, multiclass
    clus
vv   OR6C1 MUTATED OR6C1 WILD-TYPE
  R0             2             343
  R1             0               4
  R2             0              31
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1003V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OR6C1 MUTATED                                  0     2
  OR6C1 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  OR6C1 MUTATED                           0     5
  OR6C1 WILD-TYPE                        22   221
D1003V13, multiclass
                                  clus
vv                                 OR6C1 MUTATED OR6C1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               9
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        5             221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1004) Variable = GDE1 MUTATION ANALYSIS
D1004V1, survival
                sevent
clus2              0   1
  GDE1 MUTATED     5   1
  GDE1 WILD-TYPE 373  92
  GDE1 MUTATED GDE1 WILD-TYPE 
             6            465 
  GDE1 MUTATED GDE1 WILD-TYPE 
             1             92 
$`GDE1 MUTATED`
TCGA-A6-5656 TCGA-AZ-4315 TCGA-CA-6717 TCGA-CK-4950 TCGA-D5-6898 TCGA-F5-6464 
       32.91        58.39        12.76        85.45         1.48         9.96 

$`GDE1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        33.01        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 
       12.20        10.06        14.30        17.56       148.01        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       12.49        16.14        15.58         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
       18.28        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  GDE1 MUTATED GDE1 WILD-TYPE 
          1.48           0.00 
  GDE1 MUTATED GDE1 WILD-TYPE 
         85.45         148.01 
  GDE1 MUTATED GDE1 WILD-TYPE 
        22.835         20.190 
[1] "1.5 - 85.5 (22.8)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.5"
D1004V2, continuous
D1004V3, binary
                cls
clus               0   1
  GDE1 MUTATED     5   1
  GDE1 WILD-TYPE 361 118
[1] "tbl2"
                cls
clus             [,1] [,2]
  GDE1 MUTATED      5    1
  GDE1 WILD-TYPE  361  118
        clus
vv       GDE1 MUTATED GDE1 WILD-TYPE
  COLON             5            361
  RECTUM            1            118
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GDE1 MUTATED         2        0        0         2         0         0
  GDE1 WILD-TYPE      89        1       32       136        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  GDE1 MUTATED           0          0          1          1        0         0
  GDE1 WILD-TYPE        24         11         58         41       48        18
                vv
clus             STAGE IVB
  GDE1 MUTATED           0
  GDE1 WILD-TYPE         1
D1004V4, multiclass
            clus
vv           GDE1 MUTATED GDE1 WILD-TYPE
  STAGE I               2             89
  STAGE IA              0              1
  STAGE II              0             32
  STAGE IIA             2            136
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            1             58
  STAGE IIIC            1             41
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  GDE1 MUTATED     0   2   3   1
  GDE1 WILD-TYPE  17  90 326  49
D1004V5, multiclass
    clus
vv   GDE1 MUTATED GDE1 WILD-TYPE
  T1            0             17
  T2            2             90
  T3            3            326
  T4            1             49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  GDE1 MUTATED     4   1   1
  GDE1 WILD-TYPE 283 112  86
D1004V6, multiclass
    clus
vv   GDE1 MUTATED GDE1 WILD-TYPE
  N0            4            283
  N1            1            112
  N2            1             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1004V7, binary
                cls
clus               0   1
  GDE1 MUTATED     6   0
  GDE1 WILD-TYPE 369  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  GDE1 MUTATED      6    0
  GDE1 WILD-TYPE  369   65
   clus
vv  GDE1 MUTATED GDE1 WILD-TYPE
  0            6            369
  1            0             65
[1] 2 2
[1] FALSE
D1004V8, binary
                cls
clus               0   1
  GDE1 MUTATED     3   3
  GDE1 WILD-TYPE 222 261
[1] "tbl2"
                cls
clus             [,1] [,2]
  GDE1 MUTATED      3    3
  GDE1 WILD-TYPE  222  261
        clus
vv       GDE1 MUTATED GDE1 WILD-TYPE
  FEMALE            3            222
  MALE              3            261
[1] 2 2
[1] FALSE
D1004V9, binary
                cls
clus               0   1
  GDE1 MUTATED     5   0
  GDE1 WILD-TYPE 345  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  GDE1 MUTATED      5    0
  GDE1 WILD-TYPE  345   22
     clus
vv    GDE1 MUTATED GDE1 WILD-TYPE
  NO             5            345
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  GDE1 MUTATED                      4                             1
  GDE1 WILD-TYPE                  311                            46
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  GDE1 MUTATED                       1                              0
  GDE1 WILD-TYPE                   105                             10
D1004V10, multiclass
                                clus
vv                               GDE1 MUTATED GDE1 WILD-TYPE
  COLON ADENOCARCINOMA                      4            311
  COLON MUCINOUS ADENOCARCINOMA             1             46
  RECTAL ADENOCARCINOMA                     1            105
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  GDE1 MUTATED     3   1   0   1
  GDE1 WILD-TYPE 342   3  31  24
D1004V11, multiclass
    clus
vv   GDE1 MUTATED GDE1 WILD-TYPE
  R0            3            342
  R1            1              3
  R2            0             31
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1004V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GDE1 MUTATED                                  0     1
  GDE1 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  GDE1 MUTATED                           1     4
  GDE1 WILD-TYPE                        21   222
D1004V13, multiclass
                                  clus
vv                                 GDE1 MUTATED GDE1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                       4            222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1005) Variable = GRINA MUTATION ANALYSIS
D1005V1, survival
                 sevent
clus2               0   1
  GRINA MUTATED     3   1
  GRINA WILD-TYPE 375  92
  GRINA MUTATED GRINA WILD-TYPE 
              4             467 
  GRINA MUTATED GRINA WILD-TYPE 
              1              92 
$`GRINA MUTATED`
TCGA-A6-5665 TCGA-CM-5341 TCGA-G4-6309 TCGA-G4-6626 
       22.06        29.06        85.48        46.75 

$`GRINA WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       37.02        25.02        13.02        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 
       74.56        65.85        53.62        44.68        55.04        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       91.79        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  GRINA MUTATED GRINA WILD-TYPE 
          22.06            0.00 
  GRINA MUTATED GRINA WILD-TYPE 
          85.48          148.01 
  GRINA MUTATED GRINA WILD-TYPE 
         37.905          20.050 
[1] "22.1 - 85.5 (37.9)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.4"
D1005V2, continuous
D1005V3, binary
                 cls
clus                0   1
  GRINA MUTATED     4   0
  GRINA WILD-TYPE 362 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GRINA MUTATED      4    0
  GRINA WILD-TYPE  362  119
        clus
vv       GRINA MUTATED GRINA WILD-TYPE
  COLON              4             362
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GRINA MUTATED         0        0        0         2         0         0
  GRINA WILD-TYPE      91        1       32       136        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  GRINA MUTATED           0          1          1          0        0         0
  GRINA WILD-TYPE        24         10         58         42       48        18
                 vv
clus              STAGE IVB
  GRINA MUTATED           0
  GRINA WILD-TYPE         1
D1005V4, multiclass
            clus
vv           GRINA MUTATED GRINA WILD-TYPE
  STAGE I                0              91
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              2             136
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             1              10
  STAGE IIIB             1              58
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  GRINA MUTATED     0   1   3   0
  GRINA WILD-TYPE  17  91 326  50
D1005V5, multiclass
    clus
vv   GRINA MUTATED GRINA WILD-TYPE
  T1             0              17
  T2             1              91
  T3             3             326
  T4             0              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  GRINA MUTATED     2   2   0
  GRINA WILD-TYPE 285 111  87
D1005V6, multiclass
    clus
vv   GRINA MUTATED GRINA WILD-TYPE
  N0             2             285
  N1             2             111
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1005V7, binary
                 cls
clus                0   1
  GRINA MUTATED     4   0
  GRINA WILD-TYPE 371  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GRINA MUTATED      4    0
  GRINA WILD-TYPE  371   65
   clus
vv  GRINA MUTATED GRINA WILD-TYPE
  0             4             371
  1             0              65
[1] 2 2
[1] FALSE
D1005V8, binary
                 cls
clus                0   1
  GRINA MUTATED     3   1
  GRINA WILD-TYPE 222 263
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GRINA MUTATED      3    1
  GRINA WILD-TYPE  222  263
        clus
vv       GRINA MUTATED GRINA WILD-TYPE
  FEMALE             3             222
  MALE               1             263
[1] 2 2
[1] FALSE
D1005V9, binary
                 cls
clus                0   1
  GRINA MUTATED     4   0
  GRINA WILD-TYPE 346  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GRINA MUTATED      4    0
  GRINA WILD-TYPE  346   22
     clus
vv    GRINA MUTATED GRINA WILD-TYPE
  NO              4             346
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  GRINA MUTATED                      4                             0
  GRINA WILD-TYPE                  311                            47
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  GRINA MUTATED                       0                              0
  GRINA WILD-TYPE                   106                             10
D1005V10, multiclass
                                clus
vv                               GRINA MUTATED GRINA WILD-TYPE
  COLON ADENOCARCINOMA                       4             311
  COLON MUCINOUS ADENOCARCINOMA              0              47
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  GRINA MUTATED     4   0   0   0
  GRINA WILD-TYPE 341   4  31  25
D1005V11, multiclass
    clus
vv   GRINA MUTATED GRINA WILD-TYPE
  R0             4             341
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1005V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GRINA MUTATED                                  0     0
  GRINA WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  GRINA MUTATED                           1     3
  GRINA WILD-TYPE                        21   223
D1005V13, multiclass
                                  clus
vv                                 GRINA MUTATED GRINA WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        3             223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1006) Variable = FRMD4B MUTATION ANALYSIS
D1006V1, survival
                  sevent
clus2                0   1
  FRMD4B MUTATED     7   1
  FRMD4B WILD-TYPE 371  92
  FRMD4B MUTATED FRMD4B WILD-TYPE 
               8              463 
  FRMD4B MUTATED FRMD4B WILD-TYPE 
               1               92 
$`FRMD4B MUTATED`
TCGA-AA-A01T TCGA-AY-6197 TCGA-AZ-6599 TCGA-CA-6717 TCGA-CM-6679 TCGA-G4-6304 
       33.04        21.44         6.77        12.76        10.06        53.62 
TCGA-AG-A002 TCGA-EI-6506 
       20.98        20.55 

$`FRMD4B WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
       35.01         1.02        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        33.01        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 
      106.75        22.36        62.79        88.21        49.41        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.08        11.01        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 
       47.41        35.31       133.18        74.56        65.85        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
        0.49        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  FRMD4B MUTATED FRMD4B WILD-TYPE 
            6.77             0.00 
  FRMD4B MUTATED FRMD4B WILD-TYPE 
           53.62           148.01 
  FRMD4B MUTATED FRMD4B WILD-TYPE 
          20.765           20.120 
[1] "6.8 - 53.6 (20.8)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.4"
D1006V2, continuous
D1006V3, binary
                  cls
clus                 0   1
  FRMD4B MUTATED     6   2
  FRMD4B WILD-TYPE 360 117
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FRMD4B MUTATED      6    2
  FRMD4B WILD-TYPE  360  117
        clus
vv       FRMD4B MUTATED FRMD4B WILD-TYPE
  COLON               6              360
  RECTUM              2              117
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FRMD4B MUTATED         2        0        0         4         1         0
  FRMD4B WILD-TYPE      89        1       32       134         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FRMD4B MUTATED           1          0          0          0        0
  FRMD4B WILD-TYPE        23         11         59         42       48
                  vv
clus               STAGE IVA STAGE IVB
  FRMD4B MUTATED           0         0
  FRMD4B WILD-TYPE        18         1
D1006V4, multiclass
            clus
vv           FRMD4B MUTATED FRMD4B WILD-TYPE
  STAGE I                 2               89
  STAGE IA                0                1
  STAGE II                0               32
  STAGE IIA               4              134
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               1               23
  STAGE IIIA              0               11
  STAGE IIIB              0               59
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  FRMD4B MUTATED     0   2   5   1
  FRMD4B WILD-TYPE  17  90 324  49
D1006V5, multiclass
    clus
vv   FRMD4B MUTATED FRMD4B WILD-TYPE
  T1              0               17
  T2              2               90
  T3              5              324
  T4              1               49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  FRMD4B MUTATED     7   1   0
  FRMD4B WILD-TYPE 280 112  87
D1006V6, multiclass
    clus
vv   FRMD4B MUTATED FRMD4B WILD-TYPE
  N0              7              280
  N1              1              112
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1006V7, binary
                  cls
clus                 0   1
  FRMD4B MUTATED     6   0
  FRMD4B WILD-TYPE 369  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FRMD4B MUTATED      6    0
  FRMD4B WILD-TYPE  369   65
   clus
vv  FRMD4B MUTATED FRMD4B WILD-TYPE
  0              6              369
  1              0               65
[1] 2 2
[1] FALSE
D1006V8, binary
                  cls
clus                 0   1
  FRMD4B MUTATED     3   5
  FRMD4B WILD-TYPE 222 259
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FRMD4B MUTATED      3    5
  FRMD4B WILD-TYPE  222  259
        clus
vv       FRMD4B MUTATED FRMD4B WILD-TYPE
  FEMALE              3              222
  MALE                5              259
[1] 2 2
[1] FALSE
D1006V9, binary
                  cls
clus                 0   1
  FRMD4B MUTATED     8   0
  FRMD4B WILD-TYPE 342  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FRMD4B MUTATED      8    0
  FRMD4B WILD-TYPE  342   22
     clus
vv    FRMD4B MUTATED FRMD4B WILD-TYPE
  NO               8              342
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  FRMD4B MUTATED                      5                             1
  FRMD4B WILD-TYPE                  310                            46
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  FRMD4B MUTATED                       2                              0
  FRMD4B WILD-TYPE                   104                             10
D1006V10, multiclass
                                clus
vv                               FRMD4B MUTATED FRMD4B WILD-TYPE
  COLON ADENOCARCINOMA                        5              310
  COLON MUCINOUS ADENOCARCINOMA               1               46
  RECTAL ADENOCARCINOMA                       2              104
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  FRMD4B MUTATED     6   0   0   1
  FRMD4B WILD-TYPE 339   4  31  24
D1006V11, multiclass
    clus
vv   FRMD4B MUTATED FRMD4B WILD-TYPE
  R0              6              339
  R1              0                4
  R2              0               31
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1006V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FRMD4B MUTATED                                  0     1
  FRMD4B WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  FRMD4B MUTATED                           0     5
  FRMD4B WILD-TYPE                        22   221
D1006V13, multiclass
                                  clus
vv                                 FRMD4B MUTATED FRMD4B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         5              221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1007) Variable = ARHGAP11A MUTATION ANALYSIS
D1007V1, survival
                     sevent
clus2                   0   1
  ARHGAP11A MUTATED    13   2
  ARHGAP11A WILD-TYPE 365  91
  ARHGAP11A MUTATED ARHGAP11A WILD-TYPE 
                 15                 456 
  ARHGAP11A MUTATED ARHGAP11A WILD-TYPE 
                  2                  91 
$`ARHGAP11A MUTATED`
TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3662 TCGA-AA-3977 TCGA-AA-A01X TCGA-AD-6889 
       20.12        19.66         6.05        25.02        26.01        56.55 
TCGA-AD-6964 TCGA-AU-6004 TCGA-AZ-6601 TCGA-CA-6717 TCGA-CM-5348 TCGA-CM-6166 
       10.88        27.09       100.01        12.76        22.98        21.99 
TCGA-D5-5541 TCGA-AG-3892 TCGA-AG-A002 
       55.92        13.02        20.98 

$`ARHGAP11A WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       23.87        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
        0.07        21.37        15.52         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 
       22.42        27.42         0.20        14.50        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
       12.10        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       29.06        22.03        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       29.03        16.04        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       56.09        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       17.03        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  ARHGAP11A MUTATED ARHGAP11A WILD-TYPE 
               6.05                0.00 
  ARHGAP11A MUTATED ARHGAP11A WILD-TYPE 
             100.01              148.01 
  ARHGAP11A MUTATED ARHGAP11A WILD-TYPE 
             21.990              20.035 
[1] "6.0 - 100.0 (22.0)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.7"
D1007V2, continuous
D1007V3, binary
                     cls
clus                    0   1
  ARHGAP11A MUTATED    14   2
  ARHGAP11A WILD-TYPE 352 117
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  ARHGAP11A MUTATED     14    2
  ARHGAP11A WILD-TYPE  352  117
        clus
vv       ARHGAP11A MUTATED ARHGAP11A WILD-TYPE
  COLON                 14                 352
  RECTUM                 2                 117
[1] 2 2
[1] FALSE
                     vv
clus                  STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ARHGAP11A MUTATED         4        0        1         4         0         0
  ARHGAP11A WILD-TYPE      87        1       31       134        10         1
                     vv
clus                  STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ARHGAP11A MUTATED           1          0          2          1        1
  ARHGAP11A WILD-TYPE        23         11         57         41       47
                     vv
clus                  STAGE IVA STAGE IVB
  ARHGAP11A MUTATED           0         0
  ARHGAP11A WILD-TYPE        18         1
D1007V4, multiclass
            clus
vv           ARHGAP11A MUTATED ARHGAP11A WILD-TYPE
  STAGE I                    4                  87
  STAGE IA                   0                   1
  STAGE II                   1                  31
  STAGE IIA                  4                 134
  STAGE IIB                  0                  10
  STAGE IIC                  0                   1
  STAGE III                  1                  23
  STAGE IIIA                 0                  11
  STAGE IIIB                 2                  57
  STAGE IIIC                 1                  41
  STAGE IV                   1                  47
  STAGE IVA                  0                  18
  STAGE IVB                  0                   1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                   T1  T2  T3  T4
  ARHGAP11A MUTATED     1   5   7   3
  ARHGAP11A WILD-TYPE  16  87 322  47
D1007V5, multiclass
    clus
vv   ARHGAP11A MUTATED ARHGAP11A WILD-TYPE
  T1                 1                  16
  T2                 5                  87
  T3                 7                 322
  T4                 3                  47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                   N0  N1  N2
  ARHGAP11A MUTATED    10   4   2
  ARHGAP11A WILD-TYPE 277 109  85
D1007V6, multiclass
    clus
vv   ARHGAP11A MUTATED ARHGAP11A WILD-TYPE
  N0                10                 277
  N1                 4                 109
  N2                 2                  85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1007V7, binary
                     cls
clus                    0   1
  ARHGAP11A MUTATED    11   1
  ARHGAP11A WILD-TYPE 364  64
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  ARHGAP11A MUTATED     11    1
  ARHGAP11A WILD-TYPE  364   64
   clus
vv  ARHGAP11A MUTATED ARHGAP11A WILD-TYPE
  0                11                 364
  1                 1                  64
[1] 2 2
[1] FALSE
D1007V8, binary
                     cls
clus                    0   1
  ARHGAP11A MUTATED     6  10
  ARHGAP11A WILD-TYPE 219 254
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  ARHGAP11A MUTATED      6   10
  ARHGAP11A WILD-TYPE  219  254
        clus
vv       ARHGAP11A MUTATED ARHGAP11A WILD-TYPE
  FEMALE                 6                 219
  MALE                  10                 254
[1] 2 2
[1] FALSE
D1007V9, binary
                     cls
clus                    0   1
  ARHGAP11A MUTATED    13   0
  ARHGAP11A WILD-TYPE 337  22
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  ARHGAP11A MUTATED     13    0
  ARHGAP11A WILD-TYPE  337   22
     clus
vv    ARHGAP11A MUTATED ARHGAP11A WILD-TYPE
  NO                 13                 337
  YES                 0                  22
[1] 2 2
[1] FALSE
                     vv
clus                  COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ARHGAP11A MUTATED                     11                             3
  ARHGAP11A WILD-TYPE                  304                            44
                     vv
clus                  RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ARHGAP11A MUTATED                       2                              0
  ARHGAP11A WILD-TYPE                   104                             10
D1007V10, multiclass
                                clus
vv                               ARHGAP11A MUTATED ARHGAP11A WILD-TYPE
  COLON ADENOCARCINOMA                          11                 304
  COLON MUCINOUS ADENOCARCINOMA                  3                  44
  RECTAL ADENOCARCINOMA                          2                 104
  RECTAL MUCINOUS ADENOCARCINOMA                 0                  10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                   R0  R1  R2  RX
  ARHGAP11A MUTATED     8   0   1   2
  ARHGAP11A WILD-TYPE 337   4  30  23
D1007V11, multiclass
    clus
vv   ARHGAP11A MUTATED ARHGAP11A WILD-TYPE
  R0                 8                 337
  R1                 0                   4
  R2                 1                  30
  RX                 2                  23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1007V12, continuous
                     vv
clus                  AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ARHGAP11A MUTATED                                  0     2
  ARHGAP11A WILD-TYPE                                1     9
                     vv
clus                  BLACK OR AFRICAN AMERICAN WHITE
  ARHGAP11A MUTATED                           0     8
  ARHGAP11A WILD-TYPE                        22   218
D1007V13, multiclass
                                  clus
vv                                 ARHGAP11A MUTATED ARHGAP11A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                 0                   1
  ASIAN                                            2                   9
  BLACK OR AFRICAN AMERICAN                        0                  22
  WHITE                                            8                 218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1008) Variable = CHRM2 MUTATION ANALYSIS
D1008V1, survival
                 sevent
clus2               0   1
  CHRM2 MUTATED    20   3
  CHRM2 WILD-TYPE 358  90
  CHRM2 MUTATED CHRM2 WILD-TYPE 
             23             448 
  CHRM2 MUTATED CHRM2 WILD-TYPE 
              3              90 
$`CHRM2 MUTATED`
TCGA-A6-5664 TCGA-A6-6141 TCGA-A6-6651 TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3688 
       22.09         8.38        21.76         3.02        63.98        19.00 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-A00N TCGA-AA-A010 TCGA-AD-6889 
       26.99        19.04        19.04         4.01        34.98        56.55 
TCGA-CA-6717 TCGA-CK-5913 TCGA-CM-6172 TCGA-D5-6923 TCGA-D5-6931 TCGA-DM-A1HA 
       12.76        51.32        11.01        12.43        12.00       131.51 
TCGA-G4-6293 TCGA-G4-6304 TCGA-AG-3593 TCGA-AG-A002 TCGA-EI-6506 
      133.18        53.62        34.03        20.98        20.55 

$`CHRM2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 
       22.06        32.71        27.09        22.52        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       24.16        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 
       20.28         7.04         1.02        35.01         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
       13.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       36.03         8.05        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       78.08         6.05         6.97        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3811 TCGA-AA-3812 
       37.05        36.00         5.03        85.05        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
        0.07        21.37        15.52         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07        12.20        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 
      148.01        85.45        15.62        49.08         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6674 
       14.99        12.99        13.02        15.02        14.04        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
        4.41        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
        1.51        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
        7.50        44.32       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       35.31        74.56        65.85        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
        1.02        46.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6507 TCGA-EI-6508 
       24.13        51.48        32.61         0.49        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  CHRM2 MUTATED CHRM2 WILD-TYPE 
           3.02            0.00 
  CHRM2 MUTATED CHRM2 WILD-TYPE 
         133.18          148.01 
  CHRM2 MUTATED CHRM2 WILD-TYPE 
         20.980          20.085 
[1] "3.0 - 133.2 (21.0)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.9"
D1008V2, continuous
D1008V3, binary
                 cls
clus                0   1
  CHRM2 MUTATED    23   3
  CHRM2 WILD-TYPE 343 116
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CHRM2 MUTATED     23    3
  CHRM2 WILD-TYPE  343  116
        clus
vv       CHRM2 MUTATED CHRM2 WILD-TYPE
  COLON             23             343
  RECTUM             3             116
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CHRM2 MUTATED         2        0        4         7         3         0
  CHRM2 WILD-TYPE      89        1       28       131         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CHRM2 MUTATED           1          0          2          3        4         0
  CHRM2 WILD-TYPE        23         11         57         39       44        18
                 vv
clus              STAGE IVB
  CHRM2 MUTATED           0
  CHRM2 WILD-TYPE         1
D1008V4, multiclass
            clus
vv           CHRM2 MUTATED CHRM2 WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               4              28
  STAGE IIA              7             131
  STAGE IIB              3               7
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             2              57
  STAGE IIIC             3              39
  STAGE IV               4              44
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CHRM2 MUTATED     0   2  17   7
  CHRM2 WILD-TYPE  17  90 312  43
D1008V5, multiclass
    clus
vv   CHRM2 MUTATED CHRM2 WILD-TYPE
  T1             0              17
  T2             2              90
  T3            17             312
  T4             7              43
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  CHRM2 MUTATED    17   4   5
  CHRM2 WILD-TYPE 270 109  82
D1008V6, multiclass
    clus
vv   CHRM2 MUTATED CHRM2 WILD-TYPE
  N0            17             270
  N1             4             109
  N2             5              82
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1008V7, binary
                 cls
clus                0   1
  CHRM2 MUTATED    19   4
  CHRM2 WILD-TYPE 356  61
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CHRM2 MUTATED     19    4
  CHRM2 WILD-TYPE  356   61
   clus
vv  CHRM2 MUTATED CHRM2 WILD-TYPE
  0            19             356
  1             4              61
[1] 2 2
[1] FALSE
D1008V8, binary
                 cls
clus                0   1
  CHRM2 MUTATED    13  13
  CHRM2 WILD-TYPE 212 251
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CHRM2 MUTATED     13   13
  CHRM2 WILD-TYPE  212  251
        clus
vv       CHRM2 MUTATED CHRM2 WILD-TYPE
  FEMALE            13             212
  MALE              13             251
[1] 2 2
[1] FALSE
D1008V9, binary
                 cls
clus                0   1
  CHRM2 MUTATED    18   2
  CHRM2 WILD-TYPE 332  20
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CHRM2 MUTATED     18    2
  CHRM2 WILD-TYPE  332   20
     clus
vv    CHRM2 MUTATED CHRM2 WILD-TYPE
  NO             18             332
  YES             2              20
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CHRM2 MUTATED                     20                             3
  CHRM2 WILD-TYPE                  295                            44
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CHRM2 MUTATED                       3                              0
  CHRM2 WILD-TYPE                   103                             10
D1008V10, multiclass
                                clus
vv                               CHRM2 MUTATED CHRM2 WILD-TYPE
  COLON ADENOCARCINOMA                      20             295
  COLON MUCINOUS ADENOCARCINOMA              3              44
  RECTAL ADENOCARCINOMA                      3             103
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  CHRM2 MUTATED    15   0   4   2
  CHRM2 WILD-TYPE 330   4  27  23
D1008V11, multiclass
    clus
vv   CHRM2 MUTATED CHRM2 WILD-TYPE
  R0            15             330
  R1             0               4
  R2             4              27
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1008V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CHRM2 MUTATED                                  0     2
  CHRM2 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CHRM2 MUTATED                           2     9
  CHRM2 WILD-TYPE                        20   217
D1008V13, multiclass
                                  clus
vv                                 CHRM2 MUTATED CHRM2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               9
  BLACK OR AFRICAN AMERICAN                    2              20
  WHITE                                        9             217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1009) Variable = CEP290 MUTATION ANALYSIS
D1009V1, survival
                  sevent
clus2                0   1
  CEP290 MUTATED    24   4
  CEP290 WILD-TYPE 354  89
  CEP290 MUTATED CEP290 WILD-TYPE 
              28              443 
  CEP290 MUTATED CEP290 WILD-TYPE 
               4               89 
$`CEP290 MUTATED`
TCGA-A6-4105 TCGA-A6-6141 TCGA-A6-6651 TCGA-AA-3663 TCGA-AA-3672 TCGA-AA-3710 
       14.53         8.38        21.76         6.97         0.92        26.99 
TCGA-AA-3715 TCGA-AA-3815 TCGA-AA-3864 TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A010 
       19.04        33.04        53.00        25.02         4.01        34.98 
TCGA-AZ-4315 TCGA-AZ-5407 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-5913 TCGA-D5-6540 
       58.39        88.21        12.76        10.06        51.32        16.14 
TCGA-DM-A1HB TCGA-G4-6321 TCGA-G4-6323 TCGA-AF-6655 TCGA-AG-3898 TCGA-AG-A002 
      135.65        22.09        13.78        20.02        48.03        20.98 
TCGA-AH-6549 TCGA-CI-6619 TCGA-DY-A0XA TCGA-G5-6641 
       17.49         6.05       126.44        26.43 

$`CEP290 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 
       16.57        34.65        33.34        32.75        36.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 
       22.06        32.71        27.09        22.52        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       24.16        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02        78.08         6.05        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
       14.01        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 
       37.05        19.00        36.00         5.03        85.05        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       10.06        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 
        0.99        31.07        31.07        30.05        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
       16.31         0.95        33.01        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 
        5.13       106.75        22.36        62.79        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       12.20        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       49.08         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
       44.32       131.51       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6586 TCGA-G4-6588 
       85.48        63.62        61.91        36.00        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       15.39        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
       14.01         1.02        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.69         0.72        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC 
       19.99         5.95         4.01         5.03         5.29        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       28.57        32.19         0.66         0.69        55.76 

  CEP290 MUTATED CEP290 WILD-TYPE 
            0.92             0.00 
  CEP290 MUTATED CEP290 WILD-TYPE 
          135.65           148.01 
  CEP290 MUTATED CEP290 WILD-TYPE 
           21.37            20.12 
[1] "0.9 - 135.7 (21.4)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.7"
D1009V2, continuous
D1009V3, binary
                  cls
clus                 0   1
  CEP290 MUTATED    24   7
  CEP290 WILD-TYPE 342 112
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CEP290 MUTATED     24    7
  CEP290 WILD-TYPE  342  112
        clus
vv       CEP290 MUTATED CEP290 WILD-TYPE
  COLON              24              342
  RECTUM              7              112
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CEP290 MUTATED         3        1        3        11         2         0
  CEP290 WILD-TYPE      88        0       29       127         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CEP290 MUTATED           3          2          2          0        2
  CEP290 WILD-TYPE        21          9         57         42       46
                  vv
clus               STAGE IVA STAGE IVB
  CEP290 MUTATED           0         0
  CEP290 WILD-TYPE        18         1
D1009V4, multiclass
            clus
vv           CEP290 MUTATED CEP290 WILD-TYPE
  STAGE I                 3               88
  STAGE IA                1                0
  STAGE II                3               29
  STAGE IIA              11              127
  STAGE IIB               2                8
  STAGE IIC               0                1
  STAGE III               3               21
  STAGE IIIA              2                9
  STAGE IIIB              2               57
  STAGE IIIC              0               42
  STAGE IV                2               46
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  CEP290 MUTATED     2   5  20   3
  CEP290 WILD-TYPE  15  87 309  47
D1009V5, multiclass
    clus
vv   CEP290 MUTATED CEP290 WILD-TYPE
  T1              2               15
  T2              5               87
  T3             20              309
  T4              3               47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  CEP290 MUTATED    21   7   2
  CEP290 WILD-TYPE 266 106  85
D1009V6, multiclass
    clus
vv   CEP290 MUTATED CEP290 WILD-TYPE
  N0             21              266
  N1              7              106
  N2              2               85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1009V7, binary
                  cls
clus                 0   1
  CEP290 MUTATED    22   2
  CEP290 WILD-TYPE 353  63
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CEP290 MUTATED     22    2
  CEP290 WILD-TYPE  353   63
   clus
vv  CEP290 MUTATED CEP290 WILD-TYPE
  0             22              353
  1              2               63
[1] 2 2
[1] FALSE
D1009V8, binary
                  cls
clus                 0   1
  CEP290 MUTATED    11  20
  CEP290 WILD-TYPE 214 244
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CEP290 MUTATED     11   20
  CEP290 WILD-TYPE  214  244
        clus
vv       CEP290 MUTATED CEP290 WILD-TYPE
  FEMALE             11              214
  MALE               20              244
[1] 2 2
[1] FALSE
D1009V9, binary
                  cls
clus                 0   1
  CEP290 MUTATED    24   0
  CEP290 WILD-TYPE 326  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CEP290 MUTATED     24    0
  CEP290 WILD-TYPE  326   22
     clus
vv    CEP290 MUTATED CEP290 WILD-TYPE
  NO              24              326
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CEP290 MUTATED                     19                             4
  CEP290 WILD-TYPE                  296                            43
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CEP290 MUTATED                       6                              1
  CEP290 WILD-TYPE                   100                              9
D1009V10, multiclass
                                clus
vv                               CEP290 MUTATED CEP290 WILD-TYPE
  COLON ADENOCARCINOMA                       19              296
  COLON MUCINOUS ADENOCARCINOMA               4               43
  RECTAL ADENOCARCINOMA                       6              100
  RECTAL MUCINOUS ADENOCARCINOMA              1                9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  CEP290 MUTATED    18   0   1   4
  CEP290 WILD-TYPE 327   4  30  21
D1009V11, multiclass
    clus
vv   CEP290 MUTATED CEP290 WILD-TYPE
  R0             18              327
  R1              0                4
  R2              1               30
  RX              4               21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1009V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CEP290 MUTATED                                  0     2
  CEP290 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  CEP290 MUTATED                           2    13
  CEP290 WILD-TYPE                        20   213
D1009V13, multiclass
                                  clus
vv                                 CEP290 MUTATED CEP290 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                9
  BLACK OR AFRICAN AMERICAN                     2               20
  WHITE                                        13              213
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1010) Variable = MYBPH MUTATION ANALYSIS
D1010V1, survival
                 sevent
clus2               0   1
  MYBPH MUTATED     5   2
  MYBPH WILD-TYPE 373  91
  MYBPH MUTATED MYBPH WILD-TYPE 
              7             464 
  MYBPH MUTATED MYBPH WILD-TYPE 
              2              91 
$`MYBPH MUTATED`
TCGA-A6-2683 TCGA-AA-3688 TCGA-AA-3811 TCGA-AA-3842 TCGA-AD-6889 TCGA-G4-6586 
       16.57        19.00        10.06        37.02        56.55        35.80 
TCGA-AG-A02N 
       61.97 

$`MYBPH WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3692 
       47.01        15.02        11.01         5.98        37.05        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        19.04        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       38.99        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 
       40.96         0.07        21.37        15.52         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       22.09        13.78        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  MYBPH MUTATED MYBPH WILD-TYPE 
          10.06            0.00 
  MYBPH MUTATED MYBPH WILD-TYPE 
          61.97          148.01 
  MYBPH MUTATED MYBPH WILD-TYPE 
         35.800          20.155 
[1] "10.1 - 62.0 (35.8)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.1"
D1010V2, continuous
D1010V3, binary
                 cls
clus                0   1
  MYBPH MUTATED     6   1
  MYBPH WILD-TYPE 360 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYBPH MUTATED      6    1
  MYBPH WILD-TYPE  360  118
        clus
vv       MYBPH MUTATED MYBPH WILD-TYPE
  COLON              6             360
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MYBPH MUTATED         0        0        1         2         0         0
  MYBPH WILD-TYPE      91        1       31       136        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MYBPH MUTATED           1          1          0          0        2         0
  MYBPH WILD-TYPE        23         10         59         42       46        18
                 vv
clus              STAGE IVB
  MYBPH MUTATED           0
  MYBPH WILD-TYPE         1
D1010V4, multiclass
            clus
vv           MYBPH MUTATED MYBPH WILD-TYPE
  STAGE I                0              91
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              2             136
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             1              10
  STAGE IIIB             0              59
  STAGE IIIC             0              42
  STAGE IV               2              46
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  MYBPH MUTATED     0   1   5   1
  MYBPH WILD-TYPE  17  91 324  49
D1010V5, multiclass
    clus
vv   MYBPH MUTATED MYBPH WILD-TYPE
  T1             0              17
  T2             1              91
  T3             5             324
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  MYBPH MUTATED     4   2   1
  MYBPH WILD-TYPE 283 111  86
D1010V6, multiclass
    clus
vv   MYBPH MUTATED MYBPH WILD-TYPE
  N0             4             283
  N1             2             111
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1010V7, binary
                 cls
clus                0   1
  MYBPH MUTATED     5   2
  MYBPH WILD-TYPE 370  63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYBPH MUTATED      5    2
  MYBPH WILD-TYPE  370   63
   clus
vv  MYBPH MUTATED MYBPH WILD-TYPE
  0             5             370
  1             2              63
[1] 2 2
[1] FALSE
D1010V8, binary
                 cls
clus                0   1
  MYBPH MUTATED     3   4
  MYBPH WILD-TYPE 222 260
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYBPH MUTATED      3    4
  MYBPH WILD-TYPE  222  260
        clus
vv       MYBPH MUTATED MYBPH WILD-TYPE
  FEMALE             3             222
  MALE               4             260
[1] 2 2
[1] FALSE
D1010V9, binary
                 cls
clus                0   1
  MYBPH MUTATED     5   0
  MYBPH WILD-TYPE 345  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYBPH MUTATED      5    0
  MYBPH WILD-TYPE  345   22
     clus
vv    MYBPH MUTATED MYBPH WILD-TYPE
  NO              5             345
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MYBPH MUTATED                      6                             0
  MYBPH WILD-TYPE                  309                            47
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MYBPH MUTATED                       1                              0
  MYBPH WILD-TYPE                   105                             10
D1010V10, multiclass
                                clus
vv                               MYBPH MUTATED MYBPH WILD-TYPE
  COLON ADENOCARCINOMA                       6             309
  COLON MUCINOUS ADENOCARCINOMA              0              47
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  MYBPH MUTATED     5   0   1   0
  MYBPH WILD-TYPE 340   4  30  25
D1010V11, multiclass
    clus
vv   MYBPH MUTATED MYBPH WILD-TYPE
  R0             5             340
  R1             0               4
  R2             1              30
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1010V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MYBPH MUTATED                                  0     1
  MYBPH WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  MYBPH MUTATED                           0     2
  MYBPH WILD-TYPE                        22   224
D1010V13, multiclass
                                  clus
vv                                 MYBPH MUTATED MYBPH WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        2             224
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1011) Variable = A2M MUTATION ANALYSIS
D1011V1, survival
               sevent
clus2             0   1
  A2M MUTATED    19   6
  A2M WILD-TYPE 359  87
  A2M MUTATED A2M WILD-TYPE 
           25           446 
  A2M MUTATED A2M WILD-TYPE 
            6            87 
$`A2M MUTATED`
TCGA-A6-5660 TCGA-A6-6141 TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3492 TCGA-AA-3502 
       29.19         8.38        20.12        19.66         3.02        35.01 
TCGA-AA-3510 TCGA-AA-3672 TCGA-AA-3877 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-A00N 
       63.98         0.92        31.00        26.01        24.00         4.01 
TCGA-AD-6889 TCGA-AZ-4616 TCGA-AZ-6605 TCGA-CA-6717 TCGA-D5-5537 TCGA-D5-6927 
       56.55         5.13         5.23        12.76        45.40         9.44 
TCGA-D5-6930 TCGA-G4-6299 TCGA-G4-6306 TCGA-AG-A002 TCGA-CI-6624 TCGA-DC-6158 
        1.51        74.56        44.68        20.98         4.73        10.98 
TCGA-DC-6683 
        5.03 

$`A2M WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 
       22.06        32.71        27.09        22.52        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6782 
       24.16        21.76        24.69        24.39        23.87        20.28 
TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        7.04         1.02         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 
        6.97        54.02         2.01        14.01        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 
       24.03        27.02        29.98        18.05         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       21.37        15.52         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
       12.10       100.01        29.56        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5538 
       11.08        11.08        11.01        10.06        12.03        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 
       14.30         9.04        11.64         4.80        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
      133.18        65.85        53.62        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
       33.17         6.97        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DT-5265 
       13.97        27.95        19.99         5.95         4.01         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  A2M MUTATED A2M WILD-TYPE 
         0.92          0.00 
  A2M MUTATED A2M WILD-TYPE 
        74.56        148.01 
  A2M MUTATED A2M WILD-TYPE 
       19.660        20.415 
[1] "0.9 - 74.6 (19.7)"  "0.0 - 148.0 (20.4)"
[1] "hr=" "1.4"
D1011V2, continuous
D1011V3, binary
               cls
clus              0   1
  A2M MUTATED    24   4
  A2M WILD-TYPE 342 115
[1] "tbl2"
               cls
clus            [,1] [,2]
  A2M MUTATED     24    4
  A2M WILD-TYPE  342  115
        clus
vv       A2M MUTATED A2M WILD-TYPE
  COLON           24           342
  RECTUM           4           115
[1] 2 2
[1] FALSE
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  A2M MUTATED         5        0        2        10         1         0
  A2M WILD-TYPE      86        1       30       128         9         1
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  A2M MUTATED           1          0          3          3        3         0
  A2M WILD-TYPE        23         11         56         39       45        18
               vv
clus            STAGE IVB
  A2M MUTATED           0
  A2M WILD-TYPE         1
D1011V4, multiclass
            clus
vv           A2M MUTATED A2M WILD-TYPE
  STAGE I              5            86
  STAGE IA             0             1
  STAGE II             2            30
  STAGE IIA           10           128
  STAGE IIB            1             9
  STAGE IIC            0             1
  STAGE III            1            23
  STAGE IIIA           0            11
  STAGE IIIB           3            56
  STAGE IIIC           3            39
  STAGE IV             3            45
  STAGE IVA            0            18
  STAGE IVB            0             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  A2M MUTATED     1   5  17   5
  A2M WILD-TYPE  16  87 312  45
D1011V5, multiclass
    clus
vv   A2M MUTATED A2M WILD-TYPE
  T1           1            16
  T2           5            87
  T3          17           312
  T4           5            45
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2
  A2M MUTATED    17   6   5
  A2M WILD-TYPE 270 107  82
D1011V6, multiclass
    clus
vv   A2M MUTATED A2M WILD-TYPE
  N0          17           270
  N1           6           107
  N2           5            82
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1011V7, binary
               cls
clus              0   1
  A2M MUTATED    22   3
  A2M WILD-TYPE 353  62
[1] "tbl2"
               cls
clus            [,1] [,2]
  A2M MUTATED     22    3
  A2M WILD-TYPE  353   62
   clus
vv  A2M MUTATED A2M WILD-TYPE
  0          22           353
  1           3            62
[1] 2 2
[1] FALSE
D1011V8, binary
               cls
clus              0   1
  A2M MUTATED     9  19
  A2M WILD-TYPE 216 245
[1] "tbl2"
               cls
clus            [,1] [,2]
  A2M MUTATED      9   19
  A2M WILD-TYPE  216  245
        clus
vv       A2M MUTATED A2M WILD-TYPE
  FEMALE           9           216
  MALE            19           245
[1] 2 2
[1] FALSE
D1011V9, binary
               cls
clus              0   1
  A2M MUTATED    20   0
  A2M WILD-TYPE 330  22
[1] "tbl2"
               cls
clus            [,1] [,2]
  A2M MUTATED     20    0
  A2M WILD-TYPE  330   22
     clus
vv    A2M MUTATED A2M WILD-TYPE
  NO           20           330
  YES           0            22
[1] 2 2
[1] FALSE
               vv
clus            COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  A2M MUTATED                     16                             8
  A2M WILD-TYPE                  299                            39
               vv
clus            RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  A2M MUTATED                       4                              0
  A2M WILD-TYPE                   102                             10
D1011V10, multiclass
                                clus
vv                               A2M MUTATED A2M WILD-TYPE
  COLON ADENOCARCINOMA                    16           299
  COLON MUCINOUS ADENOCARCINOMA            8            39
  RECTAL ADENOCARCINOMA                    4           102
  RECTAL MUCINOUS ADENOCARCINOMA           0            10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             R0  R1  R2  RX
  A2M MUTATED    17   0   2   2
  A2M WILD-TYPE 328   4  29  23
D1011V11, multiclass
    clus
vv   A2M MUTATED A2M WILD-TYPE
  R0          17           328
  R1           0             4
  R2           2            29
  RX           2            23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1011V12, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  A2M MUTATED                                  0     2
  A2M WILD-TYPE                                1     9
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  A2M MUTATED                           2    12
  A2M WILD-TYPE                        20   214
D1011V13, multiclass
                                  clus
vv                                 A2M MUTATED A2M WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      2             9
  BLACK OR AFRICAN AMERICAN                  2            20
  WHITE                                     12           214
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1012) Variable = ADM MUTATION ANALYSIS
D1012V1, survival
               sevent
clus2             0   1
  ADM MUTATED     5   1
  ADM WILD-TYPE 373  92
  ADM MUTATED ADM WILD-TYPE 
            6           465 
  ADM MUTATED ADM WILD-TYPE 
            1            92 
$`ADM MUTATED`
TCGA-A6-5661 TCGA-AA-3510 TCGA-AA-3977 TCGA-AA-A01D TCGA-CM-4743 TCGA-G4-6588 
       33.53        63.98        25.02        10.98        23.05        26.17 

$`ADM WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       34.98         1.02        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
      124.27        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       22.09        13.78        35.80        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  ADM MUTATED ADM WILD-TYPE 
        10.98          0.00 
  ADM MUTATED ADM WILD-TYPE 
        63.98        148.01 
  ADM MUTATED ADM WILD-TYPE 
       25.595        20.050 
[1] "11.0 - 64.0 (25.6)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.4"
D1012V2, continuous
D1012V3, binary
               cls
clus              0   1
  ADM MUTATED     6   0
  ADM WILD-TYPE 360 119
[1] "tbl2"
               cls
clus            [,1] [,2]
  ADM MUTATED      6    0
  ADM WILD-TYPE  360  119
        clus
vv       ADM MUTATED ADM WILD-TYPE
  COLON            6           360
  RECTUM           0           119
[1] 2 2
[1] FALSE
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ADM MUTATED         0        0        1         3         0         0
  ADM WILD-TYPE      91        1       31       135        10         1
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ADM MUTATED           0          0          0          1        0         0
  ADM WILD-TYPE        24         11         59         41       48        18
               vv
clus            STAGE IVB
  ADM MUTATED           0
  ADM WILD-TYPE         1
D1012V4, multiclass
            clus
vv           ADM MUTATED ADM WILD-TYPE
  STAGE I              0            91
  STAGE IA             0             1
  STAGE II             1            31
  STAGE IIA            3           135
  STAGE IIB            0            10
  STAGE IIC            0             1
  STAGE III            0            24
  STAGE IIIA           0            11
  STAGE IIIB           0            59
  STAGE IIIC           1            41
  STAGE IV             0            48
  STAGE IVA            0            18
  STAGE IVB            0             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  ADM MUTATED     0   1   5   0
  ADM WILD-TYPE  17  91 324  50
D1012V5, multiclass
    clus
vv   ADM MUTATED ADM WILD-TYPE
  T1           0            17
  T2           1            91
  T3           5           324
  T4           0            50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2
  ADM MUTATED     5   0   1
  ADM WILD-TYPE 282 113  86
D1012V6, multiclass
    clus
vv   ADM MUTATED ADM WILD-TYPE
  N0           5           282
  N1           0           113
  N2           1            86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1012V7, binary
               cls
clus              0   1
  ADM MUTATED     5   0
  ADM WILD-TYPE 370  65
[1] "tbl2"
               cls
clus            [,1] [,2]
  ADM MUTATED      5    0
  ADM WILD-TYPE  370   65
   clus
vv  ADM MUTATED ADM WILD-TYPE
  0           5           370
  1           0            65
[1] 2 2
[1] FALSE
D1012V8, binary
               cls
clus              0   1
  ADM MUTATED     3   3
  ADM WILD-TYPE 222 261
[1] "tbl2"
               cls
clus            [,1] [,2]
  ADM MUTATED      3    3
  ADM WILD-TYPE  222  261
        clus
vv       ADM MUTATED ADM WILD-TYPE
  FEMALE           3           222
  MALE             3           261
[1] 2 2
[1] FALSE
D1012V9, binary
               cls
clus              0   1
  ADM MUTATED     6   0
  ADM WILD-TYPE 344  22
[1] "tbl2"
               cls
clus            [,1] [,2]
  ADM MUTATED      6    0
  ADM WILD-TYPE  344   22
     clus
vv    ADM MUTATED ADM WILD-TYPE
  NO            6           344
  YES           0            22
[1] 2 2
[1] FALSE
               vv
clus            COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ADM MUTATED                      5                             1
  ADM WILD-TYPE                  310                            46
               vv
clus            RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ADM MUTATED                       0                              0
  ADM WILD-TYPE                   106                             10
D1012V10, multiclass
                                clus
vv                               ADM MUTATED ADM WILD-TYPE
  COLON ADENOCARCINOMA                     5           310
  COLON MUCINOUS ADENOCARCINOMA            1            46
  RECTAL ADENOCARCINOMA                    0           106
  RECTAL MUCINOUS ADENOCARCINOMA           0            10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             R0  R1  R2  RX
  ADM MUTATED     5   0   0   0
  ADM WILD-TYPE 340   4  31  25
D1012V11, multiclass
    clus
vv   ADM MUTATED ADM WILD-TYPE
  R0           5           340
  R1           0             4
  R2           0            31
  RX           0            25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1012V12, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ADM MUTATED                                  0     0
  ADM WILD-TYPE                                1    11
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  ADM MUTATED                           1     2
  ADM WILD-TYPE                        21   224
D1012V13, multiclass
                                  clus
vv                                 ADM MUTATED ADM WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      0            11
  BLACK OR AFRICAN AMERICAN                  1            21
  WHITE                                      2           224
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1013) Variable = COL3A1 MUTATION ANALYSIS
D1013V1, survival
                  sevent
clus2                0   1
  COL3A1 MUTATED    28   3
  COL3A1 WILD-TYPE 350  90
  COL3A1 MUTATED COL3A1 WILD-TYPE 
              31              440 
  COL3A1 MUTATED COL3A1 WILD-TYPE 
               3               90 
$`COL3A1 MUTATED`
TCGA-A6-2676 TCGA-A6-6137 TCGA-A6-6142 TCGA-AA-3510 TCGA-AA-3554 TCGA-AA-3663 
       42.90        27.09        25.08        63.98        17.95         6.97 
TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3846 TCGA-AA-3947 TCGA-AA-3950 
       85.05        19.04        19.04        17.03        33.01        24.00 
TCGA-AA-3977 TCGA-AA-A00R TCGA-AA-A01Q TCGA-AA-A01S TCGA-AY-5543 TCGA-CA-6718 
       25.02         0.99         1.02         1.02        33.01        10.06 
TCGA-CK-4950 TCGA-CK-6751 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6164 TCGA-D5-5540 
       85.45       124.27        15.02        12.00        29.03        56.09 
TCGA-G4-6588 TCGA-G4-6625 TCGA-AG-3892 TCGA-AG-A002 TCGA-CI-6622 TCGA-EI-6506 
       26.17        91.79        13.02        20.98         6.97        20.55 
TCGA-EI-6508 
       20.91 

$`COL3A1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6649 
       22.06        32.71        22.52         8.38        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 
       20.28         7.04         3.02         1.02        35.01         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3555 
       14.01        33.99        21.01        13.02        24.00        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
       78.08         6.05        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
       19.00        36.00         5.03        26.99        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3848 TCGA-AA-3850 
       38.99        37.02        14.93         0.00        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       26.01         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W 
       38.04         4.01        27.02        42.02        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01R TCGA-AA-A01T TCGA-AA-A01V 
       31.00        31.00        38.07        35.01        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6197 TCGA-AY-6386 
       14.50        27.09        16.31         0.95        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 
        3.25         3.29         0.07        12.20        12.76        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
       17.56       148.01        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       21.14        82.95         1.91        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6163 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
        2.96        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       19.59        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       13.78        35.80        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
       33.17         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6507 TCGA-EI-6510 TCGA-F5-6464 
       51.48        32.61         0.49        19.96        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  COL3A1 MUTATED COL3A1 WILD-TYPE 
            0.99             0.00 
  COL3A1 MUTATED COL3A1 WILD-TYPE 
          124.27           148.01 
  COL3A1 MUTATED COL3A1 WILD-TYPE 
          20.980           20.035 
[1] "1.0 - 124.3 (21.0)" "0.0 - 148.0 (20.0)"
[1] "hr=" "2.5"
D1013V2, continuous
D1013V3, binary
                  cls
clus                 0   1
  COL3A1 MUTATED    26   6
  COL3A1 WILD-TYPE 340 113
[1] "tbl2"
                  cls
clus               [,1] [,2]
  COL3A1 MUTATED     26    6
  COL3A1 WILD-TYPE  340  113
        clus
vv       COL3A1 MUTATED COL3A1 WILD-TYPE
  COLON              26              340
  RECTUM              6              113
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  COL3A1 MUTATED         5        0        4         9         3         0
  COL3A1 WILD-TYPE      86        1       28       129         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  COL3A1 MUTATED           3          0          4          0        1
  COL3A1 WILD-TYPE        21         11         55         42       47
                  vv
clus               STAGE IVA STAGE IVB
  COL3A1 MUTATED           2         0
  COL3A1 WILD-TYPE        16         1
D1013V4, multiclass
            clus
vv           COL3A1 MUTATED COL3A1 WILD-TYPE
  STAGE I                 5               86
  STAGE IA                0                1
  STAGE II                4               28
  STAGE IIA               9              129
  STAGE IIB               3                7
  STAGE IIC               0                1
  STAGE III               3               21
  STAGE IIIA              0               11
  STAGE IIIB              4               55
  STAGE IIIC              0               42
  STAGE IV                1               47
  STAGE IVA               2               16
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  COL3A1 MUTATED     1   5  23   3
  COL3A1 WILD-TYPE  16  87 306  47
D1013V5, multiclass
    clus
vv   COL3A1 MUTATED COL3A1 WILD-TYPE
  T1              1               16
  T2              5               87
  T3             23              306
  T4              3               47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  COL3A1 MUTATED    24   8   0
  COL3A1 WILD-TYPE 263 105  87
D1013V6, multiclass
    clus
vv   COL3A1 MUTATED COL3A1 WILD-TYPE
  N0             24              263
  N1              8              105
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1013V7, binary
                  cls
clus                 0   1
  COL3A1 MUTATED    26   3
  COL3A1 WILD-TYPE 349  62
[1] "tbl2"
                  cls
clus               [,1] [,2]
  COL3A1 MUTATED     26    3
  COL3A1 WILD-TYPE  349   62
   clus
vv  COL3A1 MUTATED COL3A1 WILD-TYPE
  0             26              349
  1              3               62
[1] 2 2
[1] FALSE
D1013V8, binary
                  cls
clus                 0   1
  COL3A1 MUTATED    20  12
  COL3A1 WILD-TYPE 205 252
[1] "tbl2"
                  cls
clus               [,1] [,2]
  COL3A1 MUTATED     20   12
  COL3A1 WILD-TYPE  205  252
        clus
vv       COL3A1 MUTATED COL3A1 WILD-TYPE
  FEMALE             20              205
  MALE               12              252
[1] 2 2
[1] FALSE
D1013V9, binary
                  cls
clus                 0   1
  COL3A1 MUTATED    26   1
  COL3A1 WILD-TYPE 324  21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  COL3A1 MUTATED     26    1
  COL3A1 WILD-TYPE  324   21
     clus
vv    COL3A1 MUTATED COL3A1 WILD-TYPE
  NO              26              324
  YES              1               21
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  COL3A1 MUTATED                     22                             4
  COL3A1 WILD-TYPE                  293                            43
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  COL3A1 MUTATED                       6                              0
  COL3A1 WILD-TYPE                   100                             10
D1013V10, multiclass
                                clus
vv                               COL3A1 MUTATED COL3A1 WILD-TYPE
  COLON ADENOCARCINOMA                       22              293
  COLON MUCINOUS ADENOCARCINOMA               4               43
  RECTAL ADENOCARCINOMA                       6              100
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  COL3A1 MUTATED    23   1   1   2
  COL3A1 WILD-TYPE 322   3  30  23
D1013V11, multiclass
    clus
vv   COL3A1 MUTATED COL3A1 WILD-TYPE
  R0             23              322
  R1              1                3
  R2              1               30
  RX              2               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1013V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  COL3A1 MUTATED                                  0     1
  COL3A1 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  COL3A1 MUTATED                           2    14
  COL3A1 WILD-TYPE                        20   212
D1013V13, multiclass
                                  clus
vv                                 COL3A1 MUTATED COL3A1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     2               20
  WHITE                                        14              212
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1014) Variable = CCAR1 MUTATION ANALYSIS
D1014V1, survival
                 sevent
clus2               0   1
  CCAR1 MUTATED    16   3
  CCAR1 WILD-TYPE 362  90
  CCAR1 MUTATED CCAR1 WILD-TYPE 
             19             452 
  CCAR1 MUTATED CCAR1 WILD-TYPE 
              3              90 
$`CCAR1 MUTATED`
TCGA-A6-5665 TCGA-A6-6651 TCGA-A6-6781 TCGA-AA-3510 TCGA-AA-3855 TCGA-AA-3966 
       22.06        21.76        19.66        63.98        32.05         2.01 
TCGA-AA-A00J TCGA-AZ-4315 TCGA-AZ-6598 TCGA-CA-6719 TCGA-CM-6162 TCGA-CM-6680 
       18.05        58.39        49.41        14.30        12.00        12.03 
TCGA-D5-6929 TCGA-DM-A1D4 TCGA-G4-6304 TCGA-G4-6626 TCGA-G4-6628 TCGA-AG-A002 
        4.80        92.75        53.62        46.75        79.69        20.98 
TCGA-AG-A02N 
       61.97 

$`CCAR1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       25.18        24.16        24.69        24.39        23.87        20.12 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 
       20.28         7.04         3.02         1.02        35.01         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
       33.07         0.00        36.03         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 
       26.01        24.00         2.01        20.98        34.03        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        33.01        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 
      106.75        22.36        62.79        88.21         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       12.76        10.06        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 
        5.03        15.02        15.02        17.03        15.02         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.08        11.01        10.06        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.04         9.44        11.64         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D6 
       10.26       119.70        24.43        38.20       130.65        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       74.56        65.85        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       91.79        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  CCAR1 MUTATED CCAR1 WILD-TYPE 
           2.01            0.00 
  CCAR1 MUTATED CCAR1 WILD-TYPE 
          92.75          148.01 
  CCAR1 MUTATED CCAR1 WILD-TYPE 
         22.060          20.035 
[1] "2.0 - 92.8 (22.1)"  "0.0 - 148.0 (20.0)"
[1] "hr=" "1.9"
D1014V2, continuous
D1014V3, binary
                 cls
clus                0   1
  CCAR1 MUTATED    18   2
  CCAR1 WILD-TYPE 348 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CCAR1 MUTATED     18    2
  CCAR1 WILD-TYPE  348  117
        clus
vv       CCAR1 MUTATED CCAR1 WILD-TYPE
  COLON             18             348
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CCAR1 MUTATED         3        0        3         7         1         0
  CCAR1 WILD-TYPE      88        1       29       131         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CCAR1 MUTATED           0          0          4          1        1         0
  CCAR1 WILD-TYPE        24         11         55         41       47        18
                 vv
clus              STAGE IVB
  CCAR1 MUTATED           0
  CCAR1 WILD-TYPE         1
D1014V4, multiclass
            clus
vv           CCAR1 MUTATED CCAR1 WILD-TYPE
  STAGE I                3              88
  STAGE IA               0               1
  STAGE II               3              29
  STAGE IIA              7             131
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             4              55
  STAGE IIIC             1              41
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CCAR1 MUTATED     0   3  14   3
  CCAR1 WILD-TYPE  17  89 315  47
D1014V5, multiclass
    clus
vv   CCAR1 MUTATED CCAR1 WILD-TYPE
  T1             0              17
  T2             3              89
  T3            14             315
  T4             3              47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  CCAR1 MUTATED    14   5   1
  CCAR1 WILD-TYPE 273 108  86
D1014V6, multiclass
    clus
vv   CCAR1 MUTATED CCAR1 WILD-TYPE
  N0            14             273
  N1             5             108
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1014V7, binary
                 cls
clus                0   1
  CCAR1 MUTATED    16   1
  CCAR1 WILD-TYPE 359  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CCAR1 MUTATED     16    1
  CCAR1 WILD-TYPE  359   64
   clus
vv  CCAR1 MUTATED CCAR1 WILD-TYPE
  0            16             359
  1             1              64
[1] 2 2
[1] FALSE
D1014V8, binary
                 cls
clus                0   1
  CCAR1 MUTATED     9  11
  CCAR1 WILD-TYPE 216 253
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CCAR1 MUTATED      9   11
  CCAR1 WILD-TYPE  216  253
        clus
vv       CCAR1 MUTATED CCAR1 WILD-TYPE
  FEMALE             9             216
  MALE              11             253
[1] 2 2
[1] FALSE
D1014V9, binary
                 cls
clus                0   1
  CCAR1 MUTATED    15   0
  CCAR1 WILD-TYPE 335  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CCAR1 MUTATED     15    0
  CCAR1 WILD-TYPE  335   22
     clus
vv    CCAR1 MUTATED CCAR1 WILD-TYPE
  NO             15             335
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CCAR1 MUTATED                     14                             4
  CCAR1 WILD-TYPE                  301                            43
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CCAR1 MUTATED                       2                              0
  CCAR1 WILD-TYPE                   104                             10
D1014V10, multiclass
                                clus
vv                               CCAR1 MUTATED CCAR1 WILD-TYPE
  COLON ADENOCARCINOMA                      14             301
  COLON MUCINOUS ADENOCARCINOMA              4              43
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  CCAR1 MUTATED    15   0   0   1
  CCAR1 WILD-TYPE 330   4  31  24
D1014V11, multiclass
    clus
vv   CCAR1 MUTATED CCAR1 WILD-TYPE
  R0            15             330
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1014V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CCAR1 MUTATED                                  0     1
  CCAR1 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CCAR1 MUTATED                           0    12
  CCAR1 WILD-TYPE                        22   214
D1014V13, multiclass
                                  clus
vv                                 CCAR1 MUTATED CCAR1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                       12             214
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1015) Variable = ZNF182 MUTATION ANALYSIS
D1015V1, survival
                  sevent
clus2                0   1
  ZNF182 MUTATED    14   1
  ZNF182 WILD-TYPE 364  92
  ZNF182 MUTATED ZNF182 WILD-TYPE 
              15              456 
  ZNF182 MUTATED ZNF182 WILD-TYPE 
               1               92 
$`ZNF182 MUTATED`
TCGA-A6-5661 TCGA-A6-6651 TCGA-AA-3555 TCGA-AA-3977 TCGA-AA-A010 TCGA-AZ-5407 
       33.53        21.76        29.95        25.02        34.98        88.21 
TCGA-CA-6717 TCGA-CK-5913 TCGA-CM-5348 TCGA-CM-5349 TCGA-DM-A1HB TCGA-G4-6303 
       12.76        51.32        22.98        30.08       135.65        65.85 
TCGA-AG-3892 TCGA-AG-A002 TCGA-EI-6510 
       13.02        20.98        18.28 

$`ZNF182 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       25.18        24.16        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       24.00        17.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07        12.20        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 
      148.01        85.45        15.62        49.08         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5860 TCGA-CM-5861 
       25.02        13.02        29.06        22.03        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 
      140.38         7.50        44.32       131.51       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6304 TCGA-G4-6306 
       47.41        35.31       133.18        74.56        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       36.95        17.03        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       20.55        19.96        20.91         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  ZNF182 MUTATED ZNF182 WILD-TYPE 
           12.76             0.00 
  ZNF182 MUTATED ZNF182 WILD-TYPE 
          135.65           148.01 
  ZNF182 MUTATED ZNF182 WILD-TYPE 
          29.950           20.005 
[1] "12.8 - 135.7 (29.9)" "0.0 - 148.0 (20.0)" 
[1] "hr=" "4.4"
D1015V2, continuous
D1015V3, binary
                  cls
clus                 0   1
  ZNF182 MUTATED    13   3
  ZNF182 WILD-TYPE 353 116
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF182 MUTATED     13    3
  ZNF182 WILD-TYPE  353  116
        clus
vv       ZNF182 MUTATED ZNF182 WILD-TYPE
  COLON              13              353
  RECTUM              3              116
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZNF182 MUTATED         3        0        0         6         1         0
  ZNF182 WILD-TYPE      88        1       32       132         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF182 MUTATED           0          0          3          0        1
  ZNF182 WILD-TYPE        24         11         56         42       47
                  vv
clus               STAGE IVA STAGE IVB
  ZNF182 MUTATED           1         0
  ZNF182 WILD-TYPE        17         1
D1015V4, multiclass
            clus
vv           ZNF182 MUTATED ZNF182 WILD-TYPE
  STAGE I                 3               88
  STAGE IA                0                1
  STAGE II                0               32
  STAGE IIA               6              132
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              3               56
  STAGE IIIC              0               42
  STAGE IV                1               47
  STAGE IVA               1               17
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZNF182 MUTATED     2   3  10   1
  ZNF182 WILD-TYPE  15  89 319  49
D1015V5, multiclass
    clus
vv   ZNF182 MUTATED ZNF182 WILD-TYPE
  T1              2               15
  T2              3               89
  T3             10              319
  T4              1               49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  ZNF182 MUTATED    12   4   0
  ZNF182 WILD-TYPE 275 109  87
D1015V6, multiclass
    clus
vv   ZNF182 MUTATED ZNF182 WILD-TYPE
  N0             12              275
  N1              4              109
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1015V7, binary
                  cls
clus                 0   1
  ZNF182 MUTATED    11   1
  ZNF182 WILD-TYPE 364  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF182 MUTATED     11    1
  ZNF182 WILD-TYPE  364   64
   clus
vv  ZNF182 MUTATED ZNF182 WILD-TYPE
  0             11              364
  1              1               64
[1] 2 2
[1] FALSE
D1015V8, binary
                  cls
clus                 0   1
  ZNF182 MUTATED    11   5
  ZNF182 WILD-TYPE 214 259
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF182 MUTATED     11    5
  ZNF182 WILD-TYPE  214  259
        clus
vv       ZNF182 MUTATED ZNF182 WILD-TYPE
  FEMALE             11              214
  MALE                5              259
[1] 2 2
[1] FALSE
D1015V9, binary
                  cls
clus                 0   1
  ZNF182 MUTATED    14   0
  ZNF182 WILD-TYPE 336  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF182 MUTATED     14    0
  ZNF182 WILD-TYPE  336   22
     clus
vv    ZNF182 MUTATED ZNF182 WILD-TYPE
  NO              14              336
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ZNF182 MUTATED                     10                             2
  ZNF182 WILD-TYPE                  305                            45
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ZNF182 MUTATED                       3                              0
  ZNF182 WILD-TYPE                   103                             10
D1015V10, multiclass
                                clus
vv                               ZNF182 MUTATED ZNF182 WILD-TYPE
  COLON ADENOCARCINOMA                       10              305
  COLON MUCINOUS ADENOCARCINOMA               2               45
  RECTAL ADENOCARCINOMA                       3              103
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ZNF182 MUTATED    10   0   0   2
  ZNF182 WILD-TYPE 335   4  31  23
D1015V11, multiclass
    clus
vv   ZNF182 MUTATED ZNF182 WILD-TYPE
  R0             10              335
  R1              0                4
  R2              0               31
  RX              2               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1015V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF182 MUTATED                                  0     1
  ZNF182 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZNF182 MUTATED                           1     8
  ZNF182 WILD-TYPE                        21   218
D1015V13, multiclass
                                  clus
vv                                 ZNF182 MUTATED ZNF182 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                         8              218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1016) Variable = CXXC5 MUTATION ANALYSIS
D1016V1, survival
                 sevent
clus2               0   1
  CXXC5 MUTATED     4   1
  CXXC5 WILD-TYPE 374  92
  CXXC5 MUTATED CXXC5 WILD-TYPE 
              5             466 
  CXXC5 MUTATED CXXC5 WILD-TYPE 
              1              92 
$`CXXC5 MUTATED`
TCGA-A6-6780 TCGA-AA-3673 TCGA-AD-6899 TCGA-CM-5861 TCGA-CM-6674 
       20.12        50.04         5.79        15.02        12.95 

$`CXXC5 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3678 
        6.97        54.02         2.01        14.01         0.92        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
       56.55         0.79         0.72        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6676 
       13.02        15.02        14.04        11.01        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  CXXC5 MUTATED CXXC5 WILD-TYPE 
           5.79            0.00 
  CXXC5 MUTATED CXXC5 WILD-TYPE 
          50.04          148.01 
  CXXC5 MUTATED CXXC5 WILD-TYPE 
         15.020          20.415 
[1] "5.8 - 50.0 (15.0)"  "0.0 - 148.0 (20.4)"
[1] "hr=" "1.1"
D1016V2, continuous
D1016V3, binary
                 cls
clus                0   1
  CXXC5 MUTATED     6   0
  CXXC5 WILD-TYPE 360 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CXXC5 MUTATED      6    0
  CXXC5 WILD-TYPE  360  119
        clus
vv       CXXC5 MUTATED CXXC5 WILD-TYPE
  COLON              6             360
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CXXC5 MUTATED         0        0        1         3         1         0
  CXXC5 WILD-TYPE      91        1       31       135         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CXXC5 MUTATED           0          0          0          1        0         0
  CXXC5 WILD-TYPE        24         11         59         41       48        18
                 vv
clus              STAGE IVB
  CXXC5 MUTATED           0
  CXXC5 WILD-TYPE         1
D1016V4, multiclass
            clus
vv           CXXC5 MUTATED CXXC5 WILD-TYPE
  STAGE I                0              91
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              3             135
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             1              41
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CXXC5 MUTATED     0   0   4   2
  CXXC5 WILD-TYPE  17  92 325  48
D1016V5, multiclass
    clus
vv   CXXC5 MUTATED CXXC5 WILD-TYPE
  T1             0              17
  T2             0              92
  T3             4             325
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  CXXC5 MUTATED     5   0   1
  CXXC5 WILD-TYPE 282 113  86
D1016V6, multiclass
    clus
vv   CXXC5 MUTATED CXXC5 WILD-TYPE
  N0             5             282
  N1             0             113
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1016V7, binary
                 cls
clus                0   1
  CXXC5 MUTATED     3   0
  CXXC5 WILD-TYPE 372  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CXXC5 MUTATED      3    0
  CXXC5 WILD-TYPE  372   65
   clus
vv  CXXC5 MUTATED CXXC5 WILD-TYPE
  0             3             372
  1             0              65
[1] 2 2
[1] FALSE
D1016V8, binary
                 cls
clus                0   1
  CXXC5 MUTATED     3   3
  CXXC5 WILD-TYPE 222 261
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CXXC5 MUTATED      3    3
  CXXC5 WILD-TYPE  222  261
        clus
vv       CXXC5 MUTATED CXXC5 WILD-TYPE
  FEMALE             3             222
  MALE               3             261
[1] 2 2
[1] FALSE
D1016V9, binary
                 cls
clus                0   1
  CXXC5 MUTATED     5   0
  CXXC5 WILD-TYPE 345  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CXXC5 MUTATED      5    0
  CXXC5 WILD-TYPE  345   22
     clus
vv    CXXC5 MUTATED CXXC5 WILD-TYPE
  NO              5             345
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CXXC5 MUTATED                      4                             2
  CXXC5 WILD-TYPE                  311                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CXXC5 MUTATED                       0                              0
  CXXC5 WILD-TYPE                   106                             10
D1016V10, multiclass
                                clus
vv                               CXXC5 MUTATED CXXC5 WILD-TYPE
  COLON ADENOCARCINOMA                       4             311
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  CXXC5 MUTATED     3   0   0   1
  CXXC5 WILD-TYPE 342   4  31  24
D1016V11, multiclass
    clus
vv   CXXC5 MUTATED CXXC5 WILD-TYPE
  R0             3             342
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1016V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CXXC5 MUTATED                                  0     0
  CXXC5 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CXXC5 MUTATED                           0     5
  CXXC5 WILD-TYPE                        22   221
D1016V13, multiclass
                                  clus
vv                                 CXXC5 MUTATED CXXC5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        5             221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1017) Variable = SPAG1 MUTATION ANALYSIS
D1017V1, survival
                 sevent
clus2               0   1
  SPAG1 MUTATED     9   2
  SPAG1 WILD-TYPE 369  91
  SPAG1 MUTATED SPAG1 WILD-TYPE 
             11             460 
  SPAG1 MUTATED SPAG1 WILD-TYPE 
              2              91 
$`SPAG1 MUTATED`
TCGA-AA-3864 TCGA-AA-A010 TCGA-AD-6964 TCGA-AU-3779 TCGA-CA-6717 TCGA-CM-6172 
       53.00        34.98        10.88        14.50        12.76        11.01 
TCGA-G4-6321 TCGA-AF-3913 TCGA-AG-3598 TCGA-AG-3731 TCGA-AG-A002 
       22.09        10.39        50.04        37.02        20.98 

$`SPAG1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
        0.20        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07        12.20        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       15.02        14.04        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 
       55.04        85.48        63.62        61.91        36.00        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-4110 
       39.48        43.04        13.55        19.10        34.49        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3599 TCGA-AG-3600 
        1.02        46.03        34.03         2.01        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
        0.99        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  SPAG1 MUTATED SPAG1 WILD-TYPE 
          10.39            0.00 
  SPAG1 MUTATED SPAG1 WILD-TYPE 
          53.00          148.01 
  SPAG1 MUTATED SPAG1 WILD-TYPE 
         20.980          20.155 
[1] "10.4 - 53.0 (21.0)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.1"
D1017V2, continuous
D1017V3, binary
                 cls
clus                0   1
  SPAG1 MUTATED     8   4
  SPAG1 WILD-TYPE 358 115
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SPAG1 MUTATED      8    4
  SPAG1 WILD-TYPE  358  115
        clus
vv       SPAG1 MUTATED SPAG1 WILD-TYPE
  COLON              8             358
  RECTUM             4             115
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SPAG1 MUTATED         1        0        1         4         1         0
  SPAG1 WILD-TYPE      90        1       31       134         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SPAG1 MUTATED           1          0          1          0        2         0
  SPAG1 WILD-TYPE        23         11         58         42       46        18
                 vv
clus              STAGE IVB
  SPAG1 MUTATED           0
  SPAG1 WILD-TYPE         1
D1017V4, multiclass
            clus
vv           SPAG1 MUTATED SPAG1 WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              4             134
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             0              42
  STAGE IV               2              46
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  SPAG1 MUTATED     0   2   8   2
  SPAG1 WILD-TYPE  17  90 321  48
D1017V5, multiclass
    clus
vv   SPAG1 MUTATED SPAG1 WILD-TYPE
  T1             0              17
  T2             2              90
  T3             8             321
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  SPAG1 MUTATED     7   4   1
  SPAG1 WILD-TYPE 280 109  86
D1017V6, multiclass
    clus
vv   SPAG1 MUTATED SPAG1 WILD-TYPE
  N0             7             280
  N1             4             109
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1017V7, binary
                 cls
clus                0   1
  SPAG1 MUTATED     8   2
  SPAG1 WILD-TYPE 367  63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SPAG1 MUTATED      8    2
  SPAG1 WILD-TYPE  367   63
   clus
vv  SPAG1 MUTATED SPAG1 WILD-TYPE
  0             8             367
  1             2              63
[1] 2 2
[1] FALSE
D1017V8, binary
                 cls
clus                0   1
  SPAG1 MUTATED     5   7
  SPAG1 WILD-TYPE 220 257
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SPAG1 MUTATED      5    7
  SPAG1 WILD-TYPE  220  257
        clus
vv       SPAG1 MUTATED SPAG1 WILD-TYPE
  FEMALE             5             220
  MALE               7             257
[1] 2 2
[1] FALSE
D1017V9, binary
                 cls
clus                0   1
  SPAG1 MUTATED    11   0
  SPAG1 WILD-TYPE 339  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SPAG1 MUTATED     11    0
  SPAG1 WILD-TYPE  339   22
     clus
vv    SPAG1 MUTATED SPAG1 WILD-TYPE
  NO             11             339
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SPAG1 MUTATED                      7                             1
  SPAG1 WILD-TYPE                  308                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SPAG1 MUTATED                       4                              0
  SPAG1 WILD-TYPE                   102                             10
D1017V10, multiclass
                                clus
vv                               SPAG1 MUTATED SPAG1 WILD-TYPE
  COLON ADENOCARCINOMA                       7             308
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      4             102
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  SPAG1 MUTATED     9   0   1   1
  SPAG1 WILD-TYPE 336   4  30  24
D1017V11, multiclass
    clus
vv   SPAG1 MUTATED SPAG1 WILD-TYPE
  R0             9             336
  R1             0               4
  R2             1              30
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1017V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SPAG1 MUTATED                                  0     1
  SPAG1 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  SPAG1 MUTATED                           1     4
  SPAG1 WILD-TYPE                        21   222
D1017V13, multiclass
                                  clus
vv                                 SPAG1 MUTATED SPAG1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        4             222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1018) Variable = KIAA0649 MUTATION ANALYSIS
D1018V1, survival
                    sevent
clus2                  0   1
  KIAA0649 MUTATED     7   3
  KIAA0649 WILD-TYPE 371  90
  KIAA0649 MUTATED KIAA0649 WILD-TYPE 
                10                461 
  KIAA0649 MUTATED KIAA0649 WILD-TYPE 
                 3                 90 
$`KIAA0649 MUTATED`
TCGA-A6-5665 TCGA-AA-3492 TCGA-AA-3663 TCGA-AA-3672 TCGA-AA-3818 TCGA-AD-5900 
       22.06         3.02         6.97         0.92         0.99         0.07 
TCGA-CK-5913 TCGA-CM-5348 TCGA-F4-6570 TCGA-G4-6588 
       51.32        22.98         6.18        26.17 

$`KIAA0649 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 
       20.12        19.66        20.28         7.04         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
        2.01        14.01        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 
       17.56       148.01        85.45        15.62        49.08         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5349 
       37.02        25.02        13.02        29.06        22.03        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 
       61.91        36.00        22.09        13.78        35.80        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  KIAA0649 MUTATED KIAA0649 WILD-TYPE 
              0.07               0.00 
  KIAA0649 MUTATED KIAA0649 WILD-TYPE 
             51.32             148.01 
  KIAA0649 MUTATED KIAA0649 WILD-TYPE 
             6.575             20.280 
[1] "0.1 - 51.3 (6.6)"   "0.0 - 148.0 (20.3)"
[1] "hr=" "2.7"
D1018V2, continuous
D1018V3, binary
                    cls
clus                   0   1
  KIAA0649 MUTATED    10   0
  KIAA0649 WILD-TYPE 356 119
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0649 MUTATED     10    0
  KIAA0649 WILD-TYPE  356  119
        clus
vv       KIAA0649 MUTATED KIAA0649 WILD-TYPE
  COLON                10                356
  RECTUM                0                119
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KIAA0649 MUTATED         1        0        2         5         0         0
  KIAA0649 WILD-TYPE      90        1       30       133        10         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIAA0649 MUTATED           1          0          1          0        0
  KIAA0649 WILD-TYPE        23         11         58         42       48
                    vv
clus                 STAGE IVA STAGE IVB
  KIAA0649 MUTATED           0         0
  KIAA0649 WILD-TYPE        18         1
D1018V4, multiclass
            clus
vv           KIAA0649 MUTATED KIAA0649 WILD-TYPE
  STAGE I                   1                 90
  STAGE IA                  0                  1
  STAGE II                  2                 30
  STAGE IIA                 5                133
  STAGE IIB                 0                 10
  STAGE IIC                 0                  1
  STAGE III                 1                 23
  STAGE IIIA                0                 11
  STAGE IIIB                1                 58
  STAGE IIIC                0                 42
  STAGE IV                  0                 48
  STAGE IVA                 0                 18
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  KIAA0649 MUTATED     0   1   9   0
  KIAA0649 WILD-TYPE  17  91 320  50
D1018V5, multiclass
    clus
vv   KIAA0649 MUTATED KIAA0649 WILD-TYPE
  T1                0                 17
  T2                1                 91
  T3                9                320
  T4                0                 50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  KIAA0649 MUTATED     8   2   0
  KIAA0649 WILD-TYPE 279 111  87
D1018V6, multiclass
    clus
vv   KIAA0649 MUTATED KIAA0649 WILD-TYPE
  N0                8                279
  N1                2                111
  N2                0                 87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1018V7, binary
                    cls
clus                   0   1
  KIAA0649 MUTATED     8   0
  KIAA0649 WILD-TYPE 367  65
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0649 MUTATED      8    0
  KIAA0649 WILD-TYPE  367   65
   clus
vv  KIAA0649 MUTATED KIAA0649 WILD-TYPE
  0                8                367
  1                0                 65
[1] 2 2
[1] FALSE
D1018V8, binary
                    cls
clus                   0   1
  KIAA0649 MUTATED     7   3
  KIAA0649 WILD-TYPE 218 261
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0649 MUTATED      7    3
  KIAA0649 WILD-TYPE  218  261
        clus
vv       KIAA0649 MUTATED KIAA0649 WILD-TYPE
  FEMALE                7                218
  MALE                  3                261
[1] 2 2
[1] FALSE
D1018V9, binary
                    cls
clus                   0   1
  KIAA0649 MUTATED     8   0
  KIAA0649 WILD-TYPE 342  22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0649 MUTATED      8    0
  KIAA0649 WILD-TYPE  342   22
     clus
vv    KIAA0649 MUTATED KIAA0649 WILD-TYPE
  NO                 8                342
  YES                0                 22
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  KIAA0649 MUTATED                      9                             1
  KIAA0649 WILD-TYPE                  306                            46
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  KIAA0649 MUTATED                       0                              0
  KIAA0649 WILD-TYPE                   106                             10
D1018V10, multiclass
                                clus
vv                               KIAA0649 MUTATED KIAA0649 WILD-TYPE
  COLON ADENOCARCINOMA                          9                306
  COLON MUCINOUS ADENOCARCINOMA                 1                 46
  RECTAL ADENOCARCINOMA                         0                106
  RECTAL MUCINOUS ADENOCARCINOMA                0                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  KIAA0649 MUTATED     9   0   0   1
  KIAA0649 WILD-TYPE 336   4  31  24
D1018V11, multiclass
    clus
vv   KIAA0649 MUTATED KIAA0649 WILD-TYPE
  R0                9                336
  R1                0                  4
  R2                0                 31
  RX                1                 24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1018V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KIAA0649 MUTATED                                  0     0
  KIAA0649 WILD-TYPE                                1    11
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  KIAA0649 MUTATED                           0     6
  KIAA0649 WILD-TYPE                        22   220
D1018V13, multiclass
                                  clus
vv                                 KIAA0649 MUTATED KIAA0649 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 11
  BLACK OR AFRICAN AMERICAN                       0                 22
  WHITE                                           6                220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1019) Variable = SPZ1 MUTATION ANALYSIS
D1019V1, survival
                sevent
clus2              0   1
  SPZ1 MUTATED     9   1
  SPZ1 WILD-TYPE 369  92
  SPZ1 MUTATED SPZ1 WILD-TYPE 
            10            461 
  SPZ1 MUTATED SPZ1 WILD-TYPE 
             1             92 
$`SPZ1 MUTATED`
TCGA-AA-3977 TCGA-AU-3779 TCGA-CA-6717 TCGA-CA-6718 TCGA-D5-6931 TCGA-G4-6628 
       25.02        14.50        12.76        10.06        12.00        79.69 
TCGA-AG-3892 TCGA-AG-A002 TCGA-CI-6620 TCGA-DC-5337 
       13.02        20.98        33.17        15.02 

$`SPZ1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        10.88         0.20        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       12.20        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
        1.51        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       36.95        17.03        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        0.72         6.05         6.97         4.73        78.12         7.17 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  SPZ1 MUTATED SPZ1 WILD-TYPE 
         10.06           0.00 
  SPZ1 MUTATED SPZ1 WILD-TYPE 
         79.69         148.01 
  SPZ1 MUTATED SPZ1 WILD-TYPE 
         14.76          20.28 
[1] "10.1 - 79.7 (14.8)" "0.0 - 148.0 (20.3)"
[1] "hr=" "1.8"
D1019V2, continuous
D1019V3, binary
                cls
clus               0   1
  SPZ1 MUTATED     7   4
  SPZ1 WILD-TYPE 359 115
[1] "tbl2"
                cls
clus             [,1] [,2]
  SPZ1 MUTATED      7    4
  SPZ1 WILD-TYPE  359  115
        clus
vv       SPZ1 MUTATED SPZ1 WILD-TYPE
  COLON             7            359
  RECTUM            4            115
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SPZ1 MUTATED         4        0        0         4         0         0
  SPZ1 WILD-TYPE      87        1       32       134        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SPZ1 MUTATED           0          0          0          1        0         1
  SPZ1 WILD-TYPE        24         11         59         41       48        17
                vv
clus             STAGE IVB
  SPZ1 MUTATED           0
  SPZ1 WILD-TYPE         1
D1019V4, multiclass
            clus
vv           SPZ1 MUTATED SPZ1 WILD-TYPE
  STAGE I               4             87
  STAGE IA              0              1
  STAGE II              0             32
  STAGE IIA             4            134
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            0             59
  STAGE IIIC            1             41
  STAGE IV              0             48
  STAGE IVA             1             17
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  SPZ1 MUTATED     2   3   5   1
  SPZ1 WILD-TYPE  15  89 324  49
D1019V5, multiclass
    clus
vv   SPZ1 MUTATED SPZ1 WILD-TYPE
  T1            2             15
  T2            3             89
  T3            5            324
  T4            1             49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  SPZ1 MUTATED     9   1   1
  SPZ1 WILD-TYPE 278 112  86
D1019V6, multiclass
    clus
vv   SPZ1 MUTATED SPZ1 WILD-TYPE
  N0            9            278
  N1            1            112
  N2            1             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1019V7, binary
                cls
clus               0   1
  SPZ1 MUTATED     9   1
  SPZ1 WILD-TYPE 366  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  SPZ1 MUTATED      9    1
  SPZ1 WILD-TYPE  366   64
   clus
vv  SPZ1 MUTATED SPZ1 WILD-TYPE
  0            9            366
  1            1             64
[1] 2 2
[1] FALSE
D1019V8, binary
                cls
clus               0   1
  SPZ1 MUTATED     4   7
  SPZ1 WILD-TYPE 221 257
[1] "tbl2"
                cls
clus             [,1] [,2]
  SPZ1 MUTATED      4    7
  SPZ1 WILD-TYPE  221  257
        clus
vv       SPZ1 MUTATED SPZ1 WILD-TYPE
  FEMALE            4            221
  MALE              7            257
[1] 2 2
[1] FALSE
D1019V9, binary
                cls
clus               0   1
  SPZ1 MUTATED    10   0
  SPZ1 WILD-TYPE 340  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  SPZ1 MUTATED     10    0
  SPZ1 WILD-TYPE  340   22
     clus
vv    SPZ1 MUTATED SPZ1 WILD-TYPE
  NO            10            340
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SPZ1 MUTATED                      6                             1
  SPZ1 WILD-TYPE                  309                            46
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SPZ1 MUTATED                       4                              0
  SPZ1 WILD-TYPE                   102                             10
D1019V10, multiclass
                                clus
vv                               SPZ1 MUTATED SPZ1 WILD-TYPE
  COLON ADENOCARCINOMA                      6            309
  COLON MUCINOUS ADENOCARCINOMA             1             46
  RECTAL ADENOCARCINOMA                     4            102
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  SPZ1 MUTATED     7   0   0   2
  SPZ1 WILD-TYPE 338   4  31  23
D1019V11, multiclass
    clus
vv   SPZ1 MUTATED SPZ1 WILD-TYPE
  R0            7            338
  R1            0              4
  R2            0             31
  RX            2             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1019V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SPZ1 MUTATED                                  0     2
  SPZ1 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  SPZ1 MUTATED                           0     5
  SPZ1 WILD-TYPE                        22   221
D1019V13, multiclass
                                  clus
vv                                 SPZ1 MUTATED SPZ1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              9
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       5            221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1020) Variable = MLLT1 MUTATION ANALYSIS
D1020V1, survival
                 sevent
clus2               0   1
  MLLT1 MUTATED     5   1
  MLLT1 WILD-TYPE 373  92
  MLLT1 MUTATED MLLT1 WILD-TYPE 
              6             465 
  MLLT1 MUTATED MLLT1 WILD-TYPE 
              1              92 
$`MLLT1 MUTATED`
TCGA-A6-5665 TCGA-A6-5666 TCGA-AA-3713 TCGA-AA-3715 TCGA-D5-6922 TCGA-AF-6672 
       22.06        32.71        19.04        19.04         4.41        10.39 

$`MLLT1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       22.09        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
        5.03        85.05        26.99        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6923 
       12.49        16.14        15.58         1.48         3.68        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  MLLT1 MUTATED MLLT1 WILD-TYPE 
           4.41            0.00 
  MLLT1 MUTATED MLLT1 WILD-TYPE 
          32.71          148.01 
  MLLT1 MUTATED MLLT1 WILD-TYPE 
          19.04           20.28 
[1] "4.4 - 32.7 (19.0)"  "0.0 - 148.0 (20.3)"
[1] "hr=" "1.3"
D1020V2, continuous
D1020V3, binary
                 cls
clus                0   1
  MLLT1 MUTATED     5   1
  MLLT1 WILD-TYPE 361 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MLLT1 MUTATED      5    1
  MLLT1 WILD-TYPE  361  118
        clus
vv       MLLT1 MUTATED MLLT1 WILD-TYPE
  COLON              5             361
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MLLT1 MUTATED         0        0        1         1         0         1
  MLLT1 WILD-TYPE      91        1       31       137        10         0
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MLLT1 MUTATED           0          1          0          0        2         0
  MLLT1 WILD-TYPE        24         10         59         42       46        18
                 vv
clus              STAGE IVB
  MLLT1 MUTATED           0
  MLLT1 WILD-TYPE         1
D1020V4, multiclass
            clus
vv           MLLT1 MUTATED MLLT1 WILD-TYPE
  STAGE I                0              91
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              1             137
  STAGE IIB              0              10
  STAGE IIC              1               0
  STAGE III              0              24
  STAGE IIIA             1              10
  STAGE IIIB             0              59
  STAGE IIIC             0              42
  STAGE IV               2              46
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  MLLT1 MUTATED     0   0   4   2
  MLLT1 WILD-TYPE  17  92 325  48
D1020V5, multiclass
    clus
vv   MLLT1 MUTATED MLLT1 WILD-TYPE
  T1             0              17
  T2             0              92
  T3             4             325
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  MLLT1 MUTATED     4   1   1
  MLLT1 WILD-TYPE 283 112  86
D1020V6, multiclass
    clus
vv   MLLT1 MUTATED MLLT1 WILD-TYPE
  N0             4             283
  N1             1             112
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1020V7, binary
                 cls
clus                0   1
  MLLT1 MUTATED     4   1
  MLLT1 WILD-TYPE 371  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MLLT1 MUTATED      4    1
  MLLT1 WILD-TYPE  371   64
   clus
vv  MLLT1 MUTATED MLLT1 WILD-TYPE
  0             4             371
  1             1              64
[1] 2 2
[1] FALSE
D1020V8, binary
                 cls
clus                0   1
  MLLT1 MUTATED     1   5
  MLLT1 WILD-TYPE 224 259
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MLLT1 MUTATED      1    5
  MLLT1 WILD-TYPE  224  259
        clus
vv       MLLT1 MUTATED MLLT1 WILD-TYPE
  FEMALE             1             224
  MALE               5             259
[1] 2 2
[1] FALSE
D1020V9, binary
                 cls
clus                0   1
  MLLT1 MUTATED     3   2
  MLLT1 WILD-TYPE 347  20
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MLLT1 MUTATED      3    2
  MLLT1 WILD-TYPE  347   20
     clus
vv    MLLT1 MUTATED MLLT1 WILD-TYPE
  NO              3             347
  YES             2              20
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MLLT1 MUTATED                      5                             0
  MLLT1 WILD-TYPE                  310                            47
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MLLT1 MUTATED                       1                              0
  MLLT1 WILD-TYPE                   105                             10
D1020V10, multiclass
                                clus
vv                               MLLT1 MUTATED MLLT1 WILD-TYPE
  COLON ADENOCARCINOMA                       5             310
  COLON MUCINOUS ADENOCARCINOMA              0              47
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  MLLT1 MUTATED     3   0   1   0
  MLLT1 WILD-TYPE 342   4  30  25
D1020V11, multiclass
    clus
vv   MLLT1 MUTATED MLLT1 WILD-TYPE
  R0             3             342
  R1             0               4
  R2             1              30
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1020V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MLLT1 MUTATED                                  0     0
  MLLT1 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  MLLT1 MUTATED                           0     4
  MLLT1 WILD-TYPE                        22   222
D1020V13, multiclass
                                  clus
vv                                 MLLT1 MUTATED MLLT1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        4             222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1021) Variable = DLL3 MUTATION ANALYSIS
D1021V1, survival
                sevent
clus2              0   1
  DLL3 MUTATED     6   1
  DLL3 WILD-TYPE 372  92
  DLL3 MUTATED DLL3 WILD-TYPE 
             7            464 
  DLL3 MUTATED DLL3 WILD-TYPE 
             1             92 
$`DLL3 MUTATED`
TCGA-A6-6653 TCGA-AA-3947 TCGA-AA-A010 TCGA-AZ-6598 TCGA-CM-6162 TCGA-D5-6927 
       24.39        33.01        34.98        49.41        12.00         9.44 
TCGA-AG-3892 
       13.02 

$`DLL3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
       25.08        25.18        24.16        21.76        24.69        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
        2.01        12.99        24.00        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        88.21         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 
        5.03        15.02        15.02        17.03        15.02         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
       14.30         9.04        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       36.95        17.03        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  DLL3 MUTATED DLL3 WILD-TYPE 
          9.44           0.00 
  DLL3 MUTATED DLL3 WILD-TYPE 
         49.41         148.01 
  DLL3 MUTATED DLL3 WILD-TYPE 
        24.390         20.155 
[1] "9.4 - 49.4 (24.4)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.3"
D1021V2, continuous
D1021V3, binary
                cls
clus               0   1
  DLL3 MUTATED     6   1
  DLL3 WILD-TYPE 360 118
[1] "tbl2"
                cls
clus             [,1] [,2]
  DLL3 MUTATED      6    1
  DLL3 WILD-TYPE  360  118
        clus
vv       DLL3 MUTATED DLL3 WILD-TYPE
  COLON             6            360
  RECTUM            1            118
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DLL3 MUTATED         2        0        1         1         2         0
  DLL3 WILD-TYPE      89        1       31       137         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DLL3 MUTATED           0          0          1          0        0         0
  DLL3 WILD-TYPE        24         11         58         42       48        18
                vv
clus             STAGE IVB
  DLL3 MUTATED           0
  DLL3 WILD-TYPE         1
D1021V4, multiclass
            clus
vv           DLL3 MUTATED DLL3 WILD-TYPE
  STAGE I               2             89
  STAGE IA              0              1
  STAGE II              1             31
  STAGE IIA             1            137
  STAGE IIB             2              8
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            1             58
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  DLL3 MUTATED     1   1   3   2
  DLL3 WILD-TYPE  16  91 326  48
D1021V5, multiclass
    clus
vv   DLL3 MUTATED DLL3 WILD-TYPE
  T1            1             16
  T2            1             91
  T3            3            326
  T4            2             48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  DLL3 MUTATED     6   1   0
  DLL3 WILD-TYPE 281 112  87
D1021V6, multiclass
    clus
vv   DLL3 MUTATED DLL3 WILD-TYPE
  N0            6            281
  N1            1            112
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1021V7, binary
                cls
clus               0   1
  DLL3 MUTATED     6   0
  DLL3 WILD-TYPE 369  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  DLL3 MUTATED      6    0
  DLL3 WILD-TYPE  369   65
   clus
vv  DLL3 MUTATED DLL3 WILD-TYPE
  0            6            369
  1            0             65
[1] 2 2
[1] FALSE
D1021V8, binary
                cls
clus               0   1
  DLL3 MUTATED     5   2
  DLL3 WILD-TYPE 220 262
[1] "tbl2"
                cls
clus             [,1] [,2]
  DLL3 MUTATED      5    2
  DLL3 WILD-TYPE  220  262
        clus
vv       DLL3 MUTATED DLL3 WILD-TYPE
  FEMALE            5            220
  MALE              2            262
[1] 2 2
[1] FALSE
D1021V9, binary
                cls
clus               0   1
  DLL3 MUTATED     7   0
  DLL3 WILD-TYPE 343  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  DLL3 MUTATED      7    0
  DLL3 WILD-TYPE  343   22
     clus
vv    DLL3 MUTATED DLL3 WILD-TYPE
  NO             7            343
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  DLL3 MUTATED                      4                             2
  DLL3 WILD-TYPE                  311                            45
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  DLL3 MUTATED                       1                              0
  DLL3 WILD-TYPE                   105                             10
D1021V10, multiclass
                                clus
vv                               DLL3 MUTATED DLL3 WILD-TYPE
  COLON ADENOCARCINOMA                      4            311
  COLON MUCINOUS ADENOCARCINOMA             2             45
  RECTAL ADENOCARCINOMA                     1            105
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  DLL3 MUTATED     5   0   0   0
  DLL3 WILD-TYPE 340   4  31  25
D1021V11, multiclass
    clus
vv   DLL3 MUTATED DLL3 WILD-TYPE
  R0            5            340
  R1            0              4
  R2            0             31
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1021V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DLL3 MUTATED                                  0     0
  DLL3 WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  DLL3 MUTATED                           0     4
  DLL3 WILD-TYPE                        22   222
D1021V13, multiclass
                                  clus
vv                                 DLL3 MUTATED DLL3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       4            222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1022) Variable = PHF1 MUTATION ANALYSIS
D1022V1, survival
                sevent
clus2              0   1
  PHF1 MUTATED     5   2
  PHF1 WILD-TYPE 373  91
  PHF1 MUTATED PHF1 WILD-TYPE 
             7            464 
  PHF1 MUTATED PHF1 WILD-TYPE 
             2             91 
$`PHF1 MUTATED`
TCGA-A6-5665 TCGA-A6-6781 TCGA-AZ-6598 TCGA-CA-6717 TCGA-F4-6570 TCGA-G4-6315 
       22.06        19.66        49.41        12.76         6.18        61.91 
TCGA-AG-A014 
       15.95 

$`PHF1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 
      106.75        22.36        62.79        88.21         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 
       98.24         8.61        31.96        35.74        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6317 TCGA-G4-6321 
       44.68        55.04        85.48        63.62        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       23.01        37.02        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  PHF1 MUTATED PHF1 WILD-TYPE 
          6.18           0.00 
  PHF1 MUTATED PHF1 WILD-TYPE 
         61.91         148.01 
  PHF1 MUTATED PHF1 WILD-TYPE 
        19.660         20.235 
[1] "6.2 - 61.9 (19.7)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.3"
D1022V2, continuous
D1022V3, binary
                cls
clus               0   1
  PHF1 MUTATED     6   1
  PHF1 WILD-TYPE 360 118
[1] "tbl2"
                cls
clus             [,1] [,2]
  PHF1 MUTATED      6    1
  PHF1 WILD-TYPE  360  118
        clus
vv       PHF1 MUTATED PHF1 WILD-TYPE
  COLON             6            360
  RECTUM            1            118
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PHF1 MUTATED         1        0        1         3         0         0
  PHF1 WILD-TYPE      90        1       31       135        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PHF1 MUTATED           0          0          0          1        1         0
  PHF1 WILD-TYPE        24         11         59         41       47        18
                vv
clus             STAGE IVB
  PHF1 MUTATED           0
  PHF1 WILD-TYPE         1
D1022V4, multiclass
            clus
vv           PHF1 MUTATED PHF1 WILD-TYPE
  STAGE I               1             90
  STAGE IA              0              1
  STAGE II              1             31
  STAGE IIA             3            135
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            0             59
  STAGE IIIC            1             41
  STAGE IV              1             47
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  PHF1 MUTATED     0   1   5   1
  PHF1 WILD-TYPE  17  91 324  49
D1022V5, multiclass
    clus
vv   PHF1 MUTATED PHF1 WILD-TYPE
  T1            0             17
  T2            1             91
  T3            5            324
  T4            1             49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  PHF1 MUTATED     5   2   0
  PHF1 WILD-TYPE 282 111  87
D1022V6, multiclass
    clus
vv   PHF1 MUTATED PHF1 WILD-TYPE
  N0            5            282
  N1            2            111
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1022V7, binary
                cls
clus               0   1
  PHF1 MUTATED     4   1
  PHF1 WILD-TYPE 371  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  PHF1 MUTATED      4    1
  PHF1 WILD-TYPE  371   64
   clus
vv  PHF1 MUTATED PHF1 WILD-TYPE
  0            4            371
  1            1             64
[1] 2 2
[1] FALSE
D1022V8, binary
                cls
clus               0   1
  PHF1 MUTATED     3   4
  PHF1 WILD-TYPE 222 260
[1] "tbl2"
                cls
clus             [,1] [,2]
  PHF1 MUTATED      3    4
  PHF1 WILD-TYPE  222  260
        clus
vv       PHF1 MUTATED PHF1 WILD-TYPE
  FEMALE            3            222
  MALE              4            260
[1] 2 2
[1] FALSE
D1022V9, binary
                cls
clus               0   1
  PHF1 MUTATED     6   0
  PHF1 WILD-TYPE 344  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  PHF1 MUTATED      6    0
  PHF1 WILD-TYPE  344   22
     clus
vv    PHF1 MUTATED PHF1 WILD-TYPE
  NO             6            344
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PHF1 MUTATED                      4                             2
  PHF1 WILD-TYPE                  311                            45
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PHF1 MUTATED                       1                              0
  PHF1 WILD-TYPE                   105                             10
D1022V10, multiclass
                                clus
vv                               PHF1 MUTATED PHF1 WILD-TYPE
  COLON ADENOCARCINOMA                      4            311
  COLON MUCINOUS ADENOCARCINOMA             2             45
  RECTAL ADENOCARCINOMA                     1            105
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  PHF1 MUTATED     5   0   0   1
  PHF1 WILD-TYPE 340   4  31  24
D1022V11, multiclass
    clus
vv   PHF1 MUTATED PHF1 WILD-TYPE
  R0            5            340
  R1            0              4
  R2            0             31
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1022V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PHF1 MUTATED                                  0     1
  PHF1 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  PHF1 MUTATED                           0     5
  PHF1 WILD-TYPE                        22   221
D1022V13, multiclass
                                  clus
vv                                 PHF1 MUTATED PHF1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       5            221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1023) Variable = IFNAR1 MUTATION ANALYSIS
D1023V1, survival
                  sevent
clus2                0   1
  IFNAR1 MUTATED     6   1
  IFNAR1 WILD-TYPE 372  92
  IFNAR1 MUTATED IFNAR1 WILD-TYPE 
               7              464 
  IFNAR1 MUTATED IFNAR1 WILD-TYPE 
               1               92 
$`IFNAR1 MUTATED`
TCGA-AA-3672 TCGA-AA-3815 TCGA-AA-3855 TCGA-AA-A010 TCGA-CK-5912 TCGA-CM-5860 
        0.92        33.04        32.05        34.98        49.08        32.02 
TCGA-CM-6678 
       11.01 

$`IFNAR1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
        6.05         6.97        54.02         2.01        14.01        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       10.06        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3856 
       10.06         0.00        33.07         0.00        36.03         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.03        22.98        30.08        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  IFNAR1 MUTATED IFNAR1 WILD-TYPE 
            0.92             0.00 
  IFNAR1 MUTATED IFNAR1 WILD-TYPE 
           49.08           148.01 
  IFNAR1 MUTATED IFNAR1 WILD-TYPE 
          32.050           20.085 
[1] "0.9 - 49.1 (32.0)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.4"
D1023V2, continuous
D1023V3, binary
                  cls
clus                 0   1
  IFNAR1 MUTATED     7   0
  IFNAR1 WILD-TYPE 359 119
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IFNAR1 MUTATED      7    0
  IFNAR1 WILD-TYPE  359  119
        clus
vv       IFNAR1 MUTATED IFNAR1 WILD-TYPE
  COLON               7              359
  RECTUM              0              119
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  IFNAR1 MUTATED         2        0        0         2         1         0
  IFNAR1 WILD-TYPE      89        1       32       136         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  IFNAR1 MUTATED           1          0          0          0        0
  IFNAR1 WILD-TYPE        23         11         59         42       48
                  vv
clus               STAGE IVA STAGE IVB
  IFNAR1 MUTATED           1         0
  IFNAR1 WILD-TYPE        17         1
D1023V4, multiclass
            clus
vv           IFNAR1 MUTATED IFNAR1 WILD-TYPE
  STAGE I                 2               89
  STAGE IA                0                1
  STAGE II                0               32
  STAGE IIA               2              136
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               1               23
  STAGE IIIA              0               11
  STAGE IIIB              0               59
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               1               17
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  IFNAR1 MUTATED     0   2   3   2
  IFNAR1 WILD-TYPE  17  90 326  48
D1023V5, multiclass
    clus
vv   IFNAR1 MUTATED IFNAR1 WILD-TYPE
  T1              0               17
  T2              2               90
  T3              3              326
  T4              2               48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  IFNAR1 MUTATED     5   2   0
  IFNAR1 WILD-TYPE 282 111  87
D1023V6, multiclass
    clus
vv   IFNAR1 MUTATED IFNAR1 WILD-TYPE
  N0              5              282
  N1              2              111
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1023V7, binary
                  cls
clus                 0   1
  IFNAR1 MUTATED     5   1
  IFNAR1 WILD-TYPE 370  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IFNAR1 MUTATED      5    1
  IFNAR1 WILD-TYPE  370   64
   clus
vv  IFNAR1 MUTATED IFNAR1 WILD-TYPE
  0              5              370
  1              1               64
[1] 2 2
[1] FALSE
D1023V8, binary
                  cls
clus                 0   1
  IFNAR1 MUTATED     4   3
  IFNAR1 WILD-TYPE 221 261
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IFNAR1 MUTATED      4    3
  IFNAR1 WILD-TYPE  221  261
        clus
vv       IFNAR1 MUTATED IFNAR1 WILD-TYPE
  FEMALE              4              221
  MALE                3              261
[1] 2 2
[1] FALSE
D1023V9, binary
                  cls
clus                 0   1
  IFNAR1 MUTATED     7   0
  IFNAR1 WILD-TYPE 343  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IFNAR1 MUTATED      7    0
  IFNAR1 WILD-TYPE  343   22
     clus
vv    IFNAR1 MUTATED IFNAR1 WILD-TYPE
  NO               7              343
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  IFNAR1 MUTATED                      7                             0
  IFNAR1 WILD-TYPE                  308                            47
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  IFNAR1 MUTATED                       0                              0
  IFNAR1 WILD-TYPE                   106                             10
D1023V10, multiclass
                                clus
vv                               IFNAR1 MUTATED IFNAR1 WILD-TYPE
  COLON ADENOCARCINOMA                        7              308
  COLON MUCINOUS ADENOCARCINOMA               0               47
  RECTAL ADENOCARCINOMA                       0              106
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  IFNAR1 MUTATED     6   0   0   1
  IFNAR1 WILD-TYPE 339   4  31  24
D1023V11, multiclass
    clus
vv   IFNAR1 MUTATED IFNAR1 WILD-TYPE
  R0              6              339
  R1              0                4
  R2              0               31
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1023V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  IFNAR1 MUTATED                                  0     0
  IFNAR1 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  IFNAR1 MUTATED                           0     3
  IFNAR1 WILD-TYPE                        22   223
D1023V13, multiclass
                                  clus
vv                                 IFNAR1 MUTATED IFNAR1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         3              223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1024) Variable = MAP4K4 MUTATION ANALYSIS
D1024V1, survival
                  sevent
clus2                0   1
  MAP4K4 MUTATED    15   4
  MAP4K4 WILD-TYPE 363  89
  MAP4K4 MUTATED MAP4K4 WILD-TYPE 
              19              452 
  MAP4K4 MUTATED MAP4K4 WILD-TYPE 
               4               89 
$`MAP4K4 MUTATED`
TCGA-A6-5661 TCGA-AA-3492 TCGA-AA-3713 TCGA-AA-3845 TCGA-AA-3864 TCGA-AA-3949 
       33.53         3.02        19.04         0.00        53.00        26.01 
TCGA-AA-A00N TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-5913 TCGA-CM-5344 TCGA-CM-5348 
        4.01        12.76        10.06        51.32        22.03        22.98 
TCGA-CM-6162 TCGA-D5-6541 TCGA-D5-6928 TCGA-G4-6588 TCGA-AG-3731 TCGA-AG-3892 
       12.00        15.58        11.64        26.17        37.02        13.02 
TCGA-AG-A002 
       20.98 

$`MAP4K4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 
       20.12        19.66        20.28         7.04         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       38.99        37.02        14.93        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       31.07        30.05        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.07        12.20        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        49.08         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       29.06        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       15.02        17.03        15.02         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6898 
       17.85         4.80        17.13        12.49        16.14         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 
       61.91        36.00        22.09        13.78        35.80        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       17.95        36.95        17.03        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  MAP4K4 MUTATED MAP4K4 WILD-TYPE 
               0                0 
  MAP4K4 MUTATED MAP4K4 WILD-TYPE 
           53.00           148.01 
  MAP4K4 MUTATED MAP4K4 WILD-TYPE 
          19.040           20.235 
[1] "0.0 - 53.0 (19.0)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.3"
D1024V2, continuous
D1024V3, binary
                  cls
clus                 0   1
  MAP4K4 MUTATED    18   3
  MAP4K4 WILD-TYPE 348 116
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP4K4 MUTATED     18    3
  MAP4K4 WILD-TYPE  348  116
        clus
vv       MAP4K4 MUTATED MAP4K4 WILD-TYPE
  COLON              18              348
  RECTUM              3              116
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MAP4K4 MUTATED         2        0        2         8         1         0
  MAP4K4 WILD-TYPE      89        1       30       130         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MAP4K4 MUTATED           1          0          4          1        2
  MAP4K4 WILD-TYPE        23         11         55         41       46
                  vv
clus               STAGE IVA STAGE IVB
  MAP4K4 MUTATED           0         0
  MAP4K4 WILD-TYPE        18         1
D1024V4, multiclass
            clus
vv           MAP4K4 MUTATED MAP4K4 WILD-TYPE
  STAGE I                 2               89
  STAGE IA                0                1
  STAGE II                2               30
  STAGE IIA               8              130
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               1               23
  STAGE IIIA              0               11
  STAGE IIIB              4               55
  STAGE IIIC              1               41
  STAGE IV                2               46
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  MAP4K4 MUTATED     1   1  18   1
  MAP4K4 WILD-TYPE  16  91 311  49
D1024V5, multiclass
    clus
vv   MAP4K4 MUTATED MAP4K4 WILD-TYPE
  T1              1               16
  T2              1               91
  T3             18              311
  T4              1               49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  MAP4K4 MUTATED    14   5   2
  MAP4K4 WILD-TYPE 273 108  85
D1024V6, multiclass
    clus
vv   MAP4K4 MUTATED MAP4K4 WILD-TYPE
  N0             14              273
  N1              5              108
  N2              2               85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1024V7, binary
                  cls
clus                 0   1
  MAP4K4 MUTATED    17   2
  MAP4K4 WILD-TYPE 358  63
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP4K4 MUTATED     17    2
  MAP4K4 WILD-TYPE  358   63
   clus
vv  MAP4K4 MUTATED MAP4K4 WILD-TYPE
  0             17              358
  1              2               63
[1] 2 2
[1] FALSE
D1024V8, binary
                  cls
clus                 0   1
  MAP4K4 MUTATED     9  12
  MAP4K4 WILD-TYPE 216 252
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP4K4 MUTATED      9   12
  MAP4K4 WILD-TYPE  216  252
        clus
vv       MAP4K4 MUTATED MAP4K4 WILD-TYPE
  FEMALE              9              216
  MALE               12              252
[1] 2 2
[1] FALSE
D1024V9, binary
                  cls
clus                 0   1
  MAP4K4 MUTATED    16   1
  MAP4K4 WILD-TYPE 334  21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP4K4 MUTATED     16    1
  MAP4K4 WILD-TYPE  334   21
     clus
vv    MAP4K4 MUTATED MAP4K4 WILD-TYPE
  NO              16              334
  YES              1               21
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MAP4K4 MUTATED                     12                             6
  MAP4K4 WILD-TYPE                  303                            41
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MAP4K4 MUTATED                       3                              0
  MAP4K4 WILD-TYPE                   103                             10
D1024V10, multiclass
                                clus
vv                               MAP4K4 MUTATED MAP4K4 WILD-TYPE
  COLON ADENOCARCINOMA                       12              303
  COLON MUCINOUS ADENOCARCINOMA               6               41
  RECTAL ADENOCARCINOMA                       3              103
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  MAP4K4 MUTATED    16   0   2   3
  MAP4K4 WILD-TYPE 329   4  29  22
D1024V11, multiclass
    clus
vv   MAP4K4 MUTATED MAP4K4 WILD-TYPE
  R0             16              329
  R1              0                4
  R2              2               29
  RX              3               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1024V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MAP4K4 MUTATED                                  0     2
  MAP4K4 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  MAP4K4 MUTATED                           1     8
  MAP4K4 WILD-TYPE                        21   218
D1024V13, multiclass
                                  clus
vv                                 MAP4K4 MUTATED MAP4K4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                9
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                         8              218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1025) Variable = CSNK2A2 MUTATION ANALYSIS
D1025V1, survival
                   sevent
clus2                 0   1
  CSNK2A2 MUTATED     4   2
  CSNK2A2 WILD-TYPE 374  91
  CSNK2A2 MUTATED CSNK2A2 WILD-TYPE 
                6               465 
  CSNK2A2 MUTATED CSNK2A2 WILD-TYPE 
                2                91 
$`CSNK2A2 MUTATED`
TCGA-AZ-6599 TCGA-CM-5868 TCGA-D5-6535 TCGA-D5-6927 TCGA-F4-6570 TCGA-G4-6588 
        6.77        17.03        15.12         9.44         6.18        26.17 

$`CSNK2A2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       49.41        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 
       20.19        18.25         1.32        43.27        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6929 
        4.41        12.43        14.30         9.04        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 
       98.24         8.61        31.96        35.74        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       22.09        13.78        35.80        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  CSNK2A2 MUTATED CSNK2A2 WILD-TYPE 
             6.18              0.00 
  CSNK2A2 MUTATED CSNK2A2 WILD-TYPE 
            26.17            148.01 
  CSNK2A2 MUTATED CSNK2A2 WILD-TYPE 
            12.28             20.55 
[1] "6.2 - 26.2 (12.3)"  "0.0 - 148.0 (20.6)"
[1] "hr=" "3.1"
D1025V2, continuous
D1025V3, binary
                   cls
clus                  0   1
  CSNK2A2 MUTATED     7   0
  CSNK2A2 WILD-TYPE 359 119
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CSNK2A2 MUTATED      7    0
  CSNK2A2 WILD-TYPE  359  119
        clus
vv       CSNK2A2 MUTATED CSNK2A2 WILD-TYPE
  COLON                7               359
  RECTUM               0               119
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CSNK2A2 MUTATED         1        0        0         3         0         0
  CSNK2A2 WILD-TYPE      90        1       32       135        10         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CSNK2A2 MUTATED           0          0          1          0        1
  CSNK2A2 WILD-TYPE        24         11         58         42       47
                   vv
clus                STAGE IVA STAGE IVB
  CSNK2A2 MUTATED           1         0
  CSNK2A2 WILD-TYPE        17         1
D1025V4, multiclass
            clus
vv           CSNK2A2 MUTATED CSNK2A2 WILD-TYPE
  STAGE I                  1                90
  STAGE IA                 0                 1
  STAGE II                 0                32
  STAGE IIA                3               135
  STAGE IIB                0                10
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               0                11
  STAGE IIIB               1                58
  STAGE IIIC               0                42
  STAGE IV                 1                47
  STAGE IVA                1                17
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  CSNK2A2 MUTATED     0   1   4   2
  CSNK2A2 WILD-TYPE  17  91 325  48
D1025V5, multiclass
    clus
vv   CSNK2A2 MUTATED CSNK2A2 WILD-TYPE
  T1               0                17
  T2               1                91
  T3               4               325
  T4               2                48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  CSNK2A2 MUTATED     4   3   0
  CSNK2A2 WILD-TYPE 283 110  87
D1025V6, multiclass
    clus
vv   CSNK2A2 MUTATED CSNK2A2 WILD-TYPE
  N0               4               283
  N1               3               110
  N2               0                87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1025V7, binary
                   cls
clus                  0   1
  CSNK2A2 MUTATED     3   2
  CSNK2A2 WILD-TYPE 372  63
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CSNK2A2 MUTATED      3    2
  CSNK2A2 WILD-TYPE  372   63
   clus
vv  CSNK2A2 MUTATED CSNK2A2 WILD-TYPE
  0               3               372
  1               2                63
[1] 2 2
[1] FALSE
D1025V8, binary
                   cls
clus                  0   1
  CSNK2A2 MUTATED     5   2
  CSNK2A2 WILD-TYPE 220 262
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CSNK2A2 MUTATED      5    2
  CSNK2A2 WILD-TYPE  220  262
        clus
vv       CSNK2A2 MUTATED CSNK2A2 WILD-TYPE
  FEMALE               5               220
  MALE                 2               262
[1] 2 2
[1] FALSE
D1025V9, binary
                   cls
clus                  0   1
  CSNK2A2 MUTATED     6   0
  CSNK2A2 WILD-TYPE 344  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CSNK2A2 MUTATED      6    0
  CSNK2A2 WILD-TYPE  344   22
     clus
vv    CSNK2A2 MUTATED CSNK2A2 WILD-TYPE
  NO                6               344
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CSNK2A2 MUTATED                      7                             0
  CSNK2A2 WILD-TYPE                  308                            47
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CSNK2A2 MUTATED                       0                              0
  CSNK2A2 WILD-TYPE                   106                             10
D1025V10, multiclass
                                clus
vv                               CSNK2A2 MUTATED CSNK2A2 WILD-TYPE
  COLON ADENOCARCINOMA                         7               308
  COLON MUCINOUS ADENOCARCINOMA                0                47
  RECTAL ADENOCARCINOMA                        0               106
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  CSNK2A2 MUTATED     4   0   1   1
  CSNK2A2 WILD-TYPE 341   4  30  24
D1025V11, multiclass
    clus
vv   CSNK2A2 MUTATED CSNK2A2 WILD-TYPE
  R0               4               341
  R1               0                 4
  R2               1                30
  RX               1                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1025V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CSNK2A2 MUTATED                                  0     0
  CSNK2A2 WILD-TYPE                                1    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  CSNK2A2 MUTATED                           0     6
  CSNK2A2 WILD-TYPE                        22   220
D1025V13, multiclass
                                  clus
vv                                 CSNK2A2 MUTATED CSNK2A2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                      0                22
  WHITE                                          6               220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1026) Variable = CBX3 MUTATION ANALYSIS
D1026V1, survival
                sevent
clus2              0   1
  CBX3 MUTATED     7   0
  CBX3 WILD-TYPE 371  93
  CBX3 MUTATED CBX3 WILD-TYPE 
             7            464 
  CBX3 MUTATED CBX3 WILD-TYPE 
             0             93 
$`CBX3 MUTATED`
TCGA-A6-5661 TCGA-A6-6780 TCGA-AA-3950 TCGA-AA-3977 TCGA-AD-6889 TCGA-G4-6586 
       33.53        20.12        24.00        25.02        56.55        35.80 
TCGA-AG-A00C 
        6.02 

$`CBX3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 
       12.99        24.00        33.01        26.01         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 
       40.96         0.07        21.37        15.52         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       22.09        13.78        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        20.98        13.94        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  CBX3 MUTATED CBX3 WILD-TYPE 
          6.02           0.00 
  CBX3 MUTATED CBX3 WILD-TYPE 
         56.55         148.01 
  CBX3 MUTATED CBX3 WILD-TYPE 
        25.020         20.035 
[1] "6.0 - 56.5 (25.0)"  "0.0 - 148.0 (20.0)"
[1] "hr="     "9100000"
D1026V2, continuous
D1026V3, binary
                cls
clus               0   1
  CBX3 MUTATED     6   1
  CBX3 WILD-TYPE 360 118
[1] "tbl2"
                cls
clus             [,1] [,2]
  CBX3 MUTATED      6    1
  CBX3 WILD-TYPE  360  118
        clus
vv       CBX3 MUTATED CBX3 WILD-TYPE
  COLON             6            360
  RECTUM            1            118
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CBX3 MUTATED         0        0        0         5         0         0
  CBX3 WILD-TYPE      91        1       32       133        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CBX3 MUTATED           0          0          1          0        0         0
  CBX3 WILD-TYPE        24         11         58         42       48        18
                vv
clus             STAGE IVB
  CBX3 MUTATED           0
  CBX3 WILD-TYPE         1
D1026V4, multiclass
            clus
vv           CBX3 MUTATED CBX3 WILD-TYPE
  STAGE I               0             91
  STAGE IA              0              1
  STAGE II              0             32
  STAGE IIA             5            133
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            1             58
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  CBX3 MUTATED     0   1   6   0
  CBX3 WILD-TYPE  17  91 323  50
D1026V5, multiclass
    clus
vv   CBX3 MUTATED CBX3 WILD-TYPE
  T1            0             17
  T2            1             91
  T3            6            323
  T4            0             50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  CBX3 MUTATED     6   1   0
  CBX3 WILD-TYPE 281 112  87
D1026V6, multiclass
    clus
vv   CBX3 MUTATED CBX3 WILD-TYPE
  N0            6            281
  N1            1            112
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1026V7, binary
                cls
clus               0   1
  CBX3 MUTATED     5   0
  CBX3 WILD-TYPE 370  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  CBX3 MUTATED      5    0
  CBX3 WILD-TYPE  370   65
   clus
vv  CBX3 MUTATED CBX3 WILD-TYPE
  0            5            370
  1            0             65
[1] 2 2
[1] FALSE
D1026V8, binary
                cls
clus               0   1
  CBX3 MUTATED     4   3
  CBX3 WILD-TYPE 221 261
[1] "tbl2"
                cls
clus             [,1] [,2]
  CBX3 MUTATED      4    3
  CBX3 WILD-TYPE  221  261
        clus
vv       CBX3 MUTATED CBX3 WILD-TYPE
  FEMALE            4            221
  MALE              3            261
[1] 2 2
[1] FALSE
D1026V9, binary
                cls
clus               0   1
  CBX3 MUTATED     5   1
  CBX3 WILD-TYPE 345  21
[1] "tbl2"
                cls
clus             [,1] [,2]
  CBX3 MUTATED      5    1
  CBX3 WILD-TYPE  345   21
     clus
vv    CBX3 MUTATED CBX3 WILD-TYPE
  NO             5            345
  YES            1             21
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CBX3 MUTATED                      4                             2
  CBX3 WILD-TYPE                  311                            45
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CBX3 MUTATED                       1                              0
  CBX3 WILD-TYPE                   105                             10
D1026V10, multiclass
                                clus
vv                               CBX3 MUTATED CBX3 WILD-TYPE
  COLON ADENOCARCINOMA                      4            311
  COLON MUCINOUS ADENOCARCINOMA             2             45
  RECTAL ADENOCARCINOMA                     1            105
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  CBX3 MUTATED     4   0   0   0
  CBX3 WILD-TYPE 341   4  31  25
D1026V11, multiclass
    clus
vv   CBX3 MUTATED CBX3 WILD-TYPE
  R0            4            341
  R1            0              4
  R2            0             31
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1026V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CBX3 MUTATED                                  0     1
  CBX3 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  CBX3 MUTATED                           1     2
  CBX3 WILD-TYPE                        21   224
D1026V13, multiclass
                                  clus
vv                                 CBX3 MUTATED CBX3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                       2            224
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1027) Variable = MCART1 MUTATION ANALYSIS
D1027V1, survival
                  sevent
clus2                0   1
  MCART1 MUTATED    12   1
  MCART1 WILD-TYPE 366  92
  MCART1 MUTATED MCART1 WILD-TYPE 
              13              458 
  MCART1 MUTATED MCART1 WILD-TYPE 
               1               92 
$`MCART1 MUTATED`
TCGA-A6-5661 TCGA-AA-3489 TCGA-AA-3877 TCGA-AA-3947 TCGA-AZ-4315 TCGA-CK-4950 
       33.53         7.04        31.00        33.01        58.39        85.45 
TCGA-CM-4746 TCGA-CM-5348 TCGA-D5-6540 TCGA-DM-A0X9 TCGA-DM-A1D9 TCGA-G4-6309 
       37.02        22.98        16.14       119.70       140.38        85.48 
TCGA-CI-6620 
       33.17 

$`MCART1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        19.66        20.28         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 
       24.03        27.02        29.98        18.05         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       14.30        17.56       148.01        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5349 
       20.02        25.02        13.02        29.06        22.03        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
        4.80        17.13        12.49        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0XD 
        4.80         1.51        12.00        11.38        10.26        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       44.68        55.04        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6622 TCGA-CI-6624 
       17.49         0.69         0.72         6.05         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  MCART1 MUTATED MCART1 WILD-TYPE 
            7.04             0.00 
  MCART1 MUTATED MCART1 WILD-TYPE 
          140.38           148.01 
  MCART1 MUTATED MCART1 WILD-TYPE 
          33.530           20.005 
[1] "7.0 - 140.4 (33.5)" "0.0 - 148.0 (20.0)"
[1] "hr=" "4.9"
D1027V2, continuous
D1027V3, binary
                  cls
clus                 0   1
  MCART1 MUTATED    12   1
  MCART1 WILD-TYPE 354 118
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MCART1 MUTATED     12    1
  MCART1 WILD-TYPE  354  118
        clus
vv       MCART1 MUTATED MCART1 WILD-TYPE
  COLON              12              354
  RECTUM              1              118
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MCART1 MUTATED         3        0        1         4         1         0
  MCART1 WILD-TYPE      88        1       31       134         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MCART1 MUTATED           0          0          3          0        0
  MCART1 WILD-TYPE        24         11         56         42       48
                  vv
clus               STAGE IVA STAGE IVB
  MCART1 MUTATED           1         0
  MCART1 WILD-TYPE        17         1
D1027V4, multiclass
            clus
vv           MCART1 MUTATED MCART1 WILD-TYPE
  STAGE I                 3               88
  STAGE IA                0                1
  STAGE II                1               31
  STAGE IIA               4              134
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              3               56
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               1               17
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  MCART1 MUTATED     1   2   9   1
  MCART1 WILD-TYPE  16  90 320  49
D1027V5, multiclass
    clus
vv   MCART1 MUTATED MCART1 WILD-TYPE
  T1              1               16
  T2              2               90
  T3              9              320
  T4              1               49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  MCART1 MUTATED     9   4   0
  MCART1 WILD-TYPE 278 109  87
D1027V6, multiclass
    clus
vv   MCART1 MUTATED MCART1 WILD-TYPE
  N0              9              278
  N1              4              109
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1027V7, binary
                  cls
clus                 0   1
  MCART1 MUTATED    12   1
  MCART1 WILD-TYPE 363  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MCART1 MUTATED     12    1
  MCART1 WILD-TYPE  363   64
   clus
vv  MCART1 MUTATED MCART1 WILD-TYPE
  0             12              363
  1              1               64
[1] 2 2
[1] FALSE
D1027V8, binary
                  cls
clus                 0   1
  MCART1 MUTATED     8   5
  MCART1 WILD-TYPE 217 259
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MCART1 MUTATED      8    5
  MCART1 WILD-TYPE  217  259
        clus
vv       MCART1 MUTATED MCART1 WILD-TYPE
  FEMALE              8              217
  MALE                5              259
[1] 2 2
[1] FALSE
D1027V9, binary
                  cls
clus                 0   1
  MCART1 MUTATED    11   0
  MCART1 WILD-TYPE 339  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MCART1 MUTATED     11    0
  MCART1 WILD-TYPE  339   22
     clus
vv    MCART1 MUTATED MCART1 WILD-TYPE
  NO              11              339
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MCART1 MUTATED                      9                             3
  MCART1 WILD-TYPE                  306                            44
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MCART1 MUTATED                       1                              0
  MCART1 WILD-TYPE                   105                             10
D1027V10, multiclass
                                clus
vv                               MCART1 MUTATED MCART1 WILD-TYPE
  COLON ADENOCARCINOMA                        9              306
  COLON MUCINOUS ADENOCARCINOMA               3               44
  RECTAL ADENOCARCINOMA                       1              105
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  MCART1 MUTATED     9   1   0   0
  MCART1 WILD-TYPE 336   3  31  25
D1027V11, multiclass
    clus
vv   MCART1 MUTATED MCART1 WILD-TYPE
  R0              9              336
  R1              1                3
  R2              0               31
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1027V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MCART1 MUTATED                                  0     0
  MCART1 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  MCART1 MUTATED                           4     6
  MCART1 WILD-TYPE                        18   220
D1027V13, multiclass
                                  clus
vv                                 MCART1 MUTATED MCART1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     4               18
  WHITE                                         6              220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1028) Variable = USP28 MUTATION ANALYSIS
D1028V1, survival
                 sevent
clus2               0   1
  USP28 MUTATED    20   6
  USP28 WILD-TYPE 358  87
  USP28 MUTATED USP28 WILD-TYPE 
             26             445 
  USP28 MUTATED USP28 WILD-TYPE 
              6              87 
$`USP28 MUTATED`
TCGA-A6-3809 TCGA-A6-5661 TCGA-A6-6780 TCGA-AA-3510 TCGA-AA-3516 TCGA-AA-3660 
       32.75        33.53        20.12        63.98        13.02        78.08 
TCGA-AA-3692 TCGA-AA-3710 TCGA-AA-3815 TCGA-AA-3864 TCGA-AA-A00N TCGA-AA-A010 
       36.00        26.99        33.04        53.00         4.01        34.98 
TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-6599 TCGA-CA-6717 TCGA-D5-6533 TCGA-D5-6922 
       21.44        58.39         6.77        12.76         1.32         4.41 
TCGA-DM-A1HB TCGA-DM-A28E TCGA-G4-6299 TCGA-AF-2692 TCGA-AG-A002 TCGA-AG-A02N 
      135.65       119.93        74.56        13.55        20.98        61.97 
TCGA-DY-A1DC TCGA-DY-A1DD 
       41.36        57.24 

$`USP28 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       31.63        30.44        29.19        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6781 
       24.16        21.76        24.69        24.39        23.87        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 
       20.28         7.04         3.02         1.02        35.01         6.97 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
        1.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       36.03         8.05        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
       19.00         5.03        85.05        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       35.05         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        31.07        30.05        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
       16.31         0.95        33.01        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 
      106.75        22.36        62.79        88.21        49.41        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6923 TCGA-D5-6924 
       16.14        15.58         1.48         3.68        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28F 
       44.32       131.51       139.17         6.12        81.37        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       38.96        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
        5.29       126.44        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  USP28 MUTATED USP28 WILD-TYPE 
           1.32            0.00 
  USP28 MUTATED USP28 WILD-TYPE 
         135.65          148.01 
  USP28 MUTATED USP28 WILD-TYPE 
         33.285          19.990 
[1] "1.3 - 135.7 (33.3)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.3"
D1028V2, continuous
D1028V3, binary
                 cls
clus                0   1
  USP28 MUTATED    23   4
  USP28 WILD-TYPE 343 115
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP28 MUTATED     23    4
  USP28 WILD-TYPE  343  115
        clus
vv       USP28 MUTATED USP28 WILD-TYPE
  COLON             23             343
  RECTUM             4             115
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  USP28 MUTATED         2        0        4        11         3         0
  USP28 WILD-TYPE      89        1       28       127         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  USP28 MUTATED           1          1          3          1        2         0
  USP28 WILD-TYPE        23         10         56         41       46        18
                 vv
clus              STAGE IVB
  USP28 MUTATED           0
  USP28 WILD-TYPE         1
D1028V4, multiclass
            clus
vv           USP28 MUTATED USP28 WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               4              28
  STAGE IIA             11             127
  STAGE IIB              3               7
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             1              10
  STAGE IIIB             3              56
  STAGE IIIC             1              41
  STAGE IV               2              46
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  USP28 MUTATED     0   2  21   5
  USP28 WILD-TYPE  17  90 308  45
D1028V5, multiclass
    clus
vv   USP28 MUTATED USP28 WILD-TYPE
  T1             0              17
  T2             2              90
  T3            21             308
  T4             5              45
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  USP28 MUTATED    21   4   3
  USP28 WILD-TYPE 266 109  84
D1028V6, multiclass
    clus
vv   USP28 MUTATED USP28 WILD-TYPE
  N0            21             266
  N1             4             109
  N2             3              84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1028V7, binary
                 cls
clus                0   1
  USP28 MUTATED    23   2
  USP28 WILD-TYPE 352  63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP28 MUTATED     23    2
  USP28 WILD-TYPE  352   63
   clus
vv  USP28 MUTATED USP28 WILD-TYPE
  0            23             352
  1             2              63
[1] 2 2
[1] FALSE
D1028V8, binary
                 cls
clus                0   1
  USP28 MUTATED    15  13
  USP28 WILD-TYPE 210 251
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP28 MUTATED     15   13
  USP28 WILD-TYPE  210  251
        clus
vv       USP28 MUTATED USP28 WILD-TYPE
  FEMALE            15             210
  MALE              13             251
[1] 2 2
[1] FALSE
D1028V9, binary
                 cls
clus                0   1
  USP28 MUTATED    17   1
  USP28 WILD-TYPE 333  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP28 MUTATED     17    1
  USP28 WILD-TYPE  333   21
     clus
vv    USP28 MUTATED USP28 WILD-TYPE
  NO             17             333
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  USP28 MUTATED                     16                             6
  USP28 WILD-TYPE                  299                            41
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  USP28 MUTATED                       4                              0
  USP28 WILD-TYPE                   102                             10
D1028V10, multiclass
                                clus
vv                               USP28 MUTATED USP28 WILD-TYPE
  COLON ADENOCARCINOMA                      16             299
  COLON MUCINOUS ADENOCARCINOMA              6              41
  RECTAL ADENOCARCINOMA                      4             102
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  USP28 MUTATED    18   0   2   1
  USP28 WILD-TYPE 327   4  29  24
D1028V11, multiclass
    clus
vv   USP28 MUTATED USP28 WILD-TYPE
  R0            18             327
  R1             0               4
  R2             2              29
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1028V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  USP28 MUTATED                                  0     1
  USP28 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  USP28 MUTATED                           1    13
  USP28 WILD-TYPE                        21   213
D1028V13, multiclass
                                  clus
vv                                 USP28 MUTATED USP28 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                       13             213
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1029) Variable = ZBP1 MUTATION ANALYSIS
D1029V1, survival
                sevent
clus2              0   1
  ZBP1 MUTATED     9   3
  ZBP1 WILD-TYPE 369  90
  ZBP1 MUTATED ZBP1 WILD-TYPE 
            12            459 
  ZBP1 MUTATED ZBP1 WILD-TYPE 
             3             90 
$`ZBP1 MUTATED`
TCGA-AA-3524 TCGA-AA-3715 TCGA-AA-A00J TCGA-AA-A00R TCGA-AA-A010 TCGA-AZ-4681 
       36.03        19.04        18.05         0.99        34.98       106.75 
TCGA-AZ-6598 TCGA-AZ-6600 TCGA-CM-6172 TCGA-AG-3892 TCGA-AH-6547 TCGA-EI-6507 
       49.41        12.10        11.01        13.02         1.45        19.96 

$`ZBP1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3525 
       38.99         1.02         9.07        24.03        37.05         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 
       36.00         5.03        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       19.00        30.02        34.03        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       27.02        42.02        17.03        14.99        21.99         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
       58.39         1.41         5.13        22.36        62.79        88.21 
TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6674 
       14.99        12.99        13.02        15.02        14.04        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 
       19.99         1.02        17.95        36.95        17.03        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
       38.56        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6510 
       51.48        32.61         0.49        20.55        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  ZBP1 MUTATED ZBP1 WILD-TYPE 
          0.99           0.00 
  ZBP1 MUTATED ZBP1 WILD-TYPE 
        106.75         148.01 
  ZBP1 MUTATED ZBP1 WILD-TYPE 
        18.545         20.550 
[1] "1.0 - 106.8 (18.5)" "0.0 - 148.0 (20.6)"
[1] "hr=" "1.3"
D1029V2, continuous
D1029V3, binary
                cls
clus               0   1
  ZBP1 MUTATED    10   3
  ZBP1 WILD-TYPE 356 116
[1] "tbl2"
                cls
clus             [,1] [,2]
  ZBP1 MUTATED     10    3
  ZBP1 WILD-TYPE  356  116
        clus
vv       ZBP1 MUTATED ZBP1 WILD-TYPE
  COLON            10            356
  RECTUM            3            116
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZBP1 MUTATED         2        0        3         3         1         0
  ZBP1 WILD-TYPE      89        1       29       135         9         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ZBP1 MUTATED           0          0          2          0        1         0
  ZBP1 WILD-TYPE        24         11         57         42       47        18
                vv
clus             STAGE IVB
  ZBP1 MUTATED           0
  ZBP1 WILD-TYPE         1
D1029V4, multiclass
            clus
vv           ZBP1 MUTATED ZBP1 WILD-TYPE
  STAGE I               2             89
  STAGE IA              0              1
  STAGE II              3             29
  STAGE IIA             3            135
  STAGE IIB             1              9
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            2             57
  STAGE IIIC            0             42
  STAGE IV              1             47
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  ZBP1 MUTATED     1   1   8   3
  ZBP1 WILD-TYPE  16  91 321  47
D1029V5, multiclass
    clus
vv   ZBP1 MUTATED ZBP1 WILD-TYPE
  T1            1             16
  T2            1             91
  T3            8            321
  T4            3             47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  ZBP1 MUTATED    10   3   0
  ZBP1 WILD-TYPE 277 110  87
D1029V6, multiclass
    clus
vv   ZBP1 MUTATED ZBP1 WILD-TYPE
  N0           10            277
  N1            3            110
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1029V7, binary
                cls
clus               0   1
  ZBP1 MUTATED    10   1
  ZBP1 WILD-TYPE 365  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  ZBP1 MUTATED     10    1
  ZBP1 WILD-TYPE  365   64
   clus
vv  ZBP1 MUTATED ZBP1 WILD-TYPE
  0           10            365
  1            1             64
[1] 2 2
[1] FALSE
D1029V8, binary
                cls
clus               0   1
  ZBP1 MUTATED     8   5
  ZBP1 WILD-TYPE 217 259
[1] "tbl2"
                cls
clus             [,1] [,2]
  ZBP1 MUTATED      8    5
  ZBP1 WILD-TYPE  217  259
        clus
vv       ZBP1 MUTATED ZBP1 WILD-TYPE
  FEMALE            8            217
  MALE              5            259
[1] 2 2
[1] FALSE
D1029V9, binary
                cls
clus               0   1
  ZBP1 MUTATED     9   0
  ZBP1 WILD-TYPE 341  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  ZBP1 MUTATED      9    0
  ZBP1 WILD-TYPE  341   22
     clus
vv    ZBP1 MUTATED ZBP1 WILD-TYPE
  NO             9            341
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ZBP1 MUTATED                      9                             1
  ZBP1 WILD-TYPE                  306                            46
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ZBP1 MUTATED                       3                              0
  ZBP1 WILD-TYPE                   103                             10
D1029V10, multiclass
                                clus
vv                               ZBP1 MUTATED ZBP1 WILD-TYPE
  COLON ADENOCARCINOMA                      9            306
  COLON MUCINOUS ADENOCARCINOMA             1             46
  RECTAL ADENOCARCINOMA                     3            103
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  ZBP1 MUTATED    10   0   0   0
  ZBP1 WILD-TYPE 335   4  31  25
D1029V11, multiclass
    clus
vv   ZBP1 MUTATED ZBP1 WILD-TYPE
  R0           10            335
  R1            0              4
  R2            0             31
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1029V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZBP1 MUTATED                                  0     0
  ZBP1 WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  ZBP1 MUTATED                           1     5
  ZBP1 WILD-TYPE                        21   221
D1029V13, multiclass
                                  clus
vv                                 ZBP1 MUTATED ZBP1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                       5            221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1030) Variable = MYLK4 MUTATION ANALYSIS
D1030V1, survival
                 sevent
clus2               0   1
  MYLK4 MUTATED    13   1
  MYLK4 WILD-TYPE 365  92
  MYLK4 MUTATED MYLK4 WILD-TYPE 
             14             457 
  MYLK4 MUTATED MYLK4 WILD-TYPE 
              1              92 
$`MYLK4 MUTATED`
TCGA-A6-5662 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3815 
       23.61        63.98         6.97        85.05        19.04        33.04 
TCGA-AZ-6601 TCGA-CA-6717 TCGA-CK-5914 TCGA-CM-5860 TCGA-CM-5861 TCGA-D5-6539 
      100.01        12.76         9.99        32.02        15.02        12.49 
TCGA-AF-2687 TCGA-DC-6157 
       24.13        27.95 

$`MYLK4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        33.53        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
       35.01         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
       26.99        19.04        10.06        35.05         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       49.41         6.77        12.10        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07        12.20        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 
       85.45        15.62        49.08        51.32        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5862 
       13.02        29.06        22.03        22.98        30.08         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 
       43.27        15.12        17.85         4.80        17.13        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6158 
       78.12         7.17        15.02         5.03        13.97        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  MYLK4 MUTATED MYLK4 WILD-TYPE 
           6.97            0.00 
  MYLK4 MUTATED MYLK4 WILD-TYPE 
         100.01          148.01 
  MYLK4 MUTATED MYLK4 WILD-TYPE 
          23.87           20.12 
[1] "7.0 - 100.0 (23.9)" "0.0 - 148.0 (20.1)"
[1] "hr=" "3.6"
D1030V2, continuous
D1030V3, binary
                 cls
clus                0   1
  MYLK4 MUTATED    12   2
  MYLK4 WILD-TYPE 354 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYLK4 MUTATED     12    2
  MYLK4 WILD-TYPE  354  117
        clus
vv       MYLK4 MUTATED MYLK4 WILD-TYPE
  COLON             12             354
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MYLK4 MUTATED         1        0        3         4         0         0
  MYLK4 WILD-TYPE      90        1       29       134        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MYLK4 MUTATED           1          1          1          1        1         1
  MYLK4 WILD-TYPE        23         10         58         41       47        17
                 vv
clus              STAGE IVB
  MYLK4 MUTATED           0
  MYLK4 WILD-TYPE         1
D1030V4, multiclass
            clus
vv           MYLK4 MUTATED MYLK4 WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               3              29
  STAGE IIA              4             134
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             1              10
  STAGE IIIB             1              58
  STAGE IIIC             1              41
  STAGE IV               1              47
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  MYLK4 MUTATED     0   1  12   1
  MYLK4 WILD-TYPE  17  91 317  49
D1030V5, multiclass
    clus
vv   MYLK4 MUTATED MYLK4 WILD-TYPE
  T1             0              17
  T2             1              91
  T3            12             317
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  MYLK4 MUTATED    11   1   2
  MYLK4 WILD-TYPE 276 112  85
D1030V6, multiclass
    clus
vv   MYLK4 MUTATED MYLK4 WILD-TYPE
  N0            11             276
  N1             1             112
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1030V7, binary
                 cls
clus                0   1
  MYLK4 MUTATED    11   2
  MYLK4 WILD-TYPE 364  63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYLK4 MUTATED     11    2
  MYLK4 WILD-TYPE  364   63
   clus
vv  MYLK4 MUTATED MYLK4 WILD-TYPE
  0            11             364
  1             2              63
[1] 2 2
[1] FALSE
D1030V8, binary
                 cls
clus                0   1
  MYLK4 MUTATED     3  11
  MYLK4 WILD-TYPE 222 253
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYLK4 MUTATED      3   11
  MYLK4 WILD-TYPE  222  253
        clus
vv       MYLK4 MUTATED MYLK4 WILD-TYPE
  FEMALE             3             222
  MALE              11             253
[1] 2 2
[1] FALSE
D1030V9, binary
                 cls
clus                0   1
  MYLK4 MUTATED    10   2
  MYLK4 WILD-TYPE 340  20
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYLK4 MUTATED     10    2
  MYLK4 WILD-TYPE  340   20
     clus
vv    MYLK4 MUTATED MYLK4 WILD-TYPE
  NO             10             340
  YES             2              20
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MYLK4 MUTATED                     11                             1
  MYLK4 WILD-TYPE                  304                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MYLK4 MUTATED                       2                              0
  MYLK4 WILD-TYPE                   104                             10
D1030V10, multiclass
                                clus
vv                               MYLK4 MUTATED MYLK4 WILD-TYPE
  COLON ADENOCARCINOMA                      11             304
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  MYLK4 MUTATED     9   0   1   2
  MYLK4 WILD-TYPE 336   4  30  23
D1030V11, multiclass
    clus
vv   MYLK4 MUTATED MYLK4 WILD-TYPE
  R0             9             336
  R1             0               4
  R2             1              30
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1030V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MYLK4 MUTATED                                  0     1
  MYLK4 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  MYLK4 MUTATED                           1     7
  MYLK4 WILD-TYPE                        21   219
D1030V13, multiclass
                                  clus
vv                                 MYLK4 MUTATED MYLK4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        7             219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1031) Variable = FER MUTATION ANALYSIS
D1031V1, survival
               sevent
clus2             0   1
  FER MUTATED    14   2
  FER WILD-TYPE 364  91
  FER MUTATED FER WILD-TYPE 
           16           455 
  FER MUTATED FER WILD-TYPE 
            2            91 
$`FER MUTATED`
TCGA-AA-3867 TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-A010 TCGA-AZ-4315 TCGA-CK-5914 
       24.03        33.01        24.00        34.98        58.39         9.99 
TCGA-CK-5916 TCGA-CM-5862 TCGA-CM-6172 TCGA-CM-6674 TCGA-D5-6930 TCGA-G4-6306 
       21.14         5.03        11.01        12.95         1.51        44.68 
TCGA-G4-6586 TCGA-G4-6628 TCGA-AG-A002 TCGA-DC-6157 
       35.80        79.69        20.98        27.95 

$`FER WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       53.00        17.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 
        2.01        12.99        24.00        26.01         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       51.32        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       30.08        32.02        15.02        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6675 
       14.99        12.99        13.02        15.02        14.04        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 
       13.78        26.17        91.79        46.75        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
       15.02         5.03        13.97        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  FER MUTATED FER WILD-TYPE 
         1.51          0.00 
  FER MUTATED FER WILD-TYPE 
        79.69        148.01 
  FER MUTATED FER WILD-TYPE 
       24.015        20.020 
[1] "1.5 - 79.7 (24.0)"  "0.0 - 148.0 (20.0)"
[1] "hr=" "1.6"
D1031V2, continuous
D1031V3, binary
               cls
clus              0   1
  FER MUTATED    15   2
  FER WILD-TYPE 351 117
[1] "tbl2"
               cls
clus            [,1] [,2]
  FER MUTATED     15    2
  FER WILD-TYPE  351  117
        clus
vv       FER MUTATED FER WILD-TYPE
  COLON           15           351
  RECTUM           2           117
[1] 2 2
[1] FALSE
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FER MUTATED         4        0        0         7         2         0
  FER WILD-TYPE      87        1       32       131         8         1
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  FER MUTATED           0          0          2          0        1         1
  FER WILD-TYPE        24         11         57         42       47        17
               vv
clus            STAGE IVB
  FER MUTATED           0
  FER WILD-TYPE         1
D1031V4, multiclass
            clus
vv           FER MUTATED FER WILD-TYPE
  STAGE I              4            87
  STAGE IA             0             1
  STAGE II             0            32
  STAGE IIA            7           131
  STAGE IIB            2             8
  STAGE IIC            0             1
  STAGE III            0            24
  STAGE IIIA           0            11
  STAGE IIIB           2            57
  STAGE IIIC           0            42
  STAGE IV             1            47
  STAGE IVA            1            17
  STAGE IVB            0             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  FER MUTATED     1   4  10   2
  FER WILD-TYPE  16  88 319  48
D1031V5, multiclass
    clus
vv   FER MUTATED FER WILD-TYPE
  T1           1            16
  T2           4            88
  T3          10           319
  T4           2            48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2
  FER MUTATED    13   3   1
  FER WILD-TYPE 274 110  86
D1031V6, multiclass
    clus
vv   FER MUTATED FER WILD-TYPE
  N0          13           274
  N1           3           110
  N2           1            86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1031V7, binary
               cls
clus              0   1
  FER MUTATED    14   2
  FER WILD-TYPE 361  63
[1] "tbl2"
               cls
clus            [,1] [,2]
  FER MUTATED     14    2
  FER WILD-TYPE  361   63
   clus
vv  FER MUTATED FER WILD-TYPE
  0          14           361
  1           2            63
[1] 2 2
[1] FALSE
D1031V8, binary
               cls
clus              0   1
  FER MUTATED     7  10
  FER WILD-TYPE 218 254
[1] "tbl2"
               cls
clus            [,1] [,2]
  FER MUTATED      7   10
  FER WILD-TYPE  218  254
        clus
vv       FER MUTATED FER WILD-TYPE
  FEMALE           7           218
  MALE            10           254
[1] 2 2
[1] FALSE
D1031V9, binary
               cls
clus              0   1
  FER MUTATED    13   0
  FER WILD-TYPE 337  22
[1] "tbl2"
               cls
clus            [,1] [,2]
  FER MUTATED     13    0
  FER WILD-TYPE  337   22
     clus
vv    FER MUTATED FER WILD-TYPE
  NO           13           337
  YES           0            22
[1] 2 2
[1] FALSE
               vv
clus            COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  FER MUTATED                     12                             3
  FER WILD-TYPE                  303                            44
               vv
clus            RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  FER MUTATED                       2                              0
  FER WILD-TYPE                   104                             10
D1031V10, multiclass
                                clus
vv                               FER MUTATED FER WILD-TYPE
  COLON ADENOCARCINOMA                    12           303
  COLON MUCINOUS ADENOCARCINOMA            3            44
  RECTAL ADENOCARCINOMA                    2           104
  RECTAL MUCINOUS ADENOCARCINOMA           0            10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             R0  R1  R2  RX
  FER MUTATED    14   0   1   2
  FER WILD-TYPE 331   4  30  23
D1031V11, multiclass
    clus
vv   FER MUTATED FER WILD-TYPE
  R0          14           331
  R1           0             4
  R2           1            30
  RX           2            23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1031V12, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FER MUTATED                                  0     0
  FER WILD-TYPE                                1    11
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  FER MUTATED                           1    10
  FER WILD-TYPE                        21   216
D1031V13, multiclass
                                  clus
vv                                 FER MUTATED FER WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      0            11
  BLACK OR AFRICAN AMERICAN                  1            21
  WHITE                                     10           216
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1032) Variable = GNA11 MUTATION ANALYSIS
D1032V1, survival
                 sevent
clus2               0   1
  GNA11 MUTATED     7   0
  GNA11 WILD-TYPE 371  93
  GNA11 MUTATED GNA11 WILD-TYPE 
              7             464 
  GNA11 MUTATED GNA11 WILD-TYPE 
              0              93 
$`GNA11 MUTATED`
TCGA-A6-5661 TCGA-A6-6141 TCGA-A6-6654 TCGA-A6-6780 TCGA-AA-3526 TCGA-AU-6004 
       33.53         8.38        23.87        20.12        19.07        27.09 
TCGA-D5-6536 
       17.85 

$`GNA11 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 
       22.06        32.71        27.09        22.52        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6781 TCGA-A6-6782 
       24.16        21.76        24.69        24.39        19.66        20.28 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
        7.04         3.02         1.02        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       37.05        36.03         8.05         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       78.08         6.05         6.97        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       15.12         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  GNA11 MUTATED GNA11 WILD-TYPE 
           8.38            0.00 
  GNA11 MUTATED GNA11 WILD-TYPE 
          33.53          148.01 
  GNA11 MUTATED GNA11 WILD-TYPE 
         20.120          20.235 
[1] "8.4 - 33.5 (20.1)"  "0.0 - 148.0 (20.2)"
[1] "hr="     "9100000"
D1032V2, continuous
D1032V3, binary
                 cls
clus                0   1
  GNA11 MUTATED     7   0
  GNA11 WILD-TYPE 359 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GNA11 MUTATED      7    0
  GNA11 WILD-TYPE  359  119
        clus
vv       GNA11 MUTATED GNA11 WILD-TYPE
  COLON              7             359
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GNA11 MUTATED         2        0        0         4         0         0
  GNA11 WILD-TYPE      89        1       32       134        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  GNA11 MUTATED           0          0          1          0        0         0
  GNA11 WILD-TYPE        24         11         58         42       48        18
                 vv
clus              STAGE IVB
  GNA11 MUTATED           0
  GNA11 WILD-TYPE         1
D1032V4, multiclass
            clus
vv           GNA11 MUTATED GNA11 WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              4             134
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  GNA11 MUTATED     0   2   5   0
  GNA11 WILD-TYPE  17  90 324  50
D1032V5, multiclass
    clus
vv   GNA11 MUTATED GNA11 WILD-TYPE
  T1             0              17
  T2             2              90
  T3             5             324
  T4             0              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  GNA11 MUTATED     6   1   0
  GNA11 WILD-TYPE 281 112  87
D1032V6, multiclass
    clus
vv   GNA11 MUTATED GNA11 WILD-TYPE
  N0             6             281
  N1             1             112
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1032V7, binary
                 cls
clus                0   1
  GNA11 MUTATED     6   0
  GNA11 WILD-TYPE 369  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GNA11 MUTATED      6    0
  GNA11 WILD-TYPE  369   65
   clus
vv  GNA11 MUTATED GNA11 WILD-TYPE
  0             6             369
  1             0              65
[1] 2 2
[1] FALSE
D1032V8, binary
                 cls
clus                0   1
  GNA11 MUTATED     3   4
  GNA11 WILD-TYPE 222 260
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GNA11 MUTATED      3    4
  GNA11 WILD-TYPE  222  260
        clus
vv       GNA11 MUTATED GNA11 WILD-TYPE
  FEMALE             3             222
  MALE               4             260
[1] 2 2
[1] FALSE
D1032V9, binary
                 cls
clus                0   1
  GNA11 MUTATED     6   0
  GNA11 WILD-TYPE 344  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GNA11 MUTATED      6    0
  GNA11 WILD-TYPE  344   22
     clus
vv    GNA11 MUTATED GNA11 WILD-TYPE
  NO              6             344
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  GNA11 MUTATED                      6                             1
  GNA11 WILD-TYPE                  309                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  GNA11 MUTATED                       0                              0
  GNA11 WILD-TYPE                   106                             10
D1032V10, multiclass
                                clus
vv                               GNA11 MUTATED GNA11 WILD-TYPE
  COLON ADENOCARCINOMA                       6             309
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  GNA11 MUTATED     4   0   0   0
  GNA11 WILD-TYPE 341   4  31  25
D1032V11, multiclass
    clus
vv   GNA11 MUTATED GNA11 WILD-TYPE
  R0             4             341
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1032V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GNA11 MUTATED                                  0     0
  GNA11 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  GNA11 MUTATED                           2     4
  GNA11 WILD-TYPE                        20   222
D1032V13, multiclass
                                  clus
vv                                 GNA11 MUTATED GNA11 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    2              20
  WHITE                                        4             222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1033) Variable = CHRNA1 MUTATION ANALYSIS
D1033V1, survival
                  sevent
clus2                0   1
  CHRNA1 MUTATED     9   3
  CHRNA1 WILD-TYPE 369  90
  CHRNA1 MUTATED CHRNA1 WILD-TYPE 
              12              459 
  CHRNA1 MUTATED CHRNA1 WILD-TYPE 
               3               90 
$`CHRNA1 MUTATED`
TCGA-A6-5665 TCGA-A6-6781 TCGA-AA-3549 TCGA-AA-3554 TCGA-AA-3697 TCGA-CA-6717 
       22.06        19.66        21.01        17.95        85.05        12.76 
TCGA-D5-6532 TCGA-D5-6537 TCGA-DM-A285 TCGA-AG-3909 TCGA-AG-A002 TCGA-DY-A1DD 
       18.25         4.80         6.12        19.99        20.98        57.24 

$`CHRNA1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3552 TCGA-AA-3553 
       12.99         0.99        14.01        33.99        13.02        24.00 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 
        5.98        37.05        19.00        36.00         5.03        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07        12.20        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       56.09        55.92        20.19         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
       17.85        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      135.65       139.17        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3999 
       35.01        14.01         1.02        48.03        32.02        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DF TCGA-DY-A1DG 
        5.03         5.29       126.44        41.36        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  CHRNA1 MUTATED CHRNA1 WILD-TYPE 
             4.8              0.0 
  CHRNA1 MUTATED CHRNA1 WILD-TYPE 
           85.05           148.01 
  CHRNA1 MUTATED CHRNA1 WILD-TYPE 
          19.825           20.280 
[1] "4.8 - 85.0 (19.8)"  "0.0 - 148.0 (20.3)"
[1] "hr=" "1.3"
D1033V2, continuous
D1033V3, binary
                  cls
clus                 0   1
  CHRNA1 MUTATED     9   3
  CHRNA1 WILD-TYPE 357 116
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CHRNA1 MUTATED      9    3
  CHRNA1 WILD-TYPE  357  116
        clus
vv       CHRNA1 MUTATED CHRNA1 WILD-TYPE
  COLON               9              357
  RECTUM              3              116
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CHRNA1 MUTATED         2        0        0         4         0         0
  CHRNA1 WILD-TYPE      89        1       32       134        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CHRNA1 MUTATED           1          0          3          1        1
  CHRNA1 WILD-TYPE        23         11         56         41       47
                  vv
clus               STAGE IVA STAGE IVB
  CHRNA1 MUTATED           0         0
  CHRNA1 WILD-TYPE        18         1
D1033V4, multiclass
            clus
vv           CHRNA1 MUTATED CHRNA1 WILD-TYPE
  STAGE I                 2               89
  STAGE IA                0                1
  STAGE II                0               32
  STAGE IIA               4              134
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               1               23
  STAGE IIIA              0               11
  STAGE IIIB              3               56
  STAGE IIIC              1               41
  STAGE IV                1               47
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  CHRNA1 MUTATED     0   2   9   1
  CHRNA1 WILD-TYPE  17  90 320  49
D1033V5, multiclass
    clus
vv   CHRNA1 MUTATED CHRNA1 WILD-TYPE
  T1              0               17
  T2              2               90
  T3              9              320
  T4              1               49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  CHRNA1 MUTATED     7   4   1
  CHRNA1 WILD-TYPE 280 109  86
D1033V6, multiclass
    clus
vv   CHRNA1 MUTATED CHRNA1 WILD-TYPE
  N0              7              280
  N1              4              109
  N2              1               86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1033V7, binary
                  cls
clus                 0   1
  CHRNA1 MUTATED     9   1
  CHRNA1 WILD-TYPE 366  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CHRNA1 MUTATED      9    1
  CHRNA1 WILD-TYPE  366   64
   clus
vv  CHRNA1 MUTATED CHRNA1 WILD-TYPE
  0              9              366
  1              1               64
[1] 2 2
[1] FALSE
D1033V8, binary
                  cls
clus                 0   1
  CHRNA1 MUTATED     5   7
  CHRNA1 WILD-TYPE 220 257
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CHRNA1 MUTATED      5    7
  CHRNA1 WILD-TYPE  220  257
        clus
vv       CHRNA1 MUTATED CHRNA1 WILD-TYPE
  FEMALE              5              220
  MALE                7              257
[1] 2 2
[1] FALSE
D1033V9, binary
                  cls
clus                 0   1
  CHRNA1 MUTATED     9   1
  CHRNA1 WILD-TYPE 341  21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CHRNA1 MUTATED      9    1
  CHRNA1 WILD-TYPE  341   21
     clus
vv    CHRNA1 MUTATED CHRNA1 WILD-TYPE
  NO               9              341
  YES              1               21
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CHRNA1 MUTATED                      6                             3
  CHRNA1 WILD-TYPE                  309                            44
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CHRNA1 MUTATED                       3                              0
  CHRNA1 WILD-TYPE                   103                             10
D1033V10, multiclass
                                clus
vv                               CHRNA1 MUTATED CHRNA1 WILD-TYPE
  COLON ADENOCARCINOMA                        6              309
  COLON MUCINOUS ADENOCARCINOMA               3               44
  RECTAL ADENOCARCINOMA                       3              103
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  CHRNA1 MUTATED     9   0   0   1
  CHRNA1 WILD-TYPE 336   4  31  24
D1033V11, multiclass
    clus
vv   CHRNA1 MUTATED CHRNA1 WILD-TYPE
  R0              9              336
  R1              0                4
  R2              0               31
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1033V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CHRNA1 MUTATED                                  0     1
  CHRNA1 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  CHRNA1 MUTATED                           0     6
  CHRNA1 WILD-TYPE                        22   220
D1033V13, multiclass
                                  clus
vv                                 CHRNA1 MUTATED CHRNA1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         6              220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1034) Variable = SLC16A1 MUTATION ANALYSIS
D1034V1, survival
                   sevent
clus2                 0   1
  SLC16A1 MUTATED     8   2
  SLC16A1 WILD-TYPE 370  91
  SLC16A1 MUTATED SLC16A1 WILD-TYPE 
               10               461 
  SLC16A1 MUTATED SLC16A1 WILD-TYPE 
                2                91 
$`SLC16A1 MUTATED`
TCGA-A6-5665 TCGA-AA-3663 TCGA-AA-3715 TCGA-AA-3966 TCGA-CA-6717 TCGA-CK-5916 
       22.06         6.97        19.04         2.01        12.76        21.14 
TCGA-G4-6293 TCGA-AG-3885 TCGA-AG-A02N TCGA-F5-6813 
      133.18        17.95        61.97         0.69 

$`SLC16A1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
       34.03        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07        12.20        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       51.32         9.99        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
       35.31        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 
        0.99        19.04        19.99         1.02        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 
       10.98        49.97         1.94        38.96        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66        55.76        26.43 

  SLC16A1 MUTATED SLC16A1 WILD-TYPE 
             0.69              0.00 
  SLC16A1 MUTATED SLC16A1 WILD-TYPE 
           133.18            148.01 
  SLC16A1 MUTATED SLC16A1 WILD-TYPE 
           18.495            20.280 
[1] "0.7 - 133.2 (18.5)" "0.0 - 148.0 (20.3)"
[1] "hr=" "1"  
D1034V2, continuous
D1034V3, binary
                   cls
clus                  0   1
  SLC16A1 MUTATED     7   3
  SLC16A1 WILD-TYPE 359 116
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC16A1 MUTATED      7    3
  SLC16A1 WILD-TYPE  359  116
        clus
vv       SLC16A1 MUTATED SLC16A1 WILD-TYPE
  COLON                7               359
  RECTUM               3               116
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SLC16A1 MUTATED         1        0        3         3         0         0
  SLC16A1 WILD-TYPE      90        1       29       135        10         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC16A1 MUTATED           1          0          1          1        0
  SLC16A1 WILD-TYPE        23         11         58         41       48
                   vv
clus                STAGE IVA STAGE IVB
  SLC16A1 MUTATED           0         0
  SLC16A1 WILD-TYPE        18         1
D1034V4, multiclass
            clus
vv           SLC16A1 MUTATED SLC16A1 WILD-TYPE
  STAGE I                  1                90
  STAGE IA                 0                 1
  STAGE II                 3                29
  STAGE IIA                3               135
  STAGE IIB                0                10
  STAGE IIC                0                 1
  STAGE III                1                23
  STAGE IIIA               0                11
  STAGE IIIB               1                58
  STAGE IIIC               1                41
  STAGE IV                 0                48
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  SLC16A1 MUTATED     1   0   8   1
  SLC16A1 WILD-TYPE  16  92 321  49
D1034V5, multiclass
    clus
vv   SLC16A1 MUTATED SLC16A1 WILD-TYPE
  T1               1                16
  T2               0                92
  T3               8               321
  T4               1                49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  SLC16A1 MUTATED     7   2   1
  SLC16A1 WILD-TYPE 280 111  86
D1034V6, multiclass
    clus
vv   SLC16A1 MUTATED SLC16A1 WILD-TYPE
  N0               7               280
  N1               2               111
  N2               1                86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1034V7, binary
                   cls
clus                  0   1
  SLC16A1 MUTATED    10   0
  SLC16A1 WILD-TYPE 365  65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC16A1 MUTATED     10    0
  SLC16A1 WILD-TYPE  365   65
   clus
vv  SLC16A1 MUTATED SLC16A1 WILD-TYPE
  0              10               365
  1               0                65
[1] 2 2
[1] FALSE
D1034V8, binary
                   cls
clus                  0   1
  SLC16A1 MUTATED     5   5
  SLC16A1 WILD-TYPE 220 259
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC16A1 MUTATED      5    5
  SLC16A1 WILD-TYPE  220  259
        clus
vv       SLC16A1 MUTATED SLC16A1 WILD-TYPE
  FEMALE               5               220
  MALE                 5               259
[1] 2 2
[1] FALSE
D1034V9, binary
                   cls
clus                  0   1
  SLC16A1 MUTATED     6   1
  SLC16A1 WILD-TYPE 344  21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC16A1 MUTATED      6    1
  SLC16A1 WILD-TYPE  344   21
     clus
vv    SLC16A1 MUTATED SLC16A1 WILD-TYPE
  NO                6               344
  YES               1                21
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SLC16A1 MUTATED                      5                             2
  SLC16A1 WILD-TYPE                  310                            45
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SLC16A1 MUTATED                       3                              0
  SLC16A1 WILD-TYPE                   103                             10
D1034V10, multiclass
                                clus
vv                               SLC16A1 MUTATED SLC16A1 WILD-TYPE
  COLON ADENOCARCINOMA                         5               310
  COLON MUCINOUS ADENOCARCINOMA                2                45
  RECTAL ADENOCARCINOMA                        3               103
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  SLC16A1 MUTATED     7   0   0   2
  SLC16A1 WILD-TYPE 338   4  31  23
D1034V11, multiclass
    clus
vv   SLC16A1 MUTATED SLC16A1 WILD-TYPE
  R0               7               338
  R1               0                 4
  R2               0                31
  RX               2                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1034V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SLC16A1 MUTATED                                  0     1
  SLC16A1 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  SLC16A1 MUTATED                           0     4
  SLC16A1 WILD-TYPE                        22   222
D1034V13, multiclass
                                  clus
vv                                 SLC16A1 MUTATED SLC16A1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                10
  BLACK OR AFRICAN AMERICAN                      0                22
  WHITE                                          4               222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1035) Variable = TRAM1L1 MUTATION ANALYSIS
D1035V1, survival
                   sevent
clus2                 0   1
  TRAM1L1 MUTATED    10   4
  TRAM1L1 WILD-TYPE 368  89
  TRAM1L1 MUTATED TRAM1L1 WILD-TYPE 
               14               457 
  TRAM1L1 MUTATED TRAM1L1 WILD-TYPE 
                4                89 
$`TRAM1L1 MUTATED`
TCGA-AA-3713 TCGA-AA-3815 TCGA-AA-3950 TCGA-AA-A00N TCGA-AA-A010 TCGA-AZ-6598 
       19.04        33.04        24.00         4.01        34.98        49.41 
TCGA-CA-6719 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5861 TCGA-CM-6171 TCGA-CM-6674 
       14.30        29.06        22.03        15.02        14.04        12.95 
TCGA-DY-A1DD TCGA-DY-A1DF 
       57.24        24.13 

$`TRAM1L1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       10.06        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 
       12.99        24.00        33.01        26.01         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       88.21         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 
        3.29         0.07        12.20        12.76        10.06        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       37.02        25.02        13.02        22.98        30.08        32.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       13.02        15.02        11.01        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
        5.29       126.44        41.36        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  TRAM1L1 MUTATED TRAM1L1 WILD-TYPE 
             4.01              0.00 
  TRAM1L1 MUTATED TRAM1L1 WILD-TYPE 
            57.24            148.01 
  TRAM1L1 MUTATED TRAM1L1 WILD-TYPE 
           23.015            20.120 
[1] "4.0 - 57.2 (23.0)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.5"
D1035V2, continuous
D1035V3, binary
                   cls
clus                  0   1
  TRAM1L1 MUTATED    12   2
  TRAM1L1 WILD-TYPE 354 117
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TRAM1L1 MUTATED     12    2
  TRAM1L1 WILD-TYPE  354  117
        clus
vv       TRAM1L1 MUTATED TRAM1L1 WILD-TYPE
  COLON               12               354
  RECTUM               2               117
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TRAM1L1 MUTATED         1        0        1         5         2         0
  TRAM1L1 WILD-TYPE      90        1       31       133         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TRAM1L1 MUTATED           0          1          2          1        1
  TRAM1L1 WILD-TYPE        24         10         57         41       47
                   vv
clus                STAGE IVA STAGE IVB
  TRAM1L1 MUTATED           0         0
  TRAM1L1 WILD-TYPE        18         1
D1035V4, multiclass
            clus
vv           TRAM1L1 MUTATED TRAM1L1 WILD-TYPE
  STAGE I                  1                90
  STAGE IA                 0                 1
  STAGE II                 1                31
  STAGE IIA                5               133
  STAGE IIB                2                 8
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               1                10
  STAGE IIIB               2                57
  STAGE IIIC               1                41
  STAGE IV                 1                47
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  TRAM1L1 MUTATED     0   2  10   2
  TRAM1L1 WILD-TYPE  17  90 319  48
D1035V5, multiclass
    clus
vv   TRAM1L1 MUTATED TRAM1L1 WILD-TYPE
  T1               0                17
  T2               2                90
  T3              10               319
  T4               2                48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  TRAM1L1 MUTATED    10   3   1
  TRAM1L1 WILD-TYPE 277 110  86
D1035V6, multiclass
    clus
vv   TRAM1L1 MUTATED TRAM1L1 WILD-TYPE
  N0              10               277
  N1               3               110
  N2               1                86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1035V7, binary
                   cls
clus                  0   1
  TRAM1L1 MUTATED    12   1
  TRAM1L1 WILD-TYPE 363  64
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TRAM1L1 MUTATED     12    1
  TRAM1L1 WILD-TYPE  363   64
   clus
vv  TRAM1L1 MUTATED TRAM1L1 WILD-TYPE
  0              12               363
  1               1                64
[1] 2 2
[1] FALSE
D1035V8, binary
                   cls
clus                  0   1
  TRAM1L1 MUTATED    10   4
  TRAM1L1 WILD-TYPE 215 260
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TRAM1L1 MUTATED     10    4
  TRAM1L1 WILD-TYPE  215  260
        clus
vv       TRAM1L1 MUTATED TRAM1L1 WILD-TYPE
  FEMALE              10               215
  MALE                 4               260
[1] 2 2
[1] FALSE
D1035V9, binary
                   cls
clus                  0   1
  TRAM1L1 MUTATED    10   1
  TRAM1L1 WILD-TYPE 340  21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TRAM1L1 MUTATED     10    1
  TRAM1L1 WILD-TYPE  340   21
     clus
vv    TRAM1L1 MUTATED TRAM1L1 WILD-TYPE
  NO               10               340
  YES               1                21
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  TRAM1L1 MUTATED                     10                             2
  TRAM1L1 WILD-TYPE                  305                            45
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  TRAM1L1 MUTATED                       2                              0
  TRAM1L1 WILD-TYPE                   104                             10
D1035V10, multiclass
                                clus
vv                               TRAM1L1 MUTATED TRAM1L1 WILD-TYPE
  COLON ADENOCARCINOMA                        10               305
  COLON MUCINOUS ADENOCARCINOMA                2                45
  RECTAL ADENOCARCINOMA                        2               104
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  TRAM1L1 MUTATED     9   0   1   1
  TRAM1L1 WILD-TYPE 336   4  30  24
D1035V11, multiclass
    clus
vv   TRAM1L1 MUTATED TRAM1L1 WILD-TYPE
  R0               9               336
  R1               0                 4
  R2               1                30
  RX               1                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1035V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TRAM1L1 MUTATED                                  0     1
  TRAM1L1 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  TRAM1L1 MUTATED                           0     8
  TRAM1L1 WILD-TYPE                        22   218
D1035V13, multiclass
                                  clus
vv                                 TRAM1L1 MUTATED TRAM1L1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                10
  BLACK OR AFRICAN AMERICAN                      0                22
  WHITE                                          8               218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1036) Variable = MRPL13 MUTATION ANALYSIS
D1036V1, survival
                  sevent
clus2                0   1
  MRPL13 MUTATED     7   1
  MRPL13 WILD-TYPE 371  92
  MRPL13 MUTATED MRPL13 WILD-TYPE 
               8              463 
  MRPL13 MUTATED MRPL13 WILD-TYPE 
               1               92 
$`MRPL13 MUTATED`
TCGA-AA-3950 TCGA-AU-6004 TCGA-AZ-4315 TCGA-AZ-5403 TCGA-CM-6161 TCGA-D5-5538 
       24.00        27.09        58.39        62.79        15.02        12.26 
TCGA-AG-3892 TCGA-EI-6507 
       13.02        19.96 

$`MRPL13 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 
       27.42        10.88         0.20        14.50        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       33.01        21.44        17.82         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6162 TCGA-CM-6163 
        5.03        15.02        15.02        17.03        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5539 
       11.08        11.01        10.06        12.03        45.40        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       36.95        17.03        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
        0.49        20.55        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  MRPL13 MUTATED MRPL13 WILD-TYPE 
           12.26             0.00 
  MRPL13 MUTATED MRPL13 WILD-TYPE 
           62.79           148.01 
  MRPL13 MUTATED MRPL13 WILD-TYPE 
           21.98            20.19 
[1] "12.3 - 62.8 (22.0)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.9"
D1036V2, continuous
D1036V3, binary
                  cls
clus                 0   1
  MRPL13 MUTATED     6   2
  MRPL13 WILD-TYPE 360 117
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MRPL13 MUTATED      6    2
  MRPL13 WILD-TYPE  360  117
        clus
vv       MRPL13 MUTATED MRPL13 WILD-TYPE
  COLON               6              360
  RECTUM              2              117
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MRPL13 MUTATED         3        0        1         3         0         0
  MRPL13 WILD-TYPE      88        1       31       135        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MRPL13 MUTATED           0          0          1          0        0
  MRPL13 WILD-TYPE        24         11         58         42       48
                  vv
clus               STAGE IVA STAGE IVB
  MRPL13 MUTATED           0         0
  MRPL13 WILD-TYPE        18         1
D1036V4, multiclass
            clus
vv           MRPL13 MUTATED MRPL13 WILD-TYPE
  STAGE I                 3               88
  STAGE IA                0                1
  STAGE II                1               31
  STAGE IIA               3              135
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              1               58
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  MRPL13 MUTATED     1   2   5   0
  MRPL13 WILD-TYPE  16  90 324  50
D1036V5, multiclass
    clus
vv   MRPL13 MUTATED MRPL13 WILD-TYPE
  T1              1               16
  T2              2               90
  T3              5              324
  T4              0               50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  MRPL13 MUTATED     7   1   0
  MRPL13 WILD-TYPE 280 112  87
D1036V6, multiclass
    clus
vv   MRPL13 MUTATED MRPL13 WILD-TYPE
  N0              7              280
  N1              1              112
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1036V7, binary
                  cls
clus                 0   1
  MRPL13 MUTATED     7   0
  MRPL13 WILD-TYPE 368  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MRPL13 MUTATED      7    0
  MRPL13 WILD-TYPE  368   65
   clus
vv  MRPL13 MUTATED MRPL13 WILD-TYPE
  0              7              368
  1              0               65
[1] 2 2
[1] FALSE
D1036V8, binary
                  cls
clus                 0   1
  MRPL13 MUTATED     5   3
  MRPL13 WILD-TYPE 220 261
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MRPL13 MUTATED      5    3
  MRPL13 WILD-TYPE  220  261
        clus
vv       MRPL13 MUTATED MRPL13 WILD-TYPE
  FEMALE              5              220
  MALE                3              261
[1] 2 2
[1] FALSE
D1036V9, binary
                  cls
clus                 0   1
  MRPL13 MUTATED     7   0
  MRPL13 WILD-TYPE 343  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MRPL13 MUTATED      7    0
  MRPL13 WILD-TYPE  343   22
     clus
vv    MRPL13 MUTATED MRPL13 WILD-TYPE
  NO               7              343
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MRPL13 MUTATED                      5                             1
  MRPL13 WILD-TYPE                  310                            46
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MRPL13 MUTATED                       2                              0
  MRPL13 WILD-TYPE                   104                             10
D1036V10, multiclass
                                clus
vv                               MRPL13 MUTATED MRPL13 WILD-TYPE
  COLON ADENOCARCINOMA                        5              310
  COLON MUCINOUS ADENOCARCINOMA               1               46
  RECTAL ADENOCARCINOMA                       2              104
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  MRPL13 MUTATED     7   0   0   0
  MRPL13 WILD-TYPE 338   4  31  25
D1036V11, multiclass
    clus
vv   MRPL13 MUTATED MRPL13 WILD-TYPE
  R0              7              338
  R1              0                4
  R2              0               31
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1036V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MRPL13 MUTATED                                  0     0
  MRPL13 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  MRPL13 MUTATED                           0     6
  MRPL13 WILD-TYPE                        22   220
D1036V13, multiclass
                                  clus
vv                                 MRPL13 MUTATED MRPL13 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         6              220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1037) Variable = MARVELD2 MUTATION ANALYSIS
D1037V1, survival
                    sevent
clus2                  0   1
  MARVELD2 MUTATED     9   2
  MARVELD2 WILD-TYPE 369  91
  MARVELD2 MUTATED MARVELD2 WILD-TYPE 
                11                460 
  MARVELD2 MUTATED MARVELD2 WILD-TYPE 
                 2                 91 
$`MARVELD2 MUTATED`
TCGA-A6-5661 TCGA-AA-3852 TCGA-AA-A00E TCGA-AU-6004 TCGA-AZ-4315 TCGA-AZ-6601 
       33.53         0.00        30.02        27.09        58.39       100.01 
TCGA-CK-5913 TCGA-CM-4743 TCGA-F4-6856 TCGA-G4-6309 TCGA-AG-A036 
       51.32        23.05        35.31        85.48       117.11 

$`MARVELD2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 
       17.03        10.06         0.00        33.07        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       19.00        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
        0.20        14.50        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 
       88.21        49.41         6.77        12.10        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 
       17.56       148.01        85.45        15.62        49.08         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 
       21.14        82.95         1.91       124.27        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 
       33.67        13.25         0.53        47.41       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 
       65.85        53.62        44.68        55.04        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 
        1.94        38.96        61.97        41.00        38.04        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  MARVELD2 MUTATED MARVELD2 WILD-TYPE 
                 0                  0 
  MARVELD2 MUTATED MARVELD2 WILD-TYPE 
            117.11             148.01 
  MARVELD2 MUTATED MARVELD2 WILD-TYPE 
            35.310             20.005 
[1] "0.0 - 117.1 (35.3)" "0.0 - 148.0 (20.0)"
[1] "hr=" "2.1"
D1037V2, continuous
D1037V3, binary
                    cls
clus                   0   1
  MARVELD2 MUTATED    10   1
  MARVELD2 WILD-TYPE 356 118
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  MARVELD2 MUTATED     10    1
  MARVELD2 WILD-TYPE  356  118
        clus
vv       MARVELD2 MUTATED MARVELD2 WILD-TYPE
  COLON                10                356
  RECTUM                1                118
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MARVELD2 MUTATED         2        0        1         6         0         0
  MARVELD2 WILD-TYPE      89        1       31       132        10         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MARVELD2 MUTATED           1          0          1          0        0
  MARVELD2 WILD-TYPE        23         11         58         42       48
                    vv
clus                 STAGE IVA STAGE IVB
  MARVELD2 MUTATED           0         0
  MARVELD2 WILD-TYPE        18         1
D1037V4, multiclass
            clus
vv           MARVELD2 MUTATED MARVELD2 WILD-TYPE
  STAGE I                   2                 89
  STAGE IA                  0                  1
  STAGE II                  1                 31
  STAGE IIA                 6                132
  STAGE IIB                 0                 10
  STAGE IIC                 0                  1
  STAGE III                 1                 23
  STAGE IIIA                0                 11
  STAGE IIIB                1                 58
  STAGE IIIC                0                 42
  STAGE IV                  0                 48
  STAGE IVA                 0                 18
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  MARVELD2 MUTATED     0   2   9   0
  MARVELD2 WILD-TYPE  17  90 320  50
D1037V5, multiclass
    clus
vv   MARVELD2 MUTATED MARVELD2 WILD-TYPE
  T1                0                 17
  T2                2                 90
  T3                9                320
  T4                0                 50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  MARVELD2 MUTATED     9   1   1
  MARVELD2 WILD-TYPE 278 112  86
D1037V6, multiclass
    clus
vv   MARVELD2 MUTATED MARVELD2 WILD-TYPE
  N0                9                278
  N1                1                112
  N2                1                 86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1037V7, binary
                    cls
clus                   0   1
  MARVELD2 MUTATED    10   0
  MARVELD2 WILD-TYPE 365  65
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  MARVELD2 MUTATED     10    0
  MARVELD2 WILD-TYPE  365   65
   clus
vv  MARVELD2 MUTATED MARVELD2 WILD-TYPE
  0               10                365
  1                0                 65
[1] 2 2
[1] FALSE
D1037V8, binary
                    cls
clus                   0   1
  MARVELD2 MUTATED     4   7
  MARVELD2 WILD-TYPE 221 257
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  MARVELD2 MUTATED      4    7
  MARVELD2 WILD-TYPE  221  257
        clus
vv       MARVELD2 MUTATED MARVELD2 WILD-TYPE
  FEMALE                4                221
  MALE                  7                257
[1] 2 2
[1] FALSE
D1037V9, binary
                    cls
clus                   0   1
  MARVELD2 MUTATED     8   1
  MARVELD2 WILD-TYPE 342  21
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  MARVELD2 MUTATED      8    1
  MARVELD2 WILD-TYPE  342   21
     clus
vv    MARVELD2 MUTATED MARVELD2 WILD-TYPE
  NO                 8                342
  YES                1                 21
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MARVELD2 MUTATED                      8                             2
  MARVELD2 WILD-TYPE                  307                            45
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MARVELD2 MUTATED                       1                              0
  MARVELD2 WILD-TYPE                   105                             10
D1037V10, multiclass
                                clus
vv                               MARVELD2 MUTATED MARVELD2 WILD-TYPE
  COLON ADENOCARCINOMA                          8                307
  COLON MUCINOUS ADENOCARCINOMA                 2                 45
  RECTAL ADENOCARCINOMA                         1                105
  RECTAL MUCINOUS ADENOCARCINOMA                0                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  MARVELD2 MUTATED     9   0   0   1
  MARVELD2 WILD-TYPE 336   4  31  24
D1037V11, multiclass
    clus
vv   MARVELD2 MUTATED MARVELD2 WILD-TYPE
  R0                9                336
  R1                0                  4
  R2                0                 31
  RX                1                 24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1037V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MARVELD2 MUTATED                                  0     0
  MARVELD2 WILD-TYPE                                1    11
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  MARVELD2 MUTATED                           2     6
  MARVELD2 WILD-TYPE                        20   220
D1037V13, multiclass
                                  clus
vv                                 MARVELD2 MUTATED MARVELD2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 11
  BLACK OR AFRICAN AMERICAN                       2                 20
  WHITE                                           6                220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1038) Variable = PAX6 MUTATION ANALYSIS
D1038V1, survival
                sevent
clus2              0   1
  PAX6 MUTATED    14   2
  PAX6 WILD-TYPE 364  91
  PAX6 MUTATED PAX6 WILD-TYPE 
            16            455 
  PAX6 MUTATED PAX6 WILD-TYPE 
             2             91 
$`PAX6 MUTATED`
TCGA-A6-6138 TCGA-A6-6781 TCGA-AA-3811 TCGA-AA-3950 TCGA-AA-A00J TCGA-AA-A00R 
       22.52        19.66        10.06        24.00        18.05         0.99 
TCGA-AZ-4315 TCGA-CA-6717 TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-6171 TCGA-D5-6539 
       58.39        12.76        23.05        37.02        14.04        12.49 
TCGA-DM-A28F TCGA-DM-A28K TCGA-AG-A002 TCGA-AG-A02N 
       35.97        98.24        20.98        61.97 

$`PAX6 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6141 TCGA-A6-6142 
       22.09        22.06        32.71        27.09         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        19.04        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        33.01        26.01         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
       16.31         0.95        33.01        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07        12.20        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4752 
       82.95         1.91       124.27        20.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       13.02        15.02        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 
       43.27        15.12        17.85         4.80        17.13        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
      119.93        60.79       117.07         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
       49.97         1.94        38.96        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  PAX6 MUTATED PAX6 WILD-TYPE 
          0.99           0.00 
  PAX6 MUTATED PAX6 WILD-TYPE 
         98.24         148.01 
  PAX6 MUTATED PAX6 WILD-TYPE 
         21.75          20.12 
[1] "1.0 - 98.2 (21.8)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.8"
D1038V2, continuous
D1038V3, binary
                cls
clus               0   1
  PAX6 MUTATED    14   2
  PAX6 WILD-TYPE 352 117
[1] "tbl2"
                cls
clus             [,1] [,2]
  PAX6 MUTATED     14    2
  PAX6 WILD-TYPE  352  117
        clus
vv       PAX6 MUTATED PAX6 WILD-TYPE
  COLON            14            352
  RECTUM            2            117
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PAX6 MUTATED         5        0        1         5         0         0
  PAX6 WILD-TYPE      86        1       31       133        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PAX6 MUTATED           1          1          2          1        0         0
  PAX6 WILD-TYPE        23         10         57         41       48        18
                vv
clus             STAGE IVB
  PAX6 MUTATED           0
  PAX6 WILD-TYPE         1
D1038V4, multiclass
            clus
vv           PAX6 MUTATED PAX6 WILD-TYPE
  STAGE I               5             86
  STAGE IA              0              1
  STAGE II              1             31
  STAGE IIA             5            133
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             1             23
  STAGE IIIA            1             10
  STAGE IIIB            2             57
  STAGE IIIC            1             41
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  PAX6 MUTATED     0   5   9   2
  PAX6 WILD-TYPE  17  87 320  48
D1038V5, multiclass
    clus
vv   PAX6 MUTATED PAX6 WILD-TYPE
  T1            0             17
  T2            5             87
  T3            9            320
  T4            2             48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  PAX6 MUTATED    12   3   1
  PAX6 WILD-TYPE 275 110  86
D1038V6, multiclass
    clus
vv   PAX6 MUTATED PAX6 WILD-TYPE
  N0           12            275
  N1            3            110
  N2            1             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1038V7, binary
                cls
clus               0   1
  PAX6 MUTATED    15   0
  PAX6 WILD-TYPE 360  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  PAX6 MUTATED     15    0
  PAX6 WILD-TYPE  360   65
   clus
vv  PAX6 MUTATED PAX6 WILD-TYPE
  0           15            360
  1            0             65
[1] 2 2
[1] FALSE
D1038V8, binary
                cls
clus               0   1
  PAX6 MUTATED     5  11
  PAX6 WILD-TYPE 220 253
[1] "tbl2"
                cls
clus             [,1] [,2]
  PAX6 MUTATED      5   11
  PAX6 WILD-TYPE  220  253
        clus
vv       PAX6 MUTATED PAX6 WILD-TYPE
  FEMALE            5            220
  MALE             11            253
[1] 2 2
[1] FALSE
D1038V9, binary
                cls
clus               0   1
  PAX6 MUTATED    12   0
  PAX6 WILD-TYPE 338  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  PAX6 MUTATED     12    0
  PAX6 WILD-TYPE  338   22
     clus
vv    PAX6 MUTATED PAX6 WILD-TYPE
  NO            12            338
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PAX6 MUTATED                      9                             5
  PAX6 WILD-TYPE                  306                            42
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PAX6 MUTATED                       2                              0
  PAX6 WILD-TYPE                   104                             10
D1038V10, multiclass
                                clus
vv                               PAX6 MUTATED PAX6 WILD-TYPE
  COLON ADENOCARCINOMA                      9            306
  COLON MUCINOUS ADENOCARCINOMA             5             42
  RECTAL ADENOCARCINOMA                     2            104
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  PAX6 MUTATED    12   0   0   1
  PAX6 WILD-TYPE 333   4  31  24
D1038V11, multiclass
    clus
vv   PAX6 MUTATED PAX6 WILD-TYPE
  R0           12            333
  R1            0              4
  R2            0             31
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1038V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PAX6 MUTATED                                  0     1
  PAX6 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  PAX6 MUTATED                           1     8
  PAX6 WILD-TYPE                        21   218
D1038V13, multiclass
                                  clus
vv                                 PAX6 MUTATED PAX6 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                       8            218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1039) Variable = ZNF547 MUTATION ANALYSIS
D1039V1, survival
                  sevent
clus2                0   1
  ZNF547 MUTATED     9   1
  ZNF547 WILD-TYPE 369  92
  ZNF547 MUTATED ZNF547 WILD-TYPE 
              10              461 
  ZNF547 MUTATED ZNF547 WILD-TYPE 
               1               92 
$`ZNF547 MUTATED`
TCGA-AA-3697 TCGA-AU-6004 TCGA-AZ-6608 TCGA-CA-6717 TCGA-CM-4744 TCGA-CM-6168 
       85.05        27.09         1.61        12.76        20.02        12.99 
TCGA-DM-A1D9 TCGA-G4-6588 TCGA-AG-3892 TCGA-AG-A002 
      140.38        26.17        13.02        20.98 

$`ZNF547 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       19.00        36.00         5.03        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 
       27.42        10.88         0.20        14.50        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
      124.27        23.05        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6169 TCGA-CM-6170 
       29.03        16.04        21.99        14.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A1DB 
       92.75        49.91        13.32        12.59         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       35.80        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  ZNF547 MUTATED ZNF547 WILD-TYPE 
            1.61             0.00 
  ZNF547 MUTATED ZNF547 WILD-TYPE 
          140.38           148.01 
  ZNF547 MUTATED ZNF547 WILD-TYPE 
           20.50            20.19 
[1] "1.6 - 140.4 (20.5)" "0.0 - 148.0 (20.2)"
[1] "hr=" "2.4"
D1039V2, continuous
D1039V3, binary
                  cls
clus                 0   1
  ZNF547 MUTATED     8   2
  ZNF547 WILD-TYPE 358 117
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF547 MUTATED      8    2
  ZNF547 WILD-TYPE  358  117
        clus
vv       ZNF547 MUTATED ZNF547 WILD-TYPE
  COLON               8              358
  RECTUM              2              117
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZNF547 MUTATED         4        0        0         4         0         0
  ZNF547 WILD-TYPE      87        1       32       134        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF547 MUTATED           1          1          0          0        0
  ZNF547 WILD-TYPE        23         10         59         42       48
                  vv
clus               STAGE IVA STAGE IVB
  ZNF547 MUTATED           0         0
  ZNF547 WILD-TYPE        18         1
D1039V4, multiclass
            clus
vv           ZNF547 MUTATED ZNF547 WILD-TYPE
  STAGE I                 4               87
  STAGE IA                0                1
  STAGE II                0               32
  STAGE IIA               4              134
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               1               23
  STAGE IIIA              1               10
  STAGE IIIB              0               59
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZNF547 MUTATED     1   4   5   0
  ZNF547 WILD-TYPE  16  88 324  50
D1039V5, multiclass
    clus
vv   ZNF547 MUTATED ZNF547 WILD-TYPE
  T1              1               16
  T2              4               88
  T3              5              324
  T4              0               50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  ZNF547 MUTATED     9   1   0
  ZNF547 WILD-TYPE 278 112  87
D1039V6, multiclass
    clus
vv   ZNF547 MUTATED ZNF547 WILD-TYPE
  N0              9              278
  N1              1              112
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1039V7, binary
                  cls
clus                 0   1
  ZNF547 MUTATED    10   0
  ZNF547 WILD-TYPE 365  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF547 MUTATED     10    0
  ZNF547 WILD-TYPE  365   65
   clus
vv  ZNF547 MUTATED ZNF547 WILD-TYPE
  0             10              365
  1              0               65
[1] 2 2
[1] FALSE
D1039V8, binary
                  cls
clus                 0   1
  ZNF547 MUTATED     6   4
  ZNF547 WILD-TYPE 219 260
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF547 MUTATED      6    4
  ZNF547 WILD-TYPE  219  260
        clus
vv       ZNF547 MUTATED ZNF547 WILD-TYPE
  FEMALE              6              219
  MALE                4              260
[1] 2 2
[1] FALSE
D1039V9, binary
                  cls
clus                 0   1
  ZNF547 MUTATED     8   0
  ZNF547 WILD-TYPE 342  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF547 MUTATED      8    0
  ZNF547 WILD-TYPE  342   22
     clus
vv    ZNF547 MUTATED ZNF547 WILD-TYPE
  NO               8              342
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ZNF547 MUTATED                      7                             1
  ZNF547 WILD-TYPE                  308                            46
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ZNF547 MUTATED                       2                              0
  ZNF547 WILD-TYPE                   104                             10
D1039V10, multiclass
                                clus
vv                               ZNF547 MUTATED ZNF547 WILD-TYPE
  COLON ADENOCARCINOMA                        7              308
  COLON MUCINOUS ADENOCARCINOMA               1               46
  RECTAL ADENOCARCINOMA                       2              104
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ZNF547 MUTATED     7   0   0   1
  ZNF547 WILD-TYPE 338   4  31  24
D1039V11, multiclass
    clus
vv   ZNF547 MUTATED ZNF547 WILD-TYPE
  R0              7              338
  R1              0                4
  R2              0               31
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1039V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF547 MUTATED                                  0     1
  ZNF547 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZNF547 MUTATED                           1     5
  ZNF547 WILD-TYPE                        21   221
D1039V13, multiclass
                                  clus
vv                                 ZNF547 MUTATED ZNF547 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                         5              221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1040) Variable = ADCY9 MUTATION ANALYSIS
D1040V1, survival
                 sevent
clus2               0   1
  ADCY9 MUTATED    17   1
  ADCY9 WILD-TYPE 361  92
  ADCY9 MUTATED ADCY9 WILD-TYPE 
             18             453 
  ADCY9 MUTATED ADCY9 WILD-TYPE 
              1              92 
$`ADCY9 MUTATED`
TCGA-A6-6653 TCGA-AA-3511 TCGA-AA-3713 TCGA-AA-3867 TCGA-AA-3972 TCGA-AA-3977 
       24.39         6.97        19.04        24.03        50.99        25.02 
TCGA-AA-A01R TCGA-AZ-4315 TCGA-AZ-5407 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4952 
       35.01        58.39        88.21        12.76        10.06        15.62 
TCGA-CM-6162 TCGA-D5-6533 TCGA-D5-6540 TCGA-F4-6703 TCGA-AG-A002 TCGA-F5-6702 
       12.00         1.32        16.14        47.87        20.98        28.57 

$`ADCY9 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
       25.08        25.18        24.16        21.76        24.69        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01        63.98         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
       31.07        31.07        30.05        53.00        17.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
        2.01        21.99        16.08        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        33.01        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
      106.75        22.36        62.79        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 
       14.30        17.56       148.01        85.45        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       15.02        17.03        15.02         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       55.92        20.19        18.25        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
        4.80        17.13        12.49        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6811 TCGA-F5-6812 
       18.28         9.96        49.51        31.30        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  ADCY9 MUTATED ADCY9 WILD-TYPE 
           1.32            0.00 
  ADCY9 MUTATED ADCY9 WILD-TYPE 
          88.21          148.01 
  ADCY9 MUTATED ADCY9 WILD-TYPE 
         22.505          20.120 
[1] "1.3 - 88.2 (22.5)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "3.9"
D1040V2, continuous
D1040V3, binary
                 cls
clus                0   1
  ADCY9 MUTATED    18   2
  ADCY9 WILD-TYPE 348 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ADCY9 MUTATED     18    2
  ADCY9 WILD-TYPE  348  117
        clus
vv       ADCY9 MUTATED ADCY9 WILD-TYPE
  COLON             18             348
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ADCY9 MUTATED         4        0        1         4         1         0
  ADCY9 WILD-TYPE      87        1       31       134         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ADCY9 MUTATED           2          0          2          1        3         1
  ADCY9 WILD-TYPE        22         11         57         41       45        17
                 vv
clus              STAGE IVB
  ADCY9 MUTATED           0
  ADCY9 WILD-TYPE         1
D1040V4, multiclass
            clus
vv           ADCY9 MUTATED ADCY9 WILD-TYPE
  STAGE I                4              87
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              4             134
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              2              22
  STAGE IIIA             0              11
  STAGE IIIB             2              57
  STAGE IIIC             1              41
  STAGE IV               3              45
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ADCY9 MUTATED     1   4  11   4
  ADCY9 WILD-TYPE  16  88 318  46
D1040V5, multiclass
    clus
vv   ADCY9 MUTATED ADCY9 WILD-TYPE
  T1             1              16
  T2             4              88
  T3            11             318
  T4             4              46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  ADCY9 MUTATED    13   3   4
  ADCY9 WILD-TYPE 274 110  83
D1040V6, multiclass
    clus
vv   ADCY9 MUTATED ADCY9 WILD-TYPE
  N0            13             274
  N1             3             110
  N2             4              83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1040V7, binary
                 cls
clus                0   1
  ADCY9 MUTATED    14   4
  ADCY9 WILD-TYPE 361  61
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ADCY9 MUTATED     14    4
  ADCY9 WILD-TYPE  361   61
   clus
vv  ADCY9 MUTATED ADCY9 WILD-TYPE
  0            14             361
  1             4              61
[1] 2 2
[1] FALSE
D1040V8, binary
                 cls
clus                0   1
  ADCY9 MUTATED     5  15
  ADCY9 WILD-TYPE 220 249
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ADCY9 MUTATED      5   15
  ADCY9 WILD-TYPE  220  249
        clus
vv       ADCY9 MUTATED ADCY9 WILD-TYPE
  FEMALE             5             220
  MALE              15             249
[1] 2 2
[1] FALSE
D1040V9, binary
                 cls
clus                0   1
  ADCY9 MUTATED    14   2
  ADCY9 WILD-TYPE 336  20
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ADCY9 MUTATED     14    2
  ADCY9 WILD-TYPE  336   20
     clus
vv    ADCY9 MUTATED ADCY9 WILD-TYPE
  NO             14             336
  YES             2              20
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ADCY9 MUTATED                     13                             5
  ADCY9 WILD-TYPE                  302                            42
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ADCY9 MUTATED                       2                              0
  ADCY9 WILD-TYPE                   104                             10
D1040V10, multiclass
                                clus
vv                               ADCY9 MUTATED ADCY9 WILD-TYPE
  COLON ADENOCARCINOMA                      13             302
  COLON MUCINOUS ADENOCARCINOMA              5              42
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  ADCY9 MUTATED    10   0   3   4
  ADCY9 WILD-TYPE 335   4  28  21
D1040V11, multiclass
    clus
vv   ADCY9 MUTATED ADCY9 WILD-TYPE
  R0            10             335
  R1             0               4
  R2             3              28
  RX             4              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1040V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ADCY9 MUTATED                                  0     2
  ADCY9 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ADCY9 MUTATED                           0    10
  ADCY9 WILD-TYPE                        22   216
D1040V13, multiclass
                                  clus
vv                                 ADCY9 MUTATED ADCY9 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               9
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                       10             216
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1041) Variable = AGAP4 MUTATION ANALYSIS
D1041V1, survival
                 sevent
clus2               0   1
  AGAP4 MUTATED     4   0
  AGAP4 WILD-TYPE 374  93
  AGAP4 MUTATED AGAP4 WILD-TYPE 
              4             467 
  AGAP4 MUTATED AGAP4 WILD-TYPE 
              0              93 
$`AGAP4 MUTATED`
TCGA-AD-6963 TCGA-AU-6004 TCGA-AF-2687 TCGA-AF-2693 
       27.42        27.09        24.13        19.10 

$`AGAP4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 
       22.42        10.88         0.20        14.50        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2689 TCGA-AF-2691 
       26.17        91.79        46.75        79.69        39.48        43.04 
TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       13.55        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  AGAP4 MUTATED AGAP4 WILD-TYPE 
           19.1             0.0 
  AGAP4 MUTATED AGAP4 WILD-TYPE 
          27.42          148.01 
  AGAP4 MUTATED AGAP4 WILD-TYPE 
          25.61           20.12 
[1] "19.1 - 27.4 (25.6)" "0.0 - 148.0 (20.1)"
[1] "hr="     "3300000"
D1041V2, continuous
D1041V3, binary
                 cls
clus                0   1
  AGAP4 MUTATED     2   1
  AGAP4 WILD-TYPE 364 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AGAP4 MUTATED      2    1
  AGAP4 WILD-TYPE  364  118
        clus
vv       AGAP4 MUTATED AGAP4 WILD-TYPE
  COLON              2             364
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  AGAP4 MUTATED         2        0        0         0         0         0
  AGAP4 WILD-TYPE      89        1       32       138        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AGAP4 MUTATED           0          0          0          1        0         0
  AGAP4 WILD-TYPE        24         11         59         41       48        18
                 vv
clus              STAGE IVB
  AGAP4 MUTATED           0
  AGAP4 WILD-TYPE         1
D1041V4, multiclass
            clus
vv           AGAP4 MUTATED AGAP4 WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              0             138
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             1              41
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  AGAP4 MUTATED     0   2   2   0
  AGAP4 WILD-TYPE  17  90 327  50
D1041V5, multiclass
    clus
vv   AGAP4 MUTATED AGAP4 WILD-TYPE
  T1             0              17
  T2             2              90
  T3             2             327
  T4             0              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  AGAP4 MUTATED     3   0   1
  AGAP4 WILD-TYPE 284 113  86
D1041V6, multiclass
    clus
vv   AGAP4 MUTATED AGAP4 WILD-TYPE
  N0             3             284
  N1             0             113
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1041V7, binary
                 cls
clus                0   1
  AGAP4 MUTATED     2   0
  AGAP4 WILD-TYPE 373  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AGAP4 MUTATED      2    0
  AGAP4 WILD-TYPE  373   65
   clus
vv  AGAP4 MUTATED AGAP4 WILD-TYPE
  0             2             373
  1             0              65
[1] 2 2
[1] FALSE
D1041V8, binary
                 cls
clus                0   1
  AGAP4 MUTATED     1   3
  AGAP4 WILD-TYPE 224 261
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AGAP4 MUTATED      1    3
  AGAP4 WILD-TYPE  224  261
        clus
vv       AGAP4 MUTATED AGAP4 WILD-TYPE
  FEMALE             1             224
  MALE               3             261
[1] 2 2
[1] FALSE
D1041V9, binary
                 cls
clus                0   1
  AGAP4 MUTATED     2   1
  AGAP4 WILD-TYPE 348  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AGAP4 MUTATED      2    1
  AGAP4 WILD-TYPE  348   21
     clus
vv    AGAP4 MUTATED AGAP4 WILD-TYPE
  NO              2             348
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  AGAP4 MUTATED                      2                             0
  AGAP4 WILD-TYPE                  313                            47
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  AGAP4 MUTATED                       1                              0
  AGAP4 WILD-TYPE                   105                             10
D1041V10, multiclass
                                clus
vv                               AGAP4 MUTATED AGAP4 WILD-TYPE
  COLON ADENOCARCINOMA                       2             313
  COLON MUCINOUS ADENOCARCINOMA              0              47
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  AGAP4 MUTATED     2   0   0   0
  AGAP4 WILD-TYPE 343   4  31  25
D1041V11, multiclass
[1] "Remove cluster labels:" "AGAP4 MUTATED"         
clus
  AGAP4 MUTATED AGAP4 WILD-TYPE 
              2             403 
     TCGA-A6-2671      TCGA-A6-2672      TCGA-A6-2674      TCGA-A6-2676 
"AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" 
     TCGA-A6-2677      TCGA-A6-2678      TCGA-A6-2683      TCGA-A6-3807 
"AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" 
     TCGA-A6-3808      TCGA-A6-3809      TCGA-A6-3810      TCGA-A6-5657 
"AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" 
     TCGA-A6-5659      TCGA-A6-5661      TCGA-A6-5665      TCGA-A6-6781 
"AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" 
     TCGA-AA-3489      TCGA-AA-3492      TCGA-AA-3496      TCGA-AA-3502 
"AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" 
     TCGA-AA-3510      TCGA-AA-3511      TCGA-AA-3514      TCGA-AA-3517 
"AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" 
     TCGA-AA-3518      TCGA-AA-3519      TCGA-AA-3520      TCGA-AA-3521 
"AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" 
     TCGA-AA-3522      TCGA-AA-3524      TCGA-AA-3525      TCGA-AA-3526 
"AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" 
     TCGA-AA-3527      TCGA-AA-3529      TCGA-AA-3530      TCGA-AA-3531 
"AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" 
     TCGA-AA-3532      TCGA-AA-3534      TCGA-AA-3538      TCGA-AA-3542 
"AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" 
     TCGA-AA-3543      TCGA-AA-3544      TCGA-AA-3548      TCGA-AA-3549 
"AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" 
     TCGA-AA-3552      TCGA-AA-3553      TCGA-AA-3554      TCGA-AA-3555 
"AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" 
     TCGA-AA-3556      TCGA-AA-3558      TCGA-AA-3560      TCGA-AA-3561 
"AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" 
     TCGA-AA-3562      TCGA-AA-3655      TCGA-AA-3660      TCGA-AA-3662 
"AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" 
     TCGA-AA-3663      TCGA-AA-3664      TCGA-AA-3666      TCGA-AA-3667 
"AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" 
     TCGA-AA-3672      TCGA-AA-3673      TCGA-AA-3678      TCGA-AA-3679 
"AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" 
     TCGA-AA-3680      TCGA-AA-3681      TCGA-AA-3684      TCGA-AA-3685 
"AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" 
     TCGA-AA-3688      TCGA-AA-3692      TCGA-AA-3693      TCGA-AA-3695 
"AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" 
     TCGA-AA-3696      TCGA-AA-3697      TCGA-AA-3710      TCGA-AA-3712 
"AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" 
     TCGA-AA-3713      TCGA-AA-3715      TCGA-AA-3811      TCGA-AA-3812 
"AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" 
     TCGA-AA-3814      TCGA-AA-3815      TCGA-AA-3818      TCGA-AA-3819 
"AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" 
     TCGA-AA-3821      TCGA-AA-3831      TCGA-AA-3833      TCGA-AA-3837 
"AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" 
     TCGA-AA-3842      TCGA-AA-3844      TCGA-AA-3845      TCGA-AA-3846 
"AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" 
     TCGA-AA-3848      TCGA-AA-3850      TCGA-AA-3851      TCGA-AA-3852 
"AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" 
     TCGA-AA-3854      TCGA-AA-3855      TCGA-AA-3856      TCGA-AA-3858 
"AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" 
     TCGA-AA-3860      TCGA-AA-3861      TCGA-AA-3864      TCGA-AA-3866 
"AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" 
     TCGA-AA-3867      TCGA-AA-3869      TCGA-AA-3870      TCGA-AA-3872 
"AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" 
     TCGA-AA-3875      TCGA-AA-3877      TCGA-AA-3930      TCGA-AA-3939 
"AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" 
     TCGA-AA-3941      TCGA-AA-3947      TCGA-AA-3949      TCGA-AA-3950 
"AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" 
     TCGA-AA-3952      TCGA-AA-3955      TCGA-AA-3956      TCGA-AA-3968 
"AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" 
     TCGA-AA-3971      TCGA-AA-3972      TCGA-AA-3973      TCGA-AA-3975 
"AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" 
     TCGA-AA-3976      TCGA-AA-3979      TCGA-AA-3984      TCGA-AA-3986 
"AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" 
     TCGA-AA-3989      TCGA-AA-3994      TCGA-AA-A004      TCGA-AA-A00A 
"AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" 
     TCGA-AA-A00D      TCGA-AA-A00E      TCGA-AA-A00F      TCGA-AA-A00J 
"AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" 
     TCGA-AA-A00K      TCGA-AA-A00L      TCGA-AA-A00N      TCGA-AA-A00O 
"AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" 
     TCGA-AA-A00Q      TCGA-AA-A00R      TCGA-AA-A00U      TCGA-AA-A00W 
"AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" 
     TCGA-AA-A00Z      TCGA-AA-A010      TCGA-AA-A017      TCGA-AA-A01D 
"AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" 
     TCGA-AA-A01F      TCGA-AA-A01G      TCGA-AA-A01I      TCGA-AA-A01K 
"AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" 
     TCGA-AA-A01P      TCGA-AA-A01Q      TCGA-AA-A01R      TCGA-AA-A01S 
"AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" 
     TCGA-AA-A01T      TCGA-AA-A01V      TCGA-AA-A01X      TCGA-AA-A01Z 
"AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" 
     TCGA-AA-A022      TCGA-AA-A024      TCGA-AA-A029      TCGA-AA-A02F 
"AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" 
     TCGA-AA-A02H      TCGA-AA-A02J      TCGA-AA-A02K      TCGA-AA-A02O 
"AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" 
     TCGA-AA-A02W      TCGA-AA-A02Y      TCGA-AA-A03F      TCGA-AA-A03J 
"AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" 
     TCGA-AD-5900      TCGA-AD-6548      TCGA-AD-6888      TCGA-AU-3779 
"AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" 
     TCGA-AY-4070      TCGA-AY-4071      TCGA-AY-5543      TCGA-AY-6196 
"AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" 
     TCGA-AY-6197      TCGA-AY-6386      TCGA-AZ-4315      TCGA-AZ-4681 
"AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" 
     TCGA-AZ-4682      TCGA-CA-5254      TCGA-CA-5255      TCGA-CA-5796 
"AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" 
     TCGA-CA-5797      TCGA-CA-6715      TCGA-CA-6716      TCGA-CA-6717 
"AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" 
     TCGA-CA-6718      TCGA-CA-6719      TCGA-CK-4947      TCGA-CK-4948 
"AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" 
     TCGA-CK-4950      TCGA-CK-4952      TCGA-CK-5912      TCGA-CK-5913 
"AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" 
     TCGA-CK-5914      TCGA-CK-5915      TCGA-CK-5916      TCGA-CK-6746 
"AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" 
     TCGA-CK-6747      TCGA-CK-6748      TCGA-CK-6751      TCGA-CM-4743 
"AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" 
     TCGA-CM-4744      TCGA-CM-4746      TCGA-CM-4747      TCGA-CM-4752 
"AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" 
     TCGA-CM-5341      TCGA-CM-5344      TCGA-CM-5348      TCGA-CM-5349 
"AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" 
     TCGA-CM-5860      TCGA-CM-5861      TCGA-CM-5862      TCGA-CM-5863 
"AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" 
     TCGA-CM-5864      TCGA-CM-5868      TCGA-CM-6161      TCGA-CM-6162 
"AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" 
     TCGA-CM-6163      TCGA-CM-6164      TCGA-CM-6165      TCGA-CM-6166 
"AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" 
     TCGA-CM-6167      TCGA-CM-6168      TCGA-CM-6169      TCGA-CM-6170 
"AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" 
     TCGA-CM-6171      TCGA-CM-6172      TCGA-CM-6674      TCGA-CM-6675 
"AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" 
     TCGA-CM-6676      TCGA-CM-6677      TCGA-CM-6678      TCGA-CM-6679 
"AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" 
     TCGA-CM-6680      TCGA-D5-5537      TCGA-D5-5538      TCGA-D5-5539 
"AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" 
     TCGA-D5-5540      TCGA-D5-5541      TCGA-D5-6529      TCGA-D5-6532 
"AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" 
     TCGA-D5-6533      TCGA-D5-6534      TCGA-D5-6535      TCGA-D5-6536 
"AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" 
     TCGA-D5-6537      TCGA-D5-6538      TCGA-D5-6539      TCGA-D5-6540 
"AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" 
     TCGA-D5-6541      TCGA-D5-6898      TCGA-D5-6920      TCGA-D5-6922 
"AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" 
     TCGA-D5-6923      TCGA-D5-6924      TCGA-D5-6926      TCGA-D5-6927 
"AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" 
     TCGA-D5-6928      TCGA-D5-6929      TCGA-D5-6930      TCGA-D5-6931 
"AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" 
     TCGA-D5-6932      TCGA-D5-7000      TCGA-F4-6459      TCGA-F4-6460 
"AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" 
     TCGA-F4-6569      TCGA-F4-6570      TCGA-F4-6703      TCGA-F4-6704 
"AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" 
     TCGA-F4-6805      TCGA-F4-6806      TCGA-F4-6807      TCGA-F4-6808 
"AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" 
     TCGA-F4-6809      TCGA-F4-6854      TCGA-F4-6855      TCGA-F4-6856 
"AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" 
     TCGA-G4-6293      TCGA-G4-6299      TCGA-G4-6303      TCGA-G4-6304 
"AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" 
     TCGA-G4-6306      TCGA-G4-6307      TCGA-G4-6309      TCGA-G4-6310 
"AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" 
     TCGA-G4-6315      TCGA-G4-6317      TCGA-G4-6321      TCGA-G4-6323 
"AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" 
     TCGA-G4-6586      TCGA-G4-6588      TCGA-G4-6625      TCGA-G4-6626 
"AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" 
     TCGA-G4-6628      TCGA-AF-2689      TCGA-AF-2691      TCGA-AF-2692 
"AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" 
     TCGA-AF-3400      TCGA-AF-3913      TCGA-AF-4110      TCGA-AF-5654 
"AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" 
     TCGA-AF-6655      TCGA-AG-3574      TCGA-AG-3575      TCGA-AG-3578 
"AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" 
     TCGA-AG-3580      TCGA-AG-3581      TCGA-AG-3582      TCGA-AG-3583 
"AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" 
     TCGA-AG-3584      TCGA-AG-3586      TCGA-AG-3587      TCGA-AG-3593 
"AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" 
     TCGA-AG-3594      TCGA-AG-3598      TCGA-AG-3599      TCGA-AG-3600 
"AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" 
     TCGA-AG-3601      TCGA-AG-3602      TCGA-AG-3605      TCGA-AG-3608 
"AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" 
     TCGA-AG-3609      TCGA-AG-3611      TCGA-AG-3612      TCGA-AG-3726 
"AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" 
     TCGA-AG-3727      TCGA-AG-3731      TCGA-AG-3732      TCGA-AG-3742 
"AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" 
     TCGA-AG-3878      TCGA-AG-3882      TCGA-AG-3883      TCGA-AG-3885 
"AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" 
     TCGA-AG-3887      TCGA-AG-3890      TCGA-AG-3892      TCGA-AG-3893 
"AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" 
     TCGA-AG-3894      TCGA-AG-3896      TCGA-AG-3898      TCGA-AG-3901 
"AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" 
     TCGA-AG-3902      TCGA-AG-3909      TCGA-AG-3999      TCGA-AG-4001 
"AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" 
     TCGA-AG-4005      TCGA-AG-4007      TCGA-AG-4008      TCGA-AG-4015 
"AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" 
     TCGA-AG-A002      TCGA-AG-A008      TCGA-AG-A00C      TCGA-AG-A00H 
"AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" 
     TCGA-AG-A00Y      TCGA-AG-A011      TCGA-AG-A014      TCGA-AG-A015 
"AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" 
     TCGA-AG-A016      TCGA-AG-A01L      TCGA-AG-A01W      TCGA-AG-A01Y 
"AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" 
     TCGA-AG-A020      TCGA-AG-A025      TCGA-AG-A026      TCGA-AG-A02G 
"AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" 
     TCGA-AG-A02N      TCGA-AG-A02X      TCGA-AG-A032      TCGA-AG-A036 
"AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" 
     TCGA-AH-6549      TCGA-AH-6643      TCGA-CL-5917      TCGA-CL-5918 
"AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" 
     TCGA-DC-5337      TCGA-DC-5869      TCGA-DC-6155      TCGA-DC-6157 
"AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" 
     TCGA-DC-6158      TCGA-DC-6160      TCGA-DC-6681      TCGA-DC-6682 
"AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" 
     TCGA-DC-6683      TCGA-DT-5265      TCGA-EF-5830      TCGA-EI-6506 
"AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" 
     TCGA-EI-6507      TCGA-EI-6508      TCGA-EI-6510      TCGA-F5-6464 
"AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" 
     TCGA-F5-6465      TCGA-F5-6571      TCGA-F5-6702      TCGA-F5-6812 
"AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" 
     TCGA-F5-6813      TCGA-G5-6235      TCGA-G5-6641 
"AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" "AGAP4 WILD-TYPE" 
D1041V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AGAP4 MUTATED                                  0     0
  AGAP4 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  AGAP4 MUTATED                           0     4
  AGAP4 WILD-TYPE                        22   222
D1041V13, multiclass
                                  clus
vv                                 AGAP4 MUTATED AGAP4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        4             222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1042) Variable = OR11H12 MUTATION ANALYSIS
D1042V1, survival
                   sevent
clus2                 0   1
  OR11H12 MUTATED     5   0
  OR11H12 WILD-TYPE 373  93
  OR11H12 MUTATED OR11H12 WILD-TYPE 
                5               466 
  OR11H12 MUTATED OR11H12 WILD-TYPE 
                0                93 
$`OR11H12 MUTATED`
TCGA-AU-3779 TCGA-D5-6535 TCGA-G4-6628 TCGA-AG-4008 TCGA-G5-6235 
       14.50        15.12        79.69        17.03        55.76 

$`OR11H12 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        10.88         0.20        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 
       55.92        20.19        18.25         1.32        43.27        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       26.17        91.79        46.75        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-A002 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6641 
       32.19         0.66         0.69        26.43 

  OR11H12 MUTATED OR11H12 WILD-TYPE 
             14.5               0.0 
  OR11H12 MUTATED OR11H12 WILD-TYPE 
            79.69            148.01 
  OR11H12 MUTATED OR11H12 WILD-TYPE 
           17.030            20.235 
[1] "14.5 - 79.7 (17.0)" "0.0 - 148.0 (20.2)"
[1] "hr="     "9200000"
D1042V2, continuous
D1042V3, binary
                   cls
clus                  0   1
  OR11H12 MUTATED     3   2
  OR11H12 WILD-TYPE 363 117
[1] "tbl2"
                   cls
clus                [,1] [,2]
  OR11H12 MUTATED      3    2
  OR11H12 WILD-TYPE  363  117
        clus
vv       OR11H12 MUTATED OR11H12 WILD-TYPE
  COLON                3               363
  RECTUM               2               117
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  OR11H12 MUTATED         1        0        0         2         0         0
  OR11H12 WILD-TYPE      90        1       32       136        10         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  OR11H12 MUTATED           0          0          2          0        0
  OR11H12 WILD-TYPE        24         11         57         42       48
                   vv
clus                STAGE IVA STAGE IVB
  OR11H12 MUTATED           0         0
  OR11H12 WILD-TYPE        18         1
D1042V4, multiclass
            clus
vv           OR11H12 MUTATED OR11H12 WILD-TYPE
  STAGE I                  1                90
  STAGE IA                 0                 1
  STAGE II                 0                32
  STAGE IIA                2               136
  STAGE IIB                0                10
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               0                11
  STAGE IIIB               2                57
  STAGE IIIC               0                42
  STAGE IV                 0                48
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  OR11H12 MUTATED     0   1   4   0
  OR11H12 WILD-TYPE  17  91 325  50
D1042V5, multiclass
    clus
vv   OR11H12 MUTATED OR11H12 WILD-TYPE
  T1               0                17
  T2               1                91
  T3               4               325
  T4               0                50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  OR11H12 MUTATED     3   2   0
  OR11H12 WILD-TYPE 284 111  87
D1042V6, multiclass
    clus
vv   OR11H12 MUTATED OR11H12 WILD-TYPE
  N0               3               284
  N1               2               111
  N2               0                87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1042V7, binary
                   cls
clus                  0   1
  OR11H12 MUTATED     3   0
  OR11H12 WILD-TYPE 372  65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  OR11H12 MUTATED      3    0
  OR11H12 WILD-TYPE  372   65
   clus
vv  OR11H12 MUTATED OR11H12 WILD-TYPE
  0               3               372
  1               0                65
[1] 2 2
[1] FALSE
D1042V8, binary
                   cls
clus                  0   1
  OR11H12 MUTATED     2   3
  OR11H12 WILD-TYPE 223 261
[1] "tbl2"
                   cls
clus                [,1] [,2]
  OR11H12 MUTATED      2    3
  OR11H12 WILD-TYPE  223  261
        clus
vv       OR11H12 MUTATED OR11H12 WILD-TYPE
  FEMALE               2               223
  MALE                 3               261
[1] 2 2
[1] FALSE
D1042V9, binary
                   cls
clus                  0   1
  OR11H12 MUTATED     5   0
  OR11H12 WILD-TYPE 345  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  OR11H12 MUTATED      5    0
  OR11H12 WILD-TYPE  345   22
     clus
vv    OR11H12 MUTATED OR11H12 WILD-TYPE
  NO                5               345
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  OR11H12 MUTATED                      3                             0
  OR11H12 WILD-TYPE                  312                            47
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  OR11H12 MUTATED                       2                              0
  OR11H12 WILD-TYPE                   104                             10
D1042V10, multiclass
                                clus
vv                               OR11H12 MUTATED OR11H12 WILD-TYPE
  COLON ADENOCARCINOMA                         3               312
  COLON MUCINOUS ADENOCARCINOMA                0                47
  RECTAL ADENOCARCINOMA                        2               104
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  OR11H12 MUTATED     3   1   0   1
  OR11H12 WILD-TYPE 342   3  31  24
D1042V11, multiclass
    clus
vv   OR11H12 MUTATED OR11H12 WILD-TYPE
  R0               3               342
  R1               1                 3
  R2               0                31
  RX               1                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1042V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OR11H12 MUTATED                                  0     0
  OR11H12 WILD-TYPE                                1    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  OR11H12 MUTATED                           0     4
  OR11H12 WILD-TYPE                        22   222
D1042V13, multiclass
                                  clus
vv                                 OR11H12 MUTATED OR11H12 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                      0                22
  WHITE                                          4               222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1043) Variable = SLC22A3 MUTATION ANALYSIS
D1043V1, survival
                   sevent
clus2                 0   1
  SLC22A3 MUTATED    11   2
  SLC22A3 WILD-TYPE 367  91
  SLC22A3 MUTATED SLC22A3 WILD-TYPE 
               13               458 
  SLC22A3 MUTATED SLC22A3 WILD-TYPE 
                2                91 
$`SLC22A3 MUTATED`
TCGA-A6-6781 TCGA-AA-3510 TCGA-AA-3877 TCGA-AA-A010 TCGA-AD-6889 TCGA-AU-6004 
       19.66        63.98        31.00        34.98        56.55        27.09 
TCGA-AY-6386 TCGA-CK-4948 TCGA-CM-6168 TCGA-F4-6570 TCGA-F4-6806 TCGA-G4-6626 
       17.82       148.01        12.99         6.18        41.42        46.75 
TCGA-AG-A002 
       20.98 

$`SLC22A3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 
       24.03        27.02        29.98        18.05         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 
       40.96         0.07        21.37        15.52         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-4323 
       16.31         0.95        33.01        21.44        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       14.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 
      117.07        98.24         8.61        31.96        35.74        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
        1.55        34.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 
       22.09        13.78        35.80        26.17        91.79        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  SLC22A3 MUTATED SLC22A3 WILD-TYPE 
             6.18              0.00 
  SLC22A3 MUTATED SLC22A3 WILD-TYPE 
           148.01            140.38 
  SLC22A3 MUTATED SLC22A3 WILD-TYPE 
           31.000            20.035 
[1] "6.2 - 148.0 (31.0)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1.9"
D1043V2, continuous
D1043V3, binary
                   cls
clus                  0   1
  SLC22A3 MUTATED    12   1
  SLC22A3 WILD-TYPE 354 118
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC22A3 MUTATED     12    1
  SLC22A3 WILD-TYPE  354  118
        clus
vv       SLC22A3 MUTATED SLC22A3 WILD-TYPE
  COLON               12               354
  RECTUM               1               118
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SLC22A3 MUTATED         4        0        1         4         1         0
  SLC22A3 WILD-TYPE      87        1       31       134         9         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC22A3 MUTATED           1          0          1          1        0
  SLC22A3 WILD-TYPE        23         11         58         41       48
                   vv
clus                STAGE IVA STAGE IVB
  SLC22A3 MUTATED           0         0
  SLC22A3 WILD-TYPE        18         1
D1043V4, multiclass
            clus
vv           SLC22A3 MUTATED SLC22A3 WILD-TYPE
  STAGE I                  4                87
  STAGE IA                 0                 1
  STAGE II                 1                31
  STAGE IIA                4               134
  STAGE IIB                1                 9
  STAGE IIC                0                 1
  STAGE III                1                23
  STAGE IIIA               0                11
  STAGE IIIB               1                58
  STAGE IIIC               1                41
  STAGE IV                 0                48
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  SLC22A3 MUTATED     1   3   7   2
  SLC22A3 WILD-TYPE  16  89 322  48
D1043V5, multiclass
    clus
vv   SLC22A3 MUTATED SLC22A3 WILD-TYPE
  T1               1                16
  T2               3                89
  T3               7               322
  T4               2                48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  SLC22A3 MUTATED    10   3   0
  SLC22A3 WILD-TYPE 277 110  87
D1043V6, multiclass
    clus
vv   SLC22A3 MUTATED SLC22A3 WILD-TYPE
  N0              10               277
  N1               3               110
  N2               0                87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1043V7, binary
                   cls
clus                  0   1
  SLC22A3 MUTATED    12   0
  SLC22A3 WILD-TYPE 363  65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC22A3 MUTATED     12    0
  SLC22A3 WILD-TYPE  363   65
   clus
vv  SLC22A3 MUTATED SLC22A3 WILD-TYPE
  0              12               363
  1               0                65
[1] 2 2
[1] FALSE
D1043V8, binary
                   cls
clus                  0   1
  SLC22A3 MUTATED     8   5
  SLC22A3 WILD-TYPE 217 259
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC22A3 MUTATED      8    5
  SLC22A3 WILD-TYPE  217  259
        clus
vv       SLC22A3 MUTATED SLC22A3 WILD-TYPE
  FEMALE               8               217
  MALE                 5               259
[1] 2 2
[1] FALSE
D1043V9, binary
                   cls
clus                  0   1
  SLC22A3 MUTATED    11   0
  SLC22A3 WILD-TYPE 339  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC22A3 MUTATED     11    0
  SLC22A3 WILD-TYPE  339   22
     clus
vv    SLC22A3 MUTATED SLC22A3 WILD-TYPE
  NO               11               339
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SLC22A3 MUTATED                     10                             2
  SLC22A3 WILD-TYPE                  305                            45
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SLC22A3 MUTATED                       1                              0
  SLC22A3 WILD-TYPE                   105                             10
D1043V10, multiclass
                                clus
vv                               SLC22A3 MUTATED SLC22A3 WILD-TYPE
  COLON ADENOCARCINOMA                        10               305
  COLON MUCINOUS ADENOCARCINOMA                2                45
  RECTAL ADENOCARCINOMA                        1               105
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  SLC22A3 MUTATED    12   0   0   0
  SLC22A3 WILD-TYPE 333   4  31  25
D1043V11, multiclass
    clus
vv   SLC22A3 MUTATED SLC22A3 WILD-TYPE
  R0              12               333
  R1               0                 4
  R2               0                31
  RX               0                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1043V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SLC22A3 MUTATED                                  0     1
  SLC22A3 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  SLC22A3 MUTATED                           2     6
  SLC22A3 WILD-TYPE                        20   220
D1043V13, multiclass
                                  clus
vv                                 SLC22A3 MUTATED SLC22A3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                10
  BLACK OR AFRICAN AMERICAN                      2                20
  WHITE                                          6               220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1044) Variable = ATAD2B MUTATION ANALYSIS
D1044V1, survival
                  sevent
clus2                0   1
  ATAD2B MUTATED    15   3
  ATAD2B WILD-TYPE 363  90
  ATAD2B MUTATED ATAD2B WILD-TYPE 
              18              453 
  ATAD2B MUTATED ATAD2B WILD-TYPE 
               3               90 
$`ATAD2B MUTATED`
TCGA-A6-3809 TCGA-A6-5665 TCGA-A6-6782 TCGA-AA-3977 TCGA-AA-A010 TCGA-AA-A01K 
       32.75        22.06        20.28        25.02        34.98        31.00 
TCGA-AD-5900 TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-CA-6717 TCGA-CM-5348 
        0.07       100.01         5.23         3.19        12.76        22.98 
TCGA-CM-6171 TCGA-D5-6930 TCGA-DM-A1D9 TCGA-AG-3898 TCGA-AG-A002 TCGA-EI-6507 
       14.04         1.51       140.38        48.03        20.98        19.96 

$`ATAD2B WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       19.66         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q 
       10.98        32.02        12.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 
        0.92        41.00        39.98        18.05        40.96        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5254 
        6.77        12.10        29.56        11.74         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07        12.20        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.03        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
        9.44        11.64         4.80        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       13.32        12.59         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       35.01        14.01         1.02        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6510 
       51.48        32.61         0.49        20.55        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  ATAD2B MUTATED ATAD2B WILD-TYPE 
            0.07             0.00 
  ATAD2B MUTATED ATAD2B WILD-TYPE 
          140.38           148.01 
  ATAD2B MUTATED ATAD2B WILD-TYPE 
           21.52            20.05 
[1] "0.1 - 140.4 (21.5)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.3"
D1044V2, continuous
D1044V3, binary
                  cls
clus                 0   1
  ATAD2B MUTATED    15   3
  ATAD2B WILD-TYPE 351 116
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATAD2B MUTATED     15    3
  ATAD2B WILD-TYPE  351  116
        clus
vv       ATAD2B MUTATED ATAD2B WILD-TYPE
  COLON              15              351
  RECTUM              3              116
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ATAD2B MUTATED         3        0        1         6         3         0
  ATAD2B WILD-TYPE      88        1       31       132         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ATAD2B MUTATED           0          0          2          1        1
  ATAD2B WILD-TYPE        24         11         57         41       47
                  vv
clus               STAGE IVA STAGE IVB
  ATAD2B MUTATED           0         0
  ATAD2B WILD-TYPE        18         1
D1044V4, multiclass
            clus
vv           ATAD2B MUTATED ATAD2B WILD-TYPE
  STAGE I                 3               88
  STAGE IA                0                1
  STAGE II                1               31
  STAGE IIA               6              132
  STAGE IIB               3                7
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              2               57
  STAGE IIIC              1               41
  STAGE IV                1               47
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ATAD2B MUTATED     0   4   9   5
  ATAD2B WILD-TYPE  17  88 320  45
D1044V5, multiclass
    clus
vv   ATAD2B MUTATED ATAD2B WILD-TYPE
  T1              0               17
  T2              4               88
  T3              9              320
  T4              5               45
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  ATAD2B MUTATED    14   2   2
  ATAD2B WILD-TYPE 273 111  85
D1044V6, multiclass
    clus
vv   ATAD2B MUTATED ATAD2B WILD-TYPE
  N0             14              273
  N1              2              111
  N2              2               85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1044V7, binary
                  cls
clus                 0   1
  ATAD2B MUTATED    14   1
  ATAD2B WILD-TYPE 361  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATAD2B MUTATED     14    1
  ATAD2B WILD-TYPE  361   64
   clus
vv  ATAD2B MUTATED ATAD2B WILD-TYPE
  0             14              361
  1              1               64
[1] 2 2
[1] FALSE
D1044V8, binary
                  cls
clus                 0   1
  ATAD2B MUTATED     6  12
  ATAD2B WILD-TYPE 219 252
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATAD2B MUTATED      6   12
  ATAD2B WILD-TYPE  219  252
        clus
vv       ATAD2B MUTATED ATAD2B WILD-TYPE
  FEMALE              6              219
  MALE               12              252
[1] 2 2
[1] FALSE
D1044V9, binary
                  cls
clus                 0   1
  ATAD2B MUTATED    15   0
  ATAD2B WILD-TYPE 335  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATAD2B MUTATED     15    0
  ATAD2B WILD-TYPE  335   22
     clus
vv    ATAD2B MUTATED ATAD2B WILD-TYPE
  NO              15              335
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ATAD2B MUTATED                     11                             4
  ATAD2B WILD-TYPE                  304                            43
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ATAD2B MUTATED                       3                              0
  ATAD2B WILD-TYPE                   103                             10
D1044V10, multiclass
                                clus
vv                               ATAD2B MUTATED ATAD2B WILD-TYPE
  COLON ADENOCARCINOMA                       11              304
  COLON MUCINOUS ADENOCARCINOMA               4               43
  RECTAL ADENOCARCINOMA                       3              103
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ATAD2B MUTATED    11   0   0   1
  ATAD2B WILD-TYPE 334   4  31  24
D1044V11, multiclass
    clus
vv   ATAD2B MUTATED ATAD2B WILD-TYPE
  R0             11              334
  R1              0                4
  R2              0               31
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1044V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ATAD2B MUTATED                                  0     1
  ATAD2B WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ATAD2B MUTATED                           0    12
  ATAD2B WILD-TYPE                        22   214
D1044V13, multiclass
                                  clus
vv                                 ATAD2B MUTATED ATAD2B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                        12              214
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1045) Variable = GPR126 MUTATION ANALYSIS
D1045V1, survival
                  sevent
clus2                0   1
  GPR126 MUTATED    15   2
  GPR126 WILD-TYPE 363  91
  GPR126 MUTATED GPR126 WILD-TYPE 
              17              454 
  GPR126 MUTATED GPR126 WILD-TYPE 
               2               91 
$`GPR126 MUTATED`
TCGA-A6-5665 TCGA-A6-6141 TCGA-AA-3492 TCGA-AA-3672 TCGA-AA-3715 TCGA-AA-3864 
       22.06         8.38         3.02         0.92        19.04        53.00 
TCGA-AA-3947 TCGA-AA-A010 TCGA-AZ-4315 TCGA-AZ-5407 TCGA-CA-6717 TCGA-D5-6539 
       33.01        34.98        58.39        88.21        12.76        12.49 
TCGA-D5-6929 TCGA-F4-6856 TCGA-AG-3896 TCGA-AG-A002 TCGA-AG-A02N 
        4.80        35.31         1.02        20.98        61.97 

$`GPR126 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 
       22.09        32.71        27.09        22.52        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       19.66        20.28         7.04         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
        2.01        14.01        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       26.99        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       30.05        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 
       31.00         2.01        12.99        24.00        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       33.01        21.44        17.82         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07        12.20        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 
       43.27        15.12        17.85         4.80        17.13        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.04         9.44        11.64         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 
       16.24        33.67        13.25         0.53        47.41       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       13.02        35.01        14.01        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
        1.94        38.96        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  GPR126 MUTATED GPR126 WILD-TYPE 
            0.92             0.00 
  GPR126 MUTATED GPR126 WILD-TYPE 
           88.21           148.01 
  GPR126 MUTATED GPR126 WILD-TYPE 
          20.980           20.155 
[1] "0.9 - 88.2 (21.0)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.8"
D1045V2, continuous
D1045V3, binary
                  cls
clus                 0   1
  GPR126 MUTATED    16   3
  GPR126 WILD-TYPE 350 116
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR126 MUTATED     16    3
  GPR126 WILD-TYPE  350  116
        clus
vv       GPR126 MUTATED GPR126 WILD-TYPE
  COLON              16              350
  RECTUM              3              116
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GPR126 MUTATED         4        0        5         5         2         0
  GPR126 WILD-TYPE      87        1       27       133         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GPR126 MUTATED           1          1          0          0        1
  GPR126 WILD-TYPE        23         10         59         42       47
                  vv
clus               STAGE IVA STAGE IVB
  GPR126 MUTATED           0         0
  GPR126 WILD-TYPE        18         1
D1045V4, multiclass
            clus
vv           GPR126 MUTATED GPR126 WILD-TYPE
  STAGE I                 4               87
  STAGE IA                0                1
  STAGE II                5               27
  STAGE IIA               5              133
  STAGE IIB               2                8
  STAGE IIC               0                1
  STAGE III               1               23
  STAGE IIIA              1               10
  STAGE IIIB              0               59
  STAGE IIIC              0               42
  STAGE IV                1               47
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  GPR126 MUTATED     1   3  12   3
  GPR126 WILD-TYPE  16  89 317  47
D1045V5, multiclass
    clus
vv   GPR126 MUTATED GPR126 WILD-TYPE
  T1              1               16
  T2              3               89
  T3             12              317
  T4              3               47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  GPR126 MUTATED    17   2   0
  GPR126 WILD-TYPE 270 111  87
D1045V6, multiclass
    clus
vv   GPR126 MUTATED GPR126 WILD-TYPE
  N0             17              270
  N1              2              111
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1045V7, binary
                  cls
clus                 0   1
  GPR126 MUTATED    18   1
  GPR126 WILD-TYPE 357  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR126 MUTATED     18    1
  GPR126 WILD-TYPE  357   64
   clus
vv  GPR126 MUTATED GPR126 WILD-TYPE
  0             18              357
  1              1               64
[1] 2 2
[1] FALSE
D1045V8, binary
                  cls
clus                 0   1
  GPR126 MUTATED    11   8
  GPR126 WILD-TYPE 214 256
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR126 MUTATED     11    8
  GPR126 WILD-TYPE  214  256
        clus
vv       GPR126 MUTATED GPR126 WILD-TYPE
  FEMALE             11              214
  MALE                8              256
[1] 2 2
[1] FALSE
D1045V9, binary
                  cls
clus                 0   1
  GPR126 MUTATED    14   0
  GPR126 WILD-TYPE 336  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR126 MUTATED     14    0
  GPR126 WILD-TYPE  336   22
     clus
vv    GPR126 MUTATED GPR126 WILD-TYPE
  NO              14              336
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  GPR126 MUTATED                     13                             3
  GPR126 WILD-TYPE                  302                            44
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  GPR126 MUTATED                       3                              0
  GPR126 WILD-TYPE                   103                             10
D1045V10, multiclass
                                clus
vv                               GPR126 MUTATED GPR126 WILD-TYPE
  COLON ADENOCARCINOMA                       13              302
  COLON MUCINOUS ADENOCARCINOMA               3               44
  RECTAL ADENOCARCINOMA                       3              103
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  GPR126 MUTATED    16   0   0   1
  GPR126 WILD-TYPE 329   4  31  24
D1045V11, multiclass
    clus
vv   GPR126 MUTATED GPR126 WILD-TYPE
  R0             16              329
  R1              0                4
  R2              0               31
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1045V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GPR126 MUTATED                                  0     1
  GPR126 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  GPR126 MUTATED                           1     6
  GPR126 WILD-TYPE                        21   220
D1045V13, multiclass
                                  clus
vv                                 GPR126 MUTATED GPR126 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                         6              220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1046) Variable = CHMP4C MUTATION ANALYSIS
D1046V1, survival
                  sevent
clus2                0   1
  CHMP4C MUTATED     3   1
  CHMP4C WILD-TYPE 375  92
  CHMP4C MUTATED CHMP4C WILD-TYPE 
               4              467 
  CHMP4C MUTATED CHMP4C WILD-TYPE 
               1               92 
$`CHMP4C MUTATED`
TCGA-AU-6004 TCGA-AZ-6606 TCGA-CK-4952 TCGA-AG-A002 
       27.09        11.74        15.62        20.98 

$`CHMP4C WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 
       22.42        27.42        10.88         0.20        14.50        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 
        6.77        12.10       100.01        29.56         5.23         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       85.45        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  CHMP4C MUTATED CHMP4C WILD-TYPE 
           11.74             0.00 
  CHMP4C MUTATED CHMP4C WILD-TYPE 
           27.09           148.01 
  CHMP4C MUTATED CHMP4C WILD-TYPE 
           18.30            20.19 
[1] "11.7 - 27.1 (18.3)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.7"
D1046V2, continuous
D1046V3, binary
                  cls
clus                 0   1
  CHMP4C MUTATED     3   1
  CHMP4C WILD-TYPE 363 118
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CHMP4C MUTATED      3    1
  CHMP4C WILD-TYPE  363  118
        clus
vv       CHMP4C MUTATED CHMP4C WILD-TYPE
  COLON               3              363
  RECTUM              1              118
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CHMP4C MUTATED         2        0        0         0         0         0
  CHMP4C WILD-TYPE      89        1       32       138        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CHMP4C MUTATED           0          0          0          1        1
  CHMP4C WILD-TYPE        24         11         59         41       47
                  vv
clus               STAGE IVA STAGE IVB
  CHMP4C MUTATED           0         0
  CHMP4C WILD-TYPE        18         1
D1046V4, multiclass
            clus
vv           CHMP4C MUTATED CHMP4C WILD-TYPE
  STAGE I                 2               89
  STAGE IA                0                1
  STAGE II                0               32
  STAGE IIA               0              138
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              0               59
  STAGE IIIC              1               41
  STAGE IV                1               47
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  CHMP4C MUTATED     0   2   0   2
  CHMP4C WILD-TYPE  17  90 329  48
D1046V5, multiclass
    clus
vv   CHMP4C MUTATED CHMP4C WILD-TYPE
  T1              0               17
  T2              2               90
  T3              0              329
  T4              2               48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  CHMP4C MUTATED     2   0   2
  CHMP4C WILD-TYPE 285 113  85
D1046V6, multiclass
    clus
vv   CHMP4C MUTATED CHMP4C WILD-TYPE
  N0              2              285
  N1              0              113
  N2              2               85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1046V7, binary
                  cls
clus                 0   1
  CHMP4C MUTATED     3   1
  CHMP4C WILD-TYPE 372  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CHMP4C MUTATED      3    1
  CHMP4C WILD-TYPE  372   64
   clus
vv  CHMP4C MUTATED CHMP4C WILD-TYPE
  0              3              372
  1              1               64
[1] 2 2
[1] FALSE
D1046V8, binary
                  cls
clus                 0   1
  CHMP4C MUTATED     2   2
  CHMP4C WILD-TYPE 223 262
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CHMP4C MUTATED      2    2
  CHMP4C WILD-TYPE  223  262
        clus
vv       CHMP4C MUTATED CHMP4C WILD-TYPE
  FEMALE              2              223
  MALE                2              262
[1] 2 2
[1] FALSE
D1046V9, binary
                  cls
clus                 0   1
  CHMP4C MUTATED     2   0
  CHMP4C WILD-TYPE 348  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CHMP4C MUTATED      2    0
  CHMP4C WILD-TYPE  348   22
     clus
vv    CHMP4C MUTATED CHMP4C WILD-TYPE
  NO               2              348
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CHMP4C MUTATED                      2                             1
  CHMP4C WILD-TYPE                  313                            46
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CHMP4C MUTATED                       1                              0
  CHMP4C WILD-TYPE                   105                             10
D1046V10, multiclass
                                clus
vv                               CHMP4C MUTATED CHMP4C WILD-TYPE
  COLON ADENOCARCINOMA                        2              313
  COLON MUCINOUS ADENOCARCINOMA               1               46
  RECTAL ADENOCARCINOMA                       1              105
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  CHMP4C MUTATED     2   0   0   1
  CHMP4C WILD-TYPE 343   4  31  24
D1046V11, multiclass
    clus
vv   CHMP4C MUTATED CHMP4C WILD-TYPE
  R0              2              343
  R1              0                4
  R2              0               31
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1046V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CHMP4C MUTATED                                  0     0
  CHMP4C WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  CHMP4C MUTATED                           0     3
  CHMP4C WILD-TYPE                        22   223
D1046V13, multiclass
                                  clus
vv                                 CHMP4C MUTATED CHMP4C WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         3              223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1047) Variable = POLQ MUTATION ANALYSIS
D1047V1, survival
                sevent
clus2              0   1
  POLQ MUTATED    26   6
  POLQ WILD-TYPE 352  87
  POLQ MUTATED POLQ WILD-TYPE 
            32            439 
  POLQ MUTATED POLQ WILD-TYPE 
             6             87 
$`POLQ MUTATED`
TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3510 TCGA-AA-3518 TCGA-AA-3672 TCGA-AA-3713 
       20.12        19.66        63.98         1.02         0.92        19.04 
TCGA-AA-3947 TCGA-AA-3971 TCGA-AA-3977 TCGA-AA-A010 TCGA-AD-6889 TCGA-AZ-5403 
       33.01        16.08        25.02        34.98        56.55        62.79 
TCGA-AZ-6598 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4746 
       49.41        12.76        10.06       124.27        23.05        37.02 
TCGA-CM-5861 TCGA-CM-6162 TCGA-CM-6675 TCGA-D5-6537 TCGA-D5-6540 TCGA-DM-A1D4 
       15.02        12.00        13.05         4.80        16.14        92.75 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6303 TCGA-G4-6588 TCGA-G4-6628 TCGA-AG-3892 
       47.41        35.31        65.85        26.17        79.69        13.02 
TCGA-AG-A002 TCGA-DC-6157 
       20.98        27.95 

$`POLQ WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       23.87        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3520 
        6.97         1.02        13.02        38.99         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
       14.01        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 
       31.00         2.01        12.99        24.00        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3972 
        2.01        20.98        34.03         2.01        21.99        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 
       40.96         0.07        21.37        15.52         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5407 
       58.39         1.41         5.13       106.75        22.36        88.21 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.07        12.20        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
        1.91        20.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       22.98        30.08        32.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       17.03        15.02         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       12.95        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6538 
       18.25         1.32        43.27        15.12        17.85        17.13 
TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       12.49        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
      130.65        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-G4-6293 
       41.42        16.24        33.67        13.25         0.53       133.18 
TCGA-G4-6299 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       74.56        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 
       61.91        36.00        22.09        13.78        35.80        91.79 
TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       46.75        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       17.95        36.95        17.03        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6158 
       78.12         7.17        15.02         5.03        13.97        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  POLQ MUTATED POLQ WILD-TYPE 
          0.92           0.00 
  POLQ MUTATED POLQ WILD-TYPE 
        124.27         148.01 
  POLQ MUTATED POLQ WILD-TYPE 
        24.035         20.020 
[1] "0.9 - 124.3 (24.0)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.4"
D1047V2, continuous
D1047V3, binary
                cls
clus               0   1
  POLQ MUTATED    30   3
  POLQ WILD-TYPE 336 116
[1] "tbl2"
                cls
clus             [,1] [,2]
  POLQ MUTATED     30    3
  POLQ WILD-TYPE  336  116
        clus
vv       POLQ MUTATED POLQ WILD-TYPE
  COLON            30            336
  RECTUM            3            116
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  POLQ MUTATED         8        0        3        11         2         0
  POLQ WILD-TYPE      83        1       29       127         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  POLQ MUTATED           2          0          2          1        2         0
  POLQ WILD-TYPE        22         11         57         41       46        18
                vv
clus             STAGE IVB
  POLQ MUTATED           1
  POLQ WILD-TYPE         0
D1047V4, multiclass
            clus
vv           POLQ MUTATED POLQ WILD-TYPE
  STAGE I               8             83
  STAGE IA              0              1
  STAGE II              3             29
  STAGE IIA            11            127
  STAGE IIB             2              8
  STAGE IIC             0              1
  STAGE III             2             22
  STAGE IIIA            0             11
  STAGE IIIB            2             57
  STAGE IIIC            1             41
  STAGE IV              2             46
  STAGE IVA             0             18
  STAGE IVB             1              0
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  POLQ MUTATED     1   8  21   3
  POLQ WILD-TYPE  16  84 308  47
D1047V5, multiclass
    clus
vv   POLQ MUTATED POLQ WILD-TYPE
  T1            1             16
  T2            8             84
  T3           21            308
  T4            3             47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  POLQ MUTATED    26   6   1
  POLQ WILD-TYPE 261 107  86
D1047V6, multiclass
    clus
vv   POLQ MUTATED POLQ WILD-TYPE
  N0           26            261
  N1            6            107
  N2            1             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1047V7, binary
                cls
clus               0   1
  POLQ MUTATED    23   3
  POLQ WILD-TYPE 352  62
[1] "tbl2"
                cls
clus             [,1] [,2]
  POLQ MUTATED     23    3
  POLQ WILD-TYPE  352   62
   clus
vv  POLQ MUTATED POLQ WILD-TYPE
  0           23            352
  1            3             62
[1] 2 2
[1] FALSE
D1047V8, binary
                cls
clus               0   1
  POLQ MUTATED    13  20
  POLQ WILD-TYPE 212 244
[1] "tbl2"
                cls
clus             [,1] [,2]
  POLQ MUTATED     13   20
  POLQ WILD-TYPE  212  244
        clus
vv       POLQ MUTATED POLQ WILD-TYPE
  FEMALE           13            212
  MALE             20            244
[1] 2 2
[1] FALSE
D1047V9, binary
                cls
clus               0   1
  POLQ MUTATED    27   1
  POLQ WILD-TYPE 323  21
[1] "tbl2"
                cls
clus             [,1] [,2]
  POLQ MUTATED     27    1
  POLQ WILD-TYPE  323   21
     clus
vv    POLQ MUTATED POLQ WILD-TYPE
  NO            27            323
  YES            1             21
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  POLQ MUTATED                     22                             8
  POLQ WILD-TYPE                  293                            39
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  POLQ MUTATED                       3                              0
  POLQ WILD-TYPE                   103                             10
D1047V10, multiclass
                                clus
vv                               POLQ MUTATED POLQ WILD-TYPE
  COLON ADENOCARCINOMA                     22            293
  COLON MUCINOUS ADENOCARCINOMA             8             39
  RECTAL ADENOCARCINOMA                     3            103
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  POLQ MUTATED    23   0   1   3
  POLQ WILD-TYPE 322   4  30  22
D1047V11, multiclass
    clus
vv   POLQ MUTATED POLQ WILD-TYPE
  R0           23            322
  R1            0              4
  R2            1             30
  RX            3             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1047V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  POLQ MUTATED                                  0     3
  POLQ WILD-TYPE                                1     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  POLQ MUTATED                           3    16
  POLQ WILD-TYPE                        19   210
D1047V13, multiclass
                                  clus
vv                                 POLQ MUTATED POLQ WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       3              8
  BLACK OR AFRICAN AMERICAN                   3             19
  WHITE                                      16            210
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1048) Variable = CLGN MUTATION ANALYSIS
D1048V1, survival
                sevent
clus2              0   1
  CLGN MUTATED    11   1
  CLGN WILD-TYPE 367  92
  CLGN MUTATED CLGN WILD-TYPE 
            12            459 
  CLGN MUTATED CLGN WILD-TYPE 
             1             92 
$`CLGN MUTATED`
TCGA-A6-4105 TCGA-A6-5660 TCGA-A6-5661 TCGA-AA-3510 TCGA-AA-3710 TCGA-AD-5900 
       14.53        29.19        33.53        63.98        26.99         0.07 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-CA-6717 TCGA-CM-4746 TCGA-AG-A002 TCGA-DC-6681 
       17.82        58.39        12.76        37.02        20.98         5.95 

$`CLGN WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 
       16.57        34.65        33.34        32.75        36.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 
       31.63        30.44        23.61        22.09        22.06        32.71 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       27.09        22.52         8.38        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 
       20.28         7.04         3.02         1.02        35.01         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AZ-4323 TCGA-AZ-4616 
       16.31         0.95        33.01        21.44         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.20        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4752 
        1.91       124.27        23.05        20.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6682 TCGA-DC-6683 
       13.97        27.95        10.98        19.99         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  CLGN MUTATED CLGN WILD-TYPE 
          0.07           0.00 
  CLGN MUTATED CLGN WILD-TYPE 
         63.98         148.01 
  CLGN MUTATED CLGN WILD-TYPE 
        23.985         20.120 
[1] "0.1 - 64.0 (24.0)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "2.5"
D1048V2, continuous
D1048V3, binary
                cls
clus               0   1
  CLGN MUTATED    11   2
  CLGN WILD-TYPE 355 117
[1] "tbl2"
                cls
clus             [,1] [,2]
  CLGN MUTATED     11    2
  CLGN WILD-TYPE  355  117
        clus
vv       CLGN MUTATED CLGN WILD-TYPE
  COLON            11            355
  RECTUM            2            117
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CLGN MUTATED         3        0        1         5         1         0
  CLGN WILD-TYPE      88        1       31       133         9         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CLGN MUTATED           0          0          1          1        0         1
  CLGN WILD-TYPE        24         11         58         41       48        17
                vv
clus             STAGE IVB
  CLGN MUTATED           0
  CLGN WILD-TYPE         1
D1048V4, multiclass
            clus
vv           CLGN MUTATED CLGN WILD-TYPE
  STAGE I               3             88
  STAGE IA              0              1
  STAGE II              1             31
  STAGE IIA             5            133
  STAGE IIB             1              9
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            1             58
  STAGE IIIC            1             41
  STAGE IV              0             48
  STAGE IVA             1             17
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  CLGN MUTATED     0   3   9   1
  CLGN WILD-TYPE  17  89 320  49
D1048V5, multiclass
    clus
vv   CLGN MUTATED CLGN WILD-TYPE
  T1            0             17
  T2            3             89
  T3            9            320
  T4            1             49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  CLGN MUTATED    10   1   2
  CLGN WILD-TYPE 277 112  85
D1048V6, multiclass
    clus
vv   CLGN MUTATED CLGN WILD-TYPE
  N0           10            277
  N1            1            112
  N2            2             85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1048V7, binary
                cls
clus               0   1
  CLGN MUTATED    10   1
  CLGN WILD-TYPE 365  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  CLGN MUTATED     10    1
  CLGN WILD-TYPE  365   64
   clus
vv  CLGN MUTATED CLGN WILD-TYPE
  0           10            365
  1            1             64
[1] 2 2
[1] FALSE
D1048V8, binary
                cls
clus               0   1
  CLGN MUTATED     5   8
  CLGN WILD-TYPE 220 256
[1] "tbl2"
                cls
clus             [,1] [,2]
  CLGN MUTATED      5    8
  CLGN WILD-TYPE  220  256
        clus
vv       CLGN MUTATED CLGN WILD-TYPE
  FEMALE            5            220
  MALE              8            256
[1] 2 2
[1] FALSE
D1048V9, binary
                cls
clus               0   1
  CLGN MUTATED    10   0
  CLGN WILD-TYPE 340  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  CLGN MUTATED     10    0
  CLGN WILD-TYPE  340   22
     clus
vv    CLGN MUTATED CLGN WILD-TYPE
  NO            10            340
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CLGN MUTATED                      9                             2
  CLGN WILD-TYPE                  306                            45
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CLGN MUTATED                       2                              0
  CLGN WILD-TYPE                   104                             10
D1048V10, multiclass
                                clus
vv                               CLGN MUTATED CLGN WILD-TYPE
  COLON ADENOCARCINOMA                      9            306
  COLON MUCINOUS ADENOCARCINOMA             2             45
  RECTAL ADENOCARCINOMA                     2            104
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  CLGN MUTATED     9   0   0   2
  CLGN WILD-TYPE 336   4  31  23
D1048V11, multiclass
    clus
vv   CLGN MUTATED CLGN WILD-TYPE
  R0            9            336
  R1            0              4
  R2            0             31
  RX            2             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1048V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CLGN MUTATED                                  0     1
  CLGN WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  CLGN MUTATED                           4     5
  CLGN WILD-TYPE                        18   221
D1048V13, multiclass
                                  clus
vv                                 CLGN MUTATED CLGN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   4             18
  WHITE                                       5            221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1049) Variable = EML4 MUTATION ANALYSIS
D1049V1, survival
                sevent
clus2              0   1
  EML4 MUTATED     8   1
  EML4 WILD-TYPE 370  92
  EML4 MUTATED EML4 WILD-TYPE 
             9            462 
  EML4 MUTATED EML4 WILD-TYPE 
             1             92 
$`EML4 MUTATED`
TCGA-AA-3697 TCGA-AA-3950 TCGA-AA-3977 TCGA-AU-3779 TCGA-AZ-4315 TCGA-CA-6717 
       85.05        24.00        25.02        14.50        58.39        12.76 
TCGA-D5-6540 TCGA-DM-A0X9 TCGA-F4-6459 
       16.14       119.70         8.61 

$`EML4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       19.00        36.00         5.03        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 
        2.01        12.99        24.00        33.01        26.01         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
        0.20        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07        12.20        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 
       15.12        17.85         4.80        17.13        12.49        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
       10.26        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
       60.79       117.07        98.24        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  EML4 MUTATED EML4 WILD-TYPE 
          8.61           0.00 
  EML4 MUTATED EML4 WILD-TYPE 
        119.70         148.01 
  EML4 MUTATED EML4 WILD-TYPE 
        24.000         20.155 
[1] "8.6 - 119.7 (24.0)" "0.0 - 148.0 (20.2)"
[1] "hr=" "2.7"
D1049V2, continuous
D1049V3, binary
                cls
clus               0   1
  EML4 MUTATED    10   0
  EML4 WILD-TYPE 356 119
[1] "tbl2"
                cls
clus             [,1] [,2]
  EML4 MUTATED     10    0
  EML4 WILD-TYPE  356  119
        clus
vv       EML4 MUTATED EML4 WILD-TYPE
  COLON            10            356
  RECTUM            0            119
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  EML4 MUTATED         1        0        0         6         0         0
  EML4 WILD-TYPE      90        1       32       132        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  EML4 MUTATED           1          0          1          0        0         0
  EML4 WILD-TYPE        23         11         58         42       48        18
                vv
clus             STAGE IVB
  EML4 MUTATED           0
  EML4 WILD-TYPE         1
D1049V4, multiclass
            clus
vv           EML4 MUTATED EML4 WILD-TYPE
  STAGE I               1             90
  STAGE IA              0              1
  STAGE II              0             32
  STAGE IIA             6            132
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             1             23
  STAGE IIIA            0             11
  STAGE IIIB            1             58
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  EML4 MUTATED     0   2   8   0
  EML4 WILD-TYPE  17  90 321  50
D1049V5, multiclass
    clus
vv   EML4 MUTATED EML4 WILD-TYPE
  T1            0             17
  T2            2             90
  T3            8            321
  T4            0             50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  EML4 MUTATED     9   0   1
  EML4 WILD-TYPE 278 113  86
D1049V6, multiclass
    clus
vv   EML4 MUTATED EML4 WILD-TYPE
  N0            9            278
  N1            0            113
  N2            1             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1049V7, binary
                cls
clus               0   1
  EML4 MUTATED     9   0
  EML4 WILD-TYPE 366  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  EML4 MUTATED      9    0
  EML4 WILD-TYPE  366   65
   clus
vv  EML4 MUTATED EML4 WILD-TYPE
  0            9            366
  1            0             65
[1] 2 2
[1] FALSE
D1049V8, binary
                cls
clus               0   1
  EML4 MUTATED     5   5
  EML4 WILD-TYPE 220 259
[1] "tbl2"
                cls
clus             [,1] [,2]
  EML4 MUTATED      5    5
  EML4 WILD-TYPE  220  259
        clus
vv       EML4 MUTATED EML4 WILD-TYPE
  FEMALE            5            220
  MALE              5            259
[1] 2 2
[1] FALSE
D1049V9, binary
                cls
clus               0   1
  EML4 MUTATED     8   0
  EML4 WILD-TYPE 342  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  EML4 MUTATED      8    0
  EML4 WILD-TYPE  342   22
     clus
vv    EML4 MUTATED EML4 WILD-TYPE
  NO             8            342
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  EML4 MUTATED                      7                             3
  EML4 WILD-TYPE                  308                            44
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  EML4 MUTATED                       0                              0
  EML4 WILD-TYPE                   106                             10
D1049V10, multiclass
                                clus
vv                               EML4 MUTATED EML4 WILD-TYPE
  COLON ADENOCARCINOMA                      7            308
  COLON MUCINOUS ADENOCARCINOMA             3             44
  RECTAL ADENOCARCINOMA                     0            106
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  EML4 MUTATED     7   0   0   1
  EML4 WILD-TYPE 338   4  31  24
D1049V11, multiclass
    clus
vv   EML4 MUTATED EML4 WILD-TYPE
  R0            7            338
  R1            0              4
  R2            0             31
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1049V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  EML4 MUTATED                                  0     1
  EML4 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  EML4 MUTATED                           0     5
  EML4 WILD-TYPE                        22   221
D1049V13, multiclass
                                  clus
vv                                 EML4 MUTATED EML4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       5            221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1050) Variable = AP1G2 MUTATION ANALYSIS
D1050V1, survival
                 sevent
clus2               0   1
  AP1G2 MUTATED    14   1
  AP1G2 WILD-TYPE 364  92
  AP1G2 MUTATED AP1G2 WILD-TYPE 
             15             456 
  AP1G2 MUTATED AP1G2 WILD-TYPE 
              1              92 
$`AP1G2 MUTATED`
TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3518 TCGA-AA-3554 TCGA-AA-3672 TCGA-AA-3966 
       20.12        19.66         1.02        17.95         0.92         2.01 
TCGA-AA-3977 TCGA-AA-A00A TCGA-AA-A01P TCGA-CM-5348 TCGA-CM-5861 TCGA-D5-6536 
       25.02        38.04        38.07        22.98        15.02        17.85 
TCGA-G4-6299 TCGA-AG-A002 TCGA-EI-6507 
       74.56        20.98        19.96 

$`AP1G2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       23.87        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3519 
       63.98         6.97         1.02        13.02        38.99         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
       14.01        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 
       26.01        24.00         2.01        20.98        34.03        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        31.00         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 
       13.02        29.06        22.03        30.08        32.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       43.27        15.12         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
       35.31       133.18        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       20.55        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  AP1G2 MUTATED AP1G2 WILD-TYPE 
           0.92            0.00 
  AP1G2 MUTATED AP1G2 WILD-TYPE 
          74.56          148.01 
  AP1G2 MUTATED AP1G2 WILD-TYPE 
         19.960          20.415 
[1] "0.9 - 74.6 (20.0)"  "0.0 - 148.0 (20.4)"
[1] "hr=" "2.5"
D1050V2, continuous
D1050V3, binary
                 cls
clus                0   1
  AP1G2 MUTATED    13   2
  AP1G2 WILD-TYPE 353 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AP1G2 MUTATED     13    2
  AP1G2 WILD-TYPE  353  117
        clus
vv       AP1G2 MUTATED AP1G2 WILD-TYPE
  COLON             13             353
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  AP1G2 MUTATED         1        0        0         8         0         0
  AP1G2 WILD-TYPE      90        1       32       130        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AP1G2 MUTATED           2          0          1          2        0         0
  AP1G2 WILD-TYPE        22         11         58         40       48        18
                 vv
clus              STAGE IVB
  AP1G2 MUTATED           0
  AP1G2 WILD-TYPE         1
D1050V4, multiclass
            clus
vv           AP1G2 MUTATED AP1G2 WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              8             130
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              2              22
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             2              40
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  AP1G2 MUTATED     0   2  12   1
  AP1G2 WILD-TYPE  17  90 317  49
D1050V5, multiclass
    clus
vv   AP1G2 MUTATED AP1G2 WILD-TYPE
  T1             0              17
  T2             2              90
  T3            12             317
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  AP1G2 MUTATED    10   4   1
  AP1G2 WILD-TYPE 277 109  86
D1050V6, multiclass
    clus
vv   AP1G2 MUTATED AP1G2 WILD-TYPE
  N0            10             277
  N1             4             109
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1050V7, binary
                 cls
clus                0   1
  AP1G2 MUTATED    12   0
  AP1G2 WILD-TYPE 363  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AP1G2 MUTATED     12    0
  AP1G2 WILD-TYPE  363   65
   clus
vv  AP1G2 MUTATED AP1G2 WILD-TYPE
  0            12             363
  1             0              65
[1] 2 2
[1] FALSE
D1050V8, binary
                 cls
clus                0   1
  AP1G2 MUTATED     6   9
  AP1G2 WILD-TYPE 219 255
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AP1G2 MUTATED      6    9
  AP1G2 WILD-TYPE  219  255
        clus
vv       AP1G2 MUTATED AP1G2 WILD-TYPE
  FEMALE             6             219
  MALE               9             255
[1] 2 2
[1] FALSE
D1050V9, binary
                 cls
clus                0   1
  AP1G2 MUTATED    13   0
  AP1G2 WILD-TYPE 337  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AP1G2 MUTATED     13    0
  AP1G2 WILD-TYPE  337   22
     clus
vv    AP1G2 MUTATED AP1G2 WILD-TYPE
  NO             13             337
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  AP1G2 MUTATED                     10                             3
  AP1G2 WILD-TYPE                  305                            44
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  AP1G2 MUTATED                       2                              0
  AP1G2 WILD-TYPE                   104                             10
D1050V10, multiclass
                                clus
vv                               AP1G2 MUTATED AP1G2 WILD-TYPE
  COLON ADENOCARCINOMA                      10             305
  COLON MUCINOUS ADENOCARCINOMA              3              44
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  AP1G2 MUTATED    12   0   0   0
  AP1G2 WILD-TYPE 333   4  31  25
D1050V11, multiclass
    clus
vv   AP1G2 MUTATED AP1G2 WILD-TYPE
  R0            12             333
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1050V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AP1G2 MUTATED                                  0     0
  AP1G2 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  AP1G2 MUTATED                           0     7
  AP1G2 WILD-TYPE                        22   219
D1050V13, multiclass
                                  clus
vv                                 AP1G2 MUTATED AP1G2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        7             219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1051) Variable = CD3D MUTATION ANALYSIS
D1051V1, survival
                sevent
clus2              0   1
  CD3D MUTATED     3   2
  CD3D WILD-TYPE 375  91
  CD3D MUTATED CD3D WILD-TYPE 
             5            466 
  CD3D MUTATED CD3D WILD-TYPE 
             2             91 
$`CD3D MUTATED`
TCGA-A6-5657 TCGA-AA-A00N TCGA-AZ-6608 TCGA-CA-5254 TCGA-AH-6544 
       31.63         4.01         1.61        12.69        38.56 

$`CD3D WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  CD3D MUTATED CD3D WILD-TYPE 
          1.61           0.00 
  CD3D MUTATED CD3D WILD-TYPE 
         38.56         148.01 
  CD3D MUTATED CD3D WILD-TYPE 
        12.690         20.235 
[1] "1.6 - 38.6 (12.7)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "3.2"
D1051V2, continuous
D1051V3, binary
                cls
clus               0   1
  CD3D MUTATED     4   1
  CD3D WILD-TYPE 362 118
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD3D MUTATED      4    1
  CD3D WILD-TYPE  362  118
        clus
vv       CD3D MUTATED CD3D WILD-TYPE
  COLON             4            362
  RECTUM            1            118
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CD3D MUTATED         0        0        0         1         1         0
  CD3D WILD-TYPE      91        1       32       137         9         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CD3D MUTATED           0          1          1          0        0         0
  CD3D WILD-TYPE        24         10         58         42       48        18
                vv
clus             STAGE IVB
  CD3D MUTATED           0
  CD3D WILD-TYPE         1
D1051V4, multiclass
            clus
vv           CD3D MUTATED CD3D WILD-TYPE
  STAGE I               0             91
  STAGE IA              0              1
  STAGE II              0             32
  STAGE IIA             1            137
  STAGE IIB             1              9
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            1             10
  STAGE IIIB            1             58
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  CD3D MUTATED     0   1   3   1
  CD3D WILD-TYPE  17  91 326  49
D1051V5, multiclass
    clus
vv   CD3D MUTATED CD3D WILD-TYPE
  T1            0             17
  T2            1             91
  T3            3            326
  T4            1             49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  CD3D MUTATED     2   3   0
  CD3D WILD-TYPE 285 110  87
D1051V6, multiclass
    clus
vv   CD3D MUTATED CD3D WILD-TYPE
  N0            2            285
  N1            3            110
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1051V7, binary
                cls
clus               0   1
  CD3D MUTATED     4   1
  CD3D WILD-TYPE 371  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD3D MUTATED      4    1
  CD3D WILD-TYPE  371   64
   clus
vv  CD3D MUTATED CD3D WILD-TYPE
  0            4            371
  1            1             64
[1] 2 2
[1] FALSE
D1051V8, binary
                cls
clus               0   1
  CD3D MUTATED     2   3
  CD3D WILD-TYPE 223 261
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD3D MUTATED      2    3
  CD3D WILD-TYPE  223  261
        clus
vv       CD3D MUTATED CD3D WILD-TYPE
  FEMALE            2            223
  MALE              3            261
[1] 2 2
[1] FALSE
D1051V9, binary
                cls
clus               0   1
  CD3D MUTATED     4   0
  CD3D WILD-TYPE 346  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD3D MUTATED      4    0
  CD3D WILD-TYPE  346   22
     clus
vv    CD3D MUTATED CD3D WILD-TYPE
  NO             4            346
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CD3D MUTATED                      3                             1
  CD3D WILD-TYPE                  312                            46
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CD3D MUTATED                       1                              0
  CD3D WILD-TYPE                   105                             10
D1051V10, multiclass
                                clus
vv                               CD3D MUTATED CD3D WILD-TYPE
  COLON ADENOCARCINOMA                      3            312
  COLON MUCINOUS ADENOCARCINOMA             1             46
  RECTAL ADENOCARCINOMA                     1            105
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  CD3D MUTATED     2   0   0   1
  CD3D WILD-TYPE 343   4  31  24
D1051V11, multiclass
    clus
vv   CD3D MUTATED CD3D WILD-TYPE
  R0            2            343
  R1            0              4
  R2            0             31
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1051V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CD3D MUTATED                                  0     1
  CD3D WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  CD3D MUTATED                           1     2
  CD3D WILD-TYPE                        21   224
D1051V13, multiclass
                                  clus
vv                                 CD3D MUTATED CD3D WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                       2            224
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1052) Variable = CCDC69 MUTATION ANALYSIS
D1052V1, survival
                  sevent
clus2                0   1
  CCDC69 MUTATED     5   0
  CCDC69 WILD-TYPE 373  93
  CCDC69 MUTATED CCDC69 WILD-TYPE 
               5              466 
  CCDC69 MUTATED CCDC69 WILD-TYPE 
               0               93 
$`CCDC69 MUTATED`
TCGA-CM-4746 TCGA-D5-6922 TCGA-AG-A002 TCGA-DC-6682 TCGA-EI-6510 
       37.02         4.41        20.98         4.01        18.28 

$`CCDC69 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       20.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        1.48         3.68        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        5.95         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       20.91         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  CCDC69 MUTATED CCDC69 WILD-TYPE 
            4.01             0.00 
  CCDC69 MUTATED CCDC69 WILD-TYPE 
           37.02           148.01 
  CCDC69 MUTATED CCDC69 WILD-TYPE 
          18.280           20.235 
[1] "4.0 - 37.0 (18.3)"  "0.0 - 148.0 (20.2)"
[1] "hr="     "3300000"
D1052V2, continuous
D1052V3, binary
                  cls
clus                 0   1
  CCDC69 MUTATED     2   3
  CCDC69 WILD-TYPE 364 116
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC69 MUTATED      2    3
  CCDC69 WILD-TYPE  364  116
        clus
vv       CCDC69 MUTATED CCDC69 WILD-TYPE
  COLON               2              364
  RECTUM              3              116
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CCDC69 MUTATED         2        0        0         1         0         0
  CCDC69 WILD-TYPE      89        1       32       137        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CCDC69 MUTATED           0          1          0          0        0
  CCDC69 WILD-TYPE        24         10         59         42       48
                  vv
clus               STAGE IVA STAGE IVB
  CCDC69 MUTATED           1         0
  CCDC69 WILD-TYPE        17         1
D1052V4, multiclass
            clus
vv           CCDC69 MUTATED CCDC69 WILD-TYPE
  STAGE I                 2               89
  STAGE IA                0                1
  STAGE II                0               32
  STAGE IIA               1              137
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              1               10
  STAGE IIIB              0               59
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               1               17
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  CCDC69 MUTATED     0   3   2   0
  CCDC69 WILD-TYPE  17  89 327  50
D1052V5, multiclass
    clus
vv   CCDC69 MUTATED CCDC69 WILD-TYPE
  T1              0               17
  T2              3               89
  T3              2              327
  T4              0               50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  CCDC69 MUTATED     4   1   0
  CCDC69 WILD-TYPE 283 112  87
D1052V6, multiclass
    clus
vv   CCDC69 MUTATED CCDC69 WILD-TYPE
  N0              4              283
  N1              1              112
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1052V7, binary
                  cls
clus                 0   1
  CCDC69 MUTATED     4   0
  CCDC69 WILD-TYPE 371  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC69 MUTATED      4    0
  CCDC69 WILD-TYPE  371   65
   clus
vv  CCDC69 MUTATED CCDC69 WILD-TYPE
  0              4              371
  1              0               65
[1] 2 2
[1] FALSE
D1052V8, binary
                  cls
clus                 0   1
  CCDC69 MUTATED     1   4
  CCDC69 WILD-TYPE 224 260
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC69 MUTATED      1    4
  CCDC69 WILD-TYPE  224  260
        clus
vv       CCDC69 MUTATED CCDC69 WILD-TYPE
  FEMALE              1              224
  MALE                4              260
[1] 2 2
[1] FALSE
D1052V9, binary
                  cls
clus                 0   1
  CCDC69 MUTATED     3   0
  CCDC69 WILD-TYPE 347  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC69 MUTATED      3    0
  CCDC69 WILD-TYPE  347   22
     clus
vv    CCDC69 MUTATED CCDC69 WILD-TYPE
  NO               3              347
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CCDC69 MUTATED                      2                             0
  CCDC69 WILD-TYPE                  313                            47
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CCDC69 MUTATED                       3                              0
  CCDC69 WILD-TYPE                   103                             10
D1052V10, multiclass
                                clus
vv                               CCDC69 MUTATED CCDC69 WILD-TYPE
  COLON ADENOCARCINOMA                        2              313
  COLON MUCINOUS ADENOCARCINOMA               0               47
  RECTAL ADENOCARCINOMA                       3              103
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  CCDC69 MUTATED     5   0   0   0
  CCDC69 WILD-TYPE 340   4  31  25
D1052V11, multiclass
    clus
vv   CCDC69 MUTATED CCDC69 WILD-TYPE
  R0              5              340
  R1              0                4
  R2              0               31
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1052V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CCDC69 MUTATED                                  0     0
  CCDC69 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  CCDC69 MUTATED                           1     3
  CCDC69 WILD-TYPE                        21   223
D1052V13, multiclass
                                  clus
vv                                 CCDC69 MUTATED CCDC69 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                         3              223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1053) Variable = NOL9 MUTATION ANALYSIS
D1053V1, survival
                sevent
clus2              0   1
  NOL9 MUTATED     7   0
  NOL9 WILD-TYPE 371  93
  NOL9 MUTATED NOL9 WILD-TYPE 
             7            464 
  NOL9 MUTATED NOL9 WILD-TYPE 
             0             93 
$`NOL9 MUTATED`
TCGA-AA-3982 TCGA-AA-A02F TCGA-CA-6719 TCGA-DM-A1HB TCGA-G4-6586 TCGA-G4-6588 
       27.02        39.98        14.30       135.65        35.80        26.17 
TCGA-G4-6628 
       79.69 

$`NOL9 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       24.00        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       51.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.20        12.76        10.06        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 
       12.59       140.38         7.50        44.32       131.51       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 
       36.00        22.09        13.78        91.79        46.75        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  NOL9 MUTATED NOL9 WILD-TYPE 
          14.3            0.0 
  NOL9 MUTATED NOL9 WILD-TYPE 
        135.65         148.01 
  NOL9 MUTATED NOL9 WILD-TYPE 
        35.800         20.035 
[1] "14.3 - 135.7 (35.8)" "0.0 - 148.0 (20.0)" 
[1] "hr="     "9300000"
D1053V2, continuous
D1053V3, binary
                cls
clus               0   1
  NOL9 MUTATED     7   0
  NOL9 WILD-TYPE 359 119
[1] "tbl2"
                cls
clus             [,1] [,2]
  NOL9 MUTATED      7    0
  NOL9 WILD-TYPE  359  119
        clus
vv       NOL9 MUTATED NOL9 WILD-TYPE
  COLON             7            359
  RECTUM            0            119
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NOL9 MUTATED         1        0        0         3         0         0
  NOL9 WILD-TYPE      90        1       32       135        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NOL9 MUTATED           0          0          2          0        1         0
  NOL9 WILD-TYPE        24         11         57         42       47        18
                vv
clus             STAGE IVB
  NOL9 MUTATED           0
  NOL9 WILD-TYPE         1
D1053V4, multiclass
            clus
vv           NOL9 MUTATED NOL9 WILD-TYPE
  STAGE I               1             90
  STAGE IA              0              1
  STAGE II              0             32
  STAGE IIA             3            135
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            2             57
  STAGE IIIC            0             42
  STAGE IV              1             47
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  NOL9 MUTATED     0   1   6   0
  NOL9 WILD-TYPE  17  91 323  50
D1053V5, multiclass
    clus
vv   NOL9 MUTATED NOL9 WILD-TYPE
  T1            0             17
  T2            1             91
  T3            6            323
  T4            0             50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  NOL9 MUTATED     4   3   0
  NOL9 WILD-TYPE 283 110  87
D1053V6, multiclass
    clus
vv   NOL9 MUTATED NOL9 WILD-TYPE
  N0            4            283
  N1            3            110
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1053V7, binary
                cls
clus               0   1
  NOL9 MUTATED     6   1
  NOL9 WILD-TYPE 369  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  NOL9 MUTATED      6    1
  NOL9 WILD-TYPE  369   64
   clus
vv  NOL9 MUTATED NOL9 WILD-TYPE
  0            6            369
  1            1             64
[1] 2 2
[1] FALSE
D1053V8, binary
                cls
clus               0   1
  NOL9 MUTATED     3   4
  NOL9 WILD-TYPE 222 260
[1] "tbl2"
                cls
clus             [,1] [,2]
  NOL9 MUTATED      3    4
  NOL9 WILD-TYPE  222  260
        clus
vv       NOL9 MUTATED NOL9 WILD-TYPE
  FEMALE            3            222
  MALE              4            260
[1] 2 2
[1] FALSE
D1053V9, binary
                cls
clus               0   1
  NOL9 MUTATED     6   0
  NOL9 WILD-TYPE 344  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  NOL9 MUTATED      6    0
  NOL9 WILD-TYPE  344   22
     clus
vv    NOL9 MUTATED NOL9 WILD-TYPE
  NO             6            344
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  NOL9 MUTATED                      6                             0
  NOL9 WILD-TYPE                  309                            47
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  NOL9 MUTATED                       0                              0
  NOL9 WILD-TYPE                   106                             10
D1053V10, multiclass
                                clus
vv                               NOL9 MUTATED NOL9 WILD-TYPE
  COLON ADENOCARCINOMA                      6            309
  COLON MUCINOUS ADENOCARCINOMA             0             47
  RECTAL ADENOCARCINOMA                     0            106
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  NOL9 MUTATED     3   0   1   1
  NOL9 WILD-TYPE 342   4  30  24
D1053V11, multiclass
    clus
vv   NOL9 MUTATED NOL9 WILD-TYPE
  R0            3            342
  R1            0              4
  R2            1             30
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1053V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NOL9 MUTATED                                  0     1
  NOL9 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  NOL9 MUTATED                           0     4
  NOL9 WILD-TYPE                        22   222
D1053V13, multiclass
                                  clus
vv                                 NOL9 MUTATED NOL9 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       4            222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1054) Variable = DSC2 MUTATION ANALYSIS
D1054V1, survival
                sevent
clus2              0   1
  DSC2 MUTATED    11   4
  DSC2 WILD-TYPE 367  89
  DSC2 MUTATED DSC2 WILD-TYPE 
            15            456 
  DSC2 MUTATED DSC2 WILD-TYPE 
             4             89 
$`DSC2 MUTATED`
TCGA-A6-2672 TCGA-A6-5666 TCGA-A6-6142 TCGA-AA-3662 TCGA-AA-A00N TCGA-AZ-4315 
       46.65        32.71        25.08         6.05         4.01        58.39 
TCGA-AZ-6598 TCGA-AZ-6601 TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-4746 TCGA-CM-6161 
       49.41       100.01        12.76        10.06        37.02        15.02 
TCGA-D5-6540 TCGA-DM-A0X9 TCGA-AF-2693 
       16.14       119.70        19.10 

$`DSC2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6649 
       22.06        27.09        22.52         8.38        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02        78.08         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77        12.10        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       12.20        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
      124.27        23.05        20.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        15.02        17.03        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 
       15.12        17.85         4.80        17.13        12.49        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
       10.26        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       43.04        13.55        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  DSC2 MUTATED DSC2 WILD-TYPE 
          4.01           0.00 
  DSC2 MUTATED DSC2 WILD-TYPE 
        119.70         148.01 
  DSC2 MUTATED DSC2 WILD-TYPE 
        25.080         20.155 
[1] "4.0 - 119.7 (25.1)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1"  
D1054V2, continuous
D1054V3, binary
                cls
clus               0   1
  DSC2 MUTATED    14   0
  DSC2 WILD-TYPE 352 119
[1] "tbl2"
                cls
clus             [,1] [,2]
  DSC2 MUTATED     14    0
  DSC2 WILD-TYPE  352  119
        clus
vv       DSC2 MUTATED DSC2 WILD-TYPE
  COLON            14            352
  RECTUM            0            119
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DSC2 MUTATED         4        0        2         4         1         1
  DSC2 WILD-TYPE      87        1       30       134         9         0
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DSC2 MUTATED           0          0          1          0        1         1
  DSC2 WILD-TYPE        24         11         58         42       47        17
                vv
clus             STAGE IVB
  DSC2 MUTATED           0
  DSC2 WILD-TYPE         1
D1054V4, multiclass
            clus
vv           DSC2 MUTATED DSC2 WILD-TYPE
  STAGE I               4             87
  STAGE IA              0              1
  STAGE II              2             30
  STAGE IIA             4            134
  STAGE IIB             1              9
  STAGE IIC             1              0
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            1             58
  STAGE IIIC            0             42
  STAGE IV              1             47
  STAGE IVA             1             17
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  DSC2 MUTATED     0   4   8   3
  DSC2 WILD-TYPE  17  88 321  47
D1054V5, multiclass
    clus
vv   DSC2 MUTATED DSC2 WILD-TYPE
  T1            0             17
  T2            4             88
  T3            8            321
  T4            3             47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  DSC2 MUTATED    12   2   1
  DSC2 WILD-TYPE 275 111  86
D1054V6, multiclass
    clus
vv   DSC2 MUTATED DSC2 WILD-TYPE
  N0           12            275
  N1            2            111
  N2            1             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1054V7, binary
                cls
clus               0   1
  DSC2 MUTATED    11   2
  DSC2 WILD-TYPE 364  63
[1] "tbl2"
                cls
clus             [,1] [,2]
  DSC2 MUTATED     11    2
  DSC2 WILD-TYPE  364   63
   clus
vv  DSC2 MUTATED DSC2 WILD-TYPE
  0           11            364
  1            2             63
[1] 2 2
[1] FALSE
D1054V8, binary
                cls
clus               0   1
  DSC2 MUTATED     6   9
  DSC2 WILD-TYPE 219 255
[1] "tbl2"
                cls
clus             [,1] [,2]
  DSC2 MUTATED      6    9
  DSC2 WILD-TYPE  219  255
        clus
vv       DSC2 MUTATED DSC2 WILD-TYPE
  FEMALE            6            219
  MALE              9            255
[1] 2 2
[1] FALSE
D1054V9, binary
                cls
clus               0   1
  DSC2 MUTATED    13   0
  DSC2 WILD-TYPE 337  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  DSC2 MUTATED     13    0
  DSC2 WILD-TYPE  337   22
     clus
vv    DSC2 MUTATED DSC2 WILD-TYPE
  NO            13            337
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  DSC2 MUTATED                     11                             3
  DSC2 WILD-TYPE                  304                            44
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  DSC2 MUTATED                       0                              0
  DSC2 WILD-TYPE                   106                             10
D1054V10, multiclass
                                clus
vv                               DSC2 MUTATED DSC2 WILD-TYPE
  COLON ADENOCARCINOMA                     11            304
  COLON MUCINOUS ADENOCARCINOMA             3             44
  RECTAL ADENOCARCINOMA                     0            106
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  DSC2 MUTATED     6   0   1   2
  DSC2 WILD-TYPE 339   4  30  23
D1054V11, multiclass
    clus
vv   DSC2 MUTATED DSC2 WILD-TYPE
  R0            6            339
  R1            0              4
  R2            1             30
  RX            2             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1054V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DSC2 MUTATED                                  0     2
  DSC2 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  DSC2 MUTATED                           1    10
  DSC2 WILD-TYPE                        21   216
D1054V13, multiclass
                                  clus
vv                                 DSC2 MUTATED DSC2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              9
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                      10            216
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1055) Variable = AGTPBP1 MUTATION ANALYSIS
D1055V1, survival
                   sevent
clus2                 0   1
  AGTPBP1 MUTATED    17   3
  AGTPBP1 WILD-TYPE 361  90
  AGTPBP1 MUTATED AGTPBP1 WILD-TYPE 
               20               451 
  AGTPBP1 MUTATED AGTPBP1 WILD-TYPE 
                3                90 
$`AGTPBP1 MUTATED`
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5666 TCGA-A6-6649 TCGA-A6-6780 TCGA-AA-3510 
       33.53        23.61        32.71        24.16        20.12        63.98 
TCGA-AA-A00J TCGA-AA-A02J TCGA-AD-6964 TCGA-AY-6197 TCGA-AZ-4315 TCGA-CA-6717 
       18.05         5.03        10.88        21.44        58.39        12.76 
TCGA-CM-5349 TCGA-D5-6534 TCGA-DM-A1HA TCGA-F4-6570 TCGA-AF-2693 TCGA-AG-3586 
       30.08        43.27       131.51         6.18        19.10         1.02 
TCGA-AG-A002 TCGA-F5-6813 
       20.98         0.69 

$`AGTPBP1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5664 TCGA-A6-5665 
       32.91        31.63        30.44        29.19        22.09        22.06 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 
       27.09        22.52         8.38        25.08        25.18        21.76 
TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 
       24.69        24.39        23.87        19.66        20.28         7.04 
TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        3.02         1.02        35.01         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       51.98        39.98         2.01        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07        12.20        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       22.98        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6536 
       55.92        20.19        18.25         1.32        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HB 
       13.32        12.59       140.38         7.50        44.32       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 
      117.07        98.24         8.61        31.96        35.74        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       36.03        20.05        24.00        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-G5-6235 
       49.51        31.30        28.57        32.19         0.66        55.76 
TCGA-G5-6641 
       26.43 

  AGTPBP1 MUTATED AGTPBP1 WILD-TYPE 
             0.69              0.00 
  AGTPBP1 MUTATED AGTPBP1 WILD-TYPE 
           131.51            148.01 
  AGTPBP1 MUTATED AGTPBP1 WILD-TYPE 
            21.21             20.05 
[1] "0.7 - 131.5 (21.2)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.4"
D1055V2, continuous
D1055V3, binary
                   cls
clus                  0   1
  AGTPBP1 MUTATED    17   3
  AGTPBP1 WILD-TYPE 349 116
[1] "tbl2"
                   cls
clus                [,1] [,2]
  AGTPBP1 MUTATED     17    3
  AGTPBP1 WILD-TYPE  349  116
        clus
vv       AGTPBP1 MUTATED AGTPBP1 WILD-TYPE
  COLON               17               349
  RECTUM               3               116
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  AGTPBP1 MUTATED         2        0        2         8         0         1
  AGTPBP1 WILD-TYPE      89        1       30       130        10         0
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  AGTPBP1 MUTATED           1          0          2          2        1
  AGTPBP1 WILD-TYPE        23         11         57         40       47
                   vv
clus                STAGE IVA STAGE IVB
  AGTPBP1 MUTATED           1         0
  AGTPBP1 WILD-TYPE        17         1
D1055V4, multiclass
            clus
vv           AGTPBP1 MUTATED AGTPBP1 WILD-TYPE
  STAGE I                  2                89
  STAGE IA                 0                 1
  STAGE II                 2                30
  STAGE IIA                8               130
  STAGE IIB                0                10
  STAGE IIC                1                 0
  STAGE III                1                23
  STAGE IIIA               0                11
  STAGE IIIB               2                57
  STAGE IIIC               2                40
  STAGE IV                 1                47
  STAGE IVA                1                17
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  AGTPBP1 MUTATED     0   2  14   5
  AGTPBP1 WILD-TYPE  17  90 315  45
D1055V5, multiclass
    clus
vv   AGTPBP1 MUTATED AGTPBP1 WILD-TYPE
  T1               0                17
  T2               2                90
  T3              14               315
  T4               5                45
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  AGTPBP1 MUTATED    14   2   5
  AGTPBP1 WILD-TYPE 273 111  82
D1055V6, multiclass
    clus
vv   AGTPBP1 MUTATED AGTPBP1 WILD-TYPE
  N0              14               273
  N1               2               111
  N2               5                82
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1055V7, binary
                   cls
clus                  0   1
  AGTPBP1 MUTATED    15   2
  AGTPBP1 WILD-TYPE 360  63
[1] "tbl2"
                   cls
clus                [,1] [,2]
  AGTPBP1 MUTATED     15    2
  AGTPBP1 WILD-TYPE  360   63
   clus
vv  AGTPBP1 MUTATED AGTPBP1 WILD-TYPE
  0              15               360
  1               2                63
[1] 2 2
[1] FALSE
D1055V8, binary
                   cls
clus                  0   1
  AGTPBP1 MUTATED     7  14
  AGTPBP1 WILD-TYPE 218 250
[1] "tbl2"
                   cls
clus                [,1] [,2]
  AGTPBP1 MUTATED      7   14
  AGTPBP1 WILD-TYPE  218  250
        clus
vv       AGTPBP1 MUTATED AGTPBP1 WILD-TYPE
  FEMALE               7               218
  MALE                14               250
[1] 2 2
[1] FALSE
D1055V9, binary
                   cls
clus                  0   1
  AGTPBP1 MUTATED    16   0
  AGTPBP1 WILD-TYPE 334  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  AGTPBP1 MUTATED     16    0
  AGTPBP1 WILD-TYPE  334   22
     clus
vv    AGTPBP1 MUTATED AGTPBP1 WILD-TYPE
  NO               16               334
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  AGTPBP1 MUTATED                     13                             4
  AGTPBP1 WILD-TYPE                  302                            43
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  AGTPBP1 MUTATED                       2                              0
  AGTPBP1 WILD-TYPE                   104                             10
D1055V10, multiclass
                                clus
vv                               AGTPBP1 MUTATED AGTPBP1 WILD-TYPE
  COLON ADENOCARCINOMA                        13               302
  COLON MUCINOUS ADENOCARCINOMA                4                43
  RECTAL ADENOCARCINOMA                        2               104
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  AGTPBP1 MUTATED    12   0   1   1
  AGTPBP1 WILD-TYPE 333   4  30  24
D1055V11, multiclass
    clus
vv   AGTPBP1 MUTATED AGTPBP1 WILD-TYPE
  R0              12               333
  R1               0                 4
  R2               1                30
  RX               1                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1055V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AGTPBP1 MUTATED                                  0     1
  AGTPBP1 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  AGTPBP1 MUTATED                           1    13
  AGTPBP1 WILD-TYPE                        21   213
D1055V13, multiclass
                                  clus
vv                                 AGTPBP1 MUTATED AGTPBP1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                10
  BLACK OR AFRICAN AMERICAN                      1                21
  WHITE                                         13               213
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1056) Variable = C18ORF19 MUTATION ANALYSIS
D1056V1, survival
                    sevent
clus2                  0   1
  C18ORF19 MUTATED     9   0
  C18ORF19 WILD-TYPE 369  93
  C18ORF19 MUTATED C18ORF19 WILD-TYPE 
                 9                462 
  C18ORF19 MUTATED C18ORF19 WILD-TYPE 
                 0                 93 
$`C18ORF19 MUTATED`
TCGA-A6-6654 TCGA-AA-3710 TCGA-AA-3821 TCGA-AA-A00J TCGA-AD-6889 TCGA-AY-5543 
       23.87        26.99         1.02        18.05        56.55        33.01 
TCGA-CM-5349 TCGA-D5-6930 TCGA-AG-A002 
       30.08         1.51        20.98 

$`C18ORF19 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        85.05        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 
       35.05        33.04         0.99        25.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 
       40.96         0.07        21.37        15.52         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       27.09        16.31         0.95        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       22.98        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
        9.44        11.64         4.80        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  C18ORF19 MUTATED C18ORF19 WILD-TYPE 
              1.02               0.00 
  C18ORF19 MUTATED C18ORF19 WILD-TYPE 
             56.55             148.01 
  C18ORF19 MUTATED C18ORF19 WILD-TYPE 
            23.870             20.085 
[1] "1.0 - 56.5 (23.9)"  "0.0 - 148.0 (20.1)"
[1] "hr="     "9200000"
D1056V2, continuous
D1056V3, binary
                    cls
clus                   0   1
  C18ORF19 MUTATED     8   1
  C18ORF19 WILD-TYPE 358 118
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C18ORF19 MUTATED      8    1
  C18ORF19 WILD-TYPE  358  118
        clus
vv       C18ORF19 MUTATED C18ORF19 WILD-TYPE
  COLON                 8                358
  RECTUM                1                118
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  C18ORF19 MUTATED         2        0        0         4         0         0
  C18ORF19 WILD-TYPE      89        1       32       134        10         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C18ORF19 MUTATED           0          0          2          0        0
  C18ORF19 WILD-TYPE        24         11         57         42       48
                    vv
clus                 STAGE IVA STAGE IVB
  C18ORF19 MUTATED           1         0
  C18ORF19 WILD-TYPE        17         1
D1056V4, multiclass
            clus
vv           C18ORF19 MUTATED C18ORF19 WILD-TYPE
  STAGE I                   2                 89
  STAGE IA                  0                  1
  STAGE II                  0                 32
  STAGE IIA                 4                134
  STAGE IIB                 0                 10
  STAGE IIC                 0                  1
  STAGE III                 0                 24
  STAGE IIIA                0                 11
  STAGE IIIB                2                 57
  STAGE IIIC                0                 42
  STAGE IV                  0                 48
  STAGE IVA                 1                 17
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  C18ORF19 MUTATED     0   2   6   1
  C18ORF19 WILD-TYPE  17  90 323  49
D1056V5, multiclass
    clus
vv   C18ORF19 MUTATED C18ORF19 WILD-TYPE
  T1                0                 17
  T2                2                 90
  T3                6                323
  T4                1                 49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  C18ORF19 MUTATED     6   3   0
  C18ORF19 WILD-TYPE 281 110  87
D1056V6, multiclass
    clus
vv   C18ORF19 MUTATED C18ORF19 WILD-TYPE
  N0                6                281
  N1                3                110
  N2                0                 87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1056V7, binary
                    cls
clus                   0   1
  C18ORF19 MUTATED     8   1
  C18ORF19 WILD-TYPE 367  64
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C18ORF19 MUTATED      8    1
  C18ORF19 WILD-TYPE  367   64
   clus
vv  C18ORF19 MUTATED C18ORF19 WILD-TYPE
  0                8                367
  1                1                 64
[1] 2 2
[1] FALSE
D1056V8, binary
                    cls
clus                   0   1
  C18ORF19 MUTATED     5   4
  C18ORF19 WILD-TYPE 220 260
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C18ORF19 MUTATED      5    4
  C18ORF19 WILD-TYPE  220  260
        clus
vv       C18ORF19 MUTATED C18ORF19 WILD-TYPE
  FEMALE                5                220
  MALE                  4                260
[1] 2 2
[1] FALSE
D1056V9, binary
                    cls
clus                   0   1
  C18ORF19 MUTATED     7   0
  C18ORF19 WILD-TYPE 343  22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C18ORF19 MUTATED      7    0
  C18ORF19 WILD-TYPE  343   22
     clus
vv    C18ORF19 MUTATED C18ORF19 WILD-TYPE
  NO                 7                343
  YES                0                 22
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  C18ORF19 MUTATED                      5                             3
  C18ORF19 WILD-TYPE                  310                            44
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  C18ORF19 MUTATED                       1                              0
  C18ORF19 WILD-TYPE                   105                             10
D1056V10, multiclass
                                clus
vv                               C18ORF19 MUTATED C18ORF19 WILD-TYPE
  COLON ADENOCARCINOMA                          5                310
  COLON MUCINOUS ADENOCARCINOMA                 3                 44
  RECTAL ADENOCARCINOMA                         1                105
  RECTAL MUCINOUS ADENOCARCINOMA                0                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  C18ORF19 MUTATED     7   0   0   0
  C18ORF19 WILD-TYPE 338   4  31  25
D1056V11, multiclass
    clus
vv   C18ORF19 MUTATED C18ORF19 WILD-TYPE
  R0                7                338
  R1                0                  4
  R2                0                 31
  RX                0                 25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1056V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C18ORF19 MUTATED                                  0     1
  C18ORF19 WILD-TYPE                                1    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  C18ORF19 MUTATED                           1     3
  C18ORF19 WILD-TYPE                        21   223
D1056V13, multiclass
                                  clus
vv                                 C18ORF19 MUTATED C18ORF19 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                 10
  BLACK OR AFRICAN AMERICAN                       1                 21
  WHITE                                           3                223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1057) Variable = AWAT1 MUTATION ANALYSIS
D1057V1, survival
                 sevent
clus2               0   1
  AWAT1 MUTATED     8   1
  AWAT1 WILD-TYPE 370  92
  AWAT1 MUTATED AWAT1 WILD-TYPE 
              9             462 
  AWAT1 MUTATED AWAT1 WILD-TYPE 
              1              92 
$`AWAT1 MUTATED`
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-A024 TCGA-CA-6717 TCGA-D5-5540 TCGA-D5-6536 
       33.01        26.01        39.06        12.76        56.09        17.85 
TCGA-D5-6538 TCGA-G4-6588 TCGA-AG-A002 
       17.13        26.17        20.98 

$`AWAT1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3950 TCGA-AA-3952 
       31.00         2.01        12.99        24.00        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02F 
       33.04        35.01        26.01        37.02        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       12.26        19.59        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       43.27        15.12         4.80        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       35.80        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  AWAT1 MUTATED AWAT1 WILD-TYPE 
          12.76            0.00 
  AWAT1 MUTATED AWAT1 WILD-TYPE 
          56.09          148.01 
  AWAT1 MUTATED AWAT1 WILD-TYPE 
         26.010          20.085 
[1] "12.8 - 56.1 (26.0)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.9"
D1057V2, continuous
D1057V3, binary
                 cls
clus                0   1
  AWAT1 MUTATED     8   1
  AWAT1 WILD-TYPE 358 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AWAT1 MUTATED      8    1
  AWAT1 WILD-TYPE  358  118
        clus
vv       AWAT1 MUTATED AWAT1 WILD-TYPE
  COLON              8             358
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  AWAT1 MUTATED         1        0        1         4         1         0
  AWAT1 WILD-TYPE      90        1       31       134         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AWAT1 MUTATED           0          0          2          0        0         0
  AWAT1 WILD-TYPE        24         11         57         42       48        18
                 vv
clus              STAGE IVB
  AWAT1 MUTATED           0
  AWAT1 WILD-TYPE         1
D1057V4, multiclass
            clus
vv           AWAT1 MUTATED AWAT1 WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              4             134
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             2              57
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  AWAT1 MUTATED     0   1   7   1
  AWAT1 WILD-TYPE  17  91 322  49
D1057V5, multiclass
    clus
vv   AWAT1 MUTATED AWAT1 WILD-TYPE
  T1             0              17
  T2             1              91
  T3             7             322
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  AWAT1 MUTATED     7   1   1
  AWAT1 WILD-TYPE 280 112  86
D1057V6, multiclass
    clus
vv   AWAT1 MUTATED AWAT1 WILD-TYPE
  N0             7             280
  N1             1             112
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1057V7, binary
                 cls
clus                0   1
  AWAT1 MUTATED     9   0
  AWAT1 WILD-TYPE 366  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AWAT1 MUTATED      9    0
  AWAT1 WILD-TYPE  366   65
   clus
vv  AWAT1 MUTATED AWAT1 WILD-TYPE
  0             9             366
  1             0              65
[1] 2 2
[1] FALSE
D1057V8, binary
                 cls
clus                0   1
  AWAT1 MUTATED     4   5
  AWAT1 WILD-TYPE 221 259
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AWAT1 MUTATED      4    5
  AWAT1 WILD-TYPE  221  259
        clus
vv       AWAT1 MUTATED AWAT1 WILD-TYPE
  FEMALE             4             221
  MALE               5             259
[1] 2 2
[1] FALSE
D1057V9, binary
                 cls
clus                0   1
  AWAT1 MUTATED     9   0
  AWAT1 WILD-TYPE 341  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AWAT1 MUTATED      9    0
  AWAT1 WILD-TYPE  341   22
     clus
vv    AWAT1 MUTATED AWAT1 WILD-TYPE
  NO              9             341
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  AWAT1 MUTATED                      4                             4
  AWAT1 WILD-TYPE                  311                            43
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  AWAT1 MUTATED                       1                              0
  AWAT1 WILD-TYPE                   105                             10
D1057V10, multiclass
                                clus
vv                               AWAT1 MUTATED AWAT1 WILD-TYPE
  COLON ADENOCARCINOMA                       4             311
  COLON MUCINOUS ADENOCARCINOMA              4              43
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  AWAT1 MUTATED     8   0   0   1
  AWAT1 WILD-TYPE 337   4  31  24
D1057V11, multiclass
    clus
vv   AWAT1 MUTATED AWAT1 WILD-TYPE
  R0             8             337
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1057V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AWAT1 MUTATED                                  0     1
  AWAT1 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  AWAT1 MUTATED                           0     4
  AWAT1 WILD-TYPE                        22   222
D1057V13, multiclass
                                  clus
vv                                 AWAT1 MUTATED AWAT1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        4             222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1058) Variable = YSK4 MUTATION ANALYSIS
D1058V1, survival
                sevent
clus2              0   1
  YSK4 MUTATED    24   6
  YSK4 WILD-TYPE 354  87
  YSK4 MUTATED YSK4 WILD-TYPE 
            30            441 
  YSK4 MUTATED YSK4 WILD-TYPE 
             6             87 
$`YSK4 MUTATED`
TCGA-A6-6138 TCGA-A6-6653 TCGA-AA-3516 TCGA-AA-3555 TCGA-AA-3697 TCGA-AA-3713 
       22.52        24.39        13.02        29.95        85.05        19.04 
TCGA-AA-3715 TCGA-AA-3833 TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A010 TCGA-AD-6895 
       19.04        15.95        25.02         4.01        34.98         0.72 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AZ-4315 TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-4752 
       33.01        21.44        58.39        12.76        10.06        13.02 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6537 TCGA-D5-6540 TCGA-DM-A1D9 TCGA-DM-A28E 
       20.19        18.25         4.80        16.14       140.38       119.93 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AG-3892 TCGA-AG-4008 TCGA-AG-A002 TCGA-EI-6510 
       46.75        79.69        13.02        17.03        20.98        18.28 

$`YSK4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6141 TCGA-A6-6142 
       22.09        22.06        32.71        27.09         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 
       25.18        24.16        21.76        24.69        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
       63.98         6.97         1.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       17.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 
        5.98        37.05        19.00        36.00         5.03        26.99 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       17.98        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 
        0.07        21.37        15.52        56.55         0.79         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       16.31         0.95        17.82         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-5341 TCGA-CM-5344 
       23.05        20.02        37.02        25.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       56.09        55.92         1.32        43.27        15.12        17.85 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       17.13        12.49        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
       81.37        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-AF-2687 TCGA-AF-2689 
       13.78        35.80        26.17        91.79        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-A008 TCGA-AG-A00C 
       28.04        36.03        14.04         1.02        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  YSK4 MUTATED YSK4 WILD-TYPE 
          0.72           0.00 
  YSK4 MUTATED YSK4 WILD-TYPE 
        140.38         148.01 
  YSK4 MUTATED YSK4 WILD-TYPE 
        19.615         20.280 
[1] "0.7 - 140.4 (19.6)" "0.0 - 148.0 (20.3)"
[1] "hr=" "1.1"
D1058V2, continuous
D1058V3, binary
                cls
clus               0   1
  YSK4 MUTATED    26   4
  YSK4 WILD-TYPE 340 115
[1] "tbl2"
                cls
clus             [,1] [,2]
  YSK4 MUTATED     26    4
  YSK4 WILD-TYPE  340  115
        clus
vv       YSK4 MUTATED YSK4 WILD-TYPE
  COLON            26            340
  RECTUM            4            115
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  YSK4 MUTATED         6        0        1        13         2         0
  YSK4 WILD-TYPE      85        1       31       125         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  YSK4 MUTATED           2          0          1          0        1         2
  YSK4 WILD-TYPE        22         11         58         42       47        16
                vv
clus             STAGE IVB
  YSK4 MUTATED           0
  YSK4 WILD-TYPE         1
D1058V4, multiclass
            clus
vv           YSK4 MUTATED YSK4 WILD-TYPE
  STAGE I               6             85
  STAGE IA              0              1
  STAGE II              1             31
  STAGE IIA            13            125
  STAGE IIB             2              8
  STAGE IIC             0              1
  STAGE III             2             22
  STAGE IIIA            0             11
  STAGE IIIB            1             58
  STAGE IIIC            0             42
  STAGE IV              1             47
  STAGE IVA             2             16
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  YSK4 MUTATED     1   7  20   2
  YSK4 WILD-TYPE  16  85 309  48
D1058V5, multiclass
    clus
vv   YSK4 MUTATED YSK4 WILD-TYPE
  T1            1             16
  T2            7             85
  T3           20            309
  T4            2             48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  YSK4 MUTATED    26   3   1
  YSK4 WILD-TYPE 261 110  86
D1058V6, multiclass
    clus
vv   YSK4 MUTATED YSK4 WILD-TYPE
  N0           26            261
  N1            3            110
  N2            1             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1058V7, binary
                cls
clus               0   1
  YSK4 MUTATED    23   2
  YSK4 WILD-TYPE 352  63
[1] "tbl2"
                cls
clus             [,1] [,2]
  YSK4 MUTATED     23    2
  YSK4 WILD-TYPE  352   63
   clus
vv  YSK4 MUTATED YSK4 WILD-TYPE
  0           23            352
  1            2             63
[1] 2 2
[1] FALSE
D1058V8, binary
                cls
clus               0   1
  YSK4 MUTATED     9  21
  YSK4 WILD-TYPE 216 243
[1] "tbl2"
                cls
clus             [,1] [,2]
  YSK4 MUTATED      9   21
  YSK4 WILD-TYPE  216  243
        clus
vv       YSK4 MUTATED YSK4 WILD-TYPE
  FEMALE            9            216
  MALE             21            243
[1] 2 2
[1] FALSE
D1058V9, binary
                cls
clus               0   1
  YSK4 MUTATED    25   1
  YSK4 WILD-TYPE 325  21
[1] "tbl2"
                cls
clus             [,1] [,2]
  YSK4 MUTATED     25    1
  YSK4 WILD-TYPE  325   21
     clus
vv    YSK4 MUTATED YSK4 WILD-TYPE
  NO            25            325
  YES            1             21
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  YSK4 MUTATED                     21                             5
  YSK4 WILD-TYPE                  294                            42
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  YSK4 MUTATED                       4                              0
  YSK4 WILD-TYPE                   102                             10
D1058V10, multiclass
                                clus
vv                               YSK4 MUTATED YSK4 WILD-TYPE
  COLON ADENOCARCINOMA                     21            294
  COLON MUCINOUS ADENOCARCINOMA             5             42
  RECTAL ADENOCARCINOMA                     4            102
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  YSK4 MUTATED    20   0   1   2
  YSK4 WILD-TYPE 325   4  30  23
D1058V11, multiclass
    clus
vv   YSK4 MUTATED YSK4 WILD-TYPE
  R0           20            325
  R1            0              4
  R2            1             30
  RX            2             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1058V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  YSK4 MUTATED                                  0     2
  YSK4 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  YSK4 MUTATED                           2    14
  YSK4 WILD-TYPE                        20   212
D1058V13, multiclass
                                  clus
vv                                 YSK4 MUTATED YSK4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              9
  BLACK OR AFRICAN AMERICAN                   2             20
  WHITE                                      14            212
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1059) Variable = GSTA5 MUTATION ANALYSIS
D1059V1, survival
                 sevent
clus2               0   1
  GSTA5 MUTATED     7   1
  GSTA5 WILD-TYPE 371  92
  GSTA5 MUTATED GSTA5 WILD-TYPE 
              8             463 
  GSTA5 MUTATED GSTA5 WILD-TYPE 
              1              92 
$`GSTA5 MUTATED`
TCGA-AA-3697 TCGA-AA-3977 TCGA-AZ-4315 TCGA-CM-5348 TCGA-D5-6534 TCGA-G4-6303 
       85.05        25.02        58.39        22.98        43.27        65.85 
TCGA-AG-3892 TCGA-AH-6644 
       13.02         0.72 

$`GSTA5 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       19.00        36.00         5.03        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       33.01        21.44        17.82         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       13.02        29.06        22.03        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
        1.32        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6304 TCGA-G4-6306 
       47.41        35.31       133.18        74.56        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       36.95        17.03        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.69         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  GSTA5 MUTATED GSTA5 WILD-TYPE 
           0.72            0.00 
  GSTA5 MUTATED GSTA5 WILD-TYPE 
          85.05          148.01 
  GSTA5 MUTATED GSTA5 WILD-TYPE 
         34.145          20.050 
[1] "0.7 - 85.0 (34.1)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "2.5"
D1059V2, continuous
D1059V3, binary
                 cls
clus                0   1
  GSTA5 MUTATED     6   2
  GSTA5 WILD-TYPE 360 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GSTA5 MUTATED      6    2
  GSTA5 WILD-TYPE  360  117
        clus
vv       GSTA5 MUTATED GSTA5 WILD-TYPE
  COLON              6             360
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GSTA5 MUTATED         1        0        0         2         0         0
  GSTA5 WILD-TYPE      90        1       32       136        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  GSTA5 MUTATED           1          0          1          0        1         0
  GSTA5 WILD-TYPE        23         11         58         42       47        18
                 vv
clus              STAGE IVB
  GSTA5 MUTATED           0
  GSTA5 WILD-TYPE         1
D1059V4, multiclass
            clus
vv           GSTA5 MUTATED GSTA5 WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              2             136
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             0              42
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  GSTA5 MUTATED     1   1   6   0
  GSTA5 WILD-TYPE  16  91 323  50
D1059V5, multiclass
    clus
vv   GSTA5 MUTATED GSTA5 WILD-TYPE
  T1             1              16
  T2             1              91
  T3             6             323
  T4             0              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  GSTA5 MUTATED     5   2   0
  GSTA5 WILD-TYPE 282 111  87
D1059V6, multiclass
    clus
vv   GSTA5 MUTATED GSTA5 WILD-TYPE
  N0             5             282
  N1             2             111
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1059V7, binary
                 cls
clus                0   1
  GSTA5 MUTATED     5   1
  GSTA5 WILD-TYPE 370  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GSTA5 MUTATED      5    1
  GSTA5 WILD-TYPE  370   64
   clus
vv  GSTA5 MUTATED GSTA5 WILD-TYPE
  0             5             370
  1             1              64
[1] 2 2
[1] FALSE
D1059V8, binary
                 cls
clus                0   1
  GSTA5 MUTATED     3   5
  GSTA5 WILD-TYPE 222 259
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GSTA5 MUTATED      3    5
  GSTA5 WILD-TYPE  222  259
        clus
vv       GSTA5 MUTATED GSTA5 WILD-TYPE
  FEMALE             3             222
  MALE               5             259
[1] 2 2
[1] FALSE
D1059V9, binary
                 cls
clus                0   1
  GSTA5 MUTATED     7   0
  GSTA5 WILD-TYPE 343  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GSTA5 MUTATED      7    0
  GSTA5 WILD-TYPE  343   22
     clus
vv    GSTA5 MUTATED GSTA5 WILD-TYPE
  NO              7             343
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  GSTA5 MUTATED                      5                             1
  GSTA5 WILD-TYPE                  310                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  GSTA5 MUTATED                       2                              0
  GSTA5 WILD-TYPE                   104                             10
D1059V10, multiclass
                                clus
vv                               GSTA5 MUTATED GSTA5 WILD-TYPE
  COLON ADENOCARCINOMA                       5             310
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  GSTA5 MUTATED     6   0   0   0
  GSTA5 WILD-TYPE 339   4  31  25
D1059V11, multiclass
    clus
vv   GSTA5 MUTATED GSTA5 WILD-TYPE
  R0             6             339
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1059V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GSTA5 MUTATED                                  0     0
  GSTA5 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  GSTA5 MUTATED                           0     5
  GSTA5 WILD-TYPE                        22   221
D1059V13, multiclass
                                  clus
vv                                 GSTA5 MUTATED GSTA5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        5             221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1060) Variable = PCOLCE2 MUTATION ANALYSIS
D1060V1, survival
                   sevent
clus2                 0   1
  PCOLCE2 MUTATED    12   1
  PCOLCE2 WILD-TYPE 366  92
  PCOLCE2 MUTATED PCOLCE2 WILD-TYPE 
               13               458 
  PCOLCE2 MUTATED PCOLCE2 WILD-TYPE 
                1                92 
$`PCOLCE2 MUTATED`
TCGA-AA-3845 TCGA-AA-3856 TCGA-AA-A00A TCGA-AA-A00J TCGA-AA-A010 TCGA-CK-5914 
        0.00         0.99        38.04        18.05        34.98         9.99 
TCGA-CM-5861 TCGA-CM-6164 TCGA-D5-6923 TCGA-G4-6309 TCGA-AF-4110 TCGA-AG-A002 
       15.02        29.03        12.43        85.48        14.50        20.98 
TCGA-DC-6682 
        4.01 

$`PCOLCE2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
       32.05        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00D 
       27.02        19.07         7.96        27.02        13.94        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       51.32        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       22.98        30.08        32.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6165 TCGA-CM-6166 
       17.03        15.02        12.00         2.96        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        3.68         4.41        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 
       65.85        53.62        44.68        55.04        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       19.10        34.49        10.39        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 
       27.95        10.98        19.99         5.95         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  PCOLCE2 MUTATED PCOLCE2 WILD-TYPE 
                0                 0 
  PCOLCE2 MUTATED PCOLCE2 WILD-TYPE 
            85.48            148.01 
  PCOLCE2 MUTATED PCOLCE2 WILD-TYPE 
           15.020            20.415 
[1] "0.0 - 85.5 (15.0)"  "0.0 - 148.0 (20.4)"
[1] "hr=" "2.1"
D1060V2, continuous
D1060V3, binary
                   cls
clus                  0   1
  PCOLCE2 MUTATED    12   2
  PCOLCE2 WILD-TYPE 354 117
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PCOLCE2 MUTATED     12    2
  PCOLCE2 WILD-TYPE  354  117
        clus
vv       PCOLCE2 MUTATED PCOLCE2 WILD-TYPE
  COLON               12               354
  RECTUM               2               117
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PCOLCE2 MUTATED         2        0        0         6         2         0
  PCOLCE2 WILD-TYPE      89        1       32       132         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PCOLCE2 MUTATED           0          0          3          0        1
  PCOLCE2 WILD-TYPE        24         11         56         42       47
                   vv
clus                STAGE IVA STAGE IVB
  PCOLCE2 MUTATED           1         0
  PCOLCE2 WILD-TYPE        17         1
D1060V4, multiclass
            clus
vv           PCOLCE2 MUTATED PCOLCE2 WILD-TYPE
  STAGE I                  2                89
  STAGE IA                 0                 1
  STAGE II                 0                32
  STAGE IIA                6               132
  STAGE IIB                2                 8
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               0                11
  STAGE IIIB               3                56
  STAGE IIIC               0                42
  STAGE IV                 1                47
  STAGE IVA                1                17
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  PCOLCE2 MUTATED     0   2   8   5
  PCOLCE2 WILD-TYPE  17  90 321  45
D1060V5, multiclass
    clus
vv   PCOLCE2 MUTATED PCOLCE2 WILD-TYPE
  T1               0                17
  T2               2                90
  T3               8               321
  T4               5                45
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  PCOLCE2 MUTATED    10   4   1
  PCOLCE2 WILD-TYPE 277 109  86
D1060V6, multiclass
    clus
vv   PCOLCE2 MUTATED PCOLCE2 WILD-TYPE
  N0              10               277
  N1               4               109
  N2               1                86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1060V7, binary
                   cls
clus                  0   1
  PCOLCE2 MUTATED    11   1
  PCOLCE2 WILD-TYPE 364  64
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PCOLCE2 MUTATED     11    1
  PCOLCE2 WILD-TYPE  364   64
   clus
vv  PCOLCE2 MUTATED PCOLCE2 WILD-TYPE
  0              11               364
  1               1                64
[1] 2 2
[1] FALSE
D1060V8, binary
                   cls
clus                  0   1
  PCOLCE2 MUTATED     7   8
  PCOLCE2 WILD-TYPE 218 256
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PCOLCE2 MUTATED      7    8
  PCOLCE2 WILD-TYPE  218  256
        clus
vv       PCOLCE2 MUTATED PCOLCE2 WILD-TYPE
  FEMALE               7               218
  MALE                 8               256
[1] 2 2
[1] FALSE
D1060V9, binary
                   cls
clus                  0   1
  PCOLCE2 MUTATED     9   0
  PCOLCE2 WILD-TYPE 341  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PCOLCE2 MUTATED      9    0
  PCOLCE2 WILD-TYPE  341   22
     clus
vv    PCOLCE2 MUTATED PCOLCE2 WILD-TYPE
  NO                9               341
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PCOLCE2 MUTATED                     11                             1
  PCOLCE2 WILD-TYPE                  304                            46
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PCOLCE2 MUTATED                       2                              0
  PCOLCE2 WILD-TYPE                   104                             10
D1060V10, multiclass
                                clus
vv                               PCOLCE2 MUTATED PCOLCE2 WILD-TYPE
  COLON ADENOCARCINOMA                        11               304
  COLON MUCINOUS ADENOCARCINOMA                1                46
  RECTAL ADENOCARCINOMA                        2               104
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  PCOLCE2 MUTATED    12   0   1   2
  PCOLCE2 WILD-TYPE 333   4  30  23
D1060V11, multiclass
    clus
vv   PCOLCE2 MUTATED PCOLCE2 WILD-TYPE
  R0              12               333
  R1               0                 4
  R2               1                30
  RX               2                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1060V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PCOLCE2 MUTATED                                  0     0
  PCOLCE2 WILD-TYPE                                1    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  PCOLCE2 MUTATED                           1     7
  PCOLCE2 WILD-TYPE                        21   219
D1060V13, multiclass
                                  clus
vv                                 PCOLCE2 MUTATED PCOLCE2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                      1                21
  WHITE                                          7               219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1061) Variable = BUB1B MUTATION ANALYSIS
D1061V1, survival
                 sevent
clus2               0   1
  BUB1B MUTATED     7   3
  BUB1B WILD-TYPE 371  90
  BUB1B MUTATED BUB1B WILD-TYPE 
             10             461 
  BUB1B MUTATED BUB1B WILD-TYPE 
              3              90 
$`BUB1B MUTATED`
TCGA-AA-3869 TCGA-AA-3949 TCGA-AZ-4315 TCGA-AZ-6600 TCGA-CM-5868 TCGA-CM-6678 
       27.02        26.01        58.39        12.10        17.03        11.01 
TCGA-DM-A1HB TCGA-F4-6570 TCGA-AG-3892 TCGA-AG-A002 
      135.65         6.18        13.02        20.98 

$`BUB1B WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       53.00        17.03        24.03        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-3952 
        2.01        12.99        24.00        33.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       33.01        21.44        17.82         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 
       22.36        62.79        88.21        49.41         6.77       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
        5.03        15.02        15.02        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.08        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
       44.32       131.51       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       35.74        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  BUB1B MUTATED BUB1B WILD-TYPE 
           6.18            0.00 
  BUB1B MUTATED BUB1B WILD-TYPE 
         135.65          148.01 
  BUB1B MUTATED BUB1B WILD-TYPE 
         19.005          20.190 
[1] "6.2 - 135.7 (19.0)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.3"
D1061V2, continuous
D1061V3, binary
                 cls
clus                0   1
  BUB1B MUTATED     9   2
  BUB1B WILD-TYPE 357 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BUB1B MUTATED      9    2
  BUB1B WILD-TYPE  357  117
        clus
vv       BUB1B MUTATED BUB1B WILD-TYPE
  COLON              9             357
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  BUB1B MUTATED         2        0        0         3         0         0
  BUB1B WILD-TYPE      89        1       32       135        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  BUB1B MUTATED           0          0          2          0        2         2
  BUB1B WILD-TYPE        24         11         57         42       46        16
                 vv
clus              STAGE IVB
  BUB1B MUTATED           0
  BUB1B WILD-TYPE         1
D1061V4, multiclass
            clus
vv           BUB1B MUTATED BUB1B WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              3             135
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             2              57
  STAGE IIIC             0              42
  STAGE IV               2              46
  STAGE IVA              2              16
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  BUB1B MUTATED     1   1   5   4
  BUB1B WILD-TYPE  16  91 324  46
D1061V5, multiclass
    clus
vv   BUB1B MUTATED BUB1B WILD-TYPE
  T1             1              16
  T2             1              91
  T3             5             324
  T4             4              46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  BUB1B MUTATED     5   5   1
  BUB1B WILD-TYPE 282 108  86
D1061V6, multiclass
    clus
vv   BUB1B MUTATED BUB1B WILD-TYPE
  N0             5             282
  N1             5             108
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1061V7, binary
                 cls
clus                0   1
  BUB1B MUTATED     7   4
  BUB1B WILD-TYPE 368  61
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BUB1B MUTATED      7    4
  BUB1B WILD-TYPE  368   61
   clus
vv  BUB1B MUTATED BUB1B WILD-TYPE
  0             7             368
  1             4              61
[1] 2 2
[1] FALSE
D1061V8, binary
                 cls
clus                0   1
  BUB1B MUTATED     6   5
  BUB1B WILD-TYPE 219 259
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BUB1B MUTATED      6    5
  BUB1B WILD-TYPE  219  259
        clus
vv       BUB1B MUTATED BUB1B WILD-TYPE
  FEMALE             6             219
  MALE               5             259
[1] 2 2
[1] FALSE
D1061V9, binary
                 cls
clus                0   1
  BUB1B MUTATED     8   0
  BUB1B WILD-TYPE 342  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BUB1B MUTATED      8    0
  BUB1B WILD-TYPE  342   22
     clus
vv    BUB1B MUTATED BUB1B WILD-TYPE
  NO              8             342
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  BUB1B MUTATED                      7                             1
  BUB1B WILD-TYPE                  308                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  BUB1B MUTATED                       2                              0
  BUB1B WILD-TYPE                   104                             10
D1061V10, multiclass
                                clus
vv                               BUB1B MUTATED BUB1B WILD-TYPE
  COLON ADENOCARCINOMA                       7             308
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  BUB1B MUTATED     8   0   1   0
  BUB1B WILD-TYPE 337   4  30  25
D1061V11, multiclass
    clus
vv   BUB1B MUTATED BUB1B WILD-TYPE
  R0             8             337
  R1             0               4
  R2             1              30
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1061V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  BUB1B MUTATED                                  0     0
  BUB1B WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  BUB1B MUTATED                           1     5
  BUB1B WILD-TYPE                        21   221
D1061V13, multiclass
                                  clus
vv                                 BUB1B MUTATED BUB1B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        5             221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1062) Variable = MC3R MUTATION ANALYSIS
D1062V1, survival
                sevent
clus2              0   1
  MC3R MUTATED     9   4
  MC3R WILD-TYPE 369  89
  MC3R MUTATED MC3R WILD-TYPE 
            13            458 
  MC3R MUTATED MC3R WILD-TYPE 
             4             89 
$`MC3R MUTATED`
TCGA-AA-A010 TCGA-CK-5914 TCGA-CM-4743 TCGA-CM-6163 TCGA-CM-6166 TCGA-CM-6679 
       34.98         9.99        23.05         2.96        21.99        10.06 
TCGA-DM-A1D4 TCGA-DM-A1DB TCGA-F4-6808 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6586 
       92.75        44.32        33.67        65.85        53.62        35.80 
TCGA-DY-A1DC 
       41.36 

$`MC3R WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5916 
      148.01        85.45        15.62        49.08        51.32        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
       82.95         1.91       124.27        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       12.00        29.03        16.04        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.08        11.01        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HA 
       49.91        13.32        12.59       140.38         7.50       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       22.09        13.78        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
        5.29       126.44        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  MC3R MUTATED MC3R WILD-TYPE 
          2.96           0.00 
  MC3R MUTATED MC3R WILD-TYPE 
         92.75         148.01 
  MC3R MUTATED MC3R WILD-TYPE 
         34.98          20.02 
[1] "3.0 - 92.8 (35.0)"  "0.0 - 148.0 (20.0)"
[1] "hr=" "1.1"
D1062V2, continuous
D1062V3, binary
                cls
clus               0   1
  MC3R MUTATED    13   1
  MC3R WILD-TYPE 353 118
[1] "tbl2"
                cls
clus             [,1] [,2]
  MC3R MUTATED     13    1
  MC3R WILD-TYPE  353  118
        clus
vv       MC3R MUTATED MC3R WILD-TYPE
  COLON            13            353
  RECTUM            1            118
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MC3R MUTATED         3        0        0         6         2         0
  MC3R WILD-TYPE      88        1       32       132         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MC3R MUTATED           0          0          1          1        1         0
  MC3R WILD-TYPE        24         11         58         41       47        18
                vv
clus             STAGE IVB
  MC3R MUTATED           0
  MC3R WILD-TYPE         1
D1062V4, multiclass
            clus
vv           MC3R MUTATED MC3R WILD-TYPE
  STAGE I               3             88
  STAGE IA              0              1
  STAGE II              0             32
  STAGE IIA             6            132
  STAGE IIB             2              8
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            1             58
  STAGE IIIC            1             41
  STAGE IV              1             47
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  MC3R MUTATED     2   1   9   2
  MC3R WILD-TYPE  15  91 320  48
D1062V5, multiclass
    clus
vv   MC3R MUTATED MC3R WILD-TYPE
  T1            2             15
  T2            1             91
  T3            9            320
  T4            2             48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  MC3R MUTATED    11   2   1
  MC3R WILD-TYPE 276 111  86
D1062V6, multiclass
    clus
vv   MC3R MUTATED MC3R WILD-TYPE
  N0           11            276
  N1            2            111
  N2            1             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1062V7, binary
                cls
clus               0   1
  MC3R MUTATED    11   1
  MC3R WILD-TYPE 364  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  MC3R MUTATED     11    1
  MC3R WILD-TYPE  364   64
   clus
vv  MC3R MUTATED MC3R WILD-TYPE
  0           11            364
  1            1             64
[1] 2 2
[1] FALSE
D1062V8, binary
                cls
clus               0   1
  MC3R MUTATED     7   7
  MC3R WILD-TYPE 218 257
[1] "tbl2"
                cls
clus             [,1] [,2]
  MC3R MUTATED      7    7
  MC3R WILD-TYPE  218  257
        clus
vv       MC3R MUTATED MC3R WILD-TYPE
  FEMALE            7            218
  MALE              7            257
[1] 2 2
[1] FALSE
D1062V9, binary
                cls
clus               0   1
  MC3R MUTATED     9   0
  MC3R WILD-TYPE 341  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  MC3R MUTATED      9    0
  MC3R WILD-TYPE  341   22
     clus
vv    MC3R MUTATED MC3R WILD-TYPE
  NO             9            341
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MC3R MUTATED                     12                             1
  MC3R WILD-TYPE                  303                            46
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MC3R MUTATED                       1                              0
  MC3R WILD-TYPE                   105                             10
D1062V10, multiclass
                                clus
vv                               MC3R MUTATED MC3R WILD-TYPE
  COLON ADENOCARCINOMA                     12            303
  COLON MUCINOUS ADENOCARCINOMA             1             46
  RECTAL ADENOCARCINOMA                     1            105
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  MC3R MUTATED    10   0   0   1
  MC3R WILD-TYPE 335   4  31  24
D1062V11, multiclass
    clus
vv   MC3R MUTATED MC3R WILD-TYPE
  R0           10            335
  R1            0              4
  R2            0             31
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1062V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MC3R MUTATED                                  0     0
  MC3R WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  MC3R MUTATED                           0    13
  MC3R WILD-TYPE                        22   213
D1062V13, multiclass
                                  clus
vv                                 MC3R MUTATED MC3R WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                      13            213
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1063) Variable = DNASE1L3 MUTATION ANALYSIS
D1063V1, survival
                    sevent
clus2                  0   1
  DNASE1L3 MUTATED     5   3
  DNASE1L3 WILD-TYPE 373  90
  DNASE1L3 MUTATED DNASE1L3 WILD-TYPE 
                 8                463 
  DNASE1L3 MUTATED DNASE1L3 WILD-TYPE 
                 3                 90 
$`DNASE1L3 MUTATED`
TCGA-A6-2671 TCGA-AA-3510 TCGA-AA-3877 TCGA-AA-A02W TCGA-AZ-5403 TCGA-AZ-6601 
       43.76        63.98        31.00        41.00        62.79       100.01 
TCGA-CA-6717 TCGA-CK-4952 
       12.76        15.62 

$`DNASE1L3 WILD-TYPE`
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       46.65        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 
       24.03        27.02        29.98        18.05         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02Y TCGA-AA-A03F 
        2.01         5.03        14.01         0.92        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 
       88.21        49.41         6.77        12.10        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07        12.20        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
      148.01        85.45        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  DNASE1L3 MUTATED DNASE1L3 WILD-TYPE 
             12.76               0.00 
  DNASE1L3 MUTATED DNASE1L3 WILD-TYPE 
            100.01             148.01 
  DNASE1L3 MUTATED DNASE1L3 WILD-TYPE 
             42.38              20.05 
[1] "12.8 - 100.0 (42.4)" "0.0 - 148.0 (20.1)" 
[1] "hr=" "1"  
D1063V2, continuous
D1063V3, binary
                    cls
clus                   0   1
  DNASE1L3 MUTATED     8   0
  DNASE1L3 WILD-TYPE 358 119
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  DNASE1L3 MUTATED      8    0
  DNASE1L3 WILD-TYPE  358  119
        clus
vv       DNASE1L3 MUTATED DNASE1L3 WILD-TYPE
  COLON                 8                358
  RECTUM                0                119
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DNASE1L3 MUTATED         2        0        3         1         0         0
  DNASE1L3 WILD-TYPE      89        1       29       137        10         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DNASE1L3 MUTATED           0          0          0          1        1
  DNASE1L3 WILD-TYPE        24         11         59         41       47
                    vv
clus                 STAGE IVA STAGE IVB
  DNASE1L3 MUTATED           0         0
  DNASE1L3 WILD-TYPE        18         1
D1063V4, multiclass
            clus
vv           DNASE1L3 MUTATED DNASE1L3 WILD-TYPE
  STAGE I                   2                 89
  STAGE IA                  0                  1
  STAGE II                  3                 29
  STAGE IIA                 1                137
  STAGE IIB                 0                 10
  STAGE IIC                 0                  1
  STAGE III                 0                 24
  STAGE IIIA                0                 11
  STAGE IIIB                0                 59
  STAGE IIIC                1                 41
  STAGE IV                  1                 47
  STAGE IVA                 0                 18
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  DNASE1L3 MUTATED     1   1   5   1
  DNASE1L3 WILD-TYPE  16  91 324  49
D1063V5, multiclass
    clus
vv   DNASE1L3 MUTATED DNASE1L3 WILD-TYPE
  T1                1                 16
  T2                1                 91
  T3                5                324
  T4                1                 49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  DNASE1L3 MUTATED     6   0   2
  DNASE1L3 WILD-TYPE 281 113  85
D1063V6, multiclass
    clus
vv   DNASE1L3 MUTATED DNASE1L3 WILD-TYPE
  N0                6                281
  N1                0                113
  N2                2                 85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1063V7, binary
                    cls
clus                   0   1
  DNASE1L3 MUTATED     6   1
  DNASE1L3 WILD-TYPE 369  64
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  DNASE1L3 MUTATED      6    1
  DNASE1L3 WILD-TYPE  369   64
   clus
vv  DNASE1L3 MUTATED DNASE1L3 WILD-TYPE
  0                6                369
  1                1                 64
[1] 2 2
[1] FALSE
D1063V8, binary
                    cls
clus                   0   1
  DNASE1L3 MUTATED     3   5
  DNASE1L3 WILD-TYPE 222 259
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  DNASE1L3 MUTATED      3    5
  DNASE1L3 WILD-TYPE  222  259
        clus
vv       DNASE1L3 MUTATED DNASE1L3 WILD-TYPE
  FEMALE                3                222
  MALE                  5                259
[1] 2 2
[1] FALSE
D1063V9, binary
                    cls
clus                   0   1
  DNASE1L3 MUTATED     7   0
  DNASE1L3 WILD-TYPE 343  22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  DNASE1L3 MUTATED      7    0
  DNASE1L3 WILD-TYPE  343   22
     clus
vv    DNASE1L3 MUTATED DNASE1L3 WILD-TYPE
  NO                 7                343
  YES                0                 22
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  DNASE1L3 MUTATED                      5                             3
  DNASE1L3 WILD-TYPE                  310                            44
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  DNASE1L3 MUTATED                       0                              0
  DNASE1L3 WILD-TYPE                   106                             10
D1063V10, multiclass
                                clus
vv                               DNASE1L3 MUTATED DNASE1L3 WILD-TYPE
  COLON ADENOCARCINOMA                          5                310
  COLON MUCINOUS ADENOCARCINOMA                 3                 44
  RECTAL ADENOCARCINOMA                         0                106
  RECTAL MUCINOUS ADENOCARCINOMA                0                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  DNASE1L3 MUTATED     4   0   0   2
  DNASE1L3 WILD-TYPE 341   4  31  23
D1063V11, multiclass
    clus
vv   DNASE1L3 MUTATED DNASE1L3 WILD-TYPE
  R0                4                341
  R1                0                  4
  R2                0                 31
  RX                2                 23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1063V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DNASE1L3 MUTATED                                  0     1
  DNASE1L3 WILD-TYPE                                1    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  DNASE1L3 MUTATED                           0     4
  DNASE1L3 WILD-TYPE                        22   222
D1063V13, multiclass
                                  clus
vv                                 DNASE1L3 MUTATED DNASE1L3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                 10
  BLACK OR AFRICAN AMERICAN                       0                 22
  WHITE                                           4                222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1064) Variable = FAM98B MUTATION ANALYSIS
D1064V1, survival
                  sevent
clus2                0   1
  FAM98B MUTATED     5   0
  FAM98B WILD-TYPE 373  93
  FAM98B MUTATED FAM98B WILD-TYPE 
               5              466 
  FAM98B MUTATED FAM98B WILD-TYPE 
               0               93 
$`FAM98B MUTATED`
TCGA-AA-3977 TCGA-CK-4947 TCGA-CM-6674 TCGA-D5-6923 TCGA-AG-A002 
       25.02        17.56        12.95        12.43        20.98 

$`FAM98B WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4948 
        0.07        12.20        12.76        10.06        14.30       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
        4.41        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  FAM98B MUTATED FAM98B WILD-TYPE 
           12.43             0.00 
  FAM98B MUTATED FAM98B WILD-TYPE 
           25.02           148.01 
  FAM98B MUTATED FAM98B WILD-TYPE 
          17.560           20.235 
[1] "12.4 - 25.0 (17.6)" "0.0 - 148.0 (20.2)"
[1] "hr="     "3300000"
D1064V2, continuous
D1064V3, binary
                  cls
clus                 0   1
  FAM98B MUTATED     4   1
  FAM98B WILD-TYPE 362 118
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM98B MUTATED      4    1
  FAM98B WILD-TYPE  362  118
        clus
vv       FAM98B MUTATED FAM98B WILD-TYPE
  COLON               4              362
  RECTUM              1              118
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FAM98B MUTATED         2        0        0         1         0         0
  FAM98B WILD-TYPE      89        1       32       137        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FAM98B MUTATED           0          0          1          0        0
  FAM98B WILD-TYPE        24         11         58         42       48
                  vv
clus               STAGE IVA STAGE IVB
  FAM98B MUTATED           0         0
  FAM98B WILD-TYPE        18         1
D1064V4, multiclass
            clus
vv           FAM98B MUTATED FAM98B WILD-TYPE
  STAGE I                 2               89
  STAGE IA                0                1
  STAGE II                0               32
  STAGE IIA               1              137
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              1               58
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  FAM98B MUTATED     0   3   1   1
  FAM98B WILD-TYPE  17  89 328  49
D1064V5, multiclass
    clus
vv   FAM98B MUTATED FAM98B WILD-TYPE
  T1              0               17
  T2              3               89
  T3              1              328
  T4              1               49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  FAM98B MUTATED     4   1   0
  FAM98B WILD-TYPE 283 112  87
D1064V6, multiclass
    clus
vv   FAM98B MUTATED FAM98B WILD-TYPE
  N0              4              283
  N1              1              112
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1064V7, binary
                  cls
clus                 0   1
  FAM98B MUTATED     4   0
  FAM98B WILD-TYPE 371  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM98B MUTATED      4    0
  FAM98B WILD-TYPE  371   65
   clus
vv  FAM98B MUTATED FAM98B WILD-TYPE
  0              4              371
  1              0               65
[1] 2 2
[1] FALSE
D1064V8, binary
                  cls
clus                 0   1
  FAM98B MUTATED     1   4
  FAM98B WILD-TYPE 224 260
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM98B MUTATED      1    4
  FAM98B WILD-TYPE  224  260
        clus
vv       FAM98B MUTATED FAM98B WILD-TYPE
  FEMALE              1              224
  MALE                4              260
[1] 2 2
[1] FALSE
D1064V9, binary
                  cls
clus                 0   1
  FAM98B MUTATED     5   0
  FAM98B WILD-TYPE 345  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM98B MUTATED      5    0
  FAM98B WILD-TYPE  345   22
     clus
vv    FAM98B MUTATED FAM98B WILD-TYPE
  NO               5              345
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  FAM98B MUTATED                      4                             0
  FAM98B WILD-TYPE                  311                            47
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  FAM98B MUTATED                       1                              0
  FAM98B WILD-TYPE                   105                             10
D1064V10, multiclass
                                clus
vv                               FAM98B MUTATED FAM98B WILD-TYPE
  COLON ADENOCARCINOMA                        4              311
  COLON MUCINOUS ADENOCARCINOMA               0               47
  RECTAL ADENOCARCINOMA                       1              105
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  FAM98B MUTATED     3   0   0   1
  FAM98B WILD-TYPE 342   4  31  24
D1064V11, multiclass
    clus
vv   FAM98B MUTATED FAM98B WILD-TYPE
  R0              3              342
  R1              0                4
  R2              0               31
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1064V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FAM98B MUTATED                                  0     0
  FAM98B WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  FAM98B MUTATED                           0     3
  FAM98B WILD-TYPE                        22   223
D1064V13, multiclass
                                  clus
vv                                 FAM98B MUTATED FAM98B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         3              223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1065) Variable = DCTN5 MUTATION ANALYSIS
D1065V1, survival
                 sevent
clus2               0   1
  DCTN5 MUTATED     5   1
  DCTN5 WILD-TYPE 373  92
  DCTN5 MUTATED DCTN5 WILD-TYPE 
              6             465 
  DCTN5 MUTATED DCTN5 WILD-TYPE 
              1              92 
$`DCTN5 MUTATED`
TCGA-A6-3809 TCGA-AA-3713 TCGA-AZ-6598 TCGA-CK-5914 TCGA-CM-6164 TCGA-G4-6588 
       32.75        19.04        49.41         9.99        29.03        26.17 

$`DCTN5 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 
      106.75        22.36        62.79        88.21         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        49.08        51.32        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
        2.96        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       22.09        13.78        35.80        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  DCTN5 MUTATED DCTN5 WILD-TYPE 
           9.99            0.00 
  DCTN5 MUTATED DCTN5 WILD-TYPE 
          49.41          148.01 
  DCTN5 MUTATED DCTN5 WILD-TYPE 
          27.60           20.12 
[1] "10.0 - 49.4 (27.6)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.2"
D1065V2, continuous
D1065V3, binary
                 cls
clus                0   1
  DCTN5 MUTATED     6   0
  DCTN5 WILD-TYPE 360 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DCTN5 MUTATED      6    0
  DCTN5 WILD-TYPE  360  119
        clus
vv       DCTN5 MUTATED DCTN5 WILD-TYPE
  COLON              6             360
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DCTN5 MUTATED         0        0        1         2         1         0
  DCTN5 WILD-TYPE      91        1       31       136         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DCTN5 MUTATED           0          0          1          0        1         0
  DCTN5 WILD-TYPE        24         11         58         42       47        18
                 vv
clus              STAGE IVB
  DCTN5 MUTATED           0
  DCTN5 WILD-TYPE         1
D1065V4, multiclass
            clus
vv           DCTN5 MUTATED DCTN5 WILD-TYPE
  STAGE I                0              91
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              2             136
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             0              42
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  DCTN5 MUTATED     0   0   5   1
  DCTN5 WILD-TYPE  17  92 324  49
D1065V5, multiclass
    clus
vv   DCTN5 MUTATED DCTN5 WILD-TYPE
  T1             0              17
  T2             0              92
  T3             5             324
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  DCTN5 MUTATED     5   1   0
  DCTN5 WILD-TYPE 282 112  87
D1065V6, multiclass
    clus
vv   DCTN5 MUTATED DCTN5 WILD-TYPE
  N0             5             282
  N1             1             112
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1065V7, binary
                 cls
clus                0   1
  DCTN5 MUTATED     3   1
  DCTN5 WILD-TYPE 372  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DCTN5 MUTATED      3    1
  DCTN5 WILD-TYPE  372   64
   clus
vv  DCTN5 MUTATED DCTN5 WILD-TYPE
  0             3             372
  1             1              64
[1] 2 2
[1] FALSE
D1065V8, binary
                 cls
clus                0   1
  DCTN5 MUTATED     4   2
  DCTN5 WILD-TYPE 221 262
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DCTN5 MUTATED      4    2
  DCTN5 WILD-TYPE  221  262
        clus
vv       DCTN5 MUTATED DCTN5 WILD-TYPE
  FEMALE             4             221
  MALE               2             262
[1] 2 2
[1] FALSE
D1065V9, binary
                 cls
clus                0   1
  DCTN5 MUTATED     4   1
  DCTN5 WILD-TYPE 346  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DCTN5 MUTATED      4    1
  DCTN5 WILD-TYPE  346   21
     clus
vv    DCTN5 MUTATED DCTN5 WILD-TYPE
  NO              4             346
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  DCTN5 MUTATED                      5                             1
  DCTN5 WILD-TYPE                  310                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  DCTN5 MUTATED                       0                              0
  DCTN5 WILD-TYPE                   106                             10
D1065V10, multiclass
                                clus
vv                               DCTN5 MUTATED DCTN5 WILD-TYPE
  COLON ADENOCARCINOMA                       5             310
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  DCTN5 MUTATED     3   0   1   1
  DCTN5 WILD-TYPE 342   4  30  24
D1065V11, multiclass
    clus
vv   DCTN5 MUTATED DCTN5 WILD-TYPE
  R0             3             342
  R1             0               4
  R2             1              30
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1065V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DCTN5 MUTATED                                  0     0
  DCTN5 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  DCTN5 MUTATED                           0     5
  DCTN5 WILD-TYPE                        22   221
D1065V13, multiclass
                                  clus
vv                                 DCTN5 MUTATED DCTN5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        5             221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1066) Variable = SLC11A2 MUTATION ANALYSIS
D1066V1, survival
                   sevent
clus2                 0   1
  SLC11A2 MUTATED     7   1
  SLC11A2 WILD-TYPE 371  92
  SLC11A2 MUTATED SLC11A2 WILD-TYPE 
                8               463 
  SLC11A2 MUTATED SLC11A2 WILD-TYPE 
                1                92 
$`SLC11A2 MUTATED`
TCGA-AA-3949 TCGA-AA-3950 TCGA-AD-6895 TCGA-AD-6964 TCGA-CM-6171 TCGA-D5-6928 
       26.01        24.00         0.72        10.88        14.04        11.64 
TCGA-G4-6586 TCGA-AG-A002 
       35.80        20.98 

$`SLC11A2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3952 
       31.00         2.01        12.99        24.00        33.01         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       56.55         0.79         5.79        22.42        27.42         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       13.02        15.02        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
       14.30         9.04         9.44         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       13.78        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  SLC11A2 MUTATED SLC11A2 WILD-TYPE 
             0.72              0.00 
  SLC11A2 MUTATED SLC11A2 WILD-TYPE 
            35.80            148.01 
  SLC11A2 MUTATED SLC11A2 WILD-TYPE 
            17.51             20.19 
[1] "0.7 - 35.8 (17.5)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1"  
D1066V2, continuous
D1066V3, binary
                   cls
clus                  0   1
  SLC11A2 MUTATED     8   1
  SLC11A2 WILD-TYPE 358 118
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC11A2 MUTATED      8    1
  SLC11A2 WILD-TYPE  358  118
        clus
vv       SLC11A2 MUTATED SLC11A2 WILD-TYPE
  COLON                8               358
  RECTUM               1               118
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SLC11A2 MUTATED         2        0        0         4         0         0
  SLC11A2 WILD-TYPE      89        1       32       134        10         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC11A2 MUTATED           0          0          1          0        0
  SLC11A2 WILD-TYPE        24         11         58         42       48
                   vv
clus                STAGE IVA STAGE IVB
  SLC11A2 MUTATED           0         0
  SLC11A2 WILD-TYPE        18         1
D1066V4, multiclass
            clus
vv           SLC11A2 MUTATED SLC11A2 WILD-TYPE
  STAGE I                  2                89
  STAGE IA                 0                 1
  STAGE II                 0                32
  STAGE IIA                4               134
  STAGE IIB                0                10
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               0                11
  STAGE IIIB               1                58
  STAGE IIIC               0                42
  STAGE IV                 0                48
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  SLC11A2 MUTATED     0   2   6   1
  SLC11A2 WILD-TYPE  17  90 323  49
D1066V5, multiclass
    clus
vv   SLC11A2 MUTATED SLC11A2 WILD-TYPE
  T1               0                17
  T2               2                90
  T3               6               323
  T4               1                49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  SLC11A2 MUTATED     6   2   1
  SLC11A2 WILD-TYPE 281 111  86
D1066V6, multiclass
    clus
vv   SLC11A2 MUTATED SLC11A2 WILD-TYPE
  N0               6               281
  N1               2               111
  N2               1                86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1066V7, binary
                   cls
clus                  0   1
  SLC11A2 MUTATED     7   0
  SLC11A2 WILD-TYPE 368  65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC11A2 MUTATED      7    0
  SLC11A2 WILD-TYPE  368   65
   clus
vv  SLC11A2 MUTATED SLC11A2 WILD-TYPE
  0               7               368
  1               0                65
[1] 2 2
[1] FALSE
D1066V8, binary
                   cls
clus                  0   1
  SLC11A2 MUTATED     5   4
  SLC11A2 WILD-TYPE 220 260
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC11A2 MUTATED      5    4
  SLC11A2 WILD-TYPE  220  260
        clus
vv       SLC11A2 MUTATED SLC11A2 WILD-TYPE
  FEMALE               5               220
  MALE                 4               260
[1] 2 2
[1] FALSE
D1066V9, binary
                   cls
clus                  0   1
  SLC11A2 MUTATED     7   0
  SLC11A2 WILD-TYPE 343  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC11A2 MUTATED      7    0
  SLC11A2 WILD-TYPE  343   22
     clus
vv    SLC11A2 MUTATED SLC11A2 WILD-TYPE
  NO                7               343
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SLC11A2 MUTATED                      5                             3
  SLC11A2 WILD-TYPE                  310                            44
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SLC11A2 MUTATED                       1                              0
  SLC11A2 WILD-TYPE                   105                             10
D1066V10, multiclass
                                clus
vv                               SLC11A2 MUTATED SLC11A2 WILD-TYPE
  COLON ADENOCARCINOMA                         5               310
  COLON MUCINOUS ADENOCARCINOMA                3                44
  RECTAL ADENOCARCINOMA                        1               105
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  SLC11A2 MUTATED     7   0   0   0
  SLC11A2 WILD-TYPE 338   4  31  25
D1066V11, multiclass
    clus
vv   SLC11A2 MUTATED SLC11A2 WILD-TYPE
  R0               7               338
  R1               0                 4
  R2               0                31
  RX               0                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1066V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SLC11A2 MUTATED                                  0     0
  SLC11A2 WILD-TYPE                                1    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  SLC11A2 MUTATED                           0     5
  SLC11A2 WILD-TYPE                        22   221
D1066V13, multiclass
                                  clus
vv                                 SLC11A2 MUTATED SLC11A2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                      0                22
  WHITE                                          5               221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1067) Variable = SERPINB7 MUTATION ANALYSIS
D1067V1, survival
                    sevent
clus2                  0   1
  SERPINB7 MUTATED     6   2
  SERPINB7 WILD-TYPE 372  91
  SERPINB7 MUTATED SERPINB7 WILD-TYPE 
                 8                463 
  SERPINB7 MUTATED SERPINB7 WILD-TYPE 
                 2                 91 
$`SERPINB7 MUTATED`
TCGA-A6-5665 TCGA-A6-6654 TCGA-AA-3555 TCGA-AA-A010 TCGA-AZ-4315 TCGA-AZ-6598 
       22.06        23.87        29.95        34.98        58.39        49.41 
TCGA-F4-6460 TCGA-G4-6628 
       31.96        79.69 

$`SERPINB7 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 
       25.18        24.16        21.76        24.69        24.39        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       24.00        17.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       88.21         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 
       35.80        26.17        91.79        46.75        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  SERPINB7 MUTATED SERPINB7 WILD-TYPE 
             22.06               0.00 
  SERPINB7 MUTATED SERPINB7 WILD-TYPE 
             79.69             148.01 
  SERPINB7 MUTATED SERPINB7 WILD-TYPE 
             33.47              20.02 
[1] "22.1 - 79.7 (33.5)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.2"
D1067V2, continuous
D1067V3, binary
                    cls
clus                   0   1
  SERPINB7 MUTATED     8   0
  SERPINB7 WILD-TYPE 358 119
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SERPINB7 MUTATED      8    0
  SERPINB7 WILD-TYPE  358  119
        clus
vv       SERPINB7 MUTATED SERPINB7 WILD-TYPE
  COLON                 8                358
  RECTUM                0                119
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SERPINB7 MUTATED         1        0        1         3         1         0
  SERPINB7 WILD-TYPE      90        1       31       135         9         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SERPINB7 MUTATED           0          0          2          0        0
  SERPINB7 WILD-TYPE        24         11         57         42       48
                    vv
clus                 STAGE IVA STAGE IVB
  SERPINB7 MUTATED           0         0
  SERPINB7 WILD-TYPE        18         1
D1067V4, multiclass
            clus
vv           SERPINB7 MUTATED SERPINB7 WILD-TYPE
  STAGE I                   1                 90
  STAGE IA                  0                  1
  STAGE II                  1                 31
  STAGE IIA                 3                135
  STAGE IIB                 1                  9
  STAGE IIC                 0                  1
  STAGE III                 0                 24
  STAGE IIIA                0                 11
  STAGE IIIB                2                 57
  STAGE IIIC                0                 42
  STAGE IV                  0                 48
  STAGE IVA                 0                 18
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  SERPINB7 MUTATED     0   1   6   1
  SERPINB7 WILD-TYPE  17  91 323  49
D1067V5, multiclass
    clus
vv   SERPINB7 MUTATED SERPINB7 WILD-TYPE
  T1                0                 17
  T2                1                 91
  T3                6                323
  T4                1                 49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  SERPINB7 MUTATED     6   2   0
  SERPINB7 WILD-TYPE 281 111  87
D1067V6, multiclass
    clus
vv   SERPINB7 MUTATED SERPINB7 WILD-TYPE
  N0                6                281
  N1                2                111
  N2                0                 87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1067V7, binary
                    cls
clus                   0   1
  SERPINB7 MUTATED     7   0
  SERPINB7 WILD-TYPE 368  65
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SERPINB7 MUTATED      7    0
  SERPINB7 WILD-TYPE  368   65
   clus
vv  SERPINB7 MUTATED SERPINB7 WILD-TYPE
  0                7                368
  1                0                 65
[1] 2 2
[1] FALSE
D1067V8, binary
                    cls
clus                   0   1
  SERPINB7 MUTATED     6   2
  SERPINB7 WILD-TYPE 219 262
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SERPINB7 MUTATED      6    2
  SERPINB7 WILD-TYPE  219  262
        clus
vv       SERPINB7 MUTATED SERPINB7 WILD-TYPE
  FEMALE                6                219
  MALE                  2                262
[1] 2 2
[1] FALSE
D1067V9, binary
                    cls
clus                   0   1
  SERPINB7 MUTATED     8   0
  SERPINB7 WILD-TYPE 342  22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SERPINB7 MUTATED      8    0
  SERPINB7 WILD-TYPE  342   22
     clus
vv    SERPINB7 MUTATED SERPINB7 WILD-TYPE
  NO                 8                342
  YES                0                 22
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SERPINB7 MUTATED                      7                             1
  SERPINB7 WILD-TYPE                  308                            46
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SERPINB7 MUTATED                       0                              0
  SERPINB7 WILD-TYPE                   106                             10
D1067V10, multiclass
                                clus
vv                               SERPINB7 MUTATED SERPINB7 WILD-TYPE
  COLON ADENOCARCINOMA                          7                308
  COLON MUCINOUS ADENOCARCINOMA                 1                 46
  RECTAL ADENOCARCINOMA                         0                106
  RECTAL MUCINOUS ADENOCARCINOMA                0                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  SERPINB7 MUTATED     6   0   0   0
  SERPINB7 WILD-TYPE 339   4  31  25
D1067V11, multiclass
    clus
vv   SERPINB7 MUTATED SERPINB7 WILD-TYPE
  R0                6                339
  R1                0                  4
  R2                0                 31
  RX                0                 25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1067V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SERPINB7 MUTATED                                  0     0
  SERPINB7 WILD-TYPE                                1    11
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  SERPINB7 MUTATED                           0     6
  SERPINB7 WILD-TYPE                        22   220
D1067V13, multiclass
                                  clus
vv                                 SERPINB7 MUTATED SERPINB7 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 11
  BLACK OR AFRICAN AMERICAN                       0                 22
  WHITE                                           6                220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1068) Variable = PTPRJ MUTATION ANALYSIS
D1068V1, survival
                 sevent
clus2               0   1
  PTPRJ MUTATED    13   5
  PTPRJ WILD-TYPE 365  88
  PTPRJ MUTATED PTPRJ WILD-TYPE 
             18             453 
  PTPRJ MUTATED PTPRJ WILD-TYPE 
              5              88 
$`PTPRJ MUTATED`
TCGA-A6-6653 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3877 TCGA-AA-3977 TCGA-AA-A02K 
       24.39         1.02        13.02        31.00        25.02        14.01 
TCGA-AU-6004 TCGA-AZ-6599 TCGA-AZ-6603 TCGA-CA-6717 TCGA-CK-5913 TCGA-CK-6748 
       27.09         6.77        29.56        12.76        51.32         1.91 
TCGA-CM-5860 TCGA-CM-5861 TCGA-D5-6537 TCGA-AG-A002 TCGA-DC-6682 TCGA-F5-6465 
       32.02        15.02         4.80        20.98         4.01        49.51 

$`PTPRJ WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
       25.08        25.18        24.16        21.76        24.69        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 
       20.12        19.66        20.28         7.04         3.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
       63.98         6.97         1.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       27.02        29.98        18.05         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 
       22.42        27.42        10.88         0.20        14.50        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
       12.10       100.01         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 
       49.08         9.99        21.14        82.95       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       22.98        30.08         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
       18.28         9.96        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  PTPRJ MUTATED PTPRJ WILD-TYPE 
           1.02            0.00 
  PTPRJ MUTATED PTPRJ WILD-TYPE 
          51.32          148.01 
  PTPRJ MUTATED PTPRJ WILD-TYPE 
          18.00           20.19 
[1] "1.0 - 51.3 (18.0)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.8"
D1068V2, continuous
D1068V3, binary
                 cls
clus                0   1
  PTPRJ MUTATED    15   3
  PTPRJ WILD-TYPE 351 116
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPRJ MUTATED     15    3
  PTPRJ WILD-TYPE  351  116
        clus
vv       PTPRJ MUTATED PTPRJ WILD-TYPE
  COLON             15             351
  RECTUM             3             116
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PTPRJ MUTATED         5        0        1         6         0         0
  PTPRJ WILD-TYPE      86        1       31       132        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PTPRJ MUTATED           1          0          1          0        2         0
  PTPRJ WILD-TYPE        23         11         58         42       46        18
                 vv
clus              STAGE IVB
  PTPRJ MUTATED           0
  PTPRJ WILD-TYPE         1
D1068V4, multiclass
            clus
vv           PTPRJ MUTATED PTPRJ WILD-TYPE
  STAGE I                5              86
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              6             132
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             0              42
  STAGE IV               2              46
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PTPRJ MUTATED     1   6  10   1
  PTPRJ WILD-TYPE  16  86 319  49
D1068V5, multiclass
    clus
vv   PTPRJ MUTATED PTPRJ WILD-TYPE
  T1             1              16
  T2             6              86
  T3            10             319
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  PTPRJ MUTATED    13   3   2
  PTPRJ WILD-TYPE 274 110  85
D1068V6, multiclass
    clus
vv   PTPRJ MUTATED PTPRJ WILD-TYPE
  N0            13             274
  N1             3             110
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1068V7, binary
                 cls
clus                0   1
  PTPRJ MUTATED    11   2
  PTPRJ WILD-TYPE 364  63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPRJ MUTATED     11    2
  PTPRJ WILD-TYPE  364   63
   clus
vv  PTPRJ MUTATED PTPRJ WILD-TYPE
  0            11             364
  1             2              63
[1] 2 2
[1] FALSE
D1068V8, binary
                 cls
clus                0   1
  PTPRJ MUTATED     9   9
  PTPRJ WILD-TYPE 216 255
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPRJ MUTATED      9    9
  PTPRJ WILD-TYPE  216  255
        clus
vv       PTPRJ MUTATED PTPRJ WILD-TYPE
  FEMALE             9             216
  MALE               9             255
[1] 2 2
[1] FALSE
D1068V9, binary
                 cls
clus                0   1
  PTPRJ MUTATED    15   0
  PTPRJ WILD-TYPE 335  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPRJ MUTATED     15    0
  PTPRJ WILD-TYPE  335   22
     clus
vv    PTPRJ MUTATED PTPRJ WILD-TYPE
  NO             15             335
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PTPRJ MUTATED                     11                             4
  PTPRJ WILD-TYPE                  304                            43
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PTPRJ MUTATED                       3                              0
  PTPRJ WILD-TYPE                   103                             10
D1068V10, multiclass
                                clus
vv                               PTPRJ MUTATED PTPRJ WILD-TYPE
  COLON ADENOCARCINOMA                      11             304
  COLON MUCINOUS ADENOCARCINOMA              4              43
  RECTAL ADENOCARCINOMA                      3             103
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  PTPRJ MUTATED     9   0   1   3
  PTPRJ WILD-TYPE 336   4  30  22
D1068V11, multiclass
    clus
vv   PTPRJ MUTATED PTPRJ WILD-TYPE
  R0             9             336
  R1             0               4
  R2             1              30
  RX             3              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1068V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PTPRJ MUTATED                                  0     1
  PTPRJ WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PTPRJ MUTATED                           0    11
  PTPRJ WILD-TYPE                        22   215
D1068V13, multiclass
                                  clus
vv                                 PTPRJ MUTATED PTPRJ WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                       11             215
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1069) Variable = WDR5 MUTATION ANALYSIS
D1069V1, survival
                sevent
clus2              0   1
  WDR5 MUTATED     5   1
  WDR5 WILD-TYPE 373  92
  WDR5 MUTATED WDR5 WILD-TYPE 
             6            465 
  WDR5 MUTATED WDR5 WILD-TYPE 
             1             92 
$`WDR5 MUTATED`
TCGA-AA-3864 TCGA-AU-6004 TCGA-D5-6538 TCGA-F4-6809 TCGA-G4-6309 TCGA-G4-6586 
       53.00        27.09        17.13        13.25        85.48        35.80 

$`WDR5 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 
       27.42        10.88         0.20        14.50        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
        4.80        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       53.62        44.68        55.04        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       22.09        13.78        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  WDR5 MUTATED WDR5 WILD-TYPE 
         13.25           0.00 
  WDR5 MUTATED WDR5 WILD-TYPE 
         85.48         148.01 
  WDR5 MUTATED WDR5 WILD-TYPE 
        31.445         20.120 
[1] "13.2 - 85.5 (31.4)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.8"
D1069V2, continuous
D1069V3, binary
                cls
clus               0   1
  WDR5 MUTATED     6   0
  WDR5 WILD-TYPE 360 119
[1] "tbl2"
                cls
clus             [,1] [,2]
  WDR5 MUTATED      6    0
  WDR5 WILD-TYPE  360  119
        clus
vv       WDR5 MUTATED WDR5 WILD-TYPE
  COLON             6            360
  RECTUM            0            119
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  WDR5 MUTATED         1        0        1         1         0         0
  WDR5 WILD-TYPE      90        1       31       137        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  WDR5 MUTATED           0          0          2          0        0         1
  WDR5 WILD-TYPE        24         11         57         42       48        17
                vv
clus             STAGE IVB
  WDR5 MUTATED           0
  WDR5 WILD-TYPE         1
D1069V4, multiclass
            clus
vv           WDR5 MUTATED WDR5 WILD-TYPE
  STAGE I               1             90
  STAGE IA              0              1
  STAGE II              1             31
  STAGE IIA             1            137
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            2             57
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             1             17
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  WDR5 MUTATED     0   1   5   0
  WDR5 WILD-TYPE  17  91 324  50
D1069V5, multiclass
    clus
vv   WDR5 MUTATED WDR5 WILD-TYPE
  T1            0             17
  T2            1             91
  T3            5            324
  T4            0             50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  WDR5 MUTATED     3   2   1
  WDR5 WILD-TYPE 284 111  86
D1069V6, multiclass
    clus
vv   WDR5 MUTATED WDR5 WILD-TYPE
  N0            3            284
  N1            2            111
  N2            1             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1069V7, binary
                cls
clus               0   1
  WDR5 MUTATED     5   1
  WDR5 WILD-TYPE 370  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  WDR5 MUTATED      5    1
  WDR5 WILD-TYPE  370   64
   clus
vv  WDR5 MUTATED WDR5 WILD-TYPE
  0            5            370
  1            1             64
[1] 2 2
[1] FALSE
D1069V8, binary
                cls
clus               0   1
  WDR5 MUTATED     5   1
  WDR5 WILD-TYPE 220 263
[1] "tbl2"
                cls
clus             [,1] [,2]
  WDR5 MUTATED      5    1
  WDR5 WILD-TYPE  220  263
        clus
vv       WDR5 MUTATED WDR5 WILD-TYPE
  FEMALE            5            220
  MALE              1            263
[1] 2 2
[1] FALSE
D1069V9, binary
                cls
clus               0   1
  WDR5 MUTATED     5   0
  WDR5 WILD-TYPE 345  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  WDR5 MUTATED      5    0
  WDR5 WILD-TYPE  345   22
     clus
vv    WDR5 MUTATED WDR5 WILD-TYPE
  NO             5            345
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  WDR5 MUTATED                      6                             0
  WDR5 WILD-TYPE                  309                            47
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  WDR5 MUTATED                       0                              0
  WDR5 WILD-TYPE                   106                             10
D1069V10, multiclass
                                clus
vv                               WDR5 MUTATED WDR5 WILD-TYPE
  COLON ADENOCARCINOMA                      6            309
  COLON MUCINOUS ADENOCARCINOMA             0             47
  RECTAL ADENOCARCINOMA                     0            106
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  WDR5 MUTATED     6   0   0   0
  WDR5 WILD-TYPE 339   4  31  25
D1069V11, multiclass
    clus
vv   WDR5 MUTATED WDR5 WILD-TYPE
  R0            6            339
  R1            0              4
  R2            0             31
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1069V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  WDR5 MUTATED                                  0     0
  WDR5 WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  WDR5 MUTATED                           1     4
  WDR5 WILD-TYPE                        21   222
D1069V13, multiclass
                                  clus
vv                                 WDR5 MUTATED WDR5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                       4            222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1070) Variable = MAP3K4 MUTATION ANALYSIS
D1070V1, survival
                  sevent
clus2                0   1
  MAP3K4 MUTATED    25  12
  MAP3K4 WILD-TYPE 353  81
  MAP3K4 MUTATED MAP3K4 WILD-TYPE 
              37              434 
  MAP3K4 MUTATED MAP3K4 WILD-TYPE 
              12               81 
$`MAP3K4 MUTATED`
TCGA-A6-2676 TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3516 TCGA-AA-3697 TCGA-AA-3715 
       42.90         3.02        63.98        13.02        85.05        19.04 
TCGA-AA-3821 TCGA-AA-3833 TCGA-AA-3947 TCGA-AA-3968 TCGA-AA-3977 TCGA-AA-A00J 
        1.02        15.95        33.01        21.99        25.02        18.05 
TCGA-AA-A00K TCGA-AA-A01P TCGA-AA-A01R TCGA-AA-A02K TCGA-AD-6888 TCGA-AD-6889 
       18.05        38.07        35.01        14.01        15.52        56.55 
TCGA-AD-6964 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-6598 TCGA-AZ-6601 TCGA-CA-5254 
       10.88        58.39         1.41        49.41       100.01        12.69 
TCGA-CA-6716 TCGA-CM-4746 TCGA-CM-5349 TCGA-CM-5862 TCGA-CM-6165 TCGA-D5-6534 
       12.20        37.02        30.08         5.03        16.04        43.27 
TCGA-D5-6927 TCGA-F4-6703 TCGA-F4-6806 TCGA-G4-6628 TCGA-AG-3892 TCGA-AG-4001 
        9.44        47.87        41.42        79.69        13.02        36.03 
TCGA-AG-A02N 
       61.97 

$`MAP3K4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 
       20.12        19.66        20.28         7.04         1.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        6.97         1.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 
        5.98        37.05        19.00        36.00         5.03        26.99 
TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3831 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       17.98        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       12.99        24.00        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T 
       12.00        31.00        31.00         1.02         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        2.01         5.03         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       40.96         0.07        21.37         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4616 TCGA-AZ-4681 
        0.95        33.01        21.44        17.82         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 
       22.36        62.79        88.21         6.77        12.10        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19         1.61         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5860 
       25.02        13.02        29.06        22.03        22.98        32.02 
TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
       15.02        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
        2.96        29.03        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.04        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6807 TCGA-F4-6808 
       35.74         6.18         1.55        34.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       91.79        46.75        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 
        1.02        17.95        36.95        17.03        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4005 
        1.02        48.03        32.02        19.99        28.04        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  MAP3K4 MUTATED MAP3K4 WILD-TYPE 
            1.02             0.00 
  MAP3K4 MUTATED MAP3K4 WILD-TYPE 
          100.01           148.01 
  MAP3K4 MUTATED MAP3K4 WILD-TYPE 
          25.020           20.085 
[1] "1.0 - 100.0 (25.0)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.4"
D1070V2, continuous
D1070V3, binary
                  cls
clus                 0   1
  MAP3K4 MUTATED    36   3
  MAP3K4 WILD-TYPE 330 116
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP3K4 MUTATED     36    3
  MAP3K4 WILD-TYPE  330  116
        clus
vv       MAP3K4 MUTATED MAP3K4 WILD-TYPE
  COLON              36              330
  RECTUM              3              116
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MAP3K4 MUTATED         6        0        7        13         2         0
  MAP3K4 WILD-TYPE      85        1       25       125         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MAP3K4 MUTATED           4          0          2          0        2
  MAP3K4 WILD-TYPE        20         11         57         42       46
                  vv
clus               STAGE IVA STAGE IVB
  MAP3K4 MUTATED           1         0
  MAP3K4 WILD-TYPE        17         1
D1070V4, multiclass
            clus
vv           MAP3K4 MUTATED MAP3K4 WILD-TYPE
  STAGE I                 6               85
  STAGE IA                0                1
  STAGE II                7               25
  STAGE IIA              13              125
  STAGE IIB               2                8
  STAGE IIC               0                1
  STAGE III               4               20
  STAGE IIIA              0               11
  STAGE IIIB              2               57
  STAGE IIIC              0               42
  STAGE IV                2               46
  STAGE IVA               1               17
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  MAP3K4 MUTATED     1   6  25   7
  MAP3K4 WILD-TYPE  16  86 304  43
D1070V5, multiclass
    clus
vv   MAP3K4 MUTATED MAP3K4 WILD-TYPE
  T1              1               16
  T2              6               86
  T3             25              304
  T4              7               43
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  MAP3K4 MUTATED    30   4   5
  MAP3K4 WILD-TYPE 257 109  82
D1070V6, multiclass
    clus
vv   MAP3K4 MUTATED MAP3K4 WILD-TYPE
  N0             30              257
  N1              4              109
  N2              5               82
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1070V7, binary
                  cls
clus                 0   1
  MAP3K4 MUTATED    33   3
  MAP3K4 WILD-TYPE 342  62
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP3K4 MUTATED     33    3
  MAP3K4 WILD-TYPE  342   62
   clus
vv  MAP3K4 MUTATED MAP3K4 WILD-TYPE
  0             33              342
  1              3               62
[1] 2 2
[1] FALSE
D1070V8, binary
                  cls
clus                 0   1
  MAP3K4 MUTATED    17  22
  MAP3K4 WILD-TYPE 208 242
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP3K4 MUTATED     17   22
  MAP3K4 WILD-TYPE  208  242
        clus
vv       MAP3K4 MUTATED MAP3K4 WILD-TYPE
  FEMALE             17              208
  MALE               22              242
[1] 2 2
[1] FALSE
D1070V9, binary
                  cls
clus                 0   1
  MAP3K4 MUTATED    33   1
  MAP3K4 WILD-TYPE 317  21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP3K4 MUTATED     33    1
  MAP3K4 WILD-TYPE  317   21
     clus
vv    MAP3K4 MUTATED MAP3K4 WILD-TYPE
  NO              33              317
  YES              1               21
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MAP3K4 MUTATED                     30                             6
  MAP3K4 WILD-TYPE                  285                            41
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MAP3K4 MUTATED                       3                              0
  MAP3K4 WILD-TYPE                   103                             10
D1070V10, multiclass
                                clus
vv                               MAP3K4 MUTATED MAP3K4 WILD-TYPE
  COLON ADENOCARCINOMA                       30              285
  COLON MUCINOUS ADENOCARCINOMA               6               41
  RECTAL ADENOCARCINOMA                       3              103
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  MAP3K4 MUTATED    29   0   1   2
  MAP3K4 WILD-TYPE 316   4  30  23
D1070V11, multiclass
    clus
vv   MAP3K4 MUTATED MAP3K4 WILD-TYPE
  R0             29              316
  R1              0                4
  R2              1               30
  RX              2               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1070V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MAP3K4 MUTATED                                  0     3
  MAP3K4 WILD-TYPE                                1     8
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  MAP3K4 MUTATED                           1    15
  MAP3K4 WILD-TYPE                        21   211
D1070V13, multiclass
                                  clus
vv                                 MAP3K4 MUTATED MAP3K4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         3                8
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                        15              211
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1071) Variable = KRTAP5-3 MUTATION ANALYSIS
D1071V1, survival
                    sevent
clus2                  0   1
  KRTAP5-3 MUTATED     4   0
  KRTAP5-3 WILD-TYPE 374  93
  KRTAP5-3 MUTATED KRTAP5-3 WILD-TYPE 
                 4                467 
  KRTAP5-3 MUTATED KRTAP5-3 WILD-TYPE 
                 0                 93 
$`KRTAP5-3 MUTATED`
TCGA-AA-3966 TCGA-CA-6717 TCGA-CM-6169 TCGA-G4-6310 
        2.01        12.76        13.02        63.62 

$`KRTAP5-3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 
       24.00         2.01        20.98        34.03        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07        12.20        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       14.99        12.99        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6315 
       65.85        53.62        44.68        55.04        85.48        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  KRTAP5-3 MUTATED KRTAP5-3 WILD-TYPE 
              2.01               0.00 
  KRTAP5-3 MUTATED KRTAP5-3 WILD-TYPE 
             63.62             148.01 
  KRTAP5-3 MUTATED KRTAP5-3 WILD-TYPE 
             12.89              20.28 
[1] "2.0 - 63.6 (12.9)"  "0.0 - 148.0 (20.3)"
[1] "hr="     "3300000"
D1071V2, continuous
D1071V3, binary
                    cls
clus                   0   1
  KRTAP5-3 MUTATED     4   0
  KRTAP5-3 WILD-TYPE 362 119
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KRTAP5-3 MUTATED      4    0
  KRTAP5-3 WILD-TYPE  362  119
        clus
vv       KRTAP5-3 MUTATED KRTAP5-3 WILD-TYPE
  COLON                 4                362
  RECTUM                0                119
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KRTAP5-3 MUTATED         0        0        0         3         0         0
  KRTAP5-3 WILD-TYPE      91        1       32       135        10         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KRTAP5-3 MUTATED           0          0          1          0        0
  KRTAP5-3 WILD-TYPE        24         11         58         42       48
                    vv
clus                 STAGE IVA STAGE IVB
  KRTAP5-3 MUTATED           0         0
  KRTAP5-3 WILD-TYPE        18         1
D1071V4, multiclass
            clus
vv           KRTAP5-3 MUTATED KRTAP5-3 WILD-TYPE
  STAGE I                   0                 91
  STAGE IA                  0                  1
  STAGE II                  0                 32
  STAGE IIA                 3                135
  STAGE IIB                 0                 10
  STAGE IIC                 0                  1
  STAGE III                 0                 24
  STAGE IIIA                0                 11
  STAGE IIIB                1                 58
  STAGE IIIC                0                 42
  STAGE IV                  0                 48
  STAGE IVA                 0                 18
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  KRTAP5-3 MUTATED     0   0   4   0
  KRTAP5-3 WILD-TYPE  17  92 325  50
D1071V5, multiclass
    clus
vv   KRTAP5-3 MUTATED KRTAP5-3 WILD-TYPE
  T1                0                 17
  T2                0                 92
  T3                4                325
  T4                0                 50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  KRTAP5-3 MUTATED     3   1   0
  KRTAP5-3 WILD-TYPE 284 112  87
D1071V6, multiclass
    clus
vv   KRTAP5-3 MUTATED KRTAP5-3 WILD-TYPE
  N0                3                284
  N1                1                112
  N2                0                 87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1071V7, binary
                    cls
clus                   0   1
  KRTAP5-3 MUTATED     4   0
  KRTAP5-3 WILD-TYPE 371  65
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KRTAP5-3 MUTATED      4    0
  KRTAP5-3 WILD-TYPE  371   65
   clus
vv  KRTAP5-3 MUTATED KRTAP5-3 WILD-TYPE
  0                4                371
  1                0                 65
[1] 2 2
[1] FALSE
D1071V8, binary
                    cls
clus                   0   1
  KRTAP5-3 MUTATED     1   3
  KRTAP5-3 WILD-TYPE 224 261
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KRTAP5-3 MUTATED      1    3
  KRTAP5-3 WILD-TYPE  224  261
        clus
vv       KRTAP5-3 MUTATED KRTAP5-3 WILD-TYPE
  FEMALE                1                224
  MALE                  3                261
[1] 2 2
[1] FALSE
D1071V9, binary
                    cls
clus                   0   1
  KRTAP5-3 MUTATED     2   1
  KRTAP5-3 WILD-TYPE 348  21
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KRTAP5-3 MUTATED      2    1
  KRTAP5-3 WILD-TYPE  348   21
     clus
vv    KRTAP5-3 MUTATED KRTAP5-3 WILD-TYPE
  NO                 2                348
  YES                1                 21
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  KRTAP5-3 MUTATED                      2                             2
  KRTAP5-3 WILD-TYPE                  313                            45
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  KRTAP5-3 MUTATED                       0                              0
  KRTAP5-3 WILD-TYPE                   106                             10
D1071V10, multiclass
                                clus
vv                               KRTAP5-3 MUTATED KRTAP5-3 WILD-TYPE
  COLON ADENOCARCINOMA                          2                313
  COLON MUCINOUS ADENOCARCINOMA                 2                 45
  RECTAL ADENOCARCINOMA                         0                106
  RECTAL MUCINOUS ADENOCARCINOMA                0                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  KRTAP5-3 MUTATED     2   0   0   1
  KRTAP5-3 WILD-TYPE 343   4  31  24
D1071V11, multiclass
    clus
vv   KRTAP5-3 MUTATED KRTAP5-3 WILD-TYPE
  R0                2                343
  R1                0                  4
  R2                0                 31
  RX                1                 24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1071V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KRTAP5-3 MUTATED                                  0     1
  KRTAP5-3 WILD-TYPE                                1    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  KRTAP5-3 MUTATED                           1     1
  KRTAP5-3 WILD-TYPE                        21   225
D1071V13, multiclass
                                  clus
vv                                 KRTAP5-3 MUTATED KRTAP5-3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                 10
  BLACK OR AFRICAN AMERICAN                       1                 21
  WHITE                                           1                225
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1072) Variable = CPS1 MUTATION ANALYSIS
D1072V1, survival
                sevent
clus2              0   1
  CPS1 MUTATED    27   6
  CPS1 WILD-TYPE 351  87
  CPS1 MUTATED CPS1 WILD-TYPE 
            33            438 
  CPS1 MUTATED CPS1 WILD-TYPE 
             6             87 
$`CPS1 MUTATED`
TCGA-A6-5660 TCGA-A6-5665 TCGA-AA-3516 TCGA-AA-3672 TCGA-AA-3811 TCGA-AA-3861 
       29.19        22.06        13.02         0.92        10.06        30.05 
TCGA-AA-3947 TCGA-AA-3968 TCGA-AA-3977 TCGA-AA-A010 TCGA-AA-A01K TCGA-AD-6889 
       33.01        21.99        25.02        34.98        31.00        56.55 
TCGA-AZ-4315 TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-5861 
       58.39        12.76        10.06        23.05        37.02        15.02 
TCGA-CM-6169 TCGA-CM-6172 TCGA-D5-5541 TCGA-D5-6537 TCGA-D5-6930 TCGA-DM-A0XF 
       13.02        11.01        55.92         4.80         1.51        38.20 
TCGA-DM-A1D6 TCGA-G4-6299 TCGA-G4-6307 TCGA-G4-6321 TCGA-G4-6628 TCGA-AG-3892 
       49.91        74.56        55.04        22.09        79.69        13.02 
TCGA-AG-A002 TCGA-CI-6622 TCGA-G5-6235 
       20.98         6.97        55.76 

$`CPS1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        33.53        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
       63.98         6.97         1.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
        2.01        14.01        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       26.99        19.04        19.04        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 
       31.00         2.01        12.99        24.00        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3972 
        2.01        20.98        34.03         2.01        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01P 
        1.02        10.98        32.02        12.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
        0.07        21.37        15.52         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
       16.31         0.95        33.01        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.07        12.20        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
        1.91       124.27        20.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 
       22.03        22.98        30.08        32.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6170 TCGA-CM-6171 
       16.04        21.99        14.99        12.99        15.02        14.04 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-6529 
       12.03        45.40        12.26        19.59        56.09        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6538 
       18.25         1.32        43.27        15.12        17.85        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A1D0 
       12.00        11.38        10.26       119.70        24.43       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       92.75        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6310 
      133.18        65.85        53.62        44.68        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       61.91        36.00        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       46.75        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       17.95        36.95        17.03        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6624 TCGA-CL-5917 
        0.69         0.72         6.05        33.17         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6641 
       31.30        28.57        32.19         0.66         0.69        26.43 

  CPS1 MUTATED CPS1 WILD-TYPE 
          0.92           0.00 
  CPS1 MUTATED CPS1 WILD-TYPE 
         79.69         148.01 
  CPS1 MUTATED CPS1 WILD-TYPE 
        23.050         20.005 
[1] "0.9 - 79.7 (23.1)"  "0.0 - 148.0 (20.0)"
[1] "hr=" "1.3"
D1072V2, continuous
D1072V3, binary
                cls
clus               0   1
  CPS1 MUTATED    30   4
  CPS1 WILD-TYPE 336 115
[1] "tbl2"
                cls
clus             [,1] [,2]
  CPS1 MUTATED     30    4
  CPS1 WILD-TYPE  336  115
        clus
vv       CPS1 MUTATED CPS1 WILD-TYPE
  COLON            30            336
  RECTUM            4            115
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CPS1 MUTATED         5        0        0        12         3         0
  CPS1 WILD-TYPE      86        1       32       126         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CPS1 MUTATED           4          0          5          4        0         0
  CPS1 WILD-TYPE        20         11         54         38       48        18
                vv
clus             STAGE IVB
  CPS1 MUTATED           0
  CPS1 WILD-TYPE         1
D1072V4, multiclass
            clus
vv           CPS1 MUTATED CPS1 WILD-TYPE
  STAGE I               5             86
  STAGE IA              0              1
  STAGE II              0             32
  STAGE IIA            12            126
  STAGE IIB             3              7
  STAGE IIC             0              1
  STAGE III             4             20
  STAGE IIIA            0             11
  STAGE IIIB            5             54
  STAGE IIIC            4             38
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  CPS1 MUTATED     1   6  24   3
  CPS1 WILD-TYPE  16  86 305  47
D1072V5, multiclass
    clus
vv   CPS1 MUTATED CPS1 WILD-TYPE
  T1            1             16
  T2            6             86
  T3           24            305
  T4            3             47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  CPS1 MUTATED    21   7   6
  CPS1 WILD-TYPE 266 106  81
D1072V6, multiclass
    clus
vv   CPS1 MUTATED CPS1 WILD-TYPE
  N0           21            266
  N1            7            106
  N2            6             81
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1072V7, binary
                cls
clus               0   1
  CPS1 MUTATED    30   0
  CPS1 WILD-TYPE 345  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  CPS1 MUTATED     30    0
  CPS1 WILD-TYPE  345   65
   clus
vv  CPS1 MUTATED CPS1 WILD-TYPE
  0           30            345
  1            0             65
[1] 2 2
[1] FALSE
D1072V8, binary
                cls
clus               0   1
  CPS1 MUTATED    15  19
  CPS1 WILD-TYPE 210 245
[1] "tbl2"
                cls
clus             [,1] [,2]
  CPS1 MUTATED     15   19
  CPS1 WILD-TYPE  210  245
        clus
vv       CPS1 MUTATED CPS1 WILD-TYPE
  FEMALE           15            210
  MALE             19            245
[1] 2 2
[1] FALSE
D1072V9, binary
                cls
clus               0   1
  CPS1 MUTATED    28   0
  CPS1 WILD-TYPE 322  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  CPS1 MUTATED     28    0
  CPS1 WILD-TYPE  322   22
     clus
vv    CPS1 MUTATED CPS1 WILD-TYPE
  NO            28            322
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CPS1 MUTATED                     24                             5
  CPS1 WILD-TYPE                  291                            42
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CPS1 MUTATED                       4                              0
  CPS1 WILD-TYPE                   102                             10
D1072V10, multiclass
                                clus
vv                               CPS1 MUTATED CPS1 WILD-TYPE
  COLON ADENOCARCINOMA                     24            291
  COLON MUCINOUS ADENOCARCINOMA             5             42
  RECTAL ADENOCARCINOMA                     4            102
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  CPS1 MUTATED    24   1   0   2
  CPS1 WILD-TYPE 321   3  31  23
D1072V11, multiclass
    clus
vv   CPS1 MUTATED CPS1 WILD-TYPE
  R0           24            321
  R1            1              3
  R2            0             31
  RX            2             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1072V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CPS1 MUTATED                                  0     3
  CPS1 WILD-TYPE                                1     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  CPS1 MUTATED                           3    16
  CPS1 WILD-TYPE                        19   210
D1072V13, multiclass
                                  clus
vv                                 CPS1 MUTATED CPS1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       3              8
  BLACK OR AFRICAN AMERICAN                   3             19
  WHITE                                      16            210
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1073) Variable = MDN1 MUTATION ANALYSIS
D1073V1, survival
                sevent
clus2              0   1
  MDN1 MUTATED    41  14
  MDN1 WILD-TYPE 337  79
  MDN1 MUTATED MDN1 WILD-TYPE 
            55            416 
  MDN1 MUTATED MDN1 WILD-TYPE 
            14             79 
$`MDN1 MUTATED`
TCGA-A6-2676 TCGA-A6-4105 TCGA-A6-5665 TCGA-A6-6653 TCGA-A6-6780 TCGA-AA-3492 
       42.90        14.53        22.06        24.39        20.12         3.02 
TCGA-AA-3510 TCGA-AA-3516 TCGA-AA-3555 TCGA-AA-3655 TCGA-AA-3672 TCGA-AA-3685 
       63.98        13.02        29.95        61.02         0.92        37.05 
TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3815 TCGA-AA-3821 TCGA-AA-3842 TCGA-AA-3845 
       85.05        19.04        33.04         1.02        37.02         0.00 
TCGA-AA-3855 TCGA-AA-3877 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3977 TCGA-AA-A004 
       32.05        31.00        33.01        26.01        25.02        13.94 
TCGA-AA-A00J TCGA-AA-A00N TCGA-AA-A010 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6963 
       18.05         4.01        34.98        15.52        56.55        27.42 
TCGA-AY-4070 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-CA-6717 TCGA-CA-6718 
       16.31        58.39        49.41        12.10        12.76        10.06 
TCGA-CK-4950 TCGA-CK-5916 TCGA-CM-5349 TCGA-CM-6162 TCGA-CM-6168 TCGA-CM-6680 
       85.45        21.14        30.08        12.00        12.99        12.03 
TCGA-DM-A1HB TCGA-DM-A28C TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6304 
      135.65        81.37        35.31       133.18        74.56        53.62 
TCGA-G4-6317 TCGA-G4-6588 TCGA-G4-6628 TCGA-AG-3593 TCGA-AG-3600 TCGA-AG-A002 
       36.00        26.17        79.69        34.03         6.05        20.98 
TCGA-DY-A0XA 
      126.44 

$`MDN1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 
       34.65        33.34        32.75        36.53        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 
       30.44        29.19        33.53        23.61        22.09        32.71 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       27.09        22.52         8.38        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 
       21.76        24.69        23.87        19.66        20.28         7.04 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 
        1.02        35.01         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       24.00        17.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       19.99        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
       14.01        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 
       19.00        36.00         5.03        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
       35.05         0.99        25.02        17.98        15.95        38.99 
TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
       14.93        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       36.03         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 
       17.03        24.03        27.02        29.98        18.05         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       12.99        24.00        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K 
       27.02        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6890 TCGA-AD-6895 
       18.05        40.96         0.07        21.37         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        10.88         0.20        14.50        27.09 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        33.01        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6601 
      106.75        22.36        62.79        88.21         6.77       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 
        3.06         3.25         3.29         0.07        12.20        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
       17.56       148.01        15.62        49.08        51.32         9.99 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5860 
       25.02        13.02        29.06        22.03        22.98        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6169 
        2.96        29.03        16.04        21.99        14.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.08        11.01        10.06        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28E TCGA-DM-A28F 
       44.32       131.51       139.17         6.12       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6303 TCGA-G4-6306 
       33.67        13.25         0.53        47.41        65.85        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6321 TCGA-G4-6323 
       55.04        85.48        63.62        61.91        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       35.80        91.79        46.75        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 
       46.03         2.01        50.04        12.03         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
        5.29        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  MDN1 MUTATED MDN1 WILD-TYPE 
             0              0 
  MDN1 MUTATED MDN1 WILD-TYPE 
        135.65         148.01 
  MDN1 MUTATED MDN1 WILD-TYPE 
         27.42          19.99 
[1] "0.0 - 135.7 (27.4)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1"  
D1073V2, continuous
D1073V3, binary
                cls
clus               0   1
  MDN1 MUTATED    53   4
  MDN1 WILD-TYPE 313 115
[1] "tbl2"
                cls
clus             [,1] [,2]
  MDN1 MUTATED     53    4
  MDN1 WILD-TYPE  313  115
        clus
vv       MDN1 MUTATED MDN1 WILD-TYPE
  COLON            53            313
  RECTUM            4            115
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MDN1 MUTATED         8        0        7        18         5         0
  MDN1 WILD-TYPE      83        1       25       120         5         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MDN1 MUTATED           4          1          7          4        1         0
  MDN1 WILD-TYPE        20         10         52         38       47        18
                vv
clus             STAGE IVB
  MDN1 MUTATED           0
  MDN1 WILD-TYPE         1
D1073V4, multiclass
            clus
vv           MDN1 MUTATED MDN1 WILD-TYPE
  STAGE I               8             83
  STAGE IA              0              1
  STAGE II              7             25
  STAGE IIA            18            120
  STAGE IIB             5              5
  STAGE IIC             0              1
  STAGE III             4             20
  STAGE IIIA            1             10
  STAGE IIIB            7             52
  STAGE IIIC            4             38
  STAGE IV              1             47
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  MDN1 MUTATED     2   8  39   8
  MDN1 WILD-TYPE  15  84 290  42
D1073V5, multiclass
    clus
vv   MDN1 MUTATED MDN1 WILD-TYPE
  T1            2             15
  T2            8             84
  T3           39            290
  T4            8             42
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  MDN1 MUTATED    41  10   6
  MDN1 WILD-TYPE 246 103  81
D1073V6, multiclass
    clus
vv   MDN1 MUTATED MDN1 WILD-TYPE
  N0           41            246
  N1           10            103
  N2            6             81
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1073V7, binary
                cls
clus               0   1
  MDN1 MUTATED    51   1
  MDN1 WILD-TYPE 324  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  MDN1 MUTATED     51    1
  MDN1 WILD-TYPE  324   64
   clus
vv  MDN1 MUTATED MDN1 WILD-TYPE
  0           51            324
  1            1             64
[1] 2 2
[1] FALSE
D1073V8, binary
                cls
clus               0   1
  MDN1 MUTATED    29  28
  MDN1 WILD-TYPE 196 236
[1] "tbl2"
                cls
clus             [,1] [,2]
  MDN1 MUTATED     29   28
  MDN1 WILD-TYPE  196  236
        clus
vv       MDN1 MUTATED MDN1 WILD-TYPE
  FEMALE           29            196
  MALE             28            236
[1] 2 2
[1] FALSE
D1073V9, binary
                cls
clus               0   1
  MDN1 MUTATED    46   2
  MDN1 WILD-TYPE 304  20
[1] "tbl2"
                cls
clus             [,1] [,2]
  MDN1 MUTATED     46    2
  MDN1 WILD-TYPE  304   20
     clus
vv    MDN1 MUTATED MDN1 WILD-TYPE
  NO            46            304
  YES            2             20
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MDN1 MUTATED                     40                            12
  MDN1 WILD-TYPE                  275                            35
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MDN1 MUTATED                       4                              0
  MDN1 WILD-TYPE                   102                             10
D1073V10, multiclass
                                clus
vv                               MDN1 MUTATED MDN1 WILD-TYPE
  COLON ADENOCARCINOMA                     40            275
  COLON MUCINOUS ADENOCARCINOMA            12             35
  RECTAL ADENOCARCINOMA                     4            102
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  MDN1 MUTATED    40   2   0   3
  MDN1 WILD-TYPE 305   2  31  22
D1073V11, multiclass
    clus
vv   MDN1 MUTATED MDN1 WILD-TYPE
  R0           40            305
  R1            2              2
  R2            0             31
  RX            3             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1073V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MDN1 MUTATED                                  0     3
  MDN1 WILD-TYPE                                1     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  MDN1 MUTATED                           4    23
  MDN1 WILD-TYPE                        18   203
D1073V13, multiclass
                                  clus
vv                                 MDN1 MUTATED MDN1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       3              8
  BLACK OR AFRICAN AMERICAN                   4             18
  WHITE                                      23            203
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1074) Variable = COCH MUTATION ANALYSIS
D1074V1, survival
                sevent
clus2              0   1
  COCH MUTATED     5   1
  COCH WILD-TYPE 373  92
  COCH MUTATED COCH WILD-TYPE 
             6            465 
  COCH MUTATED COCH WILD-TYPE 
             1             92 
$`COCH MUTATED`
TCGA-AA-3496 TCGA-AA-3713 TCGA-AA-3949 TCGA-CA-6717 TCGA-CM-5860 TCGA-AF-5654 
        1.02        19.04        26.01        12.76        32.02        16.83 

$`COCH WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       12.99        24.00        33.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-5862 
       29.06        22.03        22.98        30.08        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       34.49        10.39        14.50        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  COCH MUTATED COCH WILD-TYPE 
          1.02           0.00 
  COCH MUTATED COCH WILD-TYPE 
         32.02         148.01 
  COCH MUTATED COCH WILD-TYPE 
        17.935         20.280 
[1] "1.0 - 32.0 (17.9)"  "0.0 - 148.0 (20.3)"
[1] "hr=" "1.3"
D1074V2, continuous
D1074V3, binary
                cls
clus               0   1
  COCH MUTATED     6   1
  COCH WILD-TYPE 360 118
[1] "tbl2"
                cls
clus             [,1] [,2]
  COCH MUTATED      6    1
  COCH WILD-TYPE  360  118
        clus
vv       COCH MUTATED COCH WILD-TYPE
  COLON             6            360
  RECTUM            1            118
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  COCH MUTATED         1        0        1         3         0         0
  COCH WILD-TYPE      90        1       31       135        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  COCH MUTATED           0          0          1          0        1         0
  COCH WILD-TYPE        24         11         58         42       47        18
                vv
clus             STAGE IVB
  COCH MUTATED           0
  COCH WILD-TYPE         1
D1074V4, multiclass
            clus
vv           COCH MUTATED COCH WILD-TYPE
  STAGE I               1             90
  STAGE IA              0              1
  STAGE II              1             31
  STAGE IIA             3            135
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            1             58
  STAGE IIIC            0             42
  STAGE IV              1             47
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  COCH MUTATED     0   1   6   0
  COCH WILD-TYPE  17  91 323  50
D1074V5, multiclass
    clus
vv   COCH MUTATED COCH WILD-TYPE
  T1            0             17
  T2            1             91
  T3            6            323
  T4            0             50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  COCH MUTATED     6   1   0
  COCH WILD-TYPE 281 112  87
D1074V6, multiclass
    clus
vv   COCH MUTATED COCH WILD-TYPE
  N0            6            281
  N1            1            112
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1074V7, binary
                cls
clus               0   1
  COCH MUTATED     6   1
  COCH WILD-TYPE 369  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  COCH MUTATED      6    1
  COCH WILD-TYPE  369   64
   clus
vv  COCH MUTATED COCH WILD-TYPE
  0            6            369
  1            1             64
[1] 2 2
[1] FALSE
D1074V8, binary
                cls
clus               0   1
  COCH MUTATED     4   3
  COCH WILD-TYPE 221 261
[1] "tbl2"
                cls
clus             [,1] [,2]
  COCH MUTATED      4    3
  COCH WILD-TYPE  221  261
        clus
vv       COCH MUTATED COCH WILD-TYPE
  FEMALE            4            221
  MALE              3            261
[1] 2 2
[1] FALSE
D1074V9, binary
                cls
clus               0   1
  COCH MUTATED     4   1
  COCH WILD-TYPE 346  21
[1] "tbl2"
                cls
clus             [,1] [,2]
  COCH MUTATED      4    1
  COCH WILD-TYPE  346   21
     clus
vv    COCH MUTATED COCH WILD-TYPE
  NO             4            346
  YES            1             21
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  COCH MUTATED                      4                             2
  COCH WILD-TYPE                  311                            45
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  COCH MUTATED                       1                              0
  COCH WILD-TYPE                   105                             10
D1074V10, multiclass
                                clus
vv                               COCH MUTATED COCH WILD-TYPE
  COLON ADENOCARCINOMA                      4            311
  COLON MUCINOUS ADENOCARCINOMA             2             45
  RECTAL ADENOCARCINOMA                     1            105
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  COCH MUTATED     5   0   1   1
  COCH WILD-TYPE 340   4  30  24
D1074V11, multiclass
    clus
vv   COCH MUTATED COCH WILD-TYPE
  R0            5            340
  R1            0              4
  R2            1             30
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1074V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  COCH MUTATED                                  0     1
  COCH WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  COCH MUTATED                           0     2
  COCH WILD-TYPE                        22   224
D1074V13, multiclass
                                  clus
vv                                 COCH MUTATED COCH WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       2            224
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1075) Variable = MFSD9 MUTATION ANALYSIS
D1075V1, survival
                 sevent
clus2               0   1
  MFSD9 MUTATED     8   3
  MFSD9 WILD-TYPE 370  90
  MFSD9 MUTATED MFSD9 WILD-TYPE 
             11             460 
  MFSD9 MUTATED MFSD9 WILD-TYPE 
              3              90 
$`MFSD9 MUTATED`
TCGA-A6-6781 TCGA-AA-3492 TCGA-AA-3518 TCGA-AA-A024 TCGA-AU-6004 TCGA-CK-6747 
       19.66         3.02         1.02        39.06        27.09        82.95 
TCGA-CM-4743 TCGA-DM-A28F TCGA-DM-A28H TCGA-G4-6299 TCGA-G4-6588 
       23.05        35.97       117.07        74.56        26.17 

$`MFSD9 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 
       23.87        20.12        20.28         7.04         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3519 
       63.98         6.97         1.02        13.02        38.99         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       35.01        26.01        37.02        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       14.50        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 
       51.32         9.99        21.14         1.91       124.27        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28G TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
       60.79        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6303 
       13.25         0.53        47.41        35.31       133.18        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        35.80        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  MFSD9 MUTATED MFSD9 WILD-TYPE 
           1.02            0.00 
  MFSD9 MUTATED MFSD9 WILD-TYPE 
         117.07          148.01 
  MFSD9 MUTATED MFSD9 WILD-TYPE 
         27.090          20.035 
[1] "1.0 - 117.1 (27.1)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.1"
D1075V2, continuous
D1075V3, binary
                 cls
clus                0   1
  MFSD9 MUTATED    12   0
  MFSD9 WILD-TYPE 354 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MFSD9 MUTATED     12    0
  MFSD9 WILD-TYPE  354  119
        clus
vv       MFSD9 MUTATED MFSD9 WILD-TYPE
  COLON             12             354
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MFSD9 MUTATED         1        0        2         5         0         0
  MFSD9 WILD-TYPE      90        1       30       133        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MFSD9 MUTATED           0          0          1          3        0         0
  MFSD9 WILD-TYPE        24         11         58         39       48        18
                 vv
clus              STAGE IVB
  MFSD9 MUTATED           0
  MFSD9 WILD-TYPE         1
D1075V4, multiclass
            clus
vv           MFSD9 MUTATED MFSD9 WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA              5             133
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             3              39
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  MFSD9 MUTATED     0   1  10   1
  MFSD9 WILD-TYPE  17  91 319  49
D1075V5, multiclass
    clus
vv   MFSD9 MUTATED MFSD9 WILD-TYPE
  T1             0              17
  T2             1              91
  T3            10             319
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  MFSD9 MUTATED     8   2   2
  MFSD9 WILD-TYPE 279 111  85
D1075V6, multiclass
    clus
vv   MFSD9 MUTATED MFSD9 WILD-TYPE
  N0             8             279
  N1             2             111
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1075V7, binary
                 cls
clus                0   1
  MFSD9 MUTATED    10   0
  MFSD9 WILD-TYPE 365  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MFSD9 MUTATED     10    0
  MFSD9 WILD-TYPE  365   65
   clus
vv  MFSD9 MUTATED MFSD9 WILD-TYPE
  0            10             365
  1             0              65
[1] 2 2
[1] FALSE
D1075V8, binary
                 cls
clus                0   1
  MFSD9 MUTATED     6   6
  MFSD9 WILD-TYPE 219 258
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MFSD9 MUTATED      6    6
  MFSD9 WILD-TYPE  219  258
        clus
vv       MFSD9 MUTATED MFSD9 WILD-TYPE
  FEMALE             6             219
  MALE               6             258
[1] 2 2
[1] FALSE
D1075V9, binary
                 cls
clus                0   1
  MFSD9 MUTATED     7   0
  MFSD9 WILD-TYPE 343  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MFSD9 MUTATED      7    0
  MFSD9 WILD-TYPE  343   22
     clus
vv    MFSD9 MUTATED MFSD9 WILD-TYPE
  NO              7             343
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MFSD9 MUTATED                     10                             2
  MFSD9 WILD-TYPE                  305                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MFSD9 MUTATED                       0                              0
  MFSD9 WILD-TYPE                   106                             10
D1075V10, multiclass
                                clus
vv                               MFSD9 MUTATED MFSD9 WILD-TYPE
  COLON ADENOCARCINOMA                      10             305
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  MFSD9 MUTATED     9   0   0   1
  MFSD9 WILD-TYPE 336   4  31  24
D1075V11, multiclass
    clus
vv   MFSD9 MUTATED MFSD9 WILD-TYPE
  R0             9             336
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1075V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MFSD9 MUTATED                                  0     0
  MFSD9 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  MFSD9 MUTATED                           0     8
  MFSD9 WILD-TYPE                        22   218
D1075V13, multiclass
                                  clus
vv                                 MFSD9 MUTATED MFSD9 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        8             218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1076) Variable = HSPA4L MUTATION ANALYSIS
D1076V1, survival
                  sevent
clus2                0   1
  HSPA4L MUTATED     9   3
  HSPA4L WILD-TYPE 369  90
  HSPA4L MUTATED HSPA4L WILD-TYPE 
              12              459 
  HSPA4L MUTATED HSPA4L WILD-TYPE 
               3               90 
$`HSPA4L MUTATED`
TCGA-AA-3555 TCGA-AA-3663 TCGA-AA-3715 TCGA-AA-3950 TCGA-AZ-4315 TCGA-CA-6717 
       29.95         6.97        19.04        24.00        58.39        12.76 
TCGA-DM-A28H TCGA-G4-6310 TCGA-AG-3892 TCGA-AG-A002 TCGA-DY-A1DF TCGA-DY-A1H8 
      117.07        63.62        13.02        20.98        24.13        32.61 

$`HSPA4L WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 
       21.01        13.02        24.00        17.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        33.01        26.01         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07        12.20        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
      119.93        35.97        60.79        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       85.48        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DG TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       51.48         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  HSPA4L MUTATED HSPA4L WILD-TYPE 
            6.97             0.00 
  HSPA4L MUTATED HSPA4L WILD-TYPE 
          117.07           148.01 
  HSPA4L MUTATED HSPA4L WILD-TYPE 
          24.065           20.050 
[1] "7.0 - 117.1 (24.1)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1"  
D1076V2, continuous
D1076V3, binary
                  cls
clus                 0   1
  HSPA4L MUTATED     8   4
  HSPA4L WILD-TYPE 358 115
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HSPA4L MUTATED      8    4
  HSPA4L WILD-TYPE  358  115
        clus
vv       HSPA4L MUTATED HSPA4L WILD-TYPE
  COLON               8              358
  RECTUM              4              115
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  HSPA4L MUTATED         2        0        2         4         0         0
  HSPA4L WILD-TYPE      89        1       30       134        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HSPA4L MUTATED           0          1          1          2        0
  HSPA4L WILD-TYPE        24         10         58         40       48
                  vv
clus               STAGE IVA STAGE IVB
  HSPA4L MUTATED           0         0
  HSPA4L WILD-TYPE        18         1
D1076V4, multiclass
            clus
vv           HSPA4L MUTATED HSPA4L WILD-TYPE
  STAGE I                 2               89
  STAGE IA                0                1
  STAGE II                2               30
  STAGE IIA               4              134
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              1               10
  STAGE IIIB              1               58
  STAGE IIIC              2               40
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  HSPA4L MUTATED     1   2   9   0
  HSPA4L WILD-TYPE  16  90 320  50
D1076V5, multiclass
    clus
vv   HSPA4L MUTATED HSPA4L WILD-TYPE
  T1              1               16
  T2              2               90
  T3              9              320
  T4              0               50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  HSPA4L MUTATED     8   2   2
  HSPA4L WILD-TYPE 279 111  85
D1076V6, multiclass
    clus
vv   HSPA4L MUTATED HSPA4L WILD-TYPE
  N0              8              279
  N1              2              111
  N2              2               85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1076V7, binary
                  cls
clus                 0   1
  HSPA4L MUTATED    12   0
  HSPA4L WILD-TYPE 363  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HSPA4L MUTATED     12    0
  HSPA4L WILD-TYPE  363   65
   clus
vv  HSPA4L MUTATED HSPA4L WILD-TYPE
  0             12              363
  1              0               65
[1] 2 2
[1] FALSE
D1076V8, binary
                  cls
clus                 0   1
  HSPA4L MUTATED     5   7
  HSPA4L WILD-TYPE 220 257
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HSPA4L MUTATED      5    7
  HSPA4L WILD-TYPE  220  257
        clus
vv       HSPA4L MUTATED HSPA4L WILD-TYPE
  FEMALE              5              220
  MALE                7              257
[1] 2 2
[1] FALSE
D1076V9, binary
                  cls
clus                 0   1
  HSPA4L MUTATED     8   1
  HSPA4L WILD-TYPE 342  21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HSPA4L MUTATED      8    1
  HSPA4L WILD-TYPE  342   21
     clus
vv    HSPA4L MUTATED HSPA4L WILD-TYPE
  NO               8              342
  YES              1               21
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  HSPA4L MUTATED                      5                             3
  HSPA4L WILD-TYPE                  310                            44
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  HSPA4L MUTATED                       4                              0
  HSPA4L WILD-TYPE                   102                             10
D1076V10, multiclass
                                clus
vv                               HSPA4L MUTATED HSPA4L WILD-TYPE
  COLON ADENOCARCINOMA                        5              310
  COLON MUCINOUS ADENOCARCINOMA               3               44
  RECTAL ADENOCARCINOMA                       4              102
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  HSPA4L MUTATED     8   0   0   1
  HSPA4L WILD-TYPE 337   4  31  24
D1076V11, multiclass
    clus
vv   HSPA4L MUTATED HSPA4L WILD-TYPE
  R0              8              337
  R1              0                4
  R2              0               31
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1076V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HSPA4L MUTATED                                  0     1
  HSPA4L WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  HSPA4L MUTATED                           0     5
  HSPA4L WILD-TYPE                        22   221
D1076V13, multiclass
                                  clus
vv                                 HSPA4L MUTATED HSPA4L WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         5              221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1077) Variable = TMTC4 MUTATION ANALYSIS
D1077V1, survival
                 sevent
clus2               0   1
  TMTC4 MUTATED    13   2
  TMTC4 WILD-TYPE 365  91
  TMTC4 MUTATED TMTC4 WILD-TYPE 
             15             456 
  TMTC4 MUTATED TMTC4 WILD-TYPE 
              2              91 
$`TMTC4 MUTATED`
TCGA-A6-6138 TCGA-A6-6141 TCGA-AA-3542 TCGA-AA-3864 TCGA-AA-3950 TCGA-AD-6889 
       22.52         8.38        12.99        53.00        24.00        56.55 
TCGA-AU-6004 TCGA-AY-6386 TCGA-AZ-6601 TCGA-CM-5348 TCGA-CM-5860 TCGA-D5-5537 
       27.09        17.82       100.01        22.98        32.02        45.40 
TCGA-DM-A1D0 TCGA-AG-3575 TCGA-DC-6157 
      130.65        12.00        27.95 

$`TMTC4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6142 TCGA-A6-6648 
       22.09        22.06        32.71        27.09        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        31.07        30.05        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       33.01        26.01         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
        0.07        21.37        15.52         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 
       22.42        27.42        10.88         0.20        14.50        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        33.01        21.44        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
       12.10        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-5862 
       13.02        29.06        22.03        30.08        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5538 TCGA-D5-5539 
       11.08        11.01        10.06        12.03        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D4 
       11.38        10.26       119.70        24.43        38.20        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6158 TCGA-DC-6160 
        7.17        15.02         5.03        13.97        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  TMTC4 MUTATED TMTC4 WILD-TYPE 
           8.38            0.00 
  TMTC4 MUTATED TMTC4 WILD-TYPE 
         130.65          148.01 
  TMTC4 MUTATED TMTC4 WILD-TYPE 
          27.09           20.02 
[1] "8.4 - 130.7 (27.1)" "0.0 - 148.0 (20.0)"
[1] "hr=" "2.2"
D1077V2, continuous
D1077V3, binary
                 cls
clus                0   1
  TMTC4 MUTATED    13   2
  TMTC4 WILD-TYPE 353 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TMTC4 MUTATED     13    2
  TMTC4 WILD-TYPE  353  117
        clus
vv       TMTC4 MUTATED TMTC4 WILD-TYPE
  COLON             13             353
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TMTC4 MUTATED         3        0        3         6         0         0
  TMTC4 WILD-TYPE      88        1       29       132        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TMTC4 MUTATED           0          0          2          1        0         0
  TMTC4 WILD-TYPE        24         11         57         41       48        18
                 vv
clus              STAGE IVB
  TMTC4 MUTATED           0
  TMTC4 WILD-TYPE         1
D1077V4, multiclass
            clus
vv           TMTC4 MUTATED TMTC4 WILD-TYPE
  STAGE I                3              88
  STAGE IA               0               1
  STAGE II               3              29
  STAGE IIA              6             132
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             2              57
  STAGE IIIC             1              41
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  TMTC4 MUTATED     0   3  12   0
  TMTC4 WILD-TYPE  17  89 317  50
D1077V5, multiclass
    clus
vv   TMTC4 MUTATED TMTC4 WILD-TYPE
  T1             0              17
  T2             3              89
  T3            12             317
  T4             0              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  TMTC4 MUTATED    11   2   2
  TMTC4 WILD-TYPE 276 111  85
D1077V6, multiclass
    clus
vv   TMTC4 MUTATED TMTC4 WILD-TYPE
  N0            11             276
  N1             2             111
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1077V7, binary
                 cls
clus                0   1
  TMTC4 MUTATED    14   0
  TMTC4 WILD-TYPE 361  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TMTC4 MUTATED     14    0
  TMTC4 WILD-TYPE  361   65
   clus
vv  TMTC4 MUTATED TMTC4 WILD-TYPE
  0            14             361
  1             0              65
[1] 2 2
[1] FALSE
D1077V8, binary
                 cls
clus                0   1
  TMTC4 MUTATED     4  11
  TMTC4 WILD-TYPE 221 253
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TMTC4 MUTATED      4   11
  TMTC4 WILD-TYPE  221  253
        clus
vv       TMTC4 MUTATED TMTC4 WILD-TYPE
  FEMALE             4             221
  MALE              11             253
[1] 2 2
[1] FALSE
D1077V9, binary
                 cls
clus                0   1
  TMTC4 MUTATED    11   0
  TMTC4 WILD-TYPE 339  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TMTC4 MUTATED     11    0
  TMTC4 WILD-TYPE  339   22
     clus
vv    TMTC4 MUTATED TMTC4 WILD-TYPE
  NO             11             339
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  TMTC4 MUTATED                     12                             1
  TMTC4 WILD-TYPE                  303                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  TMTC4 MUTATED                       2                              0
  TMTC4 WILD-TYPE                   104                             10
D1077V10, multiclass
                                clus
vv                               TMTC4 MUTATED TMTC4 WILD-TYPE
  COLON ADENOCARCINOMA                      12             303
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  TMTC4 MUTATED     9   0   0   1
  TMTC4 WILD-TYPE 336   4  31  24
D1077V11, multiclass
    clus
vv   TMTC4 MUTATED TMTC4 WILD-TYPE
  R0             9             336
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1077V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TMTC4 MUTATED                                  0     1
  TMTC4 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  TMTC4 MUTATED                           3     7
  TMTC4 WILD-TYPE                        19   219
D1077V13, multiclass
                                  clus
vv                                 TMTC4 MUTATED TMTC4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    3              19
  WHITE                                        7             219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1078) Variable = TGIF1 MUTATION ANALYSIS
D1078V1, survival
                 sevent
clus2               0   1
  TGIF1 MUTATED     8   2
  TGIF1 WILD-TYPE 370  91
  TGIF1 MUTATED TGIF1 WILD-TYPE 
             10             461 
  TGIF1 MUTATED TGIF1 WILD-TYPE 
              2              91 
$`TGIF1 MUTATED`
TCGA-AA-3510 TCGA-AA-3848 TCGA-CA-6716 TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6927 
       63.98        10.06        12.20        15.58         3.68         9.44 
TCGA-D5-6932 TCGA-DM-A28C TCGA-AG-3878 TCGA-AG-A00C 
       11.38        81.37         0.99         6.02 

$`TGIF1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       17.03         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6923 
       17.13        12.49        16.14         1.48         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
       14.30         9.04        11.64         4.80         1.51        12.00 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28E TCGA-DM-A28F 
      131.51       135.65       139.17         6.12       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3881 
        7.99         0.99        37.02        32.98         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
       13.94        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  TGIF1 MUTATED TGIF1 WILD-TYPE 
           0.99            0.00 
  TGIF1 MUTATED TGIF1 WILD-TYPE 
          81.37          148.01 
  TGIF1 MUTATED TGIF1 WILD-TYPE 
          10.72           20.91 
[1] "1.0 - 81.4 (10.7)"  "0.0 - 148.0 (20.9)"
[1] "hr=" "1.1"
D1078V2, continuous
D1078V3, binary
                 cls
clus                0   1
  TGIF1 MUTATED     9   2
  TGIF1 WILD-TYPE 357 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TGIF1 MUTATED      9    2
  TGIF1 WILD-TYPE  357  117
        clus
vv       TGIF1 MUTATED TGIF1 WILD-TYPE
  COLON              9             357
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TGIF1 MUTATED         2        0        1         6         0         0
  TGIF1 WILD-TYPE      89        1       31       132        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TGIF1 MUTATED           0          0          1          1        0         0
  TGIF1 WILD-TYPE        24         11         58         41       48        18
                 vv
clus              STAGE IVB
  TGIF1 MUTATED           0
  TGIF1 WILD-TYPE         1
D1078V4, multiclass
            clus
vv           TGIF1 MUTATED TGIF1 WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              6             132
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             1              41
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  TGIF1 MUTATED     0   2   9   0
  TGIF1 WILD-TYPE  17  90 320  50
D1078V5, multiclass
    clus
vv   TGIF1 MUTATED TGIF1 WILD-TYPE
  T1             0              17
  T2             2              90
  T3             9             320
  T4             0              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  TGIF1 MUTATED     9   1   1
  TGIF1 WILD-TYPE 278 112  86
D1078V6, multiclass
    clus
vv   TGIF1 MUTATED TGIF1 WILD-TYPE
  N0             9             278
  N1             1             112
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1078V7, binary
                 cls
clus                0   1
  TGIF1 MUTATED    10   0
  TGIF1 WILD-TYPE 365  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TGIF1 MUTATED     10    0
  TGIF1 WILD-TYPE  365   65
   clus
vv  TGIF1 MUTATED TGIF1 WILD-TYPE
  0            10             365
  1             0              65
[1] 2 2
[1] FALSE
D1078V8, binary
                 cls
clus                0   1
  TGIF1 MUTATED     3   8
  TGIF1 WILD-TYPE 222 256
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TGIF1 MUTATED      3    8
  TGIF1 WILD-TYPE  222  256
        clus
vv       TGIF1 MUTATED TGIF1 WILD-TYPE
  FEMALE             3             222
  MALE               8             256
[1] 2 2
[1] FALSE
D1078V9, binary
                 cls
clus                0   1
  TGIF1 MUTATED     6   1
  TGIF1 WILD-TYPE 344  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TGIF1 MUTATED      6    1
  TGIF1 WILD-TYPE  344   21
     clus
vv    TGIF1 MUTATED TGIF1 WILD-TYPE
  NO              6             344
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  TGIF1 MUTATED                      9                             0
  TGIF1 WILD-TYPE                  306                            47
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  TGIF1 MUTATED                       2                              0
  TGIF1 WILD-TYPE                   104                             10
D1078V10, multiclass
                                clus
vv                               TGIF1 MUTATED TGIF1 WILD-TYPE
  COLON ADENOCARCINOMA                       9             306
  COLON MUCINOUS ADENOCARCINOMA              0              47
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  TGIF1 MUTATED     8   0   0   2
  TGIF1 WILD-TYPE 337   4  31  23
D1078V11, multiclass
    clus
vv   TGIF1 MUTATED TGIF1 WILD-TYPE
  R0             8             337
  R1             0               4
  R2             0              31
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1078V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TGIF1 MUTATED                                  0     1
  TGIF1 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  TGIF1 MUTATED                           0     6
  TGIF1 WILD-TYPE                        22   220
D1078V13, multiclass
                                  clus
vv                                 TGIF1 MUTATED TGIF1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        6             220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1079) Variable = TBL1XR1 MUTATION ANALYSIS
D1079V1, survival
                   sevent
clus2                 0   1
  TBL1XR1 MUTATED    10   1
  TBL1XR1 WILD-TYPE 368  92
  TBL1XR1 MUTATED TBL1XR1 WILD-TYPE 
               11               460 
  TBL1XR1 MUTATED TBL1XR1 WILD-TYPE 
                1                92 
$`TBL1XR1 MUTATED`
TCGA-A6-6654 TCGA-AA-3510 TCGA-AA-3713 TCGA-AA-3877 TCGA-AA-3977 TCGA-AA-A00N 
       23.87        63.98        19.04        31.00        25.02         4.01 
TCGA-AA-A010 TCGA-CK-6748 TCGA-D5-6927 TCGA-D5-6928 TCGA-F4-6856 
       34.98         1.91         9.44        11.64        35.31 

$`TBL1XR1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       27.02        29.98        18.05         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       21.14        82.95       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6929 
        3.68         4.41        12.43        14.30         9.04         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
        0.53        47.41       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  TBL1XR1 MUTATED TBL1XR1 WILD-TYPE 
             1.91              0.00 
  TBL1XR1 MUTATED TBL1XR1 WILD-TYPE 
            63.98            148.01 
  TBL1XR1 MUTATED TBL1XR1 WILD-TYPE 
           23.870            20.155 
[1] "1.9 - 64.0 (23.9)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.9"
D1079V2, continuous
D1079V3, binary
                   cls
clus                  0   1
  TBL1XR1 MUTATED    13   0
  TBL1XR1 WILD-TYPE 353 119
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TBL1XR1 MUTATED     13    0
  TBL1XR1 WILD-TYPE  353  119
        clus
vv       TBL1XR1 MUTATED TBL1XR1 WILD-TYPE
  COLON               13               353
  RECTUM               0               119
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TBL1XR1 MUTATED         2        0        2         3         2         0
  TBL1XR1 WILD-TYPE      89        1       30       135         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TBL1XR1 MUTATED           0          0          1          0        2
  TBL1XR1 WILD-TYPE        24         11         58         42       46
                   vv
clus                STAGE IVA STAGE IVB
  TBL1XR1 MUTATED           0         0
  TBL1XR1 WILD-TYPE        18         1
D1079V4, multiclass
            clus
vv           TBL1XR1 MUTATED TBL1XR1 WILD-TYPE
  STAGE I                  2                89
  STAGE IA                 0                 1
  STAGE II                 2                30
  STAGE IIA                3               135
  STAGE IIB                2                 8
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               0                11
  STAGE IIIB               1                58
  STAGE IIIC               0                42
  STAGE IV                 2                46
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  TBL1XR1 MUTATED     1   2   7   3
  TBL1XR1 WILD-TYPE  16  90 322  47
D1079V5, multiclass
    clus
vv   TBL1XR1 MUTATED TBL1XR1 WILD-TYPE
  T1               1                16
  T2               2                90
  T3               7               322
  T4               3                47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  TBL1XR1 MUTATED    11   2   0
  TBL1XR1 WILD-TYPE 276 111  87
D1079V6, multiclass
    clus
vv   TBL1XR1 MUTATED TBL1XR1 WILD-TYPE
  N0              11               276
  N1               2               111
  N2               0                87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1079V7, binary
                   cls
clus                  0   1
  TBL1XR1 MUTATED    10   2
  TBL1XR1 WILD-TYPE 365  63
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TBL1XR1 MUTATED     10    2
  TBL1XR1 WILD-TYPE  365   63
   clus
vv  TBL1XR1 MUTATED TBL1XR1 WILD-TYPE
  0              10               365
  1               2                63
[1] 2 2
[1] FALSE
D1079V8, binary
                   cls
clus                  0   1
  TBL1XR1 MUTATED     6   7
  TBL1XR1 WILD-TYPE 219 257
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TBL1XR1 MUTATED      6    7
  TBL1XR1 WILD-TYPE  219  257
        clus
vv       TBL1XR1 MUTATED TBL1XR1 WILD-TYPE
  FEMALE               6               219
  MALE                 7               257
[1] 2 2
[1] FALSE
D1079V9, binary
                   cls
clus                  0   1
  TBL1XR1 MUTATED     9   1
  TBL1XR1 WILD-TYPE 341  21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TBL1XR1 MUTATED      9    1
  TBL1XR1 WILD-TYPE  341   21
     clus
vv    TBL1XR1 MUTATED TBL1XR1 WILD-TYPE
  NO                9               341
  YES               1                21
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  TBL1XR1 MUTATED                      8                             5
  TBL1XR1 WILD-TYPE                  307                            42
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  TBL1XR1 MUTATED                       0                              0
  TBL1XR1 WILD-TYPE                   106                             10
D1079V10, multiclass
                                clus
vv                               TBL1XR1 MUTATED TBL1XR1 WILD-TYPE
  COLON ADENOCARCINOMA                         8               307
  COLON MUCINOUS ADENOCARCINOMA                5                42
  RECTAL ADENOCARCINOMA                        0               106
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  TBL1XR1 MUTATED     9   0   1   1
  TBL1XR1 WILD-TYPE 336   4  30  24
D1079V11, multiclass
    clus
vv   TBL1XR1 MUTATED TBL1XR1 WILD-TYPE
  R0               9               336
  R1               0                 4
  R2               1                30
  RX               1                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1079V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TBL1XR1 MUTATED                                  0     0
  TBL1XR1 WILD-TYPE                                1    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  TBL1XR1 MUTATED                           0     5
  TBL1XR1 WILD-TYPE                        22   221
D1079V13, multiclass
                                  clus
vv                                 TBL1XR1 MUTATED TBL1XR1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                      0                22
  WHITE                                          5               221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1080) Variable = NXF3 MUTATION ANALYSIS
D1080V1, survival
                sevent
clus2              0   1
  NXF3 MUTATED     8   4
  NXF3 WILD-TYPE 370  89
  NXF3 MUTATED NXF3 WILD-TYPE 
            12            459 
  NXF3 MUTATED NXF3 WILD-TYPE 
             4             89 
$`NXF3 MUTATED`
TCGA-A6-6781 TCGA-AA-3821 TCGA-AU-3779 TCGA-AZ-6608 TCGA-CA-6717 TCGA-CK-5912 
       19.66         1.02        14.50         1.61        12.76        49.08 
TCGA-CK-5913 TCGA-CM-5862 TCGA-DM-A1DB TCGA-G4-6317 TCGA-AG-A002 TCGA-EI-6507 
       51.32         5.03        44.32        36.00        20.98        19.96 

$`NXF3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 
       10.06        35.05        33.04         0.99        25.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       10.88         0.20        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 
      100.01        29.56         5.23        11.74         3.19        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07        12.20        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5914 
       14.30        17.56       148.01        85.45        15.62         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       30.08        32.02        15.02        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A1HB 
       13.32        12.59       140.38         7.50       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       61.91        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6510 
       51.48        32.61         0.49        20.55        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  NXF3 MUTATED NXF3 WILD-TYPE 
          1.02           0.00 
  NXF3 MUTATED NXF3 WILD-TYPE 
         51.32         148.01 
  NXF3 MUTATED NXF3 WILD-TYPE 
         19.81          20.28 
[1] "1.0 - 51.3 (19.8)"  "0.0 - 148.0 (20.3)"
[1] "hr=" "1.9"
D1080V2, continuous
D1080V3, binary
                cls
clus               0   1
  NXF3 MUTATED    10   2
  NXF3 WILD-TYPE 356 117
[1] "tbl2"
                cls
clus             [,1] [,2]
  NXF3 MUTATED     10    2
  NXF3 WILD-TYPE  356  117
        clus
vv       NXF3 MUTATED NXF3 WILD-TYPE
  COLON            10            356
  RECTUM            2            117
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NXF3 MUTATED         3        0        0         5         0         0
  NXF3 WILD-TYPE      88        1       32       133        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NXF3 MUTATED           0          1          0          2        0         1
  NXF3 WILD-TYPE        24         10         59         40       48        17
                vv
clus             STAGE IVB
  NXF3 MUTATED           0
  NXF3 WILD-TYPE         1
D1080V4, multiclass
            clus
vv           NXF3 MUTATED NXF3 WILD-TYPE
  STAGE I               3             88
  STAGE IA              0              1
  STAGE II              0             32
  STAGE IIA             5            133
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            1             10
  STAGE IIIB            0             59
  STAGE IIIC            2             40
  STAGE IV              0             48
  STAGE IVA             1             17
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  NXF3 MUTATED     0   4   7   1
  NXF3 WILD-TYPE  17  88 322  49
D1080V5, multiclass
    clus
vv   NXF3 MUTATED NXF3 WILD-TYPE
  T1            0             17
  T2            4             88
  T3            7            322
  T4            1             49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  NXF3 MUTATED     8   3   1
  NXF3 WILD-TYPE 279 110  86
D1080V6, multiclass
    clus
vv   NXF3 MUTATED NXF3 WILD-TYPE
  N0            8            279
  N1            3            110
  N2            1             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1080V7, binary
                cls
clus               0   1
  NXF3 MUTATED     7   1
  NXF3 WILD-TYPE 368  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  NXF3 MUTATED      7    1
  NXF3 WILD-TYPE  368   64
   clus
vv  NXF3 MUTATED NXF3 WILD-TYPE
  0            7            368
  1            1             64
[1] 2 2
[1] FALSE
D1080V8, binary
                cls
clus               0   1
  NXF3 MUTATED     5   7
  NXF3 WILD-TYPE 220 257
[1] "tbl2"
                cls
clus             [,1] [,2]
  NXF3 MUTATED      5    7
  NXF3 WILD-TYPE  220  257
        clus
vv       NXF3 MUTATED NXF3 WILD-TYPE
  FEMALE            5            220
  MALE              7            257
[1] 2 2
[1] FALSE
D1080V9, binary
                cls
clus               0   1
  NXF3 MUTATED    11   0
  NXF3 WILD-TYPE 339  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  NXF3 MUTATED     11    0
  NXF3 WILD-TYPE  339   22
     clus
vv    NXF3 MUTATED NXF3 WILD-TYPE
  NO            11            339
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  NXF3 MUTATED                      7                             3
  NXF3 WILD-TYPE                  308                            44
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  NXF3 MUTATED                       2                              0
  NXF3 WILD-TYPE                   104                             10
D1080V10, multiclass
                                clus
vv                               NXF3 MUTATED NXF3 WILD-TYPE
  COLON ADENOCARCINOMA                      7            308
  COLON MUCINOUS ADENOCARCINOMA             3             44
  RECTAL ADENOCARCINOMA                     2            104
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  NXF3 MUTATED     7   0   0   3
  NXF3 WILD-TYPE 338   4  31  22
D1080V11, multiclass
    clus
vv   NXF3 MUTATED NXF3 WILD-TYPE
  R0            7            338
  R1            0              4
  R2            0             31
  RX            3             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1080V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NXF3 MUTATED                                  0     1
  NXF3 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  NXF3 MUTATED                           0     9
  NXF3 WILD-TYPE                        22   217
D1080V13, multiclass
                                  clus
vv                                 NXF3 MUTATED NXF3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       9            217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1081) Variable = SBNO1 MUTATION ANALYSIS
D1081V1, survival
                 sevent
clus2               0   1
  SBNO1 MUTATED    16   2
  SBNO1 WILD-TYPE 362  91
  SBNO1 MUTATED SBNO1 WILD-TYPE 
             18             453 
  SBNO1 MUTATED SBNO1 WILD-TYPE 
              2              91 
$`SBNO1 MUTATED`
TCGA-A6-6653 TCGA-A6-6781 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3864 TCGA-AA-A010 
       24.39        19.66         0.92        19.00        53.00        34.98 
TCGA-AZ-5407 TCGA-AZ-6601 TCGA-CA-6718 TCGA-CK-4952 TCGA-CM-4743 TCGA-CM-5344 
       88.21       100.01        10.06        15.62        23.05        22.03 
TCGA-CM-5349 TCGA-CM-5868 TCGA-G4-6588 TCGA-AF-6672 TCGA-AG-3892 TCGA-AG-A002 
       30.08        17.03        26.17        10.39        13.02        20.98 

$`SBNO1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
       25.08        25.18        24.16        21.76        24.69        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
       54.02         2.01        14.01        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
       11.01         5.98        37.05        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       31.07        30.05        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6598 
        1.41         5.13       106.75        22.36        62.79        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77        12.10        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.20        12.76        14.30        17.56       148.01        85.45 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
      124.27        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       22.98        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       15.39        20.02        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 
        1.02        17.95        36.95        17.03        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  SBNO1 MUTATED SBNO1 WILD-TYPE 
           0.92            0.00 
  SBNO1 MUTATED SBNO1 WILD-TYPE 
         100.01          148.01 
  SBNO1 MUTATED SBNO1 WILD-TYPE 
         21.505          20.120 
[1] "0.9 - 100.0 (21.5)" "0.0 - 148.0 (20.1)"
[1] "hr=" "2"  
D1081V2, continuous
D1081V3, binary
                 cls
clus                0   1
  SBNO1 MUTATED    15   3
  SBNO1 WILD-TYPE 351 116
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SBNO1 MUTATED     15    3
  SBNO1 WILD-TYPE  351  116
        clus
vv       SBNO1 MUTATED SBNO1 WILD-TYPE
  COLON             15             351
  RECTUM             3             116
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SBNO1 MUTATED         4        0        2         4         1         0
  SBNO1 WILD-TYPE      87        1       30       134         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SBNO1 MUTATED           1          0          1          2        2         1
  SBNO1 WILD-TYPE        23         11         58         40       46        17
                 vv
clus              STAGE IVB
  SBNO1 MUTATED           0
  SBNO1 WILD-TYPE         1
D1081V4, multiclass
            clus
vv           SBNO1 MUTATED SBNO1 WILD-TYPE
  STAGE I                4              87
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA              4             134
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             2              40
  STAGE IV               2              46
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  SBNO1 MUTATED     2   2   9   5
  SBNO1 WILD-TYPE  15  90 320  45
D1081V5, multiclass
    clus
vv   SBNO1 MUTATED SBNO1 WILD-TYPE
  T1             2              15
  T2             2              90
  T3             9             320
  T4             5              45
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  SBNO1 MUTATED    11   5   2
  SBNO1 WILD-TYPE 276 108  85
D1081V6, multiclass
    clus
vv   SBNO1 MUTATED SBNO1 WILD-TYPE
  N0            11             276
  N1             5             108
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1081V7, binary
                 cls
clus                0   1
  SBNO1 MUTATED    14   2
  SBNO1 WILD-TYPE 361  63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SBNO1 MUTATED     14    2
  SBNO1 WILD-TYPE  361   63
   clus
vv  SBNO1 MUTATED SBNO1 WILD-TYPE
  0            14             361
  1             2              63
[1] 2 2
[1] FALSE
D1081V8, binary
                 cls
clus                0   1
  SBNO1 MUTATED     9   9
  SBNO1 WILD-TYPE 216 255
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SBNO1 MUTATED      9    9
  SBNO1 WILD-TYPE  216  255
        clus
vv       SBNO1 MUTATED SBNO1 WILD-TYPE
  FEMALE             9             216
  MALE               9             255
[1] 2 2
[1] FALSE
D1081V9, binary
                 cls
clus                0   1
  SBNO1 MUTATED    16   1
  SBNO1 WILD-TYPE 334  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SBNO1 MUTATED     16    1
  SBNO1 WILD-TYPE  334   21
     clus
vv    SBNO1 MUTATED SBNO1 WILD-TYPE
  NO             16             334
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SBNO1 MUTATED                     13                             2
  SBNO1 WILD-TYPE                  302                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SBNO1 MUTATED                       3                              0
  SBNO1 WILD-TYPE                   103                             10
D1081V10, multiclass
                                clus
vv                               SBNO1 MUTATED SBNO1 WILD-TYPE
  COLON ADENOCARCINOMA                      13             302
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      3             103
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  SBNO1 MUTATED    11   0   1   2
  SBNO1 WILD-TYPE 334   4  30  23
D1081V11, multiclass
    clus
vv   SBNO1 MUTATED SBNO1 WILD-TYPE
  R0            11             334
  R1             0               4
  R2             1              30
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1081V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SBNO1 MUTATED                                  0     1
  SBNO1 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  SBNO1 MUTATED                           0    11
  SBNO1 WILD-TYPE                        22   215
D1081V13, multiclass
                                  clus
vv                                 SBNO1 MUTATED SBNO1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                       11             215
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1082) Variable = FLT1 MUTATION ANALYSIS
D1082V1, survival
                sevent
clus2              0   1
  FLT1 MUTATED    27   8
  FLT1 WILD-TYPE 351  85
  FLT1 MUTATED FLT1 WILD-TYPE 
            35            436 
  FLT1 MUTATED FLT1 WILD-TYPE 
             8             85 
$`FLT1 MUTATED`
TCGA-A6-5662 TCGA-A6-6780 TCGA-AA-3548 TCGA-AA-3663 TCGA-AA-3715 TCGA-AA-3877 
       23.61        20.12        33.99         6.97        19.04        31.00 
TCGA-AA-3949 TCGA-AA-3966 TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01Q 
       26.01         2.01        25.02         4.01        34.98         1.02 
TCGA-AU-3779 TCGA-AZ-4315 TCGA-AZ-5403 TCGA-AZ-6599 TCGA-CA-5797 TCGA-CA-6717 
       14.50        58.39        62.79         6.77         3.29        12.76 
TCGA-CA-6718 TCGA-CK-4947 TCGA-CM-5860 TCGA-CM-5862 TCGA-DM-A28E TCGA-F4-6703 
       10.06        17.56        32.02         5.03       119.93        47.87 
TCGA-F4-6854 TCGA-G4-6293 TCGA-G4-6588 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
        0.53       133.18        26.17        14.50        16.83        15.39 
TCGA-AG-3878 TCGA-AG-A002 TCGA-DY-A0XA TCGA-DY-A1DD TCGA-EI-6507 
        0.99        20.98       126.44        57.24        19.96 

$`FLT1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        33.53        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
       12.99         0.99        14.01        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02        78.08         6.05        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       26.99        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3950 
       18.05         2.01        12.99        24.00        33.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
        2.01        20.98        34.03        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        10.88         0.20        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        33.01        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6601 
      106.75        22.36        88.21        49.41        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4948 
        3.06         3.25         0.07        12.20        14.30       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
       15.02        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
        6.12        81.37        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6704 TCGA-F4-6805 
        8.61        31.96        35.74         6.18         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6855 TCGA-F4-6856 
       41.42        16.24        33.67        13.25        47.41        35.31 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-6655 TCGA-AF-6672 
       13.55        19.10        34.49        10.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC 
       19.99         5.95         4.01         5.03         5.29        41.36 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6508 
       24.13        51.48        32.61         0.49        20.55        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  FLT1 MUTATED FLT1 WILD-TYPE 
          0.53           0.00 
  FLT1 MUTATED FLT1 WILD-TYPE 
        133.18         148.01 
  FLT1 MUTATED FLT1 WILD-TYPE 
        19.960         20.415 
[1] "0.5 - 133.2 (20.0)" "0.0 - 148.0 (20.4)"
[1] "hr=" "1.1"
D1082V2, continuous
D1082V3, binary
                cls
clus               0   1
  FLT1 MUTATED    27   7
  FLT1 WILD-TYPE 339 112
[1] "tbl2"
                cls
clus             [,1] [,2]
  FLT1 MUTATED     27    7
  FLT1 WILD-TYPE  339  112
        clus
vv       FLT1 MUTATED FLT1 WILD-TYPE
  COLON            27            339
  RECTUM            7            112
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FLT1 MUTATED         5        0        4        14         2         0
  FLT1 WILD-TYPE      86        1       28       124         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  FLT1 MUTATED           1          0          4          1        0         3
  FLT1 WILD-TYPE        23         11         55         41       48        15
                vv
clus             STAGE IVB
  FLT1 MUTATED           0
  FLT1 WILD-TYPE         1
D1082V4, multiclass
            clus
vv           FLT1 MUTATED FLT1 WILD-TYPE
  STAGE I               5             86
  STAGE IA              0              1
  STAGE II              4             28
  STAGE IIA            14            124
  STAGE IIB             2              8
  STAGE IIC             0              1
  STAGE III             1             23
  STAGE IIIA            0             11
  STAGE IIIB            4             55
  STAGE IIIC            1             41
  STAGE IV              0             48
  STAGE IVA             3             15
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  FLT1 MUTATED     1   5  25   4
  FLT1 WILD-TYPE  16  87 304  46
D1082V5, multiclass
    clus
vv   FLT1 MUTATED FLT1 WILD-TYPE
  T1            1             16
  T2            5             87
  T3           25            304
  T4            4             46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  FLT1 MUTATED    26   6   3
  FLT1 WILD-TYPE 261 107  84
D1082V6, multiclass
    clus
vv   FLT1 MUTATED FLT1 WILD-TYPE
  N0           26            261
  N1            6            107
  N2            3             84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1082V7, binary
                cls
clus               0   1
  FLT1 MUTATED    27   2
  FLT1 WILD-TYPE 348  63
[1] "tbl2"
                cls
clus             [,1] [,2]
  FLT1 MUTATED     27    2
  FLT1 WILD-TYPE  348   63
   clus
vv  FLT1 MUTATED FLT1 WILD-TYPE
  0           27            348
  1            2             63
[1] 2 2
[1] FALSE
D1082V8, binary
                cls
clus               0   1
  FLT1 MUTATED    16  19
  FLT1 WILD-TYPE 209 245
[1] "tbl2"
                cls
clus             [,1] [,2]
  FLT1 MUTATED     16   19
  FLT1 WILD-TYPE  209  245
        clus
vv       FLT1 MUTATED FLT1 WILD-TYPE
  FEMALE           16            209
  MALE             19            245
[1] 2 2
[1] FALSE
D1082V9, binary
                cls
clus               0   1
  FLT1 MUTATED    27   1
  FLT1 WILD-TYPE 323  21
[1] "tbl2"
                cls
clus             [,1] [,2]
  FLT1 MUTATED     27    1
  FLT1 WILD-TYPE  323   21
     clus
vv    FLT1 MUTATED FLT1 WILD-TYPE
  NO            27            323
  YES            1             21
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  FLT1 MUTATED                     21                             6
  FLT1 WILD-TYPE                  294                            41
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  FLT1 MUTATED                       7                              0
  FLT1 WILD-TYPE                    99                             10
D1082V10, multiclass
                                clus
vv                               FLT1 MUTATED FLT1 WILD-TYPE
  COLON ADENOCARCINOMA                     21            294
  COLON MUCINOUS ADENOCARCINOMA             6             41
  RECTAL ADENOCARCINOMA                     7             99
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  FLT1 MUTATED    22   0   0   3
  FLT1 WILD-TYPE 323   4  31  22
D1082V11, multiclass
    clus
vv   FLT1 MUTATED FLT1 WILD-TYPE
  R0           22            323
  R1            0              4
  R2            0             31
  RX            3             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1082V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FLT1 MUTATED                                  0     3
  FLT1 WILD-TYPE                                1     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  FLT1 MUTATED                           0    20
  FLT1 WILD-TYPE                        22   206
D1082V13, multiclass
                                  clus
vv                                 FLT1 MUTATED FLT1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       3              8
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                      20            206
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1083) Variable = NCL MUTATION ANALYSIS
D1083V1, survival
               sevent
clus2             0   1
  NCL MUTATED     8   4
  NCL WILD-TYPE 370  89
  NCL MUTATED NCL WILD-TYPE 
           12           459 
  NCL MUTATED NCL WILD-TYPE 
            4            89 
$`NCL MUTATED`
TCGA-AA-3697 TCGA-AA-3845 TCGA-AA-A00N TCGA-AD-6889 TCGA-AD-6964 TCGA-AU-3779 
       85.05         0.00         4.01        56.55        10.88        14.50 
TCGA-AZ-6608 TCGA-CM-5341 TCGA-CM-6674 TCGA-DM-A28H TCGA-AG-A02N TCGA-F5-6811 
        1.61        29.06        12.95       117.07        61.97        32.19 

$`NCL WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       19.00        36.00         5.03        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 
       17.98        15.95        38.99        37.02        14.93        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 
       18.05        40.96         0.07        21.37        15.52         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-6004 
        0.72         5.79        22.42        27.42         0.20        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
       11.74         3.19        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       37.02        25.02        13.02        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
        1.94        38.96        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6812 
       18.28         9.96        49.51        31.30        28.57         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  NCL MUTATED NCL WILD-TYPE 
            0             0 
  NCL MUTATED NCL WILD-TYPE 
       117.07        148.01 
  NCL MUTATED NCL WILD-TYPE 
        21.78         20.19 
[1] "0.0 - 117.1 (21.8)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.3"
D1083V2, continuous
D1083V3, binary
               cls
clus              0   1
  NCL MUTATED    10   2
  NCL WILD-TYPE 356 117
[1] "tbl2"
               cls
clus            [,1] [,2]
  NCL MUTATED     10    2
  NCL WILD-TYPE  356  117
        clus
vv       NCL MUTATED NCL WILD-TYPE
  COLON           10           356
  RECTUM           2           117
[1] 2 2
[1] FALSE
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NCL MUTATED         0        0        1         5         1         0
  NCL WILD-TYPE      91        1       31       133         9         1
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NCL MUTATED           1          2          0          1        0         0
  NCL WILD-TYPE        23          9         59         41       48        18
               vv
clus            STAGE IVB
  NCL MUTATED           0
  NCL WILD-TYPE         1
D1083V4, multiclass
            clus
vv           NCL MUTATED NCL WILD-TYPE
  STAGE I              0            91
  STAGE IA             0             1
  STAGE II             1            31
  STAGE IIA            5           133
  STAGE IIB            1             9
  STAGE IIC            0             1
  STAGE III            1            23
  STAGE IIIA           2             9
  STAGE IIIB           0            59
  STAGE IIIC           1            41
  STAGE IV             0            48
  STAGE IVA            0            18
  STAGE IVB            0             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  NCL MUTATED     0   2   8   2
  NCL WILD-TYPE  17  90 321  48
D1083V5, multiclass
    clus
vv   NCL MUTATED NCL WILD-TYPE
  T1           0            17
  T2           2            90
  T3           8           321
  T4           2            48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2
  NCL MUTATED     8   2   2
  NCL WILD-TYPE 279 111  85
D1083V6, multiclass
    clus
vv   NCL MUTATED NCL WILD-TYPE
  N0           8           279
  N1           2           111
  N2           2            85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1083V7, binary
               cls
clus              0   1
  NCL MUTATED    11   0
  NCL WILD-TYPE 364  65
[1] "tbl2"
               cls
clus            [,1] [,2]
  NCL MUTATED     11    0
  NCL WILD-TYPE  364   65
   clus
vv  NCL MUTATED NCL WILD-TYPE
  0          11           364
  1           0            65
[1] 2 2
[1] FALSE
D1083V8, binary
               cls
clus              0   1
  NCL MUTATED     5   7
  NCL WILD-TYPE 220 257
[1] "tbl2"
               cls
clus            [,1] [,2]
  NCL MUTATED      5    7
  NCL WILD-TYPE  220  257
        clus
vv       NCL MUTATED NCL WILD-TYPE
  FEMALE           5           220
  MALE             7           257
[1] 2 2
[1] FALSE
D1083V9, binary
               cls
clus              0   1
  NCL MUTATED     7   0
  NCL WILD-TYPE 343  22
[1] "tbl2"
               cls
clus            [,1] [,2]
  NCL MUTATED      7    0
  NCL WILD-TYPE  343   22
     clus
vv    NCL MUTATED NCL WILD-TYPE
  NO            7           343
  YES           0            22
[1] 2 2
[1] FALSE
               vv
clus            COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  NCL MUTATED                      9                             1
  NCL WILD-TYPE                  306                            46
               vv
clus            RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  NCL MUTATED                       2                              0
  NCL WILD-TYPE                   104                             10
D1083V10, multiclass
                                clus
vv                               NCL MUTATED NCL WILD-TYPE
  COLON ADENOCARCINOMA                     9           306
  COLON MUCINOUS ADENOCARCINOMA            1            46
  RECTAL ADENOCARCINOMA                    2           104
  RECTAL MUCINOUS ADENOCARCINOMA           0            10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             R0  R1  R2  RX
  NCL MUTATED     7   0   0   0
  NCL WILD-TYPE 338   4  31  25
D1083V11, multiclass
    clus
vv   NCL MUTATED NCL WILD-TYPE
  R0           7           338
  R1           0             4
  R2           0            31
  RX           0            25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1083V12, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NCL MUTATED                                  0     1
  NCL WILD-TYPE                                1    10
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  NCL MUTATED                           0     7
  NCL WILD-TYPE                        22   219
D1083V13, multiclass
                                  clus
vv                                 NCL MUTATED NCL WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      1            10
  BLACK OR AFRICAN AMERICAN                  0            22
  WHITE                                      7           219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1084) Variable = SMC1B MUTATION ANALYSIS
D1084V1, survival
                 sevent
clus2               0   1
  SMC1B MUTATED    16   5
  SMC1B WILD-TYPE 362  88
  SMC1B MUTATED SMC1B WILD-TYPE 
             21             450 
  SMC1B MUTATED SMC1B WILD-TYPE 
              5              88 
$`SMC1B MUTATED`
TCGA-A6-3809 TCGA-A6-6653 TCGA-A6-6654 TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3511 
       32.75        24.39        23.87         3.02        63.98         6.97 
TCGA-AA-3715 TCGA-AA-3950 TCGA-AA-A010 TCGA-AZ-4315 TCGA-AZ-6601 TCGA-CA-6717 
       19.04        24.00        34.98        58.39       100.01        12.76 
TCGA-CA-6718 TCGA-CM-6680 TCGA-D5-6931 TCGA-F4-6809 TCGA-G4-6309 TCGA-G4-6586 
       10.06        12.03        12.00        13.25        85.48        35.80 
TCGA-AG-3732 TCGA-AG-3892 TCGA-AG-A002 
       32.98        13.02        20.98 

$`SMC1B WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6780 TCGA-A6-6781 
       25.18        24.16        21.76        24.69        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3514 TCGA-AA-3516 
       20.28         7.04         1.02        35.01         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 
        2.01        12.99        24.00        33.01        26.01         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 
       62.79        88.21        49.41         6.77        12.10        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 
        3.25         3.29         0.07        12.20        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       10.06        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       11.64         4.80         1.51        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       53.62        44.68        55.04        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       22.09        13.78        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 
       13.94        19.99         7.99         0.99        37.02         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       17.03        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  SMC1B MUTATED SMC1B WILD-TYPE 
           3.02            0.00 
  SMC1B MUTATED SMC1B WILD-TYPE 
         100.01          148.01 
  SMC1B MUTATED SMC1B WILD-TYPE 
         23.870          20.085 
[1] "3.0 - 100.0 (23.9)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1"  
D1084V2, continuous
D1084V3, binary
                 cls
clus                0   1
  SMC1B MUTATED    19   3
  SMC1B WILD-TYPE 347 116
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMC1B MUTATED     19    3
  SMC1B WILD-TYPE  347  116
        clus
vv       SMC1B MUTATED SMC1B WILD-TYPE
  COLON             19             347
  RECTUM             3             116
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SMC1B MUTATED         4        0        5         6         2         0
  SMC1B WILD-TYPE      87        1       27       132         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SMC1B MUTATED           0          0          3          1        0         1
  SMC1B WILD-TYPE        24         11         56         41       48        17
                 vv
clus              STAGE IVB
  SMC1B MUTATED           0
  SMC1B WILD-TYPE         1
D1084V4, multiclass
            clus
vv           SMC1B MUTATED SMC1B WILD-TYPE
  STAGE I                4              87
  STAGE IA               0               1
  STAGE II               5              27
  STAGE IIA              6             132
  STAGE IIB              2               8
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             3              56
  STAGE IIIC             1              41
  STAGE IV               0              48
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  SMC1B MUTATED     1   3  14   4
  SMC1B WILD-TYPE  16  89 315  46
D1084V5, multiclass
    clus
vv   SMC1B MUTATED SMC1B WILD-TYPE
  T1             1              16
  T2             3              89
  T3            14             315
  T4             4              46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  SMC1B MUTATED    17   3   2
  SMC1B WILD-TYPE 270 110  85
D1084V6, multiclass
    clus
vv   SMC1B MUTATED SMC1B WILD-TYPE
  N0            17             270
  N1             3             110
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1084V7, binary
                 cls
clus                0   1
  SMC1B MUTATED    21   1
  SMC1B WILD-TYPE 354  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMC1B MUTATED     21    1
  SMC1B WILD-TYPE  354   64
   clus
vv  SMC1B MUTATED SMC1B WILD-TYPE
  0            21             354
  1             1              64
[1] 2 2
[1] FALSE
D1084V8, binary
                 cls
clus                0   1
  SMC1B MUTATED    12  10
  SMC1B WILD-TYPE 213 254
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMC1B MUTATED     12   10
  SMC1B WILD-TYPE  213  254
        clus
vv       SMC1B MUTATED SMC1B WILD-TYPE
  FEMALE            12             213
  MALE              10             254
[1] 2 2
[1] FALSE
D1084V9, binary
                 cls
clus                0   1
  SMC1B MUTATED    21   0
  SMC1B WILD-TYPE 329  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMC1B MUTATED     21    0
  SMC1B WILD-TYPE  329   22
     clus
vv    SMC1B MUTATED SMC1B WILD-TYPE
  NO             21             329
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SMC1B MUTATED                     16                             3
  SMC1B WILD-TYPE                  299                            44
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SMC1B MUTATED                       3                              0
  SMC1B WILD-TYPE                   103                             10
D1084V10, multiclass
                                clus
vv                               SMC1B MUTATED SMC1B WILD-TYPE
  COLON ADENOCARCINOMA                      16             299
  COLON MUCINOUS ADENOCARCINOMA              3              44
  RECTAL ADENOCARCINOMA                      3             103
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  SMC1B MUTATED    17   0   0   2
  SMC1B WILD-TYPE 328   4  31  23
D1084V11, multiclass
    clus
vv   SMC1B MUTATED SMC1B WILD-TYPE
  R0            17             328
  R1             0               4
  R2             0              31
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1084V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SMC1B MUTATED                                  0     2
  SMC1B WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  SMC1B MUTATED                           1     9
  SMC1B WILD-TYPE                        21   217
D1084V13, multiclass
                                  clus
vv                                 SMC1B MUTATED SMC1B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               9
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        9             217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1085) Variable = HRSP12 MUTATION ANALYSIS
D1085V1, survival
                  sevent
clus2                0   1
  HRSP12 MUTATED     6   1
  HRSP12 WILD-TYPE 372  92
  HRSP12 MUTATED HRSP12 WILD-TYPE 
               7              464 
  HRSP12 MUTATED HRSP12 WILD-TYPE 
               1               92 
$`HRSP12 MUTATED`
TCGA-AA-3510 TCGA-AA-3662 TCGA-AA-3947 TCGA-AA-A010 TCGA-AZ-4315 TCGA-AZ-6598 
       63.98         6.05        33.01        34.98        58.39        49.41 
TCGA-AG-A002 
       20.98 

$`HRSP12 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       19.99        13.94        19.99        61.02        78.08         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       12.99        24.00        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       88.21         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  HRSP12 MUTATED HRSP12 WILD-TYPE 
            6.05             0.00 
  HRSP12 MUTATED HRSP12 WILD-TYPE 
           63.98           148.01 
  HRSP12 MUTATED HRSP12 WILD-TYPE 
          34.980           20.035 
[1] "6.0 - 64.0 (35.0)"  "0.0 - 148.0 (20.0)"
[1] "hr=" "2.1"
D1085V2, continuous
D1085V3, binary
                  cls
clus                 0   1
  HRSP12 MUTATED     6   1
  HRSP12 WILD-TYPE 360 118
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HRSP12 MUTATED      6    1
  HRSP12 WILD-TYPE  360  118
        clus
vv       HRSP12 MUTATED HRSP12 WILD-TYPE
  COLON               6              360
  RECTUM              1              118
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  HRSP12 MUTATED         1        0        2         1         2         0
  HRSP12 WILD-TYPE      90        1       30       137         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HRSP12 MUTATED           0          0          0          0        1
  HRSP12 WILD-TYPE        24         11         59         42       47
                  vv
clus               STAGE IVA STAGE IVB
  HRSP12 MUTATED           0         0
  HRSP12 WILD-TYPE        18         1
D1085V4, multiclass
            clus
vv           HRSP12 MUTATED HRSP12 WILD-TYPE
  STAGE I                 1               90
  STAGE IA                0                1
  STAGE II                2               30
  STAGE IIA               1              137
  STAGE IIB               2                8
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              0               59
  STAGE IIIC              0               42
  STAGE IV                1               47
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  HRSP12 MUTATED     0   1   3   3
  HRSP12 WILD-TYPE  17  91 326  47
D1085V5, multiclass
    clus
vv   HRSP12 MUTATED HRSP12 WILD-TYPE
  T1              0               17
  T2              1               91
  T3              3              326
  T4              3               47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  HRSP12 MUTATED     6   0   1
  HRSP12 WILD-TYPE 281 113  86
D1085V6, multiclass
    clus
vv   HRSP12 MUTATED HRSP12 WILD-TYPE
  N0              6              281
  N1              0              113
  N2              1               86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1085V7, binary
                  cls
clus                 0   1
  HRSP12 MUTATED     5   1
  HRSP12 WILD-TYPE 370  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HRSP12 MUTATED      5    1
  HRSP12 WILD-TYPE  370   64
   clus
vv  HRSP12 MUTATED HRSP12 WILD-TYPE
  0              5              370
  1              1               64
[1] 2 2
[1] FALSE
D1085V8, binary
                  cls
clus                 0   1
  HRSP12 MUTATED     4   3
  HRSP12 WILD-TYPE 221 261
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HRSP12 MUTATED      4    3
  HRSP12 WILD-TYPE  221  261
        clus
vv       HRSP12 MUTATED HRSP12 WILD-TYPE
  FEMALE              4              221
  MALE                3              261
[1] 2 2
[1] FALSE
D1085V9, binary
                  cls
clus                 0   1
  HRSP12 MUTATED     7   0
  HRSP12 WILD-TYPE 343  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HRSP12 MUTATED      7    0
  HRSP12 WILD-TYPE  343   22
     clus
vv    HRSP12 MUTATED HRSP12 WILD-TYPE
  NO               7              343
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  HRSP12 MUTATED                      5                             1
  HRSP12 WILD-TYPE                  310                            46
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  HRSP12 MUTATED                       1                              0
  HRSP12 WILD-TYPE                   105                             10
D1085V10, multiclass
                                clus
vv                               HRSP12 MUTATED HRSP12 WILD-TYPE
  COLON ADENOCARCINOMA                        5              310
  COLON MUCINOUS ADENOCARCINOMA               1               46
  RECTAL ADENOCARCINOMA                       1              105
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  HRSP12 MUTATED     5   0   1   0
  HRSP12 WILD-TYPE 340   4  30  25
D1085V11, multiclass
    clus
vv   HRSP12 MUTATED HRSP12 WILD-TYPE
  R0              5              340
  R1              0                4
  R2              1               30
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1085V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HRSP12 MUTATED                                  0     0
  HRSP12 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  HRSP12 MUTATED                           0     2
  HRSP12 WILD-TYPE                        22   224
D1085V13, multiclass
[1] "Remove cluster labels:" "HRSP12 MUTATED"        
clus
  HRSP12 MUTATED HRSP12 WILD-TYPE 
               2              258 
      TCGA-A6-2671       TCGA-A6-2672       TCGA-A6-2674       TCGA-A6-2676 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-A6-2677       TCGA-A6-2678       TCGA-A6-2683       TCGA-A6-3807 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-A6-3808       TCGA-A6-3809       TCGA-A6-3810       TCGA-A6-4105 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-A6-5656       TCGA-A6-5657       TCGA-A6-5659       TCGA-A6-5660 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-A6-5661       TCGA-A6-5662       TCGA-A6-5664       TCGA-A6-5665 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-A6-5666       TCGA-A6-6137       TCGA-A6-6138       TCGA-A6-6141 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-A6-6142       TCGA-A6-6648       TCGA-A6-6649       TCGA-A6-6651 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-A6-6652       TCGA-A6-6653       TCGA-A6-6654       TCGA-A6-6780 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-A6-6781       TCGA-A6-6782       TCGA-AD-5900       TCGA-AD-6548 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-AD-6888       TCGA-AD-6889       TCGA-AD-6890       TCGA-AD-6895 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-AD-6899       TCGA-AD-6901       TCGA-AD-6963       TCGA-AD-6964 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-AD-6965       TCGA-AU-3779       TCGA-AU-6004       TCGA-AY-4070 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-AY-4071       TCGA-AY-5543       TCGA-AY-6196       TCGA-AY-6197 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-AY-6386       TCGA-AZ-4323       TCGA-AZ-4616       TCGA-AZ-4681 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-AZ-4682       TCGA-AZ-5403       TCGA-AZ-5407       TCGA-AZ-6599 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-AZ-6600       TCGA-AZ-6601       TCGA-AZ-6603       TCGA-AZ-6605 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-AZ-6606       TCGA-AZ-6607       TCGA-AZ-6608       TCGA-CA-5254 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-CA-5255       TCGA-CA-5796       TCGA-CA-5797       TCGA-CA-6715 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-CA-6716       TCGA-CA-6717       TCGA-CA-6718       TCGA-CA-6719 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-CK-4947       TCGA-CK-4948       TCGA-CK-4950       TCGA-CK-4952 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-CK-5912       TCGA-CK-5913       TCGA-CK-5914       TCGA-CK-5915 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-CK-5916       TCGA-CK-6746       TCGA-CK-6747       TCGA-CK-6748 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-CK-6751       TCGA-CM-4743       TCGA-CM-4744       TCGA-CM-4746 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-CM-4747       TCGA-CM-4752       TCGA-CM-5341       TCGA-CM-5344 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-CM-5348       TCGA-CM-5349       TCGA-CM-5860       TCGA-CM-5861 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-CM-5862       TCGA-CM-5863       TCGA-CM-5864       TCGA-CM-5868 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-CM-6161       TCGA-CM-6162       TCGA-CM-6163       TCGA-CM-6164 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-CM-6165       TCGA-CM-6166       TCGA-CM-6167       TCGA-CM-6168 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-CM-6169       TCGA-CM-6170       TCGA-CM-6171       TCGA-CM-6172 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-CM-6674       TCGA-CM-6675       TCGA-CM-6676       TCGA-CM-6677 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-CM-6678       TCGA-CM-6679       TCGA-CM-6680       TCGA-D5-5537 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-D5-5538       TCGA-D5-5539       TCGA-D5-5540       TCGA-D5-5541 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-D5-6529       TCGA-D5-6532       TCGA-D5-6533       TCGA-D5-6534 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-D5-6535       TCGA-D5-6536       TCGA-D5-6537       TCGA-D5-6538 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-D5-6539       TCGA-D5-6540       TCGA-D5-6541       TCGA-D5-6898 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-D5-6920       TCGA-D5-6922       TCGA-D5-6923       TCGA-D5-6924 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-D5-6926       TCGA-D5-6927       TCGA-D5-6928       TCGA-D5-6929 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-D5-6930       TCGA-D5-6931       TCGA-D5-6932       TCGA-D5-7000 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-DM-A0X9       TCGA-DM-A0XD       TCGA-DM-A0XF       TCGA-DM-A1D0 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-DM-A1D4       TCGA-DM-A1D6       TCGA-DM-A1D7       TCGA-DM-A1D8 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-DM-A1D9       TCGA-DM-A1DA       TCGA-DM-A1DB       TCGA-DM-A1HA 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-DM-A1HB       TCGA-DM-A282       TCGA-DM-A285       TCGA-DM-A28C 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-DM-A28E       TCGA-DM-A28F       TCGA-DM-A28G       TCGA-DM-A28H 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-DM-A28K       TCGA-F4-6459       TCGA-F4-6460       TCGA-F4-6569 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-F4-6570       TCGA-F4-6703       TCGA-F4-6704       TCGA-F4-6805 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-F4-6806       TCGA-F4-6807       TCGA-F4-6808       TCGA-F4-6809 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-F4-6854       TCGA-F4-6855       TCGA-F4-6856       TCGA-G4-6293 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-G4-6299       TCGA-G4-6303       TCGA-G4-6304       TCGA-G4-6306 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-G4-6307       TCGA-G4-6309       TCGA-G4-6310       TCGA-G4-6315 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-G4-6317       TCGA-G4-6321       TCGA-G4-6323       TCGA-G4-6586 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-G4-6588       TCGA-G4-6625       TCGA-G4-6626       TCGA-G4-6628 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-AF-2687       TCGA-AF-2689       TCGA-AF-2691       TCGA-AF-2692 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-AF-2693       TCGA-AF-3400       TCGA-AF-3913       TCGA-AF-4110 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-AF-5654       TCGA-AF-6136       TCGA-AF-6655       TCGA-AF-6672 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-AH-6544       TCGA-AH-6547       TCGA-AH-6549       TCGA-AH-6643 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-AH-6644       TCGA-CI-6619       TCGA-CI-6620       TCGA-CI-6621 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-CI-6622       TCGA-CI-6624       TCGA-CL-5917       TCGA-CL-5918 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-DC-5337       TCGA-DC-5869       TCGA-DC-6155       TCGA-DC-6157 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-DC-6158       TCGA-DC-6160       TCGA-DC-6681       TCGA-DC-6682 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-DC-6683       TCGA-DT-5265       TCGA-DY-A0XA       TCGA-DY-A1DC 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-DY-A1DD       TCGA-DY-A1DF       TCGA-DY-A1DG       TCGA-DY-A1H8 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-EF-5830       TCGA-EI-6506       TCGA-EI-6507       TCGA-EI-6508 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-EI-6510       TCGA-F5-6464       TCGA-F5-6465       TCGA-F5-6571 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-F5-6702       TCGA-F5-6811       TCGA-F5-6812       TCGA-F5-6813 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 
      TCGA-G5-6235       TCGA-G5-6641 
"HRSP12 WILD-TYPE" "HRSP12 WILD-TYPE" 

Clustering(1086) Variable = RRS1 MUTATION ANALYSIS
D1086V1, survival
                sevent
clus2              0   1
  RRS1 MUTATED     4   0
  RRS1 WILD-TYPE 374  93
  RRS1 MUTATED RRS1 WILD-TYPE 
             4            467 
  RRS1 MUTATED RRS1 WILD-TYPE 
             0             93 
$`RRS1 MUTATED`
TCGA-CM-6170 TCGA-D5-6540 TCGA-D5-6928 TCGA-G4-6588 
       15.02        16.14        11.64        26.17 

$`RRS1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6171 
       16.04        21.99        14.99        12.99        13.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 
       17.85         4.80        17.13        12.49        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 
       61.91        36.00        22.09        13.78        35.80        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  RRS1 MUTATED RRS1 WILD-TYPE 
         11.64           0.00 
  RRS1 MUTATED RRS1 WILD-TYPE 
         26.17         148.01 
  RRS1 MUTATED RRS1 WILD-TYPE 
         15.58          20.28 
[1] "11.6 - 26.2 (15.6)" "0.0 - 148.0 (20.3)"
[1] "hr="     "3300000"
D1086V2, continuous
D1086V3, binary
                cls
clus               0   1
  RRS1 MUTATED     4   0
  RRS1 WILD-TYPE 362 119
[1] "tbl2"
                cls
clus             [,1] [,2]
  RRS1 MUTATED      4    0
  RRS1 WILD-TYPE  362  119
        clus
vv       RRS1 MUTATED RRS1 WILD-TYPE
  COLON             4            362
  RECTUM            0            119
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RRS1 MUTATED         2        0        0         2         0         0
  RRS1 WILD-TYPE      89        1       32       136        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RRS1 MUTATED           0          0          0          0        0         0
  RRS1 WILD-TYPE        24         11         59         42       48        18
                vv
clus             STAGE IVB
  RRS1 MUTATED           0
  RRS1 WILD-TYPE         1
D1086V4, multiclass
            clus
vv           RRS1 MUTATED RRS1 WILD-TYPE
  STAGE I               2             89
  STAGE IA              0              1
  STAGE II              0             32
  STAGE IIA             2            136
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            0             59
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  RRS1 MUTATED     0   2   2   0
  RRS1 WILD-TYPE  17  90 327  50
D1086V5, multiclass
    clus
vv   RRS1 MUTATED RRS1 WILD-TYPE
  T1            0             17
  T2            2             90
  T3            2            327
  T4            0             50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  RRS1 MUTATED     4   0   0
  RRS1 WILD-TYPE 283 113  87
D1086V6, multiclass
    clus
vv   RRS1 MUTATED RRS1 WILD-TYPE
  N0            4            283
  N1            0            113
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1086V7, binary
                cls
clus               0   1
  RRS1 MUTATED     4   0
  RRS1 WILD-TYPE 371  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  RRS1 MUTATED      4    0
  RRS1 WILD-TYPE  371   65
   clus
vv  RRS1 MUTATED RRS1 WILD-TYPE
  0            4            371
  1            0             65
[1] 2 2
[1] FALSE
D1086V8, binary
                cls
clus               0   1
  RRS1 MUTATED     2   2
  RRS1 WILD-TYPE 223 262
[1] "tbl2"
                cls
clus             [,1] [,2]
  RRS1 MUTATED      2    2
  RRS1 WILD-TYPE  223  262
        clus
vv       RRS1 MUTATED RRS1 WILD-TYPE
  FEMALE            2            223
  MALE              2            262
[1] 2 2
[1] FALSE
D1086V9, binary
                cls
clus               0   1
  RRS1 MUTATED     4   0
  RRS1 WILD-TYPE 346  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  RRS1 MUTATED      4    0
  RRS1 WILD-TYPE  346   22
     clus
vv    RRS1 MUTATED RRS1 WILD-TYPE
  NO             4            346
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  RRS1 MUTATED                      2                             2
  RRS1 WILD-TYPE                  313                            45
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  RRS1 MUTATED                       0                              0
  RRS1 WILD-TYPE                   106                             10
D1086V10, multiclass
                                clus
vv                               RRS1 MUTATED RRS1 WILD-TYPE
  COLON ADENOCARCINOMA                      2            313
  COLON MUCINOUS ADENOCARCINOMA             2             45
  RECTAL ADENOCARCINOMA                     0            106
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  RRS1 MUTATED     4   0   0   0
  RRS1 WILD-TYPE 341   4  31  25
D1086V11, multiclass
    clus
vv   RRS1 MUTATED RRS1 WILD-TYPE
  R0            4            341
  R1            0              4
  R2            0             31
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1086V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RRS1 MUTATED                                  0     0
  RRS1 WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  RRS1 MUTATED                           0     4
  RRS1 WILD-TYPE                        22   222
D1086V13, multiclass
                                  clus
vv                                 RRS1 MUTATED RRS1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       4            222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1087) Variable = CTCF MUTATION ANALYSIS
D1087V1, survival
                sevent
clus2              0   1
  CTCF MUTATED    15   4
  CTCF WILD-TYPE 363  89
  CTCF MUTATED CTCF WILD-TYPE 
            19            452 
  CTCF MUTATED CTCF WILD-TYPE 
             4             89 
$`CTCF MUTATED`
TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-5665 TCGA-AA-3518 TCGA-AA-3667 TCGA-AA-3845 
       46.65        42.90        22.06         1.02        14.01         0.00 
TCGA-AA-A00D TCGA-AA-A010 TCGA-AY-6197 TCGA-AZ-6600 TCGA-CA-5254 TCGA-CM-4743 
       19.00        34.98        21.44        12.10        12.69        23.05 
TCGA-CM-5348 TCGA-CM-5864 TCGA-D5-6920 TCGA-D5-6927 TCGA-G4-6309 TCGA-AG-A002 
       22.98        15.02         3.68         9.44        85.48        20.98 
TCGA-AG-A026 
        1.94 

$`CTCF WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       43.76        43.76        24.33        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5657 
       33.34        32.75        36.53        14.53        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 
       30.44        29.19        33.53        23.61        22.09        32.71 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       27.09        22.52         8.38        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3520 
        6.97         1.02        13.02        38.99         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
       14.93        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       13.94        38.04        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       33.01        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 
       22.36        62.79        88.21        49.41         6.77       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5255 
       29.56         5.23        11.74         3.19         1.61         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5868 
       30.08        32.02        15.02         5.03        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6929 
        4.41        12.43        14.30         9.04        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       53.62        44.68        55.04        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A02G TCGA-AG-A02N 
       70.03        64.01        10.98        49.97        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  CTCF MUTATED CTCF WILD-TYPE 
             0              0 
  CTCF MUTATED CTCF WILD-TYPE 
         85.48         148.01 
  CTCF MUTATED CTCF WILD-TYPE 
        19.000         20.235 
[1] "0.0 - 85.5 (19.0)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.3"
D1087V2, continuous
D1087V3, binary
                cls
clus               0   1
  CTCF MUTATED    17   2
  CTCF WILD-TYPE 349 117
[1] "tbl2"
                cls
clus             [,1] [,2]
  CTCF MUTATED     17    2
  CTCF WILD-TYPE  349  117
        clus
vv       CTCF MUTATED CTCF WILD-TYPE
  COLON            17            349
  RECTUM            2            117
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CTCF MUTATED         4        0        1         8         2         0
  CTCF WILD-TYPE      87        1       31       130         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CTCF MUTATED           0          0          3          0        1         0
  CTCF WILD-TYPE        24         11         56         42       47        18
                vv
clus             STAGE IVB
  CTCF MUTATED           0
  CTCF WILD-TYPE         1
D1087V4, multiclass
            clus
vv           CTCF MUTATED CTCF WILD-TYPE
  STAGE I               4             87
  STAGE IA              0              1
  STAGE II              1             31
  STAGE IIA             8            130
  STAGE IIB             2              8
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            3             56
  STAGE IIIC            0             42
  STAGE IV              1             47
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  CTCF MUTATED     0   4  11   4
  CTCF WILD-TYPE  17  88 318  46
D1087V5, multiclass
    clus
vv   CTCF MUTATED CTCF WILD-TYPE
  T1            0             17
  T2            4             88
  T3           11            318
  T4            4             46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  CTCF MUTATED    15   4   0
  CTCF WILD-TYPE 272 109  87
D1087V6, multiclass
    clus
vv   CTCF MUTATED CTCF WILD-TYPE
  N0           15            272
  N1            4            109
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1087V7, binary
                cls
clus               0   1
  CTCF MUTATED    17   1
  CTCF WILD-TYPE 358  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  CTCF MUTATED     17    1
  CTCF WILD-TYPE  358   64
   clus
vv  CTCF MUTATED CTCF WILD-TYPE
  0           17            358
  1            1             64
[1] 2 2
[1] FALSE
D1087V8, binary
                cls
clus               0   1
  CTCF MUTATED    10   9
  CTCF WILD-TYPE 215 255
[1] "tbl2"
                cls
clus             [,1] [,2]
  CTCF MUTATED     10    9
  CTCF WILD-TYPE  215  255
        clus
vv       CTCF MUTATED CTCF WILD-TYPE
  FEMALE           10            215
  MALE              9            255
[1] 2 2
[1] FALSE
D1087V9, binary
                cls
clus               0   1
  CTCF MUTATED    14   0
  CTCF WILD-TYPE 336  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  CTCF MUTATED     14    0
  CTCF WILD-TYPE  336   22
     clus
vv    CTCF MUTATED CTCF WILD-TYPE
  NO            14            336
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CTCF MUTATED                     17                             0
  CTCF WILD-TYPE                  298                            47
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CTCF MUTATED                       2                              0
  CTCF WILD-TYPE                   104                             10
D1087V10, multiclass
                                clus
vv                               CTCF MUTATED CTCF WILD-TYPE
  COLON ADENOCARCINOMA                     17            298
  COLON MUCINOUS ADENOCARCINOMA             0             47
  RECTAL ADENOCARCINOMA                     2            104
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  CTCF MUTATED    16   1   0   1
  CTCF WILD-TYPE 329   3  31  24
D1087V11, multiclass
    clus
vv   CTCF MUTATED CTCF WILD-TYPE
  R0           16            329
  R1            1              3
  R2            0             31
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1087V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CTCF MUTATED                                  0     1
  CTCF WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  CTCF MUTATED                           2     9
  CTCF WILD-TYPE                        20   217
D1087V13, multiclass
                                  clus
vv                                 CTCF MUTATED CTCF WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   2             20
  WHITE                                       9            217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1088) Variable = RNF38 MUTATION ANALYSIS
D1088V1, survival
                 sevent
clus2               0   1
  RNF38 MUTATED     4   2
  RNF38 WILD-TYPE 374  91
  RNF38 MUTATED RNF38 WILD-TYPE 
              6             465 
  RNF38 MUTATED RNF38 WILD-TYPE 
              2              91 
$`RNF38 MUTATED`
TCGA-A6-5665 TCGA-A6-6781 TCGA-AA-A010 TCGA-AY-4071 TCGA-F4-6570 TCGA-AF-6672 
       22.06        19.66        34.98         0.95         6.18        10.39 

$`RNF38 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-5543 TCGA-AY-6197 
        0.20        14.50        27.09        16.31        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 
       98.24         8.61        31.96        35.74        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  RNF38 MUTATED RNF38 WILD-TYPE 
           0.95            0.00 
  RNF38 MUTATED RNF38 WILD-TYPE 
          34.98          148.01 
  RNF38 MUTATED RNF38 WILD-TYPE 
         15.025          20.280 
[1] "0.9 - 35.0 (15.0)"  "0.0 - 148.0 (20.3)"
[1] "hr=" "3"  
D1088V2, continuous
D1088V3, binary
                 cls
clus                0   1
  RNF38 MUTATED     4   1
  RNF38 WILD-TYPE 362 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RNF38 MUTATED      4    1
  RNF38 WILD-TYPE  362  118
        clus
vv       RNF38 MUTATED RNF38 WILD-TYPE
  COLON              4             362
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RNF38 MUTATED         1        0        0         2         1         0
  RNF38 WILD-TYPE      90        1       32       136         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RNF38 MUTATED           0          0          0          1        1         0
  RNF38 WILD-TYPE        24         11         59         41       47        18
                 vv
clus              STAGE IVB
  RNF38 MUTATED           0
  RNF38 WILD-TYPE         1
D1088V4, multiclass
            clus
vv           RNF38 MUTATED RNF38 WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              2             136
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             1              41
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  RNF38 MUTATED     1   0   2   3
  RNF38 WILD-TYPE  16  92 327  47
D1088V5, multiclass
    clus
vv   RNF38 MUTATED RNF38 WILD-TYPE
  T1             1              16
  T2             0              92
  T3             2             327
  T4             3              47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  RNF38 MUTATED     4   1   1
  RNF38 WILD-TYPE 283 112  86
D1088V6, multiclass
    clus
vv   RNF38 MUTATED RNF38 WILD-TYPE
  N0             4             283
  N1             1             112
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1088V7, binary
                 cls
clus                0   1
  RNF38 MUTATED     3   0
  RNF38 WILD-TYPE 372  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RNF38 MUTATED      3    0
  RNF38 WILD-TYPE  372   65
   clus
vv  RNF38 MUTATED RNF38 WILD-TYPE
  0             3             372
  1             0              65
[1] 2 2
[1] FALSE
D1088V8, binary
                 cls
clus                0   1
  RNF38 MUTATED     4   2
  RNF38 WILD-TYPE 221 262
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RNF38 MUTATED      4    2
  RNF38 WILD-TYPE  221  262
        clus
vv       RNF38 MUTATED RNF38 WILD-TYPE
  FEMALE             4             221
  MALE               2             262
[1] 2 2
[1] FALSE
D1088V9, binary
                 cls
clus                0   1
  RNF38 MUTATED     5   1
  RNF38 WILD-TYPE 345  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RNF38 MUTATED      5    1
  RNF38 WILD-TYPE  345   21
     clus
vv    RNF38 MUTATED RNF38 WILD-TYPE
  NO              5             345
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  RNF38 MUTATED                      3                             1
  RNF38 WILD-TYPE                  312                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  RNF38 MUTATED                       1                              0
  RNF38 WILD-TYPE                   105                             10
D1088V10, multiclass
                                clus
vv                               RNF38 MUTATED RNF38 WILD-TYPE
  COLON ADENOCARCINOMA                       3             312
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  RNF38 MUTATED     5   0   0   0
  RNF38 WILD-TYPE 340   4  31  25
D1088V11, multiclass
    clus
vv   RNF38 MUTATED RNF38 WILD-TYPE
  R0             5             340
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1088V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RNF38 MUTATED                                  0     0
  RNF38 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  RNF38 MUTATED                           0     5
  RNF38 WILD-TYPE                        22   221
D1088V13, multiclass
                                  clus
vv                                 RNF38 MUTATED RNF38 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        5             221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1089) Variable = ANKRD50 MUTATION ANALYSIS
D1089V1, survival
                   sevent
clus2                 0   1
  ANKRD50 MUTATED    11   9
  ANKRD50 WILD-TYPE 367  84
  ANKRD50 MUTATED ANKRD50 WILD-TYPE 
               20               451 
  ANKRD50 MUTATED ANKRD50 WILD-TYPE 
                9                84 
$`ANKRD50 MUTATED`
TCGA-AA-3492 TCGA-AA-3516 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3977 TCGA-AA-A00E 
        3.02        13.02        19.04        19.04        25.02        30.02 
TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01P TCGA-AZ-6598 TCGA-AZ-6601 TCGA-CK-4948 
        4.01        34.98        38.07        49.41       100.01       148.01 
TCGA-CM-6171 TCGA-DM-A1HB TCGA-AF-6136 TCGA-AG-3892 TCGA-AG-A002 TCGA-AG-A02N 
       14.04       135.65        15.39        13.02        20.98        61.97 
TCGA-DY-A1DF TCGA-F5-6464 
       24.13         9.96 

$`ANKRD50 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
        5.03        85.05        26.99        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00J 
       27.02        13.94        38.04        19.00        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        31.00         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 
       22.36        62.79        88.21         6.77        12.10        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       14.30        17.56        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      131.51       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       16.83        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 
       19.99         1.02        17.95        36.95        17.03        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       38.96        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DG TCGA-DY-A1H8 
        5.29       126.44        41.36        57.24        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6465 
        0.49        20.55        19.96        20.91        18.28        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  ANKRD50 MUTATED ANKRD50 WILD-TYPE 
             3.02              0.00 
  ANKRD50 MUTATED ANKRD50 WILD-TYPE 
           148.01            140.38 
  ANKRD50 MUTATED ANKRD50 WILD-TYPE 
           22.555            20.120 
[1] "3.0 - 148.0 (22.6)" "0.0 - 140.4 (20.1)"
[1] "hr=" "1.8"
D1089V2, continuous
D1089V3, binary
                   cls
clus                  0   1
  ANKRD50 MUTATED    15   6
  ANKRD50 WILD-TYPE 351 113
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD50 MUTATED     15    6
  ANKRD50 WILD-TYPE  351  113
        clus
vv       ANKRD50 MUTATED ANKRD50 WILD-TYPE
  COLON               15               351
  RECTUM               6               113
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ANKRD50 MUTATED         3        0        6         1         2         0
  ANKRD50 WILD-TYPE      88        1       26       137         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ANKRD50 MUTATED           3          0          2          2        1
  ANKRD50 WILD-TYPE        21         11         57         40       47
                   vv
clus                STAGE IVA STAGE IVB
  ANKRD50 MUTATED           0         0
  ANKRD50 WILD-TYPE        18         1
D1089V4, multiclass
            clus
vv           ANKRD50 MUTATED ANKRD50 WILD-TYPE
  STAGE I                  3                88
  STAGE IA                 0                 1
  STAGE II                 6                26
  STAGE IIA                1               137
  STAGE IIB                2                 8
  STAGE IIC                0                 1
  STAGE III                3                21
  STAGE IIIA               0                11
  STAGE IIIB               2                57
  STAGE IIIC               2                40
  STAGE IV                 1                47
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  ANKRD50 MUTATED     1   3  13   4
  ANKRD50 WILD-TYPE  16  89 316  46
D1089V5, multiclass
    clus
vv   ANKRD50 MUTATED ANKRD50 WILD-TYPE
  T1               1                16
  T2               3                89
  T3              13               316
  T4               4                46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  ANKRD50 MUTATED    14   4   3
  ANKRD50 WILD-TYPE 273 109  84
D1089V6, multiclass
    clus
vv   ANKRD50 MUTATED ANKRD50 WILD-TYPE
  N0              14               273
  N1               4               109
  N2               3                84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1089V7, binary
                   cls
clus                  0   1
  ANKRD50 MUTATED    17   1
  ANKRD50 WILD-TYPE 358  64
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD50 MUTATED     17    1
  ANKRD50 WILD-TYPE  358   64
   clus
vv  ANKRD50 MUTATED ANKRD50 WILD-TYPE
  0              17               358
  1               1                64
[1] 2 2
[1] FALSE
D1089V8, binary
                   cls
clus                  0   1
  ANKRD50 MUTATED    12   9
  ANKRD50 WILD-TYPE 213 255
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD50 MUTATED     12    9
  ANKRD50 WILD-TYPE  213  255
        clus
vv       ANKRD50 MUTATED ANKRD50 WILD-TYPE
  FEMALE              12               213
  MALE                 9               255
[1] 2 2
[1] FALSE
D1089V9, binary
                   cls
clus                  0   1
  ANKRD50 MUTATED    14   2
  ANKRD50 WILD-TYPE 336  20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD50 MUTATED     14    2
  ANKRD50 WILD-TYPE  336   20
     clus
vv    ANKRD50 MUTATED ANKRD50 WILD-TYPE
  NO               14               336
  YES               2                20
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ANKRD50 MUTATED                     12                             2
  ANKRD50 WILD-TYPE                  303                            45
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ANKRD50 MUTATED                       6                              0
  ANKRD50 WILD-TYPE                   100                             10
D1089V10, multiclass
                                clus
vv                               ANKRD50 MUTATED ANKRD50 WILD-TYPE
  COLON ADENOCARCINOMA                        12               303
  COLON MUCINOUS ADENOCARCINOMA                2                45
  RECTAL ADENOCARCINOMA                        6               100
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  ANKRD50 MUTATED    13   0   1   0
  ANKRD50 WILD-TYPE 332   4  30  25
D1089V11, multiclass
    clus
vv   ANKRD50 MUTATED ANKRD50 WILD-TYPE
  R0              13               332
  R1               0                 4
  R2               1                30
  RX               0                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1089V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ANKRD50 MUTATED                                  0     0
  ANKRD50 WILD-TYPE                                1    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  ANKRD50 MUTATED                           0     8
  ANKRD50 WILD-TYPE                        22   218
D1089V13, multiclass
                                  clus
vv                                 ANKRD50 MUTATED ANKRD50 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                      0                22
  WHITE                                          8               218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1090) Variable = DNAJC16 MUTATION ANALYSIS
D1090V1, survival
                   sevent
clus2                 0   1
  DNAJC16 MUTATED     8   3
  DNAJC16 WILD-TYPE 370  90
  DNAJC16 MUTATED DNAJC16 WILD-TYPE 
               11               460 
  DNAJC16 MUTATED DNAJC16 WILD-TYPE 
                3                90 
$`DNAJC16 MUTATED`
TCGA-A6-3809 TCGA-AA-3553 TCGA-AA-3663 TCGA-AA-A010 TCGA-AZ-4315 TCGA-AZ-5407 
       32.75        24.00         6.97        34.98        58.39        88.21 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-G4-6628 TCGA-AG-A002 TCGA-DY-A1DG 
       12.10       100.01        79.69        20.98        51.48 

$`DNAJC16 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       13.02        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       49.41         6.77        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       26.17        91.79        46.75        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       24.13        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  DNAJC16 MUTATED DNAJC16 WILD-TYPE 
             6.97              0.00 
  DNAJC16 MUTATED DNAJC16 WILD-TYPE 
           100.01            148.01 
  DNAJC16 MUTATED DNAJC16 WILD-TYPE 
            34.98             20.02 
[1] "7.0 - 100.0 (35.0)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.3"
D1090V2, continuous
D1090V3, binary
                   cls
clus                  0   1
  DNAJC16 MUTATED     9   2
  DNAJC16 WILD-TYPE 357 117
[1] "tbl2"
                   cls
clus                [,1] [,2]
  DNAJC16 MUTATED      9    2
  DNAJC16 WILD-TYPE  357  117
        clus
vv       DNAJC16 MUTATED DNAJC16 WILD-TYPE
  COLON                9               357
  RECTUM               2               117
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DNAJC16 MUTATED         4        0        2         1         2         0
  DNAJC16 WILD-TYPE      87        1       30       137         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DNAJC16 MUTATED           0          0          0          0        1
  DNAJC16 WILD-TYPE        24         11         59         42       47
                   vv
clus                STAGE IVA STAGE IVB
  DNAJC16 MUTATED           1         0
  DNAJC16 WILD-TYPE        17         1
D1090V4, multiclass
            clus
vv           DNAJC16 MUTATED DNAJC16 WILD-TYPE
  STAGE I                  4                87
  STAGE IA                 0                 1
  STAGE II                 2                30
  STAGE IIA                1               137
  STAGE IIB                2                 8
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               0                11
  STAGE IIIB               0                59
  STAGE IIIC               0                42
  STAGE IV                 1                47
  STAGE IVA                1                17
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  DNAJC16 MUTATED     1   3   4   3
  DNAJC16 WILD-TYPE  16  89 325  47
D1090V5, multiclass
    clus
vv   DNAJC16 MUTATED DNAJC16 WILD-TYPE
  T1               1                16
  T2               3                89
  T3               4               325
  T4               3                47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  DNAJC16 MUTATED     9   2   0
  DNAJC16 WILD-TYPE 278 111  87
D1090V6, multiclass
    clus
vv   DNAJC16 MUTATED DNAJC16 WILD-TYPE
  N0               9               278
  N1               2               111
  N2               0                87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1090V7, binary
                   cls
clus                  0   1
  DNAJC16 MUTATED     9   2
  DNAJC16 WILD-TYPE 366  63
[1] "tbl2"
                   cls
clus                [,1] [,2]
  DNAJC16 MUTATED      9    2
  DNAJC16 WILD-TYPE  366   63
   clus
vv  DNAJC16 MUTATED DNAJC16 WILD-TYPE
  0               9               366
  1               2                63
[1] 2 2
[1] FALSE
D1090V8, binary
                   cls
clus                  0   1
  DNAJC16 MUTATED     4   7
  DNAJC16 WILD-TYPE 221 257
[1] "tbl2"
                   cls
clus                [,1] [,2]
  DNAJC16 MUTATED      4    7
  DNAJC16 WILD-TYPE  221  257
        clus
vv       DNAJC16 MUTATED DNAJC16 WILD-TYPE
  FEMALE               4               221
  MALE                 7               257
[1] 2 2
[1] FALSE
D1090V9, binary
                   cls
clus                  0   1
  DNAJC16 MUTATED     9   0
  DNAJC16 WILD-TYPE 341  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  DNAJC16 MUTATED      9    0
  DNAJC16 WILD-TYPE  341   22
     clus
vv    DNAJC16 MUTATED DNAJC16 WILD-TYPE
  NO                9               341
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  DNAJC16 MUTATED                      8                             1
  DNAJC16 WILD-TYPE                  307                            46
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  DNAJC16 MUTATED                       2                              0
  DNAJC16 WILD-TYPE                   104                             10
D1090V10, multiclass
                                clus
vv                               DNAJC16 MUTATED DNAJC16 WILD-TYPE
  COLON ADENOCARCINOMA                         8               307
  COLON MUCINOUS ADENOCARCINOMA                1                46
  RECTAL ADENOCARCINOMA                        2               104
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  DNAJC16 MUTATED     7   0   0   0
  DNAJC16 WILD-TYPE 338   4  31  25
D1090V11, multiclass
    clus
vv   DNAJC16 MUTATED DNAJC16 WILD-TYPE
  R0               7               338
  R1               0                 4
  R2               0                31
  RX               0                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1090V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DNAJC16 MUTATED                                  0     0
  DNAJC16 WILD-TYPE                                1    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  DNAJC16 MUTATED                           1     6
  DNAJC16 WILD-TYPE                        21   220
D1090V13, multiclass
                                  clus
vv                                 DNAJC16 MUTATED DNAJC16 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                      1                21
  WHITE                                          6               220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1091) Variable = PIGK MUTATION ANALYSIS
D1091V1, survival
                sevent
clus2              0   1
  PIGK MUTATED    10   2
  PIGK WILD-TYPE 368  91
  PIGK MUTATED PIGK WILD-TYPE 
            12            459 
  PIGK MUTATED PIGK WILD-TYPE 
             2             91 
$`PIGK MUTATED`
TCGA-A6-5660 TCGA-AA-3516 TCGA-AA-3663 TCGA-AA-3864 TCGA-AA-A00J TCGA-AD-6888 
       29.19        13.02         6.97        53.00        18.05        15.52 
TCGA-AY-5543 TCGA-CK-4947 TCGA-D5-6930 TCGA-G4-6321 TCGA-AG-A002 TCGA-CL-5917 
       33.01        17.56         1.51        22.09        20.98        78.12 

$`PIGK WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        31.07        30.05        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
        0.07        21.37        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       16.31         0.95        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4948 
        0.07        12.20        12.76        10.06        14.30       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       11.64         4.80        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       61.91        36.00        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        6.97         4.73         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  PIGK MUTATED PIGK WILD-TYPE 
          1.51           0.00 
  PIGK MUTATED PIGK WILD-TYPE 
         78.12         148.01 
  PIGK MUTATED PIGK WILD-TYPE 
        19.515         20.190 
[1] "1.5 - 78.1 (19.5)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.2"
D1091V2, continuous
D1091V3, binary
                cls
clus               0   1
  PIGK MUTATED    10   2
  PIGK WILD-TYPE 356 117
[1] "tbl2"
                cls
clus             [,1] [,2]
  PIGK MUTATED     10    2
  PIGK WILD-TYPE  356  117
        clus
vv       PIGK MUTATED PIGK WILD-TYPE
  COLON            10            356
  RECTUM            2            117
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PIGK MUTATED         1        0        2         1         0         0
  PIGK WILD-TYPE      90        1       30       137        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PIGK MUTATED           2          0          3          2        0         1
  PIGK WILD-TYPE        22         11         56         40       48        17
                vv
clus             STAGE IVB
  PIGK MUTATED           0
  PIGK WILD-TYPE         1
D1091V4, multiclass
            clus
vv           PIGK MUTATED PIGK WILD-TYPE
  STAGE I               1             90
  STAGE IA              0              1
  STAGE II              2             30
  STAGE IIA             1            137
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             2             22
  STAGE IIIA            0             11
  STAGE IIIB            3             56
  STAGE IIIC            2             40
  STAGE IV              0             48
  STAGE IVA             1             17
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  PIGK MUTATED     0   2   8   2
  PIGK WILD-TYPE  17  90 321  48
D1091V5, multiclass
    clus
vv   PIGK MUTATED PIGK WILD-TYPE
  T1            0             17
  T2            2             90
  T3            8            321
  T4            2             48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  PIGK MUTATED     4   5   3
  PIGK WILD-TYPE 283 108  84
D1091V6, multiclass
    clus
vv   PIGK MUTATED PIGK WILD-TYPE
  N0            4            283
  N1            5            108
  N2            3             84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1091V7, binary
                cls
clus               0   1
  PIGK MUTATED     9   1
  PIGK WILD-TYPE 366  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  PIGK MUTATED      9    1
  PIGK WILD-TYPE  366   64
   clus
vv  PIGK MUTATED PIGK WILD-TYPE
  0            9            366
  1            1             64
[1] 2 2
[1] FALSE
D1091V8, binary
                cls
clus               0   1
  PIGK MUTATED     5   7
  PIGK WILD-TYPE 220 257
[1] "tbl2"
                cls
clus             [,1] [,2]
  PIGK MUTATED      5    7
  PIGK WILD-TYPE  220  257
        clus
vv       PIGK MUTATED PIGK WILD-TYPE
  FEMALE            5            220
  MALE              7            257
[1] 2 2
[1] FALSE
D1091V9, binary
                cls
clus               0   1
  PIGK MUTATED    11   0
  PIGK WILD-TYPE 339  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  PIGK MUTATED     11    0
  PIGK WILD-TYPE  339   22
     clus
vv    PIGK MUTATED PIGK WILD-TYPE
  NO            11            339
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PIGK MUTATED                      7                             3
  PIGK WILD-TYPE                  308                            44
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PIGK MUTATED                       2                              0
  PIGK WILD-TYPE                   104                             10
D1091V10, multiclass
                                clus
vv                               PIGK MUTATED PIGK WILD-TYPE
  COLON ADENOCARCINOMA                      7            308
  COLON MUCINOUS ADENOCARCINOMA             3             44
  RECTAL ADENOCARCINOMA                     2            104
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  PIGK MUTATED     8   0   0   2
  PIGK WILD-TYPE 337   4  31  23
D1091V11, multiclass
    clus
vv   PIGK MUTATED PIGK WILD-TYPE
  R0            8            337
  R1            0              4
  R2            0             31
  RX            2             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1091V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PIGK MUTATED                                  0     0
  PIGK WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  PIGK MUTATED                           2     5
  PIGK WILD-TYPE                        20   221
D1091V13, multiclass
                                  clus
vv                                 PIGK MUTATED PIGK WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   2             20
  WHITE                                       5            221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1092) Variable = COPB2 MUTATION ANALYSIS
D1092V1, survival
                 sevent
clus2               0   1
  COPB2 MUTATED    11   5
  COPB2 WILD-TYPE 367  88
  COPB2 MUTATED COPB2 WILD-TYPE 
             16             455 
  COPB2 MUTATED COPB2 WILD-TYPE 
              5              88 
$`COPB2 MUTATED`
TCGA-AA-3492 TCGA-AA-3819 TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A010 TCGA-AZ-6598 
        3.02        25.02        25.02         4.01        34.98        49.41 
TCGA-AZ-6605 TCGA-CM-4743 TCGA-CM-5862 TCGA-CM-6166 TCGA-CM-6171 TCGA-D5-6924 
        5.23        23.05         5.03        21.99        14.04        14.30 
TCGA-DM-A1HB TCGA-AG-A002 TCGA-DC-6682 TCGA-EI-6507 
      135.65        20.98         4.01        19.96 

$`COPB2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3821 TCGA-AA-3831 
       10.06        35.05        33.04         0.99         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6606 
       88.21         6.77        12.10       100.01        29.56        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 
       21.14        82.95         1.91       124.27        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       32.02        15.02        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6168 
       12.00         2.96        29.03        16.04        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       13.02        15.02        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
       44.32       131.51       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
       19.99         5.95         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  COPB2 MUTATED COPB2 WILD-TYPE 
           3.02            0.00 
  COPB2 MUTATED COPB2 WILD-TYPE 
         135.65          148.01 
  COPB2 MUTATED COPB2 WILD-TYPE 
          20.47           20.19 
[1] "3.0 - 135.7 (20.5)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.8"
D1092V2, continuous
D1092V3, binary
                 cls
clus                0   1
  COPB2 MUTATED    13   3
  COPB2 WILD-TYPE 353 116
[1] "tbl2"
                 cls
clus              [,1] [,2]
  COPB2 MUTATED     13    3
  COPB2 WILD-TYPE  353  116
        clus
vv       COPB2 MUTATED COPB2 WILD-TYPE
  COLON             13             353
  RECTUM             3             116
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  COPB2 MUTATED         3        0        2         5         2         0
  COPB2 WILD-TYPE      88        1       30       133         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  COPB2 MUTATED           0          0          2          0        0         1
  COPB2 WILD-TYPE        24         11         57         42       48        17
                 vv
clus              STAGE IVB
  COPB2 MUTATED           0
  COPB2 WILD-TYPE         1
D1092V4, multiclass
            clus
vv           COPB2 MUTATED COPB2 WILD-TYPE
  STAGE I                3              88
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA              5             133
  STAGE IIB              2               8
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             2              57
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  COPB2 MUTATED     0   4   9   3
  COPB2 WILD-TYPE  17  88 320  47
D1092V5, multiclass
    clus
vv   COPB2 MUTATED COPB2 WILD-TYPE
  T1             0              17
  T2             4              88
  T3             9             320
  T4             3              47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  COPB2 MUTATED    13   3   0
  COPB2 WILD-TYPE 274 110  87
D1092V6, multiclass
    clus
vv   COPB2 MUTATED COPB2 WILD-TYPE
  N0            13             274
  N1             3             110
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1092V7, binary
                 cls
clus                0   1
  COPB2 MUTATED    13   1
  COPB2 WILD-TYPE 362  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  COPB2 MUTATED     13    1
  COPB2 WILD-TYPE  362   64
   clus
vv  COPB2 MUTATED COPB2 WILD-TYPE
  0            13             362
  1             1              64
[1] 2 2
[1] FALSE
D1092V8, binary
                 cls
clus                0   1
  COPB2 MUTATED     6  10
  COPB2 WILD-TYPE 219 254
[1] "tbl2"
                 cls
clus              [,1] [,2]
  COPB2 MUTATED      6   10
  COPB2 WILD-TYPE  219  254
        clus
vv       COPB2 MUTATED COPB2 WILD-TYPE
  FEMALE             6             219
  MALE              10             254
[1] 2 2
[1] FALSE
D1092V9, binary
                 cls
clus                0   1
  COPB2 MUTATED    13   0
  COPB2 WILD-TYPE 337  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  COPB2 MUTATED     13    0
  COPB2 WILD-TYPE  337   22
     clus
vv    COPB2 MUTATED COPB2 WILD-TYPE
  NO             13             337
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  COPB2 MUTATED                     11                             1
  COPB2 WILD-TYPE                  304                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  COPB2 MUTATED                       3                              0
  COPB2 WILD-TYPE                   103                             10
D1092V10, multiclass
                                clus
vv                               COPB2 MUTATED COPB2 WILD-TYPE
  COLON ADENOCARCINOMA                      11             304
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      3             103
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  COPB2 MUTATED    12   0   0   0
  COPB2 WILD-TYPE 333   4  31  25
D1092V11, multiclass
    clus
vv   COPB2 MUTATED COPB2 WILD-TYPE
  R0            12             333
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1092V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  COPB2 MUTATED                                  0     0
  COPB2 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  COPB2 MUTATED                           0    10
  COPB2 WILD-TYPE                        22   216
D1092V13, multiclass
                                  clus
vv                                 COPB2 MUTATED COPB2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                       10             216
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1093) Variable = CIZ1 MUTATION ANALYSIS
D1093V1, survival
                sevent
clus2              0   1
  CIZ1 MUTATED    13   2
  CIZ1 WILD-TYPE 365  91
  CIZ1 MUTATED CIZ1 WILD-TYPE 
            15            456 
  CIZ1 MUTATED CIZ1 WILD-TYPE 
             2             91 
$`CIZ1 MUTATED`
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6653 TCGA-AA-3542 TCGA-AA-3558 TCGA-AA-3715 
       22.06        32.71        24.39        12.99        20.98        19.04 
TCGA-AA-3877 TCGA-AA-3980 TCGA-AA-3982 TCGA-AD-5900 TCGA-AY-5543 TCGA-AZ-6598 
       31.00        27.02        27.02         0.07        33.01        49.41 
TCGA-CK-6751 TCGA-CM-6162 TCGA-AG-A002 
      124.27        12.00        20.98 

$`CIZ1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       22.09        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       24.16        21.76        24.69        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3543 
       19.07        34.03        29.00        29.00        26.01         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       29.95        23.01        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       78.08         6.05         6.97        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       18.05        40.96        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6197 TCGA-AY-6386 
       14.50        27.09        16.31         0.95        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       88.21         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CM-4743 TCGA-CM-4744 
        9.99        21.14        82.95         1.91        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       17.03        15.02         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  CIZ1 MUTATED CIZ1 WILD-TYPE 
          0.07           0.00 
  CIZ1 MUTATED CIZ1 WILD-TYPE 
        124.27         148.01 
  CIZ1 MUTATED CIZ1 WILD-TYPE 
         24.39          20.02 
[1] "0.1 - 124.3 (24.4)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.6"
D1093V2, continuous
D1093V3, binary
                cls
clus               0   1
  CIZ1 MUTATED    15   1
  CIZ1 WILD-TYPE 351 118
[1] "tbl2"
                cls
clus             [,1] [,2]
  CIZ1 MUTATED     15    1
  CIZ1 WILD-TYPE  351  118
        clus
vv       CIZ1 MUTATED CIZ1 WILD-TYPE
  COLON            15            351
  RECTUM            1            118
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CIZ1 MUTATED         7        0        3         1         0         1
  CIZ1 WILD-TYPE      84        1       29       137        10         0
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CIZ1 MUTATED           0          0          2          1        0         1
  CIZ1 WILD-TYPE        24         11         57         41       48        17
                vv
clus             STAGE IVB
  CIZ1 MUTATED           0
  CIZ1 WILD-TYPE         1
D1093V4, multiclass
            clus
vv           CIZ1 MUTATED CIZ1 WILD-TYPE
  STAGE I               7             84
  STAGE IA              0              1
  STAGE II              3             29
  STAGE IIA             1            137
  STAGE IIB             0             10
  STAGE IIC             1              0
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            2             57
  STAGE IIIC            1             41
  STAGE IV              0             48
  STAGE IVA             1             17
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  CIZ1 MUTATED     1   6   7   2
  CIZ1 WILD-TYPE  16  86 322  48
D1093V5, multiclass
    clus
vv   CIZ1 MUTATED CIZ1 WILD-TYPE
  T1            1             16
  T2            6             86
  T3            7            322
  T4            2             48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  CIZ1 MUTATED    12   3   1
  CIZ1 WILD-TYPE 275 110  86
D1093V6, multiclass
    clus
vv   CIZ1 MUTATED CIZ1 WILD-TYPE
  N0           12            275
  N1            3            110
  N2            1             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1093V7, binary
                cls
clus               0   1
  CIZ1 MUTATED    12   1
  CIZ1 WILD-TYPE 363  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  CIZ1 MUTATED     12    1
  CIZ1 WILD-TYPE  363   64
   clus
vv  CIZ1 MUTATED CIZ1 WILD-TYPE
  0           12            363
  1            1             64
[1] 2 2
[1] FALSE
D1093V8, binary
                cls
clus               0   1
  CIZ1 MUTATED     8   8
  CIZ1 WILD-TYPE 217 256
[1] "tbl2"
                cls
clus             [,1] [,2]
  CIZ1 MUTATED      8    8
  CIZ1 WILD-TYPE  217  256
        clus
vv       CIZ1 MUTATED CIZ1 WILD-TYPE
  FEMALE            8            217
  MALE              8            256
[1] 2 2
[1] FALSE
D1093V9, binary
                cls
clus               0   1
  CIZ1 MUTATED    14   0
  CIZ1 WILD-TYPE 336  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  CIZ1 MUTATED     14    0
  CIZ1 WILD-TYPE  336   22
     clus
vv    CIZ1 MUTATED CIZ1 WILD-TYPE
  NO            14            336
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CIZ1 MUTATED                     11                             4
  CIZ1 WILD-TYPE                  304                            43
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CIZ1 MUTATED                       1                              0
  CIZ1 WILD-TYPE                   105                             10
D1093V10, multiclass
                                clus
vv                               CIZ1 MUTATED CIZ1 WILD-TYPE
  COLON ADENOCARCINOMA                     11            304
  COLON MUCINOUS ADENOCARCINOMA             4             43
  RECTAL ADENOCARCINOMA                     1            105
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  CIZ1 MUTATED     9   0   1   1
  CIZ1 WILD-TYPE 336   4  30  24
D1093V11, multiclass
    clus
vv   CIZ1 MUTATED CIZ1 WILD-TYPE
  R0            9            336
  R1            0              4
  R2            1             30
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1093V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CIZ1 MUTATED                                  0     0
  CIZ1 WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  CIZ1 MUTATED                           1     7
  CIZ1 WILD-TYPE                        21   219
D1093V13, multiclass
                                  clus
vv                                 CIZ1 MUTATED CIZ1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                       7            219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1094) Variable = TMEM92 MUTATION ANALYSIS
D1094V1, survival
                  sevent
clus2                0   1
  TMEM92 MUTATED     3   0
  TMEM92 WILD-TYPE 375  93
  TMEM92 MUTATED TMEM92 WILD-TYPE 
               3              468 
  TMEM92 MUTATED TMEM92 WILD-TYPE 
               0               93 
$`TMEM92 MUTATED`
TCGA-AA-3947 TCGA-AD-6889 TCGA-CK-5913 
       33.01        56.55        51.32 

$`TMEM92 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 
       31.00         2.01        12.99        24.00        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       15.52         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       85.45        15.62        49.08         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  TMEM92 MUTATED TMEM92 WILD-TYPE 
           33.01             0.00 
  TMEM92 MUTATED TMEM92 WILD-TYPE 
           56.55           148.01 
  TMEM92 MUTATED TMEM92 WILD-TYPE 
          51.320           20.085 
[1] "33.0 - 56.5 (51.3)" "0.0 - 148.0 (20.1)"
[1] "hr="     "9100000"
D1094V2, continuous
[1] "Remove cluster labels:" "TMEM92 MUTATED"        
clus
  TMEM92 MUTATED TMEM92 WILD-TYPE 
               2              486 
      TCGA-A6-2671       TCGA-A6-2672       TCGA-A6-2674       TCGA-A6-2676 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-A6-2677       TCGA-A6-2678       TCGA-A6-2683       TCGA-A6-3807 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-A6-3808       TCGA-A6-3809       TCGA-A6-3810       TCGA-A6-4105 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-A6-5656       TCGA-A6-5657       TCGA-A6-5659       TCGA-A6-5660 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-A6-5661       TCGA-A6-5662       TCGA-A6-5664       TCGA-A6-5665 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-A6-5666       TCGA-A6-6137       TCGA-A6-6138       TCGA-A6-6141 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-A6-6142       TCGA-A6-6648       TCGA-A6-6649       TCGA-A6-6651 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-A6-6652       TCGA-A6-6653       TCGA-A6-6654       TCGA-A6-6780 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-A6-6781       TCGA-A6-6782       TCGA-AA-3489       TCGA-AA-3492 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3496       TCGA-AA-3502       TCGA-AA-3510       TCGA-AA-3511 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3514       TCGA-AA-3516       TCGA-AA-3517       TCGA-AA-3518 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3519       TCGA-AA-3520       TCGA-AA-3521       TCGA-AA-3522 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3524       TCGA-AA-3525       TCGA-AA-3526       TCGA-AA-3527 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3529       TCGA-AA-3530       TCGA-AA-3531       TCGA-AA-3532 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3534       TCGA-AA-3538       TCGA-AA-3542       TCGA-AA-3543 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3544       TCGA-AA-3548       TCGA-AA-3549       TCGA-AA-3552 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3553       TCGA-AA-3554       TCGA-AA-3555       TCGA-AA-3556 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3558       TCGA-AA-3560       TCGA-AA-3561       TCGA-AA-3562 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3655       TCGA-AA-3660       TCGA-AA-3662       TCGA-AA-3663 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3664       TCGA-AA-3666       TCGA-AA-3667       TCGA-AA-3672 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3673       TCGA-AA-3678       TCGA-AA-3679       TCGA-AA-3680 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3681       TCGA-AA-3684       TCGA-AA-3685       TCGA-AA-3688 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3692       TCGA-AA-3693       TCGA-AA-3695       TCGA-AA-3696 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3697       TCGA-AA-3710       TCGA-AA-3712       TCGA-AA-3713 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3715       TCGA-AA-3811       TCGA-AA-3812       TCGA-AA-3814 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3815       TCGA-AA-3818       TCGA-AA-3819       TCGA-AA-3821 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3831       TCGA-AA-3833       TCGA-AA-3837       TCGA-AA-3842 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3844       TCGA-AA-3845       TCGA-AA-3846       TCGA-AA-3848 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3850       TCGA-AA-3851       TCGA-AA-3852       TCGA-AA-3854 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3855       TCGA-AA-3856       TCGA-AA-3858       TCGA-AA-3860 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3861       TCGA-AA-3864       TCGA-AA-3866       TCGA-AA-3867 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3869       TCGA-AA-3870       TCGA-AA-3872       TCGA-AA-3875 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3877       TCGA-AA-3930       TCGA-AA-3939       TCGA-AA-3941 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3949       TCGA-AA-3950       TCGA-AA-3952       TCGA-AA-3955 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3956       TCGA-AA-3966       TCGA-AA-3968       TCGA-AA-3971 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3972       TCGA-AA-3973       TCGA-AA-3975       TCGA-AA-3976 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3977       TCGA-AA-3979       TCGA-AA-3980       TCGA-AA-3982 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3984       TCGA-AA-3986       TCGA-AA-3989       TCGA-AA-3994 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-A004       TCGA-AA-A00A       TCGA-AA-A00D       TCGA-AA-A00E 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-A00F       TCGA-AA-A00J       TCGA-AA-A00K       TCGA-AA-A00L 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-A00N       TCGA-AA-A00O       TCGA-AA-A00Q       TCGA-AA-A00R 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-A00U       TCGA-AA-A00W       TCGA-AA-A00Z       TCGA-AA-A010 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-A017       TCGA-AA-A01D       TCGA-AA-A01F       TCGA-AA-A01G 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-A01I       TCGA-AA-A01K       TCGA-AA-A01P       TCGA-AA-A01Q 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-A01R       TCGA-AA-A01S       TCGA-AA-A01T       TCGA-AA-A01V 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-A01X       TCGA-AA-A01Z       TCGA-AA-A022       TCGA-AA-A024 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-A029       TCGA-AA-A02F       TCGA-AA-A02H       TCGA-AA-A02J 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-A02K       TCGA-AA-A02O       TCGA-AA-A02W       TCGA-AA-A02Y 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-A03F       TCGA-AA-A03J       TCGA-AD-5900       TCGA-AD-6548 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AD-6888       TCGA-AD-6890       TCGA-AD-6895       TCGA-AD-6899 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AD-6901       TCGA-AD-6963       TCGA-AD-6964       TCGA-AD-6965 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AU-3779       TCGA-AU-6004       TCGA-AY-4070       TCGA-AY-4071 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AY-5543       TCGA-AY-6196       TCGA-AY-6197       TCGA-AY-6386 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AZ-4315       TCGA-AZ-4323       TCGA-AZ-4616       TCGA-AZ-4681 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AZ-4682       TCGA-AZ-5403       TCGA-AZ-5407       TCGA-AZ-6598 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AZ-6599       TCGA-AZ-6600       TCGA-AZ-6601       TCGA-AZ-6603 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AZ-6605       TCGA-AZ-6606       TCGA-AZ-6607       TCGA-AZ-6608 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-CA-5254       TCGA-CA-5255       TCGA-CA-5796       TCGA-CA-5797 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-CA-6715       TCGA-CA-6716       TCGA-CA-6717       TCGA-CA-6718 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-CA-6719       TCGA-CK-4947       TCGA-CK-4948       TCGA-CK-4950 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-CK-4952       TCGA-CK-5912       TCGA-CK-5914       TCGA-CK-5915 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-CK-5916       TCGA-CK-6746       TCGA-CK-6747       TCGA-CK-6748 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-CK-6751       TCGA-CM-4743       TCGA-CM-4744       TCGA-CM-4746 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-CM-4747       TCGA-CM-4752       TCGA-CM-5341       TCGA-CM-5344 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-CM-5348       TCGA-CM-5349       TCGA-CM-5860       TCGA-CM-5861 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-CM-5862       TCGA-CM-5863       TCGA-CM-5864       TCGA-CM-5868 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-CM-6161       TCGA-CM-6162       TCGA-CM-6163       TCGA-CM-6164 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-CM-6165       TCGA-CM-6166       TCGA-CM-6167       TCGA-CM-6168 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-CM-6169       TCGA-CM-6170       TCGA-CM-6171       TCGA-CM-6172 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-CM-6674       TCGA-CM-6675       TCGA-CM-6676       TCGA-CM-6677 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-CM-6678       TCGA-CM-6679       TCGA-CM-6680       TCGA-D5-5537 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-D5-5538       TCGA-D5-5539       TCGA-D5-5540       TCGA-D5-5541 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-D5-6529       TCGA-D5-6532       TCGA-D5-6533       TCGA-D5-6534 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-D5-6535       TCGA-D5-6536       TCGA-D5-6537       TCGA-D5-6538 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-D5-6539       TCGA-D5-6540       TCGA-D5-6541       TCGA-D5-6898 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-D5-6920       TCGA-D5-6922       TCGA-D5-6923       TCGA-D5-6924 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-D5-6926       TCGA-D5-6927       TCGA-D5-6928       TCGA-D5-6929 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-D5-6930       TCGA-D5-6931       TCGA-D5-6932       TCGA-D5-7000 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-DM-A0X9       TCGA-DM-A0XD       TCGA-DM-A0XF       TCGA-DM-A1D0 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-DM-A1D4       TCGA-DM-A1D6       TCGA-DM-A1D7       TCGA-DM-A1D8 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-DM-A1D9       TCGA-DM-A1DA       TCGA-DM-A1DB       TCGA-DM-A1HA 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-DM-A1HB       TCGA-DM-A282       TCGA-DM-A285       TCGA-DM-A28C 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-DM-A28E       TCGA-DM-A28F       TCGA-DM-A28G       TCGA-DM-A28H 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-DM-A28K       TCGA-F4-6459       TCGA-F4-6460       TCGA-F4-6569 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-F4-6570       TCGA-F4-6703       TCGA-F4-6704       TCGA-F4-6805 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-F4-6806       TCGA-F4-6807       TCGA-F4-6808       TCGA-F4-6809 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-F4-6854       TCGA-F4-6855       TCGA-F4-6856       TCGA-G4-6293 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-G4-6299       TCGA-G4-6303       TCGA-G4-6304       TCGA-G4-6306 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-G4-6307       TCGA-G4-6309       TCGA-G4-6310       TCGA-G4-6315 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-G4-6317       TCGA-G4-6321       TCGA-G4-6323       TCGA-G4-6586 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-G4-6588       TCGA-G4-6625       TCGA-G4-6626       TCGA-G4-6628 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AF-2687       TCGA-AF-2689       TCGA-AF-2691       TCGA-AF-2692 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AF-2693       TCGA-AF-3400       TCGA-AF-3913       TCGA-AF-4110 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AF-5654       TCGA-AF-6136       TCGA-AF-6655       TCGA-AF-6672 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AG-3574       TCGA-AG-3575       TCGA-AG-3578       TCGA-AG-3580 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AG-3581       TCGA-AG-3582       TCGA-AG-3583       TCGA-AG-3584 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AG-3586       TCGA-AG-3587       TCGA-AG-3593       TCGA-AG-3594 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AG-3598       TCGA-AG-3599       TCGA-AG-3600       TCGA-AG-3601 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AG-3602       TCGA-AG-3605       TCGA-AG-3608       TCGA-AG-3609 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AG-3611       TCGA-AG-3612       TCGA-AG-3726       TCGA-AG-3727 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AG-3731       TCGA-AG-3732       TCGA-AG-3742       TCGA-AG-3878 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AG-3881       TCGA-AG-3882       TCGA-AG-3883       TCGA-AG-3885 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AG-3887       TCGA-AG-3890       TCGA-AG-3892       TCGA-AG-3893 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AG-3894       TCGA-AG-3896       TCGA-AG-3898       TCGA-AG-3901 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AG-3902       TCGA-AG-3909       TCGA-AG-3999       TCGA-AG-4001 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AG-4005       TCGA-AG-4007       TCGA-AG-4008       TCGA-AG-4015 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AG-A002       TCGA-AG-A008       TCGA-AG-A00C       TCGA-AG-A00H 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AG-A00Y       TCGA-AG-A011       TCGA-AG-A014       TCGA-AG-A015 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AG-A016       TCGA-AG-A01L       TCGA-AG-A01W       TCGA-AG-A01Y 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AG-A020       TCGA-AG-A025       TCGA-AG-A026       TCGA-AG-A02G 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AG-A02N       TCGA-AG-A02X       TCGA-AG-A032       TCGA-AG-A036 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AH-6544       TCGA-AH-6547       TCGA-AH-6549       TCGA-AH-6643 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AH-6644       TCGA-CI-6619       TCGA-CI-6620       TCGA-CI-6621 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-CI-6622       TCGA-CI-6624       TCGA-CL-5917       TCGA-CL-5918 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-DC-5337       TCGA-DC-5869       TCGA-DC-6155       TCGA-DC-6157 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-DC-6158       TCGA-DC-6160       TCGA-DC-6681       TCGA-DC-6682 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-DC-6683       TCGA-DT-5265       TCGA-DY-A0XA       TCGA-DY-A1DC 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-DY-A1DD       TCGA-DY-A1DF       TCGA-DY-A1DG       TCGA-DY-A1H8 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-EF-5830       TCGA-EI-6506       TCGA-EI-6507       TCGA-EI-6508 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-EI-6510       TCGA-F5-6464       TCGA-F5-6465       TCGA-F5-6571 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-F5-6702       TCGA-F5-6811       TCGA-F5-6812       TCGA-F5-6813 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-G5-6235       TCGA-G5-6641 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
D1094V3, binary
                  cls
clus                 0   1
  TMEM92 MUTATED     3   0
  TMEM92 WILD-TYPE 363 119
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TMEM92 MUTATED      3    0
  TMEM92 WILD-TYPE  363  119
        clus
vv       TMEM92 MUTATED TMEM92 WILD-TYPE
  COLON               3              363
  RECTUM              0              119
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TMEM92 MUTATED         0        0        0         2         1         0
  TMEM92 WILD-TYPE      91        1       32       136         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TMEM92 MUTATED           0          0          0          0        0
  TMEM92 WILD-TYPE        24         11         59         42       48
                  vv
clus               STAGE IVA STAGE IVB
  TMEM92 MUTATED           0         0
  TMEM92 WILD-TYPE        18         1
D1094V4, multiclass
            clus
vv           TMEM92 MUTATED TMEM92 WILD-TYPE
  STAGE I                 0               91
  STAGE IA                0                1
  STAGE II                0               32
  STAGE IIA               2              136
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              0               59
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  TMEM92 MUTATED     0   0   2   1
  TMEM92 WILD-TYPE  17  92 327  49
D1094V5, multiclass
    clus
vv   TMEM92 MUTATED TMEM92 WILD-TYPE
  T1              0               17
  T2              0               92
  T3              2              327
  T4              1               49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  TMEM92 MUTATED     3   0   0
  TMEM92 WILD-TYPE 284 113  87
D1094V6, multiclass
    clus
vv   TMEM92 MUTATED TMEM92 WILD-TYPE
  N0              3              284
  N1              0              113
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1094V7, binary
                  cls
clus                 0   1
  TMEM92 MUTATED     2   0
  TMEM92 WILD-TYPE 373  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TMEM92 MUTATED      2    0
  TMEM92 WILD-TYPE  373   65
   clus
vv  TMEM92 MUTATED TMEM92 WILD-TYPE
  0              2              373
  1              0               65
[1] 2 2
[1] FALSE
D1094V8, binary
                  cls
clus                 0   1
  TMEM92 MUTATED     2   1
  TMEM92 WILD-TYPE 223 263
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TMEM92 MUTATED      2    1
  TMEM92 WILD-TYPE  223  263
        clus
vv       TMEM92 MUTATED TMEM92 WILD-TYPE
  FEMALE              2              223
  MALE                1              263
[1] 2 2
[1] FALSE
D1094V9, binary
                  cls
clus                 0   1
  TMEM92 MUTATED     2   0
  TMEM92 WILD-TYPE 348  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TMEM92 MUTATED      2    0
  TMEM92 WILD-TYPE  348   22
     clus
vv    TMEM92 MUTATED TMEM92 WILD-TYPE
  NO               2              348
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  TMEM92 MUTATED                      2                             1
  TMEM92 WILD-TYPE                  313                            46
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  TMEM92 MUTATED                       0                              0
  TMEM92 WILD-TYPE                   106                             10
D1094V10, multiclass
                                clus
vv                               TMEM92 MUTATED TMEM92 WILD-TYPE
  COLON ADENOCARCINOMA                        2              313
  COLON MUCINOUS ADENOCARCINOMA               1               46
  RECTAL ADENOCARCINOMA                       0              106
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  TMEM92 MUTATED     1   0   0   1
  TMEM92 WILD-TYPE 344   4  31  24
D1094V11, multiclass
[1] "Remove cluster labels:" "TMEM92 MUTATED"        
clus
  TMEM92 MUTATED TMEM92 WILD-TYPE 
               2              403 
      TCGA-A6-2671       TCGA-A6-2672       TCGA-A6-2674       TCGA-A6-2676 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-A6-2677       TCGA-A6-2678       TCGA-A6-2683       TCGA-A6-3807 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-A6-3808       TCGA-A6-3809       TCGA-A6-3810       TCGA-A6-5657 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-A6-5659       TCGA-A6-5661       TCGA-A6-5665       TCGA-A6-6781 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3489       TCGA-AA-3492       TCGA-AA-3496       TCGA-AA-3502 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3510       TCGA-AA-3511       TCGA-AA-3514       TCGA-AA-3517 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3518       TCGA-AA-3519       TCGA-AA-3520       TCGA-AA-3521 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3522       TCGA-AA-3524       TCGA-AA-3525       TCGA-AA-3526 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3527       TCGA-AA-3529       TCGA-AA-3530       TCGA-AA-3531 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3532       TCGA-AA-3534       TCGA-AA-3538       TCGA-AA-3542 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3543       TCGA-AA-3544       TCGA-AA-3548       TCGA-AA-3549 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3552       TCGA-AA-3553       TCGA-AA-3554       TCGA-AA-3555 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3556       TCGA-AA-3558       TCGA-AA-3560       TCGA-AA-3561 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3562       TCGA-AA-3655       TCGA-AA-3660       TCGA-AA-3662 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3663       TCGA-AA-3664       TCGA-AA-3666       TCGA-AA-3667 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3672       TCGA-AA-3673       TCGA-AA-3678       TCGA-AA-3679 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3680       TCGA-AA-3681       TCGA-AA-3684       TCGA-AA-3685 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3688       TCGA-AA-3692       TCGA-AA-3693       TCGA-AA-3695 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3696       TCGA-AA-3697       TCGA-AA-3710       TCGA-AA-3712 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3713       TCGA-AA-3715       TCGA-AA-3811       TCGA-AA-3812 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3814       TCGA-AA-3815       TCGA-AA-3818       TCGA-AA-3819 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3821       TCGA-AA-3831       TCGA-AA-3833       TCGA-AA-3837 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3842       TCGA-AA-3844       TCGA-AA-3845       TCGA-AA-3846 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3848       TCGA-AA-3850       TCGA-AA-3851       TCGA-AA-3852 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3854       TCGA-AA-3855       TCGA-AA-3856       TCGA-AA-3858 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3860       TCGA-AA-3861       TCGA-AA-3864       TCGA-AA-3866 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3867       TCGA-AA-3869       TCGA-AA-3870       TCGA-AA-3872 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3875       TCGA-AA-3877       TCGA-AA-3930       TCGA-AA-3939 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3941       TCGA-AA-3949       TCGA-AA-3950       TCGA-AA-3952 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3955       TCGA-AA-3956       TCGA-AA-3968       TCGA-AA-3971 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3972       TCGA-AA-3973       TCGA-AA-3975       TCGA-AA-3976 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3979       TCGA-AA-3984       TCGA-AA-3986       TCGA-AA-3989 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3994       TCGA-AA-A004       TCGA-AA-A00A       TCGA-AA-A00D 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-A00E       TCGA-AA-A00F       TCGA-AA-A00J       TCGA-AA-A00K 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-A00L       TCGA-AA-A00N       TCGA-AA-A00O       TCGA-AA-A00Q 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-A00R       TCGA-AA-A00U       TCGA-AA-A00W       TCGA-AA-A00Z 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-A010       TCGA-AA-A017       TCGA-AA-A01D       TCGA-AA-A01F 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-A01G       TCGA-AA-A01I       TCGA-AA-A01K       TCGA-AA-A01P 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-A01Q       TCGA-AA-A01R       TCGA-AA-A01S       TCGA-AA-A01T 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-A01V       TCGA-AA-A01X       TCGA-AA-A01Z       TCGA-AA-A022 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-A024       TCGA-AA-A029       TCGA-AA-A02F       TCGA-AA-A02H 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-A02J       TCGA-AA-A02K       TCGA-AA-A02O       TCGA-AA-A02W 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-A02Y       TCGA-AA-A03F       TCGA-AA-A03J       TCGA-AD-5900 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AD-6548       TCGA-AD-6888       TCGA-AU-3779       TCGA-AU-6004 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AY-4070       TCGA-AY-4071       TCGA-AY-5543       TCGA-AY-6196 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AY-6197       TCGA-AY-6386       TCGA-AZ-4315       TCGA-AZ-4681 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AZ-4682       TCGA-CA-5254       TCGA-CA-5255       TCGA-CA-5796 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-CA-5797       TCGA-CA-6715       TCGA-CA-6716       TCGA-CA-6717 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-CA-6718       TCGA-CA-6719       TCGA-CK-4947       TCGA-CK-4948 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-CK-4950       TCGA-CK-4952       TCGA-CK-5912       TCGA-CK-5914 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-CK-5915       TCGA-CK-5916       TCGA-CK-6746       TCGA-CK-6747 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-CK-6748       TCGA-CK-6751       TCGA-CM-4743       TCGA-CM-4744 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-CM-4746       TCGA-CM-4747       TCGA-CM-4752       TCGA-CM-5341 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-CM-5344       TCGA-CM-5348       TCGA-CM-5349       TCGA-CM-5860 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-CM-5861       TCGA-CM-5862       TCGA-CM-5863       TCGA-CM-5864 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-CM-5868       TCGA-CM-6161       TCGA-CM-6162       TCGA-CM-6163 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-CM-6164       TCGA-CM-6165       TCGA-CM-6166       TCGA-CM-6167 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-CM-6168       TCGA-CM-6169       TCGA-CM-6170       TCGA-CM-6171 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-CM-6172       TCGA-CM-6674       TCGA-CM-6675       TCGA-CM-6676 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-CM-6677       TCGA-CM-6678       TCGA-CM-6679       TCGA-CM-6680 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-D5-5537       TCGA-D5-5538       TCGA-D5-5539       TCGA-D5-5540 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-D5-5541       TCGA-D5-6529       TCGA-D5-6532       TCGA-D5-6533 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-D5-6534       TCGA-D5-6535       TCGA-D5-6536       TCGA-D5-6537 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-D5-6538       TCGA-D5-6539       TCGA-D5-6540       TCGA-D5-6541 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-D5-6898       TCGA-D5-6920       TCGA-D5-6922       TCGA-D5-6923 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-D5-6924       TCGA-D5-6926       TCGA-D5-6927       TCGA-D5-6928 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-D5-6929       TCGA-D5-6930       TCGA-D5-6931       TCGA-D5-6932 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-D5-7000       TCGA-F4-6459       TCGA-F4-6460       TCGA-F4-6569 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-F4-6570       TCGA-F4-6703       TCGA-F4-6704       TCGA-F4-6805 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-F4-6806       TCGA-F4-6807       TCGA-F4-6808       TCGA-F4-6809 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-F4-6854       TCGA-F4-6855       TCGA-F4-6856       TCGA-G4-6293 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-G4-6299       TCGA-G4-6303       TCGA-G4-6304       TCGA-G4-6306 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-G4-6307       TCGA-G4-6309       TCGA-G4-6310       TCGA-G4-6315 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-G4-6317       TCGA-G4-6321       TCGA-G4-6323       TCGA-G4-6586 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-G4-6588       TCGA-G4-6625       TCGA-G4-6626       TCGA-G4-6628 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AF-2687       TCGA-AF-2689       TCGA-AF-2691       TCGA-AF-2692 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AF-3400       TCGA-AF-3913       TCGA-AF-4110       TCGA-AF-5654 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AF-6655       TCGA-AG-3574       TCGA-AG-3575       TCGA-AG-3578 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AG-3580       TCGA-AG-3581       TCGA-AG-3582       TCGA-AG-3583 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AG-3584       TCGA-AG-3586       TCGA-AG-3587       TCGA-AG-3593 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AG-3594       TCGA-AG-3598       TCGA-AG-3599       TCGA-AG-3600 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AG-3601       TCGA-AG-3602       TCGA-AG-3605       TCGA-AG-3608 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AG-3609       TCGA-AG-3611       TCGA-AG-3612       TCGA-AG-3726 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AG-3727       TCGA-AG-3731       TCGA-AG-3732       TCGA-AG-3742 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AG-3878       TCGA-AG-3882       TCGA-AG-3883       TCGA-AG-3885 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AG-3887       TCGA-AG-3890       TCGA-AG-3892       TCGA-AG-3893 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AG-3894       TCGA-AG-3896       TCGA-AG-3898       TCGA-AG-3901 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AG-3902       TCGA-AG-3909       TCGA-AG-3999       TCGA-AG-4001 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AG-4005       TCGA-AG-4007       TCGA-AG-4008       TCGA-AG-4015 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AG-A002       TCGA-AG-A008       TCGA-AG-A00C       TCGA-AG-A00H 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AG-A00Y       TCGA-AG-A011       TCGA-AG-A014       TCGA-AG-A015 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AG-A016       TCGA-AG-A01L       TCGA-AG-A01W       TCGA-AG-A01Y 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AG-A020       TCGA-AG-A025       TCGA-AG-A026       TCGA-AG-A02G 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AG-A02N       TCGA-AG-A02X       TCGA-AG-A032       TCGA-AG-A036 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AH-6549       TCGA-AH-6643       TCGA-CL-5917       TCGA-CL-5918 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-DC-5337       TCGA-DC-5869       TCGA-DC-6155       TCGA-DC-6157 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-DC-6158       TCGA-DC-6160       TCGA-DC-6681       TCGA-DC-6682 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-DC-6683       TCGA-DT-5265       TCGA-EF-5830       TCGA-EI-6506 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-EI-6507       TCGA-EI-6508       TCGA-EI-6510       TCGA-F5-6464 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-F5-6465       TCGA-F5-6571       TCGA-F5-6702       TCGA-F5-6812 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-F5-6813       TCGA-G5-6235       TCGA-G5-6641 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
D1094V12, continuous
[1] "Remove cluster labels:" "TMEM92 MUTATED"        
clus
  TMEM92 MUTATED TMEM92 WILD-TYPE 
               2              456 
      TCGA-A6-2671       TCGA-A6-2672       TCGA-A6-2674       TCGA-A6-2676 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-A6-2677       TCGA-A6-2678       TCGA-A6-2683       TCGA-A6-3807 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-A6-3808       TCGA-A6-3809       TCGA-A6-3810       TCGA-A6-4105 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-A6-5656       TCGA-A6-5657       TCGA-A6-5659       TCGA-A6-5660 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-A6-5661       TCGA-A6-5662       TCGA-A6-5664       TCGA-A6-5665 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-A6-5666       TCGA-A6-6137       TCGA-A6-6138       TCGA-A6-6141 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-A6-6142       TCGA-A6-6648       TCGA-A6-6649       TCGA-A6-6651 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-A6-6652       TCGA-A6-6653       TCGA-A6-6654       TCGA-A6-6780 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-A6-6781       TCGA-A6-6782       TCGA-AA-3489       TCGA-AA-3492 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3496       TCGA-AA-3502       TCGA-AA-3510       TCGA-AA-3511 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3514       TCGA-AA-3516       TCGA-AA-3517       TCGA-AA-3518 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3519       TCGA-AA-3520       TCGA-AA-3521       TCGA-AA-3522 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3524       TCGA-AA-3525       TCGA-AA-3526       TCGA-AA-3527 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3529       TCGA-AA-3530       TCGA-AA-3531       TCGA-AA-3532 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3534       TCGA-AA-3538       TCGA-AA-3542       TCGA-AA-3543 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3544       TCGA-AA-3548       TCGA-AA-3549       TCGA-AA-3552 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3553       TCGA-AA-3554       TCGA-AA-3555       TCGA-AA-3556 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3558       TCGA-AA-3560       TCGA-AA-3562       TCGA-AA-3655 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3660       TCGA-AA-3662       TCGA-AA-3663       TCGA-AA-3664 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3666       TCGA-AA-3667       TCGA-AA-3672       TCGA-AA-3673 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3678       TCGA-AA-3679       TCGA-AA-3680       TCGA-AA-3681 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3684       TCGA-AA-3685       TCGA-AA-3688       TCGA-AA-3692 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3693       TCGA-AA-3695       TCGA-AA-3696       TCGA-AA-3697 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3710       TCGA-AA-3712       TCGA-AA-3713       TCGA-AA-3715 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3811       TCGA-AA-3812       TCGA-AA-3814       TCGA-AA-3815 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3818       TCGA-AA-3819       TCGA-AA-3821       TCGA-AA-3831 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3833       TCGA-AA-3837       TCGA-AA-3842       TCGA-AA-3844 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3845       TCGA-AA-3846       TCGA-AA-3848       TCGA-AA-3850 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3851       TCGA-AA-3852       TCGA-AA-3854       TCGA-AA-3855 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3856       TCGA-AA-3858       TCGA-AA-3860       TCGA-AA-3861 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3864       TCGA-AA-3866       TCGA-AA-3867       TCGA-AA-3869 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3870       TCGA-AA-3872       TCGA-AA-3875       TCGA-AA-3877 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3930       TCGA-AA-3939       TCGA-AA-3941       TCGA-AA-3949 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3950       TCGA-AA-3952       TCGA-AA-3955       TCGA-AA-3956 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3966       TCGA-AA-3968       TCGA-AA-3971       TCGA-AA-3972 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3973       TCGA-AA-3975       TCGA-AA-3976       TCGA-AA-3977 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3979       TCGA-AA-3980       TCGA-AA-3982       TCGA-AA-3984 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-3986       TCGA-AA-3989       TCGA-AA-3994       TCGA-AA-A004 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-A00A       TCGA-AA-A00D       TCGA-AA-A00E       TCGA-AA-A00F 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-A00J       TCGA-AA-A00K       TCGA-AA-A00L       TCGA-AA-A00N 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-A00O       TCGA-AA-A00Q       TCGA-AA-A00R       TCGA-AA-A00U 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-A00W       TCGA-AA-A00Z       TCGA-AA-A010       TCGA-AA-A017 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-A01D       TCGA-AA-A01F       TCGA-AA-A01G       TCGA-AA-A01I 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-A01K       TCGA-AA-A01P       TCGA-AA-A01Q       TCGA-AA-A01R 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-A01S       TCGA-AA-A01T       TCGA-AA-A01V       TCGA-AA-A01X 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-A01Z       TCGA-AA-A022       TCGA-AA-A024       TCGA-AA-A029 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-A02F       TCGA-AA-A02H       TCGA-AA-A02J       TCGA-AA-A02K 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-A02O       TCGA-AA-A02W       TCGA-AA-A02Y       TCGA-AA-A03F 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AA-A03J       TCGA-AD-5900       TCGA-AD-6548       TCGA-AD-6888 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AD-6890       TCGA-AD-6895       TCGA-AD-6899       TCGA-AD-6901 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AD-6963       TCGA-AD-6964       TCGA-AD-6965       TCGA-AU-3779 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AU-6004       TCGA-AY-4070       TCGA-AY-4071       TCGA-AY-5543 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AY-6196       TCGA-AY-6197       TCGA-AY-6386       TCGA-AZ-4323 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AZ-4616       TCGA-AZ-4682       TCGA-AZ-5403       TCGA-AZ-5407 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AZ-6598       TCGA-AZ-6599       TCGA-AZ-6600       TCGA-AZ-6601 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AZ-6603       TCGA-AZ-6605       TCGA-AZ-6606       TCGA-AZ-6607 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AZ-6608       TCGA-CK-4947       TCGA-CK-4948       TCGA-CK-4950 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-CK-4952       TCGA-CM-4743       TCGA-CM-4744       TCGA-CM-4746 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-CM-4747       TCGA-CM-4752       TCGA-CM-5341       TCGA-CM-5344 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-CM-5348       TCGA-CM-5349       TCGA-CM-5860       TCGA-CM-5861 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-CM-5862       TCGA-CM-5863       TCGA-CM-5864       TCGA-CM-5868 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-CM-6161       TCGA-CM-6162       TCGA-CM-6163       TCGA-CM-6164 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-CM-6165       TCGA-CM-6166       TCGA-CM-6167       TCGA-CM-6168 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-CM-6169       TCGA-CM-6170       TCGA-CM-6171       TCGA-CM-6172 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-CM-6674       TCGA-CM-6675       TCGA-CM-6676       TCGA-CM-6677 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-CM-6678       TCGA-CM-6679       TCGA-CM-6680       TCGA-D5-5537 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-D5-5538       TCGA-D5-5539       TCGA-D5-5540       TCGA-D5-5541 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-D5-6529       TCGA-D5-6532       TCGA-D5-6533       TCGA-D5-6534 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-D5-6535       TCGA-D5-6536       TCGA-D5-6537       TCGA-D5-6538 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-D5-6539       TCGA-D5-6540       TCGA-D5-6541       TCGA-D5-6898 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-D5-6920       TCGA-D5-6922       TCGA-D5-6923       TCGA-D5-6924 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-D5-6926       TCGA-D5-6927       TCGA-D5-6928       TCGA-D5-6929 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-D5-6930       TCGA-D5-6931       TCGA-D5-6932       TCGA-D5-7000 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-DM-A0X9       TCGA-DM-A0XD       TCGA-DM-A0XF       TCGA-DM-A1D0 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-DM-A1D4       TCGA-DM-A1D6       TCGA-DM-A1D7       TCGA-DM-A1D8 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-DM-A1D9       TCGA-DM-A1DA       TCGA-DM-A1DB       TCGA-DM-A1HA 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-DM-A1HB       TCGA-DM-A282       TCGA-DM-A285       TCGA-DM-A28C 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-DM-A28E       TCGA-DM-A28F       TCGA-DM-A28G       TCGA-DM-A28H 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-DM-A28K       TCGA-F4-6459       TCGA-F4-6460       TCGA-F4-6569 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-F4-6570       TCGA-F4-6703       TCGA-F4-6704       TCGA-F4-6806 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-F4-6807       TCGA-F4-6808       TCGA-F4-6809       TCGA-F4-6854 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-F4-6855       TCGA-F4-6856       TCGA-G4-6293       TCGA-G4-6299 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-G4-6303       TCGA-G4-6304       TCGA-G4-6306       TCGA-G4-6307 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-G4-6309       TCGA-G4-6310       TCGA-G4-6315       TCGA-G4-6317 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-G4-6321       TCGA-G4-6323       TCGA-G4-6586       TCGA-G4-6588 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-G4-6625       TCGA-G4-6626       TCGA-G4-6628       TCGA-AF-2687 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AF-2689       TCGA-AF-2691       TCGA-AF-2692       TCGA-AF-2693 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AF-3400       TCGA-AF-3913       TCGA-AF-4110       TCGA-AF-5654 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AF-6136       TCGA-AF-6655       TCGA-AF-6672       TCGA-AG-3574 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AG-3575       TCGA-AG-3578       TCGA-AG-3580       TCGA-AG-3581 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AG-3582       TCGA-AG-3583       TCGA-AG-3584       TCGA-AG-3586 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AG-3587       TCGA-AG-3593       TCGA-AG-3594       TCGA-AG-3598 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AG-3599       TCGA-AG-3600       TCGA-AG-3601       TCGA-AG-3602 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AG-3605       TCGA-AG-3608       TCGA-AG-3609       TCGA-AG-3611 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AG-3612       TCGA-AG-3726       TCGA-AG-3727       TCGA-AG-3731 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AG-3732       TCGA-AG-3742       TCGA-AG-3878       TCGA-AG-3881 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AG-3882       TCGA-AG-3883       TCGA-AG-3885       TCGA-AG-3887 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AG-3890       TCGA-AG-3892       TCGA-AG-3893       TCGA-AG-3894 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AG-3896       TCGA-AG-3898       TCGA-AG-3901       TCGA-AG-3902 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AG-3909       TCGA-AG-3999       TCGA-AG-4001       TCGA-AG-4005 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AG-4007       TCGA-AG-4008       TCGA-AG-4015       TCGA-AG-A002 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AG-A008       TCGA-AG-A00C       TCGA-AG-A00H       TCGA-AG-A00Y 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AG-A011       TCGA-AG-A014       TCGA-AG-A015       TCGA-AG-A016 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AG-A01L       TCGA-AG-A01W       TCGA-AG-A01Y       TCGA-AG-A020 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AG-A025       TCGA-AG-A026       TCGA-AG-A02G       TCGA-AG-A02N 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AG-A02X       TCGA-AG-A032       TCGA-AG-A036       TCGA-AH-6544 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AH-6547       TCGA-AH-6643       TCGA-AH-6644       TCGA-CI-6622 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-DC-5337       TCGA-DC-5869       TCGA-DC-6155       TCGA-DC-6157 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-DC-6158       TCGA-DC-6160       TCGA-DC-6681       TCGA-DC-6682 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-DC-6683       TCGA-DY-A0XA       TCGA-DY-A1DC       TCGA-DY-A1DD 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-DY-A1DF       TCGA-DY-A1DG       TCGA-DY-A1H8       TCGA-EI-6506 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-EI-6507       TCGA-EI-6508       TCGA-EI-6510       TCGA-F5-6464 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-F5-6465       TCGA-F5-6571       TCGA-F5-6702       TCGA-F5-6811 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-F5-6812       TCGA-F5-6813       TCGA-G5-6235       TCGA-G5-6641 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TMEM92 MUTATED                                  0     1
  TMEM92 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  TMEM92 MUTATED                           0     1
  TMEM92 WILD-TYPE                        22   225
D1094V13, multiclass
[1] "Remove cluster labels:" "TMEM92 MUTATED"        
clus
  TMEM92 MUTATED TMEM92 WILD-TYPE 
               2              258 
      TCGA-A6-2671       TCGA-A6-2672       TCGA-A6-2674       TCGA-A6-2676 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-A6-2677       TCGA-A6-2678       TCGA-A6-2683       TCGA-A6-3807 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-A6-3808       TCGA-A6-3809       TCGA-A6-3810       TCGA-A6-4105 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-A6-5656       TCGA-A6-5657       TCGA-A6-5659       TCGA-A6-5660 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-A6-5661       TCGA-A6-5662       TCGA-A6-5664       TCGA-A6-5665 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-A6-5666       TCGA-A6-6137       TCGA-A6-6138       TCGA-A6-6141 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-A6-6142       TCGA-A6-6648       TCGA-A6-6649       TCGA-A6-6651 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-A6-6652       TCGA-A6-6653       TCGA-A6-6654       TCGA-A6-6780 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-A6-6781       TCGA-A6-6782       TCGA-AD-5900       TCGA-AD-6548 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AD-6888       TCGA-AD-6890       TCGA-AD-6895       TCGA-AD-6899 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AD-6901       TCGA-AD-6963       TCGA-AD-6964       TCGA-AD-6965 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AU-3779       TCGA-AU-6004       TCGA-AY-4070       TCGA-AY-4071 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AY-5543       TCGA-AY-6196       TCGA-AY-6197       TCGA-AY-6386 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AZ-4315       TCGA-AZ-4323       TCGA-AZ-4616       TCGA-AZ-4681 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AZ-4682       TCGA-AZ-5403       TCGA-AZ-5407       TCGA-AZ-6598 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AZ-6599       TCGA-AZ-6600       TCGA-AZ-6601       TCGA-AZ-6603 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AZ-6605       TCGA-AZ-6606       TCGA-AZ-6607       TCGA-AZ-6608 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-CA-5254       TCGA-CA-5255       TCGA-CA-5796       TCGA-CA-5797 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-CA-6715       TCGA-CA-6716       TCGA-CA-6717       TCGA-CA-6718 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-CA-6719       TCGA-CK-4947       TCGA-CK-4948       TCGA-CK-4950 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-CK-4952       TCGA-CK-5912       TCGA-CK-5914       TCGA-CK-5915 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-CK-5916       TCGA-CK-6746       TCGA-CK-6747       TCGA-CK-6748 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-CK-6751       TCGA-CM-4743       TCGA-CM-4744       TCGA-CM-4746 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-CM-4747       TCGA-CM-4752       TCGA-CM-5341       TCGA-CM-5344 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-CM-5348       TCGA-CM-5349       TCGA-CM-5860       TCGA-CM-5861 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-CM-5862       TCGA-CM-5863       TCGA-CM-5864       TCGA-CM-5868 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-CM-6161       TCGA-CM-6162       TCGA-CM-6163       TCGA-CM-6164 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-CM-6165       TCGA-CM-6166       TCGA-CM-6167       TCGA-CM-6168 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-CM-6169       TCGA-CM-6170       TCGA-CM-6171       TCGA-CM-6172 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-CM-6674       TCGA-CM-6675       TCGA-CM-6676       TCGA-CM-6677 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-CM-6678       TCGA-CM-6679       TCGA-CM-6680       TCGA-D5-5537 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-D5-5538       TCGA-D5-5539       TCGA-D5-5540       TCGA-D5-5541 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-D5-6529       TCGA-D5-6532       TCGA-D5-6533       TCGA-D5-6534 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-D5-6535       TCGA-D5-6536       TCGA-D5-6537       TCGA-D5-6538 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-D5-6539       TCGA-D5-6540       TCGA-D5-6541       TCGA-D5-6898 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-D5-6920       TCGA-D5-6922       TCGA-D5-6923       TCGA-D5-6924 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-D5-6926       TCGA-D5-6927       TCGA-D5-6928       TCGA-D5-6929 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-D5-6930       TCGA-D5-6931       TCGA-D5-6932       TCGA-D5-7000 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-DM-A0X9       TCGA-DM-A0XD       TCGA-DM-A0XF       TCGA-DM-A1D0 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-DM-A1D4       TCGA-DM-A1D6       TCGA-DM-A1D7       TCGA-DM-A1D8 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-DM-A1D9       TCGA-DM-A1DA       TCGA-DM-A1DB       TCGA-DM-A1HA 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-DM-A1HB       TCGA-DM-A282       TCGA-DM-A285       TCGA-DM-A28C 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-DM-A28E       TCGA-DM-A28F       TCGA-DM-A28G       TCGA-DM-A28H 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-DM-A28K       TCGA-F4-6459       TCGA-F4-6460       TCGA-F4-6569 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-F4-6570       TCGA-F4-6703       TCGA-F4-6704       TCGA-F4-6805 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-F4-6806       TCGA-F4-6807       TCGA-F4-6808       TCGA-F4-6809 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-F4-6854       TCGA-F4-6855       TCGA-F4-6856       TCGA-G4-6293 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-G4-6299       TCGA-G4-6303       TCGA-G4-6304       TCGA-G4-6306 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-G4-6307       TCGA-G4-6309       TCGA-G4-6310       TCGA-G4-6315 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-G4-6317       TCGA-G4-6321       TCGA-G4-6323       TCGA-G4-6586 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-G4-6588       TCGA-G4-6625       TCGA-G4-6626       TCGA-G4-6628 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AF-2687       TCGA-AF-2689       TCGA-AF-2691       TCGA-AF-2692 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AF-2693       TCGA-AF-3400       TCGA-AF-3913       TCGA-AF-4110 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AF-5654       TCGA-AF-6136       TCGA-AF-6655       TCGA-AF-6672 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AH-6544       TCGA-AH-6547       TCGA-AH-6549       TCGA-AH-6643 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-AH-6644       TCGA-CI-6619       TCGA-CI-6620       TCGA-CI-6621 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-CI-6622       TCGA-CI-6624       TCGA-CL-5917       TCGA-CL-5918 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-DC-5337       TCGA-DC-5869       TCGA-DC-6155       TCGA-DC-6157 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-DC-6158       TCGA-DC-6160       TCGA-DC-6681       TCGA-DC-6682 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-DC-6683       TCGA-DT-5265       TCGA-DY-A0XA       TCGA-DY-A1DC 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-DY-A1DD       TCGA-DY-A1DF       TCGA-DY-A1DG       TCGA-DY-A1H8 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-EF-5830       TCGA-EI-6506       TCGA-EI-6507       TCGA-EI-6508 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-EI-6510       TCGA-F5-6464       TCGA-F5-6465       TCGA-F5-6571 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-F5-6702       TCGA-F5-6811       TCGA-F5-6812       TCGA-F5-6813 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 
      TCGA-G5-6235       TCGA-G5-6641 
"TMEM92 WILD-TYPE" "TMEM92 WILD-TYPE" 

Clustering(1095) Variable = TAS2R1 MUTATION ANALYSIS
D1095V1, survival
                  sevent
clus2                0   1
  TAS2R1 MUTATED     3   0
  TAS2R1 WILD-TYPE 375  93
  TAS2R1 MUTATED TAS2R1 WILD-TYPE 
               3              468 
  TAS2R1 MUTATED TAS2R1 WILD-TYPE 
               0               93 
$`TAS2R1 MUTATED`
TCGA-AA-3662 TCGA-CM-5861 TCGA-AG-3892 
        6.05        15.02        13.02 

$`TAS2R1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       30.08        32.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  TAS2R1 MUTATED TAS2R1 WILD-TYPE 
            6.05             0.00 
  TAS2R1 MUTATED TAS2R1 WILD-TYPE 
           15.02           148.01 
  TAS2R1 MUTATED TAS2R1 WILD-TYPE 
          13.020           20.415 
[1] "6.0 - 15.0 (13.0)"  "0.0 - 148.0 (20.4)"
[1] "hr="     "1200000"
D1095V2, continuous
D1095V3, binary
                  cls
clus                 0   1
  TAS2R1 MUTATED     4   1
  TAS2R1 WILD-TYPE 362 118
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TAS2R1 MUTATED      4    1
  TAS2R1 WILD-TYPE  362  118
        clus
vv       TAS2R1 MUTATED TAS2R1 WILD-TYPE
  COLON               4              362
  RECTUM              1              118
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TAS2R1 MUTATED         1        0        0         2         1         0
  TAS2R1 WILD-TYPE      90        1       32       136         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TAS2R1 MUTATED           0          0          0          0        1
  TAS2R1 WILD-TYPE        24         11         59         42       47
                  vv
clus               STAGE IVA STAGE IVB
  TAS2R1 MUTATED           0         0
  TAS2R1 WILD-TYPE        18         1
D1095V4, multiclass
            clus
vv           TAS2R1 MUTATED TAS2R1 WILD-TYPE
  STAGE I                 1               90
  STAGE IA                0                1
  STAGE II                0               32
  STAGE IIA               2              136
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              0               59
  STAGE IIIC              0               42
  STAGE IV                1               47
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  TAS2R1 MUTATED     1   0   2   2
  TAS2R1 WILD-TYPE  16  92 327  48
D1095V5, multiclass
    clus
vv   TAS2R1 MUTATED TAS2R1 WILD-TYPE
  T1              1               16
  T2              0               92
  T3              2              327
  T4              2               48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  TAS2R1 MUTATED     4   0   1
  TAS2R1 WILD-TYPE 283 113  86
D1095V6, multiclass
    clus
vv   TAS2R1 MUTATED TAS2R1 WILD-TYPE
  N0              4              283
  N1              0              113
  N2              1               86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1095V7, binary
                  cls
clus                 0   1
  TAS2R1 MUTATED     3   1
  TAS2R1 WILD-TYPE 372  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TAS2R1 MUTATED      3    1
  TAS2R1 WILD-TYPE  372   64
   clus
vv  TAS2R1 MUTATED TAS2R1 WILD-TYPE
  0              3              372
  1              1               64
[1] 2 2
[1] FALSE
D1095V8, binary
                  cls
clus                 0   1
  TAS2R1 MUTATED     5   0
  TAS2R1 WILD-TYPE 220 264
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TAS2R1 MUTATED      5    0
  TAS2R1 WILD-TYPE  220  264
        clus
vv       TAS2R1 MUTATED TAS2R1 WILD-TYPE
  FEMALE              5              220
  MALE                0              264
[1] 2 2
[1] FALSE
D1095V9, binary
                  cls
clus                 0   1
  TAS2R1 MUTATED     3   0
  TAS2R1 WILD-TYPE 347  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TAS2R1 MUTATED      3    0
  TAS2R1 WILD-TYPE  347   22
     clus
vv    TAS2R1 MUTATED TAS2R1 WILD-TYPE
  NO               3              347
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  TAS2R1 MUTATED                      4                             0
  TAS2R1 WILD-TYPE                  311                            47
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  TAS2R1 MUTATED                       1                              0
  TAS2R1 WILD-TYPE                   105                             10
D1095V10, multiclass
                                clus
vv                               TAS2R1 MUTATED TAS2R1 WILD-TYPE
  COLON ADENOCARCINOMA                        4              311
  COLON MUCINOUS ADENOCARCINOMA               0               47
  RECTAL ADENOCARCINOMA                       1              105
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  TAS2R1 MUTATED     3   0   1   1
  TAS2R1 WILD-TYPE 342   4  30  24
D1095V11, multiclass
    clus
vv   TAS2R1 MUTATED TAS2R1 WILD-TYPE
  R0              3              342
  R1              0                4
  R2              1               30
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1095V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TAS2R1 MUTATED                                  0     0
  TAS2R1 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  TAS2R1 MUTATED                           0     2
  TAS2R1 WILD-TYPE                        22   224
D1095V13, multiclass
[1] "Remove cluster labels:" "TAS2R1 MUTATED"        
clus
  TAS2R1 MUTATED TAS2R1 WILD-TYPE 
               2              258 
      TCGA-A6-2671       TCGA-A6-2672       TCGA-A6-2674       TCGA-A6-2676 
"TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" 
      TCGA-A6-2677       TCGA-A6-2678       TCGA-A6-2683       TCGA-A6-3807 
"TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" 
      TCGA-A6-3808       TCGA-A6-3809       TCGA-A6-3810       TCGA-A6-4105 
"TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" 
      TCGA-A6-5656       TCGA-A6-5657       TCGA-A6-5659       TCGA-A6-5660 
"TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" 
      TCGA-A6-5661       TCGA-A6-5662       TCGA-A6-5664       TCGA-A6-5665 
"TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" 
      TCGA-A6-5666       TCGA-A6-6137       TCGA-A6-6138       TCGA-A6-6141 
"TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" 
      TCGA-A6-6142       TCGA-A6-6648       TCGA-A6-6649       TCGA-A6-6651 
"TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" 
      TCGA-A6-6652       TCGA-A6-6653       TCGA-A6-6654       TCGA-A6-6780 
"TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" 
      TCGA-A6-6781       TCGA-A6-6782       TCGA-AD-5900       TCGA-AD-6548 
"TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" 
      TCGA-AD-6888       TCGA-AD-6889       TCGA-AD-6890       TCGA-AD-6895 
"TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" 
      TCGA-AD-6899       TCGA-AD-6901       TCGA-AD-6963       TCGA-AD-6964 
"TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" 
      TCGA-AD-6965       TCGA-AU-3779       TCGA-AU-6004       TCGA-AY-4070 
"TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" 
      TCGA-AY-4071       TCGA-AY-5543       TCGA-AY-6196       TCGA-AY-6197 
"TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" 
      TCGA-AY-6386       TCGA-AZ-4315       TCGA-AZ-4323       TCGA-AZ-4616 
"TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" 
      TCGA-AZ-4681       TCGA-AZ-4682       TCGA-AZ-5403       TCGA-AZ-5407 
"TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" 
      TCGA-AZ-6598       TCGA-AZ-6599       TCGA-AZ-6600       TCGA-AZ-6601 
"TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" 
      TCGA-AZ-6603       TCGA-AZ-6605       TCGA-AZ-6606       TCGA-AZ-6607 
"TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" 
      TCGA-AZ-6608       TCGA-CA-5254       TCGA-CA-5255       TCGA-CA-5796 
"TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" 
      TCGA-CA-5797       TCGA-CA-6715       TCGA-CA-6716       TCGA-CA-6717 
"TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" 
      TCGA-CA-6718       TCGA-CA-6719       TCGA-CK-4947       TCGA-CK-4948 
"TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" 
      TCGA-CK-4950       TCGA-CK-4952       TCGA-CK-5912       TCGA-CK-5913 
"TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" 
      TCGA-CK-5914       TCGA-CK-5915       TCGA-CK-5916       TCGA-CK-6747 
"TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" 
      TCGA-CK-6748       TCGA-CK-6751       TCGA-CM-4743       TCGA-CM-4744 
"TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" 
      TCGA-CM-4746       TCGA-CM-4747       TCGA-CM-4752       TCGA-CM-5341 
"TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" 
      TCGA-CM-5344       TCGA-CM-5348       TCGA-CM-5349       TCGA-CM-5860 
"TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" 
      TCGA-CM-5862       TCGA-CM-5863       TCGA-CM-5864       TCGA-CM-5868 
"TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" 
      TCGA-CM-6161       TCGA-CM-6162       TCGA-CM-6163       TCGA-CM-6164 
"TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" 
      TCGA-CM-6165       TCGA-CM-6166       TCGA-CM-6167       TCGA-CM-6168 
"TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" 
      TCGA-CM-6169       TCGA-CM-6170       TCGA-CM-6171       TCGA-CM-6172 
"TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" 
      TCGA-CM-6674       TCGA-CM-6675       TCGA-CM-6676       TCGA-CM-6677 
"TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" 
      TCGA-CM-6678       TCGA-CM-6679       TCGA-CM-6680       TCGA-D5-5537 
"TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" 
      TCGA-D5-5538       TCGA-D5-5539       TCGA-D5-5540       TCGA-D5-5541 
"TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" 
      TCGA-D5-6529       TCGA-D5-6532       TCGA-D5-6533       TCGA-D5-6534 
"TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" 
      TCGA-D5-6535       TCGA-D5-6536       TCGA-D5-6537       TCGA-D5-6538 
"TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" 
      TCGA-D5-6539       TCGA-D5-6540       TCGA-D5-6541       TCGA-D5-6898 
"TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" 
      TCGA-D5-6920       TCGA-D5-6922       TCGA-D5-6923       TCGA-D5-6924 
"TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" 
      TCGA-D5-6926       TCGA-D5-6927       TCGA-D5-6928       TCGA-D5-6929 
"TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" 
      TCGA-D5-6930       TCGA-D5-6931       TCGA-D5-6932       TCGA-D5-7000 
"TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" 
      TCGA-DM-A0X9       TCGA-DM-A0XD       TCGA-DM-A0XF       TCGA-DM-A1D0 
"TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" 
      TCGA-DM-A1D4       TCGA-DM-A1D6       TCGA-DM-A1D7       TCGA-DM-A1D8 
"TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" 
      TCGA-DM-A1D9       TCGA-DM-A1DA       TCGA-DM-A1DB       TCGA-DM-A1HA 
"TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" 
      TCGA-DM-A1HB       TCGA-DM-A282       TCGA-DM-A285       TCGA-DM-A28C 
"TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" 
      TCGA-DM-A28E       TCGA-DM-A28F       TCGA-DM-A28G       TCGA-DM-A28H 
"TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" 
      TCGA-DM-A28K       TCGA-F4-6459       TCGA-F4-6460       TCGA-F4-6569 
"TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" 
      TCGA-F4-6570       TCGA-F4-6703       TCGA-F4-6704       TCGA-F4-6805 
"TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" 
      TCGA-F4-6806       TCGA-F4-6807       TCGA-F4-6808       TCGA-F4-6809 
"TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" 
      TCGA-F4-6854       TCGA-F4-6855       TCGA-F4-6856       TCGA-G4-6293 
"TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" 
      TCGA-G4-6299       TCGA-G4-6303       TCGA-G4-6304       TCGA-G4-6306 
"TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" 
      TCGA-G4-6307       TCGA-G4-6309       TCGA-G4-6310       TCGA-G4-6315 
"TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" 
      TCGA-G4-6317       TCGA-G4-6321       TCGA-G4-6323       TCGA-G4-6586 
"TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" 
      TCGA-G4-6588       TCGA-G4-6625       TCGA-G4-6626       TCGA-G4-6628 
"TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" 
      TCGA-AF-2687       TCGA-AF-2689       TCGA-AF-2691       TCGA-AF-2692 
"TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" 
      TCGA-AF-2693       TCGA-AF-3400       TCGA-AF-3913       TCGA-AF-4110 
"TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" 
      TCGA-AF-5654       TCGA-AF-6136       TCGA-AF-6655       TCGA-AF-6672 
"TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" 
      TCGA-AH-6544       TCGA-AH-6547       TCGA-AH-6549       TCGA-AH-6643 
"TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" 
      TCGA-AH-6644       TCGA-CI-6619       TCGA-CI-6620       TCGA-CI-6621 
"TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" 
      TCGA-CI-6622       TCGA-CI-6624       TCGA-CL-5917       TCGA-CL-5918 
"TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" 
      TCGA-DC-5337       TCGA-DC-5869       TCGA-DC-6155       TCGA-DC-6157 
"TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" 
      TCGA-DC-6158       TCGA-DC-6160       TCGA-DC-6681       TCGA-DC-6682 
"TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" 
      TCGA-DC-6683       TCGA-DT-5265       TCGA-DY-A0XA       TCGA-DY-A1DC 
"TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" 
      TCGA-DY-A1DD       TCGA-DY-A1DF       TCGA-DY-A1DG       TCGA-DY-A1H8 
"TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" 
      TCGA-EF-5830       TCGA-EI-6506       TCGA-EI-6507       TCGA-EI-6508 
"TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" 
      TCGA-EI-6510       TCGA-F5-6464       TCGA-F5-6465       TCGA-F5-6571 
"TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" 
      TCGA-F5-6702       TCGA-F5-6811       TCGA-F5-6812       TCGA-F5-6813 
"TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" 
      TCGA-G5-6235       TCGA-G5-6641 
"TAS2R1 WILD-TYPE" "TAS2R1 WILD-TYPE" 

Clustering(1096) Variable = EHHADH MUTATION ANALYSIS
D1096V1, survival
                  sevent
clus2                0   1
  EHHADH MUTATED    12   3
  EHHADH WILD-TYPE 366  90
  EHHADH MUTATED EHHADH WILD-TYPE 
              15              456 
  EHHADH MUTATED EHHADH WILD-TYPE 
               3               90 
$`EHHADH MUTATED`
TCGA-AA-3815 TCGA-AA-A00N TCGA-AA-A010 TCGA-AD-6895 TCGA-AD-6899 TCGA-AZ-6598 
       33.04         4.01        34.98         0.72         5.79        49.41 
TCGA-CA-6717 TCGA-CK-5913 TCGA-CM-4746 TCGA-CM-4752 TCGA-CM-6167 TCGA-D5-6536 
       12.76        51.32        37.02        13.02        14.99        17.85 
TCGA-F4-6704 TCGA-AF-2693 TCGA-AF-6672 
        1.55        19.10        10.39 

$`EHHADH WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       19.04        10.06        35.05         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        0.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       88.21         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07        12.20        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 
      148.01        85.45        15.62        49.08         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4747 
       82.95         1.91       124.27        23.05        20.02        25.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6168 TCGA-CM-6169 
        2.96        29.03        16.04        21.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       43.27        15.12         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 
       31.96        35.74         6.18        47.87        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       39.48        43.04        13.55        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       16.83        15.39        20.02        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  EHHADH MUTATED EHHADH WILD-TYPE 
            0.72             0.00 
  EHHADH MUTATED EHHADH WILD-TYPE 
           51.32           148.01 
  EHHADH MUTATED EHHADH WILD-TYPE 
           14.99            20.73 
[1] "0.7 - 51.3 (15.0)"  "0.0 - 148.0 (20.7)"
[1] "hr=" "1.3"
D1096V2, continuous
D1096V3, binary
                  cls
clus                 0   1
  EHHADH MUTATED    13   1
  EHHADH WILD-TYPE 353 118
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EHHADH MUTATED     13    1
  EHHADH WILD-TYPE  353  118
        clus
vv       EHHADH MUTATED EHHADH WILD-TYPE
  COLON              13              353
  RECTUM              1              118
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  EHHADH MUTATED         2        0        1         5         2         0
  EHHADH WILD-TYPE      89        1       31       133         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  EHHADH MUTATED           0          0          0          3        1
  EHHADH WILD-TYPE        24         11         59         39       47
                  vv
clus               STAGE IVA STAGE IVB
  EHHADH MUTATED           0         0
  EHHADH WILD-TYPE        18         1
D1096V4, multiclass
            clus
vv           EHHADH MUTATED EHHADH WILD-TYPE
  STAGE I                 2               89
  STAGE IA                0                1
  STAGE II                1               31
  STAGE IIA               5              133
  STAGE IIB               2                8
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              0               59
  STAGE IIIC              3               39
  STAGE IV                1               47
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  EHHADH MUTATED     0   2   9   4
  EHHADH WILD-TYPE  17  90 320  46
D1096V5, multiclass
    clus
vv   EHHADH MUTATED EHHADH WILD-TYPE
  T1              0               17
  T2              2               90
  T3              9              320
  T4              4               46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  EHHADH MUTATED    10   1   4
  EHHADH WILD-TYPE 277 112  83
D1096V6, multiclass
    clus
vv   EHHADH MUTATED EHHADH WILD-TYPE
  N0             10              277
  N1              1              112
  N2              4               83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1096V7, binary
                  cls
clus                 0   1
  EHHADH MUTATED     8   0
  EHHADH WILD-TYPE 367  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EHHADH MUTATED      8    0
  EHHADH WILD-TYPE  367   65
   clus
vv  EHHADH MUTATED EHHADH WILD-TYPE
  0              8              367
  1              0               65
[1] 2 2
[1] FALSE
D1096V8, binary
                  cls
clus                 0   1
  EHHADH MUTATED     5  10
  EHHADH WILD-TYPE 220 254
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EHHADH MUTATED      5   10
  EHHADH WILD-TYPE  220  254
        clus
vv       EHHADH MUTATED EHHADH WILD-TYPE
  FEMALE              5              220
  MALE               10              254
[1] 2 2
[1] FALSE
D1096V9, binary
                  cls
clus                 0   1
  EHHADH MUTATED    11   1
  EHHADH WILD-TYPE 339  21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EHHADH MUTATED     11    1
  EHHADH WILD-TYPE  339   21
     clus
vv    EHHADH MUTATED EHHADH WILD-TYPE
  NO              11              339
  YES              1               21
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  EHHADH MUTATED                      9                             4
  EHHADH WILD-TYPE                  306                            43
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  EHHADH MUTATED                       1                              0
  EHHADH WILD-TYPE                   105                             10
D1096V10, multiclass
                                clus
vv                               EHHADH MUTATED EHHADH WILD-TYPE
  COLON ADENOCARCINOMA                        9              306
  COLON MUCINOUS ADENOCARCINOMA               4               43
  RECTAL ADENOCARCINOMA                       1              105
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  EHHADH MUTATED     8   0   0   2
  EHHADH WILD-TYPE 337   4  31  23
D1096V11, multiclass
    clus
vv   EHHADH MUTATED EHHADH WILD-TYPE
  R0              8              337
  R1              0                4
  R2              0               31
  RX              2               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1096V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  EHHADH MUTATED                                  1     1
  EHHADH WILD-TYPE                                0    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  EHHADH MUTATED                           3     7
  EHHADH WILD-TYPE                        19   219
D1096V13, multiclass
                                  clus
vv                                 EHHADH MUTATED EHHADH WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              1                0
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     3               19
  WHITE                                         7              219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1097) Variable = KDM2B MUTATION ANALYSIS
D1097V1, survival
                 sevent
clus2               0   1
  KDM2B MUTATED    16   4
  KDM2B WILD-TYPE 362  89
  KDM2B MUTATED KDM2B WILD-TYPE 
             20             451 
  KDM2B MUTATED KDM2B WILD-TYPE 
              4              89 
$`KDM2B MUTATED`
TCGA-A6-3809 TCGA-A6-5665 TCGA-A6-6653 TCGA-A6-6781 TCGA-AA-3492 TCGA-AA-3663 
       32.75        22.06        24.39        19.66         3.02         6.97 
TCGA-AA-3672 TCGA-AA-3697 TCGA-AA-3815 TCGA-AA-3848 TCGA-AA-3877 TCGA-AY-4070 
        0.92        85.05        33.04        10.06        31.00        16.31 
TCGA-AZ-6598 TCGA-CK-5913 TCGA-CM-5868 TCGA-CM-6162 TCGA-G4-6586 TCGA-G4-6588 
       49.41        51.32        17.03        12.00        35.80        26.17 
TCGA-AG-A002 TCGA-DC-5869 
       20.98         5.03 

$`KDM2B WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 
       24.16        21.76        24.69        23.87        20.12        20.28 
TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
        7.04         1.02        35.01        63.98         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
       13.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       36.03         8.05        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
       78.08         6.05        54.02         2.01        14.01        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       35.05         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3850 
       38.99        37.02        14.93         0.00        17.03         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       29.98        18.05         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       27.09         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 
      148.01        85.45        15.62        49.08         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6161 
       32.02        15.02         5.03        15.02        15.02        15.02 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       36.00        22.09        13.78        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
       78.12         7.17        15.02        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  KDM2B MUTATED KDM2B WILD-TYPE 
           0.92            0.00 
  KDM2B MUTATED KDM2B WILD-TYPE 
          85.05          148.01 
  KDM2B MUTATED KDM2B WILD-TYPE 
          21.52           20.12 
[1] "0.9 - 85.0 (21.5)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.1"
D1097V2, continuous
D1097V3, binary
                 cls
clus                0   1
  KDM2B MUTATED    20   2
  KDM2B WILD-TYPE 346 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM2B MUTATED     20    2
  KDM2B WILD-TYPE  346  117
        clus
vv       KDM2B MUTATED KDM2B WILD-TYPE
  COLON             20             346
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KDM2B MUTATED         4        0        3         5         2         0
  KDM2B WILD-TYPE      87        1       29       133         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  KDM2B MUTATED           2          0          2          3        0         1
  KDM2B WILD-TYPE        22         11         57         39       48        17
                 vv
clus              STAGE IVB
  KDM2B MUTATED           0
  KDM2B WILD-TYPE         1
D1097V4, multiclass
            clus
vv           KDM2B MUTATED KDM2B WILD-TYPE
  STAGE I                4              87
  STAGE IA               0               1
  STAGE II               3              29
  STAGE IIA              5             133
  STAGE IIB              2               8
  STAGE IIC              0               1
  STAGE III              2              22
  STAGE IIIA             0              11
  STAGE IIIB             2              57
  STAGE IIIC             3              39
  STAGE IV               0              48
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  KDM2B MUTATED     1   3  14   4
  KDM2B WILD-TYPE  16  89 315  46
D1097V5, multiclass
    clus
vv   KDM2B MUTATED KDM2B WILD-TYPE
  T1             1              16
  T2             3              89
  T3            14             315
  T4             4              46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  KDM2B MUTATED    15   5   2
  KDM2B WILD-TYPE 272 108  85
D1097V6, multiclass
    clus
vv   KDM2B MUTATED KDM2B WILD-TYPE
  N0            15             272
  N1             5             108
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1097V7, binary
                 cls
clus                0   1
  KDM2B MUTATED    16   1
  KDM2B WILD-TYPE 359  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM2B MUTATED     16    1
  KDM2B WILD-TYPE  359   64
   clus
vv  KDM2B MUTATED KDM2B WILD-TYPE
  0            16             359
  1             1              64
[1] 2 2
[1] FALSE
D1097V8, binary
                 cls
clus                0   1
  KDM2B MUTATED    16   6
  KDM2B WILD-TYPE 209 258
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM2B MUTATED     16    6
  KDM2B WILD-TYPE  209  258
        clus
vv       KDM2B MUTATED KDM2B WILD-TYPE
  FEMALE            16             209
  MALE               6             258
[1] 2 2
[1] FALSE
D1097V9, binary
                 cls
clus                0   1
  KDM2B MUTATED    19   0
  KDM2B WILD-TYPE 331  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM2B MUTATED     19    0
  KDM2B WILD-TYPE  331   22
     clus
vv    KDM2B MUTATED KDM2B WILD-TYPE
  NO             19             331
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  KDM2B MUTATED                     16                             4
  KDM2B WILD-TYPE                  299                            43
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  KDM2B MUTATED                       2                              0
  KDM2B WILD-TYPE                   104                             10
D1097V10, multiclass
                                clus
vv                               KDM2B MUTATED KDM2B WILD-TYPE
  COLON ADENOCARCINOMA                      16             299
  COLON MUCINOUS ADENOCARCINOMA              4              43
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  KDM2B MUTATED    16   1   0   3
  KDM2B WILD-TYPE 329   3  31  22
D1097V11, multiclass
    clus
vv   KDM2B MUTATED KDM2B WILD-TYPE
  R0            16             329
  R1             1               3
  R2             0              31
  RX             3              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1097V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KDM2B MUTATED                                  0     0
  KDM2B WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  KDM2B MUTATED                           2    12
  KDM2B WILD-TYPE                        20   214
D1097V13, multiclass
                                  clus
vv                                 KDM2B MUTATED KDM2B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    2              20
  WHITE                                       12             214
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1098) Variable = ITGB6 MUTATION ANALYSIS
D1098V1, survival
                 sevent
clus2               0   1
  ITGB6 MUTATED    14   4
  ITGB6 WILD-TYPE 364  89
  ITGB6 MUTATED ITGB6 WILD-TYPE 
             18             453 
  ITGB6 MUTATED ITGB6 WILD-TYPE 
              4              89 
$`ITGB6 MUTATED`
TCGA-A6-2676 TCGA-A6-5666 TCGA-A6-6781 TCGA-AA-3525 TCGA-AA-3864 TCGA-AA-A010 
       42.90        32.71        19.66         8.05        53.00        34.98 
TCGA-AD-6889 TCGA-AD-6964 TCGA-AY-6197 TCGA-AZ-6598 TCGA-CA-6717 TCGA-CA-6718 
       56.55        10.88        21.44        49.41        12.76        10.06 
TCGA-CM-6169 TCGA-D5-6536 TCGA-DM-A1HB TCGA-AF-6672 TCGA-AH-6644 TCGA-EF-5830 
       13.02        17.85       135.65        10.39         0.72         0.49 

$`ITGB6 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       22.06        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       24.03        37.05        36.03        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       31.07        30.05        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       21.37        15.52         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       33.01        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        88.21         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 
        3.06         3.25         3.29         0.07        12.20        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6170 TCGA-CM-6171 
       16.04        21.99        14.99        12.99        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       15.39        20.02        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-CI-6619 TCGA-CI-6620 
       38.56         1.45        17.49         0.69         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       51.48        32.61        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  ITGB6 MUTATED ITGB6 WILD-TYPE 
           0.49            0.00 
  ITGB6 MUTATED ITGB6 WILD-TYPE 
         135.65          148.01 
  ITGB6 MUTATED ITGB6 WILD-TYPE 
         18.755          20.280 
[1] "0.5 - 135.7 (18.8)" "0.0 - 148.0 (20.3)"
[1] "hr=" "1"  
D1098V2, continuous
D1098V3, binary
                 cls
clus                0   1
  ITGB6 MUTATED    15   3
  ITGB6 WILD-TYPE 351 116
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITGB6 MUTATED     15    3
  ITGB6 WILD-TYPE  351  116
        clus
vv       ITGB6 MUTATED ITGB6 WILD-TYPE
  COLON             15             351
  RECTUM             3             116
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ITGB6 MUTATED         0        0        2         6         3         1
  ITGB6 WILD-TYPE      91        1       30       132         7         0
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ITGB6 MUTATED           0          0          2          1        1         0
  ITGB6 WILD-TYPE        24         11         57         41       47        18
                 vv
clus              STAGE IVB
  ITGB6 MUTATED           0
  ITGB6 WILD-TYPE         1
D1098V4, multiclass
            clus
vv           ITGB6 MUTATED ITGB6 WILD-TYPE
  STAGE I                0              91
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA              6             132
  STAGE IIB              3               7
  STAGE IIC              1               0
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             2              57
  STAGE IIIC             1              41
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ITGB6 MUTATED     0   0  11   7
  ITGB6 WILD-TYPE  17  92 318  43
D1098V5, multiclass
    clus
vv   ITGB6 MUTATED ITGB6 WILD-TYPE
  T1             0              17
  T2             0              92
  T3            11             318
  T4             7              43
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  ITGB6 MUTATED    12   3   2
  ITGB6 WILD-TYPE 275 110  85
D1098V6, multiclass
    clus
vv   ITGB6 MUTATED ITGB6 WILD-TYPE
  N0            12             275
  N1             3             110
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1098V7, binary
                 cls
clus                0   1
  ITGB6 MUTATED    12   0
  ITGB6 WILD-TYPE 363  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITGB6 MUTATED     12    0
  ITGB6 WILD-TYPE  363   65
   clus
vv  ITGB6 MUTATED ITGB6 WILD-TYPE
  0            12             363
  1             0              65
[1] 2 2
[1] FALSE
D1098V8, binary
                 cls
clus                0   1
  ITGB6 MUTATED     3  15
  ITGB6 WILD-TYPE 222 249
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITGB6 MUTATED      3   15
  ITGB6 WILD-TYPE  222  249
        clus
vv       ITGB6 MUTATED ITGB6 WILD-TYPE
  FEMALE             3             222
  MALE              15             249
[1] 2 2
[1] FALSE
D1098V9, binary
                 cls
clus                0   1
  ITGB6 MUTATED    13   1
  ITGB6 WILD-TYPE 337  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITGB6 MUTATED     13    1
  ITGB6 WILD-TYPE  337   21
     clus
vv    ITGB6 MUTATED ITGB6 WILD-TYPE
  NO             13             337
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ITGB6 MUTATED                     12                             2
  ITGB6 WILD-TYPE                  303                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ITGB6 MUTATED                       3                              0
  ITGB6 WILD-TYPE                   103                             10
D1098V10, multiclass
                                clus
vv                               ITGB6 MUTATED ITGB6 WILD-TYPE
  COLON ADENOCARCINOMA                      12             303
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      3             103
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  ITGB6 MUTATED     9   0   0   2
  ITGB6 WILD-TYPE 336   4  31  23
D1098V11, multiclass
    clus
vv   ITGB6 MUTATED ITGB6 WILD-TYPE
  R0             9             336
  R1             0               4
  R2             0              31
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1098V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ITGB6 MUTATED                                  0     3
  ITGB6 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ITGB6 MUTATED                           1    11
  ITGB6 WILD-TYPE                        21   215
D1098V13, multiclass
                                  clus
vv                                 ITGB6 MUTATED ITGB6 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        3               8
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                       11             215
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1099) Variable = ESCO1 MUTATION ANALYSIS
D1099V1, survival
                 sevent
clus2               0   1
  ESCO1 MUTATED    14   2
  ESCO1 WILD-TYPE 364  91
  ESCO1 MUTATED ESCO1 WILD-TYPE 
             16             455 
  ESCO1 MUTATED ESCO1 WILD-TYPE 
              2              91 
$`ESCO1 MUTATED`
TCGA-A6-3809 TCGA-A6-6141 TCGA-AA-3510 TCGA-AA-3555 TCGA-AA-3697 TCGA-AA-3947 
       32.75         8.38        63.98        29.95        85.05        33.01 
TCGA-AA-3977 TCGA-AD-6889 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-CA-6717 TCGA-CK-5916 
       25.02        56.55        58.39        49.41        12.76        21.14 
TCGA-AG-3732 TCGA-AG-3892 TCGA-AG-A002 TCGA-DY-A0XA 
       32.98        13.02        20.98       126.44 

$`ESCO1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 
       22.06        32.71        27.09        22.52        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       17.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 
        5.98        37.05        19.00        36.00         5.03        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 
       18.05        31.00         2.01        12.99        24.00        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       15.52         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       33.01        21.44        17.82         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        88.21         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07        12.20        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       51.32         9.99        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 
       13.94        19.99         7.99         0.99        37.02         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       17.03        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD 
        5.95         4.01         5.03         5.29        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  ESCO1 MUTATED ESCO1 WILD-TYPE 
           8.38            0.00 
  ESCO1 MUTATED ESCO1 WILD-TYPE 
         126.44          148.01 
  ESCO1 MUTATED ESCO1 WILD-TYPE 
         32.865          19.990 
[1] "8.4 - 126.4 (32.9)" "0.0 - 148.0 (20.0)"
[1] "hr=" "2.5"
D1099V2, continuous
D1099V3, binary
                 cls
clus                0   1
  ESCO1 MUTATED    13   4
  ESCO1 WILD-TYPE 353 115
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ESCO1 MUTATED     13    4
  ESCO1 WILD-TYPE  353  115
        clus
vv       ESCO1 MUTATED ESCO1 WILD-TYPE
  COLON             13             353
  RECTUM             4             115
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ESCO1 MUTATED         4        0        2         7         2         0
  ESCO1 WILD-TYPE      87        1       30       131         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ESCO1 MUTATED           1          0          0          0        0         0
  ESCO1 WILD-TYPE        23         11         59         42       48        18
                 vv
clus              STAGE IVB
  ESCO1 MUTATED           0
  ESCO1 WILD-TYPE         1
D1099V4, multiclass
            clus
vv           ESCO1 MUTATED ESCO1 WILD-TYPE
  STAGE I                4              87
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA              7             131
  STAGE IIB              2               8
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ESCO1 MUTATED     2   3  10   2
  ESCO1 WILD-TYPE  15  89 319  48
D1099V5, multiclass
    clus
vv   ESCO1 MUTATED ESCO1 WILD-TYPE
  T1             2              15
  T2             3              89
  T3            10             319
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  ESCO1 MUTATED    17   0   0
  ESCO1 WILD-TYPE 270 113  87
D1099V6, multiclass
    clus
vv   ESCO1 MUTATED ESCO1 WILD-TYPE
  N0            17             270
  N1             0             113
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1099V7, binary
                 cls
clus                0   1
  ESCO1 MUTATED    15   0
  ESCO1 WILD-TYPE 360  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ESCO1 MUTATED     15    0
  ESCO1 WILD-TYPE  360   65
   clus
vv  ESCO1 MUTATED ESCO1 WILD-TYPE
  0            15             360
  1             0              65
[1] 2 2
[1] FALSE
D1099V8, binary
                 cls
clus                0   1
  ESCO1 MUTATED     9   8
  ESCO1 WILD-TYPE 216 256
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ESCO1 MUTATED      9    8
  ESCO1 WILD-TYPE  216  256
        clus
vv       ESCO1 MUTATED ESCO1 WILD-TYPE
  FEMALE             9             216
  MALE               8             256
[1] 2 2
[1] FALSE
D1099V9, binary
                 cls
clus                0   1
  ESCO1 MUTATED    14   0
  ESCO1 WILD-TYPE 336  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ESCO1 MUTATED     14    0
  ESCO1 WILD-TYPE  336   22
     clus
vv    ESCO1 MUTATED ESCO1 WILD-TYPE
  NO             14             336
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ESCO1 MUTATED                      9                             4
  ESCO1 WILD-TYPE                  306                            43
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ESCO1 MUTATED                       4                              0
  ESCO1 WILD-TYPE                   102                             10
D1099V10, multiclass
                                clus
vv                               ESCO1 MUTATED ESCO1 WILD-TYPE
  COLON ADENOCARCINOMA                       9             306
  COLON MUCINOUS ADENOCARCINOMA              4              43
  RECTAL ADENOCARCINOMA                      4             102
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  ESCO1 MUTATED    10   0   0   2
  ESCO1 WILD-TYPE 335   4  31  23
D1099V11, multiclass
    clus
vv   ESCO1 MUTATED ESCO1 WILD-TYPE
  R0            10             335
  R1             0               4
  R2             0              31
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1099V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ESCO1 MUTATED                                  0     2
  ESCO1 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ESCO1 MUTATED                           1     5
  ESCO1 WILD-TYPE                        21   221
D1099V13, multiclass
                                  clus
vv                                 ESCO1 MUTATED ESCO1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               9
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        5             221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1100) Variable = SERPINB10 MUTATION ANALYSIS
D1100V1, survival
                     sevent
clus2                   0   1
  SERPINB10 MUTATED     9   3
  SERPINB10 WILD-TYPE 369  90
  SERPINB10 MUTATED SERPINB10 WILD-TYPE 
                 12                 459 
  SERPINB10 MUTATED SERPINB10 WILD-TYPE 
                  3                  90 
$`SERPINB10 MUTATED`
TCGA-A6-6649 TCGA-AA-3660 TCGA-AA-3950 TCGA-AA-A00N TCGA-AA-A010 TCGA-AD-6964 
       24.16        78.08        24.00         4.01        34.98        10.88 
TCGA-AZ-4681 TCGA-AZ-6598 TCGA-CA-6717 TCGA-G4-6628 TCGA-AG-A002 TCGA-EI-6510 
      106.75        49.41        12.76        79.69        20.98        18.28 

$`SERPINB10 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.08        25.18        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 
       19.99        13.94        19.99        61.02         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 
       12.99        24.00        33.01        26.01         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 
        1.41         5.13        22.36        62.79        88.21         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.20        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       91.79        46.75        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  SERPINB10 MUTATED SERPINB10 WILD-TYPE 
               4.01                0.00 
  SERPINB10 MUTATED SERPINB10 WILD-TYPE 
             106.75              148.01 
  SERPINB10 MUTATED SERPINB10 WILD-TYPE 
              24.08               20.05 
[1] "4.0 - 106.8 (24.1)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.1"
D1100V2, continuous
D1100V3, binary
                     cls
clus                    0   1
  SERPINB10 MUTATED    10   2
  SERPINB10 WILD-TYPE 356 117
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  SERPINB10 MUTATED     10    2
  SERPINB10 WILD-TYPE  356  117
        clus
vv       SERPINB10 MUTATED SERPINB10 WILD-TYPE
  COLON                 10                 356
  RECTUM                 2                 117
[1] 2 2
[1] FALSE
                     vv
clus                  STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SERPINB10 MUTATED         2        0        2         3         2         0
  SERPINB10 WILD-TYPE      89        1       30       135         8         1
                     vv
clus                  STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SERPINB10 MUTATED           0          0          1          0        0
  SERPINB10 WILD-TYPE        24         11         58         42       48
                     vv
clus                  STAGE IVA STAGE IVB
  SERPINB10 MUTATED           1         0
  SERPINB10 WILD-TYPE        17         1
D1100V4, multiclass
            clus
vv           SERPINB10 MUTATED SERPINB10 WILD-TYPE
  STAGE I                    2                  89
  STAGE IA                   0                   1
  STAGE II                   2                  30
  STAGE IIA                  3                 135
  STAGE IIB                  2                   8
  STAGE IIC                  0                   1
  STAGE III                  0                  24
  STAGE IIIA                 0                  11
  STAGE IIIB                 1                  58
  STAGE IIIC                 0                  42
  STAGE IV                   0                  48
  STAGE IVA                  1                  17
  STAGE IVB                  0                   1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                   T1  T2  T3  T4
  SERPINB10 MUTATED     0   3   6   3
  SERPINB10 WILD-TYPE  17  89 323  47
D1100V5, multiclass
    clus
vv   SERPINB10 MUTATED SERPINB10 WILD-TYPE
  T1                 0                  17
  T2                 3                  89
  T3                 6                 323
  T4                 3                  47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                   N0  N1  N2
  SERPINB10 MUTATED    10   1   1
  SERPINB10 WILD-TYPE 277 112  86
D1100V6, multiclass
    clus
vv   SERPINB10 MUTATED SERPINB10 WILD-TYPE
  N0                10                 277
  N1                 1                 112
  N2                 1                  86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1100V7, binary
                     cls
clus                    0   1
  SERPINB10 MUTATED     9   0
  SERPINB10 WILD-TYPE 366  65
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  SERPINB10 MUTATED      9    0
  SERPINB10 WILD-TYPE  366   65
   clus
vv  SERPINB10 MUTATED SERPINB10 WILD-TYPE
  0                 9                 366
  1                 0                  65
[1] 2 2
[1] FALSE
D1100V8, binary
                     cls
clus                    0   1
  SERPINB10 MUTATED     6   6
  SERPINB10 WILD-TYPE 219 258
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  SERPINB10 MUTATED      6    6
  SERPINB10 WILD-TYPE  219  258
        clus
vv       SERPINB10 MUTATED SERPINB10 WILD-TYPE
  FEMALE                 6                 219
  MALE                   6                 258
[1] 2 2
[1] FALSE
D1100V9, binary
                     cls
clus                    0   1
  SERPINB10 MUTATED    11   0
  SERPINB10 WILD-TYPE 339  22
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  SERPINB10 MUTATED     11    0
  SERPINB10 WILD-TYPE  339   22
     clus
vv    SERPINB10 MUTATED SERPINB10 WILD-TYPE
  NO                 11                 339
  YES                 0                  22
[1] 2 2
[1] FALSE
                     vv
clus                  COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SERPINB10 MUTATED                      7                             3
  SERPINB10 WILD-TYPE                  308                            44
                     vv
clus                  RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SERPINB10 MUTATED                       2                              0
  SERPINB10 WILD-TYPE                   104                             10
D1100V10, multiclass
                                clus
vv                               SERPINB10 MUTATED SERPINB10 WILD-TYPE
  COLON ADENOCARCINOMA                           7                 308
  COLON MUCINOUS ADENOCARCINOMA                  3                  44
  RECTAL ADENOCARCINOMA                          2                 104
  RECTAL MUCINOUS ADENOCARCINOMA                 0                  10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                   R0  R1  R2  RX
  SERPINB10 MUTATED     8   0   0   1
  SERPINB10 WILD-TYPE 337   4  31  24
D1100V11, multiclass
    clus
vv   SERPINB10 MUTATED SERPINB10 WILD-TYPE
  R0                 8                 337
  R1                 0                   4
  R2                 0                  31
  RX                 1                  24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1100V12, continuous
                     vv
clus                  AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SERPINB10 MUTATED                                  0     1
  SERPINB10 WILD-TYPE                                1    10
                     vv
clus                  BLACK OR AFRICAN AMERICAN WHITE
  SERPINB10 MUTATED                           0     6
  SERPINB10 WILD-TYPE                        22   220
D1100V13, multiclass
                                  clus
vv                                 SERPINB10 MUTATED SERPINB10 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                 0                   1
  ASIAN                                            1                  10
  BLACK OR AFRICAN AMERICAN                        0                  22
  WHITE                                            6                 220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1101) Variable = GRB14 MUTATION ANALYSIS
D1101V1, survival
                 sevent
clus2               0   1
  GRB14 MUTATED     6   3
  GRB14 WILD-TYPE 372  90
  GRB14 MUTATED GRB14 WILD-TYPE 
              9             462 
  GRB14 MUTATED GRB14 WILD-TYPE 
              3              90 
$`GRB14 MUTATED`
TCGA-AA-3516 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3949 TCGA-AZ-6599 TCGA-CM-6163 
       13.02        26.99        19.04        26.01         6.77         2.96 
TCGA-D5-6536 TCGA-DM-A1D6 TCGA-AG-A002 
       17.85        49.91        20.98 

$`GRB14 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        1.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       36.00         5.03        85.05        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        33.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        88.21        49.41        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6164 
       15.02        15.02        17.03        15.02        12.00        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       15.12         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  GRB14 MUTATED GRB14 WILD-TYPE 
           2.96            0.00 
  GRB14 MUTATED GRB14 WILD-TYPE 
          49.91          148.01 
  GRB14 MUTATED GRB14 WILD-TYPE 
         19.040          20.235 
[1] "3.0 - 49.9 (19.0)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "2.1"
D1101V2, continuous
D1101V3, binary
                 cls
clus                0   1
  GRB14 MUTATED     9   2
  GRB14 WILD-TYPE 357 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GRB14 MUTATED      9    2
  GRB14 WILD-TYPE  357  117
        clus
vv       GRB14 MUTATED GRB14 WILD-TYPE
  COLON              9             357
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GRB14 MUTATED         3        0        0         4         0         0
  GRB14 WILD-TYPE      88        1       32       134        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  GRB14 MUTATED           2          0          1          0        1         0
  GRB14 WILD-TYPE        22         11         58         42       47        18
                 vv
clus              STAGE IVB
  GRB14 MUTATED           0
  GRB14 WILD-TYPE         1
D1101V4, multiclass
            clus
vv           GRB14 MUTATED GRB14 WILD-TYPE
  STAGE I                3              88
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              4             134
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              2              22
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             0              42
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  GRB14 MUTATED     1   2   8   0
  GRB14 WILD-TYPE  16  90 321  50
D1101V5, multiclass
    clus
vv   GRB14 MUTATED GRB14 WILD-TYPE
  T1             1              16
  T2             2              90
  T3             8             321
  T4             0              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  GRB14 MUTATED     8   2   1
  GRB14 WILD-TYPE 279 111  86
D1101V6, multiclass
    clus
vv   GRB14 MUTATED GRB14 WILD-TYPE
  N0             8             279
  N1             2             111
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1101V7, binary
                 cls
clus                0   1
  GRB14 MUTATED     8   1
  GRB14 WILD-TYPE 367  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GRB14 MUTATED      8    1
  GRB14 WILD-TYPE  367   64
   clus
vv  GRB14 MUTATED GRB14 WILD-TYPE
  0             8             367
  1             1              64
[1] 2 2
[1] FALSE
D1101V8, binary
                 cls
clus                0   1
  GRB14 MUTATED     4   7
  GRB14 WILD-TYPE 221 257
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GRB14 MUTATED      4    7
  GRB14 WILD-TYPE  221  257
        clus
vv       GRB14 MUTATED GRB14 WILD-TYPE
  FEMALE             4             221
  MALE               7             257
[1] 2 2
[1] FALSE
D1101V9, binary
                 cls
clus                0   1
  GRB14 MUTATED     7   1
  GRB14 WILD-TYPE 343  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GRB14 MUTATED      7    1
  GRB14 WILD-TYPE  343   21
     clus
vv    GRB14 MUTATED GRB14 WILD-TYPE
  NO              7             343
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  GRB14 MUTATED                      6                             3
  GRB14 WILD-TYPE                  309                            44
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  GRB14 MUTATED                       2                              0
  GRB14 WILD-TYPE                   104                             10
D1101V10, multiclass
                                clus
vv                               GRB14 MUTATED GRB14 WILD-TYPE
  COLON ADENOCARCINOMA                       6             309
  COLON MUCINOUS ADENOCARCINOMA              3              44
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  GRB14 MUTATED     6   0   1   0
  GRB14 WILD-TYPE 339   4  30  25
D1101V11, multiclass
    clus
vv   GRB14 MUTATED GRB14 WILD-TYPE
  R0             6             339
  R1             0               4
  R2             1              30
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1101V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GRB14 MUTATED                                  0     0
  GRB14 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  GRB14 MUTATED                           0     5
  GRB14 WILD-TYPE                        22   221
D1101V13, multiclass
                                  clus
vv                                 GRB14 MUTATED GRB14 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        5             221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1102) Variable = OR6K2 MUTATION ANALYSIS
D1102V1, survival
                 sevent
clus2               0   1
  OR6K2 MUTATED    13   3
  OR6K2 WILD-TYPE 365  90
  OR6K2 MUTATED OR6K2 WILD-TYPE 
             16             455 
  OR6K2 MUTATED OR6K2 WILD-TYPE 
              3              90 
$`OR6K2 MUTATED`
TCGA-A6-3809 TCGA-AA-3554 TCGA-AA-3663 TCGA-AA-3989 TCGA-AA-A00N TCGA-AD-5900 
       32.75        17.95         6.97         7.96         4.01         0.07 
TCGA-AY-6197 TCGA-AZ-4315 TCGA-CA-6718 TCGA-D5-6920 TCGA-DM-A0X9 TCGA-F4-6856 
       21.44        58.39        10.06         3.68       119.70        35.31 
TCGA-G4-6586 TCGA-G4-6588 TCGA-AG-A002 TCGA-AG-A008 
       35.80        26.17        20.98        13.94 

$`OR6K2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       13.02        24.00        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
       19.07        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
       16.31         0.95        33.01        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.20        12.76        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6922 
       17.13        12.49        16.14        15.58         1.48         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0XD TCGA-DM-A0XF 
        1.51        12.00        11.38        10.26        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       47.41       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       13.78        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  OR6K2 MUTATED OR6K2 WILD-TYPE 
           0.07            0.00 
  OR6K2 MUTATED OR6K2 WILD-TYPE 
         119.70          148.01 
  OR6K2 MUTATED OR6K2 WILD-TYPE 
         19.465          20.190 
[1] "0.1 - 119.7 (19.5)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1"  
D1102V2, continuous
D1102V3, binary
                 cls
clus                0   1
  OR6K2 MUTATED    14   2
  OR6K2 WILD-TYPE 352 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR6K2 MUTATED     14    2
  OR6K2 WILD-TYPE  352  117
        clus
vv       OR6K2 MUTATED OR6K2 WILD-TYPE
  COLON             14             352
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  OR6K2 MUTATED         4        0        1         8         2         0
  OR6K2 WILD-TYPE      87        1       31       130         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  OR6K2 MUTATED           0          0          0          0        1         0
  OR6K2 WILD-TYPE        24         11         59         42       47        18
                 vv
clus              STAGE IVB
  OR6K2 MUTATED           0
  OR6K2 WILD-TYPE         1
D1102V4, multiclass
            clus
vv           OR6K2 MUTATED OR6K2 WILD-TYPE
  STAGE I                4              87
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              8             130
  STAGE IIB              2               8
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             0              42
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  OR6K2 MUTATED     0   4  10   2
  OR6K2 WILD-TYPE  17  88 319  48
D1102V5, multiclass
    clus
vv   OR6K2 MUTATED OR6K2 WILD-TYPE
  T1             0              17
  T2             4              88
  T3            10             319
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  OR6K2 MUTATED    15   0   1
  OR6K2 WILD-TYPE 272 113  86
D1102V6, multiclass
    clus
vv   OR6K2 MUTATED OR6K2 WILD-TYPE
  N0            15             272
  N1             0             113
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1102V7, binary
                 cls
clus                0   1
  OR6K2 MUTATED    13   1
  OR6K2 WILD-TYPE 362  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR6K2 MUTATED     13    1
  OR6K2 WILD-TYPE  362   64
   clus
vv  OR6K2 MUTATED OR6K2 WILD-TYPE
  0            13             362
  1             1              64
[1] 2 2
[1] FALSE
D1102V8, binary
                 cls
clus                0   1
  OR6K2 MUTATED     7   9
  OR6K2 WILD-TYPE 218 255
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR6K2 MUTATED      7    9
  OR6K2 WILD-TYPE  218  255
        clus
vv       OR6K2 MUTATED OR6K2 WILD-TYPE
  FEMALE             7             218
  MALE               9             255
[1] 2 2
[1] FALSE
D1102V9, binary
                 cls
clus                0   1
  OR6K2 MUTATED    12   0
  OR6K2 WILD-TYPE 338  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR6K2 MUTATED     12    0
  OR6K2 WILD-TYPE  338   22
     clus
vv    OR6K2 MUTATED OR6K2 WILD-TYPE
  NO             12             338
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  OR6K2 MUTATED                     10                             4
  OR6K2 WILD-TYPE                  305                            43
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  OR6K2 MUTATED                       1                              1
  OR6K2 WILD-TYPE                   105                              9
D1102V10, multiclass
                                clus
vv                               OR6K2 MUTATED OR6K2 WILD-TYPE
  COLON ADENOCARCINOMA                      10             305
  COLON MUCINOUS ADENOCARCINOMA              4              43
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             1               9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  OR6K2 MUTATED    13   0   1   1
  OR6K2 WILD-TYPE 332   4  30  24
D1102V11, multiclass
    clus
vv   OR6K2 MUTATED OR6K2 WILD-TYPE
  R0            13             332
  R1             0               4
  R2             1              30
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1102V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OR6K2 MUTATED                                  0     1
  OR6K2 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  OR6K2 MUTATED                           0     9
  OR6K2 WILD-TYPE                        22   217
D1102V13, multiclass
                                  clus
vv                                 OR6K2 MUTATED OR6K2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        9             217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1103) Variable = ARAP3 MUTATION ANALYSIS
D1103V1, survival
                 sevent
clus2               0   1
  ARAP3 MUTATED    16   6
  ARAP3 WILD-TYPE 362  87
  ARAP3 MUTATED ARAP3 WILD-TYPE 
             22             449 
  ARAP3 MUTATED ARAP3 WILD-TYPE 
              6              87 
$`ARAP3 MUTATED`
TCGA-AA-3518 TCGA-AA-3663 TCGA-AA-3715 TCGA-AA-3815 TCGA-AA-3833 TCGA-AA-A00N 
        1.02         6.97        19.04        33.04        15.95         4.01 
TCGA-AA-A01R TCGA-AU-3779 TCGA-AU-6004 TCGA-AZ-4315 TCGA-AZ-5403 TCGA-AZ-6601 
       35.01        14.50        27.09        58.39        62.79       100.01 
TCGA-CK-5916 TCGA-CM-5860 TCGA-CM-6162 TCGA-F4-6460 TCGA-G4-6586 TCGA-G4-6588 
       21.14        32.02        12.00        31.96        35.80        26.17 
TCGA-G4-6628 TCGA-AG-A002 TCGA-AG-A02N TCGA-CI-6619 
       79.69        20.98        61.97         6.05 

$`ARAP3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
       38.99         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3837 TCGA-AA-3842 
        0.99        25.02         1.02        17.98        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       27.42        10.88         0.20        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13       106.75        22.36 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 
       88.21        49.41         6.77        12.10        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
        9.99        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       30.08        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       15.02         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
      117.07        98.24         8.61        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 
       36.00        22.09        13.78        91.79        46.75        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 
       10.98        49.97         1.94        38.96        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  ARAP3 MUTATED ARAP3 WILD-TYPE 
           1.02            0.00 
  ARAP3 MUTATED ARAP3 WILD-TYPE 
         100.01          148.01 
  ARAP3 MUTATED ARAP3 WILD-TYPE 
          26.63           20.02 
[1] "1.0 - 100.0 (26.6)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.1"
D1103V2, continuous
D1103V3, binary
                 cls
clus                0   1
  ARAP3 MUTATED    21   3
  ARAP3 WILD-TYPE 345 116
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ARAP3 MUTATED     21    3
  ARAP3 WILD-TYPE  345  116
        clus
vv       ARAP3 MUTATED ARAP3 WILD-TYPE
  COLON             21             345
  RECTUM             3             116
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ARAP3 MUTATED         5        0        5         8         2         0
  ARAP3 WILD-TYPE      86        1       27       130         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ARAP3 MUTATED           1          0          2          0        1         0
  ARAP3 WILD-TYPE        23         11         57         42       47        18
                 vv
clus              STAGE IVB
  ARAP3 MUTATED           0
  ARAP3 WILD-TYPE         1
D1103V4, multiclass
            clus
vv           ARAP3 MUTATED ARAP3 WILD-TYPE
  STAGE I                5              86
  STAGE IA               0               1
  STAGE II               5              27
  STAGE IIA              8             130
  STAGE IIB              2               8
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             2              57
  STAGE IIIC             0              42
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ARAP3 MUTATED     1   4  17   2
  ARAP3 WILD-TYPE  16  88 312  48
D1103V5, multiclass
    clus
vv   ARAP3 MUTATED ARAP3 WILD-TYPE
  T1             1              16
  T2             4              88
  T3            17             312
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  ARAP3 MUTATED    20   3   1
  ARAP3 WILD-TYPE 267 110  86
D1103V6, multiclass
    clus
vv   ARAP3 MUTATED ARAP3 WILD-TYPE
  N0            20             267
  N1             3             110
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1103V7, binary
                 cls
clus                0   1
  ARAP3 MUTATED    20   1
  ARAP3 WILD-TYPE 355  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ARAP3 MUTATED     20    1
  ARAP3 WILD-TYPE  355   64
   clus
vv  ARAP3 MUTATED ARAP3 WILD-TYPE
  0            20             355
  1             1              64
[1] 2 2
[1] FALSE
D1103V8, binary
                 cls
clus                0   1
  ARAP3 MUTATED    11  13
  ARAP3 WILD-TYPE 214 251
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ARAP3 MUTATED     11   13
  ARAP3 WILD-TYPE  214  251
        clus
vv       ARAP3 MUTATED ARAP3 WILD-TYPE
  FEMALE            11             214
  MALE              13             251
[1] 2 2
[1] FALSE
D1103V9, binary
                 cls
clus                0   1
  ARAP3 MUTATED    16   1
  ARAP3 WILD-TYPE 334  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ARAP3 MUTATED     16    1
  ARAP3 WILD-TYPE  334   21
     clus
vv    ARAP3 MUTATED ARAP3 WILD-TYPE
  NO             16             334
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ARAP3 MUTATED                     18                             3
  ARAP3 WILD-TYPE                  297                            44
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ARAP3 MUTATED                       3                              0
  ARAP3 WILD-TYPE                   103                             10
D1103V10, multiclass
                                clus
vv                               ARAP3 MUTATED ARAP3 WILD-TYPE
  COLON ADENOCARCINOMA                      18             297
  COLON MUCINOUS ADENOCARCINOMA              3              44
  RECTAL ADENOCARCINOMA                      3             103
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  ARAP3 MUTATED    18   0   0   3
  ARAP3 WILD-TYPE 327   4  31  22
D1103V11, multiclass
    clus
vv   ARAP3 MUTATED ARAP3 WILD-TYPE
  R0            18             327
  R1             0               4
  R2             0              31
  RX             3              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1103V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ARAP3 MUTATED                                  0     0
  ARAP3 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ARAP3 MUTATED                           0    15
  ARAP3 WILD-TYPE                        22   211
D1103V13, multiclass
                                  clus
vv                                 ARAP3 MUTATED ARAP3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                       15             211
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1104) Variable = ZNF334 MUTATION ANALYSIS
D1104V1, survival
                  sevent
clus2                0   1
  ZNF334 MUTATED    19   2
  ZNF334 WILD-TYPE 359  91
  ZNF334 MUTATED ZNF334 WILD-TYPE 
              21              450 
  ZNF334 MUTATED ZNF334 WILD-TYPE 
               2               91 
$`ZNF334 MUTATED`
TCGA-AA-3510 TCGA-AA-3518 TCGA-AA-3544 TCGA-AA-3678 TCGA-AA-3821 TCGA-AA-3947 
       63.98         1.02        14.01        47.01         1.02        33.01 
TCGA-AA-3977 TCGA-AA-A010 TCGA-AZ-4315 TCGA-AZ-6605 TCGA-CA-6717 TCGA-CM-4746 
       25.02        34.98        58.39         5.23        12.76        37.02 
TCGA-CM-5349 TCGA-CM-6166 TCGA-D5-6536 TCGA-D5-6931 TCGA-DM-A1D7 TCGA-F4-6569 
       30.08        21.99        17.85        12.00        13.32        35.74 
TCGA-G4-6628 TCGA-AF-6655 TCGA-AG-3892 
       79.69        20.02        13.02 

$`ZNF334 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
       12.99         0.99        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3679 TCGA-AA-3680 
        2.01        14.01         0.92        50.04        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
        0.99        25.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 
       18.05        31.00         2.01        12.99        24.00        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       33.01        21.44        17.82         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
      100.01        29.56        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07        12.20        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       23.05        20.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       22.98        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 
       20.19        18.25         1.32        43.27        15.12         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        4.80         1.51        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D8 TCGA-DM-A1D9 
       38.20       130.65        92.75        49.91        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
        8.61        31.96         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 
       13.78        35.80        26.17        91.79        46.75        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       14.50        16.83        15.39        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  ZNF334 MUTATED ZNF334 WILD-TYPE 
            1.02             0.00 
  ZNF334 MUTATED ZNF334 WILD-TYPE 
           79.69           148.01 
  ZNF334 MUTATED ZNF334 WILD-TYPE 
          21.990           20.155 
[1] "1.0 - 79.7 (22.0)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "2.2"
D1104V2, continuous
D1104V3, binary
                  cls
clus                 0   1
  ZNF334 MUTATED    19   2
  ZNF334 WILD-TYPE 347 117
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF334 MUTATED     19    2
  ZNF334 WILD-TYPE  347  117
        clus
vv       ZNF334 MUTATED ZNF334 WILD-TYPE
  COLON              19              347
  RECTUM              2              117
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZNF334 MUTATED         7        0        1         6         2         0
  ZNF334 WILD-TYPE      84        1       31       132         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF334 MUTATED           1          1          1          1        0
  ZNF334 WILD-TYPE        23         10         58         41       48
                  vv
clus               STAGE IVA STAGE IVB
  ZNF334 MUTATED           0         0
  ZNF334 WILD-TYPE        18         1
D1104V4, multiclass
            clus
vv           ZNF334 MUTATED ZNF334 WILD-TYPE
  STAGE I                 7               84
  STAGE IA                0                1
  STAGE II                1               31
  STAGE IIA               6              132
  STAGE IIB               2                8
  STAGE IIC               0                1
  STAGE III               1               23
  STAGE IIIA              1               10
  STAGE IIIB              1               58
  STAGE IIIC              1               41
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZNF334 MUTATED     1   9   7   4
  ZNF334 WILD-TYPE  16  83 322  46
D1104V5, multiclass
    clus
vv   ZNF334 MUTATED ZNF334 WILD-TYPE
  T1              1               16
  T2              9               83
  T3              7              322
  T4              4               46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  ZNF334 MUTATED    17   3   1
  ZNF334 WILD-TYPE 270 110  86
D1104V6, multiclass
    clus
vv   ZNF334 MUTATED ZNF334 WILD-TYPE
  N0             17              270
  N1              3              110
  N2              1               86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1104V7, binary
                  cls
clus                 0   1
  ZNF334 MUTATED    20   0
  ZNF334 WILD-TYPE 355  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF334 MUTATED     20    0
  ZNF334 WILD-TYPE  355   65
   clus
vv  ZNF334 MUTATED ZNF334 WILD-TYPE
  0             20              355
  1              0               65
[1] 2 2
[1] FALSE
D1104V8, binary
                  cls
clus                 0   1
  ZNF334 MUTATED     8  13
  ZNF334 WILD-TYPE 217 251
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF334 MUTATED      8   13
  ZNF334 WILD-TYPE  217  251
        clus
vv       ZNF334 MUTATED ZNF334 WILD-TYPE
  FEMALE              8              217
  MALE               13              251
[1] 2 2
[1] FALSE
D1104V9, binary
                  cls
clus                 0   1
  ZNF334 MUTATED    19   0
  ZNF334 WILD-TYPE 331  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF334 MUTATED     19    0
  ZNF334 WILD-TYPE  331   22
     clus
vv    ZNF334 MUTATED ZNF334 WILD-TYPE
  NO              19              331
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ZNF334 MUTATED                     15                             3
  ZNF334 WILD-TYPE                  300                            44
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ZNF334 MUTATED                       2                              0
  ZNF334 WILD-TYPE                   104                             10
D1104V10, multiclass
                                clus
vv                               ZNF334 MUTATED ZNF334 WILD-TYPE
  COLON ADENOCARCINOMA                       15              300
  COLON MUCINOUS ADENOCARCINOMA               3               44
  RECTAL ADENOCARCINOMA                       2              104
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ZNF334 MUTATED    17   0   0   1
  ZNF334 WILD-TYPE 328   4  31  24
D1104V11, multiclass
    clus
vv   ZNF334 MUTATED ZNF334 WILD-TYPE
  R0             17              328
  R1              0                4
  R2              0               31
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1104V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF334 MUTATED                                  0     1
  ZNF334 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZNF334 MUTATED                           1    10
  ZNF334 WILD-TYPE                        21   216
D1104V13, multiclass
                                  clus
vv                                 ZNF334 MUTATED ZNF334 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                        10              216
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1105) Variable = SIRT4 MUTATION ANALYSIS
D1105V1, survival
                 sevent
clus2               0   1
  SIRT4 MUTATED     4   2
  SIRT4 WILD-TYPE 374  91
  SIRT4 MUTATED SIRT4 WILD-TYPE 
              6             465 
  SIRT4 MUTATED SIRT4 WILD-TYPE 
              2              91 
$`SIRT4 MUTATED`
TCGA-AA-3864 TCGA-AA-A00N TCGA-AY-6197 TCGA-AZ-6601 TCGA-DM-A1HB TCGA-AG-A002 
       53.00         4.01        21.44       100.01       135.65        20.98 

$`SIRT4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       33.01        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 
      140.38         7.50        44.32       131.51       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  SIRT4 MUTATED SIRT4 WILD-TYPE 
           4.01            0.00 
  SIRT4 MUTATED SIRT4 WILD-TYPE 
         135.65          148.01 
  SIRT4 MUTATED SIRT4 WILD-TYPE 
          37.22           20.05 
[1] "4.0 - 135.7 (37.2)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.2"
D1105V2, continuous
D1105V3, binary
                 cls
clus                0   1
  SIRT4 MUTATED     6   1
  SIRT4 WILD-TYPE 360 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SIRT4 MUTATED      6    1
  SIRT4 WILD-TYPE  360  118
        clus
vv       SIRT4 MUTATED SIRT4 WILD-TYPE
  COLON              6             360
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SIRT4 MUTATED         1        0        2         2         1         0
  SIRT4 WILD-TYPE      90        1       30       136         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SIRT4 MUTATED           0          0          1          0        0         0
  SIRT4 WILD-TYPE        24         11         58         42       48        18
                 vv
clus              STAGE IVB
  SIRT4 MUTATED           0
  SIRT4 WILD-TYPE         1
D1105V4, multiclass
            clus
vv           SIRT4 MUTATED SIRT4 WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA              2             136
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  SIRT4 MUTATED     0   1   5   1
  SIRT4 WILD-TYPE  17  91 324  49
D1105V5, multiclass
    clus
vv   SIRT4 MUTATED SIRT4 WILD-TYPE
  T1             0              17
  T2             1              91
  T3             5             324
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  SIRT4 MUTATED     6   1   0
  SIRT4 WILD-TYPE 281 112  87
D1105V6, multiclass
    clus
vv   SIRT4 MUTATED SIRT4 WILD-TYPE
  N0             6             281
  N1             1             112
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1105V7, binary
                 cls
clus                0   1
  SIRT4 MUTATED     6   0
  SIRT4 WILD-TYPE 369  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SIRT4 MUTATED      6    0
  SIRT4 WILD-TYPE  369   65
   clus
vv  SIRT4 MUTATED SIRT4 WILD-TYPE
  0             6             369
  1             0              65
[1] 2 2
[1] FALSE
D1105V8, binary
                 cls
clus                0   1
  SIRT4 MUTATED     1   6
  SIRT4 WILD-TYPE 224 258
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SIRT4 MUTATED      1    6
  SIRT4 WILD-TYPE  224  258
        clus
vv       SIRT4 MUTATED SIRT4 WILD-TYPE
  FEMALE             1             224
  MALE               6             258
[1] 2 2
[1] FALSE
D1105V9, binary
                 cls
clus                0   1
  SIRT4 MUTATED     4   0
  SIRT4 WILD-TYPE 346  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SIRT4 MUTATED      4    0
  SIRT4 WILD-TYPE  346   22
     clus
vv    SIRT4 MUTATED SIRT4 WILD-TYPE
  NO              4             346
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SIRT4 MUTATED                      4                             1
  SIRT4 WILD-TYPE                  311                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SIRT4 MUTATED                       1                              0
  SIRT4 WILD-TYPE                   105                             10
D1105V10, multiclass
                                clus
vv                               SIRT4 MUTATED SIRT4 WILD-TYPE
  COLON ADENOCARCINOMA                       4             311
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  SIRT4 MUTATED     5   0   0   0
  SIRT4 WILD-TYPE 340   4  31  25
D1105V11, multiclass
    clus
vv   SIRT4 MUTATED SIRT4 WILD-TYPE
  R0             5             340
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1105V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SIRT4 MUTATED                                  0     0
  SIRT4 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  SIRT4 MUTATED                           0     3
  SIRT4 WILD-TYPE                        22   223
D1105V13, multiclass
                                  clus
vv                                 SIRT4 MUTATED SIRT4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        3             223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1106) Variable = C1ORF35 MUTATION ANALYSIS
D1106V1, survival
                   sevent
clus2                 0   1
  C1ORF35 MUTATED     4   1
  C1ORF35 WILD-TYPE 374  92
  C1ORF35 MUTATED C1ORF35 WILD-TYPE 
                5               466 
  C1ORF35 MUTATED C1ORF35 WILD-TYPE 
                1                92 
$`C1ORF35 MUTATED`
TCGA-AA-3713 TCGA-CA-6717 TCGA-CK-5913 TCGA-CK-5916 TCGA-AG-3883 
       19.04        12.76        51.32        21.14         1.02 

$`C1ORF35 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07        12.20        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 
       85.45        15.62        49.08         9.99        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  C1ORF35 MUTATED C1ORF35 WILD-TYPE 
             1.02              0.00 
  C1ORF35 MUTATED C1ORF35 WILD-TYPE 
            51.32            148.01 
  C1ORF35 MUTATED C1ORF35 WILD-TYPE 
           19.040            20.235 
[1] "1.0 - 51.3 (19.0)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.2"
D1106V2, continuous
D1106V3, binary
                   cls
clus                  0   1
  C1ORF35 MUTATED     4   1
  C1ORF35 WILD-TYPE 362 118
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C1ORF35 MUTATED      4    1
  C1ORF35 WILD-TYPE  362  118
        clus
vv       C1ORF35 MUTATED C1ORF35 WILD-TYPE
  COLON                4               362
  RECTUM               1               118
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  C1ORF35 MUTATED         2        0        0         2         0         0
  C1ORF35 WILD-TYPE      89        1       32       136        10         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C1ORF35 MUTATED           0          0          0          0        1
  C1ORF35 WILD-TYPE        24         11         59         42       47
                   vv
clus                STAGE IVA STAGE IVB
  C1ORF35 MUTATED           0         0
  C1ORF35 WILD-TYPE        18         1
D1106V4, multiclass
            clus
vv           C1ORF35 MUTATED C1ORF35 WILD-TYPE
  STAGE I                  2                89
  STAGE IA                 0                 1
  STAGE II                 0                32
  STAGE IIA                2               136
  STAGE IIB                0                10
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               0                11
  STAGE IIIB               0                59
  STAGE IIIC               0                42
  STAGE IV                 1                47
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  C1ORF35 MUTATED     1   1   3   0
  C1ORF35 WILD-TYPE  16  91 326  50
D1106V5, multiclass
    clus
vv   C1ORF35 MUTATED C1ORF35 WILD-TYPE
  T1               1                16
  T2               1                91
  T3               3               326
  T4               0                50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  C1ORF35 MUTATED     5   0   0
  C1ORF35 WILD-TYPE 282 113  87
D1106V6, multiclass
    clus
vv   C1ORF35 MUTATED C1ORF35 WILD-TYPE
  N0               5               282
  N1               0               113
  N2               0                87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1106V7, binary
                   cls
clus                  0   1
  C1ORF35 MUTATED     3   1
  C1ORF35 WILD-TYPE 372  64
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C1ORF35 MUTATED      3    1
  C1ORF35 WILD-TYPE  372   64
   clus
vv  C1ORF35 MUTATED C1ORF35 WILD-TYPE
  0               3               372
  1               1                64
[1] 2 2
[1] FALSE
D1106V8, binary
                   cls
clus                  0   1
  C1ORF35 MUTATED     2   3
  C1ORF35 WILD-TYPE 223 261
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C1ORF35 MUTATED      2    3
  C1ORF35 WILD-TYPE  223  261
        clus
vv       C1ORF35 MUTATED C1ORF35 WILD-TYPE
  FEMALE               2               223
  MALE                 3               261
[1] 2 2
[1] FALSE
D1106V9, binary
                   cls
clus                  0   1
  C1ORF35 MUTATED     3   1
  C1ORF35 WILD-TYPE 347  21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C1ORF35 MUTATED      3    1
  C1ORF35 WILD-TYPE  347   21
     clus
vv    C1ORF35 MUTATED C1ORF35 WILD-TYPE
  NO                3               347
  YES               1                21
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  C1ORF35 MUTATED                      3                             1
  C1ORF35 WILD-TYPE                  312                            46
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  C1ORF35 MUTATED                       1                              0
  C1ORF35 WILD-TYPE                   105                             10
D1106V10, multiclass
                                clus
vv                               C1ORF35 MUTATED C1ORF35 WILD-TYPE
  COLON ADENOCARCINOMA                         3               312
  COLON MUCINOUS ADENOCARCINOMA                1                46
  RECTAL ADENOCARCINOMA                        1               105
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  C1ORF35 MUTATED     1   0   1   3
  C1ORF35 WILD-TYPE 344   4  30  22
D1106V11, multiclass
    clus
vv   C1ORF35 MUTATED C1ORF35 WILD-TYPE
  R0               1               344
  R1               0                 4
  R2               1                30
  RX               3                22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1106V12, continuous
[1] "Remove cluster labels:" "C1ORF35 MUTATED"       
clus
  C1ORF35 MUTATED C1ORF35 WILD-TYPE 
                2               456 
       TCGA-A6-2671        TCGA-A6-2672        TCGA-A6-2674        TCGA-A6-2676 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-A6-2677        TCGA-A6-2678        TCGA-A6-2683        TCGA-A6-3807 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-A6-3808        TCGA-A6-3809        TCGA-A6-3810        TCGA-A6-4105 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-A6-5656        TCGA-A6-5657        TCGA-A6-5659        TCGA-A6-5660 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-A6-5661        TCGA-A6-5662        TCGA-A6-5664        TCGA-A6-5665 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-A6-5666        TCGA-A6-6137        TCGA-A6-6138        TCGA-A6-6141 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-A6-6142        TCGA-A6-6648        TCGA-A6-6649        TCGA-A6-6651 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-A6-6652        TCGA-A6-6653        TCGA-A6-6654        TCGA-A6-6780 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-A6-6781        TCGA-A6-6782        TCGA-AA-3489        TCGA-AA-3492 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AA-3496        TCGA-AA-3502        TCGA-AA-3510        TCGA-AA-3511 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AA-3514        TCGA-AA-3516        TCGA-AA-3517        TCGA-AA-3518 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AA-3519        TCGA-AA-3520        TCGA-AA-3521        TCGA-AA-3522 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AA-3524        TCGA-AA-3525        TCGA-AA-3526        TCGA-AA-3527 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AA-3529        TCGA-AA-3530        TCGA-AA-3531        TCGA-AA-3532 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AA-3534        TCGA-AA-3538        TCGA-AA-3542        TCGA-AA-3543 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AA-3544        TCGA-AA-3548        TCGA-AA-3549        TCGA-AA-3552 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AA-3553        TCGA-AA-3554        TCGA-AA-3555        TCGA-AA-3556 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AA-3558        TCGA-AA-3560        TCGA-AA-3562        TCGA-AA-3655 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AA-3660        TCGA-AA-3662        TCGA-AA-3663        TCGA-AA-3664 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AA-3666        TCGA-AA-3667        TCGA-AA-3672        TCGA-AA-3673 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AA-3678        TCGA-AA-3679        TCGA-AA-3680        TCGA-AA-3681 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AA-3684        TCGA-AA-3685        TCGA-AA-3688        TCGA-AA-3692 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AA-3693        TCGA-AA-3695        TCGA-AA-3696        TCGA-AA-3697 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AA-3710        TCGA-AA-3712        TCGA-AA-3715        TCGA-AA-3811 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AA-3812        TCGA-AA-3814        TCGA-AA-3815        TCGA-AA-3818 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AA-3819        TCGA-AA-3821        TCGA-AA-3831        TCGA-AA-3833 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AA-3837        TCGA-AA-3842        TCGA-AA-3844        TCGA-AA-3845 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AA-3846        TCGA-AA-3848        TCGA-AA-3850        TCGA-AA-3851 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AA-3852        TCGA-AA-3854        TCGA-AA-3855        TCGA-AA-3856 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AA-3858        TCGA-AA-3860        TCGA-AA-3861        TCGA-AA-3864 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AA-3866        TCGA-AA-3867        TCGA-AA-3869        TCGA-AA-3870 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AA-3872        TCGA-AA-3875        TCGA-AA-3877        TCGA-AA-3930 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AA-3939        TCGA-AA-3941        TCGA-AA-3947        TCGA-AA-3949 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AA-3950        TCGA-AA-3952        TCGA-AA-3955        TCGA-AA-3956 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AA-3966        TCGA-AA-3968        TCGA-AA-3971        TCGA-AA-3972 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AA-3973        TCGA-AA-3975        TCGA-AA-3976        TCGA-AA-3977 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AA-3979        TCGA-AA-3980        TCGA-AA-3982        TCGA-AA-3984 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AA-3986        TCGA-AA-3989        TCGA-AA-3994        TCGA-AA-A004 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AA-A00A        TCGA-AA-A00D        TCGA-AA-A00E        TCGA-AA-A00F 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AA-A00J        TCGA-AA-A00K        TCGA-AA-A00L        TCGA-AA-A00N 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AA-A00O        TCGA-AA-A00Q        TCGA-AA-A00R        TCGA-AA-A00U 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AA-A00W        TCGA-AA-A00Z        TCGA-AA-A010        TCGA-AA-A017 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AA-A01D        TCGA-AA-A01F        TCGA-AA-A01G        TCGA-AA-A01I 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AA-A01K        TCGA-AA-A01P        TCGA-AA-A01Q        TCGA-AA-A01R 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AA-A01S        TCGA-AA-A01T        TCGA-AA-A01V        TCGA-AA-A01X 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AA-A01Z        TCGA-AA-A022        TCGA-AA-A024        TCGA-AA-A029 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AA-A02F        TCGA-AA-A02H        TCGA-AA-A02J        TCGA-AA-A02K 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AA-A02O        TCGA-AA-A02W        TCGA-AA-A02Y        TCGA-AA-A03F 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AA-A03J        TCGA-AD-5900        TCGA-AD-6548        TCGA-AD-6888 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AD-6889        TCGA-AD-6890        TCGA-AD-6895        TCGA-AD-6899 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AD-6901        TCGA-AD-6963        TCGA-AD-6964        TCGA-AD-6965 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AU-3779        TCGA-AU-6004        TCGA-AY-4070        TCGA-AY-4071 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AY-5543        TCGA-AY-6196        TCGA-AY-6197        TCGA-AY-6386 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AZ-4323        TCGA-AZ-4616        TCGA-AZ-4682        TCGA-AZ-5403 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AZ-5407        TCGA-AZ-6598        TCGA-AZ-6599        TCGA-AZ-6600 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AZ-6601        TCGA-AZ-6603        TCGA-AZ-6605        TCGA-AZ-6606 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AZ-6607        TCGA-AZ-6608        TCGA-CK-4947        TCGA-CK-4948 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-CK-4950        TCGA-CK-4952        TCGA-CM-4743        TCGA-CM-4744 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-CM-4746        TCGA-CM-4747        TCGA-CM-4752        TCGA-CM-5341 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-CM-5344        TCGA-CM-5348        TCGA-CM-5349        TCGA-CM-5860 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-CM-5861        TCGA-CM-5862        TCGA-CM-5863        TCGA-CM-5864 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-CM-5868        TCGA-CM-6161        TCGA-CM-6162        TCGA-CM-6163 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-CM-6164        TCGA-CM-6165        TCGA-CM-6166        TCGA-CM-6167 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-CM-6168        TCGA-CM-6169        TCGA-CM-6170        TCGA-CM-6171 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-CM-6172        TCGA-CM-6674        TCGA-CM-6675        TCGA-CM-6676 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-CM-6677        TCGA-CM-6678        TCGA-CM-6679        TCGA-CM-6680 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-D5-5537        TCGA-D5-5538        TCGA-D5-5539        TCGA-D5-5540 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-D5-5541        TCGA-D5-6529        TCGA-D5-6532        TCGA-D5-6533 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-D5-6534        TCGA-D5-6535        TCGA-D5-6536        TCGA-D5-6537 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-D5-6538        TCGA-D5-6539        TCGA-D5-6540        TCGA-D5-6541 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-D5-6898        TCGA-D5-6920        TCGA-D5-6922        TCGA-D5-6923 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-D5-6924        TCGA-D5-6926        TCGA-D5-6927        TCGA-D5-6928 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-D5-6929        TCGA-D5-6930        TCGA-D5-6931        TCGA-D5-6932 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-D5-7000        TCGA-DM-A0X9        TCGA-DM-A0XD        TCGA-DM-A0XF 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-DM-A1D0        TCGA-DM-A1D4        TCGA-DM-A1D6        TCGA-DM-A1D7 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-DM-A1D8        TCGA-DM-A1D9        TCGA-DM-A1DA        TCGA-DM-A1DB 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-DM-A1HA        TCGA-DM-A1HB        TCGA-DM-A282        TCGA-DM-A285 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-DM-A28C        TCGA-DM-A28E        TCGA-DM-A28F        TCGA-DM-A28G 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-DM-A28H        TCGA-DM-A28K        TCGA-F4-6459        TCGA-F4-6460 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-F4-6569        TCGA-F4-6570        TCGA-F4-6703        TCGA-F4-6704 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-F4-6806        TCGA-F4-6807        TCGA-F4-6808        TCGA-F4-6809 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-F4-6854        TCGA-F4-6855        TCGA-F4-6856        TCGA-G4-6293 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-G4-6299        TCGA-G4-6303        TCGA-G4-6304        TCGA-G4-6306 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-G4-6307        TCGA-G4-6309        TCGA-G4-6310        TCGA-G4-6315 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-G4-6317        TCGA-G4-6321        TCGA-G4-6323        TCGA-G4-6586 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-G4-6588        TCGA-G4-6625        TCGA-G4-6626        TCGA-G4-6628 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2691        TCGA-AF-2692 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3913        TCGA-AF-4110 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AF-5654        TCGA-AF-6136        TCGA-AF-6655        TCGA-AF-6672 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AG-3574        TCGA-AG-3575        TCGA-AG-3578        TCGA-AG-3580 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AG-3581        TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3584 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AG-3586        TCGA-AG-3587        TCGA-AG-3593        TCGA-AG-3594 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AG-3598        TCGA-AG-3599        TCGA-AG-3600        TCGA-AG-3601 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AG-3602        TCGA-AG-3605        TCGA-AG-3608        TCGA-AG-3609 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AG-3611        TCGA-AG-3612        TCGA-AG-3726        TCGA-AG-3727 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3732        TCGA-AG-3742        TCGA-AG-3878 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AG-3881        TCGA-AG-3882        TCGA-AG-3885        TCGA-AG-3887 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AG-3890        TCGA-AG-3892        TCGA-AG-3893        TCGA-AG-3894 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AG-3896        TCGA-AG-3898        TCGA-AG-3901        TCGA-AG-3902 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AG-3909        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4005 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AG-4007        TCGA-AG-4008        TCGA-AG-4015        TCGA-AG-A002 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AG-A008        TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AG-A011        TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01W        TCGA-AG-A01Y        TCGA-AG-A020 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AG-A025        TCGA-AG-A026        TCGA-AG-A02G        TCGA-AG-A02N 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AG-A02X        TCGA-AG-A032        TCGA-AG-A036        TCGA-AH-6544 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644        TCGA-CI-6622 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6155        TCGA-DC-6157 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-DC-6158        TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-DC-6683        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8        TCGA-EI-6506 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-EI-6507        TCGA-EI-6508        TCGA-EI-6510        TCGA-F5-6464 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-F5-6465        TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6811 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-G5-6235        TCGA-G5-6641 
"C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" "C1ORF35 WILD-TYPE" 
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C1ORF35 MUTATED                                  0     1
  C1ORF35 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  C1ORF35 MUTATED                           0     2
  C1ORF35 WILD-TYPE                        22   224
D1106V13, multiclass
                                  clus
vv                                 C1ORF35 MUTATED C1ORF35 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                10
  BLACK OR AFRICAN AMERICAN                      0                22
  WHITE                                          2               224
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1107) Variable = PLK2 MUTATION ANALYSIS
D1107V1, survival
                sevent
clus2              0   1
  PLK2 MUTATED     4   2
  PLK2 WILD-TYPE 374  91
  PLK2 MUTATED PLK2 WILD-TYPE 
             6            465 
  PLK2 MUTATED PLK2 WILD-TYPE 
             2             91 
$`PLK2 MUTATED`
TCGA-AA-3516 TCGA-D5-6541 TCGA-DM-A1HB TCGA-DM-A28C TCGA-G4-6588 TCGA-AG-A002 
       13.02        15.58       135.65        81.37        26.17        20.98 

$`PLK2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        1.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6898 
       17.85         4.80        17.13        12.49        16.14         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
      139.17         6.12       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        35.80        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  PLK2 MUTATED PLK2 WILD-TYPE 
         13.02           0.00 
  PLK2 MUTATED PLK2 WILD-TYPE 
        135.65         148.01 
  PLK2 MUTATED PLK2 WILD-TYPE 
        23.575         20.120 
[1] "13.0 - 135.7 (23.6)" "0.0 - 148.0 (20.1)" 
[1] "hr=" "1"  
D1107V2, continuous
D1107V3, binary
                cls
clus               0   1
  PLK2 MUTATED     6   1
  PLK2 WILD-TYPE 360 118
[1] "tbl2"
                cls
clus             [,1] [,2]
  PLK2 MUTATED      6    1
  PLK2 WILD-TYPE  360  118
        clus
vv       PLK2 MUTATED PLK2 WILD-TYPE
  COLON             6            360
  RECTUM            1            118
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PLK2 MUTATED         1        0        0         4         0         0
  PLK2 WILD-TYPE      90        1       32       134        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PLK2 MUTATED           1          0          1          0        0         0
  PLK2 WILD-TYPE        23         11         58         42       48        18
                vv
clus             STAGE IVB
  PLK2 MUTATED           0
  PLK2 WILD-TYPE         1
D1107V4, multiclass
            clus
vv           PLK2 MUTATED PLK2 WILD-TYPE
  STAGE I               1             90
  STAGE IA              0              1
  STAGE II              0             32
  STAGE IIA             4            134
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             1             23
  STAGE IIIA            0             11
  STAGE IIIB            1             58
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  PLK2 MUTATED     0   1   6   0
  PLK2 WILD-TYPE  17  91 323  50
D1107V5, multiclass
    clus
vv   PLK2 MUTATED PLK2 WILD-TYPE
  T1            0             17
  T2            1             91
  T3            6            323
  T4            0             50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  PLK2 MUTATED     5   1   1
  PLK2 WILD-TYPE 282 112  86
D1107V6, multiclass
    clus
vv   PLK2 MUTATED PLK2 WILD-TYPE
  N0            5            282
  N1            1            112
  N2            1             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1107V7, binary
                cls
clus               0   1
  PLK2 MUTATED     7   0
  PLK2 WILD-TYPE 368  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  PLK2 MUTATED      7    0
  PLK2 WILD-TYPE  368   65
   clus
vv  PLK2 MUTATED PLK2 WILD-TYPE
  0            7            368
  1            0             65
[1] 2 2
[1] FALSE
D1107V8, binary
                cls
clus               0   1
  PLK2 MUTATED     3   4
  PLK2 WILD-TYPE 222 260
[1] "tbl2"
                cls
clus             [,1] [,2]
  PLK2 MUTATED      3    4
  PLK2 WILD-TYPE  222  260
        clus
vv       PLK2 MUTATED PLK2 WILD-TYPE
  FEMALE            3            222
  MALE              4            260
[1] 2 2
[1] FALSE
D1107V9, binary
                cls
clus               0   1
  PLK2 MUTATED     4   0
  PLK2 WILD-TYPE 346  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  PLK2 MUTATED      4    0
  PLK2 WILD-TYPE  346   22
     clus
vv    PLK2 MUTATED PLK2 WILD-TYPE
  NO             4            346
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PLK2 MUTATED                      4                             1
  PLK2 WILD-TYPE                  311                            46
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PLK2 MUTATED                       1                              0
  PLK2 WILD-TYPE                   105                             10
D1107V10, multiclass
                                clus
vv                               PLK2 MUTATED PLK2 WILD-TYPE
  COLON ADENOCARCINOMA                      4            311
  COLON MUCINOUS ADENOCARCINOMA             1             46
  RECTAL ADENOCARCINOMA                     1            105
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  PLK2 MUTATED     4   0   0   0
  PLK2 WILD-TYPE 341   4  31  25
D1107V11, multiclass
    clus
vv   PLK2 MUTATED PLK2 WILD-TYPE
  R0            4            341
  R1            0              4
  R2            0             31
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1107V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PLK2 MUTATED                                  0     0
  PLK2 WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  PLK2 MUTATED                           0     4
  PLK2 WILD-TYPE                        22   222
D1107V13, multiclass
                                  clus
vv                                 PLK2 MUTATED PLK2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       4            222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1108) Variable = CCT4 MUTATION ANALYSIS
D1108V1, survival
                sevent
clus2              0   1
  CCT4 MUTATED    13   0
  CCT4 WILD-TYPE 365  93
  CCT4 MUTATED CCT4 WILD-TYPE 
            13            458 
  CCT4 MUTATED CCT4 WILD-TYPE 
             0             93 
$`CCT4 MUTATED`
TCGA-A6-6780 TCGA-AA-3496 TCGA-AA-3713 TCGA-AA-3950 TCGA-AD-6895 TCGA-CM-5341 
       20.12         1.02        19.04        24.00         0.72        29.06 
TCGA-D5-5538 TCGA-D5-6536 TCGA-D5-6538 TCGA-G4-6310 TCGA-G4-6628 TCGA-AG-4001 
       12.26        17.85        17.13        63.62        79.69        36.03 
TCGA-DC-6683 
        5.03 

$`CCT4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 
       23.87        19.66        20.28         7.04         3.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        33.01        26.01         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5344 
       23.05        20.02        37.02        25.02        13.02        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5539 TCGA-D5-5540 
       11.01        10.06        12.03        45.40        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6537 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
        4.80        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6315 
       65.85        53.62        44.68        55.04        85.48        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       46.75        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4005 
        1.02        48.03        32.02        19.99        28.04        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DT-5265 
       27.95        10.98        19.99         5.95         4.01         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  CCT4 MUTATED CCT4 WILD-TYPE 
          0.72           0.00 
  CCT4 MUTATED CCT4 WILD-TYPE 
         79.69         148.01 
  CCT4 MUTATED CCT4 WILD-TYPE 
        19.040         20.415 
[1] "0.7 - 79.7 (19.0)"  "0.0 - 148.0 (20.4)"
[1] "hr="     "9300000"
D1108V2, continuous
D1108V3, binary
                cls
clus               0   1
  CCT4 MUTATED    12   2
  CCT4 WILD-TYPE 354 117
[1] "tbl2"
                cls
clus             [,1] [,2]
  CCT4 MUTATED     12    2
  CCT4 WILD-TYPE  354  117
        clus
vv       CCT4 MUTATED CCT4 WILD-TYPE
  COLON            12            354
  RECTUM            2            117
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CCT4 MUTATED         1        0        1         5         0         0
  CCT4 WILD-TYPE      90        1       31       133        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CCT4 MUTATED           0          1          4          0        1         0
  CCT4 WILD-TYPE        24         10         55         42       47        18
                vv
clus             STAGE IVB
  CCT4 MUTATED           0
  CCT4 WILD-TYPE         1
D1108V4, multiclass
            clus
vv           CCT4 MUTATED CCT4 WILD-TYPE
  STAGE I               1             90
  STAGE IA              0              1
  STAGE II              1             31
  STAGE IIA             5            133
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            1             10
  STAGE IIIB            4             55
  STAGE IIIC            0             42
  STAGE IV              1             47
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  CCT4 MUTATED     0   2  12   0
  CCT4 WILD-TYPE  17  90 317  50
D1108V5, multiclass
    clus
vv   CCT4 MUTATED CCT4 WILD-TYPE
  T1            0             17
  T2            2             90
  T3           12            317
  T4            0             50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  CCT4 MUTATED     8   5   1
  CCT4 WILD-TYPE 279 108  86
D1108V6, multiclass
    clus
vv   CCT4 MUTATED CCT4 WILD-TYPE
  N0            8            279
  N1            5            108
  N2            1             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1108V7, binary
                cls
clus               0   1
  CCT4 MUTATED    11   1
  CCT4 WILD-TYPE 364  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  CCT4 MUTATED     11    1
  CCT4 WILD-TYPE  364   64
   clus
vv  CCT4 MUTATED CCT4 WILD-TYPE
  0           11            364
  1            1             64
[1] 2 2
[1] FALSE
D1108V8, binary
                cls
clus               0   1
  CCT4 MUTATED     7   7
  CCT4 WILD-TYPE 218 257
[1] "tbl2"
                cls
clus             [,1] [,2]
  CCT4 MUTATED      7    7
  CCT4 WILD-TYPE  218  257
        clus
vv       CCT4 MUTATED CCT4 WILD-TYPE
  FEMALE            7            218
  MALE              7            257
[1] 2 2
[1] FALSE
D1108V9, binary
                cls
clus               0   1
  CCT4 MUTATED     8   2
  CCT4 WILD-TYPE 342  20
[1] "tbl2"
                cls
clus             [,1] [,2]
  CCT4 MUTATED      8    2
  CCT4 WILD-TYPE  342   20
     clus
vv    CCT4 MUTATED CCT4 WILD-TYPE
  NO             8            342
  YES            2             20
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CCT4 MUTATED                     10                             2
  CCT4 WILD-TYPE                  305                            45
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CCT4 MUTATED                       2                              0
  CCT4 WILD-TYPE                   104                             10
D1108V10, multiclass
                                clus
vv                               CCT4 MUTATED CCT4 WILD-TYPE
  COLON ADENOCARCINOMA                     10            305
  COLON MUCINOUS ADENOCARCINOMA             2             45
  RECTAL ADENOCARCINOMA                     2            104
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  CCT4 MUTATED    11   0   1   0
  CCT4 WILD-TYPE 334   4  30  25
D1108V11, multiclass
    clus
vv   CCT4 MUTATED CCT4 WILD-TYPE
  R0           11            334
  R1            0              4
  R2            1             30
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1108V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CCT4 MUTATED                                  0     0
  CCT4 WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  CCT4 MUTATED                           0     9
  CCT4 WILD-TYPE                        22   217
D1108V13, multiclass
                                  clus
vv                                 CCT4 MUTATED CCT4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       9            217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1109) Variable = MAP3K12 MUTATION ANALYSIS
D1109V1, survival
                   sevent
clus2                 0   1
  MAP3K12 MUTATED     9   4
  MAP3K12 WILD-TYPE 369  89
  MAP3K12 MUTATED MAP3K12 WILD-TYPE 
               13               458 
  MAP3K12 MUTATED MAP3K12 WILD-TYPE 
                4                89 
$`MAP3K12 MUTATED`
TCGA-AA-3713 TCGA-AA-3856 TCGA-AA-3864 TCGA-AA-A010 TCGA-AZ-6598 TCGA-AZ-6599 
       19.04         0.99        53.00        34.98        49.41         6.77 
TCGA-CK-5916 TCGA-CM-4746 TCGA-DM-A1DA TCGA-AG-3611 TCGA-AG-A002 TCGA-EI-6507 
       21.14        37.02         7.50        13.94        20.98        19.96 
TCGA-F5-6465 
       49.51 

$`MAP3K12 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 
       32.05        31.07        31.07        30.05        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       62.79        88.21        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
        9.99        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       13.32        12.59       140.38        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
        0.99        15.95        19.99        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6510 
       51.48        32.61         0.49        20.55        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
        9.96        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  MAP3K12 MUTATED MAP3K12 WILD-TYPE 
             0.99              0.00 
  MAP3K12 MUTATED MAP3K12 WILD-TYPE 
            53.00            148.01 
  MAP3K12 MUTATED MAP3K12 WILD-TYPE 
           20.980            20.155 
[1] "1.0 - 53.0 (21.0)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.5"
D1109V2, continuous
D1109V3, binary
                   cls
clus                  0   1
  MAP3K12 MUTATED    10   4
  MAP3K12 WILD-TYPE 356 115
[1] "tbl2"
                   cls
clus                [,1] [,2]
  MAP3K12 MUTATED     10    4
  MAP3K12 WILD-TYPE  356  115
        clus
vv       MAP3K12 MUTATED MAP3K12 WILD-TYPE
  COLON               10               356
  RECTUM               4               115
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MAP3K12 MUTATED         4        0        2         4         1         0
  MAP3K12 WILD-TYPE      87        1       30       134         9         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MAP3K12 MUTATED           0          0          0          1        2
  MAP3K12 WILD-TYPE        24         11         59         41       46
                   vv
clus                STAGE IVA STAGE IVB
  MAP3K12 MUTATED           0         0
  MAP3K12 WILD-TYPE        18         1
D1109V4, multiclass
            clus
vv           MAP3K12 MUTATED MAP3K12 WILD-TYPE
  STAGE I                  4                87
  STAGE IA                 0                 1
  STAGE II                 2                30
  STAGE IIA                4               134
  STAGE IIB                1                 9
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               0                11
  STAGE IIIB               0                59
  STAGE IIIC               1                41
  STAGE IV                 2                46
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  MAP3K12 MUTATED     1   3   8   2
  MAP3K12 WILD-TYPE  16  89 321  48
D1109V5, multiclass
    clus
vv   MAP3K12 MUTATED MAP3K12 WILD-TYPE
  T1               1                16
  T2               3                89
  T3               8               321
  T4               2                48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  MAP3K12 MUTATED    12   1   1
  MAP3K12 WILD-TYPE 275 112  86
D1109V6, multiclass
    clus
vv   MAP3K12 MUTATED MAP3K12 WILD-TYPE
  N0              12               275
  N1               1               112
  N2               1                86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1109V7, binary
                   cls
clus                  0   1
  MAP3K12 MUTATED    10   2
  MAP3K12 WILD-TYPE 365  63
[1] "tbl2"
                   cls
clus                [,1] [,2]
  MAP3K12 MUTATED     10    2
  MAP3K12 WILD-TYPE  365   63
   clus
vv  MAP3K12 MUTATED MAP3K12 WILD-TYPE
  0              10               365
  1               2                63
[1] 2 2
[1] FALSE
D1109V8, binary
                   cls
clus                  0   1
  MAP3K12 MUTATED     6   8
  MAP3K12 WILD-TYPE 219 256
[1] "tbl2"
                   cls
clus                [,1] [,2]
  MAP3K12 MUTATED      6    8
  MAP3K12 WILD-TYPE  219  256
        clus
vv       MAP3K12 MUTATED MAP3K12 WILD-TYPE
  FEMALE               6               219
  MALE                 8               256
[1] 2 2
[1] FALSE
D1109V9, binary
                   cls
clus                  0   1
  MAP3K12 MUTATED    10   1
  MAP3K12 WILD-TYPE 340  21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  MAP3K12 MUTATED     10    1
  MAP3K12 WILD-TYPE  340   21
     clus
vv    MAP3K12 MUTATED MAP3K12 WILD-TYPE
  NO               10               340
  YES               1                21
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MAP3K12 MUTATED                     10                             0
  MAP3K12 WILD-TYPE                  305                            47
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MAP3K12 MUTATED                       4                              0
  MAP3K12 WILD-TYPE                   102                             10
D1109V10, multiclass
                                clus
vv                               MAP3K12 MUTATED MAP3K12 WILD-TYPE
  COLON ADENOCARCINOMA                        10               305
  COLON MUCINOUS ADENOCARCINOMA                0                47
  RECTAL ADENOCARCINOMA                        4               102
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  MAP3K12 MUTATED     8   0   2   1
  MAP3K12 WILD-TYPE 337   4  29  24
D1109V11, multiclass
    clus
vv   MAP3K12 MUTATED MAP3K12 WILD-TYPE
  R0               8               337
  R1               0                 4
  R2               2                29
  RX               1                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1109V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MAP3K12 MUTATED                                  0     0
  MAP3K12 WILD-TYPE                                1    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  MAP3K12 MUTATED                           1     6
  MAP3K12 WILD-TYPE                        21   220
D1109V13, multiclass
                                  clus
vv                                 MAP3K12 MUTATED MAP3K12 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                      1                21
  WHITE                                          6               220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1110) Variable = FGD3 MUTATION ANALYSIS
D1110V1, survival
                sevent
clus2              0   1
  FGD3 MUTATED    11   3
  FGD3 WILD-TYPE 367  90
  FGD3 MUTATED FGD3 WILD-TYPE 
            14            457 
  FGD3 MUTATED FGD3 WILD-TYPE 
             3             90 
$`FGD3 MUTATED`
TCGA-A6-5661 TCGA-A6-6781 TCGA-AA-3815 TCGA-AA-3966 TCGA-AU-6004 TCGA-AZ-6598 
       33.53        19.66        33.04         2.01        27.09        49.41 
TCGA-AZ-6600 TCGA-CM-4743 TCGA-CM-5348 TCGA-D5-6927 TCGA-DM-A285 TCGA-F4-6703 
       12.10        23.05        22.98         9.44         6.12        47.87 
TCGA-G4-6309 TCGA-AG-3878 
       85.48         0.99 

$`FGD3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       35.05         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
       34.03        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       14.50        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       88.21         6.77       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 
       21.14        82.95         1.91       124.27        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5860 
       25.02        13.02        29.06        22.03        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6929 
        4.41        12.43        14.30         9.04        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6704 TCGA-F4-6805 
        8.61        31.96        35.74         6.18         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       55.04        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  FGD3 MUTATED FGD3 WILD-TYPE 
          0.99           0.00 
  FGD3 MUTATED FGD3 WILD-TYPE 
         85.48         148.01 
  FGD3 MUTATED FGD3 WILD-TYPE 
        23.015         20.120 
[1] "1.0 - 85.5 (23.0)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.1"
D1110V2, continuous
D1110V3, binary
                cls
clus               0   1
  FGD3 MUTATED    13   1
  FGD3 WILD-TYPE 353 118
[1] "tbl2"
                cls
clus             [,1] [,2]
  FGD3 MUTATED     13    1
  FGD3 WILD-TYPE  353  118
        clus
vv       FGD3 MUTATED FGD3 WILD-TYPE
  COLON            13            353
  RECTUM            1            118
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FGD3 MUTATED         2        0        1         6         0         0
  FGD3 WILD-TYPE      89        1       31       132        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  FGD3 MUTATED           0          0          2          1        2         0
  FGD3 WILD-TYPE        24         11         57         41       46        18
                vv
clus             STAGE IVB
  FGD3 MUTATED           0
  FGD3 WILD-TYPE         1
D1110V4, multiclass
            clus
vv           FGD3 MUTATED FGD3 WILD-TYPE
  STAGE I               2             89
  STAGE IA              0              1
  STAGE II              1             31
  STAGE IIA             6            132
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            2             57
  STAGE IIIC            1             41
  STAGE IV              2             46
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  FGD3 MUTATED     0   2  10   2
  FGD3 WILD-TYPE  17  90 319  48
D1110V5, multiclass
    clus
vv   FGD3 MUTATED FGD3 WILD-TYPE
  T1            0             17
  T2            2             90
  T3           10            319
  T4            2             48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  FGD3 MUTATED     9   4   1
  FGD3 WILD-TYPE 278 109  86
D1110V6, multiclass
    clus
vv   FGD3 MUTATED FGD3 WILD-TYPE
  N0            9            278
  N1            4            109
  N2            1             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1110V7, binary
                cls
clus               0   1
  FGD3 MUTATED    10   2
  FGD3 WILD-TYPE 365  63
[1] "tbl2"
                cls
clus             [,1] [,2]
  FGD3 MUTATED     10    2
  FGD3 WILD-TYPE  365   63
   clus
vv  FGD3 MUTATED FGD3 WILD-TYPE
  0           10            365
  1            2             63
[1] 2 2
[1] FALSE
D1110V8, binary
                cls
clus               0   1
  FGD3 MUTATED     7   7
  FGD3 WILD-TYPE 218 257
[1] "tbl2"
                cls
clus             [,1] [,2]
  FGD3 MUTATED      7    7
  FGD3 WILD-TYPE  218  257
        clus
vv       FGD3 MUTATED FGD3 WILD-TYPE
  FEMALE            7            218
  MALE              7            257
[1] 2 2
[1] FALSE
D1110V9, binary
                cls
clus               0   1
  FGD3 MUTATED     9   0
  FGD3 WILD-TYPE 341  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  FGD3 MUTATED      9    0
  FGD3 WILD-TYPE  341   22
     clus
vv    FGD3 MUTATED FGD3 WILD-TYPE
  NO             9            341
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  FGD3 MUTATED                     10                             3
  FGD3 WILD-TYPE                  305                            44
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  FGD3 MUTATED                       1                              0
  FGD3 WILD-TYPE                   105                             10
D1110V10, multiclass
                                clus
vv                               FGD3 MUTATED FGD3 WILD-TYPE
  COLON ADENOCARCINOMA                     10            305
  COLON MUCINOUS ADENOCARCINOMA             3             44
  RECTAL ADENOCARCINOMA                     1            105
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  FGD3 MUTATED    10   0   0   0
  FGD3 WILD-TYPE 335   4  31  25
D1110V11, multiclass
    clus
vv   FGD3 MUTATED FGD3 WILD-TYPE
  R0           10            335
  R1            0              4
  R2            0             31
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1110V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FGD3 MUTATED                                  0     0
  FGD3 WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  FGD3 MUTATED                           3     8
  FGD3 WILD-TYPE                        19   218
D1110V13, multiclass
                                  clus
vv                                 FGD3 MUTATED FGD3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   3             19
  WHITE                                       8            218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1111) Variable = ACAT2 MUTATION ANALYSIS
D1111V1, survival
                 sevent
clus2               0   1
  ACAT2 MUTATED     5   4
  ACAT2 WILD-TYPE 373  89
  ACAT2 MUTATED ACAT2 WILD-TYPE 
              9             462 
  ACAT2 MUTATED ACAT2 WILD-TYPE 
              4              89 
$`ACAT2 MUTATED`
TCGA-AA-3715 TCGA-AA-A010 TCGA-AD-6889 TCGA-CA-6718 TCGA-CK-4948 TCGA-CK-6747 
       19.04        34.98        56.55        10.06       148.01        82.95 
TCGA-CM-5862 TCGA-D5-6537 TCGA-CI-6619 
        5.03         4.80         6.05 

$`ACAT2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       12.76        14.30        17.56        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       51.32         9.99        21.14         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5864 
       22.98        30.08        32.02        15.02        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
       17.85        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        0.72        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  ACAT2 MUTATED ACAT2 WILD-TYPE 
            4.8             0.0 
  ACAT2 MUTATED ACAT2 WILD-TYPE 
         148.01          140.38 
  ACAT2 MUTATED ACAT2 WILD-TYPE 
         19.040          20.235 
[1] "4.8 - 148.0 (19.0)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.7"
D1111V2, continuous
D1111V3, binary
                 cls
clus                0   1
  ACAT2 MUTATED     8   1
  ACAT2 WILD-TYPE 358 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ACAT2 MUTATED      8    1
  ACAT2 WILD-TYPE  358  118
        clus
vv       ACAT2 MUTATED ACAT2 WILD-TYPE
  COLON              8             358
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ACAT2 MUTATED         0        0        1         3         1         0
  ACAT2 WILD-TYPE      91        1       31       135         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ACAT2 MUTATED           1          0          1          0        1         1
  ACAT2 WILD-TYPE        23         11         58         42       47        17
                 vv
clus              STAGE IVB
  ACAT2 MUTATED           0
  ACAT2 WILD-TYPE         1
D1111V4, multiclass
            clus
vv           ACAT2 MUTATED ACAT2 WILD-TYPE
  STAGE I                0              91
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              3             135
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             0              42
  STAGE IV               1              47
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ACAT2 MUTATED     0   0   8   1
  ACAT2 WILD-TYPE  17  92 321  49
D1111V5, multiclass
    clus
vv   ACAT2 MUTATED ACAT2 WILD-TYPE
  T1             0              17
  T2             0              92
  T3             8             321
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  ACAT2 MUTATED     5   4   0
  ACAT2 WILD-TYPE 282 109  87
D1111V6, multiclass
    clus
vv   ACAT2 MUTATED ACAT2 WILD-TYPE
  N0             5             282
  N1             4             109
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1111V7, binary
                 cls
clus                0   1
  ACAT2 MUTATED     5   2
  ACAT2 WILD-TYPE 370  63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ACAT2 MUTATED      5    2
  ACAT2 WILD-TYPE  370   63
   clus
vv  ACAT2 MUTATED ACAT2 WILD-TYPE
  0             5             370
  1             2              63
[1] 2 2
[1] FALSE
D1111V8, binary
                 cls
clus                0   1
  ACAT2 MUTATED     3   6
  ACAT2 WILD-TYPE 222 258
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ACAT2 MUTATED      3    6
  ACAT2 WILD-TYPE  222  258
        clus
vv       ACAT2 MUTATED ACAT2 WILD-TYPE
  FEMALE             3             222
  MALE               6             258
[1] 2 2
[1] FALSE
D1111V9, binary
                 cls
clus                0   1
  ACAT2 MUTATED     7   0
  ACAT2 WILD-TYPE 343  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ACAT2 MUTATED      7    0
  ACAT2 WILD-TYPE  343   22
     clus
vv    ACAT2 MUTATED ACAT2 WILD-TYPE
  NO              7             343
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ACAT2 MUTATED                      8                             0
  ACAT2 WILD-TYPE                  307                            47
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ACAT2 MUTATED                       1                              0
  ACAT2 WILD-TYPE                   105                             10
D1111V10, multiclass
                                clus
vv                               ACAT2 MUTATED ACAT2 WILD-TYPE
  COLON ADENOCARCINOMA                       8             307
  COLON MUCINOUS ADENOCARCINOMA              0              47
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  ACAT2 MUTATED     5   0   0   2
  ACAT2 WILD-TYPE 340   4  31  23
D1111V11, multiclass
    clus
vv   ACAT2 MUTATED ACAT2 WILD-TYPE
  R0             5             340
  R1             0               4
  R2             0              31
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1111V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ACAT2 MUTATED                                  0     2
  ACAT2 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ACAT2 MUTATED                           0     5
  ACAT2 WILD-TYPE                        22   221
D1111V13, multiclass
                                  clus
vv                                 ACAT2 MUTATED ACAT2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               9
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        5             221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1112) Variable = PRRT2 MUTATION ANALYSIS
D1112V1, survival
                 sevent
clus2               0   1
  PRRT2 MUTATED     6   0
  PRRT2 WILD-TYPE 372  93
  PRRT2 MUTATED PRRT2 WILD-TYPE 
              6             465 
  PRRT2 MUTATED PRRT2 WILD-TYPE 
              0              93 
$`PRRT2 MUTATED`
TCGA-AA-3663 TCGA-AD-5900 TCGA-AY-6197 TCGA-CK-4948 TCGA-G4-6306 TCGA-G4-6588 
        6.97         0.07        21.44       148.01        44.68        26.17 

$`PRRT2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.05        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 
       41.00        39.98        18.05        40.96        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       33.01        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4952 
       12.76        10.06        14.30        17.56        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       53.62        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       22.09        13.78        35.80        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  PRRT2 MUTATED PRRT2 WILD-TYPE 
           0.07            0.00 
  PRRT2 MUTATED PRRT2 WILD-TYPE 
         148.01          140.38 
  PRRT2 MUTATED PRRT2 WILD-TYPE 
         23.805          20.120 
[1] "0.1 - 148.0 (23.8)" "0.0 - 140.4 (20.1)"
[1] "hr="     "9200000"
D1112V2, continuous
D1112V3, binary
                 cls
clus                0   1
  PRRT2 MUTATED     6   0
  PRRT2 WILD-TYPE 360 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRRT2 MUTATED      6    0
  PRRT2 WILD-TYPE  360  119
        clus
vv       PRRT2 MUTATED PRRT2 WILD-TYPE
  COLON              6             360
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PRRT2 MUTATED         1        0        1         3         0         0
  PRRT2 WILD-TYPE      90        1       31       135        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PRRT2 MUTATED           1          0          0          0        0         0
  PRRT2 WILD-TYPE        23         11         59         42       48        18
                 vv
clus              STAGE IVB
  PRRT2 MUTATED           0
  PRRT2 WILD-TYPE         1
D1112V4, multiclass
            clus
vv           PRRT2 MUTATED PRRT2 WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              3             135
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PRRT2 MUTATED     0   2   4   0
  PRRT2 WILD-TYPE  17  90 325  50
D1112V5, multiclass
    clus
vv   PRRT2 MUTATED PRRT2 WILD-TYPE
  T1             0              17
  T2             2              90
  T3             4             325
  T4             0              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  PRRT2 MUTATED     5   1   0
  PRRT2 WILD-TYPE 282 112  87
D1112V6, multiclass
    clus
vv   PRRT2 MUTATED PRRT2 WILD-TYPE
  N0             5             282
  N1             1             112
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1112V7, binary
                 cls
clus                0   1
  PRRT2 MUTATED     4   0
  PRRT2 WILD-TYPE 371  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRRT2 MUTATED      4    0
  PRRT2 WILD-TYPE  371   65
   clus
vv  PRRT2 MUTATED PRRT2 WILD-TYPE
  0             4             371
  1             0              65
[1] 2 2
[1] FALSE
D1112V8, binary
                 cls
clus                0   1
  PRRT2 MUTATED     2   4
  PRRT2 WILD-TYPE 223 260
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRRT2 MUTATED      2    4
  PRRT2 WILD-TYPE  223  260
        clus
vv       PRRT2 MUTATED PRRT2 WILD-TYPE
  FEMALE             2             223
  MALE               4             260
[1] 2 2
[1] FALSE
D1112V9, binary
                 cls
clus                0   1
  PRRT2 MUTATED     5   0
  PRRT2 WILD-TYPE 345  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRRT2 MUTATED      5    0
  PRRT2 WILD-TYPE  345   22
     clus
vv    PRRT2 MUTATED PRRT2 WILD-TYPE
  NO              5             345
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PRRT2 MUTATED                      5                             1
  PRRT2 WILD-TYPE                  310                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PRRT2 MUTATED                       0                              0
  PRRT2 WILD-TYPE                   106                             10
D1112V10, multiclass
                                clus
vv                               PRRT2 MUTATED PRRT2 WILD-TYPE
  COLON ADENOCARCINOMA                       5             310
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  PRRT2 MUTATED     6   0   0   0
  PRRT2 WILD-TYPE 339   4  31  25
D1112V11, multiclass
    clus
vv   PRRT2 MUTATED PRRT2 WILD-TYPE
  R0             6             339
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1112V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PRRT2 MUTATED                                  0     0
  PRRT2 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PRRT2 MUTATED                           0     5
  PRRT2 WILD-TYPE                        22   221
D1112V13, multiclass
                                  clus
vv                                 PRRT2 MUTATED PRRT2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        5             221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1113) Variable = C14ORF50 MUTATION ANALYSIS
D1113V1, survival
                    sevent
clus2                  0   1
  C14ORF50 MUTATED     5   2
  C14ORF50 WILD-TYPE 373  91
  C14ORF50 MUTATED C14ORF50 WILD-TYPE 
                 7                464 
  C14ORF50 MUTATED C14ORF50 WILD-TYPE 
                 2                 91 
$`C14ORF50 MUTATED`
TCGA-AA-3492 TCGA-AA-3543 TCGA-AA-3837 TCGA-AA-3994 TCGA-CK-5916 TCGA-AG-3600 
        3.02         0.99        38.99        27.02        21.14         6.05 
TCGA-AG-3885 
       17.95 

$`C14ORF50 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       26.01        12.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       15.95        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
       19.07         7.96        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       49.08        51.32         9.99        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
        2.01        50.04        12.03         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 
        0.99         0.99        19.04        19.99         1.02        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  C14ORF50 MUTATED C14ORF50 WILD-TYPE 
              0.99               0.00 
  C14ORF50 MUTATED C14ORF50 WILD-TYPE 
             38.99             148.01 
  C14ORF50 MUTATED C14ORF50 WILD-TYPE 
            17.950             20.235 
[1] "1.0 - 39.0 (17.9)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "2.3"
D1113V2, continuous
D1113V3, binary
                    cls
clus                   0   1
  C14ORF50 MUTATED     6   2
  C14ORF50 WILD-TYPE 360 117
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C14ORF50 MUTATED      6    2
  C14ORF50 WILD-TYPE  360  117
        clus
vv       C14ORF50 MUTATED C14ORF50 WILD-TYPE
  COLON                 6                360
  RECTUM                2                117
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  C14ORF50 MUTATED         2        0        1         1         1         0
  C14ORF50 WILD-TYPE      89        1       31       137         9         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C14ORF50 MUTATED           0          0          2          1        0
  C14ORF50 WILD-TYPE        24         11         57         41       48
                    vv
clus                 STAGE IVA STAGE IVB
  C14ORF50 MUTATED           0         0
  C14ORF50 WILD-TYPE        18         1
D1113V4, multiclass
            clus
vv           C14ORF50 MUTATED C14ORF50 WILD-TYPE
  STAGE I                   2                 89
  STAGE IA                  0                  1
  STAGE II                  1                 31
  STAGE IIA                 1                137
  STAGE IIB                 1                  9
  STAGE IIC                 0                  1
  STAGE III                 0                 24
  STAGE IIIA                0                 11
  STAGE IIIB                2                 57
  STAGE IIIC                1                 41
  STAGE IV                  0                 48
  STAGE IVA                 0                 18
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  C14ORF50 MUTATED     1   1   5   1
  C14ORF50 WILD-TYPE  16  91 324  49
D1113V5, multiclass
    clus
vv   C14ORF50 MUTATED C14ORF50 WILD-TYPE
  T1                1                 16
  T2                1                 91
  T3                5                324
  T4                1                 49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  C14ORF50 MUTATED     5   2   1
  C14ORF50 WILD-TYPE 282 111  86
D1113V6, multiclass
    clus
vv   C14ORF50 MUTATED C14ORF50 WILD-TYPE
  N0                5                282
  N1                2                111
  N2                1                 86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1113V7, binary
                    cls
clus                   0   1
  C14ORF50 MUTATED     7   0
  C14ORF50 WILD-TYPE 368  65
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C14ORF50 MUTATED      7    0
  C14ORF50 WILD-TYPE  368   65
   clus
vv  C14ORF50 MUTATED C14ORF50 WILD-TYPE
  0                7                368
  1                0                 65
[1] 2 2
[1] FALSE
D1113V8, binary
                    cls
clus                   0   1
  C14ORF50 MUTATED     4   4
  C14ORF50 WILD-TYPE 221 260
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C14ORF50 MUTATED      4    4
  C14ORF50 WILD-TYPE  221  260
        clus
vv       C14ORF50 MUTATED C14ORF50 WILD-TYPE
  FEMALE                4                221
  MALE                  4                260
[1] 2 2
[1] FALSE
D1113V9, binary
                    cls
clus                   0   1
  C14ORF50 MUTATED     5   2
  C14ORF50 WILD-TYPE 345  20
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C14ORF50 MUTATED      5    2
  C14ORF50 WILD-TYPE  345   20
     clus
vv    C14ORF50 MUTATED C14ORF50 WILD-TYPE
  NO                 5                345
  YES                2                 20
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  C14ORF50 MUTATED                      3                             3
  C14ORF50 WILD-TYPE                  312                            44
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  C14ORF50 MUTATED                       2                              0
  C14ORF50 WILD-TYPE                   104                             10
D1113V10, multiclass
                                clus
vv                               C14ORF50 MUTATED C14ORF50 WILD-TYPE
  COLON ADENOCARCINOMA                          3                312
  COLON MUCINOUS ADENOCARCINOMA                 3                 44
  RECTAL ADENOCARCINOMA                         2                104
  RECTAL MUCINOUS ADENOCARCINOMA                0                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  C14ORF50 MUTATED     6   0   0   2
  C14ORF50 WILD-TYPE 339   4  31  23
D1113V11, multiclass
    clus
vv   C14ORF50 MUTATED C14ORF50 WILD-TYPE
  R0                6                339
  R1                0                  4
  R2                0                 31
  RX                2                 23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1113V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C14ORF50 MUTATED                                  0     0
  C14ORF50 WILD-TYPE                                1    11
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  C14ORF50 MUTATED                           0     2
  C14ORF50 WILD-TYPE                        22   224
D1113V13, multiclass
[1] "Remove cluster labels:" "C14ORF50 MUTATED"      
clus
  C14ORF50 MUTATED C14ORF50 WILD-TYPE 
                 2                258 
        TCGA-A6-2671         TCGA-A6-2672         TCGA-A6-2674 
"C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" 
        TCGA-A6-2676         TCGA-A6-2677         TCGA-A6-2678 
"C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" 
        TCGA-A6-2683         TCGA-A6-3807         TCGA-A6-3808 
"C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" 
        TCGA-A6-3809         TCGA-A6-3810         TCGA-A6-4105 
"C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" 
        TCGA-A6-5656         TCGA-A6-5657         TCGA-A6-5659 
"C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" 
        TCGA-A6-5660         TCGA-A6-5661         TCGA-A6-5662 
"C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" 
        TCGA-A6-5664         TCGA-A6-5665         TCGA-A6-5666 
"C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" 
        TCGA-A6-6137         TCGA-A6-6138         TCGA-A6-6141 
"C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" 
        TCGA-A6-6142         TCGA-A6-6648         TCGA-A6-6649 
"C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" 
        TCGA-A6-6651         TCGA-A6-6652         TCGA-A6-6653 
"C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" 
        TCGA-A6-6654         TCGA-A6-6780         TCGA-A6-6781 
"C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" 
        TCGA-A6-6782         TCGA-AD-5900         TCGA-AD-6548 
"C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" 
        TCGA-AD-6888         TCGA-AD-6889         TCGA-AD-6890 
"C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" 
        TCGA-AD-6895         TCGA-AD-6899         TCGA-AD-6901 
"C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" 
        TCGA-AD-6963         TCGA-AD-6964         TCGA-AD-6965 
"C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" 
        TCGA-AU-3779         TCGA-AU-6004         TCGA-AY-4070 
"C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" 
        TCGA-AY-4071         TCGA-AY-5543         TCGA-AY-6196 
"C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" 
        TCGA-AY-6197         TCGA-AY-6386         TCGA-AZ-4315 
"C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" 
        TCGA-AZ-4323         TCGA-AZ-4616         TCGA-AZ-4681 
"C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" 
        TCGA-AZ-4682         TCGA-AZ-5403         TCGA-AZ-5407 
"C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" 
        TCGA-AZ-6598         TCGA-AZ-6599         TCGA-AZ-6600 
"C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" 
        TCGA-AZ-6601         TCGA-AZ-6603         TCGA-AZ-6605 
"C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" 
        TCGA-AZ-6606         TCGA-AZ-6607         TCGA-AZ-6608 
"C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" 
        TCGA-CA-5254         TCGA-CA-5255         TCGA-CA-5796 
"C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" 
        TCGA-CA-5797         TCGA-CA-6715         TCGA-CA-6716 
"C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" 
        TCGA-CA-6717         TCGA-CA-6718         TCGA-CA-6719 
"C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" 
        TCGA-CK-4947         TCGA-CK-4948         TCGA-CK-4950 
"C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" 
        TCGA-CK-4952         TCGA-CK-5912         TCGA-CK-5913 
"C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" 
        TCGA-CK-5914         TCGA-CK-5915         TCGA-CK-6747 
"C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" 
        TCGA-CK-6748         TCGA-CK-6751         TCGA-CM-4743 
"C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" 
        TCGA-CM-4744         TCGA-CM-4746         TCGA-CM-4747 
"C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" 
        TCGA-CM-4752         TCGA-CM-5341         TCGA-CM-5344 
"C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" 
        TCGA-CM-5348         TCGA-CM-5349         TCGA-CM-5860 
"C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" 
        TCGA-CM-5861         TCGA-CM-5862         TCGA-CM-5863 
"C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" 
        TCGA-CM-5864         TCGA-CM-5868         TCGA-CM-6161 
"C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" 
        TCGA-CM-6162         TCGA-CM-6163         TCGA-CM-6164 
"C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" 
        TCGA-CM-6165         TCGA-CM-6166         TCGA-CM-6167 
"C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" 
        TCGA-CM-6168         TCGA-CM-6169         TCGA-CM-6170 
"C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" 
        TCGA-CM-6171         TCGA-CM-6172         TCGA-CM-6674 
"C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" 
        TCGA-CM-6675         TCGA-CM-6676         TCGA-CM-6677 
"C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" 
        TCGA-CM-6678         TCGA-CM-6679         TCGA-CM-6680 
"C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" 
        TCGA-D5-5537         TCGA-D5-5538         TCGA-D5-5539 
"C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" 
        TCGA-D5-5540         TCGA-D5-5541         TCGA-D5-6529 
"C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" 
        TCGA-D5-6532         TCGA-D5-6533         TCGA-D5-6534 
"C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" 
        TCGA-D5-6535         TCGA-D5-6536         TCGA-D5-6537 
"C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" 
        TCGA-D5-6538         TCGA-D5-6539         TCGA-D5-6540 
"C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" 
        TCGA-D5-6541         TCGA-D5-6898         TCGA-D5-6920 
"C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" 
        TCGA-D5-6922         TCGA-D5-6923         TCGA-D5-6924 
"C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" 
        TCGA-D5-6926         TCGA-D5-6927         TCGA-D5-6928 
"C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" 
        TCGA-D5-6929         TCGA-D5-6930         TCGA-D5-6931 
"C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" 
        TCGA-D5-6932         TCGA-D5-7000         TCGA-DM-A0X9 
"C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" 
        TCGA-DM-A0XD         TCGA-DM-A0XF         TCGA-DM-A1D0 
"C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" 
        TCGA-DM-A1D4         TCGA-DM-A1D6         TCGA-DM-A1D7 
"C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" 
        TCGA-DM-A1D8         TCGA-DM-A1D9         TCGA-DM-A1DA 
"C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" 
        TCGA-DM-A1DB         TCGA-DM-A1HA         TCGA-DM-A1HB 
"C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" 
        TCGA-DM-A282         TCGA-DM-A285         TCGA-DM-A28C 
"C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" 
        TCGA-DM-A28E         TCGA-DM-A28F         TCGA-DM-A28G 
"C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" 
        TCGA-DM-A28H         TCGA-DM-A28K         TCGA-F4-6459 
"C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" 
        TCGA-F4-6460         TCGA-F4-6569         TCGA-F4-6570 
"C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" 
        TCGA-F4-6703         TCGA-F4-6704         TCGA-F4-6805 
"C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" 
        TCGA-F4-6806         TCGA-F4-6807         TCGA-F4-6808 
"C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" 
        TCGA-F4-6809         TCGA-F4-6854         TCGA-F4-6855 
"C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" 
        TCGA-F4-6856         TCGA-G4-6293         TCGA-G4-6299 
"C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" 
        TCGA-G4-6303         TCGA-G4-6304         TCGA-G4-6306 
"C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" 
        TCGA-G4-6307         TCGA-G4-6309         TCGA-G4-6310 
"C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" 
        TCGA-G4-6315         TCGA-G4-6317         TCGA-G4-6321 
"C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" 
        TCGA-G4-6323         TCGA-G4-6586         TCGA-G4-6588 
"C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" 
        TCGA-G4-6625         TCGA-G4-6626         TCGA-G4-6628 
"C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2691 
"C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" 
        TCGA-AF-2692         TCGA-AF-2693         TCGA-AF-3400 
"C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" 
        TCGA-AF-3913         TCGA-AF-4110         TCGA-AF-5654 
"C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" 
        TCGA-AF-6136         TCGA-AF-6655         TCGA-AF-6672 
"C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6549 
"C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" 
        TCGA-AH-6643         TCGA-AH-6644         TCGA-CI-6619 
"C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" 
        TCGA-CI-6620         TCGA-CI-6621         TCGA-CI-6622 
"C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" 
        TCGA-CI-6624         TCGA-CL-5917         TCGA-CL-5918 
"C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" 
        TCGA-DC-5337         TCGA-DC-5869         TCGA-DC-6155 
"C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" 
        TCGA-DC-6157         TCGA-DC-6158         TCGA-DC-6160 
"C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" 
        TCGA-DC-6681         TCGA-DC-6682         TCGA-DC-6683 
"C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" 
        TCGA-DT-5265         TCGA-DY-A0XA         TCGA-DY-A1DC 
"C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" 
        TCGA-DY-A1DD         TCGA-DY-A1DF         TCGA-DY-A1DG 
"C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" 
        TCGA-DY-A1H8         TCGA-EF-5830         TCGA-EI-6506 
"C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6510 
"C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" 
        TCGA-F5-6464         TCGA-F5-6465         TCGA-F5-6571 
"C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6811         TCGA-F5-6812 
"C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" 
        TCGA-F5-6813         TCGA-G5-6235         TCGA-G5-6641 
"C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" "C14ORF50 WILD-TYPE" 

Clustering(1114) Variable = KCNG4 MUTATION ANALYSIS
D1114V1, survival
                 sevent
clus2               0   1
  KCNG4 MUTATED     6   3
  KCNG4 WILD-TYPE 372  90
  KCNG4 MUTATED KCNG4 WILD-TYPE 
              9             462 
  KCNG4 MUTATED KCNG4 WILD-TYPE 
              3              90 
$`KCNG4 MUTATED`
TCGA-A6-5665 TCGA-AA-3941 TCGA-AA-A010 TCGA-AD-6889 TCGA-AD-6965 TCGA-D5-6536 
       22.06        24.00        34.98        56.55         0.20        17.85 
TCGA-DM-A1D4 TCGA-DM-A1D7 TCGA-DM-A285 
       92.75        13.32         6.12 

$`KCNG4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
        2.01        12.99        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 
       18.05        40.96         0.07        21.37        15.52         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AU-3779 
        0.72         5.79        22.42        27.42        10.88        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       43.27        15.12         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D6 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       49.91        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      135.65       139.17        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  KCNG4 MUTATED KCNG4 WILD-TYPE 
            0.2             0.0 
  KCNG4 MUTATED KCNG4 WILD-TYPE 
          92.75          148.01 
  KCNG4 MUTATED KCNG4 WILD-TYPE 
         22.060          20.155 
[1] "0.2 - 92.8 (22.1)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.5"
D1114V2, continuous
D1114V3, binary
                 cls
clus                0   1
  KCNG4 MUTATED    10   0
  KCNG4 WILD-TYPE 356 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNG4 MUTATED     10    0
  KCNG4 WILD-TYPE  356  119
        clus
vv       KCNG4 MUTATED KCNG4 WILD-TYPE
  COLON             10             356
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KCNG4 MUTATED         0        0        0         5         1         0
  KCNG4 WILD-TYPE      91        1       32       133         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  KCNG4 MUTATED           0          0          0          1        1         1
  KCNG4 WILD-TYPE        24         11         59         41       47        17
                 vv
clus              STAGE IVB
  KCNG4 MUTATED           0
  KCNG4 WILD-TYPE         1
D1114V4, multiclass
            clus
vv           KCNG4 MUTATED KCNG4 WILD-TYPE
  STAGE I                0              91
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              5             133
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             1              41
  STAGE IV               1              47
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  KCNG4 MUTATED     0   0   7   3
  KCNG4 WILD-TYPE  17  92 322  47
D1114V5, multiclass
    clus
vv   KCNG4 MUTATED KCNG4 WILD-TYPE
  T1             0              17
  T2             0              92
  T3             7             322
  T4             3              47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  KCNG4 MUTATED     6   1   3
  KCNG4 WILD-TYPE 281 112  84
D1114V6, multiclass
    clus
vv   KCNG4 MUTATED KCNG4 WILD-TYPE
  N0             6             281
  N1             1             112
  N2             3              84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1114V7, binary
                 cls
clus                0   1
  KCNG4 MUTATED     6   2
  KCNG4 WILD-TYPE 369  63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNG4 MUTATED      6    2
  KCNG4 WILD-TYPE  369   63
   clus
vv  KCNG4 MUTATED KCNG4 WILD-TYPE
  0             6             369
  1             2              63
[1] 2 2
[1] FALSE
D1114V8, binary
                 cls
clus                0   1
  KCNG4 MUTATED     4   6
  KCNG4 WILD-TYPE 221 258
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNG4 MUTATED      4    6
  KCNG4 WILD-TYPE  221  258
        clus
vv       KCNG4 MUTATED KCNG4 WILD-TYPE
  FEMALE             4             221
  MALE               6             258
[1] 2 2
[1] FALSE
D1114V9, binary
                 cls
clus                0   1
  KCNG4 MUTATED     4   0
  KCNG4 WILD-TYPE 346  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNG4 MUTATED      4    0
  KCNG4 WILD-TYPE  346   22
     clus
vv    KCNG4 MUTATED KCNG4 WILD-TYPE
  NO              4             346
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  KCNG4 MUTATED                      7                             2
  KCNG4 WILD-TYPE                  308                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  KCNG4 MUTATED                       0                              0
  KCNG4 WILD-TYPE                   106                             10
D1114V10, multiclass
                                clus
vv                               KCNG4 MUTATED KCNG4 WILD-TYPE
  COLON ADENOCARCINOMA                       7             308
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  KCNG4 MUTATED     5   0   0   0
  KCNG4 WILD-TYPE 340   4  31  25
D1114V11, multiclass
    clus
vv   KCNG4 MUTATED KCNG4 WILD-TYPE
  R0             5             340
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1114V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KCNG4 MUTATED                                  0     1
  KCNG4 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  KCNG4 MUTATED                           0     7
  KCNG4 WILD-TYPE                        22   219
D1114V13, multiclass
                                  clus
vv                                 KCNG4 MUTATED KCNG4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        7             219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1115) Variable = ANKRD23 MUTATION ANALYSIS
D1115V1, survival
                   sevent
clus2                 0   1
  ANKRD23 MUTATED     4   1
  ANKRD23 WILD-TYPE 374  92
  ANKRD23 MUTATED ANKRD23 WILD-TYPE 
                5               466 
  ANKRD23 MUTATED ANKRD23 WILD-TYPE 
                1                92 
$`ANKRD23 MUTATED`
TCGA-AA-3492 TCGA-CM-4743 TCGA-CM-6171 TCGA-G4-6628 TCGA-AF-2693 
        3.02        23.05        14.04        79.69        19.10 

$`ANKRD23 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 
       21.14        82.95         1.91       124.27        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 
       14.99        12.99        13.02        15.02        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       91.79        46.75        24.13        39.48        43.04        13.55 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  ANKRD23 MUTATED ANKRD23 WILD-TYPE 
             3.02              0.00 
  ANKRD23 MUTATED ANKRD23 WILD-TYPE 
            79.69            148.01 
  ANKRD23 MUTATED ANKRD23 WILD-TYPE 
           19.100            20.235 
[1] "3.0 - 79.7 (19.1)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1"  
D1115V2, continuous
D1115V3, binary
                   cls
clus                  0   1
  ANKRD23 MUTATED     4   0
  ANKRD23 WILD-TYPE 362 119
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD23 MUTATED      4    0
  ANKRD23 WILD-TYPE  362  119
        clus
vv       ANKRD23 MUTATED ANKRD23 WILD-TYPE
  COLON                4               362
  RECTUM               0               119
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ANKRD23 MUTATED         3        0        1         1         0         0
  ANKRD23 WILD-TYPE      88        1       31       137        10         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ANKRD23 MUTATED           0          0          0          0        0
  ANKRD23 WILD-TYPE        24         11         59         42       48
                   vv
clus                STAGE IVA STAGE IVB
  ANKRD23 MUTATED           0         0
  ANKRD23 WILD-TYPE        18         1
D1115V4, multiclass
            clus
vv           ANKRD23 MUTATED ANKRD23 WILD-TYPE
  STAGE I                  3                88
  STAGE IA                 0                 1
  STAGE II                 1                31
  STAGE IIA                1               137
  STAGE IIB                0                10
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               0                11
  STAGE IIIB               0                59
  STAGE IIIC               0                42
  STAGE IV                 0                48
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  ANKRD23 MUTATED     0   3   2   0
  ANKRD23 WILD-TYPE  17  89 327  50
D1115V5, multiclass
    clus
vv   ANKRD23 MUTATED ANKRD23 WILD-TYPE
  T1               0                17
  T2               3                89
  T3               2               327
  T4               0                50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  ANKRD23 MUTATED     5   0   0
  ANKRD23 WILD-TYPE 282 113  87
D1115V6, multiclass
    clus
vv   ANKRD23 MUTATED ANKRD23 WILD-TYPE
  N0               5               282
  N1               0               113
  N2               0                87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1115V7, binary
                   cls
clus                  0   1
  ANKRD23 MUTATED     4   0
  ANKRD23 WILD-TYPE 371  65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD23 MUTATED      4    0
  ANKRD23 WILD-TYPE  371   65
   clus
vv  ANKRD23 MUTATED ANKRD23 WILD-TYPE
  0               4               371
  1               0                65
[1] 2 2
[1] FALSE
D1115V8, binary
                   cls
clus                  0   1
  ANKRD23 MUTATED     2   3
  ANKRD23 WILD-TYPE 223 261
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD23 MUTATED      2    3
  ANKRD23 WILD-TYPE  223  261
        clus
vv       ANKRD23 MUTATED ANKRD23 WILD-TYPE
  FEMALE               2               223
  MALE                 3               261
[1] 2 2
[1] FALSE
D1115V9, binary
                   cls
clus                  0   1
  ANKRD23 MUTATED     5   0
  ANKRD23 WILD-TYPE 345  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD23 MUTATED      5    0
  ANKRD23 WILD-TYPE  345   22
     clus
vv    ANKRD23 MUTATED ANKRD23 WILD-TYPE
  NO                5               345
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ANKRD23 MUTATED                      4                             0
  ANKRD23 WILD-TYPE                  311                            47
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ANKRD23 MUTATED                       0                              0
  ANKRD23 WILD-TYPE                   106                             10
D1115V10, multiclass
                                clus
vv                               ANKRD23 MUTATED ANKRD23 WILD-TYPE
  COLON ADENOCARCINOMA                         4               311
  COLON MUCINOUS ADENOCARCINOMA                0                47
  RECTAL ADENOCARCINOMA                        0               106
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  ANKRD23 MUTATED     4   0   0   0
  ANKRD23 WILD-TYPE 341   4  31  25
D1115V11, multiclass
    clus
vv   ANKRD23 MUTATED ANKRD23 WILD-TYPE
  R0               4               341
  R1               0                 4
  R2               0                31
  RX               0                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1115V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ANKRD23 MUTATED                                  0     0
  ANKRD23 WILD-TYPE                                1    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  ANKRD23 MUTATED                           0     4
  ANKRD23 WILD-TYPE                        22   222
D1115V13, multiclass
                                  clus
vv                                 ANKRD23 MUTATED ANKRD23 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                      0                22
  WHITE                                          4               222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1116) Variable = KIAA0556 MUTATION ANALYSIS
D1116V1, survival
                    sevent
clus2                  0   1
  KIAA0556 MUTATED    17   4
  KIAA0556 WILD-TYPE 361  89
  KIAA0556 MUTATED KIAA0556 WILD-TYPE 
                21                450 
  KIAA0556 MUTATED KIAA0556 WILD-TYPE 
                 4                 89 
$`KIAA0556 MUTATED`
TCGA-A6-5665 TCGA-A6-6781 TCGA-AA-3520 TCGA-AA-3663 TCGA-AA-3852 TCGA-AA-3966 
       22.06        19.66        24.03         6.97         0.00         2.01 
TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A01T TCGA-AD-5900 TCGA-AD-6895 TCGA-AU-3779 
       25.02         4.01        33.04         0.07         0.72        14.50 
TCGA-AZ-4315 TCGA-AZ-5403 TCGA-AZ-6601 TCGA-CA-6717 TCGA-D5-6540 TCGA-F4-6703 
       58.39        62.79       100.01        12.76        16.14        47.87 
TCGA-F4-6856 TCGA-G4-6586 TCGA-AG-A002 
       35.31        35.80        20.98 

$`KIAA0556 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
        9.07        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02        78.08         6.05        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
       33.07        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 
       26.01        24.00         2.01        20.98        34.03        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       18.05        40.96        21.37        15.52        56.55         0.79 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-6004 
        5.79        22.42        27.42        10.88         0.20        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
       16.31         0.95        33.01        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
        5.13       106.75        22.36        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
       12.10        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       12.49        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6704 TCGA-F4-6805 
        8.61        31.96        35.74         6.18         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  KIAA0556 MUTATED KIAA0556 WILD-TYPE 
                 0                  0 
  KIAA0556 MUTATED KIAA0556 WILD-TYPE 
            100.01             148.01 
  KIAA0556 MUTATED KIAA0556 WILD-TYPE 
            20.980             20.155 
[1] "0.0 - 100.0 (21.0)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1"  
D1116V2, continuous
D1116V3, binary
                    cls
clus                   0   1
  KIAA0556 MUTATED    22   2
  KIAA0556 WILD-TYPE 344 117
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0556 MUTATED     22    2
  KIAA0556 WILD-TYPE  344  117
        clus
vv       KIAA0556 MUTATED KIAA0556 WILD-TYPE
  COLON                22                344
  RECTUM                2                117
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KIAA0556 MUTATED         5        0        4         8         1         0
  KIAA0556 WILD-TYPE      86        1       28       130         9         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIAA0556 MUTATED           3          0          0          1        0
  KIAA0556 WILD-TYPE        21         11         59         41       48
                    vv
clus                 STAGE IVA STAGE IVB
  KIAA0556 MUTATED           0         0
  KIAA0556 WILD-TYPE        18         1
D1116V4, multiclass
            clus
vv           KIAA0556 MUTATED KIAA0556 WILD-TYPE
  STAGE I                   5                 86
  STAGE IA                  0                  1
  STAGE II                  4                 28
  STAGE IIA                 8                130
  STAGE IIB                 1                  9
  STAGE IIC                 0                  1
  STAGE III                 3                 21
  STAGE IIIA                0                 11
  STAGE IIIB                0                 59
  STAGE IIIC                1                 41
  STAGE IV                  0                 48
  STAGE IVA                 0                 18
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  KIAA0556 MUTATED     0   6  16   2
  KIAA0556 WILD-TYPE  17  86 313  48
D1116V5, multiclass
    clus
vv   KIAA0556 MUTATED KIAA0556 WILD-TYPE
  T1                0                 17
  T2                6                 86
  T3               16                313
  T4                2                 48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  KIAA0556 MUTATED    19   4   1
  KIAA0556 WILD-TYPE 268 109  86
D1116V6, multiclass
    clus
vv   KIAA0556 MUTATED KIAA0556 WILD-TYPE
  N0               19                268
  N1                4                109
  N2                1                 86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1116V7, binary
                    cls
clus                   0   1
  KIAA0556 MUTATED    17   0
  KIAA0556 WILD-TYPE 358  65
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0556 MUTATED     17    0
  KIAA0556 WILD-TYPE  358   65
   clus
vv  KIAA0556 MUTATED KIAA0556 WILD-TYPE
  0               17                358
  1                0                 65
[1] 2 2
[1] FALSE
D1116V8, binary
                    cls
clus                   0   1
  KIAA0556 MUTATED     6  18
  KIAA0556 WILD-TYPE 219 246
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0556 MUTATED      6   18
  KIAA0556 WILD-TYPE  219  246
        clus
vv       KIAA0556 MUTATED KIAA0556 WILD-TYPE
  FEMALE                6                219
  MALE                 18                246
[1] 2 2
[1] FALSE
D1116V9, binary
                    cls
clus                   0   1
  KIAA0556 MUTATED    16   0
  KIAA0556 WILD-TYPE 334  22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0556 MUTATED     16    0
  KIAA0556 WILD-TYPE  334   22
     clus
vv    KIAA0556 MUTATED KIAA0556 WILD-TYPE
  NO                16                334
  YES                0                 22
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  KIAA0556 MUTATED                     14                             8
  KIAA0556 WILD-TYPE                  301                            39
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  KIAA0556 MUTATED                       2                              0
  KIAA0556 WILD-TYPE                   104                             10
D1116V10, multiclass
                                clus
vv                               KIAA0556 MUTATED KIAA0556 WILD-TYPE
  COLON ADENOCARCINOMA                         14                301
  COLON MUCINOUS ADENOCARCINOMA                 8                 39
  RECTAL ADENOCARCINOMA                         2                104
  RECTAL MUCINOUS ADENOCARCINOMA                0                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  KIAA0556 MUTATED    16   0   0   2
  KIAA0556 WILD-TYPE 329   4  31  23
D1116V11, multiclass
    clus
vv   KIAA0556 MUTATED KIAA0556 WILD-TYPE
  R0               16                329
  R1                0                  4
  R2                0                 31
  RX                2                 23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1116V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KIAA0556 MUTATED                                  0     1
  KIAA0556 WILD-TYPE                                1    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  KIAA0556 MUTATED                           0    14
  KIAA0556 WILD-TYPE                        22   212
D1116V13, multiclass
                                  clus
vv                                 KIAA0556 MUTATED KIAA0556 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                 10
  BLACK OR AFRICAN AMERICAN                       0                 22
  WHITE                                          14                212
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1117) Variable = SLC25A44 MUTATION ANALYSIS
D1117V1, survival
                    sevent
clus2                  0   1
  SLC25A44 MUTATED     5   0
  SLC25A44 WILD-TYPE 373  93
  SLC25A44 MUTATED SLC25A44 WILD-TYPE 
                 5                466 
  SLC25A44 MUTATED SLC25A44 WILD-TYPE 
                 0                 93 
$`SLC25A44 MUTATED`
TCGA-AA-3966 TCGA-AA-A01Q TCGA-CA-6715 TCGA-CM-6162 TCGA-D5-5541 
        2.01         1.02         0.07        12.00        55.92 

$`SLC25A44 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 
       24.00         2.01        20.98        34.03        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01R TCGA-AA-A01S 
       12.00        31.00        31.00        38.07        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6716 
        1.61        12.69         3.06         3.25         3.29        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       12.26        19.59        56.09        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  SLC25A44 MUTATED SLC25A44 WILD-TYPE 
              0.07               0.00 
  SLC25A44 MUTATED SLC25A44 WILD-TYPE 
             55.92             148.01 
  SLC25A44 MUTATED SLC25A44 WILD-TYPE 
             2.010             20.415 
[1] "0.1 - 55.9 (2.0)"   "0.0 - 148.0 (20.4)"
[1] "hr="     "3300000"
D1117V2, continuous
D1117V3, binary
                    cls
clus                   0   1
  SLC25A44 MUTATED     5   0
  SLC25A44 WILD-TYPE 361 119
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SLC25A44 MUTATED      5    0
  SLC25A44 WILD-TYPE  361  119
        clus
vv       SLC25A44 MUTATED SLC25A44 WILD-TYPE
  COLON                 5                361
  RECTUM                0                119
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SLC25A44 MUTATED         0        0        1         1         0         0
  SLC25A44 WILD-TYPE      91        1       31       137        10         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC25A44 MUTATED           0          0          3          0        0
  SLC25A44 WILD-TYPE        24         11         56         42       48
                    vv
clus                 STAGE IVA STAGE IVB
  SLC25A44 MUTATED           0         0
  SLC25A44 WILD-TYPE        18         1
D1117V4, multiclass
            clus
vv           SLC25A44 MUTATED SLC25A44 WILD-TYPE
  STAGE I                   0                 91
  STAGE IA                  0                  1
  STAGE II                  1                 31
  STAGE IIA                 1                137
  STAGE IIB                 0                 10
  STAGE IIC                 0                  1
  STAGE III                 0                 24
  STAGE IIIA                0                 11
  STAGE IIIB                3                 56
  STAGE IIIC                0                 42
  STAGE IV                  0                 48
  STAGE IVA                 0                 18
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  SLC25A44 MUTATED     0   0   5   0
  SLC25A44 WILD-TYPE  17  92 324  50
D1117V5, multiclass
    clus
vv   SLC25A44 MUTATED SLC25A44 WILD-TYPE
  T1                0                 17
  T2                0                 92
  T3                5                324
  T4                0                 50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  SLC25A44 MUTATED     2   3   0
  SLC25A44 WILD-TYPE 285 110  87
D1117V6, multiclass
    clus
vv   SLC25A44 MUTATED SLC25A44 WILD-TYPE
  N0                2                285
  N1                3                110
  N2                0                 87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1117V7, binary
                    cls
clus                   0   1
  SLC25A44 MUTATED     5   0
  SLC25A44 WILD-TYPE 370  65
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SLC25A44 MUTATED      5    0
  SLC25A44 WILD-TYPE  370   65
   clus
vv  SLC25A44 MUTATED SLC25A44 WILD-TYPE
  0                5                370
  1                0                 65
[1] 2 2
[1] FALSE
D1117V8, binary
                    cls
clus                   0   1
  SLC25A44 MUTATED     3   2
  SLC25A44 WILD-TYPE 222 262
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SLC25A44 MUTATED      3    2
  SLC25A44 WILD-TYPE  222  262
        clus
vv       SLC25A44 MUTATED SLC25A44 WILD-TYPE
  FEMALE                3                222
  MALE                  2                262
[1] 2 2
[1] FALSE
D1117V9, binary
                    cls
clus                   0   1
  SLC25A44 MUTATED     2   0
  SLC25A44 WILD-TYPE 348  22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SLC25A44 MUTATED      2    0
  SLC25A44 WILD-TYPE  348   22
     clus
vv    SLC25A44 MUTATED SLC25A44 WILD-TYPE
  NO                 2                348
  YES                0                 22
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SLC25A44 MUTATED                      3                             2
  SLC25A44 WILD-TYPE                  312                            45
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SLC25A44 MUTATED                       0                              0
  SLC25A44 WILD-TYPE                   106                             10
D1117V10, multiclass
                                clus
vv                               SLC25A44 MUTATED SLC25A44 WILD-TYPE
  COLON ADENOCARCINOMA                          3                312
  COLON MUCINOUS ADENOCARCINOMA                 2                 45
  RECTAL ADENOCARCINOMA                         0                106
  RECTAL MUCINOUS ADENOCARCINOMA                0                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  SLC25A44 MUTATED     3   0   0   1
  SLC25A44 WILD-TYPE 342   4  31  24
D1117V11, multiclass
    clus
vv   SLC25A44 MUTATED SLC25A44 WILD-TYPE
  R0                3                342
  R1                0                  4
  R2                0                 31
  RX                1                 24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1117V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SLC25A44 MUTATED                                  0     1
  SLC25A44 WILD-TYPE                                1    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  SLC25A44 MUTATED                           0     2
  SLC25A44 WILD-TYPE                        22   224
D1117V13, multiclass
                                  clus
vv                                 SLC25A44 MUTATED SLC25A44 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                 10
  BLACK OR AFRICAN AMERICAN                       0                 22
  WHITE                                           2                224
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1118) Variable = VPS13C MUTATION ANALYSIS
D1118V1, survival
                  sevent
clus2                0   1
  VPS13C MUTATED    24   3
  VPS13C WILD-TYPE 354  90
  VPS13C MUTATED VPS13C WILD-TYPE 
              27              444 
  VPS13C MUTATED VPS13C WILD-TYPE 
               3               90 
$`VPS13C MUTATED`
TCGA-A6-5665 TCGA-A6-6142 TCGA-A6-6781 TCGA-AA-3510 TCGA-AA-3525 TCGA-AA-3552 
       22.06        25.08        19.66        63.98         8.05        13.02 
TCGA-AA-3555 TCGA-AA-3663 TCGA-AA-3713 TCGA-AA-3864 TCGA-AA-3950 TCGA-AA-3955 
       29.95         6.97        19.04        53.00        24.00        20.98 
TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01R TCGA-AA-A03J TCGA-AD-6895 TCGA-AZ-4315 
        4.01        34.98        35.01        40.96         0.72        58.39 
TCGA-CA-6717 TCGA-CK-6747 TCGA-D5-6922 TCGA-DM-A1HB TCGA-DM-A28H TCGA-AG-3583 
       12.76        82.95         4.41       135.65       117.07        20.05 
TCGA-AG-3892 TCGA-AG-A002 TCGA-AG-A02N 
       13.02        20.98        61.97 

$`VPS13C WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6648 
       22.09        32.71        27.09        22.52         8.38        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 
       20.28         7.04         3.02         1.02        35.01         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       37.05        36.03        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 
       33.99        21.01        24.00        17.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        31.07        30.05        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01         2.01        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T 
       31.00        31.00        38.07         1.02         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       18.05         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07        12.20        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       21.14         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        3.68        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 
       12.59       140.38         7.50        44.32       131.51       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28K 
        6.12        81.37       119.93        35.97        60.79        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       36.03        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       36.95        17.03        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 
       10.98        49.97         1.94        38.96        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  VPS13C MUTATED VPS13C WILD-TYPE 
            0.72             0.00 
  VPS13C MUTATED VPS13C WILD-TYPE 
          135.65           148.01 
  VPS13C MUTATED VPS13C WILD-TYPE 
           22.06            20.02 
[1] "0.7 - 135.7 (22.1)" "0.0 - 148.0 (20.0)"
[1] "hr=" "2.4"
D1118V2, continuous
D1118V3, binary
                  cls
clus                 0   1
  VPS13C MUTATED    24   4
  VPS13C WILD-TYPE 342 115
[1] "tbl2"
                  cls
clus               [,1] [,2]
  VPS13C MUTATED     24    4
  VPS13C WILD-TYPE  342  115
        clus
vv       VPS13C MUTATED VPS13C WILD-TYPE
  COLON              24              342
  RECTUM              4              115
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  VPS13C MUTATED         3        0        4         7         2         0
  VPS13C WILD-TYPE      88        1       28       131         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  VPS13C MUTATED           1          1          3          3        2
  VPS13C WILD-TYPE        23         10         56         39       46
                  vv
clus               STAGE IVA STAGE IVB
  VPS13C MUTATED           1         0
  VPS13C WILD-TYPE        17         1
D1118V4, multiclass
            clus
vv           VPS13C MUTATED VPS13C WILD-TYPE
  STAGE I                 3               88
  STAGE IA                0                1
  STAGE II                4               28
  STAGE IIA               7              131
  STAGE IIB               2                8
  STAGE IIC               0                1
  STAGE III               1               23
  STAGE IIIA              1               10
  STAGE IIIB              3               56
  STAGE IIIC              3               39
  STAGE IV                2               46
  STAGE IVA               1               17
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  VPS13C MUTATED     1   3  21   3
  VPS13C WILD-TYPE  16  89 308  47
D1118V5, multiclass
    clus
vv   VPS13C MUTATED VPS13C WILD-TYPE
  T1              1               16
  T2              3               89
  T3             21              308
  T4              3               47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  VPS13C MUTATED    17   6   5
  VPS13C WILD-TYPE 270 107  82
D1118V6, multiclass
    clus
vv   VPS13C MUTATED VPS13C WILD-TYPE
  N0             17              270
  N1              6              107
  N2              5               82
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1118V7, binary
                  cls
clus                 0   1
  VPS13C MUTATED    22   3
  VPS13C WILD-TYPE 353  62
[1] "tbl2"
                  cls
clus               [,1] [,2]
  VPS13C MUTATED     22    3
  VPS13C WILD-TYPE  353   62
   clus
vv  VPS13C MUTATED VPS13C WILD-TYPE
  0             22              353
  1              3               62
[1] 2 2
[1] FALSE
D1118V8, binary
                  cls
clus                 0   1
  VPS13C MUTATED     9  19
  VPS13C WILD-TYPE 216 245
[1] "tbl2"
                  cls
clus               [,1] [,2]
  VPS13C MUTATED      9   19
  VPS13C WILD-TYPE  216  245
        clus
vv       VPS13C MUTATED VPS13C WILD-TYPE
  FEMALE              9              216
  MALE               19              245
[1] 2 2
[1] FALSE
D1118V9, binary
                  cls
clus                 0   1
  VPS13C MUTATED    19   2
  VPS13C WILD-TYPE 331  20
[1] "tbl2"
                  cls
clus               [,1] [,2]
  VPS13C MUTATED     19    2
  VPS13C WILD-TYPE  331   20
     clus
vv    VPS13C MUTATED VPS13C WILD-TYPE
  NO              19              331
  YES              2               20
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  VPS13C MUTATED                     17                             6
  VPS13C WILD-TYPE                  298                            41
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  VPS13C MUTATED                       3                              1
  VPS13C WILD-TYPE                   103                              9
D1118V10, multiclass
                                clus
vv                               VPS13C MUTATED VPS13C WILD-TYPE
  COLON ADENOCARCINOMA                       17              298
  COLON MUCINOUS ADENOCARCINOMA               6               41
  RECTAL ADENOCARCINOMA                       3              103
  RECTAL MUCINOUS ADENOCARCINOMA              1                9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  VPS13C MUTATED    20   0   2   2
  VPS13C WILD-TYPE 325   4  29  23
D1118V11, multiclass
    clus
vv   VPS13C MUTATED VPS13C WILD-TYPE
  R0             20              325
  R1              0                4
  R2              2               29
  RX              2               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1118V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  VPS13C MUTATED                                  0     1
  VPS13C WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  VPS13C MUTATED                           0     9
  VPS13C WILD-TYPE                        22   217
D1118V13, multiclass
                                  clus
vv                                 VPS13C MUTATED VPS13C WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         9              217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1119) Variable = PGAP3 MUTATION ANALYSIS
D1119V1, survival
                 sevent
clus2               0   1
  PGAP3 MUTATED     5   3
  PGAP3 WILD-TYPE 373  90
  PGAP3 MUTATED PGAP3 WILD-TYPE 
              8             463 
  PGAP3 MUTATED PGAP3 WILD-TYPE 
              3              90 
$`PGAP3 MUTATED`
TCGA-AA-3525 TCGA-AA-3710 TCGA-AA-3972 TCGA-AD-6895 TCGA-AZ-6598 TCGA-AZ-6601 
        8.05        26.99        50.99         0.72        49.41       100.01 
TCGA-F4-6459 TCGA-CI-6619 
        8.61         6.05 

$`PGAP3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        85.05        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 
       20.98        34.03         2.01        21.99        16.08        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.79         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 
       62.79        88.21         6.77        12.10        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6460 
      119.93        35.97        60.79       117.07        98.24        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.69         0.72        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  PGAP3 MUTATED PGAP3 WILD-TYPE 
           0.72            0.00 
  PGAP3 MUTATED PGAP3 WILD-TYPE 
         100.01          148.01 
  PGAP3 MUTATED PGAP3 WILD-TYPE 
          17.80           20.19 
[1] "0.7 - 100.0 (17.8)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.5"
D1119V2, continuous
D1119V3, binary
                 cls
clus                0   1
  PGAP3 MUTATED     7   1
  PGAP3 WILD-TYPE 359 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PGAP3 MUTATED      7    1
  PGAP3 WILD-TYPE  359  118
        clus
vv       PGAP3 MUTATED PGAP3 WILD-TYPE
  COLON              7             359
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PGAP3 MUTATED         0        0        2         1         0         0
  PGAP3 WILD-TYPE      91        1       30       137        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PGAP3 MUTATED           0          0          2          0        2         0
  PGAP3 WILD-TYPE        24         11         57         42       46        18
                 vv
clus              STAGE IVB
  PGAP3 MUTATED           0
  PGAP3 WILD-TYPE         1
D1119V4, multiclass
            clus
vv           PGAP3 MUTATED PGAP3 WILD-TYPE
  STAGE I                0              91
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA              1             137
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             2              57
  STAGE IIIC             0              42
  STAGE IV               2              46
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PGAP3 MUTATED     0   0   8   0
  PGAP3 WILD-TYPE  17  92 321  50
D1119V5, multiclass
    clus
vv   PGAP3 MUTATED PGAP3 WILD-TYPE
  T1             0              17
  T2             0              92
  T3             8             321
  T4             0              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  PGAP3 MUTATED     3   4   1
  PGAP3 WILD-TYPE 284 109  86
D1119V6, multiclass
    clus
vv   PGAP3 MUTATED PGAP3 WILD-TYPE
  N0             3             284
  N1             4             109
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1119V7, binary
                 cls
clus                0   1
  PGAP3 MUTATED     4   2
  PGAP3 WILD-TYPE 371  63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PGAP3 MUTATED      4    2
  PGAP3 WILD-TYPE  371   63
   clus
vv  PGAP3 MUTATED PGAP3 WILD-TYPE
  0             4             371
  1             2              63
[1] 2 2
[1] FALSE
D1119V8, binary
                 cls
clus                0   1
  PGAP3 MUTATED     3   5
  PGAP3 WILD-TYPE 222 259
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PGAP3 MUTATED      3    5
  PGAP3 WILD-TYPE  222  259
        clus
vv       PGAP3 MUTATED PGAP3 WILD-TYPE
  FEMALE             3             222
  MALE               5             259
[1] 2 2
[1] FALSE
D1119V9, binary
                 cls
clus                0   1
  PGAP3 MUTATED     6   0
  PGAP3 WILD-TYPE 344  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PGAP3 MUTATED      6    0
  PGAP3 WILD-TYPE  344   22
     clus
vv    PGAP3 MUTATED PGAP3 WILD-TYPE
  NO              6             344
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PGAP3 MUTATED                      7                             0
  PGAP3 WILD-TYPE                  308                            47
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PGAP3 MUTATED                       1                              0
  PGAP3 WILD-TYPE                   105                             10
D1119V10, multiclass
                                clus
vv                               PGAP3 MUTATED PGAP3 WILD-TYPE
  COLON ADENOCARCINOMA                       7             308
  COLON MUCINOUS ADENOCARCINOMA              0              47
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  PGAP3 MUTATED     3   0   1   0
  PGAP3 WILD-TYPE 342   4  30  25
D1119V11, multiclass
    clus
vv   PGAP3 MUTATED PGAP3 WILD-TYPE
  R0             3             342
  R1             0               4
  R2             1              30
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1119V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PGAP3 MUTATED                                  0     0
  PGAP3 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PGAP3 MUTATED                           0     5
  PGAP3 WILD-TYPE                        22   221
D1119V13, multiclass
                                  clus
vv                                 PGAP3 MUTATED PGAP3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        5             221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1120) Variable = PARP1 MUTATION ANALYSIS
D1120V1, survival
                 sevent
clus2               0   1
  PARP1 MUTATED    13   1
  PARP1 WILD-TYPE 365  92
  PARP1 MUTATED PARP1 WILD-TYPE 
             14             457 
  PARP1 MUTATED PARP1 WILD-TYPE 
              1              92 
$`PARP1 MUTATED`
TCGA-A6-5662 TCGA-A6-5665 TCGA-AA-3949 TCGA-AA-A010 TCGA-AA-A01R TCGA-AA-A03F 
       23.61        22.06        26.01        34.98        35.01        18.05 
TCGA-AZ-4315 TCGA-CA-6717 TCGA-CK-4947 TCGA-CM-5861 TCGA-CM-6676 TCGA-DM-A1HB 
       58.39        12.76        17.56        15.02        11.08       135.65 
TCGA-F4-6704 TCGA-EI-6507 
        1.55        19.96 

$`PARP1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        33.53        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       12.99        24.00        33.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
       38.07         1.02         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03J TCGA-AD-5900 
       14.01         0.92        41.00        39.98        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
       16.31         0.95        33.01        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-4950 
        0.07        12.20        10.06        14.30       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
        7.50        44.32       131.51       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 
       31.96        35.74         6.18        47.87        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
        0.49        20.55        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  PARP1 MUTATED PARP1 WILD-TYPE 
           1.55            0.00 
  PARP1 MUTATED PARP1 WILD-TYPE 
         135.65          148.01 
  PARP1 MUTATED PARP1 WILD-TYPE 
          21.01           20.19 
[1] "1.6 - 135.7 (21.0)" "0.0 - 148.0 (20.2)"
[1] "hr=" "3"  
D1120V2, continuous
D1120V3, binary
                 cls
clus                0   1
  PARP1 MUTATED    14   1
  PARP1 WILD-TYPE 352 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PARP1 MUTATED     14    1
  PARP1 WILD-TYPE  352  118
        clus
vv       PARP1 MUTATED PARP1 WILD-TYPE
  COLON             14             352
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PARP1 MUTATED         1        0        0         5         1         0
  PARP1 WILD-TYPE      90        1       32       133         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PARP1 MUTATED           2          0          3          2        0         1
  PARP1 WILD-TYPE        22         11         56         40       48        17
                 vv
clus              STAGE IVB
  PARP1 MUTATED           0
  PARP1 WILD-TYPE         1
D1120V4, multiclass
            clus
vv           PARP1 MUTATED PARP1 WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              5             133
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              2              22
  STAGE IIIA             0              11
  STAGE IIIB             3              56
  STAGE IIIC             2              40
  STAGE IV               0              48
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PARP1 MUTATED     0   1  12   2
  PARP1 WILD-TYPE  17  91 317  48
D1120V5, multiclass
    clus
vv   PARP1 MUTATED PARP1 WILD-TYPE
  T1             0              17
  T2             1              91
  T3            12             317
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  PARP1 MUTATED     7   3   5
  PARP1 WILD-TYPE 280 110  82
D1120V6, multiclass
    clus
vv   PARP1 MUTATED PARP1 WILD-TYPE
  N0             7             280
  N1             3             110
  N2             5              82
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1120V7, binary
                 cls
clus                0   1
  PARP1 MUTATED    12   1
  PARP1 WILD-TYPE 363  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PARP1 MUTATED     12    1
  PARP1 WILD-TYPE  363   64
   clus
vv  PARP1 MUTATED PARP1 WILD-TYPE
  0            12             363
  1             1              64
[1] 2 2
[1] FALSE
D1120V8, binary
                 cls
clus                0   1
  PARP1 MUTATED     6   9
  PARP1 WILD-TYPE 219 255
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PARP1 MUTATED      6    9
  PARP1 WILD-TYPE  219  255
        clus
vv       PARP1 MUTATED PARP1 WILD-TYPE
  FEMALE             6             219
  MALE               9             255
[1] 2 2
[1] FALSE
D1120V9, binary
                 cls
clus                0   1
  PARP1 MUTATED    10   1
  PARP1 WILD-TYPE 340  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PARP1 MUTATED     10    1
  PARP1 WILD-TYPE  340   21
     clus
vv    PARP1 MUTATED PARP1 WILD-TYPE
  NO             10             340
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PARP1 MUTATED                      7                             6
  PARP1 WILD-TYPE                  308                            41
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PARP1 MUTATED                       1                              0
  PARP1 WILD-TYPE                   105                             10
D1120V10, multiclass
                                clus
vv                               PARP1 MUTATED PARP1 WILD-TYPE
  COLON ADENOCARCINOMA                       7             308
  COLON MUCINOUS ADENOCARCINOMA              6              41
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  PARP1 MUTATED    11   0   0   2
  PARP1 WILD-TYPE 334   4  31  23
D1120V11, multiclass
    clus
vv   PARP1 MUTATED PARP1 WILD-TYPE
  R0            11             334
  R1             0               4
  R2             0              31
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1120V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PARP1 MUTATED                                  1     1
  PARP1 WILD-TYPE                                0    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PARP1 MUTATED                           0     9
  PARP1 WILD-TYPE                        22   217
D1120V13, multiclass
                                  clus
vv                                 PARP1 MUTATED PARP1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             1               0
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        9             217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1121) Variable = EPC1 MUTATION ANALYSIS
D1121V1, survival
                sevent
clus2              0   1
  EPC1 MUTATED     7   6
  EPC1 WILD-TYPE 371  87
  EPC1 MUTATED EPC1 WILD-TYPE 
            13            458 
  EPC1 MUTATED EPC1 WILD-TYPE 
             6             87 
$`EPC1 MUTATED`
TCGA-A6-2676 TCGA-A6-5659 TCGA-A6-6781 TCGA-AA-A010 TCGA-AZ-6598 TCGA-AZ-6599 
       42.90        30.44        19.66        34.98        49.41         6.77 
TCGA-AZ-6608 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CM-5349 TCGA-CM-5860 
        1.61        12.76        10.06        17.56        30.08        32.02 
TCGA-G4-6303 
       65.85 

$`EPC1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       31.63        29.19        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       62.79        88.21        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
       11.74         3.19        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.07        12.20        14.30       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       29.06        22.03        22.98        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
       35.31       133.18        74.56        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  EPC1 MUTATED EPC1 WILD-TYPE 
          1.61           0.00 
  EPC1 MUTATED EPC1 WILD-TYPE 
         65.85         148.01 
  EPC1 MUTATED EPC1 WILD-TYPE 
        30.080         20.155 
[1] "1.6 - 65.8 (30.1)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "2.3"
D1121V2, continuous
D1121V3, binary
                cls
clus               0   1
  EPC1 MUTATED    13   0
  EPC1 WILD-TYPE 353 119
[1] "tbl2"
                cls
clus             [,1] [,2]
  EPC1 MUTATED     13    0
  EPC1 WILD-TYPE  353  119
        clus
vv       EPC1 MUTATED EPC1 WILD-TYPE
  COLON            13            353
  RECTUM            0            119
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  EPC1 MUTATED         2        0        1         4         2         0
  EPC1 WILD-TYPE      89        1       31       134         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  EPC1 MUTATED           0          1          1          1        1         0
  EPC1 WILD-TYPE        24         10         58         41       47        18
                vv
clus             STAGE IVB
  EPC1 MUTATED           0
  EPC1 WILD-TYPE         1
D1121V4, multiclass
            clus
vv           EPC1 MUTATED EPC1 WILD-TYPE
  STAGE I               2             89
  STAGE IA              0              1
  STAGE II              1             31
  STAGE IIA             4            134
  STAGE IIB             2              8
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            1             10
  STAGE IIIB            1             58
  STAGE IIIC            1             41
  STAGE IV              1             47
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  EPC1 MUTATED     0   3   6   4
  EPC1 WILD-TYPE  17  89 323  46
D1121V5, multiclass
    clus
vv   EPC1 MUTATED EPC1 WILD-TYPE
  T1            0             17
  T2            3             89
  T3            6            323
  T4            4             46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  EPC1 MUTATED     9   4   0
  EPC1 WILD-TYPE 278 109  87
D1121V6, multiclass
    clus
vv   EPC1 MUTATED EPC1 WILD-TYPE
  N0            9            278
  N1            4            109
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1121V7, binary
                cls
clus               0   1
  EPC1 MUTATED     9   1
  EPC1 WILD-TYPE 366  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  EPC1 MUTATED      9    1
  EPC1 WILD-TYPE  366   64
   clus
vv  EPC1 MUTATED EPC1 WILD-TYPE
  0            9            366
  1            1             64
[1] 2 2
[1] FALSE
D1121V8, binary
                cls
clus               0   1
  EPC1 MUTATED     7   6
  EPC1 WILD-TYPE 218 258
[1] "tbl2"
                cls
clus             [,1] [,2]
  EPC1 MUTATED      7    6
  EPC1 WILD-TYPE  218  258
        clus
vv       EPC1 MUTATED EPC1 WILD-TYPE
  FEMALE            7            218
  MALE              6            258
[1] 2 2
[1] FALSE
D1121V9, binary
                cls
clus               0   1
  EPC1 MUTATED    13   0
  EPC1 WILD-TYPE 337  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  EPC1 MUTATED     13    0
  EPC1 WILD-TYPE  337   22
     clus
vv    EPC1 MUTATED EPC1 WILD-TYPE
  NO            13            337
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  EPC1 MUTATED                     11                             2
  EPC1 WILD-TYPE                  304                            45
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  EPC1 MUTATED                       0                              0
  EPC1 WILD-TYPE                   106                             10
D1121V10, multiclass
                                clus
vv                               EPC1 MUTATED EPC1 WILD-TYPE
  COLON ADENOCARCINOMA                     11            304
  COLON MUCINOUS ADENOCARCINOMA             2             45
  RECTAL ADENOCARCINOMA                     0            106
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  EPC1 MUTATED     7   0   0   3
  EPC1 WILD-TYPE 338   4  31  22
D1121V11, multiclass
    clus
vv   EPC1 MUTATED EPC1 WILD-TYPE
  R0            7            338
  R1            0              4
  R2            0             31
  RX            3             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1121V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  EPC1 MUTATED                                  0     2
  EPC1 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  EPC1 MUTATED                           0    10
  EPC1 WILD-TYPE                        22   216
D1121V13, multiclass
                                  clus
vv                                 EPC1 MUTATED EPC1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              9
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                      10            216
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1122) Variable = ST6GALNAC3 MUTATION ANALYSIS
D1122V1, survival
                      sevent
clus2                    0   1
  ST6GALNAC3 MUTATED    10   3
  ST6GALNAC3 WILD-TYPE 368  90
  ST6GALNAC3 MUTATED ST6GALNAC3 WILD-TYPE 
                  13                  458 
  ST6GALNAC3 MUTATED ST6GALNAC3 WILD-TYPE 
                   3                   90 
$`ST6GALNAC3 MUTATED`
TCGA-A6-5665 TCGA-A6-6142 TCGA-A6-6652 TCGA-AA-A00N TCGA-AA-A01P TCGA-CA-6717 
       22.06        25.08        24.69         4.01        38.07        12.76 
TCGA-CA-6718 TCGA-CM-5348 TCGA-CM-6167 TCGA-CM-6674 TCGA-D5-6532 TCGA-D5-6540 
       10.06        22.98        14.99        12.95        18.25        16.14 
TCGA-AG-A002 
       20.98 

$`ST6GALNAC3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6648 
       22.09        32.71        27.09        22.52         8.38        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       24.16        21.76        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 
        3.25         3.29         0.07        12.20        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5349 
       37.02        25.02        13.02        29.06        22.03        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6675 
       12.99        13.02        15.02        14.04        11.01        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6533 
       12.26        19.59        56.09        55.92        20.19         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  ST6GALNAC3 MUTATED ST6GALNAC3 WILD-TYPE 
                4.01                 0.00 
  ST6GALNAC3 MUTATED ST6GALNAC3 WILD-TYPE 
               38.07               148.01 
  ST6GALNAC3 MUTATED ST6GALNAC3 WILD-TYPE 
              18.250               20.235 
[1] "4.0 - 38.1 (18.2)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.7"
D1122V2, continuous
D1122V3, binary
                      cls
clus                     0   1
  ST6GALNAC3 MUTATED    12   1
  ST6GALNAC3 WILD-TYPE 354 118
[1] "tbl2"
                      cls
clus                   [,1] [,2]
  ST6GALNAC3 MUTATED     12    1
  ST6GALNAC3 WILD-TYPE  354  118
        clus
vv       ST6GALNAC3 MUTATED ST6GALNAC3 WILD-TYPE
  COLON                  12                  354
  RECTUM                  1                  118
[1] 2 2
[1] FALSE
                      vv
clus                   STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ST6GALNAC3 MUTATED         2        0        0         5         1         0
  ST6GALNAC3 WILD-TYPE      89        1       32       133         9         1
                      vv
clus                   STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ST6GALNAC3 MUTATED           1          0          1          1        0
  ST6GALNAC3 WILD-TYPE        23         11         58         41       48
                      vv
clus                   STAGE IVA STAGE IVB
  ST6GALNAC3 MUTATED           2         0
  ST6GALNAC3 WILD-TYPE        16         1
D1122V4, multiclass
            clus
vv           ST6GALNAC3 MUTATED ST6GALNAC3 WILD-TYPE
  STAGE I                     2                   89
  STAGE IA                    0                    1
  STAGE II                    0                   32
  STAGE IIA                   5                  133
  STAGE IIB                   1                    9
  STAGE IIC                   0                    1
  STAGE III                   1                   23
  STAGE IIIA                  0                   11
  STAGE IIIB                  1                   58
  STAGE IIIC                  1                   41
  STAGE IV                    0                   48
  STAGE IVA                   2                   16
  STAGE IVB                   0                    1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                      vv
clus                    T1  T2  T3  T4
  ST6GALNAC3 MUTATED     0   2  10   1
  ST6GALNAC3 WILD-TYPE  17  90 319  49
D1122V5, multiclass
    clus
vv   ST6GALNAC3 MUTATED ST6GALNAC3 WILD-TYPE
  T1                  0                   17
  T2                  2                   90
  T3                 10                  319
  T4                  1                   49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                      vv
clus                    N0  N1  N2
  ST6GALNAC3 MUTATED     9   3   1
  ST6GALNAC3 WILD-TYPE 278 110  86
D1122V6, multiclass
    clus
vv   ST6GALNAC3 MUTATED ST6GALNAC3 WILD-TYPE
  N0                  9                  278
  N1                  3                  110
  N2                  1                   86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1122V7, binary
                      cls
clus                     0   1
  ST6GALNAC3 MUTATED    11   2
  ST6GALNAC3 WILD-TYPE 364  63
[1] "tbl2"
                      cls
clus                   [,1] [,2]
  ST6GALNAC3 MUTATED     11    2
  ST6GALNAC3 WILD-TYPE  364   63
   clus
vv  ST6GALNAC3 MUTATED ST6GALNAC3 WILD-TYPE
  0                 11                  364
  1                  2                   63
[1] 2 2
[1] FALSE
D1122V8, binary
                      cls
clus                     0   1
  ST6GALNAC3 MUTATED     4   9
  ST6GALNAC3 WILD-TYPE 221 255
[1] "tbl2"
                      cls
clus                   [,1] [,2]
  ST6GALNAC3 MUTATED      4    9
  ST6GALNAC3 WILD-TYPE  221  255
        clus
vv       ST6GALNAC3 MUTATED ST6GALNAC3 WILD-TYPE
  FEMALE                  4                  221
  MALE                    9                  255
[1] 2 2
[1] FALSE
D1122V9, binary
                      cls
clus                     0   1
  ST6GALNAC3 MUTATED    12   0
  ST6GALNAC3 WILD-TYPE 338  22
[1] "tbl2"
                      cls
clus                   [,1] [,2]
  ST6GALNAC3 MUTATED     12    0
  ST6GALNAC3 WILD-TYPE  338   22
     clus
vv    ST6GALNAC3 MUTATED ST6GALNAC3 WILD-TYPE
  NO                  12                  338
  YES                  0                   22
[1] 2 2
[1] FALSE
                      vv
clus                   COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ST6GALNAC3 MUTATED                      9                             3
  ST6GALNAC3 WILD-TYPE                  306                            44
                      vv
clus                   RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ST6GALNAC3 MUTATED                       1                              0
  ST6GALNAC3 WILD-TYPE                   105                             10
D1122V10, multiclass
                                clus
vv                               ST6GALNAC3 MUTATED ST6GALNAC3 WILD-TYPE
  COLON ADENOCARCINOMA                            9                  306
  COLON MUCINOUS ADENOCARCINOMA                   3                   44
  RECTAL ADENOCARCINOMA                           1                  105
  RECTAL MUCINOUS ADENOCARCINOMA                  0                   10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                      vv
clus                    R0  R1  R2  RX
  ST6GALNAC3 MUTATED     9   0   0   2
  ST6GALNAC3 WILD-TYPE 336   4  31  23
D1122V11, multiclass
    clus
vv   ST6GALNAC3 MUTATED ST6GALNAC3 WILD-TYPE
  R0                  9                  336
  R1                  0                    4
  R2                  0                   31
  RX                  2                   23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1122V12, continuous
                      vv
clus                   AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ST6GALNAC3 MUTATED                                  0     2
  ST6GALNAC3 WILD-TYPE                                1     9
                      vv
clus                   BLACK OR AFRICAN AMERICAN WHITE
  ST6GALNAC3 MUTATED                           2     6
  ST6GALNAC3 WILD-TYPE                        20   220
D1122V13, multiclass
                                  clus
vv                                 ST6GALNAC3 MUTATED ST6GALNAC3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                  0                    1
  ASIAN                                             2                    9
  BLACK OR AFRICAN AMERICAN                         2                   20
  WHITE                                             6                  220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1123) Variable = BRSK1 MUTATION ANALYSIS
D1123V1, survival
                 sevent
clus2               0   1
  BRSK1 MUTATED    11   7
  BRSK1 WILD-TYPE 367  86
  BRSK1 MUTATED BRSK1 WILD-TYPE 
             18             453 
  BRSK1 MUTATED BRSK1 WILD-TYPE 
              7              86 
$`BRSK1 MUTATED`
TCGA-A6-2676 TCGA-AA-3492 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3710 TCGA-AA-3715 
       42.90         3.02         6.05         6.97        26.99        19.04 
TCGA-AA-3811 TCGA-AA-3821 TCGA-AA-3848 TCGA-AA-3977 TCGA-AA-A00J TCGA-AZ-6598 
       10.06         1.02        10.06        25.02        18.05        49.41 
TCGA-AZ-6599 TCGA-CM-6676 TCGA-D5-6536 TCGA-G4-6307 TCGA-G4-6588 TCGA-CI-6622 
        6.77        11.08        17.85        55.04        26.17         6.97 

$`BRSK1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 
       20.12        19.66        20.28         7.04         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 
       13.94        19.99        61.02        78.08        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3713 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 
       19.04        35.05        33.04         0.99        25.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       88.21        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       11.01        12.95        13.05        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 
       20.19        18.25         1.32        43.27        15.12         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       65.85        53.62        44.68        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        35.80        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  BRSK1 MUTATED BRSK1 WILD-TYPE 
           1.02            0.00 
  BRSK1 MUTATED BRSK1 WILD-TYPE 
          55.04          148.01 
  BRSK1 MUTATED BRSK1 WILD-TYPE 
         14.465          20.910 
[1] "1.0 - 55.0 (14.5)"  "0.0 - 148.0 (20.9)"
[1] "hr=" "2.7"
D1123V2, continuous
D1123V3, binary
                 cls
clus                0   1
  BRSK1 MUTATED    17   1
  BRSK1 WILD-TYPE 349 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BRSK1 MUTATED     17    1
  BRSK1 WILD-TYPE  349  118
        clus
vv       BRSK1 MUTATED BRSK1 WILD-TYPE
  COLON             17             349
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  BRSK1 MUTATED         3        0        4         3         2         0
  BRSK1 WILD-TYPE      88        1       28       135         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  BRSK1 MUTATED           1          0          2          1        1         0
  BRSK1 WILD-TYPE        23         11         57         41       47        18
                 vv
clus              STAGE IVB
  BRSK1 MUTATED           0
  BRSK1 WILD-TYPE         1
D1123V4, multiclass
            clus
vv           BRSK1 MUTATED BRSK1 WILD-TYPE
  STAGE I                3              88
  STAGE IA               0               1
  STAGE II               4              28
  STAGE IIA              3             135
  STAGE IIB              2               8
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             2              57
  STAGE IIIC             1              41
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  BRSK1 MUTATED     0   4  10   4
  BRSK1 WILD-TYPE  17  88 319  46
D1123V5, multiclass
    clus
vv   BRSK1 MUTATED BRSK1 WILD-TYPE
  T1             0              17
  T2             4              88
  T3            10             319
  T4             4              46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  BRSK1 MUTATED    13   2   3
  BRSK1 WILD-TYPE 274 111  84
D1123V6, multiclass
    clus
vv   BRSK1 MUTATED BRSK1 WILD-TYPE
  N0            13             274
  N1             2             111
  N2             3              84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1123V7, binary
                 cls
clus                0   1
  BRSK1 MUTATED    14   1
  BRSK1 WILD-TYPE 361  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BRSK1 MUTATED     14    1
  BRSK1 WILD-TYPE  361   64
   clus
vv  BRSK1 MUTATED BRSK1 WILD-TYPE
  0            14             361
  1             1              64
[1] 2 2
[1] FALSE
D1123V8, binary
                 cls
clus                0   1
  BRSK1 MUTATED    10   8
  BRSK1 WILD-TYPE 215 256
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BRSK1 MUTATED     10    8
  BRSK1 WILD-TYPE  215  256
        clus
vv       BRSK1 MUTATED BRSK1 WILD-TYPE
  FEMALE            10             215
  MALE               8             256
[1] 2 2
[1] FALSE
D1123V9, binary
                 cls
clus                0   1
  BRSK1 MUTATED    17   0
  BRSK1 WILD-TYPE 333  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BRSK1 MUTATED     17    0
  BRSK1 WILD-TYPE  333   22
     clus
vv    BRSK1 MUTATED BRSK1 WILD-TYPE
  NO             17             333
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  BRSK1 MUTATED                     15                             2
  BRSK1 WILD-TYPE                  300                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  BRSK1 MUTATED                       1                              0
  BRSK1 WILD-TYPE                   105                             10
D1123V10, multiclass
                                clus
vv                               BRSK1 MUTATED BRSK1 WILD-TYPE
  COLON ADENOCARCINOMA                      15             300
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  BRSK1 MUTATED    13   0   1   0
  BRSK1 WILD-TYPE 332   4  30  25
D1123V11, multiclass
    clus
vv   BRSK1 MUTATED BRSK1 WILD-TYPE
  R0            13             332
  R1             0               4
  R2             1              30
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1123V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  BRSK1 MUTATED                                  0     0
  BRSK1 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  BRSK1 MUTATED                           0     8
  BRSK1 WILD-TYPE                        22   218
D1123V13, multiclass
                                  clus
vv                                 BRSK1 MUTATED BRSK1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        8             218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1124) Variable = FAM91A1 MUTATION ANALYSIS
D1124V1, survival
                   sevent
clus2                 0   1
  FAM91A1 MUTATED     7   5
  FAM91A1 WILD-TYPE 371  88
  FAM91A1 MUTATED FAM91A1 WILD-TYPE 
               12               459 
  FAM91A1 MUTATED FAM91A1 WILD-TYPE 
                5                88 
$`FAM91A1 MUTATED`
TCGA-A6-4105 TCGA-AA-3815 TCGA-AA-A010 TCGA-AD-6889 TCGA-AD-6964 TCGA-AZ-4315 
       14.53        33.04        34.98        56.55        10.88        58.39 
TCGA-AZ-6599 TCGA-CA-6717 TCGA-D5-6532 TCGA-DM-A1D4 TCGA-AG-A002 TCGA-DY-A1DF 
        6.77        12.76        18.25        92.75        20.98        24.13 

$`FAM91A1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 
       16.57        34.65        33.34        32.75        36.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       10.06        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 
       18.05        40.96         0.07        21.37        15.52         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
        0.72         5.79        22.42        27.42         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       49.41        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07        12.20        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       20.19         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       24.43        38.20       130.65        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DG 
        5.03         5.29       126.44        41.36        57.24        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  FAM91A1 MUTATED FAM91A1 WILD-TYPE 
             6.77              0.00 
  FAM91A1 MUTATED FAM91A1 WILD-TYPE 
            92.75            148.01 
  FAM91A1 MUTATED FAM91A1 WILD-TYPE 
           22.555            20.120 
[1] "6.8 - 92.8 (22.6)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.8"
D1124V2, continuous
D1124V3, binary
                   cls
clus                  0   1
  FAM91A1 MUTATED    10   2
  FAM91A1 WILD-TYPE 356 117
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM91A1 MUTATED     10    2
  FAM91A1 WILD-TYPE  356  117
        clus
vv       FAM91A1 MUTATED FAM91A1 WILD-TYPE
  COLON               10               356
  RECTUM               2               117
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FAM91A1 MUTATED         2        0        0         7         1         0
  FAM91A1 WILD-TYPE      89        1       32       131         9         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FAM91A1 MUTATED           0          0          0          1        0
  FAM91A1 WILD-TYPE        24         11         59         41       48
                   vv
clus                STAGE IVA STAGE IVB
  FAM91A1 MUTATED           0         0
  FAM91A1 WILD-TYPE        18         1
D1124V4, multiclass
            clus
vv           FAM91A1 MUTATED FAM91A1 WILD-TYPE
  STAGE I                  2                89
  STAGE IA                 0                 1
  STAGE II                 0                32
  STAGE IIA                7               131
  STAGE IIB                1                 9
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               0                11
  STAGE IIIB               0                59
  STAGE IIIC               1                41
  STAGE IV                 0                48
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  FAM91A1 MUTATED     0   2   8   2
  FAM91A1 WILD-TYPE  17  90 321  48
D1124V5, multiclass
    clus
vv   FAM91A1 MUTATED FAM91A1 WILD-TYPE
  T1               0                17
  T2               2                90
  T3               8               321
  T4               2                48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  FAM91A1 MUTATED    10   0   2
  FAM91A1 WILD-TYPE 277 113  85
D1124V6, multiclass
    clus
vv   FAM91A1 MUTATED FAM91A1 WILD-TYPE
  N0              10               277
  N1               0               113
  N2               2                85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1124V7, binary
                   cls
clus                  0   1
  FAM91A1 MUTATED    10   0
  FAM91A1 WILD-TYPE 365  65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM91A1 MUTATED     10    0
  FAM91A1 WILD-TYPE  365   65
   clus
vv  FAM91A1 MUTATED FAM91A1 WILD-TYPE
  0              10               365
  1               0                65
[1] 2 2
[1] FALSE
D1124V8, binary
                   cls
clus                  0   1
  FAM91A1 MUTATED     3   9
  FAM91A1 WILD-TYPE 222 255
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM91A1 MUTATED      3    9
  FAM91A1 WILD-TYPE  222  255
        clus
vv       FAM91A1 MUTATED FAM91A1 WILD-TYPE
  FEMALE               3               222
  MALE                 9               255
[1] 2 2
[1] FALSE
D1124V9, binary
                   cls
clus                  0   1
  FAM91A1 MUTATED     9   0
  FAM91A1 WILD-TYPE 341  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM91A1 MUTATED      9    0
  FAM91A1 WILD-TYPE  341   22
     clus
vv    FAM91A1 MUTATED FAM91A1 WILD-TYPE
  NO                9               341
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  FAM91A1 MUTATED                      9                             1
  FAM91A1 WILD-TYPE                  306                            46
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  FAM91A1 MUTATED                       2                              0
  FAM91A1 WILD-TYPE                   104                             10
D1124V10, multiclass
                                clus
vv                               FAM91A1 MUTATED FAM91A1 WILD-TYPE
  COLON ADENOCARCINOMA                         9               306
  COLON MUCINOUS ADENOCARCINOMA                1                46
  RECTAL ADENOCARCINOMA                        2               104
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  FAM91A1 MUTATED     5   0   0   1
  FAM91A1 WILD-TYPE 340   4  31  24
D1124V11, multiclass
    clus
vv   FAM91A1 MUTATED FAM91A1 WILD-TYPE
  R0               5               340
  R1               0                 4
  R2               0                31
  RX               1                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1124V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FAM91A1 MUTATED                                  0     2
  FAM91A1 WILD-TYPE                                1     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  FAM91A1 MUTATED                           0     7
  FAM91A1 WILD-TYPE                        22   219
D1124V13, multiclass
                                  clus
vv                                 FAM91A1 MUTATED FAM91A1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          2                 9
  BLACK OR AFRICAN AMERICAN                      0                22
  WHITE                                          7               219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1125) Variable = FAM119A MUTATION ANALYSIS
D1125V1, survival
                   sevent
clus2                 0   1
  FAM119A MUTATED     4   2
  FAM119A WILD-TYPE 374  91
  FAM119A MUTATED FAM119A WILD-TYPE 
                6               465 
  FAM119A MUTATED FAM119A WILD-TYPE 
                2                91 
$`FAM119A MUTATED`
TCGA-AA-3977 TCGA-AA-A00N TCGA-AD-6895 TCGA-AU-3779 TCGA-AZ-6599 TCGA-AG-A002 
       25.02         4.01         0.72        14.50         6.77        20.98 

$`FAM119A WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
       56.55         0.79         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
        0.20        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        88.21        49.41        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  FAM119A MUTATED FAM119A WILD-TYPE 
             0.72              0.00 
  FAM119A MUTATED FAM119A WILD-TYPE 
            25.02            148.01 
  FAM119A MUTATED FAM119A WILD-TYPE 
           10.635            20.280 
[1] "0.7 - 25.0 (10.6)"  "0.0 - 148.0 (20.3)"
[1] "hr=" "3.6"
D1125V2, continuous
D1125V3, binary
                   cls
clus                  0   1
  FAM119A MUTATED     5   1
  FAM119A WILD-TYPE 361 118
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM119A MUTATED      5    1
  FAM119A WILD-TYPE  361  118
        clus
vv       FAM119A MUTATED FAM119A WILD-TYPE
  COLON                5               361
  RECTUM               1               118
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FAM119A MUTATED         2        0        0         1         1         0
  FAM119A WILD-TYPE      89        1       32       137         9         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FAM119A MUTATED           0          0          0          0        0
  FAM119A WILD-TYPE        24         11         59         42       48
                   vv
clus                STAGE IVA STAGE IVB
  FAM119A MUTATED           0         0
  FAM119A WILD-TYPE        18         1
D1125V4, multiclass
            clus
vv           FAM119A MUTATED FAM119A WILD-TYPE
  STAGE I                  2                89
  STAGE IA                 0                 1
  STAGE II                 0                32
  STAGE IIA                1               137
  STAGE IIB                1                 9
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               0                11
  STAGE IIIB               0                59
  STAGE IIIC               0                42
  STAGE IV                 0                48
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  FAM119A MUTATED     0   3   2   1
  FAM119A WILD-TYPE  17  89 327  49
D1125V5, multiclass
    clus
vv   FAM119A MUTATED FAM119A WILD-TYPE
  T1               0                17
  T2               3                89
  T3               2               327
  T4               1                49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  FAM119A MUTATED     5   1   0
  FAM119A WILD-TYPE 282 112  87
D1125V6, multiclass
    clus
vv   FAM119A MUTATED FAM119A WILD-TYPE
  N0               5               282
  N1               1               112
  N2               0                87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1125V7, binary
                   cls
clus                  0   1
  FAM119A MUTATED     3   0
  FAM119A WILD-TYPE 372  65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM119A MUTATED      3    0
  FAM119A WILD-TYPE  372   65
   clus
vv  FAM119A MUTATED FAM119A WILD-TYPE
  0               3               372
  1               0                65
[1] 2 2
[1] FALSE
D1125V8, binary
                   cls
clus                  0   1
  FAM119A MUTATED     1   5
  FAM119A WILD-TYPE 224 259
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM119A MUTATED      1    5
  FAM119A WILD-TYPE  224  259
        clus
vv       FAM119A MUTATED FAM119A WILD-TYPE
  FEMALE               1               224
  MALE                 5               259
[1] 2 2
[1] FALSE
D1125V9, binary
                   cls
clus                  0   1
  FAM119A MUTATED     4   0
  FAM119A WILD-TYPE 346  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM119A MUTATED      4    0
  FAM119A WILD-TYPE  346   22
     clus
vv    FAM119A MUTATED FAM119A WILD-TYPE
  NO                4               346
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  FAM119A MUTATED                      4                             1
  FAM119A WILD-TYPE                  311                            46
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  FAM119A MUTATED                       1                              0
  FAM119A WILD-TYPE                   105                             10
D1125V10, multiclass
                                clus
vv                               FAM119A MUTATED FAM119A WILD-TYPE
  COLON ADENOCARCINOMA                         4               311
  COLON MUCINOUS ADENOCARCINOMA                1                46
  RECTAL ADENOCARCINOMA                        1               105
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  FAM119A MUTATED     3   0   0   0
  FAM119A WILD-TYPE 342   4  31  25
D1125V11, multiclass
    clus
vv   FAM119A MUTATED FAM119A WILD-TYPE
  R0               3               342
  R1               0                 4
  R2               0                31
  RX               0                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1125V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FAM119A MUTATED                                  0     0
  FAM119A WILD-TYPE                                1    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  FAM119A MUTATED                           0     3
  FAM119A WILD-TYPE                        22   223
D1125V13, multiclass
                                  clus
vv                                 FAM119A MUTATED FAM119A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                      0                22
  WHITE                                          3               223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1126) Variable = ZKSCAN2 MUTATION ANALYSIS
D1126V1, survival
                   sevent
clus2                 0   1
  ZKSCAN2 MUTATED    15   2
  ZKSCAN2 WILD-TYPE 363  91
  ZKSCAN2 MUTATED ZKSCAN2 WILD-TYPE 
               17               454 
  ZKSCAN2 MUTATED ZKSCAN2 WILD-TYPE 
                2                91 
$`ZKSCAN2 MUTATED`
TCGA-AA-3492 TCGA-AA-3821 TCGA-AA-3941 TCGA-AA-3966 TCGA-AA-3977 TCGA-AA-A00N 
        3.02         1.02        24.00         2.01        25.02         4.01 
TCGA-AD-6965 TCGA-AZ-4315 TCGA-CK-4947 TCGA-CM-5349 TCGA-CM-6676 TCGA-D5-6928 
        0.20        58.39        17.56        30.08        11.08        11.64 
TCGA-G4-6306 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3892 TCGA-DC-6683 
       44.68        32.98         0.99        13.02         5.03 

$`ZKSCAN2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 
       10.06        35.05        33.04         0.99        25.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       12.99        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
       34.03        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42        10.88        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        33.01        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-4950 
       12.20        12.76        10.06        14.30       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5861 
       13.02        29.06        22.03        22.98        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
       14.30         9.04         9.44         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6307 
       35.31       133.18        74.56        65.85        53.62        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3878 TCGA-AG-3881 
       19.99         7.99         0.99        37.02         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 
       19.99         1.02        17.95        36.95        17.03        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        4.01         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  ZKSCAN2 MUTATED ZKSCAN2 WILD-TYPE 
              0.2               0.0 
  ZKSCAN2 MUTATED ZKSCAN2 WILD-TYPE 
            58.39            148.01 
  ZKSCAN2 MUTATED ZKSCAN2 WILD-TYPE 
            11.64             20.73 
[1] "0.2 - 58.4 (11.6)"  "0.0 - 148.0 (20.7)"
[1] "hr=" "1.1"
D1126V2, continuous
D1126V3, binary
                   cls
clus                  0   1
  ZKSCAN2 MUTATED    13   4
  ZKSCAN2 WILD-TYPE 353 115
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZKSCAN2 MUTATED     13    4
  ZKSCAN2 WILD-TYPE  353  115
        clus
vv       ZKSCAN2 MUTATED ZKSCAN2 WILD-TYPE
  COLON               13               353
  RECTUM               4               115
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZKSCAN2 MUTATED         5        0        1         5         1         0
  ZKSCAN2 WILD-TYPE      86        1       31       133         9         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZKSCAN2 MUTATED           0          0          2          0        0
  ZKSCAN2 WILD-TYPE        24         11         57         42       48
                   vv
clus                STAGE IVA STAGE IVB
  ZKSCAN2 MUTATED           1         0
  ZKSCAN2 WILD-TYPE        17         1
D1126V4, multiclass
            clus
vv           ZKSCAN2 MUTATED ZKSCAN2 WILD-TYPE
  STAGE I                  5                86
  STAGE IA                 0                 1
  STAGE II                 1                31
  STAGE IIA                5               133
  STAGE IIB                1                 9
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               0                11
  STAGE IIIB               2                57
  STAGE IIIC               0                42
  STAGE IV                 0                48
  STAGE IVA                1                17
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  ZKSCAN2 MUTATED     2   5   6   4
  ZKSCAN2 WILD-TYPE  15  87 323  46
D1126V5, multiclass
    clus
vv   ZKSCAN2 MUTATED ZKSCAN2 WILD-TYPE
  T1               2                15
  T2               5                87
  T3               6               323
  T4               4                46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  ZKSCAN2 MUTATED    13   3   1
  ZKSCAN2 WILD-TYPE 274 110  86
D1126V6, multiclass
    clus
vv   ZKSCAN2 MUTATED ZKSCAN2 WILD-TYPE
  N0              13               274
  N1               3               110
  N2               1                86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1126V7, binary
                   cls
clus                  0   1
  ZKSCAN2 MUTATED    14   1
  ZKSCAN2 WILD-TYPE 361  64
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZKSCAN2 MUTATED     14    1
  ZKSCAN2 WILD-TYPE  361   64
   clus
vv  ZKSCAN2 MUTATED ZKSCAN2 WILD-TYPE
  0              14               361
  1               1                64
[1] 2 2
[1] FALSE
D1126V8, binary
                   cls
clus                  0   1
  ZKSCAN2 MUTATED     9   8
  ZKSCAN2 WILD-TYPE 216 256
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZKSCAN2 MUTATED      9    8
  ZKSCAN2 WILD-TYPE  216  256
        clus
vv       ZKSCAN2 MUTATED ZKSCAN2 WILD-TYPE
  FEMALE               9               216
  MALE                 8               256
[1] 2 2
[1] FALSE
D1126V9, binary
                   cls
clus                  0   1
  ZKSCAN2 MUTATED    12   0
  ZKSCAN2 WILD-TYPE 338  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZKSCAN2 MUTATED     12    0
  ZKSCAN2 WILD-TYPE  338   22
     clus
vv    ZKSCAN2 MUTATED ZKSCAN2 WILD-TYPE
  NO               12               338
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ZKSCAN2 MUTATED                      9                             4
  ZKSCAN2 WILD-TYPE                  306                            43
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ZKSCAN2 MUTATED                       4                              0
  ZKSCAN2 WILD-TYPE                   102                             10
D1126V10, multiclass
                                clus
vv                               ZKSCAN2 MUTATED ZKSCAN2 WILD-TYPE
  COLON ADENOCARCINOMA                         9               306
  COLON MUCINOUS ADENOCARCINOMA                4                43
  RECTAL ADENOCARCINOMA                        4               102
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  ZKSCAN2 MUTATED    13   0   0   1
  ZKSCAN2 WILD-TYPE 332   4  31  24
D1126V11, multiclass
    clus
vv   ZKSCAN2 MUTATED ZKSCAN2 WILD-TYPE
  R0              13               332
  R1               0                 4
  R2               0                31
  RX               1                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1126V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZKSCAN2 MUTATED                                  0     0
  ZKSCAN2 WILD-TYPE                                1    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  ZKSCAN2 MUTATED                           0     8
  ZKSCAN2 WILD-TYPE                        22   218
D1126V13, multiclass
                                  clus
vv                                 ZKSCAN2 MUTATED ZKSCAN2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                      0                22
  WHITE                                          8               218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1127) Variable = HLA-B MUTATION ANALYSIS
D1127V1, survival
                 sevent
clus2               0   1
  HLA-B MUTATED    11   0
  HLA-B WILD-TYPE 367  93
  HLA-B MUTATED HLA-B WILD-TYPE 
             11             460 
  HLA-B MUTATED HLA-B WILD-TYPE 
              0              93 
$`HLA-B MUTATED`
TCGA-A6-5665 TCGA-AA-3555 TCGA-AD-5900 TCGA-CK-4950 TCGA-CK-6751 TCGA-D5-6920 
       22.06        29.95         0.07        85.45       124.27         3.68 
TCGA-D5-6930 TCGA-D5-6931 TCGA-G4-6304 TCGA-G4-6588 TCGA-DC-6157 
        1.51        12.00        53.62        26.17        27.95 

$`HLA-B WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       13.02        24.00        17.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       39.98        18.05        40.96        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 
       12.76        10.06        14.30        17.56       148.01        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       16.14        15.58         1.48         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6932 TCGA-D5-7000 
        9.04         9.44        11.64         4.80        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       74.56        65.85        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 
       61.91        36.00        22.09        13.78        35.80        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
        5.03        13.97        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  HLA-B MUTATED HLA-B WILD-TYPE 
           0.07            0.00 
  HLA-B MUTATED HLA-B WILD-TYPE 
         124.27          148.01 
  HLA-B MUTATED HLA-B WILD-TYPE 
         26.170          20.085 
[1] "0.1 - 124.3 (26.2)" "0.0 - 148.0 (20.1)"
[1] "hr="     "2.6e+07"
D1127V2, continuous
D1127V3, binary
                 cls
clus                0   1
  HLA-B MUTATED    11   1
  HLA-B WILD-TYPE 355 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-B MUTATED     11    1
  HLA-B WILD-TYPE  355  118
        clus
vv       HLA-B MUTATED HLA-B WILD-TYPE
  COLON             11             355
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  HLA-B MUTATED         3        0        0         5         2         0
  HLA-B WILD-TYPE      88        1       32       133         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  HLA-B MUTATED           0          0          1          1        0         0
  HLA-B WILD-TYPE        24         11         58         41       48        18
                 vv
clus              STAGE IVB
  HLA-B MUTATED           0
  HLA-B WILD-TYPE         1
D1127V4, multiclass
            clus
vv           HLA-B MUTATED HLA-B WILD-TYPE
  STAGE I                3              88
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              5             133
  STAGE IIB              2               8
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             1              41
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  HLA-B MUTATED     0   3   6   3
  HLA-B WILD-TYPE  17  89 323  47
D1127V5, multiclass
    clus
vv   HLA-B MUTATED HLA-B WILD-TYPE
  T1             0              17
  T2             3              89
  T3             6             323
  T4             3              47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  HLA-B MUTATED    10   1   1
  HLA-B WILD-TYPE 277 112  86
D1127V6, multiclass
    clus
vv   HLA-B MUTATED HLA-B WILD-TYPE
  N0            10             277
  N1             1             112
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1127V7, binary
                 cls
clus                0   1
  HLA-B MUTATED     9   0
  HLA-B WILD-TYPE 366  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-B MUTATED      9    0
  HLA-B WILD-TYPE  366   65
   clus
vv  HLA-B MUTATED HLA-B WILD-TYPE
  0             9             366
  1             0              65
[1] 2 2
[1] FALSE
D1127V8, binary
                 cls
clus                0   1
  HLA-B MUTATED     8   4
  HLA-B WILD-TYPE 217 260
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-B MUTATED      8    4
  HLA-B WILD-TYPE  217  260
        clus
vv       HLA-B MUTATED HLA-B WILD-TYPE
  FEMALE             8             217
  MALE               4             260
[1] 2 2
[1] FALSE
D1127V9, binary
                 cls
clus                0   1
  HLA-B MUTATED     7   0
  HLA-B WILD-TYPE 343  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HLA-B MUTATED      7    0
  HLA-B WILD-TYPE  343   22
     clus
vv    HLA-B MUTATED HLA-B WILD-TYPE
  NO              7             343
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  HLA-B MUTATED                      7                             4
  HLA-B WILD-TYPE                  308                            43
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  HLA-B MUTATED                       1                              0
  HLA-B WILD-TYPE                   105                             10
D1127V10, multiclass
                                clus
vv                               HLA-B MUTATED HLA-B WILD-TYPE
  COLON ADENOCARCINOMA                       7             308
  COLON MUCINOUS ADENOCARCINOMA              4              43
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  HLA-B MUTATED     9   1   0   2
  HLA-B WILD-TYPE 336   3  31  23
D1127V11, multiclass
    clus
vv   HLA-B MUTATED HLA-B WILD-TYPE
  R0             9             336
  R1             1               3
  R2             0              31
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1127V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HLA-B MUTATED                                  0     0
  HLA-B WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  HLA-B MUTATED                           2     9
  HLA-B WILD-TYPE                        20   217
D1127V13, multiclass
                                  clus
vv                                 HLA-B MUTATED HLA-B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    2              20
  WHITE                                        9             217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1128) Variable = NHLRC2 MUTATION ANALYSIS
D1128V1, survival
                  sevent
clus2                0   1
  NHLRC2 MUTATED     8   0
  NHLRC2 WILD-TYPE 370  93
  NHLRC2 MUTATED NHLRC2 WILD-TYPE 
               8              463 
  NHLRC2 MUTATED NHLRC2 WILD-TYPE 
               0               93 
$`NHLRC2 MUTATED`
TCGA-AA-3510 TCGA-AA-A01R TCGA-AD-6889 TCGA-AD-6965 TCGA-AY-5543 TCGA-CM-4746 
       63.98        35.01        56.55         0.20        33.01        37.02 
TCGA-D5-6536 TCGA-G4-6309 
       17.85        85.48 

$`NHLRC2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S 
       12.00        31.00        31.00        38.07         1.02         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6197 TCGA-AY-6386 
       14.50        27.09        16.31         0.95        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       23.05        20.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       15.12         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  NHLRC2 MUTATED NHLRC2 WILD-TYPE 
             0.2              0.0 
  NHLRC2 MUTATED NHLRC2 WILD-TYPE 
           85.48           148.01 
  NHLRC2 MUTATED NHLRC2 WILD-TYPE 
          36.015           20.050 
[1] "0.2 - 85.5 (36.0)"  "0.0 - 148.0 (20.1)"
[1] "hr="     "9400000"
D1128V2, continuous
D1128V3, binary
                  cls
clus                 0   1
  NHLRC2 MUTATED     9   0
  NHLRC2 WILD-TYPE 357 119
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NHLRC2 MUTATED      9    0
  NHLRC2 WILD-TYPE  357  119
        clus
vv       NHLRC2 MUTATED NHLRC2 WILD-TYPE
  COLON               9              357
  RECTUM              0              119
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NHLRC2 MUTATED         1        0        1         3         0         0
  NHLRC2 WILD-TYPE      90        1       31       135        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NHLRC2 MUTATED           1          0          1          0        0
  NHLRC2 WILD-TYPE        23         11         58         42       48
                  vv
clus               STAGE IVA STAGE IVB
  NHLRC2 MUTATED           1         0
  NHLRC2 WILD-TYPE        17         1
D1128V4, multiclass
            clus
vv           NHLRC2 MUTATED NHLRC2 WILD-TYPE
  STAGE I                 1               90
  STAGE IA                0                1
  STAGE II                1               31
  STAGE IIA               3              135
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               1               23
  STAGE IIIA              0               11
  STAGE IIIB              1               58
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               1               17
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  NHLRC2 MUTATED     0   1   7   1
  NHLRC2 WILD-TYPE  17  91 322  49
D1128V5, multiclass
    clus
vv   NHLRC2 MUTATED NHLRC2 WILD-TYPE
  T1              0               17
  T2              1               91
  T3              7              322
  T4              1               49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  NHLRC2 MUTATED     5   2   2
  NHLRC2 WILD-TYPE 282 111  85
D1128V6, multiclass
    clus
vv   NHLRC2 MUTATED NHLRC2 WILD-TYPE
  N0              5              282
  N1              2              111
  N2              2               85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1128V7, binary
                  cls
clus                 0   1
  NHLRC2 MUTATED     7   1
  NHLRC2 WILD-TYPE 368  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NHLRC2 MUTATED      7    1
  NHLRC2 WILD-TYPE  368   64
   clus
vv  NHLRC2 MUTATED NHLRC2 WILD-TYPE
  0              7              368
  1              1               64
[1] 2 2
[1] FALSE
D1128V8, binary
                  cls
clus                 0   1
  NHLRC2 MUTATED     3   6
  NHLRC2 WILD-TYPE 222 258
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NHLRC2 MUTATED      3    6
  NHLRC2 WILD-TYPE  222  258
        clus
vv       NHLRC2 MUTATED NHLRC2 WILD-TYPE
  FEMALE              3              222
  MALE                6              258
[1] 2 2
[1] FALSE
D1128V9, binary
                  cls
clus                 0   1
  NHLRC2 MUTATED     5   1
  NHLRC2 WILD-TYPE 345  21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NHLRC2 MUTATED      5    1
  NHLRC2 WILD-TYPE  345   21
     clus
vv    NHLRC2 MUTATED NHLRC2 WILD-TYPE
  NO               5              345
  YES              1               21
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  NHLRC2 MUTATED                      8                             1
  NHLRC2 WILD-TYPE                  307                            46
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  NHLRC2 MUTATED                       0                              0
  NHLRC2 WILD-TYPE                   106                             10
D1128V10, multiclass
                                clus
vv                               NHLRC2 MUTATED NHLRC2 WILD-TYPE
  COLON ADENOCARCINOMA                        8              307
  COLON MUCINOUS ADENOCARCINOMA               1               46
  RECTAL ADENOCARCINOMA                       0              106
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  NHLRC2 MUTATED     7   0   0   0
  NHLRC2 WILD-TYPE 338   4  31  25
D1128V11, multiclass
    clus
vv   NHLRC2 MUTATED NHLRC2 WILD-TYPE
  R0              7              338
  R1              0                4
  R2              0               31
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1128V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NHLRC2 MUTATED                                  0     1
  NHLRC2 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  NHLRC2 MUTATED                           3     2
  NHLRC2 WILD-TYPE                        19   224
D1128V13, multiclass
                                  clus
vv                                 NHLRC2 MUTATED NHLRC2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     3               19
  WHITE                                         2              224
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1129) Variable = BST2 MUTATION ANALYSIS
D1129V1, survival
                sevent
clus2              0   1
  BST2 MUTATED     5   1
  BST2 WILD-TYPE 373  92
  BST2 MUTATED BST2 WILD-TYPE 
             6            465 
  BST2 MUTATED BST2 WILD-TYPE 
             1             92 
$`BST2 MUTATED`
TCGA-AA-3833 TCGA-AY-6386 TCGA-AZ-6601 TCGA-CM-4743 TCGA-CM-5861 TCGA-D5-6541 
       15.95        17.82       100.01        23.05        15.02        15.58 

$`BST2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
        1.02        17.98        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        33.01        21.44        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
       12.10        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
        1.91       124.27        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 
       29.06        22.03        22.98        30.08        32.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       16.14         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  BST2 MUTATED BST2 WILD-TYPE 
         15.02           0.00 
  BST2 MUTATED BST2 WILD-TYPE 
        100.01         148.01 
  BST2 MUTATED BST2 WILD-TYPE 
        16.885         20.280 
[1] "15.0 - 100.0 (16.9)" "0.0 - 148.0 (20.3)" 
[1] "hr=" "1.4"
D1129V2, continuous
D1129V3, binary
                cls
clus               0   1
  BST2 MUTATED     6   0
  BST2 WILD-TYPE 360 119
[1] "tbl2"
                cls
clus             [,1] [,2]
  BST2 MUTATED      6    0
  BST2 WILD-TYPE  360  119
        clus
vv       BST2 MUTATED BST2 WILD-TYPE
  COLON             6            360
  RECTUM            0            119
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  BST2 MUTATED         0        0        1         4         0         0
  BST2 WILD-TYPE      91        1       31       134        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  BST2 MUTATED           0          0          1          0        0         0
  BST2 WILD-TYPE        24         11         58         42       48        18
                vv
clus             STAGE IVB
  BST2 MUTATED           0
  BST2 WILD-TYPE         1
D1129V4, multiclass
            clus
vv           BST2 MUTATED BST2 WILD-TYPE
  STAGE I               0             91
  STAGE IA              0              1
  STAGE II              1             31
  STAGE IIA             4            134
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            1             58
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  BST2 MUTATED     0   0   6   0
  BST2 WILD-TYPE  17  92 323  50
D1129V5, multiclass
    clus
vv   BST2 MUTATED BST2 WILD-TYPE
  T1            0             17
  T2            0             92
  T3            6            323
  T4            0             50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  BST2 MUTATED     5   1   0
  BST2 WILD-TYPE 282 112  87
D1129V6, multiclass
    clus
vv   BST2 MUTATED BST2 WILD-TYPE
  N0            5            282
  N1            1            112
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1129V7, binary
                cls
clus               0   1
  BST2 MUTATED     6   0
  BST2 WILD-TYPE 369  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  BST2 MUTATED      6    0
  BST2 WILD-TYPE  369   65
   clus
vv  BST2 MUTATED BST2 WILD-TYPE
  0            6            369
  1            0             65
[1] 2 2
[1] FALSE
D1129V8, binary
                cls
clus               0   1
  BST2 MUTATED     3   3
  BST2 WILD-TYPE 222 261
[1] "tbl2"
                cls
clus             [,1] [,2]
  BST2 MUTATED      3    3
  BST2 WILD-TYPE  222  261
        clus
vv       BST2 MUTATED BST2 WILD-TYPE
  FEMALE            3            222
  MALE              3            261
[1] 2 2
[1] FALSE
D1129V9, binary
                cls
clus               0   1
  BST2 MUTATED     6   0
  BST2 WILD-TYPE 344  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  BST2 MUTATED      6    0
  BST2 WILD-TYPE  344   22
     clus
vv    BST2 MUTATED BST2 WILD-TYPE
  NO             6            344
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  BST2 MUTATED                      6                             0
  BST2 WILD-TYPE                  309                            47
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  BST2 MUTATED                       0                              0
  BST2 WILD-TYPE                   106                             10
D1129V10, multiclass
                                clus
vv                               BST2 MUTATED BST2 WILD-TYPE
  COLON ADENOCARCINOMA                      6            309
  COLON MUCINOUS ADENOCARCINOMA             0             47
  RECTAL ADENOCARCINOMA                     0            106
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  BST2 MUTATED     5   0   0   0
  BST2 WILD-TYPE 340   4  31  25
D1129V11, multiclass
    clus
vv   BST2 MUTATED BST2 WILD-TYPE
  R0            5            340
  R1            0              4
  R2            0             31
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1129V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  BST2 MUTATED                                  0     0
  BST2 WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  BST2 MUTATED                           1     4
  BST2 WILD-TYPE                        21   222
D1129V13, multiclass
                                  clus
vv                                 BST2 MUTATED BST2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                       4            222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1130) Variable = VASH1 MUTATION ANALYSIS
D1130V1, survival
                 sevent
clus2               0   1
  VASH1 MUTATED     4   0
  VASH1 WILD-TYPE 374  93
  VASH1 MUTATED VASH1 WILD-TYPE 
              4             467 
  VASH1 MUTATED VASH1 WILD-TYPE 
              0              93 
$`VASH1 MUTATED`
TCGA-A6-5665 TCGA-CM-5861 TCGA-D5-6540 TCGA-DM-A1HB 
       22.06        15.02        16.14       135.65 

$`VASH1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       30.08        32.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
        4.80        17.13        12.49        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 
       12.59       140.38         7.50        44.32       131.51       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  VASH1 MUTATED VASH1 WILD-TYPE 
          15.02            0.00 
  VASH1 MUTATED VASH1 WILD-TYPE 
         135.65          148.01 
  VASH1 MUTATED VASH1 WILD-TYPE 
          19.10           20.19 
[1] "15.0 - 135.7 (19.1)" "0.0 - 148.0 (20.2)" 
[1] "hr="     "9200000"
D1130V2, continuous
D1130V3, binary
                 cls
clus                0   1
  VASH1 MUTATED     5   0
  VASH1 WILD-TYPE 361 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VASH1 MUTATED      5    0
  VASH1 WILD-TYPE  361  119
        clus
vv       VASH1 MUTATED VASH1 WILD-TYPE
  COLON              5             361
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  VASH1 MUTATED         1        0        0         2         1         0
  VASH1 WILD-TYPE      90        1       32       136         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  VASH1 MUTATED           0          0          1          0        0         0
  VASH1 WILD-TYPE        24         11         58         42       48        18
                 vv
clus              STAGE IVB
  VASH1 MUTATED           0
  VASH1 WILD-TYPE         1
D1130V4, multiclass
            clus
vv           VASH1 MUTATED VASH1 WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              2             136
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  VASH1 MUTATED     0   1   3   1
  VASH1 WILD-TYPE  17  91 326  49
D1130V5, multiclass
    clus
vv   VASH1 MUTATED VASH1 WILD-TYPE
  T1             0              17
  T2             1              91
  T3             3             326
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  VASH1 MUTATED     4   1   0
  VASH1 WILD-TYPE 283 112  87
D1130V6, multiclass
    clus
vv   VASH1 MUTATED VASH1 WILD-TYPE
  N0             4             283
  N1             1             112
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1130V7, binary
                 cls
clus                0   1
  VASH1 MUTATED     4   0
  VASH1 WILD-TYPE 371  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VASH1 MUTATED      4    0
  VASH1 WILD-TYPE  371   65
   clus
vv  VASH1 MUTATED VASH1 WILD-TYPE
  0             4             371
  1             0              65
[1] 2 2
[1] FALSE
D1130V8, binary
                 cls
clus                0   1
  VASH1 MUTATED     3   2
  VASH1 WILD-TYPE 222 262
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VASH1 MUTATED      3    2
  VASH1 WILD-TYPE  222  262
        clus
vv       VASH1 MUTATED VASH1 WILD-TYPE
  FEMALE             3             222
  MALE               2             262
[1] 2 2
[1] FALSE
D1130V9, binary
                 cls
clus                0   1
  VASH1 MUTATED     3   0
  VASH1 WILD-TYPE 347  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VASH1 MUTATED      3    0
  VASH1 WILD-TYPE  347   22
     clus
vv    VASH1 MUTATED VASH1 WILD-TYPE
  NO              3             347
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  VASH1 MUTATED                      3                             1
  VASH1 WILD-TYPE                  312                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  VASH1 MUTATED                       0                              0
  VASH1 WILD-TYPE                   106                             10
D1130V10, multiclass
                                clus
vv                               VASH1 MUTATED VASH1 WILD-TYPE
  COLON ADENOCARCINOMA                       3             312
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  VASH1 MUTATED     3   0   0   1
  VASH1 WILD-TYPE 342   4  31  24
D1130V11, multiclass
    clus
vv   VASH1 MUTATED VASH1 WILD-TYPE
  R0             3             342
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1130V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  VASH1 MUTATED                                  0     0
  VASH1 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  VASH1 MUTATED                           0     5
  VASH1 WILD-TYPE                        22   221
D1130V13, multiclass
                                  clus
vv                                 VASH1 MUTATED VASH1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        5             221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1131) Variable = CT47B1 MUTATION ANALYSIS
D1131V1, survival
                  sevent
clus2                0   1
  CT47B1 MUTATED     6   2
  CT47B1 WILD-TYPE 372  91
  CT47B1 MUTATED CT47B1 WILD-TYPE 
               8              463 
  CT47B1 MUTATED CT47B1 WILD-TYPE 
               2               91 
$`CT47B1 MUTATED`
TCGA-A6-6138 TCGA-AZ-5403 TCGA-CM-5862 TCGA-D5-6535 TCGA-D5-6930 TCGA-DM-A1HB 
       22.52        62.79         5.03        15.12         1.51       135.65 
TCGA-G4-6625 TCGA-F5-6571 
       91.79        31.30 

$`CT47B1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6141 TCGA-A6-6142 
       22.09        22.06        32.71        27.09         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
        5.13       106.75        22.36        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       32.02        15.02        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       18.25         1.32        43.27        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
        7.50        44.32       131.51       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       13.78        35.80        26.17        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       49.51        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  CT47B1 MUTATED CT47B1 WILD-TYPE 
            1.51             0.00 
  CT47B1 MUTATED CT47B1 WILD-TYPE 
          135.65           148.01 
  CT47B1 MUTATED CT47B1 WILD-TYPE 
           26.91            20.12 
[1] "1.5 - 135.7 (26.9)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.2"
D1131V2, continuous
D1131V3, binary
                  cls
clus                 0   1
  CT47B1 MUTATED     7   1
  CT47B1 WILD-TYPE 359 118
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CT47B1 MUTATED      7    1
  CT47B1 WILD-TYPE  359  118
        clus
vv       CT47B1 MUTATED CT47B1 WILD-TYPE
  COLON               7              359
  RECTUM              1              118
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CT47B1 MUTATED         1        0        1         3         0         0
  CT47B1 WILD-TYPE      90        1       31       135        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CT47B1 MUTATED           0          0          2          0        0
  CT47B1 WILD-TYPE        24         11         57         42       48
                  vv
clus               STAGE IVA STAGE IVB
  CT47B1 MUTATED           1         0
  CT47B1 WILD-TYPE        17         1
D1131V4, multiclass
            clus
vv           CT47B1 MUTATED CT47B1 WILD-TYPE
  STAGE I                 1               90
  STAGE IA                0                1
  STAGE II                1               31
  STAGE IIA               3              135
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              2               57
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               1               17
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  CT47B1 MUTATED     0   1   7   0
  CT47B1 WILD-TYPE  17  91 322  50
D1131V5, multiclass
    clus
vv   CT47B1 MUTATED CT47B1 WILD-TYPE
  T1              0               17
  T2              1               91
  T3              7              322
  T4              0               50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  CT47B1 MUTATED     5   3   0
  CT47B1 WILD-TYPE 282 110  87
D1131V6, multiclass
    clus
vv   CT47B1 MUTATED CT47B1 WILD-TYPE
  N0              5              282
  N1              3              110
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1131V7, binary
                  cls
clus                 0   1
  CT47B1 MUTATED     5   1
  CT47B1 WILD-TYPE 370  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CT47B1 MUTATED      5    1
  CT47B1 WILD-TYPE  370   64
   clus
vv  CT47B1 MUTATED CT47B1 WILD-TYPE
  0              5              370
  1              1               64
[1] 2 2
[1] FALSE
D1131V8, binary
                  cls
clus                 0   1
  CT47B1 MUTATED     3   5
  CT47B1 WILD-TYPE 222 259
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CT47B1 MUTATED      3    5
  CT47B1 WILD-TYPE  222  259
        clus
vv       CT47B1 MUTATED CT47B1 WILD-TYPE
  FEMALE              3              222
  MALE                5              259
[1] 2 2
[1] FALSE
D1131V9, binary
                  cls
clus                 0   1
  CT47B1 MUTATED     6   0
  CT47B1 WILD-TYPE 344  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CT47B1 MUTATED      6    0
  CT47B1 WILD-TYPE  344   22
     clus
vv    CT47B1 MUTATED CT47B1 WILD-TYPE
  NO               6              344
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CT47B1 MUTATED                      5                             1
  CT47B1 WILD-TYPE                  310                            46
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CT47B1 MUTATED                       1                              0
  CT47B1 WILD-TYPE                   105                             10
D1131V10, multiclass
                                clus
vv                               CT47B1 MUTATED CT47B1 WILD-TYPE
  COLON ADENOCARCINOMA                        5              310
  COLON MUCINOUS ADENOCARCINOMA               1               46
  RECTAL ADENOCARCINOMA                       1              105
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  CT47B1 MUTATED     4   0   0   1
  CT47B1 WILD-TYPE 341   4  31  24
D1131V11, multiclass
    clus
vv   CT47B1 MUTATED CT47B1 WILD-TYPE
  R0              4              341
  R1              0                4
  R2              0               31
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1131V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CT47B1 MUTATED                                  0     0
  CT47B1 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  CT47B1 MUTATED                           0     8
  CT47B1 WILD-TYPE                        22   218
D1131V13, multiclass
                                  clus
vv                                 CT47B1 MUTATED CT47B1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         8              218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1132) Variable = ZNF619 MUTATION ANALYSIS
D1132V1, survival
                  sevent
clus2                0   1
  ZNF619 MUTATED     8   2
  ZNF619 WILD-TYPE 370  91
  ZNF619 MUTATED ZNF619 WILD-TYPE 
              10              461 
  ZNF619 MUTATED ZNF619 WILD-TYPE 
               2               91 
$`ZNF619 MUTATED`
TCGA-A6-6781 TCGA-AA-3510 TCGA-AA-3663 TCGA-AA-3845 TCGA-AA-3877 TCGA-AA-A00N 
       19.66        63.98         6.97         0.00        31.00         4.01 
TCGA-AA-A010 TCGA-AA-A01R TCGA-AZ-4315 TCGA-D5-6928 
       34.98        35.01        58.39        11.64 

$`ZNF619 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       38.99        37.02        14.93        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       29.98        18.05         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S 
       12.00        31.00        31.00        38.07         1.02         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       33.01        21.44        17.82         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 
        4.41        12.43        14.30         9.04         9.44         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  ZNF619 MUTATED ZNF619 WILD-TYPE 
               0                0 
  ZNF619 MUTATED ZNF619 WILD-TYPE 
           63.98           148.01 
  ZNF619 MUTATED ZNF619 WILD-TYPE 
           25.33            20.19 
[1] "0.0 - 64.0 (25.3)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1"  
D1132V2, continuous
D1132V3, binary
                  cls
clus                 0   1
  ZNF619 MUTATED    11   0
  ZNF619 WILD-TYPE 355 119
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF619 MUTATED     11    0
  ZNF619 WILD-TYPE  355  119
        clus
vv       ZNF619 MUTATED ZNF619 WILD-TYPE
  COLON              11              355
  RECTUM              0              119
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZNF619 MUTATED         1        0        2         3         3         0
  ZNF619 WILD-TYPE      90        1       30       135         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF619 MUTATED           1          0          0          1        0
  ZNF619 WILD-TYPE        23         11         59         41       48
                  vv
clus               STAGE IVA STAGE IVB
  ZNF619 MUTATED           0         0
  ZNF619 WILD-TYPE        18         1
D1132V4, multiclass
            clus
vv           ZNF619 MUTATED ZNF619 WILD-TYPE
  STAGE I                 1               90
  STAGE IA                0                1
  STAGE II                2               30
  STAGE IIA               3              135
  STAGE IIB               3                7
  STAGE IIC               0                1
  STAGE III               1               23
  STAGE IIIA              0               11
  STAGE IIIB              0               59
  STAGE IIIC              1               41
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZNF619 MUTATED     1   0   6   4
  ZNF619 WILD-TYPE  16  92 323  46
D1132V5, multiclass
    clus
vv   ZNF619 MUTATED ZNF619 WILD-TYPE
  T1              1               16
  T2              0               92
  T3              6              323
  T4              4               46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  ZNF619 MUTATED     9   1   1
  ZNF619 WILD-TYPE 278 112  86
D1132V6, multiclass
    clus
vv   ZNF619 MUTATED ZNF619 WILD-TYPE
  N0              9              278
  N1              1              112
  N2              1               86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1132V7, binary
                  cls
clus                 0   1
  ZNF619 MUTATED     9   0
  ZNF619 WILD-TYPE 366  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF619 MUTATED      9    0
  ZNF619 WILD-TYPE  366   65
   clus
vv  ZNF619 MUTATED ZNF619 WILD-TYPE
  0              9              366
  1              0               65
[1] 2 2
[1] FALSE
D1132V8, binary
                  cls
clus                 0   1
  ZNF619 MUTATED     4   7
  ZNF619 WILD-TYPE 221 257
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF619 MUTATED      4    7
  ZNF619 WILD-TYPE  221  257
        clus
vv       ZNF619 MUTATED ZNF619 WILD-TYPE
  FEMALE              4              221
  MALE                7              257
[1] 2 2
[1] FALSE
D1132V9, binary
                  cls
clus                 0   1
  ZNF619 MUTATED     7   1
  ZNF619 WILD-TYPE 343  21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF619 MUTATED      7    1
  ZNF619 WILD-TYPE  343   21
     clus
vv    ZNF619 MUTATED ZNF619 WILD-TYPE
  NO               7              343
  YES              1               21
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ZNF619 MUTATED                      6                             5
  ZNF619 WILD-TYPE                  309                            42
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ZNF619 MUTATED                       0                              0
  ZNF619 WILD-TYPE                   106                             10
D1132V10, multiclass
                                clus
vv                               ZNF619 MUTATED ZNF619 WILD-TYPE
  COLON ADENOCARCINOMA                        6              309
  COLON MUCINOUS ADENOCARCINOMA               5               42
  RECTAL ADENOCARCINOMA                       0              106
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ZNF619 MUTATED    10   0   0   1
  ZNF619 WILD-TYPE 335   4  31  24
D1132V11, multiclass
    clus
vv   ZNF619 MUTATED ZNF619 WILD-TYPE
  R0             10              335
  R1              0                4
  R2              0               31
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1132V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF619 MUTATED                                  0     0
  ZNF619 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZNF619 MUTATED                           0     4
  ZNF619 WILD-TYPE                        22   222
D1132V13, multiclass
                                  clus
vv                                 ZNF619 MUTATED ZNF619 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         4              222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1133) Variable = LIX1 MUTATION ANALYSIS
D1133V1, survival
                sevent
clus2              0   1
  LIX1 MUTATED     8   2
  LIX1 WILD-TYPE 370  91
  LIX1 MUTATED LIX1 WILD-TYPE 
            10            461 
  LIX1 MUTATED LIX1 WILD-TYPE 
             2             91 
$`LIX1 MUTATED`
TCGA-AA-3555 TCGA-AA-3713 TCGA-AA-3977 TCGA-AA-A010 TCGA-AZ-6600 TCGA-AZ-6601 
       29.95        19.04        25.02        34.98        12.10       100.01 
TCGA-CM-4744 TCGA-D5-6928 TCGA-AG-A002 TCGA-EI-6510 
       20.02        11.64        20.98        18.28 

$`LIX1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 
       21.01        13.02        24.00        17.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6603 TCGA-AZ-6605 
       62.79        88.21        49.41         6.77        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
        9.44         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       19.96        20.91         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  LIX1 MUTATED LIX1 WILD-TYPE 
         11.64           0.00 
  LIX1 MUTATED LIX1 WILD-TYPE 
        100.01         148.01 
  LIX1 MUTATED LIX1 WILD-TYPE 
         20.50          20.19 
[1] "11.6 - 100.0 (20.5)" "0.0 - 148.0 (20.2)" 
[1] "hr=" "1.1"
D1133V2, continuous
D1133V3, binary
                cls
clus               0   1
  LIX1 MUTATED     9   2
  LIX1 WILD-TYPE 357 117
[1] "tbl2"
                cls
clus             [,1] [,2]
  LIX1 MUTATED      9    2
  LIX1 WILD-TYPE  357  117
        clus
vv       LIX1 MUTATED LIX1 WILD-TYPE
  COLON             9            357
  RECTUM            2            117
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  LIX1 MUTATED         2        0        1         2         1         0
  LIX1 WILD-TYPE      89        1       31       136         9         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  LIX1 MUTATED           1          0          0          0        2         1
  LIX1 WILD-TYPE        23         11         59         42       46        17
                vv
clus             STAGE IVB
  LIX1 MUTATED           0
  LIX1 WILD-TYPE         1
D1133V4, multiclass
            clus
vv           LIX1 MUTATED LIX1 WILD-TYPE
  STAGE I               2             89
  STAGE IA              0              1
  STAGE II              1             31
  STAGE IIA             2            136
  STAGE IIB             1              9
  STAGE IIC             0              1
  STAGE III             1             23
  STAGE IIIA            0             11
  STAGE IIIB            0             59
  STAGE IIIC            0             42
  STAGE IV              2             46
  STAGE IVA             1             17
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  LIX1 MUTATED     0   4   5   2
  LIX1 WILD-TYPE  17  88 324  48
D1133V5, multiclass
    clus
vv   LIX1 MUTATED LIX1 WILD-TYPE
  T1            0             17
  T2            4             88
  T3            5            324
  T4            2             48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  LIX1 MUTATED     9   1   1
  LIX1 WILD-TYPE 278 112  86
D1133V6, multiclass
    clus
vv   LIX1 MUTATED LIX1 WILD-TYPE
  N0            9            278
  N1            1            112
  N2            1             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1133V7, binary
                cls
clus               0   1
  LIX1 MUTATED     7   2
  LIX1 WILD-TYPE 368  63
[1] "tbl2"
                cls
clus             [,1] [,2]
  LIX1 MUTATED      7    2
  LIX1 WILD-TYPE  368   63
   clus
vv  LIX1 MUTATED LIX1 WILD-TYPE
  0            7            368
  1            2             63
[1] 2 2
[1] FALSE
D1133V8, binary
                cls
clus               0   1
  LIX1 MUTATED     3   8
  LIX1 WILD-TYPE 222 256
[1] "tbl2"
                cls
clus             [,1] [,2]
  LIX1 MUTATED      3    8
  LIX1 WILD-TYPE  222  256
        clus
vv       LIX1 MUTATED LIX1 WILD-TYPE
  FEMALE            3            222
  MALE              8            256
[1] 2 2
[1] FALSE
D1133V9, binary
                cls
clus               0   1
  LIX1 MUTATED     8   1
  LIX1 WILD-TYPE 342  21
[1] "tbl2"
                cls
clus             [,1] [,2]
  LIX1 MUTATED      8    1
  LIX1 WILD-TYPE  342   21
     clus
vv    LIX1 MUTATED LIX1 WILD-TYPE
  NO             8            342
  YES            1             21
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  LIX1 MUTATED                      7                             2
  LIX1 WILD-TYPE                  308                            45
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  LIX1 MUTATED                       2                              0
  LIX1 WILD-TYPE                   104                             10
D1133V10, multiclass
                                clus
vv                               LIX1 MUTATED LIX1 WILD-TYPE
  COLON ADENOCARCINOMA                      7            308
  COLON MUCINOUS ADENOCARCINOMA             2             45
  RECTAL ADENOCARCINOMA                     2            104
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  LIX1 MUTATED     7   0   1   0
  LIX1 WILD-TYPE 338   4  30  25
D1133V11, multiclass
    clus
vv   LIX1 MUTATED LIX1 WILD-TYPE
  R0            7            338
  R1            0              4
  R2            1             30
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1133V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  LIX1 MUTATED                                  0     0
  LIX1 WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  LIX1 MUTATED                           1     4
  LIX1 WILD-TYPE                        21   222
D1133V13, multiclass
                                  clus
vv                                 LIX1 MUTATED LIX1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                       4            222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1134) Variable = BCLAF1 MUTATION ANALYSIS
D1134V1, survival
                  sevent
clus2                0   1
  BCLAF1 MUTATED    15   7
  BCLAF1 WILD-TYPE 363  86
  BCLAF1 MUTATED BCLAF1 WILD-TYPE 
              22              449 
  BCLAF1 MUTATED BCLAF1 WILD-TYPE 
               7               86 
$`BCLAF1 MUTATED`
TCGA-A6-5665 TCGA-AA-3489 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3558 TCGA-AA-3845 
       22.06         7.04        63.98         6.97        20.98         0.00 
TCGA-AA-3867 TCGA-AA-3975 TCGA-AA-A00N TCGA-AA-A010 TCGA-AD-6901 TCGA-AY-5543 
       24.03        34.06         4.01        34.98        22.42        33.01 
TCGA-AZ-4682 TCGA-AZ-6598 TCGA-CA-6717 TCGA-CA-6718 TCGA-D5-6924 TCGA-D5-6930 
       22.36        49.41        12.76        10.06        14.30         1.51 
TCGA-AF-6655 TCGA-AG-3883 TCGA-AG-A002 TCGA-G5-6641 
       20.02         1.02        20.98        26.43 

$`BCLAF1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        19.66        20.28         3.02         1.02        35.01 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       29.95        23.01        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       78.08         6.05         6.97        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
       14.93        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       53.00        17.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        0.72         5.79        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       27.09        16.31         0.95        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 
        1.41         5.13       106.75        62.79        88.21         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       12.20        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6931 
       12.43         9.04         9.44        11.64         4.80        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6672 TCGA-AG-3574 
       10.39        14.50        16.83        15.39        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
        0.99        19.04        19.99        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       28.57        32.19         0.66         0.69        55.76 

  BCLAF1 MUTATED BCLAF1 WILD-TYPE 
               0                0 
  BCLAF1 MUTATED BCLAF1 WILD-TYPE 
           63.98           148.01 
  BCLAF1 MUTATED BCLAF1 WILD-TYPE 
           20.98            20.12 
[1] "0.0 - 64.0 (21.0)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "2.1"
D1134V2, continuous
D1134V3, binary
                  cls
clus                 0   1
  BCLAF1 MUTATED    18   4
  BCLAF1 WILD-TYPE 348 115
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BCLAF1 MUTATED     18    4
  BCLAF1 WILD-TYPE  348  115
        clus
vv       BCLAF1 MUTATED BCLAF1 WILD-TYPE
  COLON              18              348
  RECTUM              4              115
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  BCLAF1 MUTATED         4        0        4         6         2         0
  BCLAF1 WILD-TYPE      87        1       28       132         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  BCLAF1 MUTATED           0          2          0          0        1
  BCLAF1 WILD-TYPE        24          9         59         42       47
                  vv
clus               STAGE IVA STAGE IVB
  BCLAF1 MUTATED           2         0
  BCLAF1 WILD-TYPE        16         1
D1134V4, multiclass
            clus
vv           BCLAF1 MUTATED BCLAF1 WILD-TYPE
  STAGE I                 4               87
  STAGE IA                0                1
  STAGE II                4               28
  STAGE IIA               6              132
  STAGE IIB               2                8
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              2                9
  STAGE IIIB              0               59
  STAGE IIIC              0               42
  STAGE IV                1               47
  STAGE IVA               2               16
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  BCLAF1 MUTATED     1   5  13   3
  BCLAF1 WILD-TYPE  16  87 316  47
D1134V5, multiclass
    clus
vv   BCLAF1 MUTATED BCLAF1 WILD-TYPE
  T1              1               16
  T2              5               87
  T3             13              316
  T4              3               47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  BCLAF1 MUTATED    18   3   1
  BCLAF1 WILD-TYPE 269 110  86
D1134V6, multiclass
    clus
vv   BCLAF1 MUTATED BCLAF1 WILD-TYPE
  N0             18              269
  N1              3              110
  N2              1               86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1134V7, binary
                  cls
clus                 0   1
  BCLAF1 MUTATED    16   3
  BCLAF1 WILD-TYPE 359  62
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BCLAF1 MUTATED     16    3
  BCLAF1 WILD-TYPE  359   62
   clus
vv  BCLAF1 MUTATED BCLAF1 WILD-TYPE
  0             16              359
  1              3               62
[1] 2 2
[1] FALSE
D1134V8, binary
                  cls
clus                 0   1
  BCLAF1 MUTATED     5  17
  BCLAF1 WILD-TYPE 220 247
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BCLAF1 MUTATED      5   17
  BCLAF1 WILD-TYPE  220  247
        clus
vv       BCLAF1 MUTATED BCLAF1 WILD-TYPE
  FEMALE              5              220
  MALE               17              247
[1] 2 2
[1] FALSE
D1134V9, binary
                  cls
clus                 0   1
  BCLAF1 MUTATED    18   0
  BCLAF1 WILD-TYPE 332  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BCLAF1 MUTATED     18    0
  BCLAF1 WILD-TYPE  332   22
     clus
vv    BCLAF1 MUTATED BCLAF1 WILD-TYPE
  NO              18              332
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  BCLAF1 MUTATED                     15                             3
  BCLAF1 WILD-TYPE                  300                            44
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  BCLAF1 MUTATED                       3                              1
  BCLAF1 WILD-TYPE                   103                              9
D1134V10, multiclass
                                clus
vv                               BCLAF1 MUTATED BCLAF1 WILD-TYPE
  COLON ADENOCARCINOMA                       15              300
  COLON MUCINOUS ADENOCARCINOMA               3               44
  RECTAL ADENOCARCINOMA                       3              103
  RECTAL MUCINOUS ADENOCARCINOMA              1                9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  BCLAF1 MUTATED    16   0   2   2
  BCLAF1 WILD-TYPE 329   4  29  23
D1134V11, multiclass
    clus
vv   BCLAF1 MUTATED BCLAF1 WILD-TYPE
  R0             16              329
  R1              0                4
  R2              2               29
  RX              2               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1134V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  BCLAF1 MUTATED                                  0     2
  BCLAF1 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  BCLAF1 MUTATED                           1     8
  BCLAF1 WILD-TYPE                        21   218
D1134V13, multiclass
                                  clus
vv                                 BCLAF1 MUTATED BCLAF1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                9
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                         8              218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1135) Variable = OR2Y1 MUTATION ANALYSIS
D1135V1, survival
                 sevent
clus2               0   1
  OR2Y1 MUTATED     6   1
  OR2Y1 WILD-TYPE 372  92
  OR2Y1 MUTATED OR2Y1 WILD-TYPE 
              7             464 
  OR2Y1 MUTATED OR2Y1 WILD-TYPE 
              1              92 
$`OR2Y1 MUTATED`
TCGA-A6-6653 TCGA-AA-A00N TCGA-CA-5254 TCGA-CM-6166 TCGA-D5-6540 TCGA-G4-6586 
       24.39         4.01        12.69        21.99        16.14        35.80 
TCGA-G4-6588 
       26.17 

$`OR2Y1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
       25.08        25.18        24.16        21.76        24.69        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        1.61         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6168 
       12.00         2.96        29.03        16.04        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       12.49        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       22.09        13.78        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  OR2Y1 MUTATED OR2Y1 WILD-TYPE 
           4.01            0.00 
  OR2Y1 MUTATED OR2Y1 WILD-TYPE 
          35.80          148.01 
  OR2Y1 MUTATED OR2Y1 WILD-TYPE 
         21.990          20.155 
[1] "4.0 - 35.8 (22.0)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1"  
D1135V2, continuous
D1135V3, binary
                 cls
clus                0   1
  OR2Y1 MUTATED     7   1
  OR2Y1 WILD-TYPE 359 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR2Y1 MUTATED      7    1
  OR2Y1 WILD-TYPE  359  118
        clus
vv       OR2Y1 MUTATED OR2Y1 WILD-TYPE
  COLON              7             359
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  OR2Y1 MUTATED         3        0        0         3         1         0
  OR2Y1 WILD-TYPE      88        1       32       135         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  OR2Y1 MUTATED           0          0          1          0        0         0
  OR2Y1 WILD-TYPE        24         11         58         42       48        18
                 vv
clus              STAGE IVB
  OR2Y1 MUTATED           0
  OR2Y1 WILD-TYPE         1
D1135V4, multiclass
            clus
vv           OR2Y1 MUTATED OR2Y1 WILD-TYPE
  STAGE I                3              88
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              3             135
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  OR2Y1 MUTATED     0   3   3   2
  OR2Y1 WILD-TYPE  17  89 326  48
D1135V5, multiclass
    clus
vv   OR2Y1 MUTATED OR2Y1 WILD-TYPE
  T1             0              17
  T2             3              89
  T3             3             326
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  OR2Y1 MUTATED     7   1   0
  OR2Y1 WILD-TYPE 280 112  87
D1135V6, multiclass
    clus
vv   OR2Y1 MUTATED OR2Y1 WILD-TYPE
  N0             7             280
  N1             1             112
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1135V7, binary
                 cls
clus                0   1
  OR2Y1 MUTATED     8   0
  OR2Y1 WILD-TYPE 367  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR2Y1 MUTATED      8    0
  OR2Y1 WILD-TYPE  367   65
   clus
vv  OR2Y1 MUTATED OR2Y1 WILD-TYPE
  0             8             367
  1             0              65
[1] 2 2
[1] FALSE
D1135V8, binary
                 cls
clus                0   1
  OR2Y1 MUTATED     4   4
  OR2Y1 WILD-TYPE 221 260
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR2Y1 MUTATED      4    4
  OR2Y1 WILD-TYPE  221  260
        clus
vv       OR2Y1 MUTATED OR2Y1 WILD-TYPE
  FEMALE             4             221
  MALE               4             260
[1] 2 2
[1] FALSE
D1135V9, binary
                 cls
clus                0   1
  OR2Y1 MUTATED     6   0
  OR2Y1 WILD-TYPE 344  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR2Y1 MUTATED      6    0
  OR2Y1 WILD-TYPE  344   22
     clus
vv    OR2Y1 MUTATED OR2Y1 WILD-TYPE
  NO              6             344
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  OR2Y1 MUTATED                      5                             2
  OR2Y1 WILD-TYPE                  310                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  OR2Y1 MUTATED                       1                              0
  OR2Y1 WILD-TYPE                   105                             10
D1135V10, multiclass
                                clus
vv                               OR2Y1 MUTATED OR2Y1 WILD-TYPE
  COLON ADENOCARCINOMA                       5             310
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  OR2Y1 MUTATED     5   0   1   1
  OR2Y1 WILD-TYPE 340   4  30  24
D1135V11, multiclass
    clus
vv   OR2Y1 MUTATED OR2Y1 WILD-TYPE
  R0             5             340
  R1             0               4
  R2             1              30
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1135V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OR2Y1 MUTATED                                  0     1
  OR2Y1 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  OR2Y1 MUTATED                           0     5
  OR2Y1 WILD-TYPE                        22   221
D1135V13, multiclass
                                  clus
vv                                 OR2Y1 MUTATED OR2Y1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        5             221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1136) Variable = KTN1 MUTATION ANALYSIS
D1136V1, survival
                sevent
clus2              0   1
  KTN1 MUTATED    17   2
  KTN1 WILD-TYPE 361  91
  KTN1 MUTATED KTN1 WILD-TYPE 
            19            452 
  KTN1 MUTATED KTN1 WILD-TYPE 
             2             91 
$`KTN1 MUTATED`
TCGA-A6-2672 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5665 TCGA-AA-3518 TCGA-AA-3947 
       46.65        33.53        23.61        22.06         1.02        33.01 
TCGA-AA-A00E TCGA-AA-A00N TCGA-AA-A01R TCGA-AD-6889 TCGA-AD-6895 TCGA-AZ-4315 
       30.02         4.01        35.01        56.55         0.72        58.39 
TCGA-CM-6162 TCGA-CM-6171 TCGA-D5-6540 TCGA-F4-6703 TCGA-G4-6303 TCGA-AG-3599 
       12.00        14.04        16.14        47.87        65.85        12.03 
TCGA-AG-A002 
       20.98 

$`KTN1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 
       31.63        30.44        29.19        22.09        32.71        27.09 
TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 
       22.52         8.38        25.08        25.18        24.16        21.76 
TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       24.69        24.39        23.87        20.12        19.66        20.28 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
        7.04         3.02         1.02        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
        1.02        13.02        38.99         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       36.03         8.05        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       78.08         6.05         6.97        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 
       18.05        31.00         2.01        12.99        24.00        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       13.94        38.04        19.00        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T 
       31.00        31.00        38.07         1.02         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 
       18.05        40.96         0.07        21.37        15.52         0.79 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       15.02        17.03        15.02         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 
       21.99        14.99        12.99        13.02        15.02        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
        4.80        17.13        12.49        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6304 
        0.53        47.41        35.31       133.18        74.56        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
        2.01        50.04         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  KTN1 MUTATED KTN1 WILD-TYPE 
          0.72           0.00 
  KTN1 MUTATED KTN1 WILD-TYPE 
         65.85         148.01 
  KTN1 MUTATED KTN1 WILD-TYPE 
        23.610         20.035 
[1] "0.7 - 65.8 (23.6)"  "0.0 - 148.0 (20.0)"
[1] "hr=" "2.1"
D1136V2, continuous
D1136V3, binary
                cls
clus               0   1
  KTN1 MUTATED    18   2
  KTN1 WILD-TYPE 348 117
[1] "tbl2"
                cls
clus             [,1] [,2]
  KTN1 MUTATED     18    2
  KTN1 WILD-TYPE  348  117
        clus
vv       KTN1 MUTATED KTN1 WILD-TYPE
  COLON            18            348
  RECTUM            2            117
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KTN1 MUTATED         4        0        0         7         2         0
  KTN1 WILD-TYPE      87        1       32       131         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  KTN1 MUTATED           2          0          2          0        1         1
  KTN1 WILD-TYPE        22         11         57         42       47        17
                vv
clus             STAGE IVB
  KTN1 MUTATED           0
  KTN1 WILD-TYPE         1
D1136V4, multiclass
            clus
vv           KTN1 MUTATED KTN1 WILD-TYPE
  STAGE I               4             87
  STAGE IA              0              1
  STAGE II              0             32
  STAGE IIA             7            131
  STAGE IIB             2              8
  STAGE IIC             0              1
  STAGE III             2             22
  STAGE IIIA            0             11
  STAGE IIIB            2             57
  STAGE IIIC            0             42
  STAGE IV              1             47
  STAGE IVA             1             17
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  KTN1 MUTATED     0   4  14   2
  KTN1 WILD-TYPE  17  88 315  48
D1136V5, multiclass
    clus
vv   KTN1 MUTATED KTN1 WILD-TYPE
  T1            0             17
  T2            4             88
  T3           14            315
  T4            2             48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  KTN1 MUTATED    13   4   3
  KTN1 WILD-TYPE 274 109  84
D1136V6, multiclass
    clus
vv   KTN1 MUTATED KTN1 WILD-TYPE
  N0           13            274
  N1            4            109
  N2            3             84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1136V7, binary
                cls
clus               0   1
  KTN1 MUTATED    17   2
  KTN1 WILD-TYPE 358  63
[1] "tbl2"
                cls
clus             [,1] [,2]
  KTN1 MUTATED     17    2
  KTN1 WILD-TYPE  358   63
   clus
vv  KTN1 MUTATED KTN1 WILD-TYPE
  0           17            358
  1            2             63
[1] 2 2
[1] FALSE
D1136V8, binary
                cls
clus               0   1
  KTN1 MUTATED     8  12
  KTN1 WILD-TYPE 217 252
[1] "tbl2"
                cls
clus             [,1] [,2]
  KTN1 MUTATED      8   12
  KTN1 WILD-TYPE  217  252
        clus
vv       KTN1 MUTATED KTN1 WILD-TYPE
  FEMALE            8            217
  MALE             12            252
[1] 2 2
[1] FALSE
D1136V9, binary
                cls
clus               0   1
  KTN1 MUTATED    14   1
  KTN1 WILD-TYPE 336  21
[1] "tbl2"
                cls
clus             [,1] [,2]
  KTN1 MUTATED     14    1
  KTN1 WILD-TYPE  336   21
     clus
vv    KTN1 MUTATED KTN1 WILD-TYPE
  NO            14            336
  YES            1             21
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  KTN1 MUTATED                     13                             5
  KTN1 WILD-TYPE                  302                            42
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  KTN1 MUTATED                       1                              0
  KTN1 WILD-TYPE                   105                             10
D1136V10, multiclass
                                clus
vv                               KTN1 MUTATED KTN1 WILD-TYPE
  COLON ADENOCARCINOMA                     13            302
  COLON MUCINOUS ADENOCARCINOMA             5             42
  RECTAL ADENOCARCINOMA                     1            105
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  KTN1 MUTATED    17   0   0   0
  KTN1 WILD-TYPE 328   4  31  25
D1136V11, multiclass
    clus
vv   KTN1 MUTATED KTN1 WILD-TYPE
  R0           17            328
  R1            0              4
  R2            0             31
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1136V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KTN1 MUTATED                                  0     1
  KTN1 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  KTN1 MUTATED                           1    10
  KTN1 WILD-TYPE                        21   216
D1136V13, multiclass
                                  clus
vv                                 KTN1 MUTATED KTN1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                      10            216
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1137) Variable = CBLL1 MUTATION ANALYSIS
D1137V1, survival
                 sevent
clus2               0   1
  CBLL1 MUTATED     5   1
  CBLL1 WILD-TYPE 373  92
  CBLL1 MUTATED CBLL1 WILD-TYPE 
              6             465 
  CBLL1 MUTATED CBLL1 WILD-TYPE 
              1              92 
$`CBLL1 MUTATED`
TCGA-A6-5657 TCGA-AA-3663 TCGA-AY-6197 TCGA-AZ-5407 TCGA-F4-6570 TCGA-AG-A002 
       31.63         6.97        21.44        88.21         6.18        20.98 

$`CBLL1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       33.01        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 
       98.24         8.61        31.96        35.74        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  CBLL1 MUTATED CBLL1 WILD-TYPE 
           6.18            0.00 
  CBLL1 MUTATED CBLL1 WILD-TYPE 
          88.21          148.01 
  CBLL1 MUTATED CBLL1 WILD-TYPE 
          21.21           20.12 
[1] "6.2 - 88.2 (21.2)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.3"
D1137V2, continuous
D1137V3, binary
                 cls
clus                0   1
  CBLL1 MUTATED     5   1
  CBLL1 WILD-TYPE 361 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CBLL1 MUTATED      5    1
  CBLL1 WILD-TYPE  361  118
        clus
vv       CBLL1 MUTATED CBLL1 WILD-TYPE
  COLON              5             361
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CBLL1 MUTATED         2        0        1         2         0         0
  CBLL1 WILD-TYPE      89        1       31       136        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CBLL1 MUTATED           0          0          1          0        0         0
  CBLL1 WILD-TYPE        24         11         58         42       48        18
                 vv
clus              STAGE IVB
  CBLL1 MUTATED           0
  CBLL1 WILD-TYPE         1
D1137V4, multiclass
            clus
vv           CBLL1 MUTATED CBLL1 WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              2             136
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CBLL1 MUTATED     1   1   4   0
  CBLL1 WILD-TYPE  16  91 325  50
D1137V5, multiclass
    clus
vv   CBLL1 MUTATED CBLL1 WILD-TYPE
  T1             1              16
  T2             1              91
  T3             4             325
  T4             0              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  CBLL1 MUTATED     5   1   0
  CBLL1 WILD-TYPE 282 112  87
D1137V6, multiclass
    clus
vv   CBLL1 MUTATED CBLL1 WILD-TYPE
  N0             5             282
  N1             1             112
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1137V7, binary
                 cls
clus                0   1
  CBLL1 MUTATED     5   0
  CBLL1 WILD-TYPE 370  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CBLL1 MUTATED      5    0
  CBLL1 WILD-TYPE  370   65
   clus
vv  CBLL1 MUTATED CBLL1 WILD-TYPE
  0             5             370
  1             0              65
[1] 2 2
[1] FALSE
D1137V8, binary
                 cls
clus                0   1
  CBLL1 MUTATED     2   4
  CBLL1 WILD-TYPE 223 260
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CBLL1 MUTATED      2    4
  CBLL1 WILD-TYPE  223  260
        clus
vv       CBLL1 MUTATED CBLL1 WILD-TYPE
  FEMALE             2             223
  MALE               4             260
[1] 2 2
[1] FALSE
D1137V9, binary
                 cls
clus                0   1
  CBLL1 MUTATED     6   0
  CBLL1 WILD-TYPE 344  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CBLL1 MUTATED      6    0
  CBLL1 WILD-TYPE  344   22
     clus
vv    CBLL1 MUTATED CBLL1 WILD-TYPE
  NO              6             344
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CBLL1 MUTATED                      5                             0
  CBLL1 WILD-TYPE                  310                            47
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CBLL1 MUTATED                       1                              0
  CBLL1 WILD-TYPE                   105                             10
D1137V10, multiclass
                                clus
vv                               CBLL1 MUTATED CBLL1 WILD-TYPE
  COLON ADENOCARCINOMA                       5             310
  COLON MUCINOUS ADENOCARCINOMA              0              47
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  CBLL1 MUTATED     5   0   0   0
  CBLL1 WILD-TYPE 340   4  31  25
D1137V11, multiclass
    clus
vv   CBLL1 MUTATED CBLL1 WILD-TYPE
  R0             5             340
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1137V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CBLL1 MUTATED                                  0     0
  CBLL1 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CBLL1 MUTATED                           1     3
  CBLL1 WILD-TYPE                        21   223
D1137V13, multiclass
                                  clus
vv                                 CBLL1 MUTATED CBLL1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        3             223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1138) Variable = CTSZ MUTATION ANALYSIS
D1138V1, survival
                sevent
clus2              0   1
  CTSZ MUTATED     4   2
  CTSZ WILD-TYPE 374  91
  CTSZ MUTATED CTSZ WILD-TYPE 
             6            465 
  CTSZ MUTATED CTSZ WILD-TYPE 
             2             91 
$`CTSZ MUTATED`
TCGA-A6-6652 TCGA-AA-3715 TCGA-AA-3968 TCGA-D5-6932 TCGA-F4-6856 TCGA-G4-6303 
       24.69        19.04        21.99        11.38        35.31        65.85 

$`CTSZ WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6654 
       25.08        25.18        24.16        21.76        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 
       36.00         5.03        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       20.98        34.03         2.01        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        4.80         1.51        12.00        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6304 TCGA-G4-6306 
        0.53        47.41       133.18        74.56        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  CTSZ MUTATED CTSZ WILD-TYPE 
         11.38           0.00 
  CTSZ MUTATED CTSZ WILD-TYPE 
         65.85         148.01 
  CTSZ MUTATED CTSZ WILD-TYPE 
         23.34          20.12 
[1] "11.4 - 65.8 (23.3)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.5"
D1138V2, continuous
D1138V3, binary
                cls
clus               0   1
  CTSZ MUTATED     6   0
  CTSZ WILD-TYPE 360 119
[1] "tbl2"
                cls
clus             [,1] [,2]
  CTSZ MUTATED      6    0
  CTSZ WILD-TYPE  360  119
        clus
vv       CTSZ MUTATED CTSZ WILD-TYPE
  COLON             6            360
  RECTUM            0            119
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CTSZ MUTATED         2        0        1         1         0         0
  CTSZ WILD-TYPE      89        1       31       137        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CTSZ MUTATED           0          0          0          0        1         1
  CTSZ WILD-TYPE        24         11         59         42       47        17
                vv
clus             STAGE IVB
  CTSZ MUTATED           0
  CTSZ WILD-TYPE         1
D1138V4, multiclass
            clus
vv           CTSZ MUTATED CTSZ WILD-TYPE
  STAGE I               2             89
  STAGE IA              0              1
  STAGE II              1             31
  STAGE IIA             1            137
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            0             59
  STAGE IIIC            0             42
  STAGE IV              1             47
  STAGE IVA             1             17
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  CTSZ MUTATED     0   2   4   0
  CTSZ WILD-TYPE  17  90 325  50
D1138V5, multiclass
    clus
vv   CTSZ MUTATED CTSZ WILD-TYPE
  T1            0             17
  T2            2             90
  T3            4            325
  T4            0             50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  CTSZ MUTATED     5   1   0
  CTSZ WILD-TYPE 282 112  87
D1138V6, multiclass
    clus
vv   CTSZ MUTATED CTSZ WILD-TYPE
  N0            5            282
  N1            1            112
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1138V7, binary
                cls
clus               0   1
  CTSZ MUTATED     4   2
  CTSZ WILD-TYPE 371  63
[1] "tbl2"
                cls
clus             [,1] [,2]
  CTSZ MUTATED      4    2
  CTSZ WILD-TYPE  371   63
   clus
vv  CTSZ MUTATED CTSZ WILD-TYPE
  0            4            371
  1            2             63
[1] 2 2
[1] FALSE
D1138V8, binary
                cls
clus               0   1
  CTSZ MUTATED     2   4
  CTSZ WILD-TYPE 223 260
[1] "tbl2"
                cls
clus             [,1] [,2]
  CTSZ MUTATED      2    4
  CTSZ WILD-TYPE  223  260
        clus
vv       CTSZ MUTATED CTSZ WILD-TYPE
  FEMALE            2            223
  MALE              4            260
[1] 2 2
[1] FALSE
D1138V9, binary
                cls
clus               0   1
  CTSZ MUTATED     6   0
  CTSZ WILD-TYPE 344  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  CTSZ MUTATED      6    0
  CTSZ WILD-TYPE  344   22
     clus
vv    CTSZ MUTATED CTSZ WILD-TYPE
  NO             6            344
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CTSZ MUTATED                      5                             1
  CTSZ WILD-TYPE                  310                            46
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CTSZ MUTATED                       0                              0
  CTSZ WILD-TYPE                   106                             10
D1138V10, multiclass
                                clus
vv                               CTSZ MUTATED CTSZ WILD-TYPE
  COLON ADENOCARCINOMA                      5            310
  COLON MUCINOUS ADENOCARCINOMA             1             46
  RECTAL ADENOCARCINOMA                     0            106
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  CTSZ MUTATED     5   0   0   0
  CTSZ WILD-TYPE 340   4  31  25
D1138V11, multiclass
    clus
vv   CTSZ MUTATED CTSZ WILD-TYPE
  R0            5            340
  R1            0              4
  R2            0             31
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1138V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CTSZ MUTATED                                  0     0
  CTSZ WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  CTSZ MUTATED                           1     3
  CTSZ WILD-TYPE                        21   223
D1138V13, multiclass
                                  clus
vv                                 CTSZ MUTATED CTSZ WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                       3            223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1139) Variable = GLDN MUTATION ANALYSIS
D1139V1, survival
                sevent
clus2              0   1
  GLDN MUTATED     6   2
  GLDN WILD-TYPE 372  91
  GLDN MUTATED GLDN WILD-TYPE 
             8            463 
  GLDN MUTATED GLDN WILD-TYPE 
             2             91 
$`GLDN MUTATED`
TCGA-AA-3977 TCGA-CA-6718 TCGA-D5-6537 TCGA-D5-6927 TCGA-F4-6856 TCGA-G4-6306 
       25.02        10.06         4.80         9.44        35.31        44.68 
TCGA-AG-3581 TCGA-AG-3892 
        7.07        13.02 

$`GLDN WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07        12.20        12.76        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6929 
        4.41        12.43        14.30         9.04        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
        0.53        47.41       133.18        74.56        65.85        53.62 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3582 TCGA-AG-3583 
       36.03        12.00        32.02         8.02        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       17.03        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  GLDN MUTATED GLDN WILD-TYPE 
           4.8            0.0 
  GLDN MUTATED GLDN WILD-TYPE 
         44.68         148.01 
  GLDN MUTATED GLDN WILD-TYPE 
         11.54          20.28 
[1] "4.8 - 44.7 (11.5)"  "0.0 - 148.0 (20.3)"
[1] "hr=" "1.8"
D1139V2, continuous
D1139V3, binary
                cls
clus               0   1
  GLDN MUTATED     7   2
  GLDN WILD-TYPE 359 117
[1] "tbl2"
                cls
clus             [,1] [,2]
  GLDN MUTATED      7    2
  GLDN WILD-TYPE  359  117
        clus
vv       GLDN MUTATED GLDN WILD-TYPE
  COLON             7            359
  RECTUM            2            117
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GLDN MUTATED         3        0        0         4         0         0
  GLDN WILD-TYPE      88        1       32       134        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  GLDN MUTATED           0          0          1          0        0         0
  GLDN WILD-TYPE        24         11         58         42       48        18
                vv
clus             STAGE IVB
  GLDN MUTATED           0
  GLDN WILD-TYPE         1
D1139V4, multiclass
            clus
vv           GLDN MUTATED GLDN WILD-TYPE
  STAGE I               3             88
  STAGE IA              0              1
  STAGE II              0             32
  STAGE IIA             4            134
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            1             58
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  GLDN MUTATED     1   4   4   0
  GLDN WILD-TYPE  16  88 325  50
D1139V5, multiclass
    clus
vv   GLDN MUTATED GLDN WILD-TYPE
  T1            1             16
  T2            4             88
  T3            4            325
  T4            0             50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  GLDN MUTATED     8   1   0
  GLDN WILD-TYPE 279 112  87
D1139V6, multiclass
    clus
vv   GLDN MUTATED GLDN WILD-TYPE
  N0            8            279
  N1            1            112
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1139V7, binary
                cls
clus               0   1
  GLDN MUTATED     7   0
  GLDN WILD-TYPE 368  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  GLDN MUTATED      7    0
  GLDN WILD-TYPE  368   65
   clus
vv  GLDN MUTATED GLDN WILD-TYPE
  0            7            368
  1            0             65
[1] 2 2
[1] FALSE
D1139V8, binary
                cls
clus               0   1
  GLDN MUTATED     2   7
  GLDN WILD-TYPE 223 257
[1] "tbl2"
                cls
clus             [,1] [,2]
  GLDN MUTATED      2    7
  GLDN WILD-TYPE  223  257
        clus
vv       GLDN MUTATED GLDN WILD-TYPE
  FEMALE            2            223
  MALE              7            257
[1] 2 2
[1] FALSE
D1139V9, binary
                cls
clus               0   1
  GLDN MUTATED     8   0
  GLDN WILD-TYPE 342  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  GLDN MUTATED      8    0
  GLDN WILD-TYPE  342   22
     clus
vv    GLDN MUTATED GLDN WILD-TYPE
  NO             8            342
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  GLDN MUTATED                      6                             1
  GLDN WILD-TYPE                  309                            46
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  GLDN MUTATED                       2                              0
  GLDN WILD-TYPE                   104                             10
D1139V10, multiclass
                                clus
vv                               GLDN MUTATED GLDN WILD-TYPE
  COLON ADENOCARCINOMA                      6            309
  COLON MUCINOUS ADENOCARCINOMA             1             46
  RECTAL ADENOCARCINOMA                     2            104
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  GLDN MUTATED     7   0   0   1
  GLDN WILD-TYPE 338   4  31  24
D1139V11, multiclass
    clus
vv   GLDN MUTATED GLDN WILD-TYPE
  R0            7            338
  R1            0              4
  R2            0             31
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1139V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GLDN MUTATED                                  0     1
  GLDN WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  GLDN MUTATED                           0     4
  GLDN WILD-TYPE                        22   222
D1139V13, multiclass
                                  clus
vv                                 GLDN MUTATED GLDN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       4            222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1140) Variable = RARRES3 MUTATION ANALYSIS
D1140V1, survival
                   sevent
clus2                 0   1
  RARRES3 MUTATED     3   1
  RARRES3 WILD-TYPE 375  92
  RARRES3 MUTATED RARRES3 WILD-TYPE 
                4               467 
  RARRES3 MUTATED RARRES3 WILD-TYPE 
                1                92 
$`RARRES3 MUTATED`
TCGA-AA-3710 TCGA-CA-5797 TCGA-CM-6168 TCGA-DM-A1DA 
       26.99         3.29        12.99         7.50 

$`RARRES3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
       19.00        36.00         5.03        85.05        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-6715 
        3.19         1.61        12.69         3.06         3.25         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       14.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
       12.59       140.38        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  RARRES3 MUTATED RARRES3 WILD-TYPE 
             3.29              0.00 
  RARRES3 MUTATED RARRES3 WILD-TYPE 
            26.99            148.01 
  RARRES3 MUTATED RARRES3 WILD-TYPE 
           10.245            20.280 
[1] "3.3 - 27.0 (10.2)"  "0.0 - 148.0 (20.3)"
[1] "hr=" "2.5"
D1140V2, continuous
D1140V3, binary
                   cls
clus                  0   1
  RARRES3 MUTATED     5   0
  RARRES3 WILD-TYPE 361 119
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RARRES3 MUTATED      5    0
  RARRES3 WILD-TYPE  361  119
        clus
vv       RARRES3 MUTATED RARRES3 WILD-TYPE
  COLON                5               361
  RECTUM               0               119
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RARRES3 MUTATED         0        0        0         3         0         0
  RARRES3 WILD-TYPE      91        1       32       135        10         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RARRES3 MUTATED           0          0          0          2        0
  RARRES3 WILD-TYPE        24         11         59         40       48
                   vv
clus                STAGE IVA STAGE IVB
  RARRES3 MUTATED           0         0
  RARRES3 WILD-TYPE        18         1
D1140V4, multiclass
            clus
vv           RARRES3 MUTATED RARRES3 WILD-TYPE
  STAGE I                  0                91
  STAGE IA                 0                 1
  STAGE II                 0                32
  STAGE IIA                3               135
  STAGE IIB                0                10
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               0                11
  STAGE IIIB               0                59
  STAGE IIIC               2                40
  STAGE IV                 0                48
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  RARRES3 MUTATED     0   0   5   0
  RARRES3 WILD-TYPE  17  92 324  50
D1140V5, multiclass
    clus
vv   RARRES3 MUTATED RARRES3 WILD-TYPE
  T1               0                17
  T2               0                92
  T3               5               324
  T4               0                50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  RARRES3 MUTATED     3   0   2
  RARRES3 WILD-TYPE 284 113  85
D1140V6, multiclass
    clus
vv   RARRES3 MUTATED RARRES3 WILD-TYPE
  N0               3               284
  N1               0               113
  N2               2                85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1140V7, binary
                   cls
clus                  0   1
  RARRES3 MUTATED     4   0
  RARRES3 WILD-TYPE 371  65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RARRES3 MUTATED      4    0
  RARRES3 WILD-TYPE  371   65
   clus
vv  RARRES3 MUTATED RARRES3 WILD-TYPE
  0               4               371
  1               0                65
[1] 2 2
[1] FALSE
D1140V8, binary
                   cls
clus                  0   1
  RARRES3 MUTATED     3   2
  RARRES3 WILD-TYPE 222 262
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RARRES3 MUTATED      3    2
  RARRES3 WILD-TYPE  222  262
        clus
vv       RARRES3 MUTATED RARRES3 WILD-TYPE
  FEMALE               3               222
  MALE                 2               262
[1] 2 2
[1] FALSE
D1140V9, binary
                   cls
clus                  0   1
  RARRES3 MUTATED     3   0
  RARRES3 WILD-TYPE 347  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RARRES3 MUTATED      3    0
  RARRES3 WILD-TYPE  347   22
     clus
vv    RARRES3 MUTATED RARRES3 WILD-TYPE
  NO                3               347
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  RARRES3 MUTATED                      4                             1
  RARRES3 WILD-TYPE                  311                            46
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  RARRES3 MUTATED                       0                              0
  RARRES3 WILD-TYPE                   106                             10
D1140V10, multiclass
                                clus
vv                               RARRES3 MUTATED RARRES3 WILD-TYPE
  COLON ADENOCARCINOMA                         4               311
  COLON MUCINOUS ADENOCARCINOMA                1                46
  RECTAL ADENOCARCINOMA                        0               106
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  RARRES3 MUTATED     4   0   0   0
  RARRES3 WILD-TYPE 341   4  31  25
D1140V11, multiclass
    clus
vv   RARRES3 MUTATED RARRES3 WILD-TYPE
  R0               4               341
  R1               0                 4
  R2               0                31
  RX               0                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1140V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RARRES3 MUTATED                                  0     1
  RARRES3 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  RARRES3 MUTATED                           1     2
  RARRES3 WILD-TYPE                        21   224
D1140V13, multiclass
                                  clus
vv                                 RARRES3 MUTATED RARRES3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                10
  BLACK OR AFRICAN AMERICAN                      1                21
  WHITE                                          2               224
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1141) Variable = CBLN3 MUTATION ANALYSIS
D1141V1, survival
                 sevent
clus2               0   1
  CBLN3 MUTATED     6   0
  CBLN3 WILD-TYPE 372  93
  CBLN3 MUTATED CBLN3 WILD-TYPE 
              6             465 
  CBLN3 MUTATED CBLN3 WILD-TYPE 
              0              93 
$`CBLN3 MUTATED`
TCGA-AA-3713 TCGA-CA-6717 TCGA-CM-6171 TCGA-D5-6536 TCGA-F4-6856 TCGA-G4-6321 
       19.04        12.76        14.04        17.85        35.31        22.09 

$`CBLN3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07        12.20        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 
       14.99        12.99        13.02        15.02        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 
       18.25         1.32        43.27        15.12         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
        0.53        47.41       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  CBLN3 MUTATED CBLN3 WILD-TYPE 
          12.76            0.00 
  CBLN3 MUTATED CBLN3 WILD-TYPE 
          35.31          148.01 
  CBLN3 MUTATED CBLN3 WILD-TYPE 
         18.445          20.280 
[1] "12.8 - 35.3 (18.4)" "0.0 - 148.0 (20.3)"
[1] "hr="     "3300000"
D1141V2, continuous
D1141V3, binary
                 cls
clus                0   1
  CBLN3 MUTATED     6   0
  CBLN3 WILD-TYPE 360 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CBLN3 MUTATED      6    0
  CBLN3 WILD-TYPE  360  119
        clus
vv       CBLN3 MUTATED CBLN3 WILD-TYPE
  COLON              6             360
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CBLN3 MUTATED         2        0        0         2         0         0
  CBLN3 WILD-TYPE      89        1       32       136        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CBLN3 MUTATED           1          0          0          0        1         0
  CBLN3 WILD-TYPE        23         11         59         42       47        18
                 vv
clus              STAGE IVB
  CBLN3 MUTATED           0
  CBLN3 WILD-TYPE         1
D1141V4, multiclass
            clus
vv           CBLN3 MUTATED CBLN3 WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              2             136
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             0              42
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CBLN3 MUTATED     0   3   3   0
  CBLN3 WILD-TYPE  17  89 326  50
D1141V5, multiclass
    clus
vv   CBLN3 MUTATED CBLN3 WILD-TYPE
  T1             0              17
  T2             3              89
  T3             3             326
  T4             0              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  CBLN3 MUTATED     5   1   0
  CBLN3 WILD-TYPE 282 112  87
D1141V6, multiclass
    clus
vv   CBLN3 MUTATED CBLN3 WILD-TYPE
  N0             5             282
  N1             1             112
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1141V7, binary
                 cls
clus                0   1
  CBLN3 MUTATED     4   1
  CBLN3 WILD-TYPE 371  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CBLN3 MUTATED      4    1
  CBLN3 WILD-TYPE  371   64
   clus
vv  CBLN3 MUTATED CBLN3 WILD-TYPE
  0             4             371
  1             1              64
[1] 2 2
[1] FALSE
D1141V8, binary
                 cls
clus                0   1
  CBLN3 MUTATED     2   4
  CBLN3 WILD-TYPE 223 260
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CBLN3 MUTATED      2    4
  CBLN3 WILD-TYPE  223  260
        clus
vv       CBLN3 MUTATED CBLN3 WILD-TYPE
  FEMALE             2             223
  MALE               4             260
[1] 2 2
[1] FALSE
D1141V9, binary
                 cls
clus                0   1
  CBLN3 MUTATED     5   1
  CBLN3 WILD-TYPE 345  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CBLN3 MUTATED      5    1
  CBLN3 WILD-TYPE  345   21
     clus
vv    CBLN3 MUTATED CBLN3 WILD-TYPE
  NO              5             345
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CBLN3 MUTATED                      4                             2
  CBLN3 WILD-TYPE                  311                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CBLN3 MUTATED                       0                              0
  CBLN3 WILD-TYPE                   106                             10
D1141V10, multiclass
                                clus
vv                               CBLN3 MUTATED CBLN3 WILD-TYPE
  COLON ADENOCARCINOMA                       4             311
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  CBLN3 MUTATED     4   0   1   1
  CBLN3 WILD-TYPE 341   4  30  24
D1141V11, multiclass
    clus
vv   CBLN3 MUTATED CBLN3 WILD-TYPE
  R0             4             341
  R1             0               4
  R2             1              30
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1141V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CBLN3 MUTATED                                  0     1
  CBLN3 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CBLN3 MUTATED                           0     4
  CBLN3 WILD-TYPE                        22   222
D1141V13, multiclass
                                  clus
vv                                 CBLN3 MUTATED CBLN3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        4             222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1142) Variable = LRRN3 MUTATION ANALYSIS
D1142V1, survival
                 sevent
clus2               0   1
  LRRN3 MUTATED    18   4
  LRRN3 WILD-TYPE 360  89
  LRRN3 MUTATED LRRN3 WILD-TYPE 
             22             449 
  LRRN3 MUTATED LRRN3 WILD-TYPE 
              4              89 
$`LRRN3 MUTATED`
TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-5666 TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3672 
       34.65        32.75        32.71         3.02        63.98         0.92 
TCGA-AA-3715 TCGA-AA-3941 TCGA-AA-A00E TCGA-AA-A00R TCGA-AA-A01P TCGA-AA-A01R 
       19.04        24.00        30.02         0.99        38.07        35.01 
TCGA-AZ-4315 TCGA-CM-4743 TCGA-CM-6165 TCGA-CM-6676 TCGA-D5-6930 TCGA-F4-6570 
       58.39        23.05        16.04        11.08         1.51         6.18 
TCGA-G4-6293 TCGA-G4-6628 TCGA-AF-6136 TCGA-AG-A00C 
      133.18        79.69        15.39         6.02 

$`LRRN3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5657 
       16.57        33.34        36.53        14.53        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       30.44        29.19        33.53        23.61        22.09        22.06 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       27.09        22.52         8.38        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 
       20.28         7.04         1.02        35.01         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
       13.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       36.03         8.05        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       78.08         6.05         6.97        54.02         2.01        14.01 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
        2.01        12.99        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       19.00        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       27.02        42.02        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
        1.02         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
       16.31         0.95        33.01        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 
       21.14        82.95         1.91       124.27        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6166 TCGA-CM-6167 
       15.02        12.00         2.96        29.03        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       13.05        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
        8.61        31.96        35.74        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
       35.31        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 
       35.80        26.17        91.79        46.75        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       16.83        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
       13.94        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  LRRN3 MUTATED LRRN3 WILD-TYPE 
           0.92            0.00 
  LRRN3 MUTATED LRRN3 WILD-TYPE 
         133.18          148.01 
  LRRN3 MUTATED LRRN3 WILD-TYPE 
         23.525          20.120 
[1] "0.9 - 133.2 (23.5)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.2"
D1142V2, continuous
D1142V3, binary
                 cls
clus                0   1
  LRRN3 MUTATED    21   2
  LRRN3 WILD-TYPE 345 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LRRN3 MUTATED     21    2
  LRRN3 WILD-TYPE  345  117
        clus
vv       LRRN3 MUTATED LRRN3 WILD-TYPE
  COLON             21             345
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  LRRN3 MUTATED         3        0        3         6         1         1
  LRRN3 WILD-TYPE      88        1       29       132         9         0
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  LRRN3 MUTATED           4          0          2          1        1         1
  LRRN3 WILD-TYPE        20         11         57         41       47        17
                 vv
clus              STAGE IVB
  LRRN3 MUTATED           0
  LRRN3 WILD-TYPE         1
D1142V4, multiclass
            clus
vv           LRRN3 MUTATED LRRN3 WILD-TYPE
  STAGE I                3              88
  STAGE IA               0               1
  STAGE II               3              29
  STAGE IIA              6             132
  STAGE IIB              1               9
  STAGE IIC              1               0
  STAGE III              4              20
  STAGE IIIA             0              11
  STAGE IIIB             2              57
  STAGE IIIC             1              41
  STAGE IV               1              47
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  LRRN3 MUTATED     0   3  16   4
  LRRN3 WILD-TYPE  17  89 313  46
D1142V5, multiclass
    clus
vv   LRRN3 MUTATED LRRN3 WILD-TYPE
  T1             0              17
  T2             3              89
  T3            16             313
  T4             4              46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  LRRN3 MUTATED    14   6   3
  LRRN3 WILD-TYPE 273 107  84
D1142V6, multiclass
    clus
vv   LRRN3 MUTATED LRRN3 WILD-TYPE
  N0            14             273
  N1             6             107
  N2             3              84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1142V7, binary
                 cls
clus                0   1
  LRRN3 MUTATED    20   2
  LRRN3 WILD-TYPE 355  63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LRRN3 MUTATED     20    2
  LRRN3 WILD-TYPE  355   63
   clus
vv  LRRN3 MUTATED LRRN3 WILD-TYPE
  0            20             355
  1             2              63
[1] 2 2
[1] FALSE
D1142V8, binary
                 cls
clus                0   1
  LRRN3 MUTATED    11  12
  LRRN3 WILD-TYPE 214 252
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LRRN3 MUTATED     11   12
  LRRN3 WILD-TYPE  214  252
        clus
vv       LRRN3 MUTATED LRRN3 WILD-TYPE
  FEMALE            11             214
  MALE              12             252
[1] 2 2
[1] FALSE
D1142V9, binary
                 cls
clus                0   1
  LRRN3 MUTATED    17   3
  LRRN3 WILD-TYPE 333  19
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LRRN3 MUTATED     17    3
  LRRN3 WILD-TYPE  333   19
     clus
vv    LRRN3 MUTATED LRRN3 WILD-TYPE
  NO             17             333
  YES             3              19
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  LRRN3 MUTATED                     18                             3
  LRRN3 WILD-TYPE                  297                            44
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  LRRN3 MUTATED                       2                              0
  LRRN3 WILD-TYPE                   104                             10
D1142V10, multiclass
                                clus
vv                               LRRN3 MUTATED LRRN3 WILD-TYPE
  COLON ADENOCARCINOMA                      18             297
  COLON MUCINOUS ADENOCARCINOMA              3              44
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  LRRN3 MUTATED    20   0   1   0
  LRRN3 WILD-TYPE 325   4  30  25
D1142V11, multiclass
    clus
vv   LRRN3 MUTATED LRRN3 WILD-TYPE
  R0            20             325
  R1             0               4
  R2             1              30
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1142V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  LRRN3 MUTATED                                  0     0
  LRRN3 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  LRRN3 MUTATED                           0    12
  LRRN3 WILD-TYPE                        22   214
D1142V13, multiclass
                                  clus
vv                                 LRRN3 MUTATED LRRN3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                       12             214
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1143) Variable = WDR5B MUTATION ANALYSIS
D1143V1, survival
                 sevent
clus2               0   1
  WDR5B MUTATED     9   4
  WDR5B WILD-TYPE 369  89
  WDR5B MUTATED WDR5B WILD-TYPE 
             13             458 
  WDR5B MUTATED WDR5B WILD-TYPE 
              4              89 
$`WDR5B MUTATED`
TCGA-AA-3950 TCGA-AA-A010 TCGA-AA-A01K TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-6162 
       24.00        34.98        31.00        12.76        10.06        12.00 
TCGA-CM-6164 TCGA-CM-6678 TCGA-D5-6924 TCGA-G4-6303 TCGA-G4-6626 TCGA-AF-3913 
       29.03        11.01        14.30        65.85        46.75        10.39 
TCGA-AH-6643 
        0.69 

$`WDR5B WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6165 
       15.02        15.02        17.03        15.02         2.96        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6679 
       11.01        12.95        13.05        11.08        11.08        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        3.68         4.41        12.43         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       34.49        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
       17.49         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  WDR5B MUTATED WDR5B WILD-TYPE 
           0.69            0.00 
  WDR5B MUTATED WDR5B WILD-TYPE 
          65.85          148.01 
  WDR5B MUTATED WDR5B WILD-TYPE 
         14.300          20.235 
[1] "0.7 - 65.8 (14.3)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.7"
D1143V2, continuous
D1143V3, binary
                 cls
clus                0   1
  WDR5B MUTATED    11   2
  WDR5B WILD-TYPE 355 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WDR5B MUTATED     11    2
  WDR5B WILD-TYPE  355  117
        clus
vv       WDR5B MUTATED WDR5B WILD-TYPE
  COLON             11             355
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  WDR5B MUTATED         0        0        0         6         1         0
  WDR5B WILD-TYPE      91        1       32       132         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  WDR5B MUTATED           0          0          1          2        2         1
  WDR5B WILD-TYPE        24         11         58         40       46        17
                 vv
clus              STAGE IVB
  WDR5B MUTATED           0
  WDR5B WILD-TYPE         1
D1143V4, multiclass
            clus
vv           WDR5B MUTATED WDR5B WILD-TYPE
  STAGE I                0              91
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              6             132
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             2              40
  STAGE IV               2              46
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  WDR5B MUTATED     0   0  11   2
  WDR5B WILD-TYPE  17  92 318  48
D1143V5, multiclass
    clus
vv   WDR5B MUTATED WDR5B WILD-TYPE
  T1             0              17
  T2             0              92
  T3            11             318
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  WDR5B MUTATED     7   4   2
  WDR5B WILD-TYPE 280 109  85
D1143V6, multiclass
    clus
vv   WDR5B MUTATED WDR5B WILD-TYPE
  N0             7             280
  N1             4             109
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1143V7, binary
                 cls
clus                0   1
  WDR5B MUTATED    10   3
  WDR5B WILD-TYPE 365  62
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WDR5B MUTATED     10    3
  WDR5B WILD-TYPE  365   62
   clus
vv  WDR5B MUTATED WDR5B WILD-TYPE
  0            10             365
  1             3              62
[1] 2 2
[1] FALSE
D1143V8, binary
                 cls
clus                0   1
  WDR5B MUTATED     7   6
  WDR5B WILD-TYPE 218 258
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WDR5B MUTATED      7    6
  WDR5B WILD-TYPE  218  258
        clus
vv       WDR5B MUTATED WDR5B WILD-TYPE
  FEMALE             7             218
  MALE               6             258
[1] 2 2
[1] FALSE
D1143V9, binary
                 cls
clus                0   1
  WDR5B MUTATED    12   0
  WDR5B WILD-TYPE 338  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WDR5B MUTATED     12    0
  WDR5B WILD-TYPE  338   22
     clus
vv    WDR5B MUTATED WDR5B WILD-TYPE
  NO             12             338
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  WDR5B MUTATED                      8                             3
  WDR5B WILD-TYPE                  307                            44
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  WDR5B MUTATED                       2                              0
  WDR5B WILD-TYPE                   104                             10
D1143V10, multiclass
                                clus
vv                               WDR5B MUTATED WDR5B WILD-TYPE
  COLON ADENOCARCINOMA                       8             307
  COLON MUCINOUS ADENOCARCINOMA              3              44
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  WDR5B MUTATED    11   0   0   2
  WDR5B WILD-TYPE 334   4  31  23
D1143V11, multiclass
    clus
vv   WDR5B MUTATED WDR5B WILD-TYPE
  R0            11             334
  R1             0               4
  R2             0              31
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1143V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  WDR5B MUTATED                                  0     2
  WDR5B WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  WDR5B MUTATED                           1     7
  WDR5B WILD-TYPE                        21   219
D1143V13, multiclass
                                  clus
vv                                 WDR5B MUTATED WDR5B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               9
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        7             219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1144) Variable = CLDND1 MUTATION ANALYSIS
D1144V1, survival
                  sevent
clus2                0   1
  CLDND1 MUTATED     9   0
  CLDND1 WILD-TYPE 369  93
  CLDND1 MUTATED CLDND1 WILD-TYPE 
               9              462 
  CLDND1 MUTATED CLDND1 WILD-TYPE 
               0               93 
$`CLDND1 MUTATED`
TCGA-A6-3809 TCGA-A6-6138 TCGA-AZ-4315 TCGA-CK-4952 TCGA-CM-5349 TCGA-D5-5538 
       32.75        22.52        58.39        15.62        30.08        12.26 
TCGA-D5-6540 TCGA-AG-A002 TCGA-EI-6506 
       16.14        20.98        20.55 

$`CLDND1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       22.06        32.71        27.09         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       33.01        21.44        17.82         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       29.06        22.03        22.98        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5539 
       11.08        11.01        10.06        12.03        45.40        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 
       15.12        17.85         4.80        17.13        12.49        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  CLDND1 MUTATED CLDND1 WILD-TYPE 
           12.26             0.00 
  CLDND1 MUTATED CLDND1 WILD-TYPE 
           58.39           148.01 
  CLDND1 MUTATED CLDND1 WILD-TYPE 
          20.980           20.085 
[1] "12.3 - 58.4 (21.0)" "0.0 - 148.0 (20.1)"
[1] "hr="     "9200000"
D1144V2, continuous
D1144V3, binary
                  cls
clus                 0   1
  CLDND1 MUTATED     8   2
  CLDND1 WILD-TYPE 358 117
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CLDND1 MUTATED      8    2
  CLDND1 WILD-TYPE  358  117
        clus
vv       CLDND1 MUTATED CLDND1 WILD-TYPE
  COLON               8              358
  RECTUM              2              117
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CLDND1 MUTATED         3        0        1         3         1         0
  CLDND1 WILD-TYPE      88        1       31       135         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CLDND1 MUTATED           0          0          1          1        0
  CLDND1 WILD-TYPE        24         11         58         41       48
                  vv
clus               STAGE IVA STAGE IVB
  CLDND1 MUTATED           0         0
  CLDND1 WILD-TYPE        18         1
D1144V4, multiclass
            clus
vv           CLDND1 MUTATED CLDND1 WILD-TYPE
  STAGE I                 3               88
  STAGE IA                0                1
  STAGE II                1               31
  STAGE IIA               3              135
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              1               58
  STAGE IIIC              1               41
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  CLDND1 MUTATED     0   3   4   3
  CLDND1 WILD-TYPE  17  89 325  47
D1144V5, multiclass
    clus
vv   CLDND1 MUTATED CLDND1 WILD-TYPE
  T1              0               17
  T2              3               89
  T3              4              325
  T4              3               47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  CLDND1 MUTATED     8   1   1
  CLDND1 WILD-TYPE 279 112  86
D1144V6, multiclass
    clus
vv   CLDND1 MUTATED CLDND1 WILD-TYPE
  N0              8              279
  N1              1              112
  N2              1               86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1144V7, binary
                  cls
clus                 0   1
  CLDND1 MUTATED    10   0
  CLDND1 WILD-TYPE 365  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CLDND1 MUTATED     10    0
  CLDND1 WILD-TYPE  365   65
   clus
vv  CLDND1 MUTATED CLDND1 WILD-TYPE
  0             10              365
  1              0               65
[1] 2 2
[1] FALSE
D1144V8, binary
                  cls
clus                 0   1
  CLDND1 MUTATED     6   4
  CLDND1 WILD-TYPE 219 260
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CLDND1 MUTATED      6    4
  CLDND1 WILD-TYPE  219  260
        clus
vv       CLDND1 MUTATED CLDND1 WILD-TYPE
  FEMALE              6              219
  MALE                4              260
[1] 2 2
[1] FALSE
D1144V9, binary
                  cls
clus                 0   1
  CLDND1 MUTATED     8   0
  CLDND1 WILD-TYPE 342  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CLDND1 MUTATED      8    0
  CLDND1 WILD-TYPE  342   22
     clus
vv    CLDND1 MUTATED CLDND1 WILD-TYPE
  NO               8              342
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CLDND1 MUTATED                      5                             3
  CLDND1 WILD-TYPE                  310                            44
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CLDND1 MUTATED                       2                              0
  CLDND1 WILD-TYPE                   104                             10
D1144V10, multiclass
                                clus
vv                               CLDND1 MUTATED CLDND1 WILD-TYPE
  COLON ADENOCARCINOMA                        5              310
  COLON MUCINOUS ADENOCARCINOMA               3               44
  RECTAL ADENOCARCINOMA                       2              104
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  CLDND1 MUTATED     8   0   0   1
  CLDND1 WILD-TYPE 337   4  31  24
D1144V11, multiclass
    clus
vv   CLDND1 MUTATED CLDND1 WILD-TYPE
  R0              8              337
  R1              0                4
  R2              0               31
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1144V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CLDND1 MUTATED                                  0     0
  CLDND1 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  CLDND1 MUTATED                           0     8
  CLDND1 WILD-TYPE                        22   218
D1144V13, multiclass
                                  clus
vv                                 CLDND1 MUTATED CLDND1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         8              218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1145) Variable = MERTK MUTATION ANALYSIS
D1145V1, survival
                 sevent
clus2               0   1
  MERTK MUTATED    17   3
  MERTK WILD-TYPE 361  90
  MERTK MUTATED MERTK WILD-TYPE 
             20             451 
  MERTK MUTATED MERTK WILD-TYPE 
              3              90 
$`MERTK MUTATED`
TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3833 TCGA-AA-3866 TCGA-AA-A01Q TCGA-AD-6889 
        3.02        63.98        15.95        17.03         1.02        56.55 
TCGA-AY-5543 TCGA-AZ-6601 TCGA-CA-6717 TCGA-CM-5349 TCGA-D5-6539 TCGA-D5-6923 
       33.01       100.01        12.76        30.08        12.49        12.43 
TCGA-F4-6570 TCGA-G4-6299 TCGA-G4-6588 TCGA-AF-6655 TCGA-AG-3890 TCGA-AG-A002 
        6.18        74.56        26.17        20.02        17.03        20.98 
TCGA-DC-6682 TCGA-DY-A0XA 
        4.01       126.44 

$`MERTK WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3867 TCGA-AA-3869 
       31.07        31.07        30.05        53.00        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
       38.07        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
        0.07        21.37        15.52         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       16.31         0.95        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77        12.10        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.20        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5861 
       13.02        29.06        22.03        22.98        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6924 
       16.14        15.58         1.48         3.68         4.41        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       31.96        35.74        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
      133.18        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       15.39        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
        1.02        17.95        36.95        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 
       27.95        10.98        19.99         5.95         5.03         5.29 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  MERTK MUTATED MERTK WILD-TYPE 
           1.02            0.00 
  MERTK MUTATED MERTK WILD-TYPE 
         126.44          148.01 
  MERTK MUTATED MERTK WILD-TYPE 
         18.525          20.280 
[1] "1.0 - 126.4 (18.5)" "0.0 - 148.0 (20.3)"
[1] "hr=" "1.7"
D1145V2, continuous
D1145V3, binary
                 cls
clus                0   1
  MERTK MUTATED    15   5
  MERTK WILD-TYPE 351 114
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MERTK MUTATED     15    5
  MERTK WILD-TYPE  351  114
        clus
vv       MERTK MUTATED MERTK WILD-TYPE
  COLON             15             351
  RECTUM             5             114
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MERTK MUTATED         4        0        4         8         0         0
  MERTK WILD-TYPE      87        1       28       130        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MERTK MUTATED           0          2          0          1        0         1
  MERTK WILD-TYPE        24          9         59         41       48        17
                 vv
clus              STAGE IVB
  MERTK MUTATED           0
  MERTK WILD-TYPE         1
D1145V4, multiclass
            clus
vv           MERTK MUTATED MERTK WILD-TYPE
  STAGE I                4              87
  STAGE IA               0               1
  STAGE II               4              28
  STAGE IIA              8             130
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             2               9
  STAGE IIIB             0              59
  STAGE IIIC             1              41
  STAGE IV               0              48
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  MERTK MUTATED     0   5  15   0
  MERTK WILD-TYPE  17  87 314  50
D1145V5, multiclass
    clus
vv   MERTK MUTATED MERTK WILD-TYPE
  T1             0              17
  T2             5              87
  T3            15             314
  T4             0              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  MERTK MUTATED    17   2   1
  MERTK WILD-TYPE 270 111  86
D1145V6, multiclass
    clus
vv   MERTK MUTATED MERTK WILD-TYPE
  N0            17             270
  N1             2             111
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1145V7, binary
                 cls
clus                0   1
  MERTK MUTATED    19   1
  MERTK WILD-TYPE 356  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MERTK MUTATED     19    1
  MERTK WILD-TYPE  356   64
   clus
vv  MERTK MUTATED MERTK WILD-TYPE
  0            19             356
  1             1              64
[1] 2 2
[1] FALSE
D1145V8, binary
                 cls
clus                0   1
  MERTK MUTATED    10  10
  MERTK WILD-TYPE 215 254
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MERTK MUTATED     10   10
  MERTK WILD-TYPE  215  254
        clus
vv       MERTK MUTATED MERTK WILD-TYPE
  FEMALE            10             215
  MALE              10             254
[1] 2 2
[1] FALSE
D1145V9, binary
                 cls
clus                0   1
  MERTK MUTATED    16   0
  MERTK WILD-TYPE 334  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MERTK MUTATED     16    0
  MERTK WILD-TYPE  334   22
     clus
vv    MERTK MUTATED MERTK WILD-TYPE
  NO             16             334
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MERTK MUTATED                     14                             1
  MERTK WILD-TYPE                  301                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MERTK MUTATED                       5                              0
  MERTK WILD-TYPE                   101                             10
D1145V10, multiclass
                                clus
vv                               MERTK MUTATED MERTK WILD-TYPE
  COLON ADENOCARCINOMA                      14             301
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      5             101
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  MERTK MUTATED    16   0   0   1
  MERTK WILD-TYPE 329   4  31  24
D1145V11, multiclass
    clus
vv   MERTK MUTATED MERTK WILD-TYPE
  R0            16             329
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1145V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MERTK MUTATED                                  0     2
  MERTK WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  MERTK MUTATED                           1    10
  MERTK WILD-TYPE                        21   216
D1145V13, multiclass
                                  clus
vv                                 MERTK MUTATED MERTK WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               9
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                       10             216
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1146) Variable = PRMT8 MUTATION ANALYSIS
D1146V1, survival
                 sevent
clus2               0   1
  PRMT8 MUTATED    11   3
  PRMT8 WILD-TYPE 367  90
  PRMT8 MUTATED PRMT8 WILD-TYPE 
             14             457 
  PRMT8 MUTATED PRMT8 WILD-TYPE 
              3              90 
$`PRMT8 MUTATED`
TCGA-A6-6781 TCGA-AA-3516 TCGA-AA-3663 TCGA-AA-3666 TCGA-AA-3710 TCGA-AA-3846 
       19.66        13.02         6.97         2.01        26.99        17.03 
TCGA-AZ-4315 TCGA-CM-6680 TCGA-D5-6539 TCGA-F4-6570 TCGA-G4-6588 TCGA-AG-A016 
       58.39        12.03        12.49         6.18        26.17         9.07 
TCGA-AG-A02N TCGA-G5-6641 
       61.97        26.43 

$`PRMT8 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
       14.93         0.00        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
       16.31         0.95        33.01        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       10.06        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
        4.80        17.13        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 
      117.07        98.24         8.61        31.96        35.74        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        35.80        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01L 
       25.97        23.01        37.02        15.95        36.03        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 
       55.76 

  PRMT8 MUTATED PRMT8 WILD-TYPE 
           2.01            0.00 
  PRMT8 MUTATED PRMT8 WILD-TYPE 
          61.97          148.01 
  PRMT8 MUTATED PRMT8 WILD-TYPE 
         15.025          20.550 
[1] "2.0 - 62.0 (15.0)"  "0.0 - 148.0 (20.6)"
[1] "hr=" "1.3"
D1146V2, continuous
D1146V3, binary
                 cls
clus                0   1
  PRMT8 MUTATED    11   3
  PRMT8 WILD-TYPE 355 116
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRMT8 MUTATED     11    3
  PRMT8 WILD-TYPE  355  116
        clus
vv       PRMT8 MUTATED PRMT8 WILD-TYPE
  COLON             11             355
  RECTUM             3             116
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PRMT8 MUTATED         0        0        2         5         0         0
  PRMT8 WILD-TYPE      91        1       30       133        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PRMT8 MUTATED           2          2          1          1        1         0
  PRMT8 WILD-TYPE        22          9         58         41       47        18
                 vv
clus              STAGE IVB
  PRMT8 MUTATED           0
  PRMT8 WILD-TYPE         1
D1146V4, multiclass
            clus
vv           PRMT8 MUTATED PRMT8 WILD-TYPE
  STAGE I                0              91
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA              5             133
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              2              22
  STAGE IIIA             2               9
  STAGE IIIB             1              58
  STAGE IIIC             1              41
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PRMT8 MUTATED     1   0  12   1
  PRMT8 WILD-TYPE  16  92 317  49
D1146V5, multiclass
    clus
vv   PRMT8 MUTATED PRMT8 WILD-TYPE
  T1             1              16
  T2             0              92
  T3            12             317
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  PRMT8 MUTATED     8   3   3
  PRMT8 WILD-TYPE 279 110  84
D1146V6, multiclass
    clus
vv   PRMT8 MUTATED PRMT8 WILD-TYPE
  N0             8             279
  N1             3             110
  N2             3              84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1146V7, binary
                 cls
clus                0   1
  PRMT8 MUTATED    11   1
  PRMT8 WILD-TYPE 364  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRMT8 MUTATED     11    1
  PRMT8 WILD-TYPE  364   64
   clus
vv  PRMT8 MUTATED PRMT8 WILD-TYPE
  0            11             364
  1             1              64
[1] 2 2
[1] FALSE
D1146V8, binary
                 cls
clus                0   1
  PRMT8 MUTATED     7   7
  PRMT8 WILD-TYPE 218 257
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRMT8 MUTATED      7    7
  PRMT8 WILD-TYPE  218  257
        clus
vv       PRMT8 MUTATED PRMT8 WILD-TYPE
  FEMALE             7             218
  MALE               7             257
[1] 2 2
[1] FALSE
D1146V9, binary
                 cls
clus                0   1
  PRMT8 MUTATED    12   0
  PRMT8 WILD-TYPE 338  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRMT8 MUTATED     12    0
  PRMT8 WILD-TYPE  338   22
     clus
vv    PRMT8 MUTATED PRMT8 WILD-TYPE
  NO             12             338
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PRMT8 MUTATED                      9                             2
  PRMT8 WILD-TYPE                  306                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PRMT8 MUTATED                       2                              1
  PRMT8 WILD-TYPE                   104                              9
D1146V10, multiclass
                                clus
vv                               PRMT8 MUTATED PRMT8 WILD-TYPE
  COLON ADENOCARCINOMA                       9             306
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             1               9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  PRMT8 MUTATED    12   0   1   0
  PRMT8 WILD-TYPE 333   4  30  25
D1146V11, multiclass
    clus
vv   PRMT8 MUTATED PRMT8 WILD-TYPE
  R0            12             333
  R1             0               4
  R2             1              30
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1146V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PRMT8 MUTATED                                  0     0
  PRMT8 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PRMT8 MUTATED                           0     7
  PRMT8 WILD-TYPE                        22   219
D1146V13, multiclass
                                  clus
vv                                 PRMT8 MUTATED PRMT8 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        7             219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1147) Variable = TCEAL5 MUTATION ANALYSIS
D1147V1, survival
                  sevent
clus2                0   1
  TCEAL5 MUTATED     4   1
  TCEAL5 WILD-TYPE 374  92
  TCEAL5 MUTATED TCEAL5 WILD-TYPE 
               5              466 
  TCEAL5 MUTATED TCEAL5 WILD-TYPE 
               1               92 
$`TCEAL5 MUTATED`
TCGA-A6-6138 TCGA-AA-A01P TCGA-AD-6889 TCGA-CM-6162 TCGA-G4-6306 
       22.52        38.07        56.55        12.00        44.68 

$`TCEAL5 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6141 TCGA-A6-6142 
       22.09        22.06        32.71        27.09         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       12.00        31.00        31.00         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       53.62        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  TCEAL5 MUTATED TCEAL5 WILD-TYPE 
              12                0 
  TCEAL5 MUTATED TCEAL5 WILD-TYPE 
           56.55           148.01 
  TCEAL5 MUTATED TCEAL5 WILD-TYPE 
          38.070           20.085 
[1] "12.0 - 56.5 (38.1)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.4"
D1147V2, continuous
D1147V3, binary
                  cls
clus                 0   1
  TCEAL5 MUTATED     5   0
  TCEAL5 WILD-TYPE 361 119
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TCEAL5 MUTATED      5    0
  TCEAL5 WILD-TYPE  361  119
        clus
vv       TCEAL5 MUTATED TCEAL5 WILD-TYPE
  COLON               5              361
  RECTUM              0              119
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TCEAL5 MUTATED         1        0        0         2         0         0
  TCEAL5 WILD-TYPE      90        1       32       136        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TCEAL5 MUTATED           1          0          1          0        0
  TCEAL5 WILD-TYPE        23         11         58         42       48
                  vv
clus               STAGE IVA STAGE IVB
  TCEAL5 MUTATED           0         0
  TCEAL5 WILD-TYPE        18         1
D1147V4, multiclass
            clus
vv           TCEAL5 MUTATED TCEAL5 WILD-TYPE
  STAGE I                 1               90
  STAGE IA                0                1
  STAGE II                0               32
  STAGE IIA               2              136
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               1               23
  STAGE IIIA              0               11
  STAGE IIIB              1               58
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  TCEAL5 MUTATED     0   2   3   0
  TCEAL5 WILD-TYPE  17  90 326  50
D1147V5, multiclass
    clus
vv   TCEAL5 MUTATED TCEAL5 WILD-TYPE
  T1              0               17
  T2              2               90
  T3              3              326
  T4              0               50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  TCEAL5 MUTATED     3   2   0
  TCEAL5 WILD-TYPE 284 111  87
D1147V6, multiclass
    clus
vv   TCEAL5 MUTATED TCEAL5 WILD-TYPE
  N0              3              284
  N1              2              111
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1147V7, binary
                  cls
clus                 0   1
  TCEAL5 MUTATED     5   0
  TCEAL5 WILD-TYPE 370  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TCEAL5 MUTATED      5    0
  TCEAL5 WILD-TYPE  370   65
   clus
vv  TCEAL5 MUTATED TCEAL5 WILD-TYPE
  0              5              370
  1              0               65
[1] 2 2
[1] FALSE
D1147V8, binary
                  cls
clus                 0   1
  TCEAL5 MUTATED     2   3
  TCEAL5 WILD-TYPE 223 261
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TCEAL5 MUTATED      2    3
  TCEAL5 WILD-TYPE  223  261
        clus
vv       TCEAL5 MUTATED TCEAL5 WILD-TYPE
  FEMALE              2              223
  MALE                3              261
[1] 2 2
[1] FALSE
D1147V9, binary
                  cls
clus                 0   1
  TCEAL5 MUTATED     4   0
  TCEAL5 WILD-TYPE 346  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TCEAL5 MUTATED      4    0
  TCEAL5 WILD-TYPE  346   22
     clus
vv    TCEAL5 MUTATED TCEAL5 WILD-TYPE
  NO               4              346
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  TCEAL5 MUTATED                      4                             1
  TCEAL5 WILD-TYPE                  311                            46
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  TCEAL5 MUTATED                       0                              0
  TCEAL5 WILD-TYPE                   106                             10
D1147V10, multiclass
                                clus
vv                               TCEAL5 MUTATED TCEAL5 WILD-TYPE
  COLON ADENOCARCINOMA                        4              311
  COLON MUCINOUS ADENOCARCINOMA               1               46
  RECTAL ADENOCARCINOMA                       0              106
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  TCEAL5 MUTATED     3   0   0   0
  TCEAL5 WILD-TYPE 342   4  31  25
D1147V11, multiclass
    clus
vv   TCEAL5 MUTATED TCEAL5 WILD-TYPE
  R0              3              342
  R1              0                4
  R2              0               31
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1147V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TCEAL5 MUTATED                                  0     1
  TCEAL5 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  TCEAL5 MUTATED                           0     3
  TCEAL5 WILD-TYPE                        22   223
D1147V13, multiclass
                                  clus
vv                                 TCEAL5 MUTATED TCEAL5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         3              223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1148) Variable = OR9Q2 MUTATION ANALYSIS
D1148V1, survival
                 sevent
clus2               0   1
  OR9Q2 MUTATED     8   5
  OR9Q2 WILD-TYPE 370  88
  OR9Q2 MUTATED OR9Q2 WILD-TYPE 
             13             458 
  OR9Q2 MUTATED OR9Q2 WILD-TYPE 
              5              88 
$`OR9Q2 MUTATED`
TCGA-AA-3510 TCGA-AA-3715 TCGA-AA-A010 TCGA-AY-6197 TCGA-AZ-6606 TCGA-CM-5862 
       63.98        19.04        34.98        21.44        11.74         5.03 
TCGA-CM-6680 TCGA-D5-6540 TCGA-DM-A1DB TCGA-DM-A28H TCGA-G4-6303 TCGA-G4-6310 
       12.03        16.14        44.32       117.07        65.85        63.62 
TCGA-G4-6586 
       35.80 

$`OR9Q2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 
       36.00         5.03        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
       29.56         5.23         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 
       22.03        22.98        30.08        32.02        15.02        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       11.01        10.06        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 
       17.85         4.80        17.13        12.49        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A1HB 
       13.32        12.59       140.38         7.50       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6304 
        0.53        47.41        35.31       133.18        74.56        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       44.68        55.04        85.48        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       13.78        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  OR9Q2 MUTATED OR9Q2 WILD-TYPE 
           5.03            0.00 
  OR9Q2 MUTATED OR9Q2 WILD-TYPE 
         117.07          148.01 
  OR9Q2 MUTATED OR9Q2 WILD-TYPE 
         34.980          20.085 
[1] "5.0 - 117.1 (35.0)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.3"
D1148V2, continuous
D1148V3, binary
                 cls
clus                0   1
  OR9Q2 MUTATED    14   0
  OR9Q2 WILD-TYPE 352 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR9Q2 MUTATED     14    0
  OR9Q2 WILD-TYPE  352  119
        clus
vv       OR9Q2 MUTATED OR9Q2 WILD-TYPE
  COLON             14             352
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  OR9Q2 MUTATED         1        0        2         4         1         0
  OR9Q2 WILD-TYPE      90        1       30       134         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  OR9Q2 MUTATED           0          0          2          1        2         1
  OR9Q2 WILD-TYPE        24         11         57         41       46        17
                 vv
clus              STAGE IVB
  OR9Q2 MUTATED           0
  OR9Q2 WILD-TYPE         1
D1148V4, multiclass
            clus
vv           OR9Q2 MUTATED OR9Q2 WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA              4             134
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             2              57
  STAGE IIIC             1              41
  STAGE IV               2              46
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  OR9Q2 MUTATED     0   1  11   2
  OR9Q2 WILD-TYPE  17  91 318  48
D1148V5, multiclass
    clus
vv   OR9Q2 MUTATED OR9Q2 WILD-TYPE
  T1             0              17
  T2             1              91
  T3            11             318
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  OR9Q2 MUTATED     8   3   3
  OR9Q2 WILD-TYPE 279 110  84
D1148V6, multiclass
    clus
vv   OR9Q2 MUTATED OR9Q2 WILD-TYPE
  N0             8             279
  N1             3             110
  N2             3              84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1148V7, binary
                 cls
clus                0   1
  OR9Q2 MUTATED    10   3
  OR9Q2 WILD-TYPE 365  62
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR9Q2 MUTATED     10    3
  OR9Q2 WILD-TYPE  365   62
   clus
vv  OR9Q2 MUTATED OR9Q2 WILD-TYPE
  0            10             365
  1             3              62
[1] 2 2
[1] FALSE
D1148V8, binary
                 cls
clus                0   1
  OR9Q2 MUTATED     5   9
  OR9Q2 WILD-TYPE 220 255
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR9Q2 MUTATED      5    9
  OR9Q2 WILD-TYPE  220  255
        clus
vv       OR9Q2 MUTATED OR9Q2 WILD-TYPE
  FEMALE             5             220
  MALE               9             255
[1] 2 2
[1] FALSE
D1148V9, binary
                 cls
clus                0   1
  OR9Q2 MUTATED    10   1
  OR9Q2 WILD-TYPE 340  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR9Q2 MUTATED     10    1
  OR9Q2 WILD-TYPE  340   21
     clus
vv    OR9Q2 MUTATED OR9Q2 WILD-TYPE
  NO             10             340
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  OR9Q2 MUTATED                     13                             1
  OR9Q2 WILD-TYPE                  302                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  OR9Q2 MUTATED                       0                              0
  OR9Q2 WILD-TYPE                   106                             10
D1148V10, multiclass
                                clus
vv                               OR9Q2 MUTATED OR9Q2 WILD-TYPE
  COLON ADENOCARCINOMA                      13             302
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  OR9Q2 MUTATED    11   0   0   0
  OR9Q2 WILD-TYPE 334   4  31  25
D1148V11, multiclass
    clus
vv   OR9Q2 MUTATED OR9Q2 WILD-TYPE
  R0            11             334
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1148V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OR9Q2 MUTATED                                  0     0
  OR9Q2 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  OR9Q2 MUTATED                           0    10
  OR9Q2 WILD-TYPE                        22   216
D1148V13, multiclass
                                  clus
vv                                 OR9Q2 MUTATED OR9Q2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                       10             216
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1149) Variable = CTNNA3 MUTATION ANALYSIS
D1149V1, survival
                  sevent
clus2                0   1
  CTNNA3 MUTATED    20   6
  CTNNA3 WILD-TYPE 358  87
  CTNNA3 MUTATED CTNNA3 WILD-TYPE 
              26              445 
  CTNNA3 MUTATED CTNNA3 WILD-TYPE 
               6               87 
$`CTNNA3 MUTATED`
TCGA-A6-2678 TCGA-A6-6653 TCGA-AA-3496 TCGA-AA-3511 TCGA-AA-3715 TCGA-AA-3850 
       42.28        24.39         1.02         6.97        19.04         0.00 
TCGA-AA-3864 TCGA-AA-3966 TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A02Y 
       53.00         2.01        25.02         4.01        34.98        39.98 
TCGA-AD-6964 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-5407 TCGA-AZ-6601 TCGA-CM-6171 
       10.88        21.44        17.82        88.21       100.01        14.04 
TCGA-D5-6540 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-7000 TCGA-F4-6570 TCGA-F4-6855 
       16.14         4.80         1.51        10.26         6.18        47.41 
TCGA-G4-6586 TCGA-G4-6588 
       35.80        26.17 

$`CTNNA3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2683 
       43.76        46.65        43.76        42.90        24.33        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 
       25.18        24.16        21.76        24.69        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3510 
       19.66        20.28         7.04         3.02        35.01        63.98 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       26.99        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3852 
       14.93         0.00        17.03        10.06        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
        2.01        20.98        34.03        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
       14.01         0.92        41.00        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
        0.95        33.01        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 
       22.36        62.79        49.41         6.77        12.10        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       15.02        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 
       15.12        17.85         4.80        17.13        12.49        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6931 TCGA-D5-6932 TCGA-DM-A0X9 TCGA-DM-A0XD 
        9.44        11.64        12.00        11.38       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 
       98.24         8.61        31.96        35.74        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       13.78        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  CTNNA3 MUTATED CTNNA3 WILD-TYPE 
               0                0 
  CTNNA3 MUTATED CTNNA3 WILD-TYPE 
          100.01           148.01 
  CTNNA3 MUTATED CTNNA3 WILD-TYPE 
           18.43            20.28 
[1] "0.0 - 100.0 (18.4)" "0.0 - 148.0 (20.3)"
[1] "hr=" "1.2"
D1149V2, continuous
D1149V3, binary
                  cls
clus                 0   1
  CTNNA3 MUTATED    26   0
  CTNNA3 WILD-TYPE 340 119
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CTNNA3 MUTATED     26    0
  CTNNA3 WILD-TYPE  340  119
        clus
vv       CTNNA3 MUTATED CTNNA3 WILD-TYPE
  COLON              26              340
  RECTUM              0              119
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CTNNA3 MUTATED         7        0        5         7         2         0
  CTNNA3 WILD-TYPE      84        1       27       131         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CTNNA3 MUTATED           0          0          2          0        1
  CTNNA3 WILD-TYPE        24         11         57         42       47
                  vv
clus               STAGE IVA STAGE IVB
  CTNNA3 MUTATED           0         0
  CTNNA3 WILD-TYPE        18         1
D1149V4, multiclass
            clus
vv           CTNNA3 MUTATED CTNNA3 WILD-TYPE
  STAGE I                 7               84
  STAGE IA                0                1
  STAGE II                5               27
  STAGE IIA               7              131
  STAGE IIB               2                8
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              2               57
  STAGE IIIC              0               42
  STAGE IV                1               47
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  CTNNA3 MUTATED     1   7  14   4
  CTNNA3 WILD-TYPE  16  85 315  46
D1149V5, multiclass
    clus
vv   CTNNA3 MUTATED CTNNA3 WILD-TYPE
  T1              1               16
  T2              7               85
  T3             14              315
  T4              4               46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  CTNNA3 MUTATED    22   3   1
  CTNNA3 WILD-TYPE 265 110  86
D1149V6, multiclass
    clus
vv   CTNNA3 MUTATED CTNNA3 WILD-TYPE
  N0             22              265
  N1              3              110
  N2              1               86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1149V7, binary
                  cls
clus                 0   1
  CTNNA3 MUTATED    22   1
  CTNNA3 WILD-TYPE 353  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CTNNA3 MUTATED     22    1
  CTNNA3 WILD-TYPE  353   64
   clus
vv  CTNNA3 MUTATED CTNNA3 WILD-TYPE
  0             22              353
  1              1               64
[1] 2 2
[1] FALSE
D1149V8, binary
                  cls
clus                 0   1
  CTNNA3 MUTATED    13  13
  CTNNA3 WILD-TYPE 212 251
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CTNNA3 MUTATED     13   13
  CTNNA3 WILD-TYPE  212  251
        clus
vv       CTNNA3 MUTATED CTNNA3 WILD-TYPE
  FEMALE             13              212
  MALE               13              251
[1] 2 2
[1] FALSE
D1149V9, binary
                  cls
clus                 0   1
  CTNNA3 MUTATED    20   0
  CTNNA3 WILD-TYPE 330  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CTNNA3 MUTATED     20    0
  CTNNA3 WILD-TYPE  330   22
     clus
vv    CTNNA3 MUTATED CTNNA3 WILD-TYPE
  NO              20              330
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CTNNA3 MUTATED                     21                             5
  CTNNA3 WILD-TYPE                  294                            42
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CTNNA3 MUTATED                       0                              0
  CTNNA3 WILD-TYPE                   106                             10
D1149V10, multiclass
                                clus
vv                               CTNNA3 MUTATED CTNNA3 WILD-TYPE
  COLON ADENOCARCINOMA                       21              294
  COLON MUCINOUS ADENOCARCINOMA               5               42
  RECTAL ADENOCARCINOMA                       0              106
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  CTNNA3 MUTATED    20   0   0   0
  CTNNA3 WILD-TYPE 325   4  31  25
D1149V11, multiclass
    clus
vv   CTNNA3 MUTATED CTNNA3 WILD-TYPE
  R0             20              325
  R1              0                4
  R2              0               31
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1149V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CTNNA3 MUTATED                                  0     0
  CTNNA3 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  CTNNA3 MUTATED                           1    15
  CTNNA3 WILD-TYPE                        21   211
D1149V13, multiclass
                                  clus
vv                                 CTNNA3 MUTATED CTNNA3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                        15              211
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1150) Variable = C14ORF39 MUTATION ANALYSIS
D1150V1, survival
                    sevent
clus2                  0   1
  C14ORF39 MUTATED    14   2
  C14ORF39 WILD-TYPE 364  91
  C14ORF39 MUTATED C14ORF39 WILD-TYPE 
                16                455 
  C14ORF39 MUTATED C14ORF39 WILD-TYPE 
                 2                 91 
$`C14ORF39 MUTATED`
TCGA-AA-3510 TCGA-AA-3977 TCGA-AA-A010 TCGA-AU-6004 TCGA-AY-5543 TCGA-AZ-4315 
       63.98        25.02        34.98        27.09        33.01        58.39 
TCGA-CA-6717 TCGA-CA-6718 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-6930 TCGA-DM-A28E 
       12.76        10.06        45.40        12.26         1.51       119.93 
TCGA-AF-6136 TCGA-AG-A002 TCGA-AH-6549 TCGA-DY-A0XA 
       15.39        20.98        17.49       126.44 

$`C14ORF39 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6197 TCGA-AY-6386 
        0.20        14.50        16.31         0.95        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        3.29         0.07        12.20        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.03        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
       81.37        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       10.39        14.50        16.83        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 
       38.04       117.11        38.56         1.45         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD 
        5.95         4.01         5.03         5.29        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  C14ORF39 MUTATED C14ORF39 WILD-TYPE 
              1.51               0.00 
  C14ORF39 MUTATED C14ORF39 WILD-TYPE 
            126.44             148.01 
  C14ORF39 MUTATED C14ORF39 WILD-TYPE 
            26.055             20.050 
[1] "1.5 - 126.4 (26.1)" "0.0 - 148.0 (20.1)"
[1] "hr=" "2.3"
D1150V2, continuous
D1150V3, binary
                    cls
clus                   0   1
  C14ORF39 MUTATED    13   4
  C14ORF39 WILD-TYPE 353 115
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C14ORF39 MUTATED     13    4
  C14ORF39 WILD-TYPE  353  115
        clus
vv       C14ORF39 MUTATED C14ORF39 WILD-TYPE
  COLON                13                353
  RECTUM                4                115
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  C14ORF39 MUTATED         2        0        1         7         2         0
  C14ORF39 WILD-TYPE      89        1       31       131         8         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C14ORF39 MUTATED           0          0          2          0        0
  C14ORF39 WILD-TYPE        24         11         57         42       48
                    vv
clus                 STAGE IVA STAGE IVB
  C14ORF39 MUTATED           1         0
  C14ORF39 WILD-TYPE        17         1
D1150V4, multiclass
            clus
vv           C14ORF39 MUTATED C14ORF39 WILD-TYPE
  STAGE I                   2                 89
  STAGE IA                  0                  1
  STAGE II                  1                 31
  STAGE IIA                 7                131
  STAGE IIB                 2                  8
  STAGE IIC                 0                  1
  STAGE III                 0                 24
  STAGE IIIA                0                 11
  STAGE IIIB                2                 57
  STAGE IIIC                0                 42
  STAGE IV                  0                 48
  STAGE IVA                 1                 17
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  C14ORF39 MUTATED     0   3  12   2
  C14ORF39 WILD-TYPE  17  89 317  48
D1150V5, multiclass
    clus
vv   C14ORF39 MUTATED C14ORF39 WILD-TYPE
  T1                0                 17
  T2                3                 89
  T3               12                317
  T4                2                 48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  C14ORF39 MUTATED    12   3   1
  C14ORF39 WILD-TYPE 275 110  86
D1150V6, multiclass
    clus
vv   C14ORF39 MUTATED C14ORF39 WILD-TYPE
  N0               12                275
  N1                3                110
  N2                1                 86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1150V7, binary
                    cls
clus                   0   1
  C14ORF39 MUTATED    11   1
  C14ORF39 WILD-TYPE 364  64
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C14ORF39 MUTATED     11    1
  C14ORF39 WILD-TYPE  364   64
   clus
vv  C14ORF39 MUTATED C14ORF39 WILD-TYPE
  0               11                364
  1                1                 64
[1] 2 2
[1] FALSE
D1150V8, binary
                    cls
clus                   0   1
  C14ORF39 MUTATED     8   9
  C14ORF39 WILD-TYPE 217 255
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C14ORF39 MUTATED      8    9
  C14ORF39 WILD-TYPE  217  255
        clus
vv       C14ORF39 MUTATED C14ORF39 WILD-TYPE
  FEMALE                8                217
  MALE                  9                255
[1] 2 2
[1] FALSE
D1150V9, binary
                    cls
clus                   0   1
  C14ORF39 MUTATED    11   1
  C14ORF39 WILD-TYPE 339  21
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C14ORF39 MUTATED     11    1
  C14ORF39 WILD-TYPE  339   21
     clus
vv    C14ORF39 MUTATED C14ORF39 WILD-TYPE
  NO                11                339
  YES                1                 21
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  C14ORF39 MUTATED                     11                             2
  C14ORF39 WILD-TYPE                  304                            45
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  C14ORF39 MUTATED                       4                              0
  C14ORF39 WILD-TYPE                   102                             10
D1150V10, multiclass
                                clus
vv                               C14ORF39 MUTATED C14ORF39 WILD-TYPE
  COLON ADENOCARCINOMA                         11                304
  COLON MUCINOUS ADENOCARCINOMA                 2                 45
  RECTAL ADENOCARCINOMA                         4                102
  RECTAL MUCINOUS ADENOCARCINOMA                0                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  C14ORF39 MUTATED     8   0   0   5
  C14ORF39 WILD-TYPE 337   4  31  20
D1150V11, multiclass
    clus
vv   C14ORF39 MUTATED C14ORF39 WILD-TYPE
  R0                8                337
  R1                0                  4
  R2                0                 31
  RX                5                 20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1150V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C14ORF39 MUTATED                                  0     2
  C14ORF39 WILD-TYPE                                1     9
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  C14ORF39 MUTATED                           1    10
  C14ORF39 WILD-TYPE                        21   216
D1150V13, multiclass
                                  clus
vv                                 C14ORF39 MUTATED C14ORF39 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           2                  9
  BLACK OR AFRICAN AMERICAN                       1                 21
  WHITE                                          10                216
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1151) Variable = SAPS3 MUTATION ANALYSIS
D1151V1, survival
                 sevent
clus2               0   1
  SAPS3 MUTATED    11   3
  SAPS3 WILD-TYPE 367  90
  SAPS3 MUTATED SAPS3 WILD-TYPE 
             14             457 
  SAPS3 MUTATED SAPS3 WILD-TYPE 
              3              90 
$`SAPS3 MUTATED`
TCGA-A6-5665 TCGA-A6-6781 TCGA-AA-3947 TCGA-AA-A00N TCGA-AA-A01X TCGA-AD-5900 
       22.06        19.66        33.01         4.01        26.01         0.07 
TCGA-CA-6717 TCGA-DM-A28C TCGA-G4-6303 TCGA-G4-6628 TCGA-AG-3575 TCGA-AG-3892 
       12.76        81.37        65.85        79.69        12.00        13.02 
TCGA-AG-3894 TCGA-AG-A002 
       14.01        20.98 

$`SAPS3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       12.99        24.00        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07        12.20        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28E TCGA-DM-A28F 
      131.51       135.65       139.17         6.12       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       74.56        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       91.79        46.75        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       20.02        10.39        36.03        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3898 
       17.95        36.95        17.03        35.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  SAPS3 MUTATED SAPS3 WILD-TYPE 
           0.07            0.00 
  SAPS3 MUTATED SAPS3 WILD-TYPE 
          81.37          148.01 
  SAPS3 MUTATED SAPS3 WILD-TYPE 
          20.32           20.19 
[1] "0.1 - 81.4 (20.3)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1"  
D1151V2, continuous
D1151V3, binary
                 cls
clus                0   1
  SAPS3 MUTATED    11   4
  SAPS3 WILD-TYPE 355 115
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SAPS3 MUTATED     11    4
  SAPS3 WILD-TYPE  355  115
        clus
vv       SAPS3 MUTATED SAPS3 WILD-TYPE
  COLON             11             355
  RECTUM             4             115
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SAPS3 MUTATED         4        0        1         5         2         0
  SAPS3 WILD-TYPE      87        1       31       133         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SAPS3 MUTATED           1          0          0          1        1         0
  SAPS3 WILD-TYPE        23         11         59         41       47        18
                 vv
clus              STAGE IVB
  SAPS3 MUTATED           0
  SAPS3 WILD-TYPE         1
D1151V4, multiclass
            clus
vv           SAPS3 MUTATED SAPS3 WILD-TYPE
  STAGE I                4              87
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              5             133
  STAGE IIB              2               8
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             1              41
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  SAPS3 MUTATED     1   4   7   3
  SAPS3 WILD-TYPE  16  88 322  47
D1151V5, multiclass
    clus
vv   SAPS3 MUTATED SAPS3 WILD-TYPE
  T1             1              16
  T2             4              88
  T3             7             322
  T4             3              47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  SAPS3 MUTATED    12   3   0
  SAPS3 WILD-TYPE 275 110  87
D1151V6, multiclass
    clus
vv   SAPS3 MUTATED SAPS3 WILD-TYPE
  N0            12             275
  N1             3             110
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1151V7, binary
                 cls
clus                0   1
  SAPS3 MUTATED    12   1
  SAPS3 WILD-TYPE 363  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SAPS3 MUTATED     12    1
  SAPS3 WILD-TYPE  363   64
   clus
vv  SAPS3 MUTATED SAPS3 WILD-TYPE
  0            12             363
  1             1              64
[1] 2 2
[1] FALSE
D1151V8, binary
                 cls
clus                0   1
  SAPS3 MUTATED     6   9
  SAPS3 WILD-TYPE 219 255
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SAPS3 MUTATED      6    9
  SAPS3 WILD-TYPE  219  255
        clus
vv       SAPS3 MUTATED SAPS3 WILD-TYPE
  FEMALE             6             219
  MALE               9             255
[1] 2 2
[1] FALSE
D1151V9, binary
                 cls
clus                0   1
  SAPS3 MUTATED    10   1
  SAPS3 WILD-TYPE 340  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SAPS3 MUTATED     10    1
  SAPS3 WILD-TYPE  340   21
     clus
vv    SAPS3 MUTATED SAPS3 WILD-TYPE
  NO             10             340
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SAPS3 MUTATED                      6                             5
  SAPS3 WILD-TYPE                  309                            42
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SAPS3 MUTATED                       4                              0
  SAPS3 WILD-TYPE                   102                             10
D1151V10, multiclass
                                clus
vv                               SAPS3 MUTATED SAPS3 WILD-TYPE
  COLON ADENOCARCINOMA                       6             309
  COLON MUCINOUS ADENOCARCINOMA              5              42
  RECTAL ADENOCARCINOMA                      4             102
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  SAPS3 MUTATED    12   0   0   2
  SAPS3 WILD-TYPE 333   4  31  23
D1151V11, multiclass
    clus
vv   SAPS3 MUTATED SAPS3 WILD-TYPE
  R0            12             333
  R1             0               4
  R2             0              31
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1151V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SAPS3 MUTATED                                  0     1
  SAPS3 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  SAPS3 MUTATED                           0     6
  SAPS3 WILD-TYPE                        22   220
D1151V13, multiclass
                                  clus
vv                                 SAPS3 MUTATED SAPS3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        6             220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1152) Variable = TRIM31 MUTATION ANALYSIS
D1152V1, survival
                  sevent
clus2                0   1
  TRIM31 MUTATED     5   0
  TRIM31 WILD-TYPE 373  93
  TRIM31 MUTATED TRIM31 WILD-TYPE 
               5              466 
  TRIM31 MUTATED TRIM31 WILD-TYPE 
               0               93 
$`TRIM31 MUTATED`
TCGA-AA-3525 TCGA-AA-3672 TCGA-AZ-4315 TCGA-CM-5861 TCGA-F5-6811 
        8.05         0.92        58.39        15.02        32.19 

$`TRIM31 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 
        6.97        54.02         2.01        14.01        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       33.01        21.44        17.82         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  TRIM31 MUTATED TRIM31 WILD-TYPE 
            0.92             0.00 
  TRIM31 MUTATED TRIM31 WILD-TYPE 
           58.39           148.01 
  TRIM31 MUTATED TRIM31 WILD-TYPE 
          15.020           20.235 
[1] "0.9 - 58.4 (15.0)"  "0.0 - 148.0 (20.2)"
[1] "hr="     "3300000"
D1152V2, continuous
D1152V3, binary
                  cls
clus                 0   1
  TRIM31 MUTATED     4   1
  TRIM31 WILD-TYPE 362 118
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIM31 MUTATED      4    1
  TRIM31 WILD-TYPE  362  118
        clus
vv       TRIM31 MUTATED TRIM31 WILD-TYPE
  COLON               4              362
  RECTUM              1              118
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TRIM31 MUTATED         0        0        0         3         0         0
  TRIM31 WILD-TYPE      91        1       32       135        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TRIM31 MUTATED           1          0          1          0        0
  TRIM31 WILD-TYPE        23         11         58         42       48
                  vv
clus               STAGE IVA STAGE IVB
  TRIM31 MUTATED           0         0
  TRIM31 WILD-TYPE        18         1
D1152V4, multiclass
            clus
vv           TRIM31 MUTATED TRIM31 WILD-TYPE
  STAGE I                 0               91
  STAGE IA                0                1
  STAGE II                0               32
  STAGE IIA               3              135
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               1               23
  STAGE IIIA              0               11
  STAGE IIIB              1               58
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  TRIM31 MUTATED     0   0   5   0
  TRIM31 WILD-TYPE  17  92 324  50
D1152V5, multiclass
    clus
vv   TRIM31 MUTATED TRIM31 WILD-TYPE
  T1              0               17
  T2              0               92
  T3              5              324
  T4              0               50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  TRIM31 MUTATED     3   2   0
  TRIM31 WILD-TYPE 284 111  87
D1152V6, multiclass
    clus
vv   TRIM31 MUTATED TRIM31 WILD-TYPE
  N0              3              284
  N1              2              111
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1152V7, binary
                  cls
clus                 0   1
  TRIM31 MUTATED     5   0
  TRIM31 WILD-TYPE 370  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIM31 MUTATED      5    0
  TRIM31 WILD-TYPE  370   65
   clus
vv  TRIM31 MUTATED TRIM31 WILD-TYPE
  0              5              370
  1              0               65
[1] 2 2
[1] FALSE
D1152V8, binary
                  cls
clus                 0   1
  TRIM31 MUTATED     3   2
  TRIM31 WILD-TYPE 222 262
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIM31 MUTATED      3    2
  TRIM31 WILD-TYPE  222  262
        clus
vv       TRIM31 MUTATED TRIM31 WILD-TYPE
  FEMALE              3              222
  MALE                2              262
[1] 2 2
[1] FALSE
D1152V9, binary
                  cls
clus                 0   1
  TRIM31 MUTATED     5   0
  TRIM31 WILD-TYPE 345  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIM31 MUTATED      5    0
  TRIM31 WILD-TYPE  345   22
     clus
vv    TRIM31 MUTATED TRIM31 WILD-TYPE
  NO               5              345
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  TRIM31 MUTATED                      4                             0
  TRIM31 WILD-TYPE                  311                            47
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  TRIM31 MUTATED                       1                              0
  TRIM31 WILD-TYPE                   105                             10
D1152V10, multiclass
                                clus
vv                               TRIM31 MUTATED TRIM31 WILD-TYPE
  COLON ADENOCARCINOMA                        4              311
  COLON MUCINOUS ADENOCARCINOMA               0               47
  RECTAL ADENOCARCINOMA                       1              105
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  TRIM31 MUTATED     4   0   0   0
  TRIM31 WILD-TYPE 341   4  31  25
D1152V11, multiclass
    clus
vv   TRIM31 MUTATED TRIM31 WILD-TYPE
  R0              4              341
  R1              0                4
  R2              0               31
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1152V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TRIM31 MUTATED                                  0     0
  TRIM31 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  TRIM31 MUTATED                           0     3
  TRIM31 WILD-TYPE                        22   223
D1152V13, multiclass
                                  clus
vv                                 TRIM31 MUTATED TRIM31 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         3              223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1153) Variable = PHF14 MUTATION ANALYSIS
D1153V1, survival
                 sevent
clus2               0   1
  PHF14 MUTATED    12   3
  PHF14 WILD-TYPE 366  90
  PHF14 MUTATED PHF14 WILD-TYPE 
             15             456 
  PHF14 MUTATED PHF14 WILD-TYPE 
              3              90 
$`PHF14 MUTATED`
TCGA-A6-6780 TCGA-AA-3511 TCGA-AA-3715 TCGA-AA-3949 TCGA-AY-6197 TCGA-CA-6718 
       20.12         6.97        19.04        26.01        21.44        10.06 
TCGA-CM-5861 TCGA-CM-6162 TCGA-D5-6930 TCGA-DM-A28G TCGA-G4-6323 TCGA-AG-3902 
       15.02        12.00         1.51        60.79        13.78        32.02 
TCGA-AG-A002 TCGA-EI-6507 TCGA-F5-6813 
       20.98        19.96         0.69 

$`PHF14 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01        63.98         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        33.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 
       14.50        27.09        16.31         0.95        33.01        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 
        3.25         3.29         0.07        12.20        12.76        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       22.98        30.08        32.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       17.03        15.02         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       11.64         4.80        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28H 
      139.17         6.12        81.37       119.93        35.97       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
        1.02        48.03        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
        0.49        20.55        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-G5-6235 TCGA-G5-6641 
       31.30        28.57        32.19         0.66        55.76        26.43 

  PHF14 MUTATED PHF14 WILD-TYPE 
           0.69            0.00 
  PHF14 MUTATED PHF14 WILD-TYPE 
          60.79          148.01 
  PHF14 MUTATED PHF14 WILD-TYPE 
          19.04           20.73 
[1] "0.7 - 60.8 (19.0)"  "0.0 - 148.0 (20.7)"
[1] "hr=" "1.4"
D1153V2, continuous
D1153V3, binary
                 cls
clus                0   1
  PHF14 MUTATED    12   4
  PHF14 WILD-TYPE 354 115
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PHF14 MUTATED     12    4
  PHF14 WILD-TYPE  354  115
        clus
vv       PHF14 MUTATED PHF14 WILD-TYPE
  COLON             12             354
  RECTUM             4             115
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PHF14 MUTATED         1        1        2         8         1         0
  PHF14 WILD-TYPE      90        0       30       130         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PHF14 MUTATED           0          0          2          1        0         0
  PHF14 WILD-TYPE        24         11         57         41       48        18
                 vv
clus              STAGE IVB
  PHF14 MUTATED           0
  PHF14 WILD-TYPE         1
D1153V4, multiclass
            clus
vv           PHF14 MUTATED PHF14 WILD-TYPE
  STAGE I                1              90
  STAGE IA               1               0
  STAGE II               2              30
  STAGE IIA              8             130
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             2              57
  STAGE IIIC             1              41
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PHF14 MUTATED     0   1  11   3
  PHF14 WILD-TYPE  17  91 318  47
D1153V5, multiclass
    clus
vv   PHF14 MUTATED PHF14 WILD-TYPE
  T1             0              17
  T2             1              91
  T3            11             318
  T4             3              47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  PHF14 MUTATED    13   2   1
  PHF14 WILD-TYPE 274 111  86
D1153V6, multiclass
    clus
vv   PHF14 MUTATED PHF14 WILD-TYPE
  N0            13             274
  N1             2             111
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1153V7, binary
                 cls
clus                0   1
  PHF14 MUTATED    12   0
  PHF14 WILD-TYPE 363  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PHF14 MUTATED     12    0
  PHF14 WILD-TYPE  363   65
   clus
vv  PHF14 MUTATED PHF14 WILD-TYPE
  0            12             363
  1             0              65
[1] 2 2
[1] FALSE
D1153V8, binary
                 cls
clus                0   1
  PHF14 MUTATED     4  12
  PHF14 WILD-TYPE 221 252
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PHF14 MUTATED      4   12
  PHF14 WILD-TYPE  221  252
        clus
vv       PHF14 MUTATED PHF14 WILD-TYPE
  FEMALE             4             221
  MALE              12             252
[1] 2 2
[1] FALSE
D1153V9, binary
                 cls
clus                0   1
  PHF14 MUTATED    12   0
  PHF14 WILD-TYPE 338  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PHF14 MUTATED     12    0
  PHF14 WILD-TYPE  338   22
     clus
vv    PHF14 MUTATED PHF14 WILD-TYPE
  NO             12             338
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PHF14 MUTATED                      8                             4
  PHF14 WILD-TYPE                  307                            43
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PHF14 MUTATED                       4                              0
  PHF14 WILD-TYPE                   102                             10
D1153V10, multiclass
                                clus
vv                               PHF14 MUTATED PHF14 WILD-TYPE
  COLON ADENOCARCINOMA                       8             307
  COLON MUCINOUS ADENOCARCINOMA              4              43
  RECTAL ADENOCARCINOMA                      4             102
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  PHF14 MUTATED    12   0   0   2
  PHF14 WILD-TYPE 333   4  31  23
D1153V11, multiclass
    clus
vv   PHF14 MUTATED PHF14 WILD-TYPE
  R0            12             333
  R1             0               4
  R2             0              31
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1153V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PHF14 MUTATED                                  0     1
  PHF14 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PHF14 MUTATED                           1     9
  PHF14 WILD-TYPE                        21   217
D1153V13, multiclass
                                  clus
vv                                 PHF14 MUTATED PHF14 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        9             217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1154) Variable = MOV10 MUTATION ANALYSIS
D1154V1, survival
                 sevent
clus2               0   1
  MOV10 MUTATED    14   0
  MOV10 WILD-TYPE 364  93
  MOV10 MUTATED MOV10 WILD-TYPE 
             14             457 
  MOV10 MUTATED MOV10 WILD-TYPE 
              0              93 
$`MOV10 MUTATED`
TCGA-A6-6781 TCGA-AA-3655 TCGA-AA-3812 TCGA-AA-3966 TCGA-AA-A00E TCGA-AU-3779 
       19.66        61.02        35.05         2.01        30.02        14.50 
TCGA-CK-4947 TCGA-CK-5914 TCGA-CM-5344 TCGA-CM-5349 TCGA-DM-A1HA TCGA-G4-6293 
       17.56         9.99        22.03        30.08       131.51       133.18 
TCGA-G4-6586 TCGA-AG-A002 
       35.80        20.98 

$`MOV10 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       19.99        13.94        19.99        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
       34.03        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00F 
        7.96        27.02        13.94        38.04        19.00        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-6004 
        5.79        22.42        27.42        10.88         0.20        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07        12.20        12.76        10.06        14.30 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5916 
      148.01        85.45        15.62        49.08        51.32        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5861 
       25.02        13.02        29.06        22.98        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
      140.38         7.50        44.32       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       47.41        35.31        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       13.78        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  MOV10 MUTATED MOV10 WILD-TYPE 
           2.01            0.00 
  MOV10 MUTATED MOV10 WILD-TYPE 
         133.18          148.01 
  MOV10 MUTATED MOV10 WILD-TYPE 
         26.025          20.050 
[1] "2.0 - 133.2 (26.0)" "0.0 - 148.0 (20.1)"
[1] "hr="     "2.6e+07"
D1154V2, continuous
D1154V3, binary
                 cls
clus                0   1
  MOV10 MUTATED    13   1
  MOV10 WILD-TYPE 353 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MOV10 MUTATED     13    1
  MOV10 WILD-TYPE  353  118
        clus
vv       MOV10 MUTATED MOV10 WILD-TYPE
  COLON             13             353
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MOV10 MUTATED         1        0        1         6         0         0
  MOV10 WILD-TYPE      90        1       31       132        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MOV10 MUTATED           1          0          3          2        0         0
  MOV10 WILD-TYPE        23         11         56         40       48        18
                 vv
clus              STAGE IVB
  MOV10 MUTATED           0
  MOV10 WILD-TYPE         1
D1154V4, multiclass
            clus
vv           MOV10 MUTATED MOV10 WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              6             132
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             3              56
  STAGE IIIC             2              40
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  MOV10 MUTATED     0   1  11   2
  MOV10 WILD-TYPE  17  91 318  48
D1154V5, multiclass
    clus
vv   MOV10 MUTATED MOV10 WILD-TYPE
  T1             0              17
  T2             1              91
  T3            11             318
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  MOV10 MUTATED     8   5   1
  MOV10 WILD-TYPE 279 108  86
D1154V6, multiclass
    clus
vv   MOV10 MUTATED MOV10 WILD-TYPE
  N0             8             279
  N1             5             108
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1154V7, binary
                 cls
clus                0   1
  MOV10 MUTATED    12   0
  MOV10 WILD-TYPE 363  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MOV10 MUTATED     12    0
  MOV10 WILD-TYPE  363   65
   clus
vv  MOV10 MUTATED MOV10 WILD-TYPE
  0            12             363
  1             0              65
[1] 2 2
[1] FALSE
D1154V8, binary
                 cls
clus                0   1
  MOV10 MUTATED     8   6
  MOV10 WILD-TYPE 217 258
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MOV10 MUTATED      8    6
  MOV10 WILD-TYPE  217  258
        clus
vv       MOV10 MUTATED MOV10 WILD-TYPE
  FEMALE             8             217
  MALE               6             258
[1] 2 2
[1] FALSE
D1154V9, binary
                 cls
clus                0   1
  MOV10 MUTATED    11   0
  MOV10 WILD-TYPE 339  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MOV10 MUTATED     11    0
  MOV10 WILD-TYPE  339   22
     clus
vv    MOV10 MUTATED MOV10 WILD-TYPE
  NO             11             339
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MOV10 MUTATED                     11                             2
  MOV10 WILD-TYPE                  304                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MOV10 MUTATED                       1                              0
  MOV10 WILD-TYPE                   105                             10
D1154V10, multiclass
                                clus
vv                               MOV10 MUTATED MOV10 WILD-TYPE
  COLON ADENOCARCINOMA                      11             304
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  MOV10 MUTATED    10   0   0   2
  MOV10 WILD-TYPE 335   4  31  23
D1154V11, multiclass
    clus
vv   MOV10 MUTATED MOV10 WILD-TYPE
  R0            10             335
  R1             0               4
  R2             0              31
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1154V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MOV10 MUTATED                                  0     0
  MOV10 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  MOV10 MUTATED                           0     9
  MOV10 WILD-TYPE                        22   217
D1154V13, multiclass
                                  clus
vv                                 MOV10 MUTATED MOV10 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        9             217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1155) Variable = PTCH2 MUTATION ANALYSIS
D1155V1, survival
                 sevent
clus2               0   1
  PTCH2 MUTATED    16   3
  PTCH2 WILD-TYPE 362  90
  PTCH2 MUTATED PTCH2 WILD-TYPE 
             19             452 
  PTCH2 MUTATED PTCH2 WILD-TYPE 
              3              90 
$`PTCH2 MUTATED`
TCGA-A6-6653 TCGA-AA-3510 TCGA-AA-3660 TCGA-AA-3811 TCGA-AA-3821 TCGA-AA-3947 
       24.39        63.98        78.08        10.06         1.02        33.01 
TCGA-AA-A00E TCGA-AD-6889 TCGA-AU-6004 TCGA-AZ-6601 TCGA-CM-4743 TCGA-CM-5348 
       30.02        56.55        27.09       100.01        23.05        22.98 
TCGA-CM-5861 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6928 TCGA-DM-A1D7 TCGA-AG-3893 
       15.02        17.13        12.49        11.64        13.32        35.01 
TCGA-AG-A02N 
       61.97 

$`PTCH2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
       25.08        25.18        24.16        21.76        24.69        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       13.94        19.99        61.02         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3815 
       85.05        26.99        19.04        19.04        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
        0.99        25.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 
       18.05        31.00         2.01        12.99        24.00        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       13.94        38.04        19.00        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       15.52         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       10.88         0.20        14.50        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
      124.27        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       22.03        30.08        32.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.85         4.80        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 
        4.41        12.43        14.30         9.04         9.44         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D8 TCGA-DM-A1D9 
       38.20       130.65        92.75        49.91        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-3896 
       17.95        36.95        17.03        13.02        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  PTCH2 MUTATED PTCH2 WILD-TYPE 
           1.02            0.00 
  PTCH2 MUTATED PTCH2 WILD-TYPE 
         100.01          148.01 
  PTCH2 MUTATED PTCH2 WILD-TYPE 
         24.390          20.035 
[1] "1.0 - 100.0 (24.4)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.7"
D1155V2, continuous
D1155V3, binary
                 cls
clus                0   1
  PTCH2 MUTATED    17   2
  PTCH2 WILD-TYPE 349 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTCH2 MUTATED     17    2
  PTCH2 WILD-TYPE  349  117
        clus
vv       PTCH2 MUTATED PTCH2 WILD-TYPE
  COLON             17             349
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PTCH2 MUTATED         3        0        4         6         1         0
  PTCH2 WILD-TYPE      88        1       28       132         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PTCH2 MUTATED           1          1          3          0        0         0
  PTCH2 WILD-TYPE        23         10         56         42       48        18
                 vv
clus              STAGE IVB
  PTCH2 MUTATED           0
  PTCH2 WILD-TYPE         1
D1155V4, multiclass
            clus
vv           PTCH2 MUTATED PTCH2 WILD-TYPE
  STAGE I                3              88
  STAGE IA               0               1
  STAGE II               4              28
  STAGE IIA              6             132
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             1              10
  STAGE IIIB             3              56
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PTCH2 MUTATED     0   3  15   1
  PTCH2 WILD-TYPE  17  89 314  49
D1155V5, multiclass
    clus
vv   PTCH2 MUTATED PTCH2 WILD-TYPE
  T1             0              17
  T2             3              89
  T3            15             314
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  PTCH2 MUTATED    15   2   2
  PTCH2 WILD-TYPE 272 111  85
D1155V6, multiclass
    clus
vv   PTCH2 MUTATED PTCH2 WILD-TYPE
  N0            15             272
  N1             2             111
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1155V7, binary
                 cls
clus                0   1
  PTCH2 MUTATED    19   0
  PTCH2 WILD-TYPE 356  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTCH2 MUTATED     19    0
  PTCH2 WILD-TYPE  356   65
   clus
vv  PTCH2 MUTATED PTCH2 WILD-TYPE
  0            19             356
  1             0              65
[1] 2 2
[1] FALSE
D1155V8, binary
                 cls
clus                0   1
  PTCH2 MUTATED     8  11
  PTCH2 WILD-TYPE 217 253
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTCH2 MUTATED      8   11
  PTCH2 WILD-TYPE  217  253
        clus
vv       PTCH2 MUTATED PTCH2 WILD-TYPE
  FEMALE             8             217
  MALE              11             253
[1] 2 2
[1] FALSE
D1155V9, binary
                 cls
clus                0   1
  PTCH2 MUTATED    15   0
  PTCH2 WILD-TYPE 335  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTCH2 MUTATED     15    0
  PTCH2 WILD-TYPE  335   22
     clus
vv    PTCH2 MUTATED PTCH2 WILD-TYPE
  NO             15             335
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PTCH2 MUTATED                     13                             3
  PTCH2 WILD-TYPE                  302                            44
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PTCH2 MUTATED                       2                              0
  PTCH2 WILD-TYPE                   104                             10
D1155V10, multiclass
                                clus
vv                               PTCH2 MUTATED PTCH2 WILD-TYPE
  COLON ADENOCARCINOMA                      13             302
  COLON MUCINOUS ADENOCARCINOMA              3              44
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  PTCH2 MUTATED    15   0   0   0
  PTCH2 WILD-TYPE 330   4  31  25
D1155V11, multiclass
    clus
vv   PTCH2 MUTATED PTCH2 WILD-TYPE
  R0            15             330
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1155V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PTCH2 MUTATED                                  0     1
  PTCH2 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PTCH2 MUTATED                           0    10
  PTCH2 WILD-TYPE                        22   216
D1155V13, multiclass
                                  clus
vv                                 PTCH2 MUTATED PTCH2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                       10             216
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1156) Variable = POMGNT1 MUTATION ANALYSIS
D1156V1, survival
                   sevent
clus2                 0   1
  POMGNT1 MUTATED     6   2
  POMGNT1 WILD-TYPE 372  91
  POMGNT1 MUTATED POMGNT1 WILD-TYPE 
                8               463 
  POMGNT1 MUTATED POMGNT1 WILD-TYPE 
                2                91 
$`POMGNT1 MUTATED`
TCGA-AA-3715 TCGA-AA-3966 TCGA-CM-4743 TCGA-CM-5349 TCGA-D5-6537 TCGA-D5-6540 
       19.04         2.01        23.05        30.08         4.80        16.14 
TCGA-D5-6930 TCGA-G4-6588 
        1.51        26.17 

$`POMGNT1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
        2.01        20.98        34.03        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
       82.95         1.91       124.27        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5861 
       13.02        29.06        22.03        22.98        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6539 
        1.32        43.27        15.12        17.85        17.13        12.49 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 
        9.04         9.44        11.64         4.80        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       35.80        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  POMGNT1 MUTATED POMGNT1 WILD-TYPE 
             1.51              0.00 
  POMGNT1 MUTATED POMGNT1 WILD-TYPE 
            30.08            148.01 
  POMGNT1 MUTATED POMGNT1 WILD-TYPE 
            17.59             20.28 
[1] "1.5 - 30.1 (17.6)"  "0.0 - 148.0 (20.3)"
[1] "hr=" "2.2"
D1156V2, continuous
D1156V3, binary
                   cls
clus                  0   1
  POMGNT1 MUTATED     8   0
  POMGNT1 WILD-TYPE 358 119
[1] "tbl2"
                   cls
clus                [,1] [,2]
  POMGNT1 MUTATED      8    0
  POMGNT1 WILD-TYPE  358  119
        clus
vv       POMGNT1 MUTATED POMGNT1 WILD-TYPE
  COLON                8               358
  RECTUM               0               119
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  POMGNT1 MUTATED         1        0        1         5         0         0
  POMGNT1 WILD-TYPE      90        1       31       133        10         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  POMGNT1 MUTATED           0          0          1          0        0
  POMGNT1 WILD-TYPE        24         11         58         42       48
                   vv
clus                STAGE IVA STAGE IVB
  POMGNT1 MUTATED           0         0
  POMGNT1 WILD-TYPE        18         1
D1156V4, multiclass
            clus
vv           POMGNT1 MUTATED POMGNT1 WILD-TYPE
  STAGE I                  1                90
  STAGE IA                 0                 1
  STAGE II                 1                31
  STAGE IIA                5               133
  STAGE IIB                0                10
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               0                11
  STAGE IIIB               1                58
  STAGE IIIC               0                42
  STAGE IV                 0                48
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  POMGNT1 MUTATED     0   1   7   0
  POMGNT1 WILD-TYPE  17  91 322  50
D1156V5, multiclass
    clus
vv   POMGNT1 MUTATED POMGNT1 WILD-TYPE
  T1               0                17
  T2               1                91
  T3               7               322
  T4               0                50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  POMGNT1 MUTATED     7   1   0
  POMGNT1 WILD-TYPE 280 112  87
D1156V6, multiclass
    clus
vv   POMGNT1 MUTATED POMGNT1 WILD-TYPE
  N0               7               280
  N1               1               112
  N2               0                87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1156V7, binary
                   cls
clus                  0   1
  POMGNT1 MUTATED     7   0
  POMGNT1 WILD-TYPE 368  65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  POMGNT1 MUTATED      7    0
  POMGNT1 WILD-TYPE  368   65
   clus
vv  POMGNT1 MUTATED POMGNT1 WILD-TYPE
  0               7               368
  1               0                65
[1] 2 2
[1] FALSE
D1156V8, binary
                   cls
clus                  0   1
  POMGNT1 MUTATED     3   5
  POMGNT1 WILD-TYPE 222 259
[1] "tbl2"
                   cls
clus                [,1] [,2]
  POMGNT1 MUTATED      3    5
  POMGNT1 WILD-TYPE  222  259
        clus
vv       POMGNT1 MUTATED POMGNT1 WILD-TYPE
  FEMALE               3               222
  MALE                 5               259
[1] 2 2
[1] FALSE
D1156V9, binary
                   cls
clus                  0   1
  POMGNT1 MUTATED     6   0
  POMGNT1 WILD-TYPE 344  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  POMGNT1 MUTATED      6    0
  POMGNT1 WILD-TYPE  344   22
     clus
vv    POMGNT1 MUTATED POMGNT1 WILD-TYPE
  NO                6               344
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  POMGNT1 MUTATED                      5                             3
  POMGNT1 WILD-TYPE                  310                            44
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  POMGNT1 MUTATED                       0                              0
  POMGNT1 WILD-TYPE                   106                             10
D1156V10, multiclass
                                clus
vv                               POMGNT1 MUTATED POMGNT1 WILD-TYPE
  COLON ADENOCARCINOMA                         5               310
  COLON MUCINOUS ADENOCARCINOMA                3                44
  RECTAL ADENOCARCINOMA                        0               106
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  POMGNT1 MUTATED     7   0   0   0
  POMGNT1 WILD-TYPE 338   4  31  25
D1156V11, multiclass
    clus
vv   POMGNT1 MUTATED POMGNT1 WILD-TYPE
  R0               7               338
  R1               0                 4
  R2               0                31
  RX               0                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1156V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  POMGNT1 MUTATED                                  0     0
  POMGNT1 WILD-TYPE                                1    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  POMGNT1 MUTATED                           0     6
  POMGNT1 WILD-TYPE                        22   220
D1156V13, multiclass
                                  clus
vv                                 POMGNT1 MUTATED POMGNT1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                      0                22
  WHITE                                          6               220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1157) Variable = NAA10 MUTATION ANALYSIS
D1157V1, survival
                 sevent
clus2               0   1
  NAA10 MUTATED     3   0
  NAA10 WILD-TYPE 375  93
  NAA10 MUTATED NAA10 WILD-TYPE 
              3             468 
  NAA10 MUTATED NAA10 WILD-TYPE 
              0              93 
$`NAA10 MUTATED`
TCGA-AA-3510 TCGA-CK-6751 TCGA-AF-2693 
       63.98       124.27        19.10 

$`NAA10 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       21.14        82.95         1.91        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       43.04        13.55        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  NAA10 MUTATED NAA10 WILD-TYPE 
           19.1             0.0 
  NAA10 MUTATED NAA10 WILD-TYPE 
         124.27          148.01 
  NAA10 MUTATED NAA10 WILD-TYPE 
         63.980          20.155 
[1] "19.1 - 124.3 (64.0)" "0.0 - 148.0 (20.2)" 
[1] "hr="     "9300000"
D1157V2, continuous
D1157V3, binary
                 cls
clus                0   1
  NAA10 MUTATED     2   0
  NAA10 WILD-TYPE 364 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NAA10 MUTATED      2    0
  NAA10 WILD-TYPE  364  119
        clus
vv       NAA10 MUTATED NAA10 WILD-TYPE
  COLON              2             364
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NAA10 MUTATED         2        0        1         0         0         0
  NAA10 WILD-TYPE      89        1       31       138        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NAA10 MUTATED           0          0          0          0        0         0
  NAA10 WILD-TYPE        24         11         59         42       48        18
                 vv
clus              STAGE IVB
  NAA10 MUTATED           0
  NAA10 WILD-TYPE         1
D1157V4, multiclass
            clus
vv           NAA10 MUTATED NAA10 WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              0             138
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  NAA10 MUTATED     0   2   1   0
  NAA10 WILD-TYPE  17  90 328  50
D1157V5, multiclass
    clus
vv   NAA10 MUTATED NAA10 WILD-TYPE
  T1             0              17
  T2             2              90
  T3             1             328
  T4             0              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  NAA10 MUTATED     3   0   0
  NAA10 WILD-TYPE 284 113  87
D1157V6, multiclass
    clus
vv   NAA10 MUTATED NAA10 WILD-TYPE
  N0             3             284
  N1             0             113
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1157V7, binary
                 cls
clus                0   1
  NAA10 MUTATED     1   0
  NAA10 WILD-TYPE 374  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NAA10 MUTATED      1    0
  NAA10 WILD-TYPE  374   65
   clus
vv  NAA10 MUTATED NAA10 WILD-TYPE
  0             1             374
  1             0              65
[1] 2 2
[1] FALSE
D1157V8, binary
                 cls
clus                0   1
  NAA10 MUTATED     1   2
  NAA10 WILD-TYPE 224 262
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NAA10 MUTATED      1    2
  NAA10 WILD-TYPE  224  262
        clus
vv       NAA10 MUTATED NAA10 WILD-TYPE
  FEMALE             1             224
  MALE               2             262
[1] 2 2
[1] FALSE
D1157V9, binary
                 cls
clus                0   1
  NAA10 MUTATED     3   0
  NAA10 WILD-TYPE 347  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NAA10 MUTATED      3    0
  NAA10 WILD-TYPE  347   22
     clus
vv    NAA10 MUTATED NAA10 WILD-TYPE
  NO              3             347
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  NAA10 MUTATED                      1                             1
  NAA10 WILD-TYPE                  314                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  NAA10 MUTATED                       0                              0
  NAA10 WILD-TYPE                   106                             10
D1157V10, multiclass
[1] "Remove cluster labels:" "NAA10 MUTATED"         
clus
  NAA10 MUTATED NAA10 WILD-TYPE 
              2             476 
     TCGA-A6-2671      TCGA-A6-2672      TCGA-A6-2674      TCGA-A6-2676 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-A6-2677      TCGA-A6-2678      TCGA-A6-2683      TCGA-A6-3807 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-A6-3808      TCGA-A6-3809      TCGA-A6-3810      TCGA-A6-4105 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-A6-5656      TCGA-A6-5657      TCGA-A6-5659      TCGA-A6-5660 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-A6-5661      TCGA-A6-5662      TCGA-A6-5664      TCGA-A6-5665 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-A6-5666      TCGA-A6-6137      TCGA-A6-6138      TCGA-A6-6141 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-A6-6142      TCGA-A6-6648      TCGA-A6-6649      TCGA-A6-6651 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-A6-6652      TCGA-A6-6653      TCGA-A6-6654      TCGA-A6-6780 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-A6-6781      TCGA-A6-6782      TCGA-AA-3489      TCGA-AA-3492 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AA-3496      TCGA-AA-3502      TCGA-AA-3511      TCGA-AA-3514 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AA-3516      TCGA-AA-3517      TCGA-AA-3518      TCGA-AA-3519 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AA-3520      TCGA-AA-3521      TCGA-AA-3522      TCGA-AA-3524 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AA-3525      TCGA-AA-3526      TCGA-AA-3527      TCGA-AA-3529 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AA-3530      TCGA-AA-3531      TCGA-AA-3532      TCGA-AA-3534 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AA-3538      TCGA-AA-3542      TCGA-AA-3543      TCGA-AA-3544 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AA-3548      TCGA-AA-3549      TCGA-AA-3552      TCGA-AA-3553 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AA-3554      TCGA-AA-3555      TCGA-AA-3558      TCGA-AA-3560 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AA-3561      TCGA-AA-3562      TCGA-AA-3655      TCGA-AA-3660 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AA-3662      TCGA-AA-3663      TCGA-AA-3664      TCGA-AA-3666 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AA-3667      TCGA-AA-3672      TCGA-AA-3673      TCGA-AA-3678 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AA-3679      TCGA-AA-3680      TCGA-AA-3681      TCGA-AA-3684 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AA-3685      TCGA-AA-3688      TCGA-AA-3692      TCGA-AA-3693 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AA-3695      TCGA-AA-3696      TCGA-AA-3697      TCGA-AA-3710 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AA-3712      TCGA-AA-3713      TCGA-AA-3715      TCGA-AA-3811 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AA-3812      TCGA-AA-3814      TCGA-AA-3815      TCGA-AA-3818 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AA-3819      TCGA-AA-3821      TCGA-AA-3831      TCGA-AA-3833 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AA-3837      TCGA-AA-3842      TCGA-AA-3844      TCGA-AA-3845 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AA-3846      TCGA-AA-3848      TCGA-AA-3850      TCGA-AA-3851 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AA-3852      TCGA-AA-3854      TCGA-AA-3855      TCGA-AA-3856 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AA-3858      TCGA-AA-3860      TCGA-AA-3861      TCGA-AA-3864 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AA-3866      TCGA-AA-3867      TCGA-AA-3869      TCGA-AA-3870 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AA-3872      TCGA-AA-3875      TCGA-AA-3877      TCGA-AA-3930 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AA-3939      TCGA-AA-3941      TCGA-AA-3947      TCGA-AA-3949 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AA-3950      TCGA-AA-3952      TCGA-AA-3955      TCGA-AA-3956 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AA-3966      TCGA-AA-3968      TCGA-AA-3971      TCGA-AA-3972 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AA-3973      TCGA-AA-3975      TCGA-AA-3976      TCGA-AA-3977 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AA-3979      TCGA-AA-3980      TCGA-AA-3982      TCGA-AA-3984 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AA-3986      TCGA-AA-3989      TCGA-AA-3994      TCGA-AA-A004 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AA-A00A      TCGA-AA-A00D      TCGA-AA-A00E      TCGA-AA-A00F 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AA-A00J      TCGA-AA-A00K      TCGA-AA-A00L      TCGA-AA-A00N 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AA-A00O      TCGA-AA-A00Q      TCGA-AA-A00R      TCGA-AA-A00U 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AA-A00W      TCGA-AA-A00Z      TCGA-AA-A010      TCGA-AA-A017 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AA-A01D      TCGA-AA-A01F      TCGA-AA-A01G      TCGA-AA-A01I 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AA-A01K      TCGA-AA-A01P      TCGA-AA-A01Q      TCGA-AA-A01R 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AA-A01S      TCGA-AA-A01T      TCGA-AA-A01V      TCGA-AA-A01X 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AA-A01Z      TCGA-AA-A022      TCGA-AA-A024      TCGA-AA-A029 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AA-A02F      TCGA-AA-A02H      TCGA-AA-A02J      TCGA-AA-A02K 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AA-A02O      TCGA-AA-A02W      TCGA-AA-A02Y      TCGA-AA-A03F 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AA-A03J      TCGA-AD-5900      TCGA-AD-6548      TCGA-AD-6888 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AD-6889      TCGA-AD-6890      TCGA-AD-6895      TCGA-AD-6899 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AD-6901      TCGA-AD-6963      TCGA-AD-6964      TCGA-AD-6965 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AU-3779      TCGA-AU-6004      TCGA-AY-4070      TCGA-AY-5543 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AY-6196      TCGA-AY-6197      TCGA-AY-6386      TCGA-AZ-4315 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AZ-4323      TCGA-AZ-4616      TCGA-AZ-4681      TCGA-AZ-4682 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AZ-5403      TCGA-AZ-5407      TCGA-AZ-6598      TCGA-AZ-6599 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AZ-6600      TCGA-AZ-6601      TCGA-AZ-6603      TCGA-AZ-6605 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AZ-6606      TCGA-AZ-6607      TCGA-AZ-6608      TCGA-CA-5254 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-CA-5255      TCGA-CA-5796      TCGA-CA-5797      TCGA-CA-6715 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-CA-6716      TCGA-CA-6717      TCGA-CA-6718      TCGA-CA-6719 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-CK-4947      TCGA-CK-4948      TCGA-CK-4950      TCGA-CK-4952 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-CK-5912      TCGA-CK-5913      TCGA-CK-5914      TCGA-CK-5915 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-CK-5916      TCGA-CK-6746      TCGA-CK-6747      TCGA-CK-6748 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-CM-4743      TCGA-CM-4744      TCGA-CM-4746      TCGA-CM-4747 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-CM-4752      TCGA-CM-5341      TCGA-CM-5344      TCGA-CM-5348 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-CM-5349      TCGA-CM-5860      TCGA-CM-5861      TCGA-CM-5862 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-CM-5863      TCGA-CM-5864      TCGA-CM-5868      TCGA-CM-6161 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-CM-6162      TCGA-CM-6163      TCGA-CM-6164      TCGA-CM-6165 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-CM-6166      TCGA-CM-6167      TCGA-CM-6168      TCGA-CM-6169 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-CM-6170      TCGA-CM-6171      TCGA-CM-6172      TCGA-CM-6674 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-CM-6675      TCGA-CM-6676      TCGA-CM-6677      TCGA-CM-6678 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-CM-6679      TCGA-CM-6680      TCGA-D5-5537      TCGA-D5-5538 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-D5-5539      TCGA-D5-5540      TCGA-D5-5541      TCGA-D5-6529 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-D5-6532      TCGA-D5-6533      TCGA-D5-6534      TCGA-D5-6535 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-D5-6536      TCGA-D5-6537      TCGA-D5-6538      TCGA-D5-6539 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-D5-6540      TCGA-D5-6541      TCGA-D5-6898      TCGA-D5-6920 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-D5-6922      TCGA-D5-6923      TCGA-D5-6924      TCGA-D5-6926 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-D5-6927      TCGA-D5-6928      TCGA-D5-6929      TCGA-D5-6930 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-D5-6931      TCGA-D5-6932      TCGA-D5-7000      TCGA-DM-A0X9 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-DM-A0XD      TCGA-DM-A1D0      TCGA-DM-A1D4      TCGA-DM-A1D6 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-DM-A1D8      TCGA-DM-A1D9      TCGA-DM-A1DA      TCGA-DM-A1DB 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-DM-A1HA      TCGA-DM-A282      TCGA-DM-A285      TCGA-DM-A28C 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-DM-A28E      TCGA-DM-A28F      TCGA-DM-A28G      TCGA-DM-A28H 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-DM-A28K      TCGA-F4-6459      TCGA-F4-6460      TCGA-F4-6569 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-F4-6570      TCGA-F4-6703      TCGA-F4-6704      TCGA-F4-6805 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-F4-6806      TCGA-F4-6807      TCGA-F4-6808      TCGA-F4-6809 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-F4-6854      TCGA-F4-6855      TCGA-F4-6856      TCGA-G4-6293 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-G4-6299      TCGA-G4-6303      TCGA-G4-6304      TCGA-G4-6306 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-G4-6307      TCGA-G4-6309      TCGA-G4-6310      TCGA-G4-6315 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-G4-6317      TCGA-G4-6321      TCGA-G4-6323      TCGA-G4-6586 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-G4-6588      TCGA-G4-6625      TCGA-G4-6626      TCGA-G4-6628 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AF-2687      TCGA-AF-2689      TCGA-AF-2691      TCGA-AF-3400 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AF-3913      TCGA-AF-5654      TCGA-AF-6136      TCGA-AF-6655 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AF-6672      TCGA-AG-3574      TCGA-AG-3575      TCGA-AG-3578 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AG-3580      TCGA-AG-3581      TCGA-AG-3582      TCGA-AG-3583 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AG-3584      TCGA-AG-3587      TCGA-AG-3593      TCGA-AG-3594 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AG-3598      TCGA-AG-3600      TCGA-AG-3601      TCGA-AG-3602 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AG-3605      TCGA-AG-3608      TCGA-AG-3609      TCGA-AG-3611 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AG-3612      TCGA-AG-3726      TCGA-AG-3727      TCGA-AG-3731 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AG-3732      TCGA-AG-3742      TCGA-AG-3878      TCGA-AG-3882 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AG-3883      TCGA-AG-3885      TCGA-AG-3887      TCGA-AG-3890 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AG-3892      TCGA-AG-3893      TCGA-AG-3894      TCGA-AG-3896 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AG-3898      TCGA-AG-3901      TCGA-AG-3902      TCGA-AG-3909 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AG-3999      TCGA-AG-4001      TCGA-AG-4005      TCGA-AG-4007 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AG-4008      TCGA-AG-4015      TCGA-AG-A002      TCGA-AG-A008 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AG-A00C      TCGA-AG-A00H      TCGA-AG-A00Y      TCGA-AG-A011 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AG-A014      TCGA-AG-A015      TCGA-AG-A016      TCGA-AG-A01L 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AG-A01W      TCGA-AG-A01Y      TCGA-AG-A020      TCGA-AG-A025 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AG-A026      TCGA-AG-A02G      TCGA-AG-A02N      TCGA-AG-A02X 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AG-A032      TCGA-AG-A036      TCGA-AH-6544      TCGA-AH-6547 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AH-6549      TCGA-AH-6643      TCGA-AH-6644      TCGA-CI-6619 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-CI-6620      TCGA-CI-6621      TCGA-CI-6622      TCGA-CI-6624 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-CL-5917      TCGA-CL-5918      TCGA-DC-5337      TCGA-DC-5869 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-DC-6155      TCGA-DC-6157      TCGA-DC-6158      TCGA-DC-6160 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-DC-6681      TCGA-DC-6682      TCGA-DC-6683      TCGA-DT-5265 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-DY-A0XA      TCGA-DY-A1DC      TCGA-DY-A1DD      TCGA-DY-A1DF 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-DY-A1DG      TCGA-DY-A1H8      TCGA-EF-5830      TCGA-EI-6506 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-EI-6507      TCGA-EI-6508      TCGA-EI-6510      TCGA-F5-6464 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-F5-6465      TCGA-F5-6571      TCGA-F5-6702      TCGA-F5-6811 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-F5-6812      TCGA-F5-6813      TCGA-G5-6235      TCGA-G5-6641 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
                 vv
clus               R0  R1  R2  RX
  NAA10 MUTATED     1   0   0   1
  NAA10 WILD-TYPE 344   4  31  24
D1157V11, multiclass
[1] "Remove cluster labels:" "NAA10 MUTATED"         
clus
  NAA10 MUTATED NAA10 WILD-TYPE 
              2             403 
     TCGA-A6-2671      TCGA-A6-2672      TCGA-A6-2674      TCGA-A6-2676 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-A6-2677      TCGA-A6-2678      TCGA-A6-2683      TCGA-A6-3807 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-A6-3808      TCGA-A6-3809      TCGA-A6-3810      TCGA-A6-5657 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-A6-5659      TCGA-A6-5661      TCGA-A6-5665      TCGA-A6-6781 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AA-3489      TCGA-AA-3492      TCGA-AA-3496      TCGA-AA-3502 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AA-3511      TCGA-AA-3514      TCGA-AA-3517      TCGA-AA-3518 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AA-3519      TCGA-AA-3520      TCGA-AA-3521      TCGA-AA-3522 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AA-3524      TCGA-AA-3525      TCGA-AA-3526      TCGA-AA-3527 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AA-3529      TCGA-AA-3530      TCGA-AA-3531      TCGA-AA-3532 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AA-3534      TCGA-AA-3538      TCGA-AA-3542      TCGA-AA-3543 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AA-3544      TCGA-AA-3548      TCGA-AA-3549      TCGA-AA-3552 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AA-3553      TCGA-AA-3554      TCGA-AA-3555      TCGA-AA-3556 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AA-3558      TCGA-AA-3560      TCGA-AA-3561      TCGA-AA-3562 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AA-3655      TCGA-AA-3660      TCGA-AA-3662      TCGA-AA-3663 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AA-3664      TCGA-AA-3666      TCGA-AA-3667      TCGA-AA-3672 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AA-3673      TCGA-AA-3678      TCGA-AA-3679      TCGA-AA-3680 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AA-3681      TCGA-AA-3684      TCGA-AA-3685      TCGA-AA-3688 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AA-3692      TCGA-AA-3693      TCGA-AA-3695      TCGA-AA-3696 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AA-3697      TCGA-AA-3710      TCGA-AA-3712      TCGA-AA-3713 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AA-3715      TCGA-AA-3811      TCGA-AA-3812      TCGA-AA-3814 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AA-3815      TCGA-AA-3818      TCGA-AA-3819      TCGA-AA-3821 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AA-3831      TCGA-AA-3833      TCGA-AA-3837      TCGA-AA-3842 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AA-3844      TCGA-AA-3845      TCGA-AA-3846      TCGA-AA-3848 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AA-3850      TCGA-AA-3851      TCGA-AA-3852      TCGA-AA-3854 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AA-3855      TCGA-AA-3856      TCGA-AA-3858      TCGA-AA-3860 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AA-3861      TCGA-AA-3864      TCGA-AA-3866      TCGA-AA-3867 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AA-3869      TCGA-AA-3870      TCGA-AA-3872      TCGA-AA-3875 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AA-3877      TCGA-AA-3930      TCGA-AA-3939      TCGA-AA-3941 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AA-3947      TCGA-AA-3949      TCGA-AA-3950      TCGA-AA-3952 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AA-3955      TCGA-AA-3956      TCGA-AA-3968      TCGA-AA-3971 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AA-3972      TCGA-AA-3973      TCGA-AA-3975      TCGA-AA-3976 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AA-3979      TCGA-AA-3984      TCGA-AA-3986      TCGA-AA-3989 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AA-3994      TCGA-AA-A004      TCGA-AA-A00A      TCGA-AA-A00D 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AA-A00E      TCGA-AA-A00F      TCGA-AA-A00J      TCGA-AA-A00K 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AA-A00L      TCGA-AA-A00N      TCGA-AA-A00O      TCGA-AA-A00Q 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AA-A00R      TCGA-AA-A00U      TCGA-AA-A00W      TCGA-AA-A00Z 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AA-A010      TCGA-AA-A017      TCGA-AA-A01D      TCGA-AA-A01F 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AA-A01G      TCGA-AA-A01I      TCGA-AA-A01K      TCGA-AA-A01P 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AA-A01Q      TCGA-AA-A01R      TCGA-AA-A01S      TCGA-AA-A01T 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AA-A01V      TCGA-AA-A01X      TCGA-AA-A01Z      TCGA-AA-A022 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AA-A024      TCGA-AA-A029      TCGA-AA-A02F      TCGA-AA-A02H 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AA-A02J      TCGA-AA-A02K      TCGA-AA-A02O      TCGA-AA-A02W 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AA-A02Y      TCGA-AA-A03F      TCGA-AA-A03J      TCGA-AD-5900 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AD-6548      TCGA-AD-6888      TCGA-AU-3779      TCGA-AU-6004 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AY-4070      TCGA-AY-4071      TCGA-AY-5543      TCGA-AY-6196 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AY-6197      TCGA-AY-6386      TCGA-AZ-4315      TCGA-AZ-4681 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AZ-4682      TCGA-CA-5254      TCGA-CA-5255      TCGA-CA-5796 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-CA-5797      TCGA-CA-6715      TCGA-CA-6716      TCGA-CA-6717 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-CA-6718      TCGA-CA-6719      TCGA-CK-4947      TCGA-CK-4948 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-CK-4950      TCGA-CK-4952      TCGA-CK-5912      TCGA-CK-5913 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-CK-5914      TCGA-CK-5915      TCGA-CK-5916      TCGA-CK-6746 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-CK-6747      TCGA-CK-6748      TCGA-CM-4743      TCGA-CM-4744 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-CM-4746      TCGA-CM-4747      TCGA-CM-4752      TCGA-CM-5341 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-CM-5344      TCGA-CM-5348      TCGA-CM-5349      TCGA-CM-5860 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-CM-5861      TCGA-CM-5862      TCGA-CM-5863      TCGA-CM-5864 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-CM-5868      TCGA-CM-6161      TCGA-CM-6162      TCGA-CM-6163 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-CM-6164      TCGA-CM-6165      TCGA-CM-6166      TCGA-CM-6167 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-CM-6168      TCGA-CM-6169      TCGA-CM-6170      TCGA-CM-6171 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-CM-6172      TCGA-CM-6674      TCGA-CM-6675      TCGA-CM-6676 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-CM-6677      TCGA-CM-6678      TCGA-CM-6679      TCGA-CM-6680 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-D5-5537      TCGA-D5-5538      TCGA-D5-5539      TCGA-D5-5540 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-D5-5541      TCGA-D5-6529      TCGA-D5-6532      TCGA-D5-6533 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-D5-6534      TCGA-D5-6535      TCGA-D5-6536      TCGA-D5-6537 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-D5-6538      TCGA-D5-6539      TCGA-D5-6540      TCGA-D5-6541 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-D5-6898      TCGA-D5-6920      TCGA-D5-6922      TCGA-D5-6923 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-D5-6924      TCGA-D5-6926      TCGA-D5-6927      TCGA-D5-6928 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-D5-6929      TCGA-D5-6930      TCGA-D5-6931      TCGA-D5-6932 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-D5-7000      TCGA-F4-6459      TCGA-F4-6460      TCGA-F4-6569 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-F4-6570      TCGA-F4-6703      TCGA-F4-6704      TCGA-F4-6805 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-F4-6806      TCGA-F4-6807      TCGA-F4-6808      TCGA-F4-6809 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-F4-6854      TCGA-F4-6855      TCGA-F4-6856      TCGA-G4-6293 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-G4-6299      TCGA-G4-6303      TCGA-G4-6304      TCGA-G4-6306 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-G4-6307      TCGA-G4-6309      TCGA-G4-6310      TCGA-G4-6315 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-G4-6317      TCGA-G4-6321      TCGA-G4-6323      TCGA-G4-6586 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-G4-6588      TCGA-G4-6625      TCGA-G4-6626      TCGA-G4-6628 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AF-2687      TCGA-AF-2689      TCGA-AF-2691      TCGA-AF-2692 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AF-3400      TCGA-AF-3913      TCGA-AF-4110      TCGA-AF-5654 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AF-6655      TCGA-AG-3574      TCGA-AG-3575      TCGA-AG-3578 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AG-3580      TCGA-AG-3581      TCGA-AG-3582      TCGA-AG-3583 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AG-3584      TCGA-AG-3586      TCGA-AG-3587      TCGA-AG-3593 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AG-3594      TCGA-AG-3598      TCGA-AG-3599      TCGA-AG-3600 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AG-3601      TCGA-AG-3602      TCGA-AG-3605      TCGA-AG-3608 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AG-3609      TCGA-AG-3611      TCGA-AG-3612      TCGA-AG-3726 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AG-3727      TCGA-AG-3731      TCGA-AG-3732      TCGA-AG-3742 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AG-3878      TCGA-AG-3882      TCGA-AG-3883      TCGA-AG-3885 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AG-3887      TCGA-AG-3890      TCGA-AG-3892      TCGA-AG-3893 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AG-3894      TCGA-AG-3896      TCGA-AG-3898      TCGA-AG-3901 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AG-3902      TCGA-AG-3909      TCGA-AG-3999      TCGA-AG-4001 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AG-4005      TCGA-AG-4007      TCGA-AG-4008      TCGA-AG-4015 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AG-A002      TCGA-AG-A008      TCGA-AG-A00C      TCGA-AG-A00H 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AG-A00Y      TCGA-AG-A011      TCGA-AG-A014      TCGA-AG-A015 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AG-A016      TCGA-AG-A01L      TCGA-AG-A01W      TCGA-AG-A01Y 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AG-A020      TCGA-AG-A025      TCGA-AG-A026      TCGA-AG-A02G 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AG-A02N      TCGA-AG-A02X      TCGA-AG-A032      TCGA-AG-A036 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AH-6549      TCGA-AH-6643      TCGA-CL-5917      TCGA-CL-5918 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-DC-5337      TCGA-DC-5869      TCGA-DC-6155      TCGA-DC-6157 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-DC-6158      TCGA-DC-6160      TCGA-DC-6681      TCGA-DC-6682 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-DC-6683      TCGA-DT-5265      TCGA-EF-5830      TCGA-EI-6506 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-EI-6507      TCGA-EI-6508      TCGA-EI-6510      TCGA-F5-6464 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-F5-6465      TCGA-F5-6571      TCGA-F5-6702      TCGA-F5-6812 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-F5-6813      TCGA-G5-6235      TCGA-G5-6641 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
D1157V12, continuous
[1] "Remove cluster labels:" "NAA10 MUTATED"         
clus
  NAA10 MUTATED NAA10 WILD-TYPE 
              2             456 
     TCGA-A6-2671      TCGA-A6-2672      TCGA-A6-2674      TCGA-A6-2676 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-A6-2677      TCGA-A6-2678      TCGA-A6-2683      TCGA-A6-3807 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-A6-3808      TCGA-A6-3809      TCGA-A6-3810      TCGA-A6-4105 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-A6-5656      TCGA-A6-5657      TCGA-A6-5659      TCGA-A6-5660 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-A6-5661      TCGA-A6-5662      TCGA-A6-5664      TCGA-A6-5665 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-A6-5666      TCGA-A6-6137      TCGA-A6-6138      TCGA-A6-6141 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-A6-6142      TCGA-A6-6648      TCGA-A6-6649      TCGA-A6-6651 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-A6-6652      TCGA-A6-6653      TCGA-A6-6654      TCGA-A6-6780 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-A6-6781      TCGA-A6-6782      TCGA-AA-3489      TCGA-AA-3492 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AA-3496      TCGA-AA-3502      TCGA-AA-3511      TCGA-AA-3514 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AA-3516      TCGA-AA-3517      TCGA-AA-3518      TCGA-AA-3519 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AA-3520      TCGA-AA-3521      TCGA-AA-3522      TCGA-AA-3524 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AA-3525      TCGA-AA-3526      TCGA-AA-3527      TCGA-AA-3529 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AA-3530      TCGA-AA-3531      TCGA-AA-3532      TCGA-AA-3534 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AA-3538      TCGA-AA-3542      TCGA-AA-3543      TCGA-AA-3544 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AA-3548      TCGA-AA-3549      TCGA-AA-3552      TCGA-AA-3553 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AA-3554      TCGA-AA-3555      TCGA-AA-3556      TCGA-AA-3558 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AA-3560      TCGA-AA-3562      TCGA-AA-3655      TCGA-AA-3660 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AA-3662      TCGA-AA-3663      TCGA-AA-3664      TCGA-AA-3666 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AA-3667      TCGA-AA-3672      TCGA-AA-3673      TCGA-AA-3678 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AA-3679      TCGA-AA-3680      TCGA-AA-3681      TCGA-AA-3684 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AA-3685      TCGA-AA-3688      TCGA-AA-3692      TCGA-AA-3693 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AA-3695      TCGA-AA-3696      TCGA-AA-3697      TCGA-AA-3710 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AA-3712      TCGA-AA-3713      TCGA-AA-3715      TCGA-AA-3811 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AA-3812      TCGA-AA-3814      TCGA-AA-3815      TCGA-AA-3818 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AA-3819      TCGA-AA-3821      TCGA-AA-3831      TCGA-AA-3833 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AA-3837      TCGA-AA-3842      TCGA-AA-3844      TCGA-AA-3845 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AA-3846      TCGA-AA-3848      TCGA-AA-3850      TCGA-AA-3851 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AA-3852      TCGA-AA-3854      TCGA-AA-3855      TCGA-AA-3856 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AA-3858      TCGA-AA-3860      TCGA-AA-3861      TCGA-AA-3864 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AA-3866      TCGA-AA-3867      TCGA-AA-3869      TCGA-AA-3870 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AA-3872      TCGA-AA-3875      TCGA-AA-3877      TCGA-AA-3930 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AA-3939      TCGA-AA-3941      TCGA-AA-3947      TCGA-AA-3949 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AA-3950      TCGA-AA-3952      TCGA-AA-3955      TCGA-AA-3956 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AA-3966      TCGA-AA-3968      TCGA-AA-3971      TCGA-AA-3972 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AA-3973      TCGA-AA-3975      TCGA-AA-3976      TCGA-AA-3977 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AA-3979      TCGA-AA-3980      TCGA-AA-3982      TCGA-AA-3984 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AA-3986      TCGA-AA-3989      TCGA-AA-3994      TCGA-AA-A004 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AA-A00A      TCGA-AA-A00D      TCGA-AA-A00E      TCGA-AA-A00F 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AA-A00J      TCGA-AA-A00K      TCGA-AA-A00L      TCGA-AA-A00N 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AA-A00O      TCGA-AA-A00Q      TCGA-AA-A00R      TCGA-AA-A00U 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AA-A00W      TCGA-AA-A00Z      TCGA-AA-A010      TCGA-AA-A017 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AA-A01D      TCGA-AA-A01F      TCGA-AA-A01G      TCGA-AA-A01I 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AA-A01K      TCGA-AA-A01P      TCGA-AA-A01Q      TCGA-AA-A01R 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AA-A01S      TCGA-AA-A01T      TCGA-AA-A01V      TCGA-AA-A01X 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AA-A01Z      TCGA-AA-A022      TCGA-AA-A024      TCGA-AA-A029 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AA-A02F      TCGA-AA-A02H      TCGA-AA-A02J      TCGA-AA-A02K 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AA-A02O      TCGA-AA-A02W      TCGA-AA-A02Y      TCGA-AA-A03F 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AA-A03J      TCGA-AD-5900      TCGA-AD-6548      TCGA-AD-6888 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AD-6889      TCGA-AD-6890      TCGA-AD-6895      TCGA-AD-6899 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AD-6901      TCGA-AD-6963      TCGA-AD-6964      TCGA-AD-6965 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AU-3779      TCGA-AU-6004      TCGA-AY-4070      TCGA-AY-4071 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AY-5543      TCGA-AY-6196      TCGA-AY-6197      TCGA-AY-6386 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AZ-4323      TCGA-AZ-4616      TCGA-AZ-4682      TCGA-AZ-5403 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AZ-5407      TCGA-AZ-6598      TCGA-AZ-6599      TCGA-AZ-6600 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AZ-6601      TCGA-AZ-6603      TCGA-AZ-6605      TCGA-AZ-6606 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AZ-6607      TCGA-AZ-6608      TCGA-CK-4947      TCGA-CK-4948 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-CK-4950      TCGA-CK-4952      TCGA-CM-4743      TCGA-CM-4744 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-CM-4746      TCGA-CM-4747      TCGA-CM-4752      TCGA-CM-5341 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-CM-5344      TCGA-CM-5348      TCGA-CM-5349      TCGA-CM-5860 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-CM-5861      TCGA-CM-5862      TCGA-CM-5863      TCGA-CM-5864 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-CM-5868      TCGA-CM-6161      TCGA-CM-6162      TCGA-CM-6163 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-CM-6164      TCGA-CM-6165      TCGA-CM-6166      TCGA-CM-6167 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-CM-6168      TCGA-CM-6169      TCGA-CM-6170      TCGA-CM-6171 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-CM-6172      TCGA-CM-6674      TCGA-CM-6675      TCGA-CM-6676 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-CM-6677      TCGA-CM-6678      TCGA-CM-6679      TCGA-CM-6680 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-D5-5537      TCGA-D5-5538      TCGA-D5-5539      TCGA-D5-5540 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-D5-5541      TCGA-D5-6529      TCGA-D5-6532      TCGA-D5-6533 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-D5-6534      TCGA-D5-6535      TCGA-D5-6536      TCGA-D5-6537 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-D5-6538      TCGA-D5-6539      TCGA-D5-6540      TCGA-D5-6541 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-D5-6898      TCGA-D5-6920      TCGA-D5-6922      TCGA-D5-6923 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-D5-6924      TCGA-D5-6926      TCGA-D5-6927      TCGA-D5-6928 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-D5-6929      TCGA-D5-6930      TCGA-D5-6931      TCGA-D5-6932 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-D5-7000      TCGA-DM-A0X9      TCGA-DM-A0XD      TCGA-DM-A0XF 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-DM-A1D0      TCGA-DM-A1D4      TCGA-DM-A1D6      TCGA-DM-A1D7 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-DM-A1D8      TCGA-DM-A1D9      TCGA-DM-A1DA      TCGA-DM-A1DB 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-DM-A1HA      TCGA-DM-A1HB      TCGA-DM-A282      TCGA-DM-A285 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-DM-A28C      TCGA-DM-A28E      TCGA-DM-A28F      TCGA-DM-A28G 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-DM-A28H      TCGA-DM-A28K      TCGA-F4-6459      TCGA-F4-6460 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-F4-6569      TCGA-F4-6570      TCGA-F4-6703      TCGA-F4-6704 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-F4-6806      TCGA-F4-6807      TCGA-F4-6808      TCGA-F4-6809 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-F4-6854      TCGA-F4-6855      TCGA-F4-6856      TCGA-G4-6293 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-G4-6299      TCGA-G4-6303      TCGA-G4-6304      TCGA-G4-6306 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-G4-6307      TCGA-G4-6309      TCGA-G4-6310      TCGA-G4-6315 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-G4-6317      TCGA-G4-6321      TCGA-G4-6323      TCGA-G4-6586 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-G4-6588      TCGA-G4-6625      TCGA-G4-6626      TCGA-G4-6628 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AF-2687      TCGA-AF-2689      TCGA-AF-2691      TCGA-AF-2692 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AF-3400      TCGA-AF-3913      TCGA-AF-4110      TCGA-AF-5654 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AF-6136      TCGA-AF-6655      TCGA-AF-6672      TCGA-AG-3574 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AG-3575      TCGA-AG-3578      TCGA-AG-3580      TCGA-AG-3581 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AG-3582      TCGA-AG-3583      TCGA-AG-3584      TCGA-AG-3586 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AG-3587      TCGA-AG-3593      TCGA-AG-3594      TCGA-AG-3598 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AG-3599      TCGA-AG-3600      TCGA-AG-3601      TCGA-AG-3602 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AG-3605      TCGA-AG-3608      TCGA-AG-3609      TCGA-AG-3611 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AG-3612      TCGA-AG-3726      TCGA-AG-3727      TCGA-AG-3731 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AG-3732      TCGA-AG-3742      TCGA-AG-3878      TCGA-AG-3881 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AG-3882      TCGA-AG-3883      TCGA-AG-3885      TCGA-AG-3887 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AG-3890      TCGA-AG-3892      TCGA-AG-3893      TCGA-AG-3894 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AG-3896      TCGA-AG-3898      TCGA-AG-3901      TCGA-AG-3902 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AG-3909      TCGA-AG-3999      TCGA-AG-4001      TCGA-AG-4005 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AG-4007      TCGA-AG-4008      TCGA-AG-4015      TCGA-AG-A002 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AG-A008      TCGA-AG-A00C      TCGA-AG-A00H      TCGA-AG-A00Y 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AG-A011      TCGA-AG-A014      TCGA-AG-A015      TCGA-AG-A016 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AG-A01L      TCGA-AG-A01W      TCGA-AG-A01Y      TCGA-AG-A020 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AG-A025      TCGA-AG-A026      TCGA-AG-A02G      TCGA-AG-A02N 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AG-A02X      TCGA-AG-A032      TCGA-AG-A036      TCGA-AH-6544 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AH-6547      TCGA-AH-6643      TCGA-AH-6644      TCGA-CI-6622 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-DC-5337      TCGA-DC-5869      TCGA-DC-6155      TCGA-DC-6157 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-DC-6158      TCGA-DC-6160      TCGA-DC-6681      TCGA-DC-6682 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-DC-6683      TCGA-DY-A0XA      TCGA-DY-A1DC      TCGA-DY-A1DD 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-DY-A1DF      TCGA-DY-A1DG      TCGA-DY-A1H8      TCGA-EI-6506 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-EI-6507      TCGA-EI-6508      TCGA-EI-6510      TCGA-F5-6464 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-F5-6465      TCGA-F5-6571      TCGA-F5-6702      TCGA-F5-6811 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-F5-6812      TCGA-F5-6813      TCGA-G5-6235      TCGA-G5-6641 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NAA10 MUTATED                                  0     0
  NAA10 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  NAA10 MUTATED                           0     2
  NAA10 WILD-TYPE                        22   224
D1157V13, multiclass
[1] "Remove cluster labels:" "NAA10 MUTATED"         
clus
  NAA10 MUTATED NAA10 WILD-TYPE 
              2             258 
     TCGA-A6-2671      TCGA-A6-2672      TCGA-A6-2674      TCGA-A6-2676 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-A6-2677      TCGA-A6-2678      TCGA-A6-2683      TCGA-A6-3807 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-A6-3808      TCGA-A6-3809      TCGA-A6-3810      TCGA-A6-4105 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-A6-5656      TCGA-A6-5657      TCGA-A6-5659      TCGA-A6-5660 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-A6-5661      TCGA-A6-5662      TCGA-A6-5664      TCGA-A6-5665 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-A6-5666      TCGA-A6-6137      TCGA-A6-6138      TCGA-A6-6141 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-A6-6142      TCGA-A6-6648      TCGA-A6-6649      TCGA-A6-6651 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-A6-6652      TCGA-A6-6653      TCGA-A6-6654      TCGA-A6-6780 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-A6-6781      TCGA-A6-6782      TCGA-AD-5900      TCGA-AD-6548 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AD-6888      TCGA-AD-6889      TCGA-AD-6890      TCGA-AD-6895 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AD-6899      TCGA-AD-6901      TCGA-AD-6963      TCGA-AD-6964 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AD-6965      TCGA-AU-3779      TCGA-AU-6004      TCGA-AY-4070 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AY-4071      TCGA-AY-5543      TCGA-AY-6196      TCGA-AY-6197 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AY-6386      TCGA-AZ-4315      TCGA-AZ-4323      TCGA-AZ-4616 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AZ-4681      TCGA-AZ-4682      TCGA-AZ-5403      TCGA-AZ-5407 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AZ-6598      TCGA-AZ-6599      TCGA-AZ-6600      TCGA-AZ-6601 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AZ-6603      TCGA-AZ-6605      TCGA-AZ-6606      TCGA-AZ-6607 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AZ-6608      TCGA-CA-5254      TCGA-CA-5255      TCGA-CA-5796 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-CA-5797      TCGA-CA-6715      TCGA-CA-6716      TCGA-CA-6717 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-CA-6718      TCGA-CA-6719      TCGA-CK-4947      TCGA-CK-4948 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-CK-4950      TCGA-CK-4952      TCGA-CK-5912      TCGA-CK-5913 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-CK-5914      TCGA-CK-5915      TCGA-CK-5916      TCGA-CK-6746 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-CK-6747      TCGA-CK-6748      TCGA-CM-4743      TCGA-CM-4744 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-CM-4746      TCGA-CM-4747      TCGA-CM-4752      TCGA-CM-5341 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-CM-5344      TCGA-CM-5348      TCGA-CM-5349      TCGA-CM-5860 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-CM-5861      TCGA-CM-5862      TCGA-CM-5863      TCGA-CM-5864 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-CM-5868      TCGA-CM-6161      TCGA-CM-6162      TCGA-CM-6163 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-CM-6164      TCGA-CM-6165      TCGA-CM-6166      TCGA-CM-6167 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-CM-6168      TCGA-CM-6169      TCGA-CM-6170      TCGA-CM-6171 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-CM-6172      TCGA-CM-6674      TCGA-CM-6675      TCGA-CM-6676 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-CM-6677      TCGA-CM-6678      TCGA-CM-6679      TCGA-CM-6680 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-D5-5537      TCGA-D5-5538      TCGA-D5-5539      TCGA-D5-5540 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-D5-5541      TCGA-D5-6529      TCGA-D5-6532      TCGA-D5-6533 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-D5-6534      TCGA-D5-6535      TCGA-D5-6536      TCGA-D5-6537 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-D5-6538      TCGA-D5-6539      TCGA-D5-6540      TCGA-D5-6541 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-D5-6898      TCGA-D5-6920      TCGA-D5-6922      TCGA-D5-6923 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-D5-6924      TCGA-D5-6926      TCGA-D5-6927      TCGA-D5-6928 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-D5-6929      TCGA-D5-6930      TCGA-D5-6931      TCGA-D5-6932 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-D5-7000      TCGA-DM-A0X9      TCGA-DM-A0XD      TCGA-DM-A0XF 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-DM-A1D0      TCGA-DM-A1D4      TCGA-DM-A1D6      TCGA-DM-A1D7 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-DM-A1D8      TCGA-DM-A1D9      TCGA-DM-A1DA      TCGA-DM-A1DB 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-DM-A1HA      TCGA-DM-A1HB      TCGA-DM-A282      TCGA-DM-A285 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-DM-A28C      TCGA-DM-A28E      TCGA-DM-A28F      TCGA-DM-A28G 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-DM-A28H      TCGA-DM-A28K      TCGA-F4-6459      TCGA-F4-6460 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-F4-6569      TCGA-F4-6570      TCGA-F4-6703      TCGA-F4-6704 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-F4-6805      TCGA-F4-6806      TCGA-F4-6807      TCGA-F4-6808 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-F4-6809      TCGA-F4-6854      TCGA-F4-6855      TCGA-F4-6856 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-G4-6293      TCGA-G4-6299      TCGA-G4-6303      TCGA-G4-6304 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-G4-6306      TCGA-G4-6307      TCGA-G4-6309      TCGA-G4-6310 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-G4-6315      TCGA-G4-6317      TCGA-G4-6321      TCGA-G4-6323 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-G4-6586      TCGA-G4-6588      TCGA-G4-6625      TCGA-G4-6626 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-G4-6628      TCGA-AF-2687      TCGA-AF-2689      TCGA-AF-2691 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AF-2692      TCGA-AF-3400      TCGA-AF-3913      TCGA-AF-4110 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AF-5654      TCGA-AF-6136      TCGA-AF-6655      TCGA-AF-6672 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AH-6544      TCGA-AH-6547      TCGA-AH-6549      TCGA-AH-6643 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-AH-6644      TCGA-CI-6619      TCGA-CI-6620      TCGA-CI-6621 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-CI-6622      TCGA-CI-6624      TCGA-CL-5917      TCGA-CL-5918 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-DC-5337      TCGA-DC-5869      TCGA-DC-6155      TCGA-DC-6157 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-DC-6158      TCGA-DC-6160      TCGA-DC-6681      TCGA-DC-6682 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-DC-6683      TCGA-DT-5265      TCGA-DY-A0XA      TCGA-DY-A1DC 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-DY-A1DD      TCGA-DY-A1DF      TCGA-DY-A1DG      TCGA-DY-A1H8 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-EF-5830      TCGA-EI-6506      TCGA-EI-6507      TCGA-EI-6508 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-EI-6510      TCGA-F5-6464      TCGA-F5-6465      TCGA-F5-6571 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-F5-6702      TCGA-F5-6811      TCGA-F5-6812      TCGA-F5-6813 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 
     TCGA-G5-6235      TCGA-G5-6641 
"NAA10 WILD-TYPE" "NAA10 WILD-TYPE" 

Clustering(1158) Variable = OR2A5 MUTATION ANALYSIS
D1158V1, survival
                 sevent
clus2               0   1
  OR2A5 MUTATED    10   1
  OR2A5 WILD-TYPE 368  92
  OR2A5 MUTATED OR2A5 WILD-TYPE 
             11             460 
  OR2A5 MUTATED OR2A5 WILD-TYPE 
              1              92 
$`OR2A5 MUTATED`
TCGA-AA-3713 TCGA-AA-3947 TCGA-AA-3977 TCGA-CA-6717 TCGA-CM-5349 TCGA-CM-6676 
       19.04        33.01        25.02        12.76        30.08        11.08 
TCGA-DM-A0XF TCGA-G4-6628 TCGA-AG-3892 TCGA-CI-6622 TCGA-G5-6235 
       38.20        79.69        13.02         6.97        55.76 

$`OR2A5 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
        2.01        12.99        24.00        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       29.06        22.03        22.98        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6677 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A1D0 TCGA-DM-A1D4 
       11.38        10.26       119.70        24.43       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 
       35.80        26.17        91.79        46.75        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
        6.05        33.17         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6641 
       32.19         0.66         0.69        26.43 

  OR2A5 MUTATED OR2A5 WILD-TYPE 
           6.97            0.00 
  OR2A5 MUTATED OR2A5 WILD-TYPE 
          79.69          148.01 
  OR2A5 MUTATED OR2A5 WILD-TYPE 
         25.020          20.155 
[1] "7.0 - 79.7 (25.0)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "2.5"
D1158V2, continuous
D1158V3, binary
                 cls
clus                0   1
  OR2A5 MUTATED    10   3
  OR2A5 WILD-TYPE 356 116
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR2A5 MUTATED     10    3
  OR2A5 WILD-TYPE  356  116
        clus
vv       OR2A5 MUTATED OR2A5 WILD-TYPE
  COLON             10             356
  RECTUM             3             116
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  OR2A5 MUTATED         3        0        0         3         2         0
  OR2A5 WILD-TYPE      88        1       32       135         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  OR2A5 MUTATED           0          0          1          1        2         0
  OR2A5 WILD-TYPE        24         11         58         41       46        18
                 vv
clus              STAGE IVB
  OR2A5 MUTATED           0
  OR2A5 WILD-TYPE         1
D1158V4, multiclass
            clus
vv           OR2A5 MUTATED OR2A5 WILD-TYPE
  STAGE I                3              88
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              3             135
  STAGE IIB              2               8
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             1              41
  STAGE IV               2              46
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  OR2A5 MUTATED     1   3   7   2
  OR2A5 WILD-TYPE  16  89 322  48
D1158V5, multiclass
    clus
vv   OR2A5 MUTATED OR2A5 WILD-TYPE
  T1             1              16
  T2             3              89
  T3             7             322
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  OR2A5 MUTATED    10   1   2
  OR2A5 WILD-TYPE 277 112  85
D1158V6, multiclass
    clus
vv   OR2A5 MUTATED OR2A5 WILD-TYPE
  N0            10             277
  N1             1             112
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1158V7, binary
                 cls
clus                0   1
  OR2A5 MUTATED     9   2
  OR2A5 WILD-TYPE 366  63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR2A5 MUTATED      9    2
  OR2A5 WILD-TYPE  366   63
   clus
vv  OR2A5 MUTATED OR2A5 WILD-TYPE
  0             9             366
  1             2              63
[1] 2 2
[1] FALSE
D1158V8, binary
                 cls
clus                0   1
  OR2A5 MUTATED     6   7
  OR2A5 WILD-TYPE 219 257
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR2A5 MUTATED      6    7
  OR2A5 WILD-TYPE  219  257
        clus
vv       OR2A5 MUTATED OR2A5 WILD-TYPE
  FEMALE             6             219
  MALE               7             257
[1] 2 2
[1] FALSE
D1158V9, binary
                 cls
clus                0   1
  OR2A5 MUTATED     8   1
  OR2A5 WILD-TYPE 342  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR2A5 MUTATED      8    1
  OR2A5 WILD-TYPE  342   21
     clus
vv    OR2A5 MUTATED OR2A5 WILD-TYPE
  NO              8             342
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  OR2A5 MUTATED                      7                             2
  OR2A5 WILD-TYPE                  308                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  OR2A5 MUTATED                       3                              0
  OR2A5 WILD-TYPE                   103                             10
D1158V10, multiclass
                                clus
vv                               OR2A5 MUTATED OR2A5 WILD-TYPE
  COLON ADENOCARCINOMA                       7             308
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      3             103
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  OR2A5 MUTATED     6   1   2   1
  OR2A5 WILD-TYPE 339   3  29  24
D1158V11, multiclass
    clus
vv   OR2A5 MUTATED OR2A5 WILD-TYPE
  R0             6             339
  R1             1               3
  R2             2              29
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1158V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OR2A5 MUTATED                                  0     1
  OR2A5 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  OR2A5 MUTATED                           0     6
  OR2A5 WILD-TYPE                        22   220
D1158V13, multiclass
                                  clus
vv                                 OR2A5 MUTATED OR2A5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        6             220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1159) Variable = HAUS3 MUTATION ANALYSIS
D1159V1, survival
                 sevent
clus2               0   1
  HAUS3 MUTATED     7   3
  HAUS3 WILD-TYPE 371  90
  HAUS3 MUTATED HAUS3 WILD-TYPE 
             10             461 
  HAUS3 MUTATED HAUS3 WILD-TYPE 
              3              90 
$`HAUS3 MUTATED`
TCGA-A6-5665 TCGA-AA-3510 TCGA-AA-A00N TCGA-AA-A010 TCGA-CK-5912 TCGA-D5-6932 
       22.06        63.98         4.01        34.98        49.08        11.38 
TCGA-DM-A1D0 TCGA-DM-A1HB TCGA-F4-6570 TCGA-AG-A002 
      130.65       135.65         6.18        20.98 

$`HAUS3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D4 
       12.00        10.26       119.70        24.43        38.20        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      131.51       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  HAUS3 MUTATED HAUS3 WILD-TYPE 
           4.01            0.00 
  HAUS3 MUTATED HAUS3 WILD-TYPE 
         135.65          148.01 
  HAUS3 MUTATED HAUS3 WILD-TYPE 
          28.52           20.05 
[1] "4.0 - 135.7 (28.5)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.1"
D1159V2, continuous
D1159V3, binary
                 cls
clus                0   1
  HAUS3 MUTATED     9   1
  HAUS3 WILD-TYPE 357 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HAUS3 MUTATED      9    1
  HAUS3 WILD-TYPE  357  118
        clus
vv       HAUS3 MUTATED HAUS3 WILD-TYPE
  COLON              9             357
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  HAUS3 MUTATED         2        0        1         4         2         0
  HAUS3 WILD-TYPE      89        1       31       134         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  HAUS3 MUTATED           0          0          1          0        0         0
  HAUS3 WILD-TYPE        24         11         58         42       48        18
                 vv
clus              STAGE IVB
  HAUS3 MUTATED           0
  HAUS3 WILD-TYPE         1
D1159V4, multiclass
            clus
vv           HAUS3 MUTATED HAUS3 WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              4             134
  STAGE IIB              2               8
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  HAUS3 MUTATED     0   2   6   2
  HAUS3 WILD-TYPE  17  90 323  48
D1159V5, multiclass
    clus
vv   HAUS3 MUTATED HAUS3 WILD-TYPE
  T1             0              17
  T2             2              90
  T3             6             323
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  HAUS3 MUTATED     9   1   0
  HAUS3 WILD-TYPE 278 112  87
D1159V6, multiclass
    clus
vv   HAUS3 MUTATED HAUS3 WILD-TYPE
  N0             9             278
  N1             1             112
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1159V7, binary
                 cls
clus                0   1
  HAUS3 MUTATED     9   0
  HAUS3 WILD-TYPE 366  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HAUS3 MUTATED      9    0
  HAUS3 WILD-TYPE  366   65
   clus
vv  HAUS3 MUTATED HAUS3 WILD-TYPE
  0             9             366
  1             0              65
[1] 2 2
[1] FALSE
D1159V8, binary
                 cls
clus                0   1
  HAUS3 MUTATED     4   6
  HAUS3 WILD-TYPE 221 258
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HAUS3 MUTATED      4    6
  HAUS3 WILD-TYPE  221  258
        clus
vv       HAUS3 MUTATED HAUS3 WILD-TYPE
  FEMALE             4             221
  MALE               6             258
[1] 2 2
[1] FALSE
D1159V9, binary
                 cls
clus                0   1
  HAUS3 MUTATED     7   0
  HAUS3 WILD-TYPE 343  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HAUS3 MUTATED      7    0
  HAUS3 WILD-TYPE  343   22
     clus
vv    HAUS3 MUTATED HAUS3 WILD-TYPE
  NO              7             343
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  HAUS3 MUTATED                      7                             1
  HAUS3 WILD-TYPE                  308                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  HAUS3 MUTATED                       1                              0
  HAUS3 WILD-TYPE                   105                             10
D1159V10, multiclass
                                clus
vv                               HAUS3 MUTATED HAUS3 WILD-TYPE
  COLON ADENOCARCINOMA                       7             308
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  HAUS3 MUTATED     7   0   0   1
  HAUS3 WILD-TYPE 338   4  31  24
D1159V11, multiclass
    clus
vv   HAUS3 MUTATED HAUS3 WILD-TYPE
  R0             7             338
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1159V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HAUS3 MUTATED                                  0     0
  HAUS3 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  HAUS3 MUTATED                           0     6
  HAUS3 WILD-TYPE                        22   220
D1159V13, multiclass
                                  clus
vv                                 HAUS3 MUTATED HAUS3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        6             220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1160) Variable = IFIH1 MUTATION ANALYSIS
D1160V1, survival
                 sevent
clus2               0   1
  IFIH1 MUTATED    12   4
  IFIH1 WILD-TYPE 366  89
  IFIH1 MUTATED IFIH1 WILD-TYPE 
             16             455 
  IFIH1 MUTATED IFIH1 WILD-TYPE 
              4              89 
$`IFIH1 MUTATED`
TCGA-A6-2672 TCGA-A6-6651 TCGA-A6-6654 TCGA-AA-3526 TCGA-AA-3663 TCGA-AA-A00N 
       46.65        21.76        23.87        19.07         6.97         4.01 
TCGA-AA-A010 TCGA-AZ-4315 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6601 TCGA-CA-5254 
       34.98        58.39        62.79        49.41       100.01        12.69 
TCGA-CA-5796 TCGA-CA-6717 TCGA-AH-6644 TCGA-CI-6624 
        3.25        12.76         0.72         4.73 

$`IFIH1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 
       25.18        24.16        24.69        24.39        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3529 TCGA-AA-3530 
       24.03        37.05        36.03         8.05         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       61.02        78.08         6.05        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        33.01        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 
      106.75        22.36        88.21         6.77        12.10        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5255 TCGA-CA-5797 
        5.23        11.74         3.19         1.61         3.06         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07        12.20        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
        6.05        33.17         6.97        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  IFIH1 MUTATED IFIH1 WILD-TYPE 
           0.72            0.00 
  IFIH1 MUTATED IFIH1 WILD-TYPE 
         100.01          148.01 
  IFIH1 MUTATED IFIH1 WILD-TYPE 
         20.415          20.190 
[1] "0.7 - 100.0 (20.4)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.1"
D1160V2, continuous
D1160V3, binary
                 cls
clus                0   1
  IFIH1 MUTATED    14   2
  IFIH1 WILD-TYPE 352 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IFIH1 MUTATED     14    2
  IFIH1 WILD-TYPE  352  117
        clus
vv       IFIH1 MUTATED IFIH1 WILD-TYPE
  COLON             14             352
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  IFIH1 MUTATED         2        0        4         4         2         0
  IFIH1 WILD-TYPE      89        1       28       134         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  IFIH1 MUTATED           0          0          3          0        0         0
  IFIH1 WILD-TYPE        24         11         56         42       48        18
                 vv
clus              STAGE IVB
  IFIH1 MUTATED           0
  IFIH1 WILD-TYPE         1
D1160V4, multiclass
            clus
vv           IFIH1 MUTATED IFIH1 WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               4              28
  STAGE IIA              4             134
  STAGE IIB              2               8
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             3              56
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  IFIH1 MUTATED     0   2  12   2
  IFIH1 WILD-TYPE  17  90 317  48
D1160V5, multiclass
    clus
vv   IFIH1 MUTATED IFIH1 WILD-TYPE
  T1             0              17
  T2             2              90
  T3            12             317
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  IFIH1 MUTATED    12   3   0
  IFIH1 WILD-TYPE 275 110  87
D1160V6, multiclass
    clus
vv   IFIH1 MUTATED IFIH1 WILD-TYPE
  N0            12             275
  N1             3             110
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1160V7, binary
                 cls
clus                0   1
  IFIH1 MUTATED    12   0
  IFIH1 WILD-TYPE 363  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IFIH1 MUTATED     12    0
  IFIH1 WILD-TYPE  363   65
   clus
vv  IFIH1 MUTATED IFIH1 WILD-TYPE
  0            12             363
  1             0              65
[1] 2 2
[1] FALSE
D1160V8, binary
                 cls
clus                0   1
  IFIH1 MUTATED     8   8
  IFIH1 WILD-TYPE 217 256
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IFIH1 MUTATED      8    8
  IFIH1 WILD-TYPE  217  256
        clus
vv       IFIH1 MUTATED IFIH1 WILD-TYPE
  FEMALE             8             217
  MALE               8             256
[1] 2 2
[1] FALSE
D1160V9, binary
                 cls
clus                0   1
  IFIH1 MUTATED    13   0
  IFIH1 WILD-TYPE 337  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IFIH1 MUTATED     13    0
  IFIH1 WILD-TYPE  337   22
     clus
vv    IFIH1 MUTATED IFIH1 WILD-TYPE
  NO             13             337
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  IFIH1 MUTATED                     11                             3
  IFIH1 WILD-TYPE                  304                            44
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  IFIH1 MUTATED                       2                              0
  IFIH1 WILD-TYPE                   104                             10
D1160V10, multiclass
                                clus
vv                               IFIH1 MUTATED IFIH1 WILD-TYPE
  COLON ADENOCARCINOMA                      11             304
  COLON MUCINOUS ADENOCARCINOMA              3              44
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  IFIH1 MUTATED     7   0   0   2
  IFIH1 WILD-TYPE 338   4  31  23
D1160V11, multiclass
    clus
vv   IFIH1 MUTATED IFIH1 WILD-TYPE
  R0             7             338
  R1             0               4
  R2             0              31
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1160V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  IFIH1 MUTATED                                  0     3
  IFIH1 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  IFIH1 MUTATED                           0     9
  IFIH1 WILD-TYPE                        22   217
D1160V13, multiclass
                                  clus
vv                                 IFIH1 MUTATED IFIH1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        3               8
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        9             217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1161) Variable = AKAP11 MUTATION ANALYSIS
D1161V1, survival
                  sevent
clus2                0   1
  AKAP11 MUTATED    20   4
  AKAP11 WILD-TYPE 358  89
  AKAP11 MUTATED AKAP11 WILD-TYPE 
              24              447 
  AKAP11 MUTATED AKAP11 WILD-TYPE 
               4               89 
$`AKAP11 MUTATED`
TCGA-A6-3809 TCGA-AA-3663 TCGA-AA-3861 TCGA-AA-3950 TCGA-AA-A00E TCGA-AA-A00R 
       32.75         6.97        30.05        24.00        30.02         0.99 
TCGA-AA-A010 TCGA-AD-6895 TCGA-AD-6901 TCGA-CA-5797 TCGA-CA-6717 TCGA-CA-6718 
       34.98         0.72        22.42         3.29        12.76        10.06 
TCGA-CK-4952 TCGA-CK-5916 TCGA-CM-5348 TCGA-CM-6163 TCGA-D5-5538 TCGA-D5-6929 
       15.62        21.14        22.98         2.96        12.26         4.80 
TCGA-DM-A1DA TCGA-F4-6856 TCGA-G4-6307 TCGA-AG-3902 TCGA-AG-A002 TCGA-CI-6624 
        7.50        35.31        55.04        32.02        20.98         4.73 

$`AKAP11 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
        0.99        31.07        31.07        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        33.01        26.01         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00F 
        7.96        27.02        13.94        38.04        19.00        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6964 
       15.52        56.55         0.79         5.79        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 
       12.69         3.06         3.25         0.07        12.20        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
       17.56       148.01        85.45        49.08        51.32         9.99 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5860 
       25.02        13.02        29.06        22.03        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
       12.00        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 
       14.30         9.04         9.44        11.64         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB 
       92.75        49.91        13.32        12.59       140.38        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 
       16.24        33.67        13.25         0.53        47.41       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6310 
       74.56        65.85        53.62        44.68        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3909 TCGA-AG-3999 
       35.01        14.01         1.02        48.03        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        6.97        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  AKAP11 MUTATED AKAP11 WILD-TYPE 
            0.72             0.00 
  AKAP11 MUTATED AKAP11 WILD-TYPE 
           55.04           148.01 
  AKAP11 MUTATED AKAP11 WILD-TYPE 
           18.30            20.19 
[1] "0.7 - 55.0 (18.3)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.2"
D1161V2, continuous
D1161V3, binary
                  cls
clus                 0   1
  AKAP11 MUTATED    22   3
  AKAP11 WILD-TYPE 344 116
[1] "tbl2"
                  cls
clus               [,1] [,2]
  AKAP11 MUTATED     22    3
  AKAP11 WILD-TYPE  344  116
        clus
vv       AKAP11 MUTATED AKAP11 WILD-TYPE
  COLON              22              344
  RECTUM              3              116
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  AKAP11 MUTATED         6        0        1         8         2         0
  AKAP11 WILD-TYPE      85        1       31       130         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  AKAP11 MUTATED           0          0          3          2        1
  AKAP11 WILD-TYPE        24         11         56         40       47
                  vv
clus               STAGE IVA STAGE IVB
  AKAP11 MUTATED           0         0
  AKAP11 WILD-TYPE        18         1
D1161V4, multiclass
            clus
vv           AKAP11 MUTATED AKAP11 WILD-TYPE
  STAGE I                 6               85
  STAGE IA                0                1
  STAGE II                1               31
  STAGE IIA               8              130
  STAGE IIB               2                8
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              3               56
  STAGE IIIC              2               40
  STAGE IV                1               47
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  AKAP11 MUTATED     2   4  16   3
  AKAP11 WILD-TYPE  15  88 313  47
D1161V5, multiclass
    clus
vv   AKAP11 MUTATED AKAP11 WILD-TYPE
  T1              2               15
  T2              4               88
  T3             16              313
  T4              3               47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  AKAP11 MUTATED    18   5   2
  AKAP11 WILD-TYPE 269 108  85
D1161V6, multiclass
    clus
vv   AKAP11 MUTATED AKAP11 WILD-TYPE
  N0             18              269
  N1              5              108
  N2              2               85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1161V7, binary
                  cls
clus                 0   1
  AKAP11 MUTATED    22   1
  AKAP11 WILD-TYPE 353  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  AKAP11 MUTATED     22    1
  AKAP11 WILD-TYPE  353   64
   clus
vv  AKAP11 MUTATED AKAP11 WILD-TYPE
  0             22              353
  1              1               64
[1] 2 2
[1] FALSE
D1161V8, binary
                  cls
clus                 0   1
  AKAP11 MUTATED    12  13
  AKAP11 WILD-TYPE 213 251
[1] "tbl2"
                  cls
clus               [,1] [,2]
  AKAP11 MUTATED     12   13
  AKAP11 WILD-TYPE  213  251
        clus
vv       AKAP11 MUTATED AKAP11 WILD-TYPE
  FEMALE             12              213
  MALE               13              251
[1] 2 2
[1] FALSE
D1161V9, binary
                  cls
clus                 0   1
  AKAP11 MUTATED    18   0
  AKAP11 WILD-TYPE 332  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  AKAP11 MUTATED     18    0
  AKAP11 WILD-TYPE  332   22
     clus
vv    AKAP11 MUTATED AKAP11 WILD-TYPE
  NO              18              332
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  AKAP11 MUTATED                     17                             5
  AKAP11 WILD-TYPE                  298                            42
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  AKAP11 MUTATED                       3                              0
  AKAP11 WILD-TYPE                   103                             10
D1161V10, multiclass
                                clus
vv                               AKAP11 MUTATED AKAP11 WILD-TYPE
  COLON ADENOCARCINOMA                       17              298
  COLON MUCINOUS ADENOCARCINOMA               5               42
  RECTAL ADENOCARCINOMA                       3              103
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  AKAP11 MUTATED    17   0   0   4
  AKAP11 WILD-TYPE 328   4  31  21
D1161V11, multiclass
    clus
vv   AKAP11 MUTATED AKAP11 WILD-TYPE
  R0             17              328
  R1              0                4
  R2              0               31
  RX              4               21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1161V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AKAP11 MUTATED                                  0     3
  AKAP11 WILD-TYPE                                1     8
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  AKAP11 MUTATED                           0    13
  AKAP11 WILD-TYPE                        22   213
D1161V13, multiclass
                                  clus
vv                                 AKAP11 MUTATED AKAP11 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         3                8
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                        13              213
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1162) Variable = CRTC1 MUTATION ANALYSIS
D1162V1, survival
                 sevent
clus2               0   1
  CRTC1 MUTATED    11   2
  CRTC1 WILD-TYPE 367  91
  CRTC1 MUTATED CRTC1 WILD-TYPE 
             13             458 
  CRTC1 MUTATED CRTC1 WILD-TYPE 
              2              91 
$`CRTC1 MUTATED`
TCGA-A6-5665 TCGA-A6-6653 TCGA-A6-6780 TCGA-AA-3492 TCGA-AA-3667 TCGA-AD-6964 
       22.06        24.39        20.12         3.02        14.01        10.88 
TCGA-AY-6197 TCGA-CM-6162 TCGA-D5-6930 TCGA-G4-6315 TCGA-G4-6586 TCGA-G4-6588 
       21.44        12.00         1.51        61.91        35.80        26.17 
TCGA-G4-6628 
       79.69 

$`CRTC1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6781 
       25.18        24.16        21.76        24.69        23.87        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
       20.28         7.04         1.02        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       16.31         0.95        33.01        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       17.03        15.02         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       11.64         4.80        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 
       36.00        22.09        13.78        91.79        46.75        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  CRTC1 MUTATED CRTC1 WILD-TYPE 
           1.51            0.00 
  CRTC1 MUTATED CRTC1 WILD-TYPE 
          79.69          148.01 
  CRTC1 MUTATED CRTC1 WILD-TYPE 
          21.44           20.12 
[1] "1.5 - 79.7 (21.4)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.3"
D1162V2, continuous
D1162V3, binary
                 cls
clus                0   1
  CRTC1 MUTATED    13   0
  CRTC1 WILD-TYPE 353 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CRTC1 MUTATED     13    0
  CRTC1 WILD-TYPE  353  119
        clus
vv       CRTC1 MUTATED CRTC1 WILD-TYPE
  COLON             13             353
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CRTC1 MUTATED         3        0        1         6         0         0
  CRTC1 WILD-TYPE      88        1       31       132        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CRTC1 MUTATED           0          0          1          0        1         0
  CRTC1 WILD-TYPE        24         11         58         42       47        18
                 vv
clus              STAGE IVB
  CRTC1 MUTATED           0
  CRTC1 WILD-TYPE         1
D1162V4, multiclass
            clus
vv           CRTC1 MUTATED CRTC1 WILD-TYPE
  STAGE I                3              88
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              6             132
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             0              42
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CRTC1 MUTATED     0   3   9   1
  CRTC1 WILD-TYPE  17  89 320  49
D1162V5, multiclass
    clus
vv   CRTC1 MUTATED CRTC1 WILD-TYPE
  T1             0              17
  T2             3              89
  T3             9             320
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  CRTC1 MUTATED    10   2   1
  CRTC1 WILD-TYPE 277 111  86
D1162V6, multiclass
    clus
vv   CRTC1 MUTATED CRTC1 WILD-TYPE
  N0            10             277
  N1             2             111
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1162V7, binary
                 cls
clus                0   1
  CRTC1 MUTATED     9   1
  CRTC1 WILD-TYPE 366  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CRTC1 MUTATED      9    1
  CRTC1 WILD-TYPE  366   64
   clus
vv  CRTC1 MUTATED CRTC1 WILD-TYPE
  0             9             366
  1             1              64
[1] 2 2
[1] FALSE
D1162V8, binary
                 cls
clus                0   1
  CRTC1 MUTATED     6   7
  CRTC1 WILD-TYPE 219 257
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CRTC1 MUTATED      6    7
  CRTC1 WILD-TYPE  219  257
        clus
vv       CRTC1 MUTATED CRTC1 WILD-TYPE
  FEMALE             6             219
  MALE               7             257
[1] 2 2
[1] FALSE
D1162V9, binary
                 cls
clus                0   1
  CRTC1 MUTATED    12   0
  CRTC1 WILD-TYPE 338  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CRTC1 MUTATED     12    0
  CRTC1 WILD-TYPE  338   22
     clus
vv    CRTC1 MUTATED CRTC1 WILD-TYPE
  NO             12             338
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CRTC1 MUTATED                     10                             3
  CRTC1 WILD-TYPE                  305                            44
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CRTC1 MUTATED                       0                              0
  CRTC1 WILD-TYPE                   106                             10
D1162V10, multiclass
                                clus
vv                               CRTC1 MUTATED CRTC1 WILD-TYPE
  COLON ADENOCARCINOMA                      10             305
  COLON MUCINOUS ADENOCARCINOMA              3              44
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  CRTC1 MUTATED    10   0   0   0
  CRTC1 WILD-TYPE 335   4  31  25
D1162V11, multiclass
    clus
vv   CRTC1 MUTATED CRTC1 WILD-TYPE
  R0            10             335
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1162V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CRTC1 MUTATED                                  0     0
  CRTC1 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CRTC1 MUTATED                           0    11
  CRTC1 WILD-TYPE                        22   215
D1162V13, multiclass
                                  clus
vv                                 CRTC1 MUTATED CRTC1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                       11             215
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1163) Variable = PKHD1L1 MUTATION ANALYSIS
D1163V1, survival
                   sevent
clus2                 0   1
  PKHD1L1 MUTATED    31  13
  PKHD1L1 WILD-TYPE 347  80
  PKHD1L1 MUTATED PKHD1L1 WILD-TYPE 
               44               427 
  PKHD1L1 MUTATED PKHD1L1 WILD-TYPE 
               13                80 
$`PKHD1L1 MUTATED`
TCGA-A6-3809 TCGA-A6-5665 TCGA-A6-6781 TCGA-AA-3663 TCGA-AA-3681 TCGA-AA-3710 
       32.75        22.06        19.66         6.97         5.98        26.99 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3844 TCGA-AA-3864 TCGA-AA-3877 TCGA-AA-3949 
       19.04        10.06        14.93        53.00        31.00        26.01 
TCGA-AA-3966 TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A010 TCGA-AD-6964 TCGA-AZ-4315 
        2.01        25.02         4.01        34.98        10.88        58.39 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CA-6717 TCGA-CA-6718 
       49.41         6.77       100.01         1.61        12.76        10.06 
TCGA-CA-6719 TCGA-CK-5914 TCGA-CK-5916 TCGA-CM-4746 TCGA-CM-5344 TCGA-CM-6171 
       14.30         9.99        21.14        37.02        22.03        14.04 
TCGA-D5-6535 TCGA-D5-6920 TCGA-D5-6928 TCGA-D5-6929 TCGA-DM-A28F TCGA-F4-6570 
       15.12         3.68        11.64         4.80        35.97         6.18 
TCGA-G4-6321 TCGA-G4-6588 TCGA-G4-6628 TCGA-AG-3902 TCGA-AG-A002 TCGA-CI-6620 
       22.09        26.17        79.69        32.02        20.98        33.17 
TCGA-DC-6158 TCGA-F5-6571 
       10.98        31.30 

$`PKHD1L1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02        78.08         6.05        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 
       37.05        19.00        36.00         5.03        85.05        19.04 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       15.95        38.99        37.02         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        31.07        30.05        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       29.98        18.05         2.01        12.99        24.00        33.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 
       24.00         2.01        20.98        34.03        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
        0.72         5.79        22.42        27.42         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 
       12.10        29.56         5.23        11.74         3.19        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CK-4947 
        3.06         3.25         3.29         0.07        12.20        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-6747 
      148.01        85.45        15.62        49.08        51.32        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4752 
        1.91       124.27        23.05        20.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       29.06        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       15.02        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        1.48         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
        6.12        81.37       119.93        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
        8.61        31.96        35.74        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 
       55.04        85.48        63.62        61.91        36.00        13.78 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       35.80        91.79        46.75        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3909 TCGA-AG-3999 
       35.01        14.01         1.02        48.03        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6622 
        1.45        17.49         0.69         0.72         6.05         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       27.95        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       49.51        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  PKHD1L1 MUTATED PKHD1L1 WILD-TYPE 
             1.61              0.00 
  PKHD1L1 MUTATED PKHD1L1 WILD-TYPE 
           100.01            148.01 
  PKHD1L1 MUTATED PKHD1L1 WILD-TYPE 
            20.32             20.19 
[1] "1.6 - 100.0 (20.3)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.8"
D1163V2, continuous
D1163V3, binary
                   cls
clus                  0   1
  PKHD1L1 MUTATED    41   5
  PKHD1L1 WILD-TYPE 325 114
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PKHD1L1 MUTATED     41    5
  PKHD1L1 WILD-TYPE  325  114
        clus
vv       PKHD1L1 MUTATED PKHD1L1 WILD-TYPE
  COLON               41               325
  RECTUM               5               114
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PKHD1L1 MUTATED         8        0        5        14         3         0
  PKHD1L1 WILD-TYPE      83        1       27       124         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PKHD1L1 MUTATED           4          1          5          2        1
  PKHD1L1 WILD-TYPE        20         10         54         40       47
                   vv
clus                STAGE IVA STAGE IVB
  PKHD1L1 MUTATED           1         0
  PKHD1L1 WILD-TYPE        17         1
D1163V4, multiclass
            clus
vv           PKHD1L1 MUTATED PKHD1L1 WILD-TYPE
  STAGE I                  8                83
  STAGE IA                 0                 1
  STAGE II                 5                27
  STAGE IIA               14               124
  STAGE IIB                3                 7
  STAGE IIC                0                 1
  STAGE III                4                20
  STAGE IIIA               1                10
  STAGE IIIB               5                54
  STAGE IIIC               2                40
  STAGE IV                 1                47
  STAGE IVA                1                17
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  PKHD1L1 MUTATED     2   9  30   5
  PKHD1L1 WILD-TYPE  15  83 299  45
D1163V5, multiclass
    clus
vv   PKHD1L1 MUTATED PKHD1L1 WILD-TYPE
  T1               2                15
  T2               9                83
  T3              30               299
  T4               5                45
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  PKHD1L1 MUTATED    31  11   4
  PKHD1L1 WILD-TYPE 256 102  83
D1163V6, multiclass
    clus
vv   PKHD1L1 MUTATED PKHD1L1 WILD-TYPE
  N0              31               256
  N1              11               102
  N2               4                83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1163V7, binary
                   cls
clus                  0   1
  PKHD1L1 MUTATED    36   2
  PKHD1L1 WILD-TYPE 339  63
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PKHD1L1 MUTATED     36    2
  PKHD1L1 WILD-TYPE  339   63
   clus
vv  PKHD1L1 MUTATED PKHD1L1 WILD-TYPE
  0              36               339
  1               2                63
[1] 2 2
[1] FALSE
D1163V8, binary
                   cls
clus                  0   1
  PKHD1L1 MUTATED    24  22
  PKHD1L1 WILD-TYPE 201 242
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PKHD1L1 MUTATED     24   22
  PKHD1L1 WILD-TYPE  201  242
        clus
vv       PKHD1L1 MUTATED PKHD1L1 WILD-TYPE
  FEMALE              24               201
  MALE                22               242
[1] 2 2
[1] FALSE
D1163V9, binary
                   cls
clus                  0   1
  PKHD1L1 MUTATED    37   1
  PKHD1L1 WILD-TYPE 313  21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PKHD1L1 MUTATED     37    1
  PKHD1L1 WILD-TYPE  313   21
     clus
vv    PKHD1L1 MUTATED PKHD1L1 WILD-TYPE
  NO               37               313
  YES               1                21
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PKHD1L1 MUTATED                     33                             8
  PKHD1L1 WILD-TYPE                  282                            39
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PKHD1L1 MUTATED                       5                              0
  PKHD1L1 WILD-TYPE                   101                             10
D1163V10, multiclass
                                clus
vv                               PKHD1L1 MUTATED PKHD1L1 WILD-TYPE
  COLON ADENOCARCINOMA                        33               282
  COLON MUCINOUS ADENOCARCINOMA                8                39
  RECTAL ADENOCARCINOMA                        5               101
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  PKHD1L1 MUTATED    31   0   0   6
  PKHD1L1 WILD-TYPE 314   4  31  19
D1163V11, multiclass
    clus
vv   PKHD1L1 MUTATED PKHD1L1 WILD-TYPE
  R0              31               314
  R1               0                 4
  R2               0                31
  RX               6                19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1163V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PKHD1L1 MUTATED                                  0     3
  PKHD1L1 WILD-TYPE                                1     8
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  PKHD1L1 MUTATED                           1    25
  PKHD1L1 WILD-TYPE                        21   201
D1163V13, multiclass
                                  clus
vv                                 PKHD1L1 MUTATED PKHD1L1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          3                 8
  BLACK OR AFRICAN AMERICAN                      1                21
  WHITE                                         25               201
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1164) Variable = UFSP2 MUTATION ANALYSIS
D1164V1, survival
                 sevent
clus2               0   1
  UFSP2 MUTATED     4   1
  UFSP2 WILD-TYPE 374  92
  UFSP2 MUTATED UFSP2 WILD-TYPE 
              5             466 
  UFSP2 MUTATED UFSP2 WILD-TYPE 
              1              92 
$`UFSP2 MUTATED`
TCGA-AA-3510 TCGA-AA-3663 TCGA-AA-A00N TCGA-AD-6889 TCGA-AG-A002 
       63.98         6.97         4.01        56.55        20.98 

$`UFSP2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 
       18.05        40.96         0.07        21.37        15.52         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  UFSP2 MUTATED UFSP2 WILD-TYPE 
           4.01            0.00 
  UFSP2 MUTATED UFSP2 WILD-TYPE 
          63.98          148.01 
  UFSP2 MUTATED UFSP2 WILD-TYPE 
         20.980          20.155 
[1] "4.0 - 64.0 (21.0)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.3"
D1164V2, continuous
D1164V3, binary
                 cls
clus                0   1
  UFSP2 MUTATED     4   1
  UFSP2 WILD-TYPE 362 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UFSP2 MUTATED      4    1
  UFSP2 WILD-TYPE  362  118
        clus
vv       UFSP2 MUTATED UFSP2 WILD-TYPE
  COLON              4             362
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  UFSP2 MUTATED         1        0        2         1         1         0
  UFSP2 WILD-TYPE      90        1       30       137         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  UFSP2 MUTATED           0          0          0          0        0         0
  UFSP2 WILD-TYPE        24         11         59         42       48        18
                 vv
clus              STAGE IVB
  UFSP2 MUTATED           0
  UFSP2 WILD-TYPE         1
D1164V4, multiclass
            clus
vv           UFSP2 MUTATED UFSP2 WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA              1             137
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  UFSP2 MUTATED     0   1   3   1
  UFSP2 WILD-TYPE  17  91 326  49
D1164V5, multiclass
    clus
vv   UFSP2 MUTATED UFSP2 WILD-TYPE
  T1             0              17
  T2             1              91
  T3             3             326
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  UFSP2 MUTATED     5   0   0
  UFSP2 WILD-TYPE 282 113  87
D1164V6, multiclass
    clus
vv   UFSP2 MUTATED UFSP2 WILD-TYPE
  N0             5             282
  N1             0             113
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1164V7, binary
                 cls
clus                0   1
  UFSP2 MUTATED     5   0
  UFSP2 WILD-TYPE 370  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UFSP2 MUTATED      5    0
  UFSP2 WILD-TYPE  370   65
   clus
vv  UFSP2 MUTATED UFSP2 WILD-TYPE
  0             5             370
  1             0              65
[1] 2 2
[1] FALSE
D1164V8, binary
                 cls
clus                0   1
  UFSP2 MUTATED     0   5
  UFSP2 WILD-TYPE 225 259
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UFSP2 MUTATED      0    5
  UFSP2 WILD-TYPE  225  259
        clus
vv       UFSP2 MUTATED UFSP2 WILD-TYPE
  FEMALE             0             225
  MALE               5             259
[1] 2 2
[1] FALSE
D1164V9, binary
                 cls
clus                0   1
  UFSP2 MUTATED     3   0
  UFSP2 WILD-TYPE 347  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UFSP2 MUTATED      3    0
  UFSP2 WILD-TYPE  347   22
     clus
vv    UFSP2 MUTATED UFSP2 WILD-TYPE
  NO              3             347
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  UFSP2 MUTATED                      3                             1
  UFSP2 WILD-TYPE                  312                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  UFSP2 MUTATED                       1                              0
  UFSP2 WILD-TYPE                   105                             10
D1164V10, multiclass
                                clus
vv                               UFSP2 MUTATED UFSP2 WILD-TYPE
  COLON ADENOCARCINOMA                       3             312
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  UFSP2 MUTATED     4   0   0   0
  UFSP2 WILD-TYPE 341   4  31  25
D1164V11, multiclass
    clus
vv   UFSP2 MUTATED UFSP2 WILD-TYPE
  R0             4             341
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1164V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  UFSP2 MUTATED                                  0     1
  UFSP2 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  UFSP2 MUTATED                           0     0
  UFSP2 WILD-TYPE                        22   226
D1164V13, multiclass
[1] "Remove cluster labels:" "UFSP2 MUTATED"         
clus
  UFSP2 MUTATED UFSP2 WILD-TYPE 
              1             259 
     TCGA-A6-2671      TCGA-A6-2672      TCGA-A6-2674      TCGA-A6-2676 
"UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" 
     TCGA-A6-2677      TCGA-A6-2678      TCGA-A6-2683      TCGA-A6-3807 
"UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" 
     TCGA-A6-3808      TCGA-A6-3809      TCGA-A6-3810      TCGA-A6-4105 
"UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" 
     TCGA-A6-5656      TCGA-A6-5657      TCGA-A6-5659      TCGA-A6-5660 
"UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" 
     TCGA-A6-5661      TCGA-A6-5662      TCGA-A6-5664      TCGA-A6-5665 
"UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" 
     TCGA-A6-5666      TCGA-A6-6137      TCGA-A6-6138      TCGA-A6-6141 
"UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" 
     TCGA-A6-6142      TCGA-A6-6648      TCGA-A6-6649      TCGA-A6-6651 
"UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" 
     TCGA-A6-6652      TCGA-A6-6653      TCGA-A6-6654      TCGA-A6-6780 
"UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" 
     TCGA-A6-6781      TCGA-A6-6782      TCGA-AD-5900      TCGA-AD-6548 
"UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" 
     TCGA-AD-6888      TCGA-AD-6890      TCGA-AD-6895      TCGA-AD-6899 
"UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" 
     TCGA-AD-6901      TCGA-AD-6963      TCGA-AD-6964      TCGA-AD-6965 
"UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" 
     TCGA-AU-3779      TCGA-AU-6004      TCGA-AY-4070      TCGA-AY-4071 
"UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" 
     TCGA-AY-5543      TCGA-AY-6196      TCGA-AY-6197      TCGA-AY-6386 
"UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" 
     TCGA-AZ-4315      TCGA-AZ-4323      TCGA-AZ-4616      TCGA-AZ-4681 
"UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" 
     TCGA-AZ-4682      TCGA-AZ-5403      TCGA-AZ-5407      TCGA-AZ-6598 
"UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" 
     TCGA-AZ-6599      TCGA-AZ-6600      TCGA-AZ-6601      TCGA-AZ-6603 
"UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" 
     TCGA-AZ-6605      TCGA-AZ-6606      TCGA-AZ-6607      TCGA-AZ-6608 
"UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" 
     TCGA-CA-5254      TCGA-CA-5255      TCGA-CA-5796      TCGA-CA-5797 
"UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" 
     TCGA-CA-6715      TCGA-CA-6716      TCGA-CA-6717      TCGA-CA-6718 
"UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" 
     TCGA-CA-6719      TCGA-CK-4947      TCGA-CK-4948      TCGA-CK-4950 
"UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" 
     TCGA-CK-4952      TCGA-CK-5912      TCGA-CK-5913      TCGA-CK-5914 
"UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" 
     TCGA-CK-5915      TCGA-CK-5916      TCGA-CK-6746      TCGA-CK-6747 
"UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" 
     TCGA-CK-6748      TCGA-CK-6751      TCGA-CM-4743      TCGA-CM-4744 
"UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" 
     TCGA-CM-4746      TCGA-CM-4747      TCGA-CM-4752      TCGA-CM-5341 
"UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" 
     TCGA-CM-5344      TCGA-CM-5348      TCGA-CM-5349      TCGA-CM-5860 
"UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" 
     TCGA-CM-5861      TCGA-CM-5862      TCGA-CM-5863      TCGA-CM-5864 
"UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" 
     TCGA-CM-5868      TCGA-CM-6161      TCGA-CM-6162      TCGA-CM-6163 
"UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" 
     TCGA-CM-6164      TCGA-CM-6165      TCGA-CM-6166      TCGA-CM-6167 
"UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" 
     TCGA-CM-6168      TCGA-CM-6169      TCGA-CM-6170      TCGA-CM-6171 
"UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" 
     TCGA-CM-6172      TCGA-CM-6674      TCGA-CM-6675      TCGA-CM-6676 
"UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" 
     TCGA-CM-6677      TCGA-CM-6678      TCGA-CM-6679      TCGA-CM-6680 
"UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" 
     TCGA-D5-5537      TCGA-D5-5538      TCGA-D5-5539      TCGA-D5-5540 
"UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" 
     TCGA-D5-5541      TCGA-D5-6529      TCGA-D5-6532      TCGA-D5-6533 
"UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" 
     TCGA-D5-6534      TCGA-D5-6535      TCGA-D5-6536      TCGA-D5-6537 
"UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" 
     TCGA-D5-6538      TCGA-D5-6539      TCGA-D5-6540      TCGA-D5-6541 
"UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" 
     TCGA-D5-6898      TCGA-D5-6920      TCGA-D5-6922      TCGA-D5-6923 
"UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" 
     TCGA-D5-6924      TCGA-D5-6926      TCGA-D5-6927      TCGA-D5-6928 
"UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" 
     TCGA-D5-6929      TCGA-D5-6930      TCGA-D5-6931      TCGA-D5-6932 
"UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" 
     TCGA-D5-7000      TCGA-DM-A0X9      TCGA-DM-A0XD      TCGA-DM-A0XF 
"UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" 
     TCGA-DM-A1D0      TCGA-DM-A1D4      TCGA-DM-A1D6      TCGA-DM-A1D7 
"UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" 
     TCGA-DM-A1D8      TCGA-DM-A1D9      TCGA-DM-A1DA      TCGA-DM-A1DB 
"UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" 
     TCGA-DM-A1HA      TCGA-DM-A1HB      TCGA-DM-A282      TCGA-DM-A285 
"UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" 
     TCGA-DM-A28C      TCGA-DM-A28E      TCGA-DM-A28F      TCGA-DM-A28G 
"UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" 
     TCGA-DM-A28H      TCGA-DM-A28K      TCGA-F4-6459      TCGA-F4-6460 
"UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" 
     TCGA-F4-6569      TCGA-F4-6570      TCGA-F4-6703      TCGA-F4-6704 
"UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" 
     TCGA-F4-6805      TCGA-F4-6806      TCGA-F4-6807      TCGA-F4-6808 
"UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" 
     TCGA-F4-6809      TCGA-F4-6854      TCGA-F4-6855      TCGA-F4-6856 
"UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" 
     TCGA-G4-6293      TCGA-G4-6299      TCGA-G4-6303      TCGA-G4-6304 
"UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" 
     TCGA-G4-6306      TCGA-G4-6307      TCGA-G4-6309      TCGA-G4-6310 
"UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" 
     TCGA-G4-6315      TCGA-G4-6317      TCGA-G4-6321      TCGA-G4-6323 
"UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" 
     TCGA-G4-6586      TCGA-G4-6588      TCGA-G4-6625      TCGA-G4-6626 
"UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" 
     TCGA-G4-6628      TCGA-AF-2687      TCGA-AF-2689      TCGA-AF-2691 
"UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" 
     TCGA-AF-2692      TCGA-AF-2693      TCGA-AF-3400      TCGA-AF-3913 
"UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" 
     TCGA-AF-4110      TCGA-AF-5654      TCGA-AF-6136      TCGA-AF-6655 
"UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" 
     TCGA-AF-6672      TCGA-AH-6544      TCGA-AH-6547      TCGA-AH-6549 
"UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" 
     TCGA-AH-6643      TCGA-AH-6644      TCGA-CI-6619      TCGA-CI-6620 
"UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" 
     TCGA-CI-6621      TCGA-CI-6622      TCGA-CI-6624      TCGA-CL-5917 
"UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" 
     TCGA-CL-5918      TCGA-DC-5337      TCGA-DC-5869      TCGA-DC-6155 
"UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" 
     TCGA-DC-6157      TCGA-DC-6158      TCGA-DC-6160      TCGA-DC-6681 
"UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" 
     TCGA-DC-6682      TCGA-DC-6683      TCGA-DT-5265      TCGA-DY-A0XA 
"UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" 
     TCGA-DY-A1DC      TCGA-DY-A1DD      TCGA-DY-A1DF      TCGA-DY-A1DG 
"UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" 
     TCGA-DY-A1H8      TCGA-EF-5830      TCGA-EI-6506      TCGA-EI-6507 
"UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" 
     TCGA-EI-6508      TCGA-EI-6510      TCGA-F5-6464      TCGA-F5-6465 
"UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" 
     TCGA-F5-6571      TCGA-F5-6702      TCGA-F5-6811      TCGA-F5-6812 
"UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" 
     TCGA-F5-6813      TCGA-G5-6235      TCGA-G5-6641 
"UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" "UFSP2 WILD-TYPE" 

Clustering(1165) Variable = MUC7 MUTATION ANALYSIS
D1165V1, survival
                sevent
clus2              0   1
  MUC7 MUTATED     7   3
  MUC7 WILD-TYPE 371  90
  MUC7 MUTATED MUC7 WILD-TYPE 
            10            461 
  MUC7 MUTATED MUC7 WILD-TYPE 
             3             90 
$`MUC7 MUTATED`
TCGA-A6-6141 TCGA-AA-3715 TCGA-AZ-4315 TCGA-AZ-5407 TCGA-AZ-6603 TCGA-D5-6536 
        8.38        19.04        58.39        88.21        29.56        17.85 
TCGA-DM-A1DA TCGA-G4-6309 TCGA-AG-3600 TCGA-EI-6510 
        7.50        85.48         6.05        18.28 

$`MUC7 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 
       22.09        22.06        32.71        27.09        22.52        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 
       36.00         5.03        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       33.01        21.44        17.82         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        49.41         6.77        12.10       100.01 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       43.27        15.12         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB 
       92.75        49.91        13.32        12.59       140.38        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       19.96        20.91         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  MUC7 MUTATED MUC7 WILD-TYPE 
          6.05           0.00 
  MUC7 MUTATED MUC7 WILD-TYPE 
         88.21         148.01 
  MUC7 MUTATED MUC7 WILD-TYPE 
         18.66          20.28 
[1] "6.0 - 88.2 (18.7)"  "0.0 - 148.0 (20.3)"
[1] "hr=" "1.2"
D1165V2, continuous
D1165V3, binary
                cls
clus               0   1
  MUC7 MUTATED     9   2
  MUC7 WILD-TYPE 357 117
[1] "tbl2"
                cls
clus             [,1] [,2]
  MUC7 MUTATED      9    2
  MUC7 WILD-TYPE  357  117
        clus
vv       MUC7 MUTATED MUC7 WILD-TYPE
  COLON             9            357
  RECTUM            2            117
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MUC7 MUTATED         1        0        1         3         0         0
  MUC7 WILD-TYPE      90        1       31       135        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MUC7 MUTATED           0          0          1          3        0         1
  MUC7 WILD-TYPE        24         11         58         39       48        17
                vv
clus             STAGE IVB
  MUC7 MUTATED           0
  MUC7 WILD-TYPE         1
D1165V4, multiclass
            clus
vv           MUC7 MUTATED MUC7 WILD-TYPE
  STAGE I               1             90
  STAGE IA              0              1
  STAGE II              1             31
  STAGE IIA             3            135
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            1             58
  STAGE IIIC            3             39
  STAGE IV              0             48
  STAGE IVA             1             17
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  MUC7 MUTATED     1   2   8   0
  MUC7 WILD-TYPE  16  90 321  50
D1165V5, multiclass
    clus
vv   MUC7 MUTATED MUC7 WILD-TYPE
  T1            1             16
  T2            2             90
  T3            8            321
  T4            0             50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  MUC7 MUTATED     6   2   3
  MUC7 WILD-TYPE 281 111  84
D1165V6, multiclass
    clus
vv   MUC7 MUTATED MUC7 WILD-TYPE
  N0            6            281
  N1            2            111
  N2            3             84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1165V7, binary
                cls
clus               0   1
  MUC7 MUTATED     8   0
  MUC7 WILD-TYPE 367  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  MUC7 MUTATED      8    0
  MUC7 WILD-TYPE  367   65
   clus
vv  MUC7 MUTATED MUC7 WILD-TYPE
  0            8            367
  1            0             65
[1] 2 2
[1] FALSE
D1165V8, binary
                cls
clus               0   1
  MUC7 MUTATED     5   6
  MUC7 WILD-TYPE 220 258
[1] "tbl2"
                cls
clus             [,1] [,2]
  MUC7 MUTATED      5    6
  MUC7 WILD-TYPE  220  258
        clus
vv       MUC7 MUTATED MUC7 WILD-TYPE
  FEMALE            5            220
  MALE              6            258
[1] 2 2
[1] FALSE
D1165V9, binary
                cls
clus               0   1
  MUC7 MUTATED     8   1
  MUC7 WILD-TYPE 342  21
[1] "tbl2"
                cls
clus             [,1] [,2]
  MUC7 MUTATED      8    1
  MUC7 WILD-TYPE  342   21
     clus
vv    MUC7 MUTATED MUC7 WILD-TYPE
  NO             8            342
  YES            1             21
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MUC7 MUTATED                      8                             1
  MUC7 WILD-TYPE                  307                            46
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MUC7 MUTATED                       2                              0
  MUC7 WILD-TYPE                   104                             10
D1165V10, multiclass
                                clus
vv                               MUC7 MUTATED MUC7 WILD-TYPE
  COLON ADENOCARCINOMA                      8            307
  COLON MUCINOUS ADENOCARCINOMA             1             46
  RECTAL ADENOCARCINOMA                     2            104
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  MUC7 MUTATED     7   0   0   0
  MUC7 WILD-TYPE 338   4  31  25
D1165V11, multiclass
    clus
vv   MUC7 MUTATED MUC7 WILD-TYPE
  R0            7            338
  R1            0              4
  R2            0             31
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1165V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MUC7 MUTATED                                  0     0
  MUC7 WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  MUC7 MUTATED                           2     7
  MUC7 WILD-TYPE                        20   219
D1165V13, multiclass
                                  clus
vv                                 MUC7 MUTATED MUC7 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   2             20
  WHITE                                       7            219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1166) Variable = RIMBP3 MUTATION ANALYSIS
D1166V1, survival
                  sevent
clus2                0   1
  RIMBP3 MUTATED     6   0
  RIMBP3 WILD-TYPE 372  93
  RIMBP3 MUTATED RIMBP3 WILD-TYPE 
               6              465 
  RIMBP3 MUTATED RIMBP3 WILD-TYPE 
               0               93 
$`RIMBP3 MUTATED`
TCGA-AA-A010 TCGA-AD-5900 TCGA-AU-3779 TCGA-D5-6928 TCGA-G4-6293 TCGA-G4-6310 
       34.98         0.07        14.50        11.64       133.18        63.62 

$`RIMBP3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 
       41.00        39.98        18.05        40.96        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       10.88         0.20        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 
        4.41        12.43        14.30         9.04         9.44         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
        0.53        47.41        35.31        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       44.68        55.04        85.48        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  RIMBP3 MUTATED RIMBP3 WILD-TYPE 
            0.07             0.00 
  RIMBP3 MUTATED RIMBP3 WILD-TYPE 
          133.18           148.01 
  RIMBP3 MUTATED RIMBP3 WILD-TYPE 
           24.74            20.19 
[1] "0.1 - 133.2 (24.7)" "0.0 - 148.0 (20.2)"
[1] "hr="     "9300000"
D1166V2, continuous
D1166V3, binary
                  cls
clus                 0   1
  RIMBP3 MUTATED     6   0
  RIMBP3 WILD-TYPE 360 119
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RIMBP3 MUTATED      6    0
  RIMBP3 WILD-TYPE  360  119
        clus
vv       RIMBP3 MUTATED RIMBP3 WILD-TYPE
  COLON               6              360
  RECTUM              0              119
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RIMBP3 MUTATED         1        0        0         2         1         0
  RIMBP3 WILD-TYPE      90        1       32       136         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RIMBP3 MUTATED           1          0          1          0        0
  RIMBP3 WILD-TYPE        23         11         58         42       48
                  vv
clus               STAGE IVA STAGE IVB
  RIMBP3 MUTATED           0         0
  RIMBP3 WILD-TYPE        18         1
D1166V4, multiclass
            clus
vv           RIMBP3 MUTATED RIMBP3 WILD-TYPE
  STAGE I                 1               90
  STAGE IA                0                1
  STAGE II                0               32
  STAGE IIA               2              136
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               1               23
  STAGE IIIA              0               11
  STAGE IIIB              1               58
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  RIMBP3 MUTATED     0   1   4   1
  RIMBP3 WILD-TYPE  17  91 325  49
D1166V5, multiclass
    clus
vv   RIMBP3 MUTATED RIMBP3 WILD-TYPE
  T1              0               17
  T2              1               91
  T3              4              325
  T4              1               49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  RIMBP3 MUTATED     4   2   0
  RIMBP3 WILD-TYPE 283 111  87
D1166V6, multiclass
    clus
vv   RIMBP3 MUTATED RIMBP3 WILD-TYPE
  N0              4              283
  N1              2              111
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1166V7, binary
                  cls
clus                 0   1
  RIMBP3 MUTATED     5   0
  RIMBP3 WILD-TYPE 370  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RIMBP3 MUTATED      5    0
  RIMBP3 WILD-TYPE  370   65
   clus
vv  RIMBP3 MUTATED RIMBP3 WILD-TYPE
  0              5              370
  1              0               65
[1] 2 2
[1] FALSE
D1166V8, binary
                  cls
clus                 0   1
  RIMBP3 MUTATED     3   3
  RIMBP3 WILD-TYPE 222 261
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RIMBP3 MUTATED      3    3
  RIMBP3 WILD-TYPE  222  261
        clus
vv       RIMBP3 MUTATED RIMBP3 WILD-TYPE
  FEMALE              3              222
  MALE                3              261
[1] 2 2
[1] FALSE
D1166V9, binary
                  cls
clus                 0   1
  RIMBP3 MUTATED     4   1
  RIMBP3 WILD-TYPE 346  21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RIMBP3 MUTATED      4    1
  RIMBP3 WILD-TYPE  346   21
     clus
vv    RIMBP3 MUTATED RIMBP3 WILD-TYPE
  NO               4              346
  YES              1               21
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  RIMBP3 MUTATED                      4                             2
  RIMBP3 WILD-TYPE                  311                            45
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  RIMBP3 MUTATED                       0                              0
  RIMBP3 WILD-TYPE                   106                             10
D1166V10, multiclass
                                clus
vv                               RIMBP3 MUTATED RIMBP3 WILD-TYPE
  COLON ADENOCARCINOMA                        4              311
  COLON MUCINOUS ADENOCARCINOMA               2               45
  RECTAL ADENOCARCINOMA                       0              106
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  RIMBP3 MUTATED     6   0   0   0
  RIMBP3 WILD-TYPE 339   4  31  25
D1166V11, multiclass
    clus
vv   RIMBP3 MUTATED RIMBP3 WILD-TYPE
  R0              6              339
  R1              0                4
  R2              0               31
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1166V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RIMBP3 MUTATED                                  0     0
  RIMBP3 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  RIMBP3 MUTATED                           0     5
  RIMBP3 WILD-TYPE                        22   221
D1166V13, multiclass
                                  clus
vv                                 RIMBP3 MUTATED RIMBP3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         5              221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1167) Variable = S100A2 MUTATION ANALYSIS
D1167V1, survival
                  sevent
clus2                0   1
  S100A2 MUTATED     5   2
  S100A2 WILD-TYPE 373  91
  S100A2 MUTATED S100A2 WILD-TYPE 
               7              464 
  S100A2 MUTATED S100A2 WILD-TYPE 
               2               91 
$`S100A2 MUTATED`
TCGA-A6-5657 TCGA-AA-3966 TCGA-AA-A010 TCGA-CA-6719 TCGA-DM-A1D4 TCGA-DM-A28K 
       31.63         2.01        34.98        14.30        92.75        98.24 
TCGA-DY-A1DG 
       51.48 

$`S100A2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
        2.01        20.98        34.03        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       12.76        10.06        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
       38.20       130.65        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-F4-6459 
       81.37       119.93        35.97        60.79       117.07         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1H8 
        5.29       126.44        41.36        57.24        24.13        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  S100A2 MUTATED S100A2 WILD-TYPE 
            2.01             0.00 
  S100A2 MUTATED S100A2 WILD-TYPE 
           98.24           148.01 
  S100A2 MUTATED S100A2 WILD-TYPE 
          34.980           20.085 
[1] "2.0 - 98.2 (35.0)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.2"
D1167V2, continuous
D1167V3, binary
                  cls
clus                 0   1
  S100A2 MUTATED     7   1
  S100A2 WILD-TYPE 359 118
[1] "tbl2"
                  cls
clus               [,1] [,2]
  S100A2 MUTATED      7    1
  S100A2 WILD-TYPE  359  118
        clus
vv       S100A2 MUTATED S100A2 WILD-TYPE
  COLON               7              359
  RECTUM              1              118
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  S100A2 MUTATED         1        0        0         4         1         0
  S100A2 WILD-TYPE      90        1       32       134         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  S100A2 MUTATED           0          0          1          0        0
  S100A2 WILD-TYPE        24         11         58         42       48
                  vv
clus               STAGE IVA STAGE IVB
  S100A2 MUTATED           1         0
  S100A2 WILD-TYPE        17         1
D1167V4, multiclass
            clus
vv           S100A2 MUTATED S100A2 WILD-TYPE
  STAGE I                 1               90
  STAGE IA                0                1
  STAGE II                0               32
  STAGE IIA               4              134
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              1               58
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               1               17
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  S100A2 MUTATED     0   1   6   1
  S100A2 WILD-TYPE  17  91 323  49
D1167V5, multiclass
    clus
vv   S100A2 MUTATED S100A2 WILD-TYPE
  T1              0               17
  T2              1               91
  T3              6              323
  T4              1               49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  S100A2 MUTATED     6   2   0
  S100A2 WILD-TYPE 281 111  87
D1167V6, multiclass
    clus
vv   S100A2 MUTATED S100A2 WILD-TYPE
  N0              6              281
  N1              2              111
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1167V7, binary
                  cls
clus                 0   1
  S100A2 MUTATED     6   1
  S100A2 WILD-TYPE 369  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  S100A2 MUTATED      6    1
  S100A2 WILD-TYPE  369   64
   clus
vv  S100A2 MUTATED S100A2 WILD-TYPE
  0              6              369
  1              1               64
[1] 2 2
[1] FALSE
D1167V8, binary
                  cls
clus                 0   1
  S100A2 MUTATED     2   6
  S100A2 WILD-TYPE 223 258
[1] "tbl2"
                  cls
clus               [,1] [,2]
  S100A2 MUTATED      2    6
  S100A2 WILD-TYPE  223  258
        clus
vv       S100A2 MUTATED S100A2 WILD-TYPE
  FEMALE              2              223
  MALE                6              258
[1] 2 2
[1] FALSE
D1167V9, binary
                  cls
clus                 0   1
  S100A2 MUTATED     3   0
  S100A2 WILD-TYPE 347  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  S100A2 MUTATED      3    0
  S100A2 WILD-TYPE  347   22
     clus
vv    S100A2 MUTATED S100A2 WILD-TYPE
  NO               3              347
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  S100A2 MUTATED                      5                             2
  S100A2 WILD-TYPE                  310                            45
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  S100A2 MUTATED                       1                              0
  S100A2 WILD-TYPE                   105                             10
D1167V10, multiclass
                                clus
vv                               S100A2 MUTATED S100A2 WILD-TYPE
  COLON ADENOCARCINOMA                        5              310
  COLON MUCINOUS ADENOCARCINOMA               2               45
  RECTAL ADENOCARCINOMA                       1              105
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  S100A2 MUTATED     2   0   0   2
  S100A2 WILD-TYPE 343   4  31  23
D1167V11, multiclass
    clus
vv   S100A2 MUTATED S100A2 WILD-TYPE
  R0              2              343
  R1              0                4
  R2              0               31
  RX              2               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1167V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  S100A2 MUTATED                                  0     1
  S100A2 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  S100A2 MUTATED                           1     4
  S100A2 WILD-TYPE                        21   222
D1167V13, multiclass
                                  clus
vv                                 S100A2 MUTATED S100A2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                         4              222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1168) Variable = PCSK1 MUTATION ANALYSIS
D1168V1, survival
                 sevent
clus2               0   1
  PCSK1 MUTATED    15   4
  PCSK1 WILD-TYPE 363  89
  PCSK1 MUTATED PCSK1 WILD-TYPE 
             19             452 
  PCSK1 MUTATED PCSK1 WILD-TYPE 
              4              89 
$`PCSK1 MUTATED`
TCGA-AA-3555 TCGA-AA-3663 TCGA-AA-3966 TCGA-AA-A010 TCGA-AD-6899 TCGA-AD-6963 
       29.95         6.97         2.01        34.98         5.79        27.42 
TCGA-AD-6964 TCGA-AZ-4315 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-CA-5254 TCGA-CA-6717 
       10.88        58.39        62.79        49.41        12.69        12.76 
TCGA-CK-4950 TCGA-CM-4746 TCGA-D5-6536 TCGA-G4-6628 TCGA-AG-3885 TCGA-AG-A002 
       85.45        37.02        17.85        79.69        17.95        20.98 
TCGA-DC-6682 
        4.01 

$`PCSK1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 
       21.01        13.02        24.00        17.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       20.98        34.03        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6901 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
        0.72        22.42         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        33.01        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
      106.75        22.36        88.21         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5255 
       29.56         5.23        11.74         3.19         1.61         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07        12.20        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
       17.56       148.01        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 
       20.19        18.25         1.32        43.27        15.12         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       91.79        46.75        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
        1.02        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 
       27.95        10.98        19.99         5.95         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  PCSK1 MUTATED PCSK1 WILD-TYPE 
           2.01            0.00 
  PCSK1 MUTATED PCSK1 WILD-TYPE 
          85.45          148.01 
  PCSK1 MUTATED PCSK1 WILD-TYPE 
         20.980          20.155 
[1] "2.0 - 85.5 (21.0)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.1"
D1168V2, continuous
D1168V3, binary
                 cls
clus                0   1
  PCSK1 MUTATED    16   3
  PCSK1 WILD-TYPE 350 116
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PCSK1 MUTATED     16    3
  PCSK1 WILD-TYPE  350  116
        clus
vv       PCSK1 MUTATED PCSK1 WILD-TYPE
  COLON             16             350
  RECTUM             3             116
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PCSK1 MUTATED         3        0        3         7         1         0
  PCSK1 WILD-TYPE      88        1       29       131         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PCSK1 MUTATED           0          0          2          1        0         0
  PCSK1 WILD-TYPE        24         11         57         41       48        18
                 vv
clus              STAGE IVB
  PCSK1 MUTATED           0
  PCSK1 WILD-TYPE         1
D1168V4, multiclass
            clus
vv           PCSK1 MUTATED PCSK1 WILD-TYPE
  STAGE I                3              88
  STAGE IA               0               1
  STAGE II               3              29
  STAGE IIA              7             131
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             2              57
  STAGE IIIC             1              41
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PCSK1 MUTATED     0   3  13   3
  PCSK1 WILD-TYPE  17  89 316  47
D1168V5, multiclass
    clus
vv   PCSK1 MUTATED PCSK1 WILD-TYPE
  T1             0              17
  T2             3              89
  T3            13             316
  T4             3              47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  PCSK1 MUTATED    15   2   2
  PCSK1 WILD-TYPE 272 111  85
D1168V6, multiclass
    clus
vv   PCSK1 MUTATED PCSK1 WILD-TYPE
  N0            15             272
  N1             2             111
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1168V7, binary
                 cls
clus                0   1
  PCSK1 MUTATED    14   0
  PCSK1 WILD-TYPE 361  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PCSK1 MUTATED     14    0
  PCSK1 WILD-TYPE  361   65
   clus
vv  PCSK1 MUTATED PCSK1 WILD-TYPE
  0            14             361
  1             0              65
[1] 2 2
[1] FALSE
D1168V8, binary
                 cls
clus                0   1
  PCSK1 MUTATED     7  12
  PCSK1 WILD-TYPE 218 252
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PCSK1 MUTATED      7   12
  PCSK1 WILD-TYPE  218  252
        clus
vv       PCSK1 MUTATED PCSK1 WILD-TYPE
  FEMALE             7             218
  MALE              12             252
[1] 2 2
[1] FALSE
D1168V9, binary
                 cls
clus                0   1
  PCSK1 MUTATED    16   1
  PCSK1 WILD-TYPE 334  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PCSK1 MUTATED     16    1
  PCSK1 WILD-TYPE  334   21
     clus
vv    PCSK1 MUTATED PCSK1 WILD-TYPE
  NO             16             334
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PCSK1 MUTATED                     12                             4
  PCSK1 WILD-TYPE                  303                            43
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PCSK1 MUTATED                       3                              0
  PCSK1 WILD-TYPE                   103                             10
D1168V10, multiclass
                                clus
vv                               PCSK1 MUTATED PCSK1 WILD-TYPE
  COLON ADENOCARCINOMA                      12             303
  COLON MUCINOUS ADENOCARCINOMA              4              43
  RECTAL ADENOCARCINOMA                      3             103
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  PCSK1 MUTATED    10   1   0   2
  PCSK1 WILD-TYPE 335   3  31  23
D1168V11, multiclass
    clus
vv   PCSK1 MUTATED PCSK1 WILD-TYPE
  R0            10             335
  R1             1               3
  R2             0              31
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1168V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PCSK1 MUTATED                                  0     2
  PCSK1 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PCSK1 MUTATED                           2     9
  PCSK1 WILD-TYPE                        20   217
D1168V13, multiclass
                                  clus
vv                                 PCSK1 MUTATED PCSK1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               9
  BLACK OR AFRICAN AMERICAN                    2              20
  WHITE                                        9             217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1169) Variable = RTN4 MUTATION ANALYSIS
D1169V1, survival
                sevent
clus2              0   1
  RTN4 MUTATED    18   3
  RTN4 WILD-TYPE 360  90
  RTN4 MUTATED RTN4 WILD-TYPE 
            21            450 
  RTN4 MUTATED RTN4 WILD-TYPE 
             3             90 
$`RTN4 MUTATED`
TCGA-A6-3809 TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3518 TCGA-AA-3555 
       32.75         3.02        63.98         1.02         1.02        29.95 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-A00R TCGA-AA-A010 TCGA-AD-5900 TCGA-AZ-4315 
       19.04        19.04         0.99        34.98         0.07        58.39 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4950 TCGA-CM-6171 TCGA-D5-6540 
       12.20        12.76        10.06        85.45        14.04        16.14 
TCGA-G4-6628 TCGA-AG-A002 TCGA-EI-6507 
       79.69        20.98        19.96 

$`RTN4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 
       20.12        19.66        20.28         7.04         1.02        35.01 
TCGA-AA-3511 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
        6.97        13.02        38.99         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       36.03         8.05        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 
       33.99        21.01        13.02        24.00        17.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3811 
       19.00        36.00         5.03        85.05        26.99        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
        4.01        27.02        42.02        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
       40.96        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 
        3.29         0.07        14.30        17.56       148.01        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       13.02        15.02        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 
       13.78        35.80        26.17        91.79        46.75        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       20.55        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  RTN4 MUTATED RTN4 WILD-TYPE 
          0.07           0.00 
  RTN4 MUTATED RTN4 WILD-TYPE 
         85.45         148.01 
  RTN4 MUTATED RTN4 WILD-TYPE 
         19.04          20.73 
[1] "0.1 - 85.5 (19.0)"  "0.0 - 148.0 (20.7)"
[1] "hr=" "1.4"
D1169V2, continuous
D1169V3, binary
                cls
clus               0   1
  RTN4 MUTATED    19   2
  RTN4 WILD-TYPE 347 117
[1] "tbl2"
                cls
clus             [,1] [,2]
  RTN4 MUTATED     19    2
  RTN4 WILD-TYPE  347  117
        clus
vv       RTN4 MUTATED RTN4 WILD-TYPE
  COLON            19            347
  RECTUM            2            117
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RTN4 MUTATED         7        0        3         7         2         0
  RTN4 WILD-TYPE      84        1       29       131         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RTN4 MUTATED           0          0          1          0        1         0
  RTN4 WILD-TYPE        24         11         58         42       47        18
                vv
clus             STAGE IVB
  RTN4 MUTATED           0
  RTN4 WILD-TYPE         1
D1169V4, multiclass
            clus
vv           RTN4 MUTATED RTN4 WILD-TYPE
  STAGE I               7             84
  STAGE IA              0              1
  STAGE II              3             29
  STAGE IIA             7            131
  STAGE IIB             2              8
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            1             58
  STAGE IIIC            0             42
  STAGE IV              1             47
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  RTN4 MUTATED     0   7  12   2
  RTN4 WILD-TYPE  17  85 317  48
D1169V5, multiclass
    clus
vv   RTN4 MUTATED RTN4 WILD-TYPE
  T1            0             17
  T2            7             85
  T3           12            317
  T4            2             48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  RTN4 MUTATED    20   1   0
  RTN4 WILD-TYPE 267 112  87
D1169V6, multiclass
    clus
vv   RTN4 MUTATED RTN4 WILD-TYPE
  N0           20            267
  N1            1            112
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1169V7, binary
                cls
clus               0   1
  RTN4 MUTATED    19   1
  RTN4 WILD-TYPE 356  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  RTN4 MUTATED     19    1
  RTN4 WILD-TYPE  356   64
   clus
vv  RTN4 MUTATED RTN4 WILD-TYPE
  0           19            356
  1            1             64
[1] 2 2
[1] FALSE
D1169V8, binary
                cls
clus               0   1
  RTN4 MUTATED     9  12
  RTN4 WILD-TYPE 216 252
[1] "tbl2"
                cls
clus             [,1] [,2]
  RTN4 MUTATED      9   12
  RTN4 WILD-TYPE  216  252
        clus
vv       RTN4 MUTATED RTN4 WILD-TYPE
  FEMALE            9            216
  MALE             12            252
[1] 2 2
[1] FALSE
D1169V9, binary
                cls
clus               0   1
  RTN4 MUTATED    17   1
  RTN4 WILD-TYPE 333  21
[1] "tbl2"
                cls
clus             [,1] [,2]
  RTN4 MUTATED     17    1
  RTN4 WILD-TYPE  333   21
     clus
vv    RTN4 MUTATED RTN4 WILD-TYPE
  NO            17            333
  YES            1             21
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  RTN4 MUTATED                     14                             5
  RTN4 WILD-TYPE                  301                            42
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  RTN4 MUTATED                       2                              0
  RTN4 WILD-TYPE                   104                             10
D1169V10, multiclass
                                clus
vv                               RTN4 MUTATED RTN4 WILD-TYPE
  COLON ADENOCARCINOMA                     14            301
  COLON MUCINOUS ADENOCARCINOMA             5             42
  RECTAL ADENOCARCINOMA                     2            104
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  RTN4 MUTATED    16   1   1   3
  RTN4 WILD-TYPE 329   3  30  22
D1169V11, multiclass
    clus
vv   RTN4 MUTATED RTN4 WILD-TYPE
  R0           16            329
  R1            1              3
  R2            1             30
  RX            3             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1169V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RTN4 MUTATED                                  0     3
  RTN4 WILD-TYPE                                1     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  RTN4 MUTATED                           1     7
  RTN4 WILD-TYPE                        21   219
D1169V13, multiclass
                                  clus
vv                                 RTN4 MUTATED RTN4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       3              8
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                       7            219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1170) Variable = C14ORF104 MUTATION ANALYSIS
D1170V1, survival
                     sevent
clus2                   0   1
  C14ORF104 MUTATED     4   0
  C14ORF104 WILD-TYPE 374  93
  C14ORF104 MUTATED C14ORF104 WILD-TYPE 
                  4                 467 
  C14ORF104 MUTATED C14ORF104 WILD-TYPE 
                  0                  93 
$`C14ORF104 MUTATED`
TCGA-AA-A010 TCGA-AD-6963 TCGA-D5-6930 TCGA-AG-A002 
       34.98        27.42         1.51        20.98 

$`C14ORF104 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       11.64         4.80        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  C14ORF104 MUTATED C14ORF104 WILD-TYPE 
               1.51                0.00 
  C14ORF104 MUTATED C14ORF104 WILD-TYPE 
              34.98              148.01 
  C14ORF104 MUTATED C14ORF104 WILD-TYPE 
              24.20               20.12 
[1] "1.5 - 35.0 (24.2)"  "0.0 - 148.0 (20.1)"
[1] "hr="     "3300000"
D1170V2, continuous
D1170V3, binary
                     cls
clus                    0   1
  C14ORF104 MUTATED     4   1
  C14ORF104 WILD-TYPE 362 118
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  C14ORF104 MUTATED      4    1
  C14ORF104 WILD-TYPE  362  118
        clus
vv       C14ORF104 MUTATED C14ORF104 WILD-TYPE
  COLON                  4                 362
  RECTUM                 1                 118
[1] 2 2
[1] FALSE
                     vv
clus                  STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  C14ORF104 MUTATED         1        0        0         2         1         0
  C14ORF104 WILD-TYPE      90        1       32       136         9         1
                     vv
clus                  STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C14ORF104 MUTATED           0          0          0          0        0
  C14ORF104 WILD-TYPE        24         11         59         42       48
                     vv
clus                  STAGE IVA STAGE IVB
  C14ORF104 MUTATED           0         0
  C14ORF104 WILD-TYPE        18         1
D1170V4, multiclass
            clus
vv           C14ORF104 MUTATED C14ORF104 WILD-TYPE
  STAGE I                    1                  90
  STAGE IA                   0                   1
  STAGE II                   0                  32
  STAGE IIA                  2                 136
  STAGE IIB                  1                   9
  STAGE IIC                  0                   1
  STAGE III                  0                  24
  STAGE IIIA                 0                  11
  STAGE IIIB                 0                  59
  STAGE IIIC                 0                  42
  STAGE IV                   0                  48
  STAGE IVA                  0                  18
  STAGE IVB                  0                   1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                   T1  T2  T3  T4
  C14ORF104 MUTATED     0   1   3   1
  C14ORF104 WILD-TYPE  17  91 326  49
D1170V5, multiclass
    clus
vv   C14ORF104 MUTATED C14ORF104 WILD-TYPE
  T1                 0                  17
  T2                 1                  91
  T3                 3                 326
  T4                 1                  49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                   N0  N1  N2
  C14ORF104 MUTATED     5   0   0
  C14ORF104 WILD-TYPE 282 113  87
D1170V6, multiclass
    clus
vv   C14ORF104 MUTATED C14ORF104 WILD-TYPE
  N0                 5                 282
  N1                 0                 113
  N2                 0                  87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1170V7, binary
                     cls
clus                    0   1
  C14ORF104 MUTATED     4   0
  C14ORF104 WILD-TYPE 371  65
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  C14ORF104 MUTATED      4    0
  C14ORF104 WILD-TYPE  371   65
   clus
vv  C14ORF104 MUTATED C14ORF104 WILD-TYPE
  0                 4                 371
  1                 0                  65
[1] 2 2
[1] FALSE
D1170V8, binary
                     cls
clus                    0   1
  C14ORF104 MUTATED     2   3
  C14ORF104 WILD-TYPE 223 261
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  C14ORF104 MUTATED      2    3
  C14ORF104 WILD-TYPE  223  261
        clus
vv       C14ORF104 MUTATED C14ORF104 WILD-TYPE
  FEMALE                 2                 223
  MALE                   3                 261
[1] 2 2
[1] FALSE
D1170V9, binary
                     cls
clus                    0   1
  C14ORF104 MUTATED     3   0
  C14ORF104 WILD-TYPE 347  22
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  C14ORF104 MUTATED      3    0
  C14ORF104 WILD-TYPE  347   22
     clus
vv    C14ORF104 MUTATED C14ORF104 WILD-TYPE
  NO                  3                 347
  YES                 0                  22
[1] 2 2
[1] FALSE
                     vv
clus                  COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  C14ORF104 MUTATED                      3                             1
  C14ORF104 WILD-TYPE                  312                            46
                     vv
clus                  RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  C14ORF104 MUTATED                       1                              0
  C14ORF104 WILD-TYPE                   105                             10
D1170V10, multiclass
                                clus
vv                               C14ORF104 MUTATED C14ORF104 WILD-TYPE
  COLON ADENOCARCINOMA                           3                 312
  COLON MUCINOUS ADENOCARCINOMA                  1                  46
  RECTAL ADENOCARCINOMA                          1                 105
  RECTAL MUCINOUS ADENOCARCINOMA                 0                  10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                   R0  R1  R2  RX
  C14ORF104 MUTATED     4   0   0   0
  C14ORF104 WILD-TYPE 341   4  31  25
D1170V11, multiclass
    clus
vv   C14ORF104 MUTATED C14ORF104 WILD-TYPE
  R0                 4                 341
  R1                 0                   4
  R2                 0                  31
  RX                 0                  25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1170V12, continuous
                     vv
clus                  AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C14ORF104 MUTATED                                  0     0
  C14ORF104 WILD-TYPE                                1    11
                     vv
clus                  BLACK OR AFRICAN AMERICAN WHITE
  C14ORF104 MUTATED                           0     2
  C14ORF104 WILD-TYPE                        22   224
D1170V13, multiclass
[1] "Remove cluster labels:" "C14ORF104 MUTATED"     
clus
  C14ORF104 MUTATED C14ORF104 WILD-TYPE 
                  2                 258 
         TCGA-A6-2671          TCGA-A6-2672          TCGA-A6-2674 
"C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" 
         TCGA-A6-2676          TCGA-A6-2677          TCGA-A6-2678 
"C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" 
         TCGA-A6-2683          TCGA-A6-3807          TCGA-A6-3808 
"C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" 
         TCGA-A6-3809          TCGA-A6-3810          TCGA-A6-4105 
"C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" 
         TCGA-A6-5656          TCGA-A6-5657          TCGA-A6-5659 
"C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" 
         TCGA-A6-5660          TCGA-A6-5661          TCGA-A6-5662 
"C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" 
         TCGA-A6-5664          TCGA-A6-5665          TCGA-A6-5666 
"C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" 
         TCGA-A6-6137          TCGA-A6-6138          TCGA-A6-6141 
"C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" 
         TCGA-A6-6142          TCGA-A6-6648          TCGA-A6-6649 
"C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" 
         TCGA-A6-6651          TCGA-A6-6652          TCGA-A6-6653 
"C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" 
         TCGA-A6-6654          TCGA-A6-6780          TCGA-A6-6781 
"C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" 
         TCGA-A6-6782          TCGA-AD-5900          TCGA-AD-6548 
"C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" 
         TCGA-AD-6888          TCGA-AD-6889          TCGA-AD-6890 
"C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" 
         TCGA-AD-6895          TCGA-AD-6899          TCGA-AD-6901 
"C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" 
         TCGA-AD-6964          TCGA-AD-6965          TCGA-AU-3779 
"C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" 
         TCGA-AU-6004          TCGA-AY-4070          TCGA-AY-4071 
"C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" 
         TCGA-AY-5543          TCGA-AY-6196          TCGA-AY-6197 
"C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" 
         TCGA-AY-6386          TCGA-AZ-4315          TCGA-AZ-4323 
"C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" 
         TCGA-AZ-4616          TCGA-AZ-4681          TCGA-AZ-4682 
"C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" 
         TCGA-AZ-5403          TCGA-AZ-5407          TCGA-AZ-6598 
"C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" 
         TCGA-AZ-6599          TCGA-AZ-6600          TCGA-AZ-6601 
"C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" 
         TCGA-AZ-6603          TCGA-AZ-6605          TCGA-AZ-6606 
"C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" 
         TCGA-AZ-6607          TCGA-AZ-6608          TCGA-CA-5254 
"C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" 
         TCGA-CA-5255          TCGA-CA-5796          TCGA-CA-5797 
"C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" 
         TCGA-CA-6715          TCGA-CA-6716          TCGA-CA-6717 
"C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" 
         TCGA-CA-6718          TCGA-CA-6719          TCGA-CK-4947 
"C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" 
         TCGA-CK-4948          TCGA-CK-4950          TCGA-CK-4952 
"C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" 
         TCGA-CK-5912          TCGA-CK-5913          TCGA-CK-5914 
"C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" 
         TCGA-CK-5915          TCGA-CK-5916          TCGA-CK-6746 
"C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" 
         TCGA-CK-6747          TCGA-CK-6748          TCGA-CK-6751 
"C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" 
         TCGA-CM-4743          TCGA-CM-4744          TCGA-CM-4746 
"C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" 
         TCGA-CM-4747          TCGA-CM-4752          TCGA-CM-5341 
"C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" 
         TCGA-CM-5344          TCGA-CM-5348          TCGA-CM-5349 
"C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" 
         TCGA-CM-5860          TCGA-CM-5861          TCGA-CM-5862 
"C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" 
         TCGA-CM-5863          TCGA-CM-5864          TCGA-CM-5868 
"C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" 
         TCGA-CM-6161          TCGA-CM-6162          TCGA-CM-6163 
"C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" 
         TCGA-CM-6164          TCGA-CM-6165          TCGA-CM-6166 
"C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" 
         TCGA-CM-6167          TCGA-CM-6168          TCGA-CM-6169 
"C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" 
         TCGA-CM-6170          TCGA-CM-6171          TCGA-CM-6172 
"C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" 
         TCGA-CM-6674          TCGA-CM-6675          TCGA-CM-6676 
"C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" 
         TCGA-CM-6677          TCGA-CM-6678          TCGA-CM-6679 
"C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" 
         TCGA-CM-6680          TCGA-D5-5537          TCGA-D5-5538 
"C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" 
         TCGA-D5-5539          TCGA-D5-5540          TCGA-D5-5541 
"C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" 
         TCGA-D5-6529          TCGA-D5-6532          TCGA-D5-6533 
"C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" 
         TCGA-D5-6534          TCGA-D5-6535          TCGA-D5-6536 
"C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" 
         TCGA-D5-6537          TCGA-D5-6538          TCGA-D5-6539 
"C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" 
         TCGA-D5-6540          TCGA-D5-6541          TCGA-D5-6898 
"C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" 
         TCGA-D5-6920          TCGA-D5-6922          TCGA-D5-6923 
"C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" 
         TCGA-D5-6924          TCGA-D5-6926          TCGA-D5-6927 
"C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" 
         TCGA-D5-6928          TCGA-D5-6929          TCGA-D5-6931 
"C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" 
         TCGA-D5-6932          TCGA-D5-7000          TCGA-DM-A0X9 
"C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" 
         TCGA-DM-A0XD          TCGA-DM-A0XF          TCGA-DM-A1D0 
"C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" 
         TCGA-DM-A1D4          TCGA-DM-A1D6          TCGA-DM-A1D7 
"C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" 
         TCGA-DM-A1D8          TCGA-DM-A1D9          TCGA-DM-A1DA 
"C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" 
         TCGA-DM-A1DB          TCGA-DM-A1HA          TCGA-DM-A1HB 
"C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" 
         TCGA-DM-A282          TCGA-DM-A285          TCGA-DM-A28C 
"C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" 
         TCGA-DM-A28E          TCGA-DM-A28F          TCGA-DM-A28G 
"C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" 
         TCGA-DM-A28H          TCGA-DM-A28K          TCGA-F4-6459 
"C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" 
         TCGA-F4-6460          TCGA-F4-6569          TCGA-F4-6570 
"C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" 
         TCGA-F4-6703          TCGA-F4-6704          TCGA-F4-6805 
"C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" 
         TCGA-F4-6806          TCGA-F4-6807          TCGA-F4-6808 
"C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" 
         TCGA-F4-6809          TCGA-F4-6854          TCGA-F4-6855 
"C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" 
         TCGA-F4-6856          TCGA-G4-6293          TCGA-G4-6299 
"C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" 
         TCGA-G4-6303          TCGA-G4-6304          TCGA-G4-6306 
"C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" 
         TCGA-G4-6307          TCGA-G4-6309          TCGA-G4-6310 
"C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" 
         TCGA-G4-6315          TCGA-G4-6317          TCGA-G4-6321 
"C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" 
         TCGA-G4-6323          TCGA-G4-6586          TCGA-G4-6588 
"C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" 
         TCGA-G4-6625          TCGA-G4-6626          TCGA-G4-6628 
"C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" 
         TCGA-AF-2687          TCGA-AF-2689          TCGA-AF-2691 
"C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" 
         TCGA-AF-2692          TCGA-AF-2693          TCGA-AF-3400 
"C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" 
         TCGA-AF-3913          TCGA-AF-4110          TCGA-AF-5654 
"C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" 
         TCGA-AF-6136          TCGA-AF-6655          TCGA-AF-6672 
"C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" 
         TCGA-AH-6544          TCGA-AH-6547          TCGA-AH-6549 
"C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" 
         TCGA-AH-6643          TCGA-AH-6644          TCGA-CI-6619 
"C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" 
         TCGA-CI-6620          TCGA-CI-6621          TCGA-CI-6622 
"C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" 
         TCGA-CI-6624          TCGA-CL-5917          TCGA-CL-5918 
"C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" 
         TCGA-DC-5337          TCGA-DC-5869          TCGA-DC-6155 
"C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" 
         TCGA-DC-6157          TCGA-DC-6158          TCGA-DC-6160 
"C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" 
         TCGA-DC-6681          TCGA-DC-6682          TCGA-DC-6683 
"C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" 
         TCGA-DT-5265          TCGA-DY-A0XA          TCGA-DY-A1DC 
"C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" 
         TCGA-DY-A1DD          TCGA-DY-A1DF          TCGA-DY-A1DG 
"C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" 
         TCGA-DY-A1H8          TCGA-EF-5830          TCGA-EI-6506 
"C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" 
         TCGA-EI-6507          TCGA-EI-6508          TCGA-EI-6510 
"C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" 
         TCGA-F5-6464          TCGA-F5-6465          TCGA-F5-6571 
"C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" 
         TCGA-F5-6702          TCGA-F5-6811          TCGA-F5-6812 
"C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" 
         TCGA-F5-6813          TCGA-G5-6235          TCGA-G5-6641 
"C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" "C14ORF104 WILD-TYPE" 

Clustering(1171) Variable = USF1 MUTATION ANALYSIS
D1171V1, survival
                sevent
clus2              0   1
  USF1 MUTATED     4   1
  USF1 WILD-TYPE 374  92
  USF1 MUTATED USF1 WILD-TYPE 
             5            466 
  USF1 MUTATED USF1 WILD-TYPE 
             1             92 
$`USF1 MUTATED`
TCGA-AA-3947 TCGA-AA-A010 TCGA-AD-5900 TCGA-AZ-5407 TCGA-AZ-6598 
       33.01        34.98         0.07        88.21        49.41 

$`USF1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 
       31.00         2.01        12.99        24.00        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       39.98        18.05        40.96        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       22.36        62.79         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  USF1 MUTATED USF1 WILD-TYPE 
          0.07           0.00 
  USF1 MUTATED USF1 WILD-TYPE 
         88.21         148.01 
  USF1 MUTATED USF1 WILD-TYPE 
        34.980         20.085 
[1] "0.1 - 88.2 (35.0)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.5"
D1171V2, continuous
D1171V3, binary
                cls
clus               0   1
  USF1 MUTATED     5   0
  USF1 WILD-TYPE 361 119
[1] "tbl2"
                cls
clus             [,1] [,2]
  USF1 MUTATED      5    0
  USF1 WILD-TYPE  361  119
        clus
vv       USF1 MUTATED USF1 WILD-TYPE
  COLON             5            361
  RECTUM            0            119
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  USF1 MUTATED         2        0        1         0         2         0
  USF1 WILD-TYPE      89        1       31       138         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  USF1 MUTATED           0          0          0          0        0         0
  USF1 WILD-TYPE        24         11         59         42       48        18
                vv
clus             STAGE IVB
  USF1 MUTATED           0
  USF1 WILD-TYPE         1
D1171V4, multiclass
            clus
vv           USF1 MUTATED USF1 WILD-TYPE
  STAGE I               2             89
  STAGE IA              0              1
  STAGE II              1             31
  STAGE IIA             0            138
  STAGE IIB             2              8
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            0             59
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  USF1 MUTATED     1   1   1   2
  USF1 WILD-TYPE  16  91 328  48
D1171V5, multiclass
    clus
vv   USF1 MUTATED USF1 WILD-TYPE
  T1            1             16
  T2            1             91
  T3            1            328
  T4            2             48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  USF1 MUTATED     5   0   0
  USF1 WILD-TYPE 282 113  87
D1171V6, multiclass
    clus
vv   USF1 MUTATED USF1 WILD-TYPE
  N0            5            282
  N1            0            113
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1171V7, binary
                cls
clus               0   1
  USF1 MUTATED     3   0
  USF1 WILD-TYPE 372  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  USF1 MUTATED      3    0
  USF1 WILD-TYPE  372   65
   clus
vv  USF1 MUTATED USF1 WILD-TYPE
  0            3            372
  1            0             65
[1] 2 2
[1] FALSE
D1171V8, binary
                cls
clus               0   1
  USF1 MUTATED     4   1
  USF1 WILD-TYPE 221 263
[1] "tbl2"
                cls
clus             [,1] [,2]
  USF1 MUTATED      4    1
  USF1 WILD-TYPE  221  263
        clus
vv       USF1 MUTATED USF1 WILD-TYPE
  FEMALE            4            221
  MALE              1            263
[1] 2 2
[1] FALSE
D1171V9, binary
                cls
clus               0   1
  USF1 MUTATED     4   0
  USF1 WILD-TYPE 346  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  USF1 MUTATED      4    0
  USF1 WILD-TYPE  346   22
     clus
vv    USF1 MUTATED USF1 WILD-TYPE
  NO             4            346
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  USF1 MUTATED                      3                             2
  USF1 WILD-TYPE                  312                            45
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  USF1 MUTATED                       0                              0
  USF1 WILD-TYPE                   106                             10
D1171V10, multiclass
                                clus
vv                               USF1 MUTATED USF1 WILD-TYPE
  COLON ADENOCARCINOMA                      3            312
  COLON MUCINOUS ADENOCARCINOMA             2             45
  RECTAL ADENOCARCINOMA                     0            106
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  USF1 MUTATED     3   0   0   0
  USF1 WILD-TYPE 342   4  31  25
D1171V11, multiclass
    clus
vv   USF1 MUTATED USF1 WILD-TYPE
  R0            3            342
  R1            0              4
  R2            0             31
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1171V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  USF1 MUTATED                                  0     0
  USF1 WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  USF1 MUTATED                           0     3
  USF1 WILD-TYPE                        22   223
D1171V13, multiclass
                                  clus
vv                                 USF1 MUTATED USF1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       3            223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1172) Variable = KLF12 MUTATION ANALYSIS
D1172V1, survival
                 sevent
clus2               0   1
  KLF12 MUTATED     5   0
  KLF12 WILD-TYPE 373  93
  KLF12 MUTATED KLF12 WILD-TYPE 
              5             466 
  KLF12 MUTATED KLF12 WILD-TYPE 
              0              93 
$`KLF12 MUTATED`
TCGA-AA-3949 TCGA-CA-5797 TCGA-G4-6321 TCGA-AG-3882 TCGA-EI-6506 
       26.01         3.29        22.09        19.99        20.55 

$`KLF12 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3950 
       31.00         2.01        12.99        24.00        33.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-6715 
        3.19         1.61        12.69         3.06         3.25         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       63.62        61.91        36.00        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6507 TCGA-EI-6508 
       24.13        51.48        32.61         0.49        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  KLF12 MUTATED KLF12 WILD-TYPE 
           3.29            0.00 
  KLF12 MUTATED KLF12 WILD-TYPE 
          26.01          148.01 
  KLF12 MUTATED KLF12 WILD-TYPE 
         20.550          20.155 
[1] "3.3 - 26.0 (20.6)"  "0.0 - 148.0 (20.2)"
[1] "hr="     "3300000"
D1172V2, continuous
D1172V3, binary
                 cls
clus                0   1
  KLF12 MUTATED     3   2
  KLF12 WILD-TYPE 363 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLF12 MUTATED      3    2
  KLF12 WILD-TYPE  363  117
        clus
vv       KLF12 MUTATED KLF12 WILD-TYPE
  COLON              3             363
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KLF12 MUTATED         1        0        0         2         0         0
  KLF12 WILD-TYPE      90        1       32       136        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  KLF12 MUTATED           1          0          1          0        0         0
  KLF12 WILD-TYPE        23         11         58         42       48        18
                 vv
clus              STAGE IVB
  KLF12 MUTATED           0
  KLF12 WILD-TYPE         1
D1172V4, multiclass
            clus
vv           KLF12 MUTATED KLF12 WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              2             136
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  KLF12 MUTATED     0   2   3   0
  KLF12 WILD-TYPE  17  90 326  50
D1172V5, multiclass
    clus
vv   KLF12 MUTATED KLF12 WILD-TYPE
  T1             0              17
  T2             2              90
  T3             3             326
  T4             0              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  KLF12 MUTATED     3   2   0
  KLF12 WILD-TYPE 284 111  87
D1172V6, multiclass
    clus
vv   KLF12 MUTATED KLF12 WILD-TYPE
  N0             3             284
  N1             2             111
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1172V7, binary
                 cls
clus                0   1
  KLF12 MUTATED     4   0
  KLF12 WILD-TYPE 371  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLF12 MUTATED      4    0
  KLF12 WILD-TYPE  371   65
   clus
vv  KLF12 MUTATED KLF12 WILD-TYPE
  0             4             371
  1             0              65
[1] 2 2
[1] FALSE
D1172V8, binary
                 cls
clus                0   1
  KLF12 MUTATED     4   1
  KLF12 WILD-TYPE 221 263
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLF12 MUTATED      4    1
  KLF12 WILD-TYPE  221  263
        clus
vv       KLF12 MUTATED KLF12 WILD-TYPE
  FEMALE             4             221
  MALE               1             263
[1] 2 2
[1] FALSE
D1172V9, binary
                 cls
clus                0   1
  KLF12 MUTATED     5   0
  KLF12 WILD-TYPE 345  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLF12 MUTATED      5    0
  KLF12 WILD-TYPE  345   22
     clus
vv    KLF12 MUTATED KLF12 WILD-TYPE
  NO              5             345
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  KLF12 MUTATED                      2                             1
  KLF12 WILD-TYPE                  313                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  KLF12 MUTATED                       2                              0
  KLF12 WILD-TYPE                   104                             10
D1172V10, multiclass
                                clus
vv                               KLF12 MUTATED KLF12 WILD-TYPE
  COLON ADENOCARCINOMA                       2             313
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  KLF12 MUTATED     5   0   0   0
  KLF12 WILD-TYPE 340   4  31  25
D1172V11, multiclass
    clus
vv   KLF12 MUTATED KLF12 WILD-TYPE
  R0             5             340
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1172V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KLF12 MUTATED                                  0     1
  KLF12 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  KLF12 MUTATED                           0     2
  KLF12 WILD-TYPE                        22   224
D1172V13, multiclass
                                  clus
vv                                 KLF12 MUTATED KLF12 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        2             224
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1173) Variable = VIM MUTATION ANALYSIS
D1173V1, survival
               sevent
clus2             0   1
  VIM MUTATED     7   2
  VIM WILD-TYPE 371  91
  VIM MUTATED VIM WILD-TYPE 
            9           462 
  VIM MUTATED VIM WILD-TYPE 
            2            91 
$`VIM MUTATED`
TCGA-AA-3510 TCGA-AA-3713 TCGA-AA-A00K TCGA-AA-A00R TCGA-AA-A02K TCGA-CK-4950 
       63.98        19.04        18.05         0.99        14.01        85.45 
TCGA-D5-5537 TCGA-AG-3892 TCGA-AH-6643 
       45.40        13.02         0.69 

$`VIM WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00L TCGA-AA-A00N 
       19.00        30.02        34.03        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       27.02        42.02        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
        5.03         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       14.30        17.56       148.01        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       11.01        10.06        12.03        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       17.03        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6644 
       38.04       117.11        38.56         1.45        17.49         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  VIM MUTATED VIM WILD-TYPE 
         0.69          0.00 
  VIM MUTATED VIM WILD-TYPE 
        85.45        148.01 
  VIM MUTATED VIM WILD-TYPE 
       18.050        20.415 
[1] "0.7 - 85.5 (18.1)"  "0.0 - 148.0 (20.4)"
[1] "hr=" "1"  
D1173V2, continuous
D1173V3, binary
               cls
clus              0   1
  VIM MUTATED     7   2
  VIM WILD-TYPE 359 117
[1] "tbl2"
               cls
clus            [,1] [,2]
  VIM MUTATED      7    2
  VIM WILD-TYPE  359  117
        clus
vv       VIM MUTATED VIM WILD-TYPE
  COLON            7           359
  RECTUM           2           117
[1] 2 2
[1] FALSE
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  VIM MUTATED         2        0        1         2         0         0
  VIM WILD-TYPE      89        1       31       136        10         1
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  VIM MUTATED           0          0          1          1        2         0
  VIM WILD-TYPE        24         11         58         41       46        18
               vv
clus            STAGE IVB
  VIM MUTATED           0
  VIM WILD-TYPE         1
D1173V4, multiclass
            clus
vv           VIM MUTATED VIM WILD-TYPE
  STAGE I              2            89
  STAGE IA             0             1
  STAGE II             1            31
  STAGE IIA            2           136
  STAGE IIB            0            10
  STAGE IIC            0             1
  STAGE III            0            24
  STAGE IIIA           0            11
  STAGE IIIB           1            58
  STAGE IIIC           1            41
  STAGE IV             2            46
  STAGE IVA            0            18
  STAGE IVB            0             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  VIM MUTATED     1   1   6   1
  VIM WILD-TYPE  16  91 323  49
D1173V5, multiclass
    clus
vv   VIM MUTATED VIM WILD-TYPE
  T1           1            16
  T2           1            91
  T3           6           323
  T4           1            49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2
  VIM MUTATED     5   1   3
  VIM WILD-TYPE 282 112  84
D1173V6, multiclass
    clus
vv   VIM MUTATED VIM WILD-TYPE
  N0           5           282
  N1           1           112
  N2           3            84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1173V7, binary
               cls
clus              0   1
  VIM MUTATED     6   2
  VIM WILD-TYPE 369  63
[1] "tbl2"
               cls
clus            [,1] [,2]
  VIM MUTATED      6    2
  VIM WILD-TYPE  369   63
   clus
vv  VIM MUTATED VIM WILD-TYPE
  0           6           369
  1           2            63
[1] 2 2
[1] FALSE
D1173V8, binary
               cls
clus              0   1
  VIM MUTATED     3   6
  VIM WILD-TYPE 222 258
[1] "tbl2"
               cls
clus            [,1] [,2]
  VIM MUTATED      3    6
  VIM WILD-TYPE  222  258
        clus
vv       VIM MUTATED VIM WILD-TYPE
  FEMALE           3           222
  MALE             6           258
[1] 2 2
[1] FALSE
D1173V9, binary
               cls
clus              0   1
  VIM MUTATED     5   1
  VIM WILD-TYPE 345  21
[1] "tbl2"
               cls
clus            [,1] [,2]
  VIM MUTATED      5    1
  VIM WILD-TYPE  345   21
     clus
vv    VIM MUTATED VIM WILD-TYPE
  NO            5           345
  YES           1            21
[1] 2 2
[1] FALSE
               vv
clus            COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  VIM MUTATED                      7                             0
  VIM WILD-TYPE                  308                            47
               vv
clus            RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  VIM MUTATED                       2                              0
  VIM WILD-TYPE                   104                             10
D1173V10, multiclass
                                clus
vv                               VIM MUTATED VIM WILD-TYPE
  COLON ADENOCARCINOMA                     7           308
  COLON MUCINOUS ADENOCARCINOMA            0            47
  RECTAL ADENOCARCINOMA                    2           104
  RECTAL MUCINOUS ADENOCARCINOMA           0            10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             R0  R1  R2  RX
  VIM MUTATED     5   1   2   1
  VIM WILD-TYPE 340   3  29  24
D1173V11, multiclass
    clus
vv   VIM MUTATED VIM WILD-TYPE
  R0           5           340
  R1           1             3
  R2           2            29
  RX           1            24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1173V12, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  VIM MUTATED                                  0     0
  VIM WILD-TYPE                                1    11
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  VIM MUTATED                           1     2
  VIM WILD-TYPE                        21   224
D1173V13, multiclass
                                  clus
vv                                 VIM MUTATED VIM WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      0            11
  BLACK OR AFRICAN AMERICAN                  1            21
  WHITE                                      2           224
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1174) Variable = GLG1 MUTATION ANALYSIS
D1174V1, survival
                sevent
clus2              0   1
  GLG1 MUTATED    10   4
  GLG1 WILD-TYPE 368  89
  GLG1 MUTATED GLG1 WILD-TYPE 
            14            457 
  GLG1 MUTATED GLG1 WILD-TYPE 
             4             89 
$`GLG1 MUTATED`
TCGA-A6-2683 TCGA-A6-3809 TCGA-AA-3710 TCGA-AA-A00N TCGA-AA-A010 TCGA-AU-6004 
       16.57        32.75        26.99         4.01        34.98        27.09 
TCGA-CA-6717 TCGA-CM-6674 TCGA-D5-6540 TCGA-D5-6930 TCGA-DM-A28K TCGA-F4-6460 
       12.76        12.95        16.14         1.51        98.24        31.96 
TCGA-DY-A1DG TCGA-F5-6571 
       51.48        31.30 

$`GLG1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5657 
       34.65        33.34        36.53        14.53        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       30.44        29.19        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07        12.20        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       11.01        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
        4.80        17.13        12.49        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        4.80        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-F4-6459 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
        8.61        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1H8 
        5.29       126.44        41.36        57.24        24.13        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       49.51        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  GLG1 MUTATED GLG1 WILD-TYPE 
          1.51           0.00 
  GLG1 MUTATED GLG1 WILD-TYPE 
         98.24         148.01 
  GLG1 MUTATED GLG1 WILD-TYPE 
         27.04          20.12 
[1] "1.5 - 98.2 (27.0)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.4"
D1174V2, continuous
D1174V3, binary
                cls
clus               0   1
  GLG1 MUTATED    12   2
  GLG1 WILD-TYPE 354 117
[1] "tbl2"
                cls
clus             [,1] [,2]
  GLG1 MUTATED     12    2
  GLG1 WILD-TYPE  354  117
        clus
vv       GLG1 MUTATED GLG1 WILD-TYPE
  COLON            12            354
  RECTUM            2            117
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GLG1 MUTATED         2        0        0         6         3         0
  GLG1 WILD-TYPE      89        1       32       132         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  GLG1 MUTATED           0          0          1          0        1         1
  GLG1 WILD-TYPE        24         11         58         42       47        17
                vv
clus             STAGE IVB
  GLG1 MUTATED           0
  GLG1 WILD-TYPE         1
D1174V4, multiclass
            clus
vv           GLG1 MUTATED GLG1 WILD-TYPE
  STAGE I               2             89
  STAGE IA              0              1
  STAGE II              0             32
  STAGE IIA             6            132
  STAGE IIB             3              7
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            1             58
  STAGE IIIC            0             42
  STAGE IV              1             47
  STAGE IVA             1             17
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  GLG1 MUTATED     0   2   8   4
  GLG1 WILD-TYPE  17  90 321  46
D1174V5, multiclass
    clus
vv   GLG1 MUTATED GLG1 WILD-TYPE
  T1            0             17
  T2            2             90
  T3            8            321
  T4            4             46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  GLG1 MUTATED    12   2   0
  GLG1 WILD-TYPE 275 111  87
D1174V6, multiclass
    clus
vv   GLG1 MUTATED GLG1 WILD-TYPE
  N0           12            275
  N1            2            111
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1174V7, binary
                cls
clus               0   1
  GLG1 MUTATED    12   2
  GLG1 WILD-TYPE 363  63
[1] "tbl2"
                cls
clus             [,1] [,2]
  GLG1 MUTATED     12    2
  GLG1 WILD-TYPE  363   63
   clus
vv  GLG1 MUTATED GLG1 WILD-TYPE
  0           12            363
  1            2             63
[1] 2 2
[1] FALSE
D1174V8, binary
                cls
clus               0   1
  GLG1 MUTATED     7   7
  GLG1 WILD-TYPE 218 257
[1] "tbl2"
                cls
clus             [,1] [,2]
  GLG1 MUTATED      7    7
  GLG1 WILD-TYPE  218  257
        clus
vv       GLG1 MUTATED GLG1 WILD-TYPE
  FEMALE            7            218
  MALE              7            257
[1] 2 2
[1] FALSE
D1174V9, binary
                cls
clus               0   1
  GLG1 MUTATED     9   0
  GLG1 WILD-TYPE 341  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  GLG1 MUTATED      9    0
  GLG1 WILD-TYPE  341   22
     clus
vv    GLG1 MUTATED GLG1 WILD-TYPE
  NO             9            341
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  GLG1 MUTATED                      6                             6
  GLG1 WILD-TYPE                  309                            41
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  GLG1 MUTATED                       2                              0
  GLG1 WILD-TYPE                   104                             10
D1174V10, multiclass
                                clus
vv                               GLG1 MUTATED GLG1 WILD-TYPE
  COLON ADENOCARCINOMA                      6            309
  COLON MUCINOUS ADENOCARCINOMA             6             41
  RECTAL ADENOCARCINOMA                     2            104
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  GLG1 MUTATED    11   0   0   1
  GLG1 WILD-TYPE 334   4  31  24
D1174V11, multiclass
    clus
vv   GLG1 MUTATED GLG1 WILD-TYPE
  R0           11            334
  R1            0              4
  R2            0             31
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1174V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GLG1 MUTATED                                  0     1
  GLG1 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  GLG1 MUTATED                           0    10
  GLG1 WILD-TYPE                        22   216
D1174V13, multiclass
                                  clus
vv                                 GLG1 MUTATED GLG1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                      10            216
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1175) Variable = CETN3 MUTATION ANALYSIS
D1175V1, survival
                 sevent
clus2               0   1
  CETN3 MUTATED     6   0
  CETN3 WILD-TYPE 372  93
  CETN3 MUTATED CETN3 WILD-TYPE 
              6             465 
  CETN3 MUTATED CETN3 WILD-TYPE 
              0              93 
$`CETN3 MUTATED`
TCGA-A6-6781 TCGA-CA-6717 TCGA-CM-6162 TCGA-CM-6171 TCGA-G4-6586 TCGA-G4-6628 
       19.66        12.76        12.00        14.04        35.80        79.69 

$`CETN3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07        12.20        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       15.02         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       12.99        13.02        15.02        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        26.17        91.79        46.75 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  CETN3 MUTATED CETN3 WILD-TYPE 
             12               0 
  CETN3 MUTATED CETN3 WILD-TYPE 
          79.69          148.01 
  CETN3 MUTATED CETN3 WILD-TYPE 
          16.85           20.28 
[1] "12.0 - 79.7 (16.9)" "0.0 - 148.0 (20.3)"
[1] "hr="     "9100000"
D1175V2, continuous
D1175V3, binary
                 cls
clus                0   1
  CETN3 MUTATED     6   0
  CETN3 WILD-TYPE 360 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CETN3 MUTATED      6    0
  CETN3 WILD-TYPE  360  119
        clus
vv       CETN3 MUTATED CETN3 WILD-TYPE
  COLON              6             360
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CETN3 MUTATED         2        0        0         2         0         0
  CETN3 WILD-TYPE      89        1       32       136        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CETN3 MUTATED           0          0          1          1        0         0
  CETN3 WILD-TYPE        24         11         58         41       48        18
                 vv
clus              STAGE IVB
  CETN3 MUTATED           0
  CETN3 WILD-TYPE         1
D1175V4, multiclass
            clus
vv           CETN3 MUTATED CETN3 WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              2             136
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             1              41
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CETN3 MUTATED     0   2   3   1
  CETN3 WILD-TYPE  17  90 326  49
D1175V5, multiclass
    clus
vv   CETN3 MUTATED CETN3 WILD-TYPE
  T1             0              17
  T2             2              90
  T3             3             326
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  CETN3 MUTATED     4   2   0
  CETN3 WILD-TYPE 283 111  87
D1175V6, multiclass
    clus
vv   CETN3 MUTATED CETN3 WILD-TYPE
  N0             4             283
  N1             2             111
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1175V7, binary
                 cls
clus                0   1
  CETN3 MUTATED     5   0
  CETN3 WILD-TYPE 370  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CETN3 MUTATED      5    0
  CETN3 WILD-TYPE  370   65
   clus
vv  CETN3 MUTATED CETN3 WILD-TYPE
  0             5             370
  1             0              65
[1] 2 2
[1] FALSE
D1175V8, binary
                 cls
clus                0   1
  CETN3 MUTATED     3   3
  CETN3 WILD-TYPE 222 261
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CETN3 MUTATED      3    3
  CETN3 WILD-TYPE  222  261
        clus
vv       CETN3 MUTATED CETN3 WILD-TYPE
  FEMALE             3             222
  MALE               3             261
[1] 2 2
[1] FALSE
D1175V9, binary
                 cls
clus                0   1
  CETN3 MUTATED     6   0
  CETN3 WILD-TYPE 344  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CETN3 MUTATED      6    0
  CETN3 WILD-TYPE  344   22
     clus
vv    CETN3 MUTATED CETN3 WILD-TYPE
  NO              6             344
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CETN3 MUTATED                      3                             3
  CETN3 WILD-TYPE                  312                            44
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CETN3 MUTATED                       0                              0
  CETN3 WILD-TYPE                   106                             10
D1175V10, multiclass
                                clus
vv                               CETN3 MUTATED CETN3 WILD-TYPE
  COLON ADENOCARCINOMA                       3             312
  COLON MUCINOUS ADENOCARCINOMA              3              44
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  CETN3 MUTATED     5   0   0   1
  CETN3 WILD-TYPE 340   4  31  24
D1175V11, multiclass
    clus
vv   CETN3 MUTATED CETN3 WILD-TYPE
  R0             5             340
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1175V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CETN3 MUTATED                                  0     1
  CETN3 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CETN3 MUTATED                           0     5
  CETN3 WILD-TYPE                        22   221
D1175V13, multiclass
                                  clus
vv                                 CETN3 MUTATED CETN3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        5             221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1176) Variable = SFRS15 MUTATION ANALYSIS
D1176V1, survival
                  sevent
clus2                0   1
  SFRS15 MUTATED    17   2
  SFRS15 WILD-TYPE 361  91
  SFRS15 MUTATED SFRS15 WILD-TYPE 
              19              452 
  SFRS15 MUTATED SFRS15 WILD-TYPE 
               2               91 
$`SFRS15 MUTATED`
TCGA-A6-3809 TCGA-AA-3510 TCGA-AA-3524 TCGA-AA-3555 TCGA-AA-3710 TCGA-AA-3877 
       32.75        63.98        36.03        29.95        26.99        31.00 
TCGA-AA-3977 TCGA-AA-A010 TCGA-AD-6889 TCGA-AD-6964 TCGA-AZ-4315 TCGA-AZ-6598 
       25.02        34.98        56.55        10.88        58.39        49.41 
TCGA-CA-6717 TCGA-D5-6538 TCGA-D5-6927 TCGA-D5-6928 TCGA-DM-A0X9 TCGA-G4-6309 
       12.76        17.13         9.44        11.64       119.70        85.48 
TCGA-AG-3892 
       13.02 

$`SFRS15 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
        9.07        24.03        37.05         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       17.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       18.05         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
        0.79         0.72         5.79        22.42        27.42         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       88.21         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07        12.20        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
       17.85         4.80        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6929 
        3.68         4.41        12.43        14.30         9.04         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0XD TCGA-DM-A0XF 
        1.51        12.00        11.38        10.26        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       44.68        55.04        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       36.95        17.03        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  SFRS15 MUTATED SFRS15 WILD-TYPE 
            9.44             0.00 
  SFRS15 MUTATED SFRS15 WILD-TYPE 
          119.70           148.01 
  SFRS15 MUTATED SFRS15 WILD-TYPE 
           31.00            20.02 
[1] "9.4 - 119.7 (31.0)" "0.0 - 148.0 (20.0)"
[1] "hr=" "2.8"
D1176V2, continuous
D1176V3, binary
                  cls
clus                 0   1
  SFRS15 MUTATED    19   1
  SFRS15 WILD-TYPE 347 118
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SFRS15 MUTATED     19    1
  SFRS15 WILD-TYPE  347  118
        clus
vv       SFRS15 MUTATED SFRS15 WILD-TYPE
  COLON              19              347
  RECTUM              1              118
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SFRS15 MUTATED         2        0        3         9         2         0
  SFRS15 WILD-TYPE      89        1       29       129         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SFRS15 MUTATED           0          0          2          0        0
  SFRS15 WILD-TYPE        24         11         57         42       48
                  vv
clus               STAGE IVA STAGE IVB
  SFRS15 MUTATED           0         0
  SFRS15 WILD-TYPE        18         1
D1176V4, multiclass
            clus
vv           SFRS15 MUTATED SFRS15 WILD-TYPE
  STAGE I                 2               89
  STAGE IA                0                1
  STAGE II                3               29
  STAGE IIA               9              129
  STAGE IIB               2                8
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              2               57
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  SFRS15 MUTATED     2   1  14   3
  SFRS15 WILD-TYPE  15  91 315  47
D1176V5, multiclass
    clus
vv   SFRS15 MUTATED SFRS15 WILD-TYPE
  T1              2               15
  T2              1               91
  T3             14              315
  T4              3               47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  SFRS15 MUTATED    17   1   2
  SFRS15 WILD-TYPE 270 112  85
D1176V6, multiclass
    clus
vv   SFRS15 MUTATED SFRS15 WILD-TYPE
  N0             17              270
  N1              1              112
  N2              2               85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1176V7, binary
                  cls
clus                 0   1
  SFRS15 MUTATED    17   0
  SFRS15 WILD-TYPE 358  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SFRS15 MUTATED     17    0
  SFRS15 WILD-TYPE  358   65
   clus
vv  SFRS15 MUTATED SFRS15 WILD-TYPE
  0             17              358
  1              0               65
[1] 2 2
[1] FALSE
D1176V8, binary
                  cls
clus                 0   1
  SFRS15 MUTATED    11   9
  SFRS15 WILD-TYPE 214 255
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SFRS15 MUTATED     11    9
  SFRS15 WILD-TYPE  214  255
        clus
vv       SFRS15 MUTATED SFRS15 WILD-TYPE
  FEMALE             11              214
  MALE                9              255
[1] 2 2
[1] FALSE
D1176V9, binary
                  cls
clus                 0   1
  SFRS15 MUTATED    17   0
  SFRS15 WILD-TYPE 333  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SFRS15 MUTATED     17    0
  SFRS15 WILD-TYPE  333   22
     clus
vv    SFRS15 MUTATED SFRS15 WILD-TYPE
  NO              17              333
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SFRS15 MUTATED                     14                             5
  SFRS15 WILD-TYPE                  301                            42
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SFRS15 MUTATED                       1                              0
  SFRS15 WILD-TYPE                   105                             10
D1176V10, multiclass
                                clus
vv                               SFRS15 MUTATED SFRS15 WILD-TYPE
  COLON ADENOCARCINOMA                       14              301
  COLON MUCINOUS ADENOCARCINOMA               5               42
  RECTAL ADENOCARCINOMA                       1              105
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  SFRS15 MUTATED    14   0   0   1
  SFRS15 WILD-TYPE 331   4  31  24
D1176V11, multiclass
    clus
vv   SFRS15 MUTATED SFRS15 WILD-TYPE
  R0             14              331
  R1              0                4
  R2              0               31
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1176V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SFRS15 MUTATED                                  0     2
  SFRS15 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  SFRS15 MUTATED                           1     8
  SFRS15 WILD-TYPE                        21   218
D1176V13, multiclass
                                  clus
vv                                 SFRS15 MUTATED SFRS15 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                9
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                         8              218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1177) Variable = ADAMTSL3 MUTATION ANALYSIS
D1177V1, survival
                    sevent
clus2                  0   1
  ADAMTSL3 MUTATED    35   9
  ADAMTSL3 WILD-TYPE 343  84
  ADAMTSL3 MUTATED ADAMTSL3 WILD-TYPE 
                44                427 
  ADAMTSL3 MUTATED ADAMTSL3 WILD-TYPE 
                 9                 84 
$`ADAMTSL3 MUTATED`
TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3543 TCGA-AA-3555 TCGA-AA-3662 
       24.16         1.02        35.01         0.99        29.95         6.05 
TCGA-AA-3663 TCGA-AA-3846 TCGA-AA-3877 TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-3966 
        6.97        17.03        31.00        33.01        24.00         2.01 
TCGA-AA-3977 TCGA-AA-A010 TCGA-AA-A01D TCGA-AA-A01Z TCGA-AZ-5407 TCGA-AZ-6598 
       25.02        34.98        10.98        37.02        88.21        49.41 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-5916 TCGA-CM-5344 
      100.01        29.56        12.76        10.06        21.14        22.03 
TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-6674 TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6927 
       30.08        15.02        12.95        19.59        55.92         9.44 
TCGA-D5-6929 TCGA-DM-A28F TCGA-F4-6569 TCGA-F4-6570 TCGA-G4-6299 TCGA-G4-6310 
        4.80        35.97        35.74         6.18        74.56        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-AF-3913 TCGA-AG-3731 TCGA-AG-3892 
       22.09        35.80        26.17        10.39        37.02        13.02 
TCGA-AG-A002 TCGA-EI-6510 
       20.98        18.28 

$`ADAMTSL3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.08        25.18        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3510 
       20.12        19.66        20.28         7.04         3.02        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
       78.08        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 
       24.03        27.02        29.98        18.05         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 
       24.00        26.01         2.01        20.98        34.03        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       14.99        21.99         1.02        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       35.01        26.01        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       62.79         6.77        12.10         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       12.20        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       49.08        51.32         9.99        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       22.98        32.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       45.40        12.26        56.09        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
       14.30         9.04        11.64         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6703 
       60.79       117.07        98.24         8.61        31.96        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6303 TCGA-G4-6304 
        0.53        47.41        35.31       133.18        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 
       44.68        55.04        85.48        61.91        36.00        13.78 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       13.55        19.10        34.49        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       17.95        36.95        17.03        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-F5-6464 TCGA-F5-6465 
        0.49        20.55        19.96        20.91         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  ADAMTSL3 MUTATED ADAMTSL3 WILD-TYPE 
              0.99               0.00 
  ADAMTSL3 MUTATED ADAMTSL3 WILD-TYPE 
            100.01             148.01 
  ADAMTSL3 MUTATED ADAMTSL3 WILD-TYPE 
            23.045             20.020 
[1] "1.0 - 100.0 (23.0)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1"  
D1177V2, continuous
D1177V3, binary
                    cls
clus                   0   1
  ADAMTSL3 MUTATED    41   5
  ADAMTSL3 WILD-TYPE 325 114
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ADAMTSL3 MUTATED     41    5
  ADAMTSL3 WILD-TYPE  325  114
        clus
vv       ADAMTSL3 MUTATED ADAMTSL3 WILD-TYPE
  COLON                41                325
  RECTUM                5                114
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ADAMTSL3 MUTATED         8        0        5        14         2         0
  ADAMTSL3 WILD-TYPE      83        1       27       124         8         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ADAMTSL3 MUTATED           1          1          5          3        4
  ADAMTSL3 WILD-TYPE        23         10         54         39       44
                    vv
clus                 STAGE IVA STAGE IVB
  ADAMTSL3 MUTATED           1         0
  ADAMTSL3 WILD-TYPE        17         1
D1177V4, multiclass
            clus
vv           ADAMTSL3 MUTATED ADAMTSL3 WILD-TYPE
  STAGE I                   8                 83
  STAGE IA                  0                  1
  STAGE II                  5                 27
  STAGE IIA                14                124
  STAGE IIB                 2                  8
  STAGE IIC                 0                  1
  STAGE III                 1                 23
  STAGE IIIA                1                 10
  STAGE IIIB                5                 54
  STAGE IIIC                3                 39
  STAGE IV                  4                 44
  STAGE IVA                 1                 17
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  ADAMTSL3 MUTATED     4   8  31   3
  ADAMTSL3 WILD-TYPE  13  84 298  47
D1177V5, multiclass
    clus
vv   ADAMTSL3 MUTATED ADAMTSL3 WILD-TYPE
  T1                4                 13
  T2                8                 84
  T3               31                298
  T4                3                 47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  ADAMTSL3 MUTATED    31  11   4
  ADAMTSL3 WILD-TYPE 256 102  83
D1177V6, multiclass
    clus
vv   ADAMTSL3 MUTATED ADAMTSL3 WILD-TYPE
  N0               31                256
  N1               11                102
  N2                4                 83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1177V7, binary
                    cls
clus                   0   1
  ADAMTSL3 MUTATED    36   4
  ADAMTSL3 WILD-TYPE 339  61
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ADAMTSL3 MUTATED     36    4
  ADAMTSL3 WILD-TYPE  339   61
   clus
vv  ADAMTSL3 MUTATED ADAMTSL3 WILD-TYPE
  0               36                339
  1                4                 61
[1] 2 2
[1] FALSE
D1177V8, binary
                    cls
clus                   0   1
  ADAMTSL3 MUTATED    25  21
  ADAMTSL3 WILD-TYPE 200 243
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ADAMTSL3 MUTATED     25   21
  ADAMTSL3 WILD-TYPE  200  243
        clus
vv       ADAMTSL3 MUTATED ADAMTSL3 WILD-TYPE
  FEMALE               25                200
  MALE                 21                243
[1] 2 2
[1] FALSE
D1177V9, binary
                    cls
clus                   0   1
  ADAMTSL3 MUTATED    39   1
  ADAMTSL3 WILD-TYPE 311  21
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ADAMTSL3 MUTATED     39    1
  ADAMTSL3 WILD-TYPE  311   21
     clus
vv    ADAMTSL3 MUTATED ADAMTSL3 WILD-TYPE
  NO                39                311
  YES                1                 21
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ADAMTSL3 MUTATED                     31                            10
  ADAMTSL3 WILD-TYPE                  284                            37
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ADAMTSL3 MUTATED                       5                              0
  ADAMTSL3 WILD-TYPE                   101                             10
D1177V10, multiclass
                                clus
vv                               ADAMTSL3 MUTATED ADAMTSL3 WILD-TYPE
  COLON ADENOCARCINOMA                         31                284
  COLON MUCINOUS ADENOCARCINOMA                10                 37
  RECTAL ADENOCARCINOMA                         5                101
  RECTAL MUCINOUS ADENOCARCINOMA                0                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  ADAMTSL3 MUTATED    33   0   2   3
  ADAMTSL3 WILD-TYPE 312   4  29  22
D1177V11, multiclass
    clus
vv   ADAMTSL3 MUTATED ADAMTSL3 WILD-TYPE
  R0               33                312
  R1                0                  4
  R2                2                 29
  RX                3                 22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1177V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ADAMTSL3 MUTATED                                  0     2
  ADAMTSL3 WILD-TYPE                                1     9
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  ADAMTSL3 MUTATED                           1    24
  ADAMTSL3 WILD-TYPE                        21   202
D1177V13, multiclass
                                  clus
vv                                 ADAMTSL3 MUTATED ADAMTSL3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           2                  9
  BLACK OR AFRICAN AMERICAN                       1                 21
  WHITE                                          24                202
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1178) Variable = CASP1 MUTATION ANALYSIS
D1178V1, survival
                 sevent
clus2               0   1
  CASP1 MUTATED     4   1
  CASP1 WILD-TYPE 374  92
  CASP1 MUTATED CASP1 WILD-TYPE 
              5             466 
  CASP1 MUTATED CASP1 WILD-TYPE 
              1              92 
$`CASP1 MUTATED`
TCGA-AA-3663 TCGA-AA-3811 TCGA-AA-3977 TCGA-CK-4952 TCGA-G4-6628 
        6.97        10.06        25.02        15.62        79.69 

$`CASP1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.05        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       46.75        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  CASP1 MUTATED CASP1 WILD-TYPE 
           6.97            0.00 
  CASP1 MUTATED CASP1 WILD-TYPE 
          79.69          148.01 
  CASP1 MUTATED CASP1 WILD-TYPE 
         15.620          20.235 
[1] "7.0 - 79.7 (15.6)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1"  
D1178V2, continuous
D1178V3, binary
                 cls
clus                0   1
  CASP1 MUTATED     6   0
  CASP1 WILD-TYPE 360 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASP1 MUTATED      6    0
  CASP1 WILD-TYPE  360  119
        clus
vv       CASP1 MUTATED CASP1 WILD-TYPE
  COLON              6             360
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CASP1 MUTATED         1        0        1         0         1         0
  CASP1 WILD-TYPE      90        1       31       138         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CASP1 MUTATED           1          0          0          1        0         0
  CASP1 WILD-TYPE        23         11         59         41       48        18
                 vv
clus              STAGE IVB
  CASP1 MUTATED           0
  CASP1 WILD-TYPE         1
D1178V4, multiclass
            clus
vv           CASP1 MUTATED CASP1 WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              0             138
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             1              41
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CASP1 MUTATED     0   2   2   2
  CASP1 WILD-TYPE  17  90 327  48
D1178V5, multiclass
    clus
vv   CASP1 MUTATED CASP1 WILD-TYPE
  T1             0              17
  T2             2              90
  T3             2             327
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  CASP1 MUTATED     4   0   2
  CASP1 WILD-TYPE 283 113  85
D1178V6, multiclass
    clus
vv   CASP1 MUTATED CASP1 WILD-TYPE
  N0             4             283
  N1             0             113
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1178V7, binary
                 cls
clus                0   1
  CASP1 MUTATED     4   0
  CASP1 WILD-TYPE 371  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASP1 MUTATED      4    0
  CASP1 WILD-TYPE  371   65
   clus
vv  CASP1 MUTATED CASP1 WILD-TYPE
  0             4             371
  1             0              65
[1] 2 2
[1] FALSE
D1178V8, binary
                 cls
clus                0   1
  CASP1 MUTATED     3   3
  CASP1 WILD-TYPE 222 261
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASP1 MUTATED      3    3
  CASP1 WILD-TYPE  222  261
        clus
vv       CASP1 MUTATED CASP1 WILD-TYPE
  FEMALE             3             222
  MALE               3             261
[1] 2 2
[1] FALSE
D1178V9, binary
                 cls
clus                0   1
  CASP1 MUTATED     4   0
  CASP1 WILD-TYPE 346  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASP1 MUTATED      4    0
  CASP1 WILD-TYPE  346   22
     clus
vv    CASP1 MUTATED CASP1 WILD-TYPE
  NO              4             346
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CASP1 MUTATED                      5                             1
  CASP1 WILD-TYPE                  310                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CASP1 MUTATED                       0                              0
  CASP1 WILD-TYPE                   106                             10
D1178V10, multiclass
                                clus
vv                               CASP1 MUTATED CASP1 WILD-TYPE
  COLON ADENOCARCINOMA                       5             310
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  CASP1 MUTATED     3   0   0   2
  CASP1 WILD-TYPE 342   4  31  23
D1178V11, multiclass
    clus
vv   CASP1 MUTATED CASP1 WILD-TYPE
  R0             3             342
  R1             0               4
  R2             0              31
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1178V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CASP1 MUTATED                                  0     0
  CASP1 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CASP1 MUTATED                           0     3
  CASP1 WILD-TYPE                        22   223
D1178V13, multiclass
                                  clus
vv                                 CASP1 MUTATED CASP1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        3             223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1179) Variable = B4GALT6 MUTATION ANALYSIS
D1179V1, survival
                   sevent
clus2                 0   1
  B4GALT6 MUTATED     8   2
  B4GALT6 WILD-TYPE 370  91
  B4GALT6 MUTATED B4GALT6 WILD-TYPE 
               10               461 
  B4GALT6 MUTATED B4GALT6 WILD-TYPE 
                2                91 
$`B4GALT6 MUTATED`
TCGA-A6-2676 TCGA-A6-6649 TCGA-AA-3977 TCGA-AA-A00J TCGA-AA-A010 TCGA-AA-A01R 
       42.90        24.16        25.02        18.05        34.98        35.01 
TCGA-AD-6895 TCGA-AZ-4315 TCGA-AZ-6607 TCGA-CM-6162 
        0.72        58.39         3.19        12.00 

$`B4GALT6 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       25.18        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
        1.02         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       21.37        15.52        56.55         0.79         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        33.01        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6608 
       12.10       100.01        29.56         5.23        11.74         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  B4GALT6 MUTATED B4GALT6 WILD-TYPE 
             0.72              0.00 
  B4GALT6 MUTATED B4GALT6 WILD-TYPE 
            58.39            148.01 
  B4GALT6 MUTATED B4GALT6 WILD-TYPE 
            24.59             20.12 
[1] "0.7 - 58.4 (24.6)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.1"
D1179V2, continuous
D1179V3, binary
                   cls
clus                  0   1
  B4GALT6 MUTATED    10   0
  B4GALT6 WILD-TYPE 356 119
[1] "tbl2"
                   cls
clus                [,1] [,2]
  B4GALT6 MUTATED     10    0
  B4GALT6 WILD-TYPE  356  119
        clus
vv       B4GALT6 MUTATED B4GALT6 WILD-TYPE
  COLON               10               356
  RECTUM               0               119
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  B4GALT6 MUTATED         0        0        0         1         2         0
  B4GALT6 WILD-TYPE      91        1       32       137         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  B4GALT6 MUTATED           1          0          3          0        1
  B4GALT6 WILD-TYPE        23         11         56         42       47
                   vv
clus                STAGE IVA STAGE IVB
  B4GALT6 MUTATED           0         0
  B4GALT6 WILD-TYPE        18         1
D1179V4, multiclass
            clus
vv           B4GALT6 MUTATED B4GALT6 WILD-TYPE
  STAGE I                  0                91
  STAGE IA                 0                 1
  STAGE II                 0                32
  STAGE IIA                1               137
  STAGE IIB                2                 8
  STAGE IIC                0                 1
  STAGE III                1                23
  STAGE IIIA               0                11
  STAGE IIIB               3                56
  STAGE IIIC               0                42
  STAGE IV                 1                47
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  B4GALT6 MUTATED     0   1   5   4
  B4GALT6 WILD-TYPE  17  91 324  46
D1179V5, multiclass
    clus
vv   B4GALT6 MUTATED B4GALT6 WILD-TYPE
  T1               0                17
  T2               1                91
  T3               5               324
  T4               4                46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  B4GALT6 MUTATED     4   4   2
  B4GALT6 WILD-TYPE 283 109  85
D1179V6, multiclass
    clus
vv   B4GALT6 MUTATED B4GALT6 WILD-TYPE
  N0               4               283
  N1               4               109
  N2               2                85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1179V7, binary
                   cls
clus                  0   1
  B4GALT6 MUTATED     7   1
  B4GALT6 WILD-TYPE 368  64
[1] "tbl2"
                   cls
clus                [,1] [,2]
  B4GALT6 MUTATED      7    1
  B4GALT6 WILD-TYPE  368   64
   clus
vv  B4GALT6 MUTATED B4GALT6 WILD-TYPE
  0               7               368
  1               1                64
[1] 2 2
[1] FALSE
D1179V8, binary
                   cls
clus                  0   1
  B4GALT6 MUTATED     3   7
  B4GALT6 WILD-TYPE 222 257
[1] "tbl2"
                   cls
clus                [,1] [,2]
  B4GALT6 MUTATED      3    7
  B4GALT6 WILD-TYPE  222  257
        clus
vv       B4GALT6 MUTATED B4GALT6 WILD-TYPE
  FEMALE               3               222
  MALE                 7               257
[1] 2 2
[1] FALSE
D1179V9, binary
                   cls
clus                  0   1
  B4GALT6 MUTATED     8   1
  B4GALT6 WILD-TYPE 342  21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  B4GALT6 MUTATED      8    1
  B4GALT6 WILD-TYPE  342   21
     clus
vv    B4GALT6 MUTATED B4GALT6 WILD-TYPE
  NO                8               342
  YES               1                21
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  B4GALT6 MUTATED                      7                             3
  B4GALT6 WILD-TYPE                  308                            44
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  B4GALT6 MUTATED                       0                              0
  B4GALT6 WILD-TYPE                   106                             10
D1179V10, multiclass
                                clus
vv                               B4GALT6 MUTATED B4GALT6 WILD-TYPE
  COLON ADENOCARCINOMA                         7               308
  COLON MUCINOUS ADENOCARCINOMA                3                44
  RECTAL ADENOCARCINOMA                        0               106
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  B4GALT6 MUTATED     6   0   0   0
  B4GALT6 WILD-TYPE 339   4  31  25
D1179V11, multiclass
    clus
vv   B4GALT6 MUTATED B4GALT6 WILD-TYPE
  R0               6               339
  R1               0                 4
  R2               0                31
  RX               0                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1179V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  B4GALT6 MUTATED                                  0     0
  B4GALT6 WILD-TYPE                                1    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  B4GALT6 MUTATED                           0     6
  B4GALT6 WILD-TYPE                        22   220
D1179V13, multiclass
                                  clus
vv                                 B4GALT6 MUTATED B4GALT6 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                      0                22
  WHITE                                          6               220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1180) Variable = RAD21 MUTATION ANALYSIS
D1180V1, survival
                 sevent
clus2               0   1
  RAD21 MUTATED    11   6
  RAD21 WILD-TYPE 367  87
  RAD21 MUTATED RAD21 WILD-TYPE 
             17             454 
  RAD21 MUTATED RAD21 WILD-TYPE 
              6              87 
$`RAD21 MUTATED`
TCGA-A6-6141 TCGA-A6-6780 TCGA-AA-3492 TCGA-AA-3516 TCGA-AA-3555 TCGA-AA-A00N 
        8.38        20.12         3.02        13.02        29.95         4.01 
TCGA-AA-A01Q TCGA-AZ-5403 TCGA-AZ-6598 TCGA-CA-6717 TCGA-CK-6751 TCGA-CM-6674 
        1.02        62.79        49.41        12.76       124.27        12.95 
TCGA-F4-6570 TCGA-AG-3896 TCGA-AG-A011 TCGA-DC-6155 TCGA-EF-5830 
        6.18         1.02        37.02        13.97         0.49 

$`RAD21 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 
       22.09        22.06        32.71        27.09        22.52        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       19.66        20.28         7.04         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        6.97         1.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       78.08         6.05         6.97        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01R 
       32.02        12.00        31.00        31.00        38.07        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 
        5.13       106.75        22.36        88.21         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       15.02        14.04        11.01        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       31.96        35.74        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3902 
       17.03        13.02        35.01        14.01        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A014 
       20.98        13.94         6.02        25.97        23.01        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
       15.02         5.03        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       24.13        51.48        32.61        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  RAD21 MUTATED RAD21 WILD-TYPE 
           0.49            0.00 
  RAD21 MUTATED RAD21 WILD-TYPE 
         124.27          148.01 
  RAD21 MUTATED RAD21 WILD-TYPE 
         12.950          20.945 
[1] "0.5 - 124.3 (12.9)" "0.0 - 148.0 (20.9)"
[1] "hr=" "2.1"
D1180V2, continuous
D1180V3, binary
                 cls
clus                0   1
  RAD21 MUTATED    13   4
  RAD21 WILD-TYPE 353 115
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RAD21 MUTATED     13    4
  RAD21 WILD-TYPE  353  115
        clus
vv       RAD21 MUTATED RAD21 WILD-TYPE
  COLON             13             353
  RECTUM             4             115
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RAD21 MUTATED         2        0        4         7         2         0
  RAD21 WILD-TYPE      89        1       28       131         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RAD21 MUTATED           1          1          0          0        0         0
  RAD21 WILD-TYPE        23         10         59         42       48        18
                 vv
clus              STAGE IVB
  RAD21 MUTATED           0
  RAD21 WILD-TYPE         1
D1180V4, multiclass
            clus
vv           RAD21 MUTATED RAD21 WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               4              28
  STAGE IIA              7             131
  STAGE IIB              2               8
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             1              10
  STAGE IIIB             0              59
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  RAD21 MUTATED     0   3  12   2
  RAD21 WILD-TYPE  17  89 317  48
D1180V5, multiclass
    clus
vv   RAD21 MUTATED RAD21 WILD-TYPE
  T1             0              17
  T2             3              89
  T3            12             317
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  RAD21 MUTATED    15   1   1
  RAD21 WILD-TYPE 272 112  86
D1180V6, multiclass
    clus
vv   RAD21 MUTATED RAD21 WILD-TYPE
  N0            15             272
  N1             1             112
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1180V7, binary
                 cls
clus                0   1
  RAD21 MUTATED    13   0
  RAD21 WILD-TYPE 362  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RAD21 MUTATED     13    0
  RAD21 WILD-TYPE  362   65
   clus
vv  RAD21 MUTATED RAD21 WILD-TYPE
  0            13             362
  1             0              65
[1] 2 2
[1] FALSE
D1180V8, binary
                 cls
clus                0   1
  RAD21 MUTATED     9   8
  RAD21 WILD-TYPE 216 256
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RAD21 MUTATED      9    8
  RAD21 WILD-TYPE  216  256
        clus
vv       RAD21 MUTATED RAD21 WILD-TYPE
  FEMALE             9             216
  MALE               8             256
[1] 2 2
[1] FALSE
D1180V9, binary
                 cls
clus                0   1
  RAD21 MUTATED    13   0
  RAD21 WILD-TYPE 337  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RAD21 MUTATED     13    0
  RAD21 WILD-TYPE  337   22
     clus
vv    RAD21 MUTATED RAD21 WILD-TYPE
  NO             13             337
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  RAD21 MUTATED                      7                             6
  RAD21 WILD-TYPE                  308                            41
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  RAD21 MUTATED                       4                              0
  RAD21 WILD-TYPE                   102                             10
D1180V10, multiclass
                                clus
vv                               RAD21 MUTATED RAD21 WILD-TYPE
  COLON ADENOCARCINOMA                       7             308
  COLON MUCINOUS ADENOCARCINOMA              6              41
  RECTAL ADENOCARCINOMA                      4             102
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  RAD21 MUTATED    10   0   0   2
  RAD21 WILD-TYPE 335   4  31  23
D1180V11, multiclass
    clus
vv   RAD21 MUTATED RAD21 WILD-TYPE
  R0            10             335
  R1             0               4
  R2             0              31
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1180V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RAD21 MUTATED                                  0     1
  RAD21 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  RAD21 MUTATED                           1     8
  RAD21 WILD-TYPE                        21   218
D1180V13, multiclass
                                  clus
vv                                 RAD21 MUTATED RAD21 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        8             218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1181) Variable = HUS1 MUTATION ANALYSIS
D1181V1, survival
                sevent
clus2              0   1
  HUS1 MUTATED     5   3
  HUS1 WILD-TYPE 373  90
  HUS1 MUTATED HUS1 WILD-TYPE 
             8            463 
  HUS1 MUTATED HUS1 WILD-TYPE 
             3             90 
$`HUS1 MUTATED`
TCGA-A6-5657 TCGA-AA-3510 TCGA-AA-3713 TCGA-AA-A010 TCGA-AZ-6598 TCGA-AZ-6601 
       31.63        63.98        19.04        34.98        49.41       100.01 
TCGA-DM-A1HA TCGA-DY-A1DD 
      131.51        57.24 

$`HUS1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 
       62.79        88.21         6.77        12.10        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
       44.32       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
      126.44        41.36        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  HUS1 MUTATED HUS1 WILD-TYPE 
         19.04           0.00 
  HUS1 MUTATED HUS1 WILD-TYPE 
        131.51         148.01 
  HUS1 MUTATED HUS1 WILD-TYPE 
        53.325         20.020 
[1] "19.0 - 131.5 (53.3)" "0.0 - 148.0 (20.0)" 
[1] "hr=" "1.2"
D1181V2, continuous
D1181V3, binary
                cls
clus               0   1
  HUS1 MUTATED     7   1
  HUS1 WILD-TYPE 359 118
[1] "tbl2"
                cls
clus             [,1] [,2]
  HUS1 MUTATED      7    1
  HUS1 WILD-TYPE  359  118
        clus
vv       HUS1 MUTATED HUS1 WILD-TYPE
  COLON             7            359
  RECTUM            1            118
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  HUS1 MUTATED         0        0        3         0         1         0
  HUS1 WILD-TYPE      91        1       29       138         9         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  HUS1 MUTATED           0          0          2          1        1         0
  HUS1 WILD-TYPE        24         11         57         41       47        18
                vv
clus             STAGE IVB
  HUS1 MUTATED           0
  HUS1 WILD-TYPE         1
D1181V4, multiclass
            clus
vv           HUS1 MUTATED HUS1 WILD-TYPE
  STAGE I               0             91
  STAGE IA              0              1
  STAGE II              3             29
  STAGE IIA             0            138
  STAGE IIB             1              9
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            2             57
  STAGE IIIC            1             41
  STAGE IV              1             47
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  HUS1 MUTATED     0   0   7   1
  HUS1 WILD-TYPE  17  92 322  49
D1181V5, multiclass
    clus
vv   HUS1 MUTATED HUS1 WILD-TYPE
  T1            0             17
  T2            0             92
  T3            7            322
  T4            1             49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  HUS1 MUTATED     5   2   1
  HUS1 WILD-TYPE 282 111  86
D1181V6, multiclass
    clus
vv   HUS1 MUTATED HUS1 WILD-TYPE
  N0            5            282
  N1            2            111
  N2            1             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1181V7, binary
                cls
clus               0   1
  HUS1 MUTATED     6   1
  HUS1 WILD-TYPE 369  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  HUS1 MUTATED      6    1
  HUS1 WILD-TYPE  369   64
   clus
vv  HUS1 MUTATED HUS1 WILD-TYPE
  0            6            369
  1            1             64
[1] 2 2
[1] FALSE
D1181V8, binary
                cls
clus               0   1
  HUS1 MUTATED     3   5
  HUS1 WILD-TYPE 222 259
[1] "tbl2"
                cls
clus             [,1] [,2]
  HUS1 MUTATED      3    5
  HUS1 WILD-TYPE  222  259
        clus
vv       HUS1 MUTATED HUS1 WILD-TYPE
  FEMALE            3            222
  MALE              5            259
[1] 2 2
[1] FALSE
D1181V9, binary
                cls
clus               0   1
  HUS1 MUTATED     5   1
  HUS1 WILD-TYPE 345  21
[1] "tbl2"
                cls
clus             [,1] [,2]
  HUS1 MUTATED      5    1
  HUS1 WILD-TYPE  345   21
     clus
vv    HUS1 MUTATED HUS1 WILD-TYPE
  NO             5            345
  YES            1             21
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  HUS1 MUTATED                      7                             0
  HUS1 WILD-TYPE                  308                            47
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  HUS1 MUTATED                       1                              0
  HUS1 WILD-TYPE                   105                             10
D1181V10, multiclass
                                clus
vv                               HUS1 MUTATED HUS1 WILD-TYPE
  COLON ADENOCARCINOMA                      7            308
  COLON MUCINOUS ADENOCARCINOMA             0             47
  RECTAL ADENOCARCINOMA                     1            105
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  HUS1 MUTATED     3   0   1   0
  HUS1 WILD-TYPE 342   4  30  25
D1181V11, multiclass
    clus
vv   HUS1 MUTATED HUS1 WILD-TYPE
  R0            3            342
  R1            0              4
  R2            1             30
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1181V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HUS1 MUTATED                                  0     0
  HUS1 WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  HUS1 MUTATED                           1     4
  HUS1 WILD-TYPE                        21   222
D1181V13, multiclass
                                  clus
vv                                 HUS1 MUTATED HUS1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                       4            222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1182) Variable = PTPN14 MUTATION ANALYSIS
D1182V1, survival
                  sevent
clus2                0   1
  PTPN14 MUTATED    17   3
  PTPN14 WILD-TYPE 361  90
  PTPN14 MUTATED PTPN14 WILD-TYPE 
              20              451 
  PTPN14 MUTATED PTPN14 WILD-TYPE 
               3               90 
$`PTPN14 MUTATED`
TCGA-A6-5665 TCGA-A6-6138 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3710 
       22.06        22.52        24.39        20.12        19.66        26.99 
TCGA-AA-3864 TCGA-AA-3950 TCGA-AA-3966 TCGA-AA-A01R TCGA-AY-6197 TCGA-AZ-4315 
       53.00        24.00         2.01        35.01        21.44        58.39 
TCGA-AZ-6598 TCGA-CA-6717 TCGA-CA-6718 TCGA-D5-6533 TCGA-D5-6928 TCGA-AG-A002 
       49.41        12.76        10.06         1.32        11.64        20.98 
TCGA-AH-6549 TCGA-DC-6158 
       17.49        10.98 

$`PTPN14 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       22.09        32.71        27.09         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6782 TCGA-AA-3489 
       24.16        21.76        24.69        23.87        20.28         7.04 
TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
        3.02         1.02        35.01        63.98         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
       13.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       36.03         8.05        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       78.08         6.05         6.97        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 
       37.05        19.00        36.00         5.03        85.05        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 
        2.01        12.99        24.00        33.01        26.01         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       20.98        34.03        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       31.00        38.07         1.02         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 
       14.50        27.09        16.31         0.95        33.01        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.07        12.20        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       18.25        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6930 
       12.43        14.30         9.04         9.44         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  PTPN14 MUTATED PTPN14 WILD-TYPE 
            1.32             0.00 
  PTPN14 MUTATED PTPN14 WILD-TYPE 
           58.39           148.01 
  PTPN14 MUTATED PTPN14 WILD-TYPE 
           21.21            20.05 
[1] "1.3 - 58.4 (21.2)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.2"
D1182V2, continuous
D1182V3, binary
                  cls
clus                 0   1
  PTPN14 MUTATED    18   3
  PTPN14 WILD-TYPE 348 116
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PTPN14 MUTATED     18    3
  PTPN14 WILD-TYPE  348  116
        clus
vv       PTPN14 MUTATED PTPN14 WILD-TYPE
  COLON              18              348
  RECTUM              3              116
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PTPN14 MUTATED         4        0        2        11         0         0
  PTPN14 WILD-TYPE      87        1       30       127        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PTPN14 MUTATED           1          0          1          1        0
  PTPN14 WILD-TYPE        23         11         58         41       48
                  vv
clus               STAGE IVA STAGE IVB
  PTPN14 MUTATED           0         0
  PTPN14 WILD-TYPE        18         1
D1182V4, multiclass
            clus
vv           PTPN14 MUTATED PTPN14 WILD-TYPE
  STAGE I                 4               87
  STAGE IA                0                1
  STAGE II                2               30
  STAGE IIA              11              127
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               1               23
  STAGE IIIA              0               11
  STAGE IIIB              1               58
  STAGE IIIC              1               41
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  PTPN14 MUTATED     0   4  15   2
  PTPN14 WILD-TYPE  17  88 314  48
D1182V5, multiclass
    clus
vv   PTPN14 MUTATED PTPN14 WILD-TYPE
  T1              0               17
  T2              4               88
  T3             15              314
  T4              2               48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  PTPN14 MUTATED    18   1   1
  PTPN14 WILD-TYPE 269 112  86
D1182V6, multiclass
    clus
vv   PTPN14 MUTATED PTPN14 WILD-TYPE
  N0             18              269
  N1              1              112
  N2              1               86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1182V7, binary
                  cls
clus                 0   1
  PTPN14 MUTATED    16   0
  PTPN14 WILD-TYPE 359  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PTPN14 MUTATED     16    0
  PTPN14 WILD-TYPE  359   65
   clus
vv  PTPN14 MUTATED PTPN14 WILD-TYPE
  0             16              359
  1              0               65
[1] 2 2
[1] FALSE
D1182V8, binary
                  cls
clus                 0   1
  PTPN14 MUTATED     7  14
  PTPN14 WILD-TYPE 218 250
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PTPN14 MUTATED      7   14
  PTPN14 WILD-TYPE  218  250
        clus
vv       PTPN14 MUTATED PTPN14 WILD-TYPE
  FEMALE              7              218
  MALE               14              250
[1] 2 2
[1] FALSE
D1182V9, binary
                  cls
clus                 0   1
  PTPN14 MUTATED    17   1
  PTPN14 WILD-TYPE 333  21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PTPN14 MUTATED     17    1
  PTPN14 WILD-TYPE  333   21
     clus
vv    PTPN14 MUTATED PTPN14 WILD-TYPE
  NO              17              333
  YES              1               21
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PTPN14 MUTATED                     11                             7
  PTPN14 WILD-TYPE                  304                            40
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PTPN14 MUTATED                       3                              0
  PTPN14 WILD-TYPE                   103                             10
D1182V10, multiclass
                                clus
vv                               PTPN14 MUTATED PTPN14 WILD-TYPE
  COLON ADENOCARCINOMA                       11              304
  COLON MUCINOUS ADENOCARCINOMA               7               40
  RECTAL ADENOCARCINOMA                       3              103
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  PTPN14 MUTATED    13   0   0   3
  PTPN14 WILD-TYPE 332   4  31  22
D1182V11, multiclass
    clus
vv   PTPN14 MUTATED PTPN14 WILD-TYPE
  R0             13              332
  R1              0                4
  R2              0               31
  RX              3               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1182V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PTPN14 MUTATED                                  0     2
  PTPN14 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  PTPN14 MUTATED                           0    12
  PTPN14 WILD-TYPE                        22   214
D1182V13, multiclass
                                  clus
vv                                 PTPN14 MUTATED PTPN14 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                9
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                        12              214
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1183) Variable = FZD6 MUTATION ANALYSIS
D1183V1, survival
                sevent
clus2              0   1
  FZD6 MUTATED    13   2
  FZD6 WILD-TYPE 365  91
  FZD6 MUTATED FZD6 WILD-TYPE 
            15            456 
  FZD6 MUTATED FZD6 WILD-TYPE 
             2             91 
$`FZD6 MUTATED`
TCGA-A6-5665 TCGA-AA-A00N TCGA-AA-A00R TCGA-AA-A010 TCGA-AY-6197 TCGA-AZ-4315 
       22.06         4.01         0.99        34.98        21.44        58.39 
TCGA-CA-6718 TCGA-CK-4950 TCGA-CM-4746 TCGA-CM-6170 TCGA-G4-6309 TCGA-AG-3902 
       10.06        85.45        37.02        15.02        85.48        32.02 
TCGA-AG-A002 TCGA-EI-6507 TCGA-F5-6811 
       20.98        19.96        32.19 

$`FZD6 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       38.04        27.02        42.02        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 
       14.50        27.09        16.31         0.95        33.01        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07        12.20        12.76        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
      148.01        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4747 
       82.95         1.91       124.27        23.05        20.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       12.99        13.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       53.62        44.68        55.04        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
        1.02        48.03        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
        0.49        20.55        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       31.30        28.57         0.66         0.69        55.76        26.43 

  FZD6 MUTATED FZD6 WILD-TYPE 
          0.99           0.00 
  FZD6 MUTATED FZD6 WILD-TYPE 
         85.48         148.01 
  FZD6 MUTATED FZD6 WILD-TYPE 
        22.060         20.035 
[1] "1.0 - 85.5 (22.1)"  "0.0 - 148.0 (20.0)"
[1] "hr=" "1.8"
D1183V2, continuous
D1183V3, binary
                cls
clus               0   1
  FZD6 MUTATED    11   4
  FZD6 WILD-TYPE 355 115
[1] "tbl2"
                cls
clus             [,1] [,2]
  FZD6 MUTATED     11    4
  FZD6 WILD-TYPE  355  115
        clus
vv       FZD6 MUTATED FZD6 WILD-TYPE
  COLON            11            355
  RECTUM            4            115
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FZD6 MUTATED         4        0        0         7         2         0
  FZD6 WILD-TYPE      87        1       32       131         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  FZD6 MUTATED           0          0          2          0        0         0
  FZD6 WILD-TYPE        24         11         57         42       48        18
                vv
clus             STAGE IVB
  FZD6 MUTATED           0
  FZD6 WILD-TYPE         1
D1183V4, multiclass
            clus
vv           FZD6 MUTATED FZD6 WILD-TYPE
  STAGE I               4             87
  STAGE IA              0              1
  STAGE II              0             32
  STAGE IIA             7            131
  STAGE IIB             2              8
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            2             57
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  FZD6 MUTATED     0   4   9   2
  FZD6 WILD-TYPE  17  88 320  48
D1183V5, multiclass
    clus
vv   FZD6 MUTATED FZD6 WILD-TYPE
  T1            0             17
  T2            4             88
  T3            9            320
  T4            2             48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  FZD6 MUTATED    13   2   0
  FZD6 WILD-TYPE 274 111  87
D1183V6, multiclass
    clus
vv   FZD6 MUTATED FZD6 WILD-TYPE
  N0           13            274
  N1            2            111
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1183V7, binary
                cls
clus               0   1
  FZD6 MUTATED    14   0
  FZD6 WILD-TYPE 361  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  FZD6 MUTATED     14    0
  FZD6 WILD-TYPE  361   65
   clus
vv  FZD6 MUTATED FZD6 WILD-TYPE
  0           14            361
  1            0             65
[1] 2 2
[1] FALSE
D1183V8, binary
                cls
clus               0   1
  FZD6 MUTATED     7   8
  FZD6 WILD-TYPE 218 256
[1] "tbl2"
                cls
clus             [,1] [,2]
  FZD6 MUTATED      7    8
  FZD6 WILD-TYPE  218  256
        clus
vv       FZD6 MUTATED FZD6 WILD-TYPE
  FEMALE            7            218
  MALE              8            256
[1] 2 2
[1] FALSE
D1183V9, binary
                cls
clus               0   1
  FZD6 MUTATED    13   0
  FZD6 WILD-TYPE 337  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  FZD6 MUTATED     13    0
  FZD6 WILD-TYPE  337   22
     clus
vv    FZD6 MUTATED FZD6 WILD-TYPE
  NO            13            337
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  FZD6 MUTATED                     10                             1
  FZD6 WILD-TYPE                  305                            46
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  FZD6 MUTATED                       4                              0
  FZD6 WILD-TYPE                   102                             10
D1183V10, multiclass
                                clus
vv                               FZD6 MUTATED FZD6 WILD-TYPE
  COLON ADENOCARCINOMA                     10            305
  COLON MUCINOUS ADENOCARCINOMA             1             46
  RECTAL ADENOCARCINOMA                     4            102
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  FZD6 MUTATED    12   1   0   1
  FZD6 WILD-TYPE 333   3  31  24
D1183V11, multiclass
    clus
vv   FZD6 MUTATED FZD6 WILD-TYPE
  R0           12            333
  R1            1              3
  R2            0             31
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1183V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FZD6 MUTATED                                  0     1
  FZD6 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  FZD6 MUTATED                           3     6
  FZD6 WILD-TYPE                        19   220
D1183V13, multiclass
                                  clus
vv                                 FZD6 MUTATED FZD6 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   3             19
  WHITE                                       6            220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1184) Variable = C6ORF222 MUTATION ANALYSIS
D1184V1, survival
                    sevent
clus2                  0   1
  C6ORF222 MUTATED     5   1
  C6ORF222 WILD-TYPE 373  92
  C6ORF222 MUTATED C6ORF222 WILD-TYPE 
                 6                465 
  C6ORF222 MUTATED C6ORF222 WILD-TYPE 
                 1                 92 
$`C6ORF222 MUTATED`
TCGA-A6-5665 TCGA-A6-6653 TCGA-AA-3663 TCGA-AA-3710 TCGA-AA-A00N TCGA-AA-A010 
       22.06        24.39         6.97        26.99         4.01        34.98 

$`C6ORF222 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 
       25.18        24.16        21.76        24.69        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       85.05        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  C6ORF222 MUTATED C6ORF222 WILD-TYPE 
              4.01               0.00 
  C6ORF222 MUTATED C6ORF222 WILD-TYPE 
             34.98             148.01 
  C6ORF222 MUTATED C6ORF222 WILD-TYPE 
            23.225             20.120 
[1] "4.0 - 35.0 (23.2)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.2"
D1184V2, continuous
D1184V3, binary
                    cls
clus                   0   1
  C6ORF222 MUTATED     6   0
  C6ORF222 WILD-TYPE 360 119
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C6ORF222 MUTATED      6    0
  C6ORF222 WILD-TYPE  360  119
        clus
vv       C6ORF222 MUTATED C6ORF222 WILD-TYPE
  COLON                 6                360
  RECTUM                0                119
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  C6ORF222 MUTATED         1        0        1         2         2         0
  C6ORF222 WILD-TYPE      90        1       31       136         8         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C6ORF222 MUTATED           0          0          0          0        0
  C6ORF222 WILD-TYPE        24         11         59         42       48
                    vv
clus                 STAGE IVA STAGE IVB
  C6ORF222 MUTATED           0         0
  C6ORF222 WILD-TYPE        18         1
D1184V4, multiclass
            clus
vv           C6ORF222 MUTATED C6ORF222 WILD-TYPE
  STAGE I                   1                 90
  STAGE IA                  0                  1
  STAGE II                  1                 31
  STAGE IIA                 2                136
  STAGE IIB                 2                  8
  STAGE IIC                 0                  1
  STAGE III                 0                 24
  STAGE IIIA                0                 11
  STAGE IIIB                0                 59
  STAGE IIIC                0                 42
  STAGE IV                  0                 48
  STAGE IVA                 0                 18
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  C6ORF222 MUTATED     0   1   3   2
  C6ORF222 WILD-TYPE  17  91 326  48
D1184V5, multiclass
    clus
vv   C6ORF222 MUTATED C6ORF222 WILD-TYPE
  T1                0                 17
  T2                1                 91
  T3                3                326
  T4                2                 48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  C6ORF222 MUTATED     6   0   0
  C6ORF222 WILD-TYPE 281 113  87
D1184V6, multiclass
    clus
vv   C6ORF222 MUTATED C6ORF222 WILD-TYPE
  N0                6                281
  N1                0                113
  N2                0                 87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1184V7, binary
                    cls
clus                   0   1
  C6ORF222 MUTATED     6   0
  C6ORF222 WILD-TYPE 369  65
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C6ORF222 MUTATED      6    0
  C6ORF222 WILD-TYPE  369   65
   clus
vv  C6ORF222 MUTATED C6ORF222 WILD-TYPE
  0                6                369
  1                0                 65
[1] 2 2
[1] FALSE
D1184V8, binary
                    cls
clus                   0   1
  C6ORF222 MUTATED     3   3
  C6ORF222 WILD-TYPE 222 261
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C6ORF222 MUTATED      3    3
  C6ORF222 WILD-TYPE  222  261
        clus
vv       C6ORF222 MUTATED C6ORF222 WILD-TYPE
  FEMALE                3                222
  MALE                  3                261
[1] 2 2
[1] FALSE
D1184V9, binary
                    cls
clus                   0   1
  C6ORF222 MUTATED     5   0
  C6ORF222 WILD-TYPE 345  22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C6ORF222 MUTATED      5    0
  C6ORF222 WILD-TYPE  345   22
     clus
vv    C6ORF222 MUTATED C6ORF222 WILD-TYPE
  NO                 5                345
  YES                0                 22
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  C6ORF222 MUTATED                      5                             1
  C6ORF222 WILD-TYPE                  310                            46
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  C6ORF222 MUTATED                       0                              0
  C6ORF222 WILD-TYPE                   106                             10
D1184V10, multiclass
                                clus
vv                               C6ORF222 MUTATED C6ORF222 WILD-TYPE
  COLON ADENOCARCINOMA                          5                310
  COLON MUCINOUS ADENOCARCINOMA                 1                 46
  RECTAL ADENOCARCINOMA                         0                106
  RECTAL MUCINOUS ADENOCARCINOMA                0                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  C6ORF222 MUTATED     5   0   0   0
  C6ORF222 WILD-TYPE 340   4  31  25
D1184V11, multiclass
    clus
vv   C6ORF222 MUTATED C6ORF222 WILD-TYPE
  R0                5                340
  R1                0                  4
  R2                0                 31
  RX                0                 25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1184V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C6ORF222 MUTATED                                  0     0
  C6ORF222 WILD-TYPE                                1    11
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  C6ORF222 MUTATED                           0     2
  C6ORF222 WILD-TYPE                        22   224
D1184V13, multiclass
[1] "Remove cluster labels:" "C6ORF222 MUTATED"      
clus
  C6ORF222 MUTATED C6ORF222 WILD-TYPE 
                 2                258 
        TCGA-A6-2671         TCGA-A6-2672         TCGA-A6-2674 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-A6-2676         TCGA-A6-2677         TCGA-A6-2678 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-A6-2683         TCGA-A6-3807         TCGA-A6-3808 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-A6-3809         TCGA-A6-3810         TCGA-A6-4105 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-A6-5656         TCGA-A6-5657         TCGA-A6-5659 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-A6-5660         TCGA-A6-5661         TCGA-A6-5662 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-A6-5664         TCGA-A6-5666         TCGA-A6-6137 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-A6-6138         TCGA-A6-6141         TCGA-A6-6142 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-A6-6648         TCGA-A6-6649         TCGA-A6-6651 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-A6-6652         TCGA-A6-6654         TCGA-A6-6780 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-A6-6781         TCGA-A6-6782         TCGA-AD-5900 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-AD-6548         TCGA-AD-6888         TCGA-AD-6889 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-AD-6890         TCGA-AD-6895         TCGA-AD-6899 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-AD-6901         TCGA-AD-6963         TCGA-AD-6964 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-AD-6965         TCGA-AU-3779         TCGA-AU-6004 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-AY-4070         TCGA-AY-4071         TCGA-AY-5543 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-AY-6196         TCGA-AY-6197         TCGA-AY-6386 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-AZ-4315         TCGA-AZ-4323         TCGA-AZ-4616 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-AZ-4681         TCGA-AZ-4682         TCGA-AZ-5403 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-AZ-5407         TCGA-AZ-6598         TCGA-AZ-6599 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-AZ-6600         TCGA-AZ-6601         TCGA-AZ-6603 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-AZ-6605         TCGA-AZ-6606         TCGA-AZ-6607 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-AZ-6608         TCGA-CA-5254         TCGA-CA-5255 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-CA-5796         TCGA-CA-5797         TCGA-CA-6715 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-CA-6716         TCGA-CA-6717         TCGA-CA-6718 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-CA-6719         TCGA-CK-4947         TCGA-CK-4948 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-CK-4950         TCGA-CK-4952         TCGA-CK-5912 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-CK-5913         TCGA-CK-5914         TCGA-CK-5915 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-CK-5916         TCGA-CK-6746         TCGA-CK-6747 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-CK-6748         TCGA-CK-6751         TCGA-CM-4743 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-CM-4744         TCGA-CM-4746         TCGA-CM-4747 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-CM-4752         TCGA-CM-5341         TCGA-CM-5344 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-CM-5348         TCGA-CM-5349         TCGA-CM-5860 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-CM-5861         TCGA-CM-5862         TCGA-CM-5863 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-CM-5864         TCGA-CM-5868         TCGA-CM-6161 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-CM-6162         TCGA-CM-6163         TCGA-CM-6164 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-CM-6165         TCGA-CM-6166         TCGA-CM-6167 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-CM-6168         TCGA-CM-6169         TCGA-CM-6170 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-CM-6171         TCGA-CM-6172         TCGA-CM-6674 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-CM-6675         TCGA-CM-6676         TCGA-CM-6677 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-CM-6678         TCGA-CM-6679         TCGA-CM-6680 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-D5-5537         TCGA-D5-5538         TCGA-D5-5539 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-D5-5540         TCGA-D5-5541         TCGA-D5-6529 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-D5-6532         TCGA-D5-6533         TCGA-D5-6534 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-D5-6535         TCGA-D5-6536         TCGA-D5-6537 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-D5-6538         TCGA-D5-6539         TCGA-D5-6540 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-D5-6541         TCGA-D5-6898         TCGA-D5-6920 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-D5-6922         TCGA-D5-6923         TCGA-D5-6924 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-D5-6926         TCGA-D5-6927         TCGA-D5-6928 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-D5-6929         TCGA-D5-6930         TCGA-D5-6931 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-D5-6932         TCGA-D5-7000         TCGA-DM-A0X9 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-DM-A0XD         TCGA-DM-A0XF         TCGA-DM-A1D0 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-DM-A1D4         TCGA-DM-A1D6         TCGA-DM-A1D7 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-DM-A1D8         TCGA-DM-A1D9         TCGA-DM-A1DA 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-DM-A1DB         TCGA-DM-A1HA         TCGA-DM-A1HB 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-DM-A282         TCGA-DM-A285         TCGA-DM-A28C 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-DM-A28E         TCGA-DM-A28F         TCGA-DM-A28G 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-DM-A28H         TCGA-DM-A28K         TCGA-F4-6459 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-F4-6460         TCGA-F4-6569         TCGA-F4-6570 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-F4-6703         TCGA-F4-6704         TCGA-F4-6805 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-F4-6806         TCGA-F4-6807         TCGA-F4-6808 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-F4-6809         TCGA-F4-6854         TCGA-F4-6855 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-F4-6856         TCGA-G4-6293         TCGA-G4-6299 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-G4-6303         TCGA-G4-6304         TCGA-G4-6306 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-G4-6307         TCGA-G4-6309         TCGA-G4-6310 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-G4-6315         TCGA-G4-6317         TCGA-G4-6321 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-G4-6323         TCGA-G4-6586         TCGA-G4-6588 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-G4-6625         TCGA-G4-6626         TCGA-G4-6628 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2691 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-AF-2692         TCGA-AF-2693         TCGA-AF-3400 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-AF-3913         TCGA-AF-4110         TCGA-AF-5654 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-AF-6136         TCGA-AF-6655         TCGA-AF-6672 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6549 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-AH-6643         TCGA-AH-6644         TCGA-CI-6619 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-CI-6620         TCGA-CI-6621         TCGA-CI-6622 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-CI-6624         TCGA-CL-5917         TCGA-CL-5918 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-DC-5337         TCGA-DC-5869         TCGA-DC-6155 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-DC-6157         TCGA-DC-6158         TCGA-DC-6160 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-DC-6681         TCGA-DC-6682         TCGA-DC-6683 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-DT-5265         TCGA-DY-A0XA         TCGA-DY-A1DC 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-DY-A1DD         TCGA-DY-A1DF         TCGA-DY-A1DG 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-DY-A1H8         TCGA-EF-5830         TCGA-EI-6506 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6510 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-F5-6464         TCGA-F5-6465         TCGA-F5-6571 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6811         TCGA-F5-6812 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 
        TCGA-F5-6813         TCGA-G5-6235         TCGA-G5-6641 
"C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" "C6ORF222 WILD-TYPE" 

Clustering(1185) Variable = ANKRD26 MUTATION ANALYSIS
D1185V1, survival
                   sevent
clus2                 0   1
  ANKRD26 MUTATED    20   2
  ANKRD26 WILD-TYPE 358  91
  ANKRD26 MUTATED ANKRD26 WILD-TYPE 
               22               449 
  ANKRD26 MUTATED ANKRD26 WILD-TYPE 
                2                91 
$`ANKRD26 MUTATED`
TCGA-A6-3809 TCGA-A6-5659 TCGA-AA-3663 TCGA-AA-3710 TCGA-AA-3977 TCGA-AA-A00N 
       32.75        30.44         6.97        26.99        25.02         4.01 
TCGA-AA-A010 TCGA-AD-6889 TCGA-AZ-4315 TCGA-CA-6717 TCGA-CK-6748 TCGA-CM-4744 
       34.98        56.55        58.39        12.76         1.91        20.02 
TCGA-CM-5860 TCGA-CM-6162 TCGA-D5-5539 TCGA-DM-A1D4 TCGA-DM-A28K TCGA-G4-6588 
       32.02        12.00        19.59        92.75        98.24        26.17 
TCGA-AG-A002 TCGA-AH-6544 TCGA-CI-6624 TCGA-EI-6510 
       20.98        38.56         4.73        18.28 

$`ANKRD26 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       31.63        29.19        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       85.05        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       15.52         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       33.01        21.44        17.82         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 
       49.08        51.32         9.99        21.14        82.95       124.27 
TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       23.05        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       22.98        30.08        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       17.03        15.02         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       12.03        45.40        12.26        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       24.43        38.20       130.65        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       22.09        13.78        35.80        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       41.00        38.04       117.11         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CL-5917 TCGA-CL-5918 
        0.72         6.05        33.17         6.97        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       19.96        20.91         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  ANKRD26 MUTATED ANKRD26 WILD-TYPE 
             1.91              0.00 
  ANKRD26 MUTATED ANKRD26 WILD-TYPE 
            98.24            148.01 
  ANKRD26 MUTATED ANKRD26 WILD-TYPE 
           25.595            20.050 
[1] "1.9 - 98.2 (25.6)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "2.5"
D1185V2, continuous
D1185V3, binary
                   cls
clus                  0   1
  ANKRD26 MUTATED    19   4
  ANKRD26 WILD-TYPE 347 115
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD26 MUTATED     19    4
  ANKRD26 WILD-TYPE  347  115
        clus
vv       ANKRD26 MUTATED ANKRD26 WILD-TYPE
  COLON               19               347
  RECTUM               4               115
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ANKRD26 MUTATED         5        0        1         8         3         0
  ANKRD26 WILD-TYPE      86        1       31       130         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ANKRD26 MUTATED           0          1          1          0        1
  ANKRD26 WILD-TYPE        24         10         58         42       47
                   vv
clus                STAGE IVA STAGE IVB
  ANKRD26 MUTATED           1         0
  ANKRD26 WILD-TYPE        17         1
D1185V4, multiclass
            clus
vv           ANKRD26 MUTATED ANKRD26 WILD-TYPE
  STAGE I                  5                86
  STAGE IA                 0                 1
  STAGE II                 1                31
  STAGE IIA                8               130
  STAGE IIB                3                 7
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               1                10
  STAGE IIIB               1                58
  STAGE IIIC               0                42
  STAGE IV                 1                47
  STAGE IVA                1                17
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  ANKRD26 MUTATED     0   7  13   3
  ANKRD26 WILD-TYPE  17  85 316  47
D1185V5, multiclass
    clus
vv   ANKRD26 MUTATED ANKRD26 WILD-TYPE
  T1               0                17
  T2               7                85
  T3              13               316
  T4               3                47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  ANKRD26 MUTATED    19   4   0
  ANKRD26 WILD-TYPE 268 109  87
D1185V6, multiclass
    clus
vv   ANKRD26 MUTATED ANKRD26 WILD-TYPE
  N0              19               268
  N1               4               109
  N2               0                87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1185V7, binary
                   cls
clus                  0   1
  ANKRD26 MUTATED    18   2
  ANKRD26 WILD-TYPE 357  63
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD26 MUTATED     18    2
  ANKRD26 WILD-TYPE  357   63
   clus
vv  ANKRD26 MUTATED ANKRD26 WILD-TYPE
  0              18               357
  1               2                63
[1] 2 2
[1] FALSE
D1185V8, binary
                   cls
clus                  0   1
  ANKRD26 MUTATED     8  15
  ANKRD26 WILD-TYPE 217 249
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD26 MUTATED      8   15
  ANKRD26 WILD-TYPE  217  249
        clus
vv       ANKRD26 MUTATED ANKRD26 WILD-TYPE
  FEMALE               8               217
  MALE                15               249
[1] 2 2
[1] FALSE
D1185V9, binary
                   cls
clus                  0   1
  ANKRD26 MUTATED    17   0
  ANKRD26 WILD-TYPE 333  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD26 MUTATED     17    0
  ANKRD26 WILD-TYPE  333   22
     clus
vv    ANKRD26 MUTATED ANKRD26 WILD-TYPE
  NO               17               333
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ANKRD26 MUTATED                     12                             7
  ANKRD26 WILD-TYPE                  303                            40
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ANKRD26 MUTATED                       4                              0
  ANKRD26 WILD-TYPE                   102                             10
D1185V10, multiclass
                                clus
vv                               ANKRD26 MUTATED ANKRD26 WILD-TYPE
  COLON ADENOCARCINOMA                        12               303
  COLON MUCINOUS ADENOCARCINOMA                7                40
  RECTAL ADENOCARCINOMA                        4               102
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  ANKRD26 MUTATED    14   0   0   3
  ANKRD26 WILD-TYPE 331   4  31  22
D1185V11, multiclass
    clus
vv   ANKRD26 MUTATED ANKRD26 WILD-TYPE
  R0              14               331
  R1               0                 4
  R2               0                31
  RX               3                22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1185V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ANKRD26 MUTATED                                  0     2
  ANKRD26 WILD-TYPE                                1     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  ANKRD26 MUTATED                           0    15
  ANKRD26 WILD-TYPE                        22   211
D1185V13, multiclass
                                  clus
vv                                 ANKRD26 MUTATED ANKRD26 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          2                 9
  BLACK OR AFRICAN AMERICAN                      0                22
  WHITE                                         15               211
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1186) Variable = TDRD7 MUTATION ANALYSIS
D1186V1, survival
                 sevent
clus2               0   1
  TDRD7 MUTATED    13   3
  TDRD7 WILD-TYPE 365  90
  TDRD7 MUTATED TDRD7 WILD-TYPE 
             16             455 
  TDRD7 MUTATED TDRD7 WILD-TYPE 
              3              90 
$`TDRD7 MUTATED`
TCGA-A6-5659 TCGA-A6-5665 TCGA-A6-6141 TCGA-AA-3492 TCGA-AA-3681 TCGA-AA-3710 
       30.44        22.06         8.38         3.02         5.98        26.99 
TCGA-AA-A00N TCGA-AA-A010 TCGA-AZ-4315 TCGA-AZ-6601 TCGA-CA-6717 TCGA-CM-5864 
        4.01        34.98        58.39       100.01        12.76        15.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-D5-6532 TCGA-AG-A002 
       15.02        14.04        18.25        20.98 

$`TDRD7 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        29.19        33.53        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       32.71        27.09        22.52        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
       20.28         7.04         1.02        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 
       37.05        19.00        36.00         5.03        85.05        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       33.01        21.44        17.82         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07        12.20        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6172 
       16.04        21.99        14.99        12.99        13.02        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       20.19         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  TDRD7 MUTATED TDRD7 WILD-TYPE 
           3.02            0.00 
  TDRD7 MUTATED TDRD7 WILD-TYPE 
         100.01          148.01 
  TDRD7 MUTATED TDRD7 WILD-TYPE 
         16.635          20.280 
[1] "3.0 - 100.0 (16.6)" "0.0 - 148.0 (20.3)"
[1] "hr=" "1"  
D1186V2, continuous
D1186V3, binary
                 cls
clus                0   1
  TDRD7 MUTATED    15   1
  TDRD7 WILD-TYPE 351 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TDRD7 MUTATED     15    1
  TDRD7 WILD-TYPE  351  118
        clus
vv       TDRD7 MUTATED TDRD7 WILD-TYPE
  COLON             15             351
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TDRD7 MUTATED         5        0        2         6         2         0
  TDRD7 WILD-TYPE      86        1       30       132         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TDRD7 MUTATED           1          0          0          0        0         0
  TDRD7 WILD-TYPE        23         11         59         42       48        18
                 vv
clus              STAGE IVB
  TDRD7 MUTATED           0
  TDRD7 WILD-TYPE         1
D1186V4, multiclass
            clus
vv           TDRD7 MUTATED TDRD7 WILD-TYPE
  STAGE I                5              86
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA              6             132
  STAGE IIB              2               8
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  TDRD7 MUTATED     0   5   9   2
  TDRD7 WILD-TYPE  17  87 320  48
D1186V5, multiclass
    clus
vv   TDRD7 MUTATED TDRD7 WILD-TYPE
  T1             0              17
  T2             5              87
  T3             9             320
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  TDRD7 MUTATED    15   1   0
  TDRD7 WILD-TYPE 272 112  87
D1186V6, multiclass
    clus
vv   TDRD7 MUTATED TDRD7 WILD-TYPE
  N0            15             272
  N1             1             112
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1186V7, binary
                 cls
clus                0   1
  TDRD7 MUTATED    16   0
  TDRD7 WILD-TYPE 359  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TDRD7 MUTATED     16    0
  TDRD7 WILD-TYPE  359   65
   clus
vv  TDRD7 MUTATED TDRD7 WILD-TYPE
  0            16             359
  1             0              65
[1] 2 2
[1] FALSE
D1186V8, binary
                 cls
clus                0   1
  TDRD7 MUTATED     7   9
  TDRD7 WILD-TYPE 218 255
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TDRD7 MUTATED      7    9
  TDRD7 WILD-TYPE  218  255
        clus
vv       TDRD7 MUTATED TDRD7 WILD-TYPE
  FEMALE             7             218
  MALE               9             255
[1] 2 2
[1] FALSE
D1186V9, binary
                 cls
clus                0   1
  TDRD7 MUTATED    15   0
  TDRD7 WILD-TYPE 335  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TDRD7 MUTATED     15    0
  TDRD7 WILD-TYPE  335   22
     clus
vv    TDRD7 MUTATED TDRD7 WILD-TYPE
  NO             15             335
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  TDRD7 MUTATED                     13                             2
  TDRD7 WILD-TYPE                  302                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  TDRD7 MUTATED                       1                              0
  TDRD7 WILD-TYPE                   105                             10
D1186V10, multiclass
                                clus
vv                               TDRD7 MUTATED TDRD7 WILD-TYPE
  COLON ADENOCARCINOMA                      13             302
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  TDRD7 MUTATED    13   0   0   1
  TDRD7 WILD-TYPE 332   4  31  24
D1186V11, multiclass
    clus
vv   TDRD7 MUTATED TDRD7 WILD-TYPE
  R0            13             332
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1186V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TDRD7 MUTATED                                  0     1
  TDRD7 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  TDRD7 MUTATED                           1     8
  TDRD7 WILD-TYPE                        21   218
D1186V13, multiclass
                                  clus
vv                                 TDRD7 MUTATED TDRD7 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        8             218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1187) Variable = MFSD6 MUTATION ANALYSIS
D1187V1, survival
                 sevent
clus2               0   1
  MFSD6 MUTATED     7   1
  MFSD6 WILD-TYPE 371  92
  MFSD6 MUTATED MFSD6 WILD-TYPE 
              8             463 
  MFSD6 MUTATED MFSD6 WILD-TYPE 
              1              92 
$`MFSD6 MUTATED`
TCGA-A6-5662 TCGA-AA-3949 TCGA-AD-5900 TCGA-AZ-4616 TCGA-D5-6533 TCGA-D5-6539 
       23.61        26.01         0.07         5.13         1.32        12.49 
TCGA-F4-6808 TCGA-CI-6624 
       33.67         4.73 

$`MFSD6 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        33.53        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-3952 
        2.01        12.99        24.00        33.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       39.98        18.05        40.96        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82        58.39         1.41       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 
       43.27        15.12        17.85         4.80        17.13        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       41.42        16.24        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CL-5917 
        0.69         0.72         6.05        33.17         6.97        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  MFSD6 MUTATED MFSD6 WILD-TYPE 
           0.07            0.00 
  MFSD6 MUTATED MFSD6 WILD-TYPE 
          33.67          148.01 
  MFSD6 MUTATED MFSD6 WILD-TYPE 
           8.81           20.28 
[1] "0.1 - 33.7 (8.8)"   "0.0 - 148.0 (20.3)"
[1] "hr=" "1.3"
D1187V2, continuous
D1187V3, binary
                 cls
clus                0   1
  MFSD6 MUTATED     7   1
  MFSD6 WILD-TYPE 359 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MFSD6 MUTATED      7    1
  MFSD6 WILD-TYPE  359  118
        clus
vv       MFSD6 MUTATED MFSD6 WILD-TYPE
  COLON              7             359
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MFSD6 MUTATED         3        0        0         0         0         0
  MFSD6 WILD-TYPE      88        1       32       138        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MFSD6 MUTATED           0          1          2          0        1         1
  MFSD6 WILD-TYPE        24         10         57         42       47        17
                 vv
clus              STAGE IVB
  MFSD6 MUTATED           0
  MFSD6 WILD-TYPE         1
D1187V4, multiclass
            clus
vv           MFSD6 MUTATED MFSD6 WILD-TYPE
  STAGE I                3              88
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              0             138
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             1              10
  STAGE IIIB             2              57
  STAGE IIIC             0              42
  STAGE IV               1              47
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  MFSD6 MUTATED     1   2   4   1
  MFSD6 WILD-TYPE  16  90 325  49
D1187V5, multiclass
    clus
vv   MFSD6 MUTATED MFSD6 WILD-TYPE
  T1             1              16
  T2             2              90
  T3             4             325
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  MFSD6 MUTATED     5   1   2
  MFSD6 WILD-TYPE 282 112  85
D1187V6, multiclass
    clus
vv   MFSD6 MUTATED MFSD6 WILD-TYPE
  N0             5             282
  N1             1             112
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1187V7, binary
                 cls
clus                0   1
  MFSD6 MUTATED     5   2
  MFSD6 WILD-TYPE 370  63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MFSD6 MUTATED      5    2
  MFSD6 WILD-TYPE  370   63
   clus
vv  MFSD6 MUTATED MFSD6 WILD-TYPE
  0             5             370
  1             2              63
[1] 2 2
[1] FALSE
D1187V8, binary
                 cls
clus                0   1
  MFSD6 MUTATED     6   2
  MFSD6 WILD-TYPE 219 262
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MFSD6 MUTATED      6    2
  MFSD6 WILD-TYPE  219  262
        clus
vv       MFSD6 MUTATED MFSD6 WILD-TYPE
  FEMALE             6             219
  MALE               2             262
[1] 2 2
[1] FALSE
D1187V9, binary
                 cls
clus                0   1
  MFSD6 MUTATED     5   0
  MFSD6 WILD-TYPE 345  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MFSD6 MUTATED      5    0
  MFSD6 WILD-TYPE  345   22
     clus
vv    MFSD6 MUTATED MFSD6 WILD-TYPE
  NO              5             345
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MFSD6 MUTATED                      5                             2
  MFSD6 WILD-TYPE                  310                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MFSD6 MUTATED                       1                              0
  MFSD6 WILD-TYPE                   105                             10
D1187V10, multiclass
                                clus
vv                               MFSD6 MUTATED MFSD6 WILD-TYPE
  COLON ADENOCARCINOMA                       5             310
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  MFSD6 MUTATED     5   0   0   0
  MFSD6 WILD-TYPE 340   4  31  25
D1187V11, multiclass
    clus
vv   MFSD6 MUTATED MFSD6 WILD-TYPE
  R0             5             340
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1187V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MFSD6 MUTATED                                  0     0
  MFSD6 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  MFSD6 MUTATED                           0     7
  MFSD6 WILD-TYPE                        22   219
D1187V13, multiclass
                                  clus
vv                                 MFSD6 MUTATED MFSD6 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        7             219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1188) Variable = KIAA1632 MUTATION ANALYSIS
D1188V1, survival
                    sevent
clus2                  0   1
  KIAA1632 MUTATED    23   6
  KIAA1632 WILD-TYPE 355  87
  KIAA1632 MUTATED KIAA1632 WILD-TYPE 
                29                442 
  KIAA1632 MUTATED KIAA1632 WILD-TYPE 
                 6                 87 
$`KIAA1632 MUTATED`
TCGA-A6-5659 TCGA-A6-5666 TCGA-A6-6141 TCGA-AA-3655 TCGA-AA-3680 TCGA-AA-3815 
       30.44        32.71         8.38        61.02        11.01        33.04 
TCGA-AA-3818 TCGA-AA-3845 TCGA-AA-3864 TCGA-AA-3966 TCGA-AA-3972 TCGA-AA-A00N 
        0.99         0.00        53.00         2.01        50.99         4.01 
TCGA-AA-A010 TCGA-AA-A01R TCGA-AD-5900 TCGA-AZ-4315 TCGA-CA-6717 TCGA-CK-4952 
       34.98        35.01         0.07        58.39        12.76        15.62 
TCGA-CK-6751 TCGA-CM-6161 TCGA-DM-A1D4 TCGA-DM-A1D7 TCGA-G4-6628 TCGA-AF-4110 
      124.27        15.02        92.75        13.32        79.69        14.50 
TCGA-AG-3732 TCGA-AG-3892 TCGA-AG-A002 TCGA-AG-A036 TCGA-G5-6235 
       32.98        13.02        20.98       117.11        55.76 

$`KIAA1632 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       22.06        27.09        22.52        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       19.99        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3681 
       14.01         0.92        50.04        47.01        15.02         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3819 TCGA-AA-3821 
       19.04        19.04        10.06        35.05        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 
       17.98        15.95        38.99        37.02        14.93        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 
        0.99        31.07        31.07        30.05        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       34.03        21.99        16.08        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S 
       12.00        31.00        31.00        38.07         1.02         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       39.98        18.05        40.96        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07        12.20        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 
       14.30        17.56       148.01        85.45        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CM-4743 TCGA-CM-4744 
        9.99        21.14        82.95         1.91        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       17.03        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-DM-A1D8 
      119.70        24.43        38.20       130.65        49.91        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       46.75        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       34.49        10.39        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 
       13.94        19.99         7.99         0.99        37.02         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       17.03        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6641 
       32.19         0.66         0.69        26.43 

  KIAA1632 MUTATED KIAA1632 WILD-TYPE 
                 0                  0 
  KIAA1632 MUTATED KIAA1632 WILD-TYPE 
            124.27             148.01 
  KIAA1632 MUTATED KIAA1632 WILD-TYPE 
            30.440             20.085 
[1] "0.0 - 124.3 (30.4)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.3"
D1188V2, continuous
D1188V3, binary
                    cls
clus                   0   1
  KIAA1632 MUTATED    24   6
  KIAA1632 WILD-TYPE 342 113
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1632 MUTATED     24    6
  KIAA1632 WILD-TYPE  342  113
        clus
vv       KIAA1632 MUTATED KIAA1632 WILD-TYPE
  COLON                24                342
  RECTUM                6                113
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KIAA1632 MUTATED         8        0        2        10         2         1
  KIAA1632 WILD-TYPE      83        1       30       128         8         0
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIAA1632 MUTATED           3          0          1          1        2
  KIAA1632 WILD-TYPE        21         11         58         41       46
                    vv
clus                 STAGE IVA STAGE IVB
  KIAA1632 MUTATED           1         0
  KIAA1632 WILD-TYPE        17         1
D1188V4, multiclass
            clus
vv           KIAA1632 MUTATED KIAA1632 WILD-TYPE
  STAGE I                   8                 83
  STAGE IA                  0                  1
  STAGE II                  2                 30
  STAGE IIA                10                128
  STAGE IIB                 2                  8
  STAGE IIC                 1                  0
  STAGE III                 3                 21
  STAGE IIIA                0                 11
  STAGE IIIB                1                 58
  STAGE IIIC                1                 41
  STAGE IV                  2                 46
  STAGE IVA                 1                 17
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  KIAA1632 MUTATED     1   7  17   6
  KIAA1632 WILD-TYPE  16  85 312  44
D1188V5, multiclass
    clus
vv   KIAA1632 MUTATED KIAA1632 WILD-TYPE
  T1                1                 16
  T2                7                 85
  T3               17                312
  T4                6                 44
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  KIAA1632 MUTATED    23   3   5
  KIAA1632 WILD-TYPE 264 110  82
D1188V6, multiclass
    clus
vv   KIAA1632 MUTATED KIAA1632 WILD-TYPE
  N0               23                264
  N1                3                110
  N2                5                 82
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1188V7, binary
                    cls
clus                   0   1
  KIAA1632 MUTATED    24   2
  KIAA1632 WILD-TYPE 351  63
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1632 MUTATED     24    2
  KIAA1632 WILD-TYPE  351   63
   clus
vv  KIAA1632 MUTATED KIAA1632 WILD-TYPE
  0               24                351
  1                2                 63
[1] 2 2
[1] FALSE
D1188V8, binary
                    cls
clus                   0   1
  KIAA1632 MUTATED    12  19
  KIAA1632 WILD-TYPE 213 245
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1632 MUTATED     12   19
  KIAA1632 WILD-TYPE  213  245
        clus
vv       KIAA1632 MUTATED KIAA1632 WILD-TYPE
  FEMALE               12                213
  MALE                 19                245
[1] 2 2
[1] FALSE
D1188V9, binary
                    cls
clus                   0   1
  KIAA1632 MUTATED    19   2
  KIAA1632 WILD-TYPE 331  20
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1632 MUTATED     19    2
  KIAA1632 WILD-TYPE  331   20
     clus
vv    KIAA1632 MUTATED KIAA1632 WILD-TYPE
  NO                19                331
  YES                2                 20
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  KIAA1632 MUTATED                     16                             7
  KIAA1632 WILD-TYPE                  299                            40
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  KIAA1632 MUTATED                       6                              0
  KIAA1632 WILD-TYPE                   100                             10
D1188V10, multiclass
                                clus
vv                               KIAA1632 MUTATED KIAA1632 WILD-TYPE
  COLON ADENOCARCINOMA                         16                299
  COLON MUCINOUS ADENOCARCINOMA                 7                 40
  RECTAL ADENOCARCINOMA                         6                100
  RECTAL MUCINOUS ADENOCARCINOMA                0                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  KIAA1632 MUTATED    19   1   2   3
  KIAA1632 WILD-TYPE 326   3  29  22
D1188V11, multiclass
    clus
vv   KIAA1632 MUTATED KIAA1632 WILD-TYPE
  R0               19                326
  R1                1                  3
  R2                2                 29
  RX                3                 22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1188V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KIAA1632 MUTATED                                  0     1
  KIAA1632 WILD-TYPE                                1    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  KIAA1632 MUTATED                           1    13
  KIAA1632 WILD-TYPE                        21   213
D1188V13, multiclass
                                  clus
vv                                 KIAA1632 MUTATED KIAA1632 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                 10
  BLACK OR AFRICAN AMERICAN                       1                 21
  WHITE                                          13                213
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1189) Variable = ADK MUTATION ANALYSIS
D1189V1, survival
               sevent
clus2             0   1
  ADK MUTATED     7   0
  ADK WILD-TYPE 371  93
  ADK MUTATED ADK WILD-TYPE 
            7           464 
  ADK MUTATED ADK WILD-TYPE 
            0            93 
$`ADK MUTATED`
TCGA-AA-A010 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-CA-5254 TCGA-CM-5349 
       34.98        21.44        17.82        58.39        12.69        30.08 
TCGA-G4-6588 
       26.17 

$`ADK WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
        0.95        33.01         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5255 
       29.56         5.23        11.74         3.19         1.61         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.03        22.98        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       13.78        35.80        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  ADK MUTATED ADK WILD-TYPE 
        12.69          0.00 
  ADK MUTATED ADK WILD-TYPE 
        58.39        148.01 
  ADK MUTATED ADK WILD-TYPE 
       26.170        20.085 
[1] "12.7 - 58.4 (26.2)" "0.0 - 148.0 (20.1)"
[1] "hr="     "9100000"
D1189V2, continuous
D1189V3, binary
               cls
clus              0   1
  ADK MUTATED     7   0
  ADK WILD-TYPE 359 119
[1] "tbl2"
               cls
clus            [,1] [,2]
  ADK MUTATED      7    0
  ADK WILD-TYPE  359  119
        clus
vv       ADK MUTATED ADK WILD-TYPE
  COLON            7           359
  RECTUM           0           119
[1] 2 2
[1] FALSE
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ADK MUTATED         0        0        0         5         1         0
  ADK WILD-TYPE      91        1       32       133         9         1
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ADK MUTATED           0          0          1          0        0         0
  ADK WILD-TYPE        24         11         58         42       48        18
               vv
clus            STAGE IVB
  ADK MUTATED           0
  ADK WILD-TYPE         1
D1189V4, multiclass
            clus
vv           ADK MUTATED ADK WILD-TYPE
  STAGE I              0            91
  STAGE IA             0             1
  STAGE II             0            32
  STAGE IIA            5           133
  STAGE IIB            1             9
  STAGE IIC            0             1
  STAGE III            0            24
  STAGE IIIA           0            11
  STAGE IIIB           1            58
  STAGE IIIC           0            42
  STAGE IV             0            48
  STAGE IVA            0            18
  STAGE IVB            0             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  ADK MUTATED     0   0   6   1
  ADK WILD-TYPE  17  92 323  49
D1189V5, multiclass
    clus
vv   ADK MUTATED ADK WILD-TYPE
  T1           0            17
  T2           0            92
  T3           6           323
  T4           1            49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2
  ADK MUTATED     6   1   0
  ADK WILD-TYPE 281 112  87
D1189V6, multiclass
    clus
vv   ADK MUTATED ADK WILD-TYPE
  N0           6           281
  N1           1           112
  N2           0            87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1189V7, binary
               cls
clus              0   1
  ADK MUTATED     6   0
  ADK WILD-TYPE 369  65
[1] "tbl2"
               cls
clus            [,1] [,2]
  ADK MUTATED      6    0
  ADK WILD-TYPE  369   65
   clus
vv  ADK MUTATED ADK WILD-TYPE
  0           6           369
  1           0            65
[1] 2 2
[1] FALSE
D1189V8, binary
               cls
clus              0   1
  ADK MUTATED     5   2
  ADK WILD-TYPE 220 262
[1] "tbl2"
               cls
clus            [,1] [,2]
  ADK MUTATED      5    2
  ADK WILD-TYPE  220  262
        clus
vv       ADK MUTATED ADK WILD-TYPE
  FEMALE           5           220
  MALE             2           262
[1] 2 2
[1] FALSE
D1189V9, binary
               cls
clus              0   1
  ADK MUTATED     7   0
  ADK WILD-TYPE 343  22
[1] "tbl2"
               cls
clus            [,1] [,2]
  ADK MUTATED      7    0
  ADK WILD-TYPE  343   22
     clus
vv    ADK MUTATED ADK WILD-TYPE
  NO            7           343
  YES           0            22
[1] 2 2
[1] FALSE
               vv
clus            COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ADK MUTATED                      7                             0
  ADK WILD-TYPE                  308                            47
               vv
clus            RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ADK MUTATED                       0                              0
  ADK WILD-TYPE                   106                             10
D1189V10, multiclass
                                clus
vv                               ADK MUTATED ADK WILD-TYPE
  COLON ADENOCARCINOMA                     7           308
  COLON MUCINOUS ADENOCARCINOMA            0            47
  RECTAL ADENOCARCINOMA                    0           106
  RECTAL MUCINOUS ADENOCARCINOMA           0            10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             R0  R1  R2  RX
  ADK MUTATED     6   0   0   1
  ADK WILD-TYPE 339   4  31  24
D1189V11, multiclass
    clus
vv   ADK MUTATED ADK WILD-TYPE
  R0           6           339
  R1           0             4
  R2           0            31
  RX           1            24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1189V12, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ADK MUTATED                                  0     1
  ADK WILD-TYPE                                1    10
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  ADK MUTATED                           1     4
  ADK WILD-TYPE                        21   222
D1189V13, multiclass
                                  clus
vv                                 ADK MUTATED ADK WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      1            10
  BLACK OR AFRICAN AMERICAN                  1            21
  WHITE                                      4           222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1190) Variable = PTPRB MUTATION ANALYSIS
D1190V1, survival
                 sevent
clus2               0   1
  PTPRB MUTATED    14   1
  PTPRB WILD-TYPE 364  92
  PTPRB MUTATED PTPRB WILD-TYPE 
             15             456 
  PTPRB MUTATED PTPRB WILD-TYPE 
              1              92 
$`PTPRB MUTATED`
TCGA-A6-5659 TCGA-A6-6653 TCGA-AA-3510 TCGA-AA-3713 TCGA-AA-3845 TCGA-AA-3864 
       30.44        24.39        63.98        19.04         0.00        53.00 
TCGA-AA-3949 TCGA-AU-6004 TCGA-CA-6717 TCGA-CM-4743 TCGA-D5-6928 TCGA-D5-6930 
       26.01        27.09        12.76        23.05        11.64         1.51 
TCGA-DM-A1D0 TCGA-G4-6293 TCGA-AH-6549 
      130.65       133.18        17.49 

$`PTPRB WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 
       25.18        24.16        21.76        24.69        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       85.05        26.99        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02        14.93        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       30.05        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3950 
       31.00         2.01        12.99        24.00        33.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 
       27.42        10.88         0.20        14.50        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.20        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
        1.91       124.27        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6931 
       12.43        14.30         9.04         9.44         4.80        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D4 
       11.38        10.26       119.70        24.43        38.20        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 
       38.04       117.11        38.56         1.45         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  PTPRB MUTATED PTPRB WILD-TYPE 
              0               0 
  PTPRB MUTATED PTPRB WILD-TYPE 
         133.18          148.01 
  PTPRB MUTATED PTPRB WILD-TYPE 
         24.390          20.085 
[1] "0.0 - 133.2 (24.4)" "0.0 - 148.0 (20.1)"
[1] "hr=" "4.1"
D1190V2, continuous
D1190V3, binary
                 cls
clus                0   1
  PTPRB MUTATED    17   1
  PTPRB WILD-TYPE 349 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPRB MUTATED     17    1
  PTPRB WILD-TYPE  349  118
        clus
vv       PTPRB MUTATED PTPRB WILD-TYPE
  COLON             17             349
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PTPRB MUTATED         4        0        2         7         0         0
  PTPRB WILD-TYPE      87        1       30       131        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PTPRB MUTATED           1          0          1          1        1         0
  PTPRB WILD-TYPE        23         11         58         41       47        18
                 vv
clus              STAGE IVB
  PTPRB MUTATED           0
  PTPRB WILD-TYPE         1
D1190V4, multiclass
            clus
vv           PTPRB MUTATED PTPRB WILD-TYPE
  STAGE I                4              87
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA              7             131
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             1              41
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PTPRB MUTATED     0   4  14   0
  PTPRB WILD-TYPE  17  88 315  50
D1190V5, multiclass
    clus
vv   PTPRB MUTATED PTPRB WILD-TYPE
  T1             0              17
  T2             4              88
  T3            14             315
  T4             0              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  PTPRB MUTATED    14   2   1
  PTPRB WILD-TYPE 273 111  86
D1190V6, multiclass
    clus
vv   PTPRB MUTATED PTPRB WILD-TYPE
  N0            14             273
  N1             2             111
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1190V7, binary
                 cls
clus                0   1
  PTPRB MUTATED    14   1
  PTPRB WILD-TYPE 361  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPRB MUTATED     14    1
  PTPRB WILD-TYPE  361   64
   clus
vv  PTPRB MUTATED PTPRB WILD-TYPE
  0            14             361
  1             1              64
[1] 2 2
[1] FALSE
D1190V8, binary
                 cls
clus                0   1
  PTPRB MUTATED     6  12
  PTPRB WILD-TYPE 219 252
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPRB MUTATED      6   12
  PTPRB WILD-TYPE  219  252
        clus
vv       PTPRB MUTATED PTPRB WILD-TYPE
  FEMALE             6             219
  MALE              12             252
[1] 2 2
[1] FALSE
D1190V9, binary
                 cls
clus                0   1
  PTPRB MUTATED    10   1
  PTPRB WILD-TYPE 340  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPRB MUTATED     10    1
  PTPRB WILD-TYPE  340   21
     clus
vv    PTPRB MUTATED PTPRB WILD-TYPE
  NO             10             340
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PTPRB MUTATED                     12                             5
  PTPRB WILD-TYPE                  303                            42
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PTPRB MUTATED                       1                              0
  PTPRB WILD-TYPE                   105                             10
D1190V10, multiclass
                                clus
vv                               PTPRB MUTATED PTPRB WILD-TYPE
  COLON ADENOCARCINOMA                      12             303
  COLON MUCINOUS ADENOCARCINOMA              5              42
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  PTPRB MUTATED    12   0   1   3
  PTPRB WILD-TYPE 333   4  30  22
D1190V11, multiclass
    clus
vv   PTPRB MUTATED PTPRB WILD-TYPE
  R0            12             333
  R1             0               4
  R2             1              30
  RX             3              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1190V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PTPRB MUTATED                                  0     1
  PTPRB WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PTPRB MUTATED                           0    11
  PTPRB WILD-TYPE                        22   215
D1190V13, multiclass
                                  clus
vv                                 PTPRB MUTATED PTPRB WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                       11             215
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1191) Variable = ZNF280C MUTATION ANALYSIS
D1191V1, survival
                   sevent
clus2                 0   1
  ZNF280C MUTATED    11   3
  ZNF280C WILD-TYPE 367  90
  ZNF280C MUTATED ZNF280C WILD-TYPE 
               14               457 
  ZNF280C MUTATED ZNF280C WILD-TYPE 
                3                90 
$`ZNF280C MUTATED`
TCGA-A6-5665 TCGA-A6-5666 TCGA-AA-3518 TCGA-AA-3866 TCGA-AZ-4315 TCGA-CM-6168 
       22.06        32.71         1.02        17.03        58.39        12.99 
TCGA-CM-6678 TCGA-F4-6460 TCGA-G4-6628 TCGA-AF-4110 TCGA-AG-3892 TCGA-AG-A002 
       11.01        31.96        79.69        14.50        13.02        20.98 
TCGA-AG-A026 TCGA-DC-6158 
        1.94        10.98 

$`ZNF280C WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       22.09        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3519 
       63.98         6.97         1.02        13.02        38.99         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3867 TCGA-AA-3869 
       31.07        31.07        30.05        53.00        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6169 TCGA-CM-6170 
       29.03        16.04        21.99        14.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6569 
       35.97        60.79       117.07        98.24         8.61        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       26.17        91.79        46.75        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6136 
       13.55        19.10        34.49        10.39        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 
        1.02        17.95        36.95        17.03        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A02G TCGA-AG-A02N 
       70.03        64.01        10.98        49.97        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  ZNF280C MUTATED ZNF280C WILD-TYPE 
             1.02              0.00 
  ZNF280C MUTATED ZNF280C WILD-TYPE 
            79.69            148.01 
  ZNF280C MUTATED ZNF280C WILD-TYPE 
           15.765            20.280 
[1] "1.0 - 79.7 (15.8)"  "0.0 - 148.0 (20.3)"
[1] "hr=" "1.2"
D1191V2, continuous
D1191V3, binary
                   cls
clus                  0   1
  ZNF280C MUTATED     9   4
  ZNF280C WILD-TYPE 357 115
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZNF280C MUTATED      9    4
  ZNF280C WILD-TYPE  357  115
        clus
vv       ZNF280C MUTATED ZNF280C WILD-TYPE
  COLON                9               357
  RECTUM               4               115
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZNF280C MUTATED         5        0        1         4         0         1
  ZNF280C WILD-TYPE      86        1       31       134        10         0
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF280C MUTATED           0          0          1          0        0
  ZNF280C WILD-TYPE        24         11         58         42       48
                   vv
clus                STAGE IVA STAGE IVB
  ZNF280C MUTATED           2         0
  ZNF280C WILD-TYPE        16         1
D1191V4, multiclass
            clus
vv           ZNF280C MUTATED ZNF280C WILD-TYPE
  STAGE I                  5                86
  STAGE IA                 0                 1
  STAGE II                 1                31
  STAGE IIA                4               134
  STAGE IIB                0                10
  STAGE IIC                1                 0
  STAGE III                0                24
  STAGE IIIA               0                11
  STAGE IIIB               1                58
  STAGE IIIC               0                42
  STAGE IV                 0                48
  STAGE IVA                2                16
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  ZNF280C MUTATED     1   4   5   4
  ZNF280C WILD-TYPE  16  88 324  46
D1191V5, multiclass
    clus
vv   ZNF280C MUTATED ZNF280C WILD-TYPE
  T1               1                16
  T2               4                88
  T3               5               324
  T4               4                46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  ZNF280C MUTATED    11   2   1
  ZNF280C WILD-TYPE 276 111  86
D1191V6, multiclass
    clus
vv   ZNF280C MUTATED ZNF280C WILD-TYPE
  N0              11               276
  N1               2               111
  N2               1                86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1191V7, binary
                   cls
clus                  0   1
  ZNF280C MUTATED    12   1
  ZNF280C WILD-TYPE 363  64
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZNF280C MUTATED     12    1
  ZNF280C WILD-TYPE  363   64
   clus
vv  ZNF280C MUTATED ZNF280C WILD-TYPE
  0              12               363
  1               1                64
[1] 2 2
[1] FALSE
D1191V8, binary
                   cls
clus                  0   1
  ZNF280C MUTATED     7   7
  ZNF280C WILD-TYPE 218 257
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZNF280C MUTATED      7    7
  ZNF280C WILD-TYPE  218  257
        clus
vv       ZNF280C MUTATED ZNF280C WILD-TYPE
  FEMALE               7               218
  MALE                 7               257
[1] 2 2
[1] FALSE
D1191V9, binary
                   cls
clus                  0   1
  ZNF280C MUTATED    12   0
  ZNF280C WILD-TYPE 338  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZNF280C MUTATED     12    0
  ZNF280C WILD-TYPE  338   22
     clus
vv    ZNF280C MUTATED ZNF280C WILD-TYPE
  NO               12               338
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ZNF280C MUTATED                      9                             0
  ZNF280C WILD-TYPE                  306                            47
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ZNF280C MUTATED                       4                              0
  ZNF280C WILD-TYPE                   102                             10
D1191V10, multiclass
                                clus
vv                               ZNF280C MUTATED ZNF280C WILD-TYPE
  COLON ADENOCARCINOMA                         9               306
  COLON MUCINOUS ADENOCARCINOMA                0                47
  RECTAL ADENOCARCINOMA                        4               102
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  ZNF280C MUTATED    12   1   0   0
  ZNF280C WILD-TYPE 333   3  31  25
D1191V11, multiclass
    clus
vv   ZNF280C MUTATED ZNF280C WILD-TYPE
  R0              12               333
  R1               1                 3
  R2               0                31
  RX               0                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1191V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF280C MUTATED                                  0     0
  ZNF280C WILD-TYPE                                1    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  ZNF280C MUTATED                           1     8
  ZNF280C WILD-TYPE                        21   218
D1191V13, multiclass
                                  clus
vv                                 ZNF280C MUTATED ZNF280C WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                      1                21
  WHITE                                          8               218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1192) Variable = ATIC MUTATION ANALYSIS
D1192V1, survival
                sevent
clus2              0   1
  ATIC MUTATED     9   5
  ATIC WILD-TYPE 369  88
  ATIC MUTATED ATIC WILD-TYPE 
            14            457 
  ATIC MUTATED ATIC WILD-TYPE 
             5             88 
$`ATIC MUTATED`
TCGA-A6-5666 TCGA-A6-6781 TCGA-AA-3516 TCGA-AA-3663 TCGA-AA-3672 TCGA-AA-A00N 
       32.71        19.66        13.02         6.97         0.92         4.01 
TCGA-AA-A01R TCGA-AZ-6599 TCGA-CA-5796 TCGA-CK-4950 TCGA-CK-5916 TCGA-DM-A1D4 
       35.01         6.77         3.25        85.45        21.14        92.75 
TCGA-G4-6310 TCGA-AH-6544 
       63.62        38.56 

$`ATIC WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        22.06        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
       63.98         6.97         1.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02        78.08         6.05        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
       14.01        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        1.61        12.69         3.06         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 
       12.76        10.06        14.30        17.56       148.01        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       49.08        51.32         9.99        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
      130.65        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       55.04        85.48        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       41.00        38.04       117.11         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  ATIC MUTATED ATIC WILD-TYPE 
          0.92           0.00 
  ATIC MUTATED ATIC WILD-TYPE 
         92.75         148.01 
  ATIC MUTATED ATIC WILD-TYPE 
         20.40          20.19 
[1] "0.9 - 92.8 (20.4)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.6"
D1192V2, continuous
D1192V3, binary
                cls
clus               0   1
  ATIC MUTATED    13   1
  ATIC WILD-TYPE 353 118
[1] "tbl2"
                cls
clus             [,1] [,2]
  ATIC MUTATED     13    1
  ATIC WILD-TYPE  353  118
        clus
vv       ATIC MUTATED ATIC WILD-TYPE
  COLON            13            353
  RECTUM            1            118
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ATIC MUTATED         2        0        1         2         1         1
  ATIC WILD-TYPE      89        1       31       136         9         0
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ATIC MUTATED           3          0          2          1        0         0
  ATIC WILD-TYPE        21         11         57         41       48        18
                vv
clus             STAGE IVB
  ATIC MUTATED           0
  ATIC WILD-TYPE         1
D1192V4, multiclass
            clus
vv           ATIC MUTATED ATIC WILD-TYPE
  STAGE I               2             89
  STAGE IA              0              1
  STAGE II              1             31
  STAGE IIA             2            136
  STAGE IIB             1              9
  STAGE IIC             1              0
  STAGE III             3             21
  STAGE IIIA            0             11
  STAGE IIIB            2             57
  STAGE IIIC            1             41
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  ATIC MUTATED     1   1   9   3
  ATIC WILD-TYPE  16  91 320  47
D1192V5, multiclass
    clus
vv   ATIC MUTATED ATIC WILD-TYPE
  T1            1             16
  T2            1             91
  T3            9            320
  T4            3             47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  ATIC MUTATED     7   5   2
  ATIC WILD-TYPE 280 108  85
D1192V6, multiclass
    clus
vv   ATIC MUTATED ATIC WILD-TYPE
  N0            7            280
  N1            5            108
  N2            2             85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1192V7, binary
                cls
clus               0   1
  ATIC MUTATED    11   1
  ATIC WILD-TYPE 364  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  ATIC MUTATED     11    1
  ATIC WILD-TYPE  364   64
   clus
vv  ATIC MUTATED ATIC WILD-TYPE
  0           11            364
  1            1             64
[1] 2 2
[1] FALSE
D1192V8, binary
                cls
clus               0   1
  ATIC MUTATED     5   9
  ATIC WILD-TYPE 220 255
[1] "tbl2"
                cls
clus             [,1] [,2]
  ATIC MUTATED      5    9
  ATIC WILD-TYPE  220  255
        clus
vv       ATIC MUTATED ATIC WILD-TYPE
  FEMALE            5            220
  MALE              9            255
[1] 2 2
[1] FALSE
D1192V9, binary
                cls
clus               0   1
  ATIC MUTATED    10   2
  ATIC WILD-TYPE 340  20
[1] "tbl2"
                cls
clus             [,1] [,2]
  ATIC MUTATED     10    2
  ATIC WILD-TYPE  340   20
     clus
vv    ATIC MUTATED ATIC WILD-TYPE
  NO            10            340
  YES            2             20
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ATIC MUTATED                      8                             5
  ATIC WILD-TYPE                  307                            42
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ATIC MUTATED                       1                              0
  ATIC WILD-TYPE                   105                             10
D1192V10, multiclass
                                clus
vv                               ATIC MUTATED ATIC WILD-TYPE
  COLON ADENOCARCINOMA                      8            307
  COLON MUCINOUS ADENOCARCINOMA             5             42
  RECTAL ADENOCARCINOMA                     1            105
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  ATIC MUTATED     7   1   0   1
  ATIC WILD-TYPE 338   3  31  24
D1192V11, multiclass
    clus
vv   ATIC MUTATED ATIC WILD-TYPE
  R0            7            338
  R1            1              3
  R2            0             31
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1192V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ATIC MUTATED                                  0     1
  ATIC WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  ATIC MUTATED                           1     7
  ATIC WILD-TYPE                        21   219
D1192V13, multiclass
                                  clus
vv                                 ATIC MUTATED ATIC WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                       7            219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1193) Variable = USP16 MUTATION ANALYSIS
D1193V1, survival
                 sevent
clus2               0   1
  USP16 MUTATED     6   1
  USP16 WILD-TYPE 372  92
  USP16 MUTATED USP16 WILD-TYPE 
              7             464 
  USP16 MUTATED USP16 WILD-TYPE 
              1              92 
$`USP16 MUTATED`
TCGA-AA-3520 TCGA-AA-3877 TCGA-AA-A00N TCGA-AU-6004 TCGA-AY-5543 TCGA-CK-5913 
       24.03        31.00         4.01        27.09        33.01        51.32 
TCGA-D5-5538 
       12.26 

$`USP16 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
       38.99         1.02         9.07        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 
       17.03        24.03        27.02        29.98        18.05         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6197 TCGA-AY-6386 
        0.20        14.50        16.31         0.95        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5539 TCGA-D5-5540 
       11.01        10.06        12.03        45.40        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  USP16 MUTATED USP16 WILD-TYPE 
           4.01            0.00 
  USP16 MUTATED USP16 WILD-TYPE 
          51.32          148.01 
  USP16 MUTATED USP16 WILD-TYPE 
         27.090          20.085 
[1] "4.0 - 51.3 (27.1)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.4"
D1193V2, continuous
D1193V3, binary
                 cls
clus                0   1
  USP16 MUTATED     8   0
  USP16 WILD-TYPE 358 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP16 MUTATED      8    0
  USP16 WILD-TYPE  358  119
        clus
vv       USP16 MUTATED USP16 WILD-TYPE
  COLON              8             358
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  USP16 MUTATED         2        0        1         2         1         0
  USP16 WILD-TYPE      89        1       31       136         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  USP16 MUTATED           0          0          1          0        0         1
  USP16 WILD-TYPE        24         11         58         42       48        17
                 vv
clus              STAGE IVB
  USP16 MUTATED           0
  USP16 WILD-TYPE         1
D1193V4, multiclass
            clus
vv           USP16 MUTATED USP16 WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              2             136
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  USP16 MUTATED     1   1   5   1
  USP16 WILD-TYPE  16  91 324  49
D1193V5, multiclass
    clus
vv   USP16 MUTATED USP16 WILD-TYPE
  T1             1              16
  T2             1              91
  T3             5             324
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  USP16 MUTATED     6   2   0
  USP16 WILD-TYPE 281 111  87
D1193V6, multiclass
    clus
vv   USP16 MUTATED USP16 WILD-TYPE
  N0             6             281
  N1             2             111
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1193V7, binary
                 cls
clus                0   1
  USP16 MUTATED     6   1
  USP16 WILD-TYPE 369  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP16 MUTATED      6    1
  USP16 WILD-TYPE  369   64
   clus
vv  USP16 MUTATED USP16 WILD-TYPE
  0             6             369
  1             1              64
[1] 2 2
[1] FALSE
D1193V8, binary
                 cls
clus                0   1
  USP16 MUTATED     7   1
  USP16 WILD-TYPE 218 263
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP16 MUTATED      7    1
  USP16 WILD-TYPE  218  263
        clus
vv       USP16 MUTATED USP16 WILD-TYPE
  FEMALE             7             218
  MALE               1             263
[1] 2 2
[1] FALSE
D1193V9, binary
                 cls
clus                0   1
  USP16 MUTATED     5   0
  USP16 WILD-TYPE 345  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP16 MUTATED      5    0
  USP16 WILD-TYPE  345   22
     clus
vv    USP16 MUTATED USP16 WILD-TYPE
  NO              5             345
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  USP16 MUTATED                      6                             2
  USP16 WILD-TYPE                  309                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  USP16 MUTATED                       0                              0
  USP16 WILD-TYPE                   106                             10
D1193V10, multiclass
                                clus
vv                               USP16 MUTATED USP16 WILD-TYPE
  COLON ADENOCARCINOMA                       6             309
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  USP16 MUTATED     7   0   0   1
  USP16 WILD-TYPE 338   4  31  24
D1193V11, multiclass
    clus
vv   USP16 MUTATED USP16 WILD-TYPE
  R0             7             338
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1193V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  USP16 MUTATED                                  0     0
  USP16 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  USP16 MUTATED                           1     3
  USP16 WILD-TYPE                        21   223
D1193V13, multiclass
                                  clus
vv                                 USP16 MUTATED USP16 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        3             223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1194) Variable = CIR1 MUTATION ANALYSIS
D1194V1, survival
                sevent
clus2              0   1
  CIR1 MUTATED     6   3
  CIR1 WILD-TYPE 372  90
  CIR1 MUTATED CIR1 WILD-TYPE 
             9            462 
  CIR1 MUTATED CIR1 WILD-TYPE 
             3             90 
$`CIR1 MUTATED`
TCGA-AA-3870 TCGA-AA-A00N TCGA-AA-A010 TCGA-AZ-4315 TCGA-AZ-6600 TCGA-CK-4947 
       29.98         4.01        34.98        58.39        12.10        17.56 
TCGA-AF-2693 TCGA-DC-5337 TCGA-DY-A1DD 
       19.10        15.02        57.24 

$`CIR1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       53.00        17.03        24.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        88.21        49.41         6.77       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       14.30       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3913 
       24.13        39.48        43.04        13.55        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
       78.12         7.17         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       41.36        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  CIR1 MUTATED CIR1 WILD-TYPE 
          4.01           0.00 
  CIR1 MUTATED CIR1 WILD-TYPE 
         58.39         148.01 
  CIR1 MUTATED CIR1 WILD-TYPE 
        19.100         20.235 
[1] "4.0 - 58.4 (19.1)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.6"
D1194V2, continuous
D1194V3, binary
                cls
clus               0   1
  CIR1 MUTATED     7   2
  CIR1 WILD-TYPE 359 117
[1] "tbl2"
                cls
clus             [,1] [,2]
  CIR1 MUTATED      7    2
  CIR1 WILD-TYPE  359  117
        clus
vv       CIR1 MUTATED CIR1 WILD-TYPE
  COLON             7            359
  RECTUM            2            117
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CIR1 MUTATED         2        0        0         2         2         0
  CIR1 WILD-TYPE      89        1       32       136         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CIR1 MUTATED           0          0          2          0        2         0
  CIR1 WILD-TYPE        24         11         57         42       46        18
                vv
clus             STAGE IVB
  CIR1 MUTATED           0
  CIR1 WILD-TYPE         1
D1194V4, multiclass
            clus
vv           CIR1 MUTATED CIR1 WILD-TYPE
  STAGE I               2             89
  STAGE IA              0              1
  STAGE II              0             32
  STAGE IIA             2            136
  STAGE IIB             2              8
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            2             57
  STAGE IIIC            0             42
  STAGE IV              2             46
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  CIR1 MUTATED     1   1   4   4
  CIR1 WILD-TYPE  16  91 325  46
D1194V5, multiclass
    clus
vv   CIR1 MUTATED CIR1 WILD-TYPE
  T1            1             16
  T2            1             91
  T3            4            325
  T4            4             46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  CIR1 MUTATED     6   3   1
  CIR1 WILD-TYPE 281 110  86
D1194V6, multiclass
    clus
vv   CIR1 MUTATED CIR1 WILD-TYPE
  N0            6            281
  N1            3            110
  N2            1             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1194V7, binary
                cls
clus               0   1
  CIR1 MUTATED     7   2
  CIR1 WILD-TYPE 368  63
[1] "tbl2"
                cls
clus             [,1] [,2]
  CIR1 MUTATED      7    2
  CIR1 WILD-TYPE  368   63
   clus
vv  CIR1 MUTATED CIR1 WILD-TYPE
  0            7            368
  1            2             63
[1] 2 2
[1] FALSE
D1194V8, binary
                cls
clus               0   1
  CIR1 MUTATED     5   5
  CIR1 WILD-TYPE 220 259
[1] "tbl2"
                cls
clus             [,1] [,2]
  CIR1 MUTATED      5    5
  CIR1 WILD-TYPE  220  259
        clus
vv       CIR1 MUTATED CIR1 WILD-TYPE
  FEMALE            5            220
  MALE              5            259
[1] 2 2
[1] FALSE
D1194V9, binary
                cls
clus               0   1
  CIR1 MUTATED     5   0
  CIR1 WILD-TYPE 345  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  CIR1 MUTATED      5    0
  CIR1 WILD-TYPE  345   22
     clus
vv    CIR1 MUTATED CIR1 WILD-TYPE
  NO             5            345
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CIR1 MUTATED                      6                             1
  CIR1 WILD-TYPE                  309                            46
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CIR1 MUTATED                       2                              0
  CIR1 WILD-TYPE                   104                             10
D1194V10, multiclass
                                clus
vv                               CIR1 MUTATED CIR1 WILD-TYPE
  COLON ADENOCARCINOMA                      6            309
  COLON MUCINOUS ADENOCARCINOMA             1             46
  RECTAL ADENOCARCINOMA                     2            104
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  CIR1 MUTATED     6   0   0   1
  CIR1 WILD-TYPE 339   4  31  24
D1194V11, multiclass
    clus
vv   CIR1 MUTATED CIR1 WILD-TYPE
  R0            6            339
  R1            0              4
  R2            0             31
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1194V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CIR1 MUTATED                                  0     0
  CIR1 WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  CIR1 MUTATED                           1     5
  CIR1 WILD-TYPE                        21   221
D1194V13, multiclass
                                  clus
vv                                 CIR1 MUTATED CIR1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                       5            221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1195) Variable = OR4C15 MUTATION ANALYSIS
D1195V1, survival
                  sevent
clus2                0   1
  OR4C15 MUTATED    10   5
  OR4C15 WILD-TYPE 368  88
  OR4C15 MUTATED OR4C15 WILD-TYPE 
              15              456 
  OR4C15 MUTATED OR4C15 WILD-TYPE 
               5               88 
$`OR4C15 MUTATED`
TCGA-A6-5665 TCGA-AA-3510 TCGA-AA-3713 TCGA-AA-A00N TCGA-AZ-4315 TCGA-AZ-6605 
       22.06        63.98        19.04         4.01        58.39         5.23 
TCGA-AZ-6608 TCGA-CA-6718 TCGA-CM-6162 TCGA-D5-6920 TCGA-DM-A1D9 TCGA-DM-A28G 
        1.61        10.06        12.00         3.68       140.38        60.79 
TCGA-AG-3883 TCGA-AG-A002 TCGA-G5-6235 
        1.02        20.98        55.76 

$`OR4C15 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
       11.74         3.19        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07        12.20        12.76        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       15.02         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6922 
       17.13        12.49        16.14        15.58         1.48         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
       81.37       119.93        35.97       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3885 TCGA-AG-3887 
        0.99         0.99        19.04        19.99        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6641 
       31.30        28.57        32.19         0.66         0.69        26.43 

  OR4C15 MUTATED OR4C15 WILD-TYPE 
            1.02             0.00 
  OR4C15 MUTATED OR4C15 WILD-TYPE 
          140.38           148.01 
  OR4C15 MUTATED OR4C15 WILD-TYPE 
          19.040           20.235 
[1] "1.0 - 140.4 (19.0)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.4"
D1195V2, continuous
D1195V3, binary
                  cls
clus                 0   1
  OR4C15 MUTATED    13   3
  OR4C15 WILD-TYPE 353 116
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR4C15 MUTATED     13    3
  OR4C15 WILD-TYPE  353  116
        clus
vv       OR4C15 MUTATED OR4C15 WILD-TYPE
  COLON              13              353
  RECTUM              3              116
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  OR4C15 MUTATED         2        0        2         6         1         0
  OR4C15 WILD-TYPE      89        1       30       132         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  OR4C15 MUTATED           0          1          3          0        1
  OR4C15 WILD-TYPE        24         10         56         42       47
                  vv
clus               STAGE IVA STAGE IVB
  OR4C15 MUTATED           0         0
  OR4C15 WILD-TYPE        18         1
D1195V4, multiclass
            clus
vv           OR4C15 MUTATED OR4C15 WILD-TYPE
  STAGE I                 2               89
  STAGE IA                0                1
  STAGE II                2               30
  STAGE IIA               6              132
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              1               10
  STAGE IIIB              3               56
  STAGE IIIC              0               42
  STAGE IV                1               47
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  OR4C15 MUTATED     0   3  10   3
  OR4C15 WILD-TYPE  17  89 319  47
D1195V5, multiclass
    clus
vv   OR4C15 MUTATED OR4C15 WILD-TYPE
  T1              0               17
  T2              3               89
  T3             10              319
  T4              3               47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  OR4C15 MUTATED    12   4   0
  OR4C15 WILD-TYPE 275 109  87
D1195V6, multiclass
    clus
vv   OR4C15 MUTATED OR4C15 WILD-TYPE
  N0             12              275
  N1              4              109
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1195V7, binary
                  cls
clus                 0   1
  OR4C15 MUTATED    14   1
  OR4C15 WILD-TYPE 361  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR4C15 MUTATED     14    1
  OR4C15 WILD-TYPE  361   64
   clus
vv  OR4C15 MUTATED OR4C15 WILD-TYPE
  0             14              361
  1              1               64
[1] 2 2
[1] FALSE
D1195V8, binary
                  cls
clus                 0   1
  OR4C15 MUTATED     6  10
  OR4C15 WILD-TYPE 219 254
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR4C15 MUTATED      6   10
  OR4C15 WILD-TYPE  219  254
        clus
vv       OR4C15 MUTATED OR4C15 WILD-TYPE
  FEMALE              6              219
  MALE               10              254
[1] 2 2
[1] FALSE
D1195V9, binary
                  cls
clus                 0   1
  OR4C15 MUTATED     9   1
  OR4C15 WILD-TYPE 341  21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR4C15 MUTATED      9    1
  OR4C15 WILD-TYPE  341   21
     clus
vv    OR4C15 MUTATED OR4C15 WILD-TYPE
  NO               9              341
  YES              1               21
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  OR4C15 MUTATED                     11                             2
  OR4C15 WILD-TYPE                  304                            45
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  OR4C15 MUTATED                       3                              0
  OR4C15 WILD-TYPE                   103                             10
D1195V10, multiclass
                                clus
vv                               OR4C15 MUTATED OR4C15 WILD-TYPE
  COLON ADENOCARCINOMA                       11              304
  COLON MUCINOUS ADENOCARCINOMA               2               45
  RECTAL ADENOCARCINOMA                       3              103
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  OR4C15 MUTATED     9   1   1   1
  OR4C15 WILD-TYPE 336   3  30  24
D1195V11, multiclass
    clus
vv   OR4C15 MUTATED OR4C15 WILD-TYPE
  R0              9              336
  R1              1                3
  R2              1               30
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1195V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OR4C15 MUTATED                                  0     1
  OR4C15 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  OR4C15 MUTATED                           0     9
  OR4C15 WILD-TYPE                        22   217
D1195V13, multiclass
                                  clus
vv                                 OR4C15 MUTATED OR4C15 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         9              217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1196) Variable = ANK3 MUTATION ANALYSIS
D1196V1, survival
                sevent
clus2              0   1
  ANK3 MUTATED    40  11
  ANK3 WILD-TYPE 338  82
  ANK3 MUTATED ANK3 WILD-TYPE 
            51            420 
  ANK3 MUTATED ANK3 WILD-TYPE 
            11             82 
$`ANK3 MUTATED`
TCGA-A6-2677 TCGA-A6-5661 TCGA-A6-5665 TCGA-A6-6141 TCGA-AA-3492 TCGA-AA-3496 
       24.33        33.53        22.06         8.38         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3516 TCGA-AA-3554 TCGA-AA-3663 TCGA-AA-3672 
       35.01        63.98        13.02        17.95         6.97         0.92 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3950 TCGA-AA-3977 TCGA-AA-A00J 
       19.04        19.04        10.06        24.00        25.02        18.05 
TCGA-AA-A00N TCGA-AA-A00U TCGA-AA-A010 TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
        4.01        17.03        34.98        38.07         1.02        35.01 
TCGA-AD-5900 TCGA-AD-6889 TCGA-AU-3779 TCGA-AU-6004 TCGA-AZ-4315 TCGA-AZ-6598 
        0.07        56.55        14.50        27.09        58.39        49.41 
TCGA-AZ-6601 TCGA-CA-6717 TCGA-CK-6747 TCGA-CM-6168 TCGA-CM-6171 TCGA-D5-6540 
      100.01        12.76        82.95        12.99        14.04        16.14 
TCGA-D5-6920 TCGA-D5-6928 TCGA-DM-A1HB TCGA-F4-6703 TCGA-F4-6808 TCGA-G4-6304 
        3.68        11.64       135.65        47.87        33.67        53.62 
TCGA-G4-6309 TCGA-G4-6586 TCGA-G4-6628 TCGA-AF-5654 TCGA-AG-3892 TCGA-AG-A002 
       85.48        35.80        79.69        16.83        13.02        20.98 
TCGA-DY-A0XA TCGA-DY-A1DG TCGA-EI-6507 
      126.44        51.48        19.96 

$`ANK3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        42.90        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 
       31.63        30.44        29.19        23.61        22.09        32.71 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 
       27.09        22.52        25.08        25.18        24.16        21.76 
TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       24.69        24.39        23.87        20.12        19.66        20.28 
TCGA-AA-3489 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        7.04         6.97         1.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       61.02        78.08         6.05        54.02         2.01        14.01 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3812 
       19.00        36.00         5.03        85.05        26.99        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        33.01        26.01         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00W 
       18.05        38.04        27.02        42.02         0.99        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       31.00         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 
        0.92        41.00        39.98        18.05        40.96        21.37 
TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       15.52         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       10.88         0.20        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       88.21         6.77        12.10        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07        12.20        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       13.02        15.02        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
       15.58         1.48         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
        9.44         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6854 
        1.55        34.42        41.42        16.24        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 
       47.41        35.31       133.18        74.56        65.85        44.68 
TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       55.04        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       26.17        91.79        46.75        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-6136 
       13.55        19.10        34.49        10.39        14.50        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 
        1.02        17.95        36.95        17.03        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 
        5.29        41.36        57.24        24.13        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       20.55        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  ANK3 MUTATED ANK3 WILD-TYPE 
          0.07           0.00 
  ANK3 MUTATED ANK3 WILD-TYPE 
        135.65         148.01 
  ANK3 MUTATED ANK3 WILD-TYPE 
        20.980         20.155 
[1] "0.1 - 135.7 (21.0)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.1"
D1196V2, continuous
D1196V3, binary
                cls
clus               0   1
  ANK3 MUTATED    48   6
  ANK3 WILD-TYPE 318 113
[1] "tbl2"
                cls
clus             [,1] [,2]
  ANK3 MUTATED     48    6
  ANK3 WILD-TYPE  318  113
        clus
vv       ANK3 MUTATED ANK3 WILD-TYPE
  COLON            48            318
  RECTUM            6            113
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ANK3 MUTATED        10        0        8        19         3         0
  ANK3 WILD-TYPE      81        1       24       119         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ANK3 MUTATED           6          0          4          1        1         1
  ANK3 WILD-TYPE        18         11         55         41       47        17
                vv
clus             STAGE IVB
  ANK3 MUTATED           0
  ANK3 WILD-TYPE         1
D1196V4, multiclass
            clus
vv           ANK3 MUTATED ANK3 WILD-TYPE
  STAGE I              10             81
  STAGE IA              0              1
  STAGE II              8             24
  STAGE IIA            19            119
  STAGE IIB             3              7
  STAGE IIC             0              1
  STAGE III             6             18
  STAGE IIIA            0             11
  STAGE IIIB            4             55
  STAGE IIIC            1             41
  STAGE IV              1             47
  STAGE IVA             1             17
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  ANK3 MUTATED     2   9  39   4
  ANK3 WILD-TYPE  15  83 290  46
D1196V5, multiclass
    clus
vv   ANK3 MUTATED ANK3 WILD-TYPE
  T1            2             15
  T2            9             83
  T3           39            290
  T4            4             46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  ANK3 MUTATED    42   7   5
  ANK3 WILD-TYPE 245 106  82
D1196V6, multiclass
    clus
vv   ANK3 MUTATED ANK3 WILD-TYPE
  N0           42            245
  N1            7            106
  N2            5             82
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1196V7, binary
                cls
clus               0   1
  ANK3 MUTATED    48   2
  ANK3 WILD-TYPE 327  63
[1] "tbl2"
                cls
clus             [,1] [,2]
  ANK3 MUTATED     48    2
  ANK3 WILD-TYPE  327   63
   clus
vv  ANK3 MUTATED ANK3 WILD-TYPE
  0           48            327
  1            2             63
[1] 2 2
[1] FALSE
D1196V8, binary
                cls
clus               0   1
  ANK3 MUTATED    29  25
  ANK3 WILD-TYPE 196 239
[1] "tbl2"
                cls
clus             [,1] [,2]
  ANK3 MUTATED     29   25
  ANK3 WILD-TYPE  196  239
        clus
vv       ANK3 MUTATED ANK3 WILD-TYPE
  FEMALE           29            196
  MALE             25            239
[1] 2 2
[1] FALSE
D1196V9, binary
                cls
clus               0   1
  ANK3 MUTATED    39   2
  ANK3 WILD-TYPE 311  20
[1] "tbl2"
                cls
clus             [,1] [,2]
  ANK3 MUTATED     39    2
  ANK3 WILD-TYPE  311   20
     clus
vv    ANK3 MUTATED ANK3 WILD-TYPE
  NO            39            311
  YES            2             20
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ANK3 MUTATED                     38                             9
  ANK3 WILD-TYPE                  277                            38
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ANK3 MUTATED                       6                              0
  ANK3 WILD-TYPE                   100                             10
D1196V10, multiclass
                                clus
vv                               ANK3 MUTATED ANK3 WILD-TYPE
  COLON ADENOCARCINOMA                     38            277
  COLON MUCINOUS ADENOCARCINOMA             9             38
  RECTAL ADENOCARCINOMA                     6            100
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  ANK3 MUTATED    42   0   1   2
  ANK3 WILD-TYPE 303   4  30  23
D1196V11, multiclass
    clus
vv   ANK3 MUTATED ANK3 WILD-TYPE
  R0           42            303
  R1            0              4
  R2            1             30
  RX            2             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1196V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ANK3 MUTATED                                  0     2
  ANK3 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  ANK3 MUTATED                           4    23
  ANK3 WILD-TYPE                        18   203
D1196V13, multiclass
                                  clus
vv                                 ANK3 MUTATED ANK3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              9
  BLACK OR AFRICAN AMERICAN                   4             18
  WHITE                                      23            203
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1197) Variable = PPFIBP1 MUTATION ANALYSIS
D1197V1, survival
                   sevent
clus2                 0   1
  PPFIBP1 MUTATED    11   2
  PPFIBP1 WILD-TYPE 367  91
  PPFIBP1 MUTATED PPFIBP1 WILD-TYPE 
               13               458 
  PPFIBP1 MUTATED PPFIBP1 WILD-TYPE 
                2                91 
$`PPFIBP1 MUTATED`
TCGA-A6-2672 TCGA-A6-5665 TCGA-AA-3672 TCGA-AA-3877 TCGA-AZ-6600 TCGA-AZ-6601 
       46.65        22.06         0.92        31.00        12.10       100.01 
TCGA-CA-6716 TCGA-CM-4743 TCGA-CM-6674 TCGA-D5-6924 TCGA-D5-6930 TCGA-AG-A002 
       12.20        23.05        12.95        14.30         1.51        20.98 
TCGA-DC-5337 
       15.02 

$`PPFIBP1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
       54.02         2.01        14.01        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       27.02        29.98        18.05         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6603 TCGA-AZ-6605 
       62.79        88.21        49.41         6.77        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 
       21.14        82.95         1.91       124.27        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
        4.41        12.43         9.04         9.44        11.64         4.80 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
        4.73        78.12         7.17         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  PPFIBP1 MUTATED PPFIBP1 WILD-TYPE 
             0.92              0.00 
  PPFIBP1 MUTATED PPFIBP1 WILD-TYPE 
           100.01            148.01 
  PPFIBP1 MUTATED PPFIBP1 WILD-TYPE 
           15.020            20.235 
[1] "0.9 - 100.0 (15.0)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.2"
D1197V2, continuous
D1197V3, binary
                   cls
clus                  0   1
  PPFIBP1 MUTATED    12   2
  PPFIBP1 WILD-TYPE 354 117
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PPFIBP1 MUTATED     12    2
  PPFIBP1 WILD-TYPE  354  117
        clus
vv       PPFIBP1 MUTATED PPFIBP1 WILD-TYPE
  COLON               12               354
  RECTUM               2               117
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PPFIBP1 MUTATED         3        0        1         6         0         0
  PPFIBP1 WILD-TYPE      88        1       31       132        10         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PPFIBP1 MUTATED           2          0          1          0        1
  PPFIBP1 WILD-TYPE        22         11         58         42       47
                   vv
clus                STAGE IVA STAGE IVB
  PPFIBP1 MUTATED           0         0
  PPFIBP1 WILD-TYPE        18         1
D1197V4, multiclass
            clus
vv           PPFIBP1 MUTATED PPFIBP1 WILD-TYPE
  STAGE I                  3                88
  STAGE IA                 0                 1
  STAGE II                 1                31
  STAGE IIA                6               132
  STAGE IIB                0                10
  STAGE IIC                0                 1
  STAGE III                2                22
  STAGE IIIA               0                11
  STAGE IIIB               1                58
  STAGE IIIC               0                42
  STAGE IV                 1                47
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  PPFIBP1 MUTATED     2   1  10   1
  PPFIBP1 WILD-TYPE  15  91 319  49
D1197V5, multiclass
    clus
vv   PPFIBP1 MUTATED PPFIBP1 WILD-TYPE
  T1               2                15
  T2               1                91
  T3              10               319
  T4               1                49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  PPFIBP1 MUTATED    10   3   1
  PPFIBP1 WILD-TYPE 277 110  86
D1197V6, multiclass
    clus
vv   PPFIBP1 MUTATED PPFIBP1 WILD-TYPE
  N0              10               277
  N1               3               110
  N2               1                86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1197V7, binary
                   cls
clus                  0   1
  PPFIBP1 MUTATED    13   1
  PPFIBP1 WILD-TYPE 362  64
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PPFIBP1 MUTATED     13    1
  PPFIBP1 WILD-TYPE  362   64
   clus
vv  PPFIBP1 MUTATED PPFIBP1 WILD-TYPE
  0              13               362
  1               1                64
[1] 2 2
[1] FALSE
D1197V8, binary
                   cls
clus                  0   1
  PPFIBP1 MUTATED     4  10
  PPFIBP1 WILD-TYPE 221 254
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PPFIBP1 MUTATED      4   10
  PPFIBP1 WILD-TYPE  221  254
        clus
vv       PPFIBP1 MUTATED PPFIBP1 WILD-TYPE
  FEMALE               4               221
  MALE                10               254
[1] 2 2
[1] FALSE
D1197V9, binary
                   cls
clus                  0   1
  PPFIBP1 MUTATED    11   0
  PPFIBP1 WILD-TYPE 339  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PPFIBP1 MUTATED     11    0
  PPFIBP1 WILD-TYPE  339   22
     clus
vv    PPFIBP1 MUTATED PPFIBP1 WILD-TYPE
  NO               11               339
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PPFIBP1 MUTATED                     10                             2
  PPFIBP1 WILD-TYPE                  305                            45
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PPFIBP1 MUTATED                       2                              0
  PPFIBP1 WILD-TYPE                   104                             10
D1197V10, multiclass
                                clus
vv                               PPFIBP1 MUTATED PPFIBP1 WILD-TYPE
  COLON ADENOCARCINOMA                        10               305
  COLON MUCINOUS ADENOCARCINOMA                2                45
  RECTAL ADENOCARCINOMA                        2               104
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  PPFIBP1 MUTATED    11   0   0   1
  PPFIBP1 WILD-TYPE 334   4  31  24
D1197V11, multiclass
    clus
vv   PPFIBP1 MUTATED PPFIBP1 WILD-TYPE
  R0              11               334
  R1               0                 4
  R2               0                31
  RX               1                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1197V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PPFIBP1 MUTATED                                  0     1
  PPFIBP1 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  PPFIBP1 MUTATED                           1     8
  PPFIBP1 WILD-TYPE                        21   218
D1197V13, multiclass
                                  clus
vv                                 PPFIBP1 MUTATED PPFIBP1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                10
  BLACK OR AFRICAN AMERICAN                      1                21
  WHITE                                          8               218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1198) Variable = NTNG1 MUTATION ANALYSIS
D1198V1, survival
                 sevent
clus2               0   1
  NTNG1 MUTATED    14   3
  NTNG1 WILD-TYPE 364  90
  NTNG1 MUTATED NTNG1 WILD-TYPE 
             17             454 
  NTNG1 MUTATED NTNG1 WILD-TYPE 
              3              90 
$`NTNG1 MUTATED`
TCGA-A6-4105 TCGA-A6-5661 TCGA-A6-5665 TCGA-AA-3510 TCGA-AA-3555 TCGA-AA-3655 
       14.53        33.53        22.06        63.98        29.95        61.02 
TCGA-AA-A01K TCGA-AD-6899 TCGA-CM-5344 TCGA-CM-5861 TCGA-DM-A1DA TCGA-DM-A1HB 
       31.00         5.79        22.03        15.02         7.50       135.65 
TCGA-F4-6569 TCGA-G4-6309 TCGA-AG-A002 TCGA-AG-A016 TCGA-EI-6506 
       35.74        85.48        20.98         9.07        20.55 

$`NTNG1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 
       16.57        34.65        33.34        32.75        36.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 
       31.63        30.44        29.19        23.61        22.09        32.71 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       27.09        22.52         8.38        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 
       20.28         7.04         3.02         1.02        35.01         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3660 
       23.01        20.98        19.99        13.94        19.99        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       32.02        12.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6901 TCGA-AD-6963 
       15.52        56.55         0.79         0.72        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       25.02        13.02        29.06        22.98        30.08        32.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
      140.38        44.32       131.51       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       31.96         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
       36.03        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6507 TCGA-EI-6508 
       24.13        51.48        32.61         0.49        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  NTNG1 MUTATED NTNG1 WILD-TYPE 
           5.79            0.00 
  NTNG1 MUTATED NTNG1 WILD-TYPE 
         135.65          148.01 
  NTNG1 MUTATED NTNG1 WILD-TYPE 
          22.06           20.02 
[1] "5.8 - 135.7 (22.1)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.5"
D1198V2, continuous
D1198V3, binary
                 cls
clus                0   1
  NTNG1 MUTATED    14   3
  NTNG1 WILD-TYPE 352 116
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NTNG1 MUTATED     14    3
  NTNG1 WILD-TYPE  352  116
        clus
vv       NTNG1 MUTATED NTNG1 WILD-TYPE
  COLON             14             352
  RECTUM             3             116
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NTNG1 MUTATED         2        0        2         6         0         0
  NTNG1 WILD-TYPE      89        1       30       132        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NTNG1 MUTATED           0          0          3          3        1         0
  NTNG1 WILD-TYPE        24         11         56         39       47        18
                 vv
clus              STAGE IVB
  NTNG1 MUTATED           0
  NTNG1 WILD-TYPE         1
D1198V4, multiclass
            clus
vv           NTNG1 MUTATED NTNG1 WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA              6             132
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             3              56
  STAGE IIIC             3              39
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  NTNG1 MUTATED     0   2  14   1
  NTNG1 WILD-TYPE  17  90 315  49
D1198V5, multiclass
    clus
vv   NTNG1 MUTATED NTNG1 WILD-TYPE
  T1             0              17
  T2             2              90
  T3            14             315
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  NTNG1 MUTATED    10   3   4
  NTNG1 WILD-TYPE 277 110  83
D1198V6, multiclass
    clus
vv   NTNG1 MUTATED NTNG1 WILD-TYPE
  N0            10             277
  N1             3             110
  N2             4              83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1198V7, binary
                 cls
clus                0   1
  NTNG1 MUTATED    15   1
  NTNG1 WILD-TYPE 360  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NTNG1 MUTATED     15    1
  NTNG1 WILD-TYPE  360   64
   clus
vv  NTNG1 MUTATED NTNG1 WILD-TYPE
  0            15             360
  1             1              64
[1] 2 2
[1] FALSE
D1198V8, binary
                 cls
clus                0   1
  NTNG1 MUTATED     9   8
  NTNG1 WILD-TYPE 216 256
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NTNG1 MUTATED      9    8
  NTNG1 WILD-TYPE  216  256
        clus
vv       NTNG1 MUTATED NTNG1 WILD-TYPE
  FEMALE             9             216
  MALE               8             256
[1] 2 2
[1] FALSE
D1198V9, binary
                 cls
clus                0   1
  NTNG1 MUTATED    15   0
  NTNG1 WILD-TYPE 335  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NTNG1 MUTATED     15    0
  NTNG1 WILD-TYPE  335   22
     clus
vv    NTNG1 MUTATED NTNG1 WILD-TYPE
  NO             15             335
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  NTNG1 MUTATED                     11                             2
  NTNG1 WILD-TYPE                  304                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  NTNG1 MUTATED                       3                              0
  NTNG1 WILD-TYPE                   103                             10
D1198V10, multiclass
                                clus
vv                               NTNG1 MUTATED NTNG1 WILD-TYPE
  COLON ADENOCARCINOMA                      11             304
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      3             103
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  NTNG1 MUTATED    12   0   1   0
  NTNG1 WILD-TYPE 333   4  30  25
D1198V11, multiclass
    clus
vv   NTNG1 MUTATED NTNG1 WILD-TYPE
  R0            12             333
  R1             0               4
  R2             1              30
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1198V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NTNG1 MUTATED                                  0     0
  NTNG1 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  NTNG1 MUTATED                           2     9
  NTNG1 WILD-TYPE                        20   217
D1198V13, multiclass
                                  clus
vv                                 NTNG1 MUTATED NTNG1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    2              20
  WHITE                                        9             217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1199) Variable = TRPA1 MUTATION ANALYSIS
D1199V1, survival
                 sevent
clus2               0   1
  TRPA1 MUTATED    27   5
  TRPA1 WILD-TYPE 351  88
  TRPA1 MUTATED TRPA1 WILD-TYPE 
             32             439 
  TRPA1 MUTATED TRPA1 WILD-TYPE 
              5              88 
$`TRPA1 MUTATED`
TCGA-A6-5660 TCGA-A6-6652 TCGA-AA-3672 TCGA-AA-3955 TCGA-AA-3977 TCGA-AA-A010 
       29.19        24.69         0.92        20.98        25.02        34.98 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A02O TCGA-AD-6889 TCGA-AZ-4315 TCGA-CA-6717 
        1.02        35.01         0.92        56.55        58.39        12.76 
TCGA-CA-6718 TCGA-CM-5861 TCGA-CM-6169 TCGA-CM-6171 TCGA-CM-6675 TCGA-CM-6676 
       10.06        15.02        13.02        14.04        13.05        11.08 
TCGA-D5-5538 TCGA-D5-6532 TCGA-D5-6533 TCGA-DM-A1D0 TCGA-DM-A1D8 TCGA-F4-6570 
       12.26        18.25         1.32       130.65        12.59         6.18 
TCGA-G4-6303 TCGA-G4-6315 TCGA-G4-6588 TCGA-AF-2689 TCGA-AG-3599 TCGA-AG-3600 
       65.85        61.91        26.17        39.48        12.03         6.05 
TCGA-AG-3999 TCGA-AG-A002 
       28.04        20.98 

$`TRPA1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       25.18        24.16        21.76        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
       54.02         2.01        14.01        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3956 
       24.00        33.01        26.01        24.00         2.01        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01S 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02W TCGA-AA-A02Y 
       39.98         2.01         5.03        14.01        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 
       18.05        40.96         0.07        21.37        15.52         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 
        3.25         3.29         0.07        12.20        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       30.08        32.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6677 
       14.99        12.99        15.02        11.01        12.95        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5539 TCGA-D5-5540 
       11.01        10.06        12.03        45.40        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       55.92        20.19        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D9 
       24.43        38.20        92.75        49.91        13.32       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
        8.61        31.96        35.74        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
       35.31       133.18        74.56        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       85.48        63.62        36.00        22.09        13.78        35.80 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2691 TCGA-AF-2692 
       91.79        46.75        79.69        24.13        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       34.03         2.01        50.04         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       48.03        32.02        19.99        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  TRPA1 MUTATED TRPA1 WILD-TYPE 
           0.92            0.00 
  TRPA1 MUTATED TRPA1 WILD-TYPE 
         130.65          148.01 
  TRPA1 MUTATED TRPA1 WILD-TYPE 
         16.635          20.280 
[1] "0.9 - 130.7 (16.6)" "0.0 - 148.0 (20.3)"
[1] "hr=" "1.2"
D1199V2, continuous
D1199V3, binary
                 cls
clus                0   1
  TRPA1 MUTATED    27   5
  TRPA1 WILD-TYPE 339 114
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRPA1 MUTATED     27    5
  TRPA1 WILD-TYPE  339  114
        clus
vv       TRPA1 MUTATED TRPA1 WILD-TYPE
  COLON             27             339
  RECTUM             5             114
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TRPA1 MUTATED         4        0        2        10         1         0
  TRPA1 WILD-TYPE      87        1       30       128         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TRPA1 MUTATED           2          0          3          3        3         1
  TRPA1 WILD-TYPE        22         11         56         39       45        17
                 vv
clus              STAGE IVB
  TRPA1 MUTATED           1
  TRPA1 WILD-TYPE         0
D1199V4, multiclass
            clus
vv           TRPA1 MUTATED TRPA1 WILD-TYPE
  STAGE I                4              87
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA             10             128
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              2              22
  STAGE IIIA             0              11
  STAGE IIIB             3              56
  STAGE IIIC             3              39
  STAGE IV               3              45
  STAGE IVA              1              17
  STAGE IVB              1               0
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  TRPA1 MUTATED     0   6  24   2
  TRPA1 WILD-TYPE  17  86 305  48
D1199V5, multiclass
    clus
vv   TRPA1 MUTATED TRPA1 WILD-TYPE
  T1             0              17
  T2             6              86
  T3            24             305
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  TRPA1 MUTATED    20   5   7
  TRPA1 WILD-TYPE 267 108  80
D1199V6, multiclass
    clus
vv   TRPA1 MUTATED TRPA1 WILD-TYPE
  N0            20             267
  N1             5             108
  N2             7              80
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1199V7, binary
                 cls
clus                0   1
  TRPA1 MUTATED    25   5
  TRPA1 WILD-TYPE 350  60
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRPA1 MUTATED     25    5
  TRPA1 WILD-TYPE  350   60
   clus
vv  TRPA1 MUTATED TRPA1 WILD-TYPE
  0            25             350
  1             5              60
[1] 2 2
[1] FALSE
D1199V8, binary
                 cls
clus                0   1
  TRPA1 MUTATED    14  18
  TRPA1 WILD-TYPE 211 246
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRPA1 MUTATED     14   18
  TRPA1 WILD-TYPE  211  246
        clus
vv       TRPA1 MUTATED TRPA1 WILD-TYPE
  FEMALE            14             211
  MALE              18             246
[1] 2 2
[1] FALSE
D1199V9, binary
                 cls
clus                0   1
  TRPA1 MUTATED    24   2
  TRPA1 WILD-TYPE 326  20
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRPA1 MUTATED     24    2
  TRPA1 WILD-TYPE  326   20
     clus
vv    TRPA1 MUTATED TRPA1 WILD-TYPE
  NO             24             326
  YES             2              20
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  TRPA1 MUTATED                     25                             2
  TRPA1 WILD-TYPE                  290                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  TRPA1 MUTATED                       4                              0
  TRPA1 WILD-TYPE                   102                             10
D1199V10, multiclass
                                clus
vv                               TRPA1 MUTATED TRPA1 WILD-TYPE
  COLON ADENOCARCINOMA                      25             290
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      4             102
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  TRPA1 MUTATED    24   0   0   2
  TRPA1 WILD-TYPE 321   4  31  23
D1199V11, multiclass
    clus
vv   TRPA1 MUTATED TRPA1 WILD-TYPE
  R0            24             321
  R1             0               4
  R2             0              31
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1199V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TRPA1 MUTATED                                  0     3
  TRPA1 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  TRPA1 MUTATED                           4    14
  TRPA1 WILD-TYPE                        18   212
D1199V13, multiclass
                                  clus
vv                                 TRPA1 MUTATED TRPA1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        3               8
  BLACK OR AFRICAN AMERICAN                    4              18
  WHITE                                       14             212
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1200) Variable = CWF19L2 MUTATION ANALYSIS
D1200V1, survival
                   sevent
clus2                 0   1
  CWF19L2 MUTATED    17   1
  CWF19L2 WILD-TYPE 361  92
  CWF19L2 MUTATED CWF19L2 WILD-TYPE 
               18               453 
  CWF19L2 MUTATED CWF19L2 WILD-TYPE 
                1                92 
$`CWF19L2 MUTATED`
TCGA-A6-5659 TCGA-A6-6653 TCGA-A6-6781 TCGA-AA-3543 TCGA-AA-3663 TCGA-AA-3977 
       30.44        24.39        19.66         0.99         6.97        25.02 
TCGA-AA-A00J TCGA-AA-A010 TCGA-AU-6004 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-5913 
       18.05        34.98        27.09        12.76        10.06        51.32 
TCGA-CM-4743 TCGA-CM-5868 TCGA-AG-3883 TCGA-AG-3892 TCGA-AG-A002 TCGA-CI-6624 
       23.05        17.03         1.02        13.02        20.98         4.73 

$`CWF19L2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 
       25.18        24.16        21.76        24.69        23.87        20.12 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       61.02        78.08         6.05        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       10.88         0.20        14.50        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 
        9.99        21.14        82.95         1.91       124.27        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 
       19.04        19.99        17.95        36.95        17.03        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        6.97        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  CWF19L2 MUTATED CWF19L2 WILD-TYPE 
             0.99              0.00 
  CWF19L2 MUTATED CWF19L2 WILD-TYPE 
            51.32            148.01 
  CWF19L2 MUTATED CWF19L2 WILD-TYPE 
           18.855            20.280 
[1] "1.0 - 51.3 (18.9)"  "0.0 - 148.0 (20.3)"
[1] "hr=" "2.7"
D1200V2, continuous
D1200V3, binary
                   cls
clus                  0   1
  CWF19L2 MUTATED    15   4
  CWF19L2 WILD-TYPE 351 115
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CWF19L2 MUTATED     15    4
  CWF19L2 WILD-TYPE  351  115
        clus
vv       CWF19L2 MUTATED CWF19L2 WILD-TYPE
  COLON               15               351
  RECTUM               4               115
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CWF19L2 MUTATED         8        0        1         5         1         0
  CWF19L2 WILD-TYPE      83        1       31       133         9         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CWF19L2 MUTATED           0          0          1          1        0
  CWF19L2 WILD-TYPE        24         11         58         41       48
                   vv
clus                STAGE IVA STAGE IVB
  CWF19L2 MUTATED           1         0
  CWF19L2 WILD-TYPE        17         1
D1200V4, multiclass
            clus
vv           CWF19L2 MUTATED CWF19L2 WILD-TYPE
  STAGE I                  8                83
  STAGE IA                 0                 1
  STAGE II                 1                31
  STAGE IIA                5               133
  STAGE IIB                1                 9
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               0                11
  STAGE IIIB               1                58
  STAGE IIIC               1                41
  STAGE IV                 0                48
  STAGE IVA                1                17
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  CWF19L2 MUTATED     1   8   6   4
  CWF19L2 WILD-TYPE  16  84 323  46
D1200V5, multiclass
    clus
vv   CWF19L2 MUTATED CWF19L2 WILD-TYPE
  T1               1                16
  T2               8                84
  T3               6               323
  T4               4                46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  CWF19L2 MUTATED    16   3   0
  CWF19L2 WILD-TYPE 271 110  87
D1200V6, multiclass
    clus
vv   CWF19L2 MUTATED CWF19L2 WILD-TYPE
  N0              16               271
  N1               3               110
  N2               0                87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1200V7, binary
                   cls
clus                  0   1
  CWF19L2 MUTATED    15   1
  CWF19L2 WILD-TYPE 360  64
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CWF19L2 MUTATED     15    1
  CWF19L2 WILD-TYPE  360   64
   clus
vv  CWF19L2 MUTATED CWF19L2 WILD-TYPE
  0              15               360
  1               1                64
[1] 2 2
[1] FALSE
D1200V8, binary
                   cls
clus                  0   1
  CWF19L2 MUTATED     7  12
  CWF19L2 WILD-TYPE 218 252
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CWF19L2 MUTATED      7   12
  CWF19L2 WILD-TYPE  218  252
        clus
vv       CWF19L2 MUTATED CWF19L2 WILD-TYPE
  FEMALE               7               218
  MALE                12               252
[1] 2 2
[1] FALSE
D1200V9, binary
                   cls
clus                  0   1
  CWF19L2 MUTATED    15   0
  CWF19L2 WILD-TYPE 335  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CWF19L2 MUTATED     15    0
  CWF19L2 WILD-TYPE  335   22
     clus
vv    CWF19L2 MUTATED CWF19L2 WILD-TYPE
  NO               15               335
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CWF19L2 MUTATED                     11                             4
  CWF19L2 WILD-TYPE                  304                            43
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CWF19L2 MUTATED                       4                              0
  CWF19L2 WILD-TYPE                   102                             10
D1200V10, multiclass
                                clus
vv                               CWF19L2 MUTATED CWF19L2 WILD-TYPE
  COLON ADENOCARCINOMA                        11               304
  COLON MUCINOUS ADENOCARCINOMA                4                43
  RECTAL ADENOCARCINOMA                        4               102
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  CWF19L2 MUTATED    13   0   0   3
  CWF19L2 WILD-TYPE 332   4  31  22
D1200V11, multiclass
    clus
vv   CWF19L2 MUTATED CWF19L2 WILD-TYPE
  R0              13               332
  R1               0                 4
  R2               0                31
  RX               3                22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1200V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CWF19L2 MUTATED                                  0     2
  CWF19L2 WILD-TYPE                                1     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  CWF19L2 MUTATED                           0     8
  CWF19L2 WILD-TYPE                        22   218
D1200V13, multiclass
                                  clus
vv                                 CWF19L2 MUTATED CWF19L2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          2                 9
  BLACK OR AFRICAN AMERICAN                      0                22
  WHITE                                          8               218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1201) Variable = SERPINA9 MUTATION ANALYSIS
D1201V1, survival
                    sevent
clus2                  0   1
  SERPINA9 MUTATED     7   3
  SERPINA9 WILD-TYPE 371  90
  SERPINA9 MUTATED SERPINA9 WILD-TYPE 
                10                461 
  SERPINA9 MUTATED SERPINA9 WILD-TYPE 
                 3                 90 
$`SERPINA9 MUTATED`
TCGA-A6-5657 TCGA-AD-6901 TCGA-AZ-6598 TCGA-CA-6718 TCGA-CM-4743 TCGA-CM-5344 
       31.63        22.42        49.41        10.06        23.05        22.03 
TCGA-CM-5348 TCGA-CM-6675 TCGA-D5-6923 TCGA-AG-3726 
       22.98        13.05        12.43         7.99 

$`SERPINA9 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6963 
       15.52        56.55         0.79         0.72         5.79        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 
      106.75        22.36        62.79        88.21         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       12.76        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
      124.27        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       11.01        12.95        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        3.68         4.41        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3727 
        0.99        15.95        19.99        13.94        19.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  SERPINA9 MUTATED SERPINA9 WILD-TYPE 
              7.99               0.00 
  SERPINA9 MUTATED SERPINA9 WILD-TYPE 
             49.41             148.01 
  SERPINA9 MUTATED SERPINA9 WILD-TYPE 
            22.225             20.120 
[1] "8.0 - 49.4 (22.2)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.8"
D1201V2, continuous
D1201V3, binary
                    cls
clus                   0   1
  SERPINA9 MUTATED    10   1
  SERPINA9 WILD-TYPE 356 118
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SERPINA9 MUTATED     10    1
  SERPINA9 WILD-TYPE  356  118
        clus
vv       SERPINA9 MUTATED SERPINA9 WILD-TYPE
  COLON                10                356
  RECTUM                1                118
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SERPINA9 MUTATED         2        0        1         2         0         0
  SERPINA9 WILD-TYPE      89        1       31       136        10         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SERPINA9 MUTATED           1          0          3          0        0
  SERPINA9 WILD-TYPE        23         11         56         42       48
                    vv
clus                 STAGE IVA STAGE IVB
  SERPINA9 MUTATED           0         1
  SERPINA9 WILD-TYPE        18         0
D1201V4, multiclass
            clus
vv           SERPINA9 MUTATED SERPINA9 WILD-TYPE
  STAGE I                   2                 89
  STAGE IA                  0                  1
  STAGE II                  1                 31
  STAGE IIA                 2                136
  STAGE IIB                 0                 10
  STAGE IIC                 0                  1
  STAGE III                 1                 23
  STAGE IIIA                0                 11
  STAGE IIIB                3                 56
  STAGE IIIC                0                 42
  STAGE IV                  0                 48
  STAGE IVA                 0                 18
  STAGE IVB                 1                  0
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  SERPINA9 MUTATED     0   2   9   0
  SERPINA9 WILD-TYPE  17  90 320  50
D1201V5, multiclass
    clus
vv   SERPINA9 MUTATED SERPINA9 WILD-TYPE
  T1                0                 17
  T2                2                 90
  T3                9                320
  T4                0                 50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  SERPINA9 MUTATED     6   3   2
  SERPINA9 WILD-TYPE 281 110  85
D1201V6, multiclass
    clus
vv   SERPINA9 MUTATED SERPINA9 WILD-TYPE
  N0                6                281
  N1                3                110
  N2                2                 85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1201V7, binary
                    cls
clus                   0   1
  SERPINA9 MUTATED     8   1
  SERPINA9 WILD-TYPE 367  64
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SERPINA9 MUTATED      8    1
  SERPINA9 WILD-TYPE  367   64
   clus
vv  SERPINA9 MUTATED SERPINA9 WILD-TYPE
  0                8                367
  1                1                 64
[1] 2 2
[1] FALSE
D1201V8, binary
                    cls
clus                   0   1
  SERPINA9 MUTATED     3   8
  SERPINA9 WILD-TYPE 222 256
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SERPINA9 MUTATED      3    8
  SERPINA9 WILD-TYPE  222  256
        clus
vv       SERPINA9 MUTATED SERPINA9 WILD-TYPE
  FEMALE                3                222
  MALE                  8                256
[1] 2 2
[1] FALSE
D1201V9, binary
                    cls
clus                   0   1
  SERPINA9 MUTATED    10   0
  SERPINA9 WILD-TYPE 340  22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SERPINA9 MUTATED     10    0
  SERPINA9 WILD-TYPE  340   22
     clus
vv    SERPINA9 MUTATED SERPINA9 WILD-TYPE
  NO                10                340
  YES                0                 22
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SERPINA9 MUTATED                     10                             0
  SERPINA9 WILD-TYPE                  305                            47
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SERPINA9 MUTATED                       1                              0
  SERPINA9 WILD-TYPE                   105                             10
D1201V10, multiclass
                                clus
vv                               SERPINA9 MUTATED SERPINA9 WILD-TYPE
  COLON ADENOCARCINOMA                         10                305
  COLON MUCINOUS ADENOCARCINOMA                 0                 47
  RECTAL ADENOCARCINOMA                         1                105
  RECTAL MUCINOUS ADENOCARCINOMA                0                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  SERPINA9 MUTATED     8   0   0   1
  SERPINA9 WILD-TYPE 337   4  31  24
D1201V11, multiclass
    clus
vv   SERPINA9 MUTATED SERPINA9 WILD-TYPE
  R0                8                337
  R1                0                  4
  R2                0                 31
  RX                1                 24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1201V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SERPINA9 MUTATED                                  0     1
  SERPINA9 WILD-TYPE                                1    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  SERPINA9 MUTATED                           2     6
  SERPINA9 WILD-TYPE                        20   220
D1201V13, multiclass
                                  clus
vv                                 SERPINA9 MUTATED SERPINA9 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                 10
  BLACK OR AFRICAN AMERICAN                       2                 20
  WHITE                                           6                220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1202) Variable = HSP90AA1 MUTATION ANALYSIS
D1202V1, survival
                    sevent
clus2                  0   1
  HSP90AA1 MUTATED     6   2
  HSP90AA1 WILD-TYPE 372  91
  HSP90AA1 MUTATED HSP90AA1 WILD-TYPE 
                 8                463 
  HSP90AA1 MUTATED HSP90AA1 WILD-TYPE 
                 2                 91 
$`HSP90AA1 MUTATED`
TCGA-A6-4105 TCGA-A6-5659 TCGA-A6-6781 TCGA-AA-3710 TCGA-AA-A010 TCGA-AZ-6605 
       14.53        30.44        19.66        26.99        34.98         5.23 
TCGA-CM-6171 TCGA-AG-A002 
       14.04        20.98 

$`HSP90AA1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 
       16.57        34.65        33.34        32.75        36.53        32.91 
TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       31.63        29.19        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       85.05        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  HSP90AA1 MUTATED HSP90AA1 WILD-TYPE 
              5.23               0.00 
  HSP90AA1 MUTATED HSP90AA1 WILD-TYPE 
             34.98             148.01 
  HSP90AA1 MUTATED HSP90AA1 WILD-TYPE 
             20.32              20.19 
[1] "5.2 - 35.0 (20.3)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.7"
D1202V2, continuous
D1202V3, binary
                    cls
clus                   0   1
  HSP90AA1 MUTATED     7   2
  HSP90AA1 WILD-TYPE 359 117
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HSP90AA1 MUTATED      7    2
  HSP90AA1 WILD-TYPE  359  117
        clus
vv       HSP90AA1 MUTATED HSP90AA1 WILD-TYPE
  COLON                 7                359
  RECTUM                2                117
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  HSP90AA1 MUTATED         3        0        0         2         1         0
  HSP90AA1 WILD-TYPE      88        1       32       136         9         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HSP90AA1 MUTATED           1          0          1          1        0
  HSP90AA1 WILD-TYPE        23         11         58         41       48
                    vv
clus                 STAGE IVA STAGE IVB
  HSP90AA1 MUTATED           0         0
  HSP90AA1 WILD-TYPE        18         1
D1202V4, multiclass
            clus
vv           HSP90AA1 MUTATED HSP90AA1 WILD-TYPE
  STAGE I                   3                 88
  STAGE IA                  0                  1
  STAGE II                  0                 32
  STAGE IIA                 2                136
  STAGE IIB                 1                  9
  STAGE IIC                 0                  1
  STAGE III                 1                 23
  STAGE IIIA                0                 11
  STAGE IIIB                1                 58
  STAGE IIIC                1                 41
  STAGE IV                  0                 48
  STAGE IVA                 0                 18
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  HSP90AA1 MUTATED     0   3   3   3
  HSP90AA1 WILD-TYPE  17  89 326  47
D1202V5, multiclass
    clus
vv   HSP90AA1 MUTATED HSP90AA1 WILD-TYPE
  T1                0                 17
  T2                3                 89
  T3                3                326
  T4                3                 47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  HSP90AA1 MUTATED     6   3   0
  HSP90AA1 WILD-TYPE 281 110  87
D1202V6, multiclass
    clus
vv   HSP90AA1 MUTATED HSP90AA1 WILD-TYPE
  N0                6                281
  N1                3                110
  N2                0                 87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1202V7, binary
                    cls
clus                   0   1
  HSP90AA1 MUTATED     7   0
  HSP90AA1 WILD-TYPE 368  65
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HSP90AA1 MUTATED      7    0
  HSP90AA1 WILD-TYPE  368   65
   clus
vv  HSP90AA1 MUTATED HSP90AA1 WILD-TYPE
  0                7                368
  1                0                 65
[1] 2 2
[1] FALSE
D1202V8, binary
                    cls
clus                   0   1
  HSP90AA1 MUTATED     3   6
  HSP90AA1 WILD-TYPE 222 258
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HSP90AA1 MUTATED      3    6
  HSP90AA1 WILD-TYPE  222  258
        clus
vv       HSP90AA1 MUTATED HSP90AA1 WILD-TYPE
  FEMALE                3                222
  MALE                  6                258
[1] 2 2
[1] FALSE
D1202V9, binary
                    cls
clus                   0   1
  HSP90AA1 MUTATED     8   0
  HSP90AA1 WILD-TYPE 342  22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HSP90AA1 MUTATED      8    0
  HSP90AA1 WILD-TYPE  342   22
     clus
vv    HSP90AA1 MUTATED HSP90AA1 WILD-TYPE
  NO                 8                342
  YES                0                 22
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  HSP90AA1 MUTATED                      6                             1
  HSP90AA1 WILD-TYPE                  309                            46
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  HSP90AA1 MUTATED                       2                              0
  HSP90AA1 WILD-TYPE                   104                             10
D1202V10, multiclass
                                clus
vv                               HSP90AA1 MUTATED HSP90AA1 WILD-TYPE
  COLON ADENOCARCINOMA                          6                309
  COLON MUCINOUS ADENOCARCINOMA                 1                 46
  RECTAL ADENOCARCINOMA                         2                104
  RECTAL MUCINOUS ADENOCARCINOMA                0                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  HSP90AA1 MUTATED     6   0   0   0
  HSP90AA1 WILD-TYPE 339   4  31  25
D1202V11, multiclass
    clus
vv   HSP90AA1 MUTATED HSP90AA1 WILD-TYPE
  R0                6                339
  R1                0                  4
  R2                0                 31
  RX                0                 25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1202V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HSP90AA1 MUTATED                                  0     0
  HSP90AA1 WILD-TYPE                                1    11
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  HSP90AA1 MUTATED                           0     6
  HSP90AA1 WILD-TYPE                        22   220
D1202V13, multiclass
                                  clus
vv                                 HSP90AA1 MUTATED HSP90AA1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 11
  BLACK OR AFRICAN AMERICAN                       0                 22
  WHITE                                           6                220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1203) Variable = SATB1 MUTATION ANALYSIS
D1203V1, survival
                 sevent
clus2               0   1
  SATB1 MUTATED    12   3
  SATB1 WILD-TYPE 366  90
  SATB1 MUTATED SATB1 WILD-TYPE 
             15             456 
  SATB1 MUTATED SATB1 WILD-TYPE 
              3              90 
$`SATB1 MUTATED`
TCGA-A6-6648 TCGA-A6-6780 TCGA-AA-3815 TCGA-AD-6889 TCGA-AZ-6598 TCGA-CA-6718 
       25.18        20.12        33.04        56.55        49.41        10.06 
TCGA-D5-6532 TCGA-D5-6540 TCGA-D5-6928 TCGA-DM-A1HB TCGA-F4-6856 TCGA-G4-6315 
       18.25        16.14        11.64       135.65        35.31        61.91 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AG-A002 
       46.75        79.69        20.98 

$`SATB1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.08        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       35.05         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 
       18.05        40.96         0.07        21.37        15.52         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        88.21         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 
        3.25         3.29         0.07        12.20        12.76        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       56.09        55.92        20.19         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 
       17.85         4.80        17.13        12.49        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 
       12.59       140.38         7.50        44.32       131.51       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
        0.53        47.41       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6317 TCGA-G4-6321 
       44.68        55.04        85.48        63.62        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-AF-2687 TCGA-AF-2689 
       13.78        35.80        26.17        91.79        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  SATB1 MUTATED SATB1 WILD-TYPE 
          10.06            0.00 
  SATB1 MUTATED SATB1 WILD-TYPE 
         135.65          148.01 
  SATB1 MUTATED SATB1 WILD-TYPE 
          33.04           20.02 
[1] "10.1 - 135.7 (33.0)" "0.0 - 148.0 (20.0)" 
[1] "hr=" "1.5"
D1203V2, continuous
D1203V3, binary
                 cls
clus                0   1
  SATB1 MUTATED    16   1
  SATB1 WILD-TYPE 350 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SATB1 MUTATED     16    1
  SATB1 WILD-TYPE  350  118
        clus
vv       SATB1 MUTATED SATB1 WILD-TYPE
  COLON             16             350
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SATB1 MUTATED         4        0        1         7         0         0
  SATB1 WILD-TYPE      87        1       31       131        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SATB1 MUTATED           1          0          1          0        2         1
  SATB1 WILD-TYPE        23         11         58         42       46        17
                 vv
clus              STAGE IVB
  SATB1 MUTATED           0
  SATB1 WILD-TYPE         1
D1203V4, multiclass
            clus
vv           SATB1 MUTATED SATB1 WILD-TYPE
  STAGE I                4              87
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              7             131
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             0              42
  STAGE IV               2              46
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  SATB1 MUTATED     0   4  12   1
  SATB1 WILD-TYPE  17  88 317  49
D1203V5, multiclass
    clus
vv   SATB1 MUTATED SATB1 WILD-TYPE
  T1             0              17
  T2             4              88
  T3            12             317
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  SATB1 MUTATED    13   3   1
  SATB1 WILD-TYPE 274 110  86
D1203V6, multiclass
    clus
vv   SATB1 MUTATED SATB1 WILD-TYPE
  N0            13             274
  N1             3             110
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1203V7, binary
                 cls
clus                0   1
  SATB1 MUTATED    12   3
  SATB1 WILD-TYPE 363  62
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SATB1 MUTATED     12    3
  SATB1 WILD-TYPE  363   62
   clus
vv  SATB1 MUTATED SATB1 WILD-TYPE
  0            12             363
  1             3              62
[1] 2 2
[1] FALSE
D1203V8, binary
                 cls
clus                0   1
  SATB1 MUTATED     3  14
  SATB1 WILD-TYPE 222 250
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SATB1 MUTATED      3   14
  SATB1 WILD-TYPE  222  250
        clus
vv       SATB1 MUTATED SATB1 WILD-TYPE
  FEMALE             3             222
  MALE              14             250
[1] 2 2
[1] FALSE
D1203V9, binary
                 cls
clus                0   1
  SATB1 MUTATED    13   0
  SATB1 WILD-TYPE 337  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SATB1 MUTATED     13    0
  SATB1 WILD-TYPE  337   22
     clus
vv    SATB1 MUTATED SATB1 WILD-TYPE
  NO             13             337
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SATB1 MUTATED                     11                             4
  SATB1 WILD-TYPE                  304                            43
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SATB1 MUTATED                       1                              0
  SATB1 WILD-TYPE                   105                             10
D1203V10, multiclass
                                clus
vv                               SATB1 MUTATED SATB1 WILD-TYPE
  COLON ADENOCARCINOMA                      11             304
  COLON MUCINOUS ADENOCARCINOMA              4              43
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  SATB1 MUTATED    10   0   1   1
  SATB1 WILD-TYPE 335   4  30  24
D1203V11, multiclass
    clus
vv   SATB1 MUTATED SATB1 WILD-TYPE
  R0            10             335
  R1             0               4
  R2             1              30
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1203V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SATB1 MUTATED                                  0     2
  SATB1 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  SATB1 MUTATED                           0    11
  SATB1 WILD-TYPE                        22   215
D1203V13, multiclass
                                  clus
vv                                 SATB1 MUTATED SATB1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               9
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                       11             215
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1204) Variable = FBXO45 MUTATION ANALYSIS
D1204V1, survival
                  sevent
clus2                0   1
  FBXO45 MUTATED     5   1
  FBXO45 WILD-TYPE 373  92
  FBXO45 MUTATED FBXO45 WILD-TYPE 
               6              465 
  FBXO45 MUTATED FBXO45 WILD-TYPE 
               1               92 
$`FBXO45 MUTATED`
TCGA-AA-A010 TCGA-CA-6717 TCGA-CM-5349 TCGA-AG-3731 TCGA-AG-A002 TCGA-DY-A1DF 
       34.98        12.76        30.08        37.02        20.98        24.13 

$`FBXO45 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07        12.20        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5860 
       25.02        13.02        29.06        22.03        22.98        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
        0.99        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DG 
        5.03         5.29       126.44        41.36        57.24        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  FBXO45 MUTATED FBXO45 WILD-TYPE 
           12.76             0.00 
  FBXO45 MUTATED FBXO45 WILD-TYPE 
           37.02           148.01 
  FBXO45 MUTATED FBXO45 WILD-TYPE 
          27.105           20.050 
[1] "12.8 - 37.0 (27.1)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.1"
D1204V2, continuous
D1204V3, binary
                  cls
clus                 0   1
  FBXO45 MUTATED     3   3
  FBXO45 WILD-TYPE 363 116
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FBXO45 MUTATED      3    3
  FBXO45 WILD-TYPE  363  116
        clus
vv       FBXO45 MUTATED FBXO45 WILD-TYPE
  COLON               3              363
  RECTUM              3              116
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FBXO45 MUTATED         1        0        0         2         1         0
  FBXO45 WILD-TYPE      90        1       32       136         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FBXO45 MUTATED           0          0          0          1        1
  FBXO45 WILD-TYPE        24         11         59         41       47
                  vv
clus               STAGE IVA STAGE IVB
  FBXO45 MUTATED           0         0
  FBXO45 WILD-TYPE        18         1
D1204V4, multiclass
            clus
vv           FBXO45 MUTATED FBXO45 WILD-TYPE
  STAGE I                 1               90
  STAGE IA                0                1
  STAGE II                0               32
  STAGE IIA               2              136
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              0               59
  STAGE IIIC              1               41
  STAGE IV                1               47
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  FBXO45 MUTATED     0   1   4   1
  FBXO45 WILD-TYPE  17  91 325  49
D1204V5, multiclass
    clus
vv   FBXO45 MUTATED FBXO45 WILD-TYPE
  T1              0               17
  T2              1               91
  T3              4              325
  T4              1               49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  FBXO45 MUTATED     4   1   1
  FBXO45 WILD-TYPE 283 112  86
D1204V6, multiclass
    clus
vv   FBXO45 MUTATED FBXO45 WILD-TYPE
  N0              4              283
  N1              1              112
  N2              1               86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1204V7, binary
                  cls
clus                 0   1
  FBXO45 MUTATED     5   1
  FBXO45 WILD-TYPE 370  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FBXO45 MUTATED      5    1
  FBXO45 WILD-TYPE  370   64
   clus
vv  FBXO45 MUTATED FBXO45 WILD-TYPE
  0              5              370
  1              1               64
[1] 2 2
[1] FALSE
D1204V8, binary
                  cls
clus                 0   1
  FBXO45 MUTATED     3   3
  FBXO45 WILD-TYPE 222 261
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FBXO45 MUTATED      3    3
  FBXO45 WILD-TYPE  222  261
        clus
vv       FBXO45 MUTATED FBXO45 WILD-TYPE
  FEMALE              3              222
  MALE                3              261
[1] 2 2
[1] FALSE
D1204V9, binary
                  cls
clus                 0   1
  FBXO45 MUTATED     5   0
  FBXO45 WILD-TYPE 345  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FBXO45 MUTATED      5    0
  FBXO45 WILD-TYPE  345   22
     clus
vv    FBXO45 MUTATED FBXO45 WILD-TYPE
  NO               5              345
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  FBXO45 MUTATED                      2                             1
  FBXO45 WILD-TYPE                  313                            46
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  FBXO45 MUTATED                       3                              0
  FBXO45 WILD-TYPE                   103                             10
D1204V10, multiclass
                                clus
vv                               FBXO45 MUTATED FBXO45 WILD-TYPE
  COLON ADENOCARCINOMA                        2              313
  COLON MUCINOUS ADENOCARCINOMA               1               46
  RECTAL ADENOCARCINOMA                       3              103
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  FBXO45 MUTATED     3   0   1   1
  FBXO45 WILD-TYPE 342   4  30  24
D1204V11, multiclass
    clus
vv   FBXO45 MUTATED FBXO45 WILD-TYPE
  R0              3              342
  R1              0                4
  R2              1               30
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1204V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FBXO45 MUTATED                                  0     1
  FBXO45 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  FBXO45 MUTATED                           0     2
  FBXO45 WILD-TYPE                        22   224
D1204V13, multiclass
                                  clus
vv                                 FBXO45 MUTATED FBXO45 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         2              224
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1205) Variable = MMP7 MUTATION ANALYSIS
D1205V1, survival
                sevent
clus2              0   1
  MMP7 MUTATED     8   2
  MMP7 WILD-TYPE 370  91
  MMP7 MUTATED MMP7 WILD-TYPE 
            10            461 
  MMP7 MUTATED MMP7 WILD-TYPE 
             2             91 
$`MMP7 MUTATED`
TCGA-A6-6141 TCGA-AA-3811 TCGA-AA-3950 TCGA-AA-A00N TCGA-AA-A01X TCGA-AY-5543 
        8.38        10.06        24.00         4.01        26.01        33.01 
TCGA-AZ-4315 TCGA-G4-6588 TCGA-AG-A00H TCGA-AG-A02N 
       58.39        26.17        25.97        61.97 

$`MMP7 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 
       22.09        22.06        32.71        27.09        22.52        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 
       12.99        24.00        33.01        26.01         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
       27.09        16.31         0.95        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       35.80        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       20.98        13.94         6.02        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
       49.97         1.94        38.96        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  MMP7 MUTATED MMP7 WILD-TYPE 
          4.01           0.00 
  MMP7 MUTATED MMP7 WILD-TYPE 
         61.97         148.01 
  MMP7 MUTATED MMP7 WILD-TYPE 
         25.99          20.05 
[1] "4.0 - 62.0 (26.0)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.1"
D1205V2, continuous
D1205V3, binary
                cls
clus               0   1
  MMP7 MUTATED     8   2
  MMP7 WILD-TYPE 358 117
[1] "tbl2"
                cls
clus             [,1] [,2]
  MMP7 MUTATED      8    2
  MMP7 WILD-TYPE  358  117
        clus
vv       MMP7 MUTATED MMP7 WILD-TYPE
  COLON             8            358
  RECTUM            2            117
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MMP7 MUTATED         0        0        1         5         1         0
  MMP7 WILD-TYPE      91        1       31       133         9         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MMP7 MUTATED           2          0          0          0        0         1
  MMP7 WILD-TYPE        22         11         59         42       48        17
                vv
clus             STAGE IVB
  MMP7 MUTATED           0
  MMP7 WILD-TYPE         1
D1205V4, multiclass
            clus
vv           MMP7 MUTATED MMP7 WILD-TYPE
  STAGE I               0             91
  STAGE IA              0              1
  STAGE II              1             31
  STAGE IIA             5            133
  STAGE IIB             1              9
  STAGE IIC             0              1
  STAGE III             2             22
  STAGE IIIA            0             11
  STAGE IIIB            0             59
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             1             17
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  MMP7 MUTATED     0   1   8   1
  MMP7 WILD-TYPE  17  91 321  49
D1205V5, multiclass
    clus
vv   MMP7 MUTATED MMP7 WILD-TYPE
  T1            0             17
  T2            1             91
  T3            8            321
  T4            1             49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  MMP7 MUTATED     7   2   1
  MMP7 WILD-TYPE 280 111  86
D1205V6, multiclass
    clus
vv   MMP7 MUTATED MMP7 WILD-TYPE
  N0            7            280
  N1            2            111
  N2            1             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1205V7, binary
                cls
clus               0   1
  MMP7 MUTATED     9   1
  MMP7 WILD-TYPE 366  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  MMP7 MUTATED      9    1
  MMP7 WILD-TYPE  366   64
   clus
vv  MMP7 MUTATED MMP7 WILD-TYPE
  0            9            366
  1            1             64
[1] 2 2
[1] FALSE
D1205V8, binary
                cls
clus               0   1
  MMP7 MUTATED     5   5
  MMP7 WILD-TYPE 220 259
[1] "tbl2"
                cls
clus             [,1] [,2]
  MMP7 MUTATED      5    5
  MMP7 WILD-TYPE  220  259
        clus
vv       MMP7 MUTATED MMP7 WILD-TYPE
  FEMALE            5            220
  MALE              5            259
[1] 2 2
[1] FALSE
D1205V9, binary
                cls
clus               0   1
  MMP7 MUTATED     7   1
  MMP7 WILD-TYPE 343  21
[1] "tbl2"
                cls
clus             [,1] [,2]
  MMP7 MUTATED      7    1
  MMP7 WILD-TYPE  343   21
     clus
vv    MMP7 MUTATED MMP7 WILD-TYPE
  NO             7            343
  YES            1             21
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MMP7 MUTATED                      6                             2
  MMP7 WILD-TYPE                  309                            45
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MMP7 MUTATED                       2                              0
  MMP7 WILD-TYPE                   104                             10
D1205V10, multiclass
                                clus
vv                               MMP7 MUTATED MMP7 WILD-TYPE
  COLON ADENOCARCINOMA                      6            309
  COLON MUCINOUS ADENOCARCINOMA             2             45
  RECTAL ADENOCARCINOMA                     2            104
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  MMP7 MUTATED     8   0   0   1
  MMP7 WILD-TYPE 337   4  31  24
D1205V11, multiclass
    clus
vv   MMP7 MUTATED MMP7 WILD-TYPE
  R0            8            337
  R1            0              4
  R2            0             31
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1205V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MMP7 MUTATED                                  0     0
  MMP7 WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  MMP7 MUTATED                           2     2
  MMP7 WILD-TYPE                        20   224
D1205V13, multiclass
                                  clus
vv                                 MMP7 MUTATED MMP7 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   2             20
  WHITE                                       2            224
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1206) Variable = TMCO6 MUTATION ANALYSIS
D1206V1, survival
                 sevent
clus2               0   1
  TMCO6 MUTATED     6   1
  TMCO6 WILD-TYPE 372  92
  TMCO6 MUTATED TMCO6 WILD-TYPE 
              7             464 
  TMCO6 MUTATED TMCO6 WILD-TYPE 
              1              92 
$`TMCO6 MUTATED`
TCGA-AA-3821 TCGA-AA-3947 TCGA-AA-A010 TCGA-AD-6895 TCGA-AZ-6598 TCGA-CM-4746 
        1.02        33.01        34.98         0.72        49.41        37.02 
TCGA-G4-6307 
       55.04 

$`TMCO6 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
        2.01        12.99        24.00        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.79         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        88.21         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       23.05        20.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  TMCO6 MUTATED TMCO6 WILD-TYPE 
           0.72            0.00 
  TMCO6 MUTATED TMCO6 WILD-TYPE 
          55.04          148.01 
  TMCO6 MUTATED TMCO6 WILD-TYPE 
         34.980          20.085 
[1] "0.7 - 55.0 (35.0)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.6"
D1206V2, continuous
D1206V3, binary
                 cls
clus                0   1
  TMCO6 MUTATED     7   0
  TMCO6 WILD-TYPE 359 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TMCO6 MUTATED      7    0
  TMCO6 WILD-TYPE  359  119
        clus
vv       TMCO6 MUTATED TMCO6 WILD-TYPE
  COLON              7             359
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TMCO6 MUTATED         2        0        1         0         2         0
  TMCO6 WILD-TYPE      89        1       31       138         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TMCO6 MUTATED           0          0          1          0        0         0
  TMCO6 WILD-TYPE        24         11         58         42       48        18
                 vv
clus              STAGE IVB
  TMCO6 MUTATED           0
  TMCO6 WILD-TYPE         1
D1206V4, multiclass
            clus
vv           TMCO6 MUTATED TMCO6 WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              0             138
  STAGE IIB              2               8
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  TMCO6 MUTATED     0   2   3   2
  TMCO6 WILD-TYPE  17  90 326  48
D1206V5, multiclass
    clus
vv   TMCO6 MUTATED TMCO6 WILD-TYPE
  T1             0              17
  T2             2              90
  T3             3             326
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  TMCO6 MUTATED     5   2   0
  TMCO6 WILD-TYPE 282 111  87
D1206V6, multiclass
    clus
vv   TMCO6 MUTATED TMCO6 WILD-TYPE
  N0             5             282
  N1             2             111
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1206V7, binary
                 cls
clus                0   1
  TMCO6 MUTATED     5   0
  TMCO6 WILD-TYPE 370  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TMCO6 MUTATED      5    0
  TMCO6 WILD-TYPE  370   65
   clus
vv  TMCO6 MUTATED TMCO6 WILD-TYPE
  0             5             370
  1             0              65
[1] 2 2
[1] FALSE
D1206V8, binary
                 cls
clus                0   1
  TMCO6 MUTATED     5   2
  TMCO6 WILD-TYPE 220 262
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TMCO6 MUTATED      5    2
  TMCO6 WILD-TYPE  220  262
        clus
vv       TMCO6 MUTATED TMCO6 WILD-TYPE
  FEMALE             5             220
  MALE               2             262
[1] 2 2
[1] FALSE
D1206V9, binary
                 cls
clus                0   1
  TMCO6 MUTATED     6   0
  TMCO6 WILD-TYPE 344  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TMCO6 MUTATED      6    0
  TMCO6 WILD-TYPE  344   22
     clus
vv    TMCO6 MUTATED TMCO6 WILD-TYPE
  NO              6             344
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  TMCO6 MUTATED                      5                             2
  TMCO6 WILD-TYPE                  310                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  TMCO6 MUTATED                       0                              0
  TMCO6 WILD-TYPE                   106                             10
D1206V10, multiclass
                                clus
vv                               TMCO6 MUTATED TMCO6 WILD-TYPE
  COLON ADENOCARCINOMA                       5             310
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  TMCO6 MUTATED     5   0   0   0
  TMCO6 WILD-TYPE 340   4  31  25
D1206V11, multiclass
    clus
vv   TMCO6 MUTATED TMCO6 WILD-TYPE
  R0             5             340
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1206V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TMCO6 MUTATED                                  0     0
  TMCO6 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  TMCO6 MUTATED                           1     3
  TMCO6 WILD-TYPE                        21   223
D1206V13, multiclass
                                  clus
vv                                 TMCO6 MUTATED TMCO6 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        3             223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1207) Variable = APAF1 MUTATION ANALYSIS
D1207V1, survival
                 sevent
clus2               0   1
  APAF1 MUTATED    17   3
  APAF1 WILD-TYPE 361  90
  APAF1 MUTATED APAF1 WILD-TYPE 
             20             451 
  APAF1 MUTATED APAF1 WILD-TYPE 
              3              90 
$`APAF1 MUTATED`
TCGA-A6-5665 TCGA-A6-5666 TCGA-AA-3502 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3833 
       22.06        32.71        35.01        19.04        19.04        15.95 
TCGA-AA-3950 TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A010 TCGA-CA-6718 TCGA-CK-4947 
       24.00        25.02         4.01        34.98        10.06        17.56 
TCGA-CM-5341 TCGA-CM-6170 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-6540 TCGA-G4-6299 
       29.06        15.02        12.26        56.09        16.14        74.56 
TCGA-DC-6155 TCGA-DY-A0XA 
       13.97       126.44 

$`APAF1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       22.09        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3510 
       19.66        20.28         7.04         3.02         1.02        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       85.05        26.99        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
       25.02         1.02        17.98        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       14.30       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-5348 
       20.02        37.02        25.02        13.02        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6171 TCGA-CM-6172 
       21.99        14.99        12.99        13.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.03        45.40        19.59        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       12.49        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       47.41        35.31       133.18        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6157 
        4.73        78.12         7.17        15.02         5.03        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  APAF1 MUTATED APAF1 WILD-TYPE 
           4.01            0.00 
  APAF1 MUTATED APAF1 WILD-TYPE 
         126.44          148.01 
  APAF1 MUTATED APAF1 WILD-TYPE 
          20.55           20.19 
[1] "4.0 - 126.4 (20.5)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.5"
D1207V2, continuous
D1207V3, binary
                 cls
clus                0   1
  APAF1 MUTATED    18   2
  APAF1 WILD-TYPE 348 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  APAF1 MUTATED     18    2
  APAF1 WILD-TYPE  348  117
        clus
vv       APAF1 MUTATED APAF1 WILD-TYPE
  COLON             18             348
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  APAF1 MUTATED         3        0        1         6         2         1
  APAF1 WILD-TYPE      88        1       31       132         8         0
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  APAF1 MUTATED           0          2          2          1        1         0
  APAF1 WILD-TYPE        24          9         57         41       47        18
                 vv
clus              STAGE IVB
  APAF1 MUTATED           0
  APAF1 WILD-TYPE         1
D1207V4, multiclass
            clus
vv           APAF1 MUTATED APAF1 WILD-TYPE
  STAGE I                3              88
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              6             132
  STAGE IIB              2               8
  STAGE IIC              1               0
  STAGE III              0              24
  STAGE IIIA             2               9
  STAGE IIIB             2              57
  STAGE IIIC             1              41
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  APAF1 MUTATED     0   6  10   4
  APAF1 WILD-TYPE  17  86 319  46
D1207V5, multiclass
    clus
vv   APAF1 MUTATED APAF1 WILD-TYPE
  T1             0              17
  T2             6              86
  T3            10             319
  T4             4              46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  APAF1 MUTATED    15   4   1
  APAF1 WILD-TYPE 272 109  86
D1207V6, multiclass
    clus
vv   APAF1 MUTATED APAF1 WILD-TYPE
  N0            15             272
  N1             4             109
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1207V7, binary
                 cls
clus                0   1
  APAF1 MUTATED    18   1
  APAF1 WILD-TYPE 357  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  APAF1 MUTATED     18    1
  APAF1 WILD-TYPE  357   64
   clus
vv  APAF1 MUTATED APAF1 WILD-TYPE
  0            18             357
  1             1              64
[1] 2 2
[1] FALSE
D1207V8, binary
                 cls
clus                0   1
  APAF1 MUTATED    10  10
  APAF1 WILD-TYPE 215 254
[1] "tbl2"
                 cls
clus              [,1] [,2]
  APAF1 MUTATED     10   10
  APAF1 WILD-TYPE  215  254
        clus
vv       APAF1 MUTATED APAF1 WILD-TYPE
  FEMALE            10             215
  MALE              10             254
[1] 2 2
[1] FALSE
D1207V9, binary
                 cls
clus                0   1
  APAF1 MUTATED    17   1
  APAF1 WILD-TYPE 333  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  APAF1 MUTATED     17    1
  APAF1 WILD-TYPE  333   21
     clus
vv    APAF1 MUTATED APAF1 WILD-TYPE
  NO             17             333
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  APAF1 MUTATED                     15                             3
  APAF1 WILD-TYPE                  300                            44
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  APAF1 MUTATED                       2                              0
  APAF1 WILD-TYPE                   104                             10
D1207V10, multiclass
                                clus
vv                               APAF1 MUTATED APAF1 WILD-TYPE
  COLON ADENOCARCINOMA                      15             300
  COLON MUCINOUS ADENOCARCINOMA              3              44
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  APAF1 MUTATED    14   0   1   2
  APAF1 WILD-TYPE 331   4  30  23
D1207V11, multiclass
    clus
vv   APAF1 MUTATED APAF1 WILD-TYPE
  R0            14             331
  R1             0               4
  R2             1              30
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1207V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  APAF1 MUTATED                                  0     1
  APAF1 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  APAF1 MUTATED                           0    11
  APAF1 WILD-TYPE                        22   215
D1207V13, multiclass
                                  clus
vv                                 APAF1 MUTATED APAF1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                       11             215
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1208) Variable = FGB MUTATION ANALYSIS
D1208V1, survival
               sevent
clus2             0   1
  FGB MUTATED     5   1
  FGB WILD-TYPE 373  92
  FGB MUTATED FGB WILD-TYPE 
            6           465 
  FGB MUTATED FGB WILD-TYPE 
            1            92 
$`FGB MUTATED`
TCGA-AA-A010 TCGA-AZ-4315 TCGA-CK-5914 TCGA-CM-6167 TCGA-AG-A002 TCGA-DC-6158 
       34.98        58.39         9.99        14.99        20.98        10.98 

$`FGB WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        33.01        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 
       85.45        15.62        49.08        51.32        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6168 
       12.00         2.96        29.03        16.04        21.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       13.97        27.95        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  FGB MUTATED FGB WILD-TYPE 
         9.99          0.00 
  FGB MUTATED FGB WILD-TYPE 
        58.39        148.01 
  FGB MUTATED FGB WILD-TYPE 
       17.985        20.190 
[1] "10.0 - 58.4 (18.0)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.2"
D1208V2, continuous
D1208V3, binary
               cls
clus              0   1
  FGB MUTATED     4   2
  FGB WILD-TYPE 362 117
[1] "tbl2"
               cls
clus            [,1] [,2]
  FGB MUTATED      4    2
  FGB WILD-TYPE  362  117
        clus
vv       FGB MUTATED FGB WILD-TYPE
  COLON            4           362
  RECTUM           2           117
[1] 2 2
[1] FALSE
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FGB MUTATED         2        0        0         1         1         0
  FGB WILD-TYPE      89        1       32       137         9         1
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  FGB MUTATED           0          0          1          1        0         0
  FGB WILD-TYPE        24         11         58         41       48        18
               vv
clus            STAGE IVB
  FGB MUTATED           0
  FGB WILD-TYPE         1
D1208V4, multiclass
            clus
vv           FGB MUTATED FGB WILD-TYPE
  STAGE I              2            89
  STAGE IA             0             1
  STAGE II             0            32
  STAGE IIA            1           137
  STAGE IIB            1             9
  STAGE IIC            0             1
  STAGE III            0            24
  STAGE IIIA           0            11
  STAGE IIIB           1            58
  STAGE IIIC           1            41
  STAGE IV             0            48
  STAGE IVA            0            18
  STAGE IVB            0             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  FGB MUTATED     0   2   3   1
  FGB WILD-TYPE  17  90 326  49
D1208V5, multiclass
    clus
vv   FGB MUTATED FGB WILD-TYPE
  T1           0            17
  T2           2            90
  T3           3           326
  T4           1            49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2
  FGB MUTATED     4   1   1
  FGB WILD-TYPE 283 112  86
D1208V6, multiclass
    clus
vv   FGB MUTATED FGB WILD-TYPE
  N0           4           283
  N1           1           112
  N2           1            86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1208V7, binary
               cls
clus              0   1
  FGB MUTATED     5   0
  FGB WILD-TYPE 370  65
[1] "tbl2"
               cls
clus            [,1] [,2]
  FGB MUTATED      5    0
  FGB WILD-TYPE  370   65
   clus
vv  FGB MUTATED FGB WILD-TYPE
  0           5           370
  1           0            65
[1] 2 2
[1] FALSE
D1208V8, binary
               cls
clus              0   1
  FGB MUTATED     2   4
  FGB WILD-TYPE 223 260
[1] "tbl2"
               cls
clus            [,1] [,2]
  FGB MUTATED      2    4
  FGB WILD-TYPE  223  260
        clus
vv       FGB MUTATED FGB WILD-TYPE
  FEMALE           2           223
  MALE             4           260
[1] 2 2
[1] FALSE
D1208V9, binary
               cls
clus              0   1
  FGB MUTATED     5   0
  FGB WILD-TYPE 345  22
[1] "tbl2"
               cls
clus            [,1] [,2]
  FGB MUTATED      5    0
  FGB WILD-TYPE  345   22
     clus
vv    FGB MUTATED FGB WILD-TYPE
  NO            5           345
  YES           0            22
[1] 2 2
[1] FALSE
               vv
clus            COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  FGB MUTATED                      4                             0
  FGB WILD-TYPE                  311                            47
               vv
clus            RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  FGB MUTATED                       2                              0
  FGB WILD-TYPE                   104                             10
D1208V10, multiclass
                                clus
vv                               FGB MUTATED FGB WILD-TYPE
  COLON ADENOCARCINOMA                     4           311
  COLON MUCINOUS ADENOCARCINOMA            0            47
  RECTAL ADENOCARCINOMA                    2           104
  RECTAL MUCINOUS ADENOCARCINOMA           0            10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             R0  R1  R2  RX
  FGB MUTATED     5   0   0   1
  FGB WILD-TYPE 340   4  31  24
D1208V11, multiclass
    clus
vv   FGB MUTATED FGB WILD-TYPE
  R0           5           340
  R1           0             4
  R2           0            31
  RX           1            24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1208V12, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FGB MUTATED                                  0     0
  FGB WILD-TYPE                                1    11
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  FGB MUTATED                           1     3
  FGB WILD-TYPE                        21   223
D1208V13, multiclass
                                  clus
vv                                 FGB MUTATED FGB WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      0            11
  BLACK OR AFRICAN AMERICAN                  1            21
  WHITE                                      3           223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1209) Variable = POLD3 MUTATION ANALYSIS
D1209V1, survival
                 sevent
clus2               0   1
  POLD3 MUTATED    10   1
  POLD3 WILD-TYPE 368  92
  POLD3 MUTATED POLD3 WILD-TYPE 
             11             460 
  POLD3 MUTATED POLD3 WILD-TYPE 
              1              92 
$`POLD3 MUTATED`
TCGA-A6-6141 TCGA-A6-6781 TCGA-AA-3518 TCGA-AA-3672 TCGA-AZ-4315 TCGA-D5-6540 
        8.38        19.66         1.02         0.92        58.39        16.14 
TCGA-D5-6931 TCGA-DM-A1D4 TCGA-F4-6856 TCGA-G4-6588 TCGA-G4-6628 
       12.00        92.75        35.31        26.17        79.69 

$`POLD3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 
       22.09        22.06        32.71        27.09        22.52        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3519 
       63.98         6.97         1.02        13.02        38.99         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
        2.01        14.01        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6932 
        9.04         9.44        11.64         4.80         1.51        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D6 
       10.26       119.70        24.43        38.20       130.65        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 
       33.67        13.25         0.53        47.41       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 
       61.91        36.00        22.09        13.78        35.80        91.79 
TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       46.75        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  POLD3 MUTATED POLD3 WILD-TYPE 
           0.92            0.00 
  POLD3 MUTATED POLD3 WILD-TYPE 
          92.75          148.01 
  POLD3 MUTATED POLD3 WILD-TYPE 
         19.660          20.235 
[1] "0.9 - 92.8 (19.7)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "2.7"
D1209V2, continuous
D1209V3, binary
                 cls
clus                0   1
  POLD3 MUTATED    11   0
  POLD3 WILD-TYPE 355 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  POLD3 MUTATED     11    0
  POLD3 WILD-TYPE  355  119
        clus
vv       POLD3 MUTATED POLD3 WILD-TYPE
  COLON             11             355
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  POLD3 MUTATED         3        0        0         5         0         0
  POLD3 WILD-TYPE      88        1       32       133        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  POLD3 MUTATED           1          0          0          2        0         0
  POLD3 WILD-TYPE        23         11         59         40       48        18
                 vv
clus              STAGE IVB
  POLD3 MUTATED           0
  POLD3 WILD-TYPE         1
D1209V4, multiclass
            clus
vv           POLD3 MUTATED POLD3 WILD-TYPE
  STAGE I                3              88
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              5             133
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             2              40
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  POLD3 MUTATED     0   3   6   2
  POLD3 WILD-TYPE  17  89 323  48
D1209V5, multiclass
    clus
vv   POLD3 MUTATED POLD3 WILD-TYPE
  T1             0              17
  T2             3              89
  T3             6             323
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  POLD3 MUTATED     8   2   1
  POLD3 WILD-TYPE 279 111  86
D1209V6, multiclass
    clus
vv   POLD3 MUTATED POLD3 WILD-TYPE
  N0             8             279
  N1             2             111
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1209V7, binary
                 cls
clus                0   1
  POLD3 MUTATED    10   0
  POLD3 WILD-TYPE 365  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  POLD3 MUTATED     10    0
  POLD3 WILD-TYPE  365   65
   clus
vv  POLD3 MUTATED POLD3 WILD-TYPE
  0            10             365
  1             0              65
[1] 2 2
[1] FALSE
D1209V8, binary
                 cls
clus                0   1
  POLD3 MUTATED     3   8
  POLD3 WILD-TYPE 222 256
[1] "tbl2"
                 cls
clus              [,1] [,2]
  POLD3 MUTATED      3    8
  POLD3 WILD-TYPE  222  256
        clus
vv       POLD3 MUTATED POLD3 WILD-TYPE
  FEMALE             3             222
  MALE               8             256
[1] 2 2
[1] FALSE
D1209V9, binary
                 cls
clus                0   1
  POLD3 MUTATED     9   0
  POLD3 WILD-TYPE 341  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  POLD3 MUTATED      9    0
  POLD3 WILD-TYPE  341   22
     clus
vv    POLD3 MUTATED POLD3 WILD-TYPE
  NO              9             341
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  POLD3 MUTATED                      8                             3
  POLD3 WILD-TYPE                  307                            44
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  POLD3 MUTATED                       0                              0
  POLD3 WILD-TYPE                   106                             10
D1209V10, multiclass
                                clus
vv                               POLD3 MUTATED POLD3 WILD-TYPE
  COLON ADENOCARCINOMA                       8             307
  COLON MUCINOUS ADENOCARCINOMA              3              44
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  POLD3 MUTATED     9   0   0   0
  POLD3 WILD-TYPE 336   4  31  25
D1209V11, multiclass
    clus
vv   POLD3 MUTATED POLD3 WILD-TYPE
  R0             9             336
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1209V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  POLD3 MUTATED                                  0     0
  POLD3 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  POLD3 MUTATED                           1     8
  POLD3 WILD-TYPE                        21   218
D1209V13, multiclass
                                  clus
vv                                 POLD3 MUTATED POLD3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        8             218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1210) Variable = CYP7B1 MUTATION ANALYSIS
D1210V1, survival
                  sevent
clus2                0   1
  CYP7B1 MUTATED    16   5
  CYP7B1 WILD-TYPE 362  88
  CYP7B1 MUTATED CYP7B1 WILD-TYPE 
              21              450 
  CYP7B1 MUTATED CYP7B1 WILD-TYPE 
               5               88 
$`CYP7B1 MUTATED`
TCGA-A6-5665 TCGA-AA-3510 TCGA-AA-3852 TCGA-AA-3869 TCGA-AA-A00E TCGA-AA-A00N 
       22.06        63.98         0.00        27.02        30.02         4.01 
TCGA-AA-A010 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-5860 
       34.98        58.39        49.41        12.76        10.06        32.02 
TCGA-CM-6161 TCGA-CM-6674 TCGA-D5-5538 TCGA-D5-6540 TCGA-D5-6931 TCGA-AG-A020 
       15.02        12.95        12.26        16.14        12.00        10.98 
TCGA-AG-A02N TCGA-AH-6644 TCGA-CI-6620 
       61.97         0.72        33.17 

$`CYP7B1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
       10.06         0.00        33.07        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00F 
        7.96        27.02        13.94        38.04        19.00        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        33.01        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 
      106.75        22.36        62.79        88.21         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.03        22.98        30.08        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       15.02        17.03        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       11.01        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       12.03        45.40        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       17.13        12.49        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
        1.51        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       12.00        70.03        64.01        49.97         1.94        38.96 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-CI-6619 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        0.69         6.05         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  CYP7B1 MUTATED CYP7B1 WILD-TYPE 
               0                0 
  CYP7B1 MUTATED CYP7B1 WILD-TYPE 
           63.98           148.01 
  CYP7B1 MUTATED CYP7B1 WILD-TYPE 
          16.140           20.235 
[1] "0.0 - 64.0 (16.1)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.2"
D1210V2, continuous
D1210V3, binary
                  cls
clus                 0   1
  CYP7B1 MUTATED    17   4
  CYP7B1 WILD-TYPE 349 115
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CYP7B1 MUTATED     17    4
  CYP7B1 WILD-TYPE  349  115
        clus
vv       CYP7B1 MUTATED CYP7B1 WILD-TYPE
  COLON              17              349
  RECTUM              4              115
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CYP7B1 MUTATED         2        0        3         8         2         0
  CYP7B1 WILD-TYPE      89        1       29       130         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CYP7B1 MUTATED           1          0          1          1        1
  CYP7B1 WILD-TYPE        23         11         58         41       47
                  vv
clus               STAGE IVA STAGE IVB
  CYP7B1 MUTATED           1         0
  CYP7B1 WILD-TYPE        17         1
D1210V4, multiclass
            clus
vv           CYP7B1 MUTATED CYP7B1 WILD-TYPE
  STAGE I                 2               89
  STAGE IA                0                1
  STAGE II                3               29
  STAGE IIA               8              130
  STAGE IIB               2                8
  STAGE IIC               0                1
  STAGE III               1               23
  STAGE IIIA              0               11
  STAGE IIIB              1               58
  STAGE IIIC              1               41
  STAGE IV                1               47
  STAGE IVA               1               17
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  CYP7B1 MUTATED     0   2  15   4
  CYP7B1 WILD-TYPE  17  90 314  46
D1210V5, multiclass
    clus
vv   CYP7B1 MUTATED CYP7B1 WILD-TYPE
  T1              0               17
  T2              2               90
  T3             15              314
  T4              4               46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  CYP7B1 MUTATED    15   3   2
  CYP7B1 WILD-TYPE 272 110  85
D1210V6, multiclass
    clus
vv   CYP7B1 MUTATED CYP7B1 WILD-TYPE
  N0             15              272
  N1              3              110
  N2              2               85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1210V7, binary
                  cls
clus                 0   1
  CYP7B1 MUTATED    17   2
  CYP7B1 WILD-TYPE 358  63
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CYP7B1 MUTATED     17    2
  CYP7B1 WILD-TYPE  358   63
   clus
vv  CYP7B1 MUTATED CYP7B1 WILD-TYPE
  0             17              358
  1              2               63
[1] 2 2
[1] FALSE
D1210V8, binary
                  cls
clus                 0   1
  CYP7B1 MUTATED     7  14
  CYP7B1 WILD-TYPE 218 250
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CYP7B1 MUTATED      7   14
  CYP7B1 WILD-TYPE  218  250
        clus
vv       CYP7B1 MUTATED CYP7B1 WILD-TYPE
  FEMALE              7              218
  MALE               14              250
[1] 2 2
[1] FALSE
D1210V9, binary
                  cls
clus                 0   1
  CYP7B1 MUTATED    16   0
  CYP7B1 WILD-TYPE 334  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CYP7B1 MUTATED     16    0
  CYP7B1 WILD-TYPE  334   22
     clus
vv    CYP7B1 MUTATED CYP7B1 WILD-TYPE
  NO              16              334
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CYP7B1 MUTATED                     13                             4
  CYP7B1 WILD-TYPE                  302                            43
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CYP7B1 MUTATED                       3                              1
  CYP7B1 WILD-TYPE                   103                              9
D1210V10, multiclass
                                clus
vv                               CYP7B1 MUTATED CYP7B1 WILD-TYPE
  COLON ADENOCARCINOMA                       13              302
  COLON MUCINOUS ADENOCARCINOMA               4               43
  RECTAL ADENOCARCINOMA                       3              103
  RECTAL MUCINOUS ADENOCARCINOMA              1                9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  CYP7B1 MUTATED    15   0   1   2
  CYP7B1 WILD-TYPE 330   4  30  23
D1210V11, multiclass
    clus
vv   CYP7B1 MUTATED CYP7B1 WILD-TYPE
  R0             15              330
  R1              0                4
  R2              1               30
  RX              2               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1210V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CYP7B1 MUTATED                                  0     2
  CYP7B1 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  CYP7B1 MUTATED                           0    11
  CYP7B1 WILD-TYPE                        22   215
D1210V13, multiclass
                                  clus
vv                                 CYP7B1 MUTATED CYP7B1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                9
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                        11              215
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1211) Variable = ZNF605 MUTATION ANALYSIS
D1211V1, survival
                  sevent
clus2                0   1
  ZNF605 MUTATED     5   3
  ZNF605 WILD-TYPE 373  90
  ZNF605 MUTATED ZNF605 WILD-TYPE 
               8              463 
  ZNF605 MUTATED ZNF605 WILD-TYPE 
               3               90 
$`ZNF605 MUTATED`
TCGA-A6-2672 TCGA-A6-6141 TCGA-AZ-4315 TCGA-AZ-6608 TCGA-CA-6718 TCGA-D5-6539 
       46.65         8.38        58.39         1.61        10.06        12.49 
TCGA-DM-A0XD TCGA-G4-6588 
       24.43        26.17 

$`ZNF605 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 
       22.06        32.71        27.09        22.52        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       33.01        21.44        17.82         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 
      100.01        29.56         5.23        11.74         3.19        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 
       43.27        15.12        17.85         4.80        17.13        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       11.38        10.26       119.70        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       35.80        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  ZNF605 MUTATED ZNF605 WILD-TYPE 
            1.61             0.00 
  ZNF605 MUTATED ZNF605 WILD-TYPE 
           58.39           148.01 
  ZNF605 MUTATED ZNF605 WILD-TYPE 
           18.46            20.19 
[1] "1.6 - 58.4 (18.5)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "2"  
D1211V2, continuous
D1211V3, binary
                  cls
clus                 0   1
  ZNF605 MUTATED     8   0
  ZNF605 WILD-TYPE 358 119
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF605 MUTATED      8    0
  ZNF605 WILD-TYPE  358  119
        clus
vv       ZNF605 MUTATED ZNF605 WILD-TYPE
  COLON               8              358
  RECTUM              0              119
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZNF605 MUTATED         0        0        0         5         0         0
  ZNF605 WILD-TYPE      91        1       32       133        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF605 MUTATED           0          2          1          0        0
  ZNF605 WILD-TYPE        24          9         58         42       48
                  vv
clus               STAGE IVA STAGE IVB
  ZNF605 MUTATED           0         0
  ZNF605 WILD-TYPE        18         1
D1211V4, multiclass
            clus
vv           ZNF605 MUTATED ZNF605 WILD-TYPE
  STAGE I                 0               91
  STAGE IA                0                1
  STAGE II                0               32
  STAGE IIA               5              133
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              2                9
  STAGE IIIB              1               58
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZNF605 MUTATED     0   1   7   0
  ZNF605 WILD-TYPE  17  91 322  50
D1211V5, multiclass
    clus
vv   ZNF605 MUTATED ZNF605 WILD-TYPE
  T1              0               17
  T2              1               91
  T3              7              322
  T4              0               50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  ZNF605 MUTATED     6   2   0
  ZNF605 WILD-TYPE 281 111  87
D1211V6, multiclass
    clus
vv   ZNF605 MUTATED ZNF605 WILD-TYPE
  N0              6              281
  N1              2              111
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1211V7, binary
                  cls
clus                 0   1
  ZNF605 MUTATED     8   0
  ZNF605 WILD-TYPE 367  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF605 MUTATED      8    0
  ZNF605 WILD-TYPE  367   65
   clus
vv  ZNF605 MUTATED ZNF605 WILD-TYPE
  0              8              367
  1              0               65
[1] 2 2
[1] FALSE
D1211V8, binary
                  cls
clus                 0   1
  ZNF605 MUTATED     4   4
  ZNF605 WILD-TYPE 221 260
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF605 MUTATED      4    4
  ZNF605 WILD-TYPE  221  260
        clus
vv       ZNF605 MUTATED ZNF605 WILD-TYPE
  FEMALE              4              221
  MALE                4              260
[1] 2 2
[1] FALSE
D1211V9, binary
                  cls
clus                 0   1
  ZNF605 MUTATED     7   0
  ZNF605 WILD-TYPE 343  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF605 MUTATED      7    0
  ZNF605 WILD-TYPE  343   22
     clus
vv    ZNF605 MUTATED ZNF605 WILD-TYPE
  NO               7              343
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ZNF605 MUTATED                      8                             0
  ZNF605 WILD-TYPE                  307                            47
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ZNF605 MUTATED                       0                              0
  ZNF605 WILD-TYPE                   106                             10
D1211V10, multiclass
                                clus
vv                               ZNF605 MUTATED ZNF605 WILD-TYPE
  COLON ADENOCARCINOMA                        8              307
  COLON MUCINOUS ADENOCARCINOMA               0               47
  RECTAL ADENOCARCINOMA                       0              106
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ZNF605 MUTATED     4   0   0   1
  ZNF605 WILD-TYPE 341   4  31  24
D1211V11, multiclass
    clus
vv   ZNF605 MUTATED ZNF605 WILD-TYPE
  R0              4              341
  R1              0                4
  R2              0               31
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1211V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF605 MUTATED                                  0     1
  ZNF605 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZNF605 MUTATED                           1     6
  ZNF605 WILD-TYPE                        21   220
D1211V13, multiclass
                                  clus
vv                                 ZNF605 MUTATED ZNF605 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                         6              220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1212) Variable = ITPR2 MUTATION ANALYSIS
D1212V1, survival
                 sevent
clus2               0   1
  ITPR2 MUTATED    21   6
  ITPR2 WILD-TYPE 357  87
  ITPR2 MUTATED ITPR2 WILD-TYPE 
             27             444 
  ITPR2 MUTATED ITPR2 WILD-TYPE 
              6              87 
$`ITPR2 MUTATED`
TCGA-AA-3510 TCGA-AA-3713 TCGA-AA-3864 TCGA-AA-3968 TCGA-AA-3977 TCGA-AA-A00N 
       63.98        19.04        53.00        21.99        25.02         4.01 
TCGA-AA-A010 TCGA-AU-3779 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-6598 
       34.98        14.50        21.44        17.82        58.39        49.41 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-5912 TCGA-CM-5862 TCGA-D5-6539 TCGA-D5-6927 
       12.76        10.06        49.08         5.03        12.49         9.44 
TCGA-DM-A1HB TCGA-G4-6588 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-6655 TCGA-AG-3892 
      135.65        26.17        46.75        79.69        20.02        13.02 
TCGA-AG-A002 TCGA-AG-A01W TCGA-DC-6681 
       20.98        70.03         5.95 

$`ITPR2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 
        0.99        31.07        31.07        30.05        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        10.88         0.20        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       33.01         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       88.21         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        3.29         0.07        12.20        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       85.45        15.62        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
       15.02        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
       14.30         9.04        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
       44.32       131.51       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6625 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       35.80        91.79        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       17.95        36.95        17.03        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01Y 
       37.02        15.95        36.03         9.07        12.00        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
       19.99         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  ITPR2 MUTATED ITPR2 WILD-TYPE 
           4.01            0.00 
  ITPR2 MUTATED ITPR2 WILD-TYPE 
         135.65          148.01 
  ITPR2 MUTATED ITPR2 WILD-TYPE 
         21.440          20.085 
[1] "4.0 - 135.7 (21.4)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.2"
D1212V2, continuous
D1212V3, binary
                 cls
clus                0   1
  ITPR2 MUTATED    23   5
  ITPR2 WILD-TYPE 343 114
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITPR2 MUTATED     23    5
  ITPR2 WILD-TYPE  343  114
        clus
vv       ITPR2 MUTATED ITPR2 WILD-TYPE
  COLON             23             343
  RECTUM             5             114
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ITPR2 MUTATED         5        0        4         9         2         0
  ITPR2 WILD-TYPE      86        1       28       129         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ITPR2 MUTATED           0          2          2          0        1         2
  ITPR2 WILD-TYPE        24          9         57         42       47        16
                 vv
clus              STAGE IVB
  ITPR2 MUTATED           0
  ITPR2 WILD-TYPE         1
D1212V4, multiclass
            clus
vv           ITPR2 MUTATED ITPR2 WILD-TYPE
  STAGE I                5              86
  STAGE IA               0               1
  STAGE II               4              28
  STAGE IIA              9             129
  STAGE IIB              2               8
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             2               9
  STAGE IIIB             2              57
  STAGE IIIC             0              42
  STAGE IV               1              47
  STAGE IVA              2              16
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ITPR2 MUTATED     1   6  19   2
  ITPR2 WILD-TYPE  16  86 310  48
D1212V5, multiclass
    clus
vv   ITPR2 MUTATED ITPR2 WILD-TYPE
  T1             1              16
  T2             6              86
  T3            19             310
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  ITPR2 MUTATED    23   4   1
  ITPR2 WILD-TYPE 264 109  86
D1212V6, multiclass
    clus
vv   ITPR2 MUTATED ITPR2 WILD-TYPE
  N0            23             264
  N1             4             109
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1212V7, binary
                 cls
clus                0   1
  ITPR2 MUTATED    21   3
  ITPR2 WILD-TYPE 354  62
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITPR2 MUTATED     21    3
  ITPR2 WILD-TYPE  354   62
   clus
vv  ITPR2 MUTATED ITPR2 WILD-TYPE
  0            21             354
  1             3              62
[1] 2 2
[1] FALSE
D1212V8, binary
                 cls
clus                0   1
  ITPR2 MUTATED    11  17
  ITPR2 WILD-TYPE 214 247
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITPR2 MUTATED     11   17
  ITPR2 WILD-TYPE  214  247
        clus
vv       ITPR2 MUTATED ITPR2 WILD-TYPE
  FEMALE            11             214
  MALE              17             247
[1] 2 2
[1] FALSE
D1212V9, binary
                 cls
clus                0   1
  ITPR2 MUTATED    22   1
  ITPR2 WILD-TYPE 328  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITPR2 MUTATED     22    1
  ITPR2 WILD-TYPE  328   21
     clus
vv    ITPR2 MUTATED ITPR2 WILD-TYPE
  NO             22             328
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ITPR2 MUTATED                     20                             2
  ITPR2 WILD-TYPE                  295                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ITPR2 MUTATED                       5                              0
  ITPR2 WILD-TYPE                   101                             10
D1212V10, multiclass
                                clus
vv                               ITPR2 MUTATED ITPR2 WILD-TYPE
  COLON ADENOCARCINOMA                      20             295
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      5             101
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  ITPR2 MUTATED    21   0   1   3
  ITPR2 WILD-TYPE 324   4  30  22
D1212V11, multiclass
    clus
vv   ITPR2 MUTATED ITPR2 WILD-TYPE
  R0            21             324
  R1             0               4
  R2             1              30
  RX             3              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1212V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ITPR2 MUTATED                                  0     2
  ITPR2 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ITPR2 MUTATED                           1    14
  ITPR2 WILD-TYPE                        21   212
D1212V13, multiclass
                                  clus
vv                                 ITPR2 MUTATED ITPR2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               9
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                       14             212
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1213) Variable = ZBTB33 MUTATION ANALYSIS
D1213V1, survival
                  sevent
clus2                0   1
  ZBTB33 MUTATED    10   6
  ZBTB33 WILD-TYPE 368  87
  ZBTB33 MUTATED ZBTB33 WILD-TYPE 
              16              455 
  ZBTB33 MUTATED ZBTB33 WILD-TYPE 
               6               87 
$`ZBTB33 MUTATED`
TCGA-A6-6780 TCGA-AA-3510 TCGA-AA-3552 TCGA-AA-3660 TCGA-AA-3715 TCGA-AA-3947 
       20.12        63.98        13.02        78.08        19.04        33.01 
TCGA-AA-A01P TCGA-AA-A01R TCGA-AD-6889 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-CK-5916 
       38.07        35.01        56.55         6.77       100.01        21.14 
TCGA-CM-6170 TCGA-CM-6171 TCGA-D5-6541 TCGA-G4-6586 
       15.02        14.04        15.58        35.80 

$`ZBTB33 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 
       12.99         0.99        14.01        33.99        21.01        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       26.99        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 
       18.05        31.00         2.01        12.99        24.00        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01Q TCGA-AA-A01S 
       32.02        12.00        31.00        31.00         1.02         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6603 
       22.36        62.79        88.21        49.41        12.10        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       51.32         9.99        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6172 
       16.04        21.99        14.99        12.99        13.02        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6898 TCGA-D5-6920 
        4.80        17.13        12.49        16.14         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 
       61.91        36.00        22.09        13.78        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  ZBTB33 MUTATED ZBTB33 WILD-TYPE 
            6.77             0.00 
  ZBTB33 MUTATED ZBTB33 WILD-TYPE 
          100.01           148.01 
  ZBTB33 MUTATED ZBTB33 WILD-TYPE 
          27.075           20.050 
[1] "6.8 - 100.0 (27.1)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.4"
D1213V2, continuous
D1213V3, binary
                  cls
clus                 0   1
  ZBTB33 MUTATED    16   0
  ZBTB33 WILD-TYPE 350 119
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZBTB33 MUTATED     16    0
  ZBTB33 WILD-TYPE  350  119
        clus
vv       ZBTB33 MUTATED ZBTB33 WILD-TYPE
  COLON              16              350
  RECTUM              0              119
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZBTB33 MUTATED         4        0        4         4         1         0
  ZBTB33 WILD-TYPE      87        1       28       134         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZBTB33 MUTATED           2          0          0          1        0
  ZBTB33 WILD-TYPE        22         11         59         41       48
                  vv
clus               STAGE IVA STAGE IVB
  ZBTB33 MUTATED           0         0
  ZBTB33 WILD-TYPE        18         1
D1213V4, multiclass
            clus
vv           ZBTB33 MUTATED ZBTB33 WILD-TYPE
  STAGE I                 4               87
  STAGE IA                0                1
  STAGE II                4               28
  STAGE IIA               4              134
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               2               22
  STAGE IIIA              0               11
  STAGE IIIB              0               59
  STAGE IIIC              1               41
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZBTB33 MUTATED     1   3  11   1
  ZBTB33 WILD-TYPE  16  89 318  49
D1213V5, multiclass
    clus
vv   ZBTB33 MUTATED ZBTB33 WILD-TYPE
  T1              1               16
  T2              3               89
  T3             11              318
  T4              1               49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  ZBTB33 MUTATED    13   1   2
  ZBTB33 WILD-TYPE 274 112  85
D1213V6, multiclass
    clus
vv   ZBTB33 MUTATED ZBTB33 WILD-TYPE
  N0             13              274
  N1              1              112
  N2              2               85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1213V7, binary
                  cls
clus                 0   1
  ZBTB33 MUTATED    14   0
  ZBTB33 WILD-TYPE 361  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZBTB33 MUTATED     14    0
  ZBTB33 WILD-TYPE  361   65
   clus
vv  ZBTB33 MUTATED ZBTB33 WILD-TYPE
  0             14              361
  1              0               65
[1] 2 2
[1] FALSE
D1213V8, binary
                  cls
clus                 0   1
  ZBTB33 MUTATED     7   9
  ZBTB33 WILD-TYPE 218 255
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZBTB33 MUTATED      7    9
  ZBTB33 WILD-TYPE  218  255
        clus
vv       ZBTB33 MUTATED ZBTB33 WILD-TYPE
  FEMALE              7              218
  MALE                9              255
[1] 2 2
[1] FALSE
D1213V9, binary
                  cls
clus                 0   1
  ZBTB33 MUTATED    14   1
  ZBTB33 WILD-TYPE 336  21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZBTB33 MUTATED     14    1
  ZBTB33 WILD-TYPE  336   21
     clus
vv    ZBTB33 MUTATED ZBTB33 WILD-TYPE
  NO              14              336
  YES              1               21
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ZBTB33 MUTATED                     13                             3
  ZBTB33 WILD-TYPE                  302                            44
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ZBTB33 MUTATED                       0                              0
  ZBTB33 WILD-TYPE                   106                             10
D1213V10, multiclass
                                clus
vv                               ZBTB33 MUTATED ZBTB33 WILD-TYPE
  COLON ADENOCARCINOMA                       13              302
  COLON MUCINOUS ADENOCARCINOMA               3               44
  RECTAL ADENOCARCINOMA                       0              106
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ZBTB33 MUTATED    11   0   0   1
  ZBTB33 WILD-TYPE 334   4  31  24
D1213V11, multiclass
    clus
vv   ZBTB33 MUTATED ZBTB33 WILD-TYPE
  R0             11              334
  R1              0                4
  R2              0               31
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1213V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZBTB33 MUTATED                                  0     1
  ZBTB33 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZBTB33 MUTATED                           0     8
  ZBTB33 WILD-TYPE                        22   218
D1213V13, multiclass
                                  clus
vv                                 ZBTB33 MUTATED ZBTB33 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         8              218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1214) Variable = PHF21A MUTATION ANALYSIS
D1214V1, survival
                  sevent
clus2                0   1
  PHF21A MUTATED     9   3
  PHF21A WILD-TYPE 369  90
  PHF21A MUTATED PHF21A WILD-TYPE 
              12              459 
  PHF21A MUTATED PHF21A WILD-TYPE 
               3               90 
$`PHF21A MUTATED`
TCGA-AA-3492 TCGA-AA-3525 TCGA-AA-3672 TCGA-AA-3947 TCGA-AA-3949 TCGA-AD-6964 
        3.02         8.05         0.92        33.01        26.01        10.88 
TCGA-AZ-4681 TCGA-CK-5916 TCGA-D5-6930 TCGA-G4-6304 TCGA-G4-6588 TCGA-AG-A002 
      106.75        21.14         1.51        53.62        26.17        20.98 

$`PHF21A WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3526 
        1.02         9.07        24.03        37.05        36.03        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
       54.02         2.01        14.01        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        1.41         5.13        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       11.64         4.80        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       65.85        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        35.80        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  PHF21A MUTATED PHF21A WILD-TYPE 
            0.92             0.00 
  PHF21A MUTATED PHF21A WILD-TYPE 
          106.75           148.01 
  PHF21A MUTATED PHF21A WILD-TYPE 
           21.06            20.12 
[1] "0.9 - 106.8 (21.1)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.3"
D1214V2, continuous
D1214V3, binary
                  cls
clus                 0   1
  PHF21A MUTATED    11   1
  PHF21A WILD-TYPE 355 118
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PHF21A MUTATED     11    1
  PHF21A WILD-TYPE  355  118
        clus
vv       PHF21A MUTATED PHF21A WILD-TYPE
  COLON              11              355
  RECTUM              1              118
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PHF21A MUTATED         2        0        1         3         2         0
  PHF21A WILD-TYPE      89        1       31       135         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PHF21A MUTATED           1          0          2          0        0
  PHF21A WILD-TYPE        23         11         57         42       48
                  vv
clus               STAGE IVA STAGE IVB
  PHF21A MUTATED           0         0
  PHF21A WILD-TYPE        18         1
D1214V4, multiclass
            clus
vv           PHF21A MUTATED PHF21A WILD-TYPE
  STAGE I                 2               89
  STAGE IA                0                1
  STAGE II                1               31
  STAGE IIA               3              135
  STAGE IIB               2                8
  STAGE IIC               0                1
  STAGE III               1               23
  STAGE IIIA              0               11
  STAGE IIIB              2               57
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  PHF21A MUTATED     1   1   7   3
  PHF21A WILD-TYPE  16  91 322  47
D1214V5, multiclass
    clus
vv   PHF21A MUTATED PHF21A WILD-TYPE
  T1              1               16
  T2              1               91
  T3              7              322
  T4              3               47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  PHF21A MUTATED     8   3   1
  PHF21A WILD-TYPE 279 110  86
D1214V6, multiclass
    clus
vv   PHF21A MUTATED PHF21A WILD-TYPE
  N0              8              279
  N1              3              110
  N2              1               86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1214V7, binary
                  cls
clus                 0   1
  PHF21A MUTATED    11   0
  PHF21A WILD-TYPE 364  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PHF21A MUTATED     11    0
  PHF21A WILD-TYPE  364   65
   clus
vv  PHF21A MUTATED PHF21A WILD-TYPE
  0             11              364
  1              0               65
[1] 2 2
[1] FALSE
D1214V8, binary
                  cls
clus                 0   1
  PHF21A MUTATED     8   4
  PHF21A WILD-TYPE 217 260
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PHF21A MUTATED      8    4
  PHF21A WILD-TYPE  217  260
        clus
vv       PHF21A MUTATED PHF21A WILD-TYPE
  FEMALE              8              217
  MALE                4              260
[1] 2 2
[1] FALSE
D1214V9, binary
                  cls
clus                 0   1
  PHF21A MUTATED    11   0
  PHF21A WILD-TYPE 339  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PHF21A MUTATED     11    0
  PHF21A WILD-TYPE  339   22
     clus
vv    PHF21A MUTATED PHF21A WILD-TYPE
  NO              11              339
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PHF21A MUTATED                      8                             3
  PHF21A WILD-TYPE                  307                            44
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PHF21A MUTATED                       1                              0
  PHF21A WILD-TYPE                   105                             10
D1214V10, multiclass
                                clus
vv                               PHF21A MUTATED PHF21A WILD-TYPE
  COLON ADENOCARCINOMA                        8              307
  COLON MUCINOUS ADENOCARCINOMA               3               44
  RECTAL ADENOCARCINOMA                       1              105
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  PHF21A MUTATED    10   0   0   1
  PHF21A WILD-TYPE 335   4  31  24
D1214V11, multiclass
    clus
vv   PHF21A MUTATED PHF21A WILD-TYPE
  R0             10              335
  R1              0                4
  R2              0               31
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1214V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PHF21A MUTATED                                  0     0
  PHF21A WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  PHF21A MUTATED                           0     6
  PHF21A WILD-TYPE                        22   220
D1214V13, multiclass
                                  clus
vv                                 PHF21A MUTATED PHF21A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         6              220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1215) Variable = INADL MUTATION ANALYSIS
D1215V1, survival
                 sevent
clus2               0   1
  INADL MUTATED    12   3
  INADL WILD-TYPE 366  90
  INADL MUTATED INADL WILD-TYPE 
             15             456 
  INADL MUTATED INADL WILD-TYPE 
              3              90 
$`INADL MUTATED`
TCGA-AA-3663 TCGA-AA-3845 TCGA-AA-3977 TCGA-AA-A01R TCGA-AZ-4315 TCGA-AZ-6601 
        6.97         0.00        25.02        35.01        58.39       100.01 
TCGA-CA-6717 TCGA-CM-5861 TCGA-DM-A1D8 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       12.76        15.02        12.59        22.09        13.78        35.80 
TCGA-AG-4007 TCGA-AG-A002 TCGA-EI-6506 
        1.02        20.98        20.55 

$`INADL WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.05        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 
       17.98        15.95        38.99        37.02        14.93        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       31.00        38.07         1.02         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 
       88.21        49.41         6.77        12.10        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07        12.20        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       30.08        32.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       13.32       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       61.91        36.00        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  INADL MUTATED INADL WILD-TYPE 
              0               0 
  INADL MUTATED INADL WILD-TYPE 
         100.01          148.01 
  INADL MUTATED INADL WILD-TYPE 
         20.550          20.155 
[1] "0.0 - 100.0 (20.6)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.1"
D1215V2, continuous
D1215V3, binary
                 cls
clus                0   1
  INADL MUTATED    13   3
  INADL WILD-TYPE 353 116
[1] "tbl2"
                 cls
clus              [,1] [,2]
  INADL MUTATED     13    3
  INADL WILD-TYPE  353  116
        clus
vv       INADL MUTATED INADL WILD-TYPE
  COLON             13             353
  RECTUM             3             116
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  INADL MUTATED         1        1        2         6         0         0
  INADL WILD-TYPE      90        0       30       132        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  INADL MUTATED           2          0          0          1        1         0
  INADL WILD-TYPE        22         11         59         41       47        18
                 vv
clus              STAGE IVB
  INADL MUTATED           0
  INADL WILD-TYPE         1
D1215V4, multiclass
            clus
vv           INADL MUTATED INADL WILD-TYPE
  STAGE I                1              90
  STAGE IA               1               0
  STAGE II               2              30
  STAGE IIA              6             132
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              2              22
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             1              41
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  INADL MUTATED     0   3  11   1
  INADL WILD-TYPE  17  89 318  49
D1215V5, multiclass
    clus
vv   INADL MUTATED INADL WILD-TYPE
  T1             0              17
  T2             3              89
  T3            11             318
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  INADL MUTATED    11   2   3
  INADL WILD-TYPE 276 111  84
D1215V6, multiclass
    clus
vv   INADL MUTATED INADL WILD-TYPE
  N0            11             276
  N1             2             111
  N2             3              84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1215V7, binary
                 cls
clus                0   1
  INADL MUTATED    10   1
  INADL WILD-TYPE 365  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  INADL MUTATED     10    1
  INADL WILD-TYPE  365   64
   clus
vv  INADL MUTATED INADL WILD-TYPE
  0            10             365
  1             1              64
[1] 2 2
[1] FALSE
D1215V8, binary
                 cls
clus                0   1
  INADL MUTATED     6  10
  INADL WILD-TYPE 219 254
[1] "tbl2"
                 cls
clus              [,1] [,2]
  INADL MUTATED      6   10
  INADL WILD-TYPE  219  254
        clus
vv       INADL MUTATED INADL WILD-TYPE
  FEMALE             6             219
  MALE              10             254
[1] 2 2
[1] FALSE
D1215V9, binary
                 cls
clus                0   1
  INADL MUTATED    11   1
  INADL WILD-TYPE 339  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  INADL MUTATED     11    1
  INADL WILD-TYPE  339   21
     clus
vv    INADL MUTATED INADL WILD-TYPE
  NO             11             339
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  INADL MUTATED                     10                             3
  INADL WILD-TYPE                  305                            44
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  INADL MUTATED                       3                              0
  INADL WILD-TYPE                   103                             10
D1215V10, multiclass
                                clus
vv                               INADL MUTATED INADL WILD-TYPE
  COLON ADENOCARCINOMA                      10             305
  COLON MUCINOUS ADENOCARCINOMA              3              44
  RECTAL ADENOCARCINOMA                      3             103
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  INADL MUTATED    11   0   1   1
  INADL WILD-TYPE 334   4  30  24
D1215V11, multiclass
    clus
vv   INADL MUTATED INADL WILD-TYPE
  R0            11             334
  R1             0               4
  R2             1              30
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1215V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  INADL MUTATED                                  0     1
  INADL WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  INADL MUTATED                           1     8
  INADL WILD-TYPE                        21   218
D1215V13, multiclass
                                  clus
vv                                 INADL MUTATED INADL WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        8             218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1216) Variable = DDX17 MUTATION ANALYSIS
D1216V1, survival
                 sevent
clus2               0   1
  DDX17 MUTATED     4   4
  DDX17 WILD-TYPE 374  89
  DDX17 MUTATED DDX17 WILD-TYPE 
              8             463 
  DDX17 MUTATED DDX17 WILD-TYPE 
              4              89 
$`DDX17 MUTATED`
TCGA-A6-2676 TCGA-AA-3852 TCGA-AA-A00N TCGA-AD-6889 TCGA-AZ-6598 TCGA-CM-4746 
       42.90         0.00         4.01        56.55        49.41        37.02 
TCGA-CM-6674 TCGA-G4-6628 
       12.95        79.69 

$`DDX17 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 
       17.03        10.06         0.00        33.07        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 
       18.05        40.96         0.07        21.37        15.52         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        88.21         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       23.05        20.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       14.04        11.01        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 
       35.80        26.17        91.79        46.75        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  DDX17 MUTATED DDX17 WILD-TYPE 
              0               0 
  DDX17 MUTATED DDX17 WILD-TYPE 
          79.69          148.01 
  DDX17 MUTATED DDX17 WILD-TYPE 
          39.96           20.12 
[1] "0.0 - 79.7 (40.0)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.9"
D1216V2, continuous
D1216V3, binary
                 cls
clus                0   1
  DDX17 MUTATED     8   0
  DDX17 WILD-TYPE 358 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX17 MUTATED      8    0
  DDX17 WILD-TYPE  358  119
        clus
vv       DDX17 MUTATED DDX17 WILD-TYPE
  COLON              8             358
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DDX17 MUTATED         2        0        1         3         2         0
  DDX17 WILD-TYPE      89        1       31       135         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DDX17 MUTATED           0          0          0          0        0         0
  DDX17 WILD-TYPE        24         11         59         42       48        18
                 vv
clus              STAGE IVB
  DDX17 MUTATED           0
  DDX17 WILD-TYPE         1
D1216V4, multiclass
            clus
vv           DDX17 MUTATED DDX17 WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              3             135
  STAGE IIB              2               8
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  DDX17 MUTATED     0   2   4   2
  DDX17 WILD-TYPE  17  90 325  48
D1216V5, multiclass
    clus
vv   DDX17 MUTATED DDX17 WILD-TYPE
  T1             0              17
  T2             2              90
  T3             4             325
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  DDX17 MUTATED     8   0   0
  DDX17 WILD-TYPE 279 113  87
D1216V6, multiclass
    clus
vv   DDX17 MUTATED DDX17 WILD-TYPE
  N0             8             279
  N1             0             113
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1216V7, binary
                 cls
clus                0   1
  DDX17 MUTATED     7   0
  DDX17 WILD-TYPE 368  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX17 MUTATED      7    0
  DDX17 WILD-TYPE  368   65
   clus
vv  DDX17 MUTATED DDX17 WILD-TYPE
  0             7             368
  1             0              65
[1] 2 2
[1] FALSE
D1216V8, binary
                 cls
clus                0   1
  DDX17 MUTATED     2   6
  DDX17 WILD-TYPE 223 258
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX17 MUTATED      2    6
  DDX17 WILD-TYPE  223  258
        clus
vv       DDX17 MUTATED DDX17 WILD-TYPE
  FEMALE             2             223
  MALE               6             258
[1] 2 2
[1] FALSE
D1216V9, binary
                 cls
clus                0   1
  DDX17 MUTATED     5   0
  DDX17 WILD-TYPE 345  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX17 MUTATED      5    0
  DDX17 WILD-TYPE  345   22
     clus
vv    DDX17 MUTATED DDX17 WILD-TYPE
  NO              5             345
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  DDX17 MUTATED                      6                             2
  DDX17 WILD-TYPE                  309                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  DDX17 MUTATED                       0                              0
  DDX17 WILD-TYPE                   106                             10
D1216V10, multiclass
                                clus
vv                               DDX17 MUTATED DDX17 WILD-TYPE
  COLON ADENOCARCINOMA                       6             309
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  DDX17 MUTATED     6   0   0   0
  DDX17 WILD-TYPE 339   4  31  25
D1216V11, multiclass
    clus
vv   DDX17 MUTATED DDX17 WILD-TYPE
  R0             6             339
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1216V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DDX17 MUTATED                                  0     1
  DDX17 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  DDX17 MUTATED                           1     4
  DDX17 WILD-TYPE                        21   222
D1216V13, multiclass
                                  clus
vv                                 DDX17 MUTATED DDX17 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        4             222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1217) Variable = DMXL2 MUTATION ANALYSIS
D1217V1, survival
                 sevent
clus2               0   1
  DMXL2 MUTATED    26   9
  DMXL2 WILD-TYPE 352  84
  DMXL2 MUTATED DMXL2 WILD-TYPE 
             35             436 
  DMXL2 MUTATED DMXL2 WILD-TYPE 
              9              84 
$`DMXL2 MUTATED`
TCGA-A6-2676 TCGA-A6-3809 TCGA-A6-5665 TCGA-A6-6782 TCGA-AA-3496 TCGA-AA-3510 
       42.90        32.75        22.06        20.28         1.02        63.98 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3662 TCGA-AA-3713 TCGA-AA-3833 TCGA-AA-3842 
       17.95        29.95         6.05        19.04        15.95        37.02 
TCGA-AA-3864 TCGA-AA-3869 TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A010 TCGA-AD-5900 
       53.00        27.02        25.02         4.01        34.98         0.07 
TCGA-AY-6197 TCGA-AZ-4323 TCGA-AZ-6601 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-5916 
       21.44         1.41       100.01        12.76        10.06        21.14 
TCGA-CM-6674 TCGA-D5-6928 TCGA-DM-A28E TCGA-F4-6460 TCGA-G4-6293 TCGA-G4-6303 
       12.95        11.64       119.93        31.96       133.18        65.85 
TCGA-G4-6588 TCGA-AG-3878 TCGA-AG-A002 TCGA-AG-A02N TCGA-DT-5265 
       26.17         0.99        20.98        61.97         5.29 

$`DMXL2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5657 
       34.65        33.34        36.53        14.53        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 
       30.44        29.19        33.53        23.61        22.09        32.71 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       27.09        22.52         8.38        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        7.04         3.02        35.01         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       21.01        13.02        24.00        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       85.05        26.99        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3837 TCGA-AA-3844 
        0.99        25.02         1.02        17.98        38.99        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       17.03        24.03        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4616 
       16.31         0.95        33.01        17.82        58.39         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
       12.10        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       51.32         9.99        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       14.04        11.01        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
        9.44         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28F TCGA-DM-A28G 
      135.65       139.17         6.12        81.37        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
      117.07        98.24         8.61        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6304 TCGA-G4-6306 
        0.53        47.41        35.31        74.56        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       13.78        35.80        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
       49.97         1.94        38.96        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        4.01         5.03       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  DMXL2 MUTATED DMXL2 WILD-TYPE 
           0.07            0.00 
  DMXL2 MUTATED DMXL2 WILD-TYPE 
         133.18          148.01 
  DMXL2 MUTATED DMXL2 WILD-TYPE 
          21.44           20.02 
[1] "0.1 - 133.2 (21.4)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.1"
D1217V2, continuous
D1217V3, binary
                 cls
clus                0   1
  DMXL2 MUTATED    33   4
  DMXL2 WILD-TYPE 333 115
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DMXL2 MUTATED     33    4
  DMXL2 WILD-TYPE  333  115
        clus
vv       DMXL2 MUTATED DMXL2 WILD-TYPE
  COLON             33             333
  RECTUM             4             115
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DMXL2 MUTATED         4        0        6        12         6         0
  DMXL2 WILD-TYPE      87        1       26       126         4         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DMXL2 MUTATED           1          1          1          0        5         0
  DMXL2 WILD-TYPE        23         10         58         42       43        18
                 vv
clus              STAGE IVB
  DMXL2 MUTATED           0
  DMXL2 WILD-TYPE         1
D1217V4, multiclass
            clus
vv           DMXL2 MUTATED DMXL2 WILD-TYPE
  STAGE I                4              87
  STAGE IA               0               1
  STAGE II               6              26
  STAGE IIA             12             126
  STAGE IIB              6               4
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             1              10
  STAGE IIIB             1              58
  STAGE IIIC             0              42
  STAGE IV               5              43
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  DMXL2 MUTATED     1   5  22   9
  DMXL2 WILD-TYPE  16  87 307  41
D1217V5, multiclass
    clus
vv   DMXL2 MUTATED DMXL2 WILD-TYPE
  T1             1              16
  T2             5              87
  T3            22             307
  T4             9              41
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  DMXL2 MUTATED    30   4   3
  DMXL2 WILD-TYPE 257 109  84
D1217V6, multiclass
    clus
vv   DMXL2 MUTATED DMXL2 WILD-TYPE
  N0            30             257
  N1             4             109
  N2             3              84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1217V7, binary
                 cls
clus                0   1
  DMXL2 MUTATED    27   5
  DMXL2 WILD-TYPE 348  60
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DMXL2 MUTATED     27    5
  DMXL2 WILD-TYPE  348   60
   clus
vv  DMXL2 MUTATED DMXL2 WILD-TYPE
  0            27             348
  1             5              60
[1] 2 2
[1] FALSE
D1217V8, binary
                 cls
clus                0   1
  DMXL2 MUTATED    17  20
  DMXL2 WILD-TYPE 208 244
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DMXL2 MUTATED     17   20
  DMXL2 WILD-TYPE  208  244
        clus
vv       DMXL2 MUTATED DMXL2 WILD-TYPE
  FEMALE            17             208
  MALE              20             244
[1] 2 2
[1] FALSE
D1217V9, binary
                 cls
clus                0   1
  DMXL2 MUTATED    28   1
  DMXL2 WILD-TYPE 322  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DMXL2 MUTATED     28    1
  DMXL2 WILD-TYPE  322   21
     clus
vv    DMXL2 MUTATED DMXL2 WILD-TYPE
  NO             28             322
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  DMXL2 MUTATED                     27                             6
  DMXL2 WILD-TYPE                  288                            41
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  DMXL2 MUTATED                       3                              1
  DMXL2 WILD-TYPE                   103                              9
D1217V10, multiclass
                                clus
vv                               DMXL2 MUTATED DMXL2 WILD-TYPE
  COLON ADENOCARCINOMA                      27             288
  COLON MUCINOUS ADENOCARCINOMA              6              41
  RECTAL ADENOCARCINOMA                      3             103
  RECTAL MUCINOUS ADENOCARCINOMA             1               9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  DMXL2 MUTATED    24   0   3   5
  DMXL2 WILD-TYPE 321   4  28  20
D1217V11, multiclass
    clus
vv   DMXL2 MUTATED DMXL2 WILD-TYPE
  R0            24             321
  R1             0               4
  R2             3              28
  RX             5              20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1217V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DMXL2 MUTATED                                  0     3
  DMXL2 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  DMXL2 MUTATED                           0    17
  DMXL2 WILD-TYPE                        22   209
D1217V13, multiclass
                                  clus
vv                                 DMXL2 MUTATED DMXL2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        3               8
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                       17             209
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1218) Variable = DPAGT1 MUTATION ANALYSIS
D1218V1, survival
                  sevent
clus2                0   1
  DPAGT1 MUTATED     7   1
  DPAGT1 WILD-TYPE 371  92
  DPAGT1 MUTATED DPAGT1 WILD-TYPE 
               8              463 
  DPAGT1 MUTATED DPAGT1 WILD-TYPE 
               1               92 
$`DPAGT1 MUTATED`
TCGA-AA-3710 TCGA-AU-6004 TCGA-AZ-6599 TCGA-CM-6161 TCGA-D5-6533 TCGA-D5-6929 
       26.99        27.09         6.77        15.02         1.32         4.80 
TCGA-AG-A00C TCGA-DT-5265 
        6.02         5.29 

$`DPAGT1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
       19.00        36.00         5.03        85.05        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 
       27.42        10.88         0.20        14.50        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 
      106.75        22.36        62.79        88.21        49.41        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6162 
       15.02         5.03        15.02        15.02        17.03        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 
       14.30         9.04         9.44        11.64         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        20.98        13.94        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A0XA 
       10.98        19.99         5.95         4.01         5.03       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  DPAGT1 MUTATED DPAGT1 WILD-TYPE 
            1.32             0.00 
  DPAGT1 MUTATED DPAGT1 WILD-TYPE 
           27.09           148.01 
  DPAGT1 MUTATED DPAGT1 WILD-TYPE 
           6.395           20.550 
[1] "1.3 - 27.1 (6.4)"   "0.0 - 148.0 (20.6)"
[1] "hr=" "1.4"
D1218V2, continuous
D1218V3, binary
                  cls
clus                 0   1
  DPAGT1 MUTATED     6   2
  DPAGT1 WILD-TYPE 360 117
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DPAGT1 MUTATED      6    2
  DPAGT1 WILD-TYPE  360  117
        clus
vv       DPAGT1 MUTATED DPAGT1 WILD-TYPE
  COLON               6              360
  RECTUM              2              117
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DPAGT1 MUTATED         3        0        1         1         0         0
  DPAGT1 WILD-TYPE      88        1       31       137        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DPAGT1 MUTATED           0          0          2          0        1
  DPAGT1 WILD-TYPE        24         11         57         42       47
                  vv
clus               STAGE IVA STAGE IVB
  DPAGT1 MUTATED           0         0
  DPAGT1 WILD-TYPE        18         1
D1218V4, multiclass
            clus
vv           DPAGT1 MUTATED DPAGT1 WILD-TYPE
  STAGE I                 3               88
  STAGE IA                0                1
  STAGE II                1               31
  STAGE IIA               1              137
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              2               57
  STAGE IIIC              0               42
  STAGE IV                1               47
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  DPAGT1 MUTATED     0   3   4   1
  DPAGT1 WILD-TYPE  17  89 325  49
D1218V5, multiclass
    clus
vv   DPAGT1 MUTATED DPAGT1 WILD-TYPE
  T1              0               17
  T2              3               89
  T3              4              325
  T4              1               49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  DPAGT1 MUTATED     6   2   0
  DPAGT1 WILD-TYPE 281 111  87
D1218V6, multiclass
    clus
vv   DPAGT1 MUTATED DPAGT1 WILD-TYPE
  N0              6              281
  N1              2              111
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1218V7, binary
                  cls
clus                 0   1
  DPAGT1 MUTATED     6   1
  DPAGT1 WILD-TYPE 369  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DPAGT1 MUTATED      6    1
  DPAGT1 WILD-TYPE  369   64
   clus
vv  DPAGT1 MUTATED DPAGT1 WILD-TYPE
  0              6              369
  1              1               64
[1] 2 2
[1] FALSE
D1218V8, binary
                  cls
clus                 0   1
  DPAGT1 MUTATED     6   2
  DPAGT1 WILD-TYPE 219 262
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DPAGT1 MUTATED      6    2
  DPAGT1 WILD-TYPE  219  262
        clus
vv       DPAGT1 MUTATED DPAGT1 WILD-TYPE
  FEMALE              6              219
  MALE                2              262
[1] 2 2
[1] FALSE
D1218V9, binary
                  cls
clus                 0   1
  DPAGT1 MUTATED     4   1
  DPAGT1 WILD-TYPE 346  21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DPAGT1 MUTATED      4    1
  DPAGT1 WILD-TYPE  346   21
     clus
vv    DPAGT1 MUTATED DPAGT1 WILD-TYPE
  NO               4              346
  YES              1               21
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  DPAGT1 MUTATED                      6                             0
  DPAGT1 WILD-TYPE                  309                            47
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  DPAGT1 MUTATED                       1                              1
  DPAGT1 WILD-TYPE                   105                              9
D1218V10, multiclass
                                clus
vv                               DPAGT1 MUTATED DPAGT1 WILD-TYPE
  COLON ADENOCARCINOMA                        6              309
  COLON MUCINOUS ADENOCARCINOMA               0               47
  RECTAL ADENOCARCINOMA                       1              105
  RECTAL MUCINOUS ADENOCARCINOMA              1                9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  DPAGT1 MUTATED     6   0   0   1
  DPAGT1 WILD-TYPE 339   4  31  24
D1218V11, multiclass
    clus
vv   DPAGT1 MUTATED DPAGT1 WILD-TYPE
  R0              6              339
  R1              0                4
  R2              0               31
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1218V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DPAGT1 MUTATED                                  0     1
  DPAGT1 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  DPAGT1 MUTATED                           0     5
  DPAGT1 WILD-TYPE                        22   221
D1218V13, multiclass
                                  clus
vv                                 DPAGT1 MUTATED DPAGT1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         5              221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1219) Variable = SLC38A9 MUTATION ANALYSIS
D1219V1, survival
                   sevent
clus2                 0   1
  SLC38A9 MUTATED    10   1
  SLC38A9 WILD-TYPE 368  92
  SLC38A9 MUTATED SLC38A9 WILD-TYPE 
               11               460 
  SLC38A9 MUTATED SLC38A9 WILD-TYPE 
                1                92 
$`SLC38A9 MUTATED`
TCGA-A6-5665 TCGA-AA-3663 TCGA-AA-3815 TCGA-AA-3864 TCGA-AU-6004 TCGA-AZ-4315 
       22.06         6.97        33.04        53.00        27.09        58.39 
TCGA-CA-6718 TCGA-CM-4743 TCGA-CM-4746 TCGA-D5-6928 TCGA-AG-A002 
       10.06        23.05        37.02        11.64        20.98 

$`SLC38A9 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       35.05         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        31.07        30.05        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       14.50        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07        12.20        12.76        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4747 
       21.14        82.95         1.91       124.27        20.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 
        4.41        12.43        14.30         9.04         9.44         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  SLC38A9 MUTATED SLC38A9 WILD-TYPE 
             6.97              0.00 
  SLC38A9 MUTATED SLC38A9 WILD-TYPE 
            58.39            148.01 
  SLC38A9 MUTATED SLC38A9 WILD-TYPE 
           23.050            20.035 
[1] "7.0 - 58.4 (23.1)"  "0.0 - 148.0 (20.0)"
[1] "hr=" "2.4"
D1219V2, continuous
D1219V3, binary
                   cls
clus                  0   1
  SLC38A9 MUTATED    11   1
  SLC38A9 WILD-TYPE 355 118
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC38A9 MUTATED     11    1
  SLC38A9 WILD-TYPE  355  118
        clus
vv       SLC38A9 MUTATED SLC38A9 WILD-TYPE
  COLON               11               355
  RECTUM               1               118
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SLC38A9 MUTATED         3        0        2         7         0         0
  SLC38A9 WILD-TYPE      88        1       30       131        10         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC38A9 MUTATED           0          0          0          0        0
  SLC38A9 WILD-TYPE        24         11         59         42       48
                   vv
clus                STAGE IVA STAGE IVB
  SLC38A9 MUTATED           0         0
  SLC38A9 WILD-TYPE        18         1
D1219V4, multiclass
            clus
vv           SLC38A9 MUTATED SLC38A9 WILD-TYPE
  STAGE I                  3                88
  STAGE IA                 0                 1
  STAGE II                 2                30
  STAGE IIA                7               131
  STAGE IIB                0                10
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               0                11
  STAGE IIIB               0                59
  STAGE IIIC               0                42
  STAGE IV                 0                48
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  SLC38A9 MUTATED     0   3   9   0
  SLC38A9 WILD-TYPE  17  89 320  50
D1219V5, multiclass
    clus
vv   SLC38A9 MUTATED SLC38A9 WILD-TYPE
  T1               0                17
  T2               3                89
  T3               9               320
  T4               0                50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  SLC38A9 MUTATED    12   0   0
  SLC38A9 WILD-TYPE 275 113  87
D1219V6, multiclass
    clus
vv   SLC38A9 MUTATED SLC38A9 WILD-TYPE
  N0              12               275
  N1               0               113
  N2               0                87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1219V7, binary
                   cls
clus                  0   1
  SLC38A9 MUTATED    12   0
  SLC38A9 WILD-TYPE 363  65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC38A9 MUTATED     12    0
  SLC38A9 WILD-TYPE  363   65
   clus
vv  SLC38A9 MUTATED SLC38A9 WILD-TYPE
  0              12               363
  1               0                65
[1] 2 2
[1] FALSE
D1219V8, binary
                   cls
clus                  0   1
  SLC38A9 MUTATED     4   8
  SLC38A9 WILD-TYPE 221 256
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC38A9 MUTATED      4    8
  SLC38A9 WILD-TYPE  221  256
        clus
vv       SLC38A9 MUTATED SLC38A9 WILD-TYPE
  FEMALE               4               221
  MALE                 8               256
[1] 2 2
[1] FALSE
D1219V9, binary
                   cls
clus                  0   1
  SLC38A9 MUTATED    10   0
  SLC38A9 WILD-TYPE 340  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC38A9 MUTATED     10    0
  SLC38A9 WILD-TYPE  340   22
     clus
vv    SLC38A9 MUTATED SLC38A9 WILD-TYPE
  NO               10               340
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SLC38A9 MUTATED                     10                             1
  SLC38A9 WILD-TYPE                  305                            46
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SLC38A9 MUTATED                       1                              0
  SLC38A9 WILD-TYPE                   105                             10
D1219V10, multiclass
                                clus
vv                               SLC38A9 MUTATED SLC38A9 WILD-TYPE
  COLON ADENOCARCINOMA                        10               305
  COLON MUCINOUS ADENOCARCINOMA                1                46
  RECTAL ADENOCARCINOMA                        1               105
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  SLC38A9 MUTATED    11   0   0   1
  SLC38A9 WILD-TYPE 334   4  31  24
D1219V11, multiclass
    clus
vv   SLC38A9 MUTATED SLC38A9 WILD-TYPE
  R0              11               334
  R1               0                 4
  R2               0                31
  RX               1                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1219V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SLC38A9 MUTATED                                  0     1
  SLC38A9 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  SLC38A9 MUTATED                           1     5
  SLC38A9 WILD-TYPE                        21   221
D1219V13, multiclass
                                  clus
vv                                 SLC38A9 MUTATED SLC38A9 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                10
  BLACK OR AFRICAN AMERICAN                      1                21
  WHITE                                          5               221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1220) Variable = HIST2H2AC MUTATION ANALYSIS
D1220V1, survival
                     sevent
clus2                   0   1
  HIST2H2AC MUTATED     6   0
  HIST2H2AC WILD-TYPE 372  93
  HIST2H2AC MUTATED HIST2H2AC WILD-TYPE 
                  6                 465 
  HIST2H2AC MUTATED HIST2H2AC WILD-TYPE 
                  0                  93 
$`HIST2H2AC MUTATED`
TCGA-AD-6895 TCGA-CM-5861 TCGA-CM-6172 TCGA-AF-2687 TCGA-AF-4110 TCGA-F5-6812 
        0.72        15.02        11.01        24.13        14.50         0.66 

$`HIST2H2AC WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       21.37        15.52        56.55         0.79         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       30.08        32.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6674 
       14.99        12.99        13.02        15.02        14.04        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       91.79        46.75        79.69        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       19.10        34.49        10.39        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  HIST2H2AC MUTATED HIST2H2AC WILD-TYPE 
               0.66                0.00 
  HIST2H2AC MUTATED HIST2H2AC WILD-TYPE 
              24.13              148.01 
  HIST2H2AC MUTATED HIST2H2AC WILD-TYPE 
             12.755              20.550 
[1] "0.7 - 24.1 (12.8)"  "0.0 - 148.0 (20.6)"
[1] "hr="     "3300000"
D1220V2, continuous
D1220V3, binary
                     cls
clus                    0   1
  HIST2H2AC MUTATED     3   2
  HIST2H2AC WILD-TYPE 363 117
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  HIST2H2AC MUTATED      3    2
  HIST2H2AC WILD-TYPE  363  117
        clus
vv       HIST2H2AC MUTATED HIST2H2AC WILD-TYPE
  COLON                  3                 363
  RECTUM                 2                 117
[1] 2 2
[1] FALSE
                     vv
clus                  STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  HIST2H2AC MUTATED         0        0        0         2         0         0
  HIST2H2AC WILD-TYPE      91        1       32       136        10         1
                     vv
clus                  STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HIST2H2AC MUTATED           0          0          1          1        0
  HIST2H2AC WILD-TYPE        24         11         58         41       48
                     vv
clus                  STAGE IVA STAGE IVB
  HIST2H2AC MUTATED           1         0
  HIST2H2AC WILD-TYPE        17         1
D1220V4, multiclass
            clus
vv           HIST2H2AC MUTATED HIST2H2AC WILD-TYPE
  STAGE I                    0                  91
  STAGE IA                   0                   1
  STAGE II                   0                  32
  STAGE IIA                  2                 136
  STAGE IIB                  0                  10
  STAGE IIC                  0                   1
  STAGE III                  0                  24
  STAGE IIIA                 0                  11
  STAGE IIIB                 1                  58
  STAGE IIIC                 1                  41
  STAGE IV                   0                  48
  STAGE IVA                  1                  17
  STAGE IVB                  0                   1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                   T1  T2  T3  T4
  HIST2H2AC MUTATED     0   0   5   1
  HIST2H2AC WILD-TYPE  17  92 324  49
D1220V5, multiclass
    clus
vv   HIST2H2AC MUTATED HIST2H2AC WILD-TYPE
  T1                 0                  17
  T2                 0                  92
  T3                 5                 324
  T4                 1                  49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                   N0  N1  N2
  HIST2H2AC MUTATED     2   2   2
  HIST2H2AC WILD-TYPE 285 111  85
D1220V6, multiclass
    clus
vv   HIST2H2AC MUTATED HIST2H2AC WILD-TYPE
  N0                 2                 285
  N1                 2                 111
  N2                 2                  85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1220V7, binary
                     cls
clus                    0   1
  HIST2H2AC MUTATED     4   0
  HIST2H2AC WILD-TYPE 371  65
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  HIST2H2AC MUTATED      4    0
  HIST2H2AC WILD-TYPE  371   65
   clus
vv  HIST2H2AC MUTATED HIST2H2AC WILD-TYPE
  0                 4                 371
  1                 0                  65
[1] 2 2
[1] FALSE
D1220V8, binary
                     cls
clus                    0   1
  HIST2H2AC MUTATED     2   4
  HIST2H2AC WILD-TYPE 223 260
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  HIST2H2AC MUTATED      2    4
  HIST2H2AC WILD-TYPE  223  260
        clus
vv       HIST2H2AC MUTATED HIST2H2AC WILD-TYPE
  FEMALE                 2                 223
  MALE                   4                 260
[1] 2 2
[1] FALSE
D1220V9, binary
                     cls
clus                    0   1
  HIST2H2AC MUTATED     3   1
  HIST2H2AC WILD-TYPE 347  21
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  HIST2H2AC MUTATED      3    1
  HIST2H2AC WILD-TYPE  347   21
     clus
vv    HIST2H2AC MUTATED HIST2H2AC WILD-TYPE
  NO                  3                 347
  YES                 1                  21
[1] 2 2
[1] FALSE
                     vv
clus                  COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  HIST2H2AC MUTATED                      3                             0
  HIST2H2AC WILD-TYPE                  312                            47
                     vv
clus                  RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  HIST2H2AC MUTATED                       2                              0
  HIST2H2AC WILD-TYPE                   104                             10
D1220V10, multiclass
                                clus
vv                               HIST2H2AC MUTATED HIST2H2AC WILD-TYPE
  COLON ADENOCARCINOMA                           3                 312
  COLON MUCINOUS ADENOCARCINOMA                  0                  47
  RECTAL ADENOCARCINOMA                          2                 104
  RECTAL MUCINOUS ADENOCARCINOMA                 0                  10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                   R0  R1  R2  RX
  HIST2H2AC MUTATED     5   0   0   0
  HIST2H2AC WILD-TYPE 340   4  31  25
D1220V11, multiclass
    clus
vv   HIST2H2AC MUTATED HIST2H2AC WILD-TYPE
  R0                 5                 340
  R1                 0                   4
  R2                 0                  31
  RX                 0                  25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1220V12, continuous
                     vv
clus                  AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HIST2H2AC MUTATED                                  0     0
  HIST2H2AC WILD-TYPE                                1    11
                     vv
clus                  BLACK OR AFRICAN AMERICAN WHITE
  HIST2H2AC MUTATED                           0     6
  HIST2H2AC WILD-TYPE                        22   220
D1220V13, multiclass
                                  clus
vv                                 HIST2H2AC MUTATED HIST2H2AC WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                 0                   1
  ASIAN                                            0                  11
  BLACK OR AFRICAN AMERICAN                        0                  22
  WHITE                                            6                 220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1221) Variable = SLCO1B1 MUTATION ANALYSIS
D1221V1, survival
                   sevent
clus2                 0   1
  SLCO1B1 MUTATED    16   6
  SLCO1B1 WILD-TYPE 362  87
  SLCO1B1 MUTATED SLCO1B1 WILD-TYPE 
               22               449 
  SLCO1B1 MUTATED SLCO1B1 WILD-TYPE 
                6                87 
$`SLCO1B1 MUTATED`
TCGA-A6-5657 TCGA-A6-6653 TCGA-AA-3552 TCGA-AA-3697 TCGA-AA-3821 TCGA-AA-3977 
       31.63        24.39        13.02        85.05         1.02        25.02 
TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01R TCGA-AZ-5403 TCGA-CA-6716 TCGA-CA-6718 
        4.01        34.98        35.01        62.79        12.20        10.06 
TCGA-D5-6537 TCGA-G4-6307 TCGA-G4-6317 TCGA-G4-6323 TCGA-AF-4110 TCGA-AF-6655 
        4.80        55.04        36.00        13.78        14.50        20.02 
TCGA-AG-A002 TCGA-DC-6681 TCGA-DY-A0XA TCGA-DY-A1DF 
       20.98         5.95       126.44        24.13 

$`SLCO1B1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 
       25.18        24.16        21.76        24.69        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 
       12.99         0.99        14.01        33.99        21.01        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
        0.99        25.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T 
       31.00        31.00        38.07         1.02         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6719 
        3.06         3.25         3.29         0.07        12.76        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       15.12        17.85        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 
      133.18        74.56        65.85        53.62        44.68        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       63.62        61.91        22.09        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6672 
       19.10        34.49        10.39        16.83        15.39        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC 
       10.98        19.99         4.01         5.03         5.29        41.36 
TCGA-DY-A1DD TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       57.24        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  SLCO1B1 MUTATED SLCO1B1 WILD-TYPE 
             1.02              0.00 
  SLCO1B1 MUTATED SLCO1B1 WILD-TYPE 
           126.44            148.01 
  SLCO1B1 MUTATED SLCO1B1 WILD-TYPE 
           22.555            20.120 
[1] "1.0 - 126.4 (22.6)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.3"
D1221V2, continuous
D1221V3, binary
                   cls
clus                  0   1
  SLCO1B1 MUTATED    17   5
  SLCO1B1 WILD-TYPE 349 114
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLCO1B1 MUTATED     17    5
  SLCO1B1 WILD-TYPE  349  114
        clus
vv       SLCO1B1 MUTATED SLCO1B1 WILD-TYPE
  COLON               17               349
  RECTUM               5               114
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SLCO1B1 MUTATED         3        1        1         4         2         0
  SLCO1B1 WILD-TYPE      88        0       31       134         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLCO1B1 MUTATED           2          1          3          3        0
  SLCO1B1 WILD-TYPE        22         10         56         39       48
                   vv
clus                STAGE IVA STAGE IVB
  SLCO1B1 MUTATED           2         0
  SLCO1B1 WILD-TYPE        16         1
D1221V4, multiclass
            clus
vv           SLCO1B1 MUTATED SLCO1B1 WILD-TYPE
  STAGE I                  3                88
  STAGE IA                 1                 0
  STAGE II                 1                31
  STAGE IIA                4               134
  STAGE IIB                2                 8
  STAGE IIC                0                 1
  STAGE III                2                22
  STAGE IIIA               1                10
  STAGE IIIB               3                56
  STAGE IIIC               3                39
  STAGE IV                 0                48
  STAGE IVA                2                16
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  SLCO1B1 MUTATED     0   5  14   3
  SLCO1B1 WILD-TYPE  17  87 315  47
D1221V5, multiclass
    clus
vv   SLCO1B1 MUTATED SLCO1B1 WILD-TYPE
  T1               0                17
  T2               5                87
  T3              14               315
  T4               3                47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  SLCO1B1 MUTATED    13   4   6
  SLCO1B1 WILD-TYPE 274 109  81
D1221V6, multiclass
    clus
vv   SLCO1B1 MUTATED SLCO1B1 WILD-TYPE
  N0              13               274
  N1               4               109
  N2               6                81
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1221V7, binary
                   cls
clus                  0   1
  SLCO1B1 MUTATED    16   1
  SLCO1B1 WILD-TYPE 359  64
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLCO1B1 MUTATED     16    1
  SLCO1B1 WILD-TYPE  359   64
   clus
vv  SLCO1B1 MUTATED SLCO1B1 WILD-TYPE
  0              16               359
  1               1                64
[1] 2 2
[1] FALSE
D1221V8, binary
                   cls
clus                  0   1
  SLCO1B1 MUTATED     8  15
  SLCO1B1 WILD-TYPE 217 249
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLCO1B1 MUTATED      8   15
  SLCO1B1 WILD-TYPE  217  249
        clus
vv       SLCO1B1 MUTATED SLCO1B1 WILD-TYPE
  FEMALE               8               217
  MALE                15               249
[1] 2 2
[1] FALSE
D1221V9, binary
                   cls
clus                  0   1
  SLCO1B1 MUTATED    17   1
  SLCO1B1 WILD-TYPE 333  21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLCO1B1 MUTATED     17    1
  SLCO1B1 WILD-TYPE  333   21
     clus
vv    SLCO1B1 MUTATED SLCO1B1 WILD-TYPE
  NO               17               333
  YES               1                21
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SLCO1B1 MUTATED                     14                             3
  SLCO1B1 WILD-TYPE                  301                            44
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SLCO1B1 MUTATED                       5                              0
  SLCO1B1 WILD-TYPE                   101                             10
D1221V10, multiclass
                                clus
vv                               SLCO1B1 MUTATED SLCO1B1 WILD-TYPE
  COLON ADENOCARCINOMA                        14               301
  COLON MUCINOUS ADENOCARCINOMA                3                44
  RECTAL ADENOCARCINOMA                        5               101
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  SLCO1B1 MUTATED    16   0   0   2
  SLCO1B1 WILD-TYPE 329   4  31  23
D1221V11, multiclass
    clus
vv   SLCO1B1 MUTATED SLCO1B1 WILD-TYPE
  R0              16               329
  R1               0                 4
  R2               0                31
  RX               2                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1221V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SLCO1B1 MUTATED                                  0     2
  SLCO1B1 WILD-TYPE                                1     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  SLCO1B1 MUTATED                           2    10
  SLCO1B1 WILD-TYPE                        20   216
D1221V13, multiclass
                                  clus
vv                                 SLCO1B1 MUTATED SLCO1B1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          2                 9
  BLACK OR AFRICAN AMERICAN                      2                20
  WHITE                                         10               216
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1222) Variable = LBP MUTATION ANALYSIS
D1222V1, survival
               sevent
clus2             0   1
  LBP MUTATED     7   0
  LBP WILD-TYPE 371  93
  LBP MUTATED LBP WILD-TYPE 
            7           464 
  LBP MUTATED LBP WILD-TYPE 
            0            93 
$`LBP MUTATED`
TCGA-AA-3660 TCGA-AD-5900 TCGA-CK-5913 TCGA-F4-6856 TCGA-G4-6306 TCGA-G4-6307 
       78.08         0.07        51.32        35.31        44.68        55.04 
TCGA-F5-6465 
       49.51 

$`LBP WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 
       20.98        19.99        13.94        19.99        61.02         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 
       41.00        39.98        18.05        40.96        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       85.45        15.62        49.08         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
       13.25         0.53        47.41       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       53.62        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
        9.96        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  LBP MUTATED LBP WILD-TYPE 
         0.07          0.00 
  LBP MUTATED LBP WILD-TYPE 
        78.08        148.01 
  LBP MUTATED LBP WILD-TYPE 
       49.510        20.035 
[1] "0.1 - 78.1 (49.5)"  "0.0 - 148.0 (20.0)"
[1] "hr="     "9500000"
D1222V2, continuous
D1222V3, binary
               cls
clus              0   1
  LBP MUTATED     7   1
  LBP WILD-TYPE 359 118
[1] "tbl2"
               cls
clus            [,1] [,2]
  LBP MUTATED      7    1
  LBP WILD-TYPE  359  118
        clus
vv       LBP MUTATED LBP WILD-TYPE
  COLON            7           359
  RECTUM           1           118
[1] 2 2
[1] FALSE
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  LBP MUTATED         2        0        1         3         0         0
  LBP WILD-TYPE      89        1       31       135        10         1
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  LBP MUTATED           0          0          1          0        1         0
  LBP WILD-TYPE        24         11         58         42       47        18
               vv
clus            STAGE IVB
  LBP MUTATED           0
  LBP WILD-TYPE         1
D1222V4, multiclass
            clus
vv           LBP MUTATED LBP WILD-TYPE
  STAGE I              2            89
  STAGE IA             0             1
  STAGE II             1            31
  STAGE IIA            3           135
  STAGE IIB            0            10
  STAGE IIC            0             1
  STAGE III            0            24
  STAGE IIIA           0            11
  STAGE IIIB           1            58
  STAGE IIIC           0            42
  STAGE IV             1            47
  STAGE IVA            0            18
  STAGE IVB            0             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  LBP MUTATED     0   3   4   1
  LBP WILD-TYPE  17  89 325  49
D1222V5, multiclass
    clus
vv   LBP MUTATED LBP WILD-TYPE
  T1           0            17
  T2           3            89
  T3           4           325
  T4           1            49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2
  LBP MUTATED     6   1   1
  LBP WILD-TYPE 281 112  86
D1222V6, multiclass
    clus
vv   LBP MUTATED LBP WILD-TYPE
  N0           6           281
  N1           1           112
  N2           1            86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1222V7, binary
               cls
clus              0   1
  LBP MUTATED     5   1
  LBP WILD-TYPE 370  64
[1] "tbl2"
               cls
clus            [,1] [,2]
  LBP MUTATED      5    1
  LBP WILD-TYPE  370   64
   clus
vv  LBP MUTATED LBP WILD-TYPE
  0           5           370
  1           1            64
[1] 2 2
[1] FALSE
D1222V8, binary
               cls
clus              0   1
  LBP MUTATED     4   4
  LBP WILD-TYPE 221 260
[1] "tbl2"
               cls
clus            [,1] [,2]
  LBP MUTATED      4    4
  LBP WILD-TYPE  221  260
        clus
vv       LBP MUTATED LBP WILD-TYPE
  FEMALE           4           221
  MALE             4           260
[1] 2 2
[1] FALSE
D1222V9, binary
               cls
clus              0   1
  LBP MUTATED     6   0
  LBP WILD-TYPE 344  22
[1] "tbl2"
               cls
clus            [,1] [,2]
  LBP MUTATED      6    0
  LBP WILD-TYPE  344   22
     clus
vv    LBP MUTATED LBP WILD-TYPE
  NO            6           344
  YES           0            22
[1] 2 2
[1] FALSE
               vv
clus            COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  LBP MUTATED                      5                             2
  LBP WILD-TYPE                  310                            45
               vv
clus            RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  LBP MUTATED                       1                              0
  LBP WILD-TYPE                   105                             10
D1222V10, multiclass
                                clus
vv                               LBP MUTATED LBP WILD-TYPE
  COLON ADENOCARCINOMA                     5           310
  COLON MUCINOUS ADENOCARCINOMA            2            45
  RECTAL ADENOCARCINOMA                    1           105
  RECTAL MUCINOUS ADENOCARCINOMA           0            10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             R0  R1  R2  RX
  LBP MUTATED     6   0   1   1
  LBP WILD-TYPE 339   4  30  24
D1222V11, multiclass
    clus
vv   LBP MUTATED LBP WILD-TYPE
  R0           6           339
  R1           0             4
  R2           1            30
  RX           1            24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1222V12, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  LBP MUTATED                                  0     0
  LBP WILD-TYPE                                1    11
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  LBP MUTATED                           0     6
  LBP WILD-TYPE                        22   220
D1222V13, multiclass
                                  clus
vv                                 LBP MUTATED LBP WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      0            11
  BLACK OR AFRICAN AMERICAN                  0            22
  WHITE                                      6           220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1223) Variable = THUMPD3 MUTATION ANALYSIS
D1223V1, survival
                   sevent
clus2                 0   1
  THUMPD3 MUTATED     9   2
  THUMPD3 WILD-TYPE 369  91
  THUMPD3 MUTATED THUMPD3 WILD-TYPE 
               11               460 
  THUMPD3 MUTATED THUMPD3 WILD-TYPE 
                2                91 
$`THUMPD3 MUTATED`
TCGA-AA-A00E TCGA-AA-A010 TCGA-AZ-4315 TCGA-AZ-6600 TCGA-CA-6717 TCGA-CM-6169 
       30.02        34.98        58.39        12.10        12.76        13.02 
TCGA-D5-6539 TCGA-F4-6569 TCGA-G4-6303 TCGA-G4-6304 TCGA-AG-A002 
       12.49        35.74        65.85        53.62        20.98 

$`THUMPD3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       13.94        38.04        19.00        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       33.01        21.44        17.82         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 
       22.36        62.79        88.21        49.41         6.77       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07        12.20        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6170 
       29.03        16.04        21.99        14.99        12.99        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 
       15.12        17.85         4.80        17.13        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       74.56        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  THUMPD3 MUTATED THUMPD3 WILD-TYPE 
             12.1               0.0 
  THUMPD3 MUTATED THUMPD3 WILD-TYPE 
            65.85            148.01 
  THUMPD3 MUTATED THUMPD3 WILD-TYPE 
           30.020            20.085 
[1] "12.1 - 65.8 (30.0)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.4"
D1223V2, continuous
D1223V3, binary
                   cls
clus                  0   1
  THUMPD3 MUTATED    11   1
  THUMPD3 WILD-TYPE 355 118
[1] "tbl2"
                   cls
clus                [,1] [,2]
  THUMPD3 MUTATED     11    1
  THUMPD3 WILD-TYPE  355  118
        clus
vv       THUMPD3 MUTATED THUMPD3 WILD-TYPE
  COLON               11               355
  RECTUM               1               118
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  THUMPD3 MUTATED         2        0        0         4         3         0
  THUMPD3 WILD-TYPE      89        1       32       134         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  THUMPD3 MUTATED           0          1          0          0        2
  THUMPD3 WILD-TYPE        24         10         59         42       46
                   vv
clus                STAGE IVA STAGE IVB
  THUMPD3 MUTATED           0         0
  THUMPD3 WILD-TYPE        18         1
D1223V4, multiclass
            clus
vv           THUMPD3 MUTATED THUMPD3 WILD-TYPE
  STAGE I                  2                89
  STAGE IA                 0                 1
  STAGE II                 0                32
  STAGE IIA                4               134
  STAGE IIB                3                 7
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               1                10
  STAGE IIIB               0                59
  STAGE IIIC               0                42
  STAGE IV                 2                46
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  THUMPD3 MUTATED     0   2   6   4
  THUMPD3 WILD-TYPE  17  90 323  46
D1223V5, multiclass
    clus
vv   THUMPD3 MUTATED THUMPD3 WILD-TYPE
  T1               0                17
  T2               2                90
  T3               6               323
  T4               4                46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  THUMPD3 MUTATED    10   2   0
  THUMPD3 WILD-TYPE 277 111  87
D1223V6, multiclass
    clus
vv   THUMPD3 MUTATED THUMPD3 WILD-TYPE
  N0              10               277
  N1               2               111
  N2               0                87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1223V7, binary
                   cls
clus                  0   1
  THUMPD3 MUTATED     9   2
  THUMPD3 WILD-TYPE 366  63
[1] "tbl2"
                   cls
clus                [,1] [,2]
  THUMPD3 MUTATED      9    2
  THUMPD3 WILD-TYPE  366   63
   clus
vv  THUMPD3 MUTATED THUMPD3 WILD-TYPE
  0               9               366
  1               2                63
[1] 2 2
[1] FALSE
D1223V8, binary
                   cls
clus                  0   1
  THUMPD3 MUTATED     5   7
  THUMPD3 WILD-TYPE 220 257
[1] "tbl2"
                   cls
clus                [,1] [,2]
  THUMPD3 MUTATED      5    7
  THUMPD3 WILD-TYPE  220  257
        clus
vv       THUMPD3 MUTATED THUMPD3 WILD-TYPE
  FEMALE               5               220
  MALE                 7               257
[1] 2 2
[1] FALSE
D1223V9, binary
                   cls
clus                  0   1
  THUMPD3 MUTATED    10   0
  THUMPD3 WILD-TYPE 340  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  THUMPD3 MUTATED     10    0
  THUMPD3 WILD-TYPE  340   22
     clus
vv    THUMPD3 MUTATED THUMPD3 WILD-TYPE
  NO               10               340
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  THUMPD3 MUTATED                     10                             1
  THUMPD3 WILD-TYPE                  305                            46
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  THUMPD3 MUTATED                       1                              0
  THUMPD3 WILD-TYPE                   105                             10
D1223V10, multiclass
                                clus
vv                               THUMPD3 MUTATED THUMPD3 WILD-TYPE
  COLON ADENOCARCINOMA                        10               305
  COLON MUCINOUS ADENOCARCINOMA                1                46
  RECTAL ADENOCARCINOMA                        1               105
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  THUMPD3 MUTATED     9   0   0   2
  THUMPD3 WILD-TYPE 336   4  31  23
D1223V11, multiclass
    clus
vv   THUMPD3 MUTATED THUMPD3 WILD-TYPE
  R0               9               336
  R1               0                 4
  R2               0                31
  RX               2                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1223V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  THUMPD3 MUTATED                                  0     1
  THUMPD3 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  THUMPD3 MUTATED                           2     6
  THUMPD3 WILD-TYPE                        20   220
D1223V13, multiclass
                                  clus
vv                                 THUMPD3 MUTATED THUMPD3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                10
  BLACK OR AFRICAN AMERICAN                      2                20
  WHITE                                          6               220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1224) Variable = GPSM2 MUTATION ANALYSIS
D1224V1, survival
                 sevent
clus2               0   1
  GPSM2 MUTATED     9   3
  GPSM2 WILD-TYPE 369  90
  GPSM2 MUTATED GPSM2 WILD-TYPE 
             12             459 
  GPSM2 MUTATED GPSM2 WILD-TYPE 
              3              90 
$`GPSM2 MUTATED`
TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3713 TCGA-AA-A010 TCGA-AD-6895 TCGA-AZ-4315 
        3.02        63.98        19.04        34.98         0.72        58.39 
TCGA-AZ-6600 TCGA-CA-6717 TCGA-CK-5914 TCGA-DM-A1DA TCGA-G4-6628 TCGA-EI-6506 
       12.10        12.76         9.99         7.50        79.69        20.55 

$`GPSM2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       49.41         6.77       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07        12.20        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 
       85.45        15.62        49.08        51.32        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
       12.59       140.38        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       46.75        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       51.48        32.61         0.49        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  GPSM2 MUTATED GPSM2 WILD-TYPE 
           0.72            0.00 
  GPSM2 MUTATED GPSM2 WILD-TYPE 
          79.69          148.01 
  GPSM2 MUTATED GPSM2 WILD-TYPE 
          15.90           20.28 
[1] "0.7 - 79.7 (15.9)"  "0.0 - 148.0 (20.3)"
[1] "hr=" "1.2"
D1224V2, continuous
D1224V3, binary
                 cls
clus                0   1
  GPSM2 MUTATED    12   1
  GPSM2 WILD-TYPE 354 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPSM2 MUTATED     12    1
  GPSM2 WILD-TYPE  354  118
        clus
vv       GPSM2 MUTATED GPSM2 WILD-TYPE
  COLON             12             354
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GPSM2 MUTATED         1        0        3         3         1         0
  GPSM2 WILD-TYPE      90        1       29       135         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  GPSM2 MUTATED           0          0          1          1        2         0
  GPSM2 WILD-TYPE        24         11         58         41       46        18
                 vv
clus              STAGE IVB
  GPSM2 MUTATED           0
  GPSM2 WILD-TYPE         1
D1224V4, multiclass
            clus
vv           GPSM2 MUTATED GPSM2 WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               3              29
  STAGE IIA              3             135
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             1              41
  STAGE IV               2              46
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  GPSM2 MUTATED     0   1   9   3
  GPSM2 WILD-TYPE  17  91 320  47
D1224V5, multiclass
    clus
vv   GPSM2 MUTATED GPSM2 WILD-TYPE
  T1             0              17
  T2             1              91
  T3             9             320
  T4             3              47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  GPSM2 MUTATED     9   3   1
  GPSM2 WILD-TYPE 278 110  86
D1224V6, multiclass
    clus
vv   GPSM2 MUTATED GPSM2 WILD-TYPE
  N0             9             278
  N1             3             110
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1224V7, binary
                 cls
clus                0   1
  GPSM2 MUTATED     9   2
  GPSM2 WILD-TYPE 366  63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPSM2 MUTATED      9    2
  GPSM2 WILD-TYPE  366   63
   clus
vv  GPSM2 MUTATED GPSM2 WILD-TYPE
  0             9             366
  1             2              63
[1] 2 2
[1] FALSE
D1224V8, binary
                 cls
clus                0   1
  GPSM2 MUTATED     5   8
  GPSM2 WILD-TYPE 220 256
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPSM2 MUTATED      5    8
  GPSM2 WILD-TYPE  220  256
        clus
vv       GPSM2 MUTATED GPSM2 WILD-TYPE
  FEMALE             5             220
  MALE               8             256
[1] 2 2
[1] FALSE
D1224V9, binary
                 cls
clus                0   1
  GPSM2 MUTATED     7   1
  GPSM2 WILD-TYPE 343  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPSM2 MUTATED      7    1
  GPSM2 WILD-TYPE  343   21
     clus
vv    GPSM2 MUTATED GPSM2 WILD-TYPE
  NO              7             343
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  GPSM2 MUTATED                     11                             1
  GPSM2 WILD-TYPE                  304                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  GPSM2 MUTATED                       1                              0
  GPSM2 WILD-TYPE                   105                             10
D1224V10, multiclass
                                clus
vv                               GPSM2 MUTATED GPSM2 WILD-TYPE
  COLON ADENOCARCINOMA                      11             304
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  GPSM2 MUTATED     7   0   1   2
  GPSM2 WILD-TYPE 338   4  30  23
D1224V11, multiclass
    clus
vv   GPSM2 MUTATED GPSM2 WILD-TYPE
  R0             7             338
  R1             0               4
  R2             1              30
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1224V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GPSM2 MUTATED                                  0     1
  GPSM2 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  GPSM2 MUTATED                           1     6
  GPSM2 WILD-TYPE                        21   220
D1224V13, multiclass
                                  clus
vv                                 GPSM2 MUTATED GPSM2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        6             220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1225) Variable = OR4B1 MUTATION ANALYSIS
D1225V1, survival
                 sevent
clus2               0   1
  OR4B1 MUTATED     6   0
  OR4B1 WILD-TYPE 372  93
  OR4B1 MUTATED OR4B1 WILD-TYPE 
              6             465 
  OR4B1 MUTATED OR4B1 WILD-TYPE 
              0              93 
$`OR4B1 MUTATED`
TCGA-AA-3966 TCGA-D5-6536 TCGA-DM-A1HB TCGA-G4-6323 TCGA-AG-A002 TCGA-AH-6544 
        2.01        17.85       135.65        13.78        20.98        38.56 

$`OR4B1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 
       24.00         2.01        20.98        34.03        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       61.91        36.00        22.09        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6547 
       38.96        61.97        41.00        38.04       117.11         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  OR4B1 MUTATED OR4B1 WILD-TYPE 
           2.01            0.00 
  OR4B1 MUTATED OR4B1 WILD-TYPE 
         135.65          148.01 
  OR4B1 MUTATED OR4B1 WILD-TYPE 
         19.415          20.190 
[1] "2.0 - 135.7 (19.4)" "0.0 - 148.0 (20.2)"
[1] "hr="     "9200000"
D1225V2, continuous
D1225V3, binary
                 cls
clus                0   1
  OR4B1 MUTATED     4   2
  OR4B1 WILD-TYPE 362 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR4B1 MUTATED      4    2
  OR4B1 WILD-TYPE  362  117
        clus
vv       OR4B1 MUTATED OR4B1 WILD-TYPE
  COLON              4             362
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  OR4B1 MUTATED         1        1        0         2         0         0
  OR4B1 WILD-TYPE      90        0       32       136        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  OR4B1 MUTATED           0          0          1          0        0         0
  OR4B1 WILD-TYPE        24         11         58         42       48        18
                 vv
clus              STAGE IVB
  OR4B1 MUTATED           0
  OR4B1 WILD-TYPE         1
D1225V4, multiclass
            clus
vv           OR4B1 MUTATED OR4B1 WILD-TYPE
  STAGE I                1              90
  STAGE IA               1               0
  STAGE II               0              32
  STAGE IIA              2             136
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  OR4B1 MUTATED     0   1   4   0
  OR4B1 WILD-TYPE  17  91 325  50
D1225V5, multiclass
    clus
vv   OR4B1 MUTATED OR4B1 WILD-TYPE
  T1             0              17
  T2             1              91
  T3             4             325
  T4             0              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  OR4B1 MUTATED     4   2   0
  OR4B1 WILD-TYPE 283 111  87
D1225V6, multiclass
    clus
vv   OR4B1 MUTATED OR4B1 WILD-TYPE
  N0             4             283
  N1             2             111
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1225V7, binary
                 cls
clus                0   1
  OR4B1 MUTATED     4   1
  OR4B1 WILD-TYPE 371  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR4B1 MUTATED      4    1
  OR4B1 WILD-TYPE  371   64
   clus
vv  OR4B1 MUTATED OR4B1 WILD-TYPE
  0             4             371
  1             1              64
[1] 2 2
[1] FALSE
D1225V8, binary
                 cls
clus                0   1
  OR4B1 MUTATED     1   5
  OR4B1 WILD-TYPE 224 259
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR4B1 MUTATED      1    5
  OR4B1 WILD-TYPE  224  259
        clus
vv       OR4B1 MUTATED OR4B1 WILD-TYPE
  FEMALE             1             224
  MALE               5             259
[1] 2 2
[1] FALSE
D1225V9, binary
                 cls
clus                0   1
  OR4B1 MUTATED     4   0
  OR4B1 WILD-TYPE 346  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR4B1 MUTATED      4    0
  OR4B1 WILD-TYPE  346   22
     clus
vv    OR4B1 MUTATED OR4B1 WILD-TYPE
  NO              4             346
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  OR4B1 MUTATED                      2                             1
  OR4B1 WILD-TYPE                  313                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  OR4B1 MUTATED                       2                              0
  OR4B1 WILD-TYPE                   104                             10
D1225V10, multiclass
                                clus
vv                               OR4B1 MUTATED OR4B1 WILD-TYPE
  COLON ADENOCARCINOMA                       2             313
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  OR4B1 MUTATED     3   0   0   0
  OR4B1 WILD-TYPE 342   4  31  25
D1225V11, multiclass
    clus
vv   OR4B1 MUTATED OR4B1 WILD-TYPE
  R0             3             342
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1225V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OR4B1 MUTATED                                  0     0
  OR4B1 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  OR4B1 MUTATED                           1     3
  OR4B1 WILD-TYPE                        21   223
D1225V13, multiclass
                                  clus
vv                                 OR4B1 MUTATED OR4B1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        3             223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1226) Variable = LEO1 MUTATION ANALYSIS
D1226V1, survival
                sevent
clus2              0   1
  LEO1 MUTATED    10   2
  LEO1 WILD-TYPE 368  91
  LEO1 MUTATED LEO1 WILD-TYPE 
            12            459 
  LEO1 MUTATED LEO1 WILD-TYPE 
             2             91 
$`LEO1 MUTATED`
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3510 TCGA-AA-3864 TCGA-AA-A00N 
       23.87        20.12        20.28        63.98        53.00         4.01 
TCGA-AD-6895 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-CA-6717 TCGA-AG-3892 TCGA-AG-3902 
        0.72        58.39        49.41        12.76        13.02        32.02 

$`LEO1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6781 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 
       19.66         7.04         3.02         1.02        35.01         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       31.07        30.05        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       21.37        15.52        56.55         0.79         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        33.01        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 
      106.75        22.36        62.79        88.21         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 
        1.02        17.95        36.95        17.03        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
        1.02        48.03        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  LEO1 MUTATED LEO1 WILD-TYPE 
          0.72           0.00 
  LEO1 MUTATED LEO1 WILD-TYPE 
         63.98         148.01 
  LEO1 MUTATED LEO1 WILD-TYPE 
        22.075         20.050 
[1] "0.7 - 64.0 (22.1)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.4"
D1226V2, continuous
D1226V3, binary
                cls
clus               0   1
  LEO1 MUTATED    10   2
  LEO1 WILD-TYPE 356 117
[1] "tbl2"
                cls
clus             [,1] [,2]
  LEO1 MUTATED     10    2
  LEO1 WILD-TYPE  356  117
        clus
vv       LEO1 MUTATED LEO1 WILD-TYPE
  COLON            10            356
  RECTUM            2            117
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  LEO1 MUTATED         1        0        3         4         2         0
  LEO1 WILD-TYPE      90        1       29       134         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  LEO1 MUTATED           0          0          1          0        0         0
  LEO1 WILD-TYPE        24         11         58         42       48        18
                vv
clus             STAGE IVB
  LEO1 MUTATED           0
  LEO1 WILD-TYPE         1
D1226V4, multiclass
            clus
vv           LEO1 MUTATED LEO1 WILD-TYPE
  STAGE I               1             90
  STAGE IA              0              1
  STAGE II              3             29
  STAGE IIA             4            134
  STAGE IIB             2              8
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            1             58
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  LEO1 MUTATED     1   0   9   2
  LEO1 WILD-TYPE  16  92 320  48
D1226V5, multiclass
    clus
vv   LEO1 MUTATED LEO1 WILD-TYPE
  T1            1             16
  T2            0             92
  T3            9            320
  T4            2             48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  LEO1 MUTATED    10   2   0
  LEO1 WILD-TYPE 277 111  87
D1226V6, multiclass
    clus
vv   LEO1 MUTATED LEO1 WILD-TYPE
  N0           10            277
  N1            2            111
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1226V7, binary
                cls
clus               0   1
  LEO1 MUTATED     8   0
  LEO1 WILD-TYPE 367  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  LEO1 MUTATED      8    0
  LEO1 WILD-TYPE  367   65
   clus
vv  LEO1 MUTATED LEO1 WILD-TYPE
  0            8            367
  1            0             65
[1] 2 2
[1] FALSE
D1226V8, binary
                cls
clus               0   1
  LEO1 MUTATED     3   9
  LEO1 WILD-TYPE 222 255
[1] "tbl2"
                cls
clus             [,1] [,2]
  LEO1 MUTATED      3    9
  LEO1 WILD-TYPE  222  255
        clus
vv       LEO1 MUTATED LEO1 WILD-TYPE
  FEMALE            3            222
  MALE              9            255
[1] 2 2
[1] FALSE
D1226V9, binary
                cls
clus               0   1
  LEO1 MUTATED    10   0
  LEO1 WILD-TYPE 340  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  LEO1 MUTATED     10    0
  LEO1 WILD-TYPE  340   22
     clus
vv    LEO1 MUTATED LEO1 WILD-TYPE
  NO            10            340
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  LEO1 MUTATED                      7                             3
  LEO1 WILD-TYPE                  308                            44
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  LEO1 MUTATED                       2                              0
  LEO1 WILD-TYPE                   104                             10
D1226V10, multiclass
                                clus
vv                               LEO1 MUTATED LEO1 WILD-TYPE
  COLON ADENOCARCINOMA                      7            308
  COLON MUCINOUS ADENOCARCINOMA             3             44
  RECTAL ADENOCARCINOMA                     2            104
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  LEO1 MUTATED     6   0   0   1
  LEO1 WILD-TYPE 339   4  31  24
D1226V11, multiclass
    clus
vv   LEO1 MUTATED LEO1 WILD-TYPE
  R0            6            339
  R1            0              4
  R2            0             31
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1226V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  LEO1 MUTATED                                  0     1
  LEO1 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  LEO1 MUTATED                           0     6
  LEO1 WILD-TYPE                        22   220
D1226V13, multiclass
                                  clus
vv                                 LEO1 MUTATED LEO1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       6            220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1227) Variable = SETX MUTATION ANALYSIS
D1227V1, survival
                sevent
clus2              0   1
  SETX MUTATED    26   6
  SETX WILD-TYPE 352  87
  SETX MUTATED SETX WILD-TYPE 
            32            439 
  SETX MUTATED SETX WILD-TYPE 
             6             87 
$`SETX MUTATED`
TCGA-A6-5665 TCGA-A6-6782 TCGA-AA-3510 TCGA-AA-3663 TCGA-AA-3815 TCGA-AA-3848 
       22.06        20.28        63.98         6.97        33.04        10.06 
TCGA-AA-3966 TCGA-AA-3977 TCGA-AA-A00J TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A02O 
        2.01        25.02        18.05         4.01        34.98         0.92 
TCGA-AD-6889 TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-CA-6717 TCGA-CA-6718 
       56.55        21.44        58.39        49.41        12.76        10.06 
TCGA-CK-5916 TCGA-CM-4744 TCGA-CM-6162 TCGA-CM-6172 TCGA-F4-6570 TCGA-F4-6854 
       21.14        20.02        12.00        11.01         6.18         0.53 
TCGA-AG-3600 TCGA-AG-3892 TCGA-AG-3902 TCGA-AG-4001 TCGA-AG-A002 TCGA-AG-A015 
        6.05        13.02        32.02        36.03        20.98        36.03 
TCGA-AG-A01Y TCGA-DC-5869 
       64.01         5.03 

$`SETX WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        19.66         7.04         3.02         1.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02        78.08         6.05        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
       26.99        19.04        19.04        10.06        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
       14.93         0.00        17.03         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 
       24.00         2.01        20.98        34.03        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       19.00        30.02        34.03        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
       14.01        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       21.37        15.52         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
        0.95        33.01        17.82         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        88.21         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 
        3.06         3.25         3.29         0.07        12.20        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4746 
        9.99        82.95         1.91       124.27        23.05        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       15.02         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 
       12.99        13.02        15.02        14.04        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 
       98.24         8.61        31.96        35.74        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6855 
       34.42        41.42        16.24        33.67        13.25        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       50.04        12.03         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3909 
       17.03        35.01        14.01         1.02        48.03        19.99 
TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       28.04        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A016 TCGA-AG-A01L 
       25.97        23.01        37.02        15.95         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       70.03        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
       78.12         7.17        15.02        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  SETX MUTATED SETX WILD-TYPE 
          0.53           0.00 
  SETX MUTATED SETX WILD-TYPE 
         64.01         148.01 
  SETX MUTATED SETX WILD-TYPE 
         20.15          20.19 
[1] "0.5 - 64.0 (20.1)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1"  
D1227V2, continuous
D1227V3, binary
                cls
clus               0   1
  SETX MUTATED    26   8
  SETX WILD-TYPE 340 111
[1] "tbl2"
                cls
clus             [,1] [,2]
  SETX MUTATED     26    8
  SETX WILD-TYPE  340  111
        clus
vv       SETX MUTATED SETX WILD-TYPE
  COLON            26            340
  RECTUM            8            111
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SETX MUTATED         5        0        5        13         4         0
  SETX WILD-TYPE      86        1       27       125         6         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SETX MUTATED           0          0          4          2        0         0
  SETX WILD-TYPE        24         11         55         40       48        18
                vv
clus             STAGE IVB
  SETX MUTATED           0
  SETX WILD-TYPE         1
D1227V4, multiclass
            clus
vv           SETX MUTATED SETX WILD-TYPE
  STAGE I               5             86
  STAGE IA              0              1
  STAGE II              5             27
  STAGE IIA            13            125
  STAGE IIB             4              6
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            4             55
  STAGE IIIC            2             40
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  SETX MUTATED     3   3  23   5
  SETX WILD-TYPE  14  89 306  45
D1227V5, multiclass
    clus
vv   SETX MUTATED SETX WILD-TYPE
  T1            3             14
  T2            3             89
  T3           23            306
  T4            5             45
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  SETX MUTATED    28   4   2
  SETX WILD-TYPE 259 109  85
D1227V6, multiclass
    clus
vv   SETX MUTATED SETX WILD-TYPE
  N0           28            259
  N1            4            109
  N2            2             85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1227V7, binary
                cls
clus               0   1
  SETX MUTATED    29   0
  SETX WILD-TYPE 346  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  SETX MUTATED     29    0
  SETX WILD-TYPE  346   65
   clus
vv  SETX MUTATED SETX WILD-TYPE
  0           29            346
  1            0             65
[1] 2 2
[1] FALSE
D1227V8, binary
                cls
clus               0   1
  SETX MUTATED    18  16
  SETX WILD-TYPE 207 248
[1] "tbl2"
                cls
clus             [,1] [,2]
  SETX MUTATED     18   16
  SETX WILD-TYPE  207  248
        clus
vv       SETX MUTATED SETX WILD-TYPE
  FEMALE           18            207
  MALE             16            248
[1] 2 2
[1] FALSE
D1227V9, binary
                cls
clus               0   1
  SETX MUTATED    25   1
  SETX WILD-TYPE 325  21
[1] "tbl2"
                cls
clus             [,1] [,2]
  SETX MUTATED     25    1
  SETX WILD-TYPE  325   21
     clus
vv    SETX MUTATED SETX WILD-TYPE
  NO            25            325
  YES            1             21
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SETX MUTATED                     21                             5
  SETX WILD-TYPE                  294                            42
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SETX MUTATED                       8                              0
  SETX WILD-TYPE                    98                             10
D1227V10, multiclass
                                clus
vv                               SETX MUTATED SETX WILD-TYPE
  COLON ADENOCARCINOMA                     21            294
  COLON MUCINOUS ADENOCARCINOMA             5             42
  RECTAL ADENOCARCINOMA                     8             98
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  SETX MUTATED    25   0   0   4
  SETX WILD-TYPE 320   4  31  21
D1227V11, multiclass
    clus
vv   SETX MUTATED SETX WILD-TYPE
  R0           25            320
  R1            0              4
  R2            0             31
  RX            4             21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1227V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SETX MUTATED                                  0     3
  SETX WILD-TYPE                                1     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  SETX MUTATED                           1    12
  SETX WILD-TYPE                        21   214
D1227V13, multiclass
                                  clus
vv                                 SETX MUTATED SETX WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       3              8
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                      12            214
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1228) Variable = ZBTB5 MUTATION ANALYSIS
D1228V1, survival
                 sevent
clus2               0   1
  ZBTB5 MUTATED     5   2
  ZBTB5 WILD-TYPE 373  91
  ZBTB5 MUTATED ZBTB5 WILD-TYPE 
              7             464 
  ZBTB5 MUTATED ZBTB5 WILD-TYPE 
              2              91 
$`ZBTB5 MUTATED`
TCGA-AA-3864 TCGA-AD-6895 TCGA-AD-6964 TCGA-CA-6717 TCGA-CK-5916 TCGA-D5-6927 
       53.00         0.72        10.88        12.76        21.14         9.44 
TCGA-EI-6507 
       19.96 

$`ZBTB5 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       15.52        56.55         0.79         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       49.08        51.32         9.99        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
       14.30         9.04        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
       32.61         0.49        20.55        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  ZBTB5 MUTATED ZBTB5 WILD-TYPE 
           0.72            0.00 
  ZBTB5 MUTATED ZBTB5 WILD-TYPE 
          53.00          148.01 
  ZBTB5 MUTATED ZBTB5 WILD-TYPE 
         12.760          20.415 
[1] "0.7 - 53.0 (12.8)"  "0.0 - 148.0 (20.4)"
[1] "hr=" "1.9"
D1228V2, continuous
D1228V3, binary
                 cls
clus                0   1
  ZBTB5 MUTATED     6   1
  ZBTB5 WILD-TYPE 360 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZBTB5 MUTATED      6    1
  ZBTB5 WILD-TYPE  360  118
        clus
vv       ZBTB5 MUTATED ZBTB5 WILD-TYPE
  COLON              6             360
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZBTB5 MUTATED         1        0        1         3         0         0
  ZBTB5 WILD-TYPE      90        1       31       135        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ZBTB5 MUTATED           0          0          0          0        0         0
  ZBTB5 WILD-TYPE        24         11         59         42       48        18
                 vv
clus              STAGE IVB
  ZBTB5 MUTATED           0
  ZBTB5 WILD-TYPE         1
D1228V4, multiclass
            clus
vv           ZBTB5 MUTATED ZBTB5 WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              3             135
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ZBTB5 MUTATED     1   0   5   1
  ZBTB5 WILD-TYPE  16  92 324  49
D1228V5, multiclass
    clus
vv   ZBTB5 MUTATED ZBTB5 WILD-TYPE
  T1             1              16
  T2             0              92
  T3             5             324
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  ZBTB5 MUTATED     5   1   1
  ZBTB5 WILD-TYPE 282 112  86
D1228V6, multiclass
    clus
vv   ZBTB5 MUTATED ZBTB5 WILD-TYPE
  N0             5             282
  N1             1             112
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1228V7, binary
                 cls
clus                0   1
  ZBTB5 MUTATED     5   0
  ZBTB5 WILD-TYPE 370  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZBTB5 MUTATED      5    0
  ZBTB5 WILD-TYPE  370   65
   clus
vv  ZBTB5 MUTATED ZBTB5 WILD-TYPE
  0             5             370
  1             0              65
[1] 2 2
[1] FALSE
D1228V8, binary
                 cls
clus                0   1
  ZBTB5 MUTATED     1   6
  ZBTB5 WILD-TYPE 224 258
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZBTB5 MUTATED      1    6
  ZBTB5 WILD-TYPE  224  258
        clus
vv       ZBTB5 MUTATED ZBTB5 WILD-TYPE
  FEMALE             1             224
  MALE               6             258
[1] 2 2
[1] FALSE
D1228V9, binary
                 cls
clus                0   1
  ZBTB5 MUTATED     6   0
  ZBTB5 WILD-TYPE 344  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZBTB5 MUTATED      6    0
  ZBTB5 WILD-TYPE  344   22
     clus
vv    ZBTB5 MUTATED ZBTB5 WILD-TYPE
  NO              6             344
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ZBTB5 MUTATED                      5                             1
  ZBTB5 WILD-TYPE                  310                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ZBTB5 MUTATED                       1                              0
  ZBTB5 WILD-TYPE                   105                             10
D1228V10, multiclass
                                clus
vv                               ZBTB5 MUTATED ZBTB5 WILD-TYPE
  COLON ADENOCARCINOMA                       5             310
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  ZBTB5 MUTATED     3   0   0   2
  ZBTB5 WILD-TYPE 342   4  31  23
D1228V11, multiclass
    clus
vv   ZBTB5 MUTATED ZBTB5 WILD-TYPE
  R0             3             342
  R1             0               4
  R2             0              31
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1228V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZBTB5 MUTATED                                  0     1
  ZBTB5 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ZBTB5 MUTATED                           0     5
  ZBTB5 WILD-TYPE                        22   221
D1228V13, multiclass
                                  clus
vv                                 ZBTB5 MUTATED ZBTB5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        5             221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1229) Variable = C16ORF45 MUTATION ANALYSIS
D1229V1, survival
                    sevent
clus2                  0   1
  C16ORF45 MUTATED     6   0
  C16ORF45 WILD-TYPE 372  93
  C16ORF45 MUTATED C16ORF45 WILD-TYPE 
                 6                465 
  C16ORF45 MUTATED C16ORF45 WILD-TYPE 
                 0                 93 
$`C16ORF45 MUTATED`
TCGA-A6-6141 TCGA-AA-3941 TCGA-AA-3982 TCGA-F4-6703 TCGA-G4-6306 TCGA-AG-A002 
        8.38        24.00        27.02        47.87        44.68        20.98 

$`C16ORF45 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 
       22.09        22.06        32.71        27.09        22.52        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
        2.01        12.99        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       53.62        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  C16ORF45 MUTATED C16ORF45 WILD-TYPE 
              8.38               0.00 
  C16ORF45 MUTATED C16ORF45 WILD-TYPE 
             47.87             148.01 
  C16ORF45 MUTATED C16ORF45 WILD-TYPE 
             25.51              20.05 
[1] "8.4 - 47.9 (25.5)"  "0.0 - 148.0 (20.1)"
[1] "hr="     "9100000"
D1229V2, continuous
D1229V3, binary
                    cls
clus                   0   1
  C16ORF45 MUTATED     5   1
  C16ORF45 WILD-TYPE 361 118
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C16ORF45 MUTATED      5    1
  C16ORF45 WILD-TYPE  361  118
        clus
vv       C16ORF45 MUTATED C16ORF45 WILD-TYPE
  COLON                 5                361
  RECTUM                1                118
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  C16ORF45 MUTATED         1        0        0         3         0         0
  C16ORF45 WILD-TYPE      90        1       32       135        10         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C16ORF45 MUTATED           0          0          1          0        0
  C16ORF45 WILD-TYPE        24         11         58         42       48
                    vv
clus                 STAGE IVA STAGE IVB
  C16ORF45 MUTATED           1         0
  C16ORF45 WILD-TYPE        17         1
D1229V4, multiclass
            clus
vv           C16ORF45 MUTATED C16ORF45 WILD-TYPE
  STAGE I                   1                 90
  STAGE IA                  0                  1
  STAGE II                  0                 32
  STAGE IIA                 3                135
  STAGE IIB                 0                 10
  STAGE IIC                 0                  1
  STAGE III                 0                 24
  STAGE IIIA                0                 11
  STAGE IIIB                1                 58
  STAGE IIIC                0                 42
  STAGE IV                  0                 48
  STAGE IVA                 1                 17
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  C16ORF45 MUTATED     0   2   3   1
  C16ORF45 WILD-TYPE  17  90 326  49
D1229V5, multiclass
    clus
vv   C16ORF45 MUTATED C16ORF45 WILD-TYPE
  T1                0                 17
  T2                2                 90
  T3                3                326
  T4                1                 49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  C16ORF45 MUTATED     4   2   0
  C16ORF45 WILD-TYPE 283 111  87
D1229V6, multiclass
    clus
vv   C16ORF45 MUTATED C16ORF45 WILD-TYPE
  N0                4                283
  N1                2                111
  N2                0                 87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1229V7, binary
                    cls
clus                   0   1
  C16ORF45 MUTATED     5   1
  C16ORF45 WILD-TYPE 370  64
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C16ORF45 MUTATED      5    1
  C16ORF45 WILD-TYPE  370   64
   clus
vv  C16ORF45 MUTATED C16ORF45 WILD-TYPE
  0                5                370
  1                1                 64
[1] 2 2
[1] FALSE
D1229V8, binary
                    cls
clus                   0   1
  C16ORF45 MUTATED     1   5
  C16ORF45 WILD-TYPE 224 259
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C16ORF45 MUTATED      1    5
  C16ORF45 WILD-TYPE  224  259
        clus
vv       C16ORF45 MUTATED C16ORF45 WILD-TYPE
  FEMALE                1                224
  MALE                  5                259
[1] 2 2
[1] FALSE
D1229V9, binary
                    cls
clus                   0   1
  C16ORF45 MUTATED     6   0
  C16ORF45 WILD-TYPE 344  22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C16ORF45 MUTATED      6    0
  C16ORF45 WILD-TYPE  344   22
     clus
vv    C16ORF45 MUTATED C16ORF45 WILD-TYPE
  NO                 6                344
  YES                0                 22
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  C16ORF45 MUTATED                      5                             0
  C16ORF45 WILD-TYPE                  310                            47
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  C16ORF45 MUTATED                       1                              0
  C16ORF45 WILD-TYPE                   105                             10
D1229V10, multiclass
                                clus
vv                               C16ORF45 MUTATED C16ORF45 WILD-TYPE
  COLON ADENOCARCINOMA                          5                310
  COLON MUCINOUS ADENOCARCINOMA                 0                 47
  RECTAL ADENOCARCINOMA                         1                105
  RECTAL MUCINOUS ADENOCARCINOMA                0                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  C16ORF45 MUTATED     4   0   0   0
  C16ORF45 WILD-TYPE 341   4  31  25
D1229V11, multiclass
    clus
vv   C16ORF45 MUTATED C16ORF45 WILD-TYPE
  R0                4                341
  R1                0                  4
  R2                0                 31
  RX                0                 25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1229V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C16ORF45 MUTATED                                  0     0
  C16ORF45 WILD-TYPE                                1    11
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  C16ORF45 MUTATED                           1     2
  C16ORF45 WILD-TYPE                        21   224
D1229V13, multiclass
                                  clus
vv                                 C16ORF45 MUTATED C16ORF45 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 11
  BLACK OR AFRICAN AMERICAN                       1                 21
  WHITE                                           2                224
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1230) Variable = HCLS1 MUTATION ANALYSIS
D1230V1, survival
                 sevent
clus2               0   1
  HCLS1 MUTATED    14   2
  HCLS1 WILD-TYPE 364  91
  HCLS1 MUTATED HCLS1 WILD-TYPE 
             16             455 
  HCLS1 MUTATED HCLS1 WILD-TYPE 
              2              91 
$`HCLS1 MUTATED`
TCGA-AA-3511 TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3548 TCGA-AA-3663 TCGA-AA-3977 
        6.97        13.02         1.02        33.99         6.97        25.02 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A010 TCGA-AZ-4315 TCGA-AZ-6601 TCGA-CA-6717 
       18.05        18.05        34.98        58.39       100.01        12.76 
TCGA-CM-5861 TCGA-D5-6930 TCGA-G4-6588 TCGA-AG-A002 
       15.02         1.51        26.17        20.98 

$`HCLS1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3519 
        1.02        35.01        63.98         1.02        38.99         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
        0.99        14.01        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       61.02        78.08         6.05        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00L 
       13.94        38.04        19.00        30.02        34.03        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 
       62.79        88.21        49.41         6.77        12.10        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07        12.20        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       22.98        30.08        32.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
        9.44        11.64         4.80        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  HCLS1 MUTATED HCLS1 WILD-TYPE 
           1.02            0.00 
  HCLS1 MUTATED HCLS1 WILD-TYPE 
         100.01          148.01 
  HCLS1 MUTATED HCLS1 WILD-TYPE 
          18.05           20.28 
[1] "1.0 - 100.0 (18.1)" "0.0 - 148.0 (20.3)"
[1] "hr=" "1.5"
D1230V2, continuous
D1230V3, binary
                 cls
clus                0   1
  HCLS1 MUTATED    15   1
  HCLS1 WILD-TYPE 351 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HCLS1 MUTATED     15    1
  HCLS1 WILD-TYPE  351  118
        clus
vv       HCLS1 MUTATED HCLS1 WILD-TYPE
  COLON             15             351
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  HCLS1 MUTATED         1        0        3         7         1         0
  HCLS1 WILD-TYPE      90        1       29       131         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  HCLS1 MUTATED           1          0          1          1        0         0
  HCLS1 WILD-TYPE        23         11         58         41       48        18
                 vv
clus              STAGE IVB
  HCLS1 MUTATED           0
  HCLS1 WILD-TYPE         1
D1230V4, multiclass
            clus
vv           HCLS1 MUTATED HCLS1 WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               3              29
  STAGE IIA              7             131
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             1              41
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  HCLS1 MUTATED     0   2  11   3
  HCLS1 WILD-TYPE  17  90 318  47
D1230V5, multiclass
    clus
vv   HCLS1 MUTATED HCLS1 WILD-TYPE
  T1             0              17
  T2             2              90
  T3            11             318
  T4             3              47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  HCLS1 MUTATED    13   1   2
  HCLS1 WILD-TYPE 274 112  85
D1230V6, multiclass
    clus
vv   HCLS1 MUTATED HCLS1 WILD-TYPE
  N0            13             274
  N1             1             112
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1230V7, binary
                 cls
clus                0   1
  HCLS1 MUTATED    15   0
  HCLS1 WILD-TYPE 360  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HCLS1 MUTATED     15    0
  HCLS1 WILD-TYPE  360   65
   clus
vv  HCLS1 MUTATED HCLS1 WILD-TYPE
  0            15             360
  1             0              65
[1] 2 2
[1] FALSE
D1230V8, binary
                 cls
clus                0   1
  HCLS1 MUTATED     6  10
  HCLS1 WILD-TYPE 219 254
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HCLS1 MUTATED      6   10
  HCLS1 WILD-TYPE  219  254
        clus
vv       HCLS1 MUTATED HCLS1 WILD-TYPE
  FEMALE             6             219
  MALE              10             254
[1] 2 2
[1] FALSE
D1230V9, binary
                 cls
clus                0   1
  HCLS1 MUTATED    13   0
  HCLS1 WILD-TYPE 337  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HCLS1 MUTATED     13    0
  HCLS1 WILD-TYPE  337   22
     clus
vv    HCLS1 MUTATED HCLS1 WILD-TYPE
  NO             13             337
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  HCLS1 MUTATED                     11                             4
  HCLS1 WILD-TYPE                  304                            43
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  HCLS1 MUTATED                       1                              0
  HCLS1 WILD-TYPE                   105                             10
D1230V10, multiclass
                                clus
vv                               HCLS1 MUTATED HCLS1 WILD-TYPE
  COLON ADENOCARCINOMA                      11             304
  COLON MUCINOUS ADENOCARCINOMA              4              43
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  HCLS1 MUTATED    12   0   0   1
  HCLS1 WILD-TYPE 333   4  31  24
D1230V11, multiclass
    clus
vv   HCLS1 MUTATED HCLS1 WILD-TYPE
  R0            12             333
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1230V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HCLS1 MUTATED                                  0     1
  HCLS1 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  HCLS1 MUTATED                           0     5
  HCLS1 WILD-TYPE                        22   221
D1230V13, multiclass
                                  clus
vv                                 HCLS1 MUTATED HCLS1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        5             221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1231) Variable = DNAJB9 MUTATION ANALYSIS
D1231V1, survival
                  sevent
clus2                0   1
  DNAJB9 MUTATED     5   1
  DNAJB9 WILD-TYPE 373  92
  DNAJB9 MUTATED DNAJB9 WILD-TYPE 
               6              465 
  DNAJB9 MUTATED DNAJB9 WILD-TYPE 
               1               92 
$`DNAJB9 MUTATED`
TCGA-A6-6781 TCGA-AA-A010 TCGA-CA-6717 TCGA-CA-6718 TCGA-DM-A1HB TCGA-AG-A002 
       19.66        34.98        12.76        10.06       135.65        20.98 

$`DNAJB9 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       12.20        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 
      140.38         7.50        44.32       131.51       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  DNAJB9 MUTATED DNAJB9 WILD-TYPE 
           10.06             0.00 
  DNAJB9 MUTATED DNAJB9 WILD-TYPE 
          135.65           148.01 
  DNAJB9 MUTATED DNAJB9 WILD-TYPE 
           20.32            20.19 
[1] "10.1 - 135.7 (20.3)" "0.0 - 148.0 (20.2)" 
[1] "hr=" "1.5"
D1231V2, continuous
D1231V3, binary
                  cls
clus                 0   1
  DNAJB9 MUTATED     5   1
  DNAJB9 WILD-TYPE 361 118
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DNAJB9 MUTATED      5    1
  DNAJB9 WILD-TYPE  361  118
        clus
vv       DNAJB9 MUTATED DNAJB9 WILD-TYPE
  COLON               5              361
  RECTUM              1              118
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DNAJB9 MUTATED         1        0        0         2         1         0
  DNAJB9 WILD-TYPE      90        1       32       136         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DNAJB9 MUTATED           0          0          1          1        0
  DNAJB9 WILD-TYPE        24         11         58         41       48
                  vv
clus               STAGE IVA STAGE IVB
  DNAJB9 MUTATED           0         0
  DNAJB9 WILD-TYPE        18         1
D1231V4, multiclass
            clus
vv           DNAJB9 MUTATED DNAJB9 WILD-TYPE
  STAGE I                 1               90
  STAGE IA                0                1
  STAGE II                0               32
  STAGE IIA               2              136
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              1               58
  STAGE IIIC              1               41
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  DNAJB9 MUTATED     0   1   3   2
  DNAJB9 WILD-TYPE  17  91 326  48
D1231V5, multiclass
    clus
vv   DNAJB9 MUTATED DNAJB9 WILD-TYPE
  T1              0               17
  T2              1               91
  T3              3              326
  T4              2               48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  DNAJB9 MUTATED     4   2   0
  DNAJB9 WILD-TYPE 283 111  87
D1231V6, multiclass
    clus
vv   DNAJB9 MUTATED DNAJB9 WILD-TYPE
  N0              4              283
  N1              2              111
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1231V7, binary
                  cls
clus                 0   1
  DNAJB9 MUTATED     5   0
  DNAJB9 WILD-TYPE 370  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DNAJB9 MUTATED      5    0
  DNAJB9 WILD-TYPE  370   65
   clus
vv  DNAJB9 MUTATED DNAJB9 WILD-TYPE
  0              5              370
  1              0               65
[1] 2 2
[1] FALSE
D1231V8, binary
                  cls
clus                 0   1
  DNAJB9 MUTATED     1   5
  DNAJB9 WILD-TYPE 224 259
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DNAJB9 MUTATED      1    5
  DNAJB9 WILD-TYPE  224  259
        clus
vv       DNAJB9 MUTATED DNAJB9 WILD-TYPE
  FEMALE              1              224
  MALE                5              259
[1] 2 2
[1] FALSE
D1231V9, binary
                  cls
clus                 0   1
  DNAJB9 MUTATED     5   0
  DNAJB9 WILD-TYPE 345  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DNAJB9 MUTATED      5    0
  DNAJB9 WILD-TYPE  345   22
     clus
vv    DNAJB9 MUTATED DNAJB9 WILD-TYPE
  NO               5              345
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  DNAJB9 MUTATED                      2                             2
  DNAJB9 WILD-TYPE                  313                            45
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  DNAJB9 MUTATED                       1                              0
  DNAJB9 WILD-TYPE                   105                             10
D1231V10, multiclass
                                clus
vv                               DNAJB9 MUTATED DNAJB9 WILD-TYPE
  COLON ADENOCARCINOMA                        2              313
  COLON MUCINOUS ADENOCARCINOMA               2               45
  RECTAL ADENOCARCINOMA                       1              105
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  DNAJB9 MUTATED     3   0   0   2
  DNAJB9 WILD-TYPE 342   4  31  23
D1231V11, multiclass
    clus
vv   DNAJB9 MUTATED DNAJB9 WILD-TYPE
  R0              3              342
  R1              0                4
  R2              0               31
  RX              2               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1231V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DNAJB9 MUTATED                                  0     2
  DNAJB9 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  DNAJB9 MUTATED                           0     2
  DNAJB9 WILD-TYPE                        22   224
D1231V13, multiclass
                                  clus
vv                                 DNAJB9 MUTATED DNAJB9 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                9
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         2              224
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1232) Variable = ICA1 MUTATION ANALYSIS
D1232V1, survival
                sevent
clus2              0   1
  ICA1 MUTATED     7   0
  ICA1 WILD-TYPE 371  93
  ICA1 MUTATED ICA1 WILD-TYPE 
             7            464 
  ICA1 MUTATED ICA1 WILD-TYPE 
             0             93 
$`ICA1 MUTATED`
TCGA-AA-3949 TCGA-AA-3950 TCGA-AD-6895 TCGA-CA-6717 TCGA-CM-5860 TCGA-D5-5540 
       26.01        24.00         0.72        12.76        32.02        56.09 
TCGA-DC-6155 
       13.97 

$`ICA1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3952 
       31.00         2.01        12.99        24.00        33.01         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
       56.55         0.79         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-5862 
       29.06        22.03        22.98        30.08        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       19.59        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6157 
        4.73        78.12         7.17        15.02         5.03        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  ICA1 MUTATED ICA1 WILD-TYPE 
          0.72           0.00 
  ICA1 MUTATED ICA1 WILD-TYPE 
         56.09         148.01 
  ICA1 MUTATED ICA1 WILD-TYPE 
        24.000         20.155 
[1] "0.7 - 56.1 (24.0)"  "0.0 - 148.0 (20.2)"
[1] "hr="     "9100000"
D1232V2, continuous
D1232V3, binary
                cls
clus               0   1
  ICA1 MUTATED     6   1
  ICA1 WILD-TYPE 360 118
[1] "tbl2"
                cls
clus             [,1] [,2]
  ICA1 MUTATED      6    1
  ICA1 WILD-TYPE  360  118
        clus
vv       ICA1 MUTATED ICA1 WILD-TYPE
  COLON             6            360
  RECTUM            1            118
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ICA1 MUTATED         0        0        0         4         0         0
  ICA1 WILD-TYPE      91        1       32       134        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ICA1 MUTATED           0          1          1          0        0         0
  ICA1 WILD-TYPE        24         10         58         42       48        18
                vv
clus             STAGE IVB
  ICA1 MUTATED           0
  ICA1 WILD-TYPE         1
D1232V4, multiclass
            clus
vv           ICA1 MUTATED ICA1 WILD-TYPE
  STAGE I               0             91
  STAGE IA              0              1
  STAGE II              0             32
  STAGE IIA             4            134
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            1             10
  STAGE IIIB            1             58
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  ICA1 MUTATED     0   1   6   0
  ICA1 WILD-TYPE  17  91 323  50
D1232V5, multiclass
    clus
vv   ICA1 MUTATED ICA1 WILD-TYPE
  T1            0             17
  T2            1             91
  T3            6            323
  T4            0             50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  ICA1 MUTATED     4   3   0
  ICA1 WILD-TYPE 283 110  87
D1232V6, multiclass
    clus
vv   ICA1 MUTATED ICA1 WILD-TYPE
  N0            4            283
  N1            3            110
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1232V7, binary
                cls
clus               0   1
  ICA1 MUTATED     6   0
  ICA1 WILD-TYPE 369  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  ICA1 MUTATED      6    0
  ICA1 WILD-TYPE  369   65
   clus
vv  ICA1 MUTATED ICA1 WILD-TYPE
  0            6            369
  1            0             65
[1] 2 2
[1] FALSE
D1232V8, binary
                cls
clus               0   1
  ICA1 MUTATED     3   4
  ICA1 WILD-TYPE 222 260
[1] "tbl2"
                cls
clus             [,1] [,2]
  ICA1 MUTATED      3    4
  ICA1 WILD-TYPE  222  260
        clus
vv       ICA1 MUTATED ICA1 WILD-TYPE
  FEMALE            3            222
  MALE              4            260
[1] 2 2
[1] FALSE
D1232V9, binary
                cls
clus               0   1
  ICA1 MUTATED     6   0
  ICA1 WILD-TYPE 344  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  ICA1 MUTATED      6    0
  ICA1 WILD-TYPE  344   22
     clus
vv    ICA1 MUTATED ICA1 WILD-TYPE
  NO             6            344
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ICA1 MUTATED                      3                             3
  ICA1 WILD-TYPE                  312                            44
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ICA1 MUTATED                       1                              0
  ICA1 WILD-TYPE                   105                             10
D1232V10, multiclass
                                clus
vv                               ICA1 MUTATED ICA1 WILD-TYPE
  COLON ADENOCARCINOMA                      3            312
  COLON MUCINOUS ADENOCARCINOMA             3             44
  RECTAL ADENOCARCINOMA                     1            105
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  ICA1 MUTATED     5   0   0   1
  ICA1 WILD-TYPE 340   4  31  24
D1232V11, multiclass
    clus
vv   ICA1 MUTATED ICA1 WILD-TYPE
  R0            5            340
  R1            0              4
  R2            0             31
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1232V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ICA1 MUTATED                                  0     1
  ICA1 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  ICA1 MUTATED                           0     4
  ICA1 WILD-TYPE                        22   222
D1232V13, multiclass
                                  clus
vv                                 ICA1 MUTATED ICA1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       4            222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1233) Variable = SMARCB1 MUTATION ANALYSIS
D1233V1, survival
                   sevent
clus2                 0   1
  SMARCB1 MUTATED    18   5
  SMARCB1 WILD-TYPE 360  88
  SMARCB1 MUTATED SMARCB1 WILD-TYPE 
               23               448 
  SMARCB1 MUTATED SMARCB1 WILD-TYPE 
                5                88 
$`SMARCB1 MUTATED`
TCGA-AA-3542 TCGA-AA-3663 TCGA-AA-3713 TCGA-AA-A010 TCGA-AA-A02W TCGA-AU-3779 
       12.99         6.97        19.04        34.98        41.00        14.50 
TCGA-AZ-4315 TCGA-AZ-6599 TCGA-CM-4746 TCGA-CM-5344 TCGA-CM-6172 TCGA-CM-6674 
       58.39         6.77        37.02        22.03        11.01        12.95 
TCGA-D5-6537 TCGA-D5-6540 TCGA-D5-6928 TCGA-DM-A1D7 TCGA-G4-6293 TCGA-G4-6303 
        4.80        16.14        11.64        13.32       133.18        65.85 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6588 TCGA-G4-6626 TCGA-EF-5830 
       36.00        22.09        26.17        46.75         0.49 

$`SMARCB1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       29.00        26.01         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
        5.03        14.01         0.92        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-6004 
        5.79        22.42        27.42        10.88         0.20        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
       16.31         0.95        33.01        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4747 
       82.95         1.91       124.27        23.05        20.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       13.02        29.06        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       13.02        15.02        14.04        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 
       15.12        17.85        17.13        12.49        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D8 
       24.43        38.20       130.65        92.75        49.91        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6304 TCGA-G4-6306 
        0.53        47.41        35.31        74.56        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6323 TCGA-G4-6586 
       55.04        85.48        63.62        61.91        13.78        35.80 
TCGA-G4-6625 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       91.79        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       24.13        51.48        32.61        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  SMARCB1 MUTATED SMARCB1 WILD-TYPE 
             0.49              0.00 
  SMARCB1 MUTATED SMARCB1 WILD-TYPE 
           133.18            148.01 
  SMARCB1 MUTATED SMARCB1 WILD-TYPE 
           19.040            20.235 
[1] "0.5 - 133.2 (19.0)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1"  
D1233V2, continuous
D1233V3, binary
                   cls
clus                  0   1
  SMARCB1 MUTATED    23   1
  SMARCB1 WILD-TYPE 343 118
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SMARCB1 MUTATED     23    1
  SMARCB1 WILD-TYPE  343  118
        clus
vv       SMARCB1 MUTATED SMARCB1 WILD-TYPE
  COLON               23               343
  RECTUM               1               118
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SMARCB1 MUTATED         5        0        1         7         2         0
  SMARCB1 WILD-TYPE      86        1       31       131         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SMARCB1 MUTATED           2          0          3          2        2
  SMARCB1 WILD-TYPE        22         11         56         40       46
                   vv
clus                STAGE IVA STAGE IVB
  SMARCB1 MUTATED           0         0
  SMARCB1 WILD-TYPE        18         1
D1233V4, multiclass
            clus
vv           SMARCB1 MUTATED SMARCB1 WILD-TYPE
  STAGE I                  5                86
  STAGE IA                 0                 1
  STAGE II                 1                31
  STAGE IIA                7               131
  STAGE IIB                2                 8
  STAGE IIC                0                 1
  STAGE III                2                22
  STAGE IIIA               0                11
  STAGE IIIB               3                56
  STAGE IIIC               2                40
  STAGE IV                 2                46
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  SMARCB1 MUTATED     0   6  16   2
  SMARCB1 WILD-TYPE  17  86 313  48
D1233V5, multiclass
    clus
vv   SMARCB1 MUTATED SMARCB1 WILD-TYPE
  T1               0                17
  T2               6                86
  T3              16               313
  T4               2                48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  SMARCB1 MUTATED    16   6   2
  SMARCB1 WILD-TYPE 271 107  85
D1233V6, multiclass
    clus
vv   SMARCB1 MUTATED SMARCB1 WILD-TYPE
  N0              16               271
  N1               6               107
  N2               2                85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1233V7, binary
                   cls
clus                  0   1
  SMARCB1 MUTATED    17   2
  SMARCB1 WILD-TYPE 358  63
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SMARCB1 MUTATED     17    2
  SMARCB1 WILD-TYPE  358   63
   clus
vv  SMARCB1 MUTATED SMARCB1 WILD-TYPE
  0              17               358
  1               2                63
[1] 2 2
[1] FALSE
D1233V8, binary
                   cls
clus                  0   1
  SMARCB1 MUTATED    10  14
  SMARCB1 WILD-TYPE 215 250
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SMARCB1 MUTATED     10   14
  SMARCB1 WILD-TYPE  215  250
        clus
vv       SMARCB1 MUTATED SMARCB1 WILD-TYPE
  FEMALE              10               215
  MALE                14               250
[1] 2 2
[1] FALSE
D1233V9, binary
                   cls
clus                  0   1
  SMARCB1 MUTATED    20   1
  SMARCB1 WILD-TYPE 330  21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SMARCB1 MUTATED     20    1
  SMARCB1 WILD-TYPE  330   21
     clus
vv    SMARCB1 MUTATED SMARCB1 WILD-TYPE
  NO               20               330
  YES               1                21
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SMARCB1 MUTATED                     20                             2
  SMARCB1 WILD-TYPE                  295                            45
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SMARCB1 MUTATED                       1                              0
  SMARCB1 WILD-TYPE                   105                             10
D1233V10, multiclass
                                clus
vv                               SMARCB1 MUTATED SMARCB1 WILD-TYPE
  COLON ADENOCARCINOMA                        20               295
  COLON MUCINOUS ADENOCARCINOMA                2                45
  RECTAL ADENOCARCINOMA                        1               105
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  SMARCB1 MUTATED    20   0   1   1
  SMARCB1 WILD-TYPE 325   4  30  24
D1233V11, multiclass
    clus
vv   SMARCB1 MUTATED SMARCB1 WILD-TYPE
  R0              20               325
  R1               0                 4
  R2               1                30
  RX               1                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1233V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SMARCB1 MUTATED                                  0     0
  SMARCB1 WILD-TYPE                                1    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  SMARCB1 MUTATED                           1    18
  SMARCB1 WILD-TYPE                        21   208
D1233V13, multiclass
                                  clus
vv                                 SMARCB1 MUTATED SMARCB1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                      1                21
  WHITE                                         18               208
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1234) Variable = MTOR MUTATION ANALYSIS
D1234V1, survival
                sevent
clus2              0   1
  MTOR MUTATED    30   7
  MTOR WILD-TYPE 348  86
  MTOR MUTATED MTOR WILD-TYPE 
            37            434 
  MTOR MUTATED MTOR WILD-TYPE 
             7             86 
$`MTOR MUTATED`
TCGA-A6-4105 TCGA-A6-5666 TCGA-A6-6141 TCGA-A6-6781 TCGA-AA-3555 TCGA-AA-3663 
       14.53        32.71         8.38        19.66        29.95         6.97 
TCGA-AA-3666 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3821 TCGA-AA-3854 TCGA-AA-3867 
        2.01        26.99        19.04         1.02        36.03        24.03 
TCGA-AA-3877 TCGA-AA-3949 TCGA-AA-3956 TCGA-AA-3980 TCGA-AA-A00K TCGA-AA-A010 
       31.00        26.01        34.03        27.02        18.05        34.98 
TCGA-AU-6004 TCGA-AY-5543 TCGA-AY-6197 TCGA-AZ-6598 TCGA-AZ-6601 TCGA-CA-6716 
       27.09        33.01        21.44        49.41       100.01        12.20 
TCGA-CM-4752 TCGA-DM-A1D4 TCGA-DM-A282 TCGA-DM-A28K TCGA-F4-6570 TCGA-F4-6806 
       13.02        92.75       139.17        98.24         6.18        41.42 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6586 TCGA-AG-3892 TCGA-AG-A002 TCGA-DT-5265 
       55.04        85.48        35.80        13.02        20.98         5.29 
TCGA-EF-5830 
        0.49 

$`MTOR WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 
       16.57        34.65        33.34        32.75        36.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       22.06        27.09        22.52        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 
       21.76        24.69        24.39        23.87        20.12        20.28 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
        7.04         3.02         1.02        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
       78.08         6.05        54.02        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 
       36.00         5.03        85.05        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
       33.04         0.99        25.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
       33.07         0.00        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       30.05        53.00        17.03        27.02        29.98        18.05 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-3952 
        2.01        12.99        24.00        33.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       20.98         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        25.02        24.00        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 
       22.42        27.42        10.88         0.20        14.50        16.31 
TCGA-AY-4071 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
        0.95        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 
       22.36        62.79        88.21         6.77        12.10        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       20.02        37.02        25.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D6 
       10.26       119.70        24.43        38.20       130.65        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      135.65         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 
      117.07         8.61        31.96        35.74        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       34.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 
       63.62        61.91        36.00        22.09        13.78        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 
       19.99         1.02        17.95        36.95        17.03        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.03       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
       32.61        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  MTOR MUTATED MTOR WILD-TYPE 
          0.49           0.00 
  MTOR MUTATED MTOR WILD-TYPE 
        139.17         148.01 
  MTOR MUTATED MTOR WILD-TYPE 
        26.990         20.005 
[1] "0.5 - 139.2 (27.0)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.3"
D1234V2, continuous
D1234V3, binary
                cls
clus               0   1
  MTOR MUTATED    34   4
  MTOR WILD-TYPE 332 115
[1] "tbl2"
                cls
clus             [,1] [,2]
  MTOR MUTATED     34    4
  MTOR WILD-TYPE  332  115
        clus
vv       MTOR MUTATED MTOR WILD-TYPE
  COLON            34            332
  RECTUM            4            115
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MTOR MUTATED         8        0        5        15         2         1
  MTOR WILD-TYPE      83        1       27       123         8         0
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MTOR MUTATED           1          0          3          1        1         1
  MTOR WILD-TYPE        23         11         56         41       47        17
                vv
clus             STAGE IVB
  MTOR MUTATED           0
  MTOR WILD-TYPE         1
D1234V4, multiclass
            clus
vv           MTOR MUTATED MTOR WILD-TYPE
  STAGE I               8             83
  STAGE IA              0              1
  STAGE II              5             27
  STAGE IIA            15            123
  STAGE IIB             2              8
  STAGE IIC             1              0
  STAGE III             1             23
  STAGE IIIA            0             11
  STAGE IIIB            3             56
  STAGE IIIC            1             41
  STAGE IV              1             47
  STAGE IVA             1             17
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  MTOR MUTATED     2   6  26   4
  MTOR WILD-TYPE  15  86 303  46
D1234V5, multiclass
    clus
vv   MTOR MUTATED MTOR WILD-TYPE
  T1            2             15
  T2            6             86
  T3           26            303
  T4            4             46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  MTOR MUTATED    31   6   1
  MTOR WILD-TYPE 256 107  86
D1234V6, multiclass
    clus
vv   MTOR MUTATED MTOR WILD-TYPE
  N0           31            256
  N1            6            107
  N2            1             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1234V7, binary
                cls
clus               0   1
  MTOR MUTATED    33   2
  MTOR WILD-TYPE 342  63
[1] "tbl2"
                cls
clus             [,1] [,2]
  MTOR MUTATED     33    2
  MTOR WILD-TYPE  342   63
   clus
vv  MTOR MUTATED MTOR WILD-TYPE
  0           33            342
  1            2             63
[1] 2 2
[1] FALSE
D1234V8, binary
                cls
clus               0   1
  MTOR MUTATED    19  19
  MTOR WILD-TYPE 206 245
[1] "tbl2"
                cls
clus             [,1] [,2]
  MTOR MUTATED     19   19
  MTOR WILD-TYPE  206  245
        clus
vv       MTOR MUTATED MTOR WILD-TYPE
  FEMALE           19            206
  MALE             19            245
[1] 2 2
[1] FALSE
D1234V9, binary
                cls
clus               0   1
  MTOR MUTATED    30   0
  MTOR WILD-TYPE 320  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  MTOR MUTATED     30    0
  MTOR WILD-TYPE  320   22
     clus
vv    MTOR MUTATED MTOR WILD-TYPE
  NO            30            320
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MTOR MUTATED                     27                             7
  MTOR WILD-TYPE                  288                            40
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MTOR MUTATED                       3                              1
  MTOR WILD-TYPE                   103                              9
D1234V10, multiclass
                                clus
vv                               MTOR MUTATED MTOR WILD-TYPE
  COLON ADENOCARCINOMA                     27            288
  COLON MUCINOUS ADENOCARCINOMA             7             40
  RECTAL ADENOCARCINOMA                     3            103
  RECTAL MUCINOUS ADENOCARCINOMA            1              9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  MTOR MUTATED    26   0   1   2
  MTOR WILD-TYPE 319   4  30  23
D1234V11, multiclass
    clus
vv   MTOR MUTATED MTOR WILD-TYPE
  R0           26            319
  R1            0              4
  R2            1             30
  RX            2             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1234V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MTOR MUTATED                                  0     2
  MTOR WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  MTOR MUTATED                           4    15
  MTOR WILD-TYPE                        18   211
D1234V13, multiclass
                                  clus
vv                                 MTOR MUTATED MTOR WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              9
  BLACK OR AFRICAN AMERICAN                   4             18
  WHITE                                      15            211
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1235) Variable = RNF219 MUTATION ANALYSIS
D1235V1, survival
                  sevent
clus2                0   1
  RNF219 MUTATED    16   2
  RNF219 WILD-TYPE 362  91
  RNF219 MUTATED RNF219 WILD-TYPE 
              18              453 
  RNF219 MUTATED RNF219 WILD-TYPE 
               2               91 
$`RNF219 MUTATED`
TCGA-A6-5660 TCGA-AA-A01Q TCGA-AU-3779 TCGA-AZ-6598 TCGA-CA-6717 TCGA-CA-6718 
       29.19         1.02        14.50        49.41        12.76        10.06 
TCGA-CM-5861 TCGA-D5-5539 TCGA-D5-6540 TCGA-D5-6923 TCGA-D5-6928 TCGA-G4-6309 
       15.02        19.59        16.14        12.43        11.64        85.48 
TCGA-G4-6323 TCGA-AG-3599 TCGA-AG-3612 TCGA-AG-3892 TCGA-AG-A002 TCGA-CI-6624 
       13.78        12.03        19.99        13.02        20.98         4.73 

$`RNF219 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01R TCGA-AA-A01S 
       12.00        31.00        31.00        38.07        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       10.88         0.20        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        88.21         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 
        3.06         3.25         3.29         0.07        12.20        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       22.98        30.08        32.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-5541 
       10.06        12.03        45.40        12.26        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
        4.80        17.13        12.49        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6930 
        4.41        14.30         9.04         9.44         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       44.68        55.04        63.62        61.91        36.00        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3726 
        6.05         0.99        15.95        19.99        13.94         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 
       19.99         1.02        17.95        36.95        17.03        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        6.97        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  RNF219 MUTATED RNF219 WILD-TYPE 
            1.02             0.00 
  RNF219 MUTATED RNF219 WILD-TYPE 
           85.48           148.01 
  RNF219 MUTATED RNF219 WILD-TYPE 
           14.14            20.98 
[1] "1.0 - 85.5 (14.1)"  "0.0 - 148.0 (21.0)"
[1] "hr=" "1.4"
D1235V2, continuous
D1235V3, binary
                  cls
clus                 0   1
  RNF219 MUTATED    14   5
  RNF219 WILD-TYPE 352 114
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF219 MUTATED     14    5
  RNF219 WILD-TYPE  352  114
        clus
vv       RNF219 MUTATED RNF219 WILD-TYPE
  COLON              14              352
  RECTUM              5              114
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RNF219 MUTATED         6        1        2         5         0         0
  RNF219 WILD-TYPE      85        0       30       133        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RNF219 MUTATED           0          1          2          2        0
  RNF219 WILD-TYPE        24         10         57         40       48
                  vv
clus               STAGE IVA STAGE IVB
  RNF219 MUTATED           0         0
  RNF219 WILD-TYPE        18         1
D1235V4, multiclass
            clus
vv           RNF219 MUTATED RNF219 WILD-TYPE
  STAGE I                 6               85
  STAGE IA                1                0
  STAGE II                2               30
  STAGE IIA               5              133
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              1               10
  STAGE IIIB              2               57
  STAGE IIIC              2               40
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  RNF219 MUTATED     1   5  12   0
  RNF219 WILD-TYPE  16  87 317  50
D1235V5, multiclass
    clus
vv   RNF219 MUTATED RNF219 WILD-TYPE
  T1              1               16
  T2              5               87
  T3             12              317
  T4              0               50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  RNF219 MUTATED    14   3   2
  RNF219 WILD-TYPE 273 110  85
D1235V6, multiclass
    clus
vv   RNF219 MUTATED RNF219 WILD-TYPE
  N0             14              273
  N1              3              110
  N2              2               85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1235V7, binary
                  cls
clus                 0   1
  RNF219 MUTATED    16   0
  RNF219 WILD-TYPE 359  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF219 MUTATED     16    0
  RNF219 WILD-TYPE  359   65
   clus
vv  RNF219 MUTATED RNF219 WILD-TYPE
  0             16              359
  1              0               65
[1] 2 2
[1] FALSE
D1235V8, binary
                  cls
clus                 0   1
  RNF219 MUTATED     8  11
  RNF219 WILD-TYPE 217 253
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF219 MUTATED      8   11
  RNF219 WILD-TYPE  217  253
        clus
vv       RNF219 MUTATED RNF219 WILD-TYPE
  FEMALE              8              217
  MALE               11              253
[1] 2 2
[1] FALSE
D1235V9, binary
                  cls
clus                 0   1
  RNF219 MUTATED    16   0
  RNF219 WILD-TYPE 334  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF219 MUTATED     16    0
  RNF219 WILD-TYPE  334   22
     clus
vv    RNF219 MUTATED RNF219 WILD-TYPE
  NO              16              334
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  RNF219 MUTATED                      9                             5
  RNF219 WILD-TYPE                  306                            42
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  RNF219 MUTATED                       4                              0
  RNF219 WILD-TYPE                   102                             10
D1235V10, multiclass
                                clus
vv                               RNF219 MUTATED RNF219 WILD-TYPE
  COLON ADENOCARCINOMA                        9              306
  COLON MUCINOUS ADENOCARCINOMA               5               42
  RECTAL ADENOCARCINOMA                       4              102
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  RNF219 MUTATED    14   0   0   2
  RNF219 WILD-TYPE 331   4  31  23
D1235V11, multiclass
    clus
vv   RNF219 MUTATED RNF219 WILD-TYPE
  R0             14              331
  R1              0                4
  R2              0               31
  RX              2               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1235V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RNF219 MUTATED                                  0     2
  RNF219 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  RNF219 MUTATED                           3     9
  RNF219 WILD-TYPE                        19   217
D1235V13, multiclass
                                  clus
vv                                 RNF219 MUTATED RNF219 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                9
  BLACK OR AFRICAN AMERICAN                     3               19
  WHITE                                         9              217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1236) Variable = KIAA0528 MUTATION ANALYSIS
D1236V1, survival
                    sevent
clus2                  0   1
  KIAA0528 MUTATED    12   4
  KIAA0528 WILD-TYPE 366  89
  KIAA0528 MUTATED KIAA0528 WILD-TYPE 
                16                455 
  KIAA0528 MUTATED KIAA0528 WILD-TYPE 
                 4                 89 
$`KIAA0528 MUTATED`
TCGA-AA-3510 TCGA-AA-3543 TCGA-AA-3663 TCGA-AA-3956 TCGA-AA-3977 TCGA-AA-A010 
       63.98         0.99         6.97        34.03        25.02        34.98 
TCGA-AA-A02K TCGA-AD-6964 TCGA-AU-6004 TCGA-AZ-4315 TCGA-AZ-6601 TCGA-CM-5861 
       14.01        10.88        27.09        58.39       100.01        15.02 
TCGA-CM-6165 TCGA-CM-6166 TCGA-AG-A002 TCGA-DY-A1H8 
       16.04        21.99        20.98        32.61 

$`KIAA0528 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       26.01        12.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O 
       39.06        51.98        39.98         2.01         5.03         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       27.42         0.20        14.50        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 
       62.79        88.21        49.41         6.77        12.10        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 
       22.03        22.98        30.08        32.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       57.24        24.13        51.48         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  KIAA0528 MUTATED KIAA0528 WILD-TYPE 
              0.99               0.00 
  KIAA0528 MUTATED KIAA0528 WILD-TYPE 
            100.01             148.01 
  KIAA0528 MUTATED KIAA0528 WILD-TYPE 
            23.505             20.050 
[1] "1.0 - 100.0 (23.5)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.1"
D1236V2, continuous
D1236V3, binary
                    cls
clus                   0   1
  KIAA0528 MUTATED    15   2
  KIAA0528 WILD-TYPE 351 117
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0528 MUTATED     15    2
  KIAA0528 WILD-TYPE  351  117
        clus
vv       KIAA0528 MUTATED KIAA0528 WILD-TYPE
  COLON                15                351
  RECTUM                2                117
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KIAA0528 MUTATED         4        0        3         4         2         0
  KIAA0528 WILD-TYPE      87        1       29       134         8         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIAA0528 MUTATED           0          1          0          0        1
  KIAA0528 WILD-TYPE        24         10         59         42       47
                    vv
clus                 STAGE IVA STAGE IVB
  KIAA0528 MUTATED           0         0
  KIAA0528 WILD-TYPE        18         1
D1236V4, multiclass
            clus
vv           KIAA0528 MUTATED KIAA0528 WILD-TYPE
  STAGE I                   4                 87
  STAGE IA                  0                  1
  STAGE II                  3                 29
  STAGE IIA                 4                134
  STAGE IIB                 2                  8
  STAGE IIC                 0                  1
  STAGE III                 0                 24
  STAGE IIIA                1                 10
  STAGE IIIB                0                 59
  STAGE IIIC                0                 42
  STAGE IV                  1                 47
  STAGE IVA                 0                 18
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  KIAA0528 MUTATED     0   6   7   4
  KIAA0528 WILD-TYPE  17  86 322  46
D1236V5, multiclass
    clus
vv   KIAA0528 MUTATED KIAA0528 WILD-TYPE
  T1                0                 17
  T2                6                 86
  T3                7                322
  T4                4                 46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  KIAA0528 MUTATED    14   1   2
  KIAA0528 WILD-TYPE 273 112  85
D1236V6, multiclass
    clus
vv   KIAA0528 MUTATED KIAA0528 WILD-TYPE
  N0               14                273
  N1                1                112
  N2                2                 85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1236V7, binary
                    cls
clus                   0   1
  KIAA0528 MUTATED    13   1
  KIAA0528 WILD-TYPE 362  64
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0528 MUTATED     13    1
  KIAA0528 WILD-TYPE  362   64
   clus
vv  KIAA0528 MUTATED KIAA0528 WILD-TYPE
  0               13                362
  1                1                 64
[1] 2 2
[1] FALSE
D1236V8, binary
                    cls
clus                   0   1
  KIAA0528 MUTATED     6  11
  KIAA0528 WILD-TYPE 219 253
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0528 MUTATED      6   11
  KIAA0528 WILD-TYPE  219  253
        clus
vv       KIAA0528 MUTATED KIAA0528 WILD-TYPE
  FEMALE                6                219
  MALE                 11                253
[1] 2 2
[1] FALSE
D1236V9, binary
                    cls
clus                   0   1
  KIAA0528 MUTATED    14   0
  KIAA0528 WILD-TYPE 336  22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0528 MUTATED     14    0
  KIAA0528 WILD-TYPE  336   22
     clus
vv    KIAA0528 MUTATED KIAA0528 WILD-TYPE
  NO                14                336
  YES                0                 22
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  KIAA0528 MUTATED                     14                             1
  KIAA0528 WILD-TYPE                  301                            46
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  KIAA0528 MUTATED                       2                              0
  KIAA0528 WILD-TYPE                   104                             10
D1236V10, multiclass
                                clus
vv                               KIAA0528 MUTATED KIAA0528 WILD-TYPE
  COLON ADENOCARCINOMA                         14                301
  COLON MUCINOUS ADENOCARCINOMA                 1                 46
  RECTAL ADENOCARCINOMA                         2                104
  RECTAL MUCINOUS ADENOCARCINOMA                0                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  KIAA0528 MUTATED    11   0   1   1
  KIAA0528 WILD-TYPE 334   4  30  24
D1236V11, multiclass
    clus
vv   KIAA0528 MUTATED KIAA0528 WILD-TYPE
  R0               11                334
  R1                0                  4
  R2                1                 30
  RX                1                 24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1236V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KIAA0528 MUTATED                                  0     0
  KIAA0528 WILD-TYPE                                1    11
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  KIAA0528 MUTATED                           0     9
  KIAA0528 WILD-TYPE                        22   217
D1236V13, multiclass
                                  clus
vv                                 KIAA0528 MUTATED KIAA0528 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 11
  BLACK OR AFRICAN AMERICAN                       0                 22
  WHITE                                           9                217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1237) Variable = GABPA MUTATION ANALYSIS
D1237V1, survival
                 sevent
clus2               0   1
  GABPA MUTATED    10   2
  GABPA WILD-TYPE 368  91
  GABPA MUTATED GABPA WILD-TYPE 
             12             459 
  GABPA MUTATED GABPA WILD-TYPE 
              2              91 
$`GABPA MUTATED`
TCGA-A6-6142 TCGA-AA-3672 TCGA-AA-3950 TCGA-AA-A00N TCGA-AA-A010 TCGA-AD-6889 
       25.08         0.92        24.00         4.01        34.98        56.55 
TCGA-AD-6895 TCGA-CM-6161 TCGA-D5-6533 TCGA-DM-A0XD TCGA-G4-6588 TCGA-CI-6620 
        0.72        15.02         1.32        24.43        26.17        33.17 

$`GABPA WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 
        6.97        54.02         2.01        14.01        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 
       12.99        24.00        33.01        26.01         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
        0.07        21.37        15.52         0.79         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       17.03        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       20.19        18.25        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        35.80        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6622 
        1.45        17.49         0.69         0.72         6.05         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  GABPA MUTATED GABPA WILD-TYPE 
           0.72            0.00 
  GABPA MUTATED GABPA WILD-TYPE 
          56.55          148.01 
  GABPA MUTATED GABPA WILD-TYPE 
         24.215          20.120 
[1] "0.7 - 56.5 (24.2)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.1"
D1237V2, continuous
D1237V3, binary
                 cls
clus                0   1
  GABPA MUTATED    11   1
  GABPA WILD-TYPE 355 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GABPA MUTATED     11    1
  GABPA WILD-TYPE  355  118
        clus
vv       GABPA MUTATED GABPA WILD-TYPE
  COLON             11             355
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GABPA MUTATED         1        0        0         4         2         0
  GABPA WILD-TYPE      90        1       32       134         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  GABPA MUTATED           1          0          1          0        0         2
  GABPA WILD-TYPE        23         11         58         42       48        16
                 vv
clus              STAGE IVB
  GABPA MUTATED           0
  GABPA WILD-TYPE         1
D1237V4, multiclass
            clus
vv           GABPA MUTATED GABPA WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              4             134
  STAGE IIB              2               8
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              2              16
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  GABPA MUTATED     0   1   8   3
  GABPA WILD-TYPE  17  91 321  47
D1237V5, multiclass
    clus
vv   GABPA MUTATED GABPA WILD-TYPE
  T1             0              17
  T2             1              91
  T3             8             321
  T4             3              47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  GABPA MUTATED     8   4   0
  GABPA WILD-TYPE 279 109  87
D1237V6, multiclass
    clus
vv   GABPA MUTATED GABPA WILD-TYPE
  N0             8             279
  N1             4             109
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1237V7, binary
                 cls
clus                0   1
  GABPA MUTATED     9   2
  GABPA WILD-TYPE 366  63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GABPA MUTATED      9    2
  GABPA WILD-TYPE  366   63
   clus
vv  GABPA MUTATED GABPA WILD-TYPE
  0             9             366
  1             2              63
[1] 2 2
[1] FALSE
D1237V8, binary
                 cls
clus                0   1
  GABPA MUTATED     8   4
  GABPA WILD-TYPE 217 260
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GABPA MUTATED      8    4
  GABPA WILD-TYPE  217  260
        clus
vv       GABPA MUTATED GABPA WILD-TYPE
  FEMALE             8             217
  MALE               4             260
[1] 2 2
[1] FALSE
D1237V9, binary
                 cls
clus                0   1
  GABPA MUTATED     7   0
  GABPA WILD-TYPE 343  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GABPA MUTATED      7    0
  GABPA WILD-TYPE  343   22
     clus
vv    GABPA MUTATED GABPA WILD-TYPE
  NO              7             343
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  GABPA MUTATED                      9                             2
  GABPA WILD-TYPE                  306                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  GABPA MUTATED                       1                              0
  GABPA WILD-TYPE                   105                             10
D1237V10, multiclass
                                clus
vv                               GABPA MUTATED GABPA WILD-TYPE
  COLON ADENOCARCINOMA                       9             306
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  GABPA MUTATED     7   0   0   0
  GABPA WILD-TYPE 338   4  31  25
D1237V11, multiclass
    clus
vv   GABPA MUTATED GABPA WILD-TYPE
  R0             7             338
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1237V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GABPA MUTATED                                  0     1
  GABPA WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  GABPA MUTATED                           0     7
  GABPA WILD-TYPE                        22   219
D1237V13, multiclass
                                  clus
vv                                 GABPA MUTATED GABPA WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        7             219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1238) Variable = PPP2R2B MUTATION ANALYSIS
D1238V1, survival
                   sevent
clus2                 0   1
  PPP2R2B MUTATED     7   4
  PPP2R2B WILD-TYPE 371  89
  PPP2R2B MUTATED PPP2R2B WILD-TYPE 
               11               460 
  PPP2R2B MUTATED PPP2R2B WILD-TYPE 
                4                89 
$`PPP2R2B MUTATED`
TCGA-A6-5659 TCGA-A6-6653 TCGA-AA-3877 TCGA-AD-6889 TCGA-AD-6895 TCGA-AD-6964 
       30.44        24.39        31.00        56.55         0.72        10.88 
TCGA-D5-6927 TCGA-DM-A1D6 TCGA-AG-3574 TCGA-AG-3892 TCGA-DY-A1DD 
        9.44        49.91        36.03        13.02        57.24 

$`PPP2R2B WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 
       25.18        24.16        21.76        24.69        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 
       24.03        27.02        29.98        18.05         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 
       18.05        40.96         0.07        21.37        15.52         0.79 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.04        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3575 TCGA-AG-3578 
       16.83        15.39        20.02        10.39        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 
       19.99         1.02        17.95        36.95        17.03        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DF 
        4.01         5.03         5.29       126.44        41.36        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  PPP2R2B MUTATED PPP2R2B WILD-TYPE 
             0.72              0.00 
  PPP2R2B MUTATED PPP2R2B WILD-TYPE 
            57.24            148.01 
  PPP2R2B MUTATED PPP2R2B WILD-TYPE 
           30.440            20.085 
[1] "0.7 - 57.2 (30.4)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.6"
D1238V2, continuous
D1238V3, binary
                   cls
clus                  0   1
  PPP2R2B MUTATED     8   3
  PPP2R2B WILD-TYPE 358 116
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PPP2R2B MUTATED      8    3
  PPP2R2B WILD-TYPE  358  116
        clus
vv       PPP2R2B MUTATED PPP2R2B WILD-TYPE
  COLON                8               358
  RECTUM               3               116
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PPP2R2B MUTATED         4        0        1         3         0         0
  PPP2R2B WILD-TYPE      87        1       31       135        10         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PPP2R2B MUTATED           0          0          1          0        0
  PPP2R2B WILD-TYPE        24         11         58         42       48
                   vv
clus                STAGE IVA STAGE IVB
  PPP2R2B MUTATED           0         0
  PPP2R2B WILD-TYPE        18         1
D1238V4, multiclass
            clus
vv           PPP2R2B MUTATED PPP2R2B WILD-TYPE
  STAGE I                  4                87
  STAGE IA                 0                 1
  STAGE II                 1                31
  STAGE IIA                3               135
  STAGE IIB                0                10
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               0                11
  STAGE IIIB               1                58
  STAGE IIIC               0                42
  STAGE IV                 0                48
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  PPP2R2B MUTATED     2   2   6   1
  PPP2R2B WILD-TYPE  15  90 323  49
D1238V5, multiclass
    clus
vv   PPP2R2B MUTATED PPP2R2B WILD-TYPE
  T1               2                15
  T2               2                90
  T3               6               323
  T4               1                49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  PPP2R2B MUTATED     8   2   1
  PPP2R2B WILD-TYPE 279 111  86
D1238V6, multiclass
    clus
vv   PPP2R2B MUTATED PPP2R2B WILD-TYPE
  N0               8               279
  N1               2               111
  N2               1                86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1238V7, binary
                   cls
clus                  0   1
  PPP2R2B MUTATED     9   0
  PPP2R2B WILD-TYPE 366  65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PPP2R2B MUTATED      9    0
  PPP2R2B WILD-TYPE  366   65
   clus
vv  PPP2R2B MUTATED PPP2R2B WILD-TYPE
  0               9               366
  1               0                65
[1] 2 2
[1] FALSE
D1238V8, binary
                   cls
clus                  0   1
  PPP2R2B MUTATED     4   7
  PPP2R2B WILD-TYPE 221 257
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PPP2R2B MUTATED      4    7
  PPP2R2B WILD-TYPE  221  257
        clus
vv       PPP2R2B MUTATED PPP2R2B WILD-TYPE
  FEMALE               4               221
  MALE                 7               257
[1] 2 2
[1] FALSE
D1238V9, binary
                   cls
clus                  0   1
  PPP2R2B MUTATED     7   0
  PPP2R2B WILD-TYPE 343  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PPP2R2B MUTATED      7    0
  PPP2R2B WILD-TYPE  343   22
     clus
vv    PPP2R2B MUTATED PPP2R2B WILD-TYPE
  NO                7               343
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PPP2R2B MUTATED                      6                             2
  PPP2R2B WILD-TYPE                  309                            45
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PPP2R2B MUTATED                       3                              0
  PPP2R2B WILD-TYPE                   103                             10
D1238V10, multiclass
                                clus
vv                               PPP2R2B MUTATED PPP2R2B WILD-TYPE
  COLON ADENOCARCINOMA                         6               309
  COLON MUCINOUS ADENOCARCINOMA                2                45
  RECTAL ADENOCARCINOMA                        3               103
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  PPP2R2B MUTATED     5   0   0   0
  PPP2R2B WILD-TYPE 340   4  31  25
D1238V11, multiclass
    clus
vv   PPP2R2B MUTATED PPP2R2B WILD-TYPE
  R0               5               340
  R1               0                 4
  R2               0                31
  RX               0                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1238V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PPP2R2B MUTATED                                  0     1
  PPP2R2B WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  PPP2R2B MUTATED                           0     7
  PPP2R2B WILD-TYPE                        22   219
D1238V13, multiclass
                                  clus
vv                                 PPP2R2B MUTATED PPP2R2B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                10
  BLACK OR AFRICAN AMERICAN                      0                22
  WHITE                                          7               219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1239) Variable = NEK1 MUTATION ANALYSIS
D1239V1, survival
                sevent
clus2              0   1
  NEK1 MUTATED    12   1
  NEK1 WILD-TYPE 366  92
  NEK1 MUTATED NEK1 WILD-TYPE 
            13            458 
  NEK1 MUTATED NEK1 WILD-TYPE 
             1             92 
$`NEK1 MUTATED`
TCGA-A6-5665 TCGA-A6-6653 TCGA-AA-3950 TCGA-AA-3977 TCGA-AA-A010 TCGA-AD-5900 
       22.06        24.39        24.00        25.02        34.98         0.07 
TCGA-AU-6004 TCGA-CA-6717 TCGA-D5-6539 TCGA-D5-6931 TCGA-DM-A28F TCGA-AG-3892 
       27.09        12.76        12.49        12.00        35.97        13.02 
TCGA-AG-3893 
       35.01 

$`NEK1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 
       25.18        24.16        21.76        24.69        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 
       12.99        24.00        33.01        26.01         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 
       22.42        27.42        10.88         0.20        14.50        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07        12.20        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
        4.80        17.13        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        4.80         1.51        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
        6.12        81.37       119.93        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.95        36.95        17.03        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  NEK1 MUTATED NEK1 WILD-TYPE 
          0.07           0.00 
  NEK1 MUTATED NEK1 WILD-TYPE 
         35.97         148.01 
  NEK1 MUTATED NEK1 WILD-TYPE 
        24.000         20.085 
[1] "0.1 - 36.0 (24.0)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "2"  
D1239V2, continuous
D1239V3, binary
                cls
clus               0   1
  NEK1 MUTATED    12   2
  NEK1 WILD-TYPE 354 117
[1] "tbl2"
                cls
clus             [,1] [,2]
  NEK1 MUTATED     12    2
  NEK1 WILD-TYPE  354  117
        clus
vv       NEK1 MUTATED NEK1 WILD-TYPE
  COLON            12            354
  RECTUM            2            117
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NEK1 MUTATED         4        0        0         4         1         0
  NEK1 WILD-TYPE      87        1       32       134         9         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NEK1 MUTATED           0          1          2          1        0         0
  NEK1 WILD-TYPE        24         10         57         41       48        18
                vv
clus             STAGE IVB
  NEK1 MUTATED           0
  NEK1 WILD-TYPE         1
D1239V4, multiclass
            clus
vv           NEK1 MUTATED NEK1 WILD-TYPE
  STAGE I               4             87
  STAGE IA              0              1
  STAGE II              0             32
  STAGE IIA             4            134
  STAGE IIB             1              9
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            1             10
  STAGE IIIB            2             57
  STAGE IIIC            1             41
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  NEK1 MUTATED     1   4   7   2
  NEK1 WILD-TYPE  16  88 322  48
D1239V5, multiclass
    clus
vv   NEK1 MUTATED NEK1 WILD-TYPE
  T1            1             16
  T2            4             88
  T3            7            322
  T4            2             48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  NEK1 MUTATED    11   2   1
  NEK1 WILD-TYPE 276 111  86
D1239V6, multiclass
    clus
vv   NEK1 MUTATED NEK1 WILD-TYPE
  N0           11            276
  N1            2            111
  N2            1             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1239V7, binary
                cls
clus               0   1
  NEK1 MUTATED    12   0
  NEK1 WILD-TYPE 363  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  NEK1 MUTATED     12    0
  NEK1 WILD-TYPE  363   65
   clus
vv  NEK1 MUTATED NEK1 WILD-TYPE
  0           12            363
  1            0             65
[1] 2 2
[1] FALSE
D1239V8, binary
                cls
clus               0   1
  NEK1 MUTATED     7   7
  NEK1 WILD-TYPE 218 257
[1] "tbl2"
                cls
clus             [,1] [,2]
  NEK1 MUTATED      7    7
  NEK1 WILD-TYPE  218  257
        clus
vv       NEK1 MUTATED NEK1 WILD-TYPE
  FEMALE            7            218
  MALE              7            257
[1] 2 2
[1] FALSE
D1239V9, binary
                cls
clus               0   1
  NEK1 MUTATED    10   0
  NEK1 WILD-TYPE 340  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  NEK1 MUTATED     10    0
  NEK1 WILD-TYPE  340   22
     clus
vv    NEK1 MUTATED NEK1 WILD-TYPE
  NO            10            340
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  NEK1 MUTATED                      9                             3
  NEK1 WILD-TYPE                  306                            44
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  NEK1 MUTATED                       2                              0
  NEK1 WILD-TYPE                   104                             10
D1239V10, multiclass
                                clus
vv                               NEK1 MUTATED NEK1 WILD-TYPE
  COLON ADENOCARCINOMA                      9            306
  COLON MUCINOUS ADENOCARCINOMA             3             44
  RECTAL ADENOCARCINOMA                     2            104
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  NEK1 MUTATED    10   0   0   1
  NEK1 WILD-TYPE 335   4  31  24
D1239V11, multiclass
    clus
vv   NEK1 MUTATED NEK1 WILD-TYPE
  R0           10            335
  R1            0              4
  R2            0             31
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1239V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NEK1 MUTATED                                  0     1
  NEK1 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  NEK1 MUTATED                           0     7
  NEK1 WILD-TYPE                        22   219
D1239V13, multiclass
                                  clus
vv                                 NEK1 MUTATED NEK1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       7            219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1240) Variable = CEACAM6 MUTATION ANALYSIS
D1240V1, survival
                   sevent
clus2                 0   1
  CEACAM6 MUTATED     2   2
  CEACAM6 WILD-TYPE 376  91
  CEACAM6 MUTATED CEACAM6 WILD-TYPE 
                4               467 
  CEACAM6 MUTATED CEACAM6 WILD-TYPE 
                2                91 
$`CEACAM6 MUTATED`
TCGA-AZ-6600 TCGA-DM-A28H TCGA-F4-6570 TCGA-G4-6293 
       12.10       117.07         6.18       133.18 

$`CEACAM6 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       49.41         6.77       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       35.97        60.79        98.24         8.61        31.96        35.74 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6303 
       13.25         0.53        47.41        35.31        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  CEACAM6 MUTATED CEACAM6 WILD-TYPE 
             6.18              0.00 
  CEACAM6 MUTATED CEACAM6 WILD-TYPE 
           133.18            148.01 
  CEACAM6 MUTATED CEACAM6 WILD-TYPE 
           64.585            20.190 
[1] "6.2 - 133.2 (64.6)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.2"
D1240V2, continuous
D1240V3, binary
                   cls
clus                  0   1
  CEACAM6 MUTATED     4   0
  CEACAM6 WILD-TYPE 362 119
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CEACAM6 MUTATED      4    0
  CEACAM6 WILD-TYPE  362  119
        clus
vv       CEACAM6 MUTATED CEACAM6 WILD-TYPE
  COLON                4               362
  RECTUM               0               119
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CEACAM6 MUTATED         0        0        0         1         0         0
  CEACAM6 WILD-TYPE      91        1       32       137        10         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CEACAM6 MUTATED           1          0          0          1        1
  CEACAM6 WILD-TYPE        23         11         59         41       47
                   vv
clus                STAGE IVA STAGE IVB
  CEACAM6 MUTATED           0         0
  CEACAM6 WILD-TYPE        18         1
D1240V4, multiclass
            clus
vv           CEACAM6 MUTATED CEACAM6 WILD-TYPE
  STAGE I                  0                91
  STAGE IA                 0                 1
  STAGE II                 0                32
  STAGE IIA                1               137
  STAGE IIB                0                10
  STAGE IIC                0                 1
  STAGE III                1                23
  STAGE IIIA               0                11
  STAGE IIIB               0                59
  STAGE IIIC               1                41
  STAGE IV                 1                47
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  CEACAM6 MUTATED     0   0   3   1
  CEACAM6 WILD-TYPE  17  92 326  49
D1240V5, multiclass
    clus
vv   CEACAM6 MUTATED CEACAM6 WILD-TYPE
  T1               0                17
  T2               0                92
  T3               3               326
  T4               1                49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  CEACAM6 MUTATED     1   2   1
  CEACAM6 WILD-TYPE 286 111  86
D1240V6, multiclass
    clus
vv   CEACAM6 MUTATED CEACAM6 WILD-TYPE
  N0               1               286
  N1               2               111
  N2               1                86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1240V7, binary
                   cls
clus                  0   1
  CEACAM6 MUTATED     3   1
  CEACAM6 WILD-TYPE 372  64
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CEACAM6 MUTATED      3    1
  CEACAM6 WILD-TYPE  372   64
   clus
vv  CEACAM6 MUTATED CEACAM6 WILD-TYPE
  0               3               372
  1               1                64
[1] 2 2
[1] FALSE
D1240V8, binary
                   cls
clus                  0   1
  CEACAM6 MUTATED     2   2
  CEACAM6 WILD-TYPE 223 262
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CEACAM6 MUTATED      2    2
  CEACAM6 WILD-TYPE  223  262
        clus
vv       CEACAM6 MUTATED CEACAM6 WILD-TYPE
  FEMALE               2               223
  MALE                 2               262
[1] 2 2
[1] FALSE
D1240V9, binary
                   cls
clus                  0   1
  CEACAM6 MUTATED     2   0
  CEACAM6 WILD-TYPE 348  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CEACAM6 MUTATED      2    0
  CEACAM6 WILD-TYPE  348   22
     clus
vv    CEACAM6 MUTATED CEACAM6 WILD-TYPE
  NO                2               348
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CEACAM6 MUTATED                      4                             0
  CEACAM6 WILD-TYPE                  311                            47
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CEACAM6 MUTATED                       0                              0
  CEACAM6 WILD-TYPE                   106                             10
D1240V10, multiclass
                                clus
vv                               CEACAM6 MUTATED CEACAM6 WILD-TYPE
  COLON ADENOCARCINOMA                         4               311
  COLON MUCINOUS ADENOCARCINOMA                0                47
  RECTAL ADENOCARCINOMA                        0               106
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  CEACAM6 MUTATED     2   0   0   0
  CEACAM6 WILD-TYPE 343   4  31  25
D1240V11, multiclass
[1] "Remove cluster labels:" "CEACAM6 MUTATED"       
clus
  CEACAM6 MUTATED CEACAM6 WILD-TYPE 
                2               403 
       TCGA-A6-2671        TCGA-A6-2672        TCGA-A6-2674        TCGA-A6-2676 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-A6-2677        TCGA-A6-2678        TCGA-A6-2683        TCGA-A6-3807 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-A6-3808        TCGA-A6-3809        TCGA-A6-3810        TCGA-A6-5657 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-A6-5659        TCGA-A6-5661        TCGA-A6-5665        TCGA-A6-6781 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-AA-3489        TCGA-AA-3492        TCGA-AA-3496        TCGA-AA-3502 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-AA-3510        TCGA-AA-3511        TCGA-AA-3514        TCGA-AA-3517 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-AA-3518        TCGA-AA-3519        TCGA-AA-3520        TCGA-AA-3521 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-AA-3522        TCGA-AA-3524        TCGA-AA-3525        TCGA-AA-3526 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-AA-3527        TCGA-AA-3529        TCGA-AA-3530        TCGA-AA-3531 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-AA-3532        TCGA-AA-3534        TCGA-AA-3538        TCGA-AA-3542 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-AA-3543        TCGA-AA-3544        TCGA-AA-3548        TCGA-AA-3549 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-AA-3552        TCGA-AA-3553        TCGA-AA-3554        TCGA-AA-3555 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-AA-3556        TCGA-AA-3558        TCGA-AA-3560        TCGA-AA-3561 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-AA-3562        TCGA-AA-3655        TCGA-AA-3660        TCGA-AA-3662 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-AA-3663        TCGA-AA-3664        TCGA-AA-3666        TCGA-AA-3667 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-AA-3672        TCGA-AA-3673        TCGA-AA-3678        TCGA-AA-3679 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-AA-3680        TCGA-AA-3681        TCGA-AA-3684        TCGA-AA-3685 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-AA-3688        TCGA-AA-3692        TCGA-AA-3693        TCGA-AA-3695 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-AA-3696        TCGA-AA-3697        TCGA-AA-3710        TCGA-AA-3712 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-AA-3713        TCGA-AA-3715        TCGA-AA-3811        TCGA-AA-3812 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-AA-3814        TCGA-AA-3815        TCGA-AA-3818        TCGA-AA-3819 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-AA-3821        TCGA-AA-3831        TCGA-AA-3833        TCGA-AA-3837 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-AA-3842        TCGA-AA-3844        TCGA-AA-3845        TCGA-AA-3846 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-AA-3848        TCGA-AA-3850        TCGA-AA-3851        TCGA-AA-3852 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-AA-3854        TCGA-AA-3855        TCGA-AA-3856        TCGA-AA-3858 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-AA-3860        TCGA-AA-3861        TCGA-AA-3864        TCGA-AA-3866 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-AA-3867        TCGA-AA-3869        TCGA-AA-3870        TCGA-AA-3872 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-AA-3875        TCGA-AA-3877        TCGA-AA-3930        TCGA-AA-3939 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-AA-3941        TCGA-AA-3947        TCGA-AA-3949        TCGA-AA-3950 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-AA-3952        TCGA-AA-3955        TCGA-AA-3956        TCGA-AA-3968 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-AA-3971        TCGA-AA-3972        TCGA-AA-3973        TCGA-AA-3975 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-AA-3976        TCGA-AA-3979        TCGA-AA-3984        TCGA-AA-3986 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-AA-3989        TCGA-AA-3994        TCGA-AA-A004        TCGA-AA-A00A 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-AA-A00D        TCGA-AA-A00E        TCGA-AA-A00F        TCGA-AA-A00J 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-AA-A00K        TCGA-AA-A00L        TCGA-AA-A00N        TCGA-AA-A00O 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-AA-A00Q        TCGA-AA-A00R        TCGA-AA-A00U        TCGA-AA-A00W 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-AA-A00Z        TCGA-AA-A010        TCGA-AA-A017        TCGA-AA-A01D 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-AA-A01F        TCGA-AA-A01G        TCGA-AA-A01I        TCGA-AA-A01K 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-AA-A01P        TCGA-AA-A01Q        TCGA-AA-A01R        TCGA-AA-A01S 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-AA-A01T        TCGA-AA-A01V        TCGA-AA-A01X        TCGA-AA-A01Z 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-AA-A022        TCGA-AA-A024        TCGA-AA-A029        TCGA-AA-A02F 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-AA-A02H        TCGA-AA-A02J        TCGA-AA-A02K        TCGA-AA-A02O 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-AA-A02W        TCGA-AA-A02Y        TCGA-AA-A03F        TCGA-AA-A03J 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-AD-5900        TCGA-AD-6548        TCGA-AD-6888        TCGA-AU-3779 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-AU-6004        TCGA-AY-4070        TCGA-AY-4071        TCGA-AY-5543 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-AY-6196        TCGA-AY-6197        TCGA-AY-6386        TCGA-AZ-4315 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-AZ-4681        TCGA-AZ-4682        TCGA-CA-5254        TCGA-CA-5255 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-CA-5796        TCGA-CA-5797        TCGA-CA-6715        TCGA-CA-6716 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-CA-6717        TCGA-CA-6718        TCGA-CA-6719        TCGA-CK-4947 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-CK-4948        TCGA-CK-4950        TCGA-CK-4952        TCGA-CK-5912 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-CK-5913        TCGA-CK-5914        TCGA-CK-5915        TCGA-CK-5916 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-CK-6746        TCGA-CK-6747        TCGA-CK-6748        TCGA-CK-6751 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-CM-4743        TCGA-CM-4744        TCGA-CM-4746        TCGA-CM-4747 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-CM-4752        TCGA-CM-5341        TCGA-CM-5344        TCGA-CM-5348 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-CM-5349        TCGA-CM-5860        TCGA-CM-5861        TCGA-CM-5862 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-CM-5863        TCGA-CM-5864        TCGA-CM-5868        TCGA-CM-6161 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-CM-6162        TCGA-CM-6163        TCGA-CM-6164        TCGA-CM-6165 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-CM-6166        TCGA-CM-6167        TCGA-CM-6168        TCGA-CM-6169 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-CM-6170        TCGA-CM-6171        TCGA-CM-6172        TCGA-CM-6674 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-CM-6675        TCGA-CM-6676        TCGA-CM-6677        TCGA-CM-6678 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-CM-6679        TCGA-CM-6680        TCGA-D5-5537        TCGA-D5-5538 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-D5-5539        TCGA-D5-5540        TCGA-D5-5541        TCGA-D5-6529 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-D5-6532        TCGA-D5-6533        TCGA-D5-6534        TCGA-D5-6535 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-D5-6536        TCGA-D5-6537        TCGA-D5-6538        TCGA-D5-6539 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-D5-6540        TCGA-D5-6541        TCGA-D5-6898        TCGA-D5-6920 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-D5-6922        TCGA-D5-6923        TCGA-D5-6924        TCGA-D5-6926 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-D5-6927        TCGA-D5-6928        TCGA-D5-6929        TCGA-D5-6930 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-D5-6931        TCGA-D5-6932        TCGA-D5-7000        TCGA-F4-6459 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-F4-6460        TCGA-F4-6569        TCGA-F4-6703        TCGA-F4-6704 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-F4-6805        TCGA-F4-6806        TCGA-F4-6807        TCGA-F4-6808 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-F4-6809        TCGA-F4-6854        TCGA-F4-6855        TCGA-F4-6856 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-G4-6299        TCGA-G4-6303        TCGA-G4-6304        TCGA-G4-6306 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-G4-6307        TCGA-G4-6309        TCGA-G4-6310        TCGA-G4-6315 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-G4-6317        TCGA-G4-6321        TCGA-G4-6323        TCGA-G4-6586 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-G4-6588        TCGA-G4-6625        TCGA-G4-6626        TCGA-G4-6628 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2691        TCGA-AF-2692 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-AF-3400        TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-AF-6655        TCGA-AG-3574        TCGA-AG-3575        TCGA-AG-3578 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-AG-3580        TCGA-AG-3581        TCGA-AG-3582        TCGA-AG-3583 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-AG-3584        TCGA-AG-3586        TCGA-AG-3587        TCGA-AG-3593 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-AG-3594        TCGA-AG-3598        TCGA-AG-3599        TCGA-AG-3600 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-AG-3601        TCGA-AG-3602        TCGA-AG-3605        TCGA-AG-3608 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-AG-3609        TCGA-AG-3611        TCGA-AG-3612        TCGA-AG-3726 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-AG-3727        TCGA-AG-3731        TCGA-AG-3732        TCGA-AG-3742 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-AG-3878        TCGA-AG-3882        TCGA-AG-3883        TCGA-AG-3885 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3890        TCGA-AG-3892        TCGA-AG-3893 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-AG-3894        TCGA-AG-3896        TCGA-AG-3898        TCGA-AG-3901 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-AG-3902        TCGA-AG-3909        TCGA-AG-3999        TCGA-AG-4001 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-AG-4005        TCGA-AG-4007        TCGA-AG-4008        TCGA-AG-4015 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-AG-A002        TCGA-AG-A008        TCGA-AG-A00C        TCGA-AG-A00H 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-AG-A00Y        TCGA-AG-A011        TCGA-AG-A014        TCGA-AG-A015 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-AG-A016        TCGA-AG-A01L        TCGA-AG-A01W        TCGA-AG-A01Y 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A025        TCGA-AG-A026        TCGA-AG-A02G 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032        TCGA-AG-A036 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-AH-6549        TCGA-AH-6643        TCGA-CL-5917        TCGA-CL-5918 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6155        TCGA-DC-6157 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-DC-6158        TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-DC-6683        TCGA-DT-5265        TCGA-EF-5830        TCGA-EI-6506 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-EI-6507        TCGA-EI-6508        TCGA-EI-6510        TCGA-F5-6464 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-F5-6465        TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6812 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
       TCGA-F5-6813        TCGA-G5-6235        TCGA-G5-6641 
"CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" "CEACAM6 WILD-TYPE" 
D1240V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CEACAM6 MUTATED                                  0     0
  CEACAM6 WILD-TYPE                                1    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  CEACAM6 MUTATED                           1     3
  CEACAM6 WILD-TYPE                        21   223
D1240V13, multiclass
                                  clus
vv                                 CEACAM6 MUTATED CEACAM6 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                      1                21
  WHITE                                          3               223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1241) Variable = MED14 MUTATION ANALYSIS
D1241V1, survival
                 sevent
clus2               0   1
  MED14 MUTATED    13   6
  MED14 WILD-TYPE 365  87
  MED14 MUTATED MED14 WILD-TYPE 
             19             452 
  MED14 MUTATED MED14 WILD-TYPE 
              6              87 
$`MED14 MUTATED`
TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3534 TCGA-AA-3672 TCGA-AA-3715 TCGA-AA-3947 
       13.02         1.02        29.00         0.92        19.04        33.01 
TCGA-AA-3950 TCGA-AD-5900 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-CA-6717 TCGA-CK-5913 
       24.00         0.07        49.41        12.10        12.76        51.32 
TCGA-CK-6751 TCGA-CM-6678 TCGA-F4-6459 TCGA-F4-6570 TCGA-F4-6704 TCGA-F4-6805 
      124.27        11.01         8.61         6.18         1.55        34.42 
TCGA-G4-6307 
       55.04 

$`MED14 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        1.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3538 TCGA-AA-3542 
        0.00        19.07        34.03        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
        2.01        14.01        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       26.99        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 
       18.05        31.00         2.01        12.99        24.00        26.01 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 
       41.00        39.98        18.05        40.96        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6601 
      106.75        22.36        62.79        88.21         6.77       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07        12.20        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CM-4743 TCGA-CM-4744 
        9.99        21.14        82.95         1.91        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6679 
       11.01        12.95        13.05        11.08        11.08        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 
       60.79       117.07        98.24        31.96        35.74        47.87 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  MED14 MUTATED MED14 WILD-TYPE 
           0.07            0.00 
  MED14 MUTATED MED14 WILD-TYPE 
         124.27          148.01 
  MED14 MUTATED MED14 WILD-TYPE 
         13.020          20.415 
[1] "0.1 - 124.3 (13.0)" "0.0 - 148.0 (20.4)"
[1] "hr=" "1.7"
D1241V2, continuous
D1241V3, binary
                 cls
clus                0   1
  MED14 MUTATED    19   0
  MED14 WILD-TYPE 347 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MED14 MUTATED     19    0
  MED14 WILD-TYPE  347  119
        clus
vv       MED14 MUTATED MED14 WILD-TYPE
  COLON             19             347
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MED14 MUTATED         2        0        2         7         1         0
  MED14 WILD-TYPE      89        1       30       131         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MED14 MUTATED           2          0          2          1        1         1
  MED14 WILD-TYPE        22         11         57         41       47        17
                 vv
clus              STAGE IVB
  MED14 MUTATED           0
  MED14 WILD-TYPE         1
D1241V4, multiclass
            clus
vv           MED14 MUTATED MED14 WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA              7             131
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              2              22
  STAGE IIIA             0              11
  STAGE IIIB             2              57
  STAGE IIIC             1              41
  STAGE IV               1              47
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  MED14 MUTATED     0   2  14   3
  MED14 WILD-TYPE  17  90 315  47
D1241V5, multiclass
    clus
vv   MED14 MUTATED MED14 WILD-TYPE
  T1             0              17
  T2             2              90
  T3            14             315
  T4             3              47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  MED14 MUTATED    12   4   3
  MED14 WILD-TYPE 275 109  84
D1241V6, multiclass
    clus
vv   MED14 MUTATED MED14 WILD-TYPE
  N0            12             275
  N1             4             109
  N2             3              84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1241V7, binary
                 cls
clus                0   1
  MED14 MUTATED    12   2
  MED14 WILD-TYPE 363  63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MED14 MUTATED     12    2
  MED14 WILD-TYPE  363   63
   clus
vv  MED14 MUTATED MED14 WILD-TYPE
  0            12             363
  1             2              63
[1] 2 2
[1] FALSE
D1241V8, binary
                 cls
clus                0   1
  MED14 MUTATED    14   5
  MED14 WILD-TYPE 211 259
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MED14 MUTATED     14    5
  MED14 WILD-TYPE  211  259
        clus
vv       MED14 MUTATED MED14 WILD-TYPE
  FEMALE            14             211
  MALE               5             259
[1] 2 2
[1] FALSE
D1241V9, binary
                 cls
clus                0   1
  MED14 MUTATED    15   0
  MED14 WILD-TYPE 335  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MED14 MUTATED     15    0
  MED14 WILD-TYPE  335   22
     clus
vv    MED14 MUTATED MED14 WILD-TYPE
  NO             15             335
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MED14 MUTATED                     12                             7
  MED14 WILD-TYPE                  303                            40
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MED14 MUTATED                       0                              0
  MED14 WILD-TYPE                   106                             10
D1241V10, multiclass
                                clus
vv                               MED14 MUTATED MED14 WILD-TYPE
  COLON ADENOCARCINOMA                      12             303
  COLON MUCINOUS ADENOCARCINOMA              7              40
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  MED14 MUTATED    13   0   0   3
  MED14 WILD-TYPE 332   4  31  22
D1241V11, multiclass
    clus
vv   MED14 MUTATED MED14 WILD-TYPE
  R0            13             332
  R1             0               4
  R2             0              31
  RX             3              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1241V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MED14 MUTATED                                  1     1
  MED14 WILD-TYPE                                0    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  MED14 MUTATED                           1     9
  MED14 WILD-TYPE                        21   217
D1241V13, multiclass
                                  clus
vv                                 MED14 MUTATED MED14 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             1               0
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        9             217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1242) Variable = AGTR2 MUTATION ANALYSIS
D1242V1, survival
                 sevent
clus2               0   1
  AGTR2 MUTATED    12   5
  AGTR2 WILD-TYPE 366  88
  AGTR2 MUTATED AGTR2 WILD-TYPE 
             17             454 
  AGTR2 MUTATED AGTR2 WILD-TYPE 
              5              88 
$`AGTR2 MUTATED`
TCGA-A6-3809 TCGA-A6-5666 TCGA-AA-3821 TCGA-AA-3989 TCGA-AA-A00N TCGA-AA-A017 
       32.75        32.71         1.02         7.96         4.01         1.02 
TCGA-AD-6889 TCGA-AD-6895 TCGA-AD-6899 TCGA-AZ-6601 TCGA-CA-6717 TCGA-CM-6171 
       56.55         0.72         5.79       100.01        12.76        14.04 
TCGA-D5-6539 TCGA-DM-A285 TCGA-G4-6323 TCGA-AF-2693 TCGA-AG-3892 
       12.49         6.12        13.78        19.10        13.02 

$`AGTR2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       22.06        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 
       35.05        33.04         0.99        25.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
       19.07        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99        34.98        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
       21.37        15.52         0.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07        12.20        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       15.02        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 
       15.12        17.85         4.80        17.13        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      131.51       135.65       139.17        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
       63.62        61.91        36.00        22.09        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       13.55        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 
        1.02        17.95        36.95        17.03        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  AGTR2 MUTATED AGTR2 WILD-TYPE 
           0.72            0.00 
  AGTR2 MUTATED AGTR2 WILD-TYPE 
         100.01          148.01 
  AGTR2 MUTATED AGTR2 WILD-TYPE 
          12.76           20.98 
[1] "0.7 - 100.0 (12.8)" "0.0 - 148.0 (21.0)"
[1] "hr=" "2"  
D1242V2, continuous
D1242V3, binary
                 cls
clus                0   1
  AGTR2 MUTATED    15   1
  AGTR2 WILD-TYPE 351 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AGTR2 MUTATED     15    1
  AGTR2 WILD-TYPE  351  118
        clus
vv       AGTR2 MUTATED AGTR2 WILD-TYPE
  COLON             15             351
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  AGTR2 MUTATED         4        1        1         3         2         1
  AGTR2 WILD-TYPE      87        0       31       135         8         0
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AGTR2 MUTATED           0          1          0          1        2         0
  AGTR2 WILD-TYPE        24         10         59         41       46        18
                 vv
clus              STAGE IVB
  AGTR2 MUTATED           0
  AGTR2 WILD-TYPE         1
D1242V4, multiclass
            clus
vv           AGTR2 MUTATED AGTR2 WILD-TYPE
  STAGE I                4              87
  STAGE IA               1               0
  STAGE II               1              31
  STAGE IIA              3             135
  STAGE IIB              2               8
  STAGE IIC              1               0
  STAGE III              0              24
  STAGE IIIA             1              10
  STAGE IIIB             0              59
  STAGE IIIC             1              41
  STAGE IV               2              46
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  AGTR2 MUTATED     1   3   8   4
  AGTR2 WILD-TYPE  16  89 321  46
D1242V5, multiclass
    clus
vv   AGTR2 MUTATED AGTR2 WILD-TYPE
  T1             1              16
  T2             3              89
  T3             8             321
  T4             4              46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  AGTR2 MUTATED    13   1   3
  AGTR2 WILD-TYPE 274 112  84
D1242V6, multiclass
    clus
vv   AGTR2 MUTATED AGTR2 WILD-TYPE
  N0            13             274
  N1             1             112
  N2             3              84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1242V7, binary
                 cls
clus                0   1
  AGTR2 MUTATED    11   2
  AGTR2 WILD-TYPE 364  63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AGTR2 MUTATED     11    2
  AGTR2 WILD-TYPE  364   63
   clus
vv  AGTR2 MUTATED AGTR2 WILD-TYPE
  0            11             364
  1             2              63
[1] 2 2
[1] FALSE
D1242V8, binary
                 cls
clus                0   1
  AGTR2 MUTATED     7  10
  AGTR2 WILD-TYPE 218 254
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AGTR2 MUTATED      7   10
  AGTR2 WILD-TYPE  218  254
        clus
vv       AGTR2 MUTATED AGTR2 WILD-TYPE
  FEMALE             7             218
  MALE              10             254
[1] 2 2
[1] FALSE
D1242V9, binary
                 cls
clus                0   1
  AGTR2 MUTATED    12   0
  AGTR2 WILD-TYPE 338  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AGTR2 MUTATED     12    0
  AGTR2 WILD-TYPE  338   22
     clus
vv    AGTR2 MUTATED AGTR2 WILD-TYPE
  NO             12             338
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  AGTR2 MUTATED                      9                             6
  AGTR2 WILD-TYPE                  306                            41
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  AGTR2 MUTATED                       1                              0
  AGTR2 WILD-TYPE                   105                             10
D1242V10, multiclass
                                clus
vv                               AGTR2 MUTATED AGTR2 WILD-TYPE
  COLON ADENOCARCINOMA                       9             306
  COLON MUCINOUS ADENOCARCINOMA              6              41
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  AGTR2 MUTATED     8   0   1   1
  AGTR2 WILD-TYPE 337   4  30  24
D1242V11, multiclass
    clus
vv   AGTR2 MUTATED AGTR2 WILD-TYPE
  R0             8             337
  R1             0               4
  R2             1              30
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1242V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AGTR2 MUTATED                                  0     2
  AGTR2 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  AGTR2 MUTATED                           1     9
  AGTR2 WILD-TYPE                        21   217
D1242V13, multiclass
                                  clus
vv                                 AGTR2 MUTATED AGTR2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               9
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        9             217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1243) Variable = COL4A6 MUTATION ANALYSIS
D1243V1, survival
                  sevent
clus2                0   1
  COL4A6 MUTATED    18   3
  COL4A6 WILD-TYPE 360  90
  COL4A6 MUTATED COL4A6 WILD-TYPE 
              21              450 
  COL4A6 MUTATED COL4A6 WILD-TYPE 
               3               90 
$`COL4A6 MUTATED`
TCGA-A6-5661 TCGA-A6-5666 TCGA-AA-3542 TCGA-AA-3672 TCGA-AA-3846 TCGA-AA-A00K 
       33.53        32.71        12.99         0.92        17.03        18.05 
TCGA-AA-A00N TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A01K TCGA-AA-A01Q TCGA-AD-5900 
        4.01        21.99        34.98        31.00         1.02         0.07 
TCGA-AZ-4323 TCGA-CA-6717 TCGA-CK-5913 TCGA-CK-5914 TCGA-CM-5349 TCGA-CM-6162 
        1.41        12.76        51.32         9.99        30.08        12.00 
TCGA-DM-A0XD TCGA-F4-6807 TCGA-F5-6813 
       24.43        16.24         0.69 

$`COL4A6 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       22.06        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
        2.01        14.01        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02        14.93         0.00        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       14.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01P TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
       38.07        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07        12.20        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       85.45        15.62        49.08        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       29.06        22.03        22.98        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 
       15.02        15.02        17.03        15.02         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       11.38        10.26       119.70        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-G5-6235 TCGA-G5-6641 
       31.30        28.57        32.19         0.66        55.76        26.43 

  COL4A6 MUTATED COL4A6 WILD-TYPE 
            0.07             0.00 
  COL4A6 MUTATED COL4A6 WILD-TYPE 
           51.32           148.01 
  COL4A6 MUTATED COL4A6 WILD-TYPE 
           16.24            20.73 
[1] "0.1 - 51.3 (16.2)"  "0.0 - 148.0 (20.7)"
[1] "hr=" "1.1"
D1243V2, continuous
D1243V3, binary
                  cls
clus                 0   1
  COL4A6 MUTATED    21   1
  COL4A6 WILD-TYPE 345 118
[1] "tbl2"
                  cls
clus               [,1] [,2]
  COL4A6 MUTATED     21    1
  COL4A6 WILD-TYPE  345  118
        clus
vv       COL4A6 MUTATED COL4A6 WILD-TYPE
  COLON              21              345
  RECTUM              1              118
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  COL4A6 MUTATED         1        0        1         9         2         1
  COL4A6 WILD-TYPE      90        1       31       129         8         0
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  COL4A6 MUTATED           1          0          2          4        1
  COL4A6 WILD-TYPE        23         11         57         38       47
                  vv
clus               STAGE IVA STAGE IVB
  COL4A6 MUTATED           0         0
  COL4A6 WILD-TYPE        18         1
D1243V4, multiclass
            clus
vv           COL4A6 MUTATED COL4A6 WILD-TYPE
  STAGE I                 1               90
  STAGE IA                0                1
  STAGE II                1               31
  STAGE IIA               9              129
  STAGE IIB               2                8
  STAGE IIC               1                0
  STAGE III               1               23
  STAGE IIIA              0               11
  STAGE IIIB              2               57
  STAGE IIIC              4               38
  STAGE IV                1               47
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  COL4A6 MUTATED     0   1  16   5
  COL4A6 WILD-TYPE  17  91 313  45
D1243V5, multiclass
    clus
vv   COL4A6 MUTATED COL4A6 WILD-TYPE
  T1              0               17
  T2              1               91
  T3             16              313
  T4              5               45
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  COL4A6 MUTATED    14   3   5
  COL4A6 WILD-TYPE 273 110  82
D1243V6, multiclass
    clus
vv   COL4A6 MUTATED COL4A6 WILD-TYPE
  N0             14              273
  N1              3              110
  N2              5               82
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1243V7, binary
                  cls
clus                 0   1
  COL4A6 MUTATED    18   1
  COL4A6 WILD-TYPE 357  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  COL4A6 MUTATED     18    1
  COL4A6 WILD-TYPE  357   64
   clus
vv  COL4A6 MUTATED COL4A6 WILD-TYPE
  0             18              357
  1              1               64
[1] 2 2
[1] FALSE
D1243V8, binary
                  cls
clus                 0   1
  COL4A6 MUTATED    11  11
  COL4A6 WILD-TYPE 214 253
[1] "tbl2"
                  cls
clus               [,1] [,2]
  COL4A6 MUTATED     11   11
  COL4A6 WILD-TYPE  214  253
        clus
vv       COL4A6 MUTATED COL4A6 WILD-TYPE
  FEMALE             11              214
  MALE               11              253
[1] 2 2
[1] FALSE
D1243V9, binary
                  cls
clus                 0   1
  COL4A6 MUTATED    14   0
  COL4A6 WILD-TYPE 336  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  COL4A6 MUTATED     14    0
  COL4A6 WILD-TYPE  336   22
     clus
vv    COL4A6 MUTATED COL4A6 WILD-TYPE
  NO              14              336
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  COL4A6 MUTATED                     17                             4
  COL4A6 WILD-TYPE                  298                            43
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  COL4A6 MUTATED                       1                              0
  COL4A6 WILD-TYPE                   105                             10
D1243V10, multiclass
                                clus
vv                               COL4A6 MUTATED COL4A6 WILD-TYPE
  COLON ADENOCARCINOMA                       17              298
  COLON MUCINOUS ADENOCARCINOMA               4               43
  RECTAL ADENOCARCINOMA                       1              105
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  COL4A6 MUTATED    16   0   0   3
  COL4A6 WILD-TYPE 329   4  31  22
D1243V11, multiclass
    clus
vv   COL4A6 MUTATED COL4A6 WILD-TYPE
  R0             16              329
  R1              0                4
  R2              0               31
  RX              3               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1243V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  COL4A6 MUTATED                                  0     1
  COL4A6 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  COL4A6 MUTATED                           1    10
  COL4A6 WILD-TYPE                        21   216
D1243V13, multiclass
                                  clus
vv                                 COL4A6 MUTATED COL4A6 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                        10              216
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1244) Variable = KRTAP12-3 MUTATION ANALYSIS
D1244V1, survival
                     sevent
clus2                   0   1
  KRTAP12-3 MUTATED     2   1
  KRTAP12-3 WILD-TYPE 376  92
  KRTAP12-3 MUTATED KRTAP12-3 WILD-TYPE 
                  3                 468 
  KRTAP12-3 MUTATED KRTAP12-3 WILD-TYPE 
                  1                  92 
$`KRTAP12-3 MUTATED`
TCGA-AZ-6599 TCGA-D5-6931 TCGA-G4-6586 
        6.77        12.00        35.80 

$`KRTAP12-3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       49.41        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6932 TCGA-D5-7000 
        9.44        11.64         4.80         1.51        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 
       63.62        61.91        36.00        22.09        13.78        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  KRTAP12-3 MUTATED KRTAP12-3 WILD-TYPE 
               6.77                0.00 
  KRTAP12-3 MUTATED KRTAP12-3 WILD-TYPE 
              35.80              148.01 
  KRTAP12-3 MUTATED KRTAP12-3 WILD-TYPE 
             12.000              20.235 
[1] "6.8 - 35.8 (12.0)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "2.7"
D1244V2, continuous
D1244V3, binary
                     cls
clus                    0   1
  KRTAP12-3 MUTATED     3   0
  KRTAP12-3 WILD-TYPE 363 119
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  KRTAP12-3 MUTATED      3    0
  KRTAP12-3 WILD-TYPE  363  119
        clus
vv       KRTAP12-3 MUTATED KRTAP12-3 WILD-TYPE
  COLON                  3                 363
  RECTUM                 0                 119
[1] 2 2
[1] FALSE
                     vv
clus                  STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KRTAP12-3 MUTATED         1        0        0         1         0         0
  KRTAP12-3 WILD-TYPE      90        1       32       137        10         1
                     vv
clus                  STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KRTAP12-3 MUTATED           0          0          0          1        0
  KRTAP12-3 WILD-TYPE        24         11         59         41       48
                     vv
clus                  STAGE IVA STAGE IVB
  KRTAP12-3 MUTATED           0         0
  KRTAP12-3 WILD-TYPE        18         1
D1244V4, multiclass
            clus
vv           KRTAP12-3 MUTATED KRTAP12-3 WILD-TYPE
  STAGE I                    1                  90
  STAGE IA                   0                   1
  STAGE II                   0                  32
  STAGE IIA                  1                 137
  STAGE IIB                  0                  10
  STAGE IIC                  0                   1
  STAGE III                  0                  24
  STAGE IIIA                 0                  11
  STAGE IIIB                 0                  59
  STAGE IIIC                 1                  41
  STAGE IV                   0                  48
  STAGE IVA                  0                  18
  STAGE IVB                  0                   1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                   T1  T2  T3  T4
  KRTAP12-3 MUTATED     0   1   1   1
  KRTAP12-3 WILD-TYPE  17  91 328  49
D1244V5, multiclass
    clus
vv   KRTAP12-3 MUTATED KRTAP12-3 WILD-TYPE
  T1                 0                  17
  T2                 1                  91
  T3                 1                 328
  T4                 1                  49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                   N0  N1  N2
  KRTAP12-3 MUTATED     2   0   1
  KRTAP12-3 WILD-TYPE 285 113  86
D1244V6, multiclass
    clus
vv   KRTAP12-3 MUTATED KRTAP12-3 WILD-TYPE
  N0                 2                 285
  N1                 0                 113
  N2                 1                  86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1244V7, binary
                     cls
clus                    0   1
  KRTAP12-3 MUTATED     2   0
  KRTAP12-3 WILD-TYPE 373  65
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  KRTAP12-3 MUTATED      2    0
  KRTAP12-3 WILD-TYPE  373   65
   clus
vv  KRTAP12-3 MUTATED KRTAP12-3 WILD-TYPE
  0                 2                 373
  1                 0                  65
[1] 2 2
[1] FALSE
D1244V8, binary
                     cls
clus                    0   1
  KRTAP12-3 MUTATED     1   2
  KRTAP12-3 WILD-TYPE 224 262
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  KRTAP12-3 MUTATED      1    2
  KRTAP12-3 WILD-TYPE  224  262
        clus
vv       KRTAP12-3 MUTATED KRTAP12-3 WILD-TYPE
  FEMALE                 1                 224
  MALE                   2                 262
[1] 2 2
[1] FALSE
D1244V9, binary
                     cls
clus                    0   1
  KRTAP12-3 MUTATED     3   0
  KRTAP12-3 WILD-TYPE 347  22
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  KRTAP12-3 MUTATED      3    0
  KRTAP12-3 WILD-TYPE  347   22
     clus
vv    KRTAP12-3 MUTATED KRTAP12-3 WILD-TYPE
  NO                  3                 347
  YES                 0                  22
[1] 2 2
[1] FALSE
                     vv
clus                  COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  KRTAP12-3 MUTATED                      3                             0
  KRTAP12-3 WILD-TYPE                  312                            47
                     vv
clus                  RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  KRTAP12-3 MUTATED                       0                              0
  KRTAP12-3 WILD-TYPE                   106                             10
D1244V10, multiclass
                                clus
vv                               KRTAP12-3 MUTATED KRTAP12-3 WILD-TYPE
  COLON ADENOCARCINOMA                           3                 312
  COLON MUCINOUS ADENOCARCINOMA                  0                  47
  RECTAL ADENOCARCINOMA                          0                 106
  RECTAL MUCINOUS ADENOCARCINOMA                 0                  10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                   R0  R1  R2  RX
  KRTAP12-3 MUTATED     2   0   0   0
  KRTAP12-3 WILD-TYPE 343   4  31  25
D1244V11, multiclass
[1] "Remove cluster labels:" "KRTAP12-3 MUTATED"     
clus
  KRTAP12-3 MUTATED KRTAP12-3 WILD-TYPE 
                  2                 403 
         TCGA-A6-2671          TCGA-A6-2672          TCGA-A6-2674 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-A6-2676          TCGA-A6-2677          TCGA-A6-2678 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-A6-2683          TCGA-A6-3807          TCGA-A6-3808 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-A6-3809          TCGA-A6-3810          TCGA-A6-5657 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-A6-5659          TCGA-A6-5661          TCGA-A6-5665 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-A6-6781          TCGA-AA-3489          TCGA-AA-3492 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-3496          TCGA-AA-3502          TCGA-AA-3510 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-3511          TCGA-AA-3514          TCGA-AA-3517 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-3518          TCGA-AA-3519          TCGA-AA-3520 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-3521          TCGA-AA-3522          TCGA-AA-3524 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-3525          TCGA-AA-3526          TCGA-AA-3527 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-3529          TCGA-AA-3530          TCGA-AA-3531 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-3532          TCGA-AA-3534          TCGA-AA-3538 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-3542          TCGA-AA-3543          TCGA-AA-3544 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-3548          TCGA-AA-3549          TCGA-AA-3552 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-3553          TCGA-AA-3554          TCGA-AA-3555 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-3556          TCGA-AA-3558          TCGA-AA-3560 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-3561          TCGA-AA-3562          TCGA-AA-3655 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-3660          TCGA-AA-3662          TCGA-AA-3663 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-3664          TCGA-AA-3666          TCGA-AA-3667 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-3672          TCGA-AA-3673          TCGA-AA-3678 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-3679          TCGA-AA-3680          TCGA-AA-3681 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-3684          TCGA-AA-3685          TCGA-AA-3688 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-3692          TCGA-AA-3693          TCGA-AA-3695 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-3696          TCGA-AA-3697          TCGA-AA-3710 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-3712          TCGA-AA-3713          TCGA-AA-3715 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-3811          TCGA-AA-3812          TCGA-AA-3814 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-3815          TCGA-AA-3818          TCGA-AA-3819 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-3821          TCGA-AA-3831          TCGA-AA-3833 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-3837          TCGA-AA-3842          TCGA-AA-3844 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-3845          TCGA-AA-3846          TCGA-AA-3848 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-3850          TCGA-AA-3851          TCGA-AA-3852 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-3854          TCGA-AA-3855          TCGA-AA-3856 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-3858          TCGA-AA-3860          TCGA-AA-3861 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-3864          TCGA-AA-3866          TCGA-AA-3867 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-3869          TCGA-AA-3870          TCGA-AA-3872 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-3875          TCGA-AA-3877          TCGA-AA-3930 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-3939          TCGA-AA-3941          TCGA-AA-3947 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-3949          TCGA-AA-3950          TCGA-AA-3952 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-3955          TCGA-AA-3956          TCGA-AA-3968 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-3971          TCGA-AA-3972          TCGA-AA-3973 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-3975          TCGA-AA-3976          TCGA-AA-3979 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-3984          TCGA-AA-3986          TCGA-AA-3989 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-3994          TCGA-AA-A004          TCGA-AA-A00A 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-A00D          TCGA-AA-A00E          TCGA-AA-A00F 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-A00J          TCGA-AA-A00K          TCGA-AA-A00L 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-A00N          TCGA-AA-A00O          TCGA-AA-A00Q 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-A00R          TCGA-AA-A00U          TCGA-AA-A00W 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-A00Z          TCGA-AA-A010          TCGA-AA-A017 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-A01D          TCGA-AA-A01F          TCGA-AA-A01G 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-A01I          TCGA-AA-A01K          TCGA-AA-A01P 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-A01Q          TCGA-AA-A01R          TCGA-AA-A01S 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-A01T          TCGA-AA-A01V          TCGA-AA-A01X 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-A01Z          TCGA-AA-A022          TCGA-AA-A024 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-A029          TCGA-AA-A02F          TCGA-AA-A02H 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-A02J          TCGA-AA-A02K          TCGA-AA-A02O 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-A02W          TCGA-AA-A02Y          TCGA-AA-A03F 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AA-A03J          TCGA-AD-5900          TCGA-AD-6548 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AD-6888          TCGA-AU-3779          TCGA-AU-6004 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AY-4070          TCGA-AY-4071          TCGA-AY-5543 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AY-6196          TCGA-AY-6197          TCGA-AY-6386 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AZ-4315          TCGA-AZ-4681          TCGA-AZ-4682 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-CA-5254          TCGA-CA-5255          TCGA-CA-5796 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-CA-5797          TCGA-CA-6715          TCGA-CA-6716 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-CA-6717          TCGA-CA-6718          TCGA-CA-6719 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-CK-4947          TCGA-CK-4948          TCGA-CK-4950 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-CK-4952          TCGA-CK-5912          TCGA-CK-5913 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-CK-5914          TCGA-CK-5915          TCGA-CK-5916 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-CK-6746          TCGA-CK-6747          TCGA-CK-6748 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-CK-6751          TCGA-CM-4743          TCGA-CM-4744 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-CM-4746          TCGA-CM-4747          TCGA-CM-4752 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-CM-5341          TCGA-CM-5344          TCGA-CM-5348 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-CM-5349          TCGA-CM-5860          TCGA-CM-5861 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-CM-5862          TCGA-CM-5863          TCGA-CM-5864 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-CM-5868          TCGA-CM-6161          TCGA-CM-6162 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-CM-6163          TCGA-CM-6164          TCGA-CM-6165 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-CM-6166          TCGA-CM-6167          TCGA-CM-6168 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-CM-6169          TCGA-CM-6170          TCGA-CM-6171 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-CM-6172          TCGA-CM-6674          TCGA-CM-6675 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-CM-6676          TCGA-CM-6677          TCGA-CM-6678 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-CM-6679          TCGA-CM-6680          TCGA-D5-5537 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-D5-5538          TCGA-D5-5539          TCGA-D5-5540 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-D5-5541          TCGA-D5-6529          TCGA-D5-6532 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-D5-6533          TCGA-D5-6534          TCGA-D5-6535 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-D5-6536          TCGA-D5-6537          TCGA-D5-6538 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-D5-6539          TCGA-D5-6540          TCGA-D5-6541 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-D5-6898          TCGA-D5-6920          TCGA-D5-6922 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-D5-6923          TCGA-D5-6924          TCGA-D5-6926 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-D5-6927          TCGA-D5-6928          TCGA-D5-6929 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-D5-6930          TCGA-D5-6932          TCGA-D5-7000 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-F4-6459          TCGA-F4-6460          TCGA-F4-6569 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-F4-6570          TCGA-F4-6703          TCGA-F4-6704 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-F4-6805          TCGA-F4-6806          TCGA-F4-6807 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-F4-6808          TCGA-F4-6809          TCGA-F4-6854 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-F4-6855          TCGA-F4-6856          TCGA-G4-6293 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-G4-6299          TCGA-G4-6303          TCGA-G4-6304 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-G4-6306          TCGA-G4-6307          TCGA-G4-6309 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-G4-6310          TCGA-G4-6315          TCGA-G4-6317 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-G4-6321          TCGA-G4-6323          TCGA-G4-6588 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-G4-6625          TCGA-G4-6626          TCGA-G4-6628 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AF-2687          TCGA-AF-2689          TCGA-AF-2691 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AF-2692          TCGA-AF-3400          TCGA-AF-3913 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AF-4110          TCGA-AF-5654          TCGA-AF-6655 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AG-3574          TCGA-AG-3575          TCGA-AG-3578 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AG-3580          TCGA-AG-3581          TCGA-AG-3582 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AG-3583          TCGA-AG-3584          TCGA-AG-3586 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AG-3587          TCGA-AG-3593          TCGA-AG-3594 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AG-3598          TCGA-AG-3599          TCGA-AG-3600 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AG-3601          TCGA-AG-3602          TCGA-AG-3605 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AG-3608          TCGA-AG-3609          TCGA-AG-3611 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AG-3612          TCGA-AG-3726          TCGA-AG-3727 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AG-3731          TCGA-AG-3732          TCGA-AG-3742 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AG-3878          TCGA-AG-3882          TCGA-AG-3883 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AG-3885          TCGA-AG-3887          TCGA-AG-3890 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AG-3892          TCGA-AG-3893          TCGA-AG-3894 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AG-3896          TCGA-AG-3898          TCGA-AG-3901 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AG-3902          TCGA-AG-3909          TCGA-AG-3999 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AG-4001          TCGA-AG-4005          TCGA-AG-4007 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AG-4008          TCGA-AG-4015          TCGA-AG-A002 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AG-A008          TCGA-AG-A00C          TCGA-AG-A00H 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AG-A00Y          TCGA-AG-A011          TCGA-AG-A014 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AG-A015          TCGA-AG-A016          TCGA-AG-A01L 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AG-A01W          TCGA-AG-A01Y          TCGA-AG-A020 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AG-A025          TCGA-AG-A026          TCGA-AG-A02G 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AG-A02N          TCGA-AG-A02X          TCGA-AG-A032 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-AG-A036          TCGA-AH-6549          TCGA-AH-6643 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-CL-5917          TCGA-CL-5918          TCGA-DC-5337 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-DC-5869          TCGA-DC-6155          TCGA-DC-6157 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-DC-6158          TCGA-DC-6160          TCGA-DC-6681 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-DC-6682          TCGA-DC-6683          TCGA-DT-5265 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-EF-5830          TCGA-EI-6506          TCGA-EI-6507 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-EI-6508          TCGA-EI-6510          TCGA-F5-6464 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-F5-6465          TCGA-F5-6571          TCGA-F5-6702 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-F5-6812          TCGA-F5-6813          TCGA-G5-6235 
"KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" "KRTAP12-3 WILD-TYPE" 
         TCGA-G5-6641 
"KRTAP12-3 WILD-TYPE" 
D1244V12, continuous
                     vv
clus                  AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KRTAP12-3 MUTATED                                  0     0
  KRTAP12-3 WILD-TYPE                                1    11
                     vv
clus                  BLACK OR AFRICAN AMERICAN WHITE
  KRTAP12-3 MUTATED                           0     3
  KRTAP12-3 WILD-TYPE                        22   223
D1244V13, multiclass
                                  clus
vv                                 KRTAP12-3 MUTATED KRTAP12-3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                 0                   1
  ASIAN                                            0                  11
  BLACK OR AFRICAN AMERICAN                        0                  22
  WHITE                                            3                 223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1245) Variable = EMR3 MUTATION ANALYSIS
D1245V1, survival
                sevent
clus2              0   1
  EMR3 MUTATED    12   4
  EMR3 WILD-TYPE 366  89
  EMR3 MUTATED EMR3 WILD-TYPE 
            16            455 
  EMR3 MUTATED EMR3 WILD-TYPE 
             4             89 
$`EMR3 MUTATED`
TCGA-A6-2671 TCGA-A6-4105 TCGA-A6-5665 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3525 
       43.76        14.53        22.06        35.01        63.98         8.05 
TCGA-AA-3710 TCGA-AA-3870 TCGA-AA-A00N TCGA-AA-A010 TCGA-AD-6895 TCGA-CM-4743 
       26.99        29.98         4.01        34.98         0.72        23.05 
TCGA-CM-6172 TCGA-D5-6537 TCGA-G4-6588 TCGA-AG-A002 
       11.01         4.80        26.17        20.98 

$`EMR3 WILD-TYPE`
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       46.65        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 
       34.65        33.34        32.75        36.53        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 
       30.44        29.19        33.53        23.61        22.09        32.71 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       27.09        22.52         8.38        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3511 TCGA-AA-3514 
       20.28         7.04         3.02         1.02         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
       13.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
       36.03        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
       19.00        36.00         5.03        85.05        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       17.03        24.03        27.02        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       14.04        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
       17.85        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  EMR3 MUTATED EMR3 WILD-TYPE 
          0.72           0.00 
  EMR3 MUTATED EMR3 WILD-TYPE 
         63.98         148.01 
  EMR3 MUTATED EMR3 WILD-TYPE 
        22.555         20.050 
[1] "0.7 - 64.0 (22.6)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.5"
D1245V2, continuous
D1245V3, binary
                cls
clus               0   1
  EMR3 MUTATED    16   1
  EMR3 WILD-TYPE 350 118
[1] "tbl2"
                cls
clus             [,1] [,2]
  EMR3 MUTATED     16    1
  EMR3 WILD-TYPE  350  118
        clus
vv       EMR3 MUTATED EMR3 WILD-TYPE
  COLON            16            350
  RECTUM            1            118
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  EMR3 MUTATED         2        0        1         5         2         0
  EMR3 WILD-TYPE      89        1       31       133         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  EMR3 MUTATED           0          0          3          1        2         0
  EMR3 WILD-TYPE        24         11         56         41       46        18
                vv
clus             STAGE IVB
  EMR3 MUTATED           0
  EMR3 WILD-TYPE         1
D1245V4, multiclass
            clus
vv           EMR3 MUTATED EMR3 WILD-TYPE
  STAGE I               2             89
  STAGE IA              0              1
  STAGE II              1             31
  STAGE IIA             5            133
  STAGE IIB             2              8
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            3             56
  STAGE IIIC            1             41
  STAGE IV              2             46
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  EMR3 MUTATED     0   2  13   2
  EMR3 WILD-TYPE  17  90 316  48
D1245V5, multiclass
    clus
vv   EMR3 MUTATED EMR3 WILD-TYPE
  T1            0             17
  T2            2             90
  T3           13            316
  T4            2             48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  EMR3 MUTATED    10   4   3
  EMR3 WILD-TYPE 277 109  84
D1245V6, multiclass
    clus
vv   EMR3 MUTATED EMR3 WILD-TYPE
  N0           10            277
  N1            4            109
  N2            3             84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1245V7, binary
                cls
clus               0   1
  EMR3 MUTATED    12   2
  EMR3 WILD-TYPE 363  63
[1] "tbl2"
                cls
clus             [,1] [,2]
  EMR3 MUTATED     12    2
  EMR3 WILD-TYPE  363   63
   clus
vv  EMR3 MUTATED EMR3 WILD-TYPE
  0           12            363
  1            2             63
[1] 2 2
[1] FALSE
D1245V8, binary
                cls
clus               0   1
  EMR3 MUTATED     6  11
  EMR3 WILD-TYPE 219 253
[1] "tbl2"
                cls
clus             [,1] [,2]
  EMR3 MUTATED      6   11
  EMR3 WILD-TYPE  219  253
        clus
vv       EMR3 MUTATED EMR3 WILD-TYPE
  FEMALE            6            219
  MALE             11            253
[1] 2 2
[1] FALSE
D1245V9, binary
                cls
clus               0   1
  EMR3 MUTATED    13   0
  EMR3 WILD-TYPE 337  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  EMR3 MUTATED     13    0
  EMR3 WILD-TYPE  337   22
     clus
vv    EMR3 MUTATED EMR3 WILD-TYPE
  NO            13            337
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  EMR3 MUTATED                     14                             2
  EMR3 WILD-TYPE                  301                            45
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  EMR3 MUTATED                       1                              0
  EMR3 WILD-TYPE                   105                             10
D1245V10, multiclass
                                clus
vv                               EMR3 MUTATED EMR3 WILD-TYPE
  COLON ADENOCARCINOMA                     14            301
  COLON MUCINOUS ADENOCARCINOMA             2             45
  RECTAL ADENOCARCINOMA                     1            105
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  EMR3 MUTATED    15   0   0   0
  EMR3 WILD-TYPE 330   4  31  25
D1245V11, multiclass
    clus
vv   EMR3 MUTATED EMR3 WILD-TYPE
  R0           15            330
  R1            0              4
  R2            0             31
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1245V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  EMR3 MUTATED                                  0     0
  EMR3 WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  EMR3 MUTATED                           0     9
  EMR3 WILD-TYPE                        22   217
D1245V13, multiclass
                                  clus
vv                                 EMR3 MUTATED EMR3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       9            217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1246) Variable = STAU2 MUTATION ANALYSIS
D1246V1, survival
                 sevent
clus2               0   1
  STAU2 MUTATED     7   2
  STAU2 WILD-TYPE 371  91
  STAU2 MUTATED STAU2 WILD-TYPE 
              9             462 
  STAU2 MUTATED STAU2 WILD-TYPE 
              2              91 
$`STAU2 MUTATED`
TCGA-AA-3821 TCGA-AA-A00A TCGA-AD-5900 TCGA-AZ-4315 TCGA-CA-6717 TCGA-CK-5913 
        1.02        38.04         0.07        58.39        12.76        51.32 
TCGA-CK-5916 TCGA-F4-6460 TCGA-G4-6586 
       21.14        31.96        35.80 

$`STAU2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       39.98        18.05        40.96        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07        12.20        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
        9.99        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6569 
       35.97        60.79       117.07        98.24         8.61        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 
       63.62        61.91        36.00        22.09        13.78        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  STAU2 MUTATED STAU2 WILD-TYPE 
           0.07            0.00 
  STAU2 MUTATED STAU2 WILD-TYPE 
          58.39          148.01 
  STAU2 MUTATED STAU2 WILD-TYPE 
         31.960          20.085 
[1] "0.1 - 58.4 (32.0)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.1"
D1246V2, continuous
D1246V3, binary
                 cls
clus                0   1
  STAU2 MUTATED    10   0
  STAU2 WILD-TYPE 356 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STAU2 MUTATED     10    0
  STAU2 WILD-TYPE  356  119
        clus
vv       STAU2 MUTATED STAU2 WILD-TYPE
  COLON             10             356
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  STAU2 MUTATED         3        0        0         6         0         0
  STAU2 WILD-TYPE      88        1       32       132        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  STAU2 MUTATED           0          0          1          0        0         0
  STAU2 WILD-TYPE        24         11         58         42       48        18
                 vv
clus              STAGE IVB
  STAU2 MUTATED           0
  STAU2 WILD-TYPE         1
D1246V4, multiclass
            clus
vv           STAU2 MUTATED STAU2 WILD-TYPE
  STAGE I                3              88
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              6             132
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  STAU2 MUTATED     1   2   7   0
  STAU2 WILD-TYPE  16  90 322  50
D1246V5, multiclass
    clus
vv   STAU2 MUTATED STAU2 WILD-TYPE
  T1             1              16
  T2             2              90
  T3             7             322
  T4             0              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  STAU2 MUTATED     9   1   0
  STAU2 WILD-TYPE 278 112  87
D1246V6, multiclass
    clus
vv   STAU2 MUTATED STAU2 WILD-TYPE
  N0             9             278
  N1             1             112
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1246V7, binary
                 cls
clus                0   1
  STAU2 MUTATED     8   0
  STAU2 WILD-TYPE 367  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STAU2 MUTATED      8    0
  STAU2 WILD-TYPE  367   65
   clus
vv  STAU2 MUTATED STAU2 WILD-TYPE
  0             8             367
  1             0              65
[1] 2 2
[1] FALSE
D1246V8, binary
                 cls
clus                0   1
  STAU2 MUTATED     6   4
  STAU2 WILD-TYPE 219 260
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STAU2 MUTATED      6    4
  STAU2 WILD-TYPE  219  260
        clus
vv       STAU2 MUTATED STAU2 WILD-TYPE
  FEMALE             6             219
  MALE               4             260
[1] 2 2
[1] FALSE
D1246V9, binary
                 cls
clus                0   1
  STAU2 MUTATED     8   0
  STAU2 WILD-TYPE 342  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STAU2 MUTATED      8    0
  STAU2 WILD-TYPE  342   22
     clus
vv    STAU2 MUTATED STAU2 WILD-TYPE
  NO              8             342
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  STAU2 MUTATED                      7                             3
  STAU2 WILD-TYPE                  308                            44
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  STAU2 MUTATED                       0                              0
  STAU2 WILD-TYPE                   106                             10
D1246V10, multiclass
                                clus
vv                               STAU2 MUTATED STAU2 WILD-TYPE
  COLON ADENOCARCINOMA                       7             308
  COLON MUCINOUS ADENOCARCINOMA              3              44
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  STAU2 MUTATED     7   0   0   3
  STAU2 WILD-TYPE 338   4  31  22
D1246V11, multiclass
    clus
vv   STAU2 MUTATED STAU2 WILD-TYPE
  R0             7             338
  R1             0               4
  R2             0              31
  RX             3              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1246V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  STAU2 MUTATED                                  0     1
  STAU2 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  STAU2 MUTATED                           0     6
  STAU2 WILD-TYPE                        22   220
D1246V13, multiclass
                                  clus
vv                                 STAU2 MUTATED STAU2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        6             220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1247) Variable = GGA2 MUTATION ANALYSIS
D1247V1, survival
                sevent
clus2              0   1
  GGA2 MUTATED     9   3
  GGA2 WILD-TYPE 369  90
  GGA2 MUTATED GGA2 WILD-TYPE 
            12            459 
  GGA2 MUTATED GGA2 WILD-TYPE 
             3             90 
$`GGA2 MUTATED`
TCGA-A6-5665 TCGA-AA-3510 TCGA-AA-3516 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3877 
       22.06        63.98        13.02        26.99        10.06        31.00 
TCGA-AA-3955 TCGA-AA-A00N TCGA-AA-A010 TCGA-AZ-4315 TCGA-DM-A1HB TCGA-EI-6507 
       20.98         4.01        34.98        58.39       135.65        19.96 

$`GGA2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
       35.01         6.97         1.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       85.05        19.04        19.04        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       18.05         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       24.00         2.01        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 
      140.38         7.50        44.32       131.51       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6510 
       51.48        32.61         0.49        20.55        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  GGA2 MUTATED GGA2 WILD-TYPE 
          4.01           0.00 
  GGA2 MUTATED GGA2 WILD-TYPE 
        135.65         148.01 
  GGA2 MUTATED GGA2 WILD-TYPE 
        24.525         20.050 
[1] "4.0 - 135.7 (24.5)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1"  
D1247V2, continuous
D1247V3, binary
                cls
clus               0   1
  GGA2 MUTATED    12   1
  GGA2 WILD-TYPE 354 118
[1] "tbl2"
                cls
clus             [,1] [,2]
  GGA2 MUTATED     12    1
  GGA2 WILD-TYPE  354  118
        clus
vv       GGA2 MUTATED GGA2 WILD-TYPE
  COLON            12            354
  RECTUM            1            118
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GGA2 MUTATED         1        0        1         5         2         0
  GGA2 WILD-TYPE      90        1       31       133         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  GGA2 MUTATED           2          0          2          0        0         0
  GGA2 WILD-TYPE        22         11         57         42       48        18
                vv
clus             STAGE IVB
  GGA2 MUTATED           0
  GGA2 WILD-TYPE         1
D1247V4, multiclass
            clus
vv           GGA2 MUTATED GGA2 WILD-TYPE
  STAGE I               1             90
  STAGE IA              0              1
  STAGE II              1             31
  STAGE IIA             5            133
  STAGE IIB             2              8
  STAGE IIC             0              1
  STAGE III             2             22
  STAGE IIIA            0             11
  STAGE IIIB            2             57
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  GGA2 MUTATED     1   1   9   2
  GGA2 WILD-TYPE  16  91 320  48
D1247V5, multiclass
    clus
vv   GGA2 MUTATED GGA2 WILD-TYPE
  T1            1             16
  T2            1             91
  T3            9            320
  T4            2             48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  GGA2 MUTATED     9   1   3
  GGA2 WILD-TYPE 278 112  84
D1247V6, multiclass
    clus
vv   GGA2 MUTATED GGA2 WILD-TYPE
  N0            9            278
  N1            1            112
  N2            3             84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1247V7, binary
                cls
clus               0   1
  GGA2 MUTATED    13   0
  GGA2 WILD-TYPE 362  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  GGA2 MUTATED     13    0
  GGA2 WILD-TYPE  362   65
   clus
vv  GGA2 MUTATED GGA2 WILD-TYPE
  0           13            362
  1            0             65
[1] 2 2
[1] FALSE
D1247V8, binary
                cls
clus               0   1
  GGA2 MUTATED     7   6
  GGA2 WILD-TYPE 218 258
[1] "tbl2"
                cls
clus             [,1] [,2]
  GGA2 MUTATED      7    6
  GGA2 WILD-TYPE  218  258
        clus
vv       GGA2 MUTATED GGA2 WILD-TYPE
  FEMALE            7            218
  MALE              6            258
[1] 2 2
[1] FALSE
D1247V9, binary
                cls
clus               0   1
  GGA2 MUTATED    10   0
  GGA2 WILD-TYPE 340  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  GGA2 MUTATED     10    0
  GGA2 WILD-TYPE  340   22
     clus
vv    GGA2 MUTATED GGA2 WILD-TYPE
  NO            10            340
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  GGA2 MUTATED                      8                             3
  GGA2 WILD-TYPE                  307                            44
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  GGA2 MUTATED                       1                              0
  GGA2 WILD-TYPE                   105                             10
D1247V10, multiclass
                                clus
vv                               GGA2 MUTATED GGA2 WILD-TYPE
  COLON ADENOCARCINOMA                      8            307
  COLON MUCINOUS ADENOCARCINOMA             3             44
  RECTAL ADENOCARCINOMA                     1            105
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  GGA2 MUTATED    11   0   0   0
  GGA2 WILD-TYPE 334   4  31  25
D1247V11, multiclass
    clus
vv   GGA2 MUTATED GGA2 WILD-TYPE
  R0           11            334
  R1            0              4
  R2            0             31
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1247V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GGA2 MUTATED                                  0     0
  GGA2 WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  GGA2 MUTATED                           0     4
  GGA2 WILD-TYPE                        22   222
D1247V13, multiclass
                                  clus
vv                                 GGA2 MUTATED GGA2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       4            222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1248) Variable = ATRNL1 MUTATION ANALYSIS
D1248V1, survival
                  sevent
clus2                0   1
  ATRNL1 MUTATED    19   5
  ATRNL1 WILD-TYPE 359  88
  ATRNL1 MUTATED ATRNL1 WILD-TYPE 
              24              447 
  ATRNL1 MUTATED ATRNL1 WILD-TYPE 
               5               88 
$`ATRNL1 MUTATED`
TCGA-A6-5661 TCGA-AA-3555 TCGA-AA-3663 TCGA-AA-3833 TCGA-AA-3977 TCGA-AA-A00N 
       33.53        29.95         6.97        15.95        25.02         4.01 
TCGA-AD-6890 TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-6608 TCGA-CA-5797 TCGA-CA-6717 
        0.79        21.44        58.39         1.61         3.29        12.76 
TCGA-CM-6171 TCGA-D5-6535 TCGA-D5-6928 TCGA-DM-A0XF TCGA-DM-A1HB TCGA-DM-A285 
       14.04        15.12        11.64        38.20       135.65         6.12 
TCGA-G4-6628 TCGA-AG-3894 TCGA-AG-A002 TCGA-AG-A026 TCGA-EI-6506 TCGA-EI-6507 
       79.69        14.01        20.98         1.94        20.55        19.96 

$`ATRNL1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       13.02        24.00        17.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3837 
       33.04         0.99        25.02         1.02        17.98        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       21.37        15.52        56.55         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
        0.95        33.01        17.82         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 
      100.01        29.56         5.23        11.74         3.19        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.06         3.25         0.07        12.20        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 
       55.92        20.19        18.25         1.32        43.27        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       24.43       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A28C 
      140.38         7.50        44.32       131.51       139.17        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 
       13.78        35.80        26.17        91.79        46.75        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       17.03        13.02        35.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
       49.97        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6508 TCGA-EI-6510 
       24.13        51.48        32.61         0.49        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  ATRNL1 MUTATED ATRNL1 WILD-TYPE 
            0.79             0.00 
  ATRNL1 MUTATED ATRNL1 WILD-TYPE 
          135.65           148.01 
  ATRNL1 MUTATED ATRNL1 WILD-TYPE 
          15.535           20.910 
[1] "0.8 - 135.7 (15.5)" "0.0 - 148.0 (20.9)"
[1] "hr=" "1.2"
D1248V2, continuous
D1248V3, binary
                  cls
clus                 0   1
  ATRNL1 MUTATED    22   5
  ATRNL1 WILD-TYPE 344 114
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATRNL1 MUTATED     22    5
  ATRNL1 WILD-TYPE  344  114
        clus
vv       ATRNL1 MUTATED ATRNL1 WILD-TYPE
  COLON              22              344
  RECTUM              5              114
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ATRNL1 MUTATED         3        0        3        12         1         0
  ATRNL1 WILD-TYPE      88        1       29       126         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ATRNL1 MUTATED           0          1          2          2        1
  ATRNL1 WILD-TYPE        24         10         57         40       47
                  vv
clus               STAGE IVA STAGE IVB
  ATRNL1 MUTATED           0         0
  ATRNL1 WILD-TYPE        18         1
D1248V4, multiclass
            clus
vv           ATRNL1 MUTATED ATRNL1 WILD-TYPE
  STAGE I                 3               88
  STAGE IA                0                1
  STAGE II                3               29
  STAGE IIA              12              126
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              1               10
  STAGE IIIB              2               57
  STAGE IIIC              2               40
  STAGE IV                1               47
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ATRNL1 MUTATED     1   5  18   3
  ATRNL1 WILD-TYPE  16  87 311  47
D1248V5, multiclass
    clus
vv   ATRNL1 MUTATED ATRNL1 WILD-TYPE
  T1              1               16
  T2              5               87
  T3             18              311
  T4              3               47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  ATRNL1 MUTATED    21   3   3
  ATRNL1 WILD-TYPE 266 110  84
D1248V6, multiclass
    clus
vv   ATRNL1 MUTATED ATRNL1 WILD-TYPE
  N0             21              266
  N1              3              110
  N2              3               84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1248V7, binary
                  cls
clus                 0   1
  ATRNL1 MUTATED    21   1
  ATRNL1 WILD-TYPE 354  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATRNL1 MUTATED     21    1
  ATRNL1 WILD-TYPE  354   64
   clus
vv  ATRNL1 MUTATED ATRNL1 WILD-TYPE
  0             21              354
  1              1               64
[1] 2 2
[1] FALSE
D1248V8, binary
                  cls
clus                 0   1
  ATRNL1 MUTATED    11  16
  ATRNL1 WILD-TYPE 214 248
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATRNL1 MUTATED     11   16
  ATRNL1 WILD-TYPE  214  248
        clus
vv       ATRNL1 MUTATED ATRNL1 WILD-TYPE
  FEMALE             11              214
  MALE               16              248
[1] 2 2
[1] FALSE
D1248V9, binary
                  cls
clus                 0   1
  ATRNL1 MUTATED    17   1
  ATRNL1 WILD-TYPE 333  21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATRNL1 MUTATED     17    1
  ATRNL1 WILD-TYPE  333   21
     clus
vv    ATRNL1 MUTATED ATRNL1 WILD-TYPE
  NO              17              333
  YES              1               21
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ATRNL1 MUTATED                     14                             6
  ATRNL1 WILD-TYPE                  301                            41
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ATRNL1 MUTATED                       5                              0
  ATRNL1 WILD-TYPE                   101                             10
D1248V10, multiclass
                                clus
vv                               ATRNL1 MUTATED ATRNL1 WILD-TYPE
  COLON ADENOCARCINOMA                       14              301
  COLON MUCINOUS ADENOCARCINOMA               6               41
  RECTAL ADENOCARCINOMA                       5              101
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ATRNL1 MUTATED    18   1   0   2
  ATRNL1 WILD-TYPE 327   3  31  23
D1248V11, multiclass
    clus
vv   ATRNL1 MUTATED ATRNL1 WILD-TYPE
  R0             18              327
  R1              1                3
  R2              0               31
  RX              2               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1248V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ATRNL1 MUTATED                                  0     2
  ATRNL1 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ATRNL1 MUTATED                           1    14
  ATRNL1 WILD-TYPE                        21   212
D1248V13, multiclass
                                  clus
vv                                 ATRNL1 MUTATED ATRNL1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                9
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                        14              212
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1249) Variable = OSR1 MUTATION ANALYSIS
D1249V1, survival
                sevent
clus2              0   1
  OSR1 MUTATED     3   1
  OSR1 WILD-TYPE 375  92
  OSR1 MUTATED OSR1 WILD-TYPE 
             4            467 
  OSR1 MUTATED OSR1 WILD-TYPE 
             1             92 
$`OSR1 MUTATED`
TCGA-CK-4950 TCGA-CM-5863 TCGA-G4-6293 TCGA-G4-6626 
       85.45        15.02       133.18        46.75 

$`OSR1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
       17.56       148.01        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-5868 
       30.08        32.02        15.02         5.03        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6299 
       33.67        13.25         0.53        47.41        35.31        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       91.79        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  OSR1 MUTATED OSR1 WILD-TYPE 
         15.02           0.00 
  OSR1 MUTATED OSR1 WILD-TYPE 
        133.18         148.01 
  OSR1 MUTATED OSR1 WILD-TYPE 
         66.10          20.12 
[1] "15.0 - 133.2 (66.1)" "0.0 - 148.0 (20.1)" 
[1] "hr=" "1.9"
D1249V2, continuous
D1249V3, binary
                cls
clus               0   1
  OSR1 MUTATED     4   0
  OSR1 WILD-TYPE 362 119
[1] "tbl2"
                cls
clus             [,1] [,2]
  OSR1 MUTATED      4    0
  OSR1 WILD-TYPE  362  119
        clus
vv       OSR1 MUTATED OSR1 WILD-TYPE
  COLON             4            362
  RECTUM            0            119
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  OSR1 MUTATED         0        0        0         1         0         0
  OSR1 WILD-TYPE      91        1       32       137        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  OSR1 MUTATED           1          0          2          0        0         0
  OSR1 WILD-TYPE        23         11         57         42       48        18
                vv
clus             STAGE IVB
  OSR1 MUTATED           0
  OSR1 WILD-TYPE         1
D1249V4, multiclass
            clus
vv           OSR1 MUTATED OSR1 WILD-TYPE
  STAGE I               0             91
  STAGE IA              0              1
  STAGE II              0             32
  STAGE IIA             1            137
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             1             23
  STAGE IIIA            0             11
  STAGE IIIB            2             57
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  OSR1 MUTATED     0   0   4   0
  OSR1 WILD-TYPE  17  92 325  50
D1249V5, multiclass
    clus
vv   OSR1 MUTATED OSR1 WILD-TYPE
  T1            0             17
  T2            0             92
  T3            4            325
  T4            0             50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  OSR1 MUTATED     1   3   0
  OSR1 WILD-TYPE 286 110  87
D1249V6, multiclass
    clus
vv   OSR1 MUTATED OSR1 WILD-TYPE
  N0            1            286
  N1            3            110
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1249V7, binary
                cls
clus               0   1
  OSR1 MUTATED     4   0
  OSR1 WILD-TYPE 371  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  OSR1 MUTATED      4    0
  OSR1 WILD-TYPE  371   65
   clus
vv  OSR1 MUTATED OSR1 WILD-TYPE
  0            4            371
  1            0             65
[1] 2 2
[1] FALSE
D1249V8, binary
                cls
clus               0   1
  OSR1 MUTATED     3   1
  OSR1 WILD-TYPE 222 263
[1] "tbl2"
                cls
clus             [,1] [,2]
  OSR1 MUTATED      3    1
  OSR1 WILD-TYPE  222  263
        clus
vv       OSR1 MUTATED OSR1 WILD-TYPE
  FEMALE            3            222
  MALE              1            263
[1] 2 2
[1] FALSE
D1249V9, binary
                cls
clus               0   1
  OSR1 MUTATED     4   0
  OSR1 WILD-TYPE 346  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  OSR1 MUTATED      4    0
  OSR1 WILD-TYPE  346   22
     clus
vv    OSR1 MUTATED OSR1 WILD-TYPE
  NO             4            346
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  OSR1 MUTATED                      3                             1
  OSR1 WILD-TYPE                  312                            46
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  OSR1 MUTATED                       0                              0
  OSR1 WILD-TYPE                   106                             10
D1249V10, multiclass
                                clus
vv                               OSR1 MUTATED OSR1 WILD-TYPE
  COLON ADENOCARCINOMA                      3            312
  COLON MUCINOUS ADENOCARCINOMA             1             46
  RECTAL ADENOCARCINOMA                     0            106
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  OSR1 MUTATED     3   1   0   0
  OSR1 WILD-TYPE 342   3  31  25
D1249V11, multiclass
    clus
vv   OSR1 MUTATED OSR1 WILD-TYPE
  R0            3            342
  R1            1              3
  R2            0             31
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1249V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OSR1 MUTATED                                  0     0
  OSR1 WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  OSR1 MUTATED                           1     3
  OSR1 WILD-TYPE                        21   223
D1249V13, multiclass
                                  clus
vv                                 OSR1 MUTATED OSR1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                       3            223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1250) Variable = IRS4 MUTATION ANALYSIS
D1250V1, survival
                sevent
clus2              0   1
  IRS4 MUTATED    22   7
  IRS4 WILD-TYPE 356  86
  IRS4 MUTATED IRS4 WILD-TYPE 
            29            442 
  IRS4 MUTATED IRS4 WILD-TYPE 
             7             86 
$`IRS4 MUTATED`
TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-5657 TCGA-A6-5661 TCGA-A6-5665 TCGA-AA-3510 
       46.65        42.90        31.63        33.53        22.06        63.98 
TCGA-AA-3663 TCGA-AA-3696 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3977 TCGA-AA-3979 
        6.97         5.03        19.04        10.06        25.02        24.00 
TCGA-AA-A00N TCGA-AA-A00R TCGA-AA-A01Q TCGA-AD-6889 TCGA-AD-6965 TCGA-AZ-4315 
        4.01         0.99         1.02        56.55         0.20        58.39 
TCGA-AZ-6598 TCGA-AZ-6601 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-6170 TCGA-CM-6171 
       49.41       100.01        15.02        15.02        15.02        14.04 
TCGA-G4-6315 TCGA-AG-4007 TCGA-AG-A002 TCGA-AH-6644 TCGA-DY-A1DD 
       61.91         1.02        20.98         0.72        57.24 

$`IRS4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       43.76        43.76        24.33        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5659 
       33.34        32.75        36.53        14.53        32.91        30.44 
TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 
       29.19        23.61        22.09        32.71        27.09        22.52 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 
        8.38        25.08        25.18        24.16        21.76        24.69 
TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 
       24.39        23.87        20.12        19.66        20.28         7.04 
TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        3.02         1.02        35.01         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.05        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3815 
       36.00        85.05        26.99        19.04        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       26.01        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W 
       18.05        38.04        27.02        42.02        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        31.00        38.07        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 
       18.05        40.96         0.07        21.37        15.52         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AU-3779 
        0.72         5.79        22.42        27.42        10.88        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77        12.10        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
       32.02         5.03        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       13.02        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       55.04        85.48        63.62        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4008 
       32.02        19.99        28.04        36.03        14.04        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-CI-6619 
      117.11        38.56         1.45        17.49         0.69         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DF 
        4.01         5.03         5.29       126.44        41.36        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  IRS4 MUTATED IRS4 WILD-TYPE 
           0.2            0.0 
  IRS4 MUTATED IRS4 WILD-TYPE 
        100.01         148.01 
  IRS4 MUTATED IRS4 WILD-TYPE 
        20.980         20.155 
[1] "0.2 - 100.0 (21.0)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.1"
D1250V2, continuous
D1250V3, binary
                cls
clus               0   1
  IRS4 MUTATED    27   4
  IRS4 WILD-TYPE 339 115
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRS4 MUTATED     27    4
  IRS4 WILD-TYPE  339  115
        clus
vv       IRS4 MUTATED IRS4 WILD-TYPE
  COLON            27            339
  RECTUM            4            115
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  IRS4 MUTATED         4        0        6         6         3         0
  IRS4 WILD-TYPE      87        1       26       132         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  IRS4 MUTATED           1          0          4          0        4         0
  IRS4 WILD-TYPE        23         11         55         42       44        18
                vv
clus             STAGE IVB
  IRS4 MUTATED           0
  IRS4 WILD-TYPE         1
D1250V4, multiclass
            clus
vv           IRS4 MUTATED IRS4 WILD-TYPE
  STAGE I               4             87
  STAGE IA              0              1
  STAGE II              6             26
  STAGE IIA             6            132
  STAGE IIB             3              7
  STAGE IIC             0              1
  STAGE III             1             23
  STAGE IIIA            0             11
  STAGE IIIB            4             55
  STAGE IIIC            0             42
  STAGE IV              4             44
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  IRS4 MUTATED     0   5  20   6
  IRS4 WILD-TYPE  17  87 309  44
D1250V5, multiclass
    clus
vv   IRS4 MUTATED IRS4 WILD-TYPE
  T1            0             17
  T2            5             87
  T3           20            309
  T4            6             44
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  IRS4 MUTATED    21   6   3
  IRS4 WILD-TYPE 266 107  84
D1250V6, multiclass
    clus
vv   IRS4 MUTATED IRS4 WILD-TYPE
  N0           21            266
  N1            6            107
  N2            3             84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1250V7, binary
                cls
clus               0   1
  IRS4 MUTATED    22   4
  IRS4 WILD-TYPE 353  61
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRS4 MUTATED     22    4
  IRS4 WILD-TYPE  353   61
   clus
vv  IRS4 MUTATED IRS4 WILD-TYPE
  0           22            353
  1            4             61
[1] 2 2
[1] FALSE
D1250V8, binary
                cls
clus               0   1
  IRS4 MUTATED    16  15
  IRS4 WILD-TYPE 209 249
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRS4 MUTATED     16   15
  IRS4 WILD-TYPE  209  249
        clus
vv       IRS4 MUTATED IRS4 WILD-TYPE
  FEMALE           16            209
  MALE             15            249
[1] 2 2
[1] FALSE
D1250V9, binary
                cls
clus               0   1
  IRS4 MUTATED    20   1
  IRS4 WILD-TYPE 330  21
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRS4 MUTATED     20    1
  IRS4 WILD-TYPE  330   21
     clus
vv    IRS4 MUTATED IRS4 WILD-TYPE
  NO            20            330
  YES            1             21
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  IRS4 MUTATED                     25                             2
  IRS4 WILD-TYPE                  290                            45
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  IRS4 MUTATED                       4                              0
  IRS4 WILD-TYPE                   102                             10
D1250V10, multiclass
                                clus
vv                               IRS4 MUTATED IRS4 WILD-TYPE
  COLON ADENOCARCINOMA                     25            290
  COLON MUCINOUS ADENOCARCINOMA             2             45
  RECTAL ADENOCARCINOMA                     4            102
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  IRS4 MUTATED    20   0   3   1
  IRS4 WILD-TYPE 325   4  28  24
D1250V11, multiclass
    clus
vv   IRS4 MUTATED IRS4 WILD-TYPE
  R0           20            325
  R1            0              4
  R2            3             28
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1250V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  IRS4 MUTATED                                  0     1
  IRS4 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  IRS4 MUTATED                           2    15
  IRS4 WILD-TYPE                        20   211
D1250V13, multiclass
                                  clus
vv                                 IRS4 MUTATED IRS4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   2             20
  WHITE                                      15            211
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1251) Variable = CEL MUTATION ANALYSIS
D1251V1, survival
               sevent
clus2             0   1
  CEL MUTATED     7   2
  CEL WILD-TYPE 371  91
  CEL MUTATED CEL WILD-TYPE 
            9           462 
  CEL MUTATED CEL WILD-TYPE 
            2            91 
$`CEL MUTATED`
TCGA-A6-6781 TCGA-AA-3713 TCGA-AA-3980 TCGA-AZ-6598 TCGA-CM-6171 TCGA-F4-6570 
       19.66        19.04        27.02        49.41        14.04         6.18 
TCGA-G4-6309 TCGA-G4-6588 TCGA-G4-6628 
       85.48        26.17        79.69 

$`CEL WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        88.21         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       13.02        15.02        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
        8.61        31.96        35.74        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       55.04        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       35.80        91.79        46.75        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  CEL MUTATED CEL WILD-TYPE 
         6.18          0.00 
  CEL MUTATED CEL WILD-TYPE 
        85.48        148.01 
  CEL MUTATED CEL WILD-TYPE 
       26.170        20.155 
[1] "6.2 - 85.5 (26.2)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.2"
D1251V2, continuous
D1251V3, binary
               cls
clus              0   1
  CEL MUTATED     9   0
  CEL WILD-TYPE 357 119
[1] "tbl2"
               cls
clus            [,1] [,2]
  CEL MUTATED      9    0
  CEL WILD-TYPE  357  119
        clus
vv       CEL MUTATED CEL WILD-TYPE
  COLON            9           357
  RECTUM           0           119
[1] 2 2
[1] FALSE
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CEL MUTATED         3        0        1         2         0         0
  CEL WILD-TYPE      88        1       31       136        10         1
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CEL MUTATED           0          0          1          1        1         0
  CEL WILD-TYPE        24         11         58         41       47        18
               vv
clus            STAGE IVB
  CEL MUTATED           0
  CEL WILD-TYPE         1
D1251V4, multiclass
            clus
vv           CEL MUTATED CEL WILD-TYPE
  STAGE I              3            88
  STAGE IA             0             1
  STAGE II             1            31
  STAGE IIA            2           136
  STAGE IIB            0            10
  STAGE IIC            0             1
  STAGE III            0            24
  STAGE IIIA           0            11
  STAGE IIIB           1            58
  STAGE IIIC           1            41
  STAGE IV             1            47
  STAGE IVA            0            18
  STAGE IVB            0             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  CEL MUTATED     0   3   5   1
  CEL WILD-TYPE  17  89 324  49
D1251V5, multiclass
    clus
vv   CEL MUTATED CEL WILD-TYPE
  T1           0            17
  T2           3            89
  T3           5           324
  T4           1            49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2
  CEL MUTATED     7   2   0
  CEL WILD-TYPE 280 111  87
D1251V6, multiclass
    clus
vv   CEL MUTATED CEL WILD-TYPE
  N0           7           280
  N1           2           111
  N2           0            87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1251V7, binary
               cls
clus              0   1
  CEL MUTATED     6   1
  CEL WILD-TYPE 369  64
[1] "tbl2"
               cls
clus            [,1] [,2]
  CEL MUTATED      6    1
  CEL WILD-TYPE  369   64
   clus
vv  CEL MUTATED CEL WILD-TYPE
  0           6           369
  1           1            64
[1] 2 2
[1] FALSE
D1251V8, binary
               cls
clus              0   1
  CEL MUTATED     6   3
  CEL WILD-TYPE 219 261
[1] "tbl2"
               cls
clus            [,1] [,2]
  CEL MUTATED      6    3
  CEL WILD-TYPE  219  261
        clus
vv       CEL MUTATED CEL WILD-TYPE
  FEMALE           6           219
  MALE             3           261
[1] 2 2
[1] FALSE
D1251V9, binary
               cls
clus              0   1
  CEL MUTATED     8   1
  CEL WILD-TYPE 342  21
[1] "tbl2"
               cls
clus            [,1] [,2]
  CEL MUTATED      8    1
  CEL WILD-TYPE  342   21
     clus
vv    CEL MUTATED CEL WILD-TYPE
  NO            8           342
  YES           1            21
[1] 2 2
[1] FALSE
               vv
clus            COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CEL MUTATED                      8                             1
  CEL WILD-TYPE                  307                            46
               vv
clus            RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CEL MUTATED                       0                              0
  CEL WILD-TYPE                   106                             10
D1251V10, multiclass
                                clus
vv                               CEL MUTATED CEL WILD-TYPE
  COLON ADENOCARCINOMA                     8           307
  COLON MUCINOUS ADENOCARCINOMA            1            46
  RECTAL ADENOCARCINOMA                    0           106
  RECTAL MUCINOUS ADENOCARCINOMA           0            10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             R0  R1  R2  RX
  CEL MUTATED     6   0   1   0
  CEL WILD-TYPE 339   4  30  25
D1251V11, multiclass
    clus
vv   CEL MUTATED CEL WILD-TYPE
  R0           6           339
  R1           0             4
  R2           1            30
  RX           0            25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1251V12, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CEL MUTATED                                  0     0
  CEL WILD-TYPE                                1    11
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  CEL MUTATED                           1     6
  CEL WILD-TYPE                        21   220
D1251V13, multiclass
                                  clus
vv                                 CEL MUTATED CEL WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      0            11
  BLACK OR AFRICAN AMERICAN                  1            21
  WHITE                                      6           220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1252) Variable = ZHX2 MUTATION ANALYSIS
D1252V1, survival
                sevent
clus2              0   1
  ZHX2 MUTATED    17   1
  ZHX2 WILD-TYPE 361  92
  ZHX2 MUTATED ZHX2 WILD-TYPE 
            18            453 
  ZHX2 MUTATED ZHX2 WILD-TYPE 
             1             92 
$`ZHX2 MUTATED`
TCGA-A6-2672 TCGA-A6-5661 TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3663 TCGA-AA-3976 
       46.65        33.53         3.02        63.98         6.97        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-A00A TCGA-AA-A00R TCGA-AA-A010 TCGA-AU-6004 
       25.02        24.00        38.04         0.99        34.98        27.09 
TCGA-CA-6717 TCGA-CM-6162 TCGA-DM-A1HB TCGA-AG-3605 TCGA-AG-3883 TCGA-EI-6507 
       12.76        12.00       135.65         0.99         1.02        19.96 

$`ZHX2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       31.63        30.44        29.19        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 
       19.66        20.28         7.04         1.02        35.01         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       61.02        78.08         6.05        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3980 
       21.99        16.08        50.99        13.05        34.06        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00D 
       27.02        19.07         7.96        27.02        13.94        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       27.02        42.02        17.03        14.99        21.99         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07        12.20        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       17.03        15.02         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6510 
       51.48        32.61         0.49        20.55        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  ZHX2 MUTATED ZHX2 WILD-TYPE 
          0.99           0.00 
  ZHX2 MUTATED ZHX2 WILD-TYPE 
        135.65         148.01 
  ZHX2 MUTATED ZHX2 WILD-TYPE 
         24.51          20.12 
[1] "1.0 - 135.7 (24.5)" "0.0 - 148.0 (20.1)"
[1] "hr=" "3.7"
D1252V2, continuous
D1252V3, binary
                cls
clus               0   1
  ZHX2 MUTATED    17   3
  ZHX2 WILD-TYPE 349 116
[1] "tbl2"
                cls
clus             [,1] [,2]
  ZHX2 MUTATED     17    3
  ZHX2 WILD-TYPE  349  116
        clus
vv       ZHX2 MUTATED ZHX2 WILD-TYPE
  COLON            17            349
  RECTUM            3            116
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZHX2 MUTATED         3        0        4         5         2         0
  ZHX2 WILD-TYPE      88        1       28       133         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ZHX2 MUTATED           0          1          3          0        1         0
  ZHX2 WILD-TYPE        24         10         56         42       47        18
                vv
clus             STAGE IVB
  ZHX2 MUTATED           0
  ZHX2 WILD-TYPE         1
D1252V4, multiclass
            clus
vv           ZHX2 MUTATED ZHX2 WILD-TYPE
  STAGE I               3             88
  STAGE IA              0              1
  STAGE II              4             28
  STAGE IIA             5            133
  STAGE IIB             2              8
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            1             10
  STAGE IIIB            3             56
  STAGE IIIC            0             42
  STAGE IV              1             47
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  ZHX2 MUTATED     0   5  12   3
  ZHX2 WILD-TYPE  17  87 317  47
D1252V5, multiclass
    clus
vv   ZHX2 MUTATED ZHX2 WILD-TYPE
  T1            0             17
  T2            5             87
  T3           12            317
  T4            3             47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  ZHX2 MUTATED    15   5   0
  ZHX2 WILD-TYPE 272 108  87
D1252V6, multiclass
    clus
vv   ZHX2 MUTATED ZHX2 WILD-TYPE
  N0           15            272
  N1            5            108
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1252V7, binary
                cls
clus               0   1
  ZHX2 MUTATED    17   1
  ZHX2 WILD-TYPE 358  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  ZHX2 MUTATED     17    1
  ZHX2 WILD-TYPE  358   64
   clus
vv  ZHX2 MUTATED ZHX2 WILD-TYPE
  0           17            358
  1            1             64
[1] 2 2
[1] FALSE
D1252V8, binary
                cls
clus               0   1
  ZHX2 MUTATED    10  10
  ZHX2 WILD-TYPE 215 254
[1] "tbl2"
                cls
clus             [,1] [,2]
  ZHX2 MUTATED     10   10
  ZHX2 WILD-TYPE  215  254
        clus
vv       ZHX2 MUTATED ZHX2 WILD-TYPE
  FEMALE           10            215
  MALE             10            254
[1] 2 2
[1] FALSE
D1252V9, binary
                cls
clus               0   1
  ZHX2 MUTATED    13   0
  ZHX2 WILD-TYPE 337  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  ZHX2 MUTATED     13    0
  ZHX2 WILD-TYPE  337   22
     clus
vv    ZHX2 MUTATED ZHX2 WILD-TYPE
  NO            13            337
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ZHX2 MUTATED                     14                             2
  ZHX2 WILD-TYPE                  301                            45
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ZHX2 MUTATED                       3                              0
  ZHX2 WILD-TYPE                   103                             10
D1252V10, multiclass
                                clus
vv                               ZHX2 MUTATED ZHX2 WILD-TYPE
  COLON ADENOCARCINOMA                     14            301
  COLON MUCINOUS ADENOCARCINOMA             2             45
  RECTAL ADENOCARCINOMA                     3            103
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  ZHX2 MUTATED    15   0   1   2
  ZHX2 WILD-TYPE 330   4  30  23
D1252V11, multiclass
    clus
vv   ZHX2 MUTATED ZHX2 WILD-TYPE
  R0           15            330
  R1            0              4
  R2            1             30
  RX            2             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1252V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZHX2 MUTATED                                  0     1
  ZHX2 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  ZHX2 MUTATED                           1     6
  ZHX2 WILD-TYPE                        21   220
D1252V13, multiclass
                                  clus
vv                                 ZHX2 MUTATED ZHX2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                       6            220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1253) Variable = HEATR3 MUTATION ANALYSIS
D1253V1, survival
                  sevent
clus2                0   1
  HEATR3 MUTATED     6   3
  HEATR3 WILD-TYPE 372  90
  HEATR3 MUTATED HEATR3 WILD-TYPE 
               9              462 
  HEATR3 MUTATED HEATR3 WILD-TYPE 
               3               90 
$`HEATR3 MUTATED`
TCGA-AA-3663 TCGA-AA-3975 TCGA-AA-A00N TCGA-AZ-4315 TCGA-AZ-6598 TCGA-CA-6717 
        6.97        34.06         4.01        58.39        49.41        12.76 
TCGA-CM-4747 TCGA-AG-A002 TCGA-F5-6464 
       25.02        20.98         9.96 

$`HEATR3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.05        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        88.21         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07        12.20        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       20.02        37.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6465 TCGA-F5-6571 
       20.55        19.96        20.91        18.28        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  HEATR3 MUTATED HEATR3 WILD-TYPE 
            4.01             0.00 
  HEATR3 MUTATED HEATR3 WILD-TYPE 
           58.39           148.01 
  HEATR3 MUTATED HEATR3 WILD-TYPE 
          20.980           20.155 
[1] "4.0 - 58.4 (21.0)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.7"
D1253V2, continuous
D1253V3, binary
                  cls
clus                 0   1
  HEATR3 MUTATED     8   2
  HEATR3 WILD-TYPE 358 117
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HEATR3 MUTATED      8    2
  HEATR3 WILD-TYPE  358  117
        clus
vv       HEATR3 MUTATED HEATR3 WILD-TYPE
  COLON               8              358
  RECTUM              2              117
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  HEATR3 MUTATED         2        0        2         2         2         0
  HEATR3 WILD-TYPE      89        1       30       136         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HEATR3 MUTATED           0          0          0          1        0
  HEATR3 WILD-TYPE        24         11         59         41       48
                  vv
clus               STAGE IVA STAGE IVB
  HEATR3 MUTATED           1         0
  HEATR3 WILD-TYPE        17         1
D1253V4, multiclass
            clus
vv           HEATR3 MUTATED HEATR3 WILD-TYPE
  STAGE I                 2               89
  STAGE IA                0                1
  STAGE II                2               30
  STAGE IIA               2              136
  STAGE IIB               2                8
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              0               59
  STAGE IIIC              1               41
  STAGE IV                0               48
  STAGE IVA               1               17
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  HEATR3 MUTATED     0   2   4   4
  HEATR3 WILD-TYPE  17  90 325  46
D1253V5, multiclass
    clus
vv   HEATR3 MUTATED HEATR3 WILD-TYPE
  T1              0               17
  T2              2               90
  T3              4              325
  T4              4               46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  HEATR3 MUTATED     8   1   1
  HEATR3 WILD-TYPE 279 112  86
D1253V6, multiclass
    clus
vv   HEATR3 MUTATED HEATR3 WILD-TYPE
  N0              8              279
  N1              1              112
  N2              1               86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1253V7, binary
                  cls
clus                 0   1
  HEATR3 MUTATED     7   1
  HEATR3 WILD-TYPE 368  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HEATR3 MUTATED      7    1
  HEATR3 WILD-TYPE  368   64
   clus
vv  HEATR3 MUTATED HEATR3 WILD-TYPE
  0              7              368
  1              1               64
[1] 2 2
[1] FALSE
D1253V8, binary
                  cls
clus                 0   1
  HEATR3 MUTATED     3   7
  HEATR3 WILD-TYPE 222 257
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HEATR3 MUTATED      3    7
  HEATR3 WILD-TYPE  222  257
        clus
vv       HEATR3 MUTATED HEATR3 WILD-TYPE
  FEMALE              3              222
  MALE                7              257
[1] 2 2
[1] FALSE
D1253V9, binary
                  cls
clus                 0   1
  HEATR3 MUTATED     8   0
  HEATR3 WILD-TYPE 342  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HEATR3 MUTATED      8    0
  HEATR3 WILD-TYPE  342   22
     clus
vv    HEATR3 MUTATED HEATR3 WILD-TYPE
  NO               8              342
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  HEATR3 MUTATED                      6                             2
  HEATR3 WILD-TYPE                  309                            45
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  HEATR3 MUTATED                       2                              0
  HEATR3 WILD-TYPE                   104                             10
D1253V10, multiclass
                                clus
vv                               HEATR3 MUTATED HEATR3 WILD-TYPE
  COLON ADENOCARCINOMA                        6              309
  COLON MUCINOUS ADENOCARCINOMA               2               45
  RECTAL ADENOCARCINOMA                       2              104
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  HEATR3 MUTATED     7   0   0   2
  HEATR3 WILD-TYPE 338   4  31  23
D1253V11, multiclass
    clus
vv   HEATR3 MUTATED HEATR3 WILD-TYPE
  R0              7              338
  R1              0                4
  R2              0               31
  RX              2               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1253V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HEATR3 MUTATED                                  0     1
  HEATR3 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  HEATR3 MUTATED                           0     5
  HEATR3 WILD-TYPE                        22   221
D1253V13, multiclass
                                  clus
vv                                 HEATR3 MUTATED HEATR3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         5              221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1254) Variable = STAT3 MUTATION ANALYSIS
D1254V1, survival
                 sevent
clus2               0   1
  STAT3 MUTATED     8   1
  STAT3 WILD-TYPE 370  92
  STAT3 MUTATED STAT3 WILD-TYPE 
              9             462 
  STAT3 MUTATED STAT3 WILD-TYPE 
              1              92 
$`STAT3 MUTATED`
TCGA-AA-3510 TCGA-AA-A010 TCGA-AD-5900 TCGA-AU-3779 TCGA-D5-6532 TCGA-D5-6536 
       63.98        34.98         0.07        14.50        18.25        17.85 
TCGA-DM-A1HA TCGA-F4-6570 TCGA-G4-6628 
      131.51         6.18        79.69 

$`STAT3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       39.98        18.05        40.96        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
        0.20        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6533 
       12.26        19.59        56.09        55.92        20.19         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       43.27        15.12         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
       44.32       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       35.74        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       26.17        91.79        46.75        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  STAT3 MUTATED STAT3 WILD-TYPE 
           0.07            0.00 
  STAT3 MUTATED STAT3 WILD-TYPE 
         131.51          148.01 
  STAT3 MUTATED STAT3 WILD-TYPE 
         18.250          20.235 
[1] "0.1 - 131.5 (18.2)" "0.0 - 148.0 (20.2)"
[1] "hr=" "2.6"
D1254V2, continuous
D1254V3, binary
                 cls
clus                0   1
  STAT3 MUTATED     9   0
  STAT3 WILD-TYPE 357 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STAT3 MUTATED      9    0
  STAT3 WILD-TYPE  357  119
        clus
vv       STAT3 MUTATED STAT3 WILD-TYPE
  COLON              9             357
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  STAT3 MUTATED         2        0        1         4         1         0
  STAT3 WILD-TYPE      89        1       31       134         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  STAT3 MUTATED           0          0          0          1        0         0
  STAT3 WILD-TYPE        24         11         59         41       48        18
                 vv
clus              STAGE IVB
  STAT3 MUTATED           0
  STAT3 WILD-TYPE         1
D1254V4, multiclass
            clus
vv           STAT3 MUTATED STAT3 WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              4             134
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             1              41
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  STAT3 MUTATED     0   2   6   1
  STAT3 WILD-TYPE  17  90 323  49
D1254V5, multiclass
    clus
vv   STAT3 MUTATED STAT3 WILD-TYPE
  T1             0              17
  T2             2              90
  T3             6             323
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  STAT3 MUTATED     8   0   1
  STAT3 WILD-TYPE 279 113  86
D1254V6, multiclass
    clus
vv   STAT3 MUTATED STAT3 WILD-TYPE
  N0             8             279
  N1             0             113
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1254V7, binary
                 cls
clus                0   1
  STAT3 MUTATED     8   0
  STAT3 WILD-TYPE 367  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STAT3 MUTATED      8    0
  STAT3 WILD-TYPE  367   65
   clus
vv  STAT3 MUTATED STAT3 WILD-TYPE
  0             8             367
  1             0              65
[1] 2 2
[1] FALSE
D1254V8, binary
                 cls
clus                0   1
  STAT3 MUTATED     3   6
  STAT3 WILD-TYPE 222 258
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STAT3 MUTATED      3    6
  STAT3 WILD-TYPE  222  258
        clus
vv       STAT3 MUTATED STAT3 WILD-TYPE
  FEMALE             3             222
  MALE               6             258
[1] 2 2
[1] FALSE
D1254V9, binary
                 cls
clus                0   1
  STAT3 MUTATED     7   0
  STAT3 WILD-TYPE 343  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STAT3 MUTATED      7    0
  STAT3 WILD-TYPE  343   22
     clus
vv    STAT3 MUTATED STAT3 WILD-TYPE
  NO              7             343
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  STAT3 MUTATED                      8                             1
  STAT3 WILD-TYPE                  307                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  STAT3 MUTATED                       0                              0
  STAT3 WILD-TYPE                   106                             10
D1254V10, multiclass
                                clus
vv                               STAT3 MUTATED STAT3 WILD-TYPE
  COLON ADENOCARCINOMA                       8             307
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  STAT3 MUTATED     8   0   0   0
  STAT3 WILD-TYPE 337   4  31  25
D1254V11, multiclass
    clus
vv   STAT3 MUTATED STAT3 WILD-TYPE
  R0             8             337
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1254V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  STAT3 MUTATED                                  0     0
  STAT3 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  STAT3 MUTATED                           0     7
  STAT3 WILD-TYPE                        22   219
D1254V13, multiclass
                                  clus
vv                                 STAT3 MUTATED STAT3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        7             219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1255) Variable = STK35 MUTATION ANALYSIS
D1255V1, survival
                 sevent
clus2               0   1
  STK35 MUTATED     5   1
  STK35 WILD-TYPE 373  92
  STK35 MUTATED STK35 WILD-TYPE 
              6             465 
  STK35 MUTATED STK35 WILD-TYPE 
              1              92 
$`STK35 MUTATED`
TCGA-A6-6651 TCGA-AA-3977 TCGA-AU-6004 TCGA-AY-6386 TCGA-F4-6570 TCGA-G4-6588 
       21.76        25.02        27.09        17.82         6.18        26.17 

$`STK35 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.08        25.18        24.16        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       10.88         0.20        14.50        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 
       98.24         8.61        31.96        35.74        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       22.09        13.78        35.80        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  STK35 MUTATED STK35 WILD-TYPE 
           6.18            0.00 
  STK35 MUTATED STK35 WILD-TYPE 
          27.09          148.01 
  STK35 MUTATED STK35 WILD-TYPE 
          23.39           20.12 
[1] "6.2 - 27.1 (23.4)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.1"
D1255V2, continuous
D1255V3, binary
                 cls
clus                0   1
  STK35 MUTATED     6   0
  STK35 WILD-TYPE 360 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STK35 MUTATED      6    0
  STK35 WILD-TYPE  360  119
        clus
vv       STK35 MUTATED STK35 WILD-TYPE
  COLON              6             360
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  STK35 MUTATED         1        0        0         2         0         0
  STK35 WILD-TYPE      90        1       32       136        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  STK35 MUTATED           0          0          2          0        0         0
  STK35 WILD-TYPE        24         11         57         42       48        18
                 vv
clus              STAGE IVB
  STK35 MUTATED           0
  STK35 WILD-TYPE         1
D1255V4, multiclass
            clus
vv           STK35 MUTATED STK35 WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              2             136
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             2              57
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  STK35 MUTATED     0   2   4   0
  STK35 WILD-TYPE  17  90 325  50
D1255V5, multiclass
    clus
vv   STK35 MUTATED STK35 WILD-TYPE
  T1             0              17
  T2             2              90
  T3             4             325
  T4             0              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  STK35 MUTATED     4   2   0
  STK35 WILD-TYPE 283 111  87
D1255V6, multiclass
    clus
vv   STK35 MUTATED STK35 WILD-TYPE
  N0             4             283
  N1             2             111
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1255V7, binary
                 cls
clus                0   1
  STK35 MUTATED     4   0
  STK35 WILD-TYPE 371  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STK35 MUTATED      4    0
  STK35 WILD-TYPE  371   65
   clus
vv  STK35 MUTATED STK35 WILD-TYPE
  0             4             371
  1             0              65
[1] 2 2
[1] FALSE
D1255V8, binary
                 cls
clus                0   1
  STK35 MUTATED     5   1
  STK35 WILD-TYPE 220 263
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STK35 MUTATED      5    1
  STK35 WILD-TYPE  220  263
        clus
vv       STK35 MUTATED STK35 WILD-TYPE
  FEMALE             5             220
  MALE               1             263
[1] 2 2
[1] FALSE
D1255V9, binary
                 cls
clus                0   1
  STK35 MUTATED     5   0
  STK35 WILD-TYPE 345  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STK35 MUTATED      5    0
  STK35 WILD-TYPE  345   22
     clus
vv    STK35 MUTATED STK35 WILD-TYPE
  NO              5             345
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  STK35 MUTATED                      6                             0
  STK35 WILD-TYPE                  309                            47
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  STK35 MUTATED                       0                              0
  STK35 WILD-TYPE                   106                             10
D1255V10, multiclass
                                clus
vv                               STK35 MUTATED STK35 WILD-TYPE
  COLON ADENOCARCINOMA                       6             309
  COLON MUCINOUS ADENOCARCINOMA              0              47
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  STK35 MUTATED     4   0   0   0
  STK35 WILD-TYPE 341   4  31  25
D1255V11, multiclass
    clus
vv   STK35 MUTATED STK35 WILD-TYPE
  R0             4             341
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1255V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  STK35 MUTATED                                  0     0
  STK35 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  STK35 MUTATED                           1     4
  STK35 WILD-TYPE                        21   222
D1255V13, multiclass
                                  clus
vv                                 STK35 MUTATED STK35 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        4             222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1256) Variable = ASB11 MUTATION ANALYSIS
D1256V1, survival
                 sevent
clus2               0   1
  ASB11 MUTATED     7   1
  ASB11 WILD-TYPE 371  92
  ASB11 MUTATED ASB11 WILD-TYPE 
              8             463 
  ASB11 MUTATED ASB11 WILD-TYPE 
              1              92 
$`ASB11 MUTATED`
TCGA-A6-5665 TCGA-AD-6901 TCGA-AZ-4315 TCGA-CA-6717 TCGA-CK-5913 TCGA-F4-6856 
       22.06        22.42        58.39        12.76        51.32        35.31 
TCGA-G4-6588 TCGA-G4-6628 
       26.17        79.69 

$`ASB11 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6963 
       15.52        56.55         0.79         0.72         5.79        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       33.01        21.44        17.82         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       49.08         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       47.41       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 
       13.78        35.80        91.79        46.75        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  ASB11 MUTATED ASB11 WILD-TYPE 
          12.76            0.00 
  ASB11 MUTATED ASB11 WILD-TYPE 
          79.69          148.01 
  ASB11 MUTATED ASB11 WILD-TYPE 
          30.74           20.02 
[1] "12.8 - 79.7 (30.7)" "0.0 - 148.0 (20.0)"
[1] "hr=" "2.4"
D1256V2, continuous
D1256V3, binary
                 cls
clus                0   1
  ASB11 MUTATED     8   0
  ASB11 WILD-TYPE 358 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASB11 MUTATED      8    0
  ASB11 WILD-TYPE  358  119
        clus
vv       ASB11 MUTATED ASB11 WILD-TYPE
  COLON              8             358
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ASB11 MUTATED         2        0        0         5         0         0
  ASB11 WILD-TYPE      89        1       32       133        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ASB11 MUTATED           0          0          0          0        0         0
  ASB11 WILD-TYPE        24         11         59         42       48        18
                 vv
clus              STAGE IVB
  ASB11 MUTATED           0
  ASB11 WILD-TYPE         1
D1256V4, multiclass
            clus
vv           ASB11 MUTATED ASB11 WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              5             133
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ASB11 MUTATED     0   2   6   0
  ASB11 WILD-TYPE  17  90 323  50
D1256V5, multiclass
    clus
vv   ASB11 MUTATED ASB11 WILD-TYPE
  T1             0              17
  T2             2              90
  T3             6             323
  T4             0              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  ASB11 MUTATED     8   0   0
  ASB11 WILD-TYPE 279 113  87
D1256V6, multiclass
    clus
vv   ASB11 MUTATED ASB11 WILD-TYPE
  N0             8             279
  N1             0             113
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1256V7, binary
                 cls
clus                0   1
  ASB11 MUTATED     6   0
  ASB11 WILD-TYPE 369  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASB11 MUTATED      6    0
  ASB11 WILD-TYPE  369   65
   clus
vv  ASB11 MUTATED ASB11 WILD-TYPE
  0             6             369
  1             0              65
[1] 2 2
[1] FALSE
D1256V8, binary
                 cls
clus                0   1
  ASB11 MUTATED     3   5
  ASB11 WILD-TYPE 222 259
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASB11 MUTATED      3    5
  ASB11 WILD-TYPE  222  259
        clus
vv       ASB11 MUTATED ASB11 WILD-TYPE
  FEMALE             3             222
  MALE               5             259
[1] 2 2
[1] FALSE
D1256V9, binary
                 cls
clus                0   1
  ASB11 MUTATED     8   0
  ASB11 WILD-TYPE 342  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASB11 MUTATED      8    0
  ASB11 WILD-TYPE  342   22
     clus
vv    ASB11 MUTATED ASB11 WILD-TYPE
  NO              8             342
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ASB11 MUTATED                      6                             2
  ASB11 WILD-TYPE                  309                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ASB11 MUTATED                       0                              0
  ASB11 WILD-TYPE                   106                             10
D1256V10, multiclass
                                clus
vv                               ASB11 MUTATED ASB11 WILD-TYPE
  COLON ADENOCARCINOMA                       6             309
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  ASB11 MUTATED     5   0   0   2
  ASB11 WILD-TYPE 340   4  31  23
D1256V11, multiclass
    clus
vv   ASB11 MUTATED ASB11 WILD-TYPE
  R0             5             340
  R1             0               4
  R2             0              31
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1256V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ASB11 MUTATED                                  0     1
  ASB11 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ASB11 MUTATED                           0     7
  ASB11 WILD-TYPE                        22   219
D1256V13, multiclass
                                  clus
vv                                 ASB11 MUTATED ASB11 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        7             219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1257) Variable = C7ORF50 MUTATION ANALYSIS
D1257V1, survival
                   sevent
clus2                 0   1
  C7ORF50 MUTATED     4   1
  C7ORF50 WILD-TYPE 374  92
  C7ORF50 MUTATED C7ORF50 WILD-TYPE 
                5               466 
  C7ORF50 MUTATED C7ORF50 WILD-TYPE 
                1                92 
$`C7ORF50 MUTATED`
TCGA-A6-5665 TCGA-AA-3667 TCGA-AZ-6598 TCGA-CM-6171 TCGA-DM-A1HB 
       22.06        14.01        49.41        14.04       135.65 

$`C7ORF50 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
        6.97        54.02         2.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 
      106.75        22.36        62.79        88.21         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       12.99        13.02        15.02        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 
      140.38         7.50        44.32       131.51       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  C7ORF50 MUTATED C7ORF50 WILD-TYPE 
            14.01              0.00 
  C7ORF50 MUTATED C7ORF50 WILD-TYPE 
           135.65            148.01 
  C7ORF50 MUTATED C7ORF50 WILD-TYPE 
           22.060            20.155 
[1] "14.0 - 135.7 (22.1)" "0.0 - 148.0 (20.2)" 
[1] "hr=" "1.6"
D1257V2, continuous
D1257V3, binary
                   cls
clus                  0   1
  C7ORF50 MUTATED     5   0
  C7ORF50 WILD-TYPE 361 119
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C7ORF50 MUTATED      5    0
  C7ORF50 WILD-TYPE  361  119
        clus
vv       C7ORF50 MUTATED C7ORF50 WILD-TYPE
  COLON                5               361
  RECTUM               0               119
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  C7ORF50 MUTATED         2        0        1         1         0         0
  C7ORF50 WILD-TYPE      89        1       31       137        10         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C7ORF50 MUTATED           0          0          1          0        0
  C7ORF50 WILD-TYPE        24         11         58         42       48
                   vv
clus                STAGE IVA STAGE IVB
  C7ORF50 MUTATED           0         0
  C7ORF50 WILD-TYPE        18         1
D1257V4, multiclass
            clus
vv           C7ORF50 MUTATED C7ORF50 WILD-TYPE
  STAGE I                  2                89
  STAGE IA                 0                 1
  STAGE II                 1                31
  STAGE IIA                1               137
  STAGE IIB                0                10
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               0                11
  STAGE IIIB               1                58
  STAGE IIIC               0                42
  STAGE IV                 0                48
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  C7ORF50 MUTATED     0   2   3   0
  C7ORF50 WILD-TYPE  17  90 326  50
D1257V5, multiclass
    clus
vv   C7ORF50 MUTATED C7ORF50 WILD-TYPE
  T1               0                17
  T2               2                90
  T3               3               326
  T4               0                50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  C7ORF50 MUTATED     4   1   0
  C7ORF50 WILD-TYPE 283 112  87
D1257V6, multiclass
    clus
vv   C7ORF50 MUTATED C7ORF50 WILD-TYPE
  N0               4               283
  N1               1               112
  N2               0                87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1257V7, binary
                   cls
clus                  0   1
  C7ORF50 MUTATED     4   0
  C7ORF50 WILD-TYPE 371  65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C7ORF50 MUTATED      4    0
  C7ORF50 WILD-TYPE  371   65
   clus
vv  C7ORF50 MUTATED C7ORF50 WILD-TYPE
  0               4               371
  1               0                65
[1] 2 2
[1] FALSE
D1257V8, binary
                   cls
clus                  0   1
  C7ORF50 MUTATED     4   1
  C7ORF50 WILD-TYPE 221 263
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C7ORF50 MUTATED      4    1
  C7ORF50 WILD-TYPE  221  263
        clus
vv       C7ORF50 MUTATED C7ORF50 WILD-TYPE
  FEMALE               4               221
  MALE                 1               263
[1] 2 2
[1] FALSE
D1257V9, binary
                   cls
clus                  0   1
  C7ORF50 MUTATED     4   0
  C7ORF50 WILD-TYPE 346  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C7ORF50 MUTATED      4    0
  C7ORF50 WILD-TYPE  346   22
     clus
vv    C7ORF50 MUTATED C7ORF50 WILD-TYPE
  NO                4               346
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  C7ORF50 MUTATED                      4                             0
  C7ORF50 WILD-TYPE                  311                            47
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  C7ORF50 MUTATED                       0                              0
  C7ORF50 WILD-TYPE                   106                             10
D1257V10, multiclass
                                clus
vv                               C7ORF50 MUTATED C7ORF50 WILD-TYPE
  COLON ADENOCARCINOMA                         4               311
  COLON MUCINOUS ADENOCARCINOMA                0                47
  RECTAL ADENOCARCINOMA                        0               106
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  C7ORF50 MUTATED     3   0   0   0
  C7ORF50 WILD-TYPE 342   4  31  25
D1257V11, multiclass
    clus
vv   C7ORF50 MUTATED C7ORF50 WILD-TYPE
  R0               3               342
  R1               0                 4
  R2               0                31
  RX               0                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1257V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C7ORF50 MUTATED                                  0     0
  C7ORF50 WILD-TYPE                                1    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  C7ORF50 MUTATED                           0     4
  C7ORF50 WILD-TYPE                        22   222
D1257V13, multiclass
                                  clus
vv                                 C7ORF50 MUTATED C7ORF50 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                      0                22
  WHITE                                          4               222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1258) Variable = ATP13A5 MUTATION ANALYSIS
D1258V1, survival
                   sevent
clus2                 0   1
  ATP13A5 MUTATED    24   3
  ATP13A5 WILD-TYPE 354  90
  ATP13A5 MUTATED ATP13A5 WILD-TYPE 
               27               444 
  ATP13A5 MUTATED ATP13A5 WILD-TYPE 
                3                90 
$`ATP13A5 MUTATED`
TCGA-A6-5661 TCGA-A6-6142 TCGA-A6-6651 TCGA-A6-6780 TCGA-AA-3510 TCGA-AA-3713 
       33.53        25.08        21.76        20.12        63.98        19.04 
TCGA-AA-3966 TCGA-AA-3977 TCGA-AA-A010 TCGA-AD-5900 TCGA-AD-6963 TCGA-AZ-4315 
        2.01        25.02        34.98         0.07        27.42        58.39 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4952 TCGA-CK-6747 TCGA-CM-6167 TCGA-CM-6168 
       12.76        10.06        15.62        82.95        14.99        12.99 
TCGA-DM-A1HA TCGA-F4-6570 TCGA-G4-6293 TCGA-G4-6588 TCGA-AG-3582 TCGA-AG-3587 
      131.51         6.18       133.18        26.17        36.03        46.03 
TCGA-AG-3892 TCGA-AG-A002 TCGA-AG-A01L 
       13.02        20.98        12.00 

$`ATP13A5 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6648 
       22.06        32.71        27.09        22.52         8.38        25.18 
TCGA-A6-6649 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 
       24.16        24.69        24.39        23.87        19.66        20.28 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 
        7.04         3.02         1.02        35.01         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
       13.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       36.03         8.05        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       78.08         6.05         6.97        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 
       24.00         2.01        20.98        34.03        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       18.05        40.96        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        0.72         5.79        22.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        3.29         0.07        12.20        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6748 
       85.45        49.08        51.32         9.99        21.14         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6169 TCGA-CM-6170 
        2.96        29.03        16.04        21.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
       44.32       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       35.74        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6299 
       33.67        13.25         0.53        47.41        35.31        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 
       61.91        36.00        22.09        13.78        35.80        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3593 TCGA-AG-3594 
        7.07        20.05        24.00         1.02        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       36.95        17.03        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       15.95        36.03         9.07        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  ATP13A5 MUTATED ATP13A5 WILD-TYPE 
             0.07              0.00 
  ATP13A5 MUTATED ATP13A5 WILD-TYPE 
           133.18            148.01 
  ATP13A5 MUTATED ATP13A5 WILD-TYPE 
           21.760            20.035 
[1] "0.1 - 133.2 (21.8)" "0.0 - 148.0 (20.0)"
[1] "hr=" "2.2"
D1258V2, continuous
D1258V3, binary
                   cls
clus                  0   1
  ATP13A5 MUTATED    22   5
  ATP13A5 WILD-TYPE 344 114
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ATP13A5 MUTATED     22    5
  ATP13A5 WILD-TYPE  344  114
        clus
vv       ATP13A5 MUTATED ATP13A5 WILD-TYPE
  COLON               22               344
  RECTUM               5               114
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ATP13A5 MUTATED         4        0        1        10         1         0
  ATP13A5 WILD-TYPE      87        1       31       128         9         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ATP13A5 MUTATED           1          0          2          3        2
  ATP13A5 WILD-TYPE        23         11         57         39       46
                   vv
clus                STAGE IVA STAGE IVB
  ATP13A5 MUTATED           1         0
  ATP13A5 WILD-TYPE        17         1
D1258V4, multiclass
            clus
vv           ATP13A5 MUTATED ATP13A5 WILD-TYPE
  STAGE I                  4                87
  STAGE IA                 0                 1
  STAGE II                 1                31
  STAGE IIA               10               128
  STAGE IIB                1                 9
  STAGE IIC                0                 1
  STAGE III                1                23
  STAGE IIIA               0                11
  STAGE IIIB               2                57
  STAGE IIIC               3                39
  STAGE IV                 2                46
  STAGE IVA                1                17
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  ATP13A5 MUTATED     1   4  20   2
  ATP13A5 WILD-TYPE  16  88 309  48
D1258V5, multiclass
    clus
vv   ATP13A5 MUTATED ATP13A5 WILD-TYPE
  T1               1                16
  T2               4                88
  T3              20               309
  T4               2                48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  ATP13A5 MUTATED    19   5   3
  ATP13A5 WILD-TYPE 268 108  84
D1258V6, multiclass
    clus
vv   ATP13A5 MUTATED ATP13A5 WILD-TYPE
  N0              19               268
  N1               5               108
  N2               3                84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1258V7, binary
                   cls
clus                  0   1
  ATP13A5 MUTATED    18   3
  ATP13A5 WILD-TYPE 357  62
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ATP13A5 MUTATED     18    3
  ATP13A5 WILD-TYPE  357   62
   clus
vv  ATP13A5 MUTATED ATP13A5 WILD-TYPE
  0              18               357
  1               3                62
[1] 2 2
[1] FALSE
D1258V8, binary
                   cls
clus                  0   1
  ATP13A5 MUTATED    13  14
  ATP13A5 WILD-TYPE 212 250
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ATP13A5 MUTATED     13   14
  ATP13A5 WILD-TYPE  212  250
        clus
vv       ATP13A5 MUTATED ATP13A5 WILD-TYPE
  FEMALE              13               212
  MALE                14               250
[1] 2 2
[1] FALSE
D1258V9, binary
                   cls
clus                  0   1
  ATP13A5 MUTATED    20   2
  ATP13A5 WILD-TYPE 330  20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ATP13A5 MUTATED     20    2
  ATP13A5 WILD-TYPE  330   20
     clus
vv    ATP13A5 MUTATED ATP13A5 WILD-TYPE
  NO               20               330
  YES               2                20
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ATP13A5 MUTATED                     17                             5
  ATP13A5 WILD-TYPE                  298                            42
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ATP13A5 MUTATED                       5                              0
  ATP13A5 WILD-TYPE                   101                             10
D1258V10, multiclass
                                clus
vv                               ATP13A5 MUTATED ATP13A5 WILD-TYPE
  COLON ADENOCARCINOMA                        17               298
  COLON MUCINOUS ADENOCARCINOMA                5                42
  RECTAL ADENOCARCINOMA                        5               101
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  ATP13A5 MUTATED    14   0   2   4
  ATP13A5 WILD-TYPE 331   4  29  21
D1258V11, multiclass
    clus
vv   ATP13A5 MUTATED ATP13A5 WILD-TYPE
  R0              14               331
  R1               0                 4
  R2               2                29
  RX               4                21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1258V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ATP13A5 MUTATED                                  0     2
  ATP13A5 WILD-TYPE                                1     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  ATP13A5 MUTATED                           3    12
  ATP13A5 WILD-TYPE                        19   214
D1258V13, multiclass
                                  clus
vv                                 ATP13A5 MUTATED ATP13A5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          2                 9
  BLACK OR AFRICAN AMERICAN                      3                19
  WHITE                                         12               214
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1259) Variable = ZNF43 MUTATION ANALYSIS
D1259V1, survival
                 sevent
clus2               0   1
  ZNF43 MUTATED    17   4
  ZNF43 WILD-TYPE 361  89
  ZNF43 MUTATED ZNF43 WILD-TYPE 
             21             450 
  ZNF43 MUTATED ZNF43 WILD-TYPE 
              4              89 
$`ZNF43 MUTATED`
TCGA-A6-6138 TCGA-AA-3555 TCGA-AA-3672 TCGA-AA-3815 TCGA-AA-3947 TCGA-AA-3977 
       22.52        29.95         0.92        33.04        33.01        25.02 
TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01P TCGA-AY-6197 TCGA-CA-6717 TCGA-CM-6162 
        4.01        34.98        38.07        21.44        12.76        12.00 
TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6932 TCGA-DM-A1DA TCGA-AG-3885 TCGA-AG-3894 
        1.32        15.12        11.38         7.50        17.95        14.01 
TCGA-AG-A002 TCGA-DC-6158 TCGA-DC-6682 
       20.98        10.98         4.01 

$`ZNF43 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6141 TCGA-A6-6142 
       22.09        22.06        32.71        27.09         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       13.02        24.00        17.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
       54.02         2.01        14.01        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        31.00         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07        12.20        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 
       15.02        15.02        17.03        15.02         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6536 
       56.09        55.92        20.19        18.25        43.27        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 
       11.64         4.80         1.51        12.00        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
       12.59       140.38        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3896 
        1.02        36.95        17.03        13.02        35.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
       19.99         5.95         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  ZNF43 MUTATED ZNF43 WILD-TYPE 
           0.92            0.00 
  ZNF43 MUTATED ZNF43 WILD-TYPE 
          38.07          148.01 
  ZNF43 MUTATED ZNF43 WILD-TYPE 
         15.120          20.415 
[1] "0.9 - 38.1 (15.1)"  "0.0 - 148.0 (20.4)"
[1] "hr=" "1.5"
D1259V2, continuous
D1259V3, binary
                 cls
clus                0   1
  ZNF43 MUTATED    17   5
  ZNF43 WILD-TYPE 349 114
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZNF43 MUTATED     17    5
  ZNF43 WILD-TYPE  349  114
        clus
vv       ZNF43 MUTATED ZNF43 WILD-TYPE
  COLON             17             349
  RECTUM             5             114
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZNF43 MUTATED         3        0        0         8         3         0
  ZNF43 WILD-TYPE      88        1       32       130         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ZNF43 MUTATED           2          0          4          1        0         0
  ZNF43 WILD-TYPE        22         11         55         41       48        18
                 vv
clus              STAGE IVB
  ZNF43 MUTATED           0
  ZNF43 WILD-TYPE         1
D1259V4, multiclass
            clus
vv           ZNF43 MUTATED ZNF43 WILD-TYPE
  STAGE I                3              88
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              8             130
  STAGE IIB              3               7
  STAGE IIC              0               1
  STAGE III              2              22
  STAGE IIIA             0              11
  STAGE IIIB             4              55
  STAGE IIIC             1              41
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ZNF43 MUTATED     0   4  14   4
  ZNF43 WILD-TYPE  17  88 315  46
D1259V5, multiclass
    clus
vv   ZNF43 MUTATED ZNF43 WILD-TYPE
  T1             0              17
  T2             4              88
  T3            14             315
  T4             4              46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  ZNF43 MUTATED    16   5   1
  ZNF43 WILD-TYPE 271 108  86
D1259V6, multiclass
    clus
vv   ZNF43 MUTATED ZNF43 WILD-TYPE
  N0            16             271
  N1             5             108
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1259V7, binary
                 cls
clus                0   1
  ZNF43 MUTATED    19   0
  ZNF43 WILD-TYPE 356  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZNF43 MUTATED     19    0
  ZNF43 WILD-TYPE  356   65
   clus
vv  ZNF43 MUTATED ZNF43 WILD-TYPE
  0            19             356
  1             0              65
[1] 2 2
[1] FALSE
D1259V8, binary
                 cls
clus                0   1
  ZNF43 MUTATED    12  10
  ZNF43 WILD-TYPE 213 254
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZNF43 MUTATED     12   10
  ZNF43 WILD-TYPE  213  254
        clus
vv       ZNF43 MUTATED ZNF43 WILD-TYPE
  FEMALE            12             213
  MALE              10             254
[1] 2 2
[1] FALSE
D1259V9, binary
                 cls
clus                0   1
  ZNF43 MUTATED    15   2
  ZNF43 WILD-TYPE 335  20
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZNF43 MUTATED     15    2
  ZNF43 WILD-TYPE  335   20
     clus
vv    ZNF43 MUTATED ZNF43 WILD-TYPE
  NO             15             335
  YES             2              20
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ZNF43 MUTATED                     12                             5
  ZNF43 WILD-TYPE                  303                            42
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ZNF43 MUTATED                       5                              0
  ZNF43 WILD-TYPE                   101                             10
D1259V10, multiclass
                                clus
vv                               ZNF43 MUTATED ZNF43 WILD-TYPE
  COLON ADENOCARCINOMA                      12             303
  COLON MUCINOUS ADENOCARCINOMA              5              42
  RECTAL ADENOCARCINOMA                      5             101
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  ZNF43 MUTATED    17   0   0   2
  ZNF43 WILD-TYPE 328   4  31  23
D1259V11, multiclass
    clus
vv   ZNF43 MUTATED ZNF43 WILD-TYPE
  R0            17             328
  R1             0               4
  R2             0              31
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1259V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF43 MUTATED                                  0     1
  ZNF43 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ZNF43 MUTATED                           0     9
  ZNF43 WILD-TYPE                        22   217
D1259V13, multiclass
                                  clus
vv                                 ZNF43 MUTATED ZNF43 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        9             217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1260) Variable = INPPL1 MUTATION ANALYSIS
D1260V1, survival
                  sevent
clus2                0   1
  INPPL1 MUTATED    10   4
  INPPL1 WILD-TYPE 368  89
  INPPL1 MUTATED INPPL1 WILD-TYPE 
              14              457 
  INPPL1 MUTATED INPPL1 WILD-TYPE 
               4               89 
$`INPPL1 MUTATED`
TCGA-A6-6781 TCGA-AA-3516 TCGA-AA-3529 TCGA-AA-3815 TCGA-AA-3966 TCGA-AZ-5407 
       19.66        13.02         0.00        33.04         2.01        88.21 
TCGA-AZ-6601 TCGA-CK-4952 TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-4752 TCGA-G4-6299 
      100.01        15.62        23.05        37.02        13.02        74.56 
TCGA-G4-6626 TCGA-EI-6507 
       46.75        19.96 

$`INPPL1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       49.41         6.77        12.10        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
      148.01        85.45        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-5341 
       82.95         1.91       124.27        20.02        25.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       47.41        35.31       133.18        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-AF-2687 
       13.78        35.80        26.17        91.79        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
        0.49        20.55        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  INPPL1 MUTATED INPPL1 WILD-TYPE 
               0                0 
  INPPL1 MUTATED INPPL1 WILD-TYPE 
          100.01           148.01 
  INPPL1 MUTATED INPPL1 WILD-TYPE 
          21.505           20.190 
[1] "0.0 - 100.0 (21.5)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.1"
D1260V2, continuous
D1260V3, binary
                  cls
clus                 0   1
  INPPL1 MUTATED    13   1
  INPPL1 WILD-TYPE 353 118
[1] "tbl2"
                  cls
clus               [,1] [,2]
  INPPL1 MUTATED     13    1
  INPPL1 WILD-TYPE  353  118
        clus
vv       INPPL1 MUTATED INPPL1 WILD-TYPE
  COLON              13              353
  RECTUM              1              118
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  INPPL1 MUTATED         2        0        1         6         0         0
  INPPL1 WILD-TYPE      89        1       31       132        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  INPPL1 MUTATED           1          0          0          4        0
  INPPL1 WILD-TYPE        23         11         59         38       48
                  vv
clus               STAGE IVA STAGE IVB
  INPPL1 MUTATED           0         0
  INPPL1 WILD-TYPE        18         1
D1260V4, multiclass
            clus
vv           INPPL1 MUTATED INPPL1 WILD-TYPE
  STAGE I                 2               89
  STAGE IA                0                1
  STAGE II                1               31
  STAGE IIA               6              132
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               1               23
  STAGE IIIA              0               11
  STAGE IIIB              0               59
  STAGE IIIC              4               38
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  INPPL1 MUTATED     1   1  10   2
  INPPL1 WILD-TYPE  16  91 319  48
D1260V5, multiclass
    clus
vv   INPPL1 MUTATED INPPL1 WILD-TYPE
  T1              1               16
  T2              1               91
  T3             10              319
  T4              2               48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  INPPL1 MUTATED     9   1   4
  INPPL1 WILD-TYPE 278 112  83
D1260V6, multiclass
    clus
vv   INPPL1 MUTATED INPPL1 WILD-TYPE
  N0              9              278
  N1              1              112
  N2              4               83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1260V7, binary
                  cls
clus                 0   1
  INPPL1 MUTATED    13   0
  INPPL1 WILD-TYPE 362  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  INPPL1 MUTATED     13    0
  INPPL1 WILD-TYPE  362   65
   clus
vv  INPPL1 MUTATED INPPL1 WILD-TYPE
  0             13              362
  1              0               65
[1] 2 2
[1] FALSE
D1260V8, binary
                  cls
clus                 0   1
  INPPL1 MUTATED     6   8
  INPPL1 WILD-TYPE 219 256
[1] "tbl2"
                  cls
clus               [,1] [,2]
  INPPL1 MUTATED      6    8
  INPPL1 WILD-TYPE  219  256
        clus
vv       INPPL1 MUTATED INPPL1 WILD-TYPE
  FEMALE              6              219
  MALE                8              256
[1] 2 2
[1] FALSE
D1260V9, binary
                  cls
clus                 0   1
  INPPL1 MUTATED    11   0
  INPPL1 WILD-TYPE 339  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  INPPL1 MUTATED     11    0
  INPPL1 WILD-TYPE  339   22
     clus
vv    INPPL1 MUTATED INPPL1 WILD-TYPE
  NO              11              339
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  INPPL1 MUTATED                      9                             4
  INPPL1 WILD-TYPE                  306                            43
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  INPPL1 MUTATED                       1                              0
  INPPL1 WILD-TYPE                   105                             10
D1260V10, multiclass
                                clus
vv                               INPPL1 MUTATED INPPL1 WILD-TYPE
  COLON ADENOCARCINOMA                        9              306
  COLON MUCINOUS ADENOCARCINOMA               4               43
  RECTAL ADENOCARCINOMA                       1              105
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  INPPL1 MUTATED     9   0   0   1
  INPPL1 WILD-TYPE 336   4  31  24
D1260V11, multiclass
    clus
vv   INPPL1 MUTATED INPPL1 WILD-TYPE
  R0              9              336
  R1              0                4
  R2              0               31
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1260V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  INPPL1 MUTATED                                  0     0
  INPPL1 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  INPPL1 MUTATED                           2     8
  INPPL1 WILD-TYPE                        20   218
D1260V13, multiclass
                                  clus
vv                                 INPPL1 MUTATED INPPL1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     2               20
  WHITE                                         8              218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1261) Variable = TFAP2C MUTATION ANALYSIS
D1261V1, survival
                  sevent
clus2                0   1
  TFAP2C MUTATED     8   2
  TFAP2C WILD-TYPE 370  91
  TFAP2C MUTATED TFAP2C WILD-TYPE 
              10              461 
  TFAP2C MUTATED TFAP2C WILD-TYPE 
               2               91 
$`TFAP2C MUTATED`
TCGA-AA-3663 TCGA-AA-3812 TCGA-CM-4743 TCGA-CM-6162 TCGA-D5-5539 TCGA-D5-6538 
        6.97        35.05        23.05        12.00        19.59        17.13 
TCGA-D5-6928 TCGA-D5-6929 TCGA-DM-A1D8 TCGA-DY-A1DG 
       11.64         4.80        12.59        51.48 

$`TFAP2C WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.05        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       10.06        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
       82.95         1.91       124.27        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       12.26        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6539 TCGA-D5-6540 
       43.27        15.12        17.85         4.80        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
        9.04         9.44         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       13.32       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       57.24        24.13        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  TFAP2C MUTATED TFAP2C WILD-TYPE 
             4.8              0.0 
  TFAP2C MUTATED TFAP2C WILD-TYPE 
           51.48           148.01 
  TFAP2C MUTATED TFAP2C WILD-TYPE 
           14.86            20.55 
[1] "4.8 - 51.5 (14.9)"  "0.0 - 148.0 (20.6)"
[1] "hr=" "1.3"
D1261V2, continuous
D1261V3, binary
                  cls
clus                 0   1
  TFAP2C MUTATED    10   1
  TFAP2C WILD-TYPE 356 118
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TFAP2C MUTATED     10    1
  TFAP2C WILD-TYPE  356  118
        clus
vv       TFAP2C MUTATED TFAP2C WILD-TYPE
  COLON              10              356
  RECTUM              1              118
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TFAP2C MUTATED         0        0        1         4         0         0
  TFAP2C WILD-TYPE      91        1       31       134        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TFAP2C MUTATED           0          1          2          0        1
  TFAP2C WILD-TYPE        24         10         57         42       47
                  vv
clus               STAGE IVA STAGE IVB
  TFAP2C MUTATED           1         0
  TFAP2C WILD-TYPE        17         1
D1261V4, multiclass
            clus
vv           TFAP2C MUTATED TFAP2C WILD-TYPE
  STAGE I                 0               91
  STAGE IA                0                1
  STAGE II                1               31
  STAGE IIA               4              134
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              1               10
  STAGE IIIB              2               57
  STAGE IIIC              0               42
  STAGE IV                1               47
  STAGE IVA               1               17
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  TFAP2C MUTATED     0   0  11   0
  TFAP2C WILD-TYPE  17  92 318  50
D1261V5, multiclass
    clus
vv   TFAP2C MUTATED TFAP2C WILD-TYPE
  T1              0               17
  T2              0               92
  T3             11              318
  T4              0               50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  TFAP2C MUTATED     5   5   1
  TFAP2C WILD-TYPE 282 108  86
D1261V6, multiclass
    clus
vv   TFAP2C MUTATED TFAP2C WILD-TYPE
  N0              5              282
  N1              5              108
  N2              1               86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1261V7, binary
                  cls
clus                 0   1
  TFAP2C MUTATED     8   2
  TFAP2C WILD-TYPE 367  63
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TFAP2C MUTATED      8    2
  TFAP2C WILD-TYPE  367   63
   clus
vv  TFAP2C MUTATED TFAP2C WILD-TYPE
  0              8              367
  1              2               63
[1] 2 2
[1] FALSE
D1261V8, binary
                  cls
clus                 0   1
  TFAP2C MUTATED     6   5
  TFAP2C WILD-TYPE 219 259
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TFAP2C MUTATED      6    5
  TFAP2C WILD-TYPE  219  259
        clus
vv       TFAP2C MUTATED TFAP2C WILD-TYPE
  FEMALE              6              219
  MALE                5              259
[1] 2 2
[1] FALSE
D1261V9, binary
                  cls
clus                 0   1
  TFAP2C MUTATED     7   0
  TFAP2C WILD-TYPE 343  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TFAP2C MUTATED      7    0
  TFAP2C WILD-TYPE  343   22
     clus
vv    TFAP2C MUTATED TFAP2C WILD-TYPE
  NO               7              343
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  TFAP2C MUTATED                      7                             3
  TFAP2C WILD-TYPE                  308                            44
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  TFAP2C MUTATED                       1                              0
  TFAP2C WILD-TYPE                   105                             10
D1261V10, multiclass
                                clus
vv                               TFAP2C MUTATED TFAP2C WILD-TYPE
  COLON ADENOCARCINOMA                        7              308
  COLON MUCINOUS ADENOCARCINOMA               3               44
  RECTAL ADENOCARCINOMA                       1              105
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  TFAP2C MUTATED     9   0   0   0
  TFAP2C WILD-TYPE 336   4  31  25
D1261V11, multiclass
    clus
vv   TFAP2C MUTATED TFAP2C WILD-TYPE
  R0              9              336
  R1              0                4
  R2              0               31
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1261V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TFAP2C MUTATED                                  0     0
  TFAP2C WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  TFAP2C MUTATED                           0     8
  TFAP2C WILD-TYPE                        22   218
D1261V13, multiclass
                                  clus
vv                                 TFAP2C MUTATED TFAP2C WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         8              218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1262) Variable = GAD2 MUTATION ANALYSIS
D1262V1, survival
                sevent
clus2              0   1
  GAD2 MUTATED    11   5
  GAD2 WILD-TYPE 367  88
  GAD2 MUTATED GAD2 WILD-TYPE 
            16            455 
  GAD2 MUTATED GAD2 WILD-TYPE 
             5             88 
$`GAD2 MUTATED`
TCGA-A6-2676 TCGA-A6-6141 TCGA-A6-6654 TCGA-AA-3950 TCGA-AA-3966 TCGA-AA-3989 
       42.90         8.38        23.87        24.00         2.01         7.96 
TCGA-AA-A00A TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-5862 TCGA-CM-6165 TCGA-D5-6537 
       38.04       124.27        23.05         5.03        16.04         4.80 
TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A1HB TCGA-F4-6460 
       12.00        10.26       135.65        31.96 

$`GAD2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 
       22.06        32.71        27.09        22.52        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 
       24.16        21.76        24.69        24.39        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        33.01        26.01         2.01        20.98        34.03 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3994 
       25.02        24.00        27.02        27.02        19.07        27.02 
TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       13.94        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
       21.14        82.95         1.91        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
       15.02        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
        2.96        29.03        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       43.27        15.12        17.85        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6932 
        9.04         9.44        11.64         4.80         1.51        11.38 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
      117.07        98.24         8.61        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  GAD2 MUTATED GAD2 WILD-TYPE 
          2.01           0.00 
  GAD2 MUTATED GAD2 WILD-TYPE 
        135.65         148.01 
  GAD2 MUTATED GAD2 WILD-TYPE 
        19.545         20.190 
[1] "2.0 - 135.7 (19.5)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.5"
D1262V2, continuous
D1262V3, binary
                cls
clus               0   1
  GAD2 MUTATED    16   0
  GAD2 WILD-TYPE 350 119
[1] "tbl2"
                cls
clus             [,1] [,2]
  GAD2 MUTATED     16    0
  GAD2 WILD-TYPE  350  119
        clus
vv       GAD2 MUTATED GAD2 WILD-TYPE
  COLON            16            350
  RECTUM            0            119
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GAD2 MUTATED         2        0        0         6         1         0
  GAD2 WILD-TYPE      89        1       32       132         9         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  GAD2 MUTATED           0          0          4          1        1         1
  GAD2 WILD-TYPE        24         11         55         41       47        17
                vv
clus             STAGE IVB
  GAD2 MUTATED           0
  GAD2 WILD-TYPE         1
D1262V4, multiclass
            clus
vv           GAD2 MUTATED GAD2 WILD-TYPE
  STAGE I               2             89
  STAGE IA              0              1
  STAGE II              0             32
  STAGE IIA             6            132
  STAGE IIB             1              9
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            4             55
  STAGE IIIC            1             41
  STAGE IV              1             47
  STAGE IVA             1             17
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  GAD2 MUTATED     0   2  12   2
  GAD2 WILD-TYPE  17  90 317  48
D1262V5, multiclass
    clus
vv   GAD2 MUTATED GAD2 WILD-TYPE
  T1            0             17
  T2            2             90
  T3           12            317
  T4            2             48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  GAD2 MUTATED     9   5   2
  GAD2 WILD-TYPE 278 108  85
D1262V6, multiclass
    clus
vv   GAD2 MUTATED GAD2 WILD-TYPE
  N0            9            278
  N1            5            108
  N2            2             85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1262V7, binary
                cls
clus               0   1
  GAD2 MUTATED    12   2
  GAD2 WILD-TYPE 363  63
[1] "tbl2"
                cls
clus             [,1] [,2]
  GAD2 MUTATED     12    2
  GAD2 WILD-TYPE  363   63
   clus
vv  GAD2 MUTATED GAD2 WILD-TYPE
  0           12            363
  1            2             63
[1] 2 2
[1] FALSE
D1262V8, binary
                cls
clus               0   1
  GAD2 MUTATED     7   9
  GAD2 WILD-TYPE 218 255
[1] "tbl2"
                cls
clus             [,1] [,2]
  GAD2 MUTATED      7    9
  GAD2 WILD-TYPE  218  255
        clus
vv       GAD2 MUTATED GAD2 WILD-TYPE
  FEMALE            7            218
  MALE              9            255
[1] 2 2
[1] FALSE
D1262V9, binary
                cls
clus               0   1
  GAD2 MUTATED    14   0
  GAD2 WILD-TYPE 336  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  GAD2 MUTATED     14    0
  GAD2 WILD-TYPE  336   22
     clus
vv    GAD2 MUTATED GAD2 WILD-TYPE
  NO            14            336
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  GAD2 MUTATED                     11                             4
  GAD2 WILD-TYPE                  304                            43
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  GAD2 MUTATED                       0                              0
  GAD2 WILD-TYPE                   106                             10
D1262V10, multiclass
                                clus
vv                               GAD2 MUTATED GAD2 WILD-TYPE
  COLON ADENOCARCINOMA                     11            304
  COLON MUCINOUS ADENOCARCINOMA             4             43
  RECTAL ADENOCARCINOMA                     0            106
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  GAD2 MUTATED    10   0   1   1
  GAD2 WILD-TYPE 335   4  30  24
D1262V11, multiclass
    clus
vv   GAD2 MUTATED GAD2 WILD-TYPE
  R0           10            335
  R1            0              4
  R2            1             30
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1262V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GAD2 MUTATED                                  0     0
  GAD2 WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  GAD2 MUTATED                           1    11
  GAD2 WILD-TYPE                        21   215
D1262V13, multiclass
                                  clus
vv                                 GAD2 MUTATED GAD2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                      11            215
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1263) Variable = CCDC66 MUTATION ANALYSIS
D1263V1, survival
                  sevent
clus2                0   1
  CCDC66 MUTATED     9   4
  CCDC66 WILD-TYPE 369  89
  CCDC66 MUTATED CCDC66 WILD-TYPE 
              13              458 
  CCDC66 MUTATED CCDC66 WILD-TYPE 
               4               89 
$`CCDC66 MUTATED`
TCGA-A6-5665 TCGA-AA-3877 TCGA-AA-A02K TCGA-AD-6964 TCGA-CA-6717 TCGA-CA-6718 
       22.06        31.00        14.01        10.88        12.76        10.06 
TCGA-CK-5913 TCGA-D5-6540 TCGA-F4-6570 TCGA-AG-3892 TCGA-AG-A002 TCGA-DY-A0XA 
       51.32        16.14         6.18        13.02        20.98       126.44 
TCGA-EI-6507 
       19.96 

$`CCDC66 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 
       17.03        24.03        27.02        29.98        18.05         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
       39.98         2.01         5.03         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
        0.79         0.72         5.79        22.42        27.42         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 
        3.06         3.25         3.29         0.07        12.20        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 
       17.56       148.01        85.45        15.62        49.08         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 
       17.85         4.80        17.13        12.49        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 
       19.99         1.02        17.95        36.95        17.03        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.03         5.29        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
       32.61         0.49        20.55        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  CCDC66 MUTATED CCDC66 WILD-TYPE 
            6.18             0.00 
  CCDC66 MUTATED CCDC66 WILD-TYPE 
          126.44           148.01 
  CCDC66 MUTATED CCDC66 WILD-TYPE 
          16.140           20.415 
[1] "6.2 - 126.4 (16.1)" "0.0 - 148.0 (20.4)"
[1] "hr=" "1.6"
D1263V2, continuous
D1263V3, binary
                  cls
clus                 0   1
  CCDC66 MUTATED     9   4
  CCDC66 WILD-TYPE 357 115
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC66 MUTATED      9    4
  CCDC66 WILD-TYPE  357  115
        clus
vv       CCDC66 MUTATED CCDC66 WILD-TYPE
  COLON               9              357
  RECTUM              4              115
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CCDC66 MUTATED         4        0        0         7         0         0
  CCDC66 WILD-TYPE      87        1       32       131        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CCDC66 MUTATED           0          0          0          0        1
  CCDC66 WILD-TYPE        24         11         59         42       47
                  vv
clus               STAGE IVA STAGE IVB
  CCDC66 MUTATED           0         0
  CCDC66 WILD-TYPE        18         1
D1263V4, multiclass
            clus
vv           CCDC66 MUTATED CCDC66 WILD-TYPE
  STAGE I                 4               87
  STAGE IA                0                1
  STAGE II                0               32
  STAGE IIA               7              131
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              0               59
  STAGE IIIC              0               42
  STAGE IV                1               47
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  CCDC66 MUTATED     2   2   7   2
  CCDC66 WILD-TYPE  15  90 322  48
D1263V5, multiclass
    clus
vv   CCDC66 MUTATED CCDC66 WILD-TYPE
  T1              2               15
  T2              2               90
  T3              7              322
  T4              2               48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  CCDC66 MUTATED    11   0   2
  CCDC66 WILD-TYPE 276 113  85
D1263V6, multiclass
    clus
vv   CCDC66 MUTATED CCDC66 WILD-TYPE
  N0             11              276
  N1              0              113
  N2              2               85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1263V7, binary
                  cls
clus                 0   1
  CCDC66 MUTATED    10   1
  CCDC66 WILD-TYPE 365  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC66 MUTATED     10    1
  CCDC66 WILD-TYPE  365   64
   clus
vv  CCDC66 MUTATED CCDC66 WILD-TYPE
  0             10              365
  1              1               64
[1] 2 2
[1] FALSE
D1263V8, binary
                  cls
clus                 0   1
  CCDC66 MUTATED     6   7
  CCDC66 WILD-TYPE 219 257
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC66 MUTATED      6    7
  CCDC66 WILD-TYPE  219  257
        clus
vv       CCDC66 MUTATED CCDC66 WILD-TYPE
  FEMALE              6              219
  MALE                7              257
[1] 2 2
[1] FALSE
D1263V9, binary
                  cls
clus                 0   1
  CCDC66 MUTATED    12   0
  CCDC66 WILD-TYPE 338  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC66 MUTATED     12    0
  CCDC66 WILD-TYPE  338   22
     clus
vv    CCDC66 MUTATED CCDC66 WILD-TYPE
  NO              12              338
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CCDC66 MUTATED                      6                             3
  CCDC66 WILD-TYPE                  309                            44
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CCDC66 MUTATED                       4                              0
  CCDC66 WILD-TYPE                   102                             10
D1263V10, multiclass
                                clus
vv                               CCDC66 MUTATED CCDC66 WILD-TYPE
  COLON ADENOCARCINOMA                        6              309
  COLON MUCINOUS ADENOCARCINOMA               3               44
  RECTAL ADENOCARCINOMA                       4              102
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  CCDC66 MUTATED     7   0   1   3
  CCDC66 WILD-TYPE 338   4  30  22
D1263V11, multiclass
    clus
vv   CCDC66 MUTATED CCDC66 WILD-TYPE
  R0              7              338
  R1              0                4
  R2              1               30
  RX              3               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1263V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CCDC66 MUTATED                                  0     2
  CCDC66 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  CCDC66 MUTATED                           0     7
  CCDC66 WILD-TYPE                        22   219
D1263V13, multiclass
                                  clus
vv                                 CCDC66 MUTATED CCDC66 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                9
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         7              219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1264) Variable = C10ORF119 MUTATION ANALYSIS
D1264V1, survival
                     sevent
clus2                   0   1
  C10ORF119 MUTATED     6   2
  C10ORF119 WILD-TYPE 372  91
  C10ORF119 MUTATED C10ORF119 WILD-TYPE 
                  8                 463 
  C10ORF119 MUTATED C10ORF119 WILD-TYPE 
                  2                  91 
$`C10ORF119 MUTATED`
TCGA-A6-6780 TCGA-AA-3660 TCGA-AA-A010 TCGA-AD-6964 TCGA-AZ-4315 TCGA-CM-5344 
       20.12        78.08        34.98        10.88        58.39        22.03 
TCGA-DM-A1D4 TCGA-G4-6628 
       92.75        79.69 

$`C10ORF119 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 
       19.99        13.94        19.99        61.02         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
        0.79         0.72         5.79        22.42        27.42         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 
       35.80        26.17        91.79        46.75        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  C10ORF119 MUTATED C10ORF119 WILD-TYPE 
              10.88                0.00 
  C10ORF119 MUTATED C10ORF119 WILD-TYPE 
              92.75              148.01 
  C10ORF119 MUTATED C10ORF119 WILD-TYPE 
             46.685              20.020 
[1] "10.9 - 92.8 (46.7)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.5"
D1264V2, continuous
D1264V3, binary
                     cls
clus                    0   1
  C10ORF119 MUTATED     9   0
  C10ORF119 WILD-TYPE 357 119
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  C10ORF119 MUTATED      9    0
  C10ORF119 WILD-TYPE  357  119
        clus
vv       C10ORF119 MUTATED C10ORF119 WILD-TYPE
  COLON                  9                 357
  RECTUM                 0                 119
[1] 2 2
[1] FALSE
                     vv
clus                  STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  C10ORF119 MUTATED         1        0        1         4         1         0
  C10ORF119 WILD-TYPE      90        1       31       134         9         1
                     vv
clus                  STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C10ORF119 MUTATED           0          0          1          0        0
  C10ORF119 WILD-TYPE        24         11         58         42       48
                     vv
clus                  STAGE IVA STAGE IVB
  C10ORF119 MUTATED           0         0
  C10ORF119 WILD-TYPE        18         1
D1264V4, multiclass
            clus
vv           C10ORF119 MUTATED C10ORF119 WILD-TYPE
  STAGE I                    1                  90
  STAGE IA                   0                   1
  STAGE II                   1                  31
  STAGE IIA                  4                 134
  STAGE IIB                  1                   9
  STAGE IIC                  0                   1
  STAGE III                  0                  24
  STAGE IIIA                 0                  11
  STAGE IIIB                 1                  58
  STAGE IIIC                 0                  42
  STAGE IV                   0                  48
  STAGE IVA                  0                  18
  STAGE IVB                  0                   1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                   T1  T2  T3  T4
  C10ORF119 MUTATED     0   1   6   2
  C10ORF119 WILD-TYPE  17  91 323  48
D1264V5, multiclass
    clus
vv   C10ORF119 MUTATED C10ORF119 WILD-TYPE
  T1                 0                  17
  T2                 1                  91
  T3                 6                 323
  T4                 2                  48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                   N0  N1  N2
  C10ORF119 MUTATED     7   1   1
  C10ORF119 WILD-TYPE 280 112  86
D1264V6, multiclass
    clus
vv   C10ORF119 MUTATED C10ORF119 WILD-TYPE
  N0                 7                 280
  N1                 1                 112
  N2                 1                  86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1264V7, binary
                     cls
clus                    0   1
  C10ORF119 MUTATED     7   0
  C10ORF119 WILD-TYPE 368  65
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  C10ORF119 MUTATED      7    0
  C10ORF119 WILD-TYPE  368   65
   clus
vv  C10ORF119 MUTATED C10ORF119 WILD-TYPE
  0                 7                 368
  1                 0                  65
[1] 2 2
[1] FALSE
D1264V8, binary
                     cls
clus                    0   1
  C10ORF119 MUTATED     4   5
  C10ORF119 WILD-TYPE 221 259
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  C10ORF119 MUTATED      4    5
  C10ORF119 WILD-TYPE  221  259
        clus
vv       C10ORF119 MUTATED C10ORF119 WILD-TYPE
  FEMALE                 4                 221
  MALE                   5                 259
[1] 2 2
[1] FALSE
D1264V9, binary
                     cls
clus                    0   1
  C10ORF119 MUTATED     7   0
  C10ORF119 WILD-TYPE 343  22
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  C10ORF119 MUTATED      7    0
  C10ORF119 WILD-TYPE  343   22
     clus
vv    C10ORF119 MUTATED C10ORF119 WILD-TYPE
  NO                  7                 343
  YES                 0                  22
[1] 2 2
[1] FALSE
                     vv
clus                  COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  C10ORF119 MUTATED                      8                             1
  C10ORF119 WILD-TYPE                  307                            46
                     vv
clus                  RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  C10ORF119 MUTATED                       0                              0
  C10ORF119 WILD-TYPE                   106                             10
D1264V10, multiclass
                                clus
vv                               C10ORF119 MUTATED C10ORF119 WILD-TYPE
  COLON ADENOCARCINOMA                           8                 307
  COLON MUCINOUS ADENOCARCINOMA                  1                  46
  RECTAL ADENOCARCINOMA                          0                 106
  RECTAL MUCINOUS ADENOCARCINOMA                 0                  10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                   R0  R1  R2  RX
  C10ORF119 MUTATED     6   0   0   0
  C10ORF119 WILD-TYPE 339   4  31  25
D1264V11, multiclass
    clus
vv   C10ORF119 MUTATED C10ORF119 WILD-TYPE
  R0                 6                 339
  R1                 0                   4
  R2                 0                  31
  RX                 0                  25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1264V12, continuous
                     vv
clus                  AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C10ORF119 MUTATED                                  0     0
  C10ORF119 WILD-TYPE                                1    11
                     vv
clus                  BLACK OR AFRICAN AMERICAN WHITE
  C10ORF119 MUTATED                           0     6
  C10ORF119 WILD-TYPE                        22   220
D1264V13, multiclass
                                  clus
vv                                 C10ORF119 MUTATED C10ORF119 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                 0                   1
  ASIAN                                            0                  11
  BLACK OR AFRICAN AMERICAN                        0                  22
  WHITE                                            6                 220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1265) Variable = ZMYND8 MUTATION ANALYSIS
D1265V1, survival
                  sevent
clus2                0   1
  ZMYND8 MUTATED    23   6
  ZMYND8 WILD-TYPE 355  87
  ZMYND8 MUTATED ZMYND8 WILD-TYPE 
              29              442 
  ZMYND8 MUTATED ZMYND8 WILD-TYPE 
               6               87 
$`ZMYND8 MUTATED`
TCGA-A6-6780 TCGA-AA-3510 TCGA-AA-3542 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3815 
       20.12        63.98        12.99        78.08         6.05        33.04 
TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01P TCGA-AD-6895 TCGA-AZ-4315 
       25.02         4.01        34.98        38.07         0.72        58.39 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-CK-4952 TCGA-CK-6751 TCGA-CM-4744 
       88.21        49.41        12.10        15.62       124.27        20.02 
TCGA-CM-6675 TCGA-D5-5538 TCGA-DM-A0XD TCGA-DM-A1D7 TCGA-DM-A1HB TCGA-G4-6309 
       13.05        12.26        24.43        13.32       135.65        85.48 
TCGA-G4-6586 TCGA-AG-3575 TCGA-AG-A002 TCGA-AH-6643 TCGA-DC-6682 
       35.80        12.00        20.98         0.69         4.01 

$`ZMYND8 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       19.99        61.02         6.97        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
       19.04        19.04        10.06        35.05         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       31.00         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6599 
        1.41         5.13       106.75        22.36        62.79         6.77 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       23.05        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       14.04        11.01        12.95        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       10.06        12.03        45.40        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D8 
      119.70        38.20       130.65        92.75        49.91        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 
      140.38         7.50        44.32       131.51       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       44.68        55.04        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       13.78        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6644 TCGA-CI-6619 
      117.11        38.56         1.45        17.49         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  ZMYND8 MUTATED ZMYND8 WILD-TYPE 
            0.69             0.00 
  ZMYND8 MUTATED ZMYND8 WILD-TYPE 
          135.65           148.01 
  ZMYND8 MUTATED ZMYND8 WILD-TYPE 
           20.98            20.12 
[1] "0.7 - 135.7 (21.0)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.3"
D1265V2, continuous
D1265V3, binary
                  cls
clus                 0   1
  ZMYND8 MUTATED    25   4
  ZMYND8 WILD-TYPE 341 115
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZMYND8 MUTATED     25    4
  ZMYND8 WILD-TYPE  341  115
        clus
vv       ZMYND8 MUTATED ZMYND8 WILD-TYPE
  COLON              25              341
  RECTUM              4              115
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZMYND8 MUTATED         4        0        4         7         2         0
  ZMYND8 WILD-TYPE      87        1       28       131         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZMYND8 MUTATED           1          0          3          3        2
  ZMYND8 WILD-TYPE        23         11         56         39       46
                  vv
clus               STAGE IVA STAGE IVB
  ZMYND8 MUTATED           0         1
  ZMYND8 WILD-TYPE        18         0
D1265V4, multiclass
            clus
vv           ZMYND8 MUTATED ZMYND8 WILD-TYPE
  STAGE I                 4               87
  STAGE IA                0                1
  STAGE II                4               28
  STAGE IIA               7              131
  STAGE IIB               2                8
  STAGE IIC               0                1
  STAGE III               1               23
  STAGE IIIA              0               11
  STAGE IIIB              3               56
  STAGE IIIC              3               39
  STAGE IV                2               46
  STAGE IVA               0               18
  STAGE IVB               1                0
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZMYND8 MUTATED     1   4  19   5
  ZMYND8 WILD-TYPE  16  88 310  45
D1265V5, multiclass
    clus
vv   ZMYND8 MUTATED ZMYND8 WILD-TYPE
  T1              1               16
  T2              4               88
  T3             19              310
  T4              5               45
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  ZMYND8 MUTATED    18   6   5
  ZMYND8 WILD-TYPE 269 107  82
D1265V6, multiclass
    clus
vv   ZMYND8 MUTATED ZMYND8 WILD-TYPE
  N0             18              269
  N1              6              107
  N2              5               82
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1265V7, binary
                  cls
clus                 0   1
  ZMYND8 MUTATED    21   3
  ZMYND8 WILD-TYPE 354  62
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZMYND8 MUTATED     21    3
  ZMYND8 WILD-TYPE  354   62
   clus
vv  ZMYND8 MUTATED ZMYND8 WILD-TYPE
  0             21              354
  1              3               62
[1] 2 2
[1] FALSE
D1265V8, binary
                  cls
clus                 0   1
  ZMYND8 MUTATED    12  17
  ZMYND8 WILD-TYPE 213 247
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZMYND8 MUTATED     12   17
  ZMYND8 WILD-TYPE  213  247
        clus
vv       ZMYND8 MUTATED ZMYND8 WILD-TYPE
  FEMALE             12              213
  MALE               17              247
[1] 2 2
[1] FALSE
D1265V9, binary
                  cls
clus                 0   1
  ZMYND8 MUTATED    20   0
  ZMYND8 WILD-TYPE 330  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZMYND8 MUTATED     20    0
  ZMYND8 WILD-TYPE  330   22
     clus
vv    ZMYND8 MUTATED ZMYND8 WILD-TYPE
  NO              20              330
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ZMYND8 MUTATED                     19                             4
  ZMYND8 WILD-TYPE                  296                            43
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ZMYND8 MUTATED                       4                              0
  ZMYND8 WILD-TYPE                   102                             10
D1265V10, multiclass
                                clus
vv                               ZMYND8 MUTATED ZMYND8 WILD-TYPE
  COLON ADENOCARCINOMA                       19              296
  COLON MUCINOUS ADENOCARCINOMA               4               43
  RECTAL ADENOCARCINOMA                       4              102
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ZMYND8 MUTATED    17   0   1   2
  ZMYND8 WILD-TYPE 328   4  30  23
D1265V11, multiclass
    clus
vv   ZMYND8 MUTATED ZMYND8 WILD-TYPE
  R0             17              328
  R1              0                4
  R2              1               30
  RX              2               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1265V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZMYND8 MUTATED                                  0     0
  ZMYND8 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZMYND8 MUTATED                           3    15
  ZMYND8 WILD-TYPE                        19   211
D1265V13, multiclass
                                  clus
vv                                 ZMYND8 MUTATED ZMYND8 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     3               19
  WHITE                                        15              211
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1266) Variable = NFASC MUTATION ANALYSIS
D1266V1, survival
                 sevent
clus2               0   1
  NFASC MUTATED    30   4
  NFASC WILD-TYPE 348  89
  NFASC MUTATED NFASC WILD-TYPE 
             34             437 
  NFASC MUTATED NFASC WILD-TYPE 
              4              89 
$`NFASC MUTATED`
TCGA-A6-6653 TCGA-A6-6780 TCGA-AA-3543 TCGA-AA-3660 TCGA-AA-3697 TCGA-AA-3713 
       24.39        20.12         0.99        78.08        85.05        19.04 
TCGA-AA-3815 TCGA-AA-3844 TCGA-AA-3866 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3966 
       33.04        14.93        17.03        33.01        26.01         2.01 
TCGA-AA-3982 TCGA-AA-A00J TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01R TCGA-AY-6197 
       27.02        18.05         4.01        34.98        35.01        21.44 
TCGA-AZ-4315 TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-4743 TCGA-CM-5341 TCGA-CM-6162 
       58.39        12.76        10.06        23.05        29.06        12.00 
TCGA-D5-6533 TCGA-D5-6930 TCGA-DM-A1D4 TCGA-DM-A1HB TCGA-DM-A28C TCGA-DM-A28H 
        1.32         1.51        92.75       135.65        81.37       117.07 
TCGA-F4-6704 TCGA-AG-3609 TCGA-AG-3999 TCGA-AG-A002 
        1.55        19.99        28.04        20.98 

$`NFASC WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
       25.08        25.18        24.16        21.76        24.69        23.87 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
       12.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 
        5.98        37.05        19.00        36.00         5.03        26.99 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       19.04        10.06        35.05         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3846 
       17.98        15.95        38.99        37.02         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3867 
        0.99        31.07        31.07        30.05        53.00        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 
       24.00        24.00         2.01        20.98        34.03        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       24.00        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L 
       38.04        19.00        30.02        34.03        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
       38.07         1.02         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4323 
       27.09        16.31         0.95        33.01        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.07        12.20        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
        1.91       124.27        20.02        37.02        25.02        13.02 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 
       15.02        15.02        17.03        15.02         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 
       56.09        55.92        20.19        18.25        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
        9.44        11.64         4.80        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-DM-A1D7 
      119.70        24.43        38.20       130.65        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 
       12.59       140.38         7.50        44.32       131.51       139.17 
TCGA-DM-A285 TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28K TCGA-F4-6459 
        6.12       119.93        35.97        60.79        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 
       31.96        35.74         6.18        47.87        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3611 TCGA-AG-3612 
       12.03         6.05         0.99        15.95        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       19.99        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  NFASC MUTATED NFASC WILD-TYPE 
           0.99            0.00 
  NFASC MUTATED NFASC WILD-TYPE 
         135.65          148.01 
  NFASC MUTATED NFASC WILD-TYPE 
         22.245          20.020 
[1] "1.0 - 135.7 (22.2)" "0.0 - 148.0 (20.0)"
[1] "hr=" "2.1"
D1266V2, continuous
D1266V3, binary
                 cls
clus                0   1
  NFASC MUTATED    32   3
  NFASC WILD-TYPE 334 116
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NFASC MUTATED     32    3
  NFASC WILD-TYPE  334  116
        clus
vv       NFASC MUTATED NFASC WILD-TYPE
  COLON             32             334
  RECTUM             3             116
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NFASC MUTATED         4        0        1        12         3         0
  NFASC WILD-TYPE      87        1       31       126         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NFASC MUTATED           2          1          6          5        1         0
  NFASC WILD-TYPE        22         10         53         37       47        18
                 vv
clus              STAGE IVB
  NFASC MUTATED           0
  NFASC WILD-TYPE         1
D1266V4, multiclass
            clus
vv           NFASC MUTATED NFASC WILD-TYPE
  STAGE I                4              87
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA             12             126
  STAGE IIB              3               7
  STAGE IIC              0               1
  STAGE III              2              22
  STAGE IIIA             1              10
  STAGE IIIB             6              53
  STAGE IIIC             5              37
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  NFASC MUTATED     0   5  25   5
  NFASC WILD-TYPE  17  87 304  45
D1266V5, multiclass
    clus
vv   NFASC MUTATED NFASC WILD-TYPE
  T1             0              17
  T2             5              87
  T3            25             304
  T4             5              45
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  NFASC MUTATED    23   6   6
  NFASC WILD-TYPE 264 107  81
D1266V6, multiclass
    clus
vv   NFASC MUTATED NFASC WILD-TYPE
  N0            23             264
  N1             6             107
  N2             6              81
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1266V7, binary
                 cls
clus                0   1
  NFASC MUTATED    31   1
  NFASC WILD-TYPE 344  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NFASC MUTATED     31    1
  NFASC WILD-TYPE  344   64
   clus
vv  NFASC MUTATED NFASC WILD-TYPE
  0            31             344
  1             1              64
[1] 2 2
[1] FALSE
D1266V8, binary
                 cls
clus                0   1
  NFASC MUTATED    14  21
  NFASC WILD-TYPE 211 243
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NFASC MUTATED     14   21
  NFASC WILD-TYPE  211  243
        clus
vv       NFASC MUTATED NFASC WILD-TYPE
  FEMALE            14             211
  MALE              21             243
[1] 2 2
[1] FALSE
D1266V9, binary
                 cls
clus                0   1
  NFASC MUTATED    22   3
  NFASC WILD-TYPE 328  19
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NFASC MUTATED     22    3
  NFASC WILD-TYPE  328   19
     clus
vv    NFASC MUTATED NFASC WILD-TYPE
  NO             22             328
  YES             3              19
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  NFASC MUTATED                     19                            12
  NFASC WILD-TYPE                  296                            35
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  NFASC MUTATED                       3                              0
  NFASC WILD-TYPE                   103                             10
D1266V10, multiclass
                                clus
vv                               NFASC MUTATED NFASC WILD-TYPE
  COLON ADENOCARCINOMA                      19             296
  COLON MUCINOUS ADENOCARCINOMA             12              35
  RECTAL ADENOCARCINOMA                      3             103
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  NFASC MUTATED    24   0   1   2
  NFASC WILD-TYPE 321   4  30  23
D1266V11, multiclass
    clus
vv   NFASC MUTATED NFASC WILD-TYPE
  R0            24             321
  R1             0               4
  R2             1              30
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1266V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NFASC MUTATED                                  1     2
  NFASC WILD-TYPE                                0     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  NFASC MUTATED                           0    13
  NFASC WILD-TYPE                        22   213
D1266V13, multiclass
                                  clus
vv                                 NFASC MUTATED NFASC WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             1               0
  ASIAN                                        2               9
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                       13             213
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1267) Variable = ACTA1 MUTATION ANALYSIS
D1267V1, survival
                 sevent
clus2               0   1
  ACTA1 MUTATED     9   5
  ACTA1 WILD-TYPE 369  88
  ACTA1 MUTATED ACTA1 WILD-TYPE 
             14             457 
  ACTA1 MUTATED ACTA1 WILD-TYPE 
              5              88 
$`ACTA1 MUTATED`
TCGA-A6-5665 TCGA-AA-3715 TCGA-AA-3833 TCGA-AA-A01R TCGA-AD-6964 TCGA-AZ-6598 
       22.06        19.04        15.95        35.01        10.88        49.41 
TCGA-CA-6717 TCGA-D5-6928 TCGA-DM-A0XD TCGA-F4-6460 TCGA-F4-6704 TCGA-G4-6586 
       12.76        11.64        24.43        31.96         1.55        35.80 
TCGA-AG-A002 TCGA-DC-6155 
       20.98        13.97 

$`ACTA1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 
       36.00         5.03        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       31.00        38.07         1.02         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
        0.72         5.79        22.42        27.42         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       88.21         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07        12.20        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
        9.44         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
      119.70        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
      117.07        98.24         8.61        35.74         6.18        47.87 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       22.09        13.78        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6157 TCGA-DC-6158 
       78.12         7.17        15.02         5.03        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  ACTA1 MUTATED ACTA1 WILD-TYPE 
           1.55            0.00 
  ACTA1 MUTATED ACTA1 WILD-TYPE 
          49.41          148.01 
  ACTA1 MUTATED ACTA1 WILD-TYPE 
          20.01           20.19 
[1] "1.6 - 49.4 (20.0)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "2.3"
D1267V2, continuous
D1267V3, binary
                 cls
clus                0   1
  ACTA1 MUTATED    12   2
  ACTA1 WILD-TYPE 354 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ACTA1 MUTATED     12    2
  ACTA1 WILD-TYPE  354  117
        clus
vv       ACTA1 MUTATED ACTA1 WILD-TYPE
  COLON             12             354
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ACTA1 MUTATED         1        0        2         6         0         0
  ACTA1 WILD-TYPE      90        1       30       132        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ACTA1 MUTATED           1          1          1          1        0         0
  ACTA1 WILD-TYPE        23         10         58         41       48        18
                 vv
clus              STAGE IVB
  ACTA1 MUTATED           0
  ACTA1 WILD-TYPE         1
D1267V4, multiclass
            clus
vv           ACTA1 MUTATED ACTA1 WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA              6             132
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             1              10
  STAGE IIIB             1              58
  STAGE IIIC             1              41
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ACTA1 MUTATED     0   2  11   1
  ACTA1 WILD-TYPE  17  90 318  49
D1267V5, multiclass
    clus
vv   ACTA1 MUTATED ACTA1 WILD-TYPE
  T1             0              17
  T2             2              90
  T3            11             318
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  ACTA1 MUTATED     9   2   3
  ACTA1 WILD-TYPE 278 111  84
D1267V6, multiclass
    clus
vv   ACTA1 MUTATED ACTA1 WILD-TYPE
  N0             9             278
  N1             2             111
  N2             3              84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1267V7, binary
                 cls
clus                0   1
  ACTA1 MUTATED    11   0
  ACTA1 WILD-TYPE 364  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ACTA1 MUTATED     11    0
  ACTA1 WILD-TYPE  364   65
   clus
vv  ACTA1 MUTATED ACTA1 WILD-TYPE
  0            11             364
  1             0              65
[1] 2 2
[1] FALSE
D1267V8, binary
                 cls
clus                0   1
  ACTA1 MUTATED     6   8
  ACTA1 WILD-TYPE 219 256
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ACTA1 MUTATED      6    8
  ACTA1 WILD-TYPE  219  256
        clus
vv       ACTA1 MUTATED ACTA1 WILD-TYPE
  FEMALE             6             219
  MALE               8             256
[1] 2 2
[1] FALSE
D1267V9, binary
                 cls
clus                0   1
  ACTA1 MUTATED    11   1
  ACTA1 WILD-TYPE 339  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ACTA1 MUTATED     11    1
  ACTA1 WILD-TYPE  339   21
     clus
vv    ACTA1 MUTATED ACTA1 WILD-TYPE
  NO             11             339
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ACTA1 MUTATED                      8                             4
  ACTA1 WILD-TYPE                  307                            43
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ACTA1 MUTATED                       2                              0
  ACTA1 WILD-TYPE                   104                             10
D1267V10, multiclass
                                clus
vv                               ACTA1 MUTATED ACTA1 WILD-TYPE
  COLON ADENOCARCINOMA                       8             307
  COLON MUCINOUS ADENOCARCINOMA              4              43
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  ACTA1 MUTATED    10   0   0   1
  ACTA1 WILD-TYPE 335   4  31  24
D1267V11, multiclass
    clus
vv   ACTA1 MUTATED ACTA1 WILD-TYPE
  R0            10             335
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1267V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ACTA1 MUTATED                                  1     1
  ACTA1 WILD-TYPE                                0    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ACTA1 MUTATED                           0     8
  ACTA1 WILD-TYPE                        22   218
D1267V13, multiclass
                                  clus
vv                                 ACTA1 MUTATED ACTA1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             1               0
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        8             218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1268) Variable = LYG1 MUTATION ANALYSIS
D1268V1, survival
                sevent
clus2              0   1
  LYG1 MUTATED     5   1
  LYG1 WILD-TYPE 373  92
  LYG1 MUTATED LYG1 WILD-TYPE 
             6            465 
  LYG1 MUTATED LYG1 WILD-TYPE 
             1             92 
$`LYG1 MUTATED`
TCGA-AA-3510 TCGA-AA-3663 TCGA-AA-3855 TCGA-AA-3977 TCGA-AA-A01R TCGA-CA-6718 
       63.98         6.97        32.05        25.02        35.01        10.06 

$`LYG1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3856 
       10.06         0.00        33.07         0.00        36.03         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
       38.07         1.02         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 
        3.25         3.29         0.07        12.20        12.76        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  LYG1 MUTATED LYG1 WILD-TYPE 
          6.97           0.00 
  LYG1 MUTATED LYG1 WILD-TYPE 
         63.98         148.01 
  LYG1 MUTATED LYG1 WILD-TYPE 
        28.535         20.120 
[1] "7.0 - 64.0 (28.5)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.3"
D1268V2, continuous
D1268V3, binary
                cls
clus               0   1
  LYG1 MUTATED     6   0
  LYG1 WILD-TYPE 360 119
[1] "tbl2"
                cls
clus             [,1] [,2]
  LYG1 MUTATED      6    0
  LYG1 WILD-TYPE  360  119
        clus
vv       LYG1 MUTATED LYG1 WILD-TYPE
  COLON             6            360
  RECTUM            0            119
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  LYG1 MUTATED         1        0        2         1         0         0
  LYG1 WILD-TYPE      90        1       30       137        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  LYG1 MUTATED           1          0          0          0        0         0
  LYG1 WILD-TYPE        23         11         59         42       48        18
                vv
clus             STAGE IVB
  LYG1 MUTATED           0
  LYG1 WILD-TYPE         1
D1268V4, multiclass
            clus
vv           LYG1 MUTATED LYG1 WILD-TYPE
  STAGE I               1             90
  STAGE IA              0              1
  STAGE II              2             30
  STAGE IIA             1            137
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             1             23
  STAGE IIIA            0             11
  STAGE IIIB            0             59
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  LYG1 MUTATED     0   2   4   0
  LYG1 WILD-TYPE  17  90 325  50
D1268V5, multiclass
    clus
vv   LYG1 MUTATED LYG1 WILD-TYPE
  T1            0             17
  T2            2             90
  T3            4            325
  T4            0             50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  LYG1 MUTATED     5   0   1
  LYG1 WILD-TYPE 282 113  86
D1268V6, multiclass
    clus
vv   LYG1 MUTATED LYG1 WILD-TYPE
  N0            5            282
  N1            0            113
  N2            1             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1268V7, binary
                cls
clus               0   1
  LYG1 MUTATED     5   0
  LYG1 WILD-TYPE 370  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  LYG1 MUTATED      5    0
  LYG1 WILD-TYPE  370   65
   clus
vv  LYG1 MUTATED LYG1 WILD-TYPE
  0            5            370
  1            0             65
[1] 2 2
[1] FALSE
D1268V8, binary
                cls
clus               0   1
  LYG1 MUTATED     0   6
  LYG1 WILD-TYPE 225 258
[1] "tbl2"
                cls
clus             [,1] [,2]
  LYG1 MUTATED      0    6
  LYG1 WILD-TYPE  225  258
        clus
vv       LYG1 MUTATED LYG1 WILD-TYPE
  FEMALE            0            225
  MALE              6            258
[1] 2 2
[1] FALSE
D1268V9, binary
                cls
clus               0   1
  LYG1 MUTATED     5   1
  LYG1 WILD-TYPE 345  21
[1] "tbl2"
                cls
clus             [,1] [,2]
  LYG1 MUTATED      5    1
  LYG1 WILD-TYPE  345   21
     clus
vv    LYG1 MUTATED LYG1 WILD-TYPE
  NO             5            345
  YES            1             21
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  LYG1 MUTATED                      5                             1
  LYG1 WILD-TYPE                  310                            46
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  LYG1 MUTATED                       0                              0
  LYG1 WILD-TYPE                   106                             10
D1268V10, multiclass
                                clus
vv                               LYG1 MUTATED LYG1 WILD-TYPE
  COLON ADENOCARCINOMA                      5            310
  COLON MUCINOUS ADENOCARCINOMA             1             46
  RECTAL ADENOCARCINOMA                     0            106
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  LYG1 MUTATED     4   0   0   1
  LYG1 WILD-TYPE 341   4  31  24
D1268V11, multiclass
    clus
vv   LYG1 MUTATED LYG1 WILD-TYPE
  R0            4            341
  R1            0              4
  R2            0             31
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1268V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  LYG1 MUTATED                                  0     1
  LYG1 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  LYG1 MUTATED                           0     0
  LYG1 WILD-TYPE                        22   226
D1268V13, multiclass
[1] "Remove cluster labels:" "LYG1 MUTATED"          
clus
  LYG1 MUTATED LYG1 WILD-TYPE 
             1            259 
    TCGA-A6-2671     TCGA-A6-2672     TCGA-A6-2674     TCGA-A6-2676 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-A6-2677     TCGA-A6-2678     TCGA-A6-2683     TCGA-A6-3807 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-A6-3808     TCGA-A6-3809     TCGA-A6-3810     TCGA-A6-4105 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-A6-5656     TCGA-A6-5657     TCGA-A6-5659     TCGA-A6-5660 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-A6-5661     TCGA-A6-5662     TCGA-A6-5664     TCGA-A6-5665 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-A6-5666     TCGA-A6-6137     TCGA-A6-6138     TCGA-A6-6141 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-A6-6142     TCGA-A6-6648     TCGA-A6-6649     TCGA-A6-6651 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-A6-6652     TCGA-A6-6653     TCGA-A6-6654     TCGA-A6-6780 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-A6-6781     TCGA-A6-6782     TCGA-AD-5900     TCGA-AD-6548 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-AD-6888     TCGA-AD-6889     TCGA-AD-6890     TCGA-AD-6895 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-AD-6899     TCGA-AD-6901     TCGA-AD-6963     TCGA-AD-6964 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-AD-6965     TCGA-AU-3779     TCGA-AU-6004     TCGA-AY-4070 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-AY-4071     TCGA-AY-5543     TCGA-AY-6196     TCGA-AY-6197 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-AY-6386     TCGA-AZ-4315     TCGA-AZ-4323     TCGA-AZ-4616 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-AZ-4681     TCGA-AZ-4682     TCGA-AZ-5403     TCGA-AZ-5407 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-AZ-6598     TCGA-AZ-6599     TCGA-AZ-6600     TCGA-AZ-6601 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-AZ-6603     TCGA-AZ-6605     TCGA-AZ-6606     TCGA-AZ-6607 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-AZ-6608     TCGA-CA-5254     TCGA-CA-5255     TCGA-CA-5796 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-CA-5797     TCGA-CA-6715     TCGA-CA-6716     TCGA-CA-6717 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-CA-6719     TCGA-CK-4947     TCGA-CK-4948     TCGA-CK-4950 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-CK-4952     TCGA-CK-5912     TCGA-CK-5913     TCGA-CK-5914 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-CK-5915     TCGA-CK-5916     TCGA-CK-6746     TCGA-CK-6747 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-CK-6748     TCGA-CK-6751     TCGA-CM-4743     TCGA-CM-4744 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-CM-4746     TCGA-CM-4747     TCGA-CM-4752     TCGA-CM-5341 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-CM-5344     TCGA-CM-5348     TCGA-CM-5349     TCGA-CM-5860 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-CM-5861     TCGA-CM-5862     TCGA-CM-5863     TCGA-CM-5864 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-CM-5868     TCGA-CM-6161     TCGA-CM-6162     TCGA-CM-6163 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-CM-6164     TCGA-CM-6165     TCGA-CM-6166     TCGA-CM-6167 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-CM-6168     TCGA-CM-6169     TCGA-CM-6170     TCGA-CM-6171 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-CM-6172     TCGA-CM-6674     TCGA-CM-6675     TCGA-CM-6676 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-CM-6677     TCGA-CM-6678     TCGA-CM-6679     TCGA-CM-6680 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-D5-5537     TCGA-D5-5538     TCGA-D5-5539     TCGA-D5-5540 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-D5-5541     TCGA-D5-6529     TCGA-D5-6532     TCGA-D5-6533 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-D5-6534     TCGA-D5-6535     TCGA-D5-6536     TCGA-D5-6537 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-D5-6538     TCGA-D5-6539     TCGA-D5-6540     TCGA-D5-6541 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-D5-6898     TCGA-D5-6920     TCGA-D5-6922     TCGA-D5-6923 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-D5-6924     TCGA-D5-6926     TCGA-D5-6927     TCGA-D5-6928 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-D5-6929     TCGA-D5-6930     TCGA-D5-6931     TCGA-D5-6932 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-D5-7000     TCGA-DM-A0X9     TCGA-DM-A0XD     TCGA-DM-A0XF 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-DM-A1D0     TCGA-DM-A1D4     TCGA-DM-A1D6     TCGA-DM-A1D7 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-DM-A1D8     TCGA-DM-A1D9     TCGA-DM-A1DA     TCGA-DM-A1DB 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-DM-A1HA     TCGA-DM-A1HB     TCGA-DM-A282     TCGA-DM-A285 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-DM-A28C     TCGA-DM-A28E     TCGA-DM-A28F     TCGA-DM-A28G 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-DM-A28H     TCGA-DM-A28K     TCGA-F4-6459     TCGA-F4-6460 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-F4-6569     TCGA-F4-6570     TCGA-F4-6703     TCGA-F4-6704 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-F4-6805     TCGA-F4-6806     TCGA-F4-6807     TCGA-F4-6808 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-F4-6809     TCGA-F4-6854     TCGA-F4-6855     TCGA-F4-6856 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-G4-6293     TCGA-G4-6299     TCGA-G4-6303     TCGA-G4-6304 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-G4-6306     TCGA-G4-6307     TCGA-G4-6309     TCGA-G4-6310 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-G4-6315     TCGA-G4-6317     TCGA-G4-6321     TCGA-G4-6323 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-G4-6586     TCGA-G4-6588     TCGA-G4-6625     TCGA-G4-6626 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-G4-6628     TCGA-AF-2687     TCGA-AF-2689     TCGA-AF-2691 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-AF-2692     TCGA-AF-2693     TCGA-AF-3400     TCGA-AF-3913 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-AF-4110     TCGA-AF-5654     TCGA-AF-6136     TCGA-AF-6655 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-AF-6672     TCGA-AH-6544     TCGA-AH-6547     TCGA-AH-6549 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-AH-6643     TCGA-AH-6644     TCGA-CI-6619     TCGA-CI-6620 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-CI-6621     TCGA-CI-6622     TCGA-CI-6624     TCGA-CL-5917 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-CL-5918     TCGA-DC-5337     TCGA-DC-5869     TCGA-DC-6155 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-DC-6157     TCGA-DC-6158     TCGA-DC-6160     TCGA-DC-6681 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-DC-6682     TCGA-DC-6683     TCGA-DT-5265     TCGA-DY-A0XA 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-DY-A1DC     TCGA-DY-A1DD     TCGA-DY-A1DF     TCGA-DY-A1DG 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-DY-A1H8     TCGA-EF-5830     TCGA-EI-6506     TCGA-EI-6507 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-EI-6508     TCGA-EI-6510     TCGA-F5-6464     TCGA-F5-6465 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-F5-6571     TCGA-F5-6702     TCGA-F5-6811     TCGA-F5-6812 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 
    TCGA-F5-6813     TCGA-G5-6235     TCGA-G5-6641 
"LYG1 WILD-TYPE" "LYG1 WILD-TYPE" "LYG1 WILD-TYPE" 

Clustering(1269) Variable = EXPH5 MUTATION ANALYSIS
D1269V1, survival
                 sevent
clus2               0   1
  EXPH5 MUTATED    17   6
  EXPH5 WILD-TYPE 361  87
  EXPH5 MUTATED EXPH5 WILD-TYPE 
             23             448 
  EXPH5 MUTATED EXPH5 WILD-TYPE 
              6              87 
$`EXPH5 MUTATED`
TCGA-A6-5665 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6781 TCGA-AA-3555 TCGA-AA-3877 
       22.06         8.38        25.08        19.66        29.95        31.00 
TCGA-AA-3949 TCGA-AA-A00J TCGA-AA-A00N TCGA-AA-A01R TCGA-AZ-5403 TCGA-AZ-6605 
       26.01        18.05         4.01        35.01        62.79         5.23 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-4743 TCGA-CM-5862 TCGA-D5-5539 TCGA-DM-A28F 
       12.76        10.06        23.05         5.03        19.59        35.97 
TCGA-G4-6588 TCGA-G4-6628 TCGA-AF-2693 TCGA-AG-3892 TCGA-AG-A002 
       26.17        79.69        19.10        13.02        20.98 

$`EXPH5 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6648 TCGA-A6-6649 
       22.09        32.71        27.09        22.52        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 
       21.76        24.69        24.39        23.87        20.12        20.28 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
        7.04         3.02         1.02        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       78.08         6.05         6.97        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3950 
       18.05         2.01        12.99        24.00        33.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L 
       38.04        19.00        30.02        34.03        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       31.00        38.07         1.02         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        3.29         0.07        12.20        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
       82.95         1.91       124.27        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
       15.02        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       12.26        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
       81.37       119.93        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 
       13.78        35.80        91.79        46.75        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       43.04        13.55        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 
       19.99         1.02        17.95        36.95        17.03        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  EXPH5 MUTATED EXPH5 WILD-TYPE 
           4.01            0.00 
  EXPH5 MUTATED EXPH5 WILD-TYPE 
          79.69          148.01 
  EXPH5 MUTATED EXPH5 WILD-TYPE 
         20.980          20.155 
[1] "4.0 - 79.7 (21.0)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.5"
D1269V2, continuous
D1269V3, binary
                 cls
clus                0   1
  EXPH5 MUTATED    21   2
  EXPH5 WILD-TYPE 345 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EXPH5 MUTATED     21    2
  EXPH5 WILD-TYPE  345  117
        clus
vv       EXPH5 MUTATED EXPH5 WILD-TYPE
  COLON             21             345
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  EXPH5 MUTATED         5        0        1         8         1         0
  EXPH5 WILD-TYPE      86        1       31       130         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  EXPH5 MUTATED           1          1          4          1        0         2
  EXPH5 WILD-TYPE        23         10         55         41       48        16
                 vv
clus              STAGE IVB
  EXPH5 MUTATED           0
  EXPH5 WILD-TYPE         1
D1269V4, multiclass
            clus
vv           EXPH5 MUTATED EXPH5 WILD-TYPE
  STAGE I                5              86
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              8             130
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             1              10
  STAGE IIIB             4              55
  STAGE IIIC             1              41
  STAGE IV               0              48
  STAGE IVA              2              16
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  EXPH5 MUTATED     2   3  15   4
  EXPH5 WILD-TYPE  15  89 314  46
D1269V5, multiclass
    clus
vv   EXPH5 MUTATED EXPH5 WILD-TYPE
  T1             2              15
  T2             3              89
  T3            15             314
  T4             4              46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  EXPH5 MUTATED    15   8   1
  EXPH5 WILD-TYPE 272 105  86
D1269V6, multiclass
    clus
vv   EXPH5 MUTATED EXPH5 WILD-TYPE
  N0            15             272
  N1             8             105
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1269V7, binary
                 cls
clus                0   1
  EXPH5 MUTATED    19   2
  EXPH5 WILD-TYPE 356  63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EXPH5 MUTATED     19    2
  EXPH5 WILD-TYPE  356   63
   clus
vv  EXPH5 MUTATED EXPH5 WILD-TYPE
  0            19             356
  1             2              63
[1] 2 2
[1] FALSE
D1269V8, binary
                 cls
clus                0   1
  EXPH5 MUTATED     8  16
  EXPH5 WILD-TYPE 217 248
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EXPH5 MUTATED      8   16
  EXPH5 WILD-TYPE  217  248
        clus
vv       EXPH5 MUTATED EXPH5 WILD-TYPE
  FEMALE             8             217
  MALE              16             248
[1] 2 2
[1] FALSE
D1269V9, binary
                 cls
clus                0   1
  EXPH5 MUTATED    20   1
  EXPH5 WILD-TYPE 330  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EXPH5 MUTATED     20    1
  EXPH5 WILD-TYPE  330   21
     clus
vv    EXPH5 MUTATED EXPH5 WILD-TYPE
  NO             20             330
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  EXPH5 MUTATED                     12                             9
  EXPH5 WILD-TYPE                  303                            38
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  EXPH5 MUTATED                       2                              0
  EXPH5 WILD-TYPE                   104                             10
D1269V10, multiclass
                                clus
vv                               EXPH5 MUTATED EXPH5 WILD-TYPE
  COLON ADENOCARCINOMA                      12             303
  COLON MUCINOUS ADENOCARCINOMA              9              38
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  EXPH5 MUTATED    16   0   0   2
  EXPH5 WILD-TYPE 329   4  31  23
D1269V11, multiclass
    clus
vv   EXPH5 MUTATED EXPH5 WILD-TYPE
  R0            16             329
  R1             0               4
  R2             0              31
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1269V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  EXPH5 MUTATED                                  0     2
  EXPH5 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  EXPH5 MUTATED                           1    12
  EXPH5 WILD-TYPE                        21   214
D1269V13, multiclass
                                  clus
vv                                 EXPH5 MUTATED EXPH5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               9
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                       12             214
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1270) Variable = LEPRE1 MUTATION ANALYSIS
D1270V1, survival
                  sevent
clus2                0   1
  LEPRE1 MUTATED     6   3
  LEPRE1 WILD-TYPE 372  90
  LEPRE1 MUTATED LEPRE1 WILD-TYPE 
               9              462 
  LEPRE1 MUTATED LEPRE1 WILD-TYPE 
               3               90 
$`LEPRE1 MUTATED`
TCGA-A6-6781 TCGA-AA-3713 TCGA-AY-6197 TCGA-AZ-6598 TCGA-CM-5861 TCGA-D5-6539 
       19.66        19.04        21.44        49.41        15.02        12.49 
TCGA-F4-6570 TCGA-F4-6809 TCGA-G4-6588 
        6.18        13.25        26.17 

$`LEPRE1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       33.01        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        88.21         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 
       29.06        22.03        22.98        30.08        32.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 
       43.27        15.12        17.85         4.80        17.13        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       31.96        35.74        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       16.24        33.67         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  LEPRE1 MUTATED LEPRE1 WILD-TYPE 
            6.18             0.00 
  LEPRE1 MUTATED LEPRE1 WILD-TYPE 
           49.41           148.01 
  LEPRE1 MUTATED LEPRE1 WILD-TYPE 
          19.040           20.415 
[1] "6.2 - 49.4 (19.0)"  "0.0 - 148.0 (20.4)"
[1] "hr=" "2.1"
D1270V2, continuous
D1270V3, binary
                  cls
clus                 0   1
  LEPRE1 MUTATED     9   0
  LEPRE1 WILD-TYPE 357 119
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LEPRE1 MUTATED      9    0
  LEPRE1 WILD-TYPE  357  119
        clus
vv       LEPRE1 MUTATED LEPRE1 WILD-TYPE
  COLON               9              357
  RECTUM              0              119
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  LEPRE1 MUTATED         0        0        1         4         0         0
  LEPRE1 WILD-TYPE      91        1       31       134        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  LEPRE1 MUTATED           0          1          0          1        1
  LEPRE1 WILD-TYPE        24         10         59         41       47
                  vv
clus               STAGE IVA STAGE IVB
  LEPRE1 MUTATED           1         0
  LEPRE1 WILD-TYPE        17         1
D1270V4, multiclass
            clus
vv           LEPRE1 MUTATED LEPRE1 WILD-TYPE
  STAGE I                 0               91
  STAGE IA                0                1
  STAGE II                1               31
  STAGE IIA               4              134
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              1               10
  STAGE IIIB              0               59
  STAGE IIIC              1               41
  STAGE IV                1               47
  STAGE IVA               1               17
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  LEPRE1 MUTATED     0   0   8   1
  LEPRE1 WILD-TYPE  17  92 321  49
D1270V5, multiclass
    clus
vv   LEPRE1 MUTATED LEPRE1 WILD-TYPE
  T1              0               17
  T2              0               92
  T3              8              321
  T4              1               49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  LEPRE1 MUTATED     7   2   0
  LEPRE1 WILD-TYPE 280 111  87
D1270V6, multiclass
    clus
vv   LEPRE1 MUTATED LEPRE1 WILD-TYPE
  N0              7              280
  N1              2              111
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1270V7, binary
                  cls
clus                 0   1
  LEPRE1 MUTATED     4   2
  LEPRE1 WILD-TYPE 371  63
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LEPRE1 MUTATED      4    2
  LEPRE1 WILD-TYPE  371   63
   clus
vv  LEPRE1 MUTATED LEPRE1 WILD-TYPE
  0              4              371
  1              2               63
[1] 2 2
[1] FALSE
D1270V8, binary
                  cls
clus                 0   1
  LEPRE1 MUTATED     6   3
  LEPRE1 WILD-TYPE 219 261
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LEPRE1 MUTATED      6    3
  LEPRE1 WILD-TYPE  219  261
        clus
vv       LEPRE1 MUTATED LEPRE1 WILD-TYPE
  FEMALE              6              219
  MALE                3              261
[1] 2 2
[1] FALSE
D1270V9, binary
                  cls
clus                 0   1
  LEPRE1 MUTATED     8   1
  LEPRE1 WILD-TYPE 342  21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LEPRE1 MUTATED      8    1
  LEPRE1 WILD-TYPE  342   21
     clus
vv    LEPRE1 MUTATED LEPRE1 WILD-TYPE
  NO               8              342
  YES              1               21
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  LEPRE1 MUTATED                      8                             1
  LEPRE1 WILD-TYPE                  307                            46
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  LEPRE1 MUTATED                       0                              0
  LEPRE1 WILD-TYPE                   106                             10
D1270V10, multiclass
                                clus
vv                               LEPRE1 MUTATED LEPRE1 WILD-TYPE
  COLON ADENOCARCINOMA                        8              307
  COLON MUCINOUS ADENOCARCINOMA               1               46
  RECTAL ADENOCARCINOMA                       0              106
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  LEPRE1 MUTATED     7   0   1   0
  LEPRE1 WILD-TYPE 338   4  30  25
D1270V11, multiclass
    clus
vv   LEPRE1 MUTATED LEPRE1 WILD-TYPE
  R0              7              338
  R1              0                4
  R2              1               30
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1270V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  LEPRE1 MUTATED                                  0     0
  LEPRE1 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  LEPRE1 MUTATED                           0     8
  LEPRE1 WILD-TYPE                        22   218
D1270V13, multiclass
                                  clus
vv                                 LEPRE1 MUTATED LEPRE1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         8              218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1271) Variable = COL6A5 MUTATION ANALYSIS
D1271V1, survival
                  sevent
clus2                0   1
  COL6A5 MUTATED    28   6
  COL6A5 WILD-TYPE 350  87
  COL6A5 MUTATED COL6A5 WILD-TYPE 
              34              437 
  COL6A5 MUTATED COL6A5 WILD-TYPE 
               6               87 
$`COL6A5 MUTATED`
TCGA-A6-5661 TCGA-A6-6141 TCGA-A6-6653 TCGA-AA-3510 TCGA-AA-3815 TCGA-AA-3955 
       33.53         8.38        24.39        63.98        33.04        20.98 
TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A01R TCGA-AU-3779 TCGA-AZ-4315 TCGA-AZ-6598 
       25.02         4.01        35.01        14.50        58.39        49.41 
TCGA-AZ-6608 TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-4743 TCGA-CM-5864 TCGA-CM-6164 
        1.61        12.76        10.06        23.05        15.02        29.03 
TCGA-CM-6168 TCGA-CM-6171 TCGA-CM-6675 TCGA-CM-6676 TCGA-D5-6923 TCGA-D5-6924 
       12.99        14.04        13.05        11.08        12.43        14.30 
TCGA-D5-6930 TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-F4-6460 TCGA-F4-6805 TCGA-G4-6588 
        1.51       130.65        92.75        31.96        34.42        26.17 
TCGA-G4-6628 TCGA-AG-3885 TCGA-AG-A002 TCGA-F5-6812 
       79.69        17.95        20.98         0.66 

$`COL6A5 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 
       22.06        32.71        27.09        22.52        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       24.16        21.76        24.69        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 
       20.28         7.04         3.02         1.02        35.01         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
       26.99        19.04        19.04        10.06        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       26.01        24.00         2.01        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T 
       31.00        31.00        38.07         1.02         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
        0.20        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       88.21         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
       11.74         3.19        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.07        12.20        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
        1.91       124.27        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
        5.03        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 
       16.04        21.99        14.99        13.02        15.02        11.01 
TCGA-CM-6674 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       12.95        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 
        9.04         9.44        11.64         4.80        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D6 TCGA-DM-A1D7 
       10.26       119.70        24.43        38.20        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
      117.07        98.24         8.61        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
        1.55        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 
       22.09        13.78        35.80        91.79        46.75        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 
        0.99        19.04        19.99         1.02        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.69        55.76        26.43 

  COL6A5 MUTATED COL6A5 WILD-TYPE 
            0.66             0.00 
  COL6A5 MUTATED COL6A5 WILD-TYPE 
          130.65           148.01 
  COL6A5 MUTATED COL6A5 WILD-TYPE 
           20.98            20.12 
[1] "0.7 - 130.7 (21.0)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.2"
D1271V2, continuous
D1271V3, binary
                  cls
clus                 0   1
  COL6A5 MUTATED    33   3
  COL6A5 WILD-TYPE 333 116
[1] "tbl2"
                  cls
clus               [,1] [,2]
  COL6A5 MUTATED     33    3
  COL6A5 WILD-TYPE  333  116
        clus
vv       COL6A5 MUTATED COL6A5 WILD-TYPE
  COLON              33              333
  RECTUM              3              116
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  COL6A5 MUTATED         7        0        2        18         2         0
  COL6A5 WILD-TYPE      84        1       30       120         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  COL6A5 MUTATED           1          1          3          0        0
  COL6A5 WILD-TYPE        23         10         56         42       48
                  vv
clus               STAGE IVA STAGE IVB
  COL6A5 MUTATED           0         1
  COL6A5 WILD-TYPE        18         0
D1271V4, multiclass
            clus
vv           COL6A5 MUTATED COL6A5 WILD-TYPE
  STAGE I                 7               84
  STAGE IA                0                1
  STAGE II                2               30
  STAGE IIA              18              120
  STAGE IIB               2                8
  STAGE IIC               0                1
  STAGE III               1               23
  STAGE IIIA              1               10
  STAGE IIIB              3               56
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               1                0
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  COL6A5 MUTATED     0  10  24   2
  COL6A5 WILD-TYPE  17  82 305  48
D1271V5, multiclass
    clus
vv   COL6A5 MUTATED COL6A5 WILD-TYPE
  T1              0               17
  T2             10               82
  T3             24              305
  T4              2               48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  COL6A5 MUTATED    30   3   3
  COL6A5 WILD-TYPE 257 110  84
D1271V6, multiclass
    clus
vv   COL6A5 MUTATED COL6A5 WILD-TYPE
  N0             30              257
  N1              3              110
  N2              3               84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1271V7, binary
                  cls
clus                 0   1
  COL6A5 MUTATED    32   1
  COL6A5 WILD-TYPE 343  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  COL6A5 MUTATED     32    1
  COL6A5 WILD-TYPE  343   64
   clus
vv  COL6A5 MUTATED COL6A5 WILD-TYPE
  0             32              343
  1              1               64
[1] 2 2
[1] FALSE
D1271V8, binary
                  cls
clus                 0   1
  COL6A5 MUTATED    15  21
  COL6A5 WILD-TYPE 210 243
[1] "tbl2"
                  cls
clus               [,1] [,2]
  COL6A5 MUTATED     15   21
  COL6A5 WILD-TYPE  210  243
        clus
vv       COL6A5 MUTATED COL6A5 WILD-TYPE
  FEMALE             15              210
  MALE               21              243
[1] 2 2
[1] FALSE
D1271V9, binary
                  cls
clus                 0   1
  COL6A5 MUTATED    27   2
  COL6A5 WILD-TYPE 323  20
[1] "tbl2"
                  cls
clus               [,1] [,2]
  COL6A5 MUTATED     27    2
  COL6A5 WILD-TYPE  323   20
     clus
vv    COL6A5 MUTATED COL6A5 WILD-TYPE
  NO              27              323
  YES              2               20
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  COL6A5 MUTATED                     29                             4
  COL6A5 WILD-TYPE                  286                            43
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  COL6A5 MUTATED                       3                              0
  COL6A5 WILD-TYPE                   103                             10
D1271V10, multiclass
                                clus
vv                               COL6A5 MUTATED COL6A5 WILD-TYPE
  COLON ADENOCARCINOMA                       29              286
  COLON MUCINOUS ADENOCARCINOMA               4               43
  RECTAL ADENOCARCINOMA                       3              103
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  COL6A5 MUTATED    26   0   0   3
  COL6A5 WILD-TYPE 319   4  31  22
D1271V11, multiclass
    clus
vv   COL6A5 MUTATED COL6A5 WILD-TYPE
  R0             26              319
  R1              0                4
  R2              0               31
  RX              3               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1271V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  COL6A5 MUTATED                                  0     2
  COL6A5 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  COL6A5 MUTATED                           4    21
  COL6A5 WILD-TYPE                        18   205
D1271V13, multiclass
                                  clus
vv                                 COL6A5 MUTATED COL6A5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                9
  BLACK OR AFRICAN AMERICAN                     4               18
  WHITE                                        21              205
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1272) Variable = RAB3C MUTATION ANALYSIS
D1272V1, survival
                 sevent
clus2               0   1
  RAB3C MUTATED    10   4
  RAB3C WILD-TYPE 368  89
  RAB3C MUTATED RAB3C WILD-TYPE 
             14             457 
  RAB3C MUTATED RAB3C WILD-TYPE 
              4              89 
$`RAB3C MUTATED`
TCGA-A6-5662 TCGA-A6-6651 TCGA-AA-3510 TCGA-AA-3811 TCGA-AA-3982 TCGA-AZ-6606 
       23.61        21.76        63.98        10.06        27.02        11.74 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-4743 TCGA-CM-4752 TCGA-DM-A1D6 TCGA-G4-6321 
       12.76        10.06        23.05        13.02        49.91        22.09 
TCGA-AG-A002 TCGA-CI-6619 
       20.98         6.05 

$`RAB3C WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        33.53        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       25.18        24.16        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3815 
       85.05        26.99        19.04        19.04        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3986 TCGA-AA-3989 
       26.01        25.02        24.00        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        3.29         0.07        12.20        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
       82.95         1.91       124.27        20.02        37.02        25.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
       38.20       130.65        92.75        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.69         0.72        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  RAB3C MUTATED RAB3C WILD-TYPE 
           6.05            0.00 
  RAB3C MUTATED RAB3C WILD-TYPE 
          63.98          148.01 
  RAB3C MUTATED RAB3C WILD-TYPE 
          21.37           20.12 
[1] "6.0 - 64.0 (21.4)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.6"
D1272V2, continuous
D1272V3, binary
                 cls
clus                0   1
  RAB3C MUTATED    13   2
  RAB3C WILD-TYPE 353 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RAB3C MUTATED     13    2
  RAB3C WILD-TYPE  353  117
        clus
vv       RAB3C MUTATED RAB3C WILD-TYPE
  COLON             13             353
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RAB3C MUTATED         1        0        2         5         0         0
  RAB3C WILD-TYPE      90        1       30       133        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RAB3C MUTATED           2          0          2          0        2         1
  RAB3C WILD-TYPE        22         11         57         42       46        17
                 vv
clus              STAGE IVB
  RAB3C MUTATED           0
  RAB3C WILD-TYPE         1
D1272V4, multiclass
            clus
vv           RAB3C MUTATED RAB3C WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA              5             133
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              2              22
  STAGE IIIA             0              11
  STAGE IIIB             2              57
  STAGE IIIC             0              42
  STAGE IV               2              46
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  RAB3C MUTATED     0   2  11   2
  RAB3C WILD-TYPE  17  90 318  48
D1272V5, multiclass
    clus
vv   RAB3C MUTATED RAB3C WILD-TYPE
  T1             0              17
  T2             2              90
  T3            11             318
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  RAB3C MUTATED     8   4   3
  RAB3C WILD-TYPE 279 109  84
D1272V6, multiclass
    clus
vv   RAB3C MUTATED RAB3C WILD-TYPE
  N0             8             279
  N1             4             109
  N2             3              84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1272V7, binary
                 cls
clus                0   1
  RAB3C MUTATED    10   3
  RAB3C WILD-TYPE 365  62
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RAB3C MUTATED     10    3
  RAB3C WILD-TYPE  365   62
   clus
vv  RAB3C MUTATED RAB3C WILD-TYPE
  0            10             365
  1             3              62
[1] 2 2
[1] FALSE
D1272V8, binary
                 cls
clus                0   1
  RAB3C MUTATED     4  11
  RAB3C WILD-TYPE 221 253
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RAB3C MUTATED      4   11
  RAB3C WILD-TYPE  221  253
        clus
vv       RAB3C MUTATED RAB3C WILD-TYPE
  FEMALE             4             221
  MALE              11             253
[1] 2 2
[1] FALSE
D1272V9, binary
                 cls
clus                0   1
  RAB3C MUTATED    12   0
  RAB3C WILD-TYPE 338  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RAB3C MUTATED     12    0
  RAB3C WILD-TYPE  338   22
     clus
vv    RAB3C MUTATED RAB3C WILD-TYPE
  NO             12             338
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  RAB3C MUTATED                     11                             2
  RAB3C WILD-TYPE                  304                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  RAB3C MUTATED                       2                              0
  RAB3C WILD-TYPE                   104                             10
D1272V10, multiclass
                                clus
vv                               RAB3C MUTATED RAB3C WILD-TYPE
  COLON ADENOCARCINOMA                      11             304
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  RAB3C MUTATED     7   0   0   2
  RAB3C WILD-TYPE 338   4  31  23
D1272V11, multiclass
    clus
vv   RAB3C MUTATED RAB3C WILD-TYPE
  R0             7             338
  R1             0               4
  R2             0              31
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1272V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RAB3C MUTATED                                  0     2
  RAB3C WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  RAB3C MUTATED                           1     7
  RAB3C WILD-TYPE                        21   219
D1272V13, multiclass
                                  clus
vv                                 RAB3C MUTATED RAB3C WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               9
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        7             219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1273) Variable = MAP2K1 MUTATION ANALYSIS
D1273V1, survival
                  sevent
clus2                0   1
  MAP2K1 MUTATED    10   2
  MAP2K1 WILD-TYPE 368  91
  MAP2K1 MUTATED MAP2K1 WILD-TYPE 
              12              459 
  MAP2K1 MUTATED MAP2K1 WILD-TYPE 
               2               91 
$`MAP2K1 MUTATED`
TCGA-A6-5661 TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3555 TCGA-AA-3815 TCGA-AA-3867 
       33.53         3.02        63.98        29.95        33.04        24.03 
TCGA-AY-4071 TCGA-AZ-4315 TCGA-D5-6931 TCGA-G4-6309 TCGA-AG-A002 TCGA-EI-6506 
        0.95        58.39        12.00        85.48        20.98        20.55 

$`MAP2K1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 
       20.12        19.66        20.28         7.04         1.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       17.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
       26.99        19.04        19.04        10.06        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       30.05        53.00        17.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
       16.31        33.01        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       11.64         4.80         1.51        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 
       65.85        53.62        44.68        55.04        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       51.48        32.61         0.49        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  MAP2K1 MUTATED MAP2K1 WILD-TYPE 
            0.95             0.00 
  MAP2K1 MUTATED MAP2K1 WILD-TYPE 
           85.48           148.01 
  MAP2K1 MUTATED MAP2K1 WILD-TYPE 
           26.99            20.02 
[1] "0.9 - 85.5 (27.0)"  "0.0 - 148.0 (20.0)"
[1] "hr=" "1.5"
D1273V2, continuous
D1273V3, binary
                  cls
clus                 0   1
  MAP2K1 MUTATED     9   2
  MAP2K1 WILD-TYPE 357 117
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP2K1 MUTATED      9    2
  MAP2K1 WILD-TYPE  357  117
        clus
vv       MAP2K1 MUTATED MAP2K1 WILD-TYPE
  COLON               9              357
  RECTUM              2              117
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MAP2K1 MUTATED         2        0        2         5         0         0
  MAP2K1 WILD-TYPE      89        1       30       133        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MAP2K1 MUTATED           0          0          1          1        1
  MAP2K1 WILD-TYPE        24         11         58         41       47
                  vv
clus               STAGE IVA STAGE IVB
  MAP2K1 MUTATED           0         0
  MAP2K1 WILD-TYPE        18         1
D1273V4, multiclass
            clus
vv           MAP2K1 MUTATED MAP2K1 WILD-TYPE
  STAGE I                 2               89
  STAGE IA                0                1
  STAGE II                2               30
  STAGE IIA               5              133
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              1               58
  STAGE IIIC              1               41
  STAGE IV                1               47
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  MAP2K1 MUTATED     1   1   9   1
  MAP2K1 WILD-TYPE  16  91 320  49
D1273V5, multiclass
    clus
vv   MAP2K1 MUTATED MAP2K1 WILD-TYPE
  T1              1               16
  T2              1               91
  T3              9              320
  T4              1               49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  MAP2K1 MUTATED     9   1   2
  MAP2K1 WILD-TYPE 278 112  85
D1273V6, multiclass
    clus
vv   MAP2K1 MUTATED MAP2K1 WILD-TYPE
  N0              9              278
  N1              1              112
  N2              2               85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1273V7, binary
                  cls
clus                 0   1
  MAP2K1 MUTATED    10   1
  MAP2K1 WILD-TYPE 365  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP2K1 MUTATED     10    1
  MAP2K1 WILD-TYPE  365   64
   clus
vv  MAP2K1 MUTATED MAP2K1 WILD-TYPE
  0             10              365
  1              1               64
[1] 2 2
[1] FALSE
D1273V8, binary
                  cls
clus                 0   1
  MAP2K1 MUTATED     7   5
  MAP2K1 WILD-TYPE 218 259
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP2K1 MUTATED      7    5
  MAP2K1 WILD-TYPE  218  259
        clus
vv       MAP2K1 MUTATED MAP2K1 WILD-TYPE
  FEMALE              7              218
  MALE                5              259
[1] 2 2
[1] FALSE
D1273V9, binary
                  cls
clus                 0   1
  MAP2K1 MUTATED    12   0
  MAP2K1 WILD-TYPE 338  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAP2K1 MUTATED     12    0
  MAP2K1 WILD-TYPE  338   22
     clus
vv    MAP2K1 MUTATED MAP2K1 WILD-TYPE
  NO              12              338
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MAP2K1 MUTATED                      8                             1
  MAP2K1 WILD-TYPE                  307                            46
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MAP2K1 MUTATED                       2                              0
  MAP2K1 WILD-TYPE                   104                             10
D1273V10, multiclass
                                clus
vv                               MAP2K1 MUTATED MAP2K1 WILD-TYPE
  COLON ADENOCARCINOMA                        8              307
  COLON MUCINOUS ADENOCARCINOMA               1               46
  RECTAL ADENOCARCINOMA                       2              104
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  MAP2K1 MUTATED    11   0   1   0
  MAP2K1 WILD-TYPE 334   4  30  25
D1273V11, multiclass
    clus
vv   MAP2K1 MUTATED MAP2K1 WILD-TYPE
  R0             11              334
  R1              0                4
  R2              1               30
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1273V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MAP2K1 MUTATED                                  0     0
  MAP2K1 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  MAP2K1 MUTATED                           2     4
  MAP2K1 WILD-TYPE                        20   222
D1273V13, multiclass
                                  clus
vv                                 MAP2K1 MUTATED MAP2K1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     2               20
  WHITE                                         4              222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1274) Variable = RRAS2 MUTATION ANALYSIS
D1274V1, survival
                 sevent
clus2               0   1
  RRAS2 MUTATED     5   1
  RRAS2 WILD-TYPE 373  92
  RRAS2 MUTATED RRAS2 WILD-TYPE 
              6             465 
  RRAS2 MUTATED RRAS2 WILD-TYPE 
              1              92 
$`RRAS2 MUTATED`
TCGA-A6-5665 TCGA-CA-6717 TCGA-F4-6808 TCGA-AF-5654 TCGA-AG-A002 TCGA-CL-5918 
       22.06        12.76        33.67        16.83        20.98         7.17 

$`RRAS2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07        12.20        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-6136 
       13.55        19.10        34.49        10.39        14.50        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        6.97         4.73        78.12        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  RRAS2 MUTATED RRAS2 WILD-TYPE 
           7.17            0.00 
  RRAS2 MUTATED RRAS2 WILD-TYPE 
          33.67          148.01 
  RRAS2 MUTATED RRAS2 WILD-TYPE 
         18.905          20.190 
[1] "7.2 - 33.7 (18.9)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.2"
D1274V2, continuous
D1274V3, binary
                 cls
clus                0   1
  RRAS2 MUTATED     4   3
  RRAS2 WILD-TYPE 362 116
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RRAS2 MUTATED      4    3
  RRAS2 WILD-TYPE  362  116
        clus
vv       RRAS2 MUTATED RRAS2 WILD-TYPE
  COLON              4             362
  RECTUM             3             116
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RRAS2 MUTATED         3        0        0         4         0         0
  RRAS2 WILD-TYPE      88        1       32       134        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RRAS2 MUTATED           0          0          0          0        0         0
  RRAS2 WILD-TYPE        24         11         59         42       48        18
                 vv
clus              STAGE IVB
  RRAS2 MUTATED           0
  RRAS2 WILD-TYPE         1
D1274V4, multiclass
            clus
vv           RRAS2 MUTATED RRAS2 WILD-TYPE
  STAGE I                3              88
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              4             134
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  RRAS2 MUTATED     1   2   4   0
  RRAS2 WILD-TYPE  16  90 325  50
D1274V5, multiclass
    clus
vv   RRAS2 MUTATED RRAS2 WILD-TYPE
  T1             1              16
  T2             2              90
  T3             4             325
  T4             0              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  RRAS2 MUTATED     7   0   0
  RRAS2 WILD-TYPE 280 113  87
D1274V6, multiclass
    clus
vv   RRAS2 MUTATED RRAS2 WILD-TYPE
  N0             7             280
  N1             0             113
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1274V7, binary
                 cls
clus                0   1
  RRAS2 MUTATED     6   0
  RRAS2 WILD-TYPE 369  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RRAS2 MUTATED      6    0
  RRAS2 WILD-TYPE  369   65
   clus
vv  RRAS2 MUTATED RRAS2 WILD-TYPE
  0             6             369
  1             0              65
[1] 2 2
[1] FALSE
D1274V8, binary
                 cls
clus                0   1
  RRAS2 MUTATED     5   2
  RRAS2 WILD-TYPE 220 262
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RRAS2 MUTATED      5    2
  RRAS2 WILD-TYPE  220  262
        clus
vv       RRAS2 MUTATED RRAS2 WILD-TYPE
  FEMALE             5             220
  MALE               2             262
[1] 2 2
[1] FALSE
D1274V9, binary
                 cls
clus                0   1
  RRAS2 MUTATED     6   0
  RRAS2 WILD-TYPE 344  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RRAS2 MUTATED      6    0
  RRAS2 WILD-TYPE  344   22
     clus
vv    RRAS2 MUTATED RRAS2 WILD-TYPE
  NO              6             344
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  RRAS2 MUTATED                      3                             1
  RRAS2 WILD-TYPE                  312                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  RRAS2 MUTATED                       3                              0
  RRAS2 WILD-TYPE                   103                             10
D1274V10, multiclass
                                clus
vv                               RRAS2 MUTATED RRAS2 WILD-TYPE
  COLON ADENOCARCINOMA                       3             312
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      3             103
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  RRAS2 MUTATED     5   0   0   2
  RRAS2 WILD-TYPE 340   4  31  23
D1274V11, multiclass
    clus
vv   RRAS2 MUTATED RRAS2 WILD-TYPE
  R0             5             340
  R1             0               4
  R2             0              31
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1274V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RRAS2 MUTATED                                  0     1
  RRAS2 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  RRAS2 MUTATED                           0     4
  RRAS2 WILD-TYPE                        22   222
D1274V13, multiclass
                                  clus
vv                                 RRAS2 MUTATED RRAS2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        4             222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1275) Variable = TMLHE MUTATION ANALYSIS
D1275V1, survival
                 sevent
clus2               0   1
  TMLHE MUTATED     5   0
  TMLHE WILD-TYPE 373  93
  TMLHE MUTATED TMLHE WILD-TYPE 
              5             466 
  TMLHE MUTATED TMLHE WILD-TYPE 
              0              93 
$`TMLHE MUTATED`
TCGA-AA-3982 TCGA-G4-6309 TCGA-G4-6315 TCGA-AG-A002 TCGA-AH-6549 
       27.02        85.48        61.91        20.98        17.49 

$`TMLHE WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       24.00        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6310 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       63.62        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
       38.56         1.45         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  TMLHE MUTATED TMLHE WILD-TYPE 
          17.49            0.00 
  TMLHE MUTATED TMLHE WILD-TYPE 
          85.48          148.01 
  TMLHE MUTATED TMLHE WILD-TYPE 
         27.020          20.085 
[1] "17.5 - 85.5 (27.0)" "0.0 - 148.0 (20.1)"
[1] "hr="     "9200000"
D1275V2, continuous
D1275V3, binary
                 cls
clus                0   1
  TMLHE MUTATED     3   2
  TMLHE WILD-TYPE 363 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TMLHE MUTATED      3    2
  TMLHE WILD-TYPE  363  117
        clus
vv       TMLHE MUTATED TMLHE WILD-TYPE
  COLON              3             363
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TMLHE MUTATED         1        0        0         0         0         0
  TMLHE WILD-TYPE      90        1       32       138        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TMLHE MUTATED           0          0          2          0        1         0
  TMLHE WILD-TYPE        24         11         57         42       47        18
                 vv
clus              STAGE IVB
  TMLHE MUTATED           0
  TMLHE WILD-TYPE         1
D1275V4, multiclass
            clus
vv           TMLHE MUTATED TMLHE WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              0             138
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             2              57
  STAGE IIIC             0              42
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  TMLHE MUTATED     0   1   4   0
  TMLHE WILD-TYPE  17  91 325  50
D1275V5, multiclass
    clus
vv   TMLHE MUTATED TMLHE WILD-TYPE
  T1             0              17
  T2             1              91
  T3             4             325
  T4             0              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  TMLHE MUTATED     1   3   0
  TMLHE WILD-TYPE 286 110  87
D1275V6, multiclass
    clus
vv   TMLHE MUTATED TMLHE WILD-TYPE
  N0             1             286
  N1             3             110
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1275V7, binary
                 cls
clus                0   1
  TMLHE MUTATED     3   1
  TMLHE WILD-TYPE 372  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TMLHE MUTATED      3    1
  TMLHE WILD-TYPE  372   64
   clus
vv  TMLHE MUTATED TMLHE WILD-TYPE
  0             3             372
  1             1              64
[1] 2 2
[1] FALSE
D1275V8, binary
                 cls
clus                0   1
  TMLHE MUTATED     1   4
  TMLHE WILD-TYPE 224 260
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TMLHE MUTATED      1    4
  TMLHE WILD-TYPE  224  260
        clus
vv       TMLHE MUTATED TMLHE WILD-TYPE
  FEMALE             1             224
  MALE               4             260
[1] 2 2
[1] FALSE
D1275V9, binary
                 cls
clus                0   1
  TMLHE MUTATED     5   0
  TMLHE WILD-TYPE 345  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TMLHE MUTATED      5    0
  TMLHE WILD-TYPE  345   22
     clus
vv    TMLHE MUTATED TMLHE WILD-TYPE
  NO              5             345
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  TMLHE MUTATED                      3                             0
  TMLHE WILD-TYPE                  312                            47
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  TMLHE MUTATED                       2                              0
  TMLHE WILD-TYPE                   104                             10
D1275V10, multiclass
                                clus
vv                               TMLHE MUTATED TMLHE WILD-TYPE
  COLON ADENOCARCINOMA                       3             312
  COLON MUCINOUS ADENOCARCINOMA              0              47
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  TMLHE MUTATED     3   0   0   1
  TMLHE WILD-TYPE 342   4  31  24
D1275V11, multiclass
    clus
vv   TMLHE MUTATED TMLHE WILD-TYPE
  R0             3             342
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1275V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TMLHE MUTATED                                  0     0
  TMLHE WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  TMLHE MUTATED                           1     2
  TMLHE WILD-TYPE                        21   224
D1275V13, multiclass
                                  clus
vv                                 TMLHE MUTATED TMLHE WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        2             224
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1276) Variable = UGT1A1 MUTATION ANALYSIS
D1276V1, survival
                  sevent
clus2                0   1
  UGT1A1 MUTATED     4   7
  UGT1A1 WILD-TYPE 374  86
  UGT1A1 MUTATED UGT1A1 WILD-TYPE 
              11              460 
  UGT1A1 MUTATED UGT1A1 WILD-TYPE 
               7               86 
$`UGT1A1 MUTATED`
TCGA-AA-3663 TCGA-AA-3715 TCGA-AA-3947 TCGA-AA-A01P TCGA-AY-4070 TCGA-AZ-6598 
        6.97        19.04        33.01        38.07        16.31        49.41 
TCGA-AZ-6601 TCGA-CM-6161 TCGA-D5-5537 TCGA-D5-6537 TCGA-G4-6628 
      100.01        15.02        45.40         4.80        79.69 

$`UGT1A1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.05        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 
       36.00         5.03        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       12.99        24.00        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       31.00         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       14.50        27.09         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       88.21         6.77        12.10        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       17.03        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       12.03        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6538 
       18.25         1.32        43.27        15.12        17.85        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       46.75        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  UGT1A1 MUTATED UGT1A1 WILD-TYPE 
             4.8              0.0 
  UGT1A1 MUTATED UGT1A1 WILD-TYPE 
          100.01           148.01 
  UGT1A1 MUTATED UGT1A1 WILD-TYPE 
          33.010           20.155 
[1] "4.8 - 100.0 (33.0)" "0.0 - 148.0 (20.2)"
[1] "hr=" "2.4"
D1276V2, continuous
D1276V3, binary
                  cls
clus                 0   1
  UGT1A1 MUTATED    11   0
  UGT1A1 WILD-TYPE 355 119
[1] "tbl2"
                  cls
clus               [,1] [,2]
  UGT1A1 MUTATED     11    0
  UGT1A1 WILD-TYPE  355  119
        clus
vv       UGT1A1 MUTATED UGT1A1 WILD-TYPE
  COLON              11              355
  RECTUM              0              119
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  UGT1A1 MUTATED         2        0        4         1         1         0
  UGT1A1 WILD-TYPE      89        1       28       137         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  UGT1A1 MUTATED           1          0          1          1        0
  UGT1A1 WILD-TYPE        23         11         58         41       48
                  vv
clus               STAGE IVA STAGE IVB
  UGT1A1 MUTATED           0         0
  UGT1A1 WILD-TYPE        18         1
D1276V4, multiclass
            clus
vv           UGT1A1 MUTATED UGT1A1 WILD-TYPE
  STAGE I                 2               89
  STAGE IA                0                1
  STAGE II                4               28
  STAGE IIA               1              137
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               1               23
  STAGE IIIA              0               11
  STAGE IIIB              1               58
  STAGE IIIC              1               41
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  UGT1A1 MUTATED     0   2   8   1
  UGT1A1 WILD-TYPE  17  90 321  49
D1276V5, multiclass
    clus
vv   UGT1A1 MUTATED UGT1A1 WILD-TYPE
  T1              0               17
  T2              2               90
  T3              8              321
  T4              1               49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  UGT1A1 MUTATED     7   2   2
  UGT1A1 WILD-TYPE 280 111  85
D1276V6, multiclass
    clus
vv   UGT1A1 MUTATED UGT1A1 WILD-TYPE
  N0              7              280
  N1              2              111
  N2              2               85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1276V7, binary
                  cls
clus                 0   1
  UGT1A1 MUTATED     8   0
  UGT1A1 WILD-TYPE 367  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  UGT1A1 MUTATED      8    0
  UGT1A1 WILD-TYPE  367   65
   clus
vv  UGT1A1 MUTATED UGT1A1 WILD-TYPE
  0              8              367
  1              0               65
[1] 2 2
[1] FALSE
D1276V8, binary
                  cls
clus                 0   1
  UGT1A1 MUTATED     5   6
  UGT1A1 WILD-TYPE 220 258
[1] "tbl2"
                  cls
clus               [,1] [,2]
  UGT1A1 MUTATED      5    6
  UGT1A1 WILD-TYPE  220  258
        clus
vv       UGT1A1 MUTATED UGT1A1 WILD-TYPE
  FEMALE              5              220
  MALE                6              258
[1] 2 2
[1] FALSE
D1276V9, binary
                  cls
clus                 0   1
  UGT1A1 MUTATED    11   0
  UGT1A1 WILD-TYPE 339  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  UGT1A1 MUTATED     11    0
  UGT1A1 WILD-TYPE  339   22
     clus
vv    UGT1A1 MUTATED UGT1A1 WILD-TYPE
  NO              11              339
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  UGT1A1 MUTATED                     10                             1
  UGT1A1 WILD-TYPE                  305                            46
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  UGT1A1 MUTATED                       0                              0
  UGT1A1 WILD-TYPE                   106                             10
D1276V10, multiclass
                                clus
vv                               UGT1A1 MUTATED UGT1A1 WILD-TYPE
  COLON ADENOCARCINOMA                       10              305
  COLON MUCINOUS ADENOCARCINOMA               1               46
  RECTAL ADENOCARCINOMA                       0              106
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  UGT1A1 MUTATED     7   1   0   1
  UGT1A1 WILD-TYPE 338   3  31  24
D1276V11, multiclass
    clus
vv   UGT1A1 MUTATED UGT1A1 WILD-TYPE
  R0              7              338
  R1              1                3
  R2              0               31
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1276V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  UGT1A1 MUTATED                                  0     0
  UGT1A1 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  UGT1A1 MUTATED                           1     6
  UGT1A1 WILD-TYPE                        21   220
D1276V13, multiclass
                                  clus
vv                                 UGT1A1 MUTATED UGT1A1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                         6              220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1277) Variable = NCR3 MUTATION ANALYSIS
D1277V1, survival
                sevent
clus2              0   1
  NCR3 MUTATED     3   1
  NCR3 WILD-TYPE 375  92
  NCR3 MUTATED NCR3 WILD-TYPE 
             4            467 
  NCR3 MUTATED NCR3 WILD-TYPE 
             1             92 
$`NCR3 MUTATED`
TCGA-AA-3864 TCGA-AZ-6598 TCGA-CK-4952 TCGA-D5-6931 
       53.00        49.41        15.62        12.00 

$`NCR3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 
        5.13       106.75        22.36        62.79        88.21         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       85.45        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        4.80         1.51        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  NCR3 MUTATED NCR3 WILD-TYPE 
            12              0 
  NCR3 MUTATED NCR3 WILD-TYPE 
         53.00         148.01 
  NCR3 MUTATED NCR3 WILD-TYPE 
        32.515         20.190 
[1] "12.0 - 53.0 (32.5)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.1"
D1277V2, continuous
D1277V3, binary
                cls
clus               0   1
  NCR3 MUTATED     5   0
  NCR3 WILD-TYPE 361 119
[1] "tbl2"
                cls
clus             [,1] [,2]
  NCR3 MUTATED      5    0
  NCR3 WILD-TYPE  361  119
        clus
vv       NCR3 MUTATED NCR3 WILD-TYPE
  COLON             5            361
  RECTUM            0            119
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NCR3 MUTATED         0        0        2         0         1         0
  NCR3 WILD-TYPE      91        1       30       138         9         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NCR3 MUTATED           0          0          0          2        0         0
  NCR3 WILD-TYPE        24         11         59         40       48        18
                vv
clus             STAGE IVB
  NCR3 MUTATED           0
  NCR3 WILD-TYPE         1
D1277V4, multiclass
            clus
vv           NCR3 MUTATED NCR3 WILD-TYPE
  STAGE I               0             91
  STAGE IA              0              1
  STAGE II              2             30
  STAGE IIA             0            138
  STAGE IIB             1              9
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            0             59
  STAGE IIIC            2             40
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  NCR3 MUTATED     0   0   2   3
  NCR3 WILD-TYPE  17  92 327  47
D1277V5, multiclass
    clus
vv   NCR3 MUTATED NCR3 WILD-TYPE
  T1            0             17
  T2            0             92
  T3            2            327
  T4            3             47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  NCR3 MUTATED     3   0   2
  NCR3 WILD-TYPE 284 113  85
D1277V6, multiclass
    clus
vv   NCR3 MUTATED NCR3 WILD-TYPE
  N0            3            284
  N1            0            113
  N2            2             85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1277V7, binary
                cls
clus               0   1
  NCR3 MUTATED     3   0
  NCR3 WILD-TYPE 372  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  NCR3 MUTATED      3    0
  NCR3 WILD-TYPE  372   65
   clus
vv  NCR3 MUTATED NCR3 WILD-TYPE
  0            3            372
  1            0             65
[1] 2 2
[1] FALSE
D1277V8, binary
                cls
clus               0   1
  NCR3 MUTATED     3   2
  NCR3 WILD-TYPE 222 262
[1] "tbl2"
                cls
clus             [,1] [,2]
  NCR3 MUTATED      3    2
  NCR3 WILD-TYPE  222  262
        clus
vv       NCR3 MUTATED NCR3 WILD-TYPE
  FEMALE            3            222
  MALE              2            262
[1] 2 2
[1] FALSE
D1277V9, binary
                cls
clus               0   1
  NCR3 MUTATED     3   0
  NCR3 WILD-TYPE 347  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  NCR3 MUTATED      3    0
  NCR3 WILD-TYPE  347   22
     clus
vv    NCR3 MUTATED NCR3 WILD-TYPE
  NO             3            347
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  NCR3 MUTATED                      4                             1
  NCR3 WILD-TYPE                  311                            46
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  NCR3 MUTATED                       0                              0
  NCR3 WILD-TYPE                   106                             10
D1277V10, multiclass
                                clus
vv                               NCR3 MUTATED NCR3 WILD-TYPE
  COLON ADENOCARCINOMA                      4            311
  COLON MUCINOUS ADENOCARCINOMA             1             46
  RECTAL ADENOCARCINOMA                     0            106
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  NCR3 MUTATED     2   0   0   2
  NCR3 WILD-TYPE 343   4  31  23
D1277V11, multiclass
    clus
vv   NCR3 MUTATED NCR3 WILD-TYPE
  R0            2            343
  R1            0              4
  R2            0             31
  RX            2             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1277V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NCR3 MUTATED                                  0     0
  NCR3 WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  NCR3 MUTATED                           0     4
  NCR3 WILD-TYPE                        22   222
D1277V13, multiclass
                                  clus
vv                                 NCR3 MUTATED NCR3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       4            222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1278) Variable = AP1M1 MUTATION ANALYSIS
D1278V1, survival
                 sevent
clus2               0   1
  AP1M1 MUTATED     8   1
  AP1M1 WILD-TYPE 370  92
  AP1M1 MUTATED AP1M1 WILD-TYPE 
              9             462 
  AP1M1 MUTATED AP1M1 WILD-TYPE 
              1              92 
$`AP1M1 MUTATED`
TCGA-A6-5665 TCGA-AA-3819 TCGA-AA-A01R TCGA-AY-6197 TCGA-AZ-5407 TCGA-AZ-6601 
       22.06        25.02        35.01        21.44        88.21       100.01 
TCGA-CK-5913 TCGA-D5-6533 TCGA-D5-6536 
       51.32         1.32        17.85 

$`AP1M1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3821 TCGA-AA-3831 
       10.06        35.05        33.04         0.99         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T 
       31.00        31.00        38.07         1.02         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 
       62.79        49.41         6.77        12.10        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 
       17.56       148.01        85.45        15.62        49.08         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 
       55.92        20.19        18.25        43.27        15.12         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  AP1M1 MUTATED AP1M1 WILD-TYPE 
           1.32            0.00 
  AP1M1 MUTATED AP1M1 WILD-TYPE 
         100.01          148.01 
  AP1M1 MUTATED AP1M1 WILD-TYPE 
         25.020          20.035 
[1] "1.3 - 100.0 (25.0)" "0.0 - 148.0 (20.0)"
[1] "hr=" "2.7"
D1278V2, continuous
D1278V3, binary
                 cls
clus                0   1
  AP1M1 MUTATED     9   0
  AP1M1 WILD-TYPE 357 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AP1M1 MUTATED      9    0
  AP1M1 WILD-TYPE  357  119
        clus
vv       AP1M1 MUTATED AP1M1 WILD-TYPE
  COLON              9             357
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  AP1M1 MUTATED         1        0        1         5         0         0
  AP1M1 WILD-TYPE      90        1       31       133        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AP1M1 MUTATED           1          0          1          0        0         0
  AP1M1 WILD-TYPE        23         11         58         42       48        18
                 vv
clus              STAGE IVB
  AP1M1 MUTATED           0
  AP1M1 WILD-TYPE         1
D1278V4, multiclass
            clus
vv           AP1M1 MUTATED AP1M1 WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              5             133
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  AP1M1 MUTATED     1   0   7   1
  AP1M1 WILD-TYPE  16  92 322  49
D1278V5, multiclass
    clus
vv   AP1M1 MUTATED AP1M1 WILD-TYPE
  T1             1              16
  T2             0              92
  T3             7             322
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  AP1M1 MUTATED     8   0   1
  AP1M1 WILD-TYPE 279 113  86
D1278V6, multiclass
    clus
vv   AP1M1 MUTATED AP1M1 WILD-TYPE
  N0             8             279
  N1             0             113
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1278V7, binary
                 cls
clus                0   1
  AP1M1 MUTATED     7   0
  AP1M1 WILD-TYPE 368  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AP1M1 MUTATED      7    0
  AP1M1 WILD-TYPE  368   65
   clus
vv  AP1M1 MUTATED AP1M1 WILD-TYPE
  0             7             368
  1             0              65
[1] 2 2
[1] FALSE
D1278V8, binary
                 cls
clus                0   1
  AP1M1 MUTATED     5   4
  AP1M1 WILD-TYPE 220 260
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AP1M1 MUTATED      5    4
  AP1M1 WILD-TYPE  220  260
        clus
vv       AP1M1 MUTATED AP1M1 WILD-TYPE
  FEMALE             5             220
  MALE               4             260
[1] 2 2
[1] FALSE
D1278V9, binary
                 cls
clus                0   1
  AP1M1 MUTATED     7   1
  AP1M1 WILD-TYPE 343  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AP1M1 MUTATED      7    1
  AP1M1 WILD-TYPE  343   21
     clus
vv    AP1M1 MUTATED AP1M1 WILD-TYPE
  NO              7             343
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  AP1M1 MUTATED                      8                             1
  AP1M1 WILD-TYPE                  307                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  AP1M1 MUTATED                       0                              0
  AP1M1 WILD-TYPE                   106                             10
D1278V10, multiclass
                                clus
vv                               AP1M1 MUTATED AP1M1 WILD-TYPE
  COLON ADENOCARCINOMA                       8             307
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  AP1M1 MUTATED     6   0   0   1
  AP1M1 WILD-TYPE 339   4  31  24
D1278V11, multiclass
    clus
vv   AP1M1 MUTATED AP1M1 WILD-TYPE
  R0             6             339
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1278V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AP1M1 MUTATED                                  0     0
  AP1M1 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  AP1M1 MUTATED                           0     7
  AP1M1 WILD-TYPE                        22   219
D1278V13, multiclass
                                  clus
vv                                 AP1M1 MUTATED AP1M1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        7             219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1279) Variable = FBXL4 MUTATION ANALYSIS
D1279V1, survival
                 sevent
clus2               0   1
  FBXL4 MUTATED     7   0
  FBXL4 WILD-TYPE 371  93
  FBXL4 MUTATED FBXL4 WILD-TYPE 
              7             464 
  FBXL4 MUTATED FBXL4 WILD-TYPE 
              0              93 
$`FBXL4 MUTATED`
TCGA-A6-6780 TCGA-AZ-4315 TCGA-D5-6538 TCGA-DM-A1HA TCGA-AG-A002 TCGA-DY-A0XA 
       20.12        58.39        17.13       131.51        20.98       126.44 
TCGA-G5-6235 
       55.76 

$`FBXL4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        33.01        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
        4.80        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A282 
       12.59       140.38         7.50        44.32       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.03         5.29        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6641 
        0.69        26.43 

  FBXL4 MUTATED FBXL4 WILD-TYPE 
          17.13            0.00 
  FBXL4 MUTATED FBXL4 WILD-TYPE 
         131.51          148.01 
  FBXL4 MUTATED FBXL4 WILD-TYPE 
         55.760          20.035 
[1] "17.1 - 131.5 (55.8)" "0.0 - 148.0 (20.0)" 
[1] "hr="     "2.6e+07"
D1279V2, continuous
D1279V3, binary
                 cls
clus                0   1
  FBXL4 MUTATED     5   3
  FBXL4 WILD-TYPE 361 116
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FBXL4 MUTATED      5    3
  FBXL4 WILD-TYPE  361  116
        clus
vv       FBXL4 MUTATED FBXL4 WILD-TYPE
  COLON              5             361
  RECTUM             3             116
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FBXL4 MUTATED         1        0        1         3         0         0
  FBXL4 WILD-TYPE      90        1       31       135        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  FBXL4 MUTATED           0          0          2          1        0         0
  FBXL4 WILD-TYPE        24         11         57         41       48        18
                 vv
clus              STAGE IVB
  FBXL4 MUTATED           0
  FBXL4 WILD-TYPE         1
D1279V4, multiclass
            clus
vv           FBXL4 MUTATED FBXL4 WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              3             135
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             2              57
  STAGE IIIC             1              41
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  FBXL4 MUTATED     0   1   6   1
  FBXL4 WILD-TYPE  17  91 323  49
D1279V5, multiclass
    clus
vv   FBXL4 MUTATED FBXL4 WILD-TYPE
  T1             0              17
  T2             1              91
  T3             6             323
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  FBXL4 MUTATED     5   1   2
  FBXL4 WILD-TYPE 282 112  85
D1279V6, multiclass
    clus
vv   FBXL4 MUTATED FBXL4 WILD-TYPE
  N0             5             282
  N1             1             112
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1279V7, binary
                 cls
clus                0   1
  FBXL4 MUTATED     6   0
  FBXL4 WILD-TYPE 369  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FBXL4 MUTATED      6    0
  FBXL4 WILD-TYPE  369   65
   clus
vv  FBXL4 MUTATED FBXL4 WILD-TYPE
  0             6             369
  1             0              65
[1] 2 2
[1] FALSE
D1279V8, binary
                 cls
clus                0   1
  FBXL4 MUTATED     3   5
  FBXL4 WILD-TYPE 222 259
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FBXL4 MUTATED      3    5
  FBXL4 WILD-TYPE  222  259
        clus
vv       FBXL4 MUTATED FBXL4 WILD-TYPE
  FEMALE             3             222
  MALE               5             259
[1] 2 2
[1] FALSE
D1279V9, binary
                 cls
clus                0   1
  FBXL4 MUTATED     5   0
  FBXL4 WILD-TYPE 345  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FBXL4 MUTATED      5    0
  FBXL4 WILD-TYPE  345   22
     clus
vv    FBXL4 MUTATED FBXL4 WILD-TYPE
  NO              5             345
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  FBXL4 MUTATED                      4                             1
  FBXL4 WILD-TYPE                  311                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  FBXL4 MUTATED                       3                              0
  FBXL4 WILD-TYPE                   103                             10
D1279V10, multiclass
                                clus
vv                               FBXL4 MUTATED FBXL4 WILD-TYPE
  COLON ADENOCARCINOMA                       4             311
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      3             103
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  FBXL4 MUTATED     4   1   0   0
  FBXL4 WILD-TYPE 341   3  31  25
D1279V11, multiclass
    clus
vv   FBXL4 MUTATED FBXL4 WILD-TYPE
  R0             4             341
  R1             1               3
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1279V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FBXL4 MUTATED                                  0     0
  FBXL4 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  FBXL4 MUTATED                           0     6
  FBXL4 WILD-TYPE                        22   220
D1279V13, multiclass
                                  clus
vv                                 FBXL4 MUTATED FBXL4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        6             220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1280) Variable = KRT222 MUTATION ANALYSIS
D1280V1, survival
                  sevent
clus2                0   1
  KRT222 MUTATED     7   1
  KRT222 WILD-TYPE 371  92
  KRT222 MUTATED KRT222 WILD-TYPE 
               8              463 
  KRT222 MUTATED KRT222 WILD-TYPE 
               1               92 
$`KRT222 MUTATED`
TCGA-AA-A00N TCGA-AA-A010 TCGA-AZ-4315 TCGA-F4-6704 TCGA-G4-6586 TCGA-AG-A002 
        4.01        34.98        58.39         1.55        35.80        20.98 
TCGA-AH-6549 TCGA-DC-5337 
       17.49        15.02 

$`KRT222 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       33.01        21.44        17.82         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
       47.87        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
       78.12         7.17         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  KRT222 MUTATED KRT222 WILD-TYPE 
            1.55             0.00 
  KRT222 MUTATED KRT222 WILD-TYPE 
           58.39           148.01 
  KRT222 MUTATED KRT222 WILD-TYPE 
          19.235           20.190 
[1] "1.6 - 58.4 (19.2)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.4"
D1280V2, continuous
D1280V3, binary
                  cls
clus                 0   1
  KRT222 MUTATED     5   3
  KRT222 WILD-TYPE 361 116
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KRT222 MUTATED      5    3
  KRT222 WILD-TYPE  361  116
        clus
vv       KRT222 MUTATED KRT222 WILD-TYPE
  COLON               5              361
  RECTUM              3              116
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KRT222 MUTATED         2        0        0         2         2         0
  KRT222 WILD-TYPE      89        1       32       136         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KRT222 MUTATED           0          0          0          1        0
  KRT222 WILD-TYPE        24         11         59         41       48
                  vv
clus               STAGE IVA STAGE IVB
  KRT222 MUTATED           0         0
  KRT222 WILD-TYPE        18         1
D1280V4, multiclass
            clus
vv           KRT222 MUTATED KRT222 WILD-TYPE
  STAGE I                 2               89
  STAGE IA                0                1
  STAGE II                0               32
  STAGE IIA               2              136
  STAGE IIB               2                8
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              0               59
  STAGE IIIC              1               41
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  KRT222 MUTATED     1   1   4   2
  KRT222 WILD-TYPE  16  91 325  48
D1280V5, multiclass
    clus
vv   KRT222 MUTATED KRT222 WILD-TYPE
  T1              1               16
  T2              1               91
  T3              4              325
  T4              2               48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  KRT222 MUTATED     6   0   1
  KRT222 WILD-TYPE 281 113  86
D1280V6, multiclass
    clus
vv   KRT222 MUTATED KRT222 WILD-TYPE
  N0              6              281
  N1              0              113
  N2              1               86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1280V7, binary
                  cls
clus                 0   1
  KRT222 MUTATED     6   0
  KRT222 WILD-TYPE 369  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KRT222 MUTATED      6    0
  KRT222 WILD-TYPE  369   65
   clus
vv  KRT222 MUTATED KRT222 WILD-TYPE
  0              6              369
  1              0               65
[1] 2 2
[1] FALSE
D1280V8, binary
                  cls
clus                 0   1
  KRT222 MUTATED     2   6
  KRT222 WILD-TYPE 223 258
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KRT222 MUTATED      2    6
  KRT222 WILD-TYPE  223  258
        clus
vv       KRT222 MUTATED KRT222 WILD-TYPE
  FEMALE              2              223
  MALE                6              258
[1] 2 2
[1] FALSE
D1280V9, binary
                  cls
clus                 0   1
  KRT222 MUTATED     6   0
  KRT222 WILD-TYPE 344  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KRT222 MUTATED      6    0
  KRT222 WILD-TYPE  344   22
     clus
vv    KRT222 MUTATED KRT222 WILD-TYPE
  NO               6              344
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  KRT222 MUTATED                      3                             2
  KRT222 WILD-TYPE                  312                            45
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  KRT222 MUTATED                       3                              0
  KRT222 WILD-TYPE                   103                             10
D1280V10, multiclass
                                clus
vv                               KRT222 MUTATED KRT222 WILD-TYPE
  COLON ADENOCARCINOMA                        3              312
  COLON MUCINOUS ADENOCARCINOMA               2               45
  RECTAL ADENOCARCINOMA                       3              103
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  KRT222 MUTATED     7   0   0   1
  KRT222 WILD-TYPE 338   4  31  24
D1280V11, multiclass
    clus
vv   KRT222 MUTATED KRT222 WILD-TYPE
  R0              7              338
  R1              0                4
  R2              0               31
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1280V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KRT222 MUTATED                                  1     0
  KRT222 WILD-TYPE                                0    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  KRT222 MUTATED                           0     4
  KRT222 WILD-TYPE                        22   222
D1280V13, multiclass
                                  clus
vv                                 KRT222 MUTATED KRT222 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              1                0
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         4              222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1281) Variable = CDC42BPA MUTATION ANALYSIS
D1281V1, survival
                    sevent
clus2                  0   1
  CDC42BPA MUTATED    19  11
  CDC42BPA WILD-TYPE 359  82
  CDC42BPA MUTATED CDC42BPA WILD-TYPE 
                30                441 
  CDC42BPA MUTATED CDC42BPA WILD-TYPE 
                11                 82 
$`CDC42BPA MUTATED`
TCGA-A6-2672 TCGA-A6-4105 TCGA-A6-5657 TCGA-A6-5661 TCGA-AA-3492 TCGA-AA-3516 
       46.65        14.53        31.63        33.53         3.02        13.02 
TCGA-AA-3655 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3864 TCGA-AA-3950 
       61.02        85.05        26.99        19.04        53.00        24.00 
TCGA-AA-3977 TCGA-AA-A00J TCGA-AA-A00N TCGA-AA-A02J TCGA-AD-6888 TCGA-AD-6889 
       25.02        18.05         4.01         5.03        15.52        56.55 
TCGA-AZ-4315 TCGA-AZ-4616 TCGA-AZ-6601 TCGA-CA-6717 TCGA-CM-5349 TCGA-DM-A1DB 
       58.39         5.13       100.01        12.76        30.08        44.32 
TCGA-DM-A28G TCGA-F4-6703 TCGA-F4-6856 TCGA-G4-6588 TCGA-G4-6626 TCGA-AG-A002 
       60.79        47.87        35.31        26.17        46.75        20.98 

$`CDC42BPA WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5659 
       34.65        33.34        32.75        36.53        32.91        30.44 
TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 
       29.19        23.61        22.09        22.06        32.71        27.09 
TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 
       22.52         8.38        25.08        25.18        24.16        21.76 
TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       24.69        24.39        23.87        20.12        19.66        20.28 
TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
        7.04         1.02        35.01        63.98         6.97         1.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 
       20.98        19.99        13.94        19.99        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       36.00         5.03        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       31.07        30.05        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       26.01         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L 
       38.04        19.00        30.02        34.03        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        2.01        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       40.96         0.07        21.37         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
       16.31         0.95        33.01        21.44        17.82         1.41 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
       12.10        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       29.06        22.03        22.98        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
        7.50       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
      119.93        35.97       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       35.74         6.18         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 
       33.67        13.25         0.53        47.41       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 
       61.91        36.00        22.09        13.78        35.80        91.79 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  CDC42BPA MUTATED CDC42BPA WILD-TYPE 
              3.02               0.00 
  CDC42BPA MUTATED CDC42BPA WILD-TYPE 
            100.01             148.01 
  CDC42BPA MUTATED CDC42BPA WILD-TYPE 
            28.535             19.990 
[1] "3.0 - 100.0 (28.5)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.4"
D1281V2, continuous
D1281V3, binary
                    cls
clus                   0   1
  CDC42BPA MUTATED    29   1
  CDC42BPA WILD-TYPE 337 118
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  CDC42BPA MUTATED     29    1
  CDC42BPA WILD-TYPE  337  118
        clus
vv       CDC42BPA MUTATED CDC42BPA WILD-TYPE
  COLON                29                337
  RECTUM                1                118
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CDC42BPA MUTATED         2        0        4        13         1         0
  CDC42BPA WILD-TYPE      89        1       28       125         9         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CDC42BPA MUTATED           2          0          4          0        3
  CDC42BPA WILD-TYPE        22         11         55         42       45
                    vv
clus                 STAGE IVA STAGE IVB
  CDC42BPA MUTATED           0         0
  CDC42BPA WILD-TYPE        18         1
D1281V4, multiclass
            clus
vv           CDC42BPA MUTATED CDC42BPA WILD-TYPE
  STAGE I                   2                 89
  STAGE IA                  0                  1
  STAGE II                  4                 28
  STAGE IIA                13                125
  STAGE IIB                 1                  9
  STAGE IIC                 0                  1
  STAGE III                 2                 22
  STAGE IIIA                0                 11
  STAGE IIIB                4                 55
  STAGE IIIC                0                 42
  STAGE IV                  3                 45
  STAGE IVA                 0                 18
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  CDC42BPA MUTATED     0   3  25   2
  CDC42BPA WILD-TYPE  17  89 304  48
D1281V5, multiclass
    clus
vv   CDC42BPA MUTATED CDC42BPA WILD-TYPE
  T1                0                 17
  T2                3                 89
  T3               25                304
  T4                2                 48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  CDC42BPA MUTATED    24   4   2
  CDC42BPA WILD-TYPE 263 109  85
D1281V6, multiclass
    clus
vv   CDC42BPA MUTATED CDC42BPA WILD-TYPE
  N0               24                263
  N1                4                109
  N2                2                 85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1281V7, binary
                    cls
clus                   0   1
  CDC42BPA MUTATED    26   3
  CDC42BPA WILD-TYPE 349  62
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  CDC42BPA MUTATED     26    3
  CDC42BPA WILD-TYPE  349   62
   clus
vv  CDC42BPA MUTATED CDC42BPA WILD-TYPE
  0               26                349
  1                3                 62
[1] 2 2
[1] FALSE
D1281V8, binary
                    cls
clus                   0   1
  CDC42BPA MUTATED    10  20
  CDC42BPA WILD-TYPE 215 244
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  CDC42BPA MUTATED     10   20
  CDC42BPA WILD-TYPE  215  244
        clus
vv       CDC42BPA MUTATED CDC42BPA WILD-TYPE
  FEMALE               10                215
  MALE                 20                244
[1] 2 2
[1] FALSE
D1281V9, binary
                    cls
clus                   0   1
  CDC42BPA MUTATED    24   1
  CDC42BPA WILD-TYPE 326  21
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  CDC42BPA MUTATED     24    1
  CDC42BPA WILD-TYPE  326   21
     clus
vv    CDC42BPA MUTATED CDC42BPA WILD-TYPE
  NO                24                326
  YES                1                 21
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CDC42BPA MUTATED                     23                             6
  CDC42BPA WILD-TYPE                  292                            41
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CDC42BPA MUTATED                       1                              0
  CDC42BPA WILD-TYPE                   105                             10
D1281V10, multiclass
                                clus
vv                               CDC42BPA MUTATED CDC42BPA WILD-TYPE
  COLON ADENOCARCINOMA                         23                292
  COLON MUCINOUS ADENOCARCINOMA                 6                 41
  RECTAL ADENOCARCINOMA                         1                105
  RECTAL MUCINOUS ADENOCARCINOMA                0                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  CDC42BPA MUTATED    19   0   2   1
  CDC42BPA WILD-TYPE 326   4  29  24
D1281V11, multiclass
    clus
vv   CDC42BPA MUTATED CDC42BPA WILD-TYPE
  R0               19                326
  R1                0                  4
  R2                2                 29
  RX                1                 24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1281V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CDC42BPA MUTATED                                  0     2
  CDC42BPA WILD-TYPE                                1     9
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  CDC42BPA MUTATED                           2    13
  CDC42BPA WILD-TYPE                        20   213
D1281V13, multiclass
                                  clus
vv                                 CDC42BPA MUTATED CDC42BPA WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           2                  9
  BLACK OR AFRICAN AMERICAN                       2                 20
  WHITE                                          13                213
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1282) Variable = USP44 MUTATION ANALYSIS
D1282V1, survival
                 sevent
clus2               0   1
  USP44 MUTATED    13   2
  USP44 WILD-TYPE 365  91
  USP44 MUTATED USP44 WILD-TYPE 
             15             456 
  USP44 MUTATED USP44 WILD-TYPE 
              2              91 
$`USP44 MUTATED`
TCGA-AA-3672 TCGA-AA-3713 TCGA-AA-3864 TCGA-AA-3966 TCGA-AA-3977 TCGA-AA-A00A 
        0.92        19.04        53.00         2.01        25.02        38.04 
TCGA-AA-A00N TCGA-AA-A010 TCGA-AD-6889 TCGA-CM-5344 TCGA-DM-A1D0 TCGA-DM-A1DA 
        4.01        34.98        56.55        22.03       130.65         7.50 
TCGA-F4-6807 TCGA-G4-6588 TCGA-AG-A002 
       16.24        26.17        20.98 

$`USP44 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
        6.05         6.97        54.02         2.01        14.01        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 
        0.99        31.07        31.07        30.05        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
       34.03        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       27.02        13.94        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       13.02        29.06        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
       38.20        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       41.42        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       35.80        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  USP44 MUTATED USP44 WILD-TYPE 
           0.92            0.00 
  USP44 MUTATED USP44 WILD-TYPE 
         130.65          148.01 
  USP44 MUTATED USP44 WILD-TYPE 
         22.030          20.085 
[1] "0.9 - 130.7 (22.0)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.6"
D1282V2, continuous
D1282V3, binary
                 cls
clus                0   1
  USP44 MUTATED    16   1
  USP44 WILD-TYPE 350 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP44 MUTATED     16    1
  USP44 WILD-TYPE  350  118
        clus
vv       USP44 MUTATED USP44 WILD-TYPE
  COLON             16             350
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  USP44 MUTATED         1        0        2         6         2         0
  USP44 WILD-TYPE      90        1       30       132         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  USP44 MUTATED           1          0          1          2        1         0
  USP44 WILD-TYPE        23         11         58         40       47        18
                 vv
clus              STAGE IVB
  USP44 MUTATED           0
  USP44 WILD-TYPE         1
D1282V4, multiclass
            clus
vv           USP44 MUTATED USP44 WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA              6             132
  STAGE IIB              2               8
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             2              40
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  USP44 MUTATED     0   2  12   3
  USP44 WILD-TYPE  17  90 317  47
D1282V5, multiclass
    clus
vv   USP44 MUTATED USP44 WILD-TYPE
  T1             0              17
  T2             2              90
  T3            12             317
  T4             3              47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  USP44 MUTATED    13   2   2
  USP44 WILD-TYPE 274 111  85
D1282V6, multiclass
    clus
vv   USP44 MUTATED USP44 WILD-TYPE
  N0            13             274
  N1             2             111
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1282V7, binary
                 cls
clus                0   1
  USP44 MUTATED    15   1
  USP44 WILD-TYPE 360  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP44 MUTATED     15    1
  USP44 WILD-TYPE  360   64
   clus
vv  USP44 MUTATED USP44 WILD-TYPE
  0            15             360
  1             1              64
[1] 2 2
[1] FALSE
D1282V8, binary
                 cls
clus                0   1
  USP44 MUTATED    10   7
  USP44 WILD-TYPE 215 257
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP44 MUTATED     10    7
  USP44 WILD-TYPE  215  257
        clus
vv       USP44 MUTATED USP44 WILD-TYPE
  FEMALE            10             215
  MALE               7             257
[1] 2 2
[1] FALSE
D1282V9, binary
                 cls
clus                0   1
  USP44 MUTATED     9   1
  USP44 WILD-TYPE 341  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP44 MUTATED      9    1
  USP44 WILD-TYPE  341   21
     clus
vv    USP44 MUTATED USP44 WILD-TYPE
  NO              9             341
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  USP44 MUTATED                     14                             2
  USP44 WILD-TYPE                  301                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  USP44 MUTATED                       1                              0
  USP44 WILD-TYPE                   105                             10
D1282V10, multiclass
                                clus
vv                               USP44 MUTATED USP44 WILD-TYPE
  COLON ADENOCARCINOMA                      14             301
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  USP44 MUTATED    11   0   1   0
  USP44 WILD-TYPE 334   4  30  25
D1282V11, multiclass
    clus
vv   USP44 MUTATED USP44 WILD-TYPE
  R0            11             334
  R1             0               4
  R2             1              30
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1282V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  USP44 MUTATED                                  0     1
  USP44 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  USP44 MUTATED                           0     5
  USP44 WILD-TYPE                        22   221
D1282V13, multiclass
                                  clus
vv                                 USP44 MUTATED USP44 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        5             221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1283) Variable = PLCG2 MUTATION ANALYSIS
D1283V1, survival
                 sevent
clus2               0   1
  PLCG2 MUTATED    16   5
  PLCG2 WILD-TYPE 362  88
  PLCG2 MUTATED PLCG2 WILD-TYPE 
             21             450 
  PLCG2 MUTATED PLCG2 WILD-TYPE 
              5              88 
$`PLCG2 MUTATED`
TCGA-A6-6138 TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3662 TCGA-AA-3715 TCGA-AA-3812 
       22.52         3.02        63.98         6.05        19.04        35.05 
TCGA-AA-3855 TCGA-AA-3947 TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01P TCGA-AZ-4315 
       32.05        33.01         4.01        34.98        38.07        58.39 
TCGA-CA-6717 TCGA-CM-6164 TCGA-CM-6171 TCGA-D5-6930 TCGA-G4-6586 TCGA-G4-6588 
       12.76        29.03        14.04         1.51        35.80        26.17 
TCGA-AG-A002 TCGA-AG-A020 TCGA-DY-A1H8 
       20.98        10.98        32.61 

$`PLCG2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6141 TCGA-A6-6142 
       22.09        22.06        32.71        27.09         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 
       20.12        19.66        20.28         7.04         1.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02        78.08         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       26.99        19.04        10.06        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       36.03         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
        2.01        12.99        24.00        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07        12.20        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6165 TCGA-CM-6166 
       17.03        15.02        12.00         2.96        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 
       14.99        12.99        13.02        15.02        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        4.80        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       36.00        22.09        13.78        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       64.01        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EF-5830 TCGA-EI-6506 
       41.36        57.24        24.13        51.48         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  PLCG2 MUTATED PLCG2 WILD-TYPE 
           1.51            0.00 
  PLCG2 MUTATED PLCG2 WILD-TYPE 
          63.98          148.01 
  PLCG2 MUTATED PLCG2 WILD-TYPE 
         26.170          20.035 
[1] "1.5 - 64.0 (26.2)"  "0.0 - 148.0 (20.0)"
[1] "hr=" "1.3"
D1283V2, continuous
D1283V3, binary
                 cls
clus                0   1
  PLCG2 MUTATED    18   3
  PLCG2 WILD-TYPE 348 116
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PLCG2 MUTATED     18    3
  PLCG2 WILD-TYPE  348  116
        clus
vv       PLCG2 MUTATED PLCG2 WILD-TYPE
  COLON             18             348
  RECTUM             3             116
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PLCG2 MUTATED         4        0        3         7         3         0
  PLCG2 WILD-TYPE      87        1       29       131         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PLCG2 MUTATED           2          1          0          0        1         0
  PLCG2 WILD-TYPE        22         10         59         42       47        18
                 vv
clus              STAGE IVB
  PLCG2 MUTATED           0
  PLCG2 WILD-TYPE         1
D1283V4, multiclass
            clus
vv           PLCG2 MUTATED PLCG2 WILD-TYPE
  STAGE I                4              87
  STAGE IA               0               1
  STAGE II               3              29
  STAGE IIA              7             131
  STAGE IIB              3               7
  STAGE IIC              0               1
  STAGE III              2              22
  STAGE IIIA             1              10
  STAGE IIIB             0              59
  STAGE IIIC             0              42
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PLCG2 MUTATED     0   5  12   4
  PLCG2 WILD-TYPE  17  87 317  46
D1283V5, multiclass
    clus
vv   PLCG2 MUTATED PLCG2 WILD-TYPE
  T1             0              17
  T2             5              87
  T3            12             317
  T4             4              46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  PLCG2 MUTATED    17   3   1
  PLCG2 WILD-TYPE 270 110  86
D1283V6, multiclass
    clus
vv   PLCG2 MUTATED PLCG2 WILD-TYPE
  N0            17             270
  N1             3             110
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1283V7, binary
                 cls
clus                0   1
  PLCG2 MUTATED    20   1
  PLCG2 WILD-TYPE 355  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PLCG2 MUTATED     20    1
  PLCG2 WILD-TYPE  355   64
   clus
vv  PLCG2 MUTATED PLCG2 WILD-TYPE
  0            20             355
  1             1              64
[1] 2 2
[1] FALSE
D1283V8, binary
                 cls
clus                0   1
  PLCG2 MUTATED    12   9
  PLCG2 WILD-TYPE 213 255
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PLCG2 MUTATED     12    9
  PLCG2 WILD-TYPE  213  255
        clus
vv       PLCG2 MUTATED PLCG2 WILD-TYPE
  FEMALE            12             213
  MALE               9             255
[1] 2 2
[1] FALSE
D1283V9, binary
                 cls
clus                0   1
  PLCG2 MUTATED    17   0
  PLCG2 WILD-TYPE 333  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PLCG2 MUTATED     17    0
  PLCG2 WILD-TYPE  333   22
     clus
vv    PLCG2 MUTATED PLCG2 WILD-TYPE
  NO             17             333
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PLCG2 MUTATED                     14                             4
  PLCG2 WILD-TYPE                  301                            43
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PLCG2 MUTATED                       2                              1
  PLCG2 WILD-TYPE                   104                              9
D1283V10, multiclass
                                clus
vv                               PLCG2 MUTATED PLCG2 WILD-TYPE
  COLON ADENOCARCINOMA                      14             301
  COLON MUCINOUS ADENOCARCINOMA              4              43
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             1               9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  PLCG2 MUTATED    17   0   1   1
  PLCG2 WILD-TYPE 328   4  30  24
D1283V11, multiclass
    clus
vv   PLCG2 MUTATED PLCG2 WILD-TYPE
  R0            17             328
  R1             0               4
  R2             1              30
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1283V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PLCG2 MUTATED                                  0     1
  PLCG2 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PLCG2 MUTATED                           0     8
  PLCG2 WILD-TYPE                        22   218
D1283V13, multiclass
                                  clus
vv                                 PLCG2 MUTATED PLCG2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        8             218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1284) Variable = RDBP MUTATION ANALYSIS
D1284V1, survival
                sevent
clus2              0   1
  RDBP MUTATED     7   0
  RDBP WILD-TYPE 371  93
  RDBP MUTATED RDBP WILD-TYPE 
             7            464 
  RDBP MUTATED RDBP WILD-TYPE 
             0             93 
$`RDBP MUTATED`
TCGA-A6-3809 TCGA-A6-6653 TCGA-AA-3663 TCGA-AY-6197 TCGA-CK-5913 TCGA-CM-6162 
       32.75        24.39         6.97        21.44        51.32        12.00 
TCGA-AG-3892 
       13.02 

$`RDBP WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 
       25.18        24.16        21.76        24.69        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       49.08         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 
       15.02        15.02        17.03        15.02         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       36.95        17.03        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  RDBP MUTATED RDBP WILD-TYPE 
          6.97           0.00 
  RDBP MUTATED RDBP WILD-TYPE 
         51.32         148.01 
  RDBP MUTATED RDBP WILD-TYPE 
        21.440         20.155 
[1] "7.0 - 51.3 (21.4)"  "0.0 - 148.0 (20.2)"
[1] "hr="     "9100000"
D1284V2, continuous
D1284V3, binary
                cls
clus               0   1
  RDBP MUTATED     6   1
  RDBP WILD-TYPE 360 118
[1] "tbl2"
                cls
clus             [,1] [,2]
  RDBP MUTATED      6    1
  RDBP WILD-TYPE  360  118
        clus
vv       RDBP MUTATED RDBP WILD-TYPE
  COLON             6            360
  RECTUM            1            118
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RDBP MUTATED         2        0        1         2         1         0
  RDBP WILD-TYPE      89        1       31       136         9         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RDBP MUTATED           0          0          1          0        0         0
  RDBP WILD-TYPE        24         11         58         42       48        18
                vv
clus             STAGE IVB
  RDBP MUTATED           0
  RDBP WILD-TYPE         1
D1284V4, multiclass
            clus
vv           RDBP MUTATED RDBP WILD-TYPE
  STAGE I               2             89
  STAGE IA              0              1
  STAGE II              1             31
  STAGE IIA             2            136
  STAGE IIB             1              9
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            1             58
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  RDBP MUTATED     1   1   4   1
  RDBP WILD-TYPE  16  91 325  49
D1284V5, multiclass
    clus
vv   RDBP MUTATED RDBP WILD-TYPE
  T1            1             16
  T2            1             91
  T3            4            325
  T4            1             49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  RDBP MUTATED     6   1   0
  RDBP WILD-TYPE 281 112  87
D1284V6, multiclass
    clus
vv   RDBP MUTATED RDBP WILD-TYPE
  N0            6            281
  N1            1            112
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1284V7, binary
                cls
clus               0   1
  RDBP MUTATED     5   0
  RDBP WILD-TYPE 370  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  RDBP MUTATED      5    0
  RDBP WILD-TYPE  370   65
   clus
vv  RDBP MUTATED RDBP WILD-TYPE
  0            5            370
  1            0             65
[1] 2 2
[1] FALSE
D1284V8, binary
                cls
clus               0   1
  RDBP MUTATED     4   3
  RDBP WILD-TYPE 221 261
[1] "tbl2"
                cls
clus             [,1] [,2]
  RDBP MUTATED      4    3
  RDBP WILD-TYPE  221  261
        clus
vv       RDBP MUTATED RDBP WILD-TYPE
  FEMALE            4            221
  MALE              3            261
[1] 2 2
[1] FALSE
D1284V9, binary
                cls
clus               0   1
  RDBP MUTATED     7   0
  RDBP WILD-TYPE 343  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  RDBP MUTATED      7    0
  RDBP WILD-TYPE  343   22
     clus
vv    RDBP MUTATED RDBP WILD-TYPE
  NO             7            343
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  RDBP MUTATED                      4                             2
  RDBP WILD-TYPE                  311                            45
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  RDBP MUTATED                       1                              0
  RDBP WILD-TYPE                   105                             10
D1284V10, multiclass
                                clus
vv                               RDBP MUTATED RDBP WILD-TYPE
  COLON ADENOCARCINOMA                      4            311
  COLON MUCINOUS ADENOCARCINOMA             2             45
  RECTAL ADENOCARCINOMA                     1            105
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  RDBP MUTATED     5   0   0   1
  RDBP WILD-TYPE 340   4  31  24
D1284V11, multiclass
    clus
vv   RDBP MUTATED RDBP WILD-TYPE
  R0            5            340
  R1            0              4
  R2            0             31
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1284V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RDBP MUTATED                                  0     0
  RDBP WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  RDBP MUTATED                           0     5
  RDBP WILD-TYPE                        22   221
D1284V13, multiclass
                                  clus
vv                                 RDBP MUTATED RDBP WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       5            221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1285) Variable = RAPGEF2 MUTATION ANALYSIS
D1285V1, survival
                   sevent
clus2                 0   1
  RAPGEF2 MUTATED    19   4
  RAPGEF2 WILD-TYPE 359  89
  RAPGEF2 MUTATED RAPGEF2 WILD-TYPE 
               23               448 
  RAPGEF2 MUTATED RAPGEF2 WILD-TYPE 
                4                89 
$`RAPGEF2 MUTATED`
TCGA-A6-5665 TCGA-A6-6141 TCGA-A6-6781 TCGA-AA-3655 TCGA-AA-3821 TCGA-AA-3833 
       22.06         8.38        19.66        61.02         1.02        15.95 
TCGA-AA-3864 TCGA-AA-3977 TCGA-AA-A010 TCGA-AA-A01P TCGA-AD-5900 TCGA-AD-6895 
       53.00        25.02        34.98        38.07         0.07         0.72 
TCGA-AZ-4315 TCGA-AZ-6601 TCGA-CA-6717 TCGA-CK-5916 TCGA-DM-A0XD TCGA-DM-A1HB 
       58.39       100.01        12.76        21.14        24.43       135.65 
TCGA-G4-6586 TCGA-G4-6588 TCGA-AG-3892 TCGA-AG-A002 TCGA-AH-6549 
       35.80        26.17        13.02        20.98        17.49 

$`RAPGEF2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 
       22.09        32.71        27.09        22.52        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       19.99        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        0.99        25.02        17.98        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       31.00         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 
       40.96        21.37        15.52        56.55         0.79         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
       16.31         0.95        33.01        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77        12.10        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.20        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 
       15.62        49.08        51.32         9.99        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XF 
        1.51        12.00        11.38        10.26       119.70        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
        7.50        44.32       131.51       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       13.78        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
       38.56         1.45         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  RAPGEF2 MUTATED RAPGEF2 WILD-TYPE 
             0.07              0.00 
  RAPGEF2 MUTATED RAPGEF2 WILD-TYPE 
           135.65            148.01 
  RAPGEF2 MUTATED RAPGEF2 WILD-TYPE 
           22.060            20.035 
[1] "0.1 - 135.7 (22.1)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.4"
D1285V2, continuous
D1285V3, binary
                   cls
clus                  0   1
  RAPGEF2 MUTATED    21   3
  RAPGEF2 WILD-TYPE 345 116
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RAPGEF2 MUTATED     21    3
  RAPGEF2 WILD-TYPE  345  116
        clus
vv       RAPGEF2 MUTATED RAPGEF2 WILD-TYPE
  COLON               21               345
  RECTUM               3               116
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RAPGEF2 MUTATED         5        0        3         9         1         0
  RAPGEF2 WILD-TYPE      86        1       29       129         9         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RAPGEF2 MUTATED           1          0          1          1        0
  RAPGEF2 WILD-TYPE        23         11         58         41       48
                   vv
clus                STAGE IVA STAGE IVB
  RAPGEF2 MUTATED           0         0
  RAPGEF2 WILD-TYPE        18         1
D1285V4, multiclass
            clus
vv           RAPGEF2 MUTATED RAPGEF2 WILD-TYPE
  STAGE I                  5                86
  STAGE IA                 0                 1
  STAGE II                 3                29
  STAGE IIA                9               129
  STAGE IIB                1                 9
  STAGE IIC                0                 1
  STAGE III                1                23
  STAGE IIIA               0                11
  STAGE IIIB               1                58
  STAGE IIIC               1                41
  STAGE IV                 0                48
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  RAPGEF2 MUTATED     2   4  16   2
  RAPGEF2 WILD-TYPE  15  88 313  48
D1285V5, multiclass
    clus
vv   RAPGEF2 MUTATED RAPGEF2 WILD-TYPE
  T1               2                15
  T2               4                88
  T3              16               313
  T4               2                48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  RAPGEF2 MUTATED    19   4   0
  RAPGEF2 WILD-TYPE 268 109  87
D1285V6, multiclass
    clus
vv   RAPGEF2 MUTATED RAPGEF2 WILD-TYPE
  N0              19               268
  N1               4               109
  N2               0                87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1285V7, binary
                   cls
clus                  0   1
  RAPGEF2 MUTATED    19   0
  RAPGEF2 WILD-TYPE 356  65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RAPGEF2 MUTATED     19    0
  RAPGEF2 WILD-TYPE  356   65
   clus
vv  RAPGEF2 MUTATED RAPGEF2 WILD-TYPE
  0              19               356
  1               0                65
[1] 2 2
[1] FALSE
D1285V8, binary
                   cls
clus                  0   1
  RAPGEF2 MUTATED    10  14
  RAPGEF2 WILD-TYPE 215 250
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RAPGEF2 MUTATED     10   14
  RAPGEF2 WILD-TYPE  215  250
        clus
vv       RAPGEF2 MUTATED RAPGEF2 WILD-TYPE
  FEMALE              10               215
  MALE                14               250
[1] 2 2
[1] FALSE
D1285V9, binary
                   cls
clus                  0   1
  RAPGEF2 MUTATED    19   0
  RAPGEF2 WILD-TYPE 331  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RAPGEF2 MUTATED     19    0
  RAPGEF2 WILD-TYPE  331   22
     clus
vv    RAPGEF2 MUTATED RAPGEF2 WILD-TYPE
  NO               19               331
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  RAPGEF2 MUTATED                     16                             4
  RAPGEF2 WILD-TYPE                  299                            43
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  RAPGEF2 MUTATED                       3                              0
  RAPGEF2 WILD-TYPE                   103                             10
D1285V10, multiclass
                                clus
vv                               RAPGEF2 MUTATED RAPGEF2 WILD-TYPE
  COLON ADENOCARCINOMA                        16               299
  COLON MUCINOUS ADENOCARCINOMA                4                43
  RECTAL ADENOCARCINOMA                        3               103
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  RAPGEF2 MUTATED    15   0   0   3
  RAPGEF2 WILD-TYPE 330   4  31  22
D1285V11, multiclass
    clus
vv   RAPGEF2 MUTATED RAPGEF2 WILD-TYPE
  R0              15               330
  R1               0                 4
  R2               0                31
  RX               3                22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1285V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RAPGEF2 MUTATED                                  0     1
  RAPGEF2 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  RAPGEF2 MUTATED                           1    12
  RAPGEF2 WILD-TYPE                        21   214
D1285V13, multiclass
                                  clus
vv                                 RAPGEF2 MUTATED RAPGEF2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                10
  BLACK OR AFRICAN AMERICAN                      1                21
  WHITE                                         12               214
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1286) Variable = GDA MUTATION ANALYSIS
D1286V1, survival
               sevent
clus2             0   1
  GDA MUTATED     6   1
  GDA WILD-TYPE 372  92
  GDA MUTATED GDA WILD-TYPE 
            7           464 
  GDA MUTATED GDA WILD-TYPE 
            1            92 
$`GDA MUTATED`
TCGA-AZ-6600 TCGA-CK-5914 TCGA-CM-6163 TCGA-CM-6676 TCGA-D5-6535 TCGA-G4-6309 
       12.10         9.99         2.96        11.08        15.12        85.48 
TCGA-F5-6571 
       31.30 

$`GDA WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       49.41         6.77       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5916 
      148.01        85.45        15.62        49.08        51.32        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       15.02        12.00        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       13.05        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
        1.32        43.27        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       44.68        55.04        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
        9.96        49.51        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  GDA MUTATED GDA WILD-TYPE 
         2.96          0.00 
  GDA MUTATED GDA WILD-TYPE 
        85.48        148.01 
  GDA MUTATED GDA WILD-TYPE 
       12.100        20.415 
[1] "3.0 - 85.5 (12.1)"  "0.0 - 148.0 (20.4)"
[1] "hr=" "1.3"
D1286V2, continuous
D1286V3, binary
               cls
clus              0   1
  GDA MUTATED     6   1
  GDA WILD-TYPE 360 118
[1] "tbl2"
               cls
clus            [,1] [,2]
  GDA MUTATED      6    1
  GDA WILD-TYPE  360  118
        clus
vv       GDA MUTATED GDA WILD-TYPE
  COLON            6           360
  RECTUM           1           118
[1] 2 2
[1] FALSE
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GDA MUTATED         2        0        0         1         0         0
  GDA WILD-TYPE      89        1       32       137        10         1
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  GDA MUTATED           0          0          3          0        1         0
  GDA WILD-TYPE        24         11         56         42       47        18
               vv
clus            STAGE IVB
  GDA MUTATED           0
  GDA WILD-TYPE         1
D1286V4, multiclass
            clus
vv           GDA MUTATED GDA WILD-TYPE
  STAGE I              2            89
  STAGE IA             0             1
  STAGE II             0            32
  STAGE IIA            1           137
  STAGE IIB            0            10
  STAGE IIC            0             1
  STAGE III            0            24
  STAGE IIIA           0            11
  STAGE IIIB           3            56
  STAGE IIIC           0            42
  STAGE IV             1            47
  STAGE IVA            0            18
  STAGE IVB            0             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  GDA MUTATED     1   1   4   1
  GDA WILD-TYPE  16  91 325  49
D1286V5, multiclass
    clus
vv   GDA MUTATED GDA WILD-TYPE
  T1           1            16
  T2           1            91
  T3           4           325
  T4           1            49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2
  GDA MUTATED     3   4   0
  GDA WILD-TYPE 284 109  87
D1286V6, multiclass
    clus
vv   GDA MUTATED GDA WILD-TYPE
  N0           3           284
  N1           4           109
  N2           0            87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1286V7, binary
               cls
clus              0   1
  GDA MUTATED     4   1
  GDA WILD-TYPE 371  64
[1] "tbl2"
               cls
clus            [,1] [,2]
  GDA MUTATED      4    1
  GDA WILD-TYPE  371   64
   clus
vv  GDA MUTATED GDA WILD-TYPE
  0           4           371
  1           1            64
[1] 2 2
[1] FALSE
D1286V8, binary
               cls
clus              0   1
  GDA MUTATED     3   4
  GDA WILD-TYPE 222 260
[1] "tbl2"
               cls
clus            [,1] [,2]
  GDA MUTATED      3    4
  GDA WILD-TYPE  222  260
        clus
vv       GDA MUTATED GDA WILD-TYPE
  FEMALE           3           222
  MALE             4           260
[1] 2 2
[1] FALSE
D1286V9, binary
               cls
clus              0   1
  GDA MUTATED     5   0
  GDA WILD-TYPE 345  22
[1] "tbl2"
               cls
clus            [,1] [,2]
  GDA MUTATED      5    0
  GDA WILD-TYPE  345   22
     clus
vv    GDA MUTATED GDA WILD-TYPE
  NO            5           345
  YES           0            22
[1] 2 2
[1] FALSE
               vv
clus            COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  GDA MUTATED                      6                             0
  GDA WILD-TYPE                  309                            47
               vv
clus            RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  GDA MUTATED                       1                              0
  GDA WILD-TYPE                   105                             10
D1286V10, multiclass
                                clus
vv                               GDA MUTATED GDA WILD-TYPE
  COLON ADENOCARCINOMA                     6           309
  COLON MUCINOUS ADENOCARCINOMA            0            47
  RECTAL ADENOCARCINOMA                    1           105
  RECTAL MUCINOUS ADENOCARCINOMA           0            10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             R0  R1  R2  RX
  GDA MUTATED     4   0   0   2
  GDA WILD-TYPE 341   4  31  23
D1286V11, multiclass
    clus
vv   GDA MUTATED GDA WILD-TYPE
  R0           4           341
  R1           0             4
  R2           0            31
  RX           2            23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1286V12, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GDA MUTATED                                  0     0
  GDA WILD-TYPE                                1    11
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  GDA MUTATED                           2     5
  GDA WILD-TYPE                        20   221
D1286V13, multiclass
                                  clus
vv                                 GDA MUTATED GDA WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      0            11
  BLACK OR AFRICAN AMERICAN                  2            20
  WHITE                                      5           221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1287) Variable = PEBP4 MUTATION ANALYSIS
D1287V1, survival
                 sevent
clus2               0   1
  PEBP4 MUTATED     4   2
  PEBP4 WILD-TYPE 374  91
  PEBP4 MUTATED PEBP4 WILD-TYPE 
              6             465 
  PEBP4 MUTATED PEBP4 WILD-TYPE 
              2              91 
$`PEBP4 MUTATED`
TCGA-AA-3663 TCGA-AZ-6599 TCGA-D5-6540 TCGA-D5-6927 TCGA-DM-A1DB TCGA-G4-6306 
        6.97         6.77        16.14         9.44        44.32        44.68 

$`PEBP4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.05        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
        4.80        17.13        12.49        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6929 
        4.41        12.43        14.30         9.04        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
      140.38         7.50       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  PEBP4 MUTATED PEBP4 WILD-TYPE 
           6.77            0.00 
  PEBP4 MUTATED PEBP4 WILD-TYPE 
          44.68          148.01 
  PEBP4 MUTATED PEBP4 WILD-TYPE 
          12.79           20.28 
[1] "6.8 - 44.7 (12.8)"  "0.0 - 148.0 (20.3)"
[1] "hr=" "1.9"
D1287V2, continuous
D1287V3, binary
                 cls
clus                0   1
  PEBP4 MUTATED     7   0
  PEBP4 WILD-TYPE 359 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PEBP4 MUTATED      7    0
  PEBP4 WILD-TYPE  359  119
        clus
vv       PEBP4 MUTATED PEBP4 WILD-TYPE
  COLON              7             359
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PEBP4 MUTATED         2        0        1         3         1         0
  PEBP4 WILD-TYPE      89        1       31       135         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PEBP4 MUTATED           0          0          0          0        0         0
  PEBP4 WILD-TYPE        24         11         59         42       48        18
                 vv
clus              STAGE IVB
  PEBP4 MUTATED           0
  PEBP4 WILD-TYPE         1
D1287V4, multiclass
            clus
vv           PEBP4 MUTATED PEBP4 WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              3             135
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PEBP4 MUTATED     0   3   3   1
  PEBP4 WILD-TYPE  17  89 326  49
D1287V5, multiclass
    clus
vv   PEBP4 MUTATED PEBP4 WILD-TYPE
  T1             0              17
  T2             3              89
  T3             3             326
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  PEBP4 MUTATED     7   0   0
  PEBP4 WILD-TYPE 280 113  87
D1287V6, multiclass
    clus
vv   PEBP4 MUTATED PEBP4 WILD-TYPE
  N0             7             280
  N1             0             113
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1287V7, binary
                 cls
clus                0   1
  PEBP4 MUTATED     5   0
  PEBP4 WILD-TYPE 370  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PEBP4 MUTATED      5    0
  PEBP4 WILD-TYPE  370   65
   clus
vv  PEBP4 MUTATED PEBP4 WILD-TYPE
  0             5             370
  1             0              65
[1] 2 2
[1] FALSE
D1287V8, binary
                 cls
clus                0   1
  PEBP4 MUTATED     1   6
  PEBP4 WILD-TYPE 224 258
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PEBP4 MUTATED      1    6
  PEBP4 WILD-TYPE  224  258
        clus
vv       PEBP4 MUTATED PEBP4 WILD-TYPE
  FEMALE             1             224
  MALE               6             258
[1] 2 2
[1] FALSE
D1287V9, binary
                 cls
clus                0   1
  PEBP4 MUTATED     5   0
  PEBP4 WILD-TYPE 345  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PEBP4 MUTATED      5    0
  PEBP4 WILD-TYPE  345   22
     clus
vv    PEBP4 MUTATED PEBP4 WILD-TYPE
  NO              5             345
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PEBP4 MUTATED                      6                             1
  PEBP4 WILD-TYPE                  309                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PEBP4 MUTATED                       0                              0
  PEBP4 WILD-TYPE                   106                             10
D1287V10, multiclass
                                clus
vv                               PEBP4 MUTATED PEBP4 WILD-TYPE
  COLON ADENOCARCINOMA                       6             309
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  PEBP4 MUTATED     4   0   0   1
  PEBP4 WILD-TYPE 341   4  31  24
D1287V11, multiclass
    clus
vv   PEBP4 MUTATED PEBP4 WILD-TYPE
  R0             4             341
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1287V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PEBP4 MUTATED                                  0     0
  PEBP4 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PEBP4 MUTATED                           0     6
  PEBP4 WILD-TYPE                        22   220
D1287V13, multiclass
                                  clus
vv                                 PEBP4 MUTATED PEBP4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        6             220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1288) Variable = CYP2A6 MUTATION ANALYSIS
D1288V1, survival
                  sevent
clus2                0   1
  CYP2A6 MUTATED     8   4
  CYP2A6 WILD-TYPE 370  89
  CYP2A6 MUTATED CYP2A6 WILD-TYPE 
              12              459 
  CYP2A6 MUTATED CYP2A6 WILD-TYPE 
               4               89 
$`CYP2A6 MUTATED`
TCGA-AA-3845 TCGA-AA-A010 TCGA-AA-A01P TCGA-AD-6889 TCGA-AU-6004 TCGA-CM-6166 
        0.00        34.98        38.07        56.55        27.09        21.99 
TCGA-D5-5538 TCGA-D5-6533 TCGA-F4-6459 TCGA-AG-A002 TCGA-AG-A026 TCGA-DC-5869 
       12.26         1.32         8.61        20.98         1.94         5.03 

$`CYP2A6 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        31.00         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 
       18.05        40.96         0.07        21.37        15.52         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       14.50        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       29.03        16.04        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5539 TCGA-D5-5540 
       11.01        10.06        12.03        45.40        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       55.92        20.19        18.25        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
       60.79       117.07        98.24        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-6155 
        6.97         4.73        78.12         7.17        15.02        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  CYP2A6 MUTATED CYP2A6 WILD-TYPE 
               0                0 
  CYP2A6 MUTATED CYP2A6 WILD-TYPE 
           56.55           148.01 
  CYP2A6 MUTATED CYP2A6 WILD-TYPE 
           16.62            20.19 
[1] "0.0 - 56.5 (16.6)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "2.4"
D1288V2, continuous
D1288V3, binary
                  cls
clus                 0   1
  CYP2A6 MUTATED     9   3
  CYP2A6 WILD-TYPE 357 116
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CYP2A6 MUTATED      9    3
  CYP2A6 WILD-TYPE  357  116
        clus
vv       CYP2A6 MUTATED CYP2A6 WILD-TYPE
  COLON               9              357
  RECTUM              3              116
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CYP2A6 MUTATED         3        0        1         2         1         0
  CYP2A6 WILD-TYPE      88        1       31       136         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CYP2A6 MUTATED           1          0          4          0        0
  CYP2A6 WILD-TYPE        23         11         55         42       48
                  vv
clus               STAGE IVA STAGE IVB
  CYP2A6 MUTATED           0         0
  CYP2A6 WILD-TYPE        18         1
D1288V4, multiclass
            clus
vv           CYP2A6 MUTATED CYP2A6 WILD-TYPE
  STAGE I                 3               88
  STAGE IA                0                1
  STAGE II                1               31
  STAGE IIA               2              136
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               1               23
  STAGE IIIA              0               11
  STAGE IIIB              4               55
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  CYP2A6 MUTATED     0   3   6   3
  CYP2A6 WILD-TYPE  17  89 323  47
D1288V5, multiclass
    clus
vv   CYP2A6 MUTATED CYP2A6 WILD-TYPE
  T1              0               17
  T2              3               89
  T3              6              323
  T4              3               47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  CYP2A6 MUTATED     8   3   1
  CYP2A6 WILD-TYPE 279 110  86
D1288V6, multiclass
    clus
vv   CYP2A6 MUTATED CYP2A6 WILD-TYPE
  N0              8              279
  N1              3              110
  N2              1               86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1288V7, binary
                  cls
clus                 0   1
  CYP2A6 MUTATED    12   0
  CYP2A6 WILD-TYPE 363  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CYP2A6 MUTATED     12    0
  CYP2A6 WILD-TYPE  363   65
   clus
vv  CYP2A6 MUTATED CYP2A6 WILD-TYPE
  0             12              363
  1              0               65
[1] 2 2
[1] FALSE
D1288V8, binary
                  cls
clus                 0   1
  CYP2A6 MUTATED     9   3
  CYP2A6 WILD-TYPE 216 261
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CYP2A6 MUTATED      9    3
  CYP2A6 WILD-TYPE  216  261
        clus
vv       CYP2A6 MUTATED CYP2A6 WILD-TYPE
  FEMALE              9              216
  MALE                3              261
[1] 2 2
[1] FALSE
D1288V9, binary
                  cls
clus                 0   1
  CYP2A6 MUTATED     6   0
  CYP2A6 WILD-TYPE 344  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CYP2A6 MUTATED      6    0
  CYP2A6 WILD-TYPE  344   22
     clus
vv    CYP2A6 MUTATED CYP2A6 WILD-TYPE
  NO               6              344
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CYP2A6 MUTATED                      9                             0
  CYP2A6 WILD-TYPE                  306                            47
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CYP2A6 MUTATED                       3                              0
  CYP2A6 WILD-TYPE                   103                             10
D1288V10, multiclass
                                clus
vv                               CYP2A6 MUTATED CYP2A6 WILD-TYPE
  COLON ADENOCARCINOMA                        9              306
  COLON MUCINOUS ADENOCARCINOMA               0               47
  RECTAL ADENOCARCINOMA                       3              103
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  CYP2A6 MUTATED    10   1   0   0
  CYP2A6 WILD-TYPE 335   3  31  25
D1288V11, multiclass
    clus
vv   CYP2A6 MUTATED CYP2A6 WILD-TYPE
  R0             10              335
  R1              1                3
  R2              0               31
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1288V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CYP2A6 MUTATED                                  0     1
  CYP2A6 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  CYP2A6 MUTATED                           1     5
  CYP2A6 WILD-TYPE                        21   221
D1288V13, multiclass
                                  clus
vv                                 CYP2A6 MUTATED CYP2A6 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                         5              221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1289) Variable = DEK MUTATION ANALYSIS
D1289V1, survival
               sevent
clus2             0   1
  DEK MUTATED     4   2
  DEK WILD-TYPE 374  91
  DEK MUTATED DEK WILD-TYPE 
            6           465 
  DEK MUTATED DEK WILD-TYPE 
            2            91 
$`DEK MUTATED`
TCGA-A6-5660 TCGA-AA-A00N TCGA-AY-6197 TCGA-CA-6717 TCGA-G4-6586 TCGA-G4-6626 
       29.19         4.01        21.44        12.76        35.80        46.75 

$`DEK WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       33.01        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 
       36.00        22.09        13.78        26.17        91.79        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  DEK MUTATED DEK WILD-TYPE 
         4.01          0.00 
  DEK MUTATED DEK WILD-TYPE 
        46.75        148.01 
  DEK MUTATED DEK WILD-TYPE 
       25.315        20.120 
[1] "4.0 - 46.8 (25.3)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.8"
D1289V2, continuous
D1289V3, binary
               cls
clus              0   1
  DEK MUTATED     6   0
  DEK WILD-TYPE 360 119
[1] "tbl2"
               cls
clus            [,1] [,2]
  DEK MUTATED      6    0
  DEK WILD-TYPE  360  119
        clus
vv       DEK MUTATED DEK WILD-TYPE
  COLON            6           360
  RECTUM           0           119
[1] 2 2
[1] FALSE
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEK MUTATED         0        0        0         4         1         0
  DEK WILD-TYPE      91        1       32       134         9         1
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DEK MUTATED           0          0          0          1        0         0
  DEK WILD-TYPE        24         11         59         41       48        18
               vv
clus            STAGE IVB
  DEK MUTATED           0
  DEK WILD-TYPE         1
D1289V4, multiclass
            clus
vv           DEK MUTATED DEK WILD-TYPE
  STAGE I              0            91
  STAGE IA             0             1
  STAGE II             0            32
  STAGE IIA            4           134
  STAGE IIB            1             9
  STAGE IIC            0             1
  STAGE III            0            24
  STAGE IIIA           0            11
  STAGE IIIB           0            59
  STAGE IIIC           1            41
  STAGE IV             0            48
  STAGE IVA            0            18
  STAGE IVB            0             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  DEK MUTATED     0   0   5   1
  DEK WILD-TYPE  17  92 324  49
D1289V5, multiclass
    clus
vv   DEK MUTATED DEK WILD-TYPE
  T1           0            17
  T2           0            92
  T3           5           324
  T4           1            49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2
  DEK MUTATED     5   0   1
  DEK WILD-TYPE 282 113  86
D1289V6, multiclass
    clus
vv   DEK MUTATED DEK WILD-TYPE
  N0           5           282
  N1           0           113
  N2           1            86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1289V7, binary
               cls
clus              0   1
  DEK MUTATED     5   0
  DEK WILD-TYPE 370  65
[1] "tbl2"
               cls
clus            [,1] [,2]
  DEK MUTATED      5    0
  DEK WILD-TYPE  370   65
   clus
vv  DEK MUTATED DEK WILD-TYPE
  0           5           370
  1           0            65
[1] 2 2
[1] FALSE
D1289V8, binary
               cls
clus              0   1
  DEK MUTATED     1   5
  DEK WILD-TYPE 224 259
[1] "tbl2"
               cls
clus            [,1] [,2]
  DEK MUTATED      1    5
  DEK WILD-TYPE  224  259
        clus
vv       DEK MUTATED DEK WILD-TYPE
  FEMALE           1           224
  MALE             5           259
[1] 2 2
[1] FALSE
D1289V9, binary
               cls
clus              0   1
  DEK MUTATED     5   0
  DEK WILD-TYPE 345  22
[1] "tbl2"
               cls
clus            [,1] [,2]
  DEK MUTATED      5    0
  DEK WILD-TYPE  345   22
     clus
vv    DEK MUTATED DEK WILD-TYPE
  NO            5           345
  YES           0            22
[1] 2 2
[1] FALSE
               vv
clus            COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  DEK MUTATED                      4                             2
  DEK WILD-TYPE                  311                            45
               vv
clus            RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  DEK MUTATED                       0                              0
  DEK WILD-TYPE                   106                             10
D1289V10, multiclass
                                clus
vv                               DEK MUTATED DEK WILD-TYPE
  COLON ADENOCARCINOMA                     4           311
  COLON MUCINOUS ADENOCARCINOMA            2            45
  RECTAL ADENOCARCINOMA                    0           106
  RECTAL MUCINOUS ADENOCARCINOMA           0            10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             R0  R1  R2  RX
  DEK MUTATED     4   0   0   1
  DEK WILD-TYPE 341   4  31  24
D1289V11, multiclass
    clus
vv   DEK MUTATED DEK WILD-TYPE
  R0           4           341
  R1           0             4
  R2           0            31
  RX           1            24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1289V12, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEK MUTATED                                  0     1
  DEK WILD-TYPE                                1    10
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  DEK MUTATED                           1     3
  DEK WILD-TYPE                        21   223
D1289V13, multiclass
                                  clus
vv                                 DEK MUTATED DEK WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      1            10
  BLACK OR AFRICAN AMERICAN                  1            21
  WHITE                                      3           223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1290) Variable = HAUS1 MUTATION ANALYSIS
D1290V1, survival
                 sevent
clus2               0   1
  HAUS1 MUTATED     4   2
  HAUS1 WILD-TYPE 374  91
  HAUS1 MUTATED HAUS1 WILD-TYPE 
              6             465 
  HAUS1 MUTATED HAUS1 WILD-TYPE 
              2              91 
$`HAUS1 MUTATED`
TCGA-A6-6141 TCGA-AA-3715 TCGA-AA-A01Q TCGA-AZ-4323 TCGA-CM-6161 TCGA-G4-6307 
        8.38        19.04         1.02         1.41        15.02        55.04 

$`HAUS1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 
       22.09        22.06        32.71        27.09        22.52        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 
       36.00         5.03        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        31.00        38.07        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82        58.39         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6162 TCGA-CM-6163 
        5.03        15.02        15.02        17.03        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       44.68        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  HAUS1 MUTATED HAUS1 WILD-TYPE 
           1.02            0.00 
  HAUS1 MUTATED HAUS1 WILD-TYPE 
          55.04          148.01 
  HAUS1 MUTATED HAUS1 WILD-TYPE 
          11.70           20.55 
[1] "1.0 - 55.0 (11.7)"  "0.0 - 148.0 (20.6)"
[1] "hr=" "2.4"
D1290V2, continuous
D1290V3, binary
                 cls
clus                0   1
  HAUS1 MUTATED     6   0
  HAUS1 WILD-TYPE 360 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HAUS1 MUTATED      6    0
  HAUS1 WILD-TYPE  360  119
        clus
vv       HAUS1 MUTATED HAUS1 WILD-TYPE
  COLON              6             360
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  HAUS1 MUTATED         1        0        2         1         0         0
  HAUS1 WILD-TYPE      90        1       30       137        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  HAUS1 MUTATED           0          0          1          0        1         0
  HAUS1 WILD-TYPE        24         11         58         42       47        18
                 vv
clus              STAGE IVB
  HAUS1 MUTATED           0
  HAUS1 WILD-TYPE         1
D1290V4, multiclass
            clus
vv           HAUS1 MUTATED HAUS1 WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA              1             137
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             0              42
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  HAUS1 MUTATED     0   1   4   1
  HAUS1 WILD-TYPE  17  91 325  49
D1290V5, multiclass
    clus
vv   HAUS1 MUTATED HAUS1 WILD-TYPE
  T1             0              17
  T2             1              91
  T3             4             325
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  HAUS1 MUTATED     4   1   1
  HAUS1 WILD-TYPE 283 112  86
D1290V6, multiclass
    clus
vv   HAUS1 MUTATED HAUS1 WILD-TYPE
  N0             4             283
  N1             1             112
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1290V7, binary
                 cls
clus                0   1
  HAUS1 MUTATED     5   1
  HAUS1 WILD-TYPE 370  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HAUS1 MUTATED      5    1
  HAUS1 WILD-TYPE  370   64
   clus
vv  HAUS1 MUTATED HAUS1 WILD-TYPE
  0             5             370
  1             1              64
[1] 2 2
[1] FALSE
D1290V8, binary
                 cls
clus                0   1
  HAUS1 MUTATED     3   3
  HAUS1 WILD-TYPE 222 261
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HAUS1 MUTATED      3    3
  HAUS1 WILD-TYPE  222  261
        clus
vv       HAUS1 MUTATED HAUS1 WILD-TYPE
  FEMALE             3             222
  MALE               3             261
[1] 2 2
[1] FALSE
D1290V9, binary
                 cls
clus                0   1
  HAUS1 MUTATED     5   0
  HAUS1 WILD-TYPE 345  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HAUS1 MUTATED      5    0
  HAUS1 WILD-TYPE  345   22
     clus
vv    HAUS1 MUTATED HAUS1 WILD-TYPE
  NO              5             345
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  HAUS1 MUTATED                      6                             0
  HAUS1 WILD-TYPE                  309                            47
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  HAUS1 MUTATED                       0                              0
  HAUS1 WILD-TYPE                   106                             10
D1290V10, multiclass
                                clus
vv                               HAUS1 MUTATED HAUS1 WILD-TYPE
  COLON ADENOCARCINOMA                       6             309
  COLON MUCINOUS ADENOCARCINOMA              0              47
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  HAUS1 MUTATED     4   0   0   0
  HAUS1 WILD-TYPE 341   4  31  25
D1290V11, multiclass
    clus
vv   HAUS1 MUTATED HAUS1 WILD-TYPE
  R0             4             341
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1290V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HAUS1 MUTATED                                  0     0
  HAUS1 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  HAUS1 MUTATED                           1     3
  HAUS1 WILD-TYPE                        21   223
D1290V13, multiclass
                                  clus
vv                                 HAUS1 MUTATED HAUS1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        3             223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1291) Variable = DBF4B MUTATION ANALYSIS
D1291V1, survival
                 sevent
clus2               0   1
  DBF4B MUTATED     5   1
  DBF4B WILD-TYPE 373  92
  DBF4B MUTATED DBF4B WILD-TYPE 
              6             465 
  DBF4B MUTATED DBF4B WILD-TYPE 
              1              92 
$`DBF4B MUTATED`
TCGA-A6-5656 TCGA-AA-3715 TCGA-AA-A010 TCGA-CA-6717 TCGA-CM-6171 TCGA-D5-6930 
       32.91        19.04        34.98        12.76        14.04         1.51 

$`DBF4B WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 
       36.00         5.03        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       13.02        15.02        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6931 
       14.30         9.04         9.44        11.64         4.80        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  DBF4B MUTATED DBF4B WILD-TYPE 
           1.51            0.00 
  DBF4B MUTATED DBF4B WILD-TYPE 
          34.98          148.01 
  DBF4B MUTATED DBF4B WILD-TYPE 
          16.54           20.28 
[1] "1.5 - 35.0 (16.5)"  "0.0 - 148.0 (20.3)"
[1] "hr=" "1.2"
D1291V2, continuous
D1291V3, binary
                 cls
clus                0   1
  DBF4B MUTATED     7   0
  DBF4B WILD-TYPE 359 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DBF4B MUTATED      7    0
  DBF4B WILD-TYPE  359  119
        clus
vv       DBF4B MUTATED DBF4B WILD-TYPE
  COLON              7             359
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DBF4B MUTATED         2        0        1         3         1         0
  DBF4B WILD-TYPE      89        1       31       135         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DBF4B MUTATED           0          0          0          0        0         0
  DBF4B WILD-TYPE        24         11         59         42       48        18
                 vv
clus              STAGE IVB
  DBF4B MUTATED           0
  DBF4B WILD-TYPE         1
D1291V4, multiclass
            clus
vv           DBF4B MUTATED DBF4B WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              3             135
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  DBF4B MUTATED     0   2   4   1
  DBF4B WILD-TYPE  17  90 325  49
D1291V5, multiclass
    clus
vv   DBF4B MUTATED DBF4B WILD-TYPE
  T1             0              17
  T2             2              90
  T3             4             325
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  DBF4B MUTATED     7   0   0
  DBF4B WILD-TYPE 280 113  87
D1291V6, multiclass
    clus
vv   DBF4B MUTATED DBF4B WILD-TYPE
  N0             7             280
  N1             0             113
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1291V7, binary
                 cls
clus                0   1
  DBF4B MUTATED     7   0
  DBF4B WILD-TYPE 368  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DBF4B MUTATED      7    0
  DBF4B WILD-TYPE  368   65
   clus
vv  DBF4B MUTATED DBF4B WILD-TYPE
  0             7             368
  1             0              65
[1] 2 2
[1] FALSE
D1291V8, binary
                 cls
clus                0   1
  DBF4B MUTATED     3   4
  DBF4B WILD-TYPE 222 260
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DBF4B MUTATED      3    4
  DBF4B WILD-TYPE  222  260
        clus
vv       DBF4B MUTATED DBF4B WILD-TYPE
  FEMALE             3             222
  MALE               4             260
[1] 2 2
[1] FALSE
D1291V9, binary
                 cls
clus                0   1
  DBF4B MUTATED     5   0
  DBF4B WILD-TYPE 345  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DBF4B MUTATED      5    0
  DBF4B WILD-TYPE  345   22
     clus
vv    DBF4B MUTATED DBF4B WILD-TYPE
  NO              5             345
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  DBF4B MUTATED                      5                             2
  DBF4B WILD-TYPE                  310                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  DBF4B MUTATED                       0                              0
  DBF4B WILD-TYPE                   106                             10
D1291V10, multiclass
                                clus
vv                               DBF4B MUTATED DBF4B WILD-TYPE
  COLON ADENOCARCINOMA                       5             310
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  DBF4B MUTATED     5   0   0   1
  DBF4B WILD-TYPE 340   4  31  24
D1291V11, multiclass
    clus
vv   DBF4B MUTATED DBF4B WILD-TYPE
  R0             5             340
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1291V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DBF4B MUTATED                                  0     1
  DBF4B WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  DBF4B MUTATED                           0     3
  DBF4B WILD-TYPE                        22   223
D1291V13, multiclass
                                  clus
vv                                 DBF4B MUTATED DBF4B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        3             223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1292) Variable = PLA2G15 MUTATION ANALYSIS
D1292V1, survival
                   sevent
clus2                 0   1
  PLA2G15 MUTATED     3   3
  PLA2G15 WILD-TYPE 375  90
  PLA2G15 MUTATED PLA2G15 WILD-TYPE 
                6               465 
  PLA2G15 MUTATED PLA2G15 WILD-TYPE 
                3                90 
$`PLA2G15 MUTATED`
TCGA-AA-3811 TCGA-AZ-6601 TCGA-CM-4743 TCGA-D5-6534 TCGA-DM-A1D7 TCGA-AG-A02X 
       10.06       100.01        23.05        43.27        13.32        41.00 

$`PLA2G15 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       19.04        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77        12.10        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
       82.95         1.91       124.27        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       18.25         1.32        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D8 TCGA-DM-A1D9 
       38.20       130.65        92.75        49.91        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       38.96        61.97        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  PLA2G15 MUTATED PLA2G15 WILD-TYPE 
            10.06              0.00 
  PLA2G15 MUTATED PLA2G15 WILD-TYPE 
           100.01            148.01 
  PLA2G15 MUTATED PLA2G15 WILD-TYPE 
           32.025            20.120 
[1] "10.1 - 100.0 (32.0)" "0.0 - 148.0 (20.1)" 
[1] "hr=" "1.7"
D1292V2, continuous
D1292V3, binary
                   cls
clus                  0   1
  PLA2G15 MUTATED     5   1
  PLA2G15 WILD-TYPE 361 118
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLA2G15 MUTATED      5    1
  PLA2G15 WILD-TYPE  361  118
        clus
vv       PLA2G15 MUTATED PLA2G15 WILD-TYPE
  COLON                5               361
  RECTUM               1               118
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PLA2G15 MUTATED         1        0        1         3         0         0
  PLA2G15 WILD-TYPE      90        1       31       135        10         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PLA2G15 MUTATED           1          0          0          0        0
  PLA2G15 WILD-TYPE        23         11         59         42       48
                   vv
clus                STAGE IVA STAGE IVB
  PLA2G15 MUTATED           0         0
  PLA2G15 WILD-TYPE        18         1
D1292V4, multiclass
            clus
vv           PLA2G15 MUTATED PLA2G15 WILD-TYPE
  STAGE I                  1                90
  STAGE IA                 0                 1
  STAGE II                 1                31
  STAGE IIA                3               135
  STAGE IIB                0                10
  STAGE IIC                0                 1
  STAGE III                1                23
  STAGE IIIA               0                11
  STAGE IIIB               0                59
  STAGE IIIC               0                42
  STAGE IV                 0                48
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  PLA2G15 MUTATED     0   1   5   0
  PLA2G15 WILD-TYPE  17  91 324  50
D1292V5, multiclass
    clus
vv   PLA2G15 MUTATED PLA2G15 WILD-TYPE
  T1               0                17
  T2               1                91
  T3               5               324
  T4               0                50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  PLA2G15 MUTATED     5   0   1
  PLA2G15 WILD-TYPE 282 113  86
D1292V6, multiclass
    clus
vv   PLA2G15 MUTATED PLA2G15 WILD-TYPE
  N0               5               282
  N1               0               113
  N2               1                86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1292V7, binary
                   cls
clus                  0   1
  PLA2G15 MUTATED     6   0
  PLA2G15 WILD-TYPE 369  65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLA2G15 MUTATED      6    0
  PLA2G15 WILD-TYPE  369   65
   clus
vv  PLA2G15 MUTATED PLA2G15 WILD-TYPE
  0               6               369
  1               0                65
[1] 2 2
[1] FALSE
D1292V8, binary
                   cls
clus                  0   1
  PLA2G15 MUTATED     2   4
  PLA2G15 WILD-TYPE 223 260
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLA2G15 MUTATED      2    4
  PLA2G15 WILD-TYPE  223  260
        clus
vv       PLA2G15 MUTATED PLA2G15 WILD-TYPE
  FEMALE               2               223
  MALE                 4               260
[1] 2 2
[1] FALSE
D1292V9, binary
                   cls
clus                  0   1
  PLA2G15 MUTATED     4   0
  PLA2G15 WILD-TYPE 346  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLA2G15 MUTATED      4    0
  PLA2G15 WILD-TYPE  346   22
     clus
vv    PLA2G15 MUTATED PLA2G15 WILD-TYPE
  NO                4               346
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PLA2G15 MUTATED                      3                             1
  PLA2G15 WILD-TYPE                  312                            46
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PLA2G15 MUTATED                       1                              0
  PLA2G15 WILD-TYPE                   105                             10
D1292V10, multiclass
                                clus
vv                               PLA2G15 MUTATED PLA2G15 WILD-TYPE
  COLON ADENOCARCINOMA                         3               312
  COLON MUCINOUS ADENOCARCINOMA                1                46
  RECTAL ADENOCARCINOMA                        1               105
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  PLA2G15 MUTATED     4   0   0   0
  PLA2G15 WILD-TYPE 341   4  31  25
D1292V11, multiclass
    clus
vv   PLA2G15 MUTATED PLA2G15 WILD-TYPE
  R0               4               341
  R1               0                 4
  R2               0                31
  RX               0                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1292V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PLA2G15 MUTATED                                  0     0
  PLA2G15 WILD-TYPE                                1    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  PLA2G15 MUTATED                           0     4
  PLA2G15 WILD-TYPE                        22   222
D1292V13, multiclass
                                  clus
vv                                 PLA2G15 MUTATED PLA2G15 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                      0                22
  WHITE                                          4               222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1293) Variable = STAT5B MUTATION ANALYSIS
D1293V1, survival
                  sevent
clus2                0   1
  STAT5B MUTATED    10   2
  STAT5B WILD-TYPE 368  91
  STAT5B MUTATED STAT5B WILD-TYPE 
              12              459 
  STAT5B MUTATED STAT5B WILD-TYPE 
               2               91 
$`STAT5B MUTATED`
TCGA-A6-3809 TCGA-A6-6653 TCGA-A6-6780 TCGA-AA-3815 TCGA-AA-3950 TCGA-AA-A00N 
       32.75        24.39        20.12        33.04        24.00         4.01 
TCGA-AA-A010 TCGA-AU-6004 TCGA-CA-6717 TCGA-G4-6303 TCGA-G4-6628 TCGA-AG-A002 
       34.98        27.09        12.76        65.85        79.69        20.98 

$`STAT5B WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6781 
       25.18        24.16        21.76        24.69        23.87        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       33.01        26.01         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 
       27.42        10.88         0.20        14.50        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.20        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       46.75        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  STAT5B MUTATED STAT5B WILD-TYPE 
            4.01             0.00 
  STAT5B MUTATED STAT5B WILD-TYPE 
           79.69           148.01 
  STAT5B MUTATED STAT5B WILD-TYPE 
           25.74            20.02 
[1] "4.0 - 79.7 (25.7)"  "0.0 - 148.0 (20.0)"
[1] "hr=" "1.4"
D1293V2, continuous
D1293V3, binary
                  cls
clus                 0   1
  STAT5B MUTATED    12   1
  STAT5B WILD-TYPE 354 118
[1] "tbl2"
                  cls
clus               [,1] [,2]
  STAT5B MUTATED     12    1
  STAT5B WILD-TYPE  354  118
        clus
vv       STAT5B MUTATED STAT5B WILD-TYPE
  COLON              12              354
  RECTUM              1              118
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  STAT5B MUTATED         4        0        0         4         3         0
  STAT5B WILD-TYPE      87        1       32       134         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  STAT5B MUTATED           0          0          0          1        1
  STAT5B WILD-TYPE        24         11         59         41       47
                  vv
clus               STAGE IVA STAGE IVB
  STAT5B MUTATED           0         0
  STAT5B WILD-TYPE        18         1
D1293V4, multiclass
            clus
vv           STAT5B MUTATED STAT5B WILD-TYPE
  STAGE I                 4               87
  STAGE IA                0                1
  STAGE II                0               32
  STAGE IIA               4              134
  STAGE IIB               3                7
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              0               59
  STAGE IIIC              1               41
  STAGE IV                1               47
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  STAT5B MUTATED     0   4   6   3
  STAT5B WILD-TYPE  17  88 323  47
D1293V5, multiclass
    clus
vv   STAT5B MUTATED STAT5B WILD-TYPE
  T1              0               17
  T2              4               88
  T3              6              323
  T4              3               47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  STAT5B MUTATED    11   1   1
  STAT5B WILD-TYPE 276 112  86
D1293V6, multiclass
    clus
vv   STAT5B MUTATED STAT5B WILD-TYPE
  N0             11              276
  N1              1              112
  N2              1               86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1293V7, binary
                  cls
clus                 0   1
  STAT5B MUTATED    10   1
  STAT5B WILD-TYPE 365  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  STAT5B MUTATED     10    1
  STAT5B WILD-TYPE  365   64
   clus
vv  STAT5B MUTATED STAT5B WILD-TYPE
  0             10              365
  1              1               64
[1] 2 2
[1] FALSE
D1293V8, binary
                  cls
clus                 0   1
  STAT5B MUTATED     6   7
  STAT5B WILD-TYPE 219 257
[1] "tbl2"
                  cls
clus               [,1] [,2]
  STAT5B MUTATED      6    7
  STAT5B WILD-TYPE  219  257
        clus
vv       STAT5B MUTATED STAT5B WILD-TYPE
  FEMALE              6              219
  MALE                7              257
[1] 2 2
[1] FALSE
D1293V9, binary
                  cls
clus                 0   1
  STAT5B MUTATED    10   0
  STAT5B WILD-TYPE 340  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  STAT5B MUTATED     10    0
  STAT5B WILD-TYPE  340   22
     clus
vv    STAT5B MUTATED STAT5B WILD-TYPE
  NO              10              340
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  STAT5B MUTATED                      6                             6
  STAT5B WILD-TYPE                  309                            41
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  STAT5B MUTATED                       1                              0
  STAT5B WILD-TYPE                   105                             10
D1293V10, multiclass
                                clus
vv                               STAT5B MUTATED STAT5B WILD-TYPE
  COLON ADENOCARCINOMA                        6              309
  COLON MUCINOUS ADENOCARCINOMA               6               41
  RECTAL ADENOCARCINOMA                       1              105
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  STAT5B MUTATED    10   0   0   1
  STAT5B WILD-TYPE 335   4  31  24
D1293V11, multiclass
    clus
vv   STAT5B MUTATED STAT5B WILD-TYPE
  R0             10              335
  R1              0                4
  R2              0               31
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1293V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  STAT5B MUTATED                                  0     1
  STAT5B WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  STAT5B MUTATED                           0     7
  STAT5B WILD-TYPE                        22   219
D1293V13, multiclass
                                  clus
vv                                 STAT5B MUTATED STAT5B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         7              219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1294) Variable = NCOA5 MUTATION ANALYSIS
D1294V1, survival
                 sevent
clus2               0   1
  NCOA5 MUTATED    11   2
  NCOA5 WILD-TYPE 367  91
  NCOA5 MUTATED NCOA5 WILD-TYPE 
             13             458 
  NCOA5 MUTATED NCOA5 WILD-TYPE 
              2              91 
$`NCOA5 MUTATED`
TCGA-AA-3655 TCGA-AA-3877 TCGA-AA-3947 TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A02O 
       61.02        31.00        33.01        25.02         4.01         0.92 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-CM-4743 TCGA-CM-6674 TCGA-G4-6293 TCGA-EI-6506 
       88.21        49.41        23.05        12.95       133.18        20.55 
TCGA-EI-6507 
       19.96 

$`NCOA5 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 
       20.98        19.99        13.94        19.99        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 
       17.03        24.03        27.02        29.98        18.05         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       12.99        24.00        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
       14.01        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6599 
        1.41         5.13       106.75        22.36        62.79         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
       82.95         1.91       124.27        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6675 
       12.99        13.02        15.02        14.04        11.01        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
        0.53        47.41        35.31        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
       51.48        32.61         0.49        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  NCOA5 MUTATED NCOA5 WILD-TYPE 
           0.92            0.00 
  NCOA5 MUTATED NCOA5 WILD-TYPE 
         133.18          148.01 
  NCOA5 MUTATED NCOA5 WILD-TYPE 
         25.020          20.035 
[1] "0.9 - 133.2 (25.0)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.8"
D1294V2, continuous
D1294V3, binary
                 cls
clus                0   1
  NCOA5 MUTATED    11   2
  NCOA5 WILD-TYPE 355 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NCOA5 MUTATED     11    2
  NCOA5 WILD-TYPE  355  117
        clus
vv       NCOA5 MUTATED NCOA5 WILD-TYPE
  COLON             11             355
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NCOA5 MUTATED         2        0        3         4         2         0
  NCOA5 WILD-TYPE      89        1       29       134         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NCOA5 MUTATED           1          0          0          0        0         0
  NCOA5 WILD-TYPE        23         11         59         42       48        18
                 vv
clus              STAGE IVB
  NCOA5 MUTATED           0
  NCOA5 WILD-TYPE         1
D1294V4, multiclass
            clus
vv           NCOA5 MUTATED NCOA5 WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               3              29
  STAGE IIA              4             134
  STAGE IIB              2               8
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  NCOA5 MUTATED     2   1   8   2
  NCOA5 WILD-TYPE  15  91 321  48
D1294V5, multiclass
    clus
vv   NCOA5 MUTATED NCOA5 WILD-TYPE
  T1             2              15
  T2             1              91
  T3             8             321
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  NCOA5 MUTATED    12   1   0
  NCOA5 WILD-TYPE 275 112  87
D1294V6, multiclass
    clus
vv   NCOA5 MUTATED NCOA5 WILD-TYPE
  N0            12             275
  N1             1             112
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1294V7, binary
                 cls
clus                0   1
  NCOA5 MUTATED    11   0
  NCOA5 WILD-TYPE 364  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NCOA5 MUTATED     11    0
  NCOA5 WILD-TYPE  364   65
   clus
vv  NCOA5 MUTATED NCOA5 WILD-TYPE
  0            11             364
  1             0              65
[1] 2 2
[1] FALSE
D1294V8, binary
                 cls
clus                0   1
  NCOA5 MUTATED     6   7
  NCOA5 WILD-TYPE 219 257
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NCOA5 MUTATED      6    7
  NCOA5 WILD-TYPE  219  257
        clus
vv       NCOA5 MUTATED NCOA5 WILD-TYPE
  FEMALE             6             219
  MALE               7             257
[1] 2 2
[1] FALSE
D1294V9, binary
                 cls
clus                0   1
  NCOA5 MUTATED    11   0
  NCOA5 WILD-TYPE 339  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NCOA5 MUTATED     11    0
  NCOA5 WILD-TYPE  339   22
     clus
vv    NCOA5 MUTATED NCOA5 WILD-TYPE
  NO             11             339
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  NCOA5 MUTATED                      8                             3
  NCOA5 WILD-TYPE                  307                            44
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  NCOA5 MUTATED                       2                              0
  NCOA5 WILD-TYPE                   104                             10
D1294V10, multiclass
                                clus
vv                               NCOA5 MUTATED NCOA5 WILD-TYPE
  COLON ADENOCARCINOMA                       8             307
  COLON MUCINOUS ADENOCARCINOMA              3              44
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  NCOA5 MUTATED    10   0   0   0
  NCOA5 WILD-TYPE 335   4  31  25
D1294V11, multiclass
    clus
vv   NCOA5 MUTATED NCOA5 WILD-TYPE
  R0            10             335
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1294V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NCOA5 MUTATED                                  0     0
  NCOA5 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  NCOA5 MUTATED                           0     7
  NCOA5 WILD-TYPE                        22   219
D1294V13, multiclass
                                  clus
vv                                 NCOA5 MUTATED NCOA5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        7             219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1295) Variable = MR1 MUTATION ANALYSIS
D1295V1, survival
               sevent
clus2             0   1
  MR1 MUTATED     5   2
  MR1 WILD-TYPE 373  91
  MR1 MUTATED MR1 WILD-TYPE 
            7           464 
  MR1 MUTATED MR1 WILD-TYPE 
            2            91 
$`MR1 MUTATED`
TCGA-A6-6782 TCGA-AA-3510 TCGA-AA-3977 TCGA-CA-6717 TCGA-CA-6718 TCGA-AG-A002 
       20.28        63.98        25.02        12.76        10.06        20.98 
TCGA-DY-A1DG 
       51.48 

$`MR1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        19.66         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1H8 
        5.29       126.44        41.36        57.24        24.13        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  MR1 MUTATED MR1 WILD-TYPE 
        10.06          0.00 
  MR1 MUTATED MR1 WILD-TYPE 
        63.98        148.01 
  MR1 MUTATED MR1 WILD-TYPE 
       20.980        20.085 
[1] "10.1 - 64.0 (21.0)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.2"
D1295V2, continuous
D1295V3, binary
               cls
clus              0   1
  MR1 MUTATED     5   2
  MR1 WILD-TYPE 361 117
[1] "tbl2"
               cls
clus            [,1] [,2]
  MR1 MUTATED      5    2
  MR1 WILD-TYPE  361  117
        clus
vv       MR1 MUTATED MR1 WILD-TYPE
  COLON            5           361
  RECTUM           2           117
[1] 2 2
[1] FALSE
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MR1 MUTATED         1        0        1         2         1         0
  MR1 WILD-TYPE      90        1       31       136         9         1
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MR1 MUTATED           0          0          0          0        0         1
  MR1 WILD-TYPE        24         11         59         42       48        17
               vv
clus            STAGE IVB
  MR1 MUTATED           0
  MR1 WILD-TYPE         1
D1295V4, multiclass
            clus
vv           MR1 MUTATED MR1 WILD-TYPE
  STAGE I              1            90
  STAGE IA             0             1
  STAGE II             1            31
  STAGE IIA            2           136
  STAGE IIB            1             9
  STAGE IIC            0             1
  STAGE III            0            24
  STAGE IIIA           0            11
  STAGE IIIB           0            59
  STAGE IIIC           0            42
  STAGE IV             0            48
  STAGE IVA            1            17
  STAGE IVB            0             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  MR1 MUTATED     0   2   4   1
  MR1 WILD-TYPE  17  90 325  49
D1295V5, multiclass
    clus
vv   MR1 MUTATED MR1 WILD-TYPE
  T1           0            17
  T2           2            90
  T3           4           325
  T4           1            49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2
  MR1 MUTATED     6   1   0
  MR1 WILD-TYPE 281 112  87
D1295V6, multiclass
    clus
vv   MR1 MUTATED MR1 WILD-TYPE
  N0           6           281
  N1           1           112
  N2           0            87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1295V7, binary
               cls
clus              0   1
  MR1 MUTATED     4   1
  MR1 WILD-TYPE 371  64
[1] "tbl2"
               cls
clus            [,1] [,2]
  MR1 MUTATED      4    1
  MR1 WILD-TYPE  371   64
   clus
vv  MR1 MUTATED MR1 WILD-TYPE
  0           4           371
  1           1            64
[1] 2 2
[1] FALSE
D1295V8, binary
               cls
clus              0   1
  MR1 MUTATED     0   7
  MR1 WILD-TYPE 225 257
[1] "tbl2"
               cls
clus            [,1] [,2]
  MR1 MUTATED      0    7
  MR1 WILD-TYPE  225  257
        clus
vv       MR1 MUTATED MR1 WILD-TYPE
  FEMALE           0           225
  MALE             7           257
[1] 2 2
[1] FALSE
D1295V9, binary
               cls
clus              0   1
  MR1 MUTATED     6   0
  MR1 WILD-TYPE 344  22
[1] "tbl2"
               cls
clus            [,1] [,2]
  MR1 MUTATED      6    0
  MR1 WILD-TYPE  344   22
     clus
vv    MR1 MUTATED MR1 WILD-TYPE
  NO            6           344
  YES           0            22
[1] 2 2
[1] FALSE
               vv
clus            COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MR1 MUTATED                      4                             1
  MR1 WILD-TYPE                  311                            46
               vv
clus            RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MR1 MUTATED                       2                              0
  MR1 WILD-TYPE                   104                             10
D1295V10, multiclass
                                clus
vv                               MR1 MUTATED MR1 WILD-TYPE
  COLON ADENOCARCINOMA                     4           311
  COLON MUCINOUS ADENOCARCINOMA            1            46
  RECTAL ADENOCARCINOMA                    2           104
  RECTAL MUCINOUS ADENOCARCINOMA           0            10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             R0  R1  R2  RX
  MR1 MUTATED     2   0   0   2
  MR1 WILD-TYPE 343   4  31  23
D1295V11, multiclass
    clus
vv   MR1 MUTATED MR1 WILD-TYPE
  R0           2           343
  R1           0             4
  R2           0            31
  RX           2            23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1295V12, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MR1 MUTATED                                  0     2
  MR1 WILD-TYPE                                1     9
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  MR1 MUTATED                           0     2
  MR1 WILD-TYPE                        22   224
D1295V13, multiclass
                                  clus
vv                                 MR1 MUTATED MR1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      2             9
  BLACK OR AFRICAN AMERICAN                  0            22
  WHITE                                      2           224
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1296) Variable = FAM155B MUTATION ANALYSIS
D1296V1, survival
                   sevent
clus2                 0   1
  FAM155B MUTATED     7   1
  FAM155B WILD-TYPE 371  92
  FAM155B MUTATED FAM155B WILD-TYPE 
                8               463 
  FAM155B MUTATED FAM155B WILD-TYPE 
                1                92 
$`FAM155B MUTATED`
TCGA-AA-3815 TCGA-AA-3819 TCGA-AD-6889 TCGA-AY-5543 TCGA-AZ-4315 TCGA-AZ-5403 
       33.04        25.02        56.55        33.01        58.39        62.79 
TCGA-CK-5913 TCGA-CM-5348 
       51.32        22.98 

$`FAM155B WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3821 TCGA-AA-3831 
       19.04        10.06        35.05         0.99         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6197 
        0.20        14.50        27.09        16.31         0.95        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5407 
       17.82         1.41         5.13       106.75        22.36        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 
       17.56       148.01        85.45        15.62        49.08         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5349 
       37.02        25.02        13.02        29.06        22.03        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  FAM155B MUTATED FAM155B WILD-TYPE 
            22.98              0.00 
  FAM155B MUTATED FAM155B WILD-TYPE 
            62.79            148.01 
  FAM155B MUTATED FAM155B WILD-TYPE 
            42.18             20.02 
[1] "23.0 - 62.8 (42.2)" "0.0 - 148.0 (20.0)"
[1] "hr=" "2.8"
D1296V2, continuous
D1296V3, binary
                   cls
clus                  0   1
  FAM155B MUTATED     8   0
  FAM155B WILD-TYPE 358 119
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM155B MUTATED      8    0
  FAM155B WILD-TYPE  358  119
        clus
vv       FAM155B MUTATED FAM155B WILD-TYPE
  COLON                8               358
  RECTUM               0               119
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FAM155B MUTATED         0        0        1         5         0         0
  FAM155B WILD-TYPE      91        1       31       133        10         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FAM155B MUTATED           0          0          1          0        0
  FAM155B WILD-TYPE        24         11         58         42       48
                   vv
clus                STAGE IVA STAGE IVB
  FAM155B MUTATED           1         0
  FAM155B WILD-TYPE        17         1
D1296V4, multiclass
            clus
vv           FAM155B MUTATED FAM155B WILD-TYPE
  STAGE I                  0                91
  STAGE IA                 0                 1
  STAGE II                 1                31
  STAGE IIA                5               133
  STAGE IIB                0                10
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               0                11
  STAGE IIIB               1                58
  STAGE IIIC               0                42
  STAGE IV                 0                48
  STAGE IVA                1                17
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  FAM155B MUTATED     0   0   8   0
  FAM155B WILD-TYPE  17  92 321  50
D1296V5, multiclass
    clus
vv   FAM155B MUTATED FAM155B WILD-TYPE
  T1               0                17
  T2               0                92
  T3               8               321
  T4               0                50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  FAM155B MUTATED     6   2   0
  FAM155B WILD-TYPE 281 111  87
D1296V6, multiclass
    clus
vv   FAM155B MUTATED FAM155B WILD-TYPE
  N0               6               281
  N1               2               111
  N2               0                87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1296V7, binary
                   cls
clus                  0   1
  FAM155B MUTATED     5   1
  FAM155B WILD-TYPE 370  64
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM155B MUTATED      5    1
  FAM155B WILD-TYPE  370   64
   clus
vv  FAM155B MUTATED FAM155B WILD-TYPE
  0               5               370
  1               1                64
[1] 2 2
[1] FALSE
D1296V8, binary
                   cls
clus                  0   1
  FAM155B MUTATED     4   4
  FAM155B WILD-TYPE 221 260
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM155B MUTATED      4    4
  FAM155B WILD-TYPE  221  260
        clus
vv       FAM155B MUTATED FAM155B WILD-TYPE
  FEMALE               4               221
  MALE                 4               260
[1] 2 2
[1] FALSE
D1296V9, binary
                   cls
clus                  0   1
  FAM155B MUTATED     7   0
  FAM155B WILD-TYPE 343  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM155B MUTATED      7    0
  FAM155B WILD-TYPE  343   22
     clus
vv    FAM155B MUTATED FAM155B WILD-TYPE
  NO                7               343
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  FAM155B MUTATED                      8                             0
  FAM155B WILD-TYPE                  307                            47
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  FAM155B MUTATED                       0                              0
  FAM155B WILD-TYPE                   106                             10
D1296V10, multiclass
                                clus
vv                               FAM155B MUTATED FAM155B WILD-TYPE
  COLON ADENOCARCINOMA                         8               307
  COLON MUCINOUS ADENOCARCINOMA                0                47
  RECTAL ADENOCARCINOMA                        0               106
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  FAM155B MUTATED     5   0   0   1
  FAM155B WILD-TYPE 340   4  31  24
D1296V11, multiclass
    clus
vv   FAM155B MUTATED FAM155B WILD-TYPE
  R0               5               340
  R1               0                 4
  R2               0                31
  RX               1                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1296V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FAM155B MUTATED                                  0     1
  FAM155B WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  FAM155B MUTATED                           1     4
  FAM155B WILD-TYPE                        21   222
D1296V13, multiclass
                                  clus
vv                                 FAM155B MUTATED FAM155B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                10
  BLACK OR AFRICAN AMERICAN                      1                21
  WHITE                                          4               222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1297) Variable = MCF2 MUTATION ANALYSIS
D1297V1, survival
                sevent
clus2              0   1
  MCF2 MUTATED    29   3
  MCF2 WILD-TYPE 349  90
  MCF2 MUTATED MCF2 WILD-TYPE 
            32            439 
  MCF2 MUTATED MCF2 WILD-TYPE 
             3             90 
$`MCF2 MUTATED`
TCGA-A6-5665 TCGA-A6-6653 TCGA-AA-3510 TCGA-AA-3538 TCGA-AA-3555 TCGA-AA-3662 
       22.06        24.39        63.98        26.01        29.95         6.05 
TCGA-AA-3663 TCGA-AA-3672 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3930 TCGA-AA-3968 
        6.97         0.92        85.05        19.04         2.01        21.99 
TCGA-AA-3977 TCGA-AA-A00J TCGA-AA-A00N TCGA-AA-A010 TCGA-AZ-4315 TCGA-AZ-5407 
       25.02        18.05         4.01        34.98        58.39        88.21 
TCGA-CA-5254 TCGA-CA-6717 TCGA-CA-6718 TCGA-D5-6534 TCGA-D5-6541 TCGA-D5-7000 
       12.69        12.76        10.06        43.27        15.58        10.26 
TCGA-DM-A28E TCGA-G4-6304 TCGA-G4-6586 TCGA-G4-6588 TCGA-AG-3612 TCGA-AG-3882 
      119.93        53.62        35.80        26.17        19.99        19.99 
TCGA-AG-3890 TCGA-AG-3892 
       17.03        13.02 

$`MCF2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 
       25.18        24.16        21.76        24.69        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3542 TCGA-AA-3543 
       19.07        34.03        29.00        29.00        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 
       78.08        54.02         2.01        14.01        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
        5.03        26.99        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       29.98        18.05        31.00        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L 
       38.04        19.00        30.02        34.03        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
       11.74         3.19         1.61         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.07        12.20        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       18.25         1.32        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       12.49        16.14         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       12.00        11.38       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
      133.18        74.56        65.85        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6625 
       63.62        61.91        36.00        22.09        13.78        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       15.95        19.99        13.94         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3883 TCGA-AG-3885 
       32.98         0.99         0.99        19.04         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       36.95        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  MCF2 MUTATED MCF2 WILD-TYPE 
          0.92           0.00 
  MCF2 MUTATED MCF2 WILD-TYPE 
        119.93         148.01 
  MCF2 MUTATED MCF2 WILD-TYPE 
         20.99          20.19 
[1] "0.9 - 119.9 (21.0)" "0.0 - 148.0 (20.2)"
[1] "hr=" "2.5"
D1297V2, continuous
D1297V3, binary
                cls
clus               0   1
  MCF2 MUTATED    28   4
  MCF2 WILD-TYPE 338 115
[1] "tbl2"
                cls
clus             [,1] [,2]
  MCF2 MUTATED     28    4
  MCF2 WILD-TYPE  338  115
        clus
vv       MCF2 MUTATED MCF2 WILD-TYPE
  COLON            28            338
  RECTUM            4            115
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MCF2 MUTATED         8        0        2        11         3         0
  MCF2 WILD-TYPE      83        1       30       127         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MCF2 MUTATED           2          0          2          0        3         0
  MCF2 WILD-TYPE        22         11         57         42       45        18
                vv
clus             STAGE IVB
  MCF2 MUTATED           0
  MCF2 WILD-TYPE         1
D1297V4, multiclass
            clus
vv           MCF2 MUTATED MCF2 WILD-TYPE
  STAGE I               8             83
  STAGE IA              0              1
  STAGE II              2             30
  STAGE IIA            11            127
  STAGE IIB             3              7
  STAGE IIC             0              1
  STAGE III             2             22
  STAGE IIIA            0             11
  STAGE IIIB            2             57
  STAGE IIIC            0             42
  STAGE IV              3             45
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  MCF2 MUTATED     2   7  18   5
  MCF2 WILD-TYPE  15  85 311  45
D1297V5, multiclass
    clus
vv   MCF2 MUTATED MCF2 WILD-TYPE
  T1            2             15
  T2            7             85
  T3           18            311
  T4            5             45
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  MCF2 MUTATED    27   3   2
  MCF2 WILD-TYPE 260 110  85
D1297V6, multiclass
    clus
vv   MCF2 MUTATED MCF2 WILD-TYPE
  N0           27            260
  N1            3            110
  N2            2             85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1297V7, binary
                cls
clus               0   1
  MCF2 MUTATED    28   3
  MCF2 WILD-TYPE 347  62
[1] "tbl2"
                cls
clus             [,1] [,2]
  MCF2 MUTATED     28    3
  MCF2 WILD-TYPE  347   62
   clus
vv  MCF2 MUTATED MCF2 WILD-TYPE
  0           28            347
  1            3             62
[1] 2 2
[1] FALSE
D1297V8, binary
                cls
clus               0   1
  MCF2 MUTATED    18  14
  MCF2 WILD-TYPE 207 250
[1] "tbl2"
                cls
clus             [,1] [,2]
  MCF2 MUTATED     18   14
  MCF2 WILD-TYPE  207  250
        clus
vv       MCF2 MUTATED MCF2 WILD-TYPE
  FEMALE           18            207
  MALE             14            250
[1] 2 2
[1] FALSE
D1297V9, binary
                cls
clus               0   1
  MCF2 MUTATED    29   1
  MCF2 WILD-TYPE 321  21
[1] "tbl2"
                cls
clus             [,1] [,2]
  MCF2 MUTATED     29    1
  MCF2 WILD-TYPE  321   21
     clus
vv    MCF2 MUTATED MCF2 WILD-TYPE
  NO            29            321
  YES            1             21
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MCF2 MUTATED                     22                             6
  MCF2 WILD-TYPE                  293                            41
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MCF2 MUTATED                       4                              0
  MCF2 WILD-TYPE                   102                             10
D1297V10, multiclass
                                clus
vv                               MCF2 MUTATED MCF2 WILD-TYPE
  COLON ADENOCARCINOMA                     22            293
  COLON MUCINOUS ADENOCARCINOMA             6             41
  RECTAL ADENOCARCINOMA                     4            102
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  MCF2 MUTATED    22   0   3   3
  MCF2 WILD-TYPE 323   4  28  22
D1297V11, multiclass
    clus
vv   MCF2 MUTATED MCF2 WILD-TYPE
  R0           22            323
  R1            0              4
  R2            3             28
  RX            3             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1297V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MCF2 MUTATED                                  0     3
  MCF2 WILD-TYPE                                1     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  MCF2 MUTATED                           0    11
  MCF2 WILD-TYPE                        22   215
D1297V13, multiclass
                                  clus
vv                                 MCF2 MUTATED MCF2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       3              8
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                      11            215
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1298) Variable = PSD3 MUTATION ANALYSIS
D1298V1, survival
                sevent
clus2              0   1
  PSD3 MUTATED     9   2
  PSD3 WILD-TYPE 369  91
  PSD3 MUTATED PSD3 WILD-TYPE 
            11            460 
  PSD3 MUTATED PSD3 WILD-TYPE 
             2             91 
$`PSD3 MUTATED`
TCGA-A6-5661 TCGA-AA-3510 TCGA-AA-3663 TCGA-AA-3815 TCGA-AD-6899 TCGA-AZ-6599 
       33.53        63.98         6.97        33.04         5.79         6.77 
TCGA-CM-4743 TCGA-CM-4747 TCGA-D5-6529 TCGA-G4-6588 TCGA-AG-A002 
       23.05        25.02        20.19        26.17        20.98 

$`PSD3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        0.72        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       88.21        49.41        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 
        9.99        21.14        82.95         1.91       124.27        20.02 
TCGA-CM-4746 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       37.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 
       61.91        36.00        22.09        13.78        35.80        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  PSD3 MUTATED PSD3 WILD-TYPE 
          5.79           0.00 
  PSD3 MUTATED PSD3 WILD-TYPE 
         63.98         148.01 
  PSD3 MUTATED PSD3 WILD-TYPE 
        23.050         20.035 
[1] "5.8 - 64.0 (23.1)"  "0.0 - 148.0 (20.0)"
[1] "hr=" "1"  
D1298V2, continuous
D1298V3, binary
                cls
clus               0   1
  PSD3 MUTATED    10   1
  PSD3 WILD-TYPE 356 118
[1] "tbl2"
                cls
clus             [,1] [,2]
  PSD3 MUTATED     10    1
  PSD3 WILD-TYPE  356  118
        clus
vv       PSD3 MUTATED PSD3 WILD-TYPE
  COLON            10            356
  RECTUM            1            118
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PSD3 MUTATED         2        0        2         5         0         0
  PSD3 WILD-TYPE      89        1       30       133        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PSD3 MUTATED           0          0          0          1        0         1
  PSD3 WILD-TYPE        24         11         59         41       48        17
                vv
clus             STAGE IVB
  PSD3 MUTATED           0
  PSD3 WILD-TYPE         1
D1298V4, multiclass
            clus
vv           PSD3 MUTATED PSD3 WILD-TYPE
  STAGE I               2             89
  STAGE IA              0              1
  STAGE II              2             30
  STAGE IIA             5            133
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            0             59
  STAGE IIIC            1             41
  STAGE IV              0             48
  STAGE IVA             1             17
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  PSD3 MUTATED     0   2   7   2
  PSD3 WILD-TYPE  17  90 322  48
D1298V5, multiclass
    clus
vv   PSD3 MUTATED PSD3 WILD-TYPE
  T1            0             17
  T2            2             90
  T3            7            322
  T4            2             48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  PSD3 MUTATED     9   1   1
  PSD3 WILD-TYPE 278 112  86
D1298V6, multiclass
    clus
vv   PSD3 MUTATED PSD3 WILD-TYPE
  N0            9            278
  N1            1            112
  N2            1             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1298V7, binary
                cls
clus               0   1
  PSD3 MUTATED     8   1
  PSD3 WILD-TYPE 367  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  PSD3 MUTATED      8    1
  PSD3 WILD-TYPE  367   64
   clus
vv  PSD3 MUTATED PSD3 WILD-TYPE
  0            8            367
  1            1             64
[1] 2 2
[1] FALSE
D1298V8, binary
                cls
clus               0   1
  PSD3 MUTATED     3   8
  PSD3 WILD-TYPE 222 256
[1] "tbl2"
                cls
clus             [,1] [,2]
  PSD3 MUTATED      3    8
  PSD3 WILD-TYPE  222  256
        clus
vv       PSD3 MUTATED PSD3 WILD-TYPE
  FEMALE            3            222
  MALE              8            256
[1] 2 2
[1] FALSE
D1298V9, binary
                cls
clus               0   1
  PSD3 MUTATED    11   0
  PSD3 WILD-TYPE 339  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  PSD3 MUTATED     11    0
  PSD3 WILD-TYPE  339   22
     clus
vv    PSD3 MUTATED PSD3 WILD-TYPE
  NO            11            339
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PSD3 MUTATED                      9                             1
  PSD3 WILD-TYPE                  306                            46
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PSD3 MUTATED                       1                              0
  PSD3 WILD-TYPE                   105                             10
D1298V10, multiclass
                                clus
vv                               PSD3 MUTATED PSD3 WILD-TYPE
  COLON ADENOCARCINOMA                      9            306
  COLON MUCINOUS ADENOCARCINOMA             1             46
  RECTAL ADENOCARCINOMA                     1            105
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  PSD3 MUTATED     9   0   0   0
  PSD3 WILD-TYPE 336   4  31  25
D1298V11, multiclass
    clus
vv   PSD3 MUTATED PSD3 WILD-TYPE
  R0            9            336
  R1            0              4
  R2            0             31
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1298V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PSD3 MUTATED                                  0     0
  PSD3 WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  PSD3 MUTATED                           1     6
  PSD3 WILD-TYPE                        21   220
D1298V13, multiclass
                                  clus
vv                                 PSD3 MUTATED PSD3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                       6            220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1299) Variable = ARHGAP27 MUTATION ANALYSIS
D1299V1, survival
                    sevent
clus2                  0   1
  ARHGAP27 MUTATED     9   3
  ARHGAP27 WILD-TYPE 369  90
  ARHGAP27 MUTATED ARHGAP27 WILD-TYPE 
                12                459 
  ARHGAP27 MUTATED ARHGAP27 WILD-TYPE 
                 3                 90 
$`ARHGAP27 MUTATED`
TCGA-A6-6653 TCGA-A6-6781 TCGA-AA-3516 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3877 
       24.39        19.66        13.02        19.04        10.06        31.00 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-D5-6532 TCGA-F4-6856 TCGA-G4-6588 TCGA-AG-A002 
        1.02        35.01        18.25        35.31        26.17        20.98 

$`ARHGAP27 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
       25.08        25.18        24.16        21.76        24.69        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
       63.98         6.97         1.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       85.05        26.99        19.04        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       18.05         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01S 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       20.19         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
       13.25         0.53        47.41       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        35.80        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  ARHGAP27 MUTATED ARHGAP27 WILD-TYPE 
              1.02               0.00 
  ARHGAP27 MUTATED ARHGAP27 WILD-TYPE 
             35.31             148.01 
  ARHGAP27 MUTATED ARHGAP27 WILD-TYPE 
             20.32              20.19 
[1] "1.0 - 35.3 (20.3)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.7"
D1299V2, continuous
D1299V3, binary
                    cls
clus                   0   1
  ARHGAP27 MUTATED    11   1
  ARHGAP27 WILD-TYPE 355 118
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ARHGAP27 MUTATED     11    1
  ARHGAP27 WILD-TYPE  355  118
        clus
vv       ARHGAP27 MUTATED ARHGAP27 WILD-TYPE
  COLON                11                355
  RECTUM                1                118
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ARHGAP27 MUTATED         4        0        2         2         0         0
  ARHGAP27 WILD-TYPE      87        1       30       136        10         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ARHGAP27 MUTATED           3          0          0          1        0
  ARHGAP27 WILD-TYPE        21         11         59         41       48
                    vv
clus                 STAGE IVA STAGE IVB
  ARHGAP27 MUTATED           0         0
  ARHGAP27 WILD-TYPE        18         1
D1299V4, multiclass
            clus
vv           ARHGAP27 MUTATED ARHGAP27 WILD-TYPE
  STAGE I                   4                 87
  STAGE IA                  0                  1
  STAGE II                  2                 30
  STAGE IIA                 2                136
  STAGE IIB                 0                 10
  STAGE IIC                 0                  1
  STAGE III                 3                 21
  STAGE IIIA                0                 11
  STAGE IIIB                0                 59
  STAGE IIIC                1                 41
  STAGE IV                  0                 48
  STAGE IVA                 0                 18
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  ARHGAP27 MUTATED     1   3   7   1
  ARHGAP27 WILD-TYPE  16  89 322  49
D1299V5, multiclass
    clus
vv   ARHGAP27 MUTATED ARHGAP27 WILD-TYPE
  T1                1                 16
  T2                3                 89
  T3                7                322
  T4                1                 49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  ARHGAP27 MUTATED     8   1   3
  ARHGAP27 WILD-TYPE 279 112  84
D1299V6, multiclass
    clus
vv   ARHGAP27 MUTATED ARHGAP27 WILD-TYPE
  N0                8                279
  N1                1                112
  N2                3                 84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1299V7, binary
                    cls
clus                   0   1
  ARHGAP27 MUTATED    11   0
  ARHGAP27 WILD-TYPE 364  65
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ARHGAP27 MUTATED     11    0
  ARHGAP27 WILD-TYPE  364   65
   clus
vv  ARHGAP27 MUTATED ARHGAP27 WILD-TYPE
  0               11                364
  1                0                 65
[1] 2 2
[1] FALSE
D1299V8, binary
                    cls
clus                   0   1
  ARHGAP27 MUTATED     5   7
  ARHGAP27 WILD-TYPE 220 257
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ARHGAP27 MUTATED      5    7
  ARHGAP27 WILD-TYPE  220  257
        clus
vv       ARHGAP27 MUTATED ARHGAP27 WILD-TYPE
  FEMALE                5                220
  MALE                  7                257
[1] 2 2
[1] FALSE
D1299V9, binary
                    cls
clus                   0   1
  ARHGAP27 MUTATED    10   1
  ARHGAP27 WILD-TYPE 340  21
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ARHGAP27 MUTATED     10    1
  ARHGAP27 WILD-TYPE  340   21
     clus
vv    ARHGAP27 MUTATED ARHGAP27 WILD-TYPE
  NO                10                340
  YES                1                 21
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ARHGAP27 MUTATED                      6                             5
  ARHGAP27 WILD-TYPE                  309                            42
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ARHGAP27 MUTATED                       1                              0
  ARHGAP27 WILD-TYPE                   105                             10
D1299V10, multiclass
                                clus
vv                               ARHGAP27 MUTATED ARHGAP27 WILD-TYPE
  COLON ADENOCARCINOMA                          6                309
  COLON MUCINOUS ADENOCARCINOMA                 5                 42
  RECTAL ADENOCARCINOMA                         1                105
  RECTAL MUCINOUS ADENOCARCINOMA                0                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  ARHGAP27 MUTATED    10   0   0   0
  ARHGAP27 WILD-TYPE 335   4  31  25
D1299V11, multiclass
    clus
vv   ARHGAP27 MUTATED ARHGAP27 WILD-TYPE
  R0               10                335
  R1                0                  4
  R2                0                 31
  RX                0                 25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1299V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ARHGAP27 MUTATED                                  0     0
  ARHGAP27 WILD-TYPE                                1    11
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  ARHGAP27 MUTATED                           0     5
  ARHGAP27 WILD-TYPE                        22   221
D1299V13, multiclass
                                  clus
vv                                 ARHGAP27 MUTATED ARHGAP27 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 11
  BLACK OR AFRICAN AMERICAN                       0                 22
  WHITE                                           5                221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1300) Variable = C20ORF117 MUTATION ANALYSIS
D1300V1, survival
                     sevent
clus2                   0   1
  C20ORF117 MUTATED    10   6
  C20ORF117 WILD-TYPE 368  87
  C20ORF117 MUTATED C20ORF117 WILD-TYPE 
                 16                 455 
  C20ORF117 MUTATED C20ORF117 WILD-TYPE 
                  6                  87 
$`C20ORF117 MUTATED`
TCGA-A6-5665 TCGA-AA-3492 TCGA-AA-3815 TCGA-AA-3950 TCGA-AA-A02W TCGA-AD-5900 
       22.06         3.02        33.04        24.00        41.00         0.07 
TCGA-AD-6964 TCGA-AU-6004 TCGA-AZ-6598 TCGA-CA-6718 TCGA-CM-5861 TCGA-CM-6162 
       10.88        27.09        49.41        10.06        15.02        12.00 
TCGA-F4-6570 TCGA-AG-A026 TCGA-EI-6507 TCGA-F5-6702 
        6.18         1.94        19.96        28.57 

$`C20ORF117 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 
       20.12        19.66        20.28         7.04         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       35.05         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        33.01        26.01         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
        5.03        14.01         0.92        39.98        18.05        40.96 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 
       22.42        27.42         0.20        14.50        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 
      106.75        22.36        62.79        88.21         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       12.76        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 
       29.06        22.03        22.98        30.08        32.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 
       15.02        15.02        17.03        15.02         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       31.96        35.74        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       64.01        10.98        49.97        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       20.55        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  C20ORF117 MUTATED C20ORF117 WILD-TYPE 
               0.07                0.00 
  C20ORF117 MUTATED C20ORF117 WILD-TYPE 
              49.41              148.01 
  C20ORF117 MUTATED C20ORF117 WILD-TYPE 
              17.49               20.28 
[1] "0.1 - 49.4 (17.5)"  "0.0 - 148.0 (20.3)"
[1] "hr=" "2.7"
D1300V2, continuous
D1300V3, binary
                     cls
clus                    0   1
  C20ORF117 MUTATED    15   3
  C20ORF117 WILD-TYPE 351 116
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  C20ORF117 MUTATED     15    3
  C20ORF117 WILD-TYPE  351  116
        clus
vv       C20ORF117 MUTATED C20ORF117 WILD-TYPE
  COLON                 15                 351
  RECTUM                 3                 116
[1] 2 2
[1] FALSE
                     vv
clus                  STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  C20ORF117 MUTATED         3        0        4         8         0         0
  C20ORF117 WILD-TYPE      88        1       28       130        10         1
                     vv
clus                  STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C20ORF117 MUTATED           0          0          1          0        0
  C20ORF117 WILD-TYPE        24         11         58         42       48
                     vv
clus                  STAGE IVA STAGE IVB
  C20ORF117 MUTATED           1         0
  C20ORF117 WILD-TYPE        17         1
D1300V4, multiclass
            clus
vv           C20ORF117 MUTATED C20ORF117 WILD-TYPE
  STAGE I                    3                  88
  STAGE IA                   0                   1
  STAGE II                   4                  28
  STAGE IIA                  8                 130
  STAGE IIB                  0                  10
  STAGE IIC                  0                   1
  STAGE III                  0                  24
  STAGE IIIA                 0                  11
  STAGE IIIB                 1                  58
  STAGE IIIC                 0                  42
  STAGE IV                   0                  48
  STAGE IVA                  1                  17
  STAGE IVB                  0                   1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                   T1  T2  T3  T4
  C20ORF117 MUTATED     0   3  12   3
  C20ORF117 WILD-TYPE  17  89 317  47
D1300V5, multiclass
    clus
vv   C20ORF117 MUTATED C20ORF117 WILD-TYPE
  T1                 0                  17
  T2                 3                  89
  T3                12                 317
  T4                 3                  47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                   N0  N1  N2
  C20ORF117 MUTATED    15   2   1
  C20ORF117 WILD-TYPE 272 111  86
D1300V6, multiclass
    clus
vv   C20ORF117 MUTATED C20ORF117 WILD-TYPE
  N0                15                 272
  N1                 2                 111
  N2                 1                  86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1300V7, binary
                     cls
clus                    0   1
  C20ORF117 MUTATED    14   1
  C20ORF117 WILD-TYPE 361  64
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  C20ORF117 MUTATED     14    1
  C20ORF117 WILD-TYPE  361   64
   clus
vv  C20ORF117 MUTATED C20ORF117 WILD-TYPE
  0                14                 361
  1                 1                  64
[1] 2 2
[1] FALSE
D1300V8, binary
                     cls
clus                    0   1
  C20ORF117 MUTATED    12   6
  C20ORF117 WILD-TYPE 213 258
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  C20ORF117 MUTATED     12    6
  C20ORF117 WILD-TYPE  213  258
        clus
vv       C20ORF117 MUTATED C20ORF117 WILD-TYPE
  FEMALE                12                 213
  MALE                   6                 258
[1] 2 2
[1] FALSE
D1300V9, binary
                     cls
clus                    0   1
  C20ORF117 MUTATED    13   0
  C20ORF117 WILD-TYPE 337  22
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  C20ORF117 MUTATED     13    0
  C20ORF117 WILD-TYPE  337   22
     clus
vv    C20ORF117 MUTATED C20ORF117 WILD-TYPE
  NO                 13                 337
  YES                 0                  22
[1] 2 2
[1] FALSE
                     vv
clus                  COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  C20ORF117 MUTATED                     12                             3
  C20ORF117 WILD-TYPE                  303                            44
                     vv
clus                  RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  C20ORF117 MUTATED                       3                              0
  C20ORF117 WILD-TYPE                   103                             10
D1300V10, multiclass
                                clus
vv                               C20ORF117 MUTATED C20ORF117 WILD-TYPE
  COLON ADENOCARCINOMA                          12                 303
  COLON MUCINOUS ADENOCARCINOMA                  3                  44
  RECTAL ADENOCARCINOMA                          3                 103
  RECTAL MUCINOUS ADENOCARCINOMA                 0                  10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                   R0  R1  R2  RX
  C20ORF117 MUTATED    14   1   0   1
  C20ORF117 WILD-TYPE 331   3  31  24
D1300V11, multiclass
    clus
vv   C20ORF117 MUTATED C20ORF117 WILD-TYPE
  R0                14                 331
  R1                 1                   3
  R2                 0                  31
  RX                 1                  24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1300V12, continuous
                     vv
clus                  AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C20ORF117 MUTATED                                  0     1
  C20ORF117 WILD-TYPE                                1    10
                     vv
clus                  BLACK OR AFRICAN AMERICAN WHITE
  C20ORF117 MUTATED                           0    10
  C20ORF117 WILD-TYPE                        22   216
D1300V13, multiclass
                                  clus
vv                                 C20ORF117 MUTATED C20ORF117 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                 0                   1
  ASIAN                                            1                  10
  BLACK OR AFRICAN AMERICAN                        0                  22
  WHITE                                           10                 216
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1301) Variable = NKTR MUTATION ANALYSIS
D1301V1, survival
                sevent
clus2              0   1
  NKTR MUTATED     9   5
  NKTR WILD-TYPE 369  88
  NKTR MUTATED NKTR WILD-TYPE 
            14            457 
  NKTR MUTATED NKTR WILD-TYPE 
             5             88 
$`NKTR MUTATED`
TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3663 TCGA-AA-3815 TCGA-AA-3864 TCGA-AA-A00E 
        3.02        63.98         6.97        33.04        53.00        30.02 
TCGA-AA-A00Z TCGA-AD-6889 TCGA-AZ-6601 TCGA-D5-6532 TCGA-DM-A1D8 TCGA-DM-A28F 
       21.99        56.55       100.01        18.25        12.59        35.97 
TCGA-G4-6626 TCGA-AG-A002 
       46.75        20.98 

$`NKTR WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       31.07        30.05        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00J 
       27.02        13.94        38.04        19.00        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       15.52         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
       12.10        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D9 
       38.20       130.65        92.75        49.91        13.32       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
       81.37       119.93        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-AF-2687 
       13.78        35.80        26.17        91.79        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  NKTR MUTATED NKTR WILD-TYPE 
          3.02           0.00 
  NKTR MUTATED NKTR WILD-TYPE 
        100.01         148.01 
  NKTR MUTATED NKTR WILD-TYPE 
         31.53          20.02 
[1] "3.0 - 100.0 (31.5)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.3"
D1301V2, continuous
D1301V3, binary
                cls
clus               0   1
  NKTR MUTATED    13   1
  NKTR WILD-TYPE 353 118
[1] "tbl2"
                cls
clus             [,1] [,2]
  NKTR MUTATED     13    1
  NKTR WILD-TYPE  353  118
        clus
vv       NKTR MUTATED NKTR WILD-TYPE
  COLON            13            353
  RECTUM            1            118
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NKTR MUTATED         1        0        5         6         0         0
  NKTR WILD-TYPE      90        1       27       132        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NKTR MUTATED           0          0          1          0        0         0
  NKTR WILD-TYPE        24         11         58         42       48        18
                vv
clus             STAGE IVB
  NKTR MUTATED           0
  NKTR WILD-TYPE         1
D1301V4, multiclass
            clus
vv           NKTR MUTATED NKTR WILD-TYPE
  STAGE I               1             90
  STAGE IA              0              1
  STAGE II              5             27
  STAGE IIA             6            132
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            1             58
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  NKTR MUTATED     0   1  13   0
  NKTR WILD-TYPE  17  91 316  50
D1301V5, multiclass
    clus
vv   NKTR MUTATED NKTR WILD-TYPE
  T1            0             17
  T2            1             91
  T3           13            316
  T4            0             50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  NKTR MUTATED    12   2   0
  NKTR WILD-TYPE 275 111  87
D1301V6, multiclass
    clus
vv   NKTR MUTATED NKTR WILD-TYPE
  N0           12            275
  N1            2            111
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1301V7, binary
                cls
clus               0   1
  NKTR MUTATED    13   0
  NKTR WILD-TYPE 362  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  NKTR MUTATED     13    0
  NKTR WILD-TYPE  362   65
   clus
vv  NKTR MUTATED NKTR WILD-TYPE
  0           13            362
  1            0             65
[1] 2 2
[1] FALSE
D1301V8, binary
                cls
clus               0   1
  NKTR MUTATED     3  11
  NKTR WILD-TYPE 222 253
[1] "tbl2"
                cls
clus             [,1] [,2]
  NKTR MUTATED      3   11
  NKTR WILD-TYPE  222  253
        clus
vv       NKTR MUTATED NKTR WILD-TYPE
  FEMALE            3            222
  MALE             11            253
[1] 2 2
[1] FALSE
D1301V9, binary
                cls
clus               0   1
  NKTR MUTATED    11   0
  NKTR WILD-TYPE 339  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  NKTR MUTATED     11    0
  NKTR WILD-TYPE  339   22
     clus
vv    NKTR MUTATED NKTR WILD-TYPE
  NO            11            339
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  NKTR MUTATED                     13                             0
  NKTR WILD-TYPE                  302                            47
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  NKTR MUTATED                       1                              0
  NKTR WILD-TYPE                   105                             10
D1301V10, multiclass
                                clus
vv                               NKTR MUTATED NKTR WILD-TYPE
  COLON ADENOCARCINOMA                     13            302
  COLON MUCINOUS ADENOCARCINOMA             0             47
  RECTAL ADENOCARCINOMA                     1            105
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  NKTR MUTATED    10   0   0   0
  NKTR WILD-TYPE 335   4  31  25
D1301V11, multiclass
    clus
vv   NKTR MUTATED NKTR WILD-TYPE
  R0           10            335
  R1            0              4
  R2            0             31
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1301V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NKTR MUTATED                                  0     1
  NKTR WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  NKTR MUTATED                           0     5
  NKTR WILD-TYPE                        22   221
D1301V13, multiclass
                                  clus
vv                                 NKTR MUTATED NKTR WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       5            221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1302) Variable = KLF5 MUTATION ANALYSIS
D1302V1, survival
                sevent
clus2              0   1
  KLF5 MUTATED     9   3
  KLF5 WILD-TYPE 369  90
  KLF5 MUTATED KLF5 WILD-TYPE 
            12            459 
  KLF5 MUTATED KLF5 WILD-TYPE 
             3             90 
$`KLF5 MUTATED`
TCGA-A6-5666 TCGA-AA-A01Q TCGA-AU-6004 TCGA-AZ-6599 TCGA-AZ-6608 TCGA-CM-6161 
       32.71         1.02        27.09         6.77         1.61        15.02 
TCGA-CM-6163 TCGA-D5-5539 TCGA-F4-6569 TCGA-G4-6588 TCGA-G4-6626 TCGA-AG-3598 
        2.96        19.59        35.74        26.17        46.75        50.04 

$`KLF5 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        22.06        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01R TCGA-AA-A01S 
       12.00        31.00        31.00        38.07        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       10.88         0.20        14.50        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        88.21        49.41        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6162 TCGA-CM-6164 TCGA-CM-6165 
       15.02        15.02        17.03        12.00        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-5541 
       10.06        12.03        45.40        12.26        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6570 
       60.79       117.07        98.24         8.61        31.96         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 
       61.91        36.00        22.09        13.78        35.80        91.79 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
        2.01        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  KLF5 MUTATED KLF5 WILD-TYPE 
          1.02           0.00 
  KLF5 MUTATED KLF5 WILD-TYPE 
         50.04         148.01 
  KLF5 MUTATED KLF5 WILD-TYPE 
         22.88          20.19 
[1] "1.0 - 50.0 (22.9)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.5"
D1302V2, continuous
D1302V3, binary
                cls
clus               0   1
  KLF5 MUTATED    11   1
  KLF5 WILD-TYPE 355 118
[1] "tbl2"
                cls
clus             [,1] [,2]
  KLF5 MUTATED     11    1
  KLF5 WILD-TYPE  355  118
        clus
vv       KLF5 MUTATED KLF5 WILD-TYPE
  COLON            11            355
  RECTUM            1            118
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KLF5 MUTATED         5        0        1         3         0         1
  KLF5 WILD-TYPE      86        1       31       135        10         0
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  KLF5 MUTATED           0          2          0          0        0         0
  KLF5 WILD-TYPE        24          9         59         42       48        18
                vv
clus             STAGE IVB
  KLF5 MUTATED           0
  KLF5 WILD-TYPE         1
D1302V4, multiclass
            clus
vv           KLF5 MUTATED KLF5 WILD-TYPE
  STAGE I               5             86
  STAGE IA              0              1
  STAGE II              1             31
  STAGE IIA             3            135
  STAGE IIB             0             10
  STAGE IIC             1              0
  STAGE III             0             24
  STAGE IIIA            2              9
  STAGE IIIB            0             59
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  KLF5 MUTATED     1   5   5   1
  KLF5 WILD-TYPE  16  87 324  49
D1302V5, multiclass
    clus
vv   KLF5 MUTATED KLF5 WILD-TYPE
  T1            1             16
  T2            5             87
  T3            5            324
  T4            1             49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  KLF5 MUTATED    10   2   0
  KLF5 WILD-TYPE 277 111  87
D1302V6, multiclass
    clus
vv   KLF5 MUTATED KLF5 WILD-TYPE
  N0           10            277
  N1            2            111
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1302V7, binary
                cls
clus               0   1
  KLF5 MUTATED    11   0
  KLF5 WILD-TYPE 364  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  KLF5 MUTATED     11    0
  KLF5 WILD-TYPE  364   65
   clus
vv  KLF5 MUTATED KLF5 WILD-TYPE
  0           11            364
  1            0             65
[1] 2 2
[1] FALSE
D1302V8, binary
                cls
clus               0   1
  KLF5 MUTATED     5   7
  KLF5 WILD-TYPE 220 257
[1] "tbl2"
                cls
clus             [,1] [,2]
  KLF5 MUTATED      5    7
  KLF5 WILD-TYPE  220  257
        clus
vv       KLF5 MUTATED KLF5 WILD-TYPE
  FEMALE            5            220
  MALE              7            257
[1] 2 2
[1] FALSE
D1302V9, binary
                cls
clus               0   1
  KLF5 MUTATED    10   0
  KLF5 WILD-TYPE 340  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  KLF5 MUTATED     10    0
  KLF5 WILD-TYPE  340   22
     clus
vv    KLF5 MUTATED KLF5 WILD-TYPE
  NO            10            340
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  KLF5 MUTATED                     10                             1
  KLF5 WILD-TYPE                  305                            46
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  KLF5 MUTATED                       1                              0
  KLF5 WILD-TYPE                   105                             10
D1302V10, multiclass
                                clus
vv                               KLF5 MUTATED KLF5 WILD-TYPE
  COLON ADENOCARCINOMA                     10            305
  COLON MUCINOUS ADENOCARCINOMA             1             46
  RECTAL ADENOCARCINOMA                     1            105
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  KLF5 MUTATED     9   0   0   0
  KLF5 WILD-TYPE 336   4  31  25
D1302V11, multiclass
    clus
vv   KLF5 MUTATED KLF5 WILD-TYPE
  R0            9            336
  R1            0              4
  R2            0             31
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1302V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KLF5 MUTATED                                  0     0
  KLF5 WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  KLF5 MUTATED                           0    10
  KLF5 WILD-TYPE                        22   216
D1302V13, multiclass
                                  clus
vv                                 KLF5 MUTATED KLF5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                      10            216
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1303) Variable = PARG MUTATION ANALYSIS
D1303V1, survival
                sevent
clus2              0   1
  PARG MUTATED    10   2
  PARG WILD-TYPE 368  91
  PARG MUTATED PARG WILD-TYPE 
            12            459 
  PARG MUTATED PARG WILD-TYPE 
             2             91 
$`PARG MUTATED`
TCGA-A6-5665 TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3662 TCGA-CA-6717 TCGA-CM-6171 
       22.06         3.02        63.98         6.05        12.76        14.04 
TCGA-CM-6674 TCGA-D5-6529 TCGA-D5-6928 TCGA-F4-6459 TCGA-G4-6588 TCGA-CI-6622 
       12.95        20.19        11.64         8.61        26.17         6.97 

$`PARG WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 
       20.12        19.66        20.28         7.04         1.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02        78.08         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07        12.20        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       15.02        11.01        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       55.92        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
      117.07        98.24        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        35.80        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  PARG MUTATED PARG WILD-TYPE 
          3.02           0.00 
  PARG MUTATED PARG WILD-TYPE 
         63.98         148.01 
  PARG MUTATED PARG WILD-TYPE 
        12.855         20.910 
[1] "3.0 - 64.0 (12.9)"  "0.0 - 148.0 (20.9)"
[1] "hr=" "1.2"
D1303V2, continuous
D1303V3, binary
                cls
clus               0   1
  PARG MUTATED    11   1
  PARG WILD-TYPE 355 118
[1] "tbl2"
                cls
clus             [,1] [,2]
  PARG MUTATED     11    1
  PARG WILD-TYPE  355  118
        clus
vv       PARG MUTATED PARG WILD-TYPE
  COLON            11            355
  RECTUM            1            118
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PARG MUTATED         1        0        2         6         1         0
  PARG WILD-TYPE      90        1       30       132         9         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PARG MUTATED           0          0          1          0        1         0
  PARG WILD-TYPE        24         11         58         42       47        18
                vv
clus             STAGE IVB
  PARG MUTATED           0
  PARG WILD-TYPE         1
D1303V4, multiclass
            clus
vv           PARG MUTATED PARG WILD-TYPE
  STAGE I               1             90
  STAGE IA              0              1
  STAGE II              2             30
  STAGE IIA             6            132
  STAGE IIB             1              9
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            1             58
  STAGE IIIC            0             42
  STAGE IV              1             47
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  PARG MUTATED     0   1   9   2
  PARG WILD-TYPE  17  91 320  48
D1303V5, multiclass
    clus
vv   PARG MUTATED PARG WILD-TYPE
  T1            0             17
  T2            1             91
  T3            9            320
  T4            2             48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  PARG MUTATED    10   0   2
  PARG WILD-TYPE 277 113  85
D1303V6, multiclass
    clus
vv   PARG MUTATED PARG WILD-TYPE
  N0           10            277
  N1            0            113
  N2            2             85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1303V7, binary
                cls
clus               0   1
  PARG MUTATED    11   1
  PARG WILD-TYPE 364  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  PARG MUTATED     11    1
  PARG WILD-TYPE  364   64
   clus
vv  PARG MUTATED PARG WILD-TYPE
  0           11            364
  1            1             64
[1] 2 2
[1] FALSE
D1303V8, binary
                cls
clus               0   1
  PARG MUTATED     6   6
  PARG WILD-TYPE 219 258
[1] "tbl2"
                cls
clus             [,1] [,2]
  PARG MUTATED      6    6
  PARG WILD-TYPE  219  258
        clus
vv       PARG MUTATED PARG WILD-TYPE
  FEMALE            6            219
  MALE              6            258
[1] 2 2
[1] FALSE
D1303V9, binary
                cls
clus               0   1
  PARG MUTATED    11   0
  PARG WILD-TYPE 339  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  PARG MUTATED     11    0
  PARG WILD-TYPE  339   22
     clus
vv    PARG MUTATED PARG WILD-TYPE
  NO            11            339
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PARG MUTATED                      9                             2
  PARG WILD-TYPE                  306                            45
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PARG MUTATED                       1                              0
  PARG WILD-TYPE                   105                             10
D1303V10, multiclass
                                clus
vv                               PARG MUTATED PARG WILD-TYPE
  COLON ADENOCARCINOMA                      9            306
  COLON MUCINOUS ADENOCARCINOMA             2             45
  RECTAL ADENOCARCINOMA                     1            105
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  PARG MUTATED     9   0   1   1
  PARG WILD-TYPE 336   4  30  24
D1303V11, multiclass
    clus
vv   PARG MUTATED PARG WILD-TYPE
  R0            9            336
  R1            0              4
  R2            1             30
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1303V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PARG MUTATED                                  0     1
  PARG WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  PARG MUTATED                           0     8
  PARG WILD-TYPE                        22   218
D1303V13, multiclass
                                  clus
vv                                 PARG MUTATED PARG WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       8            218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1304) Variable = OR6A2 MUTATION ANALYSIS
D1304V1, survival
                 sevent
clus2               0   1
  OR6A2 MUTATED     6   2
  OR6A2 WILD-TYPE 372  91
  OR6A2 MUTATED OR6A2 WILD-TYPE 
              8             463 
  OR6A2 MUTATED OR6A2 WILD-TYPE 
              2              91 
$`OR6A2 MUTATED`
TCGA-AA-3516 TCGA-AA-A00N TCGA-CA-6717 TCGA-CK-4948 TCGA-CM-5348 TCGA-CM-6168 
       13.02         4.01        12.76       148.01        22.98        12.99 
TCGA-D5-6541 TCGA-G4-6317 
       15.58        36.00 

$`OR6A2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        1.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4952 
       12.20        10.06        14.30        17.56        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       29.06        22.03        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6169 TCGA-CM-6170 
       29.03        16.04        21.99        14.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       85.48        63.62        61.91        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  OR6A2 MUTATED OR6A2 WILD-TYPE 
           4.01            0.00 
  OR6A2 MUTATED OR6A2 WILD-TYPE 
         148.01          140.38 
  OR6A2 MUTATED OR6A2 WILD-TYPE 
          14.30           20.28 
[1] "4.0 - 148.0 (14.3)" "0.0 - 140.4 (20.3)"
[1] "hr=" "1.2"
D1304V2, continuous
D1304V3, binary
                 cls
clus                0   1
  OR6A2 MUTATED     8   0
  OR6A2 WILD-TYPE 358 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR6A2 MUTATED      8    0
  OR6A2 WILD-TYPE  358  119
        clus
vv       OR6A2 MUTATED OR6A2 WILD-TYPE
  COLON              8             358
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  OR6A2 MUTATED         0        0        0         3         1         0
  OR6A2 WILD-TYPE      91        1       32       135         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  OR6A2 MUTATED           2          0          1          1        0         0
  OR6A2 WILD-TYPE        22         11         58         41       48        18
                 vv
clus              STAGE IVB
  OR6A2 MUTATED           0
  OR6A2 WILD-TYPE         1
D1304V4, multiclass
            clus
vv           OR6A2 MUTATED OR6A2 WILD-TYPE
  STAGE I                0              91
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              3             135
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              2              22
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             1              41
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  OR6A2 MUTATED     0   0   7   1
  OR6A2 WILD-TYPE  17  92 322  49
D1304V5, multiclass
    clus
vv   OR6A2 MUTATED OR6A2 WILD-TYPE
  T1             0              17
  T2             0              92
  T3             7             322
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  OR6A2 MUTATED     4   2   2
  OR6A2 WILD-TYPE 283 111  85
D1304V6, multiclass
    clus
vv   OR6A2 MUTATED OR6A2 WILD-TYPE
  N0             4             283
  N1             2             111
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1304V7, binary
                 cls
clus                0   1
  OR6A2 MUTATED     7   0
  OR6A2 WILD-TYPE 368  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR6A2 MUTATED      7    0
  OR6A2 WILD-TYPE  368   65
   clus
vv  OR6A2 MUTATED OR6A2 WILD-TYPE
  0             7             368
  1             0              65
[1] 2 2
[1] FALSE
D1304V8, binary
                 cls
clus                0   1
  OR6A2 MUTATED     4   4
  OR6A2 WILD-TYPE 221 260
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR6A2 MUTATED      4    4
  OR6A2 WILD-TYPE  221  260
        clus
vv       OR6A2 MUTATED OR6A2 WILD-TYPE
  FEMALE             4             221
  MALE               4             260
[1] 2 2
[1] FALSE
D1304V9, binary
                 cls
clus                0   1
  OR6A2 MUTATED     7   0
  OR6A2 WILD-TYPE 343  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR6A2 MUTATED      7    0
  OR6A2 WILD-TYPE  343   22
     clus
vv    OR6A2 MUTATED OR6A2 WILD-TYPE
  NO              7             343
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  OR6A2 MUTATED                      5                             3
  OR6A2 WILD-TYPE                  310                            44
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  OR6A2 MUTATED                       0                              0
  OR6A2 WILD-TYPE                   106                             10
D1304V10, multiclass
                                clus
vv                               OR6A2 MUTATED OR6A2 WILD-TYPE
  COLON ADENOCARCINOMA                       5             310
  COLON MUCINOUS ADENOCARCINOMA              3              44
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  OR6A2 MUTATED     6   0   0   1
  OR6A2 WILD-TYPE 339   4  31  24
D1304V11, multiclass
    clus
vv   OR6A2 MUTATED OR6A2 WILD-TYPE
  R0             6             339
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1304V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OR6A2 MUTATED                                  0     1
  OR6A2 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  OR6A2 MUTATED                           1     4
  OR6A2 WILD-TYPE                        21   222
D1304V13, multiclass
                                  clus
vv                                 OR6A2 MUTATED OR6A2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        4             222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1305) Variable = MAGI1 MUTATION ANALYSIS
D1305V1, survival
                 sevent
clus2               0   1
  MAGI1 MUTATED    22   3
  MAGI1 WILD-TYPE 356  90
  MAGI1 MUTATED MAGI1 WILD-TYPE 
             25             446 
  MAGI1 MUTATED MAGI1 WILD-TYPE 
              3              90 
$`MAGI1 MUTATED`
TCGA-A6-6652 TCGA-A6-6653 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3518 
       24.69        24.39         3.02        35.01        63.98         1.02 
TCGA-AA-3543 TCGA-AA-3560 TCGA-AA-3672 TCGA-AA-3831 TCGA-AA-3864 TCGA-AA-A01I 
        0.99        19.99         0.92        17.98        53.00        31.00 
TCGA-AA-A01R TCGA-AY-6197 TCGA-AZ-4323 TCGA-CA-6717 TCGA-CM-5861 TCGA-CM-6171 
       35.01        21.44         1.41        12.76        15.02        14.04 
TCGA-CM-6172 TCGA-F4-6570 TCGA-G4-6309 TCGA-G4-6315 TCGA-AG-A002 TCGA-AG-A02N 
       11.01         6.18        85.48        61.91        20.98        61.97 
TCGA-EI-6507 
       19.96 

$`MAGI1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6654 TCGA-A6-6780 
       25.08        25.18        24.16        21.76        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3511 TCGA-AA-3514 
       19.66        20.28         7.04         1.02         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       13.02        38.99         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       29.00        26.01        12.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
       54.02         2.01        14.01        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3833 TCGA-AA-3837 
       33.04         0.99        25.02         1.02        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       31.07        30.05        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       10.98        32.02        12.00        31.00        38.07         1.02 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4616 TCGA-AZ-4681 
        0.95        33.01        17.82        58.39         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 
       29.06        22.03        22.98        30.08        32.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       15.02        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       35.74        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 
       74.56        65.85        53.62        44.68        55.04        63.62 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       38.96        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
       32.61         0.49        20.55        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  MAGI1 MUTATED MAGI1 WILD-TYPE 
           0.92            0.00 
  MAGI1 MUTATED MAGI1 WILD-TYPE 
          85.48          148.01 
  MAGI1 MUTATED MAGI1 WILD-TYPE 
         19.990          20.235 
[1] "0.9 - 85.5 (20.0)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.7"
D1305V2, continuous
D1305V3, binary
                 cls
clus                0   1
  MAGI1 MUTATED    23   3
  MAGI1 WILD-TYPE 343 116
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MAGI1 MUTATED     23    3
  MAGI1 WILD-TYPE  343  116
        clus
vv       MAGI1 MUTATED MAGI1 WILD-TYPE
  COLON             23             343
  RECTUM             3             116
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MAGI1 MUTATED         6        0        4         8         0         0
  MAGI1 WILD-TYPE      85        1       28       130        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MAGI1 MUTATED           2          0          2          1        2         1
  MAGI1 WILD-TYPE        22         11         57         41       46        17
                 vv
clus              STAGE IVB
  MAGI1 MUTATED           0
  MAGI1 WILD-TYPE         1
D1305V4, multiclass
            clus
vv           MAGI1 MUTATED MAGI1 WILD-TYPE
  STAGE I                6              85
  STAGE IA               0               1
  STAGE II               4              28
  STAGE IIA              8             130
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              2              22
  STAGE IIIA             0              11
  STAGE IIIB             2              57
  STAGE IIIC             1              41
  STAGE IV               2              46
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  MAGI1 MUTATED     0   6  19   1
  MAGI1 WILD-TYPE  17  86 310  49
D1305V5, multiclass
    clus
vv   MAGI1 MUTATED MAGI1 WILD-TYPE
  T1             0              17
  T2             6              86
  T3            19             310
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  MAGI1 MUTATED    19   4   3
  MAGI1 WILD-TYPE 268 109  84
D1305V6, multiclass
    clus
vv   MAGI1 MUTATED MAGI1 WILD-TYPE
  N0            19             268
  N1             4             109
  N2             3              84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1305V7, binary
                 cls
clus                0   1
  MAGI1 MUTATED    22   3
  MAGI1 WILD-TYPE 353  62
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MAGI1 MUTATED     22    3
  MAGI1 WILD-TYPE  353   62
   clus
vv  MAGI1 MUTATED MAGI1 WILD-TYPE
  0            22             353
  1             3              62
[1] 2 2
[1] FALSE
D1305V8, binary
                 cls
clus                0   1
  MAGI1 MUTATED    10  16
  MAGI1 WILD-TYPE 215 248
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MAGI1 MUTATED     10   16
  MAGI1 WILD-TYPE  215  248
        clus
vv       MAGI1 MUTATED MAGI1 WILD-TYPE
  FEMALE            10             215
  MALE              16             248
[1] 2 2
[1] FALSE
D1305V9, binary
                 cls
clus                0   1
  MAGI1 MUTATED    22   1
  MAGI1 WILD-TYPE 328  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MAGI1 MUTATED     22    1
  MAGI1 WILD-TYPE  328   21
     clus
vv    MAGI1 MUTATED MAGI1 WILD-TYPE
  NO             22             328
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MAGI1 MUTATED                     20                             3
  MAGI1 WILD-TYPE                  295                            44
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MAGI1 MUTATED                       3                              0
  MAGI1 WILD-TYPE                   103                             10
D1305V10, multiclass
                                clus
vv                               MAGI1 MUTATED MAGI1 WILD-TYPE
  COLON ADENOCARCINOMA                      20             295
  COLON MUCINOUS ADENOCARCINOMA              3              44
  RECTAL ADENOCARCINOMA                      3             103
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  MAGI1 MUTATED    22   0   0   1
  MAGI1 WILD-TYPE 323   4  31  24
D1305V11, multiclass
    clus
vv   MAGI1 MUTATED MAGI1 WILD-TYPE
  R0            22             323
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1305V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MAGI1 MUTATED                                  0     1
  MAGI1 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  MAGI1 MUTATED                           2     9
  MAGI1 WILD-TYPE                        20   217
D1305V13, multiclass
                                  clus
vv                                 MAGI1 MUTATED MAGI1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    2              20
  WHITE                                        9             217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1306) Variable = CALCOCO2 MUTATION ANALYSIS
D1306V1, survival
                    sevent
clus2                  0   1
  CALCOCO2 MUTATED     6   1
  CALCOCO2 WILD-TYPE 372  92
  CALCOCO2 MUTATED CALCOCO2 WILD-TYPE 
                 7                464 
  CALCOCO2 MUTATED CALCOCO2 WILD-TYPE 
                 1                 92 
$`CALCOCO2 MUTATED`
TCGA-AA-3692 TCGA-AA-3713 TCGA-AA-A00J TCGA-CA-6717 TCGA-CM-5860 TCGA-G4-6315 
       36.00        19.04        18.05        12.76        32.02        61.91 
TCGA-AG-A01Y 
       64.01 

$`CALCOCO2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 
       19.00         5.03        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       19.00        30.02        34.03        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-5862 
       29.06        22.03        22.98        30.08        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6317 TCGA-G4-6321 
       44.68        55.04        85.48        63.62        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       70.03        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  CALCOCO2 MUTATED CALCOCO2 WILD-TYPE 
             12.76               0.00 
  CALCOCO2 MUTATED CALCOCO2 WILD-TYPE 
             64.01             148.01 
  CALCOCO2 MUTATED CALCOCO2 WILD-TYPE 
            32.020             20.155 
[1] "12.8 - 64.0 (32.0)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.9"
D1306V2, continuous
D1306V3, binary
                    cls
clus                   0   1
  CALCOCO2 MUTATED     7   1
  CALCOCO2 WILD-TYPE 359 118
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  CALCOCO2 MUTATED      7    1
  CALCOCO2 WILD-TYPE  359  118
        clus
vv       CALCOCO2 MUTATED CALCOCO2 WILD-TYPE
  COLON                 7                359
  RECTUM                1                118
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CALCOCO2 MUTATED         0        0        1         2         1         0
  CALCOCO2 WILD-TYPE      91        1       31       136         9         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CALCOCO2 MUTATED           0          0          1          0        3
  CALCOCO2 WILD-TYPE        24         11         58         42       45
                    vv
clus                 STAGE IVA STAGE IVB
  CALCOCO2 MUTATED           0         0
  CALCOCO2 WILD-TYPE        18         1
D1306V4, multiclass
            clus
vv           CALCOCO2 MUTATED CALCOCO2 WILD-TYPE
  STAGE I                   0                 91
  STAGE IA                  0                  1
  STAGE II                  1                 31
  STAGE IIA                 2                136
  STAGE IIB                 1                  9
  STAGE IIC                 0                  1
  STAGE III                 0                 24
  STAGE IIIA                0                 11
  STAGE IIIB                1                 58
  STAGE IIIC                0                 42
  STAGE IV                  3                 45
  STAGE IVA                 0                 18
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  CALCOCO2 MUTATED     0   0   6   2
  CALCOCO2 WILD-TYPE  17  92 323  48
D1306V5, multiclass
    clus
vv   CALCOCO2 MUTATED CALCOCO2 WILD-TYPE
  T1                0                 17
  T2                0                 92
  T3                6                323
  T4                2                 48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  CALCOCO2 MUTATED     5   2   1
  CALCOCO2 WILD-TYPE 282 111  86
D1306V6, multiclass
    clus
vv   CALCOCO2 MUTATED CALCOCO2 WILD-TYPE
  N0                5                282
  N1                2                111
  N2                1                 86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1306V7, binary
                    cls
clus                   0   1
  CALCOCO2 MUTATED     4   3
  CALCOCO2 WILD-TYPE 371  62
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  CALCOCO2 MUTATED      4    3
  CALCOCO2 WILD-TYPE  371   62
   clus
vv  CALCOCO2 MUTATED CALCOCO2 WILD-TYPE
  0                4                371
  1                3                 62
[1] 2 2
[1] FALSE
D1306V8, binary
                    cls
clus                   0   1
  CALCOCO2 MUTATED     3   5
  CALCOCO2 WILD-TYPE 222 259
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  CALCOCO2 MUTATED      3    5
  CALCOCO2 WILD-TYPE  222  259
        clus
vv       CALCOCO2 MUTATED CALCOCO2 WILD-TYPE
  FEMALE                3                222
  MALE                  5                259
[1] 2 2
[1] FALSE
D1306V9, binary
                    cls
clus                   0   1
  CALCOCO2 MUTATED     4   2
  CALCOCO2 WILD-TYPE 346  20
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  CALCOCO2 MUTATED      4    2
  CALCOCO2 WILD-TYPE  346   20
     clus
vv    CALCOCO2 MUTATED CALCOCO2 WILD-TYPE
  NO                 4                346
  YES                2                 20
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CALCOCO2 MUTATED                      4                             3
  CALCOCO2 WILD-TYPE                  311                            44
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CALCOCO2 MUTATED                       1                              0
  CALCOCO2 WILD-TYPE                   105                             10
D1306V10, multiclass
                                clus
vv                               CALCOCO2 MUTATED CALCOCO2 WILD-TYPE
  COLON ADENOCARCINOMA                          4                311
  COLON MUCINOUS ADENOCARCINOMA                 3                 44
  RECTAL ADENOCARCINOMA                         1                105
  RECTAL MUCINOUS ADENOCARCINOMA                0                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  CALCOCO2 MUTATED     4   0   2   2
  CALCOCO2 WILD-TYPE 341   4  29  23
D1306V11, multiclass
    clus
vv   CALCOCO2 MUTATED CALCOCO2 WILD-TYPE
  R0                4                341
  R1                0                  4
  R2                2                 29
  RX                2                 23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1306V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CALCOCO2 MUTATED                                  0     1
  CALCOCO2 WILD-TYPE                                1    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  CALCOCO2 MUTATED                           0     3
  CALCOCO2 WILD-TYPE                        22   223
D1306V13, multiclass
                                  clus
vv                                 CALCOCO2 MUTATED CALCOCO2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                 10
  BLACK OR AFRICAN AMERICAN                       0                 22
  WHITE                                           3                223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1307) Variable = IKBKE MUTATION ANALYSIS
D1307V1, survival
                 sevent
clus2               0   1
  IKBKE MUTATED     4   3
  IKBKE WILD-TYPE 374  90
  IKBKE MUTATED IKBKE WILD-TYPE 
              7             464 
  IKBKE MUTATED IKBKE WILD-TYPE 
              3              90 
$`IKBKE MUTATED`
TCGA-AA-3492 TCGA-AA-A01R TCGA-AY-6197 TCGA-AZ-6598 TCGA-DM-A1D9 TCGA-G4-6303 
        3.02        35.01        21.44        49.41       140.38        65.85 
TCGA-AG-A002 
       20.98 

$`IKBKE WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S 
       12.00        31.00        31.00        38.07         1.02         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       33.01        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        88.21         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6304 TCGA-G4-6306 
       47.41        35.31       133.18        74.56        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  IKBKE MUTATED IKBKE WILD-TYPE 
           3.02            0.00 
  IKBKE MUTATED IKBKE WILD-TYPE 
         140.38          148.01 
  IKBKE MUTATED IKBKE WILD-TYPE 
         35.010          20.035 
[1] "3.0 - 140.4 (35.0)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.3"
D1307V2, continuous
D1307V3, binary
                 cls
clus                0   1
  IKBKE MUTATED     7   1
  IKBKE WILD-TYPE 359 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IKBKE MUTATED      7    1
  IKBKE WILD-TYPE  359  118
        clus
vv       IKBKE MUTATED IKBKE WILD-TYPE
  COLON              7             359
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  IKBKE MUTATED         1        0        2         3         0         0
  IKBKE WILD-TYPE      90        1       30       135        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  IKBKE MUTATED           1          0          0          0        1         0
  IKBKE WILD-TYPE        23         11         59         42       47        18
                 vv
clus              STAGE IVB
  IKBKE MUTATED           0
  IKBKE WILD-TYPE         1
D1307V4, multiclass
            clus
vv           IKBKE MUTATED IKBKE WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA              3             135
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             0              42
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  IKBKE MUTATED     0   1   7   0
  IKBKE WILD-TYPE  17  91 322  50
D1307V5, multiclass
    clus
vv   IKBKE MUTATED IKBKE WILD-TYPE
  T1             0              17
  T2             1              91
  T3             7             322
  T4             0              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  IKBKE MUTATED     6   1   1
  IKBKE WILD-TYPE 281 112  86
D1307V6, multiclass
    clus
vv   IKBKE MUTATED IKBKE WILD-TYPE
  N0             6             281
  N1             1             112
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1307V7, binary
                 cls
clus                0   1
  IKBKE MUTATED     5   1
  IKBKE WILD-TYPE 370  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IKBKE MUTATED      5    1
  IKBKE WILD-TYPE  370   64
   clus
vv  IKBKE MUTATED IKBKE WILD-TYPE
  0             5             370
  1             1              64
[1] 2 2
[1] FALSE
D1307V8, binary
                 cls
clus                0   1
  IKBKE MUTATED     5   3
  IKBKE WILD-TYPE 220 261
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IKBKE MUTATED      5    3
  IKBKE WILD-TYPE  220  261
        clus
vv       IKBKE MUTATED IKBKE WILD-TYPE
  FEMALE             5             220
  MALE               3             261
[1] 2 2
[1] FALSE
D1307V9, binary
                 cls
clus                0   1
  IKBKE MUTATED     5   1
  IKBKE WILD-TYPE 345  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IKBKE MUTATED      5    1
  IKBKE WILD-TYPE  345   21
     clus
vv    IKBKE MUTATED IKBKE WILD-TYPE
  NO              5             345
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  IKBKE MUTATED                      6                             1
  IKBKE WILD-TYPE                  309                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  IKBKE MUTATED                       1                              0
  IKBKE WILD-TYPE                   105                             10
D1307V10, multiclass
                                clus
vv                               IKBKE MUTATED IKBKE WILD-TYPE
  COLON ADENOCARCINOMA                       6             309
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  IKBKE MUTATED     6   0   0   0
  IKBKE WILD-TYPE 339   4  31  25
D1307V11, multiclass
    clus
vv   IKBKE MUTATED IKBKE WILD-TYPE
  R0             6             339
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1307V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  IKBKE MUTATED                                  0     0
  IKBKE WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  IKBKE MUTATED                           0     4
  IKBKE WILD-TYPE                        22   222
D1307V13, multiclass
                                  clus
vv                                 IKBKE MUTATED IKBKE WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        4             222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1308) Variable = SLC44A4 MUTATION ANALYSIS
D1308V1, survival
                   sevent
clus2                 0   1
  SLC44A4 MUTATED     8   3
  SLC44A4 WILD-TYPE 370  90
  SLC44A4 MUTATED SLC44A4 WILD-TYPE 
               11               460 
  SLC44A4 MUTATED SLC44A4 WILD-TYPE 
                3                90 
$`SLC44A4 MUTATED`
TCGA-A6-5665 TCGA-A6-6781 TCGA-AA-3811 TCGA-AA-A010 TCGA-AD-6889 TCGA-AZ-6598 
       22.06        19.66        10.06        34.98        56.55        49.41 
TCGA-CK-5916 TCGA-CM-4743 TCGA-CM-5861 TCGA-CM-6168 TCGA-D5-6540 
       21.14        23.05        15.02        12.99        16.14 

$`SLC44A4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        19.04        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 
       40.96         0.07        21.37        15.52         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       88.21         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 
        9.99        82.95         1.91       124.27        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       32.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       12.49        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  SLC44A4 MUTATED SLC44A4 WILD-TYPE 
            10.06              0.00 
  SLC44A4 MUTATED SLC44A4 WILD-TYPE 
            56.55            148.01 
  SLC44A4 MUTATED SLC44A4 WILD-TYPE 
           21.140            20.155 
[1] "10.1 - 56.5 (21.1)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.4"
D1308V2, continuous
D1308V3, binary
                   cls
clus                  0   1
  SLC44A4 MUTATED    12   0
  SLC44A4 WILD-TYPE 354 119
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC44A4 MUTATED     12    0
  SLC44A4 WILD-TYPE  354  119
        clus
vv       SLC44A4 MUTATED SLC44A4 WILD-TYPE
  COLON               12               354
  RECTUM               0               119
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SLC44A4 MUTATED         2        0        1         6         1         0
  SLC44A4 WILD-TYPE      89        1       31       132         9         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC44A4 MUTATED           1          0          0          1        0
  SLC44A4 WILD-TYPE        23         11         59         41       48
                   vv
clus                STAGE IVA STAGE IVB
  SLC44A4 MUTATED           0         0
  SLC44A4 WILD-TYPE        18         1
D1308V4, multiclass
            clus
vv           SLC44A4 MUTATED SLC44A4 WILD-TYPE
  STAGE I                  2                89
  STAGE IA                 0                 1
  STAGE II                 1                31
  STAGE IIA                6               132
  STAGE IIB                1                 9
  STAGE IIC                0                 1
  STAGE III                1                23
  STAGE IIIA               0                11
  STAGE IIIB               0                59
  STAGE IIIC               1                41
  STAGE IV                 0                48
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  SLC44A4 MUTATED     1   1   8   2
  SLC44A4 WILD-TYPE  16  91 321  48
D1308V5, multiclass
    clus
vv   SLC44A4 MUTATED SLC44A4 WILD-TYPE
  T1               1                16
  T2               1                91
  T3               8               321
  T4               2                48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  SLC44A4 MUTATED    10   1   1
  SLC44A4 WILD-TYPE 277 112  86
D1308V6, multiclass
    clus
vv   SLC44A4 MUTATED SLC44A4 WILD-TYPE
  N0              10               277
  N1               1               112
  N2               1                86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1308V7, binary
                   cls
clus                  0   1
  SLC44A4 MUTATED    10   0
  SLC44A4 WILD-TYPE 365  65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC44A4 MUTATED     10    0
  SLC44A4 WILD-TYPE  365   65
   clus
vv  SLC44A4 MUTATED SLC44A4 WILD-TYPE
  0              10               365
  1               0                65
[1] 2 2
[1] FALSE
D1308V8, binary
                   cls
clus                  0   1
  SLC44A4 MUTATED     8   4
  SLC44A4 WILD-TYPE 217 260
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC44A4 MUTATED      8    4
  SLC44A4 WILD-TYPE  217  260
        clus
vv       SLC44A4 MUTATED SLC44A4 WILD-TYPE
  FEMALE               8               217
  MALE                 4               260
[1] 2 2
[1] FALSE
D1308V9, binary
                   cls
clus                  0   1
  SLC44A4 MUTATED    10   0
  SLC44A4 WILD-TYPE 340  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC44A4 MUTATED     10    0
  SLC44A4 WILD-TYPE  340   22
     clus
vv    SLC44A4 MUTATED SLC44A4 WILD-TYPE
  NO               10               340
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SLC44A4 MUTATED                     10                             2
  SLC44A4 WILD-TYPE                  305                            45
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SLC44A4 MUTATED                       0                              0
  SLC44A4 WILD-TYPE                   106                             10
D1308V10, multiclass
                                clus
vv                               SLC44A4 MUTATED SLC44A4 WILD-TYPE
  COLON ADENOCARCINOMA                        10               305
  COLON MUCINOUS ADENOCARCINOMA                2                45
  RECTAL ADENOCARCINOMA                        0               106
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  SLC44A4 MUTATED     9   0   0   1
  SLC44A4 WILD-TYPE 336   4  31  24
D1308V11, multiclass
    clus
vv   SLC44A4 MUTATED SLC44A4 WILD-TYPE
  R0               9               336
  R1               0                 4
  R2               0                31
  RX               1                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1308V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SLC44A4 MUTATED                                  0     1
  SLC44A4 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  SLC44A4 MUTATED                           1     7
  SLC44A4 WILD-TYPE                        21   219
D1308V13, multiclass
                                  clus
vv                                 SLC44A4 MUTATED SLC44A4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                10
  BLACK OR AFRICAN AMERICAN                      1                21
  WHITE                                          7               219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1309) Variable = GANAB MUTATION ANALYSIS
D1309V1, survival
                 sevent
clus2               0   1
  GANAB MUTATED     8   6
  GANAB WILD-TYPE 370  87
  GANAB MUTATED GANAB WILD-TYPE 
             14             457 
  GANAB MUTATED GANAB WILD-TYPE 
              6              87 
$`GANAB MUTATED`
TCGA-A6-3809 TCGA-A6-6781 TCGA-AA-3516 TCGA-AA-3846 TCGA-AA-A01P TCGA-AY-4071 
       32.75        19.66        13.02        17.03        38.07         0.95 
TCGA-AZ-4315 TCGA-AZ-6605 TCGA-AZ-6608 TCGA-CA-6717 TCGA-CA-6719 TCGA-CM-4743 
       58.39         5.23         1.61        12.76        14.30        23.05 
TCGA-CM-5349 TCGA-F5-6464 
       30.08         9.96 

$`GANAB WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
       63.98         6.97         1.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3848 TCGA-AA-3850 
       38.99        37.02        14.93         0.00        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
       27.09        16.31        33.01        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77        12.10       100.01        29.56        11.74         3.19 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       10.06        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       22.98        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6465 
        0.49        20.55        19.96        20.91        18.28        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  GANAB MUTATED GANAB WILD-TYPE 
           0.95            0.00 
  GANAB MUTATED GANAB WILD-TYPE 
          58.39          148.01 
  GANAB MUTATED GANAB WILD-TYPE 
         15.665          20.550 
[1] "0.9 - 58.4 (15.7)"  "0.0 - 148.0 (20.6)"
[1] "hr=" "3"  
D1309V2, continuous
D1309V3, binary
                 cls
clus                0   1
  GANAB MUTATED    12   1
  GANAB WILD-TYPE 354 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GANAB MUTATED     12    1
  GANAB WILD-TYPE  354  118
        clus
vv       GANAB MUTATED GANAB WILD-TYPE
  COLON             12             354
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GANAB MUTATED         1        0        0         6         1         0
  GANAB WILD-TYPE      90        1       32       132         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  GANAB MUTATED           2          1          1          2        0         0
  GANAB WILD-TYPE        22         10         58         40       48        18
                 vv
clus              STAGE IVB
  GANAB MUTATED           0
  GANAB WILD-TYPE         1
D1309V4, multiclass
            clus
vv           GANAB MUTATED GANAB WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              6             132
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              2              22
  STAGE IIIA             1              10
  STAGE IIIB             1              58
  STAGE IIIC             2              40
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  GANAB MUTATED     1   1   8   4
  GANAB WILD-TYPE  16  91 321  46
D1309V5, multiclass
    clus
vv   GANAB MUTATED GANAB WILD-TYPE
  T1             1              16
  T2             1              91
  T3             8             321
  T4             4              46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  GANAB MUTATED     8   4   2
  GANAB WILD-TYPE 279 109  85
D1309V6, multiclass
    clus
vv   GANAB MUTATED GANAB WILD-TYPE
  N0             8             279
  N1             4             109
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1309V7, binary
                 cls
clus                0   1
  GANAB MUTATED    12   0
  GANAB WILD-TYPE 363  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GANAB MUTATED     12    0
  GANAB WILD-TYPE  363   65
   clus
vv  GANAB MUTATED GANAB WILD-TYPE
  0            12             363
  1             0              65
[1] 2 2
[1] FALSE
D1309V8, binary
                 cls
clus                0   1
  GANAB MUTATED     8   6
  GANAB WILD-TYPE 217 258
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GANAB MUTATED      8    6
  GANAB WILD-TYPE  217  258
        clus
vv       GANAB MUTATED GANAB WILD-TYPE
  FEMALE             8             217
  MALE               6             258
[1] 2 2
[1] FALSE
D1309V9, binary
                 cls
clus                0   1
  GANAB MUTATED    14   0
  GANAB WILD-TYPE 336  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GANAB MUTATED     14    0
  GANAB WILD-TYPE  336   22
     clus
vv    GANAB MUTATED GANAB WILD-TYPE
  NO             14             336
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  GANAB MUTATED                      8                             4
  GANAB WILD-TYPE                  307                            43
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  GANAB MUTATED                       1                              0
  GANAB WILD-TYPE                   105                             10
D1309V10, multiclass
                                clus
vv                               GANAB MUTATED GANAB WILD-TYPE
  COLON ADENOCARCINOMA                       8             307
  COLON MUCINOUS ADENOCARCINOMA              4              43
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  GANAB MUTATED     9   0   0   2
  GANAB WILD-TYPE 336   4  31  23
D1309V11, multiclass
    clus
vv   GANAB MUTATED GANAB WILD-TYPE
  R0             9             336
  R1             0               4
  R2             0              31
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1309V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GANAB MUTATED                                  0     2
  GANAB WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  GANAB MUTATED                           0     9
  GANAB WILD-TYPE                        22   217
D1309V13, multiclass
                                  clus
vv                                 GANAB MUTATED GANAB WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               9
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        9             217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1310) Variable = SAMD9L MUTATION ANALYSIS
D1310V1, survival
                  sevent
clus2                0   1
  SAMD9L MUTATED    20   8
  SAMD9L WILD-TYPE 358  85
  SAMD9L MUTATED SAMD9L WILD-TYPE 
              28              443 
  SAMD9L MUTATED SAMD9L WILD-TYPE 
               8               85 
$`SAMD9L MUTATED`
TCGA-A6-3809 TCGA-AA-3496 TCGA-AA-3696 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3977 
       32.75         1.02         5.03        19.04        10.06        25.02 
TCGA-AA-A00N TCGA-AA-A010 TCGA-AD-6895 TCGA-AZ-4315 TCGA-AZ-4681 TCGA-AZ-6598 
        4.01        34.98         0.72        58.39       106.75        49.41 
TCGA-CA-6717 TCGA-CM-6170 TCGA-CM-6676 TCGA-DM-A0XD TCGA-DM-A282 TCGA-G4-6309 
       12.76        15.02        11.08        24.43       139.17        85.48 
TCGA-G4-6586 TCGA-G4-6588 TCGA-AF-2691 TCGA-AG-3584 TCGA-AG-3731 TCGA-AG-3881 
       35.80        26.17        43.04        24.00        37.02        19.04 
TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-A002 TCGA-DY-A1H8 
       13.02        14.01        20.98        32.61 

$`SAMD9L WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 
       20.12        19.66        20.28         7.04         3.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       85.05        26.99        19.04        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
       56.55         0.79         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5403 
       21.44        17.82         1.41         5.13        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       88.21         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07        12.20        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6171 TCGA-CM-6172 
       21.99        14.99        12.99        13.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       12.95        13.05        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A285 
      140.38         7.50        44.32       131.51       135.65         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       44.68        55.04        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       13.78        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3587 
        8.02         7.07        36.03        20.05         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
       32.98         0.99         0.99        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       36.95        17.03        35.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       57.24        24.13        51.48         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  SAMD9L MUTATED SAMD9L WILD-TYPE 
            0.72             0.00 
  SAMD9L MUTATED SAMD9L WILD-TYPE 
          139.17           148.01 
  SAMD9L MUTATED SAMD9L WILD-TYPE 
          24.215           20.050 
[1] "0.7 - 139.2 (24.2)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.3"
D1310V2, continuous
D1310V3, binary
                  cls
clus                 0   1
  SAMD9L MUTATED    22   8
  SAMD9L WILD-TYPE 344 111
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SAMD9L MUTATED     22    8
  SAMD9L WILD-TYPE  344  111
        clus
vv       SAMD9L MUTATED SAMD9L WILD-TYPE
  COLON              22              344
  RECTUM              8              111
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SAMD9L MUTATED         5        0        3        10         3         0
  SAMD9L WILD-TYPE      86        1       29       128         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SAMD9L MUTATED           2          1          1          0        3
  SAMD9L WILD-TYPE        22         10         58         42       45
                  vv
clus               STAGE IVA STAGE IVB
  SAMD9L MUTATED           0         0
  SAMD9L WILD-TYPE        18         1
D1310V4, multiclass
            clus
vv           SAMD9L MUTATED SAMD9L WILD-TYPE
  STAGE I                 5               86
  STAGE IA                0                1
  STAGE II                3               29
  STAGE IIA              10              128
  STAGE IIB               3                7
  STAGE IIC               0                1
  STAGE III               2               22
  STAGE IIIA              1               10
  STAGE IIIB              1               58
  STAGE IIIC              0               42
  STAGE IV                3               45
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  SAMD9L MUTATED     2   5  20   3
  SAMD9L WILD-TYPE  15  87 309  47
D1310V5, multiclass
    clus
vv   SAMD9L MUTATED SAMD9L WILD-TYPE
  T1              2               15
  T2              5               87
  T3             20              309
  T4              3               47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  SAMD9L MUTATED    22   5   3
  SAMD9L WILD-TYPE 265 108  84
D1310V6, multiclass
    clus
vv   SAMD9L MUTATED SAMD9L WILD-TYPE
  N0             22              265
  N1              5              108
  N2              3               84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1310V7, binary
                  cls
clus                 0   1
  SAMD9L MUTATED    24   3
  SAMD9L WILD-TYPE 351  62
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SAMD9L MUTATED     24    3
  SAMD9L WILD-TYPE  351   62
   clus
vv  SAMD9L MUTATED SAMD9L WILD-TYPE
  0             24              351
  1              3               62
[1] 2 2
[1] FALSE
D1310V8, binary
                  cls
clus                 0   1
  SAMD9L MUTATED    17  13
  SAMD9L WILD-TYPE 208 251
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SAMD9L MUTATED     17   13
  SAMD9L WILD-TYPE  208  251
        clus
vv       SAMD9L MUTATED SAMD9L WILD-TYPE
  FEMALE             17              208
  MALE               13              251
[1] 2 2
[1] FALSE
D1310V9, binary
                  cls
clus                 0   1
  SAMD9L MUTATED    21   1
  SAMD9L WILD-TYPE 329  21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SAMD9L MUTATED     21    1
  SAMD9L WILD-TYPE  329   21
     clus
vv    SAMD9L MUTATED SAMD9L WILD-TYPE
  NO              21              329
  YES              1               21
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SAMD9L MUTATED                     19                             3
  SAMD9L WILD-TYPE                  296                            44
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SAMD9L MUTATED                       7                              0
  SAMD9L WILD-TYPE                    99                             10
D1310V10, multiclass
                                clus
vv                               SAMD9L MUTATED SAMD9L WILD-TYPE
  COLON ADENOCARCINOMA                       19              296
  COLON MUCINOUS ADENOCARCINOMA               3               44
  RECTAL ADENOCARCINOMA                       7               99
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  SAMD9L MUTATED    19   0   3   1
  SAMD9L WILD-TYPE 326   4  28  24
D1310V11, multiclass
    clus
vv   SAMD9L MUTATED SAMD9L WILD-TYPE
  R0             19              326
  R1              0                4
  R2              3               28
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1310V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SAMD9L MUTATED                                  0     1
  SAMD9L WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  SAMD9L MUTATED                           1    13
  SAMD9L WILD-TYPE                        21   213
D1310V13, multiclass
                                  clus
vv                                 SAMD9L MUTATED SAMD9L WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                        13              213
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1311) Variable = CLPTM1 MUTATION ANALYSIS
D1311V1, survival
                  sevent
clus2                0   1
  CLPTM1 MUTATED    11   1
  CLPTM1 WILD-TYPE 367  92
  CLPTM1 MUTATED CLPTM1 WILD-TYPE 
              12              459 
  CLPTM1 MUTATED CLPTM1 WILD-TYPE 
               1               92 
$`CLPTM1 MUTATED`
TCGA-A6-5665 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3715 TCGA-D5-6928 
       22.06        24.39        20.12        19.66        19.04        11.64 
TCGA-F4-6703 TCGA-G4-6323 TCGA-G4-6588 TCGA-AG-3586 TCGA-AG-A02N TCGA-DC-5337 
       47.87        13.78        26.17         1.02        61.97        15.02 

$`CLPTM1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6782 
       25.18        24.16        21.76        24.69        23.87        20.28 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
        7.04         3.02         1.02        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       26.99        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
       14.30         9.04         9.44         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       31.96        35.74         6.18         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6586 
       85.48        63.62        61.91        36.00        22.09        35.80 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3587 
        8.02         7.07        36.03        20.05        24.00        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
        1.94        38.96        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5869 TCGA-DC-6155 
        6.97         4.73        78.12         7.17         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  CLPTM1 MUTATED CLPTM1 WILD-TYPE 
            1.02             0.00 
  CLPTM1 MUTATED CLPTM1 WILD-TYPE 
           61.97           148.01 
  CLPTM1 MUTATED CLPTM1 WILD-TYPE 
           19.89            20.28 
[1] "1.0 - 62.0 (19.9)"  "0.0 - 148.0 (20.3)"
[1] "hr=" "2.3"
D1311V2, continuous
D1311V3, binary
                  cls
clus                 0   1
  CLPTM1 MUTATED     9   3
  CLPTM1 WILD-TYPE 357 116
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CLPTM1 MUTATED      9    3
  CLPTM1 WILD-TYPE  357  116
        clus
vv       CLPTM1 MUTATED CLPTM1 WILD-TYPE
  COLON               9              357
  RECTUM              3              116
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CLPTM1 MUTATED         2        1        2         5         0         0
  CLPTM1 WILD-TYPE      89        0       30       133        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CLPTM1 MUTATED           1          0          0          1        0
  CLPTM1 WILD-TYPE        23         11         59         41       48
                  vv
clus               STAGE IVA STAGE IVB
  CLPTM1 MUTATED           0         0
  CLPTM1 WILD-TYPE        18         1
D1311V4, multiclass
            clus
vv           CLPTM1 MUTATED CLPTM1 WILD-TYPE
  STAGE I                 2               89
  STAGE IA                1                0
  STAGE II                2               30
  STAGE IIA               5              133
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               1               23
  STAGE IIIA              0               11
  STAGE IIIB              0               59
  STAGE IIIC              1               41
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  CLPTM1 MUTATED     1   1   8   1
  CLPTM1 WILD-TYPE  16  91 321  49
D1311V5, multiclass
    clus
vv   CLPTM1 MUTATED CLPTM1 WILD-TYPE
  T1              1               16
  T2              1               91
  T3              8              321
  T4              1               49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  CLPTM1 MUTATED    10   1   1
  CLPTM1 WILD-TYPE 277 112  86
D1311V6, multiclass
    clus
vv   CLPTM1 MUTATED CLPTM1 WILD-TYPE
  N0             10              277
  N1              1              112
  N2              1               86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1311V7, binary
                  cls
clus                 0   1
  CLPTM1 MUTATED     9   0
  CLPTM1 WILD-TYPE 366  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CLPTM1 MUTATED      9    0
  CLPTM1 WILD-TYPE  366   65
   clus
vv  CLPTM1 MUTATED CLPTM1 WILD-TYPE
  0              9              366
  1              0               65
[1] 2 2
[1] FALSE
D1311V8, binary
                  cls
clus                 0   1
  CLPTM1 MUTATED     3   9
  CLPTM1 WILD-TYPE 222 255
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CLPTM1 MUTATED      3    9
  CLPTM1 WILD-TYPE  222  255
        clus
vv       CLPTM1 MUTATED CLPTM1 WILD-TYPE
  FEMALE              3              222
  MALE                9              255
[1] 2 2
[1] FALSE
D1311V9, binary
                  cls
clus                 0   1
  CLPTM1 MUTATED    10   0
  CLPTM1 WILD-TYPE 340  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CLPTM1 MUTATED     10    0
  CLPTM1 WILD-TYPE  340   22
     clus
vv    CLPTM1 MUTATED CLPTM1 WILD-TYPE
  NO              10              340
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CLPTM1 MUTATED                      6                             3
  CLPTM1 WILD-TYPE                  309                            44
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CLPTM1 MUTATED                       2                              0
  CLPTM1 WILD-TYPE                   104                             10
D1311V10, multiclass
                                clus
vv                               CLPTM1 MUTATED CLPTM1 WILD-TYPE
  COLON ADENOCARCINOMA                        6              309
  COLON MUCINOUS ADENOCARCINOMA               3               44
  RECTAL ADENOCARCINOMA                       2              104
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  CLPTM1 MUTATED    10   0   0   0
  CLPTM1 WILD-TYPE 335   4  31  25
D1311V11, multiclass
    clus
vv   CLPTM1 MUTATED CLPTM1 WILD-TYPE
  R0             10              335
  R1              0                4
  R2              0               31
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1311V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CLPTM1 MUTATED                                  0     0
  CLPTM1 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  CLPTM1 MUTATED                           1     8
  CLPTM1 WILD-TYPE                        21   218
D1311V13, multiclass
                                  clus
vv                                 CLPTM1 MUTATED CLPTM1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                         8              218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1312) Variable = SCARA5 MUTATION ANALYSIS
D1312V1, survival
                  sevent
clus2                0   1
  SCARA5 MUTATED     9   6
  SCARA5 WILD-TYPE 369  87
  SCARA5 MUTATED SCARA5 WILD-TYPE 
              15              456 
  SCARA5 MUTATED SCARA5 WILD-TYPE 
               6               87 
$`SCARA5 MUTATED`
TCGA-AA-3715 TCGA-AA-3864 TCGA-AA-A00O TCGA-AA-A02H TCGA-AZ-4315 TCGA-AZ-6598 
       19.04        53.00        27.02         2.01        58.39        49.41 
TCGA-AZ-6601 TCGA-CK-4952 TCGA-D5-6540 TCGA-DM-A1D4 TCGA-DM-A1HB TCGA-F4-6570 
      100.01        15.62        16.14        92.75       135.65         6.18 
TCGA-AG-3883 TCGA-AG-3887 TCGA-EI-6507 
        1.02        36.95        19.96 

$`SCARA5 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 
       32.05         0.99        31.07        31.07        30.05        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
        4.01        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       88.21         6.77        12.10        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
      148.01        85.45        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
        4.80        17.13        12.49        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       24.43        38.20       130.65        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 
      140.38         7.50        44.32       131.51       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
        8.61        31.96        35.74        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3885 TCGA-AG-3890 
        0.99         0.99        19.04        19.99        17.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       20.55        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  SCARA5 MUTATED SCARA5 WILD-TYPE 
            1.02             0.00 
  SCARA5 MUTATED SCARA5 WILD-TYPE 
          135.65           148.01 
  SCARA5 MUTATED SCARA5 WILD-TYPE 
          27.020           20.155 
[1] "1.0 - 135.7 (27.0)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.3"
D1312V2, continuous
D1312V3, binary
                  cls
clus                 0   1
  SCARA5 MUTATED    12   3
  SCARA5 WILD-TYPE 354 116
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SCARA5 MUTATED     12    3
  SCARA5 WILD-TYPE  354  116
        clus
vv       SCARA5 MUTATED SCARA5 WILD-TYPE
  COLON              12              354
  RECTUM              3              116
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SCARA5 MUTATED         2        0        4         5         0         0
  SCARA5 WILD-TYPE      89        1       28       133        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SCARA5 MUTATED           0          0          1          2        1
  SCARA5 WILD-TYPE        24         11         58         40       47
                  vv
clus               STAGE IVA STAGE IVB
  SCARA5 MUTATED           0         0
  SCARA5 WILD-TYPE        18         1
D1312V4, multiclass
            clus
vv           SCARA5 MUTATED SCARA5 WILD-TYPE
  STAGE I                 2               89
  STAGE IA                0                1
  STAGE II                4               28
  STAGE IIA               5              133
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              1               58
  STAGE IIIC              2               40
  STAGE IV                1               47
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  SCARA5 MUTATED     0   2  12   1
  SCARA5 WILD-TYPE  17  90 317  49
D1312V5, multiclass
    clus
vv   SCARA5 MUTATED SCARA5 WILD-TYPE
  T1              0               17
  T2              2               90
  T3             12              317
  T4              1               49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  SCARA5 MUTATED    11   1   3
  SCARA5 WILD-TYPE 276 112  84
D1312V6, multiclass
    clus
vv   SCARA5 MUTATED SCARA5 WILD-TYPE
  N0             11              276
  N1              1              112
  N2              3               84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1312V7, binary
                  cls
clus                 0   1
  SCARA5 MUTATED    13   1
  SCARA5 WILD-TYPE 362  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SCARA5 MUTATED     13    1
  SCARA5 WILD-TYPE  362   64
   clus
vv  SCARA5 MUTATED SCARA5 WILD-TYPE
  0             13              362
  1              1               64
[1] 2 2
[1] FALSE
D1312V8, binary
                  cls
clus                 0   1
  SCARA5 MUTATED     5  10
  SCARA5 WILD-TYPE 220 254
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SCARA5 MUTATED      5   10
  SCARA5 WILD-TYPE  220  254
        clus
vv       SCARA5 MUTATED SCARA5 WILD-TYPE
  FEMALE              5              220
  MALE               10              254
[1] 2 2
[1] FALSE
D1312V9, binary
                  cls
clus                 0   1
  SCARA5 MUTATED     9   1
  SCARA5 WILD-TYPE 341  21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SCARA5 MUTATED      9    1
  SCARA5 WILD-TYPE  341   21
     clus
vv    SCARA5 MUTATED SCARA5 WILD-TYPE
  NO               9              341
  YES              1               21
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SCARA5 MUTATED                      9                             2
  SCARA5 WILD-TYPE                  306                            45
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SCARA5 MUTATED                       2                              1
  SCARA5 WILD-TYPE                   104                              9
D1312V10, multiclass
                                clus
vv                               SCARA5 MUTATED SCARA5 WILD-TYPE
  COLON ADENOCARCINOMA                        9              306
  COLON MUCINOUS ADENOCARCINOMA               2               45
  RECTAL ADENOCARCINOMA                       2              104
  RECTAL MUCINOUS ADENOCARCINOMA              1                9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  SCARA5 MUTATED     9   0   1   1
  SCARA5 WILD-TYPE 336   4  30  24
D1312V11, multiclass
    clus
vv   SCARA5 MUTATED SCARA5 WILD-TYPE
  R0              9              336
  R1              0                4
  R2              1               30
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1312V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SCARA5 MUTATED                                  0     0
  SCARA5 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  SCARA5 MUTATED                           0     9
  SCARA5 WILD-TYPE                        22   217
D1312V13, multiclass
                                  clus
vv                                 SCARA5 MUTATED SCARA5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         9              217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1313) Variable = RAPGEF6 MUTATION ANALYSIS
D1313V1, survival
                   sevent
clus2                 0   1
  RAPGEF6 MUTATED    16   4
  RAPGEF6 WILD-TYPE 362  89
  RAPGEF6 MUTATED RAPGEF6 WILD-TYPE 
               20               451 
  RAPGEF6 MUTATED RAPGEF6 WILD-TYPE 
                4                89 
$`RAPGEF6 MUTATED`
TCGA-A6-5664 TCGA-A6-6781 TCGA-AA-3516 TCGA-AA-3554 TCGA-AA-3660 TCGA-AA-3848 
       22.09        19.66        13.02        17.95        78.08        10.06 
TCGA-AA-A010 TCGA-AA-A01F TCGA-AD-6895 TCGA-AU-6004 TCGA-CA-6717 TCGA-CK-5913 
       34.98        32.02         0.72        27.09        12.76        51.32 
TCGA-CM-5348 TCGA-D5-6928 TCGA-F4-6459 TCGA-F4-6570 TCGA-G4-6309 TCGA-AG-3902 
       22.98        11.64         8.61         6.18        85.48        32.02 
TCGA-AG-A002 TCGA-CI-6622 
       20.98         6.97 

$`RAPGEF6 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
       63.98         6.97         1.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       61.02         6.05         6.97        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
       14.93         0.00        17.03         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01G 
       17.03        14.99        21.99         1.02        10.98        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
       56.55         0.79         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
        0.20        14.50        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07        12.20        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
        9.44         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 
       60.79       117.07        98.24        31.96        35.74        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       53.62        44.68        55.04        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
        1.02        48.03        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6624 TCGA-CL-5917 
        0.69         0.72         6.05        33.17         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  RAPGEF6 MUTATED RAPGEF6 WILD-TYPE 
             0.72              0.00 
  RAPGEF6 MUTATED RAPGEF6 WILD-TYPE 
            85.48            148.01 
  RAPGEF6 MUTATED RAPGEF6 WILD-TYPE 
            20.32             20.19 
[1] "0.7 - 85.5 (20.3)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1"  
D1313V2, continuous
D1313V3, binary
                   cls
clus                  0   1
  RAPGEF6 MUTATED    17   3
  RAPGEF6 WILD-TYPE 349 116
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RAPGEF6 MUTATED     17    3
  RAPGEF6 WILD-TYPE  349  116
        clus
vv       RAPGEF6 MUTATED RAPGEF6 WILD-TYPE
  COLON               17               349
  RECTUM               3               116
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RAPGEF6 MUTATED         2        0        1         6         2         0
  RAPGEF6 WILD-TYPE      89        1       31       132         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RAPGEF6 MUTATED           1          0          4          3        0
  RAPGEF6 WILD-TYPE        23         11         55         39       48
                   vv
clus                STAGE IVA STAGE IVB
  RAPGEF6 MUTATED           0         0
  RAPGEF6 WILD-TYPE        18         1
D1313V4, multiclass
            clus
vv           RAPGEF6 MUTATED RAPGEF6 WILD-TYPE
  STAGE I                  2                89
  STAGE IA                 0                 1
  STAGE II                 1                31
  STAGE IIA                6               132
  STAGE IIB                2                 8
  STAGE IIC                0                 1
  STAGE III                1                23
  STAGE IIIA               0                11
  STAGE IIIB               4                55
  STAGE IIIC               3                39
  STAGE IV                 0                48
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  RAPGEF6 MUTATED     0   2  14   4
  RAPGEF6 WILD-TYPE  17  90 315  46
D1313V5, multiclass
    clus
vv   RAPGEF6 MUTATED RAPGEF6 WILD-TYPE
  T1               0                17
  T2               2                90
  T3              14               315
  T4               4                46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  RAPGEF6 MUTATED    11   5   4
  RAPGEF6 WILD-TYPE 276 108  83
D1313V6, multiclass
    clus
vv   RAPGEF6 MUTATED RAPGEF6 WILD-TYPE
  N0              11               276
  N1               5               108
  N2               4                83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1313V7, binary
                   cls
clus                  0   1
  RAPGEF6 MUTATED    16   0
  RAPGEF6 WILD-TYPE 359  65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RAPGEF6 MUTATED     16    0
  RAPGEF6 WILD-TYPE  359   65
   clus
vv  RAPGEF6 MUTATED RAPGEF6 WILD-TYPE
  0              16               359
  1               0                65
[1] 2 2
[1] FALSE
D1313V8, binary
                   cls
clus                  0   1
  RAPGEF6 MUTATED    10  10
  RAPGEF6 WILD-TYPE 215 254
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RAPGEF6 MUTATED     10   10
  RAPGEF6 WILD-TYPE  215  254
        clus
vv       RAPGEF6 MUTATED RAPGEF6 WILD-TYPE
  FEMALE              10               215
  MALE                10               254
[1] 2 2
[1] FALSE
D1313V9, binary
                   cls
clus                  0   1
  RAPGEF6 MUTATED    17   0
  RAPGEF6 WILD-TYPE 333  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RAPGEF6 MUTATED     17    0
  RAPGEF6 WILD-TYPE  333   22
     clus
vv    RAPGEF6 MUTATED RAPGEF6 WILD-TYPE
  NO               17               333
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  RAPGEF6 MUTATED                     13                             4
  RAPGEF6 WILD-TYPE                  302                            43
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  RAPGEF6 MUTATED                       3                              0
  RAPGEF6 WILD-TYPE                   103                             10
D1313V10, multiclass
                                clus
vv                               RAPGEF6 MUTATED RAPGEF6 WILD-TYPE
  COLON ADENOCARCINOMA                        13               302
  COLON MUCINOUS ADENOCARCINOMA                4                43
  RECTAL ADENOCARCINOMA                        3               103
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  RAPGEF6 MUTATED    14   0   0   2
  RAPGEF6 WILD-TYPE 331   4  31  23
D1313V11, multiclass
    clus
vv   RAPGEF6 MUTATED RAPGEF6 WILD-TYPE
  R0              14               331
  R1               0                 4
  R2               0                31
  RX               2                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1313V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RAPGEF6 MUTATED                                  0     1
  RAPGEF6 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  RAPGEF6 MUTATED                           2     9
  RAPGEF6 WILD-TYPE                        20   217
D1313V13, multiclass
                                  clus
vv                                 RAPGEF6 MUTATED RAPGEF6 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                10
  BLACK OR AFRICAN AMERICAN                      2                20
  WHITE                                          9               217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1314) Variable = CEP164 MUTATION ANALYSIS
D1314V1, survival
                  sevent
clus2                0   1
  CEP164 MUTATED    22   2
  CEP164 WILD-TYPE 356  91
  CEP164 MUTATED CEP164 WILD-TYPE 
              24              447 
  CEP164 MUTATED CEP164 WILD-TYPE 
               2               91 
$`CEP164 MUTATED`
TCGA-A6-4105 TCGA-A6-5665 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3518 
       14.53        22.06        23.87        20.12        19.66         1.02 
TCGA-AA-3555 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3833 TCGA-AA-3966 TCGA-AA-3994 
       29.95        26.99        19.04        15.95         2.01        27.02 
TCGA-AA-A010 TCGA-AA-A01R TCGA-AD-6889 TCGA-AD-6895 TCGA-AU-3779 TCGA-AU-6004 
       34.98        35.01        56.55         0.72        14.50        27.09 
TCGA-AZ-6598 TCGA-CA-6717 TCGA-D5-6535 TCGA-G4-6588 TCGA-AG-A002 TCGA-CI-6624 
       49.41        12.76        15.12        26.17        20.98         4.73 

$`CEP164 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 
       16.57        34.65        33.34        32.75        36.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6782 TCGA-AA-3489 
       24.16        21.76        24.69        24.39        20.28         7.04 
TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
        3.02         1.02        35.01        63.98         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       13.02        38.99         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 
       21.01        13.02        24.00        17.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       36.00         5.03        85.05        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3837 
       33.04         0.99        25.02         1.02        17.98        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S 
       12.00        31.00        31.00        38.07         1.02         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.79         5.79        22.42        27.42        10.88         0.20 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07        12.20        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 
       20.19        18.25         1.32        43.27        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 
       61.91        36.00        22.09        13.78        35.80        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        6.97        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  CEP164 MUTATED CEP164 WILD-TYPE 
            0.72             0.00 
  CEP164 MUTATED CEP164 WILD-TYPE 
           56.55           148.01 
  CEP164 MUTATED CEP164 WILD-TYPE 
           20.55            20.19 
[1] "0.7 - 56.5 (20.6)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "2"  
D1314V2, continuous
D1314V3, binary
                  cls
clus                 0   1
  CEP164 MUTATED    23   2
  CEP164 WILD-TYPE 343 117
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CEP164 MUTATED     23    2
  CEP164 WILD-TYPE  343  117
        clus
vv       CEP164 MUTATED CEP164 WILD-TYPE
  COLON              23              343
  RECTUM              2              117
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CEP164 MUTATED         3        0        1        12         2         0
  CEP164 WILD-TYPE      88        1       31       126         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CEP164 MUTATED           1          0          3          1        1
  CEP164 WILD-TYPE        23         11         56         41       47
                  vv
clus               STAGE IVA STAGE IVB
  CEP164 MUTATED           0         0
  CEP164 WILD-TYPE        18         1
D1314V4, multiclass
            clus
vv           CEP164 MUTATED CEP164 WILD-TYPE
  STAGE I                 3               88
  STAGE IA                0                1
  STAGE II                1               31
  STAGE IIA              12              126
  STAGE IIB               2                8
  STAGE IIC               0                1
  STAGE III               1               23
  STAGE IIIA              0               11
  STAGE IIIB              3               56
  STAGE IIIC              1               41
  STAGE IV                1               47
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  CEP164 MUTATED     0   3  19   3
  CEP164 WILD-TYPE  17  89 310  47
D1314V5, multiclass
    clus
vv   CEP164 MUTATED CEP164 WILD-TYPE
  T1              0               17
  T2              3               89
  T3             19              310
  T4              3               47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  CEP164 MUTATED    19   5   1
  CEP164 WILD-TYPE 268 108  86
D1314V6, multiclass
    clus
vv   CEP164 MUTATED CEP164 WILD-TYPE
  N0             19              268
  N1              5              108
  N2              1               86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1314V7, binary
                  cls
clus                 0   1
  CEP164 MUTATED    18   1
  CEP164 WILD-TYPE 357  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CEP164 MUTATED     18    1
  CEP164 WILD-TYPE  357   64
   clus
vv  CEP164 MUTATED CEP164 WILD-TYPE
  0             18              357
  1              1               64
[1] 2 2
[1] FALSE
D1314V8, binary
                  cls
clus                 0   1
  CEP164 MUTATED    15  10
  CEP164 WILD-TYPE 210 254
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CEP164 MUTATED     15   10
  CEP164 WILD-TYPE  210  254
        clus
vv       CEP164 MUTATED CEP164 WILD-TYPE
  FEMALE             15              210
  MALE               10              254
[1] 2 2
[1] FALSE
D1314V9, binary
                  cls
clus                 0   1
  CEP164 MUTATED    16   2
  CEP164 WILD-TYPE 334  20
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CEP164 MUTATED     16    2
  CEP164 WILD-TYPE  334   20
     clus
vv    CEP164 MUTATED CEP164 WILD-TYPE
  NO              16              334
  YES              2               20
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CEP164 MUTATED                     16                             7
  CEP164 WILD-TYPE                  299                            40
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CEP164 MUTATED                       2                              0
  CEP164 WILD-TYPE                   104                             10
D1314V10, multiclass
                                clus
vv                               CEP164 MUTATED CEP164 WILD-TYPE
  COLON ADENOCARCINOMA                       16              299
  COLON MUCINOUS ADENOCARCINOMA               7               40
  RECTAL ADENOCARCINOMA                       2              104
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  CEP164 MUTATED    13   0   1   3
  CEP164 WILD-TYPE 332   4  30  22
D1314V11, multiclass
    clus
vv   CEP164 MUTATED CEP164 WILD-TYPE
  R0             13              332
  R1              0                4
  R2              1               30
  RX              3               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1314V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CEP164 MUTATED                                  0     2
  CEP164 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  CEP164 MUTATED                           0    13
  CEP164 WILD-TYPE                        22   213
D1314V13, multiclass
                                  clus
vv                                 CEP164 MUTATED CEP164 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                9
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                        13              213
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1315) Variable = PAK4 MUTATION ANALYSIS
D1315V1, survival
                sevent
clus2              0   1
  PAK4 MUTATED     5   0
  PAK4 WILD-TYPE 373  93
  PAK4 MUTATED PAK4 WILD-TYPE 
             5            466 
  PAK4 MUTATED PAK4 WILD-TYPE 
             0             93 
$`PAK4 MUTATED`
TCGA-AY-5543 TCGA-CM-4743 TCGA-CM-6171 TCGA-DM-A1HB TCGA-G4-6628 
       33.01        23.05        14.04       135.65        79.69 

$`PAK4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       16.31         0.95        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 
       21.14        82.95         1.91       124.27        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 
       14.99        12.99        13.02        15.02        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 
       12.59       140.38         7.50        44.32       131.51       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       46.75        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  PAK4 MUTATED PAK4 WILD-TYPE 
         14.04           0.00 
  PAK4 MUTATED PAK4 WILD-TYPE 
        135.65         148.01 
  PAK4 MUTATED PAK4 WILD-TYPE 
        33.010         20.085 
[1] "14.0 - 135.7 (33.0)" "0.0 - 148.0 (20.1)" 
[1] "hr="     "9300000"
D1315V2, continuous
D1315V3, binary
                cls
clus               0   1
  PAK4 MUTATED     6   0
  PAK4 WILD-TYPE 360 119
[1] "tbl2"
                cls
clus             [,1] [,2]
  PAK4 MUTATED      6    0
  PAK4 WILD-TYPE  360  119
        clus
vv       PAK4 MUTATED PAK4 WILD-TYPE
  COLON             6            360
  RECTUM            0            119
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PAK4 MUTATED         2        0        0         1         0         0
  PAK4 WILD-TYPE      89        1       32       137        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PAK4 MUTATED           0          0          1          1        0         1
  PAK4 WILD-TYPE        24         11         58         41       48        17
                vv
clus             STAGE IVB
  PAK4 MUTATED           0
  PAK4 WILD-TYPE         1
D1315V4, multiclass
            clus
vv           PAK4 MUTATED PAK4 WILD-TYPE
  STAGE I               2             89
  STAGE IA              0              1
  STAGE II              0             32
  STAGE IIA             1            137
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            1             58
  STAGE IIIC            1             41
  STAGE IV              0             48
  STAGE IVA             1             17
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  PAK4 MUTATED     0   2   4   0
  PAK4 WILD-TYPE  17  90 325  50
D1315V5, multiclass
    clus
vv   PAK4 MUTATED PAK4 WILD-TYPE
  T1            0             17
  T2            2             90
  T3            4            325
  T4            0             50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  PAK4 MUTATED     3   2   1
  PAK4 WILD-TYPE 284 111  86
D1315V6, multiclass
    clus
vv   PAK4 MUTATED PAK4 WILD-TYPE
  N0            3            284
  N1            2            111
  N2            1             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1315V7, binary
                cls
clus               0   1
  PAK4 MUTATED     4   1
  PAK4 WILD-TYPE 371  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  PAK4 MUTATED      4    1
  PAK4 WILD-TYPE  371   64
   clus
vv  PAK4 MUTATED PAK4 WILD-TYPE
  0            4            371
  1            1             64
[1] 2 2
[1] FALSE
D1315V8, binary
                cls
clus               0   1
  PAK4 MUTATED     2   4
  PAK4 WILD-TYPE 223 260
[1] "tbl2"
                cls
clus             [,1] [,2]
  PAK4 MUTATED      2    4
  PAK4 WILD-TYPE  223  260
        clus
vv       PAK4 MUTATED PAK4 WILD-TYPE
  FEMALE            2            223
  MALE              4            260
[1] 2 2
[1] FALSE
D1315V9, binary
                cls
clus               0   1
  PAK4 MUTATED     4   0
  PAK4 WILD-TYPE 346  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  PAK4 MUTATED      4    0
  PAK4 WILD-TYPE  346   22
     clus
vv    PAK4 MUTATED PAK4 WILD-TYPE
  NO             4            346
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PAK4 MUTATED                      4                             1
  PAK4 WILD-TYPE                  311                            46
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PAK4 MUTATED                       0                              0
  PAK4 WILD-TYPE                   106                             10
D1315V10, multiclass
                                clus
vv                               PAK4 MUTATED PAK4 WILD-TYPE
  COLON ADENOCARCINOMA                      4            311
  COLON MUCINOUS ADENOCARCINOMA             1             46
  RECTAL ADENOCARCINOMA                     0            106
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  PAK4 MUTATED     5   0   0   0
  PAK4 WILD-TYPE 340   4  31  25
D1315V11, multiclass
    clus
vv   PAK4 MUTATED PAK4 WILD-TYPE
  R0            5            340
  R1            0              4
  R2            0             31
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1315V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PAK4 MUTATED                                  0     0
  PAK4 WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  PAK4 MUTATED                           1     5
  PAK4 WILD-TYPE                        21   221
D1315V13, multiclass
                                  clus
vv                                 PAK4 MUTATED PAK4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                       5            221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1316) Variable = DIMT1L MUTATION ANALYSIS
D1316V1, survival
                  sevent
clus2                0   1
  DIMT1L MUTATED     4   2
  DIMT1L WILD-TYPE 374  91
  DIMT1L MUTATED DIMT1L WILD-TYPE 
               6              465 
  DIMT1L MUTATED DIMT1L WILD-TYPE 
               2               91 
$`DIMT1L MUTATED`
TCGA-AA-3492 TCGA-AY-5543 TCGA-AZ-6601 TCGA-CA-6717 TCGA-G4-6586 TCGA-EF-5830 
        3.02        33.01       100.01        12.76        35.80         0.49 

$`DIMT1L WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
       12.10        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       51.48        32.61        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  DIMT1L MUTATED DIMT1L WILD-TYPE 
            0.49             0.00 
  DIMT1L MUTATED DIMT1L WILD-TYPE 
          100.01           148.01 
  DIMT1L MUTATED DIMT1L WILD-TYPE 
          22.885           20.190 
[1] "0.5 - 100.0 (22.9)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.5"
D1316V2, continuous
D1316V3, binary
                  cls
clus                 0   1
  DIMT1L MUTATED     5   1
  DIMT1L WILD-TYPE 361 118
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DIMT1L MUTATED      5    1
  DIMT1L WILD-TYPE  361  118
        clus
vv       DIMT1L MUTATED DIMT1L WILD-TYPE
  COLON               5              361
  RECTUM              1              118
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DIMT1L MUTATED         0        0        2         2         1         0
  DIMT1L WILD-TYPE      91        1       30       136         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DIMT1L MUTATED           0          0          0          0        0
  DIMT1L WILD-TYPE        24         11         59         42       48
                  vv
clus               STAGE IVA STAGE IVB
  DIMT1L MUTATED           1         0
  DIMT1L WILD-TYPE        17         1
D1316V4, multiclass
            clus
vv           DIMT1L MUTATED DIMT1L WILD-TYPE
  STAGE I                 0               91
  STAGE IA                0                1
  STAGE II                2               30
  STAGE IIA               2              136
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              0               59
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               1               17
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  DIMT1L MUTATED     0   0   5   1
  DIMT1L WILD-TYPE  17  92 324  49
D1316V5, multiclass
    clus
vv   DIMT1L MUTATED DIMT1L WILD-TYPE
  T1              0               17
  T2              0               92
  T3              5              324
  T4              1               49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  DIMT1L MUTATED     5   1   0
  DIMT1L WILD-TYPE 282 112  87
D1316V6, multiclass
    clus
vv   DIMT1L MUTATED DIMT1L WILD-TYPE
  N0              5              282
  N1              1              112
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1316V7, binary
                  cls
clus                 0   1
  DIMT1L MUTATED     5   1
  DIMT1L WILD-TYPE 370  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DIMT1L MUTATED      5    1
  DIMT1L WILD-TYPE  370   64
   clus
vv  DIMT1L MUTATED DIMT1L WILD-TYPE
  0              5              370
  1              1               64
[1] 2 2
[1] FALSE
D1316V8, binary
                  cls
clus                 0   1
  DIMT1L MUTATED     3   3
  DIMT1L WILD-TYPE 222 261
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DIMT1L MUTATED      3    3
  DIMT1L WILD-TYPE  222  261
        clus
vv       DIMT1L MUTATED DIMT1L WILD-TYPE
  FEMALE              3              222
  MALE                3              261
[1] 2 2
[1] FALSE
D1316V9, binary
                  cls
clus                 0   1
  DIMT1L MUTATED     5   0
  DIMT1L WILD-TYPE 345  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DIMT1L MUTATED      5    0
  DIMT1L WILD-TYPE  345   22
     clus
vv    DIMT1L MUTATED DIMT1L WILD-TYPE
  NO               5              345
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  DIMT1L MUTATED                      4                             1
  DIMT1L WILD-TYPE                  311                            46
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  DIMT1L MUTATED                       1                              0
  DIMT1L WILD-TYPE                   105                             10
D1316V10, multiclass
                                clus
vv                               DIMT1L MUTATED DIMT1L WILD-TYPE
  COLON ADENOCARCINOMA                        4              311
  COLON MUCINOUS ADENOCARCINOMA               1               46
  RECTAL ADENOCARCINOMA                       1              105
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  DIMT1L MUTATED     4   0   0   1
  DIMT1L WILD-TYPE 341   4  31  24
D1316V11, multiclass
    clus
vv   DIMT1L MUTATED DIMT1L WILD-TYPE
  R0              4              341
  R1              0                4
  R2              0               31
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1316V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DIMT1L MUTATED                                  0     1
  DIMT1L WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  DIMT1L MUTATED                           1     3
  DIMT1L WILD-TYPE                        21   223
D1316V13, multiclass
                                  clus
vv                                 DIMT1L MUTATED DIMT1L WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                         3              223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1317) Variable = TAF2 MUTATION ANALYSIS
D1317V1, survival
                sevent
clus2              0   1
  TAF2 MUTATED    16   3
  TAF2 WILD-TYPE 362  90
  TAF2 MUTATED TAF2 WILD-TYPE 
            19            452 
  TAF2 MUTATED TAF2 WILD-TYPE 
             3             90 
$`TAF2 MUTATED`
TCGA-A6-6653 TCGA-A6-6780 TCGA-AA-3510 TCGA-AA-3555 TCGA-AA-3561 TCGA-AA-3821 
       24.39        20.12        63.98        29.95        13.94         1.02 
TCGA-AA-3877 TCGA-AA-A010 TCGA-AZ-4315 TCGA-AZ-6601 TCGA-CA-6717 TCGA-CA-6718 
       31.00        34.98        58.39       100.01        12.76        10.06 
TCGA-CK-4948 TCGA-D5-6539 TCGA-DM-A1D7 TCGA-G4-6315 TCGA-AG-3892 TCGA-AG-A002 
      148.01        12.49        13.32        61.91        13.02        20.98 
TCGA-DC-6157 
       27.95 

$`TAF2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
       25.08        25.18        24.16        21.76        24.69        23.87 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3655 
       17.95        23.01        20.98        19.99        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       78.08         6.05         6.97        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
       25.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       33.01        21.44        17.82         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 
        3.06         3.25         3.29         0.07        12.20        14.30 
TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
       17.56        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
       17.85         4.80        17.13        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 
        1.02        17.95        36.95        17.03        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  TAF2 MUTATED TAF2 WILD-TYPE 
          1.02           0.00 
  TAF2 MUTATED TAF2 WILD-TYPE 
        148.01         140.38 
  TAF2 MUTATED TAF2 WILD-TYPE 
        24.390         20.035 
[1] "1.0 - 148.0 (24.4)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1.7"
D1317V2, continuous
D1317V3, binary
                cls
clus               0   1
  TAF2 MUTATED    17   3
  TAF2 WILD-TYPE 349 116
[1] "tbl2"
                cls
clus             [,1] [,2]
  TAF2 MUTATED     17    3
  TAF2 WILD-TYPE  349  116
        clus
vv       TAF2 MUTATED TAF2 WILD-TYPE
  COLON            17            349
  RECTUM            3            116
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TAF2 MUTATED         6        0        2         7         1         0
  TAF2 WILD-TYPE      85        1       30       131         9         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TAF2 MUTATED           1          1          0          1        1         0
  TAF2 WILD-TYPE        23         10         59         41       47        18
                vv
clus             STAGE IVB
  TAF2 MUTATED           0
  TAF2 WILD-TYPE         1
D1317V4, multiclass
            clus
vv           TAF2 MUTATED TAF2 WILD-TYPE
  STAGE I               6             85
  STAGE IA              0              1
  STAGE II              2             30
  STAGE IIA             7            131
  STAGE IIB             1              9
  STAGE IIC             0              1
  STAGE III             1             23
  STAGE IIIA            1             10
  STAGE IIIB            0             59
  STAGE IIIC            1             41
  STAGE IV              1             47
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  TAF2 MUTATED     2   4  13   1
  TAF2 WILD-TYPE  15  88 316  49
D1317V5, multiclass
    clus
vv   TAF2 MUTATED TAF2 WILD-TYPE
  T1            2             15
  T2            4             88
  T3           13            316
  T4            1             49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  TAF2 MUTATED    17   2   1
  TAF2 WILD-TYPE 270 111  86
D1317V6, multiclass
    clus
vv   TAF2 MUTATED TAF2 WILD-TYPE
  N0           17            270
  N1            2            111
  N2            1             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1317V7, binary
                cls
clus               0   1
  TAF2 MUTATED    17   1
  TAF2 WILD-TYPE 358  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  TAF2 MUTATED     17    1
  TAF2 WILD-TYPE  358   64
   clus
vv  TAF2 MUTATED TAF2 WILD-TYPE
  0           17            358
  1            1             64
[1] 2 2
[1] FALSE
D1317V8, binary
                cls
clus               0   1
  TAF2 MUTATED     7  13
  TAF2 WILD-TYPE 218 251
[1] "tbl2"
                cls
clus             [,1] [,2]
  TAF2 MUTATED      7   13
  TAF2 WILD-TYPE  218  251
        clus
vv       TAF2 MUTATED TAF2 WILD-TYPE
  FEMALE            7            218
  MALE             13            251
[1] 2 2
[1] FALSE
D1317V9, binary
                cls
clus               0   1
  TAF2 MUTATED    17   0
  TAF2 WILD-TYPE 333  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  TAF2 MUTATED     17    0
  TAF2 WILD-TYPE  333   22
     clus
vv    TAF2 MUTATED TAF2 WILD-TYPE
  NO            17            333
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  TAF2 MUTATED                     10                             6
  TAF2 WILD-TYPE                  305                            41
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  TAF2 MUTATED                       3                              0
  TAF2 WILD-TYPE                   103                             10
D1317V10, multiclass
                                clus
vv                               TAF2 MUTATED TAF2 WILD-TYPE
  COLON ADENOCARCINOMA                     10            305
  COLON MUCINOUS ADENOCARCINOMA             6             41
  RECTAL ADENOCARCINOMA                     3            103
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  TAF2 MUTATED    14   0   0   2
  TAF2 WILD-TYPE 331   4  31  23
D1317V11, multiclass
    clus
vv   TAF2 MUTATED TAF2 WILD-TYPE
  R0           14            331
  R1            0              4
  R2            0             31
  RX            2             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1317V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TAF2 MUTATED                                  0     2
  TAF2 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  TAF2 MUTATED                           1     9
  TAF2 WILD-TYPE                        21   217
D1317V13, multiclass
                                  clus
vv                                 TAF2 MUTATED TAF2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              9
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                       9            217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1318) Variable = NR3C1 MUTATION ANALYSIS
D1318V1, survival
                 sevent
clus2               0   1
  NR3C1 MUTATED     8   2
  NR3C1 WILD-TYPE 370  91
  NR3C1 MUTATED NR3C1 WILD-TYPE 
             10             461 
  NR3C1 MUTATED NR3C1 WILD-TYPE 
              2              91 
$`NR3C1 MUTATED`
TCGA-A6-5666 TCGA-A6-6781 TCGA-AA-A00N TCGA-AA-A010 TCGA-AD-6964 TCGA-CK-5914 
       32.71        19.66         4.01        34.98        10.88         9.99 
TCGA-CM-6161 TCGA-AF-4110 TCGA-AG-A002 TCGA-F5-6571 
       15.02        14.50        20.98        31.30 

$`NR3C1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        22.06        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
        0.72         5.79        22.42        27.42         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       51.32        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       15.02        17.03        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6702 
       19.96        20.91        18.28         9.96        49.51        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  NR3C1 MUTATED NR3C1 WILD-TYPE 
           4.01            0.00 
  NR3C1 MUTATED NR3C1 WILD-TYPE 
          34.98          148.01 
  NR3C1 MUTATED NR3C1 WILD-TYPE 
          17.34           20.28 
[1] "4.0 - 35.0 (17.3)"  "0.0 - 148.0 (20.3)"
[1] "hr=" "1.5"
D1318V2, continuous
D1318V3, binary
                 cls
clus                0   1
  NR3C1 MUTATED     7   2
  NR3C1 WILD-TYPE 359 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NR3C1 MUTATED      7    2
  NR3C1 WILD-TYPE  359  117
        clus
vv       NR3C1 MUTATED NR3C1 WILD-TYPE
  COLON              7             359
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NR3C1 MUTATED         2        0        0         1         2         1
  NR3C1 WILD-TYPE      89        1       32       137         8         0
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NR3C1 MUTATED           0          0          1          1        0         1
  NR3C1 WILD-TYPE        24         11         58         41       48        17
                 vv
clus              STAGE IVB
  NR3C1 MUTATED           0
  NR3C1 WILD-TYPE         1
D1318V4, multiclass
            clus
vv           NR3C1 MUTATED NR3C1 WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              1             137
  STAGE IIB              2               8
  STAGE IIC              1               0
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             1              41
  STAGE IV               0              48
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  NR3C1 MUTATED     0   2   2   6
  NR3C1 WILD-TYPE  17  90 327  44
D1318V5, multiclass
    clus
vv   NR3C1 MUTATED NR3C1 WILD-TYPE
  T1             0              17
  T2             2              90
  T3             2             327
  T4             6              44
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  NR3C1 MUTATED     6   2   2
  NR3C1 WILD-TYPE 281 111  85
D1318V6, multiclass
    clus
vv   NR3C1 MUTATED NR3C1 WILD-TYPE
  N0             6             281
  N1             2             111
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1318V7, binary
                 cls
clus                0   1
  NR3C1 MUTATED     6   0
  NR3C1 WILD-TYPE 369  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NR3C1 MUTATED      6    0
  NR3C1 WILD-TYPE  369   65
   clus
vv  NR3C1 MUTATED NR3C1 WILD-TYPE
  0             6             369
  1             0              65
[1] 2 2
[1] FALSE
D1318V8, binary
                 cls
clus                0   1
  NR3C1 MUTATED     3   7
  NR3C1 WILD-TYPE 222 257
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NR3C1 MUTATED      3    7
  NR3C1 WILD-TYPE  222  257
        clus
vv       NR3C1 MUTATED NR3C1 WILD-TYPE
  FEMALE             3             222
  MALE               7             257
[1] 2 2
[1] FALSE
D1318V9, binary
                 cls
clus                0   1
  NR3C1 MUTATED     8   0
  NR3C1 WILD-TYPE 342  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NR3C1 MUTATED      8    0
  NR3C1 WILD-TYPE  342   22
     clus
vv    NR3C1 MUTATED NR3C1 WILD-TYPE
  NO              8             342
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  NR3C1 MUTATED                      5                             2
  NR3C1 WILD-TYPE                  310                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  NR3C1 MUTATED                       2                              0
  NR3C1 WILD-TYPE                   104                             10
D1318V10, multiclass
                                clus
vv                               NR3C1 MUTATED NR3C1 WILD-TYPE
  COLON ADENOCARCINOMA                       5             310
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  NR3C1 MUTATED     7   0   0   1
  NR3C1 WILD-TYPE 338   4  31  24
D1318V11, multiclass
    clus
vv   NR3C1 MUTATED NR3C1 WILD-TYPE
  R0             7             338
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1318V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NR3C1 MUTATED                                  0     0
  NR3C1 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  NR3C1 MUTATED                           0     7
  NR3C1 WILD-TYPE                        22   219
D1318V13, multiclass
                                  clus
vv                                 NR3C1 MUTATED NR3C1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        7             219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1319) Variable = HEATR4 MUTATION ANALYSIS
D1319V1, survival
                  sevent
clus2                0   1
  HEATR4 MUTATED    13   4
  HEATR4 WILD-TYPE 365  89
  HEATR4 MUTATED HEATR4 WILD-TYPE 
              17              454 
  HEATR4 MUTATED HEATR4 WILD-TYPE 
               4               89 
$`HEATR4 MUTATED`
TCGA-A6-5661 TCGA-AA-3492 TCGA-AA-3672 TCGA-AA-3819 TCGA-AA-A00A TCGA-AA-A01R 
       33.53         3.02         0.92        25.02        38.04        35.01 
TCGA-AD-6964 TCGA-CA-6717 TCGA-CA-6718 TCGA-D5-6920 TCGA-DM-A0XF TCGA-G4-6299 
       10.88        12.76        10.06         3.68        38.20        74.56 
TCGA-G4-6304 TCGA-G4-6588 TCGA-AG-3892 TCGA-AG-A002 TCGA-EI-6507 
       53.62        26.17        13.02        20.98        19.96 

$`HEATR4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 
       20.12        19.66        20.28         7.04         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
       54.02         2.01        14.01        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
       33.04         0.99         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
        7.96        27.02        13.94        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
        1.02         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.07        12.20        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6922 
       17.13        12.49        16.14        15.58         1.48         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 
       47.41        35.31       133.18        65.85        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       35.80        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6508 
       24.13        51.48        32.61         0.49        20.55        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  HEATR4 MUTATED HEATR4 WILD-TYPE 
            0.92             0.00 
  HEATR4 MUTATED HEATR4 WILD-TYPE 
           74.56           148.01 
  HEATR4 MUTATED HEATR4 WILD-TYPE 
          20.980           20.155 
[1] "0.9 - 74.6 (21.0)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.3"
D1319V2, continuous
D1319V3, binary
                  cls
clus                 0   1
  HEATR4 MUTATED    14   3
  HEATR4 WILD-TYPE 352 116
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HEATR4 MUTATED     14    3
  HEATR4 WILD-TYPE  352  116
        clus
vv       HEATR4 MUTATED HEATR4 WILD-TYPE
  COLON              14              352
  RECTUM              3              116
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  HEATR4 MUTATED         2        0        1         8         1         0
  HEATR4 WILD-TYPE      89        1       31       130         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HEATR4 MUTATED           2          0          0          2        0
  HEATR4 WILD-TYPE        22         11         59         40       48
                  vv
clus               STAGE IVA STAGE IVB
  HEATR4 MUTATED           0         0
  HEATR4 WILD-TYPE        18         1
D1319V4, multiclass
            clus
vv           HEATR4 MUTATED HEATR4 WILD-TYPE
  STAGE I                 2               89
  STAGE IA                0                1
  STAGE II                1               31
  STAGE IIA               8              130
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               2               22
  STAGE IIIA              0               11
  STAGE IIIB              0               59
  STAGE IIIC              2               40
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  HEATR4 MUTATED     1   1  13   2
  HEATR4 WILD-TYPE  16  91 316  48
D1319V5, multiclass
    clus
vv   HEATR4 MUTATED HEATR4 WILD-TYPE
  T1              1               16
  T2              1               91
  T3             13              316
  T4              2               48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  HEATR4 MUTATED    12   1   4
  HEATR4 WILD-TYPE 275 112  83
D1319V6, multiclass
    clus
vv   HEATR4 MUTATED HEATR4 WILD-TYPE
  N0             12              275
  N1              1              112
  N2              4               83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1319V7, binary
                  cls
clus                 0   1
  HEATR4 MUTATED    16   0
  HEATR4 WILD-TYPE 359  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HEATR4 MUTATED     16    0
  HEATR4 WILD-TYPE  359   65
   clus
vv  HEATR4 MUTATED HEATR4 WILD-TYPE
  0             16              359
  1              0               65
[1] 2 2
[1] FALSE
D1319V8, binary
                  cls
clus                 0   1
  HEATR4 MUTATED     9   8
  HEATR4 WILD-TYPE 216 256
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HEATR4 MUTATED      9    8
  HEATR4 WILD-TYPE  216  256
        clus
vv       HEATR4 MUTATED HEATR4 WILD-TYPE
  FEMALE              9              216
  MALE                8              256
[1] 2 2
[1] FALSE
D1319V9, binary
                  cls
clus                 0   1
  HEATR4 MUTATED    14   1
  HEATR4 WILD-TYPE 336  21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HEATR4 MUTATED     14    1
  HEATR4 WILD-TYPE  336   21
     clus
vv    HEATR4 MUTATED HEATR4 WILD-TYPE
  NO              14              336
  YES              1               21
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  HEATR4 MUTATED                     11                             2
  HEATR4 WILD-TYPE                  304                            45
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  HEATR4 MUTATED                       3                              0
  HEATR4 WILD-TYPE                   103                             10
D1319V10, multiclass
                                clus
vv                               HEATR4 MUTATED HEATR4 WILD-TYPE
  COLON ADENOCARCINOMA                       11              304
  COLON MUCINOUS ADENOCARCINOMA               2               45
  RECTAL ADENOCARCINOMA                       3              103
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  HEATR4 MUTATED    13   0   0   2
  HEATR4 WILD-TYPE 332   4  31  23
D1319V11, multiclass
    clus
vv   HEATR4 MUTATED HEATR4 WILD-TYPE
  R0             13              332
  R1              0                4
  R2              0               31
  RX              2               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1319V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HEATR4 MUTATED                                  0     2
  HEATR4 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  HEATR4 MUTATED                           1     7
  HEATR4 WILD-TYPE                        21   219
D1319V13, multiclass
                                  clus
vv                                 HEATR4 MUTATED HEATR4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                9
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                         7              219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1320) Variable = BCAR3 MUTATION ANALYSIS
D1320V1, survival
                 sevent
clus2               0   1
  BCAR3 MUTATED    10   3
  BCAR3 WILD-TYPE 368  90
  BCAR3 MUTATED BCAR3 WILD-TYPE 
             13             458 
  BCAR3 MUTATED BCAR3 WILD-TYPE 
              3              90 
$`BCAR3 MUTATED`
TCGA-A6-6141 TCGA-A6-6781 TCGA-AA-3663 TCGA-AA-3949 TCGA-AD-6901 TCGA-AZ-6601 
        8.38        19.66         6.97        26.01        22.42       100.01 
TCGA-CA-6717 TCGA-CK-5916 TCGA-CM-6162 TCGA-D5-6928 TCGA-G4-6309 TCGA-AG-A02N 
       12.76        21.14        12.00        11.64        85.48        61.97 
TCGA-CI-6622 
        6.97 

$`BCAR3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 
       22.09        22.06        32.71        27.09        22.52        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        33.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        0.72         5.79        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 
       88.21        49.41         6.77        12.10        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07        12.20        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       15.02         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 
        4.41        12.43        14.30         9.04         9.44         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       53.62        44.68        55.04        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       38.96        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6624 
       17.49         0.69         0.72         6.05        33.17         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  BCAR3 MUTATED BCAR3 WILD-TYPE 
           6.97            0.00 
  BCAR3 MUTATED BCAR3 WILD-TYPE 
         100.01          148.01 
  BCAR3 MUTATED BCAR3 WILD-TYPE 
         19.660          20.235 
[1] "7.0 - 100.0 (19.7)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1"  
D1320V2, continuous
D1320V3, binary
                 cls
clus                0   1
  BCAR3 MUTATED    11   2
  BCAR3 WILD-TYPE 355 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BCAR3 MUTATED     11    2
  BCAR3 WILD-TYPE  355  117
        clus
vv       BCAR3 MUTATED BCAR3 WILD-TYPE
  COLON             11             355
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  BCAR3 MUTATED         1        0        3         3         1         0
  BCAR3 WILD-TYPE      90        1       29       135         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  BCAR3 MUTATED           0          0          3          1        0         0
  BCAR3 WILD-TYPE        24         11         56         41       48        18
                 vv
clus              STAGE IVB
  BCAR3 MUTATED           0
  BCAR3 WILD-TYPE         1
D1320V4, multiclass
            clus
vv           BCAR3 MUTATED BCAR3 WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               3              29
  STAGE IIA              3             135
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             3              56
  STAGE IIIC             1              41
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  BCAR3 MUTATED     1   0  10   2
  BCAR3 WILD-TYPE  16  92 319  48
D1320V5, multiclass
    clus
vv   BCAR3 MUTATED BCAR3 WILD-TYPE
  T1             1              16
  T2             0              92
  T3            10             319
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  BCAR3 MUTATED     9   4   0
  BCAR3 WILD-TYPE 278 109  87
D1320V6, multiclass
    clus
vv   BCAR3 MUTATED BCAR3 WILD-TYPE
  N0             9             278
  N1             4             109
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1320V7, binary
                 cls
clus                0   1
  BCAR3 MUTATED    11   0
  BCAR3 WILD-TYPE 364  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BCAR3 MUTATED     11    0
  BCAR3 WILD-TYPE  364   65
   clus
vv  BCAR3 MUTATED BCAR3 WILD-TYPE
  0            11             364
  1             0              65
[1] 2 2
[1] FALSE
D1320V8, binary
                 cls
clus                0   1
  BCAR3 MUTATED     4   9
  BCAR3 WILD-TYPE 221 255
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BCAR3 MUTATED      4    9
  BCAR3 WILD-TYPE  221  255
        clus
vv       BCAR3 MUTATED BCAR3 WILD-TYPE
  FEMALE             4             221
  MALE               9             255
[1] 2 2
[1] FALSE
D1320V9, binary
                 cls
clus                0   1
  BCAR3 MUTATED    11   0
  BCAR3 WILD-TYPE 339  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BCAR3 MUTATED     11    0
  BCAR3 WILD-TYPE  339   22
     clus
vv    BCAR3 MUTATED BCAR3 WILD-TYPE
  NO             11             339
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  BCAR3 MUTATED                      6                             5
  BCAR3 WILD-TYPE                  309                            42
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  BCAR3 MUTATED                       2                              0
  BCAR3 WILD-TYPE                   104                             10
D1320V10, multiclass
                                clus
vv                               BCAR3 MUTATED BCAR3 WILD-TYPE
  COLON ADENOCARCINOMA                       6             309
  COLON MUCINOUS ADENOCARCINOMA              5              42
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  BCAR3 MUTATED     7   0   0   2
  BCAR3 WILD-TYPE 338   4  31  23
D1320V11, multiclass
    clus
vv   BCAR3 MUTATED BCAR3 WILD-TYPE
  R0             7             338
  R1             0               4
  R2             0              31
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1320V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  BCAR3 MUTATED                                  0     1
  BCAR3 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  BCAR3 MUTATED                           2     7
  BCAR3 WILD-TYPE                        20   219
D1320V13, multiclass
                                  clus
vv                                 BCAR3 MUTATED BCAR3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    2              20
  WHITE                                        7             219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1321) Variable = OR2T34 MUTATION ANALYSIS
D1321V1, survival
                  sevent
clus2                0   1
  OR2T34 MUTATED     5   0
  OR2T34 WILD-TYPE 373  93
  OR2T34 MUTATED OR2T34 WILD-TYPE 
               5              466 
  OR2T34 MUTATED OR2T34 WILD-TYPE 
               0               93 
$`OR2T34 MUTATED`
TCGA-AA-3975 TCGA-AA-A010 TCGA-AD-6963 TCGA-AG-3742 TCGA-AG-A002 
       34.06        34.98        27.42         0.99        20.98 

$`OR2T34 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       16.08        50.99        13.05        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6964 
       56.55         0.79         0.72         5.79        22.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
        0.99        37.02        32.98         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  OR2T34 MUTATED OR2T34 WILD-TYPE 
            0.99             0.00 
  OR2T34 MUTATED OR2T34 WILD-TYPE 
           34.98           148.01 
  OR2T34 MUTATED OR2T34 WILD-TYPE 
          27.420           20.085 
[1] "1.0 - 35.0 (27.4)"  "0.0 - 148.0 (20.1)"
[1] "hr="     "3300000"
D1321V2, continuous
D1321V3, binary
                  cls
clus                 0   1
  OR2T34 MUTATED     4   2
  OR2T34 WILD-TYPE 362 117
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR2T34 MUTATED      4    2
  OR2T34 WILD-TYPE  362  117
        clus
vv       OR2T34 MUTATED OR2T34 WILD-TYPE
  COLON               4              362
  RECTUM              2              117
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  OR2T34 MUTATED         3        0        1         0         1         0
  OR2T34 WILD-TYPE      88        1       31       138         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  OR2T34 MUTATED           0          0          0          0        0
  OR2T34 WILD-TYPE        24         11         59         42       48
                  vv
clus               STAGE IVA STAGE IVB
  OR2T34 MUTATED           0         0
  OR2T34 WILD-TYPE        18         1
D1321V4, multiclass
            clus
vv           OR2T34 MUTATED OR2T34 WILD-TYPE
  STAGE I                 3               88
  STAGE IA                0                1
  STAGE II                1               31
  STAGE IIA               0              138
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              0               59
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  OR2T34 MUTATED     1   2   1   2
  OR2T34 WILD-TYPE  16  90 328  48
D1321V5, multiclass
    clus
vv   OR2T34 MUTATED OR2T34 WILD-TYPE
  T1              1               16
  T2              2               90
  T3              1              328
  T4              2               48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  OR2T34 MUTATED     6   0   0
  OR2T34 WILD-TYPE 281 113  87
D1321V6, multiclass
    clus
vv   OR2T34 MUTATED OR2T34 WILD-TYPE
  N0              6              281
  N1              0              113
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1321V7, binary
                  cls
clus                 0   1
  OR2T34 MUTATED     5   0
  OR2T34 WILD-TYPE 370  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR2T34 MUTATED      5    0
  OR2T34 WILD-TYPE  370   65
   clus
vv  OR2T34 MUTATED OR2T34 WILD-TYPE
  0              5              370
  1              0               65
[1] 2 2
[1] FALSE
D1321V8, binary
                  cls
clus                 0   1
  OR2T34 MUTATED     3   3
  OR2T34 WILD-TYPE 222 261
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR2T34 MUTATED      3    3
  OR2T34 WILD-TYPE  222  261
        clus
vv       OR2T34 MUTATED OR2T34 WILD-TYPE
  FEMALE              3              222
  MALE                3              261
[1] 2 2
[1] FALSE
D1321V9, binary
                  cls
clus                 0   1
  OR2T34 MUTATED     4   0
  OR2T34 WILD-TYPE 346  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR2T34 MUTATED      4    0
  OR2T34 WILD-TYPE  346   22
     clus
vv    OR2T34 MUTATED OR2T34 WILD-TYPE
  NO               4              346
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  OR2T34 MUTATED                      4                             0
  OR2T34 WILD-TYPE                  311                            47
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  OR2T34 MUTATED                       2                              0
  OR2T34 WILD-TYPE                   104                             10
D1321V10, multiclass
                                clus
vv                               OR2T34 MUTATED OR2T34 WILD-TYPE
  COLON ADENOCARCINOMA                        4              311
  COLON MUCINOUS ADENOCARCINOMA               0               47
  RECTAL ADENOCARCINOMA                       2              104
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  OR2T34 MUTATED     5   0   0   0
  OR2T34 WILD-TYPE 340   4  31  25
D1321V11, multiclass
    clus
vv   OR2T34 MUTATED OR2T34 WILD-TYPE
  R0              5              340
  R1              0                4
  R2              0               31
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1321V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OR2T34 MUTATED                                  0     0
  OR2T34 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  OR2T34 MUTATED                           0     1
  OR2T34 WILD-TYPE                        22   225
D1321V13, multiclass
[1] "Remove cluster labels:" "OR2T34 MUTATED"        
clus
  OR2T34 MUTATED OR2T34 WILD-TYPE 
               1              259 
      TCGA-A6-2671       TCGA-A6-2672       TCGA-A6-2674       TCGA-A6-2676 
"OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" 
      TCGA-A6-2677       TCGA-A6-2678       TCGA-A6-2683       TCGA-A6-3807 
"OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" 
      TCGA-A6-3808       TCGA-A6-3809       TCGA-A6-3810       TCGA-A6-4105 
"OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" 
      TCGA-A6-5656       TCGA-A6-5657       TCGA-A6-5659       TCGA-A6-5660 
"OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" 
      TCGA-A6-5661       TCGA-A6-5662       TCGA-A6-5664       TCGA-A6-5665 
"OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" 
      TCGA-A6-5666       TCGA-A6-6137       TCGA-A6-6138       TCGA-A6-6141 
"OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" 
      TCGA-A6-6142       TCGA-A6-6648       TCGA-A6-6649       TCGA-A6-6651 
"OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" 
      TCGA-A6-6652       TCGA-A6-6653       TCGA-A6-6654       TCGA-A6-6780 
"OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" 
      TCGA-A6-6781       TCGA-A6-6782       TCGA-AD-5900       TCGA-AD-6548 
"OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" 
      TCGA-AD-6888       TCGA-AD-6889       TCGA-AD-6890       TCGA-AD-6895 
"OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" 
      TCGA-AD-6899       TCGA-AD-6901       TCGA-AD-6964       TCGA-AD-6965 
"OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" 
      TCGA-AU-3779       TCGA-AU-6004       TCGA-AY-4070       TCGA-AY-4071 
"OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" 
      TCGA-AY-5543       TCGA-AY-6196       TCGA-AY-6197       TCGA-AY-6386 
"OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" 
      TCGA-AZ-4315       TCGA-AZ-4323       TCGA-AZ-4616       TCGA-AZ-4681 
"OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" 
      TCGA-AZ-4682       TCGA-AZ-5403       TCGA-AZ-5407       TCGA-AZ-6598 
"OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" 
      TCGA-AZ-6599       TCGA-AZ-6600       TCGA-AZ-6601       TCGA-AZ-6603 
"OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" 
      TCGA-AZ-6605       TCGA-AZ-6606       TCGA-AZ-6607       TCGA-AZ-6608 
"OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" 
      TCGA-CA-5254       TCGA-CA-5255       TCGA-CA-5796       TCGA-CA-5797 
"OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" 
      TCGA-CA-6715       TCGA-CA-6716       TCGA-CA-6717       TCGA-CA-6718 
"OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" 
      TCGA-CA-6719       TCGA-CK-4947       TCGA-CK-4948       TCGA-CK-4950 
"OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" 
      TCGA-CK-4952       TCGA-CK-5912       TCGA-CK-5913       TCGA-CK-5914 
"OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" 
      TCGA-CK-5915       TCGA-CK-5916       TCGA-CK-6746       TCGA-CK-6747 
"OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" 
      TCGA-CK-6748       TCGA-CK-6751       TCGA-CM-4743       TCGA-CM-4744 
"OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" 
      TCGA-CM-4746       TCGA-CM-4747       TCGA-CM-4752       TCGA-CM-5341 
"OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" 
      TCGA-CM-5344       TCGA-CM-5348       TCGA-CM-5349       TCGA-CM-5860 
"OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" 
      TCGA-CM-5861       TCGA-CM-5862       TCGA-CM-5863       TCGA-CM-5864 
"OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" 
      TCGA-CM-5868       TCGA-CM-6161       TCGA-CM-6162       TCGA-CM-6163 
"OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" 
      TCGA-CM-6164       TCGA-CM-6165       TCGA-CM-6166       TCGA-CM-6167 
"OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" 
      TCGA-CM-6168       TCGA-CM-6169       TCGA-CM-6170       TCGA-CM-6171 
"OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" 
      TCGA-CM-6172       TCGA-CM-6674       TCGA-CM-6675       TCGA-CM-6676 
"OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" 
      TCGA-CM-6677       TCGA-CM-6678       TCGA-CM-6679       TCGA-CM-6680 
"OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" 
      TCGA-D5-5537       TCGA-D5-5538       TCGA-D5-5539       TCGA-D5-5540 
"OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" 
      TCGA-D5-5541       TCGA-D5-6529       TCGA-D5-6532       TCGA-D5-6533 
"OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" 
      TCGA-D5-6534       TCGA-D5-6535       TCGA-D5-6536       TCGA-D5-6537 
"OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" 
      TCGA-D5-6538       TCGA-D5-6539       TCGA-D5-6540       TCGA-D5-6541 
"OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" 
      TCGA-D5-6898       TCGA-D5-6920       TCGA-D5-6922       TCGA-D5-6923 
"OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" 
      TCGA-D5-6924       TCGA-D5-6926       TCGA-D5-6927       TCGA-D5-6928 
"OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" 
      TCGA-D5-6929       TCGA-D5-6930       TCGA-D5-6931       TCGA-D5-6932 
"OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" 
      TCGA-D5-7000       TCGA-DM-A0X9       TCGA-DM-A0XD       TCGA-DM-A0XF 
"OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" 
      TCGA-DM-A1D0       TCGA-DM-A1D4       TCGA-DM-A1D6       TCGA-DM-A1D7 
"OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" 
      TCGA-DM-A1D8       TCGA-DM-A1D9       TCGA-DM-A1DA       TCGA-DM-A1DB 
"OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" 
      TCGA-DM-A1HA       TCGA-DM-A1HB       TCGA-DM-A282       TCGA-DM-A285 
"OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" 
      TCGA-DM-A28C       TCGA-DM-A28E       TCGA-DM-A28F       TCGA-DM-A28G 
"OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" 
      TCGA-DM-A28H       TCGA-DM-A28K       TCGA-F4-6459       TCGA-F4-6460 
"OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" 
      TCGA-F4-6569       TCGA-F4-6570       TCGA-F4-6703       TCGA-F4-6704 
"OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" 
      TCGA-F4-6805       TCGA-F4-6806       TCGA-F4-6807       TCGA-F4-6808 
"OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" 
      TCGA-F4-6809       TCGA-F4-6854       TCGA-F4-6855       TCGA-F4-6856 
"OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" 
      TCGA-G4-6293       TCGA-G4-6299       TCGA-G4-6303       TCGA-G4-6304 
"OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" 
      TCGA-G4-6306       TCGA-G4-6307       TCGA-G4-6309       TCGA-G4-6310 
"OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" 
      TCGA-G4-6315       TCGA-G4-6317       TCGA-G4-6321       TCGA-G4-6323 
"OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" 
      TCGA-G4-6586       TCGA-G4-6588       TCGA-G4-6625       TCGA-G4-6626 
"OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" 
      TCGA-G4-6628       TCGA-AF-2687       TCGA-AF-2689       TCGA-AF-2691 
"OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" 
      TCGA-AF-2692       TCGA-AF-2693       TCGA-AF-3400       TCGA-AF-3913 
"OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" 
      TCGA-AF-4110       TCGA-AF-5654       TCGA-AF-6136       TCGA-AF-6655 
"OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" 
      TCGA-AF-6672       TCGA-AH-6544       TCGA-AH-6547       TCGA-AH-6549 
"OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" 
      TCGA-AH-6643       TCGA-AH-6644       TCGA-CI-6619       TCGA-CI-6620 
"OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" 
      TCGA-CI-6621       TCGA-CI-6622       TCGA-CI-6624       TCGA-CL-5917 
"OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" 
      TCGA-CL-5918       TCGA-DC-5337       TCGA-DC-5869       TCGA-DC-6155 
"OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" 
      TCGA-DC-6157       TCGA-DC-6158       TCGA-DC-6160       TCGA-DC-6681 
"OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" 
      TCGA-DC-6682       TCGA-DC-6683       TCGA-DT-5265       TCGA-DY-A0XA 
"OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" 
      TCGA-DY-A1DC       TCGA-DY-A1DD       TCGA-DY-A1DF       TCGA-DY-A1DG 
"OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" 
      TCGA-DY-A1H8       TCGA-EF-5830       TCGA-EI-6506       TCGA-EI-6507 
"OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" 
      TCGA-EI-6508       TCGA-EI-6510       TCGA-F5-6464       TCGA-F5-6465 
"OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" 
      TCGA-F5-6571       TCGA-F5-6702       TCGA-F5-6811       TCGA-F5-6812 
"OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" 
      TCGA-F5-6813       TCGA-G5-6235       TCGA-G5-6641 
"OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" "OR2T34 WILD-TYPE" 

Clustering(1322) Variable = POLDIP3 MUTATION ANALYSIS
D1322V1, survival
                   sevent
clus2                 0   1
  POLDIP3 MUTATED     5   2
  POLDIP3 WILD-TYPE 373  91
  POLDIP3 MUTATED POLDIP3 WILD-TYPE 
                7               464 
  POLDIP3 MUTATED POLDIP3 WILD-TYPE 
                2                91 
$`POLDIP3 MUTATED`
TCGA-AA-3811 TCGA-AA-3949 TCGA-AA-A01R TCGA-AD-6889 TCGA-F4-6570 TCGA-AG-3892 
       10.06        26.01        35.01        56.55         6.18        13.02 
TCGA-AG-A002 
       20.98 

$`POLDIP3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       19.04        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-3952 
        2.01        12.99        24.00        33.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T 
       31.00        31.00        38.07         1.02         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 
       18.05        40.96         0.07        21.37        15.52         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 
       98.24         8.61        31.96        35.74        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       17.95        36.95        17.03        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  POLDIP3 MUTATED POLDIP3 WILD-TYPE 
             6.18              0.00 
  POLDIP3 MUTATED POLDIP3 WILD-TYPE 
            56.55            148.01 
  POLDIP3 MUTATED POLDIP3 WILD-TYPE 
           20.980            20.155 
[1] "6.2 - 56.5 (21.0)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.6"
D1322V2, continuous
D1322V3, binary
                   cls
clus                  0   1
  POLDIP3 MUTATED     5   2
  POLDIP3 WILD-TYPE 361 117
[1] "tbl2"
                   cls
clus                [,1] [,2]
  POLDIP3 MUTATED      5    2
  POLDIP3 WILD-TYPE  361  117
        clus
vv       POLDIP3 MUTATED POLDIP3 WILD-TYPE
  COLON                5               361
  RECTUM               2               117
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  POLDIP3 MUTATED         2        0        0         2         0         0
  POLDIP3 WILD-TYPE      89        1       32       136        10         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  POLDIP3 MUTATED           2          0          1          0        0
  POLDIP3 WILD-TYPE        22         11         58         42       48
                   vv
clus                STAGE IVA STAGE IVB
  POLDIP3 MUTATED           0         0
  POLDIP3 WILD-TYPE        18         1
D1322V4, multiclass
            clus
vv           POLDIP3 MUTATED POLDIP3 WILD-TYPE
  STAGE I                  2                89
  STAGE IA                 0                 1
  STAGE II                 0                32
  STAGE IIA                2               136
  STAGE IIB                0                10
  STAGE IIC                0                 1
  STAGE III                2                22
  STAGE IIIA               0                11
  STAGE IIIB               1                58
  STAGE IIIC               0                42
  STAGE IV                 0                48
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  POLDIP3 MUTATED     1   1   5   0
  POLDIP3 WILD-TYPE  16  91 324  50
D1322V5, multiclass
    clus
vv   POLDIP3 MUTATED POLDIP3 WILD-TYPE
  T1               1                16
  T2               1                91
  T3               5               324
  T4               0                50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  POLDIP3 MUTATED     4   1   2
  POLDIP3 WILD-TYPE 283 112  85
D1322V6, multiclass
    clus
vv   POLDIP3 MUTATED POLDIP3 WILD-TYPE
  N0               4               283
  N1               1               112
  N2               2                85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1322V7, binary
                   cls
clus                  0   1
  POLDIP3 MUTATED     7   0
  POLDIP3 WILD-TYPE 368  65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  POLDIP3 MUTATED      7    0
  POLDIP3 WILD-TYPE  368   65
   clus
vv  POLDIP3 MUTATED POLDIP3 WILD-TYPE
  0               7               368
  1               0                65
[1] 2 2
[1] FALSE
D1322V8, binary
                   cls
clus                  0   1
  POLDIP3 MUTATED     4   3
  POLDIP3 WILD-TYPE 221 261
[1] "tbl2"
                   cls
clus                [,1] [,2]
  POLDIP3 MUTATED      4    3
  POLDIP3 WILD-TYPE  221  261
        clus
vv       POLDIP3 MUTATED POLDIP3 WILD-TYPE
  FEMALE               4               221
  MALE                 3               261
[1] 2 2
[1] FALSE
D1322V9, binary
                   cls
clus                  0   1
  POLDIP3 MUTATED     5   1
  POLDIP3 WILD-TYPE 345  21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  POLDIP3 MUTATED      5    1
  POLDIP3 WILD-TYPE  345   21
     clus
vv    POLDIP3 MUTATED POLDIP3 WILD-TYPE
  NO                5               345
  YES               1                21
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  POLDIP3 MUTATED                      3                             2
  POLDIP3 WILD-TYPE                  312                            45
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  POLDIP3 MUTATED                       2                              0
  POLDIP3 WILD-TYPE                   104                             10
D1322V10, multiclass
                                clus
vv                               POLDIP3 MUTATED POLDIP3 WILD-TYPE
  COLON ADENOCARCINOMA                         3               312
  COLON MUCINOUS ADENOCARCINOMA                2                45
  RECTAL ADENOCARCINOMA                        2               104
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  POLDIP3 MUTATED     6   0   0   0
  POLDIP3 WILD-TYPE 339   4  31  25
D1322V11, multiclass
    clus
vv   POLDIP3 MUTATED POLDIP3 WILD-TYPE
  R0               6               339
  R1               0                 4
  R2               0                31
  RX               0                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1322V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  POLDIP3 MUTATED                                  0     1
  POLDIP3 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  POLDIP3 MUTATED                           0     1
  POLDIP3 WILD-TYPE                        22   225
D1322V13, multiclass
[1] "Remove cluster labels:" "POLDIP3 MUTATED"       
clus
  POLDIP3 MUTATED POLDIP3 WILD-TYPE 
                2               258 
       TCGA-A6-2671        TCGA-A6-2672        TCGA-A6-2674        TCGA-A6-2676 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-A6-2677        TCGA-A6-2678        TCGA-A6-2683        TCGA-A6-3807 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-A6-3808        TCGA-A6-3809        TCGA-A6-3810        TCGA-A6-4105 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-A6-5656        TCGA-A6-5657        TCGA-A6-5659        TCGA-A6-5660 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-A6-5661        TCGA-A6-5662        TCGA-A6-5664        TCGA-A6-5665 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-A6-5666        TCGA-A6-6137        TCGA-A6-6138        TCGA-A6-6141 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-A6-6142        TCGA-A6-6648        TCGA-A6-6649        TCGA-A6-6651 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-A6-6652        TCGA-A6-6653        TCGA-A6-6654        TCGA-A6-6780 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-A6-6781        TCGA-A6-6782        TCGA-AD-5900        TCGA-AD-6548 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-AD-6888        TCGA-AD-6890        TCGA-AD-6895        TCGA-AD-6899 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-AD-6901        TCGA-AD-6963        TCGA-AD-6964        TCGA-AD-6965 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-AU-3779        TCGA-AU-6004        TCGA-AY-4070        TCGA-AY-4071 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-AY-5543        TCGA-AY-6196        TCGA-AY-6197        TCGA-AY-6386 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-AZ-4315        TCGA-AZ-4323        TCGA-AZ-4616        TCGA-AZ-4681 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-AZ-4682        TCGA-AZ-5403        TCGA-AZ-5407        TCGA-AZ-6598 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-AZ-6599        TCGA-AZ-6600        TCGA-AZ-6601        TCGA-AZ-6603 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-AZ-6605        TCGA-AZ-6606        TCGA-AZ-6607        TCGA-AZ-6608 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-CA-5254        TCGA-CA-5255        TCGA-CA-5796        TCGA-CA-5797 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-CA-6715        TCGA-CA-6716        TCGA-CA-6717        TCGA-CA-6718 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-CA-6719        TCGA-CK-4947        TCGA-CK-4948        TCGA-CK-4950 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-CK-4952        TCGA-CK-5912        TCGA-CK-5913        TCGA-CK-5914 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-CK-5915        TCGA-CK-5916        TCGA-CK-6746        TCGA-CK-6747 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-CK-6748        TCGA-CK-6751        TCGA-CM-4743        TCGA-CM-4744 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-CM-4746        TCGA-CM-4747        TCGA-CM-4752        TCGA-CM-5341 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-CM-5344        TCGA-CM-5348        TCGA-CM-5349        TCGA-CM-5860 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-CM-5861        TCGA-CM-5862        TCGA-CM-5863        TCGA-CM-5864 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-CM-5868        TCGA-CM-6161        TCGA-CM-6162        TCGA-CM-6163 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-CM-6164        TCGA-CM-6165        TCGA-CM-6166        TCGA-CM-6167 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-CM-6168        TCGA-CM-6169        TCGA-CM-6170        TCGA-CM-6171 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-CM-6172        TCGA-CM-6674        TCGA-CM-6675        TCGA-CM-6676 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-CM-6677        TCGA-CM-6678        TCGA-CM-6679        TCGA-CM-6680 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-D5-5537        TCGA-D5-5538        TCGA-D5-5539        TCGA-D5-5540 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-D5-5541        TCGA-D5-6529        TCGA-D5-6532        TCGA-D5-6533 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-D5-6534        TCGA-D5-6535        TCGA-D5-6536        TCGA-D5-6537 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-D5-6538        TCGA-D5-6539        TCGA-D5-6540        TCGA-D5-6541 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-D5-6898        TCGA-D5-6920        TCGA-D5-6922        TCGA-D5-6923 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-D5-6924        TCGA-D5-6926        TCGA-D5-6927        TCGA-D5-6928 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-D5-6929        TCGA-D5-6930        TCGA-D5-6931        TCGA-D5-6932 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-D5-7000        TCGA-DM-A0X9        TCGA-DM-A0XD        TCGA-DM-A0XF 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-DM-A1D0        TCGA-DM-A1D4        TCGA-DM-A1D6        TCGA-DM-A1D7 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-DM-A1D8        TCGA-DM-A1D9        TCGA-DM-A1DA        TCGA-DM-A1DB 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-DM-A1HA        TCGA-DM-A1HB        TCGA-DM-A282        TCGA-DM-A285 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-DM-A28C        TCGA-DM-A28E        TCGA-DM-A28F        TCGA-DM-A28G 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-DM-A28H        TCGA-DM-A28K        TCGA-F4-6459        TCGA-F4-6460 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-F4-6569        TCGA-F4-6703        TCGA-F4-6704        TCGA-F4-6805 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-F4-6806        TCGA-F4-6807        TCGA-F4-6808        TCGA-F4-6809 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-F4-6854        TCGA-F4-6855        TCGA-F4-6856        TCGA-G4-6293 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-G4-6299        TCGA-G4-6303        TCGA-G4-6304        TCGA-G4-6306 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-G4-6307        TCGA-G4-6309        TCGA-G4-6310        TCGA-G4-6315 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-G4-6317        TCGA-G4-6321        TCGA-G4-6323        TCGA-G4-6586 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-G4-6588        TCGA-G4-6625        TCGA-G4-6626        TCGA-G4-6628 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2691        TCGA-AF-2692 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3913        TCGA-AF-4110 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-AF-5654        TCGA-AF-6136        TCGA-AF-6655        TCGA-AF-6672 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6549        TCGA-AH-6643 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-AH-6644        TCGA-CI-6619        TCGA-CI-6620        TCGA-CI-6621 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-CI-6622        TCGA-CI-6624        TCGA-CL-5917        TCGA-CL-5918 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6155        TCGA-DC-6157 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-DC-6158        TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-DC-6683        TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-DY-A1DD        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-EF-5830        TCGA-EI-6506        TCGA-EI-6507        TCGA-EI-6508 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-EI-6510        TCGA-F5-6464        TCGA-F5-6465        TCGA-F5-6571 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-F5-6702        TCGA-F5-6811        TCGA-F5-6812        TCGA-F5-6813 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 
       TCGA-G5-6235        TCGA-G5-6641 
"POLDIP3 WILD-TYPE" "POLDIP3 WILD-TYPE" 

Clustering(1323) Variable = PNPLA8 MUTATION ANALYSIS
D1323V1, survival
                  sevent
clus2                0   1
  PNPLA8 MUTATED    14   5
  PNPLA8 WILD-TYPE 364  88
  PNPLA8 MUTATED PNPLA8 WILD-TYPE 
              19              452 
  PNPLA8 MUTATED PNPLA8 WILD-TYPE 
               5               88 
$`PNPLA8 MUTATED`
TCGA-A6-3809 TCGA-A6-6653 TCGA-AA-3710 TCGA-AA-3977 TCGA-AA-A00N TCGA-AD-6895 
       32.75        24.39        26.99        25.02         4.01         0.72 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-6717 TCGA-CA-6718 
       17.82        58.39         3.19         1.61        12.76        10.06 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5916 TCGA-CK-6747 TCGA-CM-5344 TCGA-CM-6161 
      148.01        85.45        21.14        82.95        22.03        15.02 
TCGA-AG-A002 
       20.98 

$`PNPLA8 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 
       25.18        24.16        21.76        24.69        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 
        0.07        21.37        15.52        56.55         0.79         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AZ-4323 TCGA-AZ-4616 
       16.31         0.95        33.01        21.44         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-CA-5254 
       12.10       100.01        29.56         5.23        11.74        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 
        3.06         3.25         3.29         0.07        12.20        14.30 
TCGA-CK-4947 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6748 
       17.56        15.62        49.08        51.32         9.99         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       29.06        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        15.02        17.03        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  PNPLA8 MUTATED PNPLA8 WILD-TYPE 
            0.72             0.00 
  PNPLA8 MUTATED PNPLA8 WILD-TYPE 
          148.01           140.38 
  PNPLA8 MUTATED PNPLA8 WILD-TYPE 
          21.140           20.085 
[1] "0.7 - 148.0 (21.1)" "0.0 - 140.4 (20.1)"
[1] "hr=" "1.2"
D1323V2, continuous
D1323V3, binary
                  cls
clus                 0   1
  PNPLA8 MUTATED    18   1
  PNPLA8 WILD-TYPE 348 118
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PNPLA8 MUTATED     18    1
  PNPLA8 WILD-TYPE  348  118
        clus
vv       PNPLA8 MUTATED PNPLA8 WILD-TYPE
  COLON              18              348
  RECTUM              1              118
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PNPLA8 MUTATED         4        0        0         5         2         0
  PNPLA8 WILD-TYPE      87        1       32       133         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PNPLA8 MUTATED           1          1          3          0        1
  PNPLA8 WILD-TYPE        23         10         56         42       47
                  vv
clus               STAGE IVA STAGE IVB
  PNPLA8 MUTATED           0         0
  PNPLA8 WILD-TYPE        18         1
D1323V4, multiclass
            clus
vv           PNPLA8 MUTATED PNPLA8 WILD-TYPE
  STAGE I                 4               87
  STAGE IA                0                1
  STAGE II                0               32
  STAGE IIA               5              133
  STAGE IIB               2                8
  STAGE IIC               0                1
  STAGE III               1               23
  STAGE IIIA              1               10
  STAGE IIIB              3               56
  STAGE IIIC              0               42
  STAGE IV                1               47
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  PNPLA8 MUTATED     1   5  10   3
  PNPLA8 WILD-TYPE  16  87 319  47
D1323V5, multiclass
    clus
vv   PNPLA8 MUTATED PNPLA8 WILD-TYPE
  T1              1               16
  T2              5               87
  T3             10              319
  T4              3               47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  PNPLA8 MUTATED    12   6   1
  PNPLA8 WILD-TYPE 275 107  86
D1323V6, multiclass
    clus
vv   PNPLA8 MUTATED PNPLA8 WILD-TYPE
  N0             12              275
  N1              6              107
  N2              1               86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1323V7, binary
                  cls
clus                 0   1
  PNPLA8 MUTATED    15   1
  PNPLA8 WILD-TYPE 360  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PNPLA8 MUTATED     15    1
  PNPLA8 WILD-TYPE  360   64
   clus
vv  PNPLA8 MUTATED PNPLA8 WILD-TYPE
  0             15              360
  1              1               64
[1] 2 2
[1] FALSE
D1323V8, binary
                  cls
clus                 0   1
  PNPLA8 MUTATED    10   9
  PNPLA8 WILD-TYPE 215 255
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PNPLA8 MUTATED     10    9
  PNPLA8 WILD-TYPE  215  255
        clus
vv       PNPLA8 MUTATED PNPLA8 WILD-TYPE
  FEMALE             10              215
  MALE                9              255
[1] 2 2
[1] FALSE
D1323V9, binary
                  cls
clus                 0   1
  PNPLA8 MUTATED    17   0
  PNPLA8 WILD-TYPE 333  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PNPLA8 MUTATED     17    0
  PNPLA8 WILD-TYPE  333   22
     clus
vv    PNPLA8 MUTATED PNPLA8 WILD-TYPE
  NO              17              333
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PNPLA8 MUTATED                     15                             3
  PNPLA8 WILD-TYPE                  300                            44
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PNPLA8 MUTATED                       1                              0
  PNPLA8 WILD-TYPE                   105                             10
D1323V10, multiclass
                                clus
vv                               PNPLA8 MUTATED PNPLA8 WILD-TYPE
  COLON ADENOCARCINOMA                       15              300
  COLON MUCINOUS ADENOCARCINOMA               3               44
  RECTAL ADENOCARCINOMA                       1              105
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  PNPLA8 MUTATED     9   1   0   4
  PNPLA8 WILD-TYPE 336   3  31  21
D1323V11, multiclass
    clus
vv   PNPLA8 MUTATED PNPLA8 WILD-TYPE
  R0              9              336
  R1              1                3
  R2              0               31
  RX              4               21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1323V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PNPLA8 MUTATED                                  0     2
  PNPLA8 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  PNPLA8 MUTATED                           2    11
  PNPLA8 WILD-TYPE                        20   215
D1323V13, multiclass
                                  clus
vv                                 PNPLA8 MUTATED PNPLA8 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                9
  BLACK OR AFRICAN AMERICAN                     2               20
  WHITE                                        11              215
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1324) Variable = C7ORF60 MUTATION ANALYSIS
D1324V1, survival
                   sevent
clus2                 0   1
  C7ORF60 MUTATED     5   1
  C7ORF60 WILD-TYPE 373  92
  C7ORF60 MUTATED C7ORF60 WILD-TYPE 
                6               465 
  C7ORF60 MUTATED C7ORF60 WILD-TYPE 
                1                92 
$`C7ORF60 MUTATED`
TCGA-A6-6137 TCGA-A6-6651 TCGA-AZ-4315 TCGA-AZ-4616 TCGA-CM-6161 TCGA-G4-6323 
       27.09        21.76        58.39         5.13        15.02        13.78 

$`C7ORF60 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        22.06        32.71        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       25.18        24.16        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4681 TCGA-AZ-4682 
       33.01        21.44        17.82         1.41       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6162 TCGA-CM-6163 
        5.03        15.02        15.02        17.03        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       22.09        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  C7ORF60 MUTATED C7ORF60 WILD-TYPE 
             5.13              0.00 
  C7ORF60 MUTATED C7ORF60 WILD-TYPE 
            58.39            148.01 
  C7ORF60 MUTATED C7ORF60 WILD-TYPE 
            18.39             20.19 
[1] "5.1 - 58.4 (18.4)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.1"
D1324V2, continuous
D1324V3, binary
                   cls
clus                  0   1
  C7ORF60 MUTATED     6   0
  C7ORF60 WILD-TYPE 360 119
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C7ORF60 MUTATED      6    0
  C7ORF60 WILD-TYPE  360  119
        clus
vv       C7ORF60 MUTATED C7ORF60 WILD-TYPE
  COLON                6               360
  RECTUM               0               119
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  C7ORF60 MUTATED         1        1        0         1         0         0
  C7ORF60 WILD-TYPE      90        0       32       137        10         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C7ORF60 MUTATED           0          0          2          0        1
  C7ORF60 WILD-TYPE        24         11         57         42       47
                   vv
clus                STAGE IVA STAGE IVB
  C7ORF60 MUTATED           0         0
  C7ORF60 WILD-TYPE        18         1
D1324V4, multiclass
            clus
vv           C7ORF60 MUTATED C7ORF60 WILD-TYPE
  STAGE I                  1                90
  STAGE IA                 1                 0
  STAGE II                 0                32
  STAGE IIA                1               137
  STAGE IIB                0                10
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               0                11
  STAGE IIIB               2                57
  STAGE IIIC               0                42
  STAGE IV                 1                47
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  C7ORF60 MUTATED     0   1   4   0
  C7ORF60 WILD-TYPE  17  91 325  50
D1324V5, multiclass
    clus
vv   C7ORF60 MUTATED C7ORF60 WILD-TYPE
  T1               0                17
  T2               1                91
  T3               4               325
  T4               0                50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  C7ORF60 MUTATED     3   2   1
  C7ORF60 WILD-TYPE 284 111  86
D1324V6, multiclass
    clus
vv   C7ORF60 MUTATED C7ORF60 WILD-TYPE
  N0               3               284
  N1               2               111
  N2               1                86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1324V7, binary
                   cls
clus                  0   1
  C7ORF60 MUTATED     3   1
  C7ORF60 WILD-TYPE 372  64
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C7ORF60 MUTATED      3    1
  C7ORF60 WILD-TYPE  372   64
   clus
vv  C7ORF60 MUTATED C7ORF60 WILD-TYPE
  0               3               372
  1               1                64
[1] 2 2
[1] FALSE
D1324V8, binary
                   cls
clus                  0   1
  C7ORF60 MUTATED     3   3
  C7ORF60 WILD-TYPE 222 261
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C7ORF60 MUTATED      3    3
  C7ORF60 WILD-TYPE  222  261
        clus
vv       C7ORF60 MUTATED C7ORF60 WILD-TYPE
  FEMALE               3               222
  MALE                 3               261
[1] 2 2
[1] FALSE
D1324V9, binary
                   cls
clus                  0   1
  C7ORF60 MUTATED     6   0
  C7ORF60 WILD-TYPE 344  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C7ORF60 MUTATED      6    0
  C7ORF60 WILD-TYPE  344   22
     clus
vv    C7ORF60 MUTATED C7ORF60 WILD-TYPE
  NO                6               344
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  C7ORF60 MUTATED                      6                             0
  C7ORF60 WILD-TYPE                  309                            47
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  C7ORF60 MUTATED                       0                              0
  C7ORF60 WILD-TYPE                   106                             10
D1324V10, multiclass
                                clus
vv                               C7ORF60 MUTATED C7ORF60 WILD-TYPE
  COLON ADENOCARCINOMA                         6               309
  COLON MUCINOUS ADENOCARCINOMA                0                47
  RECTAL ADENOCARCINOMA                        0               106
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  C7ORF60 MUTATED     3   0   0   0
  C7ORF60 WILD-TYPE 342   4  31  25
D1324V11, multiclass
    clus
vv   C7ORF60 MUTATED C7ORF60 WILD-TYPE
  R0               3               342
  R1               0                 4
  R2               0                31
  RX               0                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1324V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C7ORF60 MUTATED                                  0     0
  C7ORF60 WILD-TYPE                                1    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  C7ORF60 MUTATED                           1     5
  C7ORF60 WILD-TYPE                        21   221
D1324V13, multiclass
                                  clus
vv                                 C7ORF60 MUTATED C7ORF60 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                      1                21
  WHITE                                          5               221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1325) Variable = SLC25A17 MUTATION ANALYSIS
D1325V1, survival
                    sevent
clus2                  0   1
  SLC25A17 MUTATED     5   3
  SLC25A17 WILD-TYPE 373  90
  SLC25A17 MUTATED SLC25A17 WILD-TYPE 
                 8                463 
  SLC25A17 MUTATED SLC25A17 WILD-TYPE 
                 3                 90 
$`SLC25A17 MUTATED`
TCGA-A6-5665 TCGA-AA-3510 TCGA-AA-3715 TCGA-AA-3950 TCGA-AA-A00N TCGA-AD-5900 
       22.06        63.98        19.04        24.00         4.01         0.07 
TCGA-AZ-6601 TCGA-AG-A002 
      100.01        20.98 

$`SLC25A17 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        33.01        26.01         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       49.41         6.77        12.10        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  SLC25A17 MUTATED SLC25A17 WILD-TYPE 
              0.07               0.00 
  SLC25A17 MUTATED SLC25A17 WILD-TYPE 
            100.01             148.01 
  SLC25A17 MUTATED SLC25A17 WILD-TYPE 
             21.52              20.12 
[1] "0.1 - 100.0 (21.5)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.6"
D1325V2, continuous
D1325V3, binary
                    cls
clus                   0   1
  SLC25A17 MUTATED     7   1
  SLC25A17 WILD-TYPE 359 118
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SLC25A17 MUTATED      7    1
  SLC25A17 WILD-TYPE  359  118
        clus
vv       SLC25A17 MUTATED SLC25A17 WILD-TYPE
  COLON                 7                359
  RECTUM                1                118
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SLC25A17 MUTATED         2        0        3         2         1         0
  SLC25A17 WILD-TYPE      89        1       29       136         9         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC25A17 MUTATED           0          0          0          0        0
  SLC25A17 WILD-TYPE        24         11         59         42       48
                    vv
clus                 STAGE IVA STAGE IVB
  SLC25A17 MUTATED           0         0
  SLC25A17 WILD-TYPE        18         1
D1325V4, multiclass
            clus
vv           SLC25A17 MUTATED SLC25A17 WILD-TYPE
  STAGE I                   2                 89
  STAGE IA                  0                  1
  STAGE II                  3                 29
  STAGE IIA                 2                136
  STAGE IIB                 1                  9
  STAGE IIC                 0                  1
  STAGE III                 0                 24
  STAGE IIIA                0                 11
  STAGE IIIB                0                 59
  STAGE IIIC                0                 42
  STAGE IV                  0                 48
  STAGE IVA                 0                 18
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  SLC25A17 MUTATED     0   2   5   1
  SLC25A17 WILD-TYPE  17  90 324  49
D1325V5, multiclass
    clus
vv   SLC25A17 MUTATED SLC25A17 WILD-TYPE
  T1                0                 17
  T2                2                 90
  T3                5                324
  T4                1                 49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  SLC25A17 MUTATED     8   0   0
  SLC25A17 WILD-TYPE 279 113  87
D1325V6, multiclass
    clus
vv   SLC25A17 MUTATED SLC25A17 WILD-TYPE
  N0                8                279
  N1                0                113
  N2                0                 87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1325V7, binary
                    cls
clus                   0   1
  SLC25A17 MUTATED     7   0
  SLC25A17 WILD-TYPE 368  65
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SLC25A17 MUTATED      7    0
  SLC25A17 WILD-TYPE  368   65
   clus
vv  SLC25A17 MUTATED SLC25A17 WILD-TYPE
  0                7                368
  1                0                 65
[1] 2 2
[1] FALSE
D1325V8, binary
                    cls
clus                   0   1
  SLC25A17 MUTATED     2   6
  SLC25A17 WILD-TYPE 223 258
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SLC25A17 MUTATED      2    6
  SLC25A17 WILD-TYPE  223  258
        clus
vv       SLC25A17 MUTATED SLC25A17 WILD-TYPE
  FEMALE                2                223
  MALE                  6                258
[1] 2 2
[1] FALSE
D1325V9, binary
                    cls
clus                   0   1
  SLC25A17 MUTATED     6   0
  SLC25A17 WILD-TYPE 344  22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SLC25A17 MUTATED      6    0
  SLC25A17 WILD-TYPE  344   22
     clus
vv    SLC25A17 MUTATED SLC25A17 WILD-TYPE
  NO                 6                344
  YES                0                 22
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SLC25A17 MUTATED                      4                             3
  SLC25A17 WILD-TYPE                  311                            44
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SLC25A17 MUTATED                       1                              0
  SLC25A17 WILD-TYPE                   105                             10
D1325V10, multiclass
                                clus
vv                               SLC25A17 MUTATED SLC25A17 WILD-TYPE
  COLON ADENOCARCINOMA                          4                311
  COLON MUCINOUS ADENOCARCINOMA                 3                 44
  RECTAL ADENOCARCINOMA                         1                105
  RECTAL MUCINOUS ADENOCARCINOMA                0                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  SLC25A17 MUTATED     7   0   0   0
  SLC25A17 WILD-TYPE 338   4  31  25
D1325V11, multiclass
    clus
vv   SLC25A17 MUTATED SLC25A17 WILD-TYPE
  R0                7                338
  R1                0                  4
  R2                0                 31
  RX                0                 25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1325V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SLC25A17 MUTATED                                  0     0
  SLC25A17 WILD-TYPE                                1    11
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  SLC25A17 MUTATED                           0     3
  SLC25A17 WILD-TYPE                        22   223
D1325V13, multiclass
                                  clus
vv                                 SLC25A17 MUTATED SLC25A17 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 11
  BLACK OR AFRICAN AMERICAN                       0                 22
  WHITE                                           3                223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1326) Variable = KRTAP10-11 MUTATION ANALYSIS
D1326V1, survival
                      sevent
clus2                    0   1
  KRTAP10-11 MUTATED     5   1
  KRTAP10-11 WILD-TYPE 373  92
  KRTAP10-11 MUTATED KRTAP10-11 WILD-TYPE 
                   6                  465 
  KRTAP10-11 MUTATED KRTAP10-11 WILD-TYPE 
                   1                   92 
$`KRTAP10-11 MUTATED`
TCGA-A6-5660 TCGA-A6-6781 TCGA-AA-A010 TCGA-DM-A0XF TCGA-G4-6588 TCGA-CL-5918 
       29.19        19.66        34.98        38.20        26.17         7.17 

$`KRTAP10-11 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       24.43       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        35.80        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        6.97         4.73        78.12        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  KRTAP10-11 MUTATED KRTAP10-11 WILD-TYPE 
                7.17                 0.00 
  KRTAP10-11 MUTATED KRTAP10-11 WILD-TYPE 
               38.20               148.01 
  KRTAP10-11 MUTATED KRTAP10-11 WILD-TYPE 
               27.68                20.12 
[1] "7.2 - 38.2 (27.7)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.1"
D1326V2, continuous
D1326V3, binary
                      cls
clus                     0   1
  KRTAP10-11 MUTATED     5   1
  KRTAP10-11 WILD-TYPE 361 118
[1] "tbl2"
                      cls
clus                   [,1] [,2]
  KRTAP10-11 MUTATED      5    1
  KRTAP10-11 WILD-TYPE  361  118
        clus
vv       KRTAP10-11 MUTATED KRTAP10-11 WILD-TYPE
  COLON                   5                  361
  RECTUM                  1                  118
[1] 2 2
[1] FALSE
                      vv
clus                   STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KRTAP10-11 MUTATED         0        0        0         2         1         0
  KRTAP10-11 WILD-TYPE      91        1       32       136         9         1
                      vv
clus                   STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KRTAP10-11 MUTATED           0          0          0          3        0
  KRTAP10-11 WILD-TYPE        24         11         59         39       48
                      vv
clus                   STAGE IVA STAGE IVB
  KRTAP10-11 MUTATED           0         0
  KRTAP10-11 WILD-TYPE        18         1
D1326V4, multiclass
            clus
vv           KRTAP10-11 MUTATED KRTAP10-11 WILD-TYPE
  STAGE I                     0                   91
  STAGE IA                    0                    1
  STAGE II                    0                   32
  STAGE IIA                   2                  136
  STAGE IIB                   1                    9
  STAGE IIC                   0                    1
  STAGE III                   0                   24
  STAGE IIIA                  0                   11
  STAGE IIIB                  0                   59
  STAGE IIIC                  3                   39
  STAGE IV                    0                   48
  STAGE IVA                   0                   18
  STAGE IVB                   0                    1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                      vv
clus                    T1  T2  T3  T4
  KRTAP10-11 MUTATED     0   0   4   2
  KRTAP10-11 WILD-TYPE  17  92 325  48
D1326V5, multiclass
    clus
vv   KRTAP10-11 MUTATED KRTAP10-11 WILD-TYPE
  T1                  0                   17
  T2                  0                   92
  T3                  4                  325
  T4                  2                   48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                      vv
clus                    N0  N1  N2
  KRTAP10-11 MUTATED     3   1   2
  KRTAP10-11 WILD-TYPE 284 112  85
D1326V6, multiclass
    clus
vv   KRTAP10-11 MUTATED KRTAP10-11 WILD-TYPE
  N0                  3                  284
  N1                  1                  112
  N2                  2                   85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1326V7, binary
                      cls
clus                     0   1
  KRTAP10-11 MUTATED     4   0
  KRTAP10-11 WILD-TYPE 371  65
[1] "tbl2"
                      cls
clus                   [,1] [,2]
  KRTAP10-11 MUTATED      4    0
  KRTAP10-11 WILD-TYPE  371   65
   clus
vv  KRTAP10-11 MUTATED KRTAP10-11 WILD-TYPE
  0                  4                  371
  1                  0                   65
[1] 2 2
[1] FALSE
D1326V8, binary
                      cls
clus                     0   1
  KRTAP10-11 MUTATED     4   2
  KRTAP10-11 WILD-TYPE 221 262
[1] "tbl2"
                      cls
clus                   [,1] [,2]
  KRTAP10-11 MUTATED      4    2
  KRTAP10-11 WILD-TYPE  221  262
        clus
vv       KRTAP10-11 MUTATED KRTAP10-11 WILD-TYPE
  FEMALE                  4                  221
  MALE                    2                  262
[1] 2 2
[1] FALSE
D1326V9, binary
                      cls
clus                     0   1
  KRTAP10-11 MUTATED     5   0
  KRTAP10-11 WILD-TYPE 345  22
[1] "tbl2"
                      cls
clus                   [,1] [,2]
  KRTAP10-11 MUTATED      5    0
  KRTAP10-11 WILD-TYPE  345   22
     clus
vv    KRTAP10-11 MUTATED KRTAP10-11 WILD-TYPE
  NO                   5                  345
  YES                  0                   22
[1] 2 2
[1] FALSE
                      vv
clus                   COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  KRTAP10-11 MUTATED                      3                             1
  KRTAP10-11 WILD-TYPE                  312                            46
                      vv
clus                   RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  KRTAP10-11 MUTATED                       1                              0
  KRTAP10-11 WILD-TYPE                   105                             10
D1326V10, multiclass
                                clus
vv                               KRTAP10-11 MUTATED KRTAP10-11 WILD-TYPE
  COLON ADENOCARCINOMA                            3                  312
  COLON MUCINOUS ADENOCARCINOMA                   1                   46
  RECTAL ADENOCARCINOMA                           1                  105
  RECTAL MUCINOUS ADENOCARCINOMA                  0                   10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                      vv
clus                    R0  R1  R2  RX
  KRTAP10-11 MUTATED     3   0   0   1
  KRTAP10-11 WILD-TYPE 342   4  31  24
D1326V11, multiclass
    clus
vv   KRTAP10-11 MUTATED KRTAP10-11 WILD-TYPE
  R0                  3                  342
  R1                  0                    4
  R2                  0                   31
  RX                  1                   24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1326V12, continuous
                      vv
clus                   AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KRTAP10-11 MUTATED                                  0     0
  KRTAP10-11 WILD-TYPE                                1    11
                      vv
clus                   BLACK OR AFRICAN AMERICAN WHITE
  KRTAP10-11 MUTATED                           1     4
  KRTAP10-11 WILD-TYPE                        21   222
D1326V13, multiclass
                                  clus
vv                                 KRTAP10-11 MUTATED KRTAP10-11 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                  0                    1
  ASIAN                                             0                   11
  BLACK OR AFRICAN AMERICAN                         1                   21
  WHITE                                             4                  222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1327) Variable = GTF3C1 MUTATION ANALYSIS
D1327V1, survival
                  sevent
clus2                0   1
  GTF3C1 MUTATED    28   2
  GTF3C1 WILD-TYPE 350  91
  GTF3C1 MUTATED GTF3C1 WILD-TYPE 
              30              441 
  GTF3C1 MUTATED GTF3C1 WILD-TYPE 
               2               91 
$`GTF3C1 MUTATED`
TCGA-A6-3809 TCGA-A6-5665 TCGA-A6-6653 TCGA-A6-6780 TCGA-AA-3561 TCGA-AA-3663 
       32.75        22.06        24.39        20.12        13.94         6.97 
TCGA-AA-3672 TCGA-AA-3713 TCGA-AA-3837 TCGA-AA-3864 TCGA-AA-3870 TCGA-AA-3949 
        0.92        19.04        38.99        53.00        29.98        26.01 
TCGA-AA-A00A TCGA-AA-A010 TCGA-AD-5900 TCGA-AY-5543 TCGA-CK-5916 TCGA-CM-6162 
       38.04        34.98         0.07        33.01        21.14        12.00 
TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6680 TCGA-D5-6540 TCGA-D5-6928 TCGA-F4-6570 
       14.04        12.95        12.03        16.14        11.64         6.18 
TCGA-G4-6588 TCGA-G4-6628 TCGA-AF-2693 TCGA-AG-A002 TCGA-AG-A020 TCGA-F5-6702 
       26.17        79.69        19.10        20.98        10.98        28.57 

$`GTF3C1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 
       24.16        21.76        24.69        23.87        19.66        20.28 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
        7.04         3.02         1.02        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3655 
       29.95        23.01        20.98        19.99        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
       78.08         6.05        54.02         2.01        14.01        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       15.95        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        31.07        30.05        17.03        24.03        27.02 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       13.94        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       39.98        18.05        40.96        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6197 
        0.20        14.50        27.09        16.31         0.95        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       49.08        51.32         9.99        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 
       15.02        15.02        17.03        15.02         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       11.01        13.05        11.08        11.08        11.01        10.06 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       17.13        12.49        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6930 
       12.43        14.30         9.04         9.44         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
        8.61        31.96        35.74        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 
       13.78        35.80        91.79        46.75        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       43.04        13.55        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A025 TCGA-AG-A026 
        9.07        12.00        70.03        64.01        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6811 TCGA-F5-6812 
       18.28         9.96        49.51        31.30        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  GTF3C1 MUTATED GTF3C1 WILD-TYPE 
            0.07             0.00 
  GTF3C1 MUTATED GTF3C1 WILD-TYPE 
           79.69           148.01 
  GTF3C1 MUTATED GTF3C1 WILD-TYPE 
           20.55            20.19 
[1] "0.1 - 79.7 (20.6)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "2.6"
D1327V2, continuous
D1327V3, binary
                  cls
clus                 0   1
  GTF3C1 MUTATED    26   3
  GTF3C1 WILD-TYPE 340 116
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GTF3C1 MUTATED     26    3
  GTF3C1 WILD-TYPE  340  116
        clus
vv       GTF3C1 MUTATED GTF3C1 WILD-TYPE
  COLON              26              340
  RECTUM              3              116
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GTF3C1 MUTATED         8        0        2         9         2         0
  GTF3C1 WILD-TYPE      83        1       30       129         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GTF3C1 MUTATED           2          0          3          0        2
  GTF3C1 WILD-TYPE        22         11         56         42       46
                  vv
clus               STAGE IVA STAGE IVB
  GTF3C1 MUTATED           2         0
  GTF3C1 WILD-TYPE        16         1
D1327V4, multiclass
            clus
vv           GTF3C1 MUTATED GTF3C1 WILD-TYPE
  STAGE I                 8               83
  STAGE IA                0                1
  STAGE II                2               30
  STAGE IIA               9              129
  STAGE IIB               2                8
  STAGE IIC               0                1
  STAGE III               2               22
  STAGE IIIA              0               11
  STAGE IIIB              3               56
  STAGE IIIC              0               42
  STAGE IV                2               46
  STAGE IVA               2               16
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  GTF3C1 MUTATED     1   7  20   2
  GTF3C1 WILD-TYPE  16  85 309  48
D1327V5, multiclass
    clus
vv   GTF3C1 MUTATED GTF3C1 WILD-TYPE
  T1              1               16
  T2              7               85
  T3             20              309
  T4              2               48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  GTF3C1 MUTATED    22   6   2
  GTF3C1 WILD-TYPE 265 107  85
D1327V6, multiclass
    clus
vv   GTF3C1 MUTATED GTF3C1 WILD-TYPE
  N0             22              265
  N1              6              107
  N2              2               85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1327V7, binary
                  cls
clus                 0   1
  GTF3C1 MUTATED    23   4
  GTF3C1 WILD-TYPE 352  61
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GTF3C1 MUTATED     23    4
  GTF3C1 WILD-TYPE  352   61
   clus
vv  GTF3C1 MUTATED GTF3C1 WILD-TYPE
  0             23              352
  1              4               61
[1] 2 2
[1] FALSE
D1327V8, binary
                  cls
clus                 0   1
  GTF3C1 MUTATED    14  16
  GTF3C1 WILD-TYPE 211 248
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GTF3C1 MUTATED     14   16
  GTF3C1 WILD-TYPE  211  248
        clus
vv       GTF3C1 MUTATED GTF3C1 WILD-TYPE
  FEMALE             14              211
  MALE               16              248
[1] 2 2
[1] FALSE
D1327V9, binary
                  cls
clus                 0   1
  GTF3C1 MUTATED    26   1
  GTF3C1 WILD-TYPE 324  21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GTF3C1 MUTATED     26    1
  GTF3C1 WILD-TYPE  324   21
     clus
vv    GTF3C1 MUTATED GTF3C1 WILD-TYPE
  NO              26              324
  YES              1               21
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  GTF3C1 MUTATED                     18                             8
  GTF3C1 WILD-TYPE                  297                            39
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  GTF3C1 MUTATED                       2                              1
  GTF3C1 WILD-TYPE                   104                              9
D1327V10, multiclass
                                clus
vv                               GTF3C1 MUTATED GTF3C1 WILD-TYPE
  COLON ADENOCARCINOMA                       18              297
  COLON MUCINOUS ADENOCARCINOMA               8               39
  RECTAL ADENOCARCINOMA                       2              104
  RECTAL MUCINOUS ADENOCARCINOMA              1                9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  GTF3C1 MUTATED    25   0   1   1
  GTF3C1 WILD-TYPE 320   4  30  24
D1327V11, multiclass
    clus
vv   GTF3C1 MUTATED GTF3C1 WILD-TYPE
  R0             25              320
  R1              0                4
  R2              1               30
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1327V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GTF3C1 MUTATED                                  0     0
  GTF3C1 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  GTF3C1 MUTATED                           1    17
  GTF3C1 WILD-TYPE                        21   209
D1327V13, multiclass
                                  clus
vv                                 GTF3C1 MUTATED GTF3C1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                        17              209
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1328) Variable = WAC MUTATION ANALYSIS
D1328V1, survival
               sevent
clus2             0   1
  WAC MUTATED    10   4
  WAC WILD-TYPE 368  89
  WAC MUTATED WAC WILD-TYPE 
           14           457 
  WAC MUTATED WAC WILD-TYPE 
            4            89 
$`WAC MUTATED`
TCGA-A6-5659 TCGA-A6-6141 TCGA-AA-3516 TCGA-AA-3977 TCGA-AD-6901 TCGA-AY-6197 
       30.44         8.38        13.02        25.02        22.42        21.44 
TCGA-AZ-6607 TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-4746 TCGA-CM-5868 TCGA-AG-3892 
        3.19        12.76        10.06        37.02        17.03        13.02 
TCGA-AG-A036 TCGA-EI-6507 
      117.11        19.96 

$`WAC WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 
       22.06        32.71        27.09        22.52        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
       63.98         6.97         1.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        0.72         5.79        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4315 
       27.09        16.31         0.95        33.01        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
       11.74         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.07        12.20        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4752 
        1.91       124.27        23.05        20.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
        5.03        15.02        15.02        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       17.95        36.95        17.03        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       61.97        41.00        38.04        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
        0.49        20.55        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  WAC MUTATED WAC WILD-TYPE 
         3.19          0.00 
  WAC MUTATED WAC WILD-TYPE 
       117.11        148.01 
  WAC MUTATED WAC WILD-TYPE 
       18.495        20.280 
[1] "3.2 - 117.1 (18.5)" "0.0 - 148.0 (20.3)"
[1] "hr=" "1.6"
D1328V2, continuous
D1328V3, binary
               cls
clus              0   1
  WAC MUTATED    12   3
  WAC WILD-TYPE 354 116
[1] "tbl2"
               cls
clus            [,1] [,2]
  WAC MUTATED     12    3
  WAC WILD-TYPE  354  116
        clus
vv       WAC MUTATED WAC WILD-TYPE
  COLON           12           354
  RECTUM           3           116
[1] 2 2
[1] FALSE
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  WAC MUTATED         3        0        0         6         0         0
  WAC WILD-TYPE      88        1       32       132        10         1
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  WAC MUTATED           2          0          0          0        1         1
  WAC WILD-TYPE        22         11         59         42       47        17
               vv
clus            STAGE IVB
  WAC MUTATED           0
  WAC WILD-TYPE         1
D1328V4, multiclass
            clus
vv           WAC MUTATED WAC WILD-TYPE
  STAGE I              3            88
  STAGE IA             0             1
  STAGE II             0            32
  STAGE IIA            6           132
  STAGE IIB            0            10
  STAGE IIC            0             1
  STAGE III            2            22
  STAGE IIIA           0            11
  STAGE IIIB           0            59
  STAGE IIIC           0            42
  STAGE IV             1            47
  STAGE IVA            1            17
  STAGE IVB            0             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  WAC MUTATED     1   3   9   2
  WAC WILD-TYPE  16  89 320  48
D1328V5, multiclass
    clus
vv   WAC MUTATED WAC WILD-TYPE
  T1           1            16
  T2           3            89
  T3           9           320
  T4           2            48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2
  WAC MUTATED    11   1   3
  WAC WILD-TYPE 276 112  84
D1328V6, multiclass
    clus
vv   WAC MUTATED WAC WILD-TYPE
  N0          11           276
  N1           1           112
  N2           3            84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1328V7, binary
               cls
clus              0   1
  WAC MUTATED    10   2
  WAC WILD-TYPE 365  63
[1] "tbl2"
               cls
clus            [,1] [,2]
  WAC MUTATED     10    2
  WAC WILD-TYPE  365   63
   clus
vv  WAC MUTATED WAC WILD-TYPE
  0          10           365
  1           2            63
[1] 2 2
[1] FALSE
D1328V8, binary
               cls
clus              0   1
  WAC MUTATED     4  11
  WAC WILD-TYPE 221 253
[1] "tbl2"
               cls
clus            [,1] [,2]
  WAC MUTATED      4   11
  WAC WILD-TYPE  221  253
        clus
vv       WAC MUTATED WAC WILD-TYPE
  FEMALE           4           221
  MALE            11           253
[1] 2 2
[1] FALSE
D1328V9, binary
               cls
clus              0   1
  WAC MUTATED    13   1
  WAC WILD-TYPE 337  21
[1] "tbl2"
               cls
clus            [,1] [,2]
  WAC MUTATED     13    1
  WAC WILD-TYPE  337   21
     clus
vv    WAC MUTATED WAC WILD-TYPE
  NO           13           337
  YES           1            21
[1] 2 2
[1] FALSE
               vv
clus            COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  WAC MUTATED                     10                             2
  WAC WILD-TYPE                  305                            45
               vv
clus            RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  WAC MUTATED                       3                              0
  WAC WILD-TYPE                   103                             10
D1328V10, multiclass
                                clus
vv                               WAC MUTATED WAC WILD-TYPE
  COLON ADENOCARCINOMA                    10           305
  COLON MUCINOUS ADENOCARCINOMA            2            45
  RECTAL ADENOCARCINOMA                    3           103
  RECTAL MUCINOUS ADENOCARCINOMA           0            10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             R0  R1  R2  RX
  WAC MUTATED     8   0   0   2
  WAC WILD-TYPE 337   4  31  23
D1328V11, multiclass
    clus
vv   WAC MUTATED WAC WILD-TYPE
  R0           8           337
  R1           0             4
  R2           0            31
  RX           2            23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1328V12, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  WAC MUTATED                                  0     2
  WAC WILD-TYPE                                1     9
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  WAC MUTATED                           2     6
  WAC WILD-TYPE                        20   220
D1328V13, multiclass
                                  clus
vv                                 WAC MUTATED WAC WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      2             9
  BLACK OR AFRICAN AMERICAN                  2            20
  WHITE                                      6           220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1329) Variable = NFKBIE MUTATION ANALYSIS
D1329V1, survival
                  sevent
clus2                0   1
  NFKBIE MUTATED     3   1
  NFKBIE WILD-TYPE 375  92
  NFKBIE MUTATED NFKBIE WILD-TYPE 
               4              467 
  NFKBIE MUTATED NFKBIE WILD-TYPE 
               1               92 
$`NFKBIE MUTATED`
TCGA-AA-3697 TCGA-AA-A010 TCGA-CA-6717 TCGA-DY-A1DG 
       85.05        34.98        12.76        51.48 

$`NFKBIE WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       19.00        36.00         5.03        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.20        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       57.24        24.13        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  NFKBIE MUTATED NFKBIE WILD-TYPE 
           12.76             0.00 
  NFKBIE MUTATED NFKBIE WILD-TYPE 
           85.05           148.01 
  NFKBIE MUTATED NFKBIE WILD-TYPE 
           43.23            20.12 
[1] "12.8 - 85.0 (43.2)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.4"
D1329V2, continuous
D1329V3, binary
                  cls
clus                 0   1
  NFKBIE MUTATED     3   1
  NFKBIE WILD-TYPE 363 118
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NFKBIE MUTATED      3    1
  NFKBIE WILD-TYPE  363  118
        clus
vv       NFKBIE MUTATED NFKBIE WILD-TYPE
  COLON               3              363
  RECTUM              1              118
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NFKBIE MUTATED         0        0        0         1         1         0
  NFKBIE WILD-TYPE      91        1       32       137         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NFKBIE MUTATED           1          0          0          0        0
  NFKBIE WILD-TYPE        23         11         59         42       48
                  vv
clus               STAGE IVA STAGE IVB
  NFKBIE MUTATED           1         0
  NFKBIE WILD-TYPE        17         1
D1329V4, multiclass
            clus
vv           NFKBIE MUTATED NFKBIE WILD-TYPE
  STAGE I                 0               91
  STAGE IA                0                1
  STAGE II                0               32
  STAGE IIA               1              137
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               1               23
  STAGE IIIA              0               11
  STAGE IIIB              0               59
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               1               17
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  NFKBIE MUTATED     0   0   3   1
  NFKBIE WILD-TYPE  17  92 326  49
D1329V5, multiclass
    clus
vv   NFKBIE MUTATED NFKBIE WILD-TYPE
  T1              0               17
  T2              0               92
  T3              3              326
  T4              1               49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  NFKBIE MUTATED     3   1   0
  NFKBIE WILD-TYPE 284 112  87
D1329V6, multiclass
    clus
vv   NFKBIE MUTATED NFKBIE WILD-TYPE
  N0              3              284
  N1              1              112
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1329V7, binary
                  cls
clus                 0   1
  NFKBIE MUTATED     3   1
  NFKBIE WILD-TYPE 372  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NFKBIE MUTATED      3    1
  NFKBIE WILD-TYPE  372   64
   clus
vv  NFKBIE MUTATED NFKBIE WILD-TYPE
  0              3              372
  1              1               64
[1] 2 2
[1] FALSE
D1329V8, binary
                  cls
clus                 0   1
  NFKBIE MUTATED     1   3
  NFKBIE WILD-TYPE 224 261
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NFKBIE MUTATED      1    3
  NFKBIE WILD-TYPE  224  261
        clus
vv       NFKBIE MUTATED NFKBIE WILD-TYPE
  FEMALE              1              224
  MALE                3              261
[1] 2 2
[1] FALSE
D1329V9, binary
                  cls
clus                 0   1
  NFKBIE MUTATED     3   0
  NFKBIE WILD-TYPE 347  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NFKBIE MUTATED      3    0
  NFKBIE WILD-TYPE  347   22
     clus
vv    NFKBIE MUTATED NFKBIE WILD-TYPE
  NO               3              347
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  NFKBIE MUTATED                      2                             1
  NFKBIE WILD-TYPE                  313                            46
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  NFKBIE MUTATED                       1                              0
  NFKBIE WILD-TYPE                   105                             10
D1329V10, multiclass
                                clus
vv                               NFKBIE MUTATED NFKBIE WILD-TYPE
  COLON ADENOCARCINOMA                        2              313
  COLON MUCINOUS ADENOCARCINOMA               1               46
  RECTAL ADENOCARCINOMA                       1              105
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  NFKBIE MUTATED     2   0   0   1
  NFKBIE WILD-TYPE 343   4  31  24
D1329V11, multiclass
    clus
vv   NFKBIE MUTATED NFKBIE WILD-TYPE
  R0              2              343
  R1              0                4
  R2              0               31
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1329V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NFKBIE MUTATED                                  0     1
  NFKBIE WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  NFKBIE MUTATED                           0     1
  NFKBIE WILD-TYPE                        22   225
D1329V13, multiclass
[1] "Remove cluster labels:" "NFKBIE MUTATED"        
clus
  NFKBIE MUTATED NFKBIE WILD-TYPE 
               2              258 
      TCGA-A6-2671       TCGA-A6-2672       TCGA-A6-2674       TCGA-A6-2676 
"NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" 
      TCGA-A6-2677       TCGA-A6-2678       TCGA-A6-2683       TCGA-A6-3807 
"NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" 
      TCGA-A6-3808       TCGA-A6-3809       TCGA-A6-3810       TCGA-A6-4105 
"NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" 
      TCGA-A6-5656       TCGA-A6-5657       TCGA-A6-5659       TCGA-A6-5660 
"NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" 
      TCGA-A6-5661       TCGA-A6-5662       TCGA-A6-5664       TCGA-A6-5665 
"NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" 
      TCGA-A6-5666       TCGA-A6-6137       TCGA-A6-6138       TCGA-A6-6141 
"NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" 
      TCGA-A6-6142       TCGA-A6-6648       TCGA-A6-6649       TCGA-A6-6651 
"NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" 
      TCGA-A6-6652       TCGA-A6-6653       TCGA-A6-6654       TCGA-A6-6780 
"NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" 
      TCGA-A6-6781       TCGA-A6-6782       TCGA-AD-5900       TCGA-AD-6548 
"NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" 
      TCGA-AD-6888       TCGA-AD-6889       TCGA-AD-6890       TCGA-AD-6895 
"NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" 
      TCGA-AD-6899       TCGA-AD-6901       TCGA-AD-6963       TCGA-AD-6964 
"NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" 
      TCGA-AD-6965       TCGA-AU-3779       TCGA-AU-6004       TCGA-AY-4070 
"NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" 
      TCGA-AY-4071       TCGA-AY-5543       TCGA-AY-6196       TCGA-AY-6197 
"NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" 
      TCGA-AY-6386       TCGA-AZ-4315       TCGA-AZ-4323       TCGA-AZ-4616 
"NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" 
      TCGA-AZ-4681       TCGA-AZ-4682       TCGA-AZ-5403       TCGA-AZ-5407 
"NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" 
      TCGA-AZ-6598       TCGA-AZ-6599       TCGA-AZ-6600       TCGA-AZ-6601 
"NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" 
      TCGA-AZ-6603       TCGA-AZ-6605       TCGA-AZ-6606       TCGA-AZ-6607 
"NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" 
      TCGA-AZ-6608       TCGA-CA-5254       TCGA-CA-5255       TCGA-CA-5796 
"NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" 
      TCGA-CA-5797       TCGA-CA-6715       TCGA-CA-6716       TCGA-CA-6718 
"NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" 
      TCGA-CA-6719       TCGA-CK-4947       TCGA-CK-4948       TCGA-CK-4950 
"NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" 
      TCGA-CK-4952       TCGA-CK-5912       TCGA-CK-5913       TCGA-CK-5914 
"NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" 
      TCGA-CK-5915       TCGA-CK-5916       TCGA-CK-6746       TCGA-CK-6747 
"NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" 
      TCGA-CK-6748       TCGA-CK-6751       TCGA-CM-4743       TCGA-CM-4744 
"NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" 
      TCGA-CM-4746       TCGA-CM-4747       TCGA-CM-4752       TCGA-CM-5341 
"NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" 
      TCGA-CM-5344       TCGA-CM-5348       TCGA-CM-5349       TCGA-CM-5860 
"NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" 
      TCGA-CM-5861       TCGA-CM-5862       TCGA-CM-5863       TCGA-CM-5864 
"NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" 
      TCGA-CM-5868       TCGA-CM-6161       TCGA-CM-6162       TCGA-CM-6163 
"NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" 
      TCGA-CM-6164       TCGA-CM-6165       TCGA-CM-6166       TCGA-CM-6167 
"NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" 
      TCGA-CM-6168       TCGA-CM-6169       TCGA-CM-6170       TCGA-CM-6171 
"NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" 
      TCGA-CM-6172       TCGA-CM-6674       TCGA-CM-6675       TCGA-CM-6676 
"NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" 
      TCGA-CM-6677       TCGA-CM-6678       TCGA-CM-6679       TCGA-CM-6680 
"NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" 
      TCGA-D5-5537       TCGA-D5-5538       TCGA-D5-5539       TCGA-D5-5540 
"NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" 
      TCGA-D5-5541       TCGA-D5-6529       TCGA-D5-6532       TCGA-D5-6533 
"NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" 
      TCGA-D5-6534       TCGA-D5-6535       TCGA-D5-6536       TCGA-D5-6537 
"NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" 
      TCGA-D5-6538       TCGA-D5-6539       TCGA-D5-6540       TCGA-D5-6541 
"NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" 
      TCGA-D5-6898       TCGA-D5-6920       TCGA-D5-6922       TCGA-D5-6923 
"NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" 
      TCGA-D5-6924       TCGA-D5-6926       TCGA-D5-6927       TCGA-D5-6928 
"NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" 
      TCGA-D5-6929       TCGA-D5-6930       TCGA-D5-6931       TCGA-D5-6932 
"NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" 
      TCGA-D5-7000       TCGA-DM-A0X9       TCGA-DM-A0XD       TCGA-DM-A0XF 
"NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" 
      TCGA-DM-A1D0       TCGA-DM-A1D4       TCGA-DM-A1D6       TCGA-DM-A1D7 
"NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" 
      TCGA-DM-A1D8       TCGA-DM-A1D9       TCGA-DM-A1DA       TCGA-DM-A1DB 
"NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" 
      TCGA-DM-A1HA       TCGA-DM-A1HB       TCGA-DM-A282       TCGA-DM-A285 
"NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" 
      TCGA-DM-A28C       TCGA-DM-A28E       TCGA-DM-A28F       TCGA-DM-A28G 
"NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" 
      TCGA-DM-A28H       TCGA-DM-A28K       TCGA-F4-6459       TCGA-F4-6460 
"NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" 
      TCGA-F4-6569       TCGA-F4-6570       TCGA-F4-6703       TCGA-F4-6704 
"NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" 
      TCGA-F4-6805       TCGA-F4-6806       TCGA-F4-6807       TCGA-F4-6808 
"NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" 
      TCGA-F4-6809       TCGA-F4-6854       TCGA-F4-6855       TCGA-F4-6856 
"NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" 
      TCGA-G4-6293       TCGA-G4-6299       TCGA-G4-6303       TCGA-G4-6304 
"NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" 
      TCGA-G4-6306       TCGA-G4-6307       TCGA-G4-6309       TCGA-G4-6310 
"NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" 
      TCGA-G4-6315       TCGA-G4-6317       TCGA-G4-6321       TCGA-G4-6323 
"NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" 
      TCGA-G4-6586       TCGA-G4-6588       TCGA-G4-6625       TCGA-G4-6626 
"NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" 
      TCGA-G4-6628       TCGA-AF-2687       TCGA-AF-2689       TCGA-AF-2691 
"NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" 
      TCGA-AF-2692       TCGA-AF-2693       TCGA-AF-3400       TCGA-AF-3913 
"NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" 
      TCGA-AF-4110       TCGA-AF-5654       TCGA-AF-6136       TCGA-AF-6655 
"NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" 
      TCGA-AF-6672       TCGA-AH-6544       TCGA-AH-6547       TCGA-AH-6549 
"NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" 
      TCGA-AH-6643       TCGA-AH-6644       TCGA-CI-6619       TCGA-CI-6620 
"NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" 
      TCGA-CI-6621       TCGA-CI-6622       TCGA-CI-6624       TCGA-CL-5917 
"NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" 
      TCGA-CL-5918       TCGA-DC-5337       TCGA-DC-5869       TCGA-DC-6155 
"NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" 
      TCGA-DC-6157       TCGA-DC-6158       TCGA-DC-6160       TCGA-DC-6681 
"NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" 
      TCGA-DC-6682       TCGA-DC-6683       TCGA-DT-5265       TCGA-DY-A0XA 
"NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" 
      TCGA-DY-A1DC       TCGA-DY-A1DD       TCGA-DY-A1DF       TCGA-DY-A1H8 
"NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" 
      TCGA-EF-5830       TCGA-EI-6506       TCGA-EI-6507       TCGA-EI-6508 
"NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" 
      TCGA-EI-6510       TCGA-F5-6464       TCGA-F5-6465       TCGA-F5-6571 
"NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" 
      TCGA-F5-6702       TCGA-F5-6811       TCGA-F5-6812       TCGA-F5-6813 
"NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" 
      TCGA-G5-6235       TCGA-G5-6641 
"NFKBIE WILD-TYPE" "NFKBIE WILD-TYPE" 

Clustering(1330) Variable = RRM2B MUTATION ANALYSIS
D1330V1, survival
                 sevent
clus2               0   1
  RRM2B MUTATED     2   3
  RRM2B WILD-TYPE 376  90
  RRM2B MUTATED RRM2B WILD-TYPE 
              5             466 
  RRM2B MUTATED RRM2B WILD-TYPE 
              3              90 
$`RRM2B MUTATED`
TCGA-AA-3510 TCGA-AY-6197 TCGA-CA-6718 TCGA-D5-6537 TCGA-DM-A1DB 
       63.98        21.44        10.06         4.80        44.32 

$`RRM2B WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        33.01        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.20        12.76        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6538 
       18.25         1.32        43.27        15.12        17.85        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
      140.38         7.50       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  RRM2B MUTATED RRM2B WILD-TYPE 
            4.8             0.0 
  RRM2B MUTATED RRM2B WILD-TYPE 
          63.98          148.01 
  RRM2B MUTATED RRM2B WILD-TYPE 
         21.440          20.155 
[1] "4.8 - 64.0 (21.4)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "2.6"
D1330V2, continuous
D1330V3, binary
                 cls
clus                0   1
  RRM2B MUTATED     5   0
  RRM2B WILD-TYPE 361 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RRM2B MUTATED      5    0
  RRM2B WILD-TYPE  361  119
        clus
vv       RRM2B MUTATED RRM2B WILD-TYPE
  COLON              5             361
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RRM2B MUTATED         0        0        1         3         0         0
  RRM2B WILD-TYPE      91        1       31       135        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RRM2B MUTATED           0          0          1          0        0         0
  RRM2B WILD-TYPE        24         11         58         42       48        18
                 vv
clus              STAGE IVB
  RRM2B MUTATED           0
  RRM2B WILD-TYPE         1
D1330V4, multiclass
            clus
vv           RRM2B MUTATED RRM2B WILD-TYPE
  STAGE I                0              91
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              3             135
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  RRM2B MUTATED     0   0   5   0
  RRM2B WILD-TYPE  17  92 324  50
D1330V5, multiclass
    clus
vv   RRM2B MUTATED RRM2B WILD-TYPE
  T1             0              17
  T2             0              92
  T3             5             324
  T4             0              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  RRM2B MUTATED     4   1   0
  RRM2B WILD-TYPE 283 112  87
D1330V6, multiclass
    clus
vv   RRM2B MUTATED RRM2B WILD-TYPE
  N0             4             283
  N1             1             112
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1330V7, binary
                 cls
clus                0   1
  RRM2B MUTATED     3   0
  RRM2B WILD-TYPE 372  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RRM2B MUTATED      3    0
  RRM2B WILD-TYPE  372   65
   clus
vv  RRM2B MUTATED RRM2B WILD-TYPE
  0             3             372
  1             0              65
[1] 2 2
[1] FALSE
D1330V8, binary
                 cls
clus                0   1
  RRM2B MUTATED     0   5
  RRM2B WILD-TYPE 225 259
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RRM2B MUTATED      0    5
  RRM2B WILD-TYPE  225  259
        clus
vv       RRM2B MUTATED RRM2B WILD-TYPE
  FEMALE             0             225
  MALE               5             259
[1] 2 2
[1] FALSE
D1330V9, binary
                 cls
clus                0   1
  RRM2B MUTATED     4   0
  RRM2B WILD-TYPE 346  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RRM2B MUTATED      4    0
  RRM2B WILD-TYPE  346   22
     clus
vv    RRM2B MUTATED RRM2B WILD-TYPE
  NO              4             346
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  RRM2B MUTATED                      5                             0
  RRM2B WILD-TYPE                  310                            47
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  RRM2B MUTATED                       0                              0
  RRM2B WILD-TYPE                   106                             10
D1330V10, multiclass
                                clus
vv                               RRM2B MUTATED RRM2B WILD-TYPE
  COLON ADENOCARCINOMA                       5             310
  COLON MUCINOUS ADENOCARCINOMA              0              47
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  RRM2B MUTATED     3   0   0   1
  RRM2B WILD-TYPE 342   4  31  24
D1330V11, multiclass
    clus
vv   RRM2B MUTATED RRM2B WILD-TYPE
  R0             3             342
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1330V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RRM2B MUTATED                                  0     1
  RRM2B WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  RRM2B MUTATED                           0     3
  RRM2B WILD-TYPE                        22   223
D1330V13, multiclass
                                  clus
vv                                 RRM2B MUTATED RRM2B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        3             223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1331) Variable = KRTAP20-1 MUTATION ANALYSIS
D1331V1, survival
                     sevent
clus2                   0   1
  KRTAP20-1 MUTATED     3   0
  KRTAP20-1 WILD-TYPE 375  93
  KRTAP20-1 MUTATED KRTAP20-1 WILD-TYPE 
                  3                 468 
  KRTAP20-1 MUTATED KRTAP20-1 WILD-TYPE 
                  0                  93 
$`KRTAP20-1 MUTATED`
TCGA-A6-6137 TCGA-D5-6929 TCGA-EI-6510 
       27.09         4.80        18.28 

$`KRTAP20-1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        22.06        32.71        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
        9.44        11.64         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       20.55        19.96        20.91         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  KRTAP20-1 MUTATED KRTAP20-1 WILD-TYPE 
                4.8                 0.0 
  KRTAP20-1 MUTATED KRTAP20-1 WILD-TYPE 
              27.09              148.01 
  KRTAP20-1 MUTATED KRTAP20-1 WILD-TYPE 
             18.280              20.235 
[1] "4.8 - 27.1 (18.3)"  "0.0 - 148.0 (20.2)"
[1] "hr="     "3300000"
D1331V2, continuous
D1331V3, binary
                     cls
clus                    0   1
  KRTAP20-1 MUTATED     2   1
  KRTAP20-1 WILD-TYPE 364 118
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  KRTAP20-1 MUTATED      2    1
  KRTAP20-1 WILD-TYPE  364  118
        clus
vv       KRTAP20-1 MUTATED KRTAP20-1 WILD-TYPE
  COLON                  2                 364
  RECTUM                 1                 118
[1] 2 2
[1] FALSE
                     vv
clus                  STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KRTAP20-1 MUTATED         0        0        0         0         0         0
  KRTAP20-1 WILD-TYPE      91        1       32       138        10         1
                     vv
clus                  STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KRTAP20-1 MUTATED           0          0          1          0        1
  KRTAP20-1 WILD-TYPE        24         11         58         42       47
                     vv
clus                  STAGE IVA STAGE IVB
  KRTAP20-1 MUTATED           1         0
  KRTAP20-1 WILD-TYPE        17         1
D1331V4, multiclass
            clus
vv           KRTAP20-1 MUTATED KRTAP20-1 WILD-TYPE
  STAGE I                    0                  91
  STAGE IA                   0                   1
  STAGE II                   0                  32
  STAGE IIA                  0                 138
  STAGE IIB                  0                  10
  STAGE IIC                  0                   1
  STAGE III                  0                  24
  STAGE IIIA                 0                  11
  STAGE IIIB                 1                  58
  STAGE IIIC                 0                  42
  STAGE IV                   1                  47
  STAGE IVA                  1                  17
  STAGE IVB                  0                   1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                   T1  T2  T3  T4
  KRTAP20-1 MUTATED     0   1   2   0
  KRTAP20-1 WILD-TYPE  17  91 327  50
D1331V5, multiclass
    clus
vv   KRTAP20-1 MUTATED KRTAP20-1 WILD-TYPE
  T1                 0                  17
  T2                 1                  91
  T3                 2                 327
  T4                 0                  50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                   N0  N1  N2
  KRTAP20-1 MUTATED     1   2   0
  KRTAP20-1 WILD-TYPE 286 111  87
D1331V6, multiclass
    clus
vv   KRTAP20-1 MUTATED KRTAP20-1 WILD-TYPE
  N0                 1                 286
  N1                 2                 111
  N2                 0                  87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1331V7, binary
                     cls
clus                    0   1
  KRTAP20-1 MUTATED     1   1
  KRTAP20-1 WILD-TYPE 374  64
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  KRTAP20-1 MUTATED      1    1
  KRTAP20-1 WILD-TYPE  374   64
   clus
vv  KRTAP20-1 MUTATED KRTAP20-1 WILD-TYPE
  0                 1                 374
  1                 1                  64
[1] 2 2
[1] FALSE
D1331V8, binary
                     cls
clus                    0   1
  KRTAP20-1 MUTATED     2   1
  KRTAP20-1 WILD-TYPE 223 263
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  KRTAP20-1 MUTATED      2    1
  KRTAP20-1 WILD-TYPE  223  263
        clus
vv       KRTAP20-1 MUTATED KRTAP20-1 WILD-TYPE
  FEMALE                 2                 223
  MALE                   1                 263
[1] 2 2
[1] FALSE
D1331V9, binary
                     cls
clus                    0   1
  KRTAP20-1 MUTATED     2   0
  KRTAP20-1 WILD-TYPE 348  22
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  KRTAP20-1 MUTATED      2    0
  KRTAP20-1 WILD-TYPE  348   22
     clus
vv    KRTAP20-1 MUTATED KRTAP20-1 WILD-TYPE
  NO                  2                 348
  YES                 0                  22
[1] 2 2
[1] FALSE
                     vv
clus                  COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  KRTAP20-1 MUTATED                      2                             0
  KRTAP20-1 WILD-TYPE                  313                            47
                     vv
clus                  RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  KRTAP20-1 MUTATED                       1                              0
  KRTAP20-1 WILD-TYPE                   105                             10
D1331V10, multiclass
                                clus
vv                               KRTAP20-1 MUTATED KRTAP20-1 WILD-TYPE
  COLON ADENOCARCINOMA                           2                 313
  COLON MUCINOUS ADENOCARCINOMA                  0                  47
  RECTAL ADENOCARCINOMA                          1                 105
  RECTAL MUCINOUS ADENOCARCINOMA                 0                  10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                   R0  R1  R2  RX
  KRTAP20-1 MUTATED     2   0   0   0
  KRTAP20-1 WILD-TYPE 343   4  31  25
D1331V11, multiclass
[1] "Remove cluster labels:" "KRTAP20-1 MUTATED"     
clus
  KRTAP20-1 MUTATED KRTAP20-1 WILD-TYPE 
                  2                 403 
         TCGA-A6-2671          TCGA-A6-2672          TCGA-A6-2674 
"KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" 
         TCGA-A6-2676          TCGA-A6-2677          TCGA-A6-2678 
"KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" 
         TCGA-A6-2683          TCGA-A6-3807          TCGA-A6-3808 
"KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" 
         TCGA-A6-3809          TCGA-A6-3810          TCGA-A6-5657 
"KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" 
         TCGA-A6-5659          TCGA-A6-5661          TCGA-A6-5665 
"KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" 
         TCGA-A6-6781          TCGA-AA-3489          TCGA-AA-3492 
"KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" 
         TCGA-AA-3496          TCGA-AA-3502          TCGA-AA-3510 
"KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" 
         TCGA-AA-3511          TCGA-AA-3514          TCGA-AA-3517 
"KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" 
         TCGA-AA-3518          TCGA-AA-3519          TCGA-AA-3520 
"KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" 
         TCGA-AA-3521          TCGA-AA-3522          TCGA-AA-3524 
"KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" 
         TCGA-AA-3525          TCGA-AA-3526          TCGA-AA-3527 
"KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" 
         TCGA-AA-3529          TCGA-AA-3530          TCGA-AA-3531 
"KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" 
         TCGA-AA-3532          TCGA-AA-3534          TCGA-AA-3538 
"KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" 
         TCGA-AA-3542          TCGA-AA-3543          TCGA-AA-3544 
"KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" 
         TCGA-AA-3548          TCGA-AA-3549          TCGA-AA-3552 
"KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" 
         TCGA-AA-3553          TCGA-AA-3554          TCGA-AA-3555 
"KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" 
         TCGA-AA-3556          TCGA-AA-3558          TCGA-AA-3560 
"KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" 
         TCGA-AA-3561          TCGA-AA-3562          TCGA-AA-3655 
"KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" 
         TCGA-AA-3660          TCGA-AA-3662          TCGA-AA-3663 
"KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" 
         TCGA-AA-3664          TCGA-AA-3666          TCGA-AA-3667 
"KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" 
         TCGA-AA-3672          TCGA-AA-3673          TCGA-AA-3678 
"KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" 
         TCGA-AA-3679          TCGA-AA-3680          TCGA-AA-3681 
"KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" 
         TCGA-AA-3684          TCGA-AA-3685          TCGA-AA-3688 
"KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" 
         TCGA-AA-3692          TCGA-AA-3693          TCGA-AA-3695 
"KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" 
         TCGA-AA-3696          TCGA-AA-3697          TCGA-AA-3710 
"KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" 
         TCGA-AA-3712          TCGA-AA-3713          TCGA-AA-3715 
"KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" 
         TCGA-AA-3811          TCGA-AA-3812          TCGA-AA-3814 
"KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" 
         TCGA-AA-3815          TCGA-AA-3818          TCGA-AA-3819 
"KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" 
         TCGA-AA-3821          TCGA-AA-3831          TCGA-AA-3833 
"KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" 
         TCGA-AA-3837          TCGA-AA-3842          TCGA-AA-3844 
"KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" 
         TCGA-AA-3845          TCGA-AA-3846          TCGA-AA-3848 
"KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" 
         TCGA-AA-3850          TCGA-AA-3851          TCGA-AA-3852 
"KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" 
         TCGA-AA-3854          TCGA-AA-3855          TCGA-AA-3856 
"KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" 
         TCGA-AA-3858          TCGA-AA-3860          TCGA-AA-3861 
"KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" 
         TCGA-AA-3864          TCGA-AA-3866          TCGA-AA-3867 
"KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" 
         TCGA-AA-3869          TCGA-AA-3870          TCGA-AA-3872 
"KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" 
         TCGA-AA-3875          TCGA-AA-3877          TCGA-AA-3930 
"KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" 
         TCGA-AA-3939          TCGA-AA-3941          TCGA-AA-3947 
"KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" 
         TCGA-AA-3949          TCGA-AA-3950          TCGA-AA-3952 
"KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" 
         TCGA-AA-3955          TCGA-AA-3956          TCGA-AA-3968 
"KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" 
         TCGA-AA-3971          TCGA-AA-3972          TCGA-AA-3973 
"KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" 
         TCGA-AA-3975          TCGA-AA-3976          TCGA-AA-3979 
"KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" 
         TCGA-AA-3984          TCGA-AA-3986          TCGA-AA-3989 
"KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" 
         TCGA-AA-3994          TCGA-AA-A004          TCGA-AA-A00A 
"KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" 
         TCGA-AA-A00D          TCGA-AA-A00E          TCGA-AA-A00F 
"KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" 
         TCGA-AA-A00J          TCGA-AA-A00K          TCGA-AA-A00L 
"KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" 
         TCGA-AA-A00N          TCGA-AA-A00O          TCGA-AA-A00Q 
"KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" 
         TCGA-AA-A00R          TCGA-AA-A00U          TCGA-AA-A00W 
"KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" 
         TCGA-AA-A00Z          TCGA-AA-A010          TCGA-AA-A017 
"KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" 
         TCGA-AA-A01D          TCGA-AA-A01F          TCGA-AA-A01G 
"KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" 
         TCGA-AA-A01I          TCGA-AA-A01K          TCGA-AA-A01P 
"KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" 
         TCGA-AA-A01Q          TCGA-AA-A01R          TCGA-AA-A01S 
"KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" 
         TCGA-AA-A01T          TCGA-AA-A01V          TCGA-AA-A01X 
"KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" 
         TCGA-AA-A01Z          TCGA-AA-A022          TCGA-AA-A024 
"KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" 
         TCGA-AA-A029          TCGA-AA-A02F          TCGA-AA-A02H 
"KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" 
         TCGA-AA-A02J          TCGA-AA-A02K          TCGA-AA-A02O 
"KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" 
         TCGA-AA-A02W          TCGA-AA-A02Y          TCGA-AA-A03F 
"KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" 
         TCGA-AA-A03J          TCGA-AD-5900          TCGA-AD-6548 
"KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" 
         TCGA-AD-6888          TCGA-AU-3779          TCGA-AU-6004 
"KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" 
         TCGA-AY-4070          TCGA-AY-4071          TCGA-AY-5543 
"KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" 
         TCGA-AY-6196          TCGA-AY-6197          TCGA-AY-6386 
"KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" 
         TCGA-AZ-4315          TCGA-AZ-4681          TCGA-AZ-4682 
"KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" 
         TCGA-CA-5254          TCGA-CA-5255          TCGA-CA-5796 
"KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" 
         TCGA-CA-5797          TCGA-CA-6715          TCGA-CA-6716 
"KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" 
         TCGA-CA-6717          TCGA-CA-6718          TCGA-CA-6719 
"KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" 
         TCGA-CK-4947          TCGA-CK-4948          TCGA-CK-4950 
"KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" 
         TCGA-CK-4952          TCGA-CK-5912          TCGA-CK-5913 
"KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" 
         TCGA-CK-5914          TCGA-CK-5915          TCGA-CK-5916 
"KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" 
         TCGA-CK-6746          TCGA-CK-6747          TCGA-CK-6748 
"KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" 
         TCGA-CK-6751          TCGA-CM-4743          TCGA-CM-4744 
"KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" 
         TCGA-CM-4746          TCGA-CM-4747          TCGA-CM-4752 
"KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" 
         TCGA-CM-5341          TCGA-CM-5344          TCGA-CM-5348 
"KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" 
         TCGA-CM-5349          TCGA-CM-5860          TCGA-CM-5861 
"KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" 
         TCGA-CM-5862          TCGA-CM-5863          TCGA-CM-5864 
"KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" 
         TCGA-CM-5868          TCGA-CM-6161          TCGA-CM-6162 
"KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" 
         TCGA-CM-6163          TCGA-CM-6164          TCGA-CM-6165 
"KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" 
         TCGA-CM-6166          TCGA-CM-6167          TCGA-CM-6168 
"KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" 
         TCGA-CM-6169          TCGA-CM-6170          TCGA-CM-6171 
"KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" 
         TCGA-CM-6172          TCGA-CM-6674          TCGA-CM-6675 
"KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" 
         TCGA-CM-6676          TCGA-CM-6677          TCGA-CM-6678 
"KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" 
         TCGA-CM-6679          TCGA-CM-6680          TCGA-D5-5537 
"KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" 
         TCGA-D5-5538          TCGA-D5-5539          TCGA-D5-5540 
"KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" 
         TCGA-D5-5541          TCGA-D5-6529          TCGA-D5-6532 
"KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" 
         TCGA-D5-6533          TCGA-D5-6534          TCGA-D5-6535 
"KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" 
         TCGA-D5-6536          TCGA-D5-6537          TCGA-D5-6538 
"KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" 
         TCGA-D5-6539          TCGA-D5-6540          TCGA-D5-6541 
"KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" 
         TCGA-D5-6898          TCGA-D5-6920          TCGA-D5-6922 
"KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" 
         TCGA-D5-6923          TCGA-D5-6924          TCGA-D5-6926 
"KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" 
         TCGA-D5-6927          TCGA-D5-6928          TCGA-D5-6930 
"KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" 
         TCGA-D5-6931          TCGA-D5-6932          TCGA-D5-7000 
"KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" 
         TCGA-F4-6459          TCGA-F4-6460          TCGA-F4-6569 
"KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" 
         TCGA-F4-6570          TCGA-F4-6703          TCGA-F4-6704 
"KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" 
         TCGA-F4-6805          TCGA-F4-6806          TCGA-F4-6807 
"KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" 
         TCGA-F4-6808          TCGA-F4-6809          TCGA-F4-6854 
"KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" 
         TCGA-F4-6855          TCGA-F4-6856          TCGA-G4-6293 
"KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" 
         TCGA-G4-6299          TCGA-G4-6303          TCGA-G4-6304 
"KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" 
         TCGA-G4-6306          TCGA-G4-6307          TCGA-G4-6309 
"KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" 
         TCGA-G4-6310          TCGA-G4-6315          TCGA-G4-6317 
"KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" 
         TCGA-G4-6321          TCGA-G4-6323          TCGA-G4-6586 
"KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" 
         TCGA-G4-6588          TCGA-G4-6625          TCGA-G4-6626 
"KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" 
         TCGA-G4-6628          TCGA-AF-2687          TCGA-AF-2689 
"KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" 
         TCGA-AF-2691          TCGA-AF-2692          TCGA-AF-3400 
"KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" 
         TCGA-AF-3913          TCGA-AF-4110          TCGA-AF-5654 
"KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" 
         TCGA-AF-6655          TCGA-AG-3574          TCGA-AG-3575 
"KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" 
         TCGA-AG-3578          TCGA-AG-3580          TCGA-AG-3581 
"KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" 
         TCGA-AG-3582          TCGA-AG-3583          TCGA-AG-3584 
"KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" 
         TCGA-AG-3586          TCGA-AG-3587          TCGA-AG-3593 
"KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" 
         TCGA-AG-3594          TCGA-AG-3598          TCGA-AG-3599 
"KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" 
         TCGA-AG-3600          TCGA-AG-3601          TCGA-AG-3602 
"KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" 
         TCGA-AG-3605          TCGA-AG-3608          TCGA-AG-3609 
"KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" 
         TCGA-AG-3611          TCGA-AG-3612          TCGA-AG-3726 
"KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" 
         TCGA-AG-3727          TCGA-AG-3731          TCGA-AG-3732 
"KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" 
         TCGA-AG-3742          TCGA-AG-3878          TCGA-AG-3882 
"KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" 
         TCGA-AG-3883          TCGA-AG-3885          TCGA-AG-3887 
"KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" 
         TCGA-AG-3890          TCGA-AG-3892          TCGA-AG-3893 
"KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" 
         TCGA-AG-3894          TCGA-AG-3896          TCGA-AG-3898 
"KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" 
         TCGA-AG-3901          TCGA-AG-3902          TCGA-AG-3909 
"KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" 
         TCGA-AG-3999          TCGA-AG-4001          TCGA-AG-4005 
"KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" 
         TCGA-AG-4007          TCGA-AG-4008          TCGA-AG-4015 
"KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" 
         TCGA-AG-A002          TCGA-AG-A008          TCGA-AG-A00C 
"KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" 
         TCGA-AG-A00H          TCGA-AG-A00Y          TCGA-AG-A011 
"KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" 
         TCGA-AG-A014          TCGA-AG-A015          TCGA-AG-A016 
"KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" 
         TCGA-AG-A01L          TCGA-AG-A01W          TCGA-AG-A01Y 
"KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" 
         TCGA-AG-A020          TCGA-AG-A025          TCGA-AG-A026 
"KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" 
         TCGA-AG-A02G          TCGA-AG-A02N          TCGA-AG-A02X 
"KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" 
         TCGA-AG-A032          TCGA-AG-A036          TCGA-AH-6549 
"KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" 
         TCGA-AH-6643          TCGA-CL-5917          TCGA-CL-5918 
"KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" 
         TCGA-DC-5337          TCGA-DC-5869          TCGA-DC-6155 
"KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" 
         TCGA-DC-6157          TCGA-DC-6158          TCGA-DC-6160 
"KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" 
         TCGA-DC-6681          TCGA-DC-6682          TCGA-DC-6683 
"KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" 
         TCGA-DT-5265          TCGA-EF-5830          TCGA-EI-6506 
"KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" 
         TCGA-EI-6507          TCGA-EI-6508          TCGA-F5-6464 
"KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" 
         TCGA-F5-6465          TCGA-F5-6571          TCGA-F5-6702 
"KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" 
         TCGA-F5-6812          TCGA-F5-6813          TCGA-G5-6235 
"KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" "KRTAP20-1 WILD-TYPE" 
         TCGA-G5-6641 
"KRTAP20-1 WILD-TYPE" 
D1331V12, continuous
                     vv
clus                  AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KRTAP20-1 MUTATED                                  0     0
  KRTAP20-1 WILD-TYPE                                1    11
                     vv
clus                  BLACK OR AFRICAN AMERICAN WHITE
  KRTAP20-1 MUTATED                           0     3
  KRTAP20-1 WILD-TYPE                        22   223
D1331V13, multiclass
                                  clus
vv                                 KRTAP20-1 MUTATED KRTAP20-1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                 0                   1
  ASIAN                                            0                  11
  BLACK OR AFRICAN AMERICAN                        0                  22
  WHITE                                            3                 223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1332) Variable = TAF6 MUTATION ANALYSIS
D1332V1, survival
                sevent
clus2              0   1
  TAF6 MUTATED     7   3
  TAF6 WILD-TYPE 371  90
  TAF6 MUTATED TAF6 WILD-TYPE 
            10            461 
  TAF6 MUTATED TAF6 WILD-TYPE 
             3             90 
$`TAF6 MUTATED`
TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-A00N TCGA-AD-5900 TCGA-CM-6161 TCGA-D5-6540 
       13.02         1.02         4.01         0.07        15.02        16.14 
TCGA-F4-6460 TCGA-G4-6307 TCGA-G4-6317 TCGA-AG-3902 
       31.96        55.04        36.00        32.02 

$`TAF6 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        1.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       18.05        40.96        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6162 TCGA-CM-6163 
        5.03        15.02        15.02        17.03        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 
      133.18        74.56        65.85        53.62        44.68        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       63.62        61.91        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3909 TCGA-AG-3999 
       35.01        14.01         1.02        48.03        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  TAF6 MUTATED TAF6 WILD-TYPE 
          0.07           0.00 
  TAF6 MUTATED TAF6 WILD-TYPE 
         55.04         148.01 
  TAF6 MUTATED TAF6 WILD-TYPE 
         15.58          20.28 
[1] "0.1 - 55.0 (15.6)"  "0.0 - 148.0 (20.3)"
[1] "hr=" "2"  
D1332V2, continuous
D1332V3, binary
                cls
clus               0   1
  TAF6 MUTATED     9   1
  TAF6 WILD-TYPE 357 118
[1] "tbl2"
                cls
clus             [,1] [,2]
  TAF6 MUTATED      9    1
  TAF6 WILD-TYPE  357  118
        clus
vv       TAF6 MUTATED TAF6 WILD-TYPE
  COLON             9            357
  RECTUM            1            118
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TAF6 MUTATED         3        0        0         2         1         0
  TAF6 WILD-TYPE      88        1       32       136         9         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TAF6 MUTATED           1          0          2          1        0         0
  TAF6 WILD-TYPE        23         11         57         41       48        18
                vv
clus             STAGE IVB
  TAF6 MUTATED           0
  TAF6 WILD-TYPE         1
D1332V4, multiclass
            clus
vv           TAF6 MUTATED TAF6 WILD-TYPE
  STAGE I               3             88
  STAGE IA              0              1
  STAGE II              0             32
  STAGE IIA             2            136
  STAGE IIB             1              9
  STAGE IIC             0              1
  STAGE III             1             23
  STAGE IIIA            0             11
  STAGE IIIB            2             57
  STAGE IIIC            1             41
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  TAF6 MUTATED     0   3   6   1
  TAF6 WILD-TYPE  17  89 323  49
D1332V5, multiclass
    clus
vv   TAF6 MUTATED TAF6 WILD-TYPE
  T1            0             17
  T2            3             89
  T3            6            323
  T4            1             49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  TAF6 MUTATED     6   2   2
  TAF6 WILD-TYPE 281 111  85
D1332V6, multiclass
    clus
vv   TAF6 MUTATED TAF6 WILD-TYPE
  N0            6            281
  N1            2            111
  N2            2             85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1332V7, binary
                cls
clus               0   1
  TAF6 MUTATED     8   0
  TAF6 WILD-TYPE 367  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  TAF6 MUTATED      8    0
  TAF6 WILD-TYPE  367   65
   clus
vv  TAF6 MUTATED TAF6 WILD-TYPE
  0            8            367
  1            0             65
[1] 2 2
[1] FALSE
D1332V8, binary
                cls
clus               0   1
  TAF6 MUTATED     6   4
  TAF6 WILD-TYPE 219 260
[1] "tbl2"
                cls
clus             [,1] [,2]
  TAF6 MUTATED      6    4
  TAF6 WILD-TYPE  219  260
        clus
vv       TAF6 MUTATED TAF6 WILD-TYPE
  FEMALE            6            219
  MALE              4            260
[1] 2 2
[1] FALSE
D1332V9, binary
                cls
clus               0   1
  TAF6 MUTATED     7   0
  TAF6 WILD-TYPE 343  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  TAF6 MUTATED      7    0
  TAF6 WILD-TYPE  343   22
     clus
vv    TAF6 MUTATED TAF6 WILD-TYPE
  NO             7            343
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  TAF6 MUTATED                      5                             4
  TAF6 WILD-TYPE                  310                            43
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  TAF6 MUTATED                       1                              0
  TAF6 WILD-TYPE                   105                             10
D1332V10, multiclass
                                clus
vv                               TAF6 MUTATED TAF6 WILD-TYPE
  COLON ADENOCARCINOMA                      5            310
  COLON MUCINOUS ADENOCARCINOMA             4             43
  RECTAL ADENOCARCINOMA                     1            105
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  TAF6 MUTATED     9   0   0   0
  TAF6 WILD-TYPE 336   4  31  25
D1332V11, multiclass
    clus
vv   TAF6 MUTATED TAF6 WILD-TYPE
  R0            9            336
  R1            0              4
  R2            0             31
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1332V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TAF6 MUTATED                                  0     0
  TAF6 WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  TAF6 MUTATED                           0     6
  TAF6 WILD-TYPE                        22   220
D1332V13, multiclass
                                  clus
vv                                 TAF6 MUTATED TAF6 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       6            220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1333) Variable = URGCP MUTATION ANALYSIS
D1333V1, survival
                 sevent
clus2               0   1
  URGCP MUTATED    14   4
  URGCP WILD-TYPE 364  89
  URGCP MUTATED URGCP WILD-TYPE 
             18             453 
  URGCP MUTATED URGCP WILD-TYPE 
              4              89 
$`URGCP MUTATED`
TCGA-A6-5665 TCGA-A6-6138 TCGA-AA-3655 TCGA-AA-3977 TCGA-AA-A01D TCGA-AD-6964 
       22.06        22.52        61.02        25.02        10.98        10.88 
TCGA-AZ-4315 TCGA-AZ-6601 TCGA-CA-6716 TCGA-CA-6717 TCGA-CM-5344 TCGA-CM-6167 
       58.39       100.01        12.20        12.76        22.03        14.99 
TCGA-CM-6172 TCGA-D5-6927 TCGA-G4-6309 TCGA-AG-A002 TCGA-DY-A1DD TCGA-EI-6507 
       11.01         9.44        85.48        20.98        57.24        19.96 

$`URGCP WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       22.09        32.71        27.09         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       13.94        19.99        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
        1.02        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
       16.31         0.95        33.01        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77        12.10        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       29.06        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       29.03        16.04        21.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       14.04        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 
       74.56        65.85        53.62        44.68        55.04        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DF 
        4.01         5.03         5.29       126.44        41.36        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6510 
       51.48        32.61         0.49        20.55        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  URGCP MUTATED URGCP WILD-TYPE 
           9.44            0.00 
  URGCP MUTATED URGCP WILD-TYPE 
         100.01          148.01 
  URGCP MUTATED URGCP WILD-TYPE 
         21.505          20.120 
[1] "9.4 - 100.0 (21.5)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.1"
D1333V2, continuous
D1333V3, binary
                 cls
clus                0   1
  URGCP MUTATED    15   3
  URGCP WILD-TYPE 351 116
[1] "tbl2"
                 cls
clus              [,1] [,2]
  URGCP MUTATED     15    3
  URGCP WILD-TYPE  351  116
        clus
vv       URGCP MUTATED URGCP WILD-TYPE
  COLON             15             351
  RECTUM             3             116
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  URGCP MUTATED         2        0        2         6         0         0
  URGCP WILD-TYPE      89        1       30       132        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  URGCP MUTATED           0          0          4          2        0         0
  URGCP WILD-TYPE        24         11         55         40       48        18
                 vv
clus              STAGE IVB
  URGCP MUTATED           0
  URGCP WILD-TYPE         1
D1333V4, multiclass
            clus
vv           URGCP MUTATED URGCP WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA              6             132
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             4              55
  STAGE IIIC             2              40
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  URGCP MUTATED     0   3  14   1
  URGCP WILD-TYPE  17  89 315  49
D1333V5, multiclass
    clus
vv   URGCP MUTATED URGCP WILD-TYPE
  T1             0              17
  T2             3              89
  T3            14             315
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  URGCP MUTATED    11   4   3
  URGCP WILD-TYPE 276 109  84
D1333V6, multiclass
    clus
vv   URGCP MUTATED URGCP WILD-TYPE
  N0            11             276
  N1             4             109
  N2             3              84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1333V7, binary
                 cls
clus                0   1
  URGCP MUTATED    16   0
  URGCP WILD-TYPE 359  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  URGCP MUTATED     16    0
  URGCP WILD-TYPE  359   65
   clus
vv  URGCP MUTATED URGCP WILD-TYPE
  0            16             359
  1             0              65
[1] 2 2
[1] FALSE
D1333V8, binary
                 cls
clus                0   1
  URGCP MUTATED     7  11
  URGCP WILD-TYPE 218 253
[1] "tbl2"
                 cls
clus              [,1] [,2]
  URGCP MUTATED      7   11
  URGCP WILD-TYPE  218  253
        clus
vv       URGCP MUTATED URGCP WILD-TYPE
  FEMALE             7             218
  MALE              11             253
[1] 2 2
[1] FALSE
D1333V9, binary
                 cls
clus                0   1
  URGCP MUTATED    17   0
  URGCP WILD-TYPE 333  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  URGCP MUTATED     17    0
  URGCP WILD-TYPE  333   22
     clus
vv    URGCP MUTATED URGCP WILD-TYPE
  NO             17             333
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  URGCP MUTATED                     13                             2
  URGCP WILD-TYPE                  302                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  URGCP MUTATED                       3                              0
  URGCP WILD-TYPE                   103                             10
D1333V10, multiclass
                                clus
vv                               URGCP MUTATED URGCP WILD-TYPE
  COLON ADENOCARCINOMA                      13             302
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      3             103
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  URGCP MUTATED    11   0   0   2
  URGCP WILD-TYPE 334   4  31  23
D1333V11, multiclass
    clus
vv   URGCP MUTATED URGCP WILD-TYPE
  R0            11             334
  R1             0               4
  R2             0              31
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1333V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  URGCP MUTATED                                  0     2
  URGCP WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  URGCP MUTATED                           2    10
  URGCP WILD-TYPE                        20   216
D1333V13, multiclass
                                  clus
vv                                 URGCP MUTATED URGCP WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               9
  BLACK OR AFRICAN AMERICAN                    2              20
  WHITE                                       10             216
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1334) Variable = CHRNA3 MUTATION ANALYSIS
D1334V1, survival
                  sevent
clus2                0   1
  CHRNA3 MUTATED     7   4
  CHRNA3 WILD-TYPE 371  89
  CHRNA3 MUTATED CHRNA3 WILD-TYPE 
              11              460 
  CHRNA3 MUTATED CHRNA3 WILD-TYPE 
               4               89 
$`CHRNA3 MUTATED`
TCGA-A6-5659 TCGA-AA-3655 TCGA-AA-3811 TCGA-AD-6964 TCGA-AZ-6598 TCGA-AZ-6601 
       30.44        61.02        10.06        10.88        49.41       100.01 
TCGA-CK-4952 TCGA-CM-5348 TCGA-F4-6808 TCGA-F4-6856 TCGA-EI-6506 
       15.62        22.98        33.67        35.31        20.55 

$`CHRNA3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       19.99        13.94        19.99        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        19.04        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
        0.79         0.72         5.79        22.42        27.42         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 
       62.79        88.21         6.77        12.10        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
       17.56       148.01        85.45        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5349 
       37.02        25.02        13.02        29.06        22.03        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
       13.25         0.53        47.41       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6507 TCGA-EI-6508 
       24.13        51.48        32.61         0.49        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  CHRNA3 MUTATED CHRNA3 WILD-TYPE 
           10.06             0.00 
  CHRNA3 MUTATED CHRNA3 WILD-TYPE 
          100.01           148.01 
  CHRNA3 MUTATED CHRNA3 WILD-TYPE 
          30.440           20.035 
[1] "10.1 - 100.0 (30.4)" "0.0 - 148.0 (20.0)" 
[1] "hr=" "1.4"
D1334V2, continuous
D1334V3, binary
                  cls
clus                 0   1
  CHRNA3 MUTATED    10   1
  CHRNA3 WILD-TYPE 356 118
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CHRNA3 MUTATED     10    1
  CHRNA3 WILD-TYPE  356  118
        clus
vv       CHRNA3 MUTATED CHRNA3 WILD-TYPE
  COLON              10              356
  RECTUM              1              118
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CHRNA3 MUTATED         3        0        3         1         0         0
  CHRNA3 WILD-TYPE      88        1       29       137        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CHRNA3 MUTATED           1          0          1          1        0
  CHRNA3 WILD-TYPE        23         11         58         41       48
                  vv
clus               STAGE IVA STAGE IVB
  CHRNA3 MUTATED           0         0
  CHRNA3 WILD-TYPE        18         1
D1334V4, multiclass
            clus
vv           CHRNA3 MUTATED CHRNA3 WILD-TYPE
  STAGE I                 3               88
  STAGE IA                0                1
  STAGE II                3               29
  STAGE IIA               1              137
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               1               23
  STAGE IIIA              0               11
  STAGE IIIB              1               58
  STAGE IIIC              1               41
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  CHRNA3 MUTATED     1   2   6   2
  CHRNA3 WILD-TYPE  16  90 323  48
D1334V5, multiclass
    clus
vv   CHRNA3 MUTATED CHRNA3 WILD-TYPE
  T1              1               16
  T2              2               90
  T3              6              323
  T4              2               48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  CHRNA3 MUTATED     7   1   3
  CHRNA3 WILD-TYPE 280 112  84
D1334V6, multiclass
    clus
vv   CHRNA3 MUTATED CHRNA3 WILD-TYPE
  N0              7              280
  N1              1              112
  N2              3               84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1334V7, binary
                  cls
clus                 0   1
  CHRNA3 MUTATED     9   0
  CHRNA3 WILD-TYPE 366  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CHRNA3 MUTATED      9    0
  CHRNA3 WILD-TYPE  366   65
   clus
vv  CHRNA3 MUTATED CHRNA3 WILD-TYPE
  0              9              366
  1              0               65
[1] 2 2
[1] FALSE
D1334V8, binary
                  cls
clus                 0   1
  CHRNA3 MUTATED     5   6
  CHRNA3 WILD-TYPE 220 258
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CHRNA3 MUTATED      5    6
  CHRNA3 WILD-TYPE  220  258
        clus
vv       CHRNA3 MUTATED CHRNA3 WILD-TYPE
  FEMALE              5              220
  MALE                6              258
[1] 2 2
[1] FALSE
D1334V9, binary
                  cls
clus                 0   1
  CHRNA3 MUTATED    10   0
  CHRNA3 WILD-TYPE 340  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CHRNA3 MUTATED     10    0
  CHRNA3 WILD-TYPE  340   22
     clus
vv    CHRNA3 MUTATED CHRNA3 WILD-TYPE
  NO              10              340
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CHRNA3 MUTATED                      8                             2
  CHRNA3 WILD-TYPE                  307                            45
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CHRNA3 MUTATED                       1                              0
  CHRNA3 WILD-TYPE                   105                             10
D1334V10, multiclass
                                clus
vv                               CHRNA3 MUTATED CHRNA3 WILD-TYPE
  COLON ADENOCARCINOMA                        8              307
  COLON MUCINOUS ADENOCARCINOMA               2               45
  RECTAL ADENOCARCINOMA                       1              105
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  CHRNA3 MUTATED     7   0   0   1
  CHRNA3 WILD-TYPE 338   4  31  24
D1334V11, multiclass
    clus
vv   CHRNA3 MUTATED CHRNA3 WILD-TYPE
  R0              7              338
  R1              0                4
  R2              0               31
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1334V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CHRNA3 MUTATED                                  0     0
  CHRNA3 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  CHRNA3 MUTATED                           0     9
  CHRNA3 WILD-TYPE                        22   217
D1334V13, multiclass
                                  clus
vv                                 CHRNA3 MUTATED CHRNA3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         9              217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1335) Variable = RUNX2 MUTATION ANALYSIS
D1335V1, survival
                 sevent
clus2               0   1
  RUNX2 MUTATED     6   2
  RUNX2 WILD-TYPE 372  91
  RUNX2 MUTATED RUNX2 WILD-TYPE 
              8             463 
  RUNX2 MUTATED RUNX2 WILD-TYPE 
              2              91 
$`RUNX2 MUTATED`
TCGA-A6-3809 TCGA-AA-3710 TCGA-AA-3864 TCGA-AD-5900 TCGA-AU-6004 TCGA-CK-5916 
       32.75        26.99        53.00         0.07        27.09        21.14 
TCGA-F4-6570 TCGA-EI-6507 
        6.18        19.96 

$`RUNX2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        85.05        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 
        0.99        31.07        31.07        30.05        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       18.05        40.96        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       14.50        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       51.32         9.99        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       31.96        35.74        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
        0.49        20.55        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  RUNX2 MUTATED RUNX2 WILD-TYPE 
           0.07            0.00 
  RUNX2 MUTATED RUNX2 WILD-TYPE 
          53.00          148.01 
  RUNX2 MUTATED RUNX2 WILD-TYPE 
         24.065          20.120 
[1] "0.1 - 53.0 (24.1)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.4"
D1335V2, continuous
D1335V3, binary
                 cls
clus                0   1
  RUNX2 MUTATED     8   1
  RUNX2 WILD-TYPE 358 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RUNX2 MUTATED      8    1
  RUNX2 WILD-TYPE  358  118
        clus
vv       RUNX2 MUTATED RUNX2 WILD-TYPE
  COLON              8             358
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RUNX2 MUTATED         3        0        1         4         1         0
  RUNX2 WILD-TYPE      88        1       31       134         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RUNX2 MUTATED           0          0          0          0        0         0
  RUNX2 WILD-TYPE        24         11         59         42       48        18
                 vv
clus              STAGE IVB
  RUNX2 MUTATED           0
  RUNX2 WILD-TYPE         1
D1335V4, multiclass
            clus
vv           RUNX2 MUTATED RUNX2 WILD-TYPE
  STAGE I                3              88
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              4             134
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  RUNX2 MUTATED     1   2   5   1
  RUNX2 WILD-TYPE  16  90 324  49
D1335V5, multiclass
    clus
vv   RUNX2 MUTATED RUNX2 WILD-TYPE
  T1             1              16
  T2             2              90
  T3             5             324
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  RUNX2 MUTATED     9   0   0
  RUNX2 WILD-TYPE 278 113  87
D1335V6, multiclass
    clus
vv   RUNX2 MUTATED RUNX2 WILD-TYPE
  N0             9             278
  N1             0             113
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1335V7, binary
                 cls
clus                0   1
  RUNX2 MUTATED     8   0
  RUNX2 WILD-TYPE 367  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RUNX2 MUTATED      8    0
  RUNX2 WILD-TYPE  367   65
   clus
vv  RUNX2 MUTATED RUNX2 WILD-TYPE
  0             8             367
  1             0              65
[1] 2 2
[1] FALSE
D1335V8, binary
                 cls
clus                0   1
  RUNX2 MUTATED     6   3
  RUNX2 WILD-TYPE 219 261
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RUNX2 MUTATED      6    3
  RUNX2 WILD-TYPE  219  261
        clus
vv       RUNX2 MUTATED RUNX2 WILD-TYPE
  FEMALE             6             219
  MALE               3             261
[1] 2 2
[1] FALSE
D1335V9, binary
                 cls
clus                0   1
  RUNX2 MUTATED     6   0
  RUNX2 WILD-TYPE 344  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RUNX2 MUTATED      6    0
  RUNX2 WILD-TYPE  344   22
     clus
vv    RUNX2 MUTATED RUNX2 WILD-TYPE
  NO              6             344
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  RUNX2 MUTATED                      6                             2
  RUNX2 WILD-TYPE                  309                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  RUNX2 MUTATED                       1                              0
  RUNX2 WILD-TYPE                   105                             10
D1335V10, multiclass
                                clus
vv                               RUNX2 MUTATED RUNX2 WILD-TYPE
  COLON ADENOCARCINOMA                       6             309
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  RUNX2 MUTATED     8   0   0   1
  RUNX2 WILD-TYPE 337   4  31  24
D1335V11, multiclass
    clus
vv   RUNX2 MUTATED RUNX2 WILD-TYPE
  R0             8             337
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1335V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RUNX2 MUTATED                                  0     0
  RUNX2 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  RUNX2 MUTATED                           0     6
  RUNX2 WILD-TYPE                        22   220
D1335V13, multiclass
                                  clus
vv                                 RUNX2 MUTATED RUNX2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        6             220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1336) Variable = ZNF354C MUTATION ANALYSIS
D1336V1, survival
                   sevent
clus2                 0   1
  ZNF354C MUTATED    14   4
  ZNF354C WILD-TYPE 364  89
  ZNF354C MUTATED ZNF354C WILD-TYPE 
               18               453 
  ZNF354C MUTATED ZNF354C WILD-TYPE 
                4                89 
$`ZNF354C MUTATED`
TCGA-A6-3810 TCGA-AA-3864 TCGA-AA-3877 TCGA-AA-3947 TCGA-AA-3977 TCGA-AA-A00N 
       36.53        53.00        31.00        33.01        25.02         4.01 
TCGA-AZ-4315 TCGA-AZ-6598 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-D5-6929 
       58.39        49.41        12.20        12.76        10.06         4.80 
TCGA-DM-A1D8 TCGA-AG-A002 TCGA-AH-6544 TCGA-EI-6507 TCGA-F5-6465 TCGA-F5-6813 
       12.59        20.98        38.56        19.96        49.51         0.69 

$`ZNF354C WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        32.75        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 
       32.05         0.99        31.07        31.07        30.05        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 
       24.03        27.02        29.98        18.05         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
       16.31         0.95        33.01        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 
        5.13       106.75        22.36        62.79        88.21         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 
       14.30         9.04         9.44        11.64         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       92.75        49.91        13.32       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
       38.04       117.11         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       20.91        18.28         9.96        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-G5-6235 TCGA-G5-6641 
        0.66        55.76        26.43 

  ZNF354C MUTATED ZNF354C WILD-TYPE 
             0.69              0.00 
  ZNF354C MUTATED ZNF354C WILD-TYPE 
            58.39            148.01 
  ZNF354C MUTATED ZNF354C WILD-TYPE 
            23.00             20.12 
[1] "0.7 - 58.4 (23.0)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.1"
D1336V2, continuous
D1336V3, binary
                   cls
clus                  0   1
  ZNF354C MUTATED    13   5
  ZNF354C WILD-TYPE 353 114
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZNF354C MUTATED     13    5
  ZNF354C WILD-TYPE  353  114
        clus
vv       ZNF354C MUTATED ZNF354C WILD-TYPE
  COLON               13               353
  RECTUM               5               114
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZNF354C MUTATED         2        0        2         7         2         0
  ZNF354C WILD-TYPE      89        1       30       131         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF354C MUTATED           0          0          0          1        1
  ZNF354C WILD-TYPE        24         11         59         41       47
                   vv
clus                STAGE IVA STAGE IVB
  ZNF354C MUTATED           0         0
  ZNF354C WILD-TYPE        18         1
D1336V4, multiclass
            clus
vv           ZNF354C MUTATED ZNF354C WILD-TYPE
  STAGE I                  2                89
  STAGE IA                 0                 1
  STAGE II                 2                30
  STAGE IIA                7               131
  STAGE IIB                2                 8
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               0                11
  STAGE IIIB               0                59
  STAGE IIIC               1                41
  STAGE IV                 1                47
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  ZNF354C MUTATED     1   2  12   3
  ZNF354C WILD-TYPE  16  90 317  47
D1336V5, multiclass
    clus
vv   ZNF354C MUTATED ZNF354C WILD-TYPE
  T1               1                16
  T2               2                90
  T3              12               317
  T4               3                47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  ZNF354C MUTATED    14   3   1
  ZNF354C WILD-TYPE 273 110  86
D1336V6, multiclass
    clus
vv   ZNF354C MUTATED ZNF354C WILD-TYPE
  N0              14               273
  N1               3               110
  N2               1                86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1336V7, binary
                   cls
clus                  0   1
  ZNF354C MUTATED    13   2
  ZNF354C WILD-TYPE 362  63
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZNF354C MUTATED     13    2
  ZNF354C WILD-TYPE  362   63
   clus
vv  ZNF354C MUTATED ZNF354C WILD-TYPE
  0              13               362
  1               2                63
[1] 2 2
[1] FALSE
D1336V8, binary
                   cls
clus                  0   1
  ZNF354C MUTATED     6  12
  ZNF354C WILD-TYPE 219 252
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZNF354C MUTATED      6   12
  ZNF354C WILD-TYPE  219  252
        clus
vv       ZNF354C MUTATED ZNF354C WILD-TYPE
  FEMALE               6               219
  MALE                12               252
[1] 2 2
[1] FALSE
D1336V9, binary
                   cls
clus                  0   1
  ZNF354C MUTATED    14   0
  ZNF354C WILD-TYPE 336  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZNF354C MUTATED     14    0
  ZNF354C WILD-TYPE  336   22
     clus
vv    ZNF354C MUTATED ZNF354C WILD-TYPE
  NO               14               336
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ZNF354C MUTATED                      9                             4
  ZNF354C WILD-TYPE                  306                            43
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ZNF354C MUTATED                       5                              0
  ZNF354C WILD-TYPE                   101                             10
D1336V10, multiclass
                                clus
vv                               ZNF354C MUTATED ZNF354C WILD-TYPE
  COLON ADENOCARCINOMA                         9               306
  COLON MUCINOUS ADENOCARCINOMA                4                43
  RECTAL ADENOCARCINOMA                        5               101
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  ZNF354C MUTATED    11   0   0   3
  ZNF354C WILD-TYPE 334   4  31  22
D1336V11, multiclass
    clus
vv   ZNF354C MUTATED ZNF354C WILD-TYPE
  R0              11               334
  R1               0                 4
  R2               0                31
  RX               3                22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1336V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF354C MUTATED                                  0     3
  ZNF354C WILD-TYPE                                1     8
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  ZNF354C MUTATED                           0     9
  ZNF354C WILD-TYPE                        22   217
D1336V13, multiclass
                                  clus
vv                                 ZNF354C MUTATED ZNF354C WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          3                 8
  BLACK OR AFRICAN AMERICAN                      0                22
  WHITE                                          9               217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1337) Variable = PACS2 MUTATION ANALYSIS
D1337V1, survival
                 sevent
clus2               0   1
  PACS2 MUTATED     4   1
  PACS2 WILD-TYPE 374  92
  PACS2 MUTATED PACS2 WILD-TYPE 
              5             466 
  PACS2 MUTATED PACS2 WILD-TYPE 
              1              92 
$`PACS2 MUTATED`
TCGA-AD-5900 TCGA-CK-5913 TCGA-CK-6747 TCGA-CM-6674 TCGA-F4-6570 
        0.07        51.32        82.95        12.95         6.18 

$`PACS2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 
        0.92        41.00        39.98        18.05        40.96        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 
      148.01        85.45        15.62        49.08         9.99        21.14 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6675 
       12.99        13.02        15.02        14.04        11.01        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 
       98.24         8.61        31.96        35.74        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  PACS2 MUTATED PACS2 WILD-TYPE 
           0.07            0.00 
  PACS2 MUTATED PACS2 WILD-TYPE 
          82.95          148.01 
  PACS2 MUTATED PACS2 WILD-TYPE 
         12.950          20.235 
[1] "0.1 - 83.0 (12.9)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.2"
D1337V2, continuous
D1337V3, binary
                 cls
clus                0   1
  PACS2 MUTATED     5   0
  PACS2 WILD-TYPE 361 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PACS2 MUTATED      5    0
  PACS2 WILD-TYPE  361  119
        clus
vv       PACS2 MUTATED PACS2 WILD-TYPE
  COLON              5             361
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PACS2 MUTATED         1        0        0         4         0         0
  PACS2 WILD-TYPE      90        1       32       134        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PACS2 MUTATED           0          0          0          0        0         0
  PACS2 WILD-TYPE        24         11         59         42       48        18
                 vv
clus              STAGE IVB
  PACS2 MUTATED           0
  PACS2 WILD-TYPE         1
D1337V4, multiclass
            clus
vv           PACS2 MUTATED PACS2 WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              4             134
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PACS2 MUTATED     0   1   4   0
  PACS2 WILD-TYPE  17  91 325  50
D1337V5, multiclass
    clus
vv   PACS2 MUTATED PACS2 WILD-TYPE
  T1             0              17
  T2             1              91
  T3             4             325
  T4             0              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  PACS2 MUTATED     5   0   0
  PACS2 WILD-TYPE 282 113  87
D1337V6, multiclass
    clus
vv   PACS2 MUTATED PACS2 WILD-TYPE
  N0             5             282
  N1             0             113
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1337V7, binary
                 cls
clus                0   1
  PACS2 MUTATED     2   0
  PACS2 WILD-TYPE 373  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PACS2 MUTATED      2    0
  PACS2 WILD-TYPE  373   65
   clus
vv  PACS2 MUTATED PACS2 WILD-TYPE
  0             2             373
  1             0              65
[1] 2 2
[1] FALSE
D1337V8, binary
                 cls
clus                0   1
  PACS2 MUTATED     3   2
  PACS2 WILD-TYPE 222 262
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PACS2 MUTATED      3    2
  PACS2 WILD-TYPE  222  262
        clus
vv       PACS2 MUTATED PACS2 WILD-TYPE
  FEMALE             3             222
  MALE               2             262
[1] 2 2
[1] FALSE
D1337V9, binary
                 cls
clus                0   1
  PACS2 MUTATED     4   0
  PACS2 WILD-TYPE 346  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PACS2 MUTATED      4    0
  PACS2 WILD-TYPE  346   22
     clus
vv    PACS2 MUTATED PACS2 WILD-TYPE
  NO              4             346
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PACS2 MUTATED                      4                             1
  PACS2 WILD-TYPE                  311                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PACS2 MUTATED                       0                              0
  PACS2 WILD-TYPE                   106                             10
D1337V10, multiclass
                                clus
vv                               PACS2 MUTATED PACS2 WILD-TYPE
  COLON ADENOCARCINOMA                       4             311
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  PACS2 MUTATED     3   0   0   2
  PACS2 WILD-TYPE 342   4  31  23
D1337V11, multiclass
    clus
vv   PACS2 MUTATED PACS2 WILD-TYPE
  R0             3             342
  R1             0               4
  R2             0              31
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1337V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PACS2 MUTATED                                  0     0
  PACS2 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PACS2 MUTATED                           0     5
  PACS2 WILD-TYPE                        22   221
D1337V13, multiclass
                                  clus
vv                                 PACS2 MUTATED PACS2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        5             221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1338) Variable = HIF3A MUTATION ANALYSIS
D1338V1, survival
                 sevent
clus2               0   1
  HIF3A MUTATED     9   5
  HIF3A WILD-TYPE 369  88
  HIF3A MUTATED HIF3A WILD-TYPE 
             14             457 
  HIF3A MUTATED HIF3A WILD-TYPE 
              5              88 
$`HIF3A MUTATED`
TCGA-A6-2676 TCGA-A6-6653 TCGA-AA-3877 TCGA-AA-3949 TCGA-AA-A00N TCGA-AA-A010 
       42.90        24.39        31.00        26.01         4.01        34.98 
TCGA-AD-6889 TCGA-AD-6964 TCGA-AZ-6601 TCGA-AZ-6606 TCGA-CM-5349 TCGA-CM-5861 
       56.55        10.88       100.01        11.74        30.08        15.02 
TCGA-G4-6588 TCGA-G4-6628 
       26.17        79.69 

$`HIF3A WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 
       25.18        24.16        21.76        24.69        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 
       24.03        27.02        29.98        18.05         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        33.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       21.37        15.52         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       12.10        29.56         5.23         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 
       29.06        22.03        22.98        32.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 
       13.78        35.80        91.79        46.75        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  HIF3A MUTATED HIF3A WILD-TYPE 
           4.01            0.00 
  HIF3A MUTATED HIF3A WILD-TYPE 
         100.01          148.01 
  HIF3A MUTATED HIF3A WILD-TYPE 
         28.125          20.020 
[1] "4.0 - 100.0 (28.1)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.4"
D1338V2, continuous
D1338V3, binary
                 cls
clus                0   1
  HIF3A MUTATED    15   0
  HIF3A WILD-TYPE 351 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HIF3A MUTATED     15    0
  HIF3A WILD-TYPE  351  119
        clus
vv       HIF3A MUTATED HIF3A WILD-TYPE
  COLON             15             351
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  HIF3A MUTATED         3        0        2         4         3         0
  HIF3A WILD-TYPE      88        1       30       134         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  HIF3A MUTATED           0          0          1          0        1         0
  HIF3A WILD-TYPE        24         11         58         42       47        18
                 vv
clus              STAGE IVB
  HIF3A MUTATED           0
  HIF3A WILD-TYPE         1
D1338V4, multiclass
            clus
vv           HIF3A MUTATED HIF3A WILD-TYPE
  STAGE I                3              88
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA              4             134
  STAGE IIB              3               7
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             0              42
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  HIF3A MUTATED     1   2   6   6
  HIF3A WILD-TYPE  16  90 323  44
D1338V5, multiclass
    clus
vv   HIF3A MUTATED HIF3A WILD-TYPE
  T1             1              16
  T2             2              90
  T3             6             323
  T4             6              44
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  HIF3A MUTATED    12   1   2
  HIF3A WILD-TYPE 275 112  85
D1338V6, multiclass
    clus
vv   HIF3A MUTATED HIF3A WILD-TYPE
  N0            12             275
  N1             1             112
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1338V7, binary
                 cls
clus                0   1
  HIF3A MUTATED    13   1
  HIF3A WILD-TYPE 362  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HIF3A MUTATED     13    1
  HIF3A WILD-TYPE  362   64
   clus
vv  HIF3A MUTATED HIF3A WILD-TYPE
  0            13             362
  1             1              64
[1] 2 2
[1] FALSE
D1338V8, binary
                 cls
clus                0   1
  HIF3A MUTATED     8   7
  HIF3A WILD-TYPE 217 257
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HIF3A MUTATED      8    7
  HIF3A WILD-TYPE  217  257
        clus
vv       HIF3A MUTATED HIF3A WILD-TYPE
  FEMALE             8             217
  MALE               7             257
[1] 2 2
[1] FALSE
D1338V9, binary
                 cls
clus                0   1
  HIF3A MUTATED    12   0
  HIF3A WILD-TYPE 338  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HIF3A MUTATED     12    0
  HIF3A WILD-TYPE  338   22
     clus
vv    HIF3A MUTATED HIF3A WILD-TYPE
  NO             12             338
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  HIF3A MUTATED                     12                             3
  HIF3A WILD-TYPE                  303                            44
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  HIF3A MUTATED                       0                              0
  HIF3A WILD-TYPE                   106                             10
D1338V10, multiclass
                                clus
vv                               HIF3A MUTATED HIF3A WILD-TYPE
  COLON ADENOCARCINOMA                      12             303
  COLON MUCINOUS ADENOCARCINOMA              3              44
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  HIF3A MUTATED    10   0   0   0
  HIF3A WILD-TYPE 335   4  31  25
D1338V11, multiclass
    clus
vv   HIF3A MUTATED HIF3A WILD-TYPE
  R0            10             335
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1338V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HIF3A MUTATED                                  0     1
  HIF3A WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  HIF3A MUTATED                           0     9
  HIF3A WILD-TYPE                        22   217
D1338V13, multiclass
                                  clus
vv                                 HIF3A MUTATED HIF3A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        9             217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1339) Variable = ADH7 MUTATION ANALYSIS
D1339V1, survival
                sevent
clus2              0   1
  ADH7 MUTATED     7   0
  ADH7 WILD-TYPE 371  93
  ADH7 MUTATED ADH7 WILD-TYPE 
             7            464 
  ADH7 MUTATED ADH7 WILD-TYPE 
             0             93 
$`ADH7 MUTATED`
TCGA-AA-3555 TCGA-AA-3861 TCGA-AA-A010 TCGA-AZ-4315 TCGA-CA-6716 TCGA-CM-5861 
       29.95        30.05        34.98        58.39        12.20        15.02 
TCGA-CM-6161 
       15.02 

$`ADH7 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 
       21.01        13.02        24.00        17.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 
       32.05         0.99        31.07        31.07        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 
        3.06         3.25         3.29         0.07        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 
       22.03        22.98        30.08        32.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       15.02        17.03        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  ADH7 MUTATED ADH7 WILD-TYPE 
          12.2            0.0 
  ADH7 MUTATED ADH7 WILD-TYPE 
         58.39         148.01 
  ADH7 MUTATED ADH7 WILD-TYPE 
        29.950         20.155 
[1] "12.2 - 58.4 (29.9)" "0.0 - 148.0 (20.2)"
[1] "hr="     "9100000"
D1339V2, continuous
D1339V3, binary
                cls
clus               0   1
  ADH7 MUTATED     7   0
  ADH7 WILD-TYPE 359 119
[1] "tbl2"
                cls
clus             [,1] [,2]
  ADH7 MUTATED      7    0
  ADH7 WILD-TYPE  359  119
        clus
vv       ADH7 MUTATED ADH7 WILD-TYPE
  COLON             7            359
  RECTUM            0            119
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ADH7 MUTATED         1        0        0         5         1         0
  ADH7 WILD-TYPE      90        1       32       133         9         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ADH7 MUTATED           0          0          0          0        0         0
  ADH7 WILD-TYPE        24         11         59         42       48        18
                vv
clus             STAGE IVB
  ADH7 MUTATED           0
  ADH7 WILD-TYPE         1
D1339V4, multiclass
            clus
vv           ADH7 MUTATED ADH7 WILD-TYPE
  STAGE I               1             90
  STAGE IA              0              1
  STAGE II              0             32
  STAGE IIA             5            133
  STAGE IIB             1              9
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            0             59
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  ADH7 MUTATED     0   1   5   1
  ADH7 WILD-TYPE  17  91 324  49
D1339V5, multiclass
    clus
vv   ADH7 MUTATED ADH7 WILD-TYPE
  T1            0             17
  T2            1             91
  T3            5            324
  T4            1             49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  ADH7 MUTATED     7   0   0
  ADH7 WILD-TYPE 280 113  87
D1339V6, multiclass
    clus
vv   ADH7 MUTATED ADH7 WILD-TYPE
  N0            7            280
  N1            0            113
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1339V7, binary
                cls
clus               0   1
  ADH7 MUTATED     7   0
  ADH7 WILD-TYPE 368  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  ADH7 MUTATED      7    0
  ADH7 WILD-TYPE  368   65
   clus
vv  ADH7 MUTATED ADH7 WILD-TYPE
  0            7            368
  1            0             65
[1] 2 2
[1] FALSE
D1339V8, binary
                cls
clus               0   1
  ADH7 MUTATED     4   3
  ADH7 WILD-TYPE 221 261
[1] "tbl2"
                cls
clus             [,1] [,2]
  ADH7 MUTATED      4    3
  ADH7 WILD-TYPE  221  261
        clus
vv       ADH7 MUTATED ADH7 WILD-TYPE
  FEMALE            4            221
  MALE              3            261
[1] 2 2
[1] FALSE
D1339V9, binary
                cls
clus               0   1
  ADH7 MUTATED     7   0
  ADH7 WILD-TYPE 343  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  ADH7 MUTATED      7    0
  ADH7 WILD-TYPE  343   22
     clus
vv    ADH7 MUTATED ADH7 WILD-TYPE
  NO             7            343
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ADH7 MUTATED                      6                             1
  ADH7 WILD-TYPE                  309                            46
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ADH7 MUTATED                       0                              0
  ADH7 WILD-TYPE                   106                             10
D1339V10, multiclass
                                clus
vv                               ADH7 MUTATED ADH7 WILD-TYPE
  COLON ADENOCARCINOMA                      6            309
  COLON MUCINOUS ADENOCARCINOMA             1             46
  RECTAL ADENOCARCINOMA                     0            106
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  ADH7 MUTATED     6   0   0   1
  ADH7 WILD-TYPE 339   4  31  24
D1339V11, multiclass
    clus
vv   ADH7 MUTATED ADH7 WILD-TYPE
  R0            6            339
  R1            0              4
  R2            0             31
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1339V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ADH7 MUTATED                                  0     1
  ADH7 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  ADH7 MUTATED                           0     3
  ADH7 WILD-TYPE                        22   223
D1339V13, multiclass
                                  clus
vv                                 ADH7 MUTATED ADH7 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       3            223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1340) Variable = RYR2 MUTATION ANALYSIS
D1340V1, survival
                sevent
clus2              0   1
  RYR2 MUTATED    76  25
  RYR2 WILD-TYPE 302  68
  RYR2 MUTATED RYR2 WILD-TYPE 
           101            370 
  RYR2 MUTATED RYR2 WILD-TYPE 
            25             68 
$`RYR2 MUTATED`
TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-5661 TCGA-A6-5665 TCGA-A6-6653 TCGA-A6-6780 
       34.65        32.75        33.53        22.06        24.39        20.12 
TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3666 TCGA-AA-3672 
        3.02        63.98         6.05         6.97         2.01         0.92 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3815 TCGA-AA-3864 
        5.03        26.99        19.04        19.04        33.04        53.00 
TCGA-AA-3870 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3977 
       29.98        26.01        24.00         2.01        21.99        25.02 
TCGA-AA-3982 TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01K TCGA-AA-A01R TCGA-AA-A01Z 
       27.02         4.01        34.98        31.00        35.01        37.02 
TCGA-AA-A029 TCGA-AA-A02Y TCGA-AD-5900 TCGA-AD-6901 TCGA-AU-6004 TCGA-AY-4070 
       51.98        39.98         0.07        22.42        27.09        16.31 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 
       17.82        58.39        22.36        62.79        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6608 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4950 TCGA-CK-5916 
       12.10         1.61        12.76        10.06        85.45        21.14 
TCGA-CM-4746 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-6161 TCGA-CM-6171 TCGA-CM-6172 
       37.02        32.02        15.02        15.02        14.04        11.01 
TCGA-CM-6676 TCGA-D5-6534 TCGA-D5-6540 TCGA-D5-6924 TCGA-D5-6928 TCGA-D5-6930 
       11.08        43.27        16.14        14.30        11.64         1.51 
TCGA-D5-6932 TCGA-DM-A0XD TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A282 TCGA-DM-A285 
       11.38        24.43        13.32        12.59       139.17         6.12 
TCGA-DM-A28F TCGA-F4-6460 TCGA-F4-6570 TCGA-F4-6805 TCGA-F4-6808 TCGA-G4-6293 
       35.97        31.96         6.18        34.42        33.67       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6317 
       74.56        65.85        53.62        44.68        55.04        36.00 
TCGA-G4-6321 TCGA-G4-6588 TCGA-G4-6628 TCGA-AF-2693 TCGA-AF-6136 TCGA-AG-3732 
       22.09        26.17        79.69        19.10        15.39        32.98 
TCGA-AG-3885 TCGA-AG-3909 TCGA-AG-4007 TCGA-AG-A002 TCGA-AG-A01W TCGA-AG-A025 
       17.95        19.99         1.02        20.98        70.03        49.97 
TCGA-AG-A036 TCGA-AH-6544 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5918 TCGA-DC-6158 
      117.11        38.56         6.97         4.73         7.17        10.98 
TCGA-DC-6160 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A1H8 TCGA-G5-6641 
       19.99         4.01         5.03        32.61        26.43 

$`RYR2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5657 
       16.57        33.34        36.53        14.53        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 
       30.44        29.19        23.61        22.09        32.71        27.09 
TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 
       22.52         8.38        25.08        25.18        24.16        21.76 
TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       24.69        23.87        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3667 
       13.94        19.99        61.02        78.08        54.02        14.01 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
       19.00        36.00        85.05        10.06        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       30.05        17.03        24.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3952 TCGA-AA-3955 
        2.01        12.99        24.00        33.01         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       34.03        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       24.00        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
       38.07         1.02         1.02        33.04        35.01        26.01 
TCGA-AA-A024 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       39.06        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       41.00        18.05        40.96        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.79         0.72         5.79        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AZ-4323 TCGA-AZ-4616 
       14.50         0.95        33.01        21.44         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-5407 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
      106.75        88.21       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        3.19        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5912 
       12.20        14.30        17.56       148.01        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       51.32         9.99        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       20.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6162 
       30.08         5.03        15.02        15.02        17.03        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6677 TCGA-CM-6678 
       13.02        15.02        12.95        13.05        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6536 
       55.92        20.19        18.25         1.32        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
        4.80        17.13        12.49        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6931 
        4.41        12.43         9.04         9.44         4.80        12.00 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
       10.26       119.70        38.20       130.65        92.75        49.91 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A28C 
      140.38         7.50        44.32       131.51       135.65        81.37 
TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6569 
      119.93        60.79       117.07        98.24         8.61        35.74 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6854 
       47.87         1.55        41.42        16.24        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6323 
       47.41        35.31        85.48        63.62        61.91        13.78 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       35.80        91.79        46.75        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6655 
       13.55        34.49        10.39        14.50        16.83        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 
        0.99         0.99        19.04        19.99         1.02        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4008 TCGA-AG-A008 
       32.02        28.04        36.03        14.04        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A026 TCGA-AG-A02G 
        9.07        12.00        64.01        10.98         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       61.97        41.00        38.04         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CL-5917 TCGA-DC-5337 TCGA-DC-5869 
        0.72         6.05        33.17        78.12        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6681 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
       13.97        27.95         5.95         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       57.24        24.13        51.48         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       32.19         0.66         0.69        55.76 

  RYR2 MUTATED RYR2 WILD-TYPE 
          0.07           0.00 
  RYR2 MUTATED RYR2 WILD-TYPE 
        139.17         148.01 
  RYR2 MUTATED RYR2 WILD-TYPE 
         22.36          19.99 
[1] "0.1 - 139.2 (22.4)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.2"
D1340V2, continuous
D1340V3, binary
                cls
clus               0   1
  RYR2 MUTATED    84  19
  RYR2 WILD-TYPE 282 100
[1] "tbl2"
                cls
clus             [,1] [,2]
  RYR2 MUTATED     84   19
  RYR2 WILD-TYPE  282  100
        clus
vv       RYR2 MUTATED RYR2 WILD-TYPE
  COLON            84            282
  RECTUM           19            100
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RYR2 MUTATED        22        0       11        27         5         0
  RYR2 WILD-TYPE      69        1       21       111         5         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RYR2 MUTATED           6          3         12          5        8         1
  RYR2 WILD-TYPE        18          8         47         37       40        17
                vv
clus             STAGE IVB
  RYR2 MUTATED           0
  RYR2 WILD-TYPE         1
D1340V4, multiclass
            clus
vv           RYR2 MUTATED RYR2 WILD-TYPE
  STAGE I              22             69
  STAGE IA              0              1
  STAGE II             11             21
  STAGE IIA            27            111
  STAGE IIB             5              5
  STAGE IIC             0              1
  STAGE III             6             18
  STAGE IIIA            3              8
  STAGE IIIB           12             47
  STAGE IIIC            5             37
  STAGE IV              8             40
  STAGE IVA             1             17
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  RYR2 MUTATED     4  24  67   9
  RYR2 WILD-TYPE  13  68 262  41
D1340V5, multiclass
    clus
vv   RYR2 MUTATED RYR2 WILD-TYPE
  T1            4             13
  T2           24             68
  T3           67            262
  T4            9             41
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  RYR2 MUTATED    69  24  11
  RYR2 WILD-TYPE 218  89  76
D1340V6, multiclass
    clus
vv   RYR2 MUTATED RYR2 WILD-TYPE
  N0           69            218
  N1           24             89
  N2           11             76
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1340V7, binary
                cls
clus               0   1
  RYR2 MUTATED    79  10
  RYR2 WILD-TYPE 296  55
[1] "tbl2"
                cls
clus             [,1] [,2]
  RYR2 MUTATED     79   10
  RYR2 WILD-TYPE  296   55
   clus
vv  RYR2 MUTATED RYR2 WILD-TYPE
  0           79            296
  1           10             55
[1] 2 2
[1] FALSE
D1340V8, binary
                cls
clus               0   1
  RYR2 MUTATED    54  50
  RYR2 WILD-TYPE 171 214
[1] "tbl2"
                cls
clus             [,1] [,2]
  RYR2 MUTATED     54   50
  RYR2 WILD-TYPE  171  214
        clus
vv       RYR2 MUTATED RYR2 WILD-TYPE
  FEMALE           54            171
  MALE             50            214
[1] 2 2
[1] FALSE
D1340V9, binary
                cls
clus               0   1
  RYR2 MUTATED    73   5
  RYR2 WILD-TYPE 277  17
[1] "tbl2"
                cls
clus             [,1] [,2]
  RYR2 MUTATED     73    5
  RYR2 WILD-TYPE  277   17
     clus
vv    RYR2 MUTATED RYR2 WILD-TYPE
  NO            73            277
  YES            5             17
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  RYR2 MUTATED                     69                            14
  RYR2 WILD-TYPE                  246                            33
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  RYR2 MUTATED                      18                              1
  RYR2 WILD-TYPE                    88                              9
D1340V10, multiclass
                                clus
vv                               RYR2 MUTATED RYR2 WILD-TYPE
  COLON ADENOCARCINOMA                     69            246
  COLON MUCINOUS ADENOCARCINOMA            14             33
  RECTAL ADENOCARCINOMA                    18             88
  RECTAL MUCINOUS ADENOCARCINOMA            1              9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  RYR2 MUTATED    70   2   4   5
  RYR2 WILD-TYPE 275   2  27  20
D1340V11, multiclass
    clus
vv   RYR2 MUTATED RYR2 WILD-TYPE
  R0           70            275
  R1            2              2
  R2            4             27
  RX            5             20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1340V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RYR2 MUTATED                                  0     2
  RYR2 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  RYR2 MUTATED                           6    60
  RYR2 WILD-TYPE                        16   166
D1340V13, multiclass
                                  clus
vv                                 RYR2 MUTATED RYR2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              9
  BLACK OR AFRICAN AMERICAN                   6             16
  WHITE                                      60            166
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1341) Variable = DACT1 MUTATION ANALYSIS
D1341V1, survival
                 sevent
clus2               0   1
  DACT1 MUTATED    10   3
  DACT1 WILD-TYPE 368  90
  DACT1 MUTATED DACT1 WILD-TYPE 
             13             458 
  DACT1 MUTATED DACT1 WILD-TYPE 
              3              90 
$`DACT1 MUTATED`
TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3713 TCGA-AA-3815 TCGA-AA-A00N TCGA-AA-A01P 
       20.12        19.66        19.04        33.04         4.01        38.07 
TCGA-AZ-6598 TCGA-CA-6717 TCGA-CM-5348 TCGA-D5-6927 TCGA-DM-A28K TCGA-G4-6588 
       49.41        12.76        22.98         9.44        98.24        26.17 
TCGA-AG-A002 
       20.98 

$`DACT1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       23.87        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01Q 
       10.98        32.02        12.00        31.00        31.00         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07        12.20        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5860 
       25.02        13.02        29.06        22.03        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6929 
        4.41        12.43        14.30         9.04        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       22.09        13.78        35.80        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  DACT1 MUTATED DACT1 WILD-TYPE 
           4.01            0.00 
  DACT1 MUTATED DACT1 WILD-TYPE 
          98.24          148.01 
  DACT1 MUTATED DACT1 WILD-TYPE 
          20.98           20.12 
[1] "4.0 - 98.2 (21.0)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.1"
D1341V2, continuous
D1341V3, binary
                 cls
clus                0   1
  DACT1 MUTATED    15   1
  DACT1 WILD-TYPE 351 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DACT1 MUTATED     15    1
  DACT1 WILD-TYPE  351  118
        clus
vv       DACT1 MUTATED DACT1 WILD-TYPE
  COLON             15             351
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DACT1 MUTATED         1        0        2         7         2         0
  DACT1 WILD-TYPE      90        1       30       131         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DACT1 MUTATED           1          0          1          1        1         0
  DACT1 WILD-TYPE        23         11         58         41       47        18
                 vv
clus              STAGE IVB
  DACT1 MUTATED           0
  DACT1 WILD-TYPE         1
D1341V4, multiclass
            clus
vv           DACT1 MUTATED DACT1 WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA              7             131
  STAGE IIB              2               8
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             1              41
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  DACT1 MUTATED     0   1  11   4
  DACT1 WILD-TYPE  17  91 318  46
D1341V5, multiclass
    clus
vv   DACT1 MUTATED DACT1 WILD-TYPE
  T1             0              17
  T2             1              91
  T3            11             318
  T4             4              46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  DACT1 MUTATED    13   3   0
  DACT1 WILD-TYPE 274 110  87
D1341V6, multiclass
    clus
vv   DACT1 MUTATED DACT1 WILD-TYPE
  N0            13             274
  N1             3             110
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1341V7, binary
                 cls
clus                0   1
  DACT1 MUTATED    11   1
  DACT1 WILD-TYPE 364  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DACT1 MUTATED     11    1
  DACT1 WILD-TYPE  364   64
   clus
vv  DACT1 MUTATED DACT1 WILD-TYPE
  0            11             364
  1             1              64
[1] 2 2
[1] FALSE
D1341V8, binary
                 cls
clus                0   1
  DACT1 MUTATED     7   9
  DACT1 WILD-TYPE 218 255
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DACT1 MUTATED      7    9
  DACT1 WILD-TYPE  218  255
        clus
vv       DACT1 MUTATED DACT1 WILD-TYPE
  FEMALE             7             218
  MALE               9             255
[1] 2 2
[1] FALSE
D1341V9, binary
                 cls
clus                0   1
  DACT1 MUTATED    10   1
  DACT1 WILD-TYPE 340  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DACT1 MUTATED     10    1
  DACT1 WILD-TYPE  340   21
     clus
vv    DACT1 MUTATED DACT1 WILD-TYPE
  NO             10             340
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  DACT1 MUTATED                     10                             5
  DACT1 WILD-TYPE                  305                            42
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  DACT1 MUTATED                       1                              0
  DACT1 WILD-TYPE                   105                             10
D1341V10, multiclass
                                clus
vv                               DACT1 MUTATED DACT1 WILD-TYPE
  COLON ADENOCARCINOMA                      10             305
  COLON MUCINOUS ADENOCARCINOMA              5              42
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  DACT1 MUTATED    10   0   1   2
  DACT1 WILD-TYPE 335   4  30  23
D1341V11, multiclass
    clus
vv   DACT1 MUTATED DACT1 WILD-TYPE
  R0            10             335
  R1             0               4
  R2             1              30
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1341V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DACT1 MUTATED                                  0     1
  DACT1 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  DACT1 MUTATED                           0     8
  DACT1 WILD-TYPE                        22   218
D1341V13, multiclass
                                  clus
vv                                 DACT1 MUTATED DACT1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        8             218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1342) Variable = TMC8 MUTATION ANALYSIS
D1342V1, survival
                sevent
clus2              0   1
  TMC8 MUTATED     6   1
  TMC8 WILD-TYPE 372  92
  TMC8 MUTATED TMC8 WILD-TYPE 
             7            464 
  TMC8 MUTATED TMC8 WILD-TYPE 
             1             92 
$`TMC8 MUTATED`
TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3966 TCGA-AD-5900 TCGA-AU-6004 TCGA-CK-5913 
        3.02        63.98         2.01         0.07        27.09        51.32 
TCGA-CM-6162 
       12.00 

$`TMC8 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       20.98        34.03        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       18.05        40.96        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       14.50        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       15.02        17.03        15.02         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  TMC8 MUTATED TMC8 WILD-TYPE 
          0.07           0.00 
  TMC8 MUTATED TMC8 WILD-TYPE 
         63.98         148.01 
  TMC8 MUTATED TMC8 WILD-TYPE 
        12.000         20.235 
[1] "0.1 - 64.0 (12.0)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.4"
D1342V2, continuous
D1342V3, binary
                cls
clus               0   1
  TMC8 MUTATED     7   0
  TMC8 WILD-TYPE 359 119
[1] "tbl2"
                cls
clus             [,1] [,2]
  TMC8 MUTATED      7    0
  TMC8 WILD-TYPE  359  119
        clus
vv       TMC8 MUTATED TMC8 WILD-TYPE
  COLON             7            359
  RECTUM            0            119
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TMC8 MUTATED         2        0        2         2         0         0
  TMC8 WILD-TYPE      89        1       30       136        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TMC8 MUTATED           0          0          1          0        0         0
  TMC8 WILD-TYPE        24         11         58         42       48        18
                vv
clus             STAGE IVB
  TMC8 MUTATED           0
  TMC8 WILD-TYPE         1
D1342V4, multiclass
            clus
vv           TMC8 MUTATED TMC8 WILD-TYPE
  STAGE I               2             89
  STAGE IA              0              1
  STAGE II              2             30
  STAGE IIA             2            136
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            1             58
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  TMC8 MUTATED     0   2   5   0
  TMC8 WILD-TYPE  17  90 324  50
D1342V5, multiclass
    clus
vv   TMC8 MUTATED TMC8 WILD-TYPE
  T1            0             17
  T2            2             90
  T3            5            324
  T4            0             50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  TMC8 MUTATED     6   1   0
  TMC8 WILD-TYPE 281 112  87
D1342V6, multiclass
    clus
vv   TMC8 MUTATED TMC8 WILD-TYPE
  N0            6            281
  N1            1            112
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1342V7, binary
                cls
clus               0   1
  TMC8 MUTATED     5   0
  TMC8 WILD-TYPE 370  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  TMC8 MUTATED      5    0
  TMC8 WILD-TYPE  370   65
   clus
vv  TMC8 MUTATED TMC8 WILD-TYPE
  0            5            370
  1            0             65
[1] 2 2
[1] FALSE
D1342V8, binary
                cls
clus               0   1
  TMC8 MUTATED     5   2
  TMC8 WILD-TYPE 220 262
[1] "tbl2"
                cls
clus             [,1] [,2]
  TMC8 MUTATED      5    2
  TMC8 WILD-TYPE  220  262
        clus
vv       TMC8 MUTATED TMC8 WILD-TYPE
  FEMALE            5            220
  MALE              2            262
[1] 2 2
[1] FALSE
D1342V9, binary
                cls
clus               0   1
  TMC8 MUTATED     4   0
  TMC8 WILD-TYPE 346  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  TMC8 MUTATED      4    0
  TMC8 WILD-TYPE  346   22
     clus
vv    TMC8 MUTATED TMC8 WILD-TYPE
  NO             4            346
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  TMC8 MUTATED                      4                             3
  TMC8 WILD-TYPE                  311                            44
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  TMC8 MUTATED                       0                              0
  TMC8 WILD-TYPE                   106                             10
D1342V10, multiclass
                                clus
vv                               TMC8 MUTATED TMC8 WILD-TYPE
  COLON ADENOCARCINOMA                      4            311
  COLON MUCINOUS ADENOCARCINOMA             3             44
  RECTAL ADENOCARCINOMA                     0            106
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  TMC8 MUTATED     5   0   0   1
  TMC8 WILD-TYPE 340   4  31  24
D1342V11, multiclass
    clus
vv   TMC8 MUTATED TMC8 WILD-TYPE
  R0            5            340
  R1            0              4
  R2            0             31
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1342V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TMC8 MUTATED                                  0     0
  TMC8 WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  TMC8 MUTATED                           0     4
  TMC8 WILD-TYPE                        22   222
D1342V13, multiclass
                                  clus
vv                                 TMC8 MUTATED TMC8 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       4            222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1343) Variable = SULF2 MUTATION ANALYSIS
D1343V1, survival
                 sevent
clus2               0   1
  SULF2 MUTATED    22   2
  SULF2 WILD-TYPE 356  91
  SULF2 MUTATED SULF2 WILD-TYPE 
             24             447 
  SULF2 MUTATED SULF2 WILD-TYPE 
              2              91 
$`SULF2 MUTATED`
TCGA-AA-3518 TCGA-AA-3525 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-A00E TCGA-AD-6895 
        1.02         8.05        30.05        53.00        30.02         0.72 
TCGA-CA-6718 TCGA-CM-5860 TCGA-CM-5861 TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6536 
       10.06        32.02        15.02        19.59        55.92        17.85 
TCGA-D5-6537 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6928 TCGA-D5-6929 TCGA-DM-A1D9 
        4.80        16.14        15.58        11.64         4.80       140.38 
TCGA-G4-6309 TCGA-G4-6317 TCGA-G4-6321 TCGA-AF-6655 TCGA-AG-3878 TCGA-G5-6235 
       85.48        36.00        22.09        20.02         0.99        55.76 

$`SULF2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3526 
       38.99         9.07        24.03        37.05        36.03        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
        0.99        31.07        31.07        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00F 
        7.96        27.02        13.94        38.04        19.00        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 
        0.07        21.37        15.52        56.55         0.79         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07        12.20        12.76        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       30.08         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       45.40        12.26        56.09        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6898 TCGA-D5-6920 
       43.27        15.12        17.13        12.49         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6930 
        4.41        12.43        14.30         9.04         9.44         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1DA 
      130.65        92.75        49.91        13.32        12.59         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       55.04        63.62        61.91        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       15.39        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       37.02        32.98         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6641 
        0.66         0.69        26.43 

  SULF2 MUTATED SULF2 WILD-TYPE 
           0.72            0.00 
  SULF2 MUTATED SULF2 WILD-TYPE 
         140.38          148.01 
  SULF2 MUTATED SULF2 WILD-TYPE 
          18.72           20.55 
[1] "0.7 - 140.4 (18.7)" "0.0 - 148.0 (20.6)"
[1] "hr=" "2.6"
D1343V2, continuous
D1343V3, binary
                 cls
clus                0   1
  SULF2 MUTATED    22   3
  SULF2 WILD-TYPE 344 116
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SULF2 MUTATED     22    3
  SULF2 WILD-TYPE  344  116
        clus
vv       SULF2 MUTATED SULF2 WILD-TYPE
  COLON             22             344
  RECTUM             3             116
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SULF2 MUTATED         2        0        2        10         0         0
  SULF2 WILD-TYPE      89        1       30       128        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SULF2 MUTATED           1          2          5          1        1         0
  SULF2 WILD-TYPE        23          9         54         41       47        18
                 vv
clus              STAGE IVB
  SULF2 MUTATED           0
  SULF2 WILD-TYPE         1
D1343V4, multiclass
            clus
vv           SULF2 MUTATED SULF2 WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA             10             128
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             2               9
  STAGE IIIB             5              54
  STAGE IIIC             1              41
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  SULF2 MUTATED     0   4  21   0
  SULF2 WILD-TYPE  17  88 308  50
D1343V5, multiclass
    clus
vv   SULF2 MUTATED SULF2 WILD-TYPE
  T1             0              17
  T2             4              88
  T3            21             308
  T4             0              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  SULF2 MUTATED    14  10   1
  SULF2 WILD-TYPE 273 103  86
D1343V6, multiclass
    clus
vv   SULF2 MUTATED SULF2 WILD-TYPE
  N0            14             273
  N1            10             103
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1343V7, binary
                 cls
clus                0   1
  SULF2 MUTATED    19   1
  SULF2 WILD-TYPE 356  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SULF2 MUTATED     19    1
  SULF2 WILD-TYPE  356   64
   clus
vv  SULF2 MUTATED SULF2 WILD-TYPE
  0            19             356
  1             1              64
[1] 2 2
[1] FALSE
D1343V8, binary
                 cls
clus                0   1
  SULF2 MUTATED     7  18
  SULF2 WILD-TYPE 218 246
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SULF2 MUTATED      7   18
  SULF2 WILD-TYPE  218  246
        clus
vv       SULF2 MUTATED SULF2 WILD-TYPE
  FEMALE             7             218
  MALE              18             246
[1] 2 2
[1] FALSE
D1343V9, binary
                 cls
clus                0   1
  SULF2 MUTATED    19   0
  SULF2 WILD-TYPE 331  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SULF2 MUTATED     19    0
  SULF2 WILD-TYPE  331   22
     clus
vv    SULF2 MUTATED SULF2 WILD-TYPE
  NO             19             331
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SULF2 MUTATED                     19                             3
  SULF2 WILD-TYPE                  296                            44
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SULF2 MUTATED                       3                              0
  SULF2 WILD-TYPE                   103                             10
D1343V10, multiclass
                                clus
vv                               SULF2 MUTATED SULF2 WILD-TYPE
  COLON ADENOCARCINOMA                      19             296
  COLON MUCINOUS ADENOCARCINOMA              3              44
  RECTAL ADENOCARCINOMA                      3             103
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  SULF2 MUTATED    21   1   0   1
  SULF2 WILD-TYPE 324   3  31  24
D1343V11, multiclass
    clus
vv   SULF2 MUTATED SULF2 WILD-TYPE
  R0            21             324
  R1             1               3
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1343V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SULF2 MUTATED                                  0     1
  SULF2 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  SULF2 MUTATED                           1    16
  SULF2 WILD-TYPE                        21   210
D1343V13, multiclass
                                  clus
vv                                 SULF2 MUTATED SULF2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                       16             210
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1344) Variable = AIM2 MUTATION ANALYSIS
D1344V1, survival
                sevent
clus2              0   1
  AIM2 MUTATED     7   2
  AIM2 WILD-TYPE 371  91
  AIM2 MUTATED AIM2 WILD-TYPE 
             9            462 
  AIM2 MUTATED AIM2 WILD-TYPE 
             2             91 
$`AIM2 MUTATED`
TCGA-A6-6780 TCGA-AA-3510 TCGA-AA-A010 TCGA-AD-6964 TCGA-AZ-4315 TCGA-AZ-6601 
       20.12        63.98        34.98        10.88        58.39       100.01 
TCGA-CM-4744 TCGA-CM-5864 TCGA-G4-6304 
       20.02        15.02        53.62 

$`AIM2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
        0.79         0.72         5.79        22.42        27.42         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 
       88.21        49.41         6.77        12.10        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5868 
       30.08        32.02        15.02         5.03        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       74.56        65.85        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  AIM2 MUTATED AIM2 WILD-TYPE 
         10.88           0.00 
  AIM2 MUTATED AIM2 WILD-TYPE 
        100.01         148.01 
  AIM2 MUTATED AIM2 WILD-TYPE 
         34.98          20.12 
[1] "10.9 - 100.0 (35.0)" "0.0 - 148.0 (20.1)" 
[1] "hr=" "1.5"
D1344V2, continuous
D1344V3, binary
                cls
clus               0   1
  AIM2 MUTATED     9   0
  AIM2 WILD-TYPE 357 119
[1] "tbl2"
                cls
clus             [,1] [,2]
  AIM2 MUTATED      9    0
  AIM2 WILD-TYPE  357  119
        clus
vv       AIM2 MUTATED AIM2 WILD-TYPE
  COLON             9            357
  RECTUM            0            119
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  AIM2 MUTATED         2        0        2         2         2         0
  AIM2 WILD-TYPE      89        1       30       136         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AIM2 MUTATED           0          0          0          0        0         0
  AIM2 WILD-TYPE        24         11         59         42       48        18
                vv
clus             STAGE IVB
  AIM2 MUTATED           0
  AIM2 WILD-TYPE         1
D1344V4, multiclass
            clus
vv           AIM2 MUTATED AIM2 WILD-TYPE
  STAGE I               2             89
  STAGE IA              0              1
  STAGE II              2             30
  STAGE IIA             2            136
  STAGE IIB             2              8
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            0             59
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  AIM2 MUTATED     0   2   4   3
  AIM2 WILD-TYPE  17  90 325  47
D1344V5, multiclass
    clus
vv   AIM2 MUTATED AIM2 WILD-TYPE
  T1            0             17
  T2            2             90
  T3            4            325
  T4            3             47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  AIM2 MUTATED     8   0   1
  AIM2 WILD-TYPE 279 113  86
D1344V6, multiclass
    clus
vv   AIM2 MUTATED AIM2 WILD-TYPE
  N0            8            279
  N1            0            113
  N2            1             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1344V7, binary
                cls
clus               0   1
  AIM2 MUTATED     7   0
  AIM2 WILD-TYPE 368  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  AIM2 MUTATED      7    0
  AIM2 WILD-TYPE  368   65
   clus
vv  AIM2 MUTATED AIM2 WILD-TYPE
  0            7            368
  1            0             65
[1] 2 2
[1] FALSE
D1344V8, binary
                cls
clus               0   1
  AIM2 MUTATED     2   7
  AIM2 WILD-TYPE 223 257
[1] "tbl2"
                cls
clus             [,1] [,2]
  AIM2 MUTATED      2    7
  AIM2 WILD-TYPE  223  257
        clus
vv       AIM2 MUTATED AIM2 WILD-TYPE
  FEMALE            2            223
  MALE              7            257
[1] 2 2
[1] FALSE
D1344V9, binary
                cls
clus               0   1
  AIM2 MUTATED     9   0
  AIM2 WILD-TYPE 341  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  AIM2 MUTATED      9    0
  AIM2 WILD-TYPE  341   22
     clus
vv    AIM2 MUTATED AIM2 WILD-TYPE
  NO             9            341
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  AIM2 MUTATED                      8                             1
  AIM2 WILD-TYPE                  307                            46
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  AIM2 MUTATED                       0                              0
  AIM2 WILD-TYPE                   106                             10
D1344V10, multiclass
                                clus
vv                               AIM2 MUTATED AIM2 WILD-TYPE
  COLON ADENOCARCINOMA                      8            307
  COLON MUCINOUS ADENOCARCINOMA             1             46
  RECTAL ADENOCARCINOMA                     0            106
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  AIM2 MUTATED     6   0   0   0
  AIM2 WILD-TYPE 339   4  31  25
D1344V11, multiclass
    clus
vv   AIM2 MUTATED AIM2 WILD-TYPE
  R0            6            339
  R1            0              4
  R2            0             31
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1344V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AIM2 MUTATED                                  0     0
  AIM2 WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  AIM2 MUTATED                           0     7
  AIM2 WILD-TYPE                        22   219
D1344V13, multiclass
                                  clus
vv                                 AIM2 MUTATED AIM2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       7            219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1345) Variable = SPAG7 MUTATION ANALYSIS
D1345V1, survival
                 sevent
clus2               0   1
  SPAG7 MUTATED     2   1
  SPAG7 WILD-TYPE 376  92
  SPAG7 MUTATED SPAG7 WILD-TYPE 
              3             468 
  SPAG7 MUTATED SPAG7 WILD-TYPE 
              1              92 
$`SPAG7 MUTATED`
TCGA-AY-6386 TCGA-AZ-6598 TCGA-D5-5540 
       17.82        49.41        56.09 

$`SPAG7 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-4323 
       16.31         0.95        33.01        21.44        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 
        5.13       106.75        22.36        62.79        88.21         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6529 
       12.03        45.40        12.26        19.59        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  SPAG7 MUTATED SPAG7 WILD-TYPE 
          17.82            0.00 
  SPAG7 MUTATED SPAG7 WILD-TYPE 
          56.09          148.01 
  SPAG7 MUTATED SPAG7 WILD-TYPE 
         49.410          20.155 
[1] "17.8 - 56.1 (49.4)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1"  
D1345V2, continuous
D1345V3, binary
                 cls
clus                0   1
  SPAG7 MUTATED     3   0
  SPAG7 WILD-TYPE 363 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SPAG7 MUTATED      3    0
  SPAG7 WILD-TYPE  363  119
        clus
vv       SPAG7 MUTATED SPAG7 WILD-TYPE
  COLON              3             363
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SPAG7 MUTATED         0        0        1         1         0         0
  SPAG7 WILD-TYPE      91        1       31       137        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SPAG7 MUTATED           0          0          1          0        0         0
  SPAG7 WILD-TYPE        24         11         58         42       48        18
                 vv
clus              STAGE IVB
  SPAG7 MUTATED           0
  SPAG7 WILD-TYPE         1
D1345V4, multiclass
            clus
vv           SPAG7 MUTATED SPAG7 WILD-TYPE
  STAGE I                0              91
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              1             137
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  SPAG7 MUTATED     0   0   3   0
  SPAG7 WILD-TYPE  17  92 326  50
D1345V5, multiclass
    clus
vv   SPAG7 MUTATED SPAG7 WILD-TYPE
  T1             0              17
  T2             0              92
  T3             3             326
  T4             0              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  SPAG7 MUTATED     2   1   0
  SPAG7 WILD-TYPE 285 112  87
D1345V6, multiclass
    clus
vv   SPAG7 MUTATED SPAG7 WILD-TYPE
  N0             2             285
  N1             1             112
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1345V7, binary
                 cls
clus                0   1
  SPAG7 MUTATED     2   0
  SPAG7 WILD-TYPE 373  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SPAG7 MUTATED      2    0
  SPAG7 WILD-TYPE  373   65
   clus
vv  SPAG7 MUTATED SPAG7 WILD-TYPE
  0             2             373
  1             0              65
[1] 2 2
[1] FALSE
D1345V8, binary
                 cls
clus                0   1
  SPAG7 MUTATED     2   1
  SPAG7 WILD-TYPE 223 263
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SPAG7 MUTATED      2    1
  SPAG7 WILD-TYPE  223  263
        clus
vv       SPAG7 MUTATED SPAG7 WILD-TYPE
  FEMALE             2             223
  MALE               1             263
[1] 2 2
[1] FALSE
D1345V9, binary
                 cls
clus                0   1
  SPAG7 MUTATED     3   0
  SPAG7 WILD-TYPE 347  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SPAG7 MUTATED      3    0
  SPAG7 WILD-TYPE  347   22
     clus
vv    SPAG7 MUTATED SPAG7 WILD-TYPE
  NO              3             347
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SPAG7 MUTATED                      3                             0
  SPAG7 WILD-TYPE                  312                            47
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SPAG7 MUTATED                       0                              0
  SPAG7 WILD-TYPE                   106                             10
D1345V10, multiclass
                                clus
vv                               SPAG7 MUTATED SPAG7 WILD-TYPE
  COLON ADENOCARCINOMA                       3             312
  COLON MUCINOUS ADENOCARCINOMA              0              47
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  SPAG7 MUTATED     2   0   0   0
  SPAG7 WILD-TYPE 343   4  31  25
D1345V11, multiclass
[1] "Remove cluster labels:" "SPAG7 MUTATED"         
clus
  SPAG7 MUTATED SPAG7 WILD-TYPE 
              2             403 
     TCGA-A6-2671      TCGA-A6-2672      TCGA-A6-2674      TCGA-A6-2676 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-A6-2677      TCGA-A6-2678      TCGA-A6-2683      TCGA-A6-3807 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-A6-3808      TCGA-A6-3809      TCGA-A6-3810      TCGA-A6-5657 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-A6-5659      TCGA-A6-5661      TCGA-A6-5665      TCGA-A6-6781 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-AA-3489      TCGA-AA-3492      TCGA-AA-3496      TCGA-AA-3502 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-AA-3510      TCGA-AA-3511      TCGA-AA-3514      TCGA-AA-3517 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-AA-3518      TCGA-AA-3519      TCGA-AA-3520      TCGA-AA-3521 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-AA-3522      TCGA-AA-3524      TCGA-AA-3525      TCGA-AA-3526 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-AA-3527      TCGA-AA-3529      TCGA-AA-3530      TCGA-AA-3531 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-AA-3532      TCGA-AA-3534      TCGA-AA-3538      TCGA-AA-3542 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-AA-3543      TCGA-AA-3544      TCGA-AA-3548      TCGA-AA-3549 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-AA-3552      TCGA-AA-3553      TCGA-AA-3554      TCGA-AA-3555 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-AA-3556      TCGA-AA-3558      TCGA-AA-3560      TCGA-AA-3561 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-AA-3562      TCGA-AA-3655      TCGA-AA-3660      TCGA-AA-3662 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-AA-3663      TCGA-AA-3664      TCGA-AA-3666      TCGA-AA-3667 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-AA-3672      TCGA-AA-3673      TCGA-AA-3678      TCGA-AA-3679 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-AA-3680      TCGA-AA-3681      TCGA-AA-3684      TCGA-AA-3685 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-AA-3688      TCGA-AA-3692      TCGA-AA-3693      TCGA-AA-3695 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-AA-3696      TCGA-AA-3697      TCGA-AA-3710      TCGA-AA-3712 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-AA-3713      TCGA-AA-3715      TCGA-AA-3811      TCGA-AA-3812 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-AA-3814      TCGA-AA-3815      TCGA-AA-3818      TCGA-AA-3819 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-AA-3821      TCGA-AA-3831      TCGA-AA-3833      TCGA-AA-3837 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-AA-3842      TCGA-AA-3844      TCGA-AA-3845      TCGA-AA-3846 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-AA-3848      TCGA-AA-3850      TCGA-AA-3851      TCGA-AA-3852 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-AA-3854      TCGA-AA-3855      TCGA-AA-3856      TCGA-AA-3858 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-AA-3860      TCGA-AA-3861      TCGA-AA-3864      TCGA-AA-3866 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-AA-3867      TCGA-AA-3869      TCGA-AA-3870      TCGA-AA-3872 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-AA-3875      TCGA-AA-3877      TCGA-AA-3930      TCGA-AA-3939 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-AA-3941      TCGA-AA-3947      TCGA-AA-3949      TCGA-AA-3950 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-AA-3952      TCGA-AA-3955      TCGA-AA-3956      TCGA-AA-3968 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-AA-3971      TCGA-AA-3972      TCGA-AA-3973      TCGA-AA-3975 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-AA-3976      TCGA-AA-3979      TCGA-AA-3984      TCGA-AA-3986 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-AA-3989      TCGA-AA-3994      TCGA-AA-A004      TCGA-AA-A00A 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-AA-A00D      TCGA-AA-A00E      TCGA-AA-A00F      TCGA-AA-A00J 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-AA-A00K      TCGA-AA-A00L      TCGA-AA-A00N      TCGA-AA-A00O 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-AA-A00Q      TCGA-AA-A00R      TCGA-AA-A00U      TCGA-AA-A00W 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-AA-A00Z      TCGA-AA-A010      TCGA-AA-A017      TCGA-AA-A01D 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-AA-A01F      TCGA-AA-A01G      TCGA-AA-A01I      TCGA-AA-A01K 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-AA-A01P      TCGA-AA-A01Q      TCGA-AA-A01R      TCGA-AA-A01S 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-AA-A01T      TCGA-AA-A01V      TCGA-AA-A01X      TCGA-AA-A01Z 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-AA-A022      TCGA-AA-A024      TCGA-AA-A029      TCGA-AA-A02F 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-AA-A02H      TCGA-AA-A02J      TCGA-AA-A02K      TCGA-AA-A02O 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-AA-A02W      TCGA-AA-A02Y      TCGA-AA-A03F      TCGA-AA-A03J 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-AD-5900      TCGA-AD-6548      TCGA-AD-6888      TCGA-AU-3779 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-AU-6004      TCGA-AY-4070      TCGA-AY-4071      TCGA-AY-5543 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-AY-6196      TCGA-AY-6197      TCGA-AZ-4315      TCGA-AZ-4681 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-AZ-4682      TCGA-CA-5254      TCGA-CA-5255      TCGA-CA-5796 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-CA-5797      TCGA-CA-6715      TCGA-CA-6716      TCGA-CA-6717 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-CA-6718      TCGA-CA-6719      TCGA-CK-4947      TCGA-CK-4948 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-CK-4950      TCGA-CK-4952      TCGA-CK-5912      TCGA-CK-5913 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-CK-5914      TCGA-CK-5915      TCGA-CK-5916      TCGA-CK-6746 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-CK-6747      TCGA-CK-6748      TCGA-CK-6751      TCGA-CM-4743 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-CM-4744      TCGA-CM-4746      TCGA-CM-4747      TCGA-CM-4752 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-CM-5341      TCGA-CM-5344      TCGA-CM-5348      TCGA-CM-5349 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-CM-5860      TCGA-CM-5861      TCGA-CM-5862      TCGA-CM-5863 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-CM-5864      TCGA-CM-5868      TCGA-CM-6161      TCGA-CM-6162 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-CM-6163      TCGA-CM-6164      TCGA-CM-6165      TCGA-CM-6166 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-CM-6167      TCGA-CM-6168      TCGA-CM-6169      TCGA-CM-6170 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-CM-6171      TCGA-CM-6172      TCGA-CM-6674      TCGA-CM-6675 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-CM-6676      TCGA-CM-6677      TCGA-CM-6678      TCGA-CM-6679 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-CM-6680      TCGA-D5-5537      TCGA-D5-5538      TCGA-D5-5539 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-D5-5541      TCGA-D5-6529      TCGA-D5-6532      TCGA-D5-6533 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-D5-6534      TCGA-D5-6535      TCGA-D5-6536      TCGA-D5-6537 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-D5-6538      TCGA-D5-6539      TCGA-D5-6540      TCGA-D5-6541 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-D5-6898      TCGA-D5-6920      TCGA-D5-6922      TCGA-D5-6923 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-D5-6924      TCGA-D5-6926      TCGA-D5-6927      TCGA-D5-6928 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-D5-6929      TCGA-D5-6930      TCGA-D5-6931      TCGA-D5-6932 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-D5-7000      TCGA-F4-6459      TCGA-F4-6460      TCGA-F4-6569 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-F4-6570      TCGA-F4-6703      TCGA-F4-6704      TCGA-F4-6805 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-F4-6806      TCGA-F4-6807      TCGA-F4-6808      TCGA-F4-6809 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-F4-6854      TCGA-F4-6855      TCGA-F4-6856      TCGA-G4-6293 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-G4-6299      TCGA-G4-6303      TCGA-G4-6304      TCGA-G4-6306 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-G4-6307      TCGA-G4-6309      TCGA-G4-6310      TCGA-G4-6315 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-G4-6317      TCGA-G4-6321      TCGA-G4-6323      TCGA-G4-6586 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-G4-6588      TCGA-G4-6625      TCGA-G4-6626      TCGA-G4-6628 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-AF-2687      TCGA-AF-2689      TCGA-AF-2691      TCGA-AF-2692 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-AF-3400      TCGA-AF-3913      TCGA-AF-4110      TCGA-AF-5654 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-AF-6655      TCGA-AG-3574      TCGA-AG-3575      TCGA-AG-3578 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-AG-3580      TCGA-AG-3581      TCGA-AG-3582      TCGA-AG-3583 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-AG-3584      TCGA-AG-3586      TCGA-AG-3587      TCGA-AG-3593 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-AG-3594      TCGA-AG-3598      TCGA-AG-3599      TCGA-AG-3600 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-AG-3601      TCGA-AG-3602      TCGA-AG-3605      TCGA-AG-3608 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-AG-3609      TCGA-AG-3611      TCGA-AG-3612      TCGA-AG-3726 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-AG-3727      TCGA-AG-3731      TCGA-AG-3732      TCGA-AG-3742 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-AG-3878      TCGA-AG-3882      TCGA-AG-3883      TCGA-AG-3885 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-AG-3887      TCGA-AG-3890      TCGA-AG-3892      TCGA-AG-3893 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-AG-3894      TCGA-AG-3896      TCGA-AG-3898      TCGA-AG-3901 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-AG-3902      TCGA-AG-3909      TCGA-AG-3999      TCGA-AG-4001 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-AG-4005      TCGA-AG-4007      TCGA-AG-4008      TCGA-AG-4015 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-AG-A002      TCGA-AG-A008      TCGA-AG-A00C      TCGA-AG-A00H 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-AG-A00Y      TCGA-AG-A011      TCGA-AG-A014      TCGA-AG-A015 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-AG-A016      TCGA-AG-A01L      TCGA-AG-A01W      TCGA-AG-A01Y 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-AG-A020      TCGA-AG-A025      TCGA-AG-A026      TCGA-AG-A02G 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-AG-A02N      TCGA-AG-A02X      TCGA-AG-A032      TCGA-AG-A036 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-AH-6549      TCGA-AH-6643      TCGA-CL-5917      TCGA-CL-5918 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-DC-5337      TCGA-DC-5869      TCGA-DC-6155      TCGA-DC-6157 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-DC-6158      TCGA-DC-6160      TCGA-DC-6681      TCGA-DC-6682 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-DC-6683      TCGA-DT-5265      TCGA-EF-5830      TCGA-EI-6506 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-EI-6507      TCGA-EI-6508      TCGA-EI-6510      TCGA-F5-6464 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-F5-6465      TCGA-F5-6571      TCGA-F5-6702      TCGA-F5-6812 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
     TCGA-F5-6813      TCGA-G5-6235      TCGA-G5-6641 
"SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" "SPAG7 WILD-TYPE" 
D1345V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SPAG7 MUTATED                                  0     0
  SPAG7 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  SPAG7 MUTATED                           1     2
  SPAG7 WILD-TYPE                        21   224
D1345V13, multiclass
                                  clus
vv                                 SPAG7 MUTATED SPAG7 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        2             224
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1346) Variable = WDR75 MUTATION ANALYSIS
D1346V1, survival
                 sevent
clus2               0   1
  WDR75 MUTATED     4   3
  WDR75 WILD-TYPE 374  90
  WDR75 MUTATED WDR75 WILD-TYPE 
              7             464 
  WDR75 MUTATED WDR75 WILD-TYPE 
              3              90 
$`WDR75 MUTATED`
TCGA-AA-3856 TCGA-AA-3977 TCGA-AA-A00E TCGA-AA-A00N TCGA-AD-6899 TCGA-CM-4747 
        0.99        25.02        30.02         4.01         5.79        25.02 
TCGA-F4-6570 
        6.18 

$`WDR75 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       36.03        32.05        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       19.00        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        0.72        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       23.05        20.02        37.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       31.96        35.74        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  WDR75 MUTATED WDR75 WILD-TYPE 
           0.99            0.00 
  WDR75 MUTATED WDR75 WILD-TYPE 
          30.02          148.01 
  WDR75 MUTATED WDR75 WILD-TYPE 
          6.180          20.235 
[1] "1.0 - 30.0 (6.2)"   "0.0 - 148.0 (20.2)"
[1] "hr=" "4.2"
D1346V2, continuous
D1346V3, binary
                 cls
clus                0   1
  WDR75 MUTATED     8   0
  WDR75 WILD-TYPE 358 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WDR75 MUTATED      8    0
  WDR75 WILD-TYPE  358  119
        clus
vv       WDR75 MUTATED WDR75 WILD-TYPE
  COLON              8             358
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  WDR75 MUTATED         0        0        0         4         1         0
  WDR75 WILD-TYPE      91        1       32       134         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  WDR75 MUTATED           0          0          0          1        0         1
  WDR75 WILD-TYPE        24         11         59         41       48        17
                 vv
clus              STAGE IVB
  WDR75 MUTATED           0
  WDR75 WILD-TYPE         1
D1346V4, multiclass
            clus
vv           WDR75 MUTATED WDR75 WILD-TYPE
  STAGE I                0              91
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              4             134
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             1              41
  STAGE IV               0              48
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  WDR75 MUTATED     0   1   4   3
  WDR75 WILD-TYPE  17  91 325  47
D1346V5, multiclass
    clus
vv   WDR75 MUTATED WDR75 WILD-TYPE
  T1             0              17
  T2             1              91
  T3             4             325
  T4             3              47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  WDR75 MUTATED     6   1   1
  WDR75 WILD-TYPE 281 112  86
D1346V6, multiclass
    clus
vv   WDR75 MUTATED WDR75 WILD-TYPE
  N0             6             281
  N1             1             112
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1346V7, binary
                 cls
clus                0   1
  WDR75 MUTATED     5   1
  WDR75 WILD-TYPE 370  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WDR75 MUTATED      5    1
  WDR75 WILD-TYPE  370   64
   clus
vv  WDR75 MUTATED WDR75 WILD-TYPE
  0             5             370
  1             1              64
[1] 2 2
[1] FALSE
D1346V8, binary
                 cls
clus                0   1
  WDR75 MUTATED     2   6
  WDR75 WILD-TYPE 223 258
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WDR75 MUTATED      2    6
  WDR75 WILD-TYPE  223  258
        clus
vv       WDR75 MUTATED WDR75 WILD-TYPE
  FEMALE             2             223
  MALE               6             258
[1] 2 2
[1] FALSE
D1346V9, binary
                 cls
clus                0   1
  WDR75 MUTATED     5   0
  WDR75 WILD-TYPE 345  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WDR75 MUTATED      5    0
  WDR75 WILD-TYPE  345   22
     clus
vv    WDR75 MUTATED WDR75 WILD-TYPE
  NO              5             345
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  WDR75 MUTATED                      6                             2
  WDR75 WILD-TYPE                  309                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  WDR75 MUTATED                       0                              0
  WDR75 WILD-TYPE                   106                             10
D1346V10, multiclass
                                clus
vv                               WDR75 MUTATED WDR75 WILD-TYPE
  COLON ADENOCARCINOMA                       6             309
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  WDR75 MUTATED     6   0   0   0
  WDR75 WILD-TYPE 339   4  31  25
D1346V11, multiclass
    clus
vv   WDR75 MUTATED WDR75 WILD-TYPE
  R0             6             339
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1346V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  WDR75 MUTATED                                  0     0
  WDR75 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  WDR75 MUTATED                           0     3
  WDR75 WILD-TYPE                        22   223
D1346V13, multiclass
                                  clus
vv                                 WDR75 MUTATED WDR75 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        3             223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1347) Variable = CPN2 MUTATION ANALYSIS
D1347V1, survival
                sevent
clus2              0   1
  CPN2 MUTATED     7   2
  CPN2 WILD-TYPE 371  91
  CPN2 MUTATED CPN2 WILD-TYPE 
             9            462 
  CPN2 MUTATED CPN2 WILD-TYPE 
             2             91 
$`CPN2 MUTATED`
TCGA-AA-3663 TCGA-AA-3947 TCGA-AD-6889 TCGA-AU-6004 TCGA-AZ-4315 TCGA-F4-6703 
        6.97        33.01        56.55        27.09        58.39        47.87 
TCGA-G4-6303 TCGA-AF-2687 TCGA-DY-A1H8 
       65.85        24.13        32.61 

$`CPN2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.05        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
        2.01        12.99        24.00        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
        0.20        14.50        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6704 TCGA-F4-6805 
        8.61        31.96        35.74         6.18         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
       35.31       133.18        74.56        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2689 
       35.80        26.17        91.79        46.75        79.69        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EF-5830 TCGA-EI-6506 
       41.36        57.24        24.13        51.48         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  CPN2 MUTATED CPN2 WILD-TYPE 
          6.97           0.00 
  CPN2 MUTATED CPN2 WILD-TYPE 
         65.85         148.01 
  CPN2 MUTATED CPN2 WILD-TYPE 
         33.01          20.02 
[1] "7.0 - 65.8 (33.0)"  "0.0 - 148.0 (20.0)"
[1] "hr=" "1.4"
D1347V2, continuous
D1347V3, binary
                cls
clus               0   1
  CPN2 MUTATED     8   2
  CPN2 WILD-TYPE 358 117
[1] "tbl2"
                cls
clus             [,1] [,2]
  CPN2 MUTATED      8    2
  CPN2 WILD-TYPE  358  117
        clus
vv       CPN2 MUTATED CPN2 WILD-TYPE
  COLON             8            358
  RECTUM            2            117
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CPN2 MUTATED         1        0        1         3         1         0
  CPN2 WILD-TYPE      90        1       31       135         9         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CPN2 MUTATED           1          1          0          1        1         0
  CPN2 WILD-TYPE        23         10         59         41       47        18
                vv
clus             STAGE IVB
  CPN2 MUTATED           0
  CPN2 WILD-TYPE         1
D1347V4, multiclass
            clus
vv           CPN2 MUTATED CPN2 WILD-TYPE
  STAGE I               1             90
  STAGE IA              0              1
  STAGE II              1             31
  STAGE IIA             3            135
  STAGE IIB             1              9
  STAGE IIC             0              1
  STAGE III             1             23
  STAGE IIIA            1             10
  STAGE IIIB            0             59
  STAGE IIIC            1             41
  STAGE IV              1             47
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  CPN2 MUTATED     0   2   7   1
  CPN2 WILD-TYPE  17  90 322  49
D1347V5, multiclass
    clus
vv   CPN2 MUTATED CPN2 WILD-TYPE
  T1            0             17
  T2            2             90
  T3            7            322
  T4            1             49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  CPN2 MUTATED     6   2   2
  CPN2 WILD-TYPE 281 111  85
D1347V6, multiclass
    clus
vv   CPN2 MUTATED CPN2 WILD-TYPE
  N0            6            281
  N1            2            111
  N2            2             85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1347V7, binary
                cls
clus               0   1
  CPN2 MUTATED     9   1
  CPN2 WILD-TYPE 366  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  CPN2 MUTATED      9    1
  CPN2 WILD-TYPE  366   64
   clus
vv  CPN2 MUTATED CPN2 WILD-TYPE
  0            9            366
  1            1             64
[1] 2 2
[1] FALSE
D1347V8, binary
                cls
clus               0   1
  CPN2 MUTATED     4   6
  CPN2 WILD-TYPE 221 258
[1] "tbl2"
                cls
clus             [,1] [,2]
  CPN2 MUTATED      4    6
  CPN2 WILD-TYPE  221  258
        clus
vv       CPN2 MUTATED CPN2 WILD-TYPE
  FEMALE            4            221
  MALE              6            258
[1] 2 2
[1] FALSE
D1347V9, binary
                cls
clus               0   1
  CPN2 MUTATED     5   1
  CPN2 WILD-TYPE 345  21
[1] "tbl2"
                cls
clus             [,1] [,2]
  CPN2 MUTATED      5    1
  CPN2 WILD-TYPE  345   21
     clus
vv    CPN2 MUTATED CPN2 WILD-TYPE
  NO             5            345
  YES            1             21
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CPN2 MUTATED                      7                             1
  CPN2 WILD-TYPE                  308                            46
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CPN2 MUTATED                       2                              0
  CPN2 WILD-TYPE                   104                             10
D1347V10, multiclass
                                clus
vv                               CPN2 MUTATED CPN2 WILD-TYPE
  COLON ADENOCARCINOMA                      7            308
  COLON MUCINOUS ADENOCARCINOMA             1             46
  RECTAL ADENOCARCINOMA                     2            104
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  CPN2 MUTATED     8   0   0   0
  CPN2 WILD-TYPE 337   4  31  25
D1347V11, multiclass
    clus
vv   CPN2 MUTATED CPN2 WILD-TYPE
  R0            8            337
  R1            0              4
  R2            0             31
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1347V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CPN2 MUTATED                                  0     1
  CPN2 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  CPN2 MUTATED                           0     6
  CPN2 WILD-TYPE                        22   220
D1347V13, multiclass
                                  clus
vv                                 CPN2 MUTATED CPN2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       6            220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1348) Variable = NFKBIB MUTATION ANALYSIS
D1348V1, survival
                  sevent
clus2                0   1
  NFKBIB MUTATED     2   3
  NFKBIB WILD-TYPE 376  90
  NFKBIB MUTATED NFKBIB WILD-TYPE 
               5              466 
  NFKBIB MUTATED NFKBIB WILD-TYPE 
               3               90 
$`NFKBIB MUTATED`
TCGA-AA-3875 TCGA-AZ-6605 TCGA-DM-A1D7 TCGA-G4-6303 TCGA-G4-6588 
       18.05         5.23        13.32        65.85        26.17 

$`NFKBIB WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3877 
       53.00        17.03        24.03        27.02        29.98        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77        12.10       100.01        29.56        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        35.80        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  NFKBIB MUTATED NFKBIB WILD-TYPE 
            5.23             0.00 
  NFKBIB MUTATED NFKBIB WILD-TYPE 
           65.85           148.01 
  NFKBIB MUTATED NFKBIB WILD-TYPE 
          18.050           20.235 
[1] "5.2 - 65.8 (18.1)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "2.8"
D1348V2, continuous
D1348V3, binary
                  cls
clus                 0   1
  NFKBIB MUTATED     5   0
  NFKBIB WILD-TYPE 361 119
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NFKBIB MUTATED      5    0
  NFKBIB WILD-TYPE  361  119
        clus
vv       NFKBIB MUTATED NFKBIB WILD-TYPE
  COLON               5              361
  RECTUM              0              119
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NFKBIB MUTATED         1        0        0         2         0         0
  NFKBIB WILD-TYPE      90        1       32       136        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NFKBIB MUTATED           0          0          1          0        1
  NFKBIB WILD-TYPE        24         11         58         42       47
                  vv
clus               STAGE IVA STAGE IVB
  NFKBIB MUTATED           0         0
  NFKBIB WILD-TYPE        18         1
D1348V4, multiclass
            clus
vv           NFKBIB MUTATED NFKBIB WILD-TYPE
  STAGE I                 1               90
  STAGE IA                0                1
  STAGE II                0               32
  STAGE IIA               2              136
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              1               58
  STAGE IIIC              0               42
  STAGE IV                1               47
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  NFKBIB MUTATED     1   0   3   1
  NFKBIB WILD-TYPE  16  92 326  49
D1348V5, multiclass
    clus
vv   NFKBIB MUTATED NFKBIB WILD-TYPE
  T1              1               16
  T2              0               92
  T3              3              326
  T4              1               49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  NFKBIB MUTATED     3   2   0
  NFKBIB WILD-TYPE 284 111  87
D1348V6, multiclass
    clus
vv   NFKBIB MUTATED NFKBIB WILD-TYPE
  N0              3              284
  N1              2              111
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1348V7, binary
                  cls
clus                 0   1
  NFKBIB MUTATED     4   1
  NFKBIB WILD-TYPE 371  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NFKBIB MUTATED      4    1
  NFKBIB WILD-TYPE  371   64
   clus
vv  NFKBIB MUTATED NFKBIB WILD-TYPE
  0              4              371
  1              1               64
[1] 2 2
[1] FALSE
D1348V8, binary
                  cls
clus                 0   1
  NFKBIB MUTATED     3   2
  NFKBIB WILD-TYPE 222 262
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NFKBIB MUTATED      3    2
  NFKBIB WILD-TYPE  222  262
        clus
vv       NFKBIB MUTATED NFKBIB WILD-TYPE
  FEMALE              3              222
  MALE                2              262
[1] 2 2
[1] FALSE
D1348V9, binary
                  cls
clus                 0   1
  NFKBIB MUTATED     4   0
  NFKBIB WILD-TYPE 346  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NFKBIB MUTATED      4    0
  NFKBIB WILD-TYPE  346   22
     clus
vv    NFKBIB MUTATED NFKBIB WILD-TYPE
  NO               4              346
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  NFKBIB MUTATED                      4                             0
  NFKBIB WILD-TYPE                  311                            47
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  NFKBIB MUTATED                       0                              0
  NFKBIB WILD-TYPE                   106                             10
D1348V10, multiclass
                                clus
vv                               NFKBIB MUTATED NFKBIB WILD-TYPE
  COLON ADENOCARCINOMA                        4              311
  COLON MUCINOUS ADENOCARCINOMA               0               47
  RECTAL ADENOCARCINOMA                       0              106
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  NFKBIB MUTATED     3   0   0   0
  NFKBIB WILD-TYPE 342   4  31  25
D1348V11, multiclass
    clus
vv   NFKBIB MUTATED NFKBIB WILD-TYPE
  R0              3              342
  R1              0                4
  R2              0               31
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1348V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NFKBIB MUTATED                                  0     0
  NFKBIB WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  NFKBIB MUTATED                           0     4
  NFKBIB WILD-TYPE                        22   222
D1348V13, multiclass
                                  clus
vv                                 NFKBIB MUTATED NFKBIB WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         4              222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1349) Variable = ATRX MUTATION ANALYSIS
D1349V1, survival
                sevent
clus2              0   1
  ATRX MUTATED    23   8
  ATRX WILD-TYPE 355  85
  ATRX MUTATED ATRX WILD-TYPE 
            31            440 
  ATRX MUTATED ATRX WILD-TYPE 
             8             85 
$`ATRX MUTATED`
TCGA-A6-2677 TCGA-A6-5665 TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3555 TCGA-AA-3815 
       24.33        22.06         3.02        63.98        29.95        33.04 
TCGA-AA-3947 TCGA-AA-3977 TCGA-AD-6895 TCGA-AZ-4315 TCGA-AZ-6606 TCGA-AZ-6607 
       33.01        25.02         0.72        58.39        11.74         3.19 
TCGA-CA-5255 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4950 TCGA-CM-4746 TCGA-CM-5860 
        3.06        12.76        10.06        85.45        37.02        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5868 TCGA-DM-A0XD TCGA-DM-A1D0 TCGA-F4-6570 
       15.02         5.03        17.03        24.43       130.65         6.18 
TCGA-F4-6805 TCGA-F4-6807 TCGA-F4-6854 TCGA-G4-6315 TCGA-G4-6588 TCGA-AH-6549 
       34.42        16.24         0.53        61.91        26.17        17.49 
TCGA-DT-5265 
        5.29 

$`ATRX WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        42.90        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 
       19.66        20.28         7.04         1.02        35.01         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       78.08         6.05         6.97        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
       19.04        19.04        10.06        35.05         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 
       31.00         2.01        12.99        24.00        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
       56.55         0.79         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5796 TCGA-CA-5797 
       29.56         5.23         1.61        12.69         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 
        0.07        12.20        14.30        17.56       148.01        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
      124.27        23.05        20.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6161 
       22.03        22.98        30.08        15.02        15.02        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XF TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
       38.20        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6806 
        8.61        31.96        35.74        47.87         1.55        41.42 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       33.67        13.25        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        35.80        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
        1.45         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  ATRX MUTATED ATRX WILD-TYPE 
          0.53           0.00 
  ATRX MUTATED ATRX WILD-TYPE 
        130.65         148.01 
  ATRX MUTATED ATRX WILD-TYPE 
        22.060         20.155 
[1] "0.5 - 130.7 (22.1)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.3"
D1349V2, continuous
D1349V3, binary
                cls
clus               0   1
  ATRX MUTATED    31   2
  ATRX WILD-TYPE 335 117
[1] "tbl2"
                cls
clus             [,1] [,2]
  ATRX MUTATED     31    2
  ATRX WILD-TYPE  335  117
        clus
vv       ATRX MUTATED ATRX WILD-TYPE
  COLON            31            335
  RECTUM            2            117
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ATRX MUTATED         1        0        3        16         2         0
  ATRX WILD-TYPE      90        1       29       122         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ATRX MUTATED           0          0          1          2        3         2
  ATRX WILD-TYPE        24         11         58         40       45        16
                vv
clus             STAGE IVB
  ATRX MUTATED           0
  ATRX WILD-TYPE         1
D1349V4, multiclass
            clus
vv           ATRX MUTATED ATRX WILD-TYPE
  STAGE I               1             90
  STAGE IA              0              1
  STAGE II              3             29
  STAGE IIA            16            122
  STAGE IIB             2              8
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            1             58
  STAGE IIIC            2             40
  STAGE IV              3             45
  STAGE IVA             2             16
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  ATRX MUTATED     0   2  26   5
  ATRX WILD-TYPE  17  90 303  45
D1349V5, multiclass
    clus
vv   ATRX MUTATED ATRX WILD-TYPE
  T1            0             17
  T2            2             90
  T3           26            303
  T4            5             45
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  ATRX MUTATED    23   5   4
  ATRX WILD-TYPE 264 108  83
D1349V6, multiclass
    clus
vv   ATRX MUTATED ATRX WILD-TYPE
  N0           23            264
  N1            5            108
  N2            4             83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1349V7, binary
                cls
clus               0   1
  ATRX MUTATED    24   5
  ATRX WILD-TYPE 351  60
[1] "tbl2"
                cls
clus             [,1] [,2]
  ATRX MUTATED     24    5
  ATRX WILD-TYPE  351   60
   clus
vv  ATRX MUTATED ATRX WILD-TYPE
  0           24            351
  1            5             60
[1] 2 2
[1] FALSE
D1349V8, binary
                cls
clus               0   1
  ATRX MUTATED    17  16
  ATRX WILD-TYPE 208 248
[1] "tbl2"
                cls
clus             [,1] [,2]
  ATRX MUTATED     17   16
  ATRX WILD-TYPE  208  248
        clus
vv       ATRX MUTATED ATRX WILD-TYPE
  FEMALE           17            208
  MALE             16            248
[1] 2 2
[1] FALSE
D1349V9, binary
                cls
clus               0   1
  ATRX MUTATED    27   1
  ATRX WILD-TYPE 323  21
[1] "tbl2"
                cls
clus             [,1] [,2]
  ATRX MUTATED     27    1
  ATRX WILD-TYPE  323   21
     clus
vv    ATRX MUTATED ATRX WILD-TYPE
  NO            27            323
  YES            1             21
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ATRX MUTATED                     28                             3
  ATRX WILD-TYPE                  287                            44
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ATRX MUTATED                       1                              1
  ATRX WILD-TYPE                   105                              9
D1349V10, multiclass
                                clus
vv                               ATRX MUTATED ATRX WILD-TYPE
  COLON ADENOCARCINOMA                     28            287
  COLON MUCINOUS ADENOCARCINOMA             3             44
  RECTAL ADENOCARCINOMA                     1            105
  RECTAL MUCINOUS ADENOCARCINOMA            1              9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  ATRX MUTATED    20   1   0   6
  ATRX WILD-TYPE 325   3  31  19
D1349V11, multiclass
    clus
vv   ATRX MUTATED ATRX WILD-TYPE
  R0           20            325
  R1            1              3
  R2            0             31
  RX            6             19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1349V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ATRX MUTATED                                  0     4
  ATRX WILD-TYPE                                1     7
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  ATRX MUTATED                           2    20
  ATRX WILD-TYPE                        20   206
D1349V13, multiclass
                                  clus
vv                                 ATRX MUTATED ATRX WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       4              7
  BLACK OR AFRICAN AMERICAN                   2             20
  WHITE                                      20            206
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1350) Variable = TTC24 MUTATION ANALYSIS
D1350V1, survival
                 sevent
clus2               0   1
  TTC24 MUTATED     4   3
  TTC24 WILD-TYPE 374  90
  TTC24 MUTATED TTC24 WILD-TYPE 
              7             464 
  TTC24 MUTATED TTC24 WILD-TYPE 
              3              90 
$`TTC24 MUTATED`
TCGA-AA-3492 TCGA-AA-3664 TCGA-AA-3710 TCGA-CK-5916 TCGA-G4-6304 TCGA-G4-6628 
        3.02        54.02        26.99        21.14        53.62        79.69 
TCGA-DY-A1DG 
       51.48 

$`TTC24 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
        6.97         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 
       15.62        49.08        51.32         9.99        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1H8 
        5.29       126.44        41.36        57.24        24.13        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  TTC24 MUTATED TTC24 WILD-TYPE 
           3.02            0.00 
  TTC24 MUTATED TTC24 WILD-TYPE 
          79.69          148.01 
  TTC24 MUTATED TTC24 WILD-TYPE 
         51.480          20.035 
[1] "3.0 - 79.7 (51.5)"  "0.0 - 148.0 (20.0)"
[1] "hr=" "1.3"
D1350V2, continuous
D1350V3, binary
                 cls
clus                0   1
  TTC24 MUTATED     6   1
  TTC24 WILD-TYPE 360 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TTC24 MUTATED      6    1
  TTC24 WILD-TYPE  360  118
        clus
vv       TTC24 MUTATED TTC24 WILD-TYPE
  COLON              6             360
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TTC24 MUTATED         2        0        2         1         1         0
  TTC24 WILD-TYPE      89        1       30       137         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TTC24 MUTATED           0          0          0          0        0         1
  TTC24 WILD-TYPE        24         11         59         42       48        17
                 vv
clus              STAGE IVB
  TTC24 MUTATED           0
  TTC24 WILD-TYPE         1
D1350V4, multiclass
            clus
vv           TTC24 MUTATED TTC24 WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA              1             137
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  TTC24 MUTATED     1   1   4   1
  TTC24 WILD-TYPE  16  91 325  49
D1350V5, multiclass
    clus
vv   TTC24 MUTATED TTC24 WILD-TYPE
  T1             1              16
  T2             1              91
  T3             4             325
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  TTC24 MUTATED     6   1   0
  TTC24 WILD-TYPE 281 112  87
D1350V6, multiclass
    clus
vv   TTC24 MUTATED TTC24 WILD-TYPE
  N0             6             281
  N1             1             112
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1350V7, binary
                 cls
clus                0   1
  TTC24 MUTATED     6   1
  TTC24 WILD-TYPE 369  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TTC24 MUTATED      6    1
  TTC24 WILD-TYPE  369   64
   clus
vv  TTC24 MUTATED TTC24 WILD-TYPE
  0             6             369
  1             1              64
[1] 2 2
[1] FALSE
D1350V8, binary
                 cls
clus                0   1
  TTC24 MUTATED     5   2
  TTC24 WILD-TYPE 220 262
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TTC24 MUTATED      5    2
  TTC24 WILD-TYPE  220  262
        clus
vv       TTC24 MUTATED TTC24 WILD-TYPE
  FEMALE             5             220
  MALE               2             262
[1] 2 2
[1] FALSE
D1350V9, binary
                 cls
clus                0   1
  TTC24 MUTATED     6   0
  TTC24 WILD-TYPE 344  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TTC24 MUTATED      6    0
  TTC24 WILD-TYPE  344   22
     clus
vv    TTC24 MUTATED TTC24 WILD-TYPE
  NO              6             344
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  TTC24 MUTATED                      6                             0
  TTC24 WILD-TYPE                  309                            47
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  TTC24 MUTATED                       1                              0
  TTC24 WILD-TYPE                   105                             10
D1350V10, multiclass
                                clus
vv                               TTC24 MUTATED TTC24 WILD-TYPE
  COLON ADENOCARCINOMA                       6             309
  COLON MUCINOUS ADENOCARCINOMA              0              47
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  TTC24 MUTATED     5   0   0   1
  TTC24 WILD-TYPE 340   4  31  24
D1350V11, multiclass
    clus
vv   TTC24 MUTATED TTC24 WILD-TYPE
  R0             5             340
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1350V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TTC24 MUTATED                                  0     0
  TTC24 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  TTC24 MUTATED                           0     4
  TTC24 WILD-TYPE                        22   222
D1350V13, multiclass
                                  clus
vv                                 TTC24 MUTATED TTC24 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        4             222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1351) Variable = ARMC9 MUTATION ANALYSIS
D1351V1, survival
                 sevent
clus2               0   1
  ARMC9 MUTATED     5   3
  ARMC9 WILD-TYPE 373  90
  ARMC9 MUTATED ARMC9 WILD-TYPE 
              8             463 
  ARMC9 MUTATED ARMC9 WILD-TYPE 
              3              90 
$`ARMC9 MUTATED`
TCGA-AA-3555 TCGA-AA-3663 TCGA-AA-A00N TCGA-CK-4952 TCGA-CK-5916 TCGA-F4-6856 
       29.95         6.97         4.01        15.62        21.14        35.31 
TCGA-G4-6303 TCGA-AG-A002 
       65.85        20.98 

$`ARMC9 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 
       21.01        13.02        24.00        17.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       49.08        51.32         9.99        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
       47.41       133.18        74.56        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  ARMC9 MUTATED ARMC9 WILD-TYPE 
           4.01            0.00 
  ARMC9 MUTATED ARMC9 WILD-TYPE 
          65.85          148.01 
  ARMC9 MUTATED ARMC9 WILD-TYPE 
          21.06           20.12 
[1] "4.0 - 65.8 (21.1)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "2"  
D1351V2, continuous
D1351V3, binary
                 cls
clus                0   1
  ARMC9 MUTATED     7   1
  ARMC9 WILD-TYPE 359 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ARMC9 MUTATED      7    1
  ARMC9 WILD-TYPE  359  118
        clus
vv       ARMC9 MUTATED ARMC9 WILD-TYPE
  COLON              7             359
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ARMC9 MUTATED         3        0        1         1         1         0
  ARMC9 WILD-TYPE      88        1       31       137         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ARMC9 MUTATED           0          0          0          1        1         0
  ARMC9 WILD-TYPE        24         11         59         41       47        18
                 vv
clus              STAGE IVB
  ARMC9 MUTATED           0
  ARMC9 WILD-TYPE         1
D1351V4, multiclass
            clus
vv           ARMC9 MUTATED ARMC9 WILD-TYPE
  STAGE I                3              88
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              1             137
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             1              41
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ARMC9 MUTATED     1   2   3   2
  ARMC9 WILD-TYPE  16  90 326  48
D1351V5, multiclass
    clus
vv   ARMC9 MUTATED ARMC9 WILD-TYPE
  T1             1              16
  T2             2              90
  T3             3             326
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  ARMC9 MUTATED     6   1   1
  ARMC9 WILD-TYPE 281 112  86
D1351V6, multiclass
    clus
vv   ARMC9 MUTATED ARMC9 WILD-TYPE
  N0             6             281
  N1             1             112
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1351V7, binary
                 cls
clus                0   1
  ARMC9 MUTATED     7   1
  ARMC9 WILD-TYPE 368  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ARMC9 MUTATED      7    1
  ARMC9 WILD-TYPE  368   64
   clus
vv  ARMC9 MUTATED ARMC9 WILD-TYPE
  0             7             368
  1             1              64
[1] 2 2
[1] FALSE
D1351V8, binary
                 cls
clus                0   1
  ARMC9 MUTATED     4   4
  ARMC9 WILD-TYPE 221 260
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ARMC9 MUTATED      4    4
  ARMC9 WILD-TYPE  221  260
        clus
vv       ARMC9 MUTATED ARMC9 WILD-TYPE
  FEMALE             4             221
  MALE               4             260
[1] 2 2
[1] FALSE
D1351V9, binary
                 cls
clus                0   1
  ARMC9 MUTATED     6   0
  ARMC9 WILD-TYPE 344  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ARMC9 MUTATED      6    0
  ARMC9 WILD-TYPE  344   22
     clus
vv    ARMC9 MUTATED ARMC9 WILD-TYPE
  NO              6             344
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ARMC9 MUTATED                      3                             4
  ARMC9 WILD-TYPE                  312                            43
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ARMC9 MUTATED                       1                              0
  ARMC9 WILD-TYPE                   105                             10
D1351V10, multiclass
                                clus
vv                               ARMC9 MUTATED ARMC9 WILD-TYPE
  COLON ADENOCARCINOMA                       3             312
  COLON MUCINOUS ADENOCARCINOMA              4              43
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  ARMC9 MUTATED     6   0   0   2
  ARMC9 WILD-TYPE 339   4  31  23
D1351V11, multiclass
    clus
vv   ARMC9 MUTATED ARMC9 WILD-TYPE
  R0             6             339
  R1             0               4
  R2             0              31
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1351V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ARMC9 MUTATED                                  0     0
  ARMC9 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ARMC9 MUTATED                           0     4
  ARMC9 WILD-TYPE                        22   222
D1351V13, multiclass
                                  clus
vv                                 ARMC9 MUTATED ARMC9 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        4             222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1352) Variable = SNAPC1 MUTATION ANALYSIS
D1352V1, survival
                  sevent
clus2                0   1
  SNAPC1 MUTATED     3   4
  SNAPC1 WILD-TYPE 375  89
  SNAPC1 MUTATED SNAPC1 WILD-TYPE 
               7              464 
  SNAPC1 MUTATED SNAPC1 WILD-TYPE 
               4               89 
$`SNAPC1 MUTATED`
TCGA-A6-2676 TCGA-AA-3854 TCGA-AA-3864 TCGA-AA-A00N TCGA-AZ-6598 TCGA-CA-6717 
       42.90        36.03        53.00         4.01        49.41        12.76 
TCGA-F4-6570 
        6.18 

$`SNAPC1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3855 
       17.03        10.06         0.00        33.07         0.00        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 
        0.99        31.07        31.07        30.05        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        88.21         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07        12.20        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       31.96        35.74        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  SNAPC1 MUTATED SNAPC1 WILD-TYPE 
            4.01             0.00 
  SNAPC1 MUTATED SNAPC1 WILD-TYPE 
           53.00           148.01 
  SNAPC1 MUTATED SNAPC1 WILD-TYPE 
          36.030           20.155 
[1] "4.0 - 53.0 (36.0)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "2.5"
D1352V2, continuous
D1352V3, binary
                  cls
clus                 0   1
  SNAPC1 MUTATED     7   0
  SNAPC1 WILD-TYPE 359 119
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SNAPC1 MUTATED      7    0
  SNAPC1 WILD-TYPE  359  119
        clus
vv       SNAPC1 MUTATED SNAPC1 WILD-TYPE
  COLON               7              359
  RECTUM              0              119
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SNAPC1 MUTATED         1        0        2         2         2         0
  SNAPC1 WILD-TYPE      90        1       30       136         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SNAPC1 MUTATED           0          0          0          0        0
  SNAPC1 WILD-TYPE        24         11         59         42       48
                  vv
clus               STAGE IVA STAGE IVB
  SNAPC1 MUTATED           0         0
  SNAPC1 WILD-TYPE        18         1
D1352V4, multiclass
            clus
vv           SNAPC1 MUTATED SNAPC1 WILD-TYPE
  STAGE I                 1               90
  STAGE IA                0                1
  STAGE II                2               30
  STAGE IIA               2              136
  STAGE IIB               2                8
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              0               59
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  SNAPC1 MUTATED     0   1   4   2
  SNAPC1 WILD-TYPE  17  91 325  48
D1352V5, multiclass
    clus
vv   SNAPC1 MUTATED SNAPC1 WILD-TYPE
  T1              0               17
  T2              1               91
  T3              4              325
  T4              2               48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  SNAPC1 MUTATED     7   0   0
  SNAPC1 WILD-TYPE 280 113  87
D1352V6, multiclass
    clus
vv   SNAPC1 MUTATED SNAPC1 WILD-TYPE
  N0              7              280
  N1              0              113
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1352V7, binary
                  cls
clus                 0   1
  SNAPC1 MUTATED     6   0
  SNAPC1 WILD-TYPE 369  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SNAPC1 MUTATED      6    0
  SNAPC1 WILD-TYPE  369   65
   clus
vv  SNAPC1 MUTATED SNAPC1 WILD-TYPE
  0              6              369
  1              0               65
[1] 2 2
[1] FALSE
D1352V8, binary
                  cls
clus                 0   1
  SNAPC1 MUTATED     4   3
  SNAPC1 WILD-TYPE 221 261
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SNAPC1 MUTATED      4    3
  SNAPC1 WILD-TYPE  221  261
        clus
vv       SNAPC1 MUTATED SNAPC1 WILD-TYPE
  FEMALE              4              221
  MALE                3              261
[1] 2 2
[1] FALSE
D1352V9, binary
                  cls
clus                 0   1
  SNAPC1 MUTATED     6   0
  SNAPC1 WILD-TYPE 344  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SNAPC1 MUTATED      6    0
  SNAPC1 WILD-TYPE  344   22
     clus
vv    SNAPC1 MUTATED SNAPC1 WILD-TYPE
  NO               6              344
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SNAPC1 MUTATED                      4                             3
  SNAPC1 WILD-TYPE                  311                            44
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SNAPC1 MUTATED                       0                              0
  SNAPC1 WILD-TYPE                   106                             10
D1352V10, multiclass
                                clus
vv                               SNAPC1 MUTATED SNAPC1 WILD-TYPE
  COLON ADENOCARCINOMA                        4              311
  COLON MUCINOUS ADENOCARCINOMA               3               44
  RECTAL ADENOCARCINOMA                       0              106
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  SNAPC1 MUTATED     5   0   0   1
  SNAPC1 WILD-TYPE 340   4  31  24
D1352V11, multiclass
    clus
vv   SNAPC1 MUTATED SNAPC1 WILD-TYPE
  R0              5              340
  R1              0                4
  R2              0               31
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1352V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SNAPC1 MUTATED                                  0     1
  SNAPC1 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  SNAPC1 MUTATED                           0     3
  SNAPC1 WILD-TYPE                        22   223
D1352V13, multiclass
                                  clus
vv                                 SNAPC1 MUTATED SNAPC1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         3              223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1353) Variable = C20ORF151 MUTATION ANALYSIS
D1353V1, survival
                     sevent
clus2                   0   1
  C20ORF151 MUTATED    10   0
  C20ORF151 WILD-TYPE 368  93
  C20ORF151 MUTATED C20ORF151 WILD-TYPE 
                 10                 461 
  C20ORF151 MUTATED C20ORF151 WILD-TYPE 
                  0                  93 
$`C20ORF151 MUTATED`
TCGA-AA-3713 TCGA-AA-A01R TCGA-AA-A01S TCGA-AD-6889 TCGA-CM-6674 TCGA-CM-6676 
       19.04        35.01         1.02        56.55        12.95        11.08 
TCGA-D5-6928 TCGA-F4-6855 TCGA-AG-A016 TCGA-EI-6506 
       11.64        47.41         9.07        20.55 

$`C20ORF151 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01T 
       12.00        31.00        31.00        38.07         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 
       18.05        40.96         0.07        21.37        15.52         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6677 
       13.02        15.02        14.04        11.01        13.05        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.04         9.44         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6856 TCGA-G4-6293 
       16.24        33.67        13.25         0.53        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       15.95        36.03        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6507 
       57.24        24.13        51.48        32.61         0.49        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  C20ORF151 MUTATED C20ORF151 WILD-TYPE 
               1.02                0.00 
  C20ORF151 MUTATED C20ORF151 WILD-TYPE 
              56.55              148.01 
  C20ORF151 MUTATED C20ORF151 WILD-TYPE 
             15.995              20.280 
[1] "1.0 - 56.5 (16.0)"  "0.0 - 148.0 (20.3)"
[1] "hr="     "9200000"
D1353V2, continuous
D1353V3, binary
                     cls
clus                    0   1
  C20ORF151 MUTATED     9   2
  C20ORF151 WILD-TYPE 357 117
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  C20ORF151 MUTATED      9    2
  C20ORF151 WILD-TYPE  357  117
        clus
vv       C20ORF151 MUTATED C20ORF151 WILD-TYPE
  COLON                  9                 357
  RECTUM                 2                 117
[1] 2 2
[1] FALSE
                     vv
clus                  STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  C20ORF151 MUTATED         1        0        0         5         0         0
  C20ORF151 WILD-TYPE      90        1       32       133        10         1
                     vv
clus                  STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C20ORF151 MUTATED           2          0          0          1        2
  C20ORF151 WILD-TYPE        22         11         59         41       46
                     vv
clus                  STAGE IVA STAGE IVB
  C20ORF151 MUTATED           0         0
  C20ORF151 WILD-TYPE        18         1
D1353V4, multiclass
            clus
vv           C20ORF151 MUTATED C20ORF151 WILD-TYPE
  STAGE I                    1                  90
  STAGE IA                   0                   1
  STAGE II                   0                  32
  STAGE IIA                  5                 133
  STAGE IIB                  0                  10
  STAGE IIC                  0                   1
  STAGE III                  2                  22
  STAGE IIIA                 0                  11
  STAGE IIIB                 0                  59
  STAGE IIIC                 1                  41
  STAGE IV                   2                  46
  STAGE IVA                  0                  18
  STAGE IVB                  0                   1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                   T1  T2  T3  T4
  C20ORF151 MUTATED     0   1  10   0
  C20ORF151 WILD-TYPE  17  91 319  50
D1353V5, multiclass
    clus
vv   C20ORF151 MUTATED C20ORF151 WILD-TYPE
  T1                 0                  17
  T2                 1                  91
  T3                10                 319
  T4                 0                  50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                   N0  N1  N2
  C20ORF151 MUTATED     7   1   3
  C20ORF151 WILD-TYPE 280 112  84
D1353V6, multiclass
    clus
vv   C20ORF151 MUTATED C20ORF151 WILD-TYPE
  N0                 7                 280
  N1                 1                 112
  N2                 3                  84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1353V7, binary
                     cls
clus                    0   1
  C20ORF151 MUTATED     8   2
  C20ORF151 WILD-TYPE 367  63
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  C20ORF151 MUTATED      8    2
  C20ORF151 WILD-TYPE  367   63
   clus
vv  C20ORF151 MUTATED C20ORF151 WILD-TYPE
  0                 8                 367
  1                 2                  63
[1] 2 2
[1] FALSE
D1353V8, binary
                     cls
clus                    0   1
  C20ORF151 MUTATED     3   8
  C20ORF151 WILD-TYPE 222 256
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  C20ORF151 MUTATED      3    8
  C20ORF151 WILD-TYPE  222  256
        clus
vv       C20ORF151 MUTATED C20ORF151 WILD-TYPE
  FEMALE                 3                 222
  MALE                   8                 256
[1] 2 2
[1] FALSE
D1353V9, binary
                     cls
clus                    0   1
  C20ORF151 MUTATED     6   2
  C20ORF151 WILD-TYPE 344  20
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  C20ORF151 MUTATED      6    2
  C20ORF151 WILD-TYPE  344   20
     clus
vv    C20ORF151 MUTATED C20ORF151 WILD-TYPE
  NO                  6                 344
  YES                 2                  20
[1] 2 2
[1] FALSE
                     vv
clus                  COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  C20ORF151 MUTATED                      6                             3
  C20ORF151 WILD-TYPE                  309                            44
                     vv
clus                  RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  C20ORF151 MUTATED                       2                              0
  C20ORF151 WILD-TYPE                   104                             10
D1353V10, multiclass
                                clus
vv                               C20ORF151 MUTATED C20ORF151 WILD-TYPE
  COLON ADENOCARCINOMA                           6                 309
  COLON MUCINOUS ADENOCARCINOMA                  3                  44
  RECTAL ADENOCARCINOMA                          2                 104
  RECTAL MUCINOUS ADENOCARCINOMA                 0                  10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                   R0  R1  R2  RX
  C20ORF151 MUTATED     8   0   2   0
  C20ORF151 WILD-TYPE 337   4  29  25
D1353V11, multiclass
    clus
vv   C20ORF151 MUTATED C20ORF151 WILD-TYPE
  R0                 8                 337
  R1                 0                   4
  R2                 2                  29
  RX                 0                  25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1353V12, continuous
                     vv
clus                  AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C20ORF151 MUTATED                                  0     1
  C20ORF151 WILD-TYPE                                1    10
                     vv
clus                  BLACK OR AFRICAN AMERICAN WHITE
  C20ORF151 MUTATED                           0     6
  C20ORF151 WILD-TYPE                        22   220
D1353V13, multiclass
                                  clus
vv                                 C20ORF151 MUTATED C20ORF151 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                 0                   1
  ASIAN                                            1                  10
  BLACK OR AFRICAN AMERICAN                        0                  22
  WHITE                                            6                 220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1354) Variable = DNAJC7 MUTATION ANALYSIS
D1354V1, survival
                  sevent
clus2                0   1
  DNAJC7 MUTATED     7   0
  DNAJC7 WILD-TYPE 371  93
  DNAJC7 MUTATED DNAJC7 WILD-TYPE 
               7              464 
  DNAJC7 MUTATED DNAJC7 WILD-TYPE 
               0               93 
$`DNAJC7 MUTATED`
TCGA-AA-3950 TCGA-AA-A010 TCGA-AY-6197 TCGA-CA-6717 TCGA-CK-5913 TCGA-G4-6628 
       24.00        34.98        21.44        12.76        51.32        79.69 
TCGA-AG-A002 
       20.98 

$`DNAJC7 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       33.01        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       49.08         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  DNAJC7 MUTATED DNAJC7 WILD-TYPE 
           12.76             0.00 
  DNAJC7 MUTATED DNAJC7 WILD-TYPE 
           79.69           148.01 
  DNAJC7 MUTATED DNAJC7 WILD-TYPE 
          24.000           20.035 
[1] "12.8 - 79.7 (24.0)" "0.0 - 148.0 (20.0)"
[1] "hr="     "9200000"
D1354V2, continuous
D1354V3, binary
                  cls
clus                 0   1
  DNAJC7 MUTATED     7   1
  DNAJC7 WILD-TYPE 359 118
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DNAJC7 MUTATED      7    1
  DNAJC7 WILD-TYPE  359  118
        clus
vv       DNAJC7 MUTATED DNAJC7 WILD-TYPE
  COLON               7              359
  RECTUM              1              118
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DNAJC7 MUTATED         2        0        0         4         2         0
  DNAJC7 WILD-TYPE      89        1       32       134         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DNAJC7 MUTATED           0          0          0          0        0
  DNAJC7 WILD-TYPE        24         11         59         42       48
                  vv
clus               STAGE IVA STAGE IVB
  DNAJC7 MUTATED           0         0
  DNAJC7 WILD-TYPE        18         1
D1354V4, multiclass
            clus
vv           DNAJC7 MUTATED DNAJC7 WILD-TYPE
  STAGE I                 2               89
  STAGE IA                0                1
  STAGE II                0               32
  STAGE IIA               4              134
  STAGE IIB               2                8
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              0               59
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  DNAJC7 MUTATED     0   2   4   2
  DNAJC7 WILD-TYPE  17  90 325  48
D1354V5, multiclass
    clus
vv   DNAJC7 MUTATED DNAJC7 WILD-TYPE
  T1              0               17
  T2              2               90
  T3              4              325
  T4              2               48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  DNAJC7 MUTATED     8   0   0
  DNAJC7 WILD-TYPE 279 113  87
D1354V6, multiclass
    clus
vv   DNAJC7 MUTATED DNAJC7 WILD-TYPE
  N0              8              279
  N1              0              113
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1354V7, binary
                  cls
clus                 0   1
  DNAJC7 MUTATED     5   0
  DNAJC7 WILD-TYPE 370  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DNAJC7 MUTATED      5    0
  DNAJC7 WILD-TYPE  370   65
   clus
vv  DNAJC7 MUTATED DNAJC7 WILD-TYPE
  0              5              370
  1              0               65
[1] 2 2
[1] FALSE
D1354V8, binary
                  cls
clus                 0   1
  DNAJC7 MUTATED     4   4
  DNAJC7 WILD-TYPE 221 260
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DNAJC7 MUTATED      4    4
  DNAJC7 WILD-TYPE  221  260
        clus
vv       DNAJC7 MUTATED DNAJC7 WILD-TYPE
  FEMALE              4              221
  MALE                4              260
[1] 2 2
[1] FALSE
D1354V9, binary
                  cls
clus                 0   1
  DNAJC7 MUTATED     7   0
  DNAJC7 WILD-TYPE 343  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DNAJC7 MUTATED      7    0
  DNAJC7 WILD-TYPE  343   22
     clus
vv    DNAJC7 MUTATED DNAJC7 WILD-TYPE
  NO               7              343
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  DNAJC7 MUTATED                      5                             2
  DNAJC7 WILD-TYPE                  310                            45
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  DNAJC7 MUTATED                       1                              0
  DNAJC7 WILD-TYPE                   105                             10
D1354V10, multiclass
                                clus
vv                               DNAJC7 MUTATED DNAJC7 WILD-TYPE
  COLON ADENOCARCINOMA                        5              310
  COLON MUCINOUS ADENOCARCINOMA               2               45
  RECTAL ADENOCARCINOMA                       1              105
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  DNAJC7 MUTATED     5   0   0   3
  DNAJC7 WILD-TYPE 340   4  31  22
D1354V11, multiclass
    clus
vv   DNAJC7 MUTATED DNAJC7 WILD-TYPE
  R0              5              340
  R1              0                4
  R2              0               31
  RX              3               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1354V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DNAJC7 MUTATED                                  0     1
  DNAJC7 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  DNAJC7 MUTATED                           0     4
  DNAJC7 WILD-TYPE                        22   222
D1354V13, multiclass
                                  clus
vv                                 DNAJC7 MUTATED DNAJC7 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         4              222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1355) Variable = NUP205 MUTATION ANALYSIS
D1355V1, survival
                  sevent
clus2                0   1
  NUP205 MUTATED    20   4
  NUP205 WILD-TYPE 358  89
  NUP205 MUTATED NUP205 WILD-TYPE 
              24              447 
  NUP205 MUTATED NUP205 WILD-TYPE 
               4               89 
$`NUP205 MUTATED`
TCGA-A6-6141 TCGA-AA-3510 TCGA-AA-3663 TCGA-AA-3667 TCGA-AA-3821 TCGA-AA-3870 
        8.38        63.98         6.97        14.01         1.02        29.98 
TCGA-AA-3947 TCGA-AA-A010 TCGA-AA-A01P TCGA-AD-5900 TCGA-AY-6197 TCGA-AZ-4315 
       33.01        34.98        38.07         0.07        21.44        58.39 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-6747 TCGA-CM-6162 
       22.36        62.79        12.76        10.06        82.95        12.00 
TCGA-CM-6679 TCGA-D5-6540 TCGA-D5-6927 TCGA-G4-6304 TCGA-AG-A002 TCGA-AG-A02X 
       10.06        16.14         9.44        53.62        20.98        41.00 

$`NUP205 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 
       22.09        22.06        32.71        27.09        22.52        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
        2.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
        0.99        25.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3875 
       30.05        53.00        17.03        24.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 
       31.00         2.01        12.99        24.00        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        31.00         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       18.05        40.96        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 
       14.50        27.09        16.31         0.95        33.01        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
        1.41         5.13       106.75        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       12.20        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6748 TCGA-CK-6751 
       49.08        51.32         9.99        21.14         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 
       15.02        15.02        17.03        15.02         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       11.01        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 
       17.85         4.80        17.13        12.49        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6928 
        3.68         4.41        12.43        14.30         9.04        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       65.85        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       38.96        61.97        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  NUP205 MUTATED NUP205 WILD-TYPE 
            0.07             0.00 
  NUP205 MUTATED NUP205 WILD-TYPE 
           82.95           148.01 
  NUP205 MUTATED NUP205 WILD-TYPE 
           21.21            20.12 
[1] "0.1 - 83.0 (21.2)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.3"
D1355V2, continuous
D1355V3, binary
                  cls
clus                 0   1
  NUP205 MUTATED    24   2
  NUP205 WILD-TYPE 342 117
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NUP205 MUTATED     24    2
  NUP205 WILD-TYPE  342  117
        clus
vv       NUP205 MUTATED NUP205 WILD-TYPE
  COLON              24              342
  RECTUM              2              117
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NUP205 MUTATED         6        0        3        10         3         0
  NUP205 WILD-TYPE      85        1       29       128         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NUP205 MUTATED           1          0          1          0        1
  NUP205 WILD-TYPE        23         11         58         42       47
                  vv
clus               STAGE IVA STAGE IVB
  NUP205 MUTATED           1         0
  NUP205 WILD-TYPE        17         1
D1355V4, multiclass
            clus
vv           NUP205 MUTATED NUP205 WILD-TYPE
  STAGE I                 6               85
  STAGE IA                0                1
  STAGE II                3               29
  STAGE IIA              10              128
  STAGE IIB               3                7
  STAGE IIC               0                1
  STAGE III               1               23
  STAGE IIIA              0               11
  STAGE IIIB              1               58
  STAGE IIIC              0               42
  STAGE IV                1               47
  STAGE IVA               1               17
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  NUP205 MUTATED     0   6  17   3
  NUP205 WILD-TYPE  17  86 312  47
D1355V5, multiclass
    clus
vv   NUP205 MUTATED NUP205 WILD-TYPE
  T1              0               17
  T2              6               86
  T3             17              312
  T4              3               47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  NUP205 MUTATED    23   2   1
  NUP205 WILD-TYPE 264 111  86
D1355V6, multiclass
    clus
vv   NUP205 MUTATED NUP205 WILD-TYPE
  N0             23              264
  N1              2              111
  N2              1               86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1355V7, binary
                  cls
clus                 0   1
  NUP205 MUTATED    20   2
  NUP205 WILD-TYPE 355  63
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NUP205 MUTATED     20    2
  NUP205 WILD-TYPE  355   63
   clus
vv  NUP205 MUTATED NUP205 WILD-TYPE
  0             20              355
  1              2               63
[1] 2 2
[1] FALSE
D1355V8, binary
                  cls
clus                 0   1
  NUP205 MUTATED    11  15
  NUP205 WILD-TYPE 214 249
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NUP205 MUTATED     11   15
  NUP205 WILD-TYPE  214  249
        clus
vv       NUP205 MUTATED NUP205 WILD-TYPE
  FEMALE             11              214
  MALE               15              249
[1] 2 2
[1] FALSE
D1355V9, binary
                  cls
clus                 0   1
  NUP205 MUTATED    21   0
  NUP205 WILD-TYPE 329  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NUP205 MUTATED     21    0
  NUP205 WILD-TYPE  329   22
     clus
vv    NUP205 MUTATED NUP205 WILD-TYPE
  NO              21              329
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  NUP205 MUTATED                     18                             6
  NUP205 WILD-TYPE                  297                            41
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  NUP205 MUTATED                       2                              0
  NUP205 WILD-TYPE                   104                             10
D1355V10, multiclass
                                clus
vv                               NUP205 MUTATED NUP205 WILD-TYPE
  COLON ADENOCARCINOMA                       18              297
  COLON MUCINOUS ADENOCARCINOMA               6               41
  RECTAL ADENOCARCINOMA                       2              104
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  NUP205 MUTATED    21   0   0   3
  NUP205 WILD-TYPE 324   4  31  22
D1355V11, multiclass
    clus
vv   NUP205 MUTATED NUP205 WILD-TYPE
  R0             21              324
  R1              0                4
  R2              0               31
  RX              3               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1355V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NUP205 MUTATED                                  0     2
  NUP205 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  NUP205 MUTATED                           1    11
  NUP205 WILD-TYPE                        21   215
D1355V13, multiclass
                                  clus
vv                                 NUP205 MUTATED NUP205 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                9
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                        11              215
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1356) Variable = TF MUTATION ANALYSIS
D1356V1, survival
              sevent
clus2            0   1
  TF MUTATED    13   1
  TF WILD-TYPE 365  92
  TF MUTATED TF WILD-TYPE 
          14          457 
  TF MUTATED TF WILD-TYPE 
           1           92 
$`TF MUTATED`
TCGA-A6-5660 TCGA-AA-3518 TCGA-AA-3672 TCGA-AA-3976 TCGA-AA-A00N TCGA-AA-A010 
       29.19         1.02         0.92        26.01         4.01        34.98 
TCGA-AA-A01Q TCGA-AZ-4315 TCGA-CK-4952 TCGA-DM-A1HA TCGA-AG-3892 TCGA-AG-3999 
        1.02        58.39        15.62       131.51        13.02        28.04 
TCGA-AG-A002 TCGA-CI-6624 
       20.98         4.73 

$`TF WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
       54.02         2.01        14.01        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       34.06        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01R 
       32.02        12.00        31.00        31.00        38.07        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        33.01        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       85.45        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A282 
       12.59       140.38         7.50        44.32       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 
        1.02        17.95        36.95        17.03        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-4001 TCGA-AG-4005 
        1.02        48.03        32.02        19.99        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CL-5917 
        0.69         0.72         6.05        33.17         6.97        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  TF MUTATED TF WILD-TYPE 
        0.92         0.00 
  TF MUTATED TF WILD-TYPE 
      131.51       148.01 
  TF MUTATED TF WILD-TYPE 
       18.30        20.19 
[1] "0.9 - 131.5 (18.3)" "0.0 - 148.0 (20.2)"
[1] "hr=" "2.6"
D1356V2, continuous
D1356V3, binary
              cls
clus             0   1
  TF MUTATED    10   4
  TF WILD-TYPE 356 115
[1] "tbl2"
              cls
clus           [,1] [,2]
  TF MUTATED     10    4
  TF WILD-TYPE  356  115
        clus
vv       TF MUTATED TF WILD-TYPE
  COLON          10          356
  RECTUM          4          115
[1] 2 2
[1] FALSE
              vv
clus           STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TF MUTATED         3        0        1         2         2         0
  TF WILD-TYPE      88        1       31       136         8         1
              vv
clus           STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TF MUTATED           1          1          0          4        0         0
  TF WILD-TYPE        23         10         59         38       48        18
              vv
clus           STAGE IVB
  TF MUTATED           0
  TF WILD-TYPE         1
D1356V4, multiclass
            clus
vv           TF MUTATED TF WILD-TYPE
  STAGE I             3           88
  STAGE IA            0            1
  STAGE II            1           31
  STAGE IIA           2          136
  STAGE IIB           2            8
  STAGE IIC           0            1
  STAGE III           1           23
  STAGE IIIA          1           10
  STAGE IIIB          0           59
  STAGE IIIC          4           38
  STAGE IV            0           48
  STAGE IVA           0           18
  STAGE IVB           0            1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
              vv
clus            T1  T2  T3  T4
  TF MUTATED     1   3   7   3
  TF WILD-TYPE  16  89 322  47
D1356V5, multiclass
    clus
vv   TF MUTATED TF WILD-TYPE
  T1          1           16
  T2          3           89
  T3          7          322
  T4          3           47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
              vv
clus            N0  N1  N2
  TF MUTATED     8   2   4
  TF WILD-TYPE 279 111  83
D1356V6, multiclass
    clus
vv   TF MUTATED TF WILD-TYPE
  N0          8          279
  N1          2          111
  N2          4           83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1356V7, binary
              cls
clus             0   1
  TF MUTATED    14   0
  TF WILD-TYPE 361  65
[1] "tbl2"
              cls
clus           [,1] [,2]
  TF MUTATED     14    0
  TF WILD-TYPE  361   65
   clus
vv  TF MUTATED TF WILD-TYPE
  0         14          361
  1          0           65
[1] 2 2
[1] FALSE
D1356V8, binary
              cls
clus             0   1
  TF MUTATED     8   6
  TF WILD-TYPE 217 258
[1] "tbl2"
              cls
clus           [,1] [,2]
  TF MUTATED      8    6
  TF WILD-TYPE  217  258
        clus
vv       TF MUTATED TF WILD-TYPE
  FEMALE          8          217
  MALE            6          258
[1] 2 2
[1] FALSE
D1356V9, binary
              cls
clus             0   1
  TF MUTATED     8   0
  TF WILD-TYPE 342  22
[1] "tbl2"
              cls
clus           [,1] [,2]
  TF MUTATED      8    0
  TF WILD-TYPE  342   22
     clus
vv    TF MUTATED TF WILD-TYPE
  NO           8          342
  YES          0           22
[1] 2 2
[1] FALSE
              vv
clus           COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  TF MUTATED                      8                             2
  TF WILD-TYPE                  307                            45
              vv
clus           RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  TF MUTATED                       4                              0
  TF WILD-TYPE                   102                             10
D1356V10, multiclass
                                clus
vv                               TF MUTATED TF WILD-TYPE
  COLON ADENOCARCINOMA                    8          307
  COLON MUCINOUS ADENOCARCINOMA           2           45
  RECTAL ADENOCARCINOMA                   4          102
  RECTAL MUCINOUS ADENOCARCINOMA          0           10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
              vv
clus            R0  R1  R2  RX
  TF MUTATED    10   0   0   1
  TF WILD-TYPE 335   4  31  24
D1356V11, multiclass
    clus
vv   TF MUTATED TF WILD-TYPE
  R0         10          335
  R1          0            4
  R2          0           31
  RX          1           24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1356V12, continuous
              vv
clus           AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  TF MUTATED                                  0     0                         1
  TF WILD-TYPE                                1    11                        21
              vv
clus           WHITE
  TF MUTATED       4
  TF WILD-TYPE   222
D1356V13, multiclass
                                  clus
vv                                 TF MUTATED TF WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE          0            1
  ASIAN                                     0           11
  BLACK OR AFRICAN AMERICAN                 1           21
  WHITE                                     4          222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1357) Variable = LRRC37B MUTATION ANALYSIS
D1357V1, survival
                   sevent
clus2                 0   1
  LRRC37B MUTATED     6   3
  LRRC37B WILD-TYPE 372  90
  LRRC37B MUTATED LRRC37B WILD-TYPE 
                9               462 
  LRRC37B MUTATED LRRC37B WILD-TYPE 
                3                90 
$`LRRC37B MUTATED`
TCGA-A6-4105 TCGA-AZ-6603 TCGA-CA-6717 TCGA-CK-4948 TCGA-D5-6932 TCGA-F4-6460 
       14.53        29.56        12.76       148.01        11.38        31.96 
TCGA-AG-A002 TCGA-AG-A02N TCGA-AH-6547 
       20.98        61.97         1.45 

$`LRRC37B WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 
       16.57        34.65        33.34        32.75        36.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77        12.10       100.01         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4952 
       12.20        10.06        14.30        17.56        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
        1.51        12.00        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
        8.61        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X 
       64.01        10.98        49.97         1.94        38.96        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
       38.04       117.11        38.56        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  LRRC37B MUTATED LRRC37B WILD-TYPE 
             1.45              0.00 
  LRRC37B MUTATED LRRC37B WILD-TYPE 
           148.01            140.38 
  LRRC37B MUTATED LRRC37B WILD-TYPE 
           20.980            20.155 
[1] "1.4 - 148.0 (21.0)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.4"
D1357V2, continuous
D1357V3, binary
                   cls
clus                  0   1
  LRRC37B MUTATED     6   3
  LRRC37B WILD-TYPE 360 116
[1] "tbl2"
                   cls
clus                [,1] [,2]
  LRRC37B MUTATED      6    3
  LRRC37B WILD-TYPE  360  116
        clus
vv       LRRC37B MUTATED LRRC37B WILD-TYPE
  COLON                6               360
  RECTUM               3               116
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  LRRC37B MUTATED         1        0        1         3         0         0
  LRRC37B WILD-TYPE      90        1       31       135        10         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  LRRC37B MUTATED           1          0          1          0        0
  LRRC37B WILD-TYPE        23         11         58         42       48
                   vv
clus                STAGE IVA STAGE IVB
  LRRC37B MUTATED           0         0
  LRRC37B WILD-TYPE        18         1
D1357V4, multiclass
            clus
vv           LRRC37B MUTATED LRRC37B WILD-TYPE
  STAGE I                  1                90
  STAGE IA                 0                 1
  STAGE II                 1                31
  STAGE IIA                3               135
  STAGE IIB                0                10
  STAGE IIC                0                 1
  STAGE III                1                23
  STAGE IIIA               0                11
  STAGE IIIB               1                58
  STAGE IIIC               0                42
  STAGE IV                 0                48
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  LRRC37B MUTATED     0   2   7   0
  LRRC37B WILD-TYPE  17  90 322  50
D1357V5, multiclass
    clus
vv   LRRC37B MUTATED LRRC37B WILD-TYPE
  T1               0                17
  T2               2                90
  T3               7               322
  T4               0                50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  LRRC37B MUTATED     6   3   0
  LRRC37B WILD-TYPE 281 110  87
D1357V6, multiclass
    clus
vv   LRRC37B MUTATED LRRC37B WILD-TYPE
  N0               6               281
  N1               3               110
  N2               0                87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1357V7, binary
                   cls
clus                  0   1
  LRRC37B MUTATED     7   0
  LRRC37B WILD-TYPE 368  65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  LRRC37B MUTATED      7    0
  LRRC37B WILD-TYPE  368   65
   clus
vv  LRRC37B MUTATED LRRC37B WILD-TYPE
  0               7               368
  1               0                65
[1] 2 2
[1] FALSE
D1357V8, binary
                   cls
clus                  0   1
  LRRC37B MUTATED     4   5
  LRRC37B WILD-TYPE 221 259
[1] "tbl2"
                   cls
clus                [,1] [,2]
  LRRC37B MUTATED      4    5
  LRRC37B WILD-TYPE  221  259
        clus
vv       LRRC37B MUTATED LRRC37B WILD-TYPE
  FEMALE               4               221
  MALE                 5               259
[1] 2 2
[1] FALSE
D1357V9, binary
                   cls
clus                  0   1
  LRRC37B MUTATED     7   0
  LRRC37B WILD-TYPE 343  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  LRRC37B MUTATED      7    0
  LRRC37B WILD-TYPE  343   22
     clus
vv    LRRC37B MUTATED LRRC37B WILD-TYPE
  NO                7               343
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  LRRC37B MUTATED                      5                             1
  LRRC37B WILD-TYPE                  310                            46
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  LRRC37B MUTATED                       3                              0
  LRRC37B WILD-TYPE                   103                             10
D1357V10, multiclass
                                clus
vv                               LRRC37B MUTATED LRRC37B WILD-TYPE
  COLON ADENOCARCINOMA                         5               310
  COLON MUCINOUS ADENOCARCINOMA                1                46
  RECTAL ADENOCARCINOMA                        3               103
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  LRRC37B MUTATED     5   0   0   1
  LRRC37B WILD-TYPE 340   4  31  24
D1357V11, multiclass
    clus
vv   LRRC37B MUTATED LRRC37B WILD-TYPE
  R0               5               340
  R1               0                 4
  R2               0                31
  RX               1                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1357V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  LRRC37B MUTATED                                  0     1
  LRRC37B WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  LRRC37B MUTATED                           0     6
  LRRC37B WILD-TYPE                        22   220
D1357V13, multiclass
                                  clus
vv                                 LRRC37B MUTATED LRRC37B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                10
  BLACK OR AFRICAN AMERICAN                      0                22
  WHITE                                          6               220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1358) Variable = BCHE MUTATION ANALYSIS
D1358V1, survival
                sevent
clus2              0   1
  BCHE MUTATED    22   6
  BCHE WILD-TYPE 356  87
  BCHE MUTATED BCHE WILD-TYPE 
            28            443 
  BCHE MUTATED BCHE WILD-TYPE 
             6             87 
$`BCHE MUTATED`
TCGA-AA-3492 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3544 TCGA-AA-3811 TCGA-AA-3815 
        3.02        13.02        38.99        14.01        10.06        33.04 
TCGA-AA-3977 TCGA-AA-A00E TCGA-AA-A01V TCGA-AD-6889 TCGA-AD-6964 TCGA-AU-6004 
       25.02        30.02        35.01        56.55        10.88        27.09 
TCGA-AZ-4315 TCGA-CA-5796 TCGA-CA-6717 TCGA-CK-4952 TCGA-CK-6748 TCGA-CM-5860 
       58.39         3.25        12.76        15.62         1.91        32.02 
TCGA-CM-5861 TCGA-D5-6533 TCGA-D5-6927 TCGA-D5-6930 TCGA-DM-A0XF TCGA-G4-6303 
       15.02         1.32         9.44         1.51        38.20        65.85 
TCGA-AG-4007 TCGA-AG-A002 TCGA-CL-5918 TCGA-G5-6641 
        1.02        20.98         7.17        26.43 

$`BCHE WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3518 TCGA-AA-3519 
       35.01        63.98         6.97         1.02         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
        0.99        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
       26.99        19.04        19.04        35.05         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       38.04        19.00        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       33.04        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 
       18.05        40.96         0.07        21.37        15.52         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
        0.72         5.79        22.42        27.42         0.20        14.50 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
       16.31         0.95        33.01        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5797 TCGA-CA-6715 
        3.19         1.61        12.69         3.06         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.20        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 
       49.08        51.32         9.99        21.14        82.95       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       22.03        22.98        30.08         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       55.92        20.19        18.25        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6928 
        3.68         4.41        12.43        14.30         9.04        11.64 
TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        4.80        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6304 TCGA-G4-6306 
       47.41        35.31       133.18        74.56        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       28.57        32.19         0.66         0.69        55.76 

  BCHE MUTATED BCHE WILD-TYPE 
          1.02           0.00 
  BCHE MUTATED BCHE WILD-TYPE 
         65.85         148.01 
  BCHE MUTATED BCHE WILD-TYPE 
         15.32          20.28 
[1] "1.0 - 65.8 (15.3)"  "0.0 - 148.0 (20.3)"
[1] "hr=" "1.3"
D1358V2, continuous
D1358V3, binary
                cls
clus               0   1
  BCHE MUTATED    25   4
  BCHE WILD-TYPE 341 115
[1] "tbl2"
                cls
clus             [,1] [,2]
  BCHE MUTATED     25    4
  BCHE WILD-TYPE  341  115
        clus
vv       BCHE MUTATED BCHE WILD-TYPE
  COLON            25            341
  RECTUM            4            115
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  BCHE MUTATED         4        0        1        12         0         0
  BCHE WILD-TYPE      87        1       31       126        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  BCHE MUTATED           3          1          1          2        3         0
  BCHE WILD-TYPE        21         10         58         40       45        18
                vv
clus             STAGE IVB
  BCHE MUTATED           0
  BCHE WILD-TYPE         1
D1358V4, multiclass
            clus
vv           BCHE MUTATED BCHE WILD-TYPE
  STAGE I               4             87
  STAGE IA              0              1
  STAGE II              1             31
  STAGE IIA            12            126
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             3             21
  STAGE IIIA            1             10
  STAGE IIIB            1             58
  STAGE IIIC            2             40
  STAGE IV              3             45
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  BCHE MUTATED     1   5  19   4
  BCHE WILD-TYPE  16  87 310  46
D1358V5, multiclass
    clus
vv   BCHE MUTATED BCHE WILD-TYPE
  T1            1             16
  T2            5             87
  T3           19            310
  T4            4             46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  BCHE MUTATED    19   3   7
  BCHE WILD-TYPE 268 110  80
D1358V6, multiclass
    clus
vv   BCHE MUTATED BCHE WILD-TYPE
  N0           19            268
  N1            3            110
  N2            7             80
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1358V7, binary
                cls
clus               0   1
  BCHE MUTATED    22   3
  BCHE WILD-TYPE 353  62
[1] "tbl2"
                cls
clus             [,1] [,2]
  BCHE MUTATED     22    3
  BCHE WILD-TYPE  353   62
   clus
vv  BCHE MUTATED BCHE WILD-TYPE
  0           22            353
  1            3             62
[1] 2 2
[1] FALSE
D1358V8, binary
                cls
clus               0   1
  BCHE MUTATED    13  16
  BCHE WILD-TYPE 212 248
[1] "tbl2"
                cls
clus             [,1] [,2]
  BCHE MUTATED     13   16
  BCHE WILD-TYPE  212  248
        clus
vv       BCHE MUTATED BCHE WILD-TYPE
  FEMALE           13            212
  MALE             16            248
[1] 2 2
[1] FALSE
D1358V9, binary
                cls
clus               0   1
  BCHE MUTATED    20   0
  BCHE WILD-TYPE 330  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  BCHE MUTATED     20    0
  BCHE WILD-TYPE  330   22
     clus
vv    BCHE MUTATED BCHE WILD-TYPE
  NO            20            330
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  BCHE MUTATED                     18                             6
  BCHE WILD-TYPE                  297                            41
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  BCHE MUTATED                       3                              1
  BCHE WILD-TYPE                   103                              9
D1358V10, multiclass
                                clus
vv                               BCHE MUTATED BCHE WILD-TYPE
  COLON ADENOCARCINOMA                     18            297
  COLON MUCINOUS ADENOCARCINOMA             6             41
  RECTAL ADENOCARCINOMA                     3            103
  RECTAL MUCINOUS ADENOCARCINOMA            1              9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  BCHE MUTATED    19   0   1   4
  BCHE WILD-TYPE 326   4  30  21
D1358V11, multiclass
    clus
vv   BCHE MUTATED BCHE WILD-TYPE
  R0           19            326
  R1            0              4
  R2            1             30
  RX            4             21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1358V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  BCHE MUTATED                                  0     3
  BCHE WILD-TYPE                                1     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  BCHE MUTATED                           0    14
  BCHE WILD-TYPE                        22   212
D1358V13, multiclass
                                  clus
vv                                 BCHE MUTATED BCHE WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       3              8
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                      14            212
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1359) Variable = TRYX3 MUTATION ANALYSIS
D1359V1, survival
                 sevent
clus2               0   1
  TRYX3 MUTATED     4   3
  TRYX3 WILD-TYPE 374  90
  TRYX3 MUTATED TRYX3 WILD-TYPE 
              7             464 
  TRYX3 MUTATED TRYX3 WILD-TYPE 
              3              90 
$`TRYX3 MUTATED`
TCGA-A6-5665 TCGA-AA-3660 TCGA-AA-3852 TCGA-AD-6964 TCGA-CA-6718 TCGA-D5-6926 
       22.06        78.08         0.00        10.88        10.06         9.04 
TCGA-AG-A002 
       20.98 

$`TRYX3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 
       19.99        13.94        19.99        61.02         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
       10.06         0.00        33.07        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
        0.79         0.72         5.79        22.42        27.42         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
       14.30         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  TRYX3 MUTATED TRYX3 WILD-TYPE 
              0               0 
  TRYX3 MUTATED TRYX3 WILD-TYPE 
          78.08          148.01 
  TRYX3 MUTATED TRYX3 WILD-TYPE 
         10.880          20.235 
[1] "0.0 - 78.1 (10.9)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "2.7"
D1359V2, continuous
D1359V3, binary
                 cls
clus                0   1
  TRYX3 MUTATED     6   1
  TRYX3 WILD-TYPE 360 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRYX3 MUTATED      6    1
  TRYX3 WILD-TYPE  360  118
        clus
vv       TRYX3 MUTATED TRYX3 WILD-TYPE
  COLON              6             360
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TRYX3 MUTATED         1        0        1         3         0         0
  TRYX3 WILD-TYPE      90        1       31       135        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TRYX3 MUTATED           0          0          1          0        0         0
  TRYX3 WILD-TYPE        24         11         58         42       48        18
                 vv
clus              STAGE IVB
  TRYX3 MUTATED           0
  TRYX3 WILD-TYPE         1
D1359V4, multiclass
            clus
vv           TRYX3 MUTATED TRYX3 WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              3             135
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  TRYX3 MUTATED     0   1   4   2
  TRYX3 WILD-TYPE  17  91 325  48
D1359V5, multiclass
    clus
vv   TRYX3 MUTATED TRYX3 WILD-TYPE
  T1             0              17
  T2             1              91
  T3             4             325
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  TRYX3 MUTATED     5   1   1
  TRYX3 WILD-TYPE 282 112  86
D1359V6, multiclass
    clus
vv   TRYX3 MUTATED TRYX3 WILD-TYPE
  N0             5             282
  N1             1             112
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1359V7, binary
                 cls
clus                0   1
  TRYX3 MUTATED     6   0
  TRYX3 WILD-TYPE 369  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRYX3 MUTATED      6    0
  TRYX3 WILD-TYPE  369   65
   clus
vv  TRYX3 MUTATED TRYX3 WILD-TYPE
  0             6             369
  1             0              65
[1] 2 2
[1] FALSE
D1359V8, binary
                 cls
clus                0   1
  TRYX3 MUTATED     2   5
  TRYX3 WILD-TYPE 223 259
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRYX3 MUTATED      2    5
  TRYX3 WILD-TYPE  223  259
        clus
vv       TRYX3 MUTATED TRYX3 WILD-TYPE
  FEMALE             2             223
  MALE               5             259
[1] 2 2
[1] FALSE
D1359V9, binary
                 cls
clus                0   1
  TRYX3 MUTATED     5   1
  TRYX3 WILD-TYPE 345  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRYX3 MUTATED      5    1
  TRYX3 WILD-TYPE  345   21
     clus
vv    TRYX3 MUTATED TRYX3 WILD-TYPE
  NO              5             345
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  TRYX3 MUTATED                      5                             1
  TRYX3 WILD-TYPE                  310                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  TRYX3 MUTATED                       1                              0
  TRYX3 WILD-TYPE                   105                             10
D1359V10, multiclass
                                clus
vv                               TRYX3 MUTATED TRYX3 WILD-TYPE
  COLON ADENOCARCINOMA                       5             310
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  TRYX3 MUTATED     5   0   0   1
  TRYX3 WILD-TYPE 340   4  31  24
D1359V11, multiclass
    clus
vv   TRYX3 MUTATED TRYX3 WILD-TYPE
  R0             5             340
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1359V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TRYX3 MUTATED                                  0     1
  TRYX3 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  TRYX3 MUTATED                           0     3
  TRYX3 WILD-TYPE                        22   223
D1359V13, multiclass
                                  clus
vv                                 TRYX3 MUTATED TRYX3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        3             223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1360) Variable = ZNF436 MUTATION ANALYSIS
D1360V1, survival
                  sevent
clus2                0   1
  ZNF436 MUTATED     6   1
  ZNF436 WILD-TYPE 372  92
  ZNF436 MUTATED ZNF436 WILD-TYPE 
               7              464 
  ZNF436 MUTATED ZNF436 WILD-TYPE 
               1               92 
$`ZNF436 MUTATED`
TCGA-AA-3994 TCGA-CA-6717 TCGA-CM-5861 TCGA-D5-6532 TCGA-DM-A28G TCGA-G4-6586 
       27.02        12.76        15.02        18.25        60.79        35.80 
TCGA-DY-A0XA 
      126.44 

$`ZNF436 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-A004 
       24.00        27.02        27.02        19.07         7.96        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07        12.20        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       32.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28H TCGA-DM-A28K 
        6.12        81.37       119.93        35.97       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       22.09        13.78        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
        5.29        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  ZNF436 MUTATED ZNF436 WILD-TYPE 
           12.76             0.00 
  ZNF436 MUTATED ZNF436 WILD-TYPE 
          126.44           148.01 
  ZNF436 MUTATED ZNF436 WILD-TYPE 
          27.020           20.155 
[1] "12.8 - 126.4 (27.0)" "0.0 - 148.0 (20.2)" 
[1] "hr=" "2.1"
D1360V2, continuous
D1360V3, binary
                  cls
clus                 0   1
  ZNF436 MUTATED     6   1
  ZNF436 WILD-TYPE 360 118
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF436 MUTATED      6    1
  ZNF436 WILD-TYPE  360  118
        clus
vv       ZNF436 MUTATED ZNF436 WILD-TYPE
  COLON               6              360
  RECTUM              1              118
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZNF436 MUTATED         0        0        0         6         0         0
  ZNF436 WILD-TYPE      91        1       32       132        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF436 MUTATED           0          0          1          0        0
  ZNF436 WILD-TYPE        24         11         58         42       48
                  vv
clus               STAGE IVA STAGE IVB
  ZNF436 MUTATED           0         0
  ZNF436 WILD-TYPE        18         1
D1360V4, multiclass
            clus
vv           ZNF436 MUTATED ZNF436 WILD-TYPE
  STAGE I                 0               91
  STAGE IA                0                1
  STAGE II                0               32
  STAGE IIA               6              132
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              1               58
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZNF436 MUTATED     0   0   7   0
  ZNF436 WILD-TYPE  17  92 322  50
D1360V5, multiclass
    clus
vv   ZNF436 MUTATED ZNF436 WILD-TYPE
  T1              0               17
  T2              0               92
  T3              7              322
  T4              0               50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  ZNF436 MUTATED     6   1   0
  ZNF436 WILD-TYPE 281 112  87
D1360V6, multiclass
    clus
vv   ZNF436 MUTATED ZNF436 WILD-TYPE
  N0              6              281
  N1              1              112
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1360V7, binary
                  cls
clus                 0   1
  ZNF436 MUTATED     7   0
  ZNF436 WILD-TYPE 368  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF436 MUTATED      7    0
  ZNF436 WILD-TYPE  368   65
   clus
vv  ZNF436 MUTATED ZNF436 WILD-TYPE
  0              7              368
  1              0               65
[1] 2 2
[1] FALSE
D1360V8, binary
                  cls
clus                 0   1
  ZNF436 MUTATED     3   4
  ZNF436 WILD-TYPE 222 260
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF436 MUTATED      3    4
  ZNF436 WILD-TYPE  222  260
        clus
vv       ZNF436 MUTATED ZNF436 WILD-TYPE
  FEMALE              3              222
  MALE                4              260
[1] 2 2
[1] FALSE
D1360V9, binary
                  cls
clus                 0   1
  ZNF436 MUTATED     5   0
  ZNF436 WILD-TYPE 345  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF436 MUTATED      5    0
  ZNF436 WILD-TYPE  345   22
     clus
vv    ZNF436 MUTATED ZNF436 WILD-TYPE
  NO               5              345
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ZNF436 MUTATED                      4                             2
  ZNF436 WILD-TYPE                  311                            45
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ZNF436 MUTATED                       1                              0
  ZNF436 WILD-TYPE                   105                             10
D1360V10, multiclass
                                clus
vv                               ZNF436 MUTATED ZNF436 WILD-TYPE
  COLON ADENOCARCINOMA                        4              311
  COLON MUCINOUS ADENOCARCINOMA               2               45
  RECTAL ADENOCARCINOMA                       1              105
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ZNF436 MUTATED     4   0   0   1
  ZNF436 WILD-TYPE 341   4  31  24
D1360V11, multiclass
    clus
vv   ZNF436 MUTATED ZNF436 WILD-TYPE
  R0              4              341
  R1              0                4
  R2              0               31
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1360V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF436 MUTATED                                  0     1
  ZNF436 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZNF436 MUTATED                           0     5
  ZNF436 WILD-TYPE                        22   221
D1360V13, multiclass
                                  clus
vv                                 ZNF436 MUTATED ZNF436 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         5              221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1361) Variable = A1CF MUTATION ANALYSIS
D1361V1, survival
                sevent
clus2              0   1
  A1CF MUTATED     7   0
  A1CF WILD-TYPE 371  93
  A1CF MUTATED A1CF WILD-TYPE 
             7            464 
  A1CF MUTATED A1CF WILD-TYPE 
             0             93 
$`A1CF MUTATED`
TCGA-A6-3809 TCGA-A6-5660 TCGA-AA-3977 TCGA-CA-6717 TCGA-CM-5860 TCGA-CM-6676 
       32.75        29.19        25.02        12.76        32.02        11.08 
TCGA-G4-6307 
       55.04 

$`A1CF WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       31.63        30.44        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-5862 
       29.06        22.03        22.98        30.08        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6677 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  A1CF MUTATED A1CF WILD-TYPE 
         11.08           0.00 
  A1CF MUTATED A1CF WILD-TYPE 
         55.04         148.01 
  A1CF MUTATED A1CF WILD-TYPE 
        29.190         20.085 
[1] "11.1 - 55.0 (29.2)" "0.0 - 148.0 (20.1)"
[1] "hr="     "9100000"
D1361V2, continuous
D1361V3, binary
                cls
clus               0   1
  A1CF MUTATED     8   0
  A1CF WILD-TYPE 358 119
[1] "tbl2"
                cls
clus             [,1] [,2]
  A1CF MUTATED      8    0
  A1CF WILD-TYPE  358  119
        clus
vv       A1CF MUTATED A1CF WILD-TYPE
  COLON             8            358
  RECTUM            0            119
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  A1CF MUTATED         1        0        0         3         1         0
  A1CF WILD-TYPE      90        1       32       135         9         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  A1CF MUTATED           0          0          1          1        0         0
  A1CF WILD-TYPE        24         11         58         41       48        18
                vv
clus             STAGE IVB
  A1CF MUTATED           0
  A1CF WILD-TYPE         1
D1361V4, multiclass
            clus
vv           A1CF MUTATED A1CF WILD-TYPE
  STAGE I               1             90
  STAGE IA              0              1
  STAGE II              0             32
  STAGE IIA             3            135
  STAGE IIB             1              9
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            1             58
  STAGE IIIC            1             41
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  A1CF MUTATED     0   2   5   1
  A1CF WILD-TYPE  17  90 324  49
D1361V5, multiclass
    clus
vv   A1CF MUTATED A1CF WILD-TYPE
  T1            0             17
  T2            2             90
  T3            5            324
  T4            1             49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  A1CF MUTATED     6   1   1
  A1CF WILD-TYPE 281 112  86
D1361V6, multiclass
    clus
vv   A1CF MUTATED A1CF WILD-TYPE
  N0            6            281
  N1            1            112
  N2            1             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1361V7, binary
                cls
clus               0   1
  A1CF MUTATED     7   0
  A1CF WILD-TYPE 368  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  A1CF MUTATED      7    0
  A1CF WILD-TYPE  368   65
   clus
vv  A1CF MUTATED A1CF WILD-TYPE
  0            7            368
  1            0             65
[1] 2 2
[1] FALSE
D1361V8, binary
                cls
clus               0   1
  A1CF MUTATED     3   5
  A1CF WILD-TYPE 222 259
[1] "tbl2"
                cls
clus             [,1] [,2]
  A1CF MUTATED      3    5
  A1CF WILD-TYPE  222  259
        clus
vv       A1CF MUTATED A1CF WILD-TYPE
  FEMALE            3            222
  MALE              5            259
[1] 2 2
[1] FALSE
D1361V9, binary
                cls
clus               0   1
  A1CF MUTATED     7   0
  A1CF WILD-TYPE 343  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  A1CF MUTATED      7    0
  A1CF WILD-TYPE  343   22
     clus
vv    A1CF MUTATED A1CF WILD-TYPE
  NO             7            343
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  A1CF MUTATED                      6                             2
  A1CF WILD-TYPE                  309                            45
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  A1CF MUTATED                       0                              0
  A1CF WILD-TYPE                   106                             10
D1361V10, multiclass
                                clus
vv                               A1CF MUTATED A1CF WILD-TYPE
  COLON ADENOCARCINOMA                      6            309
  COLON MUCINOUS ADENOCARCINOMA             2             45
  RECTAL ADENOCARCINOMA                     0            106
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  A1CF MUTATED     5   0   0   1
  A1CF WILD-TYPE 340   4  31  24
D1361V11, multiclass
    clus
vv   A1CF MUTATED A1CF WILD-TYPE
  R0            5            340
  R1            0              4
  R2            0             31
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1361V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  A1CF MUTATED                                  0     1
  A1CF WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  A1CF MUTATED                           1     4
  A1CF WILD-TYPE                        21   222
D1361V13, multiclass
                                  clus
vv                                 A1CF MUTATED A1CF WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                       4            222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1362) Variable = TXLNG MUTATION ANALYSIS
D1362V1, survival
                 sevent
clus2               0   1
  TXLNG MUTATED     9   1
  TXLNG WILD-TYPE 369  92
  TXLNG MUTATED TXLNG WILD-TYPE 
             10             461 
  TXLNG MUTATED TXLNG WILD-TYPE 
              1              92 
$`TXLNG MUTATED`
TCGA-AA-3949 TCGA-AA-3977 TCGA-AA-A00R TCGA-AA-A010 TCGA-AZ-4315 TCGA-AZ-6598 
       26.01        25.02         0.99        34.98        58.39        49.41 
TCGA-CA-6717 TCGA-D5-6920 TCGA-DM-A0X9 TCGA-AG-A002 
       12.76         3.68       119.70        20.98 

$`TXLNG WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3950 
       31.00         2.01        12.99        24.00        33.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
        4.01        27.02        42.02        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       88.21         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07        12.20        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        1.48         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  TXLNG MUTATED TXLNG WILD-TYPE 
           0.99            0.00 
  TXLNG MUTATED TXLNG WILD-TYPE 
         119.70          148.01 
  TXLNG MUTATED TXLNG WILD-TYPE 
         25.515          20.050 
[1] "1.0 - 119.7 (25.5)" "0.0 - 148.0 (20.1)"
[1] "hr=" "2.6"
D1362V2, continuous
D1362V3, binary
                 cls
clus                0   1
  TXLNG MUTATED     9   1
  TXLNG WILD-TYPE 357 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TXLNG MUTATED      9    1
  TXLNG WILD-TYPE  357  118
        clus
vv       TXLNG MUTATED TXLNG WILD-TYPE
  COLON              9             357
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TXLNG MUTATED         2        0        1         4         1         0
  TXLNG WILD-TYPE      89        1       31       134         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TXLNG MUTATED           0          0          1          0        0         0
  TXLNG WILD-TYPE        24         11         58         42       48        18
                 vv
clus              STAGE IVB
  TXLNG MUTATED           0
  TXLNG WILD-TYPE         1
D1362V4, multiclass
            clus
vv           TXLNG MUTATED TXLNG WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              4             134
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  TXLNG MUTATED     0   3   6   1
  TXLNG WILD-TYPE  17  89 323  49
D1362V5, multiclass
    clus
vv   TXLNG MUTATED TXLNG WILD-TYPE
  T1             0              17
  T2             3              89
  T3             6             323
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  TXLNG MUTATED     9   1   0
  TXLNG WILD-TYPE 278 112  87
D1362V6, multiclass
    clus
vv   TXLNG MUTATED TXLNG WILD-TYPE
  N0             9             278
  N1             1             112
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1362V7, binary
                 cls
clus                0   1
  TXLNG MUTATED     8   0
  TXLNG WILD-TYPE 367  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TXLNG MUTATED      8    0
  TXLNG WILD-TYPE  367   65
   clus
vv  TXLNG MUTATED TXLNG WILD-TYPE
  0             8             367
  1             0              65
[1] 2 2
[1] FALSE
D1362V8, binary
                 cls
clus                0   1
  TXLNG MUTATED     6   4
  TXLNG WILD-TYPE 219 260
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TXLNG MUTATED      6    4
  TXLNG WILD-TYPE  219  260
        clus
vv       TXLNG MUTATED TXLNG WILD-TYPE
  FEMALE             6             219
  MALE               4             260
[1] 2 2
[1] FALSE
D1362V9, binary
                 cls
clus                0   1
  TXLNG MUTATED     7   0
  TXLNG WILD-TYPE 343  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TXLNG MUTATED      7    0
  TXLNG WILD-TYPE  343   22
     clus
vv    TXLNG MUTATED TXLNG WILD-TYPE
  NO              7             343
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  TXLNG MUTATED                      7                             2
  TXLNG WILD-TYPE                  308                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  TXLNG MUTATED                       1                              0
  TXLNG WILD-TYPE                   105                             10
D1362V10, multiclass
                                clus
vv                               TXLNG MUTATED TXLNG WILD-TYPE
  COLON ADENOCARCINOMA                       7             308
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  TXLNG MUTATED     6   0   0   1
  TXLNG WILD-TYPE 339   4  31  24
D1362V11, multiclass
    clus
vv   TXLNG MUTATED TXLNG WILD-TYPE
  R0             6             339
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1362V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TXLNG MUTATED                                  0     1
  TXLNG WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  TXLNG MUTATED                           0     4
  TXLNG WILD-TYPE                        22   222
D1362V13, multiclass
                                  clus
vv                                 TXLNG MUTATED TXLNG WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        4             222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1363) Variable = P2RX7 MUTATION ANALYSIS
D1363V1, survival
                 sevent
clus2               0   1
  P2RX7 MUTATED    10   3
  P2RX7 WILD-TYPE 368  90
  P2RX7 MUTATED P2RX7 WILD-TYPE 
             13             458 
  P2RX7 MUTATED P2RX7 WILD-TYPE 
              3              90 
$`P2RX7 MUTATED`
TCGA-A6-4105 TCGA-AA-3966 TCGA-AA-A02J TCGA-AD-6895 TCGA-CK-6747 TCGA-CM-5863 
       14.53         2.01         5.03         0.72        82.95        15.02 
TCGA-CM-6165 TCGA-D5-5538 TCGA-D5-6927 TCGA-DM-A1HA TCGA-DM-A28H TCGA-G4-6588 
       16.04        12.26         9.44       131.51       117.07        26.17 
TCGA-AF-2689 
       39.48 

$`P2RX7 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 
       16.57        34.65        33.34        32.75        36.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
        2.01        20.98        34.03        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
       39.98         2.01        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.79         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6748 TCGA-CK-6751 
       49.08        51.32         9.99        21.14         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       10.06        12.03        45.40        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6928 
        3.68         4.41        12.43        14.30         9.04        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A282 
       12.59       140.38         7.50        44.32       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28K 
        6.12        81.37       119.93        35.97        60.79        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       22.09        13.78        35.80        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       24.13        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  P2RX7 MUTATED P2RX7 WILD-TYPE 
           0.72            0.00 
  P2RX7 MUTATED P2RX7 WILD-TYPE 
         131.51          148.01 
  P2RX7 MUTATED P2RX7 WILD-TYPE 
         15.020          20.415 
[1] "0.7 - 131.5 (15.0)" "0.0 - 148.0 (20.4)"
[1] "hr=" "1.1"
D1363V2, continuous
D1363V3, binary
                 cls
clus                0   1
  P2RX7 MUTATED    12   1
  P2RX7 WILD-TYPE 354 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  P2RX7 MUTATED     12    1
  P2RX7 WILD-TYPE  354  118
        clus
vv       P2RX7 MUTATED P2RX7 WILD-TYPE
  COLON             12             354
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  P2RX7 MUTATED         0        0        0         6         0         0
  P2RX7 WILD-TYPE      91        1       32       132        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  P2RX7 MUTATED           0          0          2          2        2         0
  P2RX7 WILD-TYPE        24         11         57         40       46        18
                 vv
clus              STAGE IVB
  P2RX7 MUTATED           0
  P2RX7 WILD-TYPE         1
D1363V4, multiclass
            clus
vv           P2RX7 MUTATED P2RX7 WILD-TYPE
  STAGE I                0              91
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              6             132
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             2              57
  STAGE IIIC             2              40
  STAGE IV               2              46
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  P2RX7 MUTATED     0   0  13   0
  P2RX7 WILD-TYPE  17  92 316  50
D1363V5, multiclass
    clus
vv   P2RX7 MUTATED P2RX7 WILD-TYPE
  T1             0              17
  T2             0              92
  T3            13             316
  T4             0              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  P2RX7 MUTATED     7   3   3
  P2RX7 WILD-TYPE 280 110  84
D1363V6, multiclass
    clus
vv   P2RX7 MUTATED P2RX7 WILD-TYPE
  N0             7             280
  N1             3             110
  N2             3              84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1363V7, binary
                 cls
clus                0   1
  P2RX7 MUTATED     9   2
  P2RX7 WILD-TYPE 366  63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  P2RX7 MUTATED      9    2
  P2RX7 WILD-TYPE  366   63
   clus
vv  P2RX7 MUTATED P2RX7 WILD-TYPE
  0             9             366
  1             2              63
[1] 2 2
[1] FALSE
D1363V8, binary
                 cls
clus                0   1
  P2RX7 MUTATED     7   6
  P2RX7 WILD-TYPE 218 258
[1] "tbl2"
                 cls
clus              [,1] [,2]
  P2RX7 MUTATED      7    6
  P2RX7 WILD-TYPE  218  258
        clus
vv       P2RX7 MUTATED P2RX7 WILD-TYPE
  FEMALE             7             218
  MALE               6             258
[1] 2 2
[1] FALSE
D1363V9, binary
                 cls
clus                0   1
  P2RX7 MUTATED     8   0
  P2RX7 WILD-TYPE 342  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  P2RX7 MUTATED      8    0
  P2RX7 WILD-TYPE  342   22
     clus
vv    P2RX7 MUTATED P2RX7 WILD-TYPE
  NO              8             342
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  P2RX7 MUTATED                     10                             2
  P2RX7 WILD-TYPE                  305                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  P2RX7 MUTATED                       1                              0
  P2RX7 WILD-TYPE                   105                             10
D1363V10, multiclass
                                clus
vv                               P2RX7 MUTATED P2RX7 WILD-TYPE
  COLON ADENOCARCINOMA                      10             305
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  P2RX7 MUTATED     6   0   1   1
  P2RX7 WILD-TYPE 339   4  30  24
D1363V11, multiclass
    clus
vv   P2RX7 MUTATED P2RX7 WILD-TYPE
  R0             6             339
  R1             0               4
  R2             1              30
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1363V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  P2RX7 MUTATED                                  0     0
  P2RX7 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  P2RX7 MUTATED                           0    11
  P2RX7 WILD-TYPE                        22   215
D1363V13, multiclass
                                  clus
vv                                 P2RX7 MUTATED P2RX7 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                       11             215
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1364) Variable = RCOR3 MUTATION ANALYSIS
D1364V1, survival
                 sevent
clus2               0   1
  RCOR3 MUTATED     9   2
  RCOR3 WILD-TYPE 369  91
  RCOR3 MUTATED RCOR3 WILD-TYPE 
             11             460 
  RCOR3 MUTATED RCOR3 WILD-TYPE 
              2              91 
$`RCOR3 MUTATED`
TCGA-A6-4105 TCGA-AA-3663 TCGA-AA-3877 TCGA-AA-A01Q TCGA-AD-6895 TCGA-AZ-6598 
       14.53         6.97        31.00         1.02         0.72        49.41 
TCGA-CM-5861 TCGA-D5-6927 TCGA-G4-6299 TCGA-AG-3598 TCGA-F5-6465 
       15.02         9.44        74.56        50.04        49.51 

$`RCOR3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 
       16.57        34.65        33.34        32.75        36.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 
       24.03        27.02        29.98        18.05         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       31.00        38.07        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       88.21         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       22.98        30.08        32.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       46.03        34.03         2.01        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       20.91        18.28         9.96        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  RCOR3 MUTATED RCOR3 WILD-TYPE 
           0.72            0.00 
  RCOR3 MUTATED RCOR3 WILD-TYPE 
          74.56          148.01 
  RCOR3 MUTATED RCOR3 WILD-TYPE 
         15.020          20.235 
[1] "0.7 - 74.6 (15.0)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.2"
D1364V2, continuous
D1364V3, binary
                 cls
clus                0   1
  RCOR3 MUTATED    11   2
  RCOR3 WILD-TYPE 355 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RCOR3 MUTATED     11    2
  RCOR3 WILD-TYPE  355  117
        clus
vv       RCOR3 MUTATED RCOR3 WILD-TYPE
  COLON             11             355
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RCOR3 MUTATED         1        0        3         6         0         0
  RCOR3 WILD-TYPE      90        1       29       132        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RCOR3 MUTATED           0          0          0          1        1         0
  RCOR3 WILD-TYPE        24         11         59         41       47        18
                 vv
clus              STAGE IVB
  RCOR3 MUTATED           0
  RCOR3 WILD-TYPE         1
D1364V4, multiclass
            clus
vv           RCOR3 MUTATED RCOR3 WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               3              29
  STAGE IIA              6             132
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             1              41
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  RCOR3 MUTATED     1   0  11   1
  RCOR3 WILD-TYPE  16  92 318  49
D1364V5, multiclass
    clus
vv   RCOR3 MUTATED RCOR3 WILD-TYPE
  T1             1              16
  T2             0              92
  T3            11             318
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  RCOR3 MUTATED    10   1   2
  RCOR3 WILD-TYPE 277 112  85
D1364V6, multiclass
    clus
vv   RCOR3 MUTATED RCOR3 WILD-TYPE
  N0            10             277
  N1             1             112
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1364V7, binary
                 cls
clus                0   1
  RCOR3 MUTATED    10   1
  RCOR3 WILD-TYPE 365  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RCOR3 MUTATED     10    1
  RCOR3 WILD-TYPE  365   64
   clus
vv  RCOR3 MUTATED RCOR3 WILD-TYPE
  0            10             365
  1             1              64
[1] 2 2
[1] FALSE
D1364V8, binary
                 cls
clus                0   1
  RCOR3 MUTATED     7   6
  RCOR3 WILD-TYPE 218 258
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RCOR3 MUTATED      7    6
  RCOR3 WILD-TYPE  218  258
        clus
vv       RCOR3 MUTATED RCOR3 WILD-TYPE
  FEMALE             7             218
  MALE               6             258
[1] 2 2
[1] FALSE
D1364V9, binary
                 cls
clus                0   1
  RCOR3 MUTATED     9   0
  RCOR3 WILD-TYPE 341  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RCOR3 MUTATED      9    0
  RCOR3 WILD-TYPE  341   22
     clus
vv    RCOR3 MUTATED RCOR3 WILD-TYPE
  NO              9             341
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  RCOR3 MUTATED                      9                             2
  RCOR3 WILD-TYPE                  306                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  RCOR3 MUTATED                       2                              0
  RCOR3 WILD-TYPE                   104                             10
D1364V10, multiclass
                                clus
vv                               RCOR3 MUTATED RCOR3 WILD-TYPE
  COLON ADENOCARCINOMA                       9             306
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  RCOR3 MUTATED     9   0   1   0
  RCOR3 WILD-TYPE 336   4  30  25
D1364V11, multiclass
    clus
vv   RCOR3 MUTATED RCOR3 WILD-TYPE
  R0             9             336
  R1             0               4
  R2             1              30
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1364V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RCOR3 MUTATED                                  0     0
  RCOR3 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  RCOR3 MUTATED                           0     7
  RCOR3 WILD-TYPE                        22   219
D1364V13, multiclass
                                  clus
vv                                 RCOR3 MUTATED RCOR3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        7             219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1365) Variable = HMOX1 MUTATION ANALYSIS
D1365V1, survival
                 sevent
clus2               0   1
  HMOX1 MUTATED     5   1
  HMOX1 WILD-TYPE 373  92
  HMOX1 MUTATED HMOX1 WILD-TYPE 
              6             465 
  HMOX1 MUTATED HMOX1 WILD-TYPE 
              1              92 
$`HMOX1 MUTATED`
TCGA-AA-3966 TCGA-AA-A010 TCGA-AY-6386 TCGA-DM-A1DA TCGA-G4-6310 TCGA-G4-6588 
        2.01        34.98        17.82         7.50        63.62        26.17 

$`HMOX1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 
       24.00         2.01        20.98        34.03        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       33.01        21.44        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
       12.59       140.38        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6317 
       53.62        44.68        55.04        85.48        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       22.09        13.78        35.80        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  HMOX1 MUTATED HMOX1 WILD-TYPE 
           2.01            0.00 
  HMOX1 MUTATED HMOX1 WILD-TYPE 
          63.62          148.01 
  HMOX1 MUTATED HMOX1 WILD-TYPE 
         21.995          20.190 
[1] "2.0 - 63.6 (22.0)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.2"
D1365V2, continuous
D1365V3, binary
                 cls
clus                0   1
  HMOX1 MUTATED     6   0
  HMOX1 WILD-TYPE 360 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HMOX1 MUTATED      6    0
  HMOX1 WILD-TYPE  360  119
        clus
vv       HMOX1 MUTATED HMOX1 WILD-TYPE
  COLON              6             360
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  HMOX1 MUTATED         0        0        0         2         1         0
  HMOX1 WILD-TYPE      91        1       32       136         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  HMOX1 MUTATED           0          0          2          1        0         0
  HMOX1 WILD-TYPE        24         11         57         41       48        18
                 vv
clus              STAGE IVB
  HMOX1 MUTATED           0
  HMOX1 WILD-TYPE         1
D1365V4, multiclass
            clus
vv           HMOX1 MUTATED HMOX1 WILD-TYPE
  STAGE I                0              91
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              2             136
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             2              57
  STAGE IIIC             1              41
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  HMOX1 MUTATED     0   0   5   1
  HMOX1 WILD-TYPE  17  92 324  49
D1365V5, multiclass
    clus
vv   HMOX1 MUTATED HMOX1 WILD-TYPE
  T1             0              17
  T2             0              92
  T3             5             324
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  HMOX1 MUTATED     3   2   1
  HMOX1 WILD-TYPE 284 111  86
D1365V6, multiclass
    clus
vv   HMOX1 MUTATED HMOX1 WILD-TYPE
  N0             3             284
  N1             2             111
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1365V7, binary
                 cls
clus                0   1
  HMOX1 MUTATED     6   0
  HMOX1 WILD-TYPE 369  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HMOX1 MUTATED      6    0
  HMOX1 WILD-TYPE  369   65
   clus
vv  HMOX1 MUTATED HMOX1 WILD-TYPE
  0             6             369
  1             0              65
[1] 2 2
[1] FALSE
D1365V8, binary
                 cls
clus                0   1
  HMOX1 MUTATED     5   1
  HMOX1 WILD-TYPE 220 263
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HMOX1 MUTATED      5    1
  HMOX1 WILD-TYPE  220  263
        clus
vv       HMOX1 MUTATED HMOX1 WILD-TYPE
  FEMALE             5             220
  MALE               1             263
[1] 2 2
[1] FALSE
D1365V9, binary
                 cls
clus                0   1
  HMOX1 MUTATED     3   1
  HMOX1 WILD-TYPE 347  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HMOX1 MUTATED      3    1
  HMOX1 WILD-TYPE  347   21
     clus
vv    HMOX1 MUTATED HMOX1 WILD-TYPE
  NO              3             347
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  HMOX1 MUTATED                      5                             1
  HMOX1 WILD-TYPE                  310                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  HMOX1 MUTATED                       0                              0
  HMOX1 WILD-TYPE                   106                             10
D1365V10, multiclass
                                clus
vv                               HMOX1 MUTATED HMOX1 WILD-TYPE
  COLON ADENOCARCINOMA                       5             310
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  HMOX1 MUTATED     4   0   0   0
  HMOX1 WILD-TYPE 341   4  31  25
D1365V11, multiclass
    clus
vv   HMOX1 MUTATED HMOX1 WILD-TYPE
  R0             4             341
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1365V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HMOX1 MUTATED                                  0     0
  HMOX1 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  HMOX1 MUTATED                           1     3
  HMOX1 WILD-TYPE                        21   223
D1365V13, multiclass
                                  clus
vv                                 HMOX1 MUTATED HMOX1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        3             223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1366) Variable = UCHL5 MUTATION ANALYSIS
D1366V1, survival
                 sevent
clus2               0   1
  UCHL5 MUTATED     3   2
  UCHL5 WILD-TYPE 375  91
  UCHL5 MUTATED UCHL5 WILD-TYPE 
              5             466 
  UCHL5 MUTATED UCHL5 WILD-TYPE 
              2              91 
$`UCHL5 MUTATED`
TCGA-AA-3510 TCGA-AZ-6606 TCGA-CK-5912 TCGA-CM-4746 TCGA-AG-A015 
       63.98        11.74        49.08        37.02        36.03 

$`UCHL5 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 
        6.77        12.10       100.01        29.56         5.23         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       85.45        15.62        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4752 
        1.91       124.27        23.05        20.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A016 
        6.02        25.97        23.01        37.02        15.95         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  UCHL5 MUTATED UCHL5 WILD-TYPE 
          11.74            0.00 
  UCHL5 MUTATED UCHL5 WILD-TYPE 
          63.98          148.01 
  UCHL5 MUTATED UCHL5 WILD-TYPE 
         37.020          20.085 
[1] "11.7 - 64.0 (37.0)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.3"
D1366V2, continuous
D1366V3, binary
                 cls
clus                0   1
  UCHL5 MUTATED     4   1
  UCHL5 WILD-TYPE 362 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UCHL5 MUTATED      4    1
  UCHL5 WILD-TYPE  362  118
        clus
vv       UCHL5 MUTATED UCHL5 WILD-TYPE
  COLON              4             362
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  UCHL5 MUTATED         3        0        1         0         0         0
  UCHL5 WILD-TYPE      88        1       31       138        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  UCHL5 MUTATED           0          0          0          0        1         0
  UCHL5 WILD-TYPE        24         11         59         42       47        18
                 vv
clus              STAGE IVB
  UCHL5 MUTATED           0
  UCHL5 WILD-TYPE         1
D1366V4, multiclass
            clus
vv           UCHL5 MUTATED UCHL5 WILD-TYPE
  STAGE I                3              88
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              0             138
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             0              42
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  UCHL5 MUTATED     1   2   1   1
  UCHL5 WILD-TYPE  16  90 328  49
D1366V5, multiclass
    clus
vv   UCHL5 MUTATED UCHL5 WILD-TYPE
  T1             1              16
  T2             2              90
  T3             1             328
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  UCHL5 MUTATED     4   0   1
  UCHL5 WILD-TYPE 283 113  86
D1366V6, multiclass
    clus
vv   UCHL5 MUTATED UCHL5 WILD-TYPE
  N0             4             283
  N1             0             113
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1366V7, binary
                 cls
clus                0   1
  UCHL5 MUTATED     3   1
  UCHL5 WILD-TYPE 372  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UCHL5 MUTATED      3    1
  UCHL5 WILD-TYPE  372   64
   clus
vv  UCHL5 MUTATED UCHL5 WILD-TYPE
  0             3             372
  1             1              64
[1] 2 2
[1] FALSE
D1366V8, binary
                 cls
clus                0   1
  UCHL5 MUTATED     1   4
  UCHL5 WILD-TYPE 224 260
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UCHL5 MUTATED      1    4
  UCHL5 WILD-TYPE  224  260
        clus
vv       UCHL5 MUTATED UCHL5 WILD-TYPE
  FEMALE             1             224
  MALE               4             260
[1] 2 2
[1] FALSE
D1366V9, binary
                 cls
clus                0   1
  UCHL5 MUTATED     5   0
  UCHL5 WILD-TYPE 345  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UCHL5 MUTATED      5    0
  UCHL5 WILD-TYPE  345   22
     clus
vv    UCHL5 MUTATED UCHL5 WILD-TYPE
  NO              5             345
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  UCHL5 MUTATED                      4                             0
  UCHL5 WILD-TYPE                  311                            47
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  UCHL5 MUTATED                       1                              0
  UCHL5 WILD-TYPE                   105                             10
D1366V10, multiclass
                                clus
vv                               UCHL5 MUTATED UCHL5 WILD-TYPE
  COLON ADENOCARCINOMA                       4             311
  COLON MUCINOUS ADENOCARCINOMA              0              47
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  UCHL5 MUTATED     3   0   0   1
  UCHL5 WILD-TYPE 342   4  31  24
D1366V11, multiclass
    clus
vv   UCHL5 MUTATED UCHL5 WILD-TYPE
  R0             3             342
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1366V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  UCHL5 MUTATED                                  0     0
  UCHL5 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  UCHL5 MUTATED                           1     2
  UCHL5 WILD-TYPE                        21   224
D1366V13, multiclass
                                  clus
vv                                 UCHL5 MUTATED UCHL5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        2             224
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1367) Variable = NTRK2 MUTATION ANALYSIS
D1367V1, survival
                 sevent
clus2               0   1
  NTRK2 MUTATED    19   5
  NTRK2 WILD-TYPE 359  88
  NTRK2 MUTATED NTRK2 WILD-TYPE 
             24             447 
  NTRK2 MUTATED NTRK2 WILD-TYPE 
              5              88 
$`NTRK2 MUTATED`
TCGA-A6-3810 TCGA-A6-5662 TCGA-A6-5665 TCGA-A6-5666 TCGA-AA-3492 TCGA-AA-3510 
       36.53        23.61        22.06        32.71         3.02        63.98 
TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A02K TCGA-AD-6895 TCGA-AU-6004 TCGA-AZ-6598 
        4.01        34.98        14.01         0.72        27.09        49.41 
TCGA-CA-6717 TCGA-CM-5348 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-D5-6541 
       12.76        22.98         2.96        29.03        16.04        15.58 
TCGA-D5-6922 TCGA-D5-6930 TCGA-DM-A1DB TCGA-G4-6315 TCGA-AG-3892 TCGA-DC-5337 
        4.41         1.51        44.32        61.91        13.02        15.02 

$`NTRK2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        32.75        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5664 TCGA-A6-6137 
       31.63        30.44        29.19        33.53        22.09        27.09 
TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 
       22.52         8.38        25.08        25.18        24.16        21.76 
TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       24.69        24.39        23.87        20.12        19.66        20.28 
TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        7.04         1.02        35.01         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
       39.98         2.01         5.03         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.79         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       14.50        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       88.21         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07        12.20        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5349 
       37.02        25.02        13.02        29.06        22.03        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       15.02        12.00        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
       16.14         1.48         3.68        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
        9.44        11.64         4.80        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A1HB 
       13.32        12.59       140.38         7.50       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 
        1.02        17.95        36.95        17.03        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5869 TCGA-DC-6155 
        6.97         4.73        78.12         7.17         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  NTRK2 MUTATED NTRK2 WILD-TYPE 
           0.72            0.00 
  NTRK2 MUTATED NTRK2 WILD-TYPE 
          63.98          148.01 
  NTRK2 MUTATED NTRK2 WILD-TYPE 
          19.05           20.19 
[1] "0.7 - 64.0 (19.0)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.2"
D1367V2, continuous
D1367V3, binary
                 cls
clus                0   1
  NTRK2 MUTATED    23   2
  NTRK2 WILD-TYPE 343 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NTRK2 MUTATED     23    2
  NTRK2 WILD-TYPE  343  117
        clus
vv       NTRK2 MUTATED NTRK2 WILD-TYPE
  COLON             23             343
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NTRK2 MUTATED         4        0        3         8         3         1
  NTRK2 WILD-TYPE      87        1       29       130         7         0
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NTRK2 MUTATED           0          1          1          0        2         1
  NTRK2 WILD-TYPE        24         10         58         42       46        17
                 vv
clus              STAGE IVB
  NTRK2 MUTATED           0
  NTRK2 WILD-TYPE         1
D1367V4, multiclass
            clus
vv           NTRK2 MUTATED NTRK2 WILD-TYPE
  STAGE I                4              87
  STAGE IA               0               1
  STAGE II               3              29
  STAGE IIA              8             130
  STAGE IIB              3               7
  STAGE IIC              1               0
  STAGE III              0              24
  STAGE IIIA             1              10
  STAGE IIIB             1              58
  STAGE IIIC             0              42
  STAGE IV               2              46
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  NTRK2 MUTATED     3   1  16   5
  NTRK2 WILD-TYPE  14  91 313  45
D1367V5, multiclass
    clus
vv   NTRK2 MUTATED NTRK2 WILD-TYPE
  T1             3              14
  T2             1              91
  T3            16             313
  T4             5              45
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  NTRK2 MUTATED    19   4   2
  NTRK2 WILD-TYPE 268 109  85
D1367V6, multiclass
    clus
vv   NTRK2 MUTATED NTRK2 WILD-TYPE
  N0            19             268
  N1             4             109
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1367V7, binary
                 cls
clus                0   1
  NTRK2 MUTATED    19   3
  NTRK2 WILD-TYPE 356  62
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NTRK2 MUTATED     19    3
  NTRK2 WILD-TYPE  356   62
   clus
vv  NTRK2 MUTATED NTRK2 WILD-TYPE
  0            19             356
  1             3              62
[1] 2 2
[1] FALSE
D1367V8, binary
                 cls
clus                0   1
  NTRK2 MUTATED     8  17
  NTRK2 WILD-TYPE 217 247
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NTRK2 MUTATED      8   17
  NTRK2 WILD-TYPE  217  247
        clus
vv       NTRK2 MUTATED NTRK2 WILD-TYPE
  FEMALE             8             217
  MALE              17             247
[1] 2 2
[1] FALSE
D1367V9, binary
                 cls
clus                0   1
  NTRK2 MUTATED    18   0
  NTRK2 WILD-TYPE 332  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NTRK2 MUTATED     18    0
  NTRK2 WILD-TYPE  332   22
     clus
vv    NTRK2 MUTATED NTRK2 WILD-TYPE
  NO             18             332
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  NTRK2 MUTATED                     20                             3
  NTRK2 WILD-TYPE                  295                            44
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  NTRK2 MUTATED                       2                              0
  NTRK2 WILD-TYPE                   104                             10
D1367V10, multiclass
                                clus
vv                               NTRK2 MUTATED NTRK2 WILD-TYPE
  COLON ADENOCARCINOMA                      20             295
  COLON MUCINOUS ADENOCARCINOMA              3              44
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  NTRK2 MUTATED    17   0   1   2
  NTRK2 WILD-TYPE 328   4  30  23
D1367V11, multiclass
    clus
vv   NTRK2 MUTATED NTRK2 WILD-TYPE
  R0            17             328
  R1             0               4
  R2             1              30
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1367V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NTRK2 MUTATED                                  0     1
  NTRK2 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  NTRK2 MUTATED                           0    18
  NTRK2 WILD-TYPE                        22   208
D1367V13, multiclass
                                  clus
vv                                 NTRK2 MUTATED NTRK2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                       18             208
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1368) Variable = MFAP1 MUTATION ANALYSIS
D1368V1, survival
                 sevent
clus2               0   1
  MFAP1 MUTATED     4   1
  MFAP1 WILD-TYPE 374  92
  MFAP1 MUTATED MFAP1 WILD-TYPE 
              5             466 
  MFAP1 MUTATED MFAP1 WILD-TYPE 
              1              92 
$`MFAP1 MUTATED`
TCGA-AZ-4315 TCGA-AZ-6599 TCGA-CK-4952 TCGA-CM-4743 TCGA-DC-6157 
       58.39         6.77        15.62        23.05        27.95 

$`MFAP1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
       16.31         0.95        33.01        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       85.45        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
        1.91       124.27        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
        5.03        13.97        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  MFAP1 MUTATED MFAP1 WILD-TYPE 
           6.77            0.00 
  MFAP1 MUTATED MFAP1 WILD-TYPE 
          58.39          148.01 
  MFAP1 MUTATED MFAP1 WILD-TYPE 
         23.050          20.155 
[1] "6.8 - 58.4 (23.1)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1"  
D1368V2, continuous
D1368V3, binary
                 cls
clus                0   1
  MFAP1 MUTATED     4   1
  MFAP1 WILD-TYPE 362 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MFAP1 MUTATED      4    1
  MFAP1 WILD-TYPE  362  118
        clus
vv       MFAP1 MUTATED MFAP1 WILD-TYPE
  COLON              4             362
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MFAP1 MUTATED         2        0        0         2         0         0
  MFAP1 WILD-TYPE      89        1       32       136        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MFAP1 MUTATED           0          0          0          1        0         0
  MFAP1 WILD-TYPE        24         11         59         41       48        18
                 vv
clus              STAGE IVB
  MFAP1 MUTATED           0
  MFAP1 WILD-TYPE         1
D1368V4, multiclass
            clus
vv           MFAP1 MUTATED MFAP1 WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              2             136
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             1              41
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  MFAP1 MUTATED     0   2   2   1
  MFAP1 WILD-TYPE  17  90 327  49
D1368V5, multiclass
    clus
vv   MFAP1 MUTATED MFAP1 WILD-TYPE
  T1             0              17
  T2             2              90
  T3             2             327
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  MFAP1 MUTATED     4   0   1
  MFAP1 WILD-TYPE 283 113  86
D1368V6, multiclass
    clus
vv   MFAP1 MUTATED MFAP1 WILD-TYPE
  N0             4             283
  N1             0             113
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1368V7, binary
                 cls
clus                0   1
  MFAP1 MUTATED     4   0
  MFAP1 WILD-TYPE 371  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MFAP1 MUTATED      4    0
  MFAP1 WILD-TYPE  371   65
   clus
vv  MFAP1 MUTATED MFAP1 WILD-TYPE
  0             4             371
  1             0              65
[1] 2 2
[1] FALSE
D1368V8, binary
                 cls
clus                0   1
  MFAP1 MUTATED     1   4
  MFAP1 WILD-TYPE 224 260
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MFAP1 MUTATED      1    4
  MFAP1 WILD-TYPE  224  260
        clus
vv       MFAP1 MUTATED MFAP1 WILD-TYPE
  FEMALE             1             224
  MALE               4             260
[1] 2 2
[1] FALSE
D1368V9, binary
                 cls
clus                0   1
  MFAP1 MUTATED     3   0
  MFAP1 WILD-TYPE 347  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MFAP1 MUTATED      3    0
  MFAP1 WILD-TYPE  347   22
     clus
vv    MFAP1 MUTATED MFAP1 WILD-TYPE
  NO              3             347
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MFAP1 MUTATED                      3                             1
  MFAP1 WILD-TYPE                  312                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MFAP1 MUTATED                       1                              0
  MFAP1 WILD-TYPE                   105                             10
D1368V10, multiclass
                                clus
vv                               MFAP1 MUTATED MFAP1 WILD-TYPE
  COLON ADENOCARCINOMA                       3             312
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  MFAP1 MUTATED     3   0   0   1
  MFAP1 WILD-TYPE 342   4  31  24
D1368V11, multiclass
    clus
vv   MFAP1 MUTATED MFAP1 WILD-TYPE
  R0             3             342
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1368V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MFAP1 MUTATED                                  0     0
  MFAP1 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  MFAP1 MUTATED                           1     4
  MFAP1 WILD-TYPE                        21   222
D1368V13, multiclass
                                  clus
vv                                 MFAP1 MUTATED MFAP1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        4             222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1369) Variable = RNF215 MUTATION ANALYSIS
D1369V1, survival
                  sevent
clus2                0   1
  RNF215 MUTATED     3   0
  RNF215 WILD-TYPE 375  93
  RNF215 MUTATED RNF215 WILD-TYPE 
               3              468 
  RNF215 MUTATED RNF215 WILD-TYPE 
               0               93 
$`RNF215 MUTATED`
TCGA-CA-5796 TCGA-CM-6163 TCGA-G4-6586 
        3.25         2.96        35.80 

$`RNF215 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5797 
       11.74         3.19         1.61        12.69         3.06         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       17.03        15.02        12.00        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 
       63.62        61.91        36.00        22.09        13.78        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  RNF215 MUTATED RNF215 WILD-TYPE 
            2.96             0.00 
  RNF215 MUTATED RNF215 WILD-TYPE 
           35.80           148.01 
  RNF215 MUTATED RNF215 WILD-TYPE 
           3.250           20.235 
[1] "3.0 - 35.8 (3.2)"   "0.0 - 148.0 (20.2)"
[1] "hr="     "1200000"
D1369V2, continuous
D1369V3, binary
                  cls
clus                 0   1
  RNF215 MUTATED     3   0
  RNF215 WILD-TYPE 363 119
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF215 MUTATED      3    0
  RNF215 WILD-TYPE  363  119
        clus
vv       RNF215 MUTATED RNF215 WILD-TYPE
  COLON               3              363
  RECTUM              0              119
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RNF215 MUTATED         1        0        0         2         0         0
  RNF215 WILD-TYPE      90        1       32       136        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RNF215 MUTATED           0          0          0          0        0
  RNF215 WILD-TYPE        24         11         59         42       48
                  vv
clus               STAGE IVA STAGE IVB
  RNF215 MUTATED           0         0
  RNF215 WILD-TYPE        18         1
D1369V4, multiclass
            clus
vv           RNF215 MUTATED RNF215 WILD-TYPE
  STAGE I                 1               90
  STAGE IA                0                1
  STAGE II                0               32
  STAGE IIA               2              136
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              0               59
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  RNF215 MUTATED     1   0   2   0
  RNF215 WILD-TYPE  16  92 327  50
D1369V5, multiclass
    clus
vv   RNF215 MUTATED RNF215 WILD-TYPE
  T1              1               16
  T2              0               92
  T3              2              327
  T4              0               50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  RNF215 MUTATED     3   0   0
  RNF215 WILD-TYPE 284 113  87
D1369V6, multiclass
    clus
vv   RNF215 MUTATED RNF215 WILD-TYPE
  N0              3              284
  N1              0              113
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1369V7, binary
                  cls
clus                 0   1
  RNF215 MUTATED     3   0
  RNF215 WILD-TYPE 372  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF215 MUTATED      3    0
  RNF215 WILD-TYPE  372   65
   clus
vv  RNF215 MUTATED RNF215 WILD-TYPE
  0              3              372
  1              0               65
[1] 2 2
[1] FALSE
D1369V8, binary
                  cls
clus                 0   1
  RNF215 MUTATED     2   1
  RNF215 WILD-TYPE 223 263
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF215 MUTATED      2    1
  RNF215 WILD-TYPE  223  263
        clus
vv       RNF215 MUTATED RNF215 WILD-TYPE
  FEMALE              2              223
  MALE                1              263
[1] 2 2
[1] FALSE
D1369V9, binary
                  cls
clus                 0   1
  RNF215 MUTATED     3   0
  RNF215 WILD-TYPE 347  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF215 MUTATED      3    0
  RNF215 WILD-TYPE  347   22
     clus
vv    RNF215 MUTATED RNF215 WILD-TYPE
  NO               3              347
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  RNF215 MUTATED                      2                             1
  RNF215 WILD-TYPE                  313                            46
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  RNF215 MUTATED                       0                              0
  RNF215 WILD-TYPE                   106                             10
D1369V10, multiclass
                                clus
vv                               RNF215 MUTATED RNF215 WILD-TYPE
  COLON ADENOCARCINOMA                        2              313
  COLON MUCINOUS ADENOCARCINOMA               1               46
  RECTAL ADENOCARCINOMA                       0              106
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  RNF215 MUTATED     3   0   0   0
  RNF215 WILD-TYPE 342   4  31  25
D1369V11, multiclass
    clus
vv   RNF215 MUTATED RNF215 WILD-TYPE
  R0              3              342
  R1              0                4
  R2              0               31
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1369V12, continuous
[1] "Remove cluster labels:" "RNF215 MUTATED"        
clus
  RNF215 MUTATED RNF215 WILD-TYPE 
               2              456 
      TCGA-A6-2671       TCGA-A6-2672       TCGA-A6-2674       TCGA-A6-2676 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-A6-2677       TCGA-A6-2678       TCGA-A6-2683       TCGA-A6-3807 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-A6-3808       TCGA-A6-3809       TCGA-A6-3810       TCGA-A6-4105 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-A6-5656       TCGA-A6-5657       TCGA-A6-5659       TCGA-A6-5660 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-A6-5661       TCGA-A6-5662       TCGA-A6-5664       TCGA-A6-5665 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-A6-5666       TCGA-A6-6137       TCGA-A6-6138       TCGA-A6-6141 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-A6-6142       TCGA-A6-6648       TCGA-A6-6649       TCGA-A6-6651 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-A6-6652       TCGA-A6-6653       TCGA-A6-6654       TCGA-A6-6780 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-A6-6781       TCGA-A6-6782       TCGA-AA-3489       TCGA-AA-3492 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AA-3496       TCGA-AA-3502       TCGA-AA-3510       TCGA-AA-3511 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AA-3514       TCGA-AA-3516       TCGA-AA-3517       TCGA-AA-3518 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AA-3519       TCGA-AA-3520       TCGA-AA-3521       TCGA-AA-3522 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AA-3524       TCGA-AA-3525       TCGA-AA-3526       TCGA-AA-3527 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AA-3529       TCGA-AA-3530       TCGA-AA-3531       TCGA-AA-3532 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AA-3534       TCGA-AA-3538       TCGA-AA-3542       TCGA-AA-3543 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AA-3544       TCGA-AA-3548       TCGA-AA-3549       TCGA-AA-3552 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AA-3553       TCGA-AA-3554       TCGA-AA-3555       TCGA-AA-3556 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AA-3558       TCGA-AA-3560       TCGA-AA-3562       TCGA-AA-3655 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AA-3660       TCGA-AA-3662       TCGA-AA-3663       TCGA-AA-3664 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AA-3666       TCGA-AA-3667       TCGA-AA-3672       TCGA-AA-3673 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AA-3678       TCGA-AA-3679       TCGA-AA-3680       TCGA-AA-3681 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AA-3684       TCGA-AA-3685       TCGA-AA-3688       TCGA-AA-3692 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AA-3693       TCGA-AA-3695       TCGA-AA-3696       TCGA-AA-3697 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AA-3710       TCGA-AA-3712       TCGA-AA-3713       TCGA-AA-3715 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AA-3811       TCGA-AA-3812       TCGA-AA-3814       TCGA-AA-3815 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AA-3818       TCGA-AA-3819       TCGA-AA-3821       TCGA-AA-3831 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AA-3833       TCGA-AA-3837       TCGA-AA-3842       TCGA-AA-3844 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AA-3845       TCGA-AA-3846       TCGA-AA-3848       TCGA-AA-3850 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AA-3851       TCGA-AA-3852       TCGA-AA-3854       TCGA-AA-3855 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AA-3856       TCGA-AA-3858       TCGA-AA-3860       TCGA-AA-3861 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AA-3864       TCGA-AA-3866       TCGA-AA-3867       TCGA-AA-3869 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AA-3870       TCGA-AA-3872       TCGA-AA-3875       TCGA-AA-3877 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AA-3930       TCGA-AA-3939       TCGA-AA-3941       TCGA-AA-3947 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AA-3949       TCGA-AA-3950       TCGA-AA-3952       TCGA-AA-3955 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AA-3956       TCGA-AA-3966       TCGA-AA-3968       TCGA-AA-3971 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AA-3972       TCGA-AA-3973       TCGA-AA-3975       TCGA-AA-3976 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AA-3977       TCGA-AA-3979       TCGA-AA-3980       TCGA-AA-3982 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AA-3984       TCGA-AA-3986       TCGA-AA-3989       TCGA-AA-3994 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AA-A004       TCGA-AA-A00A       TCGA-AA-A00D       TCGA-AA-A00E 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AA-A00F       TCGA-AA-A00J       TCGA-AA-A00K       TCGA-AA-A00L 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AA-A00N       TCGA-AA-A00O       TCGA-AA-A00Q       TCGA-AA-A00R 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AA-A00U       TCGA-AA-A00W       TCGA-AA-A00Z       TCGA-AA-A010 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AA-A017       TCGA-AA-A01D       TCGA-AA-A01F       TCGA-AA-A01G 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AA-A01I       TCGA-AA-A01K       TCGA-AA-A01P       TCGA-AA-A01Q 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AA-A01R       TCGA-AA-A01S       TCGA-AA-A01T       TCGA-AA-A01V 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AA-A01X       TCGA-AA-A01Z       TCGA-AA-A022       TCGA-AA-A024 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AA-A029       TCGA-AA-A02F       TCGA-AA-A02H       TCGA-AA-A02J 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AA-A02K       TCGA-AA-A02O       TCGA-AA-A02W       TCGA-AA-A02Y 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AA-A03F       TCGA-AA-A03J       TCGA-AD-5900       TCGA-AD-6548 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AD-6888       TCGA-AD-6889       TCGA-AD-6890       TCGA-AD-6895 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AD-6899       TCGA-AD-6901       TCGA-AD-6963       TCGA-AD-6964 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AD-6965       TCGA-AU-3779       TCGA-AU-6004       TCGA-AY-4070 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AY-4071       TCGA-AY-5543       TCGA-AY-6196       TCGA-AY-6197 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AY-6386       TCGA-AZ-4323       TCGA-AZ-4616       TCGA-AZ-4682 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AZ-5403       TCGA-AZ-5407       TCGA-AZ-6598       TCGA-AZ-6599 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AZ-6600       TCGA-AZ-6601       TCGA-AZ-6603       TCGA-AZ-6605 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AZ-6606       TCGA-AZ-6607       TCGA-AZ-6608       TCGA-CK-4947 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-CK-4948       TCGA-CK-4950       TCGA-CK-4952       TCGA-CM-4743 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-CM-4744       TCGA-CM-4746       TCGA-CM-4747       TCGA-CM-4752 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-CM-5341       TCGA-CM-5344       TCGA-CM-5348       TCGA-CM-5349 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-CM-5860       TCGA-CM-5861       TCGA-CM-5862       TCGA-CM-5863 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-CM-5864       TCGA-CM-5868       TCGA-CM-6161       TCGA-CM-6162 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-CM-6164       TCGA-CM-6165       TCGA-CM-6166       TCGA-CM-6167 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-CM-6168       TCGA-CM-6169       TCGA-CM-6170       TCGA-CM-6171 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-CM-6172       TCGA-CM-6674       TCGA-CM-6675       TCGA-CM-6676 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-CM-6677       TCGA-CM-6678       TCGA-CM-6679       TCGA-CM-6680 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-D5-5537       TCGA-D5-5538       TCGA-D5-5539       TCGA-D5-5540 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-D5-5541       TCGA-D5-6529       TCGA-D5-6532       TCGA-D5-6533 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-D5-6534       TCGA-D5-6535       TCGA-D5-6536       TCGA-D5-6537 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-D5-6538       TCGA-D5-6539       TCGA-D5-6540       TCGA-D5-6541 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-D5-6898       TCGA-D5-6920       TCGA-D5-6922       TCGA-D5-6923 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-D5-6924       TCGA-D5-6926       TCGA-D5-6927       TCGA-D5-6928 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-D5-6929       TCGA-D5-6930       TCGA-D5-6931       TCGA-D5-6932 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-D5-7000       TCGA-DM-A0X9       TCGA-DM-A0XD       TCGA-DM-A0XF 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-DM-A1D0       TCGA-DM-A1D4       TCGA-DM-A1D6       TCGA-DM-A1D7 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-DM-A1D8       TCGA-DM-A1D9       TCGA-DM-A1DA       TCGA-DM-A1DB 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-DM-A1HA       TCGA-DM-A1HB       TCGA-DM-A282       TCGA-DM-A285 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-DM-A28C       TCGA-DM-A28E       TCGA-DM-A28F       TCGA-DM-A28G 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-DM-A28H       TCGA-DM-A28K       TCGA-F4-6459       TCGA-F4-6460 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-F4-6569       TCGA-F4-6570       TCGA-F4-6703       TCGA-F4-6704 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-F4-6806       TCGA-F4-6807       TCGA-F4-6808       TCGA-F4-6809 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-F4-6854       TCGA-F4-6855       TCGA-F4-6856       TCGA-G4-6293 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-G4-6299       TCGA-G4-6303       TCGA-G4-6304       TCGA-G4-6306 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-G4-6307       TCGA-G4-6309       TCGA-G4-6310       TCGA-G4-6315 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-G4-6317       TCGA-G4-6321       TCGA-G4-6323       TCGA-G4-6588 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-G4-6625       TCGA-G4-6626       TCGA-G4-6628       TCGA-AF-2687 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AF-2689       TCGA-AF-2691       TCGA-AF-2692       TCGA-AF-2693 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AF-3400       TCGA-AF-3913       TCGA-AF-4110       TCGA-AF-5654 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AF-6136       TCGA-AF-6655       TCGA-AF-6672       TCGA-AG-3574 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AG-3575       TCGA-AG-3578       TCGA-AG-3580       TCGA-AG-3581 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AG-3582       TCGA-AG-3583       TCGA-AG-3584       TCGA-AG-3586 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AG-3587       TCGA-AG-3593       TCGA-AG-3594       TCGA-AG-3598 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AG-3599       TCGA-AG-3600       TCGA-AG-3601       TCGA-AG-3602 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AG-3605       TCGA-AG-3608       TCGA-AG-3609       TCGA-AG-3611 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AG-3612       TCGA-AG-3726       TCGA-AG-3727       TCGA-AG-3731 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AG-3732       TCGA-AG-3742       TCGA-AG-3878       TCGA-AG-3881 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AG-3882       TCGA-AG-3883       TCGA-AG-3885       TCGA-AG-3887 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AG-3890       TCGA-AG-3892       TCGA-AG-3893       TCGA-AG-3894 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AG-3896       TCGA-AG-3898       TCGA-AG-3901       TCGA-AG-3902 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AG-3909       TCGA-AG-3999       TCGA-AG-4001       TCGA-AG-4005 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AG-4007       TCGA-AG-4008       TCGA-AG-4015       TCGA-AG-A002 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AG-A008       TCGA-AG-A00C       TCGA-AG-A00H       TCGA-AG-A00Y 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AG-A011       TCGA-AG-A014       TCGA-AG-A015       TCGA-AG-A016 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AG-A01L       TCGA-AG-A01W       TCGA-AG-A01Y       TCGA-AG-A020 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AG-A025       TCGA-AG-A026       TCGA-AG-A02G       TCGA-AG-A02N 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AG-A02X       TCGA-AG-A032       TCGA-AG-A036       TCGA-AH-6544 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-AH-6547       TCGA-AH-6643       TCGA-AH-6644       TCGA-CI-6622 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-DC-5337       TCGA-DC-5869       TCGA-DC-6155       TCGA-DC-6157 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-DC-6158       TCGA-DC-6160       TCGA-DC-6681       TCGA-DC-6682 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-DC-6683       TCGA-DY-A0XA       TCGA-DY-A1DC       TCGA-DY-A1DD 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-DY-A1DF       TCGA-DY-A1DG       TCGA-DY-A1H8       TCGA-EI-6506 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-EI-6507       TCGA-EI-6508       TCGA-EI-6510       TCGA-F5-6464 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-F5-6465       TCGA-F5-6571       TCGA-F5-6702       TCGA-F5-6811 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
      TCGA-F5-6812       TCGA-F5-6813       TCGA-G5-6235       TCGA-G5-6641 
"RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" "RNF215 WILD-TYPE" 
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RNF215 MUTATED                                  0     1
  RNF215 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  RNF215 MUTATED                           0     2
  RNF215 WILD-TYPE                        22   224
D1369V13, multiclass
                                  clus
vv                                 RNF215 MUTATED RNF215 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         2              224
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1370) Variable = FANCD2 MUTATION ANALYSIS
D1370V1, survival
                  sevent
clus2                0   1
  FANCD2 MUTATED    11   5
  FANCD2 WILD-TYPE 367  88
  FANCD2 MUTATED FANCD2 WILD-TYPE 
              16              455 
  FANCD2 MUTATED FANCD2 WILD-TYPE 
               5               88 
$`FANCD2 MUTATED`
TCGA-AA-3663 TCGA-AA-3715 TCGA-AA-3845 TCGA-AA-3947 TCGA-AA-A00J TCGA-AA-A00N 
        6.97        19.04         0.00        33.01        18.05         4.01 
TCGA-AA-A02F TCGA-AD-6964 TCGA-AZ-6600 TCGA-CK-4950 TCGA-D5-6532 TCGA-G4-6299 
       39.98        10.88        12.10        85.45        18.25        74.56 
TCGA-G4-6588 TCGA-AG-3892 TCGA-AG-A002 TCGA-DC-6160 
       26.17        13.02        20.98        19.99 

$`FANCD2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.05        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 
       36.00         5.03        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 
       15.95        38.99        37.02        14.93        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       34.03        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       39.06        51.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 
       12.76        10.06        14.30        17.56       148.01        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6533 
       12.26        19.59        56.09        55.92        20.19         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       47.41        35.31       133.18        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       13.78        35.80        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       17.03        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6681 
       15.02         5.03        13.97        27.95        10.98         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  FANCD2 MUTATED FANCD2 WILD-TYPE 
               0                0 
  FANCD2 MUTATED FANCD2 WILD-TYPE 
           85.45           148.01 
  FANCD2 MUTATED FANCD2 WILD-TYPE 
          18.645           20.550 
[1] "0.0 - 85.5 (18.6)"  "0.0 - 148.0 (20.6)"
[1] "hr=" "1.7"
D1370V2, continuous
D1370V3, binary
                  cls
clus                 0   1
  FANCD2 MUTATED    15   3
  FANCD2 WILD-TYPE 351 116
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FANCD2 MUTATED     15    3
  FANCD2 WILD-TYPE  351  116
        clus
vv       FANCD2 MUTATED FANCD2 WILD-TYPE
  COLON              15              351
  RECTUM              3              116
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FANCD2 MUTATED         3        0        2         4         3         0
  FANCD2 WILD-TYPE      88        1       30       134         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FANCD2 MUTATED           0          0          2          1        2
  FANCD2 WILD-TYPE        24         11         57         41       46
                  vv
clus               STAGE IVA STAGE IVB
  FANCD2 MUTATED           0         0
  FANCD2 WILD-TYPE        18         1
D1370V4, multiclass
            clus
vv           FANCD2 MUTATED FANCD2 WILD-TYPE
  STAGE I                 3               88
  STAGE IA                0                1
  STAGE II                2               30
  STAGE IIA               4              134
  STAGE IIB               3                7
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              2               57
  STAGE IIIC              1               41
  STAGE IV                2               46
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  FANCD2 MUTATED     1   2   9   6
  FANCD2 WILD-TYPE  16  90 320  44
D1370V5, multiclass
    clus
vv   FANCD2 MUTATED FANCD2 WILD-TYPE
  T1              1               16
  T2              2               90
  T3              9              320
  T4              6               44
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  FANCD2 MUTATED    12   4   2
  FANCD2 WILD-TYPE 275 109  85
D1370V6, multiclass
    clus
vv   FANCD2 MUTATED FANCD2 WILD-TYPE
  N0             12              275
  N1              4              109
  N2              2               85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1370V7, binary
                  cls
clus                 0   1
  FANCD2 MUTATED    14   2
  FANCD2 WILD-TYPE 361  63
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FANCD2 MUTATED     14    2
  FANCD2 WILD-TYPE  361   63
   clus
vv  FANCD2 MUTATED FANCD2 WILD-TYPE
  0             14              361
  1              2               63
[1] 2 2
[1] FALSE
D1370V8, binary
                  cls
clus                 0   1
  FANCD2 MUTATED     8  10
  FANCD2 WILD-TYPE 217 254
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FANCD2 MUTATED      8   10
  FANCD2 WILD-TYPE  217  254
        clus
vv       FANCD2 MUTATED FANCD2 WILD-TYPE
  FEMALE              8              217
  MALE               10              254
[1] 2 2
[1] FALSE
D1370V9, binary
                  cls
clus                 0   1
  FANCD2 MUTATED    12   0
  FANCD2 WILD-TYPE 338  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FANCD2 MUTATED     12    0
  FANCD2 WILD-TYPE  338   22
     clus
vv    FANCD2 MUTATED FANCD2 WILD-TYPE
  NO              12              338
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  FANCD2 MUTATED                     12                             3
  FANCD2 WILD-TYPE                  303                            44
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  FANCD2 MUTATED                       3                              0
  FANCD2 WILD-TYPE                   103                             10
D1370V10, multiclass
                                clus
vv                               FANCD2 MUTATED FANCD2 WILD-TYPE
  COLON ADENOCARCINOMA                       12              303
  COLON MUCINOUS ADENOCARCINOMA               3               44
  RECTAL ADENOCARCINOMA                       3              103
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  FANCD2 MUTATED    13   1   1   1
  FANCD2 WILD-TYPE 332   3  30  24
D1370V11, multiclass
    clus
vv   FANCD2 MUTATED FANCD2 WILD-TYPE
  R0             13              332
  R1              1                3
  R2              1               30
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1370V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FANCD2 MUTATED                                  0     0
  FANCD2 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  FANCD2 MUTATED                           2     6
  FANCD2 WILD-TYPE                        20   220
D1370V13, multiclass
                                  clus
vv                                 FANCD2 MUTATED FANCD2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     2               20
  WHITE                                         6              220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1371) Variable = CD34 MUTATION ANALYSIS
D1371V1, survival
                sevent
clus2              0   1
  CD34 MUTATED     4   2
  CD34 WILD-TYPE 374  91
  CD34 MUTATED CD34 WILD-TYPE 
             6            465 
  CD34 MUTATED CD34 WILD-TYPE 
             2             91 
$`CD34 MUTATED`
TCGA-AA-3489 TCGA-AA-3662 TCGA-AA-3966 TCGA-AZ-4315 TCGA-AZ-6606 TCGA-CA-6717 
        7.04         6.05         2.01        58.39        11.74        12.76 

$`CD34 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       19.99        13.94        19.99        61.02        78.08         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       20.98        34.03        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
       29.56         5.23         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07        12.20        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  CD34 MUTATED CD34 WILD-TYPE 
          2.01           0.00 
  CD34 MUTATED CD34 WILD-TYPE 
         58.39         148.01 
  CD34 MUTATED CD34 WILD-TYPE 
          9.39          20.55 
[1] "2.0 - 58.4 (9.4)"   "0.0 - 148.0 (20.6)"
[1] "hr=" "2.4"
D1371V2, continuous
D1371V3, binary
                cls
clus               0   1
  CD34 MUTATED     6   0
  CD34 WILD-TYPE 360 119
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD34 MUTATED      6    0
  CD34 WILD-TYPE  360  119
        clus
vv       CD34 MUTATED CD34 WILD-TYPE
  COLON             6            360
  RECTUM            0            119
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CD34 MUTATED         0        0        1         3         0         0
  CD34 WILD-TYPE      91        1       31       135        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CD34 MUTATED           0          0          0          0        2         0
  CD34 WILD-TYPE        24         11         59         42       46        18
                vv
clus             STAGE IVB
  CD34 MUTATED           0
  CD34 WILD-TYPE         1
D1371V4, multiclass
            clus
vv           CD34 MUTATED CD34 WILD-TYPE
  STAGE I               0             91
  STAGE IA              0              1
  STAGE II              1             31
  STAGE IIA             3            135
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            0             59
  STAGE IIIC            0             42
  STAGE IV              2             46
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  CD34 MUTATED     0   0   4   2
  CD34 WILD-TYPE  17  92 325  48
D1371V5, multiclass
    clus
vv   CD34 MUTATED CD34 WILD-TYPE
  T1            0             17
  T2            0             92
  T3            4            325
  T4            2             48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  CD34 MUTATED     4   0   2
  CD34 WILD-TYPE 283 113  85
D1371V6, multiclass
    clus
vv   CD34 MUTATED CD34 WILD-TYPE
  N0            4            283
  N1            0            113
  N2            2             85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1371V7, binary
                cls
clus               0   1
  CD34 MUTATED     4   2
  CD34 WILD-TYPE 371  63
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD34 MUTATED      4    2
  CD34 WILD-TYPE  371   63
   clus
vv  CD34 MUTATED CD34 WILD-TYPE
  0            4            371
  1            2             63
[1] 2 2
[1] FALSE
D1371V8, binary
                cls
clus               0   1
  CD34 MUTATED     2   4
  CD34 WILD-TYPE 223 260
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD34 MUTATED      2    4
  CD34 WILD-TYPE  223  260
        clus
vv       CD34 MUTATED CD34 WILD-TYPE
  FEMALE            2            223
  MALE              4            260
[1] 2 2
[1] FALSE
D1371V9, binary
                cls
clus               0   1
  CD34 MUTATED     5   0
  CD34 WILD-TYPE 345  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD34 MUTATED      5    0
  CD34 WILD-TYPE  345   22
     clus
vv    CD34 MUTATED CD34 WILD-TYPE
  NO             5            345
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CD34 MUTATED                      4                             2
  CD34 WILD-TYPE                  311                            45
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CD34 MUTATED                       0                              0
  CD34 WILD-TYPE                   106                             10
D1371V10, multiclass
                                clus
vv                               CD34 MUTATED CD34 WILD-TYPE
  COLON ADENOCARCINOMA                      4            311
  COLON MUCINOUS ADENOCARCINOMA             2             45
  RECTAL ADENOCARCINOMA                     0            106
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  CD34 MUTATED     2   0   1   1
  CD34 WILD-TYPE 343   4  30  24
D1371V11, multiclass
    clus
vv   CD34 MUTATED CD34 WILD-TYPE
  R0            2            343
  R1            0              4
  R2            1             30
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1371V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CD34 MUTATED                                  0     1
  CD34 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  CD34 MUTATED                           0     2
  CD34 WILD-TYPE                        22   224
D1371V13, multiclass
                                  clus
vv                                 CD34 MUTATED CD34 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       2            224
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1372) Variable = ZSWIM3 MUTATION ANALYSIS
D1372V1, survival
                  sevent
clus2                0   1
  ZSWIM3 MUTATED    11   2
  ZSWIM3 WILD-TYPE 367  91
  ZSWIM3 MUTATED ZSWIM3 WILD-TYPE 
              13              458 
  ZSWIM3 MUTATED ZSWIM3 WILD-TYPE 
               2               91 
$`ZSWIM3 MUTATED`
TCGA-AA-3492 TCGA-AA-3518 TCGA-AA-3542 TCGA-AA-3554 TCGA-AA-A00A TCGA-AA-A010 
        3.02         1.02        12.99        17.95        38.04        34.98 
TCGA-CK-4950 TCGA-D5-6540 TCGA-D5-6541 TCGA-DM-A1D4 TCGA-DM-A1HB TCGA-G4-6310 
       85.45        16.14        15.58        92.75       135.65        63.62 
TCGA-AG-4007 
        1.02 

$`ZSWIM3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
        7.96        27.02        13.94        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
       17.56       148.01        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6898 TCGA-D5-6920 
       17.85         4.80        17.13        12.49         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       24.43        38.20       130.65        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 
      140.38         7.50        44.32       131.51       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       44.68        55.04        85.48        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  ZSWIM3 MUTATED ZSWIM3 WILD-TYPE 
            1.02             0.00 
  ZSWIM3 MUTATED ZSWIM3 WILD-TYPE 
          135.65           148.01 
  ZSWIM3 MUTATED ZSWIM3 WILD-TYPE 
          17.950           20.235 
[1] "1.0 - 135.7 (17.9)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.8"
D1372V2, continuous
D1372V3, binary
                  cls
clus                 0   1
  ZSWIM3 MUTATED    12   1
  ZSWIM3 WILD-TYPE 354 118
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZSWIM3 MUTATED     12    1
  ZSWIM3 WILD-TYPE  354  118
        clus
vv       ZSWIM3 MUTATED ZSWIM3 WILD-TYPE
  COLON              12              354
  RECTUM              1              118
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZSWIM3 MUTATED         1        0        1         5         1         0
  ZSWIM3 WILD-TYPE      90        1       31       133         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZSWIM3 MUTATED           0          0          3          1        1
  ZSWIM3 WILD-TYPE        24         11         56         41       47
                  vv
clus               STAGE IVA STAGE IVB
  ZSWIM3 MUTATED           0         0
  ZSWIM3 WILD-TYPE        18         1
D1372V4, multiclass
            clus
vv           ZSWIM3 MUTATED ZSWIM3 WILD-TYPE
  STAGE I                 1               90
  STAGE IA                0                1
  STAGE II                1               31
  STAGE IIA               5              133
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              3               56
  STAGE IIIC              1               41
  STAGE IV                1               47
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZSWIM3 MUTATED     0   1  10   2
  ZSWIM3 WILD-TYPE  17  91 319  48
D1372V5, multiclass
    clus
vv   ZSWIM3 MUTATED ZSWIM3 WILD-TYPE
  T1              0               17
  T2              1               91
  T3             10              319
  T4              2               48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  ZSWIM3 MUTATED     8   3   2
  ZSWIM3 WILD-TYPE 279 110  85
D1372V6, multiclass
    clus
vv   ZSWIM3 MUTATED ZSWIM3 WILD-TYPE
  N0              8              279
  N1              3              110
  N2              2               85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1372V7, binary
                  cls
clus                 0   1
  ZSWIM3 MUTATED    12   1
  ZSWIM3 WILD-TYPE 363  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZSWIM3 MUTATED     12    1
  ZSWIM3 WILD-TYPE  363   64
   clus
vv  ZSWIM3 MUTATED ZSWIM3 WILD-TYPE
  0             12              363
  1              1               64
[1] 2 2
[1] FALSE
D1372V8, binary
                  cls
clus                 0   1
  ZSWIM3 MUTATED     5   8
  ZSWIM3 WILD-TYPE 220 256
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZSWIM3 MUTATED      5    8
  ZSWIM3 WILD-TYPE  220  256
        clus
vv       ZSWIM3 MUTATED ZSWIM3 WILD-TYPE
  FEMALE              5              220
  MALE                8              256
[1] 2 2
[1] FALSE
D1372V9, binary
                  cls
clus                 0   1
  ZSWIM3 MUTATED     8   1
  ZSWIM3 WILD-TYPE 342  21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZSWIM3 MUTATED      8    1
  ZSWIM3 WILD-TYPE  342   21
     clus
vv    ZSWIM3 MUTATED ZSWIM3 WILD-TYPE
  NO               8              342
  YES              1               21
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ZSWIM3 MUTATED                     10                             1
  ZSWIM3 WILD-TYPE                  305                            46
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ZSWIM3 MUTATED                       1                              0
  ZSWIM3 WILD-TYPE                   105                             10
D1372V10, multiclass
                                clus
vv                               ZSWIM3 MUTATED ZSWIM3 WILD-TYPE
  COLON ADENOCARCINOMA                       10              305
  COLON MUCINOUS ADENOCARCINOMA               1               46
  RECTAL ADENOCARCINOMA                       1              105
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ZSWIM3 MUTATED     9   1   1   0
  ZSWIM3 WILD-TYPE 336   3  30  25
D1372V11, multiclass
    clus
vv   ZSWIM3 MUTATED ZSWIM3 WILD-TYPE
  R0              9              336
  R1              1                3
  R2              1               30
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1372V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZSWIM3 MUTATED                                  0     0
  ZSWIM3 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZSWIM3 MUTATED                           1     5
  ZSWIM3 WILD-TYPE                        21   221
D1372V13, multiclass
                                  clus
vv                                 ZSWIM3 MUTATED ZSWIM3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                         5              221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1373) Variable = SLC16A2 MUTATION ANALYSIS
D1373V1, survival
                   sevent
clus2                 0   1
  SLC16A2 MUTATED     6   2
  SLC16A2 WILD-TYPE 372  91
  SLC16A2 MUTATED SLC16A2 WILD-TYPE 
                8               463 
  SLC16A2 MUTATED SLC16A2 WILD-TYPE 
                2                91 
$`SLC16A2 MUTATED`
TCGA-AA-3516 TCGA-AA-3877 TCGA-CM-6165 TCGA-DM-A1D9 TCGA-F4-6809 TCGA-AG-3732 
       13.02        31.00        16.04       140.38        13.25        32.98 
TCGA-AG-4001 TCGA-DY-A0XA 
       36.03       126.44 

$`SLC16A2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        1.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 
       17.03        24.03        27.02        29.98        18.05         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6166 TCGA-CM-6167 
       15.02        12.00         2.96        29.03        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
       12.59         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6854 
        1.55        34.42        41.42        16.24        33.67         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4007 
       48.03        32.02        19.99        28.04        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  SLC16A2 MUTATED SLC16A2 WILD-TYPE 
            13.02              0.00 
  SLC16A2 MUTATED SLC16A2 WILD-TYPE 
           140.38            148.01 
  SLC16A2 MUTATED SLC16A2 WILD-TYPE 
            31.99             20.12 
[1] "13.0 - 140.4 (32.0)" "0.0 - 148.0 (20.1)" 
[1] "hr=" "1.3"
D1373V2, continuous
D1373V3, binary
                   cls
clus                  0   1
  SLC16A2 MUTATED     5   3
  SLC16A2 WILD-TYPE 361 116
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC16A2 MUTATED      5    3
  SLC16A2 WILD-TYPE  361  116
        clus
vv       SLC16A2 MUTATED SLC16A2 WILD-TYPE
  COLON                5               361
  RECTUM               3               116
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SLC16A2 MUTATED         2        0        0         4         0         0
  SLC16A2 WILD-TYPE      89        1       32       134        10         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC16A2 MUTATED           1          0          0          0        0
  SLC16A2 WILD-TYPE        23         11         59         42       48
                   vv
clus                STAGE IVA STAGE IVB
  SLC16A2 MUTATED           1         0
  SLC16A2 WILD-TYPE        17         1
D1373V4, multiclass
            clus
vv           SLC16A2 MUTATED SLC16A2 WILD-TYPE
  STAGE I                  2                89
  STAGE IA                 0                 1
  STAGE II                 0                32
  STAGE IIA                4               134
  STAGE IIB                0                10
  STAGE IIC                0                 1
  STAGE III                1                23
  STAGE IIIA               0                11
  STAGE IIIB               0                59
  STAGE IIIC               0                42
  STAGE IV                 0                48
  STAGE IVA                1                17
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  SLC16A2 MUTATED     1   1   6   0
  SLC16A2 WILD-TYPE  16  91 323  50
D1373V5, multiclass
    clus
vv   SLC16A2 MUTATED SLC16A2 WILD-TYPE
  T1               1                16
  T2               1                91
  T3               6               323
  T4               0                50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  SLC16A2 MUTATED     6   1   1
  SLC16A2 WILD-TYPE 281 112  86
D1373V6, multiclass
    clus
vv   SLC16A2 MUTATED SLC16A2 WILD-TYPE
  N0               6               281
  N1               1               112
  N2               1                86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1373V7, binary
                   cls
clus                  0   1
  SLC16A2 MUTATED     7   1
  SLC16A2 WILD-TYPE 368  64
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC16A2 MUTATED      7    1
  SLC16A2 WILD-TYPE  368   64
   clus
vv  SLC16A2 MUTATED SLC16A2 WILD-TYPE
  0               7               368
  1               1                64
[1] 2 2
[1] FALSE
D1373V8, binary
                   cls
clus                  0   1
  SLC16A2 MUTATED     7   1
  SLC16A2 WILD-TYPE 218 263
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC16A2 MUTATED      7    1
  SLC16A2 WILD-TYPE  218  263
        clus
vv       SLC16A2 MUTATED SLC16A2 WILD-TYPE
  FEMALE               7               218
  MALE                 1               263
[1] 2 2
[1] FALSE
D1373V9, binary
                   cls
clus                  0   1
  SLC16A2 MUTATED     6   0
  SLC16A2 WILD-TYPE 344  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC16A2 MUTATED      6    0
  SLC16A2 WILD-TYPE  344   22
     clus
vv    SLC16A2 MUTATED SLC16A2 WILD-TYPE
  NO                6               344
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SLC16A2 MUTATED                      3                             2
  SLC16A2 WILD-TYPE                  312                            45
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SLC16A2 MUTATED                       3                              0
  SLC16A2 WILD-TYPE                   103                             10
D1373V10, multiclass
                                clus
vv                               SLC16A2 MUTATED SLC16A2 WILD-TYPE
  COLON ADENOCARCINOMA                         3               312
  COLON MUCINOUS ADENOCARCINOMA                2                45
  RECTAL ADENOCARCINOMA                        3               103
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  SLC16A2 MUTATED     5   0   0   0
  SLC16A2 WILD-TYPE 340   4  31  25
D1373V11, multiclass
    clus
vv   SLC16A2 MUTATED SLC16A2 WILD-TYPE
  R0               5               340
  R1               0                 4
  R2               0                31
  RX               0                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1373V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SLC16A2 MUTATED                                  0     0
  SLC16A2 WILD-TYPE                                1    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  SLC16A2 MUTATED                           0     4
  SLC16A2 WILD-TYPE                        22   222
D1373V13, multiclass
                                  clus
vv                                 SLC16A2 MUTATED SLC16A2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                      0                22
  WHITE                                          4               222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1374) Variable = DDHD2 MUTATION ANALYSIS
D1374V1, survival
                 sevent
clus2               0   1
  DDHD2 MUTATED     8   3
  DDHD2 WILD-TYPE 370  90
  DDHD2 MUTATED DDHD2 WILD-TYPE 
             11             460 
  DDHD2 MUTATED DDHD2 WILD-TYPE 
              3              90 
$`DDHD2 MUTATED`
TCGA-A6-6781 TCGA-AA-3555 TCGA-AA-3715 TCGA-AA-3947 TCGA-AZ-6599 TCGA-CK-5913 
       19.66        29.95        19.04        33.01         6.77        51.32 
TCGA-CM-6161 TCGA-D5-6923 TCGA-G4-6626 TCGA-CL-5918 TCGA-EI-6507 
       15.02        12.43        46.75         7.17        19.96 

$`DDHD2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       13.02        24.00        17.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        88.21        49.41        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       15.02        17.03        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        1.48         3.68         4.41        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       26.17        91.79        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-DC-5337 
        6.05        33.17         6.97         4.73        78.12        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6508 
       24.13        51.48        32.61         0.49        20.55        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  DDHD2 MUTATED DDHD2 WILD-TYPE 
           6.77            0.00 
  DDHD2 MUTATED DDHD2 WILD-TYPE 
          51.32          148.01 
  DDHD2 MUTATED DDHD2 WILD-TYPE 
         19.660          20.415 
[1] "6.8 - 51.3 (19.7)"  "0.0 - 148.0 (20.4)"
[1] "hr=" "1.5"
D1374V2, continuous
D1374V3, binary
                 cls
clus                0   1
  DDHD2 MUTATED     9   2
  DDHD2 WILD-TYPE 357 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDHD2 MUTATED      9    2
  DDHD2 WILD-TYPE  357  117
        clus
vv       DDHD2 MUTATED DDHD2 WILD-TYPE
  COLON              9             357
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DDHD2 MUTATED         3        0        1         5         1         0
  DDHD2 WILD-TYPE      88        1       31       133         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DDHD2 MUTATED           0          0          0          1        0         0
  DDHD2 WILD-TYPE        24         11         59         41       48        18
                 vv
clus              STAGE IVB
  DDHD2 MUTATED           0
  DDHD2 WILD-TYPE         1
D1374V4, multiclass
            clus
vv           DDHD2 MUTATED DDHD2 WILD-TYPE
  STAGE I                3              88
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              5             133
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             1              41
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  DDHD2 MUTATED     0   3   6   2
  DDHD2 WILD-TYPE  17  89 323  48
D1374V5, multiclass
    clus
vv   DDHD2 MUTATED DDHD2 WILD-TYPE
  T1             0              17
  T2             3              89
  T3             6             323
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  DDHD2 MUTATED    10   1   0
  DDHD2 WILD-TYPE 277 112  87
D1374V6, multiclass
    clus
vv   DDHD2 MUTATED DDHD2 WILD-TYPE
  N0            10             277
  N1             1             112
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1374V7, binary
                 cls
clus                0   1
  DDHD2 MUTATED     7   0
  DDHD2 WILD-TYPE 368  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDHD2 MUTATED      7    0
  DDHD2 WILD-TYPE  368   65
   clus
vv  DDHD2 MUTATED DDHD2 WILD-TYPE
  0             7             368
  1             0              65
[1] 2 2
[1] FALSE
D1374V8, binary
                 cls
clus                0   1
  DDHD2 MUTATED     5   6
  DDHD2 WILD-TYPE 220 258
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDHD2 MUTATED      5    6
  DDHD2 WILD-TYPE  220  258
        clus
vv       DDHD2 MUTATED DDHD2 WILD-TYPE
  FEMALE             5             220
  MALE               6             258
[1] 2 2
[1] FALSE
D1374V9, binary
                 cls
clus                0   1
  DDHD2 MUTATED    11   0
  DDHD2 WILD-TYPE 339  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDHD2 MUTATED     11    0
  DDHD2 WILD-TYPE  339   22
     clus
vv    DDHD2 MUTATED DDHD2 WILD-TYPE
  NO             11             339
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  DDHD2 MUTATED                      6                             3
  DDHD2 WILD-TYPE                  309                            44
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  DDHD2 MUTATED                       2                              0
  DDHD2 WILD-TYPE                   104                             10
D1374V10, multiclass
                                clus
vv                               DDHD2 MUTATED DDHD2 WILD-TYPE
  COLON ADENOCARCINOMA                       6             309
  COLON MUCINOUS ADENOCARCINOMA              3              44
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  DDHD2 MUTATED     8   0   0   2
  DDHD2 WILD-TYPE 337   4  31  23
D1374V11, multiclass
    clus
vv   DDHD2 MUTATED DDHD2 WILD-TYPE
  R0             8             337
  R1             0               4
  R2             0              31
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1374V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DDHD2 MUTATED                                  0     0
  DDHD2 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  DDHD2 MUTATED                           0     8
  DDHD2 WILD-TYPE                        22   218
D1374V13, multiclass
                                  clus
vv                                 DDHD2 MUTATED DDHD2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        8             218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1375) Variable = GKN1 MUTATION ANALYSIS
D1375V1, survival
                sevent
clus2              0   1
  GKN1 MUTATED     4   2
  GKN1 WILD-TYPE 374  91
  GKN1 MUTATED GKN1 WILD-TYPE 
             6            465 
  GKN1 MUTATED GKN1 WILD-TYPE 
             2             91 
$`GKN1 MUTATED`
TCGA-AA-3818 TCGA-AA-A00D TCGA-D5-6541 TCGA-DM-A1DB TCGA-AF-2693 TCGA-AG-A002 
        0.99        19.00        15.58        44.32        19.10        20.98 

$`GKN1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3819 TCGA-AA-3821 
       19.04        10.06        35.05        33.04        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       38.04        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6898 TCGA-D5-6920 
        4.80        17.13        12.49        16.14         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
       12.59       140.38         7.50       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  GKN1 MUTATED GKN1 WILD-TYPE 
          0.99           0.00 
  GKN1 MUTATED GKN1 WILD-TYPE 
         44.32         148.01 
  GKN1 MUTATED GKN1 WILD-TYPE 
         19.05          20.28 
[1] "1.0 - 44.3 (19.1)"  "0.0 - 148.0 (20.3)"
[1] "hr=" "2.1"
D1375V2, continuous
D1375V3, binary
                cls
clus               0   1
  GKN1 MUTATED     4   1
  GKN1 WILD-TYPE 362 118
[1] "tbl2"
                cls
clus             [,1] [,2]
  GKN1 MUTATED      4    1
  GKN1 WILD-TYPE  362  118
        clus
vv       GKN1 MUTATED GKN1 WILD-TYPE
  COLON             4            362
  RECTUM            1            118
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GKN1 MUTATED         3        0        0         3         0         0
  GKN1 WILD-TYPE      88        1       32       135        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  GKN1 MUTATED           0          0          0          0        0         0
  GKN1 WILD-TYPE        24         11         59         42       48        18
                vv
clus             STAGE IVB
  GKN1 MUTATED           0
  GKN1 WILD-TYPE         1
D1375V4, multiclass
            clus
vv           GKN1 MUTATED GKN1 WILD-TYPE
  STAGE I               3             88
  STAGE IA              0              1
  STAGE II              0             32
  STAGE IIA             3            135
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            0             59
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  GKN1 MUTATED     0   3   3   0
  GKN1 WILD-TYPE  17  89 326  50
D1375V5, multiclass
    clus
vv   GKN1 MUTATED GKN1 WILD-TYPE
  T1            0             17
  T2            3             89
  T3            3            326
  T4            0             50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  GKN1 MUTATED     6   0   0
  GKN1 WILD-TYPE 281 113  87
D1375V6, multiclass
    clus
vv   GKN1 MUTATED GKN1 WILD-TYPE
  N0            6            281
  N1            0            113
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1375V7, binary
                cls
clus               0   1
  GKN1 MUTATED     5   0
  GKN1 WILD-TYPE 370  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  GKN1 MUTATED      5    0
  GKN1 WILD-TYPE  370   65
   clus
vv  GKN1 MUTATED GKN1 WILD-TYPE
  0            5            370
  1            0             65
[1] 2 2
[1] FALSE
D1375V8, binary
                cls
clus               0   1
  GKN1 MUTATED     1   5
  GKN1 WILD-TYPE 224 259
[1] "tbl2"
                cls
clus             [,1] [,2]
  GKN1 MUTATED      1    5
  GKN1 WILD-TYPE  224  259
        clus
vv       GKN1 MUTATED GKN1 WILD-TYPE
  FEMALE            1            224
  MALE              5            259
[1] 2 2
[1] FALSE
D1375V9, binary
                cls
clus               0   1
  GKN1 MUTATED     4   0
  GKN1 WILD-TYPE 346  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  GKN1 MUTATED      4    0
  GKN1 WILD-TYPE  346   22
     clus
vv    GKN1 MUTATED GKN1 WILD-TYPE
  NO             4            346
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  GKN1 MUTATED                      4                             0
  GKN1 WILD-TYPE                  311                            47
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  GKN1 MUTATED                       1                              0
  GKN1 WILD-TYPE                   105                             10
D1375V10, multiclass
                                clus
vv                               GKN1 MUTATED GKN1 WILD-TYPE
  COLON ADENOCARCINOMA                      4            311
  COLON MUCINOUS ADENOCARCINOMA             0             47
  RECTAL ADENOCARCINOMA                     1            105
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  GKN1 MUTATED     4   0   0   0
  GKN1 WILD-TYPE 341   4  31  25
D1375V11, multiclass
    clus
vv   GKN1 MUTATED GKN1 WILD-TYPE
  R0            4            341
  R1            0              4
  R2            0             31
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1375V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GKN1 MUTATED                                  0     0
  GKN1 WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  GKN1 MUTATED                           0     3
  GKN1 WILD-TYPE                        22   223
D1375V13, multiclass
                                  clus
vv                                 GKN1 MUTATED GKN1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       3            223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1376) Variable = F2R MUTATION ANALYSIS
D1376V1, survival
               sevent
clus2             0   1
  F2R MUTATED    10   1
  F2R WILD-TYPE 368  92
  F2R MUTATED F2R WILD-TYPE 
           11           460 
  F2R MUTATED F2R WILD-TYPE 
            1            92 
$`F2R MUTATED`
TCGA-A6-6780 TCGA-AA-3511 TCGA-AA-3663 TCGA-AA-3950 TCGA-AZ-6599 TCGA-CA-6717 
       20.12         6.97         6.97        24.00         6.77        12.76 
TCGA-CK-4950 TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-6161 TCGA-D5-6540 
       85.45        30.08        15.02        15.02        16.14 

$`F2R WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01        63.98         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        33.01        26.01         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        88.21        49.41        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07        12.20        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
       17.56       148.01        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6162 
       32.02         5.03        15.02        15.02        17.03        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       12.49        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  F2R MUTATED F2R WILD-TYPE 
         6.77          0.00 
  F2R MUTATED F2R WILD-TYPE 
        85.45        148.01 
  F2R MUTATED F2R WILD-TYPE 
        15.02         20.73 
[1] "6.8 - 85.5 (15.0)"  "0.0 - 148.0 (20.7)"
[1] "hr=" "1.8"
D1376V2, continuous
D1376V3, binary
               cls
clus              0   1
  F2R MUTATED    11   0
  F2R WILD-TYPE 355 119
[1] "tbl2"
               cls
clus            [,1] [,2]
  F2R MUTATED     11    0
  F2R WILD-TYPE  355  119
        clus
vv       F2R MUTATED F2R WILD-TYPE
  COLON           11           355
  RECTUM           0           119
[1] 2 2
[1] FALSE
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  F2R MUTATED         3        0        2         5         0         0
  F2R WILD-TYPE      88        1       30       133        10         1
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  F2R MUTATED           0          0          1          0        0         0
  F2R WILD-TYPE        24         11         58         42       48        18
               vv
clus            STAGE IVB
  F2R MUTATED           0
  F2R WILD-TYPE         1
D1376V4, multiclass
            clus
vv           F2R MUTATED F2R WILD-TYPE
  STAGE I              3            88
  STAGE IA             0             1
  STAGE II             2            30
  STAGE IIA            5           133
  STAGE IIB            0            10
  STAGE IIC            0             1
  STAGE III            0            24
  STAGE IIIA           0            11
  STAGE IIIB           1            58
  STAGE IIIC           0            42
  STAGE IV             0            48
  STAGE IVA            0            18
  STAGE IVB            0             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  F2R MUTATED     0   3   7   1
  F2R WILD-TYPE  17  89 322  49
D1376V5, multiclass
    clus
vv   F2R MUTATED F2R WILD-TYPE
  T1           0            17
  T2           3            89
  T3           7           322
  T4           1            49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2
  F2R MUTATED    10   1   0
  F2R WILD-TYPE 277 112  87
D1376V6, multiclass
    clus
vv   F2R MUTATED F2R WILD-TYPE
  N0          10           277
  N1           1           112
  N2           0            87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1376V7, binary
               cls
clus              0   1
  F2R MUTATED     9   0
  F2R WILD-TYPE 366  65
[1] "tbl2"
               cls
clus            [,1] [,2]
  F2R MUTATED      9    0
  F2R WILD-TYPE  366   65
   clus
vv  F2R MUTATED F2R WILD-TYPE
  0           9           366
  1           0            65
[1] 2 2
[1] FALSE
D1376V8, binary
               cls
clus              0   1
  F2R MUTATED     5   6
  F2R WILD-TYPE 220 258
[1] "tbl2"
               cls
clus            [,1] [,2]
  F2R MUTATED      5    6
  F2R WILD-TYPE  220  258
        clus
vv       F2R MUTATED F2R WILD-TYPE
  FEMALE           5           220
  MALE             6           258
[1] 2 2
[1] FALSE
D1376V9, binary
               cls
clus              0   1
  F2R MUTATED    11   0
  F2R WILD-TYPE 339  22
[1] "tbl2"
               cls
clus            [,1] [,2]
  F2R MUTATED     11    0
  F2R WILD-TYPE  339   22
     clus
vv    F2R MUTATED F2R WILD-TYPE
  NO           11           339
  YES           0            22
[1] 2 2
[1] FALSE
               vv
clus            COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  F2R MUTATED                      7                             4
  F2R WILD-TYPE                  308                            43
               vv
clus            RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  F2R MUTATED                       0                              0
  F2R WILD-TYPE                   106                             10
D1376V10, multiclass
                                clus
vv                               F2R MUTATED F2R WILD-TYPE
  COLON ADENOCARCINOMA                     7           308
  COLON MUCINOUS ADENOCARCINOMA            4            43
  RECTAL ADENOCARCINOMA                    0           106
  RECTAL MUCINOUS ADENOCARCINOMA           0            10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             R0  R1  R2  RX
  F2R MUTATED     7   1   0   1
  F2R WILD-TYPE 338   3  31  24
D1376V11, multiclass
    clus
vv   F2R MUTATED F2R WILD-TYPE
  R0           7           338
  R1           1             3
  R2           0            31
  RX           1            24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1376V12, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  F2R MUTATED                                  0     1
  F2R WILD-TYPE                                1    10
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  F2R MUTATED                           1     6
  F2R WILD-TYPE                        21   220
D1376V13, multiclass
                                  clus
vv                                 F2R MUTATED F2R WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      1            10
  BLACK OR AFRICAN AMERICAN                  1            21
  WHITE                                      6           220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1377) Variable = CYP20A1 MUTATION ANALYSIS
D1377V1, survival
                   sevent
clus2                 0   1
  CYP20A1 MUTATED     6   2
  CYP20A1 WILD-TYPE 372  91
  CYP20A1 MUTATED CYP20A1 WILD-TYPE 
                8               463 
  CYP20A1 MUTATED CYP20A1 WILD-TYPE 
                2                91 
$`CYP20A1 MUTATED`
TCGA-A6-6781 TCGA-AA-3663 TCGA-AA-3672 TCGA-AA-3856 TCGA-AD-6964 TCGA-AY-6197 
       19.66         6.97         0.92         0.99        10.88        21.44 
TCGA-AZ-4315 TCGA-D5-6537 
       58.39         4.80 

$`CYP20A1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
       54.02         2.01        14.01        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3858 
        0.00        33.07         0.00        36.03        32.05        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
        0.72         5.79        22.42        27.42         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4323 
       27.09        16.31         0.95        33.01        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
       17.85        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  CYP20A1 MUTATED CYP20A1 WILD-TYPE 
             0.92              0.00 
  CYP20A1 MUTATED CYP20A1 WILD-TYPE 
            58.39            148.01 
  CYP20A1 MUTATED CYP20A1 WILD-TYPE 
            8.925            20.550 
[1] "0.9 - 58.4 (8.9)"   "0.0 - 148.0 (20.6)"
[1] "hr=" "2"  
D1377V2, continuous
D1377V3, binary
                   cls
clus                  0   1
  CYP20A1 MUTATED     8   0
  CYP20A1 WILD-TYPE 358 119
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CYP20A1 MUTATED      8    0
  CYP20A1 WILD-TYPE  358  119
        clus
vv       CYP20A1 MUTATED CYP20A1 WILD-TYPE
  COLON                8               358
  RECTUM               0               119
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CYP20A1 MUTATED         0        0        1         3         0         0
  CYP20A1 WILD-TYPE      91        1       31       135        10         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CYP20A1 MUTATED           1          0          1          1        0
  CYP20A1 WILD-TYPE        23         11         58         41       48
                   vv
clus                STAGE IVA STAGE IVB
  CYP20A1 MUTATED           0         0
  CYP20A1 WILD-TYPE        18         1
D1377V4, multiclass
            clus
vv           CYP20A1 MUTATED CYP20A1 WILD-TYPE
  STAGE I                  0                91
  STAGE IA                 0                 1
  STAGE II                 1                31
  STAGE IIA                3               135
  STAGE IIB                0                10
  STAGE IIC                0                 1
  STAGE III                1                23
  STAGE IIIA               0                11
  STAGE IIIB               1                58
  STAGE IIIC               1                41
  STAGE IV                 0                48
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  CYP20A1 MUTATED     0   0   6   2
  CYP20A1 WILD-TYPE  17  92 323  48
D1377V5, multiclass
    clus
vv   CYP20A1 MUTATED CYP20A1 WILD-TYPE
  T1               0                17
  T2               0                92
  T3               6               323
  T4               2                48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  CYP20A1 MUTATED     4   3   1
  CYP20A1 WILD-TYPE 283 110  86
D1377V6, multiclass
    clus
vv   CYP20A1 MUTATED CYP20A1 WILD-TYPE
  N0               4               283
  N1               3               110
  N2               1                86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1377V7, binary
                   cls
clus                  0   1
  CYP20A1 MUTATED     4   0
  CYP20A1 WILD-TYPE 371  65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CYP20A1 MUTATED      4    0
  CYP20A1 WILD-TYPE  371   65
   clus
vv  CYP20A1 MUTATED CYP20A1 WILD-TYPE
  0               4               371
  1               0                65
[1] 2 2
[1] FALSE
D1377V8, binary
                   cls
clus                  0   1
  CYP20A1 MUTATED     1   7
  CYP20A1 WILD-TYPE 224 257
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CYP20A1 MUTATED      1    7
  CYP20A1 WILD-TYPE  224  257
        clus
vv       CYP20A1 MUTATED CYP20A1 WILD-TYPE
  FEMALE               1               224
  MALE                 7               257
[1] 2 2
[1] FALSE
D1377V9, binary
                   cls
clus                  0   1
  CYP20A1 MUTATED     7   0
  CYP20A1 WILD-TYPE 343  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CYP20A1 MUTATED      7    0
  CYP20A1 WILD-TYPE  343   22
     clus
vv    CYP20A1 MUTATED CYP20A1 WILD-TYPE
  NO                7               343
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CYP20A1 MUTATED                      7                             1
  CYP20A1 WILD-TYPE                  308                            46
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CYP20A1 MUTATED                       0                              0
  CYP20A1 WILD-TYPE                   106                             10
D1377V10, multiclass
                                clus
vv                               CYP20A1 MUTATED CYP20A1 WILD-TYPE
  COLON ADENOCARCINOMA                         7               308
  COLON MUCINOUS ADENOCARCINOMA                1                46
  RECTAL ADENOCARCINOMA                        0               106
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  CYP20A1 MUTATED     7   0   0   0
  CYP20A1 WILD-TYPE 338   4  31  25
D1377V11, multiclass
    clus
vv   CYP20A1 MUTATED CYP20A1 WILD-TYPE
  R0               7               338
  R1               0                 4
  R2               0                31
  RX               0                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1377V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CYP20A1 MUTATED                                  0     0
  CYP20A1 WILD-TYPE                                1    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  CYP20A1 MUTATED                           0     5
  CYP20A1 WILD-TYPE                        22   221
D1377V13, multiclass
                                  clus
vv                                 CYP20A1 MUTATED CYP20A1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                      0                22
  WHITE                                          5               221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1378) Variable = ZP2 MUTATION ANALYSIS
D1378V1, survival
               sevent
clus2             0   1
  ZP2 MUTATED    14   0
  ZP2 WILD-TYPE 364  93
  ZP2 MUTATED ZP2 WILD-TYPE 
           14           457 
  ZP2 MUTATED ZP2 WILD-TYPE 
            0            93 
$`ZP2 MUTATED`
TCGA-A6-3809 TCGA-A6-5666 TCGA-A6-6653 TCGA-AA-3710 TCGA-AA-3864 TCGA-AA-3977 
       32.75        32.71        24.39        26.99        53.00        25.02 
TCGA-AA-A010 TCGA-CK-4948 TCGA-CM-6161 TCGA-CM-6167 TCGA-D5-6928 TCGA-G4-6306 
       34.98       148.01        15.02        14.99        11.64        44.68 
TCGA-AG-3593 TCGA-EF-5830 
       34.03         0.49 

$`ZP2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       22.06        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       24.16        21.76        24.69        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       85.05        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       31.07        30.05        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6168 
       12.00         2.96        29.03        16.04        21.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6930 
       12.43        14.30         9.04         9.44         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3594 TCGA-AG-3598 
       20.05        24.00         1.02        46.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  ZP2 MUTATED ZP2 WILD-TYPE 
         0.49          0.00 
  ZP2 MUTATED ZP2 WILD-TYPE 
       148.01        140.38 
  ZP2 MUTATED ZP2 WILD-TYPE 
        29.85         20.02 
[1] "0.5 - 148.0 (29.9)" "0.0 - 140.4 (20.0)"
[1] "hr="     "2.6e+07"
D1378V2, continuous
D1378V3, binary
               cls
clus              0   1
  ZP2 MUTATED    12   2
  ZP2 WILD-TYPE 354 117
[1] "tbl2"
               cls
clus            [,1] [,2]
  ZP2 MUTATED     12    2
  ZP2 WILD-TYPE  354  117
        clus
vv       ZP2 MUTATED ZP2 WILD-TYPE
  COLON           12           354
  RECTUM           2           117
[1] 2 2
[1] FALSE
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZP2 MUTATED         2        0        1         4         3         1
  ZP2 WILD-TYPE      89        1       31       134         7         0
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ZP2 MUTATED           1          0          0          1        0         0
  ZP2 WILD-TYPE        23         11         59         41       48        18
               vv
clus            STAGE IVB
  ZP2 MUTATED           0
  ZP2 WILD-TYPE         1
D1378V4, multiclass
            clus
vv           ZP2 MUTATED ZP2 WILD-TYPE
  STAGE I              2            89
  STAGE IA             0             1
  STAGE II             1            31
  STAGE IIA            4           134
  STAGE IIB            3             7
  STAGE IIC            1             0
  STAGE III            1            23
  STAGE IIIA           0            11
  STAGE IIIB           0            59
  STAGE IIIC           1            41
  STAGE IV             0            48
  STAGE IVA            0            18
  STAGE IVB            0             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  ZP2 MUTATED     0   4   6   4
  ZP2 WILD-TYPE  17  88 323  46
D1378V5, multiclass
    clus
vv   ZP2 MUTATED ZP2 WILD-TYPE
  T1           0            17
  T2           4            88
  T3           6           323
  T4           4            46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2
  ZP2 MUTATED    12   1   1
  ZP2 WILD-TYPE 275 112  86
D1378V6, multiclass
    clus
vv   ZP2 MUTATED ZP2 WILD-TYPE
  N0          12           275
  N1           1           112
  N2           1            86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1378V7, binary
               cls
clus              0   1
  ZP2 MUTATED    13   0
  ZP2 WILD-TYPE 362  65
[1] "tbl2"
               cls
clus            [,1] [,2]
  ZP2 MUTATED     13    0
  ZP2 WILD-TYPE  362   65
   clus
vv  ZP2 MUTATED ZP2 WILD-TYPE
  0          13           362
  1           0            65
[1] 2 2
[1] FALSE
D1378V8, binary
               cls
clus              0   1
  ZP2 MUTATED     7   7
  ZP2 WILD-TYPE 218 257
[1] "tbl2"
               cls
clus            [,1] [,2]
  ZP2 MUTATED      7    7
  ZP2 WILD-TYPE  218  257
        clus
vv       ZP2 MUTATED ZP2 WILD-TYPE
  FEMALE           7           218
  MALE             7           257
[1] 2 2
[1] FALSE
D1378V9, binary
               cls
clus              0   1
  ZP2 MUTATED    12   1
  ZP2 WILD-TYPE 338  21
[1] "tbl2"
               cls
clus            [,1] [,2]
  ZP2 MUTATED     12    1
  ZP2 WILD-TYPE  338   21
     clus
vv    ZP2 MUTATED ZP2 WILD-TYPE
  NO           12           338
  YES           1            21
[1] 2 2
[1] FALSE
               vv
clus            COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ZP2 MUTATED                     10                             2
  ZP2 WILD-TYPE                  305                            45
               vv
clus            RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ZP2 MUTATED                       2                              0
  ZP2 WILD-TYPE                   104                             10
D1378V10, multiclass
                                clus
vv                               ZP2 MUTATED ZP2 WILD-TYPE
  COLON ADENOCARCINOMA                    10           305
  COLON MUCINOUS ADENOCARCINOMA            2            45
  RECTAL ADENOCARCINOMA                    2           104
  RECTAL MUCINOUS ADENOCARCINOMA           0            10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             R0  R1  R2  RX
  ZP2 MUTATED    11   0   0   0
  ZP2 WILD-TYPE 334   4  31  25
D1378V11, multiclass
    clus
vv   ZP2 MUTATED ZP2 WILD-TYPE
  R0          11           334
  R1           0             4
  R2           0            31
  RX           0            25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1378V12, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZP2 MUTATED                                  0     0
  ZP2 WILD-TYPE                                1    11
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  ZP2 MUTATED                           1     8
  ZP2 WILD-TYPE                        21   218
D1378V13, multiclass
                                  clus
vv                                 ZP2 MUTATED ZP2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      0            11
  BLACK OR AFRICAN AMERICAN                  1            21
  WHITE                                      8           218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1379) Variable = RAB38 MUTATION ANALYSIS
D1379V1, survival
                 sevent
clus2               0   1
  RAB38 MUTATED     2   3
  RAB38 WILD-TYPE 376  90
  RAB38 MUTATED RAB38 WILD-TYPE 
              5             466 
  RAB38 MUTATED RAB38 WILD-TYPE 
              3              90 
$`RAB38 MUTATED`
TCGA-A6-2676 TCGA-A6-5665 TCGA-AD-6890 TCGA-AZ-6598 TCGA-CM-5862 
       42.90        22.06         0.79        49.41         5.03 

$`RAB38 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
       56.55         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        88.21         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  RAB38 MUTATED RAB38 WILD-TYPE 
           0.79            0.00 
  RAB38 MUTATED RAB38 WILD-TYPE 
          49.41          148.01 
  RAB38 MUTATED RAB38 WILD-TYPE 
         22.060          20.155 
[1] "0.8 - 49.4 (22.1)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "3.2"
D1379V2, continuous
D1379V3, binary
                 cls
clus                0   1
  RAB38 MUTATED     5   0
  RAB38 WILD-TYPE 361 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RAB38 MUTATED      5    0
  RAB38 WILD-TYPE  361  119
        clus
vv       RAB38 MUTATED RAB38 WILD-TYPE
  COLON              5             361
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RAB38 MUTATED         0        0        1         1         1         0
  RAB38 WILD-TYPE      91        1       31       137         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RAB38 MUTATED           0          0          0          0        0         1
  RAB38 WILD-TYPE        24         11         59         42       48        17
                 vv
clus              STAGE IVB
  RAB38 MUTATED           0
  RAB38 WILD-TYPE         1
D1379V4, multiclass
            clus
vv           RAB38 MUTATED RAB38 WILD-TYPE
  STAGE I                0              91
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              1             137
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  RAB38 MUTATED     1   0   3   1
  RAB38 WILD-TYPE  16  92 326  49
D1379V5, multiclass
    clus
vv   RAB38 MUTATED RAB38 WILD-TYPE
  T1             1              16
  T2             0              92
  T3             3             326
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  RAB38 MUTATED     4   1   0
  RAB38 WILD-TYPE 283 112  87
D1379V6, multiclass
    clus
vv   RAB38 MUTATED RAB38 WILD-TYPE
  N0             4             283
  N1             1             112
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1379V7, binary
                 cls
clus                0   1
  RAB38 MUTATED     2   1
  RAB38 WILD-TYPE 373  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RAB38 MUTATED      2    1
  RAB38 WILD-TYPE  373   64
   clus
vv  RAB38 MUTATED RAB38 WILD-TYPE
  0             2             373
  1             1              64
[1] 2 2
[1] FALSE
D1379V8, binary
                 cls
clus                0   1
  RAB38 MUTATED     3   2
  RAB38 WILD-TYPE 222 262
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RAB38 MUTATED      3    2
  RAB38 WILD-TYPE  222  262
        clus
vv       RAB38 MUTATED RAB38 WILD-TYPE
  FEMALE             3             222
  MALE               2             262
[1] 2 2
[1] FALSE
D1379V9, binary
                 cls
clus                0   1
  RAB38 MUTATED     4   0
  RAB38 WILD-TYPE 346  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RAB38 MUTATED      4    0
  RAB38 WILD-TYPE  346   22
     clus
vv    RAB38 MUTATED RAB38 WILD-TYPE
  NO              4             346
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  RAB38 MUTATED                      5                             0
  RAB38 WILD-TYPE                  310                            47
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  RAB38 MUTATED                       0                              0
  RAB38 WILD-TYPE                   106                             10
D1379V10, multiclass
                                clus
vv                               RAB38 MUTATED RAB38 WILD-TYPE
  COLON ADENOCARCINOMA                       5             310
  COLON MUCINOUS ADENOCARCINOMA              0              47
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  RAB38 MUTATED     3   0   0   0
  RAB38 WILD-TYPE 342   4  31  25
D1379V11, multiclass
    clus
vv   RAB38 MUTATED RAB38 WILD-TYPE
  R0             3             342
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1379V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RAB38 MUTATED                                  0     0
  RAB38 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  RAB38 MUTATED                           0     5
  RAB38 WILD-TYPE                        22   221
D1379V13, multiclass
                                  clus
vv                                 RAB38 MUTATED RAB38 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        5             221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1380) Variable = TCF7 MUTATION ANALYSIS
D1380V1, survival
                sevent
clus2              0   1
  TCF7 MUTATED    10   2
  TCF7 WILD-TYPE 368  91
  TCF7 MUTATED TCF7 WILD-TYPE 
            12            459 
  TCF7 MUTATED TCF7 WILD-TYPE 
             2             91 
$`TCF7 MUTATED`
TCGA-A6-5661 TCGA-A6-6780 TCGA-AA-3554 TCGA-AA-3558 TCGA-AA-3713 TCGA-AA-A00N 
       33.53        20.12        17.95        20.98        19.04         4.01 
TCGA-AD-6548 TCGA-AZ-6598 TCGA-CA-6717 TCGA-CM-4746 TCGA-AG-3598 TCGA-AG-A002 
       21.37        49.41        12.76        37.02        50.04        20.98 

$`TCF7 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       24.00        29.95        23.01        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       26.99        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 
        5.13       106.75        22.36        62.79        88.21         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.20        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4752 
        1.91       124.27        23.05        20.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
       34.03         2.01        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  TCF7 MUTATED TCF7 WILD-TYPE 
          4.01           0.00 
  TCF7 MUTATED TCF7 WILD-TYPE 
         50.04         148.01 
  TCF7 MUTATED TCF7 WILD-TYPE 
         20.98          20.05 
[1] "4.0 - 50.0 (21.0)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.2"
D1380V2, continuous
D1380V3, binary
                cls
clus               0   1
  TCF7 MUTATED    10   2
  TCF7 WILD-TYPE 356 117
[1] "tbl2"
                cls
clus             [,1] [,2]
  TCF7 MUTATED     10    2
  TCF7 WILD-TYPE  356  117
        clus
vv       TCF7 MUTATED TCF7 WILD-TYPE
  COLON            10            356
  RECTUM            2            117
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TCF7 MUTATED         4        0        1         5         1         0
  TCF7 WILD-TYPE      87        1       31       133         9         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TCF7 MUTATED           0          0          0          0        1         0
  TCF7 WILD-TYPE        24         11         59         42       47        18
                vv
clus             STAGE IVB
  TCF7 MUTATED           0
  TCF7 WILD-TYPE         1
D1380V4, multiclass
            clus
vv           TCF7 MUTATED TCF7 WILD-TYPE
  STAGE I               4             87
  STAGE IA              0              1
  STAGE II              1             31
  STAGE IIA             5            133
  STAGE IIB             1              9
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            0             59
  STAGE IIIC            0             42
  STAGE IV              1             47
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  TCF7 MUTATED     0   4   7   1
  TCF7 WILD-TYPE  17  88 322  49
D1380V5, multiclass
    clus
vv   TCF7 MUTATED TCF7 WILD-TYPE
  T1            0             17
  T2            4             88
  T3            7            322
  T4            1             49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  TCF7 MUTATED    12   0   0
  TCF7 WILD-TYPE 275 113  87
D1380V6, multiclass
    clus
vv   TCF7 MUTATED TCF7 WILD-TYPE
  N0           12            275
  N1            0            113
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1380V7, binary
                cls
clus               0   1
  TCF7 MUTATED     9   1
  TCF7 WILD-TYPE 366  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  TCF7 MUTATED      9    1
  TCF7 WILD-TYPE  366   64
   clus
vv  TCF7 MUTATED TCF7 WILD-TYPE
  0            9            366
  1            1             64
[1] 2 2
[1] FALSE
D1380V8, binary
                cls
clus               0   1
  TCF7 MUTATED     4   8
  TCF7 WILD-TYPE 221 256
[1] "tbl2"
                cls
clus             [,1] [,2]
  TCF7 MUTATED      4    8
  TCF7 WILD-TYPE  221  256
        clus
vv       TCF7 MUTATED TCF7 WILD-TYPE
  FEMALE            4            221
  MALE              8            256
[1] 2 2
[1] FALSE
D1380V9, binary
                cls
clus               0   1
  TCF7 MUTATED    10   1
  TCF7 WILD-TYPE 340  21
[1] "tbl2"
                cls
clus             [,1] [,2]
  TCF7 MUTATED     10    1
  TCF7 WILD-TYPE  340   21
     clus
vv    TCF7 MUTATED TCF7 WILD-TYPE
  NO            10            340
  YES            1             21
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  TCF7 MUTATED                      7                             3
  TCF7 WILD-TYPE                  308                            44
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  TCF7 MUTATED                       2                              0
  TCF7 WILD-TYPE                   104                             10
D1380V10, multiclass
                                clus
vv                               TCF7 MUTATED TCF7 WILD-TYPE
  COLON ADENOCARCINOMA                      7            308
  COLON MUCINOUS ADENOCARCINOMA             3             44
  RECTAL ADENOCARCINOMA                     2            104
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  TCF7 MUTATED     7   0   2   1
  TCF7 WILD-TYPE 338   4  29  24
D1380V11, multiclass
    clus
vv   TCF7 MUTATED TCF7 WILD-TYPE
  R0            7            338
  R1            0              4
  R2            2             29
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1380V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TCF7 MUTATED                                  0     1
  TCF7 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  TCF7 MUTATED                           2     3
  TCF7 WILD-TYPE                        20   223
D1380V13, multiclass
                                  clus
vv                                 TCF7 MUTATED TCF7 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   2             20
  WHITE                                       3            223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1381) Variable = NUFIP1 MUTATION ANALYSIS
D1381V1, survival
                  sevent
clus2                0   1
  NUFIP1 MUTATED     7   0
  NUFIP1 WILD-TYPE 371  93
  NUFIP1 MUTATED NUFIP1 WILD-TYPE 
               7              464 
  NUFIP1 MUTATED NUFIP1 WILD-TYPE 
               0               93 
$`NUFIP1 MUTATED`
TCGA-A6-6780 TCGA-AA-3510 TCGA-AA-3663 TCGA-AA-A010 TCGA-AZ-4315 TCGA-CA-6717 
       20.12        63.98         6.97        34.98        58.39        12.76 
TCGA-CK-5913 
       51.32 

$`NUFIP1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07        12.20        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 
       17.56       148.01        85.45        15.62        49.08         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  NUFIP1 MUTATED NUFIP1 WILD-TYPE 
            6.97             0.00 
  NUFIP1 MUTATED NUFIP1 WILD-TYPE 
           63.98           148.01 
  NUFIP1 MUTATED NUFIP1 WILD-TYPE 
           34.98            20.12 
[1] "7.0 - 64.0 (35.0)"  "0.0 - 148.0 (20.1)"
[1] "hr="     "9300000"
D1381V2, continuous
D1381V3, binary
                  cls
clus                 0   1
  NUFIP1 MUTATED     8   0
  NUFIP1 WILD-TYPE 358 119
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NUFIP1 MUTATED      8    0
  NUFIP1 WILD-TYPE  358  119
        clus
vv       NUFIP1 MUTATED NUFIP1 WILD-TYPE
  COLON               8              358
  RECTUM              0              119
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NUFIP1 MUTATED         0        0        3         4         1         0
  NUFIP1 WILD-TYPE      91        1       29       134         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NUFIP1 MUTATED           0          0          0          0        0
  NUFIP1 WILD-TYPE        24         11         59         42       48
                  vv
clus               STAGE IVA STAGE IVB
  NUFIP1 MUTATED           0         0
  NUFIP1 WILD-TYPE        18         1
D1381V4, multiclass
            clus
vv           NUFIP1 MUTATED NUFIP1 WILD-TYPE
  STAGE I                 0               91
  STAGE IA                0                1
  STAGE II                3               29
  STAGE IIA               4              134
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              0               59
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  NUFIP1 MUTATED     0   0   6   2
  NUFIP1 WILD-TYPE  17  92 323  48
D1381V5, multiclass
    clus
vv   NUFIP1 MUTATED NUFIP1 WILD-TYPE
  T1              0               17
  T2              0               92
  T3              6              323
  T4              2               48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  NUFIP1 MUTATED     8   0   0
  NUFIP1 WILD-TYPE 279 113  87
D1381V6, multiclass
    clus
vv   NUFIP1 MUTATED NUFIP1 WILD-TYPE
  N0              8              279
  N1              0              113
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1381V7, binary
                  cls
clus                 0   1
  NUFIP1 MUTATED     6   0
  NUFIP1 WILD-TYPE 369  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NUFIP1 MUTATED      6    0
  NUFIP1 WILD-TYPE  369   65
   clus
vv  NUFIP1 MUTATED NUFIP1 WILD-TYPE
  0              6              369
  1              0               65
[1] 2 2
[1] FALSE
D1381V8, binary
                  cls
clus                 0   1
  NUFIP1 MUTATED     3   5
  NUFIP1 WILD-TYPE 222 259
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NUFIP1 MUTATED      3    5
  NUFIP1 WILD-TYPE  222  259
        clus
vv       NUFIP1 MUTATED NUFIP1 WILD-TYPE
  FEMALE              3              222
  MALE                5              259
[1] 2 2
[1] FALSE
D1381V9, binary
                  cls
clus                 0   1
  NUFIP1 MUTATED     7   0
  NUFIP1 WILD-TYPE 343  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NUFIP1 MUTATED      7    0
  NUFIP1 WILD-TYPE  343   22
     clus
vv    NUFIP1 MUTATED NUFIP1 WILD-TYPE
  NO               7              343
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  NUFIP1 MUTATED                      6                             2
  NUFIP1 WILD-TYPE                  309                            45
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  NUFIP1 MUTATED                       0                              0
  NUFIP1 WILD-TYPE                   106                             10
D1381V10, multiclass
                                clus
vv                               NUFIP1 MUTATED NUFIP1 WILD-TYPE
  COLON ADENOCARCINOMA                        6              309
  COLON MUCINOUS ADENOCARCINOMA               2               45
  RECTAL ADENOCARCINOMA                       0              106
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  NUFIP1 MUTATED     5   0   0   2
  NUFIP1 WILD-TYPE 340   4  31  23
D1381V11, multiclass
    clus
vv   NUFIP1 MUTATED NUFIP1 WILD-TYPE
  R0              5              340
  R1              0                4
  R2              0               31
  RX              2               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1381V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NUFIP1 MUTATED                                  0     1
  NUFIP1 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  NUFIP1 MUTATED                           0     3
  NUFIP1 WILD-TYPE                        22   223
D1381V13, multiclass
                                  clus
vv                                 NUFIP1 MUTATED NUFIP1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         3              223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1382) Variable = OR7D4 MUTATION ANALYSIS
D1382V1, survival
                 sevent
clus2               0   1
  OR7D4 MUTATED     7   2
  OR7D4 WILD-TYPE 371  91
  OR7D4 MUTATED OR7D4 WILD-TYPE 
              9             462 
  OR7D4 MUTATED OR7D4 WILD-TYPE 
              2              91 
$`OR7D4 MUTATED`
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3845 TCGA-CA-6717 TCGA-CK-6747 TCGA-CM-5860 
       63.98         6.97         0.00        12.76        82.95        32.02 
TCGA-DM-A282 TCGA-F4-6460 TCGA-AG-A002 
      139.17        31.96        20.98 

$`OR7D4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
        1.02        35.01         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 
       15.95        38.99        37.02        14.93        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6748 TCGA-CK-6751 
       49.08        51.32         9.99        21.14         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.03        22.98        30.08        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
       44.32       131.51       135.65         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6569 
       35.97        60.79       117.07        98.24         8.61        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  OR7D4 MUTATED OR7D4 WILD-TYPE 
              0               0 
  OR7D4 MUTATED OR7D4 WILD-TYPE 
         139.17          148.01 
  OR7D4 MUTATED OR7D4 WILD-TYPE 
         31.960          20.085 
[1] "0.0 - 139.2 (32.0)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.3"
D1382V2, continuous
D1382V3, binary
                 cls
clus                0   1
  OR7D4 MUTATED     9   1
  OR7D4 WILD-TYPE 357 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR7D4 MUTATED      9    1
  OR7D4 WILD-TYPE  357  118
        clus
vv       OR7D4 MUTATED OR7D4 WILD-TYPE
  COLON              9             357
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  OR7D4 MUTATED         2        0        2         5         0         0
  OR7D4 WILD-TYPE      89        1       30       133        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  OR7D4 MUTATED           0          0          1          0        0         0
  OR7D4 WILD-TYPE        24         11         58         42       48        18
                 vv
clus              STAGE IVB
  OR7D4 MUTATED           0
  OR7D4 WILD-TYPE         1
D1382V4, multiclass
            clus
vv           OR7D4 MUTATED OR7D4 WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA              5             133
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  OR7D4 MUTATED     0   2   7   1
  OR7D4 WILD-TYPE  17  90 322  49
D1382V5, multiclass
    clus
vv   OR7D4 MUTATED OR7D4 WILD-TYPE
  T1             0              17
  T2             2              90
  T3             7             322
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  OR7D4 MUTATED     9   1   0
  OR7D4 WILD-TYPE 278 112  87
D1382V6, multiclass
    clus
vv   OR7D4 MUTATED OR7D4 WILD-TYPE
  N0             9             278
  N1             1             112
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1382V7, binary
                 cls
clus                0   1
  OR7D4 MUTATED     8   0
  OR7D4 WILD-TYPE 367  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR7D4 MUTATED      8    0
  OR7D4 WILD-TYPE  367   65
   clus
vv  OR7D4 MUTATED OR7D4 WILD-TYPE
  0             8             367
  1             0              65
[1] 2 2
[1] FALSE
D1382V8, binary
                 cls
clus                0   1
  OR7D4 MUTATED     4   6
  OR7D4 WILD-TYPE 221 258
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR7D4 MUTATED      4    6
  OR7D4 WILD-TYPE  221  258
        clus
vv       OR7D4 MUTATED OR7D4 WILD-TYPE
  FEMALE             4             221
  MALE               6             258
[1] 2 2
[1] FALSE
D1382V9, binary
                 cls
clus                0   1
  OR7D4 MUTATED     7   0
  OR7D4 WILD-TYPE 343  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR7D4 MUTATED      7    0
  OR7D4 WILD-TYPE  343   22
     clus
vv    OR7D4 MUTATED OR7D4 WILD-TYPE
  NO              7             343
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  OR7D4 MUTATED                      8                             1
  OR7D4 WILD-TYPE                  307                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  OR7D4 MUTATED                       1                              0
  OR7D4 WILD-TYPE                   105                             10
D1382V10, multiclass
                                clus
vv                               OR7D4 MUTATED OR7D4 WILD-TYPE
  COLON ADENOCARCINOMA                       8             307
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  OR7D4 MUTATED     6   0   0   3
  OR7D4 WILD-TYPE 339   4  31  22
D1382V11, multiclass
    clus
vv   OR7D4 MUTATED OR7D4 WILD-TYPE
  R0             6             339
  R1             0               4
  R2             0              31
  RX             3              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1382V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OR7D4 MUTATED                                  0     1
  OR7D4 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  OR7D4 MUTATED                           0     5
  OR7D4 WILD-TYPE                        22   221
D1382V13, multiclass
                                  clus
vv                                 OR7D4 MUTATED OR7D4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        5             221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1383) Variable = NUPL2 MUTATION ANALYSIS
D1383V1, survival
                 sevent
clus2               0   1
  NUPL2 MUTATED     7   4
  NUPL2 WILD-TYPE 371  89
  NUPL2 MUTATED NUPL2 WILD-TYPE 
             11             460 
  NUPL2 MUTATED NUPL2 WILD-TYPE 
              4              89 
$`NUPL2 MUTATED`
TCGA-AA-3510 TCGA-AA-3815 TCGA-AA-A00E TCGA-AA-A00K TCGA-AA-A010 TCGA-AD-6895 
       63.98        33.04        30.02        18.05        34.98         0.72 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-CK-5916 TCGA-CM-4743 TCGA-DM-A0XF 
       12.10        29.56        21.14        23.05        38.20 

$`NUPL2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       10.06        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       19.00        34.03        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 
        0.07        21.37        15.52        56.55         0.79         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       49.41         6.77       100.01         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 
       85.45        15.62        49.08        51.32         9.99        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
        1.91       124.27        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  NUPL2 MUTATED NUPL2 WILD-TYPE 
           0.72            0.00 
  NUPL2 MUTATED NUPL2 WILD-TYPE 
          63.98          148.01 
  NUPL2 MUTATED NUPL2 WILD-TYPE 
         29.560          20.035 
[1] "0.7 - 64.0 (29.6)"  "0.0 - 148.0 (20.0)"
[1] "hr=" "1.8"
D1383V2, continuous
D1383V3, binary
                 cls
clus                0   1
  NUPL2 MUTATED    11   0
  NUPL2 WILD-TYPE 355 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NUPL2 MUTATED     11    0
  NUPL2 WILD-TYPE  355  119
        clus
vv       NUPL2 MUTATED NUPL2 WILD-TYPE
  COLON             11             355
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NUPL2 MUTATED         1        0        1         4         1         0
  NUPL2 WILD-TYPE      90        1       31       134         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NUPL2 MUTATED           0          0          0          1        1         0
  NUPL2 WILD-TYPE        24         11         59         41       47        18
                 vv
clus              STAGE IVB
  NUPL2 MUTATED           0
  NUPL2 WILD-TYPE         1
D1383V4, multiclass
            clus
vv           NUPL2 MUTATED NUPL2 WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              4             134
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             1              41
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  NUPL2 MUTATED     1   1   7   2
  NUPL2 WILD-TYPE  16  91 322  48
D1383V5, multiclass
    clus
vv   NUPL2 MUTATED NUPL2 WILD-TYPE
  T1             1              16
  T2             1              91
  T3             7             322
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  NUPL2 MUTATED     7   3   1
  NUPL2 WILD-TYPE 280 110  86
D1383V6, multiclass
    clus
vv   NUPL2 MUTATED NUPL2 WILD-TYPE
  N0             7             280
  N1             3             110
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1383V7, binary
                 cls
clus                0   1
  NUPL2 MUTATED     8   1
  NUPL2 WILD-TYPE 367  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NUPL2 MUTATED      8    1
  NUPL2 WILD-TYPE  367   64
   clus
vv  NUPL2 MUTATED NUPL2 WILD-TYPE
  0             8             367
  1             1              64
[1] 2 2
[1] FALSE
D1383V8, binary
                 cls
clus                0   1
  NUPL2 MUTATED     5   6
  NUPL2 WILD-TYPE 220 258
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NUPL2 MUTATED      5    6
  NUPL2 WILD-TYPE  220  258
        clus
vv       NUPL2 MUTATED NUPL2 WILD-TYPE
  FEMALE             5             220
  MALE               6             258
[1] 2 2
[1] FALSE
D1383V9, binary
                 cls
clus                0   1
  NUPL2 MUTATED     7   0
  NUPL2 WILD-TYPE 343  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NUPL2 MUTATED      7    0
  NUPL2 WILD-TYPE  343   22
     clus
vv    NUPL2 MUTATED NUPL2 WILD-TYPE
  NO              7             343
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  NUPL2 MUTATED                     10                             0
  NUPL2 WILD-TYPE                  305                            47
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  NUPL2 MUTATED                       0                              0
  NUPL2 WILD-TYPE                   106                             10
D1383V10, multiclass
                                clus
vv                               NUPL2 MUTATED NUPL2 WILD-TYPE
  COLON ADENOCARCINOMA                      10             305
  COLON MUCINOUS ADENOCARCINOMA              0              47
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  NUPL2 MUTATED     6   0   0   1
  NUPL2 WILD-TYPE 339   4  31  24
D1383V11, multiclass
    clus
vv   NUPL2 MUTATED NUPL2 WILD-TYPE
  R0             6             339
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1383V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NUPL2 MUTATED                                  0     0
  NUPL2 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  NUPL2 MUTATED                           1     5
  NUPL2 WILD-TYPE                        21   221
D1383V13, multiclass
                                  clus
vv                                 NUPL2 MUTATED NUPL2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        5             221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1384) Variable = GNA14 MUTATION ANALYSIS
D1384V1, survival
                 sevent
clus2               0   1
  GNA14 MUTATED    11   2
  GNA14 WILD-TYPE 367  91
  GNA14 MUTATED GNA14 WILD-TYPE 
             13             458 
  GNA14 MUTATED GNA14 WILD-TYPE 
              2              91 
$`GNA14 MUTATED`
TCGA-AA-3510 TCGA-AA-3516 TCGA-AA-3543 TCGA-AA-3821 TCGA-AA-3877 TCGA-AA-3966 
       63.98        13.02         0.99         1.02        31.00         2.01 
TCGA-AY-6197 TCGA-D5-5538 TCGA-DM-A1HB TCGA-DM-A28G TCGA-AF-2687 TCGA-AG-A002 
       21.44        12.26       135.65        60.79        24.13        20.98 
TCGA-DC-6157 
       27.95 

$`GNA14 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 
        1.02        35.01         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
       12.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
       33.04         0.99        25.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       29.98        18.05         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 
       26.01        24.00         2.01        20.98        34.03        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       16.31         0.95        33.01        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       10.06        12.03        45.40        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28H 
      139.17         6.12        81.37       119.93        35.97       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       46.75        79.69        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  GNA14 MUTATED GNA14 WILD-TYPE 
           0.99            0.00 
  GNA14 MUTATED GNA14 WILD-TYPE 
         135.65          148.01 
  GNA14 MUTATED GNA14 WILD-TYPE 
         21.440          20.085 
[1] "1.0 - 135.7 (21.4)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.5"
D1384V2, continuous
D1384V3, binary
                 cls
clus                0   1
  GNA14 MUTATED    10   3
  GNA14 WILD-TYPE 356 116
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GNA14 MUTATED     10    3
  GNA14 WILD-TYPE  356  116
        clus
vv       GNA14 MUTATED GNA14 WILD-TYPE
  COLON             10             356
  RECTUM             3             116
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GNA14 MUTATED         5        0        1         3         0         0
  GNA14 WILD-TYPE      86        1       31       135        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  GNA14 MUTATED           1          0          2          1        0         0
  GNA14 WILD-TYPE        23         11         57         41       48        18
                 vv
clus              STAGE IVB
  GNA14 MUTATED           0
  GNA14 WILD-TYPE         1
D1384V4, multiclass
            clus
vv           GNA14 MUTATED GNA14 WILD-TYPE
  STAGE I                5              86
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              3             135
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             2              57
  STAGE IIIC             1              41
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  GNA14 MUTATED     1   4   8   0
  GNA14 WILD-TYPE  16  88 321  50
D1384V5, multiclass
    clus
vv   GNA14 MUTATED GNA14 WILD-TYPE
  T1             1              16
  T2             4              88
  T3             8             321
  T4             0              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  GNA14 MUTATED     9   2   2
  GNA14 WILD-TYPE 278 111  85
D1384V6, multiclass
    clus
vv   GNA14 MUTATED GNA14 WILD-TYPE
  N0             9             278
  N1             2             111
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1384V7, binary
                 cls
clus                0   1
  GNA14 MUTATED    12   0
  GNA14 WILD-TYPE 363  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GNA14 MUTATED     12    0
  GNA14 WILD-TYPE  363   65
   clus
vv  GNA14 MUTATED GNA14 WILD-TYPE
  0            12             363
  1             0              65
[1] 2 2
[1] FALSE
D1384V8, binary
                 cls
clus                0   1
  GNA14 MUTATED     5   8
  GNA14 WILD-TYPE 220 256
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GNA14 MUTATED      5    8
  GNA14 WILD-TYPE  220  256
        clus
vv       GNA14 MUTATED GNA14 WILD-TYPE
  FEMALE             5             220
  MALE               8             256
[1] 2 2
[1] FALSE
D1384V9, binary
                 cls
clus                0   1
  GNA14 MUTATED     8   1
  GNA14 WILD-TYPE 342  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GNA14 MUTATED      8    1
  GNA14 WILD-TYPE  342   21
     clus
vv    GNA14 MUTATED GNA14 WILD-TYPE
  NO              8             342
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  GNA14 MUTATED                      4                             5
  GNA14 WILD-TYPE                  311                            42
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  GNA14 MUTATED                       3                              0
  GNA14 WILD-TYPE                   103                             10
D1384V10, multiclass
                                clus
vv                               GNA14 MUTATED GNA14 WILD-TYPE
  COLON ADENOCARCINOMA                       4             311
  COLON MUCINOUS ADENOCARCINOMA              5              42
  RECTAL ADENOCARCINOMA                      3             103
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  GNA14 MUTATED     9   0   0   0
  GNA14 WILD-TYPE 336   4  31  25
D1384V11, multiclass
    clus
vv   GNA14 MUTATED GNA14 WILD-TYPE
  R0             9             336
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1384V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GNA14 MUTATED                                  0     0
  GNA14 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  GNA14 MUTATED                           1     5
  GNA14 WILD-TYPE                        21   221
D1384V13, multiclass
                                  clus
vv                                 GNA14 MUTATED GNA14 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        5             221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1385) Variable = PREX2 MUTATION ANALYSIS
D1385V1, survival
                 sevent
clus2               0   1
  PREX2 MUTATED    27   5
  PREX2 WILD-TYPE 351  88
  PREX2 MUTATED PREX2 WILD-TYPE 
             32             439 
  PREX2 MUTATED PREX2 WILD-TYPE 
              5              88 
$`PREX2 MUTATED`
TCGA-A6-2676 TCGA-A6-5659 TCGA-A6-6142 TCGA-A6-6653 TCGA-AA-3510 TCGA-AA-3544 
       42.90        30.44        25.08        24.39        63.98        14.01 
TCGA-AA-3660 TCGA-AA-3672 TCGA-AA-3815 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-A00N 
       78.08         0.92        33.04        24.00        33.01         4.01 
TCGA-AA-A01R TCGA-AD-6548 TCGA-AZ-4315 TCGA-CA-6716 TCGA-CA-6717 TCGA-CK-4950 
       35.01        21.37        58.39        12.20        12.76        85.45 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CM-6168 TCGA-CM-6170 TCGA-CM-6676 TCGA-D5-6537 
       51.32         9.99        12.99        15.02        11.08         4.80 
TCGA-D5-6538 TCGA-D5-6540 TCGA-DM-A285 TCGA-F4-6570 TCGA-G4-6323 TCGA-AG-3902 
       17.13        16.14         6.12         6.18        13.78        32.02 
TCGA-AH-6549 TCGA-DC-6683 
       17.49         5.03 

$`PREX2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       31.63        29.19        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6649 
       32.71        27.09        22.52         8.38        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       21.76        24.69        23.87        20.12        19.66        20.28 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 
        7.04         3.02         1.02        35.01         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
       13.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       36.03         8.05        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3548 
       29.00        29.00        26.01        12.99         0.99        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 
       20.98        19.99        13.94        19.99        61.02         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 
        6.97        54.02         2.01        14.01        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       35.05         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6888 
       41.00        39.98        18.05        40.96         0.07        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       33.01        21.44        17.82         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6718 
       12.69         3.06         3.25         3.29         0.07        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5916 
       14.30        17.56       148.01        15.62        49.08        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6169 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       14.99        13.02        14.04        11.01        12.95        13.05 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 
       43.27        15.12        17.85        12.49        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      135.65       139.17        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 
      117.07        98.24         8.61        31.96        35.74        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
        1.02        48.03        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DT-5265 TCGA-DY-A0XA 
       10.98        19.99         5.95         4.01         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  PREX2 MUTATED PREX2 WILD-TYPE 
           0.92            0.00 
  PREX2 MUTATED PREX2 WILD-TYPE 
          85.45          148.01 
  PREX2 MUTATED PREX2 WILD-TYPE 
          17.31           20.28 
[1] "0.9 - 85.5 (17.3)"  "0.0 - 148.0 (20.3)"
[1] "hr=" "1.3"
D1385V2, continuous
D1385V3, binary
                 cls
clus                0   1
  PREX2 MUTATED    31   4
  PREX2 WILD-TYPE 335 115
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PREX2 MUTATED     31    4
  PREX2 WILD-TYPE  335  115
        clus
vv       PREX2 MUTATED PREX2 WILD-TYPE
  COLON             31             335
  RECTUM             4             115
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PREX2 MUTATED         7        1        2         8         3         0
  PREX2 WILD-TYPE      84        0       30       130         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PREX2 MUTATED           3          0          5          0        3         2
  PREX2 WILD-TYPE        21         11         54         42       45        16
                 vv
clus              STAGE IVB
  PREX2 MUTATED           0
  PREX2 WILD-TYPE         1
D1385V4, multiclass
            clus
vv           PREX2 MUTATED PREX2 WILD-TYPE
  STAGE I                7              84
  STAGE IA               1               0
  STAGE II               2              30
  STAGE IIA              8             130
  STAGE IIB              3               7
  STAGE IIC              0               1
  STAGE III              3              21
  STAGE IIIA             0              11
  STAGE IIIB             5              54
  STAGE IIIC             0              42
  STAGE IV               3              45
  STAGE IVA              2              16
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PREX2 MUTATED     0   7  22   5
  PREX2 WILD-TYPE  17  85 307  45
D1385V5, multiclass
    clus
vv   PREX2 MUTATED PREX2 WILD-TYPE
  T1             0              17
  T2             7              85
  T3            22             307
  T4             5              45
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  PREX2 MUTATED    21   9   4
  PREX2 WILD-TYPE 266 104  83
D1385V6, multiclass
    clus
vv   PREX2 MUTATED PREX2 WILD-TYPE
  N0            21             266
  N1             9             104
  N2             4              83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1385V7, binary
                 cls
clus                0   1
  PREX2 MUTATED    24   5
  PREX2 WILD-TYPE 351  60
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PREX2 MUTATED     24    5
  PREX2 WILD-TYPE  351   60
   clus
vv  PREX2 MUTATED PREX2 WILD-TYPE
  0            24             351
  1             5              60
[1] 2 2
[1] FALSE
D1385V8, binary
                 cls
clus                0   1
  PREX2 MUTATED    17  18
  PREX2 WILD-TYPE 208 246
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PREX2 MUTATED     17   18
  PREX2 WILD-TYPE  208  246
        clus
vv       PREX2 MUTATED PREX2 WILD-TYPE
  FEMALE            17             208
  MALE              18             246
[1] 2 2
[1] FALSE
D1385V9, binary
                 cls
clus                0   1
  PREX2 MUTATED    27   1
  PREX2 WILD-TYPE 323  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PREX2 MUTATED     27    1
  PREX2 WILD-TYPE  323   21
     clus
vv    PREX2 MUTATED PREX2 WILD-TYPE
  NO             27             323
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PREX2 MUTATED                     25                             6
  PREX2 WILD-TYPE                  290                            41
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PREX2 MUTATED                       4                              0
  PREX2 WILD-TYPE                   102                             10
D1385V10, multiclass
                                clus
vv                               PREX2 MUTATED PREX2 WILD-TYPE
  COLON ADENOCARCINOMA                      25             290
  COLON MUCINOUS ADENOCARCINOMA              6              41
  RECTAL ADENOCARCINOMA                      4             102
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  PREX2 MUTATED    23   1   2   5
  PREX2 WILD-TYPE 322   3  29  20
D1385V11, multiclass
    clus
vv   PREX2 MUTATED PREX2 WILD-TYPE
  R0            23             322
  R1             1               3
  R2             2              29
  RX             5              20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1385V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PREX2 MUTATED                                  0     2
  PREX2 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PREX2 MUTATED                           3    18
  PREX2 WILD-TYPE                        19   208
D1385V13, multiclass
                                  clus
vv                                 PREX2 MUTATED PREX2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               9
  BLACK OR AFRICAN AMERICAN                    3              19
  WHITE                                       18             208
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1386) Variable = NEB MUTATION ANALYSIS
D1386V1, survival
               sevent
clus2             0   1
  NEB MUTATED    40  24
  NEB WILD-TYPE 338  69
  NEB MUTATED NEB WILD-TYPE 
           64           407 
  NEB MUTATED NEB WILD-TYPE 
           24            69 
$`NEB MUTATED`
TCGA-A6-3810 TCGA-A6-5661 TCGA-A6-6141 TCGA-A6-6653 TCGA-A6-6654 TCGA-AA-3496 
       36.53        33.53         8.38        24.39        23.87         1.02 
TCGA-AA-3510 TCGA-AA-3655 TCGA-AA-3672 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       63.98        61.02         0.92        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3845 TCGA-AA-3848 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 
       10.06         0.00        10.06        33.01        26.01         2.01 
TCGA-AA-3966 TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01R TCGA-AD-6964 
        2.01        25.02         4.01        34.98        35.01        10.88 
TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       21.44        58.39        62.79        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4948 
      100.01        11.74         3.19        12.76        10.06       148.01 
TCGA-CK-5912 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-6162 
       49.08        82.95       124.27        22.98        32.02        12.00 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6537 TCGA-D5-6538 TCGA-DM-A1D6 TCGA-DM-A1D7 
       20.19        18.25         4.80        17.13        49.91        13.32 
TCGA-DM-A1DA TCGA-DM-A28F TCGA-G4-6293 TCGA-G4-6309 TCGA-G4-6321 TCGA-G4-6588 
        7.50        35.97       133.18        85.48        22.09        26.17 
TCGA-G4-6628 TCGA-AF-6672 TCGA-AG-3892 TCGA-AG-A002 TCGA-AG-A01W TCGA-DC-6158 
       79.69        10.39        13.02        20.98        70.03        10.98 
TCGA-DT-5265 TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EI-6507 
        5.29        24.13        51.48        19.96 

$`NEB WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        32.75        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       31.63        30.44        29.19        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       32.71        27.09        22.52        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 
       21.76        24.69        20.12        19.66        20.28         7.04 
TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        3.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       19.99        13.94        19.99        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
       54.02         2.01        14.01        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       85.05        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 
       17.98        15.95        38.99        37.02        14.93        17.03 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3950 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 
       24.00        24.00        20.98        34.03        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
       38.07         1.02         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
       16.31         0.95        33.01        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6608 
      106.75        22.36        88.21        29.56         5.23         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 
       14.30        17.56        85.45        15.62        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6748 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
       21.14         1.91        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-5862 
       13.02        29.06        22.03        30.08        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 
       15.02        15.02        17.03        15.02         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       56.09        55.92         1.32        43.27        15.12        17.85 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB 
       38.20       130.65        92.75        12.59       140.38        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6299 
       33.67        13.25         0.53        47.41        35.31        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 
       65.85        53.62        44.68        55.04        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 
       36.00        13.78        35.80        91.79        46.75        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AG-3574 TCGA-AG-3575 
       14.50        16.83        15.39        20.02        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
        9.07        12.00        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       13.97        27.95        19.99         5.95         4.01         5.03 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
      126.44        41.36        57.24        32.61         0.49        20.55 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  NEB MUTATED NEB WILD-TYPE 
            0             0 
  NEB MUTATED NEB WILD-TYPE 
       148.01        140.38 
  NEB MUTATED NEB WILD-TYPE 
       21.765        20.020 
[1] "0.0 - 148.0 (21.8)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1.8"
D1386V2, continuous
D1386V3, binary
               cls
clus              0   1
  NEB MUTATED    57   9
  NEB WILD-TYPE 309 110
[1] "tbl2"
               cls
clus            [,1] [,2]
  NEB MUTATED     57    9
  NEB WILD-TYPE  309  110
        clus
vv       NEB MUTATED NEB WILD-TYPE
  COLON           57           309
  RECTUM           9           110
[1] 2 2
[1] FALSE
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NEB MUTATED         8        0        9        19         3         0
  NEB WILD-TYPE      83        1       23       119         7         1
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NEB MUTATED           7          0          8          4        5         1
  NEB WILD-TYPE        17         11         51         38       43        17
               vv
clus            STAGE IVB
  NEB MUTATED           0
  NEB WILD-TYPE         1
D1386V4, multiclass
            clus
vv           NEB MUTATED NEB WILD-TYPE
  STAGE I              8            83
  STAGE IA             0             1
  STAGE II             9            23
  STAGE IIA           19           119
  STAGE IIB            3             7
  STAGE IIC            0             1
  STAGE III            7            17
  STAGE IIIA           0            11
  STAGE IIIB           8            51
  STAGE IIIC           4            38
  STAGE IV             5            43
  STAGE IVA            1            17
  STAGE IVB            0             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  NEB MUTATED     1   9  48   8
  NEB WILD-TYPE  16  83 281  42
D1386V5, multiclass
    clus
vv   NEB MUTATED NEB WILD-TYPE
  T1           1            16
  T2           9            83
  T3          48           281
  T4           8            42
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2
  NEB MUTATED    41  13  12
  NEB WILD-TYPE 246 100  75
D1386V6, multiclass
    clus
vv   NEB MUTATED NEB WILD-TYPE
  N0          41           246
  N1          13           100
  N2          12            75
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1386V7, binary
               cls
clus              0   1
  NEB MUTATED    49   5
  NEB WILD-TYPE 326  60
[1] "tbl2"
               cls
clus            [,1] [,2]
  NEB MUTATED     49    5
  NEB WILD-TYPE  326   60
   clus
vv  NEB MUTATED NEB WILD-TYPE
  0          49           326
  1           5            60
[1] 2 2
[1] FALSE
D1386V8, binary
               cls
clus              0   1
  NEB MUTATED    27  39
  NEB WILD-TYPE 198 225
[1] "tbl2"
               cls
clus            [,1] [,2]
  NEB MUTATED     27   39
  NEB WILD-TYPE  198  225
        clus
vv       NEB MUTATED NEB WILD-TYPE
  FEMALE          27           198
  MALE            39           225
[1] 2 2
[1] FALSE
D1386V9, binary
               cls
clus              0   1
  NEB MUTATED    48   3
  NEB WILD-TYPE 302  19
[1] "tbl2"
               cls
clus            [,1] [,2]
  NEB MUTATED     48    3
  NEB WILD-TYPE  302   19
     clus
vv    NEB MUTATED NEB WILD-TYPE
  NO           48           302
  YES           3            19
[1] 2 2
[1] FALSE
               vv
clus            COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  NEB MUTATED                     47                             9
  NEB WILD-TYPE                  268                            38
               vv
clus            RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  NEB MUTATED                       8                              1
  NEB WILD-TYPE                    98                              9
D1386V10, multiclass
                                clus
vv                               NEB MUTATED NEB WILD-TYPE
  COLON ADENOCARCINOMA                    47           268
  COLON MUCINOUS ADENOCARCINOMA            9            38
  RECTAL ADENOCARCINOMA                    8            98
  RECTAL MUCINOUS ADENOCARCINOMA           1             9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             R0  R1  R2  RX
  NEB MUTATED    39   0   1   6
  NEB WILD-TYPE 306   4  30  19
D1386V11, multiclass
    clus
vv   NEB MUTATED NEB WILD-TYPE
  R0          39           306
  R1           0             4
  R2           1            30
  RX           6            19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1386V12, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NEB MUTATED                                  0     3
  NEB WILD-TYPE                                1     8
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  NEB MUTATED                           4    36
  NEB WILD-TYPE                        18   190
D1386V13, multiclass
                                  clus
vv                                 NEB MUTATED NEB WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      3             8
  BLACK OR AFRICAN AMERICAN                  4            18
  WHITE                                     36           190
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1387) Variable = DTX3L MUTATION ANALYSIS
D1387V1, survival
                 sevent
clus2               0   1
  DTX3L MUTATED     6   4
  DTX3L WILD-TYPE 372  89
  DTX3L MUTATED DTX3L WILD-TYPE 
             10             461 
  DTX3L MUTATED DTX3L WILD-TYPE 
              4              89 
$`DTX3L MUTATED`
TCGA-AA-3977 TCGA-AA-A010 TCGA-AD-6964 TCGA-AZ-6599 TCGA-CK-5912 TCGA-CM-4743 
       25.02        34.98        10.88         6.77        49.08        23.05 
TCGA-D5-6533 TCGA-DM-A1D4 TCGA-G4-6586 TCGA-EI-6507 
        1.32        92.75        35.80        19.96 

$`DTX3L WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        88.21        49.41        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 
       56.09        55.92        20.19        18.25        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D6 
       10.26       119.70        24.43        38.20       130.65        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 
       63.62        61.91        36.00        22.09        13.78        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  DTX3L MUTATED DTX3L WILD-TYPE 
           1.32            0.00 
  DTX3L MUTATED DTX3L WILD-TYPE 
          92.75          148.01 
  DTX3L MUTATED DTX3L WILD-TYPE 
         24.035          20.120 
[1] "1.3 - 92.8 (24.0)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.9"
D1387V2, continuous
D1387V3, binary
                 cls
clus                0   1
  DTX3L MUTATED    10   1
  DTX3L WILD-TYPE 356 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DTX3L MUTATED     10    1
  DTX3L WILD-TYPE  356  118
        clus
vv       DTX3L MUTATED DTX3L WILD-TYPE
  COLON             10             356
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DTX3L MUTATED         2        0        0         5         1         0
  DTX3L WILD-TYPE      89        1       32       133         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DTX3L MUTATED           0          0          1          0        0         0
  DTX3L WILD-TYPE        24         11         58         42       48        18
                 vv
clus              STAGE IVB
  DTX3L MUTATED           0
  DTX3L WILD-TYPE         1
D1387V4, multiclass
            clus
vv           DTX3L MUTATED DTX3L WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              5             133
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  DTX3L MUTATED     0   3   5   3
  DTX3L WILD-TYPE  17  89 324  47
D1387V5, multiclass
    clus
vv   DTX3L MUTATED DTX3L WILD-TYPE
  T1             0              17
  T2             3              89
  T3             5             324
  T4             3              47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  DTX3L MUTATED    10   0   1
  DTX3L WILD-TYPE 277 113  86
D1387V6, multiclass
    clus
vv   DTX3L MUTATED DTX3L WILD-TYPE
  N0            10             277
  N1             0             113
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1387V7, binary
                 cls
clus                0   1
  DTX3L MUTATED     7   0
  DTX3L WILD-TYPE 368  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DTX3L MUTATED      7    0
  DTX3L WILD-TYPE  368   65
   clus
vv  DTX3L MUTATED DTX3L WILD-TYPE
  0             7             368
  1             0              65
[1] 2 2
[1] FALSE
D1387V8, binary
                 cls
clus                0   1
  DTX3L MUTATED     4   7
  DTX3L WILD-TYPE 221 257
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DTX3L MUTATED      4    7
  DTX3L WILD-TYPE  221  257
        clus
vv       DTX3L MUTATED DTX3L WILD-TYPE
  FEMALE             4             221
  MALE               7             257
[1] 2 2
[1] FALSE
D1387V9, binary
                 cls
clus                0   1
  DTX3L MUTATED     8   0
  DTX3L WILD-TYPE 342  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DTX3L MUTATED      8    0
  DTX3L WILD-TYPE  342   22
     clus
vv    DTX3L MUTATED DTX3L WILD-TYPE
  NO              8             342
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  DTX3L MUTATED                     10                             0
  DTX3L WILD-TYPE                  305                            47
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  DTX3L MUTATED                       1                              0
  DTX3L WILD-TYPE                   105                             10
D1387V10, multiclass
                                clus
vv                               DTX3L MUTATED DTX3L WILD-TYPE
  COLON ADENOCARCINOMA                      10             305
  COLON MUCINOUS ADENOCARCINOMA              0              47
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  DTX3L MUTATED     6   0   0   1
  DTX3L WILD-TYPE 339   4  31  24
D1387V11, multiclass
    clus
vv   DTX3L MUTATED DTX3L WILD-TYPE
  R0             6             339
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1387V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DTX3L MUTATED                                  0     0
  DTX3L WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  DTX3L MUTATED                           0     8
  DTX3L WILD-TYPE                        22   218
D1387V13, multiclass
                                  clus
vv                                 DTX3L MUTATED DTX3L WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        8             218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1388) Variable = ARHGEF1 MUTATION ANALYSIS
D1388V1, survival
                   sevent
clus2                 0   1
  ARHGEF1 MUTATED    12   3
  ARHGEF1 WILD-TYPE 366  90
  ARHGEF1 MUTATED ARHGEF1 WILD-TYPE 
               15               456 
  ARHGEF1 MUTATED ARHGEF1 WILD-TYPE 
                3                90 
$`ARHGEF1 MUTATED`
TCGA-A6-5665 TCGA-A6-6141 TCGA-AA-3660 TCGA-AA-3811 TCGA-AA-3815 TCGA-AA-3977 
       22.06         8.38        78.08        10.06        33.04        25.02 
TCGA-AA-3986 TCGA-AD-6889 TCGA-AU-6004 TCGA-CK-5916 TCGA-F4-6570 TCGA-G4-6306 
       19.07        56.55        27.09        21.14         6.18        44.68 
TCGA-G4-6588 TCGA-AG-3742 TCGA-AG-A01L 
       26.17         0.99        12.00 

$`ARHGEF1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 
       22.09        32.71        27.09        22.52        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       13.94        19.99        61.02         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3818 
       85.05        26.99        19.04        19.04        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       24.00        27.02        27.02         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       15.52         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       10.88         0.20        14.50        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 
       15.62        49.08        51.32         9.99        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 
       98.24         8.61        31.96        35.74        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       13.78        35.80        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3878 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       15.95        36.03         9.07        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  ARHGEF1 MUTATED ARHGEF1 WILD-TYPE 
             0.99              0.00 
  ARHGEF1 MUTATED ARHGEF1 WILD-TYPE 
            78.08            148.01 
  ARHGEF1 MUTATED ARHGEF1 WILD-TYPE 
           22.060            20.085 
[1] "1.0 - 78.1 (22.1)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1"  
D1388V2, continuous
D1388V3, binary
                   cls
clus                  0   1
  ARHGEF1 MUTATED    13   2
  ARHGEF1 WILD-TYPE 353 117
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ARHGEF1 MUTATED     13    2
  ARHGEF1 WILD-TYPE  353  117
        clus
vv       ARHGEF1 MUTATED ARHGEF1 WILD-TYPE
  COLON               13               353
  RECTUM               2               117
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ARHGEF1 MUTATED         4        0        1         7         0         0
  ARHGEF1 WILD-TYPE      87        1       31       131        10         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ARHGEF1 MUTATED           1          0          1          0        0
  ARHGEF1 WILD-TYPE        23         11         58         42       48
                   vv
clus                STAGE IVA STAGE IVB
  ARHGEF1 MUTATED           0         0
  ARHGEF1 WILD-TYPE        18         1
D1388V4, multiclass
            clus
vv           ARHGEF1 MUTATED ARHGEF1 WILD-TYPE
  STAGE I                  4                87
  STAGE IA                 0                 1
  STAGE II                 1                31
  STAGE IIA                7               131
  STAGE IIB                0                10
  STAGE IIC                0                 1
  STAGE III                1                23
  STAGE IIIA               0                11
  STAGE IIIB               1                58
  STAGE IIIC               0                42
  STAGE IV                 0                48
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  ARHGEF1 MUTATED     2   4   9   0
  ARHGEF1 WILD-TYPE  15  88 320  50
D1388V5, multiclass
    clus
vv   ARHGEF1 MUTATED ARHGEF1 WILD-TYPE
  T1               2                15
  T2               4                88
  T3               9               320
  T4               0                50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  ARHGEF1 MUTATED    13   1   1
  ARHGEF1 WILD-TYPE 274 112  86
D1388V6, multiclass
    clus
vv   ARHGEF1 MUTATED ARHGEF1 WILD-TYPE
  N0              13               274
  N1               1               112
  N2               1                86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1388V7, binary
                   cls
clus                  0   1
  ARHGEF1 MUTATED    14   0
  ARHGEF1 WILD-TYPE 361  65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ARHGEF1 MUTATED     14    0
  ARHGEF1 WILD-TYPE  361   65
   clus
vv  ARHGEF1 MUTATED ARHGEF1 WILD-TYPE
  0              14               361
  1               0                65
[1] 2 2
[1] FALSE
D1388V8, binary
                   cls
clus                  0   1
  ARHGEF1 MUTATED     9   6
  ARHGEF1 WILD-TYPE 216 258
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ARHGEF1 MUTATED      9    6
  ARHGEF1 WILD-TYPE  216  258
        clus
vv       ARHGEF1 MUTATED ARHGEF1 WILD-TYPE
  FEMALE               9               216
  MALE                 6               258
[1] 2 2
[1] FALSE
D1388V9, binary
                   cls
clus                  0   1
  ARHGEF1 MUTATED    11   0
  ARHGEF1 WILD-TYPE 339  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ARHGEF1 MUTATED     11    0
  ARHGEF1 WILD-TYPE  339   22
     clus
vv    ARHGEF1 MUTATED ARHGEF1 WILD-TYPE
  NO               11               339
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ARHGEF1 MUTATED                     13                             0
  ARHGEF1 WILD-TYPE                  302                            47
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ARHGEF1 MUTATED                       2                              0
  ARHGEF1 WILD-TYPE                   104                             10
D1388V10, multiclass
                                clus
vv                               ARHGEF1 MUTATED ARHGEF1 WILD-TYPE
  COLON ADENOCARCINOMA                        13               302
  COLON MUCINOUS ADENOCARCINOMA                0                47
  RECTAL ADENOCARCINOMA                        2               104
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  ARHGEF1 MUTATED    11   0   0   1
  ARHGEF1 WILD-TYPE 334   4  31  24
D1388V11, multiclass
    clus
vv   ARHGEF1 MUTATED ARHGEF1 WILD-TYPE
  R0              11               334
  R1               0                 4
  R2               0                31
  RX               1                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1388V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ARHGEF1 MUTATED                                  0     1
  ARHGEF1 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  ARHGEF1 MUTATED                           1     6
  ARHGEF1 WILD-TYPE                        21   220
D1388V13, multiclass
                                  clus
vv                                 ARHGEF1 MUTATED ARHGEF1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                10
  BLACK OR AFRICAN AMERICAN                      1                21
  WHITE                                          6               220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1389) Variable = VPS33A MUTATION ANALYSIS
D1389V1, survival
                  sevent
clus2                0   1
  VPS33A MUTATED     6   1
  VPS33A WILD-TYPE 372  92
  VPS33A MUTATED VPS33A WILD-TYPE 
               7              464 
  VPS33A MUTATED VPS33A WILD-TYPE 
               1               92 
$`VPS33A MUTATED`
TCGA-AA-3525 TCGA-AA-3833 TCGA-AA-3845 TCGA-AA-3950 TCGA-AD-5900 TCGA-AD-6895 
        8.05        15.95         0.00        24.00         0.07         0.72 
TCGA-G4-6588 
       26.17 

$`VPS33A WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 
       17.98        38.99        37.02        14.93        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        33.01        26.01         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 
       40.96        21.37        15.52        56.55         0.79         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       13.78        35.80        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  VPS33A MUTATED VPS33A WILD-TYPE 
               0                0 
  VPS33A MUTATED VPS33A WILD-TYPE 
           26.17           148.01 
  VPS33A MUTATED VPS33A WILD-TYPE 
           8.050           20.415 
[1] "0.0 - 26.2 (8.1)"   "0.0 - 148.0 (20.4)"
[1] "hr=" "1.7"
D1389V2, continuous
D1389V3, binary
                  cls
clus                 0   1
  VPS33A MUTATED     8   0
  VPS33A WILD-TYPE 358 119
[1] "tbl2"
                  cls
clus               [,1] [,2]
  VPS33A MUTATED      8    0
  VPS33A WILD-TYPE  358  119
        clus
vv       VPS33A MUTATED VPS33A WILD-TYPE
  COLON               8              358
  RECTUM              0              119
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  VPS33A MUTATED         1        0        0         4         1         0
  VPS33A WILD-TYPE      90        1       32       134         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  VPS33A MUTATED           0          0          1          0        0
  VPS33A WILD-TYPE        24         11         58         42       48
                  vv
clus               STAGE IVA STAGE IVB
  VPS33A MUTATED           0         0
  VPS33A WILD-TYPE        18         1
D1389V4, multiclass
            clus
vv           VPS33A MUTATED VPS33A WILD-TYPE
  STAGE I                 1               90
  STAGE IA                0                1
  STAGE II                0               32
  STAGE IIA               4              134
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              1               58
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  VPS33A MUTATED     0   1   6   1
  VPS33A WILD-TYPE  17  91 323  49
D1389V5, multiclass
    clus
vv   VPS33A MUTATED VPS33A WILD-TYPE
  T1              0               17
  T2              1               91
  T3              6              323
  T4              1               49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  VPS33A MUTATED     6   2   0
  VPS33A WILD-TYPE 281 111  87
D1389V6, multiclass
    clus
vv   VPS33A MUTATED VPS33A WILD-TYPE
  N0              6              281
  N1              2              111
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1389V7, binary
                  cls
clus                 0   1
  VPS33A MUTATED     5   0
  VPS33A WILD-TYPE 370  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  VPS33A MUTATED      5    0
  VPS33A WILD-TYPE  370   65
   clus
vv  VPS33A MUTATED VPS33A WILD-TYPE
  0              5              370
  1              0               65
[1] 2 2
[1] FALSE
D1389V8, binary
                  cls
clus                 0   1
  VPS33A MUTATED     5   3
  VPS33A WILD-TYPE 220 261
[1] "tbl2"
                  cls
clus               [,1] [,2]
  VPS33A MUTATED      5    3
  VPS33A WILD-TYPE  220  261
        clus
vv       VPS33A MUTATED VPS33A WILD-TYPE
  FEMALE              5              220
  MALE                3              261
[1] 2 2
[1] FALSE
D1389V9, binary
                  cls
clus                 0   1
  VPS33A MUTATED     4   0
  VPS33A WILD-TYPE 346  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  VPS33A MUTATED      4    0
  VPS33A WILD-TYPE  346   22
     clus
vv    VPS33A MUTATED VPS33A WILD-TYPE
  NO               4              346
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  VPS33A MUTATED                      6                             2
  VPS33A WILD-TYPE                  309                            45
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  VPS33A MUTATED                       0                              0
  VPS33A WILD-TYPE                   106                             10
D1389V10, multiclass
                                clus
vv                               VPS33A MUTATED VPS33A WILD-TYPE
  COLON ADENOCARCINOMA                        6              309
  COLON MUCINOUS ADENOCARCINOMA               2               45
  RECTAL ADENOCARCINOMA                       0              106
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  VPS33A MUTATED     6   0   0   1
  VPS33A WILD-TYPE 339   4  31  24
D1389V11, multiclass
    clus
vv   VPS33A MUTATED VPS33A WILD-TYPE
  R0              6              339
  R1              0                4
  R2              0               31
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1389V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  VPS33A MUTATED                                  0     0
  VPS33A WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  VPS33A MUTATED                           0     4
  VPS33A WILD-TYPE                        22   222
D1389V13, multiclass
                                  clus
vv                                 VPS33A MUTATED VPS33A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         4              222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1390) Variable = FSTL4 MUTATION ANALYSIS
D1390V1, survival
                 sevent
clus2               0   1
  FSTL4 MUTATED    15   2
  FSTL4 WILD-TYPE 363  91
  FSTL4 MUTATED FSTL4 WILD-TYPE 
             17             454 
  FSTL4 MUTATED FSTL4 WILD-TYPE 
              2              91 
$`FSTL4 MUTATED`
TCGA-A6-5665 TCGA-AA-3510 TCGA-AA-3663 TCGA-AA-3672 TCGA-AA-3986 TCGA-AD-6964 
       22.06        63.98         6.97         0.92        19.07        10.88 
TCGA-AU-6004 TCGA-AY-6197 TCGA-CA-6718 TCGA-CM-5860 TCGA-CM-5861 TCGA-D5-6536 
       27.09        21.44        10.06        32.02        15.02        17.85 
TCGA-D5-6540 TCGA-D5-6541 TCGA-DM-A1HB TCGA-AG-3892 TCGA-G5-6235 
       16.14        15.58       135.65        13.02        55.76 

$`FSTL4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
        2.01        14.01        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       26.01        25.02        24.00        27.02        27.02         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 
        5.79        22.42        27.42         0.20        14.50        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        33.01        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.20        12.76        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5862 
       13.02        29.06        22.03        22.98        30.08         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6898 
       43.27        15.12         4.80        17.13        12.49         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 
       19.99         1.02        17.95        36.95        17.03        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6641 
       32.19         0.66         0.69        26.43 

  FSTL4 MUTATED FSTL4 WILD-TYPE 
           0.92            0.00 
  FSTL4 MUTATED FSTL4 WILD-TYPE 
         135.65          148.01 
  FSTL4 MUTATED FSTL4 WILD-TYPE 
         17.850          20.415 
[1] "0.9 - 135.7 (17.9)" "0.0 - 148.0 (20.4)"
[1] "hr=" "1.8"
D1390V2, continuous
D1390V3, binary
                 cls
clus                0   1
  FSTL4 MUTATED    15   2
  FSTL4 WILD-TYPE 351 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FSTL4 MUTATED     15    2
  FSTL4 WILD-TYPE  351  117
        clus
vv       FSTL4 MUTATED FSTL4 WILD-TYPE
  COLON             15             351
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FSTL4 MUTATED         4        0        2         7         0         0
  FSTL4 WILD-TYPE      87        1       30       131        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  FSTL4 MUTATED           1          0          2          0        0         0
  FSTL4 WILD-TYPE        23         11         57         42       48        18
                 vv
clus              STAGE IVB
  FSTL4 MUTATED           0
  FSTL4 WILD-TYPE         1
D1390V4, multiclass
            clus
vv           FSTL4 MUTATED FSTL4 WILD-TYPE
  STAGE I                4              87
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA              7             131
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             2              57
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  FSTL4 MUTATED     1   3  12   1
  FSTL4 WILD-TYPE  16  89 317  49
D1390V5, multiclass
    clus
vv   FSTL4 MUTATED FSTL4 WILD-TYPE
  T1             1              16
  T2             3              89
  T3            12             317
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  FSTL4 MUTATED    13   3   1
  FSTL4 WILD-TYPE 274 110  86
D1390V6, multiclass
    clus
vv   FSTL4 MUTATED FSTL4 WILD-TYPE
  N0            13             274
  N1             3             110
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1390V7, binary
                 cls
clus                0   1
  FSTL4 MUTATED    14   0
  FSTL4 WILD-TYPE 361  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FSTL4 MUTATED     14    0
  FSTL4 WILD-TYPE  361   65
   clus
vv  FSTL4 MUTATED FSTL4 WILD-TYPE
  0            14             361
  1             0              65
[1] 2 2
[1] FALSE
D1390V8, binary
                 cls
clus                0   1
  FSTL4 MUTATED     5  12
  FSTL4 WILD-TYPE 220 252
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FSTL4 MUTATED      5   12
  FSTL4 WILD-TYPE  220  252
        clus
vv       FSTL4 MUTATED FSTL4 WILD-TYPE
  FEMALE             5             220
  MALE              12             252
[1] 2 2
[1] FALSE
D1390V9, binary
                 cls
clus                0   1
  FSTL4 MUTATED    15   0
  FSTL4 WILD-TYPE 335  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FSTL4 MUTATED     15    0
  FSTL4 WILD-TYPE  335   22
     clus
vv    FSTL4 MUTATED FSTL4 WILD-TYPE
  NO             15             335
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  FSTL4 MUTATED                     13                             1
  FSTL4 WILD-TYPE                  302                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  FSTL4 MUTATED                       2                              0
  FSTL4 WILD-TYPE                   104                             10
D1390V10, multiclass
                                clus
vv                               FSTL4 MUTATED FSTL4 WILD-TYPE
  COLON ADENOCARCINOMA                      13             302
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  FSTL4 MUTATED    13   1   0   1
  FSTL4 WILD-TYPE 332   3  31  24
D1390V11, multiclass
    clus
vv   FSTL4 MUTATED FSTL4 WILD-TYPE
  R0            13             332
  R1             1               3
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1390V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FSTL4 MUTATED                                  0     1
  FSTL4 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  FSTL4 MUTATED                           0    11
  FSTL4 WILD-TYPE                        22   215
D1390V13, multiclass
                                  clus
vv                                 FSTL4 MUTATED FSTL4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                       11             215
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1391) Variable = PTPRG MUTATION ANALYSIS
D1391V1, survival
                 sevent
clus2               0   1
  PTPRG MUTATED    16   6
  PTPRG WILD-TYPE 362  87
  PTPRG MUTATED PTPRG WILD-TYPE 
             22             449 
  PTPRG MUTATED PTPRG WILD-TYPE 
              6              87 
$`PTPRG MUTATED`
TCGA-A6-6141 TCGA-AA-3510 TCGA-AA-3525 TCGA-AA-3663 TCGA-AA-3845 TCGA-AA-3864 
        8.38        63.98         8.05         6.97         0.00        53.00 
TCGA-AA-3869 TCGA-AA-3977 TCGA-AA-A00N TCGA-AD-6889 TCGA-AD-6963 TCGA-AZ-6599 
       27.02        25.02         4.01        56.55        27.42         6.77 
TCGA-AZ-6601 TCGA-CA-6716 TCGA-CM-5864 TCGA-D5-6540 TCGA-D5-6928 TCGA-DM-A1D6 
      100.01        12.20        15.02        16.14        11.64        49.91 
TCGA-G4-6323 TCGA-AG-A002 TCGA-AG-A00Y TCGA-EF-5830 
       13.78        20.98        23.01         0.49 

$`PTPRG WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 
       22.09        22.06        32.71        27.09        22.52        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3529 
        9.07        24.03        37.05        36.03        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02        78.08         6.05        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02        14.93        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       30.05        17.03        24.03        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 
       18.05        40.96         0.07        21.37        15.52         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        0.72         5.79        22.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       88.21        49.41        12.10        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5868 TCGA-CM-6161 
       32.02        15.02         5.03        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       17.13        12.49        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6930 
       12.43        14.30         9.04         9.44         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
      130.65        92.75        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A011 TCGA-AG-A014 
       17.03        13.94         6.02        25.97        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EI-6506 TCGA-EI-6507 
       57.24        24.13        51.48        32.61        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  PTPRG MUTATED PTPRG WILD-TYPE 
              0               0 
  PTPRG MUTATED PTPRG WILD-TYPE 
         100.01          148.01 
  PTPRG MUTATED PTPRG WILD-TYPE 
          15.58           20.28 
[1] "0.0 - 100.0 (15.6)" "0.0 - 148.0 (20.3)"
[1] "hr=" "1.4"
D1391V2, continuous
D1391V3, binary
                 cls
clus                0   1
  PTPRG MUTATED    22   3
  PTPRG WILD-TYPE 344 116
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPRG MUTATED     22    3
  PTPRG WILD-TYPE  344  116
        clus
vv       PTPRG MUTATED PTPRG WILD-TYPE
  COLON             22             344
  RECTUM             3             116
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PTPRG MUTATED         4        1        5         8         2         0
  PTPRG WILD-TYPE      87        0       27       130         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PTPRG MUTATED           0          0          1          1        1         0
  PTPRG WILD-TYPE        24         11         58         41       47        18
                 vv
clus              STAGE IVB
  PTPRG MUTATED           0
  PTPRG WILD-TYPE         1
D1391V4, multiclass
            clus
vv           PTPRG MUTATED PTPRG WILD-TYPE
  STAGE I                4              87
  STAGE IA               1               0
  STAGE II               5              27
  STAGE IIA              8             130
  STAGE IIB              2               8
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             1              41
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PTPRG MUTATED     0   5  15   4
  PTPRG WILD-TYPE  17  87 314  46
D1391V5, multiclass
    clus
vv   PTPRG MUTATED PTPRG WILD-TYPE
  T1             0              17
  T2             5              87
  T3            15             314
  T4             4              46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  PTPRG MUTATED    22   1   2
  PTPRG WILD-TYPE 265 112  85
D1391V6, multiclass
    clus
vv   PTPRG MUTATED PTPRG WILD-TYPE
  N0            22             265
  N1             1             112
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1391V7, binary
                 cls
clus                0   1
  PTPRG MUTATED    19   1
  PTPRG WILD-TYPE 356  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPRG MUTATED     19    1
  PTPRG WILD-TYPE  356   64
   clus
vv  PTPRG MUTATED PTPRG WILD-TYPE
  0            19             356
  1             1              64
[1] 2 2
[1] FALSE
D1391V8, binary
                 cls
clus                0   1
  PTPRG MUTATED     3  22
  PTPRG WILD-TYPE 222 242
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPRG MUTATED      3   22
  PTPRG WILD-TYPE  222  242
        clus
vv       PTPRG MUTATED PTPRG WILD-TYPE
  FEMALE             3             222
  MALE              22             242
[1] 2 2
[1] FALSE
D1391V9, binary
                 cls
clus                0   1
  PTPRG MUTATED    17   0
  PTPRG WILD-TYPE 333  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPRG MUTATED     17    0
  PTPRG WILD-TYPE  333   22
     clus
vv    PTPRG MUTATED PTPRG WILD-TYPE
  NO             17             333
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PTPRG MUTATED                     17                             5
  PTPRG WILD-TYPE                  298                            42
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PTPRG MUTATED                       3                              0
  PTPRG WILD-TYPE                   103                             10
D1391V10, multiclass
                                clus
vv                               PTPRG MUTATED PTPRG WILD-TYPE
  COLON ADENOCARCINOMA                      17             298
  COLON MUCINOUS ADENOCARCINOMA              5              42
  RECTAL ADENOCARCINOMA                      3             103
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  PTPRG MUTATED    16   0   1   1
  PTPRG WILD-TYPE 329   4  30  24
D1391V11, multiclass
    clus
vv   PTPRG MUTATED PTPRG WILD-TYPE
  R0            16             329
  R1             0               4
  R2             1              30
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1391V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PTPRG MUTATED                                  0     2
  PTPRG WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PTPRG MUTATED                           2     9
  PTPRG WILD-TYPE                        20   217
D1391V13, multiclass
                                  clus
vv                                 PTPRG MUTATED PTPRG WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               9
  BLACK OR AFRICAN AMERICAN                    2              20
  WHITE                                        9             217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1392) Variable = ATF2 MUTATION ANALYSIS
D1392V1, survival
                sevent
clus2              0   1
  ATF2 MUTATED     4   3
  ATF2 WILD-TYPE 374  90
  ATF2 MUTATED ATF2 WILD-TYPE 
             7            464 
  ATF2 MUTATED ATF2 WILD-TYPE 
             3             90 
$`ATF2 MUTATED`
TCGA-AA-3496 TCGA-AA-A02K TCGA-CA-6716 TCGA-CA-6718 TCGA-D5-5539 TCGA-DM-A1DB 
        1.02        14.01        12.20        10.06        19.59        44.32 
TCGA-AG-A002 
       20.98 

$`ATF2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02W 
       51.98        39.98         2.01         5.03         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       12.76        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       12.26        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
        7.50       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  ATF2 MUTATED ATF2 WILD-TYPE 
          1.02           0.00 
  ATF2 MUTATED ATF2 WILD-TYPE 
         44.32         148.01 
  ATF2 MUTATED ATF2 WILD-TYPE 
        14.010         20.415 
[1] "1.0 - 44.3 (14.0)"  "0.0 - 148.0 (20.4)"
[1] "hr=" "3.1"
D1392V2, continuous
D1392V3, binary
                cls
clus               0   1
  ATF2 MUTATED     6   1
  ATF2 WILD-TYPE 360 118
[1] "tbl2"
                cls
clus             [,1] [,2]
  ATF2 MUTATED      6    1
  ATF2 WILD-TYPE  360  118
        clus
vv       ATF2 MUTATED ATF2 WILD-TYPE
  COLON             6            360
  RECTUM            1            118
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ATF2 MUTATED         1        0        1         3         0         0
  ATF2 WILD-TYPE      90        1       31       135        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ATF2 MUTATED           0          1          0          0        1         0
  ATF2 WILD-TYPE        24         10         59         42       47        18
                vv
clus             STAGE IVB
  ATF2 MUTATED           0
  ATF2 WILD-TYPE         1
D1392V4, multiclass
            clus
vv           ATF2 MUTATED ATF2 WILD-TYPE
  STAGE I               1             90
  STAGE IA              0              1
  STAGE II              1             31
  STAGE IIA             3            135
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            1             10
  STAGE IIIB            0             59
  STAGE IIIC            0             42
  STAGE IV              1             47
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  ATF2 MUTATED     0   1   5   1
  ATF2 WILD-TYPE  17  91 324  49
D1392V5, multiclass
    clus
vv   ATF2 MUTATED ATF2 WILD-TYPE
  T1            0             17
  T2            1             91
  T3            5            324
  T4            1             49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  ATF2 MUTATED     5   1   1
  ATF2 WILD-TYPE 282 112  86
D1392V6, multiclass
    clus
vv   ATF2 MUTATED ATF2 WILD-TYPE
  N0            5            282
  N1            1            112
  N2            1             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1392V7, binary
                cls
clus               0   1
  ATF2 MUTATED     6   1
  ATF2 WILD-TYPE 369  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  ATF2 MUTATED      6    1
  ATF2 WILD-TYPE  369   64
   clus
vv  ATF2 MUTATED ATF2 WILD-TYPE
  0            6            369
  1            1             64
[1] 2 2
[1] FALSE
D1392V8, binary
                cls
clus               0   1
  ATF2 MUTATED     1   6
  ATF2 WILD-TYPE 224 258
[1] "tbl2"
                cls
clus             [,1] [,2]
  ATF2 MUTATED      1    6
  ATF2 WILD-TYPE  224  258
        clus
vv       ATF2 MUTATED ATF2 WILD-TYPE
  FEMALE            1            224
  MALE              6            258
[1] 2 2
[1] FALSE
D1392V9, binary
                cls
clus               0   1
  ATF2 MUTATED     5   0
  ATF2 WILD-TYPE 345  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  ATF2 MUTATED      5    0
  ATF2 WILD-TYPE  345   22
     clus
vv    ATF2 MUTATED ATF2 WILD-TYPE
  NO             5            345
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ATF2 MUTATED                      5                             1
  ATF2 WILD-TYPE                  310                            46
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ATF2 MUTATED                       1                              0
  ATF2 WILD-TYPE                   105                             10
D1392V10, multiclass
                                clus
vv                               ATF2 MUTATED ATF2 WILD-TYPE
  COLON ADENOCARCINOMA                      5            310
  COLON MUCINOUS ADENOCARCINOMA             1             46
  RECTAL ADENOCARCINOMA                     1            105
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  ATF2 MUTATED     3   0   1   2
  ATF2 WILD-TYPE 342   4  30  23
D1392V11, multiclass
    clus
vv   ATF2 MUTATED ATF2 WILD-TYPE
  R0            3            342
  R1            0              4
  R2            1             30
  RX            2             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1392V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ATF2 MUTATED                                  0     2
  ATF2 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  ATF2 MUTATED                           0     2
  ATF2 WILD-TYPE                        22   224
D1392V13, multiclass
                                  clus
vv                                 ATF2 MUTATED ATF2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              9
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       2            224
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1393) Variable = CREG2 MUTATION ANALYSIS
D1393V1, survival
                 sevent
clus2               0   1
  CREG2 MUTATED     3   2
  CREG2 WILD-TYPE 375  91
  CREG2 MUTATED CREG2 WILD-TYPE 
              5             466 
  CREG2 MUTATED CREG2 WILD-TYPE 
              2              91 
$`CREG2 MUTATED`
TCGA-AA-3516 TCGA-AA-3552 TCGA-AU-3779 TCGA-CM-6170 TCGA-G4-6306 
       13.02        13.02        14.50        15.02        44.68 

$`CREG2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        1.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       10.88         0.20        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       12.99        13.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       53.62        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  CREG2 MUTATED CREG2 WILD-TYPE 
          13.02            0.00 
  CREG2 MUTATED CREG2 WILD-TYPE 
          44.68          148.01 
  CREG2 MUTATED CREG2 WILD-TYPE 
         14.500          20.415 
[1] "13.0 - 44.7 (14.5)" "0.0 - 148.0 (20.4)"
[1] "hr=" "2.4"
D1393V2, continuous
D1393V3, binary
                 cls
clus                0   1
  CREG2 MUTATED     5   0
  CREG2 WILD-TYPE 361 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CREG2 MUTATED      5    0
  CREG2 WILD-TYPE  361  119
        clus
vv       CREG2 MUTATED CREG2 WILD-TYPE
  COLON              5             361
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CREG2 MUTATED         1        0        0         2         0         0
  CREG2 WILD-TYPE      90        1       32       136        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CREG2 MUTATED           1          0          0          1        0         0
  CREG2 WILD-TYPE        23         11         59         41       48        18
                 vv
clus              STAGE IVB
  CREG2 MUTATED           0
  CREG2 WILD-TYPE         1
D1393V4, multiclass
            clus
vv           CREG2 MUTATED CREG2 WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              2             136
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             1              41
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CREG2 MUTATED     0   2   3   0
  CREG2 WILD-TYPE  17  90 326  50
D1393V5, multiclass
    clus
vv   CREG2 MUTATED CREG2 WILD-TYPE
  T1             0              17
  T2             2              90
  T3             3             326
  T4             0              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  CREG2 MUTATED     3   0   2
  CREG2 WILD-TYPE 284 113  85
D1393V6, multiclass
    clus
vv   CREG2 MUTATED CREG2 WILD-TYPE
  N0             3             284
  N1             0             113
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1393V7, binary
                 cls
clus                0   1
  CREG2 MUTATED     5   0
  CREG2 WILD-TYPE 370  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CREG2 MUTATED      5    0
  CREG2 WILD-TYPE  370   65
   clus
vv  CREG2 MUTATED CREG2 WILD-TYPE
  0             5             370
  1             0              65
[1] 2 2
[1] FALSE
D1393V8, binary
                 cls
clus                0   1
  CREG2 MUTATED     3   2
  CREG2 WILD-TYPE 222 262
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CREG2 MUTATED      3    2
  CREG2 WILD-TYPE  222  262
        clus
vv       CREG2 MUTATED CREG2 WILD-TYPE
  FEMALE             3             222
  MALE               2             262
[1] 2 2
[1] FALSE
D1393V9, binary
                 cls
clus                0   1
  CREG2 MUTATED     5   0
  CREG2 WILD-TYPE 345  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CREG2 MUTATED      5    0
  CREG2 WILD-TYPE  345   22
     clus
vv    CREG2 MUTATED CREG2 WILD-TYPE
  NO              5             345
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CREG2 MUTATED                      4                             1
  CREG2 WILD-TYPE                  311                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CREG2 MUTATED                       0                              0
  CREG2 WILD-TYPE                   106                             10
D1393V10, multiclass
                                clus
vv                               CREG2 MUTATED CREG2 WILD-TYPE
  COLON ADENOCARCINOMA                       4             311
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  CREG2 MUTATED     4   0   0   0
  CREG2 WILD-TYPE 341   4  31  25
D1393V11, multiclass
    clus
vv   CREG2 MUTATED CREG2 WILD-TYPE
  R0             4             341
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1393V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CREG2 MUTATED                                  0     0
  CREG2 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CREG2 MUTATED                           0     3
  CREG2 WILD-TYPE                        22   223
D1393V13, multiclass
                                  clus
vv                                 CREG2 MUTATED CREG2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        3             223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1394) Variable = GTF2A1L MUTATION ANALYSIS
D1394V1, survival
                   sevent
clus2                 0   1
  GTF2A1L MUTATED    13   5
  GTF2A1L WILD-TYPE 365  88
  GTF2A1L MUTATED GTF2A1L WILD-TYPE 
               18               453 
  GTF2A1L MUTATED GTF2A1L WILD-TYPE 
                5                88 
$`GTF2A1L MUTATED`
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3811 TCGA-AA-3968 TCGA-AA-A00N TCGA-AA-A00Z 
       78.08         6.05        10.06        21.99         4.01        21.99 
TCGA-AA-A010 TCGA-CM-6676 TCGA-DM-A28H TCGA-F4-6570 TCGA-F4-6809 TCGA-G4-6310 
       34.98        11.08       117.07         6.18        13.25        63.62 
TCGA-AG-3593 TCGA-AG-A002 TCGA-AH-6544 TCGA-CI-6619 TCGA-DY-A0XA TCGA-DY-A1DG 
       34.03        20.98        38.56         6.05       126.44        51.48 

$`GTF2A1L WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3663 
       20.98        19.99        13.94        19.99        61.02         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        19.04        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
        0.99        17.03        14.99         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       11.01        12.95        13.05        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 
       60.79        98.24         8.61        31.96        35.74        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6854 
        1.55        34.42        41.42        16.24        33.67         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       44.68        55.04        85.48        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3594 TCGA-AG-3598 
       20.05        24.00         1.02        46.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
       38.04       117.11         1.45        17.49         0.69         0.72 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        4.01         5.03         5.29        41.36        57.24        24.13 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  GTF2A1L MUTATED GTF2A1L WILD-TYPE 
             4.01              0.00 
  GTF2A1L MUTATED GTF2A1L WILD-TYPE 
           126.44            148.01 
  GTF2A1L MUTATED GTF2A1L WILD-TYPE 
            21.99             20.05 
[1] "4.0 - 126.4 (22.0)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.1"
D1394V2, continuous
D1394V3, binary
                   cls
clus                  0   1
  GTF2A1L MUTATED    15   6
  GTF2A1L WILD-TYPE 351 113
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GTF2A1L MUTATED     15    6
  GTF2A1L WILD-TYPE  351  113
        clus
vv       GTF2A1L MUTATED GTF2A1L WILD-TYPE
  COLON               15               351
  RECTUM               6               113
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GTF2A1L MUTATED         3        0        1         4         2         0
  GTF2A1L WILD-TYPE      88        1       31       134         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GTF2A1L MUTATED           1          0          1          2        4
  GTF2A1L WILD-TYPE        23         11         58         40       44
                   vv
clus                STAGE IVA STAGE IVB
  GTF2A1L MUTATED           2         0
  GTF2A1L WILD-TYPE        16         1
D1394V4, multiclass
            clus
vv           GTF2A1L MUTATED GTF2A1L WILD-TYPE
  STAGE I                  3                88
  STAGE IA                 0                 1
  STAGE II                 1                31
  STAGE IIA                4               134
  STAGE IIB                2                 8
  STAGE IIC                0                 1
  STAGE III                1                23
  STAGE IIIA               0                11
  STAGE IIIB               1                58
  STAGE IIIC               2                40
  STAGE IV                 4                44
  STAGE IVA                2                16
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  GTF2A1L MUTATED     0   3  13   5
  GTF2A1L WILD-TYPE  17  89 316  45
D1394V5, multiclass
    clus
vv   GTF2A1L MUTATED GTF2A1L WILD-TYPE
  T1               0                17
  T2               3                89
  T3              13               316
  T4               5                45
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  GTF2A1L MUTATED    10   6   5
  GTF2A1L WILD-TYPE 277 107  82
D1394V6, multiclass
    clus
vv   GTF2A1L MUTATED GTF2A1L WILD-TYPE
  N0              10               277
  N1               6               107
  N2               5                82
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1394V7, binary
                   cls
clus                  0   1
  GTF2A1L MUTATED    13   7
  GTF2A1L WILD-TYPE 362  58
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GTF2A1L MUTATED     13    7
  GTF2A1L WILD-TYPE  362   58
   clus
vv  GTF2A1L MUTATED GTF2A1L WILD-TYPE
  0              13               362
  1               7                58
[1] 2 2
[1] FALSE
D1394V8, binary
                   cls
clus                  0   1
  GTF2A1L MUTATED    11  10
  GTF2A1L WILD-TYPE 214 254
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GTF2A1L MUTATED     11   10
  GTF2A1L WILD-TYPE  214  254
        clus
vv       GTF2A1L MUTATED GTF2A1L WILD-TYPE
  FEMALE              11               214
  MALE                10               254
[1] 2 2
[1] FALSE
D1394V9, binary
                   cls
clus                  0   1
  GTF2A1L MUTATED    11   2
  GTF2A1L WILD-TYPE 339  20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GTF2A1L MUTATED     11    2
  GTF2A1L WILD-TYPE  339   20
     clus
vv    GTF2A1L MUTATED GTF2A1L WILD-TYPE
  NO               11               339
  YES               2                20
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  GTF2A1L MUTATED                     12                             3
  GTF2A1L WILD-TYPE                  303                            44
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  GTF2A1L MUTATED                       6                              0
  GTF2A1L WILD-TYPE                   100                             10
D1394V10, multiclass
                                clus
vv                               GTF2A1L MUTATED GTF2A1L WILD-TYPE
  COLON ADENOCARCINOMA                        12               303
  COLON MUCINOUS ADENOCARCINOMA                3                44
  RECTAL ADENOCARCINOMA                        6               100
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  GTF2A1L MUTATED    13   0   3   0
  GTF2A1L WILD-TYPE 332   4  28  25
D1394V11, multiclass
    clus
vv   GTF2A1L MUTATED GTF2A1L WILD-TYPE
  R0              13               332
  R1               0                 4
  R2               3                28
  RX               0                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1394V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GTF2A1L MUTATED                                  0     0
  GTF2A1L WILD-TYPE                                1    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  GTF2A1L MUTATED                           0    10
  GTF2A1L WILD-TYPE                        22   216
D1394V13, multiclass
                                  clus
vv                                 GTF2A1L MUTATED GTF2A1L WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                      0                22
  WHITE                                         10               216
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1395) Variable = MALT1 MUTATION ANALYSIS
D1395V1, survival
                 sevent
clus2               0   1
  MALT1 MUTATED     9   3
  MALT1 WILD-TYPE 369  90
  MALT1 MUTATED MALT1 WILD-TYPE 
             12             459 
  MALT1 MUTATED MALT1 WILD-TYPE 
              3              90 
$`MALT1 MUTATED`
TCGA-A6-5665 TCGA-AA-3492 TCGA-AA-3516 TCGA-AA-3662 TCGA-AA-3815 TCGA-AA-3864 
       22.06         3.02        13.02         6.05        33.04        53.00 
TCGA-AA-3877 TCGA-AA-3977 TCGA-AA-A010 TCGA-AD-6901 TCGA-G4-6625 TCGA-AG-A002 
       31.00        25.02        34.98        22.42        91.79        20.98 

$`MALT1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 
       20.12        19.66        20.28         7.04         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
       63.98         6.97         1.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02        78.08         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
       26.99        19.04        19.04        10.06        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       30.05        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.79         0.72         5.79        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6626 
       36.00        22.09        13.78        35.80        26.17        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  MALT1 MUTATED MALT1 WILD-TYPE 
           3.02            0.00 
  MALT1 MUTATED MALT1 WILD-TYPE 
          91.79          148.01 
  MALT1 MUTATED MALT1 WILD-TYPE 
          23.72           20.02 
[1] "3.0 - 91.8 (23.7)"  "0.0 - 148.0 (20.0)"
[1] "hr=" "1.2"
D1395V2, continuous
D1395V3, binary
                 cls
clus                0   1
  MALT1 MUTATED    11   1
  MALT1 WILD-TYPE 355 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MALT1 MUTATED     11    1
  MALT1 WILD-TYPE  355  118
        clus
vv       MALT1 MUTATED MALT1 WILD-TYPE
  COLON             11             355
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MALT1 MUTATED         2        0        2         3         1         0
  MALT1 WILD-TYPE      89        1       30       135         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MALT1 MUTATED           1          0          0          0        1         0
  MALT1 WILD-TYPE        23         11         59         42       47        18
                 vv
clus              STAGE IVB
  MALT1 MUTATED           0
  MALT1 WILD-TYPE         1
D1395V4, multiclass
            clus
vv           MALT1 MUTATED MALT1 WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA              3             135
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             0              42
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  MALT1 MUTATED     1   2   7   2
  MALT1 WILD-TYPE  16  90 322  48
D1395V5, multiclass
    clus
vv   MALT1 MUTATED MALT1 WILD-TYPE
  T1             1              16
  T2             2              90
  T3             7             322
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  MALT1 MUTATED    10   0   2
  MALT1 WILD-TYPE 277 113  85
D1395V6, multiclass
    clus
vv   MALT1 MUTATED MALT1 WILD-TYPE
  N0            10             277
  N1             0             113
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1395V7, binary
                 cls
clus                0   1
  MALT1 MUTATED     9   1
  MALT1 WILD-TYPE 366  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MALT1 MUTATED      9    1
  MALT1 WILD-TYPE  366   64
   clus
vv  MALT1 MUTATED MALT1 WILD-TYPE
  0             9             366
  1             1              64
[1] 2 2
[1] FALSE
D1395V8, binary
                 cls
clus                0   1
  MALT1 MUTATED     8   4
  MALT1 WILD-TYPE 217 260
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MALT1 MUTATED      8    4
  MALT1 WILD-TYPE  217  260
        clus
vv       MALT1 MUTATED MALT1 WILD-TYPE
  FEMALE             8             217
  MALE               4             260
[1] 2 2
[1] FALSE
D1395V9, binary
                 cls
clus                0   1
  MALT1 MUTATED    12   0
  MALT1 WILD-TYPE 338  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MALT1 MUTATED     12    0
  MALT1 WILD-TYPE  338   22
     clus
vv    MALT1 MUTATED MALT1 WILD-TYPE
  NO             12             338
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MALT1 MUTATED                      9                             2
  MALT1 WILD-TYPE                  306                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MALT1 MUTATED                       1                              0
  MALT1 WILD-TYPE                   105                             10
D1395V10, multiclass
                                clus
vv                               MALT1 MUTATED MALT1 WILD-TYPE
  COLON ADENOCARCINOMA                       9             306
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  MALT1 MUTATED     8   0   1   0
  MALT1 WILD-TYPE 337   4  30  25
D1395V11, multiclass
    clus
vv   MALT1 MUTATED MALT1 WILD-TYPE
  R0             8             337
  R1             0               4
  R2             1              30
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1395V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MALT1 MUTATED                                  0     0
  MALT1 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  MALT1 MUTATED                           0     3
  MALT1 WILD-TYPE                        22   223
D1395V13, multiclass
                                  clus
vv                                 MALT1 MUTATED MALT1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        3             223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1396) Variable = PSMD6 MUTATION ANALYSIS
D1396V1, survival
                 sevent
clus2               0   1
  PSMD6 MUTATED     7   1
  PSMD6 WILD-TYPE 371  92
  PSMD6 MUTATED PSMD6 WILD-TYPE 
              8             463 
  PSMD6 MUTATED PSMD6 WILD-TYPE 
              1              92 
$`PSMD6 MUTATED`
TCGA-AA-3663 TCGA-AA-3977 TCGA-AD-6895 TCGA-CK-4947 TCGA-CM-6168 TCGA-AG-A002 
        6.97        25.02         0.72        17.56        12.99        20.98 
TCGA-DY-A1H8 TCGA-EI-6510 
       32.61        18.28 

$`PSMD6 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.05        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
       56.55         0.79         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       12.76        10.06        14.30       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6169 
        2.96        29.03        16.04        21.99        14.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-F5-6464 TCGA-F5-6465 
        0.49        20.55        19.96        20.91         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  PSMD6 MUTATED PSMD6 WILD-TYPE 
           0.72            0.00 
  PSMD6 MUTATED PSMD6 WILD-TYPE 
          32.61          148.01 
  PSMD6 MUTATED PSMD6 WILD-TYPE 
          17.92           20.28 
[1] "0.7 - 32.6 (17.9)"  "0.0 - 148.0 (20.3)"
[1] "hr=" "1"  
D1396V2, continuous
D1396V3, binary
                 cls
clus                0   1
  PSMD6 MUTATED     5   3
  PSMD6 WILD-TYPE 361 116
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PSMD6 MUTATED      5    3
  PSMD6 WILD-TYPE  361  116
        clus
vv       PSMD6 MUTATED PSMD6 WILD-TYPE
  COLON              5             361
  RECTUM             3             116
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PSMD6 MUTATED         1        0        1         1         0         0
  PSMD6 WILD-TYPE      90        1       31       137        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PSMD6 MUTATED           0          1          1          0        0         1
  PSMD6 WILD-TYPE        24         10         58         42       48        17
                 vv
clus              STAGE IVB
  PSMD6 MUTATED           0
  PSMD6 WILD-TYPE         1
D1396V4, multiclass
            clus
vv           PSMD6 MUTATED PSMD6 WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              1             137
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             1              10
  STAGE IIIB             1              58
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PSMD6 MUTATED     0   4   3   1
  PSMD6 WILD-TYPE  17  88 326  49
D1396V5, multiclass
    clus
vv   PSMD6 MUTATED PSMD6 WILD-TYPE
  T1             0              17
  T2             4              88
  T3             3             326
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  PSMD6 MUTATED     5   3   0
  PSMD6 WILD-TYPE 282 110  87
D1396V6, multiclass
    clus
vv   PSMD6 MUTATED PSMD6 WILD-TYPE
  N0             5             282
  N1             3             110
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1396V7, binary
                 cls
clus                0   1
  PSMD6 MUTATED     5   0
  PSMD6 WILD-TYPE 370  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PSMD6 MUTATED      5    0
  PSMD6 WILD-TYPE  370   65
   clus
vv  PSMD6 MUTATED PSMD6 WILD-TYPE
  0             5             370
  1             0              65
[1] 2 2
[1] FALSE
D1396V8, binary
                 cls
clus                0   1
  PSMD6 MUTATED     4   4
  PSMD6 WILD-TYPE 221 260
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PSMD6 MUTATED      4    4
  PSMD6 WILD-TYPE  221  260
        clus
vv       PSMD6 MUTATED PSMD6 WILD-TYPE
  FEMALE             4             221
  MALE               4             260
[1] 2 2
[1] FALSE
D1396V9, binary
                 cls
clus                0   1
  PSMD6 MUTATED     6   0
  PSMD6 WILD-TYPE 344  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PSMD6 MUTATED      6    0
  PSMD6 WILD-TYPE  344   22
     clus
vv    PSMD6 MUTATED PSMD6 WILD-TYPE
  NO              6             344
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PSMD6 MUTATED                      5                             0
  PSMD6 WILD-TYPE                  310                            47
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PSMD6 MUTATED                       3                              0
  PSMD6 WILD-TYPE                   103                             10
D1396V10, multiclass
                                clus
vv                               PSMD6 MUTATED PSMD6 WILD-TYPE
  COLON ADENOCARCINOMA                       5             310
  COLON MUCINOUS ADENOCARCINOMA              0              47
  RECTAL ADENOCARCINOMA                      3             103
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  PSMD6 MUTATED     4   0   0   1
  PSMD6 WILD-TYPE 341   4  31  24
D1396V11, multiclass
    clus
vv   PSMD6 MUTATED PSMD6 WILD-TYPE
  R0             4             341
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1396V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PSMD6 MUTATED                                  0     0
  PSMD6 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PSMD6 MUTATED                           1     4
  PSMD6 WILD-TYPE                        21   222
D1396V13, multiclass
                                  clus
vv                                 PSMD6 MUTATED PSMD6 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        4             222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1397) Variable = DLEC1 MUTATION ANALYSIS
D1397V1, survival
                 sevent
clus2               0   1
  DLEC1 MUTATED    15   4
  DLEC1 WILD-TYPE 363  89
  DLEC1 MUTATED DLEC1 WILD-TYPE 
             19             452 
  DLEC1 MUTATED DLEC1 WILD-TYPE 
              4              89 
$`DLEC1 MUTATED`
TCGA-A6-3809 TCGA-A6-5662 TCGA-A6-5665 TCGA-AA-3663 TCGA-AA-3697 TCGA-AA-3715 
       32.75        23.61        22.06         6.97        85.05        19.04 
TCGA-AA-A010 TCGA-AA-A01P TCGA-AA-A01R TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 
       34.98        38.07        35.01        12.76        10.06        17.56 
TCGA-CK-5916 TCGA-D5-6536 TCGA-D5-6922 TCGA-G4-6588 TCGA-AF-2693 TCGA-CI-6620 
       21.14        17.85         4.41        26.17        19.10        33.17 
TCGA-EF-5830 
        0.49 

$`DLEC1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5664 TCGA-A6-5666 
       31.63        30.44        29.19        33.53        22.09        32.71 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       27.09        22.52         8.38        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02        78.08         6.05        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 
        5.98        37.05        19.00        36.00         5.03        26.99 
TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T 
       12.00        31.00        31.00         1.02         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       14.30       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
        9.99        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        3.68        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 
       61.91        36.00        22.09        13.78        35.80        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6622 
        1.45        17.49         0.69         0.72         6.05         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
       32.61        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  DLEC1 MUTATED DLEC1 WILD-TYPE 
           0.49            0.00 
  DLEC1 MUTATED DLEC1 WILD-TYPE 
          85.05          148.01 
  DLEC1 MUTATED DLEC1 WILD-TYPE 
         21.140          20.155 
[1] "0.5 - 85.0 (21.1)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.2"
D1397V2, continuous
D1397V3, binary
                 cls
clus                0   1
  DLEC1 MUTATED    16   2
  DLEC1 WILD-TYPE 350 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DLEC1 MUTATED     16    2
  DLEC1 WILD-TYPE  350  117
        clus
vv       DLEC1 MUTATED DLEC1 WILD-TYPE
  COLON             16             350
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DLEC1 MUTATED         2        0        2         5         3         0
  DLEC1 WILD-TYPE      89        1       30       133         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DLEC1 MUTATED           3          1          1          0        0         2
  DLEC1 WILD-TYPE        21         10         58         42       48        16
                 vv
clus              STAGE IVB
  DLEC1 MUTATED           0
  DLEC1 WILD-TYPE         1
D1397V4, multiclass
            clus
vv           DLEC1 MUTATED DLEC1 WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA              5             133
  STAGE IIB              3               7
  STAGE IIC              0               1
  STAGE III              3              21
  STAGE IIIA             1              10
  STAGE IIIB             1              58
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              2              16
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  DLEC1 MUTATED     1   1  13   4
  DLEC1 WILD-TYPE  16  91 316  46
D1397V5, multiclass
    clus
vv   DLEC1 MUTATED DLEC1 WILD-TYPE
  T1             1              16
  T2             1              91
  T3            13             316
  T4             4              46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  DLEC1 MUTATED    13   4   2
  DLEC1 WILD-TYPE 274 109  85
D1397V6, multiclass
    clus
vv   DLEC1 MUTATED DLEC1 WILD-TYPE
  N0            13             274
  N1             4             109
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1397V7, binary
                 cls
clus                0   1
  DLEC1 MUTATED    16   2
  DLEC1 WILD-TYPE 359  63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DLEC1 MUTATED     16    2
  DLEC1 WILD-TYPE  359   63
   clus
vv  DLEC1 MUTATED DLEC1 WILD-TYPE
  0            16             359
  1             2              63
[1] 2 2
[1] FALSE
D1397V8, binary
                 cls
clus                0   1
  DLEC1 MUTATED     8  11
  DLEC1 WILD-TYPE 217 253
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DLEC1 MUTATED      8   11
  DLEC1 WILD-TYPE  217  253
        clus
vv       DLEC1 MUTATED DLEC1 WILD-TYPE
  FEMALE             8             217
  MALE              11             253
[1] 2 2
[1] FALSE
D1397V9, binary
                 cls
clus                0   1
  DLEC1 MUTATED    16   1
  DLEC1 WILD-TYPE 334  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DLEC1 MUTATED     16    1
  DLEC1 WILD-TYPE  334   21
     clus
vv    DLEC1 MUTATED DLEC1 WILD-TYPE
  NO             16             334
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  DLEC1 MUTATED                     13                             3
  DLEC1 WILD-TYPE                  302                            44
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  DLEC1 MUTATED                       2                              0
  DLEC1 WILD-TYPE                   104                             10
D1397V10, multiclass
                                clus
vv                               DLEC1 MUTATED DLEC1 WILD-TYPE
  COLON ADENOCARCINOMA                      13             302
  COLON MUCINOUS ADENOCARCINOMA              3              44
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  DLEC1 MUTATED    12   0   0   4
  DLEC1 WILD-TYPE 333   4  31  21
D1397V11, multiclass
    clus
vv   DLEC1 MUTATED DLEC1 WILD-TYPE
  R0            12             333
  R1             0               4
  R2             0              31
  RX             4              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1397V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DLEC1 MUTATED                                  0     2
  DLEC1 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  DLEC1 MUTATED                           0    11
  DLEC1 WILD-TYPE                        22   215
D1397V13, multiclass
                                  clus
vv                                 DLEC1 MUTATED DLEC1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               9
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                       11             215
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1398) Variable = DPP8 MUTATION ANALYSIS
D1398V1, survival
                sevent
clus2              0   1
  DPP8 MUTATED    11   2
  DPP8 WILD-TYPE 367  91
  DPP8 MUTATED DPP8 WILD-TYPE 
            13            458 
  DPP8 MUTATED DPP8 WILD-TYPE 
             2             91 
$`DPP8 MUTATED`
TCGA-AA-3510 TCGA-AA-3715 TCGA-AA-3864 TCGA-AA-3949 TCGA-AA-3977 TCGA-AA-A010 
       63.98        19.04        53.00        26.01        25.02        34.98 
TCGA-AA-A01S TCGA-AA-A03J TCGA-AD-5900 TCGA-AZ-6598 TCGA-CM-6162 TCGA-G4-6304 
        1.02        40.96         0.07        49.41        12.00        53.62 
TCGA-AG-A02N 
       61.97 

$`DPP8 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 
       36.00         5.03        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 
        0.99        31.07        31.07        30.05        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        33.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
       35.01        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       41.00        39.98        18.05        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        88.21         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 
        5.03        15.02        15.02        17.03        15.02         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 
       47.41        35.31       133.18        74.56        65.85        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  DPP8 MUTATED DPP8 WILD-TYPE 
          0.07           0.00 
  DPP8 MUTATED DPP8 WILD-TYPE 
         63.98         148.01 
  DPP8 MUTATED DPP8 WILD-TYPE 
        34.980         20.035 
[1] "0.1 - 64.0 (35.0)"  "0.0 - 148.0 (20.0)"
[1] "hr=" "1.8"
D1398V2, continuous
D1398V3, binary
                cls
clus               0   1
  DPP8 MUTATED    13   1
  DPP8 WILD-TYPE 353 118
[1] "tbl2"
                cls
clus             [,1] [,2]
  DPP8 MUTATED     13    1
  DPP8 WILD-TYPE  353  118
        clus
vv       DPP8 MUTATED DPP8 WILD-TYPE
  COLON            13            353
  RECTUM            1            118
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DPP8 MUTATED         2        0        5         1         2         0
  DPP8 WILD-TYPE      89        1       27       137         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DPP8 MUTATED           1          0          2          0        0         0
  DPP8 WILD-TYPE        23         11         57         42       48        18
                vv
clus             STAGE IVB
  DPP8 MUTATED           0
  DPP8 WILD-TYPE         1
D1398V4, multiclass
            clus
vv           DPP8 MUTATED DPP8 WILD-TYPE
  STAGE I               2             89
  STAGE IA              0              1
  STAGE II              5             27
  STAGE IIA             1            137
  STAGE IIB             2              8
  STAGE IIC             0              1
  STAGE III             1             23
  STAGE IIIA            0             11
  STAGE IIIB            2             57
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  DPP8 MUTATED     0   3   9   2
  DPP8 WILD-TYPE  17  89 320  48
D1398V5, multiclass
    clus
vv   DPP8 MUTATED DPP8 WILD-TYPE
  T1            0             17
  T2            3             89
  T3            9            320
  T4            2             48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  DPP8 MUTATED    11   3   0
  DPP8 WILD-TYPE 276 110  87
D1398V6, multiclass
    clus
vv   DPP8 MUTATED DPP8 WILD-TYPE
  N0           11            276
  N1            3            110
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1398V7, binary
                cls
clus               0   1
  DPP8 MUTATED    11   0
  DPP8 WILD-TYPE 364  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  DPP8 MUTATED     11    0
  DPP8 WILD-TYPE  364   65
   clus
vv  DPP8 MUTATED DPP8 WILD-TYPE
  0           11            364
  1            0             65
[1] 2 2
[1] FALSE
D1398V8, binary
                cls
clus               0   1
  DPP8 MUTATED     8   6
  DPP8 WILD-TYPE 217 258
[1] "tbl2"
                cls
clus             [,1] [,2]
  DPP8 MUTATED      8    6
  DPP8 WILD-TYPE  217  258
        clus
vv       DPP8 MUTATED DPP8 WILD-TYPE
  FEMALE            8            217
  MALE              6            258
[1] 2 2
[1] FALSE
D1398V9, binary
                cls
clus               0   1
  DPP8 MUTATED    10   0
  DPP8 WILD-TYPE 340  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  DPP8 MUTATED     10    0
  DPP8 WILD-TYPE  340   22
     clus
vv    DPP8 MUTATED DPP8 WILD-TYPE
  NO            10            340
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  DPP8 MUTATED                     10                             3
  DPP8 WILD-TYPE                  305                            44
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  DPP8 MUTATED                       1                              0
  DPP8 WILD-TYPE                   105                             10
D1398V10, multiclass
                                clus
vv                               DPP8 MUTATED DPP8 WILD-TYPE
  COLON ADENOCARCINOMA                     10            305
  COLON MUCINOUS ADENOCARCINOMA             3             44
  RECTAL ADENOCARCINOMA                     1            105
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  DPP8 MUTATED    12   0   0   0
  DPP8 WILD-TYPE 333   4  31  25
D1398V11, multiclass
    clus
vv   DPP8 MUTATED DPP8 WILD-TYPE
  R0           12            333
  R1            0              4
  R2            0             31
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1398V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DPP8 MUTATED                                  0     0
  DPP8 WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  DPP8 MUTATED                           0     4
  DPP8 WILD-TYPE                        22   222
D1398V13, multiclass
                                  clus
vv                                 DPP8 MUTATED DPP8 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       4            222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1399) Variable = CAPRIN1 MUTATION ANALYSIS
D1399V1, survival
                   sevent
clus2                 0   1
  CAPRIN1 MUTATED     9   3
  CAPRIN1 WILD-TYPE 369  90
  CAPRIN1 MUTATED CAPRIN1 WILD-TYPE 
               12               459 
  CAPRIN1 MUTATED CAPRIN1 WILD-TYPE 
                3                90 
$`CAPRIN1 MUTATED`
TCGA-A6-2672 TCGA-A6-3809 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3548 TCGA-AA-A01R 
       46.65        32.75         3.02         1.02        33.99        35.01 
TCGA-AD-6901 TCGA-CM-4746 TCGA-CM-6171 TCGA-D5-6540 TCGA-G4-6626 TCGA-AG-A002 
       22.42        37.02        14.04        16.14        46.75        20.98 

$`CAPRIN1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5657 
       34.65        33.34        36.53        14.53        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       30.44        29.19        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
       19.66        20.28         7.04        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       14.01        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       78.08         6.05         6.97        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
        1.02         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 
       14.99        12.99        13.02        15.02        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       17.13        12.49        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  CAPRIN1 MUTATED CAPRIN1 WILD-TYPE 
             1.02              0.00 
  CAPRIN1 MUTATED CAPRIN1 WILD-TYPE 
            46.75            148.01 
  CAPRIN1 MUTATED CAPRIN1 WILD-TYPE 
           27.585            20.050 
[1] "1.0 - 46.8 (27.6)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.3"
D1399V2, continuous
D1399V3, binary
                   cls
clus                  0   1
  CAPRIN1 MUTATED    11   1
  CAPRIN1 WILD-TYPE 355 118
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CAPRIN1 MUTATED     11    1
  CAPRIN1 WILD-TYPE  355  118
        clus
vv       CAPRIN1 MUTATED CAPRIN1 WILD-TYPE
  COLON               11               355
  RECTUM               1               118
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CAPRIN1 MUTATED         4        0        2         1         1         0
  CAPRIN1 WILD-TYPE      87        1       30       137         9         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CAPRIN1 MUTATED           1          0          1          1        0
  CAPRIN1 WILD-TYPE        23         11         58         41       48
                   vv
clus                STAGE IVA STAGE IVB
  CAPRIN1 MUTATED           0         0
  CAPRIN1 WILD-TYPE        18         1
D1399V4, multiclass
            clus
vv           CAPRIN1 MUTATED CAPRIN1 WILD-TYPE
  STAGE I                  4                87
  STAGE IA                 0                 1
  STAGE II                 2                30
  STAGE IIA                1               137
  STAGE IIB                1                 9
  STAGE IIC                0                 1
  STAGE III                1                23
  STAGE IIIA               0                11
  STAGE IIIB               1                58
  STAGE IIIC               1                41
  STAGE IV                 0                48
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  CAPRIN1 MUTATED     0   4   7   1
  CAPRIN1 WILD-TYPE  17  88 322  49
D1399V5, multiclass
    clus
vv   CAPRIN1 MUTATED CAPRIN1 WILD-TYPE
  T1               0                17
  T2               4                88
  T3               7               322
  T4               1                49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  CAPRIN1 MUTATED     9   1   2
  CAPRIN1 WILD-TYPE 278 112  85
D1399V6, multiclass
    clus
vv   CAPRIN1 MUTATED CAPRIN1 WILD-TYPE
  N0               9               278
  N1               1               112
  N2               2                85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1399V7, binary
                   cls
clus                  0   1
  CAPRIN1 MUTATED    11   0
  CAPRIN1 WILD-TYPE 364  65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CAPRIN1 MUTATED     11    0
  CAPRIN1 WILD-TYPE  364   65
   clus
vv  CAPRIN1 MUTATED CAPRIN1 WILD-TYPE
  0              11               364
  1               0                65
[1] 2 2
[1] FALSE
D1399V8, binary
                   cls
clus                  0   1
  CAPRIN1 MUTATED     6   6
  CAPRIN1 WILD-TYPE 219 258
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CAPRIN1 MUTATED      6    6
  CAPRIN1 WILD-TYPE  219  258
        clus
vv       CAPRIN1 MUTATED CAPRIN1 WILD-TYPE
  FEMALE               6               219
  MALE                 6               258
[1] 2 2
[1] FALSE
D1399V9, binary
                   cls
clus                  0   1
  CAPRIN1 MUTATED    10   1
  CAPRIN1 WILD-TYPE 340  21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CAPRIN1 MUTATED     10    1
  CAPRIN1 WILD-TYPE  340   21
     clus
vv    CAPRIN1 MUTATED CAPRIN1 WILD-TYPE
  NO               10               340
  YES               1                21
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CAPRIN1 MUTATED                      8                             3
  CAPRIN1 WILD-TYPE                  307                            44
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CAPRIN1 MUTATED                       1                              0
  CAPRIN1 WILD-TYPE                   105                             10
D1399V10, multiclass
                                clus
vv                               CAPRIN1 MUTATED CAPRIN1 WILD-TYPE
  COLON ADENOCARCINOMA                         8               307
  COLON MUCINOUS ADENOCARCINOMA                3                44
  RECTAL ADENOCARCINOMA                        1               105
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  CAPRIN1 MUTATED    11   0   0   0
  CAPRIN1 WILD-TYPE 334   4  31  25
D1399V11, multiclass
    clus
vv   CAPRIN1 MUTATED CAPRIN1 WILD-TYPE
  R0              11               334
  R1               0                 4
  R2               0                31
  RX               0                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1399V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CAPRIN1 MUTATED                                  0     0
  CAPRIN1 WILD-TYPE                                1    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  CAPRIN1 MUTATED                           1     6
  CAPRIN1 WILD-TYPE                        21   220
D1399V13, multiclass
                                  clus
vv                                 CAPRIN1 MUTATED CAPRIN1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                      1                21
  WHITE                                          6               220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1400) Variable = MTA2 MUTATION ANALYSIS
D1400V1, survival
                sevent
clus2              0   1
  MTA2 MUTATED     7   5
  MTA2 WILD-TYPE 371  88
  MTA2 MUTATED MTA2 WILD-TYPE 
            12            459 
  MTA2 MUTATED MTA2 WILD-TYPE 
             5             88 
$`MTA2 MUTATED`
TCGA-A6-2672 TCGA-AA-3492 TCGA-AA-3713 TCGA-AA-3950 TCGA-AA-3977 TCGA-AA-A01D 
       46.65         3.02        19.04        24.00        25.02        10.98 
TCGA-AY-4071 TCGA-AZ-6601 TCGA-CM-5344 TCGA-F4-6809 TCGA-G4-6299 TCGA-G4-6588 
        0.95       100.01        22.03        13.25        74.56        26.17 

$`MTA2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 
       20.12        19.66        20.28         7.04         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        33.01        26.01         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       16.31        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77        12.10        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       25.02        13.02        29.06        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6303 TCGA-G4-6304 
        0.53        47.41        35.31       133.18        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       22.09        13.78        35.80        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  MTA2 MUTATED MTA2 WILD-TYPE 
          0.95           0.00 
  MTA2 MUTATED MTA2 WILD-TYPE 
        100.01         148.01 
  MTA2 MUTATED MTA2 WILD-TYPE 
        23.015         20.120 
[1] "0.9 - 100.0 (23.0)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.8"
D1400V2, continuous
D1400V3, binary
                cls
clus               0   1
  MTA2 MUTATED    11   0
  MTA2 WILD-TYPE 355 119
[1] "tbl2"
                cls
clus             [,1] [,2]
  MTA2 MUTATED     11    0
  MTA2 WILD-TYPE  355  119
        clus
vv       MTA2 MUTATED MTA2 WILD-TYPE
  COLON            11            355
  RECTUM            0            119
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MTA2 MUTATED         1        0        2         2         0         0
  MTA2 WILD-TYPE      90        1       30       136        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MTA2 MUTATED           0          0          2          2        1         1
  MTA2 WILD-TYPE        24         11         57         40       47        17
                vv
clus             STAGE IVB
  MTA2 MUTATED           0
  MTA2 WILD-TYPE         1
D1400V4, multiclass
            clus
vv           MTA2 MUTATED MTA2 WILD-TYPE
  STAGE I               1             90
  STAGE IA              0              1
  STAGE II              2             30
  STAGE IIA             2            136
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            2             57
  STAGE IIIC            2             40
  STAGE IV              1             47
  STAGE IVA             1             17
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  MTA2 MUTATED     1   1  10   0
  MTA2 WILD-TYPE  16  91 319  50
D1400V5, multiclass
    clus
vv   MTA2 MUTATED MTA2 WILD-TYPE
  T1            1             16
  T2            1             91
  T3           10            319
  T4            0             50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  MTA2 MUTATED     7   3   2
  MTA2 WILD-TYPE 280 110  85
D1400V6, multiclass
    clus
vv   MTA2 MUTATED MTA2 WILD-TYPE
  N0            7            280
  N1            3            110
  N2            2             85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1400V7, binary
                cls
clus               0   1
  MTA2 MUTATED     8   2
  MTA2 WILD-TYPE 367  63
[1] "tbl2"
                cls
clus             [,1] [,2]
  MTA2 MUTATED      8    2
  MTA2 WILD-TYPE  367   63
   clus
vv  MTA2 MUTATED MTA2 WILD-TYPE
  0            8            367
  1            2             63
[1] 2 2
[1] FALSE
D1400V8, binary
                cls
clus               0   1
  MTA2 MUTATED     8   4
  MTA2 WILD-TYPE 217 260
[1] "tbl2"
                cls
clus             [,1] [,2]
  MTA2 MUTATED      8    4
  MTA2 WILD-TYPE  217  260
        clus
vv       MTA2 MUTATED MTA2 WILD-TYPE
  FEMALE            8            217
  MALE              4            260
[1] 2 2
[1] FALSE
D1400V9, binary
                cls
clus               0   1
  MTA2 MUTATED    11   1
  MTA2 WILD-TYPE 339  21
[1] "tbl2"
                cls
clus             [,1] [,2]
  MTA2 MUTATED     11    1
  MTA2 WILD-TYPE  339   21
     clus
vv    MTA2 MUTATED MTA2 WILD-TYPE
  NO            11            339
  YES            1             21
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MTA2 MUTATED                      9                             2
  MTA2 WILD-TYPE                  306                            45
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MTA2 MUTATED                       0                              0
  MTA2 WILD-TYPE                   106                             10
D1400V10, multiclass
                                clus
vv                               MTA2 MUTATED MTA2 WILD-TYPE
  COLON ADENOCARCINOMA                      9            306
  COLON MUCINOUS ADENOCARCINOMA             2             45
  RECTAL ADENOCARCINOMA                     0            106
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  MTA2 MUTATED     9   0   1   0
  MTA2 WILD-TYPE 336   4  30  25
D1400V11, multiclass
    clus
vv   MTA2 MUTATED MTA2 WILD-TYPE
  R0            9            336
  R1            0              4
  R2            1             30
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1400V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MTA2 MUTATED                                  0     0
  MTA2 WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  MTA2 MUTATED                           0     7
  MTA2 WILD-TYPE                        22   219
D1400V13, multiclass
                                  clus
vv                                 MTA2 MUTATED MTA2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       7            219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1401) Variable = GFRA4 MUTATION ANALYSIS
D1401V1, survival
                 sevent
clus2               0   1
  GFRA4 MUTATED     3   0
  GFRA4 WILD-TYPE 375  93
  GFRA4 MUTATED GFRA4 WILD-TYPE 
              3             468 
  GFRA4 MUTATED GFRA4 WILD-TYPE 
              0              93 
$`GFRA4 MUTATED`
TCGA-AA-3510 TCGA-AA-3864 TCGA-G4-6304 
       63.98        53.00        53.62 

$`GFRA4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 
       32.05         0.99        31.07        31.07        30.05        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       74.56        65.85        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  GFRA4 MUTATED GFRA4 WILD-TYPE 
             53               0 
  GFRA4 MUTATED GFRA4 WILD-TYPE 
          63.98          148.01 
  GFRA4 MUTATED GFRA4 WILD-TYPE 
         53.620          20.085 
[1] "53.0 - 64.0 (53.6)" "0.0 - 148.0 (20.1)"
[1] "hr="     "9300000"
D1401V2, continuous
D1401V3, binary
                 cls
clus                0   1
  GFRA4 MUTATED     3   0
  GFRA4 WILD-TYPE 363 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GFRA4 MUTATED      3    0
  GFRA4 WILD-TYPE  363  119
        clus
vv       GFRA4 MUTATED GFRA4 WILD-TYPE
  COLON              3             363
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GFRA4 MUTATED         0        0        2         0         1         0
  GFRA4 WILD-TYPE      91        1       30       138         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  GFRA4 MUTATED           0          0          0          0        0         0
  GFRA4 WILD-TYPE        24         11         59         42       48        18
                 vv
clus              STAGE IVB
  GFRA4 MUTATED           0
  GFRA4 WILD-TYPE         1
D1401V4, multiclass
            clus
vv           GFRA4 MUTATED GFRA4 WILD-TYPE
  STAGE I                0              91
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA              0             138
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  GFRA4 MUTATED     0   0   2   1
  GFRA4 WILD-TYPE  17  92 327  49
D1401V5, multiclass
    clus
vv   GFRA4 MUTATED GFRA4 WILD-TYPE
  T1             0              17
  T2             0              92
  T3             2             327
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  GFRA4 MUTATED     3   0   0
  GFRA4 WILD-TYPE 284 113  87
D1401V6, multiclass
    clus
vv   GFRA4 MUTATED GFRA4 WILD-TYPE
  N0             3             284
  N1             0             113
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1401V7, binary
                 cls
clus                0   1
  GFRA4 MUTATED     3   0
  GFRA4 WILD-TYPE 372  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GFRA4 MUTATED      3    0
  GFRA4 WILD-TYPE  372   65
   clus
vv  GFRA4 MUTATED GFRA4 WILD-TYPE
  0             3             372
  1             0              65
[1] 2 2
[1] FALSE
D1401V8, binary
                 cls
clus                0   1
  GFRA4 MUTATED     1   2
  GFRA4 WILD-TYPE 224 262
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GFRA4 MUTATED      1    2
  GFRA4 WILD-TYPE  224  262
        clus
vv       GFRA4 MUTATED GFRA4 WILD-TYPE
  FEMALE             1             224
  MALE               2             262
[1] 2 2
[1] FALSE
D1401V9, binary
                 cls
clus                0   1
  GFRA4 MUTATED     3   0
  GFRA4 WILD-TYPE 347  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GFRA4 MUTATED      3    0
  GFRA4 WILD-TYPE  347   22
     clus
vv    GFRA4 MUTATED GFRA4 WILD-TYPE
  NO              3             347
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  GFRA4 MUTATED                      3                             0
  GFRA4 WILD-TYPE                  312                            47
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  GFRA4 MUTATED                       0                              0
  GFRA4 WILD-TYPE                   106                             10
D1401V10, multiclass
                                clus
vv                               GFRA4 MUTATED GFRA4 WILD-TYPE
  COLON ADENOCARCINOMA                       3             312
  COLON MUCINOUS ADENOCARCINOMA              0              47
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  GFRA4 MUTATED     3   0   0   0
  GFRA4 WILD-TYPE 342   4  31  25
D1401V11, multiclass
    clus
vv   GFRA4 MUTATED GFRA4 WILD-TYPE
  R0             3             342
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1401V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GFRA4 MUTATED                                  0     0
  GFRA4 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  GFRA4 MUTATED                           0     1
  GFRA4 WILD-TYPE                        22   225
D1401V13, multiclass
[1] "Remove cluster labels:" "GFRA4 MUTATED"         
clus
  GFRA4 MUTATED GFRA4 WILD-TYPE 
              1             259 
     TCGA-A6-2671      TCGA-A6-2672      TCGA-A6-2674      TCGA-A6-2676 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-A6-2677      TCGA-A6-2678      TCGA-A6-2683      TCGA-A6-3807 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-A6-3808      TCGA-A6-3809      TCGA-A6-3810      TCGA-A6-4105 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-A6-5656      TCGA-A6-5657      TCGA-A6-5659      TCGA-A6-5660 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-A6-5661      TCGA-A6-5662      TCGA-A6-5664      TCGA-A6-5665 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-A6-5666      TCGA-A6-6137      TCGA-A6-6138      TCGA-A6-6141 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-A6-6142      TCGA-A6-6648      TCGA-A6-6649      TCGA-A6-6651 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-A6-6652      TCGA-A6-6653      TCGA-A6-6654      TCGA-A6-6780 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-A6-6781      TCGA-A6-6782      TCGA-AD-5900      TCGA-AD-6548 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-AD-6888      TCGA-AD-6889      TCGA-AD-6890      TCGA-AD-6895 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-AD-6899      TCGA-AD-6901      TCGA-AD-6963      TCGA-AD-6964 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-AD-6965      TCGA-AU-3779      TCGA-AU-6004      TCGA-AY-4070 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-AY-4071      TCGA-AY-5543      TCGA-AY-6196      TCGA-AY-6197 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-AY-6386      TCGA-AZ-4315      TCGA-AZ-4323      TCGA-AZ-4616 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-AZ-4681      TCGA-AZ-4682      TCGA-AZ-5403      TCGA-AZ-5407 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-AZ-6598      TCGA-AZ-6599      TCGA-AZ-6600      TCGA-AZ-6601 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-AZ-6603      TCGA-AZ-6605      TCGA-AZ-6606      TCGA-AZ-6607 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-AZ-6608      TCGA-CA-5254      TCGA-CA-5255      TCGA-CA-5796 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-CA-5797      TCGA-CA-6715      TCGA-CA-6716      TCGA-CA-6717 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-CA-6718      TCGA-CA-6719      TCGA-CK-4947      TCGA-CK-4948 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-CK-4950      TCGA-CK-4952      TCGA-CK-5912      TCGA-CK-5913 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-CK-5914      TCGA-CK-5915      TCGA-CK-5916      TCGA-CK-6746 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-CK-6747      TCGA-CK-6748      TCGA-CK-6751      TCGA-CM-4743 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-CM-4744      TCGA-CM-4746      TCGA-CM-4747      TCGA-CM-4752 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-CM-5341      TCGA-CM-5344      TCGA-CM-5348      TCGA-CM-5349 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-CM-5860      TCGA-CM-5861      TCGA-CM-5862      TCGA-CM-5863 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-CM-5864      TCGA-CM-5868      TCGA-CM-6161      TCGA-CM-6162 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-CM-6163      TCGA-CM-6164      TCGA-CM-6165      TCGA-CM-6166 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-CM-6167      TCGA-CM-6168      TCGA-CM-6169      TCGA-CM-6170 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-CM-6171      TCGA-CM-6172      TCGA-CM-6674      TCGA-CM-6675 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-CM-6676      TCGA-CM-6677      TCGA-CM-6678      TCGA-CM-6679 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-CM-6680      TCGA-D5-5537      TCGA-D5-5538      TCGA-D5-5539 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-D5-5540      TCGA-D5-5541      TCGA-D5-6529      TCGA-D5-6532 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-D5-6533      TCGA-D5-6534      TCGA-D5-6535      TCGA-D5-6536 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-D5-6537      TCGA-D5-6538      TCGA-D5-6539      TCGA-D5-6540 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-D5-6541      TCGA-D5-6898      TCGA-D5-6920      TCGA-D5-6922 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-D5-6923      TCGA-D5-6924      TCGA-D5-6926      TCGA-D5-6927 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-D5-6928      TCGA-D5-6929      TCGA-D5-6930      TCGA-D5-6931 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-D5-6932      TCGA-D5-7000      TCGA-DM-A0X9      TCGA-DM-A0XD 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-DM-A0XF      TCGA-DM-A1D0      TCGA-DM-A1D4      TCGA-DM-A1D6 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-DM-A1D7      TCGA-DM-A1D8      TCGA-DM-A1D9      TCGA-DM-A1DA 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-DM-A1DB      TCGA-DM-A1HA      TCGA-DM-A1HB      TCGA-DM-A282 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-DM-A285      TCGA-DM-A28C      TCGA-DM-A28E      TCGA-DM-A28F 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-DM-A28G      TCGA-DM-A28H      TCGA-DM-A28K      TCGA-F4-6459 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-F4-6460      TCGA-F4-6569      TCGA-F4-6570      TCGA-F4-6703 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-F4-6704      TCGA-F4-6805      TCGA-F4-6806      TCGA-F4-6807 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-F4-6808      TCGA-F4-6809      TCGA-F4-6854      TCGA-F4-6855 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-F4-6856      TCGA-G4-6293      TCGA-G4-6299      TCGA-G4-6303 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-G4-6306      TCGA-G4-6307      TCGA-G4-6309      TCGA-G4-6310 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-G4-6315      TCGA-G4-6317      TCGA-G4-6321      TCGA-G4-6323 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-G4-6586      TCGA-G4-6588      TCGA-G4-6625      TCGA-G4-6626 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-G4-6628      TCGA-AF-2687      TCGA-AF-2689      TCGA-AF-2691 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-AF-2692      TCGA-AF-2693      TCGA-AF-3400      TCGA-AF-3913 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-AF-4110      TCGA-AF-5654      TCGA-AF-6136      TCGA-AF-6655 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-AF-6672      TCGA-AH-6544      TCGA-AH-6547      TCGA-AH-6549 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-AH-6643      TCGA-AH-6644      TCGA-CI-6619      TCGA-CI-6620 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-CI-6621      TCGA-CI-6622      TCGA-CI-6624      TCGA-CL-5917 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-CL-5918      TCGA-DC-5337      TCGA-DC-5869      TCGA-DC-6155 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-DC-6157      TCGA-DC-6158      TCGA-DC-6160      TCGA-DC-6681 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-DC-6682      TCGA-DC-6683      TCGA-DT-5265      TCGA-DY-A0XA 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-DY-A1DC      TCGA-DY-A1DD      TCGA-DY-A1DF      TCGA-DY-A1DG 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-DY-A1H8      TCGA-EF-5830      TCGA-EI-6506      TCGA-EI-6507 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-EI-6508      TCGA-EI-6510      TCGA-F5-6464      TCGA-F5-6465 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-F5-6571      TCGA-F5-6702      TCGA-F5-6811      TCGA-F5-6812 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 
     TCGA-F5-6813      TCGA-G5-6235      TCGA-G5-6641 
"GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" "GFRA4 WILD-TYPE" 

Clustering(1402) Variable = FGD4 MUTATION ANALYSIS
D1402V1, survival
                sevent
clus2              0   1
  FGD4 MUTATED     8   0
  FGD4 WILD-TYPE 370  93
  FGD4 MUTATED FGD4 WILD-TYPE 
             8            463 
  FGD4 MUTATED FGD4 WILD-TYPE 
             0             93 
$`FGD4 MUTATED`
TCGA-CM-4746 TCGA-D5-6533 TCGA-F4-6703 TCGA-G4-6306 TCGA-AF-6655 TCGA-AG-3605 
       37.02         1.32        47.87        44.68        20.02         0.99 
TCGA-AG-A002 TCGA-F5-6811 
       20.98        32.19 

$`FGD4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       20.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       55.92        20.19        18.25        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
        6.18         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       65.85        53.62        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3608 TCGA-AG-3609 
        2.01        50.04        12.03         6.05        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       49.51        31.30        28.57         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  FGD4 MUTATED FGD4 WILD-TYPE 
          0.99           0.00 
  FGD4 MUTATED FGD4 WILD-TYPE 
         47.87         148.01 
  FGD4 MUTATED FGD4 WILD-TYPE 
        26.585         20.120 
[1] "1.0 - 47.9 (26.6)"  "0.0 - 148.0 (20.1)"
[1] "hr="     "9200000"
D1402V2, continuous
D1402V3, binary
                cls
clus               0   1
  FGD4 MUTATED     5   5
  FGD4 WILD-TYPE 361 114
[1] "tbl2"
                cls
clus             [,1] [,2]
  FGD4 MUTATED      5    5
  FGD4 WILD-TYPE  361  114
        clus
vv       FGD4 MUTATED FGD4 WILD-TYPE
  COLON             5            361
  RECTUM            5            114
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FGD4 MUTATED         2        0        0         5         0         0
  FGD4 WILD-TYPE      89        1       32       133        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  FGD4 MUTATED           0          1          1          0        1         0
  FGD4 WILD-TYPE        24         10         58         42       47        18
                vv
clus             STAGE IVB
  FGD4 MUTATED           0
  FGD4 WILD-TYPE         1
D1402V4, multiclass
            clus
vv           FGD4 MUTATED FGD4 WILD-TYPE
  STAGE I               2             89
  STAGE IA              0              1
  STAGE II              0             32
  STAGE IIA             5            133
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            1             10
  STAGE IIIB            1             58
  STAGE IIIC            0             42
  STAGE IV              1             47
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  FGD4 MUTATED     0   4   5   1
  FGD4 WILD-TYPE  17  88 324  49
D1402V5, multiclass
    clus
vv   FGD4 MUTATED FGD4 WILD-TYPE
  T1            0             17
  T2            4             88
  T3            5            324
  T4            1             49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  FGD4 MUTATED     8   2   0
  FGD4 WILD-TYPE 279 111  87
D1402V6, multiclass
    clus
vv   FGD4 MUTATED FGD4 WILD-TYPE
  N0            8            279
  N1            2            111
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1402V7, binary
                cls
clus               0   1
  FGD4 MUTATED     9   1
  FGD4 WILD-TYPE 366  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  FGD4 MUTATED      9    1
  FGD4 WILD-TYPE  366   64
   clus
vv  FGD4 MUTATED FGD4 WILD-TYPE
  0            9            366
  1            1             64
[1] 2 2
[1] FALSE
D1402V8, binary
                cls
clus               0   1
  FGD4 MUTATED     5   5
  FGD4 WILD-TYPE 220 259
[1] "tbl2"
                cls
clus             [,1] [,2]
  FGD4 MUTATED      5    5
  FGD4 WILD-TYPE  220  259
        clus
vv       FGD4 MUTATED FGD4 WILD-TYPE
  FEMALE            5            220
  MALE              5            259
[1] 2 2
[1] FALSE
D1402V9, binary
                cls
clus               0   1
  FGD4 MUTATED     6   0
  FGD4 WILD-TYPE 344  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  FGD4 MUTATED      6    0
  FGD4 WILD-TYPE  344   22
     clus
vv    FGD4 MUTATED FGD4 WILD-TYPE
  NO             6            344
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  FGD4 MUTATED                      5                             0
  FGD4 WILD-TYPE                  310                            47
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  FGD4 MUTATED                       5                              0
  FGD4 WILD-TYPE                   101                             10
D1402V10, multiclass
                                clus
vv                               FGD4 MUTATED FGD4 WILD-TYPE
  COLON ADENOCARCINOMA                      5            310
  COLON MUCINOUS ADENOCARCINOMA             0             47
  RECTAL ADENOCARCINOMA                     5            101
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  FGD4 MUTATED     8   0   1   0
  FGD4 WILD-TYPE 337   4  30  25
D1402V11, multiclass
    clus
vv   FGD4 MUTATED FGD4 WILD-TYPE
  R0            8            337
  R1            0              4
  R2            1             30
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1402V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FGD4 MUTATED                                  0     0
  FGD4 WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  FGD4 MUTATED                           1     5
  FGD4 WILD-TYPE                        21   221
D1402V13, multiclass
                                  clus
vv                                 FGD4 MUTATED FGD4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                       5            221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1403) Variable = HPS6 MUTATION ANALYSIS
D1403V1, survival
                sevent
clus2              0   1
  HPS6 MUTATED     5   1
  HPS6 WILD-TYPE 373  92
  HPS6 MUTATED HPS6 WILD-TYPE 
             6            465 
  HPS6 MUTATED HPS6 WILD-TYPE 
             1             92 
$`HPS6 MUTATED`
TCGA-AA-3710 TCGA-AA-3821 TCGA-AA-A01S TCGA-AY-6197 TCGA-AZ-6598 TCGA-AG-A002 
       26.99         1.02         1.02        21.44        49.41        20.98 

$`HPS6 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
       19.00        36.00         5.03        85.05        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 
       10.06        35.05        33.04         0.99        25.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01T 
       31.00        31.00        38.07         1.02        35.01        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        88.21         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  HPS6 MUTATED HPS6 WILD-TYPE 
          1.02           0.00 
  HPS6 MUTATED HPS6 WILD-TYPE 
         49.41         148.01 
  HPS6 MUTATED HPS6 WILD-TYPE 
         21.21          20.12 
[1] "1.0 - 49.4 (21.2)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.1"
D1403V2, continuous
D1403V3, binary
                cls
clus               0   1
  HPS6 MUTATED     6   1
  HPS6 WILD-TYPE 360 118
[1] "tbl2"
                cls
clus             [,1] [,2]
  HPS6 MUTATED      6    1
  HPS6 WILD-TYPE  360  118
        clus
vv       HPS6 MUTATED HPS6 WILD-TYPE
  COLON             6            360
  RECTUM            1            118
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  HPS6 MUTATED         2        0        1         2         1         0
  HPS6 WILD-TYPE      89        1       31       136         9         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  HPS6 MUTATED           1          0          0          0        0         0
  HPS6 WILD-TYPE        23         11         59         42       48        18
                vv
clus             STAGE IVB
  HPS6 MUTATED           0
  HPS6 WILD-TYPE         1
D1403V4, multiclass
            clus
vv           HPS6 MUTATED HPS6 WILD-TYPE
  STAGE I               2             89
  STAGE IA              0              1
  STAGE II              1             31
  STAGE IIA             2            136
  STAGE IIB             1              9
  STAGE IIC             0              1
  STAGE III             1             23
  STAGE IIIA            0             11
  STAGE IIIB            0             59
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  HPS6 MUTATED     0   2   4   1
  HPS6 WILD-TYPE  17  90 325  49
D1403V5, multiclass
    clus
vv   HPS6 MUTATED HPS6 WILD-TYPE
  T1            0             17
  T2            2             90
  T3            4            325
  T4            1             49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  HPS6 MUTATED     6   1   0
  HPS6 WILD-TYPE 281 112  87
D1403V6, multiclass
    clus
vv   HPS6 MUTATED HPS6 WILD-TYPE
  N0            6            281
  N1            1            112
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1403V7, binary
                cls
clus               0   1
  HPS6 MUTATED     4   0
  HPS6 WILD-TYPE 371  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  HPS6 MUTATED      4    0
  HPS6 WILD-TYPE  371   65
   clus
vv  HPS6 MUTATED HPS6 WILD-TYPE
  0            4            371
  1            0             65
[1] 2 2
[1] FALSE
D1403V8, binary
                cls
clus               0   1
  HPS6 MUTATED     5   2
  HPS6 WILD-TYPE 220 262
[1] "tbl2"
                cls
clus             [,1] [,2]
  HPS6 MUTATED      5    2
  HPS6 WILD-TYPE  220  262
        clus
vv       HPS6 MUTATED HPS6 WILD-TYPE
  FEMALE            5            220
  MALE              2            262
[1] 2 2
[1] FALSE
D1403V9, binary
                cls
clus               0   1
  HPS6 MUTATED     5   0
  HPS6 WILD-TYPE 345  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  HPS6 MUTATED      5    0
  HPS6 WILD-TYPE  345   22
     clus
vv    HPS6 MUTATED HPS6 WILD-TYPE
  NO             5            345
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  HPS6 MUTATED                      5                             1
  HPS6 WILD-TYPE                  310                            46
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  HPS6 MUTATED                       1                              0
  HPS6 WILD-TYPE                   105                             10
D1403V10, multiclass
                                clus
vv                               HPS6 MUTATED HPS6 WILD-TYPE
  COLON ADENOCARCINOMA                      5            310
  COLON MUCINOUS ADENOCARCINOMA             1             46
  RECTAL ADENOCARCINOMA                     1            105
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  HPS6 MUTATED     5   0   0   1
  HPS6 WILD-TYPE 340   4  31  24
D1403V11, multiclass
    clus
vv   HPS6 MUTATED HPS6 WILD-TYPE
  R0            5            340
  R1            0              4
  R2            0             31
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1403V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HPS6 MUTATED                                  0     0
  HPS6 WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  HPS6 MUTATED                           0     3
  HPS6 WILD-TYPE                        22   223
D1403V13, multiclass
                                  clus
vv                                 HPS6 MUTATED HPS6 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       3            223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1404) Variable = AP4B1 MUTATION ANALYSIS
D1404V1, survival
                 sevent
clus2               0   1
  AP4B1 MUTATED    10   2
  AP4B1 WILD-TYPE 368  91
  AP4B1 MUTATED AP4B1 WILD-TYPE 
             12             459 
  AP4B1 MUTATED AP4B1 WILD-TYPE 
              2              91 
$`AP4B1 MUTATED`
TCGA-A6-5665 TCGA-A6-6780 TCGA-AA-3510 TCGA-AA-3713 TCGA-AA-3977 TCGA-AA-A010 
       22.06        20.12        63.98        19.04        25.02        34.98 
TCGA-CK-4952 TCGA-CM-5344 TCGA-D5-6532 TCGA-DM-A0XD TCGA-DM-A1DB TCGA-F4-6703 
       15.62        22.03        18.25        24.43        44.32        47.87 

$`AP4B1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       85.05        26.99        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
       17.56       148.01        85.45        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5349 
       37.02        25.02        13.02        29.06        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       20.19         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
      140.38         7.50       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6704 TCGA-F4-6805 
        8.61        31.96        35.74         6.18         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  AP4B1 MUTATED AP4B1 WILD-TYPE 
          15.62            0.00 
  AP4B1 MUTATED AP4B1 WILD-TYPE 
          63.98          148.01 
  AP4B1 MUTATED AP4B1 WILD-TYPE 
         23.245          20.020 
[1] "15.6 - 64.0 (23.2)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.4"
D1404V2, continuous
D1404V3, binary
                 cls
clus                0   1
  AP4B1 MUTATED    12   0
  AP4B1 WILD-TYPE 354 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AP4B1 MUTATED     12    0
  AP4B1 WILD-TYPE  354  119
        clus
vv       AP4B1 MUTATED AP4B1 WILD-TYPE
  COLON             12             354
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  AP4B1 MUTATED         0        0        1         6         1         0
  AP4B1 WILD-TYPE      91        1       31       132         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AP4B1 MUTATED           0          0          1          1        1         0
  AP4B1 WILD-TYPE        24         11         58         41       47        18
                 vv
clus              STAGE IVB
  AP4B1 MUTATED           0
  AP4B1 WILD-TYPE         1
D1404V4, multiclass
            clus
vv           AP4B1 MUTATED AP4B1 WILD-TYPE
  STAGE I                0              91
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              6             132
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             1              41
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  AP4B1 MUTATED     0   1   9   2
  AP4B1 WILD-TYPE  17  91 320  48
D1404V5, multiclass
    clus
vv   AP4B1 MUTATED AP4B1 WILD-TYPE
  T1             0              17
  T2             1              91
  T3             9             320
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  AP4B1 MUTATED    10   1   1
  AP4B1 WILD-TYPE 277 112  86
D1404V6, multiclass
    clus
vv   AP4B1 MUTATED AP4B1 WILD-TYPE
  N0            10             277
  N1             1             112
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1404V7, binary
                 cls
clus                0   1
  AP4B1 MUTATED     9   1
  AP4B1 WILD-TYPE 366  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AP4B1 MUTATED      9    1
  AP4B1 WILD-TYPE  366   64
   clus
vv  AP4B1 MUTATED AP4B1 WILD-TYPE
  0             9             366
  1             1              64
[1] 2 2
[1] FALSE
D1404V8, binary
                 cls
clus                0   1
  AP4B1 MUTATED     4   8
  AP4B1 WILD-TYPE 221 256
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AP4B1 MUTATED      4    8
  AP4B1 WILD-TYPE  221  256
        clus
vv       AP4B1 MUTATED AP4B1 WILD-TYPE
  FEMALE             4             221
  MALE               8             256
[1] 2 2
[1] FALSE
D1404V9, binary
                 cls
clus                0   1
  AP4B1 MUTATED     8   1
  AP4B1 WILD-TYPE 342  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AP4B1 MUTATED      8    1
  AP4B1 WILD-TYPE  342   21
     clus
vv    AP4B1 MUTATED AP4B1 WILD-TYPE
  NO              8             342
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  AP4B1 MUTATED                     10                             2
  AP4B1 WILD-TYPE                  305                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  AP4B1 MUTATED                       0                              0
  AP4B1 WILD-TYPE                   106                             10
D1404V10, multiclass
                                clus
vv                               AP4B1 MUTATED AP4B1 WILD-TYPE
  COLON ADENOCARCINOMA                      10             305
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  AP4B1 MUTATED     6   0   1   1
  AP4B1 WILD-TYPE 339   4  30  24
D1404V11, multiclass
    clus
vv   AP4B1 MUTATED AP4B1 WILD-TYPE
  R0             6             339
  R1             0               4
  R2             1              30
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1404V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AP4B1 MUTATED                                  0     0
  AP4B1 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  AP4B1 MUTATED                           0     8
  AP4B1 WILD-TYPE                        22   218
D1404V13, multiclass
                                  clus
vv                                 AP4B1 MUTATED AP4B1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        8             218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1405) Variable = STK38 MUTATION ANALYSIS
D1405V1, survival
                 sevent
clus2               0   1
  STK38 MUTATED    10   1
  STK38 WILD-TYPE 368  92
  STK38 MUTATED STK38 WILD-TYPE 
             11             460 
  STK38 MUTATED STK38 WILD-TYPE 
              1              92 
$`STK38 MUTATED`
TCGA-A6-6141 TCGA-AA-3856 TCGA-AZ-6599 TCGA-CK-4950 TCGA-CM-6172 TCGA-CM-6680 
        8.38         0.99         6.77        85.45        11.01        12.03 
TCGA-G4-6628 TCGA-AF-6655 TCGA-AG-A002 TCGA-EI-6510 TCGA-F5-6813 
       79.69        20.02        20.98        18.28         0.69 

$`STK38 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 
       22.09        22.06        32.71        27.09        22.52        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
       32.05        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 
      106.75        22.36        62.79        88.21        49.41        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 
       12.76        10.06        14.30        17.56       148.01        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       13.02        15.02        14.04        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.08        11.01        10.06        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 
       13.78        35.80        26.17        91.79        46.75        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       14.50        16.83        15.39        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       19.96        20.91         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66        55.76        26.43 

  STK38 MUTATED STK38 WILD-TYPE 
           0.69            0.00 
  STK38 MUTATED STK38 WILD-TYPE 
          85.45          148.01 
  STK38 MUTATED STK38 WILD-TYPE 
          12.03           20.73 
[1] "0.7 - 85.5 (12.0)"  "0.0 - 148.0 (20.7)"
[1] "hr=" "2"  
D1405V2, continuous
D1405V3, binary
                 cls
clus                0   1
  STK38 MUTATED     7   4
  STK38 WILD-TYPE 359 115
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STK38 MUTATED      7    4
  STK38 WILD-TYPE  359  115
        clus
vv       STK38 MUTATED STK38 WILD-TYPE
  COLON              7             359
  RECTUM             4             115
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  STK38 MUTATED         3        0        0         2         0         0
  STK38 WILD-TYPE      88        1       32       136        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  STK38 MUTATED           0          1          3          1        0         1
  STK38 WILD-TYPE        24         10         56         41       48        17
                 vv
clus              STAGE IVB
  STK38 MUTATED           0
  STK38 WILD-TYPE         1
D1405V4, multiclass
            clus
vv           STK38 MUTATED STK38 WILD-TYPE
  STAGE I                3              88
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              2             136
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             1              10
  STAGE IIIB             3              56
  STAGE IIIC             1              41
  STAGE IV               0              48
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  STK38 MUTATED     0   5   5   1
  STK38 WILD-TYPE  17  87 324  49
D1405V5, multiclass
    clus
vv   STK38 MUTATED STK38 WILD-TYPE
  T1             0              17
  T2             5              87
  T3             5             324
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  STK38 MUTATED     6   3   2
  STK38 WILD-TYPE 281 110  85
D1405V6, multiclass
    clus
vv   STK38 MUTATED STK38 WILD-TYPE
  N0             6             281
  N1             3             110
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1405V7, binary
                 cls
clus                0   1
  STK38 MUTATED     9   0
  STK38 WILD-TYPE 366  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STK38 MUTATED      9    0
  STK38 WILD-TYPE  366   65
   clus
vv  STK38 MUTATED STK38 WILD-TYPE
  0             9             366
  1             0              65
[1] 2 2
[1] FALSE
D1405V8, binary
                 cls
clus                0   1
  STK38 MUTATED     4   7
  STK38 WILD-TYPE 221 257
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STK38 MUTATED      4    7
  STK38 WILD-TYPE  221  257
        clus
vv       STK38 MUTATED STK38 WILD-TYPE
  FEMALE             4             221
  MALE               7             257
[1] 2 2
[1] FALSE
D1405V9, binary
                 cls
clus                0   1
  STK38 MUTATED     9   0
  STK38 WILD-TYPE 341  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STK38 MUTATED      9    0
  STK38 WILD-TYPE  341   22
     clus
vv    STK38 MUTATED STK38 WILD-TYPE
  NO              9             341
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  STK38 MUTATED                      7                             0
  STK38 WILD-TYPE                  308                            47
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  STK38 MUTATED                       4                              0
  STK38 WILD-TYPE                   102                             10
D1405V10, multiclass
                                clus
vv                               STK38 MUTATED STK38 WILD-TYPE
  COLON ADENOCARCINOMA                       7             308
  COLON MUCINOUS ADENOCARCINOMA              0              47
  RECTAL ADENOCARCINOMA                      4             102
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  STK38 MUTATED     8   1   0   0
  STK38 WILD-TYPE 337   3  31  25
D1405V11, multiclass
    clus
vv   STK38 MUTATED STK38 WILD-TYPE
  R0             8             337
  R1             1               3
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1405V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  STK38 MUTATED                                  0     0
  STK38 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  STK38 MUTATED                           2     7
  STK38 WILD-TYPE                        20   219
D1405V13, multiclass
                                  clus
vv                                 STK38 MUTATED STK38 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    2              20
  WHITE                                        7             219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1406) Variable = PRKCD MUTATION ANALYSIS
D1406V1, survival
                 sevent
clus2               0   1
  PRKCD MUTATED    12   0
  PRKCD WILD-TYPE 366  93
  PRKCD MUTATED PRKCD WILD-TYPE 
             12             459 
  PRKCD MUTATED PRKCD WILD-TYPE 
              0              93 
$`PRKCD MUTATED`
TCGA-A6-5661 TCGA-A6-5665 TCGA-A6-6781 TCGA-AA-3710 TCGA-AA-3815 TCGA-AA-A01R 
       33.53        22.06        19.66        26.99        33.04        35.01 
TCGA-AD-5900 TCGA-CK-4947 TCGA-CM-6162 TCGA-D5-6541 TCGA-D5-6930 TCGA-D5-6931 
        0.07        17.56        12.00        15.58         1.51        12.00 

$`PRKCD WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
       85.05        19.04        19.04        10.06        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
        1.02         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 
        0.92        41.00        39.98        18.05        40.96        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4948 
        0.07        12.20        12.76        10.06        14.30       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       15.02         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       17.13        12.49        16.14         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  PRKCD MUTATED PRKCD WILD-TYPE 
           0.07            0.00 
  PRKCD MUTATED PRKCD WILD-TYPE 
          35.01          148.01 
  PRKCD MUTATED PRKCD WILD-TYPE 
          18.61           20.28 
[1] "0.1 - 35.0 (18.6)"  "0.0 - 148.0 (20.3)"
[1] "hr="     "9200000"
D1406V2, continuous
D1406V3, binary
                 cls
clus                0   1
  PRKCD MUTATED    13   0
  PRKCD WILD-TYPE 353 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRKCD MUTATED     13    0
  PRKCD WILD-TYPE  353  119
        clus
vv       PRKCD MUTATED PRKCD WILD-TYPE
  COLON             13             353
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PRKCD MUTATED         1        0        0         7         0         0
  PRKCD WILD-TYPE      90        1       32       131        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PRKCD MUTATED           1          0          2          2        0         0
  PRKCD WILD-TYPE        23         11         57         40       48        18
                 vv
clus              STAGE IVB
  PRKCD MUTATED           0
  PRKCD WILD-TYPE         1
D1406V4, multiclass
            clus
vv           PRKCD MUTATED PRKCD WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              7             131
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             2              57
  STAGE IIIC             2              40
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PRKCD MUTATED     0   1   9   3
  PRKCD WILD-TYPE  17  91 320  47
D1406V5, multiclass
    clus
vv   PRKCD MUTATED PRKCD WILD-TYPE
  T1             0              17
  T2             1              91
  T3             9             320
  T4             3              47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  PRKCD MUTATED     8   3   2
  PRKCD WILD-TYPE 279 110  85
D1406V6, multiclass
    clus
vv   PRKCD MUTATED PRKCD WILD-TYPE
  N0             8             279
  N1             3             110
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1406V7, binary
                 cls
clus                0   1
  PRKCD MUTATED    11   0
  PRKCD WILD-TYPE 364  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRKCD MUTATED     11    0
  PRKCD WILD-TYPE  364   65
   clus
vv  PRKCD MUTATED PRKCD WILD-TYPE
  0            11             364
  1             0              65
[1] 2 2
[1] FALSE
D1406V8, binary
                 cls
clus                0   1
  PRKCD MUTATED     7   6
  PRKCD WILD-TYPE 218 258
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRKCD MUTATED      7    6
  PRKCD WILD-TYPE  218  258
        clus
vv       PRKCD MUTATED PRKCD WILD-TYPE
  FEMALE             7             218
  MALE               6             258
[1] 2 2
[1] FALSE
D1406V9, binary
                 cls
clus                0   1
  PRKCD MUTATED     9   1
  PRKCD WILD-TYPE 341  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRKCD MUTATED      9    1
  PRKCD WILD-TYPE  341   21
     clus
vv    PRKCD MUTATED PRKCD WILD-TYPE
  NO              9             341
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PRKCD MUTATED                      8                             5
  PRKCD WILD-TYPE                  307                            42
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PRKCD MUTATED                       0                              0
  PRKCD WILD-TYPE                   106                             10
D1406V10, multiclass
                                clus
vv                               PRKCD MUTATED PRKCD WILD-TYPE
  COLON ADENOCARCINOMA                       8             307
  COLON MUCINOUS ADENOCARCINOMA              5              42
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  PRKCD MUTATED    12   0   0   1
  PRKCD WILD-TYPE 333   4  31  24
D1406V11, multiclass
    clus
vv   PRKCD MUTATED PRKCD WILD-TYPE
  R0            12             333
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1406V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PRKCD MUTATED                                  0     0
  PRKCD WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PRKCD MUTATED                           1     8
  PRKCD WILD-TYPE                        21   218
D1406V13, multiclass
                                  clus
vv                                 PRKCD MUTATED PRKCD WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        8             218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1407) Variable = HIST1H2BC MUTATION ANALYSIS
D1407V1, survival
                     sevent
clus2                   0   1
  HIST1H2BC MUTATED     4   0
  HIST1H2BC WILD-TYPE 374  93
  HIST1H2BC MUTATED HIST1H2BC WILD-TYPE 
                  4                 467 
  HIST1H2BC MUTATED HIST1H2BC WILD-TYPE 
                  0                  93 
$`HIST1H2BC MUTATED`
TCGA-A6-5665 TCGA-AA-3510 TCGA-AA-A010 TCGA-G4-6299 
       22.06        63.98        34.98        74.56 

$`HIST1H2BC WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6303 
       13.25         0.53        47.41        35.31       133.18        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  HIST1H2BC MUTATED HIST1H2BC WILD-TYPE 
              22.06                0.00 
  HIST1H2BC MUTATED HIST1H2BC WILD-TYPE 
              74.56              148.01 
  HIST1H2BC MUTATED HIST1H2BC WILD-TYPE 
              49.48               20.05 
[1] "22.1 - 74.6 (49.5)" "0.0 - 148.0 (20.1)"
[1] "hr="     "9200000"
D1407V2, continuous
D1407V3, binary
                     cls
clus                    0   1
  HIST1H2BC MUTATED     4   0
  HIST1H2BC WILD-TYPE 362 119
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  HIST1H2BC MUTATED      4    0
  HIST1H2BC WILD-TYPE  362  119
        clus
vv       HIST1H2BC MUTATED HIST1H2BC WILD-TYPE
  COLON                  4                 362
  RECTUM                 0                 119
[1] 2 2
[1] FALSE
                     vv
clus                  STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  HIST1H2BC MUTATED         0        0        1         1         1         0
  HIST1H2BC WILD-TYPE      91        1       31       137         9         1
                     vv
clus                  STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HIST1H2BC MUTATED           0          0          0          1        0
  HIST1H2BC WILD-TYPE        24         11         59         41       48
                     vv
clus                  STAGE IVA STAGE IVB
  HIST1H2BC MUTATED           0         0
  HIST1H2BC WILD-TYPE        18         1
D1407V4, multiclass
            clus
vv           HIST1H2BC MUTATED HIST1H2BC WILD-TYPE
  STAGE I                    0                  91
  STAGE IA                   0                   1
  STAGE II                   1                  31
  STAGE IIA                  1                 137
  STAGE IIB                  1                   9
  STAGE IIC                  0                   1
  STAGE III                  0                  24
  STAGE IIIA                 0                  11
  STAGE IIIB                 0                  59
  STAGE IIIC                 1                  41
  STAGE IV                   0                  48
  STAGE IVA                  0                  18
  STAGE IVB                  0                   1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                   T1  T2  T3  T4
  HIST1H2BC MUTATED     0   0   3   1
  HIST1H2BC WILD-TYPE  17  92 326  49
D1407V5, multiclass
    clus
vv   HIST1H2BC MUTATED HIST1H2BC WILD-TYPE
  T1                 0                  17
  T2                 0                  92
  T3                 3                 326
  T4                 1                  49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                   N0  N1  N2
  HIST1H2BC MUTATED     3   0   1
  HIST1H2BC WILD-TYPE 284 113  86
D1407V6, multiclass
    clus
vv   HIST1H2BC MUTATED HIST1H2BC WILD-TYPE
  N0                 3                 284
  N1                 0                 113
  N2                 1                  86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1407V7, binary
                     cls
clus                    0   1
  HIST1H2BC MUTATED     4   0
  HIST1H2BC WILD-TYPE 371  65
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  HIST1H2BC MUTATED      4    0
  HIST1H2BC WILD-TYPE  371   65
   clus
vv  HIST1H2BC MUTATED HIST1H2BC WILD-TYPE
  0                 4                 371
  1                 0                  65
[1] 2 2
[1] FALSE
D1407V8, binary
                     cls
clus                    0   1
  HIST1H2BC MUTATED     2   2
  HIST1H2BC WILD-TYPE 223 262
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  HIST1H2BC MUTATED      2    2
  HIST1H2BC WILD-TYPE  223  262
        clus
vv       HIST1H2BC MUTATED HIST1H2BC WILD-TYPE
  FEMALE                 2                 223
  MALE                   2                 262
[1] 2 2
[1] FALSE
D1407V9, binary
                     cls
clus                    0   1
  HIST1H2BC MUTATED     4   0
  HIST1H2BC WILD-TYPE 346  22
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  HIST1H2BC MUTATED      4    0
  HIST1H2BC WILD-TYPE  346   22
     clus
vv    HIST1H2BC MUTATED HIST1H2BC WILD-TYPE
  NO                  4                 346
  YES                 0                  22
[1] 2 2
[1] FALSE
                     vv
clus                  COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  HIST1H2BC MUTATED                      4                             0
  HIST1H2BC WILD-TYPE                  311                            47
                     vv
clus                  RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  HIST1H2BC MUTATED                       0                              0
  HIST1H2BC WILD-TYPE                   106                             10
D1407V10, multiclass
                                clus
vv                               HIST1H2BC MUTATED HIST1H2BC WILD-TYPE
  COLON ADENOCARCINOMA                           4                 311
  COLON MUCINOUS ADENOCARCINOMA                  0                  47
  RECTAL ADENOCARCINOMA                          0                 106
  RECTAL MUCINOUS ADENOCARCINOMA                 0                  10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                   R0  R1  R2  RX
  HIST1H2BC MUTATED     4   0   0   0
  HIST1H2BC WILD-TYPE 341   4  31  25
D1407V11, multiclass
    clus
vv   HIST1H2BC MUTATED HIST1H2BC WILD-TYPE
  R0                 4                 341
  R1                 0                   4
  R2                 0                  31
  RX                 0                  25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1407V12, continuous
                     vv
clus                  AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HIST1H2BC MUTATED                                  0     0
  HIST1H2BC WILD-TYPE                                1    11
                     vv
clus                  BLACK OR AFRICAN AMERICAN WHITE
  HIST1H2BC MUTATED                           0     2
  HIST1H2BC WILD-TYPE                        22   224
D1407V13, multiclass
[1] "Remove cluster labels:" "HIST1H2BC MUTATED"     
clus
  HIST1H2BC MUTATED HIST1H2BC WILD-TYPE 
                  2                 258 
         TCGA-A6-2671          TCGA-A6-2672          TCGA-A6-2674 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-A6-2676          TCGA-A6-2677          TCGA-A6-2678 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-A6-2683          TCGA-A6-3807          TCGA-A6-3808 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-A6-3809          TCGA-A6-3810          TCGA-A6-4105 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-A6-5656          TCGA-A6-5657          TCGA-A6-5659 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-A6-5660          TCGA-A6-5661          TCGA-A6-5662 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-A6-5664          TCGA-A6-5666          TCGA-A6-6137 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-A6-6138          TCGA-A6-6141          TCGA-A6-6142 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-A6-6648          TCGA-A6-6649          TCGA-A6-6651 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-A6-6652          TCGA-A6-6653          TCGA-A6-6654 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-A6-6780          TCGA-A6-6781          TCGA-A6-6782 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-AD-5900          TCGA-AD-6548          TCGA-AD-6888 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-AD-6889          TCGA-AD-6890          TCGA-AD-6895 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-AD-6899          TCGA-AD-6901          TCGA-AD-6963 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-AD-6964          TCGA-AD-6965          TCGA-AU-3779 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-AU-6004          TCGA-AY-4070          TCGA-AY-4071 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-AY-5543          TCGA-AY-6196          TCGA-AY-6197 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-AY-6386          TCGA-AZ-4315          TCGA-AZ-4323 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-AZ-4616          TCGA-AZ-4681          TCGA-AZ-4682 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-AZ-5403          TCGA-AZ-5407          TCGA-AZ-6598 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-AZ-6599          TCGA-AZ-6600          TCGA-AZ-6601 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-AZ-6603          TCGA-AZ-6605          TCGA-AZ-6606 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-AZ-6607          TCGA-AZ-6608          TCGA-CA-5254 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-CA-5255          TCGA-CA-5796          TCGA-CA-5797 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-CA-6715          TCGA-CA-6716          TCGA-CA-6717 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-CA-6718          TCGA-CA-6719          TCGA-CK-4947 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-CK-4948          TCGA-CK-4950          TCGA-CK-4952 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-CK-5912          TCGA-CK-5913          TCGA-CK-5914 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-CK-5915          TCGA-CK-5916          TCGA-CK-6746 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-CK-6747          TCGA-CK-6748          TCGA-CK-6751 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-CM-4743          TCGA-CM-4744          TCGA-CM-4746 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-CM-4747          TCGA-CM-4752          TCGA-CM-5341 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-CM-5344          TCGA-CM-5348          TCGA-CM-5349 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-CM-5860          TCGA-CM-5861          TCGA-CM-5862 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-CM-5863          TCGA-CM-5864          TCGA-CM-5868 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-CM-6161          TCGA-CM-6162          TCGA-CM-6163 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-CM-6164          TCGA-CM-6165          TCGA-CM-6166 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-CM-6167          TCGA-CM-6168          TCGA-CM-6169 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-CM-6170          TCGA-CM-6171          TCGA-CM-6172 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-CM-6674          TCGA-CM-6675          TCGA-CM-6676 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-CM-6677          TCGA-CM-6678          TCGA-CM-6679 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-CM-6680          TCGA-D5-5537          TCGA-D5-5538 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-D5-5539          TCGA-D5-5540          TCGA-D5-5541 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-D5-6529          TCGA-D5-6532          TCGA-D5-6533 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-D5-6534          TCGA-D5-6535          TCGA-D5-6536 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-D5-6537          TCGA-D5-6538          TCGA-D5-6539 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-D5-6540          TCGA-D5-6541          TCGA-D5-6898 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-D5-6920          TCGA-D5-6922          TCGA-D5-6923 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-D5-6924          TCGA-D5-6926          TCGA-D5-6927 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-D5-6928          TCGA-D5-6929          TCGA-D5-6930 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-D5-6931          TCGA-D5-6932          TCGA-D5-7000 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-DM-A0X9          TCGA-DM-A0XD          TCGA-DM-A0XF 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-DM-A1D0          TCGA-DM-A1D4          TCGA-DM-A1D6 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-DM-A1D7          TCGA-DM-A1D8          TCGA-DM-A1D9 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-DM-A1DA          TCGA-DM-A1DB          TCGA-DM-A1HA 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-DM-A1HB          TCGA-DM-A282          TCGA-DM-A285 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-DM-A28C          TCGA-DM-A28E          TCGA-DM-A28F 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-DM-A28G          TCGA-DM-A28H          TCGA-DM-A28K 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-F4-6459          TCGA-F4-6460          TCGA-F4-6569 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-F4-6570          TCGA-F4-6703          TCGA-F4-6704 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-F4-6805          TCGA-F4-6806          TCGA-F4-6807 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-F4-6808          TCGA-F4-6809          TCGA-F4-6854 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-F4-6855          TCGA-F4-6856          TCGA-G4-6293 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-G4-6303          TCGA-G4-6304          TCGA-G4-6306 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-G4-6307          TCGA-G4-6309          TCGA-G4-6310 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-G4-6315          TCGA-G4-6317          TCGA-G4-6321 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-G4-6323          TCGA-G4-6586          TCGA-G4-6588 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-G4-6625          TCGA-G4-6626          TCGA-G4-6628 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-AF-2687          TCGA-AF-2689          TCGA-AF-2691 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-AF-2692          TCGA-AF-2693          TCGA-AF-3400 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-AF-3913          TCGA-AF-4110          TCGA-AF-5654 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-AF-6136          TCGA-AF-6655          TCGA-AF-6672 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-AH-6544          TCGA-AH-6547          TCGA-AH-6549 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-AH-6643          TCGA-AH-6644          TCGA-CI-6619 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-CI-6620          TCGA-CI-6621          TCGA-CI-6622 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-CI-6624          TCGA-CL-5917          TCGA-CL-5918 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-DC-5337          TCGA-DC-5869          TCGA-DC-6155 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-DC-6157          TCGA-DC-6158          TCGA-DC-6160 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-DC-6681          TCGA-DC-6682          TCGA-DC-6683 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-DT-5265          TCGA-DY-A0XA          TCGA-DY-A1DC 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-DY-A1DD          TCGA-DY-A1DF          TCGA-DY-A1DG 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-DY-A1H8          TCGA-EF-5830          TCGA-EI-6506 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-EI-6507          TCGA-EI-6508          TCGA-EI-6510 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-F5-6464          TCGA-F5-6465          TCGA-F5-6571 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-F5-6702          TCGA-F5-6811          TCGA-F5-6812 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 
         TCGA-F5-6813          TCGA-G5-6235          TCGA-G5-6641 
"HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" "HIST1H2BC WILD-TYPE" 

Clustering(1408) Variable = RIMS2 MUTATION ANALYSIS
D1408V1, survival
                 sevent
clus2               0   1
  RIMS2 MUTATED    27  12
  RIMS2 WILD-TYPE 351  81
  RIMS2 MUTATED RIMS2 WILD-TYPE 
             39             432 
  RIMS2 MUTATED RIMS2 WILD-TYPE 
             12              81 
$`RIMS2 MUTATED`
TCGA-A6-5660 TCGA-A6-6141 TCGA-AA-3672 TCGA-AA-3680 TCGA-AA-3819 TCGA-AA-3821 
       29.19         8.38         0.92        11.01        25.02         1.02 
TCGA-AA-3930 TCGA-AA-3949 TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A024 
        2.01        26.01        25.02         4.01        34.98        39.06 
TCGA-AD-6964 TCGA-AU-3779 TCGA-AZ-4315 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 
       10.88        14.50        58.39        88.21        49.41        12.10 
TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4952 TCGA-CM-4747 
        0.07        12.76        10.06        17.56        15.62        25.02 
TCGA-CM-6674 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6928 
       12.95         1.32        15.12        16.14        15.58        11.64 
TCGA-DM-A28G TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6323 TCGA-G4-6588 TCGA-AG-A002 
       60.79        55.04        85.48        13.78        26.17        20.98 
TCGA-DY-A1DC TCGA-DY-A1DG TCGA-F5-6464 
       41.36        51.48         9.96 

$`RIMS2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 
       22.06        32.71        27.09        22.52        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
       54.02         2.01        14.01        50.04        47.01        15.02 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        0.99        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-3952 
       31.00        12.99        24.00        33.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       37.02        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       22.42        27.42         0.20        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       33.01        21.44        17.82         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       22.36        62.79         6.77       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 
        3.29        12.20        14.30       148.01        85.45        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       23.05        20.02        37.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       14.04        11.01        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 
       55.92        20.19        18.25        43.27        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       17.13        12.49         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
       14.30         9.04         9.44         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
      119.93        35.97       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6310 
      133.18        74.56        65.85        53.62        44.68        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 
       61.91        36.00        22.09        35.80        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 
        5.29       126.44        57.24        24.13        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6465 TCGA-F5-6571 
       20.55        19.96        20.91        18.28        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  RIMS2 MUTATED RIMS2 WILD-TYPE 
           0.07            0.00 
  RIMS2 MUTATED RIMS2 WILD-TYPE 
          88.21          148.01 
  RIMS2 MUTATED RIMS2 WILD-TYPE 
          15.62           20.73 
[1] "0.1 - 88.2 (15.6)"  "0.0 - 148.0 (20.7)"
[1] "hr=" "1.7"
D1408V2, continuous
D1408V3, binary
                 cls
clus                0   1
  RIMS2 MUTATED    36   4
  RIMS2 WILD-TYPE 330 115
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RIMS2 MUTATED     36    4
  RIMS2 WILD-TYPE  330  115
        clus
vv       RIMS2 MUTATED RIMS2 WILD-TYPE
  COLON             36             330
  RECTUM             4             115
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RIMS2 MUTATED         4        1        2        13         2         0
  RIMS2 WILD-TYPE      87        0       30       125         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RIMS2 MUTATED           1          0          7          3        3         2
  RIMS2 WILD-TYPE        23         11         52         39       45        16
                 vv
clus              STAGE IVB
  RIMS2 MUTATED           0
  RIMS2 WILD-TYPE         1
D1408V4, multiclass
            clus
vv           RIMS2 MUTATED RIMS2 WILD-TYPE
  STAGE I                4              87
  STAGE IA               1               0
  STAGE II               2              30
  STAGE IIA             13             125
  STAGE IIB              2               8
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             7              52
  STAGE IIIC             3              39
  STAGE IV               3              45
  STAGE IVA              2              16
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  RIMS2 MUTATED     1   4  24  10
  RIMS2 WILD-TYPE  16  88 305  40
D1408V5, multiclass
    clus
vv   RIMS2 MUTATED RIMS2 WILD-TYPE
  T1             1              16
  T2             4              88
  T3            24             305
  T4            10              40
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  RIMS2 MUTATED    24  10   6
  RIMS2 WILD-TYPE 263 103  81
D1408V6, multiclass
    clus
vv   RIMS2 MUTATED RIMS2 WILD-TYPE
  N0            24             263
  N1            10             103
  N2             6              81
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1408V7, binary
                 cls
clus                0   1
  RIMS2 MUTATED    30   5
  RIMS2 WILD-TYPE 345  60
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RIMS2 MUTATED     30    5
  RIMS2 WILD-TYPE  345   60
   clus
vv  RIMS2 MUTATED RIMS2 WILD-TYPE
  0            30             345
  1             5              60
[1] 2 2
[1] FALSE
D1408V8, binary
                 cls
clus                0   1
  RIMS2 MUTATED    19  21
  RIMS2 WILD-TYPE 206 243
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RIMS2 MUTATED     19   21
  RIMS2 WILD-TYPE  206  243
        clus
vv       RIMS2 MUTATED RIMS2 WILD-TYPE
  FEMALE            19             206
  MALE              21             243
[1] 2 2
[1] FALSE
D1408V9, binary
                 cls
clus                0   1
  RIMS2 MUTATED    31   0
  RIMS2 WILD-TYPE 319  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RIMS2 MUTATED     31    0
  RIMS2 WILD-TYPE  319   22
     clus
vv    RIMS2 MUTATED RIMS2 WILD-TYPE
  NO             31             319
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  RIMS2 MUTATED                     28                             8
  RIMS2 WILD-TYPE                  287                            39
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  RIMS2 MUTATED                       4                              0
  RIMS2 WILD-TYPE                   102                             10
D1408V10, multiclass
                                clus
vv                               RIMS2 MUTATED RIMS2 WILD-TYPE
  COLON ADENOCARCINOMA                      28             287
  COLON MUCINOUS ADENOCARCINOMA              8              39
  RECTAL ADENOCARCINOMA                      4             102
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  RIMS2 MUTATED    22   0   2   6
  RIMS2 WILD-TYPE 323   4  29  19
D1408V11, multiclass
    clus
vv   RIMS2 MUTATED RIMS2 WILD-TYPE
  R0            22             323
  R1             0               4
  R2             2              29
  RX             6              19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1408V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RIMS2 MUTATED                                  0     3
  RIMS2 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  RIMS2 MUTATED                           5    20
  RIMS2 WILD-TYPE                        17   206
D1408V13, multiclass
                                  clus
vv                                 RIMS2 MUTATED RIMS2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        3               8
  BLACK OR AFRICAN AMERICAN                    5              17
  WHITE                                       20             206
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1409) Variable = LEMD1 MUTATION ANALYSIS
D1409V1, survival
                 sevent
clus2               0   1
  LEMD1 MUTATED     3   0
  LEMD1 WILD-TYPE 375  93
  LEMD1 MUTATED LEMD1 WILD-TYPE 
              3             468 
  LEMD1 MUTATED LEMD1 WILD-TYPE 
              0              93 
$`LEMD1 MUTATED`
TCGA-A6-5665 TCGA-AD-6895 TCGA-G4-6588 
       22.06         0.72        26.17 

$`LEMD1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       15.52        56.55         0.79         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  LEMD1 MUTATED LEMD1 WILD-TYPE 
           0.72            0.00 
  LEMD1 MUTATED LEMD1 WILD-TYPE 
          26.17          148.01 
  LEMD1 MUTATED LEMD1 WILD-TYPE 
         22.060          20.155 
[1] "0.7 - 26.2 (22.1)"  "0.0 - 148.0 (20.2)"
[1] "hr="     "3300000"
D1409V2, continuous
D1409V3, binary
                 cls
clus                0   1
  LEMD1 MUTATED     3   0
  LEMD1 WILD-TYPE 363 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LEMD1 MUTATED      3    0
  LEMD1 WILD-TYPE  363  119
        clus
vv       LEMD1 MUTATED LEMD1 WILD-TYPE
  COLON              3             363
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  LEMD1 MUTATED         0        0        0         2         0         0
  LEMD1 WILD-TYPE      91        1       32       136        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  LEMD1 MUTATED           0          0          0          0        0         0
  LEMD1 WILD-TYPE        24         11         59         42       48        18
                 vv
clus              STAGE IVB
  LEMD1 MUTATED           0
  LEMD1 WILD-TYPE         1
D1409V4, multiclass
[1] "Remove cluster labels:" "LEMD1 MUTATED"         
clus
  LEMD1 MUTATED LEMD1 WILD-TYPE 
              2             474 
     TCGA-A6-2671      TCGA-A6-2672      TCGA-A6-2674      TCGA-A6-2676 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-A6-2677      TCGA-A6-2678      TCGA-A6-2683      TCGA-A6-3807 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-A6-3808      TCGA-A6-3809      TCGA-A6-3810      TCGA-A6-4105 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-A6-5656      TCGA-A6-5657      TCGA-A6-5659      TCGA-A6-5660 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-A6-5661      TCGA-A6-5662      TCGA-A6-5664      TCGA-A6-5666 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-A6-6137      TCGA-A6-6138      TCGA-A6-6141      TCGA-A6-6142 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-A6-6648      TCGA-A6-6649      TCGA-A6-6651      TCGA-A6-6652 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-A6-6653      TCGA-A6-6654      TCGA-A6-6780      TCGA-A6-6781 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-A6-6782      TCGA-AA-3489      TCGA-AA-3492      TCGA-AA-3496 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-3502      TCGA-AA-3510      TCGA-AA-3511      TCGA-AA-3514 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-3516      TCGA-AA-3517      TCGA-AA-3518      TCGA-AA-3519 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-3520      TCGA-AA-3521      TCGA-AA-3522      TCGA-AA-3524 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-3525      TCGA-AA-3526      TCGA-AA-3527      TCGA-AA-3529 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-3530      TCGA-AA-3531      TCGA-AA-3532      TCGA-AA-3534 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-3538      TCGA-AA-3542      TCGA-AA-3543      TCGA-AA-3544 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-3548      TCGA-AA-3549      TCGA-AA-3552      TCGA-AA-3553 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-3554      TCGA-AA-3555      TCGA-AA-3556      TCGA-AA-3558 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-3560      TCGA-AA-3561      TCGA-AA-3562      TCGA-AA-3655 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-3660      TCGA-AA-3662      TCGA-AA-3663      TCGA-AA-3664 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-3666      TCGA-AA-3667      TCGA-AA-3672      TCGA-AA-3673 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-3678      TCGA-AA-3679      TCGA-AA-3680      TCGA-AA-3681 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-3684      TCGA-AA-3685      TCGA-AA-3688      TCGA-AA-3692 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-3693      TCGA-AA-3695      TCGA-AA-3696      TCGA-AA-3697 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-3710      TCGA-AA-3712      TCGA-AA-3713      TCGA-AA-3715 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-3811      TCGA-AA-3812      TCGA-AA-3814      TCGA-AA-3815 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-3818      TCGA-AA-3819      TCGA-AA-3821      TCGA-AA-3831 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-3833      TCGA-AA-3837      TCGA-AA-3842      TCGA-AA-3844 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-3845      TCGA-AA-3846      TCGA-AA-3848      TCGA-AA-3850 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-3851      TCGA-AA-3852      TCGA-AA-3854      TCGA-AA-3855 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-3856      TCGA-AA-3858      TCGA-AA-3860      TCGA-AA-3861 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-3864      TCGA-AA-3866      TCGA-AA-3867      TCGA-AA-3869 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-3870      TCGA-AA-3872      TCGA-AA-3875      TCGA-AA-3877 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-3930      TCGA-AA-3939      TCGA-AA-3941      TCGA-AA-3947 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-3949      TCGA-AA-3950      TCGA-AA-3952      TCGA-AA-3955 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-3956      TCGA-AA-3966      TCGA-AA-3968      TCGA-AA-3971 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-3972      TCGA-AA-3973      TCGA-AA-3975      TCGA-AA-3976 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-3979      TCGA-AA-3980      TCGA-AA-3982      TCGA-AA-3984 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-3986      TCGA-AA-3989      TCGA-AA-3994      TCGA-AA-A004 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-A00A      TCGA-AA-A00D      TCGA-AA-A00E      TCGA-AA-A00F 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-A00J      TCGA-AA-A00K      TCGA-AA-A00L      TCGA-AA-A00N 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-A00O      TCGA-AA-A00Q      TCGA-AA-A00R      TCGA-AA-A00U 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-A00W      TCGA-AA-A00Z      TCGA-AA-A010      TCGA-AA-A017 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-A01D      TCGA-AA-A01F      TCGA-AA-A01G      TCGA-AA-A01I 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-A01K      TCGA-AA-A01P      TCGA-AA-A01Q      TCGA-AA-A01R 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-A01S      TCGA-AA-A01T      TCGA-AA-A01V      TCGA-AA-A01X 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-A01Z      TCGA-AA-A022      TCGA-AA-A024      TCGA-AA-A029 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-A02F      TCGA-AA-A02H      TCGA-AA-A02J      TCGA-AA-A02K 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-A02O      TCGA-AA-A02W      TCGA-AA-A02Y      TCGA-AA-A03F 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-A03J      TCGA-AD-5900      TCGA-AD-6548      TCGA-AD-6888 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AD-6889      TCGA-AD-6899      TCGA-AU-3779      TCGA-AU-6004 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AY-4070      TCGA-AY-4071      TCGA-AY-5543      TCGA-AY-6196 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AY-6197      TCGA-AY-6386      TCGA-AZ-4315      TCGA-AZ-4323 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AZ-4616      TCGA-AZ-4681      TCGA-AZ-4682      TCGA-AZ-5403 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AZ-5407      TCGA-AZ-6598      TCGA-AZ-6599      TCGA-AZ-6600 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AZ-6601      TCGA-AZ-6605      TCGA-AZ-6606      TCGA-AZ-6607 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AZ-6608      TCGA-CA-5254      TCGA-CA-5255      TCGA-CA-5796 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-CA-5797      TCGA-CA-6715      TCGA-CA-6716      TCGA-CA-6717 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-CA-6718      TCGA-CA-6719      TCGA-CK-4947      TCGA-CK-4948 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-CK-4950      TCGA-CK-4952      TCGA-CK-5912      TCGA-CK-5913 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-CK-5914      TCGA-CK-5915      TCGA-CK-5916      TCGA-CK-6746 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-CK-6747      TCGA-CK-6748      TCGA-CK-6751      TCGA-CM-4743 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-CM-4744      TCGA-CM-4746      TCGA-CM-4747      TCGA-CM-4752 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-CM-5341      TCGA-CM-5344      TCGA-CM-5348      TCGA-CM-5349 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-CM-5860      TCGA-CM-5861      TCGA-CM-5862      TCGA-CM-5863 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-CM-5864      TCGA-CM-5868      TCGA-CM-6161      TCGA-CM-6162 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-CM-6163      TCGA-CM-6164      TCGA-CM-6165      TCGA-CM-6166 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-CM-6167      TCGA-CM-6168      TCGA-CM-6169      TCGA-CM-6170 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-CM-6171      TCGA-CM-6172      TCGA-CM-6674      TCGA-CM-6675 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-CM-6676      TCGA-CM-6677      TCGA-CM-6678      TCGA-CM-6679 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-CM-6680      TCGA-D5-5537      TCGA-D5-5538      TCGA-D5-5539 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-D5-5540      TCGA-D5-5541      TCGA-D5-6529      TCGA-D5-6532 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-D5-6533      TCGA-D5-6534      TCGA-D5-6535      TCGA-D5-6536 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-D5-6537      TCGA-D5-6538      TCGA-D5-6539      TCGA-D5-6540 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-D5-6541      TCGA-D5-6898      TCGA-D5-6920      TCGA-D5-6922 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-D5-6923      TCGA-D5-6924      TCGA-D5-6926      TCGA-D5-6927 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-D5-6928      TCGA-D5-6929      TCGA-D5-6930      TCGA-D5-6931 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-D5-6932      TCGA-D5-7000      TCGA-DM-A0X9      TCGA-DM-A0XD 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-DM-A0XF      TCGA-DM-A1D0      TCGA-DM-A1D4      TCGA-DM-A1D6 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-DM-A1D7      TCGA-DM-A1D9      TCGA-DM-A1DA      TCGA-DM-A1DB 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-DM-A1HA      TCGA-DM-A1HB      TCGA-DM-A282      TCGA-DM-A285 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-DM-A28C      TCGA-DM-A28E      TCGA-DM-A28F      TCGA-DM-A28G 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-DM-A28H      TCGA-DM-A28K      TCGA-F4-6459      TCGA-F4-6460 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-F4-6569      TCGA-F4-6570      TCGA-F4-6703      TCGA-F4-6704 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-F4-6805      TCGA-F4-6806      TCGA-F4-6807      TCGA-F4-6808 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-F4-6809      TCGA-F4-6854      TCGA-F4-6855      TCGA-F4-6856 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-G4-6293      TCGA-G4-6299      TCGA-G4-6303      TCGA-G4-6304 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-G4-6306      TCGA-G4-6307      TCGA-G4-6309      TCGA-G4-6310 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-G4-6315      TCGA-G4-6317      TCGA-G4-6321      TCGA-G4-6323 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-G4-6586      TCGA-G4-6625      TCGA-G4-6626      TCGA-G4-6628 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AF-2687      TCGA-AF-2689      TCGA-AF-2691      TCGA-AF-2692 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AF-2693      TCGA-AF-3400      TCGA-AF-3913      TCGA-AF-4110 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AF-5654      TCGA-AF-6136      TCGA-AF-6655      TCGA-AF-6672 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AG-3574      TCGA-AG-3575      TCGA-AG-3578      TCGA-AG-3580 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AG-3581      TCGA-AG-3582      TCGA-AG-3583      TCGA-AG-3584 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AG-3586      TCGA-AG-3587      TCGA-AG-3593      TCGA-AG-3594 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AG-3598      TCGA-AG-3599      TCGA-AG-3600      TCGA-AG-3601 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AG-3602      TCGA-AG-3605      TCGA-AG-3608      TCGA-AG-3609 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AG-3611      TCGA-AG-3612      TCGA-AG-3726      TCGA-AG-3727 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AG-3731      TCGA-AG-3732      TCGA-AG-3742      TCGA-AG-3878 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AG-3881      TCGA-AG-3882      TCGA-AG-3883      TCGA-AG-3885 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AG-3887      TCGA-AG-3890      TCGA-AG-3892      TCGA-AG-3893 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AG-3894      TCGA-AG-3896      TCGA-AG-3898      TCGA-AG-3901 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AG-3902      TCGA-AG-3909      TCGA-AG-3999      TCGA-AG-4001 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AG-4005      TCGA-AG-4007      TCGA-AG-4008      TCGA-AG-4015 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AG-A002      TCGA-AG-A008      TCGA-AG-A00C      TCGA-AG-A00H 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AG-A00Y      TCGA-AG-A011      TCGA-AG-A014      TCGA-AG-A015 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AG-A016      TCGA-AG-A01L      TCGA-AG-A01W      TCGA-AG-A01Y 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AG-A020      TCGA-AG-A025      TCGA-AG-A026      TCGA-AG-A02G 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AG-A02N      TCGA-AG-A02X      TCGA-AG-A032      TCGA-AG-A036 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AH-6643      TCGA-CI-6619      TCGA-CI-6620      TCGA-CI-6621 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-CI-6622      TCGA-CI-6624      TCGA-CL-5917      TCGA-CL-5918 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-DC-5337      TCGA-DC-5869      TCGA-DC-6155      TCGA-DC-6157 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-DC-6158      TCGA-DC-6160      TCGA-DC-6681      TCGA-DC-6682 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-DC-6683      TCGA-DT-5265      TCGA-DY-A0XA      TCGA-DY-A1DC 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-DY-A1DD      TCGA-DY-A1DF      TCGA-DY-A1DG      TCGA-DY-A1H8 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-EF-5830      TCGA-EI-6506      TCGA-EI-6507      TCGA-EI-6508 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-EI-6510      TCGA-F5-6464      TCGA-F5-6465      TCGA-F5-6571 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-F5-6702      TCGA-F5-6811      TCGA-F5-6812      TCGA-F5-6813 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-G5-6235      TCGA-G5-6641 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
                 vv
clus               T1  T2  T3  T4
  LEMD1 MUTATED     0   0   3   0
  LEMD1 WILD-TYPE  17  92 326  50
D1409V5, multiclass
    clus
vv   LEMD1 MUTATED LEMD1 WILD-TYPE
  T1             0              17
  T2             0              92
  T3             3             326
  T4             0              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  LEMD1 MUTATED     2   1   0
  LEMD1 WILD-TYPE 285 112  87
D1409V6, multiclass
    clus
vv   LEMD1 MUTATED LEMD1 WILD-TYPE
  N0             2             285
  N1             1             112
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1409V7, binary
                 cls
clus                0   1
  LEMD1 MUTATED     2   0
  LEMD1 WILD-TYPE 373  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LEMD1 MUTATED      2    0
  LEMD1 WILD-TYPE  373   65
   clus
vv  LEMD1 MUTATED LEMD1 WILD-TYPE
  0             2             373
  1             0              65
[1] 2 2
[1] FALSE
D1409V8, binary
                 cls
clus                0   1
  LEMD1 MUTATED     2   1
  LEMD1 WILD-TYPE 223 263
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LEMD1 MUTATED      2    1
  LEMD1 WILD-TYPE  223  263
        clus
vv       LEMD1 MUTATED LEMD1 WILD-TYPE
  FEMALE             2             223
  MALE               1             263
[1] 2 2
[1] FALSE
D1409V9, binary
                 cls
clus                0   1
  LEMD1 MUTATED     2   0
  LEMD1 WILD-TYPE 348  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LEMD1 MUTATED      2    0
  LEMD1 WILD-TYPE  348   22
     clus
vv    LEMD1 MUTATED LEMD1 WILD-TYPE
  NO              2             348
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  LEMD1 MUTATED                      3                             0
  LEMD1 WILD-TYPE                  312                            47
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  LEMD1 MUTATED                       0                              0
  LEMD1 WILD-TYPE                   106                             10
D1409V10, multiclass
                                clus
vv                               LEMD1 MUTATED LEMD1 WILD-TYPE
  COLON ADENOCARCINOMA                       3             312
  COLON MUCINOUS ADENOCARCINOMA              0              47
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  LEMD1 MUTATED     2   0   0   0
  LEMD1 WILD-TYPE 343   4  31  25
D1409V11, multiclass
[1] "Remove cluster labels:" "LEMD1 MUTATED"         
clus
  LEMD1 MUTATED LEMD1 WILD-TYPE 
              2             403 
     TCGA-A6-2671      TCGA-A6-2672      TCGA-A6-2674      TCGA-A6-2676 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-A6-2677      TCGA-A6-2678      TCGA-A6-2683      TCGA-A6-3807 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-A6-3808      TCGA-A6-3809      TCGA-A6-3810      TCGA-A6-5657 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-A6-5659      TCGA-A6-5661      TCGA-A6-6781      TCGA-AA-3489 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-3492      TCGA-AA-3496      TCGA-AA-3502      TCGA-AA-3510 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-3511      TCGA-AA-3514      TCGA-AA-3517      TCGA-AA-3518 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-3519      TCGA-AA-3520      TCGA-AA-3521      TCGA-AA-3522 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-3524      TCGA-AA-3525      TCGA-AA-3526      TCGA-AA-3527 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-3529      TCGA-AA-3530      TCGA-AA-3531      TCGA-AA-3532 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-3534      TCGA-AA-3538      TCGA-AA-3542      TCGA-AA-3543 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-3544      TCGA-AA-3548      TCGA-AA-3549      TCGA-AA-3552 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-3553      TCGA-AA-3554      TCGA-AA-3555      TCGA-AA-3556 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-3558      TCGA-AA-3560      TCGA-AA-3561      TCGA-AA-3562 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-3655      TCGA-AA-3660      TCGA-AA-3662      TCGA-AA-3663 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-3664      TCGA-AA-3666      TCGA-AA-3667      TCGA-AA-3672 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-3673      TCGA-AA-3678      TCGA-AA-3679      TCGA-AA-3680 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-3681      TCGA-AA-3684      TCGA-AA-3685      TCGA-AA-3688 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-3692      TCGA-AA-3693      TCGA-AA-3695      TCGA-AA-3696 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-3697      TCGA-AA-3710      TCGA-AA-3712      TCGA-AA-3713 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-3715      TCGA-AA-3811      TCGA-AA-3812      TCGA-AA-3814 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-3815      TCGA-AA-3818      TCGA-AA-3819      TCGA-AA-3821 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-3831      TCGA-AA-3833      TCGA-AA-3837      TCGA-AA-3842 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-3844      TCGA-AA-3845      TCGA-AA-3846      TCGA-AA-3848 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-3850      TCGA-AA-3851      TCGA-AA-3852      TCGA-AA-3854 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-3855      TCGA-AA-3856      TCGA-AA-3858      TCGA-AA-3860 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-3861      TCGA-AA-3864      TCGA-AA-3866      TCGA-AA-3867 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-3869      TCGA-AA-3870      TCGA-AA-3872      TCGA-AA-3875 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-3877      TCGA-AA-3930      TCGA-AA-3939      TCGA-AA-3941 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-3947      TCGA-AA-3949      TCGA-AA-3950      TCGA-AA-3952 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-3955      TCGA-AA-3956      TCGA-AA-3968      TCGA-AA-3971 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-3972      TCGA-AA-3973      TCGA-AA-3975      TCGA-AA-3976 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-3979      TCGA-AA-3984      TCGA-AA-3986      TCGA-AA-3989 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-3994      TCGA-AA-A004      TCGA-AA-A00A      TCGA-AA-A00D 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-A00E      TCGA-AA-A00F      TCGA-AA-A00J      TCGA-AA-A00K 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-A00L      TCGA-AA-A00N      TCGA-AA-A00O      TCGA-AA-A00Q 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-A00R      TCGA-AA-A00U      TCGA-AA-A00W      TCGA-AA-A00Z 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-A010      TCGA-AA-A017      TCGA-AA-A01D      TCGA-AA-A01F 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-A01G      TCGA-AA-A01I      TCGA-AA-A01K      TCGA-AA-A01P 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-A01Q      TCGA-AA-A01R      TCGA-AA-A01S      TCGA-AA-A01T 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-A01V      TCGA-AA-A01X      TCGA-AA-A01Z      TCGA-AA-A022 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-A024      TCGA-AA-A029      TCGA-AA-A02F      TCGA-AA-A02H 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-A02J      TCGA-AA-A02K      TCGA-AA-A02O      TCGA-AA-A02W 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AA-A02Y      TCGA-AA-A03F      TCGA-AA-A03J      TCGA-AD-5900 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AD-6548      TCGA-AD-6888      TCGA-AU-3779      TCGA-AU-6004 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AY-4070      TCGA-AY-4071      TCGA-AY-5543      TCGA-AY-6196 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AY-6197      TCGA-AY-6386      TCGA-AZ-4315      TCGA-AZ-4681 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AZ-4682      TCGA-CA-5254      TCGA-CA-5255      TCGA-CA-5796 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-CA-5797      TCGA-CA-6715      TCGA-CA-6716      TCGA-CA-6717 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-CA-6718      TCGA-CA-6719      TCGA-CK-4947      TCGA-CK-4948 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-CK-4950      TCGA-CK-4952      TCGA-CK-5912      TCGA-CK-5913 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-CK-5914      TCGA-CK-5915      TCGA-CK-5916      TCGA-CK-6746 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-CK-6747      TCGA-CK-6748      TCGA-CK-6751      TCGA-CM-4743 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-CM-4744      TCGA-CM-4746      TCGA-CM-4747      TCGA-CM-4752 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-CM-5341      TCGA-CM-5344      TCGA-CM-5348      TCGA-CM-5349 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-CM-5860      TCGA-CM-5861      TCGA-CM-5862      TCGA-CM-5863 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-CM-5864      TCGA-CM-5868      TCGA-CM-6161      TCGA-CM-6162 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-CM-6163      TCGA-CM-6164      TCGA-CM-6165      TCGA-CM-6166 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-CM-6167      TCGA-CM-6168      TCGA-CM-6169      TCGA-CM-6170 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-CM-6171      TCGA-CM-6172      TCGA-CM-6674      TCGA-CM-6675 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-CM-6676      TCGA-CM-6677      TCGA-CM-6678      TCGA-CM-6679 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-CM-6680      TCGA-D5-5537      TCGA-D5-5538      TCGA-D5-5539 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-D5-5540      TCGA-D5-5541      TCGA-D5-6529      TCGA-D5-6532 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-D5-6533      TCGA-D5-6534      TCGA-D5-6535      TCGA-D5-6536 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-D5-6537      TCGA-D5-6538      TCGA-D5-6539      TCGA-D5-6540 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-D5-6541      TCGA-D5-6898      TCGA-D5-6920      TCGA-D5-6922 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-D5-6923      TCGA-D5-6924      TCGA-D5-6926      TCGA-D5-6927 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-D5-6928      TCGA-D5-6929      TCGA-D5-6930      TCGA-D5-6931 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-D5-6932      TCGA-D5-7000      TCGA-F4-6459      TCGA-F4-6460 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-F4-6569      TCGA-F4-6570      TCGA-F4-6703      TCGA-F4-6704 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-F4-6805      TCGA-F4-6806      TCGA-F4-6807      TCGA-F4-6808 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-F4-6809      TCGA-F4-6854      TCGA-F4-6855      TCGA-F4-6856 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-G4-6293      TCGA-G4-6299      TCGA-G4-6303      TCGA-G4-6304 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-G4-6306      TCGA-G4-6307      TCGA-G4-6309      TCGA-G4-6310 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-G4-6315      TCGA-G4-6317      TCGA-G4-6321      TCGA-G4-6323 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-G4-6586      TCGA-G4-6625      TCGA-G4-6626      TCGA-G4-6628 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AF-2687      TCGA-AF-2689      TCGA-AF-2691      TCGA-AF-2692 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AF-3400      TCGA-AF-3913      TCGA-AF-4110      TCGA-AF-5654 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AF-6655      TCGA-AG-3574      TCGA-AG-3575      TCGA-AG-3578 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AG-3580      TCGA-AG-3581      TCGA-AG-3582      TCGA-AG-3583 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AG-3584      TCGA-AG-3586      TCGA-AG-3587      TCGA-AG-3593 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AG-3594      TCGA-AG-3598      TCGA-AG-3599      TCGA-AG-3600 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AG-3601      TCGA-AG-3602      TCGA-AG-3605      TCGA-AG-3608 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AG-3609      TCGA-AG-3611      TCGA-AG-3612      TCGA-AG-3726 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AG-3727      TCGA-AG-3731      TCGA-AG-3732      TCGA-AG-3742 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AG-3878      TCGA-AG-3882      TCGA-AG-3883      TCGA-AG-3885 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AG-3887      TCGA-AG-3890      TCGA-AG-3892      TCGA-AG-3893 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AG-3894      TCGA-AG-3896      TCGA-AG-3898      TCGA-AG-3901 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AG-3902      TCGA-AG-3909      TCGA-AG-3999      TCGA-AG-4001 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AG-4005      TCGA-AG-4007      TCGA-AG-4008      TCGA-AG-4015 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AG-A002      TCGA-AG-A008      TCGA-AG-A00C      TCGA-AG-A00H 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AG-A00Y      TCGA-AG-A011      TCGA-AG-A014      TCGA-AG-A015 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AG-A016      TCGA-AG-A01L      TCGA-AG-A01W      TCGA-AG-A01Y 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AG-A020      TCGA-AG-A025      TCGA-AG-A026      TCGA-AG-A02G 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AG-A02N      TCGA-AG-A02X      TCGA-AG-A032      TCGA-AG-A036 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-AH-6549      TCGA-AH-6643      TCGA-CL-5917      TCGA-CL-5918 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-DC-5337      TCGA-DC-5869      TCGA-DC-6155      TCGA-DC-6157 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-DC-6158      TCGA-DC-6160      TCGA-DC-6681      TCGA-DC-6682 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-DC-6683      TCGA-DT-5265      TCGA-EF-5830      TCGA-EI-6506 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-EI-6507      TCGA-EI-6508      TCGA-EI-6510      TCGA-F5-6464 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-F5-6465      TCGA-F5-6571      TCGA-F5-6702      TCGA-F5-6812 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
     TCGA-F5-6813      TCGA-G5-6235      TCGA-G5-6641 
"LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" "LEMD1 WILD-TYPE" 
D1409V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  LEMD1 MUTATED                                  0     0
  LEMD1 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  LEMD1 MUTATED                           0     3
  LEMD1 WILD-TYPE                        22   223
D1409V13, multiclass
                                  clus
vv                                 LEMD1 MUTATED LEMD1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        3             223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1410) Variable = RC3H2 MUTATION ANALYSIS
D1410V1, survival
                 sevent
clus2               0   1
  RC3H2 MUTATED     9   1
  RC3H2 WILD-TYPE 369  92
  RC3H2 MUTATED RC3H2 WILD-TYPE 
             10             461 
  RC3H2 MUTATED RC3H2 WILD-TYPE 
              1              92 
$`RC3H2 MUTATED`
TCGA-AA-3864 TCGA-CK-6748 TCGA-CM-4743 TCGA-CM-6169 TCGA-CM-6674 TCGA-D5-6541 
       53.00         1.91        23.05        13.02        12.95        15.58 
TCGA-F4-6460 TCGA-F4-6806 TCGA-G4-6586 TCGA-AG-A002 
       31.96        41.42        35.80        20.98 

$`RC3H2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
       21.14        82.95       124.27        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6676 
       12.99        15.02        14.04        11.01        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       16.14         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6807 
       35.74         6.18        47.87         1.55        34.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 
       63.62        61.91        36.00        22.09        13.78        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  RC3H2 MUTATED RC3H2 WILD-TYPE 
           1.91            0.00 
  RC3H2 MUTATED RC3H2 WILD-TYPE 
          53.00          148.01 
  RC3H2 MUTATED RC3H2 WILD-TYPE 
         22.015          20.120 
[1] "1.9 - 53.0 (22.0)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.9"
D1410V2, continuous
D1410V3, binary
                 cls
clus                0   1
  RC3H2 MUTATED     9   1
  RC3H2 WILD-TYPE 357 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RC3H2 MUTATED      9    1
  RC3H2 WILD-TYPE  357  118
        clus
vv       RC3H2 MUTATED RC3H2 WILD-TYPE
  COLON              9             357
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RC3H2 MUTATED         2        0        1         5         0         0
  RC3H2 WILD-TYPE      89        1       31       133        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RC3H2 MUTATED           0          0          1          0        1         0
  RC3H2 WILD-TYPE        24         11         58         42       47        18
                 vv
clus              STAGE IVB
  RC3H2 MUTATED           0
  RC3H2 WILD-TYPE         1
D1410V4, multiclass
            clus
vv           RC3H2 MUTATED RC3H2 WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              5             133
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             0              42
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  RC3H2 MUTATED     0   2   8   0
  RC3H2 WILD-TYPE  17  90 321  50
D1410V5, multiclass
    clus
vv   RC3H2 MUTATED RC3H2 WILD-TYPE
  T1             0              17
  T2             2              90
  T3             8             321
  T4             0              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  RC3H2 MUTATED     8   2   0
  RC3H2 WILD-TYPE 279 111  87
D1410V6, multiclass
    clus
vv   RC3H2 MUTATED RC3H2 WILD-TYPE
  N0             8             279
  N1             2             111
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1410V7, binary
                 cls
clus                0   1
  RC3H2 MUTATED     9   1
  RC3H2 WILD-TYPE 366  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RC3H2 MUTATED      9    1
  RC3H2 WILD-TYPE  366   64
   clus
vv  RC3H2 MUTATED RC3H2 WILD-TYPE
  0             9             366
  1             1              64
[1] 2 2
[1] FALSE
D1410V8, binary
                 cls
clus                0   1
  RC3H2 MUTATED     4   6
  RC3H2 WILD-TYPE 221 258
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RC3H2 MUTATED      4    6
  RC3H2 WILD-TYPE  221  258
        clus
vv       RC3H2 MUTATED RC3H2 WILD-TYPE
  FEMALE             4             221
  MALE               6             258
[1] 2 2
[1] FALSE
D1410V9, binary
                 cls
clus                0   1
  RC3H2 MUTATED    10   0
  RC3H2 WILD-TYPE 340  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RC3H2 MUTATED     10    0
  RC3H2 WILD-TYPE  340   22
     clus
vv    RC3H2 MUTATED RC3H2 WILD-TYPE
  NO             10             340
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  RC3H2 MUTATED                      8                             1
  RC3H2 WILD-TYPE                  307                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  RC3H2 MUTATED                       1                              0
  RC3H2 WILD-TYPE                   105                             10
D1410V10, multiclass
                                clus
vv                               RC3H2 MUTATED RC3H2 WILD-TYPE
  COLON ADENOCARCINOMA                       8             307
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  RC3H2 MUTATED     9   0   0   1
  RC3H2 WILD-TYPE 336   4  31  24
D1410V11, multiclass
    clus
vv   RC3H2 MUTATED RC3H2 WILD-TYPE
  R0             9             336
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1410V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RC3H2 MUTATED                                  0     0
  RC3H2 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  RC3H2 MUTATED                           1     7
  RC3H2 WILD-TYPE                        21   219
D1410V13, multiclass
                                  clus
vv                                 RC3H2 MUTATED RC3H2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        7             219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1411) Variable = ZFYVE16 MUTATION ANALYSIS
D1411V1, survival
                   sevent
clus2                 0   1
  ZFYVE16 MUTATED    15   1
  ZFYVE16 WILD-TYPE 363  92
  ZFYVE16 MUTATED ZFYVE16 WILD-TYPE 
               16               455 
  ZFYVE16 MUTATED ZFYVE16 WILD-TYPE 
                1                92 
$`ZFYVE16 MUTATED`
TCGA-A6-5661 TCGA-A6-5665 TCGA-AA-3667 TCGA-AA-3977 TCGA-AA-A00E TCGA-AA-A00N 
       33.53        22.06        14.01        25.02        30.02         4.01 
TCGA-AA-A010 TCGA-AD-5900 TCGA-AD-6895 TCGA-AZ-4315 TCGA-CA-6717 TCGA-CM-5861 
       34.98         0.07         0.72        58.39        12.76        15.02 
TCGA-CM-6165 TCGA-D5-6540 TCGA-D5-6928 TCGA-AG-A002 
       16.04        16.14        11.64        20.98 

$`ZFYVE16 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
       54.02         2.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00F 
        7.96        27.02        13.94        38.04        19.00        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 
       41.00        39.98        18.05        40.96        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
       56.55         0.79         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07        12.20        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 
       22.03        22.98        30.08        32.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 
       17.85         4.80        17.13        12.49        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  ZFYVE16 MUTATED ZFYVE16 WILD-TYPE 
             0.07              0.00 
  ZFYVE16 MUTATED ZFYVE16 WILD-TYPE 
            58.39            148.01 
  ZFYVE16 MUTATED ZFYVE16 WILD-TYPE 
            16.09             20.28 
[1] "0.1 - 58.4 (16.1)"  "0.0 - 148.0 (20.3)"
[1] "hr=" "2.4"
D1411V2, continuous
D1411V3, binary
                   cls
clus                  0   1
  ZFYVE16 MUTATED    17   2
  ZFYVE16 WILD-TYPE 349 117
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZFYVE16 MUTATED     17    2
  ZFYVE16 WILD-TYPE  349  117
        clus
vv       ZFYVE16 MUTATED ZFYVE16 WILD-TYPE
  COLON               17               349
  RECTUM               2               117
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZFYVE16 MUTATED         4        0        0        10         3         0
  ZFYVE16 WILD-TYPE      87        1       32       128         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZFYVE16 MUTATED           0          0          0          0        0
  ZFYVE16 WILD-TYPE        24         11         59         42       48
                   vv
clus                STAGE IVA STAGE IVB
  ZFYVE16 MUTATED           0         0
  ZFYVE16 WILD-TYPE        18         1
D1411V4, multiclass
            clus
vv           ZFYVE16 MUTATED ZFYVE16 WILD-TYPE
  STAGE I                  4                87
  STAGE IA                 0                 1
  STAGE II                 0                32
  STAGE IIA               10               128
  STAGE IIB                3                 7
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               0                11
  STAGE IIIB               0                59
  STAGE IIIC               0                42
  STAGE IV                 0                48
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  ZFYVE16 MUTATED     0   5  11   3
  ZFYVE16 WILD-TYPE  17  87 318  47
D1411V5, multiclass
    clus
vv   ZFYVE16 MUTATED ZFYVE16 WILD-TYPE
  T1               0                17
  T2               5                87
  T3              11               318
  T4               3                47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  ZFYVE16 MUTATED    18   1   0
  ZFYVE16 WILD-TYPE 269 112  87
D1411V6, multiclass
    clus
vv   ZFYVE16 MUTATED ZFYVE16 WILD-TYPE
  N0              18               269
  N1               1               112
  N2               0                87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1411V7, binary
                   cls
clus                  0   1
  ZFYVE16 MUTATED    15   0
  ZFYVE16 WILD-TYPE 360  65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZFYVE16 MUTATED     15    0
  ZFYVE16 WILD-TYPE  360   65
   clus
vv  ZFYVE16 MUTATED ZFYVE16 WILD-TYPE
  0              15               360
  1               0                65
[1] 2 2
[1] FALSE
D1411V8, binary
                   cls
clus                  0   1
  ZFYVE16 MUTATED     8  11
  ZFYVE16 WILD-TYPE 217 253
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZFYVE16 MUTATED      8   11
  ZFYVE16 WILD-TYPE  217  253
        clus
vv       ZFYVE16 MUTATED ZFYVE16 WILD-TYPE
  FEMALE               8               217
  MALE                11               253
[1] 2 2
[1] FALSE
D1411V9, binary
                   cls
clus                  0   1
  ZFYVE16 MUTATED    13   0
  ZFYVE16 WILD-TYPE 337  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZFYVE16 MUTATED     13    0
  ZFYVE16 WILD-TYPE  337   22
     clus
vv    ZFYVE16 MUTATED ZFYVE16 WILD-TYPE
  NO               13               337
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ZFYVE16 MUTATED                     12                             5
  ZFYVE16 WILD-TYPE                  303                            42
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ZFYVE16 MUTATED                       2                              0
  ZFYVE16 WILD-TYPE                   104                             10
D1411V10, multiclass
                                clus
vv                               ZFYVE16 MUTATED ZFYVE16 WILD-TYPE
  COLON ADENOCARCINOMA                        12               303
  COLON MUCINOUS ADENOCARCINOMA                5                42
  RECTAL ADENOCARCINOMA                        2               104
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  ZFYVE16 MUTATED    15   0   0   2
  ZFYVE16 WILD-TYPE 330   4  31  23
D1411V11, multiclass
    clus
vv   ZFYVE16 MUTATED ZFYVE16 WILD-TYPE
  R0              15               330
  R1               0                 4
  R2               0                31
  RX               2                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1411V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZFYVE16 MUTATED                                  0     1
  ZFYVE16 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  ZFYVE16 MUTATED                           1     9
  ZFYVE16 WILD-TYPE                        21   217
D1411V13, multiclass
                                  clus
vv                                 ZFYVE16 MUTATED ZFYVE16 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                10
  BLACK OR AFRICAN AMERICAN                      1                21
  WHITE                                          9               217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1412) Variable = APOBEC4 MUTATION ANALYSIS
D1412V1, survival
                   sevent
clus2                 0   1
  APOBEC4 MUTATED     8   1
  APOBEC4 WILD-TYPE 370  92
  APOBEC4 MUTATED APOBEC4 WILD-TYPE 
                9               462 
  APOBEC4 MUTATED APOBEC4 WILD-TYPE 
                1                92 
$`APOBEC4 MUTATED`
TCGA-A6-5665 TCGA-AA-3555 TCGA-AA-3815 TCGA-AA-A010 TCGA-CA-6717 TCGA-CA-6718 
       22.06        29.95        33.04        34.98        12.76        10.06 
TCGA-G4-6309 TCGA-AG-3892 TCGA-AG-A002 
       85.48        13.02        20.98 

$`APOBEC4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       13.02        24.00        17.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       35.05         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 
        3.06         3.25         3.29         0.07        12.20        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       55.04        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       17.03        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  APOBEC4 MUTATED APOBEC4 WILD-TYPE 
            10.06              0.00 
  APOBEC4 MUTATED APOBEC4 WILD-TYPE 
            85.48            148.01 
  APOBEC4 MUTATED APOBEC4 WILD-TYPE 
           22.060            20.085 
[1] "10.1 - 85.5 (22.1)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.9"
D1412V2, continuous
D1412V3, binary
                   cls
clus                  0   1
  APOBEC4 MUTATED     7   2
  APOBEC4 WILD-TYPE 359 117
[1] "tbl2"
                   cls
clus                [,1] [,2]
  APOBEC4 MUTATED      7    2
  APOBEC4 WILD-TYPE  359  117
        clus
vv       APOBEC4 MUTATED APOBEC4 WILD-TYPE
  COLON                7               359
  RECTUM               2               117
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  APOBEC4 MUTATED         2        0        0         5         1         0
  APOBEC4 WILD-TYPE      89        1       32       133         9         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  APOBEC4 MUTATED           0          0          1          0        0
  APOBEC4 WILD-TYPE        24         11         58         42       48
                   vv
clus                STAGE IVA STAGE IVB
  APOBEC4 MUTATED           0         0
  APOBEC4 WILD-TYPE        18         1
D1412V4, multiclass
            clus
vv           APOBEC4 MUTATED APOBEC4 WILD-TYPE
  STAGE I                  2                89
  STAGE IA                 0                 1
  STAGE II                 0                32
  STAGE IIA                5               133
  STAGE IIB                1                 9
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               0                11
  STAGE IIIB               1                58
  STAGE IIIC               0                42
  STAGE IV                 0                48
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  APOBEC4 MUTATED     1   1   6   1
  APOBEC4 WILD-TYPE  16  91 323  49
D1412V5, multiclass
    clus
vv   APOBEC4 MUTATED APOBEC4 WILD-TYPE
  T1               1                16
  T2               1                91
  T3               6               323
  T4               1                49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  APOBEC4 MUTATED     8   1   0
  APOBEC4 WILD-TYPE 279 112  87
D1412V6, multiclass
    clus
vv   APOBEC4 MUTATED APOBEC4 WILD-TYPE
  N0               8               279
  N1               1               112
  N2               0                87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1412V7, binary
                   cls
clus                  0   1
  APOBEC4 MUTATED     9   0
  APOBEC4 WILD-TYPE 366  65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  APOBEC4 MUTATED      9    0
  APOBEC4 WILD-TYPE  366   65
   clus
vv  APOBEC4 MUTATED APOBEC4 WILD-TYPE
  0               9               366
  1               0                65
[1] 2 2
[1] FALSE
D1412V8, binary
                   cls
clus                  0   1
  APOBEC4 MUTATED     6   3
  APOBEC4 WILD-TYPE 219 261
[1] "tbl2"
                   cls
clus                [,1] [,2]
  APOBEC4 MUTATED      6    3
  APOBEC4 WILD-TYPE  219  261
        clus
vv       APOBEC4 MUTATED APOBEC4 WILD-TYPE
  FEMALE               6               219
  MALE                 3               261
[1] 2 2
[1] FALSE
D1412V9, binary
                   cls
clus                  0   1
  APOBEC4 MUTATED     9   0
  APOBEC4 WILD-TYPE 341  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  APOBEC4 MUTATED      9    0
  APOBEC4 WILD-TYPE  341   22
     clus
vv    APOBEC4 MUTATED APOBEC4 WILD-TYPE
  NO                9               341
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  APOBEC4 MUTATED                      5                             2
  APOBEC4 WILD-TYPE                  310                            45
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  APOBEC4 MUTATED                       2                              0
  APOBEC4 WILD-TYPE                   104                             10
D1412V10, multiclass
                                clus
vv                               APOBEC4 MUTATED APOBEC4 WILD-TYPE
  COLON ADENOCARCINOMA                         5               310
  COLON MUCINOUS ADENOCARCINOMA                2                45
  RECTAL ADENOCARCINOMA                        2               104
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  APOBEC4 MUTATED     7   0   0   2
  APOBEC4 WILD-TYPE 338   4  31  23
D1412V11, multiclass
    clus
vv   APOBEC4 MUTATED APOBEC4 WILD-TYPE
  R0               7               338
  R1               0                 4
  R2               0                31
  RX               2                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1412V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  APOBEC4 MUTATED                                  0     2
  APOBEC4 WILD-TYPE                                1     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  APOBEC4 MUTATED                           1     1
  APOBEC4 WILD-TYPE                        21   225
D1412V13, multiclass
                                  clus
vv                                 APOBEC4 MUTATED APOBEC4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          2                 9
  BLACK OR AFRICAN AMERICAN                      1                21
  WHITE                                          1               225
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1413) Variable = ARID5A MUTATION ANALYSIS
D1413V1, survival
                  sevent
clus2                0   1
  ARID5A MUTATED     6   1
  ARID5A WILD-TYPE 372  92
  ARID5A MUTATED ARID5A WILD-TYPE 
               7              464 
  ARID5A MUTATED ARID5A WILD-TYPE 
               1               92 
$`ARID5A MUTATED`
TCGA-AA-3502 TCGA-AD-5900 TCGA-AZ-6601 TCGA-CA-6715 TCGA-CM-4743 TCGA-CM-5861 
       35.01         0.07       100.01         0.07        23.05        15.02 
TCGA-G4-6628 
       79.69 

$`ARID5A WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 
       41.00        39.98        18.05        40.96        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
       12.10        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6716 TCGA-CA-6717 
       12.69         3.06         3.25         3.29        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
      124.27        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 
       22.03        22.98        30.08        32.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 
       13.78        35.80        26.17        91.79        46.75        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  ARID5A MUTATED ARID5A WILD-TYPE 
            0.07             0.00 
  ARID5A MUTATED ARID5A WILD-TYPE 
          100.01           148.01 
  ARID5A MUTATED ARID5A WILD-TYPE 
          23.050           20.155 
[1] "0.1 - 100.0 (23.1)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.9"
D1413V2, continuous
D1413V3, binary
                  cls
clus                 0   1
  ARID5A MUTATED     8   0
  ARID5A WILD-TYPE 358 119
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID5A MUTATED      8    0
  ARID5A WILD-TYPE  358  119
        clus
vv       ARID5A MUTATED ARID5A WILD-TYPE
  COLON               8              358
  RECTUM              0              119
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ARID5A MUTATED         3        0        1         3         0         0
  ARID5A WILD-TYPE      88        1       31       135        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ARID5A MUTATED           0          0          1          0        0
  ARID5A WILD-TYPE        24         11         58         42       48
                  vv
clus               STAGE IVA STAGE IVB
  ARID5A MUTATED           0         0
  ARID5A WILD-TYPE        18         1
D1413V4, multiclass
            clus
vv           ARID5A MUTATED ARID5A WILD-TYPE
  STAGE I                 3               88
  STAGE IA                0                1
  STAGE II                1               31
  STAGE IIA               3              135
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              1               58
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ARID5A MUTATED     0   3   5   0
  ARID5A WILD-TYPE  17  89 324  50
D1413V5, multiclass
    clus
vv   ARID5A MUTATED ARID5A WILD-TYPE
  T1              0               17
  T2              3               89
  T3              5              324
  T4              0               50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  ARID5A MUTATED     7   1   0
  ARID5A WILD-TYPE 280 112  87
D1413V6, multiclass
    clus
vv   ARID5A MUTATED ARID5A WILD-TYPE
  N0              7              280
  N1              1              112
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1413V7, binary
                  cls
clus                 0   1
  ARID5A MUTATED     7   0
  ARID5A WILD-TYPE 368  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID5A MUTATED      7    0
  ARID5A WILD-TYPE  368   65
   clus
vv  ARID5A MUTATED ARID5A WILD-TYPE
  0              7              368
  1              0               65
[1] 2 2
[1] FALSE
D1413V8, binary
                  cls
clus                 0   1
  ARID5A MUTATED     2   6
  ARID5A WILD-TYPE 223 258
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID5A MUTATED      2    6
  ARID5A WILD-TYPE  223  258
        clus
vv       ARID5A MUTATED ARID5A WILD-TYPE
  FEMALE              2              223
  MALE                6              258
[1] 2 2
[1] FALSE
D1413V9, binary
                  cls
clus                 0   1
  ARID5A MUTATED     5   0
  ARID5A WILD-TYPE 345  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID5A MUTATED      5    0
  ARID5A WILD-TYPE  345   22
     clus
vv    ARID5A MUTATED ARID5A WILD-TYPE
  NO               5              345
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ARID5A MUTATED                      7                             1
  ARID5A WILD-TYPE                  308                            46
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ARID5A MUTATED                       0                              0
  ARID5A WILD-TYPE                   106                             10
D1413V10, multiclass
                                clus
vv                               ARID5A MUTATED ARID5A WILD-TYPE
  COLON ADENOCARCINOMA                        7              308
  COLON MUCINOUS ADENOCARCINOMA               1               46
  RECTAL ADENOCARCINOMA                       0              106
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ARID5A MUTATED     6   0   0   1
  ARID5A WILD-TYPE 339   4  31  24
D1413V11, multiclass
    clus
vv   ARID5A MUTATED ARID5A WILD-TYPE
  R0              6              339
  R1              0                4
  R2              0               31
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1413V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ARID5A MUTATED                                  0     1
  ARID5A WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ARID5A MUTATED                           0     5
  ARID5A WILD-TYPE                        22   221
D1413V13, multiclass
                                  clus
vv                                 ARID5A MUTATED ARID5A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         5              221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1414) Variable = CYP2C18 MUTATION ANALYSIS
D1414V1, survival
                   sevent
clus2                 0   1
  CYP2C18 MUTATED     6   1
  CYP2C18 WILD-TYPE 372  92
  CYP2C18 MUTATED CYP2C18 WILD-TYPE 
                7               464 
  CYP2C18 MUTATED CYP2C18 WILD-TYPE 
                1                92 
$`CYP2C18 MUTATED`
TCGA-AD-6889 TCGA-AZ-5403 TCGA-CM-5860 TCGA-F4-6856 TCGA-G4-6310 TCGA-AG-3892 
       56.55        62.79        32.02        35.31        63.62        13.02 
TCGA-AG-A002 
       20.98 

$`CYP2C18 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       21.37        15.52         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
        5.13       106.75        22.36        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
       13.25         0.53        47.41       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6317 
       53.62        44.68        55.04        85.48        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       17.95        36.95        17.03        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  CYP2C18 MUTATED CYP2C18 WILD-TYPE 
            13.02              0.00 
  CYP2C18 MUTATED CYP2C18 WILD-TYPE 
            63.62            148.01 
  CYP2C18 MUTATED CYP2C18 WILD-TYPE 
           35.310            20.035 
[1] "13.0 - 63.6 (35.3)" "0.0 - 148.0 (20.0)"
[1] "hr=" "2.3"
D1414V2, continuous
D1414V3, binary
                   cls
clus                  0   1
  CYP2C18 MUTATED     5   2
  CYP2C18 WILD-TYPE 361 117
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CYP2C18 MUTATED      5    2
  CYP2C18 WILD-TYPE  361  117
        clus
vv       CYP2C18 MUTATED CYP2C18 WILD-TYPE
  COLON                5               361
  RECTUM               2               117
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CYP2C18 MUTATED         3        0        1         2         0         0
  CYP2C18 WILD-TYPE      88        1       31       136        10         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CYP2C18 MUTATED           0          0          1          0        0
  CYP2C18 WILD-TYPE        24         11         58         42       48
                   vv
clus                STAGE IVA STAGE IVB
  CYP2C18 MUTATED           0         0
  CYP2C18 WILD-TYPE        18         1
D1414V4, multiclass
            clus
vv           CYP2C18 MUTATED CYP2C18 WILD-TYPE
  STAGE I                  3                88
  STAGE IA                 0                 1
  STAGE II                 1                31
  STAGE IIA                2               136
  STAGE IIB                0                10
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               0                11
  STAGE IIIB               1                58
  STAGE IIIC               0                42
  STAGE IV                 0                48
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  CYP2C18 MUTATED     1   2   4   0
  CYP2C18 WILD-TYPE  16  90 325  50
D1414V5, multiclass
    clus
vv   CYP2C18 MUTATED CYP2C18 WILD-TYPE
  T1               1                16
  T2               2                90
  T3               4               325
  T4               0                50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  CYP2C18 MUTATED     6   1   0
  CYP2C18 WILD-TYPE 281 112  87
D1414V6, multiclass
    clus
vv   CYP2C18 MUTATED CYP2C18 WILD-TYPE
  N0               6               281
  N1               1               112
  N2               0                87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1414V7, binary
                   cls
clus                  0   1
  CYP2C18 MUTATED     6   0
  CYP2C18 WILD-TYPE 369  65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CYP2C18 MUTATED      6    0
  CYP2C18 WILD-TYPE  369   65
   clus
vv  CYP2C18 MUTATED CYP2C18 WILD-TYPE
  0               6               369
  1               0                65
[1] 2 2
[1] FALSE
D1414V8, binary
                   cls
clus                  0   1
  CYP2C18 MUTATED     1   6
  CYP2C18 WILD-TYPE 224 258
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CYP2C18 MUTATED      1    6
  CYP2C18 WILD-TYPE  224  258
        clus
vv       CYP2C18 MUTATED CYP2C18 WILD-TYPE
  FEMALE               1               224
  MALE                 6               258
[1] 2 2
[1] FALSE
D1414V9, binary
                   cls
clus                  0   1
  CYP2C18 MUTATED     5   1
  CYP2C18 WILD-TYPE 345  21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CYP2C18 MUTATED      5    1
  CYP2C18 WILD-TYPE  345   21
     clus
vv    CYP2C18 MUTATED CYP2C18 WILD-TYPE
  NO                5               345
  YES               1                21
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CYP2C18 MUTATED                      4                             1
  CYP2C18 WILD-TYPE                  311                            46
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CYP2C18 MUTATED                       2                              0
  CYP2C18 WILD-TYPE                   104                             10
D1414V10, multiclass
                                clus
vv                               CYP2C18 MUTATED CYP2C18 WILD-TYPE
  COLON ADENOCARCINOMA                         4               311
  COLON MUCINOUS ADENOCARCINOMA                1                46
  RECTAL ADENOCARCINOMA                        2               104
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  CYP2C18 MUTATED     5   0   0   0
  CYP2C18 WILD-TYPE 340   4  31  25
D1414V11, multiclass
    clus
vv   CYP2C18 MUTATED CYP2C18 WILD-TYPE
  R0               5               340
  R1               0                 4
  R2               0                31
  RX               0                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1414V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CYP2C18 MUTATED                                  0     1
  CYP2C18 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  CYP2C18 MUTATED                           0     4
  CYP2C18 WILD-TYPE                        22   222
D1414V13, multiclass
                                  clus
vv                                 CYP2C18 MUTATED CYP2C18 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                10
  BLACK OR AFRICAN AMERICAN                      0                22
  WHITE                                          4               222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1415) Variable = BEND2 MUTATION ANALYSIS
D1415V1, survival
                 sevent
clus2               0   1
  BEND2 MUTATED    17   4
  BEND2 WILD-TYPE 361  89
  BEND2 MUTATED BEND2 WILD-TYPE 
             21             450 
  BEND2 MUTATED BEND2 WILD-TYPE 
              4              89 
$`BEND2 MUTATED`
TCGA-A6-3809 TCGA-A6-5666 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3666 TCGA-AA-3710 
       32.75        32.71         1.02        13.02         2.01        26.99 
TCGA-AA-3877 TCGA-AA-3947 TCGA-AA-A00J TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-6603 
       31.00        33.01        18.05        21.44        58.39        29.56 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-5914 TCGA-CM-5348 TCGA-CM-6162 TCGA-D5-5540 
       12.76        10.06         9.99        22.98        12.00        56.09 
TCGA-D5-6931 TCGA-DM-A28E TCGA-G4-6306 
       12.00       119.93        44.68 

$`BEND2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       22.06        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
       63.98         6.97        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 
       61.02        78.08         6.05         6.97        54.02        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 
       37.05        19.00        36.00         5.03        85.05        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
        2.01        12.99        24.00        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       19.00        30.02        34.03        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6605 
       88.21        49.41         6.77        12.10       100.01         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        3.29         0.07        12.20        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 
       85.45        15.62        49.08        51.32        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       13.02        29.06        22.03        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 
        5.03        15.02        15.02        17.03        15.02         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       19.59        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6932 
        9.04         9.44        11.64         4.80         1.51        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28F 
      131.51       135.65       139.17         6.12        81.37        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       74.56        65.85        53.62        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  BEND2 MUTATED BEND2 WILD-TYPE 
           1.02            0.00 
  BEND2 MUTATED BEND2 WILD-TYPE 
         119.93          148.01 
  BEND2 MUTATED BEND2 WILD-TYPE 
         22.980          20.085 
[1] "1.0 - 119.9 (23.0)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.1"
D1415V2, continuous
D1415V3, binary
                 cls
clus                0   1
  BEND2 MUTATED    23   0
  BEND2 WILD-TYPE 343 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BEND2 MUTATED     23    0
  BEND2 WILD-TYPE  343  119
        clus
vv       BEND2 MUTATED BEND2 WILD-TYPE
  COLON             23             343
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  BEND2 MUTATED         2        0        0         9         2         1
  BEND2 WILD-TYPE      89        1       32       129         8         0
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  BEND2 MUTATED           3          0          4          1        0         0
  BEND2 WILD-TYPE        21         11         55         41       48        18
                 vv
clus              STAGE IVB
  BEND2 MUTATED           0
  BEND2 WILD-TYPE         1
D1415V4, multiclass
            clus
vv           BEND2 MUTATED BEND2 WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              9             129
  STAGE IIB              2               8
  STAGE IIC              1               0
  STAGE III              3              21
  STAGE IIIA             0              11
  STAGE IIIB             4              55
  STAGE IIIC             1              41
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  BEND2 MUTATED     1   3  14   5
  BEND2 WILD-TYPE  16  89 315  45
D1415V5, multiclass
    clus
vv   BEND2 MUTATED BEND2 WILD-TYPE
  T1             1              16
  T2             3              89
  T3            14             315
  T4             5              45
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  BEND2 MUTATED    14   6   3
  BEND2 WILD-TYPE 273 107  84
D1415V6, multiclass
    clus
vv   BEND2 MUTATED BEND2 WILD-TYPE
  N0            14             273
  N1             6             107
  N2             3              84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1415V7, binary
                 cls
clus                0   1
  BEND2 MUTATED    20   0
  BEND2 WILD-TYPE 355  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BEND2 MUTATED     20    0
  BEND2 WILD-TYPE  355   65
   clus
vv  BEND2 MUTATED BEND2 WILD-TYPE
  0            20             355
  1             0              65
[1] 2 2
[1] FALSE
D1415V8, binary
                 cls
clus                0   1
  BEND2 MUTATED    10  13
  BEND2 WILD-TYPE 215 251
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BEND2 MUTATED     10   13
  BEND2 WILD-TYPE  215  251
        clus
vv       BEND2 MUTATED BEND2 WILD-TYPE
  FEMALE            10             215
  MALE              13             251
[1] 2 2
[1] FALSE
D1415V9, binary
                 cls
clus                0   1
  BEND2 MUTATED    18   0
  BEND2 WILD-TYPE 332  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BEND2 MUTATED     18    0
  BEND2 WILD-TYPE  332   22
     clus
vv    BEND2 MUTATED BEND2 WILD-TYPE
  NO             18             332
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  BEND2 MUTATED                     16                             7
  BEND2 WILD-TYPE                  299                            40
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  BEND2 MUTATED                       0                              0
  BEND2 WILD-TYPE                   106                             10
D1415V10, multiclass
                                clus
vv                               BEND2 MUTATED BEND2 WILD-TYPE
  COLON ADENOCARCINOMA                      16             299
  COLON MUCINOUS ADENOCARCINOMA              7              40
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  BEND2 MUTATED    16   0   0   3
  BEND2 WILD-TYPE 329   4  31  22
D1415V11, multiclass
    clus
vv   BEND2 MUTATED BEND2 WILD-TYPE
  R0            16             329
  R1             0               4
  R2             0              31
  RX             3              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1415V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  BEND2 MUTATED                                  0     2
  BEND2 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  BEND2 MUTATED                           0    12
  BEND2 WILD-TYPE                        22   214
D1415V13, multiclass
                                  clus
vv                                 BEND2 MUTATED BEND2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               9
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                       12             214
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1416) Variable = KCTD9 MUTATION ANALYSIS
D1416V1, survival
                 sevent
clus2               0   1
  KCTD9 MUTATED     5   0
  KCTD9 WILD-TYPE 373  93
  KCTD9 MUTATED KCTD9 WILD-TYPE 
              5             466 
  KCTD9 MUTATED KCTD9 WILD-TYPE 
              0              93 
$`KCTD9 MUTATED`
TCGA-A6-6781 TCGA-AD-5900 TCGA-CM-6162 TCGA-CM-6674 TCGA-G4-6628 
       19.66         0.07        12.00        12.95        79.69 

$`KCTD9 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 
       41.00        39.98        18.05        40.96        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       15.02         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6675 
       12.99        13.02        15.02        14.04        11.01        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       46.75        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  KCTD9 MUTATED KCTD9 WILD-TYPE 
           0.07            0.00 
  KCTD9 MUTATED KCTD9 WILD-TYPE 
          79.69          148.01 
  KCTD9 MUTATED KCTD9 WILD-TYPE 
         12.950          20.415 
[1] "0.1 - 79.7 (12.9)"  "0.0 - 148.0 (20.4)"
[1] "hr="     "3300000"
D1416V2, continuous
D1416V3, binary
                 cls
clus                0   1
  KCTD9 MUTATED     5   0
  KCTD9 WILD-TYPE 361 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCTD9 MUTATED      5    0
  KCTD9 WILD-TYPE  361  119
        clus
vv       KCTD9 MUTATED KCTD9 WILD-TYPE
  COLON              5             361
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KCTD9 MUTATED         2        0        0         1         0         0
  KCTD9 WILD-TYPE      89        1       32       137        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  KCTD9 MUTATED           0          0          1          1        0         0
  KCTD9 WILD-TYPE        24         11         58         41       48        18
                 vv
clus              STAGE IVB
  KCTD9 MUTATED           0
  KCTD9 WILD-TYPE         1
D1416V4, multiclass
            clus
vv           KCTD9 MUTATED KCTD9 WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              1             137
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             1              41
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  KCTD9 MUTATED     0   2   2   1
  KCTD9 WILD-TYPE  17  90 327  49
D1416V5, multiclass
    clus
vv   KCTD9 MUTATED KCTD9 WILD-TYPE
  T1             0              17
  T2             2              90
  T3             2             327
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  KCTD9 MUTATED     3   2   0
  KCTD9 WILD-TYPE 284 111  87
D1416V6, multiclass
    clus
vv   KCTD9 MUTATED KCTD9 WILD-TYPE
  N0             3             284
  N1             2             111
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1416V7, binary
                 cls
clus                0   1
  KCTD9 MUTATED     3   0
  KCTD9 WILD-TYPE 372  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCTD9 MUTATED      3    0
  KCTD9 WILD-TYPE  372   65
   clus
vv  KCTD9 MUTATED KCTD9 WILD-TYPE
  0             3             372
  1             0              65
[1] 2 2
[1] FALSE
D1416V8, binary
                 cls
clus                0   1
  KCTD9 MUTATED     1   4
  KCTD9 WILD-TYPE 224 260
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCTD9 MUTATED      1    4
  KCTD9 WILD-TYPE  224  260
        clus
vv       KCTD9 MUTATED KCTD9 WILD-TYPE
  FEMALE             1             224
  MALE               4             260
[1] 2 2
[1] FALSE
D1416V9, binary
                 cls
clus                0   1
  KCTD9 MUTATED     4   0
  KCTD9 WILD-TYPE 346  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCTD9 MUTATED      4    0
  KCTD9 WILD-TYPE  346   22
     clus
vv    KCTD9 MUTATED KCTD9 WILD-TYPE
  NO              4             346
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  KCTD9 MUTATED                      2                             3
  KCTD9 WILD-TYPE                  313                            44
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  KCTD9 MUTATED                       0                              0
  KCTD9 WILD-TYPE                   106                             10
D1416V10, multiclass
                                clus
vv                               KCTD9 MUTATED KCTD9 WILD-TYPE
  COLON ADENOCARCINOMA                       2             313
  COLON MUCINOUS ADENOCARCINOMA              3              44
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  KCTD9 MUTATED     5   0   0   0
  KCTD9 WILD-TYPE 340   4  31  25
D1416V11, multiclass
    clus
vv   KCTD9 MUTATED KCTD9 WILD-TYPE
  R0             5             340
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1416V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KCTD9 MUTATED                                  0     0
  KCTD9 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  KCTD9 MUTATED                           0     5
  KCTD9 WILD-TYPE                        22   221
D1416V13, multiclass
                                  clus
vv                                 KCTD9 MUTATED KCTD9 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        5             221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1417) Variable = SBDS MUTATION ANALYSIS
D1417V1, survival
                sevent
clus2              0   1
  SBDS MUTATED     2   1
  SBDS WILD-TYPE 376  92
  SBDS MUTATED SBDS WILD-TYPE 
             3            468 
  SBDS MUTATED SBDS WILD-TYPE 
             1             92 
$`SBDS MUTATED`
TCGA-AA-3660 TCGA-D5-6926 TCGA-G4-6303 
       78.08         9.04        65.85 

$`SBDS WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 
       20.98        19.99        13.94        19.99        61.02         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6927 
        1.48         3.68         4.41        12.43        14.30         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       74.56        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  SBDS MUTATED SBDS WILD-TYPE 
          9.04           0.00 
  SBDS MUTATED SBDS WILD-TYPE 
         78.08         148.01 
  SBDS MUTATED SBDS WILD-TYPE 
        65.850         20.155 
[1] "9.0 - 78.1 (65.8)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.2"
D1417V2, continuous
D1417V3, binary
                cls
clus               0   1
  SBDS MUTATED     3   0
  SBDS WILD-TYPE 363 119
[1] "tbl2"
                cls
clus             [,1] [,2]
  SBDS MUTATED      3    0
  SBDS WILD-TYPE  363  119
        clus
vv       SBDS MUTATED SBDS WILD-TYPE
  COLON             3            363
  RECTUM            0            119
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SBDS MUTATED         0        0        1         0         0         0
  SBDS WILD-TYPE      91        1       31       138        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SBDS MUTATED           0          0          1          0        1         0
  SBDS WILD-TYPE        24         11         58         42       47        18
                vv
clus             STAGE IVB
  SBDS MUTATED           0
  SBDS WILD-TYPE         1
D1417V4, multiclass
            clus
vv           SBDS MUTATED SBDS WILD-TYPE
  STAGE I               0             91
  STAGE IA              0              1
  STAGE II              1             31
  STAGE IIA             0            138
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            1             58
  STAGE IIIC            0             42
  STAGE IV              1             47
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  SBDS MUTATED     0   0   2   1
  SBDS WILD-TYPE  17  92 327  49
D1417V5, multiclass
    clus
vv   SBDS MUTATED SBDS WILD-TYPE
  T1            0             17
  T2            0             92
  T3            2            327
  T4            1             49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  SBDS MUTATED     1   2   0
  SBDS WILD-TYPE 286 111  87
D1417V6, multiclass
    clus
vv   SBDS MUTATED SBDS WILD-TYPE
  N0            1            286
  N1            2            111
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1417V7, binary
                cls
clus               0   1
  SBDS MUTATED     2   1
  SBDS WILD-TYPE 373  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  SBDS MUTATED      2    1
  SBDS WILD-TYPE  373   64
   clus
vv  SBDS MUTATED SBDS WILD-TYPE
  0            2            373
  1            1             64
[1] 2 2
[1] FALSE
D1417V8, binary
                cls
clus               0   1
  SBDS MUTATED     2   1
  SBDS WILD-TYPE 223 263
[1] "tbl2"
                cls
clus             [,1] [,2]
  SBDS MUTATED      2    1
  SBDS WILD-TYPE  223  263
        clus
vv       SBDS MUTATED SBDS WILD-TYPE
  FEMALE            2            223
  MALE              1            263
[1] 2 2
[1] FALSE
D1417V9, binary
                cls
clus               0   1
  SBDS MUTATED     2   1
  SBDS WILD-TYPE 348  21
[1] "tbl2"
                cls
clus             [,1] [,2]
  SBDS MUTATED      2    1
  SBDS WILD-TYPE  348   21
     clus
vv    SBDS MUTATED SBDS WILD-TYPE
  NO             2            348
  YES            1             21
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SBDS MUTATED                      3                             0
  SBDS WILD-TYPE                  312                            47
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SBDS MUTATED                       0                              0
  SBDS WILD-TYPE                   106                             10
D1417V10, multiclass
                                clus
vv                               SBDS MUTATED SBDS WILD-TYPE
  COLON ADENOCARCINOMA                      3            312
  COLON MUCINOUS ADENOCARCINOMA             0             47
  RECTAL ADENOCARCINOMA                     0            106
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  SBDS MUTATED     3   0   0   0
  SBDS WILD-TYPE 342   4  31  25
D1417V11, multiclass
    clus
vv   SBDS MUTATED SBDS WILD-TYPE
  R0            3            342
  R1            0              4
  R2            0             31
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1417V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SBDS MUTATED                                  0     0
  SBDS WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  SBDS MUTATED                           0     2
  SBDS WILD-TYPE                        22   224
D1417V13, multiclass
[1] "Remove cluster labels:" "SBDS MUTATED"          
clus
  SBDS MUTATED SBDS WILD-TYPE 
             2            258 
    TCGA-A6-2671     TCGA-A6-2672     TCGA-A6-2674     TCGA-A6-2676 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-A6-2677     TCGA-A6-2678     TCGA-A6-2683     TCGA-A6-3807 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-A6-3808     TCGA-A6-3809     TCGA-A6-3810     TCGA-A6-4105 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-A6-5656     TCGA-A6-5657     TCGA-A6-5659     TCGA-A6-5660 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-A6-5661     TCGA-A6-5662     TCGA-A6-5664     TCGA-A6-5665 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-A6-5666     TCGA-A6-6137     TCGA-A6-6138     TCGA-A6-6141 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-A6-6142     TCGA-A6-6648     TCGA-A6-6649     TCGA-A6-6651 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-A6-6652     TCGA-A6-6653     TCGA-A6-6654     TCGA-A6-6780 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-A6-6781     TCGA-A6-6782     TCGA-AD-5900     TCGA-AD-6548 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-AD-6888     TCGA-AD-6889     TCGA-AD-6890     TCGA-AD-6895 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-AD-6899     TCGA-AD-6901     TCGA-AD-6963     TCGA-AD-6964 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-AD-6965     TCGA-AU-3779     TCGA-AU-6004     TCGA-AY-4070 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-AY-4071     TCGA-AY-5543     TCGA-AY-6196     TCGA-AY-6197 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-AY-6386     TCGA-AZ-4315     TCGA-AZ-4323     TCGA-AZ-4616 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-AZ-4681     TCGA-AZ-4682     TCGA-AZ-5403     TCGA-AZ-5407 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-AZ-6598     TCGA-AZ-6599     TCGA-AZ-6600     TCGA-AZ-6601 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-AZ-6603     TCGA-AZ-6605     TCGA-AZ-6606     TCGA-AZ-6607 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-AZ-6608     TCGA-CA-5254     TCGA-CA-5255     TCGA-CA-5796 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-CA-5797     TCGA-CA-6715     TCGA-CA-6716     TCGA-CA-6717 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-CA-6718     TCGA-CA-6719     TCGA-CK-4947     TCGA-CK-4948 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-CK-4950     TCGA-CK-4952     TCGA-CK-5912     TCGA-CK-5913 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-CK-5914     TCGA-CK-5915     TCGA-CK-5916     TCGA-CK-6746 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-CK-6747     TCGA-CK-6748     TCGA-CK-6751     TCGA-CM-4743 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-CM-4744     TCGA-CM-4746     TCGA-CM-4747     TCGA-CM-4752 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-CM-5341     TCGA-CM-5344     TCGA-CM-5348     TCGA-CM-5349 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-CM-5860     TCGA-CM-5861     TCGA-CM-5862     TCGA-CM-5863 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-CM-5864     TCGA-CM-5868     TCGA-CM-6161     TCGA-CM-6162 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-CM-6163     TCGA-CM-6164     TCGA-CM-6165     TCGA-CM-6166 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-CM-6167     TCGA-CM-6168     TCGA-CM-6169     TCGA-CM-6170 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-CM-6171     TCGA-CM-6172     TCGA-CM-6674     TCGA-CM-6675 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-CM-6676     TCGA-CM-6677     TCGA-CM-6678     TCGA-CM-6679 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-CM-6680     TCGA-D5-5537     TCGA-D5-5538     TCGA-D5-5539 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-D5-5540     TCGA-D5-5541     TCGA-D5-6529     TCGA-D5-6532 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-D5-6533     TCGA-D5-6534     TCGA-D5-6535     TCGA-D5-6536 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-D5-6537     TCGA-D5-6538     TCGA-D5-6539     TCGA-D5-6540 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-D5-6541     TCGA-D5-6898     TCGA-D5-6920     TCGA-D5-6922 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-D5-6923     TCGA-D5-6924     TCGA-D5-6927     TCGA-D5-6928 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-D5-6929     TCGA-D5-6930     TCGA-D5-6931     TCGA-D5-6932 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-D5-7000     TCGA-DM-A0X9     TCGA-DM-A0XD     TCGA-DM-A0XF 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-DM-A1D0     TCGA-DM-A1D4     TCGA-DM-A1D6     TCGA-DM-A1D7 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-DM-A1D8     TCGA-DM-A1D9     TCGA-DM-A1DA     TCGA-DM-A1DB 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-DM-A1HA     TCGA-DM-A1HB     TCGA-DM-A282     TCGA-DM-A285 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-DM-A28C     TCGA-DM-A28E     TCGA-DM-A28F     TCGA-DM-A28G 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-DM-A28H     TCGA-DM-A28K     TCGA-F4-6459     TCGA-F4-6460 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-F4-6569     TCGA-F4-6570     TCGA-F4-6703     TCGA-F4-6704 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-F4-6805     TCGA-F4-6806     TCGA-F4-6807     TCGA-F4-6808 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-F4-6809     TCGA-F4-6854     TCGA-F4-6855     TCGA-F4-6856 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-G4-6293     TCGA-G4-6299     TCGA-G4-6304     TCGA-G4-6306 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-G4-6307     TCGA-G4-6309     TCGA-G4-6310     TCGA-G4-6315 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-G4-6317     TCGA-G4-6321     TCGA-G4-6323     TCGA-G4-6586 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-G4-6588     TCGA-G4-6625     TCGA-G4-6626     TCGA-G4-6628 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-AF-2687     TCGA-AF-2689     TCGA-AF-2691     TCGA-AF-2692 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-AF-2693     TCGA-AF-3400     TCGA-AF-3913     TCGA-AF-4110 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-AF-5654     TCGA-AF-6136     TCGA-AF-6655     TCGA-AF-6672 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-AH-6544     TCGA-AH-6547     TCGA-AH-6549     TCGA-AH-6643 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-AH-6644     TCGA-CI-6619     TCGA-CI-6620     TCGA-CI-6621 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-CI-6622     TCGA-CI-6624     TCGA-CL-5917     TCGA-CL-5918 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-DC-5337     TCGA-DC-5869     TCGA-DC-6155     TCGA-DC-6157 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-DC-6158     TCGA-DC-6160     TCGA-DC-6681     TCGA-DC-6682 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-DC-6683     TCGA-DT-5265     TCGA-DY-A0XA     TCGA-DY-A1DC 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-DY-A1DD     TCGA-DY-A1DF     TCGA-DY-A1DG     TCGA-DY-A1H8 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-EF-5830     TCGA-EI-6506     TCGA-EI-6507     TCGA-EI-6508 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-EI-6510     TCGA-F5-6464     TCGA-F5-6465     TCGA-F5-6571 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-F5-6702     TCGA-F5-6811     TCGA-F5-6812     TCGA-F5-6813 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" "SBDS WILD-TYPE" 
    TCGA-G5-6235     TCGA-G5-6641 
"SBDS WILD-TYPE" "SBDS WILD-TYPE" 

Clustering(1418) Variable = KIFC2 MUTATION ANALYSIS
D1418V1, survival
                 sevent
clus2               0   1
  KIFC2 MUTATED     6   0
  KIFC2 WILD-TYPE 372  93
  KIFC2 MUTATED KIFC2 WILD-TYPE 
              6             465 
  KIFC2 MUTATED KIFC2 WILD-TYPE 
              0              93 
$`KIFC2 MUTATED`
TCGA-A6-5665 TCGA-AA-3697 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-6386 TCGA-DM-A1HB 
       22.06        85.05        14.50        27.09        17.82       135.65 

$`KIFC2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       10.88         0.20        16.31         0.95        33.01        21.44 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
        7.50        44.32       131.51       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  KIFC2 MUTATED KIFC2 WILD-TYPE 
           14.5             0.0 
  KIFC2 MUTATED KIFC2 WILD-TYPE 
         135.65          148.01 
  KIFC2 MUTATED KIFC2 WILD-TYPE 
         24.575          20.120 
[1] "14.5 - 135.7 (24.6)" "0.0 - 148.0 (20.1)" 
[1] "hr="     "9300000"
D1418V2, continuous
D1418V3, binary
                 cls
clus                0   1
  KIFC2 MUTATED     6   0
  KIFC2 WILD-TYPE 360 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KIFC2 MUTATED      6    0
  KIFC2 WILD-TYPE  360  119
        clus
vv       KIFC2 MUTATED KIFC2 WILD-TYPE
  COLON              6             360
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KIFC2 MUTATED         1        0        0         2         0         0
  KIFC2 WILD-TYPE      90        1       32       136        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  KIFC2 MUTATED           1          0          2          0        0         0
  KIFC2 WILD-TYPE        23         11         57         42       48        18
                 vv
clus              STAGE IVB
  KIFC2 MUTATED           0
  KIFC2 WILD-TYPE         1
D1418V4, multiclass
            clus
vv           KIFC2 MUTATED KIFC2 WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              2             136
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             2              57
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  KIFC2 MUTATED     0   1   5   0
  KIFC2 WILD-TYPE  17  91 324  50
D1418V5, multiclass
    clus
vv   KIFC2 MUTATED KIFC2 WILD-TYPE
  T1             0              17
  T2             1              91
  T3             5             324
  T4             0              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  KIFC2 MUTATED     4   2   0
  KIFC2 WILD-TYPE 283 111  87
D1418V6, multiclass
    clus
vv   KIFC2 MUTATED KIFC2 WILD-TYPE
  N0             4             283
  N1             2             111
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1418V7, binary
                 cls
clus                0   1
  KIFC2 MUTATED     6   0
  KIFC2 WILD-TYPE 369  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KIFC2 MUTATED      6    0
  KIFC2 WILD-TYPE  369   65
   clus
vv  KIFC2 MUTATED KIFC2 WILD-TYPE
  0             6             369
  1             0              65
[1] 2 2
[1] FALSE
D1418V8, binary
                 cls
clus                0   1
  KIFC2 MUTATED     4   2
  KIFC2 WILD-TYPE 221 262
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KIFC2 MUTATED      4    2
  KIFC2 WILD-TYPE  221  262
        clus
vv       KIFC2 MUTATED KIFC2 WILD-TYPE
  FEMALE             4             221
  MALE               2             262
[1] 2 2
[1] FALSE
D1418V9, binary
                 cls
clus                0   1
  KIFC2 MUTATED     4   0
  KIFC2 WILD-TYPE 346  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KIFC2 MUTATED      4    0
  KIFC2 WILD-TYPE  346   22
     clus
vv    KIFC2 MUTATED KIFC2 WILD-TYPE
  NO              4             346
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  KIFC2 MUTATED                      5                             0
  KIFC2 WILD-TYPE                  310                            47
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  KIFC2 MUTATED                       0                              0
  KIFC2 WILD-TYPE                   106                             10
D1418V10, multiclass
                                clus
vv                               KIFC2 MUTATED KIFC2 WILD-TYPE
  COLON ADENOCARCINOMA                       5             310
  COLON MUCINOUS ADENOCARCINOMA              0              47
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  KIFC2 MUTATED     5   0   0   0
  KIFC2 WILD-TYPE 340   4  31  25
D1418V11, multiclass
    clus
vv   KIFC2 MUTATED KIFC2 WILD-TYPE
  R0             5             340
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1418V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KIFC2 MUTATED                                  0     0
  KIFC2 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  KIFC2 MUTATED                           1     4
  KIFC2 WILD-TYPE                        21   222
D1418V13, multiclass
                                  clus
vv                                 KIFC2 MUTATED KIFC2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        4             222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1419) Variable = PSMD11 MUTATION ANALYSIS
D1419V1, survival
                  sevent
clus2                0   1
  PSMD11 MUTATED     6   2
  PSMD11 WILD-TYPE 372  91
  PSMD11 MUTATED PSMD11 WILD-TYPE 
               8              463 
  PSMD11 MUTATED PSMD11 WILD-TYPE 
               2               91 
$`PSMD11 MUTATED`
TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01R TCGA-AD-5900 TCGA-AY-5543 TCGA-CM-6161 
        4.01        34.98        35.01         0.07        33.01        15.02 
TCGA-CM-6162 TCGA-DM-A1D8 
       12.00        12.59 

$`PSMD11 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T 
       31.00        31.00        38.07         1.02         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       18.05        40.96        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6197 TCGA-AY-6386 
       14.50        27.09        16.31         0.95        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       15.02        15.02        17.03         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       49.91        13.32       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  PSMD11 MUTATED PSMD11 WILD-TYPE 
            0.07             0.00 
  PSMD11 MUTATED PSMD11 WILD-TYPE 
           35.01           148.01 
  PSMD11 MUTATED PSMD11 WILD-TYPE 
          13.805           20.280 
[1] "0.1 - 35.0 (13.8)"  "0.0 - 148.0 (20.3)"
[1] "hr=" "2"  
D1419V2, continuous
D1419V3, binary
                  cls
clus                 0   1
  PSMD11 MUTATED     8   0
  PSMD11 WILD-TYPE 358 119
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PSMD11 MUTATED      8    0
  PSMD11 WILD-TYPE  358  119
        clus
vv       PSMD11 MUTATED PSMD11 WILD-TYPE
  COLON               8              358
  RECTUM              0              119
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PSMD11 MUTATED         2        0        0         0         2         0
  PSMD11 WILD-TYPE      89        1       32       138         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PSMD11 MUTATED           1          0          1          0        0
  PSMD11 WILD-TYPE        23         11         58         42       48
                  vv
clus               STAGE IVA STAGE IVB
  PSMD11 MUTATED           1         0
  PSMD11 WILD-TYPE        17         1
D1419V4, multiclass
            clus
vv           PSMD11 MUTATED PSMD11 WILD-TYPE
  STAGE I                 2               89
  STAGE IA                0                1
  STAGE II                0               32
  STAGE IIA               0              138
  STAGE IIB               2                8
  STAGE IIC               0                1
  STAGE III               1               23
  STAGE IIIA              0               11
  STAGE IIIB              1               58
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               1               17
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  PSMD11 MUTATED     0   2   4   2
  PSMD11 WILD-TYPE  17  90 325  48
D1419V5, multiclass
    clus
vv   PSMD11 MUTATED PSMD11 WILD-TYPE
  T1              0               17
  T2              2               90
  T3              4              325
  T4              2               48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  PSMD11 MUTATED     4   3   1
  PSMD11 WILD-TYPE 283 110  86
D1419V6, multiclass
    clus
vv   PSMD11 MUTATED PSMD11 WILD-TYPE
  N0              4              283
  N1              3              110
  N2              1               86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1419V7, binary
                  cls
clus                 0   1
  PSMD11 MUTATED     5   1
  PSMD11 WILD-TYPE 370  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PSMD11 MUTATED      5    1
  PSMD11 WILD-TYPE  370   64
   clus
vv  PSMD11 MUTATED PSMD11 WILD-TYPE
  0              5              370
  1              1               64
[1] 2 2
[1] FALSE
D1419V8, binary
                  cls
clus                 0   1
  PSMD11 MUTATED     5   3
  PSMD11 WILD-TYPE 220 261
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PSMD11 MUTATED      5    3
  PSMD11 WILD-TYPE  220  261
        clus
vv       PSMD11 MUTATED PSMD11 WILD-TYPE
  FEMALE              5              220
  MALE                3              261
[1] 2 2
[1] FALSE
D1419V9, binary
                  cls
clus                 0   1
  PSMD11 MUTATED     4   1
  PSMD11 WILD-TYPE 346  21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PSMD11 MUTATED      4    1
  PSMD11 WILD-TYPE  346   21
     clus
vv    PSMD11 MUTATED PSMD11 WILD-TYPE
  NO               4              346
  YES              1               21
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PSMD11 MUTATED                      4                             4
  PSMD11 WILD-TYPE                  311                            43
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PSMD11 MUTATED                       0                              0
  PSMD11 WILD-TYPE                   106                             10
D1419V10, multiclass
                                clus
vv                               PSMD11 MUTATED PSMD11 WILD-TYPE
  COLON ADENOCARCINOMA                        4              311
  COLON MUCINOUS ADENOCARCINOMA               4               43
  RECTAL ADENOCARCINOMA                       0              106
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  PSMD11 MUTATED     7   0   0   0
  PSMD11 WILD-TYPE 338   4  31  25
D1419V11, multiclass
    clus
vv   PSMD11 MUTATED PSMD11 WILD-TYPE
  R0              7              338
  R1              0                4
  R2              0               31
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1419V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PSMD11 MUTATED                                  0     0
  PSMD11 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  PSMD11 MUTATED                           1     4
  PSMD11 WILD-TYPE                        21   222
D1419V13, multiclass
                                  clus
vv                                 PSMD11 MUTATED PSMD11 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                         4              222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1420) Variable = PPYR1 MUTATION ANALYSIS
D1420V1, survival
                 sevent
clus2               0   1
  PPYR1 MUTATED     5   1
  PPYR1 WILD-TYPE 373  92
  PPYR1 MUTATED PPYR1 WILD-TYPE 
              6             465 
  PPYR1 MUTATED PPYR1 WILD-TYPE 
              1              92 
$`PPYR1 MUTATED`
TCGA-AU-6004 TCGA-CM-6674 TCGA-G4-6586 TCGA-G4-6626 TCGA-AG-A002 TCGA-AG-A00C 
       27.09        12.95        35.80        46.75        20.98         6.02 

$`PPYR1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 
       22.42        27.42        10.88         0.20        14.50        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       11.01        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 
       63.62        61.91        36.00        22.09        13.78        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       91.79        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00H 
       36.03        14.04         1.02        17.03        13.94        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  PPYR1 MUTATED PPYR1 WILD-TYPE 
           6.02            0.00 
  PPYR1 MUTATED PPYR1 WILD-TYPE 
          46.75          148.01 
  PPYR1 MUTATED PPYR1 WILD-TYPE 
         24.035          20.120 
[1] "6.0 - 46.8 (24.0)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.1"
D1420V2, continuous
D1420V3, binary
                 cls
clus                0   1
  PPYR1 MUTATED     5   2
  PPYR1 WILD-TYPE 361 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PPYR1 MUTATED      5    2
  PPYR1 WILD-TYPE  361  117
        clus
vv       PPYR1 MUTATED PPYR1 WILD-TYPE
  COLON              5             361
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PPYR1 MUTATED         2        0        0         4         0         0
  PPYR1 WILD-TYPE      89        1       32       134        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PPYR1 MUTATED           0          0          1          0        0         0
  PPYR1 WILD-TYPE        24         11         58         42       48        18
                 vv
clus              STAGE IVB
  PPYR1 MUTATED           0
  PPYR1 WILD-TYPE         1
D1420V4, multiclass
            clus
vv           PPYR1 MUTATED PPYR1 WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              4             134
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PPYR1 MUTATED     0   2   5   0
  PPYR1 WILD-TYPE  17  90 324  50
D1420V5, multiclass
    clus
vv   PPYR1 MUTATED PPYR1 WILD-TYPE
  T1             0              17
  T2             2              90
  T3             5             324
  T4             0              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  PPYR1 MUTATED     6   1   0
  PPYR1 WILD-TYPE 281 112  87
D1420V6, multiclass
    clus
vv   PPYR1 MUTATED PPYR1 WILD-TYPE
  N0             6             281
  N1             1             112
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1420V7, binary
                 cls
clus                0   1
  PPYR1 MUTATED     7   0
  PPYR1 WILD-TYPE 368  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PPYR1 MUTATED      7    0
  PPYR1 WILD-TYPE  368   65
   clus
vv  PPYR1 MUTATED PPYR1 WILD-TYPE
  0             7             368
  1             0              65
[1] 2 2
[1] FALSE
D1420V8, binary
                 cls
clus                0   1
  PPYR1 MUTATED     4   3
  PPYR1 WILD-TYPE 221 261
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PPYR1 MUTATED      4    3
  PPYR1 WILD-TYPE  221  261
        clus
vv       PPYR1 MUTATED PPYR1 WILD-TYPE
  FEMALE             4             221
  MALE               3             261
[1] 2 2
[1] FALSE
D1420V9, binary
                 cls
clus                0   1
  PPYR1 MUTATED     4   1
  PPYR1 WILD-TYPE 346  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PPYR1 MUTATED      4    1
  PPYR1 WILD-TYPE  346   21
     clus
vv    PPYR1 MUTATED PPYR1 WILD-TYPE
  NO              4             346
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PPYR1 MUTATED                      5                             0
  PPYR1 WILD-TYPE                  310                            47
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PPYR1 MUTATED                       2                              0
  PPYR1 WILD-TYPE                   104                             10
D1420V10, multiclass
                                clus
vv                               PPYR1 MUTATED PPYR1 WILD-TYPE
  COLON ADENOCARCINOMA                       5             310
  COLON MUCINOUS ADENOCARCINOMA              0              47
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  PPYR1 MUTATED     7   0   0   0
  PPYR1 WILD-TYPE 338   4  31  25
D1420V11, multiclass
    clus
vv   PPYR1 MUTATED PPYR1 WILD-TYPE
  R0             7             338
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1420V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PPYR1 MUTATED                                  0     0
  PPYR1 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PPYR1 MUTATED                           0     4
  PPYR1 WILD-TYPE                        22   222
D1420V13, multiclass
                                  clus
vv                                 PPYR1 MUTATED PPYR1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        4             222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1421) Variable = MCM4 MUTATION ANALYSIS
D1421V1, survival
                sevent
clus2              0   1
  MCM4 MUTATED    11   3
  MCM4 WILD-TYPE 367  90
  MCM4 MUTATED MCM4 WILD-TYPE 
            14            457 
  MCM4 MUTATED MCM4 WILD-TYPE 
             3             90 
$`MCM4 MUTATED`
TCGA-A6-6781 TCGA-AA-3821 TCGA-AA-3845 TCGA-AA-A00J TCGA-AA-A010 TCGA-AZ-6598 
       19.66         1.02         0.00        18.05        34.98        49.41 
TCGA-CA-6717 TCGA-CK-4950 TCGA-CK-5913 TCGA-CM-5348 TCGA-CM-6165 TCGA-D5-6929 
       12.76        85.45        51.32        22.98        16.04         4.80 
TCGA-AH-6544 TCGA-F5-6464 
       38.56         9.96 

$`MCM4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 
       10.06        35.05        33.04         0.99        25.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 
       15.95        38.99        37.02        14.93        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       88.21         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07        12.20        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
      148.01        15.62        49.08         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       13.02        29.06        22.03        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
        2.96        29.03        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 
       14.30         9.04         9.44        11.64         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6547 TCGA-AH-6549 
       61.97        41.00        38.04       117.11         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6465 
        0.49        20.55        19.96        20.91        18.28        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  MCM4 MUTATED MCM4 WILD-TYPE 
             0              0 
  MCM4 MUTATED MCM4 WILD-TYPE 
         85.45         148.01 
  MCM4 MUTATED MCM4 WILD-TYPE 
        18.855         20.280 
[1] "0.0 - 85.5 (18.9)"  "0.0 - 148.0 (20.3)"
[1] "hr=" "1.1"
D1421V2, continuous
D1421V3, binary
                cls
clus               0   1
  MCM4 MUTATED    12   2
  MCM4 WILD-TYPE 354 117
[1] "tbl2"
                cls
clus             [,1] [,2]
  MCM4 MUTATED     12    2
  MCM4 WILD-TYPE  354  117
        clus
vv       MCM4 MUTATED MCM4 WILD-TYPE
  COLON            12            354
  RECTUM            2            117
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MCM4 MUTATED         1        0        1         4         1         0
  MCM4 WILD-TYPE      90        1       31       134         9         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MCM4 MUTATED           0          0          3          2        1         0
  MCM4 WILD-TYPE        24         11         56         40       47        18
                vv
clus             STAGE IVB
  MCM4 MUTATED           0
  MCM4 WILD-TYPE         1
D1421V4, multiclass
            clus
vv           MCM4 MUTATED MCM4 WILD-TYPE
  STAGE I               1             90
  STAGE IA              0              1
  STAGE II              1             31
  STAGE IIA             4            134
  STAGE IIB             1              9
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            3             56
  STAGE IIIC            2             40
  STAGE IV              1             47
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  MCM4 MUTATED     0   1   9   4
  MCM4 WILD-TYPE  17  91 320  46
D1421V5, multiclass
    clus
vv   MCM4 MUTATED MCM4 WILD-TYPE
  T1            0             17
  T2            1             91
  T3            9            320
  T4            4             46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  MCM4 MUTATED     7   6   1
  MCM4 WILD-TYPE 280 107  86
D1421V6, multiclass
    clus
vv   MCM4 MUTATED MCM4 WILD-TYPE
  N0            7            280
  N1            6            107
  N2            1             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1421V7, binary
                cls
clus               0   1
  MCM4 MUTATED     9   2
  MCM4 WILD-TYPE 366  63
[1] "tbl2"
                cls
clus             [,1] [,2]
  MCM4 MUTATED      9    2
  MCM4 WILD-TYPE  366   63
   clus
vv  MCM4 MUTATED MCM4 WILD-TYPE
  0            9            366
  1            2             63
[1] 2 2
[1] FALSE
D1421V8, binary
                cls
clus               0   1
  MCM4 MUTATED     8   6
  MCM4 WILD-TYPE 217 258
[1] "tbl2"
                cls
clus             [,1] [,2]
  MCM4 MUTATED      8    6
  MCM4 WILD-TYPE  217  258
        clus
vv       MCM4 MUTATED MCM4 WILD-TYPE
  FEMALE            8            217
  MALE              6            258
[1] 2 2
[1] FALSE
D1421V9, binary
                cls
clus               0   1
  MCM4 MUTATED    12   0
  MCM4 WILD-TYPE 338  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  MCM4 MUTATED     12    0
  MCM4 WILD-TYPE  338   22
     clus
vv    MCM4 MUTATED MCM4 WILD-TYPE
  NO            12            338
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MCM4 MUTATED                      8                             4
  MCM4 WILD-TYPE                  307                            43
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MCM4 MUTATED                       2                              0
  MCM4 WILD-TYPE                   104                             10
D1421V10, multiclass
                                clus
vv                               MCM4 MUTATED MCM4 WILD-TYPE
  COLON ADENOCARCINOMA                      8            307
  COLON MUCINOUS ADENOCARCINOMA             4             43
  RECTAL ADENOCARCINOMA                     2            104
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  MCM4 MUTATED     9   1   0   2
  MCM4 WILD-TYPE 336   3  31  23
D1421V11, multiclass
    clus
vv   MCM4 MUTATED MCM4 WILD-TYPE
  R0            9            336
  R1            1              3
  R2            0             31
  RX            2             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1421V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MCM4 MUTATED                                  0     1
  MCM4 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  MCM4 MUTATED                           1     8
  MCM4 WILD-TYPE                        21   218
D1421V13, multiclass
                                  clus
vv                                 MCM4 MUTATED MCM4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                       8            218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1422) Variable = ARHGEF3 MUTATION ANALYSIS
D1422V1, survival
                   sevent
clus2                 0   1
  ARHGEF3 MUTATED     9   1
  ARHGEF3 WILD-TYPE 369  92
  ARHGEF3 MUTATED ARHGEF3 WILD-TYPE 
               10               461 
  ARHGEF3 MUTATED ARHGEF3 WILD-TYPE 
                1                92 
$`ARHGEF3 MUTATED`
TCGA-A6-6653 TCGA-AA-3663 TCGA-AA-3977 TCGA-AA-A010 TCGA-AA-A01Q TCGA-AZ-4315 
       24.39         6.97        25.02        34.98         1.02        58.39 
TCGA-AZ-6601 TCGA-CA-6717 TCGA-CM-5868 TCGA-D5-6540 
      100.01        12.76        17.03        16.14 

$`ARHGEF3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
       25.08        25.18        24.16        21.76        24.69        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
       38.07        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       49.41         6.77        12.10        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07        12.20        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6161 
       32.02        15.02         5.03        15.02        15.02        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       17.13        12.49        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  ARHGEF3 MUTATED ARHGEF3 WILD-TYPE 
             1.02              0.00 
  ARHGEF3 MUTATED ARHGEF3 WILD-TYPE 
           100.01            148.01 
  ARHGEF3 MUTATED ARHGEF3 WILD-TYPE 
            20.71             20.19 
[1] "1.0 - 100.0 (20.7)" "0.0 - 148.0 (20.2)"
[1] "hr=" "2.3"
D1422V2, continuous
D1422V3, binary
                   cls
clus                  0   1
  ARHGEF3 MUTATED    11   0
  ARHGEF3 WILD-TYPE 355 119
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ARHGEF3 MUTATED     11    0
  ARHGEF3 WILD-TYPE  355  119
        clus
vv       ARHGEF3 MUTATED ARHGEF3 WILD-TYPE
  COLON               11               355
  RECTUM               0               119
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ARHGEF3 MUTATED         2        0        3         2         1         0
  ARHGEF3 WILD-TYPE      89        1       29       136         9         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ARHGEF3 MUTATED           0          0          0          1        0
  ARHGEF3 WILD-TYPE        24         11         59         41       48
                   vv
clus                STAGE IVA STAGE IVB
  ARHGEF3 MUTATED           1         0
  ARHGEF3 WILD-TYPE        17         1
D1422V4, multiclass
            clus
vv           ARHGEF3 MUTATED ARHGEF3 WILD-TYPE
  STAGE I                  2                89
  STAGE IA                 0                 1
  STAGE II                 3                29
  STAGE IIA                2               136
  STAGE IIB                1                 9
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               0                11
  STAGE IIIB               0                59
  STAGE IIIC               1                41
  STAGE IV                 0                48
  STAGE IVA                1                17
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  ARHGEF3 MUTATED     0   3   6   2
  ARHGEF3 WILD-TYPE  17  89 323  48
D1422V5, multiclass
    clus
vv   ARHGEF3 MUTATED ARHGEF3 WILD-TYPE
  T1               0                17
  T2               3                89
  T3               6               323
  T4               2                48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  ARHGEF3 MUTATED     9   1   1
  ARHGEF3 WILD-TYPE 278 112  86
D1422V6, multiclass
    clus
vv   ARHGEF3 MUTATED ARHGEF3 WILD-TYPE
  N0               9               278
  N1               1               112
  N2               1                86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1422V7, binary
                   cls
clus                  0   1
  ARHGEF3 MUTATED     8   1
  ARHGEF3 WILD-TYPE 367  64
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ARHGEF3 MUTATED      8    1
  ARHGEF3 WILD-TYPE  367   64
   clus
vv  ARHGEF3 MUTATED ARHGEF3 WILD-TYPE
  0               8               367
  1               1                64
[1] 2 2
[1] FALSE
D1422V8, binary
                   cls
clus                  0   1
  ARHGEF3 MUTATED     3   8
  ARHGEF3 WILD-TYPE 222 256
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ARHGEF3 MUTATED      3    8
  ARHGEF3 WILD-TYPE  222  256
        clus
vv       ARHGEF3 MUTATED ARHGEF3 WILD-TYPE
  FEMALE               3               222
  MALE                 8               256
[1] 2 2
[1] FALSE
D1422V9, binary
                   cls
clus                  0   1
  ARHGEF3 MUTATED     9   0
  ARHGEF3 WILD-TYPE 341  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ARHGEF3 MUTATED      9    0
  ARHGEF3 WILD-TYPE  341   22
     clus
vv    ARHGEF3 MUTATED ARHGEF3 WILD-TYPE
  NO                9               341
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ARHGEF3 MUTATED                      8                             3
  ARHGEF3 WILD-TYPE                  307                            44
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ARHGEF3 MUTATED                       0                              0
  ARHGEF3 WILD-TYPE                   106                             10
D1422V10, multiclass
                                clus
vv                               ARHGEF3 MUTATED ARHGEF3 WILD-TYPE
  COLON ADENOCARCINOMA                         8               307
  COLON MUCINOUS ADENOCARCINOMA                3                44
  RECTAL ADENOCARCINOMA                        0               106
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  ARHGEF3 MUTATED     7   0   0   1
  ARHGEF3 WILD-TYPE 338   4  31  24
D1422V11, multiclass
    clus
vv   ARHGEF3 MUTATED ARHGEF3 WILD-TYPE
  R0               7               338
  R1               0                 4
  R2               0                31
  RX               1                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1422V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ARHGEF3 MUTATED                                  0     1
  ARHGEF3 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  ARHGEF3 MUTATED                           0     6
  ARHGEF3 WILD-TYPE                        22   220
D1422V13, multiclass
                                  clus
vv                                 ARHGEF3 MUTATED ARHGEF3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                10
  BLACK OR AFRICAN AMERICAN                      0                22
  WHITE                                          6               220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1423) Variable = KLF3 MUTATION ANALYSIS
D1423V1, survival
                sevent
clus2              0   1
  KLF3 MUTATED     4   1
  KLF3 WILD-TYPE 374  92
  KLF3 MUTATED KLF3 WILD-TYPE 
             5            466 
  KLF3 MUTATED KLF3 WILD-TYPE 
             1             92 
$`KLF3 MUTATED`
TCGA-A6-5665 TCGA-AA-3663 TCGA-AA-3930 TCGA-AD-6895 TCGA-AZ-4315 
       22.06         6.97         2.01         0.72        58.39 

$`KLF3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3939 
       24.03        27.02        29.98        18.05        31.00        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.79         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  KLF3 MUTATED KLF3 WILD-TYPE 
          0.72           0.00 
  KLF3 MUTATED KLF3 WILD-TYPE 
         58.39         148.01 
  KLF3 MUTATED KLF3 WILD-TYPE 
         6.970         20.235 
[1] "0.7 - 58.4 (7.0)"   "0.0 - 148.0 (20.2)"
[1] "hr=" "1.3"
D1423V2, continuous
D1423V3, binary
                cls
clus               0   1
  KLF3 MUTATED     7   0
  KLF3 WILD-TYPE 359 119
[1] "tbl2"
                cls
clus             [,1] [,2]
  KLF3 MUTATED      7    0
  KLF3 WILD-TYPE  359  119
        clus
vv       KLF3 MUTATED KLF3 WILD-TYPE
  COLON             7            359
  RECTUM            0            119
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KLF3 MUTATED         0        0        1         3         1         0
  KLF3 WILD-TYPE      91        1       31       135         9         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  KLF3 MUTATED           0          0          0          0        1         0
  KLF3 WILD-TYPE        24         11         59         42       47        18
                vv
clus             STAGE IVB
  KLF3 MUTATED           0
  KLF3 WILD-TYPE         1
D1423V4, multiclass
            clus
vv           KLF3 MUTATED KLF3 WILD-TYPE
  STAGE I               0             91
  STAGE IA              0              1
  STAGE II              1             31
  STAGE IIA             3            135
  STAGE IIB             1              9
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            0             59
  STAGE IIIC            0             42
  STAGE IV              1             47
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  KLF3 MUTATED     0   0   6   1
  KLF3 WILD-TYPE  17  92 323  49
D1423V5, multiclass
    clus
vv   KLF3 MUTATED KLF3 WILD-TYPE
  T1            0             17
  T2            0             92
  T3            6            323
  T4            1             49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  KLF3 MUTATED     5   1   1
  KLF3 WILD-TYPE 282 112  86
D1423V6, multiclass
    clus
vv   KLF3 MUTATED KLF3 WILD-TYPE
  N0            5            282
  N1            1            112
  N2            1             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1423V7, binary
                cls
clus               0   1
  KLF3 MUTATED     4   1
  KLF3 WILD-TYPE 371  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  KLF3 MUTATED      4    1
  KLF3 WILD-TYPE  371   64
   clus
vv  KLF3 MUTATED KLF3 WILD-TYPE
  0            4            371
  1            1             64
[1] 2 2
[1] FALSE
D1423V8, binary
                cls
clus               0   1
  KLF3 MUTATED     3   4
  KLF3 WILD-TYPE 222 260
[1] "tbl2"
                cls
clus             [,1] [,2]
  KLF3 MUTATED      3    4
  KLF3 WILD-TYPE  222  260
        clus
vv       KLF3 MUTATED KLF3 WILD-TYPE
  FEMALE            3            222
  MALE              4            260
[1] 2 2
[1] FALSE
D1423V9, binary
                cls
clus               0   1
  KLF3 MUTATED     4   0
  KLF3 WILD-TYPE 346  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  KLF3 MUTATED      4    0
  KLF3 WILD-TYPE  346   22
     clus
vv    KLF3 MUTATED KLF3 WILD-TYPE
  NO             4            346
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  KLF3 MUTATED                      7                             0
  KLF3 WILD-TYPE                  308                            47
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  KLF3 MUTATED                       0                              0
  KLF3 WILD-TYPE                   106                             10
D1423V10, multiclass
                                clus
vv                               KLF3 MUTATED KLF3 WILD-TYPE
  COLON ADENOCARCINOMA                      7            308
  COLON MUCINOUS ADENOCARCINOMA             0             47
  RECTAL ADENOCARCINOMA                     0            106
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  KLF3 MUTATED     4   0   1   1
  KLF3 WILD-TYPE 341   4  30  24
D1423V11, multiclass
    clus
vv   KLF3 MUTATED KLF3 WILD-TYPE
  R0            4            341
  R1            0              4
  R2            1             30
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1423V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KLF3 MUTATED                                  0     0
  KLF3 WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  KLF3 MUTATED                           0     4
  KLF3 WILD-TYPE                        22   222
D1423V13, multiclass
                                  clus
vv                                 KLF3 MUTATED KLF3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       4            222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1424) Variable = SENP8 MUTATION ANALYSIS
D1424V1, survival
                 sevent
clus2               0   1
  SENP8 MUTATED     3   0
  SENP8 WILD-TYPE 375  93
  SENP8 MUTATED SENP8 WILD-TYPE 
              3             468 
  SENP8 MUTATED SENP8 WILD-TYPE 
              0              93 
$`SENP8 MUTATED`
TCGA-A6-6780 TCGA-A6-6781 TCGA-CM-6674 
       20.12        19.66        12.95 

$`SENP8 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       23.87        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  SENP8 MUTATED SENP8 WILD-TYPE 
          12.95            0.00 
  SENP8 MUTATED SENP8 WILD-TYPE 
          20.12          148.01 
  SENP8 MUTATED SENP8 WILD-TYPE 
         19.660          20.415 
[1] "12.9 - 20.1 (19.7)" "0.0 - 148.0 (20.4)"
[1] "hr="     "3300000"
D1424V2, continuous
D1424V3, binary
                 cls
clus                0   1
  SENP8 MUTATED     4   0
  SENP8 WILD-TYPE 362 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SENP8 MUTATED      4    0
  SENP8 WILD-TYPE  362  119
        clus
vv       SENP8 MUTATED SENP8 WILD-TYPE
  COLON              4             362
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SENP8 MUTATED         0        0        0         2         1         0
  SENP8 WILD-TYPE      91        1       32       136         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SENP8 MUTATED           0          0          0          1        0         0
  SENP8 WILD-TYPE        24         11         59         41       48        18
                 vv
clus              STAGE IVB
  SENP8 MUTATED           0
  SENP8 WILD-TYPE         1
D1424V4, multiclass
            clus
vv           SENP8 MUTATED SENP8 WILD-TYPE
  STAGE I                0              91
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              2             136
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             1              41
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  SENP8 MUTATED     0   0   2   2
  SENP8 WILD-TYPE  17  92 327  48
D1424V5, multiclass
    clus
vv   SENP8 MUTATED SENP8 WILD-TYPE
  T1             0              17
  T2             0              92
  T3             2             327
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  SENP8 MUTATED     3   1   0
  SENP8 WILD-TYPE 284 112  87
D1424V6, multiclass
    clus
vv   SENP8 MUTATED SENP8 WILD-TYPE
  N0             3             284
  N1             1             112
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1424V7, binary
                 cls
clus                0   1
  SENP8 MUTATED     1   0
  SENP8 WILD-TYPE 374  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SENP8 MUTATED      1    0
  SENP8 WILD-TYPE  374   65
   clus
vv  SENP8 MUTATED SENP8 WILD-TYPE
  0             1             374
  1             0              65
[1] 2 2
[1] FALSE
D1424V8, binary
                 cls
clus                0   1
  SENP8 MUTATED     1   3
  SENP8 WILD-TYPE 224 261
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SENP8 MUTATED      1    3
  SENP8 WILD-TYPE  224  261
        clus
vv       SENP8 MUTATED SENP8 WILD-TYPE
  FEMALE             1             224
  MALE               3             261
[1] 2 2
[1] FALSE
D1424V9, binary
                 cls
clus                0   1
  SENP8 MUTATED     3   0
  SENP8 WILD-TYPE 347  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SENP8 MUTATED      3    0
  SENP8 WILD-TYPE  347   22
     clus
vv    SENP8 MUTATED SENP8 WILD-TYPE
  NO              3             347
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SENP8 MUTATED                      2                             2
  SENP8 WILD-TYPE                  313                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SENP8 MUTATED                       0                              0
  SENP8 WILD-TYPE                   106                             10
D1424V10, multiclass
                                clus
vv                               SENP8 MUTATED SENP8 WILD-TYPE
  COLON ADENOCARCINOMA                       2             313
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  SENP8 MUTATED     2   0   0   1
  SENP8 WILD-TYPE 343   4  31  24
D1424V11, multiclass
    clus
vv   SENP8 MUTATED SENP8 WILD-TYPE
  R0             2             343
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1424V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SENP8 MUTATED                                  0     0
  SENP8 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  SENP8 MUTATED                           0     4
  SENP8 WILD-TYPE                        22   222
D1424V13, multiclass
                                  clus
vv                                 SENP8 MUTATED SENP8 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        4             222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1425) Variable = GCM2 MUTATION ANALYSIS
D1425V1, survival
                sevent
clus2              0   1
  GCM2 MUTATED     9   4
  GCM2 WILD-TYPE 369  89
  GCM2 MUTATED GCM2 WILD-TYPE 
            13            458 
  GCM2 MUTATED GCM2 WILD-TYPE 
             4             89 
$`GCM2 MUTATED`
TCGA-A6-5665 TCGA-AA-3972 TCGA-AA-A010 TCGA-AA-A02K TCGA-AD-6889 TCGA-AD-6964 
       22.06        50.99        34.98        14.01        56.55        10.88 
TCGA-AY-5543 TCGA-AZ-6605 TCGA-CM-5344 TCGA-AG-A002 TCGA-DY-A1DG TCGA-EI-6506 
       33.01         5.23        22.03        20.98        51.48        20.55 
TCGA-EI-6507 
       19.96 

$`GCM2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        2.01         5.03         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 
       40.96         0.07        21.37        15.52         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       16.31         0.95        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77        12.10       100.01        29.56        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       25.02        13.02        29.06        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
       24.13        32.61         0.49        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  GCM2 MUTATED GCM2 WILD-TYPE 
          5.23           0.00 
  GCM2 MUTATED GCM2 WILD-TYPE 
         56.55         148.01 
  GCM2 MUTATED GCM2 WILD-TYPE 
        22.030         20.035 
[1] "5.2 - 56.5 (22.0)"  "0.0 - 148.0 (20.0)"
[1] "hr=" "1.4"
D1425V2, continuous
D1425V3, binary
                cls
clus               0   1
  GCM2 MUTATED    10   4
  GCM2 WILD-TYPE 356 115
[1] "tbl2"
                cls
clus             [,1] [,2]
  GCM2 MUTATED     10    4
  GCM2 WILD-TYPE  356  115
        clus
vv       GCM2 MUTATED GCM2 WILD-TYPE
  COLON            10            356
  RECTUM            4            115
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GCM2 MUTATED         1        0        0         5         1         0
  GCM2 WILD-TYPE      90        1       32       133         9         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  GCM2 MUTATED           0          0          2          0        2         2
  GCM2 WILD-TYPE        24         11         57         42       46        16
                vv
clus             STAGE IVB
  GCM2 MUTATED           0
  GCM2 WILD-TYPE         1
D1425V4, multiclass
            clus
vv           GCM2 MUTATED GCM2 WILD-TYPE
  STAGE I               1             90
  STAGE IA              0              1
  STAGE II              0             32
  STAGE IIA             5            133
  STAGE IIB             1              9
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            2             57
  STAGE IIIC            0             42
  STAGE IV              2             46
  STAGE IVA             2             16
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  GCM2 MUTATED     0   1   9   4
  GCM2 WILD-TYPE  17  91 320  46
D1425V5, multiclass
    clus
vv   GCM2 MUTATED GCM2 WILD-TYPE
  T1            0             17
  T2            1             91
  T3            9            320
  T4            4             46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  GCM2 MUTATED     7   5   2
  GCM2 WILD-TYPE 280 108  85
D1425V6, multiclass
    clus
vv   GCM2 MUTATED GCM2 WILD-TYPE
  N0            7            280
  N1            5            108
  N2            2             85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1425V7, binary
                cls
clus               0   1
  GCM2 MUTATED     9   4
  GCM2 WILD-TYPE 366  61
[1] "tbl2"
                cls
clus             [,1] [,2]
  GCM2 MUTATED      9    4
  GCM2 WILD-TYPE  366   61
   clus
vv  GCM2 MUTATED GCM2 WILD-TYPE
  0            9            366
  1            4             61
[1] 2 2
[1] FALSE
D1425V8, binary
                cls
clus               0   1
  GCM2 MUTATED     6   8
  GCM2 WILD-TYPE 219 256
[1] "tbl2"
                cls
clus             [,1] [,2]
  GCM2 MUTATED      6    8
  GCM2 WILD-TYPE  219  256
        clus
vv       GCM2 MUTATED GCM2 WILD-TYPE
  FEMALE            6            219
  MALE              8            256
[1] 2 2
[1] FALSE
D1425V9, binary
                cls
clus               0   1
  GCM2 MUTATED    11   0
  GCM2 WILD-TYPE 339  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  GCM2 MUTATED     11    0
  GCM2 WILD-TYPE  339   22
     clus
vv    GCM2 MUTATED GCM2 WILD-TYPE
  NO            11            339
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  GCM2 MUTATED                     10                             0
  GCM2 WILD-TYPE                  305                            47
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  GCM2 MUTATED                       4                              0
  GCM2 WILD-TYPE                   102                             10
D1425V10, multiclass
                                clus
vv                               GCM2 MUTATED GCM2 WILD-TYPE
  COLON ADENOCARCINOMA                     10            305
  COLON MUCINOUS ADENOCARCINOMA             0             47
  RECTAL ADENOCARCINOMA                     4            102
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  GCM2 MUTATED     8   0   2   0
  GCM2 WILD-TYPE 337   4  29  25
D1425V11, multiclass
    clus
vv   GCM2 MUTATED GCM2 WILD-TYPE
  R0            8            337
  R1            0              4
  R2            2             29
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1425V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GCM2 MUTATED                                  0     1
  GCM2 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  GCM2 MUTATED                           1     7
  GCM2 WILD-TYPE                        21   219
D1425V13, multiclass
                                  clus
vv                                 GCM2 MUTATED GCM2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                       7            219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1426) Variable = KRT9 MUTATION ANALYSIS
D1426V1, survival
                sevent
clus2              0   1
  KRT9 MUTATED    10   2
  KRT9 WILD-TYPE 368  91
  KRT9 MUTATED KRT9 WILD-TYPE 
            12            459 
  KRT9 MUTATED KRT9 WILD-TYPE 
             2             91 
$`KRT9 MUTATED`
TCGA-A6-2672 TCGA-AA-3492 TCGA-AA-3977 TCGA-AA-A010 TCGA-AZ-6601 TCGA-CA-6717 
       46.65         3.02        25.02        34.98       100.01        12.76 
TCGA-CM-5341 TCGA-CM-6168 TCGA-D5-6529 TCGA-D5-6927 TCGA-D5-6928 TCGA-AG-3892 
       29.06        12.99        20.19         9.44        11.64        13.02 

$`KRT9 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 
       20.12        19.66        20.28         7.04         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 
       62.79        88.21        49.41         6.77        12.10        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07        12.20        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-5348 
       20.02        37.02        25.02        13.02        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       21.99        14.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6930 
        4.41        12.43        14.30         9.04         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       17.95        36.95        17.03        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  KRT9 MUTATED KRT9 WILD-TYPE 
          3.02           0.00 
  KRT9 MUTATED KRT9 WILD-TYPE 
        100.01         148.01 
  KRT9 MUTATED KRT9 WILD-TYPE 
        16.605         20.280 
[1] "3.0 - 100.0 (16.6)" "0.0 - 148.0 (20.3)"
[1] "hr=" "1.2"
D1426V2, continuous
D1426V3, binary
                cls
clus               0   1
  KRT9 MUTATED    12   1
  KRT9 WILD-TYPE 354 118
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRT9 MUTATED     12    1
  KRT9 WILD-TYPE  354  118
        clus
vv       KRT9 MUTATED KRT9 WILD-TYPE
  COLON            12            354
  RECTUM            1            118
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KRT9 MUTATED         1        0        2         5         1         0
  KRT9 WILD-TYPE      90        1       30       133         9         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  KRT9 MUTATED           0          1          1          0        1         0
  KRT9 WILD-TYPE        24         10         58         42       47        18
                vv
clus             STAGE IVB
  KRT9 MUTATED           0
  KRT9 WILD-TYPE         1
D1426V4, multiclass
            clus
vv           KRT9 MUTATED KRT9 WILD-TYPE
  STAGE I               1             90
  STAGE IA              0              1
  STAGE II              2             30
  STAGE IIA             5            133
  STAGE IIB             1              9
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            1             10
  STAGE IIIB            1             58
  STAGE IIIC            0             42
  STAGE IV              1             47
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  KRT9 MUTATED     1   2   8   2
  KRT9 WILD-TYPE  16  90 321  48
D1426V5, multiclass
    clus
vv   KRT9 MUTATED KRT9 WILD-TYPE
  T1            1             16
  T2            2             90
  T3            8            321
  T4            2             48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  KRT9 MUTATED    10   3   0
  KRT9 WILD-TYPE 277 110  87
D1426V6, multiclass
    clus
vv   KRT9 MUTATED KRT9 WILD-TYPE
  N0           10            277
  N1            3            110
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1426V7, binary
                cls
clus               0   1
  KRT9 MUTATED    11   1
  KRT9 WILD-TYPE 364  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRT9 MUTATED     11    1
  KRT9 WILD-TYPE  364   64
   clus
vv  KRT9 MUTATED KRT9 WILD-TYPE
  0           11            364
  1            1             64
[1] 2 2
[1] FALSE
D1426V8, binary
                cls
clus               0   1
  KRT9 MUTATED     7   6
  KRT9 WILD-TYPE 218 258
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRT9 MUTATED      7    6
  KRT9 WILD-TYPE  218  258
        clus
vv       KRT9 MUTATED KRT9 WILD-TYPE
  FEMALE            7            218
  MALE              6            258
[1] 2 2
[1] FALSE
D1426V9, binary
                cls
clus               0   1
  KRT9 MUTATED    12   0
  KRT9 WILD-TYPE 338  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRT9 MUTATED     12    0
  KRT9 WILD-TYPE  338   22
     clus
vv    KRT9 MUTATED KRT9 WILD-TYPE
  NO            12            338
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  KRT9 MUTATED                     10                             2
  KRT9 WILD-TYPE                  305                            45
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  KRT9 MUTATED                       1                              0
  KRT9 WILD-TYPE                   105                             10
D1426V10, multiclass
                                clus
vv                               KRT9 MUTATED KRT9 WILD-TYPE
  COLON ADENOCARCINOMA                     10            305
  COLON MUCINOUS ADENOCARCINOMA             2             45
  RECTAL ADENOCARCINOMA                     1            105
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  KRT9 MUTATED     9   0   1   1
  KRT9 WILD-TYPE 336   4  30  24
D1426V11, multiclass
    clus
vv   KRT9 MUTATED KRT9 WILD-TYPE
  R0            9            336
  R1            0              4
  R2            1             30
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1426V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KRT9 MUTATED                                  0     1
  KRT9 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  KRT9 MUTATED                           1     6
  KRT9 WILD-TYPE                        21   220
D1426V13, multiclass
                                  clus
vv                                 KRT9 MUTATED KRT9 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                       6            220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1427) Variable = CHD7 MUTATION ANALYSIS
D1427V1, survival
                sevent
clus2              0   1
  CHD7 MUTATED    32   5
  CHD7 WILD-TYPE 346  88
  CHD7 MUTATED CHD7 WILD-TYPE 
            37            434 
  CHD7 MUTATED CHD7 WILD-TYPE 
             5             88 
$`CHD7 MUTATED`
TCGA-A6-3809 TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3672 TCGA-AA-3681 TCGA-AA-3697 
       32.75         3.02        63.98         0.92         5.98        85.05 
TCGA-AA-3713 TCGA-AA-3815 TCGA-AA-3861 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3977 
       19.04        33.04        30.05        26.01        24.00        25.02 
TCGA-AA-A004 TCGA-AA-A010 TCGA-AA-A01K TCGA-AD-6889 TCGA-AD-6895 TCGA-AU-6004 
       13.94        34.98        31.00        56.55         0.72        27.09 
TCGA-AZ-4315 TCGA-AZ-6598 TCGA-CA-6717 TCGA-CK-4952 TCGA-CM-4743 TCGA-CM-5348 
       58.39        49.41        12.76        15.62        23.05        22.98 
TCGA-CM-6161 TCGA-CM-6674 TCGA-CM-6679 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6928 
       15.02        12.95        10.06        17.13        16.14        11.64 
TCGA-DM-A0XF TCGA-DM-A1DB TCGA-G4-6309 TCGA-G4-6588 TCGA-G4-6628 TCGA-AG-A002 
       38.20        44.32        85.48        26.17        79.69        20.98 
TCGA-DY-A1H8 
       32.61 

$`CHD7 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 
       20.12        19.66        20.28         7.04         1.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
        2.01        14.01        50.04        47.01        15.02        11.01 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3715 
       37.05        19.00        36.00         5.03        26.99        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       10.06        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
        0.99        31.07        31.07        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 
       18.05        40.96         0.07        21.37        15.52         0.79 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
       16.31         0.95        33.01        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 
        5.13       106.75        22.36        62.79        88.21         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.20        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
      124.27        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.03        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       15.02        17.03        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6680 
       11.01        13.05        11.08        11.08        11.01        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       12.49        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
       14.30         9.04         9.44         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A1D0 TCGA-DM-A1D4 
       11.38        10.26       119.70        24.43       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HA 
       49.91        13.32        12.59       140.38         7.50       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 
       74.56        65.85        53.62        44.68        55.04        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 
       61.91        36.00        22.09        13.78        35.80        91.79 
TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       46.75        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  CHD7 MUTATED CHD7 WILD-TYPE 
          0.72           0.00 
  CHD7 MUTATED CHD7 WILD-TYPE 
         85.48         148.01 
  CHD7 MUTATED CHD7 WILD-TYPE 
        25.020         20.005 
[1] "0.7 - 85.5 (25.0)"  "0.0 - 148.0 (20.0)"
[1] "hr=" "1.7"
D1427V2, continuous
D1427V3, binary
                cls
clus               0   1
  CHD7 MUTATED    37   2
  CHD7 WILD-TYPE 329 117
[1] "tbl2"
                cls
clus             [,1] [,2]
  CHD7 MUTATED     37    2
  CHD7 WILD-TYPE  329  117
        clus
vv       CHD7 MUTATED CHD7 WILD-TYPE
  COLON            37            329
  RECTUM            2            117
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CHD7 MUTATED         5        0        3        14         3         0
  CHD7 WILD-TYPE      86        1       29       124         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CHD7 MUTATED           3          1          4          3        1         0
  CHD7 WILD-TYPE        21         10         55         39       47        18
                vv
clus             STAGE IVB
  CHD7 MUTATED           0
  CHD7 WILD-TYPE         1
D1427V4, multiclass
            clus
vv           CHD7 MUTATED CHD7 WILD-TYPE
  STAGE I               5             86
  STAGE IA              0              1
  STAGE II              3             29
  STAGE IIA            14            124
  STAGE IIB             3              7
  STAGE IIC             0              1
  STAGE III             3             21
  STAGE IIIA            1             10
  STAGE IIIB            4             55
  STAGE IIIC            3             39
  STAGE IV              1             47
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  CHD7 MUTATED     0   7  28   4
  CHD7 WILD-TYPE  17  85 301  46
D1427V5, multiclass
    clus
vv   CHD7 MUTATED CHD7 WILD-TYPE
  T1            0             17
  T2            7             85
  T3           28            301
  T4            4             46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  CHD7 MUTATED    28   7   4
  CHD7 WILD-TYPE 259 106  83
D1427V6, multiclass
    clus
vv   CHD7 MUTATED CHD7 WILD-TYPE
  N0           28            259
  N1            7            106
  N2            4             83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1427V7, binary
                cls
clus               0   1
  CHD7 MUTATED    34   1
  CHD7 WILD-TYPE 341  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  CHD7 MUTATED     34    1
  CHD7 WILD-TYPE  341   64
   clus
vv  CHD7 MUTATED CHD7 WILD-TYPE
  0           34            341
  1            1             64
[1] 2 2
[1] FALSE
D1427V8, binary
                cls
clus               0   1
  CHD7 MUTATED    20  19
  CHD7 WILD-TYPE 205 245
[1] "tbl2"
                cls
clus             [,1] [,2]
  CHD7 MUTATED     20   19
  CHD7 WILD-TYPE  205  245
        clus
vv       CHD7 MUTATED CHD7 WILD-TYPE
  FEMALE           20            205
  MALE             19            245
[1] 2 2
[1] FALSE
D1427V9, binary
                cls
clus               0   1
  CHD7 MUTATED    29   1
  CHD7 WILD-TYPE 321  21
[1] "tbl2"
                cls
clus             [,1] [,2]
  CHD7 MUTATED     29    1
  CHD7 WILD-TYPE  321   21
     clus
vv    CHD7 MUTATED CHD7 WILD-TYPE
  NO            29            321
  YES            1             21
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CHD7 MUTATED                     29                             7
  CHD7 WILD-TYPE                  286                            40
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CHD7 MUTATED                       2                              0
  CHD7 WILD-TYPE                   104                             10
D1427V10, multiclass
                                clus
vv                               CHD7 MUTATED CHD7 WILD-TYPE
  COLON ADENOCARCINOMA                     29            286
  COLON MUCINOUS ADENOCARCINOMA             7             40
  RECTAL ADENOCARCINOMA                     2            104
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  CHD7 MUTATED    28   0   1   3
  CHD7 WILD-TYPE 317   4  30  22
D1427V11, multiclass
    clus
vv   CHD7 MUTATED CHD7 WILD-TYPE
  R0           28            317
  R1            0              4
  R2            1             30
  RX            3             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1427V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CHD7 MUTATED                                  0     2
  CHD7 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  CHD7 MUTATED                           1    20
  CHD7 WILD-TYPE                        21   206
D1427V13, multiclass
                                  clus
vv                                 CHD7 MUTATED CHD7 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              9
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                      20            206
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1428) Variable = CHD1 MUTATION ANALYSIS
D1428V1, survival
                sevent
clus2              0   1
  CHD1 MUTATED    21   4
  CHD1 WILD-TYPE 357  89
  CHD1 MUTATED CHD1 WILD-TYPE 
            25            446 
  CHD1 MUTATED CHD1 WILD-TYPE 
             4             89 
$`CHD1 MUTATED`
TCGA-A6-5659 TCGA-A6-6138 TCGA-A6-6649 TCGA-AA-3526 TCGA-AA-3672 TCGA-AA-3713 
       30.44        22.52        24.16        19.07         0.92        19.04 
TCGA-AA-3815 TCGA-AA-3821 TCGA-AA-3864 TCGA-AA-3947 TCGA-AA-3977 TCGA-AA-3982 
       33.04         1.02        53.00        33.01        25.02        27.02 
TCGA-AA-A00A TCGA-AD-5900 TCGA-AZ-4315 TCGA-AZ-6606 TCGA-CA-6717 TCGA-CA-6718 
       38.04         0.07        58.39        11.74        12.76        10.06 
TCGA-CK-5916 TCGA-CM-6162 TCGA-D5-6930 TCGA-DM-A0XF TCGA-F4-6856 TCGA-AG-A002 
       21.14        12.00         1.51        38.20        35.31        20.98 
TCGA-EF-5830 
        0.49 

$`CHD1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       22.06        32.71        27.09         8.38        25.08        25.18 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3529 TCGA-AA-3530 
       24.03        37.05        36.03         8.05         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
       14.01        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 
       19.04        10.06        35.05         0.99        25.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 
        0.99        31.07        31.07        30.05        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       26.01        24.00        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       13.94        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 
       41.00        39.98        18.05        40.96        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       33.01        21.44        17.82         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
      100.01        29.56         5.23         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 
        3.06         3.25         3.29         0.07        12.20        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
        9.99        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       17.03        15.02         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       11.64         4.80        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       24.43       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
        0.53        47.41       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
       32.61        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  CHD1 MUTATED CHD1 WILD-TYPE 
          0.07           0.00 
  CHD1 MUTATED CHD1 WILD-TYPE 
         58.39         148.01 
  CHD1 MUTATED CHD1 WILD-TYPE 
        21.140         20.085 
[1] "0.1 - 58.4 (21.1)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1"  
D1428V2, continuous
D1428V3, binary
                cls
clus               0   1
  CHD1 MUTATED    23   2
  CHD1 WILD-TYPE 343 117
[1] "tbl2"
                cls
clus             [,1] [,2]
  CHD1 MUTATED     23    2
  CHD1 WILD-TYPE  343  117
        clus
vv       CHD1 MUTATED CHD1 WILD-TYPE
  COLON            23            343
  RECTUM            2            117
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CHD1 MUTATED         8        0        1         6         2         0
  CHD1 WILD-TYPE      83        1       31       132         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CHD1 MUTATED           1          0          3          1        2         0
  CHD1 WILD-TYPE        23         11         56         41       46        18
                vv
clus             STAGE IVB
  CHD1 MUTATED           0
  CHD1 WILD-TYPE         1
D1428V4, multiclass
            clus
vv           CHD1 MUTATED CHD1 WILD-TYPE
  STAGE I               8             83
  STAGE IA              0              1
  STAGE II              1             31
  STAGE IIA             6            132
  STAGE IIB             2              8
  STAGE IIC             0              1
  STAGE III             1             23
  STAGE IIIA            0             11
  STAGE IIIB            3             56
  STAGE IIIC            1             41
  STAGE IV              2             46
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  CHD1 MUTATED     1   8  13   3
  CHD1 WILD-TYPE  16  84 316  47
D1428V5, multiclass
    clus
vv   CHD1 MUTATED CHD1 WILD-TYPE
  T1            1             16
  T2            8             84
  T3           13            316
  T4            3             47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  CHD1 MUTATED    19   4   2
  CHD1 WILD-TYPE 268 109  85
D1428V6, multiclass
    clus
vv   CHD1 MUTATED CHD1 WILD-TYPE
  N0           19            268
  N1            4            109
  N2            2             85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1428V7, binary
                cls
clus               0   1
  CHD1 MUTATED    21   2
  CHD1 WILD-TYPE 354  63
[1] "tbl2"
                cls
clus             [,1] [,2]
  CHD1 MUTATED     21    2
  CHD1 WILD-TYPE  354   63
   clus
vv  CHD1 MUTATED CHD1 WILD-TYPE
  0           21            354
  1            2             63
[1] 2 2
[1] FALSE
D1428V8, binary
                cls
clus               0   1
  CHD1 MUTATED     7  18
  CHD1 WILD-TYPE 218 246
[1] "tbl2"
                cls
clus             [,1] [,2]
  CHD1 MUTATED      7   18
  CHD1 WILD-TYPE  218  246
        clus
vv       CHD1 MUTATED CHD1 WILD-TYPE
  FEMALE            7            218
  MALE             18            246
[1] 2 2
[1] FALSE
D1428V9, binary
                cls
clus               0   1
  CHD1 MUTATED    20   1
  CHD1 WILD-TYPE 330  21
[1] "tbl2"
                cls
clus             [,1] [,2]
  CHD1 MUTATED     20    1
  CHD1 WILD-TYPE  330   21
     clus
vv    CHD1 MUTATED CHD1 WILD-TYPE
  NO            20            330
  YES            1             21
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CHD1 MUTATED                     15                             7
  CHD1 WILD-TYPE                  300                            40
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CHD1 MUTATED                       2                              0
  CHD1 WILD-TYPE                   104                             10
D1428V10, multiclass
                                clus
vv                               CHD1 MUTATED CHD1 WILD-TYPE
  COLON ADENOCARCINOMA                     15            300
  COLON MUCINOUS ADENOCARCINOMA             7             40
  RECTAL ADENOCARCINOMA                     2            104
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  CHD1 MUTATED    15   0   1   3
  CHD1 WILD-TYPE 330   4  30  22
D1428V11, multiclass
    clus
vv   CHD1 MUTATED CHD1 WILD-TYPE
  R0           15            330
  R1            0              4
  R2            1             30
  RX            3             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1428V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CHD1 MUTATED                                  0     2
  CHD1 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  CHD1 MUTATED                           0    12
  CHD1 WILD-TYPE                        22   214
D1428V13, multiclass
                                  clus
vv                                 CHD1 MUTATED CHD1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              9
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                      12            214
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1429) Variable = LRIG2 MUTATION ANALYSIS
D1429V1, survival
                 sevent
clus2               0   1
  LRIG2 MUTATED     6   3
  LRIG2 WILD-TYPE 372  90
  LRIG2 MUTATED LRIG2 WILD-TYPE 
              9             462 
  LRIG2 MUTATED LRIG2 WILD-TYPE 
              3              90 
$`LRIG2 MUTATED`
TCGA-A6-5665 TCGA-AA-3510 TCGA-AA-3845 TCGA-AA-3947 TCGA-AY-6197 TCGA-AZ-6599 
       22.06        63.98         0.00        33.01        21.44         6.77 
TCGA-CK-4947 TCGA-D5-6541 TCGA-F4-6570 
       17.56        15.58         6.18 

$`LRIG2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 
       15.95        38.99        37.02        14.93        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 
       14.50        27.09        16.31         0.95        33.01        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       88.21        49.41        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07        12.20        12.76        10.06        14.30 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6898 
       17.85         4.80        17.13        12.49        16.14         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  LRIG2 MUTATED LRIG2 WILD-TYPE 
              0               0 
  LRIG2 MUTATED LRIG2 WILD-TYPE 
          63.98          148.01 
  LRIG2 MUTATED LRIG2 WILD-TYPE 
         17.560          20.235 
[1] "0.0 - 64.0 (17.6)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "2.1"
D1429V2, continuous
D1429V3, binary
                 cls
clus                0   1
  LRIG2 MUTATED     9   0
  LRIG2 WILD-TYPE 357 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LRIG2 MUTATED      9    0
  LRIG2 WILD-TYPE  357  119
        clus
vv       LRIG2 MUTATED LRIG2 WILD-TYPE
  COLON              9             357
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  LRIG2 MUTATED         1        0        1         5         1         0
  LRIG2 WILD-TYPE      90        1       31       133         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  LRIG2 MUTATED           0          0          1          0        0         0
  LRIG2 WILD-TYPE        24         11         58         42       48        18
                 vv
clus              STAGE IVB
  LRIG2 MUTATED           0
  LRIG2 WILD-TYPE         1
D1429V4, multiclass
            clus
vv           LRIG2 MUTATED LRIG2 WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              5             133
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  LRIG2 MUTATED     0   1   6   2
  LRIG2 WILD-TYPE  17  91 323  48
D1429V5, multiclass
    clus
vv   LRIG2 MUTATED LRIG2 WILD-TYPE
  T1             0              17
  T2             1              91
  T3             6             323
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  LRIG2 MUTATED     8   1   0
  LRIG2 WILD-TYPE 279 112  87
D1429V6, multiclass
    clus
vv   LRIG2 MUTATED LRIG2 WILD-TYPE
  N0             8             279
  N1             1             112
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1429V7, binary
                 cls
clus                0   1
  LRIG2 MUTATED     7   0
  LRIG2 WILD-TYPE 368  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LRIG2 MUTATED      7    0
  LRIG2 WILD-TYPE  368   65
   clus
vv  LRIG2 MUTATED LRIG2 WILD-TYPE
  0             7             368
  1             0              65
[1] 2 2
[1] FALSE
D1429V8, binary
                 cls
clus                0   1
  LRIG2 MUTATED     5   4
  LRIG2 WILD-TYPE 220 260
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LRIG2 MUTATED      5    4
  LRIG2 WILD-TYPE  220  260
        clus
vv       LRIG2 MUTATED LRIG2 WILD-TYPE
  FEMALE             5             220
  MALE               4             260
[1] 2 2
[1] FALSE
D1429V9, binary
                 cls
clus                0   1
  LRIG2 MUTATED     8   0
  LRIG2 WILD-TYPE 342  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LRIG2 MUTATED      8    0
  LRIG2 WILD-TYPE  342   22
     clus
vv    LRIG2 MUTATED LRIG2 WILD-TYPE
  NO              8             342
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  LRIG2 MUTATED                      8                             1
  LRIG2 WILD-TYPE                  307                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  LRIG2 MUTATED                       0                              0
  LRIG2 WILD-TYPE                   106                             10
D1429V10, multiclass
                                clus
vv                               LRIG2 MUTATED LRIG2 WILD-TYPE
  COLON ADENOCARCINOMA                       8             307
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  LRIG2 MUTATED     7   0   0   1
  LRIG2 WILD-TYPE 338   4  31  24
D1429V11, multiclass
    clus
vv   LRIG2 MUTATED LRIG2 WILD-TYPE
  R0             7             338
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1429V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  LRIG2 MUTATED                                  0     0
  LRIG2 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  LRIG2 MUTATED                           0     6
  LRIG2 WILD-TYPE                        22   220
D1429V13, multiclass
                                  clus
vv                                 LRIG2 MUTATED LRIG2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        6             220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1430) Variable = SAMD9 MUTATION ANALYSIS
D1430V1, survival
                 sevent
clus2               0   1
  SAMD9 MUTATED    24   4
  SAMD9 WILD-TYPE 354  89
  SAMD9 MUTATED SAMD9 WILD-TYPE 
             28             443 
  SAMD9 MUTATED SAMD9 WILD-TYPE 
              4              89 
$`SAMD9 MUTATED`
TCGA-A6-5665 TCGA-A6-6141 TCGA-A6-6654 TCGA-A6-6781 TCGA-AA-3492 TCGA-AA-3510 
       22.06         8.38        23.87        19.66         3.02        63.98 
TCGA-AA-3811 TCGA-AA-3866 TCGA-AA-A00A TCGA-AA-A00J TCGA-AA-A010 TCGA-AA-A02H 
       10.06        17.03        38.04        18.05        34.98         2.01 
TCGA-AD-6889 TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-6601 TCGA-CA-6717 TCGA-CK-5913 
       56.55        21.44        58.39       100.01        12.76        51.32 
TCGA-CM-4744 TCGA-CM-5861 TCGA-D5-5538 TCGA-D5-6536 TCGA-D5-6898 TCGA-D5-6923 
       20.02        15.02        12.26        17.85         1.48        12.43 
TCGA-G4-6293 TCGA-AG-3892 TCGA-AG-A002 TCGA-AG-A020 
      133.18        13.02        20.98        10.98 

$`SAMD9 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 
       22.09        32.71        27.09        22.52        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6782 
       24.16        21.76        24.69        24.39        20.12        20.28 
TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        7.04         1.02        35.01         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       19.04        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00D 
       27.02        19.07         7.96        27.02        13.94        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02J TCGA-AA-A02K 
       37.02        39.06        51.98        39.98         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       21.37        15.52         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
        0.95        33.01        17.82         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07        12.20        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       30.08        32.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       12.03        45.40        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 
       18.25         1.32        43.27        15.12         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6924 
       12.49        16.14        15.58         3.68         4.41        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
       35.31        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       17.03        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A025 
       36.03         9.07        12.00        70.03        64.01        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  SAMD9 MUTATED SAMD9 WILD-TYPE 
           1.48            0.00 
  SAMD9 MUTATED SAMD9 WILD-TYPE 
         133.18          148.01 
  SAMD9 MUTATED SAMD9 WILD-TYPE 
         18.855          20.550 
[1] "1.5 - 133.2 (18.9)" "0.0 - 148.0 (20.6)"
[1] "hr=" "1.6"
D1430V2, continuous
D1430V3, binary
                 cls
clus                0   1
  SAMD9 MUTATED    26   3
  SAMD9 WILD-TYPE 340 116
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SAMD9 MUTATED     26    3
  SAMD9 WILD-TYPE  340  116
        clus
vv       SAMD9 MUTATED SAMD9 WILD-TYPE
  COLON             26             340
  RECTUM             3             116
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SAMD9 MUTATED         6        0        4        10         1         0
  SAMD9 WILD-TYPE      85        1       28       128         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SAMD9 MUTATED           3          0          3          1        1         0
  SAMD9 WILD-TYPE        21         11         56         41       47        18
                 vv
clus              STAGE IVB
  SAMD9 MUTATED           0
  SAMD9 WILD-TYPE         1
D1430V4, multiclass
            clus
vv           SAMD9 MUTATED SAMD9 WILD-TYPE
  STAGE I                6              85
  STAGE IA               0               1
  STAGE II               4              28
  STAGE IIA             10             128
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              3              21
  STAGE IIIA             0              11
  STAGE IIIB             3              56
  STAGE IIIC             1              41
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  SAMD9 MUTATED     1   5  20   3
  SAMD9 WILD-TYPE  16  87 309  47
D1430V5, multiclass
    clus
vv   SAMD9 MUTATED SAMD9 WILD-TYPE
  T1             1              16
  T2             5              87
  T3            20             309
  T4             3              47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  SAMD9 MUTATED    21   6   2
  SAMD9 WILD-TYPE 266 107  85
D1430V6, multiclass
    clus
vv   SAMD9 MUTATED SAMD9 WILD-TYPE
  N0            21             266
  N1             6             107
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1430V7, binary
                 cls
clus                0   1
  SAMD9 MUTATED    25   1
  SAMD9 WILD-TYPE 350  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SAMD9 MUTATED     25    1
  SAMD9 WILD-TYPE  350   64
   clus
vv  SAMD9 MUTATED SAMD9 WILD-TYPE
  0            25             350
  1             1              64
[1] 2 2
[1] FALSE
D1430V8, binary
                 cls
clus                0   1
  SAMD9 MUTATED    14  15
  SAMD9 WILD-TYPE 211 249
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SAMD9 MUTATED     14   15
  SAMD9 WILD-TYPE  211  249
        clus
vv       SAMD9 MUTATED SAMD9 WILD-TYPE
  FEMALE            14             211
  MALE              15             249
[1] 2 2
[1] FALSE
D1430V9, binary
                 cls
clus                0   1
  SAMD9 MUTATED    24   0
  SAMD9 WILD-TYPE 326  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SAMD9 MUTATED     24    0
  SAMD9 WILD-TYPE  326   22
     clus
vv    SAMD9 MUTATED SAMD9 WILD-TYPE
  NO             24             326
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SAMD9 MUTATED                     23                             3
  SAMD9 WILD-TYPE                  292                            44
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SAMD9 MUTATED                       2                              1
  SAMD9 WILD-TYPE                   104                              9
D1430V10, multiclass
                                clus
vv                               SAMD9 MUTATED SAMD9 WILD-TYPE
  COLON ADENOCARCINOMA                      23             292
  COLON MUCINOUS ADENOCARCINOMA              3              44
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             1               9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  SAMD9 MUTATED    22   0   1   2
  SAMD9 WILD-TYPE 323   4  30  23
D1430V11, multiclass
    clus
vv   SAMD9 MUTATED SAMD9 WILD-TYPE
  R0            22             323
  R1             0               4
  R2             1              30
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1430V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SAMD9 MUTATED                                  0     2
  SAMD9 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  SAMD9 MUTATED                           1    14
  SAMD9 WILD-TYPE                        21   212
D1430V13, multiclass
                                  clus
vv                                 SAMD9 MUTATED SAMD9 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               9
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                       14             212
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1431) Variable = CROT MUTATION ANALYSIS
D1431V1, survival
                sevent
clus2              0   1
  CROT MUTATED    11   0
  CROT WILD-TYPE 367  93
  CROT MUTATED CROT WILD-TYPE 
            11            460 
  CROT MUTATED CROT WILD-TYPE 
             0             93 
$`CROT MUTATED`
TCGA-AA-3543 TCGA-AA-3815 TCGA-AA-A004 TCGA-AD-5900 TCGA-AZ-4315 TCGA-D5-5539 
        0.99        33.04        13.94         0.07        58.39        19.59 
TCGA-D5-5540 TCGA-G4-6628 TCGA-AF-6655 TCGA-AG-3732 TCGA-AG-A002 
       56.09        79.69        20.02        32.98        20.98 

$`CROT WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       29.00        26.01        12.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       10.06        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A00D 
       27.02        19.07         7.96        27.02        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       18.05        40.96        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 
       35.80        26.17        91.79        46.75        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       16.83        15.39        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
        0.99        37.02         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  CROT MUTATED CROT WILD-TYPE 
          0.07           0.00 
  CROT MUTATED CROT WILD-TYPE 
         79.69         148.01 
  CROT MUTATED CROT WILD-TYPE 
        20.980         20.155 
[1] "0.1 - 79.7 (21.0)"  "0.0 - 148.0 (20.2)"
[1] "hr="     "9300000"
D1431V2, continuous
D1431V3, binary
                cls
clus               0   1
  CROT MUTATED     8   3
  CROT WILD-TYPE 358 116
[1] "tbl2"
                cls
clus             [,1] [,2]
  CROT MUTATED      8    3
  CROT WILD-TYPE  358  116
        clus
vv       CROT MUTATED CROT WILD-TYPE
  COLON             8            358
  RECTUM            3            116
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CROT MUTATED         5        0        0         4         0         0
  CROT WILD-TYPE      86        1       32       134        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CROT MUTATED           0          2          0          0        0         0
  CROT WILD-TYPE        24          9         59         42       48        18
                vv
clus             STAGE IVB
  CROT MUTATED           0
  CROT WILD-TYPE         1
D1431V4, multiclass
            clus
vv           CROT MUTATED CROT WILD-TYPE
  STAGE I               5             86
  STAGE IA              0              1
  STAGE II              0             32
  STAGE IIA             4            134
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            2              9
  STAGE IIIB            0             59
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  CROT MUTATED     0   6   5   0
  CROT WILD-TYPE  17  86 324  50
D1431V5, multiclass
    clus
vv   CROT MUTATED CROT WILD-TYPE
  T1            0             17
  T2            6             86
  T3            5            324
  T4            0             50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  CROT MUTATED     9   2   0
  CROT WILD-TYPE 278 111  87
D1431V6, multiclass
    clus
vv   CROT MUTATED CROT WILD-TYPE
  N0            9            278
  N1            2            111
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1431V7, binary
                cls
clus               0   1
  CROT MUTATED    10   0
  CROT WILD-TYPE 365  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  CROT MUTATED     10    0
  CROT WILD-TYPE  365   65
   clus
vv  CROT MUTATED CROT WILD-TYPE
  0           10            365
  1            0             65
[1] 2 2
[1] FALSE
D1431V8, binary
                cls
clus               0   1
  CROT MUTATED     2   9
  CROT WILD-TYPE 223 255
[1] "tbl2"
                cls
clus             [,1] [,2]
  CROT MUTATED      2    9
  CROT WILD-TYPE  223  255
        clus
vv       CROT MUTATED CROT WILD-TYPE
  FEMALE            2            223
  MALE              9            255
[1] 2 2
[1] FALSE
D1431V9, binary
                cls
clus               0   1
  CROT MUTATED    10   0
  CROT WILD-TYPE 340  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  CROT MUTATED     10    0
  CROT WILD-TYPE  340   22
     clus
vv    CROT MUTATED CROT WILD-TYPE
  NO            10            340
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CROT MUTATED                      5                             3
  CROT WILD-TYPE                  310                            44
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CROT MUTATED                       3                              0
  CROT WILD-TYPE                   103                             10
D1431V10, multiclass
                                clus
vv                               CROT MUTATED CROT WILD-TYPE
  COLON ADENOCARCINOMA                      5            310
  COLON MUCINOUS ADENOCARCINOMA             3             44
  RECTAL ADENOCARCINOMA                     3            103
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  CROT MUTATED    11   0   0   0
  CROT WILD-TYPE 334   4  31  25
D1431V11, multiclass
    clus
vv   CROT MUTATED CROT WILD-TYPE
  R0           11            334
  R1            0              4
  R2            0             31
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1431V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CROT MUTATED                                  0     0
  CROT WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  CROT MUTATED                           0     6
  CROT WILD-TYPE                        22   220
D1431V13, multiclass
                                  clus
vv                                 CROT MUTATED CROT WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       6            220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1432) Variable = BUB1 MUTATION ANALYSIS
D1432V1, survival
                sevent
clus2              0   1
  BUB1 MUTATED    11   4
  BUB1 WILD-TYPE 367  89
  BUB1 MUTATED BUB1 WILD-TYPE 
            15            456 
  BUB1 MUTATED BUB1 WILD-TYPE 
             4             89 
$`BUB1 MUTATED`
TCGA-A6-6780 TCGA-AA-3660 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-A00N TCGA-AA-A010 
       20.12        78.08        85.05        19.04         4.01        34.98 
TCGA-AA-A01P TCGA-AZ-4315 TCGA-D5-6930 TCGA-DM-A1DA TCGA-G4-6303 TCGA-G4-6588 
       38.07        58.39         1.51         7.50        65.85        26.17 
TCGA-AG-3599 TCGA-AG-A025 TCGA-F5-6811 
       12.03        49.97        32.19 

$`BUB1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 
       19.99        13.94        19.99        61.02         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
        5.03        26.99        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01Q TCGA-AA-A01R 
       32.02        12.00        31.00        31.00         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        33.01        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       11.64         4.80        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
       12.59       140.38        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6304 
        0.53        47.41        35.31       133.18        74.56        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       22.09        13.78        35.80        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       50.04         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       64.01        10.98         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       31.30        28.57         0.66         0.69        55.76        26.43 

  BUB1 MUTATED BUB1 WILD-TYPE 
          1.51           0.00 
  BUB1 MUTATED BUB1 WILD-TYPE 
         85.05         148.01 
  BUB1 MUTATED BUB1 WILD-TYPE 
        32.190         20.035 
[1] "1.5 - 85.0 (32.2)"  "0.0 - 148.0 (20.0)"
[1] "hr=" "1"  
D1432V2, continuous
D1432V3, binary
                cls
clus               0   1
  BUB1 MUTATED    13   3
  BUB1 WILD-TYPE 353 116
[1] "tbl2"
                cls
clus             [,1] [,2]
  BUB1 MUTATED     13    3
  BUB1 WILD-TYPE  353  116
        clus
vv       BUB1 MUTATED BUB1 WILD-TYPE
  COLON            13            353
  RECTUM            3            116
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  BUB1 MUTATED         2        0        1         6         2         0
  BUB1 WILD-TYPE      89        1       31       132         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  BUB1 MUTATED           2          0          0          1        2         0
  BUB1 WILD-TYPE        22         11         59         41       46        18
                vv
clus             STAGE IVB
  BUB1 MUTATED           0
  BUB1 WILD-TYPE         1
D1432V4, multiclass
            clus
vv           BUB1 MUTATED BUB1 WILD-TYPE
  STAGE I               2             89
  STAGE IA              0              1
  STAGE II              1             31
  STAGE IIA             6            132
  STAGE IIB             2              8
  STAGE IIC             0              1
  STAGE III             2             22
  STAGE IIIA            0             11
  STAGE IIIB            0             59
  STAGE IIIC            1             41
  STAGE IV              2             46
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  BUB1 MUTATED     1   1  12   2
  BUB1 WILD-TYPE  16  91 317  48
D1432V5, multiclass
    clus
vv   BUB1 MUTATED BUB1 WILD-TYPE
  T1            1             16
  T2            1             91
  T3           12            317
  T4            2             48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  BUB1 MUTATED    13   2   1
  BUB1 WILD-TYPE 274 111  86
D1432V6, multiclass
    clus
vv   BUB1 MUTATED BUB1 WILD-TYPE
  N0           13            274
  N1            2            111
  N2            1             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1432V7, binary
                cls
clus               0   1
  BUB1 MUTATED    13   2
  BUB1 WILD-TYPE 362  63
[1] "tbl2"
                cls
clus             [,1] [,2]
  BUB1 MUTATED     13    2
  BUB1 WILD-TYPE  362   63
   clus
vv  BUB1 MUTATED BUB1 WILD-TYPE
  0           13            362
  1            2             63
[1] 2 2
[1] FALSE
D1432V8, binary
                cls
clus               0   1
  BUB1 MUTATED     9   7
  BUB1 WILD-TYPE 216 257
[1] "tbl2"
                cls
clus             [,1] [,2]
  BUB1 MUTATED      9    7
  BUB1 WILD-TYPE  216  257
        clus
vv       BUB1 MUTATED BUB1 WILD-TYPE
  FEMALE            9            216
  MALE              7            257
[1] 2 2
[1] FALSE
D1432V9, binary
                cls
clus               0   1
  BUB1 MUTATED    10   1
  BUB1 WILD-TYPE 340  21
[1] "tbl2"
                cls
clus             [,1] [,2]
  BUB1 MUTATED     10    1
  BUB1 WILD-TYPE  340   21
     clus
vv    BUB1 MUTATED BUB1 WILD-TYPE
  NO            10            340
  YES            1             21
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  BUB1 MUTATED                     10                             3
  BUB1 WILD-TYPE                  305                            44
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  BUB1 MUTATED                       2                              0
  BUB1 WILD-TYPE                   104                             10
D1432V10, multiclass
                                clus
vv                               BUB1 MUTATED BUB1 WILD-TYPE
  COLON ADENOCARCINOMA                     10            305
  COLON MUCINOUS ADENOCARCINOMA             3             44
  RECTAL ADENOCARCINOMA                     2            104
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  BUB1 MUTATED    12   0   1   0
  BUB1 WILD-TYPE 333   4  30  25
D1432V11, multiclass
    clus
vv   BUB1 MUTATED BUB1 WILD-TYPE
  R0           12            333
  R1            0              4
  R2            1             30
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1432V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  BUB1 MUTATED                                  0     0
  BUB1 WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  BUB1 MUTATED                           0     7
  BUB1 WILD-TYPE                        22   219
D1432V13, multiclass
                                  clus
vv                                 BUB1 MUTATED BUB1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       7            219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1433) Variable = SULT1E1 MUTATION ANALYSIS
D1433V1, survival
                   sevent
clus2                 0   1
  SULT1E1 MUTATED     5   0
  SULT1E1 WILD-TYPE 373  93
  SULT1E1 MUTATED SULT1E1 WILD-TYPE 
                5               466 
  SULT1E1 MUTATED SULT1E1 WILD-TYPE 
                0                93 
$`SULT1E1 MUTATED`
TCGA-AA-3510 TCGA-AA-3977 TCGA-AU-6004 TCGA-CA-6717 TCGA-AG-A002 
       63.98        25.02        27.09        12.76        20.98 

$`SULT1E1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       10.88         0.20        14.50        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  SULT1E1 MUTATED SULT1E1 WILD-TYPE 
            12.76              0.00 
  SULT1E1 MUTATED SULT1E1 WILD-TYPE 
            63.98            148.01 
  SULT1E1 MUTATED SULT1E1 WILD-TYPE 
           25.020            20.085 
[1] "12.8 - 64.0 (25.0)" "0.0 - 148.0 (20.1)"
[1] "hr="     "9100000"
D1433V2, continuous
D1433V3, binary
                   cls
clus                  0   1
  SULT1E1 MUTATED     4   1
  SULT1E1 WILD-TYPE 362 118
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SULT1E1 MUTATED      4    1
  SULT1E1 WILD-TYPE  362  118
        clus
vv       SULT1E1 MUTATED SULT1E1 WILD-TYPE
  COLON                4               362
  RECTUM               1               118
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SULT1E1 MUTATED         2        0        1         1         0         0
  SULT1E1 WILD-TYPE      89        1       31       137        10         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SULT1E1 MUTATED           0          0          0          0        0
  SULT1E1 WILD-TYPE        24         11         59         42       48
                   vv
clus                STAGE IVA STAGE IVB
  SULT1E1 MUTATED           0         0
  SULT1E1 WILD-TYPE        18         1
D1433V4, multiclass
            clus
vv           SULT1E1 MUTATED SULT1E1 WILD-TYPE
  STAGE I                  2                89
  STAGE IA                 0                 1
  STAGE II                 1                31
  STAGE IIA                1               137
  STAGE IIB                0                10
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               0                11
  STAGE IIIB               0                59
  STAGE IIIC               0                42
  STAGE IV                 0                48
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  SULT1E1 MUTATED     0   3   2   0
  SULT1E1 WILD-TYPE  17  89 327  50
D1433V5, multiclass
    clus
vv   SULT1E1 MUTATED SULT1E1 WILD-TYPE
  T1               0                17
  T2               3                89
  T3               2               327
  T4               0                50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  SULT1E1 MUTATED     5   0   0
  SULT1E1 WILD-TYPE 282 113  87
D1433V6, multiclass
    clus
vv   SULT1E1 MUTATED SULT1E1 WILD-TYPE
  N0               5               282
  N1               0               113
  N2               0                87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1433V7, binary
                   cls
clus                  0   1
  SULT1E1 MUTATED     4   0
  SULT1E1 WILD-TYPE 371  65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SULT1E1 MUTATED      4    0
  SULT1E1 WILD-TYPE  371   65
   clus
vv  SULT1E1 MUTATED SULT1E1 WILD-TYPE
  0               4               371
  1               0                65
[1] 2 2
[1] FALSE
D1433V8, binary
                   cls
clus                  0   1
  SULT1E1 MUTATED     1   4
  SULT1E1 WILD-TYPE 224 260
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SULT1E1 MUTATED      1    4
  SULT1E1 WILD-TYPE  224  260
        clus
vv       SULT1E1 MUTATED SULT1E1 WILD-TYPE
  FEMALE               1               224
  MALE                 4               260
[1] 2 2
[1] FALSE
D1433V9, binary
                   cls
clus                  0   1
  SULT1E1 MUTATED     4   0
  SULT1E1 WILD-TYPE 346  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SULT1E1 MUTATED      4    0
  SULT1E1 WILD-TYPE  346   22
     clus
vv    SULT1E1 MUTATED SULT1E1 WILD-TYPE
  NO                4               346
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SULT1E1 MUTATED                      3                             1
  SULT1E1 WILD-TYPE                  312                            46
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SULT1E1 MUTATED                       1                              0
  SULT1E1 WILD-TYPE                   105                             10
D1433V10, multiclass
                                clus
vv                               SULT1E1 MUTATED SULT1E1 WILD-TYPE
  COLON ADENOCARCINOMA                         3               312
  COLON MUCINOUS ADENOCARCINOMA                1                46
  RECTAL ADENOCARCINOMA                        1               105
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  SULT1E1 MUTATED     3   0   0   1
  SULT1E1 WILD-TYPE 342   4  31  24
D1433V11, multiclass
    clus
vv   SULT1E1 MUTATED SULT1E1 WILD-TYPE
  R0               3               342
  R1               0                 4
  R2               0                31
  RX               1                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1433V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SULT1E1 MUTATED                                  0     1
  SULT1E1 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  SULT1E1 MUTATED                           0     1
  SULT1E1 WILD-TYPE                        22   225
D1433V13, multiclass
[1] "Remove cluster labels:" "SULT1E1 MUTATED"       
clus
  SULT1E1 MUTATED SULT1E1 WILD-TYPE 
                2               258 
       TCGA-A6-2671        TCGA-A6-2672        TCGA-A6-2674        TCGA-A6-2676 
"SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" 
       TCGA-A6-2677        TCGA-A6-2678        TCGA-A6-2683        TCGA-A6-3807 
"SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" 
       TCGA-A6-3808        TCGA-A6-3809        TCGA-A6-3810        TCGA-A6-4105 
"SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" 
       TCGA-A6-5656        TCGA-A6-5657        TCGA-A6-5659        TCGA-A6-5660 
"SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" 
       TCGA-A6-5661        TCGA-A6-5662        TCGA-A6-5664        TCGA-A6-5665 
"SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" 
       TCGA-A6-5666        TCGA-A6-6137        TCGA-A6-6138        TCGA-A6-6141 
"SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" 
       TCGA-A6-6142        TCGA-A6-6648        TCGA-A6-6649        TCGA-A6-6651 
"SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" 
       TCGA-A6-6652        TCGA-A6-6653        TCGA-A6-6654        TCGA-A6-6780 
"SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" 
       TCGA-A6-6781        TCGA-A6-6782        TCGA-AD-5900        TCGA-AD-6548 
"SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" 
       TCGA-AD-6888        TCGA-AD-6889        TCGA-AD-6890        TCGA-AD-6895 
"SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" 
       TCGA-AD-6899        TCGA-AD-6901        TCGA-AD-6963        TCGA-AD-6964 
"SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" 
       TCGA-AD-6965        TCGA-AU-3779        TCGA-AY-4070        TCGA-AY-4071 
"SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" 
       TCGA-AY-5543        TCGA-AY-6196        TCGA-AY-6197        TCGA-AY-6386 
"SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" 
       TCGA-AZ-4315        TCGA-AZ-4323        TCGA-AZ-4616        TCGA-AZ-4681 
"SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" 
       TCGA-AZ-4682        TCGA-AZ-5403        TCGA-AZ-5407        TCGA-AZ-6598 
"SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" 
       TCGA-AZ-6599        TCGA-AZ-6600        TCGA-AZ-6601        TCGA-AZ-6603 
"SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" 
       TCGA-AZ-6605        TCGA-AZ-6606        TCGA-AZ-6607        TCGA-AZ-6608 
"SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" 
       TCGA-CA-5254        TCGA-CA-5255        TCGA-CA-5796        TCGA-CA-5797 
"SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" 
       TCGA-CA-6715        TCGA-CA-6716        TCGA-CA-6718        TCGA-CA-6719 
"SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" 
       TCGA-CK-4947        TCGA-CK-4948        TCGA-CK-4950        TCGA-CK-4952 
"SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" 
       TCGA-CK-5912        TCGA-CK-5913        TCGA-CK-5914        TCGA-CK-5915 
"SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" 
       TCGA-CK-5916        TCGA-CK-6746        TCGA-CK-6747        TCGA-CK-6748 
"SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" 
       TCGA-CK-6751        TCGA-CM-4743        TCGA-CM-4744        TCGA-CM-4746 
"SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" 
       TCGA-CM-4747        TCGA-CM-4752        TCGA-CM-5341        TCGA-CM-5344 
"SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" 
       TCGA-CM-5348        TCGA-CM-5349        TCGA-CM-5860        TCGA-CM-5861 
"SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" 
       TCGA-CM-5862        TCGA-CM-5863        TCGA-CM-5864        TCGA-CM-5868 
"SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" 
       TCGA-CM-6161        TCGA-CM-6162        TCGA-CM-6163        TCGA-CM-6164 
"SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" 
       TCGA-CM-6165        TCGA-CM-6166        TCGA-CM-6167        TCGA-CM-6168 
"SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" 
       TCGA-CM-6169        TCGA-CM-6170        TCGA-CM-6171        TCGA-CM-6172 
"SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" 
       TCGA-CM-6674        TCGA-CM-6675        TCGA-CM-6676        TCGA-CM-6677 
"SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" 
       TCGA-CM-6678        TCGA-CM-6679        TCGA-CM-6680        TCGA-D5-5537 
"SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" 
       TCGA-D5-5538        TCGA-D5-5539        TCGA-D5-5540        TCGA-D5-5541 
"SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" 
       TCGA-D5-6529        TCGA-D5-6532        TCGA-D5-6533        TCGA-D5-6534 
"SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" 
       TCGA-D5-6535        TCGA-D5-6536        TCGA-D5-6537        TCGA-D5-6538 
"SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" 
       TCGA-D5-6539        TCGA-D5-6540        TCGA-D5-6541        TCGA-D5-6898 
"SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" 
       TCGA-D5-6920        TCGA-D5-6922        TCGA-D5-6923        TCGA-D5-6924 
"SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" 
       TCGA-D5-6926        TCGA-D5-6927        TCGA-D5-6928        TCGA-D5-6929 
"SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" 
       TCGA-D5-6930        TCGA-D5-6931        TCGA-D5-6932        TCGA-D5-7000 
"SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" 
       TCGA-DM-A0X9        TCGA-DM-A0XD        TCGA-DM-A0XF        TCGA-DM-A1D0 
"SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" 
       TCGA-DM-A1D4        TCGA-DM-A1D6        TCGA-DM-A1D7        TCGA-DM-A1D8 
"SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" 
       TCGA-DM-A1D9        TCGA-DM-A1DA        TCGA-DM-A1DB        TCGA-DM-A1HA 
"SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" 
       TCGA-DM-A1HB        TCGA-DM-A282        TCGA-DM-A285        TCGA-DM-A28C 
"SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" 
       TCGA-DM-A28E        TCGA-DM-A28F        TCGA-DM-A28G        TCGA-DM-A28H 
"SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" 
       TCGA-DM-A28K        TCGA-F4-6459        TCGA-F4-6460        TCGA-F4-6569 
"SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" 
       TCGA-F4-6570        TCGA-F4-6703        TCGA-F4-6704        TCGA-F4-6805 
"SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" 
       TCGA-F4-6806        TCGA-F4-6807        TCGA-F4-6808        TCGA-F4-6809 
"SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" 
       TCGA-F4-6854        TCGA-F4-6855        TCGA-F4-6856        TCGA-G4-6293 
"SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" 
       TCGA-G4-6299        TCGA-G4-6303        TCGA-G4-6304        TCGA-G4-6306 
"SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" 
       TCGA-G4-6307        TCGA-G4-6309        TCGA-G4-6310        TCGA-G4-6315 
"SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" 
       TCGA-G4-6317        TCGA-G4-6321        TCGA-G4-6323        TCGA-G4-6586 
"SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" 
       TCGA-G4-6588        TCGA-G4-6625        TCGA-G4-6626        TCGA-G4-6628 
"SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2691        TCGA-AF-2692 
"SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" 
       TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3913        TCGA-AF-4110 
"SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" 
       TCGA-AF-5654        TCGA-AF-6136        TCGA-AF-6655        TCGA-AF-6672 
"SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6549        TCGA-AH-6643 
"SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" 
       TCGA-AH-6644        TCGA-CI-6619        TCGA-CI-6620        TCGA-CI-6621 
"SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" 
       TCGA-CI-6622        TCGA-CI-6624        TCGA-CL-5917        TCGA-CL-5918 
"SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" 
       TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6155        TCGA-DC-6157 
"SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" 
       TCGA-DC-6158        TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682 
"SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" 
       TCGA-DC-6683        TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC 
"SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" 
       TCGA-DY-A1DD        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" 
       TCGA-EF-5830        TCGA-EI-6506        TCGA-EI-6507        TCGA-EI-6508 
"SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" 
       TCGA-EI-6510        TCGA-F5-6464        TCGA-F5-6465        TCGA-F5-6571 
"SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" 
       TCGA-F5-6702        TCGA-F5-6811        TCGA-F5-6812        TCGA-F5-6813 
"SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" 
       TCGA-G5-6235        TCGA-G5-6641 
"SULT1E1 WILD-TYPE" "SULT1E1 WILD-TYPE" 

Clustering(1434) Variable = TTBK2 MUTATION ANALYSIS
D1434V1, survival
                 sevent
clus2               0   1
  TTBK2 MUTATED    15   2
  TTBK2 WILD-TYPE 363  91
  TTBK2 MUTATED TTBK2 WILD-TYPE 
             17             454 
  TTBK2 MUTATED TTBK2 WILD-TYPE 
              2              91 
$`TTBK2 MUTATED`
TCGA-A6-6781 TCGA-AA-3966 TCGA-AA-3977 TCGA-AA-A010 TCGA-AU-6004 TCGA-AY-6197 
       19.66         2.01        25.02        34.98        27.09        21.44 
TCGA-AZ-4315 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-CA-6717 TCGA-CK-6751 TCGA-DM-A28H 
       58.39        49.41         6.77        12.76       124.27       117.07 
TCGA-G4-6309 TCGA-G4-6628 TCGA-AG-A002 TCGA-AH-6544 TCGA-CI-6622 
       85.48        79.69        20.98        38.56         6.97 

$`TTBK2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
        2.01        20.98        34.03        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4323 
       14.50        16.31         0.95        33.01        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6600 
        5.13       106.75        22.36        62.79        88.21        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28K TCGA-F4-6459 
       81.37       119.93        35.97        60.79        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       55.04        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 
       35.80        26.17        91.79        46.75        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
      117.11         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
       33.17         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  TTBK2 MUTATED TTBK2 WILD-TYPE 
           2.01            0.00 
  TTBK2 MUTATED TTBK2 WILD-TYPE 
         124.27          148.01 
  TTBK2 MUTATED TTBK2 WILD-TYPE 
          27.09           20.02 
[1] "2.0 - 124.3 (27.1)" "0.0 - 148.0 (20.0)"
[1] "hr=" "2.7"
D1434V2, continuous
D1434V3, binary
                 cls
clus                0   1
  TTBK2 MUTATED    15   3
  TTBK2 WILD-TYPE 351 116
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TTBK2 MUTATED     15    3
  TTBK2 WILD-TYPE  351  116
        clus
vv       TTBK2 MUTATED TTBK2 WILD-TYPE
  COLON             15             351
  RECTUM             3             116
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TTBK2 MUTATED         5        0        1         5         2         0
  TTBK2 WILD-TYPE      86        1       31       133         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TTBK2 MUTATED           0          0          1          2        0         0
  TTBK2 WILD-TYPE        24         11         58         40       48        18
                 vv
clus              STAGE IVB
  TTBK2 MUTATED           0
  TTBK2 WILD-TYPE         1
D1434V4, multiclass
            clus
vv           TTBK2 MUTATED TTBK2 WILD-TYPE
  STAGE I                5              86
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              5             133
  STAGE IIB              2               8
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             2              40
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  TTBK2 MUTATED     0   6   9   3
  TTBK2 WILD-TYPE  17  86 320  47
D1434V5, multiclass
    clus
vv   TTBK2 MUTATED TTBK2 WILD-TYPE
  T1             0              17
  T2             6              86
  T3             9             320
  T4             3              47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  TTBK2 MUTATED    14   3   1
  TTBK2 WILD-TYPE 273 110  86
D1434V6, multiclass
    clus
vv   TTBK2 MUTATED TTBK2 WILD-TYPE
  N0            14             273
  N1             3             110
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1434V7, binary
                 cls
clus                0   1
  TTBK2 MUTATED    11   1
  TTBK2 WILD-TYPE 364  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TTBK2 MUTATED     11    1
  TTBK2 WILD-TYPE  364   64
   clus
vv  TTBK2 MUTATED TTBK2 WILD-TYPE
  0            11             364
  1             1              64
[1] 2 2
[1] FALSE
D1434V8, binary
                 cls
clus                0   1
  TTBK2 MUTATED     7  11
  TTBK2 WILD-TYPE 218 253
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TTBK2 MUTATED      7   11
  TTBK2 WILD-TYPE  218  253
        clus
vv       TTBK2 MUTATED TTBK2 WILD-TYPE
  FEMALE             7             218
  MALE              11             253
[1] 2 2
[1] FALSE
D1434V9, binary
                 cls
clus                0   1
  TTBK2 MUTATED    13   0
  TTBK2 WILD-TYPE 337  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TTBK2 MUTATED     13    0
  TTBK2 WILD-TYPE  337   22
     clus
vv    TTBK2 MUTATED TTBK2 WILD-TYPE
  NO             13             337
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  TTBK2 MUTATED                     11                             4
  TTBK2 WILD-TYPE                  304                            43
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  TTBK2 MUTATED                       3                              0
  TTBK2 WILD-TYPE                   103                             10
D1434V10, multiclass
                                clus
vv                               TTBK2 MUTATED TTBK2 WILD-TYPE
  COLON ADENOCARCINOMA                      11             304
  COLON MUCINOUS ADENOCARCINOMA              4              43
  RECTAL ADENOCARCINOMA                      3             103
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  TTBK2 MUTATED     9   0   0   2
  TTBK2 WILD-TYPE 336   4  31  23
D1434V11, multiclass
    clus
vv   TTBK2 MUTATED TTBK2 WILD-TYPE
  R0             9             336
  R1             0               4
  R2             0              31
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1434V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TTBK2 MUTATED                                  0     1
  TTBK2 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  TTBK2 MUTATED                           1    11
  TTBK2 WILD-TYPE                        21   215
D1434V13, multiclass
                                  clus
vv                                 TTBK2 MUTATED TTBK2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                       11             215
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1435) Variable = SMO MUTATION ANALYSIS
D1435V1, survival
               sevent
clus2             0   1
  SMO MUTATED    11   2
  SMO WILD-TYPE 367  91
  SMO MUTATED SMO WILD-TYPE 
           13           458 
  SMO MUTATED SMO WILD-TYPE 
            2            91 
$`SMO MUTATED`
TCGA-A6-6651 TCGA-AA-3663 TCGA-AY-5543 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-CM-4746 
       21.76         6.97        33.01        88.21        49.41        37.02 
TCGA-CM-6164 TCGA-CM-6168 TCGA-D5-5537 TCGA-D5-6533 TCGA-G4-6306 TCGA-AF-2687 
       29.03        12.99        45.40         1.32        44.68        24.13 
TCGA-AG-A02N 
       61.97 

$`SMO WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.08        25.18        24.16        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       22.36        62.79         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       23.05        20.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6165 
       15.02        17.03        15.02        12.00         2.96        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       21.99        14.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       12.03        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       18.25        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       53.62        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       79.69        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  SMO MUTATED SMO WILD-TYPE 
         1.32          0.00 
  SMO MUTATED SMO WILD-TYPE 
        88.21        148.01 
  SMO MUTATED SMO WILD-TYPE 
        33.01         20.02 
[1] "1.3 - 88.2 (33.0)"  "0.0 - 148.0 (20.0)"
[1] "hr=" "1.8"
D1435V2, continuous
D1435V3, binary
               cls
clus              0   1
  SMO MUTATED    11   2
  SMO WILD-TYPE 355 117
[1] "tbl2"
               cls
clus            [,1] [,2]
  SMO MUTATED     11    2
  SMO WILD-TYPE  355  117
        clus
vv       SMO MUTATED SMO WILD-TYPE
  COLON           11           355
  RECTUM           2           117
[1] 2 2
[1] FALSE
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SMO MUTATED         2        0        3         4         0         0
  SMO WILD-TYPE      89        1       29       134        10         1
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SMO MUTATED           0          0          2          1        0         1
  SMO WILD-TYPE        24         11         57         41       48        17
               vv
clus            STAGE IVB
  SMO MUTATED           0
  SMO WILD-TYPE         1
D1435V4, multiclass
            clus
vv           SMO MUTATED SMO WILD-TYPE
  STAGE I              2            89
  STAGE IA             0             1
  STAGE II             3            29
  STAGE IIA            4           134
  STAGE IIB            0            10
  STAGE IIC            0             1
  STAGE III            0            24
  STAGE IIIA           0            11
  STAGE IIIB           2            57
  STAGE IIIC           1            41
  STAGE IV             0            48
  STAGE IVA            1            17
  STAGE IVB            0             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  SMO MUTATED     1   2   9   1
  SMO WILD-TYPE  16  90 320  49
D1435V5, multiclass
    clus
vv   SMO MUTATED SMO WILD-TYPE
  T1           1            16
  T2           2            90
  T3           9           320
  T4           1            49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2
  SMO MUTATED     9   2   2
  SMO WILD-TYPE 278 111  85
D1435V6, multiclass
    clus
vv   SMO MUTATED SMO WILD-TYPE
  N0           9           278
  N1           2           111
  N2           2            85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1435V7, binary
               cls
clus              0   1
  SMO MUTATED     9   1
  SMO WILD-TYPE 366  64
[1] "tbl2"
               cls
clus            [,1] [,2]
  SMO MUTATED      9    1
  SMO WILD-TYPE  366   64
   clus
vv  SMO MUTATED SMO WILD-TYPE
  0           9           366
  1           1            64
[1] 2 2
[1] FALSE
D1435V8, binary
               cls
clus              0   1
  SMO MUTATED     7   6
  SMO WILD-TYPE 218 258
[1] "tbl2"
               cls
clus            [,1] [,2]
  SMO MUTATED      7    6
  SMO WILD-TYPE  218  258
        clus
vv       SMO MUTATED SMO WILD-TYPE
  FEMALE           7           218
  MALE             6           258
[1] 2 2
[1] FALSE
D1435V9, binary
               cls
clus              0   1
  SMO MUTATED    10   1
  SMO WILD-TYPE 340  21
[1] "tbl2"
               cls
clus            [,1] [,2]
  SMO MUTATED     10    1
  SMO WILD-TYPE  340   21
     clus
vv    SMO MUTATED SMO WILD-TYPE
  NO           10           340
  YES           1            21
[1] 2 2
[1] FALSE
               vv
clus            COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SMO MUTATED                     11                             0
  SMO WILD-TYPE                  304                            47
               vv
clus            RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SMO MUTATED                       2                              0
  SMO WILD-TYPE                   104                             10
D1435V10, multiclass
                                clus
vv                               SMO MUTATED SMO WILD-TYPE
  COLON ADENOCARCINOMA                    11           304
  COLON MUCINOUS ADENOCARCINOMA            0            47
  RECTAL ADENOCARCINOMA                    2           104
  RECTAL MUCINOUS ADENOCARCINOMA           0            10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             R0  R1  R2  RX
  SMO MUTATED     9   0   0   1
  SMO WILD-TYPE 336   4  31  24
D1435V11, multiclass
    clus
vv   SMO MUTATED SMO WILD-TYPE
  R0           9           336
  R1           0             4
  R2           0            31
  RX           1            24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1435V12, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SMO MUTATED                                  0     0
  SMO WILD-TYPE                                1    11
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  SMO MUTATED                           3     8
  SMO WILD-TYPE                        19   218
D1435V13, multiclass
                                  clus
vv                                 SMO MUTATED SMO WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      0            11
  BLACK OR AFRICAN AMERICAN                  3            19
  WHITE                                      8           218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1436) Variable = FBXO40 MUTATION ANALYSIS
D1436V1, survival
                  sevent
clus2                0   1
  FBXO40 MUTATED    18   3
  FBXO40 WILD-TYPE 360  90
  FBXO40 MUTATED FBXO40 WILD-TYPE 
              21              450 
  FBXO40 MUTATED FBXO40 WILD-TYPE 
               3               90 
$`FBXO40 MUTATED`
TCGA-A6-5666 TCGA-AA-3543 TCGA-AA-3663 TCGA-AA-3710 TCGA-AA-A00R TCGA-AA-A010 
       32.71         0.99         6.97        26.99         0.99        34.98 
TCGA-AU-6004 TCGA-AY-6197 TCGA-AZ-6598 TCGA-AZ-6601 TCGA-CA-6718 TCGA-CM-6164 
       27.09        21.44        49.41       100.01        10.06        29.03 
TCGA-CM-6169 TCGA-CM-6170 TCGA-D5-6930 TCGA-G4-6588 TCGA-AF-2693 TCGA-AF-6655 
       13.02        15.02         1.51        26.17        19.10        20.02 
TCGA-AG-3909 TCGA-AG-A002 TCGA-EI-6508 
       19.99        20.98        20.91 

$`FBXO40 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        22.06        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       26.01        12.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       85.05        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
       42.02        17.03        14.99        21.99         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 
       22.42        27.42        10.88         0.20        14.50        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        33.01        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 
      106.75        22.36        62.79        88.21         6.77        12.10 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6171 TCGA-CM-6172 
       16.04        21.99        14.99        12.99        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       11.64         4.80        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 
       61.91        36.00        22.09        13.78        35.80        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6672 
       34.49        10.39        14.50        16.83        15.39        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       48.03        32.02        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       20.55        19.96        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  FBXO40 MUTATED FBXO40 WILD-TYPE 
            0.99             0.00 
  FBXO40 MUTATED FBXO40 WILD-TYPE 
          100.01           148.01 
  FBXO40 MUTATED FBXO40 WILD-TYPE 
          20.910           20.155 
[1] "1.0 - 100.0 (20.9)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.2"
D1436V2, continuous
D1436V3, binary
                  cls
clus                 0   1
  FBXO40 MUTATED    16   4
  FBXO40 WILD-TYPE 350 115
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FBXO40 MUTATED     16    4
  FBXO40 WILD-TYPE  350  115
        clus
vv       FBXO40 MUTATED FBXO40 WILD-TYPE
  COLON              16              350
  RECTUM              4              115
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FBXO40 MUTATED         6        0        3         7         1         1
  FBXO40 WILD-TYPE      85        1       29       131         9         0
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FBXO40 MUTATED           0          1          2          0        0
  FBXO40 WILD-TYPE        24         10         57         42       48
                  vv
clus               STAGE IVA STAGE IVB
  FBXO40 MUTATED           0         0
  FBXO40 WILD-TYPE        18         1
D1436V4, multiclass
            clus
vv           FBXO40 MUTATED FBXO40 WILD-TYPE
  STAGE I                 6               85
  STAGE IA                0                1
  STAGE II                3               29
  STAGE IIA               7              131
  STAGE IIB               1                9
  STAGE IIC               1                0
  STAGE III               0               24
  STAGE IIIA              1               10
  STAGE IIIB              2               57
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  FBXO40 MUTATED     0   7  12   2
  FBXO40 WILD-TYPE  17  85 317  48
D1436V5, multiclass
    clus
vv   FBXO40 MUTATED FBXO40 WILD-TYPE
  T1              0               17
  T2              7               85
  T3             12              317
  T4              2               48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  FBXO40 MUTATED    18   3   0
  FBXO40 WILD-TYPE 269 110  87
D1436V6, multiclass
    clus
vv   FBXO40 MUTATED FBXO40 WILD-TYPE
  N0             18              269
  N1              3              110
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1436V7, binary
                  cls
clus                 0   1
  FBXO40 MUTATED    18   0
  FBXO40 WILD-TYPE 357  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FBXO40 MUTATED     18    0
  FBXO40 WILD-TYPE  357   65
   clus
vv  FBXO40 MUTATED FBXO40 WILD-TYPE
  0             18              357
  1              0               65
[1] 2 2
[1] FALSE
D1436V8, binary
                  cls
clus                 0   1
  FBXO40 MUTATED    10  11
  FBXO40 WILD-TYPE 215 253
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FBXO40 MUTATED     10   11
  FBXO40 WILD-TYPE  215  253
        clus
vv       FBXO40 MUTATED FBXO40 WILD-TYPE
  FEMALE             10              215
  MALE               11              253
[1] 2 2
[1] FALSE
D1436V9, binary
                  cls
clus                 0   1
  FBXO40 MUTATED    18   0
  FBXO40 WILD-TYPE 332  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FBXO40 MUTATED     18    0
  FBXO40 WILD-TYPE  332   22
     clus
vv    FBXO40 MUTATED FBXO40 WILD-TYPE
  NO              18              332
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  FBXO40 MUTATED                     14                             2
  FBXO40 WILD-TYPE                  301                            45
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  FBXO40 MUTATED                       4                              0
  FBXO40 WILD-TYPE                   102                             10
D1436V10, multiclass
                                clus
vv                               FBXO40 MUTATED FBXO40 WILD-TYPE
  COLON ADENOCARCINOMA                       14              301
  COLON MUCINOUS ADENOCARCINOMA               2               45
  RECTAL ADENOCARCINOMA                       4              102
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  FBXO40 MUTATED    16   0   0   1
  FBXO40 WILD-TYPE 329   4  31  24
D1436V11, multiclass
    clus
vv   FBXO40 MUTATED FBXO40 WILD-TYPE
  R0             16              329
  R1              0                4
  R2              0               31
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1436V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FBXO40 MUTATED                                  0     1
  FBXO40 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  FBXO40 MUTATED                           1    12
  FBXO40 WILD-TYPE                        21   214
D1436V13, multiclass
                                  clus
vv                                 FBXO40 MUTATED FBXO40 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                        12              214
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1437) Variable = ARHGAP29 MUTATION ANALYSIS
D1437V1, survival
                    sevent
clus2                  0   1
  ARHGAP29 MUTATED    15   3
  ARHGAP29 WILD-TYPE 363  90
  ARHGAP29 MUTATED ARHGAP29 WILD-TYPE 
                18                453 
  ARHGAP29 MUTATED ARHGAP29 WILD-TYPE 
                 3                 90 
$`ARHGAP29 MUTATED`
TCGA-A6-5665 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3672 TCGA-AA-3713 TCGA-AA-3821 
       22.06        78.08         6.97         0.92        19.04         1.02 
TCGA-AA-3947 TCGA-AA-A010 TCGA-AD-6889 TCGA-AD-6964 TCGA-AZ-6600 TCGA-CA-6717 
       33.01        34.98        56.55        10.88        12.10        12.76 
TCGA-DM-A1D7 TCGA-G4-6586 TCGA-G4-6588 TCGA-AF-6136 TCGA-AG-A002 TCGA-EI-6510 
       13.32        35.80        26.17        15.39        20.98        18.28 

$`ARHGAP29 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3664 
       19.99        13.94        19.99        61.02         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
        2.01        14.01        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       26.99        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
       25.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 
       31.00         2.01        12.99        24.00        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
        0.79         0.72         5.79        22.42        27.42         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        88.21        49.41         6.77       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07        12.20        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       92.75        49.91        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  ARHGAP29 MUTATED ARHGAP29 WILD-TYPE 
              0.92               0.00 
  ARHGAP29 MUTATED ARHGAP29 WILD-TYPE 
             78.08             148.01 
  ARHGAP29 MUTATED ARHGAP29 WILD-TYPE 
             18.66              20.28 
[1] "0.9 - 78.1 (18.7)"  "0.0 - 148.0 (20.3)"
[1] "hr=" "1"  
D1437V2, continuous
D1437V3, binary
                    cls
clus                   0   1
  ARHGAP29 MUTATED    16   3
  ARHGAP29 WILD-TYPE 350 116
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ARHGAP29 MUTATED     16    3
  ARHGAP29 WILD-TYPE  350  116
        clus
vv       ARHGAP29 MUTATED ARHGAP29 WILD-TYPE
  COLON                16                350
  RECTUM                3                116
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ARHGAP29 MUTATED         2        0        3         6         2         0
  ARHGAP29 WILD-TYPE      89        1       29       132         8         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ARHGAP29 MUTATED           1          0          1          0        2
  ARHGAP29 WILD-TYPE        23         11         58         42       46
                    vv
clus                 STAGE IVA STAGE IVB
  ARHGAP29 MUTATED           1         0
  ARHGAP29 WILD-TYPE        17         1
D1437V4, multiclass
            clus
vv           ARHGAP29 MUTATED ARHGAP29 WILD-TYPE
  STAGE I                   2                 89
  STAGE IA                  0                  1
  STAGE II                  3                 29
  STAGE IIA                 6                132
  STAGE IIB                 2                  8
  STAGE IIC                 0                  1
  STAGE III                 1                 23
  STAGE IIIA                0                 11
  STAGE IIIB                1                 58
  STAGE IIIC                0                 42
  STAGE IV                  2                 46
  STAGE IVA                 1                 17
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  ARHGAP29 MUTATED     0   3  12   4
  ARHGAP29 WILD-TYPE  17  89 317  46
D1437V5, multiclass
    clus
vv   ARHGAP29 MUTATED ARHGAP29 WILD-TYPE
  T1                0                 17
  T2                3                 89
  T3               12                317
  T4                4                 46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  ARHGAP29 MUTATED    15   3   1
  ARHGAP29 WILD-TYPE 272 110  86
D1437V6, multiclass
    clus
vv   ARHGAP29 MUTATED ARHGAP29 WILD-TYPE
  N0               15                272
  N1                3                110
  N2                1                 86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1437V7, binary
                    cls
clus                   0   1
  ARHGAP29 MUTATED    14   2
  ARHGAP29 WILD-TYPE 361  63
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ARHGAP29 MUTATED     14    2
  ARHGAP29 WILD-TYPE  361   63
   clus
vv  ARHGAP29 MUTATED ARHGAP29 WILD-TYPE
  0               14                361
  1                2                 63
[1] 2 2
[1] FALSE
D1437V8, binary
                    cls
clus                   0   1
  ARHGAP29 MUTATED    10   9
  ARHGAP29 WILD-TYPE 215 255
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ARHGAP29 MUTATED     10    9
  ARHGAP29 WILD-TYPE  215  255
        clus
vv       ARHGAP29 MUTATED ARHGAP29 WILD-TYPE
  FEMALE               10                215
  MALE                  9                255
[1] 2 2
[1] FALSE
D1437V9, binary
                    cls
clus                   0   1
  ARHGAP29 MUTATED    13   2
  ARHGAP29 WILD-TYPE 337  20
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ARHGAP29 MUTATED     13    2
  ARHGAP29 WILD-TYPE  337   20
     clus
vv    ARHGAP29 MUTATED ARHGAP29 WILD-TYPE
  NO                13                337
  YES                2                 20
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ARHGAP29 MUTATED                     12                             3
  ARHGAP29 WILD-TYPE                  303                            44
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ARHGAP29 MUTATED                       3                              0
  ARHGAP29 WILD-TYPE                   103                             10
D1437V10, multiclass
                                clus
vv                               ARHGAP29 MUTATED ARHGAP29 WILD-TYPE
  COLON ADENOCARCINOMA                         12                303
  COLON MUCINOUS ADENOCARCINOMA                 3                 44
  RECTAL ADENOCARCINOMA                         3                103
  RECTAL MUCINOUS ADENOCARCINOMA                0                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  ARHGAP29 MUTATED    12   0   1   1
  ARHGAP29 WILD-TYPE 333   4  30  24
D1437V11, multiclass
    clus
vv   ARHGAP29 MUTATED ARHGAP29 WILD-TYPE
  R0               12                333
  R1                0                  4
  R2                1                 30
  RX                1                 24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1437V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ARHGAP29 MUTATED                                  0     2
  ARHGAP29 WILD-TYPE                                1     9
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  ARHGAP29 MUTATED                           1     7
  ARHGAP29 WILD-TYPE                        21   219
D1437V13, multiclass
                                  clus
vv                                 ARHGAP29 MUTATED ARHGAP29 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           2                  9
  BLACK OR AFRICAN AMERICAN                       1                 21
  WHITE                                           7                219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1438) Variable = PAK2 MUTATION ANALYSIS
D1438V1, survival
                sevent
clus2              0   1
  PAK2 MUTATED    10   1
  PAK2 WILD-TYPE 368  92
  PAK2 MUTATED PAK2 WILD-TYPE 
            11            460 
  PAK2 MUTATED PAK2 WILD-TYPE 
             1             92 
$`PAK2 MUTATED`
TCGA-A6-2672 TCGA-A6-6781 TCGA-CK-4948 TCGA-CM-4752 TCGA-CM-5868 TCGA-CM-6171 
       46.65        19.66       148.01        13.02        17.03        14.04 
TCGA-D5-6931 TCGA-F4-6570 TCGA-G4-6293 TCGA-G4-6586 TCGA-AG-A002 
       12.00         6.18       133.18        35.80        20.98 

$`PAK2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 
       12.20        12.76        10.06        14.30        17.56        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
        5.03        15.02        15.02        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       15.02        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6932 
        9.04         9.44        11.64         4.80         1.51        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       35.74        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6299 
       33.67        13.25         0.53        47.41        35.31        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 
       61.91        36.00        22.09        13.78        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  PAK2 MUTATED PAK2 WILD-TYPE 
          6.18           0.00 
  PAK2 MUTATED PAK2 WILD-TYPE 
        148.01         140.38 
  PAK2 MUTATED PAK2 WILD-TYPE 
        19.660         20.235 
[1] "6.2 - 148.0 (19.7)" "0.0 - 140.4 (20.2)"
[1] "hr=" "3"  
D1438V2, continuous
D1438V3, binary
                cls
clus               0   1
  PAK2 MUTATED    10   1
  PAK2 WILD-TYPE 356 118
[1] "tbl2"
                cls
clus             [,1] [,2]
  PAK2 MUTATED     10    1
  PAK2 WILD-TYPE  356  118
        clus
vv       PAK2 MUTATED PAK2 WILD-TYPE
  COLON            10            356
  RECTUM            1            118
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PAK2 MUTATED         2        0        0         3         0         0
  PAK2 WILD-TYPE      89        1       32       135        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PAK2 MUTATED           2          0          1          2        0         1
  PAK2 WILD-TYPE        22         11         58         40       48        17
                vv
clus             STAGE IVB
  PAK2 MUTATED           0
  PAK2 WILD-TYPE         1
D1438V4, multiclass
            clus
vv           PAK2 MUTATED PAK2 WILD-TYPE
  STAGE I               2             89
  STAGE IA              0              1
  STAGE II              0             32
  STAGE IIA             3            135
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             2             22
  STAGE IIIA            0             11
  STAGE IIIB            1             58
  STAGE IIIC            2             40
  STAGE IV              0             48
  STAGE IVA             1             17
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  PAK2 MUTATED     0   2   6   3
  PAK2 WILD-TYPE  17  90 323  47
D1438V5, multiclass
    clus
vv   PAK2 MUTATED PAK2 WILD-TYPE
  T1            0             17
  T2            2             90
  T3            6            323
  T4            3             47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  PAK2 MUTATED     5   5   1
  PAK2 WILD-TYPE 282 108  86
D1438V6, multiclass
    clus
vv   PAK2 MUTATED PAK2 WILD-TYPE
  N0            5            282
  N1            5            108
  N2            1             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1438V7, binary
                cls
clus               0   1
  PAK2 MUTATED     9   1
  PAK2 WILD-TYPE 366  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  PAK2 MUTATED      9    1
  PAK2 WILD-TYPE  366   64
   clus
vv  PAK2 MUTATED PAK2 WILD-TYPE
  0            9            366
  1            1             64
[1] 2 2
[1] FALSE
D1438V8, binary
                cls
clus               0   1
  PAK2 MUTATED     7   4
  PAK2 WILD-TYPE 218 260
[1] "tbl2"
                cls
clus             [,1] [,2]
  PAK2 MUTATED      7    4
  PAK2 WILD-TYPE  218  260
        clus
vv       PAK2 MUTATED PAK2 WILD-TYPE
  FEMALE            7            218
  MALE              4            260
[1] 2 2
[1] FALSE
D1438V9, binary
                cls
clus               0   1
  PAK2 MUTATED    11   0
  PAK2 WILD-TYPE 339  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  PAK2 MUTATED     11    0
  PAK2 WILD-TYPE  339   22
     clus
vv    PAK2 MUTATED PAK2 WILD-TYPE
  NO            11            339
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PAK2 MUTATED                      9                             1
  PAK2 WILD-TYPE                  306                            46
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PAK2 MUTATED                       1                              0
  PAK2 WILD-TYPE                   105                             10
D1438V10, multiclass
                                clus
vv                               PAK2 MUTATED PAK2 WILD-TYPE
  COLON ADENOCARCINOMA                      9            306
  COLON MUCINOUS ADENOCARCINOMA             1             46
  RECTAL ADENOCARCINOMA                     1            105
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  PAK2 MUTATED    11   0   0   0
  PAK2 WILD-TYPE 334   4  31  25
D1438V11, multiclass
    clus
vv   PAK2 MUTATED PAK2 WILD-TYPE
  R0           11            334
  R1            0              4
  R2            0             31
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1438V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PAK2 MUTATED                                  0     0
  PAK2 WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  PAK2 MUTATED                           1     9
  PAK2 WILD-TYPE                        21   217
D1438V13, multiclass
                                  clus
vv                                 PAK2 MUTATED PAK2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                       9            217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1439) Variable = MAOA MUTATION ANALYSIS
D1439V1, survival
                sevent
clus2              0   1
  MAOA MUTATED     6   1
  MAOA WILD-TYPE 372  92
  MAOA MUTATED MAOA WILD-TYPE 
             7            464 
  MAOA MUTATED MAOA WILD-TYPE 
             1             92 
$`MAOA MUTATED`
TCGA-AA-3525 TCGA-AA-A00R TCGA-AZ-6601 TCGA-D5-6922 TCGA-G4-6317 TCGA-AG-3609 
        8.05         0.99       100.01         4.41        36.00        19.99 
TCGA-AG-3742 
        0.99 

$`MAOA WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W 
       38.04         4.01        27.02        42.02        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
       12.10        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  MAOA MUTATED MAOA WILD-TYPE 
          0.99           0.00 
  MAOA MUTATED MAOA WILD-TYPE 
        100.01         148.01 
  MAOA MUTATED MAOA WILD-TYPE 
         8.050         20.415 
[1] "1.0 - 100.0 (8.1)"  "0.0 - 148.0 (20.4)"
[1] "hr=" "1.3"
D1439V2, continuous
D1439V3, binary
                cls
clus               0   1
  MAOA MUTATED     5   2
  MAOA WILD-TYPE 361 117
[1] "tbl2"
                cls
clus             [,1] [,2]
  MAOA MUTATED      5    2
  MAOA WILD-TYPE  361  117
        clus
vv       MAOA MUTATED MAOA WILD-TYPE
  COLON             5            361
  RECTUM            2            117
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MAOA MUTATED         2        0        1         0         0         0
  MAOA WILD-TYPE      89        1       31       138        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MAOA MUTATED           0          1          1          2        0         0
  MAOA WILD-TYPE        24         10         58         40       48        18
                vv
clus             STAGE IVB
  MAOA MUTATED           0
  MAOA WILD-TYPE         1
D1439V4, multiclass
            clus
vv           MAOA MUTATED MAOA WILD-TYPE
  STAGE I               2             89
  STAGE IA              0              1
  STAGE II              1             31
  STAGE IIA             0            138
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            1             10
  STAGE IIIB            1             58
  STAGE IIIC            2             40
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  MAOA MUTATED     1   1   5   0
  MAOA WILD-TYPE  16  91 324  50
D1439V5, multiclass
    clus
vv   MAOA MUTATED MAOA WILD-TYPE
  T1            1             16
  T2            1             91
  T3            5            324
  T4            0             50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  MAOA MUTATED     3   2   2
  MAOA WILD-TYPE 284 111  85
D1439V6, multiclass
    clus
vv   MAOA MUTATED MAOA WILD-TYPE
  N0            3            284
  N1            2            111
  N2            2             85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1439V7, binary
                cls
clus               0   1
  MAOA MUTATED     6   0
  MAOA WILD-TYPE 369  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  MAOA MUTATED      6    0
  MAOA WILD-TYPE  369   65
   clus
vv  MAOA MUTATED MAOA WILD-TYPE
  0            6            369
  1            0             65
[1] 2 2
[1] FALSE
D1439V8, binary
                cls
clus               0   1
  MAOA MUTATED     4   3
  MAOA WILD-TYPE 221 261
[1] "tbl2"
                cls
clus             [,1] [,2]
  MAOA MUTATED      4    3
  MAOA WILD-TYPE  221  261
        clus
vv       MAOA MUTATED MAOA WILD-TYPE
  FEMALE            4            221
  MALE              3            261
[1] 2 2
[1] FALSE
D1439V9, binary
                cls
clus               0   1
  MAOA MUTATED     4   0
  MAOA WILD-TYPE 346  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  MAOA MUTATED      4    0
  MAOA WILD-TYPE  346   22
     clus
vv    MAOA MUTATED MAOA WILD-TYPE
  NO             4            346
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MAOA MUTATED                      5                             0
  MAOA WILD-TYPE                  310                            47
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MAOA MUTATED                       2                              0
  MAOA WILD-TYPE                   104                             10
D1439V10, multiclass
                                clus
vv                               MAOA MUTATED MAOA WILD-TYPE
  COLON ADENOCARCINOMA                      5            310
  COLON MUCINOUS ADENOCARCINOMA             0             47
  RECTAL ADENOCARCINOMA                     2            104
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  MAOA MUTATED     6   0   0   0
  MAOA WILD-TYPE 339   4  31  25
D1439V11, multiclass
    clus
vv   MAOA MUTATED MAOA WILD-TYPE
  R0            6            339
  R1            0              4
  R2            0             31
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1439V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MAOA MUTATED                                  0     0
  MAOA WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  MAOA MUTATED                           0     3
  MAOA WILD-TYPE                        22   223
D1439V13, multiclass
                                  clus
vv                                 MAOA MUTATED MAOA WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       3            223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1440) Variable = FAM120C MUTATION ANALYSIS
D1440V1, survival
                   sevent
clus2                 0   1
  FAM120C MUTATED     4   3
  FAM120C WILD-TYPE 374  90
  FAM120C MUTATED FAM120C WILD-TYPE 
                7               464 
  FAM120C MUTATED FAM120C WILD-TYPE 
                3                90 
$`FAM120C MUTATED`
TCGA-AA-3864 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-CK-4947 TCGA-CM-6161 TCGA-CM-6164 
       53.00        49.41         6.77        17.56        15.02        29.03 
TCGA-F4-6460 
       31.96 

$`FAM120C WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6600 
        5.13       106.75        22.36        62.79        88.21        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       12.76        10.06        14.30       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6162 TCGA-CM-6163 
        5.03        15.02        15.02        17.03        12.00         2.96 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  FAM120C MUTATED FAM120C WILD-TYPE 
             6.77              0.00 
  FAM120C MUTATED FAM120C WILD-TYPE 
            53.00            148.01 
  FAM120C MUTATED FAM120C WILD-TYPE 
           29.030            20.155 
[1] "6.8 - 53.0 (29.0)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.9"
D1440V2, continuous
D1440V3, binary
                   cls
clus                  0   1
  FAM120C MUTATED     8   0
  FAM120C WILD-TYPE 358 119
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM120C MUTATED      8    0
  FAM120C WILD-TYPE  358  119
        clus
vv       FAM120C MUTATED FAM120C WILD-TYPE
  COLON                8               358
  RECTUM               0               119
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FAM120C MUTATED         2        0        2         2         0         0
  FAM120C WILD-TYPE      89        1       30       136        10         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FAM120C MUTATED           0          0          2          0        0
  FAM120C WILD-TYPE        24         11         57         42       48
                   vv
clus                STAGE IVA STAGE IVB
  FAM120C MUTATED           0         0
  FAM120C WILD-TYPE        18         1
D1440V4, multiclass
            clus
vv           FAM120C MUTATED FAM120C WILD-TYPE
  STAGE I                  2                89
  STAGE IA                 0                 1
  STAGE II                 2                30
  STAGE IIA                2               136
  STAGE IIB                0                10
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               0                11
  STAGE IIIB               2                57
  STAGE IIIC               0                42
  STAGE IV                 0                48
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  FAM120C MUTATED     0   2   5   1
  FAM120C WILD-TYPE  17  90 324  49
D1440V5, multiclass
    clus
vv   FAM120C MUTATED FAM120C WILD-TYPE
  T1               0                17
  T2               2                90
  T3               5               324
  T4               1                49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  FAM120C MUTATED     6   2   0
  FAM120C WILD-TYPE 281 111  87
D1440V6, multiclass
    clus
vv   FAM120C MUTATED FAM120C WILD-TYPE
  N0               6               281
  N1               2               111
  N2               0                87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1440V7, binary
                   cls
clus                  0   1
  FAM120C MUTATED     6   0
  FAM120C WILD-TYPE 369  65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM120C MUTATED      6    0
  FAM120C WILD-TYPE  369   65
   clus
vv  FAM120C MUTATED FAM120C WILD-TYPE
  0               6               369
  1               0                65
[1] 2 2
[1] FALSE
D1440V8, binary
                   cls
clus                  0   1
  FAM120C MUTATED     6   2
  FAM120C WILD-TYPE 219 262
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM120C MUTATED      6    2
  FAM120C WILD-TYPE  219  262
        clus
vv       FAM120C MUTATED FAM120C WILD-TYPE
  FEMALE               6               219
  MALE                 2               262
[1] 2 2
[1] FALSE
D1440V9, binary
                   cls
clus                  0   1
  FAM120C MUTATED     7   0
  FAM120C WILD-TYPE 343  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM120C MUTATED      7    0
  FAM120C WILD-TYPE  343   22
     clus
vv    FAM120C MUTATED FAM120C WILD-TYPE
  NO                7               343
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  FAM120C MUTATED                      8                             0
  FAM120C WILD-TYPE                  307                            47
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  FAM120C MUTATED                       0                              0
  FAM120C WILD-TYPE                   106                             10
D1440V10, multiclass
                                clus
vv                               FAM120C MUTATED FAM120C WILD-TYPE
  COLON ADENOCARCINOMA                         8               307
  COLON MUCINOUS ADENOCARCINOMA                0                47
  RECTAL ADENOCARCINOMA                        0               106
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  FAM120C MUTATED     5   0   0   1
  FAM120C WILD-TYPE 340   4  31  24
D1440V11, multiclass
    clus
vv   FAM120C MUTATED FAM120C WILD-TYPE
  R0               5               340
  R1               0                 4
  R2               0                31
  RX               1                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1440V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FAM120C MUTATED                                  0     0
  FAM120C WILD-TYPE                                1    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  FAM120C MUTATED                           0     6
  FAM120C WILD-TYPE                        22   220
D1440V13, multiclass
                                  clus
vv                                 FAM120C MUTATED FAM120C WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                      0                22
  WHITE                                          6               220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1441) Variable = MED13 MUTATION ANALYSIS
D1441V1, survival
                 sevent
clus2               0   1
  MED13 MUTATED    18   3
  MED13 WILD-TYPE 360  90
  MED13 MUTATED MED13 WILD-TYPE 
             21             450 
  MED13 MUTATED MED13 WILD-TYPE 
              3              90 
$`MED13 MUTATED`
TCGA-A6-6653 TCGA-A6-6781 TCGA-AA-3710 TCGA-AA-3864 TCGA-AA-3877 TCGA-AA-A00N 
       24.39        19.66        26.99        53.00        31.00         4.01 
TCGA-AA-A010 TCGA-AD-6895 TCGA-AY-5543 TCGA-CA-6717 TCGA-CK-5913 TCGA-CM-4746 
       34.98         0.72        33.01        12.76        51.32        37.02 
TCGA-CM-5341 TCGA-D5-6928 TCGA-D5-6932 TCGA-F4-6570 TCGA-F4-6856 TCGA-G4-6588 
       29.06        11.64        11.38         6.18        35.31        26.17 
TCGA-G4-6626 TCGA-AG-A002 TCGA-AG-A02N 
       46.75        20.98        61.97 

$`MED13 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
       25.08        25.18        24.16        21.76        24.69        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        31.07        30.05        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       29.98        18.05         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       15.52        56.55         0.79         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       49.08         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-5348 
       23.05        20.02        25.02        13.02        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 
        9.44         4.80         1.51        12.00        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 
      117.07        98.24         8.61        31.96        35.74        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
        0.53        47.41       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-AF-2687 
       22.09        13.78        35.80        91.79        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 
       10.98        49.97         1.94        38.96        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  MED13 MUTATED MED13 WILD-TYPE 
           0.72            0.00 
  MED13 MUTATED MED13 WILD-TYPE 
          61.97          148.01 
  MED13 MUTATED MED13 WILD-TYPE 
          26.99           20.02 
[1] "0.7 - 62.0 (27.0)"  "0.0 - 148.0 (20.0)"
[1] "hr=" "1.5"
D1441V2, continuous
D1441V3, binary
                 cls
clus                0   1
  MED13 MUTATED    20   2
  MED13 WILD-TYPE 346 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MED13 MUTATED     20    2
  MED13 WILD-TYPE  346  117
        clus
vv       MED13 MUTATED MED13 WILD-TYPE
  COLON             20             346
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MED13 MUTATED         5        0        2         8         3         0
  MED13 WILD-TYPE      86        1       30       130         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MED13 MUTATED           0          1          0          1        0         1
  MED13 WILD-TYPE        24         10         59         41       48        17
                 vv
clus              STAGE IVB
  MED13 MUTATED           0
  MED13 WILD-TYPE         1
D1441V4, multiclass
            clus
vv           MED13 MUTATED MED13 WILD-TYPE
  STAGE I                5              86
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA              8             130
  STAGE IIB              3               7
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             1              10
  STAGE IIIB             0              59
  STAGE IIIC             1              41
  STAGE IV               0              48
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  MED13 MUTATED     1   5  12   4
  MED13 WILD-TYPE  16  87 317  46
D1441V5, multiclass
    clus
vv   MED13 MUTATED MED13 WILD-TYPE
  T1             1              16
  T2             5              87
  T3            12             317
  T4             4              46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  MED13 MUTATED    18   4   0
  MED13 WILD-TYPE 269 109  87
D1441V6, multiclass
    clus
vv   MED13 MUTATED MED13 WILD-TYPE
  N0            18             269
  N1             4             109
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1441V7, binary
                 cls
clus                0   1
  MED13 MUTATED    17   1
  MED13 WILD-TYPE 358  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MED13 MUTATED     17    1
  MED13 WILD-TYPE  358   64
   clus
vv  MED13 MUTATED MED13 WILD-TYPE
  0            17             358
  1             1              64
[1] 2 2
[1] FALSE
D1441V8, binary
                 cls
clus                0   1
  MED13 MUTATED     9  13
  MED13 WILD-TYPE 216 251
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MED13 MUTATED      9   13
  MED13 WILD-TYPE  216  251
        clus
vv       MED13 MUTATED MED13 WILD-TYPE
  FEMALE             9             216
  MALE              13             251
[1] 2 2
[1] FALSE
D1441V9, binary
                 cls
clus                0   1
  MED13 MUTATED    18   0
  MED13 WILD-TYPE 332  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MED13 MUTATED     18    0
  MED13 WILD-TYPE  332   22
     clus
vv    MED13 MUTATED MED13 WILD-TYPE
  NO             18             332
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MED13 MUTATED                     14                             6
  MED13 WILD-TYPE                  301                            41
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MED13 MUTATED                       2                              0
  MED13 WILD-TYPE                   104                             10
D1441V10, multiclass
                                clus
vv                               MED13 MUTATED MED13 WILD-TYPE
  COLON ADENOCARCINOMA                      14             301
  COLON MUCINOUS ADENOCARCINOMA              6              41
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  MED13 MUTATED    17   0   0   3
  MED13 WILD-TYPE 328   4  31  22
D1441V11, multiclass
    clus
vv   MED13 MUTATED MED13 WILD-TYPE
  R0            17             328
  R1             0               4
  R2             0              31
  RX             3              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1441V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MED13 MUTATED                                  0     1
  MED13 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  MED13 MUTATED                           2    12
  MED13 WILD-TYPE                        20   214
D1441V13, multiclass
                                  clus
vv                                 MED13 MUTATED MED13 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    2              20
  WHITE                                       12             214
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1442) Variable = ALCAM MUTATION ANALYSIS
D1442V1, survival
                 sevent
clus2               0   1
  ALCAM MUTATED     8   4
  ALCAM WILD-TYPE 370  89
  ALCAM MUTATED ALCAM WILD-TYPE 
             12             459 
  ALCAM MUTATED ALCAM WILD-TYPE 
              4              89 
$`ALCAM MUTATED`
TCGA-AA-3672 TCGA-AA-3864 TCGA-AD-6899 TCGA-AY-6197 TCGA-AZ-6598 TCGA-CA-6717 
        0.92        53.00         5.79        21.44        49.41        12.76 
TCGA-CA-6718 TCGA-D5-6923 TCGA-DM-A1HA TCGA-G4-6303 TCGA-G4-6315 TCGA-CI-6620 
       10.06        12.43       131.51        65.85        61.91        33.17 

$`ALCAM WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
        6.05         6.97        54.02         2.01        14.01        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 
       32.05         0.99        31.07        31.07        30.05        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
       56.55         0.79         0.72        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        88.21         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 
        3.25         3.29         0.07        12.20        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        1.48         3.68         4.41        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HB 
       13.32        12.59       140.38         7.50        44.32       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6317 
       53.62        44.68        55.04        85.48        63.62        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6622 
        1.45        17.49         0.69         0.72         6.05         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  ALCAM MUTATED ALCAM WILD-TYPE 
           0.92            0.00 
  ALCAM MUTATED ALCAM WILD-TYPE 
         131.51          148.01 
  ALCAM MUTATED ALCAM WILD-TYPE 
         27.305          20.120 
[1] "0.9 - 131.5 (27.3)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.2"
D1442V2, continuous
D1442V3, binary
                 cls
clus                0   1
  ALCAM MUTATED    11   1
  ALCAM WILD-TYPE 355 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ALCAM MUTATED     11    1
  ALCAM WILD-TYPE  355  118
        clus
vv       ALCAM MUTATED ALCAM WILD-TYPE
  COLON             11             355
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ALCAM MUTATED         1        0        2         3         0         0
  ALCAM WILD-TYPE      90        1       30       135        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ALCAM MUTATED           1          0          0          2        2         1
  ALCAM WILD-TYPE        23         11         59         40       46        17
                 vv
clus              STAGE IVB
  ALCAM MUTATED           0
  ALCAM WILD-TYPE         1
D1442V4, multiclass
            clus
vv           ALCAM MUTATED ALCAM WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA              3             135
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             2              40
  STAGE IV               2              46
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ALCAM MUTATED     0   1  10   1
  ALCAM WILD-TYPE  17  91 319  49
D1442V5, multiclass
    clus
vv   ALCAM MUTATED ALCAM WILD-TYPE
  T1             0              17
  T2             1              91
  T3            10             319
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  ALCAM MUTATED     6   4   2
  ALCAM WILD-TYPE 281 109  85
D1442V6, multiclass
    clus
vv   ALCAM MUTATED ALCAM WILD-TYPE
  N0             6             281
  N1             4             109
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1442V7, binary
                 cls
clus                0   1
  ALCAM MUTATED     6   3
  ALCAM WILD-TYPE 369  62
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ALCAM MUTATED      6    3
  ALCAM WILD-TYPE  369   62
   clus
vv  ALCAM MUTATED ALCAM WILD-TYPE
  0             6             369
  1             3              62
[1] 2 2
[1] FALSE
D1442V8, binary
                 cls
clus                0   1
  ALCAM MUTATED     4   8
  ALCAM WILD-TYPE 221 256
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ALCAM MUTATED      4    8
  ALCAM WILD-TYPE  221  256
        clus
vv       ALCAM MUTATED ALCAM WILD-TYPE
  FEMALE             4             221
  MALE               8             256
[1] 2 2
[1] FALSE
D1442V9, binary
                 cls
clus                0   1
  ALCAM MUTATED    11   0
  ALCAM WILD-TYPE 339  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ALCAM MUTATED     11    0
  ALCAM WILD-TYPE  339   22
     clus
vv    ALCAM MUTATED ALCAM WILD-TYPE
  NO             11             339
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ALCAM MUTATED                      9                             2
  ALCAM WILD-TYPE                  306                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ALCAM MUTATED                       1                              0
  ALCAM WILD-TYPE                   105                             10
D1442V10, multiclass
                                clus
vv                               ALCAM MUTATED ALCAM WILD-TYPE
  COLON ADENOCARCINOMA                       9             306
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  ALCAM MUTATED     6   0   0   2
  ALCAM WILD-TYPE 339   4  31  23
D1442V11, multiclass
    clus
vv   ALCAM MUTATED ALCAM WILD-TYPE
  R0             6             339
  R1             0               4
  R2             0              31
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1442V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ALCAM MUTATED                                  0     2
  ALCAM WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ALCAM MUTATED                           0     8
  ALCAM WILD-TYPE                        22   218
D1442V13, multiclass
                                  clus
vv                                 ALCAM MUTATED ALCAM WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               9
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        8             218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1443) Variable = MEGF8 MUTATION ANALYSIS
D1443V1, survival
                 sevent
clus2               0   1
  MEGF8 MUTATED    22   4
  MEGF8 WILD-TYPE 356  89
  MEGF8 MUTATED MEGF8 WILD-TYPE 
             26             445 
  MEGF8 MUTATED MEGF8 WILD-TYPE 
              4              89 
$`MEGF8 MUTATED`
TCGA-A6-5661 TCGA-A6-5665 TCGA-A6-6781 TCGA-AA-3492 TCGA-AA-3663 TCGA-AA-3815 
       33.53        22.06        19.66         3.02         6.97        33.04 
TCGA-AA-3821 TCGA-AA-3845 TCGA-AA-3877 TCGA-AA-3947 TCGA-AA-A010 TCGA-AD-6889 
        1.02         0.00        31.00        33.01        34.98        56.55 
TCGA-AU-6004 TCGA-AY-6197 TCGA-AZ-6598 TCGA-CA-6717 TCGA-CK-5916 TCGA-CM-5861 
       27.09        21.44        49.41        12.76        21.14        15.02 
TCGA-CM-6171 TCGA-D5-6540 TCGA-D5-6927 TCGA-DM-A0X9 TCGA-DM-A1HB TCGA-AG-A002 
       14.04        16.14         9.44       119.70       135.65        20.98 
TCGA-AG-A02N TCGA-AH-6643 
       61.97         0.69 

$`MEGF8 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
       20.28         7.04         1.02        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       61.02        78.08         6.05        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
       19.04        19.04        10.06        35.05         0.99        25.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 
       17.98        15.95        38.99        37.02        14.93        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 
       24.03        27.02        29.98        18.05         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
        0.07        21.37        15.52         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 
       22.42        27.42        10.88         0.20        14.50        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        33.01        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 
      106.75        22.36        62.79        88.21         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       49.08        51.32         9.99        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 
       22.03        22.98        30.08        32.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 
       17.85         4.80        17.13        12.49        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6928 
        3.68         4.41        12.43        14.30         9.04        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0XD 
        4.80         1.51        12.00        11.38        10.26        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 
      140.38         7.50        44.32       131.51       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  MEGF8 MUTATED MEGF8 WILD-TYPE 
              0               0 
  MEGF8 MUTATED MEGF8 WILD-TYPE 
         135.65          148.01 
  MEGF8 MUTATED MEGF8 WILD-TYPE 
          21.29           20.05 
[1] "0.0 - 135.7 (21.3)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.4"
D1443V2, continuous
D1443V3, binary
                 cls
clus                0   1
  MEGF8 MUTATED    24   3
  MEGF8 WILD-TYPE 342 116
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MEGF8 MUTATED     24    3
  MEGF8 WILD-TYPE  342  116
        clus
vv       MEGF8 MUTATED MEGF8 WILD-TYPE
  COLON             24             342
  RECTUM             3             116
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MEGF8 MUTATED         7        0        5        10         2         0
  MEGF8 WILD-TYPE      84        1       27       128         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MEGF8 MUTATED           0          0          1          2        0         0
  MEGF8 WILD-TYPE        24         11         58         40       48        18
                 vv
clus              STAGE IVB
  MEGF8 MUTATED           0
  MEGF8 WILD-TYPE         1
D1443V4, multiclass
            clus
vv           MEGF8 MUTATED MEGF8 WILD-TYPE
  STAGE I                7              84
  STAGE IA               0               1
  STAGE II               5              27
  STAGE IIA             10             128
  STAGE IIB              2               8
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             2              40
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  MEGF8 MUTATED     2   5  16   4
  MEGF8 WILD-TYPE  15  87 313  46
D1443V5, multiclass
    clus
vv   MEGF8 MUTATED MEGF8 WILD-TYPE
  T1             2              15
  T2             5              87
  T3            16             313
  T4             4              46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  MEGF8 MUTATED    24   2   1
  MEGF8 WILD-TYPE 263 111  86
D1443V6, multiclass
    clus
vv   MEGF8 MUTATED MEGF8 WILD-TYPE
  N0            24             263
  N1             2             111
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1443V7, binary
                 cls
clus                0   1
  MEGF8 MUTATED    24   0
  MEGF8 WILD-TYPE 351  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MEGF8 MUTATED     24    0
  MEGF8 WILD-TYPE  351   65
   clus
vv  MEGF8 MUTATED MEGF8 WILD-TYPE
  0            24             351
  1             0              65
[1] 2 2
[1] FALSE
D1443V8, binary
                 cls
clus                0   1
  MEGF8 MUTATED    16  11
  MEGF8 WILD-TYPE 209 253
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MEGF8 MUTATED     16   11
  MEGF8 WILD-TYPE  209  253
        clus
vv       MEGF8 MUTATED MEGF8 WILD-TYPE
  FEMALE            16             209
  MALE              11             253
[1] 2 2
[1] FALSE
D1443V9, binary
                 cls
clus                0   1
  MEGF8 MUTATED    19   0
  MEGF8 WILD-TYPE 331  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MEGF8 MUTATED     19    0
  MEGF8 WILD-TYPE  331   22
     clus
vv    MEGF8 MUTATED MEGF8 WILD-TYPE
  NO             19             331
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MEGF8 MUTATED                     17                             6
  MEGF8 WILD-TYPE                  298                            41
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MEGF8 MUTATED                       3                              0
  MEGF8 WILD-TYPE                   103                             10
D1443V10, multiclass
                                clus
vv                               MEGF8 MUTATED MEGF8 WILD-TYPE
  COLON ADENOCARCINOMA                      17             298
  COLON MUCINOUS ADENOCARCINOMA              6              41
  RECTAL ADENOCARCINOMA                      3             103
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  MEGF8 MUTATED    21   0   0   2
  MEGF8 WILD-TYPE 324   4  31  23
D1443V11, multiclass
    clus
vv   MEGF8 MUTATED MEGF8 WILD-TYPE
  R0            21             324
  R1             0               4
  R2             0              31
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1443V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MEGF8 MUTATED                                  0     2
  MEGF8 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  MEGF8 MUTATED                           1    13
  MEGF8 WILD-TYPE                        21   213
D1443V13, multiclass
                                  clus
vv                                 MEGF8 MUTATED MEGF8 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               9
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                       13             213
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1444) Variable = SLIT3 MUTATION ANALYSIS
D1444V1, survival
                 sevent
clus2               0   1
  SLIT3 MUTATED    22   4
  SLIT3 WILD-TYPE 356  89
  SLIT3 MUTATED SLIT3 WILD-TYPE 
             26             445 
  SLIT3 MUTATED SLIT3 WILD-TYPE 
              4              89 
$`SLIT3 MUTATED`
TCGA-A6-2672 TCGA-A6-6781 TCGA-AA-3517 TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3672 
       46.65        19.66        38.99        61.02         6.97         0.92 
TCGA-AA-3713 TCGA-AA-3821 TCGA-AA-3866 TCGA-AA-3986 TCGA-AA-A00N TCGA-AD-6890 
       19.04         1.02        17.03        19.07         4.01         0.79 
TCGA-AY-5543 TCGA-CA-6717 TCGA-CM-5861 TCGA-CM-6167 TCGA-CM-6171 TCGA-DM-A28C 
       33.01        12.76        15.02        14.99        14.04        81.37 
TCGA-DM-A28F TCGA-F4-6570 TCGA-G4-6293 TCGA-G4-6309 TCGA-G4-6586 TCGA-G4-6588 
       35.97         6.18       133.18        85.48        35.80        26.17 
TCGA-AG-3587 TCGA-AG-A002 
       46.03        20.98 

$`SLIT3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3519 
       63.98         6.97         1.02        13.02         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       19.99        78.08         6.05        54.02         2.01        14.01 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 
       10.06        35.05        33.04         0.99        25.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3867 
        0.99        31.07        31.07        30.05        53.00        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6895 TCGA-AD-6899 
        0.07        21.37        15.52        56.55         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       16.31         0.95        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07        12.20        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       32.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6168 
       12.00         2.96        29.03        16.04        21.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       13.02        15.02        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
      119.93        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       35.74        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6299 
       33.67        13.25         0.53        47.41        35.31        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 
       65.85        53.62        44.68        55.04        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       36.00        22.09        13.78        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       20.05        24.00         1.02        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  SLIT3 MUTATED SLIT3 WILD-TYPE 
           0.79            0.00 
  SLIT3 MUTATED SLIT3 WILD-TYPE 
         133.18          148.01 
  SLIT3 MUTATED SLIT3 WILD-TYPE 
         19.365          20.280 
[1] "0.8 - 133.2 (19.4)" "0.0 - 148.0 (20.3)"
[1] "hr=" "1.5"
D1444V2, continuous
D1444V3, binary
                 cls
clus                0   1
  SLIT3 MUTATED    25   2
  SLIT3 WILD-TYPE 341 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SLIT3 MUTATED     25    2
  SLIT3 WILD-TYPE  341  117
        clus
vv       SLIT3 MUTATED SLIT3 WILD-TYPE
  COLON             25             341
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SLIT3 MUTATED         6        0        2         7         2         0
  SLIT3 WILD-TYPE      85        1       30       131         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SLIT3 MUTATED           2          0          3          2        1         1
  SLIT3 WILD-TYPE        22         11         56         40       47        17
                 vv
clus              STAGE IVB
  SLIT3 MUTATED           0
  SLIT3 WILD-TYPE         1
D1444V4, multiclass
            clus
vv           SLIT3 MUTATED SLIT3 WILD-TYPE
  STAGE I                6              85
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA              7             131
  STAGE IIB              2               8
  STAGE IIC              0               1
  STAGE III              2              22
  STAGE IIIA             0              11
  STAGE IIIB             3              56
  STAGE IIIC             2              40
  STAGE IV               1              47
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  SLIT3 MUTATED     1   6  17   3
  SLIT3 WILD-TYPE  16  86 312  47
D1444V5, multiclass
    clus
vv   SLIT3 MUTATED SLIT3 WILD-TYPE
  T1             1              16
  T2             6              86
  T3            17             312
  T4             3              47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  SLIT3 MUTATED    19   7   1
  SLIT3 WILD-TYPE 268 106  86
D1444V6, multiclass
    clus
vv   SLIT3 MUTATED SLIT3 WILD-TYPE
  N0            19             268
  N1             7             106
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1444V7, binary
                 cls
clus                0   1
  SLIT3 MUTATED    22   2
  SLIT3 WILD-TYPE 353  63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SLIT3 MUTATED     22    2
  SLIT3 WILD-TYPE  353   63
   clus
vv  SLIT3 MUTATED SLIT3 WILD-TYPE
  0            22             353
  1             2              63
[1] 2 2
[1] FALSE
D1444V8, binary
                 cls
clus                0   1
  SLIT3 MUTATED    14  13
  SLIT3 WILD-TYPE 211 251
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SLIT3 MUTATED     14   13
  SLIT3 WILD-TYPE  211  251
        clus
vv       SLIT3 MUTATED SLIT3 WILD-TYPE
  FEMALE            14             211
  MALE              13             251
[1] 2 2
[1] FALSE
D1444V9, binary
                 cls
clus                0   1
  SLIT3 MUTATED    20   2
  SLIT3 WILD-TYPE 330  20
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SLIT3 MUTATED     20    2
  SLIT3 WILD-TYPE  330   20
     clus
vv    SLIT3 MUTATED SLIT3 WILD-TYPE
  NO             20             330
  YES             2              20
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SLIT3 MUTATED                     21                             4
  SLIT3 WILD-TYPE                  294                            43
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SLIT3 MUTATED                       2                              0
  SLIT3 WILD-TYPE                   104                             10
D1444V10, multiclass
                                clus
vv                               SLIT3 MUTATED SLIT3 WILD-TYPE
  COLON ADENOCARCINOMA                      21             294
  COLON MUCINOUS ADENOCARCINOMA              4              43
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  SLIT3 MUTATED    21   0   1   2
  SLIT3 WILD-TYPE 324   4  30  23
D1444V11, multiclass
    clus
vv   SLIT3 MUTATED SLIT3 WILD-TYPE
  R0            21             324
  R1             0               4
  R2             1              30
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1444V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SLIT3 MUTATED                                  0     1
  SLIT3 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  SLIT3 MUTATED                           3    12
  SLIT3 WILD-TYPE                        19   214
D1444V13, multiclass
                                  clus
vv                                 SLIT3 MUTATED SLIT3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    3              19
  WHITE                                       12             214
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1445) Variable = KIF14 MUTATION ANALYSIS
D1445V1, survival
                 sevent
clus2               0   1
  KIF14 MUTATED    11   2
  KIF14 WILD-TYPE 367  91
  KIF14 MUTATED KIF14 WILD-TYPE 
             13             458 
  KIF14 MUTATED KIF14 WILD-TYPE 
              2              91 
$`KIF14 MUTATED`
TCGA-A6-6141 TCGA-AA-3489 TCGA-AA-3510 TCGA-AA-3966 TCGA-AA-3977 TCGA-AA-A00N 
        8.38         7.04        63.98         2.01        25.02         4.01 
TCGA-AA-A010 TCGA-CA-6717 TCGA-DM-A1HA TCGA-DM-A28K TCGA-F4-6855 TCGA-AG-3892 
       34.98        12.76       131.51        98.24        47.41        13.02 
TCGA-AG-A002 
       20.98 

$`KIF14 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 
       22.09        22.06        32.71        27.09        22.52        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        19.66        20.28         3.02         1.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
       34.03        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07        12.20        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HB 
       13.32        12.59       140.38         7.50        44.32       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
      117.07         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
        0.53        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       17.95        36.95        17.03        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  KIF14 MUTATED KIF14 WILD-TYPE 
           2.01            0.00 
  KIF14 MUTATED KIF14 WILD-TYPE 
         131.51          148.01 
  KIF14 MUTATED KIF14 WILD-TYPE 
         20.980          20.155 
[1] "2.0 - 131.5 (21.0)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.7"
D1445V2, continuous
D1445V3, binary
                 cls
clus                0   1
  KIF14 MUTATED    11   2
  KIF14 WILD-TYPE 355 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KIF14 MUTATED     11    2
  KIF14 WILD-TYPE  355  117
        clus
vv       KIF14 MUTATED KIF14 WILD-TYPE
  COLON             11             355
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KIF14 MUTATED         2        0        2         5         2         0
  KIF14 WILD-TYPE      89        1       30       133         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  KIF14 MUTATED           0          0          0          1        0         0
  KIF14 WILD-TYPE        24         11         59         41       48        18
                 vv
clus              STAGE IVB
  KIF14 MUTATED           0
  KIF14 WILD-TYPE         1
D1445V4, multiclass
            clus
vv           KIF14 MUTATED KIF14 WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA              5             133
  STAGE IIB              2               8
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             1              41
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  KIF14 MUTATED     1   2   8   2
  KIF14 WILD-TYPE  16  90 321  48
D1445V5, multiclass
    clus
vv   KIF14 MUTATED KIF14 WILD-TYPE
  T1             1              16
  T2             2              90
  T3             8             321
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  KIF14 MUTATED    12   0   1
  KIF14 WILD-TYPE 275 113  86
D1445V6, multiclass
    clus
vv   KIF14 MUTATED KIF14 WILD-TYPE
  N0            12             275
  N1             0             113
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1445V7, binary
                 cls
clus                0   1
  KIF14 MUTATED    12   0
  KIF14 WILD-TYPE 363  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KIF14 MUTATED     12    0
  KIF14 WILD-TYPE  363   65
   clus
vv  KIF14 MUTATED KIF14 WILD-TYPE
  0            12             363
  1             0              65
[1] 2 2
[1] FALSE
D1445V8, binary
                 cls
clus                0   1
  KIF14 MUTATED     4   9
  KIF14 WILD-TYPE 221 255
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KIF14 MUTATED      4    9
  KIF14 WILD-TYPE  221  255
        clus
vv       KIF14 MUTATED KIF14 WILD-TYPE
  FEMALE             4             221
  MALE               9             255
[1] 2 2
[1] FALSE
D1445V9, binary
                 cls
clus                0   1
  KIF14 MUTATED     9   0
  KIF14 WILD-TYPE 341  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KIF14 MUTATED      9    0
  KIF14 WILD-TYPE  341   22
     clus
vv    KIF14 MUTATED KIF14 WILD-TYPE
  NO              9             341
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  KIF14 MUTATED                      7                             4
  KIF14 WILD-TYPE                  308                            43
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  KIF14 MUTATED                       2                              0
  KIF14 WILD-TYPE                   104                             10
D1445V10, multiclass
                                clus
vv                               KIF14 MUTATED KIF14 WILD-TYPE
  COLON ADENOCARCINOMA                       7             308
  COLON MUCINOUS ADENOCARCINOMA              4              43
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  KIF14 MUTATED     7   0   0   1
  KIF14 WILD-TYPE 338   4  31  24
D1445V11, multiclass
    clus
vv   KIF14 MUTATED KIF14 WILD-TYPE
  R0             7             338
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1445V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KIF14 MUTATED                                  0     1
  KIF14 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  KIF14 MUTATED                           1     3
  KIF14 WILD-TYPE                        21   223
D1445V13, multiclass
                                  clus
vv                                 KIF14 MUTATED KIF14 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        3             223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1446) Variable = CDKL2 MUTATION ANALYSIS
D1446V1, survival
                 sevent
clus2               0   1
  CDKL2 MUTATED     9   1
  CDKL2 WILD-TYPE 369  92
  CDKL2 MUTATED CDKL2 WILD-TYPE 
             10             461 
  CDKL2 MUTATED CDKL2 WILD-TYPE 
              1              92 
$`CDKL2 MUTATED`
TCGA-AA-3518 TCGA-AA-3663 TCGA-AA-A00J TCGA-AA-A010 TCGA-AY-5543 TCGA-CA-6717 
        1.02         6.97        18.05        34.98        33.01        12.76 
TCGA-CK-5913 TCGA-CM-6167 TCGA-CM-6172 TCGA-DM-A28G 
       51.32        14.99        11.01        60.79 

$`CDKL2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
       38.99         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       19.00        30.02        34.03        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6197 TCGA-AY-6386 
       14.50        27.09        16.31         0.95        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07        12.20        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 
       17.56       148.01        85.45        15.62        49.08         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6674 
       21.99        12.99        13.02        15.02        14.04        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28H 
      139.17         6.12        81.37       119.93        35.97       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  CDKL2 MUTATED CDKL2 WILD-TYPE 
           1.02            0.00 
  CDKL2 MUTATED CDKL2 WILD-TYPE 
          60.79          148.01 
  CDKL2 MUTATED CDKL2 WILD-TYPE 
          16.52           20.28 
[1] "1.0 - 60.8 (16.5)"  "0.0 - 148.0 (20.3)"
[1] "hr=" "2"  
D1446V2, continuous
D1446V3, binary
                 cls
clus                0   1
  CDKL2 MUTATED    11   0
  CDKL2 WILD-TYPE 355 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDKL2 MUTATED     11    0
  CDKL2 WILD-TYPE  355  119
        clus
vv       CDKL2 MUTATED CDKL2 WILD-TYPE
  COLON             11             355
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CDKL2 MUTATED         0        0        1         5         1         0
  CDKL2 WILD-TYPE      91        1       31       133         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CDKL2 MUTATED           0          0          2          1        0         1
  CDKL2 WILD-TYPE        24         11         57         41       48        17
                 vv
clus              STAGE IVB
  CDKL2 MUTATED           0
  CDKL2 WILD-TYPE         1
D1446V4, multiclass
            clus
vv           CDKL2 MUTATED CDKL2 WILD-TYPE
  STAGE I                0              91
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              5             133
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             2              57
  STAGE IIIC             1              41
  STAGE IV               0              48
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CDKL2 MUTATED     0   0   9   2
  CDKL2 WILD-TYPE  17  92 320  48
D1446V5, multiclass
    clus
vv   CDKL2 MUTATED CDKL2 WILD-TYPE
  T1             0              17
  T2             0              92
  T3             9             320
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  CDKL2 MUTATED     7   3   1
  CDKL2 WILD-TYPE 280 110  86
D1446V6, multiclass
    clus
vv   CDKL2 MUTATED CDKL2 WILD-TYPE
  N0             7             280
  N1             3             110
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1446V7, binary
                 cls
clus                0   1
  CDKL2 MUTATED     9   1
  CDKL2 WILD-TYPE 366  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDKL2 MUTATED      9    1
  CDKL2 WILD-TYPE  366   64
   clus
vv  CDKL2 MUTATED CDKL2 WILD-TYPE
  0             9             366
  1             1              64
[1] 2 2
[1] FALSE
D1446V8, binary
                 cls
clus                0   1
  CDKL2 MUTATED     7   4
  CDKL2 WILD-TYPE 218 260
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDKL2 MUTATED      7    4
  CDKL2 WILD-TYPE  218  260
        clus
vv       CDKL2 MUTATED CDKL2 WILD-TYPE
  FEMALE             7             218
  MALE               4             260
[1] 2 2
[1] FALSE
D1446V9, binary
                 cls
clus                0   1
  CDKL2 MUTATED     8   0
  CDKL2 WILD-TYPE 342  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDKL2 MUTATED      8    0
  CDKL2 WILD-TYPE  342   22
     clus
vv    CDKL2 MUTATED CDKL2 WILD-TYPE
  NO              8             342
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CDKL2 MUTATED                      9                             2
  CDKL2 WILD-TYPE                  306                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CDKL2 MUTATED                       0                              0
  CDKL2 WILD-TYPE                   106                             10
D1446V10, multiclass
                                clus
vv                               CDKL2 MUTATED CDKL2 WILD-TYPE
  COLON ADENOCARCINOMA                       9             306
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  CDKL2 MUTATED     8   0   0   2
  CDKL2 WILD-TYPE 337   4  31  23
D1446V11, multiclass
    clus
vv   CDKL2 MUTATED CDKL2 WILD-TYPE
  R0             8             337
  R1             0               4
  R2             0              31
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1446V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CDKL2 MUTATED                                  0     1
  CDKL2 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CDKL2 MUTATED                           2     3
  CDKL2 WILD-TYPE                        20   223
D1446V13, multiclass
                                  clus
vv                                 CDKL2 MUTATED CDKL2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    2              20
  WHITE                                        3             223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1447) Variable = ITGA5 MUTATION ANALYSIS
D1447V1, survival
                 sevent
clus2               0   1
  ITGA5 MUTATED    15   1
  ITGA5 WILD-TYPE 363  92
  ITGA5 MUTATED ITGA5 WILD-TYPE 
             16             455 
  ITGA5 MUTATED ITGA5 WILD-TYPE 
              1              92 
$`ITGA5 MUTATED`
TCGA-AA-3511 TCGA-AA-3877 TCGA-AA-A00E TCGA-AA-A00R TCGA-AA-A010 TCGA-AA-A02J 
        6.97        31.00        30.02         0.99        34.98         5.03 
TCGA-AZ-4315 TCGA-CA-6715 TCGA-CM-4746 TCGA-CM-5861 TCGA-CM-5863 TCGA-D5-6928 
       58.39         0.07        37.02        15.02        15.02        11.64 
TCGA-D5-6930 TCGA-G4-6293 TCGA-G4-6586 TCGA-DC-5337 
        1.51       133.18        35.80        15.02 

$`ITGA5 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01        63.98         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 
       17.03        24.03        27.02        29.98        18.05         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       19.00        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       27.02        42.02        17.03        14.99        21.99         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02K 
       37.02        39.06        51.98        39.98         2.01        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
       16.31         0.95        33.01        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4747 
       82.95         1.91       124.27        23.05        20.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
        5.03        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 
       14.30         9.04         9.44         4.80        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 
       63.62        61.91        36.00        22.09        13.78        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  ITGA5 MUTATED ITGA5 WILD-TYPE 
           0.07            0.00 
  ITGA5 MUTATED ITGA5 WILD-TYPE 
         133.18          148.01 
  ITGA5 MUTATED ITGA5 WILD-TYPE 
          15.02           20.28 
[1] "0.1 - 133.2 (15.0)" "0.0 - 148.0 (20.3)"
[1] "hr=" "3"  
D1447V2, continuous
D1447V3, binary
                 cls
clus                0   1
  ITGA5 MUTATED    16   1
  ITGA5 WILD-TYPE 350 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITGA5 MUTATED     16    1
  ITGA5 WILD-TYPE  350  118
        clus
vv       ITGA5 MUTATED ITGA5 WILD-TYPE
  COLON             16             350
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ITGA5 MUTATED         4        0        1         6         1         0
  ITGA5 WILD-TYPE      87        1       31       132         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ITGA5 MUTATED           1          0          2          0        2         0
  ITGA5 WILD-TYPE        23         11         57         42       46        18
                 vv
clus              STAGE IVB
  ITGA5 MUTATED           0
  ITGA5 WILD-TYPE         1
D1447V4, multiclass
            clus
vv           ITGA5 MUTATED ITGA5 WILD-TYPE
  STAGE I                4              87
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              6             132
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             2              57
  STAGE IIIC             0              42
  STAGE IV               2              46
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ITGA5 MUTATED     2   2  10   3
  ITGA5 WILD-TYPE  15  90 319  47
D1447V5, multiclass
    clus
vv   ITGA5 MUTATED ITGA5 WILD-TYPE
  T1             2              15
  T2             2              90
  T3            10             319
  T4             3              47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  ITGA5 MUTATED    13   3   1
  ITGA5 WILD-TYPE 274 110  86
D1447V6, multiclass
    clus
vv   ITGA5 MUTATED ITGA5 WILD-TYPE
  N0            13             274
  N1             3             110
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1447V7, binary
                 cls
clus                0   1
  ITGA5 MUTATED    15   2
  ITGA5 WILD-TYPE 360  63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITGA5 MUTATED     15    2
  ITGA5 WILD-TYPE  360   63
   clus
vv  ITGA5 MUTATED ITGA5 WILD-TYPE
  0            15             360
  1             2              63
[1] 2 2
[1] FALSE
D1447V8, binary
                 cls
clus                0   1
  ITGA5 MUTATED     8   9
  ITGA5 WILD-TYPE 217 255
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITGA5 MUTATED      8    9
  ITGA5 WILD-TYPE  217  255
        clus
vv       ITGA5 MUTATED ITGA5 WILD-TYPE
  FEMALE             8             217
  MALE               9             255
[1] 2 2
[1] FALSE
D1447V9, binary
                 cls
clus                0   1
  ITGA5 MUTATED    12   0
  ITGA5 WILD-TYPE 338  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITGA5 MUTATED     12    0
  ITGA5 WILD-TYPE  338   22
     clus
vv    ITGA5 MUTATED ITGA5 WILD-TYPE
  NO             12             338
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ITGA5 MUTATED                     12                             4
  ITGA5 WILD-TYPE                  303                            43
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ITGA5 MUTATED                       1                              0
  ITGA5 WILD-TYPE                   105                             10
D1447V10, multiclass
                                clus
vv                               ITGA5 MUTATED ITGA5 WILD-TYPE
  COLON ADENOCARCINOMA                      12             303
  COLON MUCINOUS ADENOCARCINOMA              4              43
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  ITGA5 MUTATED    14   0   2   1
  ITGA5 WILD-TYPE 331   4  29  24
D1447V11, multiclass
    clus
vv   ITGA5 MUTATED ITGA5 WILD-TYPE
  R0            14             331
  R1             0               4
  R2             2              29
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1447V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ITGA5 MUTATED                                  0     1
  ITGA5 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ITGA5 MUTATED                           1     8
  ITGA5 WILD-TYPE                        21   218
D1447V13, multiclass
                                  clus
vv                                 ITGA5 MUTATED ITGA5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        8             218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1448) Variable = SULT1C4 MUTATION ANALYSIS
D1448V1, survival
                   sevent
clus2                 0   1
  SULT1C4 MUTATED     2   1
  SULT1C4 WILD-TYPE 376  92
  SULT1C4 MUTATED SULT1C4 WILD-TYPE 
                3               468 
  SULT1C4 MUTATED SULT1C4 WILD-TYPE 
                1                92 
$`SULT1C4 MUTATED`
TCGA-AA-3526 TCGA-AA-3555 TCGA-AA-A00N 
       19.07        29.95         4.01 

$`SULT1C4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
        8.05         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       13.02        24.00        17.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  SULT1C4 MUTATED SULT1C4 WILD-TYPE 
             4.01              0.00 
  SULT1C4 MUTATED SULT1C4 WILD-TYPE 
            29.95            148.01 
  SULT1C4 MUTATED SULT1C4 WILD-TYPE 
           19.070            20.235 
[1] "4.0 - 29.9 (19.1)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "2.6"
D1448V2, continuous
D1448V3, binary
                   cls
clus                  0   1
  SULT1C4 MUTATED     3   0
  SULT1C4 WILD-TYPE 363 119
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SULT1C4 MUTATED      3    0
  SULT1C4 WILD-TYPE  363  119
        clus
vv       SULT1C4 MUTATED SULT1C4 WILD-TYPE
  COLON                3               363
  RECTUM               0               119
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SULT1C4 MUTATED         1        0        0         1         1         0
  SULT1C4 WILD-TYPE      90        1       32       137         9         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SULT1C4 MUTATED           0          0          0          0        0
  SULT1C4 WILD-TYPE        24         11         59         42       48
                   vv
clus                STAGE IVA STAGE IVB
  SULT1C4 MUTATED           0         0
  SULT1C4 WILD-TYPE        18         1
D1448V4, multiclass
            clus
vv           SULT1C4 MUTATED SULT1C4 WILD-TYPE
  STAGE I                  1                90
  STAGE IA                 0                 1
  STAGE II                 0                32
  STAGE IIA                1               137
  STAGE IIB                1                 9
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               0                11
  STAGE IIIB               0                59
  STAGE IIIC               0                42
  STAGE IV                 0                48
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  SULT1C4 MUTATED     0   1   1   1
  SULT1C4 WILD-TYPE  17  91 328  49
D1448V5, multiclass
    clus
vv   SULT1C4 MUTATED SULT1C4 WILD-TYPE
  T1               0                17
  T2               1                91
  T3               1               328
  T4               1                49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  SULT1C4 MUTATED     3   0   0
  SULT1C4 WILD-TYPE 284 113  87
D1448V6, multiclass
    clus
vv   SULT1C4 MUTATED SULT1C4 WILD-TYPE
  N0               3               284
  N1               0               113
  N2               0                87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1448V7, binary
                   cls
clus                  0   1
  SULT1C4 MUTATED     3   0
  SULT1C4 WILD-TYPE 372  65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SULT1C4 MUTATED      3    0
  SULT1C4 WILD-TYPE  372   65
   clus
vv  SULT1C4 MUTATED SULT1C4 WILD-TYPE
  0               3               372
  1               0                65
[1] 2 2
[1] FALSE
D1448V8, binary
                   cls
clus                  0   1
  SULT1C4 MUTATED     1   2
  SULT1C4 WILD-TYPE 224 262
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SULT1C4 MUTATED      1    2
  SULT1C4 WILD-TYPE  224  262
        clus
vv       SULT1C4 MUTATED SULT1C4 WILD-TYPE
  FEMALE               1               224
  MALE                 2               262
[1] 2 2
[1] FALSE
D1448V9, binary
                   cls
clus                  0   1
  SULT1C4 MUTATED     2   0
  SULT1C4 WILD-TYPE 348  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SULT1C4 MUTATED      2    0
  SULT1C4 WILD-TYPE  348   22
     clus
vv    SULT1C4 MUTATED SULT1C4 WILD-TYPE
  NO                2               348
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SULT1C4 MUTATED                      1                             2
  SULT1C4 WILD-TYPE                  314                            45
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SULT1C4 MUTATED                       0                              0
  SULT1C4 WILD-TYPE                   106                             10
D1448V10, multiclass
                                clus
vv                               SULT1C4 MUTATED SULT1C4 WILD-TYPE
  COLON ADENOCARCINOMA                         1               314
  COLON MUCINOUS ADENOCARCINOMA                2                45
  RECTAL ADENOCARCINOMA                        0               106
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  SULT1C4 MUTATED     3   0   0   0
  SULT1C4 WILD-TYPE 342   4  31  25
D1448V11, multiclass
    clus
vv   SULT1C4 MUTATED SULT1C4 WILD-TYPE
  R0               3               342
  R1               0                 4
  R2               0                31
  RX               0                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1448V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SULT1C4 MUTATED                                  0     0
  SULT1C4 WILD-TYPE                                1    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  SULT1C4 MUTATED                           0     0
  SULT1C4 WILD-TYPE                        22   226
D1448V13, multiclass

Clustering(1449) Variable = C6ORF146 MUTATION ANALYSIS
D1449V1, survival
                    sevent
clus2                  0   1
  C6ORF146 MUTATED     6   2
  C6ORF146 WILD-TYPE 372  91
  C6ORF146 MUTATED C6ORF146 WILD-TYPE 
                 8                463 
  C6ORF146 MUTATED C6ORF146 WILD-TYPE 
                 2                 91 
$`C6ORF146 MUTATED`
TCGA-AA-3947 TCGA-AA-A00N TCGA-AD-6889 TCGA-CA-6717 TCGA-CA-6718 TCGA-DM-A1HB 
       33.01         4.01        56.55        12.76        10.06       135.65 
TCGA-G4-6586 TCGA-AG-A002 
       35.80        20.98 

$`C6ORF146 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 
       31.00         2.01        12.99        24.00        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
        7.50        44.32       131.51       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       13.78        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  C6ORF146 MUTATED C6ORF146 WILD-TYPE 
              4.01               0.00 
  C6ORF146 MUTATED C6ORF146 WILD-TYPE 
            135.65             148.01 
  C6ORF146 MUTATED C6ORF146 WILD-TYPE 
            26.995             20.120 
[1] "4.0 - 135.7 (27.0)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1"  
D1449V2, continuous
D1449V3, binary
                    cls
clus                   0   1
  C6ORF146 MUTATED     7   1
  C6ORF146 WILD-TYPE 359 118
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C6ORF146 MUTATED      7    1
  C6ORF146 WILD-TYPE  359  118
        clus
vv       C6ORF146 MUTATED C6ORF146 WILD-TYPE
  COLON                 7                359
  RECTUM                1                118
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  C6ORF146 MUTATED         1        0        0         4         2         0
  C6ORF146 WILD-TYPE      90        1       32       134         8         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C6ORF146 MUTATED           0          0          1          0        0
  C6ORF146 WILD-TYPE        24         11         58         42       48
                    vv
clus                 STAGE IVA STAGE IVB
  C6ORF146 MUTATED           0         0
  C6ORF146 WILD-TYPE        18         1
D1449V4, multiclass
            clus
vv           C6ORF146 MUTATED C6ORF146 WILD-TYPE
  STAGE I                   1                 90
  STAGE IA                  0                  1
  STAGE II                  0                 32
  STAGE IIA                 4                134
  STAGE IIB                 2                  8
  STAGE IIC                 0                  1
  STAGE III                 0                 24
  STAGE IIIA                0                 11
  STAGE IIIB                1                 58
  STAGE IIIC                0                 42
  STAGE IV                  0                 48
  STAGE IVA                 0                 18
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  C6ORF146 MUTATED     0   1   5   2
  C6ORF146 WILD-TYPE  17  91 324  48
D1449V5, multiclass
    clus
vv   C6ORF146 MUTATED C6ORF146 WILD-TYPE
  T1                0                 17
  T2                1                 91
  T3                5                324
  T4                2                 48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  C6ORF146 MUTATED     7   1   0
  C6ORF146 WILD-TYPE 280 112  87
D1449V6, multiclass
    clus
vv   C6ORF146 MUTATED C6ORF146 WILD-TYPE
  N0                7                280
  N1                1                112
  N2                0                 87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1449V7, binary
                    cls
clus                   0   1
  C6ORF146 MUTATED     8   0
  C6ORF146 WILD-TYPE 367  65
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C6ORF146 MUTATED      8    0
  C6ORF146 WILD-TYPE  367   65
   clus
vv  C6ORF146 MUTATED C6ORF146 WILD-TYPE
  0                8                367
  1                0                 65
[1] 2 2
[1] FALSE
D1449V8, binary
                    cls
clus                   0   1
  C6ORF146 MUTATED     2   6
  C6ORF146 WILD-TYPE 223 258
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C6ORF146 MUTATED      2    6
  C6ORF146 WILD-TYPE  223  258
        clus
vv       C6ORF146 MUTATED C6ORF146 WILD-TYPE
  FEMALE                2                223
  MALE                  6                258
[1] 2 2
[1] FALSE
D1449V9, binary
                    cls
clus                   0   1
  C6ORF146 MUTATED     5   0
  C6ORF146 WILD-TYPE 345  22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C6ORF146 MUTATED      5    0
  C6ORF146 WILD-TYPE  345   22
     clus
vv    C6ORF146 MUTATED C6ORF146 WILD-TYPE
  NO                 5                345
  YES                0                 22
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  C6ORF146 MUTATED                      3                             3
  C6ORF146 WILD-TYPE                  312                            44
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  C6ORF146 MUTATED                       1                              0
  C6ORF146 WILD-TYPE                   105                             10
D1449V10, multiclass
                                clus
vv                               C6ORF146 MUTATED C6ORF146 WILD-TYPE
  COLON ADENOCARCINOMA                          3                312
  COLON MUCINOUS ADENOCARCINOMA                 3                 44
  RECTAL ADENOCARCINOMA                         1                105
  RECTAL MUCINOUS ADENOCARCINOMA                0                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  C6ORF146 MUTATED     4   0   0   2
  C6ORF146 WILD-TYPE 341   4  31  23
D1449V11, multiclass
    clus
vv   C6ORF146 MUTATED C6ORF146 WILD-TYPE
  R0                4                341
  R1                0                  4
  R2                0                 31
  RX                2                 23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1449V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C6ORF146 MUTATED                                  0     3
  C6ORF146 WILD-TYPE                                1     8
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  C6ORF146 MUTATED                           0     2
  C6ORF146 WILD-TYPE                        22   224
D1449V13, multiclass
                                  clus
vv                                 C6ORF146 MUTATED C6ORF146 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           3                  8
  BLACK OR AFRICAN AMERICAN                       0                 22
  WHITE                                           2                224
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1450) Variable = DYM MUTATION ANALYSIS
D1450V1, survival
               sevent
clus2             0   1
  DYM MUTATED     8   2
  DYM WILD-TYPE 370  91
  DYM MUTATED DYM WILD-TYPE 
           10           461 
  DYM MUTATED DYM WILD-TYPE 
            2            91 
$`DYM MUTATED`
TCGA-A6-5665 TCGA-A6-6649 TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A010 TCGA-AZ-4315 
       22.06        24.16        18.05         4.01        34.98        58.39 
TCGA-AZ-6598 TCGA-CA-6717 TCGA-CK-5914 TCGA-G4-6304 
       49.41        12.76         9.99        53.62 

$`DYM WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       25.18        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00L TCGA-AA-A00O 
       19.00        30.02        34.03        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07        12.20        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 
       85.45        15.62        49.08        51.32        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       65.85        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  DYM MUTATED DYM WILD-TYPE 
         4.01          0.00 
  DYM MUTATED DYM WILD-TYPE 
        58.39        148.01 
  DYM MUTATED DYM WILD-TYPE 
        23.11         20.12 
[1] "4.0 - 58.4 (23.1)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.1"
D1450V2, continuous
D1450V3, binary
               cls
clus              0   1
  DYM MUTATED    10   0
  DYM WILD-TYPE 356 119
[1] "tbl2"
               cls
clus            [,1] [,2]
  DYM MUTATED     10    0
  DYM WILD-TYPE  356  119
        clus
vv       DYM MUTATED DYM WILD-TYPE
  COLON           10           356
  RECTUM           0           119
[1] 2 2
[1] FALSE
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DYM MUTATED         0        0        1         4         3         0
  DYM WILD-TYPE      91        1       31       134         7         1
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DYM MUTATED           0          0          2          0        0         0
  DYM WILD-TYPE        24         11         57         42       48        18
               vv
clus            STAGE IVB
  DYM MUTATED           0
  DYM WILD-TYPE         1
D1450V4, multiclass
            clus
vv           DYM MUTATED DYM WILD-TYPE
  STAGE I              0            91
  STAGE IA             0             1
  STAGE II             1            31
  STAGE IIA            4           134
  STAGE IIB            3             7
  STAGE IIC            0             1
  STAGE III            0            24
  STAGE IIIA           0            11
  STAGE IIIB           2            57
  STAGE IIIC           0            42
  STAGE IV             0            48
  STAGE IVA            0            18
  STAGE IVB            0             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  DYM MUTATED     0   0   7   3
  DYM WILD-TYPE  17  92 322  47
D1450V5, multiclass
    clus
vv   DYM MUTATED DYM WILD-TYPE
  T1           0            17
  T2           0            92
  T3           7           322
  T4           3            47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2
  DYM MUTATED     8   2   0
  DYM WILD-TYPE 279 111  87
D1450V6, multiclass
    clus
vv   DYM MUTATED DYM WILD-TYPE
  N0           8           279
  N1           2           111
  N2           0            87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1450V7, binary
               cls
clus              0   1
  DYM MUTATED     8   0
  DYM WILD-TYPE 367  65
[1] "tbl2"
               cls
clus            [,1] [,2]
  DYM MUTATED      8    0
  DYM WILD-TYPE  367   65
   clus
vv  DYM MUTATED DYM WILD-TYPE
  0           8           367
  1           0            65
[1] 2 2
[1] FALSE
D1450V8, binary
               cls
clus              0   1
  DYM MUTATED     4   6
  DYM WILD-TYPE 221 258
[1] "tbl2"
               cls
clus            [,1] [,2]
  DYM MUTATED      4    6
  DYM WILD-TYPE  221  258
        clus
vv       DYM MUTATED DYM WILD-TYPE
  FEMALE           4           221
  MALE             6           258
[1] 2 2
[1] FALSE
D1450V9, binary
               cls
clus              0   1
  DYM MUTATED     7   0
  DYM WILD-TYPE 343  22
[1] "tbl2"
               cls
clus            [,1] [,2]
  DYM MUTATED      7    0
  DYM WILD-TYPE  343   22
     clus
vv    DYM MUTATED DYM WILD-TYPE
  NO            7           343
  YES           0            22
[1] 2 2
[1] FALSE
               vv
clus            COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  DYM MUTATED                      8                             2
  DYM WILD-TYPE                  307                            45
               vv
clus            RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  DYM MUTATED                       0                              0
  DYM WILD-TYPE                   106                             10
D1450V10, multiclass
                                clus
vv                               DYM MUTATED DYM WILD-TYPE
  COLON ADENOCARCINOMA                     8           307
  COLON MUCINOUS ADENOCARCINOMA            2            45
  RECTAL ADENOCARCINOMA                    0           106
  RECTAL MUCINOUS ADENOCARCINOMA           0            10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             R0  R1  R2  RX
  DYM MUTATED     6   0   0   2
  DYM WILD-TYPE 339   4  31  23
D1450V11, multiclass
    clus
vv   DYM MUTATED DYM WILD-TYPE
  R0           6           339
  R1           0             4
  R2           0            31
  RX           2            23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1450V12, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DYM MUTATED                                  0     1
  DYM WILD-TYPE                                1    10
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  DYM MUTATED                           0     6
  DYM WILD-TYPE                        22   220
D1450V13, multiclass
                                  clus
vv                                 DYM MUTATED DYM WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      1            10
  BLACK OR AFRICAN AMERICAN                  0            22
  WHITE                                      6           220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1451) Variable = PCDH9 MUTATION ANALYSIS
D1451V1, survival
                 sevent
clus2               0   1
  PCDH9 MUTATED    38   7
  PCDH9 WILD-TYPE 340  86
  PCDH9 MUTATED PCDH9 WILD-TYPE 
             45             426 
  PCDH9 MUTATED PCDH9 WILD-TYPE 
              7              86 
$`PCDH9 MUTATED`
TCGA-A6-6141 TCGA-AA-3510 TCGA-AA-3534 TCGA-AA-3542 TCGA-AA-3555 TCGA-AA-3679 
        8.38        63.98        29.00        12.99        29.95        15.02 
TCGA-AA-3715 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3831 TCGA-AA-3842 TCGA-AA-3939 
       19.04        33.04         0.99        17.98        37.02        12.99 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A00U TCGA-AA-A010 
       34.03         2.01        25.02         4.01        17.03        34.98 
TCGA-AA-A01K TCGA-AD-6895 TCGA-AU-6004 TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-5403 
       31.00         0.72        27.09        21.44        58.39        62.79 
TCGA-AZ-6598 TCGA-AZ-6601 TCGA-CA-5254 TCGA-CA-6715 TCGA-CA-6717 TCGA-CM-4743 
       49.41       100.01        12.69         0.07        12.76        23.05 
TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-6166 TCGA-CM-6171 TCGA-D5-6538 TCGA-D5-6898 
       13.02        22.03        21.99        14.04        17.13         1.48 
TCGA-G4-6293 TCGA-G4-6586 TCGA-AF-6136 TCGA-AG-3600 TCGA-AG-3894 TCGA-AG-3909 
      133.18        35.80        15.39         6.05        14.01        19.99 
TCGA-AG-A002 TCGA-AG-A026 TCGA-AG-A02N 
       20.98         1.94        61.97 

$`PCDH9 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 
       22.09        22.06        32.71        27.09        22.52        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3538 TCGA-AA-3543 
        0.00        19.07        34.03        29.00        26.01         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       78.08         6.05         6.97        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
        0.92        50.04        47.01        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3833 TCGA-AA-3837 
       10.06        35.05        25.02         1.02        15.95        38.99 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       18.05        31.00         2.01        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       24.00         2.01        20.98        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
       42.02         0.99        14.99        21.99         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       32.02        12.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       15.52        56.55         0.79         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       10.88         0.20        14.50        16.31         0.95        33.01 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5407 
       17.82         1.41         5.13       106.75        22.36        88.21 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77        12.10        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6716 TCGA-CA-6718 
        1.61         3.06         3.25         3.29        12.20        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5349 
       20.02        37.02        25.02        29.06        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6167 
       15.02        12.00         2.96        29.03        16.04        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       12.99        13.02        15.02        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6539 
        1.32        43.27        15.12        17.85         4.80        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       16.14        15.58         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
       35.31        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       16.83        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 
       46.03        34.03         2.01        50.04        12.03         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
        1.02        48.03        32.02        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 
       64.01        10.98        49.97        38.96        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  PCDH9 MUTATED PCDH9 WILD-TYPE 
           0.07            0.00 
  PCDH9 MUTATED PCDH9 WILD-TYPE 
         133.18          148.01 
  PCDH9 MUTATED PCDH9 WILD-TYPE 
         19.990          20.235 
[1] "0.1 - 133.2 (20.0)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.3"
D1451V2, continuous
D1451V3, binary
                 cls
clus                0   1
  PCDH9 MUTATED    38   7
  PCDH9 WILD-TYPE 328 112
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PCDH9 MUTATED     38    7
  PCDH9 WILD-TYPE  328  112
        clus
vv       PCDH9 MUTATED PCDH9 WILD-TYPE
  COLON             38             328
  RECTUM             7             112
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PCDH9 MUTATED         5        0        7        17         2         0
  PCDH9 WILD-TYPE      86        1       25       121         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PCDH9 MUTATED           1          1          6          3        1         0
  PCDH9 WILD-TYPE        23         10         53         39       47        18
                 vv
clus              STAGE IVB
  PCDH9 MUTATED           0
  PCDH9 WILD-TYPE         1
D1451V4, multiclass
            clus
vv           PCDH9 MUTATED PCDH9 WILD-TYPE
  STAGE I                5              86
  STAGE IA               0               1
  STAGE II               7              25
  STAGE IIA             17             121
  STAGE IIB              2               8
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             1              10
  STAGE IIIB             6              53
  STAGE IIIC             3              39
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PCDH9 MUTATED     0   7  35   3
  PCDH9 WILD-TYPE  17  85 294  47
D1451V5, multiclass
    clus
vv   PCDH9 MUTATED PCDH9 WILD-TYPE
  T1             0              17
  T2             7              85
  T3            35             294
  T4             3              47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  PCDH9 MUTATED    32   8   5
  PCDH9 WILD-TYPE 255 105  82
D1451V6, multiclass
    clus
vv   PCDH9 MUTATED PCDH9 WILD-TYPE
  N0            32             255
  N1             8             105
  N2             5              82
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1451V7, binary
                 cls
clus                0   1
  PCDH9 MUTATED    38   1
  PCDH9 WILD-TYPE 337  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PCDH9 MUTATED     38    1
  PCDH9 WILD-TYPE  337   64
   clus
vv  PCDH9 MUTATED PCDH9 WILD-TYPE
  0            38             337
  1             1              64
[1] 2 2
[1] FALSE
D1451V8, binary
                 cls
clus                0   1
  PCDH9 MUTATED    19  26
  PCDH9 WILD-TYPE 206 238
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PCDH9 MUTATED     19   26
  PCDH9 WILD-TYPE  206  238
        clus
vv       PCDH9 MUTATED PCDH9 WILD-TYPE
  FEMALE            19             206
  MALE              26             238
[1] 2 2
[1] FALSE
D1451V9, binary
                 cls
clus                0   1
  PCDH9 MUTATED    33   3
  PCDH9 WILD-TYPE 317  19
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PCDH9 MUTATED     33    3
  PCDH9 WILD-TYPE  317   19
     clus
vv    PCDH9 MUTATED PCDH9 WILD-TYPE
  NO             33             317
  YES             3              19
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PCDH9 MUTATED                     34                             4
  PCDH9 WILD-TYPE                  281                            43
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PCDH9 MUTATED                       7                              0
  PCDH9 WILD-TYPE                    99                             10
D1451V10, multiclass
                                clus
vv                               PCDH9 MUTATED PCDH9 WILD-TYPE
  COLON ADENOCARCINOMA                      34             281
  COLON MUCINOUS ADENOCARCINOMA              4              43
  RECTAL ADENOCARCINOMA                      7              99
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  PCDH9 MUTATED    32   1   1   3
  PCDH9 WILD-TYPE 313   3  30  22
D1451V11, multiclass
    clus
vv   PCDH9 MUTATED PCDH9 WILD-TYPE
  R0            32             313
  R1             1               3
  R2             1              30
  RX             3              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1451V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PCDH9 MUTATED                                  0     3
  PCDH9 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PCDH9 MUTATED                           2    16
  PCDH9 WILD-TYPE                        20   210
D1451V13, multiclass
                                  clus
vv                                 PCDH9 MUTATED PCDH9 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        3               8
  BLACK OR AFRICAN AMERICAN                    2              20
  WHITE                                       16             210
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1452) Variable = MRE11A MUTATION ANALYSIS
D1452V1, survival
                  sevent
clus2                0   1
  MRE11A MUTATED    11   2
  MRE11A WILD-TYPE 367  91
  MRE11A MUTATED MRE11A WILD-TYPE 
              13              458 
  MRE11A MUTATED MRE11A WILD-TYPE 
               2               91 
$`MRE11A MUTATED`
TCGA-A6-6141 TCGA-AA-A00N TCGA-CA-6717 TCGA-CM-4743 TCGA-CM-5861 TCGA-CM-6161 
        8.38         4.01        12.76        23.05        15.02        15.02 
TCGA-CM-6677 TCGA-D5-6534 TCGA-DM-A0XD TCGA-F4-6856 TCGA-G4-6588 TCGA-AG-3892 
       11.08        43.27        24.43        35.31        26.17        13.02 
TCGA-AG-A002 
       20.98 

$`MRE11A WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 
       22.09        22.06        32.71        27.09        22.52        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.20        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
        1.91       124.27        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 
       29.06        22.03        22.98        30.08        32.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        15.02        17.03        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6678 
       14.04        11.01        12.95        13.05        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6536 
       55.92        20.19        18.25         1.32        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
      119.70        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
       13.25         0.53        47.41       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        35.80        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       17.95        36.95        17.03        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  MRE11A MUTATED MRE11A WILD-TYPE 
            4.01             0.00 
  MRE11A MUTATED MRE11A WILD-TYPE 
           43.27           148.01 
  MRE11A MUTATED MRE11A WILD-TYPE 
          15.020           20.235 
[1] "4.0 - 43.3 (15.0)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1"  
D1452V2, continuous
D1452V3, binary
                  cls
clus                 0   1
  MRE11A MUTATED    12   2
  MRE11A WILD-TYPE 354 117
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MRE11A MUTATED     12    2
  MRE11A WILD-TYPE  354  117
        clus
vv       MRE11A MUTATED MRE11A WILD-TYPE
  COLON              12              354
  RECTUM              2              117
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MRE11A MUTATED         4        0        0         8         2         0
  MRE11A WILD-TYPE      87        1       32       130         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MRE11A MUTATED           0          0          0          0        0
  MRE11A WILD-TYPE        24         11         59         42       48
                  vv
clus               STAGE IVA STAGE IVB
  MRE11A MUTATED           0         0
  MRE11A WILD-TYPE        18         1
D1452V4, multiclass
            clus
vv           MRE11A MUTATED MRE11A WILD-TYPE
  STAGE I                 4               87
  STAGE IA                0                1
  STAGE II                0               32
  STAGE IIA               8              130
  STAGE IIB               2                8
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              0               59
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  MRE11A MUTATED     1   3   8   2
  MRE11A WILD-TYPE  16  89 321  48
D1452V5, multiclass
    clus
vv   MRE11A MUTATED MRE11A WILD-TYPE
  T1              1               16
  T2              3               89
  T3              8              321
  T4              2               48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  MRE11A MUTATED    14   0   0
  MRE11A WILD-TYPE 273 113  87
D1452V6, multiclass
    clus
vv   MRE11A MUTATED MRE11A WILD-TYPE
  N0             14              273
  N1              0              113
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1452V7, binary
                  cls
clus                 0   1
  MRE11A MUTATED    13   0
  MRE11A WILD-TYPE 362  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MRE11A MUTATED     13    0
  MRE11A WILD-TYPE  362   65
   clus
vv  MRE11A MUTATED MRE11A WILD-TYPE
  0             13              362
  1              0               65
[1] 2 2
[1] FALSE
D1452V8, binary
                  cls
clus                 0   1
  MRE11A MUTATED     7   7
  MRE11A WILD-TYPE 218 257
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MRE11A MUTATED      7    7
  MRE11A WILD-TYPE  218  257
        clus
vv       MRE11A MUTATED MRE11A WILD-TYPE
  FEMALE              7              218
  MALE                7              257
[1] 2 2
[1] FALSE
D1452V9, binary
                  cls
clus                 0   1
  MRE11A MUTATED    11   0
  MRE11A WILD-TYPE 339  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MRE11A MUTATED     11    0
  MRE11A WILD-TYPE  339   22
     clus
vv    MRE11A MUTATED MRE11A WILD-TYPE
  NO              11              339
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MRE11A MUTATED                      8                             4
  MRE11A WILD-TYPE                  307                            43
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MRE11A MUTATED                       2                              0
  MRE11A WILD-TYPE                   104                             10
D1452V10, multiclass
                                clus
vv                               MRE11A MUTATED MRE11A WILD-TYPE
  COLON ADENOCARCINOMA                        8              307
  COLON MUCINOUS ADENOCARCINOMA               4               43
  RECTAL ADENOCARCINOMA                       2              104
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  MRE11A MUTATED    10   0   0   2
  MRE11A WILD-TYPE 335   4  31  23
D1452V11, multiclass
    clus
vv   MRE11A MUTATED MRE11A WILD-TYPE
  R0             10              335
  R1              0                4
  R2              0               31
  RX              2               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1452V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MRE11A MUTATED                                  0     1
  MRE11A WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  MRE11A MUTATED                           1     9
  MRE11A WILD-TYPE                        21   217
D1452V13, multiclass
                                  clus
vv                                 MRE11A MUTATED MRE11A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                         9              217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1453) Variable = CASP10 MUTATION ANALYSIS
D1453V1, survival
                  sevent
clus2                0   1
  CASP10 MUTATED     6   0
  CASP10 WILD-TYPE 372  93
  CASP10 MUTATED CASP10 WILD-TYPE 
               6              465 
  CASP10 MUTATED CASP10 WILD-TYPE 
               0               93 
$`CASP10 MUTATED`
TCGA-A6-5657 TCGA-AA-3517 TCGA-AA-A010 TCGA-CA-6717 TCGA-CM-5861 TCGA-G4-6293 
       31.63        38.99        34.98        12.76        15.02       133.18 

$`CASP10 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        13.02         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 
       29.06        22.03        22.98        30.08        32.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       47.41        35.31        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  CASP10 MUTATED CASP10 WILD-TYPE 
           12.76             0.00 
  CASP10 MUTATED CASP10 WILD-TYPE 
          133.18           148.01 
  CASP10 MUTATED CASP10 WILD-TYPE 
          33.305           20.120 
[1] "12.8 - 133.2 (33.3)" "0.0 - 148.0 (20.1)" 
[1] "hr="     "9200000"
D1453V2, continuous
D1453V3, binary
                  cls
clus                 0   1
  CASP10 MUTATED     7   0
  CASP10 WILD-TYPE 359 119
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CASP10 MUTATED      7    0
  CASP10 WILD-TYPE  359  119
        clus
vv       CASP10 MUTATED CASP10 WILD-TYPE
  COLON               7              359
  RECTUM              0              119
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CASP10 MUTATED         0        0        0         3         1         0
  CASP10 WILD-TYPE      91        1       32       135         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CASP10 MUTATED           2          0          1          0        0
  CASP10 WILD-TYPE        22         11         58         42       48
                  vv
clus               STAGE IVA STAGE IVB
  CASP10 MUTATED           0         0
  CASP10 WILD-TYPE        18         1
D1453V4, multiclass
            clus
vv           CASP10 MUTATED CASP10 WILD-TYPE
  STAGE I                 0               91
  STAGE IA                0                1
  STAGE II                0               32
  STAGE IIA               3              135
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               2               22
  STAGE IIIA              0               11
  STAGE IIIB              1               58
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  CASP10 MUTATED     0   0   6   1
  CASP10 WILD-TYPE  17  92 323  49
D1453V5, multiclass
    clus
vv   CASP10 MUTATED CASP10 WILD-TYPE
  T1              0               17
  T2              0               92
  T3              6              323
  T4              1               49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  CASP10 MUTATED     4   2   1
  CASP10 WILD-TYPE 283 111  86
D1453V6, multiclass
    clus
vv   CASP10 MUTATED CASP10 WILD-TYPE
  N0              4              283
  N1              2              111
  N2              1               86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1453V7, binary
                  cls
clus                 0   1
  CASP10 MUTATED     7   0
  CASP10 WILD-TYPE 368  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CASP10 MUTATED      7    0
  CASP10 WILD-TYPE  368   65
   clus
vv  CASP10 MUTATED CASP10 WILD-TYPE
  0              7              368
  1              0               65
[1] 2 2
[1] FALSE
D1453V8, binary
                  cls
clus                 0   1
  CASP10 MUTATED     3   4
  CASP10 WILD-TYPE 222 260
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CASP10 MUTATED      3    4
  CASP10 WILD-TYPE  222  260
        clus
vv       CASP10 MUTATED CASP10 WILD-TYPE
  FEMALE              3              222
  MALE                4              260
[1] 2 2
[1] FALSE
D1453V9, binary
                  cls
clus                 0   1
  CASP10 MUTATED     6   0
  CASP10 WILD-TYPE 344  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CASP10 MUTATED      6    0
  CASP10 WILD-TYPE  344   22
     clus
vv    CASP10 MUTATED CASP10 WILD-TYPE
  NO               6              344
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CASP10 MUTATED                      6                             1
  CASP10 WILD-TYPE                  309                            46
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CASP10 MUTATED                       0                              0
  CASP10 WILD-TYPE                   106                             10
D1453V10, multiclass
                                clus
vv                               CASP10 MUTATED CASP10 WILD-TYPE
  COLON ADENOCARCINOMA                        6              309
  COLON MUCINOUS ADENOCARCINOMA               1               46
  RECTAL ADENOCARCINOMA                       0              106
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  CASP10 MUTATED     6   0   0   1
  CASP10 WILD-TYPE 339   4  31  24
D1453V11, multiclass
    clus
vv   CASP10 MUTATED CASP10 WILD-TYPE
  R0              6              339
  R1              0                4
  R2              0               31
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1453V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CASP10 MUTATED                                  0     1
  CASP10 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  CASP10 MUTATED                           1     2
  CASP10 WILD-TYPE                        21   224
D1453V13, multiclass
                                  clus
vv                                 CASP10 MUTATED CASP10 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                         2              224
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1454) Variable = TSHZ1 MUTATION ANALYSIS
D1454V1, survival
                 sevent
clus2               0   1
  TSHZ1 MUTATED    11   2
  TSHZ1 WILD-TYPE 367  91
  TSHZ1 MUTATED TSHZ1 WILD-TYPE 
             13             458 
  TSHZ1 MUTATED TSHZ1 WILD-TYPE 
              2              91 
$`TSHZ1 MUTATED`
TCGA-A6-5661 TCGA-A6-6780 TCGA-AA-3697 TCGA-AA-3821 TCGA-AA-3877 TCGA-AA-A00N 
       33.53        20.12        85.05         1.02        31.00         4.01 
TCGA-AA-A010 TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-D5-6928 TCGA-G4-6628 
       34.98        21.44        58.39        49.41        11.64        79.69 
TCGA-AG-A002 
       20.98 

$`TSHZ1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
       33.04         0.99        25.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       29.98        18.05         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
        0.95        33.01        17.82         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        88.21         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6930 
       12.43        14.30         9.04         9.44         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  TSHZ1 MUTATED TSHZ1 WILD-TYPE 
           1.02            0.00 
  TSHZ1 MUTATED TSHZ1 WILD-TYPE 
          85.05          148.01 
  TSHZ1 MUTATED TSHZ1 WILD-TYPE 
          31.00           20.02 
[1] "1.0 - 85.0 (31.0)"  "0.0 - 148.0 (20.0)"
[1] "hr=" "1.7"
D1454V2, continuous
D1454V3, binary
                 cls
clus                0   1
  TSHZ1 MUTATED    12   1
  TSHZ1 WILD-TYPE 354 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TSHZ1 MUTATED     12    1
  TSHZ1 WILD-TYPE  354  118
        clus
vv       TSHZ1 MUTATED TSHZ1 WILD-TYPE
  COLON             12             354
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TSHZ1 MUTATED         4        0        1         5         2         0
  TSHZ1 WILD-TYPE      87        1       31       133         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TSHZ1 MUTATED           1          0          0          0        0         0
  TSHZ1 WILD-TYPE        23         11         59         42       48        18
                 vv
clus              STAGE IVB
  TSHZ1 MUTATED           0
  TSHZ1 WILD-TYPE         1
D1454V4, multiclass
            clus
vv           TSHZ1 MUTATED TSHZ1 WILD-TYPE
  STAGE I                4              87
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              5             133
  STAGE IIB              2               8
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  TSHZ1 MUTATED     1   3   7   2
  TSHZ1 WILD-TYPE  16  89 322  48
D1454V5, multiclass
    clus
vv   TSHZ1 MUTATED TSHZ1 WILD-TYPE
  T1             1              16
  T2             3              89
  T3             7             322
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  TSHZ1 MUTATED    13   0   0
  TSHZ1 WILD-TYPE 274 113  87
D1454V6, multiclass
    clus
vv   TSHZ1 MUTATED TSHZ1 WILD-TYPE
  N0            13             274
  N1             0             113
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1454V7, binary
                 cls
clus                0   1
  TSHZ1 MUTATED    10   0
  TSHZ1 WILD-TYPE 365  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TSHZ1 MUTATED     10    0
  TSHZ1 WILD-TYPE  365   65
   clus
vv  TSHZ1 MUTATED TSHZ1 WILD-TYPE
  0            10             365
  1             0              65
[1] 2 2
[1] FALSE
D1454V8, binary
                 cls
clus                0   1
  TSHZ1 MUTATED     5   8
  TSHZ1 WILD-TYPE 220 256
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TSHZ1 MUTATED      5    8
  TSHZ1 WILD-TYPE  220  256
        clus
vv       TSHZ1 MUTATED TSHZ1 WILD-TYPE
  FEMALE             5             220
  MALE               8             256
[1] 2 2
[1] FALSE
D1454V9, binary
                 cls
clus                0   1
  TSHZ1 MUTATED    12   0
  TSHZ1 WILD-TYPE 338  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TSHZ1 MUTATED     12    0
  TSHZ1 WILD-TYPE  338   22
     clus
vv    TSHZ1 MUTATED TSHZ1 WILD-TYPE
  NO             12             338
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  TSHZ1 MUTATED                      7                             5
  TSHZ1 WILD-TYPE                  308                            42
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  TSHZ1 MUTATED                       1                              0
  TSHZ1 WILD-TYPE                   105                             10
D1454V10, multiclass
                                clus
vv                               TSHZ1 MUTATED TSHZ1 WILD-TYPE
  COLON ADENOCARCINOMA                       7             308
  COLON MUCINOUS ADENOCARCINOMA              5              42
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  TSHZ1 MUTATED    11   0   0   0
  TSHZ1 WILD-TYPE 334   4  31  25
D1454V11, multiclass
    clus
vv   TSHZ1 MUTATED TSHZ1 WILD-TYPE
  R0            11             334
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1454V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TSHZ1 MUTATED                                  0     0
  TSHZ1 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  TSHZ1 MUTATED                           1     6
  TSHZ1 WILD-TYPE                        21   220
D1454V13, multiclass
                                  clus
vv                                 TSHZ1 MUTATED TSHZ1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        6             220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1455) Variable = CCDC158 MUTATION ANALYSIS
D1455V1, survival
                   sevent
clus2                 0   1
  CCDC158 MUTATED    16   1
  CCDC158 WILD-TYPE 362  92
  CCDC158 MUTATED CCDC158 WILD-TYPE 
               17               454 
  CCDC158 MUTATED CCDC158 WILD-TYPE 
                1                92 
$`CCDC158 MUTATED`
TCGA-A6-5657 TCGA-A6-5661 TCGA-A6-6141 TCGA-AA-3510 TCGA-AA-3864 TCGA-AA-3950 
       31.63        33.53         8.38        63.98        53.00        24.00 
TCGA-AA-3977 TCGA-AA-A010 TCGA-AD-6889 TCGA-AZ-4315 TCGA-CA-6717 TCGA-CA-6718 
       25.02        34.98        56.55        58.39        12.76        10.06 
TCGA-CM-4752 TCGA-CM-5861 TCGA-CM-6171 TCGA-AG-3892 TCGA-AG-A002 
       13.02        15.02        14.04        13.02        20.98 

$`CCDC158 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       32.91        30.44        29.19        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       32.71        27.09        22.52        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 
       20.28         7.04         3.02         1.02        35.01         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       31.07        30.05        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       26.01         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 
        3.06         3.25         3.29         0.07        12.20        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       20.02        37.02        25.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       30.08        32.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 
       14.99        12.99        13.02        15.02        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 
       19.99         1.02        17.95        36.95        17.03        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  CCDC158 MUTATED CCDC158 WILD-TYPE 
             8.38              0.00 
  CCDC158 MUTATED CCDC158 WILD-TYPE 
            63.98            148.01 
  CCDC158 MUTATED CCDC158 WILD-TYPE 
           24.000            20.085 
[1] "8.4 - 64.0 (24.0)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "4"  
D1455V2, continuous
D1455V3, binary
                   cls
clus                  0   1
  CCDC158 MUTATED    16   3
  CCDC158 WILD-TYPE 350 116
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC158 MUTATED     16    3
  CCDC158 WILD-TYPE  350  116
        clus
vv       CCDC158 MUTATED CCDC158 WILD-TYPE
  COLON               16               350
  RECTUM               3               116
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CCDC158 MUTATED         3        0        2        11         1         0
  CCDC158 WILD-TYPE      88        1       30       127         9         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CCDC158 MUTATED           0          0          1          0        0
  CCDC158 WILD-TYPE        24         11         58         42       48
                   vv
clus                STAGE IVA STAGE IVB
  CCDC158 MUTATED           0         0
  CCDC158 WILD-TYPE        18         1
D1455V4, multiclass
            clus
vv           CCDC158 MUTATED CCDC158 WILD-TYPE
  STAGE I                  3                88
  STAGE IA                 0                 1
  STAGE II                 2                30
  STAGE IIA               11               127
  STAGE IIB                1                 9
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               0                11
  STAGE IIIB               1                58
  STAGE IIIC               0                42
  STAGE IV                 0                48
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  CCDC158 MUTATED     1   3  14   1
  CCDC158 WILD-TYPE  16  89 315  49
D1455V5, multiclass
    clus
vv   CCDC158 MUTATED CCDC158 WILD-TYPE
  T1               1                16
  T2               3                89
  T3              14               315
  T4               1                49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  CCDC158 MUTATED    18   1   0
  CCDC158 WILD-TYPE 269 112  87
D1455V6, multiclass
    clus
vv   CCDC158 MUTATED CCDC158 WILD-TYPE
  N0              18               269
  N1               1               112
  N2               0                87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1455V7, binary
                   cls
clus                  0   1
  CCDC158 MUTATED    18   0
  CCDC158 WILD-TYPE 357  65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC158 MUTATED     18    0
  CCDC158 WILD-TYPE  357   65
   clus
vv  CCDC158 MUTATED CCDC158 WILD-TYPE
  0              18               357
  1               0                65
[1] 2 2
[1] FALSE
D1455V8, binary
                   cls
clus                  0   1
  CCDC158 MUTATED     8  11
  CCDC158 WILD-TYPE 217 253
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC158 MUTATED      8   11
  CCDC158 WILD-TYPE  217  253
        clus
vv       CCDC158 MUTATED CCDC158 WILD-TYPE
  FEMALE               8               217
  MALE                11               253
[1] 2 2
[1] FALSE
D1455V9, binary
                   cls
clus                  0   1
  CCDC158 MUTATED    16   0
  CCDC158 WILD-TYPE 334  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC158 MUTATED     16    0
  CCDC158 WILD-TYPE  334   22
     clus
vv    CCDC158 MUTATED CCDC158 WILD-TYPE
  NO               16               334
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CCDC158 MUTATED                     14                             2
  CCDC158 WILD-TYPE                  301                            45
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CCDC158 MUTATED                       3                              0
  CCDC158 WILD-TYPE                   103                             10
D1455V10, multiclass
                                clus
vv                               CCDC158 MUTATED CCDC158 WILD-TYPE
  COLON ADENOCARCINOMA                        14               301
  COLON MUCINOUS ADENOCARCINOMA                2                45
  RECTAL ADENOCARCINOMA                        3               103
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  CCDC158 MUTATED    14   0   0   2
  CCDC158 WILD-TYPE 331   4  31  23
D1455V11, multiclass
    clus
vv   CCDC158 MUTATED CCDC158 WILD-TYPE
  R0              14               331
  R1               0                 4
  R2               0                31
  RX               2                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1455V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CCDC158 MUTATED                                  0     3
  CCDC158 WILD-TYPE                                1     8
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  CCDC158 MUTATED                           4     3
  CCDC158 WILD-TYPE                        18   223
D1455V13, multiclass
                                  clus
vv                                 CCDC158 MUTATED CCDC158 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          3                 8
  BLACK OR AFRICAN AMERICAN                      4                18
  WHITE                                          3               223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1456) Variable = BRD2 MUTATION ANALYSIS
D1456V1, survival
                sevent
clus2              0   1
  BRD2 MUTATED     8   2
  BRD2 WILD-TYPE 370  91
  BRD2 MUTATED BRD2 WILD-TYPE 
            10            461 
  BRD2 MUTATED BRD2 WILD-TYPE 
             2             91 
$`BRD2 MUTATED`
TCGA-A6-3809 TCGA-AA-3821 TCGA-AZ-6599 TCGA-CM-4743 TCGA-CM-4746 TCGA-D5-6924 
       32.75         1.02         6.77        23.05        37.02        14.30 
TCGA-DM-A0X9 TCGA-G4-6588 TCGA-G4-6626 TCGA-AG-A002 
      119.70        26.17        46.75        20.98 

$`BRD2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 
       10.06        35.05        33.04         0.99        25.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 
      106.75        22.36        62.79        88.21        49.41        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
        1.91       124.27        20.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       11.38        10.26        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       35.80        91.79        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  BRD2 MUTATED BRD2 WILD-TYPE 
          1.02           0.00 
  BRD2 MUTATED BRD2 WILD-TYPE 
        119.70         148.01 
  BRD2 MUTATED BRD2 WILD-TYPE 
         24.61          20.05 
[1] "1.0 - 119.7 (24.6)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.2"
D1456V2, continuous
D1456V3, binary
                cls
clus               0   1
  BRD2 MUTATED    11   1
  BRD2 WILD-TYPE 355 118
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRD2 MUTATED     11    1
  BRD2 WILD-TYPE  355  118
        clus
vv       BRD2 MUTATED BRD2 WILD-TYPE
  COLON            11            355
  RECTUM            1            118
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  BRD2 MUTATED         4        0        0         6         2         0
  BRD2 WILD-TYPE      87        1       32       132         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  BRD2 MUTATED           0          0          0          0        0         0
  BRD2 WILD-TYPE        24         11         59         42       48        18
                vv
clus             STAGE IVB
  BRD2 MUTATED           0
  BRD2 WILD-TYPE         1
D1456V4, multiclass
            clus
vv           BRD2 MUTATED BRD2 WILD-TYPE
  STAGE I               4             87
  STAGE IA              0              1
  STAGE II              0             32
  STAGE IIA             6            132
  STAGE IIB             2              8
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            0             59
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  BRD2 MUTATED     0   4   6   2
  BRD2 WILD-TYPE  17  88 323  48
D1456V5, multiclass
    clus
vv   BRD2 MUTATED BRD2 WILD-TYPE
  T1            0             17
  T2            4             88
  T3            6            323
  T4            2             48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  BRD2 MUTATED    12   0   0
  BRD2 WILD-TYPE 275 113  87
D1456V6, multiclass
    clus
vv   BRD2 MUTATED BRD2 WILD-TYPE
  N0           12            275
  N1            0            113
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1456V7, binary
                cls
clus               0   1
  BRD2 MUTATED    10   0
  BRD2 WILD-TYPE 365  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRD2 MUTATED     10    0
  BRD2 WILD-TYPE  365   65
   clus
vv  BRD2 MUTATED BRD2 WILD-TYPE
  0           10            365
  1            0             65
[1] 2 2
[1] FALSE
D1456V8, binary
                cls
clus               0   1
  BRD2 MUTATED     6   6
  BRD2 WILD-TYPE 219 258
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRD2 MUTATED      6    6
  BRD2 WILD-TYPE  219  258
        clus
vv       BRD2 MUTATED BRD2 WILD-TYPE
  FEMALE            6            219
  MALE              6            258
[1] 2 2
[1] FALSE
D1456V9, binary
                cls
clus               0   1
  BRD2 MUTATED     9   0
  BRD2 WILD-TYPE 341  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRD2 MUTATED      9    0
  BRD2 WILD-TYPE  341   22
     clus
vv    BRD2 MUTATED BRD2 WILD-TYPE
  NO             9            341
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  BRD2 MUTATED                      9                             2
  BRD2 WILD-TYPE                  306                            45
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  BRD2 MUTATED                       1                              0
  BRD2 WILD-TYPE                   105                             10
D1456V10, multiclass
                                clus
vv                               BRD2 MUTATED BRD2 WILD-TYPE
  COLON ADENOCARCINOMA                      9            306
  COLON MUCINOUS ADENOCARCINOMA             2             45
  RECTAL ADENOCARCINOMA                     1            105
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  BRD2 MUTATED     9   0   0   1
  BRD2 WILD-TYPE 336   4  31  24
D1456V11, multiclass
    clus
vv   BRD2 MUTATED BRD2 WILD-TYPE
  R0            9            336
  R1            0              4
  R2            0             31
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1456V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  BRD2 MUTATED                                  0     0
  BRD2 WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  BRD2 MUTATED                           1     8
  BRD2 WILD-TYPE                        21   218
D1456V13, multiclass
                                  clus
vv                                 BRD2 MUTATED BRD2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                       8            218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1457) Variable = KIAA2022 MUTATION ANALYSIS
D1457V1, survival
                    sevent
clus2                  0   1
  KIAA2022 MUTATED    26   9
  KIAA2022 WILD-TYPE 352  84
  KIAA2022 MUTATED KIAA2022 WILD-TYPE 
                35                436 
  KIAA2022 MUTATED KIAA2022 WILD-TYPE 
                 9                 84 
$`KIAA2022 MUTATED`
TCGA-A6-5659 TCGA-AA-3496 TCGA-AA-3660 TCGA-AA-3681 TCGA-AA-3877 TCGA-AA-3977 
       30.44         1.02        78.08         5.98        31.00        25.02 
TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01Q TCGA-AA-A02W TCGA-AD-5900 TCGA-AD-6901 
        4.01        34.98         1.02        41.00         0.07        22.42 
TCGA-AD-6964 TCGA-AZ-6605 TCGA-CK-4952 TCGA-CK-5916 TCGA-CM-5860 TCGA-CM-6162 
       10.88         5.23        15.62        21.14        32.02        12.00 
TCGA-CM-6164 TCGA-CM-6166 TCGA-D5-6536 TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A28H 
       29.03        21.99        17.85        44.32       135.65       117.07 
TCGA-F4-6460 TCGA-G4-6303 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2693 TCGA-AG-3600 
       31.96        65.85        91.79        46.75        19.10         6.05 
TCGA-AG-3909 TCGA-AG-A002 TCGA-AG-A011 TCGA-AG-A02N TCGA-DY-A0XA 
       19.99        20.98        37.02        61.97       126.44 

$`KIAA2022 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 
       20.12        19.66        20.28         7.04         3.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       13.94        19.99        61.02         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
       11.01        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       29.98        18.05         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        31.00        38.07        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02Y TCGA-AA-A03F 
        2.01         5.03        14.01         0.92        39.98        18.05 
TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
       40.96        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
        5.79        27.42         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77        12.10       100.01        29.56        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 
       85.45        49.08        51.32         9.99        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-5862 
       29.06        22.03        22.98        30.08        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6165 
       15.02        15.02        17.03        15.02         2.96        16.04 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 
       20.19        18.25         1.32        43.27        15.12         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 
       12.59       140.38         7.50       131.51       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28K TCGA-F4-6459 
       81.37       119.93        35.97        60.79        98.24         8.61 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
      133.18        74.56        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       26.17        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
        2.01        50.04        12.03         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       48.03        32.02        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A014 
       17.03        13.94         6.02        25.97        23.01        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
       49.97         1.94        38.96        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        4.01         5.03         5.29        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  KIAA2022 MUTATED KIAA2022 WILD-TYPE 
              0.07               0.00 
  KIAA2022 MUTATED KIAA2022 WILD-TYPE 
            135.65             148.01 
  KIAA2022 MUTATED KIAA2022 WILD-TYPE 
            25.020             20.005 
[1] "0.1 - 135.7 (25.0)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1"  
D1457V2, continuous
D1457V3, binary
                    cls
clus                   0   1
  KIAA2022 MUTATED    32   6
  KIAA2022 WILD-TYPE 334 113
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA2022 MUTATED     32    6
  KIAA2022 WILD-TYPE  334  113
        clus
vv       KIAA2022 MUTATED KIAA2022 WILD-TYPE
  COLON                32                334
  RECTUM                6                113
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KIAA2022 MUTATED         8        0        5         9         2         0
  KIAA2022 WILD-TYPE      83        1       27       129         8         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIAA2022 MUTATED           2          0          5          3        2
  KIAA2022 WILD-TYPE        22         11         54         39       46
                    vv
clus                 STAGE IVA STAGE IVB
  KIAA2022 MUTATED           0         0
  KIAA2022 WILD-TYPE        18         1
D1457V4, multiclass
            clus
vv           KIAA2022 MUTATED KIAA2022 WILD-TYPE
  STAGE I                   8                 83
  STAGE IA                  0                  1
  STAGE II                  5                 27
  STAGE IIA                 9                129
  STAGE IIB                 2                  8
  STAGE IIC                 0                  1
  STAGE III                 2                 22
  STAGE IIIA                0                 11
  STAGE IIIB                5                 54
  STAGE IIIC                3                 39
  STAGE IV                  2                 46
  STAGE IVA                 0                 18
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  KIAA2022 MUTATED     2   7  23   7
  KIAA2022 WILD-TYPE  15  85 306  43
D1457V5, multiclass
    clus
vv   KIAA2022 MUTATED KIAA2022 WILD-TYPE
  T1                2                 15
  T2                7                 85
  T3               23                306
  T4                7                 43
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  KIAA2022 MUTATED    26   8   5
  KIAA2022 WILD-TYPE 261 105  82
D1457V6, multiclass
    clus
vv   KIAA2022 MUTATED KIAA2022 WILD-TYPE
  N0               26                261
  N1                8                105
  N2                5                 82
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1457V7, binary
                    cls
clus                   0   1
  KIAA2022 MUTATED    32   2
  KIAA2022 WILD-TYPE 343  63
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA2022 MUTATED     32    2
  KIAA2022 WILD-TYPE  343   63
   clus
vv  KIAA2022 MUTATED KIAA2022 WILD-TYPE
  0               32                343
  1                2                 63
[1] 2 2
[1] FALSE
D1457V8, binary
                    cls
clus                   0   1
  KIAA2022 MUTATED    20  19
  KIAA2022 WILD-TYPE 205 245
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA2022 MUTATED     20   19
  KIAA2022 WILD-TYPE  205  245
        clus
vv       KIAA2022 MUTATED KIAA2022 WILD-TYPE
  FEMALE               20                205
  MALE                 19                245
[1] 2 2
[1] FALSE
D1457V9, binary
                    cls
clus                   0   1
  KIAA2022 MUTATED    24   1
  KIAA2022 WILD-TYPE 326  21
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA2022 MUTATED     24    1
  KIAA2022 WILD-TYPE  326   21
     clus
vv    KIAA2022 MUTATED KIAA2022 WILD-TYPE
  NO                24                326
  YES                1                 21
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  KIAA2022 MUTATED                     26                             5
  KIAA2022 WILD-TYPE                  289                            42
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  KIAA2022 MUTATED                       6                              0
  KIAA2022 WILD-TYPE                   100                             10
D1457V10, multiclass
                                clus
vv                               KIAA2022 MUTATED KIAA2022 WILD-TYPE
  COLON ADENOCARCINOMA                         26                289
  COLON MUCINOUS ADENOCARCINOMA                 5                 42
  RECTAL ADENOCARCINOMA                         6                100
  RECTAL MUCINOUS ADENOCARCINOMA                0                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  KIAA2022 MUTATED    27   0   1   2
  KIAA2022 WILD-TYPE 318   4  30  23
D1457V11, multiclass
    clus
vv   KIAA2022 MUTATED KIAA2022 WILD-TYPE
  R0               27                318
  R1                0                  4
  R2                1                 30
  RX                2                 23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1457V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KIAA2022 MUTATED                                  0     0
  KIAA2022 WILD-TYPE                                1    11
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  KIAA2022 MUTATED                           0    21
  KIAA2022 WILD-TYPE                        22   205
D1457V13, multiclass
                                  clus
vv                                 KIAA2022 MUTATED KIAA2022 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 11
  BLACK OR AFRICAN AMERICAN                       0                 22
  WHITE                                          21                205
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1458) Variable = GRM1 MUTATION ANALYSIS
D1458V1, survival
                sevent
clus2              0   1
  GRM1 MUTATED    24   3
  GRM1 WILD-TYPE 354  90
  GRM1 MUTATED GRM1 WILD-TYPE 
            27            444 
  GRM1 MUTATED GRM1 WILD-TYPE 
             3             90 
$`GRM1 MUTATED`
TCGA-A6-6782 TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3672 TCGA-AA-3812 TCGA-AA-3949 
       20.28         3.02        63.98         0.92        35.05        26.01 
TCGA-AA-3966 TCGA-AA-A00E TCGA-AA-A00J TCGA-AD-6963 TCGA-AZ-6598 TCGA-CA-6717 
        2.01        30.02        18.05        27.42        49.41        12.76 
TCGA-CA-6718 TCGA-CK-5913 TCGA-CK-6751 TCGA-CM-6165 TCGA-CM-6168 TCGA-CM-6674 
       10.06        51.32       124.27        16.04        12.99        12.95 
TCGA-D5-5538 TCGA-D5-6529 TCGA-D5-6540 TCGA-D5-6541 TCGA-G4-6588 TCGA-AG-3593 
       12.26        20.19        16.14        15.58        26.17        34.03 
TCGA-AG-A002 TCGA-AG-A025 TCGA-DC-6157 
       20.98        49.97        27.95 

$`GRM1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 
       23.87        20.12        19.66         7.04         1.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
        2.01        14.01        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3815 TCGA-AA-3818 
       26.99        19.04        19.04        10.06        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 
       24.00         2.01        20.98        34.03        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       38.04        19.00        34.03        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6964 TCGA-AD-6965 
        0.79         0.72         5.79        22.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        88.21         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 
        3.25         3.29         0.07        12.20        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 
      148.01        85.45        15.62        49.08         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
       82.95         1.91        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6169 
       12.00         2.96        29.03        21.99        14.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       15.02        14.04        11.01        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5539 TCGA-D5-5540 
       11.01        10.06        12.03        45.40        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       55.92        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
        4.80        17.13        12.49         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        35.80        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3594 
       36.03        20.05        24.00         1.02        46.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       64.01        10.98         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6158 TCGA-DC-6160 
        7.17        15.02         5.03        13.97        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  GRM1 MUTATED GRM1 WILD-TYPE 
          0.92           0.00 
  GRM1 MUTATED GRM1 WILD-TYPE 
        124.27         148.01 
  GRM1 MUTATED GRM1 WILD-TYPE 
        20.280         20.085 
[1] "0.9 - 124.3 (20.3)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.9"
D1458V2, continuous
D1458V3, binary
                cls
clus               0   1
  GRM1 MUTATED    27   5
  GRM1 WILD-TYPE 339 114
[1] "tbl2"
                cls
clus             [,1] [,2]
  GRM1 MUTATED     27    5
  GRM1 WILD-TYPE  339  114
        clus
vv       GRM1 MUTATED GRM1 WILD-TYPE
  COLON            27            339
  RECTUM            5            114
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GRM1 MUTATED         5        0        4        13         1         0
  GRM1 WILD-TYPE      86        1       28       125         9         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  GRM1 MUTATED           2          0          3          1        2         0
  GRM1 WILD-TYPE        22         11         56         41       46        18
                vv
clus             STAGE IVB
  GRM1 MUTATED           0
  GRM1 WILD-TYPE         1
D1458V4, multiclass
            clus
vv           GRM1 MUTATED GRM1 WILD-TYPE
  STAGE I               5             86
  STAGE IA              0              1
  STAGE II              4             28
  STAGE IIA            13            125
  STAGE IIB             1              9
  STAGE IIC             0              1
  STAGE III             2             22
  STAGE IIIA            0             11
  STAGE IIIB            3             56
  STAGE IIIC            1             41
  STAGE IV              2             46
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  GRM1 MUTATED     1   4  23   4
  GRM1 WILD-TYPE  16  88 306  46
D1458V5, multiclass
    clus
vv   GRM1 MUTATED GRM1 WILD-TYPE
  T1            1             16
  T2            4             88
  T3           23            306
  T4            4             46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  GRM1 MUTATED    24   5   3
  GRM1 WILD-TYPE 263 108  84
D1458V6, multiclass
    clus
vv   GRM1 MUTATED GRM1 WILD-TYPE
  N0           24            263
  N1            5            108
  N2            3             84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1458V7, binary
                cls
clus               0   1
  GRM1 MUTATED    23   2
  GRM1 WILD-TYPE 352  63
[1] "tbl2"
                cls
clus             [,1] [,2]
  GRM1 MUTATED     23    2
  GRM1 WILD-TYPE  352   63
   clus
vv  GRM1 MUTATED GRM1 WILD-TYPE
  0           23            352
  1            2             63
[1] 2 2
[1] FALSE
D1458V8, binary
                cls
clus               0   1
  GRM1 MUTATED    15  17
  GRM1 WILD-TYPE 210 247
[1] "tbl2"
                cls
clus             [,1] [,2]
  GRM1 MUTATED     15   17
  GRM1 WILD-TYPE  210  247
        clus
vv       GRM1 MUTATED GRM1 WILD-TYPE
  FEMALE           15            210
  MALE             17            247
[1] 2 2
[1] FALSE
D1458V9, binary
                cls
clus               0   1
  GRM1 MUTATED    23   1
  GRM1 WILD-TYPE 327  21
[1] "tbl2"
                cls
clus             [,1] [,2]
  GRM1 MUTATED     23    1
  GRM1 WILD-TYPE  327   21
     clus
vv    GRM1 MUTATED GRM1 WILD-TYPE
  NO            23            327
  YES            1             21
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  GRM1 MUTATED                     20                             7
  GRM1 WILD-TYPE                  295                            40
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  GRM1 MUTATED                       5                              0
  GRM1 WILD-TYPE                   101                             10
D1458V10, multiclass
                                clus
vv                               GRM1 MUTATED GRM1 WILD-TYPE
  COLON ADENOCARCINOMA                     20            295
  COLON MUCINOUS ADENOCARCINOMA             7             40
  RECTAL ADENOCARCINOMA                     5            101
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  GRM1 MUTATED    21   0   2   4
  GRM1 WILD-TYPE 324   4  29  21
D1458V11, multiclass
    clus
vv   GRM1 MUTATED GRM1 WILD-TYPE
  R0           21            324
  R1            0              4
  R2            2             29
  RX            4             21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1458V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GRM1 MUTATED                                  0     2
  GRM1 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  GRM1 MUTATED                           2    14
  GRM1 WILD-TYPE                        20   212
D1458V13, multiclass
                                  clus
vv                                 GRM1 MUTATED GRM1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              9
  BLACK OR AFRICAN AMERICAN                   2             20
  WHITE                                      14            212
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1459) Variable = WFDC10B MUTATION ANALYSIS
D1459V1, survival
                   sevent
clus2                 0   1
  WFDC10B MUTATED     4   1
  WFDC10B WILD-TYPE 374  92
  WFDC10B MUTATED WFDC10B WILD-TYPE 
                5               466 
  WFDC10B MUTATED WFDC10B WILD-TYPE 
                1                92 
$`WFDC10B MUTATED`
TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6676 TCGA-F4-6459 TCGA-G4-6588 
       11.01        13.05        11.08         8.61        26.17 

$`WFDC10B WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       14.04        12.95        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
      117.07        98.24        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        35.80        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  WFDC10B MUTATED WFDC10B WILD-TYPE 
             8.61              0.00 
  WFDC10B MUTATED WFDC10B WILD-TYPE 
            26.17            148.01 
  WFDC10B MUTATED WFDC10B WILD-TYPE 
           11.080            20.415 
[1] "8.6 - 26.2 (11.1)"  "0.0 - 148.0 (20.4)"
[1] "hr=" "1.8"
D1459V2, continuous
D1459V3, binary
                   cls
clus                  0   1
  WFDC10B MUTATED     5   0
  WFDC10B WILD-TYPE 361 119
[1] "tbl2"
                   cls
clus                [,1] [,2]
  WFDC10B MUTATED      5    0
  WFDC10B WILD-TYPE  361  119
        clus
vv       WFDC10B MUTATED WFDC10B WILD-TYPE
  COLON                5               361
  RECTUM               0               119
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  WFDC10B MUTATED         1        0        0         1         0         0
  WFDC10B WILD-TYPE      90        1       32       137        10         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  WFDC10B MUTATED           0          0          2          0        0
  WFDC10B WILD-TYPE        24         11         57         42       48
                   vv
clus                STAGE IVA STAGE IVB
  WFDC10B MUTATED           0         1
  WFDC10B WILD-TYPE        18         0
D1459V4, multiclass
            clus
vv           WFDC10B MUTATED WFDC10B WILD-TYPE
  STAGE I                  1                90
  STAGE IA                 0                 1
  STAGE II                 0                32
  STAGE IIA                1               137
  STAGE IIB                0                10
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               0                11
  STAGE IIIB               2                57
  STAGE IIIC               0                42
  STAGE IV                 0                48
  STAGE IVA                0                18
  STAGE IVB                1                 0
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  WFDC10B MUTATED     0   1   4   0
  WFDC10B WILD-TYPE  17  91 325  50
D1459V5, multiclass
    clus
vv   WFDC10B MUTATED WFDC10B WILD-TYPE
  T1               0                17
  T2               1                91
  T3               4               325
  T4               0                50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  WFDC10B MUTATED     2   1   2
  WFDC10B WILD-TYPE 285 112  85
D1459V6, multiclass
    clus
vv   WFDC10B MUTATED WFDC10B WILD-TYPE
  N0               2               285
  N1               1               112
  N2               2                85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1459V7, binary
                   cls
clus                  0   1
  WFDC10B MUTATED     4   1
  WFDC10B WILD-TYPE 371  64
[1] "tbl2"
                   cls
clus                [,1] [,2]
  WFDC10B MUTATED      4    1
  WFDC10B WILD-TYPE  371   64
   clus
vv  WFDC10B MUTATED WFDC10B WILD-TYPE
  0               4               371
  1               1                64
[1] 2 2
[1] FALSE
D1459V8, binary
                   cls
clus                  0   1
  WFDC10B MUTATED     3   2
  WFDC10B WILD-TYPE 222 262
[1] "tbl2"
                   cls
clus                [,1] [,2]
  WFDC10B MUTATED      3    2
  WFDC10B WILD-TYPE  222  262
        clus
vv       WFDC10B MUTATED WFDC10B WILD-TYPE
  FEMALE               3               222
  MALE                 2               262
[1] 2 2
[1] FALSE
D1459V9, binary
                   cls
clus                  0   1
  WFDC10B MUTATED     5   0
  WFDC10B WILD-TYPE 345  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  WFDC10B MUTATED      5    0
  WFDC10B WILD-TYPE  345   22
     clus
vv    WFDC10B MUTATED WFDC10B WILD-TYPE
  NO                5               345
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  WFDC10B MUTATED                      5                             0
  WFDC10B WILD-TYPE                  310                            47
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  WFDC10B MUTATED                       0                              0
  WFDC10B WILD-TYPE                   106                             10
D1459V10, multiclass
                                clus
vv                               WFDC10B MUTATED WFDC10B WILD-TYPE
  COLON ADENOCARCINOMA                         5               310
  COLON MUCINOUS ADENOCARCINOMA                0                47
  RECTAL ADENOCARCINOMA                        0               106
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  WFDC10B MUTATED     5   0   0   0
  WFDC10B WILD-TYPE 340   4  31  25
D1459V11, multiclass
    clus
vv   WFDC10B MUTATED WFDC10B WILD-TYPE
  R0               5               340
  R1               0                 4
  R2               0                31
  RX               0                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1459V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  WFDC10B MUTATED                                  0     0
  WFDC10B WILD-TYPE                                1    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  WFDC10B MUTATED                           1     4
  WFDC10B WILD-TYPE                        21   222
D1459V13, multiclass
                                  clus
vv                                 WFDC10B MUTATED WFDC10B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                      1                21
  WHITE                                          4               222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1460) Variable = KIAA0240 MUTATION ANALYSIS
D1460V1, survival
                    sevent
clus2                  0   1
  KIAA0240 MUTATED     9   2
  KIAA0240 WILD-TYPE 369  91
  KIAA0240 MUTATED KIAA0240 WILD-TYPE 
                11                460 
  KIAA0240 MUTATED KIAA0240 WILD-TYPE 
                 2                 91 
$`KIAA0240 MUTATED`
TCGA-AA-3510 TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3713 TCGA-AA-3949 TCGA-AA-A00N 
       63.98        13.02         1.02        19.04        26.01         4.01 
TCGA-CM-6171 TCGA-D5-6928 TCGA-G4-6628 TCGA-AG-A002 TCGA-AG-A02X 
       14.04        11.64        79.69        20.98        41.00 

$`KIAA0240 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3519 
        1.02        35.01         6.97         1.02        38.99         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       85.05        26.99        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       33.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
        9.44         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       26.17        91.79        46.75        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
        1.94        38.96        61.97        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  KIAA0240 MUTATED KIAA0240 WILD-TYPE 
              1.02               0.00 
  KIAA0240 MUTATED KIAA0240 WILD-TYPE 
             79.69             148.01 
  KIAA0240 MUTATED KIAA0240 WILD-TYPE 
            19.040             20.235 
[1] "1.0 - 79.7 (19.0)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.2"
D1460V2, continuous
D1460V3, binary
                    cls
clus                   0   1
  KIAA0240 MUTATED     9   2
  KIAA0240 WILD-TYPE 357 117
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0240 MUTATED      9    2
  KIAA0240 WILD-TYPE  357  117
        clus
vv       KIAA0240 MUTATED KIAA0240 WILD-TYPE
  COLON                 9                357
  RECTUM                2                117
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KIAA0240 MUTATED         4        0        1         2         1         0
  KIAA0240 WILD-TYPE      87        1       31       136         9         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIAA0240 MUTATED           1          0          1          0        1
  KIAA0240 WILD-TYPE        23         11         58         42       47
                    vv
clus                 STAGE IVA STAGE IVB
  KIAA0240 MUTATED           0         0
  KIAA0240 WILD-TYPE        18         1
D1460V4, multiclass
            clus
vv           KIAA0240 MUTATED KIAA0240 WILD-TYPE
  STAGE I                   4                 87
  STAGE IA                  0                  1
  STAGE II                  1                 31
  STAGE IIA                 2                136
  STAGE IIB                 1                  9
  STAGE IIC                 0                  1
  STAGE III                 1                 23
  STAGE IIIA                0                 11
  STAGE IIIB                1                 58
  STAGE IIIC                0                 42
  STAGE IV                  1                 47
  STAGE IVA                 0                 18
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  KIAA0240 MUTATED     0   4   6   1
  KIAA0240 WILD-TYPE  17  88 323  49
D1460V5, multiclass
    clus
vv   KIAA0240 MUTATED KIAA0240 WILD-TYPE
  T1                0                 17
  T2                4                 88
  T3                6                323
  T4                1                 49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  KIAA0240 MUTATED     9   1   1
  KIAA0240 WILD-TYPE 278 112  86
D1460V6, multiclass
    clus
vv   KIAA0240 MUTATED KIAA0240 WILD-TYPE
  N0                9                278
  N1                1                112
  N2                1                 86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1460V7, binary
                    cls
clus                   0   1
  KIAA0240 MUTATED    10   1
  KIAA0240 WILD-TYPE 365  64
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0240 MUTATED     10    1
  KIAA0240 WILD-TYPE  365   64
   clus
vv  KIAA0240 MUTATED KIAA0240 WILD-TYPE
  0               10                365
  1                1                 64
[1] 2 2
[1] FALSE
D1460V8, binary
                    cls
clus                   0   1
  KIAA0240 MUTATED     4   7
  KIAA0240 WILD-TYPE 221 257
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0240 MUTATED      4    7
  KIAA0240 WILD-TYPE  221  257
        clus
vv       KIAA0240 MUTATED KIAA0240 WILD-TYPE
  FEMALE                4                221
  MALE                  7                257
[1] 2 2
[1] FALSE
D1460V9, binary
                    cls
clus                   0   1
  KIAA0240 MUTATED     7   1
  KIAA0240 WILD-TYPE 343  21
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0240 MUTATED      7    1
  KIAA0240 WILD-TYPE  343   21
     clus
vv    KIAA0240 MUTATED KIAA0240 WILD-TYPE
  NO                 7                343
  YES                1                 21
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  KIAA0240 MUTATED                      5                             4
  KIAA0240 WILD-TYPE                  310                            43
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  KIAA0240 MUTATED                       2                              0
  KIAA0240 WILD-TYPE                   104                             10
D1460V10, multiclass
                                clus
vv                               KIAA0240 MUTATED KIAA0240 WILD-TYPE
  COLON ADENOCARCINOMA                          5                310
  COLON MUCINOUS ADENOCARCINOMA                 4                 43
  RECTAL ADENOCARCINOMA                         2                104
  RECTAL MUCINOUS ADENOCARCINOMA                0                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  KIAA0240 MUTATED     9   0   1   0
  KIAA0240 WILD-TYPE 336   4  30  25
D1460V11, multiclass
    clus
vv   KIAA0240 MUTATED KIAA0240 WILD-TYPE
  R0                9                336
  R1                0                  4
  R2                1                 30
  RX                0                 25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1460V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KIAA0240 MUTATED                                  0     0
  KIAA0240 WILD-TYPE                                1    11
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  KIAA0240 MUTATED                           0     3
  KIAA0240 WILD-TYPE                        22   223
D1460V13, multiclass
                                  clus
vv                                 KIAA0240 MUTATED KIAA0240 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 11
  BLACK OR AFRICAN AMERICAN                       0                 22
  WHITE                                           3                223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1461) Variable = PSMB8 MUTATION ANALYSIS
D1461V1, survival
                 sevent
clus2               0   1
  PSMB8 MUTATED     6   1
  PSMB8 WILD-TYPE 372  92
  PSMB8 MUTATED PSMB8 WILD-TYPE 
              7             464 
  PSMB8 MUTATED PSMB8 WILD-TYPE 
              1              92 
$`PSMB8 MUTATED`
TCGA-A6-5661 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-CM-5861 TCGA-AG-3598 TCGA-AG-3892 
       33.53        58.39        49.41        15.02        50.04        13.02 
TCGA-AG-A015 
       36.03 

$`PSMB8 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        33.01        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 
      106.75        22.36        62.79        88.21         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
       34.03         2.01        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       17.95        36.95        17.03        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       23.01        37.02        15.95         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  PSMB8 MUTATED PSMB8 WILD-TYPE 
          13.02            0.00 
  PSMB8 MUTATED PSMB8 WILD-TYPE 
          58.39          148.01 
  PSMB8 MUTATED PSMB8 WILD-TYPE 
         36.030          20.085 
[1] "13.0 - 58.4 (36.0)" "0.0 - 148.0 (20.1)"
[1] "hr=" "2.1"
D1461V2, continuous
D1461V3, binary
                 cls
clus                0   1
  PSMB8 MUTATED     4   3
  PSMB8 WILD-TYPE 362 116
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PSMB8 MUTATED      4    3
  PSMB8 WILD-TYPE  362  116
        clus
vv       PSMB8 MUTATED PSMB8 WILD-TYPE
  COLON              4             362
  RECTUM             3             116
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PSMB8 MUTATED         2        0        1         4         0         0
  PSMB8 WILD-TYPE      89        1       31       134        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PSMB8 MUTATED           0          0          0          0        0         0
  PSMB8 WILD-TYPE        24         11         59         42       48        18
                 vv
clus              STAGE IVB
  PSMB8 MUTATED           0
  PSMB8 WILD-TYPE         1
D1461V4, multiclass
            clus
vv           PSMB8 MUTATED PSMB8 WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              4             134
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PSMB8 MUTATED     2   0   5   0
  PSMB8 WILD-TYPE  15  92 324  50
D1461V5, multiclass
    clus
vv   PSMB8 MUTATED PSMB8 WILD-TYPE
  T1             2              15
  T2             0              92
  T3             5             324
  T4             0              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  PSMB8 MUTATED     7   0   0
  PSMB8 WILD-TYPE 280 113  87
D1461V6, multiclass
    clus
vv   PSMB8 MUTATED PSMB8 WILD-TYPE
  N0             7             280
  N1             0             113
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1461V7, binary
                 cls
clus                0   1
  PSMB8 MUTATED     6   0
  PSMB8 WILD-TYPE 369  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PSMB8 MUTATED      6    0
  PSMB8 WILD-TYPE  369   65
   clus
vv  PSMB8 MUTATED PSMB8 WILD-TYPE
  0             6             369
  1             0              65
[1] 2 2
[1] FALSE
D1461V8, binary
                 cls
clus                0   1
  PSMB8 MUTATED     5   2
  PSMB8 WILD-TYPE 220 262
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PSMB8 MUTATED      5    2
  PSMB8 WILD-TYPE  220  262
        clus
vv       PSMB8 MUTATED PSMB8 WILD-TYPE
  FEMALE             5             220
  MALE               2             262
[1] 2 2
[1] FALSE
D1461V9, binary
                 cls
clus                0   1
  PSMB8 MUTATED     7   0
  PSMB8 WILD-TYPE 343  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PSMB8 MUTATED      7    0
  PSMB8 WILD-TYPE  343   22
     clus
vv    PSMB8 MUTATED PSMB8 WILD-TYPE
  NO              7             343
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PSMB8 MUTATED                      4                             0
  PSMB8 WILD-TYPE                  311                            47
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PSMB8 MUTATED                       3                              0
  PSMB8 WILD-TYPE                   103                             10
D1461V10, multiclass
                                clus
vv                               PSMB8 MUTATED PSMB8 WILD-TYPE
  COLON ADENOCARCINOMA                       4             311
  COLON MUCINOUS ADENOCARCINOMA              0              47
  RECTAL ADENOCARCINOMA                      3             103
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  PSMB8 MUTATED     6   0   0   0
  PSMB8 WILD-TYPE 339   4  31  25
D1461V11, multiclass
    clus
vv   PSMB8 MUTATED PSMB8 WILD-TYPE
  R0             6             339
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1461V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PSMB8 MUTATED                                  0     0
  PSMB8 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PSMB8 MUTATED                           1     3
  PSMB8 WILD-TYPE                        21   223
D1461V13, multiclass
                                  clus
vv                                 PSMB8 MUTATED PSMB8 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        3             223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1462) Variable = BTF3L4 MUTATION ANALYSIS
D1462V1, survival
                  sevent
clus2                0   1
  BTF3L4 MUTATED     2   3
  BTF3L4 WILD-TYPE 376  90
  BTF3L4 MUTATED BTF3L4 WILD-TYPE 
               5              466 
  BTF3L4 MUTATED BTF3L4 WILD-TYPE 
               3               90 
$`BTF3L4 MUTATED`
TCGA-AD-6964 TCGA-AZ-6608 TCGA-CK-5916 TCGA-CM-4743 TCGA-D5-6539 
       10.88         1.61        21.14        23.05        12.49 

$`BTF3L4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        3.19        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 
       85.45        15.62        49.08        51.32         9.99        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
        1.91       124.27        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  BTF3L4 MUTATED BTF3L4 WILD-TYPE 
            1.61             0.00 
  BTF3L4 MUTATED BTF3L4 WILD-TYPE 
           23.05           148.01 
  BTF3L4 MUTATED BTF3L4 WILD-TYPE 
          12.490           20.235 
[1] "1.6 - 23.1 (12.5)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "5.8"
D1462V2, continuous
D1462V3, binary
                  cls
clus                 0   1
  BTF3L4 MUTATED     5   0
  BTF3L4 WILD-TYPE 361 119
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BTF3L4 MUTATED      5    0
  BTF3L4 WILD-TYPE  361  119
        clus
vv       BTF3L4 MUTATED BTF3L4 WILD-TYPE
  COLON               5              361
  RECTUM              0              119
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  BTF3L4 MUTATED         1        0        0         1         0         0
  BTF3L4 WILD-TYPE      90        1       32       137        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  BTF3L4 MUTATED           0          2          0          0        0
  BTF3L4 WILD-TYPE        24          9         59         42       48
                  vv
clus               STAGE IVA STAGE IVB
  BTF3L4 MUTATED           0         0
  BTF3L4 WILD-TYPE        18         1
D1462V4, multiclass
            clus
vv           BTF3L4 MUTATED BTF3L4 WILD-TYPE
  STAGE I                 1               90
  STAGE IA                0                1
  STAGE II                0               32
  STAGE IIA               1              137
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              2                9
  STAGE IIIB              0               59
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  BTF3L4 MUTATED     1   1   2   1
  BTF3L4 WILD-TYPE  16  91 327  49
D1462V5, multiclass
    clus
vv   BTF3L4 MUTATED BTF3L4 WILD-TYPE
  T1              1               16
  T2              1               91
  T3              2              327
  T4              1               49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  BTF3L4 MUTATED     3   1   1
  BTF3L4 WILD-TYPE 284 112  86
D1462V6, multiclass
    clus
vv   BTF3L4 MUTATED BTF3L4 WILD-TYPE
  N0              3              284
  N1              1              112
  N2              1               86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1462V7, binary
                  cls
clus                 0   1
  BTF3L4 MUTATED     4   0
  BTF3L4 WILD-TYPE 371  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BTF3L4 MUTATED      4    0
  BTF3L4 WILD-TYPE  371   65
   clus
vv  BTF3L4 MUTATED BTF3L4 WILD-TYPE
  0              4              371
  1              0               65
[1] 2 2
[1] FALSE
D1462V8, binary
                  cls
clus                 0   1
  BTF3L4 MUTATED     3   2
  BTF3L4 WILD-TYPE 222 262
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BTF3L4 MUTATED      3    2
  BTF3L4 WILD-TYPE  222  262
        clus
vv       BTF3L4 MUTATED BTF3L4 WILD-TYPE
  FEMALE              3              222
  MALE                2              262
[1] 2 2
[1] FALSE
D1462V9, binary
                  cls
clus                 0   1
  BTF3L4 MUTATED     5   0
  BTF3L4 WILD-TYPE 345  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BTF3L4 MUTATED      5    0
  BTF3L4 WILD-TYPE  345   22
     clus
vv    BTF3L4 MUTATED BTF3L4 WILD-TYPE
  NO               5              345
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  BTF3L4 MUTATED                      5                             0
  BTF3L4 WILD-TYPE                  310                            47
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  BTF3L4 MUTATED                       0                              0
  BTF3L4 WILD-TYPE                   106                             10
D1462V10, multiclass
                                clus
vv                               BTF3L4 MUTATED BTF3L4 WILD-TYPE
  COLON ADENOCARCINOMA                        5              310
  COLON MUCINOUS ADENOCARCINOMA               0               47
  RECTAL ADENOCARCINOMA                       0              106
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  BTF3L4 MUTATED     2   0   0   1
  BTF3L4 WILD-TYPE 343   4  31  24
D1462V11, multiclass
    clus
vv   BTF3L4 MUTATED BTF3L4 WILD-TYPE
  R0              2              343
  R1              0                4
  R2              0               31
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1462V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  BTF3L4 MUTATED                                  0     0
  BTF3L4 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  BTF3L4 MUTATED                           0     5
  BTF3L4 WILD-TYPE                        22   221
D1462V13, multiclass
                                  clus
vv                                 BTF3L4 MUTATED BTF3L4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         5              221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1463) Variable = SYNGR4 MUTATION ANALYSIS
D1463V1, survival
                  sevent
clus2                0   1
  SYNGR4 MUTATED     4   1
  SYNGR4 WILD-TYPE 374  92
  SYNGR4 MUTATED SYNGR4 WILD-TYPE 
               5              466 
  SYNGR4 MUTATED SYNGR4 WILD-TYPE 
               1               92 
$`SYNGR4 MUTATED`
TCGA-A6-6781 TCGA-AA-A00N TCGA-AD-5900 TCGA-AZ-4315 TCGA-D5-5539 
       19.66         4.01         0.07        58.39        19.59 

$`SYNGR4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       39.98        18.05        40.96        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       12.26        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  SYNGR4 MUTATED SYNGR4 WILD-TYPE 
            0.07             0.00 
  SYNGR4 MUTATED SYNGR4 WILD-TYPE 
           58.39           148.01 
  SYNGR4 MUTATED SYNGR4 WILD-TYPE 
          19.590           20.415 
[1] "0.1 - 58.4 (19.6)"  "0.0 - 148.0 (20.4)"
[1] "hr=" "1.2"
D1463V2, continuous
D1463V3, binary
                  cls
clus                 0   1
  SYNGR4 MUTATED     6   0
  SYNGR4 WILD-TYPE 360 119
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SYNGR4 MUTATED      6    0
  SYNGR4 WILD-TYPE  360  119
        clus
vv       SYNGR4 MUTATED SYNGR4 WILD-TYPE
  COLON               6              360
  RECTUM              0              119
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SYNGR4 MUTATED         1        0        1         1         1         0
  SYNGR4 WILD-TYPE      90        1       31       137         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SYNGR4 MUTATED           0          1          0          1        0
  SYNGR4 WILD-TYPE        24         10         59         41       48
                  vv
clus               STAGE IVA STAGE IVB
  SYNGR4 MUTATED           0         0
  SYNGR4 WILD-TYPE        18         1
D1463V4, multiclass
            clus
vv           SYNGR4 MUTATED SYNGR4 WILD-TYPE
  STAGE I                 1               90
  STAGE IA                0                1
  STAGE II                1               31
  STAGE IIA               1              137
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              1               10
  STAGE IIIB              0               59
  STAGE IIIC              1               41
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  SYNGR4 MUTATED     0   1   3   2
  SYNGR4 WILD-TYPE  17  91 326  48
D1463V5, multiclass
    clus
vv   SYNGR4 MUTATED SYNGR4 WILD-TYPE
  T1              0               17
  T2              1               91
  T3              3              326
  T4              2               48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  SYNGR4 MUTATED     4   2   0
  SYNGR4 WILD-TYPE 283 111  87
D1463V6, multiclass
    clus
vv   SYNGR4 MUTATED SYNGR4 WILD-TYPE
  N0              4              283
  N1              2              111
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1463V7, binary
                  cls
clus                 0   1
  SYNGR4 MUTATED     4   0
  SYNGR4 WILD-TYPE 371  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SYNGR4 MUTATED      4    0
  SYNGR4 WILD-TYPE  371   65
   clus
vv  SYNGR4 MUTATED SYNGR4 WILD-TYPE
  0              4              371
  1              0               65
[1] 2 2
[1] FALSE
D1463V8, binary
                  cls
clus                 0   1
  SYNGR4 MUTATED     0   6
  SYNGR4 WILD-TYPE 225 258
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SYNGR4 MUTATED      0    6
  SYNGR4 WILD-TYPE  225  258
        clus
vv       SYNGR4 MUTATED SYNGR4 WILD-TYPE
  FEMALE              0              225
  MALE                6              258
[1] 2 2
[1] FALSE
D1463V9, binary
                  cls
clus                 0   1
  SYNGR4 MUTATED     3   0
  SYNGR4 WILD-TYPE 347  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SYNGR4 MUTATED      3    0
  SYNGR4 WILD-TYPE  347   22
     clus
vv    SYNGR4 MUTATED SYNGR4 WILD-TYPE
  NO               3              347
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SYNGR4 MUTATED                      2                             4
  SYNGR4 WILD-TYPE                  313                            43
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SYNGR4 MUTATED                       0                              0
  SYNGR4 WILD-TYPE                   106                             10
D1463V10, multiclass
                                clus
vv                               SYNGR4 MUTATED SYNGR4 WILD-TYPE
  COLON ADENOCARCINOMA                        2              313
  COLON MUCINOUS ADENOCARCINOMA               4               43
  RECTAL ADENOCARCINOMA                       0              106
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  SYNGR4 MUTATED     6   0   0   0
  SYNGR4 WILD-TYPE 339   4  31  25
D1463V11, multiclass
    clus
vv   SYNGR4 MUTATED SYNGR4 WILD-TYPE
  R0              6              339
  R1              0                4
  R2              0               31
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1463V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SYNGR4 MUTATED                                  0     0
  SYNGR4 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  SYNGR4 MUTATED                           0     4
  SYNGR4 WILD-TYPE                        22   222
D1463V13, multiclass
                                  clus
vv                                 SYNGR4 MUTATED SYNGR4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         4              222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1464) Variable = OR2AE1 MUTATION ANALYSIS
D1464V1, survival
                  sevent
clus2                0   1
  OR2AE1 MUTATED     3   0
  OR2AE1 WILD-TYPE 375  93
  OR2AE1 MUTATED OR2AE1 WILD-TYPE 
               3              468 
  OR2AE1 MUTATED OR2AE1 WILD-TYPE 
               0               93 
$`OR2AE1 MUTATED`
TCGA-AA-3968 TCGA-AY-6197 TCGA-AG-A002 
       21.99        21.44        20.98 

$`OR2AE1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3971 
       24.00         2.01        20.98        34.03         2.01        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        33.01        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  OR2AE1 MUTATED OR2AE1 WILD-TYPE 
           20.98             0.00 
  OR2AE1 MUTATED OR2AE1 WILD-TYPE 
           21.99           148.01 
  OR2AE1 MUTATED OR2AE1 WILD-TYPE 
          21.440           20.085 
[1] "21.0 - 22.0 (21.4)" "0.0 - 148.0 (20.1)"
[1] "hr="     "3300000"
D1464V2, continuous
D1464V3, binary
                  cls
clus                 0   1
  OR2AE1 MUTATED     2   1
  OR2AE1 WILD-TYPE 364 118
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR2AE1 MUTATED      2    1
  OR2AE1 WILD-TYPE  364  118
        clus
vv       OR2AE1 MUTATED OR2AE1 WILD-TYPE
  COLON               2              364
  RECTUM              1              118
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  OR2AE1 MUTATED         2        0        0         1         0         0
  OR2AE1 WILD-TYPE      89        1       32       137        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  OR2AE1 MUTATED           0          0          0          0        0
  OR2AE1 WILD-TYPE        24         11         59         42       48
                  vv
clus               STAGE IVA STAGE IVB
  OR2AE1 MUTATED           0         0
  OR2AE1 WILD-TYPE        18         1
D1464V4, multiclass
            clus
vv           OR2AE1 MUTATED OR2AE1 WILD-TYPE
  STAGE I                 2               89
  STAGE IA                0                1
  STAGE II                0               32
  STAGE IIA               1              137
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              0               59
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  OR2AE1 MUTATED     0   2   1   0
  OR2AE1 WILD-TYPE  17  90 328  50
D1464V5, multiclass
    clus
vv   OR2AE1 MUTATED OR2AE1 WILD-TYPE
  T1              0               17
  T2              2               90
  T3              1              328
  T4              0               50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  OR2AE1 MUTATED     3   0   0
  OR2AE1 WILD-TYPE 284 113  87
D1464V6, multiclass
    clus
vv   OR2AE1 MUTATED OR2AE1 WILD-TYPE
  N0              3              284
  N1              0              113
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1464V7, binary
                  cls
clus                 0   1
  OR2AE1 MUTATED     2   0
  OR2AE1 WILD-TYPE 373  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR2AE1 MUTATED      2    0
  OR2AE1 WILD-TYPE  373   65
   clus
vv  OR2AE1 MUTATED OR2AE1 WILD-TYPE
  0              2              373
  1              0               65
[1] 2 2
[1] FALSE
D1464V8, binary
                  cls
clus                 0   1
  OR2AE1 MUTATED     1   2
  OR2AE1 WILD-TYPE 224 262
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR2AE1 MUTATED      1    2
  OR2AE1 WILD-TYPE  224  262
        clus
vv       OR2AE1 MUTATED OR2AE1 WILD-TYPE
  FEMALE              1              224
  MALE                2              262
[1] 2 2
[1] FALSE
D1464V9, binary
                  cls
clus                 0   1
  OR2AE1 MUTATED     3   0
  OR2AE1 WILD-TYPE 347  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR2AE1 MUTATED      3    0
  OR2AE1 WILD-TYPE  347   22
     clus
vv    OR2AE1 MUTATED OR2AE1 WILD-TYPE
  NO               3              347
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  OR2AE1 MUTATED                      2                             0
  OR2AE1 WILD-TYPE                  313                            47
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  OR2AE1 MUTATED                       1                              0
  OR2AE1 WILD-TYPE                   105                             10
D1464V10, multiclass
                                clus
vv                               OR2AE1 MUTATED OR2AE1 WILD-TYPE
  COLON ADENOCARCINOMA                        2              313
  COLON MUCINOUS ADENOCARCINOMA               0               47
  RECTAL ADENOCARCINOMA                       1              105
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  OR2AE1 MUTATED     3   0   0   0
  OR2AE1 WILD-TYPE 342   4  31  25
D1464V11, multiclass
    clus
vv   OR2AE1 MUTATED OR2AE1 WILD-TYPE
  R0              3              342
  R1              0                4
  R2              0               31
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1464V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OR2AE1 MUTATED                                  0     0
  OR2AE1 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  OR2AE1 MUTATED                           0     1
  OR2AE1 WILD-TYPE                        22   225
D1464V13, multiclass
[1] "Remove cluster labels:" "OR2AE1 MUTATED"        
clus
  OR2AE1 MUTATED OR2AE1 WILD-TYPE 
               1              259 
      TCGA-A6-2671       TCGA-A6-2672       TCGA-A6-2674       TCGA-A6-2676 
"OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" 
      TCGA-A6-2677       TCGA-A6-2678       TCGA-A6-2683       TCGA-A6-3807 
"OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" 
      TCGA-A6-3808       TCGA-A6-3809       TCGA-A6-3810       TCGA-A6-4105 
"OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" 
      TCGA-A6-5656       TCGA-A6-5657       TCGA-A6-5659       TCGA-A6-5660 
"OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" 
      TCGA-A6-5661       TCGA-A6-5662       TCGA-A6-5664       TCGA-A6-5665 
"OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" 
      TCGA-A6-5666       TCGA-A6-6137       TCGA-A6-6138       TCGA-A6-6141 
"OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" 
      TCGA-A6-6142       TCGA-A6-6648       TCGA-A6-6649       TCGA-A6-6651 
"OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" 
      TCGA-A6-6652       TCGA-A6-6653       TCGA-A6-6654       TCGA-A6-6780 
"OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" 
      TCGA-A6-6781       TCGA-A6-6782       TCGA-AD-5900       TCGA-AD-6548 
"OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" 
      TCGA-AD-6888       TCGA-AD-6889       TCGA-AD-6890       TCGA-AD-6895 
"OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" 
      TCGA-AD-6899       TCGA-AD-6901       TCGA-AD-6963       TCGA-AD-6964 
"OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" 
      TCGA-AD-6965       TCGA-AU-3779       TCGA-AU-6004       TCGA-AY-4070 
"OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" 
      TCGA-AY-4071       TCGA-AY-5543       TCGA-AY-6196       TCGA-AY-6386 
"OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" 
      TCGA-AZ-4315       TCGA-AZ-4323       TCGA-AZ-4616       TCGA-AZ-4681 
"OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" 
      TCGA-AZ-4682       TCGA-AZ-5403       TCGA-AZ-5407       TCGA-AZ-6598 
"OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" 
      TCGA-AZ-6599       TCGA-AZ-6600       TCGA-AZ-6601       TCGA-AZ-6603 
"OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" 
      TCGA-AZ-6605       TCGA-AZ-6606       TCGA-AZ-6607       TCGA-AZ-6608 
"OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" 
      TCGA-CA-5254       TCGA-CA-5255       TCGA-CA-5796       TCGA-CA-5797 
"OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" 
      TCGA-CA-6715       TCGA-CA-6716       TCGA-CA-6717       TCGA-CA-6718 
"OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" 
      TCGA-CA-6719       TCGA-CK-4947       TCGA-CK-4948       TCGA-CK-4950 
"OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" 
      TCGA-CK-4952       TCGA-CK-5912       TCGA-CK-5913       TCGA-CK-5914 
"OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" 
      TCGA-CK-5915       TCGA-CK-5916       TCGA-CK-6746       TCGA-CK-6747 
"OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" 
      TCGA-CK-6748       TCGA-CK-6751       TCGA-CM-4743       TCGA-CM-4744 
"OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" 
      TCGA-CM-4746       TCGA-CM-4747       TCGA-CM-4752       TCGA-CM-5341 
"OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" 
      TCGA-CM-5344       TCGA-CM-5348       TCGA-CM-5349       TCGA-CM-5860 
"OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" 
      TCGA-CM-5861       TCGA-CM-5862       TCGA-CM-5863       TCGA-CM-5864 
"OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" 
      TCGA-CM-5868       TCGA-CM-6161       TCGA-CM-6162       TCGA-CM-6163 
"OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" 
      TCGA-CM-6164       TCGA-CM-6165       TCGA-CM-6166       TCGA-CM-6167 
"OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" 
      TCGA-CM-6168       TCGA-CM-6169       TCGA-CM-6170       TCGA-CM-6171 
"OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" 
      TCGA-CM-6172       TCGA-CM-6674       TCGA-CM-6675       TCGA-CM-6676 
"OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" 
      TCGA-CM-6677       TCGA-CM-6678       TCGA-CM-6679       TCGA-CM-6680 
"OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" 
      TCGA-D5-5537       TCGA-D5-5538       TCGA-D5-5539       TCGA-D5-5540 
"OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" 
      TCGA-D5-5541       TCGA-D5-6529       TCGA-D5-6532       TCGA-D5-6533 
"OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" 
      TCGA-D5-6534       TCGA-D5-6535       TCGA-D5-6536       TCGA-D5-6537 
"OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" 
      TCGA-D5-6538       TCGA-D5-6539       TCGA-D5-6540       TCGA-D5-6541 
"OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" 
      TCGA-D5-6898       TCGA-D5-6920       TCGA-D5-6922       TCGA-D5-6923 
"OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" 
      TCGA-D5-6924       TCGA-D5-6926       TCGA-D5-6927       TCGA-D5-6928 
"OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" 
      TCGA-D5-6929       TCGA-D5-6930       TCGA-D5-6931       TCGA-D5-6932 
"OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" 
      TCGA-D5-7000       TCGA-DM-A0X9       TCGA-DM-A0XD       TCGA-DM-A0XF 
"OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" 
      TCGA-DM-A1D0       TCGA-DM-A1D4       TCGA-DM-A1D6       TCGA-DM-A1D7 
"OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" 
      TCGA-DM-A1D8       TCGA-DM-A1D9       TCGA-DM-A1DA       TCGA-DM-A1DB 
"OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" 
      TCGA-DM-A1HA       TCGA-DM-A1HB       TCGA-DM-A282       TCGA-DM-A285 
"OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" 
      TCGA-DM-A28C       TCGA-DM-A28E       TCGA-DM-A28F       TCGA-DM-A28G 
"OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" 
      TCGA-DM-A28H       TCGA-DM-A28K       TCGA-F4-6459       TCGA-F4-6460 
"OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" 
      TCGA-F4-6569       TCGA-F4-6570       TCGA-F4-6703       TCGA-F4-6704 
"OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" 
      TCGA-F4-6805       TCGA-F4-6806       TCGA-F4-6807       TCGA-F4-6808 
"OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" 
      TCGA-F4-6809       TCGA-F4-6854       TCGA-F4-6855       TCGA-F4-6856 
"OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" 
      TCGA-G4-6293       TCGA-G4-6299       TCGA-G4-6303       TCGA-G4-6304 
"OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" 
      TCGA-G4-6306       TCGA-G4-6307       TCGA-G4-6309       TCGA-G4-6310 
"OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" 
      TCGA-G4-6315       TCGA-G4-6317       TCGA-G4-6321       TCGA-G4-6323 
"OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" 
      TCGA-G4-6586       TCGA-G4-6588       TCGA-G4-6625       TCGA-G4-6626 
"OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" 
      TCGA-G4-6628       TCGA-AF-2687       TCGA-AF-2689       TCGA-AF-2691 
"OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" 
      TCGA-AF-2692       TCGA-AF-2693       TCGA-AF-3400       TCGA-AF-3913 
"OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" 
      TCGA-AF-4110       TCGA-AF-5654       TCGA-AF-6136       TCGA-AF-6655 
"OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" 
      TCGA-AF-6672       TCGA-AH-6544       TCGA-AH-6547       TCGA-AH-6549 
"OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" 
      TCGA-AH-6643       TCGA-AH-6644       TCGA-CI-6619       TCGA-CI-6620 
"OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" 
      TCGA-CI-6621       TCGA-CI-6622       TCGA-CI-6624       TCGA-CL-5917 
"OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" 
      TCGA-CL-5918       TCGA-DC-5337       TCGA-DC-5869       TCGA-DC-6155 
"OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" 
      TCGA-DC-6157       TCGA-DC-6158       TCGA-DC-6160       TCGA-DC-6681 
"OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" 
      TCGA-DC-6682       TCGA-DC-6683       TCGA-DT-5265       TCGA-DY-A0XA 
"OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" 
      TCGA-DY-A1DC       TCGA-DY-A1DD       TCGA-DY-A1DF       TCGA-DY-A1DG 
"OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" 
      TCGA-DY-A1H8       TCGA-EF-5830       TCGA-EI-6506       TCGA-EI-6507 
"OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" 
      TCGA-EI-6508       TCGA-EI-6510       TCGA-F5-6464       TCGA-F5-6465 
"OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" 
      TCGA-F5-6571       TCGA-F5-6702       TCGA-F5-6811       TCGA-F5-6812 
"OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" 
      TCGA-F5-6813       TCGA-G5-6235       TCGA-G5-6641 
"OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" "OR2AE1 WILD-TYPE" 

Clustering(1465) Variable = SMAP1 MUTATION ANALYSIS
D1465V1, survival
                 sevent
clus2               0   1
  SMAP1 MUTATED     2   1
  SMAP1 WILD-TYPE 376  92
  SMAP1 MUTATED SMAP1 WILD-TYPE 
              3             468 
  SMAP1 MUTATED SMAP1 WILD-TYPE 
              1              92 
$`SMAP1 MUTATED`
TCGA-AA-3663 TCGA-AA-3715 TCGA-AG-A002 
        6.97        19.04        20.98 

$`SMAP1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.05        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 
       36.00         5.03        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  SMAP1 MUTATED SMAP1 WILD-TYPE 
           6.97            0.00 
  SMAP1 MUTATED SMAP1 WILD-TYPE 
          20.98          148.01 
  SMAP1 MUTATED SMAP1 WILD-TYPE 
         19.040          20.235 
[1] "7.0 - 21.0 (19.0)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "2.8"
D1465V2, continuous
D1465V3, binary
                 cls
clus                0   1
  SMAP1 MUTATED     2   1
  SMAP1 WILD-TYPE 364 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAP1 MUTATED      2    1
  SMAP1 WILD-TYPE  364  118
        clus
vv       SMAP1 MUTATED SMAP1 WILD-TYPE
  COLON              2             364
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SMAP1 MUTATED         1        0        2         0         0         0
  SMAP1 WILD-TYPE      90        1       30       138        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SMAP1 MUTATED           0          0          0          0        0         0
  SMAP1 WILD-TYPE        24         11         59         42       48        18
                 vv
clus              STAGE IVB
  SMAP1 MUTATED           0
  SMAP1 WILD-TYPE         1
D1465V4, multiclass
            clus
vv           SMAP1 MUTATED SMAP1 WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA              0             138
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  SMAP1 MUTATED     0   1   2   0
  SMAP1 WILD-TYPE  17  91 327  50
D1465V5, multiclass
    clus
vv   SMAP1 MUTATED SMAP1 WILD-TYPE
  T1             0              17
  T2             1              91
  T3             2             327
  T4             0              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  SMAP1 MUTATED     3   0   0
  SMAP1 WILD-TYPE 284 113  87
D1465V6, multiclass
    clus
vv   SMAP1 MUTATED SMAP1 WILD-TYPE
  N0             3             284
  N1             0             113
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1465V7, binary
                 cls
clus                0   1
  SMAP1 MUTATED     3   0
  SMAP1 WILD-TYPE 372  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAP1 MUTATED      3    0
  SMAP1 WILD-TYPE  372   65
   clus
vv  SMAP1 MUTATED SMAP1 WILD-TYPE
  0             3             372
  1             0              65
[1] 2 2
[1] FALSE
D1465V8, binary
                 cls
clus                0   1
  SMAP1 MUTATED     0   3
  SMAP1 WILD-TYPE 225 261
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAP1 MUTATED      0    3
  SMAP1 WILD-TYPE  225  261
        clus
vv       SMAP1 MUTATED SMAP1 WILD-TYPE
  FEMALE             0             225
  MALE               3             261
[1] 2 2
[1] FALSE
D1465V9, binary
                 cls
clus                0   1
  SMAP1 MUTATED     3   0
  SMAP1 WILD-TYPE 347  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAP1 MUTATED      3    0
  SMAP1 WILD-TYPE  347   22
     clus
vv    SMAP1 MUTATED SMAP1 WILD-TYPE
  NO              3             347
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SMAP1 MUTATED                      2                             0
  SMAP1 WILD-TYPE                  313                            47
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SMAP1 MUTATED                       1                              0
  SMAP1 WILD-TYPE                   105                             10
D1465V10, multiclass
                                clus
vv                               SMAP1 MUTATED SMAP1 WILD-TYPE
  COLON ADENOCARCINOMA                       2             313
  COLON MUCINOUS ADENOCARCINOMA              0              47
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  SMAP1 MUTATED     3   0   0   0
  SMAP1 WILD-TYPE 342   4  31  25
D1465V11, multiclass
    clus
vv   SMAP1 MUTATED SMAP1 WILD-TYPE
  R0             3             342
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1465V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SMAP1 MUTATED                                  0     0
  SMAP1 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  SMAP1 MUTATED                           0     0
  SMAP1 WILD-TYPE                        22   226
D1465V13, multiclass

Clustering(1466) Variable = GON4L MUTATION ANALYSIS
D1466V1, survival
                 sevent
clus2               0   1
  GON4L MUTATED    20   2
  GON4L WILD-TYPE 358  91
  GON4L MUTATED GON4L WILD-TYPE 
             22             449 
  GON4L MUTATED GON4L WILD-TYPE 
              2              91 
$`GON4L MUTATED`
TCGA-A6-3809 TCGA-A6-5665 TCGA-A6-6651 TCGA-A6-6780 TCGA-AA-3510 TCGA-AA-3845 
       32.75        22.06        21.76        20.12        63.98         0.00 
TCGA-AA-3877 TCGA-AA-A010 TCGA-AA-A01Q TCGA-AD-6889 TCGA-AZ-5407 TCGA-AZ-6598 
       31.00        34.98         1.02        56.55        88.21        49.41 
TCGA-CA-6717 TCGA-CM-5341 TCGA-D5-6928 TCGA-DM-A1HA TCGA-G4-6323 TCGA-G4-6586 
       12.76        29.06        11.64       131.51        13.78        35.80 
TCGA-G4-6628 TCGA-AG-A002 TCGA-EI-6507 TCGA-G5-6641 
       79.69        20.98        19.96        26.43 

$`GON4L WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 
       24.16        24.69        24.39        23.87        19.66        20.28 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 
        7.04         3.02         1.02        35.01         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
       13.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       36.03         8.05        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       78.08         6.05         6.97        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
       14.93        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        31.00        38.07        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 
       18.05        40.96         0.07        21.37        15.52         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       62.79         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07        12.20        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       37.02        25.02        13.02        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A282 
       12.59       140.38         7.50        44.32       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 
       36.00        22.09        26.17        91.79        46.75        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       20.55        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       28.57        32.19         0.66         0.69        55.76 

  GON4L MUTATED GON4L WILD-TYPE 
              0               0 
  GON4L MUTATED GON4L WILD-TYPE 
         131.51          148.01 
  GON4L MUTATED GON4L WILD-TYPE 
         27.745          19.990 
[1] "0.0 - 131.5 (27.7)" "0.0 - 148.0 (20.0)"
[1] "hr=" "3"  
D1466V2, continuous
D1466V3, binary
                 cls
clus                0   1
  GON4L MUTATED    20   3
  GON4L WILD-TYPE 346 116
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GON4L MUTATED     20    3
  GON4L WILD-TYPE  346  116
        clus
vv       GON4L MUTATED GON4L WILD-TYPE
  COLON             20             346
  RECTUM             3             116
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GON4L MUTATED         4        1        3         9         2         0
  GON4L WILD-TYPE      87        0       29       129         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  GON4L MUTATED           0          2          1          1        0         0
  GON4L WILD-TYPE        24          9         58         41       48        18
                 vv
clus              STAGE IVB
  GON4L MUTATED           0
  GON4L WILD-TYPE         1
D1466V4, multiclass
            clus
vv           GON4L MUTATED GON4L WILD-TYPE
  STAGE I                4              87
  STAGE IA               1               0
  STAGE II               3              29
  STAGE IIA              9             129
  STAGE IIB              2               8
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             2               9
  STAGE IIIB             1              58
  STAGE IIIC             1              41
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  GON4L MUTATED     3   3  14   2
  GON4L WILD-TYPE  14  89 315  48
D1466V5, multiclass
    clus
vv   GON4L MUTATED GON4L WILD-TYPE
  T1             3              14
  T2             3              89
  T3            14             315
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  GON4L MUTATED    19   3   1
  GON4L WILD-TYPE 268 110  86
D1466V6, multiclass
    clus
vv   GON4L MUTATED GON4L WILD-TYPE
  N0            19             268
  N1             3             110
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1466V7, binary
                 cls
clus                0   1
  GON4L MUTATED    18   0
  GON4L WILD-TYPE 357  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GON4L MUTATED     18    0
  GON4L WILD-TYPE  357   65
   clus
vv  GON4L MUTATED GON4L WILD-TYPE
  0            18             357
  1             0              65
[1] 2 2
[1] FALSE
D1466V8, binary
                 cls
clus                0   1
  GON4L MUTATED    12  11
  GON4L WILD-TYPE 213 253
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GON4L MUTATED     12   11
  GON4L WILD-TYPE  213  253
        clus
vv       GON4L MUTATED GON4L WILD-TYPE
  FEMALE            12             213
  MALE              11             253
[1] 2 2
[1] FALSE
D1466V9, binary
                 cls
clus                0   1
  GON4L MUTATED    18   0
  GON4L WILD-TYPE 332  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GON4L MUTATED     18    0
  GON4L WILD-TYPE  332   22
     clus
vv    GON4L MUTATED GON4L WILD-TYPE
  NO             18             332
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  GON4L MUTATED                     15                             5
  GON4L WILD-TYPE                  300                            42
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  GON4L MUTATED                       2                              1
  GON4L WILD-TYPE                   104                              9
D1466V10, multiclass
                                clus
vv                               GON4L MUTATED GON4L WILD-TYPE
  COLON ADENOCARCINOMA                      15             300
  COLON MUCINOUS ADENOCARCINOMA              5              42
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             1               9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  GON4L MUTATED    16   0   0   1
  GON4L WILD-TYPE 329   4  31  24
D1466V11, multiclass
    clus
vv   GON4L MUTATED GON4L WILD-TYPE
  R0            16             329
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1466V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GON4L MUTATED                                  0     2
  GON4L WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  GON4L MUTATED                           1    13
  GON4L WILD-TYPE                        21   213
D1466V13, multiclass
                                  clus
vv                                 GON4L MUTATED GON4L WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               9
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                       13             213
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1467) Variable = NDST3 MUTATION ANALYSIS
D1467V1, survival
                 sevent
clus2               0   1
  NDST3 MUTATED    15   3
  NDST3 WILD-TYPE 363  90
  NDST3 MUTATED NDST3 WILD-TYPE 
             18             453 
  NDST3 MUTATED NDST3 WILD-TYPE 
              3              90 
$`NDST3 MUTATED`
TCGA-A6-2677 TCGA-A6-6141 TCGA-AA-3510 TCGA-AA-3833 TCGA-AA-3977 TCGA-AA-A00E 
       24.33         8.38        63.98        15.95        25.02        30.02 
TCGA-AA-A00J TCGA-AA-A010 TCGA-AZ-4315 TCGA-AZ-6601 TCGA-CA-6717 TCGA-D5-5541 
       18.05        34.98        58.39       100.01        12.76        55.92 
TCGA-D5-6927 TCGA-F4-6570 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-4008 TCGA-EF-5830 
        9.44         6.18        17.03        13.02        17.03         0.49 

$`NDST3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        42.90        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 
       22.06        32.71        27.09        22.52        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3837 
       33.04         0.99        25.02         1.02        17.98        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00K 
       27.02        13.94        38.04        19.00        34.03        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       33.01        21.44        17.82         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07        12.20        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       19.59        56.09        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.04        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       35.74        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3893 
       19.04        19.99         1.02        17.95        36.95        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       51.48        32.61        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  NDST3 MUTATED NDST3 WILD-TYPE 
           0.49            0.00 
  NDST3 MUTATED NDST3 WILD-TYPE 
         100.01          148.01 
  NDST3 MUTATED NDST3 WILD-TYPE 
          17.54           20.28 
[1] "0.5 - 100.0 (17.5)" "0.0 - 148.0 (20.3)"
[1] "hr=" "1.4"
D1467V2, continuous
D1467V3, binary
                 cls
clus                0   1
  NDST3 MUTATED    14   4
  NDST3 WILD-TYPE 352 115
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NDST3 MUTATED     14    4
  NDST3 WILD-TYPE  352  115
        clus
vv       NDST3 MUTATED NDST3 WILD-TYPE
  COLON             14             352
  RECTUM             4             115
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NDST3 MUTATED         2        0        2         8         2         0
  NDST3 WILD-TYPE      89        1       30       130         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NDST3 MUTATED           0          0          2          1        0         0
  NDST3 WILD-TYPE        24         11         57         41       48        18
                 vv
clus              STAGE IVB
  NDST3 MUTATED           0
  NDST3 WILD-TYPE         1
D1467V4, multiclass
            clus
vv           NDST3 MUTATED NDST3 WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA              8             130
  STAGE IIB              2               8
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             2              57
  STAGE IIIC             1              41
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  NDST3 MUTATED     1   2  12   3
  NDST3 WILD-TYPE  16  90 317  47
D1467V5, multiclass
    clus
vv   NDST3 MUTATED NDST3 WILD-TYPE
  T1             1              16
  T2             2              90
  T3            12             317
  T4             3              47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  NDST3 MUTATED    15   2   1
  NDST3 WILD-TYPE 272 111  86
D1467V6, multiclass
    clus
vv   NDST3 MUTATED NDST3 WILD-TYPE
  N0            15             272
  N1             2             111
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1467V7, binary
                 cls
clus                0   1
  NDST3 MUTATED    17   0
  NDST3 WILD-TYPE 358  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NDST3 MUTATED     17    0
  NDST3 WILD-TYPE  358   65
   clus
vv  NDST3 MUTATED NDST3 WILD-TYPE
  0            17             358
  1             0              65
[1] 2 2
[1] FALSE
D1467V8, binary
                 cls
clus                0   1
  NDST3 MUTATED     5  13
  NDST3 WILD-TYPE 220 251
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NDST3 MUTATED      5   13
  NDST3 WILD-TYPE  220  251
        clus
vv       NDST3 MUTATED NDST3 WILD-TYPE
  FEMALE             5             220
  MALE              13             251
[1] 2 2
[1] FALSE
D1467V9, binary
                 cls
clus                0   1
  NDST3 MUTATED    17   0
  NDST3 WILD-TYPE 333  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NDST3 MUTATED     17    0
  NDST3 WILD-TYPE  333   22
     clus
vv    NDST3 MUTATED NDST3 WILD-TYPE
  NO             17             333
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  NDST3 MUTATED                     12                             2
  NDST3 WILD-TYPE                  303                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  NDST3 MUTATED                       4                              0
  NDST3 WILD-TYPE                   102                             10
D1467V10, multiclass
                                clus
vv                               NDST3 MUTATED NDST3 WILD-TYPE
  COLON ADENOCARCINOMA                      12             303
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      4             102
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  NDST3 MUTATED    14   0   0   1
  NDST3 WILD-TYPE 331   4  31  24
D1467V11, multiclass
    clus
vv   NDST3 MUTATED NDST3 WILD-TYPE
  R0            14             331
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1467V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NDST3 MUTATED                                  0     1
  NDST3 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  NDST3 MUTATED                           1     7
  NDST3 WILD-TYPE                        21   219
D1467V13, multiclass
                                  clus
vv                                 NDST3 MUTATED NDST3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        7             219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1468) Variable = MAGEA4 MUTATION ANALYSIS
D1468V1, survival
                  sevent
clus2                0   1
  MAGEA4 MUTATED     3   3
  MAGEA4 WILD-TYPE 375  90
  MAGEA4 MUTATED MAGEA4 WILD-TYPE 
               6              465 
  MAGEA4 MUTATED MAGEA4 WILD-TYPE 
               3               90 
$`MAGEA4 MUTATED`
TCGA-AA-3496 TCGA-AZ-6598 TCGA-CA-6718 TCGA-F4-6459 TCGA-G4-6588 TCGA-AG-A002 
        1.02        49.41        10.06         8.61        26.17        20.98 

$`MAGEA4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 
        5.13       106.75        22.36        62.79        88.21         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.20        12.76        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
      117.07        98.24        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        35.80        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  MAGEA4 MUTATED MAGEA4 WILD-TYPE 
            1.02             0.00 
  MAGEA4 MUTATED MAGEA4 WILD-TYPE 
           49.41           148.01 
  MAGEA4 MUTATED MAGEA4 WILD-TYPE 
           15.52            20.19 
[1] "1.0 - 49.4 (15.5)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "3.3"
D1468V2, continuous
D1468V3, binary
                  cls
clus                 0   1
  MAGEA4 MUTATED     6   1
  MAGEA4 WILD-TYPE 360 118
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAGEA4 MUTATED      6    1
  MAGEA4 WILD-TYPE  360  118
        clus
vv       MAGEA4 MUTATED MAGEA4 WILD-TYPE
  COLON               6              360
  RECTUM              1              118
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MAGEA4 MUTATED         1        0        2         2         0         0
  MAGEA4 WILD-TYPE      90        1       30       136        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MAGEA4 MUTATED           0          0          1          0        1
  MAGEA4 WILD-TYPE        24         11         58         42       47
                  vv
clus               STAGE IVA STAGE IVB
  MAGEA4 MUTATED           0         0
  MAGEA4 WILD-TYPE        18         1
D1468V4, multiclass
            clus
vv           MAGEA4 MUTATED MAGEA4 WILD-TYPE
  STAGE I                 1               90
  STAGE IA                0                1
  STAGE II                2               30
  STAGE IIA               2              136
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              1               58
  STAGE IIIC              0               42
  STAGE IV                1               47
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  MAGEA4 MUTATED     0   1   6   0
  MAGEA4 WILD-TYPE  17  91 323  50
D1468V5, multiclass
    clus
vv   MAGEA4 MUTATED MAGEA4 WILD-TYPE
  T1              0               17
  T2              1               91
  T3              6              323
  T4              0               50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  MAGEA4 MUTATED     5   0   2
  MAGEA4 WILD-TYPE 282 113  85
D1468V6, multiclass
    clus
vv   MAGEA4 MUTATED MAGEA4 WILD-TYPE
  N0              5              282
  N1              0              113
  N2              2               85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1468V7, binary
                  cls
clus                 0   1
  MAGEA4 MUTATED     5   1
  MAGEA4 WILD-TYPE 370  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAGEA4 MUTATED      5    1
  MAGEA4 WILD-TYPE  370   64
   clus
vv  MAGEA4 MUTATED MAGEA4 WILD-TYPE
  0              5              370
  1              1               64
[1] 2 2
[1] FALSE
D1468V8, binary
                  cls
clus                 0   1
  MAGEA4 MUTATED     5   2
  MAGEA4 WILD-TYPE 220 262
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAGEA4 MUTATED      5    2
  MAGEA4 WILD-TYPE  220  262
        clus
vv       MAGEA4 MUTATED MAGEA4 WILD-TYPE
  FEMALE              5              220
  MALE                2              262
[1] 2 2
[1] FALSE
D1468V9, binary
                  cls
clus                 0   1
  MAGEA4 MUTATED     5   0
  MAGEA4 WILD-TYPE 345  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAGEA4 MUTATED      5    0
  MAGEA4 WILD-TYPE  345   22
     clus
vv    MAGEA4 MUTATED MAGEA4 WILD-TYPE
  NO               5              345
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MAGEA4 MUTATED                      6                             0
  MAGEA4 WILD-TYPE                  309                            47
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MAGEA4 MUTATED                       1                              0
  MAGEA4 WILD-TYPE                   105                             10
D1468V10, multiclass
                                clus
vv                               MAGEA4 MUTATED MAGEA4 WILD-TYPE
  COLON ADENOCARCINOMA                        6              309
  COLON MUCINOUS ADENOCARCINOMA               0               47
  RECTAL ADENOCARCINOMA                       1              105
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  MAGEA4 MUTATED     4   0   1   1
  MAGEA4 WILD-TYPE 341   4  30  24
D1468V11, multiclass
    clus
vv   MAGEA4 MUTATED MAGEA4 WILD-TYPE
  R0              4              341
  R1              0                4
  R2              1               30
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1468V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MAGEA4 MUTATED                                  0     1
  MAGEA4 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  MAGEA4 MUTATED                           0     3
  MAGEA4 WILD-TYPE                        22   223
D1468V13, multiclass
                                  clus
vv                                 MAGEA4 MUTATED MAGEA4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         3              223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1469) Variable = RPS6KA5 MUTATION ANALYSIS
D1469V1, survival
                   sevent
clus2                 0   1
  RPS6KA5 MUTATED     7   4
  RPS6KA5 WILD-TYPE 371  89
  RPS6KA5 MUTATED RPS6KA5 WILD-TYPE 
               11               460 
  RPS6KA5 MUTATED RPS6KA5 WILD-TYPE 
                4                89 
$`RPS6KA5 MUTATED`
TCGA-AA-3715 TCGA-AA-3950 TCGA-AA-A00N TCGA-AA-A01Q TCGA-AY-5543 TCGA-AZ-4315 
       19.04        24.00         4.01         1.02        33.01        58.39 
TCGA-AZ-6598 TCGA-CA-6717 TCGA-CM-6171 TCGA-DM-A1D4 TCGA-AG-A002 
       49.41        12.76        14.04        92.75        20.98 

$`RPS6KA5 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 
        2.01        12.99        24.00        33.01        26.01         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       31.00        38.07        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6197 TCGA-AY-6386 
       14.50        27.09        16.31         0.95        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07        12.20        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 
       14.99        12.99        13.02        15.02        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       24.43        38.20       130.65        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  RPS6KA5 MUTATED RPS6KA5 WILD-TYPE 
             1.02              0.00 
  RPS6KA5 MUTATED RPS6KA5 WILD-TYPE 
            92.75            148.01 
  RPS6KA5 MUTATED RPS6KA5 WILD-TYPE 
           20.980            20.155 
[1] "1.0 - 92.8 (21.0)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.6"
D1469V2, continuous
D1469V3, binary
                   cls
clus                  0   1
  RPS6KA5 MUTATED    10   1
  RPS6KA5 WILD-TYPE 356 118
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RPS6KA5 MUTATED     10    1
  RPS6KA5 WILD-TYPE  356  118
        clus
vv       RPS6KA5 MUTATED RPS6KA5 WILD-TYPE
  COLON               10               356
  RECTUM               1               118
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RPS6KA5 MUTATED         2        0        3         4         1         0
  RPS6KA5 WILD-TYPE      89        1       29       134         9         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RPS6KA5 MUTATED           0          0          0          0        0
  RPS6KA5 WILD-TYPE        24         11         59         42       48
                   vv
clus                STAGE IVA STAGE IVB
  RPS6KA5 MUTATED           1         0
  RPS6KA5 WILD-TYPE        17         1
D1469V4, multiclass
            clus
vv           RPS6KA5 MUTATED RPS6KA5 WILD-TYPE
  STAGE I                  2                89
  STAGE IA                 0                 1
  STAGE II                 3                29
  STAGE IIA                4               134
  STAGE IIB                1                 9
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               0                11
  STAGE IIIB               0                59
  STAGE IIIC               0                42
  STAGE IV                 0                48
  STAGE IVA                1                17
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  RPS6KA5 MUTATED     0   2   8   1
  RPS6KA5 WILD-TYPE  17  90 321  49
D1469V5, multiclass
    clus
vv   RPS6KA5 MUTATED RPS6KA5 WILD-TYPE
  T1               0                17
  T2               2                90
  T3               8               321
  T4               1                49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  RPS6KA5 MUTATED    10   1   0
  RPS6KA5 WILD-TYPE 277 112  87
D1469V6, multiclass
    clus
vv   RPS6KA5 MUTATED RPS6KA5 WILD-TYPE
  N0              10               277
  N1               1               112
  N2               0                87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1469V7, binary
                   cls
clus                  0   1
  RPS6KA5 MUTATED     9   1
  RPS6KA5 WILD-TYPE 366  64
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RPS6KA5 MUTATED      9    1
  RPS6KA5 WILD-TYPE  366   64
   clus
vv  RPS6KA5 MUTATED RPS6KA5 WILD-TYPE
  0               9               366
  1               1                64
[1] 2 2
[1] FALSE
D1469V8, binary
                   cls
clus                  0   1
  RPS6KA5 MUTATED     5   6
  RPS6KA5 WILD-TYPE 220 258
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RPS6KA5 MUTATED      5    6
  RPS6KA5 WILD-TYPE  220  258
        clus
vv       RPS6KA5 MUTATED RPS6KA5 WILD-TYPE
  FEMALE               5               220
  MALE                 6               258
[1] 2 2
[1] FALSE
D1469V9, binary
                   cls
clus                  0   1
  RPS6KA5 MUTATED     8   0
  RPS6KA5 WILD-TYPE 342  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RPS6KA5 MUTATED      8    0
  RPS6KA5 WILD-TYPE  342   22
     clus
vv    RPS6KA5 MUTATED RPS6KA5 WILD-TYPE
  NO                8               342
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  RPS6KA5 MUTATED                      7                             3
  RPS6KA5 WILD-TYPE                  308                            44
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  RPS6KA5 MUTATED                       1                              0
  RPS6KA5 WILD-TYPE                   105                             10
D1469V10, multiclass
                                clus
vv                               RPS6KA5 MUTATED RPS6KA5 WILD-TYPE
  COLON ADENOCARCINOMA                         7               308
  COLON MUCINOUS ADENOCARCINOMA                3                44
  RECTAL ADENOCARCINOMA                        1               105
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  RPS6KA5 MUTATED     8   0   0   1
  RPS6KA5 WILD-TYPE 337   4  31  24
D1469V11, multiclass
    clus
vv   RPS6KA5 MUTATED RPS6KA5 WILD-TYPE
  R0               8               337
  R1               0                 4
  R2               0                31
  RX               1                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1469V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RPS6KA5 MUTATED                                  0     1
  RPS6KA5 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  RPS6KA5 MUTATED                           1     4
  RPS6KA5 WILD-TYPE                        21   222
D1469V13, multiclass
                                  clus
vv                                 RPS6KA5 MUTATED RPS6KA5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                10
  BLACK OR AFRICAN AMERICAN                      1                21
  WHITE                                          4               222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1470) Variable = KLHL34 MUTATION ANALYSIS
D1470V1, survival
                  sevent
clus2                0   1
  KLHL34 MUTATED    11   2
  KLHL34 WILD-TYPE 367  91
  KLHL34 MUTATED KLHL34 WILD-TYPE 
              13              458 
  KLHL34 MUTATED KLHL34 WILD-TYPE 
               2               91 
$`KLHL34 MUTATED`
TCGA-A6-5665 TCGA-AU-6004 TCGA-AZ-6598 TCGA-CK-4952 TCGA-CK-5913 TCGA-CM-6171 
       22.06        27.09        49.41        15.62        51.32        14.04 
TCGA-D5-6533 TCGA-D5-6927 TCGA-DM-A1DA TCGA-DM-A1HB TCGA-G4-6586 TCGA-AG-3727 
        1.32         9.44         7.50       135.65        35.80         0.99 
TCGA-CL-5917 
       78.12 

$`KLHL34 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 
       27.42        10.88         0.20        14.50        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 
      106.75        22.36        62.79        88.21         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       49.08         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       15.02        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 
       56.09        55.92        20.19        18.25        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 
       13.32        12.59       140.38        44.32       131.51       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3731 TCGA-AG-3732 
       19.99        13.94        19.99         7.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
        4.73         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  KLHL34 MUTATED KLHL34 WILD-TYPE 
            0.99             0.00 
  KLHL34 MUTATED KLHL34 WILD-TYPE 
          135.65           148.01 
  KLHL34 MUTATED KLHL34 WILD-TYPE 
          22.060           20.155 
[1] "1.0 - 135.7 (22.1)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.6"
D1470V2, continuous
D1470V3, binary
                  cls
clus                 0   1
  KLHL34 MUTATED    11   2
  KLHL34 WILD-TYPE 355 117
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KLHL34 MUTATED     11    2
  KLHL34 WILD-TYPE  355  117
        clus
vv       KLHL34 MUTATED KLHL34 WILD-TYPE
  COLON              11              355
  RECTUM              2              117
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KLHL34 MUTATED         2        0        1         4         0         0
  KLHL34 WILD-TYPE      89        1       31       134        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KLHL34 MUTATED           1          0          2          3        0
  KLHL34 WILD-TYPE        23         11         57         39       48
                  vv
clus               STAGE IVA STAGE IVB
  KLHL34 MUTATED           0         0
  KLHL34 WILD-TYPE        18         1
D1470V4, multiclass
            clus
vv           KLHL34 MUTATED KLHL34 WILD-TYPE
  STAGE I                 2               89
  STAGE IA                0                1
  STAGE II                1               31
  STAGE IIA               4              134
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               1               23
  STAGE IIIA              0               11
  STAGE IIIB              2               57
  STAGE IIIC              3               39
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  KLHL34 MUTATED     0   2   9   2
  KLHL34 WILD-TYPE  17  90 320  48
D1470V5, multiclass
    clus
vv   KLHL34 MUTATED KLHL34 WILD-TYPE
  T1              0               17
  T2              2               90
  T3              9              320
  T4              2               48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  KLHL34 MUTATED     8   2   3
  KLHL34 WILD-TYPE 279 111  84
D1470V6, multiclass
    clus
vv   KLHL34 MUTATED KLHL34 WILD-TYPE
  N0              8              279
  N1              2              111
  N2              3               84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1470V7, binary
                  cls
clus                 0   1
  KLHL34 MUTATED    10   0
  KLHL34 WILD-TYPE 365  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KLHL34 MUTATED     10    0
  KLHL34 WILD-TYPE  365   65
   clus
vv  KLHL34 MUTATED KLHL34 WILD-TYPE
  0             10              365
  1              0               65
[1] 2 2
[1] FALSE
D1470V8, binary
                  cls
clus                 0   1
  KLHL34 MUTATED    11   2
  KLHL34 WILD-TYPE 214 262
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KLHL34 MUTATED     11    2
  KLHL34 WILD-TYPE  214  262
        clus
vv       KLHL34 MUTATED KLHL34 WILD-TYPE
  FEMALE             11              214
  MALE                2              262
[1] 2 2
[1] FALSE
D1470V9, binary
                  cls
clus                 0   1
  KLHL34 MUTATED     7   0
  KLHL34 WILD-TYPE 343  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KLHL34 MUTATED      7    0
  KLHL34 WILD-TYPE  343   22
     clus
vv    KLHL34 MUTATED KLHL34 WILD-TYPE
  NO               7              343
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  KLHL34 MUTATED                      9                             1
  KLHL34 WILD-TYPE                  306                            46
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  KLHL34 MUTATED                       2                              0
  KLHL34 WILD-TYPE                   104                             10
D1470V10, multiclass
                                clus
vv                               KLHL34 MUTATED KLHL34 WILD-TYPE
  COLON ADENOCARCINOMA                        9              306
  COLON MUCINOUS ADENOCARCINOMA               1               46
  RECTAL ADENOCARCINOMA                       2              104
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  KLHL34 MUTATED     7   0   0   3
  KLHL34 WILD-TYPE 338   4  31  22
D1470V11, multiclass
    clus
vv   KLHL34 MUTATED KLHL34 WILD-TYPE
  R0              7              338
  R1              0                4
  R2              0               31
  RX              3               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1470V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KLHL34 MUTATED                                  0     0
  KLHL34 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  KLHL34 MUTATED                           0    12
  KLHL34 WILD-TYPE                        22   214
D1470V13, multiclass
                                  clus
vv                                 KLHL34 MUTATED KLHL34 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                        12              214
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1471) Variable = EIF2AK3 MUTATION ANALYSIS
D1471V1, survival
                   sevent
clus2                 0   1
  EIF2AK3 MUTATED     8   4
  EIF2AK3 WILD-TYPE 370  89
  EIF2AK3 MUTATED EIF2AK3 WILD-TYPE 
               12               459 
  EIF2AK3 MUTATED EIF2AK3 WILD-TYPE 
                4                89 
$`EIF2AK3 MUTATED`
TCGA-A6-6141 TCGA-AA-3966 TCGA-AD-6899 TCGA-AZ-4323 TCGA-AZ-4681 TCGA-CA-6717 
        8.38         2.01         5.79         1.41       106.75        12.76 
TCGA-CM-5862 TCGA-CM-6162 TCGA-CM-6674 TCGA-F4-6570 TCGA-F4-6856 TCGA-AG-A002 
        5.03        12.00        12.95         6.18        35.31        20.98 

$`EIF2AK3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 
       22.09        22.06        32.71        27.09        22.52        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
        2.01        20.98        34.03        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
       56.55         0.79         0.72        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5403 
       21.44        17.82        58.39         5.13        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07        12.20        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5864 
       22.98        30.08        32.02        15.02        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       17.03        15.02         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 
      117.07        98.24         8.61        31.96        35.74        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
        0.53        47.41       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  EIF2AK3 MUTATED EIF2AK3 WILD-TYPE 
             1.41              0.00 
  EIF2AK3 MUTATED EIF2AK3 WILD-TYPE 
           106.75            148.01 
  EIF2AK3 MUTATED EIF2AK3 WILD-TYPE 
            10.19             20.91 
[1] "1.4 - 106.8 (10.2)" "0.0 - 148.0 (20.9)"
[1] "hr=" "2.4"
D1471V2, continuous
D1471V3, binary
                   cls
clus                  0   1
  EIF2AK3 MUTATED    11   1
  EIF2AK3 WILD-TYPE 355 118
[1] "tbl2"
                   cls
clus                [,1] [,2]
  EIF2AK3 MUTATED     11    1
  EIF2AK3 WILD-TYPE  355  118
        clus
vv       EIF2AK3 MUTATED EIF2AK3 WILD-TYPE
  COLON               11               355
  RECTUM               1               118
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  EIF2AK3 MUTATED         2        0        0         6         0         0
  EIF2AK3 WILD-TYPE      89        1       32       132        10         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  EIF2AK3 MUTATED           0          0          1          1        1
  EIF2AK3 WILD-TYPE        24         11         58         41       47
                   vv
clus                STAGE IVA STAGE IVB
  EIF2AK3 MUTATED           1         0
  EIF2AK3 WILD-TYPE        17         1
D1471V4, multiclass
            clus
vv           EIF2AK3 MUTATED EIF2AK3 WILD-TYPE
  STAGE I                  2                89
  STAGE IA                 0                 1
  STAGE II                 0                32
  STAGE IIA                6               132
  STAGE IIB                0                10
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               0                11
  STAGE IIIB               1                58
  STAGE IIIC               1                41
  STAGE IV                 1                47
  STAGE IVA                1                17
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  EIF2AK3 MUTATED     0   2   8   2
  EIF2AK3 WILD-TYPE  17  90 321  48
D1471V5, multiclass
    clus
vv   EIF2AK3 MUTATED EIF2AK3 WILD-TYPE
  T1               0                17
  T2               2                90
  T3               8               321
  T4               2                48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  EIF2AK3 MUTATED     8   2   2
  EIF2AK3 WILD-TYPE 279 111  85
D1471V6, multiclass
    clus
vv   EIF2AK3 MUTATED EIF2AK3 WILD-TYPE
  N0               8               279
  N1               2               111
  N2               2                85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1471V7, binary
                   cls
clus                  0   1
  EIF2AK3 MUTATED     9   2
  EIF2AK3 WILD-TYPE 366  63
[1] "tbl2"
                   cls
clus                [,1] [,2]
  EIF2AK3 MUTATED      9    2
  EIF2AK3 WILD-TYPE  366   63
   clus
vv  EIF2AK3 MUTATED EIF2AK3 WILD-TYPE
  0               9               366
  1               2                63
[1] 2 2
[1] FALSE
D1471V8, binary
                   cls
clus                  0   1
  EIF2AK3 MUTATED     4   8
  EIF2AK3 WILD-TYPE 221 256
[1] "tbl2"
                   cls
clus                [,1] [,2]
  EIF2AK3 MUTATED      4    8
  EIF2AK3 WILD-TYPE  221  256
        clus
vv       EIF2AK3 MUTATED EIF2AK3 WILD-TYPE
  FEMALE               4               221
  MALE                 8               256
[1] 2 2
[1] FALSE
D1471V9, binary
                   cls
clus                  0   1
  EIF2AK3 MUTATED    11   0
  EIF2AK3 WILD-TYPE 339  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  EIF2AK3 MUTATED     11    0
  EIF2AK3 WILD-TYPE  339   22
     clus
vv    EIF2AK3 MUTATED EIF2AK3 WILD-TYPE
  NO               11               339
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  EIF2AK3 MUTATED                      6                             5
  EIF2AK3 WILD-TYPE                  309                            42
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  EIF2AK3 MUTATED                       1                              0
  EIF2AK3 WILD-TYPE                   105                             10
D1471V10, multiclass
                                clus
vv                               EIF2AK3 MUTATED EIF2AK3 WILD-TYPE
  COLON ADENOCARCINOMA                         6               309
  COLON MUCINOUS ADENOCARCINOMA                5                42
  RECTAL ADENOCARCINOMA                        1               105
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  EIF2AK3 MUTATED     7   0   0   1
  EIF2AK3 WILD-TYPE 338   4  31  24
D1471V11, multiclass
    clus
vv   EIF2AK3 MUTATED EIF2AK3 WILD-TYPE
  R0               7               338
  R1               0                 4
  R2               0                31
  RX               1                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1471V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  EIF2AK3 MUTATED                                  0     1
  EIF2AK3 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  EIF2AK3 MUTATED                           1     8
  EIF2AK3 WILD-TYPE                        21   218
D1471V13, multiclass
                                  clus
vv                                 EIF2AK3 MUTATED EIF2AK3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                10
  BLACK OR AFRICAN AMERICAN                      1                21
  WHITE                                          8               218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1472) Variable = CDC73 MUTATION ANALYSIS
D1472V1, survival
                 sevent
clus2               0   1
  CDC73 MUTATED    17   4
  CDC73 WILD-TYPE 361  89
  CDC73 MUTATED CDC73 WILD-TYPE 
             21             450 
  CDC73 MUTATED CDC73 WILD-TYPE 
              4              89 
$`CDC73 MUTATED`
TCGA-A6-2683 TCGA-A6-3809 TCGA-A6-5660 TCGA-AA-3662 TCGA-AA-3681 TCGA-AA-3815 
       16.57        32.75        29.19         6.05         5.98        33.04 
TCGA-AA-3949 TCGA-AA-A00N TCGA-AA-A01Q TCGA-AZ-4315 TCGA-AZ-5407 TCGA-CM-4752 
       26.01         4.01         1.02        58.39        88.21        13.02 
TCGA-CM-6677 TCGA-D5-6535 TCGA-D5-6930 TCGA-DM-A1D4 TCGA-DM-A1DA TCGA-F4-6569 
       11.08        15.12         1.51        92.75         7.50        35.74 
TCGA-AG-3892 TCGA-EI-6506 TCGA-F5-6812 
       13.02        20.55         0.66 

$`CDC73 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5657 
       34.65        33.34        36.53        14.53        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 
       30.44        33.53        23.61        22.09        22.06        32.71 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       27.09        22.52         8.38        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02        78.08         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
       19.04        19.04        10.06        35.05         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3950 
       31.00         2.01        12.99        24.00        33.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        31.00        38.07        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-5341 TCGA-CM-5344 
       23.05        20.02        37.02        25.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6678 
       14.04        11.01        12.95        13.05        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 
       55.92        20.19        18.25         1.32        43.27        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       11.64         4.80        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       24.43        38.20       130.65        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
      140.38        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
        8.61        31.96         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       36.95        17.03        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
        0.49        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       31.30        28.57        32.19         0.69        55.76        26.43 

  CDC73 MUTATED CDC73 WILD-TYPE 
           0.66            0.00 
  CDC73 MUTATED CDC73 WILD-TYPE 
          92.75          148.01 
  CDC73 MUTATED CDC73 WILD-TYPE 
         15.120          20.595 
[1] "0.7 - 92.8 (15.1)"  "0.0 - 148.0 (20.6)"
[1] "hr=" "1.1"
D1472V2, continuous
D1472V3, binary
                 cls
clus                0   1
  CDC73 MUTATED    19   3
  CDC73 WILD-TYPE 347 116
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDC73 MUTATED     19    3
  CDC73 WILD-TYPE  347  116
        clus
vv       CDC73 MUTATED CDC73 WILD-TYPE
  COLON             19             347
  RECTUM             3             116
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CDC73 MUTATED         3        0        1         8         2         0
  CDC73 WILD-TYPE      88        1       31       130         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CDC73 MUTATED           2          0          2          2        2         0
  CDC73 WILD-TYPE        22         11         57         40       46        18
                 vv
clus              STAGE IVB
  CDC73 MUTATED           0
  CDC73 WILD-TYPE         1
D1472V4, multiclass
            clus
vv           CDC73 MUTATED CDC73 WILD-TYPE
  STAGE I                3              88
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              8             130
  STAGE IIB              2               8
  STAGE IIC              0               1
  STAGE III              2              22
  STAGE IIIA             0              11
  STAGE IIIB             2              57
  STAGE IIIC             2              40
  STAGE IV               2              46
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CDC73 MUTATED     2   1  15   4
  CDC73 WILD-TYPE  15  91 314  46
D1472V5, multiclass
    clus
vv   CDC73 MUTATED CDC73 WILD-TYPE
  T1             2              15
  T2             1              91
  T3            15             314
  T4             4              46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  CDC73 MUTATED    15   3   4
  CDC73 WILD-TYPE 272 110  83
D1472V6, multiclass
    clus
vv   CDC73 MUTATED CDC73 WILD-TYPE
  N0            15             272
  N1             3             110
  N2             4              83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1472V7, binary
                 cls
clus                0   1
  CDC73 MUTATED    19   2
  CDC73 WILD-TYPE 356  63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDC73 MUTATED     19    2
  CDC73 WILD-TYPE  356   63
   clus
vv  CDC73 MUTATED CDC73 WILD-TYPE
  0            19             356
  1             2              63
[1] 2 2
[1] FALSE
D1472V8, binary
                 cls
clus                0   1
  CDC73 MUTATED    13   9
  CDC73 WILD-TYPE 212 255
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDC73 MUTATED     13    9
  CDC73 WILD-TYPE  212  255
        clus
vv       CDC73 MUTATED CDC73 WILD-TYPE
  FEMALE            13             212
  MALE               9             255
[1] 2 2
[1] FALSE
D1472V9, binary
                 cls
clus                0   1
  CDC73 MUTATED    15   0
  CDC73 WILD-TYPE 335  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDC73 MUTATED     15    0
  CDC73 WILD-TYPE  335   22
     clus
vv    CDC73 MUTATED CDC73 WILD-TYPE
  NO             15             335
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CDC73 MUTATED                     15                             4
  CDC73 WILD-TYPE                  300                            43
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CDC73 MUTATED                       3                              0
  CDC73 WILD-TYPE                   103                             10
D1472V10, multiclass
                                clus
vv                               CDC73 MUTATED CDC73 WILD-TYPE
  COLON ADENOCARCINOMA                      15             300
  COLON MUCINOUS ADENOCARCINOMA              4              43
  RECTAL ADENOCARCINOMA                      3             103
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  CDC73 MUTATED    16   0   1   1
  CDC73 WILD-TYPE 329   4  30  24
D1472V11, multiclass
    clus
vv   CDC73 MUTATED CDC73 WILD-TYPE
  R0            16             329
  R1             0               4
  R2             1              30
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1472V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CDC73 MUTATED                                  0     0
  CDC73 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CDC73 MUTATED                           2    12
  CDC73 WILD-TYPE                        20   214
D1472V13, multiclass
                                  clus
vv                                 CDC73 MUTATED CDC73 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    2              20
  WHITE                                       12             214
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1473) Variable = MYH15 MUTATION ANALYSIS
D1473V1, survival
                 sevent
clus2               0   1
  MYH15 MUTATED    24   4
  MYH15 WILD-TYPE 354  89
  MYH15 MUTATED MYH15 WILD-TYPE 
             28             443 
  MYH15 MUTATED MYH15 WILD-TYPE 
              4              89 
$`MYH15 MUTATED`
TCGA-A6-6138 TCGA-A6-6653 TCGA-A6-6654 TCGA-AA-3510 TCGA-AA-3662 TCGA-AA-3663 
       22.52        24.39        23.87        63.98         6.05         6.97 
TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3864 TCGA-AA-3950 TCGA-AA-A010 TCGA-AD-6890 
       26.99        19.04        53.00        24.00        34.98         0.79 
TCGA-AD-6964 TCGA-AZ-4315 TCGA-CA-6717 TCGA-CM-5861 TCGA-CM-6674 TCGA-D5-5541 
       10.88        58.39        12.76        15.02        12.95        55.92 
TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6930 TCGA-DM-A0XF TCGA-DM-A1D4 TCGA-G4-6628 
       18.25        43.27         1.51        38.20        92.75        79.69 
TCGA-AG-4001 TCGA-AG-A002 TCGA-CI-6619 TCGA-CI-6620 
       36.03        20.98         6.05        33.17 

$`MYH15 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6141 TCGA-A6-6142 
       22.09        22.06        32.71        27.09         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6780 TCGA-A6-6781 
       25.18        24.16        21.76        24.69        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 
       20.28         7.04         3.02         1.02        35.01         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
       61.02        78.08        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3811 
       19.00        36.00         5.03        85.05        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 
        0.99        31.07        31.07        30.05        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        33.01        26.01         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6895 TCGA-AD-6899 
        0.07        21.37        15.52        56.55         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        33.01        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.20        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6676 
       13.02        15.02        14.04        11.01        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6536 
       19.59        56.09        20.19         1.32        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       11.64         4.80        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
       24.43       130.65        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4007 
       48.03        32.02        19.99        28.04        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
        0.72         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  MYH15 MUTATED MYH15 WILD-TYPE 
           0.79            0.00 
  MYH15 MUTATED MYH15 WILD-TYPE 
          92.75          148.01 
  MYH15 MUTATED MYH15 WILD-TYPE 
         23.935          20.020 
[1] "0.8 - 92.8 (23.9)"  "0.0 - 148.0 (20.0)"
[1] "hr=" "1.7"
D1473V2, continuous
D1473V3, binary
                 cls
clus                0   1
  MYH15 MUTATED    25   4
  MYH15 WILD-TYPE 341 115
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYH15 MUTATED     25    4
  MYH15 WILD-TYPE  341  115
        clus
vv       MYH15 MUTATED MYH15 WILD-TYPE
  COLON             25             341
  RECTUM             4             115
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MYH15 MUTATED         4        0        4        12         1         0
  MYH15 WILD-TYPE      87        1       28       126         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MYH15 MUTATED           0          0          2          1        2         1
  MYH15 WILD-TYPE        24         11         57         41       46        17
                 vv
clus              STAGE IVB
  MYH15 MUTATED           0
  MYH15 WILD-TYPE         1
D1473V4, multiclass
            clus
vv           MYH15 MUTATED MYH15 WILD-TYPE
  STAGE I                4              87
  STAGE IA               0               1
  STAGE II               4              28
  STAGE IIA             12             126
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             2              57
  STAGE IIIC             1              41
  STAGE IV               2              46
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  MYH15 MUTATED     1   4  21   3
  MYH15 WILD-TYPE  16  88 308  47
D1473V5, multiclass
    clus
vv   MYH15 MUTATED MYH15 WILD-TYPE
  T1             1              16
  T2             4              88
  T3            21             308
  T4             3              47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  MYH15 MUTATED    22   4   3
  MYH15 WILD-TYPE 265 109  84
D1473V6, multiclass
    clus
vv   MYH15 MUTATED MYH15 WILD-TYPE
  N0            22             265
  N1             4             109
  N2             3              84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1473V7, binary
                 cls
clus                0   1
  MYH15 MUTATED    24   3
  MYH15 WILD-TYPE 351  62
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYH15 MUTATED     24    3
  MYH15 WILD-TYPE  351   62
   clus
vv  MYH15 MUTATED MYH15 WILD-TYPE
  0            24             351
  1             3              62
[1] 2 2
[1] FALSE
D1473V8, binary
                 cls
clus                0   1
  MYH15 MUTATED    11  18
  MYH15 WILD-TYPE 214 246
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYH15 MUTATED     11   18
  MYH15 WILD-TYPE  214  246
        clus
vv       MYH15 MUTATED MYH15 WILD-TYPE
  FEMALE            11             214
  MALE              18             246
[1] 2 2
[1] FALSE
D1473V9, binary
                 cls
clus                0   1
  MYH15 MUTATED    23   0
  MYH15 WILD-TYPE 327  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYH15 MUTATED     23    0
  MYH15 WILD-TYPE  327   22
     clus
vv    MYH15 MUTATED MYH15 WILD-TYPE
  NO             23             327
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MYH15 MUTATED                     20                             4
  MYH15 WILD-TYPE                  295                            43
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MYH15 MUTATED                       4                              0
  MYH15 WILD-TYPE                   102                             10
D1473V10, multiclass
                                clus
vv                               MYH15 MUTATED MYH15 WILD-TYPE
  COLON ADENOCARCINOMA                      20             295
  COLON MUCINOUS ADENOCARCINOMA              4              43
  RECTAL ADENOCARCINOMA                      4             102
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  MYH15 MUTATED    18   0   1   1
  MYH15 WILD-TYPE 327   4  30  24
D1473V11, multiclass
    clus
vv   MYH15 MUTATED MYH15 WILD-TYPE
  R0            18             327
  R1             0               4
  R2             1              30
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1473V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MYH15 MUTATED                                  0     1
  MYH15 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  MYH15 MUTATED                           0    17
  MYH15 WILD-TYPE                        22   209
D1473V13, multiclass
                                  clus
vv                                 MYH15 MUTATED MYH15 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                       17             209
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1474) Variable = SPEN MUTATION ANALYSIS
D1474V1, survival
                sevent
clus2              0   1
  SPEN MUTATED    25   7
  SPEN WILD-TYPE 353  86
  SPEN MUTATED SPEN WILD-TYPE 
            32            439 
  SPEN MUTATED SPEN WILD-TYPE 
             7             86 
$`SPEN MUTATED`
TCGA-A6-3809 TCGA-A6-5661 TCGA-A6-5665 TCGA-AA-3492 TCGA-AA-3522 TCGA-AA-3543 
       32.75        33.53        22.06         3.02        37.05         0.99 
TCGA-AA-3672 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3949 TCGA-AA-3956 TCGA-AA-3977 
        0.92        26.99        10.06        26.01        34.03        25.02 
TCGA-AA-A00N TCGA-AD-5900 TCGA-AU-6004 TCGA-AY-5543 TCGA-AZ-4315 TCGA-AZ-6599 
        4.01         0.07        27.09        33.01        58.39         6.77 
TCGA-AZ-6603 TCGA-CK-5916 TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-5868 TCGA-CM-6169 
       29.56        21.14        23.05        37.02        17.03        13.02 
TCGA-D5-5538 TCGA-D5-6541 TCGA-DM-A0XD TCGA-DM-A1HB TCGA-G4-6628 TCGA-AG-A002 
       12.26        15.58        24.43       135.65        79.69        20.98 
TCGA-AG-A02X TCGA-EI-6508 
       41.00        20.91 

$`SPEN WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 
       31.63        30.44        29.19        23.61        22.09        32.71 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       27.09        22.52         8.38        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
       20.28         7.04         1.02        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       36.03         8.05        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 
       29.00        29.00        26.01        12.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
        6.05         6.97        54.02         2.01        14.01        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 
       36.00         5.03        85.05        19.04        19.04        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3966 
       24.00        33.01        24.00         2.01        20.98         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 
       41.00        39.98        18.05        40.96        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6197 
       10.88         0.20        14.50        16.31         0.95        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6606 
       88.21        49.41        12.10       100.01         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4752 
       82.95         1.91       124.27        20.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
        5.03        15.02        15.02        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6170 
       29.03        16.04        21.99        14.99        12.99        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5539 TCGA-D5-5540 
       11.01        10.06        12.03        45.40        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6898 
       17.85         4.80        17.13        12.49        16.14         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
      119.70        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 
       12.59       140.38         7.50        44.32       131.51       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       46.75        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       61.97        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
        0.49        20.55        19.96        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  SPEN MUTATED SPEN WILD-TYPE 
          0.07           0.00 
  SPEN MUTATED SPEN WILD-TYPE 
        135.65         148.01 
  SPEN MUTATED SPEN WILD-TYPE 
         23.74          19.99 
[1] "0.1 - 135.7 (23.7)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.2"
D1474V2, continuous
D1474V3, binary
                cls
clus               0   1
  SPEN MUTATED    31   3
  SPEN WILD-TYPE 335 116
[1] "tbl2"
                cls
clus             [,1] [,2]
  SPEN MUTATED     31    3
  SPEN WILD-TYPE  335  116
        clus
vv       SPEN MUTATED SPEN WILD-TYPE
  COLON            31            335
  RECTUM            3            116
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SPEN MUTATED         9        0        1        11         3         0
  SPEN WILD-TYPE      82        1       31       127         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SPEN MUTATED           2          0          4          0        0         2
  SPEN WILD-TYPE        22         11         55         42       48        16
                vv
clus             STAGE IVB
  SPEN MUTATED           0
  SPEN WILD-TYPE         1
D1474V4, multiclass
            clus
vv           SPEN MUTATED SPEN WILD-TYPE
  STAGE I               9             82
  STAGE IA              0              1
  STAGE II              1             31
  STAGE IIA            11            127
  STAGE IIB             3              7
  STAGE IIC             0              1
  STAGE III             2             22
  STAGE IIIA            0             11
  STAGE IIIB            4             55
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             2             16
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  SPEN MUTATED     1  10  19   4
  SPEN WILD-TYPE  16  82 310  46
D1474V5, multiclass
    clus
vv   SPEN MUTATED SPEN WILD-TYPE
  T1            1             16
  T2           10             82
  T3           19            310
  T4            4             46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  SPEN MUTATED    25   8   1
  SPEN WILD-TYPE 262 105  86
D1474V6, multiclass
    clus
vv   SPEN MUTATED SPEN WILD-TYPE
  N0           25            262
  N1            8            105
  N2            1             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1474V7, binary
                cls
clus               0   1
  SPEN MUTATED    27   2
  SPEN WILD-TYPE 348  63
[1] "tbl2"
                cls
clus             [,1] [,2]
  SPEN MUTATED     27    2
  SPEN WILD-TYPE  348   63
   clus
vv  SPEN MUTATED SPEN WILD-TYPE
  0           27            348
  1            2             63
[1] 2 2
[1] FALSE
D1474V8, binary
                cls
clus               0   1
  SPEN MUTATED    17  17
  SPEN WILD-TYPE 208 247
[1] "tbl2"
                cls
clus             [,1] [,2]
  SPEN MUTATED     17   17
  SPEN WILD-TYPE  208  247
        clus
vv       SPEN MUTATED SPEN WILD-TYPE
  FEMALE           17            208
  MALE             17            247
[1] 2 2
[1] FALSE
D1474V9, binary
                cls
clus               0   1
  SPEN MUTATED    26   0
  SPEN WILD-TYPE 324  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  SPEN MUTATED     26    0
  SPEN WILD-TYPE  324   22
     clus
vv    SPEN MUTATED SPEN WILD-TYPE
  NO            26            324
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SPEN MUTATED                     25                             5
  SPEN WILD-TYPE                  290                            42
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SPEN MUTATED                       3                              0
  SPEN WILD-TYPE                   103                             10
D1474V10, multiclass
                                clus
vv                               SPEN MUTATED SPEN WILD-TYPE
  COLON ADENOCARCINOMA                     25            290
  COLON MUCINOUS ADENOCARCINOMA             5             42
  RECTAL ADENOCARCINOMA                     3            103
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  SPEN MUTATED    27   0   0   2
  SPEN WILD-TYPE 318   4  31  23
D1474V11, multiclass
    clus
vv   SPEN MUTATED SPEN WILD-TYPE
  R0           27            318
  R1            0              4
  R2            0             31
  RX            2             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1474V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SPEN MUTATED                                  0     0
  SPEN WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  SPEN MUTATED                           4    17
  SPEN WILD-TYPE                        18   209
D1474V13, multiclass
                                  clus
vv                                 SPEN MUTATED SPEN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   4             18
  WHITE                                      17            209
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1475) Variable = IL1F8 MUTATION ANALYSIS
D1475V1, survival
                 sevent
clus2               0   1
  IL1F8 MUTATED     2   1
  IL1F8 WILD-TYPE 376  92
  IL1F8 MUTATED IL1F8 WILD-TYPE 
              3             468 
  IL1F8 MUTATED IL1F8 WILD-TYPE 
              1              92 
$`IL1F8 MUTATED`
TCGA-A6-5661 TCGA-AA-3663 TCGA-DC-6158 
       33.53         6.97        10.98 

$`IL1F8 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6160 
        7.17        15.02         5.03        13.97        27.95        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  IL1F8 MUTATED IL1F8 WILD-TYPE 
           6.97            0.00 
  IL1F8 MUTATED IL1F8 WILD-TYPE 
          33.53          148.01 
  IL1F8 MUTATED IL1F8 WILD-TYPE 
         10.980          20.235 
[1] "7.0 - 33.5 (11.0)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "2.7"
D1475V2, continuous
D1475V3, binary
                 cls
clus                0   1
  IL1F8 MUTATED     2   1
  IL1F8 WILD-TYPE 364 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IL1F8 MUTATED      2    1
  IL1F8 WILD-TYPE  364  118
        clus
vv       IL1F8 MUTATED IL1F8 WILD-TYPE
  COLON              2             364
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  IL1F8 MUTATED         1        0        1         1         0         0
  IL1F8 WILD-TYPE      90        1       31       137        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  IL1F8 MUTATED           0          0          0          0        0         0
  IL1F8 WILD-TYPE        24         11         59         42       48        18
                 vv
clus              STAGE IVB
  IL1F8 MUTATED           0
  IL1F8 WILD-TYPE         1
D1475V4, multiclass
            clus
vv           IL1F8 MUTATED IL1F8 WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              1             137
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  IL1F8 MUTATED     0   1   2   0
  IL1F8 WILD-TYPE  17  91 327  50
D1475V5, multiclass
    clus
vv   IL1F8 MUTATED IL1F8 WILD-TYPE
  T1             0              17
  T2             1              91
  T3             2             327
  T4             0              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  IL1F8 MUTATED     3   0   0
  IL1F8 WILD-TYPE 284 113  87
D1475V6, multiclass
    clus
vv   IL1F8 MUTATED IL1F8 WILD-TYPE
  N0             3             284
  N1             0             113
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1475V7, binary
                 cls
clus                0   1
  IL1F8 MUTATED     3   0
  IL1F8 WILD-TYPE 372  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IL1F8 MUTATED      3    0
  IL1F8 WILD-TYPE  372   65
   clus
vv  IL1F8 MUTATED IL1F8 WILD-TYPE
  0             3             372
  1             0              65
[1] 2 2
[1] FALSE
D1475V8, binary
                 cls
clus                0   1
  IL1F8 MUTATED     1   2
  IL1F8 WILD-TYPE 224 262
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IL1F8 MUTATED      1    2
  IL1F8 WILD-TYPE  224  262
        clus
vv       IL1F8 MUTATED IL1F8 WILD-TYPE
  FEMALE             1             224
  MALE               2             262
[1] 2 2
[1] FALSE
D1475V9, binary
                 cls
clus                0   1
  IL1F8 MUTATED     3   0
  IL1F8 WILD-TYPE 347  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IL1F8 MUTATED      3    0
  IL1F8 WILD-TYPE  347   22
     clus
vv    IL1F8 MUTATED IL1F8 WILD-TYPE
  NO              3             347
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  IL1F8 MUTATED                      2                             0
  IL1F8 WILD-TYPE                  313                            47
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  IL1F8 MUTATED                       1                              0
  IL1F8 WILD-TYPE                   105                             10
D1475V10, multiclass
                                clus
vv                               IL1F8 MUTATED IL1F8 WILD-TYPE
  COLON ADENOCARCINOMA                       2             313
  COLON MUCINOUS ADENOCARCINOMA              0              47
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  IL1F8 MUTATED     3   0   0   0
  IL1F8 WILD-TYPE 342   4  31  25
D1475V11, multiclass
    clus
vv   IL1F8 MUTATED IL1F8 WILD-TYPE
  R0             3             342
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1475V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  IL1F8 MUTATED                                  0     0
  IL1F8 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  IL1F8 MUTATED                           1     1
  IL1F8 WILD-TYPE                        21   225
D1475V13, multiclass
[1] "Remove cluster labels:" "IL1F8 MUTATED"         
clus
  IL1F8 MUTATED IL1F8 WILD-TYPE 
              2             258 
     TCGA-A6-2671      TCGA-A6-2672      TCGA-A6-2674      TCGA-A6-2676 
"IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" 
     TCGA-A6-2677      TCGA-A6-2678      TCGA-A6-2683      TCGA-A6-3807 
"IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" 
     TCGA-A6-3808      TCGA-A6-3809      TCGA-A6-3810      TCGA-A6-4105 
"IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" 
     TCGA-A6-5656      TCGA-A6-5657      TCGA-A6-5659      TCGA-A6-5660 
"IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" 
     TCGA-A6-5662      TCGA-A6-5664      TCGA-A6-5665      TCGA-A6-5666 
"IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" 
     TCGA-A6-6137      TCGA-A6-6138      TCGA-A6-6141      TCGA-A6-6142 
"IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" 
     TCGA-A6-6648      TCGA-A6-6649      TCGA-A6-6651      TCGA-A6-6652 
"IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" 
     TCGA-A6-6653      TCGA-A6-6654      TCGA-A6-6780      TCGA-A6-6781 
"IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" 
     TCGA-A6-6782      TCGA-AD-5900      TCGA-AD-6548      TCGA-AD-6888 
"IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" 
     TCGA-AD-6889      TCGA-AD-6890      TCGA-AD-6895      TCGA-AD-6899 
"IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" 
     TCGA-AD-6901      TCGA-AD-6963      TCGA-AD-6964      TCGA-AD-6965 
"IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" 
     TCGA-AU-3779      TCGA-AU-6004      TCGA-AY-4070      TCGA-AY-4071 
"IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" 
     TCGA-AY-5543      TCGA-AY-6196      TCGA-AY-6197      TCGA-AY-6386 
"IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" 
     TCGA-AZ-4315      TCGA-AZ-4323      TCGA-AZ-4616      TCGA-AZ-4681 
"IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" 
     TCGA-AZ-4682      TCGA-AZ-5403      TCGA-AZ-5407      TCGA-AZ-6598 
"IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" 
     TCGA-AZ-6599      TCGA-AZ-6600      TCGA-AZ-6601      TCGA-AZ-6603 
"IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" 
     TCGA-AZ-6605      TCGA-AZ-6606      TCGA-AZ-6607      TCGA-AZ-6608 
"IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" 
     TCGA-CA-5254      TCGA-CA-5255      TCGA-CA-5796      TCGA-CA-5797 
"IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" 
     TCGA-CA-6715      TCGA-CA-6716      TCGA-CA-6717      TCGA-CA-6718 
"IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" 
     TCGA-CA-6719      TCGA-CK-4947      TCGA-CK-4948      TCGA-CK-4950 
"IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" 
     TCGA-CK-4952      TCGA-CK-5912      TCGA-CK-5913      TCGA-CK-5914 
"IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" 
     TCGA-CK-5915      TCGA-CK-5916      TCGA-CK-6746      TCGA-CK-6747 
"IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" 
     TCGA-CK-6748      TCGA-CK-6751      TCGA-CM-4743      TCGA-CM-4744 
"IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" 
     TCGA-CM-4746      TCGA-CM-4747      TCGA-CM-4752      TCGA-CM-5341 
"IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" 
     TCGA-CM-5344      TCGA-CM-5348      TCGA-CM-5349      TCGA-CM-5860 
"IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" 
     TCGA-CM-5861      TCGA-CM-5862      TCGA-CM-5863      TCGA-CM-5864 
"IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" 
     TCGA-CM-5868      TCGA-CM-6161      TCGA-CM-6162      TCGA-CM-6163 
"IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" 
     TCGA-CM-6164      TCGA-CM-6165      TCGA-CM-6166      TCGA-CM-6167 
"IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" 
     TCGA-CM-6168      TCGA-CM-6169      TCGA-CM-6170      TCGA-CM-6171 
"IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" 
     TCGA-CM-6172      TCGA-CM-6674      TCGA-CM-6675      TCGA-CM-6676 
"IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" 
     TCGA-CM-6677      TCGA-CM-6678      TCGA-CM-6679      TCGA-CM-6680 
"IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" 
     TCGA-D5-5537      TCGA-D5-5538      TCGA-D5-5539      TCGA-D5-5540 
"IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" 
     TCGA-D5-5541      TCGA-D5-6529      TCGA-D5-6532      TCGA-D5-6533 
"IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" 
     TCGA-D5-6534      TCGA-D5-6535      TCGA-D5-6536      TCGA-D5-6537 
"IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" 
     TCGA-D5-6538      TCGA-D5-6539      TCGA-D5-6540      TCGA-D5-6541 
"IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" 
     TCGA-D5-6898      TCGA-D5-6920      TCGA-D5-6922      TCGA-D5-6923 
"IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" 
     TCGA-D5-6924      TCGA-D5-6926      TCGA-D5-6927      TCGA-D5-6928 
"IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" 
     TCGA-D5-6929      TCGA-D5-6930      TCGA-D5-6931      TCGA-D5-6932 
"IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" 
     TCGA-D5-7000      TCGA-DM-A0X9      TCGA-DM-A0XD      TCGA-DM-A0XF 
"IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" 
     TCGA-DM-A1D0      TCGA-DM-A1D4      TCGA-DM-A1D6      TCGA-DM-A1D7 
"IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" 
     TCGA-DM-A1D8      TCGA-DM-A1D9      TCGA-DM-A1DA      TCGA-DM-A1DB 
"IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" 
     TCGA-DM-A1HA      TCGA-DM-A1HB      TCGA-DM-A282      TCGA-DM-A285 
"IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" 
     TCGA-DM-A28C      TCGA-DM-A28E      TCGA-DM-A28F      TCGA-DM-A28G 
"IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" 
     TCGA-DM-A28H      TCGA-DM-A28K      TCGA-F4-6459      TCGA-F4-6460 
"IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" 
     TCGA-F4-6569      TCGA-F4-6570      TCGA-F4-6703      TCGA-F4-6704 
"IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" 
     TCGA-F4-6805      TCGA-F4-6806      TCGA-F4-6807      TCGA-F4-6808 
"IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" 
     TCGA-F4-6809      TCGA-F4-6854      TCGA-F4-6855      TCGA-F4-6856 
"IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" 
     TCGA-G4-6293      TCGA-G4-6299      TCGA-G4-6303      TCGA-G4-6304 
"IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" 
     TCGA-G4-6306      TCGA-G4-6307      TCGA-G4-6309      TCGA-G4-6310 
"IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" 
     TCGA-G4-6315      TCGA-G4-6317      TCGA-G4-6321      TCGA-G4-6323 
"IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" 
     TCGA-G4-6586      TCGA-G4-6588      TCGA-G4-6625      TCGA-G4-6626 
"IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" 
     TCGA-G4-6628      TCGA-AF-2687      TCGA-AF-2689      TCGA-AF-2691 
"IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" 
     TCGA-AF-2692      TCGA-AF-2693      TCGA-AF-3400      TCGA-AF-3913 
"IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" 
     TCGA-AF-4110      TCGA-AF-5654      TCGA-AF-6136      TCGA-AF-6655 
"IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" 
     TCGA-AF-6672      TCGA-AH-6544      TCGA-AH-6547      TCGA-AH-6549 
"IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" 
     TCGA-AH-6643      TCGA-AH-6644      TCGA-CI-6619      TCGA-CI-6620 
"IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" 
     TCGA-CI-6621      TCGA-CI-6622      TCGA-CI-6624      TCGA-CL-5917 
"IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" 
     TCGA-CL-5918      TCGA-DC-5337      TCGA-DC-5869      TCGA-DC-6155 
"IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" 
     TCGA-DC-6157      TCGA-DC-6160      TCGA-DC-6681      TCGA-DC-6682 
"IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" 
     TCGA-DC-6683      TCGA-DT-5265      TCGA-DY-A0XA      TCGA-DY-A1DC 
"IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" 
     TCGA-DY-A1DD      TCGA-DY-A1DF      TCGA-DY-A1DG      TCGA-DY-A1H8 
"IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" 
     TCGA-EF-5830      TCGA-EI-6506      TCGA-EI-6507      TCGA-EI-6508 
"IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" 
     TCGA-EI-6510      TCGA-F5-6464      TCGA-F5-6465      TCGA-F5-6571 
"IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" 
     TCGA-F5-6702      TCGA-F5-6811      TCGA-F5-6812      TCGA-F5-6813 
"IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" 
     TCGA-G5-6235      TCGA-G5-6641 
"IL1F8 WILD-TYPE" "IL1F8 WILD-TYPE" 

Clustering(1476) Variable = CCR8 MUTATION ANALYSIS
D1476V1, survival
                sevent
clus2              0   1
  CCR8 MUTATED     3   4
  CCR8 WILD-TYPE 375  89
  CCR8 MUTATED CCR8 WILD-TYPE 
             7            464 
  CCR8 MUTATED CCR8 WILD-TYPE 
             4             89 
$`CCR8 MUTATED`
TCGA-AA-3555 TCGA-AA-3966 TCGA-AA-A00N TCGA-AZ-6603 TCGA-AZ-6607 TCGA-D5-6924 
       29.95         2.01         4.01        29.56         3.19        14.30 
TCGA-DM-A1D4 
       92.75 

$`CCR8 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 
       21.01        13.02        24.00        17.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
        2.01        20.98        34.03        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
      100.01         5.23        11.74         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  CCR8 MUTATED CCR8 WILD-TYPE 
          2.01           0.00 
  CCR8 MUTATED CCR8 WILD-TYPE 
         92.75         148.01 
  CCR8 MUTATED CCR8 WILD-TYPE 
        14.300         20.235 
[1] "2.0 - 92.8 (14.3)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "3.2"
D1476V2, continuous
D1476V3, binary
                cls
clus               0   1
  CCR8 MUTATED     7   0
  CCR8 WILD-TYPE 359 119
[1] "tbl2"
                cls
clus             [,1] [,2]
  CCR8 MUTATED      7    0
  CCR8 WILD-TYPE  359  119
        clus
vv       CCR8 MUTATED CCR8 WILD-TYPE
  COLON             7            359
  RECTUM            0            119
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CCR8 MUTATED         0        0        0         4         1         0
  CCR8 WILD-TYPE      91        1       32       134         9         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CCR8 MUTATED           0          0          0          0        1         0
  CCR8 WILD-TYPE        24         11         59         42       47        18
                vv
clus             STAGE IVB
  CCR8 MUTATED           0
  CCR8 WILD-TYPE         1
D1476V4, multiclass
            clus
vv           CCR8 MUTATED CCR8 WILD-TYPE
  STAGE I               0             91
  STAGE IA              0              1
  STAGE II              0             32
  STAGE IIA             4            134
  STAGE IIB             1              9
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            0             59
  STAGE IIIC            0             42
  STAGE IV              1             47
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  CCR8 MUTATED     0   1   4   2
  CCR8 WILD-TYPE  17  91 325  48
D1476V5, multiclass
    clus
vv   CCR8 MUTATED CCR8 WILD-TYPE
  T1            0             17
  T2            1             91
  T3            4            325
  T4            2             48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  CCR8 MUTATED     5   1   1
  CCR8 WILD-TYPE 282 112  86
D1476V6, multiclass
    clus
vv   CCR8 MUTATED CCR8 WILD-TYPE
  N0            5            282
  N1            1            112
  N2            1             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1476V7, binary
                cls
clus               0   1
  CCR8 MUTATED     5   1
  CCR8 WILD-TYPE 370  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  CCR8 MUTATED      5    1
  CCR8 WILD-TYPE  370   64
   clus
vv  CCR8 MUTATED CCR8 WILD-TYPE
  0            5            370
  1            1             64
[1] 2 2
[1] FALSE
D1476V8, binary
                cls
clus               0   1
  CCR8 MUTATED     3   4
  CCR8 WILD-TYPE 222 260
[1] "tbl2"
                cls
clus             [,1] [,2]
  CCR8 MUTATED      3    4
  CCR8 WILD-TYPE  222  260
        clus
vv       CCR8 MUTATED CCR8 WILD-TYPE
  FEMALE            3            222
  MALE              4            260
[1] 2 2
[1] FALSE
D1476V9, binary
                cls
clus               0   1
  CCR8 MUTATED     4   0
  CCR8 WILD-TYPE 346  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  CCR8 MUTATED      4    0
  CCR8 WILD-TYPE  346   22
     clus
vv    CCR8 MUTATED CCR8 WILD-TYPE
  NO             4            346
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CCR8 MUTATED                      4                             3
  CCR8 WILD-TYPE                  311                            44
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CCR8 MUTATED                       0                              0
  CCR8 WILD-TYPE                   106                             10
D1476V10, multiclass
                                clus
vv                               CCR8 MUTATED CCR8 WILD-TYPE
  COLON ADENOCARCINOMA                      4            311
  COLON MUCINOUS ADENOCARCINOMA             3             44
  RECTAL ADENOCARCINOMA                     0            106
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  CCR8 MUTATED     3   0   0   0
  CCR8 WILD-TYPE 342   4  31  25
D1476V11, multiclass
    clus
vv   CCR8 MUTATED CCR8 WILD-TYPE
  R0            3            342
  R1            0              4
  R2            0             31
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1476V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CCR8 MUTATED                                  0     0
  CCR8 WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  CCR8 MUTATED                           0     4
  CCR8 WILD-TYPE                        22   222
D1476V13, multiclass
                                  clus
vv                                 CCR8 MUTATED CCR8 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       4            222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1477) Variable = HSPBAP1 MUTATION ANALYSIS
D1477V1, survival
                   sevent
clus2                 0   1
  HSPBAP1 MUTATED     5   3
  HSPBAP1 WILD-TYPE 373  90
  HSPBAP1 MUTATED HSPBAP1 WILD-TYPE 
                8               463 
  HSPBAP1 MUTATED HSPBAP1 WILD-TYPE 
                3                90 
$`HSPBAP1 MUTATED`
TCGA-A6-6142 TCGA-AA-A00N TCGA-AD-6889 TCGA-AZ-6598 TCGA-CK-5913 TCGA-DM-A1HB 
       25.08         4.01        56.55        49.41        51.32       135.65 
TCGA-F4-6459 TCGA-AH-6644 
        8.61         0.72 

$`HSPBAP1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        88.21         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       49.08         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
        7.50        44.32       131.51       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6460 
      119.93        35.97        60.79       117.07        98.24        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.69         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  HSPBAP1 MUTATED HSPBAP1 WILD-TYPE 
             0.72              0.00 
  HSPBAP1 MUTATED HSPBAP1 WILD-TYPE 
           135.65            148.01 
  HSPBAP1 MUTATED HSPBAP1 WILD-TYPE 
           37.245            20.120 
[1] "0.7 - 135.7 (37.2)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.3"
D1477V2, continuous
D1477V3, binary
                   cls
clus                  0   1
  HSPBAP1 MUTATED     7   1
  HSPBAP1 WILD-TYPE 359 118
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HSPBAP1 MUTATED      7    1
  HSPBAP1 WILD-TYPE  359  118
        clus
vv       HSPBAP1 MUTATED HSPBAP1 WILD-TYPE
  COLON                7               359
  RECTUM               1               118
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  HSPBAP1 MUTATED         0        0        1         2         1         0
  HSPBAP1 WILD-TYPE      91        1       31       136         9         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HSPBAP1 MUTATED           0          0          2          0        0
  HSPBAP1 WILD-TYPE        24         11         57         42       48
                   vv
clus                STAGE IVA STAGE IVB
  HSPBAP1 MUTATED           1         0
  HSPBAP1 WILD-TYPE        17         1
D1477V4, multiclass
            clus
vv           HSPBAP1 MUTATED HSPBAP1 WILD-TYPE
  STAGE I                  0                91
  STAGE IA                 0                 1
  STAGE II                 1                31
  STAGE IIA                2               136
  STAGE IIB                1                 9
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               0                11
  STAGE IIIB               2                57
  STAGE IIIC               0                42
  STAGE IV                 0                48
  STAGE IVA                1                17
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  HSPBAP1 MUTATED     0   0   7   1
  HSPBAP1 WILD-TYPE  17  92 322  49
D1477V5, multiclass
    clus
vv   HSPBAP1 MUTATED HSPBAP1 WILD-TYPE
  T1               0                17
  T2               0                92
  T3               7               322
  T4               1                49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  HSPBAP1 MUTATED     4   2   1
  HSPBAP1 WILD-TYPE 283 111  86
D1477V6, multiclass
    clus
vv   HSPBAP1 MUTATED HSPBAP1 WILD-TYPE
  N0               4               283
  N1               2               111
  N2               1                86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1477V7, binary
                   cls
clus                  0   1
  HSPBAP1 MUTATED     4   1
  HSPBAP1 WILD-TYPE 371  64
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HSPBAP1 MUTATED      4    1
  HSPBAP1 WILD-TYPE  371   64
   clus
vv  HSPBAP1 MUTATED HSPBAP1 WILD-TYPE
  0               4               371
  1               1                64
[1] 2 2
[1] FALSE
D1477V8, binary
                   cls
clus                  0   1
  HSPBAP1 MUTATED     4   4
  HSPBAP1 WILD-TYPE 221 260
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HSPBAP1 MUTATED      4    4
  HSPBAP1 WILD-TYPE  221  260
        clus
vv       HSPBAP1 MUTATED HSPBAP1 WILD-TYPE
  FEMALE               4               221
  MALE                 4               260
[1] 2 2
[1] FALSE
D1477V9, binary
                   cls
clus                  0   1
  HSPBAP1 MUTATED     4   0
  HSPBAP1 WILD-TYPE 346  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HSPBAP1 MUTATED      4    0
  HSPBAP1 WILD-TYPE  346   22
     clus
vv    HSPBAP1 MUTATED HSPBAP1 WILD-TYPE
  NO                4               346
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  HSPBAP1 MUTATED                      5                             1
  HSPBAP1 WILD-TYPE                  310                            46
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  HSPBAP1 MUTATED                       1                              0
  HSPBAP1 WILD-TYPE                   105                             10
D1477V10, multiclass
                                clus
vv                               HSPBAP1 MUTATED HSPBAP1 WILD-TYPE
  COLON ADENOCARCINOMA                         5               310
  COLON MUCINOUS ADENOCARCINOMA                1                46
  RECTAL ADENOCARCINOMA                        1               105
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  HSPBAP1 MUTATED     2   0   0   1
  HSPBAP1 WILD-TYPE 343   4  31  24
D1477V11, multiclass
    clus
vv   HSPBAP1 MUTATED HSPBAP1 WILD-TYPE
  R0               2               343
  R1               0                 4
  R2               0                31
  RX               1                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1477V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HSPBAP1 MUTATED                                  0     1
  HSPBAP1 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  HSPBAP1 MUTATED                           0     6
  HSPBAP1 WILD-TYPE                        22   220
D1477V13, multiclass
                                  clus
vv                                 HSPBAP1 MUTATED HSPBAP1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                10
  BLACK OR AFRICAN AMERICAN                      0                22
  WHITE                                          6               220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1478) Variable = XG MUTATION ANALYSIS
D1478V1, survival
              sevent
clus2            0   1
  XG MUTATED     5   2
  XG WILD-TYPE 373  91
  XG MUTATED XG WILD-TYPE 
           7          464 
  XG MUTATED XG WILD-TYPE 
           2           91 
$`XG MUTATED`
TCGA-AA-A01P TCGA-AA-A02Y TCGA-AZ-6599 TCGA-CA-5797 TCGA-D5-6533 TCGA-DC-6681 
       38.07        39.98         6.77         3.29         1.32         5.95 
TCGA-F5-6811 
       32.19 

$`XG WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01Q TCGA-AA-A01R 
       32.02        12.00        31.00        31.00         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       41.00        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 
      106.75        22.36        62.79        88.21        49.41        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
       12.69         3.06         3.25         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6682 TCGA-DC-6683 
       13.97        27.95        10.98        19.99         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6812 TCGA-F5-6813 
        9.96        49.51        31.30        28.57         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  XG MUTATED XG WILD-TYPE 
        1.32         0.00 
  XG MUTATED XG WILD-TYPE 
       39.98       148.01 
  XG MUTATED XG WILD-TYPE 
       6.770       20.235 
[1] "1.3 - 40.0 (6.8)"   "0.0 - 148.0 (20.2)"
[1] "hr=" "2.2"
D1478V2, continuous
D1478V3, binary
              cls
clus             0   1
  XG MUTATED     5   2
  XG WILD-TYPE 361 117
[1] "tbl2"
              cls
clus           [,1] [,2]
  XG MUTATED      5    2
  XG WILD-TYPE  361  117
        clus
vv       XG MUTATED XG WILD-TYPE
  COLON           5          361
  RECTUM          2          117
[1] 2 2
[1] FALSE
              vv
clus           STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  XG MUTATED         2        0        0         2         0         0
  XG WILD-TYPE      89        1       32       136        10         1
              vv
clus           STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  XG MUTATED           1          0          1          0        0         1
  XG WILD-TYPE        23         11         58         42       48        17
              vv
clus           STAGE IVB
  XG MUTATED           0
  XG WILD-TYPE         1
D1478V4, multiclass
            clus
vv           XG MUTATED XG WILD-TYPE
  STAGE I             2           89
  STAGE IA            0            1
  STAGE II            0           32
  STAGE IIA           2          136
  STAGE IIB           0           10
  STAGE IIC           0            1
  STAGE III           1           23
  STAGE IIIA          0           11
  STAGE IIIB          1           58
  STAGE IIIC          0           42
  STAGE IV            0           48
  STAGE IVA           1           17
  STAGE IVB           0            1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
              vv
clus            T1  T2  T3  T4
  XG MUTATED     0   2   4   1
  XG WILD-TYPE  17  90 325  49
D1478V5, multiclass
    clus
vv   XG MUTATED XG WILD-TYPE
  T1          0           17
  T2          2           90
  T3          4          325
  T4          1           49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
              vv
clus            N0  N1  N2
  XG MUTATED     5   1   1
  XG WILD-TYPE 282 112  86
D1478V6, multiclass
    clus
vv   XG MUTATED XG WILD-TYPE
  N0          5          282
  N1          1          112
  N2          1           86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1478V7, binary
              cls
clus             0   1
  XG MUTATED     5   1
  XG WILD-TYPE 370  64
[1] "tbl2"
              cls
clus           [,1] [,2]
  XG MUTATED      5    1
  XG WILD-TYPE  370   64
   clus
vv  XG MUTATED XG WILD-TYPE
  0          5          370
  1          1           64
[1] 2 2
[1] FALSE
D1478V8, binary
              cls
clus             0   1
  XG MUTATED     4   3
  XG WILD-TYPE 221 261
[1] "tbl2"
              cls
clus           [,1] [,2]
  XG MUTATED      4    3
  XG WILD-TYPE  221  261
        clus
vv       XG MUTATED XG WILD-TYPE
  FEMALE          4          221
  MALE            3          261
[1] 2 2
[1] FALSE
D1478V9, binary
              cls
clus             0   1
  XG MUTATED     5   0
  XG WILD-TYPE 345  22
[1] "tbl2"
              cls
clus           [,1] [,2]
  XG MUTATED      5    0
  XG WILD-TYPE  345   22
     clus
vv    XG MUTATED XG WILD-TYPE
  NO           5          345
  YES          0           22
[1] 2 2
[1] FALSE
              vv
clus           COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  XG MUTATED                      5                             0
  XG WILD-TYPE                  310                            47
              vv
clus           RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  XG MUTATED                       2                              0
  XG WILD-TYPE                   104                             10
D1478V10, multiclass
                                clus
vv                               XG MUTATED XG WILD-TYPE
  COLON ADENOCARCINOMA                    5          310
  COLON MUCINOUS ADENOCARCINOMA           0           47
  RECTAL ADENOCARCINOMA                   2          104
  RECTAL MUCINOUS ADENOCARCINOMA          0           10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
              vv
clus            R0  R1  R2  RX
  XG MUTATED     5   0   0   0
  XG WILD-TYPE 340   4  31  25
D1478V11, multiclass
    clus
vv   XG MUTATED XG WILD-TYPE
  R0          5          340
  R1          0            4
  R2          0           31
  RX          0           25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1478V12, continuous
              vv
clus           AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  XG MUTATED                                  0     1                         0
  XG WILD-TYPE                                1    10                        22
              vv
clus           WHITE
  XG MUTATED       4
  XG WILD-TYPE   222
D1478V13, multiclass
                                  clus
vv                                 XG MUTATED XG WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE          0            1
  ASIAN                                     1           10
  BLACK OR AFRICAN AMERICAN                 0           22
  WHITE                                     4          222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1479) Variable = UHRF1BP1L MUTATION ANALYSIS
D1479V1, survival
                     sevent
clus2                   0   1
  UHRF1BP1L MUTATED    12   8
  UHRF1BP1L WILD-TYPE 366  85
  UHRF1BP1L MUTATED UHRF1BP1L WILD-TYPE 
                 20                 451 
  UHRF1BP1L MUTATED UHRF1BP1L WILD-TYPE 
                  8                  85 
$`UHRF1BP1L MUTATED`
TCGA-A6-5660 TCGA-A6-5665 TCGA-AA-3715 TCGA-AA-3845 TCGA-AA-3864 TCGA-AA-3950 
       29.19        22.06        19.04         0.00        53.00        24.00 
TCGA-AA-3966 TCGA-AA-3977 TCGA-AA-A00N TCGA-AD-6889 TCGA-AD-6901 TCGA-AZ-6598 
        2.01        25.02         4.01        56.55        22.42        49.41 
TCGA-AZ-6599 TCGA-CM-5861 TCGA-CM-6161 TCGA-CM-6677 TCGA-F4-6460 TCGA-G4-6317 
        6.77        15.02        15.02        11.08        31.96        36.00 
TCGA-G4-6628 TCGA-DC-6158 
       79.69        10.98 

$`UHRF1BP1L WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        33.53        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       38.99        37.02        14.93        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       31.07        30.05        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 
       26.01         2.01        20.98        34.03        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 
       18.05        40.96         0.07        21.37        15.52         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        0.72         5.79        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       88.21        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       30.08        32.02         5.03        15.02        15.02        17.03 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       13.05        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
       98.24         8.61        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6321 
       44.68        55.04        85.48        63.62        61.91        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 
       13.78        35.80        26.17        91.79        46.75        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  UHRF1BP1L MUTATED UHRF1BP1L WILD-TYPE 
                  0                   0 
  UHRF1BP1L MUTATED UHRF1BP1L WILD-TYPE 
              79.69              148.01 
  UHRF1BP1L MUTATED UHRF1BP1L WILD-TYPE 
              22.24               20.12 
[1] "0.0 - 79.7 (22.2)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "2.1"
D1479V2, continuous
D1479V3, binary
                     cls
clus                    0   1
  UHRF1BP1L MUTATED    20   1
  UHRF1BP1L WILD-TYPE 346 118
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  UHRF1BP1L MUTATED     20    1
  UHRF1BP1L WILD-TYPE  346  118
        clus
vv       UHRF1BP1L MUTATED UHRF1BP1L WILD-TYPE
  COLON                 20                 346
  RECTUM                 1                 118
[1] 2 2
[1] FALSE
                     vv
clus                  STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  UHRF1BP1L MUTATED         4        0        3         8         1         0
  UHRF1BP1L WILD-TYPE      87        1       29       130         9         1
                     vv
clus                  STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  UHRF1BP1L MUTATED           0          0          1          2        0
  UHRF1BP1L WILD-TYPE        24         11         58         40       48
                     vv
clus                  STAGE IVA STAGE IVB
  UHRF1BP1L MUTATED           0         0
  UHRF1BP1L WILD-TYPE        18         1
D1479V4, multiclass
            clus
vv           UHRF1BP1L MUTATED UHRF1BP1L WILD-TYPE
  STAGE I                    4                  87
  STAGE IA                   0                   1
  STAGE II                   3                  29
  STAGE IIA                  8                 130
  STAGE IIB                  1                   9
  STAGE IIC                  0                   1
  STAGE III                  0                  24
  STAGE IIIA                 0                  11
  STAGE IIIB                 1                  58
  STAGE IIIC                 2                  40
  STAGE IV                   0                  48
  STAGE IVA                  0                  18
  STAGE IVB                  0                   1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                   T1  T2  T3  T4
  UHRF1BP1L MUTATED     0   5  15   1
  UHRF1BP1L WILD-TYPE  17  87 314  49
D1479V5, multiclass
    clus
vv   UHRF1BP1L MUTATED UHRF1BP1L WILD-TYPE
  T1                 0                  17
  T2                 5                  87
  T3                15                 314
  T4                 1                  49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                   N0  N1  N2
  UHRF1BP1L MUTATED    18   1   2
  UHRF1BP1L WILD-TYPE 269 112  85
D1479V6, multiclass
    clus
vv   UHRF1BP1L MUTATED UHRF1BP1L WILD-TYPE
  N0                18                 269
  N1                 1                 112
  N2                 2                  85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1479V7, binary
                     cls
clus                    0   1
  UHRF1BP1L MUTATED    16   0
  UHRF1BP1L WILD-TYPE 359  65
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  UHRF1BP1L MUTATED     16    0
  UHRF1BP1L WILD-TYPE  359   65
   clus
vv  UHRF1BP1L MUTATED UHRF1BP1L WILD-TYPE
  0                16                 359
  1                 0                  65
[1] 2 2
[1] FALSE
D1479V8, binary
                     cls
clus                    0   1
  UHRF1BP1L MUTATED    11  10
  UHRF1BP1L WILD-TYPE 214 254
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  UHRF1BP1L MUTATED     11   10
  UHRF1BP1L WILD-TYPE  214  254
        clus
vv       UHRF1BP1L MUTATED UHRF1BP1L WILD-TYPE
  FEMALE                11                 214
  MALE                  10                 254
[1] 2 2
[1] FALSE
D1479V9, binary
                     cls
clus                    0   1
  UHRF1BP1L MUTATED    16   0
  UHRF1BP1L WILD-TYPE 334  22
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  UHRF1BP1L MUTATED     16    0
  UHRF1BP1L WILD-TYPE  334   22
     clus
vv    UHRF1BP1L MUTATED UHRF1BP1L WILD-TYPE
  NO                 16                 334
  YES                 0                  22
[1] 2 2
[1] FALSE
                     vv
clus                  COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  UHRF1BP1L MUTATED                     17                             3
  UHRF1BP1L WILD-TYPE                  298                            44
                     vv
clus                  RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  UHRF1BP1L MUTATED                       1                              0
  UHRF1BP1L WILD-TYPE                   105                             10
D1479V10, multiclass
                                clus
vv                               UHRF1BP1L MUTATED UHRF1BP1L WILD-TYPE
  COLON ADENOCARCINOMA                          17                 298
  COLON MUCINOUS ADENOCARCINOMA                  3                  44
  RECTAL ADENOCARCINOMA                          1                 105
  RECTAL MUCINOUS ADENOCARCINOMA                 0                  10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                   R0  R1  R2  RX
  UHRF1BP1L MUTATED    14   0   0   0
  UHRF1BP1L WILD-TYPE 331   4  31  25
D1479V11, multiclass
    clus
vv   UHRF1BP1L MUTATED UHRF1BP1L WILD-TYPE
  R0                14                 331
  R1                 0                   4
  R2                 0                  31
  RX                 0                  25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1479V12, continuous
                     vv
clus                  AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  UHRF1BP1L MUTATED                                  0     1
  UHRF1BP1L WILD-TYPE                                1    10
                     vv
clus                  BLACK OR AFRICAN AMERICAN WHITE
  UHRF1BP1L MUTATED                           1    11
  UHRF1BP1L WILD-TYPE                        21   215
D1479V13, multiclass
                                  clus
vv                                 UHRF1BP1L MUTATED UHRF1BP1L WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                 0                   1
  ASIAN                                            1                  10
  BLACK OR AFRICAN AMERICAN                        1                  21
  WHITE                                           11                 215
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1480) Variable = CATSPER2 MUTATION ANALYSIS
D1480V1, survival
                    sevent
clus2                  0   1
  CATSPER2 MUTATED     5   2
  CATSPER2 WILD-TYPE 373  91
  CATSPER2 MUTATED CATSPER2 WILD-TYPE 
                 7                464 
  CATSPER2 MUTATED CATSPER2 WILD-TYPE 
                 2                 91 
$`CATSPER2 MUTATED`
TCGA-AA-3510 TCGA-AA-3811 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-AG-A002 TCGA-AH-6643 
       63.98        10.06        58.39        49.41        20.98         0.69 
TCGA-DT-5265 
        5.29 

$`CATSPER2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       33.01        21.44        17.82         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        88.21         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
        1.45        17.49         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  CATSPER2 MUTATED CATSPER2 WILD-TYPE 
              0.69               0.00 
  CATSPER2 MUTATED CATSPER2 WILD-TYPE 
             63.98             148.01 
  CATSPER2 MUTATED CATSPER2 WILD-TYPE 
            20.980             20.155 
[1] "0.7 - 64.0 (21.0)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.1"
D1480V2, continuous
D1480V3, binary
                    cls
clus                   0   1
  CATSPER2 MUTATED     4   3
  CATSPER2 WILD-TYPE 362 116
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  CATSPER2 MUTATED      4    3
  CATSPER2 WILD-TYPE  362  116
        clus
vv       CATSPER2 MUTATED CATSPER2 WILD-TYPE
  COLON                 4                362
  RECTUM                3                116
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CATSPER2 MUTATED         1        0        3         1         0         0
  CATSPER2 WILD-TYPE      90        1       29       137        10         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CATSPER2 MUTATED           1          0          0          1        0
  CATSPER2 WILD-TYPE        23         11         59         41       48
                    vv
clus                 STAGE IVA STAGE IVB
  CATSPER2 MUTATED           0         0
  CATSPER2 WILD-TYPE        18         1
D1480V4, multiclass
            clus
vv           CATSPER2 MUTATED CATSPER2 WILD-TYPE
  STAGE I                   1                 90
  STAGE IA                  0                  1
  STAGE II                  3                 29
  STAGE IIA                 1                137
  STAGE IIB                 0                 10
  STAGE IIC                 0                  1
  STAGE III                 1                 23
  STAGE IIIA                0                 11
  STAGE IIIB                0                 59
  STAGE IIIC                1                 41
  STAGE IV                  0                 48
  STAGE IVA                 0                 18
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  CATSPER2 MUTATED     0   1   6   0
  CATSPER2 WILD-TYPE  17  91 323  50
D1480V5, multiclass
    clus
vv   CATSPER2 MUTATED CATSPER2 WILD-TYPE
  T1                0                 17
  T2                1                 91
  T3                6                323
  T4                0                 50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  CATSPER2 MUTATED     5   0   2
  CATSPER2 WILD-TYPE 282 113  85
D1480V6, multiclass
    clus
vv   CATSPER2 MUTATED CATSPER2 WILD-TYPE
  N0                5                282
  N1                0                113
  N2                2                 85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1480V7, binary
                    cls
clus                   0   1
  CATSPER2 MUTATED     6   0
  CATSPER2 WILD-TYPE 369  65
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  CATSPER2 MUTATED      6    0
  CATSPER2 WILD-TYPE  369   65
   clus
vv  CATSPER2 MUTATED CATSPER2 WILD-TYPE
  0                6                369
  1                0                 65
[1] 2 2
[1] FALSE
D1480V8, binary
                    cls
clus                   0   1
  CATSPER2 MUTATED     2   5
  CATSPER2 WILD-TYPE 223 259
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  CATSPER2 MUTATED      2    5
  CATSPER2 WILD-TYPE  223  259
        clus
vv       CATSPER2 MUTATED CATSPER2 WILD-TYPE
  FEMALE                2                223
  MALE                  5                259
[1] 2 2
[1] FALSE
D1480V9, binary
                    cls
clus                   0   1
  CATSPER2 MUTATED     6   0
  CATSPER2 WILD-TYPE 344  22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  CATSPER2 MUTATED      6    0
  CATSPER2 WILD-TYPE  344   22
     clus
vv    CATSPER2 MUTATED CATSPER2 WILD-TYPE
  NO                 6                344
  YES                0                 22
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CATSPER2 MUTATED                      4                             0
  CATSPER2 WILD-TYPE                  311                            47
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CATSPER2 MUTATED                       2                              1
  CATSPER2 WILD-TYPE                   104                              9
D1480V10, multiclass
                                clus
vv                               CATSPER2 MUTATED CATSPER2 WILD-TYPE
  COLON ADENOCARCINOMA                          4                311
  COLON MUCINOUS ADENOCARCINOMA                 0                 47
  RECTAL ADENOCARCINOMA                         2                104
  RECTAL MUCINOUS ADENOCARCINOMA                1                  9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  CATSPER2 MUTATED     5   0   0   1
  CATSPER2 WILD-TYPE 340   4  31  24
D1480V11, multiclass
    clus
vv   CATSPER2 MUTATED CATSPER2 WILD-TYPE
  R0                5                340
  R1                0                  4
  R2                0                 31
  RX                1                 24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1480V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CATSPER2 MUTATED                                  0     1
  CATSPER2 WILD-TYPE                                1    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  CATSPER2 MUTATED                           0     3
  CATSPER2 WILD-TYPE                        22   223
D1480V13, multiclass
                                  clus
vv                                 CATSPER2 MUTATED CATSPER2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                 10
  BLACK OR AFRICAN AMERICAN                       0                 22
  WHITE                                           3                223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1481) Variable = PPP2R5E MUTATION ANALYSIS
D1481V1, survival
                   sevent
clus2                 0   1
  PPP2R5E MUTATED     8   0
  PPP2R5E WILD-TYPE 370  93
  PPP2R5E MUTATED PPP2R5E WILD-TYPE 
                8               463 
  PPP2R5E MUTATED PPP2R5E WILD-TYPE 
                0                93 
$`PPP2R5E MUTATED`
TCGA-A6-5661 TCGA-AA-A00J TCGA-AA-A01Q TCGA-AD-6895 TCGA-CA-6717 TCGA-CM-4746 
       33.53        18.05         1.02         0.72        12.76        37.02 
TCGA-D5-6541 TCGA-DM-A1HB 
       15.58       135.65 

$`PPP2R5E WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L 
       38.04        19.00        30.02        34.03        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        31.00        38.07        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.79         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07        12.20        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       23.05        20.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      131.51       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  PPP2R5E MUTATED PPP2R5E WILD-TYPE 
             0.72              0.00 
  PPP2R5E MUTATED PPP2R5E WILD-TYPE 
           135.65            148.01 
  PPP2R5E MUTATED PPP2R5E WILD-TYPE 
           16.815            20.280 
[1] "0.7 - 135.7 (16.8)" "0.0 - 148.0 (20.3)"
[1] "hr="     "9200000"
D1481V2, continuous
D1481V3, binary
                   cls
clus                  0   1
  PPP2R5E MUTATED     8   0
  PPP2R5E WILD-TYPE 358 119
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PPP2R5E MUTATED      8    0
  PPP2R5E WILD-TYPE  358  119
        clus
vv       PPP2R5E MUTATED PPP2R5E WILD-TYPE
  COLON                8               358
  RECTUM               0               119
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PPP2R5E MUTATED         1        0        1         3         0         0
  PPP2R5E WILD-TYPE      90        1       31       135        10         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PPP2R5E MUTATED           0          0          2          0        0
  PPP2R5E WILD-TYPE        24         11         57         42       48
                   vv
clus                STAGE IVA STAGE IVB
  PPP2R5E MUTATED           0         0
  PPP2R5E WILD-TYPE        18         1
D1481V4, multiclass
            clus
vv           PPP2R5E MUTATED PPP2R5E WILD-TYPE
  STAGE I                  1                90
  STAGE IA                 0                 1
  STAGE II                 1                31
  STAGE IIA                3               135
  STAGE IIB                0                10
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               0                11
  STAGE IIIB               2                57
  STAGE IIIC               0                42
  STAGE IV                 0                48
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  PPP2R5E MUTATED     0   1   6   1
  PPP2R5E WILD-TYPE  17  91 323  49
D1481V5, multiclass
    clus
vv   PPP2R5E MUTATED PPP2R5E WILD-TYPE
  T1               0                17
  T2               1                91
  T3               6               323
  T4               1                49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  PPP2R5E MUTATED     5   3   0
  PPP2R5E WILD-TYPE 282 110  87
D1481V6, multiclass
    clus
vv   PPP2R5E MUTATED PPP2R5E WILD-TYPE
  N0               5               282
  N1               3               110
  N2               0                87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1481V7, binary
                   cls
clus                  0   1
  PPP2R5E MUTATED     7   0
  PPP2R5E WILD-TYPE 368  65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PPP2R5E MUTATED      7    0
  PPP2R5E WILD-TYPE  368   65
   clus
vv  PPP2R5E MUTATED PPP2R5E WILD-TYPE
  0               7               368
  1               0                65
[1] 2 2
[1] FALSE
D1481V8, binary
                   cls
clus                  0   1
  PPP2R5E MUTATED     2   6
  PPP2R5E WILD-TYPE 223 258
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PPP2R5E MUTATED      2    6
  PPP2R5E WILD-TYPE  223  258
        clus
vv       PPP2R5E MUTATED PPP2R5E WILD-TYPE
  FEMALE               2               223
  MALE                 6               258
[1] 2 2
[1] FALSE
D1481V9, binary
                   cls
clus                  0   1
  PPP2R5E MUTATED     5   0
  PPP2R5E WILD-TYPE 345  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PPP2R5E MUTATED      5    0
  PPP2R5E WILD-TYPE  345   22
     clus
vv    PPP2R5E MUTATED PPP2R5E WILD-TYPE
  NO                5               345
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PPP2R5E MUTATED                      5                             2
  PPP2R5E WILD-TYPE                  310                            45
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PPP2R5E MUTATED                       0                              0
  PPP2R5E WILD-TYPE                   106                             10
D1481V10, multiclass
                                clus
vv                               PPP2R5E MUTATED PPP2R5E WILD-TYPE
  COLON ADENOCARCINOMA                         5               310
  COLON MUCINOUS ADENOCARCINOMA                2                45
  RECTAL ADENOCARCINOMA                        0               106
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  PPP2R5E MUTATED     5   0   0   1
  PPP2R5E WILD-TYPE 340   4  31  24
D1481V11, multiclass
    clus
vv   PPP2R5E MUTATED PPP2R5E WILD-TYPE
  R0               5               340
  R1               0                 4
  R2               0                31
  RX               1                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1481V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PPP2R5E MUTATED                                  0     1
  PPP2R5E WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  PPP2R5E MUTATED                           2     3
  PPP2R5E WILD-TYPE                        20   223
D1481V13, multiclass
                                  clus
vv                                 PPP2R5E MUTATED PPP2R5E WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                10
  BLACK OR AFRICAN AMERICAN                      2                20
  WHITE                                          3               223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1482) Variable = SPOPL MUTATION ANALYSIS
D1482V1, survival
                 sevent
clus2               0   1
  SPOPL MUTATED     8   2
  SPOPL WILD-TYPE 370  91
  SPOPL MUTATED SPOPL WILD-TYPE 
             10             461 
  SPOPL MUTATED SPOPL WILD-TYPE 
              2              91 
$`SPOPL MUTATED`
TCGA-AA-3666 TCGA-AA-3672 TCGA-AZ-4315 TCGA-AZ-6603 TCGA-CA-6716 TCGA-D5-6532 
        2.01         0.92        58.39        29.56        12.20        18.25 
TCGA-D5-6541 TCGA-DM-A28E TCGA-F4-6704 TCGA-G4-6586 
       15.58       119.93         1.55        35.80 

$`SPOPL WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 
        6.05         6.97        54.02        14.01        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       33.01        21.44        17.82         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
      100.01         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 
        3.06         3.25         3.29         0.07        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6534 
       19.59        56.09        55.92        20.19         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28F 
      131.51       135.65       139.17         6.12        81.37        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
        6.18        47.87        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 
       61.91        36.00        22.09        13.78        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  SPOPL MUTATED SPOPL WILD-TYPE 
           0.92            0.00 
  SPOPL MUTATED SPOPL WILD-TYPE 
         119.93          148.01 
  SPOPL MUTATED SPOPL WILD-TYPE 
         16.915          20.280 
[1] "0.9 - 119.9 (16.9)" "0.0 - 148.0 (20.3)"
[1] "hr=" "1"  
D1482V2, continuous
D1482V3, binary
                 cls
clus                0   1
  SPOPL MUTATED    10   0
  SPOPL WILD-TYPE 356 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SPOPL MUTATED     10    0
  SPOPL WILD-TYPE  356  119
        clus
vv       SPOPL MUTATED SPOPL WILD-TYPE
  COLON             10             356
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SPOPL MUTATED         0        0        0         6         0         0
  SPOPL WILD-TYPE      91        1       32       132        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SPOPL MUTATED           2          0          0          1        0         0
  SPOPL WILD-TYPE        22         11         59         41       48        18
                 vv
clus              STAGE IVB
  SPOPL MUTATED           0
  SPOPL WILD-TYPE         1
D1482V4, multiclass
            clus
vv           SPOPL MUTATED SPOPL WILD-TYPE
  STAGE I                0              91
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              6             132
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              2              22
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             1              41
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  SPOPL MUTATED     0   1   9   0
  SPOPL WILD-TYPE  17  91 320  50
D1482V5, multiclass
    clus
vv   SPOPL MUTATED SPOPL WILD-TYPE
  T1             0              17
  T2             1              91
  T3             9             320
  T4             0              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  SPOPL MUTATED     6   3   1
  SPOPL WILD-TYPE 281 110  86
D1482V6, multiclass
    clus
vv   SPOPL MUTATED SPOPL WILD-TYPE
  N0             6             281
  N1             3             110
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1482V7, binary
                 cls
clus                0   1
  SPOPL MUTATED     8   0
  SPOPL WILD-TYPE 367  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SPOPL MUTATED      8    0
  SPOPL WILD-TYPE  367   65
   clus
vv  SPOPL MUTATED SPOPL WILD-TYPE
  0             8             367
  1             0              65
[1] 2 2
[1] FALSE
D1482V8, binary
                 cls
clus                0   1
  SPOPL MUTATED     4   6
  SPOPL WILD-TYPE 221 258
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SPOPL MUTATED      4    6
  SPOPL WILD-TYPE  221  258
        clus
vv       SPOPL MUTATED SPOPL WILD-TYPE
  FEMALE             4             221
  MALE               6             258
[1] 2 2
[1] FALSE
D1482V9, binary
                 cls
clus                0   1
  SPOPL MUTATED     7   0
  SPOPL WILD-TYPE 343  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SPOPL MUTATED      7    0
  SPOPL WILD-TYPE  343   22
     clus
vv    SPOPL MUTATED SPOPL WILD-TYPE
  NO              7             343
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SPOPL MUTATED                      9                             1
  SPOPL WILD-TYPE                  306                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SPOPL MUTATED                       0                              0
  SPOPL WILD-TYPE                   106                             10
D1482V10, multiclass
                                clus
vv                               SPOPL MUTATED SPOPL WILD-TYPE
  COLON ADENOCARCINOMA                       9             306
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  SPOPL MUTATED     7   0   0   1
  SPOPL WILD-TYPE 338   4  31  24
D1482V11, multiclass
    clus
vv   SPOPL MUTATED SPOPL WILD-TYPE
  R0             7             338
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1482V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SPOPL MUTATED                                  1     1
  SPOPL WILD-TYPE                                0    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  SPOPL MUTATED                           0     6
  SPOPL WILD-TYPE                        22   220
D1482V13, multiclass
                                  clus
vv                                 SPOPL MUTATED SPOPL WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             1               0
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        6             220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1483) Variable = FCRL4 MUTATION ANALYSIS
D1483V1, survival
                 sevent
clus2               0   1
  FCRL4 MUTATED     9   4
  FCRL4 WILD-TYPE 369  89
  FCRL4 MUTATED FCRL4 WILD-TYPE 
             13             458 
  FCRL4 MUTATED FCRL4 WILD-TYPE 
              4              89 
$`FCRL4 MUTATED`
TCGA-AA-3542 TCGA-AA-3561 TCGA-AA-3864 TCGA-AA-A01R TCGA-AD-6964 TCGA-AZ-4315 
       12.99        13.94        53.00        35.01        10.88        58.39 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-CA-6717 TCGA-DM-A1DA TCGA-DM-A1HA TCGA-AF-6672 
       49.41         6.77        12.76         7.50       131.51        10.39 
TCGA-F5-6465 
       49.51 

$`FCRL4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       29.00        26.01         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       19.99        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 
        0.99        31.07        31.07        30.05        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       31.00        38.07         1.02         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
        0.72         5.79        22.42        27.42         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.20        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
       12.59       140.38        44.32       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
        9.96        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  FCRL4 MUTATED FCRL4 WILD-TYPE 
           6.77            0.00 
  FCRL4 MUTATED FCRL4 WILD-TYPE 
         131.51          148.01 
  FCRL4 MUTATED FCRL4 WILD-TYPE 
         13.940          20.235 
[1] "6.8 - 131.5 (13.9)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.2"
D1483V2, continuous
D1483V3, binary
                 cls
clus                0   1
  FCRL4 MUTATED    11   2
  FCRL4 WILD-TYPE 355 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FCRL4 MUTATED     11    2
  FCRL4 WILD-TYPE  355  117
        clus
vv       FCRL4 MUTATED FCRL4 WILD-TYPE
  COLON             11             355
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FCRL4 MUTATED         1        0        2         4         0         0
  FCRL4 WILD-TYPE      90        1       30       134        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  FCRL4 MUTATED           1          0          0          3        1         0
  FCRL4 WILD-TYPE        23         11         59         39       47        18
                 vv
clus              STAGE IVB
  FCRL4 MUTATED           0
  FCRL4 WILD-TYPE         1
D1483V4, multiclass
            clus
vv           FCRL4 MUTATED FCRL4 WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA              4             134
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             3              39
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  FCRL4 MUTATED     0   1  10   2
  FCRL4 WILD-TYPE  17  91 319  48
D1483V5, multiclass
    clus
vv   FCRL4 MUTATED FCRL4 WILD-TYPE
  T1             0              17
  T2             1              91
  T3            10             319
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  FCRL4 MUTATED     7   0   6
  FCRL4 WILD-TYPE 280 113  81
D1483V6, multiclass
    clus
vv   FCRL4 MUTATED FCRL4 WILD-TYPE
  N0             7             280
  N1             0             113
  N2             6              81
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1483V7, binary
                 cls
clus                0   1
  FCRL4 MUTATED     9   0
  FCRL4 WILD-TYPE 366  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FCRL4 MUTATED      9    0
  FCRL4 WILD-TYPE  366   65
   clus
vv  FCRL4 MUTATED FCRL4 WILD-TYPE
  0             9             366
  1             0              65
[1] 2 2
[1] FALSE
D1483V8, binary
                 cls
clus                0   1
  FCRL4 MUTATED     3  10
  FCRL4 WILD-TYPE 222 254
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FCRL4 MUTATED      3   10
  FCRL4 WILD-TYPE  222  254
        clus
vv       FCRL4 MUTATED FCRL4 WILD-TYPE
  FEMALE             3             222
  MALE              10             254
[1] 2 2
[1] FALSE
D1483V9, binary
                 cls
clus                0   1
  FCRL4 MUTATED     9   2
  FCRL4 WILD-TYPE 341  20
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FCRL4 MUTATED      9    2
  FCRL4 WILD-TYPE  341   20
     clus
vv    FCRL4 MUTATED FCRL4 WILD-TYPE
  NO              9             341
  YES             2              20
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  FCRL4 MUTATED                      9                             2
  FCRL4 WILD-TYPE                  306                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  FCRL4 MUTATED                       2                              0
  FCRL4 WILD-TYPE                   104                             10
D1483V10, multiclass
                                clus
vv                               FCRL4 MUTATED FCRL4 WILD-TYPE
  COLON ADENOCARCINOMA                       9             306
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  FCRL4 MUTATED     6   0   0   1
  FCRL4 WILD-TYPE 339   4  31  24
D1483V11, multiclass
    clus
vv   FCRL4 MUTATED FCRL4 WILD-TYPE
  R0             6             339
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1483V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FCRL4 MUTATED                                  0     1
  FCRL4 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  FCRL4 MUTATED                           0     8
  FCRL4 WILD-TYPE                        22   218
D1483V13, multiclass
                                  clus
vv                                 FCRL4 MUTATED FCRL4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        8             218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1484) Variable = THRAP3 MUTATION ANALYSIS
D1484V1, survival
                  sevent
clus2                0   1
  THRAP3 MUTATED     9   3
  THRAP3 WILD-TYPE 369  90
  THRAP3 MUTATED THRAP3 WILD-TYPE 
              12              459 
  THRAP3 MUTATED THRAP3 WILD-TYPE 
               3               90 
$`THRAP3 MUTATED`
TCGA-AA-3492 TCGA-AA-3815 TCGA-AA-3821 TCGA-AA-3845 TCGA-AA-A00N TCGA-AY-6386 
        3.02        33.04         1.02         0.00         4.01        17.82 
TCGA-CA-6717 TCGA-CM-4743 TCGA-D5-6540 TCGA-D5-6924 TCGA-F4-6703 TCGA-AG-A002 
       12.76        23.05        16.14        14.30        47.87        20.98 

$`THRAP3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 
       10.06        35.05         0.99        25.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       38.99        37.02        14.93        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AZ-4315 
       27.09        16.31         0.95        33.01        21.44        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07        12.20        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 
       21.14        82.95         1.91       124.27        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
        4.80        17.13        12.49        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
        4.41        12.43         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6704 
       98.24         8.61        31.96        35.74         6.18         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  THRAP3 MUTATED THRAP3 WILD-TYPE 
               0                0 
  THRAP3 MUTATED THRAP3 WILD-TYPE 
           47.87           148.01 
  THRAP3 MUTATED THRAP3 WILD-TYPE 
           15.22            20.55 
[1] "0.0 - 47.9 (15.2)"  "0.0 - 148.0 (20.6)"
[1] "hr=" "2"  
D1484V2, continuous
D1484V3, binary
                  cls
clus                 0   1
  THRAP3 MUTATED    11   1
  THRAP3 WILD-TYPE 355 118
[1] "tbl2"
                  cls
clus               [,1] [,2]
  THRAP3 MUTATED     11    1
  THRAP3 WILD-TYPE  355  118
        clus
vv       THRAP3 MUTATED THRAP3 WILD-TYPE
  COLON              11              355
  RECTUM              1              118
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  THRAP3 MUTATED         3        0        1         6         1         0
  THRAP3 WILD-TYPE      88        1       31       132         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  THRAP3 MUTATED           0          0          1          0        0
  THRAP3 WILD-TYPE        24         11         58         42       48
                  vv
clus               STAGE IVA STAGE IVB
  THRAP3 MUTATED           0         0
  THRAP3 WILD-TYPE        18         1
D1484V4, multiclass
            clus
vv           THRAP3 MUTATED THRAP3 WILD-TYPE
  STAGE I                 3               88
  STAGE IA                0                1
  STAGE II                1               31
  STAGE IIA               6              132
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              1               58
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  THRAP3 MUTATED     0   3   8   1
  THRAP3 WILD-TYPE  17  89 321  49
D1484V5, multiclass
    clus
vv   THRAP3 MUTATED THRAP3 WILD-TYPE
  T1              0               17
  T2              3               89
  T3              8              321
  T4              1               49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  THRAP3 MUTATED    11   1   0
  THRAP3 WILD-TYPE 276 112  87
D1484V6, multiclass
    clus
vv   THRAP3 MUTATED THRAP3 WILD-TYPE
  N0             11              276
  N1              1              112
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1484V7, binary
                  cls
clus                 0   1
  THRAP3 MUTATED    12   0
  THRAP3 WILD-TYPE 363  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  THRAP3 MUTATED     12    0
  THRAP3 WILD-TYPE  363   65
   clus
vv  THRAP3 MUTATED THRAP3 WILD-TYPE
  0             12              363
  1              0               65
[1] 2 2
[1] FALSE
D1484V8, binary
                  cls
clus                 0   1
  THRAP3 MUTATED     5   7
  THRAP3 WILD-TYPE 220 257
[1] "tbl2"
                  cls
clus               [,1] [,2]
  THRAP3 MUTATED      5    7
  THRAP3 WILD-TYPE  220  257
        clus
vv       THRAP3 MUTATED THRAP3 WILD-TYPE
  FEMALE              5              220
  MALE                7              257
[1] 2 2
[1] FALSE
D1484V9, binary
                  cls
clus                 0   1
  THRAP3 MUTATED    10   0
  THRAP3 WILD-TYPE 340  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  THRAP3 MUTATED     10    0
  THRAP3 WILD-TYPE  340   22
     clus
vv    THRAP3 MUTATED THRAP3 WILD-TYPE
  NO              10              340
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  THRAP3 MUTATED                      7                             4
  THRAP3 WILD-TYPE                  308                            43
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  THRAP3 MUTATED                       1                              0
  THRAP3 WILD-TYPE                   105                             10
D1484V10, multiclass
                                clus
vv                               THRAP3 MUTATED THRAP3 WILD-TYPE
  COLON ADENOCARCINOMA                        7              308
  COLON MUCINOUS ADENOCARCINOMA               4               43
  RECTAL ADENOCARCINOMA                       1              105
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  THRAP3 MUTATED    11   0   0   1
  THRAP3 WILD-TYPE 334   4  31  24
D1484V11, multiclass
    clus
vv   THRAP3 MUTATED THRAP3 WILD-TYPE
  R0             11              334
  R1              0                4
  R2              0               31
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1484V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  THRAP3 MUTATED                                  0     1
  THRAP3 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  THRAP3 MUTATED                           1     4
  THRAP3 WILD-TYPE                        21   222
D1484V13, multiclass
                                  clus
vv                                 THRAP3 MUTATED THRAP3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                         4              222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1485) Variable = ATP2B4 MUTATION ANALYSIS
D1485V1, survival
                  sevent
clus2                0   1
  ATP2B4 MUTATED    13   6
  ATP2B4 WILD-TYPE 365  87
  ATP2B4 MUTATED ATP2B4 WILD-TYPE 
              19              452 
  ATP2B4 MUTATED ATP2B4 WILD-TYPE 
               6               87 
$`ATP2B4 MUTATED`
TCGA-A6-5665 TCGA-AA-3950 TCGA-AA-3966 TCGA-AA-A010 TCGA-AA-A024 TCGA-AD-6889 
       22.06        24.00         2.01        34.98        39.06        56.55 
TCGA-AZ-5403 TCGA-AZ-6601 TCGA-CK-5914 TCGA-CM-5862 TCGA-CM-6161 TCGA-CM-6165 
       62.79       100.01         9.99         5.03        15.02        16.04 
TCGA-CM-6676 TCGA-DM-A28G TCGA-F4-6856 TCGA-G4-6588 TCGA-AG-A002 TCGA-CI-6624 
       11.08        60.79        35.31        26.17        20.98         4.73 
TCGA-F5-6464 
        9.96 

$`ATP2B4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 
        2.01        12.99        24.00        33.01        26.01         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       20.98        34.03        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       26.01        37.02        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
        0.07        21.37        15.52         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6598 
        1.41         5.13       106.75        22.36        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77        12.10        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 
       85.45        15.62        49.08        51.32        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        15.02        17.03        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       29.03        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6677 TCGA-CM-6678 
       14.04        11.01        12.95        13.05        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       35.97       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 
       33.67        13.25         0.53        47.41       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 
       61.91        36.00        22.09        13.78        35.80        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        6.97        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  ATP2B4 MUTATED ATP2B4 WILD-TYPE 
            2.01             0.00 
  ATP2B4 MUTATED ATP2B4 WILD-TYPE 
          100.01           148.01 
  ATP2B4 MUTATED ATP2B4 WILD-TYPE 
          22.060           20.085 
[1] "2.0 - 100.0 (22.1)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.4"
D1485V2, continuous
D1485V3, binary
                  cls
clus                 0   1
  ATP2B4 MUTATED    18   3
  ATP2B4 WILD-TYPE 348 116
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP2B4 MUTATED     18    3
  ATP2B4 WILD-TYPE  348  116
        clus
vv       ATP2B4 MUTATED ATP2B4 WILD-TYPE
  COLON              18              348
  RECTUM              3              116
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ATP2B4 MUTATED         6        0        3         8         1         0
  ATP2B4 WILD-TYPE      85        1       29       130         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ATP2B4 MUTATED           0          0          1          1        0
  ATP2B4 WILD-TYPE        24         11         58         41       48
                  vv
clus               STAGE IVA STAGE IVB
  ATP2B4 MUTATED           1         0
  ATP2B4 WILD-TYPE        17         1
D1485V4, multiclass
            clus
vv           ATP2B4 MUTATED ATP2B4 WILD-TYPE
  STAGE I                 6               85
  STAGE IA                0                1
  STAGE II                3               29
  STAGE IIA               8              130
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              1               58
  STAGE IIIC              1               41
  STAGE IV                0               48
  STAGE IVA               1               17
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ATP2B4 MUTATED     0   6  13   2
  ATP2B4 WILD-TYPE  17  86 316  48
D1485V5, multiclass
    clus
vv   ATP2B4 MUTATED ATP2B4 WILD-TYPE
  T1              0               17
  T2              6               86
  T3             13              316
  T4              2               48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  ATP2B4 MUTATED    18   2   1
  ATP2B4 WILD-TYPE 269 111  86
D1485V6, multiclass
    clus
vv   ATP2B4 MUTATED ATP2B4 WILD-TYPE
  N0             18              269
  N1              2              111
  N2              1               86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1485V7, binary
                  cls
clus                 0   1
  ATP2B4 MUTATED    17   1
  ATP2B4 WILD-TYPE 358  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP2B4 MUTATED     17    1
  ATP2B4 WILD-TYPE  358   64
   clus
vv  ATP2B4 MUTATED ATP2B4 WILD-TYPE
  0             17              358
  1              1               64
[1] 2 2
[1] FALSE
D1485V8, binary
                  cls
clus                 0   1
  ATP2B4 MUTATED     9  12
  ATP2B4 WILD-TYPE 216 252
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP2B4 MUTATED      9   12
  ATP2B4 WILD-TYPE  216  252
        clus
vv       ATP2B4 MUTATED ATP2B4 WILD-TYPE
  FEMALE              9              216
  MALE               12              252
[1] 2 2
[1] FALSE
D1485V9, binary
                  cls
clus                 0   1
  ATP2B4 MUTATED    14   0
  ATP2B4 WILD-TYPE 336  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP2B4 MUTATED     14    0
  ATP2B4 WILD-TYPE  336   22
     clus
vv    ATP2B4 MUTATED ATP2B4 WILD-TYPE
  NO              14              336
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ATP2B4 MUTATED                     14                             4
  ATP2B4 WILD-TYPE                  301                            43
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ATP2B4 MUTATED                       3                              0
  ATP2B4 WILD-TYPE                   103                             10
D1485V10, multiclass
                                clus
vv                               ATP2B4 MUTATED ATP2B4 WILD-TYPE
  COLON ADENOCARCINOMA                       14              301
  COLON MUCINOUS ADENOCARCINOMA               4               43
  RECTAL ADENOCARCINOMA                       3              103
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ATP2B4 MUTATED    13   0   0   2
  ATP2B4 WILD-TYPE 332   4  31  23
D1485V11, multiclass
    clus
vv   ATP2B4 MUTATED ATP2B4 WILD-TYPE
  R0             13              332
  R1              0                4
  R2              0               31
  RX              2               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1485V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ATP2B4 MUTATED                                  0     1
  ATP2B4 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ATP2B4 MUTATED                           0    14
  ATP2B4 WILD-TYPE                        22   212
D1485V13, multiclass
                                  clus
vv                                 ATP2B4 MUTATED ATP2B4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                        14              212
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1486) Variable = PCDHGA8 MUTATION ANALYSIS
D1486V1, survival
                   sevent
clus2                 0   1
  PCDHGA8 MUTATED    14   4
  PCDHGA8 WILD-TYPE 364  89
  PCDHGA8 MUTATED PCDHGA8 WILD-TYPE 
               18               453 
  PCDHGA8 MUTATED PCDHGA8 WILD-TYPE 
                4                89 
$`PCDHGA8 MUTATED`
TCGA-A6-5661 TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3663 TCGA-AA-3672 TCGA-AA-3715 
       33.53         3.02        63.98         6.97         0.92        19.04 
TCGA-AA-A010 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-CA-6716 TCGA-CA-6717 TCGA-CK-5916 
       34.98        58.39        49.41        12.20        12.76        21.14 
TCGA-G4-6304 TCGA-G4-6309 TCGA-AG-A002 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
       53.62        85.48        20.98         7.17        15.02         5.03 

$`PCDHGA8 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 
       20.12        19.66        20.28         7.04         1.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02        78.08         6.05        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
       14.01        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        33.01        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 
      106.75        22.36        62.79        88.21         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6718 
       12.69         3.06         3.25         3.29         0.07        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       51.32         9.99        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 
       35.31       133.18        74.56        65.85        44.68        55.04 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-DC-6155 
        6.05        33.17         6.97         4.73        78.12        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  PCDHGA8 MUTATED PCDHGA8 WILD-TYPE 
             0.92              0.00 
  PCDHGA8 MUTATED PCDHGA8 WILD-TYPE 
            85.48            148.01 
  PCDHGA8 MUTATED PCDHGA8 WILD-TYPE 
            20.01             20.19 
[1] "0.9 - 85.5 (20.0)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1"  
D1486V2, continuous
D1486V3, binary
                   cls
clus                  0   1
  PCDHGA8 MUTATED    14   4
  PCDHGA8 WILD-TYPE 352 115
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PCDHGA8 MUTATED     14    4
  PCDHGA8 WILD-TYPE  352  115
        clus
vv       PCDHGA8 MUTATED PCDHGA8 WILD-TYPE
  COLON               14               352
  RECTUM               4               115
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PCDHGA8 MUTATED         3        0        5         5         2         0
  PCDHGA8 WILD-TYPE      88        1       27       133         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PCDHGA8 MUTATED           1          0          2          0        0
  PCDHGA8 WILD-TYPE        23         11         57         42       48
                   vv
clus                STAGE IVA STAGE IVB
  PCDHGA8 MUTATED           0         0
  PCDHGA8 WILD-TYPE        18         1
D1486V4, multiclass
            clus
vv           PCDHGA8 MUTATED PCDHGA8 WILD-TYPE
  STAGE I                  3                88
  STAGE IA                 0                 1
  STAGE II                 5                27
  STAGE IIA                5               133
  STAGE IIB                2                 8
  STAGE IIC                0                 1
  STAGE III                1                23
  STAGE IIIA               0                11
  STAGE IIIB               2                57
  STAGE IIIC               0                42
  STAGE IV                 0                48
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  PCDHGA8 MUTATED     2   1  13   2
  PCDHGA8 WILD-TYPE  15  91 316  48
D1486V5, multiclass
    clus
vv   PCDHGA8 MUTATED PCDHGA8 WILD-TYPE
  T1               2                15
  T2               1                91
  T3              13               316
  T4               2                48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  PCDHGA8 MUTATED    15   3   0
  PCDHGA8 WILD-TYPE 272 110  87
D1486V6, multiclass
    clus
vv   PCDHGA8 MUTATED PCDHGA8 WILD-TYPE
  N0              15               272
  N1               3               110
  N2               0                87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1486V7, binary
                   cls
clus                  0   1
  PCDHGA8 MUTATED    16   0
  PCDHGA8 WILD-TYPE 359  65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PCDHGA8 MUTATED     16    0
  PCDHGA8 WILD-TYPE  359   65
   clus
vv  PCDHGA8 MUTATED PCDHGA8 WILD-TYPE
  0              16               359
  1               0                65
[1] 2 2
[1] FALSE
D1486V8, binary
                   cls
clus                  0   1
  PCDHGA8 MUTATED    10   8
  PCDHGA8 WILD-TYPE 215 256
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PCDHGA8 MUTATED     10    8
  PCDHGA8 WILD-TYPE  215  256
        clus
vv       PCDHGA8 MUTATED PCDHGA8 WILD-TYPE
  FEMALE              10               215
  MALE                 8               256
[1] 2 2
[1] FALSE
D1486V9, binary
                   cls
clus                  0   1
  PCDHGA8 MUTATED    17   0
  PCDHGA8 WILD-TYPE 333  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PCDHGA8 MUTATED     17    0
  PCDHGA8 WILD-TYPE  333   22
     clus
vv    PCDHGA8 MUTATED PCDHGA8 WILD-TYPE
  NO               17               333
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PCDHGA8 MUTATED                     13                             1
  PCDHGA8 WILD-TYPE                  302                            46
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PCDHGA8 MUTATED                       4                              0
  PCDHGA8 WILD-TYPE                   102                             10
D1486V10, multiclass
                                clus
vv                               PCDHGA8 MUTATED PCDHGA8 WILD-TYPE
  COLON ADENOCARCINOMA                        13               302
  COLON MUCINOUS ADENOCARCINOMA                1                46
  RECTAL ADENOCARCINOMA                        4               102
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  PCDHGA8 MUTATED    13   0   0   4
  PCDHGA8 WILD-TYPE 332   4  31  21
D1486V11, multiclass
    clus
vv   PCDHGA8 MUTATED PCDHGA8 WILD-TYPE
  R0              13               332
  R1               0                 4
  R2               0                31
  RX               4                21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1486V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PCDHGA8 MUTATED                                  0     2
  PCDHGA8 WILD-TYPE                                1     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  PCDHGA8 MUTATED                           3     6
  PCDHGA8 WILD-TYPE                        19   220
D1486V13, multiclass
                                  clus
vv                                 PCDHGA8 MUTATED PCDHGA8 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          2                 9
  BLACK OR AFRICAN AMERICAN                      3                19
  WHITE                                          6               220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1487) Variable = TRIM46 MUTATION ANALYSIS
D1487V1, survival
                  sevent
clus2                0   1
  TRIM46 MUTATED     9   5
  TRIM46 WILD-TYPE 369  88
  TRIM46 MUTATED TRIM46 WILD-TYPE 
              14              457 
  TRIM46 MUTATED TRIM46 WILD-TYPE 
               5               88 
$`TRIM46 MUTATED`
TCGA-AA-3715 TCGA-AA-3845 TCGA-AD-6889 TCGA-AD-6964 TCGA-AY-6197 TCGA-AZ-4315 
       19.04         0.00        56.55        10.88        21.44        58.39 
TCGA-AZ-6601 TCGA-CA-6718 TCGA-CM-4746 TCGA-CM-5344 TCGA-CM-5861 TCGA-D5-6539 
      100.01        10.06        37.02        22.03        15.02        12.49 
TCGA-DM-A0X9 TCGA-DM-A1HB 
      119.70       135.65 

$`TRIM46 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 
       17.98        15.95        38.99        37.02        14.93        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
        0.79         0.72         5.79        22.42        27.42         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 
       14.50        27.09        16.31         0.95        33.01        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       49.41         6.77        12.10        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07        12.20        12.76        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4747 
       82.95         1.91       124.27        23.05        20.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 
       13.02        29.06        22.98        30.08        32.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 
       43.27        15.12        17.85         4.80        17.13        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       11.38        10.26        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      131.51       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  TRIM46 MUTATED TRIM46 WILD-TYPE 
               0                0 
  TRIM46 MUTATED TRIM46 WILD-TYPE 
          135.65           148.01 
  TRIM46 MUTATED TRIM46 WILD-TYPE 
          21.735           20.120 
[1] "0.0 - 135.7 (21.7)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.2"
D1487V2, continuous
D1487V3, binary
                  cls
clus                 0   1
  TRIM46 MUTATED    15   0
  TRIM46 WILD-TYPE 351 119
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIM46 MUTATED     15    0
  TRIM46 WILD-TYPE  351  119
        clus
vv       TRIM46 MUTATED TRIM46 WILD-TYPE
  COLON              15              351
  RECTUM              0              119
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TRIM46 MUTATED         1        0        3         7         0         0
  TRIM46 WILD-TYPE      90        1       29       131        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TRIM46 MUTATED           0          1          2          0        0
  TRIM46 WILD-TYPE        24         10         57         42       48
                  vv
clus               STAGE IVA STAGE IVB
  TRIM46 MUTATED           0         0
  TRIM46 WILD-TYPE        18         1
D1487V4, multiclass
            clus
vv           TRIM46 MUTATED TRIM46 WILD-TYPE
  STAGE I                 1               90
  STAGE IA                0                1
  STAGE II                3               29
  STAGE IIA               7              131
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              1               10
  STAGE IIIB              2               57
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  TRIM46 MUTATED     0   1  12   2
  TRIM46 WILD-TYPE  17  91 317  48
D1487V5, multiclass
    clus
vv   TRIM46 MUTATED TRIM46 WILD-TYPE
  T1              0               17
  T2              1               91
  T3             12              317
  T4              2               48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  TRIM46 MUTATED    12   2   1
  TRIM46 WILD-TYPE 275 111  86
D1487V6, multiclass
    clus
vv   TRIM46 MUTATED TRIM46 WILD-TYPE
  N0             12              275
  N1              2              111
  N2              1               86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1487V7, binary
                  cls
clus                 0   1
  TRIM46 MUTATED    13   0
  TRIM46 WILD-TYPE 362  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIM46 MUTATED     13    0
  TRIM46 WILD-TYPE  362   65
   clus
vv  TRIM46 MUTATED TRIM46 WILD-TYPE
  0             13              362
  1              0               65
[1] 2 2
[1] FALSE
D1487V8, binary
                  cls
clus                 0   1
  TRIM46 MUTATED     6   9
  TRIM46 WILD-TYPE 219 255
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIM46 MUTATED      6    9
  TRIM46 WILD-TYPE  219  255
        clus
vv       TRIM46 MUTATED TRIM46 WILD-TYPE
  FEMALE              6              219
  MALE                9              255
[1] 2 2
[1] FALSE
D1487V9, binary
                  cls
clus                 0   1
  TRIM46 MUTATED    10   0
  TRIM46 WILD-TYPE 340  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIM46 MUTATED     10    0
  TRIM46 WILD-TYPE  340   22
     clus
vv    TRIM46 MUTATED TRIM46 WILD-TYPE
  NO              10              340
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  TRIM46 MUTATED                     14                             0
  TRIM46 WILD-TYPE                  301                            47
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  TRIM46 MUTATED                       0                              0
  TRIM46 WILD-TYPE                   106                             10
D1487V10, multiclass
                                clus
vv                               TRIM46 MUTATED TRIM46 WILD-TYPE
  COLON ADENOCARCINOMA                       14              301
  COLON MUCINOUS ADENOCARCINOMA               0               47
  RECTAL ADENOCARCINOMA                       0              106
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  TRIM46 MUTATED     9   0   0   1
  TRIM46 WILD-TYPE 336   4  31  24
D1487V11, multiclass
    clus
vv   TRIM46 MUTATED TRIM46 WILD-TYPE
  R0              9              336
  R1              0                4
  R2              0               31
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1487V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TRIM46 MUTATED                                  0     2
  TRIM46 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  TRIM46 MUTATED                           1     9
  TRIM46 WILD-TYPE                        21   217
D1487V13, multiclass
                                  clus
vv                                 TRIM46 MUTATED TRIM46 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                9
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                         9              217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1488) Variable = TNKS MUTATION ANALYSIS
D1488V1, survival
                sevent
clus2              0   1
  TNKS MUTATED     8   2
  TNKS WILD-TYPE 370  91
  TNKS MUTATED TNKS WILD-TYPE 
            10            461 
  TNKS MUTATED TNKS WILD-TYPE 
             2             91 
$`TNKS MUTATED`
TCGA-A6-3808 TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3492 TCGA-AA-3555 TCGA-AA-3855 
       33.34        20.12        19.66         3.02        29.95        32.05 
TCGA-AA-3966 TCGA-AZ-4315 TCGA-CA-6718 TCGA-EI-6507 
        2.01        58.39        10.06        19.96 

$`TNKS WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
       20.28         7.04         1.02        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       78.08         6.05         6.97        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
        0.00        36.03         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 
       24.00         2.01        20.98        34.03        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        33.01        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.20        12.76        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  TNKS MUTATED TNKS WILD-TYPE 
          2.01           0.00 
  TNKS MUTATED TNKS WILD-TYPE 
         58.39         148.01 
  TNKS MUTATED TNKS WILD-TYPE 
         20.04          20.28 
[1] "2.0 - 58.4 (20.0)"  "0.0 - 148.0 (20.3)"
[1] "hr=" "1.2"
D1488V2, continuous
D1488V3, binary
                cls
clus               0   1
  TNKS MUTATED     9   1
  TNKS WILD-TYPE 357 118
[1] "tbl2"
                cls
clus             [,1] [,2]
  TNKS MUTATED      9    1
  TNKS WILD-TYPE  357  118
        clus
vv       TNKS MUTATED TNKS WILD-TYPE
  COLON             9            357
  RECTUM            1            118
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TNKS MUTATED         1        0        1         7         0         0
  TNKS WILD-TYPE      90        1       31       131        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TNKS MUTATED           0          0          0          1        0         0
  TNKS WILD-TYPE        24         11         59         41       48        18
                vv
clus             STAGE IVB
  TNKS MUTATED           0
  TNKS WILD-TYPE         1
D1488V4, multiclass
            clus
vv           TNKS MUTATED TNKS WILD-TYPE
  STAGE I               1             90
  STAGE IA              0              1
  STAGE II              1             31
  STAGE IIA             7            131
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            0             59
  STAGE IIIC            1             41
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  TNKS MUTATED     0   1   8   1
  TNKS WILD-TYPE  17  91 321  49
D1488V5, multiclass
    clus
vv   TNKS MUTATED TNKS WILD-TYPE
  T1            0             17
  T2            1             91
  T3            8            321
  T4            1             49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  TNKS MUTATED     9   1   0
  TNKS WILD-TYPE 278 112  87
D1488V6, multiclass
    clus
vv   TNKS MUTATED TNKS WILD-TYPE
  N0            9            278
  N1            1            112
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1488V7, binary
                cls
clus               0   1
  TNKS MUTATED     8   0
  TNKS WILD-TYPE 367  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  TNKS MUTATED      8    0
  TNKS WILD-TYPE  367   65
   clus
vv  TNKS MUTATED TNKS WILD-TYPE
  0            8            367
  1            0             65
[1] 2 2
[1] FALSE
D1488V8, binary
                cls
clus               0   1
  TNKS MUTATED     3   7
  TNKS WILD-TYPE 222 257
[1] "tbl2"
                cls
clus             [,1] [,2]
  TNKS MUTATED      3    7
  TNKS WILD-TYPE  222  257
        clus
vv       TNKS MUTATED TNKS WILD-TYPE
  FEMALE            3            222
  MALE              7            257
[1] 2 2
[1] FALSE
D1488V9, binary
                cls
clus               0   1
  TNKS MUTATED     9   0
  TNKS WILD-TYPE 341  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  TNKS MUTATED      9    0
  TNKS WILD-TYPE  341   22
     clus
vv    TNKS MUTATED TNKS WILD-TYPE
  NO             9            341
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  TNKS MUTATED                      5                             4
  TNKS WILD-TYPE                  310                            43
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  TNKS MUTATED                       1                              0
  TNKS WILD-TYPE                   105                             10
D1488V10, multiclass
                                clus
vv                               TNKS MUTATED TNKS WILD-TYPE
  COLON ADENOCARCINOMA                      5            310
  COLON MUCINOUS ADENOCARCINOMA             4             43
  RECTAL ADENOCARCINOMA                     1            105
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  TNKS MUTATED     7   0   0   1
  TNKS WILD-TYPE 338   4  31  24
D1488V11, multiclass
    clus
vv   TNKS MUTATED TNKS WILD-TYPE
  R0            7            338
  R1            0              4
  R2            0             31
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1488V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TNKS MUTATED                                  0     1
  TNKS WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  TNKS MUTATED                           0     5
  TNKS WILD-TYPE                        22   221
D1488V13, multiclass
                                  clus
vv                                 TNKS MUTATED TNKS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       5            221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1489) Variable = ADAM20 MUTATION ANALYSIS
D1489V1, survival
                  sevent
clus2                0   1
  ADAM20 MUTATED     6   0
  ADAM20 WILD-TYPE 372  93
  ADAM20 MUTATED ADAM20 WILD-TYPE 
               6              465 
  ADAM20 MUTATED ADAM20 WILD-TYPE 
               0               93 
$`ADAM20 MUTATED`
TCGA-AA-3502 TCGA-AD-5900 TCGA-CM-6676 TCGA-AF-6655 TCGA-AG-3731 TCGA-AG-A008 
       35.01         0.07        11.08        20.02        37.02        13.94 

$`ADAM20 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 
       41.00        39.98        18.05        40.96        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       12.95        13.05        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       15.39        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        20.98         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  ADAM20 MUTATED ADAM20 WILD-TYPE 
            0.07             0.00 
  ADAM20 MUTATED ADAM20 WILD-TYPE 
           37.02           148.01 
  ADAM20 MUTATED ADAM20 WILD-TYPE 
           16.98            20.28 
[1] "0.1 - 37.0 (17.0)"  "0.0 - 148.0 (20.3)"
[1] "hr="     "3300000"
D1489V2, continuous
D1489V3, binary
                  cls
clus                 0   1
  ADAM20 MUTATED     3   3
  ADAM20 WILD-TYPE 363 116
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ADAM20 MUTATED      3    3
  ADAM20 WILD-TYPE  363  116
        clus
vv       ADAM20 MUTATED ADAM20 WILD-TYPE
  COLON               3              363
  RECTUM              3              116
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ADAM20 MUTATED         4        0        0         0         0         0
  ADAM20 WILD-TYPE      87        1       32       138        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ADAM20 MUTATED           0          1          0          0        1
  ADAM20 WILD-TYPE        24         10         59         42       47
                  vv
clus               STAGE IVA STAGE IVB
  ADAM20 MUTATED           0         0
  ADAM20 WILD-TYPE        18         1
D1489V4, multiclass
            clus
vv           ADAM20 MUTATED ADAM20 WILD-TYPE
  STAGE I                 4               87
  STAGE IA                0                1
  STAGE II                0               32
  STAGE IIA               0              138
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              1               10
  STAGE IIIB              0               59
  STAGE IIIC              0               42
  STAGE IV                1               47
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ADAM20 MUTATED     0   5   1   0
  ADAM20 WILD-TYPE  17  87 328  50
D1489V5, multiclass
    clus
vv   ADAM20 MUTATED ADAM20 WILD-TYPE
  T1              0               17
  T2              5               87
  T3              1              328
  T4              0               50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  ADAM20 MUTATED     4   2   0
  ADAM20 WILD-TYPE 283 111  87
D1489V6, multiclass
    clus
vv   ADAM20 MUTATED ADAM20 WILD-TYPE
  N0              4              283
  N1              2              111
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1489V7, binary
                  cls
clus                 0   1
  ADAM20 MUTATED     4   1
  ADAM20 WILD-TYPE 371  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ADAM20 MUTATED      4    1
  ADAM20 WILD-TYPE  371   64
   clus
vv  ADAM20 MUTATED ADAM20 WILD-TYPE
  0              4              371
  1              1               64
[1] 2 2
[1] FALSE
D1489V8, binary
                  cls
clus                 0   1
  ADAM20 MUTATED     1   5
  ADAM20 WILD-TYPE 224 259
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ADAM20 MUTATED      1    5
  ADAM20 WILD-TYPE  224  259
        clus
vv       ADAM20 MUTATED ADAM20 WILD-TYPE
  FEMALE              1              224
  MALE                5              259
[1] 2 2
[1] FALSE
D1489V9, binary
                  cls
clus                 0   1
  ADAM20 MUTATED     5   0
  ADAM20 WILD-TYPE 345  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ADAM20 MUTATED      5    0
  ADAM20 WILD-TYPE  345   22
     clus
vv    ADAM20 MUTATED ADAM20 WILD-TYPE
  NO               5              345
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ADAM20 MUTATED                      2                             1
  ADAM20 WILD-TYPE                  313                            46
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ADAM20 MUTATED                       2                              1
  ADAM20 WILD-TYPE                   104                              9
D1489V10, multiclass
                                clus
vv                               ADAM20 MUTATED ADAM20 WILD-TYPE
  COLON ADENOCARCINOMA                        2              313
  COLON MUCINOUS ADENOCARCINOMA               1               46
  RECTAL ADENOCARCINOMA                       2              104
  RECTAL MUCINOUS ADENOCARCINOMA              1                9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ADAM20 MUTATED     5   0   1   0
  ADAM20 WILD-TYPE 340   4  30  25
D1489V11, multiclass
    clus
vv   ADAM20 MUTATED ADAM20 WILD-TYPE
  R0              5              340
  R1              0                4
  R2              1               30
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1489V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ADAM20 MUTATED                                  0     0
  ADAM20 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ADAM20 MUTATED                           0     3
  ADAM20 WILD-TYPE                        22   223
D1489V13, multiclass
                                  clus
vv                                 ADAM20 MUTATED ADAM20 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         3              223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1490) Variable = CDK5RAP2 MUTATION ANALYSIS
D1490V1, survival
                    sevent
clus2                  0   1
  CDK5RAP2 MUTATED    23   1
  CDK5RAP2 WILD-TYPE 355  92
  CDK5RAP2 MUTATED CDK5RAP2 WILD-TYPE 
                24                447 
  CDK5RAP2 MUTATED CDK5RAP2 WILD-TYPE 
                 1                 92 
$`CDK5RAP2 MUTATED`
TCGA-A6-5659 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6653 TCGA-AA-3510 TCGA-AA-3977 
       30.44        22.06        32.71        24.39        63.98        25.02 
TCGA-AA-A00N TCGA-AA-A010 TCGA-AD-5900 TCGA-AD-6889 TCGA-AU-6004 TCGA-AZ-4315 
        4.01        34.98         0.07        56.55        27.09        58.39 
TCGA-AZ-5407 TCGA-CA-5797 TCGA-CA-6717 TCGA-CM-5861 TCGA-CM-6168 TCGA-CM-6674 
       88.21         3.29        12.76        15.02        12.99        12.95 
TCGA-D5-6930 TCGA-G4-6293 TCGA-G4-6586 TCGA-G4-6628 TCGA-AG-A002 TCGA-DY-A0XA 
        1.51       133.18        35.80        79.69        20.98       126.44 

$`CDK5RAP2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        29.19        33.53        23.61        22.09 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       27.09        22.52         8.38        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       21.76        24.69        23.87        20.12        19.66        20.28 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 
        7.04         3.02         1.02        35.01         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
       13.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       36.03         8.05        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       78.08         6.05         6.97        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 
       39.98        18.05        40.96        21.37        15.52         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       14.50        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6598 
        1.41         5.13       106.75        22.36        62.79        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-6715 
        3.19         1.61        12.69         3.06         3.25         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.20        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6169 
        2.96        29.03        16.04        21.99        14.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       15.02        14.04        11.01        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 
        9.04         9.44        11.64         4.80        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 
       63.62        61.91        36.00        22.09        13.78        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       91.79        46.75        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.03         5.29        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  CDK5RAP2 MUTATED CDK5RAP2 WILD-TYPE 
              0.07               0.00 
  CDK5RAP2 MUTATED CDK5RAP2 WILD-TYPE 
            133.18             148.01 
  CDK5RAP2 MUTATED CDK5RAP2 WILD-TYPE 
            26.055             20.020 
[1] "0.1 - 133.2 (26.1)" "0.0 - 148.0 (20.0)"
[1] "hr=" "6.9"
D1490V2, continuous
D1490V3, binary
                    cls
clus                   0   1
  CDK5RAP2 MUTATED    23   2
  CDK5RAP2 WILD-TYPE 343 117
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  CDK5RAP2 MUTATED     23    2
  CDK5RAP2 WILD-TYPE  343  117
        clus
vv       CDK5RAP2 MUTATED CDK5RAP2 WILD-TYPE
  COLON                23                343
  RECTUM                2                117
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CDK5RAP2 MUTATED         7        0        2        11         2         1
  CDK5RAP2 WILD-TYPE      84        1       30       127         8         0
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CDK5RAP2 MUTATED           1          0          0          0        0
  CDK5RAP2 WILD-TYPE        23         11         59         42       48
                    vv
clus                 STAGE IVA STAGE IVB
  CDK5RAP2 MUTATED           0         0
  CDK5RAP2 WILD-TYPE        18         1
D1490V4, multiclass
            clus
vv           CDK5RAP2 MUTATED CDK5RAP2 WILD-TYPE
  STAGE I                   7                 84
  STAGE IA                  0                  1
  STAGE II                  2                 30
  STAGE IIA                11                127
  STAGE IIB                 2                  8
  STAGE IIC                 1                  0
  STAGE III                 1                 23
  STAGE IIIA                0                 11
  STAGE IIIB                0                 59
  STAGE IIIC                0                 42
  STAGE IV                  0                 48
  STAGE IVA                 0                 18
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  CDK5RAP2 MUTATED     1   7  13   4
  CDK5RAP2 WILD-TYPE  16  85 316  46
D1490V5, multiclass
    clus
vv   CDK5RAP2 MUTATED CDK5RAP2 WILD-TYPE
  T1                1                 16
  T2                7                 85
  T3               13                316
  T4                4                 46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  CDK5RAP2 MUTATED    24   1   0
  CDK5RAP2 WILD-TYPE 263 112  87
D1490V6, multiclass
    clus
vv   CDK5RAP2 MUTATED CDK5RAP2 WILD-TYPE
  N0               24                263
  N1                1                112
  N2                0                 87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1490V7, binary
                    cls
clus                   0   1
  CDK5RAP2 MUTATED    23   0
  CDK5RAP2 WILD-TYPE 352  65
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  CDK5RAP2 MUTATED     23    0
  CDK5RAP2 WILD-TYPE  352   65
   clus
vv  CDK5RAP2 MUTATED CDK5RAP2 WILD-TYPE
  0               23                352
  1                0                 65
[1] 2 2
[1] FALSE
D1490V8, binary
                    cls
clus                   0   1
  CDK5RAP2 MUTATED    10  15
  CDK5RAP2 WILD-TYPE 215 249
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  CDK5RAP2 MUTATED     10   15
  CDK5RAP2 WILD-TYPE  215  249
        clus
vv       CDK5RAP2 MUTATED CDK5RAP2 WILD-TYPE
  FEMALE               10                215
  MALE                 15                249
[1] 2 2
[1] FALSE
D1490V9, binary
                    cls
clus                   0   1
  CDK5RAP2 MUTATED    18   0
  CDK5RAP2 WILD-TYPE 332  22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  CDK5RAP2 MUTATED     18    0
  CDK5RAP2 WILD-TYPE  332   22
     clus
vv    CDK5RAP2 MUTATED CDK5RAP2 WILD-TYPE
  NO                18                332
  YES                0                 22
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CDK5RAP2 MUTATED                     19                             4
  CDK5RAP2 WILD-TYPE                  296                            43
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CDK5RAP2 MUTATED                       2                              0
  CDK5RAP2 WILD-TYPE                   104                             10
D1490V10, multiclass
                                clus
vv                               CDK5RAP2 MUTATED CDK5RAP2 WILD-TYPE
  COLON ADENOCARCINOMA                         19                296
  COLON MUCINOUS ADENOCARCINOMA                 4                 43
  RECTAL ADENOCARCINOMA                         2                104
  RECTAL MUCINOUS ADENOCARCINOMA                0                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  CDK5RAP2 MUTATED    18   0   0   1
  CDK5RAP2 WILD-TYPE 327   4  31  24
D1490V11, multiclass
    clus
vv   CDK5RAP2 MUTATED CDK5RAP2 WILD-TYPE
  R0               18                327
  R1                0                  4
  R2                0                 31
  RX                1                 24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1490V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CDK5RAP2 MUTATED                                  0     3
  CDK5RAP2 WILD-TYPE                                1     8
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  CDK5RAP2 MUTATED                           1    15
  CDK5RAP2 WILD-TYPE                        21   211
D1490V13, multiclass
                                  clus
vv                                 CDK5RAP2 MUTATED CDK5RAP2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           3                  8
  BLACK OR AFRICAN AMERICAN                       1                 21
  WHITE                                          15                211
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1491) Variable = NXPH1 MUTATION ANALYSIS
D1491V1, survival
                 sevent
clus2               0   1
  NXPH1 MUTATED     7   1
  NXPH1 WILD-TYPE 371  92
  NXPH1 MUTATED NXPH1 WILD-TYPE 
              8             463 
  NXPH1 MUTATED NXPH1 WILD-TYPE 
              1              92 
$`NXPH1 MUTATED`
TCGA-A6-6141 TCGA-A6-6649 TCGA-AA-3861 TCGA-AA-A00N TCGA-AA-A010 TCGA-D5-6541 
        8.38        24.16        30.05         4.01        34.98        15.58 
TCGA-G4-6309 TCGA-G4-6628 
       85.48        79.69 

$`NXPH1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 
       22.09        22.06        32.71        27.09        22.52        25.08 
TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       25.18        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
        0.99        31.07        31.07        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       16.14         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       55.04        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 
       35.80        26.17        91.79        46.75        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  NXPH1 MUTATED NXPH1 WILD-TYPE 
           4.01            0.00 
  NXPH1 MUTATED NXPH1 WILD-TYPE 
          85.48          148.01 
  NXPH1 MUTATED NXPH1 WILD-TYPE 
         27.105          20.120 
[1] "4.0 - 85.5 (27.1)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "2"  
D1491V2, continuous
D1491V3, binary
                 cls
clus                0   1
  NXPH1 MUTATED     8   1
  NXPH1 WILD-TYPE 358 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NXPH1 MUTATED      8    1
  NXPH1 WILD-TYPE  358  118
        clus
vv       NXPH1 MUTATED NXPH1 WILD-TYPE
  COLON              8             358
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NXPH1 MUTATED         1        0        0         3         2         0
  NXPH1 WILD-TYPE      90        1       32       135         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NXPH1 MUTATED           1          0          2          0        0         0
  NXPH1 WILD-TYPE        23         11         57         42       48        18
                 vv
clus              STAGE IVB
  NXPH1 MUTATED           0
  NXPH1 WILD-TYPE         1
D1491V4, multiclass
            clus
vv           NXPH1 MUTATED NXPH1 WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              3             135
  STAGE IIB              2               8
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             2              57
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  NXPH1 MUTATED     0   1   6   2
  NXPH1 WILD-TYPE  17  91 323  48
D1491V5, multiclass
    clus
vv   NXPH1 MUTATED NXPH1 WILD-TYPE
  T1             0              17
  T2             1              91
  T3             6             323
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  NXPH1 MUTATED     6   3   0
  NXPH1 WILD-TYPE 281 110  87
D1491V6, multiclass
    clus
vv   NXPH1 MUTATED NXPH1 WILD-TYPE
  N0             6             281
  N1             3             110
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1491V7, binary
                 cls
clus                0   1
  NXPH1 MUTATED     8   0
  NXPH1 WILD-TYPE 367  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NXPH1 MUTATED      8    0
  NXPH1 WILD-TYPE  367   65
   clus
vv  NXPH1 MUTATED NXPH1 WILD-TYPE
  0             8             367
  1             0              65
[1] 2 2
[1] FALSE
D1491V8, binary
                 cls
clus                0   1
  NXPH1 MUTATED     2   7
  NXPH1 WILD-TYPE 223 257
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NXPH1 MUTATED      2    7
  NXPH1 WILD-TYPE  223  257
        clus
vv       NXPH1 MUTATED NXPH1 WILD-TYPE
  FEMALE             2             223
  MALE               7             257
[1] 2 2
[1] FALSE
D1491V9, binary
                 cls
clus                0   1
  NXPH1 MUTATED     7   0
  NXPH1 WILD-TYPE 343  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NXPH1 MUTATED      7    0
  NXPH1 WILD-TYPE  343   22
     clus
vv    NXPH1 MUTATED NXPH1 WILD-TYPE
  NO              7             343
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  NXPH1 MUTATED                      7                             1
  NXPH1 WILD-TYPE                  308                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  NXPH1 MUTATED                       1                              0
  NXPH1 WILD-TYPE                   105                             10
D1491V10, multiclass
                                clus
vv                               NXPH1 MUTATED NXPH1 WILD-TYPE
  COLON ADENOCARCINOMA                       7             308
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  NXPH1 MUTATED     6   0   0   0
  NXPH1 WILD-TYPE 339   4  31  25
D1491V11, multiclass
    clus
vv   NXPH1 MUTATED NXPH1 WILD-TYPE
  R0             6             339
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1491V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NXPH1 MUTATED                                  0     0
  NXPH1 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  NXPH1 MUTATED                           2     4
  NXPH1 WILD-TYPE                        20   222
D1491V13, multiclass
                                  clus
vv                                 NXPH1 MUTATED NXPH1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    2              20
  WHITE                                        4             222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1492) Variable = ATP10B MUTATION ANALYSIS
D1492V1, survival
                  sevent
clus2                0   1
  ATP10B MUTATED    11   6
  ATP10B WILD-TYPE 367  87
  ATP10B MUTATED ATP10B WILD-TYPE 
              17              454 
  ATP10B MUTATED ATP10B WILD-TYPE 
               6               87 
$`ATP10B MUTATED`
TCGA-A6-5665 TCGA-A6-6781 TCGA-AA-3655 TCGA-AA-3715 TCGA-AA-3845 TCGA-AD-6889 
       22.06        19.66        61.02        19.04         0.00        56.55 
TCGA-AY-5543 TCGA-AZ-6599 TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-4743 TCGA-CM-4747 
       33.01         6.77        12.76        10.06        23.05        25.02 
TCGA-D5-6926 TCGA-DM-A285 TCGA-F4-6854 TCGA-AG-3892 TCGA-DY-A1DG 
        9.04         6.12         0.53        13.02        51.48 

$`ATP10B WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       13.94        19.99        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       85.05        26.99        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02        14.93        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
        0.07        21.37        15.52         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       16.31         0.95        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       12.20        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
      124.27        20.02        37.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      131.51       135.65       139.17        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       33.67        13.25        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 
       19.99         1.02        17.95        36.95        17.03        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       24.13        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  ATP10B MUTATED ATP10B WILD-TYPE 
               0                0 
  ATP10B MUTATED ATP10B WILD-TYPE 
           61.02           148.01 
  ATP10B MUTATED ATP10B WILD-TYPE 
          19.040           20.415 
[1] "0.0 - 61.0 (19.0)"  "0.0 - 148.0 (20.4)"
[1] "hr=" "2.1"
D1492V2, continuous
D1492V3, binary
                  cls
clus                 0   1
  ATP10B MUTATED    15   2
  ATP10B WILD-TYPE 351 117
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP10B MUTATED     15    2
  ATP10B WILD-TYPE  351  117
        clus
vv       ATP10B MUTATED ATP10B WILD-TYPE
  COLON              15              351
  RECTUM              2              117
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ATP10B MUTATED         2        0        2         7         0         0
  ATP10B WILD-TYPE      89        1       30       131        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ATP10B MUTATED           0          0          1          1        1
  ATP10B WILD-TYPE        24         11         58         41       47
                  vv
clus               STAGE IVA STAGE IVB
  ATP10B MUTATED           3         0
  ATP10B WILD-TYPE        15         1
D1492V4, multiclass
            clus
vv           ATP10B MUTATED ATP10B WILD-TYPE
  STAGE I                 2               89
  STAGE IA                0                1
  STAGE II                2               30
  STAGE IIA               7              131
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              1               58
  STAGE IIIC              1               41
  STAGE IV                1               47
  STAGE IVA               3               15
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ATP10B MUTATED     1   1  12   3
  ATP10B WILD-TYPE  16  91 317  47
D1492V5, multiclass
    clus
vv   ATP10B MUTATED ATP10B WILD-TYPE
  T1              1               16
  T2              1               91
  T3             12              317
  T4              3               47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  ATP10B MUTATED    11   5   1
  ATP10B WILD-TYPE 276 108  86
D1492V6, multiclass
    clus
vv   ATP10B MUTATED ATP10B WILD-TYPE
  N0             11              276
  N1              5              108
  N2              1               86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1492V7, binary
                  cls
clus                 0   1
  ATP10B MUTATED    11   4
  ATP10B WILD-TYPE 364  61
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP10B MUTATED     11    4
  ATP10B WILD-TYPE  364   61
   clus
vv  ATP10B MUTATED ATP10B WILD-TYPE
  0             11              364
  1              4               61
[1] 2 2
[1] FALSE
D1492V8, binary
                  cls
clus                 0   1
  ATP10B MUTATED     6  11
  ATP10B WILD-TYPE 219 253
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP10B MUTATED      6   11
  ATP10B WILD-TYPE  219  253
        clus
vv       ATP10B MUTATED ATP10B WILD-TYPE
  FEMALE              6              219
  MALE               11              253
[1] 2 2
[1] FALSE
D1492V9, binary
                  cls
clus                 0   1
  ATP10B MUTATED    12   1
  ATP10B WILD-TYPE 338  21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP10B MUTATED     12    1
  ATP10B WILD-TYPE  338   21
     clus
vv    ATP10B MUTATED ATP10B WILD-TYPE
  NO              12              338
  YES              1               21
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ATP10B MUTATED                     12                             3
  ATP10B WILD-TYPE                  303                            44
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ATP10B MUTATED                       2                              0
  ATP10B WILD-TYPE                   104                             10
D1492V10, multiclass
                                clus
vv                               ATP10B MUTATED ATP10B WILD-TYPE
  COLON ADENOCARCINOMA                       12              303
  COLON MUCINOUS ADENOCARCINOMA               3               44
  RECTAL ADENOCARCINOMA                       2              104
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ATP10B MUTATED    11   0   0   2
  ATP10B WILD-TYPE 334   4  31  23
D1492V11, multiclass
    clus
vv   ATP10B MUTATED ATP10B WILD-TYPE
  R0             11              334
  R1              0                4
  R2              0               31
  RX              2               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1492V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ATP10B MUTATED                                  0     3
  ATP10B WILD-TYPE                                1     8
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ATP10B MUTATED                           1     9
  ATP10B WILD-TYPE                        21   217
D1492V13, multiclass
                                  clus
vv                                 ATP10B MUTATED ATP10B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         3                8
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                         9              217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1493) Variable = ERGIC1 MUTATION ANALYSIS
D1493V1, survival
                  sevent
clus2                0   1
  ERGIC1 MUTATED     5   0
  ERGIC1 WILD-TYPE 373  93
  ERGIC1 MUTATED ERGIC1 WILD-TYPE 
               5              466 
  ERGIC1 MUTATED ERGIC1 WILD-TYPE 
               0               93 
$`ERGIC1 MUTATED`
TCGA-A6-5660 TCGA-CM-6675 TCGA-CM-6677 TCGA-D5-6541 TCGA-EI-6507 
       29.19        13.05        11.08        15.58        19.96 

$`ERGIC1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6676 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       11.01        12.95        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       17.13        12.49        16.14         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6508 
       24.13        51.48        32.61         0.49        20.55        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  ERGIC1 MUTATED ERGIC1 WILD-TYPE 
           11.08             0.00 
  ERGIC1 MUTATED ERGIC1 WILD-TYPE 
           29.19           148.01 
  ERGIC1 MUTATED ERGIC1 WILD-TYPE 
          15.580           20.415 
[1] "11.1 - 29.2 (15.6)" "0.0 - 148.0 (20.4)"
[1] "hr="     "3300000"
D1493V2, continuous
D1493V3, binary
                  cls
clus                 0   1
  ERGIC1 MUTATED     4   1
  ERGIC1 WILD-TYPE 362 118
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ERGIC1 MUTATED      4    1
  ERGIC1 WILD-TYPE  362  118
        clus
vv       ERGIC1 MUTATED ERGIC1 WILD-TYPE
  COLON               4              362
  RECTUM              1              118
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ERGIC1 MUTATED         0        0        0         3         0         0
  ERGIC1 WILD-TYPE      91        1       32       135        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ERGIC1 MUTATED           0          0          0          1        0
  ERGIC1 WILD-TYPE        24         11         59         41       48
                  vv
clus               STAGE IVA STAGE IVB
  ERGIC1 MUTATED           0         1
  ERGIC1 WILD-TYPE        18         0
D1493V4, multiclass
            clus
vv           ERGIC1 MUTATED ERGIC1 WILD-TYPE
  STAGE I                 0               91
  STAGE IA                0                1
  STAGE II                0               32
  STAGE IIA               3              135
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              0               59
  STAGE IIIC              1               41
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               1                0
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ERGIC1 MUTATED     0   0   5   0
  ERGIC1 WILD-TYPE  17  92 324  50
D1493V5, multiclass
    clus
vv   ERGIC1 MUTATED ERGIC1 WILD-TYPE
  T1              0               17
  T2              0               92
  T3              5              324
  T4              0               50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  ERGIC1 MUTATED     3   0   2
  ERGIC1 WILD-TYPE 284 113  85
D1493V6, multiclass
    clus
vv   ERGIC1 MUTATED ERGIC1 WILD-TYPE
  N0              3              284
  N1              0              113
  N2              2               85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1493V7, binary
                  cls
clus                 0   1
  ERGIC1 MUTATED     4   1
  ERGIC1 WILD-TYPE 371  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ERGIC1 MUTATED      4    1
  ERGIC1 WILD-TYPE  371   64
   clus
vv  ERGIC1 MUTATED ERGIC1 WILD-TYPE
  0              4              371
  1              1               64
[1] 2 2
[1] FALSE
D1493V8, binary
                  cls
clus                 0   1
  ERGIC1 MUTATED     1   4
  ERGIC1 WILD-TYPE 224 260
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ERGIC1 MUTATED      1    4
  ERGIC1 WILD-TYPE  224  260
        clus
vv       ERGIC1 MUTATED ERGIC1 WILD-TYPE
  FEMALE              1              224
  MALE                4              260
[1] 2 2
[1] FALSE
D1493V9, binary
                  cls
clus                 0   1
  ERGIC1 MUTATED     5   0
  ERGIC1 WILD-TYPE 345  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ERGIC1 MUTATED      5    0
  ERGIC1 WILD-TYPE  345   22
     clus
vv    ERGIC1 MUTATED ERGIC1 WILD-TYPE
  NO               5              345
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ERGIC1 MUTATED                      4                             0
  ERGIC1 WILD-TYPE                  311                            47
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ERGIC1 MUTATED                       1                              0
  ERGIC1 WILD-TYPE                   105                             10
D1493V10, multiclass
                                clus
vv                               ERGIC1 MUTATED ERGIC1 WILD-TYPE
  COLON ADENOCARCINOMA                        4              311
  COLON MUCINOUS ADENOCARCINOMA               0               47
  RECTAL ADENOCARCINOMA                       1              105
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ERGIC1 MUTATED     4   0   0   0
  ERGIC1 WILD-TYPE 341   4  31  25
D1493V11, multiclass
    clus
vv   ERGIC1 MUTATED ERGIC1 WILD-TYPE
  R0              4              341
  R1              0                4
  R2              0               31
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1493V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ERGIC1 MUTATED                                  0     0
  ERGIC1 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ERGIC1 MUTATED                           2     3
  ERGIC1 WILD-TYPE                        20   223
D1493V13, multiclass
                                  clus
vv                                 ERGIC1 MUTATED ERGIC1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     2               20
  WHITE                                         3              223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1494) Variable = IVD MUTATION ANALYSIS
D1494V1, survival
               sevent
clus2             0   1
  IVD MUTATED     5   1
  IVD WILD-TYPE 373  92
  IVD MUTATED IVD WILD-TYPE 
            6           465 
  IVD MUTATED IVD WILD-TYPE 
            1            92 
$`IVD MUTATED`
TCGA-A6-6781 TCGA-AU-6004 TCGA-CA-6716 TCGA-D5-6539 TCGA-F4-6703 TCGA-DC-6158 
       19.66        27.09        12.20        12.49        47.87        10.98 

$`IVD WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 
       27.42        10.88         0.20        14.50        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       17.13        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6704 
       98.24         8.61        31.96        35.74         6.18         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       13.97        27.95        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  IVD MUTATED IVD WILD-TYPE 
        10.98          0.00 
  IVD MUTATED IVD WILD-TYPE 
        47.87        148.01 
  IVD MUTATED IVD WILD-TYPE 
       16.075        20.280 
[1] "11.0 - 47.9 (16.1)" "0.0 - 148.0 (20.3)"
[1] "hr=" "1"  
D1494V2, continuous
D1494V3, binary
               cls
clus              0   1
  IVD MUTATED     5   1
  IVD WILD-TYPE 361 118
[1] "tbl2"
               cls
clus            [,1] [,2]
  IVD MUTATED      5    1
  IVD WILD-TYPE  361  118
        clus
vv       IVD MUTATED IVD WILD-TYPE
  COLON            5           361
  RECTUM           1           118
[1] 2 2
[1] FALSE
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  IVD MUTATED         2        0        0         2         0         0
  IVD WILD-TYPE      89        1       32       136        10         1
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  IVD MUTATED           0          1          0          1        0         0
  IVD WILD-TYPE        24         10         59         41       48        18
               vv
clus            STAGE IVB
  IVD MUTATED           0
  IVD WILD-TYPE         1
D1494V4, multiclass
            clus
vv           IVD MUTATED IVD WILD-TYPE
  STAGE I              2            89
  STAGE IA             0             1
  STAGE II             0            32
  STAGE IIA            2           136
  STAGE IIB            0            10
  STAGE IIC            0             1
  STAGE III            0            24
  STAGE IIIA           1            10
  STAGE IIIB           0            59
  STAGE IIIC           1            41
  STAGE IV             0            48
  STAGE IVA            0            18
  STAGE IVB            0             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  IVD MUTATED     0   2   3   1
  IVD WILD-TYPE  17  90 326  49
D1494V5, multiclass
    clus
vv   IVD MUTATED IVD WILD-TYPE
  T1           0            17
  T2           2            90
  T3           3           326
  T4           1            49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2
  IVD MUTATED     5   1   0
  IVD WILD-TYPE 282 112  87
D1494V6, multiclass
    clus
vv   IVD MUTATED IVD WILD-TYPE
  N0           5           282
  N1           1           112
  N2           0            87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1494V7, binary
               cls
clus              0   1
  IVD MUTATED     5   0
  IVD WILD-TYPE 370  65
[1] "tbl2"
               cls
clus            [,1] [,2]
  IVD MUTATED      5    0
  IVD WILD-TYPE  370   65
   clus
vv  IVD MUTATED IVD WILD-TYPE
  0           5           370
  1           0            65
[1] 2 2
[1] FALSE
D1494V8, binary
               cls
clus              0   1
  IVD MUTATED     2   4
  IVD WILD-TYPE 223 260
[1] "tbl2"
               cls
clus            [,1] [,2]
  IVD MUTATED      2    4
  IVD WILD-TYPE  223  260
        clus
vv       IVD MUTATED IVD WILD-TYPE
  FEMALE           2           223
  MALE             4           260
[1] 2 2
[1] FALSE
D1494V9, binary
               cls
clus              0   1
  IVD MUTATED     5   0
  IVD WILD-TYPE 345  22
[1] "tbl2"
               cls
clus            [,1] [,2]
  IVD MUTATED      5    0
  IVD WILD-TYPE  345   22
     clus
vv    IVD MUTATED IVD WILD-TYPE
  NO            5           345
  YES           0            22
[1] 2 2
[1] FALSE
               vv
clus            COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  IVD MUTATED                      4                             1
  IVD WILD-TYPE                  311                            46
               vv
clus            RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  IVD MUTATED                       1                              0
  IVD WILD-TYPE                   105                             10
D1494V10, multiclass
                                clus
vv                               IVD MUTATED IVD WILD-TYPE
  COLON ADENOCARCINOMA                     4           311
  COLON MUCINOUS ADENOCARCINOMA            1            46
  RECTAL ADENOCARCINOMA                    1           105
  RECTAL MUCINOUS ADENOCARCINOMA           0            10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             R0  R1  R2  RX
  IVD MUTATED     5   0   0   1
  IVD WILD-TYPE 340   4  31  24
D1494V11, multiclass
    clus
vv   IVD MUTATED IVD WILD-TYPE
  R0           5           340
  R1           0             4
  R2           0            31
  RX           1            24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1494V12, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  IVD MUTATED                                  0     1
  IVD WILD-TYPE                                1    10
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  IVD MUTATED                           0     5
  IVD WILD-TYPE                        22   221
D1494V13, multiclass
                                  clus
vv                                 IVD MUTATED IVD WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      1            10
  BLACK OR AFRICAN AMERICAN                  0            22
  WHITE                                      5           221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1495) Variable = YTHDF2 MUTATION ANALYSIS
D1495V1, survival
                  sevent
clus2                0   1
  YTHDF2 MUTATED    10   2
  YTHDF2 WILD-TYPE 368  91
  YTHDF2 MUTATED YTHDF2 WILD-TYPE 
              12              459 
  YTHDF2 MUTATED YTHDF2 WILD-TYPE 
               2               91 
$`YTHDF2 MUTATED`
TCGA-A6-5665 TCGA-A6-6781 TCGA-AA-A010 TCGA-AD-5900 TCGA-AZ-6601 TCGA-CA-6718 
       22.06        19.66        34.98         0.07       100.01        10.06 
TCGA-CK-5913 TCGA-CM-5344 TCGA-CM-6162 TCGA-D5-6930 TCGA-AG-A002 TCGA-DC-5337 
       51.32        22.03        12.00         1.51        20.98        15.02 

$`YTHDF2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       18.05        40.96        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 
       62.79        88.21        49.41         6.77        12.10        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 
        3.25         3.29         0.07        12.20        12.76        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 
       17.56       148.01        85.45        15.62        49.08         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5349 
       37.02        25.02        13.02        29.06        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       15.02         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        4.80        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5869 TCGA-DC-6155 
        6.97         4.73        78.12         7.17         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  YTHDF2 MUTATED YTHDF2 WILD-TYPE 
            0.07             0.00 
  YTHDF2 MUTATED YTHDF2 WILD-TYPE 
          100.01           148.01 
  YTHDF2 MUTATED YTHDF2 WILD-TYPE 
           20.32            20.19 
[1] "0.1 - 100.0 (20.3)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.2"
D1495V2, continuous
D1495V3, binary
                  cls
clus                 0   1
  YTHDF2 MUTATED    10   2
  YTHDF2 WILD-TYPE 356 117
[1] "tbl2"
                  cls
clus               [,1] [,2]
  YTHDF2 MUTATED     10    2
  YTHDF2 WILD-TYPE  356  117
        clus
vv       YTHDF2 MUTATED YTHDF2 WILD-TYPE
  COLON              10              356
  RECTUM              2              117
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  YTHDF2 MUTATED         3        0        1         4         1         0
  YTHDF2 WILD-TYPE      88        1       31       134         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  YTHDF2 MUTATED           0          0          2          1        0
  YTHDF2 WILD-TYPE        24         11         57         41       48
                  vv
clus               STAGE IVA STAGE IVB
  YTHDF2 MUTATED           0         0
  YTHDF2 WILD-TYPE        18         1
D1495V4, multiclass
            clus
vv           YTHDF2 MUTATED YTHDF2 WILD-TYPE
  STAGE I                 3               88
  STAGE IA                0                1
  STAGE II                1               31
  STAGE IIA               4              134
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              2               57
  STAGE IIIC              1               41
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  YTHDF2 MUTATED     1   2   7   2
  YTHDF2 WILD-TYPE  16  90 322  48
D1495V5, multiclass
    clus
vv   YTHDF2 MUTATED YTHDF2 WILD-TYPE
  T1              1               16
  T2              2               90
  T3              7              322
  T4              2               48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  YTHDF2 MUTATED     9   3   0
  YTHDF2 WILD-TYPE 278 110  87
D1495V6, multiclass
    clus
vv   YTHDF2 MUTATED YTHDF2 WILD-TYPE
  N0              9              278
  N1              3              110
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1495V7, binary
                  cls
clus                 0   1
  YTHDF2 MUTATED     9   0
  YTHDF2 WILD-TYPE 366  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  YTHDF2 MUTATED      9    0
  YTHDF2 WILD-TYPE  366   65
   clus
vv  YTHDF2 MUTATED YTHDF2 WILD-TYPE
  0              9              366
  1              0               65
[1] 2 2
[1] FALSE
D1495V8, binary
                  cls
clus                 0   1
  YTHDF2 MUTATED     5   7
  YTHDF2 WILD-TYPE 220 257
[1] "tbl2"
                  cls
clus               [,1] [,2]
  YTHDF2 MUTATED      5    7
  YTHDF2 WILD-TYPE  220  257
        clus
vv       YTHDF2 MUTATED YTHDF2 WILD-TYPE
  FEMALE              5              220
  MALE                7              257
[1] 2 2
[1] FALSE
D1495V9, binary
                  cls
clus                 0   1
  YTHDF2 MUTATED    10   0
  YTHDF2 WILD-TYPE 340  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  YTHDF2 MUTATED     10    0
  YTHDF2 WILD-TYPE  340   22
     clus
vv    YTHDF2 MUTATED YTHDF2 WILD-TYPE
  NO              10              340
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  YTHDF2 MUTATED                      6                             4
  YTHDF2 WILD-TYPE                  309                            43
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  YTHDF2 MUTATED                       2                              0
  YTHDF2 WILD-TYPE                   104                             10
D1495V10, multiclass
                                clus
vv                               YTHDF2 MUTATED YTHDF2 WILD-TYPE
  COLON ADENOCARCINOMA                        6              309
  COLON MUCINOUS ADENOCARCINOMA               4               43
  RECTAL ADENOCARCINOMA                       2              104
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  YTHDF2 MUTATED     9   0   0   2
  YTHDF2 WILD-TYPE 336   4  31  23
D1495V11, multiclass
    clus
vv   YTHDF2 MUTATED YTHDF2 WILD-TYPE
  R0              9              336
  R1              0                4
  R2              0               31
  RX              2               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1495V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  YTHDF2 MUTATED                                  0     1
  YTHDF2 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  YTHDF2 MUTATED                           0     9
  YTHDF2 WILD-TYPE                        22   217
D1495V13, multiclass
                                  clus
vv                                 YTHDF2 MUTATED YTHDF2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         9              217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1496) Variable = KCNN4 MUTATION ANALYSIS
D1496V1, survival
                 sevent
clus2               0   1
  KCNN4 MUTATED     6   1
  KCNN4 WILD-TYPE 372  92
  KCNN4 MUTATED KCNN4 WILD-TYPE 
              7             464 
  KCNN4 MUTATED KCNN4 WILD-TYPE 
              1              92 
$`KCNN4 MUTATED`
TCGA-AD-6901 TCGA-AZ-5407 TCGA-CK-4950 TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-5860 
       22.42        88.21        85.45        13.02        22.03        32.02 
TCGA-G4-6304 
       53.62 

$`KCNN4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 
        5.13       106.75        22.36        62.79        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       29.06        22.98        30.08        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 
       35.31       133.18        74.56        65.85        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  KCNN4 MUTATED KCNN4 WILD-TYPE 
          13.02            0.00 
  KCNN4 MUTATED KCNN4 WILD-TYPE 
          88.21          148.01 
  KCNN4 MUTATED KCNN4 WILD-TYPE 
         32.020          20.035 
[1] "13.0 - 88.2 (32.0)" "0.0 - 148.0 (20.0)"
[1] "hr=" "2.4"
D1496V2, continuous
D1496V3, binary
                 cls
clus                0   1
  KCNN4 MUTATED     7   0
  KCNN4 WILD-TYPE 359 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNN4 MUTATED      7    0
  KCNN4 WILD-TYPE  359  119
        clus
vv       KCNN4 MUTATED KCNN4 WILD-TYPE
  COLON              7             359
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KCNN4 MUTATED         1        0        0         2         1         0
  KCNN4 WILD-TYPE      90        1       32       136         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  KCNN4 MUTATED           0          0          2          0        0         0
  KCNN4 WILD-TYPE        24         11         57         42       48        18
                 vv
clus              STAGE IVB
  KCNN4 MUTATED           0
  KCNN4 WILD-TYPE         1
D1496V4, multiclass
            clus
vv           KCNN4 MUTATED KCNN4 WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              2             136
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             2              57
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  KCNN4 MUTATED     1   0   5   1
  KCNN4 WILD-TYPE  16  92 324  49
D1496V5, multiclass
    clus
vv   KCNN4 MUTATED KCNN4 WILD-TYPE
  T1             1              16
  T2             0              92
  T3             5             324
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  KCNN4 MUTATED     5   2   0
  KCNN4 WILD-TYPE 282 111  87
D1496V6, multiclass
    clus
vv   KCNN4 MUTATED KCNN4 WILD-TYPE
  N0             5             282
  N1             2             111
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1496V7, binary
                 cls
clus                0   1
  KCNN4 MUTATED     6   0
  KCNN4 WILD-TYPE 369  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNN4 MUTATED      6    0
  KCNN4 WILD-TYPE  369   65
   clus
vv  KCNN4 MUTATED KCNN4 WILD-TYPE
  0             6             369
  1             0              65
[1] 2 2
[1] FALSE
D1496V8, binary
                 cls
clus                0   1
  KCNN4 MUTATED     4   3
  KCNN4 WILD-TYPE 221 261
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNN4 MUTATED      4    3
  KCNN4 WILD-TYPE  221  261
        clus
vv       KCNN4 MUTATED KCNN4 WILD-TYPE
  FEMALE             4             221
  MALE               3             261
[1] 2 2
[1] FALSE
D1496V9, binary
                 cls
clus                0   1
  KCNN4 MUTATED     7   0
  KCNN4 WILD-TYPE 343  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNN4 MUTATED      7    0
  KCNN4 WILD-TYPE  343   22
     clus
vv    KCNN4 MUTATED KCNN4 WILD-TYPE
  NO              7             343
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  KCNN4 MUTATED                      7                             0
  KCNN4 WILD-TYPE                  308                            47
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  KCNN4 MUTATED                       0                              0
  KCNN4 WILD-TYPE                   106                             10
D1496V10, multiclass
                                clus
vv                               KCNN4 MUTATED KCNN4 WILD-TYPE
  COLON ADENOCARCINOMA                       7             308
  COLON MUCINOUS ADENOCARCINOMA              0              47
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  KCNN4 MUTATED     4   1   0   0
  KCNN4 WILD-TYPE 341   3  31  25
D1496V11, multiclass
    clus
vv   KCNN4 MUTATED KCNN4 WILD-TYPE
  R0             4             341
  R1             1               3
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1496V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KCNN4 MUTATED                                  0     0
  KCNN4 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  KCNN4 MUTATED                           2     5
  KCNN4 WILD-TYPE                        20   221
D1496V13, multiclass
                                  clus
vv                                 KCNN4 MUTATED KCNN4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    2              20
  WHITE                                        5             221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1497) Variable = C20ORF177 MUTATION ANALYSIS
D1497V1, survival
                     sevent
clus2                   0   1
  C20ORF177 MUTATED    11   2
  C20ORF177 WILD-TYPE 367  91
  C20ORF177 MUTATED C20ORF177 WILD-TYPE 
                 13                 458 
  C20ORF177 MUTATED C20ORF177 WILD-TYPE 
                  2                  91 
$`C20ORF177 MUTATED`
TCGA-AA-A00N TCGA-AA-A01R TCGA-CA-6718 TCGA-CA-6719 TCGA-CM-6171 TCGA-D5-6536 
        4.01        35.01        10.06        14.30        14.04        17.85 
TCGA-DM-A1D0 TCGA-F4-6704 TCGA-G4-6304 TCGA-AF-6655 TCGA-AG-3892 TCGA-AG-A002 
      130.65         1.55        53.62        20.02        13.02        20.98 
TCGA-F5-6813 
        0.69 

$`C20ORF177 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S 
       12.00        31.00        31.00        38.07         1.02         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       12.20        12.76        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       13.02        15.02        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       43.27        15.12         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D4 
       11.38        10.26       119.70        24.43        38.20        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       35.74         6.18        47.87        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       74.56        65.85        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       15.39        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 
        1.02        17.95        36.95        17.03        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  C20ORF177 MUTATED C20ORF177 WILD-TYPE 
               0.69                0.00 
  C20ORF177 MUTATED C20ORF177 WILD-TYPE 
             130.65              148.01 
  C20ORF177 MUTATED C20ORF177 WILD-TYPE 
              14.30               20.73 
[1] "0.7 - 130.7 (14.3)" "0.0 - 148.0 (20.7)"
[1] "hr=" "1.2"
D1497V2, continuous
D1497V3, binary
                     cls
clus                    0   1
  C20ORF177 MUTATED     9   4
  C20ORF177 WILD-TYPE 357 115
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  C20ORF177 MUTATED      9    4
  C20ORF177 WILD-TYPE  357  115
        clus
vv       C20ORF177 MUTATED C20ORF177 WILD-TYPE
  COLON                  9                 357
  RECTUM                 4                 115
[1] 2 2
[1] FALSE
                     vv
clus                  STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  C20ORF177 MUTATED         3        0        0         4         2         0
  C20ORF177 WILD-TYPE      88        1       32       134         8         1
                     vv
clus                  STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C20ORF177 MUTATED           1          1          0          2        0
  C20ORF177 WILD-TYPE        23         10         59         40       48
                     vv
clus                  STAGE IVA STAGE IVB
  C20ORF177 MUTATED           0         0
  C20ORF177 WILD-TYPE        18         1
D1497V4, multiclass
            clus
vv           C20ORF177 MUTATED C20ORF177 WILD-TYPE
  STAGE I                    3                  88
  STAGE IA                   0                   1
  STAGE II                   0                  32
  STAGE IIA                  4                 134
  STAGE IIB                  2                   8
  STAGE IIC                  0                   1
  STAGE III                  1                  23
  STAGE IIIA                 1                  10
  STAGE IIIB                 0                  59
  STAGE IIIC                 2                  40
  STAGE IV                   0                  48
  STAGE IVA                  0                  18
  STAGE IVB                  0                   1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                   T1  T2  T3  T4
  C20ORF177 MUTATED     1   3   6   3
  C20ORF177 WILD-TYPE  16  89 323  47
D1497V5, multiclass
    clus
vv   C20ORF177 MUTATED C20ORF177 WILD-TYPE
  T1                 1                  16
  T2                 3                  89
  T3                 6                 323
  T4                 3                  47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                   N0  N1  N2
  C20ORF177 MUTATED     9   1   3
  C20ORF177 WILD-TYPE 278 112  84
D1497V6, multiclass
    clus
vv   C20ORF177 MUTATED C20ORF177 WILD-TYPE
  N0                 9                 278
  N1                 1                 112
  N2                 3                  84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1497V7, binary
                     cls
clus                    0   1
  C20ORF177 MUTATED    12   0
  C20ORF177 WILD-TYPE 363  65
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  C20ORF177 MUTATED     12    0
  C20ORF177 WILD-TYPE  363   65
   clus
vv  C20ORF177 MUTATED C20ORF177 WILD-TYPE
  0                12                 363
  1                 0                  65
[1] 2 2
[1] FALSE
D1497V8, binary
                     cls
clus                    0   1
  C20ORF177 MUTATED     4   9
  C20ORF177 WILD-TYPE 221 255
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  C20ORF177 MUTATED      4    9
  C20ORF177 WILD-TYPE  221  255
        clus
vv       C20ORF177 MUTATED C20ORF177 WILD-TYPE
  FEMALE                 4                 221
  MALE                   9                 255
[1] 2 2
[1] FALSE
D1497V9, binary
                     cls
clus                    0   1
  C20ORF177 MUTATED     8   1
  C20ORF177 WILD-TYPE 342  21
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  C20ORF177 MUTATED      8    1
  C20ORF177 WILD-TYPE  342   21
     clus
vv    C20ORF177 MUTATED C20ORF177 WILD-TYPE
  NO                  8                 342
  YES                 1                  21
[1] 2 2
[1] FALSE
                     vv
clus                  COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  C20ORF177 MUTATED                      6                             3
  C20ORF177 WILD-TYPE                  309                            44
                     vv
clus                  RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  C20ORF177 MUTATED                       4                              0
  C20ORF177 WILD-TYPE                   102                             10
D1497V10, multiclass
                                clus
vv                               C20ORF177 MUTATED C20ORF177 WILD-TYPE
  COLON ADENOCARCINOMA                           6                 309
  COLON MUCINOUS ADENOCARCINOMA                  3                  44
  RECTAL ADENOCARCINOMA                          4                 102
  RECTAL MUCINOUS ADENOCARCINOMA                 0                  10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                   R0  R1  R2  RX
  C20ORF177 MUTATED    10   0   0   2
  C20ORF177 WILD-TYPE 335   4  31  23
D1497V11, multiclass
    clus
vv   C20ORF177 MUTATED C20ORF177 WILD-TYPE
  R0                10                 335
  R1                 0                   4
  R2                 0                  31
  RX                 2                  23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1497V12, continuous
                     vv
clus                  AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C20ORF177 MUTATED                                  1     2
  C20ORF177 WILD-TYPE                                0     9
                     vv
clus                  BLACK OR AFRICAN AMERICAN WHITE
  C20ORF177 MUTATED                           0     6
  C20ORF177 WILD-TYPE                        22   220
D1497V13, multiclass
                                  clus
vv                                 C20ORF177 MUTATED C20ORF177 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                 1                   0
  ASIAN                                            2                   9
  BLACK OR AFRICAN AMERICAN                        0                  22
  WHITE                                            6                 220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1498) Variable = RBL1 MUTATION ANALYSIS
D1498V1, survival
                sevent
clus2              0   1
  RBL1 MUTATED    16   3
  RBL1 WILD-TYPE 362  90
  RBL1 MUTATED RBL1 WILD-TYPE 
            19            452 
  RBL1 MUTATED RBL1 WILD-TYPE 
             3             90 
$`RBL1 MUTATED`
TCGA-A6-2676 TCGA-A6-5661 TCGA-A6-6654 TCGA-A6-6780 TCGA-AA-3544 TCGA-AA-3663 
       42.90        33.53        23.87        20.12        14.01         6.97 
TCGA-AA-A00N TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-6608 TCGA-CA-6717 TCGA-CM-6679 
        4.01        17.82        58.39         1.61        12.76        10.06 
TCGA-D5-6923 TCGA-D5-6931 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6588 TCGA-AG-A002 
       12.43        12.00        47.41       133.18        26.17        20.98 
TCGA-DY-A0XA 
      126.44 

$`RBL1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       31.63        30.44        29.19        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6781 TCGA-A6-6782 
       24.16        21.76        24.69        24.39        19.66        20.28 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
        7.04         3.02         1.02        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
       78.08         6.05        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
        0.95        33.01        21.44         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 
      100.01        29.56         5.23        11.74         3.19        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07        12.20        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.08        11.01        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6924 TCGA-D5-6926 
       15.58         1.48         3.68         4.41        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6932 TCGA-D5-7000 
        9.44        11.64         4.80         1.51        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6303 
       33.67        13.25         0.53        35.31        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        35.80        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
        5.29        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  RBL1 MUTATED RBL1 WILD-TYPE 
          1.61           0.00 
  RBL1 MUTATED RBL1 WILD-TYPE 
        133.18         148.01 
  RBL1 MUTATED RBL1 WILD-TYPE 
        20.120         20.235 
[1] "1.6 - 133.2 (20.1)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.5"
D1498V2, continuous
D1498V3, binary
                cls
clus               0   1
  RBL1 MUTATED    17   2
  RBL1 WILD-TYPE 349 117
[1] "tbl2"
                cls
clus             [,1] [,2]
  RBL1 MUTATED     17    2
  RBL1 WILD-TYPE  349  117
        clus
vv       RBL1 MUTATED RBL1 WILD-TYPE
  COLON            17            349
  RECTUM            2            117
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RBL1 MUTATED         3        0        1         8         2         0
  RBL1 WILD-TYPE      88        1       31       130         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RBL1 MUTATED           1          1          2          1        0         0
  RBL1 WILD-TYPE        23         10         57         41       48        18
                vv
clus             STAGE IVB
  RBL1 MUTATED           0
  RBL1 WILD-TYPE         1
D1498V4, multiclass
            clus
vv           RBL1 MUTATED RBL1 WILD-TYPE
  STAGE I               3             88
  STAGE IA              0              1
  STAGE II              1             31
  STAGE IIA             8            130
  STAGE IIB             2              8
  STAGE IIC             0              1
  STAGE III             1             23
  STAGE IIIA            1             10
  STAGE IIIB            2             57
  STAGE IIIC            1             41
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  RBL1 MUTATED     0   4  12   3
  RBL1 WILD-TYPE  17  88 317  47
D1498V5, multiclass
    clus
vv   RBL1 MUTATED RBL1 WILD-TYPE
  T1            0             17
  T2            4             88
  T3           12            317
  T4            3             47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  RBL1 MUTATED    14   4   1
  RBL1 WILD-TYPE 273 109  86
D1498V6, multiclass
    clus
vv   RBL1 MUTATED RBL1 WILD-TYPE
  N0           14            273
  N1            4            109
  N2            1             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1498V7, binary
                cls
clus               0   1
  RBL1 MUTATED    18   0
  RBL1 WILD-TYPE 357  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  RBL1 MUTATED     18    0
  RBL1 WILD-TYPE  357   65
   clus
vv  RBL1 MUTATED RBL1 WILD-TYPE
  0           18            357
  1            0             65
[1] 2 2
[1] FALSE
D1498V8, binary
                cls
clus               0   1
  RBL1 MUTATED     9  10
  RBL1 WILD-TYPE 216 254
[1] "tbl2"
                cls
clus             [,1] [,2]
  RBL1 MUTATED      9   10
  RBL1 WILD-TYPE  216  254
        clus
vv       RBL1 MUTATED RBL1 WILD-TYPE
  FEMALE            9            216
  MALE             10            254
[1] 2 2
[1] FALSE
D1498V9, binary
                cls
clus               0   1
  RBL1 MUTATED    17   0
  RBL1 WILD-TYPE 333  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  RBL1 MUTATED     17    0
  RBL1 WILD-TYPE  333   22
     clus
vv    RBL1 MUTATED RBL1 WILD-TYPE
  NO            17            333
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  RBL1 MUTATED                     14                             3
  RBL1 WILD-TYPE                  301                            44
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  RBL1 MUTATED                       2                              0
  RBL1 WILD-TYPE                   104                             10
D1498V10, multiclass
                                clus
vv                               RBL1 MUTATED RBL1 WILD-TYPE
  COLON ADENOCARCINOMA                     14            301
  COLON MUCINOUS ADENOCARCINOMA             3             44
  RECTAL ADENOCARCINOMA                     2            104
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  RBL1 MUTATED    14   0   0   1
  RBL1 WILD-TYPE 331   4  31  24
D1498V11, multiclass
    clus
vv   RBL1 MUTATED RBL1 WILD-TYPE
  R0           14            331
  R1            0              4
  R2            0             31
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1498V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RBL1 MUTATED                                  0     1
  RBL1 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  RBL1 MUTATED                           2    12
  RBL1 WILD-TYPE                        20   214
D1498V13, multiclass
                                  clus
vv                                 RBL1 MUTATED RBL1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   2             20
  WHITE                                      12            214
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1499) Variable = RBM15B MUTATION ANALYSIS
D1499V1, survival
                  sevent
clus2                0   1
  RBM15B MUTATED     7   2
  RBM15B WILD-TYPE 371  91
  RBM15B MUTATED RBM15B WILD-TYPE 
               9              462 
  RBM15B MUTATED RBM15B WILD-TYPE 
               2               91 
$`RBM15B MUTATED`
TCGA-A6-5661 TCGA-A6-6653 TCGA-AA-3492 TCGA-AA-3864 TCGA-AA-A00K TCGA-AD-5900 
       33.53        24.39         3.02        53.00        18.05         0.07 
TCGA-CA-6718 TCGA-CM-6678 TCGA-AG-A02N 
       10.06        11.01        61.97 

$`RBM15B WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 
       25.18        24.16        21.76        24.69        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       19.66        20.28         7.04         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        31.07        30.05        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07        12.20        12.76        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6679 
       11.01        12.95        13.05        11.08        11.08        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 
       10.98        49.97         1.94        38.96        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  RBM15B MUTATED RBM15B WILD-TYPE 
            0.07             0.00 
  RBM15B MUTATED RBM15B WILD-TYPE 
           61.97           148.01 
  RBM15B MUTATED RBM15B WILD-TYPE 
          18.050           20.235 
[1] "0.1 - 62.0 (18.1)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.2"
D1499V2, continuous
D1499V3, binary
                  cls
clus                 0   1
  RBM15B MUTATED     8   1
  RBM15B WILD-TYPE 358 118
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RBM15B MUTATED      8    1
  RBM15B WILD-TYPE  358  118
        clus
vv       RBM15B MUTATED RBM15B WILD-TYPE
  COLON               8              358
  RECTUM              1              118
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RBM15B MUTATED         2        0        3         3         0         0
  RBM15B WILD-TYPE      89        1       29       135        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RBM15B MUTATED           0          0          0          0        0
  RBM15B WILD-TYPE        24         11         59         42       48
                  vv
clus               STAGE IVA STAGE IVB
  RBM15B MUTATED           1         0
  RBM15B WILD-TYPE        17         1
D1499V4, multiclass
            clus
vv           RBM15B MUTATED RBM15B WILD-TYPE
  STAGE I                 2               89
  STAGE IA                0                1
  STAGE II                3               29
  STAGE IIA               3              135
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              0               59
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               1               17
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  RBM15B MUTATED     0   2   6   1
  RBM15B WILD-TYPE  17  90 323  49
D1499V5, multiclass
    clus
vv   RBM15B MUTATED RBM15B WILD-TYPE
  T1              0               17
  T2              2               90
  T3              6              323
  T4              1               49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  RBM15B MUTATED     8   1   0
  RBM15B WILD-TYPE 279 112  87
D1499V6, multiclass
    clus
vv   RBM15B MUTATED RBM15B WILD-TYPE
  N0              8              279
  N1              1              112
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1499V7, binary
                  cls
clus                 0   1
  RBM15B MUTATED     7   1
  RBM15B WILD-TYPE 368  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RBM15B MUTATED      7    1
  RBM15B WILD-TYPE  368   64
   clus
vv  RBM15B MUTATED RBM15B WILD-TYPE
  0              7              368
  1              1               64
[1] 2 2
[1] FALSE
D1499V8, binary
                  cls
clus                 0   1
  RBM15B MUTATED     3   6
  RBM15B WILD-TYPE 222 258
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RBM15B MUTATED      3    6
  RBM15B WILD-TYPE  222  258
        clus
vv       RBM15B MUTATED RBM15B WILD-TYPE
  FEMALE              3              222
  MALE                6              258
[1] 2 2
[1] FALSE
D1499V9, binary
                  cls
clus                 0   1
  RBM15B MUTATED     6   0
  RBM15B WILD-TYPE 344  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RBM15B MUTATED      6    0
  RBM15B WILD-TYPE  344   22
     clus
vv    RBM15B MUTATED RBM15B WILD-TYPE
  NO               6              344
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  RBM15B MUTATED                      7                             1
  RBM15B WILD-TYPE                  308                            46
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  RBM15B MUTATED                       1                              0
  RBM15B WILD-TYPE                   105                             10
D1499V10, multiclass
                                clus
vv                               RBM15B MUTATED RBM15B WILD-TYPE
  COLON ADENOCARCINOMA                        7              308
  COLON MUCINOUS ADENOCARCINOMA               1               46
  RECTAL ADENOCARCINOMA                       1              105
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  RBM15B MUTATED     7   0   0   1
  RBM15B WILD-TYPE 338   4  31  24
D1499V11, multiclass
    clus
vv   RBM15B MUTATED RBM15B WILD-TYPE
  R0              7              338
  R1              0                4
  R2              0               31
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1499V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RBM15B MUTATED                                  0     1
  RBM15B WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  RBM15B MUTATED                           1     3
  RBM15B WILD-TYPE                        21   223
D1499V13, multiclass
                                  clus
vv                                 RBM15B MUTATED RBM15B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                         3              223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1500) Variable = PCDH19 MUTATION ANALYSIS
D1500V1, survival
                  sevent
clus2                0   1
  PCDH19 MUTATED    17   4
  PCDH19 WILD-TYPE 361  89
  PCDH19 MUTATED PCDH19 WILD-TYPE 
              21              450 
  PCDH19 MUTATED PCDH19 WILD-TYPE 
               4               89 
$`PCDH19 MUTATED`
TCGA-AA-3492 TCGA-AA-3672 TCGA-AA-3845 TCGA-AA-3854 TCGA-AA-3947 TCGA-AA-A004 
        3.02         0.92         0.00        36.03        33.01        13.94 
TCGA-AZ-4315 TCGA-AZ-5403 TCGA-DM-A1HB TCGA-F4-6570 TCGA-G4-6586 TCGA-G4-6588 
       58.39        62.79       135.65         6.18        35.80        26.17 
TCGA-G4-6625 TCGA-AF-4110 TCGA-AG-3892 TCGA-AG-3898 TCGA-AG-A002 TCGA-AG-A020 
       91.79        14.50        13.02        48.03        20.98        10.98 
TCGA-EI-6506 TCGA-EI-6507 TCGA-F5-6813 
       20.55        19.96         0.69 

$`PCDH19 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 
        6.97        54.02         2.01        14.01        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 
       15.95        38.99        37.02        14.93        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
        0.00        33.07         0.00        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       27.02        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
       16.31         0.95        33.01        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
        5.13       106.75        22.36        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 
      117.07        98.24         8.61        31.96        35.74        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       36.00        22.09        13.78        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       35.01        14.01         1.02        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       12.00        70.03        64.01        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       32.61         0.49        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-G5-6235 TCGA-G5-6641 
       31.30        28.57        32.19         0.66        55.76        26.43 

  PCDH19 MUTATED PCDH19 WILD-TYPE 
               0                0 
  PCDH19 MUTATED PCDH19 WILD-TYPE 
          135.65           148.01 
  PCDH19 MUTATED PCDH19 WILD-TYPE 
          20.550           20.155 
[1] "0.0 - 135.7 (20.6)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.2"
D1500V2, continuous
D1500V3, binary
                  cls
clus                 0   1
  PCDH19 MUTATED    14   7
  PCDH19 WILD-TYPE 352 112
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PCDH19 MUTATED     14    7
  PCDH19 WILD-TYPE  352  112
        clus
vv       PCDH19 MUTATED PCDH19 WILD-TYPE
  COLON              14              352
  RECTUM              7              112
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PCDH19 MUTATED         3        0        2        11         1         0
  PCDH19 WILD-TYPE      88        1       30       127         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PCDH19 MUTATED           2          0          1          1        0
  PCDH19 WILD-TYPE        22         11         58         41       48
                  vv
clus               STAGE IVA STAGE IVB
  PCDH19 MUTATED           1         0
  PCDH19 WILD-TYPE        17         1
D1500V4, multiclass
            clus
vv           PCDH19 MUTATED PCDH19 WILD-TYPE
  STAGE I                 3               88
  STAGE IA                0                1
  STAGE II                2               30
  STAGE IIA              11              127
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               2               22
  STAGE IIIA              0               11
  STAGE IIIB              1               58
  STAGE IIIC              1               41
  STAGE IV                0               48
  STAGE IVA               1               17
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  PCDH19 MUTATED     1   2  16   3
  PCDH19 WILD-TYPE  16  90 313  47
D1500V5, multiclass
    clus
vv   PCDH19 MUTATED PCDH19 WILD-TYPE
  T1              1               16
  T2              2               90
  T3             16              313
  T4              3               47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  PCDH19 MUTATED    17   3   2
  PCDH19 WILD-TYPE 270 110  85
D1500V6, multiclass
    clus
vv   PCDH19 MUTATED PCDH19 WILD-TYPE
  N0             17              270
  N1              3              110
  N2              2               85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1500V7, binary
                  cls
clus                 0   1
  PCDH19 MUTATED    20   0
  PCDH19 WILD-TYPE 355  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PCDH19 MUTATED     20    0
  PCDH19 WILD-TYPE  355   65
   clus
vv  PCDH19 MUTATED PCDH19 WILD-TYPE
  0             20              355
  1              0               65
[1] 2 2
[1] FALSE
D1500V8, binary
                  cls
clus                 0   1
  PCDH19 MUTATED    13   9
  PCDH19 WILD-TYPE 212 255
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PCDH19 MUTATED     13    9
  PCDH19 WILD-TYPE  212  255
        clus
vv       PCDH19 MUTATED PCDH19 WILD-TYPE
  FEMALE             13              212
  MALE                9              255
[1] 2 2
[1] FALSE
D1500V9, binary
                  cls
clus                 0   1
  PCDH19 MUTATED    17   0
  PCDH19 WILD-TYPE 333  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PCDH19 MUTATED     17    0
  PCDH19 WILD-TYPE  333   22
     clus
vv    PCDH19 MUTATED PCDH19 WILD-TYPE
  NO              17              333
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PCDH19 MUTATED                     11                             2
  PCDH19 WILD-TYPE                  304                            45
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PCDH19 MUTATED                       6                              1
  PCDH19 WILD-TYPE                   100                              9
D1500V10, multiclass
                                clus
vv                               PCDH19 MUTATED PCDH19 WILD-TYPE
  COLON ADENOCARCINOMA                       11              304
  COLON MUCINOUS ADENOCARCINOMA               2               45
  RECTAL ADENOCARCINOMA                       6              100
  RECTAL MUCINOUS ADENOCARCINOMA              1                9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  PCDH19 MUTATED    20   0   0   0
  PCDH19 WILD-TYPE 325   4  31  25
D1500V11, multiclass
    clus
vv   PCDH19 MUTATED PCDH19 WILD-TYPE
  R0             20              325
  R1              0                4
  R2              0               31
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1500V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PCDH19 MUTATED                                  0     0
  PCDH19 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  PCDH19 MUTATED                           0    11
  PCDH19 WILD-TYPE                        22   215
D1500V13, multiclass
                                  clus
vv                                 PCDH19 MUTATED PCDH19 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                        11              215
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1501) Variable = MOV10L1 MUTATION ANALYSIS
D1501V1, survival
                   sevent
clus2                 0   1
  MOV10L1 MUTATED    14   3
  MOV10L1 WILD-TYPE 364  90
  MOV10L1 MUTATED MOV10L1 WILD-TYPE 
               17               454 
  MOV10L1 MUTATED MOV10L1 WILD-TYPE 
                3                90 
$`MOV10L1 MUTATED`
TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-5661 TCGA-AA-3672 TCGA-AA-3947 TCGA-AA-3977 
       34.65        32.75        33.53         0.92        33.01        25.02 
TCGA-AA-A00N TCGA-AU-6004 TCGA-CM-5860 TCGA-CM-6172 TCGA-D5-6532 TCGA-D5-6537 
        4.01        27.09        32.02        11.01        18.25         4.80 
TCGA-D5-6541 TCGA-DM-A0XD TCGA-G4-6307 TCGA-AG-3892 TCGA-AG-A002 
       15.58        24.43        55.04        13.02        20.98 

$`MOV10L1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5657 
       16.57        33.34        36.53        14.53        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 
       30.44        29.19        23.61        22.09        22.06        32.71 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       27.09        22.52         8.38        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
        2.01        14.01        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 
       27.42        10.88         0.20        14.50        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 
       12.99        13.02        15.02        14.04        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6533 
       12.26        19.59        56.09        55.92        20.19         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       43.27        15.12        17.85        17.13        12.49        16.14 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
       10.26       119.70        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6310 
       74.56        65.85        53.62        44.68        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 
       19.99         1.02        17.95        36.95        17.03        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  MOV10L1 MUTATED MOV10L1 WILD-TYPE 
             0.92              0.00 
  MOV10L1 MUTATED MOV10L1 WILD-TYPE 
            55.04            148.01 
  MOV10L1 MUTATED MOV10L1 WILD-TYPE 
           24.430            20.085 
[1] "0.9 - 55.0 (24.4)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.1"
D1501V2, continuous
D1501V3, binary
                   cls
clus                  0   1
  MOV10L1 MUTATED    15   2
  MOV10L1 WILD-TYPE 351 117
[1] "tbl2"
                   cls
clus                [,1] [,2]
  MOV10L1 MUTATED     15    2
  MOV10L1 WILD-TYPE  351  117
        clus
vv       MOV10L1 MUTATED MOV10L1 WILD-TYPE
  COLON               15               351
  RECTUM               2               117
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MOV10L1 MUTATED         3        0        0         5         3         0
  MOV10L1 WILD-TYPE      88        1       32       133         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MOV10L1 MUTATED           1          0          3          1        0
  MOV10L1 WILD-TYPE        23         11         56         41       48
                   vv
clus                STAGE IVA STAGE IVB
  MOV10L1 MUTATED           0         0
  MOV10L1 WILD-TYPE        18         1
D1501V4, multiclass
            clus
vv           MOV10L1 MUTATED MOV10L1 WILD-TYPE
  STAGE I                  3                88
  STAGE IA                 0                 1
  STAGE II                 0                32
  STAGE IIA                5               133
  STAGE IIB                3                 7
  STAGE IIC                0                 1
  STAGE III                1                23
  STAGE IIIA               0                11
  STAGE IIIB               3                56
  STAGE IIIC               1                41
  STAGE IV                 0                48
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  MOV10L1 MUTATED     1   3  10   3
  MOV10L1 WILD-TYPE  16  89 319  47
D1501V5, multiclass
    clus
vv   MOV10L1 MUTATED MOV10L1 WILD-TYPE
  T1               1                16
  T2               3                89
  T3              10               319
  T4               3                47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  MOV10L1 MUTATED    12   4   1
  MOV10L1 WILD-TYPE 275 109  86
D1501V6, multiclass
    clus
vv   MOV10L1 MUTATED MOV10L1 WILD-TYPE
  N0              12               275
  N1               4               109
  N2               1                86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1501V7, binary
                   cls
clus                  0   1
  MOV10L1 MUTATED    15   0
  MOV10L1 WILD-TYPE 360  65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  MOV10L1 MUTATED     15    0
  MOV10L1 WILD-TYPE  360   65
   clus
vv  MOV10L1 MUTATED MOV10L1 WILD-TYPE
  0              15               360
  1               0                65
[1] 2 2
[1] FALSE
D1501V8, binary
                   cls
clus                  0   1
  MOV10L1 MUTATED     9   8
  MOV10L1 WILD-TYPE 216 256
[1] "tbl2"
                   cls
clus                [,1] [,2]
  MOV10L1 MUTATED      9    8
  MOV10L1 WILD-TYPE  216  256
        clus
vv       MOV10L1 MUTATED MOV10L1 WILD-TYPE
  FEMALE               9               216
  MALE                 8               256
[1] 2 2
[1] FALSE
D1501V9, binary
                   cls
clus                  0   1
  MOV10L1 MUTATED    14   0
  MOV10L1 WILD-TYPE 336  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  MOV10L1 MUTATED     14    0
  MOV10L1 WILD-TYPE  336   22
     clus
vv    MOV10L1 MUTATED MOV10L1 WILD-TYPE
  NO               14               336
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MOV10L1 MUTATED                     12                             3
  MOV10L1 WILD-TYPE                  303                            44
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MOV10L1 MUTATED                       2                              0
  MOV10L1 WILD-TYPE                   104                             10
D1501V10, multiclass
                                clus
vv                               MOV10L1 MUTATED MOV10L1 WILD-TYPE
  COLON ADENOCARCINOMA                        12               303
  COLON MUCINOUS ADENOCARCINOMA                3                44
  RECTAL ADENOCARCINOMA                        2               104
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  MOV10L1 MUTATED    15   0   0   0
  MOV10L1 WILD-TYPE 330   4  31  25
D1501V11, multiclass
    clus
vv   MOV10L1 MUTATED MOV10L1 WILD-TYPE
  R0              15               330
  R1               0                 4
  R2               0                31
  RX               0                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1501V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MOV10L1 MUTATED                                  0     0
  MOV10L1 WILD-TYPE                                1    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  MOV10L1 MUTATED                           1    10
  MOV10L1 WILD-TYPE                        21   216
D1501V13, multiclass
                                  clus
vv                                 MOV10L1 MUTATED MOV10L1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                      1                21
  WHITE                                         10               216
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1502) Variable = FAF2 MUTATION ANALYSIS
D1502V1, survival
                sevent
clus2              0   1
  FAF2 MUTATED     4   3
  FAF2 WILD-TYPE 374  90
  FAF2 MUTATED FAF2 WILD-TYPE 
             7            464 
  FAF2 MUTATED FAF2 WILD-TYPE 
             3             90 
$`FAF2 MUTATED`
TCGA-A6-2672 TCGA-A6-2676 TCGA-AA-3489 TCGA-AA-3864 TCGA-CA-6717 TCGA-CM-5861 
       46.65        42.90         7.04        53.00        12.76        15.02 
TCGA-DM-A28F 
       35.97 

$`FAF2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       43.76        43.76        24.33        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5657 
       33.34        32.75        36.53        14.53        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       30.44        29.19        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       19.66        20.28         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        31.07        30.05        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07        12.20        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 
       22.03        22.98        30.08        32.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
      119.93        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  FAF2 MUTATED FAF2 WILD-TYPE 
          7.04           0.00 
  FAF2 MUTATED FAF2 WILD-TYPE 
         53.00         148.01 
  FAF2 MUTATED FAF2 WILD-TYPE 
        35.970         20.155 
[1] "7.0 - 53.0 (36.0)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.8"
D1502V2, continuous
D1502V3, binary
                cls
clus               0   1
  FAF2 MUTATED     7   1
  FAF2 WILD-TYPE 359 118
[1] "tbl2"
                cls
clus             [,1] [,2]
  FAF2 MUTATED      7    1
  FAF2 WILD-TYPE  359  118
        clus
vv       FAF2 MUTATED FAF2 WILD-TYPE
  COLON             7            359
  RECTUM            1            118
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FAF2 MUTATED         0        0        2         2         1         0
  FAF2 WILD-TYPE      91        1       30       136         9         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  FAF2 MUTATED           1          0          2          0        0         0
  FAF2 WILD-TYPE        23         11         57         42       48        18
                vv
clus             STAGE IVB
  FAF2 MUTATED           0
  FAF2 WILD-TYPE         1
D1502V4, multiclass
            clus
vv           FAF2 MUTATED FAF2 WILD-TYPE
  STAGE I               0             91
  STAGE IA              0              1
  STAGE II              2             30
  STAGE IIA             2            136
  STAGE IIB             1              9
  STAGE IIC             0              1
  STAGE III             1             23
  STAGE IIIA            0             11
  STAGE IIIB            2             57
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  FAF2 MUTATED     0   0   7   1
  FAF2 WILD-TYPE  17  92 322  49
D1502V5, multiclass
    clus
vv   FAF2 MUTATED FAF2 WILD-TYPE
  T1            0             17
  T2            0             92
  T3            7            322
  T4            1             49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  FAF2 MUTATED     5   3   0
  FAF2 WILD-TYPE 282 110  87
D1502V6, multiclass
    clus
vv   FAF2 MUTATED FAF2 WILD-TYPE
  N0            5            282
  N1            3            110
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1502V7, binary
                cls
clus               0   1
  FAF2 MUTATED     7   0
  FAF2 WILD-TYPE 368  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  FAF2 MUTATED      7    0
  FAF2 WILD-TYPE  368   65
   clus
vv  FAF2 MUTATED FAF2 WILD-TYPE
  0            7            368
  1            0             65
[1] 2 2
[1] FALSE
D1502V8, binary
                cls
clus               0   1
  FAF2 MUTATED     3   5
  FAF2 WILD-TYPE 222 259
[1] "tbl2"
                cls
clus             [,1] [,2]
  FAF2 MUTATED      3    5
  FAF2 WILD-TYPE  222  259
        clus
vv       FAF2 MUTATED FAF2 WILD-TYPE
  FEMALE            3            222
  MALE              5            259
[1] 2 2
[1] FALSE
D1502V9, binary
                cls
clus               0   1
  FAF2 MUTATED     6   0
  FAF2 WILD-TYPE 344  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  FAF2 MUTATED      6    0
  FAF2 WILD-TYPE  344   22
     clus
vv    FAF2 MUTATED FAF2 WILD-TYPE
  NO             6            344
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  FAF2 MUTATED                      6                             1
  FAF2 WILD-TYPE                  309                            46
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  FAF2 MUTATED                       1                              0
  FAF2 WILD-TYPE                   105                             10
D1502V10, multiclass
                                clus
vv                               FAF2 MUTATED FAF2 WILD-TYPE
  COLON ADENOCARCINOMA                      6            309
  COLON MUCINOUS ADENOCARCINOMA             1             46
  RECTAL ADENOCARCINOMA                     1            105
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  FAF2 MUTATED     5   0   0   1
  FAF2 WILD-TYPE 340   4  31  24
D1502V11, multiclass
    clus
vv   FAF2 MUTATED FAF2 WILD-TYPE
  R0            5            340
  R1            0              4
  R2            0             31
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1502V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FAF2 MUTATED                                  0     1
  FAF2 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  FAF2 MUTATED                           0     5
  FAF2 WILD-TYPE                        22   221
D1502V13, multiclass
                                  clus
vv                                 FAF2 MUTATED FAF2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       5            221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1503) Variable = RBM15 MUTATION ANALYSIS
D1503V1, survival
                 sevent
clus2               0   1
  RBM15 MUTATED    19   0
  RBM15 WILD-TYPE 359  93
  RBM15 MUTATED RBM15 WILD-TYPE 
             19             452 
  RBM15 MUTATED RBM15 WILD-TYPE 
              0              93 
$`RBM15 MUTATED`
TCGA-AA-3713 TCGA-AA-3821 TCGA-AA-3877 TCGA-AA-3949 TCGA-AA-A010 TCGA-AU-3779 
       19.04         1.02        31.00        26.01        34.98        14.50 
TCGA-CA-6717 TCGA-CM-4743 TCGA-CM-6162 TCGA-CM-6171 TCGA-D5-6928 TCGA-F4-6569 
       12.76        23.05        12.00        14.04        11.64        35.74 
TCGA-F4-6856 TCGA-G4-6309 TCGA-G4-6588 TCGA-AG-3892 TCGA-AG-A002 TCGA-DY-A0XA 
       35.31        85.48        26.17        13.02        20.98       126.44 
TCGA-F5-6571 
       31.30 

$`RBM15 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 
       10.06        35.05        33.04         0.99        25.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 
       24.03        27.02        29.98        18.05         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        33.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-6004 
        5.79        22.42        27.42        10.88         0.20        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07        12.20        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 
       21.14        82.95         1.91       124.27        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       15.02         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       12.99        13.02        15.02        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6930 
       12.43        14.30         9.04         9.44         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
        8.61        31.96         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 
       19.99         1.02        17.95        36.95        17.03        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.03         5.29        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
        9.96        49.51        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  RBM15 MUTATED RBM15 WILD-TYPE 
           1.02            0.00 
  RBM15 MUTATED RBM15 WILD-TYPE 
         126.44          148.01 
  RBM15 MUTATED RBM15 WILD-TYPE 
         23.050          20.085 
[1] "1.0 - 126.4 (23.1)" "0.0 - 148.0 (20.1)"
[1] "hr="     "2.6e+07"
D1503V2, continuous
D1503V3, binary
                 cls
clus                0   1
  RBM15 MUTATED    16   4
  RBM15 WILD-TYPE 350 115
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM15 MUTATED     16    4
  RBM15 WILD-TYPE  350  115
        clus
vv       RBM15 MUTATED RBM15 WILD-TYPE
  COLON             16             350
  RECTUM             4             115
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RBM15 MUTATED         7        0        0         7         1         0
  RBM15 WILD-TYPE      84        1       32       131         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RBM15 MUTATED           1          0          3          0        1         0
  RBM15 WILD-TYPE        23         11         56         42       47        18
                 vv
clus              STAGE IVB
  RBM15 MUTATED           0
  RBM15 WILD-TYPE         1
D1503V4, multiclass
            clus
vv           RBM15 MUTATED RBM15 WILD-TYPE
  STAGE I                7              84
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              7             131
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             3              56
  STAGE IIIC             0              42
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  RBM15 MUTATED     2   5  12   1
  RBM15 WILD-TYPE  15  87 317  49
D1503V5, multiclass
    clus
vv   RBM15 MUTATED RBM15 WILD-TYPE
  T1             2              15
  T2             5              87
  T3            12             317
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  RBM15 MUTATED    16   3   1
  RBM15 WILD-TYPE 271 110  86
D1503V6, multiclass
    clus
vv   RBM15 MUTATED RBM15 WILD-TYPE
  N0            16             271
  N1             3             110
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1503V7, binary
                 cls
clus                0   1
  RBM15 MUTATED    19   1
  RBM15 WILD-TYPE 356  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM15 MUTATED     19    1
  RBM15 WILD-TYPE  356   64
   clus
vv  RBM15 MUTATED RBM15 WILD-TYPE
  0            19             356
  1             1              64
[1] 2 2
[1] FALSE
D1503V8, binary
                 cls
clus                0   1
  RBM15 MUTATED    12   8
  RBM15 WILD-TYPE 213 256
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM15 MUTATED     12    8
  RBM15 WILD-TYPE  213  256
        clus
vv       RBM15 MUTATED RBM15 WILD-TYPE
  FEMALE            12             213
  MALE               8             256
[1] 2 2
[1] FALSE
D1503V9, binary
                 cls
clus                0   1
  RBM15 MUTATED    17   1
  RBM15 WILD-TYPE 333  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM15 MUTATED     17    1
  RBM15 WILD-TYPE  333   21
     clus
vv    RBM15 MUTATED RBM15 WILD-TYPE
  NO             17             333
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  RBM15 MUTATED                      9                             7
  RBM15 WILD-TYPE                  306                            40
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  RBM15 MUTATED                       4                              0
  RBM15 WILD-TYPE                   102                             10
D1503V10, multiclass
                                clus
vv                               RBM15 MUTATED RBM15 WILD-TYPE
  COLON ADENOCARCINOMA                       9             306
  COLON MUCINOUS ADENOCARCINOMA              7              40
  RECTAL ADENOCARCINOMA                      4             102
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  RBM15 MUTATED    17   0   1   1
  RBM15 WILD-TYPE 328   4  30  24
D1503V11, multiclass
    clus
vv   RBM15 MUTATED RBM15 WILD-TYPE
  R0            17             328
  R1             0               4
  R2             1              30
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1503V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RBM15 MUTATED                                  0     1
  RBM15 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  RBM15 MUTATED                           1    10
  RBM15 WILD-TYPE                        21   216
D1503V13, multiclass
                                  clus
vv                                 RBM15 MUTATED RBM15 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                       10             216
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1504) Variable = C5ORF42 MUTATION ANALYSIS
D1504V1, survival
                   sevent
clus2                 0   1
  C5ORF42 MUTATED    31   9
  C5ORF42 WILD-TYPE 347  84
  C5ORF42 MUTATED C5ORF42 WILD-TYPE 
               40               431 
  C5ORF42 MUTATED C5ORF42 WILD-TYPE 
                9                84 
$`C5ORF42 MUTATED`
TCGA-A6-3809 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5665 TCGA-A6-6141 TCGA-A6-6653 
       32.75        29.19        33.53        22.06         8.38        24.39 
TCGA-AA-3511 TCGA-AA-3664 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3950 
        6.97        54.02        26.99        19.04        19.04        24.00 
TCGA-AA-3966 TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01P TCGA-AD-5900 TCGA-AD-6963 
        2.01         4.01        34.98        38.07         0.07        27.42 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-CA-6717 TCGA-CA-6718 
       58.39         1.41        12.10       100.01        12.76        10.06 
TCGA-CK-5913 TCGA-CM-6168 TCGA-D5-5537 TCGA-D5-6928 TCGA-F4-6569 TCGA-G4-6307 
       51.32        12.99        45.40        11.64        35.74        55.04 
TCGA-G4-6309 TCGA-AF-2693 TCGA-AF-3913 TCGA-AF-6655 TCGA-AG-3727 TCGA-AG-A002 
       85.48        19.10        10.39        20.02         0.99        20.98 
TCGA-AG-A025 TCGA-AH-6544 TCGA-CI-6620 TCGA-EI-6506 
       49.97        38.56        33.17        20.55 

$`C5ORF42 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 
       31.63        30.44        23.61        22.09        32.71        27.09 
TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 
       22.52        25.08        25.18        24.16        21.76        24.69 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01        63.98         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
        6.97         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
        5.03        85.05        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 
       26.01         2.01        20.98        34.03        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       31.00         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
       40.96        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4616 
       16.31         0.95        33.01        21.44        17.82         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 
        3.06         3.25         3.29         0.07        12.20        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 
       17.56       148.01        85.45        15.62        49.08         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       21.99        14.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       12.03        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 
        4.41        12.43        14.30         9.04         9.44         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
       98.24         8.61        31.96         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       44.68        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-4110 TCGA-AF-5654 
       39.48        43.04        13.55        34.49        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       15.39        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3731 
       15.95        19.99        13.94        19.99         7.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       70.03        64.01        10.98         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       41.00        38.04       117.11         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        0.72         6.05         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6507 
       57.24        24.13        51.48        32.61         0.49        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  C5ORF42 MUTATED C5ORF42 WILD-TYPE 
             0.07              0.00 
  C5ORF42 MUTATED C5ORF42 WILD-TYPE 
           100.01            148.01 
  C5ORF42 MUTATED C5ORF42 WILD-TYPE 
            23.03             20.02 
[1] "0.1 - 100.0 (23.0)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.1"
D1504V2, continuous
D1504V3, binary
                   cls
clus                  0   1
  C5ORF42 MUTATED    32   8
  C5ORF42 WILD-TYPE 334 111
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C5ORF42 MUTATED     32    8
  C5ORF42 WILD-TYPE  334  111
        clus
vv       C5ORF42 MUTATED C5ORF42 WILD-TYPE
  COLON               32               334
  RECTUM               8               111
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  C5ORF42 MUTATED         6        0        4        15         3         0
  C5ORF42 WILD-TYPE      85        1       28       123         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C5ORF42 MUTATED           2          1          2          1        4
  C5ORF42 WILD-TYPE        22         10         57         41       44
                   vv
clus                STAGE IVA STAGE IVB
  C5ORF42 MUTATED           1         0
  C5ORF42 WILD-TYPE        17         1
D1504V4, multiclass
            clus
vv           C5ORF42 MUTATED C5ORF42 WILD-TYPE
  STAGE I                  6                85
  STAGE IA                 0                 1
  STAGE II                 4                28
  STAGE IIA               15               123
  STAGE IIB                3                 7
  STAGE IIC                0                 1
  STAGE III                2                22
  STAGE IIIA               1                10
  STAGE IIIB               2                57
  STAGE IIIC               1                41
  STAGE IV                 4                44
  STAGE IVA                1                17
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  C5ORF42 MUTATED     1   6  28   6
  C5ORF42 WILD-TYPE  16  86 301  44
D1504V5, multiclass
    clus
vv   C5ORF42 MUTATED C5ORF42 WILD-TYPE
  T1               1                16
  T2               6                86
  T3              28               301
  T4               6                44
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  C5ORF42 MUTATED    29   9   3
  C5ORF42 WILD-TYPE 258 104  84
D1504V6, multiclass
    clus
vv   C5ORF42 MUTATED C5ORF42 WILD-TYPE
  N0              29               258
  N1               9               104
  N2               3                84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1504V7, binary
                   cls
clus                  0   1
  C5ORF42 MUTATED    30   6
  C5ORF42 WILD-TYPE 345  59
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C5ORF42 MUTATED     30    6
  C5ORF42 WILD-TYPE  345   59
   clus
vv  C5ORF42 MUTATED C5ORF42 WILD-TYPE
  0              30               345
  1               6                59
[1] 2 2
[1] FALSE
D1504V8, binary
                   cls
clus                  0   1
  C5ORF42 MUTATED    18  23
  C5ORF42 WILD-TYPE 207 241
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C5ORF42 MUTATED     18   23
  C5ORF42 WILD-TYPE  207  241
        clus
vv       C5ORF42 MUTATED C5ORF42 WILD-TYPE
  FEMALE              18               207
  MALE                23               241
[1] 2 2
[1] FALSE
D1504V9, binary
                   cls
clus                  0   1
  C5ORF42 MUTATED    33   1
  C5ORF42 WILD-TYPE 317  21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C5ORF42 MUTATED     33    1
  C5ORF42 WILD-TYPE  317   21
     clus
vv    C5ORF42 MUTATED C5ORF42 WILD-TYPE
  NO               33               317
  YES               1                21
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  C5ORF42 MUTATED                     25                             7
  C5ORF42 WILD-TYPE                  290                            40
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  C5ORF42 MUTATED                       8                              0
  C5ORF42 WILD-TYPE                    98                             10
D1504V10, multiclass
                                clus
vv                               C5ORF42 MUTATED C5ORF42 WILD-TYPE
  COLON ADENOCARCINOMA                        25               290
  COLON MUCINOUS ADENOCARCINOMA                7                40
  RECTAL ADENOCARCINOMA                        8                98
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  C5ORF42 MUTATED    25   0   1   4
  C5ORF42 WILD-TYPE 320   4  30  21
D1504V11, multiclass
    clus
vv   C5ORF42 MUTATED C5ORF42 WILD-TYPE
  R0              25               320
  R1               0                 4
  R2               1                30
  RX               4                21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1504V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C5ORF42 MUTATED                                  0     2
  C5ORF42 WILD-TYPE                                1     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  C5ORF42 MUTATED                           7    18
  C5ORF42 WILD-TYPE                        15   208
D1504V13, multiclass
                                  clus
vv                                 C5ORF42 MUTATED C5ORF42 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          2                 9
  BLACK OR AFRICAN AMERICAN                      7                15
  WHITE                                         18               208
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1505) Variable = BTBD3 MUTATION ANALYSIS
D1505V1, survival
                 sevent
clus2               0   1
  BTBD3 MUTATED    10   2
  BTBD3 WILD-TYPE 368  91
  BTBD3 MUTATED BTBD3 WILD-TYPE 
             12             459 
  BTBD3 MUTATED BTBD3 WILD-TYPE 
              2              91 
$`BTBD3 MUTATED`
TCGA-A6-5661 TCGA-A6-6137 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-A00N TCGA-AU-6004 
       33.53        27.09         6.05         6.97         4.01        27.09 
TCGA-AZ-4315 TCGA-AZ-6598 TCGA-CM-6162 TCGA-D5-6541 TCGA-G4-6315 TCGA-G4-6321 
       58.39        49.41        12.00        15.58        61.91        22.09 

$`BTBD3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       22.06        32.71        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 
       13.94        19.99        61.02        78.08        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
       16.31         0.95        33.01        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 
        5.13       106.75        22.36        62.79        88.21         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       15.02         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       17.13        12.49        16.14         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6317 
       53.62        44.68        55.04        85.48        63.62        36.00 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  BTBD3 MUTATED BTBD3 WILD-TYPE 
           4.01            0.00 
  BTBD3 MUTATED BTBD3 WILD-TYPE 
          61.91          148.01 
  BTBD3 MUTATED BTBD3 WILD-TYPE 
          24.59           20.12 
[1] "4.0 - 61.9 (24.6)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.3"
D1505V2, continuous
D1505V3, binary
                 cls
clus                0   1
  BTBD3 MUTATED    13   0
  BTBD3 WILD-TYPE 353 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BTBD3 MUTATED     13    0
  BTBD3 WILD-TYPE  353  119
        clus
vv       BTBD3 MUTATED BTBD3 WILD-TYPE
  COLON             13             353
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  BTBD3 MUTATED         1        0        3         3         1         0
  BTBD3 WILD-TYPE      90        1       29       135         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  BTBD3 MUTATED           1          0          2          0        2         0
  BTBD3 WILD-TYPE        23         11         57         42       46        18
                 vv
clus              STAGE IVB
  BTBD3 MUTATED           0
  BTBD3 WILD-TYPE         1
D1505V4, multiclass
            clus
vv           BTBD3 MUTATED BTBD3 WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               3              29
  STAGE IIA              3             135
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             2              57
  STAGE IIIC             0              42
  STAGE IV               2              46
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  BTBD3 MUTATED     0   2   8   3
  BTBD3 WILD-TYPE  17  90 321  47
D1505V5, multiclass
    clus
vv   BTBD3 MUTATED BTBD3 WILD-TYPE
  T1             0              17
  T2             2              90
  T3             8             321
  T4             3              47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  BTBD3 MUTATED     8   4   1
  BTBD3 WILD-TYPE 279 109  86
D1505V6, multiclass
    clus
vv   BTBD3 MUTATED BTBD3 WILD-TYPE
  N0             8             279
  N1             4             109
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1505V7, binary
                 cls
clus                0   1
  BTBD3 MUTATED     9   2
  BTBD3 WILD-TYPE 366  63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BTBD3 MUTATED      9    2
  BTBD3 WILD-TYPE  366   63
   clus
vv  BTBD3 MUTATED BTBD3 WILD-TYPE
  0             9             366
  1             2              63
[1] 2 2
[1] FALSE
D1505V8, binary
                 cls
clus                0   1
  BTBD3 MUTATED     7   6
  BTBD3 WILD-TYPE 218 258
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BTBD3 MUTATED      7    6
  BTBD3 WILD-TYPE  218  258
        clus
vv       BTBD3 MUTATED BTBD3 WILD-TYPE
  FEMALE             7             218
  MALE               6             258
[1] 2 2
[1] FALSE
D1505V9, binary
                 cls
clus                0   1
  BTBD3 MUTATED    10   0
  BTBD3 WILD-TYPE 340  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BTBD3 MUTATED     10    0
  BTBD3 WILD-TYPE  340   22
     clus
vv    BTBD3 MUTATED BTBD3 WILD-TYPE
  NO             10             340
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  BTBD3 MUTATED                     11                             2
  BTBD3 WILD-TYPE                  304                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  BTBD3 MUTATED                       0                              0
  BTBD3 WILD-TYPE                   106                             10
D1505V10, multiclass
                                clus
vv                               BTBD3 MUTATED BTBD3 WILD-TYPE
  COLON ADENOCARCINOMA                      11             304
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  BTBD3 MUTATED    10   0   1   0
  BTBD3 WILD-TYPE 335   4  30  25
D1505V11, multiclass
    clus
vv   BTBD3 MUTATED BTBD3 WILD-TYPE
  R0            10             335
  R1             0               4
  R2             1              30
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1505V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  BTBD3 MUTATED                                  0     0
  BTBD3 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  BTBD3 MUTATED                           1     8
  BTBD3 WILD-TYPE                        21   218
D1505V13, multiclass
                                  clus
vv                                 BTBD3 MUTATED BTBD3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        8             218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1506) Variable = NOVA1 MUTATION ANALYSIS
D1506V1, survival
                 sevent
clus2               0   1
  NOVA1 MUTATED    12   6
  NOVA1 WILD-TYPE 366  87
  NOVA1 MUTATED NOVA1 WILD-TYPE 
             18             453 
  NOVA1 MUTATED NOVA1 WILD-TYPE 
              6              87 
$`NOVA1 MUTATED`
TCGA-A6-2677 TCGA-A6-3810 TCGA-A6-6781 TCGA-AA-3710 TCGA-AA-3877 TCGA-AA-A010 
       24.33        36.53        19.66        26.99        31.00        34.98 
TCGA-AD-5900 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-CK-5916 TCGA-D5-6540 TCGA-G4-6303 
        0.07        49.41         6.77        21.14        16.14        65.85 
TCGA-G4-6310 TCGA-AF-2687 TCGA-AG-3742 TCGA-AG-A002 TCGA-DC-6682 TCGA-DY-A1H8 
       63.62        24.13         0.99        20.98         4.01        32.61 

$`NOVA1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        42.90        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5657 
       34.65        33.34        32.75        14.53        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       30.44        29.19        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       85.05        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       29.98        18.05         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 
        0.92        41.00        39.98        18.05        40.96        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6600 
        5.13       106.75        22.36        62.79        88.21        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 
       15.62        49.08        51.32         9.99        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       12.49        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6304 TCGA-G4-6306 
       47.41        35.31       133.18        74.56        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       55.04        85.48        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2689 
       35.80        26.17        91.79        46.75        79.69        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3878 TCGA-AG-3881 
        7.99         0.99        37.02        32.98         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       51.48         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  NOVA1 MUTATED NOVA1 WILD-TYPE 
           0.07            0.00 
  NOVA1 MUTATED NOVA1 WILD-TYPE 
          65.85          148.01 
  NOVA1 MUTATED NOVA1 WILD-TYPE 
          24.23           20.02 
[1] "0.1 - 65.8 (24.2)"  "0.0 - 148.0 (20.0)"
[1] "hr=" "1.7"
D1506V2, continuous
D1506V3, binary
                 cls
clus                0   1
  NOVA1 MUTATED    14   5
  NOVA1 WILD-TYPE 352 114
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NOVA1 MUTATED     14    5
  NOVA1 WILD-TYPE  352  114
        clus
vv       NOVA1 MUTATED NOVA1 WILD-TYPE
  COLON             14             352
  RECTUM             5             114
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NOVA1 MUTATED         7        0        1         3         2         0
  NOVA1 WILD-TYPE      84        1       31       135         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NOVA1 MUTATED           0          1          1          3        1         0
  NOVA1 WILD-TYPE        24         10         58         39       47        18
                 vv
clus              STAGE IVB
  NOVA1 MUTATED           0
  NOVA1 WILD-TYPE         1
D1506V4, multiclass
            clus
vv           NOVA1 MUTATED NOVA1 WILD-TYPE
  STAGE I                7              84
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              3             135
  STAGE IIB              2               8
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             1              10
  STAGE IIIB             1              58
  STAGE IIIC             3              39
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  NOVA1 MUTATED     3   5   8   3
  NOVA1 WILD-TYPE  14  87 321  47
D1506V5, multiclass
    clus
vv   NOVA1 MUTATED NOVA1 WILD-TYPE
  T1             3              14
  T2             5              87
  T3             8             321
  T4             3              47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  NOVA1 MUTATED    13   4   2
  NOVA1 WILD-TYPE 274 109  85
D1506V6, multiclass
    clus
vv   NOVA1 MUTATED NOVA1 WILD-TYPE
  N0            13             274
  N1             4             109
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1506V7, binary
                 cls
clus                0   1
  NOVA1 MUTATED    13   1
  NOVA1 WILD-TYPE 362  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NOVA1 MUTATED     13    1
  NOVA1 WILD-TYPE  362   64
   clus
vv  NOVA1 MUTATED NOVA1 WILD-TYPE
  0            13             362
  1             1              64
[1] 2 2
[1] FALSE
D1506V8, binary
                 cls
clus                0   1
  NOVA1 MUTATED    10   9
  NOVA1 WILD-TYPE 215 255
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NOVA1 MUTATED     10    9
  NOVA1 WILD-TYPE  215  255
        clus
vv       NOVA1 MUTATED NOVA1 WILD-TYPE
  FEMALE            10             215
  MALE               9             255
[1] 2 2
[1] FALSE
D1506V9, binary
                 cls
clus                0   1
  NOVA1 MUTATED    12   2
  NOVA1 WILD-TYPE 338  20
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NOVA1 MUTATED     12    2
  NOVA1 WILD-TYPE  338   20
     clus
vv    NOVA1 MUTATED NOVA1 WILD-TYPE
  NO             12             338
  YES             2              20
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  NOVA1 MUTATED                     10                             4
  NOVA1 WILD-TYPE                  305                            43
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  NOVA1 MUTATED                       5                              0
  NOVA1 WILD-TYPE                   101                             10
D1506V10, multiclass
                                clus
vv                               NOVA1 MUTATED NOVA1 WILD-TYPE
  COLON ADENOCARCINOMA                      10             305
  COLON MUCINOUS ADENOCARCINOMA              4              43
  RECTAL ADENOCARCINOMA                      5             101
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  NOVA1 MUTATED    14   0   0   2
  NOVA1 WILD-TYPE 331   4  31  23
D1506V11, multiclass
    clus
vv   NOVA1 MUTATED NOVA1 WILD-TYPE
  R0            14             331
  R1             0               4
  R2             0              31
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1506V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NOVA1 MUTATED                                  0     0
  NOVA1 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  NOVA1 MUTATED                           0    14
  NOVA1 WILD-TYPE                        22   212
D1506V13, multiclass
                                  clus
vv                                 NOVA1 MUTATED NOVA1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                       14             212
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1507) Variable = SBSN MUTATION ANALYSIS
D1507V1, survival
                sevent
clus2              0   1
  SBSN MUTATED     8   2
  SBSN WILD-TYPE 370  91
  SBSN MUTATED SBSN WILD-TYPE 
            10            461 
  SBSN MUTATED SBSN WILD-TYPE 
             2             91 
$`SBSN MUTATED`
TCGA-AA-3554 TCGA-AA-3655 TCGA-AA-3977 TCGA-AA-A00A TCGA-AA-A00E TCGA-AD-5900 
       17.95        61.02        25.02        38.04        30.02         0.07 
TCGA-AD-6895 TCGA-AZ-6600 TCGA-CM-6171 TCGA-DM-A28F 
        0.72        12.10        14.04        35.97 

$`SBSN WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       21.01        13.02        24.00        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       19.99        13.94        19.99        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00F 
       19.07         7.96        27.02        13.94        19.00        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       21.37        15.52        56.55         0.79         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 
       14.99        12.99        13.02        15.02        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H 
      139.17         6.12        81.37       119.93        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  SBSN MUTATED SBSN WILD-TYPE 
          0.07           0.00 
  SBSN MUTATED SBSN WILD-TYPE 
         61.02         148.01 
  SBSN MUTATED SBSN WILD-TYPE 
        21.485         20.190 
[1] "0.1 - 61.0 (21.5)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.1"
D1507V2, continuous
D1507V3, binary
                cls
clus               0   1
  SBSN MUTATED    10   0
  SBSN WILD-TYPE 356 119
[1] "tbl2"
                cls
clus             [,1] [,2]
  SBSN MUTATED     10    0
  SBSN WILD-TYPE  356  119
        clus
vv       SBSN MUTATED SBSN WILD-TYPE
  COLON            10            356
  RECTUM            0            119
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SBSN MUTATED         2        0        1         3         0         0
  SBSN WILD-TYPE      89        1       31       135        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SBSN MUTATED           0          0          1          0        1         0
  SBSN WILD-TYPE        24         11         58         42       47        18
                vv
clus             STAGE IVB
  SBSN MUTATED           0
  SBSN WILD-TYPE         1
D1507V4, multiclass
            clus
vv           SBSN MUTATED SBSN WILD-TYPE
  STAGE I               2             89
  STAGE IA              0              1
  STAGE II              1             31
  STAGE IIA             3            135
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            1             58
  STAGE IIIC            0             42
  STAGE IV              1             47
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  SBSN MUTATED     0   3   6   1
  SBSN WILD-TYPE  17  89 323  49
D1507V5, multiclass
    clus
vv   SBSN MUTATED SBSN WILD-TYPE
  T1            0             17
  T2            3             89
  T3            6            323
  T4            1             49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  SBSN MUTATED     7   3   0
  SBSN WILD-TYPE 280 110  87
D1507V6, multiclass
    clus
vv   SBSN MUTATED SBSN WILD-TYPE
  N0            7            280
  N1            3            110
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1507V7, binary
                cls
clus               0   1
  SBSN MUTATED     6   1
  SBSN WILD-TYPE 369  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  SBSN MUTATED      6    1
  SBSN WILD-TYPE  369   64
   clus
vv  SBSN MUTATED SBSN WILD-TYPE
  0            6            369
  1            1             64
[1] 2 2
[1] FALSE
D1507V8, binary
                cls
clus               0   1
  SBSN MUTATED     2   8
  SBSN WILD-TYPE 223 256
[1] "tbl2"
                cls
clus             [,1] [,2]
  SBSN MUTATED      2    8
  SBSN WILD-TYPE  223  256
        clus
vv       SBSN MUTATED SBSN WILD-TYPE
  FEMALE            2            223
  MALE              8            256
[1] 2 2
[1] FALSE
D1507V9, binary
                cls
clus               0   1
  SBSN MUTATED     6   0
  SBSN WILD-TYPE 344  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  SBSN MUTATED      6    0
  SBSN WILD-TYPE  344   22
     clus
vv    SBSN MUTATED SBSN WILD-TYPE
  NO             6            344
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SBSN MUTATED                      9                             1
  SBSN WILD-TYPE                  306                            46
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SBSN MUTATED                       0                              0
  SBSN WILD-TYPE                   106                             10
D1507V10, multiclass
                                clus
vv                               SBSN MUTATED SBSN WILD-TYPE
  COLON ADENOCARCINOMA                      9            306
  COLON MUCINOUS ADENOCARCINOMA             1             46
  RECTAL ADENOCARCINOMA                     0            106
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  SBSN MUTATED     6   0   0   0
  SBSN WILD-TYPE 339   4  31  25
D1507V11, multiclass
    clus
vv   SBSN MUTATED SBSN WILD-TYPE
  R0            6            339
  R1            0              4
  R2            0             31
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1507V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SBSN MUTATED                                  0     0
  SBSN WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  SBSN MUTATED                           1     4
  SBSN WILD-TYPE                        21   222
D1507V13, multiclass
                                  clus
vv                                 SBSN MUTATED SBSN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                       4            222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1508) Variable = OR8B12 MUTATION ANALYSIS
D1508V1, survival
                  sevent
clus2                0   1
  OR8B12 MUTATED     2   2
  OR8B12 WILD-TYPE 376  91
  OR8B12 MUTATED OR8B12 WILD-TYPE 
               4              467 
  OR8B12 MUTATED OR8B12 WILD-TYPE 
               2               91 
$`OR8B12 MUTATED`
TCGA-AA-3715 TCGA-AZ-4315 TCGA-CM-6169 TCGA-DY-A1DG 
       19.04        58.39        13.02        51.48 

$`OR8B12 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        33.01        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       14.99        12.99        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       57.24        24.13        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  OR8B12 MUTATED OR8B12 WILD-TYPE 
           13.02             0.00 
  OR8B12 MUTATED OR8B12 WILD-TYPE 
           58.39           148.01 
  OR8B12 MUTATED OR8B12 WILD-TYPE 
           35.26            20.19 
[1] "13.0 - 58.4 (35.3)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.7"
D1508V2, continuous
D1508V3, binary
                  cls
clus                 0   1
  OR8B12 MUTATED     3   1
  OR8B12 WILD-TYPE 363 118
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR8B12 MUTATED      3    1
  OR8B12 WILD-TYPE  363  118
        clus
vv       OR8B12 MUTATED OR8B12 WILD-TYPE
  COLON               3              363
  RECTUM              1              118
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  OR8B12 MUTATED         0        0        1         2         0         0
  OR8B12 WILD-TYPE      91        1       31       136        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  OR8B12 MUTATED           0          0          0          0        0
  OR8B12 WILD-TYPE        24         11         59         42       48
                  vv
clus               STAGE IVA STAGE IVB
  OR8B12 MUTATED           1         0
  OR8B12 WILD-TYPE        17         1
D1508V4, multiclass
            clus
vv           OR8B12 MUTATED OR8B12 WILD-TYPE
  STAGE I                 0               91
  STAGE IA                0                1
  STAGE II                1               31
  STAGE IIA               2              136
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              0               59
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               1               17
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  OR8B12 MUTATED     0   0   4   0
  OR8B12 WILD-TYPE  17  92 325  50
D1508V5, multiclass
    clus
vv   OR8B12 MUTATED OR8B12 WILD-TYPE
  T1              0               17
  T2              0               92
  T3              4              325
  T4              0               50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  OR8B12 MUTATED     3   1   0
  OR8B12 WILD-TYPE 284 112  87
D1508V6, multiclass
    clus
vv   OR8B12 MUTATED OR8B12 WILD-TYPE
  N0              3              284
  N1              1              112
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1508V7, binary
                  cls
clus                 0   1
  OR8B12 MUTATED     3   1
  OR8B12 WILD-TYPE 372  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR8B12 MUTATED      3    1
  OR8B12 WILD-TYPE  372   64
   clus
vv  OR8B12 MUTATED OR8B12 WILD-TYPE
  0              3              372
  1              1               64
[1] 2 2
[1] FALSE
D1508V8, binary
                  cls
clus                 0   1
  OR8B12 MUTATED     0   4
  OR8B12 WILD-TYPE 225 260
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR8B12 MUTATED      0    4
  OR8B12 WILD-TYPE  225  260
        clus
vv       OR8B12 MUTATED OR8B12 WILD-TYPE
  FEMALE              0              225
  MALE                4              260
[1] 2 2
[1] FALSE
D1508V9, binary
                  cls
clus                 0   1
  OR8B12 MUTATED     3   0
  OR8B12 WILD-TYPE 347  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR8B12 MUTATED      3    0
  OR8B12 WILD-TYPE  347   22
     clus
vv    OR8B12 MUTATED OR8B12 WILD-TYPE
  NO               3              347
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  OR8B12 MUTATED                      3                             0
  OR8B12 WILD-TYPE                  312                            47
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  OR8B12 MUTATED                       1                              0
  OR8B12 WILD-TYPE                   105                             10
D1508V10, multiclass
                                clus
vv                               OR8B12 MUTATED OR8B12 WILD-TYPE
  COLON ADENOCARCINOMA                        3              312
  COLON MUCINOUS ADENOCARCINOMA               0               47
  RECTAL ADENOCARCINOMA                       1              105
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  OR8B12 MUTATED     3   0   0   0
  OR8B12 WILD-TYPE 342   4  31  25
D1508V11, multiclass
    clus
vv   OR8B12 MUTATED OR8B12 WILD-TYPE
  R0              3              342
  R1              0                4
  R2              0               31
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1508V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OR8B12 MUTATED                                  0     0
  OR8B12 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  OR8B12 MUTATED                           1     2
  OR8B12 WILD-TYPE                        21   224
D1508V13, multiclass
                                  clus
vv                                 OR8B12 MUTATED OR8B12 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                         2              224
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1509) Variable = AGXT2L1 MUTATION ANALYSIS
D1509V1, survival
                   sevent
clus2                 0   1
  AGXT2L1 MUTATED    11   1
  AGXT2L1 WILD-TYPE 367  92
  AGXT2L1 MUTATED AGXT2L1 WILD-TYPE 
               12               459 
  AGXT2L1 MUTATED AGXT2L1 WILD-TYPE 
                1                92 
$`AGXT2L1 MUTATED`
TCGA-A6-2672 TCGA-AA-3510 TCGA-AA-3710 TCGA-AA-3949 TCGA-AA-A00W TCGA-AD-6895 
       46.65        63.98        26.99        26.01        14.99         0.72 
TCGA-AY-6197 TCGA-CA-6718 TCGA-CM-5349 TCGA-D5-6928 TCGA-F4-6569 TCGA-AG-A002 
       21.44        10.06        30.08        11.64        35.74        20.98 

$`AGXT2L1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        33.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 
        0.07        21.37        15.52        56.55         0.79         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       16.31         0.95        33.01        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07        12.20        12.76        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5860 
       25.02        13.02        29.06        22.03        22.98        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 
        4.41        12.43        14.30         9.04         9.44         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
       98.24         8.61        31.96         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  AGXT2L1 MUTATED AGXT2L1 WILD-TYPE 
             0.72              0.00 
  AGXT2L1 MUTATED AGXT2L1 WILD-TYPE 
            63.98            148.01 
  AGXT2L1 MUTATED AGXT2L1 WILD-TYPE 
           23.725            20.050 
[1] "0.7 - 64.0 (23.7)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "2.4"
D1509V2, continuous
D1509V3, binary
                   cls
clus                  0   1
  AGXT2L1 MUTATED    12   1
  AGXT2L1 WILD-TYPE 354 118
[1] "tbl2"
                   cls
clus                [,1] [,2]
  AGXT2L1 MUTATED     12    1
  AGXT2L1 WILD-TYPE  354  118
        clus
vv       AGXT2L1 MUTATED AGXT2L1 WILD-TYPE
  COLON               12               354
  RECTUM               1               118
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  AGXT2L1 MUTATED         3        0        1         6         0         0
  AGXT2L1 WILD-TYPE      88        1       31       132        10         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  AGXT2L1 MUTATED           0          0          2          0        0
  AGXT2L1 WILD-TYPE        24         11         57         42       48
                   vv
clus                STAGE IVA STAGE IVB
  AGXT2L1 MUTATED           0         0
  AGXT2L1 WILD-TYPE        18         1
D1509V4, multiclass
            clus
vv           AGXT2L1 MUTATED AGXT2L1 WILD-TYPE
  STAGE I                  3                88
  STAGE IA                 0                 1
  STAGE II                 1                31
  STAGE IIA                6               132
  STAGE IIB                0                10
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               0                11
  STAGE IIIB               2                57
  STAGE IIIC               0                42
  STAGE IV                 0                48
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  AGXT2L1 MUTATED     1   2  10   0
  AGXT2L1 WILD-TYPE  16  90 319  50
D1509V5, multiclass
    clus
vv   AGXT2L1 MUTATED AGXT2L1 WILD-TYPE
  T1               1                16
  T2               2                90
  T3              10               319
  T4               0                50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  AGXT2L1 MUTATED    10   3   0
  AGXT2L1 WILD-TYPE 277 110  87
D1509V6, multiclass
    clus
vv   AGXT2L1 MUTATED AGXT2L1 WILD-TYPE
  N0              10               277
  N1               3               110
  N2               0                87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1509V7, binary
                   cls
clus                  0   1
  AGXT2L1 MUTATED    11   0
  AGXT2L1 WILD-TYPE 364  65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  AGXT2L1 MUTATED     11    0
  AGXT2L1 WILD-TYPE  364   65
   clus
vv  AGXT2L1 MUTATED AGXT2L1 WILD-TYPE
  0              11               364
  1               0                65
[1] 2 2
[1] FALSE
D1509V8, binary
                   cls
clus                  0   1
  AGXT2L1 MUTATED     5   8
  AGXT2L1 WILD-TYPE 220 256
[1] "tbl2"
                   cls
clus                [,1] [,2]
  AGXT2L1 MUTATED      5    8
  AGXT2L1 WILD-TYPE  220  256
        clus
vv       AGXT2L1 MUTATED AGXT2L1 WILD-TYPE
  FEMALE               5               220
  MALE                 8               256
[1] 2 2
[1] FALSE
D1509V9, binary
                   cls
clus                  0   1
  AGXT2L1 MUTATED    11   0
  AGXT2L1 WILD-TYPE 339  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  AGXT2L1 MUTATED     11    0
  AGXT2L1 WILD-TYPE  339   22
     clus
vv    AGXT2L1 MUTATED AGXT2L1 WILD-TYPE
  NO               11               339
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  AGXT2L1 MUTATED                     10                             2
  AGXT2L1 WILD-TYPE                  305                            45
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  AGXT2L1 MUTATED                       1                              0
  AGXT2L1 WILD-TYPE                   105                             10
D1509V10, multiclass
                                clus
vv                               AGXT2L1 MUTATED AGXT2L1 WILD-TYPE
  COLON ADENOCARCINOMA                        10               305
  COLON MUCINOUS ADENOCARCINOMA                2                45
  RECTAL ADENOCARCINOMA                        1               105
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  AGXT2L1 MUTATED    11   0   0   1
  AGXT2L1 WILD-TYPE 334   4  31  24
D1509V11, multiclass
    clus
vv   AGXT2L1 MUTATED AGXT2L1 WILD-TYPE
  R0              11               334
  R1               0                 4
  R2               0                31
  RX               1                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1509V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AGXT2L1 MUTATED                                  0     1
  AGXT2L1 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  AGXT2L1 MUTATED                           0     6
  AGXT2L1 WILD-TYPE                        22   220
D1509V13, multiclass
                                  clus
vv                                 AGXT2L1 MUTATED AGXT2L1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                10
  BLACK OR AFRICAN AMERICAN                      0                22
  WHITE                                          6               220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1510) Variable = JAK1 MUTATION ANALYSIS
D1510V1, survival
                sevent
clus2              0   1
  JAK1 MUTATED    17   2
  JAK1 WILD-TYPE 361  91
  JAK1 MUTATED JAK1 WILD-TYPE 
            19            452 
  JAK1 MUTATED JAK1 WILD-TYPE 
             2             91 
$`JAK1 MUTATED`
TCGA-A6-5657 TCGA-A6-5665 TCGA-A6-6781 TCGA-AA-3710 TCGA-AA-3977 TCGA-AA-A01P 
       31.63        22.06        19.66        26.99        25.02        38.07 
TCGA-AD-6895 TCGA-AD-6964 TCGA-AY-6197 TCGA-CA-6717 TCGA-CK-4948 TCGA-CK-4952 
        0.72        10.88        21.44        12.76       148.01        15.62 
TCGA-CM-4743 TCGA-CM-6171 TCGA-D5-6928 TCGA-G4-6586 TCGA-G4-6628 TCGA-AG-A002 
       23.05        14.04        11.64        35.80        79.69        20.98 
TCGA-EI-6507 
       19.96 

$`JAK1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       85.05        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01Q 
       10.98        32.02        12.00        31.00        31.00         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       21.37        15.52        56.55         0.79         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       33.01        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 
       10.06        14.30        17.56        85.45        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 
        9.99        21.14        82.95         1.91       124.27        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 
       21.99        14.99        12.99        13.02        15.02        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 
       61.91        36.00        22.09        13.78        26.17        91.79 
TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       46.75        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
       32.61         0.49        20.55        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  JAK1 MUTATED JAK1 WILD-TYPE 
          0.72           0.00 
  JAK1 MUTATED JAK1 WILD-TYPE 
        148.01         140.38 
  JAK1 MUTATED JAK1 WILD-TYPE 
        21.440         20.085 
[1] "0.7 - 148.0 (21.4)" "0.0 - 140.4 (20.1)"
[1] "hr=" "2"  
D1510V2, continuous
D1510V3, binary
                cls
clus               0   1
  JAK1 MUTATED    18   2
  JAK1 WILD-TYPE 348 117
[1] "tbl2"
                cls
clus             [,1] [,2]
  JAK1 MUTATED     18    2
  JAK1 WILD-TYPE  348  117
        clus
vv       JAK1 MUTATED JAK1 WILD-TYPE
  COLON            18            348
  RECTUM            2            117
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  JAK1 MUTATED         3        0        0         8         0         0
  JAK1 WILD-TYPE      88        1       32       130        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  JAK1 MUTATED           2          0          1          3        0         0
  JAK1 WILD-TYPE        22         11         58         39       48        18
                vv
clus             STAGE IVB
  JAK1 MUTATED           0
  JAK1 WILD-TYPE         1
D1510V4, multiclass
            clus
vv           JAK1 MUTATED JAK1 WILD-TYPE
  STAGE I               3             88
  STAGE IA              0              1
  STAGE II              0             32
  STAGE IIA             8            130
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             2             22
  STAGE IIIA            0             11
  STAGE IIIB            1             58
  STAGE IIIC            3             39
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  JAK1 MUTATED     0   4  13   3
  JAK1 WILD-TYPE  17  88 316  47
D1510V5, multiclass
    clus
vv   JAK1 MUTATED JAK1 WILD-TYPE
  T1            0             17
  T2            4             88
  T3           13            316
  T4            3             47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  JAK1 MUTATED    12   5   3
  JAK1 WILD-TYPE 275 108  84
D1510V6, multiclass
    clus
vv   JAK1 MUTATED JAK1 WILD-TYPE
  N0           12            275
  N1            5            108
  N2            3             84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1510V7, binary
                cls
clus               0   1
  JAK1 MUTATED    14   0
  JAK1 WILD-TYPE 361  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  JAK1 MUTATED     14    0
  JAK1 WILD-TYPE  361   65
   clus
vv  JAK1 MUTATED JAK1 WILD-TYPE
  0           14            361
  1            0             65
[1] 2 2
[1] FALSE
D1510V8, binary
                cls
clus               0   1
  JAK1 MUTATED     7  13
  JAK1 WILD-TYPE 218 251
[1] "tbl2"
                cls
clus             [,1] [,2]
  JAK1 MUTATED      7   13
  JAK1 WILD-TYPE  218  251
        clus
vv       JAK1 MUTATED JAK1 WILD-TYPE
  FEMALE            7            218
  MALE             13            251
[1] 2 2
[1] FALSE
D1510V9, binary
                cls
clus               0   1
  JAK1 MUTATED    17   0
  JAK1 WILD-TYPE 333  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  JAK1 MUTATED     17    0
  JAK1 WILD-TYPE  333   22
     clus
vv    JAK1 MUTATED JAK1 WILD-TYPE
  NO            17            333
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  JAK1 MUTATED                     13                             5
  JAK1 WILD-TYPE                  302                            42
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  JAK1 MUTATED                       2                              0
  JAK1 WILD-TYPE                   104                             10
D1510V10, multiclass
                                clus
vv                               JAK1 MUTATED JAK1 WILD-TYPE
  COLON ADENOCARCINOMA                     13            302
  COLON MUCINOUS ADENOCARCINOMA             5             42
  RECTAL ADENOCARCINOMA                     2            104
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  JAK1 MUTATED    15   0   0   2
  JAK1 WILD-TYPE 330   4  31  23
D1510V11, multiclass
    clus
vv   JAK1 MUTATED JAK1 WILD-TYPE
  R0           15            330
  R1            0              4
  R2            0             31
  RX            2             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1510V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  JAK1 MUTATED                                  0     1
  JAK1 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  JAK1 MUTATED                           1    14
  JAK1 WILD-TYPE                        21   212
D1510V13, multiclass
                                  clus
vv                                 JAK1 MUTATED JAK1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                      14            212
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1511) Variable = CCDC110 MUTATION ANALYSIS
D1511V1, survival
                   sevent
clus2                 0   1
  CCDC110 MUTATED     8   4
  CCDC110 WILD-TYPE 370  89
  CCDC110 MUTATED CCDC110 WILD-TYPE 
               12               459 
  CCDC110 MUTATED CCDC110 WILD-TYPE 
                4                89 
$`CCDC110 MUTATED`
TCGA-A6-5665 TCGA-AA-3510 TCGA-AA-3680 TCGA-AA-3977 TCGA-AA-A010 TCGA-AZ-6598 
       22.06        63.98        11.01        25.02        34.98        49.41 
TCGA-AZ-6601 TCGA-CA-6717 TCGA-CM-5861 TCGA-D5-6926 TCGA-F4-6570 TCGA-AG-A002 
      100.01        12.76        15.02         9.04         6.18        20.98 

$`CCDC110 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       15.02         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       88.21         6.77        12.10        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07        12.20        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       32.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
        4.41        12.43        14.30         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 
       98.24         8.61        31.96        35.74        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  CCDC110 MUTATED CCDC110 WILD-TYPE 
             6.18              0.00 
  CCDC110 MUTATED CCDC110 WILD-TYPE 
           100.01            148.01 
  CCDC110 MUTATED CCDC110 WILD-TYPE 
            21.52             20.12 
[1] "6.2 - 100.0 (21.5)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.4"
D1511V2, continuous
D1511V3, binary
                   cls
clus                  0   1
  CCDC110 MUTATED    13   1
  CCDC110 WILD-TYPE 353 118
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC110 MUTATED     13    1
  CCDC110 WILD-TYPE  353  118
        clus
vv       CCDC110 MUTATED CCDC110 WILD-TYPE
  COLON               13               353
  RECTUM               1               118
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CCDC110 MUTATED         1        0        3         5         2         0
  CCDC110 WILD-TYPE      90        1       29       133         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CCDC110 MUTATED           0          0          1          0        1
  CCDC110 WILD-TYPE        24         11         58         42       47
                   vv
clus                STAGE IVA STAGE IVB
  CCDC110 MUTATED           0         0
  CCDC110 WILD-TYPE        18         1
D1511V4, multiclass
            clus
vv           CCDC110 MUTATED CCDC110 WILD-TYPE
  STAGE I                  1                90
  STAGE IA                 0                 1
  STAGE II                 3                29
  STAGE IIA                5               133
  STAGE IIB                2                 8
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               0                11
  STAGE IIIB               1                58
  STAGE IIIC               0                42
  STAGE IV                 1                47
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  CCDC110 MUTATED     0   2   8   4
  CCDC110 WILD-TYPE  17  90 321  46
D1511V5, multiclass
    clus
vv   CCDC110 MUTATED CCDC110 WILD-TYPE
  T1               0                17
  T2               2                90
  T3               8               321
  T4               4                46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  CCDC110 MUTATED    12   1   1
  CCDC110 WILD-TYPE 275 112  86
D1511V6, multiclass
    clus
vv   CCDC110 MUTATED CCDC110 WILD-TYPE
  N0              12               275
  N1               1               112
  N2               1                86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1511V7, binary
                   cls
clus                  0   1
  CCDC110 MUTATED    10   1
  CCDC110 WILD-TYPE 365  64
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC110 MUTATED     10    1
  CCDC110 WILD-TYPE  365   64
   clus
vv  CCDC110 MUTATED CCDC110 WILD-TYPE
  0              10               365
  1               1                64
[1] 2 2
[1] FALSE
D1511V8, binary
                   cls
clus                  0   1
  CCDC110 MUTATED     8   6
  CCDC110 WILD-TYPE 217 258
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC110 MUTATED      8    6
  CCDC110 WILD-TYPE  217  258
        clus
vv       CCDC110 MUTATED CCDC110 WILD-TYPE
  FEMALE               8               217
  MALE                 6               258
[1] 2 2
[1] FALSE
D1511V9, binary
                   cls
clus                  0   1
  CCDC110 MUTATED    11   1
  CCDC110 WILD-TYPE 339  21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC110 MUTATED     11    1
  CCDC110 WILD-TYPE  339   21
     clus
vv    CCDC110 MUTATED CCDC110 WILD-TYPE
  NO               11               339
  YES               1                21
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CCDC110 MUTATED                     12                             1
  CCDC110 WILD-TYPE                  303                            46
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CCDC110 MUTATED                       1                              0
  CCDC110 WILD-TYPE                   105                             10
D1511V10, multiclass
                                clus
vv                               CCDC110 MUTATED CCDC110 WILD-TYPE
  COLON ADENOCARCINOMA                        12               303
  COLON MUCINOUS ADENOCARCINOMA                1                46
  RECTAL ADENOCARCINOMA                        1               105
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  CCDC110 MUTATED     8   0   1   2
  CCDC110 WILD-TYPE 337   4  30  23
D1511V11, multiclass
    clus
vv   CCDC110 MUTATED CCDC110 WILD-TYPE
  R0               8               337
  R1               0                 4
  R2               1                30
  RX               2                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1511V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CCDC110 MUTATED                                  0     1
  CCDC110 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  CCDC110 MUTATED                           0     7
  CCDC110 WILD-TYPE                        22   219
D1511V13, multiclass
                                  clus
vv                                 CCDC110 MUTATED CCDC110 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                10
  BLACK OR AFRICAN AMERICAN                      0                22
  WHITE                                          7               219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1512) Variable = LMOD1 MUTATION ANALYSIS
D1512V1, survival
                 sevent
clus2               0   1
  LMOD1 MUTATED    12   1
  LMOD1 WILD-TYPE 366  92
  LMOD1 MUTATED LMOD1 WILD-TYPE 
             13             458 
  LMOD1 MUTATED LMOD1 WILD-TYPE 
              1              92 
$`LMOD1 MUTATED`
TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3672 TCGA-AA-3947 TCGA-AZ-4315 TCGA-CA-6717 
        3.02        63.98         0.92        33.01        58.39        12.76 
TCGA-CM-5861 TCGA-CM-6166 TCGA-CM-6170 TCGA-D5-5538 TCGA-D5-6540 TCGA-D5-6926 
       15.02        21.99        15.02        12.26        16.14         9.04 
TCGA-AG-A002 
       20.98 

$`LMOD1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
       54.02         2.01        14.01        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07        12.20        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       22.98        30.08        32.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       14.99        12.99        13.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       45.40        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       12.49        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
       14.30         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  LMOD1 MUTATED LMOD1 WILD-TYPE 
           0.92            0.00 
  LMOD1 MUTATED LMOD1 WILD-TYPE 
          63.98          148.01 
  LMOD1 MUTATED LMOD1 WILD-TYPE 
         15.020          20.415 
[1] "0.9 - 64.0 (15.0)"  "0.0 - 148.0 (20.4)"
[1] "hr=" "2.3"
D1512V2, continuous
D1512V3, binary
                 cls
clus                0   1
  LMOD1 MUTATED    12   1
  LMOD1 WILD-TYPE 354 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LMOD1 MUTATED     12    1
  LMOD1 WILD-TYPE  354  118
        clus
vv       LMOD1 MUTATED LMOD1 WILD-TYPE
  COLON             12             354
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  LMOD1 MUTATED         4        0        2         3         1         0
  LMOD1 WILD-TYPE      87        1       30       135         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  LMOD1 MUTATED           1          0          2          0        0         0
  LMOD1 WILD-TYPE        23         11         57         42       48        18
                 vv
clus              STAGE IVB
  LMOD1 MUTATED           0
  LMOD1 WILD-TYPE         1
D1512V4, multiclass
            clus
vv           LMOD1 MUTATED LMOD1 WILD-TYPE
  STAGE I                4              87
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA              3             135
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             2              57
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  LMOD1 MUTATED     0   4   7   2
  LMOD1 WILD-TYPE  17  88 322  48
D1512V5, multiclass
    clus
vv   LMOD1 MUTATED LMOD1 WILD-TYPE
  T1             0              17
  T2             4              88
  T3             7             322
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  LMOD1 MUTATED    10   3   0
  LMOD1 WILD-TYPE 277 110  87
D1512V6, multiclass
    clus
vv   LMOD1 MUTATED LMOD1 WILD-TYPE
  N0            10             277
  N1             3             110
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1512V7, binary
                 cls
clus                0   1
  LMOD1 MUTATED    13   0
  LMOD1 WILD-TYPE 362  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LMOD1 MUTATED     13    0
  LMOD1 WILD-TYPE  362   65
   clus
vv  LMOD1 MUTATED LMOD1 WILD-TYPE
  0            13             362
  1             0              65
[1] 2 2
[1] FALSE
D1512V8, binary
                 cls
clus                0   1
  LMOD1 MUTATED     7   6
  LMOD1 WILD-TYPE 218 258
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LMOD1 MUTATED      7    6
  LMOD1 WILD-TYPE  218  258
        clus
vv       LMOD1 MUTATED LMOD1 WILD-TYPE
  FEMALE             7             218
  MALE               6             258
[1] 2 2
[1] FALSE
D1512V9, binary
                 cls
clus                0   1
  LMOD1 MUTATED    12   1
  LMOD1 WILD-TYPE 338  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LMOD1 MUTATED     12    1
  LMOD1 WILD-TYPE  338   21
     clus
vv    LMOD1 MUTATED LMOD1 WILD-TYPE
  NO             12             338
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  LMOD1 MUTATED                      9                             3
  LMOD1 WILD-TYPE                  306                            44
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  LMOD1 MUTATED                       1                              0
  LMOD1 WILD-TYPE                   105                             10
D1512V10, multiclass
                                clus
vv                               LMOD1 MUTATED LMOD1 WILD-TYPE
  COLON ADENOCARCINOMA                       9             306
  COLON MUCINOUS ADENOCARCINOMA              3              44
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  LMOD1 MUTATED    12   0   0   1
  LMOD1 WILD-TYPE 333   4  31  24
D1512V11, multiclass
    clus
vv   LMOD1 MUTATED LMOD1 WILD-TYPE
  R0            12             333
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1512V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  LMOD1 MUTATED                                  0     1
  LMOD1 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  LMOD1 MUTATED                           0     7
  LMOD1 WILD-TYPE                        22   219
D1512V13, multiclass
                                  clus
vv                                 LMOD1 MUTATED LMOD1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        7             219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1513) Variable = C2CD3 MUTATION ANALYSIS
D1513V1, survival
                 sevent
clus2               0   1
  C2CD3 MUTATED    15   1
  C2CD3 WILD-TYPE 363  92
  C2CD3 MUTATED C2CD3 WILD-TYPE 
             16             455 
  C2CD3 MUTATED C2CD3 WILD-TYPE 
              1              92 
$`C2CD3 MUTATED`
TCGA-A6-2676 TCGA-A6-5661 TCGA-AA-3660 TCGA-AA-3864 TCGA-AA-A010 TCGA-AA-A01V 
       42.90        33.53        78.08        53.00        34.98        35.01 
TCGA-CK-5913 TCGA-CM-5863 TCGA-CM-6171 TCGA-D5-5538 TCGA-G4-6323 TCGA-G4-6588 
       51.32        15.02        14.04        12.26        13.78        26.17 
TCGA-AG-3999 TCGA-AG-A002 TCGA-CI-6624 TCGA-DC-6683 
       28.04        20.98         4.73         5.03 

$`C2CD3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       31.63        30.44        29.19        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       13.94        19.99        61.02         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        31.07        30.05        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A01Z 
        1.02        35.01         1.02        33.04        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 
       17.56       148.01        85.45        15.62        49.08         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-5868 
       30.08        32.02        15.02         5.03        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 
       14.99        12.99        13.02        15.02        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       45.40        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       36.00        22.09        35.80        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       48.03        32.02        19.99        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CL-5917 TCGA-CL-5918 
        0.72         6.05        33.17         6.97        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        5.95         4.01         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  C2CD3 MUTATED C2CD3 WILD-TYPE 
           4.73            0.00 
  C2CD3 MUTATED C2CD3 WILD-TYPE 
          78.08          148.01 
  C2CD3 MUTATED C2CD3 WILD-TYPE 
         27.105          20.050 
[1] "4.7 - 78.1 (27.1)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "3.6"
D1513V2, continuous
D1513V3, binary
                 cls
clus                0   1
  C2CD3 MUTATED    13   4
  C2CD3 WILD-TYPE 353 115
[1] "tbl2"
                 cls
clus              [,1] [,2]
  C2CD3 MUTATED     13    4
  C2CD3 WILD-TYPE  353  115
        clus
vv       C2CD3 MUTATED C2CD3 WILD-TYPE
  COLON             13             353
  RECTUM             4             115
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  C2CD3 MUTATED         4        1        2         4         2         0
  C2CD3 WILD-TYPE      87        0       30       134         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  C2CD3 MUTATED           0          0          3          1        0         0
  C2CD3 WILD-TYPE        24         11         56         41       48        18
                 vv
clus              STAGE IVB
  C2CD3 MUTATED           0
  C2CD3 WILD-TYPE         1
D1513V4, multiclass
            clus
vv           C2CD3 MUTATED C2CD3 WILD-TYPE
  STAGE I                4              87
  STAGE IA               1               0
  STAGE II               2              30
  STAGE IIA              4             134
  STAGE IIB              2               8
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             3              56
  STAGE IIIC             1              41
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  C2CD3 MUTATED     0   4  10   2
  C2CD3 WILD-TYPE  17  88 319  48
D1513V5, multiclass
    clus
vv   C2CD3 MUTATED C2CD3 WILD-TYPE
  T1             0              17
  T2             4              88
  T3            10             319
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  C2CD3 MUTATED    13   3   1
  C2CD3 WILD-TYPE 274 110  86
D1513V6, multiclass
    clus
vv   C2CD3 MUTATED C2CD3 WILD-TYPE
  N0            13             274
  N1             3             110
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1513V7, binary
                 cls
clus                0   1
  C2CD3 MUTATED    15   0
  C2CD3 WILD-TYPE 360  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  C2CD3 MUTATED     15    0
  C2CD3 WILD-TYPE  360   65
   clus
vv  C2CD3 MUTATED C2CD3 WILD-TYPE
  0            15             360
  1             0              65
[1] 2 2
[1] FALSE
D1513V8, binary
                 cls
clus                0   1
  C2CD3 MUTATED    12   5
  C2CD3 WILD-TYPE 213 259
[1] "tbl2"
                 cls
clus              [,1] [,2]
  C2CD3 MUTATED     12    5
  C2CD3 WILD-TYPE  213  259
        clus
vv       C2CD3 MUTATED C2CD3 WILD-TYPE
  FEMALE            12             213
  MALE               5             259
[1] 2 2
[1] FALSE
D1513V9, binary
                 cls
clus                0   1
  C2CD3 MUTATED    13   0
  C2CD3 WILD-TYPE 337  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  C2CD3 MUTATED     13    0
  C2CD3 WILD-TYPE  337   22
     clus
vv    C2CD3 MUTATED C2CD3 WILD-TYPE
  NO             13             337
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  C2CD3 MUTATED                     12                             1
  C2CD3 WILD-TYPE                  303                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  C2CD3 MUTATED                       4                              0
  C2CD3 WILD-TYPE                   102                             10
D1513V10, multiclass
                                clus
vv                               C2CD3 MUTATED C2CD3 WILD-TYPE
  COLON ADENOCARCINOMA                      12             303
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      4             102
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  C2CD3 MUTATED    15   0   0   1
  C2CD3 WILD-TYPE 330   4  31  24
D1513V11, multiclass
    clus
vv   C2CD3 MUTATED C2CD3 WILD-TYPE
  R0            15             330
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1513V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C2CD3 MUTATED                                  0     0
  C2CD3 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  C2CD3 MUTATED                           2     8
  C2CD3 WILD-TYPE                        20   218
D1513V13, multiclass
                                  clus
vv                                 C2CD3 MUTATED C2CD3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    2              20
  WHITE                                        8             218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1514) Variable = AFF1 MUTATION ANALYSIS
D1514V1, survival
                sevent
clus2              0   1
  AFF1 MUTATED     9   5
  AFF1 WILD-TYPE 369  88
  AFF1 MUTATED AFF1 WILD-TYPE 
            14            457 
  AFF1 MUTATED AFF1 WILD-TYPE 
             5             88 
$`AFF1 MUTATED`
TCGA-A6-6652 TCGA-AA-3869 TCGA-AA-3977 TCGA-AA-A00N TCGA-AY-6197 TCGA-AZ-6601 
       24.69        27.02        25.02         4.01        21.44       100.01 
TCGA-CA-6717 TCGA-CK-5916 TCGA-CM-6170 TCGA-CM-6677 TCGA-D5-5537 TCGA-G4-6588 
       12.76        21.14        15.02        11.08        45.40        26.17 
TCGA-AG-3892 TCGA-AG-A02N 
       13.02        61.97 

$`AFF1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6654 
       25.08        25.18        24.16        21.76        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       17.03        24.03        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 
       14.50        27.09        16.31         0.95        33.01        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 
       88.21        49.41         6.77        12.10        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07        12.20        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       14.99        12.99        13.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5538 
       13.05        11.08        11.01        10.06        12.03        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       22.09        13.78        35.80        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       36.95        17.03        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X 
       64.01        10.98        49.97         1.94        38.96        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  AFF1 MUTATED AFF1 WILD-TYPE 
          4.01           0.00 
  AFF1 MUTATED AFF1 WILD-TYPE 
        100.01         148.01 
  AFF1 MUTATED AFF1 WILD-TYPE 
        23.065         20.050 
[1] "4.0 - 100.0 (23.1)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.6"
D1514V2, continuous
D1514V3, binary
                cls
clus               0   1
  AFF1 MUTATED    12   2
  AFF1 WILD-TYPE 354 117
[1] "tbl2"
                cls
clus             [,1] [,2]
  AFF1 MUTATED     12    2
  AFF1 WILD-TYPE  354  117
        clus
vv       AFF1 MUTATED AFF1 WILD-TYPE
  COLON            12            354
  RECTUM            2            117
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  AFF1 MUTATED         3        0        2         5         1         0
  AFF1 WILD-TYPE      88        1       30       133         9         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AFF1 MUTATED           0          0          0          0        1         1
  AFF1 WILD-TYPE        24         11         59         42       47        17
                vv
clus             STAGE IVB
  AFF1 MUTATED           0
  AFF1 WILD-TYPE         1
D1514V4, multiclass
            clus
vv           AFF1 MUTATED AFF1 WILD-TYPE
  STAGE I               3             88
  STAGE IA              0              1
  STAGE II              2             30
  STAGE IIA             5            133
  STAGE IIB             1              9
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            0             59
  STAGE IIIC            0             42
  STAGE IV              1             47
  STAGE IVA             1             17
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  AFF1 MUTATED     2   2   8   2
  AFF1 WILD-TYPE  15  90 321  48
D1514V5, multiclass
    clus
vv   AFF1 MUTATED AFF1 WILD-TYPE
  T1            2             15
  T2            2             90
  T3            8            321
  T4            2             48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  AFF1 MUTATED    12   0   2
  AFF1 WILD-TYPE 275 113  85
D1514V6, multiclass
    clus
vv   AFF1 MUTATED AFF1 WILD-TYPE
  N0           12            275
  N1            0            113
  N2            2             85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1514V7, binary
                cls
clus               0   1
  AFF1 MUTATED     9   2
  AFF1 WILD-TYPE 366  63
[1] "tbl2"
                cls
clus             [,1] [,2]
  AFF1 MUTATED      9    2
  AFF1 WILD-TYPE  366   63
   clus
vv  AFF1 MUTATED AFF1 WILD-TYPE
  0            9            366
  1            2             63
[1] 2 2
[1] FALSE
D1514V8, binary
                cls
clus               0   1
  AFF1 MUTATED     5   9
  AFF1 WILD-TYPE 220 255
[1] "tbl2"
                cls
clus             [,1] [,2]
  AFF1 MUTATED      5    9
  AFF1 WILD-TYPE  220  255
        clus
vv       AFF1 MUTATED AFF1 WILD-TYPE
  FEMALE            5            220
  MALE              9            255
[1] 2 2
[1] FALSE
D1514V9, binary
                cls
clus               0   1
  AFF1 MUTATED    12   0
  AFF1 WILD-TYPE 338  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  AFF1 MUTATED     12    0
  AFF1 WILD-TYPE  338   22
     clus
vv    AFF1 MUTATED AFF1 WILD-TYPE
  NO            12            338
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  AFF1 MUTATED                     10                             2
  AFF1 WILD-TYPE                  305                            45
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  AFF1 MUTATED                       2                              0
  AFF1 WILD-TYPE                   104                             10
D1514V10, multiclass
                                clus
vv                               AFF1 MUTATED AFF1 WILD-TYPE
  COLON ADENOCARCINOMA                     10            305
  COLON MUCINOUS ADENOCARCINOMA             2             45
  RECTAL ADENOCARCINOMA                     2            104
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  AFF1 MUTATED     7   0   1   3
  AFF1 WILD-TYPE 338   4  30  22
D1514V11, multiclass
    clus
vv   AFF1 MUTATED AFF1 WILD-TYPE
  R0            7            338
  R1            0              4
  R2            1             30
  RX            3             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1514V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AFF1 MUTATED                                  0     1
  AFF1 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  AFF1 MUTATED                           1     7
  AFF1 WILD-TYPE                        21   219
D1514V13, multiclass
                                  clus
vv                                 AFF1 MUTATED AFF1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                       7            219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1515) Variable = MANBA MUTATION ANALYSIS
D1515V1, survival
                 sevent
clus2               0   1
  MANBA MUTATED    11   2
  MANBA WILD-TYPE 367  91
  MANBA MUTATED MANBA WILD-TYPE 
             13             458 
  MANBA MUTATED MANBA WILD-TYPE 
              2              91 
$`MANBA MUTATED`
TCGA-AA-3525 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3672 TCGA-AA-A00N TCGA-AA-A01Q 
        8.05        17.95        29.95         0.92         4.01         1.02 
TCGA-AD-6964 TCGA-AZ-4315 TCGA-CK-4947 TCGA-CK-5914 TCGA-CM-6168 TCGA-D5-6533 
       10.88        58.39        17.56         9.99        12.99         1.32 
TCGA-AG-A002 
       20.98 

$`MANBA WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       13.02        24.00        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
        2.01        14.01        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        33.01        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-4950 
       12.20        12.76        10.06        14.30       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        49.08        51.32        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6169 
        2.96        29.03        16.04        21.99        14.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6534 
       19.59        56.09        55.92        20.19        18.25        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  MANBA MUTATED MANBA WILD-TYPE 
           0.92            0.00 
  MANBA MUTATED MANBA WILD-TYPE 
          58.39          148.01 
  MANBA MUTATED MANBA WILD-TYPE 
         10.880          20.945 
[1] "0.9 - 58.4 (10.9)"  "0.0 - 148.0 (20.9)"
[1] "hr=" "1.3"
D1515V2, continuous
D1515V3, binary
                 cls
clus                0   1
  MANBA MUTATED    12   1
  MANBA WILD-TYPE 354 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MANBA MUTATED     12    1
  MANBA WILD-TYPE  354  118
        clus
vv       MANBA MUTATED MANBA WILD-TYPE
  COLON             12             354
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MANBA MUTATED         1        0        1         4         1         0
  MANBA WILD-TYPE      90        1       31       134         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MANBA MUTATED           1          0          4          0        0         0
  MANBA WILD-TYPE        23         11         55         42       48        18
                 vv
clus              STAGE IVB
  MANBA MUTATED           0
  MANBA WILD-TYPE         1
D1515V4, multiclass
            clus
vv           MANBA MUTATED MANBA WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              4             134
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             4              55
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  MANBA MUTATED     0   1   8   4
  MANBA WILD-TYPE  17  91 321  46
D1515V5, multiclass
    clus
vv   MANBA MUTATED MANBA WILD-TYPE
  T1             0              17
  T2             1              91
  T3             8             321
  T4             4              46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  MANBA MUTATED     8   4   1
  MANBA WILD-TYPE 279 109  86
D1515V6, multiclass
    clus
vv   MANBA MUTATED MANBA WILD-TYPE
  N0             8             279
  N1             4             109
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1515V7, binary
                 cls
clus                0   1
  MANBA MUTATED    11   0
  MANBA WILD-TYPE 364  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MANBA MUTATED     11    0
  MANBA WILD-TYPE  364   65
   clus
vv  MANBA MUTATED MANBA WILD-TYPE
  0            11             364
  1             0              65
[1] 2 2
[1] FALSE
D1515V8, binary
                 cls
clus                0   1
  MANBA MUTATED     7   6
  MANBA WILD-TYPE 218 258
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MANBA MUTATED      7    6
  MANBA WILD-TYPE  218  258
        clus
vv       MANBA MUTATED MANBA WILD-TYPE
  FEMALE             7             218
  MALE               6             258
[1] 2 2
[1] FALSE
D1515V9, binary
                 cls
clus                0   1
  MANBA MUTATED     9   0
  MANBA WILD-TYPE 341  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MANBA MUTATED      9    0
  MANBA WILD-TYPE  341   22
     clus
vv    MANBA MUTATED MANBA WILD-TYPE
  NO              9             341
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MANBA MUTATED                     10                             2
  MANBA WILD-TYPE                  305                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MANBA MUTATED                       1                              0
  MANBA WILD-TYPE                   105                             10
D1515V10, multiclass
                                clus
vv                               MANBA MUTATED MANBA WILD-TYPE
  COLON ADENOCARCINOMA                      10             305
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  MANBA MUTATED    10   0   0   2
  MANBA WILD-TYPE 335   4  31  23
D1515V11, multiclass
    clus
vv   MANBA MUTATED MANBA WILD-TYPE
  R0            10             335
  R1             0               4
  R2             0              31
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1515V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MANBA MUTATED                                  0     0
  MANBA WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  MANBA MUTATED                           1     5
  MANBA WILD-TYPE                        21   221
D1515V13, multiclass
                                  clus
vv                                 MANBA MUTATED MANBA WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        5             221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1516) Variable = PROM1 MUTATION ANALYSIS
D1516V1, survival
                 sevent
clus2               0   1
  PROM1 MUTATED    12   4
  PROM1 WILD-TYPE 366  89
  PROM1 MUTATED PROM1 WILD-TYPE 
             16             455 
  PROM1 MUTATED PROM1 WILD-TYPE 
              4              89 
$`PROM1 MUTATED`
TCGA-A6-6653 TCGA-AA-3864 TCGA-AA-A010 TCGA-AD-6964 TCGA-AZ-6608 TCGA-CM-6163 
       24.39        53.00        34.98        10.88         1.61         2.96 
TCGA-CM-6171 TCGA-CM-6172 TCGA-D5-6532 TCGA-D5-6930 TCGA-DM-A28H TCGA-G4-6588 
       14.04        11.01        18.25         1.51       117.07        26.17 
TCGA-AG-A002 TCGA-DY-A1DC TCGA-DY-A1DG TCGA-F5-6812 
       20.98        41.36        51.48         0.66 

$`PROM1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
       25.08        25.18        24.16        21.76        24.69        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 
       32.05         0.99        31.07        31.07        30.05        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
        0.79         0.72         5.79        22.42        27.42         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6164 
       15.02        15.02        17.03        15.02        12.00        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       20.19         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        4.80        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28K 
        6.12        81.37       119.93        35.97        60.79        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       22.09        13.78        35.80        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
      126.44        57.24        24.13        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.69        55.76        26.43 

  PROM1 MUTATED PROM1 WILD-TYPE 
           0.66            0.00 
  PROM1 MUTATED PROM1 WILD-TYPE 
         117.07          148.01 
  PROM1 MUTATED PROM1 WILD-TYPE 
         19.615          20.190 
[1] "0.7 - 117.1 (19.6)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.2"
D1516V2, continuous
D1516V3, binary
                 cls
clus                0   1
  PROM1 MUTATED    12   4
  PROM1 WILD-TYPE 354 115
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PROM1 MUTATED     12    4
  PROM1 WILD-TYPE  354  115
        clus
vv       PROM1 MUTATED PROM1 WILD-TYPE
  COLON             12             354
  RECTUM             4             115
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PROM1 MUTATED         4        0        1         5         1         0
  PROM1 WILD-TYPE      87        1       31       133         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PROM1 MUTATED           0          1          1          1        0         1
  PROM1 WILD-TYPE        24         10         58         41       48        17
                 vv
clus              STAGE IVB
  PROM1 MUTATED           0
  PROM1 WILD-TYPE         1
D1516V4, multiclass
            clus
vv           PROM1 MUTATED PROM1 WILD-TYPE
  STAGE I                4              87
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              5             133
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             1              10
  STAGE IIIB             1              58
  STAGE IIIC             1              41
  STAGE IV               0              48
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PROM1 MUTATED     1   4   9   2
  PROM1 WILD-TYPE  16  88 320  48
D1516V5, multiclass
    clus
vv   PROM1 MUTATED PROM1 WILD-TYPE
  T1             1              16
  T2             4              88
  T3             9             320
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  PROM1 MUTATED    11   3   2
  PROM1 WILD-TYPE 276 110  85
D1516V6, multiclass
    clus
vv   PROM1 MUTATED PROM1 WILD-TYPE
  N0            11             276
  N1             3             110
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1516V7, binary
                 cls
clus                0   1
  PROM1 MUTATED    14   1
  PROM1 WILD-TYPE 361  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PROM1 MUTATED     14    1
  PROM1 WILD-TYPE  361   64
   clus
vv  PROM1 MUTATED PROM1 WILD-TYPE
  0            14             361
  1             1              64
[1] 2 2
[1] FALSE
D1516V8, binary
                 cls
clus                0   1
  PROM1 MUTATED     6  10
  PROM1 WILD-TYPE 219 254
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PROM1 MUTATED      6   10
  PROM1 WILD-TYPE  219  254
        clus
vv       PROM1 MUTATED PROM1 WILD-TYPE
  FEMALE             6             219
  MALE              10             254
[1] 2 2
[1] FALSE
D1516V9, binary
                 cls
clus                0   1
  PROM1 MUTATED    11   0
  PROM1 WILD-TYPE 339  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PROM1 MUTATED     11    0
  PROM1 WILD-TYPE  339   22
     clus
vv    PROM1 MUTATED PROM1 WILD-TYPE
  NO             11             339
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PROM1 MUTATED                     11                             1
  PROM1 WILD-TYPE                  304                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PROM1 MUTATED                       4                              0
  PROM1 WILD-TYPE                   102                             10
D1516V10, multiclass
                                clus
vv                               PROM1 MUTATED PROM1 WILD-TYPE
  COLON ADENOCARCINOMA                      11             304
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      4             102
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  PROM1 MUTATED    10   0   0   0
  PROM1 WILD-TYPE 335   4  31  25
D1516V11, multiclass
    clus
vv   PROM1 MUTATED PROM1 WILD-TYPE
  R0            10             335
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1516V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PROM1 MUTATED                                  0     0
  PROM1 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PROM1 MUTATED                           0    13
  PROM1 WILD-TYPE                        22   213
D1516V13, multiclass
                                  clus
vv                                 PROM1 MUTATED PROM1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                       13             213
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1517) Variable = AMBRA1 MUTATION ANALYSIS
D1517V1, survival
                  sevent
clus2                0   1
  AMBRA1 MUTATED    15   4
  AMBRA1 WILD-TYPE 363  89
  AMBRA1 MUTATED AMBRA1 WILD-TYPE 
              19              452 
  AMBRA1 MUTATED AMBRA1 WILD-TYPE 
               4               89 
$`AMBRA1 MUTATED`
TCGA-AA-3492 TCGA-AA-3518 TCGA-AA-3864 TCGA-AA-A01I TCGA-AA-A01Q TCGA-AU-6004 
        3.02         1.02        53.00        31.00         1.02        27.09 
TCGA-AZ-4315 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-CK-6748 TCGA-CM-5861 TCGA-CM-6171 
       58.39         6.77       100.01         1.91        15.02        14.04 
TCGA-CM-6674 TCGA-D5-6536 TCGA-D5-6922 TCGA-DM-A1HB TCGA-DM-A28C TCGA-G4-6307 
       12.95        17.85         4.41       135.65        81.37        55.04 
TCGA-DC-5337 
       15.02 

$`AMBRA1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 
        0.99        31.07        31.07        30.05        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01K 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01P TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
       38.07        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
       16.31         0.95        33.01        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
       12.10        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 
       29.06        22.03        22.98        30.08        32.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       15.02        11.01        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        3.68        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 
       12.59       140.38         7.50        44.32       131.51       139.17 
TCGA-DM-A285 TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
        6.12       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       44.68        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
        4.73        78.12         7.17         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  AMBRA1 MUTATED AMBRA1 WILD-TYPE 
            1.02             0.00 
  AMBRA1 MUTATED AMBRA1 WILD-TYPE 
          135.65           148.01 
  AMBRA1 MUTATED AMBRA1 WILD-TYPE 
          15.020           20.415 
[1] "1.0 - 135.7 (15.0)" "0.0 - 148.0 (20.4)"
[1] "hr=" "1.2"
D1517V2, continuous
D1517V3, binary
                  cls
clus                 0   1
  AMBRA1 MUTATED    18   1
  AMBRA1 WILD-TYPE 348 118
[1] "tbl2"
                  cls
clus               [,1] [,2]
  AMBRA1 MUTATED     18    1
  AMBRA1 WILD-TYPE  348  118
        clus
vv       AMBRA1 MUTATED AMBRA1 WILD-TYPE
  COLON              18              348
  RECTUM              1              118
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  AMBRA1 MUTATED         5        0        4         6         0         0
  AMBRA1 WILD-TYPE      86        1       28       132        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  AMBRA1 MUTATED           0          1          2          0        1
  AMBRA1 WILD-TYPE        24         10         57         42       47
                  vv
clus               STAGE IVA STAGE IVB
  AMBRA1 MUTATED           0         0
  AMBRA1 WILD-TYPE        18         1
D1517V4, multiclass
            clus
vv           AMBRA1 MUTATED AMBRA1 WILD-TYPE
  STAGE I                 5               86
  STAGE IA                0                1
  STAGE II                4               28
  STAGE IIA               6              132
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              1               10
  STAGE IIIB              2               57
  STAGE IIIC              0               42
  STAGE IV                1               47
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  AMBRA1 MUTATED     1   4  14   0
  AMBRA1 WILD-TYPE  16  88 315  50
D1517V5, multiclass
    clus
vv   AMBRA1 MUTATED AMBRA1 WILD-TYPE
  T1              1               16
  T2              4               88
  T3             14              315
  T4              0               50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  AMBRA1 MUTATED    15   4   0
  AMBRA1 WILD-TYPE 272 109  87
D1517V6, multiclass
    clus
vv   AMBRA1 MUTATED AMBRA1 WILD-TYPE
  N0             15              272
  N1              4              109
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1517V7, binary
                  cls
clus                 0   1
  AMBRA1 MUTATED    17   1
  AMBRA1 WILD-TYPE 358  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  AMBRA1 MUTATED     17    1
  AMBRA1 WILD-TYPE  358   64
   clus
vv  AMBRA1 MUTATED AMBRA1 WILD-TYPE
  0             17              358
  1              1               64
[1] 2 2
[1] FALSE
D1517V8, binary
                  cls
clus                 0   1
  AMBRA1 MUTATED     8  11
  AMBRA1 WILD-TYPE 217 253
[1] "tbl2"
                  cls
clus               [,1] [,2]
  AMBRA1 MUTATED      8   11
  AMBRA1 WILD-TYPE  217  253
        clus
vv       AMBRA1 MUTATED AMBRA1 WILD-TYPE
  FEMALE              8              217
  MALE               11              253
[1] 2 2
[1] FALSE
D1517V9, binary
                  cls
clus                 0   1
  AMBRA1 MUTATED    13   0
  AMBRA1 WILD-TYPE 337  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  AMBRA1 MUTATED     13    0
  AMBRA1 WILD-TYPE  337   22
     clus
vv    AMBRA1 MUTATED AMBRA1 WILD-TYPE
  NO              13              337
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  AMBRA1 MUTATED                     16                             1
  AMBRA1 WILD-TYPE                  299                            46
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  AMBRA1 MUTATED                       1                              0
  AMBRA1 WILD-TYPE                   105                             10
D1517V10, multiclass
                                clus
vv                               AMBRA1 MUTATED AMBRA1 WILD-TYPE
  COLON ADENOCARCINOMA                       16              299
  COLON MUCINOUS ADENOCARCINOMA               1               46
  RECTAL ADENOCARCINOMA                       1              105
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  AMBRA1 MUTATED    14   0   0   1
  AMBRA1 WILD-TYPE 331   4  31  24
D1517V11, multiclass
    clus
vv   AMBRA1 MUTATED AMBRA1 WILD-TYPE
  R0             14              331
  R1              0                4
  R2              0               31
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1517V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMBRA1 MUTATED                                  0     0
  AMBRA1 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  AMBRA1 MUTATED                           0    14
  AMBRA1 WILD-TYPE                        22   212
D1517V13, multiclass
                                  clus
vv                                 AMBRA1 MUTATED AMBRA1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                        14              212
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1518) Variable = TBC1D10C MUTATION ANALYSIS
D1518V1, survival
                    sevent
clus2                  0   1
  TBC1D10C MUTATED     7   2
  TBC1D10C WILD-TYPE 371  91
  TBC1D10C MUTATED TBC1D10C WILD-TYPE 
                 9                462 
  TBC1D10C MUTATED TBC1D10C WILD-TYPE 
                 2                 91 
$`TBC1D10C MUTATED`
TCGA-A6-5661 TCGA-AA-3821 TCGA-AA-3949 TCGA-CA-5254 TCGA-D5-5537 TCGA-D5-6539 
       33.53         1.02        26.01        12.69        45.40        12.49 
TCGA-F4-6570 TCGA-G4-6299 TCGA-DC-5869 
        6.18        74.56         5.03 

$`TBC1D10C WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 
       10.06        35.05        33.04         0.99        25.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       12.99        24.00        33.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5538 
       11.08        11.08        11.01        10.06        12.03        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 
       43.27        15.12        17.85         4.80        17.13        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       31.96        35.74        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
      133.18        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
        7.17        15.02        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  TBC1D10C MUTATED TBC1D10C WILD-TYPE 
              1.02               0.00 
  TBC1D10C MUTATED TBC1D10C WILD-TYPE 
             74.56             148.01 
  TBC1D10C MUTATED TBC1D10C WILD-TYPE 
            12.690             20.235 
[1] "1.0 - 74.6 (12.7)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.2"
D1518V2, continuous
D1518V3, binary
                    cls
clus                   0   1
  TBC1D10C MUTATED     8   1
  TBC1D10C WILD-TYPE 358 118
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  TBC1D10C MUTATED      8    1
  TBC1D10C WILD-TYPE  358  118
        clus
vv       TBC1D10C MUTATED TBC1D10C WILD-TYPE
  COLON                 8                358
  RECTUM                1                118
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TBC1D10C MUTATED         1        0        0         4         0         0
  TBC1D10C WILD-TYPE      90        1       32       134        10         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TBC1D10C MUTATED           0          1          2          1        0
  TBC1D10C WILD-TYPE        24         10         57         41       48
                    vv
clus                 STAGE IVA STAGE IVB
  TBC1D10C MUTATED           0         0
  TBC1D10C WILD-TYPE        18         1
D1518V4, multiclass
            clus
vv           TBC1D10C MUTATED TBC1D10C WILD-TYPE
  STAGE I                   1                 90
  STAGE IA                  0                  1
  STAGE II                  0                 32
  STAGE IIA                 4                134
  STAGE IIB                 0                 10
  STAGE IIC                 0                  1
  STAGE III                 0                 24
  STAGE IIIA                1                 10
  STAGE IIIB                2                 57
  STAGE IIIC                1                 41
  STAGE IV                  0                 48
  STAGE IVA                 0                 18
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  TBC1D10C MUTATED     0   1   8   0
  TBC1D10C WILD-TYPE  17  91 321  50
D1518V5, multiclass
    clus
vv   TBC1D10C MUTATED TBC1D10C WILD-TYPE
  T1                0                 17
  T2                1                 91
  T3                8                321
  T4                0                 50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  TBC1D10C MUTATED     5   2   2
  TBC1D10C WILD-TYPE 282 111  85
D1518V6, multiclass
    clus
vv   TBC1D10C MUTATED TBC1D10C WILD-TYPE
  N0                5                282
  N1                2                111
  N2                2                 85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1518V7, binary
                    cls
clus                   0   1
  TBC1D10C MUTATED     8   0
  TBC1D10C WILD-TYPE 367  65
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  TBC1D10C MUTATED      8    0
  TBC1D10C WILD-TYPE  367   65
   clus
vv  TBC1D10C MUTATED TBC1D10C WILD-TYPE
  0                8                367
  1                0                 65
[1] 2 2
[1] FALSE
D1518V8, binary
                    cls
clus                   0   1
  TBC1D10C MUTATED     7   2
  TBC1D10C WILD-TYPE 218 262
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  TBC1D10C MUTATED      7    2
  TBC1D10C WILD-TYPE  218  262
        clus
vv       TBC1D10C MUTATED TBC1D10C WILD-TYPE
  FEMALE                7                218
  MALE                  2                262
[1] 2 2
[1] FALSE
D1518V9, binary
                    cls
clus                   0   1
  TBC1D10C MUTATED     8   0
  TBC1D10C WILD-TYPE 342  22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  TBC1D10C MUTATED      8    0
  TBC1D10C WILD-TYPE  342   22
     clus
vv    TBC1D10C MUTATED TBC1D10C WILD-TYPE
  NO                 8                342
  YES                0                 22
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  TBC1D10C MUTATED                      6                             2
  TBC1D10C WILD-TYPE                  309                            45
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  TBC1D10C MUTATED                       1                              0
  TBC1D10C WILD-TYPE                   105                             10
D1518V10, multiclass
                                clus
vv                               TBC1D10C MUTATED TBC1D10C WILD-TYPE
  COLON ADENOCARCINOMA                          6                309
  COLON MUCINOUS ADENOCARCINOMA                 2                 45
  RECTAL ADENOCARCINOMA                         1                105
  RECTAL MUCINOUS ADENOCARCINOMA                0                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  TBC1D10C MUTATED     7   0   0   2
  TBC1D10C WILD-TYPE 338   4  31  23
D1518V11, multiclass
    clus
vv   TBC1D10C MUTATED TBC1D10C WILD-TYPE
  R0                7                338
  R1                0                  4
  R2                0                 31
  RX                2                 23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1518V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TBC1D10C MUTATED                                  0     1
  TBC1D10C WILD-TYPE                                1    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  TBC1D10C MUTATED                           2     4
  TBC1D10C WILD-TYPE                        20   222
D1518V13, multiclass
                                  clus
vv                                 TBC1D10C MUTATED TBC1D10C WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                 10
  BLACK OR AFRICAN AMERICAN                       2                 20
  WHITE                                           4                222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1519) Variable = CD84 MUTATION ANALYSIS
D1519V1, survival
                sevent
clus2              0   1
  CD84 MUTATED    10   2
  CD84 WILD-TYPE 368  91
  CD84 MUTATED CD84 WILD-TYPE 
            12            459 
  CD84 MUTATED CD84 WILD-TYPE 
             2             91 
$`CD84 MUTATED`
TCGA-AA-3510 TCGA-AA-3854 TCGA-AA-3977 TCGA-CA-6717 TCGA-D5-6539 TCGA-D5-7000 
       63.98        36.03        25.02        12.76        12.49        10.26 
TCGA-DM-A28C TCGA-F4-6807 TCGA-G4-6588 TCGA-AG-A002 TCGA-DC-5337 TCGA-DY-A1H8 
       81.37        16.24        26.17        20.98        15.02        32.61 

$`CD84 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3855 
       17.03        10.06         0.00        33.07         0.00        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       12.00        11.38       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28E 
       44.32       131.51       135.65       139.17         6.12       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5869 
       33.17         6.97         4.73        78.12         7.17         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       51.48         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  CD84 MUTATED CD84 WILD-TYPE 
         10.26           0.00 
  CD84 MUTATED CD84 WILD-TYPE 
         81.37         148.01 
  CD84 MUTATED CD84 WILD-TYPE 
         23.00          20.12 
[1] "10.3 - 81.4 (23.0)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.4"
D1519V2, continuous
D1519V3, binary
                cls
clus               0   1
  CD84 MUTATED     9   3
  CD84 WILD-TYPE 357 116
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD84 MUTATED      9    3
  CD84 WILD-TYPE  357  116
        clus
vv       CD84 MUTATED CD84 WILD-TYPE
  COLON             9            357
  RECTUM            3            116
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CD84 MUTATED         4        0        1         3         0         0
  CD84 WILD-TYPE      87        1       31       135        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CD84 MUTATED           0          2          0          1        0         0
  CD84 WILD-TYPE        24          9         59         41       48        18
                vv
clus             STAGE IVB
  CD84 MUTATED           0
  CD84 WILD-TYPE         1
D1519V4, multiclass
            clus
vv           CD84 MUTATED CD84 WILD-TYPE
  STAGE I               4             87
  STAGE IA              0              1
  STAGE II              1             31
  STAGE IIA             3            135
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            2              9
  STAGE IIIB            0             59
  STAGE IIIC            1             41
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  CD84 MUTATED     1   5   6   0
  CD84 WILD-TYPE  16  87 323  50
D1519V5, multiclass
    clus
vv   CD84 MUTATED CD84 WILD-TYPE
  T1            1             16
  T2            5             87
  T3            6            323
  T4            0             50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  CD84 MUTATED    10   1   1
  CD84 WILD-TYPE 277 112  86
D1519V6, multiclass
    clus
vv   CD84 MUTATED CD84 WILD-TYPE
  N0           10            277
  N1            1            112
  N2            1             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1519V7, binary
                cls
clus               0   1
  CD84 MUTATED    11   0
  CD84 WILD-TYPE 364  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD84 MUTATED     11    0
  CD84 WILD-TYPE  364   65
   clus
vv  CD84 MUTATED CD84 WILD-TYPE
  0           11            364
  1            0             65
[1] 2 2
[1] FALSE
D1519V8, binary
                cls
clus               0   1
  CD84 MUTATED     6   6
  CD84 WILD-TYPE 219 258
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD84 MUTATED      6    6
  CD84 WILD-TYPE  219  258
        clus
vv       CD84 MUTATED CD84 WILD-TYPE
  FEMALE            6            219
  MALE              6            258
[1] 2 2
[1] FALSE
D1519V9, binary
                cls
clus               0   1
  CD84 MUTATED    10   0
  CD84 WILD-TYPE 340  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD84 MUTATED     10    0
  CD84 WILD-TYPE  340   22
     clus
vv    CD84 MUTATED CD84 WILD-TYPE
  NO            10            340
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CD84 MUTATED                      6                             3
  CD84 WILD-TYPE                  309                            44
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CD84 MUTATED                       3                              0
  CD84 WILD-TYPE                   103                             10
D1519V10, multiclass
                                clus
vv                               CD84 MUTATED CD84 WILD-TYPE
  COLON ADENOCARCINOMA                      6            309
  COLON MUCINOUS ADENOCARCINOMA             3             44
  RECTAL ADENOCARCINOMA                     3            103
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  CD84 MUTATED     8   0   0   1
  CD84 WILD-TYPE 337   4  31  24
D1519V11, multiclass
    clus
vv   CD84 MUTATED CD84 WILD-TYPE
  R0            8            337
  R1            0              4
  R2            0             31
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1519V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CD84 MUTATED                                  0     1
  CD84 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  CD84 MUTATED                           0     7
  CD84 WILD-TYPE                        22   219
D1519V13, multiclass
                                  clus
vv                                 CD84 MUTATED CD84 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       7            219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1520) Variable = DNMT1 MUTATION ANALYSIS
D1520V1, survival
                 sevent
clus2               0   1
  DNMT1 MUTATED    18   6
  DNMT1 WILD-TYPE 360  87
  DNMT1 MUTATED DNMT1 WILD-TYPE 
             24             447 
  DNMT1 MUTATED DNMT1 WILD-TYPE 
              6              87 
$`DNMT1 MUTATED`
TCGA-A6-2683 TCGA-AA-3492 TCGA-AA-3555 TCGA-AA-3672 TCGA-AA-3845 TCGA-AA-3877 
       16.57         3.02        29.95         0.92         0.00        31.00 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-A00J TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01Q 
       34.03         2.01        18.05         4.01        34.98         1.02 
TCGA-AA-A01Z TCGA-AZ-4315 TCGA-CA-6718 TCGA-CK-5913 TCGA-CM-5861 TCGA-D5-6540 
       37.02        58.39        10.06        51.32        15.02        16.14 
TCGA-AF-2689 TCGA-AG-3609 TCGA-AG-3882 TCGA-AG-A002 TCGA-AG-A02N TCGA-EI-6510 
       39.48        19.99        19.99        20.98        61.97        18.28 

$`DNMT1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 
       20.12        19.66        20.28         7.04         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       24.00        17.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
        2.01        14.01        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02        14.93        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       18.05         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       24.00         2.01        20.98        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       19.00        30.02        34.03        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A024 
       35.01         1.02        33.04        35.01        26.01        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        33.01        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.20        12.76        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        49.08         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 
       29.06        22.03        22.98        30.08        32.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       24.13        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3611 TCGA-AG-3612 
       12.03         6.05         0.99        15.95        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.04         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
        1.94        38.96        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  DNMT1 MUTATED DNMT1 WILD-TYPE 
              0               0 
  DNMT1 MUTATED DNMT1 WILD-TYPE 
          61.97          148.01 
  DNMT1 MUTATED DNMT1 WILD-TYPE 
         19.135          20.550 
[1] "0.0 - 62.0 (19.1)"  "0.0 - 148.0 (20.6)"
[1] "hr=" "1.5"
D1520V2, continuous
D1520V3, binary
                 cls
clus                0   1
  DNMT1 MUTATED    18   6
  DNMT1 WILD-TYPE 348 113
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DNMT1 MUTATED     18    6
  DNMT1 WILD-TYPE  348  113
        clus
vv       DNMT1 MUTATED DNMT1 WILD-TYPE
  COLON             18             348
  RECTUM             6             113
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DNMT1 MUTATED         4        0        4         8         2         0
  DNMT1 WILD-TYPE      87        1       28       130         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DNMT1 MUTATED           1          0          1          1        2         1
  DNMT1 WILD-TYPE        23         11         58         41       46        17
                 vv
clus              STAGE IVB
  DNMT1 MUTATED           0
  DNMT1 WILD-TYPE         1
D1520V4, multiclass
            clus
vv           DNMT1 MUTATED DNMT1 WILD-TYPE
  STAGE I                4              87
  STAGE IA               0               1
  STAGE II               4              28
  STAGE IIA              8             130
  STAGE IIB              2               8
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             1              41
  STAGE IV               2              46
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  DNMT1 MUTATED     1   4  15   4
  DNMT1 WILD-TYPE  16  88 314  46
D1520V5, multiclass
    clus
vv   DNMT1 MUTATED DNMT1 WILD-TYPE
  T1             1              16
  T2             4              88
  T3            15             314
  T4             4              46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  DNMT1 MUTATED    20   2   2
  DNMT1 WILD-TYPE 267 111  85
D1520V6, multiclass
    clus
vv   DNMT1 MUTATED DNMT1 WILD-TYPE
  N0            20             267
  N1             2             111
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1520V7, binary
                 cls
clus                0   1
  DNMT1 MUTATED    20   2
  DNMT1 WILD-TYPE 355  63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DNMT1 MUTATED     20    2
  DNMT1 WILD-TYPE  355   63
   clus
vv  DNMT1 MUTATED DNMT1 WILD-TYPE
  0            20             355
  1             2              63
[1] 2 2
[1] FALSE
D1520V8, binary
                 cls
clus                0   1
  DNMT1 MUTATED    15   9
  DNMT1 WILD-TYPE 210 255
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DNMT1 MUTATED     15    9
  DNMT1 WILD-TYPE  210  255
        clus
vv       DNMT1 MUTATED DNMT1 WILD-TYPE
  FEMALE            15             210
  MALE               9             255
[1] 2 2
[1] FALSE
D1520V9, binary
                 cls
clus                0   1
  DNMT1 MUTATED    19   0
  DNMT1 WILD-TYPE 331  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DNMT1 MUTATED     19    0
  DNMT1 WILD-TYPE  331   22
     clus
vv    DNMT1 MUTATED DNMT1 WILD-TYPE
  NO             19             331
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  DNMT1 MUTATED                     12                             6
  DNMT1 WILD-TYPE                  303                            41
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  DNMT1 MUTATED                       6                              0
  DNMT1 WILD-TYPE                   100                             10
D1520V10, multiclass
                                clus
vv                               DNMT1 MUTATED DNMT1 WILD-TYPE
  COLON ADENOCARCINOMA                      12             303
  COLON MUCINOUS ADENOCARCINOMA              6              41
  RECTAL ADENOCARCINOMA                      6             100
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  DNMT1 MUTATED    21   0   0   2
  DNMT1 WILD-TYPE 324   4  31  23
D1520V11, multiclass
    clus
vv   DNMT1 MUTATED DNMT1 WILD-TYPE
  R0            21             324
  R1             0               4
  R2             0              31
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1520V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DNMT1 MUTATED                                  0     1
  DNMT1 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  DNMT1 MUTATED                           0     7
  DNMT1 WILD-TYPE                        22   219
D1520V13, multiclass
                                  clus
vv                                 DNMT1 MUTATED DNMT1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        7             219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1521) Variable = TUT1 MUTATION ANALYSIS
D1521V1, survival
                sevent
clus2              0   1
  TUT1 MUTATED    10   0
  TUT1 WILD-TYPE 368  93
  TUT1 MUTATED TUT1 WILD-TYPE 
            10            461 
  TUT1 MUTATED TUT1 WILD-TYPE 
             0             93 
$`TUT1 MUTATED`
TCGA-A6-5661 TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3518 TCGA-AA-3837 TCGA-AA-3950 
       33.53        20.12        19.66         1.02        38.99        24.00 
TCGA-AU-6004 TCGA-CM-5860 TCGA-D5-6529 TCGA-AG-3892 
       27.09        32.02        20.19        13.02 

$`TUT1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3520 
        6.97         1.02        13.02        38.99         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3842 
        0.99        25.02         1.02        17.98        15.95        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       26.01         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 
       22.42        27.42        10.88         0.20        14.50        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       30.08        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 
       19.99         1.02        17.95        36.95        17.03        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  TUT1 MUTATED TUT1 WILD-TYPE 
          1.02           0.00 
  TUT1 MUTATED TUT1 WILD-TYPE 
         38.99         148.01 
  TUT1 MUTATED TUT1 WILD-TYPE 
        22.095         20.050 
[1] "1.0 - 39.0 (22.1)"  "0.0 - 148.0 (20.1)"
[1] "hr="     "9200000"
D1521V2, continuous
D1521V3, binary
                cls
clus               0   1
  TUT1 MUTATED     9   1
  TUT1 WILD-TYPE 357 118
[1] "tbl2"
                cls
clus             [,1] [,2]
  TUT1 MUTATED      9    1
  TUT1 WILD-TYPE  357  118
        clus
vv       TUT1 MUTATED TUT1 WILD-TYPE
  COLON             9            357
  RECTUM            1            118
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TUT1 MUTATED         2        0        0         7         0         0
  TUT1 WILD-TYPE      89        1       32       131        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TUT1 MUTATED           0          0          0          1        0         0
  TUT1 WILD-TYPE        24         11         59         41       48        18
                vv
clus             STAGE IVB
  TUT1 MUTATED           0
  TUT1 WILD-TYPE         1
D1521V4, multiclass
            clus
vv           TUT1 MUTATED TUT1 WILD-TYPE
  STAGE I               2             89
  STAGE IA              0              1
  STAGE II              0             32
  STAGE IIA             7            131
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            0             59
  STAGE IIIC            1             41
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  TUT1 MUTATED     1   1   7   1
  TUT1 WILD-TYPE  16  91 322  49
D1521V5, multiclass
    clus
vv   TUT1 MUTATED TUT1 WILD-TYPE
  T1            1             16
  T2            1             91
  T3            7            322
  T4            1             49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  TUT1 MUTATED     9   1   0
  TUT1 WILD-TYPE 278 112  87
D1521V6, multiclass
    clus
vv   TUT1 MUTATED TUT1 WILD-TYPE
  N0            9            278
  N1            1            112
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1521V7, binary
                cls
clus               0   1
  TUT1 MUTATED     8   0
  TUT1 WILD-TYPE 367  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  TUT1 MUTATED      8    0
  TUT1 WILD-TYPE  367   65
   clus
vv  TUT1 MUTATED TUT1 WILD-TYPE
  0            8            367
  1            0             65
[1] 2 2
[1] FALSE
D1521V8, binary
                cls
clus               0   1
  TUT1 MUTATED     5   5
  TUT1 WILD-TYPE 220 259
[1] "tbl2"
                cls
clus             [,1] [,2]
  TUT1 MUTATED      5    5
  TUT1 WILD-TYPE  220  259
        clus
vv       TUT1 MUTATED TUT1 WILD-TYPE
  FEMALE            5            220
  MALE              5            259
[1] 2 2
[1] FALSE
D1521V9, binary
                cls
clus               0   1
  TUT1 MUTATED     8   0
  TUT1 WILD-TYPE 342  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  TUT1 MUTATED      8    0
  TUT1 WILD-TYPE  342   22
     clus
vv    TUT1 MUTATED TUT1 WILD-TYPE
  NO             8            342
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  TUT1 MUTATED                      5                             4
  TUT1 WILD-TYPE                  310                            43
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  TUT1 MUTATED                       1                              0
  TUT1 WILD-TYPE                   105                             10
D1521V10, multiclass
                                clus
vv                               TUT1 MUTATED TUT1 WILD-TYPE
  COLON ADENOCARCINOMA                      5            310
  COLON MUCINOUS ADENOCARCINOMA             4             43
  RECTAL ADENOCARCINOMA                     1            105
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  TUT1 MUTATED     9   0   0   0
  TUT1 WILD-TYPE 336   4  31  25
D1521V11, multiclass
    clus
vv   TUT1 MUTATED TUT1 WILD-TYPE
  R0            9            336
  R1            0              4
  R2            0             31
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1521V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TUT1 MUTATED                                  0     0
  TUT1 WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  TUT1 MUTATED                           1     5
  TUT1 WILD-TYPE                        21   221
D1521V13, multiclass
                                  clus
vv                                 TUT1 MUTATED TUT1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                       5            221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1522) Variable = OR9G4 MUTATION ANALYSIS
D1522V1, survival
                 sevent
clus2               0   1
  OR9G4 MUTATED     7   1
  OR9G4 WILD-TYPE 371  92
  OR9G4 MUTATED OR9G4 WILD-TYPE 
              8             463 
  OR9G4 MUTATED OR9G4 WILD-TYPE 
              1              92 
$`OR9G4 MUTATED`
TCGA-AA-3502 TCGA-AA-A00N TCGA-AA-A010 TCGA-CA-5796 TCGA-CA-6717 TCGA-D5-6535 
       35.01         4.01        34.98         3.25        12.76        15.12 
TCGA-F4-6807 TCGA-F4-6808 
       16.24        33.67 

$`OR9G4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
       12.69         3.06         3.29         0.07        12.20        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       43.27        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       41.42        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  OR9G4 MUTATED OR9G4 WILD-TYPE 
           3.25            0.00 
  OR9G4 MUTATED OR9G4 WILD-TYPE 
          35.01          148.01 
  OR9G4 MUTATED OR9G4 WILD-TYPE 
          15.68           20.28 
[1] "3.2 - 35.0 (15.7)"  "0.0 - 148.0 (20.3)"
[1] "hr=" "1.1"
D1522V2, continuous
D1522V3, binary
                 cls
clus                0   1
  OR9G4 MUTATED     8   0
  OR9G4 WILD-TYPE 358 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR9G4 MUTATED      8    0
  OR9G4 WILD-TYPE  358  119
        clus
vv       OR9G4 MUTATED OR9G4 WILD-TYPE
  COLON              8             358
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  OR9G4 MUTATED         2        0        0         2         2         0
  OR9G4 WILD-TYPE      89        1       32       136         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  OR9G4 MUTATED           0          0          1          1        0         0
  OR9G4 WILD-TYPE        24         11         58         41       48        18
                 vv
clus              STAGE IVB
  OR9G4 MUTATED           0
  OR9G4 WILD-TYPE         1
D1522V4, multiclass
            clus
vv           OR9G4 MUTATED OR9G4 WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              2             136
  STAGE IIB              2               8
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             1              41
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  OR9G4 MUTATED     1   1   4   2
  OR9G4 WILD-TYPE  16  91 325  48
D1522V5, multiclass
    clus
vv   OR9G4 MUTATED OR9G4 WILD-TYPE
  T1             1              16
  T2             1              91
  T3             4             325
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  OR9G4 MUTATED     6   1   1
  OR9G4 WILD-TYPE 281 112  86
D1522V6, multiclass
    clus
vv   OR9G4 MUTATED OR9G4 WILD-TYPE
  N0             6             281
  N1             1             112
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1522V7, binary
                 cls
clus                0   1
  OR9G4 MUTATED     7   0
  OR9G4 WILD-TYPE 368  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR9G4 MUTATED      7    0
  OR9G4 WILD-TYPE  368   65
   clus
vv  OR9G4 MUTATED OR9G4 WILD-TYPE
  0             7             368
  1             0              65
[1] 2 2
[1] FALSE
D1522V8, binary
                 cls
clus                0   1
  OR9G4 MUTATED     5   3
  OR9G4 WILD-TYPE 220 261
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR9G4 MUTATED      5    3
  OR9G4 WILD-TYPE  220  261
        clus
vv       OR9G4 MUTATED OR9G4 WILD-TYPE
  FEMALE             5             220
  MALE               3             261
[1] 2 2
[1] FALSE
D1522V9, binary
                 cls
clus                0   1
  OR9G4 MUTATED     7   0
  OR9G4 WILD-TYPE 343  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR9G4 MUTATED      7    0
  OR9G4 WILD-TYPE  343   22
     clus
vv    OR9G4 MUTATED OR9G4 WILD-TYPE
  NO              7             343
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  OR9G4 MUTATED                      5                             3
  OR9G4 WILD-TYPE                  310                            44
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  OR9G4 MUTATED                       0                              0
  OR9G4 WILD-TYPE                   106                             10
D1522V10, multiclass
                                clus
vv                               OR9G4 MUTATED OR9G4 WILD-TYPE
  COLON ADENOCARCINOMA                       5             310
  COLON MUCINOUS ADENOCARCINOMA              3              44
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  OR9G4 MUTATED     6   0   0   2
  OR9G4 WILD-TYPE 339   4  31  23
D1522V11, multiclass
    clus
vv   OR9G4 MUTATED OR9G4 WILD-TYPE
  R0             6             339
  R1             0               4
  R2             0              31
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1522V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OR9G4 MUTATED                                  0     2
  OR9G4 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  OR9G4 MUTATED                           0     3
  OR9G4 WILD-TYPE                        22   223
D1522V13, multiclass
                                  clus
vv                                 OR9G4 MUTATED OR9G4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               9
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        3             223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1523) Variable = SLC45A2 MUTATION ANALYSIS
D1523V1, survival
                   sevent
clus2                 0   1
  SLC45A2 MUTATED     8   3
  SLC45A2 WILD-TYPE 370  90
  SLC45A2 MUTATED SLC45A2 WILD-TYPE 
               11               460 
  SLC45A2 MUTATED SLC45A2 WILD-TYPE 
                3                90 
$`SLC45A2 MUTATED`
TCGA-A6-5661 TCGA-AA-3544 TCGA-AA-3666 TCGA-AA-A00D TCGA-AD-6899 TCGA-CK-4948 
       33.53        14.01         2.01        19.00         5.79       148.01 
TCGA-D5-6529 TCGA-D5-6541 TCGA-G4-6588 TCGA-AG-3584 TCGA-AG-A002 
       20.19        15.58        26.17        24.00        20.98 

$`SLC45A2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       26.01        12.99         0.99        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
       54.02        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00E 
       19.07         7.96        27.02        13.94        38.04        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        0.72        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       14.30        17.56        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       56.09        55.92        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6898 
       17.85         4.80        17.13        12.49        16.14         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3587 
        8.02         7.07        36.03        20.05         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  SLC45A2 MUTATED SLC45A2 WILD-TYPE 
             2.01              0.00 
  SLC45A2 MUTATED SLC45A2 WILD-TYPE 
           148.01            140.38 
  SLC45A2 MUTATED SLC45A2 WILD-TYPE 
            20.19             20.20 
[1] "2.0 - 148.0 (20.2)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.4"
D1523V2, continuous
D1523V3, binary
                   cls
clus                  0   1
  SLC45A2 MUTATED     9   2
  SLC45A2 WILD-TYPE 357 117
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC45A2 MUTATED      9    2
  SLC45A2 WILD-TYPE  357  117
        clus
vv       SLC45A2 MUTATED SLC45A2 WILD-TYPE
  COLON                9               357
  RECTUM               2               117
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SLC45A2 MUTATED         3        0        0         4         0         0
  SLC45A2 WILD-TYPE      88        1       32       134        10         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC45A2 MUTATED           2          0          0          1        1
  SLC45A2 WILD-TYPE        22         11         59         41       47
                   vv
clus                STAGE IVA STAGE IVB
  SLC45A2 MUTATED           0         0
  SLC45A2 WILD-TYPE        18         1
D1523V4, multiclass
            clus
vv           SLC45A2 MUTATED SLC45A2 WILD-TYPE
  STAGE I                  3                88
  STAGE IA                 0                 1
  STAGE II                 0                32
  STAGE IIA                4               134
  STAGE IIB                0                10
  STAGE IIC                0                 1
  STAGE III                2                22
  STAGE IIIA               0                11
  STAGE IIIB               0                59
  STAGE IIIC               1                41
  STAGE IV                 1                47
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  SLC45A2 MUTATED     0   3   7   1
  SLC45A2 WILD-TYPE  17  89 322  49
D1523V5, multiclass
    clus
vv   SLC45A2 MUTATED SLC45A2 WILD-TYPE
  T1               0                17
  T2               3                89
  T3               7               322
  T4               1                49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  SLC45A2 MUTATED     7   2   2
  SLC45A2 WILD-TYPE 280 111  85
D1523V6, multiclass
    clus
vv   SLC45A2 MUTATED SLC45A2 WILD-TYPE
  N0               7               280
  N1               2               111
  N2               2                85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1523V7, binary
                   cls
clus                  0   1
  SLC45A2 MUTATED     9   1
  SLC45A2 WILD-TYPE 366  64
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC45A2 MUTATED      9    1
  SLC45A2 WILD-TYPE  366   64
   clus
vv  SLC45A2 MUTATED SLC45A2 WILD-TYPE
  0               9               366
  1               1                64
[1] 2 2
[1] FALSE
D1523V8, binary
                   cls
clus                  0   1
  SLC45A2 MUTATED     3   8
  SLC45A2 WILD-TYPE 222 256
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC45A2 MUTATED      3    8
  SLC45A2 WILD-TYPE  222  256
        clus
vv       SLC45A2 MUTATED SLC45A2 WILD-TYPE
  FEMALE               3               222
  MALE                 8               256
[1] 2 2
[1] FALSE
D1523V9, binary
                   cls
clus                  0   1
  SLC45A2 MUTATED    10   0
  SLC45A2 WILD-TYPE 340  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC45A2 MUTATED     10    0
  SLC45A2 WILD-TYPE  340   22
     clus
vv    SLC45A2 MUTATED SLC45A2 WILD-TYPE
  NO               10               340
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SLC45A2 MUTATED                      8                             1
  SLC45A2 WILD-TYPE                  307                            46
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SLC45A2 MUTATED                       2                              0
  SLC45A2 WILD-TYPE                   104                             10
D1523V10, multiclass
                                clus
vv                               SLC45A2 MUTATED SLC45A2 WILD-TYPE
  COLON ADENOCARCINOMA                         8               307
  COLON MUCINOUS ADENOCARCINOMA                1                46
  RECTAL ADENOCARCINOMA                        2               104
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  SLC45A2 MUTATED     9   0   1   0
  SLC45A2 WILD-TYPE 336   4  30  25
D1523V11, multiclass
    clus
vv   SLC45A2 MUTATED SLC45A2 WILD-TYPE
  R0               9               336
  R1               0                 4
  R2               1                30
  RX               0                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1523V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SLC45A2 MUTATED                                  0     0
  SLC45A2 WILD-TYPE                                1    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  SLC45A2 MUTATED                           1     5
  SLC45A2 WILD-TYPE                        21   221
D1523V13, multiclass
                                  clus
vv                                 SLC45A2 MUTATED SLC45A2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                      1                21
  WHITE                                          5               221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1524) Variable = SPARCL1 MUTATION ANALYSIS
D1524V1, survival
                   sevent
clus2                 0   1
  SPARCL1 MUTATED    13   2
  SPARCL1 WILD-TYPE 365  91
  SPARCL1 MUTATED SPARCL1 WILD-TYPE 
               15               456 
  SPARCL1 MUTATED SPARCL1 WILD-TYPE 
                2                91 
$`SPARCL1 MUTATED`
TCGA-A6-6653 TCGA-AA-3510 TCGA-AA-3543 TCGA-AA-3663 TCGA-AA-3713 TCGA-AA-3950 
       24.39        63.98         0.99         6.97        19.04        24.00 
TCGA-AA-A00J TCGA-AD-6889 TCGA-AZ-4315 TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-4746 
       18.05        56.55        58.39        12.76        10.06        37.02 
TCGA-DM-A0XD TCGA-G4-6628 TCGA-AG-A002 
       24.43        79.69        20.98 

$`SPARCL1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
       25.08        25.18        24.16        21.76        24.69        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
       12.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02        78.08         6.05        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       26.99        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       26.01         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       15.52         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       33.01        21.44        17.82         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       23.05        20.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       11.38        10.26       119.70        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 
       35.80        26.17        91.79        46.75        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  SPARCL1 MUTATED SPARCL1 WILD-TYPE 
             0.99              0.00 
  SPARCL1 MUTATED SPARCL1 WILD-TYPE 
            79.69            148.01 
  SPARCL1 MUTATED SPARCL1 WILD-TYPE 
           24.000            20.085 
[1] "1.0 - 79.7 (24.0)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.8"
D1524V2, continuous
D1524V3, binary
                   cls
clus                  0   1
  SPARCL1 MUTATED    14   1
  SPARCL1 WILD-TYPE 352 118
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SPARCL1 MUTATED     14    1
  SPARCL1 WILD-TYPE  352  118
        clus
vv       SPARCL1 MUTATED SPARCL1 WILD-TYPE
  COLON               14               352
  RECTUM               1               118
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SPARCL1 MUTATED         5        0        2         6         0         0
  SPARCL1 WILD-TYPE      86        1       30       132        10         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SPARCL1 MUTATED           0          0          1          0        1
  SPARCL1 WILD-TYPE        24         11         58         42       47
                   vv
clus                STAGE IVA STAGE IVB
  SPARCL1 MUTATED           0         0
  SPARCL1 WILD-TYPE        18         1
D1524V4, multiclass
            clus
vv           SPARCL1 MUTATED SPARCL1 WILD-TYPE
  STAGE I                  5                86
  STAGE IA                 0                 1
  STAGE II                 2                30
  STAGE IIA                6               132
  STAGE IIB                0                10
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               0                11
  STAGE IIIB               1                58
  STAGE IIIC               0                42
  STAGE IV                 1                47
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  SPARCL1 MUTATED     0   5   9   1
  SPARCL1 WILD-TYPE  17  87 320  49
D1524V5, multiclass
    clus
vv   SPARCL1 MUTATED SPARCL1 WILD-TYPE
  T1               0                17
  T2               5                87
  T3               9               320
  T4               1                49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  SPARCL1 MUTATED    14   1   0
  SPARCL1 WILD-TYPE 273 112  87
D1524V6, multiclass
    clus
vv   SPARCL1 MUTATED SPARCL1 WILD-TYPE
  N0              14               273
  N1               1               112
  N2               0                87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1524V7, binary
                   cls
clus                  0   1
  SPARCL1 MUTATED    14   1
  SPARCL1 WILD-TYPE 361  64
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SPARCL1 MUTATED     14    1
  SPARCL1 WILD-TYPE  361   64
   clus
vv  SPARCL1 MUTATED SPARCL1 WILD-TYPE
  0              14               361
  1               1                64
[1] 2 2
[1] FALSE
D1524V8, binary
                   cls
clus                  0   1
  SPARCL1 MUTATED     1  14
  SPARCL1 WILD-TYPE 224 250
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SPARCL1 MUTATED      1   14
  SPARCL1 WILD-TYPE  224  250
        clus
vv       SPARCL1 MUTATED SPARCL1 WILD-TYPE
  FEMALE               1               224
  MALE                14               250
[1] 2 2
[1] FALSE
D1524V9, binary
                   cls
clus                  0   1
  SPARCL1 MUTATED    12   1
  SPARCL1 WILD-TYPE 338  21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SPARCL1 MUTATED     12    1
  SPARCL1 WILD-TYPE  338   21
     clus
vv    SPARCL1 MUTATED SPARCL1 WILD-TYPE
  NO               12               338
  YES               1                21
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SPARCL1 MUTATED                     10                             4
  SPARCL1 WILD-TYPE                  305                            43
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SPARCL1 MUTATED                       1                              0
  SPARCL1 WILD-TYPE                   105                             10
D1524V10, multiclass
                                clus
vv                               SPARCL1 MUTATED SPARCL1 WILD-TYPE
  COLON ADENOCARCINOMA                        10               305
  COLON MUCINOUS ADENOCARCINOMA                4                43
  RECTAL ADENOCARCINOMA                        1               105
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  SPARCL1 MUTATED     9   0   1   2
  SPARCL1 WILD-TYPE 336   4  30  23
D1524V11, multiclass
    clus
vv   SPARCL1 MUTATED SPARCL1 WILD-TYPE
  R0               9               336
  R1               0                 4
  R2               1                30
  RX               2                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1524V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SPARCL1 MUTATED                                  0     3
  SPARCL1 WILD-TYPE                                1     8
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  SPARCL1 MUTATED                           1     4
  SPARCL1 WILD-TYPE                        21   222
D1524V13, multiclass
                                  clus
vv                                 SPARCL1 MUTATED SPARCL1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          3                 8
  BLACK OR AFRICAN AMERICAN                      1                21
  WHITE                                          4               222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1525) Variable = NBPF14 MUTATION ANALYSIS
D1525V1, survival
                  sevent
clus2                0   1
  NBPF14 MUTATED     2   1
  NBPF14 WILD-TYPE 376  92
  NBPF14 MUTATED NBPF14 WILD-TYPE 
               3              468 
  NBPF14 MUTATED NBPF14 WILD-TYPE 
               1               92 
$`NBPF14 MUTATED`
TCGA-A6-5664 TCGA-CA-6718 TCGA-AF-6136 
       22.09        10.06        15.39 

$`NBPF14 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07        12.20        12.76        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       16.83        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  NBPF14 MUTATED NBPF14 WILD-TYPE 
           10.06             0.00 
  NBPF14 MUTATED NBPF14 WILD-TYPE 
           22.09           148.01 
  NBPF14 MUTATED NBPF14 WILD-TYPE 
          15.390           20.235 
[1] "10.1 - 22.1 (15.4)" "0.0 - 148.0 (20.2)"
[1] "hr=" "2.8"
D1525V2, continuous
D1525V3, binary
                  cls
clus                 0   1
  NBPF14 MUTATED     2   1
  NBPF14 WILD-TYPE 364 118
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NBPF14 MUTATED      2    1
  NBPF14 WILD-TYPE  364  118
        clus
vv       NBPF14 MUTATED NBPF14 WILD-TYPE
  COLON               2              364
  RECTUM              1              118
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NBPF14 MUTATED         0        0        0         1         0         0
  NBPF14 WILD-TYPE      91        1       32       137        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NBPF14 MUTATED           0          0          1          1        0
  NBPF14 WILD-TYPE        24         11         58         41       48
                  vv
clus               STAGE IVA STAGE IVB
  NBPF14 MUTATED           0         0
  NBPF14 WILD-TYPE        18         1
D1525V4, multiclass
            clus
vv           NBPF14 MUTATED NBPF14 WILD-TYPE
  STAGE I                 0               91
  STAGE IA                0                1
  STAGE II                0               32
  STAGE IIA               1              137
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              1               58
  STAGE IIIC              1               41
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  NBPF14 MUTATED     0   0   2   1
  NBPF14 WILD-TYPE  17  92 327  49
D1525V5, multiclass
    clus
vv   NBPF14 MUTATED NBPF14 WILD-TYPE
  T1              0               17
  T2              0               92
  T3              2              327
  T4              1               49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  NBPF14 MUTATED     1   1   1
  NBPF14 WILD-TYPE 286 112  86
D1525V6, multiclass
    clus
vv   NBPF14 MUTATED NBPF14 WILD-TYPE
  N0              1              286
  N1              1              112
  N2              1               86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1525V7, binary
                  cls
clus                 0   1
  NBPF14 MUTATED     1   0
  NBPF14 WILD-TYPE 374  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NBPF14 MUTATED      1    0
  NBPF14 WILD-TYPE  374   65
   clus
vv  NBPF14 MUTATED NBPF14 WILD-TYPE
  0              1              374
  1              0               65
[1] 2 2
[1] FALSE
D1525V8, binary
                  cls
clus                 0   1
  NBPF14 MUTATED     1   2
  NBPF14 WILD-TYPE 224 262
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NBPF14 MUTATED      1    2
  NBPF14 WILD-TYPE  224  262
        clus
vv       NBPF14 MUTATED NBPF14 WILD-TYPE
  FEMALE              1              224
  MALE                2              262
[1] 2 2
[1] FALSE
D1525V9, binary
                  cls
clus                 0   1
  NBPF14 MUTATED     2   1
  NBPF14 WILD-TYPE 348  21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NBPF14 MUTATED      2    1
  NBPF14 WILD-TYPE  348   21
     clus
vv    NBPF14 MUTATED NBPF14 WILD-TYPE
  NO               2              348
  YES              1               21
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  NBPF14 MUTATED                      2                             0
  NBPF14 WILD-TYPE                  313                            47
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  NBPF14 MUTATED                       1                              0
  NBPF14 WILD-TYPE                   105                             10
D1525V10, multiclass
                                clus
vv                               NBPF14 MUTATED NBPF14 WILD-TYPE
  COLON ADENOCARCINOMA                        2              313
  COLON MUCINOUS ADENOCARCINOMA               0               47
  RECTAL ADENOCARCINOMA                       1              105
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  NBPF14 MUTATED     0   0   0   1
  NBPF14 WILD-TYPE 345   4  31  24
D1525V11, multiclass
[1] "Remove cluster labels:" "NBPF14 MUTATED"        
clus
  NBPF14 MUTATED NBPF14 WILD-TYPE 
               1              404 
      TCGA-A6-2671       TCGA-A6-2672       TCGA-A6-2674       TCGA-A6-2676 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-A6-2677       TCGA-A6-2678       TCGA-A6-2683       TCGA-A6-3807 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-A6-3808       TCGA-A6-3809       TCGA-A6-3810       TCGA-A6-5657 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-A6-5659       TCGA-A6-5661       TCGA-A6-5665       TCGA-A6-6781 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-AA-3489       TCGA-AA-3492       TCGA-AA-3496       TCGA-AA-3502 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-AA-3510       TCGA-AA-3511       TCGA-AA-3514       TCGA-AA-3517 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-AA-3518       TCGA-AA-3519       TCGA-AA-3520       TCGA-AA-3521 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-AA-3522       TCGA-AA-3524       TCGA-AA-3525       TCGA-AA-3526 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-AA-3527       TCGA-AA-3529       TCGA-AA-3530       TCGA-AA-3531 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-AA-3532       TCGA-AA-3534       TCGA-AA-3538       TCGA-AA-3542 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-AA-3543       TCGA-AA-3544       TCGA-AA-3548       TCGA-AA-3549 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-AA-3552       TCGA-AA-3553       TCGA-AA-3554       TCGA-AA-3555 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-AA-3556       TCGA-AA-3558       TCGA-AA-3560       TCGA-AA-3561 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-AA-3562       TCGA-AA-3655       TCGA-AA-3660       TCGA-AA-3662 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-AA-3663       TCGA-AA-3664       TCGA-AA-3666       TCGA-AA-3667 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-AA-3672       TCGA-AA-3673       TCGA-AA-3678       TCGA-AA-3679 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-AA-3680       TCGA-AA-3681       TCGA-AA-3684       TCGA-AA-3685 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-AA-3688       TCGA-AA-3692       TCGA-AA-3693       TCGA-AA-3695 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-AA-3696       TCGA-AA-3697       TCGA-AA-3710       TCGA-AA-3712 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-AA-3713       TCGA-AA-3715       TCGA-AA-3811       TCGA-AA-3812 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-AA-3814       TCGA-AA-3815       TCGA-AA-3818       TCGA-AA-3819 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-AA-3821       TCGA-AA-3831       TCGA-AA-3833       TCGA-AA-3837 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-AA-3842       TCGA-AA-3844       TCGA-AA-3845       TCGA-AA-3846 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-AA-3848       TCGA-AA-3850       TCGA-AA-3851       TCGA-AA-3852 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-AA-3854       TCGA-AA-3855       TCGA-AA-3856       TCGA-AA-3858 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-AA-3860       TCGA-AA-3861       TCGA-AA-3864       TCGA-AA-3866 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-AA-3867       TCGA-AA-3869       TCGA-AA-3870       TCGA-AA-3872 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-AA-3875       TCGA-AA-3877       TCGA-AA-3930       TCGA-AA-3939 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-AA-3941       TCGA-AA-3947       TCGA-AA-3949       TCGA-AA-3950 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-AA-3952       TCGA-AA-3955       TCGA-AA-3956       TCGA-AA-3968 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-AA-3971       TCGA-AA-3972       TCGA-AA-3973       TCGA-AA-3975 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-AA-3976       TCGA-AA-3979       TCGA-AA-3984       TCGA-AA-3986 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-AA-3989       TCGA-AA-3994       TCGA-AA-A004       TCGA-AA-A00A 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-AA-A00D       TCGA-AA-A00E       TCGA-AA-A00F       TCGA-AA-A00J 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-AA-A00K       TCGA-AA-A00L       TCGA-AA-A00N       TCGA-AA-A00O 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-AA-A00Q       TCGA-AA-A00R       TCGA-AA-A00U       TCGA-AA-A00W 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-AA-A00Z       TCGA-AA-A010       TCGA-AA-A017       TCGA-AA-A01D 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-AA-A01F       TCGA-AA-A01G       TCGA-AA-A01I       TCGA-AA-A01K 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-AA-A01P       TCGA-AA-A01Q       TCGA-AA-A01R       TCGA-AA-A01S 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-AA-A01T       TCGA-AA-A01V       TCGA-AA-A01X       TCGA-AA-A01Z 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-AA-A022       TCGA-AA-A024       TCGA-AA-A029       TCGA-AA-A02F 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-AA-A02H       TCGA-AA-A02J       TCGA-AA-A02K       TCGA-AA-A02O 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-AA-A02W       TCGA-AA-A02Y       TCGA-AA-A03F       TCGA-AA-A03J 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-AD-5900       TCGA-AD-6548       TCGA-AD-6888       TCGA-AU-3779 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-AU-6004       TCGA-AY-4070       TCGA-AY-4071       TCGA-AY-5543 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-AY-6196       TCGA-AY-6197       TCGA-AY-6386       TCGA-AZ-4315 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-AZ-4681       TCGA-AZ-4682       TCGA-CA-5254       TCGA-CA-5255 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-CA-5796       TCGA-CA-5797       TCGA-CA-6715       TCGA-CA-6716 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-CA-6717       TCGA-CA-6719       TCGA-CK-4947       TCGA-CK-4948 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-CK-4950       TCGA-CK-4952       TCGA-CK-5912       TCGA-CK-5913 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-CK-5914       TCGA-CK-5915       TCGA-CK-5916       TCGA-CK-6746 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-CK-6747       TCGA-CK-6748       TCGA-CK-6751       TCGA-CM-4743 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-CM-4744       TCGA-CM-4746       TCGA-CM-4747       TCGA-CM-4752 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-CM-5341       TCGA-CM-5344       TCGA-CM-5348       TCGA-CM-5349 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-CM-5860       TCGA-CM-5861       TCGA-CM-5862       TCGA-CM-5863 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-CM-5864       TCGA-CM-5868       TCGA-CM-6161       TCGA-CM-6162 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-CM-6163       TCGA-CM-6164       TCGA-CM-6165       TCGA-CM-6166 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-CM-6167       TCGA-CM-6168       TCGA-CM-6169       TCGA-CM-6170 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-CM-6171       TCGA-CM-6172       TCGA-CM-6674       TCGA-CM-6675 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-CM-6676       TCGA-CM-6677       TCGA-CM-6678       TCGA-CM-6679 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-CM-6680       TCGA-D5-5537       TCGA-D5-5538       TCGA-D5-5539 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-D5-5540       TCGA-D5-5541       TCGA-D5-6529       TCGA-D5-6532 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-D5-6533       TCGA-D5-6534       TCGA-D5-6535       TCGA-D5-6536 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-D5-6537       TCGA-D5-6538       TCGA-D5-6539       TCGA-D5-6540 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-D5-6541       TCGA-D5-6898       TCGA-D5-6920       TCGA-D5-6922 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-D5-6923       TCGA-D5-6924       TCGA-D5-6926       TCGA-D5-6927 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-D5-6928       TCGA-D5-6929       TCGA-D5-6930       TCGA-D5-6931 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-D5-6932       TCGA-D5-7000       TCGA-F4-6459       TCGA-F4-6460 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-F4-6569       TCGA-F4-6570       TCGA-F4-6703       TCGA-F4-6704 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-F4-6805       TCGA-F4-6806       TCGA-F4-6807       TCGA-F4-6808 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-F4-6809       TCGA-F4-6854       TCGA-F4-6855       TCGA-F4-6856 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-G4-6293       TCGA-G4-6299       TCGA-G4-6303       TCGA-G4-6304 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-G4-6306       TCGA-G4-6307       TCGA-G4-6309       TCGA-G4-6310 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-G4-6315       TCGA-G4-6317       TCGA-G4-6321       TCGA-G4-6323 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-G4-6586       TCGA-G4-6588       TCGA-G4-6625       TCGA-G4-6626 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-G4-6628       TCGA-AF-2687       TCGA-AF-2689       TCGA-AF-2691 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-AF-2692       TCGA-AF-3400       TCGA-AF-3913       TCGA-AF-4110 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-AF-5654       TCGA-AF-6655       TCGA-AG-3574       TCGA-AG-3575 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-AG-3578       TCGA-AG-3580       TCGA-AG-3581       TCGA-AG-3582 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-AG-3583       TCGA-AG-3584       TCGA-AG-3586       TCGA-AG-3587 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-AG-3593       TCGA-AG-3594       TCGA-AG-3598       TCGA-AG-3599 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-AG-3600       TCGA-AG-3601       TCGA-AG-3602       TCGA-AG-3605 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-AG-3608       TCGA-AG-3609       TCGA-AG-3611       TCGA-AG-3612 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-AG-3726       TCGA-AG-3727       TCGA-AG-3731       TCGA-AG-3732 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-AG-3742       TCGA-AG-3878       TCGA-AG-3882       TCGA-AG-3883 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-AG-3885       TCGA-AG-3887       TCGA-AG-3890       TCGA-AG-3892 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-AG-3893       TCGA-AG-3894       TCGA-AG-3896       TCGA-AG-3898 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-AG-3901       TCGA-AG-3902       TCGA-AG-3909       TCGA-AG-3999 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-AG-4001       TCGA-AG-4005       TCGA-AG-4007       TCGA-AG-4008 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-AG-4015       TCGA-AG-A002       TCGA-AG-A008       TCGA-AG-A00C 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-AG-A00H       TCGA-AG-A00Y       TCGA-AG-A011       TCGA-AG-A014 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-AG-A015       TCGA-AG-A016       TCGA-AG-A01L       TCGA-AG-A01W 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-AG-A01Y       TCGA-AG-A020       TCGA-AG-A025       TCGA-AG-A026 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-AG-A02G       TCGA-AG-A02N       TCGA-AG-A02X       TCGA-AG-A032 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-AG-A036       TCGA-AH-6549       TCGA-AH-6643       TCGA-CL-5917 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-CL-5918       TCGA-DC-5337       TCGA-DC-5869       TCGA-DC-6155 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-DC-6157       TCGA-DC-6158       TCGA-DC-6160       TCGA-DC-6681 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-DC-6682       TCGA-DC-6683       TCGA-DT-5265       TCGA-EF-5830 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-EI-6506       TCGA-EI-6507       TCGA-EI-6508       TCGA-EI-6510 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-F5-6464       TCGA-F5-6465       TCGA-F5-6571       TCGA-F5-6702 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-F5-6812       TCGA-F5-6813       TCGA-G5-6235       TCGA-G5-6641 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
D1525V12, continuous
[1] "Remove cluster labels:" "NBPF14 MUTATED"        
clus
  NBPF14 MUTATED NBPF14 WILD-TYPE 
               2              456 
      TCGA-A6-2671       TCGA-A6-2672       TCGA-A6-2674       TCGA-A6-2676 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-A6-2677       TCGA-A6-2678       TCGA-A6-2683       TCGA-A6-3807 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-A6-3808       TCGA-A6-3809       TCGA-A6-3810       TCGA-A6-4105 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-A6-5656       TCGA-A6-5657       TCGA-A6-5659       TCGA-A6-5660 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-A6-5661       TCGA-A6-5662       TCGA-A6-5665       TCGA-A6-5666 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-A6-6137       TCGA-A6-6138       TCGA-A6-6141       TCGA-A6-6142 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-A6-6648       TCGA-A6-6649       TCGA-A6-6651       TCGA-A6-6652 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-A6-6653       TCGA-A6-6654       TCGA-A6-6780       TCGA-A6-6781 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-A6-6782       TCGA-AA-3489       TCGA-AA-3492       TCGA-AA-3496 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-AA-3502       TCGA-AA-3510       TCGA-AA-3511       TCGA-AA-3514 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-AA-3516       TCGA-AA-3517       TCGA-AA-3518       TCGA-AA-3519 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-AA-3520       TCGA-AA-3521       TCGA-AA-3522       TCGA-AA-3524 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-AA-3525       TCGA-AA-3526       TCGA-AA-3527       TCGA-AA-3529 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-AA-3530       TCGA-AA-3531       TCGA-AA-3532       TCGA-AA-3534 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-AA-3538       TCGA-AA-3542       TCGA-AA-3543       TCGA-AA-3544 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-AA-3548       TCGA-AA-3549       TCGA-AA-3552       TCGA-AA-3553 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-AA-3554       TCGA-AA-3555       TCGA-AA-3556       TCGA-AA-3558 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-AA-3560       TCGA-AA-3562       TCGA-AA-3655       TCGA-AA-3660 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-AA-3662       TCGA-AA-3663       TCGA-AA-3664       TCGA-AA-3666 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-AA-3667       TCGA-AA-3672       TCGA-AA-3673       TCGA-AA-3678 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-AA-3679       TCGA-AA-3680       TCGA-AA-3681       TCGA-AA-3684 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-AA-3685       TCGA-AA-3688       TCGA-AA-3692       TCGA-AA-3693 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-AA-3695       TCGA-AA-3696       TCGA-AA-3697       TCGA-AA-3710 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-AA-3712       TCGA-AA-3713       TCGA-AA-3715       TCGA-AA-3811 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-AA-3812       TCGA-AA-3814       TCGA-AA-3815       TCGA-AA-3818 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-AA-3819       TCGA-AA-3821       TCGA-AA-3831       TCGA-AA-3833 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-AA-3837       TCGA-AA-3842       TCGA-AA-3844       TCGA-AA-3845 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-AA-3846       TCGA-AA-3848       TCGA-AA-3850       TCGA-AA-3851 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-AA-3852       TCGA-AA-3854       TCGA-AA-3855       TCGA-AA-3856 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-AA-3858       TCGA-AA-3860       TCGA-AA-3861       TCGA-AA-3864 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-AA-3866       TCGA-AA-3867       TCGA-AA-3869       TCGA-AA-3870 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-AA-3872       TCGA-AA-3875       TCGA-AA-3877       TCGA-AA-3930 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-AA-3939       TCGA-AA-3941       TCGA-AA-3947       TCGA-AA-3949 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-AA-3950       TCGA-AA-3952       TCGA-AA-3955       TCGA-AA-3956 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-AA-3966       TCGA-AA-3968       TCGA-AA-3971       TCGA-AA-3972 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-AA-3973       TCGA-AA-3975       TCGA-AA-3976       TCGA-AA-3977 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-AA-3979       TCGA-AA-3980       TCGA-AA-3982       TCGA-AA-3984 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-AA-3986       TCGA-AA-3989       TCGA-AA-3994       TCGA-AA-A004 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-AA-A00A       TCGA-AA-A00D       TCGA-AA-A00E       TCGA-AA-A00F 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-AA-A00J       TCGA-AA-A00K       TCGA-AA-A00L       TCGA-AA-A00N 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-AA-A00O       TCGA-AA-A00Q       TCGA-AA-A00R       TCGA-AA-A00U 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-AA-A00W       TCGA-AA-A00Z       TCGA-AA-A010       TCGA-AA-A017 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-AA-A01D       TCGA-AA-A01F       TCGA-AA-A01G       TCGA-AA-A01I 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-AA-A01K       TCGA-AA-A01P       TCGA-AA-A01Q       TCGA-AA-A01R 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-AA-A01S       TCGA-AA-A01T       TCGA-AA-A01V       TCGA-AA-A01X 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-AA-A01Z       TCGA-AA-A022       TCGA-AA-A024       TCGA-AA-A029 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-AA-A02F       TCGA-AA-A02H       TCGA-AA-A02J       TCGA-AA-A02K 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-AA-A02O       TCGA-AA-A02W       TCGA-AA-A02Y       TCGA-AA-A03F 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-AA-A03J       TCGA-AD-5900       TCGA-AD-6548       TCGA-AD-6888 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-AD-6889       TCGA-AD-6890       TCGA-AD-6895       TCGA-AD-6899 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-AD-6901       TCGA-AD-6963       TCGA-AD-6964       TCGA-AD-6965 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-AU-3779       TCGA-AU-6004       TCGA-AY-4070       TCGA-AY-4071 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-AY-5543       TCGA-AY-6196       TCGA-AY-6197       TCGA-AY-6386 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-AZ-4323       TCGA-AZ-4616       TCGA-AZ-4682       TCGA-AZ-5403 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-AZ-5407       TCGA-AZ-6598       TCGA-AZ-6599       TCGA-AZ-6600 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-AZ-6601       TCGA-AZ-6603       TCGA-AZ-6605       TCGA-AZ-6606 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-AZ-6607       TCGA-AZ-6608       TCGA-CK-4947       TCGA-CK-4948 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-CK-4950       TCGA-CK-4952       TCGA-CM-4743       TCGA-CM-4744 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-CM-4746       TCGA-CM-4747       TCGA-CM-4752       TCGA-CM-5341 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-CM-5344       TCGA-CM-5348       TCGA-CM-5349       TCGA-CM-5860 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-CM-5861       TCGA-CM-5862       TCGA-CM-5863       TCGA-CM-5864 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-CM-5868       TCGA-CM-6161       TCGA-CM-6162       TCGA-CM-6163 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-CM-6164       TCGA-CM-6165       TCGA-CM-6166       TCGA-CM-6167 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-CM-6168       TCGA-CM-6169       TCGA-CM-6170       TCGA-CM-6171 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-CM-6172       TCGA-CM-6674       TCGA-CM-6675       TCGA-CM-6676 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-CM-6677       TCGA-CM-6678       TCGA-CM-6679       TCGA-CM-6680 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-D5-5537       TCGA-D5-5538       TCGA-D5-5539       TCGA-D5-5540 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-D5-5541       TCGA-D5-6529       TCGA-D5-6532       TCGA-D5-6533 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-D5-6534       TCGA-D5-6535       TCGA-D5-6536       TCGA-D5-6537 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-D5-6538       TCGA-D5-6539       TCGA-D5-6540       TCGA-D5-6541 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-D5-6898       TCGA-D5-6920       TCGA-D5-6922       TCGA-D5-6923 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-D5-6924       TCGA-D5-6926       TCGA-D5-6927       TCGA-D5-6928 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-D5-6929       TCGA-D5-6930       TCGA-D5-6931       TCGA-D5-6932 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-D5-7000       TCGA-DM-A0X9       TCGA-DM-A0XD       TCGA-DM-A0XF 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-DM-A1D0       TCGA-DM-A1D4       TCGA-DM-A1D6       TCGA-DM-A1D7 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-DM-A1D8       TCGA-DM-A1D9       TCGA-DM-A1DA       TCGA-DM-A1DB 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-DM-A1HA       TCGA-DM-A1HB       TCGA-DM-A282       TCGA-DM-A285 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-DM-A28C       TCGA-DM-A28E       TCGA-DM-A28F       TCGA-DM-A28G 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-DM-A28H       TCGA-DM-A28K       TCGA-F4-6459       TCGA-F4-6460 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-F4-6569       TCGA-F4-6570       TCGA-F4-6703       TCGA-F4-6704 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-F4-6806       TCGA-F4-6807       TCGA-F4-6808       TCGA-F4-6809 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-F4-6854       TCGA-F4-6855       TCGA-F4-6856       TCGA-G4-6293 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-G4-6299       TCGA-G4-6303       TCGA-G4-6304       TCGA-G4-6306 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-G4-6307       TCGA-G4-6309       TCGA-G4-6310       TCGA-G4-6315 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-G4-6317       TCGA-G4-6321       TCGA-G4-6323       TCGA-G4-6586 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-G4-6588       TCGA-G4-6625       TCGA-G4-6626       TCGA-G4-6628 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-AF-2687       TCGA-AF-2689       TCGA-AF-2691       TCGA-AF-2692 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-AF-2693       TCGA-AF-3400       TCGA-AF-3913       TCGA-AF-4110 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-AF-5654       TCGA-AF-6655       TCGA-AF-6672       TCGA-AG-3574 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-AG-3575       TCGA-AG-3578       TCGA-AG-3580       TCGA-AG-3581 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-AG-3582       TCGA-AG-3583       TCGA-AG-3584       TCGA-AG-3586 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-AG-3587       TCGA-AG-3593       TCGA-AG-3594       TCGA-AG-3598 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-AG-3599       TCGA-AG-3600       TCGA-AG-3601       TCGA-AG-3602 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-AG-3605       TCGA-AG-3608       TCGA-AG-3609       TCGA-AG-3611 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-AG-3612       TCGA-AG-3726       TCGA-AG-3727       TCGA-AG-3731 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-AG-3732       TCGA-AG-3742       TCGA-AG-3878       TCGA-AG-3881 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-AG-3882       TCGA-AG-3883       TCGA-AG-3885       TCGA-AG-3887 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-AG-3890       TCGA-AG-3892       TCGA-AG-3893       TCGA-AG-3894 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-AG-3896       TCGA-AG-3898       TCGA-AG-3901       TCGA-AG-3902 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-AG-3909       TCGA-AG-3999       TCGA-AG-4001       TCGA-AG-4005 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-AG-4007       TCGA-AG-4008       TCGA-AG-4015       TCGA-AG-A002 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-AG-A008       TCGA-AG-A00C       TCGA-AG-A00H       TCGA-AG-A00Y 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-AG-A011       TCGA-AG-A014       TCGA-AG-A015       TCGA-AG-A016 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-AG-A01L       TCGA-AG-A01W       TCGA-AG-A01Y       TCGA-AG-A020 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-AG-A025       TCGA-AG-A026       TCGA-AG-A02G       TCGA-AG-A02N 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-AG-A02X       TCGA-AG-A032       TCGA-AG-A036       TCGA-AH-6544 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-AH-6547       TCGA-AH-6643       TCGA-AH-6644       TCGA-CI-6622 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-DC-5337       TCGA-DC-5869       TCGA-DC-6155       TCGA-DC-6157 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-DC-6158       TCGA-DC-6160       TCGA-DC-6681       TCGA-DC-6682 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-DC-6683       TCGA-DY-A0XA       TCGA-DY-A1DC       TCGA-DY-A1DD 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-DY-A1DF       TCGA-DY-A1DG       TCGA-DY-A1H8       TCGA-EI-6506 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-EI-6507       TCGA-EI-6508       TCGA-EI-6510       TCGA-F5-6464 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-F5-6465       TCGA-F5-6571       TCGA-F5-6702       TCGA-F5-6811 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
      TCGA-F5-6812       TCGA-F5-6813       TCGA-G5-6235       TCGA-G5-6641 
"NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" "NBPF14 WILD-TYPE" 
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NBPF14 MUTATED                                  0     1
  NBPF14 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  NBPF14 MUTATED                           1     1
  NBPF14 WILD-TYPE                        21   225
D1525V13, multiclass
                                  clus
vv                                 NBPF14 MUTATED NBPF14 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                         1              225
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1526) Variable = SLC44A1 MUTATION ANALYSIS
D1526V1, survival
                   sevent
clus2                 0   1
  SLC44A1 MUTATED     8   1
  SLC44A1 WILD-TYPE 370  92
  SLC44A1 MUTATED SLC44A1 WILD-TYPE 
                9               462 
  SLC44A1 MUTATED SLC44A1 WILD-TYPE 
                1                92 
$`SLC44A1 MUTATED`
TCGA-AA-3821 TCGA-AA-3844 TCGA-AD-6964 TCGA-AY-6386 TCGA-CA-6717 TCGA-CM-4743 
        1.02        14.93        10.88        17.82        12.76        23.05 
TCGA-D5-6535 TCGA-G4-6323 TCGA-AG-A002 
       15.12        13.78        20.98 

$`SLC44A1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3846 
       17.98        15.95        38.99        37.02         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07        12.20        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6586 
       85.48        63.62        61.91        36.00        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  SLC44A1 MUTATED SLC44A1 WILD-TYPE 
             1.02              0.00 
  SLC44A1 MUTATED SLC44A1 WILD-TYPE 
            23.05            148.01 
  SLC44A1 MUTATED SLC44A1 WILD-TYPE 
            14.93             20.73 
[1] "1.0 - 23.1 (14.9)"  "0.0 - 148.0 (20.7)"
[1] "hr=" "1"  
D1526V2, continuous
D1526V3, binary
                   cls
clus                  0   1
  SLC44A1 MUTATED     9   1
  SLC44A1 WILD-TYPE 357 118
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC44A1 MUTATED      9    1
  SLC44A1 WILD-TYPE  357  118
        clus
vv       SLC44A1 MUTATED SLC44A1 WILD-TYPE
  COLON                9               357
  RECTUM               1               118
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SLC44A1 MUTATED         2        1        0         3         0         0
  SLC44A1 WILD-TYPE      89        0       32       135        10         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC44A1 MUTATED           0          0          2          1        0
  SLC44A1 WILD-TYPE        24         11         57         41       48
                   vv
clus                STAGE IVA STAGE IVB
  SLC44A1 MUTATED           0         0
  SLC44A1 WILD-TYPE        18         1
D1526V4, multiclass
            clus
vv           SLC44A1 MUTATED SLC44A1 WILD-TYPE
  STAGE I                  2                89
  STAGE IA                 1                 0
  STAGE II                 0                32
  STAGE IIA                3               135
  STAGE IIB                0                10
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               0                11
  STAGE IIIB               2                57
  STAGE IIIC               1                41
  STAGE IV                 0                48
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  SLC44A1 MUTATED     0   2   6   1
  SLC44A1 WILD-TYPE  17  90 323  49
D1526V5, multiclass
    clus
vv   SLC44A1 MUTATED SLC44A1 WILD-TYPE
  T1               0                17
  T2               2                90
  T3               6               323
  T4               1                49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  SLC44A1 MUTATED     6   2   2
  SLC44A1 WILD-TYPE 281 111  85
D1526V6, multiclass
    clus
vv   SLC44A1 MUTATED SLC44A1 WILD-TYPE
  N0               6               281
  N1               2               111
  N2               2                85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1526V7, binary
                   cls
clus                  0   1
  SLC44A1 MUTATED     7   0
  SLC44A1 WILD-TYPE 368  65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC44A1 MUTATED      7    0
  SLC44A1 WILD-TYPE  368   65
   clus
vv  SLC44A1 MUTATED SLC44A1 WILD-TYPE
  0               7               368
  1               0                65
[1] 2 2
[1] FALSE
D1526V8, binary
                   cls
clus                  0   1
  SLC44A1 MUTATED     5   5
  SLC44A1 WILD-TYPE 220 259
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC44A1 MUTATED      5    5
  SLC44A1 WILD-TYPE  220  259
        clus
vv       SLC44A1 MUTATED SLC44A1 WILD-TYPE
  FEMALE               5               220
  MALE                 5               259
[1] 2 2
[1] FALSE
D1526V9, binary
                   cls
clus                  0   1
  SLC44A1 MUTATED     8   1
  SLC44A1 WILD-TYPE 342  21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC44A1 MUTATED      8    1
  SLC44A1 WILD-TYPE  342   21
     clus
vv    SLC44A1 MUTATED SLC44A1 WILD-TYPE
  NO                8               342
  YES               1                21
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SLC44A1 MUTATED                      7                             2
  SLC44A1 WILD-TYPE                  308                            45
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SLC44A1 MUTATED                       1                              0
  SLC44A1 WILD-TYPE                   105                             10
D1526V10, multiclass
                                clus
vv                               SLC44A1 MUTATED SLC44A1 WILD-TYPE
  COLON ADENOCARCINOMA                         7               308
  COLON MUCINOUS ADENOCARCINOMA                2                45
  RECTAL ADENOCARCINOMA                        1               105
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  SLC44A1 MUTATED     7   0   0   2
  SLC44A1 WILD-TYPE 338   4  31  23
D1526V11, multiclass
    clus
vv   SLC44A1 MUTATED SLC44A1 WILD-TYPE
  R0               7               338
  R1               0                 4
  R2               0                31
  RX               2                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1526V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SLC44A1 MUTATED                                  0     1
  SLC44A1 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  SLC44A1 MUTATED                           2     3
  SLC44A1 WILD-TYPE                        20   223
D1526V13, multiclass
                                  clus
vv                                 SLC44A1 MUTATED SLC44A1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                10
  BLACK OR AFRICAN AMERICAN                      2                20
  WHITE                                          3               223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1527) Variable = C14ORF105 MUTATION ANALYSIS
D1527V1, survival
                     sevent
clus2                   0   1
  C14ORF105 MUTATED     3   0
  C14ORF105 WILD-TYPE 375  93
  C14ORF105 MUTATED C14ORF105 WILD-TYPE 
                  3                 468 
  C14ORF105 MUTATED C14ORF105 WILD-TYPE 
                  0                  93 
$`C14ORF105 MUTATED`
TCGA-AA-3977 TCGA-AA-A010 TCGA-D5-6928 
       25.02        34.98        11.64 

$`C14ORF105 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  C14ORF105 MUTATED C14ORF105 WILD-TYPE 
              11.64                0.00 
  C14ORF105 MUTATED C14ORF105 WILD-TYPE 
              34.98              148.01 
  C14ORF105 MUTATED C14ORF105 WILD-TYPE 
             25.020              20.155 
[1] "11.6 - 35.0 (25.0)" "0.0 - 148.0 (20.2)"
[1] "hr="     "3300000"
D1527V2, continuous
D1527V3, binary
                     cls
clus                    0   1
  C14ORF105 MUTATED     3   0
  C14ORF105 WILD-TYPE 363 119
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  C14ORF105 MUTATED      3    0
  C14ORF105 WILD-TYPE  363  119
        clus
vv       C14ORF105 MUTATED C14ORF105 WILD-TYPE
  COLON                  3                 363
  RECTUM                 0                 119
[1] 2 2
[1] FALSE
                     vv
clus                  STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  C14ORF105 MUTATED         0        0        0         1         1         0
  C14ORF105 WILD-TYPE      91        1       32       137         9         1
                     vv
clus                  STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C14ORF105 MUTATED           0          0          0          0        0
  C14ORF105 WILD-TYPE        24         11         59         42       48
                     vv
clus                  STAGE IVA STAGE IVB
  C14ORF105 MUTATED           0         0
  C14ORF105 WILD-TYPE        18         1
D1527V4, multiclass
[1] "Remove cluster labels:" "C14ORF105 MUTATED"     
clus
  C14ORF105 MUTATED C14ORF105 WILD-TYPE 
                  2                 474 
         TCGA-A6-2671          TCGA-A6-2672          TCGA-A6-2674 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-A6-2676          TCGA-A6-2677          TCGA-A6-2678 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-A6-2683          TCGA-A6-3807          TCGA-A6-3808 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-A6-3809          TCGA-A6-3810          TCGA-A6-4105 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-A6-5656          TCGA-A6-5657          TCGA-A6-5659 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-A6-5660          TCGA-A6-5661          TCGA-A6-5662 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-A6-5664          TCGA-A6-5665          TCGA-A6-5666 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-A6-6137          TCGA-A6-6138          TCGA-A6-6141 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-A6-6142          TCGA-A6-6648          TCGA-A6-6649 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-A6-6651          TCGA-A6-6652          TCGA-A6-6653 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-A6-6654          TCGA-A6-6780          TCGA-A6-6781 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-A6-6782          TCGA-AA-3489          TCGA-AA-3492 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3496          TCGA-AA-3502          TCGA-AA-3510 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3511          TCGA-AA-3514          TCGA-AA-3516 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3517          TCGA-AA-3518          TCGA-AA-3519 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3520          TCGA-AA-3521          TCGA-AA-3522 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3524          TCGA-AA-3525          TCGA-AA-3526 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3527          TCGA-AA-3529          TCGA-AA-3530 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3531          TCGA-AA-3532          TCGA-AA-3534 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3538          TCGA-AA-3542          TCGA-AA-3543 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3544          TCGA-AA-3548          TCGA-AA-3549 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3552          TCGA-AA-3553          TCGA-AA-3554 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3555          TCGA-AA-3556          TCGA-AA-3558 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3560          TCGA-AA-3561          TCGA-AA-3562 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3655          TCGA-AA-3660          TCGA-AA-3662 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3663          TCGA-AA-3664          TCGA-AA-3666 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3667          TCGA-AA-3672          TCGA-AA-3673 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3678          TCGA-AA-3679          TCGA-AA-3680 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3681          TCGA-AA-3684          TCGA-AA-3685 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3688          TCGA-AA-3692          TCGA-AA-3693 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3695          TCGA-AA-3696          TCGA-AA-3697 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3710          TCGA-AA-3712          TCGA-AA-3713 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3715          TCGA-AA-3811          TCGA-AA-3812 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3814          TCGA-AA-3815          TCGA-AA-3818 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3819          TCGA-AA-3821          TCGA-AA-3831 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3833          TCGA-AA-3837          TCGA-AA-3842 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3844          TCGA-AA-3845          TCGA-AA-3846 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3848          TCGA-AA-3850          TCGA-AA-3851 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3852          TCGA-AA-3854          TCGA-AA-3855 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3856          TCGA-AA-3858          TCGA-AA-3860 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3861          TCGA-AA-3864          TCGA-AA-3866 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3867          TCGA-AA-3869          TCGA-AA-3870 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3872          TCGA-AA-3875          TCGA-AA-3877 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3930          TCGA-AA-3939          TCGA-AA-3941 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3947          TCGA-AA-3949          TCGA-AA-3950 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3952          TCGA-AA-3955          TCGA-AA-3956 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3966          TCGA-AA-3968          TCGA-AA-3971 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3972          TCGA-AA-3973          TCGA-AA-3975 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3976          TCGA-AA-3979          TCGA-AA-3980 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3982          TCGA-AA-3984          TCGA-AA-3986 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3989          TCGA-AA-3994          TCGA-AA-A004 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-A00A          TCGA-AA-A00D          TCGA-AA-A00E 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-A00F          TCGA-AA-A00J          TCGA-AA-A00K 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-A00L          TCGA-AA-A00N          TCGA-AA-A00O 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-A00Q          TCGA-AA-A00R          TCGA-AA-A00U 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-A00W          TCGA-AA-A00Z          TCGA-AA-A017 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-A01D          TCGA-AA-A01F          TCGA-AA-A01G 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-A01I          TCGA-AA-A01K          TCGA-AA-A01P 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-A01Q          TCGA-AA-A01R          TCGA-AA-A01S 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-A01T          TCGA-AA-A01V          TCGA-AA-A01X 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-A01Z          TCGA-AA-A022          TCGA-AA-A024 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-A029          TCGA-AA-A02F          TCGA-AA-A02H 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-A02J          TCGA-AA-A02K          TCGA-AA-A02O 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-A02W          TCGA-AA-A02Y          TCGA-AA-A03F 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-A03J          TCGA-AD-5900          TCGA-AD-6548 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AD-6888          TCGA-AD-6889          TCGA-AD-6899 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AU-3779          TCGA-AU-6004          TCGA-AY-4070 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AY-4071          TCGA-AY-5543          TCGA-AY-6196 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AY-6197          TCGA-AY-6386          TCGA-AZ-4315 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AZ-4323          TCGA-AZ-4616          TCGA-AZ-4681 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AZ-4682          TCGA-AZ-5403          TCGA-AZ-5407 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AZ-6598          TCGA-AZ-6599          TCGA-AZ-6600 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AZ-6601          TCGA-AZ-6605          TCGA-AZ-6606 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AZ-6607          TCGA-AZ-6608          TCGA-CA-5254 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-CA-5255          TCGA-CA-5796          TCGA-CA-5797 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-CA-6715          TCGA-CA-6716          TCGA-CA-6717 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-CA-6718          TCGA-CA-6719          TCGA-CK-4947 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-CK-4948          TCGA-CK-4950          TCGA-CK-4952 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-CK-5912          TCGA-CK-5913          TCGA-CK-5914 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-CK-5915          TCGA-CK-5916          TCGA-CK-6746 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-CK-6747          TCGA-CK-6748          TCGA-CK-6751 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-CM-4743          TCGA-CM-4744          TCGA-CM-4746 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-CM-4747          TCGA-CM-4752          TCGA-CM-5341 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-CM-5344          TCGA-CM-5348          TCGA-CM-5349 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-CM-5860          TCGA-CM-5861          TCGA-CM-5862 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-CM-5863          TCGA-CM-5864          TCGA-CM-5868 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-CM-6161          TCGA-CM-6162          TCGA-CM-6163 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-CM-6164          TCGA-CM-6165          TCGA-CM-6166 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-CM-6167          TCGA-CM-6168          TCGA-CM-6169 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-CM-6170          TCGA-CM-6171          TCGA-CM-6172 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-CM-6674          TCGA-CM-6675          TCGA-CM-6676 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-CM-6677          TCGA-CM-6678          TCGA-CM-6679 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-CM-6680          TCGA-D5-5537          TCGA-D5-5538 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-D5-5539          TCGA-D5-5540          TCGA-D5-5541 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-D5-6529          TCGA-D5-6532          TCGA-D5-6533 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-D5-6534          TCGA-D5-6535          TCGA-D5-6536 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-D5-6537          TCGA-D5-6538          TCGA-D5-6539 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-D5-6540          TCGA-D5-6541          TCGA-D5-6898 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-D5-6920          TCGA-D5-6922          TCGA-D5-6923 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-D5-6924          TCGA-D5-6926          TCGA-D5-6927 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-D5-6929          TCGA-D5-6930          TCGA-D5-6931 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-D5-6932          TCGA-D5-7000          TCGA-DM-A0X9 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-DM-A0XD          TCGA-DM-A0XF          TCGA-DM-A1D0 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-DM-A1D4          TCGA-DM-A1D6          TCGA-DM-A1D7 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-DM-A1D9          TCGA-DM-A1DA          TCGA-DM-A1DB 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-DM-A1HA          TCGA-DM-A1HB          TCGA-DM-A282 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-DM-A285          TCGA-DM-A28C          TCGA-DM-A28E 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-DM-A28F          TCGA-DM-A28G          TCGA-DM-A28H 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-DM-A28K          TCGA-F4-6459          TCGA-F4-6460 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-F4-6569          TCGA-F4-6570          TCGA-F4-6703 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-F4-6704          TCGA-F4-6805          TCGA-F4-6806 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-F4-6807          TCGA-F4-6808          TCGA-F4-6809 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-F4-6854          TCGA-F4-6855          TCGA-F4-6856 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-G4-6293          TCGA-G4-6299          TCGA-G4-6303 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-G4-6304          TCGA-G4-6306          TCGA-G4-6307 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-G4-6309          TCGA-G4-6310          TCGA-G4-6315 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-G4-6317          TCGA-G4-6321          TCGA-G4-6323 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-G4-6586          TCGA-G4-6588          TCGA-G4-6625 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-G4-6626          TCGA-G4-6628          TCGA-AF-2687 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AF-2689          TCGA-AF-2691          TCGA-AF-2692 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AF-2693          TCGA-AF-3400          TCGA-AF-3913 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AF-4110          TCGA-AF-5654          TCGA-AF-6136 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AF-6655          TCGA-AF-6672          TCGA-AG-3574 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AG-3575          TCGA-AG-3578          TCGA-AG-3580 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AG-3581          TCGA-AG-3582          TCGA-AG-3583 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AG-3584          TCGA-AG-3586          TCGA-AG-3587 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AG-3593          TCGA-AG-3594          TCGA-AG-3598 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AG-3599          TCGA-AG-3600          TCGA-AG-3601 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AG-3602          TCGA-AG-3605          TCGA-AG-3608 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AG-3609          TCGA-AG-3611          TCGA-AG-3612 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AG-3726          TCGA-AG-3727          TCGA-AG-3731 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AG-3732          TCGA-AG-3742          TCGA-AG-3878 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AG-3881          TCGA-AG-3882          TCGA-AG-3883 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AG-3885          TCGA-AG-3887          TCGA-AG-3890 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AG-3892          TCGA-AG-3893          TCGA-AG-3894 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AG-3896          TCGA-AG-3898          TCGA-AG-3901 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AG-3902          TCGA-AG-3909          TCGA-AG-3999 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AG-4001          TCGA-AG-4005          TCGA-AG-4007 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AG-4008          TCGA-AG-4015          TCGA-AG-A002 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AG-A008          TCGA-AG-A00C          TCGA-AG-A00H 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AG-A00Y          TCGA-AG-A011          TCGA-AG-A014 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AG-A015          TCGA-AG-A016          TCGA-AG-A01L 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AG-A01W          TCGA-AG-A01Y          TCGA-AG-A020 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AG-A025          TCGA-AG-A026          TCGA-AG-A02G 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AG-A02N          TCGA-AG-A02X          TCGA-AG-A032 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AG-A036          TCGA-AH-6643          TCGA-CI-6619 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-CI-6620          TCGA-CI-6621          TCGA-CI-6622 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-CI-6624          TCGA-CL-5917          TCGA-CL-5918 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-DC-5337          TCGA-DC-5869          TCGA-DC-6155 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-DC-6157          TCGA-DC-6158          TCGA-DC-6160 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-DC-6681          TCGA-DC-6682          TCGA-DC-6683 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-DT-5265          TCGA-DY-A0XA          TCGA-DY-A1DC 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-DY-A1DD          TCGA-DY-A1DF          TCGA-DY-A1DG 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-DY-A1H8          TCGA-EF-5830          TCGA-EI-6506 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-EI-6507          TCGA-EI-6508          TCGA-EI-6510 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-F5-6464          TCGA-F5-6465          TCGA-F5-6571 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-F5-6702          TCGA-F5-6811          TCGA-F5-6812 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-F5-6813          TCGA-G5-6235          TCGA-G5-6641 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
                     vv
clus                   T1  T2  T3  T4
  C14ORF105 MUTATED     0   1   1   1
  C14ORF105 WILD-TYPE  17  91 328  49
D1527V5, multiclass
    clus
vv   C14ORF105 MUTATED C14ORF105 WILD-TYPE
  T1                 0                  17
  T2                 1                  91
  T3                 1                 328
  T4                 1                  49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                   N0  N1  N2
  C14ORF105 MUTATED     3   0   0
  C14ORF105 WILD-TYPE 284 113  87
D1527V6, multiclass
    clus
vv   C14ORF105 MUTATED C14ORF105 WILD-TYPE
  N0                 3                 284
  N1                 0                 113
  N2                 0                  87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1527V7, binary
                     cls
clus                    0   1
  C14ORF105 MUTATED     2   0
  C14ORF105 WILD-TYPE 373  65
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  C14ORF105 MUTATED      2    0
  C14ORF105 WILD-TYPE  373   65
   clus
vv  C14ORF105 MUTATED C14ORF105 WILD-TYPE
  0                 2                 373
  1                 0                  65
[1] 2 2
[1] FALSE
D1527V8, binary
                     cls
clus                    0   1
  C14ORF105 MUTATED     1   2
  C14ORF105 WILD-TYPE 224 262
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  C14ORF105 MUTATED      1    2
  C14ORF105 WILD-TYPE  224  262
        clus
vv       C14ORF105 MUTATED C14ORF105 WILD-TYPE
  FEMALE                 1                 224
  MALE                   2                 262
[1] 2 2
[1] FALSE
D1527V9, binary
                     cls
clus                    0   1
  C14ORF105 MUTATED     3   0
  C14ORF105 WILD-TYPE 347  22
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  C14ORF105 MUTATED      3    0
  C14ORF105 WILD-TYPE  347   22
     clus
vv    C14ORF105 MUTATED C14ORF105 WILD-TYPE
  NO                  3                 347
  YES                 0                  22
[1] 2 2
[1] FALSE
                     vv
clus                  COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  C14ORF105 MUTATED                      2                             1
  C14ORF105 WILD-TYPE                  313                            46
                     vv
clus                  RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  C14ORF105 MUTATED                       0                              0
  C14ORF105 WILD-TYPE                   106                             10
D1527V10, multiclass
                                clus
vv                               C14ORF105 MUTATED C14ORF105 WILD-TYPE
  COLON ADENOCARCINOMA                           2                 313
  COLON MUCINOUS ADENOCARCINOMA                  1                  46
  RECTAL ADENOCARCINOMA                          0                 106
  RECTAL MUCINOUS ADENOCARCINOMA                 0                  10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                   R0  R1  R2  RX
  C14ORF105 MUTATED     2   0   0   0
  C14ORF105 WILD-TYPE 343   4  31  25
D1527V11, multiclass
[1] "Remove cluster labels:" "C14ORF105 MUTATED"     
clus
  C14ORF105 MUTATED C14ORF105 WILD-TYPE 
                  2                 403 
         TCGA-A6-2671          TCGA-A6-2672          TCGA-A6-2674 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-A6-2676          TCGA-A6-2677          TCGA-A6-2678 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-A6-2683          TCGA-A6-3807          TCGA-A6-3808 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-A6-3809          TCGA-A6-3810          TCGA-A6-5657 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-A6-5659          TCGA-A6-5661          TCGA-A6-5665 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-A6-6781          TCGA-AA-3489          TCGA-AA-3492 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3496          TCGA-AA-3502          TCGA-AA-3510 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3511          TCGA-AA-3514          TCGA-AA-3517 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3518          TCGA-AA-3519          TCGA-AA-3520 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3521          TCGA-AA-3522          TCGA-AA-3524 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3525          TCGA-AA-3526          TCGA-AA-3527 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3529          TCGA-AA-3530          TCGA-AA-3531 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3532          TCGA-AA-3534          TCGA-AA-3538 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3542          TCGA-AA-3543          TCGA-AA-3544 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3548          TCGA-AA-3549          TCGA-AA-3552 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3553          TCGA-AA-3554          TCGA-AA-3555 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3556          TCGA-AA-3558          TCGA-AA-3560 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3561          TCGA-AA-3562          TCGA-AA-3655 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3660          TCGA-AA-3662          TCGA-AA-3663 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3664          TCGA-AA-3666          TCGA-AA-3667 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3672          TCGA-AA-3673          TCGA-AA-3678 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3679          TCGA-AA-3680          TCGA-AA-3681 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3684          TCGA-AA-3685          TCGA-AA-3688 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3692          TCGA-AA-3693          TCGA-AA-3695 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3696          TCGA-AA-3697          TCGA-AA-3710 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3712          TCGA-AA-3713          TCGA-AA-3715 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3811          TCGA-AA-3812          TCGA-AA-3814 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3815          TCGA-AA-3818          TCGA-AA-3819 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3821          TCGA-AA-3831          TCGA-AA-3833 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3837          TCGA-AA-3842          TCGA-AA-3844 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3845          TCGA-AA-3846          TCGA-AA-3848 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3850          TCGA-AA-3851          TCGA-AA-3852 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3854          TCGA-AA-3855          TCGA-AA-3856 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3858          TCGA-AA-3860          TCGA-AA-3861 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3864          TCGA-AA-3866          TCGA-AA-3867 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3869          TCGA-AA-3870          TCGA-AA-3872 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3875          TCGA-AA-3877          TCGA-AA-3930 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3939          TCGA-AA-3941          TCGA-AA-3947 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3949          TCGA-AA-3950          TCGA-AA-3952 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3955          TCGA-AA-3956          TCGA-AA-3968 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3971          TCGA-AA-3972          TCGA-AA-3973 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3975          TCGA-AA-3976          TCGA-AA-3979 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3984          TCGA-AA-3986          TCGA-AA-3989 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-3994          TCGA-AA-A004          TCGA-AA-A00A 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-A00D          TCGA-AA-A00E          TCGA-AA-A00F 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-A00J          TCGA-AA-A00K          TCGA-AA-A00L 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-A00N          TCGA-AA-A00O          TCGA-AA-A00Q 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-A00R          TCGA-AA-A00U          TCGA-AA-A00W 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-A00Z          TCGA-AA-A017          TCGA-AA-A01D 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-A01F          TCGA-AA-A01G          TCGA-AA-A01I 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-A01K          TCGA-AA-A01P          TCGA-AA-A01Q 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-A01R          TCGA-AA-A01S          TCGA-AA-A01T 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-A01V          TCGA-AA-A01X          TCGA-AA-A01Z 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-A022          TCGA-AA-A024          TCGA-AA-A029 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-A02F          TCGA-AA-A02H          TCGA-AA-A02J 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-A02K          TCGA-AA-A02O          TCGA-AA-A02W 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AA-A02Y          TCGA-AA-A03F          TCGA-AA-A03J 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AD-5900          TCGA-AD-6548          TCGA-AD-6888 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AU-3779          TCGA-AU-6004          TCGA-AY-4070 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AY-4071          TCGA-AY-5543          TCGA-AY-6196 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AY-6197          TCGA-AY-6386          TCGA-AZ-4315 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AZ-4681          TCGA-AZ-4682          TCGA-CA-5254 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-CA-5255          TCGA-CA-5796          TCGA-CA-5797 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-CA-6715          TCGA-CA-6716          TCGA-CA-6717 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-CA-6718          TCGA-CA-6719          TCGA-CK-4947 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-CK-4948          TCGA-CK-4950          TCGA-CK-4952 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-CK-5912          TCGA-CK-5913          TCGA-CK-5914 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-CK-5915          TCGA-CK-5916          TCGA-CK-6746 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-CK-6747          TCGA-CK-6748          TCGA-CK-6751 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-CM-4743          TCGA-CM-4744          TCGA-CM-4746 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-CM-4747          TCGA-CM-4752          TCGA-CM-5341 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-CM-5344          TCGA-CM-5348          TCGA-CM-5349 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-CM-5860          TCGA-CM-5861          TCGA-CM-5862 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-CM-5863          TCGA-CM-5864          TCGA-CM-5868 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-CM-6161          TCGA-CM-6162          TCGA-CM-6163 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-CM-6164          TCGA-CM-6165          TCGA-CM-6166 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-CM-6167          TCGA-CM-6168          TCGA-CM-6169 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-CM-6170          TCGA-CM-6171          TCGA-CM-6172 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-CM-6674          TCGA-CM-6675          TCGA-CM-6676 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-CM-6677          TCGA-CM-6678          TCGA-CM-6679 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-CM-6680          TCGA-D5-5537          TCGA-D5-5538 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-D5-5539          TCGA-D5-5540          TCGA-D5-5541 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-D5-6529          TCGA-D5-6532          TCGA-D5-6533 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-D5-6534          TCGA-D5-6535          TCGA-D5-6536 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-D5-6537          TCGA-D5-6538          TCGA-D5-6539 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-D5-6540          TCGA-D5-6541          TCGA-D5-6898 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-D5-6920          TCGA-D5-6922          TCGA-D5-6923 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-D5-6924          TCGA-D5-6926          TCGA-D5-6927 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-D5-6929          TCGA-D5-6930          TCGA-D5-6931 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-D5-6932          TCGA-D5-7000          TCGA-F4-6459 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-F4-6460          TCGA-F4-6569          TCGA-F4-6570 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-F4-6703          TCGA-F4-6704          TCGA-F4-6805 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-F4-6806          TCGA-F4-6807          TCGA-F4-6808 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-F4-6809          TCGA-F4-6854          TCGA-F4-6855 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-F4-6856          TCGA-G4-6293          TCGA-G4-6299 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-G4-6303          TCGA-G4-6304          TCGA-G4-6306 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-G4-6307          TCGA-G4-6309          TCGA-G4-6310 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-G4-6315          TCGA-G4-6317          TCGA-G4-6321 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-G4-6323          TCGA-G4-6586          TCGA-G4-6588 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-G4-6625          TCGA-G4-6626          TCGA-G4-6628 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AF-2687          TCGA-AF-2689          TCGA-AF-2691 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AF-2692          TCGA-AF-3400          TCGA-AF-3913 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AF-4110          TCGA-AF-5654          TCGA-AF-6655 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AG-3574          TCGA-AG-3575          TCGA-AG-3578 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AG-3580          TCGA-AG-3581          TCGA-AG-3582 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AG-3583          TCGA-AG-3584          TCGA-AG-3586 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AG-3587          TCGA-AG-3593          TCGA-AG-3594 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AG-3598          TCGA-AG-3599          TCGA-AG-3600 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AG-3601          TCGA-AG-3602          TCGA-AG-3605 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AG-3608          TCGA-AG-3609          TCGA-AG-3611 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AG-3612          TCGA-AG-3726          TCGA-AG-3727 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AG-3731          TCGA-AG-3732          TCGA-AG-3742 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AG-3878          TCGA-AG-3882          TCGA-AG-3883 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AG-3885          TCGA-AG-3887          TCGA-AG-3890 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AG-3892          TCGA-AG-3893          TCGA-AG-3894 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AG-3896          TCGA-AG-3898          TCGA-AG-3901 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AG-3902          TCGA-AG-3909          TCGA-AG-3999 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AG-4001          TCGA-AG-4005          TCGA-AG-4007 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AG-4008          TCGA-AG-4015          TCGA-AG-A002 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AG-A008          TCGA-AG-A00C          TCGA-AG-A00H 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AG-A00Y          TCGA-AG-A011          TCGA-AG-A014 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AG-A015          TCGA-AG-A016          TCGA-AG-A01L 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AG-A01W          TCGA-AG-A01Y          TCGA-AG-A020 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AG-A025          TCGA-AG-A026          TCGA-AG-A02G 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AG-A02N          TCGA-AG-A02X          TCGA-AG-A032 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AG-A036          TCGA-AH-6549          TCGA-AH-6643 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-CL-5917          TCGA-CL-5918          TCGA-DC-5337 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-DC-5869          TCGA-DC-6155          TCGA-DC-6157 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-DC-6158          TCGA-DC-6160          TCGA-DC-6681 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-DC-6682          TCGA-DC-6683          TCGA-DT-5265 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-EF-5830          TCGA-EI-6506          TCGA-EI-6507 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-EI-6508          TCGA-EI-6510          TCGA-F5-6464 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-F5-6465          TCGA-F5-6571          TCGA-F5-6702 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-F5-6812          TCGA-F5-6813          TCGA-G5-6235 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-G5-6641 
"C14ORF105 WILD-TYPE" 
D1527V12, continuous
                     vv
clus                  AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C14ORF105 MUTATED                                  0     0
  C14ORF105 WILD-TYPE                                1    11
                     vv
clus                  BLACK OR AFRICAN AMERICAN WHITE
  C14ORF105 MUTATED                           0     1
  C14ORF105 WILD-TYPE                        22   225
D1527V13, multiclass
[1] "Remove cluster labels:" "C14ORF105 MUTATED"     
clus
  C14ORF105 MUTATED C14ORF105 WILD-TYPE 
                  1                 259 
         TCGA-A6-2671          TCGA-A6-2672          TCGA-A6-2674 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-A6-2676          TCGA-A6-2677          TCGA-A6-2678 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-A6-2683          TCGA-A6-3807          TCGA-A6-3808 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-A6-3809          TCGA-A6-3810          TCGA-A6-4105 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-A6-5656          TCGA-A6-5657          TCGA-A6-5659 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-A6-5660          TCGA-A6-5661          TCGA-A6-5662 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-A6-5664          TCGA-A6-5665          TCGA-A6-5666 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-A6-6137          TCGA-A6-6138          TCGA-A6-6141 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-A6-6142          TCGA-A6-6648          TCGA-A6-6649 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-A6-6651          TCGA-A6-6652          TCGA-A6-6653 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-A6-6654          TCGA-A6-6780          TCGA-A6-6781 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-A6-6782          TCGA-AD-5900          TCGA-AD-6548 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AD-6888          TCGA-AD-6889          TCGA-AD-6890 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AD-6895          TCGA-AD-6899          TCGA-AD-6901 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AD-6963          TCGA-AD-6964          TCGA-AD-6965 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AU-3779          TCGA-AU-6004          TCGA-AY-4070 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AY-4071          TCGA-AY-5543          TCGA-AY-6196 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AY-6197          TCGA-AY-6386          TCGA-AZ-4315 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AZ-4323          TCGA-AZ-4616          TCGA-AZ-4681 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AZ-4682          TCGA-AZ-5403          TCGA-AZ-5407 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AZ-6598          TCGA-AZ-6599          TCGA-AZ-6600 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AZ-6601          TCGA-AZ-6603          TCGA-AZ-6605 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AZ-6606          TCGA-AZ-6607          TCGA-AZ-6608 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-CA-5254          TCGA-CA-5255          TCGA-CA-5796 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-CA-5797          TCGA-CA-6715          TCGA-CA-6716 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-CA-6717          TCGA-CA-6718          TCGA-CA-6719 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-CK-4947          TCGA-CK-4948          TCGA-CK-4950 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-CK-4952          TCGA-CK-5912          TCGA-CK-5913 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-CK-5914          TCGA-CK-5915          TCGA-CK-5916 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-CK-6746          TCGA-CK-6747          TCGA-CK-6748 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-CK-6751          TCGA-CM-4743          TCGA-CM-4744 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-CM-4746          TCGA-CM-4747          TCGA-CM-4752 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-CM-5341          TCGA-CM-5344          TCGA-CM-5348 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-CM-5349          TCGA-CM-5860          TCGA-CM-5861 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-CM-5862          TCGA-CM-5863          TCGA-CM-5864 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-CM-5868          TCGA-CM-6161          TCGA-CM-6162 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-CM-6163          TCGA-CM-6164          TCGA-CM-6165 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-CM-6166          TCGA-CM-6167          TCGA-CM-6168 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-CM-6169          TCGA-CM-6170          TCGA-CM-6171 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-CM-6172          TCGA-CM-6674          TCGA-CM-6675 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-CM-6676          TCGA-CM-6677          TCGA-CM-6678 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-CM-6679          TCGA-CM-6680          TCGA-D5-5537 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-D5-5538          TCGA-D5-5539          TCGA-D5-5540 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-D5-5541          TCGA-D5-6529          TCGA-D5-6532 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-D5-6533          TCGA-D5-6534          TCGA-D5-6535 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-D5-6536          TCGA-D5-6537          TCGA-D5-6538 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-D5-6539          TCGA-D5-6540          TCGA-D5-6541 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-D5-6898          TCGA-D5-6920          TCGA-D5-6922 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-D5-6923          TCGA-D5-6924          TCGA-D5-6926 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-D5-6927          TCGA-D5-6929          TCGA-D5-6930 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-D5-6931          TCGA-D5-6932          TCGA-D5-7000 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-DM-A0X9          TCGA-DM-A0XD          TCGA-DM-A0XF 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-DM-A1D0          TCGA-DM-A1D4          TCGA-DM-A1D6 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-DM-A1D7          TCGA-DM-A1D8          TCGA-DM-A1D9 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-DM-A1DA          TCGA-DM-A1DB          TCGA-DM-A1HA 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-DM-A1HB          TCGA-DM-A282          TCGA-DM-A285 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-DM-A28C          TCGA-DM-A28E          TCGA-DM-A28F 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-DM-A28G          TCGA-DM-A28H          TCGA-DM-A28K 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-F4-6459          TCGA-F4-6460          TCGA-F4-6569 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-F4-6570          TCGA-F4-6703          TCGA-F4-6704 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-F4-6805          TCGA-F4-6806          TCGA-F4-6807 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-F4-6808          TCGA-F4-6809          TCGA-F4-6854 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-F4-6855          TCGA-F4-6856          TCGA-G4-6293 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-G4-6299          TCGA-G4-6303          TCGA-G4-6304 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-G4-6306          TCGA-G4-6307          TCGA-G4-6309 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-G4-6310          TCGA-G4-6315          TCGA-G4-6317 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-G4-6321          TCGA-G4-6323          TCGA-G4-6586 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-G4-6588          TCGA-G4-6625          TCGA-G4-6626 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-G4-6628          TCGA-AF-2687          TCGA-AF-2689 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AF-2691          TCGA-AF-2692          TCGA-AF-2693 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AF-3400          TCGA-AF-3913          TCGA-AF-4110 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AF-5654          TCGA-AF-6136          TCGA-AF-6655 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AF-6672          TCGA-AH-6544          TCGA-AH-6547 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-AH-6549          TCGA-AH-6643          TCGA-AH-6644 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-CI-6619          TCGA-CI-6620          TCGA-CI-6621 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-CI-6622          TCGA-CI-6624          TCGA-CL-5917 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-CL-5918          TCGA-DC-5337          TCGA-DC-5869 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-DC-6155          TCGA-DC-6157          TCGA-DC-6158 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-DC-6160          TCGA-DC-6681          TCGA-DC-6682 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-DC-6683          TCGA-DT-5265          TCGA-DY-A0XA 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-DY-A1DC          TCGA-DY-A1DD          TCGA-DY-A1DF 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-DY-A1DG          TCGA-DY-A1H8          TCGA-EF-5830 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-EI-6506          TCGA-EI-6507          TCGA-EI-6508 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-EI-6510          TCGA-F5-6464          TCGA-F5-6465 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-F5-6571          TCGA-F5-6702          TCGA-F5-6811 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-F5-6812          TCGA-F5-6813          TCGA-G5-6235 
"C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" "C14ORF105 WILD-TYPE" 
         TCGA-G5-6641 
"C14ORF105 WILD-TYPE" 

Clustering(1528) Variable = CCDC141 MUTATION ANALYSIS
D1528V1, survival
                   sevent
clus2                 0   1
  CCDC141 MUTATED    20   3
  CCDC141 WILD-TYPE 358  90
  CCDC141 MUTATED CCDC141 WILD-TYPE 
               23               448 
  CCDC141 MUTATED CCDC141 WILD-TYPE 
                3                90 
$`CCDC141 MUTATED`
TCGA-AA-3496 TCGA-AA-3510 TCGA-AA-3864 TCGA-AA-3941 TCGA-AA-3977 TCGA-AA-A00N 
        1.02        63.98        53.00        24.00        25.02         4.01 
TCGA-AA-A010 TCGA-AA-A01R TCGA-AZ-4315 TCGA-CA-6717 TCGA-CK-5912 TCGA-CM-5348 
       34.98        35.01        58.39        12.76        49.08        22.98 
TCGA-CM-6161 TCGA-CM-6166 TCGA-CM-6171 TCGA-D5-6541 TCGA-D5-6929 TCGA-D5-6932 
       15.02        21.99        14.04        15.58         4.80        11.38 
TCGA-F4-6459 TCGA-G4-6304 TCGA-G4-6628 TCGA-AG-A002 TCGA-AG-A01L 
        8.61        53.62        79.69        20.98        12.00 

$`CCDC141 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 
        0.99        31.07        31.07        30.05        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S 
       12.00        31.00        31.00        38.07         1.02         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       33.01        21.44        17.82         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.03        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       15.02        17.03        12.00         2.96        29.03        16.04 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 
       14.99        12.99        13.02        15.02        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       17.13        12.49        16.14         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 
       12.43        14.30         9.04         9.44        11.64         1.51 
TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       12.00        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6460 
      119.93        35.97        60.79       117.07        98.24        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
      133.18        74.56        65.85        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       26.17        91.79        46.75        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
        9.07        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  CCDC141 MUTATED CCDC141 WILD-TYPE 
             1.02              0.00 
  CCDC141 MUTATED CCDC141 WILD-TYPE 
            79.69            148.01 
  CCDC141 MUTATED CCDC141 WILD-TYPE 
           21.990            20.085 
[1] "1.0 - 79.7 (22.0)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.7"
D1528V2, continuous
D1528V3, binary
                   cls
clus                  0   1
  CCDC141 MUTATED    21   2
  CCDC141 WILD-TYPE 345 117
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC141 MUTATED     21    2
  CCDC141 WILD-TYPE  345  117
        clus
vv       CCDC141 MUTATED CCDC141 WILD-TYPE
  COLON               21               345
  RECTUM               2               117
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CCDC141 MUTATED         6        0        3         4         3         0
  CCDC141 WILD-TYPE      85        1       29       134         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CCDC141 MUTATED           1          0          3          0        1
  CCDC141 WILD-TYPE        23         11         56         42       47
                   vv
clus                STAGE IVA STAGE IVB
  CCDC141 MUTATED           1         0
  CCDC141 WILD-TYPE        17         1
D1528V4, multiclass
            clus
vv           CCDC141 MUTATED CCDC141 WILD-TYPE
  STAGE I                  6                85
  STAGE IA                 0                 1
  STAGE II                 3                29
  STAGE IIA                4               134
  STAGE IIB                3                 7
  STAGE IIC                0                 1
  STAGE III                1                23
  STAGE IIIA               0                11
  STAGE IIIB               3                56
  STAGE IIIC               0                42
  STAGE IV                 1                47
  STAGE IVA                1                17
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  CCDC141 MUTATED     0   7  12   4
  CCDC141 WILD-TYPE  17  85 317  46
D1528V5, multiclass
    clus
vv   CCDC141 MUTATED CCDC141 WILD-TYPE
  T1               0                17
  T2               7                85
  T3              12               317
  T4               4                46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  CCDC141 MUTATED    17   4   2
  CCDC141 WILD-TYPE 270 109  85
D1528V6, multiclass
    clus
vv   CCDC141 MUTATED CCDC141 WILD-TYPE
  N0              17               270
  N1               4               109
  N2               2                85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1528V7, binary
                   cls
clus                  0   1
  CCDC141 MUTATED    19   2
  CCDC141 WILD-TYPE 356  63
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC141 MUTATED     19    2
  CCDC141 WILD-TYPE  356   63
   clus
vv  CCDC141 MUTATED CCDC141 WILD-TYPE
  0              19               356
  1               2                63
[1] 2 2
[1] FALSE
D1528V8, binary
                   cls
clus                  0   1
  CCDC141 MUTATED     9  14
  CCDC141 WILD-TYPE 216 250
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC141 MUTATED      9   14
  CCDC141 WILD-TYPE  216  250
        clus
vv       CCDC141 MUTATED CCDC141 WILD-TYPE
  FEMALE               9               216
  MALE                14               250
[1] 2 2
[1] FALSE
D1528V9, binary
                   cls
clus                  0   1
  CCDC141 MUTATED    18   1
  CCDC141 WILD-TYPE 332  21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC141 MUTATED     18    1
  CCDC141 WILD-TYPE  332   21
     clus
vv    CCDC141 MUTATED CCDC141 WILD-TYPE
  NO               18               332
  YES               1                21
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CCDC141 MUTATED                     18                             3
  CCDC141 WILD-TYPE                  297                            44
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CCDC141 MUTATED                       2                              0
  CCDC141 WILD-TYPE                   104                             10
D1528V10, multiclass
                                clus
vv                               CCDC141 MUTATED CCDC141 WILD-TYPE
  COLON ADENOCARCINOMA                        18               297
  COLON MUCINOUS ADENOCARCINOMA                3                44
  RECTAL ADENOCARCINOMA                        2               104
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  CCDC141 MUTATED    20   0   0   2
  CCDC141 WILD-TYPE 325   4  31  23
D1528V11, multiclass
    clus
vv   CCDC141 MUTATED CCDC141 WILD-TYPE
  R0              20               325
  R1               0                 4
  R2               0                31
  RX               2                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1528V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CCDC141 MUTATED                                  0     1
  CCDC141 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  CCDC141 MUTATED                           0    12
  CCDC141 WILD-TYPE                        22   214
D1528V13, multiclass
                                  clus
vv                                 CCDC141 MUTATED CCDC141 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                10
  BLACK OR AFRICAN AMERICAN                      0                22
  WHITE                                         12               214
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1529) Variable = SSX2IP MUTATION ANALYSIS
D1529V1, survival
                  sevent
clus2                0   1
  SSX2IP MUTATED     6   2
  SSX2IP WILD-TYPE 372  91
  SSX2IP MUTATED SSX2IP WILD-TYPE 
               8              463 
  SSX2IP MUTATED SSX2IP WILD-TYPE 
               2               91 
$`SSX2IP MUTATED`
TCGA-AA-3492 TCGA-AA-3558 TCGA-AA-A010 TCGA-AZ-5403 TCGA-CM-5860 TCGA-CM-6162 
        3.02        20.98        34.98        62.79        32.02        12.00 
TCGA-D5-5539 TCGA-AG-A002 
       19.59        20.98 

$`SSX2IP WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3560 
       13.02        24.00        17.95        29.95        23.01        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-5862 
       29.06        22.03        22.98        30.08        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 
       15.02        15.02        17.03        15.02         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 
       11.01        10.06        12.03        45.40        12.26        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  SSX2IP MUTATED SSX2IP WILD-TYPE 
            3.02             0.00 
  SSX2IP MUTATED SSX2IP WILD-TYPE 
           62.79           148.01 
  SSX2IP MUTATED SSX2IP WILD-TYPE 
           20.98            20.12 
[1] "3.0 - 62.8 (21.0)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.3"
D1529V2, continuous
D1529V3, binary
                  cls
clus                 0   1
  SSX2IP MUTATED     8   1
  SSX2IP WILD-TYPE 358 118
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SSX2IP MUTATED      8    1
  SSX2IP WILD-TYPE  358  118
        clus
vv       SSX2IP MUTATED SSX2IP WILD-TYPE
  COLON               8              358
  RECTUM              1              118
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SSX2IP MUTATED         2        0        3         1         1         0
  SSX2IP WILD-TYPE      89        1       29       137         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SSX2IP MUTATED           0          1          1          0        0
  SSX2IP WILD-TYPE        24         10         58         42       48
                  vv
clus               STAGE IVA STAGE IVB
  SSX2IP MUTATED           0         0
  SSX2IP WILD-TYPE        18         1
D1529V4, multiclass
            clus
vv           SSX2IP MUTATED SSX2IP WILD-TYPE
  STAGE I                 2               89
  STAGE IA                0                1
  STAGE II                3               29
  STAGE IIA               1              137
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              1               10
  STAGE IIIB              1               58
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  SSX2IP MUTATED     0   2   5   2
  SSX2IP WILD-TYPE  17  90 324  48
D1529V5, multiclass
    clus
vv   SSX2IP MUTATED SSX2IP WILD-TYPE
  T1              0               17
  T2              2               90
  T3              5              324
  T4              2               48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  SSX2IP MUTATED     7   2   0
  SSX2IP WILD-TYPE 280 111  87
D1529V6, multiclass
    clus
vv   SSX2IP MUTATED SSX2IP WILD-TYPE
  N0              7              280
  N1              2              111
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1529V7, binary
                  cls
clus                 0   1
  SSX2IP MUTATED     8   0
  SSX2IP WILD-TYPE 367  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SSX2IP MUTATED      8    0
  SSX2IP WILD-TYPE  367   65
   clus
vv  SSX2IP MUTATED SSX2IP WILD-TYPE
  0              8              367
  1              0               65
[1] 2 2
[1] FALSE
D1529V8, binary
                  cls
clus                 0   1
  SSX2IP MUTATED     4   5
  SSX2IP WILD-TYPE 221 259
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SSX2IP MUTATED      4    5
  SSX2IP WILD-TYPE  221  259
        clus
vv       SSX2IP MUTATED SSX2IP WILD-TYPE
  FEMALE              4              221
  MALE                5              259
[1] 2 2
[1] FALSE
D1529V9, binary
                  cls
clus                 0   1
  SSX2IP MUTATED     8   0
  SSX2IP WILD-TYPE 342  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SSX2IP MUTATED      8    0
  SSX2IP WILD-TYPE  342   22
     clus
vv    SSX2IP MUTATED SSX2IP WILD-TYPE
  NO               8              342
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SSX2IP MUTATED                      6                             2
  SSX2IP WILD-TYPE                  309                            45
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SSX2IP MUTATED                       1                              0
  SSX2IP WILD-TYPE                   105                             10
D1529V10, multiclass
                                clus
vv                               SSX2IP MUTATED SSX2IP WILD-TYPE
  COLON ADENOCARCINOMA                        6              309
  COLON MUCINOUS ADENOCARCINOMA               2               45
  RECTAL ADENOCARCINOMA                       1              105
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  SSX2IP MUTATED     7   0   1   0
  SSX2IP WILD-TYPE 338   4  30  25
D1529V11, multiclass
    clus
vv   SSX2IP MUTATED SSX2IP WILD-TYPE
  R0              7              338
  R1              0                4
  R2              1               30
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1529V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SSX2IP MUTATED                                  0     0
  SSX2IP WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  SSX2IP MUTATED                           0     4
  SSX2IP WILD-TYPE                        22   222
D1529V13, multiclass
                                  clus
vv                                 SSX2IP MUTATED SSX2IP WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         4              222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1530) Variable = CSPP1 MUTATION ANALYSIS
D1530V1, survival
                 sevent
clus2               0   1
  CSPP1 MUTATED    15   2
  CSPP1 WILD-TYPE 363  91
  CSPP1 MUTATED CSPP1 WILD-TYPE 
             17             454 
  CSPP1 MUTATED CSPP1 WILD-TYPE 
              2              91 
$`CSPP1 MUTATED`
TCGA-A6-6653 TCGA-AA-3663 TCGA-AA-3710 TCGA-AA-3977 TCGA-AA-A010 TCGA-AY-5543 
       24.39         6.97        26.99        25.02        34.98        33.01 
TCGA-AZ-4315 TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-4746 TCGA-D5-6540 TCGA-DM-A1D8 
       58.39        12.76        10.06        37.02        16.14        12.59 
TCGA-DM-A28H TCGA-F4-6704 TCGA-AG-A002 TCGA-DC-6683 TCGA-F5-6811 
      117.07         1.55        20.98         5.03        32.19 

$`CSPP1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
       25.08        25.18        24.16        21.76        24.69        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
       27.09        16.31         0.95        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.07        12.20        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4752 
        1.91       124.27        23.05        20.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       12.49        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A1DA 
      130.65        92.75        49.91        13.32       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
      119.93        35.97        60.79        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       35.74         6.18        47.87        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        5.95         4.01         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  CSPP1 MUTATED CSPP1 WILD-TYPE 
           1.55            0.00 
  CSPP1 MUTATED CSPP1 WILD-TYPE 
         117.07          148.01 
  CSPP1 MUTATED CSPP1 WILD-TYPE 
         24.390          20.085 
[1] "1.6 - 117.1 (24.4)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.7"
D1530V2, continuous
D1530V3, binary
                 cls
clus                0   1
  CSPP1 MUTATED    15   3
  CSPP1 WILD-TYPE 351 116
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CSPP1 MUTATED     15    3
  CSPP1 WILD-TYPE  351  116
        clus
vv       CSPP1 MUTATED CSPP1 WILD-TYPE
  COLON             15             351
  RECTUM             3             116
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CSPP1 MUTATED         4        0        1         6         1         0
  CSPP1 WILD-TYPE      87        1       31       132         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CSPP1 MUTATED           0          0          1          2        0         1
  CSPP1 WILD-TYPE        24         11         58         40       48        17
                 vv
clus              STAGE IVB
  CSPP1 MUTATED           0
  CSPP1 WILD-TYPE         1
D1530V4, multiclass
            clus
vv           CSPP1 MUTATED CSPP1 WILD-TYPE
  STAGE I                4              87
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              6             132
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             2              40
  STAGE IV               0              48
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CSPP1 MUTATED     0   5  12   1
  CSPP1 WILD-TYPE  17  87 317  49
D1530V5, multiclass
    clus
vv   CSPP1 MUTATED CSPP1 WILD-TYPE
  T1             0              17
  T2             5              87
  T3            12             317
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  CSPP1 MUTATED    13   3   2
  CSPP1 WILD-TYPE 274 110  85
D1530V6, multiclass
    clus
vv   CSPP1 MUTATED CSPP1 WILD-TYPE
  N0            13             274
  N1             3             110
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1530V7, binary
                 cls
clus                0   1
  CSPP1 MUTATED    14   1
  CSPP1 WILD-TYPE 361  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CSPP1 MUTATED     14    1
  CSPP1 WILD-TYPE  361   64
   clus
vv  CSPP1 MUTATED CSPP1 WILD-TYPE
  0            14             361
  1             1              64
[1] 2 2
[1] FALSE
D1530V8, binary
                 cls
clus                0   1
  CSPP1 MUTATED     6  12
  CSPP1 WILD-TYPE 219 252
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CSPP1 MUTATED      6   12
  CSPP1 WILD-TYPE  219  252
        clus
vv       CSPP1 MUTATED CSPP1 WILD-TYPE
  FEMALE             6             219
  MALE              12             252
[1] 2 2
[1] FALSE
D1530V9, binary
                 cls
clus                0   1
  CSPP1 MUTATED    13   0
  CSPP1 WILD-TYPE 337  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CSPP1 MUTATED     13    0
  CSPP1 WILD-TYPE  337   22
     clus
vv    CSPP1 MUTATED CSPP1 WILD-TYPE
  NO             13             337
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CSPP1 MUTATED                     12                             3
  CSPP1 WILD-TYPE                  303                            44
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CSPP1 MUTATED                       3                              0
  CSPP1 WILD-TYPE                   103                             10
D1530V10, multiclass
                                clus
vv                               CSPP1 MUTATED CSPP1 WILD-TYPE
  COLON ADENOCARCINOMA                      12             303
  COLON MUCINOUS ADENOCARCINOMA              3              44
  RECTAL ADENOCARCINOMA                      3             103
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  CSPP1 MUTATED    11   0   0   2
  CSPP1 WILD-TYPE 334   4  31  23
D1530V11, multiclass
    clus
vv   CSPP1 MUTATED CSPP1 WILD-TYPE
  R0            11             334
  R1             0               4
  R2             0              31
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1530V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CSPP1 MUTATED                                  1     2
  CSPP1 WILD-TYPE                                0     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CSPP1 MUTATED                           2     7
  CSPP1 WILD-TYPE                        20   219
D1530V13, multiclass
                                  clus
vv                                 CSPP1 MUTATED CSPP1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             1               0
  ASIAN                                        2               9
  BLACK OR AFRICAN AMERICAN                    2              20
  WHITE                                        7             219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1531) Variable = CDS2 MUTATION ANALYSIS
D1531V1, survival
                sevent
clus2              0   1
  CDS2 MUTATED     8   1
  CDS2 WILD-TYPE 370  92
  CDS2 MUTATED CDS2 WILD-TYPE 
             9            462 
  CDS2 MUTATED CDS2 WILD-TYPE 
             1             92 
$`CDS2 MUTATED`
TCGA-AA-3492 TCGA-AA-3525 TCGA-AA-3555 TCGA-AA-3710 TCGA-AA-A010 TCGA-CM-5861 
        3.02         8.05        29.95        26.99        34.98        15.02 
TCGA-CM-5868 TCGA-G4-6628 TCGA-EF-5830 
       17.03        79.69         0.49 

$`CDS2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3526 
        1.02         9.07        24.03        37.05        36.03        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       24.00        17.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       85.05        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 
       22.03        22.98        30.08        32.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       15.02        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 
       35.80        26.17        91.79        46.75        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EI-6506 
       41.36        57.24        24.13        51.48        32.61        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  CDS2 MUTATED CDS2 WILD-TYPE 
          0.49           0.00 
  CDS2 MUTATED CDS2 WILD-TYPE 
         79.69         148.01 
  CDS2 MUTATED CDS2 WILD-TYPE 
        17.030         20.235 
[1] "0.5 - 79.7 (17.0)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.6"
D1531V2, continuous
D1531V3, binary
                cls
clus               0   1
  CDS2 MUTATED     9   1
  CDS2 WILD-TYPE 357 118
[1] "tbl2"
                cls
clus             [,1] [,2]
  CDS2 MUTATED      9    1
  CDS2 WILD-TYPE  357  118
        clus
vv       CDS2 MUTATED CDS2 WILD-TYPE
  COLON             9            357
  RECTUM            1            118
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CDS2 MUTATED         1        0        1         3         3         0
  CDS2 WILD-TYPE      90        1       31       135         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CDS2 MUTATED           0          0          1          0        0         1
  CDS2 WILD-TYPE        24         11         58         42       48        17
                vv
clus             STAGE IVB
  CDS2 MUTATED           0
  CDS2 WILD-TYPE         1
D1531V4, multiclass
            clus
vv           CDS2 MUTATED CDS2 WILD-TYPE
  STAGE I               1             90
  STAGE IA              0              1
  STAGE II              1             31
  STAGE IIA             3            135
  STAGE IIB             3              7
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            1             58
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             1             17
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  CDS2 MUTATED     0   1   5   4
  CDS2 WILD-TYPE  17  91 324  46
D1531V5, multiclass
    clus
vv   CDS2 MUTATED CDS2 WILD-TYPE
  T1            0             17
  T2            1             91
  T3            5            324
  T4            4             46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  CDS2 MUTATED     8   2   0
  CDS2 WILD-TYPE 279 111  87
D1531V6, multiclass
    clus
vv   CDS2 MUTATED CDS2 WILD-TYPE
  N0            8            279
  N1            2            111
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1531V7, binary
                cls
clus               0   1
  CDS2 MUTATED     8   1
  CDS2 WILD-TYPE 367  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  CDS2 MUTATED      8    1
  CDS2 WILD-TYPE  367   64
   clus
vv  CDS2 MUTATED CDS2 WILD-TYPE
  0            8            367
  1            1             64
[1] 2 2
[1] FALSE
D1531V8, binary
                cls
clus               0   1
  CDS2 MUTATED     7   3
  CDS2 WILD-TYPE 218 261
[1] "tbl2"
                cls
clus             [,1] [,2]
  CDS2 MUTATED      7    3
  CDS2 WILD-TYPE  218  261
        clus
vv       CDS2 MUTATED CDS2 WILD-TYPE
  FEMALE            7            218
  MALE              3            261
[1] 2 2
[1] FALSE
D1531V9, binary
                cls
clus               0   1
  CDS2 MUTATED     8   0
  CDS2 WILD-TYPE 342  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  CDS2 MUTATED      8    0
  CDS2 WILD-TYPE  342   22
     clus
vv    CDS2 MUTATED CDS2 WILD-TYPE
  NO             8            342
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CDS2 MUTATED                      8                             1
  CDS2 WILD-TYPE                  307                            46
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CDS2 MUTATED                       1                              0
  CDS2 WILD-TYPE                   105                             10
D1531V10, multiclass
                                clus
vv                               CDS2 MUTATED CDS2 WILD-TYPE
  COLON ADENOCARCINOMA                      8            307
  COLON MUCINOUS ADENOCARCINOMA             1             46
  RECTAL ADENOCARCINOMA                     1            105
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  CDS2 MUTATED     9   0   0   1
  CDS2 WILD-TYPE 336   4  31  24
D1531V11, multiclass
    clus
vv   CDS2 MUTATED CDS2 WILD-TYPE
  R0            9            336
  R1            0              4
  R2            0             31
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1531V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CDS2 MUTATED                                  0     0
  CDS2 WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  CDS2 MUTATED                           0     5
  CDS2 WILD-TYPE                        22   221
D1531V13, multiclass
                                  clus
vv                                 CDS2 MUTATED CDS2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       5            221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1532) Variable = EPHA4 MUTATION ANALYSIS
D1532V1, survival
                 sevent
clus2               0   1
  EPHA4 MUTATED    19   5
  EPHA4 WILD-TYPE 359  88
  EPHA4 MUTATED EPHA4 WILD-TYPE 
             24             447 
  EPHA4 MUTATED EPHA4 WILD-TYPE 
              5              88 
$`EPHA4 MUTATED`
TCGA-AA-3555 TCGA-AA-3663 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3815 
       29.95         6.97        19.04        19.04        10.06        33.04 
TCGA-AA-3950 TCGA-AA-A01V TCGA-AD-6889 TCGA-AY-6197 TCGA-AZ-4315 TCGA-CA-6719 
       24.00        35.01        56.55        21.44        58.39        14.30 
TCGA-CM-5861 TCGA-D5-6537 TCGA-D5-6928 TCGA-DM-A28F TCGA-F4-6570 TCGA-G4-6586 
       15.02         4.80        11.64        35.97         6.18        35.80 
TCGA-AG-3890 TCGA-AG-A002 TCGA-CL-5917 TCGA-DC-5337 TCGA-DC-5869 TCGA-EI-6507 
       17.03        20.98        78.12        15.02         5.03        19.96 

$`EPHA4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 
       21.01        13.02        24.00        17.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
        5.03        85.05        26.99        35.05         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
        1.02        33.04        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       22.98        30.08        32.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
       17.85        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H 
      139.17         6.12        81.37       119.93        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 
       98.24         8.61        31.96        35.74        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       22.09        13.78        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       36.95        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5918 
        0.72         6.05        33.17         6.97         4.73         7.17 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6510 
       51.48        32.61         0.49        20.55        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  EPHA4 MUTATED EPHA4 WILD-TYPE 
            4.8             0.0 
  EPHA4 MUTATED EPHA4 WILD-TYPE 
          78.12          148.01 
  EPHA4 MUTATED EPHA4 WILD-TYPE 
          19.50           20.28 
[1] "4.8 - 78.1 (19.5)"  "0.0 - 148.0 (20.3)"
[1] "hr=" "1.1"
D1532V2, continuous
D1532V3, binary
                 cls
clus                0   1
  EPHA4 MUTATED    19   6
  EPHA4 WILD-TYPE 347 113
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPHA4 MUTATED     19    6
  EPHA4 WILD-TYPE  347  113
        clus
vv       EPHA4 MUTATED EPHA4 WILD-TYPE
  COLON             19             347
  RECTUM             6             113
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  EPHA4 MUTATED         4        0        2        12         1         0
  EPHA4 WILD-TYPE      87        1       30       126         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  EPHA4 MUTATED           1          0          3          1        1         0
  EPHA4 WILD-TYPE        23         11         56         41       47        18
                 vv
clus              STAGE IVB
  EPHA4 MUTATED           0
  EPHA4 WILD-TYPE         1
D1532V4, multiclass
            clus
vv           EPHA4 MUTATED EPHA4 WILD-TYPE
  STAGE I                4              87
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA             12             126
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             3              56
  STAGE IIIC             1              41
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  EPHA4 MUTATED     1   3  20   1
  EPHA4 WILD-TYPE  16  89 309  49
D1532V5, multiclass
    clus
vv   EPHA4 MUTATED EPHA4 WILD-TYPE
  T1             1              16
  T2             3              89
  T3            20             309
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  EPHA4 MUTATED    20   3   2
  EPHA4 WILD-TYPE 267 110  85
D1532V6, multiclass
    clus
vv   EPHA4 MUTATED EPHA4 WILD-TYPE
  N0            20             267
  N1             3             110
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1532V7, binary
                 cls
clus                0   1
  EPHA4 MUTATED    20   1
  EPHA4 WILD-TYPE 355  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPHA4 MUTATED     20    1
  EPHA4 WILD-TYPE  355   64
   clus
vv  EPHA4 MUTATED EPHA4 WILD-TYPE
  0            20             355
  1             1              64
[1] 2 2
[1] FALSE
D1532V8, binary
                 cls
clus                0   1
  EPHA4 MUTATED    10  15
  EPHA4 WILD-TYPE 215 249
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPHA4 MUTATED     10   15
  EPHA4 WILD-TYPE  215  249
        clus
vv       EPHA4 MUTATED EPHA4 WILD-TYPE
  FEMALE            10             215
  MALE              15             249
[1] 2 2
[1] FALSE
D1532V9, binary
                 cls
clus                0   1
  EPHA4 MUTATED    19   1
  EPHA4 WILD-TYPE 331  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPHA4 MUTATED     19    1
  EPHA4 WILD-TYPE  331   21
     clus
vv    EPHA4 MUTATED EPHA4 WILD-TYPE
  NO             19             331
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  EPHA4 MUTATED                     16                             3
  EPHA4 WILD-TYPE                  299                            44
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  EPHA4 MUTATED                       6                              0
  EPHA4 WILD-TYPE                   100                             10
D1532V10, multiclass
                                clus
vv                               EPHA4 MUTATED EPHA4 WILD-TYPE
  COLON ADENOCARCINOMA                      16             299
  COLON MUCINOUS ADENOCARCINOMA              3              44
  RECTAL ADENOCARCINOMA                      6             100
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  EPHA4 MUTATED    19   0   1   3
  EPHA4 WILD-TYPE 326   4  30  22
D1532V11, multiclass
    clus
vv   EPHA4 MUTATED EPHA4 WILD-TYPE
  R0            19             326
  R1             0               4
  R2             1              30
  RX             3              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1532V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  EPHA4 MUTATED                                  0     2
  EPHA4 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  EPHA4 MUTATED                           1    12
  EPHA4 WILD-TYPE                        21   214
D1532V13, multiclass
                                  clus
vv                                 EPHA4 MUTATED EPHA4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               9
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                       12             214
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1533) Variable = TMEM195 MUTATION ANALYSIS
D1533V1, survival
                   sevent
clus2                 0   1
  TMEM195 MUTATED     8   1
  TMEM195 WILD-TYPE 370  92
  TMEM195 MUTATED TMEM195 WILD-TYPE 
                9               462 
  TMEM195 MUTATED TMEM195 WILD-TYPE 
                1                92 
$`TMEM195 MUTATED`
TCGA-A6-6653 TCGA-A6-6780 TCGA-AA-3510 TCGA-AA-3544 TCGA-AA-A010 TCGA-CA-6717 
       24.39        20.12        63.98        14.01        34.98        12.76 
TCGA-F4-6570 TCGA-AG-3892 TCGA-AG-A002 
        6.18        13.02        20.98 

$`TMEM195 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
       25.08        25.18        24.16        21.76        24.69        23.87 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
        0.99        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07        12.20        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       31.96        35.74        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       17.03        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  TMEM195 MUTATED TMEM195 WILD-TYPE 
             6.18              0.00 
  TMEM195 MUTATED TMEM195 WILD-TYPE 
            63.98            148.01 
  TMEM195 MUTATED TMEM195 WILD-TYPE 
           20.120            20.235 
[1] "6.2 - 64.0 (20.1)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.7"
D1533V2, continuous
D1533V3, binary
                   cls
clus                  0   1
  TMEM195 MUTATED     7   2
  TMEM195 WILD-TYPE 359 117
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM195 MUTATED      7    2
  TMEM195 WILD-TYPE  359  117
        clus
vv       TMEM195 MUTATED TMEM195 WILD-TYPE
  COLON                7               359
  RECTUM               2               117
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TMEM195 MUTATED         4        0        1         3         1         0
  TMEM195 WILD-TYPE      87        1       31       135         9         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TMEM195 MUTATED           0          0          0          0        0
  TMEM195 WILD-TYPE        24         11         59         42       48
                   vv
clus                STAGE IVA STAGE IVB
  TMEM195 MUTATED           0         0
  TMEM195 WILD-TYPE        18         1
D1533V4, multiclass
            clus
vv           TMEM195 MUTATED TMEM195 WILD-TYPE
  STAGE I                  4                87
  STAGE IA                 0                 1
  STAGE II                 1                31
  STAGE IIA                3               135
  STAGE IIB                1                 9
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               0                11
  STAGE IIIB               0                59
  STAGE IIIC               0                42
  STAGE IV                 0                48
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  TMEM195 MUTATED     1   3   4   1
  TMEM195 WILD-TYPE  16  89 325  49
D1533V5, multiclass
    clus
vv   TMEM195 MUTATED TMEM195 WILD-TYPE
  T1               1                16
  T2               3                89
  T3               4               325
  T4               1                49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  TMEM195 MUTATED     9   0   0
  TMEM195 WILD-TYPE 278 113  87
D1533V6, multiclass
    clus
vv   TMEM195 MUTATED TMEM195 WILD-TYPE
  N0               9               278
  N1               0               113
  N2               0                87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1533V7, binary
                   cls
clus                  0   1
  TMEM195 MUTATED     8   0
  TMEM195 WILD-TYPE 367  65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM195 MUTATED      8    0
  TMEM195 WILD-TYPE  367   65
   clus
vv  TMEM195 MUTATED TMEM195 WILD-TYPE
  0               8               367
  1               0                65
[1] 2 2
[1] FALSE
D1533V8, binary
                   cls
clus                  0   1
  TMEM195 MUTATED     3   6
  TMEM195 WILD-TYPE 222 258
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM195 MUTATED      3    6
  TMEM195 WILD-TYPE  222  258
        clus
vv       TMEM195 MUTATED TMEM195 WILD-TYPE
  FEMALE               3               222
  MALE                 6               258
[1] 2 2
[1] FALSE
D1533V9, binary
                   cls
clus                  0   1
  TMEM195 MUTATED     9   0
  TMEM195 WILD-TYPE 341  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM195 MUTATED      9    0
  TMEM195 WILD-TYPE  341   22
     clus
vv    TMEM195 MUTATED TMEM195 WILD-TYPE
  NO                9               341
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  TMEM195 MUTATED                      5                             2
  TMEM195 WILD-TYPE                  310                            45
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  TMEM195 MUTATED                       2                              0
  TMEM195 WILD-TYPE                   104                             10
D1533V10, multiclass
                                clus
vv                               TMEM195 MUTATED TMEM195 WILD-TYPE
  COLON ADENOCARCINOMA                         5               310
  COLON MUCINOUS ADENOCARCINOMA                2                45
  RECTAL ADENOCARCINOMA                        2               104
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  TMEM195 MUTATED     6   0   0   1
  TMEM195 WILD-TYPE 339   4  31  24
D1533V11, multiclass
    clus
vv   TMEM195 MUTATED TMEM195 WILD-TYPE
  R0               6               339
  R1               0                 4
  R2               0                31
  RX               1                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1533V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TMEM195 MUTATED                                  0     1
  TMEM195 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  TMEM195 MUTATED                           0     3
  TMEM195 WILD-TYPE                        22   223
D1533V13, multiclass
                                  clus
vv                                 TMEM195 MUTATED TMEM195 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                10
  BLACK OR AFRICAN AMERICAN                      0                22
  WHITE                                          3               223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1534) Variable = AGT MUTATION ANALYSIS
D1534V1, survival
               sevent
clus2             0   1
  AGT MUTATED     6   3
  AGT WILD-TYPE 372  90
  AGT MUTATED AGT WILD-TYPE 
            9           462 
  AGT MUTATED AGT WILD-TYPE 
            3            90 
$`AGT MUTATED`
TCGA-AA-3492 TCGA-AA-3864 TCGA-AA-3877 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-CA-6718 
        3.02        53.00        31.00        58.39        49.41        10.06 
TCGA-G4-6323 TCGA-AG-A002 TCGA-DC-6681 
       13.78        20.98         5.95 

$`AGT WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 
       32.05         0.99        31.07        31.07        30.05        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 
       24.03        27.02        29.98        18.05         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        88.21         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 
        3.25         3.29         0.07        12.20        12.76        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
       19.99         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  AGT MUTATED AGT WILD-TYPE 
         3.02          0.00 
  AGT MUTATED AGT WILD-TYPE 
        58.39        148.01 
  AGT MUTATED AGT WILD-TYPE 
       20.980        20.155 
[1] "3.0 - 58.4 (21.0)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.5"
D1534V2, continuous
D1534V3, binary
               cls
clus              0   1
  AGT MUTATED     8   2
  AGT WILD-TYPE 358 117
[1] "tbl2"
               cls
clus            [,1] [,2]
  AGT MUTATED      8    2
  AGT WILD-TYPE  358  117
        clus
vv       AGT MUTATED AGT WILD-TYPE
  COLON            8           358
  RECTUM           2           117
[1] 2 2
[1] FALSE
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  AGT MUTATED         2        1        4         2         0         0
  AGT WILD-TYPE      89        0       28       136        10         1
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AGT MUTATED           0          0          0          0        0         1
  AGT WILD-TYPE        24         11         59         42       48        17
               vv
clus            STAGE IVB
  AGT MUTATED           0
  AGT WILD-TYPE         1
D1534V4, multiclass
            clus
vv           AGT MUTATED AGT WILD-TYPE
  STAGE I              2            89
  STAGE IA             1             0
  STAGE II             4            28
  STAGE IIA            2           136
  STAGE IIB            0            10
  STAGE IIC            0             1
  STAGE III            0            24
  STAGE IIIA           0            11
  STAGE IIIB           0            59
  STAGE IIIC           0            42
  STAGE IV             0            48
  STAGE IVA            1            17
  STAGE IVB            0             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  AGT MUTATED     1   1   6   1
  AGT WILD-TYPE  16  91 323  49
D1534V5, multiclass
    clus
vv   AGT MUTATED AGT WILD-TYPE
  T1           1            16
  T2           1            91
  T3           6           323
  T4           1            49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2
  AGT MUTATED     9   0   1
  AGT WILD-TYPE 278 113  86
D1534V6, multiclass
    clus
vv   AGT MUTATED AGT WILD-TYPE
  N0           9           278
  N1           0           113
  N2           1            86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1534V7, binary
               cls
clus              0   1
  AGT MUTATED     7   1
  AGT WILD-TYPE 368  64
[1] "tbl2"
               cls
clus            [,1] [,2]
  AGT MUTATED      7    1
  AGT WILD-TYPE  368   64
   clus
vv  AGT MUTATED AGT WILD-TYPE
  0           7           368
  1           1            64
[1] 2 2
[1] FALSE
D1534V8, binary
               cls
clus              0   1
  AGT MUTATED     5   5
  AGT WILD-TYPE 220 259
[1] "tbl2"
               cls
clus            [,1] [,2]
  AGT MUTATED      5    5
  AGT WILD-TYPE  220  259
        clus
vv       AGT MUTATED AGT WILD-TYPE
  FEMALE           5           220
  MALE             5           259
[1] 2 2
[1] FALSE
D1534V9, binary
               cls
clus              0   1
  AGT MUTATED     8   0
  AGT WILD-TYPE 342  22
[1] "tbl2"
               cls
clus            [,1] [,2]
  AGT MUTATED      8    0
  AGT WILD-TYPE  342   22
     clus
vv    AGT MUTATED AGT WILD-TYPE
  NO            8           342
  YES           0            22
[1] 2 2
[1] FALSE
               vv
clus            COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  AGT MUTATED                      7                             1
  AGT WILD-TYPE                  308                            46
               vv
clus            RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  AGT MUTATED                       2                              0
  AGT WILD-TYPE                   104                             10
D1534V10, multiclass
                                clus
vv                               AGT MUTATED AGT WILD-TYPE
  COLON ADENOCARCINOMA                     7           308
  COLON MUCINOUS ADENOCARCINOMA            1            46
  RECTAL ADENOCARCINOMA                    2           104
  RECTAL MUCINOUS ADENOCARCINOMA           0            10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             R0  R1  R2  RX
  AGT MUTATED     8   0   0   1
  AGT WILD-TYPE 337   4  31  24
D1534V11, multiclass
    clus
vv   AGT MUTATED AGT WILD-TYPE
  R0           8           337
  R1           0             4
  R2           0            31
  RX           1            24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1534V12, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AGT MUTATED                                  0     1
  AGT WILD-TYPE                                1    10
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  AGT MUTATED                           1     3
  AGT WILD-TYPE                        21   223
D1534V13, multiclass
                                  clus
vv                                 AGT MUTATED AGT WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      1            10
  BLACK OR AFRICAN AMERICAN                  1            21
  WHITE                                      3           223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1535) Variable = ARHGEF11 MUTATION ANALYSIS
D1535V1, survival
                    sevent
clus2                  0   1
  ARHGEF11 MUTATED    15   7
  ARHGEF11 WILD-TYPE 363  86
  ARHGEF11 MUTATED ARHGEF11 WILD-TYPE 
                22                449 
  ARHGEF11 MUTATED ARHGEF11 WILD-TYPE 
                 7                 86 
$`ARHGEF11 MUTATED`
TCGA-A6-6654 TCGA-AA-3492 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3555 TCGA-AA-3672 
       23.87         3.02        13.02        38.99        29.95         0.92 
TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3950 TCGA-AA-3966 TCGA-AA-A02J TCGA-AZ-6598 
       19.04        10.06        24.00         2.01         5.03        49.41 
TCGA-AZ-6601 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-6165 TCGA-G4-6586 TCGA-G4-6628 
      100.01        15.02         5.03        16.04        35.80        79.69 
TCGA-AF-6655 TCGA-AG-3892 TCGA-AG-A002 TCGA-AH-6547 
       20.02        13.02        20.98         1.45 

$`ARHGEF11 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 
       20.12        19.66        20.28         7.04         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
       63.98         6.97         1.02         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       78.08         6.05         6.97        54.02         2.01        14.01 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 
       12.99        24.00        33.01        26.01         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
       34.03        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       88.21         6.77        12.10        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       30.08        32.02        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
       12.00         2.96        29.03        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        26.17        91.79        46.75 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6672 TCGA-AG-3574 
       10.39        14.50        16.83        15.39        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       17.03        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
      117.11        38.56        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  ARHGEF11 MUTATED ARHGEF11 WILD-TYPE 
              0.92               0.00 
  ARHGEF11 MUTATED ARHGEF11 WILD-TYPE 
            100.01             148.01 
  ARHGEF11 MUTATED ARHGEF11 WILD-TYPE 
             17.54              20.55 
[1] "0.9 - 100.0 (17.5)" "0.0 - 148.0 (20.6)"
[1] "hr=" "1.8"
D1535V2, continuous
D1535V3, binary
                    cls
clus                   0   1
  ARHGEF11 MUTATED    19   4
  ARHGEF11 WILD-TYPE 347 115
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ARHGEF11 MUTATED     19    4
  ARHGEF11 WILD-TYPE  347  115
        clus
vv       ARHGEF11 MUTATED ARHGEF11 WILD-TYPE
  COLON                19                347
  RECTUM                4                115
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ARHGEF11 MUTATED         3        0        3         8         0         0
  ARHGEF11 WILD-TYPE      88        1       29       130        10         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ARHGEF11 MUTATED           3          1          1          0        2
  ARHGEF11 WILD-TYPE        21         10         58         42       46
                    vv
clus                 STAGE IVA STAGE IVB
  ARHGEF11 MUTATED           1         0
  ARHGEF11 WILD-TYPE        17         1
D1535V4, multiclass
            clus
vv           ARHGEF11 MUTATED ARHGEF11 WILD-TYPE
  STAGE I                   3                 88
  STAGE IA                  0                  1
  STAGE II                  3                 29
  STAGE IIA                 8                130
  STAGE IIB                 0                 10
  STAGE IIC                 0                  1
  STAGE III                 3                 21
  STAGE IIIA                1                 10
  STAGE IIIB                1                 58
  STAGE IIIC                0                 42
  STAGE IV                  2                 46
  STAGE IVA                 1                 17
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  ARHGEF11 MUTATED     1   3  19   0
  ARHGEF11 WILD-TYPE  16  89 310  50
D1535V5, multiclass
    clus
vv   ARHGEF11 MUTATED ARHGEF11 WILD-TYPE
  T1                1                 16
  T2                3                 89
  T3               19                310
  T4                0                 50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  ARHGEF11 MUTATED    17   4   2
  ARHGEF11 WILD-TYPE 270 109  85
D1535V6, multiclass
    clus
vv   ARHGEF11 MUTATED ARHGEF11 WILD-TYPE
  N0               17                270
  N1                4                109
  N2                2                 85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1535V7, binary
                    cls
clus                   0   1
  ARHGEF11 MUTATED    18   3
  ARHGEF11 WILD-TYPE 357  62
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ARHGEF11 MUTATED     18    3
  ARHGEF11 WILD-TYPE  357   62
   clus
vv  ARHGEF11 MUTATED ARHGEF11 WILD-TYPE
  0               18                357
  1                3                 62
[1] 2 2
[1] FALSE
D1535V8, binary
                    cls
clus                   0   1
  ARHGEF11 MUTATED    15   8
  ARHGEF11 WILD-TYPE 210 256
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ARHGEF11 MUTATED     15    8
  ARHGEF11 WILD-TYPE  210  256
        clus
vv       ARHGEF11 MUTATED ARHGEF11 WILD-TYPE
  FEMALE               15                210
  MALE                  8                256
[1] 2 2
[1] FALSE
D1535V9, binary
                    cls
clus                   0   1
  ARHGEF11 MUTATED    18   1
  ARHGEF11 WILD-TYPE 332  21
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ARHGEF11 MUTATED     18    1
  ARHGEF11 WILD-TYPE  332   21
     clus
vv    ARHGEF11 MUTATED ARHGEF11 WILD-TYPE
  NO                18                332
  YES                1                 21
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ARHGEF11 MUTATED                     15                             4
  ARHGEF11 WILD-TYPE                  300                            43
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ARHGEF11 MUTATED                       4                              0
  ARHGEF11 WILD-TYPE                   102                             10
D1535V10, multiclass
                                clus
vv                               ARHGEF11 MUTATED ARHGEF11 WILD-TYPE
  COLON ADENOCARCINOMA                         15                300
  COLON MUCINOUS ADENOCARCINOMA                 4                 43
  RECTAL ADENOCARCINOMA                         4                102
  RECTAL MUCINOUS ADENOCARCINOMA                0                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  ARHGEF11 MUTATED    15   0   2   0
  ARHGEF11 WILD-TYPE 330   4  29  25
D1535V11, multiclass
    clus
vv   ARHGEF11 MUTATED ARHGEF11 WILD-TYPE
  R0               15                330
  R1                0                  4
  R2                2                 29
  RX                0                 25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1535V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ARHGEF11 MUTATED                                  0     0
  ARHGEF11 WILD-TYPE                                1    11
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  ARHGEF11 MUTATED                           0    10
  ARHGEF11 WILD-TYPE                        22   216
D1535V13, multiclass
                                  clus
vv                                 ARHGEF11 MUTATED ARHGEF11 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 11
  BLACK OR AFRICAN AMERICAN                       0                 22
  WHITE                                          10                216
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1536) Variable = MRPS22 MUTATION ANALYSIS
D1536V1, survival
                  sevent
clus2                0   1
  MRPS22 MUTATED     8   2
  MRPS22 WILD-TYPE 370  91
  MRPS22 MUTATED MRPS22 WILD-TYPE 
              10              461 
  MRPS22 MUTATED MRPS22 WILD-TYPE 
               2               91 
$`MRPS22 MUTATED`
TCGA-A6-5661 TCGA-AA-3977 TCGA-AA-A010 TCGA-AY-6197 TCGA-AZ-6603 TCGA-AZ-6608 
       33.53        25.02        34.98        21.44        29.56         1.61 
TCGA-CM-4743 TCGA-D5-6541 TCGA-DM-A1HB TCGA-G4-6317 
       23.05        15.58       135.65        36.00 

$`MRPS22 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 
        9.99        21.14        82.95         1.91       124.27        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6898 
       17.85         4.80        17.13        12.49        16.14         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       61.91        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  MRPS22 MUTATED MRPS22 WILD-TYPE 
            1.61             0.00 
  MRPS22 MUTATED MRPS22 WILD-TYPE 
          135.65           148.01 
  MRPS22 MUTATED MRPS22 WILD-TYPE 
           27.29            20.02 
[1] "1.6 - 135.7 (27.3)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.1"
D1536V2, continuous
D1536V3, binary
                  cls
clus                 0   1
  MRPS22 MUTATED    10   0
  MRPS22 WILD-TYPE 356 119
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MRPS22 MUTATED     10    0
  MRPS22 WILD-TYPE  356  119
        clus
vv       MRPS22 MUTATED MRPS22 WILD-TYPE
  COLON              10              356
  RECTUM              0              119
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MRPS22 MUTATED         0        0        0         4         1         0
  MRPS22 WILD-TYPE      91        1       32       134         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MRPS22 MUTATED           0          1          1          1        0
  MRPS22 WILD-TYPE        24         10         58         41       48
                  vv
clus               STAGE IVA STAGE IVB
  MRPS22 MUTATED           0         0
  MRPS22 WILD-TYPE        18         1
D1536V4, multiclass
            clus
vv           MRPS22 MUTATED MRPS22 WILD-TYPE
  STAGE I                 0               91
  STAGE IA                0                1
  STAGE II                0               32
  STAGE IIA               4              134
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              1               10
  STAGE IIIB              1               58
  STAGE IIIC              1               41
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  MRPS22 MUTATED     0   3   6   1
  MRPS22 WILD-TYPE  17  89 323  49
D1536V5, multiclass
    clus
vv   MRPS22 MUTATED MRPS22 WILD-TYPE
  T1              0               17
  T2              3               89
  T3              6              323
  T4              1               49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  MRPS22 MUTATED     6   3   1
  MRPS22 WILD-TYPE 281 110  86
D1536V6, multiclass
    clus
vv   MRPS22 MUTATED MRPS22 WILD-TYPE
  N0              6              281
  N1              3              110
  N2              1               86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1536V7, binary
                  cls
clus                 0   1
  MRPS22 MUTATED     6   0
  MRPS22 WILD-TYPE 369  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MRPS22 MUTATED      6    0
  MRPS22 WILD-TYPE  369   65
   clus
vv  MRPS22 MUTATED MRPS22 WILD-TYPE
  0              6              369
  1              0               65
[1] 2 2
[1] FALSE
D1536V8, binary
                  cls
clus                 0   1
  MRPS22 MUTATED     5   5
  MRPS22 WILD-TYPE 220 259
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MRPS22 MUTATED      5    5
  MRPS22 WILD-TYPE  220  259
        clus
vv       MRPS22 MUTATED MRPS22 WILD-TYPE
  FEMALE              5              220
  MALE                5              259
[1] 2 2
[1] FALSE
D1536V9, binary
                  cls
clus                 0   1
  MRPS22 MUTATED     9   0
  MRPS22 WILD-TYPE 341  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MRPS22 MUTATED      9    0
  MRPS22 WILD-TYPE  341   22
     clus
vv    MRPS22 MUTATED MRPS22 WILD-TYPE
  NO               9              341
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MRPS22 MUTATED                      9                             0
  MRPS22 WILD-TYPE                  306                            47
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MRPS22 MUTATED                       0                              0
  MRPS22 WILD-TYPE                   106                             10
D1536V10, multiclass
                                clus
vv                               MRPS22 MUTATED MRPS22 WILD-TYPE
  COLON ADENOCARCINOMA                        9              306
  COLON MUCINOUS ADENOCARCINOMA               0               47
  RECTAL ADENOCARCINOMA                       0              106
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  MRPS22 MUTATED     6   0   0   0
  MRPS22 WILD-TYPE 339   4  31  25
D1536V11, multiclass
    clus
vv   MRPS22 MUTATED MRPS22 WILD-TYPE
  R0              6              339
  R1              0                4
  R2              0               31
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1536V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MRPS22 MUTATED                                  0     0
  MRPS22 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  MRPS22 MUTATED                           1     7
  MRPS22 WILD-TYPE                        21   219
D1536V13, multiclass
                                  clus
vv                                 MRPS22 MUTATED MRPS22 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                         7              219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1537) Variable = TMEM229B MUTATION ANALYSIS
D1537V1, survival
                    sevent
clus2                  0   1
  TMEM229B MUTATED     4   0
  TMEM229B WILD-TYPE 374  93
  TMEM229B MUTATED TMEM229B WILD-TYPE 
                 4                467 
  TMEM229B MUTATED TMEM229B WILD-TYPE 
                 0                 93 
$`TMEM229B MUTATED`
TCGA-AD-6890 TCGA-AD-6895 TCGA-CM-4746 TCGA-CM-5344 
        0.79         0.72        37.02        22.03 

$`TMEM229B WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       21.37        15.52        56.55         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4747 
       82.95         1.91       124.27        23.05        20.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       13.02        29.06        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  TMEM229B MUTATED TMEM229B WILD-TYPE 
              0.72               0.00 
  TMEM229B MUTATED TMEM229B WILD-TYPE 
             37.02             148.01 
  TMEM229B MUTATED TMEM229B WILD-TYPE 
             11.41              20.19 
[1] "0.7 - 37.0 (11.4)"  "0.0 - 148.0 (20.2)"
[1] "hr="     "3300000"
D1537V2, continuous
D1537V3, binary
                    cls
clus                   0   1
  TMEM229B MUTATED     4   0
  TMEM229B WILD-TYPE 362 119
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  TMEM229B MUTATED      4    0
  TMEM229B WILD-TYPE  362  119
        clus
vv       TMEM229B MUTATED TMEM229B WILD-TYPE
  COLON                 4                362
  RECTUM                0                119
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TMEM229B MUTATED         1        0        0         0         0         0
  TMEM229B WILD-TYPE      90        1       32       138        10         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TMEM229B MUTATED           0          0          1          0        0
  TMEM229B WILD-TYPE        24         11         58         42       48
                    vv
clus                 STAGE IVA STAGE IVB
  TMEM229B MUTATED           0         0
  TMEM229B WILD-TYPE        18         1
D1537V4, multiclass
[1] "Remove cluster labels:" "TMEM229B MUTATED"      
clus
  TMEM229B MUTATED TMEM229B WILD-TYPE 
                 2                474 
        TCGA-A6-2671         TCGA-A6-2672         TCGA-A6-2674 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-A6-2676         TCGA-A6-2677         TCGA-A6-2678 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-A6-2683         TCGA-A6-3807         TCGA-A6-3808 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-A6-3809         TCGA-A6-3810         TCGA-A6-4105 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-A6-5656         TCGA-A6-5657         TCGA-A6-5659 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-A6-5660         TCGA-A6-5661         TCGA-A6-5662 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-A6-5664         TCGA-A6-5665         TCGA-A6-5666 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-A6-6137         TCGA-A6-6138         TCGA-A6-6141 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-A6-6142         TCGA-A6-6648         TCGA-A6-6649 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-A6-6651         TCGA-A6-6652         TCGA-A6-6653 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
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"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-CI-6624         TCGA-CL-5917         TCGA-CL-5918 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-DC-5337         TCGA-DC-5869         TCGA-DC-6155 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-DC-6157         TCGA-DC-6158         TCGA-DC-6160 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-DC-6681         TCGA-DC-6682         TCGA-DC-6683 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-DT-5265         TCGA-DY-A0XA         TCGA-DY-A1DC 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-DY-A1DD         TCGA-DY-A1DF         TCGA-DY-A1DG 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-DY-A1H8         TCGA-EF-5830         TCGA-EI-6506 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6510 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-F5-6464         TCGA-F5-6465         TCGA-F5-6571 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6811         TCGA-F5-6812 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-F5-6813         TCGA-G5-6235         TCGA-G5-6641 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
                    vv
clus                  T1  T2  T3  T4
  TMEM229B MUTATED     1   1   2   0
  TMEM229B WILD-TYPE  16  91 327  50
D1537V5, multiclass
    clus
vv   TMEM229B MUTATED TMEM229B WILD-TYPE
  T1                1                 16
  T2                1                 91
  T3                2                327
  T4                0                 50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  TMEM229B MUTATED     2   2   0
  TMEM229B WILD-TYPE 285 111  87
D1537V6, multiclass
    clus
vv   TMEM229B MUTATED TMEM229B WILD-TYPE
  N0                2                285
  N1                2                111
  N2                0                 87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1537V7, binary
                    cls
clus                   0   1
  TMEM229B MUTATED     2   0
  TMEM229B WILD-TYPE 373  65
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  TMEM229B MUTATED      2    0
  TMEM229B WILD-TYPE  373   65
   clus
vv  TMEM229B MUTATED TMEM229B WILD-TYPE
  0                2                373
  1                0                 65
[1] 2 2
[1] FALSE
D1537V8, binary
                    cls
clus                   0   1
  TMEM229B MUTATED     1   3
  TMEM229B WILD-TYPE 224 261
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  TMEM229B MUTATED      1    3
  TMEM229B WILD-TYPE  224  261
        clus
vv       TMEM229B MUTATED TMEM229B WILD-TYPE
  FEMALE                1                224
  MALE                  3                261
[1] 2 2
[1] FALSE
D1537V9, binary
                    cls
clus                   0   1
  TMEM229B MUTATED     2   0
  TMEM229B WILD-TYPE 348  22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  TMEM229B MUTATED      2    0
  TMEM229B WILD-TYPE  348   22
     clus
vv    TMEM229B MUTATED TMEM229B WILD-TYPE
  NO                 2                348
  YES                0                 22
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  TMEM229B MUTATED                      4                             0
  TMEM229B WILD-TYPE                  311                            47
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  TMEM229B MUTATED                       0                              0
  TMEM229B WILD-TYPE                   106                             10
D1537V10, multiclass
                                clus
vv                               TMEM229B MUTATED TMEM229B WILD-TYPE
  COLON ADENOCARCINOMA                          4                311
  COLON MUCINOUS ADENOCARCINOMA                 0                 47
  RECTAL ADENOCARCINOMA                         0                106
  RECTAL MUCINOUS ADENOCARCINOMA                0                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  TMEM229B MUTATED     2   0   0   0
  TMEM229B WILD-TYPE 343   4  31  25
D1537V11, multiclass
[1] "Remove cluster labels:" "TMEM229B MUTATED"      
clus
  TMEM229B MUTATED TMEM229B WILD-TYPE 
                 2                403 
        TCGA-A6-2671         TCGA-A6-2672         TCGA-A6-2674 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-A6-2676         TCGA-A6-2677         TCGA-A6-2678 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-A6-2683         TCGA-A6-3807         TCGA-A6-3808 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-A6-3809         TCGA-A6-3810         TCGA-A6-5657 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-A6-5659         TCGA-A6-5661         TCGA-A6-5665 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-A6-6781         TCGA-AA-3489         TCGA-AA-3492 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-3496         TCGA-AA-3502         TCGA-AA-3510 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-3511         TCGA-AA-3514         TCGA-AA-3517 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-3518         TCGA-AA-3519         TCGA-AA-3520 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-3521         TCGA-AA-3522         TCGA-AA-3524 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-3525         TCGA-AA-3526         TCGA-AA-3527 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-3529         TCGA-AA-3530         TCGA-AA-3531 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-3532         TCGA-AA-3534         TCGA-AA-3538 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-3542         TCGA-AA-3543         TCGA-AA-3544 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-3548         TCGA-AA-3549         TCGA-AA-3552 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-3553         TCGA-AA-3554         TCGA-AA-3555 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-3556         TCGA-AA-3558         TCGA-AA-3560 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-3561         TCGA-AA-3562         TCGA-AA-3655 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-3660         TCGA-AA-3662         TCGA-AA-3663 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-3664         TCGA-AA-3666         TCGA-AA-3667 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-3672         TCGA-AA-3673         TCGA-AA-3678 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-3679         TCGA-AA-3680         TCGA-AA-3681 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-3684         TCGA-AA-3685         TCGA-AA-3688 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-3692         TCGA-AA-3693         TCGA-AA-3695 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-3696         TCGA-AA-3697         TCGA-AA-3710 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-3712         TCGA-AA-3713         TCGA-AA-3715 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-3811         TCGA-AA-3812         TCGA-AA-3814 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-3815         TCGA-AA-3818         TCGA-AA-3819 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-3821         TCGA-AA-3831         TCGA-AA-3833 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-3837         TCGA-AA-3842         TCGA-AA-3844 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-3845         TCGA-AA-3846         TCGA-AA-3848 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-3850         TCGA-AA-3851         TCGA-AA-3852 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-3854         TCGA-AA-3855         TCGA-AA-3856 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-3858         TCGA-AA-3860         TCGA-AA-3861 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-3864         TCGA-AA-3866         TCGA-AA-3867 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-3869         TCGA-AA-3870         TCGA-AA-3872 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-3875         TCGA-AA-3877         TCGA-AA-3930 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-3939         TCGA-AA-3941         TCGA-AA-3947 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-3949         TCGA-AA-3950         TCGA-AA-3952 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-3955         TCGA-AA-3956         TCGA-AA-3968 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-3971         TCGA-AA-3972         TCGA-AA-3973 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-3975         TCGA-AA-3976         TCGA-AA-3979 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-3984         TCGA-AA-3986         TCGA-AA-3989 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-3994         TCGA-AA-A004         TCGA-AA-A00A 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-A00D         TCGA-AA-A00E         TCGA-AA-A00F 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-A00J         TCGA-AA-A00K         TCGA-AA-A00L 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-A00N         TCGA-AA-A00O         TCGA-AA-A00Q 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-A00R         TCGA-AA-A00U         TCGA-AA-A00W 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-A00Z         TCGA-AA-A010         TCGA-AA-A017 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-A01D         TCGA-AA-A01F         TCGA-AA-A01G 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-A01I         TCGA-AA-A01K         TCGA-AA-A01P 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-A01Q         TCGA-AA-A01R         TCGA-AA-A01S 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-A01T         TCGA-AA-A01V         TCGA-AA-A01X 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-A01Z         TCGA-AA-A022         TCGA-AA-A024 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-A029         TCGA-AA-A02F         TCGA-AA-A02H 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-A02J         TCGA-AA-A02K         TCGA-AA-A02O 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-A02W         TCGA-AA-A02Y         TCGA-AA-A03F 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AA-A03J         TCGA-AD-5900         TCGA-AD-6548 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AD-6888         TCGA-AU-3779         TCGA-AU-6004 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AY-4070         TCGA-AY-4071         TCGA-AY-5543 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AY-6196         TCGA-AY-6197         TCGA-AY-6386 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AZ-4315         TCGA-AZ-4681         TCGA-AZ-4682 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-CA-5254         TCGA-CA-5255         TCGA-CA-5796 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-CA-5797         TCGA-CA-6715         TCGA-CA-6716 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-CA-6717         TCGA-CA-6718         TCGA-CA-6719 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-CK-4947         TCGA-CK-4948         TCGA-CK-4950 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-CK-4952         TCGA-CK-5912         TCGA-CK-5913 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-CK-5914         TCGA-CK-5915         TCGA-CK-5916 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-CK-6746         TCGA-CK-6747         TCGA-CK-6748 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-CK-6751         TCGA-CM-4743         TCGA-CM-4744 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-CM-4747         TCGA-CM-4752         TCGA-CM-5341 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-CM-5348         TCGA-CM-5349         TCGA-CM-5860 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-CM-5861         TCGA-CM-5862         TCGA-CM-5863 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-CM-5864         TCGA-CM-5868         TCGA-CM-6161 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-CM-6162         TCGA-CM-6163         TCGA-CM-6164 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-CM-6165         TCGA-CM-6166         TCGA-CM-6167 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-CM-6168         TCGA-CM-6169         TCGA-CM-6170 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-CM-6171         TCGA-CM-6172         TCGA-CM-6674 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-CM-6675         TCGA-CM-6676         TCGA-CM-6677 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-CM-6678         TCGA-CM-6679         TCGA-CM-6680 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-D5-5537         TCGA-D5-5538         TCGA-D5-5539 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-D5-5540         TCGA-D5-5541         TCGA-D5-6529 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-D5-6532         TCGA-D5-6533         TCGA-D5-6534 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-D5-6535         TCGA-D5-6536         TCGA-D5-6537 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-D5-6538         TCGA-D5-6539         TCGA-D5-6540 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-D5-6541         TCGA-D5-6898         TCGA-D5-6920 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-D5-6922         TCGA-D5-6923         TCGA-D5-6924 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-D5-6926         TCGA-D5-6927         TCGA-D5-6928 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-D5-6929         TCGA-D5-6930         TCGA-D5-6931 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-D5-6932         TCGA-D5-7000         TCGA-F4-6459 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-F4-6460         TCGA-F4-6569         TCGA-F4-6570 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-F4-6703         TCGA-F4-6704         TCGA-F4-6805 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-F4-6806         TCGA-F4-6807         TCGA-F4-6808 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-F4-6809         TCGA-F4-6854         TCGA-F4-6855 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-F4-6856         TCGA-G4-6293         TCGA-G4-6299 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-G4-6303         TCGA-G4-6304         TCGA-G4-6306 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-G4-6307         TCGA-G4-6309         TCGA-G4-6310 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-G4-6315         TCGA-G4-6317         TCGA-G4-6321 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-G4-6323         TCGA-G4-6586         TCGA-G4-6588 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-G4-6625         TCGA-G4-6626         TCGA-G4-6628 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2691 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AF-2692         TCGA-AF-3400         TCGA-AF-3913 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6655 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AG-3574         TCGA-AG-3575         TCGA-AG-3578 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AG-3580         TCGA-AG-3581         TCGA-AG-3582 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AG-3583         TCGA-AG-3584         TCGA-AG-3586 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AG-3587         TCGA-AG-3593         TCGA-AG-3594 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AG-3598         TCGA-AG-3599         TCGA-AG-3600 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AG-3601         TCGA-AG-3602         TCGA-AG-3605 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AG-3608         TCGA-AG-3609         TCGA-AG-3611 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AG-3612         TCGA-AG-3726         TCGA-AG-3727 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3732         TCGA-AG-3742 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AG-3878         TCGA-AG-3882         TCGA-AG-3883 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AG-3885         TCGA-AG-3887         TCGA-AG-3890 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AG-3892         TCGA-AG-3893         TCGA-AG-3894 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AG-3896         TCGA-AG-3898         TCGA-AG-3901 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AG-3902         TCGA-AG-3909         TCGA-AG-3999 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AG-4001         TCGA-AG-4005         TCGA-AG-4007 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4015         TCGA-AG-A002 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01L 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AG-A01W         TCGA-AG-A01Y         TCGA-AG-A020 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-AG-A036         TCGA-AH-6549         TCGA-AH-6643 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-CL-5917         TCGA-CL-5918         TCGA-DC-5337 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6155         TCGA-DC-6157 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-DC-6158         TCGA-DC-6160         TCGA-DC-6681 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-DC-6682         TCGA-DC-6683         TCGA-DT-5265 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-EF-5830         TCGA-EI-6506         TCGA-EI-6507 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-EI-6508         TCGA-EI-6510         TCGA-F5-6464 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-F5-6465         TCGA-F5-6571         TCGA-F5-6702 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-G5-6235 
"TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" "TMEM229B WILD-TYPE" 
        TCGA-G5-6641 
"TMEM229B WILD-TYPE" 
D1537V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TMEM229B MUTATED                                  0     0
  TMEM229B WILD-TYPE                                1    11
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  TMEM229B MUTATED                           1     3
  TMEM229B WILD-TYPE                        21   223
D1537V13, multiclass
                                  clus
vv                                 TMEM229B MUTATED TMEM229B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 11
  BLACK OR AFRICAN AMERICAN                       1                 21
  WHITE                                           3                223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1538) Variable = ABCG2 MUTATION ANALYSIS
D1538V1, survival
                 sevent
clus2               0   1
  ABCG2 MUTATED    14   1
  ABCG2 WILD-TYPE 364  92
  ABCG2 MUTATED ABCG2 WILD-TYPE 
             15             456 
  ABCG2 MUTATED ABCG2 WILD-TYPE 
              1              92 
$`ABCG2 MUTATED`
TCGA-AA-3672 TCGA-AA-3977 TCGA-AA-A00A TCGA-AA-A010 TCGA-AA-A02J TCGA-AD-6965 
        0.92        25.02        38.04        34.98         5.03         0.20 
TCGA-CA-6717 TCGA-D5-6540 TCGA-D5-6922 TCGA-G4-6306 TCGA-G4-6317 TCGA-G4-6628 
       12.76        16.14         4.41        44.68        36.00        79.69 
TCGA-AG-3892 TCGA-AG-A002 TCGA-CL-5918 
       13.02        20.98         7.17 

$`ABCG2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
        6.05         6.97        54.02         2.01        14.01        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00D 
       27.02        19.07         7.96        27.02        13.94        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        10.88        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07        12.20        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 
       17.85         4.80        17.13        12.49        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        3.68        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       65.85        53.62        55.04        85.48        63.62        61.91 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       36.95        17.03        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  ABCG2 MUTATED ABCG2 WILD-TYPE 
            0.2             0.0 
  ABCG2 MUTATED ABCG2 WILD-TYPE 
          79.69          148.01 
  ABCG2 MUTATED ABCG2 WILD-TYPE 
         16.140          20.235 
[1] "0.2 - 79.7 (16.1)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "2.5"
D1538V2, continuous
D1538V3, binary
                 cls
clus                0   1
  ABCG2 MUTATED    12   3
  ABCG2 WILD-TYPE 354 116
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCG2 MUTATED     12    3
  ABCG2 WILD-TYPE  354  116
        clus
vv       ABCG2 MUTATED ABCG2 WILD-TYPE
  COLON             12             354
  RECTUM             3             116
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ABCG2 MUTATED         4        0        0         4         1         0
  ABCG2 WILD-TYPE      87        1       32       134         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ABCG2 MUTATED           1          1          0          1        1         0
  ABCG2 WILD-TYPE        23         10         59         41       47        18
                 vv
clus              STAGE IVB
  ABCG2 MUTATED           0
  ABCG2 WILD-TYPE         1
D1538V4, multiclass
            clus
vv           ABCG2 MUTATED ABCG2 WILD-TYPE
  STAGE I                4              87
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              4             134
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             1              10
  STAGE IIIB             0              59
  STAGE IIIC             1              41
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ABCG2 MUTATED     1   5   7   2
  ABCG2 WILD-TYPE  16  87 322  48
D1538V5, multiclass
    clus
vv   ABCG2 MUTATED ABCG2 WILD-TYPE
  T1             1              16
  T2             5              87
  T3             7             322
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  ABCG2 MUTATED    11   2   2
  ABCG2 WILD-TYPE 276 111  85
D1538V6, multiclass
    clus
vv   ABCG2 MUTATED ABCG2 WILD-TYPE
  N0            11             276
  N1             2             111
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1538V7, binary
                 cls
clus                0   1
  ABCG2 MUTATED    10   1
  ABCG2 WILD-TYPE 365  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCG2 MUTATED     10    1
  ABCG2 WILD-TYPE  365   64
   clus
vv  ABCG2 MUTATED ABCG2 WILD-TYPE
  0            10             365
  1             1              64
[1] 2 2
[1] FALSE
D1538V8, binary
                 cls
clus                0   1
  ABCG2 MUTATED     6   9
  ABCG2 WILD-TYPE 219 255
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCG2 MUTATED      6    9
  ABCG2 WILD-TYPE  219  255
        clus
vv       ABCG2 MUTATED ABCG2 WILD-TYPE
  FEMALE             6             219
  MALE               9             255
[1] 2 2
[1] FALSE
D1538V9, binary
                 cls
clus                0   1
  ABCG2 MUTATED    12   0
  ABCG2 WILD-TYPE 338  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCG2 MUTATED     12    0
  ABCG2 WILD-TYPE  338   22
     clus
vv    ABCG2 MUTATED ABCG2 WILD-TYPE
  NO             12             338
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ABCG2 MUTATED                     10                             2
  ABCG2 WILD-TYPE                  305                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ABCG2 MUTATED                       3                              0
  ABCG2 WILD-TYPE                   103                             10
D1538V10, multiclass
                                clus
vv                               ABCG2 MUTATED ABCG2 WILD-TYPE
  COLON ADENOCARCINOMA                      10             305
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      3             103
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  ABCG2 MUTATED    10   0   1   2
  ABCG2 WILD-TYPE 335   4  30  23
D1538V11, multiclass
    clus
vv   ABCG2 MUTATED ABCG2 WILD-TYPE
  R0            10             335
  R1             0               4
  R2             1              30
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1538V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ABCG2 MUTATED                                  0     1
  ABCG2 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ABCG2 MUTATED                           0     7
  ABCG2 WILD-TYPE                        22   219
D1538V13, multiclass
                                  clus
vv                                 ABCG2 MUTATED ABCG2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        7             219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1539) Variable = TMEM168 MUTATION ANALYSIS
D1539V1, survival
                   sevent
clus2                 0   1
  TMEM168 MUTATED    13   3
  TMEM168 WILD-TYPE 365  90
  TMEM168 MUTATED TMEM168 WILD-TYPE 
               16               455 
  TMEM168 MUTATED TMEM168 WILD-TYPE 
                3                90 
$`TMEM168 MUTATED`
TCGA-A6-5661 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3977 TCGA-AA-A010 TCGA-AA-A03F 
       33.53        19.04        19.04        25.02        34.98        18.05 
TCGA-AZ-4323 TCGA-CA-6717 TCGA-CM-5861 TCGA-D5-6928 TCGA-DM-A0X9 TCGA-AG-3885 
        1.41        12.76        15.02        11.64       119.70        17.95 
TCGA-AG-3892 TCGA-AG-A002 TCGA-AG-A02N TCGA-DY-A0XA 
       13.02        20.98        61.97       126.44 

$`TMEM168 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
       36.00         5.03        85.05        26.99        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03J TCGA-AD-5900 
       14.01         0.92        41.00        39.98        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07        12.20        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       32.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 
        4.41        12.43        14.30         9.04         9.44         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0XD TCGA-DM-A0XF 
        1.51        12.00        11.38        10.26        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       36.95        17.03        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 
       10.98        49.97         1.94        38.96        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD 
        5.95         4.01         5.03         5.29        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  TMEM168 MUTATED TMEM168 WILD-TYPE 
             1.41              0.00 
  TMEM168 MUTATED TMEM168 WILD-TYPE 
           126.44            148.01 
  TMEM168 MUTATED TMEM168 WILD-TYPE 
            19.04             20.28 
[1] "1.4 - 126.4 (19.0)" "0.0 - 148.0 (20.3)"
[1] "hr=" "1.3"
D1539V2, continuous
D1539V3, binary
                   cls
clus                  0   1
  TMEM168 MUTATED    11   5
  TMEM168 WILD-TYPE 355 114
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM168 MUTATED     11    5
  TMEM168 WILD-TYPE  355  114
        clus
vv       TMEM168 MUTATED TMEM168 WILD-TYPE
  COLON               11               355
  RECTUM               5               114
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TMEM168 MUTATED         2        0        2         6         1         0
  TMEM168 WILD-TYPE      89        1       30       132         9         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TMEM168 MUTATED           1          0          1          0        2
  TMEM168 WILD-TYPE        23         11         58         42       46
                   vv
clus                STAGE IVA STAGE IVB
  TMEM168 MUTATED           0         0
  TMEM168 WILD-TYPE        18         1
D1539V4, multiclass
            clus
vv           TMEM168 MUTATED TMEM168 WILD-TYPE
  STAGE I                  2                89
  STAGE IA                 0                 1
  STAGE II                 2                30
  STAGE IIA                6               132
  STAGE IIB                1                 9
  STAGE IIC                0                 1
  STAGE III                1                23
  STAGE IIIA               0                11
  STAGE IIIB               1                58
  STAGE IIIC               0                42
  STAGE IV                 2                46
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  TMEM168 MUTATED     1   2  11   2
  TMEM168 WILD-TYPE  16  90 318  48
D1539V5, multiclass
    clus
vv   TMEM168 MUTATED TMEM168 WILD-TYPE
  T1               1                16
  T2               2                90
  T3              11               318
  T4               2                48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  TMEM168 MUTATED    13   1   2
  TMEM168 WILD-TYPE 274 112  85
D1539V6, multiclass
    clus
vv   TMEM168 MUTATED TMEM168 WILD-TYPE
  N0              13               274
  N1               1               112
  N2               2                85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1539V7, binary
                   cls
clus                  0   1
  TMEM168 MUTATED    13   2
  TMEM168 WILD-TYPE 362  63
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM168 MUTATED     13    2
  TMEM168 WILD-TYPE  362   63
   clus
vv  TMEM168 MUTATED TMEM168 WILD-TYPE
  0              13               362
  1               2                63
[1] 2 2
[1] FALSE
D1539V8, binary
                   cls
clus                  0   1
  TMEM168 MUTATED     8   8
  TMEM168 WILD-TYPE 217 256
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM168 MUTATED      8    8
  TMEM168 WILD-TYPE  217  256
        clus
vv       TMEM168 MUTATED TMEM168 WILD-TYPE
  FEMALE               8               217
  MALE                 8               256
[1] 2 2
[1] FALSE
D1539V9, binary
                   cls
clus                  0   1
  TMEM168 MUTATED    10   2
  TMEM168 WILD-TYPE 340  20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM168 MUTATED     10    2
  TMEM168 WILD-TYPE  340   20
     clus
vv    TMEM168 MUTATED TMEM168 WILD-TYPE
  NO               10               340
  YES               2                20
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  TMEM168 MUTATED                      8                             3
  TMEM168 WILD-TYPE                  307                            44
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  TMEM168 MUTATED                       5                              0
  TMEM168 WILD-TYPE                   101                             10
D1539V10, multiclass
                                clus
vv                               TMEM168 MUTATED TMEM168 WILD-TYPE
  COLON ADENOCARCINOMA                         8               307
  COLON MUCINOUS ADENOCARCINOMA                3                44
  RECTAL ADENOCARCINOMA                        5               101
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  TMEM168 MUTATED    10   0   1   1
  TMEM168 WILD-TYPE 335   4  30  24
D1539V11, multiclass
    clus
vv   TMEM168 MUTATED TMEM168 WILD-TYPE
  R0              10               335
  R1               0                 4
  R2               1                30
  RX               1                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1539V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TMEM168 MUTATED                                  0     1
  TMEM168 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  TMEM168 MUTATED                           1     5
  TMEM168 WILD-TYPE                        21   221
D1539V13, multiclass
                                  clus
vv                                 TMEM168 MUTATED TMEM168 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                10
  BLACK OR AFRICAN AMERICAN                      1                21
  WHITE                                          5               221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1540) Variable = NUDT15 MUTATION ANALYSIS
D1540V1, survival
                  sevent
clus2                0   1
  NUDT15 MUTATED     2   1
  NUDT15 WILD-TYPE 376  92
  NUDT15 MUTATED NUDT15 WILD-TYPE 
               3              468 
  NUDT15 MUTATED NUDT15 WILD-TYPE 
               1               92 
$`NUDT15 MUTATED`
TCGA-AY-6197 TCGA-CA-6718 TCGA-AG-A002 
       21.44        10.06        20.98 

$`NUDT15 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       16.31         0.95        33.01        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07        12.20        12.76        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  NUDT15 MUTATED NUDT15 WILD-TYPE 
           10.06             0.00 
  NUDT15 MUTATED NUDT15 WILD-TYPE 
           21.44           148.01 
  NUDT15 MUTATED NUDT15 WILD-TYPE 
          20.980           20.155 
[1] "10.1 - 21.4 (21.0)" "0.0 - 148.0 (20.2)"
[1] "hr=" "2.6"
D1540V2, continuous
D1540V3, binary
                  cls
clus                 0   1
  NUDT15 MUTATED     3   1
  NUDT15 WILD-TYPE 363 118
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NUDT15 MUTATED      3    1
  NUDT15 WILD-TYPE  363  118
        clus
vv       NUDT15 MUTATED NUDT15 WILD-TYPE
  COLON               3              363
  RECTUM              1              118
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NUDT15 MUTATED         1        0        0         3         0         0
  NUDT15 WILD-TYPE      90        1       32       135        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NUDT15 MUTATED           0          0          0          0        0
  NUDT15 WILD-TYPE        24         11         59         42       48
                  vv
clus               STAGE IVA STAGE IVB
  NUDT15 MUTATED           0         0
  NUDT15 WILD-TYPE        18         1
D1540V4, multiclass
            clus
vv           NUDT15 MUTATED NUDT15 WILD-TYPE
  STAGE I                 1               90
  STAGE IA                0                1
  STAGE II                0               32
  STAGE IIA               3              135
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              0               59
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  NUDT15 MUTATED     0   1   3   0
  NUDT15 WILD-TYPE  17  91 326  50
D1540V5, multiclass
    clus
vv   NUDT15 MUTATED NUDT15 WILD-TYPE
  T1              0               17
  T2              1               91
  T3              3              326
  T4              0               50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  NUDT15 MUTATED     4   0   0
  NUDT15 WILD-TYPE 283 113  87
D1540V6, multiclass
    clus
vv   NUDT15 MUTATED NUDT15 WILD-TYPE
  N0              4              283
  N1              0              113
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1540V7, binary
                  cls
clus                 0   1
  NUDT15 MUTATED     3   0
  NUDT15 WILD-TYPE 372  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NUDT15 MUTATED      3    0
  NUDT15 WILD-TYPE  372   65
   clus
vv  NUDT15 MUTATED NUDT15 WILD-TYPE
  0              3              372
  1              0               65
[1] 2 2
[1] FALSE
D1540V8, binary
                  cls
clus                 0   1
  NUDT15 MUTATED     1   3
  NUDT15 WILD-TYPE 224 261
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NUDT15 MUTATED      1    3
  NUDT15 WILD-TYPE  224  261
        clus
vv       NUDT15 MUTATED NUDT15 WILD-TYPE
  FEMALE              1              224
  MALE                3              261
[1] 2 2
[1] FALSE
D1540V9, binary
                  cls
clus                 0   1
  NUDT15 MUTATED     3   0
  NUDT15 WILD-TYPE 347  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NUDT15 MUTATED      3    0
  NUDT15 WILD-TYPE  347   22
     clus
vv    NUDT15 MUTATED NUDT15 WILD-TYPE
  NO               3              347
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  NUDT15 MUTATED                      3                             0
  NUDT15 WILD-TYPE                  312                            47
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  NUDT15 MUTATED                       1                              0
  NUDT15 WILD-TYPE                   105                             10
D1540V10, multiclass
                                clus
vv                               NUDT15 MUTATED NUDT15 WILD-TYPE
  COLON ADENOCARCINOMA                        3              312
  COLON MUCINOUS ADENOCARCINOMA               0               47
  RECTAL ADENOCARCINOMA                       1              105
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  NUDT15 MUTATED     3   0   0   1
  NUDT15 WILD-TYPE 342   4  31  24
D1540V11, multiclass
    clus
vv   NUDT15 MUTATED NUDT15 WILD-TYPE
  R0              3              342
  R1              0                4
  R2              0               31
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1540V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NUDT15 MUTATED                                  0     1
  NUDT15 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  NUDT15 MUTATED                           0     1
  NUDT15 WILD-TYPE                        22   225
D1540V13, multiclass
[1] "Remove cluster labels:" "NUDT15 MUTATED"        
clus
  NUDT15 MUTATED NUDT15 WILD-TYPE 
               2              258 
      TCGA-A6-2671       TCGA-A6-2672       TCGA-A6-2674       TCGA-A6-2676 
"NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" 
      TCGA-A6-2677       TCGA-A6-2678       TCGA-A6-2683       TCGA-A6-3807 
"NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" 
      TCGA-A6-3808       TCGA-A6-3809       TCGA-A6-3810       TCGA-A6-4105 
"NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" 
      TCGA-A6-5656       TCGA-A6-5657       TCGA-A6-5659       TCGA-A6-5660 
"NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" 
      TCGA-A6-5661       TCGA-A6-5662       TCGA-A6-5664       TCGA-A6-5665 
"NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" 
      TCGA-A6-5666       TCGA-A6-6137       TCGA-A6-6138       TCGA-A6-6141 
"NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" 
      TCGA-A6-6142       TCGA-A6-6648       TCGA-A6-6649       TCGA-A6-6651 
"NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" 
      TCGA-A6-6652       TCGA-A6-6653       TCGA-A6-6654       TCGA-A6-6780 
"NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" 
      TCGA-A6-6781       TCGA-A6-6782       TCGA-AD-5900       TCGA-AD-6548 
"NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" 
      TCGA-AD-6888       TCGA-AD-6889       TCGA-AD-6890       TCGA-AD-6895 
"NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" 
      TCGA-AD-6899       TCGA-AD-6901       TCGA-AD-6963       TCGA-AD-6964 
"NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" 
      TCGA-AD-6965       TCGA-AU-3779       TCGA-AU-6004       TCGA-AY-4070 
"NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" 
      TCGA-AY-4071       TCGA-AY-5543       TCGA-AY-6196       TCGA-AY-6386 
"NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" 
      TCGA-AZ-4315       TCGA-AZ-4323       TCGA-AZ-4616       TCGA-AZ-4681 
"NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" 
      TCGA-AZ-4682       TCGA-AZ-5403       TCGA-AZ-5407       TCGA-AZ-6598 
"NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" 
      TCGA-AZ-6599       TCGA-AZ-6600       TCGA-AZ-6601       TCGA-AZ-6603 
"NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" 
      TCGA-AZ-6605       TCGA-AZ-6606       TCGA-AZ-6607       TCGA-AZ-6608 
"NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" 
      TCGA-CA-5254       TCGA-CA-5255       TCGA-CA-5796       TCGA-CA-5797 
"NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" 
      TCGA-CA-6715       TCGA-CA-6716       TCGA-CA-6717       TCGA-CA-6719 
"NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" 
      TCGA-CK-4947       TCGA-CK-4948       TCGA-CK-4950       TCGA-CK-4952 
"NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" 
      TCGA-CK-5912       TCGA-CK-5913       TCGA-CK-5914       TCGA-CK-5915 
"NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" 
      TCGA-CK-5916       TCGA-CK-6746       TCGA-CK-6747       TCGA-CK-6748 
"NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" 
      TCGA-CK-6751       TCGA-CM-4743       TCGA-CM-4744       TCGA-CM-4746 
"NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" 
      TCGA-CM-4747       TCGA-CM-4752       TCGA-CM-5341       TCGA-CM-5344 
"NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" 
      TCGA-CM-5348       TCGA-CM-5349       TCGA-CM-5860       TCGA-CM-5861 
"NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" 
      TCGA-CM-5862       TCGA-CM-5863       TCGA-CM-5864       TCGA-CM-5868 
"NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" 
      TCGA-CM-6161       TCGA-CM-6162       TCGA-CM-6163       TCGA-CM-6164 
"NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" 
      TCGA-CM-6165       TCGA-CM-6166       TCGA-CM-6167       TCGA-CM-6168 
"NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" 
      TCGA-CM-6169       TCGA-CM-6170       TCGA-CM-6171       TCGA-CM-6172 
"NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" 
      TCGA-CM-6674       TCGA-CM-6675       TCGA-CM-6676       TCGA-CM-6677 
"NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" 
      TCGA-CM-6678       TCGA-CM-6679       TCGA-CM-6680       TCGA-D5-5537 
"NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" 
      TCGA-D5-5538       TCGA-D5-5539       TCGA-D5-5540       TCGA-D5-5541 
"NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" 
      TCGA-D5-6529       TCGA-D5-6532       TCGA-D5-6533       TCGA-D5-6534 
"NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" 
      TCGA-D5-6535       TCGA-D5-6536       TCGA-D5-6537       TCGA-D5-6538 
"NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" 
      TCGA-D5-6539       TCGA-D5-6540       TCGA-D5-6541       TCGA-D5-6898 
"NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" 
      TCGA-D5-6920       TCGA-D5-6922       TCGA-D5-6923       TCGA-D5-6924 
"NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" 
      TCGA-D5-6926       TCGA-D5-6927       TCGA-D5-6928       TCGA-D5-6929 
"NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" 
      TCGA-D5-6930       TCGA-D5-6931       TCGA-D5-6932       TCGA-D5-7000 
"NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" 
      TCGA-DM-A0X9       TCGA-DM-A0XD       TCGA-DM-A0XF       TCGA-DM-A1D0 
"NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" 
      TCGA-DM-A1D4       TCGA-DM-A1D6       TCGA-DM-A1D7       TCGA-DM-A1D8 
"NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" 
      TCGA-DM-A1D9       TCGA-DM-A1DA       TCGA-DM-A1DB       TCGA-DM-A1HA 
"NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" 
      TCGA-DM-A1HB       TCGA-DM-A282       TCGA-DM-A285       TCGA-DM-A28C 
"NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" 
      TCGA-DM-A28E       TCGA-DM-A28F       TCGA-DM-A28G       TCGA-DM-A28H 
"NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" 
      TCGA-DM-A28K       TCGA-F4-6459       TCGA-F4-6460       TCGA-F4-6569 
"NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" 
      TCGA-F4-6570       TCGA-F4-6703       TCGA-F4-6704       TCGA-F4-6805 
"NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" 
      TCGA-F4-6806       TCGA-F4-6807       TCGA-F4-6808       TCGA-F4-6809 
"NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" 
      TCGA-F4-6854       TCGA-F4-6855       TCGA-F4-6856       TCGA-G4-6293 
"NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" 
      TCGA-G4-6299       TCGA-G4-6303       TCGA-G4-6304       TCGA-G4-6306 
"NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" 
      TCGA-G4-6307       TCGA-G4-6309       TCGA-G4-6310       TCGA-G4-6315 
"NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" 
      TCGA-G4-6317       TCGA-G4-6321       TCGA-G4-6323       TCGA-G4-6586 
"NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" 
      TCGA-G4-6588       TCGA-G4-6625       TCGA-G4-6626       TCGA-G4-6628 
"NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" 
      TCGA-AF-2687       TCGA-AF-2689       TCGA-AF-2691       TCGA-AF-2692 
"NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" 
      TCGA-AF-2693       TCGA-AF-3400       TCGA-AF-3913       TCGA-AF-4110 
"NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" 
      TCGA-AF-5654       TCGA-AF-6136       TCGA-AF-6655       TCGA-AF-6672 
"NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" 
      TCGA-AH-6544       TCGA-AH-6547       TCGA-AH-6549       TCGA-AH-6643 
"NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" 
      TCGA-AH-6644       TCGA-CI-6619       TCGA-CI-6620       TCGA-CI-6621 
"NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" 
      TCGA-CI-6622       TCGA-CI-6624       TCGA-CL-5917       TCGA-CL-5918 
"NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" 
      TCGA-DC-5337       TCGA-DC-5869       TCGA-DC-6155       TCGA-DC-6157 
"NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" 
      TCGA-DC-6158       TCGA-DC-6160       TCGA-DC-6681       TCGA-DC-6682 
"NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" 
      TCGA-DC-6683       TCGA-DT-5265       TCGA-DY-A0XA       TCGA-DY-A1DC 
"NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" 
      TCGA-DY-A1DD       TCGA-DY-A1DF       TCGA-DY-A1DG       TCGA-DY-A1H8 
"NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" 
      TCGA-EF-5830       TCGA-EI-6506       TCGA-EI-6507       TCGA-EI-6508 
"NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" 
      TCGA-EI-6510       TCGA-F5-6464       TCGA-F5-6465       TCGA-F5-6571 
"NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" 
      TCGA-F5-6702       TCGA-F5-6811       TCGA-F5-6812       TCGA-F5-6813 
"NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" 
      TCGA-G5-6235       TCGA-G5-6641 
"NUDT15 WILD-TYPE" "NUDT15 WILD-TYPE" 

Clustering(1541) Variable = PANK1 MUTATION ANALYSIS
D1541V1, survival
                 sevent
clus2               0   1
  PANK1 MUTATED     6   1
  PANK1 WILD-TYPE 372  92
  PANK1 MUTATED PANK1 WILD-TYPE 
              7             464 
  PANK1 MUTATED PANK1 WILD-TYPE 
              1              92 
$`PANK1 MUTATED`
TCGA-A6-3809 TCGA-A6-5661 TCGA-A6-6653 TCGA-AA-3713 TCGA-AA-A00N TCGA-AA-A010 
       32.75        33.53        24.39        19.04         4.01        34.98 
TCGA-AZ-4315 
       58.39 

$`PANK1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       31.63        30.44        29.19        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       24.16        21.76        24.69        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       85.05        26.99        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
       16.31         0.95        33.01        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  PANK1 MUTATED PANK1 WILD-TYPE 
           4.01            0.00 
  PANK1 MUTATED PANK1 WILD-TYPE 
          58.39          148.01 
  PANK1 MUTATED PANK1 WILD-TYPE 
         32.750          20.085 
[1] "4.0 - 58.4 (32.8)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.5"
D1541V2, continuous
D1541V3, binary
                 cls
clus                0   1
  PANK1 MUTATED     7   0
  PANK1 WILD-TYPE 359 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PANK1 MUTATED      7    0
  PANK1 WILD-TYPE  359  119
        clus
vv       PANK1 MUTATED PANK1 WILD-TYPE
  COLON              7             359
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PANK1 MUTATED         1        0        0         2         3         0
  PANK1 WILD-TYPE      90        1       32       136         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PANK1 MUTATED           0          0          0          0        1         0
  PANK1 WILD-TYPE        24         11         59         42       47        18
                 vv
clus              STAGE IVB
  PANK1 MUTATED           0
  PANK1 WILD-TYPE         1
D1541V4, multiclass
            clus
vv           PANK1 MUTATED PANK1 WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              2             136
  STAGE IIB              3               7
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             0              42
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PANK1 MUTATED     0   1   3   3
  PANK1 WILD-TYPE  17  91 326  47
D1541V5, multiclass
    clus
vv   PANK1 MUTATED PANK1 WILD-TYPE
  T1             0              17
  T2             1              91
  T3             3             326
  T4             3              47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  PANK1 MUTATED     7   0   0
  PANK1 WILD-TYPE 280 113  87
D1541V6, multiclass
    clus
vv   PANK1 MUTATED PANK1 WILD-TYPE
  N0             7             280
  N1             0             113
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1541V7, binary
                 cls
clus                0   1
  PANK1 MUTATED     6   1
  PANK1 WILD-TYPE 369  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PANK1 MUTATED      6    1
  PANK1 WILD-TYPE  369   64
   clus
vv  PANK1 MUTATED PANK1 WILD-TYPE
  0             6             369
  1             1              64
[1] 2 2
[1] FALSE
D1541V8, binary
                 cls
clus                0   1
  PANK1 MUTATED     3   4
  PANK1 WILD-TYPE 222 260
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PANK1 MUTATED      3    4
  PANK1 WILD-TYPE  222  260
        clus
vv       PANK1 MUTATED PANK1 WILD-TYPE
  FEMALE             3             222
  MALE               4             260
[1] 2 2
[1] FALSE
D1541V9, binary
                 cls
clus                0   1
  PANK1 MUTATED     5   1
  PANK1 WILD-TYPE 345  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PANK1 MUTATED      5    1
  PANK1 WILD-TYPE  345   21
     clus
vv    PANK1 MUTATED PANK1 WILD-TYPE
  NO              5             345
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PANK1 MUTATED                      5                             2
  PANK1 WILD-TYPE                  310                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PANK1 MUTATED                       0                              0
  PANK1 WILD-TYPE                   106                             10
D1541V10, multiclass
                                clus
vv                               PANK1 MUTATED PANK1 WILD-TYPE
  COLON ADENOCARCINOMA                       5             310
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  PANK1 MUTATED     5   0   1   0
  PANK1 WILD-TYPE 340   4  30  25
D1541V11, multiclass
    clus
vv   PANK1 MUTATED PANK1 WILD-TYPE
  R0             5             340
  R1             0               4
  R2             1              30
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1541V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PANK1 MUTATED                                  0     0
  PANK1 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PANK1 MUTATED                           1     3
  PANK1 WILD-TYPE                        21   223
D1541V13, multiclass
                                  clus
vv                                 PANK1 MUTATED PANK1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        3             223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1542) Variable = SYT14 MUTATION ANALYSIS
D1542V1, survival
                 sevent
clus2               0   1
  SYT14 MUTATED    10   4
  SYT14 WILD-TYPE 368  89
  SYT14 MUTATED SYT14 WILD-TYPE 
             14             457 
  SYT14 MUTATED SYT14 WILD-TYPE 
              4              89 
$`SYT14 MUTATED`
TCGA-A6-3809 TCGA-A6-6649 TCGA-AA-3518 TCGA-AA-3667 TCGA-AA-3831 TCGA-AA-A00J 
       32.75        24.16         1.02        14.01        17.98        18.05 
TCGA-AU-6004 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-6606 TCGA-CA-6717 TCGA-DM-A1D7 
       27.09         5.13        22.36        11.74        12.76        13.32 
TCGA-G4-6628 TCGA-AG-A002 
       79.69        20.98 

$`SYT14 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       25.18        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3519 
       63.98         6.97         1.02        13.02        38.99         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
        2.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
        0.99        25.02         1.02        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 
       22.42        27.42        10.88         0.20        14.50        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4681 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
      106.75        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
      100.01        29.56         5.23         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07        12.20        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
      130.65        92.75        49.91        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 
       13.78        35.80        26.17        91.79        46.75        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  SYT14 MUTATED SYT14 WILD-TYPE 
           1.02            0.00 
  SYT14 MUTATED SYT14 WILD-TYPE 
          79.69          148.01 
  SYT14 MUTATED SYT14 WILD-TYPE 
         18.015          20.280 
[1] "1.0 - 79.7 (18.0)"  "0.0 - 148.0 (20.3)"
[1] "hr=" "1.8"
D1542V2, continuous
D1542V3, binary
                 cls
clus                0   1
  SYT14 MUTATED    14   1
  SYT14 WILD-TYPE 352 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SYT14 MUTATED     14    1
  SYT14 WILD-TYPE  352  118
        clus
vv       SYT14 MUTATED SYT14 WILD-TYPE
  COLON             14             352
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SYT14 MUTATED         4        0        0         5         1         0
  SYT14 WILD-TYPE      87        1       32       133         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SYT14 MUTATED           0          0          2          0        2         1
  SYT14 WILD-TYPE        24         11         57         42       46        17
                 vv
clus              STAGE IVB
  SYT14 MUTATED           0
  SYT14 WILD-TYPE         1
D1542V4, multiclass
            clus
vv           SYT14 MUTATED SYT14 WILD-TYPE
  STAGE I                4              87
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              5             133
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             2              57
  STAGE IIIC             0              42
  STAGE IV               2              46
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  SYT14 MUTATED     0   4   8   3
  SYT14 WILD-TYPE  17  88 321  47
D1542V5, multiclass
    clus
vv   SYT14 MUTATED SYT14 WILD-TYPE
  T1             0              17
  T2             4              88
  T3             8             321
  T4             3              47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  SYT14 MUTATED    11   2   2
  SYT14 WILD-TYPE 276 111  85
D1542V6, multiclass
    clus
vv   SYT14 MUTATED SYT14 WILD-TYPE
  N0            11             276
  N1             2             111
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1542V7, binary
                 cls
clus                0   1
  SYT14 MUTATED    12   3
  SYT14 WILD-TYPE 363  62
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SYT14 MUTATED     12    3
  SYT14 WILD-TYPE  363   62
   clus
vv  SYT14 MUTATED SYT14 WILD-TYPE
  0            12             363
  1             3              62
[1] 2 2
[1] FALSE
D1542V8, binary
                 cls
clus                0   1
  SYT14 MUTATED     6   9
  SYT14 WILD-TYPE 219 255
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SYT14 MUTATED      6    9
  SYT14 WILD-TYPE  219  255
        clus
vv       SYT14 MUTATED SYT14 WILD-TYPE
  FEMALE             6             219
  MALE               9             255
[1] 2 2
[1] FALSE
D1542V9, binary
                 cls
clus                0   1
  SYT14 MUTATED    11   0
  SYT14 WILD-TYPE 339  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SYT14 MUTATED     11    0
  SYT14 WILD-TYPE  339   22
     clus
vv    SYT14 MUTATED SYT14 WILD-TYPE
  NO             11             339
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SYT14 MUTATED                     10                             3
  SYT14 WILD-TYPE                  305                            44
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SYT14 MUTATED                       1                              0
  SYT14 WILD-TYPE                   105                             10
D1542V10, multiclass
                                clus
vv                               SYT14 MUTATED SYT14 WILD-TYPE
  COLON ADENOCARCINOMA                      10             305
  COLON MUCINOUS ADENOCARCINOMA              3              44
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  SYT14 MUTATED    10   0   0   1
  SYT14 WILD-TYPE 335   4  31  24
D1542V11, multiclass
    clus
vv   SYT14 MUTATED SYT14 WILD-TYPE
  R0            10             335
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1542V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SYT14 MUTATED                                  0     1
  SYT14 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  SYT14 MUTATED                           0     8
  SYT14 WILD-TYPE                        22   218
D1542V13, multiclass
                                  clus
vv                                 SYT14 MUTATED SYT14 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        8             218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1543) Variable = ARHGAP25 MUTATION ANALYSIS
D1543V1, survival
                    sevent
clus2                  0   1
  ARHGAP25 MUTATED    11   1
  ARHGAP25 WILD-TYPE 367  92
  ARHGAP25 MUTATED ARHGAP25 WILD-TYPE 
                12                459 
  ARHGAP25 MUTATED ARHGAP25 WILD-TYPE 
                 1                 92 
$`ARHGAP25 MUTATED`
TCGA-AA-3660 TCGA-AA-3947 TCGA-AA-A01R TCGA-AU-6004 TCGA-AZ-4315 TCGA-CA-6717 
       78.08        33.01        35.01        27.09        58.39        12.76 
TCGA-D5-6533 TCGA-D5-6536 TCGA-D5-6922 TCGA-DM-A0XF TCGA-AG-A002 TCGA-AG-A00C 
        1.32        17.85         4.41        38.20        20.98         6.02 

$`ARHGAP25 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 
       20.98        19.99        13.94        19.99        61.02         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
        2.01        12.99        24.00        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T 
       31.00        31.00        38.07         1.02         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
        0.20        14.50        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07        12.20        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 
       56.09        55.92        20.19        18.25        43.27        15.12 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        3.68        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       24.43       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00H 
       36.03        14.04         1.02        17.03        13.94        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  ARHGAP25 MUTATED ARHGAP25 WILD-TYPE 
              1.32               0.00 
  ARHGAP25 MUTATED ARHGAP25 WILD-TYPE 
             78.08             148.01 
  ARHGAP25 MUTATED ARHGAP25 WILD-TYPE 
            24.035             20.120 
[1] "1.3 - 78.1 (24.0)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "2.5"
D1543V2, continuous
D1543V3, binary
                    cls
clus                   0   1
  ARHGAP25 MUTATED    10   2
  ARHGAP25 WILD-TYPE 356 117
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ARHGAP25 MUTATED     10    2
  ARHGAP25 WILD-TYPE  356  117
        clus
vv       ARHGAP25 MUTATED ARHGAP25 WILD-TYPE
  COLON                10                356
  RECTUM                2                117
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ARHGAP25 MUTATED         2        0        1         3         1         0
  ARHGAP25 WILD-TYPE      89        1       31       135         9         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ARHGAP25 MUTATED           1          1          2          1        0
  ARHGAP25 WILD-TYPE        23         10         57         41       48
                    vv
clus                 STAGE IVA STAGE IVB
  ARHGAP25 MUTATED           0         0
  ARHGAP25 WILD-TYPE        18         1
D1543V4, multiclass
            clus
vv           ARHGAP25 MUTATED ARHGAP25 WILD-TYPE
  STAGE I                   2                 89
  STAGE IA                  0                  1
  STAGE II                  1                 31
  STAGE IIA                 3                135
  STAGE IIB                 1                  9
  STAGE IIC                 0                  1
  STAGE III                 1                 23
  STAGE IIIA                1                 10
  STAGE IIIB                2                 57
  STAGE IIIC                1                 41
  STAGE IV                  0                 48
  STAGE IVA                 0                 18
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  ARHGAP25 MUTATED     0   2   8   2
  ARHGAP25 WILD-TYPE  17  90 321  48
D1543V5, multiclass
    clus
vv   ARHGAP25 MUTATED ARHGAP25 WILD-TYPE
  T1                0                 17
  T2                2                 90
  T3                8                321
  T4                2                 48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  ARHGAP25 MUTATED     8   2   2
  ARHGAP25 WILD-TYPE 279 111  85
D1543V6, multiclass
    clus
vv   ARHGAP25 MUTATED ARHGAP25 WILD-TYPE
  N0                8                279
  N1                2                111
  N2                2                 85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1543V7, binary
                    cls
clus                   0   1
  ARHGAP25 MUTATED    12   0
  ARHGAP25 WILD-TYPE 363  65
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ARHGAP25 MUTATED     12    0
  ARHGAP25 WILD-TYPE  363   65
   clus
vv  ARHGAP25 MUTATED ARHGAP25 WILD-TYPE
  0               12                363
  1                0                 65
[1] 2 2
[1] FALSE
D1543V8, binary
                    cls
clus                   0   1
  ARHGAP25 MUTATED     6   6
  ARHGAP25 WILD-TYPE 219 258
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ARHGAP25 MUTATED      6    6
  ARHGAP25 WILD-TYPE  219  258
        clus
vv       ARHGAP25 MUTATED ARHGAP25 WILD-TYPE
  FEMALE                6                219
  MALE                  6                258
[1] 2 2
[1] FALSE
D1543V9, binary
                    cls
clus                   0   1
  ARHGAP25 MUTATED     6   2
  ARHGAP25 WILD-TYPE 344  20
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ARHGAP25 MUTATED      6    2
  ARHGAP25 WILD-TYPE  344   20
     clus
vv    ARHGAP25 MUTATED ARHGAP25 WILD-TYPE
  NO                 6                344
  YES                2                 20
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ARHGAP25 MUTATED                      6                             3
  ARHGAP25 WILD-TYPE                  309                            44
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ARHGAP25 MUTATED                       2                              0
  ARHGAP25 WILD-TYPE                   104                             10
D1543V10, multiclass
                                clus
vv                               ARHGAP25 MUTATED ARHGAP25 WILD-TYPE
  COLON ADENOCARCINOMA                          6                309
  COLON MUCINOUS ADENOCARCINOMA                 3                 44
  RECTAL ADENOCARCINOMA                         2                104
  RECTAL MUCINOUS ADENOCARCINOMA                0                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  ARHGAP25 MUTATED    10   0   0   1
  ARHGAP25 WILD-TYPE 335   4  31  24
D1543V11, multiclass
    clus
vv   ARHGAP25 MUTATED ARHGAP25 WILD-TYPE
  R0               10                335
  R1                0                  4
  R2                0                 31
  RX                1                 24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1543V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ARHGAP25 MUTATED                                  0     1
  ARHGAP25 WILD-TYPE                                1    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  ARHGAP25 MUTATED                           0     6
  ARHGAP25 WILD-TYPE                        22   220
D1543V13, multiclass
                                  clus
vv                                 ARHGAP25 MUTATED ARHGAP25 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                 10
  BLACK OR AFRICAN AMERICAN                       0                 22
  WHITE                                           6                220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1544) Variable = HCFC1R1 MUTATION ANALYSIS
D1544V1, survival
                   sevent
clus2                 0   1
  HCFC1R1 MUTATED     3   2
  HCFC1R1 WILD-TYPE 375  91
  HCFC1R1 MUTATED HCFC1R1 WILD-TYPE 
                5               466 
  HCFC1R1 MUTATED HCFC1R1 WILD-TYPE 
                2                91 
$`HCFC1R1 MUTATED`
TCGA-A6-5665 TCGA-A6-6781 TCGA-AA-3845 TCGA-DM-A1D7 TCGA-G4-6586 
       22.06        19.66         0.00        13.32        35.80 

$`HCFC1R1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 
       15.95        38.99        37.02        14.93        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D8 
       24.43        38.20       130.65        92.75        49.91        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  HCFC1R1 MUTATED HCFC1R1 WILD-TYPE 
                0                 0 
  HCFC1R1 MUTATED HCFC1R1 WILD-TYPE 
            35.80            148.01 
  HCFC1R1 MUTATED HCFC1R1 WILD-TYPE 
           19.660            20.235 
[1] "0.0 - 35.8 (19.7)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "3.2"
D1544V2, continuous
D1544V3, binary
                   cls
clus                  0   1
  HCFC1R1 MUTATED     5   0
  HCFC1R1 WILD-TYPE 361 119
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HCFC1R1 MUTATED      5    0
  HCFC1R1 WILD-TYPE  361  119
        clus
vv       HCFC1R1 MUTATED HCFC1R1 WILD-TYPE
  COLON                5               361
  RECTUM               0               119
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  HCFC1R1 MUTATED         0        0        0         4         0         0
  HCFC1R1 WILD-TYPE      91        1       32       134        10         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HCFC1R1 MUTATED           0          0          0          1        0
  HCFC1R1 WILD-TYPE        24         11         59         41       48
                   vv
clus                STAGE IVA STAGE IVB
  HCFC1R1 MUTATED           0         0
  HCFC1R1 WILD-TYPE        18         1
D1544V4, multiclass
            clus
vv           HCFC1R1 MUTATED HCFC1R1 WILD-TYPE
  STAGE I                  0                91
  STAGE IA                 0                 1
  STAGE II                 0                32
  STAGE IIA                4               134
  STAGE IIB                0                10
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               0                11
  STAGE IIIB               0                59
  STAGE IIIC               1                41
  STAGE IV                 0                48
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  HCFC1R1 MUTATED     0   0   4   1
  HCFC1R1 WILD-TYPE  17  92 325  49
D1544V5, multiclass
    clus
vv   HCFC1R1 MUTATED HCFC1R1 WILD-TYPE
  T1               0                17
  T2               0                92
  T3               4               325
  T4               1                49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  HCFC1R1 MUTATED     4   1   0
  HCFC1R1 WILD-TYPE 283 112  87
D1544V6, multiclass
    clus
vv   HCFC1R1 MUTATED HCFC1R1 WILD-TYPE
  N0               4               283
  N1               1               112
  N2               0                87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1544V7, binary
                   cls
clus                  0   1
  HCFC1R1 MUTATED     4   0
  HCFC1R1 WILD-TYPE 371  65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HCFC1R1 MUTATED      4    0
  HCFC1R1 WILD-TYPE  371   65
   clus
vv  HCFC1R1 MUTATED HCFC1R1 WILD-TYPE
  0               4               371
  1               0                65
[1] 2 2
[1] FALSE
D1544V8, binary
                   cls
clus                  0   1
  HCFC1R1 MUTATED     3   2
  HCFC1R1 WILD-TYPE 222 262
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HCFC1R1 MUTATED      3    2
  HCFC1R1 WILD-TYPE  222  262
        clus
vv       HCFC1R1 MUTATED HCFC1R1 WILD-TYPE
  FEMALE               3               222
  MALE                 2               262
[1] 2 2
[1] FALSE
D1544V9, binary
                   cls
clus                  0   1
  HCFC1R1 MUTATED     3   0
  HCFC1R1 WILD-TYPE 347  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HCFC1R1 MUTATED      3    0
  HCFC1R1 WILD-TYPE  347   22
     clus
vv    HCFC1R1 MUTATED HCFC1R1 WILD-TYPE
  NO                3               347
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  HCFC1R1 MUTATED                      3                             1
  HCFC1R1 WILD-TYPE                  312                            46
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  HCFC1R1 MUTATED                       0                              0
  HCFC1R1 WILD-TYPE                   106                             10
D1544V10, multiclass
                                clus
vv                               HCFC1R1 MUTATED HCFC1R1 WILD-TYPE
  COLON ADENOCARCINOMA                         3               312
  COLON MUCINOUS ADENOCARCINOMA                1                46
  RECTAL ADENOCARCINOMA                        0               106
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  HCFC1R1 MUTATED     4   0   0   0
  HCFC1R1 WILD-TYPE 341   4  31  25
D1544V11, multiclass
    clus
vv   HCFC1R1 MUTATED HCFC1R1 WILD-TYPE
  R0               4               341
  R1               0                 4
  R2               0                31
  RX               0                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1544V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HCFC1R1 MUTATED                                  0     0
  HCFC1R1 WILD-TYPE                                1    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  HCFC1R1 MUTATED                           0     4
  HCFC1R1 WILD-TYPE                        22   222
D1544V13, multiclass
                                  clus
vv                                 HCFC1R1 MUTATED HCFC1R1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                      0                22
  WHITE                                          4               222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1545) Variable = C7ORF66 MUTATION ANALYSIS
D1545V1, survival
                   sevent
clus2                 0   1
  C7ORF66 MUTATED     7   0
  C7ORF66 WILD-TYPE 371  93
  C7ORF66 MUTATED C7ORF66 WILD-TYPE 
                7               464 
  C7ORF66 MUTATED C7ORF66 WILD-TYPE 
                0                93 
$`C7ORF66 MUTATED`
TCGA-A6-6781 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6677 TCGA-D5-7000 TCGA-DM-A1HB 
       19.66        21.99        14.99        11.08        10.26       135.65 
TCGA-AH-6644 
        0.72 

$`C7ORF66 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       13.05        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
        1.51        12.00        11.38       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
        7.50        44.32       131.51       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
       17.49         0.69         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  C7ORF66 MUTATED C7ORF66 WILD-TYPE 
             0.72              0.00 
  C7ORF66 MUTATED C7ORF66 WILD-TYPE 
           135.65            148.01 
  C7ORF66 MUTATED C7ORF66 WILD-TYPE 
           14.990            20.415 
[1] "0.7 - 135.7 (15.0)" "0.0 - 148.0 (20.4)"
[1] "hr="     "9200000"
D1545V2, continuous
D1545V3, binary
                   cls
clus                  0   1
  C7ORF66 MUTATED     7   1
  C7ORF66 WILD-TYPE 359 118
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C7ORF66 MUTATED      7    1
  C7ORF66 WILD-TYPE  359  118
        clus
vv       C7ORF66 MUTATED C7ORF66 WILD-TYPE
  COLON                7               359
  RECTUM               1               118
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  C7ORF66 MUTATED         2        0        0         2         0         0
  C7ORF66 WILD-TYPE      89        1       32       136        10         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C7ORF66 MUTATED           0          0          1          2        0
  C7ORF66 WILD-TYPE        24         11         58         40       48
                   vv
clus                STAGE IVA STAGE IVB
  C7ORF66 MUTATED           0         0
  C7ORF66 WILD-TYPE        18         1
D1545V4, multiclass
            clus
vv           C7ORF66 MUTATED C7ORF66 WILD-TYPE
  STAGE I                  2                89
  STAGE IA                 0                 1
  STAGE II                 0                32
  STAGE IIA                2               136
  STAGE IIB                0                10
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               0                11
  STAGE IIIB               1                58
  STAGE IIIC               2                40
  STAGE IV                 0                48
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  C7ORF66 MUTATED     0   2   5   1
  C7ORF66 WILD-TYPE  17  90 324  49
D1545V5, multiclass
    clus
vv   C7ORF66 MUTATED C7ORF66 WILD-TYPE
  T1               0                17
  T2               2                90
  T3               5               324
  T4               1                49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  C7ORF66 MUTATED     4   2   1
  C7ORF66 WILD-TYPE 283 111  86
D1545V6, multiclass
    clus
vv   C7ORF66 MUTATED C7ORF66 WILD-TYPE
  N0               4               283
  N1               2               111
  N2               1                86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1545V7, binary
                   cls
clus                  0   1
  C7ORF66 MUTATED     6   0
  C7ORF66 WILD-TYPE 369  65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C7ORF66 MUTATED      6    0
  C7ORF66 WILD-TYPE  369   65
   clus
vv  C7ORF66 MUTATED C7ORF66 WILD-TYPE
  0               6               369
  1               0                65
[1] 2 2
[1] FALSE
D1545V8, binary
                   cls
clus                  0   1
  C7ORF66 MUTATED     5   3
  C7ORF66 WILD-TYPE 220 261
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C7ORF66 MUTATED      5    3
  C7ORF66 WILD-TYPE  220  261
        clus
vv       C7ORF66 MUTATED C7ORF66 WILD-TYPE
  FEMALE               5               220
  MALE                 3               261
[1] 2 2
[1] FALSE
D1545V9, binary
                   cls
clus                  0   1
  C7ORF66 MUTATED     5   0
  C7ORF66 WILD-TYPE 345  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C7ORF66 MUTATED      5    0
  C7ORF66 WILD-TYPE  345   22
     clus
vv    C7ORF66 MUTATED C7ORF66 WILD-TYPE
  NO                5               345
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  C7ORF66 MUTATED                      4                             2
  C7ORF66 WILD-TYPE                  311                            45
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  C7ORF66 MUTATED                       1                              0
  C7ORF66 WILD-TYPE                   105                             10
D1545V10, multiclass
                                clus
vv                               C7ORF66 MUTATED C7ORF66 WILD-TYPE
  COLON ADENOCARCINOMA                         4               311
  COLON MUCINOUS ADENOCARCINOMA                2                45
  RECTAL ADENOCARCINOMA                        1               105
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  C7ORF66 MUTATED     6   0   0   0
  C7ORF66 WILD-TYPE 339   4  31  25
D1545V11, multiclass
    clus
vv   C7ORF66 MUTATED C7ORF66 WILD-TYPE
  R0               6               339
  R1               0                 4
  R2               0                31
  RX               0                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1545V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C7ORF66 MUTATED                                  0     0
  C7ORF66 WILD-TYPE                                1    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  C7ORF66 MUTATED                           1     6
  C7ORF66 WILD-TYPE                        21   220
D1545V13, multiclass
                                  clus
vv                                 C7ORF66 MUTATED C7ORF66 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                      1                21
  WHITE                                          6               220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1546) Variable = CD47 MUTATION ANALYSIS
D1546V1, survival
                sevent
clus2              0   1
  CD47 MUTATED     6   0
  CD47 WILD-TYPE 372  93
  CD47 MUTATED CD47 WILD-TYPE 
             6            465 
  CD47 MUTATED CD47 WILD-TYPE 
             0             93 
$`CD47 MUTATED`
TCGA-AA-3947 TCGA-AA-A010 TCGA-CA-6717 TCGA-CK-4952 TCGA-CM-5868 TCGA-D5-6541 
       33.01        34.98        12.76        15.62        17.03        15.58 

$`CD47 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 
       31.00         2.01        12.99        24.00        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.20        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
        5.03        15.02        15.02        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       16.14         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  CD47 MUTATED CD47 WILD-TYPE 
         12.76           0.00 
  CD47 MUTATED CD47 WILD-TYPE 
         34.98         148.01 
  CD47 MUTATED CD47 WILD-TYPE 
        16.325         20.280 
[1] "12.8 - 35.0 (16.3)" "0.0 - 148.0 (20.3)"
[1] "hr="     "3300000"
D1546V2, continuous
D1546V3, binary
                cls
clus               0   1
  CD47 MUTATED     8   0
  CD47 WILD-TYPE 358 119
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD47 MUTATED      8    0
  CD47 WILD-TYPE  358  119
        clus
vv       CD47 MUTATED CD47 WILD-TYPE
  COLON             8            358
  RECTUM            0            119
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CD47 MUTATED         0        0        1         2         2         0
  CD47 WILD-TYPE      91        1       31       136         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CD47 MUTATED           1          0          0          1        0         1
  CD47 WILD-TYPE        23         11         59         41       48        17
                vv
clus             STAGE IVB
  CD47 MUTATED           0
  CD47 WILD-TYPE         1
D1546V4, multiclass
            clus
vv           CD47 MUTATED CD47 WILD-TYPE
  STAGE I               0             91
  STAGE IA              0              1
  STAGE II              1             31
  STAGE IIA             2            136
  STAGE IIB             2              8
  STAGE IIC             0              1
  STAGE III             1             23
  STAGE IIIA            0             11
  STAGE IIIB            0             59
  STAGE IIIC            1             41
  STAGE IV              0             48
  STAGE IVA             1             17
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  CD47 MUTATED     0   0   3   5
  CD47 WILD-TYPE  17  92 326  45
D1546V5, multiclass
    clus
vv   CD47 MUTATED CD47 WILD-TYPE
  T1            0             17
  T2            0             92
  T3            3            326
  T4            5             45
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  CD47 MUTATED     5   1   2
  CD47 WILD-TYPE 282 112  85
D1546V6, multiclass
    clus
vv   CD47 MUTATED CD47 WILD-TYPE
  N0            5            282
  N1            1            112
  N2            2             85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1546V7, binary
                cls
clus               0   1
  CD47 MUTATED     7   1
  CD47 WILD-TYPE 368  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD47 MUTATED      7    1
  CD47 WILD-TYPE  368   64
   clus
vv  CD47 MUTATED CD47 WILD-TYPE
  0            7            368
  1            1             64
[1] 2 2
[1] FALSE
D1546V8, binary
                cls
clus               0   1
  CD47 MUTATED     5   3
  CD47 WILD-TYPE 220 261
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD47 MUTATED      5    3
  CD47 WILD-TYPE  220  261
        clus
vv       CD47 MUTATED CD47 WILD-TYPE
  FEMALE            5            220
  MALE              3            261
[1] 2 2
[1] FALSE
D1546V9, binary
                cls
clus               0   1
  CD47 MUTATED     5   0
  CD47 WILD-TYPE 345  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  CD47 MUTATED      5    0
  CD47 WILD-TYPE  345   22
     clus
vv    CD47 MUTATED CD47 WILD-TYPE
  NO             5            345
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CD47 MUTATED                      5                             3
  CD47 WILD-TYPE                  310                            44
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CD47 MUTATED                       0                              0
  CD47 WILD-TYPE                   106                             10
D1546V10, multiclass
                                clus
vv                               CD47 MUTATED CD47 WILD-TYPE
  COLON ADENOCARCINOMA                      5            310
  COLON MUCINOUS ADENOCARCINOMA             3             44
  RECTAL ADENOCARCINOMA                     0            106
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  CD47 MUTATED     6   0   0   2
  CD47 WILD-TYPE 339   4  31  23
D1546V11, multiclass
    clus
vv   CD47 MUTATED CD47 WILD-TYPE
  R0            6            339
  R1            0              4
  R2            0             31
  RX            2             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1546V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CD47 MUTATED                                  0     1
  CD47 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  CD47 MUTATED                           0     3
  CD47 WILD-TYPE                        22   223
D1546V13, multiclass
                                  clus
vv                                 CD47 MUTATED CD47 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       3            223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1547) Variable = RWDD4A MUTATION ANALYSIS
D1547V1, survival
                  sevent
clus2                0   1
  RWDD4A MUTATED     5   0
  RWDD4A WILD-TYPE 373  93
  RWDD4A MUTATED RWDD4A WILD-TYPE 
               5              466 
  RWDD4A MUTATED RWDD4A WILD-TYPE 
               0               93 
$`RWDD4A MUTATED`
TCGA-AA-3510 TCGA-AA-3520 TCGA-AD-6963 TCGA-CM-6678 TCGA-DM-A282 
       63.98        24.03        27.42        11.01       139.17 

$`RWDD4A WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        1.02         9.07        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6964 
       56.55         0.79         0.72         5.79        22.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       13.05        11.08        11.08        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A285 
      140.38         7.50        44.32       131.51       135.65         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  RWDD4A MUTATED RWDD4A WILD-TYPE 
           11.01             0.00 
  RWDD4A MUTATED RWDD4A WILD-TYPE 
          139.17           148.01 
  RWDD4A MUTATED RWDD4A WILD-TYPE 
          27.420           20.085 
[1] "11.0 - 139.2 (27.4)" "0.0 - 148.0 (20.1)" 
[1] "hr="     "9300000"
D1547V2, continuous
D1547V3, binary
                  cls
clus                 0   1
  RWDD4A MUTATED     5   0
  RWDD4A WILD-TYPE 361 119
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RWDD4A MUTATED      5    0
  RWDD4A WILD-TYPE  361  119
        clus
vv       RWDD4A MUTATED RWDD4A WILD-TYPE
  COLON               5              361
  RECTUM              0              119
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RWDD4A MUTATED         0        0        2         1         0         0
  RWDD4A WILD-TYPE      91        1       30       137        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RWDD4A MUTATED           0          0          0          0        0
  RWDD4A WILD-TYPE        24         11         59         42       48
                  vv
clus               STAGE IVA STAGE IVB
  RWDD4A MUTATED           1         0
  RWDD4A WILD-TYPE        17         1
D1547V4, multiclass
            clus
vv           RWDD4A MUTATED RWDD4A WILD-TYPE
  STAGE I                 0               91
  STAGE IA                0                1
  STAGE II                2               30
  STAGE IIA               1              137
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              0               59
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               1               17
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  RWDD4A MUTATED     0   0   4   1
  RWDD4A WILD-TYPE  17  92 325  49
D1547V5, multiclass
    clus
vv   RWDD4A MUTATED RWDD4A WILD-TYPE
  T1              0               17
  T2              0               92
  T3              4              325
  T4              1               49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  RWDD4A MUTATED     4   1   0
  RWDD4A WILD-TYPE 283 112  87
D1547V6, multiclass
    clus
vv   RWDD4A MUTATED RWDD4A WILD-TYPE
  N0              4              283
  N1              1              112
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1547V7, binary
                  cls
clus                 0   1
  RWDD4A MUTATED     3   1
  RWDD4A WILD-TYPE 372  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RWDD4A MUTATED      3    1
  RWDD4A WILD-TYPE  372   64
   clus
vv  RWDD4A MUTATED RWDD4A WILD-TYPE
  0              3              372
  1              1               64
[1] 2 2
[1] FALSE
D1547V8, binary
                  cls
clus                 0   1
  RWDD4A MUTATED     3   2
  RWDD4A WILD-TYPE 222 262
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RWDD4A MUTATED      3    2
  RWDD4A WILD-TYPE  222  262
        clus
vv       RWDD4A MUTATED RWDD4A WILD-TYPE
  FEMALE              3              222
  MALE                2              262
[1] 2 2
[1] FALSE
D1547V9, binary
                  cls
clus                 0   1
  RWDD4A MUTATED     4   0
  RWDD4A WILD-TYPE 346  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RWDD4A MUTATED      4    0
  RWDD4A WILD-TYPE  346   22
     clus
vv    RWDD4A MUTATED RWDD4A WILD-TYPE
  NO               4              346
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  RWDD4A MUTATED                      5                             0
  RWDD4A WILD-TYPE                  310                            47
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  RWDD4A MUTATED                       0                              0
  RWDD4A WILD-TYPE                   106                             10
D1547V10, multiclass
                                clus
vv                               RWDD4A MUTATED RWDD4A WILD-TYPE
  COLON ADENOCARCINOMA                        5              310
  COLON MUCINOUS ADENOCARCINOMA               0               47
  RECTAL ADENOCARCINOMA                       0              106
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  RWDD4A MUTATED     3   0   0   0
  RWDD4A WILD-TYPE 342   4  31  25
D1547V11, multiclass
    clus
vv   RWDD4A MUTATED RWDD4A WILD-TYPE
  R0              3              342
  R1              0                4
  R2              0               31
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1547V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RWDD4A MUTATED                                  0     0
  RWDD4A WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  RWDD4A MUTATED                           0     3
  RWDD4A WILD-TYPE                        22   223
D1547V13, multiclass
                                  clus
vv                                 RWDD4A MUTATED RWDD4A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         3              223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1548) Variable = EPRS MUTATION ANALYSIS
D1548V1, survival
                sevent
clus2              0   1
  EPRS MUTATED    18   3
  EPRS WILD-TYPE 360  90
  EPRS MUTATED EPRS WILD-TYPE 
            21            450 
  EPRS MUTATED EPRS WILD-TYPE 
             3             90 
$`EPRS MUTATED`
TCGA-A6-5665 TCGA-A6-6652 TCGA-A6-6780 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3966 
       22.06        24.69        20.12        26.99        10.06         2.01 
TCGA-AA-A00J TCGA-AA-A00N TCGA-AA-A010 TCGA-AD-6890 TCGA-AD-6895 TCGA-CA-6717 
       18.05         4.01        34.98         0.79         0.72        12.76 
TCGA-CM-4747 TCGA-CM-5864 TCGA-CM-6674 TCGA-D5-6929 TCGA-DM-A0XF TCGA-AG-3608 
       25.02        15.02        12.95         4.80        38.20        15.95 
TCGA-AG-3732 TCGA-AG-A002 TCGA-DC-6160 
       32.98        20.98        19.99 

$`EPRS WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6781 
       25.18        24.16        21.76        24.39        23.87        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       85.05        19.04        19.04        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 
       26.01        24.00         2.01        20.98        34.03        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07        12.20        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       20.02        37.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5868 
       30.08        32.02        15.02         5.03        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3609 
        2.01        50.04        12.03         6.05         0.99        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 
       13.94        19.99         7.99         0.99        37.02         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  EPRS MUTATED EPRS WILD-TYPE 
          0.72           0.00 
  EPRS MUTATED EPRS WILD-TYPE 
         38.20         148.01 
  EPRS MUTATED EPRS WILD-TYPE 
         18.05          20.73 
[1] "0.7 - 38.2 (18.1)"  "0.0 - 148.0 (20.7)"
[1] "hr=" "1.1"
D1548V2, continuous
D1548V3, binary
                cls
clus               0   1
  EPRS MUTATED    19   4
  EPRS WILD-TYPE 347 115
[1] "tbl2"
                cls
clus             [,1] [,2]
  EPRS MUTATED     19    4
  EPRS WILD-TYPE  347  115
        clus
vv       EPRS MUTATED EPRS WILD-TYPE
  COLON            19            347
  RECTUM            4            115
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  EPRS MUTATED         4        0        0         8         3         0
  EPRS WILD-TYPE      87        1       32       130         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  EPRS MUTATED           1          0          1          1        1         2
  EPRS WILD-TYPE        23         11         58         41       47        16
                vv
clus             STAGE IVB
  EPRS MUTATED           0
  EPRS WILD-TYPE         1
D1548V4, multiclass
            clus
vv           EPRS MUTATED EPRS WILD-TYPE
  STAGE I               4             87
  STAGE IA              0              1
  STAGE II              0             32
  STAGE IIA             8            130
  STAGE IIB             3              7
  STAGE IIC             0              1
  STAGE III             1             23
  STAGE IIIA            0             11
  STAGE IIIB            1             58
  STAGE IIIC            1             41
  STAGE IV              1             47
  STAGE IVA             2             16
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  EPRS MUTATED     1   4  13   5
  EPRS WILD-TYPE  16  88 316  45
D1548V5, multiclass
    clus
vv   EPRS MUTATED EPRS WILD-TYPE
  T1            1             16
  T2            4             88
  T3           13            316
  T4            5             45
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  EPRS MUTATED    17   4   2
  EPRS WILD-TYPE 270 109  85
D1548V6, multiclass
    clus
vv   EPRS MUTATED EPRS WILD-TYPE
  N0           17            270
  N1            4            109
  N2            2             85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1548V7, binary
                cls
clus               0   1
  EPRS MUTATED    16   3
  EPRS WILD-TYPE 359  62
[1] "tbl2"
                cls
clus             [,1] [,2]
  EPRS MUTATED     16    3
  EPRS WILD-TYPE  359   62
   clus
vv  EPRS MUTATED EPRS WILD-TYPE
  0           16            359
  1            3             62
[1] 2 2
[1] FALSE
D1548V8, binary
                cls
clus               0   1
  EPRS MUTATED    11  12
  EPRS WILD-TYPE 214 252
[1] "tbl2"
                cls
clus             [,1] [,2]
  EPRS MUTATED     11   12
  EPRS WILD-TYPE  214  252
        clus
vv       EPRS MUTATED EPRS WILD-TYPE
  FEMALE           11            214
  MALE             12            252
[1] 2 2
[1] FALSE
D1548V9, binary
                cls
clus               0   1
  EPRS MUTATED    14   0
  EPRS WILD-TYPE 336  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  EPRS MUTATED     14    0
  EPRS WILD-TYPE  336   22
     clus
vv    EPRS MUTATED EPRS WILD-TYPE
  NO            14            336
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  EPRS MUTATED                     13                             5
  EPRS WILD-TYPE                  302                            42
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  EPRS MUTATED                       4                              0
  EPRS WILD-TYPE                   102                             10
D1548V10, multiclass
                                clus
vv                               EPRS MUTATED EPRS WILD-TYPE
  COLON ADENOCARCINOMA                     13            302
  COLON MUCINOUS ADENOCARCINOMA             5             42
  RECTAL ADENOCARCINOMA                     4            102
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  EPRS MUTATED    15   0   0   2
  EPRS WILD-TYPE 330   4  31  23
D1548V11, multiclass
    clus
vv   EPRS MUTATED EPRS WILD-TYPE
  R0           15            330
  R1            0              4
  R2            0             31
  RX            2             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1548V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  EPRS MUTATED                                  0     1
  EPRS WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  EPRS MUTATED                           1    11
  EPRS WILD-TYPE                        21   215
D1548V13, multiclass
                                  clus
vv                                 EPRS MUTATED EPRS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                      11            215
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1549) Variable = DUSP9 MUTATION ANALYSIS
D1549V1, survival
                 sevent
clus2               0   1
  DUSP9 MUTATED     8   1
  DUSP9 WILD-TYPE 370  92
  DUSP9 MUTATED DUSP9 WILD-TYPE 
              9             462 
  DUSP9 MUTATED DUSP9 WILD-TYPE 
              1              92 
$`DUSP9 MUTATED`
TCGA-A6-6652 TCGA-A6-6782 TCGA-AA-3655 TCGA-AA-3821 TCGA-CM-4743 TCGA-D5-6534 
       24.69        20.28        61.02         1.02        23.05        43.27 
TCGA-D5-6930 TCGA-G4-6303 TCGA-G4-6588 
        1.51        65.85        26.17 

$`DUSP9 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6654 
       25.08        25.18        24.16        21.76        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        19.66         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       13.94        19.99        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
       33.04         0.99        25.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
      124.27        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 
        9.04         9.44        11.64         4.80        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
      133.18        74.56        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  DUSP9 MUTATED DUSP9 WILD-TYPE 
           1.02            0.00 
  DUSP9 MUTATED DUSP9 WILD-TYPE 
          65.85          148.01 
  DUSP9 MUTATED DUSP9 WILD-TYPE 
         24.690          20.035 
[1] "1.0 - 65.8 (24.7)"  "0.0 - 148.0 (20.0)"
[1] "hr=" "2.2"
D1549V2, continuous
D1549V3, binary
                 cls
clus                0   1
  DUSP9 MUTATED     9   0
  DUSP9 WILD-TYPE 357 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DUSP9 MUTATED      9    0
  DUSP9 WILD-TYPE  357  119
        clus
vv       DUSP9 MUTATED DUSP9 WILD-TYPE
  COLON              9             357
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DUSP9 MUTATED         1        0        1         4         1         0
  DUSP9 WILD-TYPE      90        1       31       134         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DUSP9 MUTATED           0          0          0          0        1         1
  DUSP9 WILD-TYPE        24         11         59         42       47        17
                 vv
clus              STAGE IVB
  DUSP9 MUTATED           0
  DUSP9 WILD-TYPE         1
D1549V4, multiclass
            clus
vv           DUSP9 MUTATED DUSP9 WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              4             134
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             0              42
  STAGE IV               1              47
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  DUSP9 MUTATED     0   1   7   1
  DUSP9 WILD-TYPE  17  91 322  49
D1549V5, multiclass
    clus
vv   DUSP9 MUTATED DUSP9 WILD-TYPE
  T1             0              17
  T2             1              91
  T3             7             322
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  DUSP9 MUTATED     8   1   0
  DUSP9 WILD-TYPE 279 112  87
D1549V6, multiclass
    clus
vv   DUSP9 MUTATED DUSP9 WILD-TYPE
  N0             8             279
  N1             1             112
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1549V7, binary
                 cls
clus                0   1
  DUSP9 MUTATED     6   2
  DUSP9 WILD-TYPE 369  63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DUSP9 MUTATED      6    2
  DUSP9 WILD-TYPE  369   63
   clus
vv  DUSP9 MUTATED DUSP9 WILD-TYPE
  0             6             369
  1             2              63
[1] 2 2
[1] FALSE
D1549V8, binary
                 cls
clus                0   1
  DUSP9 MUTATED     4   5
  DUSP9 WILD-TYPE 221 259
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DUSP9 MUTATED      4    5
  DUSP9 WILD-TYPE  221  259
        clus
vv       DUSP9 MUTATED DUSP9 WILD-TYPE
  FEMALE             4             221
  MALE               5             259
[1] 2 2
[1] FALSE
D1549V9, binary
                 cls
clus                0   1
  DUSP9 MUTATED     8   0
  DUSP9 WILD-TYPE 342  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DUSP9 MUTATED      8    0
  DUSP9 WILD-TYPE  342   22
     clus
vv    DUSP9 MUTATED DUSP9 WILD-TYPE
  NO              8             342
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  DUSP9 MUTATED                      6                             3
  DUSP9 WILD-TYPE                  309                            44
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  DUSP9 MUTATED                       0                              0
  DUSP9 WILD-TYPE                   106                             10
D1549V10, multiclass
                                clus
vv                               DUSP9 MUTATED DUSP9 WILD-TYPE
  COLON ADENOCARCINOMA                       6             309
  COLON MUCINOUS ADENOCARCINOMA              3              44
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  DUSP9 MUTATED     7   0   0   0
  DUSP9 WILD-TYPE 338   4  31  25
D1549V11, multiclass
    clus
vv   DUSP9 MUTATED DUSP9 WILD-TYPE
  R0             7             338
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1549V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DUSP9 MUTATED                                  0     0
  DUSP9 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  DUSP9 MUTATED                           1     6
  DUSP9 WILD-TYPE                        21   220
D1549V13, multiclass
                                  clus
vv                                 DUSP9 MUTATED DUSP9 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        6             220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1550) Variable = HIST1H1A MUTATION ANALYSIS
D1550V1, survival
                    sevent
clus2                  0   1
  HIST1H1A MUTATED     6   3
  HIST1H1A WILD-TYPE 372  90
  HIST1H1A MUTATED HIST1H1A WILD-TYPE 
                 9                462 
  HIST1H1A MUTATED HIST1H1A WILD-TYPE 
                 3                 90 
$`HIST1H1A MUTATED`
TCGA-A6-6141 TCGA-AA-3492 TCGA-AA-3710 TCGA-AA-A01R TCGA-AA-A024 TCGA-AZ-4315 
        8.38         3.02        26.99        35.01        39.06        58.39 
TCGA-AZ-6608 TCGA-F4-6855 TCGA-G4-6588 
        1.61        47.41        26.17 

$`HIST1H1A WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 
       22.09        22.06        32.71        27.09        22.52        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 
       20.12        19.66        20.28         7.04         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       31.00        38.07         1.02         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       26.01        37.02        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
       11.74         3.19        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6856 TCGA-G4-6293 
       16.24        33.67        13.25         0.53        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  HIST1H1A MUTATED HIST1H1A WILD-TYPE 
              1.61               0.00 
  HIST1H1A MUTATED HIST1H1A WILD-TYPE 
             58.39             148.01 
  HIST1H1A MUTATED HIST1H1A WILD-TYPE 
            26.990             20.085 
[1] "1.6 - 58.4 (27.0)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.6"
D1550V2, continuous
D1550V3, binary
                    cls
clus                   0   1
  HIST1H1A MUTATED     9   0
  HIST1H1A WILD-TYPE 357 119
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HIST1H1A MUTATED      9    0
  HIST1H1A WILD-TYPE  357  119
        clus
vv       HIST1H1A MUTATED HIST1H1A WILD-TYPE
  COLON                 9                357
  RECTUM                0                119
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  HIST1H1A MUTATED         0        0        2         5         0         0
  HIST1H1A WILD-TYPE      91        1       30       133        10         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HIST1H1A MUTATED           1          1          0          0        0
  HIST1H1A WILD-TYPE        23         10         59         42       48
                    vv
clus                 STAGE IVA STAGE IVB
  HIST1H1A MUTATED           0         0
  HIST1H1A WILD-TYPE        18         1
D1550V4, multiclass
            clus
vv           HIST1H1A MUTATED HIST1H1A WILD-TYPE
  STAGE I                   0                 91
  STAGE IA                  0                  1
  STAGE II                  2                 30
  STAGE IIA                 5                133
  STAGE IIB                 0                 10
  STAGE IIC                 0                  1
  STAGE III                 1                 23
  STAGE IIIA                1                 10
  STAGE IIIB                0                 59
  STAGE IIIC                0                 42
  STAGE IV                  0                 48
  STAGE IVA                 0                 18
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  HIST1H1A MUTATED     0   1   8   0
  HIST1H1A WILD-TYPE  17  91 321  50
D1550V5, multiclass
    clus
vv   HIST1H1A MUTATED HIST1H1A WILD-TYPE
  T1                0                 17
  T2                1                 91
  T3                8                321
  T4                0                 50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  HIST1H1A MUTATED     7   1   1
  HIST1H1A WILD-TYPE 280 112  86
D1550V6, multiclass
    clus
vv   HIST1H1A MUTATED HIST1H1A WILD-TYPE
  N0                7                280
  N1                1                112
  N2                1                 86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1550V7, binary
                    cls
clus                   0   1
  HIST1H1A MUTATED     9   0
  HIST1H1A WILD-TYPE 366  65
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HIST1H1A MUTATED      9    0
  HIST1H1A WILD-TYPE  366   65
   clus
vv  HIST1H1A MUTATED HIST1H1A WILD-TYPE
  0                9                366
  1                0                 65
[1] 2 2
[1] FALSE
D1550V8, binary
                    cls
clus                   0   1
  HIST1H1A MUTATED     5   4
  HIST1H1A WILD-TYPE 220 260
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HIST1H1A MUTATED      5    4
  HIST1H1A WILD-TYPE  220  260
        clus
vv       HIST1H1A MUTATED HIST1H1A WILD-TYPE
  FEMALE                5                220
  MALE                  4                260
[1] 2 2
[1] FALSE
D1550V9, binary
                    cls
clus                   0   1
  HIST1H1A MUTATED     8   1
  HIST1H1A WILD-TYPE 342  21
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HIST1H1A MUTATED      8    1
  HIST1H1A WILD-TYPE  342   21
     clus
vv    HIST1H1A MUTATED HIST1H1A WILD-TYPE
  NO                 8                342
  YES                1                 21
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  HIST1H1A MUTATED                      7                             2
  HIST1H1A WILD-TYPE                  308                            45
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  HIST1H1A MUTATED                       0                              0
  HIST1H1A WILD-TYPE                   106                             10
D1550V10, multiclass
                                clus
vv                               HIST1H1A MUTATED HIST1H1A WILD-TYPE
  COLON ADENOCARCINOMA                          7                308
  COLON MUCINOUS ADENOCARCINOMA                 2                 45
  RECTAL ADENOCARCINOMA                         0                106
  RECTAL MUCINOUS ADENOCARCINOMA                0                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  HIST1H1A MUTATED     7   0   0   0
  HIST1H1A WILD-TYPE 338   4  31  25
D1550V11, multiclass
    clus
vv   HIST1H1A MUTATED HIST1H1A WILD-TYPE
  R0                7                338
  R1                0                  4
  R2                0                 31
  RX                0                 25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1550V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HIST1H1A MUTATED                                  0     0
  HIST1H1A WILD-TYPE                                1    11
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  HIST1H1A MUTATED                           1     4
  HIST1H1A WILD-TYPE                        21   222
D1550V13, multiclass
                                  clus
vv                                 HIST1H1A MUTATED HIST1H1A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 11
  BLACK OR AFRICAN AMERICAN                       1                 21
  WHITE                                           4                222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1551) Variable = ZSCAN20 MUTATION ANALYSIS
D1551V1, survival
                   sevent
clus2                 0   1
  ZSCAN20 MUTATED    13   4
  ZSCAN20 WILD-TYPE 365  89
  ZSCAN20 MUTATED ZSCAN20 WILD-TYPE 
               17               454 
  ZSCAN20 MUTATED ZSCAN20 WILD-TYPE 
                4                89 
$`ZSCAN20 MUTATED`
TCGA-A6-5661 TCGA-A6-6142 TCGA-A6-6780 TCGA-AA-3848 TCGA-AA-3852 TCGA-AA-3968 
       33.53        25.08        20.12        10.06         0.00        21.99 
TCGA-AA-3977 TCGA-AY-5543 TCGA-AZ-4315 TCGA-CA-6718 TCGA-CM-4743 TCGA-D5-6930 
       25.02        33.01        58.39        10.06        23.05         1.51 
TCGA-DM-A1D4 TCGA-AG-3731 TCGA-AG-3902 TCGA-AG-A002 TCGA-AG-A011 
       92.75        37.02        32.02        20.98        37.02 

$`ZSCAN20 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6648 
       22.06        32.71        27.09        22.52         8.38        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6781 
       24.16        21.76        24.69        24.39        23.87        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3850 
       38.99        37.02        14.93         0.00        17.03         0.00 
TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
       33.07        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
        0.95        21.44        17.82         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       12.76        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
      124.27        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6931 
       14.30         9.04         9.44        11.64         4.80        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
       19.99         7.99         0.99        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3909 
       13.02        35.01        14.01         1.02        48.03        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
        6.02        25.97        23.01        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  ZSCAN20 MUTATED ZSCAN20 WILD-TYPE 
                0                 0 
  ZSCAN20 MUTATED ZSCAN20 WILD-TYPE 
            92.75            148.01 
  ZSCAN20 MUTATED ZSCAN20 WILD-TYPE 
           25.020            20.005 
[1] "0.0 - 92.8 (25.0)"  "0.0 - 148.0 (20.0)"
[1] "hr=" "1.2"
D1551V2, continuous
D1551V3, binary
                   cls
clus                  0   1
  ZSCAN20 MUTATED    13   4
  ZSCAN20 WILD-TYPE 353 115
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZSCAN20 MUTATED     13    4
  ZSCAN20 WILD-TYPE  353  115
        clus
vv       ZSCAN20 MUTATED ZSCAN20 WILD-TYPE
  COLON               13               353
  RECTUM               4               115
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZSCAN20 MUTATED         2        0        0        10         0         0
  ZSCAN20 WILD-TYPE      89        1       32       128        10         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZSCAN20 MUTATED           0          0          0          1        1
  ZSCAN20 WILD-TYPE        24         11         59         41       47
                   vv
clus                STAGE IVA STAGE IVB
  ZSCAN20 MUTATED           2         0
  ZSCAN20 WILD-TYPE        16         1
D1551V4, multiclass
            clus
vv           ZSCAN20 MUTATED ZSCAN20 WILD-TYPE
  STAGE I                  2                89
  STAGE IA                 0                 1
  STAGE II                 0                32
  STAGE IIA               10               128
  STAGE IIB                0                10
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               0                11
  STAGE IIIB               0                59
  STAGE IIIC               1                41
  STAGE IV                 1                47
  STAGE IVA                2                16
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  ZSCAN20 MUTATED     0   3  14   0
  ZSCAN20 WILD-TYPE  17  89 315  50
D1551V5, multiclass
    clus
vv   ZSCAN20 MUTATED ZSCAN20 WILD-TYPE
  T1               0                17
  T2               3                89
  T3              14               315
  T4               0                50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  ZSCAN20 MUTATED    13   3   1
  ZSCAN20 WILD-TYPE 274 110  86
D1551V6, multiclass
    clus
vv   ZSCAN20 MUTATED ZSCAN20 WILD-TYPE
  N0              13               274
  N1               3               110
  N2               1                86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1551V7, binary
                   cls
clus                  0   1
  ZSCAN20 MUTATED    12   3
  ZSCAN20 WILD-TYPE 363  62
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZSCAN20 MUTATED     12    3
  ZSCAN20 WILD-TYPE  363   62
   clus
vv  ZSCAN20 MUTATED ZSCAN20 WILD-TYPE
  0              12               363
  1               3                62
[1] 2 2
[1] FALSE
D1551V8, binary
                   cls
clus                  0   1
  ZSCAN20 MUTATED     5  12
  ZSCAN20 WILD-TYPE 220 252
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZSCAN20 MUTATED      5   12
  ZSCAN20 WILD-TYPE  220  252
        clus
vv       ZSCAN20 MUTATED ZSCAN20 WILD-TYPE
  FEMALE               5               220
  MALE                12               252
[1] 2 2
[1] FALSE
D1551V9, binary
                   cls
clus                  0   1
  ZSCAN20 MUTATED    14   0
  ZSCAN20 WILD-TYPE 336  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZSCAN20 MUTATED     14    0
  ZSCAN20 WILD-TYPE  336   22
     clus
vv    ZSCAN20 MUTATED ZSCAN20 WILD-TYPE
  NO               14               336
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ZSCAN20 MUTATED                     10                             3
  ZSCAN20 WILD-TYPE                  305                            44
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ZSCAN20 MUTATED                       4                              0
  ZSCAN20 WILD-TYPE                   102                             10
D1551V10, multiclass
                                clus
vv                               ZSCAN20 MUTATED ZSCAN20 WILD-TYPE
  COLON ADENOCARCINOMA                        10               305
  COLON MUCINOUS ADENOCARCINOMA                3                44
  RECTAL ADENOCARCINOMA                        4               102
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  ZSCAN20 MUTATED    11   0   1   1
  ZSCAN20 WILD-TYPE 334   4  30  24
D1551V11, multiclass
    clus
vv   ZSCAN20 MUTATED ZSCAN20 WILD-TYPE
  R0              11               334
  R1               0                 4
  R2               1                30
  RX               1                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1551V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZSCAN20 MUTATED                                  0     1
  ZSCAN20 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  ZSCAN20 MUTATED                           2     6
  ZSCAN20 WILD-TYPE                        20   220
D1551V13, multiclass
                                  clus
vv                                 ZSCAN20 MUTATED ZSCAN20 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                10
  BLACK OR AFRICAN AMERICAN                      2                20
  WHITE                                          6               220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1552) Variable = ERCC3 MUTATION ANALYSIS
D1552V1, survival
                 sevent
clus2               0   1
  ERCC3 MUTATED    12   6
  ERCC3 WILD-TYPE 366  87
  ERCC3 MUTATED ERCC3 WILD-TYPE 
             18             453 
  ERCC3 MUTATED ERCC3 WILD-TYPE 
              6              87 
$`ERCC3 MUTATED`
TCGA-A6-5657 TCGA-A6-5665 TCGA-AA-3492 TCGA-AA-3516 TCGA-AA-3815 TCGA-AA-3845 
       31.63        22.06         3.02        13.02        33.04         0.00 
TCGA-AA-A010 TCGA-AA-A01K TCGA-AZ-6605 TCGA-CA-6717 TCGA-CK-4950 TCGA-CM-5348 
       34.98        31.00         5.23        12.76        85.45        22.98 
TCGA-D5-6920 TCGA-D5-6930 TCGA-DM-A1D9 TCGA-F4-6570 TCGA-G4-6626 TCGA-AG-A002 
        3.68         1.51       140.38         6.18        46.75        20.98 

$`ERCC3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       19.66        20.28         7.04         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        6.97         1.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
       26.99        19.04        19.04        10.06        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
       14.93        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       12.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
       12.10       100.01        29.56        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5912 
       10.06        14.30        17.56       148.01        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.03        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
       15.58         1.48         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
        9.44        11.64         4.80        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       13.32        12.59         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 
      117.07        98.24         8.61        31.96        35.74        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  ERCC3 MUTATED ERCC3 WILD-TYPE 
              0               0 
  ERCC3 MUTATED ERCC3 WILD-TYPE 
         140.38          148.01 
  ERCC3 MUTATED ERCC3 WILD-TYPE 
          21.52           20.12 
[1] "0.0 - 140.4 (21.5)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.8"
D1552V2, continuous
D1552V3, binary
                 cls
clus                0   1
  ERCC3 MUTATED    19   1
  ERCC3 WILD-TYPE 347 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERCC3 MUTATED     19    1
  ERCC3 WILD-TYPE  347  118
        clus
vv       ERCC3 MUTATED ERCC3 WILD-TYPE
  COLON             19             347
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ERCC3 MUTATED         1        0        1        10         2         0
  ERCC3 WILD-TYPE      90        1       31       128         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ERCC3 MUTATED           1          0          4          1        0         0
  ERCC3 WILD-TYPE        23         11         55         41       48        18
                 vv
clus              STAGE IVB
  ERCC3 MUTATED           0
  ERCC3 WILD-TYPE         1
D1552V4, multiclass
            clus
vv           ERCC3 MUTATED ERCC3 WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA             10             128
  STAGE IIB              2               8
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             4              55
  STAGE IIIC             1              41
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ERCC3 MUTATED     0   1  16   3
  ERCC3 WILD-TYPE  17  91 313  47
D1552V5, multiclass
    clus
vv   ERCC3 MUTATED ERCC3 WILD-TYPE
  T1             0              17
  T2             1              91
  T3            16             313
  T4             3              47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  ERCC3 MUTATED    14   4   2
  ERCC3 WILD-TYPE 273 109  85
D1552V6, multiclass
    clus
vv   ERCC3 MUTATED ERCC3 WILD-TYPE
  N0            14             273
  N1             4             109
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1552V7, binary
                 cls
clus                0   1
  ERCC3 MUTATED    19   0
  ERCC3 WILD-TYPE 356  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERCC3 MUTATED     19    0
  ERCC3 WILD-TYPE  356   65
   clus
vv  ERCC3 MUTATED ERCC3 WILD-TYPE
  0            19             356
  1             0              65
[1] 2 2
[1] FALSE
D1552V8, binary
                 cls
clus                0   1
  ERCC3 MUTATED    13   7
  ERCC3 WILD-TYPE 212 257
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERCC3 MUTATED     13    7
  ERCC3 WILD-TYPE  212  257
        clus
vv       ERCC3 MUTATED ERCC3 WILD-TYPE
  FEMALE            13             212
  MALE               7             257
[1] 2 2
[1] FALSE
D1552V9, binary
                 cls
clus                0   1
  ERCC3 MUTATED    14   0
  ERCC3 WILD-TYPE 336  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERCC3 MUTATED     14    0
  ERCC3 WILD-TYPE  336   22
     clus
vv    ERCC3 MUTATED ERCC3 WILD-TYPE
  NO             14             336
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ERCC3 MUTATED                     16                             3
  ERCC3 WILD-TYPE                  299                            44
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ERCC3 MUTATED                       1                              0
  ERCC3 WILD-TYPE                   105                             10
D1552V10, multiclass
                                clus
vv                               ERCC3 MUTATED ERCC3 WILD-TYPE
  COLON ADENOCARCINOMA                      16             299
  COLON MUCINOUS ADENOCARCINOMA              3              44
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  ERCC3 MUTATED    14   1   0   2
  ERCC3 WILD-TYPE 331   3  31  23
D1552V11, multiclass
    clus
vv   ERCC3 MUTATED ERCC3 WILD-TYPE
  R0            14             331
  R1             1               3
  R2             0              31
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1552V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ERCC3 MUTATED                                  0     1
  ERCC3 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ERCC3 MUTATED                           2     9
  ERCC3 WILD-TYPE                        20   217
D1552V13, multiclass
                                  clus
vv                                 ERCC3 MUTATED ERCC3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    2              20
  WHITE                                        9             217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1553) Variable = XKR3 MUTATION ANALYSIS
D1553V1, survival
                sevent
clus2              0   1
  XKR3 MUTATED    13   1
  XKR3 WILD-TYPE 365  92
  XKR3 MUTATED XKR3 WILD-TYPE 
            14            457 
  XKR3 MUTATED XKR3 WILD-TYPE 
             1             92 
$`XKR3 MUTATED`
TCGA-A6-6780 TCGA-AA-3660 TCGA-AA-3710 TCGA-AA-3821 TCGA-AZ-4315 TCGA-AZ-6601 
       20.12        78.08        26.99         1.02        58.39       100.01 
TCGA-CA-6717 TCGA-CM-5861 TCGA-D5-5541 TCGA-G4-6307 TCGA-G4-6628 TCGA-AF-2687 
       12.76        15.02        55.92        55.04        79.69        24.13 
TCGA-AG-A002 TCGA-AG-A01W 
       20.98        70.03 

$`XKR3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 
       19.99        13.94        19.99        61.02         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
       33.04         0.99        25.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 
       88.21        49.41         6.77        12.10        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07        12.20        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       30.08        32.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-6529 
       12.03        45.40        12.26        19.59        56.09        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       65.85        53.62        44.68        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       46.75        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01Y 
       37.02        15.95        36.03         9.07        12.00        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  XKR3 MUTATED XKR3 WILD-TYPE 
          1.02           0.00 
  XKR3 MUTATED XKR3 WILD-TYPE 
        100.01         148.01 
  XKR3 MUTATED XKR3 WILD-TYPE 
        41.015         20.020 
[1] "1.0 - 100.0 (41.0)" "0.0 - 148.0 (20.0)"
[1] "hr=" "5.1"
D1553V2, continuous
D1553V3, binary
                cls
clus               0   1
  XKR3 MUTATED    12   3
  XKR3 WILD-TYPE 354 116
[1] "tbl2"
                cls
clus             [,1] [,2]
  XKR3 MUTATED     12    3
  XKR3 WILD-TYPE  354  116
        clus
vv       XKR3 MUTATED XKR3 WILD-TYPE
  COLON            12            354
  RECTUM            3            116
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  XKR3 MUTATED         3        0        3         6         0         0
  XKR3 WILD-TYPE      88        1       29       132        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  XKR3 MUTATED           0          0          2          1        0         0
  XKR3 WILD-TYPE        24         11         57         41       48        18
                vv
clus             STAGE IVB
  XKR3 MUTATED           0
  XKR3 WILD-TYPE         1
D1553V4, multiclass
            clus
vv           XKR3 MUTATED XKR3 WILD-TYPE
  STAGE I               3             88
  STAGE IA              0              1
  STAGE II              3             29
  STAGE IIA             6            132
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            2             57
  STAGE IIIC            1             41
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  XKR3 MUTATED     0   3  12   0
  XKR3 WILD-TYPE  17  89 317  50
D1553V5, multiclass
    clus
vv   XKR3 MUTATED XKR3 WILD-TYPE
  T1            0             17
  T2            3             89
  T3           12            317
  T4            0             50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  XKR3 MUTATED    12   2   1
  XKR3 WILD-TYPE 275 111  86
D1553V6, multiclass
    clus
vv   XKR3 MUTATED XKR3 WILD-TYPE
  N0           12            275
  N1            2            111
  N2            1             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1553V7, binary
                cls
clus               0   1
  XKR3 MUTATED    14   0
  XKR3 WILD-TYPE 361  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  XKR3 MUTATED     14    0
  XKR3 WILD-TYPE  361   65
   clus
vv  XKR3 MUTATED XKR3 WILD-TYPE
  0           14            361
  1            0             65
[1] 2 2
[1] FALSE
D1553V8, binary
                cls
clus               0   1
  XKR3 MUTATED     7   8
  XKR3 WILD-TYPE 218 256
[1] "tbl2"
                cls
clus             [,1] [,2]
  XKR3 MUTATED      7    8
  XKR3 WILD-TYPE  218  256
        clus
vv       XKR3 MUTATED XKR3 WILD-TYPE
  FEMALE            7            218
  MALE              8            256
[1] 2 2
[1] FALSE
D1553V9, binary
                cls
clus               0   1
  XKR3 MUTATED    12   1
  XKR3 WILD-TYPE 338  21
[1] "tbl2"
                cls
clus             [,1] [,2]
  XKR3 MUTATED     12    1
  XKR3 WILD-TYPE  338   21
     clus
vv    XKR3 MUTATED XKR3 WILD-TYPE
  NO            12            338
  YES            1             21
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  XKR3 MUTATED                      9                             3
  XKR3 WILD-TYPE                  306                            44
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  XKR3 MUTATED                       3                              0
  XKR3 WILD-TYPE                   103                             10
D1553V10, multiclass
                                clus
vv                               XKR3 MUTATED XKR3 WILD-TYPE
  COLON ADENOCARCINOMA                      9            306
  COLON MUCINOUS ADENOCARCINOMA             3             44
  RECTAL ADENOCARCINOMA                     3            103
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  XKR3 MUTATED    12   0   0   1
  XKR3 WILD-TYPE 333   4  31  24
D1553V11, multiclass
    clus
vv   XKR3 MUTATED XKR3 WILD-TYPE
  R0           12            333
  R1            0              4
  R2            0             31
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1553V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  XKR3 MUTATED                                  0     1
  XKR3 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  XKR3 MUTATED                           0     8
  XKR3 WILD-TYPE                        22   218
D1553V13, multiclass
                                  clus
vv                                 XKR3 MUTATED XKR3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       8            218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1554) Variable = PIGS MUTATION ANALYSIS
D1554V1, survival
                sevent
clus2              0   1
  PIGS MUTATED     5   3
  PIGS WILD-TYPE 373  90
  PIGS MUTATED PIGS WILD-TYPE 
             8            463 
  PIGS MUTATED PIGS WILD-TYPE 
             3             90 
$`PIGS MUTATED`
TCGA-AA-3558 TCGA-AA-3660 TCGA-AA-3715 TCGA-AZ-6598 TCGA-AZ-6601 TCGA-D5-6541 
       20.98        78.08        19.04        49.41       100.01        15.58 
TCGA-AH-6643 TCGA-EI-6508 
        0.69        20.91 

$`PIGS WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 
       19.99        13.94        19.99        61.02         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 
       22.36        62.79        88.21         6.77        12.10        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       16.14         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
       17.49         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
        0.49        20.55        19.96        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  PIGS MUTATED PIGS WILD-TYPE 
          0.69           0.00 
  PIGS MUTATED PIGS WILD-TYPE 
        100.01         148.01 
  PIGS MUTATED PIGS WILD-TYPE 
        20.945         20.120 
[1] "0.7 - 100.0 (20.9)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.3"
D1554V2, continuous
D1554V3, binary
                cls
clus               0   1
  PIGS MUTATED     6   2
  PIGS WILD-TYPE 360 117
[1] "tbl2"
                cls
clus             [,1] [,2]
  PIGS MUTATED      6    2
  PIGS WILD-TYPE  360  117
        clus
vv       PIGS MUTATED PIGS WILD-TYPE
  COLON             6            360
  RECTUM            2            117
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PIGS MUTATED         1        0        4         1         0         0
  PIGS WILD-TYPE      90        1       28       137        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PIGS MUTATED           0          0          1          1        0         0
  PIGS WILD-TYPE        24         11         58         41       48        18
                vv
clus             STAGE IVB
  PIGS MUTATED           0
  PIGS WILD-TYPE         1
D1554V4, multiclass
            clus
vv           PIGS MUTATED PIGS WILD-TYPE
  STAGE I               1             90
  STAGE IA              0              1
  STAGE II              4             28
  STAGE IIA             1            137
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            1             58
  STAGE IIIC            1             41
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  PIGS MUTATED     0   1   7   0
  PIGS WILD-TYPE  17  91 322  50
D1554V5, multiclass
    clus
vv   PIGS MUTATED PIGS WILD-TYPE
  T1            0             17
  T2            1             91
  T3            7            322
  T4            0             50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  PIGS MUTATED     6   1   1
  PIGS WILD-TYPE 281 112  86
D1554V6, multiclass
    clus
vv   PIGS MUTATED PIGS WILD-TYPE
  N0            6            281
  N1            1            112
  N2            1             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1554V7, binary
                cls
clus               0   1
  PIGS MUTATED     7   0
  PIGS WILD-TYPE 368  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  PIGS MUTATED      7    0
  PIGS WILD-TYPE  368   65
   clus
vv  PIGS MUTATED PIGS WILD-TYPE
  0            7            368
  1            0             65
[1] 2 2
[1] FALSE
D1554V8, binary
                cls
clus               0   1
  PIGS MUTATED     3   5
  PIGS WILD-TYPE 222 259
[1] "tbl2"
                cls
clus             [,1] [,2]
  PIGS MUTATED      3    5
  PIGS WILD-TYPE  222  259
        clus
vv       PIGS MUTATED PIGS WILD-TYPE
  FEMALE            3            222
  MALE              5            259
[1] 2 2
[1] FALSE
D1554V9, binary
                cls
clus               0   1
  PIGS MUTATED     7   0
  PIGS WILD-TYPE 343  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  PIGS MUTATED      7    0
  PIGS WILD-TYPE  343   22
     clus
vv    PIGS MUTATED PIGS WILD-TYPE
  NO             7            343
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PIGS MUTATED                      6                             0
  PIGS WILD-TYPE                  309                            47
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PIGS MUTATED                       2                              0
  PIGS WILD-TYPE                   104                             10
D1554V10, multiclass
                                clus
vv                               PIGS MUTATED PIGS WILD-TYPE
  COLON ADENOCARCINOMA                      6            309
  COLON MUCINOUS ADENOCARCINOMA             0             47
  RECTAL ADENOCARCINOMA                     2            104
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  PIGS MUTATED     5   0   1   0
  PIGS WILD-TYPE 340   4  30  25
D1554V11, multiclass
    clus
vv   PIGS MUTATED PIGS WILD-TYPE
  R0            5            340
  R1            0              4
  R2            1             30
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1554V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PIGS MUTATED                                  0     0
  PIGS WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  PIGS MUTATED                           0     5
  PIGS WILD-TYPE                        22   221
D1554V13, multiclass
                                  clus
vv                                 PIGS MUTATED PIGS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       5            221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1555) Variable = AAMP MUTATION ANALYSIS
D1555V1, survival
                sevent
clus2              0   1
  AAMP MUTATED     3   0
  AAMP WILD-TYPE 375  93
  AAMP MUTATED AAMP WILD-TYPE 
             3            468 
  AAMP MUTATED AAMP WILD-TYPE 
             0             93 
$`AAMP MUTATED`
TCGA-A6-6781 TCGA-G4-6309 TCGA-G4-6628 
       19.66        85.48        79.69 

$`AAMP WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       26.17        91.79        46.75        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  AAMP MUTATED AAMP WILD-TYPE 
         19.66           0.00 
  AAMP MUTATED AAMP WILD-TYPE 
         85.48         148.01 
  AAMP MUTATED AAMP WILD-TYPE 
        79.690         20.155 
[1] "19.7 - 85.5 (79.7)" "0.0 - 148.0 (20.2)"
[1] "hr="     "9300000"
D1555V2, continuous
D1555V3, binary
                cls
clus               0   1
  AAMP MUTATED     3   0
  AAMP WILD-TYPE 363 119
[1] "tbl2"
                cls
clus             [,1] [,2]
  AAMP MUTATED      3    0
  AAMP WILD-TYPE  363  119
        clus
vv       AAMP MUTATED AAMP WILD-TYPE
  COLON             3            363
  RECTUM            0            119
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  AAMP MUTATED         1        0        0         0         0         0
  AAMP WILD-TYPE      90        1       32       138        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AAMP MUTATED           0          0          1          1        0         0
  AAMP WILD-TYPE        24         11         58         41       48        18
                vv
clus             STAGE IVB
  AAMP MUTATED           0
  AAMP WILD-TYPE         1
D1555V4, multiclass
            clus
vv           AAMP MUTATED AAMP WILD-TYPE
  STAGE I               1             90
  STAGE IA              0              1
  STAGE II              0             32
  STAGE IIA             0            138
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            1             58
  STAGE IIIC            1             41
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  AAMP MUTATED     0   1   1   1
  AAMP WILD-TYPE  17  91 328  49
D1555V5, multiclass
    clus
vv   AAMP MUTATED AAMP WILD-TYPE
  T1            0             17
  T2            1             91
  T3            1            328
  T4            1             49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  AAMP MUTATED     1   2   0
  AAMP WILD-TYPE 286 111  87
D1555V6, multiclass
    clus
vv   AAMP MUTATED AAMP WILD-TYPE
  N0            1            286
  N1            2            111
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1555V7, binary
                cls
clus               0   1
  AAMP MUTATED     2   0
  AAMP WILD-TYPE 373  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  AAMP MUTATED      2    0
  AAMP WILD-TYPE  373   65
   clus
vv  AAMP MUTATED AAMP WILD-TYPE
  0            2            373
  1            0             65
[1] 2 2
[1] FALSE
D1555V8, binary
                cls
clus               0   1
  AAMP MUTATED     1   2
  AAMP WILD-TYPE 224 262
[1] "tbl2"
                cls
clus             [,1] [,2]
  AAMP MUTATED      1    2
  AAMP WILD-TYPE  224  262
        clus
vv       AAMP MUTATED AAMP WILD-TYPE
  FEMALE            1            224
  MALE              2            262
[1] 2 2
[1] FALSE
D1555V9, binary
                cls
clus               0   1
  AAMP MUTATED     3   0
  AAMP WILD-TYPE 347  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  AAMP MUTATED      3    0
  AAMP WILD-TYPE  347   22
     clus
vv    AAMP MUTATED AAMP WILD-TYPE
  NO             3            347
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  AAMP MUTATED                      2                             1
  AAMP WILD-TYPE                  313                            46
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  AAMP MUTATED                       0                              0
  AAMP WILD-TYPE                   106                             10
D1555V10, multiclass
                                clus
vv                               AAMP MUTATED AAMP WILD-TYPE
  COLON ADENOCARCINOMA                      2            313
  COLON MUCINOUS ADENOCARCINOMA             1             46
  RECTAL ADENOCARCINOMA                     0            106
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  AAMP MUTATED     3   0   0   0
  AAMP WILD-TYPE 342   4  31  25
D1555V11, multiclass
    clus
vv   AAMP MUTATED AAMP WILD-TYPE
  R0            3            342
  R1            0              4
  R2            0             31
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1555V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AAMP MUTATED                                  0     0
  AAMP WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  AAMP MUTATED                           1     2
  AAMP WILD-TYPE                        21   224
D1555V13, multiclass
                                  clus
vv                                 AAMP MUTATED AAMP WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                       2            224
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1556) Variable = IL21R MUTATION ANALYSIS
D1556V1, survival
                 sevent
clus2               0   1
  IL21R MUTATED    12   2
  IL21R WILD-TYPE 366  91
  IL21R MUTATED IL21R WILD-TYPE 
             14             457 
  IL21R MUTATED IL21R WILD-TYPE 
              2              91 
$`IL21R MUTATED`
TCGA-A6-5661 TCGA-A6-5666 TCGA-AA-3492 TCGA-AA-3534 TCGA-AA-3555 TCGA-AA-3662 
       33.53        32.71         3.02        29.00        29.95         6.05 
TCGA-AA-3713 TCGA-AA-3966 TCGA-AD-6895 TCGA-AZ-6598 TCGA-CM-4743 TCGA-AG-A002 
       19.04         2.01         0.72        49.41        23.05        20.98 
TCGA-AG-A02N TCGA-EI-6507 
       61.97        19.96 

$`IL21R WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       22.06        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       19.66        20.28         7.04         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       19.07        34.03        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
       78.08         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
        2.01        20.98        34.03        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
       56.55         0.79         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        88.21         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
      124.27        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
        0.49        20.55        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  IL21R MUTATED IL21R WILD-TYPE 
           0.72            0.00 
  IL21R MUTATED IL21R WILD-TYPE 
          61.97          148.01 
  IL21R MUTATED IL21R WILD-TYPE 
         22.015          20.120 
[1] "0.7 - 62.0 (22.0)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.3"
D1556V2, continuous
D1556V3, binary
                 cls
clus                0   1
  IL21R MUTATED    11   3
  IL21R WILD-TYPE 355 116
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IL21R MUTATED     11    3
  IL21R WILD-TYPE  355  116
        clus
vv       IL21R MUTATED IL21R WILD-TYPE
  COLON             11             355
  RECTUM             3             116
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  IL21R MUTATED         1        0        3         6         0         1
  IL21R WILD-TYPE      90        1       29       132        10         0
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  IL21R MUTATED           0          0          0          0        2         0
  IL21R WILD-TYPE        24         11         59         42       46        18
                 vv
clus              STAGE IVB
  IL21R MUTATED           0
  IL21R WILD-TYPE         1
D1556V4, multiclass
            clus
vv           IL21R MUTATED IL21R WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               3              29
  STAGE IIA              6             132
  STAGE IIB              0              10
  STAGE IIC              1               0
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             0              42
  STAGE IV               2              46
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  IL21R MUTATED     0   1  11   2
  IL21R WILD-TYPE  17  91 318  48
D1556V5, multiclass
    clus
vv   IL21R MUTATED IL21R WILD-TYPE
  T1             0              17
  T2             1              91
  T3            11             318
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  IL21R MUTATED    12   1   1
  IL21R WILD-TYPE 275 112  86
D1556V6, multiclass
    clus
vv   IL21R MUTATED IL21R WILD-TYPE
  N0            12             275
  N1             1             112
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1556V7, binary
                 cls
clus                0   1
  IL21R MUTATED    10   2
  IL21R WILD-TYPE 365  63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IL21R MUTATED     10    2
  IL21R WILD-TYPE  365   63
   clus
vv  IL21R MUTATED IL21R WILD-TYPE
  0            10             365
  1             2              63
[1] 2 2
[1] FALSE
D1556V8, binary
                 cls
clus                0   1
  IL21R MUTATED     7   7
  IL21R WILD-TYPE 218 257
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IL21R MUTATED      7    7
  IL21R WILD-TYPE  218  257
        clus
vv       IL21R MUTATED IL21R WILD-TYPE
  FEMALE             7             218
  MALE               7             257
[1] 2 2
[1] FALSE
D1556V9, binary
                 cls
clus                0   1
  IL21R MUTATED    10   1
  IL21R WILD-TYPE 340  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IL21R MUTATED     10    1
  IL21R WILD-TYPE  340   21
     clus
vv    IL21R MUTATED IL21R WILD-TYPE
  NO             10             340
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  IL21R MUTATED                      9                             2
  IL21R WILD-TYPE                  306                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  IL21R MUTATED                       3                              0
  IL21R WILD-TYPE                   103                             10
D1556V10, multiclass
                                clus
vv                               IL21R MUTATED IL21R WILD-TYPE
  COLON ADENOCARCINOMA                       9             306
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      3             103
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  IL21R MUTATED     8   0   2   0
  IL21R WILD-TYPE 337   4  29  25
D1556V11, multiclass
    clus
vv   IL21R MUTATED IL21R WILD-TYPE
  R0             8             337
  R1             0               4
  R2             2              29
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1556V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  IL21R MUTATED                                  0     0
  IL21R WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  IL21R MUTATED                           1     5
  IL21R WILD-TYPE                        21   221
D1556V13, multiclass
                                  clus
vv                                 IL21R MUTATED IL21R WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        5             221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1557) Variable = MBP MUTATION ANALYSIS
D1557V1, survival
               sevent
clus2             0   1
  MBP MUTATED     5   1
  MBP WILD-TYPE 373  92
  MBP MUTATED MBP WILD-TYPE 
            6           465 
  MBP MUTATED MBP WILD-TYPE 
            1            92 
$`MBP MUTATED`
TCGA-A6-2672 TCGA-AA-3833 TCGA-AA-A010 TCGA-AZ-6598 TCGA-CM-4743 TCGA-CM-6674 
       46.65        15.95        34.98        49.41        23.05        12.95 

$`MBP WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       17.98        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        88.21         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
      124.27        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       15.02        14.04        11.01        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  MBP MUTATED MBP WILD-TYPE 
        12.95          0.00 
  MBP MUTATED MBP WILD-TYPE 
        49.41        148.01 
  MBP MUTATED MBP WILD-TYPE 
       29.015        20.120 
[1] "12.9 - 49.4 (29.0)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.4"
D1557V2, continuous
D1557V3, binary
               cls
clus              0   1
  MBP MUTATED     6   0
  MBP WILD-TYPE 360 119
[1] "tbl2"
               cls
clus            [,1] [,2]
  MBP MUTATED      6    0
  MBP WILD-TYPE  360  119
        clus
vv       MBP MUTATED MBP WILD-TYPE
  COLON            6           360
  RECTUM           0           119
[1] 2 2
[1] FALSE
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MBP MUTATED         0        0        1         3         1         0
  MBP WILD-TYPE      91        1       31       135         9         1
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MBP MUTATED           0          0          1          0        0         0
  MBP WILD-TYPE        24         11         58         42       48        18
               vv
clus            STAGE IVB
  MBP MUTATED           0
  MBP WILD-TYPE         1
D1557V4, multiclass
            clus
vv           MBP MUTATED MBP WILD-TYPE
  STAGE I              0            91
  STAGE IA             0             1
  STAGE II             1            31
  STAGE IIA            3           135
  STAGE IIB            1             9
  STAGE IIC            0             1
  STAGE III            0            24
  STAGE IIIA           0            11
  STAGE IIIB           1            58
  STAGE IIIC           0            42
  STAGE IV             0            48
  STAGE IVA            0            18
  STAGE IVB            0             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  MBP MUTATED     0   0   5   1
  MBP WILD-TYPE  17  92 324  49
D1557V5, multiclass
    clus
vv   MBP MUTATED MBP WILD-TYPE
  T1           0            17
  T2           0            92
  T3           5           324
  T4           1            49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2
  MBP MUTATED     5   1   0
  MBP WILD-TYPE 282 112  87
D1557V6, multiclass
    clus
vv   MBP MUTATED MBP WILD-TYPE
  N0           5           282
  N1           1           112
  N2           0            87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1557V7, binary
               cls
clus              0   1
  MBP MUTATED     5   0
  MBP WILD-TYPE 370  65
[1] "tbl2"
               cls
clus            [,1] [,2]
  MBP MUTATED      5    0
  MBP WILD-TYPE  370   65
   clus
vv  MBP MUTATED MBP WILD-TYPE
  0           5           370
  1           0            65
[1] 2 2
[1] FALSE
D1557V8, binary
               cls
clus              0   1
  MBP MUTATED     4   2
  MBP WILD-TYPE 221 262
[1] "tbl2"
               cls
clus            [,1] [,2]
  MBP MUTATED      4    2
  MBP WILD-TYPE  221  262
        clus
vv       MBP MUTATED MBP WILD-TYPE
  FEMALE           4           221
  MALE             2           262
[1] 2 2
[1] FALSE
D1557V9, binary
               cls
clus              0   1
  MBP MUTATED     6   0
  MBP WILD-TYPE 344  22
[1] "tbl2"
               cls
clus            [,1] [,2]
  MBP MUTATED      6    0
  MBP WILD-TYPE  344   22
     clus
vv    MBP MUTATED MBP WILD-TYPE
  NO            6           344
  YES           0            22
[1] 2 2
[1] FALSE
               vv
clus            COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MBP MUTATED                      6                             0
  MBP WILD-TYPE                  309                            47
               vv
clus            RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MBP MUTATED                       0                              0
  MBP WILD-TYPE                   106                             10
D1557V10, multiclass
                                clus
vv                               MBP MUTATED MBP WILD-TYPE
  COLON ADENOCARCINOMA                     6           309
  COLON MUCINOUS ADENOCARCINOMA            0            47
  RECTAL ADENOCARCINOMA                    0           106
  RECTAL MUCINOUS ADENOCARCINOMA           0            10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             R0  R1  R2  RX
  MBP MUTATED     5   0   0   0
  MBP WILD-TYPE 340   4  31  25
D1557V11, multiclass
    clus
vv   MBP MUTATED MBP WILD-TYPE
  R0           5           340
  R1           0             4
  R2           0            31
  RX           0            25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1557V12, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MBP MUTATED                                  0     0
  MBP WILD-TYPE                                1    11
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  MBP MUTATED                           0     4
  MBP WILD-TYPE                        22   222
D1557V13, multiclass
                                  clus
vv                                 MBP MUTATED MBP WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      0            11
  BLACK OR AFRICAN AMERICAN                  0            22
  WHITE                                      4           222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1558) Variable = DLGAP5 MUTATION ANALYSIS
D1558V1, survival
                  sevent
clus2                0   1
  DLGAP5 MUTATED     7   3
  DLGAP5 WILD-TYPE 371  90
  DLGAP5 MUTATED DLGAP5 WILD-TYPE 
              10              461 
  DLGAP5 MUTATED DLGAP5 WILD-TYPE 
               3               90 
$`DLGAP5 MUTATED`
TCGA-AA-3715 TCGA-AZ-4315 TCGA-AZ-6603 TCGA-CA-6717 TCGA-CK-5914 TCGA-CM-4752 
       19.04        58.39        29.56        12.76         9.99        13.02 
TCGA-D5-6537 TCGA-G4-6315 TCGA-AG-3885 TCGA-AG-A002 
        4.80        61.91        17.95        20.98 

$`DLGAP5 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        33.01        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
       12.10       100.01         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       49.08        51.32        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-5341 TCGA-CM-5344 
       23.05        20.02        37.02        25.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       15.12        17.85        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       85.48        63.62        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.04        19.99         1.02        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  DLGAP5 MUTATED DLGAP5 WILD-TYPE 
             4.8              0.0 
  DLGAP5 MUTATED DLGAP5 WILD-TYPE 
           61.91           148.01 
  DLGAP5 MUTATED DLGAP5 WILD-TYPE 
          18.495           20.280 
[1] "4.8 - 61.9 (18.5)"  "0.0 - 148.0 (20.3)"
[1] "hr=" "1.5"
D1558V2, continuous
D1558V3, binary
                  cls
clus                 0   1
  DLGAP5 MUTATED     8   2
  DLGAP5 WILD-TYPE 358 117
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DLGAP5 MUTATED      8    2
  DLGAP5 WILD-TYPE  358  117
        clus
vv       DLGAP5 MUTATED DLGAP5 WILD-TYPE
  COLON               8              358
  RECTUM              2              117
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DLGAP5 MUTATED         1        0        1         3         0         0
  DLGAP5 WILD-TYPE      90        1       31       135        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DLGAP5 MUTATED           0          0          3          0        1
  DLGAP5 WILD-TYPE        24         11         56         42       47
                  vv
clus               STAGE IVA STAGE IVB
  DLGAP5 MUTATED           0         0
  DLGAP5 WILD-TYPE        18         1
D1558V4, multiclass
            clus
vv           DLGAP5 MUTATED DLGAP5 WILD-TYPE
  STAGE I                 1               90
  STAGE IA                0                1
  STAGE II                1               31
  STAGE IIA               3              135
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              3               56
  STAGE IIIC              0               42
  STAGE IV                1               47
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  DLGAP5 MUTATED     0   2   8   0
  DLGAP5 WILD-TYPE  17  90 321  50
D1558V5, multiclass
    clus
vv   DLGAP5 MUTATED DLGAP5 WILD-TYPE
  T1              0               17
  T2              2               90
  T3              8              321
  T4              0               50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  DLGAP5 MUTATED     5   5   0
  DLGAP5 WILD-TYPE 282 108  87
D1558V6, multiclass
    clus
vv   DLGAP5 MUTATED DLGAP5 WILD-TYPE
  N0              5              282
  N1              5              108
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1558V7, binary
                  cls
clus                 0   1
  DLGAP5 MUTATED     6   1
  DLGAP5 WILD-TYPE 369  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DLGAP5 MUTATED      6    1
  DLGAP5 WILD-TYPE  369   64
   clus
vv  DLGAP5 MUTATED DLGAP5 WILD-TYPE
  0              6              369
  1              1               64
[1] 2 2
[1] FALSE
D1558V8, binary
                  cls
clus                 0   1
  DLGAP5 MUTATED     2   8
  DLGAP5 WILD-TYPE 223 256
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DLGAP5 MUTATED      2    8
  DLGAP5 WILD-TYPE  223  256
        clus
vv       DLGAP5 MUTATED DLGAP5 WILD-TYPE
  FEMALE              2              223
  MALE                8              256
[1] 2 2
[1] FALSE
D1558V9, binary
                  cls
clus                 0   1
  DLGAP5 MUTATED     8   1
  DLGAP5 WILD-TYPE 342  21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DLGAP5 MUTATED      8    1
  DLGAP5 WILD-TYPE  342   21
     clus
vv    DLGAP5 MUTATED DLGAP5 WILD-TYPE
  NO               8              342
  YES              1               21
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  DLGAP5 MUTATED                      7                             1
  DLGAP5 WILD-TYPE                  308                            46
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  DLGAP5 MUTATED                       2                              0
  DLGAP5 WILD-TYPE                   104                             10
D1558V10, multiclass
                                clus
vv                               DLGAP5 MUTATED DLGAP5 WILD-TYPE
  COLON ADENOCARCINOMA                        7              308
  COLON MUCINOUS ADENOCARCINOMA               1               46
  RECTAL ADENOCARCINOMA                       2              104
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  DLGAP5 MUTATED     7   0   0   2
  DLGAP5 WILD-TYPE 338   4  31  23
D1558V11, multiclass
    clus
vv   DLGAP5 MUTATED DLGAP5 WILD-TYPE
  R0              7              338
  R1              0                4
  R2              0               31
  RX              2               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1558V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DLGAP5 MUTATED                                  0     1
  DLGAP5 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  DLGAP5 MUTATED                           1     5
  DLGAP5 WILD-TYPE                        21   221
D1558V13, multiclass
                                  clus
vv                                 DLGAP5 MUTATED DLGAP5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                         5              221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1559) Variable = MAP7 MUTATION ANALYSIS
D1559V1, survival
                sevent
clus2              0   1
  MAP7 MUTATED    12   1
  MAP7 WILD-TYPE 366  92
  MAP7 MUTATED MAP7 WILD-TYPE 
            13            458 
  MAP7 MUTATED MAP7 WILD-TYPE 
             1             92 
$`MAP7 MUTATED`
TCGA-A6-6653 TCGA-AA-3543 TCGA-AA-3555 TCGA-AA-3949 TCGA-AA-3966 TCGA-AA-A010 
       24.39         0.99        29.95        26.01         2.01        34.98 
TCGA-AA-A01Q TCGA-AD-6889 TCGA-CA-6718 TCGA-D5-6540 TCGA-AG-3727 TCGA-AG-3892 
        1.02        56.55        10.06        16.14         0.99        13.02 
TCGA-AG-A002 
       20.98 

$`MAP7 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
       25.08        25.18        24.16        21.76        24.69        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       26.01        12.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       24.00        17.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        33.01        24.00         2.01        20.98        34.03 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01R 
       32.02        12.00        31.00        31.00        38.07        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       15.52         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.20        12.76        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       17.13        12.49        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3731 
       15.95        19.99        13.94        19.99         7.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       17.95        36.95        17.03        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  MAP7 MUTATED MAP7 WILD-TYPE 
          0.99           0.00 
  MAP7 MUTATED MAP7 WILD-TYPE 
         56.55         148.01 
  MAP7 MUTATED MAP7 WILD-TYPE 
        16.140         20.235 
[1] "1.0 - 56.5 (16.1)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.8"
D1559V2, continuous
D1559V3, binary
                cls
clus               0   1
  MAP7 MUTATED    11   3
  MAP7 WILD-TYPE 355 116
[1] "tbl2"
                cls
clus             [,1] [,2]
  MAP7 MUTATED     11    3
  MAP7 WILD-TYPE  355  116
        clus
vv       MAP7 MUTATED MAP7 WILD-TYPE
  COLON            11            355
  RECTUM            3            116
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MAP7 MUTATED         5        0        1         5         1         0
  MAP7 WILD-TYPE      86        1       31       133         9         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MAP7 MUTATED           1          0          1          0        0         0
  MAP7 WILD-TYPE        23         11         58         42       48        18
                vv
clus             STAGE IVB
  MAP7 MUTATED           0
  MAP7 WILD-TYPE         1
D1559V4, multiclass
            clus
vv           MAP7 MUTATED MAP7 WILD-TYPE
  STAGE I               5             86
  STAGE IA              0              1
  STAGE II              1             31
  STAGE IIA             5            133
  STAGE IIB             1              9
  STAGE IIC             0              1
  STAGE III             1             23
  STAGE IIIA            0             11
  STAGE IIIB            1             58
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  MAP7 MUTATED     1   4   8   1
  MAP7 WILD-TYPE  16  88 321  49
D1559V5, multiclass
    clus
vv   MAP7 MUTATED MAP7 WILD-TYPE
  T1            1             16
  T2            4             88
  T3            8            321
  T4            1             49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  MAP7 MUTATED    12   2   0
  MAP7 WILD-TYPE 275 111  87
D1559V6, multiclass
    clus
vv   MAP7 MUTATED MAP7 WILD-TYPE
  N0           12            275
  N1            2            111
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1559V7, binary
                cls
clus               0   1
  MAP7 MUTATED    14   0
  MAP7 WILD-TYPE 361  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  MAP7 MUTATED     14    0
  MAP7 WILD-TYPE  361   65
   clus
vv  MAP7 MUTATED MAP7 WILD-TYPE
  0           14            361
  1            0             65
[1] 2 2
[1] FALSE
D1559V8, binary
                cls
clus               0   1
  MAP7 MUTATED     8   6
  MAP7 WILD-TYPE 217 258
[1] "tbl2"
                cls
clus             [,1] [,2]
  MAP7 MUTATED      8    6
  MAP7 WILD-TYPE  217  258
        clus
vv       MAP7 MUTATED MAP7 WILD-TYPE
  FEMALE            8            217
  MALE              6            258
[1] 2 2
[1] FALSE
D1559V9, binary
                cls
clus               0   1
  MAP7 MUTATED     9   0
  MAP7 WILD-TYPE 341  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  MAP7 MUTATED      9    0
  MAP7 WILD-TYPE  341   22
     clus
vv    MAP7 MUTATED MAP7 WILD-TYPE
  NO             9            341
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MAP7 MUTATED                      6                             5
  MAP7 WILD-TYPE                  309                            42
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MAP7 MUTATED                       3                              0
  MAP7 WILD-TYPE                   103                             10
D1559V10, multiclass
                                clus
vv                               MAP7 MUTATED MAP7 WILD-TYPE
  COLON ADENOCARCINOMA                      6            309
  COLON MUCINOUS ADENOCARCINOMA             5             42
  RECTAL ADENOCARCINOMA                     3            103
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  MAP7 MUTATED    10   0   0   1
  MAP7 WILD-TYPE 335   4  31  24
D1559V11, multiclass
    clus
vv   MAP7 MUTATED MAP7 WILD-TYPE
  R0           10            335
  R1            0              4
  R2            0             31
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1559V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MAP7 MUTATED                                  0     2
  MAP7 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  MAP7 MUTATED                           0     2
  MAP7 WILD-TYPE                        22   224
D1559V13, multiclass
                                  clus
vv                                 MAP7 MUTATED MAP7 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              9
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       2            224
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1560) Variable = OR4A16 MUTATION ANALYSIS
D1560V1, survival
                  sevent
clus2                0   1
  OR4A16 MUTATED    11   3
  OR4A16 WILD-TYPE 367  90
  OR4A16 MUTATED OR4A16 WILD-TYPE 
              14              457 
  OR4A16 MUTATED OR4A16 WILD-TYPE 
               3               90 
$`OR4A16 MUTATED`
TCGA-AA-3510 TCGA-AA-3950 TCGA-AA-A02J TCGA-AZ-6608 TCGA-CA-6717 TCGA-CM-4743 
       63.98        24.00         5.03         1.61        12.76        23.05 
TCGA-CM-5344 TCGA-CM-5860 TCGA-CM-6161 TCGA-CM-6677 TCGA-D5-6928 TCGA-DM-A0X9 
       22.03        32.02        15.02        11.08        11.64       119.70 
TCGA-F4-6809 TCGA-AG-3892 
       13.25        13.02 

$`OR4A16 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 
        2.01        12.99        24.00        33.01        26.01         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
       39.98         2.01        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 
      100.01        29.56         5.23        11.74         3.19        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07        12.20        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5348 
       20.02        37.02        25.02        13.02        29.06        22.98 
TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       30.08        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       13.05        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6930 
       12.43        14.30         9.04         9.44         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       12.00        11.38        10.26        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       41.42        16.24        33.67         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       17.03        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  OR4A16 MUTATED OR4A16 WILD-TYPE 
            1.61             0.00 
  OR4A16 MUTATED OR4A16 WILD-TYPE 
          119.70           148.01 
  OR4A16 MUTATED OR4A16 WILD-TYPE 
          14.135           20.280 
[1] "1.6 - 119.7 (14.1)" "0.0 - 148.0 (20.3)"
[1] "hr=" "1.1"
D1560V2, continuous
D1560V3, binary
                  cls
clus                 0   1
  OR4A16 MUTATED    14   1
  OR4A16 WILD-TYPE 352 118
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR4A16 MUTATED     14    1
  OR4A16 WILD-TYPE  352  118
        clus
vv       OR4A16 MUTATED OR4A16 WILD-TYPE
  COLON              14              352
  RECTUM              1              118
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  OR4A16 MUTATED         2        0        1         8         0         0
  OR4A16 WILD-TYPE      89        1       31       130        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  OR4A16 MUTATED           0          1          1          0        1
  OR4A16 WILD-TYPE        24         10         58         42       47
                  vv
clus               STAGE IVA STAGE IVB
  OR4A16 MUTATED           1         0
  OR4A16 WILD-TYPE        17         1
D1560V4, multiclass
            clus
vv           OR4A16 MUTATED OR4A16 WILD-TYPE
  STAGE I                 2               89
  STAGE IA                0                1
  STAGE II                1               31
  STAGE IIA               8              130
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              1               10
  STAGE IIIB              1               58
  STAGE IIIC              0               42
  STAGE IV                1               47
  STAGE IVA               1               17
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  OR4A16 MUTATED     1   2  12   0
  OR4A16 WILD-TYPE  16  90 317  50
D1560V5, multiclass
    clus
vv   OR4A16 MUTATED OR4A16 WILD-TYPE
  T1              1               16
  T2              2               90
  T3             12              317
  T4              0               50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  OR4A16 MUTATED    12   3   0
  OR4A16 WILD-TYPE 275 110  87
D1560V6, multiclass
    clus
vv   OR4A16 MUTATED OR4A16 WILD-TYPE
  N0             12              275
  N1              3              110
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1560V7, binary
                  cls
clus                 0   1
  OR4A16 MUTATED    13   2
  OR4A16 WILD-TYPE 362  63
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR4A16 MUTATED     13    2
  OR4A16 WILD-TYPE  362   63
   clus
vv  OR4A16 MUTATED OR4A16 WILD-TYPE
  0             13              362
  1              2               63
[1] 2 2
[1] FALSE
D1560V8, binary
                  cls
clus                 0   1
  OR4A16 MUTATED    10   5
  OR4A16 WILD-TYPE 215 259
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR4A16 MUTATED     10    5
  OR4A16 WILD-TYPE  215  259
        clus
vv       OR4A16 MUTATED OR4A16 WILD-TYPE
  FEMALE             10              215
  MALE                5              259
[1] 2 2
[1] FALSE
D1560V9, binary
                  cls
clus                 0   1
  OR4A16 MUTATED    12   0
  OR4A16 WILD-TYPE 338  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR4A16 MUTATED     12    0
  OR4A16 WILD-TYPE  338   22
     clus
vv    OR4A16 MUTATED OR4A16 WILD-TYPE
  NO              12              338
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  OR4A16 MUTATED                     11                             3
  OR4A16 WILD-TYPE                  304                            44
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  OR4A16 MUTATED                       1                              0
  OR4A16 WILD-TYPE                   105                             10
D1560V10, multiclass
                                clus
vv                               OR4A16 MUTATED OR4A16 WILD-TYPE
  COLON ADENOCARCINOMA                       11              304
  COLON MUCINOUS ADENOCARCINOMA               3               44
  RECTAL ADENOCARCINOMA                       1              105
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  OR4A16 MUTATED    11   0   1   1
  OR4A16 WILD-TYPE 334   4  30  24
D1560V11, multiclass
    clus
vv   OR4A16 MUTATED OR4A16 WILD-TYPE
  R0             11              334
  R1              0                4
  R2              1               30
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1560V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OR4A16 MUTATED                                  0     1
  OR4A16 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  OR4A16 MUTATED                           0     9
  OR4A16 WILD-TYPE                        22   217
D1560V13, multiclass
                                  clus
vv                                 OR4A16 MUTATED OR4A16 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         9              217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1561) Variable = IRF6 MUTATION ANALYSIS
D1561V1, survival
                sevent
clus2              0   1
  IRF6 MUTATED     3   3
  IRF6 WILD-TYPE 375  90
  IRF6 MUTATED IRF6 WILD-TYPE 
             6            465 
  IRF6 MUTATED IRF6 WILD-TYPE 
             3             90 
$`IRF6 MUTATED`
TCGA-A6-6141 TCGA-AA-3510 TCGA-AA-3715 TCGA-AA-A00N TCGA-D5-5538 TCGA-DM-A1DA 
        8.38        63.98        19.04         4.01        12.26         7.50 

$`IRF6 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 
       22.09        22.06        32.71        27.09        22.52        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  IRF6 MUTATED IRF6 WILD-TYPE 
          4.01           0.00 
  IRF6 MUTATED IRF6 WILD-TYPE 
         63.98         148.01 
  IRF6 MUTATED IRF6 WILD-TYPE 
         10.32          20.55 
[1] "4.0 - 64.0 (10.3)"  "0.0 - 148.0 (20.6)"
[1] "hr=" "3.2"
D1561V2, continuous
D1561V3, binary
                cls
clus               0   1
  IRF6 MUTATED     6   0
  IRF6 WILD-TYPE 360 119
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRF6 MUTATED      6    0
  IRF6 WILD-TYPE  360  119
        clus
vv       IRF6 MUTATED IRF6 WILD-TYPE
  COLON             6            360
  RECTUM            0            119
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  IRF6 MUTATED         0        0        2         1         1         0
  IRF6 WILD-TYPE      91        1       30       137         9         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  IRF6 MUTATED           0          0          1          1        0         0
  IRF6 WILD-TYPE        24         11         58         41       48        18
                vv
clus             STAGE IVB
  IRF6 MUTATED           0
  IRF6 WILD-TYPE         1
D1561V4, multiclass
            clus
vv           IRF6 MUTATED IRF6 WILD-TYPE
  STAGE I               0             91
  STAGE IA              0              1
  STAGE II              2             30
  STAGE IIA             1            137
  STAGE IIB             1              9
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            1             58
  STAGE IIIC            1             41
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  IRF6 MUTATED     0   0   5   1
  IRF6 WILD-TYPE  17  92 324  49
D1561V5, multiclass
    clus
vv   IRF6 MUTATED IRF6 WILD-TYPE
  T1            0             17
  T2            0             92
  T3            5            324
  T4            1             49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  IRF6 MUTATED     4   1   1
  IRF6 WILD-TYPE 283 112  86
D1561V6, multiclass
    clus
vv   IRF6 MUTATED IRF6 WILD-TYPE
  N0            4            283
  N1            1            112
  N2            1             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1561V7, binary
                cls
clus               0   1
  IRF6 MUTATED     6   0
  IRF6 WILD-TYPE 369  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRF6 MUTATED      6    0
  IRF6 WILD-TYPE  369   65
   clus
vv  IRF6 MUTATED IRF6 WILD-TYPE
  0            6            369
  1            0             65
[1] 2 2
[1] FALSE
D1561V8, binary
                cls
clus               0   1
  IRF6 MUTATED     2   4
  IRF6 WILD-TYPE 223 260
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRF6 MUTATED      2    4
  IRF6 WILD-TYPE  223  260
        clus
vv       IRF6 MUTATED IRF6 WILD-TYPE
  FEMALE            2            223
  MALE              4            260
[1] 2 2
[1] FALSE
D1561V9, binary
                cls
clus               0   1
  IRF6 MUTATED     4   0
  IRF6 WILD-TYPE 346  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRF6 MUTATED      4    0
  IRF6 WILD-TYPE  346   22
     clus
vv    IRF6 MUTATED IRF6 WILD-TYPE
  NO             4            346
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  IRF6 MUTATED                      5                             1
  IRF6 WILD-TYPE                  310                            46
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  IRF6 MUTATED                       0                              0
  IRF6 WILD-TYPE                   106                             10
D1561V10, multiclass
                                clus
vv                               IRF6 MUTATED IRF6 WILD-TYPE
  COLON ADENOCARCINOMA                      5            310
  COLON MUCINOUS ADENOCARCINOMA             1             46
  RECTAL ADENOCARCINOMA                     0            106
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  IRF6 MUTATED     4   0   0   0
  IRF6 WILD-TYPE 341   4  31  25
D1561V11, multiclass
    clus
vv   IRF6 MUTATED IRF6 WILD-TYPE
  R0            4            341
  R1            0              4
  R2            0             31
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1561V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  IRF6 MUTATED                                  0     0
  IRF6 WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  IRF6 MUTATED                           1     2
  IRF6 WILD-TYPE                        21   224
D1561V13, multiclass
                                  clus
vv                                 IRF6 MUTATED IRF6 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                       2            224
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1562) Variable = LGALS9C MUTATION ANALYSIS
D1562V1, survival
                   sevent
clus2                 0   1
  LGALS9C MUTATED     5   1
  LGALS9C WILD-TYPE 373  92
  LGALS9C MUTATED LGALS9C WILD-TYPE 
                6               465 
  LGALS9C MUTATED LGALS9C WILD-TYPE 
                1                92 
$`LGALS9C MUTATED`
TCGA-AA-3511 TCGA-AZ-6599 TCGA-CM-6164 TCGA-CM-6674 TCGA-G4-6586 TCGA-AG-A002 
        6.97         6.77        29.03        12.95        35.80        20.98 

$`LGALS9C WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01        63.98         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       15.02        12.00         2.96        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6675 
       12.99        13.02        15.02        14.04        11.01        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  LGALS9C MUTATED LGALS9C WILD-TYPE 
             6.77              0.00 
  LGALS9C MUTATED LGALS9C WILD-TYPE 
            35.80            148.01 
  LGALS9C MUTATED LGALS9C WILD-TYPE 
           16.965            20.190 
[1] "6.8 - 35.8 (17.0)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.3"
D1562V2, continuous
D1562V3, binary
                   cls
clus                  0   1
  LGALS9C MUTATED     5   1
  LGALS9C WILD-TYPE 361 118
[1] "tbl2"
                   cls
clus                [,1] [,2]
  LGALS9C MUTATED      5    1
  LGALS9C WILD-TYPE  361  118
        clus
vv       LGALS9C MUTATED LGALS9C WILD-TYPE
  COLON                5               361
  RECTUM               1               118
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  LGALS9C MUTATED         2        0        1         3         0         0
  LGALS9C WILD-TYPE      89        1       31       135        10         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  LGALS9C MUTATED           0          0          0          0        0
  LGALS9C WILD-TYPE        24         11         59         42       48
                   vv
clus                STAGE IVA STAGE IVB
  LGALS9C MUTATED           0         0
  LGALS9C WILD-TYPE        18         1
D1562V4, multiclass
            clus
vv           LGALS9C MUTATED LGALS9C WILD-TYPE
  STAGE I                  2                89
  STAGE IA                 0                 1
  STAGE II                 1                31
  STAGE IIA                3               135
  STAGE IIB                0                10
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               0                11
  STAGE IIIB               0                59
  STAGE IIIC               0                42
  STAGE IV                 0                48
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  LGALS9C MUTATED     0   2   3   1
  LGALS9C WILD-TYPE  17  90 326  49
D1562V5, multiclass
    clus
vv   LGALS9C MUTATED LGALS9C WILD-TYPE
  T1               0                17
  T2               2                90
  T3               3               326
  T4               1                49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  LGALS9C MUTATED     6   0   0
  LGALS9C WILD-TYPE 281 113  87
D1562V6, multiclass
    clus
vv   LGALS9C MUTATED LGALS9C WILD-TYPE
  N0               6               281
  N1               0               113
  N2               0                87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1562V7, binary
                   cls
clus                  0   1
  LGALS9C MUTATED     5   0
  LGALS9C WILD-TYPE 370  65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  LGALS9C MUTATED      5    0
  LGALS9C WILD-TYPE  370   65
   clus
vv  LGALS9C MUTATED LGALS9C WILD-TYPE
  0               5               370
  1               0                65
[1] 2 2
[1] FALSE
D1562V8, binary
                   cls
clus                  0   1
  LGALS9C MUTATED     2   4
  LGALS9C WILD-TYPE 223 260
[1] "tbl2"
                   cls
clus                [,1] [,2]
  LGALS9C MUTATED      2    4
  LGALS9C WILD-TYPE  223  260
        clus
vv       LGALS9C MUTATED LGALS9C WILD-TYPE
  FEMALE               2               223
  MALE                 4               260
[1] 2 2
[1] FALSE
D1562V9, binary
                   cls
clus                  0   1
  LGALS9C MUTATED     6   0
  LGALS9C WILD-TYPE 344  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  LGALS9C MUTATED      6    0
  LGALS9C WILD-TYPE  344   22
     clus
vv    LGALS9C MUTATED LGALS9C WILD-TYPE
  NO                6               344
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  LGALS9C MUTATED                      5                             0
  LGALS9C WILD-TYPE                  310                            47
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  LGALS9C MUTATED                       1                              0
  LGALS9C WILD-TYPE                   105                             10
D1562V10, multiclass
                                clus
vv                               LGALS9C MUTATED LGALS9C WILD-TYPE
  COLON ADENOCARCINOMA                         5               310
  COLON MUCINOUS ADENOCARCINOMA                0                47
  RECTAL ADENOCARCINOMA                        1               105
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  LGALS9C MUTATED     5   0   0   0
  LGALS9C WILD-TYPE 340   4  31  25
D1562V11, multiclass
    clus
vv   LGALS9C MUTATED LGALS9C WILD-TYPE
  R0               5               340
  R1               0                 4
  R2               0                31
  RX               0                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1562V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  LGALS9C MUTATED                                  0     0
  LGALS9C WILD-TYPE                                1    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  LGALS9C MUTATED                           0     4
  LGALS9C WILD-TYPE                        22   222
D1562V13, multiclass
                                  clus
vv                                 LGALS9C MUTATED LGALS9C WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                      0                22
  WHITE                                          4               222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1563) Variable = ZNF512 MUTATION ANALYSIS
D1563V1, survival
                  sevent
clus2                0   1
  ZNF512 MUTATED     2   1
  ZNF512 WILD-TYPE 376  92
  ZNF512 MUTATED ZNF512 WILD-TYPE 
               3              468 
  ZNF512 MUTATED ZNF512 WILD-TYPE 
               1               92 
$`ZNF512 MUTATED`
TCGA-AD-6963 TCGA-AZ-6600 TCGA-G4-6315 
       27.42        12.10        61.91 

$`ZNF512 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       63.62        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  ZNF512 MUTATED ZNF512 WILD-TYPE 
            12.1              0.0 
  ZNF512 MUTATED ZNF512 WILD-TYPE 
           61.91           148.01 
  ZNF512 MUTATED ZNF512 WILD-TYPE 
          27.420           20.155 
[1] "12.1 - 61.9 (27.4)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.2"
D1563V2, continuous
D1563V3, binary
                  cls
clus                 0   1
  ZNF512 MUTATED     3   0
  ZNF512 WILD-TYPE 363 119
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF512 MUTATED      3    0
  ZNF512 WILD-TYPE  363  119
        clus
vv       ZNF512 MUTATED ZNF512 WILD-TYPE
  COLON               3              363
  RECTUM              0              119
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZNF512 MUTATED         0        0        0         0         0         0
  ZNF512 WILD-TYPE      91        1       32       138        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF512 MUTATED           0          0          0          0        2
  ZNF512 WILD-TYPE        24         11         59         42       46
                  vv
clus               STAGE IVA STAGE IVB
  ZNF512 MUTATED           0         0
  ZNF512 WILD-TYPE        18         1
D1563V4, multiclass
[1] "Remove cluster labels:" "ZNF512 MUTATED"        
clus
  ZNF512 MUTATED ZNF512 WILD-TYPE 
               2              474 
      TCGA-A6-2671       TCGA-A6-2672       TCGA-A6-2674       TCGA-A6-2676 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-A6-2677       TCGA-A6-2678       TCGA-A6-2683       TCGA-A6-3807 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-A6-3808       TCGA-A6-3809       TCGA-A6-3810       TCGA-A6-4105 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-A6-5656       TCGA-A6-5657       TCGA-A6-5659       TCGA-A6-5660 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-A6-5661       TCGA-A6-5662       TCGA-A6-5664       TCGA-A6-5665 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-A6-5666       TCGA-A6-6137       TCGA-A6-6138       TCGA-A6-6141 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-A6-6142       TCGA-A6-6648       TCGA-A6-6649       TCGA-A6-6651 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-A6-6652       TCGA-A6-6653       TCGA-A6-6654       TCGA-A6-6780 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-A6-6781       TCGA-A6-6782       TCGA-AA-3489       TCGA-AA-3492 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3496       TCGA-AA-3502       TCGA-AA-3510       TCGA-AA-3511 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3514       TCGA-AA-3516       TCGA-AA-3517       TCGA-AA-3518 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3519       TCGA-AA-3520       TCGA-AA-3521       TCGA-AA-3522 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3524       TCGA-AA-3525       TCGA-AA-3526       TCGA-AA-3527 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3529       TCGA-AA-3530       TCGA-AA-3531       TCGA-AA-3532 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3534       TCGA-AA-3538       TCGA-AA-3542       TCGA-AA-3543 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3544       TCGA-AA-3548       TCGA-AA-3549       TCGA-AA-3552 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3553       TCGA-AA-3554       TCGA-AA-3555       TCGA-AA-3556 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3558       TCGA-AA-3560       TCGA-AA-3561       TCGA-AA-3562 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3655       TCGA-AA-3660       TCGA-AA-3662       TCGA-AA-3663 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3664       TCGA-AA-3666       TCGA-AA-3667       TCGA-AA-3672 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3673       TCGA-AA-3678       TCGA-AA-3679       TCGA-AA-3680 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3681       TCGA-AA-3684       TCGA-AA-3685       TCGA-AA-3688 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3692       TCGA-AA-3693       TCGA-AA-3695       TCGA-AA-3696 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3697       TCGA-AA-3710       TCGA-AA-3712       TCGA-AA-3713 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3715       TCGA-AA-3811       TCGA-AA-3812       TCGA-AA-3814 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3815       TCGA-AA-3818       TCGA-AA-3819       TCGA-AA-3821 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3831       TCGA-AA-3833       TCGA-AA-3837       TCGA-AA-3842 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3844       TCGA-AA-3845       TCGA-AA-3846       TCGA-AA-3848 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3850       TCGA-AA-3851       TCGA-AA-3852       TCGA-AA-3854 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3855       TCGA-AA-3856       TCGA-AA-3858       TCGA-AA-3860 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3861       TCGA-AA-3864       TCGA-AA-3866       TCGA-AA-3867 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3869       TCGA-AA-3870       TCGA-AA-3872       TCGA-AA-3875 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3877       TCGA-AA-3930       TCGA-AA-3939       TCGA-AA-3941 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3947       TCGA-AA-3949       TCGA-AA-3950       TCGA-AA-3952 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3955       TCGA-AA-3956       TCGA-AA-3966       TCGA-AA-3968 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3971       TCGA-AA-3972       TCGA-AA-3973       TCGA-AA-3975 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3976       TCGA-AA-3979       TCGA-AA-3980       TCGA-AA-3982 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3984       TCGA-AA-3986       TCGA-AA-3989       TCGA-AA-3994 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-A004       TCGA-AA-A00A       TCGA-AA-A00D       TCGA-AA-A00E 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-A00F       TCGA-AA-A00J       TCGA-AA-A00K       TCGA-AA-A00L 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-A00N       TCGA-AA-A00O       TCGA-AA-A00Q       TCGA-AA-A00R 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-A00U       TCGA-AA-A00W       TCGA-AA-A00Z       TCGA-AA-A010 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-A017       TCGA-AA-A01D       TCGA-AA-A01F       TCGA-AA-A01G 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-A01I       TCGA-AA-A01K       TCGA-AA-A01P       TCGA-AA-A01Q 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-A01R       TCGA-AA-A01S       TCGA-AA-A01T       TCGA-AA-A01V 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-A01X       TCGA-AA-A01Z       TCGA-AA-A022       TCGA-AA-A024 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-A029       TCGA-AA-A02F       TCGA-AA-A02H       TCGA-AA-A02J 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-A02K       TCGA-AA-A02O       TCGA-AA-A02W       TCGA-AA-A02Y 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-A03F       TCGA-AA-A03J       TCGA-AD-5900       TCGA-AD-6548 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AD-6888       TCGA-AD-6889       TCGA-AD-6899       TCGA-AU-3779 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AU-6004       TCGA-AY-4070       TCGA-AY-4071       TCGA-AY-5543 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AY-6196       TCGA-AY-6197       TCGA-AY-6386       TCGA-AZ-4315 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AZ-4323       TCGA-AZ-4616       TCGA-AZ-4681       TCGA-AZ-4682 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AZ-5403       TCGA-AZ-5407       TCGA-AZ-6598       TCGA-AZ-6599 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AZ-6601       TCGA-AZ-6605       TCGA-AZ-6606       TCGA-AZ-6607 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AZ-6608       TCGA-CA-5254       TCGA-CA-5255       TCGA-CA-5796 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-CA-5797       TCGA-CA-6715       TCGA-CA-6716       TCGA-CA-6717 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-CA-6718       TCGA-CA-6719       TCGA-CK-4947       TCGA-CK-4948 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-CK-4950       TCGA-CK-4952       TCGA-CK-5912       TCGA-CK-5913 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-CK-5914       TCGA-CK-5915       TCGA-CK-5916       TCGA-CK-6746 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-CK-6747       TCGA-CK-6748       TCGA-CK-6751       TCGA-CM-4743 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-CM-4744       TCGA-CM-4746       TCGA-CM-4747       TCGA-CM-4752 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-CM-5341       TCGA-CM-5344       TCGA-CM-5348       TCGA-CM-5349 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-CM-5860       TCGA-CM-5861       TCGA-CM-5862       TCGA-CM-5863 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-CM-5864       TCGA-CM-5868       TCGA-CM-6161       TCGA-CM-6162 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-CM-6163       TCGA-CM-6164       TCGA-CM-6165       TCGA-CM-6166 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-CM-6167       TCGA-CM-6168       TCGA-CM-6169       TCGA-CM-6170 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-CM-6171       TCGA-CM-6172       TCGA-CM-6674       TCGA-CM-6675 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-CM-6676       TCGA-CM-6677       TCGA-CM-6678       TCGA-CM-6679 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-CM-6680       TCGA-D5-5537       TCGA-D5-5538       TCGA-D5-5539 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-D5-5540       TCGA-D5-5541       TCGA-D5-6529       TCGA-D5-6532 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-D5-6533       TCGA-D5-6534       TCGA-D5-6535       TCGA-D5-6536 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-D5-6537       TCGA-D5-6538       TCGA-D5-6539       TCGA-D5-6540 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-D5-6541       TCGA-D5-6898       TCGA-D5-6920       TCGA-D5-6922 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-D5-6923       TCGA-D5-6924       TCGA-D5-6926       TCGA-D5-6927 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-D5-6928       TCGA-D5-6929       TCGA-D5-6930       TCGA-D5-6931 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-D5-6932       TCGA-D5-7000       TCGA-DM-A0X9       TCGA-DM-A0XD 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-DM-A0XF       TCGA-DM-A1D0       TCGA-DM-A1D4       TCGA-DM-A1D6 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-DM-A1D7       TCGA-DM-A1D9       TCGA-DM-A1DA       TCGA-DM-A1DB 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-DM-A1HA       TCGA-DM-A1HB       TCGA-DM-A282       TCGA-DM-A285 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-DM-A28C       TCGA-DM-A28E       TCGA-DM-A28F       TCGA-DM-A28G 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-DM-A28H       TCGA-DM-A28K       TCGA-F4-6459       TCGA-F4-6460 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-F4-6569       TCGA-F4-6570       TCGA-F4-6703       TCGA-F4-6704 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-F4-6805       TCGA-F4-6806       TCGA-F4-6807       TCGA-F4-6808 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-F4-6809       TCGA-F4-6854       TCGA-F4-6855       TCGA-F4-6856 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-G4-6293       TCGA-G4-6299       TCGA-G4-6303       TCGA-G4-6304 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-G4-6306       TCGA-G4-6307       TCGA-G4-6309       TCGA-G4-6310 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-G4-6317       TCGA-G4-6321       TCGA-G4-6323       TCGA-G4-6586 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-G4-6588       TCGA-G4-6625       TCGA-G4-6626       TCGA-G4-6628 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AF-2687       TCGA-AF-2689       TCGA-AF-2691       TCGA-AF-2692 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AF-2693       TCGA-AF-3400       TCGA-AF-3913       TCGA-AF-4110 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AF-5654       TCGA-AF-6136       TCGA-AF-6655       TCGA-AF-6672 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AG-3574       TCGA-AG-3575       TCGA-AG-3578       TCGA-AG-3580 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AG-3581       TCGA-AG-3582       TCGA-AG-3583       TCGA-AG-3584 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AG-3586       TCGA-AG-3587       TCGA-AG-3593       TCGA-AG-3594 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AG-3598       TCGA-AG-3599       TCGA-AG-3600       TCGA-AG-3601 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AG-3602       TCGA-AG-3605       TCGA-AG-3608       TCGA-AG-3609 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AG-3611       TCGA-AG-3612       TCGA-AG-3726       TCGA-AG-3727 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AG-3731       TCGA-AG-3732       TCGA-AG-3742       TCGA-AG-3878 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AG-3881       TCGA-AG-3882       TCGA-AG-3883       TCGA-AG-3885 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AG-3887       TCGA-AG-3890       TCGA-AG-3892       TCGA-AG-3893 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AG-3894       TCGA-AG-3896       TCGA-AG-3898       TCGA-AG-3901 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AG-3902       TCGA-AG-3909       TCGA-AG-3999       TCGA-AG-4001 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AG-4005       TCGA-AG-4007       TCGA-AG-4008       TCGA-AG-4015 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AG-A002       TCGA-AG-A008       TCGA-AG-A00C       TCGA-AG-A00H 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AG-A00Y       TCGA-AG-A011       TCGA-AG-A014       TCGA-AG-A015 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AG-A016       TCGA-AG-A01L       TCGA-AG-A01W       TCGA-AG-A01Y 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AG-A020       TCGA-AG-A025       TCGA-AG-A026       TCGA-AG-A02G 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AG-A02N       TCGA-AG-A02X       TCGA-AG-A032       TCGA-AG-A036 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AH-6643       TCGA-CI-6619       TCGA-CI-6620       TCGA-CI-6621 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-CI-6622       TCGA-CI-6624       TCGA-CL-5917       TCGA-CL-5918 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-DC-5337       TCGA-DC-5869       TCGA-DC-6155       TCGA-DC-6157 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-DC-6158       TCGA-DC-6160       TCGA-DC-6681       TCGA-DC-6682 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-DC-6683       TCGA-DT-5265       TCGA-DY-A0XA       TCGA-DY-A1DC 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-DY-A1DD       TCGA-DY-A1DF       TCGA-DY-A1DG       TCGA-DY-A1H8 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-EF-5830       TCGA-EI-6506       TCGA-EI-6507       TCGA-EI-6508 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-EI-6510       TCGA-F5-6464       TCGA-F5-6465       TCGA-F5-6571 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-F5-6702       TCGA-F5-6811       TCGA-F5-6812       TCGA-F5-6813 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-G5-6235       TCGA-G5-6641 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
                  vv
clus                T1  T2  T3  T4
  ZNF512 MUTATED     0   0   2   1
  ZNF512 WILD-TYPE  17  92 327  49
D1563V5, multiclass
    clus
vv   ZNF512 MUTATED ZNF512 WILD-TYPE
  T1              0               17
  T2              0               92
  T3              2              327
  T4              1               49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  ZNF512 MUTATED     1   2   0
  ZNF512 WILD-TYPE 286 111  87
D1563V6, multiclass
    clus
vv   ZNF512 MUTATED ZNF512 WILD-TYPE
  N0              1              286
  N1              2              111
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1563V7, binary
                  cls
clus                 0   1
  ZNF512 MUTATED     0   2
  ZNF512 WILD-TYPE 375  63
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF512 MUTATED      0    2
  ZNF512 WILD-TYPE  375   63
   clus
vv  ZNF512 MUTATED ZNF512 WILD-TYPE
  0              0              375
  1              2               63
[1] 2 2
[1] FALSE
D1563V8, binary
                  cls
clus                 0   1
  ZNF512 MUTATED     0   3
  ZNF512 WILD-TYPE 225 261
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF512 MUTATED      0    3
  ZNF512 WILD-TYPE  225  261
        clus
vv       ZNF512 MUTATED ZNF512 WILD-TYPE
  FEMALE              0              225
  MALE                3              261
[1] 2 2
[1] FALSE
D1563V9, binary
                  cls
clus                 0   1
  ZNF512 MUTATED     2   0
  ZNF512 WILD-TYPE 348  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF512 MUTATED      2    0
  ZNF512 WILD-TYPE  348   22
     clus
vv    ZNF512 MUTATED ZNF512 WILD-TYPE
  NO               2              348
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ZNF512 MUTATED                      3                             0
  ZNF512 WILD-TYPE                  312                            47
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ZNF512 MUTATED                       0                              0
  ZNF512 WILD-TYPE                   106                             10
D1563V10, multiclass
                                clus
vv                               ZNF512 MUTATED ZNF512 WILD-TYPE
  COLON ADENOCARCINOMA                        3              312
  COLON MUCINOUS ADENOCARCINOMA               0               47
  RECTAL ADENOCARCINOMA                       0              106
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ZNF512 MUTATED     1   0   0   0
  ZNF512 WILD-TYPE 344   4  31  25
D1563V11, multiclass
[1] "Remove cluster labels:" "ZNF512 MUTATED"        
clus
  ZNF512 MUTATED ZNF512 WILD-TYPE 
               1              404 
      TCGA-A6-2671       TCGA-A6-2672       TCGA-A6-2674       TCGA-A6-2676 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-A6-2677       TCGA-A6-2678       TCGA-A6-2683       TCGA-A6-3807 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-A6-3808       TCGA-A6-3809       TCGA-A6-3810       TCGA-A6-5657 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-A6-5659       TCGA-A6-5661       TCGA-A6-5665       TCGA-A6-6781 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3489       TCGA-AA-3492       TCGA-AA-3496       TCGA-AA-3502 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3510       TCGA-AA-3511       TCGA-AA-3514       TCGA-AA-3517 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3518       TCGA-AA-3519       TCGA-AA-3520       TCGA-AA-3521 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3522       TCGA-AA-3524       TCGA-AA-3525       TCGA-AA-3526 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3527       TCGA-AA-3529       TCGA-AA-3530       TCGA-AA-3531 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3532       TCGA-AA-3534       TCGA-AA-3538       TCGA-AA-3542 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3543       TCGA-AA-3544       TCGA-AA-3548       TCGA-AA-3549 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3552       TCGA-AA-3553       TCGA-AA-3554       TCGA-AA-3555 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3556       TCGA-AA-3558       TCGA-AA-3560       TCGA-AA-3561 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3562       TCGA-AA-3655       TCGA-AA-3660       TCGA-AA-3662 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3663       TCGA-AA-3664       TCGA-AA-3666       TCGA-AA-3667 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3672       TCGA-AA-3673       TCGA-AA-3678       TCGA-AA-3679 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3680       TCGA-AA-3681       TCGA-AA-3684       TCGA-AA-3685 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3688       TCGA-AA-3692       TCGA-AA-3693       TCGA-AA-3695 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3696       TCGA-AA-3697       TCGA-AA-3710       TCGA-AA-3712 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3713       TCGA-AA-3715       TCGA-AA-3811       TCGA-AA-3812 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3814       TCGA-AA-3815       TCGA-AA-3818       TCGA-AA-3819 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3821       TCGA-AA-3831       TCGA-AA-3833       TCGA-AA-3837 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3842       TCGA-AA-3844       TCGA-AA-3845       TCGA-AA-3846 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3848       TCGA-AA-3850       TCGA-AA-3851       TCGA-AA-3852 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3854       TCGA-AA-3855       TCGA-AA-3856       TCGA-AA-3858 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3860       TCGA-AA-3861       TCGA-AA-3864       TCGA-AA-3866 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3867       TCGA-AA-3869       TCGA-AA-3870       TCGA-AA-3872 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3875       TCGA-AA-3877       TCGA-AA-3930       TCGA-AA-3939 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3941       TCGA-AA-3947       TCGA-AA-3949       TCGA-AA-3950 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3952       TCGA-AA-3955       TCGA-AA-3956       TCGA-AA-3968 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3971       TCGA-AA-3972       TCGA-AA-3973       TCGA-AA-3975 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3976       TCGA-AA-3979       TCGA-AA-3984       TCGA-AA-3986 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-3989       TCGA-AA-3994       TCGA-AA-A004       TCGA-AA-A00A 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-A00D       TCGA-AA-A00E       TCGA-AA-A00F       TCGA-AA-A00J 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-A00K       TCGA-AA-A00L       TCGA-AA-A00N       TCGA-AA-A00O 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-A00Q       TCGA-AA-A00R       TCGA-AA-A00U       TCGA-AA-A00W 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-A00Z       TCGA-AA-A010       TCGA-AA-A017       TCGA-AA-A01D 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-A01F       TCGA-AA-A01G       TCGA-AA-A01I       TCGA-AA-A01K 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-A01P       TCGA-AA-A01Q       TCGA-AA-A01R       TCGA-AA-A01S 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-A01T       TCGA-AA-A01V       TCGA-AA-A01X       TCGA-AA-A01Z 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-A022       TCGA-AA-A024       TCGA-AA-A029       TCGA-AA-A02F 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-A02H       TCGA-AA-A02J       TCGA-AA-A02K       TCGA-AA-A02O 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AA-A02W       TCGA-AA-A02Y       TCGA-AA-A03F       TCGA-AA-A03J 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AD-5900       TCGA-AD-6548       TCGA-AD-6888       TCGA-AU-3779 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AU-6004       TCGA-AY-4070       TCGA-AY-4071       TCGA-AY-5543 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AY-6196       TCGA-AY-6197       TCGA-AY-6386       TCGA-AZ-4315 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AZ-4681       TCGA-AZ-4682       TCGA-CA-5254       TCGA-CA-5255 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-CA-5796       TCGA-CA-5797       TCGA-CA-6715       TCGA-CA-6716 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-CA-6717       TCGA-CA-6718       TCGA-CA-6719       TCGA-CK-4947 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-CK-4948       TCGA-CK-4950       TCGA-CK-4952       TCGA-CK-5912 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-CK-5913       TCGA-CK-5914       TCGA-CK-5915       TCGA-CK-5916 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-CK-6746       TCGA-CK-6747       TCGA-CK-6748       TCGA-CK-6751 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-CM-4743       TCGA-CM-4744       TCGA-CM-4746       TCGA-CM-4747 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-CM-4752       TCGA-CM-5341       TCGA-CM-5344       TCGA-CM-5348 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-CM-5349       TCGA-CM-5860       TCGA-CM-5861       TCGA-CM-5862 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-CM-5863       TCGA-CM-5864       TCGA-CM-5868       TCGA-CM-6161 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-CM-6162       TCGA-CM-6163       TCGA-CM-6164       TCGA-CM-6165 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-CM-6166       TCGA-CM-6167       TCGA-CM-6168       TCGA-CM-6169 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-CM-6170       TCGA-CM-6171       TCGA-CM-6172       TCGA-CM-6674 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-CM-6675       TCGA-CM-6676       TCGA-CM-6677       TCGA-CM-6678 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-CM-6679       TCGA-CM-6680       TCGA-D5-5537       TCGA-D5-5538 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-D5-5539       TCGA-D5-5540       TCGA-D5-5541       TCGA-D5-6529 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-D5-6532       TCGA-D5-6533       TCGA-D5-6534       TCGA-D5-6535 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-D5-6536       TCGA-D5-6537       TCGA-D5-6538       TCGA-D5-6539 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-D5-6540       TCGA-D5-6541       TCGA-D5-6898       TCGA-D5-6920 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-D5-6922       TCGA-D5-6923       TCGA-D5-6924       TCGA-D5-6926 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-D5-6927       TCGA-D5-6928       TCGA-D5-6929       TCGA-D5-6930 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-D5-6931       TCGA-D5-6932       TCGA-D5-7000       TCGA-F4-6459 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-F4-6460       TCGA-F4-6569       TCGA-F4-6570       TCGA-F4-6703 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-F4-6704       TCGA-F4-6805       TCGA-F4-6806       TCGA-F4-6807 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-F4-6808       TCGA-F4-6809       TCGA-F4-6854       TCGA-F4-6855 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-F4-6856       TCGA-G4-6293       TCGA-G4-6299       TCGA-G4-6303 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-G4-6304       TCGA-G4-6306       TCGA-G4-6307       TCGA-G4-6309 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-G4-6310       TCGA-G4-6317       TCGA-G4-6321       TCGA-G4-6323 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-G4-6586       TCGA-G4-6588       TCGA-G4-6625       TCGA-G4-6626 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-G4-6628       TCGA-AF-2687       TCGA-AF-2689       TCGA-AF-2691 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AF-2692       TCGA-AF-3400       TCGA-AF-3913       TCGA-AF-4110 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AF-5654       TCGA-AF-6655       TCGA-AG-3574       TCGA-AG-3575 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AG-3578       TCGA-AG-3580       TCGA-AG-3581       TCGA-AG-3582 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AG-3583       TCGA-AG-3584       TCGA-AG-3586       TCGA-AG-3587 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AG-3593       TCGA-AG-3594       TCGA-AG-3598       TCGA-AG-3599 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AG-3600       TCGA-AG-3601       TCGA-AG-3602       TCGA-AG-3605 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AG-3608       TCGA-AG-3609       TCGA-AG-3611       TCGA-AG-3612 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AG-3726       TCGA-AG-3727       TCGA-AG-3731       TCGA-AG-3732 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AG-3742       TCGA-AG-3878       TCGA-AG-3882       TCGA-AG-3883 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AG-3885       TCGA-AG-3887       TCGA-AG-3890       TCGA-AG-3892 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AG-3893       TCGA-AG-3894       TCGA-AG-3896       TCGA-AG-3898 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AG-3901       TCGA-AG-3902       TCGA-AG-3909       TCGA-AG-3999 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AG-4001       TCGA-AG-4005       TCGA-AG-4007       TCGA-AG-4008 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AG-4015       TCGA-AG-A002       TCGA-AG-A008       TCGA-AG-A00C 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AG-A00H       TCGA-AG-A00Y       TCGA-AG-A011       TCGA-AG-A014 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AG-A015       TCGA-AG-A016       TCGA-AG-A01L       TCGA-AG-A01W 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AG-A01Y       TCGA-AG-A020       TCGA-AG-A025       TCGA-AG-A026 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AG-A02G       TCGA-AG-A02N       TCGA-AG-A02X       TCGA-AG-A032 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-AG-A036       TCGA-AH-6549       TCGA-AH-6643       TCGA-CL-5917 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-CL-5918       TCGA-DC-5337       TCGA-DC-5869       TCGA-DC-6155 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-DC-6157       TCGA-DC-6158       TCGA-DC-6160       TCGA-DC-6681 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-DC-6682       TCGA-DC-6683       TCGA-DT-5265       TCGA-EF-5830 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-EI-6506       TCGA-EI-6507       TCGA-EI-6508       TCGA-EI-6510 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-F5-6464       TCGA-F5-6465       TCGA-F5-6571       TCGA-F5-6702 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
      TCGA-F5-6812       TCGA-F5-6813       TCGA-G5-6235       TCGA-G5-6641 
"ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" "ZNF512 WILD-TYPE" 
D1563V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF512 MUTATED                                  0     0
  ZNF512 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZNF512 MUTATED                           1     2
  ZNF512 WILD-TYPE                        21   224
D1563V13, multiclass
                                  clus
vv                                 ZNF512 MUTATED ZNF512 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                         2              224
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1564) Variable = HIF1A MUTATION ANALYSIS
D1564V1, survival
                 sevent
clus2               0   1
  HIF1A MUTATED     9   3
  HIF1A WILD-TYPE 369  90
  HIF1A MUTATED HIF1A WILD-TYPE 
             12             459 
  HIF1A MUTATED HIF1A WILD-TYPE 
              3              90 
$`HIF1A MUTATED`
TCGA-A6-3809 TCGA-AA-3950 TCGA-AA-A00E TCGA-AA-A02K TCGA-AZ-4315 TCGA-AZ-6598 
       32.75        24.00        30.02        14.01        58.39        49.41 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-6674 TCGA-D5-6928 TCGA-G4-6628 TCGA-AG-A002 
       12.76        10.06        12.95        11.64        79.69        20.98 

$`HIF1A WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 
        2.01        12.99        24.00        33.01        26.01         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       19.00        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        2.01         5.03         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       88.21         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        3.29         0.07        12.20        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 
        4.41        12.43        14.30         9.04         9.44         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       46.75        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  HIF1A MUTATED HIF1A WILD-TYPE 
          10.06            0.00 
  HIF1A MUTATED HIF1A WILD-TYPE 
          79.69          148.01 
  HIF1A MUTATED HIF1A WILD-TYPE 
          22.49           20.12 
[1] "10.1 - 79.7 (22.5)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.1"
D1564V2, continuous
D1564V3, binary
                 cls
clus                0   1
  HIF1A MUTATED    11   1
  HIF1A WILD-TYPE 355 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HIF1A MUTATED     11    1
  HIF1A WILD-TYPE  355  118
        clus
vv       HIF1A MUTATED HIF1A WILD-TYPE
  COLON             11             355
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  HIF1A MUTATED         2        0        1         7         1         0
  HIF1A WILD-TYPE      89        1       31       131         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  HIF1A MUTATED           0          0          0          0        1         0
  HIF1A WILD-TYPE        24         11         59         42       47        18
                 vv
clus              STAGE IVB
  HIF1A MUTATED           0
  HIF1A WILD-TYPE         1
D1564V4, multiclass
            clus
vv           HIF1A MUTATED HIF1A WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              7             131
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             0              42
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  HIF1A MUTATED     0   2   8   2
  HIF1A WILD-TYPE  17  90 321  48
D1564V5, multiclass
    clus
vv   HIF1A MUTATED HIF1A WILD-TYPE
  T1             0              17
  T2             2              90
  T3             8             321
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  HIF1A MUTATED    11   0   1
  HIF1A WILD-TYPE 276 113  86
D1564V6, multiclass
    clus
vv   HIF1A MUTATED HIF1A WILD-TYPE
  N0            11             276
  N1             0             113
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1564V7, binary
                 cls
clus                0   1
  HIF1A MUTATED    10   1
  HIF1A WILD-TYPE 365  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HIF1A MUTATED     10    1
  HIF1A WILD-TYPE  365   64
   clus
vv  HIF1A MUTATED HIF1A WILD-TYPE
  0            10             365
  1             1              64
[1] 2 2
[1] FALSE
D1564V8, binary
                 cls
clus                0   1
  HIF1A MUTATED     3   9
  HIF1A WILD-TYPE 222 255
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HIF1A MUTATED      3    9
  HIF1A WILD-TYPE  222  255
        clus
vv       HIF1A MUTATED HIF1A WILD-TYPE
  FEMALE             3             222
  MALE               9             255
[1] 2 2
[1] FALSE
D1564V9, binary
                 cls
clus                0   1
  HIF1A MUTATED    12   0
  HIF1A WILD-TYPE 338  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HIF1A MUTATED     12    0
  HIF1A WILD-TYPE  338   22
     clus
vv    HIF1A MUTATED HIF1A WILD-TYPE
  NO             12             338
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  HIF1A MUTATED                      7                             4
  HIF1A WILD-TYPE                  308                            43
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  HIF1A MUTATED                       1                              0
  HIF1A WILD-TYPE                   105                             10
D1564V10, multiclass
                                clus
vv                               HIF1A MUTATED HIF1A WILD-TYPE
  COLON ADENOCARCINOMA                       7             308
  COLON MUCINOUS ADENOCARCINOMA              4              43
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  HIF1A MUTATED     8   0   1   2
  HIF1A WILD-TYPE 337   4  30  23
D1564V11, multiclass
    clus
vv   HIF1A MUTATED HIF1A WILD-TYPE
  R0             8             337
  R1             0               4
  R2             1              30
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1564V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HIF1A MUTATED                                  0     2
  HIF1A WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  HIF1A MUTATED                           0     6
  HIF1A WILD-TYPE                        22   220
D1564V13, multiclass
                                  clus
vv                                 HIF1A MUTATED HIF1A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               9
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        6             220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1565) Variable = CD79A MUTATION ANALYSIS
D1565V1, survival
                 sevent
clus2               0   1
  CD79A MUTATED     5   1
  CD79A WILD-TYPE 373  92
  CD79A MUTATED CD79A WILD-TYPE 
              6             465 
  CD79A MUTATED CD79A WILD-TYPE 
              1              92 
$`CD79A MUTATED`
TCGA-A6-2676 TCGA-AA-3864 TCGA-AA-3947 TCGA-CM-4743 TCGA-CM-6169 TCGA-CM-6680 
       42.90        53.00        33.01        23.05        13.02        12.03 

$`CD79A WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 
       32.05         0.99        31.07        31.07        30.05        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       12.99        24.00        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
        1.91       124.27        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.08        11.01        10.06        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  CD79A MUTATED CD79A WILD-TYPE 
          12.03            0.00 
  CD79A MUTATED CD79A WILD-TYPE 
          53.00          148.01 
  CD79A MUTATED CD79A WILD-TYPE 
          28.03           20.12 
[1] "12.0 - 53.0 (28.0)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.4"
D1565V2, continuous
D1565V3, binary
                 cls
clus                0   1
  CD79A MUTATED     6   0
  CD79A WILD-TYPE 360 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CD79A MUTATED      6    0
  CD79A WILD-TYPE  360  119
        clus
vv       CD79A MUTATED CD79A WILD-TYPE
  COLON              6             360
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CD79A MUTATED         0        0        1         2         2         0
  CD79A WILD-TYPE      91        1       31       136         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CD79A MUTATED           0          0          1          0        0         0
  CD79A WILD-TYPE        24         11         58         42       48        18
                 vv
clus              STAGE IVB
  CD79A MUTATED           0
  CD79A WILD-TYPE         1
D1565V4, multiclass
            clus
vv           CD79A MUTATED CD79A WILD-TYPE
  STAGE I                0              91
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              2             136
  STAGE IIB              2               8
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CD79A MUTATED     0   0   4   2
  CD79A WILD-TYPE  17  92 325  48
D1565V5, multiclass
    clus
vv   CD79A MUTATED CD79A WILD-TYPE
  T1             0              17
  T2             0              92
  T3             4             325
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  CD79A MUTATED     5   0   1
  CD79A WILD-TYPE 282 113  86
D1565V6, multiclass
    clus
vv   CD79A MUTATED CD79A WILD-TYPE
  N0             5             282
  N1             0             113
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1565V7, binary
                 cls
clus                0   1
  CD79A MUTATED     6   0
  CD79A WILD-TYPE 369  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CD79A MUTATED      6    0
  CD79A WILD-TYPE  369   65
   clus
vv  CD79A MUTATED CD79A WILD-TYPE
  0             6             369
  1             0              65
[1] 2 2
[1] FALSE
D1565V8, binary
                 cls
clus                0   1
  CD79A MUTATED     3   3
  CD79A WILD-TYPE 222 261
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CD79A MUTATED      3    3
  CD79A WILD-TYPE  222  261
        clus
vv       CD79A MUTATED CD79A WILD-TYPE
  FEMALE             3             222
  MALE               3             261
[1] 2 2
[1] FALSE
D1565V9, binary
                 cls
clus                0   1
  CD79A MUTATED     6   0
  CD79A WILD-TYPE 344  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CD79A MUTATED      6    0
  CD79A WILD-TYPE  344   22
     clus
vv    CD79A MUTATED CD79A WILD-TYPE
  NO              6             344
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CD79A MUTATED                      5                             1
  CD79A WILD-TYPE                  310                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CD79A MUTATED                       0                              0
  CD79A WILD-TYPE                   106                             10
D1565V10, multiclass
                                clus
vv                               CD79A MUTATED CD79A WILD-TYPE
  COLON ADENOCARCINOMA                       5             310
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  CD79A MUTATED     6   0   0   0
  CD79A WILD-TYPE 339   4  31  25
D1565V11, multiclass
    clus
vv   CD79A MUTATED CD79A WILD-TYPE
  R0             6             339
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1565V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CD79A MUTATED                                  0     0
  CD79A WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CD79A MUTATED                           1     3
  CD79A WILD-TYPE                        21   223
D1565V13, multiclass
                                  clus
vv                                 CD79A MUTATED CD79A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        3             223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1566) Variable = HIVEP1 MUTATION ANALYSIS
D1566V1, survival
                  sevent
clus2                0   1
  HIVEP1 MUTATED    15   4
  HIVEP1 WILD-TYPE 363  89
  HIVEP1 MUTATED HIVEP1 WILD-TYPE 
              19              452 
  HIVEP1 MUTATED HIVEP1 WILD-TYPE 
               4               89 
$`HIVEP1 MUTATED`
TCGA-AA-3510 TCGA-AA-3713 TCGA-AA-3950 TCGA-AA-A00N TCGA-AA-A010 TCGA-AD-5900 
       63.98        19.04        24.00         4.01        34.98         0.07 
TCGA-AY-6386 TCGA-CA-5797 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4950 TCGA-CK-5916 
       17.82         3.29        12.76        14.30        85.45        21.14 
TCGA-CM-5349 TCGA-D5-6932 TCGA-DM-A1D6 TCGA-DM-A28F TCGA-G4-6588 TCGA-AG-3902 
       30.08        11.38        49.91        35.97        26.17        32.02 
TCGA-AG-A002 
       20.98 

$`HIVEP1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 
       12.99        24.00        33.01        26.01         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-4323 
       16.31         0.95        33.01        21.44        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-6715 
        3.19         1.61        12.69         3.06         3.25         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5912 
       12.20        10.06        17.56       148.01        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       51.32         9.99        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       22.98        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 
        9.44        11.64         4.80         1.51        12.00        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D7 
      119.70        24.43        38.20       130.65        92.75        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H 
      139.17         6.12        81.37       119.93        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        35.80        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
        1.02        48.03        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  HIVEP1 MUTATED HIVEP1 WILD-TYPE 
            0.07             0.00 
  HIVEP1 MUTATED HIVEP1 WILD-TYPE 
           85.45           148.01 
  HIVEP1 MUTATED HIVEP1 WILD-TYPE 
          21.140           20.085 
[1] "0.1 - 85.5 (21.1)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.1"
D1566V2, continuous
D1566V3, binary
                  cls
clus                 0   1
  HIVEP1 MUTATED    18   2
  HIVEP1 WILD-TYPE 348 117
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HIVEP1 MUTATED     18    2
  HIVEP1 WILD-TYPE  348  117
        clus
vv       HIVEP1 MUTATED HIVEP1 WILD-TYPE
  COLON              18              348
  RECTUM              2              117
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  HIVEP1 MUTATED         3        0        1        10         2         0
  HIVEP1 WILD-TYPE      88        1       31       128         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HIVEP1 MUTATED           0          0          3          0        1
  HIVEP1 WILD-TYPE        24         11         56         42       47
                  vv
clus               STAGE IVA STAGE IVB
  HIVEP1 MUTATED           0         0
  HIVEP1 WILD-TYPE        18         1
D1566V4, multiclass
            clus
vv           HIVEP1 MUTATED HIVEP1 WILD-TYPE
  STAGE I                 3               88
  STAGE IA                0                1
  STAGE II                1               31
  STAGE IIA              10              128
  STAGE IIB               2                8
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              3               56
  STAGE IIIC              0               42
  STAGE IV                1               47
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  HIVEP1 MUTATED     1   2  15   2
  HIVEP1 WILD-TYPE  16  90 314  48
D1566V5, multiclass
    clus
vv   HIVEP1 MUTATED HIVEP1 WILD-TYPE
  T1              1               16
  T2              2               90
  T3             15              314
  T4              2               48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  HIVEP1 MUTATED    17   3   0
  HIVEP1 WILD-TYPE 270 110  87
D1566V6, multiclass
    clus
vv   HIVEP1 MUTATED HIVEP1 WILD-TYPE
  N0             17              270
  N1              3              110
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1566V7, binary
                  cls
clus                 0   1
  HIVEP1 MUTATED    18   1
  HIVEP1 WILD-TYPE 357  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HIVEP1 MUTATED     18    1
  HIVEP1 WILD-TYPE  357   64
   clus
vv  HIVEP1 MUTATED HIVEP1 WILD-TYPE
  0             18              357
  1              1               64
[1] 2 2
[1] FALSE
D1566V8, binary
                  cls
clus                 0   1
  HIVEP1 MUTATED     8  12
  HIVEP1 WILD-TYPE 217 252
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HIVEP1 MUTATED      8   12
  HIVEP1 WILD-TYPE  217  252
        clus
vv       HIVEP1 MUTATED HIVEP1 WILD-TYPE
  FEMALE              8              217
  MALE               12              252
[1] 2 2
[1] FALSE
D1566V9, binary
                  cls
clus                 0   1
  HIVEP1 MUTATED    14   1
  HIVEP1 WILD-TYPE 336  21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HIVEP1 MUTATED     14    1
  HIVEP1 WILD-TYPE  336   21
     clus
vv    HIVEP1 MUTATED HIVEP1 WILD-TYPE
  NO              14              336
  YES              1               21
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  HIVEP1 MUTATED                     13                             5
  HIVEP1 WILD-TYPE                  302                            42
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  HIVEP1 MUTATED                       2                              0
  HIVEP1 WILD-TYPE                   104                             10
D1566V10, multiclass
                                clus
vv                               HIVEP1 MUTATED HIVEP1 WILD-TYPE
  COLON ADENOCARCINOMA                       13              302
  COLON MUCINOUS ADENOCARCINOMA               5               42
  RECTAL ADENOCARCINOMA                       2              104
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  HIVEP1 MUTATED    13   1   1   3
  HIVEP1 WILD-TYPE 332   3  30  22
D1566V11, multiclass
    clus
vv   HIVEP1 MUTATED HIVEP1 WILD-TYPE
  R0             13              332
  R1              1                3
  R2              1               30
  RX              3               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1566V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HIVEP1 MUTATED                                  0     3
  HIVEP1 WILD-TYPE                                1     8
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  HIVEP1 MUTATED                           2     7
  HIVEP1 WILD-TYPE                        20   219
D1566V13, multiclass
                                  clus
vv                                 HIVEP1 MUTATED HIVEP1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         3                8
  BLACK OR AFRICAN AMERICAN                     2               20
  WHITE                                         7              219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1567) Variable = C1S MUTATION ANALYSIS
D1567V1, survival
               sevent
clus2             0   1
  C1S MUTATED     8   5
  C1S WILD-TYPE 370  88
  C1S MUTATED C1S WILD-TYPE 
           13           458 
  C1S MUTATED C1S WILD-TYPE 
            5            88 
$`C1S MUTATED`
TCGA-A6-6780 TCGA-AA-3555 TCGA-AA-3713 TCGA-AA-3930 TCGA-AA-A00N TCGA-AZ-6598 
       20.12        29.95        19.04         2.01         4.01        49.41 
TCGA-AZ-6601 TCGA-CA-6718 TCGA-DM-A1D0 TCGA-F4-6856 TCGA-AG-3892 TCGA-AG-A002 
      100.01        10.06       130.65        35.31        13.02        20.98 
TCGA-AG-A02N 
       61.97 

$`C1S WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       13.02        24.00        17.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3939 TCGA-AA-3941 
       27.02        29.98        18.05        31.00        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       88.21         6.77        12.10        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07        12.20        12.76        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
      119.70        24.43        38.20        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
       13.25         0.53        47.41       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 
        1.02        17.95        36.95        17.03        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  C1S MUTATED C1S WILD-TYPE 
         2.01          0.00 
  C1S MUTATED C1S WILD-TYPE 
       130.65        148.01 
  C1S MUTATED C1S WILD-TYPE 
        20.98         20.12 
[1] "2.0 - 130.7 (21.0)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.4"
D1567V2, continuous
D1567V3, binary
               cls
clus              0   1
  C1S MUTATED    10   3
  C1S WILD-TYPE 356 116
[1] "tbl2"
               cls
clus            [,1] [,2]
  C1S MUTATED     10    3
  C1S WILD-TYPE  356  116
        clus
vv       C1S MUTATED C1S WILD-TYPE
  COLON           10           356
  RECTUM           3           116
[1] 2 2
[1] FALSE
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  C1S MUTATED         3        0        3         4         1         0
  C1S WILD-TYPE      88        1       29       134         9         1
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  C1S MUTATED           0          0          0          0        2         0
  C1S WILD-TYPE        24         11         59         42       46        18
               vv
clus            STAGE IVB
  C1S MUTATED           0
  C1S WILD-TYPE         1
D1567V4, multiclass
            clus
vv           C1S MUTATED C1S WILD-TYPE
  STAGE I              3            88
  STAGE IA             0             1
  STAGE II             3            29
  STAGE IIA            4           134
  STAGE IIB            1             9
  STAGE IIC            0             1
  STAGE III            0            24
  STAGE IIIA           0            11
  STAGE IIIB           0            59
  STAGE IIIC           0            42
  STAGE IV             2            46
  STAGE IVA            0            18
  STAGE IVB            0             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  C1S MUTATED     1   2   9   1
  C1S WILD-TYPE  16  90 320  49
D1567V5, multiclass
    clus
vv   C1S MUTATED C1S WILD-TYPE
  T1           1            16
  T2           2            90
  T3           9           320
  T4           1            49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2
  C1S MUTATED    12   0   1
  C1S WILD-TYPE 275 113  86
D1567V6, multiclass
    clus
vv   C1S MUTATED C1S WILD-TYPE
  N0          12           275
  N1           0           113
  N2           1            86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1567V7, binary
               cls
clus              0   1
  C1S MUTATED     9   2
  C1S WILD-TYPE 366  63
[1] "tbl2"
               cls
clus            [,1] [,2]
  C1S MUTATED      9    2
  C1S WILD-TYPE  366   63
   clus
vv  C1S MUTATED C1S WILD-TYPE
  0           9           366
  1           2            63
[1] 2 2
[1] FALSE
D1567V8, binary
               cls
clus              0   1
  C1S MUTATED     4   9
  C1S WILD-TYPE 221 255
[1] "tbl2"
               cls
clus            [,1] [,2]
  C1S MUTATED      4    9
  C1S WILD-TYPE  221  255
        clus
vv       C1S MUTATED C1S WILD-TYPE
  FEMALE           4           221
  MALE             9           255
[1] 2 2
[1] FALSE
D1567V9, binary
               cls
clus              0   1
  C1S MUTATED     9   1
  C1S WILD-TYPE 341  21
[1] "tbl2"
               cls
clus            [,1] [,2]
  C1S MUTATED      9    1
  C1S WILD-TYPE  341   21
     clus
vv    C1S MUTATED C1S WILD-TYPE
  NO            9           341
  YES           1            21
[1] 2 2
[1] FALSE
               vv
clus            COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  C1S MUTATED                      6                             4
  C1S WILD-TYPE                  309                            43
               vv
clus            RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  C1S MUTATED                       3                              0
  C1S WILD-TYPE                   103                             10
D1567V10, multiclass
                                clus
vv                               C1S MUTATED C1S WILD-TYPE
  COLON ADENOCARCINOMA                     6           309
  COLON MUCINOUS ADENOCARCINOMA            4            43
  RECTAL ADENOCARCINOMA                    3           103
  RECTAL MUCINOUS ADENOCARCINOMA           0            10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             R0  R1  R2  RX
  C1S MUTATED     6   0   2   1
  C1S WILD-TYPE 339   4  29  24
D1567V11, multiclass
    clus
vv   C1S MUTATED C1S WILD-TYPE
  R0           6           339
  R1           0             4
  R2           2            29
  RX           1            24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1567V12, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C1S MUTATED                                  0     1
  C1S WILD-TYPE                                1    10
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  C1S MUTATED                           0     5
  C1S WILD-TYPE                        22   221
D1567V13, multiclass
                                  clus
vv                                 C1S MUTATED C1S WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      1            10
  BLACK OR AFRICAN AMERICAN                  0            22
  WHITE                                      5           221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1568) Variable = OR8K3 MUTATION ANALYSIS
D1568V1, survival
                 sevent
clus2               0   1
  OR8K3 MUTATED    11   1
  OR8K3 WILD-TYPE 367  92
  OR8K3 MUTATED OR8K3 WILD-TYPE 
             12             459 
  OR8K3 MUTATED OR8K3 WILD-TYPE 
              1              92 
$`OR8K3 MUTATED`
TCGA-A6-6141 TCGA-A6-6780 TCGA-AA-3821 TCGA-AA-A010 TCGA-AU-3779 TCGA-CA-6717 
        8.38        20.12         1.02        34.98        14.50        12.76 
TCGA-CA-6718 TCGA-CK-4948 TCGA-DM-A1HB TCGA-G4-6625 TCGA-AG-3892 TCGA-AG-A02X 
       10.06       148.01       135.65        91.79        13.02        41.00 

$`OR8K3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 
       22.09        22.06        32.71        27.09        22.52        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 
       35.05        33.04         0.99        25.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 
        3.25         3.29         0.07        12.20        14.30        17.56 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 
        1.02        17.95        36.95        17.03        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       38.96        61.97        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  OR8K3 MUTATED OR8K3 WILD-TYPE 
           1.02            0.00 
  OR8K3 MUTATED OR8K3 WILD-TYPE 
         148.01          140.38 
  OR8K3 MUTATED OR8K3 WILD-TYPE 
          17.31           20.28 
[1] "1.0 - 148.0 (17.3)" "0.0 - 140.4 (20.3)"
[1] "hr=" "3.4"
D1568V2, continuous
D1568V3, binary
                 cls
clus                0   1
  OR8K3 MUTATED    10   2
  OR8K3 WILD-TYPE 356 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR8K3 MUTATED     10    2
  OR8K3 WILD-TYPE  356  117
        clus
vv       OR8K3 MUTATED OR8K3 WILD-TYPE
  COLON             10             356
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  OR8K3 MUTATED         3        0        0         6         1         0
  OR8K3 WILD-TYPE      88        1       32       132         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  OR8K3 MUTATED           1          0          1          0        0         0
  OR8K3 WILD-TYPE        23         11         58         42       48        18
                 vv
clus              STAGE IVB
  OR8K3 MUTATED           0
  OR8K3 WILD-TYPE         1
D1568V4, multiclass
            clus
vv           OR8K3 MUTATED OR8K3 WILD-TYPE
  STAGE I                3              88
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              6             132
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  OR8K3 MUTATED     1   2   8   1
  OR8K3 WILD-TYPE  16  90 321  49
D1568V5, multiclass
    clus
vv   OR8K3 MUTATED OR8K3 WILD-TYPE
  T1             1              16
  T2             2              90
  T3             8             321
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  OR8K3 MUTATED    10   2   0
  OR8K3 WILD-TYPE 277 111  87
D1568V6, multiclass
    clus
vv   OR8K3 MUTATED OR8K3 WILD-TYPE
  N0            10             277
  N1             2             111
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1568V7, binary
                 cls
clus                0   1
  OR8K3 MUTATED    11   0
  OR8K3 WILD-TYPE 364  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR8K3 MUTATED     11    0
  OR8K3 WILD-TYPE  364   65
   clus
vv  OR8K3 MUTATED OR8K3 WILD-TYPE
  0            11             364
  1             0              65
[1] 2 2
[1] FALSE
D1568V8, binary
                 cls
clus                0   1
  OR8K3 MUTATED     6   6
  OR8K3 WILD-TYPE 219 258
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR8K3 MUTATED      6    6
  OR8K3 WILD-TYPE  219  258
        clus
vv       OR8K3 MUTATED OR8K3 WILD-TYPE
  FEMALE             6             219
  MALE               6             258
[1] 2 2
[1] FALSE
D1568V9, binary
                 cls
clus                0   1
  OR8K3 MUTATED    10   0
  OR8K3 WILD-TYPE 340  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR8K3 MUTATED     10    0
  OR8K3 WILD-TYPE  340   22
     clus
vv    OR8K3 MUTATED OR8K3 WILD-TYPE
  NO             10             340
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  OR8K3 MUTATED                      6                             3
  OR8K3 WILD-TYPE                  309                            44
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  OR8K3 MUTATED                       2                              0
  OR8K3 WILD-TYPE                   104                             10
D1568V10, multiclass
                                clus
vv                               OR8K3 MUTATED OR8K3 WILD-TYPE
  COLON ADENOCARCINOMA                       6             309
  COLON MUCINOUS ADENOCARCINOMA              3              44
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  OR8K3 MUTATED     7   0   0   2
  OR8K3 WILD-TYPE 338   4  31  23
D1568V11, multiclass
    clus
vv   OR8K3 MUTATED OR8K3 WILD-TYPE
  R0             7             338
  R1             0               4
  R2             0              31
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1568V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OR8K3 MUTATED                                  0     2
  OR8K3 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  OR8K3 MUTATED                           1     5
  OR8K3 WILD-TYPE                        21   221
D1568V13, multiclass
                                  clus
vv                                 OR8K3 MUTATED OR8K3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               9
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        5             221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1569) Variable = NUP210L MUTATION ANALYSIS
D1569V1, survival
                   sevent
clus2                 0   1
  NUP210L MUTATED    17   6
  NUP210L WILD-TYPE 361  87
  NUP210L MUTATED NUP210L WILD-TYPE 
               23               448 
  NUP210L MUTATED NUP210L WILD-TYPE 
                6                87 
$`NUP210L MUTATED`
TCGA-A6-6141 TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3811 TCGA-AA-3950 TCGA-AA-3977 
        8.38         3.02        63.98        10.06        24.00        25.02 
TCGA-AA-A00N TCGA-AA-A010 TCGA-AD-6895 TCGA-AU-6004 TCGA-AZ-4315 TCGA-AZ-6598 
        4.01        34.98         0.72        27.09        58.39        49.41 
TCGA-AZ-6600 TCGA-CK-5916 TCGA-CM-6677 TCGA-D5-6533 TCGA-D5-6536 TCGA-D5-6538 
       12.10        21.14        11.08         1.32        17.85        17.13 
TCGA-D5-6928 TCGA-DM-A28H TCGA-G4-6321 TCGA-AG-3890 TCGA-AG-A002 
       11.64       117.07        22.09        17.03        20.98 

$`NUP210L WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 
       22.09        22.06        32.71        27.09        22.52        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 
       20.12        19.66        20.28         7.04         1.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3815 
       85.05        26.99        19.04        19.04        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       33.01        26.01         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
       56.55         0.79         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
        0.20        14.50        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       88.21         6.77       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       12.95        13.05        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6539 TCGA-D5-6540 
       18.25        43.27        15.12         4.80        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.04         9.44         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       35.97        60.79        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       63.62        61.91        36.00        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 
       19.99         1.02        17.95        36.95        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  NUP210L MUTATED NUP210L WILD-TYPE 
             0.72              0.00 
  NUP210L MUTATED NUP210L WILD-TYPE 
           117.07            148.01 
  NUP210L MUTATED NUP210L WILD-TYPE 
           17.850            20.235 
[1] "0.7 - 117.1 (17.9)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.4"
D1569V2, continuous
D1569V3, binary
                   cls
clus                  0   1
  NUP210L MUTATED    22   2
  NUP210L WILD-TYPE 344 117
[1] "tbl2"
                   cls
clus                [,1] [,2]
  NUP210L MUTATED     22    2
  NUP210L WILD-TYPE  344  117
        clus
vv       NUP210L MUTATED NUP210L WILD-TYPE
  COLON               22               344
  RECTUM               2               117
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NUP210L MUTATED         4        0        3         6         2         0
  NUP210L WILD-TYPE      87        1       29       132         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NUP210L MUTATED           3          0          2          1        1
  NUP210L WILD-TYPE        21         11         57         41       47
                   vv
clus                STAGE IVA STAGE IVB
  NUP210L MUTATED           0         0
  NUP210L WILD-TYPE        18         1
D1569V4, multiclass
            clus
vv           NUP210L MUTATED NUP210L WILD-TYPE
  STAGE I                  4                87
  STAGE IA                 0                 1
  STAGE II                 3                29
  STAGE IIA                6               132
  STAGE IIB                2                 8
  STAGE IIC                0                 1
  STAGE III                3                21
  STAGE IIIA               0                11
  STAGE IIIB               2                57
  STAGE IIIC               1                41
  STAGE IV                 1                47
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  NUP210L MUTATED     1   5  14   4
  NUP210L WILD-TYPE  16  87 315  46
D1569V5, multiclass
    clus
vv   NUP210L MUTATED NUP210L WILD-TYPE
  T1               1                16
  T2               5                87
  T3              14               315
  T4               4                46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  NUP210L MUTATED    17   3   4
  NUP210L WILD-TYPE 270 110  83
D1569V6, multiclass
    clus
vv   NUP210L MUTATED NUP210L WILD-TYPE
  N0              17               270
  N1               3               110
  N2               4                83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1569V7, binary
                   cls
clus                  0   1
  NUP210L MUTATED    19   1
  NUP210L WILD-TYPE 356  64
[1] "tbl2"
                   cls
clus                [,1] [,2]
  NUP210L MUTATED     19    1
  NUP210L WILD-TYPE  356   64
   clus
vv  NUP210L MUTATED NUP210L WILD-TYPE
  0              19               356
  1               1                64
[1] 2 2
[1] FALSE
D1569V8, binary
                   cls
clus                  0   1
  NUP210L MUTATED    11  13
  NUP210L WILD-TYPE 214 251
[1] "tbl2"
                   cls
clus                [,1] [,2]
  NUP210L MUTATED     11   13
  NUP210L WILD-TYPE  214  251
        clus
vv       NUP210L MUTATED NUP210L WILD-TYPE
  FEMALE              11               214
  MALE                13               251
[1] 2 2
[1] FALSE
D1569V9, binary
                   cls
clus                  0   1
  NUP210L MUTATED    17   0
  NUP210L WILD-TYPE 333  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  NUP210L MUTATED     17    0
  NUP210L WILD-TYPE  333   22
     clus
vv    NUP210L MUTATED NUP210L WILD-TYPE
  NO               17               333
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  NUP210L MUTATED                     19                             3
  NUP210L WILD-TYPE                  296                            44
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  NUP210L MUTATED                       2                              0
  NUP210L WILD-TYPE                   104                             10
D1569V10, multiclass
                                clus
vv                               NUP210L MUTATED NUP210L WILD-TYPE
  COLON ADENOCARCINOMA                        19               296
  COLON MUCINOUS ADENOCARCINOMA                3                44
  RECTAL ADENOCARCINOMA                        2               104
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  NUP210L MUTATED    17   0   0   1
  NUP210L WILD-TYPE 328   4  31  24
D1569V11, multiclass
    clus
vv   NUP210L MUTATED NUP210L WILD-TYPE
  R0              17               328
  R1               0                 4
  R2               0                31
  RX               1                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1569V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NUP210L MUTATED                                  0     0
  NUP210L WILD-TYPE                                1    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  NUP210L MUTATED                           2    12
  NUP210L WILD-TYPE                        20   214
D1569V13, multiclass
                                  clus
vv                                 NUP210L MUTATED NUP210L WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                      2                20
  WHITE                                         12               214
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1570) Variable = RRAGD MUTATION ANALYSIS
D1570V1, survival
                 sevent
clus2               0   1
  RRAGD MUTATED     7   0
  RRAGD WILD-TYPE 371  93
  RRAGD MUTATED RRAGD WILD-TYPE 
              7             464 
  RRAGD MUTATED RRAGD WILD-TYPE 
              0              93 
$`RRAGD MUTATED`
TCGA-A6-5662 TCGA-AA-3558 TCGA-AU-3779 TCGA-AZ-4315 TCGA-AZ-5407 TCGA-D5-6535 
       23.61        20.98        14.50        58.39        88.21        15.12 
TCGA-D5-6538 
       17.13 

$`RRAGD WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        33.53        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3560 
       13.02        24.00        17.95        29.95        23.01        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       10.88         0.20        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       43.27        17.85         4.80        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  RRAGD MUTATED RRAGD WILD-TYPE 
           14.5             0.0 
  RRAGD MUTATED RRAGD WILD-TYPE 
          88.21          148.01 
  RRAGD MUTATED RRAGD WILD-TYPE 
         20.980          20.155 
[1] "14.5 - 88.2 (21.0)" "0.0 - 148.0 (20.2)"
[1] "hr="     "9200000"
D1570V2, continuous
D1570V3, binary
                 cls
clus                0   1
  RRAGD MUTATED     7   0
  RRAGD WILD-TYPE 359 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RRAGD MUTATED      7    0
  RRAGD WILD-TYPE  359  119
        clus
vv       RRAGD MUTATED RRAGD WILD-TYPE
  COLON              7             359
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RRAGD MUTATED         2        0        0         2         0         0
  RRAGD WILD-TYPE      89        1       32       136        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RRAGD MUTATED           0          0          2          0        0         1
  RRAGD WILD-TYPE        24         11         57         42       48        17
                 vv
clus              STAGE IVB
  RRAGD MUTATED           0
  RRAGD WILD-TYPE         1
D1570V4, multiclass
            clus
vv           RRAGD MUTATED RRAGD WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              2             136
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             2              57
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  RRAGD MUTATED     1   1   5   0
  RRAGD WILD-TYPE  16  91 324  50
D1570V5, multiclass
    clus
vv   RRAGD MUTATED RRAGD WILD-TYPE
  T1             1              16
  T2             1              91
  T3             5             324
  T4             0              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  RRAGD MUTATED     4   1   2
  RRAGD WILD-TYPE 283 112  85
D1570V6, multiclass
    clus
vv   RRAGD MUTATED RRAGD WILD-TYPE
  N0             4             283
  N1             1             112
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1570V7, binary
                 cls
clus                0   1
  RRAGD MUTATED     5   1
  RRAGD WILD-TYPE 370  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RRAGD MUTATED      5    1
  RRAGD WILD-TYPE  370   64
   clus
vv  RRAGD MUTATED RRAGD WILD-TYPE
  0             5             370
  1             1              64
[1] 2 2
[1] FALSE
D1570V8, binary
                 cls
clus                0   1
  RRAGD MUTATED     4   3
  RRAGD WILD-TYPE 221 261
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RRAGD MUTATED      4    3
  RRAGD WILD-TYPE  221  261
        clus
vv       RRAGD MUTATED RRAGD WILD-TYPE
  FEMALE             4             221
  MALE               3             261
[1] 2 2
[1] FALSE
D1570V9, binary
                 cls
clus                0   1
  RRAGD MUTATED     7   0
  RRAGD WILD-TYPE 343  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RRAGD MUTATED      7    0
  RRAGD WILD-TYPE  343   22
     clus
vv    RRAGD MUTATED RRAGD WILD-TYPE
  NO              7             343
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  RRAGD MUTATED                      7                             0
  RRAGD WILD-TYPE                  308                            47
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  RRAGD MUTATED                       0                              0
  RRAGD WILD-TYPE                   106                             10
D1570V10, multiclass
                                clus
vv                               RRAGD MUTATED RRAGD WILD-TYPE
  COLON ADENOCARCINOMA                       7             308
  COLON MUCINOUS ADENOCARCINOMA              0              47
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  RRAGD MUTATED     3   0   1   1
  RRAGD WILD-TYPE 342   4  30  24
D1570V11, multiclass
    clus
vv   RRAGD MUTATED RRAGD WILD-TYPE
  R0             3             342
  R1             0               4
  R2             1              30
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1570V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RRAGD MUTATED                                  0     0
  RRAGD WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  RRAGD MUTATED                           0     6
  RRAGD WILD-TYPE                        22   220
D1570V13, multiclass
                                  clus
vv                                 RRAGD MUTATED RRAGD WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        6             220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1571) Variable = BLM MUTATION ANALYSIS
D1571V1, survival
               sevent
clus2             0   1
  BLM MUTATED    16   2
  BLM WILD-TYPE 362  91
  BLM MUTATED BLM WILD-TYPE 
           18           453 
  BLM MUTATED BLM WILD-TYPE 
            2            91 
$`BLM MUTATED`
TCGA-A6-2672 TCGA-A6-5665 TCGA-AA-3518 TCGA-AA-3977 TCGA-AA-A00J TCGA-AA-A00N 
       46.65        22.06         1.02        25.02        18.05         4.01 
TCGA-AA-A010 TCGA-AD-6895 TCGA-AY-5543 TCGA-AZ-4315 TCGA-CA-6718 TCGA-CM-4744 
       34.98         0.72        33.01        58.39        10.06        20.02 
TCGA-CM-6171 TCGA-CM-6678 TCGA-D5-6534 TCGA-G4-6628 TCGA-AG-3892 TCGA-AG-A002 
       14.04        11.01        43.27        79.69        13.02        20.98 

$`BLM WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3519 
       63.98         6.97         1.02        13.02        38.99         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       34.03        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       15.52        56.55         0.79         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       23.05        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6679 
       11.01        12.95        13.05        11.08        11.08        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       20.19        18.25         1.32        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       91.79        46.75        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 
        1.02        17.95        36.95        17.03        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  BLM MUTATED BLM WILD-TYPE 
         0.72          0.00 
  BLM MUTATED BLM WILD-TYPE 
        79.69        148.01 
  BLM MUTATED BLM WILD-TYPE 
        20.50         20.19 
[1] "0.7 - 79.7 (20.5)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.8"
D1571V2, continuous
D1571V3, binary
               cls
clus              0   1
  BLM MUTATED    17   2
  BLM WILD-TYPE 349 117
[1] "tbl2"
               cls
clus            [,1] [,2]
  BLM MUTATED     17    2
  BLM WILD-TYPE  349  117
        clus
vv       BLM MUTATED BLM WILD-TYPE
  COLON           17           349
  RECTUM           2           117
[1] 2 2
[1] FALSE
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  BLM MUTATED         5        0        0         6         2         0
  BLM WILD-TYPE      86        1       32       132         8         1
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  BLM MUTATED           0          0          2          0        0         2
  BLM WILD-TYPE        24         11         57         42       48        16
               vv
clus            STAGE IVB
  BLM MUTATED           0
  BLM WILD-TYPE         1
D1571V4, multiclass
            clus
vv           BLM MUTATED BLM WILD-TYPE
  STAGE I              5            86
  STAGE IA             0             1
  STAGE II             0            32
  STAGE IIA            6           132
  STAGE IIB            2             8
  STAGE IIC            0             1
  STAGE III            0            24
  STAGE IIIA           0            11
  STAGE IIIB           2            57
  STAGE IIIC           0            42
  STAGE IV             0            48
  STAGE IVA            2            16
  STAGE IVB            0             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  BLM MUTATED     1   5   9   4
  BLM WILD-TYPE  16  87 320  46
D1571V5, multiclass
    clus
vv   BLM MUTATED BLM WILD-TYPE
  T1           1            16
  T2           5            87
  T3           9           320
  T4           4            46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2
  BLM MUTATED    14   5   0
  BLM WILD-TYPE 273 108  87
D1571V6, multiclass
    clus
vv   BLM MUTATED BLM WILD-TYPE
  N0          14           273
  N1           5           108
  N2           0            87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1571V7, binary
               cls
clus              0   1
  BLM MUTATED    15   2
  BLM WILD-TYPE 360  63
[1] "tbl2"
               cls
clus            [,1] [,2]
  BLM MUTATED     15    2
  BLM WILD-TYPE  360   63
   clus
vv  BLM MUTATED BLM WILD-TYPE
  0          15           360
  1           2            63
[1] 2 2
[1] FALSE
D1571V8, binary
               cls
clus              0   1
  BLM MUTATED    10   9
  BLM WILD-TYPE 215 255
[1] "tbl2"
               cls
clus            [,1] [,2]
  BLM MUTATED     10    9
  BLM WILD-TYPE  215  255
        clus
vv       BLM MUTATED BLM WILD-TYPE
  FEMALE          10           215
  MALE             9           255
[1] 2 2
[1] FALSE
D1571V9, binary
               cls
clus              0   1
  BLM MUTATED    15   0
  BLM WILD-TYPE 335  22
[1] "tbl2"
               cls
clus            [,1] [,2]
  BLM MUTATED     15    0
  BLM WILD-TYPE  335   22
     clus
vv    BLM MUTATED BLM WILD-TYPE
  NO           15           335
  YES           0            22
[1] 2 2
[1] FALSE
               vv
clus            COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  BLM MUTATED                     14                             3
  BLM WILD-TYPE                  301                            44
               vv
clus            RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  BLM MUTATED                       2                              0
  BLM WILD-TYPE                   104                             10
D1571V10, multiclass
                                clus
vv                               BLM MUTATED BLM WILD-TYPE
  COLON ADENOCARCINOMA                    14           301
  COLON MUCINOUS ADENOCARCINOMA            3            44
  RECTAL ADENOCARCINOMA                    2           104
  RECTAL MUCINOUS ADENOCARCINOMA           0            10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             R0  R1  R2  RX
  BLM MUTATED    16   0   0   1
  BLM WILD-TYPE 329   4  31  24
D1571V11, multiclass
    clus
vv   BLM MUTATED BLM WILD-TYPE
  R0          16           329
  R1           0             4
  R2           0            31
  RX           1            24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1571V12, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  BLM MUTATED                                  0     1
  BLM WILD-TYPE                                1    10
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  BLM MUTATED                           1     9
  BLM WILD-TYPE                        21   217
D1571V13, multiclass
                                  clus
vv                                 BLM MUTATED BLM WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      1            10
  BLACK OR AFRICAN AMERICAN                  1            21
  WHITE                                      9           217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1572) Variable = CLCN3 MUTATION ANALYSIS
D1572V1, survival
                 sevent
clus2               0   1
  CLCN3 MUTATED    11   2
  CLCN3 WILD-TYPE 367  91
  CLCN3 MUTATED CLCN3 WILD-TYPE 
             13             458 
  CLCN3 MUTATED CLCN3 WILD-TYPE 
              2              91 
$`CLCN3 MUTATED`
TCGA-A6-5661 TCGA-A6-6781 TCGA-AA-3672 TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A010 
       33.53        19.66         0.92        25.02         4.01        34.98 
TCGA-AD-5900 TCGA-CM-4743 TCGA-F4-6856 TCGA-AG-A00C TCGA-DC-6681 TCGA-F5-6464 
        0.07        23.05        35.31         6.02         5.95         9.96 
TCGA-F5-6465 
       49.51 

$`CLCN3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
       54.02         2.01        14.01        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 
        0.92        41.00        39.98        18.05        40.96        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 
       21.14        82.95         1.91       124.27        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 
       33.67        13.25         0.53        47.41       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
       13.94        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6682 
        5.03        13.97        27.95        10.98        19.99         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       18.28        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  CLCN3 MUTATED CLCN3 WILD-TYPE 
           0.07            0.00 
  CLCN3 MUTATED CLCN3 WILD-TYPE 
          49.51          148.01 
  CLCN3 MUTATED CLCN3 WILD-TYPE 
         19.660          20.235 
[1] "0.1 - 49.5 (19.7)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.1"
D1572V2, continuous
D1572V3, binary
                 cls
clus                0   1
  CLCN3 MUTATED     9   4
  CLCN3 WILD-TYPE 357 115
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CLCN3 MUTATED      9    4
  CLCN3 WILD-TYPE  357  115
        clus
vv       CLCN3 MUTATED CLCN3 WILD-TYPE
  COLON              9             357
  RECTUM             4             115
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CLCN3 MUTATED         2        0        0         3         2         0
  CLCN3 WILD-TYPE      89        1       32       135         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CLCN3 MUTATED           1          0          1          2        0         1
  CLCN3 WILD-TYPE        23         11         58         40       48        17
                 vv
clus              STAGE IVB
  CLCN3 MUTATED           0
  CLCN3 WILD-TYPE         1
D1572V4, multiclass
            clus
vv           CLCN3 MUTATED CLCN3 WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              3             135
  STAGE IIB              2               8
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             2              40
  STAGE IV               0              48
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CLCN3 MUTATED     0   3   6   4
  CLCN3 WILD-TYPE  17  89 323  46
D1572V5, multiclass
    clus
vv   CLCN3 MUTATED CLCN3 WILD-TYPE
  T1             0              17
  T2             3              89
  T3             6             323
  T4             4              46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  CLCN3 MUTATED     8   3   2
  CLCN3 WILD-TYPE 279 110  85
D1572V6, multiclass
    clus
vv   CLCN3 MUTATED CLCN3 WILD-TYPE
  N0             8             279
  N1             3             110
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1572V7, binary
                 cls
clus                0   1
  CLCN3 MUTATED     9   1
  CLCN3 WILD-TYPE 366  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CLCN3 MUTATED      9    1
  CLCN3 WILD-TYPE  366   64
   clus
vv  CLCN3 MUTATED CLCN3 WILD-TYPE
  0             9             366
  1             1              64
[1] 2 2
[1] FALSE
D1572V8, binary
                 cls
clus                0   1
  CLCN3 MUTATED     7   6
  CLCN3 WILD-TYPE 218 258
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CLCN3 MUTATED      7    6
  CLCN3 WILD-TYPE  218  258
        clus
vv       CLCN3 MUTATED CLCN3 WILD-TYPE
  FEMALE             7             218
  MALE               6             258
[1] 2 2
[1] FALSE
D1572V9, binary
                 cls
clus                0   1
  CLCN3 MUTATED     9   1
  CLCN3 WILD-TYPE 341  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CLCN3 MUTATED      9    1
  CLCN3 WILD-TYPE  341   21
     clus
vv    CLCN3 MUTATED CLCN3 WILD-TYPE
  NO              9             341
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CLCN3 MUTATED                      5                             4
  CLCN3 WILD-TYPE                  310                            43
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CLCN3 MUTATED                       4                              0
  CLCN3 WILD-TYPE                   102                             10
D1572V10, multiclass
                                clus
vv                               CLCN3 MUTATED CLCN3 WILD-TYPE
  COLON ADENOCARCINOMA                       5             310
  COLON MUCINOUS ADENOCARCINOMA              4              43
  RECTAL ADENOCARCINOMA                      4             102
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  CLCN3 MUTATED    12   0   0   0
  CLCN3 WILD-TYPE 333   4  31  25
D1572V11, multiclass
    clus
vv   CLCN3 MUTATED CLCN3 WILD-TYPE
  R0            12             333
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1572V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CLCN3 MUTATED                                  0     0
  CLCN3 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CLCN3 MUTATED                           1     7
  CLCN3 WILD-TYPE                        21   219
D1572V13, multiclass
                                  clus
vv                                 CLCN3 MUTATED CLCN3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        7             219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1573) Variable = ANKRD40 MUTATION ANALYSIS
D1573V1, survival
                   sevent
clus2                 0   1
  ANKRD40 MUTATED     6   3
  ANKRD40 WILD-TYPE 372  90
  ANKRD40 MUTATED ANKRD40 WILD-TYPE 
                9               462 
  ANKRD40 MUTATED ANKRD40 WILD-TYPE 
                3                90 
$`ANKRD40 MUTATED`
TCGA-AA-3492 TCGA-AA-3811 TCGA-AA-3821 TCGA-AA-3968 TCGA-AD-5900 TCGA-AY-6197 
        3.02        10.06         1.02        21.99         0.07        21.44 
TCGA-AZ-6598 TCGA-G4-6628 TCGA-AF-2692 
       49.41        79.69        13.55 

$`ANKRD40 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 
       35.05        33.04         0.99        25.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
       40.96        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4315 
       27.09        16.31         0.95        33.01        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 
       35.80        26.17        91.79        46.75        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       43.04        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  ANKRD40 MUTATED ANKRD40 WILD-TYPE 
             0.07              0.00 
  ANKRD40 MUTATED ANKRD40 WILD-TYPE 
            79.69            148.01 
  ANKRD40 MUTATED ANKRD40 WILD-TYPE 
           13.550            20.235 
[1] "0.1 - 79.7 (13.6)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.9"
D1573V2, continuous
D1573V3, binary
                   cls
clus                  0   1
  ANKRD40 MUTATED     8   0
  ANKRD40 WILD-TYPE 358 119
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD40 MUTATED      8    0
  ANKRD40 WILD-TYPE  358  119
        clus
vv       ANKRD40 MUTATED ANKRD40 WILD-TYPE
  COLON                8               358
  RECTUM               0               119
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ANKRD40 MUTATED         4        0        2         2         0         0
  ANKRD40 WILD-TYPE      87        1       30       136        10         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ANKRD40 MUTATED           1          0          0          0        0
  ANKRD40 WILD-TYPE        23         11         59         42       48
                   vv
clus                STAGE IVA STAGE IVB
  ANKRD40 MUTATED           0         0
  ANKRD40 WILD-TYPE        18         1
D1573V4, multiclass
            clus
vv           ANKRD40 MUTATED ANKRD40 WILD-TYPE
  STAGE I                  4                87
  STAGE IA                 0                 1
  STAGE II                 2                30
  STAGE IIA                2               136
  STAGE IIB                0                10
  STAGE IIC                0                 1
  STAGE III                1                23
  STAGE IIIA               0                11
  STAGE IIIB               0                59
  STAGE IIIC               0                42
  STAGE IV                 0                48
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  ANKRD40 MUTATED     0   4   5   0
  ANKRD40 WILD-TYPE  17  88 324  50
D1573V5, multiclass
    clus
vv   ANKRD40 MUTATED ANKRD40 WILD-TYPE
  T1               0                17
  T2               4                88
  T3               5               324
  T4               0                50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  ANKRD40 MUTATED     8   0   1
  ANKRD40 WILD-TYPE 279 113  86
D1573V6, multiclass
    clus
vv   ANKRD40 MUTATED ANKRD40 WILD-TYPE
  N0               8               279
  N1               0               113
  N2               1                86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1573V7, binary
                   cls
clus                  0   1
  ANKRD40 MUTATED     6   0
  ANKRD40 WILD-TYPE 369  65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD40 MUTATED      6    0
  ANKRD40 WILD-TYPE  369   65
   clus
vv  ANKRD40 MUTATED ANKRD40 WILD-TYPE
  0               6               369
  1               0                65
[1] 2 2
[1] FALSE
D1573V8, binary
                   cls
clus                  0   1
  ANKRD40 MUTATED     6   3
  ANKRD40 WILD-TYPE 219 261
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD40 MUTATED      6    3
  ANKRD40 WILD-TYPE  219  261
        clus
vv       ANKRD40 MUTATED ANKRD40 WILD-TYPE
  FEMALE               6               219
  MALE                 3               261
[1] 2 2
[1] FALSE
D1573V9, binary
                   cls
clus                  0   1
  ANKRD40 MUTATED     8   0
  ANKRD40 WILD-TYPE 342  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD40 MUTATED      8    0
  ANKRD40 WILD-TYPE  342   22
     clus
vv    ANKRD40 MUTATED ANKRD40 WILD-TYPE
  NO                8               342
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ANKRD40 MUTATED                      6                             2
  ANKRD40 WILD-TYPE                  309                            45
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ANKRD40 MUTATED                       0                              0
  ANKRD40 WILD-TYPE                   106                             10
D1573V10, multiclass
                                clus
vv                               ANKRD40 MUTATED ANKRD40 WILD-TYPE
  COLON ADENOCARCINOMA                         6               309
  COLON MUCINOUS ADENOCARCINOMA                2                45
  RECTAL ADENOCARCINOMA                        0               106
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  ANKRD40 MUTATED     8   0   0   0
  ANKRD40 WILD-TYPE 337   4  31  25
D1573V11, multiclass
    clus
vv   ANKRD40 MUTATED ANKRD40 WILD-TYPE
  R0               8               337
  R1               0                 4
  R2               0                31
  RX               0                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1573V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ANKRD40 MUTATED                                  0     0
  ANKRD40 WILD-TYPE                                1    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  ANKRD40 MUTATED                           0     5
  ANKRD40 WILD-TYPE                        22   221
D1573V13, multiclass
                                  clus
vv                                 ANKRD40 MUTATED ANKRD40 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                      0                22
  WHITE                                          5               221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1574) Variable = SNAPC2 MUTATION ANALYSIS
D1574V1, survival
                  sevent
clus2                0   1
  SNAPC2 MUTATED     5   1
  SNAPC2 WILD-TYPE 373  92
  SNAPC2 MUTATED SNAPC2 WILD-TYPE 
               6              465 
  SNAPC2 MUTATED SNAPC2 WILD-TYPE 
               1               92 
$`SNAPC2 MUTATED`
TCGA-AA-3516 TCGA-AA-3663 TCGA-AA-3713 TCGA-AA-3977 TCGA-AD-6889 TCGA-DM-A1HB 
       13.02         6.97        19.04        25.02        56.55       135.65 

$`SNAPC2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        1.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 
       40.96         0.07        21.37        15.52         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
        7.50        44.32       131.51       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  SNAPC2 MUTATED SNAPC2 WILD-TYPE 
            6.97             0.00 
  SNAPC2 MUTATED SNAPC2 WILD-TYPE 
          135.65           148.01 
  SNAPC2 MUTATED SNAPC2 WILD-TYPE 
           22.03            20.19 
[1] "7.0 - 135.7 (22.0)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.7"
D1574V2, continuous
D1574V3, binary
                  cls
clus                 0   1
  SNAPC2 MUTATED     6   0
  SNAPC2 WILD-TYPE 360 119
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SNAPC2 MUTATED      6    0
  SNAPC2 WILD-TYPE  360  119
        clus
vv       SNAPC2 MUTATED SNAPC2 WILD-TYPE
  COLON               6              360
  RECTUM              0              119
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SNAPC2 MUTATED         0        0        1         1         0         0
  SNAPC2 WILD-TYPE      91        1       31       137        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SNAPC2 MUTATED           1          0          1          0        1
  SNAPC2 WILD-TYPE        23         11         58         42       47
                  vv
clus               STAGE IVA STAGE IVB
  SNAPC2 MUTATED           0         0
  SNAPC2 WILD-TYPE        18         1
D1574V4, multiclass
            clus
vv           SNAPC2 MUTATED SNAPC2 WILD-TYPE
  STAGE I                 0               91
  STAGE IA                0                1
  STAGE II                1               31
  STAGE IIA               1              137
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               1               23
  STAGE IIIA              0               11
  STAGE IIIB              1               58
  STAGE IIIC              0               42
  STAGE IV                1               47
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  SNAPC2 MUTATED     0   1   5   0
  SNAPC2 WILD-TYPE  17  91 324  50
D1574V5, multiclass
    clus
vv   SNAPC2 MUTATED SNAPC2 WILD-TYPE
  T1              0               17
  T2              1               91
  T3              5              324
  T4              0               50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  SNAPC2 MUTATED     4   1   1
  SNAPC2 WILD-TYPE 283 112  86
D1574V6, multiclass
    clus
vv   SNAPC2 MUTATED SNAPC2 WILD-TYPE
  N0              4              283
  N1              1              112
  N2              1               86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1574V7, binary
                  cls
clus                 0   1
  SNAPC2 MUTATED     4   1
  SNAPC2 WILD-TYPE 371  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SNAPC2 MUTATED      4    1
  SNAPC2 WILD-TYPE  371   64
   clus
vv  SNAPC2 MUTATED SNAPC2 WILD-TYPE
  0              4              371
  1              1               64
[1] 2 2
[1] FALSE
D1574V8, binary
                  cls
clus                 0   1
  SNAPC2 MUTATED     1   5
  SNAPC2 WILD-TYPE 224 259
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SNAPC2 MUTATED      1    5
  SNAPC2 WILD-TYPE  224  259
        clus
vv       SNAPC2 MUTATED SNAPC2 WILD-TYPE
  FEMALE              1              224
  MALE                5              259
[1] 2 2
[1] FALSE
D1574V9, binary
                  cls
clus                 0   1
  SNAPC2 MUTATED     3   1
  SNAPC2 WILD-TYPE 347  21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SNAPC2 MUTATED      3    1
  SNAPC2 WILD-TYPE  347   21
     clus
vv    SNAPC2 MUTATED SNAPC2 WILD-TYPE
  NO               3              347
  YES              1               21
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SNAPC2 MUTATED                      4                             1
  SNAPC2 WILD-TYPE                  311                            46
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SNAPC2 MUTATED                       0                              0
  SNAPC2 WILD-TYPE                   106                             10
D1574V10, multiclass
                                clus
vv                               SNAPC2 MUTATED SNAPC2 WILD-TYPE
  COLON ADENOCARCINOMA                        4              311
  COLON MUCINOUS ADENOCARCINOMA               1               46
  RECTAL ADENOCARCINOMA                       0              106
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  SNAPC2 MUTATED     1   0   1   0
  SNAPC2 WILD-TYPE 344   4  30  25
D1574V11, multiclass
[1] "Remove cluster labels:" "SNAPC2 MUTATED"        
clus
  SNAPC2 MUTATED SNAPC2 WILD-TYPE 
               2              403 
      TCGA-A6-2671       TCGA-A6-2672       TCGA-A6-2674       TCGA-A6-2676 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-A6-2677       TCGA-A6-2678       TCGA-A6-2683       TCGA-A6-3807 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-A6-3808       TCGA-A6-3809       TCGA-A6-3810       TCGA-A6-5657 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-A6-5659       TCGA-A6-5661       TCGA-A6-5665       TCGA-A6-6781 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-AA-3489       TCGA-AA-3492       TCGA-AA-3496       TCGA-AA-3502 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-AA-3510       TCGA-AA-3511       TCGA-AA-3514       TCGA-AA-3517 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-AA-3518       TCGA-AA-3519       TCGA-AA-3520       TCGA-AA-3521 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-AA-3522       TCGA-AA-3524       TCGA-AA-3525       TCGA-AA-3526 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-AA-3527       TCGA-AA-3529       TCGA-AA-3530       TCGA-AA-3531 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-AA-3532       TCGA-AA-3534       TCGA-AA-3538       TCGA-AA-3542 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-AA-3543       TCGA-AA-3544       TCGA-AA-3548       TCGA-AA-3549 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-AA-3552       TCGA-AA-3553       TCGA-AA-3554       TCGA-AA-3555 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-AA-3556       TCGA-AA-3558       TCGA-AA-3560       TCGA-AA-3561 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-AA-3562       TCGA-AA-3655       TCGA-AA-3660       TCGA-AA-3662 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-AA-3664       TCGA-AA-3666       TCGA-AA-3667       TCGA-AA-3672 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-AA-3673       TCGA-AA-3678       TCGA-AA-3679       TCGA-AA-3680 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-AA-3681       TCGA-AA-3684       TCGA-AA-3685       TCGA-AA-3688 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-AA-3692       TCGA-AA-3693       TCGA-AA-3695       TCGA-AA-3696 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-AA-3697       TCGA-AA-3710       TCGA-AA-3712       TCGA-AA-3715 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-AA-3811       TCGA-AA-3812       TCGA-AA-3814       TCGA-AA-3815 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-AA-3818       TCGA-AA-3819       TCGA-AA-3821       TCGA-AA-3831 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-AA-3833       TCGA-AA-3837       TCGA-AA-3842       TCGA-AA-3844 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-AA-3845       TCGA-AA-3846       TCGA-AA-3848       TCGA-AA-3850 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-AA-3851       TCGA-AA-3852       TCGA-AA-3854       TCGA-AA-3855 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-AA-3856       TCGA-AA-3858       TCGA-AA-3860       TCGA-AA-3861 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-AA-3864       TCGA-AA-3866       TCGA-AA-3867       TCGA-AA-3869 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-AA-3870       TCGA-AA-3872       TCGA-AA-3875       TCGA-AA-3877 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-AA-3930       TCGA-AA-3939       TCGA-AA-3941       TCGA-AA-3947 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-AA-3949       TCGA-AA-3950       TCGA-AA-3952       TCGA-AA-3955 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-AA-3956       TCGA-AA-3968       TCGA-AA-3971       TCGA-AA-3972 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-AA-3973       TCGA-AA-3975       TCGA-AA-3976       TCGA-AA-3979 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-AA-3984       TCGA-AA-3986       TCGA-AA-3989       TCGA-AA-3994 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-AA-A004       TCGA-AA-A00A       TCGA-AA-A00D       TCGA-AA-A00E 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-AA-A00F       TCGA-AA-A00J       TCGA-AA-A00K       TCGA-AA-A00L 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-AA-A00N       TCGA-AA-A00O       TCGA-AA-A00Q       TCGA-AA-A00R 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-AA-A00U       TCGA-AA-A00W       TCGA-AA-A00Z       TCGA-AA-A010 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-AA-A017       TCGA-AA-A01D       TCGA-AA-A01F       TCGA-AA-A01G 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-AA-A01I       TCGA-AA-A01K       TCGA-AA-A01P       TCGA-AA-A01Q 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-AA-A01R       TCGA-AA-A01S       TCGA-AA-A01T       TCGA-AA-A01V 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-AA-A01X       TCGA-AA-A01Z       TCGA-AA-A022       TCGA-AA-A024 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-AA-A029       TCGA-AA-A02F       TCGA-AA-A02H       TCGA-AA-A02J 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-AA-A02K       TCGA-AA-A02O       TCGA-AA-A02W       TCGA-AA-A02Y 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-AA-A03F       TCGA-AA-A03J       TCGA-AD-5900       TCGA-AD-6548 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-AD-6888       TCGA-AU-3779       TCGA-AU-6004       TCGA-AY-4070 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-AY-4071       TCGA-AY-5543       TCGA-AY-6196       TCGA-AY-6197 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-AY-6386       TCGA-AZ-4315       TCGA-AZ-4681       TCGA-AZ-4682 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-CA-5254       TCGA-CA-5255       TCGA-CA-5796       TCGA-CA-5797 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-CA-6715       TCGA-CA-6716       TCGA-CA-6717       TCGA-CA-6718 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-CA-6719       TCGA-CK-4947       TCGA-CK-4948       TCGA-CK-4950 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-CK-4952       TCGA-CK-5912       TCGA-CK-5913       TCGA-CK-5914 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-CK-5915       TCGA-CK-5916       TCGA-CK-6746       TCGA-CK-6747 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-CK-6748       TCGA-CK-6751       TCGA-CM-4743       TCGA-CM-4744 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-CM-4746       TCGA-CM-4747       TCGA-CM-4752       TCGA-CM-5341 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-CM-5344       TCGA-CM-5348       TCGA-CM-5349       TCGA-CM-5860 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-CM-5861       TCGA-CM-5862       TCGA-CM-5863       TCGA-CM-5864 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-CM-5868       TCGA-CM-6161       TCGA-CM-6162       TCGA-CM-6163 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-CM-6164       TCGA-CM-6165       TCGA-CM-6166       TCGA-CM-6167 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-CM-6168       TCGA-CM-6169       TCGA-CM-6170       TCGA-CM-6171 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-CM-6172       TCGA-CM-6674       TCGA-CM-6675       TCGA-CM-6676 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-CM-6677       TCGA-CM-6678       TCGA-CM-6679       TCGA-CM-6680 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-D5-5537       TCGA-D5-5538       TCGA-D5-5539       TCGA-D5-5540 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-D5-5541       TCGA-D5-6529       TCGA-D5-6532       TCGA-D5-6533 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-D5-6534       TCGA-D5-6535       TCGA-D5-6536       TCGA-D5-6537 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-D5-6538       TCGA-D5-6539       TCGA-D5-6540       TCGA-D5-6541 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-D5-6898       TCGA-D5-6920       TCGA-D5-6922       TCGA-D5-6923 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-D5-6924       TCGA-D5-6926       TCGA-D5-6927       TCGA-D5-6928 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-D5-6929       TCGA-D5-6930       TCGA-D5-6931       TCGA-D5-6932 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-D5-7000       TCGA-F4-6459       TCGA-F4-6460       TCGA-F4-6569 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-F4-6570       TCGA-F4-6703       TCGA-F4-6704       TCGA-F4-6805 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-F4-6806       TCGA-F4-6807       TCGA-F4-6808       TCGA-F4-6809 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-F4-6854       TCGA-F4-6855       TCGA-F4-6856       TCGA-G4-6293 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-G4-6299       TCGA-G4-6303       TCGA-G4-6304       TCGA-G4-6306 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-G4-6307       TCGA-G4-6309       TCGA-G4-6310       TCGA-G4-6315 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-G4-6317       TCGA-G4-6321       TCGA-G4-6323       TCGA-G4-6586 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-G4-6588       TCGA-G4-6625       TCGA-G4-6626       TCGA-G4-6628 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-AF-2687       TCGA-AF-2689       TCGA-AF-2691       TCGA-AF-2692 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-AF-3400       TCGA-AF-3913       TCGA-AF-4110       TCGA-AF-5654 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-AF-6655       TCGA-AG-3574       TCGA-AG-3575       TCGA-AG-3578 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-AG-3580       TCGA-AG-3581       TCGA-AG-3582       TCGA-AG-3583 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-AG-3584       TCGA-AG-3586       TCGA-AG-3587       TCGA-AG-3593 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-AG-3594       TCGA-AG-3598       TCGA-AG-3599       TCGA-AG-3600 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-AG-3601       TCGA-AG-3602       TCGA-AG-3605       TCGA-AG-3608 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-AG-3609       TCGA-AG-3611       TCGA-AG-3612       TCGA-AG-3726 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-AG-3727       TCGA-AG-3731       TCGA-AG-3732       TCGA-AG-3742 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-AG-3878       TCGA-AG-3882       TCGA-AG-3883       TCGA-AG-3885 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-AG-3887       TCGA-AG-3890       TCGA-AG-3892       TCGA-AG-3893 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-AG-3894       TCGA-AG-3896       TCGA-AG-3898       TCGA-AG-3901 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-AG-3902       TCGA-AG-3909       TCGA-AG-3999       TCGA-AG-4001 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-AG-4005       TCGA-AG-4007       TCGA-AG-4008       TCGA-AG-4015 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-AG-A002       TCGA-AG-A008       TCGA-AG-A00C       TCGA-AG-A00H 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-AG-A00Y       TCGA-AG-A011       TCGA-AG-A014       TCGA-AG-A015 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-AG-A016       TCGA-AG-A01L       TCGA-AG-A01W       TCGA-AG-A01Y 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-AG-A020       TCGA-AG-A025       TCGA-AG-A026       TCGA-AG-A02G 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-AG-A02N       TCGA-AG-A02X       TCGA-AG-A032       TCGA-AG-A036 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-AH-6549       TCGA-AH-6643       TCGA-CL-5917       TCGA-CL-5918 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-DC-5337       TCGA-DC-5869       TCGA-DC-6155       TCGA-DC-6157 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-DC-6158       TCGA-DC-6160       TCGA-DC-6681       TCGA-DC-6682 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-DC-6683       TCGA-DT-5265       TCGA-EF-5830       TCGA-EI-6506 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-EI-6507       TCGA-EI-6508       TCGA-EI-6510       TCGA-F5-6464 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-F5-6465       TCGA-F5-6571       TCGA-F5-6702       TCGA-F5-6812 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-F5-6813       TCGA-G5-6235       TCGA-G5-6641 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
D1574V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SNAPC2 MUTATED                                  0     1
  SNAPC2 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  SNAPC2 MUTATED                           0     1
  SNAPC2 WILD-TYPE                        22   225
D1574V13, multiclass
[1] "Remove cluster labels:" "SNAPC2 MUTATED"        
clus
  SNAPC2 MUTATED SNAPC2 WILD-TYPE 
               2              258 
      TCGA-A6-2671       TCGA-A6-2672       TCGA-A6-2674       TCGA-A6-2676 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-A6-2677       TCGA-A6-2678       TCGA-A6-2683       TCGA-A6-3807 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-A6-3808       TCGA-A6-3809       TCGA-A6-3810       TCGA-A6-4105 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-A6-5656       TCGA-A6-5657       TCGA-A6-5659       TCGA-A6-5660 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-A6-5661       TCGA-A6-5662       TCGA-A6-5664       TCGA-A6-5665 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-A6-5666       TCGA-A6-6137       TCGA-A6-6138       TCGA-A6-6141 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-A6-6142       TCGA-A6-6648       TCGA-A6-6649       TCGA-A6-6651 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-A6-6652       TCGA-A6-6653       TCGA-A6-6654       TCGA-A6-6780 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-A6-6781       TCGA-A6-6782       TCGA-AD-5900       TCGA-AD-6548 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-AD-6888       TCGA-AD-6890       TCGA-AD-6895       TCGA-AD-6899 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-AD-6901       TCGA-AD-6963       TCGA-AD-6964       TCGA-AD-6965 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-AU-3779       TCGA-AU-6004       TCGA-AY-4070       TCGA-AY-4071 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-AY-5543       TCGA-AY-6196       TCGA-AY-6197       TCGA-AY-6386 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-AZ-4315       TCGA-AZ-4323       TCGA-AZ-4616       TCGA-AZ-4681 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-AZ-4682       TCGA-AZ-5403       TCGA-AZ-5407       TCGA-AZ-6598 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-AZ-6599       TCGA-AZ-6600       TCGA-AZ-6601       TCGA-AZ-6603 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-AZ-6605       TCGA-AZ-6606       TCGA-AZ-6607       TCGA-AZ-6608 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-CA-5254       TCGA-CA-5255       TCGA-CA-5796       TCGA-CA-5797 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-CA-6715       TCGA-CA-6716       TCGA-CA-6717       TCGA-CA-6718 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-CA-6719       TCGA-CK-4947       TCGA-CK-4948       TCGA-CK-4950 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-CK-4952       TCGA-CK-5912       TCGA-CK-5913       TCGA-CK-5914 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-CK-5915       TCGA-CK-5916       TCGA-CK-6746       TCGA-CK-6747 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-CK-6748       TCGA-CK-6751       TCGA-CM-4743       TCGA-CM-4744 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-CM-4746       TCGA-CM-4747       TCGA-CM-4752       TCGA-CM-5341 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-CM-5344       TCGA-CM-5348       TCGA-CM-5349       TCGA-CM-5860 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-CM-5861       TCGA-CM-5862       TCGA-CM-5863       TCGA-CM-5864 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-CM-5868       TCGA-CM-6161       TCGA-CM-6162       TCGA-CM-6163 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-CM-6164       TCGA-CM-6165       TCGA-CM-6166       TCGA-CM-6167 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-CM-6168       TCGA-CM-6169       TCGA-CM-6170       TCGA-CM-6171 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-CM-6172       TCGA-CM-6674       TCGA-CM-6675       TCGA-CM-6676 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-CM-6677       TCGA-CM-6678       TCGA-CM-6679       TCGA-CM-6680 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-D5-5537       TCGA-D5-5538       TCGA-D5-5539       TCGA-D5-5540 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-D5-5541       TCGA-D5-6529       TCGA-D5-6532       TCGA-D5-6533 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-D5-6534       TCGA-D5-6535       TCGA-D5-6536       TCGA-D5-6537 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-D5-6538       TCGA-D5-6539       TCGA-D5-6540       TCGA-D5-6541 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-D5-6898       TCGA-D5-6920       TCGA-D5-6922       TCGA-D5-6923 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-D5-6924       TCGA-D5-6926       TCGA-D5-6927       TCGA-D5-6928 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-D5-6929       TCGA-D5-6930       TCGA-D5-6931       TCGA-D5-6932 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-D5-7000       TCGA-DM-A0X9       TCGA-DM-A0XD       TCGA-DM-A0XF 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-DM-A1D0       TCGA-DM-A1D4       TCGA-DM-A1D6       TCGA-DM-A1D7 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-DM-A1D8       TCGA-DM-A1D9       TCGA-DM-A1DA       TCGA-DM-A1DB 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-DM-A1HA       TCGA-DM-A282       TCGA-DM-A285       TCGA-DM-A28C 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-DM-A28E       TCGA-DM-A28F       TCGA-DM-A28G       TCGA-DM-A28H 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-DM-A28K       TCGA-F4-6459       TCGA-F4-6460       TCGA-F4-6569 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-F4-6570       TCGA-F4-6703       TCGA-F4-6704       TCGA-F4-6805 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-F4-6806       TCGA-F4-6807       TCGA-F4-6808       TCGA-F4-6809 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-F4-6854       TCGA-F4-6855       TCGA-F4-6856       TCGA-G4-6293 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-G4-6299       TCGA-G4-6303       TCGA-G4-6304       TCGA-G4-6306 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-G4-6307       TCGA-G4-6309       TCGA-G4-6310       TCGA-G4-6315 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-G4-6317       TCGA-G4-6321       TCGA-G4-6323       TCGA-G4-6586 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-G4-6588       TCGA-G4-6625       TCGA-G4-6626       TCGA-G4-6628 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-AF-2687       TCGA-AF-2689       TCGA-AF-2691       TCGA-AF-2692 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-AF-2693       TCGA-AF-3400       TCGA-AF-3913       TCGA-AF-4110 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-AF-5654       TCGA-AF-6136       TCGA-AF-6655       TCGA-AF-6672 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-AH-6544       TCGA-AH-6547       TCGA-AH-6549       TCGA-AH-6643 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-AH-6644       TCGA-CI-6619       TCGA-CI-6620       TCGA-CI-6621 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-CI-6622       TCGA-CI-6624       TCGA-CL-5917       TCGA-CL-5918 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-DC-5337       TCGA-DC-5869       TCGA-DC-6155       TCGA-DC-6157 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-DC-6158       TCGA-DC-6160       TCGA-DC-6681       TCGA-DC-6682 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-DC-6683       TCGA-DT-5265       TCGA-DY-A0XA       TCGA-DY-A1DC 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-DY-A1DD       TCGA-DY-A1DF       TCGA-DY-A1DG       TCGA-DY-A1H8 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-EF-5830       TCGA-EI-6506       TCGA-EI-6507       TCGA-EI-6508 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-EI-6510       TCGA-F5-6464       TCGA-F5-6465       TCGA-F5-6571 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-F5-6702       TCGA-F5-6811       TCGA-F5-6812       TCGA-F5-6813 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 
      TCGA-G5-6235       TCGA-G5-6641 
"SNAPC2 WILD-TYPE" "SNAPC2 WILD-TYPE" 

Clustering(1575) Variable = UPF3B MUTATION ANALYSIS
D1575V1, survival
                 sevent
clus2               0   1
  UPF3B MUTATED    10   1
  UPF3B WILD-TYPE 368  92
  UPF3B MUTATED UPF3B WILD-TYPE 
             11             460 
  UPF3B MUTATED UPF3B WILD-TYPE 
              1              92 
$`UPF3B MUTATED`
TCGA-AA-A010 TCGA-AA-A01Q TCGA-CM-4752 TCGA-D5-6535 TCGA-D5-6898 TCGA-D5-7000 
       34.98         1.02        13.02        15.12         1.48        10.26 
TCGA-F4-6460 TCGA-G4-6307 TCGA-AG-3731 TCGA-AG-3892 TCGA-AG-A00Y 
       31.96        55.04        37.02        13.02        23.01 

$`UPF3B WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01R TCGA-AA-A01S 
       12.00        31.00        31.00        38.07        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       25.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       18.25         1.32        43.27        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       12.49        16.14        15.58         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       12.00        11.38       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 
      133.18        74.56        65.85        53.62        44.68        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        7.99         0.99        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 
       19.99         1.02        17.95        36.95        17.03        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
        6.02        25.97        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  UPF3B MUTATED UPF3B WILD-TYPE 
           1.02            0.00 
  UPF3B MUTATED UPF3B WILD-TYPE 
          55.04          148.01 
  UPF3B MUTATED UPF3B WILD-TYPE 
         15.120          20.235 
[1] "1.0 - 55.0 (15.1)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.8"
D1575V2, continuous
D1575V3, binary
                 cls
clus                0   1
  UPF3B MUTATED     8   3
  UPF3B WILD-TYPE 358 116
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UPF3B MUTATED      8    3
  UPF3B WILD-TYPE  358  116
        clus
vv       UPF3B MUTATED UPF3B WILD-TYPE
  COLON              8             358
  RECTUM             3             116
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  UPF3B MUTATED         3        0        1         2         1         0
  UPF3B WILD-TYPE      88        1       31       136         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  UPF3B MUTATED           0          0          3          0        1         0
  UPF3B WILD-TYPE        24         11         56         42       47        18
                 vv
clus              STAGE IVB
  UPF3B MUTATED           0
  UPF3B WILD-TYPE         1
D1575V4, multiclass
            clus
vv           UPF3B MUTATED UPF3B WILD-TYPE
  STAGE I                3              88
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              2             136
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             3              56
  STAGE IIIC             0              42
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  UPF3B MUTATED     1   2   7   1
  UPF3B WILD-TYPE  16  90 322  49
D1575V5, multiclass
    clus
vv   UPF3B MUTATED UPF3B WILD-TYPE
  T1             1              16
  T2             2              90
  T3             7             322
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  UPF3B MUTATED     7   4   0
  UPF3B WILD-TYPE 280 109  87
D1575V6, multiclass
    clus
vv   UPF3B MUTATED UPF3B WILD-TYPE
  N0             7             280
  N1             4             109
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1575V7, binary
                 cls
clus                0   1
  UPF3B MUTATED     9   1
  UPF3B WILD-TYPE 366  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UPF3B MUTATED      9    1
  UPF3B WILD-TYPE  366   64
   clus
vv  UPF3B MUTATED UPF3B WILD-TYPE
  0             9             366
  1             1              64
[1] 2 2
[1] FALSE
D1575V8, binary
                 cls
clus                0   1
  UPF3B MUTATED     8   3
  UPF3B WILD-TYPE 217 261
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UPF3B MUTATED      8    3
  UPF3B WILD-TYPE  217  261
        clus
vv       UPF3B MUTATED UPF3B WILD-TYPE
  FEMALE             8             217
  MALE               3             261
[1] 2 2
[1] FALSE
D1575V9, binary
                 cls
clus                0   1
  UPF3B MUTATED     9   0
  UPF3B WILD-TYPE 341  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UPF3B MUTATED      9    0
  UPF3B WILD-TYPE  341   22
     clus
vv    UPF3B MUTATED UPF3B WILD-TYPE
  NO              9             341
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  UPF3B MUTATED                      7                             1
  UPF3B WILD-TYPE                  308                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  UPF3B MUTATED                       3                              0
  UPF3B WILD-TYPE                   103                             10
D1575V10, multiclass
                                clus
vv                               UPF3B MUTATED UPF3B WILD-TYPE
  COLON ADENOCARCINOMA                       7             308
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      3             103
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  UPF3B MUTATED     9   0   1   1
  UPF3B WILD-TYPE 336   4  30  24
D1575V11, multiclass
    clus
vv   UPF3B MUTATED UPF3B WILD-TYPE
  R0             9             336
  R1             0               4
  R2             1              30
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1575V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  UPF3B MUTATED                                  0     0
  UPF3B WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  UPF3B MUTATED                           1     5
  UPF3B WILD-TYPE                        21   221
D1575V13, multiclass
                                  clus
vv                                 UPF3B MUTATED UPF3B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        5             221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1576) Variable = LMTK3 MUTATION ANALYSIS
D1576V1, survival
                 sevent
clus2               0   1
  LMTK3 MUTATED    11   5
  LMTK3 WILD-TYPE 367  88
  LMTK3 MUTATED LMTK3 WILD-TYPE 
             16             455 
  LMTK3 MUTATED LMTK3 WILD-TYPE 
              5              88 
$`LMTK3 MUTATED`
TCGA-AD-6889 TCGA-AD-6899 TCGA-AZ-6598 TCGA-AZ-6601 TCGA-CA-6716 TCGA-CA-6717 
       56.55         5.79        49.41       100.01        12.20        12.76 
TCGA-CM-6168 TCGA-CM-6171 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6930 TCGA-F4-6459 
       12.99        14.04        15.12         4.80         1.51         8.61 
TCGA-F4-6856 TCGA-G4-6304 TCGA-G4-6628 TCGA-AG-3892 
       35.31        53.62        79.69        13.02 

$`LMTK3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6901 TCGA-AD-6963 
       21.37        15.52         0.79         0.72        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 
      106.75        22.36        62.79        88.21         6.77        12.10 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6718 TCGA-CA-6719 
        3.06         3.25         3.29         0.07        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 
       16.04        21.99        14.99        13.02        15.02        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6538 
       20.19        18.25         1.32        43.27        17.85        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
      133.18        74.56        65.85        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       26.17        91.79        46.75        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 
       19.99         1.02        17.95        36.95        17.03        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  LMTK3 MUTATED LMTK3 WILD-TYPE 
           1.51            0.00 
  LMTK3 MUTATED LMTK3 WILD-TYPE 
         100.01          148.01 
  LMTK3 MUTATED LMTK3 WILD-TYPE 
          13.53           20.55 
[1] "1.5 - 100.0 (13.5)" "0.0 - 148.0 (20.6)"
[1] "hr=" "1.4"
D1576V2, continuous
D1576V3, binary
                 cls
clus                0   1
  LMTK3 MUTATED    15   1
  LMTK3 WILD-TYPE 351 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LMTK3 MUTATED     15    1
  LMTK3 WILD-TYPE  351  118
        clus
vv       LMTK3 MUTATED LMTK3 WILD-TYPE
  COLON             15             351
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  LMTK3 MUTATED         4        0        2         5         1         0
  LMTK3 WILD-TYPE      87        1       30       133         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  LMTK3 MUTATED           0          0          3          1        0         0
  LMTK3 WILD-TYPE        24         11         56         41       48        18
                 vv
clus              STAGE IVB
  LMTK3 MUTATED           0
  LMTK3 WILD-TYPE         1
D1576V4, multiclass
            clus
vv           LMTK3 MUTATED LMTK3 WILD-TYPE
  STAGE I                4              87
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA              5             133
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             3              56
  STAGE IIIC             1              41
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  LMTK3 MUTATED     1   3  10   2
  LMTK3 WILD-TYPE  16  89 319  48
D1576V5, multiclass
    clus
vv   LMTK3 MUTATED LMTK3 WILD-TYPE
  T1             1              16
  T2             3              89
  T3            10             319
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  LMTK3 MUTATED    12   2   2
  LMTK3 WILD-TYPE 275 111  85
D1576V6, multiclass
    clus
vv   LMTK3 MUTATED LMTK3 WILD-TYPE
  N0            12             275
  N1             2             111
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1576V7, binary
                 cls
clus                0   1
  LMTK3 MUTATED    12   0
  LMTK3 WILD-TYPE 363  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LMTK3 MUTATED     12    0
  LMTK3 WILD-TYPE  363   65
   clus
vv  LMTK3 MUTATED LMTK3 WILD-TYPE
  0            12             363
  1             0              65
[1] 2 2
[1] FALSE
D1576V8, binary
                 cls
clus                0   1
  LMTK3 MUTATED     7   9
  LMTK3 WILD-TYPE 218 255
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LMTK3 MUTATED      7    9
  LMTK3 WILD-TYPE  218  255
        clus
vv       LMTK3 MUTATED LMTK3 WILD-TYPE
  FEMALE             7             218
  MALE               9             255
[1] 2 2
[1] FALSE
D1576V9, binary
                 cls
clus                0   1
  LMTK3 MUTATED    14   0
  LMTK3 WILD-TYPE 336  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LMTK3 MUTATED     14    0
  LMTK3 WILD-TYPE  336   22
     clus
vv    LMTK3 MUTATED LMTK3 WILD-TYPE
  NO             14             336
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  LMTK3 MUTATED                     11                             4
  LMTK3 WILD-TYPE                  304                            43
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  LMTK3 MUTATED                       1                              0
  LMTK3 WILD-TYPE                   105                             10
D1576V10, multiclass
                                clus
vv                               LMTK3 MUTATED LMTK3 WILD-TYPE
  COLON ADENOCARCINOMA                      11             304
  COLON MUCINOUS ADENOCARCINOMA              4              43
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  LMTK3 MUTATED     9   0   0   3
  LMTK3 WILD-TYPE 336   4  31  22
D1576V11, multiclass
    clus
vv   LMTK3 MUTATED LMTK3 WILD-TYPE
  R0             9             336
  R1             0               4
  R2             0              31
  RX             3              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1576V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  LMTK3 MUTATED                                  0     3
  LMTK3 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  LMTK3 MUTATED                           1    11
  LMTK3 WILD-TYPE                        21   215
D1576V13, multiclass
                                  clus
vv                                 LMTK3 MUTATED LMTK3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        3               8
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                       11             215
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1577) Variable = FCAMR MUTATION ANALYSIS
D1577V1, survival
                 sevent
clus2               0   1
  FCAMR MUTATED    10   1
  FCAMR WILD-TYPE 368  92
  FCAMR MUTATED FCAMR WILD-TYPE 
             11             460 
  FCAMR MUTATED FCAMR WILD-TYPE 
              1              92 
$`FCAMR MUTATED`
TCGA-A6-6653 TCGA-A6-6781 TCGA-AA-3713 TCGA-AA-3968 TCGA-AD-6889 TCGA-AD-6895 
       24.39        19.66        19.04        21.99        56.55         0.72 
TCGA-AZ-4315 TCGA-AZ-6601 TCGA-CM-6171 TCGA-AG-A002 TCGA-EI-6507 
       58.39       100.01        14.04        20.98        19.96 

$`FCAMR WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
       25.08        25.18        24.16        21.76        24.69        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6899 
       40.96         0.07        21.37        15.52         0.79         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
       16.31         0.95        33.01        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77        12.10        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 
       14.99        12.99        13.02        15.02        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6508 
       24.13        51.48        32.61         0.49        20.55        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  FCAMR MUTATED FCAMR WILD-TYPE 
           0.72            0.00 
  FCAMR MUTATED FCAMR WILD-TYPE 
         100.01          148.01 
  FCAMR MUTATED FCAMR WILD-TYPE 
         20.980          20.155 
[1] "0.7 - 100.0 (21.0)" "0.0 - 148.0 (20.2)"
[1] "hr=" "2.8"
D1577V2, continuous
D1577V3, binary
                 cls
clus                0   1
  FCAMR MUTATED    10   2
  FCAMR WILD-TYPE 356 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FCAMR MUTATED     10    2
  FCAMR WILD-TYPE  356  117
        clus
vv       FCAMR MUTATED FCAMR WILD-TYPE
  COLON             10             356
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FCAMR MUTATED         4        0        1         3         1         0
  FCAMR WILD-TYPE      87        1       31       135         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  FCAMR MUTATED           0          0          0          1        1         0
  FCAMR WILD-TYPE        24         11         59         41       47        18
                 vv
clus              STAGE IVB
  FCAMR MUTATED           0
  FCAMR WILD-TYPE         1
D1577V4, multiclass
            clus
vv           FCAMR MUTATED FCAMR WILD-TYPE
  STAGE I                4              87
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              3             135
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             1              41
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  FCAMR MUTATED     0   4   6   2
  FCAMR WILD-TYPE  17  88 323  48
D1577V5, multiclass
    clus
vv   FCAMR MUTATED FCAMR WILD-TYPE
  T1             0              17
  T2             4              88
  T3             6             323
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  FCAMR MUTATED    10   2   0
  FCAMR WILD-TYPE 277 111  87
D1577V6, multiclass
    clus
vv   FCAMR MUTATED FCAMR WILD-TYPE
  N0            10             277
  N1             2             111
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1577V7, binary
                 cls
clus                0   1
  FCAMR MUTATED     8   1
  FCAMR WILD-TYPE 367  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FCAMR MUTATED      8    1
  FCAMR WILD-TYPE  367   64
   clus
vv  FCAMR MUTATED FCAMR WILD-TYPE
  0             8             367
  1             1              64
[1] 2 2
[1] FALSE
D1577V8, binary
                 cls
clus                0   1
  FCAMR MUTATED     3   9
  FCAMR WILD-TYPE 222 255
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FCAMR MUTATED      3    9
  FCAMR WILD-TYPE  222  255
        clus
vv       FCAMR MUTATED FCAMR WILD-TYPE
  FEMALE             3             222
  MALE               9             255
[1] 2 2
[1] FALSE
D1577V9, binary
                 cls
clus                0   1
  FCAMR MUTATED     8   1
  FCAMR WILD-TYPE 342  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FCAMR MUTATED      8    1
  FCAMR WILD-TYPE  342   21
     clus
vv    FCAMR MUTATED FCAMR WILD-TYPE
  NO              8             342
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  FCAMR MUTATED                      9                             1
  FCAMR WILD-TYPE                  306                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  FCAMR MUTATED                       2                              0
  FCAMR WILD-TYPE                   104                             10
D1577V10, multiclass
                                clus
vv                               FCAMR MUTATED FCAMR WILD-TYPE
  COLON ADENOCARCINOMA                       9             306
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  FCAMR MUTATED     6   0   1   1
  FCAMR WILD-TYPE 339   4  30  24
D1577V11, multiclass
    clus
vv   FCAMR MUTATED FCAMR WILD-TYPE
  R0             6             339
  R1             0               4
  R2             1              30
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1577V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FCAMR MUTATED                                  0     1
  FCAMR WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  FCAMR MUTATED                           0     8
  FCAMR WILD-TYPE                        22   218
D1577V13, multiclass
                                  clus
vv                                 FCAMR MUTATED FCAMR WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        8             218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1578) Variable = XCL2 MUTATION ANALYSIS
D1578V1, survival
                sevent
clus2              0   1
  XCL2 MUTATED     3   1
  XCL2 WILD-TYPE 375  92
  XCL2 MUTATED XCL2 WILD-TYPE 
             4            467 
  XCL2 MUTATED XCL2 WILD-TYPE 
             1             92 
$`XCL2 MUTATED`
TCGA-A6-2676 TCGA-AD-6889 TCGA-D5-5538 TCGA-AF-2693 
       42.90        56.55        12.26        19.10 

$`XCL2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       15.52         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       12.03        45.40        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       13.55        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  XCL2 MUTATED XCL2 WILD-TYPE 
         12.26           0.00 
  XCL2 MUTATED XCL2 WILD-TYPE 
         56.55         148.01 
  XCL2 MUTATED XCL2 WILD-TYPE 
         31.00          20.19 
[1] "12.3 - 56.5 (31.0)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1"  
D1578V2, continuous
D1578V3, binary
                cls
clus               0   1
  XCL2 MUTATED     3   0
  XCL2 WILD-TYPE 363 119
[1] "tbl2"
                cls
clus             [,1] [,2]
  XCL2 MUTATED      3    0
  XCL2 WILD-TYPE  363  119
        clus
vv       XCL2 MUTATED XCL2 WILD-TYPE
  COLON             3            363
  RECTUM            0            119
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  XCL2 MUTATED         1        0        0         1         1         0
  XCL2 WILD-TYPE      90        1       32       137         9         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  XCL2 MUTATED           0          0          1          0        0         0
  XCL2 WILD-TYPE        24         11         58         42       48        18
                vv
clus             STAGE IVB
  XCL2 MUTATED           0
  XCL2 WILD-TYPE         1
D1578V4, multiclass
            clus
vv           XCL2 MUTATED XCL2 WILD-TYPE
  STAGE I               1             90
  STAGE IA              0              1
  STAGE II              0             32
  STAGE IIA             1            137
  STAGE IIB             1              9
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            1             58
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  XCL2 MUTATED     0   1   2   1
  XCL2 WILD-TYPE  17  91 327  49
D1578V5, multiclass
    clus
vv   XCL2 MUTATED XCL2 WILD-TYPE
  T1            0             17
  T2            1             91
  T3            2            327
  T4            1             49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  XCL2 MUTATED     3   1   0
  XCL2 WILD-TYPE 284 112  87
D1578V6, multiclass
    clus
vv   XCL2 MUTATED XCL2 WILD-TYPE
  N0            3            284
  N1            1            112
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1578V7, binary
                cls
clus               0   1
  XCL2 MUTATED     3   0
  XCL2 WILD-TYPE 372  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  XCL2 MUTATED      3    0
  XCL2 WILD-TYPE  372   65
   clus
vv  XCL2 MUTATED XCL2 WILD-TYPE
  0            3            372
  1            0             65
[1] 2 2
[1] FALSE
D1578V8, binary
                cls
clus               0   1
  XCL2 MUTATED     2   2
  XCL2 WILD-TYPE 223 262
[1] "tbl2"
                cls
clus             [,1] [,2]
  XCL2 MUTATED      2    2
  XCL2 WILD-TYPE  223  262
        clus
vv       XCL2 MUTATED XCL2 WILD-TYPE
  FEMALE            2            223
  MALE              2            262
[1] 2 2
[1] FALSE
D1578V9, binary
                cls
clus               0   1
  XCL2 MUTATED     3   0
  XCL2 WILD-TYPE 347  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  XCL2 MUTATED      3    0
  XCL2 WILD-TYPE  347   22
     clus
vv    XCL2 MUTATED XCL2 WILD-TYPE
  NO             3            347
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  XCL2 MUTATED                      3                             0
  XCL2 WILD-TYPE                  312                            47
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  XCL2 MUTATED                       0                              0
  XCL2 WILD-TYPE                   106                             10
D1578V10, multiclass
                                clus
vv                               XCL2 MUTATED XCL2 WILD-TYPE
  COLON ADENOCARCINOMA                      3            312
  COLON MUCINOUS ADENOCARCINOMA             0             47
  RECTAL ADENOCARCINOMA                     0            106
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  XCL2 MUTATED     2   0   0   0
  XCL2 WILD-TYPE 343   4  31  25
D1578V11, multiclass
[1] "Remove cluster labels:" "XCL2 MUTATED"          
clus
  XCL2 MUTATED XCL2 WILD-TYPE 
             2            403 
    TCGA-A6-2671     TCGA-A6-2672     TCGA-A6-2674     TCGA-A6-2677 
"XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" 
    TCGA-A6-2678     TCGA-A6-2683     TCGA-A6-3807     TCGA-A6-3808 
"XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" 
    TCGA-A6-3809     TCGA-A6-3810     TCGA-A6-5657     TCGA-A6-5659 
"XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" 
    TCGA-A6-5661     TCGA-A6-5665     TCGA-A6-6781     TCGA-AA-3489 
"XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" 
    TCGA-AA-3492     TCGA-AA-3496     TCGA-AA-3502     TCGA-AA-3510 
"XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" 
    TCGA-AA-3511     TCGA-AA-3514     TCGA-AA-3517     TCGA-AA-3518 
"XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" 
    TCGA-AA-3519     TCGA-AA-3520     TCGA-AA-3521     TCGA-AA-3522 
"XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" 
    TCGA-AA-3524     TCGA-AA-3525     TCGA-AA-3526     TCGA-AA-3527 
"XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" 
    TCGA-AA-3529     TCGA-AA-3530     TCGA-AA-3531     TCGA-AA-3532 
"XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" 
    TCGA-AA-3534     TCGA-AA-3538     TCGA-AA-3542     TCGA-AA-3543 
"XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" 
    TCGA-AA-3544     TCGA-AA-3548     TCGA-AA-3549     TCGA-AA-3552 
"XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" 
    TCGA-AA-3553     TCGA-AA-3554     TCGA-AA-3555     TCGA-AA-3556 
"XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" 
    TCGA-AA-3558     TCGA-AA-3560     TCGA-AA-3561     TCGA-AA-3562 
"XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" 
    TCGA-AA-3655     TCGA-AA-3660     TCGA-AA-3662     TCGA-AA-3663 
"XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" 
    TCGA-AA-3664     TCGA-AA-3666     TCGA-AA-3667     TCGA-AA-3672 
"XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" 
    TCGA-AA-3673     TCGA-AA-3678     TCGA-AA-3679     TCGA-AA-3680 
"XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" 
    TCGA-AA-3681     TCGA-AA-3684     TCGA-AA-3685     TCGA-AA-3688 
"XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" 
    TCGA-AA-3692     TCGA-AA-3693     TCGA-AA-3695     TCGA-AA-3696 
"XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" 
    TCGA-AA-3697     TCGA-AA-3710     TCGA-AA-3712     TCGA-AA-3713 
"XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" 
    TCGA-AA-3715     TCGA-AA-3811     TCGA-AA-3812     TCGA-AA-3814 
"XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" 
    TCGA-AA-3815     TCGA-AA-3818     TCGA-AA-3819     TCGA-AA-3821 
"XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" 
    TCGA-AA-3831     TCGA-AA-3833     TCGA-AA-3837     TCGA-AA-3842 
"XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" 
    TCGA-AA-3844     TCGA-AA-3845     TCGA-AA-3846     TCGA-AA-3848 
"XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" 
    TCGA-AA-3850     TCGA-AA-3851     TCGA-AA-3852     TCGA-AA-3854 
"XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" 
    TCGA-AA-3855     TCGA-AA-3856     TCGA-AA-3858     TCGA-AA-3860 
"XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" 
    TCGA-AA-3861     TCGA-AA-3864     TCGA-AA-3866     TCGA-AA-3867 
"XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" 
    TCGA-AA-3869     TCGA-AA-3870     TCGA-AA-3872     TCGA-AA-3875 
"XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" 
    TCGA-AA-3877     TCGA-AA-3930     TCGA-AA-3939     TCGA-AA-3941 
"XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" 
    TCGA-AA-3947     TCGA-AA-3949     TCGA-AA-3950     TCGA-AA-3952 
"XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" 
    TCGA-AA-3955     TCGA-AA-3956     TCGA-AA-3968     TCGA-AA-3971 
"XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" 
    TCGA-AA-3972     TCGA-AA-3973     TCGA-AA-3975     TCGA-AA-3976 
"XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" 
    TCGA-AA-3979     TCGA-AA-3984     TCGA-AA-3986     TCGA-AA-3989 
"XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" 
    TCGA-AA-3994     TCGA-AA-A004     TCGA-AA-A00A     TCGA-AA-A00D 
"XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" 
    TCGA-AA-A00E     TCGA-AA-A00F     TCGA-AA-A00J     TCGA-AA-A00K 
"XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" 
    TCGA-AA-A00L     TCGA-AA-A00N     TCGA-AA-A00O     TCGA-AA-A00Q 
"XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" 
    TCGA-AA-A00R     TCGA-AA-A00U     TCGA-AA-A00W     TCGA-AA-A00Z 
"XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" 
    TCGA-AA-A010     TCGA-AA-A017     TCGA-AA-A01D     TCGA-AA-A01F 
"XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" 
    TCGA-AA-A01G     TCGA-AA-A01I     TCGA-AA-A01K     TCGA-AA-A01P 
"XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" 
    TCGA-AA-A01Q     TCGA-AA-A01R     TCGA-AA-A01S     TCGA-AA-A01T 
"XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" 
    TCGA-AA-A01V     TCGA-AA-A01X     TCGA-AA-A01Z     TCGA-AA-A022 
"XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" 
    TCGA-AA-A024     TCGA-AA-A029     TCGA-AA-A02F     TCGA-AA-A02H 
"XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" 
    TCGA-AA-A02J     TCGA-AA-A02K     TCGA-AA-A02O     TCGA-AA-A02W 
"XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" 
    TCGA-AA-A02Y     TCGA-AA-A03F     TCGA-AA-A03J     TCGA-AD-5900 
"XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" 
    TCGA-AD-6548     TCGA-AD-6888     TCGA-AU-3779     TCGA-AU-6004 
"XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" 
    TCGA-AY-4070     TCGA-AY-4071     TCGA-AY-5543     TCGA-AY-6196 
"XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" 
    TCGA-AY-6197     TCGA-AY-6386     TCGA-AZ-4315     TCGA-AZ-4681 
"XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" 
    TCGA-AZ-4682     TCGA-CA-5254     TCGA-CA-5255     TCGA-CA-5796 
"XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" 
    TCGA-CA-5797     TCGA-CA-6715     TCGA-CA-6716     TCGA-CA-6717 
"XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" 
    TCGA-CA-6718     TCGA-CA-6719     TCGA-CK-4947     TCGA-CK-4948 
"XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" 
    TCGA-CK-4950     TCGA-CK-4952     TCGA-CK-5912     TCGA-CK-5913 
"XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" 
    TCGA-CK-5914     TCGA-CK-5915     TCGA-CK-5916     TCGA-CK-6746 
"XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" 
    TCGA-CK-6747     TCGA-CK-6748     TCGA-CK-6751     TCGA-CM-4743 
"XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" 
    TCGA-CM-4744     TCGA-CM-4746     TCGA-CM-4747     TCGA-CM-4752 
"XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" 
    TCGA-CM-5341     TCGA-CM-5344     TCGA-CM-5348     TCGA-CM-5349 
"XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" 
    TCGA-CM-5860     TCGA-CM-5861     TCGA-CM-5862     TCGA-CM-5863 
"XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" 
    TCGA-CM-5864     TCGA-CM-5868     TCGA-CM-6161     TCGA-CM-6162 
"XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" 
    TCGA-CM-6163     TCGA-CM-6164     TCGA-CM-6165     TCGA-CM-6166 
"XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" 
    TCGA-CM-6167     TCGA-CM-6168     TCGA-CM-6169     TCGA-CM-6170 
"XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" 
    TCGA-CM-6171     TCGA-CM-6172     TCGA-CM-6674     TCGA-CM-6675 
"XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" 
    TCGA-CM-6676     TCGA-CM-6677     TCGA-CM-6678     TCGA-CM-6679 
"XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" 
    TCGA-CM-6680     TCGA-D5-5537     TCGA-D5-5539     TCGA-D5-5540 
"XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" 
    TCGA-D5-5541     TCGA-D5-6529     TCGA-D5-6532     TCGA-D5-6533 
"XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" 
    TCGA-D5-6534     TCGA-D5-6535     TCGA-D5-6536     TCGA-D5-6537 
"XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" 
    TCGA-D5-6538     TCGA-D5-6539     TCGA-D5-6540     TCGA-D5-6541 
"XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" 
    TCGA-D5-6898     TCGA-D5-6920     TCGA-D5-6922     TCGA-D5-6923 
"XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" 
    TCGA-D5-6924     TCGA-D5-6926     TCGA-D5-6927     TCGA-D5-6928 
"XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" 
    TCGA-D5-6929     TCGA-D5-6930     TCGA-D5-6931     TCGA-D5-6932 
"XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" 
    TCGA-D5-7000     TCGA-F4-6459     TCGA-F4-6460     TCGA-F4-6569 
"XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" 
    TCGA-F4-6570     TCGA-F4-6703     TCGA-F4-6704     TCGA-F4-6805 
"XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" 
    TCGA-F4-6806     TCGA-F4-6807     TCGA-F4-6808     TCGA-F4-6809 
"XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" 
    TCGA-F4-6854     TCGA-F4-6855     TCGA-F4-6856     TCGA-G4-6293 
"XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" 
    TCGA-G4-6299     TCGA-G4-6303     TCGA-G4-6304     TCGA-G4-6306 
"XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" 
    TCGA-G4-6307     TCGA-G4-6309     TCGA-G4-6310     TCGA-G4-6315 
"XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" 
    TCGA-G4-6317     TCGA-G4-6321     TCGA-G4-6323     TCGA-G4-6586 
"XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" 
    TCGA-G4-6588     TCGA-G4-6625     TCGA-G4-6626     TCGA-G4-6628 
"XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" 
    TCGA-AF-2687     TCGA-AF-2689     TCGA-AF-2691     TCGA-AF-2692 
"XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" 
    TCGA-AF-3400     TCGA-AF-3913     TCGA-AF-4110     TCGA-AF-5654 
"XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" 
    TCGA-AF-6655     TCGA-AG-3574     TCGA-AG-3575     TCGA-AG-3578 
"XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" 
    TCGA-AG-3580     TCGA-AG-3581     TCGA-AG-3582     TCGA-AG-3583 
"XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" 
    TCGA-AG-3584     TCGA-AG-3586     TCGA-AG-3587     TCGA-AG-3593 
"XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" 
    TCGA-AG-3594     TCGA-AG-3598     TCGA-AG-3599     TCGA-AG-3600 
"XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" 
    TCGA-AG-3601     TCGA-AG-3602     TCGA-AG-3605     TCGA-AG-3608 
"XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" 
    TCGA-AG-3609     TCGA-AG-3611     TCGA-AG-3612     TCGA-AG-3726 
"XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" 
    TCGA-AG-3727     TCGA-AG-3731     TCGA-AG-3732     TCGA-AG-3742 
"XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" 
    TCGA-AG-3878     TCGA-AG-3882     TCGA-AG-3883     TCGA-AG-3885 
"XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" 
    TCGA-AG-3887     TCGA-AG-3890     TCGA-AG-3892     TCGA-AG-3893 
"XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" 
    TCGA-AG-3894     TCGA-AG-3896     TCGA-AG-3898     TCGA-AG-3901 
"XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" 
    TCGA-AG-3902     TCGA-AG-3909     TCGA-AG-3999     TCGA-AG-4001 
"XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" 
    TCGA-AG-4005     TCGA-AG-4007     TCGA-AG-4008     TCGA-AG-4015 
"XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" 
    TCGA-AG-A002     TCGA-AG-A008     TCGA-AG-A00C     TCGA-AG-A00H 
"XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" 
    TCGA-AG-A00Y     TCGA-AG-A011     TCGA-AG-A014     TCGA-AG-A015 
"XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" 
    TCGA-AG-A016     TCGA-AG-A01L     TCGA-AG-A01W     TCGA-AG-A01Y 
"XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" 
    TCGA-AG-A020     TCGA-AG-A025     TCGA-AG-A026     TCGA-AG-A02G 
"XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" 
    TCGA-AG-A02N     TCGA-AG-A02X     TCGA-AG-A032     TCGA-AG-A036 
"XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" 
    TCGA-AH-6549     TCGA-AH-6643     TCGA-CL-5917     TCGA-CL-5918 
"XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" 
    TCGA-DC-5337     TCGA-DC-5869     TCGA-DC-6155     TCGA-DC-6157 
"XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" 
    TCGA-DC-6158     TCGA-DC-6160     TCGA-DC-6681     TCGA-DC-6682 
"XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" 
    TCGA-DC-6683     TCGA-DT-5265     TCGA-EF-5830     TCGA-EI-6506 
"XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" 
    TCGA-EI-6507     TCGA-EI-6508     TCGA-EI-6510     TCGA-F5-6464 
"XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" 
    TCGA-F5-6465     TCGA-F5-6571     TCGA-F5-6702     TCGA-F5-6812 
"XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" 
    TCGA-F5-6813     TCGA-G5-6235     TCGA-G5-6641 
"XCL2 WILD-TYPE" "XCL2 WILD-TYPE" "XCL2 WILD-TYPE" 
D1578V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  XCL2 MUTATED                                  0     1
  XCL2 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  XCL2 MUTATED                           0     3
  XCL2 WILD-TYPE                        22   223
D1578V13, multiclass
                                  clus
vv                                 XCL2 MUTATED XCL2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       3            223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1579) Variable = AASS MUTATION ANALYSIS
D1579V1, survival
                sevent
clus2              0   1
  AASS MUTATED    13   0
  AASS WILD-TYPE 365  93
  AASS MUTATED AASS WILD-TYPE 
            13            458 
  AASS MUTATED AASS WILD-TYPE 
             0             93 
$`AASS MUTATED`
TCGA-AA-3663 TCGA-AA-3819 TCGA-AA-3864 TCGA-AA-3947 TCGA-AA-3966 TCGA-AA-3977 
        6.97        25.02        53.00        33.01         2.01        25.02 
TCGA-AA-A010 TCGA-AU-6004 TCGA-DM-A28E TCGA-F4-6856 TCGA-AG-3599 TCGA-AG-A002 
       34.98        27.09       119.93        35.31        12.03        20.98 
TCGA-CI-6624 
        4.73 

$`AASS WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.05        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3821 TCGA-AA-3831 
       10.06        35.05        33.04         0.99         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 
        0.99        31.07        31.07        30.05        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 
       27.42        10.88         0.20        14.50        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28F TCGA-DM-A28G 
      135.65       139.17         6.12        81.37        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
       13.25         0.53        47.41       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
       34.03         2.01        50.04         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  AASS MUTATED AASS WILD-TYPE 
          2.01           0.00 
  AASS MUTATED AASS WILD-TYPE 
        119.93         148.01 
  AASS MUTATED AASS WILD-TYPE 
        25.020         20.035 
[1] "2.0 - 119.9 (25.0)" "0.0 - 148.0 (20.0)"
[1] "hr="     "2.5e+07"
D1579V2, continuous
D1579V3, binary
                cls
clus               0   1
  AASS MUTATED    10   3
  AASS WILD-TYPE 356 116
[1] "tbl2"
                cls
clus             [,1] [,2]
  AASS MUTATED     10    3
  AASS WILD-TYPE  356  116
        clus
vv       AASS MUTATED AASS WILD-TYPE
  COLON            10            356
  RECTUM            3            116
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  AASS MUTATED         5        0        2         3         2         0
  AASS WILD-TYPE      86        1       30       135         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AASS MUTATED           0          0          0          0        0         0
  AASS WILD-TYPE        24         11         59         42       48        18
                vv
clus             STAGE IVB
  AASS MUTATED           0
  AASS WILD-TYPE         1
D1579V4, multiclass
            clus
vv           AASS MUTATED AASS WILD-TYPE
  STAGE I               5             86
  STAGE IA              0              1
  STAGE II              2             30
  STAGE IIA             3            135
  STAGE IIB             2              8
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            0             59
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  AASS MUTATED     0   6   5   2
  AASS WILD-TYPE  17  86 324  48
D1579V5, multiclass
    clus
vv   AASS MUTATED AASS WILD-TYPE
  T1            0             17
  T2            6             86
  T3            5            324
  T4            2             48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  AASS MUTATED    13   0   0
  AASS WILD-TYPE 274 113  87
D1579V6, multiclass
    clus
vv   AASS MUTATED AASS WILD-TYPE
  N0           13            274
  N1            0            113
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1579V7, binary
                cls
clus               0   1
  AASS MUTATED    12   0
  AASS WILD-TYPE 363  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  AASS MUTATED     12    0
  AASS WILD-TYPE  363   65
   clus
vv  AASS MUTATED AASS WILD-TYPE
  0           12            363
  1            0             65
[1] 2 2
[1] FALSE
D1579V8, binary
                cls
clus               0   1
  AASS MUTATED     7   6
  AASS WILD-TYPE 218 258
[1] "tbl2"
                cls
clus             [,1] [,2]
  AASS MUTATED      7    6
  AASS WILD-TYPE  218  258
        clus
vv       AASS MUTATED AASS WILD-TYPE
  FEMALE            7            218
  MALE              6            258
[1] 2 2
[1] FALSE
D1579V9, binary
                cls
clus               0   1
  AASS MUTATED     9   0
  AASS WILD-TYPE 341  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  AASS MUTATED      9    0
  AASS WILD-TYPE  341   22
     clus
vv    AASS MUTATED AASS WILD-TYPE
  NO             9            341
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  AASS MUTATED                      7                             3
  AASS WILD-TYPE                  308                            44
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  AASS MUTATED                       2                              0
  AASS WILD-TYPE                   104                             10
D1579V10, multiclass
                                clus
vv                               AASS MUTATED AASS WILD-TYPE
  COLON ADENOCARCINOMA                      7            308
  COLON MUCINOUS ADENOCARCINOMA             3             44
  RECTAL ADENOCARCINOMA                     2            104
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  AASS MUTATED     9   0   0   0
  AASS WILD-TYPE 336   4  31  25
D1579V11, multiclass
    clus
vv   AASS MUTATED AASS WILD-TYPE
  R0            9            336
  R1            0              4
  R2            0             31
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1579V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AASS MUTATED                                  0     0
  AASS WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  AASS MUTATED                           0     4
  AASS WILD-TYPE                        22   222
D1579V13, multiclass
                                  clus
vv                                 AASS MUTATED AASS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       4            222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1580) Variable = CCNH MUTATION ANALYSIS
D1580V1, survival
                sevent
clus2              0   1
  CCNH MUTATED     6   1
  CCNH WILD-TYPE 372  92
  CCNH MUTATED CCNH WILD-TYPE 
             7            464 
  CCNH MUTATED CCNH WILD-TYPE 
             1             92 
$`CCNH MUTATED`
TCGA-AA-3977 TCGA-AA-A00R TCGA-CM-6168 TCGA-D5-6536 TCGA-F4-6569 TCGA-G4-6626 
       25.02         0.99        12.99        17.85        35.74        46.75 
TCGA-G4-6628 
       79.69 

$`CCNH WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W 
       38.04         4.01        27.02        42.02        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       14.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 
       18.25         1.32        43.27        15.12         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
       98.24         8.61        31.96         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-AF-2687 
       22.09        13.78        35.80        26.17        91.79        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  CCNH MUTATED CCNH WILD-TYPE 
          0.99           0.00 
  CCNH MUTATED CCNH WILD-TYPE 
         79.69         148.01 
  CCNH MUTATED CCNH WILD-TYPE 
        25.020         20.155 
[1] "1.0 - 79.7 (25.0)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.6"
D1580V2, continuous
D1580V3, binary
                cls
clus               0   1
  CCNH MUTATED     7   0
  CCNH WILD-TYPE 359 119
[1] "tbl2"
                cls
clus             [,1] [,2]
  CCNH MUTATED      7    0
  CCNH WILD-TYPE  359  119
        clus
vv       CCNH MUTATED CCNH WILD-TYPE
  COLON             7            359
  RECTUM            0            119
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CCNH MUTATED         3        0        0         3         0         0
  CCNH WILD-TYPE      88        1       32       135        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CCNH MUTATED           0          0          0          0        0         0
  CCNH WILD-TYPE        24         11         59         42       48        18
                vv
clus             STAGE IVB
  CCNH MUTATED           0
  CCNH WILD-TYPE         1
D1580V4, multiclass
            clus
vv           CCNH MUTATED CCNH WILD-TYPE
  STAGE I               3             88
  STAGE IA              0              1
  STAGE II              0             32
  STAGE IIA             3            135
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            0             59
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  CCNH MUTATED     0   4   3   0
  CCNH WILD-TYPE  17  88 326  50
D1580V5, multiclass
    clus
vv   CCNH MUTATED CCNH WILD-TYPE
  T1            0             17
  T2            4             88
  T3            3            326
  T4            0             50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  CCNH MUTATED     7   0   0
  CCNH WILD-TYPE 280 113  87
D1580V6, multiclass
    clus
vv   CCNH MUTATED CCNH WILD-TYPE
  N0            7            280
  N1            0            113
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1580V7, binary
                cls
clus               0   1
  CCNH MUTATED     6   0
  CCNH WILD-TYPE 369  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  CCNH MUTATED      6    0
  CCNH WILD-TYPE  369   65
   clus
vv  CCNH MUTATED CCNH WILD-TYPE
  0            6            369
  1            0             65
[1] 2 2
[1] FALSE
D1580V8, binary
                cls
clus               0   1
  CCNH MUTATED     2   5
  CCNH WILD-TYPE 223 259
[1] "tbl2"
                cls
clus             [,1] [,2]
  CCNH MUTATED      2    5
  CCNH WILD-TYPE  223  259
        clus
vv       CCNH MUTATED CCNH WILD-TYPE
  FEMALE            2            223
  MALE              5            259
[1] 2 2
[1] FALSE
D1580V9, binary
                cls
clus               0   1
  CCNH MUTATED     6   0
  CCNH WILD-TYPE 344  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  CCNH MUTATED      6    0
  CCNH WILD-TYPE  344   22
     clus
vv    CCNH MUTATED CCNH WILD-TYPE
  NO             6            344
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CCNH MUTATED                      7                             0
  CCNH WILD-TYPE                  308                            47
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CCNH MUTATED                       0                              0
  CCNH WILD-TYPE                   106                             10
D1580V10, multiclass
                                clus
vv                               CCNH MUTATED CCNH WILD-TYPE
  COLON ADENOCARCINOMA                      7            308
  COLON MUCINOUS ADENOCARCINOMA             0             47
  RECTAL ADENOCARCINOMA                     0            106
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  CCNH MUTATED     6   0   0   0
  CCNH WILD-TYPE 339   4  31  25
D1580V11, multiclass
    clus
vv   CCNH MUTATED CCNH WILD-TYPE
  R0            6            339
  R1            0              4
  R2            0             31
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1580V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CCNH MUTATED                                  0     0
  CCNH WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  CCNH MUTATED                           1     4
  CCNH WILD-TYPE                        21   222
D1580V13, multiclass
                                  clus
vv                                 CCNH MUTATED CCNH WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                       4            222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1581) Variable = ITGA4 MUTATION ANALYSIS
D1581V1, survival
                 sevent
clus2               0   1
  ITGA4 MUTATED    10   7
  ITGA4 WILD-TYPE 368  86
  ITGA4 MUTATED ITGA4 WILD-TYPE 
             17             454 
  ITGA4 MUTATED ITGA4 WILD-TYPE 
              7              86 
$`ITGA4 MUTATED`
TCGA-AA-3662 TCGA-AA-3818 TCGA-AA-3950 TCGA-AA-A010 TCGA-AD-6889 TCGA-AZ-6598 
        6.05         0.99        24.00        34.98        56.55        49.41 
TCGA-AZ-6601 TCGA-CA-5796 TCGA-CA-6718 TCGA-CK-5913 TCGA-CK-5916 TCGA-CM-5341 
      100.01         3.25        10.06        51.32        21.14        29.06 
TCGA-G4-6303 TCGA-AG-3892 TCGA-AG-4005 TCGA-AG-A002 TCGA-DY-A1DD 
       65.85        13.02        14.04        20.98        57.24 

$`ITGA4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       10.06        35.05        33.04        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 
       12.99        24.00        33.01        26.01         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 
       40.96         0.07        21.37        15.52         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       88.21         6.77        12.10        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5797 TCGA-CA-6715 
        3.19         1.61        12.69         3.06         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.20        12.76        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       15.62        49.08         9.99        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5344 
       23.05        20.02        37.02        25.02        13.02        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
       35.31       133.18        74.56        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       17.03        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       19.99        28.04        36.03         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DF 
        4.01         5.03         5.29       126.44        41.36        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  ITGA4 MUTATED ITGA4 WILD-TYPE 
           0.99            0.00 
  ITGA4 MUTATED ITGA4 WILD-TYPE 
         100.01          148.01 
  ITGA4 MUTATED ITGA4 WILD-TYPE 
         24.000          20.035 
[1] "1.0 - 100.0 (24.0)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.6"
D1581V2, continuous
D1581V3, binary
                 cls
clus                0   1
  ITGA4 MUTATED    13   4
  ITGA4 WILD-TYPE 353 115
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITGA4 MUTATED     13    4
  ITGA4 WILD-TYPE  353  115
        clus
vv       ITGA4 MUTATED ITGA4 WILD-TYPE
  COLON             13             353
  RECTUM             4             115
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ITGA4 MUTATED         3        0        2         6         1         0
  ITGA4 WILD-TYPE      88        1       30       132         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ITGA4 MUTATED           0          1          1          0        3         0
  ITGA4 WILD-TYPE        24         10         58         42       45        18
                 vv
clus              STAGE IVB
  ITGA4 MUTATED           0
  ITGA4 WILD-TYPE         1
D1581V4, multiclass
            clus
vv           ITGA4 MUTATED ITGA4 WILD-TYPE
  STAGE I                3              88
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA              6             132
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             1              10
  STAGE IIIB             1              58
  STAGE IIIC             0              42
  STAGE IV               3              45
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ITGA4 MUTATED     2   2  11   2
  ITGA4 WILD-TYPE  15  90 318  48
D1581V5, multiclass
    clus
vv   ITGA4 MUTATED ITGA4 WILD-TYPE
  T1             2              15
  T2             2              90
  T3            11             318
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  ITGA4 MUTATED    12   3   2
  ITGA4 WILD-TYPE 275 110  85
D1581V6, multiclass
    clus
vv   ITGA4 MUTATED ITGA4 WILD-TYPE
  N0            12             275
  N1             3             110
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1581V7, binary
                 cls
clus                0   1
  ITGA4 MUTATED    12   3
  ITGA4 WILD-TYPE 363  62
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITGA4 MUTATED     12    3
  ITGA4 WILD-TYPE  363   62
   clus
vv  ITGA4 MUTATED ITGA4 WILD-TYPE
  0            12             363
  1             3              62
[1] 2 2
[1] FALSE
D1581V8, binary
                 cls
clus                0   1
  ITGA4 MUTATED    12   5
  ITGA4 WILD-TYPE 213 259
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITGA4 MUTATED     12    5
  ITGA4 WILD-TYPE  213  259
        clus
vv       ITGA4 MUTATED ITGA4 WILD-TYPE
  FEMALE            12             213
  MALE               5             259
[1] 2 2
[1] FALSE
D1581V9, binary
                 cls
clus                0   1
  ITGA4 MUTATED    14   0
  ITGA4 WILD-TYPE 336  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITGA4 MUTATED     14    0
  ITGA4 WILD-TYPE  336   22
     clus
vv    ITGA4 MUTATED ITGA4 WILD-TYPE
  NO             14             336
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ITGA4 MUTATED                     11                             2
  ITGA4 WILD-TYPE                  304                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ITGA4 MUTATED                       4                              0
  ITGA4 WILD-TYPE                   102                             10
D1581V10, multiclass
                                clus
vv                               ITGA4 MUTATED ITGA4 WILD-TYPE
  COLON ADENOCARCINOMA                      11             304
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      4             102
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  ITGA4 MUTATED     9   0   1   3
  ITGA4 WILD-TYPE 336   4  30  22
D1581V11, multiclass
    clus
vv   ITGA4 MUTATED ITGA4 WILD-TYPE
  R0             9             336
  R1             0               4
  R2             1              30
  RX             3              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1581V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ITGA4 MUTATED                                  0     3
  ITGA4 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ITGA4 MUTATED                           0     7
  ITGA4 WILD-TYPE                        22   219
D1581V13, multiclass
                                  clus
vv                                 ITGA4 MUTATED ITGA4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        3               8
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        7             219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1582) Variable = ST18 MUTATION ANALYSIS
D1582V1, survival
                sevent
clus2              0   1
  ST18 MUTATED    21   4
  ST18 WILD-TYPE 357  89
  ST18 MUTATED ST18 WILD-TYPE 
            25            446 
  ST18 MUTATED ST18 WILD-TYPE 
             4             89 
$`ST18 MUTATED`
TCGA-AA-3510 TCGA-AA-A00N TCGA-AA-A00R TCGA-AA-A010 TCGA-AD-6895 TCGA-AU-6004 
       63.98         4.01         0.99        34.98         0.72        27.09 
TCGA-AY-6197 TCGA-AZ-6600 TCGA-CA-6716 TCGA-CA-6718 TCGA-CK-4952 TCGA-D5-6539 
       21.44        12.10        12.20        10.06        15.62        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6932 TCGA-DM-A1HB TCGA-F4-6809 TCGA-G4-6293 
       16.14        15.58        11.38       135.65        13.25       133.18 
TCGA-G4-6307 TCGA-G4-6321 TCGA-G4-6586 TCGA-AG-3896 TCGA-AG-A002 TCGA-AG-A02N 
       55.04        22.09        35.80         1.02        20.98        61.97 
TCGA-AH-6547 
        1.45 

$`ST18 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       38.04        27.02        42.02        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       16.31         0.95        33.01        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 
       12.76        14.30        17.56       148.01        85.45        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6898 
       43.27        15.12        17.85         4.80        17.13         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 
       11.64         4.80         1.51        12.00        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 
       12.59       140.38         7.50        44.32       131.51       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6854 
        1.55        34.42        41.42        16.24        33.67         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       47.41        35.31        74.56        65.85        53.62        44.68 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6588 
       85.48        63.62        61.91        36.00        13.78        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       35.01        14.01        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6549 
       38.96        41.00        38.04       117.11        38.56        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  ST18 MUTATED ST18 WILD-TYPE 
          0.72           0.00 
  ST18 MUTATED ST18 WILD-TYPE 
        135.65         148.01 
  ST18 MUTATED ST18 WILD-TYPE 
        15.620         20.415 
[1] "0.7 - 135.7 (15.6)" "0.0 - 148.0 (20.4)"
[1] "hr=" "1.3"
D1582V2, continuous
D1582V3, binary
                cls
clus               0   1
  ST18 MUTATED    23   4
  ST18 WILD-TYPE 343 115
[1] "tbl2"
                cls
clus             [,1] [,2]
  ST18 MUTATED     23    4
  ST18 WILD-TYPE  343  115
        clus
vv       ST18 MUTATED ST18 WILD-TYPE
  COLON            23            343
  RECTUM            4            115
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ST18 MUTATED         5        0        2         7         2         0
  ST18 WILD-TYPE      86        1       30       131         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ST18 MUTATED           2          1          2          2        1         1
  ST18 WILD-TYPE        22         10         57         40       47        17
                vv
clus             STAGE IVB
  ST18 MUTATED           0
  ST18 WILD-TYPE         1
D1582V4, multiclass
            clus
vv           ST18 MUTATED ST18 WILD-TYPE
  STAGE I               5             86
  STAGE IA              0              1
  STAGE II              2             30
  STAGE IIA             7            131
  STAGE IIB             2              8
  STAGE IIC             0              1
  STAGE III             2             22
  STAGE IIIA            1             10
  STAGE IIIB            2             57
  STAGE IIIC            2             40
  STAGE IV              1             47
  STAGE IVA             1             17
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  ST18 MUTATED     0   6  17   4
  ST18 WILD-TYPE  17  86 312  46
D1582V5, multiclass
    clus
vv   ST18 MUTATED ST18 WILD-TYPE
  T1            0             17
  T2            6             86
  T3           17            312
  T4            4             46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  ST18 MUTATED    18   7   2
  ST18 WILD-TYPE 269 106  85
D1582V6, multiclass
    clus
vv   ST18 MUTATED ST18 WILD-TYPE
  N0           18            269
  N1            7            106
  N2            2             85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1582V7, binary
                cls
clus               0   1
  ST18 MUTATED    20   2
  ST18 WILD-TYPE 355  63
[1] "tbl2"
                cls
clus             [,1] [,2]
  ST18 MUTATED     20    2
  ST18 WILD-TYPE  355   63
   clus
vv  ST18 MUTATED ST18 WILD-TYPE
  0           20            355
  1            2             63
[1] 2 2
[1] FALSE
D1582V8, binary
                cls
clus               0   1
  ST18 MUTATED    13  14
  ST18 WILD-TYPE 212 250
[1] "tbl2"
                cls
clus             [,1] [,2]
  ST18 MUTATED     13   14
  ST18 WILD-TYPE  212  250
        clus
vv       ST18 MUTATED ST18 WILD-TYPE
  FEMALE           13            212
  MALE             14            250
[1] 2 2
[1] FALSE
D1582V9, binary
                cls
clus               0   1
  ST18 MUTATED    15   0
  ST18 WILD-TYPE 335  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  ST18 MUTATED     15    0
  ST18 WILD-TYPE  335   22
     clus
vv    ST18 MUTATED ST18 WILD-TYPE
  NO            15            335
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ST18 MUTATED                     18                             4
  ST18 WILD-TYPE                  297                            43
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ST18 MUTATED                       4                              0
  ST18 WILD-TYPE                   102                             10
D1582V10, multiclass
                                clus
vv                               ST18 MUTATED ST18 WILD-TYPE
  COLON ADENOCARCINOMA                     18            297
  COLON MUCINOUS ADENOCARCINOMA             4             43
  RECTAL ADENOCARCINOMA                     4            102
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  ST18 MUTATED    20   0   0   3
  ST18 WILD-TYPE 325   4  31  22
D1582V11, multiclass
    clus
vv   ST18 MUTATED ST18 WILD-TYPE
  R0           20            325
  R1            0              4
  R2            0             31
  RX            3             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1582V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ST18 MUTATED                                  0     2
  ST18 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  ST18 MUTATED                           1    16
  ST18 WILD-TYPE                        21   210
D1582V13, multiclass
                                  clus
vv                                 ST18 MUTATED ST18 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              9
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                      16            210
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1583) Variable = SECISBP2 MUTATION ANALYSIS
D1583V1, survival
                    sevent
clus2                  0   1
  SECISBP2 MUTATED     7   1
  SECISBP2 WILD-TYPE 371  92
  SECISBP2 MUTATED SECISBP2 WILD-TYPE 
                 8                463 
  SECISBP2 MUTATED SECISBP2 WILD-TYPE 
                 1                 92 
$`SECISBP2 MUTATED`
TCGA-A6-2678 TCGA-A6-6648 TCGA-AA-A01R TCGA-AZ-6605 TCGA-CA-6717 TCGA-DM-A28H 
       42.28        25.18        35.01         5.23        12.76       117.07 
TCGA-G4-6588 TCGA-DC-6157 
       26.17        27.95 

$`SECISBP2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2683 
       43.76        46.65        43.76        42.90        24.33        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T 
       31.00        31.00        38.07         1.02         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
      100.01        29.56        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07        12.20        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28K TCGA-F4-6459 
       81.37       119.93        35.97        60.79        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       13.78        35.80        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6158 
       78.12         7.17        15.02         5.03        13.97        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  SECISBP2 MUTATED SECISBP2 WILD-TYPE 
              5.23               0.00 
  SECISBP2 MUTATED SECISBP2 WILD-TYPE 
            117.07             148.01 
  SECISBP2 MUTATED SECISBP2 WILD-TYPE 
             27.06              20.05 
[1] "5.2 - 117.1 (27.1)" "0.0 - 148.0 (20.1)"
[1] "hr=" "2"  
D1583V2, continuous
D1583V3, binary
                    cls
clus                   0   1
  SECISBP2 MUTATED     7   1
  SECISBP2 WILD-TYPE 359 118
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SECISBP2 MUTATED      7    1
  SECISBP2 WILD-TYPE  359  118
        clus
vv       SECISBP2 MUTATED SECISBP2 WILD-TYPE
  COLON                 7                359
  RECTUM                1                118
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SECISBP2 MUTATED         1        0        0         2         0         0
  SECISBP2 WILD-TYPE      90        1       32       136        10         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SECISBP2 MUTATED           1          0          2          1        0
  SECISBP2 WILD-TYPE        23         11         57         41       48
                    vv
clus                 STAGE IVA STAGE IVB
  SECISBP2 MUTATED           1         0
  SECISBP2 WILD-TYPE        17         1
D1583V4, multiclass
            clus
vv           SECISBP2 MUTATED SECISBP2 WILD-TYPE
  STAGE I                   1                 90
  STAGE IA                  0                  1
  STAGE II                  0                 32
  STAGE IIA                 2                136
  STAGE IIB                 0                 10
  STAGE IIC                 0                  1
  STAGE III                 1                 23
  STAGE IIIA                0                 11
  STAGE IIIB                2                 57
  STAGE IIIC                1                 41
  STAGE IV                  0                 48
  STAGE IVA                 1                 17
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  SECISBP2 MUTATED     0   1   6   1
  SECISBP2 WILD-TYPE  17  91 323  49
D1583V5, multiclass
    clus
vv   SECISBP2 MUTATED SECISBP2 WILD-TYPE
  T1                0                 17
  T2                1                 91
  T3                6                323
  T4                1                 49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  SECISBP2 MUTATED     4   2   2
  SECISBP2 WILD-TYPE 283 111  85
D1583V6, multiclass
    clus
vv   SECISBP2 MUTATED SECISBP2 WILD-TYPE
  N0                4                283
  N1                2                111
  N2                2                 85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1583V7, binary
                    cls
clus                   0   1
  SECISBP2 MUTATED     7   1
  SECISBP2 WILD-TYPE 368  64
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SECISBP2 MUTATED      7    1
  SECISBP2 WILD-TYPE  368   64
   clus
vv  SECISBP2 MUTATED SECISBP2 WILD-TYPE
  0                7                368
  1                1                 64
[1] 2 2
[1] FALSE
D1583V8, binary
                    cls
clus                   0   1
  SECISBP2 MUTATED     2   6
  SECISBP2 WILD-TYPE 223 258
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SECISBP2 MUTATED      2    6
  SECISBP2 WILD-TYPE  223  258
        clus
vv       SECISBP2 MUTATED SECISBP2 WILD-TYPE
  FEMALE                2                223
  MALE                  6                258
[1] 2 2
[1] FALSE
D1583V9, binary
                    cls
clus                   0   1
  SECISBP2 MUTATED     5   1
  SECISBP2 WILD-TYPE 345  21
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SECISBP2 MUTATED      5    1
  SECISBP2 WILD-TYPE  345   21
     clus
vv    SECISBP2 MUTATED SECISBP2 WILD-TYPE
  NO                 5                345
  YES                1                 21
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SECISBP2 MUTATED                      5                             2
  SECISBP2 WILD-TYPE                  310                            45
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SECISBP2 MUTATED                       1                              0
  SECISBP2 WILD-TYPE                   105                             10
D1583V10, multiclass
                                clus
vv                               SECISBP2 MUTATED SECISBP2 WILD-TYPE
  COLON ADENOCARCINOMA                          5                310
  COLON MUCINOUS ADENOCARCINOMA                 2                 45
  RECTAL ADENOCARCINOMA                         1                105
  RECTAL MUCINOUS ADENOCARCINOMA                0                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  SECISBP2 MUTATED     4   0   0   1
  SECISBP2 WILD-TYPE 341   4  31  24
D1583V11, multiclass
    clus
vv   SECISBP2 MUTATED SECISBP2 WILD-TYPE
  R0                4                341
  R1                0                  4
  R2                0                 31
  RX                1                 24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1583V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SECISBP2 MUTATED                                  0     1
  SECISBP2 WILD-TYPE                                1    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  SECISBP2 MUTATED                           1     5
  SECISBP2 WILD-TYPE                        21   221
D1583V13, multiclass
                                  clus
vv                                 SECISBP2 MUTATED SECISBP2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                 10
  BLACK OR AFRICAN AMERICAN                       1                 21
  WHITE                                           5                221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1584) Variable = GPX8 MUTATION ANALYSIS
D1584V1, survival
                sevent
clus2              0   1
  GPX8 MUTATED     3   0
  GPX8 WILD-TYPE 375  93
  GPX8 MUTATED GPX8 WILD-TYPE 
             3            468 
  GPX8 MUTATED GPX8 WILD-TYPE 
             0             93 
$`GPX8 MUTATED`
TCGA-AA-3510 TCGA-AZ-4315 TCGA-AG-A002 
       63.98        58.39        20.98 

$`GPX8 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        33.01        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  GPX8 MUTATED GPX8 WILD-TYPE 
         20.98           0.00 
  GPX8 MUTATED GPX8 WILD-TYPE 
         63.98         148.01 
  GPX8 MUTATED GPX8 WILD-TYPE 
        58.390         20.085 
[1] "21.0 - 64.0 (58.4)" "0.0 - 148.0 (20.1)"
[1] "hr="     "9200000"
D1584V2, continuous
D1584V3, binary
                cls
clus               0   1
  GPX8 MUTATED     2   1
  GPX8 WILD-TYPE 364 118
[1] "tbl2"
                cls
clus             [,1] [,2]
  GPX8 MUTATED      2    1
  GPX8 WILD-TYPE  364  118
        clus
vv       GPX8 MUTATED GPX8 WILD-TYPE
  COLON             2            364
  RECTUM            1            118
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GPX8 MUTATED         1        0        1         1         0         0
  GPX8 WILD-TYPE      90        1       31       137        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  GPX8 MUTATED           0          0          0          0        0         0
  GPX8 WILD-TYPE        24         11         59         42       48        18
                vv
clus             STAGE IVB
  GPX8 MUTATED           0
  GPX8 WILD-TYPE         1
D1584V4, multiclass
            clus
vv           GPX8 MUTATED GPX8 WILD-TYPE
  STAGE I               1             90
  STAGE IA              0              1
  STAGE II              1             31
  STAGE IIA             1            137
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            0             59
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  GPX8 MUTATED     0   1   2   0
  GPX8 WILD-TYPE  17  91 327  50
D1584V5, multiclass
    clus
vv   GPX8 MUTATED GPX8 WILD-TYPE
  T1            0             17
  T2            1             91
  T3            2            327
  T4            0             50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  GPX8 MUTATED     3   0   0
  GPX8 WILD-TYPE 284 113  87
D1584V6, multiclass
    clus
vv   GPX8 MUTATED GPX8 WILD-TYPE
  N0            3            284
  N1            0            113
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1584V7, binary
                cls
clus               0   1
  GPX8 MUTATED     3   0
  GPX8 WILD-TYPE 372  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  GPX8 MUTATED      3    0
  GPX8 WILD-TYPE  372   65
   clus
vv  GPX8 MUTATED GPX8 WILD-TYPE
  0            3            372
  1            0             65
[1] 2 2
[1] FALSE
D1584V8, binary
                cls
clus               0   1
  GPX8 MUTATED     0   3
  GPX8 WILD-TYPE 225 261
[1] "tbl2"
                cls
clus             [,1] [,2]
  GPX8 MUTATED      0    3
  GPX8 WILD-TYPE  225  261
        clus
vv       GPX8 MUTATED GPX8 WILD-TYPE
  FEMALE            0            225
  MALE              3            261
[1] 2 2
[1] FALSE
D1584V9, binary
                cls
clus               0   1
  GPX8 MUTATED     3   0
  GPX8 WILD-TYPE 347  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  GPX8 MUTATED      3    0
  GPX8 WILD-TYPE  347   22
     clus
vv    GPX8 MUTATED GPX8 WILD-TYPE
  NO             3            347
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  GPX8 MUTATED                      2                             0
  GPX8 WILD-TYPE                  313                            47
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  GPX8 MUTATED                       1                              0
  GPX8 WILD-TYPE                   105                             10
D1584V10, multiclass
                                clus
vv                               GPX8 MUTATED GPX8 WILD-TYPE
  COLON ADENOCARCINOMA                      2            313
  COLON MUCINOUS ADENOCARCINOMA             0             47
  RECTAL ADENOCARCINOMA                     1            105
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  GPX8 MUTATED     3   0   0   0
  GPX8 WILD-TYPE 342   4  31  25
D1584V11, multiclass
    clus
vv   GPX8 MUTATED GPX8 WILD-TYPE
  R0            3            342
  R1            0              4
  R2            0             31
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1584V12, continuous
[1] "Remove cluster labels:" "GPX8 MUTATED"          
clus
  GPX8 MUTATED GPX8 WILD-TYPE 
             2            456 
    TCGA-A6-2671     TCGA-A6-2672     TCGA-A6-2674     TCGA-A6-2676 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-A6-2677     TCGA-A6-2678     TCGA-A6-2683     TCGA-A6-3807 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-A6-3808     TCGA-A6-3809     TCGA-A6-3810     TCGA-A6-4105 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-A6-5656     TCGA-A6-5657     TCGA-A6-5659     TCGA-A6-5660 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-A6-5661     TCGA-A6-5662     TCGA-A6-5664     TCGA-A6-5665 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-A6-5666     TCGA-A6-6137     TCGA-A6-6138     TCGA-A6-6141 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-A6-6142     TCGA-A6-6648     TCGA-A6-6649     TCGA-A6-6651 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-A6-6652     TCGA-A6-6653     TCGA-A6-6654     TCGA-A6-6780 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-A6-6781     TCGA-A6-6782     TCGA-AA-3489     TCGA-AA-3492 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-AA-3496     TCGA-AA-3502     TCGA-AA-3511     TCGA-AA-3514 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-AA-3516     TCGA-AA-3517     TCGA-AA-3518     TCGA-AA-3519 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-AA-3520     TCGA-AA-3521     TCGA-AA-3522     TCGA-AA-3524 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-AA-3525     TCGA-AA-3526     TCGA-AA-3527     TCGA-AA-3529 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-AA-3530     TCGA-AA-3531     TCGA-AA-3532     TCGA-AA-3534 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-AA-3538     TCGA-AA-3542     TCGA-AA-3543     TCGA-AA-3544 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-AA-3548     TCGA-AA-3549     TCGA-AA-3552     TCGA-AA-3553 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-AA-3554     TCGA-AA-3555     TCGA-AA-3556     TCGA-AA-3558 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-AA-3560     TCGA-AA-3562     TCGA-AA-3655     TCGA-AA-3660 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-AA-3662     TCGA-AA-3663     TCGA-AA-3664     TCGA-AA-3666 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-AA-3667     TCGA-AA-3672     TCGA-AA-3673     TCGA-AA-3678 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-AA-3679     TCGA-AA-3680     TCGA-AA-3681     TCGA-AA-3684 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-AA-3685     TCGA-AA-3688     TCGA-AA-3692     TCGA-AA-3693 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-AA-3695     TCGA-AA-3696     TCGA-AA-3697     TCGA-AA-3710 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-AA-3712     TCGA-AA-3713     TCGA-AA-3715     TCGA-AA-3811 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-AA-3812     TCGA-AA-3814     TCGA-AA-3815     TCGA-AA-3818 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-AA-3819     TCGA-AA-3821     TCGA-AA-3831     TCGA-AA-3833 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-AA-3837     TCGA-AA-3842     TCGA-AA-3844     TCGA-AA-3845 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-AA-3846     TCGA-AA-3848     TCGA-AA-3850     TCGA-AA-3851 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-AA-3852     TCGA-AA-3854     TCGA-AA-3855     TCGA-AA-3856 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-AA-3858     TCGA-AA-3860     TCGA-AA-3861     TCGA-AA-3864 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-AA-3866     TCGA-AA-3867     TCGA-AA-3869     TCGA-AA-3870 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-AA-3872     TCGA-AA-3875     TCGA-AA-3877     TCGA-AA-3930 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-AA-3939     TCGA-AA-3941     TCGA-AA-3947     TCGA-AA-3949 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-AA-3950     TCGA-AA-3952     TCGA-AA-3955     TCGA-AA-3956 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-AA-3966     TCGA-AA-3968     TCGA-AA-3971     TCGA-AA-3972 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-AA-3973     TCGA-AA-3975     TCGA-AA-3976     TCGA-AA-3977 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-AA-3979     TCGA-AA-3980     TCGA-AA-3982     TCGA-AA-3984 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-AA-3986     TCGA-AA-3989     TCGA-AA-3994     TCGA-AA-A004 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-AA-A00A     TCGA-AA-A00D     TCGA-AA-A00E     TCGA-AA-A00F 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-AA-A00J     TCGA-AA-A00K     TCGA-AA-A00L     TCGA-AA-A00N 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-AA-A00O     TCGA-AA-A00Q     TCGA-AA-A00R     TCGA-AA-A00U 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-AA-A00W     TCGA-AA-A00Z     TCGA-AA-A010     TCGA-AA-A017 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-AA-A01D     TCGA-AA-A01F     TCGA-AA-A01G     TCGA-AA-A01I 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-AA-A01K     TCGA-AA-A01P     TCGA-AA-A01Q     TCGA-AA-A01R 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-AA-A01S     TCGA-AA-A01T     TCGA-AA-A01V     TCGA-AA-A01X 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-AA-A01Z     TCGA-AA-A022     TCGA-AA-A024     TCGA-AA-A029 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-AA-A02F     TCGA-AA-A02H     TCGA-AA-A02J     TCGA-AA-A02K 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-AA-A02O     TCGA-AA-A02W     TCGA-AA-A02Y     TCGA-AA-A03F 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-AA-A03J     TCGA-AD-5900     TCGA-AD-6548     TCGA-AD-6888 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-AD-6889     TCGA-AD-6890     TCGA-AD-6895     TCGA-AD-6899 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-AD-6901     TCGA-AD-6963     TCGA-AD-6964     TCGA-AD-6965 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-AU-3779     TCGA-AU-6004     TCGA-AY-4070     TCGA-AY-4071 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-AY-5543     TCGA-AY-6196     TCGA-AY-6197     TCGA-AY-6386 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-AZ-4323     TCGA-AZ-4616     TCGA-AZ-4682     TCGA-AZ-5403 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-AZ-5407     TCGA-AZ-6598     TCGA-AZ-6599     TCGA-AZ-6600 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-AZ-6601     TCGA-AZ-6603     TCGA-AZ-6605     TCGA-AZ-6606 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-AZ-6607     TCGA-AZ-6608     TCGA-CK-4947     TCGA-CK-4948 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-CK-4950     TCGA-CK-4952     TCGA-CM-4743     TCGA-CM-4744 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-CM-4746     TCGA-CM-4747     TCGA-CM-4752     TCGA-CM-5341 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-CM-5344     TCGA-CM-5348     TCGA-CM-5349     TCGA-CM-5860 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-CM-5861     TCGA-CM-5862     TCGA-CM-5863     TCGA-CM-5864 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-CM-5868     TCGA-CM-6161     TCGA-CM-6162     TCGA-CM-6163 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-CM-6164     TCGA-CM-6165     TCGA-CM-6166     TCGA-CM-6167 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-CM-6168     TCGA-CM-6169     TCGA-CM-6170     TCGA-CM-6171 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-CM-6172     TCGA-CM-6674     TCGA-CM-6675     TCGA-CM-6676 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-CM-6677     TCGA-CM-6678     TCGA-CM-6679     TCGA-CM-6680 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-D5-5537     TCGA-D5-5538     TCGA-D5-5539     TCGA-D5-5540 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-D5-5541     TCGA-D5-6529     TCGA-D5-6532     TCGA-D5-6533 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-D5-6534     TCGA-D5-6535     TCGA-D5-6536     TCGA-D5-6537 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-D5-6538     TCGA-D5-6539     TCGA-D5-6540     TCGA-D5-6541 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-D5-6898     TCGA-D5-6920     TCGA-D5-6922     TCGA-D5-6923 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-D5-6924     TCGA-D5-6926     TCGA-D5-6927     TCGA-D5-6928 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-D5-6929     TCGA-D5-6930     TCGA-D5-6931     TCGA-D5-6932 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-D5-7000     TCGA-DM-A0X9     TCGA-DM-A0XD     TCGA-DM-A0XF 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-DM-A1D0     TCGA-DM-A1D4     TCGA-DM-A1D6     TCGA-DM-A1D7 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-DM-A1D8     TCGA-DM-A1D9     TCGA-DM-A1DA     TCGA-DM-A1DB 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-DM-A1HA     TCGA-DM-A1HB     TCGA-DM-A282     TCGA-DM-A285 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-DM-A28C     TCGA-DM-A28E     TCGA-DM-A28F     TCGA-DM-A28G 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-DM-A28H     TCGA-DM-A28K     TCGA-F4-6459     TCGA-F4-6460 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-F4-6569     TCGA-F4-6570     TCGA-F4-6703     TCGA-F4-6704 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-F4-6806     TCGA-F4-6807     TCGA-F4-6808     TCGA-F4-6809 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-F4-6854     TCGA-F4-6855     TCGA-F4-6856     TCGA-G4-6293 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-G4-6299     TCGA-G4-6303     TCGA-G4-6304     TCGA-G4-6306 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-G4-6307     TCGA-G4-6309     TCGA-G4-6310     TCGA-G4-6315 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-G4-6317     TCGA-G4-6321     TCGA-G4-6323     TCGA-G4-6586 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-G4-6588     TCGA-G4-6625     TCGA-G4-6626     TCGA-G4-6628 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-AF-2687     TCGA-AF-2689     TCGA-AF-2691     TCGA-AF-2692 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-AF-2693     TCGA-AF-3400     TCGA-AF-3913     TCGA-AF-4110 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-AF-5654     TCGA-AF-6136     TCGA-AF-6655     TCGA-AF-6672 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-AG-3574     TCGA-AG-3575     TCGA-AG-3578     TCGA-AG-3580 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-AG-3581     TCGA-AG-3582     TCGA-AG-3583     TCGA-AG-3584 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-AG-3586     TCGA-AG-3587     TCGA-AG-3593     TCGA-AG-3594 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-AG-3598     TCGA-AG-3599     TCGA-AG-3600     TCGA-AG-3601 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-AG-3602     TCGA-AG-3605     TCGA-AG-3608     TCGA-AG-3609 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-AG-3611     TCGA-AG-3612     TCGA-AG-3726     TCGA-AG-3727 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-AG-3731     TCGA-AG-3732     TCGA-AG-3742     TCGA-AG-3878 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-AG-3881     TCGA-AG-3882     TCGA-AG-3883     TCGA-AG-3885 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-AG-3887     TCGA-AG-3890     TCGA-AG-3892     TCGA-AG-3893 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-AG-3894     TCGA-AG-3896     TCGA-AG-3898     TCGA-AG-3901 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-AG-3902     TCGA-AG-3909     TCGA-AG-3999     TCGA-AG-4001 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-AG-4005     TCGA-AG-4007     TCGA-AG-4008     TCGA-AG-4015 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-AG-A008     TCGA-AG-A00C     TCGA-AG-A00H     TCGA-AG-A00Y 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-AG-A011     TCGA-AG-A014     TCGA-AG-A015     TCGA-AG-A016 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-AG-A01L     TCGA-AG-A01W     TCGA-AG-A01Y     TCGA-AG-A020 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-AG-A025     TCGA-AG-A026     TCGA-AG-A02G     TCGA-AG-A02N 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-AG-A02X     TCGA-AG-A032     TCGA-AG-A036     TCGA-AH-6544 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-AH-6547     TCGA-AH-6643     TCGA-AH-6644     TCGA-CI-6622 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-DC-5337     TCGA-DC-5869     TCGA-DC-6155     TCGA-DC-6157 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-DC-6158     TCGA-DC-6160     TCGA-DC-6681     TCGA-DC-6682 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-DC-6683     TCGA-DY-A0XA     TCGA-DY-A1DC     TCGA-DY-A1DD 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-DY-A1DF     TCGA-DY-A1DG     TCGA-DY-A1H8     TCGA-EI-6506 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-EI-6507     TCGA-EI-6508     TCGA-EI-6510     TCGA-F5-6464 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-F5-6465     TCGA-F5-6571     TCGA-F5-6702     TCGA-F5-6811 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-F5-6812     TCGA-F5-6813     TCGA-G5-6235     TCGA-G5-6641 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GPX8 MUTATED                                  0     0
  GPX8 WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  GPX8 MUTATED                           0     1
  GPX8 WILD-TYPE                        22   225
D1584V13, multiclass
[1] "Remove cluster labels:" "GPX8 MUTATED"          
clus
  GPX8 MUTATED GPX8 WILD-TYPE 
             1            259 
    TCGA-A6-2671     TCGA-A6-2672     TCGA-A6-2674     TCGA-A6-2676 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-A6-2677     TCGA-A6-2678     TCGA-A6-2683     TCGA-A6-3807 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-A6-3808     TCGA-A6-3809     TCGA-A6-3810     TCGA-A6-4105 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-A6-5656     TCGA-A6-5657     TCGA-A6-5659     TCGA-A6-5660 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-A6-5661     TCGA-A6-5662     TCGA-A6-5664     TCGA-A6-5665 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-A6-5666     TCGA-A6-6137     TCGA-A6-6138     TCGA-A6-6141 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-A6-6142     TCGA-A6-6648     TCGA-A6-6649     TCGA-A6-6651 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-A6-6652     TCGA-A6-6653     TCGA-A6-6654     TCGA-A6-6780 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-A6-6781     TCGA-A6-6782     TCGA-AD-5900     TCGA-AD-6548 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-AD-6888     TCGA-AD-6889     TCGA-AD-6890     TCGA-AD-6895 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-AD-6899     TCGA-AD-6901     TCGA-AD-6963     TCGA-AD-6964 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-AD-6965     TCGA-AU-3779     TCGA-AU-6004     TCGA-AY-4070 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-AY-4071     TCGA-AY-5543     TCGA-AY-6196     TCGA-AY-6197 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-AY-6386     TCGA-AZ-4323     TCGA-AZ-4616     TCGA-AZ-4681 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-AZ-4682     TCGA-AZ-5403     TCGA-AZ-5407     TCGA-AZ-6598 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-AZ-6599     TCGA-AZ-6600     TCGA-AZ-6601     TCGA-AZ-6603 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-AZ-6605     TCGA-AZ-6606     TCGA-AZ-6607     TCGA-AZ-6608 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-CA-5254     TCGA-CA-5255     TCGA-CA-5796     TCGA-CA-5797 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-CA-6715     TCGA-CA-6716     TCGA-CA-6717     TCGA-CA-6718 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-CA-6719     TCGA-CK-4947     TCGA-CK-4948     TCGA-CK-4950 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-CK-4952     TCGA-CK-5912     TCGA-CK-5913     TCGA-CK-5914 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-CK-5915     TCGA-CK-5916     TCGA-CK-6746     TCGA-CK-6747 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-CK-6748     TCGA-CK-6751     TCGA-CM-4743     TCGA-CM-4744 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-CM-4746     TCGA-CM-4747     TCGA-CM-4752     TCGA-CM-5341 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-CM-5344     TCGA-CM-5348     TCGA-CM-5349     TCGA-CM-5860 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-CM-5861     TCGA-CM-5862     TCGA-CM-5863     TCGA-CM-5864 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-CM-5868     TCGA-CM-6161     TCGA-CM-6162     TCGA-CM-6163 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-CM-6164     TCGA-CM-6165     TCGA-CM-6166     TCGA-CM-6167 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-CM-6168     TCGA-CM-6169     TCGA-CM-6170     TCGA-CM-6171 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-CM-6172     TCGA-CM-6674     TCGA-CM-6675     TCGA-CM-6676 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-CM-6677     TCGA-CM-6678     TCGA-CM-6679     TCGA-CM-6680 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-D5-5537     TCGA-D5-5538     TCGA-D5-5539     TCGA-D5-5540 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-D5-5541     TCGA-D5-6529     TCGA-D5-6532     TCGA-D5-6533 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-D5-6534     TCGA-D5-6535     TCGA-D5-6536     TCGA-D5-6537 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-D5-6538     TCGA-D5-6539     TCGA-D5-6540     TCGA-D5-6541 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-D5-6898     TCGA-D5-6920     TCGA-D5-6922     TCGA-D5-6923 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-D5-6924     TCGA-D5-6926     TCGA-D5-6927     TCGA-D5-6928 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-D5-6929     TCGA-D5-6930     TCGA-D5-6931     TCGA-D5-6932 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-D5-7000     TCGA-DM-A0X9     TCGA-DM-A0XD     TCGA-DM-A0XF 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-DM-A1D0     TCGA-DM-A1D4     TCGA-DM-A1D6     TCGA-DM-A1D7 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-DM-A1D8     TCGA-DM-A1D9     TCGA-DM-A1DA     TCGA-DM-A1DB 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-DM-A1HA     TCGA-DM-A1HB     TCGA-DM-A282     TCGA-DM-A285 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-DM-A28C     TCGA-DM-A28E     TCGA-DM-A28F     TCGA-DM-A28G 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-DM-A28H     TCGA-DM-A28K     TCGA-F4-6459     TCGA-F4-6460 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-F4-6569     TCGA-F4-6570     TCGA-F4-6703     TCGA-F4-6704 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-F4-6805     TCGA-F4-6806     TCGA-F4-6807     TCGA-F4-6808 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-F4-6809     TCGA-F4-6854     TCGA-F4-6855     TCGA-F4-6856 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-G4-6293     TCGA-G4-6299     TCGA-G4-6303     TCGA-G4-6304 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-G4-6306     TCGA-G4-6307     TCGA-G4-6309     TCGA-G4-6310 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-G4-6315     TCGA-G4-6317     TCGA-G4-6321     TCGA-G4-6323 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-G4-6586     TCGA-G4-6588     TCGA-G4-6625     TCGA-G4-6626 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-G4-6628     TCGA-AF-2687     TCGA-AF-2689     TCGA-AF-2691 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-AF-2692     TCGA-AF-2693     TCGA-AF-3400     TCGA-AF-3913 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-AF-4110     TCGA-AF-5654     TCGA-AF-6136     TCGA-AF-6655 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-AF-6672     TCGA-AH-6544     TCGA-AH-6547     TCGA-AH-6549 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-AH-6643     TCGA-AH-6644     TCGA-CI-6619     TCGA-CI-6620 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-CI-6621     TCGA-CI-6622     TCGA-CI-6624     TCGA-CL-5917 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-CL-5918     TCGA-DC-5337     TCGA-DC-5869     TCGA-DC-6155 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-DC-6157     TCGA-DC-6158     TCGA-DC-6160     TCGA-DC-6681 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-DC-6682     TCGA-DC-6683     TCGA-DT-5265     TCGA-DY-A0XA 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-DY-A1DC     TCGA-DY-A1DD     TCGA-DY-A1DF     TCGA-DY-A1DG 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-DY-A1H8     TCGA-EF-5830     TCGA-EI-6506     TCGA-EI-6507 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-EI-6508     TCGA-EI-6510     TCGA-F5-6464     TCGA-F5-6465 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-F5-6571     TCGA-F5-6702     TCGA-F5-6811     TCGA-F5-6812 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 
    TCGA-F5-6813     TCGA-G5-6235     TCGA-G5-6641 
"GPX8 WILD-TYPE" "GPX8 WILD-TYPE" "GPX8 WILD-TYPE" 

Clustering(1585) Variable = C6ORF150 MUTATION ANALYSIS
D1585V1, survival
                    sevent
clus2                  0   1
  C6ORF150 MUTATED     9   1
  C6ORF150 WILD-TYPE 369  92
  C6ORF150 MUTATED C6ORF150 WILD-TYPE 
                10                461 
  C6ORF150 MUTATED C6ORF150 WILD-TYPE 
                 1                 92 
$`C6ORF150 MUTATED`
TCGA-AA-3496 TCGA-AA-3510 TCGA-AA-3864 TCGA-AA-A00A TCGA-AA-A010 TCGA-AU-6004 
        1.02        63.98        53.00        38.04        34.98        27.09 
TCGA-AZ-6601 TCGA-CM-5349 TCGA-D5-5538 TCGA-AG-A002 
      100.01        30.08        12.26        20.98 

$`C6ORF150 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 
        0.99        31.07        31.07        30.05        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00E 
       19.07         7.96        27.02        13.94        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       49.41         6.77        12.10        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       12.03        45.40        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  C6ORF150 MUTATED C6ORF150 WILD-TYPE 
              1.02               0.00 
  C6ORF150 MUTATED C6ORF150 WILD-TYPE 
            100.01             148.01 
  C6ORF150 MUTATED C6ORF150 WILD-TYPE 
             32.53              20.02 
[1] "1.0 - 100.0 (32.5)" "0.0 - 148.0 (20.0)"
[1] "hr=" "2.9"
D1585V2, continuous
D1585V3, binary
                    cls
clus                   0   1
  C6ORF150 MUTATED     9   1
  C6ORF150 WILD-TYPE 357 118
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C6ORF150 MUTATED      9    1
  C6ORF150 WILD-TYPE  357  118
        clus
vv       C6ORF150 MUTATED C6ORF150 WILD-TYPE
  COLON                 9                357
  RECTUM                1                118
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  C6ORF150 MUTATED         2        0        4         2         1         0
  C6ORF150 WILD-TYPE      89        1       28       136         9         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C6ORF150 MUTATED           0          0          1          0        0
  C6ORF150 WILD-TYPE        24         11         58         42       48
                    vv
clus                 STAGE IVA STAGE IVB
  C6ORF150 MUTATED           0         0
  C6ORF150 WILD-TYPE        18         1
D1585V4, multiclass
            clus
vv           C6ORF150 MUTATED C6ORF150 WILD-TYPE
  STAGE I                   2                 89
  STAGE IA                  0                  1
  STAGE II                  4                 28
  STAGE IIA                 2                136
  STAGE IIB                 1                  9
  STAGE IIC                 0                  1
  STAGE III                 0                 24
  STAGE IIIA                0                 11
  STAGE IIIB                1                 58
  STAGE IIIC                0                 42
  STAGE IV                  0                 48
  STAGE IVA                 0                 18
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  C6ORF150 MUTATED     0   2   7   1
  C6ORF150 WILD-TYPE  17  90 322  49
D1585V5, multiclass
    clus
vv   C6ORF150 MUTATED C6ORF150 WILD-TYPE
  T1                0                 17
  T2                2                 90
  T3                7                322
  T4                1                 49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  C6ORF150 MUTATED     9   1   0
  C6ORF150 WILD-TYPE 278 112  87
D1585V6, multiclass
    clus
vv   C6ORF150 MUTATED C6ORF150 WILD-TYPE
  N0                9                278
  N1                1                112
  N2                0                 87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1585V7, binary
                    cls
clus                   0   1
  C6ORF150 MUTATED    10   0
  C6ORF150 WILD-TYPE 365  65
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C6ORF150 MUTATED     10    0
  C6ORF150 WILD-TYPE  365   65
   clus
vv  C6ORF150 MUTATED C6ORF150 WILD-TYPE
  0               10                365
  1                0                 65
[1] 2 2
[1] FALSE
D1585V8, binary
                    cls
clus                   0   1
  C6ORF150 MUTATED     5   5
  C6ORF150 WILD-TYPE 220 259
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C6ORF150 MUTATED      5    5
  C6ORF150 WILD-TYPE  220  259
        clus
vv       C6ORF150 MUTATED C6ORF150 WILD-TYPE
  FEMALE                5                220
  MALE                  5                259
[1] 2 2
[1] FALSE
D1585V9, binary
                    cls
clus                   0   1
  C6ORF150 MUTATED     8   0
  C6ORF150 WILD-TYPE 342  22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C6ORF150 MUTATED      8    0
  C6ORF150 WILD-TYPE  342   22
     clus
vv    C6ORF150 MUTATED C6ORF150 WILD-TYPE
  NO                 8                342
  YES                0                 22
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  C6ORF150 MUTATED                      9                             0
  C6ORF150 WILD-TYPE                  306                            47
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  C6ORF150 MUTATED                       1                              0
  C6ORF150 WILD-TYPE                   105                             10
D1585V10, multiclass
                                clus
vv                               C6ORF150 MUTATED C6ORF150 WILD-TYPE
  COLON ADENOCARCINOMA                          9                306
  COLON MUCINOUS ADENOCARCINOMA                 0                 47
  RECTAL ADENOCARCINOMA                         1                105
  RECTAL MUCINOUS ADENOCARCINOMA                0                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  C6ORF150 MUTATED     9   0   0   0
  C6ORF150 WILD-TYPE 336   4  31  25
D1585V11, multiclass
    clus
vv   C6ORF150 MUTATED C6ORF150 WILD-TYPE
  R0                9                336
  R1                0                  4
  R2                0                 31
  RX                0                 25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1585V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C6ORF150 MUTATED                                  0     0
  C6ORF150 WILD-TYPE                                1    11
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  C6ORF150 MUTATED                           0     4
  C6ORF150 WILD-TYPE                        22   222
D1585V13, multiclass
                                  clus
vv                                 C6ORF150 MUTATED C6ORF150 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 11
  BLACK OR AFRICAN AMERICAN                       0                 22
  WHITE                                           4                222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1586) Variable = NAP1L4 MUTATION ANALYSIS
D1586V1, survival
                  sevent
clus2                0   1
  NAP1L4 MUTATED     5   1
  NAP1L4 WILD-TYPE 373  92
  NAP1L4 MUTATED NAP1L4 WILD-TYPE 
               6              465 
  NAP1L4 MUTATED NAP1L4 WILD-TYPE 
               1               92 
$`NAP1L4 MUTATED`
TCGA-AA-3815 TCGA-AU-3779 TCGA-DM-A0XF TCGA-G4-6317 TCGA-G4-6628 TCGA-AG-A002 
       33.04        14.50        38.20        36.00        79.69        20.98 

$`NAP1L4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       19.04        10.06        35.05         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        10.88         0.20        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
      119.70        24.43       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       61.91        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       46.75        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  NAP1L4 MUTATED NAP1L4 WILD-TYPE 
            14.5              0.0 
  NAP1L4 MUTATED NAP1L4 WILD-TYPE 
           79.69           148.01 
  NAP1L4 MUTATED NAP1L4 WILD-TYPE 
           34.52            20.05 
[1] "14.5 - 79.7 (34.5)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.6"
D1586V2, continuous
D1586V3, binary
                  cls
clus                 0   1
  NAP1L4 MUTATED     5   1
  NAP1L4 WILD-TYPE 361 118
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NAP1L4 MUTATED      5    1
  NAP1L4 WILD-TYPE  361  118
        clus
vv       NAP1L4 MUTATED NAP1L4 WILD-TYPE
  COLON               5              361
  RECTUM              1              118
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NAP1L4 MUTATED         2        0        0         2         0         0
  NAP1L4 WILD-TYPE      89        1       32       136        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NAP1L4 MUTATED           0          0          0          2        0
  NAP1L4 WILD-TYPE        24         11         59         40       48
                  vv
clus               STAGE IVA STAGE IVB
  NAP1L4 MUTATED           0         0
  NAP1L4 WILD-TYPE        18         1
D1586V4, multiclass
            clus
vv           NAP1L4 MUTATED NAP1L4 WILD-TYPE
  STAGE I                 2               89
  STAGE IA                0                1
  STAGE II                0               32
  STAGE IIA               2              136
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              0               59
  STAGE IIIC              2               40
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  NAP1L4 MUTATED     0   2   4   0
  NAP1L4 WILD-TYPE  17  90 325  50
D1586V5, multiclass
    clus
vv   NAP1L4 MUTATED NAP1L4 WILD-TYPE
  T1              0               17
  T2              2               90
  T3              4              325
  T4              0               50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  NAP1L4 MUTATED     4   0   2
  NAP1L4 WILD-TYPE 283 113  85
D1586V6, multiclass
    clus
vv   NAP1L4 MUTATED NAP1L4 WILD-TYPE
  N0              4              283
  N1              0              113
  N2              2               85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1586V7, binary
                  cls
clus                 0   1
  NAP1L4 MUTATED     5   0
  NAP1L4 WILD-TYPE 370  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NAP1L4 MUTATED      5    0
  NAP1L4 WILD-TYPE  370   65
   clus
vv  NAP1L4 MUTATED NAP1L4 WILD-TYPE
  0              5              370
  1              0               65
[1] 2 2
[1] FALSE
D1586V8, binary
                  cls
clus                 0   1
  NAP1L4 MUTATED     4   2
  NAP1L4 WILD-TYPE 221 262
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NAP1L4 MUTATED      4    2
  NAP1L4 WILD-TYPE  221  262
        clus
vv       NAP1L4 MUTATED NAP1L4 WILD-TYPE
  FEMALE              4              221
  MALE                2              262
[1] 2 2
[1] FALSE
D1586V9, binary
                  cls
clus                 0   1
  NAP1L4 MUTATED     5   0
  NAP1L4 WILD-TYPE 345  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NAP1L4 MUTATED      5    0
  NAP1L4 WILD-TYPE  345   22
     clus
vv    NAP1L4 MUTATED NAP1L4 WILD-TYPE
  NO               5              345
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  NAP1L4 MUTATED                      4                             0
  NAP1L4 WILD-TYPE                  311                            47
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  NAP1L4 MUTATED                       1                              0
  NAP1L4 WILD-TYPE                   105                             10
D1586V10, multiclass
                                clus
vv                               NAP1L4 MUTATED NAP1L4 WILD-TYPE
  COLON ADENOCARCINOMA                        4              311
  COLON MUCINOUS ADENOCARCINOMA               0               47
  RECTAL ADENOCARCINOMA                       1              105
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  NAP1L4 MUTATED     5   0   0   0
  NAP1L4 WILD-TYPE 340   4  31  25
D1586V11, multiclass
    clus
vv   NAP1L4 MUTATED NAP1L4 WILD-TYPE
  R0              5              340
  R1              0                4
  R2              0               31
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1586V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NAP1L4 MUTATED                                  0     0
  NAP1L4 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  NAP1L4 MUTATED                           0     4
  NAP1L4 WILD-TYPE                        22   222
D1586V13, multiclass
                                  clus
vv                                 NAP1L4 MUTATED NAP1L4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         4              222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1587) Variable = MANF MUTATION ANALYSIS
D1587V1, survival
                sevent
clus2              0   1
  MANF MUTATED     3   1
  MANF WILD-TYPE 375  92
  MANF MUTATED MANF WILD-TYPE 
             4            467 
  MANF MUTATED MANF WILD-TYPE 
             1             92 
$`MANF MUTATED`
TCGA-A6-3809 TCGA-AD-6964 TCGA-AU-6004 TCGA-AY-6197 
       32.75        10.88        27.09        21.44 

$`MANF WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       27.42         0.20        14.50        16.31         0.95        33.01 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  MANF MUTATED MANF WILD-TYPE 
         10.88           0.00 
  MANF MUTATED MANF WILD-TYPE 
         32.75         148.01 
  MANF MUTATED MANF WILD-TYPE 
        24.265         20.120 
[1] "10.9 - 32.8 (24.3)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.5"
D1587V2, continuous
D1587V3, binary
                cls
clus               0   1
  MANF MUTATED     4   0
  MANF WILD-TYPE 362 119
[1] "tbl2"
                cls
clus             [,1] [,2]
  MANF MUTATED      4    0
  MANF WILD-TYPE  362  119
        clus
vv       MANF MUTATED MANF WILD-TYPE
  COLON             4            362
  RECTUM            0            119
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MANF MUTATED         1        0        0         1         1         0
  MANF WILD-TYPE      90        1       32       137         9         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MANF MUTATED           0          0          0          0        0         0
  MANF WILD-TYPE        24         11         59         42       48        18
                vv
clus             STAGE IVB
  MANF MUTATED           0
  MANF WILD-TYPE         1
D1587V4, multiclass
            clus
vv           MANF MUTATED MANF WILD-TYPE
  STAGE I               1             90
  STAGE IA              0              1
  STAGE II              0             32
  STAGE IIA             1            137
  STAGE IIB             1              9
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            0             59
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  MANF MUTATED     0   1   1   2
  MANF WILD-TYPE  17  91 328  48
D1587V5, multiclass
    clus
vv   MANF MUTATED MANF WILD-TYPE
  T1            0             17
  T2            1             91
  T3            1            328
  T4            2             48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  MANF MUTATED     3   0   1
  MANF WILD-TYPE 284 113  86
D1587V6, multiclass
    clus
vv   MANF MUTATED MANF WILD-TYPE
  N0            3            284
  N1            0            113
  N2            1             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1587V7, binary
                cls
clus               0   1
  MANF MUTATED     2   0
  MANF WILD-TYPE 373  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  MANF MUTATED      2    0
  MANF WILD-TYPE  373   65
   clus
vv  MANF MUTATED MANF WILD-TYPE
  0            2            373
  1            0             65
[1] 2 2
[1] FALSE
D1587V8, binary
                cls
clus               0   1
  MANF MUTATED     2   2
  MANF WILD-TYPE 223 262
[1] "tbl2"
                cls
clus             [,1] [,2]
  MANF MUTATED      2    2
  MANF WILD-TYPE  223  262
        clus
vv       MANF MUTATED MANF WILD-TYPE
  FEMALE            2            223
  MALE              2            262
[1] 2 2
[1] FALSE
D1587V9, binary
                cls
clus               0   1
  MANF MUTATED     3   0
  MANF WILD-TYPE 347  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  MANF MUTATED      3    0
  MANF WILD-TYPE  347   22
     clus
vv    MANF MUTATED MANF WILD-TYPE
  NO             3            347
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MANF MUTATED                      3                             1
  MANF WILD-TYPE                  312                            46
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MANF MUTATED                       0                              0
  MANF WILD-TYPE                   106                             10
D1587V10, multiclass
                                clus
vv                               MANF MUTATED MANF WILD-TYPE
  COLON ADENOCARCINOMA                      3            312
  COLON MUCINOUS ADENOCARCINOMA             1             46
  RECTAL ADENOCARCINOMA                     0            106
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  MANF MUTATED     3   0   0   0
  MANF WILD-TYPE 342   4  31  25
D1587V11, multiclass
    clus
vv   MANF MUTATED MANF WILD-TYPE
  R0            3            342
  R1            0              4
  R2            0             31
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1587V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MANF MUTATED                                  0     0
  MANF WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  MANF MUTATED                           0     4
  MANF WILD-TYPE                        22   222
D1587V13, multiclass
                                  clus
vv                                 MANF MUTATED MANF WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       4            222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1588) Variable = CUX1 MUTATION ANALYSIS
D1588V1, survival
                sevent
clus2              0   1
  CUX1 MUTATED    13   3
  CUX1 WILD-TYPE 365  90
  CUX1 MUTATED CUX1 WILD-TYPE 
            16            455 
  CUX1 MUTATED CUX1 WILD-TYPE 
             3             90 
$`CUX1 MUTATED`
TCGA-A6-5665 TCGA-A6-6781 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3672 TCGA-AA-3821 
       22.06        19.66        78.08        54.02         0.92         1.02 
TCGA-AA-A00F TCGA-AZ-6598 TCGA-CM-4746 TCGA-CM-5861 TCGA-CM-6171 TCGA-D5-6930 
       34.03        49.41        37.02        15.02        14.04         1.51 
TCGA-F4-6459 TCGA-F4-6570 TCGA-AG-A02N TCGA-EI-6507 
        8.61         6.18        61.97        19.96 

$`CUX1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3666 
       13.94        19.99        61.02         6.05         6.97         2.01 
TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
       14.01        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
       25.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K 
       13.94        38.04        19.00        30.02        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 
        5.13       106.75        22.36        62.79        88.21         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4747 
       82.95         1.91       124.27        23.05        20.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       13.02        15.02        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6931 
       14.30         9.04         9.44        11.64         4.80        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6460 
      119.93        35.97        60.79       117.07        98.24        31.96 
TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       35.74        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 
       10.98        49.97         1.94        38.96        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  CUX1 MUTATED CUX1 WILD-TYPE 
          0.92           0.00 
  CUX1 MUTATED CUX1 WILD-TYPE 
         78.08         148.01 
  CUX1 MUTATED CUX1 WILD-TYPE 
         19.81          20.28 
[1] "0.9 - 78.1 (19.8)"  "0.0 - 148.0 (20.3)"
[1] "hr=" "1.1"
D1588V2, continuous
D1588V3, binary
                cls
clus               0   1
  CUX1 MUTATED    15   2
  CUX1 WILD-TYPE 351 117
[1] "tbl2"
                cls
clus             [,1] [,2]
  CUX1 MUTATED     15    2
  CUX1 WILD-TYPE  351  117
        clus
vv       CUX1 MUTATED CUX1 WILD-TYPE
  COLON            15            351
  RECTUM            2            117
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CUX1 MUTATED         3        0        4         6         0         0
  CUX1 WILD-TYPE      88        1       28       132        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CUX1 MUTATED           1          0          1          2        0         0
  CUX1 WILD-TYPE        23         11         58         40       48        18
                vv
clus             STAGE IVB
  CUX1 MUTATED           0
  CUX1 WILD-TYPE         1
D1588V4, multiclass
            clus
vv           CUX1 MUTATED CUX1 WILD-TYPE
  STAGE I               3             88
  STAGE IA              0              1
  STAGE II              4             28
  STAGE IIA             6            132
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             1             23
  STAGE IIIA            0             11
  STAGE IIIB            1             58
  STAGE IIIC            2             40
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  CUX1 MUTATED     0   3  13   1
  CUX1 WILD-TYPE  17  89 316  49
D1588V5, multiclass
    clus
vv   CUX1 MUTATED CUX1 WILD-TYPE
  T1            0             17
  T2            3             89
  T3           13            316
  T4            1             49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  CUX1 MUTATED    13   2   2
  CUX1 WILD-TYPE 274 111  85
D1588V6, multiclass
    clus
vv   CUX1 MUTATED CUX1 WILD-TYPE
  N0           13            274
  N1            2            111
  N2            2             85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1588V7, binary
                cls
clus               0   1
  CUX1 MUTATED    15   0
  CUX1 WILD-TYPE 360  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  CUX1 MUTATED     15    0
  CUX1 WILD-TYPE  360   65
   clus
vv  CUX1 MUTATED CUX1 WILD-TYPE
  0           15            360
  1            0             65
[1] 2 2
[1] FALSE
D1588V8, binary
                cls
clus               0   1
  CUX1 MUTATED    11   6
  CUX1 WILD-TYPE 214 258
[1] "tbl2"
                cls
clus             [,1] [,2]
  CUX1 MUTATED     11    6
  CUX1 WILD-TYPE  214  258
        clus
vv       CUX1 MUTATED CUX1 WILD-TYPE
  FEMALE           11            214
  MALE              6            258
[1] 2 2
[1] FALSE
D1588V9, binary
                cls
clus               0   1
  CUX1 MUTATED    14   0
  CUX1 WILD-TYPE 336  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  CUX1 MUTATED     14    0
  CUX1 WILD-TYPE  336   22
     clus
vv    CUX1 MUTATED CUX1 WILD-TYPE
  NO            14            336
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CUX1 MUTATED                     12                             3
  CUX1 WILD-TYPE                  303                            44
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CUX1 MUTATED                       2                              0
  CUX1 WILD-TYPE                   104                             10
D1588V10, multiclass
                                clus
vv                               CUX1 MUTATED CUX1 WILD-TYPE
  COLON ADENOCARCINOMA                     12            303
  COLON MUCINOUS ADENOCARCINOMA             3             44
  RECTAL ADENOCARCINOMA                     2            104
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  CUX1 MUTATED    16   0   0   0
  CUX1 WILD-TYPE 329   4  31  25
D1588V11, multiclass
    clus
vv   CUX1 MUTATED CUX1 WILD-TYPE
  R0           16            329
  R1            0              4
  R2            0             31
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1588V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CUX1 MUTATED                                  0     0
  CUX1 WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  CUX1 MUTATED                           1     9
  CUX1 WILD-TYPE                        21   217
D1588V13, multiclass
                                  clus
vv                                 CUX1 MUTATED CUX1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                       9            217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1589) Variable = SLC16A5 MUTATION ANALYSIS
D1589V1, survival
                   sevent
clus2                 0   1
  SLC16A5 MUTATED     8   1
  SLC16A5 WILD-TYPE 370  92
  SLC16A5 MUTATED SLC16A5 WILD-TYPE 
                9               462 
  SLC16A5 MUTATED SLC16A5 WILD-TYPE 
                1                92 
$`SLC16A5 MUTATED`
TCGA-A6-6651 TCGA-AA-3517 TCGA-AA-3672 TCGA-AA-3815 TCGA-AA-3977 TCGA-CA-6717 
       21.76        38.99         0.92        33.04        25.02        12.76 
TCGA-D5-5539 TCGA-F4-6808 TCGA-G4-6626 
       19.59        33.67        46.75 

$`SLC16A5 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.08        25.18        24.16        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        13.02         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
       54.02         2.01        14.01        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07        12.20        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 
       11.01        10.06        12.03        45.40        12.26        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       16.24        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       26.17        91.79        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  SLC16A5 MUTATED SLC16A5 WILD-TYPE 
             0.92              0.00 
  SLC16A5 MUTATED SLC16A5 WILD-TYPE 
            46.75            148.01 
  SLC16A5 MUTATED SLC16A5 WILD-TYPE 
           25.020            20.085 
[1] "0.9 - 46.8 (25.0)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.7"
D1589V2, continuous
D1589V3, binary
                   cls
clus                  0   1
  SLC16A5 MUTATED    10   0
  SLC16A5 WILD-TYPE 356 119
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC16A5 MUTATED     10    0
  SLC16A5 WILD-TYPE  356  119
        clus
vv       SLC16A5 MUTATED SLC16A5 WILD-TYPE
  COLON               10               356
  RECTUM               0               119
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SLC16A5 MUTATED         1        0        1         4         0         0
  SLC16A5 WILD-TYPE      90        1       31       134        10         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC16A5 MUTATED           1          1          1          0        0
  SLC16A5 WILD-TYPE        23         10         58         42       48
                   vv
clus                STAGE IVA STAGE IVB
  SLC16A5 MUTATED           0         0
  SLC16A5 WILD-TYPE        18         1
D1589V4, multiclass
            clus
vv           SLC16A5 MUTATED SLC16A5 WILD-TYPE
  STAGE I                  1                90
  STAGE IA                 0                 1
  STAGE II                 1                31
  STAGE IIA                4               134
  STAGE IIB                0                10
  STAGE IIC                0                 1
  STAGE III                1                23
  STAGE IIIA               1                10
  STAGE IIIB               1                58
  STAGE IIIC               0                42
  STAGE IV                 0                48
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  SLC16A5 MUTATED     1   1   7   1
  SLC16A5 WILD-TYPE  16  91 322  49
D1589V5, multiclass
    clus
vv   SLC16A5 MUTATED SLC16A5 WILD-TYPE
  T1               1                16
  T2               1                91
  T3               7               322
  T4               1                49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  SLC16A5 MUTATED     7   3   0
  SLC16A5 WILD-TYPE 280 110  87
D1589V6, multiclass
    clus
vv   SLC16A5 MUTATED SLC16A5 WILD-TYPE
  N0               7               280
  N1               3               110
  N2               0                87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1589V7, binary
                   cls
clus                  0   1
  SLC16A5 MUTATED     8   0
  SLC16A5 WILD-TYPE 367  65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC16A5 MUTATED      8    0
  SLC16A5 WILD-TYPE  367   65
   clus
vv  SLC16A5 MUTATED SLC16A5 WILD-TYPE
  0               8               367
  1               0                65
[1] 2 2
[1] FALSE
D1589V8, binary
                   cls
clus                  0   1
  SLC16A5 MUTATED     5   5
  SLC16A5 WILD-TYPE 220 259
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC16A5 MUTATED      5    5
  SLC16A5 WILD-TYPE  220  259
        clus
vv       SLC16A5 MUTATED SLC16A5 WILD-TYPE
  FEMALE               5               220
  MALE                 5               259
[1] 2 2
[1] FALSE
D1589V9, binary
                   cls
clus                  0   1
  SLC16A5 MUTATED     9   0
  SLC16A5 WILD-TYPE 341  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC16A5 MUTATED      9    0
  SLC16A5 WILD-TYPE  341   22
     clus
vv    SLC16A5 MUTATED SLC16A5 WILD-TYPE
  NO                9               341
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SLC16A5 MUTATED                      8                             2
  SLC16A5 WILD-TYPE                  307                            45
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SLC16A5 MUTATED                       0                              0
  SLC16A5 WILD-TYPE                   106                             10
D1589V10, multiclass
                                clus
vv                               SLC16A5 MUTATED SLC16A5 WILD-TYPE
  COLON ADENOCARCINOMA                         8               307
  COLON MUCINOUS ADENOCARCINOMA                2                45
  RECTAL ADENOCARCINOMA                        0               106
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  SLC16A5 MUTATED     7   0   0   1
  SLC16A5 WILD-TYPE 338   4  31  24
D1589V11, multiclass
    clus
vv   SLC16A5 MUTATED SLC16A5 WILD-TYPE
  R0               7               338
  R1               0                 4
  R2               0                31
  RX               1                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1589V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SLC16A5 MUTATED                                  0     1
  SLC16A5 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  SLC16A5 MUTATED                           0     4
  SLC16A5 WILD-TYPE                        22   222
D1589V13, multiclass
                                  clus
vv                                 SLC16A5 MUTATED SLC16A5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                10
  BLACK OR AFRICAN AMERICAN                      0                22
  WHITE                                          4               222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1590) Variable = TUBB4 MUTATION ANALYSIS
D1590V1, survival
                 sevent
clus2               0   1
  TUBB4 MUTATED     5   0
  TUBB4 WILD-TYPE 373  93
  TUBB4 MUTATED TUBB4 WILD-TYPE 
              5             466 
  TUBB4 MUTATED TUBB4 WILD-TYPE 
              0              93 
$`TUBB4 MUTATED`
TCGA-A6-5665 TCGA-AA-3864 TCGA-D5-6930 TCGA-AG-3742 TCGA-AG-A02N 
       22.06        53.00         1.51         0.99        61.97 

$`TUBB4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 
       32.05         0.99        31.07        31.07        30.05        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       11.64         4.80        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
        0.99        37.02        32.98         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
        1.94        38.96        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  TUBB4 MUTATED TUBB4 WILD-TYPE 
           0.99            0.00 
  TUBB4 MUTATED TUBB4 WILD-TYPE 
          61.97          148.01 
  TUBB4 MUTATED TUBB4 WILD-TYPE 
         22.060          20.155 
[1] "1.0 - 62.0 (22.1)"  "0.0 - 148.0 (20.2)"
[1] "hr="     "9100000"
D1590V2, continuous
D1590V3, binary
                 cls
clus                0   1
  TUBB4 MUTATED     5   2
  TUBB4 WILD-TYPE 361 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TUBB4 MUTATED      5    2
  TUBB4 WILD-TYPE  361  117
        clus
vv       TUBB4 MUTATED TUBB4 WILD-TYPE
  COLON              5             361
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TUBB4 MUTATED         1        0        2         2         1         0
  TUBB4 WILD-TYPE      90        1       30       136         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TUBB4 MUTATED           0          0          0          0        1         0
  TUBB4 WILD-TYPE        24         11         59         42       47        18
                 vv
clus              STAGE IVB
  TUBB4 MUTATED           0
  TUBB4 WILD-TYPE         1
D1590V4, multiclass
            clus
vv           TUBB4 MUTATED TUBB4 WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA              2             136
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             0              42
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  TUBB4 MUTATED     1   0   4   2
  TUBB4 WILD-TYPE  16  92 325  48
D1590V5, multiclass
    clus
vv   TUBB4 MUTATED TUBB4 WILD-TYPE
  T1             1              16
  T2             0              92
  T3             4             325
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  TUBB4 MUTATED     6   0   1
  TUBB4 WILD-TYPE 281 113  86
D1590V6, multiclass
    clus
vv   TUBB4 MUTATED TUBB4 WILD-TYPE
  N0             6             281
  N1             0             113
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1590V7, binary
                 cls
clus                0   1
  TUBB4 MUTATED     5   1
  TUBB4 WILD-TYPE 370  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TUBB4 MUTATED      5    1
  TUBB4 WILD-TYPE  370   64
   clus
vv  TUBB4 MUTATED TUBB4 WILD-TYPE
  0             5             370
  1             1              64
[1] 2 2
[1] FALSE
D1590V8, binary
                 cls
clus                0   1
  TUBB4 MUTATED     4   3
  TUBB4 WILD-TYPE 221 261
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TUBB4 MUTATED      4    3
  TUBB4 WILD-TYPE  221  261
        clus
vv       TUBB4 MUTATED TUBB4 WILD-TYPE
  FEMALE             4             221
  MALE               3             261
[1] 2 2
[1] FALSE
D1590V9, binary
                 cls
clus                0   1
  TUBB4 MUTATED     2   0
  TUBB4 WILD-TYPE 348  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TUBB4 MUTATED      2    0
  TUBB4 WILD-TYPE  348   22
     clus
vv    TUBB4 MUTATED TUBB4 WILD-TYPE
  NO              2             348
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  TUBB4 MUTATED                      3                             2
  TUBB4 WILD-TYPE                  312                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  TUBB4 MUTATED                       2                              0
  TUBB4 WILD-TYPE                   104                             10
D1590V10, multiclass
                                clus
vv                               TUBB4 MUTATED TUBB4 WILD-TYPE
  COLON ADENOCARCINOMA                       3             312
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  TUBB4 MUTATED     5   0   1   1
  TUBB4 WILD-TYPE 340   4  30  24
D1590V11, multiclass
    clus
vv   TUBB4 MUTATED TUBB4 WILD-TYPE
  R0             5             340
  R1             0               4
  R2             1              30
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1590V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TUBB4 MUTATED                                  0     0
  TUBB4 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  TUBB4 MUTATED                           0     3
  TUBB4 WILD-TYPE                        22   223
D1590V13, multiclass
                                  clus
vv                                 TUBB4 MUTATED TUBB4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        3             223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1591) Variable = SUPT3H MUTATION ANALYSIS
D1591V1, survival
                  sevent
clus2                0   1
  SUPT3H MUTATED     6   2
  SUPT3H WILD-TYPE 372  91
  SUPT3H MUTATED SUPT3H WILD-TYPE 
               8              463 
  SUPT3H MUTATED SUPT3H WILD-TYPE 
               2               91 
$`SUPT3H MUTATED`
TCGA-AA-3510 TCGA-AA-3516 TCGA-AA-3950 TCGA-AA-A010 TCGA-AZ-6599 TCGA-CA-6719 
       63.98        13.02        24.00        34.98         6.77        14.30 
TCGA-CM-6674 TCGA-F4-6854 
       12.95         0.53 

$`SUPT3H WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 
        1.02        35.01         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 
       12.99        24.00        33.01        26.01         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        88.21        49.41        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       14.04        11.01        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       16.24        33.67        13.25        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  SUPT3H MUTATED SUPT3H WILD-TYPE 
            0.53             0.00 
  SUPT3H MUTATED SUPT3H WILD-TYPE 
           63.98           148.01 
  SUPT3H MUTATED SUPT3H WILD-TYPE 
           13.66            20.28 
[1] "0.5 - 64.0 (13.7)"  "0.0 - 148.0 (20.3)"
[1] "hr=" "1.5"
D1591V2, continuous
D1591V3, binary
                  cls
clus                 0   1
  SUPT3H MUTATED    11   0
  SUPT3H WILD-TYPE 355 119
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SUPT3H MUTATED     11    0
  SUPT3H WILD-TYPE  355  119
        clus
vv       SUPT3H MUTATED SUPT3H WILD-TYPE
  COLON              11              355
  RECTUM              0              119
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SUPT3H MUTATED         1        0        1         5         2         0
  SUPT3H WILD-TYPE      90        1       31       133         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SUPT3H MUTATED           2          0          0          0        0
  SUPT3H WILD-TYPE        22         11         59         42       48
                  vv
clus               STAGE IVA STAGE IVB
  SUPT3H MUTATED           0         0
  SUPT3H WILD-TYPE        18         1
D1591V4, multiclass
            clus
vv           SUPT3H MUTATED SUPT3H WILD-TYPE
  STAGE I                 1               90
  STAGE IA                0                1
  STAGE II                1               31
  STAGE IIA               5              133
  STAGE IIB               2                8
  STAGE IIC               0                1
  STAGE III               2               22
  STAGE IIIA              0               11
  STAGE IIIB              0               59
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  SUPT3H MUTATED     0   1   8   2
  SUPT3H WILD-TYPE  17  91 321  48
D1591V5, multiclass
    clus
vv   SUPT3H MUTATED SUPT3H WILD-TYPE
  T1              0               17
  T2              1               91
  T3              8              321
  T4              2               48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  SUPT3H MUTATED     9   0   2
  SUPT3H WILD-TYPE 278 113  85
D1591V6, multiclass
    clus
vv   SUPT3H MUTATED SUPT3H WILD-TYPE
  N0              9              278
  N1              0              113
  N2              2               85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1591V7, binary
                  cls
clus                 0   1
  SUPT3H MUTATED     9   0
  SUPT3H WILD-TYPE 366  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SUPT3H MUTATED      9    0
  SUPT3H WILD-TYPE  366   65
   clus
vv  SUPT3H MUTATED SUPT3H WILD-TYPE
  0              9              366
  1              0               65
[1] 2 2
[1] FALSE
D1591V8, binary
                  cls
clus                 0   1
  SUPT3H MUTATED     6   5
  SUPT3H WILD-TYPE 219 259
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SUPT3H MUTATED      6    5
  SUPT3H WILD-TYPE  219  259
        clus
vv       SUPT3H MUTATED SUPT3H WILD-TYPE
  FEMALE              6              219
  MALE                5              259
[1] 2 2
[1] FALSE
D1591V9, binary
                  cls
clus                 0   1
  SUPT3H MUTATED     8   0
  SUPT3H WILD-TYPE 342  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SUPT3H MUTATED      8    0
  SUPT3H WILD-TYPE  342   22
     clus
vv    SUPT3H MUTATED SUPT3H WILD-TYPE
  NO               8              342
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SUPT3H MUTATED                      9                             2
  SUPT3H WILD-TYPE                  306                            45
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SUPT3H MUTATED                       0                              0
  SUPT3H WILD-TYPE                   106                             10
D1591V10, multiclass
                                clus
vv                               SUPT3H MUTATED SUPT3H WILD-TYPE
  COLON ADENOCARCINOMA                        9              306
  COLON MUCINOUS ADENOCARCINOMA               2               45
  RECTAL ADENOCARCINOMA                       0              106
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  SUPT3H MUTATED     7   0   0   2
  SUPT3H WILD-TYPE 338   4  31  23
D1591V11, multiclass
    clus
vv   SUPT3H MUTATED SUPT3H WILD-TYPE
  R0              7              338
  R1              0                4
  R2              0               31
  RX              2               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1591V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SUPT3H MUTATED                                  0     1
  SUPT3H WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  SUPT3H MUTATED                           0     4
  SUPT3H WILD-TYPE                        22   222
D1591V13, multiclass
                                  clus
vv                                 SUPT3H MUTATED SUPT3H WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         4              222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1592) Variable = FAM151A MUTATION ANALYSIS
D1592V1, survival
                   sevent
clus2                 0   1
  FAM151A MUTATED     4   2
  FAM151A WILD-TYPE 374  91
  FAM151A MUTATED FAM151A WILD-TYPE 
                6               465 
  FAM151A MUTATED FAM151A WILD-TYPE 
                2                91 
$`FAM151A MUTATED`
TCGA-A6-6780 TCGA-AA-3811 TCGA-AZ-6601 TCGA-CA-6717 TCGA-D5-6540 TCGA-F4-6856 
       20.12        10.06       100.01        12.76        16.14        35.31 

$`FAM151A WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
       12.10        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       12.49        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       47.41       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  FAM151A MUTATED FAM151A WILD-TYPE 
            10.06              0.00 
  FAM151A MUTATED FAM151A WILD-TYPE 
           100.01            148.01 
  FAM151A MUTATED FAM151A WILD-TYPE 
            18.13             20.28 
[1] "10.1 - 100.0 (18.1)" "0.0 - 148.0 (20.3)" 
[1] "hr=" "1.4"
D1592V2, continuous
D1592V3, binary
                   cls
clus                  0   1
  FAM151A MUTATED     6   0
  FAM151A WILD-TYPE 360 119
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM151A MUTATED      6    0
  FAM151A WILD-TYPE  360  119
        clus
vv       FAM151A MUTATED FAM151A WILD-TYPE
  COLON                6               360
  RECTUM               0               119
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FAM151A MUTATED         2        0        1         2         0         0
  FAM151A WILD-TYPE      89        1       31       136        10         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FAM151A MUTATED           1          0          0          0        0
  FAM151A WILD-TYPE        23         11         59         42       48
                   vv
clus                STAGE IVA STAGE IVB
  FAM151A MUTATED           0         0
  FAM151A WILD-TYPE        18         1
D1592V4, multiclass
            clus
vv           FAM151A MUTATED FAM151A WILD-TYPE
  STAGE I                  2                89
  STAGE IA                 0                 1
  STAGE II                 1                31
  STAGE IIA                2               136
  STAGE IIB                0                10
  STAGE IIC                0                 1
  STAGE III                1                23
  STAGE IIIA               0                11
  STAGE IIIB               0                59
  STAGE IIIC               0                42
  STAGE IV                 0                48
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  FAM151A MUTATED     0   2   4   0
  FAM151A WILD-TYPE  17  90 325  50
D1592V5, multiclass
    clus
vv   FAM151A MUTATED FAM151A WILD-TYPE
  T1               0                17
  T2               2                90
  T3               4               325
  T4               0                50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  FAM151A MUTATED     5   0   1
  FAM151A WILD-TYPE 282 113  86
D1592V6, multiclass
    clus
vv   FAM151A MUTATED FAM151A WILD-TYPE
  N0               5               282
  N1               0               113
  N2               1                86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1592V7, binary
                   cls
clus                  0   1
  FAM151A MUTATED     5   0
  FAM151A WILD-TYPE 370  65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM151A MUTATED      5    0
  FAM151A WILD-TYPE  370   65
   clus
vv  FAM151A MUTATED FAM151A WILD-TYPE
  0               5               370
  1               0                65
[1] 2 2
[1] FALSE
D1592V8, binary
                   cls
clus                  0   1
  FAM151A MUTATED     1   5
  FAM151A WILD-TYPE 224 259
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM151A MUTATED      1    5
  FAM151A WILD-TYPE  224  259
        clus
vv       FAM151A MUTATED FAM151A WILD-TYPE
  FEMALE               1               224
  MALE                 5               259
[1] 2 2
[1] FALSE
D1592V9, binary
                   cls
clus                  0   1
  FAM151A MUTATED     6   0
  FAM151A WILD-TYPE 344  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM151A MUTATED      6    0
  FAM151A WILD-TYPE  344   22
     clus
vv    FAM151A MUTATED FAM151A WILD-TYPE
  NO                6               344
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  FAM151A MUTATED                      2                             4
  FAM151A WILD-TYPE                  313                            43
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  FAM151A MUTATED                       0                              0
  FAM151A WILD-TYPE                   106                             10
D1592V10, multiclass
                                clus
vv                               FAM151A MUTATED FAM151A WILD-TYPE
  COLON ADENOCARCINOMA                         2               313
  COLON MUCINOUS ADENOCARCINOMA                4                43
  RECTAL ADENOCARCINOMA                        0               106
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  FAM151A MUTATED     3   0   0   1
  FAM151A WILD-TYPE 342   4  31  24
D1592V11, multiclass
    clus
vv   FAM151A MUTATED FAM151A WILD-TYPE
  R0               3               342
  R1               0                 4
  R2               0                31
  RX               1                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1592V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FAM151A MUTATED                                  0     1
  FAM151A WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  FAM151A MUTATED                           0     4
  FAM151A WILD-TYPE                        22   222
D1592V13, multiclass
                                  clus
vv                                 FAM151A MUTATED FAM151A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                10
  BLACK OR AFRICAN AMERICAN                      0                22
  WHITE                                          4               222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1593) Variable = HERC1 MUTATION ANALYSIS
D1593V1, survival
                 sevent
clus2               0   1
  HERC1 MUTATED    25   7
  HERC1 WILD-TYPE 353  86
  HERC1 MUTATED HERC1 WILD-TYPE 
             32             439 
  HERC1 MUTATED HERC1 WILD-TYPE 
              7              86 
$`HERC1 MUTATED`
TCGA-A6-3809 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6653 TCGA-A6-6780 TCGA-AA-3660 
       32.75        22.06        32.71        24.39        20.12        78.08 
TCGA-AA-3663 TCGA-AA-3710 TCGA-AA-3870 TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-3952 
        6.97        26.99        29.98        33.01        24.00         2.01 
TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A02K TCGA-AD-5900 TCGA-AD-6889 
       25.02         4.01        34.98        14.01         0.07        56.55 
TCGA-AD-6895 TCGA-AZ-4315 TCGA-CA-5797 TCGA-CA-6716 TCGA-CK-6751 TCGA-D5-6538 
        0.72        58.39         3.29        12.20       124.27        17.13 
TCGA-D5-6928 TCGA-DM-A1D4 TCGA-DM-A28C TCGA-DM-A28F TCGA-F4-6570 TCGA-G4-6307 
       11.64        92.75        81.37        35.97         6.18        55.04 
TCGA-AF-6136 TCGA-AG-A002 
       15.39        20.98 

$`HERC1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       27.09        22.52         8.38        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 
       21.76        24.69        23.87        19.66        20.28         7.04 
TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
        3.02         1.02        35.01        63.98         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
       13.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       36.03         8.05        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.05        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        85.05        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       24.03        27.02        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        2.01         5.03         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        21.37        15.52         0.79         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        33.01        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6717 
        1.61        12.69         3.06         3.25         0.07        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6539 TCGA-D5-6540 
       43.27        15.12        17.85         4.80        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.04         9.44         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D6 
       10.26       119.70        24.43        38.20       130.65        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H 
      135.65       139.17         6.12       119.93        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 
       98.24         8.61        31.96        35.74        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       44.68        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       10.39        14.50        16.83        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  HERC1 MUTATED HERC1 WILD-TYPE 
           0.07            0.00 
  HERC1 MUTATED HERC1 WILD-TYPE 
         124.27          148.01 
  HERC1 MUTATED HERC1 WILD-TYPE 
         24.195          20.020 
[1] "0.1 - 124.3 (24.2)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1"  
D1593V2, continuous
D1593V3, binary
                 cls
clus                0   1
  HERC1 MUTATED    31   2
  HERC1 WILD-TYPE 335 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HERC1 MUTATED     31    2
  HERC1 WILD-TYPE  335  117
        clus
vv       HERC1 MUTATED HERC1 WILD-TYPE
  COLON             31             335
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  HERC1 MUTATED         4        0        2        13         4         1
  HERC1 WILD-TYPE      87        1       30       125         6         0
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  HERC1 MUTATED           0          0          4          1        2         0
  HERC1 WILD-TYPE        24         11         55         41       46        18
                 vv
clus              STAGE IVB
  HERC1 MUTATED           0
  HERC1 WILD-TYPE         1
D1593V4, multiclass
            clus
vv           HERC1 MUTATED HERC1 WILD-TYPE
  STAGE I                4              87
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA             13             125
  STAGE IIB              4               6
  STAGE IIC              1               0
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             4              55
  STAGE IIIC             1              41
  STAGE IV               2              46
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  HERC1 MUTATED     0   5  22   6
  HERC1 WILD-TYPE  17  87 307  44
D1593V5, multiclass
    clus
vv   HERC1 MUTATED HERC1 WILD-TYPE
  T1             0              17
  T2             5              87
  T3            22             307
  T4             6              44
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  HERC1 MUTATED    25   4   4
  HERC1 WILD-TYPE 262 109  83
D1593V6, multiclass
    clus
vv   HERC1 MUTATED HERC1 WILD-TYPE
  N0            25             262
  N1             4             109
  N2             4              83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1593V7, binary
                 cls
clus                0   1
  HERC1 MUTATED    25   2
  HERC1 WILD-TYPE 350  63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HERC1 MUTATED     25    2
  HERC1 WILD-TYPE  350   63
   clus
vv  HERC1 MUTATED HERC1 WILD-TYPE
  0            25             350
  1             2              63
[1] 2 2
[1] FALSE
D1593V8, binary
                 cls
clus                0   1
  HERC1 MUTATED    14  19
  HERC1 WILD-TYPE 211 245
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HERC1 MUTATED     14   19
  HERC1 WILD-TYPE  211  245
        clus
vv       HERC1 MUTATED HERC1 WILD-TYPE
  FEMALE            14             211
  MALE              19             245
[1] 2 2
[1] FALSE
D1593V9, binary
                 cls
clus                0   1
  HERC1 MUTATED    22   1
  HERC1 WILD-TYPE 328  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HERC1 MUTATED     22    1
  HERC1 WILD-TYPE  328   21
     clus
vv    HERC1 MUTATED HERC1 WILD-TYPE
  NO             22             328
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  HERC1 MUTATED                     23                             8
  HERC1 WILD-TYPE                  292                            39
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  HERC1 MUTATED                       2                              0
  HERC1 WILD-TYPE                   104                             10
D1593V10, multiclass
                                clus
vv                               HERC1 MUTATED HERC1 WILD-TYPE
  COLON ADENOCARCINOMA                      23             292
  COLON MUCINOUS ADENOCARCINOMA              8              39
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  HERC1 MUTATED    20   0   1   2
  HERC1 WILD-TYPE 325   4  30  23
D1593V11, multiclass
    clus
vv   HERC1 MUTATED HERC1 WILD-TYPE
  R0            20             325
  R1             0               4
  R2             1              30
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1593V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HERC1 MUTATED                                  0     3
  HERC1 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  HERC1 MUTATED                           0    17
  HERC1 WILD-TYPE                        22   209
D1593V13, multiclass
                                  clus
vv                                 HERC1 MUTATED HERC1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        3               8
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                       17             209
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1594) Variable = TBX4 MUTATION ANALYSIS
D1594V1, survival
                sevent
clus2              0   1
  TBX4 MUTATED     7   4
  TBX4 WILD-TYPE 371  89
  TBX4 MUTATED TBX4 WILD-TYPE 
            11            460 
  TBX4 MUTATED TBX4 WILD-TYPE 
             4             89 
$`TBX4 MUTATED`
TCGA-A6-5661 TCGA-A6-6653 TCGA-AA-3492 TCGA-AA-3864 TCGA-AA-3877 TCGA-AA-A00N 
       33.53        24.39         3.02        53.00        31.00         4.01 
TCGA-AA-A010 TCGA-AZ-5407 TCGA-AZ-6601 TCGA-CA-5254 TCGA-CA-6718 
       34.98        88.21       100.01        12.69        10.06 

$`TBX4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 
       25.18        24.16        21.76        24.69        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       19.66        20.28         7.04         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        31.07        30.05        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       29.98        18.05         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 
        5.13       106.75        22.36        62.79        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
       12.10        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  TBX4 MUTATED TBX4 WILD-TYPE 
          3.02           0.00 
  TBX4 MUTATED TBX4 WILD-TYPE 
        100.01         148.01 
  TBX4 MUTATED TBX4 WILD-TYPE 
        31.000         20.085 
[1] "3.0 - 100.0 (31.0)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.4"
D1594V2, continuous
D1594V3, binary
                cls
clus               0   1
  TBX4 MUTATED    11   0
  TBX4 WILD-TYPE 355 119
[1] "tbl2"
                cls
clus             [,1] [,2]
  TBX4 MUTATED     11    0
  TBX4 WILD-TYPE  355  119
        clus
vv       TBX4 MUTATED TBX4 WILD-TYPE
  COLON            11            355
  RECTUM            0            119
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TBX4 MUTATED         3        0        3         3         2         0
  TBX4 WILD-TYPE      88        1       29       135         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TBX4 MUTATED           0          0          0          0        0         0
  TBX4 WILD-TYPE        24         11         59         42       48        18
                vv
clus             STAGE IVB
  TBX4 MUTATED           0
  TBX4 WILD-TYPE         1
D1594V4, multiclass
            clus
vv           TBX4 MUTATED TBX4 WILD-TYPE
  STAGE I               3             88
  STAGE IA              0              1
  STAGE II              3             29
  STAGE IIA             3            135
  STAGE IIB             2              8
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            0             59
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  TBX4 MUTATED     2   1   6   2
  TBX4 WILD-TYPE  15  91 323  48
D1594V5, multiclass
    clus
vv   TBX4 MUTATED TBX4 WILD-TYPE
  T1            2             15
  T2            1             91
  T3            6            323
  T4            2             48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  TBX4 MUTATED    11   0   0
  TBX4 WILD-TYPE 276 113  87
D1594V6, multiclass
    clus
vv   TBX4 MUTATED TBX4 WILD-TYPE
  N0           11            276
  N1            0            113
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1594V7, binary
                cls
clus               0   1
  TBX4 MUTATED    11   0
  TBX4 WILD-TYPE 364  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  TBX4 MUTATED     11    0
  TBX4 WILD-TYPE  364   65
   clus
vv  TBX4 MUTATED TBX4 WILD-TYPE
  0           11            364
  1            0             65
[1] 2 2
[1] FALSE
D1594V8, binary
                cls
clus               0   1
  TBX4 MUTATED     6   5
  TBX4 WILD-TYPE 219 259
[1] "tbl2"
                cls
clus             [,1] [,2]
  TBX4 MUTATED      6    5
  TBX4 WILD-TYPE  219  259
        clus
vv       TBX4 MUTATED TBX4 WILD-TYPE
  FEMALE            6            219
  MALE              5            259
[1] 2 2
[1] FALSE
D1594V9, binary
                cls
clus               0   1
  TBX4 MUTATED    10   0
  TBX4 WILD-TYPE 340  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  TBX4 MUTATED     10    0
  TBX4 WILD-TYPE  340   22
     clus
vv    TBX4 MUTATED TBX4 WILD-TYPE
  NO            10            340
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  TBX4 MUTATED                      9                             2
  TBX4 WILD-TYPE                  306                            45
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  TBX4 MUTATED                       0                              0
  TBX4 WILD-TYPE                   106                             10
D1594V10, multiclass
                                clus
vv                               TBX4 MUTATED TBX4 WILD-TYPE
  COLON ADENOCARCINOMA                      9            306
  COLON MUCINOUS ADENOCARCINOMA             2             45
  RECTAL ADENOCARCINOMA                     0            106
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  TBX4 MUTATED     6   0   0   2
  TBX4 WILD-TYPE 339   4  31  23
D1594V11, multiclass
    clus
vv   TBX4 MUTATED TBX4 WILD-TYPE
  R0            6            339
  R1            0              4
  R2            0             31
  RX            2             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1594V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TBX4 MUTATED                                  0     2
  TBX4 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  TBX4 MUTATED                           1     3
  TBX4 WILD-TYPE                        21   223
D1594V13, multiclass
                                  clus
vv                                 TBX4 MUTATED TBX4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              9
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                       3            223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1595) Variable = TRIP6 MUTATION ANALYSIS
D1595V1, survival
                 sevent
clus2               0   1
  TRIP6 MUTATED     9   2
  TRIP6 WILD-TYPE 369  91
  TRIP6 MUTATED TRIP6 WILD-TYPE 
             11             460 
  TRIP6 MUTATED TRIP6 WILD-TYPE 
              2              91 
$`TRIP6 MUTATED`
TCGA-A6-5665 TCGA-A6-6780 TCGA-AA-3522 TCGA-AD-5900 TCGA-AD-6895 TCGA-AZ-6598 
       22.06        20.12        37.05         0.07         0.72        49.41 
TCGA-CA-6718 TCGA-CK-4952 TCGA-CK-5913 TCGA-G4-6628 TCGA-AG-3731 
       10.06        15.62        51.32        79.69        37.02 

$`TRIP6 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
        9.07        24.03        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       18.05        40.96        21.37        15.52        56.55         0.79 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       88.21         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07        12.20        12.76        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
      148.01        85.45        49.08         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       91.79        46.75        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  TRIP6 MUTATED TRIP6 WILD-TYPE 
           0.07            0.00 
  TRIP6 MUTATED TRIP6 WILD-TYPE 
          79.69          148.01 
  TRIP6 MUTATED TRIP6 WILD-TYPE 
          22.06           20.12 
[1] "0.1 - 79.7 (22.1)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.2"
D1595V2, continuous
D1595V3, binary
                 cls
clus                0   1
  TRIP6 MUTATED    10   1
  TRIP6 WILD-TYPE 356 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRIP6 MUTATED     10    1
  TRIP6 WILD-TYPE  356  118
        clus
vv       TRIP6 MUTATED TRIP6 WILD-TYPE
  COLON             10             356
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TRIP6 MUTATED         2        0        1         5         0         0
  TRIP6 WILD-TYPE      89        1       31       133        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TRIP6 MUTATED           0          0          0          1        1         0
  TRIP6 WILD-TYPE        24         11         59         41       47        18
                 vv
clus              STAGE IVB
  TRIP6 MUTATED           0
  TRIP6 WILD-TYPE         1
D1595V4, multiclass
            clus
vv           TRIP6 MUTATED TRIP6 WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              5             133
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             1              41
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  TRIP6 MUTATED     0   2   8   1
  TRIP6 WILD-TYPE  17  90 321  49
D1595V5, multiclass
    clus
vv   TRIP6 MUTATED TRIP6 WILD-TYPE
  T1             0              17
  T2             2              90
  T3             8             321
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  TRIP6 MUTATED     8   2   1
  TRIP6 WILD-TYPE 279 111  86
D1595V6, multiclass
    clus
vv   TRIP6 MUTATED TRIP6 WILD-TYPE
  N0             8             279
  N1             2             111
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1595V7, binary
                 cls
clus                0   1
  TRIP6 MUTATED     5   1
  TRIP6 WILD-TYPE 370  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRIP6 MUTATED      5    1
  TRIP6 WILD-TYPE  370   64
   clus
vv  TRIP6 MUTATED TRIP6 WILD-TYPE
  0             5             370
  1             1              64
[1] 2 2
[1] FALSE
D1595V8, binary
                 cls
clus                0   1
  TRIP6 MUTATED     4   7
  TRIP6 WILD-TYPE 221 257
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRIP6 MUTATED      4    7
  TRIP6 WILD-TYPE  221  257
        clus
vv       TRIP6 MUTATED TRIP6 WILD-TYPE
  FEMALE             4             221
  MALE               7             257
[1] 2 2
[1] FALSE
D1595V9, binary
                 cls
clus                0   1
  TRIP6 MUTATED     8   0
  TRIP6 WILD-TYPE 342  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRIP6 MUTATED      8    0
  TRIP6 WILD-TYPE  342   22
     clus
vv    TRIP6 MUTATED TRIP6 WILD-TYPE
  NO              8             342
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  TRIP6 MUTATED                      7                             3
  TRIP6 WILD-TYPE                  308                            44
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  TRIP6 MUTATED                       1                              0
  TRIP6 WILD-TYPE                   105                             10
D1595V10, multiclass
                                clus
vv                               TRIP6 MUTATED TRIP6 WILD-TYPE
  COLON ADENOCARCINOMA                       7             308
  COLON MUCINOUS ADENOCARCINOMA              3              44
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  TRIP6 MUTATED     4   0   1   3
  TRIP6 WILD-TYPE 341   4  30  22
D1595V11, multiclass
    clus
vv   TRIP6 MUTATED TRIP6 WILD-TYPE
  R0             4             341
  R1             0               4
  R2             1              30
  RX             3              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1595V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TRIP6 MUTATED                                  0     1
  TRIP6 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  TRIP6 MUTATED                           0     8
  TRIP6 WILD-TYPE                        22   218
D1595V13, multiclass
                                  clus
vv                                 TRIP6 MUTATED TRIP6 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        8             218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1596) Variable = SERPINB5 MUTATION ANALYSIS
D1596V1, survival
                    sevent
clus2                  0   1
  SERPINB5 MUTATED     6   0
  SERPINB5 WILD-TYPE 372  93
  SERPINB5 MUTATED SERPINB5 WILD-TYPE 
                 6                465 
  SERPINB5 MUTATED SERPINB5 WILD-TYPE 
                 0                 93 
$`SERPINB5 MUTATED`
TCGA-CM-4746 TCGA-D5-5539 TCGA-D5-6928 TCGA-AG-3612 TCGA-DT-5265 TCGA-DY-A0XA 
       37.02        19.59        11.64        19.99         5.29       126.44 

$`SERPINB5 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       20.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-5541 
       10.06        12.03        45.40        12.26        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3726 TCGA-AG-3727 
        0.99        15.95        19.99        13.94         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        4.01         5.03        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  SERPINB5 MUTATED SERPINB5 WILD-TYPE 
              5.29               0.00 
  SERPINB5 MUTATED SERPINB5 WILD-TYPE 
            126.44             148.01 
  SERPINB5 MUTATED SERPINB5 WILD-TYPE 
             19.79              20.28 
[1] "5.3 - 126.4 (19.8)" "0.0 - 148.0 (20.3)"
[1] "hr="     "9200000"
D1596V2, continuous
D1596V3, binary
                    cls
clus                   0   1
  SERPINB5 MUTATED     3   3
  SERPINB5 WILD-TYPE 363 116
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SERPINB5 MUTATED      3    3
  SERPINB5 WILD-TYPE  363  116
        clus
vv       SERPINB5 MUTATED SERPINB5 WILD-TYPE
  COLON                 3                363
  RECTUM                3                116
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SERPINB5 MUTATED         1        0        1         2         0         0
  SERPINB5 WILD-TYPE      90        1       31       136        10         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SERPINB5 MUTATED           0          1          1          0        0
  SERPINB5 WILD-TYPE        24         10         58         42       48
                    vv
clus                 STAGE IVA STAGE IVB
  SERPINB5 MUTATED           0         0
  SERPINB5 WILD-TYPE        18         1
D1596V4, multiclass
            clus
vv           SERPINB5 MUTATED SERPINB5 WILD-TYPE
  STAGE I                   1                 90
  STAGE IA                  0                  1
  STAGE II                  1                 31
  STAGE IIA                 2                136
  STAGE IIB                 0                 10
  STAGE IIC                 0                  1
  STAGE III                 0                 24
  STAGE IIIA                1                 10
  STAGE IIIB                1                 58
  STAGE IIIC                0                 42
  STAGE IV                  0                 48
  STAGE IVA                 0                 18
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  SERPINB5 MUTATED     0   1   5   0
  SERPINB5 WILD-TYPE  17  91 324  50
D1596V5, multiclass
    clus
vv   SERPINB5 MUTATED SERPINB5 WILD-TYPE
  T1                0                 17
  T2                1                 91
  T3                5                324
  T4                0                 50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  SERPINB5 MUTATED     4   2   0
  SERPINB5 WILD-TYPE 283 111  87
D1596V6, multiclass
    clus
vv   SERPINB5 MUTATED SERPINB5 WILD-TYPE
  N0                4                283
  N1                2                111
  N2                0                 87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1596V7, binary
                    cls
clus                   0   1
  SERPINB5 MUTATED     6   0
  SERPINB5 WILD-TYPE 369  65
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SERPINB5 MUTATED      6    0
  SERPINB5 WILD-TYPE  369   65
   clus
vv  SERPINB5 MUTATED SERPINB5 WILD-TYPE
  0                6                369
  1                0                 65
[1] 2 2
[1] FALSE
D1596V8, binary
                    cls
clus                   0   1
  SERPINB5 MUTATED     2   4
  SERPINB5 WILD-TYPE 223 260
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SERPINB5 MUTATED      2    4
  SERPINB5 WILD-TYPE  223  260
        clus
vv       SERPINB5 MUTATED SERPINB5 WILD-TYPE
  FEMALE                2                223
  MALE                  4                260
[1] 2 2
[1] FALSE
D1596V9, binary
                    cls
clus                   0   1
  SERPINB5 MUTATED     5   0
  SERPINB5 WILD-TYPE 345  22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SERPINB5 MUTATED      5    0
  SERPINB5 WILD-TYPE  345   22
     clus
vv    SERPINB5 MUTATED SERPINB5 WILD-TYPE
  NO                 5                345
  YES                0                 22
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SERPINB5 MUTATED                      1                             2
  SERPINB5 WILD-TYPE                  314                            45
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SERPINB5 MUTATED                       2                              1
  SERPINB5 WILD-TYPE                   104                              9
D1596V10, multiclass
                                clus
vv                               SERPINB5 MUTATED SERPINB5 WILD-TYPE
  COLON ADENOCARCINOMA                          1                314
  COLON MUCINOUS ADENOCARCINOMA                 2                 45
  RECTAL ADENOCARCINOMA                         2                104
  RECTAL MUCINOUS ADENOCARCINOMA                1                  9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  SERPINB5 MUTATED     4   0   0   1
  SERPINB5 WILD-TYPE 341   4  31  24
D1596V11, multiclass
    clus
vv   SERPINB5 MUTATED SERPINB5 WILD-TYPE
  R0                4                341
  R1                0                  4
  R2                0                 31
  RX                1                 24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1596V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SERPINB5 MUTATED                                  0     1
  SERPINB5 WILD-TYPE                                1    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  SERPINB5 MUTATED                           1     3
  SERPINB5 WILD-TYPE                        21   223
D1596V13, multiclass
                                  clus
vv                                 SERPINB5 MUTATED SERPINB5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                 10
  BLACK OR AFRICAN AMERICAN                       1                 21
  WHITE                                           3                223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1597) Variable = HIPK3 MUTATION ANALYSIS
D1597V1, survival
                 sevent
clus2               0   1
  HIPK3 MUTATED     8   0
  HIPK3 WILD-TYPE 370  93
  HIPK3 MUTATED HIPK3 WILD-TYPE 
              8             463 
  HIPK3 MUTATED HIPK3 WILD-TYPE 
              0              93 
$`HIPK3 MUTATED`
TCGA-A6-6649 TCGA-AA-3864 TCGA-AA-3977 TCGA-AU-6004 TCGA-CK-5913 TCGA-G4-6310 
       24.16        53.00        25.02        27.09        51.32        63.62 
TCGA-AG-A002 TCGA-G5-6641 
       20.98        26.43 

$`HIPK3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.08        25.18        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 
       32.05         0.99        31.07        31.07        30.05        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
        0.20        14.50        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       49.08         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       44.68        55.04        85.48        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 
       55.76 

  HIPK3 MUTATED HIPK3 WILD-TYPE 
          20.98            0.00 
  HIPK3 MUTATED HIPK3 WILD-TYPE 
          63.62          148.01 
  HIPK3 MUTATED HIPK3 WILD-TYPE 
          26.76           20.02 
[1] "21.0 - 63.6 (26.8)" "0.0 - 148.0 (20.0)"
[1] "hr="     "9300000"
D1597V2, continuous
D1597V3, binary
                 cls
clus                0   1
  HIPK3 MUTATED     6   2
  HIPK3 WILD-TYPE 360 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HIPK3 MUTATED      6    2
  HIPK3 WILD-TYPE  360  117
        clus
vv       HIPK3 MUTATED HIPK3 WILD-TYPE
  COLON              6             360
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  HIPK3 MUTATED         2        0        1         1         0         0
  HIPK3 WILD-TYPE      89        1       31       137        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  HIPK3 MUTATED           0          1          2          0        0         0
  HIPK3 WILD-TYPE        24         10         57         42       48        18
                 vv
clus              STAGE IVB
  HIPK3 MUTATED           0
  HIPK3 WILD-TYPE         1
D1597V4, multiclass
            clus
vv           HIPK3 MUTATED HIPK3 WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              1             137
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             1              10
  STAGE IIIB             2              57
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  HIPK3 MUTATED     1   3   4   0
  HIPK3 WILD-TYPE  16  89 325  50
D1597V5, multiclass
    clus
vv   HIPK3 MUTATED HIPK3 WILD-TYPE
  T1             1              16
  T2             3              89
  T3             4             325
  T4             0              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  HIPK3 MUTATED     5   3   0
  HIPK3 WILD-TYPE 282 110  87
D1597V6, multiclass
    clus
vv   HIPK3 MUTATED HIPK3 WILD-TYPE
  N0             5             282
  N1             3             110
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1597V7, binary
                 cls
clus                0   1
  HIPK3 MUTATED     5   0
  HIPK3 WILD-TYPE 370  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HIPK3 MUTATED      5    0
  HIPK3 WILD-TYPE  370   65
   clus
vv  HIPK3 MUTATED HIPK3 WILD-TYPE
  0             5             370
  1             0              65
[1] 2 2
[1] FALSE
D1597V8, binary
                 cls
clus                0   1
  HIPK3 MUTATED     2   6
  HIPK3 WILD-TYPE 223 258
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HIPK3 MUTATED      2    6
  HIPK3 WILD-TYPE  223  258
        clus
vv       HIPK3 MUTATED HIPK3 WILD-TYPE
  FEMALE             2             223
  MALE               6             258
[1] 2 2
[1] FALSE
D1597V9, binary
                 cls
clus                0   1
  HIPK3 MUTATED     6   1
  HIPK3 WILD-TYPE 344  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HIPK3 MUTATED      6    1
  HIPK3 WILD-TYPE  344   21
     clus
vv    HIPK3 MUTATED HIPK3 WILD-TYPE
  NO              6             344
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  HIPK3 MUTATED                      6                             0
  HIPK3 WILD-TYPE                  309                            47
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  HIPK3 MUTATED                       1                              1
  HIPK3 WILD-TYPE                   105                              9
D1597V10, multiclass
                                clus
vv                               HIPK3 MUTATED HIPK3 WILD-TYPE
  COLON ADENOCARCINOMA                       6             309
  COLON MUCINOUS ADENOCARCINOMA              0              47
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             1               9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  HIPK3 MUTATED     5   0   0   1
  HIPK3 WILD-TYPE 340   4  31  24
D1597V11, multiclass
    clus
vv   HIPK3 MUTATED HIPK3 WILD-TYPE
  R0             5             340
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1597V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HIPK3 MUTATED                                  0     0
  HIPK3 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  HIPK3 MUTATED                           0     5
  HIPK3 WILD-TYPE                        22   221
D1597V13, multiclass
                                  clus
vv                                 HIPK3 MUTATED HIPK3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        5             221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1598) Variable = NLRP11 MUTATION ANALYSIS
D1598V1, survival
                  sevent
clus2                0   1
  NLRP11 MUTATED    15   4
  NLRP11 WILD-TYPE 363  89
  NLRP11 MUTATED NLRP11 WILD-TYPE 
              19              452 
  NLRP11 MUTATED NLRP11 WILD-TYPE 
               4               89 
$`NLRP11 MUTATED`
TCGA-A6-6141 TCGA-A6-6653 TCGA-A6-6781 TCGA-AA-3510 TCGA-AA-3672 TCGA-AA-3715 
        8.38        24.39        19.66        63.98         0.92        19.04 
TCGA-AA-3833 TCGA-AA-A00E TCGA-AA-A00N TCGA-AZ-4315 TCGA-CA-5797 TCGA-CA-6717 
       15.95        30.02         4.01        58.39         3.29        12.76 
TCGA-F4-6570 TCGA-G4-6588 TCGA-AF-6136 TCGA-AG-3892 TCGA-AG-A00Y TCGA-DY-A1DC 
        6.18        26.17        15.39        13.02        23.01        41.36 
TCGA-G5-6235 
       55.76 

$`NLRP11 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 
       22.09        22.06        32.71        27.09        22.52        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 
       25.18        24.16        21.76        24.69        23.87        20.12 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 
       20.28         7.04         3.02         1.02        35.01         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
       14.01        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
        1.02        17.98        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       38.04        19.00        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.06         3.25         0.07        12.20        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       31.96        35.74        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       35.80        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       16.83        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 
       19.99         1.02        17.95        36.95        17.03        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
        6.02        25.97        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.03         5.29       126.44        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6641 
        0.69        26.43 

  NLRP11 MUTATED NLRP11 WILD-TYPE 
            0.92             0.00 
  NLRP11 MUTATED NLRP11 WILD-TYPE 
           63.98           148.01 
  NLRP11 MUTATED NLRP11 WILD-TYPE 
          19.040           20.415 
[1] "0.9 - 64.0 (19.0)"  "0.0 - 148.0 (20.4)"
[1] "hr=" "1.1"
D1598V2, continuous
D1598V3, binary
                  cls
clus                 0   1
  NLRP11 MUTATED    15   5
  NLRP11 WILD-TYPE 351 114
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NLRP11 MUTATED     15    5
  NLRP11 WILD-TYPE  351  114
        clus
vv       NLRP11 MUTATED NLRP11 WILD-TYPE
  COLON              15              351
  RECTUM              5              114
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NLRP11 MUTATED         2        0        2        11         1         0
  NLRP11 WILD-TYPE      89        1       30       127         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NLRP11 MUTATED           1          0          2          1        0
  NLRP11 WILD-TYPE        23         11         57         41       48
                  vv
clus               STAGE IVA STAGE IVB
  NLRP11 MUTATED           0         0
  NLRP11 WILD-TYPE        18         1
D1598V4, multiclass
            clus
vv           NLRP11 MUTATED NLRP11 WILD-TYPE
  STAGE I                 2               89
  STAGE IA                0                1
  STAGE II                2               30
  STAGE IIA              11              127
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               1               23
  STAGE IIIA              0               11
  STAGE IIIB              2               57
  STAGE IIIC              1               41
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  NLRP11 MUTATED     1   1  16   2
  NLRP11 WILD-TYPE  16  91 313  48
D1598V5, multiclass
    clus
vv   NLRP11 MUTATED NLRP11 WILD-TYPE
  T1              1               16
  T2              1               91
  T3             16              313
  T4              2               48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  NLRP11 MUTATED    16   4   0
  NLRP11 WILD-TYPE 271 109  87
D1598V6, multiclass
    clus
vv   NLRP11 MUTATED NLRP11 WILD-TYPE
  N0             16              271
  N1              4              109
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1598V7, binary
                  cls
clus                 0   1
  NLRP11 MUTATED    17   0
  NLRP11 WILD-TYPE 358  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NLRP11 MUTATED     17    0
  NLRP11 WILD-TYPE  358   65
   clus
vv  NLRP11 MUTATED NLRP11 WILD-TYPE
  0             17              358
  1              0               65
[1] 2 2
[1] FALSE
D1598V8, binary
                  cls
clus                 0   1
  NLRP11 MUTATED     8  12
  NLRP11 WILD-TYPE 217 252
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NLRP11 MUTATED      8   12
  NLRP11 WILD-TYPE  217  252
        clus
vv       NLRP11 MUTATED NLRP11 WILD-TYPE
  FEMALE              8              217
  MALE               12              252
[1] 2 2
[1] FALSE
D1598V9, binary
                  cls
clus                 0   1
  NLRP11 MUTATED    16   1
  NLRP11 WILD-TYPE 334  21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NLRP11 MUTATED     16    1
  NLRP11 WILD-TYPE  334   21
     clus
vv    NLRP11 MUTATED NLRP11 WILD-TYPE
  NO              16              334
  YES              1               21
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  NLRP11 MUTATED                     12                             3
  NLRP11 WILD-TYPE                  303                            44
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  NLRP11 MUTATED                       5                              0
  NLRP11 WILD-TYPE                   101                             10
D1598V10, multiclass
                                clus
vv                               NLRP11 MUTATED NLRP11 WILD-TYPE
  COLON ADENOCARCINOMA                       12              303
  COLON MUCINOUS ADENOCARCINOMA               3               44
  RECTAL ADENOCARCINOMA                       5              101
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  NLRP11 MUTATED    14   1   0   1
  NLRP11 WILD-TYPE 331   3  31  24
D1598V11, multiclass
    clus
vv   NLRP11 MUTATED NLRP11 WILD-TYPE
  R0             14              331
  R1              1                3
  R2              0               31
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1598V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NLRP11 MUTATED                                  0     2
  NLRP11 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  NLRP11 MUTATED                           1     8
  NLRP11 WILD-TYPE                        21   218
D1598V13, multiclass
                                  clus
vv                                 NLRP11 MUTATED NLRP11 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                9
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                         8              218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1599) Variable = DZIP1L MUTATION ANALYSIS
D1599V1, survival
                  sevent
clus2                0   1
  DZIP1L MUTATED    11   4
  DZIP1L WILD-TYPE 367  89
  DZIP1L MUTATED DZIP1L WILD-TYPE 
              15              456 
  DZIP1L MUTATED DZIP1L WILD-TYPE 
               4               89 
$`DZIP1L MUTATED`
TCGA-A6-6653 TCGA-AA-3510 TCGA-AA-3950 TCGA-AA-3977 TCGA-AA-A010 TCGA-AD-5900 
       24.39        63.98        24.00        25.02        34.98         0.07 
TCGA-AZ-6598 TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-6171 TCGA-F4-6460 TCGA-G4-6307 
       49.41        12.76        10.06        14.04        31.96        55.04 
TCGA-AG-A002 TCGA-AG-A02G TCGA-DC-6155 
       20.98        38.96        13.97 

$`DZIP1L WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
       25.08        25.18        24.16        21.76        24.69        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 
       12.99        24.00        33.01        26.01         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.07        12.20        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       12.99        13.02        15.02        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
       98.24         8.61        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       44.68        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02N TCGA-AG-A02X 
       64.01        10.98        49.97         1.94        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
        7.17        15.02         5.03        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  DZIP1L MUTATED DZIP1L WILD-TYPE 
            0.07             0.00 
  DZIP1L MUTATED DZIP1L WILD-TYPE 
           63.98           148.01 
  DZIP1L MUTATED DZIP1L WILD-TYPE 
          24.390           20.035 
[1] "0.1 - 64.0 (24.4)"  "0.0 - 148.0 (20.0)"
[1] "hr=" "1.2"
D1599V2, continuous
D1599V3, binary
                  cls
clus                 0   1
  DZIP1L MUTATED    13   3
  DZIP1L WILD-TYPE 353 116
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DZIP1L MUTATED     13    3
  DZIP1L WILD-TYPE  353  116
        clus
vv       DZIP1L MUTATED DZIP1L WILD-TYPE
  COLON              13              353
  RECTUM              3              116
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DZIP1L MUTATED         5        0        2         3         1         0
  DZIP1L WILD-TYPE      86        1       30       135         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DZIP1L MUTATED           0          1          2          0        1
  DZIP1L WILD-TYPE        24         10         57         42       47
                  vv
clus               STAGE IVA STAGE IVB
  DZIP1L MUTATED           0         0
  DZIP1L WILD-TYPE        18         1
D1599V4, multiclass
            clus
vv           DZIP1L MUTATED DZIP1L WILD-TYPE
  STAGE I                 5               86
  STAGE IA                0                1
  STAGE II                2               30
  STAGE IIA               3              135
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              1               10
  STAGE IIIB              2               57
  STAGE IIIC              0               42
  STAGE IV                1               47
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  DZIP1L MUTATED     0   8   7   1
  DZIP1L WILD-TYPE  17  84 322  49
D1599V5, multiclass
    clus
vv   DZIP1L MUTATED DZIP1L WILD-TYPE
  T1              0               17
  T2              8               84
  T3              7              322
  T4              1               49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  DZIP1L MUTATED    12   4   0
  DZIP1L WILD-TYPE 275 109  87
D1599V6, multiclass
    clus
vv   DZIP1L MUTATED DZIP1L WILD-TYPE
  N0             12              275
  N1              4              109
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1599V7, binary
                  cls
clus                 0   1
  DZIP1L MUTATED    11   1
  DZIP1L WILD-TYPE 364  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DZIP1L MUTATED     11    1
  DZIP1L WILD-TYPE  364   64
   clus
vv  DZIP1L MUTATED DZIP1L WILD-TYPE
  0             11              364
  1              1               64
[1] 2 2
[1] FALSE
D1599V8, binary
                  cls
clus                 0   1
  DZIP1L MUTATED     7   9
  DZIP1L WILD-TYPE 218 255
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DZIP1L MUTATED      7    9
  DZIP1L WILD-TYPE  218  255
        clus
vv       DZIP1L MUTATED DZIP1L WILD-TYPE
  FEMALE              7              218
  MALE                9              255
[1] 2 2
[1] FALSE
D1599V9, binary
                  cls
clus                 0   1
  DZIP1L MUTATED    14   0
  DZIP1L WILD-TYPE 336  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DZIP1L MUTATED     14    0
  DZIP1L WILD-TYPE  336   22
     clus
vv    DZIP1L MUTATED DZIP1L WILD-TYPE
  NO              14              336
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  DZIP1L MUTATED                     10                             3
  DZIP1L WILD-TYPE                  305                            44
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  DZIP1L MUTATED                       3                              0
  DZIP1L WILD-TYPE                   103                             10
D1599V10, multiclass
                                clus
vv                               DZIP1L MUTATED DZIP1L WILD-TYPE
  COLON ADENOCARCINOMA                       10              305
  COLON MUCINOUS ADENOCARCINOMA               3               44
  RECTAL ADENOCARCINOMA                       3              103
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  DZIP1L MUTATED     9   0   1   3
  DZIP1L WILD-TYPE 336   4  30  22
D1599V11, multiclass
    clus
vv   DZIP1L MUTATED DZIP1L WILD-TYPE
  R0              9              336
  R1              0                4
  R2              1               30
  RX              3               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1599V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DZIP1L MUTATED                                  0     2
  DZIP1L WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  DZIP1L MUTATED                           0     8
  DZIP1L WILD-TYPE                        22   218
D1599V13, multiclass
                                  clus
vv                                 DZIP1L MUTATED DZIP1L WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                9
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         8              218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1600) Variable = GSG2 MUTATION ANALYSIS
D1600V1, survival
                sevent
clus2              0   1
  GSG2 MUTATED     4   1
  GSG2 WILD-TYPE 374  92
  GSG2 MUTATED GSG2 WILD-TYPE 
             5            466 
  GSG2 MUTATED GSG2 WILD-TYPE 
             1             92 
$`GSG2 MUTATED`
TCGA-A6-5665 TCGA-A6-6780 TCGA-AA-3856 TCGA-CM-5861 TCGA-F4-6570 
       22.06        20.12         0.99        15.02         6.18 

$`GSG2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 
       98.24         8.61        31.96        35.74        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  GSG2 MUTATED GSG2 WILD-TYPE 
          0.99           0.00 
  GSG2 MUTATED GSG2 WILD-TYPE 
         22.06         148.01 
  GSG2 MUTATED GSG2 WILD-TYPE 
        15.020         20.415 
[1] "1.0 - 22.1 (15.0)"  "0.0 - 148.0 (20.4)"
[1] "hr=" "2"  
D1600V2, continuous
D1600V3, binary
                cls
clus               0   1
  GSG2 MUTATED     6   0
  GSG2 WILD-TYPE 360 119
[1] "tbl2"
                cls
clus             [,1] [,2]
  GSG2 MUTATED      6    0
  GSG2 WILD-TYPE  360  119
        clus
vv       GSG2 MUTATED GSG2 WILD-TYPE
  COLON             6            360
  RECTUM            0            119
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GSG2 MUTATED         0        0        0         6         0         0
  GSG2 WILD-TYPE      91        1       32       132        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  GSG2 MUTATED           0          0          0          0        0         0
  GSG2 WILD-TYPE        24         11         59         42       48        18
                vv
clus             STAGE IVB
  GSG2 MUTATED           0
  GSG2 WILD-TYPE         1
D1600V4, multiclass
            clus
vv           GSG2 MUTATED GSG2 WILD-TYPE
  STAGE I               0             91
  STAGE IA              0              1
  STAGE II              0             32
  STAGE IIA             6            132
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            0             59
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  GSG2 MUTATED     0   0   6   0
  GSG2 WILD-TYPE  17  92 323  50
D1600V5, multiclass
    clus
vv   GSG2 MUTATED GSG2 WILD-TYPE
  T1            0             17
  T2            0             92
  T3            6            323
  T4            0             50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  GSG2 MUTATED     6   0   0
  GSG2 WILD-TYPE 281 113  87
D1600V6, multiclass
    clus
vv   GSG2 MUTATED GSG2 WILD-TYPE
  N0            6            281
  N1            0            113
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1600V7, binary
                cls
clus               0   1
  GSG2 MUTATED     5   0
  GSG2 WILD-TYPE 370  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  GSG2 MUTATED      5    0
  GSG2 WILD-TYPE  370   65
   clus
vv  GSG2 MUTATED GSG2 WILD-TYPE
  0            5            370
  1            0             65
[1] 2 2
[1] FALSE
D1600V8, binary
                cls
clus               0   1
  GSG2 MUTATED     4   2
  GSG2 WILD-TYPE 221 262
[1] "tbl2"
                cls
clus             [,1] [,2]
  GSG2 MUTATED      4    2
  GSG2 WILD-TYPE  221  262
        clus
vv       GSG2 MUTATED GSG2 WILD-TYPE
  FEMALE            4            221
  MALE              2            262
[1] 2 2
[1] FALSE
D1600V9, binary
                cls
clus               0   1
  GSG2 MUTATED     4   0
  GSG2 WILD-TYPE 346  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  GSG2 MUTATED      4    0
  GSG2 WILD-TYPE  346   22
     clus
vv    GSG2 MUTATED GSG2 WILD-TYPE
  NO             4            346
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  GSG2 MUTATED                      5                             1
  GSG2 WILD-TYPE                  310                            46
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  GSG2 MUTATED                       0                              0
  GSG2 WILD-TYPE                   106                             10
D1600V10, multiclass
                                clus
vv                               GSG2 MUTATED GSG2 WILD-TYPE
  COLON ADENOCARCINOMA                      5            310
  COLON MUCINOUS ADENOCARCINOMA             1             46
  RECTAL ADENOCARCINOMA                     0            106
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  GSG2 MUTATED     5   0   0   0
  GSG2 WILD-TYPE 340   4  31  25
D1600V11, multiclass
    clus
vv   GSG2 MUTATED GSG2 WILD-TYPE
  R0            5            340
  R1            0              4
  R2            0             31
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1600V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GSG2 MUTATED                                  0     0
  GSG2 WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  GSG2 MUTATED                           0     4
  GSG2 WILD-TYPE                        22   222
D1600V13, multiclass
                                  clus
vv                                 GSG2 MUTATED GSG2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       4            222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1601) Variable = FAM193A MUTATION ANALYSIS
D1601V1, survival
                   sevent
clus2                 0   1
  FAM193A MUTATED    14   3
  FAM193A WILD-TYPE 364  90
  FAM193A MUTATED FAM193A WILD-TYPE 
               17               454 
  FAM193A MUTATED FAM193A WILD-TYPE 
                3                90 
$`FAM193A MUTATED`
TCGA-A6-5665 TCGA-A6-6780 TCGA-AA-3660 TCGA-AA-3947 TCGA-AD-5900 TCGA-AD-6895 
       22.06        20.12        78.08        33.01         0.07         0.72 
TCGA-AD-6964 TCGA-AZ-6598 TCGA-CA-6718 TCGA-CK-4952 TCGA-CK-5913 TCGA-CM-5861 
       10.88        49.41        10.06        15.62        51.32        15.02 
TCGA-CM-6169 TCGA-D5-6927 TCGA-D5-7000 TCGA-G4-6304 TCGA-G4-6588 
       13.02         9.44        10.26        53.62        26.17 

$`FAM193A WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       13.94        19.99        61.02         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 
       40.96        21.37        15.52        56.55         0.79         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 
        5.13       106.75        22.36        62.79        88.21         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.20        12.76        14.30        17.56       148.01        85.45 
TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       49.08         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 
       22.03        22.98        30.08        32.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6170 TCGA-CM-6171 
       16.04        21.99        14.99        12.99        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-DM-A0X9 
       11.64         4.80         1.51        12.00        11.38       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       65.85        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        35.80        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  FAM193A MUTATED FAM193A WILD-TYPE 
             0.07              0.00 
  FAM193A MUTATED FAM193A WILD-TYPE 
            78.08            148.01 
  FAM193A MUTATED FAM193A WILD-TYPE 
           15.620            20.415 
[1] "0.1 - 78.1 (15.6)"  "0.0 - 148.0 (20.4)"
[1] "hr=" "1.1"
D1601V2, continuous
D1601V3, binary
                   cls
clus                  0   1
  FAM193A MUTATED    17   0
  FAM193A WILD-TYPE 349 119
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM193A MUTATED     17    0
  FAM193A WILD-TYPE  349  119
        clus
vv       FAM193A MUTATED FAM193A WILD-TYPE
  COLON               17               349
  RECTUM               0               119
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FAM193A MUTATED         2        0        2         8         2         0
  FAM193A WILD-TYPE      89        1       30       130         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FAM193A MUTATED           0          0          0          1        0
  FAM193A WILD-TYPE        24         11         59         41       48
                   vv
clus                STAGE IVA STAGE IVB
  FAM193A MUTATED           0         0
  FAM193A WILD-TYPE        18         1
D1601V4, multiclass
            clus
vv           FAM193A MUTATED FAM193A WILD-TYPE
  STAGE I                  2                89
  STAGE IA                 0                 1
  STAGE II                 2                30
  STAGE IIA                8               130
  STAGE IIB                2                 8
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               0                11
  STAGE IIIB               0                59
  STAGE IIIC               1                41
  STAGE IV                 0                48
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  FAM193A MUTATED     0   2  11   4
  FAM193A WILD-TYPE  17  90 318  46
D1601V5, multiclass
    clus
vv   FAM193A MUTATED FAM193A WILD-TYPE
  T1               0                17
  T2               2                90
  T3              11               318
  T4               4                46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  FAM193A MUTATED    14   1   2
  FAM193A WILD-TYPE 273 112  85
D1601V6, multiclass
    clus
vv   FAM193A MUTATED FAM193A WILD-TYPE
  N0              14               273
  N1               1               112
  N2               2                85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1601V7, binary
                   cls
clus                  0   1
  FAM193A MUTATED    11   0
  FAM193A WILD-TYPE 364  65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM193A MUTATED     11    0
  FAM193A WILD-TYPE  364   65
   clus
vv  FAM193A MUTATED FAM193A WILD-TYPE
  0              11               364
  1               0                65
[1] 2 2
[1] FALSE
D1601V8, binary
                   cls
clus                  0   1
  FAM193A MUTATED    10   7
  FAM193A WILD-TYPE 215 257
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM193A MUTATED     10    7
  FAM193A WILD-TYPE  215  257
        clus
vv       FAM193A MUTATED FAM193A WILD-TYPE
  FEMALE              10               215
  MALE                 7               257
[1] 2 2
[1] FALSE
D1601V9, binary
                   cls
clus                  0   1
  FAM193A MUTATED    14   0
  FAM193A WILD-TYPE 336  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM193A MUTATED     14    0
  FAM193A WILD-TYPE  336   22
     clus
vv    FAM193A MUTATED FAM193A WILD-TYPE
  NO               14               336
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  FAM193A MUTATED                     12                             5
  FAM193A WILD-TYPE                  303                            42
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  FAM193A MUTATED                       0                              0
  FAM193A WILD-TYPE                   106                             10
D1601V10, multiclass
                                clus
vv                               FAM193A MUTATED FAM193A WILD-TYPE
  COLON ADENOCARCINOMA                        12               303
  COLON MUCINOUS ADENOCARCINOMA                5                42
  RECTAL ADENOCARCINOMA                        0               106
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  FAM193A MUTATED    10   0   0   3
  FAM193A WILD-TYPE 335   4  31  22
D1601V11, multiclass
    clus
vv   FAM193A MUTATED FAM193A WILD-TYPE
  R0              10               335
  R1               0                 4
  R2               0                31
  RX               3                22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1601V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FAM193A MUTATED                                  0     1
  FAM193A WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  FAM193A MUTATED                           1    13
  FAM193A WILD-TYPE                        21   213
D1601V13, multiclass
                                  clus
vv                                 FAM193A MUTATED FAM193A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                10
  BLACK OR AFRICAN AMERICAN                      1                21
  WHITE                                         13               213
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1602) Variable = ENC1 MUTATION ANALYSIS
D1602V1, survival
                sevent
clus2              0   1
  ENC1 MUTATED    11   2
  ENC1 WILD-TYPE 367  91
  ENC1 MUTATED ENC1 WILD-TYPE 
            13            458 
  ENC1 MUTATED ENC1 WILD-TYPE 
             2             91 
$`ENC1 MUTATED`
TCGA-AA-3510 TCGA-AA-3851 TCGA-AA-3949 TCGA-AA-A010 TCGA-AZ-4315 TCGA-AZ-6598 
       63.98        33.07        26.01        34.98        58.39        49.41 
TCGA-CM-6171 TCGA-D5-5540 TCGA-D5-6541 TCGA-F4-6808 TCGA-G4-6303 TCGA-G4-6586 
       14.04        56.09        15.58        33.67        65.85        35.80 
TCGA-AG-3742 
        0.99 

$`ENC1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       17.03        10.06         0.00         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       12.99        24.00        33.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       88.21         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5541 
       10.06        12.03        45.40        12.26        19.59        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6898 TCGA-D5-6920 
        4.80        17.13        12.49        16.14         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6809 
       47.87         1.55        34.42        41.42        16.24        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6304 
        0.53        47.41        35.31       133.18        74.56        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       22.09        13.78        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  ENC1 MUTATED ENC1 WILD-TYPE 
          0.99           0.00 
  ENC1 MUTATED ENC1 WILD-TYPE 
         65.85         148.01 
  ENC1 MUTATED ENC1 WILD-TYPE 
         34.98          20.02 
[1] "1.0 - 65.8 (35.0)"  "0.0 - 148.0 (20.0)"
[1] "hr=" "1.9"
D1602V2, continuous
D1602V3, binary
                cls
clus               0   1
  ENC1 MUTATED    12   1
  ENC1 WILD-TYPE 354 118
[1] "tbl2"
                cls
clus             [,1] [,2]
  ENC1 MUTATED     12    1
  ENC1 WILD-TYPE  354  118
        clus
vv       ENC1 MUTATED ENC1 WILD-TYPE
  COLON            12            354
  RECTUM            1            118
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ENC1 MUTATED         3        0        2         5         1         0
  ENC1 WILD-TYPE      88        1       30       133         9         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ENC1 MUTATED           0          0          1          0        1         0
  ENC1 WILD-TYPE        24         11         58         42       47        18
                vv
clus             STAGE IVB
  ENC1 MUTATED           0
  ENC1 WILD-TYPE         1
D1602V4, multiclass
            clus
vv           ENC1 MUTATED ENC1 WILD-TYPE
  STAGE I               3             88
  STAGE IA              0              1
  STAGE II              2             30
  STAGE IIA             5            133
  STAGE IIB             1              9
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            1             58
  STAGE IIIC            0             42
  STAGE IV              1             47
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  ENC1 MUTATED     2   1   9   1
  ENC1 WILD-TYPE  15  91 320  49
D1602V5, multiclass
    clus
vv   ENC1 MUTATED ENC1 WILD-TYPE
  T1            2             15
  T2            1             91
  T3            9            320
  T4            1             49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  ENC1 MUTATED    11   2   0
  ENC1 WILD-TYPE 276 111  87
D1602V6, multiclass
    clus
vv   ENC1 MUTATED ENC1 WILD-TYPE
  N0           11            276
  N1            2            111
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1602V7, binary
                cls
clus               0   1
  ENC1 MUTATED    11   1
  ENC1 WILD-TYPE 364  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  ENC1 MUTATED     11    1
  ENC1 WILD-TYPE  364   64
   clus
vv  ENC1 MUTATED ENC1 WILD-TYPE
  0           11            364
  1            1             64
[1] 2 2
[1] FALSE
D1602V8, binary
                cls
clus               0   1
  ENC1 MUTATED     8   5
  ENC1 WILD-TYPE 217 259
[1] "tbl2"
                cls
clus             [,1] [,2]
  ENC1 MUTATED      8    5
  ENC1 WILD-TYPE  217  259
        clus
vv       ENC1 MUTATED ENC1 WILD-TYPE
  FEMALE            8            217
  MALE              5            259
[1] 2 2
[1] FALSE
D1602V9, binary
                cls
clus               0   1
  ENC1 MUTATED    12   0
  ENC1 WILD-TYPE 338  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  ENC1 MUTATED     12    0
  ENC1 WILD-TYPE  338   22
     clus
vv    ENC1 MUTATED ENC1 WILD-TYPE
  NO            12            338
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ENC1 MUTATED                     11                             1
  ENC1 WILD-TYPE                  304                            46
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ENC1 MUTATED                       1                              0
  ENC1 WILD-TYPE                   105                             10
D1602V10, multiclass
                                clus
vv                               ENC1 MUTATED ENC1 WILD-TYPE
  COLON ADENOCARCINOMA                     11            304
  COLON MUCINOUS ADENOCARCINOMA             1             46
  RECTAL ADENOCARCINOMA                     1            105
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  ENC1 MUTATED    12   0   0   0
  ENC1 WILD-TYPE 333   4  31  25
D1602V11, multiclass
    clus
vv   ENC1 MUTATED ENC1 WILD-TYPE
  R0           12            333
  R1            0              4
  R2            0             31
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1602V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ENC1 MUTATED                                  0     0
  ENC1 WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  ENC1 MUTATED                           0     8
  ENC1 WILD-TYPE                        22   218
D1602V13, multiclass
                                  clus
vv                                 ENC1 MUTATED ENC1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       8            218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1603) Variable = RUSC2 MUTATION ANALYSIS
D1603V1, survival
                 sevent
clus2               0   1
  RUSC2 MUTATED    11   1
  RUSC2 WILD-TYPE 367  92
  RUSC2 MUTATED RUSC2 WILD-TYPE 
             12             459 
  RUSC2 MUTATED RUSC2 WILD-TYPE 
              1              92 
$`RUSC2 MUTATED`
TCGA-A6-6648 TCGA-AA-3715 TCGA-AA-3819 TCGA-AA-3864 TCGA-AA-A00J TCGA-AA-A010 
       25.18        19.04        25.02        53.00        18.05        34.98 
TCGA-AD-5900 TCGA-CK-4950 TCGA-CM-4746 TCGA-CM-6674 TCGA-DM-A1HB TCGA-EI-6507 
        0.07        85.45        37.02        12.95       135.65        19.96 

$`RUSC2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.08        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 
       36.00         5.03        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       35.05        33.04         0.99         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        31.07        30.05        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 
        0.92        41.00        39.98        18.05        40.96        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
      148.01        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4747 
       82.95         1.91       124.27        23.05        20.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6675 
       12.99        13.02        15.02        14.04        11.01        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 
      140.38         7.50        44.32       131.51       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6510 
       51.48        32.61         0.49        20.55        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  RUSC2 MUTATED RUSC2 WILD-TYPE 
           0.07            0.00 
  RUSC2 MUTATED RUSC2 WILD-TYPE 
         135.65          148.01 
  RUSC2 MUTATED RUSC2 WILD-TYPE 
          25.10           20.12 
[1] "0.1 - 135.7 (25.1)" "0.0 - 148.0 (20.1)"
[1] "hr=" "3.3"
D1603V2, continuous
D1603V3, binary
                 cls
clus                0   1
  RUSC2 MUTATED    12   1
  RUSC2 WILD-TYPE 354 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RUSC2 MUTATED     12    1
  RUSC2 WILD-TYPE  354  118
        clus
vv       RUSC2 MUTATED RUSC2 WILD-TYPE
  COLON             12             354
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RUSC2 MUTATED         2        0        2         3         2         0
  RUSC2 WILD-TYPE      89        1       30       135         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RUSC2 MUTATED           0          0          3          0        0         1
  RUSC2 WILD-TYPE        24         11         56         42       48        17
                 vv
clus              STAGE IVB
  RUSC2 MUTATED           0
  RUSC2 WILD-TYPE         1
D1603V4, multiclass
            clus
vv           RUSC2 MUTATED RUSC2 WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA              3             135
  STAGE IIB              2               8
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             3              56
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  RUSC2 MUTATED     0   2   8   3
  RUSC2 WILD-TYPE  17  90 321  47
D1603V5, multiclass
    clus
vv   RUSC2 MUTATED RUSC2 WILD-TYPE
  T1             0              17
  T2             2              90
  T3             8             321
  T4             3              47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  RUSC2 MUTATED    10   3   0
  RUSC2 WILD-TYPE 277 110  87
D1603V6, multiclass
    clus
vv   RUSC2 MUTATED RUSC2 WILD-TYPE
  N0            10             277
  N1             3             110
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1603V7, binary
                 cls
clus                0   1
  RUSC2 MUTATED    10   1
  RUSC2 WILD-TYPE 365  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RUSC2 MUTATED     10    1
  RUSC2 WILD-TYPE  365   64
   clus
vv  RUSC2 MUTATED RUSC2 WILD-TYPE
  0            10             365
  1             1              64
[1] 2 2
[1] FALSE
D1603V8, binary
                 cls
clus                0   1
  RUSC2 MUTATED     4   9
  RUSC2 WILD-TYPE 221 255
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RUSC2 MUTATED      4    9
  RUSC2 WILD-TYPE  221  255
        clus
vv       RUSC2 MUTATED RUSC2 WILD-TYPE
  FEMALE             4             221
  MALE               9             255
[1] 2 2
[1] FALSE
D1603V9, binary
                 cls
clus                0   1
  RUSC2 MUTATED    10   0
  RUSC2 WILD-TYPE 340  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RUSC2 MUTATED     10    0
  RUSC2 WILD-TYPE  340   22
     clus
vv    RUSC2 MUTATED RUSC2 WILD-TYPE
  NO             10             340
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  RUSC2 MUTATED                      9                             2
  RUSC2 WILD-TYPE                  306                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  RUSC2 MUTATED                       1                              0
  RUSC2 WILD-TYPE                   105                             10
D1603V10, multiclass
                                clus
vv                               RUSC2 MUTATED RUSC2 WILD-TYPE
  COLON ADENOCARCINOMA                       9             306
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  RUSC2 MUTATED     9   1   0   1
  RUSC2 WILD-TYPE 336   3  31  24
D1603V11, multiclass
    clus
vv   RUSC2 MUTATED RUSC2 WILD-TYPE
  R0             9             336
  R1             1               3
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1603V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RUSC2 MUTATED                                  0     0
  RUSC2 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  RUSC2 MUTATED                           2     6
  RUSC2 WILD-TYPE                        20   220
D1603V13, multiclass
                                  clus
vv                                 RUSC2 MUTATED RUSC2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    2              20
  WHITE                                        6             220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1604) Variable = WHAMM MUTATION ANALYSIS
D1604V1, survival
                 sevent
clus2               0   1
  WHAMM MUTATED     6   0
  WHAMM WILD-TYPE 372  93
  WHAMM MUTATED WHAMM WILD-TYPE 
              6             465 
  WHAMM MUTATED WHAMM WILD-TYPE 
              0              93 
$`WHAMM MUTATED`
TCGA-A6-3810 TCGA-AA-3864 TCGA-AA-A010 TCGA-AD-6895 TCGA-AZ-4315 TCGA-AH-6644 
       36.53        53.00        34.98         0.72        58.39         0.72 

$`WHAMM WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        32.75        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 
       32.05         0.99        31.07        31.07        30.05        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.79         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
        1.45        17.49         0.69         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  WHAMM MUTATED WHAMM WILD-TYPE 
           0.72            0.00 
  WHAMM MUTATED WHAMM WILD-TYPE 
          58.39          148.01 
  WHAMM MUTATED WHAMM WILD-TYPE 
         35.755          20.120 
[1] "0.7 - 58.4 (35.8)"  "0.0 - 148.0 (20.1)"
[1] "hr="     "9200000"
D1604V2, continuous
D1604V3, binary
                 cls
clus                0   1
  WHAMM MUTATED     5   1
  WHAMM WILD-TYPE 361 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WHAMM MUTATED      5    1
  WHAMM WILD-TYPE  361  118
        clus
vv       WHAMM MUTATED WHAMM WILD-TYPE
  COLON              5             361
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  WHAMM MUTATED         0        0        1         2         1         0
  WHAMM WILD-TYPE      91        1       31       136         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  WHAMM MUTATED           0          0          0          0        0         0
  WHAMM WILD-TYPE        24         11         59         42       48        18
                 vv
clus              STAGE IVB
  WHAMM MUTATED           0
  WHAMM WILD-TYPE         1
D1604V4, multiclass
            clus
vv           WHAMM MUTATED WHAMM WILD-TYPE
  STAGE I                0              91
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              2             136
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  WHAMM MUTATED     0   0   5   1
  WHAMM WILD-TYPE  17  92 324  49
D1604V5, multiclass
    clus
vv   WHAMM MUTATED WHAMM WILD-TYPE
  T1             0              17
  T2             0              92
  T3             5             324
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  WHAMM MUTATED     4   1   0
  WHAMM WILD-TYPE 283 112  87
D1604V6, multiclass
    clus
vv   WHAMM MUTATED WHAMM WILD-TYPE
  N0             4             283
  N1             1             112
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1604V7, binary
                 cls
clus                0   1
  WHAMM MUTATED     4   0
  WHAMM WILD-TYPE 371  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WHAMM MUTATED      4    0
  WHAMM WILD-TYPE  371   65
   clus
vv  WHAMM MUTATED WHAMM WILD-TYPE
  0             4             371
  1             0              65
[1] 2 2
[1] FALSE
D1604V8, binary
                 cls
clus                0   1
  WHAMM MUTATED     1   5
  WHAMM WILD-TYPE 224 259
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WHAMM MUTATED      1    5
  WHAMM WILD-TYPE  224  259
        clus
vv       WHAMM MUTATED WHAMM WILD-TYPE
  FEMALE             1             224
  MALE               5             259
[1] 2 2
[1] FALSE
D1604V9, binary
                 cls
clus                0   1
  WHAMM MUTATED     4   0
  WHAMM WILD-TYPE 346  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WHAMM MUTATED      4    0
  WHAMM WILD-TYPE  346   22
     clus
vv    WHAMM MUTATED WHAMM WILD-TYPE
  NO              4             346
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  WHAMM MUTATED                      5                             0
  WHAMM WILD-TYPE                  310                            47
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  WHAMM MUTATED                       1                              0
  WHAMM WILD-TYPE                   105                             10
D1604V10, multiclass
                                clus
vv                               WHAMM MUTATED WHAMM WILD-TYPE
  COLON ADENOCARCINOMA                       5             310
  COLON MUCINOUS ADENOCARCINOMA              0              47
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  WHAMM MUTATED     4   0   0   0
  WHAMM WILD-TYPE 341   4  31  25
D1604V11, multiclass
    clus
vv   WHAMM MUTATED WHAMM WILD-TYPE
  R0             4             341
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1604V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  WHAMM MUTATED                                  0     0
  WHAMM WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  WHAMM MUTATED                           0     4
  WHAMM WILD-TYPE                        22   222
D1604V13, multiclass
                                  clus
vv                                 WHAMM MUTATED WHAMM WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        4             222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1605) Variable = TAF1 MUTATION ANALYSIS
D1605V1, survival
                sevent
clus2              0   1
  TAF1 MUTATED    19   7
  TAF1 WILD-TYPE 359  86
  TAF1 MUTATED TAF1 WILD-TYPE 
            26            445 
  TAF1 MUTATED TAF1 WILD-TYPE 
             7             86 
$`TAF1 MUTATED`
TCGA-A6-2683 TCGA-A6-5657 TCGA-A6-5665 TCGA-AA-3697 TCGA-AA-3864 TCGA-AA-3977 
       16.57        31.63        22.06        85.05        53.00        25.02 
TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A03F TCGA-AZ-4315 TCGA-CA-6717 TCGA-CA-6718 
        4.01        34.98        18.05        58.39        12.76        10.06 
TCGA-CM-5349 TCGA-CM-5862 TCGA-CM-6166 TCGA-CM-6676 TCGA-D5-6922 TCGA-D5-6928 
       30.08         5.03        21.99        11.08         4.41        11.64 
TCGA-DM-A0XD TCGA-DM-A1DA TCGA-DM-A28E TCGA-G4-6309 TCGA-AG-3892 TCGA-AG-4001 
       24.43         7.50       119.93        85.48        13.02        36.03 
TCGA-AG-A002 TCGA-F5-6571 
       20.98        31.30 

$`TAF1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 
       30.44        29.19        33.53        23.61        22.09        32.71 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       27.09        22.52         8.38        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       31.07        30.05        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       39.98        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 
        3.06         3.25         3.29         0.07        12.20        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       22.98        32.02        15.02        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6167 
       15.02        12.00         2.96        29.03        16.04        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       13.05        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6923 
       12.49        16.14        15.58         1.48         3.68        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
       14.30         9.04         9.44         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       11.38        10.26       119.70        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA 
       49.91        13.32        12.59       140.38        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28F TCGA-DM-A28G 
      135.65       139.17         6.12        81.37        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 
       65.85        53.62        44.68        55.04        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 
        1.02        17.95        36.95        17.03        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4005 
        1.02        48.03        32.02        19.99        28.04        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       49.51        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  TAF1 MUTATED TAF1 WILD-TYPE 
          4.01           0.00 
  TAF1 MUTATED TAF1 WILD-TYPE 
        119.93         148.01 
  TAF1 MUTATED TAF1 WILD-TYPE 
        22.025         20.050 
[1] "4.0 - 119.9 (22.0)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.2"
D1605V2, continuous
D1605V3, binary
                cls
clus               0   1
  TAF1 MUTATED    22   4
  TAF1 WILD-TYPE 344 115
[1] "tbl2"
                cls
clus             [,1] [,2]
  TAF1 MUTATED     22    4
  TAF1 WILD-TYPE  344  115
        clus
vv       TAF1 MUTATED TAF1 WILD-TYPE
  COLON            22            344
  RECTUM            4            115
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TAF1 MUTATED         4        0        1        10         2         0
  TAF1 WILD-TYPE      87        1       31       128         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TAF1 MUTATED           2          1          2          1        1         1
  TAF1 WILD-TYPE        22         10         57         41       47        17
                vv
clus             STAGE IVB
  TAF1 MUTATED           0
  TAF1 WILD-TYPE         1
D1605V4, multiclass
            clus
vv           TAF1 MUTATED TAF1 WILD-TYPE
  STAGE I               4             87
  STAGE IA              0              1
  STAGE II              1             31
  STAGE IIA            10            128
  STAGE IIB             2              8
  STAGE IIC             0              1
  STAGE III             2             22
  STAGE IIIA            1             10
  STAGE IIIB            2             57
  STAGE IIIC            1             41
  STAGE IV              1             47
  STAGE IVA             1             17
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  TAF1 MUTATED     1   4  18   3
  TAF1 WILD-TYPE  16  88 311  47
D1605V5, multiclass
    clus
vv   TAF1 MUTATED TAF1 WILD-TYPE
  T1            1             16
  T2            4             88
  T3           18            311
  T4            3             47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  TAF1 MUTATED    20   4   2
  TAF1 WILD-TYPE 267 109  85
D1605V6, multiclass
    clus
vv   TAF1 MUTATED TAF1 WILD-TYPE
  N0           20            267
  N1            4            109
  N2            2             85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1605V7, binary
                cls
clus               0   1
  TAF1 MUTATED    23   2
  TAF1 WILD-TYPE 352  63
[1] "tbl2"
                cls
clus             [,1] [,2]
  TAF1 MUTATED     23    2
  TAF1 WILD-TYPE  352   63
   clus
vv  TAF1 MUTATED TAF1 WILD-TYPE
  0           23            352
  1            2             63
[1] 2 2
[1] FALSE
D1605V8, binary
                cls
clus               0   1
  TAF1 MUTATED    12  14
  TAF1 WILD-TYPE 213 250
[1] "tbl2"
                cls
clus             [,1] [,2]
  TAF1 MUTATED     12   14
  TAF1 WILD-TYPE  213  250
        clus
vv       TAF1 MUTATED TAF1 WILD-TYPE
  FEMALE           12            213
  MALE             14            250
[1] 2 2
[1] FALSE
D1605V9, binary
                cls
clus               0   1
  TAF1 MUTATED    20   0
  TAF1 WILD-TYPE 330  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  TAF1 MUTATED     20    0
  TAF1 WILD-TYPE  330   22
     clus
vv    TAF1 MUTATED TAF1 WILD-TYPE
  NO            20            330
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  TAF1 MUTATED                     18                             4
  TAF1 WILD-TYPE                  297                            43
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  TAF1 MUTATED                       4                              0
  TAF1 WILD-TYPE                   102                             10
D1605V10, multiclass
                                clus
vv                               TAF1 MUTATED TAF1 WILD-TYPE
  COLON ADENOCARCINOMA                     18            297
  COLON MUCINOUS ADENOCARCINOMA             4             43
  RECTAL ADENOCARCINOMA                     4            102
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  TAF1 MUTATED    20   0   0   2
  TAF1 WILD-TYPE 325   4  31  23
D1605V11, multiclass
    clus
vv   TAF1 MUTATED TAF1 WILD-TYPE
  R0           20            325
  R1            0              4
  R2            0             31
  RX            2             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1605V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TAF1 MUTATED                                  0     2
  TAF1 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  TAF1 MUTATED                           2    13
  TAF1 WILD-TYPE                        20   213
D1605V13, multiclass
                                  clus
vv                                 TAF1 MUTATED TAF1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              9
  BLACK OR AFRICAN AMERICAN                   2             20
  WHITE                                      13            213
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1606) Variable = METTL5 MUTATION ANALYSIS
D1606V1, survival
                  sevent
clus2                0   1
  METTL5 MUTATED     5   0
  METTL5 WILD-TYPE 373  93
  METTL5 MUTATED METTL5 WILD-TYPE 
               5              466 
  METTL5 MUTATED METTL5 WILD-TYPE 
               0               93 
$`METTL5 MUTATED`
TCGA-AA-3710 TCGA-AD-6889 TCGA-CM-5860 TCGA-CM-6171 TCGA-AG-A002 
       26.99        56.55        32.02        14.04        20.98 

$`METTL5 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
       19.00        36.00         5.03        85.05        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       15.52         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       12.99        13.02        15.02        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  METTL5 MUTATED METTL5 WILD-TYPE 
           14.04             0.00 
  METTL5 MUTATED METTL5 WILD-TYPE 
           56.55           148.01 
  METTL5 MUTATED METTL5 WILD-TYPE 
          26.990           20.085 
[1] "14.0 - 56.5 (27.0)" "0.0 - 148.0 (20.1)"
[1] "hr="     "9100000"
D1606V2, continuous
D1606V3, binary
                  cls
clus                 0   1
  METTL5 MUTATED     5   1
  METTL5 WILD-TYPE 361 118
[1] "tbl2"
                  cls
clus               [,1] [,2]
  METTL5 MUTATED      5    1
  METTL5 WILD-TYPE  361  118
        clus
vv       METTL5 MUTATED METTL5 WILD-TYPE
  COLON               5              361
  RECTUM              1              118
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  METTL5 MUTATED         2        0        0         3         0         0
  METTL5 WILD-TYPE      89        1       32       135        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  METTL5 MUTATED           1          0          0          0        0
  METTL5 WILD-TYPE        23         11         59         42       48
                  vv
clus               STAGE IVA STAGE IVB
  METTL5 MUTATED           0         0
  METTL5 WILD-TYPE        18         1
D1606V4, multiclass
            clus
vv           METTL5 MUTATED METTL5 WILD-TYPE
  STAGE I                 2               89
  STAGE IA                0                1
  STAGE II                0               32
  STAGE IIA               3              135
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               1               23
  STAGE IIIA              0               11
  STAGE IIIB              0               59
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  METTL5 MUTATED     0   2   4   0
  METTL5 WILD-TYPE  17  90 325  50
D1606V5, multiclass
    clus
vv   METTL5 MUTATED METTL5 WILD-TYPE
  T1              0               17
  T2              2               90
  T3              4              325
  T4              0               50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  METTL5 MUTATED     5   0   1
  METTL5 WILD-TYPE 282 113  86
D1606V6, multiclass
    clus
vv   METTL5 MUTATED METTL5 WILD-TYPE
  N0              5              282
  N1              0              113
  N2              1               86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1606V7, binary
                  cls
clus                 0   1
  METTL5 MUTATED     6   0
  METTL5 WILD-TYPE 369  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  METTL5 MUTATED      6    0
  METTL5 WILD-TYPE  369   65
   clus
vv  METTL5 MUTATED METTL5 WILD-TYPE
  0              6              369
  1              0               65
[1] 2 2
[1] FALSE
D1606V8, binary
                  cls
clus                 0   1
  METTL5 MUTATED     2   4
  METTL5 WILD-TYPE 223 260
[1] "tbl2"
                  cls
clus               [,1] [,2]
  METTL5 MUTATED      2    4
  METTL5 WILD-TYPE  223  260
        clus
vv       METTL5 MUTATED METTL5 WILD-TYPE
  FEMALE              2              223
  MALE                4              260
[1] 2 2
[1] FALSE
D1606V9, binary
                  cls
clus                 0   1
  METTL5 MUTATED     4   0
  METTL5 WILD-TYPE 346  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  METTL5 MUTATED      4    0
  METTL5 WILD-TYPE  346   22
     clus
vv    METTL5 MUTATED METTL5 WILD-TYPE
  NO               4              346
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  METTL5 MUTATED                      5                             0
  METTL5 WILD-TYPE                  310                            47
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  METTL5 MUTATED                       1                              0
  METTL5 WILD-TYPE                   105                             10
D1606V10, multiclass
                                clus
vv                               METTL5 MUTATED METTL5 WILD-TYPE
  COLON ADENOCARCINOMA                        5              310
  COLON MUCINOUS ADENOCARCINOMA               0               47
  RECTAL ADENOCARCINOMA                       1              105
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  METTL5 MUTATED     5   0   0   0
  METTL5 WILD-TYPE 340   4  31  25
D1606V11, multiclass
    clus
vv   METTL5 MUTATED METTL5 WILD-TYPE
  R0              5              340
  R1              0                4
  R2              0               31
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1606V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  METTL5 MUTATED                                  0     1
  METTL5 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  METTL5 MUTATED                           0     2
  METTL5 WILD-TYPE                        22   224
D1606V13, multiclass
                                  clus
vv                                 METTL5 MUTATED METTL5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         2              224
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1607) Variable = ITPRIPL1 MUTATION ANALYSIS
D1607V1, survival
                    sevent
clus2                  0   1
  ITPRIPL1 MUTATED     8   0
  ITPRIPL1 WILD-TYPE 370  93
  ITPRIPL1 MUTATED ITPRIPL1 WILD-TYPE 
                 8                463 
  ITPRIPL1 MUTATED ITPRIPL1 WILD-TYPE 
                 0                 93 
$`ITPRIPL1 MUTATED`
TCGA-A6-6781 TCGA-AA-3502 TCGA-AA-3949 TCGA-AZ-4315 TCGA-D5-6927 TCGA-D5-6930 
       19.66        35.01        26.01        58.39         9.44         1.51 
TCGA-G4-6625 TCGA-AG-A002 
       91.79        20.98 

$`ITPRIPL1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        20.28         7.04         3.02         1.02 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       12.99        24.00        33.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6931 
       12.43        14.30         9.04        11.64         4.80        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       13.78        35.80        26.17        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  ITPRIPL1 MUTATED ITPRIPL1 WILD-TYPE 
              1.51               0.00 
  ITPRIPL1 MUTATED ITPRIPL1 WILD-TYPE 
             91.79             148.01 
  ITPRIPL1 MUTATED ITPRIPL1 WILD-TYPE 
            23.495             20.120 
[1] "1.5 - 91.8 (23.5)"  "0.0 - 148.0 (20.1)"
[1] "hr="     "9200000"
D1607V2, continuous
D1607V3, binary
                    cls
clus                   0   1
  ITPRIPL1 MUTATED     7   1
  ITPRIPL1 WILD-TYPE 359 118
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ITPRIPL1 MUTATED      7    1
  ITPRIPL1 WILD-TYPE  359  118
        clus
vv       ITPRIPL1 MUTATED ITPRIPL1 WILD-TYPE
  COLON                 7                359
  RECTUM                1                118
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ITPRIPL1 MUTATED         2        0        0         4         0         0
  ITPRIPL1 WILD-TYPE      89        1       32       134        10         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ITPRIPL1 MUTATED           0          0          1          1        0
  ITPRIPL1 WILD-TYPE        24         11         58         41       48
                    vv
clus                 STAGE IVA STAGE IVB
  ITPRIPL1 MUTATED           0         0
  ITPRIPL1 WILD-TYPE        18         1
D1607V4, multiclass
            clus
vv           ITPRIPL1 MUTATED ITPRIPL1 WILD-TYPE
  STAGE I                   2                 89
  STAGE IA                  0                  1
  STAGE II                  0                 32
  STAGE IIA                 4                134
  STAGE IIB                 0                 10
  STAGE IIC                 0                  1
  STAGE III                 0                 24
  STAGE IIIA                0                 11
  STAGE IIIB                1                 58
  STAGE IIIC                1                 41
  STAGE IV                  0                 48
  STAGE IVA                 0                 18
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  ITPRIPL1 MUTATED     0   2   5   1
  ITPRIPL1 WILD-TYPE  17  90 324  49
D1607V5, multiclass
    clus
vv   ITPRIPL1 MUTATED ITPRIPL1 WILD-TYPE
  T1                0                 17
  T2                2                 90
  T3                5                324
  T4                1                 49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  ITPRIPL1 MUTATED     6   2   0
  ITPRIPL1 WILD-TYPE 281 111  87
D1607V6, multiclass
    clus
vv   ITPRIPL1 MUTATED ITPRIPL1 WILD-TYPE
  N0                6                281
  N1                2                111
  N2                0                 87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1607V7, binary
                    cls
clus                   0   1
  ITPRIPL1 MUTATED     7   0
  ITPRIPL1 WILD-TYPE 368  65
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ITPRIPL1 MUTATED      7    0
  ITPRIPL1 WILD-TYPE  368   65
   clus
vv  ITPRIPL1 MUTATED ITPRIPL1 WILD-TYPE
  0                7                368
  1                0                 65
[1] 2 2
[1] FALSE
D1607V8, binary
                    cls
clus                   0   1
  ITPRIPL1 MUTATED     2   6
  ITPRIPL1 WILD-TYPE 223 258
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ITPRIPL1 MUTATED      2    6
  ITPRIPL1 WILD-TYPE  223  258
        clus
vv       ITPRIPL1 MUTATED ITPRIPL1 WILD-TYPE
  FEMALE                2                223
  MALE                  6                258
[1] 2 2
[1] FALSE
D1607V9, binary
                    cls
clus                   0   1
  ITPRIPL1 MUTATED     7   0
  ITPRIPL1 WILD-TYPE 343  22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ITPRIPL1 MUTATED      7    0
  ITPRIPL1 WILD-TYPE  343   22
     clus
vv    ITPRIPL1 MUTATED ITPRIPL1 WILD-TYPE
  NO                 7                343
  YES                0                 22
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ITPRIPL1 MUTATED                      4                             3
  ITPRIPL1 WILD-TYPE                  311                            44
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ITPRIPL1 MUTATED                       1                              0
  ITPRIPL1 WILD-TYPE                   105                             10
D1607V10, multiclass
                                clus
vv                               ITPRIPL1 MUTATED ITPRIPL1 WILD-TYPE
  COLON ADENOCARCINOMA                          4                311
  COLON MUCINOUS ADENOCARCINOMA                 3                 44
  RECTAL ADENOCARCINOMA                         1                105
  RECTAL MUCINOUS ADENOCARCINOMA                0                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  ITPRIPL1 MUTATED     8   0   0   0
  ITPRIPL1 WILD-TYPE 337   4  31  25
D1607V11, multiclass
    clus
vv   ITPRIPL1 MUTATED ITPRIPL1 WILD-TYPE
  R0                8                337
  R1                0                  4
  R2                0                 31
  RX                0                 25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1607V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ITPRIPL1 MUTATED                                  0     0
  ITPRIPL1 WILD-TYPE                                1    11
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  ITPRIPL1 MUTATED                           0     5
  ITPRIPL1 WILD-TYPE                        22   221
D1607V13, multiclass
                                  clus
vv                                 ITPRIPL1 MUTATED ITPRIPL1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 11
  BLACK OR AFRICAN AMERICAN                       0                 22
  WHITE                                           5                221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1608) Variable = WFS1 MUTATION ANALYSIS
D1608V1, survival
                sevent
clus2              0   1
  WFS1 MUTATED     8   4
  WFS1 WILD-TYPE 370  89
  WFS1 MUTATED WFS1 WILD-TYPE 
            12            459 
  WFS1 MUTATED WFS1 WILD-TYPE 
             4             89 
$`WFS1 MUTATED`
TCGA-A6-6781 TCGA-AA-3713 TCGA-AA-A00K TCGA-AD-5900 TCGA-AD-6895 TCGA-AD-6964 
       19.66        19.04        18.05         0.07         0.72        10.88 
TCGA-AZ-6598 TCGA-AZ-6601 TCGA-CM-6165 TCGA-DM-A28F TCGA-G4-6310 TCGA-AH-6644 
       49.41       100.01        16.04        35.97        63.62         0.72 

$`WFS1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00L TCGA-AA-A00N 
       19.00        30.02        34.03        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       18.05        40.96        21.37        15.52        56.55         0.79 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77        12.10        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6166 TCGA-CM-6167 
       15.02        12.00         2.96        29.03        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H 
      139.17         6.12        81.37       119.93        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6317 
       53.62        44.68        55.04        85.48        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
        1.45        17.49         0.69         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  WFS1 MUTATED WFS1 WILD-TYPE 
          0.07           0.00 
  WFS1 MUTATED WFS1 WILD-TYPE 
        100.01         148.01 
  WFS1 MUTATED WFS1 WILD-TYPE 
        18.545         20.550 
[1] "0.1 - 100.0 (18.5)" "0.0 - 148.0 (20.6)"
[1] "hr=" "1.6"
D1608V2, continuous
D1608V3, binary
                cls
clus               0   1
  WFS1 MUTATED    11   1
  WFS1 WILD-TYPE 355 118
[1] "tbl2"
                cls
clus             [,1] [,2]
  WFS1 MUTATED     11    1
  WFS1 WILD-TYPE  355  118
        clus
vv       WFS1 MUTATED WFS1 WILD-TYPE
  COLON            11            355
  RECTUM            1            118
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  WFS1 MUTATED         1        0        2         2         0         0
  WFS1 WILD-TYPE      90        1       30       136        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  WFS1 MUTATED           0          0          2          1        1         0
  WFS1 WILD-TYPE        24         11         57         41       47        18
                vv
clus             STAGE IVB
  WFS1 MUTATED           0
  WFS1 WILD-TYPE         1
D1608V4, multiclass
            clus
vv           WFS1 MUTATED WFS1 WILD-TYPE
  STAGE I               1             90
  STAGE IA              0              1
  STAGE II              2             30
  STAGE IIA             2            136
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            2             57
  STAGE IIIC            1             41
  STAGE IV              1             47
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  WFS1 MUTATED     0   1   9   2
  WFS1 WILD-TYPE  17  91 320  48
D1608V5, multiclass
    clus
vv   WFS1 MUTATED WFS1 WILD-TYPE
  T1            0             17
  T2            1             91
  T3            9            320
  T4            2             48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  WFS1 MUTATED     6   4   1
  WFS1 WILD-TYPE 281 109  86
D1608V6, multiclass
    clus
vv   WFS1 MUTATED WFS1 WILD-TYPE
  N0            6            281
  N1            4            109
  N2            1             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1608V7, binary
                cls
clus               0   1
  WFS1 MUTATED     5   1
  WFS1 WILD-TYPE 370  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  WFS1 MUTATED      5    1
  WFS1 WILD-TYPE  370   64
   clus
vv  WFS1 MUTATED WFS1 WILD-TYPE
  0            5            370
  1            1             64
[1] 2 2
[1] FALSE
D1608V8, binary
                cls
clus               0   1
  WFS1 MUTATED     1  11
  WFS1 WILD-TYPE 224 253
[1] "tbl2"
                cls
clus             [,1] [,2]
  WFS1 MUTATED      1   11
  WFS1 WILD-TYPE  224  253
        clus
vv       WFS1 MUTATED WFS1 WILD-TYPE
  FEMALE            1            224
  MALE             11            253
[1] 2 2
[1] FALSE
D1608V9, binary
                cls
clus               0   1
  WFS1 MUTATED     5   2
  WFS1 WILD-TYPE 345  20
[1] "tbl2"
                cls
clus             [,1] [,2]
  WFS1 MUTATED      5    2
  WFS1 WILD-TYPE  345   20
     clus
vv    WFS1 MUTATED WFS1 WILD-TYPE
  NO             5            345
  YES            2             20
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  WFS1 MUTATED                      9                             2
  WFS1 WILD-TYPE                  306                            45
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  WFS1 MUTATED                       1                              0
  WFS1 WILD-TYPE                   105                             10
D1608V10, multiclass
                                clus
vv                               WFS1 MUTATED WFS1 WILD-TYPE
  COLON ADENOCARCINOMA                      9            306
  COLON MUCINOUS ADENOCARCINOMA             2             45
  RECTAL ADENOCARCINOMA                     1            105
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  WFS1 MUTATED     5   0   1   0
  WFS1 WILD-TYPE 340   4  30  25
D1608V11, multiclass
    clus
vv   WFS1 MUTATED WFS1 WILD-TYPE
  R0            5            340
  R1            0              4
  R2            1             30
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1608V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  WFS1 MUTATED                                  0     0
  WFS1 WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  WFS1 MUTATED                           0    10
  WFS1 WILD-TYPE                        22   216
D1608V13, multiclass
                                  clus
vv                                 WFS1 MUTATED WFS1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                      10            216
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1609) Variable = GOT1 MUTATION ANALYSIS
D1609V1, survival
                sevent
clus2              0   1
  GOT1 MUTATED     3   2
  GOT1 WILD-TYPE 375  91
  GOT1 MUTATED GOT1 WILD-TYPE 
             5            466 
  GOT1 MUTATED GOT1 WILD-TYPE 
             2             91 
$`GOT1 MUTATED`
TCGA-A6-2676 TCGA-A6-5659 TCGA-AA-3811 TCGA-AA-A010 TCGA-AG-A002 
       42.90        30.44        10.06        34.98        20.98 

$`GOT1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       31.63        29.19        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        19.04        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  GOT1 MUTATED GOT1 WILD-TYPE 
         10.06           0.00 
  GOT1 MUTATED GOT1 WILD-TYPE 
         42.90         148.01 
  GOT1 MUTATED GOT1 WILD-TYPE 
        30.440         20.085 
[1] "10.1 - 42.9 (30.4)" "0.0 - 148.0 (20.1)"
[1] "hr=" "2.1"
D1609V2, continuous
D1609V3, binary
                cls
clus               0   1
  GOT1 MUTATED     5   1
  GOT1 WILD-TYPE 361 118
[1] "tbl2"
                cls
clus             [,1] [,2]
  GOT1 MUTATED      5    1
  GOT1 WILD-TYPE  361  118
        clus
vv       GOT1 MUTATED GOT1 WILD-TYPE
  COLON             5            361
  RECTUM            1            118
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GOT1 MUTATED         2        0        0         1         2         0
  GOT1 WILD-TYPE      89        1       32       137         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  GOT1 MUTATED           1          0          0          0        0         0
  GOT1 WILD-TYPE        23         11         59         42       48        18
                vv
clus             STAGE IVB
  GOT1 MUTATED           0
  GOT1 WILD-TYPE         1
D1609V4, multiclass
            clus
vv           GOT1 MUTATED GOT1 WILD-TYPE
  STAGE I               2             89
  STAGE IA              0              1
  STAGE II              0             32
  STAGE IIA             1            137
  STAGE IIB             2              8
  STAGE IIC             0              1
  STAGE III             1             23
  STAGE IIIA            0             11
  STAGE IIIB            0             59
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  GOT1 MUTATED     0   2   2   2
  GOT1 WILD-TYPE  17  90 327  48
D1609V5, multiclass
    clus
vv   GOT1 MUTATED GOT1 WILD-TYPE
  T1            0             17
  T2            2             90
  T3            2            327
  T4            2             48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  GOT1 MUTATED     5   0   1
  GOT1 WILD-TYPE 282 113  86
D1609V6, multiclass
    clus
vv   GOT1 MUTATED GOT1 WILD-TYPE
  N0            5            282
  N1            0            113
  N2            1             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1609V7, binary
                cls
clus               0   1
  GOT1 MUTATED     6   0
  GOT1 WILD-TYPE 369  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  GOT1 MUTATED      6    0
  GOT1 WILD-TYPE  369   65
   clus
vv  GOT1 MUTATED GOT1 WILD-TYPE
  0            6            369
  1            0             65
[1] 2 2
[1] FALSE
D1609V8, binary
                cls
clus               0   1
  GOT1 MUTATED     4   2
  GOT1 WILD-TYPE 221 262
[1] "tbl2"
                cls
clus             [,1] [,2]
  GOT1 MUTATED      4    2
  GOT1 WILD-TYPE  221  262
        clus
vv       GOT1 MUTATED GOT1 WILD-TYPE
  FEMALE            4            221
  MALE              2            262
[1] 2 2
[1] FALSE
D1609V9, binary
                cls
clus               0   1
  GOT1 MUTATED     5   0
  GOT1 WILD-TYPE 345  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  GOT1 MUTATED      5    0
  GOT1 WILD-TYPE  345   22
     clus
vv    GOT1 MUTATED GOT1 WILD-TYPE
  NO             5            345
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  GOT1 MUTATED                      5                             0
  GOT1 WILD-TYPE                  310                            47
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  GOT1 MUTATED                       1                              0
  GOT1 WILD-TYPE                   105                             10
D1609V10, multiclass
                                clus
vv                               GOT1 MUTATED GOT1 WILD-TYPE
  COLON ADENOCARCINOMA                      5            310
  COLON MUCINOUS ADENOCARCINOMA             0             47
  RECTAL ADENOCARCINOMA                     1            105
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  GOT1 MUTATED     6   0   0   0
  GOT1 WILD-TYPE 339   4  31  25
D1609V11, multiclass
    clus
vv   GOT1 MUTATED GOT1 WILD-TYPE
  R0            6            339
  R1            0              4
  R2            0             31
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1609V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GOT1 MUTATED                                  0     0
  GOT1 WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  GOT1 MUTATED                           0     2
  GOT1 WILD-TYPE                        22   224
D1609V13, multiclass
[1] "Remove cluster labels:" "GOT1 MUTATED"          
clus
  GOT1 MUTATED GOT1 WILD-TYPE 
             2            258 
    TCGA-A6-2671     TCGA-A6-2672     TCGA-A6-2674     TCGA-A6-2677 
"GOT1 WILD-TYPE" "GOT1 WILD-TYPE" "GOT1 WILD-TYPE" "GOT1 WILD-TYPE" 
    TCGA-A6-2678     TCGA-A6-2683     TCGA-A6-3807     TCGA-A6-3808 
"GOT1 WILD-TYPE" "GOT1 WILD-TYPE" "GOT1 WILD-TYPE" "GOT1 WILD-TYPE" 
    TCGA-A6-3809     TCGA-A6-3810     TCGA-A6-4105     TCGA-A6-5656 
"GOT1 WILD-TYPE" "GOT1 WILD-TYPE" "GOT1 WILD-TYPE" "GOT1 WILD-TYPE" 
    TCGA-A6-5657     TCGA-A6-5660     TCGA-A6-5661     TCGA-A6-5662 
"GOT1 WILD-TYPE" "GOT1 WILD-TYPE" "GOT1 WILD-TYPE" "GOT1 WILD-TYPE" 
    TCGA-A6-5664     TCGA-A6-5665     TCGA-A6-5666     TCGA-A6-6137 
"GOT1 WILD-TYPE" "GOT1 WILD-TYPE" "GOT1 WILD-TYPE" "GOT1 WILD-TYPE" 
    TCGA-A6-6138     TCGA-A6-6141     TCGA-A6-6142     TCGA-A6-6648 
"GOT1 WILD-TYPE" "GOT1 WILD-TYPE" "GOT1 WILD-TYPE" "GOT1 WILD-TYPE" 
    TCGA-A6-6649     TCGA-A6-6651     TCGA-A6-6652     TCGA-A6-6653 
"GOT1 WILD-TYPE" "GOT1 WILD-TYPE" "GOT1 WILD-TYPE" "GOT1 WILD-TYPE" 
    TCGA-A6-6654     TCGA-A6-6780     TCGA-A6-6781     TCGA-A6-6782 
"GOT1 WILD-TYPE" "GOT1 WILD-TYPE" "GOT1 WILD-TYPE" "GOT1 WILD-TYPE" 
    TCGA-AD-5900     TCGA-AD-6548     TCGA-AD-6888     TCGA-AD-6889 
"GOT1 WILD-TYPE" "GOT1 WILD-TYPE" "GOT1 WILD-TYPE" "GOT1 WILD-TYPE" 
    TCGA-AD-6890     TCGA-AD-6895     TCGA-AD-6899     TCGA-AD-6901 
"GOT1 WILD-TYPE" "GOT1 WILD-TYPE" "GOT1 WILD-TYPE" "GOT1 WILD-TYPE" 
    TCGA-AD-6963     TCGA-AD-6964     TCGA-AD-6965     TCGA-AU-3779 
"GOT1 WILD-TYPE" "GOT1 WILD-TYPE" "GOT1 WILD-TYPE" "GOT1 WILD-TYPE" 
    TCGA-AU-6004     TCGA-AY-4070     TCGA-AY-4071     TCGA-AY-5543 
"GOT1 WILD-TYPE" "GOT1 WILD-TYPE" "GOT1 WILD-TYPE" "GOT1 WILD-TYPE" 
    TCGA-AY-6196     TCGA-AY-6197     TCGA-AY-6386     TCGA-AZ-4315 
"GOT1 WILD-TYPE" "GOT1 WILD-TYPE" "GOT1 WILD-TYPE" "GOT1 WILD-TYPE" 
    TCGA-AZ-4323     TCGA-AZ-4616     TCGA-AZ-4681     TCGA-AZ-4682 
"GOT1 WILD-TYPE" "GOT1 WILD-TYPE" "GOT1 WILD-TYPE" "GOT1 WILD-TYPE" 
    TCGA-AZ-5403     TCGA-AZ-5407     TCGA-AZ-6598     TCGA-AZ-6599 
"GOT1 WILD-TYPE" "GOT1 WILD-TYPE" "GOT1 WILD-TYPE" "GOT1 WILD-TYPE" 
    TCGA-AZ-6600     TCGA-AZ-6601     TCGA-AZ-6603     TCGA-AZ-6605 
"GOT1 WILD-TYPE" "GOT1 WILD-TYPE" "GOT1 WILD-TYPE" "GOT1 WILD-TYPE" 
    TCGA-AZ-6606     TCGA-AZ-6607     TCGA-AZ-6608     TCGA-CA-5254 
"GOT1 WILD-TYPE" "GOT1 WILD-TYPE" "GOT1 WILD-TYPE" "GOT1 WILD-TYPE" 
    TCGA-CA-5255     TCGA-CA-5796     TCGA-CA-5797     TCGA-CA-6715 
"GOT1 WILD-TYPE" "GOT1 WILD-TYPE" "GOT1 WILD-TYPE" "GOT1 WILD-TYPE" 
    TCGA-CA-6716     TCGA-CA-6717     TCGA-CA-6718     TCGA-CA-6719 
"GOT1 WILD-TYPE" "GOT1 WILD-TYPE" "GOT1 WILD-TYPE" "GOT1 WILD-TYPE" 
    TCGA-CK-4947     TCGA-CK-4948     TCGA-CK-4950     TCGA-CK-4952 
"GOT1 WILD-TYPE" "GOT1 WILD-TYPE" "GOT1 WILD-TYPE" "GOT1 WILD-TYPE" 
    TCGA-CK-5912     TCGA-CK-5913     TCGA-CK-5914     TCGA-CK-5915 
"GOT1 WILD-TYPE" "GOT1 WILD-TYPE" "GOT1 WILD-TYPE" "GOT1 WILD-TYPE" 
    TCGA-CK-5916     TCGA-CK-6746     TCGA-CK-6747     TCGA-CK-6748 
"GOT1 WILD-TYPE" "GOT1 WILD-TYPE" "GOT1 WILD-TYPE" "GOT1 WILD-TYPE" 
    TCGA-CK-6751     TCGA-CM-4743     TCGA-CM-4744     TCGA-CM-4746 
"GOT1 WILD-TYPE" "GOT1 WILD-TYPE" "GOT1 WILD-TYPE" "GOT1 WILD-TYPE" 
    TCGA-CM-4747     TCGA-CM-4752     TCGA-CM-5341     TCGA-CM-5344 
"GOT1 WILD-TYPE" "GOT1 WILD-TYPE" "GOT1 WILD-TYPE" "GOT1 WILD-TYPE" 
    TCGA-CM-5348     TCGA-CM-5349     TCGA-CM-5860     TCGA-CM-5861 
"GOT1 WILD-TYPE" "GOT1 WILD-TYPE" "GOT1 WILD-TYPE" "GOT1 WILD-TYPE" 
    TCGA-CM-5862     TCGA-CM-5863     TCGA-CM-5864     TCGA-CM-5868 
"GOT1 WILD-TYPE" "GOT1 WILD-TYPE" "GOT1 WILD-TYPE" "GOT1 WILD-TYPE" 
    TCGA-CM-6161     TCGA-CM-6162     TCGA-CM-6163     TCGA-CM-6164 
"GOT1 WILD-TYPE" "GOT1 WILD-TYPE" "GOT1 WILD-TYPE" "GOT1 WILD-TYPE" 
    TCGA-CM-6165     TCGA-CM-6166     TCGA-CM-6167     TCGA-CM-6168 
"GOT1 WILD-TYPE" "GOT1 WILD-TYPE" "GOT1 WILD-TYPE" "GOT1 WILD-TYPE" 
    TCGA-CM-6169     TCGA-CM-6170     TCGA-CM-6171     TCGA-CM-6172 
"GOT1 WILD-TYPE" "GOT1 WILD-TYPE" "GOT1 WILD-TYPE" "GOT1 WILD-TYPE" 
    TCGA-CM-6674     TCGA-CM-6675     TCGA-CM-6676     TCGA-CM-6677 
"GOT1 WILD-TYPE" "GOT1 WILD-TYPE" "GOT1 WILD-TYPE" "GOT1 WILD-TYPE" 
    TCGA-CM-6678     TCGA-CM-6679     TCGA-CM-6680     TCGA-D5-5537 
"GOT1 WILD-TYPE" "GOT1 WILD-TYPE" "GOT1 WILD-TYPE" "GOT1 WILD-TYPE" 
    TCGA-D5-5538     TCGA-D5-5539     TCGA-D5-5540     TCGA-D5-5541 
"GOT1 WILD-TYPE" "GOT1 WILD-TYPE" "GOT1 WILD-TYPE" "GOT1 WILD-TYPE" 
    TCGA-D5-6529     TCGA-D5-6532     TCGA-D5-6533     TCGA-D5-6534 
"GOT1 WILD-TYPE" "GOT1 WILD-TYPE" "GOT1 WILD-TYPE" "GOT1 WILD-TYPE" 
    TCGA-D5-6535     TCGA-D5-6536     TCGA-D5-6537     TCGA-D5-6538 
"GOT1 WILD-TYPE" "GOT1 WILD-TYPE" "GOT1 WILD-TYPE" "GOT1 WILD-TYPE" 
    TCGA-D5-6539     TCGA-D5-6540     TCGA-D5-6541     TCGA-D5-6898 
"GOT1 WILD-TYPE" "GOT1 WILD-TYPE" "GOT1 WILD-TYPE" "GOT1 WILD-TYPE" 
    TCGA-D5-6920     TCGA-D5-6922     TCGA-D5-6923     TCGA-D5-6924 
"GOT1 WILD-TYPE" "GOT1 WILD-TYPE" "GOT1 WILD-TYPE" "GOT1 WILD-TYPE" 
    TCGA-D5-6926     TCGA-D5-6927     TCGA-D5-6928     TCGA-D5-6929 
"GOT1 WILD-TYPE" "GOT1 WILD-TYPE" "GOT1 WILD-TYPE" "GOT1 WILD-TYPE" 
    TCGA-D5-6930     TCGA-D5-6931     TCGA-D5-6932     TCGA-D5-7000 
"GOT1 WILD-TYPE" "GOT1 WILD-TYPE" "GOT1 WILD-TYPE" "GOT1 WILD-TYPE" 
    TCGA-DM-A0X9     TCGA-DM-A0XD     TCGA-DM-A0XF     TCGA-DM-A1D0 
"GOT1 WILD-TYPE" "GOT1 WILD-TYPE" "GOT1 WILD-TYPE" "GOT1 WILD-TYPE" 
    TCGA-DM-A1D4     TCGA-DM-A1D6     TCGA-DM-A1D7     TCGA-DM-A1D8 
"GOT1 WILD-TYPE" "GOT1 WILD-TYPE" "GOT1 WILD-TYPE" "GOT1 WILD-TYPE" 
    TCGA-DM-A1D9     TCGA-DM-A1DA     TCGA-DM-A1DB     TCGA-DM-A1HA 
"GOT1 WILD-TYPE" "GOT1 WILD-TYPE" "GOT1 WILD-TYPE" "GOT1 WILD-TYPE" 
    TCGA-DM-A1HB     TCGA-DM-A282     TCGA-DM-A285     TCGA-DM-A28C 
"GOT1 WILD-TYPE" "GOT1 WILD-TYPE" "GOT1 WILD-TYPE" "GOT1 WILD-TYPE" 
    TCGA-DM-A28E     TCGA-DM-A28F     TCGA-DM-A28G     TCGA-DM-A28H 
"GOT1 WILD-TYPE" "GOT1 WILD-TYPE" "GOT1 WILD-TYPE" "GOT1 WILD-TYPE" 
    TCGA-DM-A28K     TCGA-F4-6459     TCGA-F4-6460     TCGA-F4-6569 
"GOT1 WILD-TYPE" "GOT1 WILD-TYPE" "GOT1 WILD-TYPE" "GOT1 WILD-TYPE" 
    TCGA-F4-6570     TCGA-F4-6703     TCGA-F4-6704     TCGA-F4-6805 
"GOT1 WILD-TYPE" "GOT1 WILD-TYPE" "GOT1 WILD-TYPE" "GOT1 WILD-TYPE" 
    TCGA-F4-6806     TCGA-F4-6807     TCGA-F4-6808     TCGA-F4-6809 
"GOT1 WILD-TYPE" "GOT1 WILD-TYPE" "GOT1 WILD-TYPE" "GOT1 WILD-TYPE" 
    TCGA-F4-6854     TCGA-F4-6855     TCGA-F4-6856     TCGA-G4-6293 
"GOT1 WILD-TYPE" "GOT1 WILD-TYPE" "GOT1 WILD-TYPE" "GOT1 WILD-TYPE" 
    TCGA-G4-6299     TCGA-G4-6303     TCGA-G4-6304     TCGA-G4-6306 
"GOT1 WILD-TYPE" "GOT1 WILD-TYPE" "GOT1 WILD-TYPE" "GOT1 WILD-TYPE" 
    TCGA-G4-6307     TCGA-G4-6309     TCGA-G4-6310     TCGA-G4-6315 
"GOT1 WILD-TYPE" "GOT1 WILD-TYPE" "GOT1 WILD-TYPE" "GOT1 WILD-TYPE" 
    TCGA-G4-6317     TCGA-G4-6321     TCGA-G4-6323     TCGA-G4-6586 
"GOT1 WILD-TYPE" "GOT1 WILD-TYPE" "GOT1 WILD-TYPE" "GOT1 WILD-TYPE" 
    TCGA-G4-6588     TCGA-G4-6625     TCGA-G4-6626     TCGA-G4-6628 
"GOT1 WILD-TYPE" "GOT1 WILD-TYPE" "GOT1 WILD-TYPE" "GOT1 WILD-TYPE" 
    TCGA-AF-2687     TCGA-AF-2689     TCGA-AF-2691     TCGA-AF-2692 
"GOT1 WILD-TYPE" "GOT1 WILD-TYPE" "GOT1 WILD-TYPE" "GOT1 WILD-TYPE" 
    TCGA-AF-2693     TCGA-AF-3400     TCGA-AF-3913     TCGA-AF-4110 
"GOT1 WILD-TYPE" "GOT1 WILD-TYPE" "GOT1 WILD-TYPE" "GOT1 WILD-TYPE" 
    TCGA-AF-5654     TCGA-AF-6136     TCGA-AF-6655     TCGA-AF-6672 
"GOT1 WILD-TYPE" "GOT1 WILD-TYPE" "GOT1 WILD-TYPE" "GOT1 WILD-TYPE" 
    TCGA-AH-6544     TCGA-AH-6547     TCGA-AH-6549     TCGA-AH-6643 
"GOT1 WILD-TYPE" "GOT1 WILD-TYPE" "GOT1 WILD-TYPE" "GOT1 WILD-TYPE" 
    TCGA-AH-6644     TCGA-CI-6619     TCGA-CI-6620     TCGA-CI-6621 
"GOT1 WILD-TYPE" "GOT1 WILD-TYPE" "GOT1 WILD-TYPE" "GOT1 WILD-TYPE" 
    TCGA-CI-6622     TCGA-CI-6624     TCGA-CL-5917     TCGA-CL-5918 
"GOT1 WILD-TYPE" "GOT1 WILD-TYPE" "GOT1 WILD-TYPE" "GOT1 WILD-TYPE" 
    TCGA-DC-5337     TCGA-DC-5869     TCGA-DC-6155     TCGA-DC-6157 
"GOT1 WILD-TYPE" "GOT1 WILD-TYPE" "GOT1 WILD-TYPE" "GOT1 WILD-TYPE" 
    TCGA-DC-6158     TCGA-DC-6160     TCGA-DC-6681     TCGA-DC-6682 
"GOT1 WILD-TYPE" "GOT1 WILD-TYPE" "GOT1 WILD-TYPE" "GOT1 WILD-TYPE" 
    TCGA-DC-6683     TCGA-DT-5265     TCGA-DY-A0XA     TCGA-DY-A1DC 
"GOT1 WILD-TYPE" "GOT1 WILD-TYPE" "GOT1 WILD-TYPE" "GOT1 WILD-TYPE" 
    TCGA-DY-A1DD     TCGA-DY-A1DF     TCGA-DY-A1DG     TCGA-DY-A1H8 
"GOT1 WILD-TYPE" "GOT1 WILD-TYPE" "GOT1 WILD-TYPE" "GOT1 WILD-TYPE" 
    TCGA-EF-5830     TCGA-EI-6506     TCGA-EI-6507     TCGA-EI-6508 
"GOT1 WILD-TYPE" "GOT1 WILD-TYPE" "GOT1 WILD-TYPE" "GOT1 WILD-TYPE" 
    TCGA-EI-6510     TCGA-F5-6464     TCGA-F5-6465     TCGA-F5-6571 
"GOT1 WILD-TYPE" "GOT1 WILD-TYPE" "GOT1 WILD-TYPE" "GOT1 WILD-TYPE" 
    TCGA-F5-6702     TCGA-F5-6811     TCGA-F5-6812     TCGA-F5-6813 
"GOT1 WILD-TYPE" "GOT1 WILD-TYPE" "GOT1 WILD-TYPE" "GOT1 WILD-TYPE" 
    TCGA-G5-6235     TCGA-G5-6641 
"GOT1 WILD-TYPE" "GOT1 WILD-TYPE" 

Clustering(1610) Variable = SRGAP3 MUTATION ANALYSIS
D1610V1, survival
                  sevent
clus2                0   1
  SRGAP3 MUTATED    15   3
  SRGAP3 WILD-TYPE 363  90
  SRGAP3 MUTATED SRGAP3 WILD-TYPE 
              18              453 
  SRGAP3 MUTATED SRGAP3 WILD-TYPE 
               3               90 
$`SRGAP3 MUTATED`
TCGA-A6-6653 TCGA-AA-3662 TCGA-AA-3666 TCGA-AA-3715 TCGA-AA-3815 TCGA-AA-3950 
       24.39         6.05         2.01        19.04        33.04        24.00 
TCGA-AA-A029 TCGA-AD-5900 TCGA-AD-6895 TCGA-CA-6717 TCGA-CM-6674 TCGA-D5-6535 
       51.98         0.07         0.72        12.76        12.95        15.12 
TCGA-D5-6927 TCGA-D5-6930 TCGA-DM-A285 TCGA-G4-6310 TCGA-AG-A002 TCGA-F5-6813 
        9.44         1.51         6.12        63.62        20.98         0.69 

$`SRGAP3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
       25.08        25.18        24.16        21.76        24.69        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       19.99        13.94        19.99        61.02        78.08         6.97 
TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
       54.02        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
       85.05        26.99        19.04        10.06        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       26.01         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       39.06        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 
       41.00        39.98        18.05        40.96        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
       56.55         0.79         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6676 
       13.02        15.02        14.04        11.01        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       43.27        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
        9.04        11.64         4.80        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      135.65       139.17        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6315 
       65.85        53.62        44.68        55.04        85.48        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-G5-6235 TCGA-G5-6641 
        0.66        55.76        26.43 

  SRGAP3 MUTATED SRGAP3 WILD-TYPE 
            0.07             0.00 
  SRGAP3 MUTATED SRGAP3 WILD-TYPE 
           63.62           148.01 
  SRGAP3 MUTATED SRGAP3 WILD-TYPE 
          12.855           20.910 
[1] "0.1 - 63.6 (12.9)"  "0.0 - 148.0 (20.9)"
[1] "hr=" "1.2"
D1610V2, continuous
D1610V3, binary
                  cls
clus                 0   1
  SRGAP3 MUTATED    17   2
  SRGAP3 WILD-TYPE 349 117
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SRGAP3 MUTATED     17    2
  SRGAP3 WILD-TYPE  349  117
        clus
vv       SRGAP3 MUTATED SRGAP3 WILD-TYPE
  COLON              17              349
  RECTUM              2              117
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SRGAP3 MUTATED         3        0        2         6         1         0
  SRGAP3 WILD-TYPE      88        1       30       132         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SRGAP3 MUTATED           1          0          2          1        2
  SRGAP3 WILD-TYPE        23         11         57         41       46
                  vv
clus               STAGE IVA STAGE IVB
  SRGAP3 MUTATED           0         0
  SRGAP3 WILD-TYPE        18         1
D1610V4, multiclass
            clus
vv           SRGAP3 MUTATED SRGAP3 WILD-TYPE
  STAGE I                 3               88
  STAGE IA                0                1
  STAGE II                2               30
  STAGE IIA               6              132
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               1               23
  STAGE IIIA              0               11
  STAGE IIIB              2               57
  STAGE IIIC              1               41
  STAGE IV                2               46
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  SRGAP3 MUTATED     0   3  13   3
  SRGAP3 WILD-TYPE  17  89 316  47
D1610V5, multiclass
    clus
vv   SRGAP3 MUTATED SRGAP3 WILD-TYPE
  T1              0               17
  T2              3               89
  T3             13              316
  T4              3               47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  SRGAP3 MUTATED    12   4   3
  SRGAP3 WILD-TYPE 275 109  84
D1610V6, multiclass
    clus
vv   SRGAP3 MUTATED SRGAP3 WILD-TYPE
  N0             12              275
  N1              4              109
  N2              3               84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1610V7, binary
                  cls
clus                 0   1
  SRGAP3 MUTATED    13   2
  SRGAP3 WILD-TYPE 362  63
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SRGAP3 MUTATED     13    2
  SRGAP3 WILD-TYPE  362   63
   clus
vv  SRGAP3 MUTATED SRGAP3 WILD-TYPE
  0             13              362
  1              2               63
[1] 2 2
[1] FALSE
D1610V8, binary
                  cls
clus                 0   1
  SRGAP3 MUTATED     6  13
  SRGAP3 WILD-TYPE 219 251
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SRGAP3 MUTATED      6   13
  SRGAP3 WILD-TYPE  219  251
        clus
vv       SRGAP3 MUTATED SRGAP3 WILD-TYPE
  FEMALE              6              219
  MALE               13              251
[1] 2 2
[1] FALSE
D1610V9, binary
                  cls
clus                 0   1
  SRGAP3 MUTATED    11   1
  SRGAP3 WILD-TYPE 339  21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SRGAP3 MUTATED     11    1
  SRGAP3 WILD-TYPE  339   21
     clus
vv    SRGAP3 MUTATED SRGAP3 WILD-TYPE
  NO              11              339
  YES              1               21
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SRGAP3 MUTATED                     12                             5
  SRGAP3 WILD-TYPE                  303                            42
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SRGAP3 MUTATED                       2                              0
  SRGAP3 WILD-TYPE                   104                             10
D1610V10, multiclass
                                clus
vv                               SRGAP3 MUTATED SRGAP3 WILD-TYPE
  COLON ADENOCARCINOMA                       12              303
  COLON MUCINOUS ADENOCARCINOMA               5               42
  RECTAL ADENOCARCINOMA                       2              104
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  SRGAP3 MUTATED    12   0   1   3
  SRGAP3 WILD-TYPE 333   4  30  22
D1610V11, multiclass
    clus
vv   SRGAP3 MUTATED SRGAP3 WILD-TYPE
  R0             12              333
  R1              0                4
  R2              1               30
  RX              3               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1610V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SRGAP3 MUTATED                                  0     1
  SRGAP3 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  SRGAP3 MUTATED                           0    11
  SRGAP3 WILD-TYPE                        22   215
D1610V13, multiclass
                                  clus
vv                                 SRGAP3 MUTATED SRGAP3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                        11              215
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1611) Variable = MTMR8 MUTATION ANALYSIS
D1611V1, survival
                 sevent
clus2               0   1
  MTMR8 MUTATED    11   4
  MTMR8 WILD-TYPE 367  89
  MTMR8 MUTATED MTMR8 WILD-TYPE 
             15             456 
  MTMR8 MUTATED MTMR8 WILD-TYPE 
              4              89 
$`MTMR8 MUTATED`
TCGA-A6-5665 TCGA-AA-3710 TCGA-AA-3947 TCGA-AA-A01D TCGA-AU-3779 TCGA-AZ-5403 
       22.06        26.99        33.01        10.98        14.50        62.79 
TCGA-AZ-6603 TCGA-CM-5344 TCGA-CM-6163 TCGA-D5-6541 TCGA-G4-6586 TCGA-AG-A002 
       29.56        22.03         2.96        15.58        35.80        20.98 
TCGA-CI-6622 TCGA-DC-6160 TCGA-F5-6464 
        6.97        19.99         9.96 

$`MTMR8 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        85.05        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       12.99        24.00        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       34.98         1.02        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5407 
       58.39         1.41         5.13       106.75        22.36        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6606 
       49.41         6.77        12.10       100.01         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5349 
       37.02        25.02        13.02        29.06        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       15.02        12.00        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       17.13        12.49        16.14         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6624 
       17.49         0.69         0.72         6.05        33.17         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       10.98         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6465 TCGA-F5-6571 
       20.55        19.96        20.91        18.28        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  MTMR8 MUTATED MTMR8 WILD-TYPE 
           2.96            0.00 
  MTMR8 MUTATED MTMR8 WILD-TYPE 
          62.79          148.01 
  MTMR8 MUTATED MTMR8 WILD-TYPE 
         20.980          20.155 
[1] "3.0 - 62.8 (21.0)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.6"
D1611V2, continuous
D1611V3, binary
                 cls
clus                0   1
  MTMR8 MUTATED    11   4
  MTMR8 WILD-TYPE 355 115
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MTMR8 MUTATED     11    4
  MTMR8 WILD-TYPE  355  115
        clus
vv       MTMR8 MUTATED MTMR8 WILD-TYPE
  COLON             11             355
  RECTUM             4             115
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MTMR8 MUTATED         3        0        1         5         2         0
  MTMR8 WILD-TYPE      88        1       31       133         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MTMR8 MUTATED           0          0          1          2        0         0
  MTMR8 WILD-TYPE        24         11         58         40       48        18
                 vv
clus              STAGE IVB
  MTMR8 MUTATED           0
  MTMR8 WILD-TYPE         1
D1611V4, multiclass
            clus
vv           MTMR8 MUTATED MTMR8 WILD-TYPE
  STAGE I                3              88
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              5             133
  STAGE IIB              2               8
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             2              40
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  MTMR8 MUTATED     1   3   8   3
  MTMR8 WILD-TYPE  16  89 321  47
D1611V5, multiclass
    clus
vv   MTMR8 MUTATED MTMR8 WILD-TYPE
  T1             1              16
  T2             3              89
  T3             8             321
  T4             3              47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  MTMR8 MUTATED    11   2   2
  MTMR8 WILD-TYPE 276 111  85
D1611V6, multiclass
    clus
vv   MTMR8 MUTATED MTMR8 WILD-TYPE
  N0            11             276
  N1             2             111
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1611V7, binary
                 cls
clus                0   1
  MTMR8 MUTATED    13   0
  MTMR8 WILD-TYPE 362  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MTMR8 MUTATED     13    0
  MTMR8 WILD-TYPE  362   65
   clus
vv  MTMR8 MUTATED MTMR8 WILD-TYPE
  0            13             362
  1             0              65
[1] 2 2
[1] FALSE
D1611V8, binary
                 cls
clus                0   1
  MTMR8 MUTATED     9   6
  MTMR8 WILD-TYPE 216 258
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MTMR8 MUTATED      9    6
  MTMR8 WILD-TYPE  216  258
        clus
vv       MTMR8 MUTATED MTMR8 WILD-TYPE
  FEMALE             9             216
  MALE               6             258
[1] 2 2
[1] FALSE
D1611V9, binary
                 cls
clus                0   1
  MTMR8 MUTATED    13   0
  MTMR8 WILD-TYPE 337  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MTMR8 MUTATED     13    0
  MTMR8 WILD-TYPE  337   22
     clus
vv    MTMR8 MUTATED MTMR8 WILD-TYPE
  NO             13             337
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MTMR8 MUTATED                      9                             2
  MTMR8 WILD-TYPE                  306                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MTMR8 MUTATED                       4                              0
  MTMR8 WILD-TYPE                   102                             10
D1611V10, multiclass
                                clus
vv                               MTMR8 MUTATED MTMR8 WILD-TYPE
  COLON ADENOCARCINOMA                       9             306
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      4             102
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  MTMR8 MUTATED    12   0   0   0
  MTMR8 WILD-TYPE 333   4  31  25
D1611V11, multiclass
    clus
vv   MTMR8 MUTATED MTMR8 WILD-TYPE
  R0            12             333
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1611V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MTMR8 MUTATED                                  0     0
  MTMR8 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  MTMR8 MUTATED                           0    11
  MTMR8 WILD-TYPE                        22   215
D1611V13, multiclass
                                  clus
vv                                 MTMR8 MUTATED MTMR8 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                       11             215
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1612) Variable = GAB3 MUTATION ANALYSIS
D1612V1, survival
                sevent
clus2              0   1
  GAB3 MUTATED     9   2
  GAB3 WILD-TYPE 369  91
  GAB3 MUTATED GAB3 WILD-TYPE 
            11            460 
  GAB3 MUTATED GAB3 WILD-TYPE 
             2             91 
$`GAB3 MUTATED`
TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3534 TCGA-AA-3663 TCGA-AA-A00R TCGA-AA-A010 
       63.98         1.02        29.00         6.97         0.99        34.98 
TCGA-AA-A01Q TCGA-AZ-6601 TCGA-D5-6534 TCGA-DM-A28F TCGA-AF-2691 
        1.02       100.01        43.27        35.97        43.04 

$`GAB3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
        1.02        35.01         6.97        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3538 TCGA-AA-3542 
        0.00        19.07        34.03        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02        78.08         6.05        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
       42.02        17.03        14.99        21.99         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01R 
       32.02        12.00        31.00        31.00        38.07        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77        12.10        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       20.19        18.25         1.32        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H 
      139.17         6.12        81.37       119.93        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2692 TCGA-AF-2693 
       46.75        79.69        24.13        39.48        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  GAB3 MUTATED GAB3 WILD-TYPE 
          0.99           0.00 
  GAB3 MUTATED GAB3 WILD-TYPE 
        100.01         148.01 
  GAB3 MUTATED GAB3 WILD-TYPE 
        34.980         20.085 
[1] "1.0 - 100.0 (35.0)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.3"
D1612V2, continuous
D1612V3, binary
                cls
clus               0   1
  GAB3 MUTATED    11   1
  GAB3 WILD-TYPE 355 118
[1] "tbl2"
                cls
clus             [,1] [,2]
  GAB3 MUTATED     11    1
  GAB3 WILD-TYPE  355  118
        clus
vv       GAB3 MUTATED GAB3 WILD-TYPE
  COLON            11            355
  RECTUM            1            118
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GAB3 MUTATED         3        0        4         3         1         0
  GAB3 WILD-TYPE      88        1       28       135         9         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  GAB3 MUTATED           0          0          1          0        0         0
  GAB3 WILD-TYPE        24         11         58         42       48        18
                vv
clus             STAGE IVB
  GAB3 MUTATED           0
  GAB3 WILD-TYPE         1
D1612V4, multiclass
            clus
vv           GAB3 MUTATED GAB3 WILD-TYPE
  STAGE I               3             88
  STAGE IA              0              1
  STAGE II              4             28
  STAGE IIA             3            135
  STAGE IIB             1              9
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            1             58
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  GAB3 MUTATED     1   2   8   1
  GAB3 WILD-TYPE  16  90 321  49
D1612V5, multiclass
    clus
vv   GAB3 MUTATED GAB3 WILD-TYPE
  T1            1             16
  T2            2             90
  T3            8            321
  T4            1             49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  GAB3 MUTATED    11   1   0
  GAB3 WILD-TYPE 276 112  87
D1612V6, multiclass
    clus
vv   GAB3 MUTATED GAB3 WILD-TYPE
  N0           11            276
  N1            1            112
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1612V7, binary
                cls
clus               0   1
  GAB3 MUTATED    12   0
  GAB3 WILD-TYPE 363  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  GAB3 MUTATED     12    0
  GAB3 WILD-TYPE  363   65
   clus
vv  GAB3 MUTATED GAB3 WILD-TYPE
  0           12            363
  1            0             65
[1] 2 2
[1] FALSE
D1612V8, binary
                cls
clus               0   1
  GAB3 MUTATED     8   4
  GAB3 WILD-TYPE 217 260
[1] "tbl2"
                cls
clus             [,1] [,2]
  GAB3 MUTATED      8    4
  GAB3 WILD-TYPE  217  260
        clus
vv       GAB3 MUTATED GAB3 WILD-TYPE
  FEMALE            8            217
  MALE              4            260
[1] 2 2
[1] FALSE
D1612V9, binary
                cls
clus               0   1
  GAB3 MUTATED     8   0
  GAB3 WILD-TYPE 342  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  GAB3 MUTATED      8    0
  GAB3 WILD-TYPE  342   22
     clus
vv    GAB3 MUTATED GAB3 WILD-TYPE
  NO             8            342
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  GAB3 MUTATED                     10                             1
  GAB3 WILD-TYPE                  305                            46
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  GAB3 MUTATED                       1                              0
  GAB3 WILD-TYPE                   105                             10
D1612V10, multiclass
                                clus
vv                               GAB3 MUTATED GAB3 WILD-TYPE
  COLON ADENOCARCINOMA                     10            305
  COLON MUCINOUS ADENOCARCINOMA             1             46
  RECTAL ADENOCARCINOMA                     1            105
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  GAB3 MUTATED    10   0   0   0
  GAB3 WILD-TYPE 335   4  31  25
D1612V11, multiclass
    clus
vv   GAB3 MUTATED GAB3 WILD-TYPE
  R0           10            335
  R1            0              4
  R2            0             31
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1612V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GAB3 MUTATED                                  0     0
  GAB3 WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  GAB3 MUTATED                           0     4
  GAB3 WILD-TYPE                        22   222
D1612V13, multiclass
                                  clus
vv                                 GAB3 MUTATED GAB3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       4            222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1613) Variable = GIMAP5 MUTATION ANALYSIS
D1613V1, survival
                  sevent
clus2                0   1
  GIMAP5 MUTATED     6   2
  GIMAP5 WILD-TYPE 372  91
  GIMAP5 MUTATED GIMAP5 WILD-TYPE 
               8              463 
  GIMAP5 MUTATED GIMAP5 WILD-TYPE 
               2               91 
$`GIMAP5 MUTATED`
TCGA-A6-5659 TCGA-A6-6653 TCGA-AA-3555 TCGA-AA-3811 TCGA-AA-A00N TCGA-AA-A01F 
       30.44        24.39        29.95        10.06         4.01        32.02 
TCGA-AG-3885 TCGA-AG-A002 
       17.95        20.98 

$`GIMAP5 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 
       25.18        24.16        21.76        24.69        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       24.00        17.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3815 
       85.05        26.99        19.04        19.04        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       10.98        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 
        0.99         0.99        19.04        19.99         1.02        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  GIMAP5 MUTATED GIMAP5 WILD-TYPE 
            4.01             0.00 
  GIMAP5 MUTATED GIMAP5 WILD-TYPE 
           32.02           148.01 
  GIMAP5 MUTATED GIMAP5 WILD-TYPE 
          22.685           20.120 
[1] "4.0 - 32.0 (22.7)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.7"
D1613V2, continuous
D1613V3, binary
                  cls
clus                 0   1
  GIMAP5 MUTATED     6   2
  GIMAP5 WILD-TYPE 360 117
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GIMAP5 MUTATED      6    2
  GIMAP5 WILD-TYPE  360  117
        clus
vv       GIMAP5 MUTATED GIMAP5 WILD-TYPE
  COLON               6              360
  RECTUM              2              117
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GIMAP5 MUTATED         3        0        0         1         1         0
  GIMAP5 WILD-TYPE      88        1       32       137         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GIMAP5 MUTATED           1          0          2          0        0
  GIMAP5 WILD-TYPE        23         11         57         42       48
                  vv
clus               STAGE IVA STAGE IVB
  GIMAP5 MUTATED           0         0
  GIMAP5 WILD-TYPE        18         1
D1613V4, multiclass
            clus
vv           GIMAP5 MUTATED GIMAP5 WILD-TYPE
  STAGE I                 3               88
  STAGE IA                0                1
  STAGE II                0               32
  STAGE IIA               1              137
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               1               23
  STAGE IIIA              0               11
  STAGE IIIB              2               57
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  GIMAP5 MUTATED     0   3   4   1
  GIMAP5 WILD-TYPE  17  89 325  49
D1613V5, multiclass
    clus
vv   GIMAP5 MUTATED GIMAP5 WILD-TYPE
  T1              0               17
  T2              3               89
  T3              4              325
  T4              1               49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  GIMAP5 MUTATED     5   2   1
  GIMAP5 WILD-TYPE 282 111  86
D1613V6, multiclass
    clus
vv   GIMAP5 MUTATED GIMAP5 WILD-TYPE
  N0              5              282
  N1              2              111
  N2              1               86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1613V7, binary
                  cls
clus                 0   1
  GIMAP5 MUTATED     8   0
  GIMAP5 WILD-TYPE 367  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GIMAP5 MUTATED      8    0
  GIMAP5 WILD-TYPE  367   65
   clus
vv  GIMAP5 MUTATED GIMAP5 WILD-TYPE
  0              8              367
  1              0               65
[1] 2 2
[1] FALSE
D1613V8, binary
                  cls
clus                 0   1
  GIMAP5 MUTATED     3   5
  GIMAP5 WILD-TYPE 222 259
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GIMAP5 MUTATED      3    5
  GIMAP5 WILD-TYPE  222  259
        clus
vv       GIMAP5 MUTATED GIMAP5 WILD-TYPE
  FEMALE              3              222
  MALE                5              259
[1] 2 2
[1] FALSE
D1613V9, binary
                  cls
clus                 0   1
  GIMAP5 MUTATED     6   1
  GIMAP5 WILD-TYPE 344  21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GIMAP5 MUTATED      6    1
  GIMAP5 WILD-TYPE  344   21
     clus
vv    GIMAP5 MUTATED GIMAP5 WILD-TYPE
  NO               6              344
  YES              1               21
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  GIMAP5 MUTATED                      4                             2
  GIMAP5 WILD-TYPE                  311                            45
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  GIMAP5 MUTATED                       2                              0
  GIMAP5 WILD-TYPE                   104                             10
D1613V10, multiclass
                                clus
vv                               GIMAP5 MUTATED GIMAP5 WILD-TYPE
  COLON ADENOCARCINOMA                        4              311
  COLON MUCINOUS ADENOCARCINOMA               2               45
  RECTAL ADENOCARCINOMA                       2              104
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  GIMAP5 MUTATED     7   0   0   0
  GIMAP5 WILD-TYPE 338   4  31  25
D1613V11, multiclass
    clus
vv   GIMAP5 MUTATED GIMAP5 WILD-TYPE
  R0              7              338
  R1              0                4
  R2              0               31
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1613V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GIMAP5 MUTATED                                  0     0
  GIMAP5 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  GIMAP5 MUTATED                           0     2
  GIMAP5 WILD-TYPE                        22   224
D1613V13, multiclass
[1] "Remove cluster labels:" "GIMAP5 MUTATED"        
clus
  GIMAP5 MUTATED GIMAP5 WILD-TYPE 
               2              258 
      TCGA-A6-2671       TCGA-A6-2672       TCGA-A6-2674       TCGA-A6-2676 
"GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" 
      TCGA-A6-2677       TCGA-A6-2678       TCGA-A6-2683       TCGA-A6-3807 
"GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" 
      TCGA-A6-3808       TCGA-A6-3809       TCGA-A6-3810       TCGA-A6-4105 
"GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" 
      TCGA-A6-5656       TCGA-A6-5657       TCGA-A6-5660       TCGA-A6-5661 
"GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" 
      TCGA-A6-5662       TCGA-A6-5664       TCGA-A6-5665       TCGA-A6-5666 
"GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" 
      TCGA-A6-6137       TCGA-A6-6138       TCGA-A6-6141       TCGA-A6-6142 
"GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" 
      TCGA-A6-6648       TCGA-A6-6649       TCGA-A6-6651       TCGA-A6-6652 
"GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" 
      TCGA-A6-6654       TCGA-A6-6780       TCGA-A6-6781       TCGA-A6-6782 
"GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" 
      TCGA-AD-5900       TCGA-AD-6548       TCGA-AD-6888       TCGA-AD-6889 
"GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" 
      TCGA-AD-6890       TCGA-AD-6895       TCGA-AD-6899       TCGA-AD-6901 
"GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" 
      TCGA-AD-6963       TCGA-AD-6964       TCGA-AD-6965       TCGA-AU-3779 
"GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" 
      TCGA-AU-6004       TCGA-AY-4070       TCGA-AY-4071       TCGA-AY-5543 
"GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" 
      TCGA-AY-6196       TCGA-AY-6197       TCGA-AY-6386       TCGA-AZ-4315 
"GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" 
      TCGA-AZ-4323       TCGA-AZ-4616       TCGA-AZ-4681       TCGA-AZ-4682 
"GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" 
      TCGA-AZ-5403       TCGA-AZ-5407       TCGA-AZ-6598       TCGA-AZ-6599 
"GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" 
      TCGA-AZ-6600       TCGA-AZ-6601       TCGA-AZ-6603       TCGA-AZ-6605 
"GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" 
      TCGA-AZ-6606       TCGA-AZ-6607       TCGA-AZ-6608       TCGA-CA-5254 
"GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" 
      TCGA-CA-5255       TCGA-CA-5796       TCGA-CA-5797       TCGA-CA-6715 
"GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" 
      TCGA-CA-6716       TCGA-CA-6717       TCGA-CA-6718       TCGA-CA-6719 
"GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" 
      TCGA-CK-4947       TCGA-CK-4948       TCGA-CK-4950       TCGA-CK-4952 
"GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" 
      TCGA-CK-5912       TCGA-CK-5913       TCGA-CK-5914       TCGA-CK-5915 
"GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" 
      TCGA-CK-5916       TCGA-CK-6746       TCGA-CK-6747       TCGA-CK-6748 
"GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" 
      TCGA-CK-6751       TCGA-CM-4743       TCGA-CM-4744       TCGA-CM-4746 
"GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" 
      TCGA-CM-4747       TCGA-CM-4752       TCGA-CM-5341       TCGA-CM-5344 
"GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" 
      TCGA-CM-5348       TCGA-CM-5349       TCGA-CM-5860       TCGA-CM-5861 
"GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" 
      TCGA-CM-5862       TCGA-CM-5863       TCGA-CM-5864       TCGA-CM-5868 
"GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" 
      TCGA-CM-6161       TCGA-CM-6162       TCGA-CM-6163       TCGA-CM-6164 
"GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" 
      TCGA-CM-6165       TCGA-CM-6166       TCGA-CM-6167       TCGA-CM-6168 
"GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" 
      TCGA-CM-6169       TCGA-CM-6170       TCGA-CM-6171       TCGA-CM-6172 
"GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" 
      TCGA-CM-6674       TCGA-CM-6675       TCGA-CM-6676       TCGA-CM-6677 
"GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" 
      TCGA-CM-6678       TCGA-CM-6679       TCGA-CM-6680       TCGA-D5-5537 
"GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" 
      TCGA-D5-5538       TCGA-D5-5539       TCGA-D5-5540       TCGA-D5-5541 
"GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" 
      TCGA-D5-6529       TCGA-D5-6532       TCGA-D5-6533       TCGA-D5-6534 
"GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" 
      TCGA-D5-6535       TCGA-D5-6536       TCGA-D5-6537       TCGA-D5-6538 
"GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" 
      TCGA-D5-6539       TCGA-D5-6540       TCGA-D5-6541       TCGA-D5-6898 
"GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" 
      TCGA-D5-6920       TCGA-D5-6922       TCGA-D5-6923       TCGA-D5-6924 
"GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" 
      TCGA-D5-6926       TCGA-D5-6927       TCGA-D5-6928       TCGA-D5-6929 
"GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" 
      TCGA-D5-6930       TCGA-D5-6931       TCGA-D5-6932       TCGA-D5-7000 
"GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" 
      TCGA-DM-A0X9       TCGA-DM-A0XD       TCGA-DM-A0XF       TCGA-DM-A1D0 
"GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" 
      TCGA-DM-A1D4       TCGA-DM-A1D6       TCGA-DM-A1D7       TCGA-DM-A1D8 
"GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" 
      TCGA-DM-A1D9       TCGA-DM-A1DA       TCGA-DM-A1DB       TCGA-DM-A1HA 
"GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" 
      TCGA-DM-A1HB       TCGA-DM-A282       TCGA-DM-A285       TCGA-DM-A28C 
"GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" 
      TCGA-DM-A28E       TCGA-DM-A28F       TCGA-DM-A28G       TCGA-DM-A28H 
"GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" 
      TCGA-DM-A28K       TCGA-F4-6459       TCGA-F4-6460       TCGA-F4-6569 
"GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" 
      TCGA-F4-6570       TCGA-F4-6703       TCGA-F4-6704       TCGA-F4-6805 
"GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" 
      TCGA-F4-6806       TCGA-F4-6807       TCGA-F4-6808       TCGA-F4-6809 
"GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" 
      TCGA-F4-6854       TCGA-F4-6855       TCGA-F4-6856       TCGA-G4-6293 
"GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" 
      TCGA-G4-6299       TCGA-G4-6303       TCGA-G4-6304       TCGA-G4-6306 
"GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" 
      TCGA-G4-6307       TCGA-G4-6309       TCGA-G4-6310       TCGA-G4-6315 
"GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" 
      TCGA-G4-6317       TCGA-G4-6321       TCGA-G4-6323       TCGA-G4-6586 
"GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" 
      TCGA-G4-6588       TCGA-G4-6625       TCGA-G4-6626       TCGA-G4-6628 
"GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" 
      TCGA-AF-2687       TCGA-AF-2689       TCGA-AF-2691       TCGA-AF-2692 
"GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" 
      TCGA-AF-2693       TCGA-AF-3400       TCGA-AF-3913       TCGA-AF-4110 
"GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" 
      TCGA-AF-5654       TCGA-AF-6136       TCGA-AF-6655       TCGA-AF-6672 
"GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" 
      TCGA-AH-6544       TCGA-AH-6547       TCGA-AH-6549       TCGA-AH-6643 
"GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" 
      TCGA-AH-6644       TCGA-CI-6619       TCGA-CI-6620       TCGA-CI-6621 
"GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" 
      TCGA-CI-6622       TCGA-CI-6624       TCGA-CL-5917       TCGA-CL-5918 
"GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" 
      TCGA-DC-5337       TCGA-DC-5869       TCGA-DC-6155       TCGA-DC-6157 
"GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" 
      TCGA-DC-6158       TCGA-DC-6160       TCGA-DC-6681       TCGA-DC-6682 
"GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" 
      TCGA-DC-6683       TCGA-DT-5265       TCGA-DY-A0XA       TCGA-DY-A1DC 
"GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" 
      TCGA-DY-A1DD       TCGA-DY-A1DF       TCGA-DY-A1DG       TCGA-DY-A1H8 
"GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" 
      TCGA-EF-5830       TCGA-EI-6506       TCGA-EI-6507       TCGA-EI-6508 
"GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" 
      TCGA-EI-6510       TCGA-F5-6464       TCGA-F5-6465       TCGA-F5-6571 
"GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" 
      TCGA-F5-6702       TCGA-F5-6811       TCGA-F5-6812       TCGA-F5-6813 
"GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" 
      TCGA-G5-6235       TCGA-G5-6641 
"GIMAP5 WILD-TYPE" "GIMAP5 WILD-TYPE" 

Clustering(1614) Variable = ZEB1 MUTATION ANALYSIS
D1614V1, survival
                sevent
clus2              0   1
  ZEB1 MUTATED    20   2
  ZEB1 WILD-TYPE 358  91
  ZEB1 MUTATED ZEB1 WILD-TYPE 
            22            449 
  ZEB1 MUTATED ZEB1 WILD-TYPE 
             2             91 
$`ZEB1 MUTATED`
TCGA-A6-2672 TCGA-AA-3510 TCGA-AA-3518 TCGA-AA-3655 TCGA-AA-3672 TCGA-AA-3852 
       46.65        63.98         1.02        61.02         0.92         0.00 
TCGA-AA-3977 TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A01R TCGA-AA-A02O TCGA-AZ-6598 
       25.02        34.03        18.05        35.01         0.92        49.41 
TCGA-CA-6717 TCGA-CK-6747 TCGA-CM-6674 TCGA-D5-6930 TCGA-F4-6703 TCGA-G4-6310 
       12.76        82.95        12.95         1.51        47.87        63.62 
TCGA-AG-3732 TCGA-AG-A02N TCGA-F5-6571 TCGA-G5-6641 
       32.98        61.97        31.30        26.43 

$`ZEB1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3519 
       35.01         6.97         1.02        13.02        38.99         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       19.99        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
       14.01        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       38.04        19.00        30.02        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       31.00        38.07         1.02         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
        5.03        14.01        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       88.21         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07        12.20        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       21.14         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        4.80        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6704 
       98.24         8.61        31.96        35.74         6.18         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       44.68        55.04        85.48        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 
       13.94        19.99         7.99         0.99        37.02         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X 
       64.01        10.98        49.97         1.94        38.96        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       28.57        32.19         0.66         0.69        55.76 

  ZEB1 MUTATED ZEB1 WILD-TYPE 
             0              0 
  ZEB1 MUTATED ZEB1 WILD-TYPE 
         82.95         148.01 
  ZEB1 MUTATED ZEB1 WILD-TYPE 
         32.14          20.02 
[1] "0.0 - 83.0 (32.1)"  "0.0 - 148.0 (20.0)"
[1] "hr=" "2.9"
D1614V2, continuous
D1614V3, binary
                cls
clus               0   1
  ZEB1 MUTATED    18   5
  ZEB1 WILD-TYPE 348 114
[1] "tbl2"
                cls
clus             [,1] [,2]
  ZEB1 MUTATED     18    5
  ZEB1 WILD-TYPE  348  114
        clus
vv       ZEB1 MUTATED ZEB1 WILD-TYPE
  COLON            18            348
  RECTUM            5            114
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZEB1 MUTATED         1        0        5         8         0         0
  ZEB1 WILD-TYPE      90        1       27       130        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ZEB1 MUTATED           2          1          3          2        0         0
  ZEB1 WILD-TYPE        22         10         56         40       48        18
                vv
clus             STAGE IVB
  ZEB1 MUTATED           0
  ZEB1 WILD-TYPE         1
D1614V4, multiclass
            clus
vv           ZEB1 MUTATED ZEB1 WILD-TYPE
  STAGE I               1             90
  STAGE IA              0              1
  STAGE II              5             27
  STAGE IIA             8            130
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             2             22
  STAGE IIIA            1             10
  STAGE IIIB            3             56
  STAGE IIIC            2             40
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  ZEB1 MUTATED     1   2  19   1
  ZEB1 WILD-TYPE  16  90 310  49
D1614V5, multiclass
    clus
vv   ZEB1 MUTATED ZEB1 WILD-TYPE
  T1            1             16
  T2            2             90
  T3           19            310
  T4            1             49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  ZEB1 MUTATED    15   5   3
  ZEB1 WILD-TYPE 272 108  84
D1614V6, multiclass
    clus
vv   ZEB1 MUTATED ZEB1 WILD-TYPE
  N0           15            272
  N1            5            108
  N2            3             84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1614V7, binary
                cls
clus               0   1
  ZEB1 MUTATED    19   0
  ZEB1 WILD-TYPE 356  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  ZEB1 MUTATED     19    0
  ZEB1 WILD-TYPE  356   65
   clus
vv  ZEB1 MUTATED ZEB1 WILD-TYPE
  0           19            356
  1            0             65
[1] 2 2
[1] FALSE
D1614V8, binary
                cls
clus               0   1
  ZEB1 MUTATED     8  15
  ZEB1 WILD-TYPE 217 249
[1] "tbl2"
                cls
clus             [,1] [,2]
  ZEB1 MUTATED      8   15
  ZEB1 WILD-TYPE  217  249
        clus
vv       ZEB1 MUTATED ZEB1 WILD-TYPE
  FEMALE            8            217
  MALE             15            249
[1] 2 2
[1] FALSE
D1614V9, binary
                cls
clus               0   1
  ZEB1 MUTATED    15   2
  ZEB1 WILD-TYPE 335  20
[1] "tbl2"
                cls
clus             [,1] [,2]
  ZEB1 MUTATED     15    2
  ZEB1 WILD-TYPE  335   20
     clus
vv    ZEB1 MUTATED ZEB1 WILD-TYPE
  NO            15            335
  YES            2             20
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ZEB1 MUTATED                     13                             5
  ZEB1 WILD-TYPE                  302                            42
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ZEB1 MUTATED                       4                              1
  ZEB1 WILD-TYPE                   102                              9
D1614V10, multiclass
                                clus
vv                               ZEB1 MUTATED ZEB1 WILD-TYPE
  COLON ADENOCARCINOMA                     13            302
  COLON MUCINOUS ADENOCARCINOMA             5             42
  RECTAL ADENOCARCINOMA                     4            102
  RECTAL MUCINOUS ADENOCARCINOMA            1              9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  ZEB1 MUTATED    19   0   0   2
  ZEB1 WILD-TYPE 326   4  31  23
D1614V11, multiclass
    clus
vv   ZEB1 MUTATED ZEB1 WILD-TYPE
  R0           19            326
  R1            0              4
  R2            0             31
  RX            2             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1614V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZEB1 MUTATED                                  0     1
  ZEB1 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  ZEB1 MUTATED                           0     9
  ZEB1 WILD-TYPE                        22   217
D1614V13, multiclass
                                  clus
vv                                 ZEB1 MUTATED ZEB1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       9            217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1615) Variable = CATSPER4 MUTATION ANALYSIS
D1615V1, survival
                    sevent
clus2                  0   1
  CATSPER4 MUTATED     8   3
  CATSPER4 WILD-TYPE 370  90
  CATSPER4 MUTATED CATSPER4 WILD-TYPE 
                11                460 
  CATSPER4 MUTATED CATSPER4 WILD-TYPE 
                 3                 90 
$`CATSPER4 MUTATED`
TCGA-A6-6654 TCGA-A6-6780 TCGA-AA-3525 TCGA-AA-3947 TCGA-AD-6895 TCGA-AD-6901 
       23.87        20.12         8.05        33.01         0.72        22.42 
TCGA-AU-6004 TCGA-AZ-6606 TCGA-CA-6718 TCGA-AG-A002 TCGA-AG-A00C 
       27.09        11.74        10.06        20.98         6.02 

$`CATSPER4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3529 
        9.07        24.03        37.05        36.03        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 
        5.79        27.42        10.88         0.20        14.50        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 
        6.77        12.10       100.01        29.56         5.23         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.20        12.76        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  CATSPER4 MUTATED CATSPER4 WILD-TYPE 
              0.72               0.00 
  CATSPER4 MUTATED CATSPER4 WILD-TYPE 
             33.01             148.01 
  CATSPER4 MUTATED CATSPER4 WILD-TYPE 
            20.120             20.235 
[1] "0.7 - 33.0 (20.1)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "2.3"
D1615V2, continuous
D1615V3, binary
                    cls
clus                   0   1
  CATSPER4 MUTATED    11   2
  CATSPER4 WILD-TYPE 355 117
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  CATSPER4 MUTATED     11    2
  CATSPER4 WILD-TYPE  355  117
        clus
vv       CATSPER4 MUTATED CATSPER4 WILD-TYPE
  COLON                11                355
  RECTUM                2                117
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CATSPER4 MUTATED         2        0        0         3         2         0
  CATSPER4 WILD-TYPE      89        1       32       135         8         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CATSPER4 MUTATED           0          0          3          0        1
  CATSPER4 WILD-TYPE        24         11         56         42       47
                    vv
clus                 STAGE IVA STAGE IVB
  CATSPER4 MUTATED           0         0
  CATSPER4 WILD-TYPE        18         1
D1615V4, multiclass
            clus
vv           CATSPER4 MUTATED CATSPER4 WILD-TYPE
  STAGE I                   2                 89
  STAGE IA                  0                  1
  STAGE II                  0                 32
  STAGE IIA                 3                135
  STAGE IIB                 2                  8
  STAGE IIC                 0                  1
  STAGE III                 0                 24
  STAGE IIIA                0                 11
  STAGE IIIB                3                 56
  STAGE IIIC                0                 42
  STAGE IV                  1                 47
  STAGE IVA                 0                 18
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  CATSPER4 MUTATED     0   2   8   3
  CATSPER4 WILD-TYPE  17  90 321  47
D1615V5, multiclass
    clus
vv   CATSPER4 MUTATED CATSPER4 WILD-TYPE
  T1                0                 17
  T2                2                 90
  T3                8                321
  T4                3                 47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  CATSPER4 MUTATED     8   4   1
  CATSPER4 WILD-TYPE 279 109  86
D1615V6, multiclass
    clus
vv   CATSPER4 MUTATED CATSPER4 WILD-TYPE
  N0                8                279
  N1                4                109
  N2                1                 86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1615V7, binary
                    cls
clus                   0   1
  CATSPER4 MUTATED     8   1
  CATSPER4 WILD-TYPE 367  64
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  CATSPER4 MUTATED      8    1
  CATSPER4 WILD-TYPE  367   64
   clus
vv  CATSPER4 MUTATED CATSPER4 WILD-TYPE
  0                8                367
  1                1                 64
[1] 2 2
[1] FALSE
D1615V8, binary
                    cls
clus                   0   1
  CATSPER4 MUTATED     6   7
  CATSPER4 WILD-TYPE 219 257
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  CATSPER4 MUTATED      6    7
  CATSPER4 WILD-TYPE  219  257
        clus
vv       CATSPER4 MUTATED CATSPER4 WILD-TYPE
  FEMALE                6                219
  MALE                  7                257
[1] 2 2
[1] FALSE
D1615V9, binary
                    cls
clus                   0   1
  CATSPER4 MUTATED     8   1
  CATSPER4 WILD-TYPE 342  21
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  CATSPER4 MUTATED      8    1
  CATSPER4 WILD-TYPE  342   21
     clus
vv    CATSPER4 MUTATED CATSPER4 WILD-TYPE
  NO                 8                342
  YES                1                 21
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CATSPER4 MUTATED                      9                             2
  CATSPER4 WILD-TYPE                  306                            45
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CATSPER4 MUTATED                       2                              0
  CATSPER4 WILD-TYPE                   104                             10
D1615V10, multiclass
                                clus
vv                               CATSPER4 MUTATED CATSPER4 WILD-TYPE
  COLON ADENOCARCINOMA                          9                306
  COLON MUCINOUS ADENOCARCINOMA                 2                 45
  RECTAL ADENOCARCINOMA                         2                104
  RECTAL MUCINOUS ADENOCARCINOMA                0                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  CATSPER4 MUTATED     6   0   0   2
  CATSPER4 WILD-TYPE 339   4  31  23
D1615V11, multiclass
    clus
vv   CATSPER4 MUTATED CATSPER4 WILD-TYPE
  R0                6                339
  R1                0                  4
  R2                0                 31
  RX                2                 23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1615V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CATSPER4 MUTATED                                  0     1
  CATSPER4 WILD-TYPE                                1    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  CATSPER4 MUTATED                           0     7
  CATSPER4 WILD-TYPE                        22   219
D1615V13, multiclass
                                  clus
vv                                 CATSPER4 MUTATED CATSPER4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                 10
  BLACK OR AFRICAN AMERICAN                       0                 22
  WHITE                                           7                219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1616) Variable = ERN1 MUTATION ANALYSIS
D1616V1, survival
                sevent
clus2              0   1
  ERN1 MUTATED     2   1
  ERN1 WILD-TYPE 376  92
  ERN1 MUTATED ERN1 WILD-TYPE 
             3            468 
  ERN1 MUTATED ERN1 WILD-TYPE 
             1             92 
$`ERN1 MUTATED`
TCGA-AA-3968 TCGA-AZ-6601 TCGA-CM-5860 
       21.99       100.01        32.02 

$`ERN1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3971 
       24.00         2.01        20.98        34.03         2.01        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77        12.10        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  ERN1 MUTATED ERN1 WILD-TYPE 
         21.99           0.00 
  ERN1 MUTATED ERN1 WILD-TYPE 
        100.01         148.01 
  ERN1 MUTATED ERN1 WILD-TYPE 
        32.020         20.085 
[1] "22.0 - 100.0 (32.0)" "0.0 - 148.0 (20.1)" 
[1] "hr=" "1.1"
D1616V2, continuous
D1616V3, binary
                cls
clus               0   1
  ERN1 MUTATED     3   0
  ERN1 WILD-TYPE 363 119
[1] "tbl2"
                cls
clus             [,1] [,2]
  ERN1 MUTATED      3    0
  ERN1 WILD-TYPE  363  119
        clus
vv       ERN1 MUTATED ERN1 WILD-TYPE
  COLON             3            363
  RECTUM            0            119
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ERN1 MUTATED         1        0        1         1         0         0
  ERN1 WILD-TYPE      90        1       31       137        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ERN1 MUTATED           0          0          0          0        0         0
  ERN1 WILD-TYPE        24         11         59         42       48        18
                vv
clus             STAGE IVB
  ERN1 MUTATED           0
  ERN1 WILD-TYPE         1
D1616V4, multiclass
            clus
vv           ERN1 MUTATED ERN1 WILD-TYPE
  STAGE I               1             90
  STAGE IA              0              1
  STAGE II              1             31
  STAGE IIA             1            137
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            0             59
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  ERN1 MUTATED     0   1   2   0
  ERN1 WILD-TYPE  17  91 327  50
D1616V5, multiclass
    clus
vv   ERN1 MUTATED ERN1 WILD-TYPE
  T1            0             17
  T2            1             91
  T3            2            327
  T4            0             50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  ERN1 MUTATED     3   0   0
  ERN1 WILD-TYPE 284 113  87
D1616V6, multiclass
    clus
vv   ERN1 MUTATED ERN1 WILD-TYPE
  N0            3            284
  N1            0            113
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1616V7, binary
                cls
clus               0   1
  ERN1 MUTATED     3   0
  ERN1 WILD-TYPE 372  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  ERN1 MUTATED      3    0
  ERN1 WILD-TYPE  372   65
   clus
vv  ERN1 MUTATED ERN1 WILD-TYPE
  0            3            372
  1            0             65
[1] 2 2
[1] FALSE
D1616V8, binary
                cls
clus               0   1
  ERN1 MUTATED     1   2
  ERN1 WILD-TYPE 224 262
[1] "tbl2"
                cls
clus             [,1] [,2]
  ERN1 MUTATED      1    2
  ERN1 WILD-TYPE  224  262
        clus
vv       ERN1 MUTATED ERN1 WILD-TYPE
  FEMALE            1            224
  MALE              2            262
[1] 2 2
[1] FALSE
D1616V9, binary
                cls
clus               0   1
  ERN1 MUTATED     3   0
  ERN1 WILD-TYPE 347  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  ERN1 MUTATED      3    0
  ERN1 WILD-TYPE  347   22
     clus
vv    ERN1 MUTATED ERN1 WILD-TYPE
  NO             3            347
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ERN1 MUTATED                      3                             0
  ERN1 WILD-TYPE                  312                            47
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ERN1 MUTATED                       0                              0
  ERN1 WILD-TYPE                   106                             10
D1616V10, multiclass
                                clus
vv                               ERN1 MUTATED ERN1 WILD-TYPE
  COLON ADENOCARCINOMA                      3            312
  COLON MUCINOUS ADENOCARCINOMA             0             47
  RECTAL ADENOCARCINOMA                     0            106
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  ERN1 MUTATED     2   0   0   0
  ERN1 WILD-TYPE 343   4  31  25
D1616V11, multiclass
[1] "Remove cluster labels:" "ERN1 MUTATED"          
clus
  ERN1 MUTATED ERN1 WILD-TYPE 
             2            403 
    TCGA-A6-2671     TCGA-A6-2672     TCGA-A6-2674     TCGA-A6-2676 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-A6-2677     TCGA-A6-2678     TCGA-A6-2683     TCGA-A6-3807 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-A6-3808     TCGA-A6-3809     TCGA-A6-3810     TCGA-A6-5657 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-A6-5659     TCGA-A6-5661     TCGA-A6-5665     TCGA-A6-6781 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AA-3489     TCGA-AA-3492     TCGA-AA-3496     TCGA-AA-3502 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AA-3510     TCGA-AA-3511     TCGA-AA-3514     TCGA-AA-3517 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AA-3518     TCGA-AA-3519     TCGA-AA-3520     TCGA-AA-3521 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AA-3522     TCGA-AA-3524     TCGA-AA-3525     TCGA-AA-3526 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AA-3527     TCGA-AA-3529     TCGA-AA-3530     TCGA-AA-3531 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AA-3532     TCGA-AA-3534     TCGA-AA-3538     TCGA-AA-3542 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AA-3543     TCGA-AA-3544     TCGA-AA-3548     TCGA-AA-3549 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AA-3552     TCGA-AA-3553     TCGA-AA-3554     TCGA-AA-3555 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AA-3556     TCGA-AA-3558     TCGA-AA-3560     TCGA-AA-3561 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AA-3562     TCGA-AA-3655     TCGA-AA-3660     TCGA-AA-3662 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AA-3663     TCGA-AA-3664     TCGA-AA-3666     TCGA-AA-3667 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AA-3672     TCGA-AA-3673     TCGA-AA-3678     TCGA-AA-3679 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AA-3680     TCGA-AA-3681     TCGA-AA-3684     TCGA-AA-3685 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AA-3688     TCGA-AA-3692     TCGA-AA-3693     TCGA-AA-3695 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AA-3696     TCGA-AA-3697     TCGA-AA-3710     TCGA-AA-3712 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AA-3713     TCGA-AA-3715     TCGA-AA-3811     TCGA-AA-3812 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AA-3814     TCGA-AA-3815     TCGA-AA-3818     TCGA-AA-3819 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AA-3821     TCGA-AA-3831     TCGA-AA-3833     TCGA-AA-3837 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AA-3842     TCGA-AA-3844     TCGA-AA-3845     TCGA-AA-3846 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AA-3848     TCGA-AA-3850     TCGA-AA-3851     TCGA-AA-3852 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AA-3854     TCGA-AA-3855     TCGA-AA-3856     TCGA-AA-3858 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AA-3860     TCGA-AA-3861     TCGA-AA-3864     TCGA-AA-3866 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AA-3867     TCGA-AA-3869     TCGA-AA-3870     TCGA-AA-3872 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AA-3875     TCGA-AA-3877     TCGA-AA-3930     TCGA-AA-3939 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AA-3941     TCGA-AA-3947     TCGA-AA-3949     TCGA-AA-3950 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AA-3952     TCGA-AA-3955     TCGA-AA-3956     TCGA-AA-3971 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AA-3972     TCGA-AA-3973     TCGA-AA-3975     TCGA-AA-3976 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AA-3979     TCGA-AA-3984     TCGA-AA-3986     TCGA-AA-3989 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AA-3994     TCGA-AA-A004     TCGA-AA-A00A     TCGA-AA-A00D 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AA-A00E     TCGA-AA-A00F     TCGA-AA-A00J     TCGA-AA-A00K 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AA-A00L     TCGA-AA-A00N     TCGA-AA-A00O     TCGA-AA-A00Q 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AA-A00R     TCGA-AA-A00U     TCGA-AA-A00W     TCGA-AA-A00Z 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AA-A010     TCGA-AA-A017     TCGA-AA-A01D     TCGA-AA-A01F 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AA-A01G     TCGA-AA-A01I     TCGA-AA-A01K     TCGA-AA-A01P 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AA-A01Q     TCGA-AA-A01R     TCGA-AA-A01S     TCGA-AA-A01T 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AA-A01V     TCGA-AA-A01X     TCGA-AA-A01Z     TCGA-AA-A022 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AA-A024     TCGA-AA-A029     TCGA-AA-A02F     TCGA-AA-A02H 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AA-A02J     TCGA-AA-A02K     TCGA-AA-A02O     TCGA-AA-A02W 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AA-A02Y     TCGA-AA-A03F     TCGA-AA-A03J     TCGA-AD-5900 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AD-6548     TCGA-AD-6888     TCGA-AU-3779     TCGA-AU-6004 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AY-4070     TCGA-AY-4071     TCGA-AY-5543     TCGA-AY-6196 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AY-6197     TCGA-AY-6386     TCGA-AZ-4315     TCGA-AZ-4681 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AZ-4682     TCGA-CA-5254     TCGA-CA-5255     TCGA-CA-5796 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-CA-5797     TCGA-CA-6715     TCGA-CA-6716     TCGA-CA-6717 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-CA-6718     TCGA-CA-6719     TCGA-CK-4947     TCGA-CK-4948 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-CK-4950     TCGA-CK-4952     TCGA-CK-5912     TCGA-CK-5913 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-CK-5914     TCGA-CK-5915     TCGA-CK-5916     TCGA-CK-6746 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-CK-6747     TCGA-CK-6748     TCGA-CK-6751     TCGA-CM-4743 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-CM-4744     TCGA-CM-4746     TCGA-CM-4747     TCGA-CM-4752 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-CM-5341     TCGA-CM-5344     TCGA-CM-5348     TCGA-CM-5349 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-CM-5861     TCGA-CM-5862     TCGA-CM-5863     TCGA-CM-5864 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-CM-5868     TCGA-CM-6161     TCGA-CM-6162     TCGA-CM-6163 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-CM-6164     TCGA-CM-6165     TCGA-CM-6166     TCGA-CM-6167 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-CM-6168     TCGA-CM-6169     TCGA-CM-6170     TCGA-CM-6171 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-CM-6172     TCGA-CM-6674     TCGA-CM-6675     TCGA-CM-6676 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-CM-6677     TCGA-CM-6678     TCGA-CM-6679     TCGA-CM-6680 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-D5-5537     TCGA-D5-5538     TCGA-D5-5539     TCGA-D5-5540 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-D5-5541     TCGA-D5-6529     TCGA-D5-6532     TCGA-D5-6533 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-D5-6534     TCGA-D5-6535     TCGA-D5-6536     TCGA-D5-6537 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-D5-6538     TCGA-D5-6539     TCGA-D5-6540     TCGA-D5-6541 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-D5-6898     TCGA-D5-6920     TCGA-D5-6922     TCGA-D5-6923 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-D5-6924     TCGA-D5-6926     TCGA-D5-6927     TCGA-D5-6928 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-D5-6929     TCGA-D5-6930     TCGA-D5-6931     TCGA-D5-6932 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-D5-7000     TCGA-F4-6459     TCGA-F4-6460     TCGA-F4-6569 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-F4-6570     TCGA-F4-6703     TCGA-F4-6704     TCGA-F4-6805 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-F4-6806     TCGA-F4-6807     TCGA-F4-6808     TCGA-F4-6809 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-F4-6854     TCGA-F4-6855     TCGA-F4-6856     TCGA-G4-6293 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-G4-6299     TCGA-G4-6303     TCGA-G4-6304     TCGA-G4-6306 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-G4-6307     TCGA-G4-6309     TCGA-G4-6310     TCGA-G4-6315 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-G4-6317     TCGA-G4-6321     TCGA-G4-6323     TCGA-G4-6586 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-G4-6588     TCGA-G4-6625     TCGA-G4-6626     TCGA-G4-6628 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AF-2687     TCGA-AF-2689     TCGA-AF-2691     TCGA-AF-2692 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AF-3400     TCGA-AF-3913     TCGA-AF-4110     TCGA-AF-5654 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AF-6655     TCGA-AG-3574     TCGA-AG-3575     TCGA-AG-3578 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AG-3580     TCGA-AG-3581     TCGA-AG-3582     TCGA-AG-3583 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AG-3584     TCGA-AG-3586     TCGA-AG-3587     TCGA-AG-3593 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AG-3594     TCGA-AG-3598     TCGA-AG-3599     TCGA-AG-3600 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AG-3601     TCGA-AG-3602     TCGA-AG-3605     TCGA-AG-3608 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AG-3609     TCGA-AG-3611     TCGA-AG-3612     TCGA-AG-3726 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AG-3727     TCGA-AG-3731     TCGA-AG-3732     TCGA-AG-3742 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AG-3878     TCGA-AG-3882     TCGA-AG-3883     TCGA-AG-3885 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AG-3887     TCGA-AG-3890     TCGA-AG-3892     TCGA-AG-3893 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AG-3894     TCGA-AG-3896     TCGA-AG-3898     TCGA-AG-3901 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AG-3902     TCGA-AG-3909     TCGA-AG-3999     TCGA-AG-4001 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AG-4005     TCGA-AG-4007     TCGA-AG-4008     TCGA-AG-4015 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AG-A002     TCGA-AG-A008     TCGA-AG-A00C     TCGA-AG-A00H 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AG-A00Y     TCGA-AG-A011     TCGA-AG-A014     TCGA-AG-A015 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AG-A016     TCGA-AG-A01L     TCGA-AG-A01W     TCGA-AG-A01Y 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AG-A020     TCGA-AG-A025     TCGA-AG-A026     TCGA-AG-A02G 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AG-A02N     TCGA-AG-A02X     TCGA-AG-A032     TCGA-AG-A036 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AH-6549     TCGA-AH-6643     TCGA-CL-5917     TCGA-CL-5918 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-DC-5337     TCGA-DC-5869     TCGA-DC-6155     TCGA-DC-6157 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-DC-6158     TCGA-DC-6160     TCGA-DC-6681     TCGA-DC-6682 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-DC-6683     TCGA-DT-5265     TCGA-EF-5830     TCGA-EI-6506 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-EI-6507     TCGA-EI-6508     TCGA-EI-6510     TCGA-F5-6464 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-F5-6465     TCGA-F5-6571     TCGA-F5-6702     TCGA-F5-6812 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-F5-6813     TCGA-G5-6235     TCGA-G5-6641 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
D1616V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ERN1 MUTATED                                  0     0
  ERN1 WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  ERN1 MUTATED                           0     2
  ERN1 WILD-TYPE                        22   224
D1616V13, multiclass
[1] "Remove cluster labels:" "ERN1 MUTATED"          
clus
  ERN1 MUTATED ERN1 WILD-TYPE 
             2            258 
    TCGA-A6-2671     TCGA-A6-2672     TCGA-A6-2674     TCGA-A6-2676 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-A6-2677     TCGA-A6-2678     TCGA-A6-2683     TCGA-A6-3807 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-A6-3808     TCGA-A6-3809     TCGA-A6-3810     TCGA-A6-4105 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-A6-5656     TCGA-A6-5657     TCGA-A6-5659     TCGA-A6-5660 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-A6-5661     TCGA-A6-5662     TCGA-A6-5664     TCGA-A6-5665 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-A6-5666     TCGA-A6-6137     TCGA-A6-6138     TCGA-A6-6141 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-A6-6142     TCGA-A6-6648     TCGA-A6-6649     TCGA-A6-6651 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-A6-6652     TCGA-A6-6653     TCGA-A6-6654     TCGA-A6-6780 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-A6-6781     TCGA-A6-6782     TCGA-AD-5900     TCGA-AD-6548 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AD-6888     TCGA-AD-6889     TCGA-AD-6890     TCGA-AD-6895 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AD-6899     TCGA-AD-6901     TCGA-AD-6963     TCGA-AD-6964 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AD-6965     TCGA-AU-3779     TCGA-AU-6004     TCGA-AY-4070 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AY-4071     TCGA-AY-5543     TCGA-AY-6196     TCGA-AY-6197 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AY-6386     TCGA-AZ-4315     TCGA-AZ-4323     TCGA-AZ-4616 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AZ-4681     TCGA-AZ-4682     TCGA-AZ-5403     TCGA-AZ-5407 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AZ-6598     TCGA-AZ-6599     TCGA-AZ-6600     TCGA-AZ-6603 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AZ-6605     TCGA-AZ-6606     TCGA-AZ-6607     TCGA-AZ-6608 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-CA-5254     TCGA-CA-5255     TCGA-CA-5796     TCGA-CA-5797 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-CA-6715     TCGA-CA-6716     TCGA-CA-6717     TCGA-CA-6718 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-CA-6719     TCGA-CK-4947     TCGA-CK-4948     TCGA-CK-4950 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-CK-4952     TCGA-CK-5912     TCGA-CK-5913     TCGA-CK-5914 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-CK-5915     TCGA-CK-5916     TCGA-CK-6746     TCGA-CK-6747 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-CK-6748     TCGA-CK-6751     TCGA-CM-4743     TCGA-CM-4744 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-CM-4746     TCGA-CM-4747     TCGA-CM-4752     TCGA-CM-5341 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-CM-5344     TCGA-CM-5348     TCGA-CM-5349     TCGA-CM-5861 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-CM-5862     TCGA-CM-5863     TCGA-CM-5864     TCGA-CM-5868 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-CM-6161     TCGA-CM-6162     TCGA-CM-6163     TCGA-CM-6164 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-CM-6165     TCGA-CM-6166     TCGA-CM-6167     TCGA-CM-6168 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-CM-6169     TCGA-CM-6170     TCGA-CM-6171     TCGA-CM-6172 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-CM-6674     TCGA-CM-6675     TCGA-CM-6676     TCGA-CM-6677 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-CM-6678     TCGA-CM-6679     TCGA-CM-6680     TCGA-D5-5537 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-D5-5538     TCGA-D5-5539     TCGA-D5-5540     TCGA-D5-5541 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-D5-6529     TCGA-D5-6532     TCGA-D5-6533     TCGA-D5-6534 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-D5-6535     TCGA-D5-6536     TCGA-D5-6537     TCGA-D5-6538 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-D5-6539     TCGA-D5-6540     TCGA-D5-6541     TCGA-D5-6898 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-D5-6920     TCGA-D5-6922     TCGA-D5-6923     TCGA-D5-6924 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-D5-6926     TCGA-D5-6927     TCGA-D5-6928     TCGA-D5-6929 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-D5-6930     TCGA-D5-6931     TCGA-D5-6932     TCGA-D5-7000 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-DM-A0X9     TCGA-DM-A0XD     TCGA-DM-A0XF     TCGA-DM-A1D0 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-DM-A1D4     TCGA-DM-A1D6     TCGA-DM-A1D7     TCGA-DM-A1D8 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-DM-A1D9     TCGA-DM-A1DA     TCGA-DM-A1DB     TCGA-DM-A1HA 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-DM-A1HB     TCGA-DM-A282     TCGA-DM-A285     TCGA-DM-A28C 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-DM-A28E     TCGA-DM-A28F     TCGA-DM-A28G     TCGA-DM-A28H 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-DM-A28K     TCGA-F4-6459     TCGA-F4-6460     TCGA-F4-6569 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-F4-6570     TCGA-F4-6703     TCGA-F4-6704     TCGA-F4-6805 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-F4-6806     TCGA-F4-6807     TCGA-F4-6808     TCGA-F4-6809 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-F4-6854     TCGA-F4-6855     TCGA-F4-6856     TCGA-G4-6293 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-G4-6299     TCGA-G4-6303     TCGA-G4-6304     TCGA-G4-6306 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-G4-6307     TCGA-G4-6309     TCGA-G4-6310     TCGA-G4-6315 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-G4-6317     TCGA-G4-6321     TCGA-G4-6323     TCGA-G4-6586 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-G4-6588     TCGA-G4-6625     TCGA-G4-6626     TCGA-G4-6628 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AF-2687     TCGA-AF-2689     TCGA-AF-2691     TCGA-AF-2692 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AF-2693     TCGA-AF-3400     TCGA-AF-3913     TCGA-AF-4110 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AF-5654     TCGA-AF-6136     TCGA-AF-6655     TCGA-AF-6672 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AH-6544     TCGA-AH-6547     TCGA-AH-6549     TCGA-AH-6643 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-AH-6644     TCGA-CI-6619     TCGA-CI-6620     TCGA-CI-6621 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-CI-6622     TCGA-CI-6624     TCGA-CL-5917     TCGA-CL-5918 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-DC-5337     TCGA-DC-5869     TCGA-DC-6155     TCGA-DC-6157 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-DC-6158     TCGA-DC-6160     TCGA-DC-6681     TCGA-DC-6682 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-DC-6683     TCGA-DT-5265     TCGA-DY-A0XA     TCGA-DY-A1DC 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-DY-A1DD     TCGA-DY-A1DF     TCGA-DY-A1DG     TCGA-DY-A1H8 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-EF-5830     TCGA-EI-6506     TCGA-EI-6507     TCGA-EI-6508 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-EI-6510     TCGA-F5-6464     TCGA-F5-6465     TCGA-F5-6571 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-F5-6702     TCGA-F5-6811     TCGA-F5-6812     TCGA-F5-6813 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 
    TCGA-G5-6235     TCGA-G5-6641 
"ERN1 WILD-TYPE" "ERN1 WILD-TYPE" 

Clustering(1617) Variable = HECW2 MUTATION ANALYSIS
D1617V1, survival
                 sevent
clus2               0   1
  HECW2 MUTATED    24   6
  HECW2 WILD-TYPE 354  87
  HECW2 MUTATED HECW2 WILD-TYPE 
             30             441 
  HECW2 MUTATED HECW2 WILD-TYPE 
              6              87 
$`HECW2 MUTATED`
TCGA-A6-2672 TCGA-A6-5656 TCGA-A6-5660 TCGA-AA-3510 TCGA-AA-3516 TCGA-AA-3672 
       46.65        32.91        29.19        63.98        13.02         0.92 
TCGA-AA-3854 TCGA-AA-3977 TCGA-AA-3986 TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A02Y 
       36.03        25.02        19.07         4.01        34.98        39.98 
TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6895 TCGA-AU-6004 TCGA-AZ-4315 TCGA-AZ-5403 
        0.07        56.55         0.72        27.09        58.39        62.79 
TCGA-AZ-6601 TCGA-CA-6717 TCGA-CK-5916 TCGA-CM-6674 TCGA-D5-6922 TCGA-D5-6924 
      100.01        12.76        21.14        12.95         4.41        14.30 
TCGA-G4-6307 TCGA-G4-6626 TCGA-AG-3731 TCGA-AG-3892 TCGA-AG-A002 TCGA-CI-6624 
       55.04        46.75        37.02        13.02        20.98         4.73 

$`HECW2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5657 
       34.65        33.34        32.75        36.53        14.53        31.63 
TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 
       30.44        33.53        23.61        22.09        22.06        32.71 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       27.09        22.52         8.38        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 
       20.28         7.04         3.02         1.02        35.01         6.97 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
        1.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       36.03         8.05        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       78.08         6.05         6.97        54.02         2.01        14.01 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       27.02         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 
       14.01         0.92        41.00        18.05        40.96        21.37 
TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
       15.52         0.79         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
        0.20        14.50        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5407 
       17.82         1.41         5.13       106.75        22.36        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       49.41         6.77        12.10        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07        12.20        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 
       85.45        15.62        49.08        51.32         9.99        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6675 
       12.99        13.02        15.02        14.04        11.01        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6923 
       12.49        16.14        15.58         1.48         3.68        12.43 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       35.80        26.17        91.79        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        7.99         0.99        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 
       19.99         1.02        17.95        36.95        17.03        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        6.97        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  HECW2 MUTATED HECW2 WILD-TYPE 
           0.07            0.00 
  HECW2 MUTATED HECW2 WILD-TYPE 
         100.01          148.01 
  HECW2 MUTATED HECW2 WILD-TYPE 
         26.055          20.020 
[1] "0.1 - 100.0 (26.1)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.2"
D1617V2, continuous
D1617V3, binary
                 cls
clus                0   1
  HECW2 MUTATED    28   4
  HECW2 WILD-TYPE 338 115
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HECW2 MUTATED     28    4
  HECW2 WILD-TYPE  338  115
        clus
vv       HECW2 MUTATED HECW2 WILD-TYPE
  COLON             28             338
  RECTUM             4             115
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  HECW2 MUTATED        10        0        3         6         3         0
  HECW2 WILD-TYPE      81        1       29       132         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  HECW2 MUTATED           3          1          2          1        1         0
  HECW2 WILD-TYPE        21         10         57         41       47        18
                 vv
clus              STAGE IVB
  HECW2 MUTATED           0
  HECW2 WILD-TYPE         1
D1617V4, multiclass
            clus
vv           HECW2 MUTATED HECW2 WILD-TYPE
  STAGE I               10              81
  STAGE IA               0               1
  STAGE II               3              29
  STAGE IIA              6             132
  STAGE IIB              3               7
  STAGE IIC              0               1
  STAGE III              3              21
  STAGE IIIA             1              10
  STAGE IIIB             2              57
  STAGE IIIC             1              41
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  HECW2 MUTATED     2   9  18   3
  HECW2 WILD-TYPE  15  83 311  47
D1617V5, multiclass
    clus
vv   HECW2 MUTATED HECW2 WILD-TYPE
  T1             2              15
  T2             9              83
  T3            18             311
  T4             3              47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  HECW2 MUTATED    23   6   3
  HECW2 WILD-TYPE 264 107  84
D1617V6, multiclass
    clus
vv   HECW2 MUTATED HECW2 WILD-TYPE
  N0            23             264
  N1             6             107
  N2             3              84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1617V7, binary
                 cls
clus                0   1
  HECW2 MUTATED    26   1
  HECW2 WILD-TYPE 349  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HECW2 MUTATED     26    1
  HECW2 WILD-TYPE  349   64
   clus
vv  HECW2 MUTATED HECW2 WILD-TYPE
  0            26             349
  1             1              64
[1] 2 2
[1] FALSE
D1617V8, binary
                 cls
clus                0   1
  HECW2 MUTATED    11  21
  HECW2 WILD-TYPE 214 243
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HECW2 MUTATED     11   21
  HECW2 WILD-TYPE  214  243
        clus
vv       HECW2 MUTATED HECW2 WILD-TYPE
  FEMALE            11             214
  MALE              21             243
[1] 2 2
[1] FALSE
D1617V9, binary
                 cls
clus                0   1
  HECW2 MUTATED    23   0
  HECW2 WILD-TYPE 327  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HECW2 MUTATED     23    0
  HECW2 WILD-TYPE  327   22
     clus
vv    HECW2 MUTATED HECW2 WILD-TYPE
  NO             23             327
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  HECW2 MUTATED                     23                             5
  HECW2 WILD-TYPE                  292                            42
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  HECW2 MUTATED                       4                              0
  HECW2 WILD-TYPE                   102                             10
D1617V10, multiclass
                                clus
vv                               HECW2 MUTATED HECW2 WILD-TYPE
  COLON ADENOCARCINOMA                      23             292
  COLON MUCINOUS ADENOCARCINOMA              5              42
  RECTAL ADENOCARCINOMA                      4             102
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  HECW2 MUTATED    19   0   1   3
  HECW2 WILD-TYPE 326   4  30  22
D1617V11, multiclass
    clus
vv   HECW2 MUTATED HECW2 WILD-TYPE
  R0            19             326
  R1             0               4
  R2             1              30
  RX             3              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1617V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HECW2 MUTATED                                  0     2
  HECW2 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  HECW2 MUTATED                           1    16
  HECW2 WILD-TYPE                        21   210
D1617V13, multiclass
                                  clus
vv                                 HECW2 MUTATED HECW2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               9
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                       16             210
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1618) Variable = CASP6 MUTATION ANALYSIS
D1618V1, survival
                 sevent
clus2               0   1
  CASP6 MUTATED     3   0
  CASP6 WILD-TYPE 375  93
  CASP6 MUTATED CASP6 WILD-TYPE 
              3             468 
  CASP6 MUTATED CASP6 WILD-TYPE 
              0              93 
$`CASP6 MUTATED`
TCGA-AA-A00E TCGA-CA-6717 TCGA-AG-A002 
       30.02        12.76        20.98 

$`CASP6 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       13.94        38.04        19.00        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07        12.20        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  CASP6 MUTATED CASP6 WILD-TYPE 
          12.76            0.00 
  CASP6 MUTATED CASP6 WILD-TYPE 
          30.02          148.01 
  CASP6 MUTATED CASP6 WILD-TYPE 
         20.980          20.155 
[1] "12.8 - 30.0 (21.0)" "0.0 - 148.0 (20.2)"
[1] "hr="     "3300000"
D1618V2, continuous
D1618V3, binary
                 cls
clus                0   1
  CASP6 MUTATED     2   1
  CASP6 WILD-TYPE 364 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASP6 MUTATED      2    1
  CASP6 WILD-TYPE  364  118
        clus
vv       CASP6 MUTATED CASP6 WILD-TYPE
  COLON              2             364
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CASP6 MUTATED         1        0        0         2         0         0
  CASP6 WILD-TYPE      90        1       32       136        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CASP6 MUTATED           0          0          0          0        0         0
  CASP6 WILD-TYPE        24         11         59         42       48        18
                 vv
clus              STAGE IVB
  CASP6 MUTATED           0
  CASP6 WILD-TYPE         1
D1618V4, multiclass
            clus
vv           CASP6 MUTATED CASP6 WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              2             136
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CASP6 MUTATED     0   1   2   0
  CASP6 WILD-TYPE  17  91 327  50
D1618V5, multiclass
    clus
vv   CASP6 MUTATED CASP6 WILD-TYPE
  T1             0              17
  T2             1              91
  T3             2             327
  T4             0              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  CASP6 MUTATED     3   0   0
  CASP6 WILD-TYPE 284 113  87
D1618V6, multiclass
    clus
vv   CASP6 MUTATED CASP6 WILD-TYPE
  N0             3             284
  N1             0             113
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1618V7, binary
                 cls
clus                0   1
  CASP6 MUTATED     3   0
  CASP6 WILD-TYPE 372  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASP6 MUTATED      3    0
  CASP6 WILD-TYPE  372   65
   clus
vv  CASP6 MUTATED CASP6 WILD-TYPE
  0             3             372
  1             0              65
[1] 2 2
[1] FALSE
D1618V8, binary
                 cls
clus                0   1
  CASP6 MUTATED     0   3
  CASP6 WILD-TYPE 225 261
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASP6 MUTATED      0    3
  CASP6 WILD-TYPE  225  261
        clus
vv       CASP6 MUTATED CASP6 WILD-TYPE
  FEMALE             0             225
  MALE               3             261
[1] 2 2
[1] FALSE
D1618V9, binary
                 cls
clus                0   1
  CASP6 MUTATED     3   0
  CASP6 WILD-TYPE 347  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASP6 MUTATED      3    0
  CASP6 WILD-TYPE  347   22
     clus
vv    CASP6 MUTATED CASP6 WILD-TYPE
  NO              3             347
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CASP6 MUTATED                      1                             1
  CASP6 WILD-TYPE                  314                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CASP6 MUTATED                       1                              0
  CASP6 WILD-TYPE                   105                             10
D1618V10, multiclass
                                clus
vv                               CASP6 MUTATED CASP6 WILD-TYPE
  COLON ADENOCARCINOMA                       1             314
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  CASP6 MUTATED     2   0   0   1
  CASP6 WILD-TYPE 343   4  31  24
D1618V11, multiclass
    clus
vv   CASP6 MUTATED CASP6 WILD-TYPE
  R0             2             343
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1618V12, continuous
[1] "Remove cluster labels:" "CASP6 MUTATED"         
clus
  CASP6 MUTATED CASP6 WILD-TYPE 
              2             456 
     TCGA-A6-2671      TCGA-A6-2672      TCGA-A6-2674      TCGA-A6-2676 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-A6-2677      TCGA-A6-2678      TCGA-A6-2683      TCGA-A6-3807 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-A6-3808      TCGA-A6-3809      TCGA-A6-3810      TCGA-A6-4105 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-A6-5656      TCGA-A6-5657      TCGA-A6-5659      TCGA-A6-5660 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-A6-5661      TCGA-A6-5662      TCGA-A6-5664      TCGA-A6-5665 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-A6-5666      TCGA-A6-6137      TCGA-A6-6138      TCGA-A6-6141 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-A6-6142      TCGA-A6-6648      TCGA-A6-6649      TCGA-A6-6651 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-A6-6652      TCGA-A6-6653      TCGA-A6-6654      TCGA-A6-6780 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-A6-6781      TCGA-A6-6782      TCGA-AA-3489      TCGA-AA-3492 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-AA-3496      TCGA-AA-3502      TCGA-AA-3510      TCGA-AA-3511 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-AA-3514      TCGA-AA-3516      TCGA-AA-3517      TCGA-AA-3518 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-AA-3519      TCGA-AA-3520      TCGA-AA-3521      TCGA-AA-3522 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-AA-3524      TCGA-AA-3525      TCGA-AA-3526      TCGA-AA-3527 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-AA-3529      TCGA-AA-3530      TCGA-AA-3531      TCGA-AA-3532 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-AA-3534      TCGA-AA-3538      TCGA-AA-3542      TCGA-AA-3543 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-AA-3544      TCGA-AA-3548      TCGA-AA-3549      TCGA-AA-3552 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-AA-3553      TCGA-AA-3554      TCGA-AA-3555      TCGA-AA-3556 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-AA-3558      TCGA-AA-3560      TCGA-AA-3562      TCGA-AA-3655 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-AA-3660      TCGA-AA-3662      TCGA-AA-3663      TCGA-AA-3664 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-AA-3666      TCGA-AA-3667      TCGA-AA-3672      TCGA-AA-3673 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-AA-3678      TCGA-AA-3679      TCGA-AA-3680      TCGA-AA-3681 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-AA-3684      TCGA-AA-3685      TCGA-AA-3688      TCGA-AA-3692 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-AA-3693      TCGA-AA-3695      TCGA-AA-3696      TCGA-AA-3697 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-AA-3710      TCGA-AA-3712      TCGA-AA-3713      TCGA-AA-3715 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-AA-3811      TCGA-AA-3812      TCGA-AA-3814      TCGA-AA-3815 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-AA-3818      TCGA-AA-3819      TCGA-AA-3821      TCGA-AA-3831 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-AA-3833      TCGA-AA-3837      TCGA-AA-3842      TCGA-AA-3844 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-AA-3845      TCGA-AA-3846      TCGA-AA-3848      TCGA-AA-3850 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-AA-3851      TCGA-AA-3852      TCGA-AA-3854      TCGA-AA-3855 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-AA-3856      TCGA-AA-3858      TCGA-AA-3860      TCGA-AA-3861 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-AA-3864      TCGA-AA-3866      TCGA-AA-3867      TCGA-AA-3869 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-AA-3870      TCGA-AA-3872      TCGA-AA-3875      TCGA-AA-3877 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-AA-3930      TCGA-AA-3939      TCGA-AA-3941      TCGA-AA-3947 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-AA-3949      TCGA-AA-3950      TCGA-AA-3952      TCGA-AA-3955 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-AA-3956      TCGA-AA-3966      TCGA-AA-3968      TCGA-AA-3971 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-AA-3972      TCGA-AA-3973      TCGA-AA-3975      TCGA-AA-3976 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-AA-3977      TCGA-AA-3979      TCGA-AA-3980      TCGA-AA-3982 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-AA-3984      TCGA-AA-3986      TCGA-AA-3989      TCGA-AA-3994 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-AA-A004      TCGA-AA-A00A      TCGA-AA-A00D      TCGA-AA-A00F 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-AA-A00J      TCGA-AA-A00K      TCGA-AA-A00L      TCGA-AA-A00N 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-AA-A00O      TCGA-AA-A00Q      TCGA-AA-A00R      TCGA-AA-A00U 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-AA-A00W      TCGA-AA-A00Z      TCGA-AA-A010      TCGA-AA-A017 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-AA-A01D      TCGA-AA-A01F      TCGA-AA-A01G      TCGA-AA-A01I 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-AA-A01K      TCGA-AA-A01P      TCGA-AA-A01Q      TCGA-AA-A01R 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-AA-A01S      TCGA-AA-A01T      TCGA-AA-A01V      TCGA-AA-A01X 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-AA-A01Z      TCGA-AA-A022      TCGA-AA-A024      TCGA-AA-A029 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-AA-A02F      TCGA-AA-A02H      TCGA-AA-A02J      TCGA-AA-A02K 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-AA-A02O      TCGA-AA-A02W      TCGA-AA-A02Y      TCGA-AA-A03F 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-AA-A03J      TCGA-AD-5900      TCGA-AD-6548      TCGA-AD-6888 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-AD-6889      TCGA-AD-6890      TCGA-AD-6895      TCGA-AD-6899 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-AD-6901      TCGA-AD-6963      TCGA-AD-6964      TCGA-AD-6965 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-AU-3779      TCGA-AU-6004      TCGA-AY-4070      TCGA-AY-4071 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-AY-5543      TCGA-AY-6196      TCGA-AY-6197      TCGA-AY-6386 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-AZ-4323      TCGA-AZ-4616      TCGA-AZ-4682      TCGA-AZ-5403 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-AZ-5407      TCGA-AZ-6598      TCGA-AZ-6599      TCGA-AZ-6600 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-AZ-6601      TCGA-AZ-6603      TCGA-AZ-6605      TCGA-AZ-6606 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-AZ-6607      TCGA-AZ-6608      TCGA-CK-4947      TCGA-CK-4948 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-CK-4950      TCGA-CK-4952      TCGA-CM-4743      TCGA-CM-4744 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-CM-4746      TCGA-CM-4747      TCGA-CM-4752      TCGA-CM-5341 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-CM-5344      TCGA-CM-5348      TCGA-CM-5349      TCGA-CM-5860 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-CM-5861      TCGA-CM-5862      TCGA-CM-5863      TCGA-CM-5864 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-CM-5868      TCGA-CM-6161      TCGA-CM-6162      TCGA-CM-6163 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-CM-6164      TCGA-CM-6165      TCGA-CM-6166      TCGA-CM-6167 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-CM-6168      TCGA-CM-6169      TCGA-CM-6170      TCGA-CM-6171 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-CM-6172      TCGA-CM-6674      TCGA-CM-6675      TCGA-CM-6676 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-CM-6677      TCGA-CM-6678      TCGA-CM-6679      TCGA-CM-6680 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-D5-5537      TCGA-D5-5538      TCGA-D5-5539      TCGA-D5-5540 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-D5-5541      TCGA-D5-6529      TCGA-D5-6532      TCGA-D5-6533 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-D5-6534      TCGA-D5-6535      TCGA-D5-6536      TCGA-D5-6537 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-D5-6538      TCGA-D5-6539      TCGA-D5-6540      TCGA-D5-6541 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-D5-6898      TCGA-D5-6920      TCGA-D5-6922      TCGA-D5-6923 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-D5-6924      TCGA-D5-6926      TCGA-D5-6927      TCGA-D5-6928 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-D5-6929      TCGA-D5-6930      TCGA-D5-6931      TCGA-D5-6932 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-D5-7000      TCGA-DM-A0X9      TCGA-DM-A0XD      TCGA-DM-A0XF 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-DM-A1D0      TCGA-DM-A1D4      TCGA-DM-A1D6      TCGA-DM-A1D7 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-DM-A1D8      TCGA-DM-A1D9      TCGA-DM-A1DA      TCGA-DM-A1DB 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-DM-A1HA      TCGA-DM-A1HB      TCGA-DM-A282      TCGA-DM-A285 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-DM-A28C      TCGA-DM-A28E      TCGA-DM-A28F      TCGA-DM-A28G 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-DM-A28H      TCGA-DM-A28K      TCGA-F4-6459      TCGA-F4-6460 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-F4-6569      TCGA-F4-6570      TCGA-F4-6703      TCGA-F4-6704 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-F4-6806      TCGA-F4-6807      TCGA-F4-6808      TCGA-F4-6809 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-F4-6854      TCGA-F4-6855      TCGA-F4-6856      TCGA-G4-6293 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-G4-6299      TCGA-G4-6303      TCGA-G4-6304      TCGA-G4-6306 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-G4-6307      TCGA-G4-6309      TCGA-G4-6310      TCGA-G4-6315 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-G4-6317      TCGA-G4-6321      TCGA-G4-6323      TCGA-G4-6586 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-G4-6588      TCGA-G4-6625      TCGA-G4-6626      TCGA-G4-6628 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-AF-2687      TCGA-AF-2689      TCGA-AF-2691      TCGA-AF-2692 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-AF-2693      TCGA-AF-3400      TCGA-AF-3913      TCGA-AF-4110 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-AF-5654      TCGA-AF-6136      TCGA-AF-6655      TCGA-AF-6672 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-AG-3574      TCGA-AG-3575      TCGA-AG-3578      TCGA-AG-3580 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-AG-3581      TCGA-AG-3582      TCGA-AG-3583      TCGA-AG-3584 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-AG-3586      TCGA-AG-3587      TCGA-AG-3593      TCGA-AG-3594 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-AG-3598      TCGA-AG-3599      TCGA-AG-3600      TCGA-AG-3601 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-AG-3602      TCGA-AG-3605      TCGA-AG-3608      TCGA-AG-3609 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-AG-3611      TCGA-AG-3612      TCGA-AG-3726      TCGA-AG-3727 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-AG-3731      TCGA-AG-3732      TCGA-AG-3742      TCGA-AG-3878 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-AG-3881      TCGA-AG-3882      TCGA-AG-3883      TCGA-AG-3885 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-AG-3887      TCGA-AG-3890      TCGA-AG-3892      TCGA-AG-3893 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-AG-3894      TCGA-AG-3896      TCGA-AG-3898      TCGA-AG-3901 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-AG-3902      TCGA-AG-3909      TCGA-AG-3999      TCGA-AG-4001 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-AG-4005      TCGA-AG-4007      TCGA-AG-4008      TCGA-AG-4015 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-AG-A008      TCGA-AG-A00C      TCGA-AG-A00H      TCGA-AG-A00Y 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-AG-A011      TCGA-AG-A014      TCGA-AG-A015      TCGA-AG-A016 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-AG-A01L      TCGA-AG-A01W      TCGA-AG-A01Y      TCGA-AG-A020 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-AG-A025      TCGA-AG-A026      TCGA-AG-A02G      TCGA-AG-A02N 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-AG-A02X      TCGA-AG-A032      TCGA-AG-A036      TCGA-AH-6544 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-AH-6547      TCGA-AH-6643      TCGA-AH-6644      TCGA-CI-6622 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-DC-5337      TCGA-DC-5869      TCGA-DC-6155      TCGA-DC-6157 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-DC-6158      TCGA-DC-6160      TCGA-DC-6681      TCGA-DC-6682 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-DC-6683      TCGA-DY-A0XA      TCGA-DY-A1DC      TCGA-DY-A1DD 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-DY-A1DF      TCGA-DY-A1DG      TCGA-DY-A1H8      TCGA-EI-6506 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-EI-6507      TCGA-EI-6508      TCGA-EI-6510      TCGA-F5-6464 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-F5-6465      TCGA-F5-6571      TCGA-F5-6702      TCGA-F5-6811 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-F5-6812      TCGA-F5-6813      TCGA-G5-6235      TCGA-G5-6641 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CASP6 MUTATED                                  0     1
  CASP6 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CASP6 MUTATED                           0     0
  CASP6 WILD-TYPE                        22   226
D1618V13, multiclass
[1] "Remove cluster labels:" "CASP6 MUTATED"         
clus
  CASP6 MUTATED CASP6 WILD-TYPE 
              1             259 
     TCGA-A6-2671      TCGA-A6-2672      TCGA-A6-2674      TCGA-A6-2676 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-A6-2677      TCGA-A6-2678      TCGA-A6-2683      TCGA-A6-3807 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-A6-3808      TCGA-A6-3809      TCGA-A6-3810      TCGA-A6-4105 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-A6-5656      TCGA-A6-5657      TCGA-A6-5659      TCGA-A6-5660 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-A6-5661      TCGA-A6-5662      TCGA-A6-5664      TCGA-A6-5665 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-A6-5666      TCGA-A6-6137      TCGA-A6-6138      TCGA-A6-6141 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-A6-6142      TCGA-A6-6648      TCGA-A6-6649      TCGA-A6-6651 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-A6-6652      TCGA-A6-6653      TCGA-A6-6654      TCGA-A6-6780 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-A6-6781      TCGA-A6-6782      TCGA-AD-5900      TCGA-AD-6548 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-AD-6888      TCGA-AD-6889      TCGA-AD-6890      TCGA-AD-6895 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-AD-6899      TCGA-AD-6901      TCGA-AD-6963      TCGA-AD-6964 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-AD-6965      TCGA-AU-3779      TCGA-AU-6004      TCGA-AY-4070 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-AY-4071      TCGA-AY-5543      TCGA-AY-6196      TCGA-AY-6197 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-AY-6386      TCGA-AZ-4315      TCGA-AZ-4323      TCGA-AZ-4616 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-AZ-4681      TCGA-AZ-4682      TCGA-AZ-5403      TCGA-AZ-5407 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-AZ-6598      TCGA-AZ-6599      TCGA-AZ-6600      TCGA-AZ-6601 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-AZ-6603      TCGA-AZ-6605      TCGA-AZ-6606      TCGA-AZ-6607 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-AZ-6608      TCGA-CA-5254      TCGA-CA-5255      TCGA-CA-5796 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-CA-5797      TCGA-CA-6715      TCGA-CA-6716      TCGA-CA-6718 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-CA-6719      TCGA-CK-4947      TCGA-CK-4948      TCGA-CK-4950 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-CK-4952      TCGA-CK-5912      TCGA-CK-5913      TCGA-CK-5914 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-CK-5915      TCGA-CK-5916      TCGA-CK-6746      TCGA-CK-6747 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-CK-6748      TCGA-CK-6751      TCGA-CM-4743      TCGA-CM-4744 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-CM-4746      TCGA-CM-4747      TCGA-CM-4752      TCGA-CM-5341 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-CM-5344      TCGA-CM-5348      TCGA-CM-5349      TCGA-CM-5860 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-CM-5861      TCGA-CM-5862      TCGA-CM-5863      TCGA-CM-5864 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-CM-5868      TCGA-CM-6161      TCGA-CM-6162      TCGA-CM-6163 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-CM-6164      TCGA-CM-6165      TCGA-CM-6166      TCGA-CM-6167 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-CM-6168      TCGA-CM-6169      TCGA-CM-6170      TCGA-CM-6171 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-CM-6172      TCGA-CM-6674      TCGA-CM-6675      TCGA-CM-6676 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-CM-6677      TCGA-CM-6678      TCGA-CM-6679      TCGA-CM-6680 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-D5-5537      TCGA-D5-5538      TCGA-D5-5539      TCGA-D5-5540 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-D5-5541      TCGA-D5-6529      TCGA-D5-6532      TCGA-D5-6533 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-D5-6534      TCGA-D5-6535      TCGA-D5-6536      TCGA-D5-6537 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-D5-6538      TCGA-D5-6539      TCGA-D5-6540      TCGA-D5-6541 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-D5-6898      TCGA-D5-6920      TCGA-D5-6922      TCGA-D5-6923 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-D5-6924      TCGA-D5-6926      TCGA-D5-6927      TCGA-D5-6928 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-D5-6929      TCGA-D5-6930      TCGA-D5-6931      TCGA-D5-6932 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-D5-7000      TCGA-DM-A0X9      TCGA-DM-A0XD      TCGA-DM-A0XF 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-DM-A1D0      TCGA-DM-A1D4      TCGA-DM-A1D6      TCGA-DM-A1D7 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-DM-A1D8      TCGA-DM-A1D9      TCGA-DM-A1DA      TCGA-DM-A1DB 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-DM-A1HA      TCGA-DM-A1HB      TCGA-DM-A282      TCGA-DM-A285 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-DM-A28C      TCGA-DM-A28E      TCGA-DM-A28F      TCGA-DM-A28G 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-DM-A28H      TCGA-DM-A28K      TCGA-F4-6459      TCGA-F4-6460 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-F4-6569      TCGA-F4-6570      TCGA-F4-6703      TCGA-F4-6704 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-F4-6805      TCGA-F4-6806      TCGA-F4-6807      TCGA-F4-6808 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-F4-6809      TCGA-F4-6854      TCGA-F4-6855      TCGA-F4-6856 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-G4-6293      TCGA-G4-6299      TCGA-G4-6303      TCGA-G4-6304 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-G4-6306      TCGA-G4-6307      TCGA-G4-6309      TCGA-G4-6310 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-G4-6315      TCGA-G4-6317      TCGA-G4-6321      TCGA-G4-6323 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-G4-6586      TCGA-G4-6588      TCGA-G4-6625      TCGA-G4-6626 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-G4-6628      TCGA-AF-2687      TCGA-AF-2689      TCGA-AF-2691 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-AF-2692      TCGA-AF-2693      TCGA-AF-3400      TCGA-AF-3913 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-AF-4110      TCGA-AF-5654      TCGA-AF-6136      TCGA-AF-6655 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-AF-6672      TCGA-AH-6544      TCGA-AH-6547      TCGA-AH-6549 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-AH-6643      TCGA-AH-6644      TCGA-CI-6619      TCGA-CI-6620 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-CI-6621      TCGA-CI-6622      TCGA-CI-6624      TCGA-CL-5917 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-CL-5918      TCGA-DC-5337      TCGA-DC-5869      TCGA-DC-6155 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-DC-6157      TCGA-DC-6158      TCGA-DC-6160      TCGA-DC-6681 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-DC-6682      TCGA-DC-6683      TCGA-DT-5265      TCGA-DY-A0XA 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-DY-A1DC      TCGA-DY-A1DD      TCGA-DY-A1DF      TCGA-DY-A1DG 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-DY-A1H8      TCGA-EF-5830      TCGA-EI-6506      TCGA-EI-6507 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-EI-6508      TCGA-EI-6510      TCGA-F5-6464      TCGA-F5-6465 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-F5-6571      TCGA-F5-6702      TCGA-F5-6811      TCGA-F5-6812 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 
     TCGA-F5-6813      TCGA-G5-6235      TCGA-G5-6641 
"CASP6 WILD-TYPE" "CASP6 WILD-TYPE" "CASP6 WILD-TYPE" 

Clustering(1619) Variable = CSGALNACT1 MUTATION ANALYSIS
D1619V1, survival
                      sevent
clus2                    0   1
  CSGALNACT1 MUTATED     7   2
  CSGALNACT1 WILD-TYPE 371  91
  CSGALNACT1 MUTATED CSGALNACT1 WILD-TYPE 
                   9                  462 
  CSGALNACT1 MUTATED CSGALNACT1 WILD-TYPE 
                   2                   91 
$`CSGALNACT1 MUTATED`
TCGA-A6-6781 TCGA-AA-3489 TCGA-AD-6899 TCGA-AU-3779 TCGA-CA-6716 TCGA-CA-6717 
       19.66         7.04         5.79        14.50        12.20        12.76 
TCGA-G4-6586 TCGA-G4-6588 TCGA-EI-6506 
       35.80        26.17        20.55 

$`CSGALNACT1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       23.87        20.12        20.28         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
       56.55         0.79         0.72        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
        0.20        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6718 TCGA-CA-6719 
        3.06         3.25         3.29         0.07        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       13.78        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  CSGALNACT1 MUTATED CSGALNACT1 WILD-TYPE 
                5.79                 0.00 
  CSGALNACT1 MUTATED CSGALNACT1 WILD-TYPE 
               35.80               148.01 
  CSGALNACT1 MUTATED CSGALNACT1 WILD-TYPE 
              14.500               20.595 
[1] "5.8 - 35.8 (14.5)"  "0.0 - 148.0 (20.6)"
[1] "hr=" "1.8"
D1619V2, continuous
D1619V3, binary
                      cls
clus                     0   1
  CSGALNACT1 MUTATED     8   1
  CSGALNACT1 WILD-TYPE 358 118
[1] "tbl2"
                      cls
clus                   [,1] [,2]
  CSGALNACT1 MUTATED      8    1
  CSGALNACT1 WILD-TYPE  358  118
        clus
vv       CSGALNACT1 MUTATED CSGALNACT1 WILD-TYPE
  COLON                   8                  358
  RECTUM                  1                  118
[1] 2 2
[1] FALSE
                      vv
clus                   STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CSGALNACT1 MUTATED         0        0        1         6         0         0
  CSGALNACT1 WILD-TYPE      91        1       31       132        10         1
                      vv
clus                   STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CSGALNACT1 MUTATED           0          0          0          2        0
  CSGALNACT1 WILD-TYPE        24         11         59         40       48
                      vv
clus                   STAGE IVA STAGE IVB
  CSGALNACT1 MUTATED           0         0
  CSGALNACT1 WILD-TYPE        18         1
D1619V4, multiclass
            clus
vv           CSGALNACT1 MUTATED CSGALNACT1 WILD-TYPE
  STAGE I                     0                   91
  STAGE IA                    0                    1
  STAGE II                    1                   31
  STAGE IIA                   6                  132
  STAGE IIB                   0                   10
  STAGE IIC                   0                    1
  STAGE III                   0                   24
  STAGE IIIA                  0                   11
  STAGE IIIB                  0                   59
  STAGE IIIC                  2                   40
  STAGE IV                    0                   48
  STAGE IVA                   0                   18
  STAGE IVB                   0                    1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                      vv
clus                    T1  T2  T3  T4
  CSGALNACT1 MUTATED     0   0   7   2
  CSGALNACT1 WILD-TYPE  17  92 322  48
D1619V5, multiclass
    clus
vv   CSGALNACT1 MUTATED CSGALNACT1 WILD-TYPE
  T1                  0                   17
  T2                  0                   92
  T3                  7                  322
  T4                  2                   48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                      vv
clus                    N0  N1  N2
  CSGALNACT1 MUTATED     7   1   1
  CSGALNACT1 WILD-TYPE 280 112  86
D1619V6, multiclass
    clus
vv   CSGALNACT1 MUTATED CSGALNACT1 WILD-TYPE
  N0                  7                  280
  N1                  1                  112
  N2                  1                   86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1619V7, binary
                      cls
clus                     0   1
  CSGALNACT1 MUTATED     7   0
  CSGALNACT1 WILD-TYPE 368  65
[1] "tbl2"
                      cls
clus                   [,1] [,2]
  CSGALNACT1 MUTATED      7    0
  CSGALNACT1 WILD-TYPE  368   65
   clus
vv  CSGALNACT1 MUTATED CSGALNACT1 WILD-TYPE
  0                  7                  368
  1                  0                   65
[1] 2 2
[1] FALSE
D1619V8, binary
                      cls
clus                     0   1
  CSGALNACT1 MUTATED     4   5
  CSGALNACT1 WILD-TYPE 221 259
[1] "tbl2"
                      cls
clus                   [,1] [,2]
  CSGALNACT1 MUTATED      4    5
  CSGALNACT1 WILD-TYPE  221  259
        clus
vv       CSGALNACT1 MUTATED CSGALNACT1 WILD-TYPE
  FEMALE                  4                  221
  MALE                    5                  259
[1] 2 2
[1] FALSE
D1619V9, binary
                      cls
clus                     0   1
  CSGALNACT1 MUTATED     9   0
  CSGALNACT1 WILD-TYPE 341  22
[1] "tbl2"
                      cls
clus                   [,1] [,2]
  CSGALNACT1 MUTATED      9    0
  CSGALNACT1 WILD-TYPE  341   22
     clus
vv    CSGALNACT1 MUTATED CSGALNACT1 WILD-TYPE
  NO                   9                  341
  YES                  0                   22
[1] 2 2
[1] FALSE
                      vv
clus                   COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CSGALNACT1 MUTATED                      5                             3
  CSGALNACT1 WILD-TYPE                  310                            44
                      vv
clus                   RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CSGALNACT1 MUTATED                       1                              0
  CSGALNACT1 WILD-TYPE                   105                             10
D1619V10, multiclass
                                clus
vv                               CSGALNACT1 MUTATED CSGALNACT1 WILD-TYPE
  COLON ADENOCARCINOMA                            5                  310
  COLON MUCINOUS ADENOCARCINOMA                   3                   44
  RECTAL ADENOCARCINOMA                           1                  105
  RECTAL MUCINOUS ADENOCARCINOMA                  0                   10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                      vv
clus                    R0  R1  R2  RX
  CSGALNACT1 MUTATED     6   0   0   2
  CSGALNACT1 WILD-TYPE 339   4  31  23
D1619V11, multiclass
    clus
vv   CSGALNACT1 MUTATED CSGALNACT1 WILD-TYPE
  R0                  6                  339
  R1                  0                    4
  R2                  0                   31
  RX                  2                   23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1619V12, continuous
                      vv
clus                   AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CSGALNACT1 MUTATED                                  0     2
  CSGALNACT1 WILD-TYPE                                1     9
                      vv
clus                   BLACK OR AFRICAN AMERICAN WHITE
  CSGALNACT1 MUTATED                           0     6
  CSGALNACT1 WILD-TYPE                        22   220
D1619V13, multiclass
                                  clus
vv                                 CSGALNACT1 MUTATED CSGALNACT1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                  0                    1
  ASIAN                                             2                    9
  BLACK OR AFRICAN AMERICAN                         0                   22
  WHITE                                             6                  220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1620) Variable = SF3B2 MUTATION ANALYSIS
D1620V1, survival
                 sevent
clus2               0   1
  SF3B2 MUTATED     6   4
  SF3B2 WILD-TYPE 372  89
  SF3B2 MUTATED SF3B2 WILD-TYPE 
             10             461 
  SF3B2 MUTATED SF3B2 WILD-TYPE 
              4              89 
$`SF3B2 MUTATED`
TCGA-A6-5665 TCGA-A6-6781 TCGA-AA-3811 TCGA-AA-A010 TCGA-AZ-5407 TCGA-AZ-6598 
       22.06        19.66        10.06        34.98        88.21        49.41 
TCGA-AZ-6599 TCGA-CM-6166 TCGA-D5-6539 TCGA-F4-6570 
        6.77        21.99        12.49         6.18 

$`SF3B2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        19.04        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       62.79        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
        4.80        17.13        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 
      117.07        98.24         8.61        31.96        35.74        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  SF3B2 MUTATED SF3B2 WILD-TYPE 
           6.18            0.00 
  SF3B2 MUTATED SF3B2 WILD-TYPE 
          88.21          148.01 
  SF3B2 MUTATED SF3B2 WILD-TYPE 
         20.825          20.190 
[1] "6.2 - 88.2 (20.8)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "2"  
D1620V2, continuous
D1620V3, binary
                 cls
clus                0   1
  SF3B2 MUTATED    10   0
  SF3B2 WILD-TYPE 356 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SF3B2 MUTATED     10    0
  SF3B2 WILD-TYPE  356  119
        clus
vv       SF3B2 MUTATED SF3B2 WILD-TYPE
  COLON             10             356
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SF3B2 MUTATED         3        0        1         2         1         0
  SF3B2 WILD-TYPE      88        1       31       136         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SF3B2 MUTATED           1          1          0          1        0         0
  SF3B2 WILD-TYPE        23         10         59         41       48        18
                 vv
clus              STAGE IVB
  SF3B2 MUTATED           0
  SF3B2 WILD-TYPE         1
D1620V4, multiclass
            clus
vv           SF3B2 MUTATED SF3B2 WILD-TYPE
  STAGE I                3              88
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              2             136
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             1              10
  STAGE IIIB             0              59
  STAGE IIIC             1              41
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  SF3B2 MUTATED     1   2   5   2
  SF3B2 WILD-TYPE  16  90 324  48
D1620V5, multiclass
    clus
vv   SF3B2 MUTATED SF3B2 WILD-TYPE
  T1             1              16
  T2             2              90
  T3             5             324
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  SF3B2 MUTATED     8   1   1
  SF3B2 WILD-TYPE 279 112  86
D1620V6, multiclass
    clus
vv   SF3B2 MUTATED SF3B2 WILD-TYPE
  N0             8             279
  N1             1             112
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1620V7, binary
                 cls
clus                0   1
  SF3B2 MUTATED     7   0
  SF3B2 WILD-TYPE 368  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SF3B2 MUTATED      7    0
  SF3B2 WILD-TYPE  368   65
   clus
vv  SF3B2 MUTATED SF3B2 WILD-TYPE
  0             7             368
  1             0              65
[1] 2 2
[1] FALSE
D1620V8, binary
                 cls
clus                0   1
  SF3B2 MUTATED     8   2
  SF3B2 WILD-TYPE 217 262
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SF3B2 MUTATED      8    2
  SF3B2 WILD-TYPE  217  262
        clus
vv       SF3B2 MUTATED SF3B2 WILD-TYPE
  FEMALE             8             217
  MALE               2             262
[1] 2 2
[1] FALSE
D1620V9, binary
                 cls
clus                0   1
  SF3B2 MUTATED    10   0
  SF3B2 WILD-TYPE 340  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SF3B2 MUTATED     10    0
  SF3B2 WILD-TYPE  340   22
     clus
vv    SF3B2 MUTATED SF3B2 WILD-TYPE
  NO             10             340
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SF3B2 MUTATED                      9                             1
  SF3B2 WILD-TYPE                  306                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SF3B2 MUTATED                       0                              0
  SF3B2 WILD-TYPE                   106                             10
D1620V10, multiclass
                                clus
vv                               SF3B2 MUTATED SF3B2 WILD-TYPE
  COLON ADENOCARCINOMA                       9             306
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  SF3B2 MUTATED     7   0   0   0
  SF3B2 WILD-TYPE 338   4  31  25
D1620V11, multiclass
    clus
vv   SF3B2 MUTATED SF3B2 WILD-TYPE
  R0             7             338
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1620V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SF3B2 MUTATED                                  0     0
  SF3B2 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  SF3B2 MUTATED                           0     8
  SF3B2 WILD-TYPE                        22   218
D1620V13, multiclass
                                  clus
vv                                 SF3B2 MUTATED SF3B2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        8             218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1621) Variable = ZNF232 MUTATION ANALYSIS
D1621V1, survival
                  sevent
clus2                0   1
  ZNF232 MUTATED     3   1
  ZNF232 WILD-TYPE 375  92
  ZNF232 MUTATED ZNF232 WILD-TYPE 
               4              467 
  ZNF232 MUTATED ZNF232 WILD-TYPE 
               1               92 
$`ZNF232 MUTATED`
TCGA-AZ-4315 TCGA-F4-6459 TCGA-G4-6586 TCGA-G4-6588 
       58.39         8.61        35.80        26.17 

$`ZNF232 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
       16.31         0.95        33.01        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6460 TCGA-F4-6569 
       35.97        60.79       117.07        98.24        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6625 
       63.62        61.91        36.00        22.09        13.78        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  ZNF232 MUTATED ZNF232 WILD-TYPE 
            8.61             0.00 
  ZNF232 MUTATED ZNF232 WILD-TYPE 
           58.39           148.01 
  ZNF232 MUTATED ZNF232 WILD-TYPE 
          30.985           20.120 
[1] "8.6 - 58.4 (31.0)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1"  
D1621V2, continuous
D1621V3, binary
                  cls
clus                 0   1
  ZNF232 MUTATED     4   0
  ZNF232 WILD-TYPE 362 119
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF232 MUTATED      4    0
  ZNF232 WILD-TYPE  362  119
        clus
vv       ZNF232 MUTATED ZNF232 WILD-TYPE
  COLON               4              362
  RECTUM              0              119
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZNF232 MUTATED         0        0        0         3         0         0
  ZNF232 WILD-TYPE      91        1       32       135        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF232 MUTATED           0          0          1          0        0
  ZNF232 WILD-TYPE        24         11         58         42       48
                  vv
clus               STAGE IVA STAGE IVB
  ZNF232 MUTATED           0         0
  ZNF232 WILD-TYPE        18         1
D1621V4, multiclass
            clus
vv           ZNF232 MUTATED ZNF232 WILD-TYPE
  STAGE I                 0               91
  STAGE IA                0                1
  STAGE II                0               32
  STAGE IIA               3              135
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              1               58
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZNF232 MUTATED     0   0   4   0
  ZNF232 WILD-TYPE  17  92 325  50
D1621V5, multiclass
    clus
vv   ZNF232 MUTATED ZNF232 WILD-TYPE
  T1              0               17
  T2              0               92
  T3              4              325
  T4              0               50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  ZNF232 MUTATED     3   0   1
  ZNF232 WILD-TYPE 284 113  86
D1621V6, multiclass
    clus
vv   ZNF232 MUTATED ZNF232 WILD-TYPE
  N0              3              284
  N1              0              113
  N2              1               86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1621V7, binary
                  cls
clus                 0   1
  ZNF232 MUTATED     4   0
  ZNF232 WILD-TYPE 371  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF232 MUTATED      4    0
  ZNF232 WILD-TYPE  371   65
   clus
vv  ZNF232 MUTATED ZNF232 WILD-TYPE
  0              4              371
  1              0               65
[1] 2 2
[1] FALSE
D1621V8, binary
                  cls
clus                 0   1
  ZNF232 MUTATED     3   1
  ZNF232 WILD-TYPE 222 263
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF232 MUTATED      3    1
  ZNF232 WILD-TYPE  222  263
        clus
vv       ZNF232 MUTATED ZNF232 WILD-TYPE
  FEMALE              3              222
  MALE                1              263
[1] 2 2
[1] FALSE
D1621V9, binary
                  cls
clus                 0   1
  ZNF232 MUTATED     4   0
  ZNF232 WILD-TYPE 346  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF232 MUTATED      4    0
  ZNF232 WILD-TYPE  346   22
     clus
vv    ZNF232 MUTATED ZNF232 WILD-TYPE
  NO               4              346
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ZNF232 MUTATED                      4                             0
  ZNF232 WILD-TYPE                  311                            47
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ZNF232 MUTATED                       0                              0
  ZNF232 WILD-TYPE                   106                             10
D1621V10, multiclass
                                clus
vv                               ZNF232 MUTATED ZNF232 WILD-TYPE
  COLON ADENOCARCINOMA                        4              311
  COLON MUCINOUS ADENOCARCINOMA               0               47
  RECTAL ADENOCARCINOMA                       0              106
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ZNF232 MUTATED     4   0   0   0
  ZNF232 WILD-TYPE 341   4  31  25
D1621V11, multiclass
    clus
vv   ZNF232 MUTATED ZNF232 WILD-TYPE
  R0              4              341
  R1              0                4
  R2              0               31
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1621V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF232 MUTATED                                  0     0
  ZNF232 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZNF232 MUTATED                           0     4
  ZNF232 WILD-TYPE                        22   222
D1621V13, multiclass
                                  clus
vv                                 ZNF232 MUTATED ZNF232 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         4              222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1622) Variable = TRIM55 MUTATION ANALYSIS
D1622V1, survival
                  sevent
clus2                0   1
  TRIM55 MUTATED    14   5
  TRIM55 WILD-TYPE 364  88
  TRIM55 MUTATED TRIM55 WILD-TYPE 
              19              452 
  TRIM55 MUTATED TRIM55 WILD-TYPE 
               5               88 
$`TRIM55 MUTATED`
TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-6781 TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3864 
       42.90        24.33        19.66        61.02         6.97        53.00 
TCGA-AA-3875 TCGA-AA-A00N TCGA-AZ-4315 TCGA-CA-6717 TCGA-CA-6718 TCGA-D5-6924 
       18.05         4.01        58.39        12.76        10.06        14.30 
TCGA-D5-6927 TCGA-DM-A28H TCGA-F4-6806 TCGA-AG-3583 TCGA-AG-3892 TCGA-AG-A002 
        9.44       117.07        41.42        20.05        13.02        20.98 
TCGA-CI-6620 
       33.17 

$`TRIM55 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       43.76        46.65        43.76        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5657 
       33.34        32.75        36.53        14.53        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       30.44        29.19        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       19.99        78.08         6.05        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3877 
       30.05        17.03        24.03        27.02        29.98        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       33.01        21.44        17.82         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.04        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       35.97        60.79        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6807 TCGA-F4-6808 
        6.18        47.87         1.55        34.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        8.02         7.07        36.03        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 
        1.02        17.95        36.95        17.03        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6622 TCGA-CI-6624 
       17.49         0.69         0.72         6.05         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  TRIM55 MUTATED TRIM55 WILD-TYPE 
            4.01             0.00 
  TRIM55 MUTATED TRIM55 WILD-TYPE 
          117.07           148.01 
  TRIM55 MUTATED TRIM55 WILD-TYPE 
          20.050           20.235 
[1] "4.0 - 117.1 (20.1)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.1"
D1622V2, continuous
D1622V3, binary
                  cls
clus                 0   1
  TRIM55 MUTATED    15   4
  TRIM55 WILD-TYPE 351 115
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIM55 MUTATED     15    4
  TRIM55 WILD-TYPE  351  115
        clus
vv       TRIM55 MUTATED TRIM55 WILD-TYPE
  COLON              15              351
  RECTUM              4              115
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TRIM55 MUTATED         4        0        3         5         2         0
  TRIM55 WILD-TYPE      87        1       29       133         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TRIM55 MUTATED           0          0          0          3        1
  TRIM55 WILD-TYPE        24         11         59         39       47
                  vv
clus               STAGE IVA STAGE IVB
  TRIM55 MUTATED           1         0
  TRIM55 WILD-TYPE        17         1
D1622V4, multiclass
            clus
vv           TRIM55 MUTATED TRIM55 WILD-TYPE
  STAGE I                 4               87
  STAGE IA                0                1
  STAGE II                3               29
  STAGE IIA               5              133
  STAGE IIB               2                8
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              0               59
  STAGE IIIC              3               39
  STAGE IV                1               47
  STAGE IVA               1               17
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  TRIM55 MUTATED     2   2  12   3
  TRIM55 WILD-TYPE  15  90 317  47
D1622V5, multiclass
    clus
vv   TRIM55 MUTATED TRIM55 WILD-TYPE
  T1              2               15
  T2              2               90
  T3             12              317
  T4              3               47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  TRIM55 MUTATED    14   2   3
  TRIM55 WILD-TYPE 273 111  84
D1622V6, multiclass
    clus
vv   TRIM55 MUTATED TRIM55 WILD-TYPE
  N0             14              273
  N1              2              111
  N2              3               84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1622V7, binary
                  cls
clus                 0   1
  TRIM55 MUTATED    16   2
  TRIM55 WILD-TYPE 359  63
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIM55 MUTATED     16    2
  TRIM55 WILD-TYPE  359   63
   clus
vv  TRIM55 MUTATED TRIM55 WILD-TYPE
  0             16              359
  1              2               63
[1] 2 2
[1] FALSE
D1622V8, binary
                  cls
clus                 0   1
  TRIM55 MUTATED     6  13
  TRIM55 WILD-TYPE 219 251
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIM55 MUTATED      6   13
  TRIM55 WILD-TYPE  219  251
        clus
vv       TRIM55 MUTATED TRIM55 WILD-TYPE
  FEMALE              6              219
  MALE               13              251
[1] 2 2
[1] FALSE
D1622V9, binary
                  cls
clus                 0   1
  TRIM55 MUTATED    17   0
  TRIM55 WILD-TYPE 333  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIM55 MUTATED     17    0
  TRIM55 WILD-TYPE  333   22
     clus
vv    TRIM55 MUTATED TRIM55 WILD-TYPE
  NO              17              333
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  TRIM55 MUTATED                     12                             3
  TRIM55 WILD-TYPE                  303                            44
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  TRIM55 MUTATED                       3                              1
  TRIM55 WILD-TYPE                   103                              9
D1622V10, multiclass
                                clus
vv                               TRIM55 MUTATED TRIM55 WILD-TYPE
  COLON ADENOCARCINOMA                       12              303
  COLON MUCINOUS ADENOCARCINOMA               3               44
  RECTAL ADENOCARCINOMA                       3              103
  RECTAL MUCINOUS ADENOCARCINOMA              1                9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  TRIM55 MUTATED    14   0   1   2
  TRIM55 WILD-TYPE 331   4  30  23
D1622V11, multiclass
    clus
vv   TRIM55 MUTATED TRIM55 WILD-TYPE
  R0             14              331
  R1              0                4
  R2              1               30
  RX              2               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1622V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TRIM55 MUTATED                                  0     2
  TRIM55 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  TRIM55 MUTATED                           0     9
  TRIM55 WILD-TYPE                        22   217
D1622V13, multiclass
                                  clus
vv                                 TRIM55 MUTATED TRIM55 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                9
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         9              217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1623) Variable = IFITM5 MUTATION ANALYSIS
D1623V1, survival
                  sevent
clus2                0   1
  IFITM5 MUTATED     3   1
  IFITM5 WILD-TYPE 375  92
  IFITM5 MUTATED IFITM5 WILD-TYPE 
               4              467 
  IFITM5 MUTATED IFITM5 WILD-TYPE 
               1               92 
$`IFITM5 MUTATED`
TCGA-A6-6653 TCGA-AA-3492 TCGA-D5-6922 TCGA-AH-6644 
       24.39         3.02         4.41         0.72 

$`IFITM5 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
       25.08        25.18        24.16        21.76        24.69        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 
       20.12        19.66        20.28         7.04         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        3.68        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-CI-6619 
      117.11        38.56         1.45        17.49         0.69         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  IFITM5 MUTATED IFITM5 WILD-TYPE 
            0.72             0.00 
  IFITM5 MUTATED IFITM5 WILD-TYPE 
           24.39           148.01 
  IFITM5 MUTATED IFITM5 WILD-TYPE 
           3.715           20.280 
[1] "0.7 - 24.4 (3.7)"   "0.0 - 148.0 (20.3)"
[1] "hr=" "3.9"
D1623V2, continuous
D1623V3, binary
                  cls
clus                 0   1
  IFITM5 MUTATED     3   1
  IFITM5 WILD-TYPE 363 118
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IFITM5 MUTATED      3    1
  IFITM5 WILD-TYPE  363  118
        clus
vv       IFITM5 MUTATED IFITM5 WILD-TYPE
  COLON               3              363
  RECTUM              1              118
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  IFITM5 MUTATED         1        0        1         0         0         0
  IFITM5 WILD-TYPE      90        1       31       138        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  IFITM5 MUTATED           0          1          0          0        0
  IFITM5 WILD-TYPE        24         10         59         42       48
                  vv
clus               STAGE IVA STAGE IVB
  IFITM5 MUTATED           0         0
  IFITM5 WILD-TYPE        18         1
D1623V4, multiclass
            clus
vv           IFITM5 MUTATED IFITM5 WILD-TYPE
  STAGE I                 1               90
  STAGE IA                0                1
  STAGE II                1               31
  STAGE IIA               0              138
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              1               10
  STAGE IIIB              0               59
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  IFITM5 MUTATED     0   1   3   0
  IFITM5 WILD-TYPE  17  91 326  50
D1623V5, multiclass
    clus
vv   IFITM5 MUTATED IFITM5 WILD-TYPE
  T1              0               17
  T2              1               91
  T3              3              326
  T4              0               50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  IFITM5 MUTATED     2   1   0
  IFITM5 WILD-TYPE 285 112  87
D1623V6, multiclass
    clus
vv   IFITM5 MUTATED IFITM5 WILD-TYPE
  N0              2              285
  N1              1              112
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1623V7, binary
                  cls
clus                 0   1
  IFITM5 MUTATED     3   0
  IFITM5 WILD-TYPE 372  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IFITM5 MUTATED      3    0
  IFITM5 WILD-TYPE  372   65
   clus
vv  IFITM5 MUTATED IFITM5 WILD-TYPE
  0              3              372
  1              0               65
[1] 2 2
[1] FALSE
D1623V8, binary
                  cls
clus                 0   1
  IFITM5 MUTATED     1   3
  IFITM5 WILD-TYPE 224 261
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IFITM5 MUTATED      1    3
  IFITM5 WILD-TYPE  224  261
        clus
vv       IFITM5 MUTATED IFITM5 WILD-TYPE
  FEMALE              1              224
  MALE                3              261
[1] 2 2
[1] FALSE
D1623V9, binary
                  cls
clus                 0   1
  IFITM5 MUTATED     2   0
  IFITM5 WILD-TYPE 348  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IFITM5 MUTATED      2    0
  IFITM5 WILD-TYPE  348   22
     clus
vv    IFITM5 MUTATED IFITM5 WILD-TYPE
  NO               2              348
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  IFITM5 MUTATED                      3                             0
  IFITM5 WILD-TYPE                  312                            47
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  IFITM5 MUTATED                       1                              0
  IFITM5 WILD-TYPE                   105                             10
D1623V10, multiclass
                                clus
vv                               IFITM5 MUTATED IFITM5 WILD-TYPE
  COLON ADENOCARCINOMA                        3              312
  COLON MUCINOUS ADENOCARCINOMA               0               47
  RECTAL ADENOCARCINOMA                       1              105
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  IFITM5 MUTATED     2   0   0   0
  IFITM5 WILD-TYPE 343   4  31  25
D1623V11, multiclass
[1] "Remove cluster labels:" "IFITM5 MUTATED"        
clus
  IFITM5 MUTATED IFITM5 WILD-TYPE 
               2              403 
      TCGA-A6-2671       TCGA-A6-2672       TCGA-A6-2674       TCGA-A6-2676 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-A6-2677       TCGA-A6-2678       TCGA-A6-2683       TCGA-A6-3807 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-A6-3808       TCGA-A6-3809       TCGA-A6-3810       TCGA-A6-5657 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-A6-5659       TCGA-A6-5661       TCGA-A6-5665       TCGA-A6-6781 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AA-3489       TCGA-AA-3496       TCGA-AA-3502       TCGA-AA-3510 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AA-3511       TCGA-AA-3514       TCGA-AA-3517       TCGA-AA-3518 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AA-3519       TCGA-AA-3520       TCGA-AA-3521       TCGA-AA-3522 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AA-3524       TCGA-AA-3525       TCGA-AA-3526       TCGA-AA-3527 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AA-3529       TCGA-AA-3530       TCGA-AA-3531       TCGA-AA-3532 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AA-3534       TCGA-AA-3538       TCGA-AA-3542       TCGA-AA-3543 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AA-3544       TCGA-AA-3548       TCGA-AA-3549       TCGA-AA-3552 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AA-3553       TCGA-AA-3554       TCGA-AA-3555       TCGA-AA-3556 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AA-3558       TCGA-AA-3560       TCGA-AA-3561       TCGA-AA-3562 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AA-3655       TCGA-AA-3660       TCGA-AA-3662       TCGA-AA-3663 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AA-3664       TCGA-AA-3666       TCGA-AA-3667       TCGA-AA-3672 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AA-3673       TCGA-AA-3678       TCGA-AA-3679       TCGA-AA-3680 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AA-3681       TCGA-AA-3684       TCGA-AA-3685       TCGA-AA-3688 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AA-3692       TCGA-AA-3693       TCGA-AA-3695       TCGA-AA-3696 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AA-3697       TCGA-AA-3710       TCGA-AA-3712       TCGA-AA-3713 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AA-3715       TCGA-AA-3811       TCGA-AA-3812       TCGA-AA-3814 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AA-3815       TCGA-AA-3818       TCGA-AA-3819       TCGA-AA-3821 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AA-3831       TCGA-AA-3833       TCGA-AA-3837       TCGA-AA-3842 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AA-3844       TCGA-AA-3845       TCGA-AA-3846       TCGA-AA-3848 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AA-3850       TCGA-AA-3851       TCGA-AA-3852       TCGA-AA-3854 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AA-3855       TCGA-AA-3856       TCGA-AA-3858       TCGA-AA-3860 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AA-3861       TCGA-AA-3864       TCGA-AA-3866       TCGA-AA-3867 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AA-3869       TCGA-AA-3870       TCGA-AA-3872       TCGA-AA-3875 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AA-3877       TCGA-AA-3930       TCGA-AA-3939       TCGA-AA-3941 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AA-3947       TCGA-AA-3949       TCGA-AA-3950       TCGA-AA-3952 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AA-3955       TCGA-AA-3956       TCGA-AA-3968       TCGA-AA-3971 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AA-3972       TCGA-AA-3973       TCGA-AA-3975       TCGA-AA-3976 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AA-3979       TCGA-AA-3984       TCGA-AA-3986       TCGA-AA-3989 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AA-3994       TCGA-AA-A004       TCGA-AA-A00A       TCGA-AA-A00D 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AA-A00E       TCGA-AA-A00F       TCGA-AA-A00J       TCGA-AA-A00K 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AA-A00L       TCGA-AA-A00N       TCGA-AA-A00O       TCGA-AA-A00Q 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AA-A00R       TCGA-AA-A00U       TCGA-AA-A00W       TCGA-AA-A00Z 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AA-A010       TCGA-AA-A017       TCGA-AA-A01D       TCGA-AA-A01F 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AA-A01G       TCGA-AA-A01I       TCGA-AA-A01K       TCGA-AA-A01P 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AA-A01Q       TCGA-AA-A01R       TCGA-AA-A01S       TCGA-AA-A01T 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AA-A01V       TCGA-AA-A01X       TCGA-AA-A01Z       TCGA-AA-A022 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AA-A024       TCGA-AA-A029       TCGA-AA-A02F       TCGA-AA-A02H 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AA-A02J       TCGA-AA-A02K       TCGA-AA-A02O       TCGA-AA-A02W 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AA-A02Y       TCGA-AA-A03F       TCGA-AA-A03J       TCGA-AD-5900 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AD-6548       TCGA-AD-6888       TCGA-AU-3779       TCGA-AU-6004 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AY-4070       TCGA-AY-4071       TCGA-AY-5543       TCGA-AY-6196 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AY-6197       TCGA-AY-6386       TCGA-AZ-4315       TCGA-AZ-4681 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AZ-4682       TCGA-CA-5254       TCGA-CA-5255       TCGA-CA-5796 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-CA-5797       TCGA-CA-6715       TCGA-CA-6716       TCGA-CA-6717 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-CA-6718       TCGA-CA-6719       TCGA-CK-4947       TCGA-CK-4948 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-CK-4950       TCGA-CK-4952       TCGA-CK-5912       TCGA-CK-5913 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-CK-5914       TCGA-CK-5915       TCGA-CK-5916       TCGA-CK-6746 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-CK-6747       TCGA-CK-6748       TCGA-CK-6751       TCGA-CM-4743 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-CM-4744       TCGA-CM-4746       TCGA-CM-4747       TCGA-CM-4752 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-CM-5341       TCGA-CM-5344       TCGA-CM-5348       TCGA-CM-5349 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-CM-5860       TCGA-CM-5861       TCGA-CM-5862       TCGA-CM-5863 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-CM-5864       TCGA-CM-5868       TCGA-CM-6161       TCGA-CM-6162 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-CM-6163       TCGA-CM-6164       TCGA-CM-6165       TCGA-CM-6166 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-CM-6167       TCGA-CM-6168       TCGA-CM-6169       TCGA-CM-6170 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-CM-6171       TCGA-CM-6172       TCGA-CM-6674       TCGA-CM-6675 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-CM-6676       TCGA-CM-6677       TCGA-CM-6678       TCGA-CM-6679 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-CM-6680       TCGA-D5-5537       TCGA-D5-5538       TCGA-D5-5539 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-D5-5540       TCGA-D5-5541       TCGA-D5-6529       TCGA-D5-6532 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-D5-6533       TCGA-D5-6534       TCGA-D5-6535       TCGA-D5-6536 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-D5-6537       TCGA-D5-6538       TCGA-D5-6539       TCGA-D5-6540 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-D5-6541       TCGA-D5-6898       TCGA-D5-6920       TCGA-D5-6923 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-D5-6924       TCGA-D5-6926       TCGA-D5-6927       TCGA-D5-6928 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-D5-6929       TCGA-D5-6930       TCGA-D5-6931       TCGA-D5-6932 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-D5-7000       TCGA-F4-6459       TCGA-F4-6460       TCGA-F4-6569 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-F4-6570       TCGA-F4-6703       TCGA-F4-6704       TCGA-F4-6805 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-F4-6806       TCGA-F4-6807       TCGA-F4-6808       TCGA-F4-6809 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-F4-6854       TCGA-F4-6855       TCGA-F4-6856       TCGA-G4-6293 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-G4-6299       TCGA-G4-6303       TCGA-G4-6304       TCGA-G4-6306 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-G4-6307       TCGA-G4-6309       TCGA-G4-6310       TCGA-G4-6315 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-G4-6317       TCGA-G4-6321       TCGA-G4-6323       TCGA-G4-6586 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-G4-6588       TCGA-G4-6625       TCGA-G4-6626       TCGA-G4-6628 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AF-2687       TCGA-AF-2689       TCGA-AF-2691       TCGA-AF-2692 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AF-3400       TCGA-AF-3913       TCGA-AF-4110       TCGA-AF-5654 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AF-6655       TCGA-AG-3574       TCGA-AG-3575       TCGA-AG-3578 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AG-3580       TCGA-AG-3581       TCGA-AG-3582       TCGA-AG-3583 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AG-3584       TCGA-AG-3586       TCGA-AG-3587       TCGA-AG-3593 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AG-3594       TCGA-AG-3598       TCGA-AG-3599       TCGA-AG-3600 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AG-3601       TCGA-AG-3602       TCGA-AG-3605       TCGA-AG-3608 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AG-3609       TCGA-AG-3611       TCGA-AG-3612       TCGA-AG-3726 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AG-3727       TCGA-AG-3731       TCGA-AG-3732       TCGA-AG-3742 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AG-3878       TCGA-AG-3882       TCGA-AG-3883       TCGA-AG-3885 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AG-3887       TCGA-AG-3890       TCGA-AG-3892       TCGA-AG-3893 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AG-3894       TCGA-AG-3896       TCGA-AG-3898       TCGA-AG-3901 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AG-3902       TCGA-AG-3909       TCGA-AG-3999       TCGA-AG-4001 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AG-4005       TCGA-AG-4007       TCGA-AG-4008       TCGA-AG-4015 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AG-A002       TCGA-AG-A008       TCGA-AG-A00C       TCGA-AG-A00H 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AG-A00Y       TCGA-AG-A011       TCGA-AG-A014       TCGA-AG-A015 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AG-A016       TCGA-AG-A01L       TCGA-AG-A01W       TCGA-AG-A01Y 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AG-A020       TCGA-AG-A025       TCGA-AG-A026       TCGA-AG-A02G 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AG-A02N       TCGA-AG-A02X       TCGA-AG-A032       TCGA-AG-A036 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-AH-6549       TCGA-AH-6643       TCGA-CL-5917       TCGA-CL-5918 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-DC-5337       TCGA-DC-5869       TCGA-DC-6155       TCGA-DC-6157 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-DC-6158       TCGA-DC-6160       TCGA-DC-6681       TCGA-DC-6682 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-DC-6683       TCGA-DT-5265       TCGA-EF-5830       TCGA-EI-6506 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-EI-6507       TCGA-EI-6508       TCGA-EI-6510       TCGA-F5-6464 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-F5-6465       TCGA-F5-6571       TCGA-F5-6702       TCGA-F5-6812 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
      TCGA-F5-6813       TCGA-G5-6235       TCGA-G5-6641 
"IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" "IFITM5 WILD-TYPE" 
D1623V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  IFITM5 MUTATED                                  0     0
  IFITM5 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  IFITM5 MUTATED                           0     3
  IFITM5 WILD-TYPE                        22   223
D1623V13, multiclass
                                  clus
vv                                 IFITM5 MUTATED IFITM5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         3              223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1624) Variable = C9ORF125 MUTATION ANALYSIS
D1624V1, survival
                    sevent
clus2                  0   1
  C9ORF125 MUTATED     9   3
  C9ORF125 WILD-TYPE 369  90
  C9ORF125 MUTATED C9ORF125 WILD-TYPE 
                12                459 
  C9ORF125 MUTATED C9ORF125 WILD-TYPE 
                 3                 90 
$`C9ORF125 MUTATED`
TCGA-A6-5665 TCGA-AA-3492 TCGA-AA-3516 TCGA-AA-3710 TCGA-AA-A00A TCGA-AA-A00E 
       22.06         3.02        13.02        26.99        38.04        30.02 
TCGA-AD-6895 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-D5-6930 TCGA-DM-A1HB TCGA-G4-6588 
        0.72        58.39        49.41         1.51       135.65        26.17 

$`C9ORF125 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 
       20.12        19.66        20.28         7.04         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
       63.98         6.97         1.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       85.05        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00J 
        7.96        27.02        13.94        19.00        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       21.37        15.52        56.55         0.79         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        33.01        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 
      106.75        22.36        62.79        88.21         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        4.80        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 
      140.38         7.50        44.32       131.51       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       22.09        13.78        35.80        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  C9ORF125 MUTATED C9ORF125 WILD-TYPE 
              0.72               0.00 
  C9ORF125 MUTATED C9ORF125 WILD-TYPE 
            135.65             148.01 
  C9ORF125 MUTATED C9ORF125 WILD-TYPE 
             26.58              20.05 
[1] "0.7 - 135.7 (26.6)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.1"
D1624V2, continuous
D1624V3, binary
                    cls
clus                   0   1
  C9ORF125 MUTATED    12   0
  C9ORF125 WILD-TYPE 354 119
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C9ORF125 MUTATED     12    0
  C9ORF125 WILD-TYPE  354  119
        clus
vv       C9ORF125 MUTATED C9ORF125 WILD-TYPE
  COLON                12                354
  RECTUM                0                119
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  C9ORF125 MUTATED         0        0        2         7         0         0
  C9ORF125 WILD-TYPE      91        1       30       131        10         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C9ORF125 MUTATED           1          0          1          0        0
  C9ORF125 WILD-TYPE        23         11         58         42       48
                    vv
clus                 STAGE IVA STAGE IVB
  C9ORF125 MUTATED           0         0
  C9ORF125 WILD-TYPE        18         1
D1624V4, multiclass
            clus
vv           C9ORF125 MUTATED C9ORF125 WILD-TYPE
  STAGE I                   0                 91
  STAGE IA                  0                  1
  STAGE II                  2                 30
  STAGE IIA                 7                131
  STAGE IIB                 0                 10
  STAGE IIC                 0                  1
  STAGE III                 1                 23
  STAGE IIIA                0                 11
  STAGE IIIB                1                 58
  STAGE IIIC                0                 42
  STAGE IV                  0                 48
  STAGE IVA                 0                 18
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  C9ORF125 MUTATED     0   0  12   0
  C9ORF125 WILD-TYPE  17  92 317  50
D1624V5, multiclass
    clus
vv   C9ORF125 MUTATED C9ORF125 WILD-TYPE
  T1                0                 17
  T2                0                 92
  T3               12                317
  T4                0                 50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  C9ORF125 MUTATED     9   2   1
  C9ORF125 WILD-TYPE 278 111  86
D1624V6, multiclass
    clus
vv   C9ORF125 MUTATED C9ORF125 WILD-TYPE
  N0                9                278
  N1                2                111
  N2                1                 86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1624V7, binary
                    cls
clus                   0   1
  C9ORF125 MUTATED    10   0
  C9ORF125 WILD-TYPE 365  65
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C9ORF125 MUTATED     10    0
  C9ORF125 WILD-TYPE  365   65
   clus
vv  C9ORF125 MUTATED C9ORF125 WILD-TYPE
  0               10                365
  1                0                 65
[1] 2 2
[1] FALSE
D1624V8, binary
                    cls
clus                   0   1
  C9ORF125 MUTATED     6   6
  C9ORF125 WILD-TYPE 219 258
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C9ORF125 MUTATED      6    6
  C9ORF125 WILD-TYPE  219  258
        clus
vv       C9ORF125 MUTATED C9ORF125 WILD-TYPE
  FEMALE                6                219
  MALE                  6                258
[1] 2 2
[1] FALSE
D1624V9, binary
                    cls
clus                   0   1
  C9ORF125 MUTATED     9   0
  C9ORF125 WILD-TYPE 341  22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C9ORF125 MUTATED      9    0
  C9ORF125 WILD-TYPE  341   22
     clus
vv    C9ORF125 MUTATED C9ORF125 WILD-TYPE
  NO                 9                341
  YES                0                 22
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  C9ORF125 MUTATED                      9                             2
  C9ORF125 WILD-TYPE                  306                            45
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  C9ORF125 MUTATED                       0                              0
  C9ORF125 WILD-TYPE                   106                             10
D1624V10, multiclass
                                clus
vv                               C9ORF125 MUTATED C9ORF125 WILD-TYPE
  COLON ADENOCARCINOMA                          9                306
  COLON MUCINOUS ADENOCARCINOMA                 2                 45
  RECTAL ADENOCARCINOMA                         0                106
  RECTAL MUCINOUS ADENOCARCINOMA                0                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  C9ORF125 MUTATED     8   0   0   0
  C9ORF125 WILD-TYPE 337   4  31  25
D1624V11, multiclass
    clus
vv   C9ORF125 MUTATED C9ORF125 WILD-TYPE
  R0                8                337
  R1                0                  4
  R2                0                 31
  RX                0                 25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1624V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C9ORF125 MUTATED                                  0     0
  C9ORF125 WILD-TYPE                                1    11
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  C9ORF125 MUTATED                           0     7
  C9ORF125 WILD-TYPE                        22   219
D1624V13, multiclass
                                  clus
vv                                 C9ORF125 MUTATED C9ORF125 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 11
  BLACK OR AFRICAN AMERICAN                       0                 22
  WHITE                                           7                219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1625) Variable = IPPK MUTATION ANALYSIS
D1625V1, survival
                sevent
clus2              0   1
  IPPK MUTATED     8   1
  IPPK WILD-TYPE 370  92
  IPPK MUTATED IPPK WILD-TYPE 
             9            462 
  IPPK MUTATED IPPK WILD-TYPE 
             1             92 
$`IPPK MUTATED`
TCGA-A6-6780 TCGA-AA-3542 TCGA-AA-3864 TCGA-AZ-6601 TCGA-CA-6717 TCGA-CM-5349 
       20.12        12.99        53.00       100.01        12.76        30.08 
TCGA-CM-6674 TCGA-D5-6533 TCGA-G4-6304 
       12.95         1.32        53.62 

$`IPPK WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       26.01         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 
        0.99        31.07        31.07        30.05        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07        12.20        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.03        22.98        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       14.04        11.01        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       55.92        20.19        18.25        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       74.56        65.85        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  IPPK MUTATED IPPK WILD-TYPE 
          1.32           0.00 
  IPPK MUTATED IPPK WILD-TYPE 
        100.01         148.01 
  IPPK MUTATED IPPK WILD-TYPE 
        20.120         20.235 
[1] "1.3 - 100.0 (20.1)" "0.0 - 148.0 (20.2)"
[1] "hr=" "2.4"
D1625V2, continuous
D1625V3, binary
                cls
clus               0   1
  IPPK MUTATED     9   0
  IPPK WILD-TYPE 357 119
[1] "tbl2"
                cls
clus             [,1] [,2]
  IPPK MUTATED      9    0
  IPPK WILD-TYPE  357  119
        clus
vv       IPPK MUTATED IPPK WILD-TYPE
  COLON             9            357
  RECTUM            0            119
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  IPPK MUTATED         0        0        2         4         1         0
  IPPK WILD-TYPE      91        1       30       134         9         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  IPPK MUTATED           0          0          1          1        0         0
  IPPK WILD-TYPE        24         11         58         41       48        18
                vv
clus             STAGE IVB
  IPPK MUTATED           0
  IPPK WILD-TYPE         1
D1625V4, multiclass
            clus
vv           IPPK MUTATED IPPK WILD-TYPE
  STAGE I               0             91
  STAGE IA              0              1
  STAGE II              2             30
  STAGE IIA             4            134
  STAGE IIB             1              9
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            1             58
  STAGE IIIC            1             41
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  IPPK MUTATED     0   0   7   2
  IPPK WILD-TYPE  17  92 322  48
D1625V5, multiclass
    clus
vv   IPPK MUTATED IPPK WILD-TYPE
  T1            0             17
  T2            0             92
  T3            7            322
  T4            2             48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  IPPK MUTATED     8   0   1
  IPPK WILD-TYPE 279 113  86
D1625V6, multiclass
    clus
vv   IPPK MUTATED IPPK WILD-TYPE
  N0            8            279
  N1            0            113
  N2            1             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1625V7, binary
                cls
clus               0   1
  IPPK MUTATED     8   0
  IPPK WILD-TYPE 367  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  IPPK MUTATED      8    0
  IPPK WILD-TYPE  367   65
   clus
vv  IPPK MUTATED IPPK WILD-TYPE
  0            8            367
  1            0             65
[1] 2 2
[1] FALSE
D1625V8, binary
                cls
clus               0   1
  IPPK MUTATED     3   6
  IPPK WILD-TYPE 222 258
[1] "tbl2"
                cls
clus             [,1] [,2]
  IPPK MUTATED      3    6
  IPPK WILD-TYPE  222  258
        clus
vv       IPPK MUTATED IPPK WILD-TYPE
  FEMALE            3            222
  MALE              6            258
[1] 2 2
[1] FALSE
D1625V9, binary
                cls
clus               0   1
  IPPK MUTATED     8   0
  IPPK WILD-TYPE 342  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  IPPK MUTATED      8    0
  IPPK WILD-TYPE  342   22
     clus
vv    IPPK MUTATED IPPK WILD-TYPE
  NO             8            342
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  IPPK MUTATED                      7                             2
  IPPK WILD-TYPE                  308                            45
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  IPPK MUTATED                       0                              0
  IPPK WILD-TYPE                   106                             10
D1625V10, multiclass
                                clus
vv                               IPPK MUTATED IPPK WILD-TYPE
  COLON ADENOCARCINOMA                      7            308
  COLON MUCINOUS ADENOCARCINOMA             2             45
  RECTAL ADENOCARCINOMA                     0            106
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  IPPK MUTATED     6   0   0   1
  IPPK WILD-TYPE 339   4  31  24
D1625V11, multiclass
    clus
vv   IPPK MUTATED IPPK WILD-TYPE
  R0            6            339
  R1            0              4
  R2            0             31
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1625V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  IPPK MUTATED                                  0     1
  IPPK WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  IPPK MUTATED                           0     6
  IPPK WILD-TYPE                        22   220
D1625V13, multiclass
                                  clus
vv                                 IPPK MUTATED IPPK WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       6            220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1626) Variable = ARHGEF7 MUTATION ANALYSIS
D1626V1, survival
                   sevent
clus2                 0   1
  ARHGEF7 MUTATED    14   6
  ARHGEF7 WILD-TYPE 364  87
  ARHGEF7 MUTATED ARHGEF7 WILD-TYPE 
               20               451 
  ARHGEF7 MUTATED ARHGEF7 WILD-TYPE 
                6                87 
$`ARHGEF7 MUTATED`
TCGA-AA-3496 TCGA-AA-3510 TCGA-AA-3663 TCGA-AA-3811 TCGA-AA-3947 TCGA-AA-A00E 
        1.02        63.98         6.97        10.06        33.01        30.02 
TCGA-AA-A00R TCGA-AD-6895 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-6197 TCGA-AZ-6601 
        0.99         0.72        14.50        16.31        21.44       100.01 
TCGA-CM-5348 TCGA-D5-6535 TCGA-DM-A0XD TCGA-DM-A1DB TCGA-G4-6309 TCGA-G4-6588 
       22.98        15.12        24.43        44.32        85.48        26.17 
TCGA-AF-6672 TCGA-DY-A1DF 
       10.39        24.13 

$`ARHGEF7 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3815 
       85.05        26.99        19.04        19.04        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00J 
       27.02        13.94        38.04        19.00        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00U 
       18.05        38.04         4.01        27.02        42.02        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       15.52        56.55         0.79         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 
       10.88         0.20        27.09         0.95        33.01        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 
       88.21        49.41         6.77        12.10        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 
       55.92        20.19        18.25         1.32        43.27        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
      119.70        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
       12.59       140.38         7.50       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       53.62        44.68        55.04        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       22.09        13.78        35.80        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AG-3574 
       10.39        14.50        16.83        15.39        20.02        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
      126.44        41.36        57.24        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  ARHGEF7 MUTATED ARHGEF7 WILD-TYPE 
             0.72              0.00 
  ARHGEF7 MUTATED ARHGEF7 WILD-TYPE 
           100.01            148.01 
  ARHGEF7 MUTATED ARHGEF7 WILD-TYPE 
            22.21             20.12 
[1] "0.7 - 100.0 (22.2)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.5"
D1626V2, continuous
D1626V3, binary
                   cls
clus                  0   1
  ARHGEF7 MUTATED    19   2
  ARHGEF7 WILD-TYPE 347 117
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ARHGEF7 MUTATED     19    2
  ARHGEF7 WILD-TYPE  347  117
        clus
vv       ARHGEF7 MUTATED ARHGEF7 WILD-TYPE
  COLON               19               347
  RECTUM               2               117
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ARHGEF7 MUTATED         1        0        5         6         1         0
  ARHGEF7 WILD-TYPE      90        1       27       132         9         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ARHGEF7 MUTATED           1          0          3          2        1
  ARHGEF7 WILD-TYPE        23         11         56         40       47
                   vv
clus                STAGE IVA STAGE IVB
  ARHGEF7 MUTATED           0         0
  ARHGEF7 WILD-TYPE        18         1
D1626V4, multiclass
            clus
vv           ARHGEF7 MUTATED ARHGEF7 WILD-TYPE
  STAGE I                  1                90
  STAGE IA                 0                 1
  STAGE II                 5                27
  STAGE IIA                6               132
  STAGE IIB                1                 9
  STAGE IIC                0                 1
  STAGE III                1                23
  STAGE IIIA               0                11
  STAGE IIIB               3                56
  STAGE IIIC               2                40
  STAGE IV                 1                47
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  ARHGEF7 MUTATED     0   1  17   3
  ARHGEF7 WILD-TYPE  17  91 312  47
D1626V5, multiclass
    clus
vv   ARHGEF7 MUTATED ARHGEF7 WILD-TYPE
  T1               0                17
  T2               1                91
  T3              17               312
  T4               3                47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  ARHGEF7 MUTATED    13   4   4
  ARHGEF7 WILD-TYPE 274 109  83
D1626V6, multiclass
    clus
vv   ARHGEF7 MUTATED ARHGEF7 WILD-TYPE
  N0              13               274
  N1               4               109
  N2               4                83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1626V7, binary
                   cls
clus                  0   1
  ARHGEF7 MUTATED    17   0
  ARHGEF7 WILD-TYPE 358  65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ARHGEF7 MUTATED     17    0
  ARHGEF7 WILD-TYPE  358   65
   clus
vv  ARHGEF7 MUTATED ARHGEF7 WILD-TYPE
  0              17               358
  1               0                65
[1] 2 2
[1] FALSE
D1626V8, binary
                   cls
clus                  0   1
  ARHGEF7 MUTATED    11  10
  ARHGEF7 WILD-TYPE 214 254
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ARHGEF7 MUTATED     11   10
  ARHGEF7 WILD-TYPE  214  254
        clus
vv       ARHGEF7 MUTATED ARHGEF7 WILD-TYPE
  FEMALE              11               214
  MALE                10               254
[1] 2 2
[1] FALSE
D1626V9, binary
                   cls
clus                  0   1
  ARHGEF7 MUTATED    13   1
  ARHGEF7 WILD-TYPE 337  21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ARHGEF7 MUTATED     13    1
  ARHGEF7 WILD-TYPE  337   21
     clus
vv    ARHGEF7 MUTATED ARHGEF7 WILD-TYPE
  NO               13               337
  YES               1                21
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ARHGEF7 MUTATED                     18                             1
  ARHGEF7 WILD-TYPE                  297                            46
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ARHGEF7 MUTATED                       2                              0
  ARHGEF7 WILD-TYPE                   104                             10
D1626V10, multiclass
                                clus
vv                               ARHGEF7 MUTATED ARHGEF7 WILD-TYPE
  COLON ADENOCARCINOMA                        18               297
  COLON MUCINOUS ADENOCARCINOMA                1                46
  RECTAL ADENOCARCINOMA                        2               104
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  ARHGEF7 MUTATED    13   1   0   1
  ARHGEF7 WILD-TYPE 332   3  31  24
D1626V11, multiclass
    clus
vv   ARHGEF7 MUTATED ARHGEF7 WILD-TYPE
  R0              13               332
  R1               1                 3
  R2               0                31
  RX               1                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1626V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ARHGEF7 MUTATED                                  0     0
  ARHGEF7 WILD-TYPE                                1    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  ARHGEF7 MUTATED                           2    11
  ARHGEF7 WILD-TYPE                        20   215
D1626V13, multiclass
                                  clus
vv                                 ARHGEF7 MUTATED ARHGEF7 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                      2                20
  WHITE                                         11               215
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1627) Variable = WDR65 MUTATION ANALYSIS
D1627V1, survival
                 sevent
clus2               0   1
  WDR65 MUTATED     5   1
  WDR65 WILD-TYPE 373  92
  WDR65 MUTATED WDR65 WILD-TYPE 
              6             465 
  WDR65 MUTATED WDR65 WILD-TYPE 
              1              92 
$`WDR65 MUTATED`
TCGA-A6-6780 TCGA-AA-3950 TCGA-AA-A00J TCGA-AD-6889 TCGA-CA-6718 TCGA-G4-6628 
       20.12        24.00        18.05        56.55        10.06        79.69 

$`WDR65 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 
        2.01        12.99        24.00        33.01        26.01         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       19.00        30.02        34.03        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 
       18.05        40.96         0.07        21.37        15.52         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  WDR65 MUTATED WDR65 WILD-TYPE 
          10.06            0.00 
  WDR65 MUTATED WDR65 WILD-TYPE 
          79.69          148.01 
  WDR65 MUTATED WDR65 WILD-TYPE 
          22.06           20.19 
[1] "10.1 - 79.7 (22.1)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.6"
D1627V2, continuous
D1627V3, binary
                 cls
clus                0   1
  WDR65 MUTATED     6   0
  WDR65 WILD-TYPE 360 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WDR65 MUTATED      6    0
  WDR65 WILD-TYPE  360  119
        clus
vv       WDR65 MUTATED WDR65 WILD-TYPE
  COLON              6             360
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  WDR65 MUTATED         1        0        0         4         0         0
  WDR65 WILD-TYPE      90        1       32       134        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  WDR65 MUTATED           0          0          1          0        0         0
  WDR65 WILD-TYPE        24         11         58         42       48        18
                 vv
clus              STAGE IVB
  WDR65 MUTATED           0
  WDR65 WILD-TYPE         1
D1627V4, multiclass
            clus
vv           WDR65 MUTATED WDR65 WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              4             134
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  WDR65 MUTATED     0   1   4   1
  WDR65 WILD-TYPE  17  91 325  49
D1627V5, multiclass
    clus
vv   WDR65 MUTATED WDR65 WILD-TYPE
  T1             0              17
  T2             1              91
  T3             4             325
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  WDR65 MUTATED     5   1   0
  WDR65 WILD-TYPE 282 112  87
D1627V6, multiclass
    clus
vv   WDR65 MUTATED WDR65 WILD-TYPE
  N0             5             282
  N1             1             112
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1627V7, binary
                 cls
clus                0   1
  WDR65 MUTATED     5   0
  WDR65 WILD-TYPE 370  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WDR65 MUTATED      5    0
  WDR65 WILD-TYPE  370   65
   clus
vv  WDR65 MUTATED WDR65 WILD-TYPE
  0             5             370
  1             0              65
[1] 2 2
[1] FALSE
D1627V8, binary
                 cls
clus                0   1
  WDR65 MUTATED     1   5
  WDR65 WILD-TYPE 224 259
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WDR65 MUTATED      1    5
  WDR65 WILD-TYPE  224  259
        clus
vv       WDR65 MUTATED WDR65 WILD-TYPE
  FEMALE             1             224
  MALE               5             259
[1] 2 2
[1] FALSE
D1627V9, binary
                 cls
clus                0   1
  WDR65 MUTATED     5   0
  WDR65 WILD-TYPE 345  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WDR65 MUTATED      5    0
  WDR65 WILD-TYPE  345   22
     clus
vv    WDR65 MUTATED WDR65 WILD-TYPE
  NO              5             345
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  WDR65 MUTATED                      3                             3
  WDR65 WILD-TYPE                  312                            44
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  WDR65 MUTATED                       0                              0
  WDR65 WILD-TYPE                   106                             10
D1627V10, multiclass
                                clus
vv                               WDR65 MUTATED WDR65 WILD-TYPE
  COLON ADENOCARCINOMA                       3             312
  COLON MUCINOUS ADENOCARCINOMA              3              44
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  WDR65 MUTATED     3   0   0   1
  WDR65 WILD-TYPE 342   4  31  24
D1627V11, multiclass
    clus
vv   WDR65 MUTATED WDR65 WILD-TYPE
  R0             3             342
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1627V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  WDR65 MUTATED                                  0     2
  WDR65 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  WDR65 MUTATED                           0     2
  WDR65 WILD-TYPE                        22   224
D1627V13, multiclass
                                  clus
vv                                 WDR65 MUTATED WDR65 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               9
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        2             224
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1628) Variable = APLP1 MUTATION ANALYSIS
D1628V1, survival
                 sevent
clus2               0   1
  APLP1 MUTATED    12   5
  APLP1 WILD-TYPE 366  88
  APLP1 MUTATED APLP1 WILD-TYPE 
             17             454 
  APLP1 MUTATED APLP1 WILD-TYPE 
              5              88 
$`APLP1 MUTATED`
TCGA-A6-2672 TCGA-A6-2677 TCGA-AA-3492 TCGA-AA-3525 TCGA-AA-3542 TCGA-AA-3821 
       46.65        24.33         3.02         8.05        12.99         1.02 
TCGA-AA-3831 TCGA-AA-3877 TCGA-AA-3977 TCGA-AA-A00N TCGA-AD-6965 TCGA-AZ-4315 
       17.98        31.00        25.02         4.01         0.20        58.39 
TCGA-AZ-6606 TCGA-CK-5913 TCGA-F4-6459 TCGA-F4-6856 TCGA-AG-4007 
       11.74        51.32         8.61        35.31         1.02 

$`APLP1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       43.76        43.76        42.90        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5657 
       33.34        32.75        36.53        14.53        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       30.44        29.19        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       19.66        20.28         7.04         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       24.03        37.05        36.03        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3543 TCGA-AA-3544 
       34.03        29.00        29.00        26.01         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       78.08         6.05         6.97        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       25.02        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 
       17.03        24.03        27.02        29.98        18.05         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AU-3779 
        0.72         5.79        22.42        27.42        10.88        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 
      148.01        85.45        15.62        49.08         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
       60.79       117.07        98.24        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
       13.25         0.53        47.41       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  APLP1 MUTATED APLP1 WILD-TYPE 
            0.2             0.0 
  APLP1 MUTATED APLP1 WILD-TYPE 
          58.39          148.01 
  APLP1 MUTATED APLP1 WILD-TYPE 
         12.990          20.415 
[1] "0.2 - 58.4 (13.0)"  "0.0 - 148.0 (20.4)"
[1] "hr=" "1.9"
D1628V2, continuous
D1628V3, binary
                 cls
clus                0   1
  APLP1 MUTATED    16   1
  APLP1 WILD-TYPE 350 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  APLP1 MUTATED     16    1
  APLP1 WILD-TYPE  350  118
        clus
vv       APLP1 MUTATED APLP1 WILD-TYPE
  COLON             16             350
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  APLP1 MUTATED         3        0        1         3         1         0
  APLP1 WILD-TYPE      88        1       31       135         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  APLP1 MUTATED           0          0          3          2        2         0
  APLP1 WILD-TYPE        24         11         56         40       46        18
                 vv
clus              STAGE IVB
  APLP1 MUTATED           0
  APLP1 WILD-TYPE         1
D1628V4, multiclass
            clus
vv           APLP1 MUTATED APLP1 WILD-TYPE
  STAGE I                3              88
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              3             135
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             3              56
  STAGE IIIC             2              40
  STAGE IV               2              46
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  APLP1 MUTATED     1   3   9   4
  APLP1 WILD-TYPE  16  89 320  46
D1628V5, multiclass
    clus
vv   APLP1 MUTATED APLP1 WILD-TYPE
  T1             1              16
  T2             3              89
  T3             9             320
  T4             4              46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  APLP1 MUTATED     9   2   6
  APLP1 WILD-TYPE 278 111  81
D1628V6, multiclass
    clus
vv   APLP1 MUTATED APLP1 WILD-TYPE
  N0             9             278
  N1             2             111
  N2             6              81
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1628V7, binary
                 cls
clus                0   1
  APLP1 MUTATED    12   2
  APLP1 WILD-TYPE 363  63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  APLP1 MUTATED     12    2
  APLP1 WILD-TYPE  363   63
   clus
vv  APLP1 MUTATED APLP1 WILD-TYPE
  0            12             363
  1             2              63
[1] 2 2
[1] FALSE
D1628V8, binary
                 cls
clus                0   1
  APLP1 MUTATED     7  10
  APLP1 WILD-TYPE 218 254
[1] "tbl2"
                 cls
clus              [,1] [,2]
  APLP1 MUTATED      7   10
  APLP1 WILD-TYPE  218  254
        clus
vv       APLP1 MUTATED APLP1 WILD-TYPE
  FEMALE             7             218
  MALE              10             254
[1] 2 2
[1] FALSE
D1628V9, binary
                 cls
clus                0   1
  APLP1 MUTATED    14   0
  APLP1 WILD-TYPE 336  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  APLP1 MUTATED     14    0
  APLP1 WILD-TYPE  336   22
     clus
vv    APLP1 MUTATED APLP1 WILD-TYPE
  NO             14             336
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  APLP1 MUTATED                     12                             4
  APLP1 WILD-TYPE                  303                            43
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  APLP1 MUTATED                       1                              0
  APLP1 WILD-TYPE                   105                             10
D1628V10, multiclass
                                clus
vv                               APLP1 MUTATED APLP1 WILD-TYPE
  COLON ADENOCARCINOMA                      12             303
  COLON MUCINOUS ADENOCARCINOMA              4              43
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  APLP1 MUTATED    12   0   1   1
  APLP1 WILD-TYPE 333   4  30  24
D1628V11, multiclass
    clus
vv   APLP1 MUTATED APLP1 WILD-TYPE
  R0            12             333
  R1             0               4
  R2             1              30
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1628V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  APLP1 MUTATED                                  0     0
  APLP1 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  APLP1 MUTATED                           0     8
  APLP1 WILD-TYPE                        22   218
D1628V13, multiclass
                                  clus
vv                                 APLP1 MUTATED APLP1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        8             218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1629) Variable = KIAA0319 MUTATION ANALYSIS
D1629V1, survival
                    sevent
clus2                  0   1
  KIAA0319 MUTATED    15   1
  KIAA0319 WILD-TYPE 363  92
  KIAA0319 MUTATED KIAA0319 WILD-TYPE 
                16                455 
  KIAA0319 MUTATED KIAA0319 WILD-TYPE 
                 1                 92 
$`KIAA0319 MUTATED`
TCGA-A6-3807 TCGA-A6-6780 TCGA-AA-3715 TCGA-AA-3941 TCGA-AA-A00J TCGA-AA-A01F 
       34.65        20.12        19.04        24.00        18.05        32.02 
TCGA-AD-6889 TCGA-AY-6197 TCGA-AZ-4315 TCGA-CA-6717 TCGA-CK-5913 TCGA-D5-6535 
       56.55        21.44        58.39        12.76        51.32        15.12 
TCGA-DM-A1HB TCGA-G4-6304 TCGA-AG-A002 TCGA-DC-6157 
      135.65        53.62        20.98        27.95 

$`KIAA0319 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       10.98        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       21.37        15.52         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
        0.95        33.01        17.82         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       49.08         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       43.27        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
       44.32       131.51       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
      133.18        74.56        65.85        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
       15.02         5.03        13.97        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  KIAA0319 MUTATED KIAA0319 WILD-TYPE 
             12.76               0.00 
  KIAA0319 MUTATED KIAA0319 WILD-TYPE 
            135.65             148.01 
  KIAA0319 MUTATED KIAA0319 WILD-TYPE 
            25.975             20.020 
[1] "12.8 - 135.7 (26.0)" "0.0 - 148.0 (20.0)" 
[1] "hr=" "4.5"
D1629V2, continuous
D1629V3, binary
                    cls
clus                   0   1
  KIAA0319 MUTATED    15   2
  KIAA0319 WILD-TYPE 351 117
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0319 MUTATED     15    2
  KIAA0319 WILD-TYPE  351  117
        clus
vv       KIAA0319 MUTATED KIAA0319 WILD-TYPE
  COLON                15                351
  RECTUM                2                117
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KIAA0319 MUTATED         2        0        1         7         1         0
  KIAA0319 WILD-TYPE      89        1       31       131         9         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIAA0319 MUTATED           0          0          4          1        0
  KIAA0319 WILD-TYPE        24         11         55         41       48
                    vv
clus                 STAGE IVA STAGE IVB
  KIAA0319 MUTATED           1         0
  KIAA0319 WILD-TYPE        17         1
D1629V4, multiclass
            clus
vv           KIAA0319 MUTATED KIAA0319 WILD-TYPE
  STAGE I                   2                 89
  STAGE IA                  0                  1
  STAGE II                  1                 31
  STAGE IIA                 7                131
  STAGE IIB                 1                  9
  STAGE IIC                 0                  1
  STAGE III                 0                 24
  STAGE IIIA                0                 11
  STAGE IIIB                4                 55
  STAGE IIIC                1                 41
  STAGE IV                  0                 48
  STAGE IVA                 1                 17
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  KIAA0319 MUTATED     0   2  12   3
  KIAA0319 WILD-TYPE  17  90 317  47
D1629V5, multiclass
    clus
vv   KIAA0319 MUTATED KIAA0319 WILD-TYPE
  T1                0                 17
  T2                2                 90
  T3               12                317
  T4                3                 47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  KIAA0319 MUTATED    11   5   1
  KIAA0319 WILD-TYPE 276 108  86
D1629V6, multiclass
    clus
vv   KIAA0319 MUTATED KIAA0319 WILD-TYPE
  N0               11                276
  N1                5                108
  N2                1                 86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1629V7, binary
                    cls
clus                   0   1
  KIAA0319 MUTATED    12   1
  KIAA0319 WILD-TYPE 363  64
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0319 MUTATED     12    1
  KIAA0319 WILD-TYPE  363   64
   clus
vv  KIAA0319 MUTATED KIAA0319 WILD-TYPE
  0               12                363
  1                1                 64
[1] 2 2
[1] FALSE
D1629V8, binary
                    cls
clus                   0   1
  KIAA0319 MUTATED     6  11
  KIAA0319 WILD-TYPE 219 253
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0319 MUTATED      6   11
  KIAA0319 WILD-TYPE  219  253
        clus
vv       KIAA0319 MUTATED KIAA0319 WILD-TYPE
  FEMALE                6                219
  MALE                 11                253
[1] 2 2
[1] FALSE
D1629V9, binary
                    cls
clus                   0   1
  KIAA0319 MUTATED    13   0
  KIAA0319 WILD-TYPE 337  22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0319 MUTATED     13    0
  KIAA0319 WILD-TYPE  337   22
     clus
vv    KIAA0319 MUTATED KIAA0319 WILD-TYPE
  NO                13                337
  YES                0                 22
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  KIAA0319 MUTATED                     11                             3
  KIAA0319 WILD-TYPE                  304                            44
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  KIAA0319 MUTATED                       2                              0
  KIAA0319 WILD-TYPE                   104                             10
D1629V10, multiclass
                                clus
vv                               KIAA0319 MUTATED KIAA0319 WILD-TYPE
  COLON ADENOCARCINOMA                         11                304
  COLON MUCINOUS ADENOCARCINOMA                 3                 44
  RECTAL ADENOCARCINOMA                         2                104
  RECTAL MUCINOUS ADENOCARCINOMA                0                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  KIAA0319 MUTATED    11   0   0   3
  KIAA0319 WILD-TYPE 334   4  31  22
D1629V11, multiclass
    clus
vv   KIAA0319 MUTATED KIAA0319 WILD-TYPE
  R0               11                334
  R1                0                  4
  R2                0                 31
  RX                3                 22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1629V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KIAA0319 MUTATED                                  0     2
  KIAA0319 WILD-TYPE                                1     9
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  KIAA0319 MUTATED                           1     8
  KIAA0319 WILD-TYPE                        21   218
D1629V13, multiclass
                                  clus
vv                                 KIAA0319 MUTATED KIAA0319 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           2                  9
  BLACK OR AFRICAN AMERICAN                       1                 21
  WHITE                                           8                218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1630) Variable = MECOM MUTATION ANALYSIS
D1630V1, survival
                 sevent
clus2               0   1
  MECOM MUTATED    17   3
  MECOM WILD-TYPE 361  90
  MECOM MUTATED MECOM WILD-TYPE 
             20             451 
  MECOM MUTATED MECOM WILD-TYPE 
              3              90 
$`MECOM MUTATED`
TCGA-A6-5661 TCGA-AA-3510 TCGA-AA-3543 TCGA-AA-3821 TCGA-AA-3864 TCGA-AA-3977 
       33.53        63.98         0.99         1.02        53.00        25.02 
TCGA-AA-A00N TCGA-AA-A010 TCGA-AD-5900 TCGA-AD-6889 TCGA-CA-6718 TCGA-D5-6540 
        4.01        34.98         0.07        56.55        10.06        16.14 
TCGA-D5-6927 TCGA-D5-6930 TCGA-DM-A1HA TCGA-G4-6317 TCGA-G4-6588 TCGA-G4-6626 
        9.44         1.51       131.51        36.00        26.17        46.75 
TCGA-AG-4008 TCGA-AG-A002 
       17.03        20.98 

$`MECOM WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
       12.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
       33.04         0.99        25.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       31.07        30.05        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 
       39.98        18.05        40.96        21.37        15.52         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
        9.04        11.64         4.80        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HB 
       13.32        12.59       140.38         7.50        44.32       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 
       61.91        22.09        13.78        35.80        91.79        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
        1.02        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  MECOM MUTATED MECOM WILD-TYPE 
           0.07            0.00 
  MECOM MUTATED MECOM WILD-TYPE 
         131.51          148.01 
  MECOM MUTATED MECOM WILD-TYPE 
          23.00           20.12 
[1] "0.1 - 131.5 (23.0)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.5"
D1630V2, continuous
D1630V3, binary
                 cls
clus                0   1
  MECOM MUTATED    19   2
  MECOM WILD-TYPE 347 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MECOM MUTATED     19    2
  MECOM WILD-TYPE  347  117
        clus
vv       MECOM MUTATED MECOM WILD-TYPE
  COLON             19             347
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MECOM MUTATED         5        0        2         8         2         0
  MECOM WILD-TYPE      86        1       30       130         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MECOM MUTATED           0          0          0          3        0         0
  MECOM WILD-TYPE        24         11         59         39       48        18
                 vv
clus              STAGE IVB
  MECOM MUTATED           0
  MECOM WILD-TYPE         1
D1630V4, multiclass
            clus
vv           MECOM MUTATED MECOM WILD-TYPE
  STAGE I                5              86
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA              8             130
  STAGE IIB              2               8
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             3              39
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  MECOM MUTATED     0   6  13   2
  MECOM WILD-TYPE  17  86 316  48
D1630V5, multiclass
    clus
vv   MECOM MUTATED MECOM WILD-TYPE
  T1             0              17
  T2             6              86
  T3            13             316
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  MECOM MUTATED    18   0   3
  MECOM WILD-TYPE 269 113  84
D1630V6, multiclass
    clus
vv   MECOM MUTATED MECOM WILD-TYPE
  N0            18             269
  N1             0             113
  N2             3              84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1630V7, binary
                 cls
clus                0   1
  MECOM MUTATED    17   0
  MECOM WILD-TYPE 358  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MECOM MUTATED     17    0
  MECOM WILD-TYPE  358   65
   clus
vv  MECOM MUTATED MECOM WILD-TYPE
  0            17             358
  1             0              65
[1] 2 2
[1] FALSE
D1630V8, binary
                 cls
clus                0   1
  MECOM MUTATED     5  16
  MECOM WILD-TYPE 220 248
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MECOM MUTATED      5   16
  MECOM WILD-TYPE  220  248
        clus
vv       MECOM MUTATED MECOM WILD-TYPE
  FEMALE             5             220
  MALE              16             248
[1] 2 2
[1] FALSE
D1630V9, binary
                 cls
clus                0   1
  MECOM MUTATED    15   0
  MECOM WILD-TYPE 335  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MECOM MUTATED     15    0
  MECOM WILD-TYPE  335   22
     clus
vv    MECOM MUTATED MECOM WILD-TYPE
  NO             15             335
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MECOM MUTATED                     12                             7
  MECOM WILD-TYPE                  303                            40
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MECOM MUTATED                       2                              0
  MECOM WILD-TYPE                   104                             10
D1630V10, multiclass
                                clus
vv                               MECOM MUTATED MECOM WILD-TYPE
  COLON ADENOCARCINOMA                      12             303
  COLON MUCINOUS ADENOCARCINOMA              7              40
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  MECOM MUTATED    17   0   0   1
  MECOM WILD-TYPE 328   4  31  24
D1630V11, multiclass
    clus
vv   MECOM MUTATED MECOM WILD-TYPE
  R0            17             328
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1630V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MECOM MUTATED                                  0     2
  MECOM WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  MECOM MUTATED                           1     9
  MECOM WILD-TYPE                        21   217
D1630V13, multiclass
                                  clus
vv                                 MECOM MUTATED MECOM WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               9
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        9             217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1631) Variable = MYO3A MUTATION ANALYSIS
D1631V1, survival
                 sevent
clus2               0   1
  MYO3A MUTATED    34   8
  MYO3A WILD-TYPE 344  85
  MYO3A MUTATED MYO3A WILD-TYPE 
             42             429 
  MYO3A MUTATED MYO3A WILD-TYPE 
              8              85 
$`MYO3A MUTATED`
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5661 TCGA-A6-6138 TCGA-A6-6652 TCGA-A6-6780 
       32.75        36.53        33.53        22.52        24.69        20.12 
TCGA-A6-6781 TCGA-AA-3510 TCGA-AA-3663 TCGA-AA-3811 TCGA-AA-3947 TCGA-AA-3966 
       19.66        63.98         6.97        10.06        33.01         2.01 
TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01Q TCGA-AD-6889 TCGA-AD-6899 
       25.02         4.01        34.98         1.02        56.55         5.79 
TCGA-AZ-4315 TCGA-AZ-6601 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4948 TCGA-CM-4743 
       58.39       100.01        12.76        10.06       148.01        23.05 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5861 TCGA-CM-6161 TCGA-CM-6163 TCGA-D5-6535 
       22.03        22.98        15.02        15.02         2.96        15.12 
TCGA-D5-6537 TCGA-DM-A28G TCGA-F4-6806 TCGA-F4-6808 TCGA-G4-6588 TCGA-G4-6626 
        4.80        60.79        41.42        33.67        26.17        46.75 
TCGA-AG-3600 TCGA-AG-3883 TCGA-AG-A002 TCGA-DC-5869 TCGA-F5-6813 TCGA-G5-6641 
        6.05         1.02        20.98         5.03         0.69        26.43 

$`MYO3A WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5657 
       16.57        34.65        33.34        14.53        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 
       30.44        29.19        23.61        22.09        22.06        32.71 
TCGA-A6-6137 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 
       27.09         8.38        25.08        25.18        24.16        21.76 
TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       24.39        23.87        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3815 
       85.05        26.99        19.04        19.04        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 
       26.01        24.00         2.01        20.98        34.03        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       31.00        38.07        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 
       40.96         0.07        21.37        15.52         0.79         0.72 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
       16.31         0.95        33.01        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77        12.10        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       12.20        14.30        17.56        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5349 
       20.02        37.02        25.02        13.02        29.06        30.08 
TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6162 
       32.02         5.03        15.02        15.02        17.03        12.00 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       43.27        17.85        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       35.97       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6807 TCGA-F4-6809 
        6.18        47.87         1.55        34.42        16.24        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 
       36.00        22.09        13.78        35.80        91.79        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       50.04        12.03         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
        0.99        19.04        19.99        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
       15.02        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-G5-6235 
       32.19         0.66        55.76 

  MYO3A MUTATED MYO3A WILD-TYPE 
           0.69            0.00 
  MYO3A MUTATED MYO3A WILD-TYPE 
         148.01          140.38 
  MYO3A MUTATED MYO3A WILD-TYPE 
         22.275          20.020 
[1] "0.7 - 148.0 (22.3)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1.1"
D1631V2, continuous
D1631V3, binary
                 cls
clus                0   1
  MYO3A MUTATED    37   6
  MYO3A WILD-TYPE 329 113
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYO3A MUTATED     37    6
  MYO3A WILD-TYPE  329  113
        clus
vv       MYO3A MUTATED MYO3A WILD-TYPE
  COLON             37             329
  RECTUM             6             113
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MYO3A MUTATED         8        0        4        13         4         0
  MYO3A WILD-TYPE      83        1       28       125         6         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MYO3A MUTATED           2          1          5          4        0         1
  MYO3A WILD-TYPE        22         10         54         38       48        17
                 vv
clus              STAGE IVB
  MYO3A MUTATED           0
  MYO3A WILD-TYPE         1
D1631V4, multiclass
            clus
vv           MYO3A MUTATED MYO3A WILD-TYPE
  STAGE I                8              83
  STAGE IA               0               1
  STAGE II               4              28
  STAGE IIA             13             125
  STAGE IIB              4               6
  STAGE IIC              0               1
  STAGE III              2              22
  STAGE IIIA             1              10
  STAGE IIIB             5              54
  STAGE IIIC             4              38
  STAGE IV               0              48
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  MYO3A MUTATED     3   7  26   7
  MYO3A WILD-TYPE  14  85 303  43
D1631V5, multiclass
    clus
vv   MYO3A MUTATED MYO3A WILD-TYPE
  T1             3              14
  T2             7              85
  T3            26             303
  T4             7              43
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  MYO3A MUTATED    31   8   4
  MYO3A WILD-TYPE 256 105  83
D1631V6, multiclass
    clus
vv   MYO3A MUTATED MYO3A WILD-TYPE
  N0            31             256
  N1             8             105
  N2             4              83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1631V7, binary
                 cls
clus                0   1
  MYO3A MUTATED    34   1
  MYO3A WILD-TYPE 341  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYO3A MUTATED     34    1
  MYO3A WILD-TYPE  341   64
   clus
vv  MYO3A MUTATED MYO3A WILD-TYPE
  0            34             341
  1             1              64
[1] 2 2
[1] FALSE
D1631V8, binary
                 cls
clus                0   1
  MYO3A MUTATED    16  27
  MYO3A WILD-TYPE 209 237
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYO3A MUTATED     16   27
  MYO3A WILD-TYPE  209  237
        clus
vv       MYO3A MUTATED MYO3A WILD-TYPE
  FEMALE            16             209
  MALE              27             237
[1] 2 2
[1] FALSE
D1631V9, binary
                 cls
clus                0   1
  MYO3A MUTATED    33   1
  MYO3A WILD-TYPE 317  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYO3A MUTATED     33    1
  MYO3A WILD-TYPE  317   21
     clus
vv    MYO3A MUTATED MYO3A WILD-TYPE
  NO             33             317
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MYO3A MUTATED                     29                             8
  MYO3A WILD-TYPE                  286                            39
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MYO3A MUTATED                       5                              1
  MYO3A WILD-TYPE                   101                              9
D1631V10, multiclass
                                clus
vv                               MYO3A MUTATED MYO3A WILD-TYPE
  COLON ADENOCARCINOMA                      29             286
  COLON MUCINOUS ADENOCARCINOMA              8              39
  RECTAL ADENOCARCINOMA                      5             101
  RECTAL MUCINOUS ADENOCARCINOMA             1               9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  MYO3A MUTATED    30   0   0   4
  MYO3A WILD-TYPE 315   4  31  21
D1631V11, multiclass
    clus
vv   MYO3A MUTATED MYO3A WILD-TYPE
  R0            30             315
  R1             0               4
  R2             0              31
  RX             4              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1631V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MYO3A MUTATED                                  0     3
  MYO3A WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  MYO3A MUTATED                           3    25
  MYO3A WILD-TYPE                        19   201
D1631V13, multiclass
                                  clus
vv                                 MYO3A MUTATED MYO3A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        3               8
  BLACK OR AFRICAN AMERICAN                    3              19
  WHITE                                       25             201
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1632) Variable = PIK3C2G MUTATION ANALYSIS
D1632V1, survival
                   sevent
clus2                 0   1
  PIK3C2G MUTATED    20   2
  PIK3C2G WILD-TYPE 358  91
  PIK3C2G MUTATED PIK3C2G WILD-TYPE 
               22               449 
  PIK3C2G MUTATED PIK3C2G WILD-TYPE 
                2                91 
$`PIK3C2G MUTATED`
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3977 TCGA-AA-A010 TCGA-AD-6895 TCGA-AZ-6599 
       25.02         1.02        25.02        34.98         0.72         6.77 
TCGA-CA-6717 TCGA-CM-5349 TCGA-CM-6161 TCGA-CM-6674 TCGA-D5-6534 TCGA-DM-A1HB 
       12.76        30.08        15.02        12.95        43.27       135.65 
TCGA-DM-A28C TCGA-F4-6856 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6317 
       81.37        35.31        53.62        44.68        85.48        36.00 
TCGA-G4-6586 TCGA-AF-2687 TCGA-AG-3883 TCGA-AG-A002 
       35.80        24.13         1.02        20.98 

$`PIK3C2G WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3831 
       19.04        10.06        35.05        33.04         0.99        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       88.21        49.41        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07        12.20        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6675 
       12.99        13.02        15.02        14.04        11.01        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
        1.32        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28E 
        7.50        44.32       131.51       139.17         6.12       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 
       16.24        33.67        13.25         0.53        47.41       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6321 
       74.56        65.85        55.04        63.62        61.91        22.09 
TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2689 
       13.78        26.17        91.79        46.75        79.69        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.04        19.99        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  PIK3C2G MUTATED PIK3C2G WILD-TYPE 
             0.72              0.00 
  PIK3C2G MUTATED PIK3C2G WILD-TYPE 
           135.65            148.01 
  PIK3C2G MUTATED PIK3C2G WILD-TYPE 
            27.55             20.02 
[1] "0.7 - 135.7 (27.5)" "0.0 - 148.0 (20.0)"
[1] "hr=" "2.8"
D1632V2, continuous
D1632V3, binary
                   cls
clus                  0   1
  PIK3C2G MUTATED    20   3
  PIK3C2G WILD-TYPE 346 116
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PIK3C2G MUTATED     20    3
  PIK3C2G WILD-TYPE  346  116
        clus
vv       PIK3C2G MUTATED PIK3C2G WILD-TYPE
  COLON               20               346
  RECTUM               3               116
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PIK3C2G MUTATED         6        0        0         9         2         0
  PIK3C2G WILD-TYPE      85        1       32       129         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PIK3C2G MUTATED           0          0          2          2        0
  PIK3C2G WILD-TYPE        24         11         57         40       48
                   vv
clus                STAGE IVA STAGE IVB
  PIK3C2G MUTATED           0         0
  PIK3C2G WILD-TYPE        18         1
D1632V4, multiclass
            clus
vv           PIK3C2G MUTATED PIK3C2G WILD-TYPE
  STAGE I                  6                85
  STAGE IA                 0                 1
  STAGE II                 0                32
  STAGE IIA                9               129
  STAGE IIB                2                 8
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               0                11
  STAGE IIIB               2                57
  STAGE IIIC               2                40
  STAGE IV                 0                48
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  PIK3C2G MUTATED     0   8  13   2
  PIK3C2G WILD-TYPE  17  84 316  48
D1632V5, multiclass
    clus
vv   PIK3C2G MUTATED PIK3C2G WILD-TYPE
  T1               0                17
  T2               8                84
  T3              13               316
  T4               2                48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  PIK3C2G MUTATED    18   3   2
  PIK3C2G WILD-TYPE 269 110  85
D1632V6, multiclass
    clus
vv   PIK3C2G MUTATED PIK3C2G WILD-TYPE
  N0              18               269
  N1               3               110
  N2               2                85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1632V7, binary
                   cls
clus                  0   1
  PIK3C2G MUTATED    19   0
  PIK3C2G WILD-TYPE 356  65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PIK3C2G MUTATED     19    0
  PIK3C2G WILD-TYPE  356   65
   clus
vv  PIK3C2G MUTATED PIK3C2G WILD-TYPE
  0              19               356
  1               0                65
[1] 2 2
[1] FALSE
D1632V8, binary
                   cls
clus                  0   1
  PIK3C2G MUTATED    11  12
  PIK3C2G WILD-TYPE 214 252
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PIK3C2G MUTATED     11   12
  PIK3C2G WILD-TYPE  214  252
        clus
vv       PIK3C2G MUTATED PIK3C2G WILD-TYPE
  FEMALE              11               214
  MALE                12               252
[1] 2 2
[1] FALSE
D1632V9, binary
                   cls
clus                  0   1
  PIK3C2G MUTATED    17   1
  PIK3C2G WILD-TYPE 333  21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PIK3C2G MUTATED     17    1
  PIK3C2G WILD-TYPE  333   21
     clus
vv    PIK3C2G MUTATED PIK3C2G WILD-TYPE
  NO               17               333
  YES               1                21
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PIK3C2G MUTATED                     15                             4
  PIK3C2G WILD-TYPE                  300                            43
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PIK3C2G MUTATED                       3                              0
  PIK3C2G WILD-TYPE                   103                             10
D1632V10, multiclass
                                clus
vv                               PIK3C2G MUTATED PIK3C2G WILD-TYPE
  COLON ADENOCARCINOMA                        15               300
  COLON MUCINOUS ADENOCARCINOMA                4                43
  RECTAL ADENOCARCINOMA                        3               103
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  PIK3C2G MUTATED    17   0   0   1
  PIK3C2G WILD-TYPE 328   4  31  24
D1632V11, multiclass
    clus
vv   PIK3C2G MUTATED PIK3C2G WILD-TYPE
  R0              17               328
  R1               0                 4
  R2               0                31
  RX               1                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1632V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PIK3C2G MUTATED                                  0     1
  PIK3C2G WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  PIK3C2G MUTATED                           1    14
  PIK3C2G WILD-TYPE                        21   212
D1632V13, multiclass
                                  clus
vv                                 PIK3C2G MUTATED PIK3C2G WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                10
  BLACK OR AFRICAN AMERICAN                      1                21
  WHITE                                         14               212
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1633) Variable = WFDC5 MUTATION ANALYSIS
D1633V1, survival
                 sevent
clus2               0   1
  WFDC5 MUTATED     3   2
  WFDC5 WILD-TYPE 375  91
  WFDC5 MUTATED WFDC5 WILD-TYPE 
              5             466 
  WFDC5 MUTATED WFDC5 WILD-TYPE 
              2              91 
$`WFDC5 MUTATED`
TCGA-A6-5656 TCGA-AA-3715 TCGA-AD-5900 TCGA-AZ-6600 TCGA-CM-6164 
       32.91        19.04         0.07        12.10        29.03 

$`WFDC5 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 
       36.00         5.03        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       39.98        18.05        40.96        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 
       22.36        62.79        88.21        49.41         6.77       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
        2.96        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  WFDC5 MUTATED WFDC5 WILD-TYPE 
           0.07            0.00 
  WFDC5 MUTATED WFDC5 WILD-TYPE 
          32.91          148.01 
  WFDC5 MUTATED WFDC5 WILD-TYPE 
         19.040          20.235 
[1] "0.1 - 32.9 (19.0)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "3.1"
D1633V2, continuous
D1633V3, binary
                 cls
clus                0   1
  WFDC5 MUTATED     5   0
  WFDC5 WILD-TYPE 361 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WFDC5 MUTATED      5    0
  WFDC5 WILD-TYPE  361  119
        clus
vv       WFDC5 MUTATED WFDC5 WILD-TYPE
  COLON              5             361
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  WFDC5 MUTATED         2        0        1         1         0         0
  WFDC5 WILD-TYPE      89        1       31       137        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  WFDC5 MUTATED           0          0          0          0        1         0
  WFDC5 WILD-TYPE        24         11         59         42       47        18
                 vv
clus              STAGE IVB
  WFDC5 MUTATED           0
  WFDC5 WILD-TYPE         1
D1633V4, multiclass
            clus
vv           WFDC5 MUTATED WFDC5 WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              1             137
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             0              42
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  WFDC5 MUTATED     0   2   2   1
  WFDC5 WILD-TYPE  17  90 327  49
D1633V5, multiclass
    clus
vv   WFDC5 MUTATED WFDC5 WILD-TYPE
  T1             0              17
  T2             2              90
  T3             2             327
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  WFDC5 MUTATED     4   1   0
  WFDC5 WILD-TYPE 283 112  87
D1633V6, multiclass
    clus
vv   WFDC5 MUTATED WFDC5 WILD-TYPE
  N0             4             283
  N1             1             112
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1633V7, binary
                 cls
clus                0   1
  WFDC5 MUTATED     3   1
  WFDC5 WILD-TYPE 372  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WFDC5 MUTATED      3    1
  WFDC5 WILD-TYPE  372   64
   clus
vv  WFDC5 MUTATED WFDC5 WILD-TYPE
  0             3             372
  1             1              64
[1] 2 2
[1] FALSE
D1633V8, binary
                 cls
clus                0   1
  WFDC5 MUTATED     1   4
  WFDC5 WILD-TYPE 224 260
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WFDC5 MUTATED      1    4
  WFDC5 WILD-TYPE  224  260
        clus
vv       WFDC5 MUTATED WFDC5 WILD-TYPE
  FEMALE             1             224
  MALE               4             260
[1] 2 2
[1] FALSE
D1633V9, binary
                 cls
clus                0   1
  WFDC5 MUTATED     3   0
  WFDC5 WILD-TYPE 347  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WFDC5 MUTATED      3    0
  WFDC5 WILD-TYPE  347   22
     clus
vv    WFDC5 MUTATED WFDC5 WILD-TYPE
  NO              3             347
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  WFDC5 MUTATED                      4                             1
  WFDC5 WILD-TYPE                  311                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  WFDC5 MUTATED                       0                              0
  WFDC5 WILD-TYPE                   106                             10
D1633V10, multiclass
                                clus
vv                               WFDC5 MUTATED WFDC5 WILD-TYPE
  COLON ADENOCARCINOMA                       4             311
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  WFDC5 MUTATED     3   0   0   0
  WFDC5 WILD-TYPE 342   4  31  25
D1633V11, multiclass
    clus
vv   WFDC5 MUTATED WFDC5 WILD-TYPE
  R0             3             342
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1633V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  WFDC5 MUTATED                                  0     0
  WFDC5 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  WFDC5 MUTATED                           1     3
  WFDC5 WILD-TYPE                        21   223
D1633V13, multiclass
                                  clus
vv                                 WFDC5 MUTATED WFDC5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        3             223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1634) Variable = ABCD4 MUTATION ANALYSIS
D1634V1, survival
                 sevent
clus2               0   1
  ABCD4 MUTATED     9   1
  ABCD4 WILD-TYPE 369  92
  ABCD4 MUTATED ABCD4 WILD-TYPE 
             10             461 
  ABCD4 MUTATED ABCD4 WILD-TYPE 
              1              92 
$`ABCD4 MUTATED`
TCGA-AA-3663 TCGA-AA-3672 TCGA-AA-3864 TCGA-AA-3877 TCGA-AA-A00E TCGA-CK-4950 
        6.97         0.92        53.00        31.00        30.02        85.45 
TCGA-D5-6930 TCGA-F4-6570 TCGA-G4-6588 TCGA-G4-6628 
        1.51         6.18        26.17        79.69 

$`ABCD4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 
        6.05        54.02         2.01        14.01        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 
        0.99        31.07        31.07        30.05        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       27.02        29.98        18.05         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00F 
        7.96        27.02        13.94        38.04        19.00        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       14.30        17.56       148.01        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 
        9.04         9.44        11.64         4.80        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       35.74        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       91.79        46.75        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  ABCD4 MUTATED ABCD4 WILD-TYPE 
           0.92            0.00 
  ABCD4 MUTATED ABCD4 WILD-TYPE 
          85.45          148.01 
  ABCD4 MUTATED ABCD4 WILD-TYPE 
         28.095          20.120 
[1] "0.9 - 85.5 (28.1)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "2.4"
D1634V2, continuous
D1634V3, binary
                 cls
clus                0   1
  ABCD4 MUTATED    10   0
  ABCD4 WILD-TYPE 356 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCD4 MUTATED     10    0
  ABCD4 WILD-TYPE  356  119
        clus
vv       ABCD4 MUTATED ABCD4 WILD-TYPE
  COLON             10             356
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ABCD4 MUTATED         2        0        2         4         0         0
  ABCD4 WILD-TYPE      89        1       30       134        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ABCD4 MUTATED           1          0          1          0        0         0
  ABCD4 WILD-TYPE        23         11         58         42       48        18
                 vv
clus              STAGE IVB
  ABCD4 MUTATED           0
  ABCD4 WILD-TYPE         1
D1634V4, multiclass
            clus
vv           ABCD4 MUTATED ABCD4 WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA              4             134
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ABCD4 MUTATED     1   1   8   0
  ABCD4 WILD-TYPE  16  91 321  50
D1634V5, multiclass
    clus
vv   ABCD4 MUTATED ABCD4 WILD-TYPE
  T1             1              16
  T2             1              91
  T3             8             321
  T4             0              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  ABCD4 MUTATED     8   2   0
  ABCD4 WILD-TYPE 279 111  87
D1634V6, multiclass
    clus
vv   ABCD4 MUTATED ABCD4 WILD-TYPE
  N0             8             279
  N1             2             111
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1634V7, binary
                 cls
clus                0   1
  ABCD4 MUTATED    10   0
  ABCD4 WILD-TYPE 365  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCD4 MUTATED     10    0
  ABCD4 WILD-TYPE  365   65
   clus
vv  ABCD4 MUTATED ABCD4 WILD-TYPE
  0            10             365
  1             0              65
[1] 2 2
[1] FALSE
D1634V8, binary
                 cls
clus                0   1
  ABCD4 MUTATED     5   5
  ABCD4 WILD-TYPE 220 259
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCD4 MUTATED      5    5
  ABCD4 WILD-TYPE  220  259
        clus
vv       ABCD4 MUTATED ABCD4 WILD-TYPE
  FEMALE             5             220
  MALE               5             259
[1] 2 2
[1] FALSE
D1634V9, binary
                 cls
clus                0   1
  ABCD4 MUTATED     9   0
  ABCD4 WILD-TYPE 341  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCD4 MUTATED      9    0
  ABCD4 WILD-TYPE  341   22
     clus
vv    ABCD4 MUTATED ABCD4 WILD-TYPE
  NO              9             341
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ABCD4 MUTATED                      8                             2
  ABCD4 WILD-TYPE                  307                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ABCD4 MUTATED                       0                              0
  ABCD4 WILD-TYPE                   106                             10
D1634V10, multiclass
                                clus
vv                               ABCD4 MUTATED ABCD4 WILD-TYPE
  COLON ADENOCARCINOMA                       8             307
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  ABCD4 MUTATED     9   1   0   0
  ABCD4 WILD-TYPE 336   3  31  25
D1634V11, multiclass
    clus
vv   ABCD4 MUTATED ABCD4 WILD-TYPE
  R0             9             336
  R1             1               3
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1634V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ABCD4 MUTATED                                  0     0
  ABCD4 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ABCD4 MUTATED                           1     4
  ABCD4 WILD-TYPE                        21   222
D1634V13, multiclass
                                  clus
vv                                 ABCD4 MUTATED ABCD4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        4             222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1635) Variable = PCSK5 MUTATION ANALYSIS
D1635V1, survival
                 sevent
clus2               0   1
  PCSK5 MUTATED    13   2
  PCSK5 WILD-TYPE 365  91
  PCSK5 MUTATED PCSK5 WILD-TYPE 
             15             456 
  PCSK5 MUTATED PCSK5 WILD-TYPE 
              2              91 
$`PCSK5 MUTATED`
TCGA-A6-6142 TCGA-A6-6653 TCGA-AA-3518 TCGA-AA-3866 TCGA-AA-3947 TCGA-AA-A00N 
       25.08        24.39         1.02        17.03        33.01         4.01 
TCGA-AA-A010 TCGA-AA-A03F TCGA-AY-5543 TCGA-CM-6163 TCGA-D5-6532 TCGA-D5-6930 
       34.98        18.05        33.01         2.96        18.25         1.51 
TCGA-DM-A282 TCGA-G4-6588 TCGA-AG-A02N 
      139.17        26.17        61.97 

$`PCSK5 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 
       25.18        24.16        21.76        24.69        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3519 
       63.98         6.97         1.02        13.02        38.99         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3867 TCGA-AA-3869 
       31.07        31.07        30.05        53.00        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       41.00        39.98        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
       12.00        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6533 
       12.26        19.59        56.09        55.92        20.19         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6931 
       14.30         9.04         9.44        11.64         4.80        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
       44.32       131.51       135.65         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       35.80        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 
       10.98        49.97         1.94        38.96        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  PCSK5 MUTATED PCSK5 WILD-TYPE 
           1.02            0.00 
  PCSK5 MUTATED PCSK5 WILD-TYPE 
         139.17          148.01 
  PCSK5 MUTATED PCSK5 WILD-TYPE 
         24.390          20.155 
[1] "1.0 - 139.2 (24.4)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.5"
D1635V2, continuous
D1635V3, binary
                 cls
clus                0   1
  PCSK5 MUTATED    14   1
  PCSK5 WILD-TYPE 352 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PCSK5 MUTATED     14    1
  PCSK5 WILD-TYPE  352  118
        clus
vv       PCSK5 MUTATED PCSK5 WILD-TYPE
  COLON             14             352
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PCSK5 MUTATED         3        0        1         5         3         0
  PCSK5 WILD-TYPE      88        1       31       133         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PCSK5 MUTATED           1          0          0          0        0         2
  PCSK5 WILD-TYPE        23         11         59         42       48        16
                 vv
clus              STAGE IVB
  PCSK5 MUTATED           0
  PCSK5 WILD-TYPE         1
D1635V4, multiclass
            clus
vv           PCSK5 MUTATED PCSK5 WILD-TYPE
  STAGE I                3              88
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              5             133
  STAGE IIB              3               7
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              2              16
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PCSK5 MUTATED     1   2   9   3
  PCSK5 WILD-TYPE  16  90 320  47
D1635V5, multiclass
    clus
vv   PCSK5 MUTATED PCSK5 WILD-TYPE
  T1             1              16
  T2             2              90
  T3             9             320
  T4             3              47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  PCSK5 MUTATED    12   2   1
  PCSK5 WILD-TYPE 275 111  86
D1635V6, multiclass
    clus
vv   PCSK5 MUTATED PCSK5 WILD-TYPE
  N0            12             275
  N1             2             111
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1635V7, binary
                 cls
clus                0   1
  PCSK5 MUTATED    13   2
  PCSK5 WILD-TYPE 362  63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PCSK5 MUTATED     13    2
  PCSK5 WILD-TYPE  362   63
   clus
vv  PCSK5 MUTATED PCSK5 WILD-TYPE
  0            13             362
  1             2              63
[1] 2 2
[1] FALSE
D1635V8, binary
                 cls
clus                0   1
  PCSK5 MUTATED     9   6
  PCSK5 WILD-TYPE 216 258
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PCSK5 MUTATED      9    6
  PCSK5 WILD-TYPE  216  258
        clus
vv       PCSK5 MUTATED PCSK5 WILD-TYPE
  FEMALE             9             216
  MALE               6             258
[1] 2 2
[1] FALSE
D1635V9, binary
                 cls
clus                0   1
  PCSK5 MUTATED     9   0
  PCSK5 WILD-TYPE 341  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PCSK5 MUTATED      9    0
  PCSK5 WILD-TYPE  341   22
     clus
vv    PCSK5 MUTATED PCSK5 WILD-TYPE
  NO              9             341
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PCSK5 MUTATED                     10                             4
  PCSK5 WILD-TYPE                  305                            43
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PCSK5 MUTATED                       1                              0
  PCSK5 WILD-TYPE                   105                             10
D1635V10, multiclass
                                clus
vv                               PCSK5 MUTATED PCSK5 WILD-TYPE
  COLON ADENOCARCINOMA                      10             305
  COLON MUCINOUS ADENOCARCINOMA              4              43
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  PCSK5 MUTATED    12   0   0   0
  PCSK5 WILD-TYPE 333   4  31  25
D1635V11, multiclass
    clus
vv   PCSK5 MUTATED PCSK5 WILD-TYPE
  R0            12             333
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1635V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PCSK5 MUTATED                                  0     0
  PCSK5 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PCSK5 MUTATED                           1     7
  PCSK5 WILD-TYPE                        21   219
D1635V13, multiclass
                                  clus
vv                                 PCSK5 MUTATED PCSK5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        7             219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1636) Variable = DLGAP3 MUTATION ANALYSIS
D1636V1, survival
                  sevent
clus2                0   1
  DLGAP3 MUTATED    14   2
  DLGAP3 WILD-TYPE 364  91
  DLGAP3 MUTATED DLGAP3 WILD-TYPE 
              16              455 
  DLGAP3 MUTATED DLGAP3 WILD-TYPE 
               2               91 
$`DLGAP3 MUTATED`
TCGA-A6-5665 TCGA-AA-3510 TCGA-AA-3663 TCGA-AA-3815 TCGA-AA-A010 TCGA-AA-A01Q 
       22.06        63.98         6.97        33.04        34.98         1.02 
TCGA-AD-6889 TCGA-AZ-6598 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4952 TCGA-CK-5913 
       56.55        49.41        12.76        10.06        15.62        51.32 
TCGA-CM-5861 TCGA-D5-6529 TCGA-D5-6928 TCGA-AG-A002 
       15.02        20.19        11.64        20.98 

$`DLGAP3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       21.37        15.52         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 
        5.13       106.75        22.36        62.79        88.21         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 
       12.20        14.30        17.56       148.01        85.45        49.08 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       22.98        30.08        32.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       55.92        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  DLGAP3 MUTATED DLGAP3 WILD-TYPE 
            1.02             0.00 
  DLGAP3 MUTATED DLGAP3 WILD-TYPE 
           63.98           148.01 
  DLGAP3 MUTATED DLGAP3 WILD-TYPE 
          20.585           20.120 
[1] "1.0 - 64.0 (20.6)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.7"
D1636V2, continuous
D1636V3, binary
                  cls
clus                 0   1
  DLGAP3 MUTATED    16   1
  DLGAP3 WILD-TYPE 350 118
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DLGAP3 MUTATED     16    1
  DLGAP3 WILD-TYPE  350  118
        clus
vv       DLGAP3 MUTATED DLGAP3 WILD-TYPE
  COLON              16              350
  RECTUM              1              118
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DLGAP3 MUTATED         1        0        4        10         1         0
  DLGAP3 WILD-TYPE      90        1       28       128         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DLGAP3 MUTATED           0          0          0          1        0
  DLGAP3 WILD-TYPE        24         11         59         41       48
                  vv
clus               STAGE IVA STAGE IVB
  DLGAP3 MUTATED           0         0
  DLGAP3 WILD-TYPE        18         1
D1636V4, multiclass
            clus
vv           DLGAP3 MUTATED DLGAP3 WILD-TYPE
  STAGE I                 1               90
  STAGE IA                0                1
  STAGE II                4               28
  STAGE IIA              10              128
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              0               59
  STAGE IIIC              1               41
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  DLGAP3 MUTATED     0   1  14   2
  DLGAP3 WILD-TYPE  17  91 315  48
D1636V5, multiclass
    clus
vv   DLGAP3 MUTATED DLGAP3 WILD-TYPE
  T1              0               17
  T2              1               91
  T3             14              315
  T4              2               48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  DLGAP3 MUTATED    16   0   1
  DLGAP3 WILD-TYPE 271 113  86
D1636V6, multiclass
    clus
vv   DLGAP3 MUTATED DLGAP3 WILD-TYPE
  N0             16              271
  N1              0              113
  N2              1               86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1636V7, binary
                  cls
clus                 0   1
  DLGAP3 MUTATED    15   0
  DLGAP3 WILD-TYPE 360  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DLGAP3 MUTATED     15    0
  DLGAP3 WILD-TYPE  360   65
   clus
vv  DLGAP3 MUTATED DLGAP3 WILD-TYPE
  0             15              360
  1              0               65
[1] 2 2
[1] FALSE
D1636V8, binary
                  cls
clus                 0   1
  DLGAP3 MUTATED     9   8
  DLGAP3 WILD-TYPE 216 256
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DLGAP3 MUTATED      9    8
  DLGAP3 WILD-TYPE  216  256
        clus
vv       DLGAP3 MUTATED DLGAP3 WILD-TYPE
  FEMALE              9              216
  MALE                8              256
[1] 2 2
[1] FALSE
D1636V9, binary
                  cls
clus                 0   1
  DLGAP3 MUTATED    13   0
  DLGAP3 WILD-TYPE 337  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DLGAP3 MUTATED     13    0
  DLGAP3 WILD-TYPE  337   22
     clus
vv    DLGAP3 MUTATED DLGAP3 WILD-TYPE
  NO              13              337
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  DLGAP3 MUTATED                     13                             3
  DLGAP3 WILD-TYPE                  302                            44
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  DLGAP3 MUTATED                       1                              0
  DLGAP3 WILD-TYPE                   105                             10
D1636V10, multiclass
                                clus
vv                               DLGAP3 MUTATED DLGAP3 WILD-TYPE
  COLON ADENOCARCINOMA                       13              302
  COLON MUCINOUS ADENOCARCINOMA               3               44
  RECTAL ADENOCARCINOMA                       1              105
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  DLGAP3 MUTATED    11   0   0   4
  DLGAP3 WILD-TYPE 334   4  31  21
D1636V11, multiclass
    clus
vv   DLGAP3 MUTATED DLGAP3 WILD-TYPE
  R0             11              334
  R1              0                4
  R2              0               31
  RX              4               21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1636V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DLGAP3 MUTATED                                  0     3
  DLGAP3 WILD-TYPE                                1     8
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  DLGAP3 MUTATED                           0     7
  DLGAP3 WILD-TYPE                        22   219
D1636V13, multiclass
                                  clus
vv                                 DLGAP3 MUTATED DLGAP3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         3                8
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         7              219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1637) Variable = MFSD4 MUTATION ANALYSIS
D1637V1, survival
                 sevent
clus2               0   1
  MFSD4 MUTATED     6   0
  MFSD4 WILD-TYPE 372  93
  MFSD4 MUTATED MFSD4 WILD-TYPE 
              6             465 
  MFSD4 MUTATED MFSD4 WILD-TYPE 
              0              93 
$`MFSD4 MUTATED`
TCGA-AA-3520 TCGA-AA-A00U TCGA-AD-6889 TCGA-AZ-4315 TCGA-CA-6716 TCGA-CA-6717 
       24.03        17.03        56.55        58.39        12.20        12.76 

$`MFSD4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
       38.99         1.02         9.07        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00W 
       38.04         4.01        27.02        42.02         0.99        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6718 TCGA-CA-6719 
        3.06         3.25         3.29         0.07        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  MFSD4 MUTATED MFSD4 WILD-TYPE 
           12.2             0.0 
  MFSD4 MUTATED MFSD4 WILD-TYPE 
          58.39          148.01 
  MFSD4 MUTATED MFSD4 WILD-TYPE 
          20.53           20.19 
[1] "12.2 - 58.4 (20.5)" "0.0 - 148.0 (20.2)"
[1] "hr="     "9200000"
D1637V2, continuous
D1637V3, binary
                 cls
clus                0   1
  MFSD4 MUTATED     6   0
  MFSD4 WILD-TYPE 360 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MFSD4 MUTATED      6    0
  MFSD4 WILD-TYPE  360  119
        clus
vv       MFSD4 MUTATED MFSD4 WILD-TYPE
  COLON              6             360
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MFSD4 MUTATED         0        0        1         4         0         0
  MFSD4 WILD-TYPE      91        1       31       134        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MFSD4 MUTATED           0          0          1          0        0         0
  MFSD4 WILD-TYPE        24         11         58         42       48        18
                 vv
clus              STAGE IVB
  MFSD4 MUTATED           0
  MFSD4 WILD-TYPE         1
D1637V4, multiclass
            clus
vv           MFSD4 MUTATED MFSD4 WILD-TYPE
  STAGE I                0              91
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              4             134
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  MFSD4 MUTATED     0   0   6   0
  MFSD4 WILD-TYPE  17  92 323  50
D1637V5, multiclass
    clus
vv   MFSD4 MUTATED MFSD4 WILD-TYPE
  T1             0              17
  T2             0              92
  T3             6             323
  T4             0              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  MFSD4 MUTATED     5   1   0
  MFSD4 WILD-TYPE 282 112  87
D1637V6, multiclass
    clus
vv   MFSD4 MUTATED MFSD4 WILD-TYPE
  N0             5             282
  N1             1             112
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1637V7, binary
                 cls
clus                0   1
  MFSD4 MUTATED     6   0
  MFSD4 WILD-TYPE 369  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MFSD4 MUTATED      6    0
  MFSD4 WILD-TYPE  369   65
   clus
vv  MFSD4 MUTATED MFSD4 WILD-TYPE
  0             6             369
  1             0              65
[1] 2 2
[1] FALSE
D1637V8, binary
                 cls
clus                0   1
  MFSD4 MUTATED     1   5
  MFSD4 WILD-TYPE 224 259
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MFSD4 MUTATED      1    5
  MFSD4 WILD-TYPE  224  259
        clus
vv       MFSD4 MUTATED MFSD4 WILD-TYPE
  FEMALE             1             224
  MALE               5             259
[1] 2 2
[1] FALSE
D1637V9, binary
                 cls
clus                0   1
  MFSD4 MUTATED     5   0
  MFSD4 WILD-TYPE 345  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MFSD4 MUTATED      5    0
  MFSD4 WILD-TYPE  345   22
     clus
vv    MFSD4 MUTATED MFSD4 WILD-TYPE
  NO              5             345
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MFSD4 MUTATED                      5                             1
  MFSD4 WILD-TYPE                  310                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MFSD4 MUTATED                       0                              0
  MFSD4 WILD-TYPE                   106                             10
D1637V10, multiclass
                                clus
vv                               MFSD4 MUTATED MFSD4 WILD-TYPE
  COLON ADENOCARCINOMA                       5             310
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  MFSD4 MUTATED     3   0   0   2
  MFSD4 WILD-TYPE 342   4  31  23
D1637V11, multiclass
    clus
vv   MFSD4 MUTATED MFSD4 WILD-TYPE
  R0             3             342
  R1             0               4
  R2             0              31
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1637V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MFSD4 MUTATED                                  0     3
  MFSD4 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  MFSD4 MUTATED                           0     1
  MFSD4 WILD-TYPE                        22   225
D1637V13, multiclass
                                  clus
vv                                 MFSD4 MUTATED MFSD4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        3               8
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        1             225
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1638) Variable = HECTD2 MUTATION ANALYSIS
D1638V1, survival
                  sevent
clus2                0   1
  HECTD2 MUTATED     8   3
  HECTD2 WILD-TYPE 370  90
  HECTD2 MUTATED HECTD2 WILD-TYPE 
              11              460 
  HECTD2 MUTATED HECTD2 WILD-TYPE 
               3               90 
$`HECTD2 MUTATED`
TCGA-AA-3950 TCGA-AA-A00E TCGA-AA-A00N TCGA-AA-A010 TCGA-AZ-6606 TCGA-CA-5796 
       24.00        30.02         4.01        34.98        11.74         3.25 
TCGA-CA-6717 TCGA-CA-6718 TCGA-D5-6927 TCGA-AG-3892 TCGA-AG-A002 
       12.76        10.06         9.44        13.02        20.98 

$`HECTD2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       38.04        19.00        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
       29.56         5.23         3.19         1.61        12.69         3.06 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        3.29         0.07        12.20        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6928 
        3.68         4.41        12.43        14.30         9.04        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 
       19.99         1.02        17.95        36.95        17.03        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  HECTD2 MUTATED HECTD2 WILD-TYPE 
            3.25             0.00 
  HECTD2 MUTATED HECTD2 WILD-TYPE 
           34.98           148.01 
  HECTD2 MUTATED HECTD2 WILD-TYPE 
          12.760           20.415 
[1] "3.2 - 35.0 (12.8)"  "0.0 - 148.0 (20.4)"
[1] "hr=" "2.4"
D1638V2, continuous
D1638V3, binary
                  cls
clus                 0   1
  HECTD2 MUTATED    10   2
  HECTD2 WILD-TYPE 356 117
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HECTD2 MUTATED     10    2
  HECTD2 WILD-TYPE  356  117
        clus
vv       HECTD2 MUTATED HECTD2 WILD-TYPE
  COLON              10              356
  RECTUM              2              117
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  HECTD2 MUTATED         2        0        0         7         2         0
  HECTD2 WILD-TYPE      89        1       32       131         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HECTD2 MUTATED           0          0          0          0        1
  HECTD2 WILD-TYPE        24         11         59         42       47
                  vv
clus               STAGE IVA STAGE IVB
  HECTD2 MUTATED           0         0
  HECTD2 WILD-TYPE        18         1
D1638V4, multiclass
            clus
vv           HECTD2 MUTATED HECTD2 WILD-TYPE
  STAGE I                 2               89
  STAGE IA                0                1
  STAGE II                0               32
  STAGE IIA               7              131
  STAGE IIB               2                8
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              0               59
  STAGE IIIC              0               42
  STAGE IV                1               47
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  HECTD2 MUTATED     1   1   7   3
  HECTD2 WILD-TYPE  16  91 322  47
D1638V5, multiclass
    clus
vv   HECTD2 MUTATED HECTD2 WILD-TYPE
  T1              1               16
  T2              1               91
  T3              7              322
  T4              3               47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  HECTD2 MUTATED    11   0   1
  HECTD2 WILD-TYPE 276 113  86
D1638V6, multiclass
    clus
vv   HECTD2 MUTATED HECTD2 WILD-TYPE
  N0             11              276
  N1              0              113
  N2              1               86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1638V7, binary
                  cls
clus                 0   1
  HECTD2 MUTATED    11   1
  HECTD2 WILD-TYPE 364  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HECTD2 MUTATED     11    1
  HECTD2 WILD-TYPE  364   64
   clus
vv  HECTD2 MUTATED HECTD2 WILD-TYPE
  0             11              364
  1              1               64
[1] 2 2
[1] FALSE
D1638V8, binary
                  cls
clus                 0   1
  HECTD2 MUTATED     5   7
  HECTD2 WILD-TYPE 220 257
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HECTD2 MUTATED      5    7
  HECTD2 WILD-TYPE  220  257
        clus
vv       HECTD2 MUTATED HECTD2 WILD-TYPE
  FEMALE              5              220
  MALE                7              257
[1] 2 2
[1] FALSE
D1638V9, binary
                  cls
clus                 0   1
  HECTD2 MUTATED    10   0
  HECTD2 WILD-TYPE 340  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HECTD2 MUTATED     10    0
  HECTD2 WILD-TYPE  340   22
     clus
vv    HECTD2 MUTATED HECTD2 WILD-TYPE
  NO              10              340
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  HECTD2 MUTATED                      6                             4
  HECTD2 WILD-TYPE                  309                            43
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  HECTD2 MUTATED                       2                              0
  HECTD2 WILD-TYPE                   104                             10
D1638V10, multiclass
                                clus
vv                               HECTD2 MUTATED HECTD2 WILD-TYPE
  COLON ADENOCARCINOMA                        6              309
  COLON MUCINOUS ADENOCARCINOMA               4               43
  RECTAL ADENOCARCINOMA                       2              104
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  HECTD2 MUTATED     9   0   0   2
  HECTD2 WILD-TYPE 336   4  31  23
D1638V11, multiclass
    clus
vv   HECTD2 MUTATED HECTD2 WILD-TYPE
  R0              9              336
  R1              0                4
  R2              0               31
  RX              2               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1638V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HECTD2 MUTATED                                  0     3
  HECTD2 WILD-TYPE                                1     8
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  HECTD2 MUTATED                           0     2
  HECTD2 WILD-TYPE                        22   224
D1638V13, multiclass
                                  clus
vv                                 HECTD2 MUTATED HECTD2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         3                8
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         2              224
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1639) Variable = CDH18 MUTATION ANALYSIS
D1639V1, survival
                 sevent
clus2               0   1
  CDH18 MUTATED    28   8
  CDH18 WILD-TYPE 350  85
  CDH18 MUTATED CDH18 WILD-TYPE 
             36             435 
  CDH18 MUTATED CDH18 WILD-TYPE 
              8              85 
$`CDH18 MUTATED`
TCGA-A6-2672 TCGA-A6-3807 TCGA-AA-3514 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3950 
       46.65        34.65         1.02        26.99        19.04        24.00 
TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A02J TCGA-AD-5900 TCGA-AD-6548 TCGA-AY-6197 
        4.01        34.98         5.03         0.07        21.37        21.44 
TCGA-AZ-4315 TCGA-AZ-4681 TCGA-AZ-5407 TCGA-AZ-6600 TCGA-AZ-6608 TCGA-CA-6717 
       58.39       106.75        88.21        12.10         1.61        12.76 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CM-6675 TCGA-CM-6676 TCGA-D5-6929 
       15.62        51.32         9.99        13.05        11.08         4.80 
TCGA-D5-6930 TCGA-D5-7000 TCGA-DM-A0XD TCGA-DM-A1D8 TCGA-F4-6570 TCGA-G4-6310 
        1.51        10.26        24.43        12.59         6.18        63.62 
TCGA-AG-3742 TCGA-AG-A002 TCGA-AG-A02N TCGA-AG-A032 TCGA-AH-6547 TCGA-G5-6641 
        0.99        20.98        61.97        38.04         1.45        26.43 

$`CDH18 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5657 
       33.34        32.75        36.53        14.53        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       30.44        29.19        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
       63.98         6.97        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       85.05        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       26.01         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
       39.98         2.01        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
       18.05        40.96        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4323 
       27.09        16.31         0.95        33.01        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 
        5.13        22.36        62.79        49.41         6.77       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07        12.20        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5916 TCGA-CK-6747 
       17.56       148.01        85.45        49.08        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6931 TCGA-D5-6932 
       14.30         9.04         9.44        11.64        12.00        11.38 
TCGA-DM-A0X9 TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
      119.70        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 
       98.24         8.61        31.96        35.74        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       44.68        55.04        85.48        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A036 
       10.98        49.97         1.94        38.96        41.00       117.11 
TCGA-AH-6544 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
       38.56        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
        0.66         0.69        55.76 

  CDH18 MUTATED CDH18 WILD-TYPE 
           0.07            0.00 
  CDH18 MUTATED CDH18 WILD-TYPE 
         106.75          148.01 
  CDH18 MUTATED CDH18 WILD-TYPE 
          17.33           20.28 
[1] "0.1 - 106.8 (17.3)" "0.0 - 148.0 (20.3)"
[1] "hr=" "1.2"
D1639V2, continuous
D1639V3, binary
                 cls
clus                0   1
  CDH18 MUTATED    31   6
  CDH18 WILD-TYPE 335 113
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDH18 MUTATED     31    6
  CDH18 WILD-TYPE  335  113
        clus
vv       CDH18 MUTATED CDH18 WILD-TYPE
  COLON             31             335
  RECTUM             6             113
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CDH18 MUTATED         8        0        2        11         2         0
  CDH18 WILD-TYPE      83        1       30       127         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CDH18 MUTATED           0          2          4          2        3         0
  CDH18 WILD-TYPE        24          9         55         40       45        18
                 vv
clus              STAGE IVB
  CDH18 MUTATED           1
  CDH18 WILD-TYPE         0
D1639V4, multiclass
            clus
vv           CDH18 MUTATED CDH18 WILD-TYPE
  STAGE I                8              83
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA             11             127
  STAGE IIB              2               8
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             2               9
  STAGE IIIB             4              55
  STAGE IIIC             2              40
  STAGE IV               3              45
  STAGE IVA              0              18
  STAGE IVB              1               0
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CDH18 MUTATED     3   7  23   4
  CDH18 WILD-TYPE  14  85 306  46
D1639V5, multiclass
    clus
vv   CDH18 MUTATED CDH18 WILD-TYPE
  T1             3              14
  T2             7              85
  T3            23             306
  T4             4              46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  CDH18 MUTATED    25   9   3
  CDH18 WILD-TYPE 262 104  84
D1639V6, multiclass
    clus
vv   CDH18 MUTATED CDH18 WILD-TYPE
  N0            25             262
  N1             9             104
  N2             3              84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1639V7, binary
                 cls
clus                0   1
  CDH18 MUTATED    26   4
  CDH18 WILD-TYPE 349  61
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDH18 MUTATED     26    4
  CDH18 WILD-TYPE  349   61
   clus
vv  CDH18 MUTATED CDH18 WILD-TYPE
  0            26             349
  1             4              61
[1] 2 2
[1] FALSE
D1639V8, binary
                 cls
clus                0   1
  CDH18 MUTATED    20  17
  CDH18 WILD-TYPE 205 247
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDH18 MUTATED     20   17
  CDH18 WILD-TYPE  205  247
        clus
vv       CDH18 MUTATED CDH18 WILD-TYPE
  FEMALE            20             205
  MALE              17             247
[1] 2 2
[1] FALSE
D1639V9, binary
                 cls
clus                0   1
  CDH18 MUTATED    21   2
  CDH18 WILD-TYPE 329  20
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDH18 MUTATED     21    2
  CDH18 WILD-TYPE  329   20
     clus
vv    CDH18 MUTATED CDH18 WILD-TYPE
  NO             21             329
  YES             2              20
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CDH18 MUTATED                     24                             7
  CDH18 WILD-TYPE                  291                            40
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CDH18 MUTATED                       5                              1
  CDH18 WILD-TYPE                   101                              9
D1639V10, multiclass
                                clus
vv                               CDH18 MUTATED CDH18 WILD-TYPE
  COLON ADENOCARCINOMA                      24             291
  COLON MUCINOUS ADENOCARCINOMA              7              40
  RECTAL ADENOCARCINOMA                      5             101
  RECTAL MUCINOUS ADENOCARCINOMA             1               9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  CDH18 MUTATED    26   0   1   4
  CDH18 WILD-TYPE 319   4  30  21
D1639V11, multiclass
    clus
vv   CDH18 MUTATED CDH18 WILD-TYPE
  R0            26             319
  R1             0               4
  R2             1              30
  RX             4              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1639V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CDH18 MUTATED                                  0     1
  CDH18 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CDH18 MUTATED                           2    22
  CDH18 WILD-TYPE                        20   204
D1639V13, multiclass
                                  clus
vv                                 CDH18 MUTATED CDH18 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    2              20
  WHITE                                       22             204
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1640) Variable = SIX5 MUTATION ANALYSIS
D1640V1, survival
                sevent
clus2              0   1
  SIX5 MUTATED     4   1
  SIX5 WILD-TYPE 374  92
  SIX5 MUTATED SIX5 WILD-TYPE 
             5            466 
  SIX5 MUTATED SIX5 WILD-TYPE 
             1             92 
$`SIX5 MUTATED`
TCGA-AA-3947 TCGA-AA-3966 TCGA-AD-5900 TCGA-F4-6570 TCGA-G4-6586 
       33.01         2.01         0.07         6.18        35.80 

$`SIX5 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 
       31.00         2.01        12.99        24.00        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
        2.01        20.98        34.03        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       39.98        18.05        40.96        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 
      117.07        98.24         8.61        31.96        35.74        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  SIX5 MUTATED SIX5 WILD-TYPE 
          0.07           0.00 
  SIX5 MUTATED SIX5 WILD-TYPE 
         35.80         148.01 
  SIX5 MUTATED SIX5 WILD-TYPE 
         6.180         20.235 
[1] "0.1 - 35.8 (6.2)"   "0.0 - 148.0 (20.2)"
[1] "hr=" "1.9"
D1640V2, continuous
D1640V3, binary
                cls
clus               0   1
  SIX5 MUTATED     5   0
  SIX5 WILD-TYPE 361 119
[1] "tbl2"
                cls
clus             [,1] [,2]
  SIX5 MUTATED      5    0
  SIX5 WILD-TYPE  361  119
        clus
vv       SIX5 MUTATED SIX5 WILD-TYPE
  COLON             5            361
  RECTUM            0            119
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SIX5 MUTATED         1        0        0         3         1         0
  SIX5 WILD-TYPE      90        1       32       135         9         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SIX5 MUTATED           0          0          0          0        0         0
  SIX5 WILD-TYPE        24         11         59         42       48        18
                vv
clus             STAGE IVB
  SIX5 MUTATED           0
  SIX5 WILD-TYPE         1
D1640V4, multiclass
            clus
vv           SIX5 MUTATED SIX5 WILD-TYPE
  STAGE I               1             90
  STAGE IA              0              1
  STAGE II              0             32
  STAGE IIA             3            135
  STAGE IIB             1              9
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            0             59
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  SIX5 MUTATED     0   1   3   1
  SIX5 WILD-TYPE  17  91 326  49
D1640V5, multiclass
    clus
vv   SIX5 MUTATED SIX5 WILD-TYPE
  T1            0             17
  T2            1             91
  T3            3            326
  T4            1             49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  SIX5 MUTATED     5   0   0
  SIX5 WILD-TYPE 282 113  87
D1640V6, multiclass
    clus
vv   SIX5 MUTATED SIX5 WILD-TYPE
  N0            5            282
  N1            0            113
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1640V7, binary
                cls
clus               0   1
  SIX5 MUTATED     4   0
  SIX5 WILD-TYPE 371  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  SIX5 MUTATED      4    0
  SIX5 WILD-TYPE  371   65
   clus
vv  SIX5 MUTATED SIX5 WILD-TYPE
  0            4            371
  1            0             65
[1] 2 2
[1] FALSE
D1640V8, binary
                cls
clus               0   1
  SIX5 MUTATED     4   1
  SIX5 WILD-TYPE 221 263
[1] "tbl2"
                cls
clus             [,1] [,2]
  SIX5 MUTATED      4    1
  SIX5 WILD-TYPE  221  263
        clus
vv       SIX5 MUTATED SIX5 WILD-TYPE
  FEMALE            4            221
  MALE              1            263
[1] 2 2
[1] FALSE
D1640V9, binary
                cls
clus               0   1
  SIX5 MUTATED     3   0
  SIX5 WILD-TYPE 347  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  SIX5 MUTATED      3    0
  SIX5 WILD-TYPE  347   22
     clus
vv    SIX5 MUTATED SIX5 WILD-TYPE
  NO             3            347
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SIX5 MUTATED                      2                             3
  SIX5 WILD-TYPE                  313                            44
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SIX5 MUTATED                       0                              0
  SIX5 WILD-TYPE                   106                             10
D1640V10, multiclass
                                clus
vv                               SIX5 MUTATED SIX5 WILD-TYPE
  COLON ADENOCARCINOMA                      2            313
  COLON MUCINOUS ADENOCARCINOMA             3             44
  RECTAL ADENOCARCINOMA                     0            106
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  SIX5 MUTATED     4   0   0   0
  SIX5 WILD-TYPE 341   4  31  25
D1640V11, multiclass
    clus
vv   SIX5 MUTATED SIX5 WILD-TYPE
  R0            4            341
  R1            0              4
  R2            0             31
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1640V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SIX5 MUTATED                                  0     0
  SIX5 WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  SIX5 MUTATED                           0     3
  SIX5 WILD-TYPE                        22   223
D1640V13, multiclass
                                  clus
vv                                 SIX5 MUTATED SIX5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       3            223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1641) Variable = C1ORF85 MUTATION ANALYSIS
D1641V1, survival
                   sevent
clus2                 0   1
  C1ORF85 MUTATED     8   0
  C1ORF85 WILD-TYPE 370  93
  C1ORF85 MUTATED C1ORF85 WILD-TYPE 
                8               463 
  C1ORF85 MUTATED C1ORF85 WILD-TYPE 
                0                93 
$`C1ORF85 MUTATED`
TCGA-AD-5900 TCGA-AZ-4315 TCGA-CA-6717 TCGA-CM-5860 TCGA-DM-A282 TCGA-G4-6588 
        0.07        58.39        12.76        32.02       139.17        26.17 
TCGA-G4-6628 TCGA-AG-A002 
       79.69        20.98 

$`C1ORF85 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 
        0.92        41.00        39.98        18.05        40.96        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        33.01        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.20        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5861 
       13.02        29.06        22.03        22.98        30.08        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A285 
      140.38         7.50        44.32       131.51       135.65         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 
       22.09        13.78        35.80        91.79        46.75        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  C1ORF85 MUTATED C1ORF85 WILD-TYPE 
             0.07              0.00 
  C1ORF85 MUTATED C1ORF85 WILD-TYPE 
           139.17            148.01 
  C1ORF85 MUTATED C1ORF85 WILD-TYPE 
           29.095            20.050 
[1] "0.1 - 139.2 (29.1)" "0.0 - 148.0 (20.1)"
[1] "hr="     "9400000"
D1641V2, continuous
D1641V3, binary
                   cls
clus                  0   1
  C1ORF85 MUTATED     7   1
  C1ORF85 WILD-TYPE 359 118
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C1ORF85 MUTATED      7    1
  C1ORF85 WILD-TYPE  359  118
        clus
vv       C1ORF85 MUTATED C1ORF85 WILD-TYPE
  COLON                7               359
  RECTUM               1               118
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  C1ORF85 MUTATED         3        0        0         5         0         0
  C1ORF85 WILD-TYPE      88        1       32       133        10         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C1ORF85 MUTATED           0          0          0          0        0
  C1ORF85 WILD-TYPE        24         11         59         42       48
                   vv
clus                STAGE IVA STAGE IVB
  C1ORF85 MUTATED           0         0
  C1ORF85 WILD-TYPE        18         1
D1641V4, multiclass
            clus
vv           C1ORF85 MUTATED C1ORF85 WILD-TYPE
  STAGE I                  3                88
  STAGE IA                 0                 1
  STAGE II                 0                32
  STAGE IIA                5               133
  STAGE IIB                0                10
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               0                11
  STAGE IIIB               0                59
  STAGE IIIC               0                42
  STAGE IV                 0                48
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  C1ORF85 MUTATED     0   3   5   0
  C1ORF85 WILD-TYPE  17  89 324  50
D1641V5, multiclass
    clus
vv   C1ORF85 MUTATED C1ORF85 WILD-TYPE
  T1               0                17
  T2               3                89
  T3               5               324
  T4               0                50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  C1ORF85 MUTATED     8   0   0
  C1ORF85 WILD-TYPE 279 113  87
D1641V6, multiclass
    clus
vv   C1ORF85 MUTATED C1ORF85 WILD-TYPE
  N0               8               279
  N1               0               113
  N2               0                87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1641V7, binary
                   cls
clus                  0   1
  C1ORF85 MUTATED     7   0
  C1ORF85 WILD-TYPE 368  65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C1ORF85 MUTATED      7    0
  C1ORF85 WILD-TYPE  368   65
   clus
vv  C1ORF85 MUTATED C1ORF85 WILD-TYPE
  0               7               368
  1               0                65
[1] 2 2
[1] FALSE
D1641V8, binary
                   cls
clus                  0   1
  C1ORF85 MUTATED     2   6
  C1ORF85 WILD-TYPE 223 258
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C1ORF85 MUTATED      2    6
  C1ORF85 WILD-TYPE  223  258
        clus
vv       C1ORF85 MUTATED C1ORF85 WILD-TYPE
  FEMALE               2               223
  MALE                 6               258
[1] 2 2
[1] FALSE
D1641V9, binary
                   cls
clus                  0   1
  C1ORF85 MUTATED     6   0
  C1ORF85 WILD-TYPE 344  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C1ORF85 MUTATED      6    0
  C1ORF85 WILD-TYPE  344   22
     clus
vv    C1ORF85 MUTATED C1ORF85 WILD-TYPE
  NO                6               344
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  C1ORF85 MUTATED                      5                             2
  C1ORF85 WILD-TYPE                  310                            45
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  C1ORF85 MUTATED                       1                              0
  C1ORF85 WILD-TYPE                   105                             10
D1641V10, multiclass
                                clus
vv                               C1ORF85 MUTATED C1ORF85 WILD-TYPE
  COLON ADENOCARCINOMA                         5               310
  COLON MUCINOUS ADENOCARCINOMA                2                45
  RECTAL ADENOCARCINOMA                        1               105
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  C1ORF85 MUTATED     6   0   0   1
  C1ORF85 WILD-TYPE 339   4  31  24
D1641V11, multiclass
    clus
vv   C1ORF85 MUTATED C1ORF85 WILD-TYPE
  R0               6               339
  R1               0                 4
  R2               0                31
  RX               1                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1641V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C1ORF85 MUTATED                                  0     1
  C1ORF85 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  C1ORF85 MUTATED                           0     6
  C1ORF85 WILD-TYPE                        22   220
D1641V13, multiclass
                                  clus
vv                                 C1ORF85 MUTATED C1ORF85 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                10
  BLACK OR AFRICAN AMERICAN                      0                22
  WHITE                                          6               220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1642) Variable = NAE1 MUTATION ANALYSIS
D1642V1, survival
                sevent
clus2              0   1
  NAE1 MUTATED     8   1
  NAE1 WILD-TYPE 370  92
  NAE1 MUTATED NAE1 WILD-TYPE 
             9            462 
  NAE1 MUTATED NAE1 WILD-TYPE 
             1             92 
$`NAE1 MUTATED`
TCGA-A6-2676 TCGA-AA-3994 TCGA-AU-6004 TCGA-CM-5868 TCGA-CM-6164 TCGA-AG-A002 
       42.90        27.02        27.09        17.03        29.03        20.98 
TCGA-AG-A00Y TCGA-F5-6812 TCGA-F5-6813 
       23.01         0.66         0.69 

$`NAE1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        27.02        19.07         7.96        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       10.88         0.20        14.50        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6162 
       15.02         5.03        15.02        15.02        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
        2.96        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-G5-6235 TCGA-G5-6641 
       49.51        31.30        28.57        32.19        55.76        26.43 

  NAE1 MUTATED NAE1 WILD-TYPE 
          0.66           0.00 
  NAE1 MUTATED NAE1 WILD-TYPE 
         42.90         148.01 
  NAE1 MUTATED NAE1 WILD-TYPE 
        23.010         20.085 
[1] "0.7 - 42.9 (23.0)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.4"
D1642V2, continuous
D1642V3, binary
                cls
clus               0   1
  NAE1 MUTATED     5   4
  NAE1 WILD-TYPE 361 115
[1] "tbl2"
                cls
clus             [,1] [,2]
  NAE1 MUTATED      5    4
  NAE1 WILD-TYPE  361  115
        clus
vv       NAE1 MUTATED NAE1 WILD-TYPE
  COLON             5            361
  RECTUM            4            115
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NAE1 MUTATED         2        0        0         3         1         0
  NAE1 WILD-TYPE      89        1       32       135         9         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NAE1 MUTATED           0          0          1          1        0         1
  NAE1 WILD-TYPE        24         11         58         41       48        17
                vv
clus             STAGE IVB
  NAE1 MUTATED           0
  NAE1 WILD-TYPE         1
D1642V4, multiclass
            clus
vv           NAE1 MUTATED NAE1 WILD-TYPE
  STAGE I               2             89
  STAGE IA              0              1
  STAGE II              0             32
  STAGE IIA             3            135
  STAGE IIB             1              9
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            1             58
  STAGE IIIC            1             41
  STAGE IV              0             48
  STAGE IVA             1             17
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  NAE1 MUTATED     0   2   4   3
  NAE1 WILD-TYPE  17  90 325  47
D1642V5, multiclass
    clus
vv   NAE1 MUTATED NAE1 WILD-TYPE
  T1            0             17
  T2            2             90
  T3            4            325
  T4            3             47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  NAE1 MUTATED     6   2   1
  NAE1 WILD-TYPE 281 111  86
D1642V6, multiclass
    clus
vv   NAE1 MUTATED NAE1 WILD-TYPE
  N0            6            281
  N1            2            111
  N2            1             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1642V7, binary
                cls
clus               0   1
  NAE1 MUTATED     8   1
  NAE1 WILD-TYPE 367  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  NAE1 MUTATED      8    1
  NAE1 WILD-TYPE  367   64
   clus
vv  NAE1 MUTATED NAE1 WILD-TYPE
  0            8            367
  1            1             64
[1] 2 2
[1] FALSE
D1642V8, binary
                cls
clus               0   1
  NAE1 MUTATED     4   5
  NAE1 WILD-TYPE 221 259
[1] "tbl2"
                cls
clus             [,1] [,2]
  NAE1 MUTATED      4    5
  NAE1 WILD-TYPE  221  259
        clus
vv       NAE1 MUTATED NAE1 WILD-TYPE
  FEMALE            4            221
  MALE              5            259
[1] 2 2
[1] FALSE
D1642V9, binary
                cls
clus               0   1
  NAE1 MUTATED     6   0
  NAE1 WILD-TYPE 344  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  NAE1 MUTATED      6    0
  NAE1 WILD-TYPE  344   22
     clus
vv    NAE1 MUTATED NAE1 WILD-TYPE
  NO             6            344
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  NAE1 MUTATED                      4                             1
  NAE1 WILD-TYPE                  311                            46
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  NAE1 MUTATED                       4                              0
  NAE1 WILD-TYPE                   102                             10
D1642V10, multiclass
                                clus
vv                               NAE1 MUTATED NAE1 WILD-TYPE
  COLON ADENOCARCINOMA                      4            311
  COLON MUCINOUS ADENOCARCINOMA             1             46
  RECTAL ADENOCARCINOMA                     4            102
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  NAE1 MUTATED     9   0   0   0
  NAE1 WILD-TYPE 336   4  31  25
D1642V11, multiclass
    clus
vv   NAE1 MUTATED NAE1 WILD-TYPE
  R0            9            336
  R1            0              4
  R2            0             31
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1642V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NAE1 MUTATED                                  0     0
  NAE1 WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  NAE1 MUTATED                           0     6
  NAE1 WILD-TYPE                        22   220
D1642V13, multiclass
                                  clus
vv                                 NAE1 MUTATED NAE1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       6            220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1643) Variable = CYP3A7 MUTATION ANALYSIS
D1643V1, survival
                  sevent
clus2                0   1
  CYP3A7 MUTATED    10   2
  CYP3A7 WILD-TYPE 368  91
  CYP3A7 MUTATED CYP3A7 WILD-TYPE 
              12              459 
  CYP3A7 MUTATED CYP3A7 WILD-TYPE 
               2               91 
$`CYP3A7 MUTATED`
TCGA-A6-2677 TCGA-AA-3697 TCGA-AA-3845 TCGA-AA-3864 TCGA-AA-3977 TCGA-AA-A010 
       24.33        85.05         0.00        53.00        25.02        34.98 
TCGA-CA-6717 TCGA-CM-6162 TCGA-DM-A28H TCGA-G4-6323 TCGA-AG-A002 TCGA-AG-A00H 
       12.76        12.00       117.07        13.78        20.98        25.97 

$`CYP3A7 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        42.90        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 
       15.95        38.99        37.02        14.93        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        31.07        30.05        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07        12.20        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       17.03        15.02         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
       60.79        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       61.91        36.00        22.09        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  CYP3A7 MUTATED CYP3A7 WILD-TYPE 
               0                0 
  CYP3A7 MUTATED CYP3A7 WILD-TYPE 
          117.07           148.01 
  CYP3A7 MUTATED CYP3A7 WILD-TYPE 
          24.675           20.050 
[1] "0.0 - 117.1 (24.7)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.6"
D1643V2, continuous
D1643V3, binary
                  cls
clus                 0   1
  CYP3A7 MUTATED    10   2
  CYP3A7 WILD-TYPE 356 117
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CYP3A7 MUTATED     10    2
  CYP3A7 WILD-TYPE  356  117
        clus
vv       CYP3A7 MUTATED CYP3A7 WILD-TYPE
  COLON              10              356
  RECTUM              2              117
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CYP3A7 MUTATED         1        1        1         3         1         0
  CYP3A7 WILD-TYPE      90        0       31       135         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CYP3A7 MUTATED           1          0          1          2        0
  CYP3A7 WILD-TYPE        23         11         58         40       48
                  vv
clus               STAGE IVA STAGE IVB
  CYP3A7 MUTATED           0         0
  CYP3A7 WILD-TYPE        18         1
D1643V4, multiclass
            clus
vv           CYP3A7 MUTATED CYP3A7 WILD-TYPE
  STAGE I                 1               90
  STAGE IA                1                0
  STAGE II                1               31
  STAGE IIA               3              135
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               1               23
  STAGE IIIA              0               11
  STAGE IIIB              1               58
  STAGE IIIC              2               40
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  CYP3A7 MUTATED     0   2   8   1
  CYP3A7 WILD-TYPE  17  90 321  49
D1643V5, multiclass
    clus
vv   CYP3A7 MUTATED CYP3A7 WILD-TYPE
  T1              0               17
  T2              2               90
  T3              8              321
  T4              1               49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  CYP3A7 MUTATED     9   1   2
  CYP3A7 WILD-TYPE 278 112  85
D1643V6, multiclass
    clus
vv   CYP3A7 MUTATED CYP3A7 WILD-TYPE
  N0              9              278
  N1              1              112
  N2              2               85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1643V7, binary
                  cls
clus                 0   1
  CYP3A7 MUTATED    10   0
  CYP3A7 WILD-TYPE 365  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CYP3A7 MUTATED     10    0
  CYP3A7 WILD-TYPE  365   65
   clus
vv  CYP3A7 MUTATED CYP3A7 WILD-TYPE
  0             10              365
  1              0               65
[1] 2 2
[1] FALSE
D1643V8, binary
                  cls
clus                 0   1
  CYP3A7 MUTATED     4   8
  CYP3A7 WILD-TYPE 221 256
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CYP3A7 MUTATED      4    8
  CYP3A7 WILD-TYPE  221  256
        clus
vv       CYP3A7 MUTATED CYP3A7 WILD-TYPE
  FEMALE              4              221
  MALE                8              256
[1] 2 2
[1] FALSE
D1643V9, binary
                  cls
clus                 0   1
  CYP3A7 MUTATED     9   1
  CYP3A7 WILD-TYPE 341  21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CYP3A7 MUTATED      9    1
  CYP3A7 WILD-TYPE  341   21
     clus
vv    CYP3A7 MUTATED CYP3A7 WILD-TYPE
  NO               9              341
  YES              1               21
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CYP3A7 MUTATED                      8                             2
  CYP3A7 WILD-TYPE                  307                            45
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CYP3A7 MUTATED                       2                              0
  CYP3A7 WILD-TYPE                   104                             10
D1643V10, multiclass
                                clus
vv                               CYP3A7 MUTATED CYP3A7 WILD-TYPE
  COLON ADENOCARCINOMA                        8              307
  COLON MUCINOUS ADENOCARCINOMA               2               45
  RECTAL ADENOCARCINOMA                       2              104
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  CYP3A7 MUTATED     9   0   0   1
  CYP3A7 WILD-TYPE 336   4  31  24
D1643V11, multiclass
    clus
vv   CYP3A7 MUTATED CYP3A7 WILD-TYPE
  R0              9              336
  R1              0                4
  R2              0               31
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1643V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CYP3A7 MUTATED                                  0     1
  CYP3A7 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  CYP3A7 MUTATED                           1     3
  CYP3A7 WILD-TYPE                        21   223
D1643V13, multiclass
                                  clus
vv                                 CYP3A7 MUTATED CYP3A7 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                         3              223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1644) Variable = DEFB129 MUTATION ANALYSIS
D1644V1, survival
                   sevent
clus2                 0   1
  DEFB129 MUTATED     4   1
  DEFB129 WILD-TYPE 374  92
  DEFB129 MUTATED DEFB129 WILD-TYPE 
                5               466 
  DEFB129 MUTATED DEFB129 WILD-TYPE 
                1                92 
$`DEFB129 MUTATED`
TCGA-AA-3516 TCGA-AA-3710 TCGA-AA-3968 TCGA-D5-6536 TCGA-G4-6628 
       13.02        26.99        21.99        17.85        79.69 

$`DEFB129 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        1.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        85.05        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       20.98        34.03         2.01        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 
       18.25         1.32        43.27        15.12         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       46.75        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  DEFB129 MUTATED DEFB129 WILD-TYPE 
            13.02              0.00 
  DEFB129 MUTATED DEFB129 WILD-TYPE 
            79.69            148.01 
  DEFB129 MUTATED DEFB129 WILD-TYPE 
           21.990            20.155 
[1] "13.0 - 79.7 (22.0)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.2"
D1644V2, continuous
D1644V3, binary
                   cls
clus                  0   1
  DEFB129 MUTATED     5   0
  DEFB129 WILD-TYPE 361 119
[1] "tbl2"
                   cls
clus                [,1] [,2]
  DEFB129 MUTATED      5    0
  DEFB129 WILD-TYPE  361  119
        clus
vv       DEFB129 MUTATED DEFB129 WILD-TYPE
  COLON                5               361
  RECTUM               0               119
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEFB129 MUTATED         2        0        0         2         0         0
  DEFB129 WILD-TYPE      89        1       32       136        10         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DEFB129 MUTATED           1          0          0          0        0
  DEFB129 WILD-TYPE        23         11         59         42       48
                   vv
clus                STAGE IVA STAGE IVB
  DEFB129 MUTATED           0         0
  DEFB129 WILD-TYPE        18         1
D1644V4, multiclass
            clus
vv           DEFB129 MUTATED DEFB129 WILD-TYPE
  STAGE I                  2                89
  STAGE IA                 0                 1
  STAGE II                 0                32
  STAGE IIA                2               136
  STAGE IIB                0                10
  STAGE IIC                0                 1
  STAGE III                1                23
  STAGE IIIA               0                11
  STAGE IIIB               0                59
  STAGE IIIC               0                42
  STAGE IV                 0                48
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  DEFB129 MUTATED     0   2   3   0
  DEFB129 WILD-TYPE  17  90 326  50
D1644V5, multiclass
    clus
vv   DEFB129 MUTATED DEFB129 WILD-TYPE
  T1               0                17
  T2               2                90
  T3               3               326
  T4               0                50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  DEFB129 MUTATED     4   0   1
  DEFB129 WILD-TYPE 283 113  86
D1644V6, multiclass
    clus
vv   DEFB129 MUTATED DEFB129 WILD-TYPE
  N0               4               283
  N1               0               113
  N2               1                86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1644V7, binary
                   cls
clus                  0   1
  DEFB129 MUTATED     5   0
  DEFB129 WILD-TYPE 370  65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  DEFB129 MUTATED      5    0
  DEFB129 WILD-TYPE  370   65
   clus
vv  DEFB129 MUTATED DEFB129 WILD-TYPE
  0               5               370
  1               0                65
[1] 2 2
[1] FALSE
D1644V8, binary
                   cls
clus                  0   1
  DEFB129 MUTATED     3   2
  DEFB129 WILD-TYPE 222 262
[1] "tbl2"
                   cls
clus                [,1] [,2]
  DEFB129 MUTATED      3    2
  DEFB129 WILD-TYPE  222  262
        clus
vv       DEFB129 MUTATED DEFB129 WILD-TYPE
  FEMALE               3               222
  MALE                 2               262
[1] 2 2
[1] FALSE
D1644V9, binary
                   cls
clus                  0   1
  DEFB129 MUTATED     5   0
  DEFB129 WILD-TYPE 345  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  DEFB129 MUTATED      5    0
  DEFB129 WILD-TYPE  345   22
     clus
vv    DEFB129 MUTATED DEFB129 WILD-TYPE
  NO                5               345
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  DEFB129 MUTATED                      4                             1
  DEFB129 WILD-TYPE                  311                            46
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  DEFB129 MUTATED                       0                              0
  DEFB129 WILD-TYPE                   106                             10
D1644V10, multiclass
                                clus
vv                               DEFB129 MUTATED DEFB129 WILD-TYPE
  COLON ADENOCARCINOMA                         4               311
  COLON MUCINOUS ADENOCARCINOMA                1                46
  RECTAL ADENOCARCINOMA                        0               106
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  DEFB129 MUTATED     4   0   0   0
  DEFB129 WILD-TYPE 341   4  31  25
D1644V11, multiclass
    clus
vv   DEFB129 MUTATED DEFB129 WILD-TYPE
  R0               4               341
  R1               0                 4
  R2               0                31
  RX               0                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1644V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEFB129 MUTATED                                  0     0
  DEFB129 WILD-TYPE                                1    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  DEFB129 MUTATED                           0     2
  DEFB129 WILD-TYPE                        22   224
D1644V13, multiclass
[1] "Remove cluster labels:" "DEFB129 MUTATED"       
clus
  DEFB129 MUTATED DEFB129 WILD-TYPE 
                2               258 
       TCGA-A6-2671        TCGA-A6-2672        TCGA-A6-2674        TCGA-A6-2676 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-A6-2677        TCGA-A6-2678        TCGA-A6-2683        TCGA-A6-3807 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-A6-3808        TCGA-A6-3809        TCGA-A6-3810        TCGA-A6-4105 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-A6-5656        TCGA-A6-5657        TCGA-A6-5659        TCGA-A6-5660 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-A6-5661        TCGA-A6-5662        TCGA-A6-5664        TCGA-A6-5665 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-A6-5666        TCGA-A6-6137        TCGA-A6-6138        TCGA-A6-6141 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-A6-6142        TCGA-A6-6648        TCGA-A6-6649        TCGA-A6-6651 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-A6-6652        TCGA-A6-6653        TCGA-A6-6654        TCGA-A6-6780 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-A6-6781        TCGA-A6-6782        TCGA-AD-5900        TCGA-AD-6548 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-AD-6888        TCGA-AD-6889        TCGA-AD-6890        TCGA-AD-6895 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-AD-6899        TCGA-AD-6901        TCGA-AD-6963        TCGA-AD-6964 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-AD-6965        TCGA-AU-3779        TCGA-AU-6004        TCGA-AY-4070 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-AY-4071        TCGA-AY-5543        TCGA-AY-6196        TCGA-AY-6197 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-AY-6386        TCGA-AZ-4315        TCGA-AZ-4323        TCGA-AZ-4616 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-AZ-4681        TCGA-AZ-4682        TCGA-AZ-5403        TCGA-AZ-5407 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-AZ-6598        TCGA-AZ-6599        TCGA-AZ-6600        TCGA-AZ-6601 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-AZ-6603        TCGA-AZ-6605        TCGA-AZ-6606        TCGA-AZ-6607 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-AZ-6608        TCGA-CA-5254        TCGA-CA-5255        TCGA-CA-5796 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-CA-5797        TCGA-CA-6715        TCGA-CA-6716        TCGA-CA-6717 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-CA-6718        TCGA-CA-6719        TCGA-CK-4947        TCGA-CK-4948 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-CK-4950        TCGA-CK-4952        TCGA-CK-5912        TCGA-CK-5913 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-CK-5914        TCGA-CK-5915        TCGA-CK-5916        TCGA-CK-6746 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-CK-6747        TCGA-CK-6748        TCGA-CK-6751        TCGA-CM-4743 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-CM-4744        TCGA-CM-4746        TCGA-CM-4747        TCGA-CM-4752 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-CM-5341        TCGA-CM-5344        TCGA-CM-5348        TCGA-CM-5349 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-CM-5860        TCGA-CM-5861        TCGA-CM-5862        TCGA-CM-5863 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-CM-5864        TCGA-CM-5868        TCGA-CM-6161        TCGA-CM-6162 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-CM-6163        TCGA-CM-6164        TCGA-CM-6165        TCGA-CM-6166 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-CM-6167        TCGA-CM-6168        TCGA-CM-6169        TCGA-CM-6170 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-CM-6171        TCGA-CM-6172        TCGA-CM-6674        TCGA-CM-6675 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-CM-6676        TCGA-CM-6677        TCGA-CM-6678        TCGA-CM-6679 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-CM-6680        TCGA-D5-5537        TCGA-D5-5538        TCGA-D5-5539 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-D5-5540        TCGA-D5-5541        TCGA-D5-6529        TCGA-D5-6532 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-D5-6533        TCGA-D5-6534        TCGA-D5-6535        TCGA-D5-6537 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-D5-6538        TCGA-D5-6539        TCGA-D5-6540        TCGA-D5-6541 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-D5-6898        TCGA-D5-6920        TCGA-D5-6922        TCGA-D5-6923 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-D5-6924        TCGA-D5-6926        TCGA-D5-6927        TCGA-D5-6928 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-D5-6929        TCGA-D5-6930        TCGA-D5-6931        TCGA-D5-6932 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-D5-7000        TCGA-DM-A0X9        TCGA-DM-A0XD        TCGA-DM-A0XF 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-DM-A1D0        TCGA-DM-A1D4        TCGA-DM-A1D6        TCGA-DM-A1D7 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-DM-A1D8        TCGA-DM-A1D9        TCGA-DM-A1DA        TCGA-DM-A1DB 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-DM-A1HA        TCGA-DM-A1HB        TCGA-DM-A282        TCGA-DM-A285 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-DM-A28C        TCGA-DM-A28E        TCGA-DM-A28F        TCGA-DM-A28G 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-DM-A28H        TCGA-DM-A28K        TCGA-F4-6459        TCGA-F4-6460 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-F4-6569        TCGA-F4-6570        TCGA-F4-6703        TCGA-F4-6704 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-F4-6805        TCGA-F4-6806        TCGA-F4-6807        TCGA-F4-6808 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-F4-6809        TCGA-F4-6854        TCGA-F4-6855        TCGA-F4-6856 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-G4-6293        TCGA-G4-6299        TCGA-G4-6303        TCGA-G4-6304 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-G4-6306        TCGA-G4-6307        TCGA-G4-6309        TCGA-G4-6310 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-G4-6315        TCGA-G4-6317        TCGA-G4-6321        TCGA-G4-6323 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-G4-6586        TCGA-G4-6588        TCGA-G4-6625        TCGA-G4-6626 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2691        TCGA-AF-2692 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3913        TCGA-AF-4110 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-AF-5654        TCGA-AF-6136        TCGA-AF-6655        TCGA-AF-6672 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6549        TCGA-AH-6643 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-AH-6644        TCGA-CI-6619        TCGA-CI-6620        TCGA-CI-6621 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-CI-6622        TCGA-CI-6624        TCGA-CL-5917        TCGA-CL-5918 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6155        TCGA-DC-6157 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-DC-6158        TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-DC-6683        TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-DY-A1DD        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-EF-5830        TCGA-EI-6506        TCGA-EI-6507        TCGA-EI-6508 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-EI-6510        TCGA-F5-6464        TCGA-F5-6465        TCGA-F5-6571 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-F5-6702        TCGA-F5-6811        TCGA-F5-6812        TCGA-F5-6813 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 
       TCGA-G5-6235        TCGA-G5-6641 
"DEFB129 WILD-TYPE" "DEFB129 WILD-TYPE" 

Clustering(1645) Variable = EFNB3 MUTATION ANALYSIS
D1645V1, survival
                 sevent
clus2               0   1
  EFNB3 MUTATED     7   2
  EFNB3 WILD-TYPE 371  91
  EFNB3 MUTATED EFNB3 WILD-TYPE 
              9             462 
  EFNB3 MUTATED EFNB3 WILD-TYPE 
              2              91 
$`EFNB3 MUTATED`
TCGA-AA-3713 TCGA-AA-3851 TCGA-AA-3950 TCGA-AA-A02O TCGA-AZ-4315 TCGA-AZ-6598 
       19.04        33.07        24.00         0.92        58.39        49.41 
TCGA-CM-5861 TCGA-DM-A1D8 TCGA-AG-A025 
       15.02        12.59        49.97 

$`EFNB3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       17.03        10.06         0.00         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 
       12.99        24.00        33.01        26.01         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        2.01         5.03        14.01        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       88.21         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       22.98        30.08        32.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       49.91        13.32       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       10.98         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  EFNB3 MUTATED EFNB3 WILD-TYPE 
           0.92            0.00 
  EFNB3 MUTATED EFNB3 WILD-TYPE 
          58.39          148.01 
  EFNB3 MUTATED EFNB3 WILD-TYPE 
         24.000          20.155 
[1] "0.9 - 58.4 (24.0)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.1"
D1645V2, continuous
D1645V3, binary
                 cls
clus                0   1
  EFNB3 MUTATED     8   1
  EFNB3 WILD-TYPE 358 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EFNB3 MUTATED      8    1
  EFNB3 WILD-TYPE  358  118
        clus
vv       EFNB3 MUTATED EFNB3 WILD-TYPE
  COLON              8             358
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  EFNB3 MUTATED         1        0        2         4         0         0
  EFNB3 WILD-TYPE      90        1       30       134        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  EFNB3 MUTATED           0          0          0          0        1         0
  EFNB3 WILD-TYPE        24         11         59         42       47        18
                 vv
clus              STAGE IVB
  EFNB3 MUTATED           0
  EFNB3 WILD-TYPE         1
D1645V4, multiclass
            clus
vv           EFNB3 MUTATED EFNB3 WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA              4             134
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             0              42
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  EFNB3 MUTATED     1   0   8   0
  EFNB3 WILD-TYPE  16  92 321  50
D1645V5, multiclass
    clus
vv   EFNB3 MUTATED EFNB3 WILD-TYPE
  T1             1              16
  T2             0              92
  T3             8             321
  T4             0              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  EFNB3 MUTATED     8   1   0
  EFNB3 WILD-TYPE 279 112  87
D1645V6, multiclass
    clus
vv   EFNB3 MUTATED EFNB3 WILD-TYPE
  N0             8             279
  N1             1             112
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1645V7, binary
                 cls
clus                0   1
  EFNB3 MUTATED     6   1
  EFNB3 WILD-TYPE 369  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EFNB3 MUTATED      6    1
  EFNB3 WILD-TYPE  369   64
   clus
vv  EFNB3 MUTATED EFNB3 WILD-TYPE
  0             6             369
  1             1              64
[1] 2 2
[1] FALSE
D1645V8, binary
                 cls
clus                0   1
  EFNB3 MUTATED     5   4
  EFNB3 WILD-TYPE 220 260
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EFNB3 MUTATED      5    4
  EFNB3 WILD-TYPE  220  260
        clus
vv       EFNB3 MUTATED EFNB3 WILD-TYPE
  FEMALE             5             220
  MALE               4             260
[1] 2 2
[1] FALSE
D1645V9, binary
                 cls
clus                0   1
  EFNB3 MUTATED     5   1
  EFNB3 WILD-TYPE 345  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EFNB3 MUTATED      5    1
  EFNB3 WILD-TYPE  345   21
     clus
vv    EFNB3 MUTATED EFNB3 WILD-TYPE
  NO              5             345
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  EFNB3 MUTATED                      7                             1
  EFNB3 WILD-TYPE                  308                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  EFNB3 MUTATED                       1                              0
  EFNB3 WILD-TYPE                   105                             10
D1645V10, multiclass
                                clus
vv                               EFNB3 MUTATED EFNB3 WILD-TYPE
  COLON ADENOCARCINOMA                       7             308
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  EFNB3 MUTATED     6   0   1   0
  EFNB3 WILD-TYPE 339   4  30  25
D1645V11, multiclass
    clus
vv   EFNB3 MUTATED EFNB3 WILD-TYPE
  R0             6             339
  R1             0               4
  R2             1              30
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1645V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  EFNB3 MUTATED                                  0     0
  EFNB3 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  EFNB3 MUTATED                           0     4
  EFNB3 WILD-TYPE                        22   222
D1645V13, multiclass
                                  clus
vv                                 EFNB3 MUTATED EFNB3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        4             222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1646) Variable = DYRK3 MUTATION ANALYSIS
D1646V1, survival
                 sevent
clus2               0   1
  DYRK3 MUTATED    11   4
  DYRK3 WILD-TYPE 367  89
  DYRK3 MUTATED DYRK3 WILD-TYPE 
             15             456 
  DYRK3 MUTATED DYRK3 WILD-TYPE 
              4              89 
$`DYRK3 MUTATED`
TCGA-AA-3510 TCGA-AA-3877 TCGA-AA-A00J TCGA-AA-A00N TCGA-AA-A010 TCGA-AZ-4315 
       63.98        31.00        18.05         4.01        34.98        58.39 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-CA-6717 TCGA-CM-5861 TCGA-D5-6537 TCGA-D5-6540 
       49.41         6.77        12.76        15.02         4.80        16.14 
TCGA-G4-6628 TCGA-AG-3726 TCGA-AG-3881 
       79.69         7.99        19.04 

$`DYRK3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 
       17.03        24.03        27.02        29.98        18.05         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       19.00        30.02        34.03        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.20        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6539 
        1.32        43.27        15.12        17.85        17.13        12.49 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 
       13.78        35.80        26.17        91.79        46.75        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
       19.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  DYRK3 MUTATED DYRK3 WILD-TYPE 
           4.01            0.00 
  DYRK3 MUTATED DYRK3 WILD-TYPE 
          79.69          148.01 
  DYRK3 MUTATED DYRK3 WILD-TYPE 
         18.050          20.415 
[1] "4.0 - 79.7 (18.1)"  "0.0 - 148.0 (20.4)"
[1] "hr=" "1.2"
D1646V2, continuous
D1646V3, binary
                 cls
clus                0   1
  DYRK3 MUTATED    14   2
  DYRK3 WILD-TYPE 352 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DYRK3 MUTATED     14    2
  DYRK3 WILD-TYPE  352  117
        clus
vv       DYRK3 MUTATED DYRK3 WILD-TYPE
  COLON             14             352
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DYRK3 MUTATED         5        0        3         4         2         0
  DYRK3 WILD-TYPE      86        1       29       134         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DYRK3 MUTATED           0          0          2          0        0         0
  DYRK3 WILD-TYPE        24         11         57         42       48        18
                 vv
clus              STAGE IVB
  DYRK3 MUTATED           0
  DYRK3 WILD-TYPE         1
D1646V4, multiclass
            clus
vv           DYRK3 MUTATED DYRK3 WILD-TYPE
  STAGE I                5              86
  STAGE IA               0               1
  STAGE II               3              29
  STAGE IIA              4             134
  STAGE IIB              2               8
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             2              57
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  DYRK3 MUTATED     1   4   7   4
  DYRK3 WILD-TYPE  16  88 322  46
D1646V5, multiclass
    clus
vv   DYRK3 MUTATED DYRK3 WILD-TYPE
  T1             1              16
  T2             4              88
  T3             7             322
  T4             4              46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  DYRK3 MUTATED    14   2   0
  DYRK3 WILD-TYPE 273 111  87
D1646V6, multiclass
    clus
vv   DYRK3 MUTATED DYRK3 WILD-TYPE
  N0            14             273
  N1             2             111
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1646V7, binary
                 cls
clus                0   1
  DYRK3 MUTATED    13   0
  DYRK3 WILD-TYPE 362  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DYRK3 MUTATED     13    0
  DYRK3 WILD-TYPE  362   65
   clus
vv  DYRK3 MUTATED DYRK3 WILD-TYPE
  0            13             362
  1             0              65
[1] 2 2
[1] FALSE
D1646V8, binary
                 cls
clus                0   1
  DYRK3 MUTATED     7   9
  DYRK3 WILD-TYPE 218 255
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DYRK3 MUTATED      7    9
  DYRK3 WILD-TYPE  218  255
        clus
vv       DYRK3 MUTATED DYRK3 WILD-TYPE
  FEMALE             7             218
  MALE               9             255
[1] 2 2
[1] FALSE
D1646V9, binary
                 cls
clus                0   1
  DYRK3 MUTATED    14   0
  DYRK3 WILD-TYPE 336  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DYRK3 MUTATED     14    0
  DYRK3 WILD-TYPE  336   22
     clus
vv    DYRK3 MUTATED DYRK3 WILD-TYPE
  NO             14             336
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  DYRK3 MUTATED                      9                             5
  DYRK3 WILD-TYPE                  306                            42
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  DYRK3 MUTATED                       1                              0
  DYRK3 WILD-TYPE                   105                             10
D1646V10, multiclass
                                clus
vv                               DYRK3 MUTATED DYRK3 WILD-TYPE
  COLON ADENOCARCINOMA                       9             306
  COLON MUCINOUS ADENOCARCINOMA              5              42
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  DYRK3 MUTATED    12   0   0   1
  DYRK3 WILD-TYPE 333   4  31  24
D1646V11, multiclass
    clus
vv   DYRK3 MUTATED DYRK3 WILD-TYPE
  R0            12             333
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1646V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DYRK3 MUTATED                                  0     1
  DYRK3 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  DYRK3 MUTATED                           0     7
  DYRK3 WILD-TYPE                        22   219
D1646V13, multiclass
                                  clus
vv                                 DYRK3 MUTATED DYRK3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        7             219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1647) Variable = ZBTB24 MUTATION ANALYSIS
D1647V1, survival
                  sevent
clus2                0   1
  ZBTB24 MUTATED     8   3
  ZBTB24 WILD-TYPE 370  90
  ZBTB24 MUTATED ZBTB24 WILD-TYPE 
              11              460 
  ZBTB24 MUTATED ZBTB24 WILD-TYPE 
               3               90 
$`ZBTB24 MUTATED`
TCGA-A6-6649 TCGA-AA-3864 TCGA-AA-A010 TCGA-CA-6718 TCGA-CM-6171 TCGA-CM-6679 
       24.16        53.00        34.98        10.06        14.04        10.06 
TCGA-DM-A0XF TCGA-DM-A1HB TCGA-AG-A002 TCGA-AG-A020 TCGA-DY-A1H8 
       38.20       135.65        20.98        10.98        32.61 

$`ZBTB24 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.08        25.18        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 
       32.05         0.99        31.07        31.07        30.05        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       12.76        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       13.02        15.02        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.08        11.01        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A1D0 TCGA-DM-A1D4 
       11.38        10.26       119.70        24.43       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      131.51       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A025 
       36.03         9.07        12.00        70.03        64.01        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       24.13        51.48         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  ZBTB24 MUTATED ZBTB24 WILD-TYPE 
           10.06             0.00 
  ZBTB24 MUTATED ZBTB24 WILD-TYPE 
          135.65           148.01 
  ZBTB24 MUTATED ZBTB24 WILD-TYPE 
          24.160           20.085 
[1] "10.1 - 135.7 (24.2)" "0.0 - 148.0 (20.1)" 
[1] "hr=" "1.2"
D1647V2, continuous
D1647V3, binary
                  cls
clus                 0   1
  ZBTB24 MUTATED     8   3
  ZBTB24 WILD-TYPE 358 116
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZBTB24 MUTATED      8    3
  ZBTB24 WILD-TYPE  358  116
        clus
vv       ZBTB24 MUTATED ZBTB24 WILD-TYPE
  COLON               8              358
  RECTUM              3              116
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZBTB24 MUTATED         2        0        1         2         1         0
  ZBTB24 WILD-TYPE      89        1       31       136         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZBTB24 MUTATED           1          1          2          1        0
  ZBTB24 WILD-TYPE        23         10         57         41       48
                  vv
clus               STAGE IVA STAGE IVB
  ZBTB24 MUTATED           0         0
  ZBTB24 WILD-TYPE        18         1
D1647V4, multiclass
            clus
vv           ZBTB24 MUTATED ZBTB24 WILD-TYPE
  STAGE I                 2               89
  STAGE IA                0                1
  STAGE II                1               31
  STAGE IIA               2              136
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               1               23
  STAGE IIIA              1               10
  STAGE IIIB              2               57
  STAGE IIIC              1               41
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZBTB24 MUTATED     0   3   7   1
  ZBTB24 WILD-TYPE  17  89 322  49
D1647V5, multiclass
    clus
vv   ZBTB24 MUTATED ZBTB24 WILD-TYPE
  T1              0               17
  T2              3               89
  T3              7              322
  T4              1               49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  ZBTB24 MUTATED     6   4   1
  ZBTB24 WILD-TYPE 281 109  86
D1647V6, multiclass
    clus
vv   ZBTB24 MUTATED ZBTB24 WILD-TYPE
  N0              6              281
  N1              4              109
  N2              1               86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1647V7, binary
                  cls
clus                 0   1
  ZBTB24 MUTATED    11   0
  ZBTB24 WILD-TYPE 364  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZBTB24 MUTATED     11    0
  ZBTB24 WILD-TYPE  364   65
   clus
vv  ZBTB24 MUTATED ZBTB24 WILD-TYPE
  0             11              364
  1              0               65
[1] 2 2
[1] FALSE
D1647V8, binary
                  cls
clus                 0   1
  ZBTB24 MUTATED     5   6
  ZBTB24 WILD-TYPE 220 258
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZBTB24 MUTATED      5    6
  ZBTB24 WILD-TYPE  220  258
        clus
vv       ZBTB24 MUTATED ZBTB24 WILD-TYPE
  FEMALE              5              220
  MALE                6              258
[1] 2 2
[1] FALSE
D1647V9, binary
                  cls
clus                 0   1
  ZBTB24 MUTATED     7   0
  ZBTB24 WILD-TYPE 343  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZBTB24 MUTATED      7    0
  ZBTB24 WILD-TYPE  343   22
     clus
vv    ZBTB24 MUTATED ZBTB24 WILD-TYPE
  NO               7              343
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ZBTB24 MUTATED                      6                             0
  ZBTB24 WILD-TYPE                  309                            47
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ZBTB24 MUTATED                       2                              1
  ZBTB24 WILD-TYPE                   104                              9
D1647V10, multiclass
                                clus
vv                               ZBTB24 MUTATED ZBTB24 WILD-TYPE
  COLON ADENOCARCINOMA                        6              309
  COLON MUCINOUS ADENOCARCINOMA               0               47
  RECTAL ADENOCARCINOMA                       2              104
  RECTAL MUCINOUS ADENOCARCINOMA              1                9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ZBTB24 MUTATED     6   0   0   1
  ZBTB24 WILD-TYPE 339   4  31  24
D1647V11, multiclass
    clus
vv   ZBTB24 MUTATED ZBTB24 WILD-TYPE
  R0              6              339
  R1              0                4
  R2              0               31
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1647V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZBTB24 MUTATED                                  0     1
  ZBTB24 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZBTB24 MUTATED                           0     6
  ZBTB24 WILD-TYPE                        22   220
D1647V13, multiclass
                                  clus
vv                                 ZBTB24 MUTATED ZBTB24 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         6              220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1648) Variable = TNRC6B MUTATION ANALYSIS
D1648V1, survival
                  sevent
clus2                0   1
  TNRC6B MUTATED    20   3
  TNRC6B WILD-TYPE 358  90
  TNRC6B MUTATED TNRC6B WILD-TYPE 
              23              448 
  TNRC6B MUTATED TNRC6B WILD-TYPE 
               3               90 
$`TNRC6B MUTATED`
TCGA-A6-5661 TCGA-A6-6141 TCGA-A6-6653 TCGA-AA-3510 TCGA-AA-3663 TCGA-AA-3673 
       33.53         8.38        24.39        63.98         6.97        50.04 
TCGA-AA-3697 TCGA-AA-3811 TCGA-AA-A01T TCGA-AA-A02Y TCGA-AD-6901 TCGA-AZ-6601 
       85.05        10.06        33.04        39.98        22.42       100.01 
TCGA-CA-6716 TCGA-CM-4746 TCGA-CM-5861 TCGA-CM-6162 TCGA-D5-6924 TCGA-DM-A1HB 
       12.20        37.02        15.02        12.00        14.30       135.65 
TCGA-G4-6304 TCGA-G4-6588 TCGA-AG-A002 TCGA-AG-A011 TCGA-AG-A01L 
       53.62        26.17        20.98        37.02        12.00 

$`TNRC6B WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 
       22.06        32.71        27.09        22.52        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       24.16        21.76        24.69        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 
       20.28         7.04         3.02         1.02        35.01         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       61.02        78.08         6.05        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
        0.92        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       19.00        36.00         5.03        26.99        19.04        19.04 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A03F 
        2.01         5.03        14.01         0.92        41.00        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        0.72         5.79        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 
       88.21        49.41         6.77        12.10        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       32.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       12.43         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
        7.50        44.32       131.51       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 
       35.31       133.18        74.56        65.85        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       35.80        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A014 TCGA-AG-A015 
       13.94         6.02        25.97        23.01        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
        9.07        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  TNRC6B MUTATED TNRC6B WILD-TYPE 
            6.97             0.00 
  TNRC6B MUTATED TNRC6B WILD-TYPE 
          135.65           148.01 
  TNRC6B MUTATED TNRC6B WILD-TYPE 
           26.17            20.02 
[1] "7.0 - 135.7 (26.2)" "0.0 - 148.0 (20.0)"
[1] "hr=" "2.2"
D1648V2, continuous
D1648V3, binary
                  cls
clus                 0   1
  TNRC6B MUTATED    20   3
  TNRC6B WILD-TYPE 346 116
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TNRC6B MUTATED     20    3
  TNRC6B WILD-TYPE  346  116
        clus
vv       TNRC6B MUTATED TNRC6B WILD-TYPE
  COLON              20              346
  RECTUM              3              116
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TNRC6B MUTATED         4        0        4         7         1         0
  TNRC6B WILD-TYPE      87        1       28       131         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TNRC6B MUTATED           3          0          3          0        0
  TNRC6B WILD-TYPE        21         11         56         42       48
                  vv
clus               STAGE IVA STAGE IVB
  TNRC6B MUTATED           0         0
  TNRC6B WILD-TYPE        18         1
D1648V4, multiclass
            clus
vv           TNRC6B MUTATED TNRC6B WILD-TYPE
  STAGE I                 4               87
  STAGE IA                0                1
  STAGE II                4               28
  STAGE IIA               7              131
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               3               21
  STAGE IIIA              0               11
  STAGE IIIB              3               56
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  TNRC6B MUTATED     0   4  18   1
  TNRC6B WILD-TYPE  17  88 311  49
D1648V5, multiclass
    clus
vv   TNRC6B MUTATED TNRC6B WILD-TYPE
  T1              0               17
  T2              4               88
  T3             18              311
  T4              1               49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  TNRC6B MUTATED    18   4   1
  TNRC6B WILD-TYPE 269 109  86
D1648V6, multiclass
    clus
vv   TNRC6B MUTATED TNRC6B WILD-TYPE
  N0             18              269
  N1              4              109
  N2              1               86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1648V7, binary
                  cls
clus                 0   1
  TNRC6B MUTATED    22   0
  TNRC6B WILD-TYPE 353  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TNRC6B MUTATED     22    0
  TNRC6B WILD-TYPE  353   65
   clus
vv  TNRC6B MUTATED TNRC6B WILD-TYPE
  0             22              353
  1              0               65
[1] 2 2
[1] FALSE
D1648V8, binary
                  cls
clus                 0   1
  TNRC6B MUTATED     8  15
  TNRC6B WILD-TYPE 217 249
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TNRC6B MUTATED      8   15
  TNRC6B WILD-TYPE  217  249
        clus
vv       TNRC6B MUTATED TNRC6B WILD-TYPE
  FEMALE              8              217
  MALE               15              249
[1] 2 2
[1] FALSE
D1648V9, binary
                  cls
clus                 0   1
  TNRC6B MUTATED    21   0
  TNRC6B WILD-TYPE 329  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TNRC6B MUTATED     21    0
  TNRC6B WILD-TYPE  329   22
     clus
vv    TNRC6B MUTATED TNRC6B WILD-TYPE
  NO              21              329
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  TNRC6B MUTATED                     18                             1
  TNRC6B WILD-TYPE                  297                            46
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  TNRC6B MUTATED                       3                              0
  TNRC6B WILD-TYPE                   103                             10
D1648V10, multiclass
                                clus
vv                               TNRC6B MUTATED TNRC6B WILD-TYPE
  COLON ADENOCARCINOMA                       18              297
  COLON MUCINOUS ADENOCARCINOMA               1               46
  RECTAL ADENOCARCINOMA                       3              103
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  TNRC6B MUTATED    17   0   0   1
  TNRC6B WILD-TYPE 328   4  31  24
D1648V11, multiclass
    clus
vv   TNRC6B MUTATED TNRC6B WILD-TYPE
  R0             17              328
  R1              0                4
  R2              0               31
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1648V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TNRC6B MUTATED                                  0     1
  TNRC6B WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  TNRC6B MUTATED                           3     9
  TNRC6B WILD-TYPE                        19   217
D1648V13, multiclass
                                  clus
vv                                 TNRC6B MUTATED TNRC6B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     3               19
  WHITE                                         9              217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1649) Variable = PAK1 MUTATION ANALYSIS
D1649V1, survival
                sevent
clus2              0   1
  PAK1 MUTATED     9   0
  PAK1 WILD-TYPE 369  93
  PAK1 MUTATED PAK1 WILD-TYPE 
             9            462 
  PAK1 MUTATED PAK1 WILD-TYPE 
             0             93 
$`PAK1 MUTATED`
TCGA-AA-3947 TCGA-AA-A010 TCGA-AZ-4315 TCGA-CA-6717 TCGA-D5-6539 TCGA-DM-A28H 
       33.01        34.98        58.39        12.76        12.49       117.07 
TCGA-G4-6588 TCGA-G4-6628 TCGA-AG-3892 
       26.17        79.69        13.02 

$`PAK1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 
       31.00         2.01        12.99        24.00        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       33.01        21.44        17.82         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28K TCGA-F4-6459 
       81.37       119.93        35.97        60.79        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 
       13.78        35.80        91.79        46.75        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  PAK1 MUTATED PAK1 WILD-TYPE 
         12.49           0.00 
  PAK1 MUTATED PAK1 WILD-TYPE 
        117.07         148.01 
  PAK1 MUTATED PAK1 WILD-TYPE 
        33.010         20.085 
[1] "12.5 - 117.1 (33.0)" "0.0 - 148.0 (20.1)" 
[1] "hr="     "2.6e+07"
D1649V2, continuous
D1649V3, binary
                cls
clus               0   1
  PAK1 MUTATED    10   1
  PAK1 WILD-TYPE 356 118
[1] "tbl2"
                cls
clus             [,1] [,2]
  PAK1 MUTATED     10    1
  PAK1 WILD-TYPE  356  118
        clus
vv       PAK1 MUTATED PAK1 WILD-TYPE
  COLON            10            356
  RECTUM            1            118
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PAK1 MUTATED         2        0        1         4         2         0
  PAK1 WILD-TYPE      89        1       31       134         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PAK1 MUTATED           0          1          0          1        0         0
  PAK1 WILD-TYPE        24         10         59         41       48        18
                vv
clus             STAGE IVB
  PAK1 MUTATED           0
  PAK1 WILD-TYPE         1
D1649V4, multiclass
            clus
vv           PAK1 MUTATED PAK1 WILD-TYPE
  STAGE I               2             89
  STAGE IA              0              1
  STAGE II              1             31
  STAGE IIA             4            134
  STAGE IIB             2              8
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            1             10
  STAGE IIIB            0             59
  STAGE IIIC            1             41
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  PAK1 MUTATED     1   1   6   3
  PAK1 WILD-TYPE  16  91 323  47
D1649V5, multiclass
    clus
vv   PAK1 MUTATED PAK1 WILD-TYPE
  T1            1             16
  T2            1             91
  T3            6            323
  T4            3             47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  PAK1 MUTATED    10   0   1
  PAK1 WILD-TYPE 277 113  86
D1649V6, multiclass
    clus
vv   PAK1 MUTATED PAK1 WILD-TYPE
  N0           10            277
  N1            0            113
  N2            1             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1649V7, binary
                cls
clus               0   1
  PAK1 MUTATED    11   0
  PAK1 WILD-TYPE 364  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  PAK1 MUTATED     11    0
  PAK1 WILD-TYPE  364   65
   clus
vv  PAK1 MUTATED PAK1 WILD-TYPE
  0           11            364
  1            0             65
[1] 2 2
[1] FALSE
D1649V8, binary
                cls
clus               0   1
  PAK1 MUTATED     7   4
  PAK1 WILD-TYPE 218 260
[1] "tbl2"
                cls
clus             [,1] [,2]
  PAK1 MUTATED      7    4
  PAK1 WILD-TYPE  218  260
        clus
vv       PAK1 MUTATED PAK1 WILD-TYPE
  FEMALE            7            218
  MALE              4            260
[1] 2 2
[1] FALSE
D1649V9, binary
                cls
clus               0   1
  PAK1 MUTATED     8   0
  PAK1 WILD-TYPE 342  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  PAK1 MUTATED      8    0
  PAK1 WILD-TYPE  342   22
     clus
vv    PAK1 MUTATED PAK1 WILD-TYPE
  NO             8            342
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PAK1 MUTATED                      8                             2
  PAK1 WILD-TYPE                  307                            45
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PAK1 MUTATED                       1                              0
  PAK1 WILD-TYPE                   105                             10
D1649V10, multiclass
                                clus
vv                               PAK1 MUTATED PAK1 WILD-TYPE
  COLON ADENOCARCINOMA                      8            307
  COLON MUCINOUS ADENOCARCINOMA             2             45
  RECTAL ADENOCARCINOMA                     1            105
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  PAK1 MUTATED     9   0   0   1
  PAK1 WILD-TYPE 336   4  31  24
D1649V11, multiclass
    clus
vv   PAK1 MUTATED PAK1 WILD-TYPE
  R0            9            336
  R1            0              4
  R2            0             31
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1649V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PAK1 MUTATED                                  0     1
  PAK1 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  PAK1 MUTATED                           0     5
  PAK1 WILD-TYPE                        22   221
D1649V13, multiclass
                                  clus
vv                                 PAK1 MUTATED PAK1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       5            221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1650) Variable = PODXL MUTATION ANALYSIS
D1650V1, survival
                 sevent
clus2               0   1
  PODXL MUTATED     8   1
  PODXL WILD-TYPE 370  92
  PODXL MUTATED PODXL WILD-TYPE 
              9             462 
  PODXL MUTATED PODXL WILD-TYPE 
              1              92 
$`PODXL MUTATED`
TCGA-AA-3672 TCGA-AA-3811 TCGA-AA-3977 TCGA-AD-6548 TCGA-AZ-4315 TCGA-CM-6166 
        0.92        10.06        25.02        21.37        58.39        21.99 
TCGA-CM-6675 TCGA-DM-A28H TCGA-AF-2687 
       13.05       117.07        24.13 

$`PODXL WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
        6.05         6.97        54.02         2.01        14.01        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       18.05        40.96         0.07        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       29.03        16.04        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       14.04        11.01        12.95        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       35.97        60.79        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2689 TCGA-AF-2691 
       26.17        91.79        46.75        79.69        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  PODXL MUTATED PODXL WILD-TYPE 
           0.92            0.00 
  PODXL MUTATED PODXL WILD-TYPE 
         117.07          148.01 
  PODXL MUTATED PODXL WILD-TYPE 
         21.990          20.085 
[1] "0.9 - 117.1 (22.0)" "0.0 - 148.0 (20.1)"
[1] "hr=" "2.1"
D1650V2, continuous
D1650V3, binary
                 cls
clus                0   1
  PODXL MUTATED     9   1
  PODXL WILD-TYPE 357 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PODXL MUTATED      9    1
  PODXL WILD-TYPE  357  118
        clus
vv       PODXL MUTATED PODXL WILD-TYPE
  COLON              9             357
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PODXL MUTATED         2        0        0         1         1         0
  PODXL WILD-TYPE      89        1       32       137         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PODXL MUTATED           2          0          0          2        0         0
  PODXL WILD-TYPE        22         11         59         40       48        18
                 vv
clus              STAGE IVB
  PODXL MUTATED           1
  PODXL WILD-TYPE         0
D1650V4, multiclass
            clus
vv           PODXL MUTATED PODXL WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              1             137
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              2              22
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             2              40
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              1               0
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PODXL MUTATED     0   3   6   1
  PODXL WILD-TYPE  17  89 323  49
D1650V5, multiclass
    clus
vv   PODXL MUTATED PODXL WILD-TYPE
  T1             0              17
  T2             3              89
  T3             6             323
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  PODXL MUTATED     5   1   4
  PODXL WILD-TYPE 282 112  83
D1650V6, multiclass
    clus
vv   PODXL MUTATED PODXL WILD-TYPE
  N0             5             282
  N1             1             112
  N2             4              83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1650V7, binary
                 cls
clus                0   1
  PODXL MUTATED     7   1
  PODXL WILD-TYPE 368  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PODXL MUTATED      7    1
  PODXL WILD-TYPE  368   64
   clus
vv  PODXL MUTATED PODXL WILD-TYPE
  0             7             368
  1             1              64
[1] 2 2
[1] FALSE
D1650V8, binary
                 cls
clus                0   1
  PODXL MUTATED     5   5
  PODXL WILD-TYPE 220 259
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PODXL MUTATED      5    5
  PODXL WILD-TYPE  220  259
        clus
vv       PODXL MUTATED PODXL WILD-TYPE
  FEMALE             5             220
  MALE               5             259
[1] 2 2
[1] FALSE
D1650V9, binary
                 cls
clus                0   1
  PODXL MUTATED     7   1
  PODXL WILD-TYPE 343  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PODXL MUTATED      7    1
  PODXL WILD-TYPE  343   21
     clus
vv    PODXL MUTATED PODXL WILD-TYPE
  NO              7             343
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PODXL MUTATED                      9                             0
  PODXL WILD-TYPE                  306                            47
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PODXL MUTATED                       1                              0
  PODXL WILD-TYPE                   105                             10
D1650V10, multiclass
                                clus
vv                               PODXL MUTATED PODXL WILD-TYPE
  COLON ADENOCARCINOMA                       9             306
  COLON MUCINOUS ADENOCARCINOMA              0              47
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  PODXL MUTATED     7   0   0   1
  PODXL WILD-TYPE 338   4  31  24
D1650V11, multiclass
    clus
vv   PODXL MUTATED PODXL WILD-TYPE
  R0             7             338
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1650V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PODXL MUTATED                                  0     0
  PODXL WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PODXL MUTATED                           1     6
  PODXL WILD-TYPE                        21   220
D1650V13, multiclass
                                  clus
vv                                 PODXL MUTATED PODXL WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        6             220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1651) Variable = OR5AK2 MUTATION ANALYSIS
D1651V1, survival
                  sevent
clus2                0   1
  OR5AK2 MUTATED     5   4
  OR5AK2 WILD-TYPE 373  89
  OR5AK2 MUTATED OR5AK2 WILD-TYPE 
               9              462 
  OR5AK2 MUTATED OR5AK2 WILD-TYPE 
               4               89 
$`OR5AK2 MUTATED`
TCGA-AA-3496 TCGA-AA-3715 TCGA-AA-3947 TCGA-AA-A010 TCGA-AZ-4616 TCGA-CA-6718 
        1.02        19.04        33.01        34.98         5.13        10.06 
TCGA-DM-A1D7 TCGA-DM-A28K TCGA-F4-6808 
       13.32        98.24        33.67 

$`OR5AK2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 
       36.00         5.03        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       12.99        24.00        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82        58.39         1.41       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 
        3.25         3.29         0.07        12.20        12.76        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       92.75        49.91        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       35.97        60.79       117.07         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  OR5AK2 MUTATED OR5AK2 WILD-TYPE 
            1.02             0.00 
  OR5AK2 MUTATED OR5AK2 WILD-TYPE 
           98.24           148.01 
  OR5AK2 MUTATED OR5AK2 WILD-TYPE 
          19.040           20.235 
[1] "1.0 - 98.2 (19.0)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "2.4"
D1651V2, continuous
D1651V3, binary
                  cls
clus                 0   1
  OR5AK2 MUTATED     9   0
  OR5AK2 WILD-TYPE 357 119
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR5AK2 MUTATED      9    0
  OR5AK2 WILD-TYPE  357  119
        clus
vv       OR5AK2 MUTATED OR5AK2 WILD-TYPE
  COLON               9              357
  RECTUM              0              119
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  OR5AK2 MUTATED         1        0        2         3         2         0
  OR5AK2 WILD-TYPE      90        1       30       135         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  OR5AK2 MUTATED           0          0          0          0        1
  OR5AK2 WILD-TYPE        24         11         59         42       47
                  vv
clus               STAGE IVA STAGE IVB
  OR5AK2 MUTATED           0         0
  OR5AK2 WILD-TYPE        18         1
D1651V4, multiclass
            clus
vv           OR5AK2 MUTATED OR5AK2 WILD-TYPE
  STAGE I                 1               90
  STAGE IA                0                1
  STAGE II                2               30
  STAGE IIA               3              135
  STAGE IIB               2                8
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              0               59
  STAGE IIIC              0               42
  STAGE IV                1               47
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  OR5AK2 MUTATED     1   0   6   2
  OR5AK2 WILD-TYPE  16  92 323  48
D1651V5, multiclass
    clus
vv   OR5AK2 MUTATED OR5AK2 WILD-TYPE
  T1              1               16
  T2              0               92
  T3              6              323
  T4              2               48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  OR5AK2 MUTATED     8   0   1
  OR5AK2 WILD-TYPE 279 113  86
D1651V6, multiclass
    clus
vv   OR5AK2 MUTATED OR5AK2 WILD-TYPE
  N0              8              279
  N1              0              113
  N2              1               86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1651V7, binary
                  cls
clus                 0   1
  OR5AK2 MUTATED     8   1
  OR5AK2 WILD-TYPE 367  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR5AK2 MUTATED      8    1
  OR5AK2 WILD-TYPE  367   64
   clus
vv  OR5AK2 MUTATED OR5AK2 WILD-TYPE
  0              8              367
  1              1               64
[1] 2 2
[1] FALSE
D1651V8, binary
                  cls
clus                 0   1
  OR5AK2 MUTATED     5   4
  OR5AK2 WILD-TYPE 220 260
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR5AK2 MUTATED      5    4
  OR5AK2 WILD-TYPE  220  260
        clus
vv       OR5AK2 MUTATED OR5AK2 WILD-TYPE
  FEMALE              5              220
  MALE                4              260
[1] 2 2
[1] FALSE
D1651V9, binary
                  cls
clus                 0   1
  OR5AK2 MUTATED     6   0
  OR5AK2 WILD-TYPE 344  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR5AK2 MUTATED      6    0
  OR5AK2 WILD-TYPE  344   22
     clus
vv    OR5AK2 MUTATED OR5AK2 WILD-TYPE
  NO               6              344
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  OR5AK2 MUTATED                      6                             2
  OR5AK2 WILD-TYPE                  309                            45
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  OR5AK2 MUTATED                       0                              0
  OR5AK2 WILD-TYPE                   106                             10
D1651V10, multiclass
                                clus
vv                               OR5AK2 MUTATED OR5AK2 WILD-TYPE
  COLON ADENOCARCINOMA                        6              309
  COLON MUCINOUS ADENOCARCINOMA               2               45
  RECTAL ADENOCARCINOMA                       0              106
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  OR5AK2 MUTATED     5   0   0   1
  OR5AK2 WILD-TYPE 340   4  31  24
D1651V11, multiclass
    clus
vv   OR5AK2 MUTATED OR5AK2 WILD-TYPE
  R0              5              340
  R1              0                4
  R2              0               31
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1651V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OR5AK2 MUTATED                                  0     1
  OR5AK2 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  OR5AK2 MUTATED                           0     4
  OR5AK2 WILD-TYPE                        22   222
D1651V13, multiclass
                                  clus
vv                                 OR5AK2 MUTATED OR5AK2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         4              222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1652) Variable = LGALS9 MUTATION ANALYSIS
D1652V1, survival
                  sevent
clus2                0   1
  LGALS9 MUTATED     3   1
  LGALS9 WILD-TYPE 375  92
  LGALS9 MUTATED LGALS9 WILD-TYPE 
               4              467 
  LGALS9 MUTATED LGALS9 WILD-TYPE 
               1               92 
$`LGALS9 MUTATED`
TCGA-A6-5665 TCGA-AA-3492 TCGA-AA-3672 TCGA-D5-6930 
       22.06         3.02         0.92         1.51 

$`LGALS9 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 
       20.12        19.66        20.28         7.04         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
       54.02         2.01        14.01        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        4.80        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  LGALS9 MUTATED LGALS9 WILD-TYPE 
            0.92             0.00 
  LGALS9 MUTATED LGALS9 WILD-TYPE 
           22.06           148.01 
  LGALS9 MUTATED LGALS9 WILD-TYPE 
           2.265           20.280 
[1] "0.9 - 22.1 (2.3)"   "0.0 - 148.0 (20.3)"
[1] "hr=" "4.7"
D1652V2, continuous
D1652V3, binary
                  cls
clus                 0   1
  LGALS9 MUTATED     4   1
  LGALS9 WILD-TYPE 362 118
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LGALS9 MUTATED      4    1
  LGALS9 WILD-TYPE  362  118
        clus
vv       LGALS9 MUTATED LGALS9 WILD-TYPE
  COLON               4              362
  RECTUM              1              118
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  LGALS9 MUTATED         0        0        1         3         0         0
  LGALS9 WILD-TYPE      91        1       31       135        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  LGALS9 MUTATED           1          0          0          0        0
  LGALS9 WILD-TYPE        23         11         59         42       48
                  vv
clus               STAGE IVA STAGE IVB
  LGALS9 MUTATED           0         0
  LGALS9 WILD-TYPE        18         1
D1652V4, multiclass
            clus
vv           LGALS9 MUTATED LGALS9 WILD-TYPE
  STAGE I                 0               91
  STAGE IA                0                1
  STAGE II                1               31
  STAGE IIA               3              135
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               1               23
  STAGE IIIA              0               11
  STAGE IIIB              0               59
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  LGALS9 MUTATED     0   0   5   0
  LGALS9 WILD-TYPE  17  92 324  50
D1652V5, multiclass
    clus
vv   LGALS9 MUTATED LGALS9 WILD-TYPE
  T1              0               17
  T2              0               92
  T3              5              324
  T4              0               50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  LGALS9 MUTATED     4   1   0
  LGALS9 WILD-TYPE 283 112  87
D1652V6, multiclass
    clus
vv   LGALS9 MUTATED LGALS9 WILD-TYPE
  N0              4              283
  N1              1              112
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1652V7, binary
                  cls
clus                 0   1
  LGALS9 MUTATED     5   0
  LGALS9 WILD-TYPE 370  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LGALS9 MUTATED      5    0
  LGALS9 WILD-TYPE  370   65
   clus
vv  LGALS9 MUTATED LGALS9 WILD-TYPE
  0              5              370
  1              0               65
[1] 2 2
[1] FALSE
D1652V8, binary
                  cls
clus                 0   1
  LGALS9 MUTATED     4   1
  LGALS9 WILD-TYPE 221 263
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LGALS9 MUTATED      4    1
  LGALS9 WILD-TYPE  221  263
        clus
vv       LGALS9 MUTATED LGALS9 WILD-TYPE
  FEMALE              4              221
  MALE                1              263
[1] 2 2
[1] FALSE
D1652V9, binary
                  cls
clus                 0   1
  LGALS9 MUTATED     3   0
  LGALS9 WILD-TYPE 347  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LGALS9 MUTATED      3    0
  LGALS9 WILD-TYPE  347   22
     clus
vv    LGALS9 MUTATED LGALS9 WILD-TYPE
  NO               3              347
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  LGALS9 MUTATED                      3                             1
  LGALS9 WILD-TYPE                  312                            46
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  LGALS9 MUTATED                       1                              0
  LGALS9 WILD-TYPE                   105                             10
D1652V10, multiclass
                                clus
vv                               LGALS9 MUTATED LGALS9 WILD-TYPE
  COLON ADENOCARCINOMA                        3              312
  COLON MUCINOUS ADENOCARCINOMA               1               46
  RECTAL ADENOCARCINOMA                       1              105
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  LGALS9 MUTATED     5   0   0   0
  LGALS9 WILD-TYPE 340   4  31  25
D1652V11, multiclass
    clus
vv   LGALS9 MUTATED LGALS9 WILD-TYPE
  R0              5              340
  R1              0                4
  R2              0               31
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1652V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  LGALS9 MUTATED                                  0     0
  LGALS9 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  LGALS9 MUTATED                           0     2
  LGALS9 WILD-TYPE                        22   224
D1652V13, multiclass
[1] "Remove cluster labels:" "LGALS9 MUTATED"        
clus
  LGALS9 MUTATED LGALS9 WILD-TYPE 
               2              258 
      TCGA-A6-2671       TCGA-A6-2672       TCGA-A6-2674       TCGA-A6-2676 
"LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" 
      TCGA-A6-2677       TCGA-A6-2678       TCGA-A6-2683       TCGA-A6-3807 
"LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" 
      TCGA-A6-3808       TCGA-A6-3809       TCGA-A6-3810       TCGA-A6-4105 
"LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" 
      TCGA-A6-5656       TCGA-A6-5657       TCGA-A6-5659       TCGA-A6-5660 
"LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" 
      TCGA-A6-5661       TCGA-A6-5662       TCGA-A6-5664       TCGA-A6-5666 
"LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" 
      TCGA-A6-6137       TCGA-A6-6138       TCGA-A6-6141       TCGA-A6-6142 
"LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" 
      TCGA-A6-6648       TCGA-A6-6649       TCGA-A6-6651       TCGA-A6-6652 
"LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" 
      TCGA-A6-6653       TCGA-A6-6654       TCGA-A6-6780       TCGA-A6-6781 
"LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" 
      TCGA-A6-6782       TCGA-AD-5900       TCGA-AD-6548       TCGA-AD-6888 
"LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" 
      TCGA-AD-6889       TCGA-AD-6890       TCGA-AD-6895       TCGA-AD-6899 
"LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" 
      TCGA-AD-6901       TCGA-AD-6963       TCGA-AD-6964       TCGA-AD-6965 
"LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" 
      TCGA-AU-3779       TCGA-AU-6004       TCGA-AY-4070       TCGA-AY-4071 
"LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" 
      TCGA-AY-5543       TCGA-AY-6196       TCGA-AY-6197       TCGA-AY-6386 
"LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" 
      TCGA-AZ-4315       TCGA-AZ-4323       TCGA-AZ-4616       TCGA-AZ-4681 
"LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" 
      TCGA-AZ-4682       TCGA-AZ-5403       TCGA-AZ-5407       TCGA-AZ-6598 
"LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" 
      TCGA-AZ-6599       TCGA-AZ-6600       TCGA-AZ-6601       TCGA-AZ-6603 
"LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" 
      TCGA-AZ-6605       TCGA-AZ-6606       TCGA-AZ-6607       TCGA-AZ-6608 
"LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" 
      TCGA-CA-5254       TCGA-CA-5255       TCGA-CA-5796       TCGA-CA-5797 
"LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" 
      TCGA-CA-6715       TCGA-CA-6716       TCGA-CA-6717       TCGA-CA-6718 
"LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" 
      TCGA-CA-6719       TCGA-CK-4947       TCGA-CK-4948       TCGA-CK-4950 
"LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" 
      TCGA-CK-4952       TCGA-CK-5912       TCGA-CK-5913       TCGA-CK-5914 
"LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" 
      TCGA-CK-5915       TCGA-CK-5916       TCGA-CK-6746       TCGA-CK-6747 
"LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" 
      TCGA-CK-6748       TCGA-CK-6751       TCGA-CM-4743       TCGA-CM-4744 
"LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" 
      TCGA-CM-4746       TCGA-CM-4747       TCGA-CM-4752       TCGA-CM-5341 
"LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" 
      TCGA-CM-5344       TCGA-CM-5348       TCGA-CM-5349       TCGA-CM-5860 
"LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" 
      TCGA-CM-5861       TCGA-CM-5862       TCGA-CM-5863       TCGA-CM-5864 
"LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" 
      TCGA-CM-5868       TCGA-CM-6161       TCGA-CM-6162       TCGA-CM-6163 
"LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" 
      TCGA-CM-6164       TCGA-CM-6165       TCGA-CM-6166       TCGA-CM-6167 
"LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" 
      TCGA-CM-6168       TCGA-CM-6169       TCGA-CM-6170       TCGA-CM-6171 
"LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" 
      TCGA-CM-6172       TCGA-CM-6674       TCGA-CM-6675       TCGA-CM-6676 
"LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" 
      TCGA-CM-6677       TCGA-CM-6678       TCGA-CM-6679       TCGA-CM-6680 
"LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" 
      TCGA-D5-5537       TCGA-D5-5538       TCGA-D5-5539       TCGA-D5-5540 
"LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" 
      TCGA-D5-5541       TCGA-D5-6529       TCGA-D5-6532       TCGA-D5-6533 
"LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" 
      TCGA-D5-6534       TCGA-D5-6535       TCGA-D5-6536       TCGA-D5-6537 
"LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" 
      TCGA-D5-6538       TCGA-D5-6539       TCGA-D5-6540       TCGA-D5-6541 
"LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" 
      TCGA-D5-6898       TCGA-D5-6920       TCGA-D5-6922       TCGA-D5-6923 
"LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" 
      TCGA-D5-6924       TCGA-D5-6926       TCGA-D5-6927       TCGA-D5-6928 
"LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" 
      TCGA-D5-6929       TCGA-D5-6931       TCGA-D5-6932       TCGA-D5-7000 
"LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" 
      TCGA-DM-A0X9       TCGA-DM-A0XD       TCGA-DM-A0XF       TCGA-DM-A1D0 
"LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" 
      TCGA-DM-A1D4       TCGA-DM-A1D6       TCGA-DM-A1D7       TCGA-DM-A1D8 
"LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" 
      TCGA-DM-A1D9       TCGA-DM-A1DA       TCGA-DM-A1DB       TCGA-DM-A1HA 
"LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" 
      TCGA-DM-A1HB       TCGA-DM-A282       TCGA-DM-A285       TCGA-DM-A28C 
"LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" 
      TCGA-DM-A28E       TCGA-DM-A28F       TCGA-DM-A28G       TCGA-DM-A28H 
"LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" 
      TCGA-DM-A28K       TCGA-F4-6459       TCGA-F4-6460       TCGA-F4-6569 
"LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" 
      TCGA-F4-6570       TCGA-F4-6703       TCGA-F4-6704       TCGA-F4-6805 
"LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" 
      TCGA-F4-6806       TCGA-F4-6807       TCGA-F4-6808       TCGA-F4-6809 
"LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" 
      TCGA-F4-6854       TCGA-F4-6855       TCGA-F4-6856       TCGA-G4-6293 
"LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" 
      TCGA-G4-6299       TCGA-G4-6303       TCGA-G4-6304       TCGA-G4-6306 
"LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" 
      TCGA-G4-6307       TCGA-G4-6309       TCGA-G4-6310       TCGA-G4-6315 
"LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" 
      TCGA-G4-6317       TCGA-G4-6321       TCGA-G4-6323       TCGA-G4-6586 
"LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" 
      TCGA-G4-6588       TCGA-G4-6625       TCGA-G4-6626       TCGA-G4-6628 
"LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" 
      TCGA-AF-2687       TCGA-AF-2689       TCGA-AF-2691       TCGA-AF-2692 
"LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" 
      TCGA-AF-2693       TCGA-AF-3400       TCGA-AF-3913       TCGA-AF-4110 
"LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" 
      TCGA-AF-5654       TCGA-AF-6136       TCGA-AF-6655       TCGA-AF-6672 
"LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" 
      TCGA-AH-6544       TCGA-AH-6547       TCGA-AH-6549       TCGA-AH-6643 
"LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" 
      TCGA-AH-6644       TCGA-CI-6619       TCGA-CI-6620       TCGA-CI-6621 
"LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" 
      TCGA-CI-6622       TCGA-CI-6624       TCGA-CL-5917       TCGA-CL-5918 
"LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" 
      TCGA-DC-5337       TCGA-DC-5869       TCGA-DC-6155       TCGA-DC-6157 
"LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" 
      TCGA-DC-6158       TCGA-DC-6160       TCGA-DC-6681       TCGA-DC-6682 
"LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" 
      TCGA-DC-6683       TCGA-DT-5265       TCGA-DY-A0XA       TCGA-DY-A1DC 
"LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" 
      TCGA-DY-A1DD       TCGA-DY-A1DF       TCGA-DY-A1DG       TCGA-DY-A1H8 
"LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" 
      TCGA-EF-5830       TCGA-EI-6506       TCGA-EI-6507       TCGA-EI-6508 
"LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" 
      TCGA-EI-6510       TCGA-F5-6464       TCGA-F5-6465       TCGA-F5-6571 
"LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" 
      TCGA-F5-6702       TCGA-F5-6811       TCGA-F5-6812       TCGA-F5-6813 
"LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" 
      TCGA-G5-6235       TCGA-G5-6641 
"LGALS9 WILD-TYPE" "LGALS9 WILD-TYPE" 

Clustering(1653) Variable = IRGQ MUTATION ANALYSIS
D1653V1, survival
                sevent
clus2              0   1
  IRGQ MUTATED     5   0
  IRGQ WILD-TYPE 373  93
  IRGQ MUTATED IRGQ WILD-TYPE 
             5            466 
  IRGQ MUTATED IRGQ WILD-TYPE 
             0             93 
$`IRGQ MUTATED`
TCGA-A6-6653 TCGA-AA-3672 TCGA-G4-6588 TCGA-EF-5830 TCGA-EI-6507 
       24.39         0.92        26.17         0.49        19.96 

$`IRGQ WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
       25.08        25.18        24.16        21.76        24.69        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 
        6.97        54.02         2.01        14.01        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EI-6506 TCGA-EI-6508 
       57.24        24.13        51.48        32.61        20.55        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  IRGQ MUTATED IRGQ WILD-TYPE 
          0.49           0.00 
  IRGQ MUTATED IRGQ WILD-TYPE 
         26.17         148.01 
  IRGQ MUTATED IRGQ WILD-TYPE 
        19.960         20.235 
[1] "0.5 - 26.2 (20.0)"  "0.0 - 148.0 (20.2)"
[1] "hr="     "3300000"
D1653V2, continuous
D1653V3, binary
                cls
clus               0   1
  IRGQ MUTATED     3   2
  IRGQ WILD-TYPE 363 117
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRGQ MUTATED      3    2
  IRGQ WILD-TYPE  363  117
        clus
vv       IRGQ MUTATED IRGQ WILD-TYPE
  COLON             3            363
  RECTUM            2            117
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  IRGQ MUTATED         1        0        0         2         1         0
  IRGQ WILD-TYPE      90        1       32       136         9         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  IRGQ MUTATED           1          0          0          0        0         0
  IRGQ WILD-TYPE        23         11         59         42       48        18
                vv
clus             STAGE IVB
  IRGQ MUTATED           0
  IRGQ WILD-TYPE         1
D1653V4, multiclass
            clus
vv           IRGQ MUTATED IRGQ WILD-TYPE
  STAGE I               1             90
  STAGE IA              0              1
  STAGE II              0             32
  STAGE IIA             2            136
  STAGE IIB             1              9
  STAGE IIC             0              1
  STAGE III             1             23
  STAGE IIIA            0             11
  STAGE IIIB            0             59
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  IRGQ MUTATED     0   1   3   1
  IRGQ WILD-TYPE  17  91 326  49
D1653V5, multiclass
    clus
vv   IRGQ MUTATED IRGQ WILD-TYPE
  T1            0             17
  T2            1             91
  T3            3            326
  T4            1             49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  IRGQ MUTATED     4   1   0
  IRGQ WILD-TYPE 283 112  87
D1653V6, multiclass
    clus
vv   IRGQ MUTATED IRGQ WILD-TYPE
  N0            4            283
  N1            1            112
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1653V7, binary
                cls
clus               0   1
  IRGQ MUTATED     5   0
  IRGQ WILD-TYPE 370  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRGQ MUTATED      5    0
  IRGQ WILD-TYPE  370   65
   clus
vv  IRGQ MUTATED IRGQ WILD-TYPE
  0            5            370
  1            0             65
[1] 2 2
[1] FALSE
D1653V8, binary
                cls
clus               0   1
  IRGQ MUTATED     2   3
  IRGQ WILD-TYPE 223 261
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRGQ MUTATED      2    3
  IRGQ WILD-TYPE  223  261
        clus
vv       IRGQ MUTATED IRGQ WILD-TYPE
  FEMALE            2            223
  MALE              3            261
[1] 2 2
[1] FALSE
D1653V9, binary
                cls
clus               0   1
  IRGQ MUTATED     4   0
  IRGQ WILD-TYPE 346  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRGQ MUTATED      4    0
  IRGQ WILD-TYPE  346   22
     clus
vv    IRGQ MUTATED IRGQ WILD-TYPE
  NO             4            346
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  IRGQ MUTATED                      3                             0
  IRGQ WILD-TYPE                  312                            47
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  IRGQ MUTATED                       2                              0
  IRGQ WILD-TYPE                   104                             10
D1653V10, multiclass
                                clus
vv                               IRGQ MUTATED IRGQ WILD-TYPE
  COLON ADENOCARCINOMA                      3            312
  COLON MUCINOUS ADENOCARCINOMA             0             47
  RECTAL ADENOCARCINOMA                     2            104
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  IRGQ MUTATED     4   0   0   0
  IRGQ WILD-TYPE 341   4  31  25
D1653V11, multiclass
    clus
vv   IRGQ MUTATED IRGQ WILD-TYPE
  R0            4            341
  R1            0              4
  R2            0             31
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1653V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  IRGQ MUTATED                                  0     0
  IRGQ WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  IRGQ MUTATED                           0     4
  IRGQ WILD-TYPE                        22   222
D1653V13, multiclass
                                  clus
vv                                 IRGQ MUTATED IRGQ WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       4            222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1654) Variable = NLRP1 MUTATION ANALYSIS
D1654V1, survival
                 sevent
clus2               0   1
  NLRP1 MUTATED    26   2
  NLRP1 WILD-TYPE 352  91
  NLRP1 MUTATED NLRP1 WILD-TYPE 
             28             443 
  NLRP1 MUTATED NLRP1 WILD-TYPE 
              2              91 
$`NLRP1 MUTATED`
TCGA-AA-3510 TCGA-AA-3525 TCGA-AA-3534 TCGA-AA-3821 TCGA-AA-3833 TCGA-AA-3977 
       63.98         8.05        29.00         1.02        15.95        25.02 
TCGA-AA-A00D TCGA-AA-A00N TCGA-AA-A010 TCGA-AD-6889 TCGA-AZ-4315 TCGA-CA-6717 
       19.00         4.01        34.98        56.55        58.39        12.76 
TCGA-CA-6719 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CM-6162 TCGA-CM-6171 
       14.30         9.99        21.14        82.95        12.00        14.04 
TCGA-D5-5538 TCGA-G4-6293 TCGA-G4-6628 TCGA-AG-3731 TCGA-AG-3892 TCGA-AG-4007 
       12.26       133.18        79.69        37.02        13.02         1.02 
TCGA-AG-A011 TCGA-CL-5917 TCGA-DC-5337 TCGA-DY-A0XA 
       37.02        78.12        15.02       126.44 

$`NLRP1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3526 
        1.02         9.07        24.03        37.05        36.03        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3538 TCGA-AA-3542 
        0.00        19.07        34.03        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3837 TCGA-AA-3842 
       33.04         0.99        25.02        17.98        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       13.94        38.04        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 
       18.05        40.96         0.07        21.37        15.52         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CK-4947 
        3.25         3.29         0.07        12.20        10.06        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-6748 
      148.01        85.45        15.62        49.08        51.32         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 
        5.03        15.02        15.02        17.03        15.02         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       15.02        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5539 TCGA-D5-5540 
       11.01        10.06        12.03        45.40        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       26.17        91.79        46.75        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
        0.99        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 
        1.02        17.95        36.95        17.03        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       23.01        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5918 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
        7.17         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD 
        5.95         4.01         5.03         5.29        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  NLRP1 MUTATED NLRP1 WILD-TYPE 
           1.02            0.00 
  NLRP1 MUTATED NLRP1 WILD-TYPE 
         133.18          148.01 
  NLRP1 MUTATED NLRP1 WILD-TYPE 
          20.07           20.19 
[1] "1.0 - 133.2 (20.1)" "0.0 - 148.0 (20.2)"
[1] "hr=" "3.9"
D1654V2, continuous
D1654V3, binary
                 cls
clus                0   1
  NLRP1 MUTATED    21   7
  NLRP1 WILD-TYPE 345 112
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NLRP1 MUTATED     21    7
  NLRP1 WILD-TYPE  345  112
        clus
vv       NLRP1 MUTATED NLRP1 WILD-TYPE
  COLON             21             345
  RECTUM             7             112
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NLRP1 MUTATED         7        0        1         9         2         0
  NLRP1 WILD-TYPE      84        1       31       129         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NLRP1 MUTATED           1          0          4          1        2         0
  NLRP1 WILD-TYPE        23         11         55         41       46        18
                 vv
clus              STAGE IVB
  NLRP1 MUTATED           0
  NLRP1 WILD-TYPE         1
D1654V4, multiclass
            clus
vv           NLRP1 MUTATED NLRP1 WILD-TYPE
  STAGE I                7              84
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              9             129
  STAGE IIB              2               8
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             4              55
  STAGE IIIC             1              41
  STAGE IV               2              46
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  NLRP1 MUTATED     3   5  17   3
  NLRP1 WILD-TYPE  14  87 312  47
D1654V5, multiclass
    clus
vv   NLRP1 MUTATED NLRP1 WILD-TYPE
  T1             3              14
  T2             5              87
  T3            17             312
  T4             3              47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  NLRP1 MUTATED    20   6   2
  NLRP1 WILD-TYPE 267 107  85
D1654V6, multiclass
    clus
vv   NLRP1 MUTATED NLRP1 WILD-TYPE
  N0            20             267
  N1             6             107
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1654V7, binary
                 cls
clus                0   1
  NLRP1 MUTATED    22   2
  NLRP1 WILD-TYPE 353  63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NLRP1 MUTATED     22    2
  NLRP1 WILD-TYPE  353   63
   clus
vv  NLRP1 MUTATED NLRP1 WILD-TYPE
  0            22             353
  1             2              63
[1] 2 2
[1] FALSE
D1654V8, binary
                 cls
clus                0   1
  NLRP1 MUTATED    13  15
  NLRP1 WILD-TYPE 212 249
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NLRP1 MUTATED     13   15
  NLRP1 WILD-TYPE  212  249
        clus
vv       NLRP1 MUTATED NLRP1 WILD-TYPE
  FEMALE            13             212
  MALE              15             249
[1] 2 2
[1] FALSE
D1654V9, binary
                 cls
clus                0   1
  NLRP1 MUTATED    23   0
  NLRP1 WILD-TYPE 327  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NLRP1 MUTATED     23    0
  NLRP1 WILD-TYPE  327   22
     clus
vv    NLRP1 MUTATED NLRP1 WILD-TYPE
  NO             23             327
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  NLRP1 MUTATED                     17                             4
  NLRP1 WILD-TYPE                  298                            43
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  NLRP1 MUTATED                       7                              0
  NLRP1 WILD-TYPE                    99                             10
D1654V10, multiclass
                                clus
vv                               NLRP1 MUTATED NLRP1 WILD-TYPE
  COLON ADENOCARCINOMA                      17             298
  COLON MUCINOUS ADENOCARCINOMA              4              43
  RECTAL ADENOCARCINOMA                      7              99
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  NLRP1 MUTATED    17   0   2   6
  NLRP1 WILD-TYPE 328   4  29  19
D1654V11, multiclass
    clus
vv   NLRP1 MUTATED NLRP1 WILD-TYPE
  R0            17             328
  R1             0               4
  R2             2              29
  RX             6              19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1654V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NLRP1 MUTATED                                  0     3
  NLRP1 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  NLRP1 MUTATED                           0    12
  NLRP1 WILD-TYPE                        22   214
D1654V13, multiclass
                                  clus
vv                                 NLRP1 MUTATED NLRP1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        3               8
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                       12             214
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1655) Variable = TPR MUTATION ANALYSIS
D1655V1, survival
               sevent
clus2             0   1
  TPR MUTATED    21   3
  TPR WILD-TYPE 357  90
  TPR MUTATED TPR WILD-TYPE 
           24           447 
  TPR MUTATED TPR WILD-TYPE 
            3            90 
$`TPR MUTATED`
TCGA-A6-5666 TCGA-A6-6141 TCGA-A6-6781 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3679 
       32.71         8.38        19.66         3.02         1.02        15.02 
TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3864 TCGA-AA-3941 TCGA-AA-3966 TCGA-AA-3977 
       26.99        10.06        53.00        24.00         2.01        25.02 
TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01R TCGA-AZ-4681 TCGA-CA-5254 TCGA-CA-6717 
        4.01        34.98        35.01       106.75        12.69        12.76 
TCGA-CM-4746 TCGA-CM-5861 TCGA-DM-A28H TCGA-G4-6299 TCGA-G4-6309 TCGA-AG-A002 
       37.02        15.02       117.07        74.56        85.48        20.98 

$`TPR WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 
       22.09        22.06        27.09        22.52        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
       20.28         7.04        35.01        63.98         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
       13.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       36.03         8.05        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       78.08         6.05         6.97        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
        0.92        50.04        47.01        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
       19.00        36.00         5.03        85.05        19.04        19.04 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 
        0.99        31.07        31.07        30.05        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T 
       31.00        31.00        38.07         1.02         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 
       21.44        17.82        58.39         1.41         5.13        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5255 
       29.56         5.23        11.74         3.19         1.61         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07        12.20        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       20.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       30.08        32.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
       60.79        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6303 
       13.25         0.53        47.41        35.31       133.18        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       53.62        44.68        55.04        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  TPR MUTATED TPR WILD-TYPE 
         1.02          0.00 
  TPR MUTATED TPR WILD-TYPE 
       117.07        148.01 
  TPR MUTATED TPR WILD-TYPE 
        22.49         20.12 
[1] "1.0 - 117.1 (22.5)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.9"
D1655V2, continuous
D1655V3, binary
               cls
clus              0   1
  TPR MUTATED    24   1
  TPR WILD-TYPE 342 118
[1] "tbl2"
               cls
clus            [,1] [,2]
  TPR MUTATED     24    1
  TPR WILD-TYPE  342  118
        clus
vv       TPR MUTATED TPR WILD-TYPE
  COLON           24           342
  RECTUM           1           118
[1] 2 2
[1] FALSE
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TPR MUTATED         2        0        3         8         2         1
  TPR WILD-TYPE      89        1       29       130         8         0
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TPR MUTATED           2          0          1          3        1         1
  TPR WILD-TYPE        22         11         58         39       47        17
               vv
clus            STAGE IVB
  TPR MUTATED           0
  TPR WILD-TYPE         1
D1655V4, multiclass
            clus
vv           TPR MUTATED TPR WILD-TYPE
  STAGE I              2            89
  STAGE IA             0             1
  STAGE II             3            29
  STAGE IIA            8           130
  STAGE IIB            2             8
  STAGE IIC            1             0
  STAGE III            2            22
  STAGE IIIA           0            11
  STAGE IIIB           1            58
  STAGE IIIC           3            39
  STAGE IV             1            47
  STAGE IVA            1            17
  STAGE IVB            0             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  TPR MUTATED     0   3  17   5
  TPR WILD-TYPE  17  89 312  45
D1655V5, multiclass
    clus
vv   TPR MUTATED TPR WILD-TYPE
  T1           0            17
  T2           3            89
  T3          17           312
  T4           5            45
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2
  TPR MUTATED    17   3   5
  TPR WILD-TYPE 270 110  82
D1655V6, multiclass
    clus
vv   TPR MUTATED TPR WILD-TYPE
  N0          17           270
  N1           3           110
  N2           5            82
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1655V7, binary
               cls
clus              0   1
  TPR MUTATED    21   2
  TPR WILD-TYPE 354  63
[1] "tbl2"
               cls
clus            [,1] [,2]
  TPR MUTATED     21    2
  TPR WILD-TYPE  354   63
   clus
vv  TPR MUTATED TPR WILD-TYPE
  0          21           354
  1           2            63
[1] 2 2
[1] FALSE
D1655V8, binary
               cls
clus              0   1
  TPR MUTATED    12  13
  TPR WILD-TYPE 213 251
[1] "tbl2"
               cls
clus            [,1] [,2]
  TPR MUTATED     12   13
  TPR WILD-TYPE  213  251
        clus
vv       TPR MUTATED TPR WILD-TYPE
  FEMALE          12           213
  MALE            13           251
[1] 2 2
[1] FALSE
D1655V9, binary
               cls
clus              0   1
  TPR MUTATED    19   1
  TPR WILD-TYPE 331  21
[1] "tbl2"
               cls
clus            [,1] [,2]
  TPR MUTATED     19    1
  TPR WILD-TYPE  331   21
     clus
vv    TPR MUTATED TPR WILD-TYPE
  NO           19           331
  YES           1            21
[1] 2 2
[1] FALSE
               vv
clus            COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  TPR MUTATED                     19                             5
  TPR WILD-TYPE                  296                            42
               vv
clus            RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  TPR MUTATED                       1                              0
  TPR WILD-TYPE                   105                             10
D1655V10, multiclass
                                clus
vv                               TPR MUTATED TPR WILD-TYPE
  COLON ADENOCARCINOMA                    19           296
  COLON MUCINOUS ADENOCARCINOMA            5            42
  RECTAL ADENOCARCINOMA                    1           105
  RECTAL MUCINOUS ADENOCARCINOMA           0            10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             R0  R1  R2  RX
  TPR MUTATED    17   0   1   2
  TPR WILD-TYPE 328   4  30  23
D1655V11, multiclass
    clus
vv   TPR MUTATED TPR WILD-TYPE
  R0          17           328
  R1           0             4
  R2           1            30
  RX           2            23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1655V12, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TPR MUTATED                                  0     2
  TPR WILD-TYPE                                1     9
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  TPR MUTATED                           3     6
  TPR WILD-TYPE                        19   220
D1655V13, multiclass
                                  clus
vv                                 TPR MUTATED TPR WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      2             9
  BLACK OR AFRICAN AMERICAN                  3            19
  WHITE                                      6           220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1656) Variable = METT5D1 MUTATION ANALYSIS
D1656V1, survival
                   sevent
clus2                 0   1
  METT5D1 MUTATED     7   0
  METT5D1 WILD-TYPE 371  93
  METT5D1 MUTATED METT5D1 WILD-TYPE 
                7               464 
  METT5D1 MUTATED METT5D1 WILD-TYPE 
                0                93 
$`METT5D1 MUTATED`
TCGA-AA-3966 TCGA-AY-6197 TCGA-DM-A1HB TCGA-DM-A282 TCGA-G4-6299 TCGA-G4-6306 
        2.01        21.44       135.65       139.17        74.56        44.68 
TCGA-AF-4110 
       14.50 

$`METT5D1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 
       24.00         2.01        20.98        34.03        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        33.01        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6303 TCGA-G4-6304 
        0.53        47.41        35.31       133.18        65.85        53.62 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       10.39        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  METT5D1 MUTATED METT5D1 WILD-TYPE 
             2.01              0.00 
  METT5D1 MUTATED METT5D1 WILD-TYPE 
           139.17            148.01 
  METT5D1 MUTATED METT5D1 WILD-TYPE 
           44.680            20.085 
[1] "2.0 - 139.2 (44.7)" "0.0 - 148.0 (20.1)"
[1] "hr="     "2.6e+07"
D1656V2, continuous
D1656V3, binary
                   cls
clus                  0   1
  METT5D1 MUTATED     6   0
  METT5D1 WILD-TYPE 360 119
[1] "tbl2"
                   cls
clus                [,1] [,2]
  METT5D1 MUTATED      6    0
  METT5D1 WILD-TYPE  360  119
        clus
vv       METT5D1 MUTATED METT5D1 WILD-TYPE
  COLON                6               360
  RECTUM               0               119
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  METT5D1 MUTATED         0        0        0         4         0         0
  METT5D1 WILD-TYPE      91        1       32       134        10         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  METT5D1 MUTATED           0          0          1          1        0
  METT5D1 WILD-TYPE        24         11         58         41       48
                   vv
clus                STAGE IVA STAGE IVB
  METT5D1 MUTATED           1         0
  METT5D1 WILD-TYPE        17         1
D1656V4, multiclass
            clus
vv           METT5D1 MUTATED METT5D1 WILD-TYPE
  STAGE I                  0                91
  STAGE IA                 0                 1
  STAGE II                 0                32
  STAGE IIA                4               134
  STAGE IIB                0                10
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               0                11
  STAGE IIIB               1                58
  STAGE IIIC               1                41
  STAGE IV                 0                48
  STAGE IVA                1                17
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  METT5D1 MUTATED     0   1   5   1
  METT5D1 WILD-TYPE  17  91 324  49
D1656V5, multiclass
    clus
vv   METT5D1 MUTATED METT5D1 WILD-TYPE
  T1               0                17
  T2               1                91
  T3               5               324
  T4               1                49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  METT5D1 MUTATED     4   1   2
  METT5D1 WILD-TYPE 283 112  85
D1656V6, multiclass
    clus
vv   METT5D1 MUTATED METT5D1 WILD-TYPE
  N0               4               283
  N1               1               112
  N2               2                85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1656V7, binary
                   cls
clus                  0   1
  METT5D1 MUTATED     5   0
  METT5D1 WILD-TYPE 370  65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  METT5D1 MUTATED      5    0
  METT5D1 WILD-TYPE  370   65
   clus
vv  METT5D1 MUTATED METT5D1 WILD-TYPE
  0               5               370
  1               0                65
[1] 2 2
[1] FALSE
D1656V8, binary
                   cls
clus                  0   1
  METT5D1 MUTATED     2   5
  METT5D1 WILD-TYPE 223 259
[1] "tbl2"
                   cls
clus                [,1] [,2]
  METT5D1 MUTATED      2    5
  METT5D1 WILD-TYPE  223  259
        clus
vv       METT5D1 MUTATED METT5D1 WILD-TYPE
  FEMALE               2               223
  MALE                 5               259
[1] 2 2
[1] FALSE
D1656V9, binary
                   cls
clus                  0   1
  METT5D1 MUTATED     4   0
  METT5D1 WILD-TYPE 346  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  METT5D1 MUTATED      4    0
  METT5D1 WILD-TYPE  346   22
     clus
vv    METT5D1 MUTATED METT5D1 WILD-TYPE
  NO                4               346
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  METT5D1 MUTATED                      4                             1
  METT5D1 WILD-TYPE                  311                            46
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  METT5D1 MUTATED                       0                              0
  METT5D1 WILD-TYPE                   106                             10
D1656V10, multiclass
                                clus
vv                               METT5D1 MUTATED METT5D1 WILD-TYPE
  COLON ADENOCARCINOMA                         4               311
  COLON MUCINOUS ADENOCARCINOMA                1                46
  RECTAL ADENOCARCINOMA                        0               106
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  METT5D1 MUTATED     4   0   0   0
  METT5D1 WILD-TYPE 341   4  31  25
D1656V11, multiclass
    clus
vv   METT5D1 MUTATED METT5D1 WILD-TYPE
  R0               4               341
  R1               0                 4
  R2               0                31
  RX               0                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1656V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  METT5D1 MUTATED                                  0     0
  METT5D1 WILD-TYPE                                1    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  METT5D1 MUTATED                           0     6
  METT5D1 WILD-TYPE                        22   220
D1656V13, multiclass
                                  clus
vv                                 METT5D1 MUTATED METT5D1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                      0                22
  WHITE                                          6               220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1657) Variable = BCAP29 MUTATION ANALYSIS
D1657V1, survival
                  sevent
clus2                0   1
  BCAP29 MUTATED     8   0
  BCAP29 WILD-TYPE 370  93
  BCAP29 MUTATED BCAP29 WILD-TYPE 
               8              463 
  BCAP29 MUTATED BCAP29 WILD-TYPE 
               0               93 
$`BCAP29 MUTATED`
TCGA-AA-3713 TCGA-AA-3977 TCGA-AD-5900 TCGA-CA-6717 TCGA-CK-4948 TCGA-CM-6675 
       19.04        25.02         0.07        12.76       148.01        13.05 
TCGA-DM-A28K TCGA-DT-5265 
       98.24         5.29 

$`BCAP29 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       39.98        18.05        40.96        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       10.06        14.30        17.56        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6676 TCGA-CM-6677 
       15.02        14.04        11.01        12.95        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-F4-6459 TCGA-F4-6460 
      119.93        35.97        60.79       117.07         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A0XA 
       10.98        19.99         5.95         4.01         5.03       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  BCAP29 MUTATED BCAP29 WILD-TYPE 
            0.07             0.00 
  BCAP29 MUTATED BCAP29 WILD-TYPE 
          148.01           140.38 
  BCAP29 MUTATED BCAP29 WILD-TYPE 
          16.045           20.280 
[1] "0.1 - 148.0 (16.0)" "0.0 - 140.4 (20.3)"
[1] "hr="     "9400000"
D1657V2, continuous
D1657V3, binary
                  cls
clus                 0   1
  BCAP29 MUTATED     7   1
  BCAP29 WILD-TYPE 359 118
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BCAP29 MUTATED      7    1
  BCAP29 WILD-TYPE  359  118
        clus
vv       BCAP29 MUTATED BCAP29 WILD-TYPE
  COLON               7              359
  RECTUM              1              118
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  BCAP29 MUTATED         1        0        1         2         0         0
  BCAP29 WILD-TYPE      90        1       31       136        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  BCAP29 MUTATED           1          0          0          0        1
  BCAP29 WILD-TYPE        23         11         59         42       47
                  vv
clus               STAGE IVA STAGE IVB
  BCAP29 MUTATED           0         1
  BCAP29 WILD-TYPE        18         0
D1657V4, multiclass
            clus
vv           BCAP29 MUTATED BCAP29 WILD-TYPE
  STAGE I                 1               90
  STAGE IA                0                1
  STAGE II                1               31
  STAGE IIA               2              136
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               1               23
  STAGE IIIA              0               11
  STAGE IIIB              0               59
  STAGE IIIC              0               42
  STAGE IV                1               47
  STAGE IVA               0               18
  STAGE IVB               1                0
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  BCAP29 MUTATED     0   2   6   0
  BCAP29 WILD-TYPE  17  90 323  50
D1657V5, multiclass
    clus
vv   BCAP29 MUTATED BCAP29 WILD-TYPE
  T1              0               17
  T2              2               90
  T3              6              323
  T4              0               50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  BCAP29 MUTATED     6   1   1
  BCAP29 WILD-TYPE 281 112  86
D1657V6, multiclass
    clus
vv   BCAP29 MUTATED BCAP29 WILD-TYPE
  N0              6              281
  N1              1              112
  N2              1               86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1657V7, binary
                  cls
clus                 0   1
  BCAP29 MUTATED     4   2
  BCAP29 WILD-TYPE 371  63
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BCAP29 MUTATED      4    2
  BCAP29 WILD-TYPE  371   63
   clus
vv  BCAP29 MUTATED BCAP29 WILD-TYPE
  0              4              371
  1              2               63
[1] 2 2
[1] FALSE
D1657V8, binary
                  cls
clus                 0   1
  BCAP29 MUTATED     1   7
  BCAP29 WILD-TYPE 224 257
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BCAP29 MUTATED      1    7
  BCAP29 WILD-TYPE  224  257
        clus
vv       BCAP29 MUTATED BCAP29 WILD-TYPE
  FEMALE              1              224
  MALE                7              257
[1] 2 2
[1] FALSE
D1657V9, binary
                  cls
clus                 0   1
  BCAP29 MUTATED     5   1
  BCAP29 WILD-TYPE 345  21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BCAP29 MUTATED      5    1
  BCAP29 WILD-TYPE  345   21
     clus
vv    BCAP29 MUTATED BCAP29 WILD-TYPE
  NO               5              345
  YES              1               21
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  BCAP29 MUTATED                      4                             3
  BCAP29 WILD-TYPE                  311                            44
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  BCAP29 MUTATED                       0                              1
  BCAP29 WILD-TYPE                   106                              9
D1657V10, multiclass
                                clus
vv                               BCAP29 MUTATED BCAP29 WILD-TYPE
  COLON ADENOCARCINOMA                        4              311
  COLON MUCINOUS ADENOCARCINOMA               3               44
  RECTAL ADENOCARCINOMA                       0              106
  RECTAL MUCINOUS ADENOCARCINOMA              1                9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  BCAP29 MUTATED     3   0   1   2
  BCAP29 WILD-TYPE 342   4  30  23
D1657V11, multiclass
    clus
vv   BCAP29 MUTATED BCAP29 WILD-TYPE
  R0              3              342
  R1              0                4
  R2              1               30
  RX              2               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1657V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  BCAP29 MUTATED                                  0     2
  BCAP29 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  BCAP29 MUTATED                           1     3
  BCAP29 WILD-TYPE                        21   223
D1657V13, multiclass
                                  clus
vv                                 BCAP29 MUTATED BCAP29 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                9
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                         3              223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1658) Variable = MSH5 MUTATION ANALYSIS
D1658V1, survival
                sevent
clus2              0   1
  MSH5 MUTATED     7   0
  MSH5 WILD-TYPE 371  93
  MSH5 MUTATED MSH5 WILD-TYPE 
             7            464 
  MSH5 MUTATED MSH5 WILD-TYPE 
             0             93 
$`MSH5 MUTATED`
TCGA-A6-2678 TCGA-AA-3710 TCGA-AA-3821 TCGA-CM-5348 TCGA-G4-6586 TCGA-G4-6588 
       42.28        26.99         1.02        22.98        35.80        26.17 
TCGA-AG-3892 
       13.02 

$`MSH5 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2683 
       43.76        46.65        43.76        42.90        24.33        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        85.05        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 
       35.05        33.04         0.99        25.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       13.02        29.06        22.03        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       36.00        22.09        13.78        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       36.95        17.03        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  MSH5 MUTATED MSH5 WILD-TYPE 
          1.02           0.00 
  MSH5 MUTATED MSH5 WILD-TYPE 
         42.28         148.01 
  MSH5 MUTATED MSH5 WILD-TYPE 
        26.170         20.085 
[1] "1.0 - 42.3 (26.2)"  "0.0 - 148.0 (20.1)"
[1] "hr="     "9100000"
D1658V2, continuous
D1658V3, binary
                cls
clus               0   1
  MSH5 MUTATED     7   1
  MSH5 WILD-TYPE 359 118
[1] "tbl2"
                cls
clus             [,1] [,2]
  MSH5 MUTATED      7    1
  MSH5 WILD-TYPE  359  118
        clus
vv       MSH5 MUTATED MSH5 WILD-TYPE
  COLON             7            359
  RECTUM            1            118
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MSH5 MUTATED         2        0        0         4         0         0
  MSH5 WILD-TYPE      89        1       32       134        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MSH5 MUTATED           0          0          2          0        0         0
  MSH5 WILD-TYPE        24         11         57         42       48        18
                vv
clus             STAGE IVB
  MSH5 MUTATED           0
  MSH5 WILD-TYPE         1
D1658V4, multiclass
            clus
vv           MSH5 MUTATED MSH5 WILD-TYPE
  STAGE I               2             89
  STAGE IA              0              1
  STAGE II              0             32
  STAGE IIA             4            134
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            2             57
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  MSH5 MUTATED     1   1   6   0
  MSH5 WILD-TYPE  16  91 323  50
D1658V5, multiclass
    clus
vv   MSH5 MUTATED MSH5 WILD-TYPE
  T1            1             16
  T2            1             91
  T3            6            323
  T4            0             50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  MSH5 MUTATED     6   2   0
  MSH5 WILD-TYPE 281 111  87
D1658V6, multiclass
    clus
vv   MSH5 MUTATED MSH5 WILD-TYPE
  N0            6            281
  N1            2            111
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1658V7, binary
                cls
clus               0   1
  MSH5 MUTATED     8   0
  MSH5 WILD-TYPE 367  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  MSH5 MUTATED      8    0
  MSH5 WILD-TYPE  367   65
   clus
vv  MSH5 MUTATED MSH5 WILD-TYPE
  0            8            367
  1            0             65
[1] 2 2
[1] FALSE
D1658V8, binary
                cls
clus               0   1
  MSH5 MUTATED     7   1
  MSH5 WILD-TYPE 218 263
[1] "tbl2"
                cls
clus             [,1] [,2]
  MSH5 MUTATED      7    1
  MSH5 WILD-TYPE  218  263
        clus
vv       MSH5 MUTATED MSH5 WILD-TYPE
  FEMALE            7            218
  MALE              1            263
[1] 2 2
[1] FALSE
D1658V9, binary
                cls
clus               0   1
  MSH5 MUTATED     7   0
  MSH5 WILD-TYPE 343  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  MSH5 MUTATED      7    0
  MSH5 WILD-TYPE  343   22
     clus
vv    MSH5 MUTATED MSH5 WILD-TYPE
  NO             7            343
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MSH5 MUTATED                      6                             1
  MSH5 WILD-TYPE                  309                            46
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MSH5 MUTATED                       1                              0
  MSH5 WILD-TYPE                   105                             10
D1658V10, multiclass
                                clus
vv                               MSH5 MUTATED MSH5 WILD-TYPE
  COLON ADENOCARCINOMA                      6            309
  COLON MUCINOUS ADENOCARCINOMA             1             46
  RECTAL ADENOCARCINOMA                     1            105
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  MSH5 MUTATED     8   0   0   0
  MSH5 WILD-TYPE 337   4  31  25
D1658V11, multiclass
    clus
vv   MSH5 MUTATED MSH5 WILD-TYPE
  R0            8            337
  R1            0              4
  R2            0             31
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1658V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MSH5 MUTATED                                  0     0
  MSH5 WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  MSH5 MUTATED                           0     4
  MSH5 WILD-TYPE                        22   222
D1658V13, multiclass
                                  clus
vv                                 MSH5 MUTATED MSH5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       4            222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1659) Variable = BTBD11 MUTATION ANALYSIS
D1659V1, survival
                  sevent
clus2                0   1
  BTBD11 MUTATED    13   9
  BTBD11 WILD-TYPE 365  84
  BTBD11 MUTATED BTBD11 WILD-TYPE 
              22              449 
  BTBD11 MUTATED BTBD11 WILD-TYPE 
               9               84 
$`BTBD11 MUTATED`
TCGA-A6-2676 TCGA-A6-6780 TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3525 TCGA-AA-3555 
       42.90        20.12         3.02        63.98         8.05        29.95 
TCGA-AA-3663 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3952 TCGA-AA-3977 
        6.97        19.04        19.04        10.06         2.01        25.02 
TCGA-AZ-4315 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-5916 
       58.39       100.01         1.61        12.76        10.06        21.14 
TCGA-CM-4743 TCGA-CM-5864 TCGA-CM-6674 TCGA-AG-3892 
       23.05        15.02        12.95        13.02 

$`BTBD11 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 
       19.66        20.28         7.04         1.02        35.01         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       37.05        36.03        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 
       33.99        21.01        13.02        24.00        17.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.05        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3812 TCGA-AA-3815 
       36.00         5.03        85.05        26.99        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       33.01        26.01        24.00        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
       16.31         0.95        33.01        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77        12.10        29.56         5.23        11.74         3.19 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 
       51.32         9.99        82.95         1.91       124.27        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5868 
       30.08        32.02        15.02         5.03        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 
       19.99         1.02        17.95        36.95        17.03        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  BTBD11 MUTATED BTBD11 WILD-TYPE 
            1.61             0.00 
  BTBD11 MUTATED BTBD11 WILD-TYPE 
          100.01           148.01 
  BTBD11 MUTATED BTBD11 WILD-TYPE 
           17.03            20.91 
[1] "1.6 - 100.0 (17.0)" "0.0 - 148.0 (20.9)"
[1] "hr=" "2.3"
D1659V2, continuous
D1659V3, binary
                  cls
clus                 0   1
  BTBD11 MUTATED    22   1
  BTBD11 WILD-TYPE 344 118
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BTBD11 MUTATED     22    1
  BTBD11 WILD-TYPE  344  118
        clus
vv       BTBD11 MUTATED BTBD11 WILD-TYPE
  COLON              22              344
  RECTUM              1              118
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  BTBD11 MUTATED         3        0        5         8         1         0
  BTBD11 WILD-TYPE      88        1       27       130         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  BTBD11 MUTATED           1          1          1          1        1
  BTBD11 WILD-TYPE        23         10         58         41       47
                  vv
clus               STAGE IVA STAGE IVB
  BTBD11 MUTATED           0         0
  BTBD11 WILD-TYPE        18         1
D1659V4, multiclass
            clus
vv           BTBD11 MUTATED BTBD11 WILD-TYPE
  STAGE I                 3               88
  STAGE IA                0                1
  STAGE II                5               27
  STAGE IIA               8              130
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               1               23
  STAGE IIIA              1               10
  STAGE IIIB              1               58
  STAGE IIIC              1               41
  STAGE IV                1               47
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  BTBD11 MUTATED     2   3  17   1
  BTBD11 WILD-TYPE  15  89 312  49
D1659V5, multiclass
    clus
vv   BTBD11 MUTATED BTBD11 WILD-TYPE
  T1              2               15
  T2              3               89
  T3             17              312
  T4              1               49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  BTBD11 MUTATED    19   2   2
  BTBD11 WILD-TYPE 268 111  85
D1659V6, multiclass
    clus
vv   BTBD11 MUTATED BTBD11 WILD-TYPE
  N0             19              268
  N1              2              111
  N2              2               85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1659V7, binary
                  cls
clus                 0   1
  BTBD11 MUTATED    20   1
  BTBD11 WILD-TYPE 355  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BTBD11 MUTATED     20    1
  BTBD11 WILD-TYPE  355   64
   clus
vv  BTBD11 MUTATED BTBD11 WILD-TYPE
  0             20              355
  1              1               64
[1] 2 2
[1] FALSE
D1659V8, binary
                  cls
clus                 0   1
  BTBD11 MUTATED     8  15
  BTBD11 WILD-TYPE 217 249
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BTBD11 MUTATED      8   15
  BTBD11 WILD-TYPE  217  249
        clus
vv       BTBD11 MUTATED BTBD11 WILD-TYPE
  FEMALE              8              217
  MALE               15              249
[1] 2 2
[1] FALSE
D1659V9, binary
                  cls
clus                 0   1
  BTBD11 MUTATED    20   1
  BTBD11 WILD-TYPE 330  21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BTBD11 MUTATED     20    1
  BTBD11 WILD-TYPE  330   21
     clus
vv    BTBD11 MUTATED BTBD11 WILD-TYPE
  NO              20              330
  YES              1               21
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  BTBD11 MUTATED                     19                             3
  BTBD11 WILD-TYPE                  296                            44
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  BTBD11 MUTATED                       1                              0
  BTBD11 WILD-TYPE                   105                             10
D1659V10, multiclass
                                clus
vv                               BTBD11 MUTATED BTBD11 WILD-TYPE
  COLON ADENOCARCINOMA                       19              296
  COLON MUCINOUS ADENOCARCINOMA               3               44
  RECTAL ADENOCARCINOMA                       1              105
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  BTBD11 MUTATED    15   0   1   3
  BTBD11 WILD-TYPE 330   4  30  22
D1659V11, multiclass
    clus
vv   BTBD11 MUTATED BTBD11 WILD-TYPE
  R0             15              330
  R1              0                4
  R2              1               30
  RX              3               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1659V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  BTBD11 MUTATED                                  0     2
  BTBD11 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  BTBD11 MUTATED                           0     9
  BTBD11 WILD-TYPE                        22   217
D1659V13, multiclass
                                  clus
vv                                 BTBD11 MUTATED BTBD11 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                9
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         9              217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1660) Variable = ATAD1 MUTATION ANALYSIS
D1660V1, survival
                 sevent
clus2               0   1
  ATAD1 MUTATED     7   2
  ATAD1 WILD-TYPE 371  91
  ATAD1 MUTATED ATAD1 WILD-TYPE 
              9             462 
  ATAD1 MUTATED ATAD1 WILD-TYPE 
              2              91 
$`ATAD1 MUTATED`
TCGA-AA-3947 TCGA-AD-6895 TCGA-AZ-4315 TCGA-CK-5916 TCGA-CM-4743 TCGA-CM-6168 
       33.01         0.72        58.39        21.14        23.05        12.99 
TCGA-D5-6920 TCGA-DM-A28F TCGA-AG-A002 
        3.68        35.97        20.98 

$`ATAD1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 
       31.00         2.01        12.99        24.00        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       15.52        56.55         0.79         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       33.01        21.44        17.82         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 
       15.62        49.08        51.32         9.99        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
      124.27        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6169 TCGA-CM-6170 
       29.03        16.04        21.99        14.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
       15.58         1.48         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  ATAD1 MUTATED ATAD1 WILD-TYPE 
           0.72            0.00 
  ATAD1 MUTATED ATAD1 WILD-TYPE 
          58.39          148.01 
  ATAD1 MUTATED ATAD1 WILD-TYPE 
         21.140          20.085 
[1] "0.7 - 58.4 (21.1)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.3"
D1660V2, continuous
D1660V3, binary
                 cls
clus                0   1
  ATAD1 MUTATED     8   1
  ATAD1 WILD-TYPE 358 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ATAD1 MUTATED      8    1
  ATAD1 WILD-TYPE  358  118
        clus
vv       ATAD1 MUTATED ATAD1 WILD-TYPE
  COLON              8             358
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ATAD1 MUTATED         2        0        0         4         1         0
  ATAD1 WILD-TYPE      89        1       32       134         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ATAD1 MUTATED           0          0          1          0        0         0
  ATAD1 WILD-TYPE        24         11         58         42       48        18
                 vv
clus              STAGE IVB
  ATAD1 MUTATED           0
  ATAD1 WILD-TYPE         1
D1660V4, multiclass
            clus
vv           ATAD1 MUTATED ATAD1 WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              4             134
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ATAD1 MUTATED     1   1   6   1
  ATAD1 WILD-TYPE  16  91 323  49
D1660V5, multiclass
    clus
vv   ATAD1 MUTATED ATAD1 WILD-TYPE
  T1             1              16
  T2             1              91
  T3             6             323
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  ATAD1 MUTATED     7   2   0
  ATAD1 WILD-TYPE 280 111  87
D1660V6, multiclass
    clus
vv   ATAD1 MUTATED ATAD1 WILD-TYPE
  N0             7             280
  N1             2             111
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1660V7, binary
                 cls
clus                0   1
  ATAD1 MUTATED     8   0
  ATAD1 WILD-TYPE 367  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ATAD1 MUTATED      8    0
  ATAD1 WILD-TYPE  367   65
   clus
vv  ATAD1 MUTATED ATAD1 WILD-TYPE
  0             8             367
  1             0              65
[1] 2 2
[1] FALSE
D1660V8, binary
                 cls
clus                0   1
  ATAD1 MUTATED     4   5
  ATAD1 WILD-TYPE 221 259
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ATAD1 MUTATED      4    5
  ATAD1 WILD-TYPE  221  259
        clus
vv       ATAD1 MUTATED ATAD1 WILD-TYPE
  FEMALE             4             221
  MALE               5             259
[1] 2 2
[1] FALSE
D1660V9, binary
                 cls
clus                0   1
  ATAD1 MUTATED     6   0
  ATAD1 WILD-TYPE 344  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ATAD1 MUTATED      6    0
  ATAD1 WILD-TYPE  344   22
     clus
vv    ATAD1 MUTATED ATAD1 WILD-TYPE
  NO              6             344
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ATAD1 MUTATED                      7                             1
  ATAD1 WILD-TYPE                  308                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ATAD1 MUTATED                       1                              0
  ATAD1 WILD-TYPE                   105                             10
D1660V10, multiclass
                                clus
vv                               ATAD1 MUTATED ATAD1 WILD-TYPE
  COLON ADENOCARCINOMA                       7             308
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  ATAD1 MUTATED     6   0   0   1
  ATAD1 WILD-TYPE 339   4  31  24
D1660V11, multiclass
    clus
vv   ATAD1 MUTATED ATAD1 WILD-TYPE
  R0             6             339
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1660V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ATAD1 MUTATED                                  0     0
  ATAD1 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ATAD1 MUTATED                           1     6
  ATAD1 WILD-TYPE                        21   220
D1660V13, multiclass
                                  clus
vv                                 ATAD1 MUTATED ATAD1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        6             220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1661) Variable = PRPF4B MUTATION ANALYSIS
D1661V1, survival
                  sevent
clus2                0   1
  PRPF4B MUTATED    15   1
  PRPF4B WILD-TYPE 363  92
  PRPF4B MUTATED PRPF4B WILD-TYPE 
              16              455 
  PRPF4B MUTATED PRPF4B WILD-TYPE 
               1               92 
$`PRPF4B MUTATED`
TCGA-A6-6781 TCGA-AA-3663 TCGA-AA-3697 TCGA-AA-3955 TCGA-AA-A00A TCGA-AA-A010 
       19.66         6.97        85.05        20.98        38.04        34.98 
TCGA-AD-6895 TCGA-CA-6717 TCGA-CK-4948 TCGA-CK-5913 TCGA-CK-5916 TCGA-CM-4746 
        0.72        12.76       148.01        51.32        21.14        37.02 
TCGA-CM-6166 TCGA-CM-6674 TCGA-D5-6533 TCGA-AG-A002 
       21.99        12.95         1.32        20.98 

$`PRPF4B WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3956 
       24.00        33.01        26.01        24.00         2.01        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
        7.96        27.02        13.94        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       21.37        15.52        56.55         0.79         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 
        0.07        12.20        10.06        14.30        17.56        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       15.62        49.08         9.99        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       23.05        20.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       16.04        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       11.01        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       20.19        18.25        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  PRPF4B MUTATED PRPF4B WILD-TYPE 
            0.72             0.00 
  PRPF4B MUTATED PRPF4B WILD-TYPE 
          148.01           140.38 
  PRPF4B MUTATED PRPF4B WILD-TYPE 
           21.06            20.05 
[1] "0.7 - 148.0 (21.1)" "0.0 - 140.4 (20.1)"
[1] "hr=" "3.7"
D1661V2, continuous
D1661V3, binary
                  cls
clus                 0   1
  PRPF4B MUTATED    15   1
  PRPF4B WILD-TYPE 351 118
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PRPF4B MUTATED     15    1
  PRPF4B WILD-TYPE  351  118
        clus
vv       PRPF4B MUTATED PRPF4B WILD-TYPE
  COLON              15              351
  RECTUM              1              118
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PRPF4B MUTATED         4        0        1         4         1         0
  PRPF4B WILD-TYPE      87        1       31       134         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PRPF4B MUTATED           2          0          2          1        0
  PRPF4B WILD-TYPE        22         11         57         41       48
                  vv
clus               STAGE IVA STAGE IVB
  PRPF4B MUTATED           0         0
  PRPF4B WILD-TYPE        18         1
D1661V4, multiclass
            clus
vv           PRPF4B MUTATED PRPF4B WILD-TYPE
  STAGE I                 4               87
  STAGE IA                0                1
  STAGE II                1               31
  STAGE IIA               4              134
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               2               22
  STAGE IIIA              0               11
  STAGE IIIB              2               57
  STAGE IIIC              1               41
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  PRPF4B MUTATED     1   4   8   3
  PRPF4B WILD-TYPE  16  88 321  47
D1661V5, multiclass
    clus
vv   PRPF4B MUTATED PRPF4B WILD-TYPE
  T1              1               16
  T2              4               88
  T3              8              321
  T4              3               47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  PRPF4B MUTATED    12   3   1
  PRPF4B WILD-TYPE 275 110  86
D1661V6, multiclass
    clus
vv   PRPF4B MUTATED PRPF4B WILD-TYPE
  N0             12              275
  N1              3              110
  N2              1               86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1661V7, binary
                  cls
clus                 0   1
  PRPF4B MUTATED    13   0
  PRPF4B WILD-TYPE 362  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PRPF4B MUTATED     13    0
  PRPF4B WILD-TYPE  362   65
   clus
vv  PRPF4B MUTATED PRPF4B WILD-TYPE
  0             13              362
  1              0               65
[1] 2 2
[1] FALSE
D1661V8, binary
                  cls
clus                 0   1
  PRPF4B MUTATED     6  10
  PRPF4B WILD-TYPE 219 254
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PRPF4B MUTATED      6   10
  PRPF4B WILD-TYPE  219  254
        clus
vv       PRPF4B MUTATED PRPF4B WILD-TYPE
  FEMALE              6              219
  MALE               10              254
[1] 2 2
[1] FALSE
D1661V9, binary
                  cls
clus                 0   1
  PRPF4B MUTATED    14   0
  PRPF4B WILD-TYPE 336  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PRPF4B MUTATED     14    0
  PRPF4B WILD-TYPE  336   22
     clus
vv    PRPF4B MUTATED PRPF4B WILD-TYPE
  NO              14              336
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PRPF4B MUTATED                     13                             2
  PRPF4B WILD-TYPE                  302                            45
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PRPF4B MUTATED                       1                              0
  PRPF4B WILD-TYPE                   105                             10
D1661V10, multiclass
                                clus
vv                               PRPF4B MUTATED PRPF4B WILD-TYPE
  COLON ADENOCARCINOMA                       13              302
  COLON MUCINOUS ADENOCARCINOMA               2               45
  RECTAL ADENOCARCINOMA                       1              105
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  PRPF4B MUTATED    12   0   0   3
  PRPF4B WILD-TYPE 333   4  31  22
D1661V11, multiclass
    clus
vv   PRPF4B MUTATED PRPF4B WILD-TYPE
  R0             12              333
  R1              0                4
  R2              0               31
  RX              3               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1661V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PRPF4B MUTATED                                  0     1
  PRPF4B WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  PRPF4B MUTATED                           1     8
  PRPF4B WILD-TYPE                        21   218
D1661V13, multiclass
                                  clus
vv                                 PRPF4B MUTATED PRPF4B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                         8              218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1662) Variable = ARHGEF6 MUTATION ANALYSIS
D1662V1, survival
                   sevent
clus2                 0   1
  ARHGEF6 MUTATED    10   4
  ARHGEF6 WILD-TYPE 368  89
  ARHGEF6 MUTATED ARHGEF6 WILD-TYPE 
               14               457 
  ARHGEF6 MUTATED ARHGEF6 WILD-TYPE 
                4                89 
$`ARHGEF6 MUTATED`
TCGA-A6-3809 TCGA-A6-5661 TCGA-AA-3672 TCGA-AA-3811 TCGA-AA-3977 TCGA-AA-A01R 
       32.75        33.53         0.92        10.06        25.02        35.01 
TCGA-AZ-4315 TCGA-CA-6717 TCGA-CA-6718 TCGA-DM-A28C TCGA-DM-A28F TCGA-G4-6586 
       58.39        12.76        10.06        81.37        35.97        35.80 
TCGA-AF-2691 TCGA-AG-A002 
       43.04        20.98 

$`ARHGEF6 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       31.63        30.44        29.19        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
       54.02         2.01        14.01        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3815 
       85.05        26.99        19.04        19.04        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
        1.02         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
       16.31         0.95        33.01        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.07        12.20        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
      139.17         6.12       119.93        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       22.09        13.78        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       24.13        39.48        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  ARHGEF6 MUTATED ARHGEF6 WILD-TYPE 
             0.92              0.00 
  ARHGEF6 MUTATED ARHGEF6 WILD-TYPE 
            81.37            148.01 
  ARHGEF6 MUTATED ARHGEF6 WILD-TYPE 
            33.14             20.02 
[1] "0.9 - 81.4 (33.1)"  "0.0 - 148.0 (20.0)"
[1] "hr=" "1.3"
D1662V2, continuous
D1662V3, binary
                   cls
clus                  0   1
  ARHGEF6 MUTATED    13   2
  ARHGEF6 WILD-TYPE 353 117
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ARHGEF6 MUTATED     13    2
  ARHGEF6 WILD-TYPE  353  117
        clus
vv       ARHGEF6 MUTATED ARHGEF6 WILD-TYPE
  COLON               13               353
  RECTUM               2               117
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ARHGEF6 MUTATED         2        0        0         7         1         0
  ARHGEF6 WILD-TYPE      89        1       32       131         9         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ARHGEF6 MUTATED           3          0          1          0        0
  ARHGEF6 WILD-TYPE        21         11         58         42       48
                   vv
clus                STAGE IVA STAGE IVB
  ARHGEF6 MUTATED           0         0
  ARHGEF6 WILD-TYPE        18         1
D1662V4, multiclass
            clus
vv           ARHGEF6 MUTATED ARHGEF6 WILD-TYPE
  STAGE I                  2                89
  STAGE IA                 0                 1
  STAGE II                 0                32
  STAGE IIA                7               131
  STAGE IIB                1                 9
  STAGE IIC                0                 1
  STAGE III                3                21
  STAGE IIIA               0                11
  STAGE IIIB               1                58
  STAGE IIIC               0                42
  STAGE IV                 0                48
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  ARHGEF6 MUTATED     1   2  11   1
  ARHGEF6 WILD-TYPE  16  90 318  49
D1662V5, multiclass
    clus
vv   ARHGEF6 MUTATED ARHGEF6 WILD-TYPE
  T1               1                16
  T2               2                90
  T3              11               318
  T4               1                49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  ARHGEF6 MUTATED    11   2   2
  ARHGEF6 WILD-TYPE 276 111  85
D1662V6, multiclass
    clus
vv   ARHGEF6 MUTATED ARHGEF6 WILD-TYPE
  N0              11               276
  N1               2               111
  N2               2                85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1662V7, binary
                   cls
clus                  0   1
  ARHGEF6 MUTATED    14   0
  ARHGEF6 WILD-TYPE 361  65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ARHGEF6 MUTATED     14    0
  ARHGEF6 WILD-TYPE  361   65
   clus
vv  ARHGEF6 MUTATED ARHGEF6 WILD-TYPE
  0              14               361
  1               0                65
[1] 2 2
[1] FALSE
D1662V8, binary
                   cls
clus                  0   1
  ARHGEF6 MUTATED     7   8
  ARHGEF6 WILD-TYPE 218 256
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ARHGEF6 MUTATED      7    8
  ARHGEF6 WILD-TYPE  218  256
        clus
vv       ARHGEF6 MUTATED ARHGEF6 WILD-TYPE
  FEMALE               7               218
  MALE                 8               256
[1] 2 2
[1] FALSE
D1662V9, binary
                   cls
clus                  0   1
  ARHGEF6 MUTATED    11   1
  ARHGEF6 WILD-TYPE 339  21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ARHGEF6 MUTATED     11    1
  ARHGEF6 WILD-TYPE  339   21
     clus
vv    ARHGEF6 MUTATED ARHGEF6 WILD-TYPE
  NO               11               339
  YES               1                21
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ARHGEF6 MUTATED                     10                             3
  ARHGEF6 WILD-TYPE                  305                            44
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ARHGEF6 MUTATED                       2                              0
  ARHGEF6 WILD-TYPE                   104                             10
D1662V10, multiclass
                                clus
vv                               ARHGEF6 MUTATED ARHGEF6 WILD-TYPE
  COLON ADENOCARCINOMA                        10               305
  COLON MUCINOUS ADENOCARCINOMA                3                44
  RECTAL ADENOCARCINOMA                        2               104
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  ARHGEF6 MUTATED    10   0   0   2
  ARHGEF6 WILD-TYPE 335   4  31  23
D1662V11, multiclass
    clus
vv   ARHGEF6 MUTATED ARHGEF6 WILD-TYPE
  R0              10               335
  R1               0                 4
  R2               0                31
  RX               2                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1662V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ARHGEF6 MUTATED                                  0     2
  ARHGEF6 WILD-TYPE                                1     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  ARHGEF6 MUTATED                           1     6
  ARHGEF6 WILD-TYPE                        21   220
D1662V13, multiclass
                                  clus
vv                                 ARHGEF6 MUTATED ARHGEF6 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          2                 9
  BLACK OR AFRICAN AMERICAN                      1                21
  WHITE                                          6               220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1663) Variable = HK3 MUTATION ANALYSIS
D1663V1, survival
               sevent
clus2             0   1
  HK3 MUTATED    19   2
  HK3 WILD-TYPE 359  91
  HK3 MUTATED HK3 WILD-TYPE 
           21           450 
  HK3 MUTATED HK3 WILD-TYPE 
            2            91 
$`HK3 MUTATED`
TCGA-A6-5661 TCGA-A6-5665 TCGA-AA-3510 TCGA-AA-3660 TCGA-AA-3864 TCGA-AA-3977 
       33.53        22.06        63.98        78.08        53.00        25.02 
TCGA-AA-A01R TCGA-AZ-4681 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5916 TCGA-DM-A1HB 
       35.01       106.75        15.62        51.32        21.14       135.65 
TCGA-DM-A28K TCGA-G4-6306 TCGA-G4-6588 TCGA-G4-6628 TCGA-AF-2693 TCGA-AF-6136 
       98.24        44.68        26.17        79.69        19.10        15.39 
TCGA-AG-A002 TCGA-DY-A1H8 TCGA-F5-6571 
       20.98        32.61        31.30 

$`HK3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       31.07        30.05        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
        5.13        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       85.45        49.08         9.99        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
        7.50        44.32       131.51       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-F4-6459 TCGA-F4-6460 
      119.93        35.97        60.79       117.07         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 
      133.18        74.56        65.85        53.62        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       91.79        46.75        24.13        39.48        43.04        13.55 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 
       34.49        10.39        14.50        16.83        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EF-5830 
      126.44        41.36        57.24        24.13        51.48         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  HK3 MUTATED HK3 WILD-TYPE 
        15.39          0.00 
  HK3 MUTATED HK3 WILD-TYPE 
       135.65        148.01 
  HK3 MUTATED HK3 WILD-TYPE 
        33.53         19.99 
[1] "15.4 - 135.7 (33.5)" "0.0 - 148.0 (20.0)" 
[1] "hr=" "3.9"
D1663V2, continuous
D1663V3, binary
               cls
clus              0   1
  HK3 MUTATED    17   4
  HK3 WILD-TYPE 349 115
[1] "tbl2"
               cls
clus            [,1] [,2]
  HK3 MUTATED     17    4
  HK3 WILD-TYPE  349  115
        clus
vv       HK3 MUTATED HK3 WILD-TYPE
  COLON           17           349
  RECTUM           4           115
[1] 2 2
[1] FALSE
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  HK3 MUTATED         4        0        4         8         0         0
  HK3 WILD-TYPE      87        1       28       130        10         1
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  HK3 MUTATED           1          1          2          1        0         0
  HK3 WILD-TYPE        23         10         57         41       48        18
               vv
clus            STAGE IVB
  HK3 MUTATED           0
  HK3 WILD-TYPE         1
D1663V4, multiclass
            clus
vv           HK3 MUTATED HK3 WILD-TYPE
  STAGE I              4            87
  STAGE IA             0             1
  STAGE II             4            28
  STAGE IIA            8           130
  STAGE IIB            0            10
  STAGE IIC            0             1
  STAGE III            1            23
  STAGE IIIA           1            10
  STAGE IIIB           2            57
  STAGE IIIC           1            41
  STAGE IV             0            48
  STAGE IVA            0            18
  STAGE IVB            0             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  HK3 MUTATED     1   6  13   2
  HK3 WILD-TYPE  16  86 316  48
D1663V5, multiclass
    clus
vv   HK3 MUTATED HK3 WILD-TYPE
  T1           1            16
  T2           6            86
  T3          13           316
  T4           2            48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2
  HK3 MUTATED    17   3   2
  HK3 WILD-TYPE 270 110  85
D1663V6, multiclass
    clus
vv   HK3 MUTATED HK3 WILD-TYPE
  N0          17           270
  N1           3           110
  N2           2            85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1663V7, binary
               cls
clus              0   1
  HK3 MUTATED    18   0
  HK3 WILD-TYPE 357  65
[1] "tbl2"
               cls
clus            [,1] [,2]
  HK3 MUTATED     18    0
  HK3 WILD-TYPE  357   65
   clus
vv  HK3 MUTATED HK3 WILD-TYPE
  0          18           357
  1           0            65
[1] 2 2
[1] FALSE
D1663V8, binary
               cls
clus              0   1
  HK3 MUTATED    12  10
  HK3 WILD-TYPE 213 254
[1] "tbl2"
               cls
clus            [,1] [,2]
  HK3 MUTATED     12   10
  HK3 WILD-TYPE  213  254
        clus
vv       HK3 MUTATED HK3 WILD-TYPE
  FEMALE          12           213
  MALE            10           254
[1] 2 2
[1] FALSE
D1663V9, binary
               cls
clus              0   1
  HK3 MUTATED    15   2
  HK3 WILD-TYPE 335  20
[1] "tbl2"
               cls
clus            [,1] [,2]
  HK3 MUTATED     15    2
  HK3 WILD-TYPE  335   20
     clus
vv    HK3 MUTATED HK3 WILD-TYPE
  NO           15           335
  YES           2            20
[1] 2 2
[1] FALSE
               vv
clus            COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  HK3 MUTATED                     13                             3
  HK3 WILD-TYPE                  302                            44
               vv
clus            RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  HK3 MUTATED                       4                              0
  HK3 WILD-TYPE                   102                             10
D1663V10, multiclass
                                clus
vv                               HK3 MUTATED HK3 WILD-TYPE
  COLON ADENOCARCINOMA                    13           302
  COLON MUCINOUS ADENOCARCINOMA            3            44
  RECTAL ADENOCARCINOMA                    4           102
  RECTAL MUCINOUS ADENOCARCINOMA           0            10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             R0  R1  R2  RX
  HK3 MUTATED    13   0   0   3
  HK3 WILD-TYPE 332   4  31  22
D1663V11, multiclass
    clus
vv   HK3 MUTATED HK3 WILD-TYPE
  R0          13           332
  R1           0             4
  R2           0            31
  RX           3            22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1663V12, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HK3 MUTATED                                  0     0
  HK3 WILD-TYPE                                1    11
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  HK3 MUTATED                           1    14
  HK3 WILD-TYPE                        21   212
D1663V13, multiclass
                                  clus
vv                                 HK3 MUTATED HK3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      0            11
  BLACK OR AFRICAN AMERICAN                  1            21
  WHITE                                     14           212
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1664) Variable = OR5R1 MUTATION ANALYSIS
D1664V1, survival
                 sevent
clus2               0   1
  OR5R1 MUTATED     9   4
  OR5R1 WILD-TYPE 369  89
  OR5R1 MUTATED OR5R1 WILD-TYPE 
             13             458 
  OR5R1 MUTATED OR5R1 WILD-TYPE 
              4              89 
$`OR5R1 MUTATED`
TCGA-AA-3510 TCGA-AA-3845 TCGA-AA-3950 TCGA-AA-3955 TCGA-AZ-4681 TCGA-AZ-6598 
       63.98         0.00        24.00        20.98       106.75        49.41 
TCGA-AZ-6599 TCGA-CA-6717 TCGA-CK-4947 TCGA-D5-6533 TCGA-D5-6929 TCGA-F4-6854 
        6.77        12.76        17.56         1.32         4.80         0.53 
TCGA-G4-6626 
       46.75 

$`OR5R1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 
       17.98        15.95        38.99        37.02        14.93        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3956 
       12.99        24.00        33.01        26.01         2.01        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82        58.39         1.41         5.13        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       88.21        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-4950 
        0.07        12.20        10.06        14.30       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       18.25        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 
       12.43        14.30         9.04         9.44        11.64         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6855 
       34.42        41.42        16.24        33.67        13.25        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-AF-2687 
       13.78        35.80        26.17        91.79        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  OR5R1 MUTATED OR5R1 WILD-TYPE 
              0               0 
  OR5R1 MUTATED OR5R1 WILD-TYPE 
         106.75          148.01 
  OR5R1 MUTATED OR5R1 WILD-TYPE 
         17.560          20.235 
[1] "0.0 - 106.8 (17.6)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.4"
D1664V2, continuous
D1664V3, binary
                 cls
clus                0   1
  OR5R1 MUTATED    14   0
  OR5R1 WILD-TYPE 352 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR5R1 MUTATED     14    0
  OR5R1 WILD-TYPE  352  119
        clus
vv       OR5R1 MUTATED OR5R1 WILD-TYPE
  COLON             14             352
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  OR5R1 MUTATED         1        0        2         7         0         0
  OR5R1 WILD-TYPE      90        1       30       131        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  OR5R1 MUTATED           0          0          3          0        1         0
  OR5R1 WILD-TYPE        24         11         56         42       47        18
                 vv
clus              STAGE IVB
  OR5R1 MUTATED           0
  OR5R1 WILD-TYPE         1
D1664V4, multiclass
            clus
vv           OR5R1 MUTATED OR5R1 WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA              7             131
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             3              56
  STAGE IIIC             0              42
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  OR5R1 MUTATED     0   2  10   2
  OR5R1 WILD-TYPE  17  90 319  48
D1664V5, multiclass
    clus
vv   OR5R1 MUTATED OR5R1 WILD-TYPE
  T1             0              17
  T2             2              90
  T3            10             319
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  OR5R1 MUTATED    11   2   1
  OR5R1 WILD-TYPE 276 111  86
D1664V6, multiclass
    clus
vv   OR5R1 MUTATED OR5R1 WILD-TYPE
  N0            11             276
  N1             2             111
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1664V7, binary
                 cls
clus                0   1
  OR5R1 MUTATED    11   1
  OR5R1 WILD-TYPE 364  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR5R1 MUTATED     11    1
  OR5R1 WILD-TYPE  364   64
   clus
vv  OR5R1 MUTATED OR5R1 WILD-TYPE
  0            11             364
  1             1              64
[1] 2 2
[1] FALSE
D1664V8, binary
                 cls
clus                0   1
  OR5R1 MUTATED     9   5
  OR5R1 WILD-TYPE 216 259
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR5R1 MUTATED      9    5
  OR5R1 WILD-TYPE  216  259
        clus
vv       OR5R1 MUTATED OR5R1 WILD-TYPE
  FEMALE             9             216
  MALE               5             259
[1] 2 2
[1] FALSE
D1664V9, binary
                 cls
clus                0   1
  OR5R1 MUTATED    10   0
  OR5R1 WILD-TYPE 340  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR5R1 MUTATED     10    0
  OR5R1 WILD-TYPE  340   22
     clus
vv    OR5R1 MUTATED OR5R1 WILD-TYPE
  NO             10             340
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  OR5R1 MUTATED                     12                             2
  OR5R1 WILD-TYPE                  303                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  OR5R1 MUTATED                       0                              0
  OR5R1 WILD-TYPE                   106                             10
D1664V10, multiclass
                                clus
vv                               OR5R1 MUTATED OR5R1 WILD-TYPE
  COLON ADENOCARCINOMA                      12             303
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  OR5R1 MUTATED    10   0   0   2
  OR5R1 WILD-TYPE 335   4  31  23
D1664V11, multiclass
    clus
vv   OR5R1 MUTATED OR5R1 WILD-TYPE
  R0            10             335
  R1             0               4
  R2             0              31
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1664V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OR5R1 MUTATED                                  0     1
  OR5R1 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  OR5R1 MUTATED                           0     8
  OR5R1 WILD-TYPE                        22   218
D1664V13, multiclass
                                  clus
vv                                 OR5R1 MUTATED OR5R1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        8             218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1665) Variable = TCEANC MUTATION ANALYSIS
D1665V1, survival
                  sevent
clus2                0   1
  TCEANC MUTATED     4   3
  TCEANC WILD-TYPE 374  90
  TCEANC MUTATED TCEANC WILD-TYPE 
               7              464 
  TCEANC MUTATED TCEANC WILD-TYPE 
               3               90 
$`TCEANC MUTATED`
TCGA-A6-6781 TCGA-AA-3672 TCGA-AA-3811 TCGA-AA-A00N TCGA-AD-6889 TCGA-CA-6718 
       19.66         0.92        10.06         4.01        56.55        10.06 
TCGA-AG-A002 
       20.98 

$`TCEANC WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 
        6.97        54.02         2.01        14.01        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        19.04        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 
       40.96         0.07        21.37        15.52         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 
        3.25         3.29         0.07        12.20        12.76        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  TCEANC MUTATED TCEANC WILD-TYPE 
            0.92             0.00 
  TCEANC MUTATED TCEANC WILD-TYPE 
           56.55           148.01 
  TCEANC MUTATED TCEANC WILD-TYPE 
          10.060           20.415 
[1] "0.9 - 56.5 (10.1)"  "0.0 - 148.0 (20.4)"
[1] "hr=" "3.2"
D1665V2, continuous
D1665V3, binary
                  cls
clus                 0   1
  TCEANC MUTATED     8   1
  TCEANC WILD-TYPE 358 118
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TCEANC MUTATED      8    1
  TCEANC WILD-TYPE  358  118
        clus
vv       TCEANC MUTATED TCEANC WILD-TYPE
  COLON               8              358
  RECTUM              1              118
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TCEANC MUTATED         1        0        0         3         2         0
  TCEANC WILD-TYPE      90        1       32       135         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TCEANC MUTATED           2          0          0          1        0
  TCEANC WILD-TYPE        22         11         59         41       48
                  vv
clus               STAGE IVA STAGE IVB
  TCEANC MUTATED           0         0
  TCEANC WILD-TYPE        18         1
D1665V4, multiclass
            clus
vv           TCEANC MUTATED TCEANC WILD-TYPE
  STAGE I                 1               90
  STAGE IA                0                1
  STAGE II                0               32
  STAGE IIA               3              135
  STAGE IIB               2                8
  STAGE IIC               0                1
  STAGE III               2               22
  STAGE IIIA              0               11
  STAGE IIIB              0               59
  STAGE IIIC              1               41
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  TCEANC MUTATED     0   1   5   3
  TCEANC WILD-TYPE  17  91 324  47
D1665V5, multiclass
    clus
vv   TCEANC MUTATED TCEANC WILD-TYPE
  T1              0               17
  T2              1               91
  T3              5              324
  T4              3               47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  TCEANC MUTATED     6   2   1
  TCEANC WILD-TYPE 281 111  86
D1665V6, multiclass
    clus
vv   TCEANC MUTATED TCEANC WILD-TYPE
  N0              6              281
  N1              2              111
  N2              1               86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1665V7, binary
                  cls
clus                 0   1
  TCEANC MUTATED     7   0
  TCEANC WILD-TYPE 368  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TCEANC MUTATED      7    0
  TCEANC WILD-TYPE  368   65
   clus
vv  TCEANC MUTATED TCEANC WILD-TYPE
  0              7              368
  1              0               65
[1] 2 2
[1] FALSE
D1665V8, binary
                  cls
clus                 0   1
  TCEANC MUTATED     4   5
  TCEANC WILD-TYPE 221 259
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TCEANC MUTATED      4    5
  TCEANC WILD-TYPE  221  259
        clus
vv       TCEANC MUTATED TCEANC WILD-TYPE
  FEMALE              4              221
  MALE                5              259
[1] 2 2
[1] FALSE
D1665V9, binary
                  cls
clus                 0   1
  TCEANC MUTATED     5   0
  TCEANC WILD-TYPE 345  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TCEANC MUTATED      5    0
  TCEANC WILD-TYPE  345   22
     clus
vv    TCEANC MUTATED TCEANC WILD-TYPE
  NO               5              345
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  TCEANC MUTATED                      6                             2
  TCEANC WILD-TYPE                  309                            45
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  TCEANC MUTATED                       1                              0
  TCEANC WILD-TYPE                   105                             10
D1665V10, multiclass
                                clus
vv                               TCEANC MUTATED TCEANC WILD-TYPE
  COLON ADENOCARCINOMA                        6              309
  COLON MUCINOUS ADENOCARCINOMA               2               45
  RECTAL ADENOCARCINOMA                       1              105
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  TCEANC MUTATED     6   0   0   2
  TCEANC WILD-TYPE 339   4  31  23
D1665V11, multiclass
    clus
vv   TCEANC MUTATED TCEANC WILD-TYPE
  R0              6              339
  R1              0                4
  R2              0               31
  RX              2               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1665V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TCEANC MUTATED                                  0     2
  TCEANC WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  TCEANC MUTATED                           0     2
  TCEANC WILD-TYPE                        22   224
D1665V13, multiclass
                                  clus
vv                                 TCEANC MUTATED TCEANC WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                9
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         2              224
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1666) Variable = GJA10 MUTATION ANALYSIS
D1666V1, survival
                 sevent
clus2               0   1
  GJA10 MUTATED    10   3
  GJA10 WILD-TYPE 368  90
  GJA10 MUTATED GJA10 WILD-TYPE 
             13             458 
  GJA10 MUTATED GJA10 WILD-TYPE 
              3              90 
$`GJA10 MUTATED`
TCGA-A6-5665 TCGA-AA-3510 TCGA-AA-3555 TCGA-AA-A010 TCGA-AA-A01R TCGA-AA-A02K 
       22.06        63.98        29.95        34.98        35.01        14.01 
TCGA-AA-A02Y TCGA-CA-6717 TCGA-CK-5916 TCGA-D5-6927 TCGA-AF-5654 TCGA-AG-A002 
       39.98        12.76        21.14         9.44        16.83        20.98 
TCGA-AG-A00H 
       25.97 

$`GJA10 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       24.00        17.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
       38.07         1.02         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
        0.92        41.00        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07        12.20        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 
       85.45        15.62        49.08        51.32         9.99        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6929 
        4.41        12.43        14.30         9.04        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6655 
       19.10        34.49        10.39        14.50        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y 
       14.04         1.02        17.03        13.94         6.02        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  GJA10 MUTATED GJA10 WILD-TYPE 
           9.44            0.00 
  GJA10 MUTATED GJA10 WILD-TYPE 
          63.98          148.01 
  GJA10 MUTATED GJA10 WILD-TYPE 
         22.060          20.035 
[1] "9.4 - 64.0 (22.1)"  "0.0 - 148.0 (20.0)"
[1] "hr=" "1.2"
D1666V2, continuous
D1666V3, binary
                 cls
clus                0   1
  GJA10 MUTATED    11   3
  GJA10 WILD-TYPE 355 116
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GJA10 MUTATED     11    3
  GJA10 WILD-TYPE  355  116
        clus
vv       GJA10 MUTATED GJA10 WILD-TYPE
  COLON             11             355
  RECTUM             3             116
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GJA10 MUTATED         4        0        1         6         1         0
  GJA10 WILD-TYPE      87        1       31       132         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  GJA10 MUTATED           1          0          0          0        1         0
  GJA10 WILD-TYPE        23         11         59         42       47        18
                 vv
clus              STAGE IVB
  GJA10 MUTATED           0
  GJA10 WILD-TYPE         1
D1666V4, multiclass
            clus
vv           GJA10 MUTATED GJA10 WILD-TYPE
  STAGE I                4              87
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              6             132
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             0              42
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  GJA10 MUTATED     1   3   8   2
  GJA10 WILD-TYPE  16  89 321  48
D1666V5, multiclass
    clus
vv   GJA10 MUTATED GJA10 WILD-TYPE
  T1             1              16
  T2             3              89
  T3             8             321
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  GJA10 MUTATED    12   0   2
  GJA10 WILD-TYPE 275 113  85
D1666V6, multiclass
    clus
vv   GJA10 MUTATED GJA10 WILD-TYPE
  N0            12             275
  N1             0             113
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1666V7, binary
                 cls
clus                0   1
  GJA10 MUTATED    13   1
  GJA10 WILD-TYPE 362  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GJA10 MUTATED     13    1
  GJA10 WILD-TYPE  362   64
   clus
vv  GJA10 MUTATED GJA10 WILD-TYPE
  0            13             362
  1             1              64
[1] 2 2
[1] FALSE
D1666V8, binary
                 cls
clus                0   1
  GJA10 MUTATED     6   8
  GJA10 WILD-TYPE 219 256
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GJA10 MUTATED      6    8
  GJA10 WILD-TYPE  219  256
        clus
vv       GJA10 MUTATED GJA10 WILD-TYPE
  FEMALE             6             219
  MALE               8             256
[1] 2 2
[1] FALSE
D1666V9, binary
                 cls
clus                0   1
  GJA10 MUTATED    11   2
  GJA10 WILD-TYPE 339  20
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GJA10 MUTATED     11    2
  GJA10 WILD-TYPE  339   20
     clus
vv    GJA10 MUTATED GJA10 WILD-TYPE
  NO             11             339
  YES             2              20
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  GJA10 MUTATED                      8                             3
  GJA10 WILD-TYPE                  307                            44
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  GJA10 MUTATED                       3                              0
  GJA10 WILD-TYPE                   103                             10
D1666V10, multiclass
                                clus
vv                               GJA10 MUTATED GJA10 WILD-TYPE
  COLON ADENOCARCINOMA                       8             307
  COLON MUCINOUS ADENOCARCINOMA              3              44
  RECTAL ADENOCARCINOMA                      3             103
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  GJA10 MUTATED    11   0   1   2
  GJA10 WILD-TYPE 334   4  30  23
D1666V11, multiclass
    clus
vv   GJA10 MUTATED GJA10 WILD-TYPE
  R0            11             334
  R1             0               4
  R2             1              30
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1666V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GJA10 MUTATED                                  0     1
  GJA10 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  GJA10 MUTATED                           0     4
  GJA10 WILD-TYPE                        22   222
D1666V13, multiclass
                                  clus
vv                                 GJA10 MUTATED GJA10 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        4             222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1667) Variable = AP1G1 MUTATION ANALYSIS
D1667V1, survival
                 sevent
clus2               0   1
  AP1G1 MUTATED     8   4
  AP1G1 WILD-TYPE 370  89
  AP1G1 MUTATED AP1G1 WILD-TYPE 
             12             459 
  AP1G1 MUTATED AP1G1 WILD-TYPE 
              4              89 
$`AP1G1 MUTATED`
TCGA-A6-4105 TCGA-AA-3710 TCGA-AA-A00N TCGA-AZ-4315 TCGA-CA-6715 TCGA-CA-6717 
       14.53        26.99         4.01        58.39         0.07        12.76 
TCGA-CM-6171 TCGA-CM-6675 TCGA-D5-6929 TCGA-F4-6460 TCGA-AG-A002 TCGA-DY-A1DG 
       14.04        13.05         4.80        31.96        20.98        51.48 

$`AP1G1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 
       16.57        34.65        33.34        32.75        36.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        85.05        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.06         3.25         3.29        12.20        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       11.01        12.95        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       11.64         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
      117.07        98.24         8.61        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  AP1G1 MUTATED AP1G1 WILD-TYPE 
           0.07            0.00 
  AP1G1 MUTATED AP1G1 WILD-TYPE 
          58.39          148.01 
  AP1G1 MUTATED AP1G1 WILD-TYPE 
         14.285          20.280 
[1] "0.1 - 58.4 (14.3)"  "0.0 - 148.0 (20.3)"
[1] "hr=" "2"  
D1667V2, continuous
D1667V3, binary
                 cls
clus                0   1
  AP1G1 MUTATED    11   2
  AP1G1 WILD-TYPE 355 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AP1G1 MUTATED     11    2
  AP1G1 WILD-TYPE  355  117
        clus
vv       AP1G1 MUTATED AP1G1 WILD-TYPE
  COLON             11             355
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  AP1G1 MUTATED         2        0        0         5         1         0
  AP1G1 WILD-TYPE      89        1       32       133         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AP1G1 MUTATED           0          0          2          0        1         1
  AP1G1 WILD-TYPE        24         11         57         42       47        17
                 vv
clus              STAGE IVB
  AP1G1 MUTATED           1
  AP1G1 WILD-TYPE         0
D1667V4, multiclass
            clus
vv           AP1G1 MUTATED AP1G1 WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              5             133
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             2              57
  STAGE IIIC             0              42
  STAGE IV               1              47
  STAGE IVA              1              17
  STAGE IVB              1               0
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  AP1G1 MUTATED     0   2  10   1
  AP1G1 WILD-TYPE  17  90 319  49
D1667V5, multiclass
    clus
vv   AP1G1 MUTATED AP1G1 WILD-TYPE
  T1             0              17
  T2             2              90
  T3            10             319
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  AP1G1 MUTATED     8   4   1
  AP1G1 WILD-TYPE 279 109  86
D1667V6, multiclass
    clus
vv   AP1G1 MUTATED AP1G1 WILD-TYPE
  N0             8             279
  N1             4             109
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1667V7, binary
                 cls
clus                0   1
  AP1G1 MUTATED    10   3
  AP1G1 WILD-TYPE 365  62
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AP1G1 MUTATED     10    3
  AP1G1 WILD-TYPE  365   62
   clus
vv  AP1G1 MUTATED AP1G1 WILD-TYPE
  0            10             365
  1             3              62
[1] 2 2
[1] FALSE
D1667V8, binary
                 cls
clus                0   1
  AP1G1 MUTATED     5   8
  AP1G1 WILD-TYPE 220 256
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AP1G1 MUTATED      5    8
  AP1G1 WILD-TYPE  220  256
        clus
vv       AP1G1 MUTATED AP1G1 WILD-TYPE
  FEMALE             5             220
  MALE               8             256
[1] 2 2
[1] FALSE
D1667V9, binary
                 cls
clus                0   1
  AP1G1 MUTATED     8   0
  AP1G1 WILD-TYPE 342  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AP1G1 MUTATED      8    0
  AP1G1 WILD-TYPE  342   22
     clus
vv    AP1G1 MUTATED AP1G1 WILD-TYPE
  NO              8             342
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  AP1G1 MUTATED                      9                             2
  AP1G1 WILD-TYPE                  306                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  AP1G1 MUTATED                       2                              0
  AP1G1 WILD-TYPE                   104                             10
D1667V10, multiclass
                                clus
vv                               AP1G1 MUTATED AP1G1 WILD-TYPE
  COLON ADENOCARCINOMA                       9             306
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  AP1G1 MUTATED     9   0   0   2
  AP1G1 WILD-TYPE 336   4  31  23
D1667V11, multiclass
    clus
vv   AP1G1 MUTATED AP1G1 WILD-TYPE
  R0             9             336
  R1             0               4
  R2             0              31
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1667V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AP1G1 MUTATED                                  0     2
  AP1G1 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  AP1G1 MUTATED                           1     6
  AP1G1 WILD-TYPE                        21   220
D1667V13, multiclass
                                  clus
vv                                 AP1G1 MUTATED AP1G1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               9
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        6             220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1668) Variable = PLEKHA3 MUTATION ANALYSIS
D1668V1, survival
                   sevent
clus2                 0   1
  PLEKHA3 MUTATED     7   1
  PLEKHA3 WILD-TYPE 371  92
  PLEKHA3 MUTATED PLEKHA3 WILD-TYPE 
                8               463 
  PLEKHA3 MUTATED PLEKHA3 WILD-TYPE 
                1                92 
$`PLEKHA3 MUTATED`
TCGA-AA-A010 TCGA-AD-6895 TCGA-AZ-6598 TCGA-CM-5861 TCGA-D5-6529 TCGA-AF-2693 
       34.98         0.72        49.41        15.02        20.19        19.10 
TCGA-AG-A002 TCGA-AG-A032 
       20.98        38.04 

$`PLEKHA3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       15.52        56.55         0.79         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 
      106.75        22.36        62.79        88.21         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6532 TCGA-D5-6533 
       12.26        19.59        56.09        55.92        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 
       79.69        24.13        39.48        43.04        13.55        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       41.00       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  PLEKHA3 MUTATED PLEKHA3 WILD-TYPE 
             0.72              0.00 
  PLEKHA3 MUTATED PLEKHA3 WILD-TYPE 
            49.41            148.01 
  PLEKHA3 MUTATED PLEKHA3 WILD-TYPE 
           20.585            20.120 
[1] "0.7 - 49.4 (20.6)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.5"
D1668V2, continuous
D1668V3, binary
                   cls
clus                  0   1
  PLEKHA3 MUTATED     5   2
  PLEKHA3 WILD-TYPE 361 117
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLEKHA3 MUTATED      5    2
  PLEKHA3 WILD-TYPE  361  117
        clus
vv       PLEKHA3 MUTATED PLEKHA3 WILD-TYPE
  COLON                5               361
  RECTUM               2               117
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PLEKHA3 MUTATED         2        0        1         2         1         0
  PLEKHA3 WILD-TYPE      89        1       31       136         9         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PLEKHA3 MUTATED           0          0          1          0        0
  PLEKHA3 WILD-TYPE        24         11         58         42       48
                   vv
clus                STAGE IVA STAGE IVB
  PLEKHA3 MUTATED           0         0
  PLEKHA3 WILD-TYPE        18         1
D1668V4, multiclass
            clus
vv           PLEKHA3 MUTATED PLEKHA3 WILD-TYPE
  STAGE I                  2                89
  STAGE IA                 0                 1
  STAGE II                 1                31
  STAGE IIA                2               136
  STAGE IIB                1                 9
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               0                11
  STAGE IIIB               1                58
  STAGE IIIC               0                42
  STAGE IV                 0                48
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  PLEKHA3 MUTATED     0   2   5   1
  PLEKHA3 WILD-TYPE  17  90 324  49
D1668V5, multiclass
    clus
vv   PLEKHA3 MUTATED PLEKHA3 WILD-TYPE
  T1               0                17
  T2               2                90
  T3               5               324
  T4               1                49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  PLEKHA3 MUTATED     6   2   0
  PLEKHA3 WILD-TYPE 281 111  87
D1668V6, multiclass
    clus
vv   PLEKHA3 MUTATED PLEKHA3 WILD-TYPE
  N0               6               281
  N1               2               111
  N2               0                87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1668V7, binary
                   cls
clus                  0   1
  PLEKHA3 MUTATED     5   0
  PLEKHA3 WILD-TYPE 370  65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLEKHA3 MUTATED      5    0
  PLEKHA3 WILD-TYPE  370   65
   clus
vv  PLEKHA3 MUTATED PLEKHA3 WILD-TYPE
  0               5               370
  1               0                65
[1] 2 2
[1] FALSE
D1668V8, binary
                   cls
clus                  0   1
  PLEKHA3 MUTATED     3   5
  PLEKHA3 WILD-TYPE 222 259
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLEKHA3 MUTATED      3    5
  PLEKHA3 WILD-TYPE  222  259
        clus
vv       PLEKHA3 MUTATED PLEKHA3 WILD-TYPE
  FEMALE               3               222
  MALE                 5               259
[1] 2 2
[1] FALSE
D1668V9, binary
                   cls
clus                  0   1
  PLEKHA3 MUTATED     6   1
  PLEKHA3 WILD-TYPE 344  21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLEKHA3 MUTATED      6    1
  PLEKHA3 WILD-TYPE  344   21
     clus
vv    PLEKHA3 MUTATED PLEKHA3 WILD-TYPE
  NO                6               344
  YES               1                21
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PLEKHA3 MUTATED                      5                             0
  PLEKHA3 WILD-TYPE                  310                            47
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PLEKHA3 MUTATED                       2                              0
  PLEKHA3 WILD-TYPE                   104                             10
D1668V10, multiclass
                                clus
vv                               PLEKHA3 MUTATED PLEKHA3 WILD-TYPE
  COLON ADENOCARCINOMA                         5               310
  COLON MUCINOUS ADENOCARCINOMA                0                47
  RECTAL ADENOCARCINOMA                        2               104
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  PLEKHA3 MUTATED     5   0   0   0
  PLEKHA3 WILD-TYPE 340   4  31  25
D1668V11, multiclass
    clus
vv   PLEKHA3 MUTATED PLEKHA3 WILD-TYPE
  R0               5               340
  R1               0                 4
  R2               0                31
  RX               0                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1668V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PLEKHA3 MUTATED                                  0     0
  PLEKHA3 WILD-TYPE                                1    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  PLEKHA3 MUTATED                           0     5
  PLEKHA3 WILD-TYPE                        22   221
D1668V13, multiclass
                                  clus
vv                                 PLEKHA3 MUTATED PLEKHA3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                      0                22
  WHITE                                          5               221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1669) Variable = PCNA MUTATION ANALYSIS
D1669V1, survival
                sevent
clus2              0   1
  PCNA MUTATED     4   1
  PCNA WILD-TYPE 374  92
  PCNA MUTATED PCNA WILD-TYPE 
             5            466 
  PCNA MUTATED PCNA WILD-TYPE 
             1             92 
$`PCNA MUTATED`
TCGA-AA-3688 TCGA-AA-A010 TCGA-AG-3999 TCGA-DY-A1DF TCGA-F5-6465 
       19.00        34.98        28.04        24.13        49.51 

$`PCNA WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       19.99        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       57.24        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       20.91        18.28         9.96        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  PCNA MUTATED PCNA WILD-TYPE 
            19              0 
  PCNA MUTATED PCNA WILD-TYPE 
         49.51         148.01 
  PCNA MUTATED PCNA WILD-TYPE 
        28.040         20.085 
[1] "19.0 - 49.5 (28.0)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.2"
D1669V2, continuous
D1669V3, binary
                cls
clus               0   1
  PCNA MUTATED     2   3
  PCNA WILD-TYPE 364 116
[1] "tbl2"
                cls
clus             [,1] [,2]
  PCNA MUTATED      2    3
  PCNA WILD-TYPE  364  116
        clus
vv       PCNA MUTATED PCNA WILD-TYPE
  COLON             2            364
  RECTUM            3            116
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PCNA MUTATED         0        0        0         1         1         0
  PCNA WILD-TYPE      91        1       32       137         9         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PCNA MUTATED           0          0          0          2        1         0
  PCNA WILD-TYPE        24         11         59         40       47        18
                vv
clus             STAGE IVB
  PCNA MUTATED           0
  PCNA WILD-TYPE         1
D1669V4, multiclass
            clus
vv           PCNA MUTATED PCNA WILD-TYPE
  STAGE I               0             91
  STAGE IA              0              1
  STAGE II              0             32
  STAGE IIA             1            137
  STAGE IIB             1              9
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            0             59
  STAGE IIIC            2             40
  STAGE IV              1             47
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  PCNA MUTATED     0   0   4   1
  PCNA WILD-TYPE  17  92 325  49
D1669V5, multiclass
    clus
vv   PCNA MUTATED PCNA WILD-TYPE
  T1            0             17
  T2            0             92
  T3            4            325
  T4            1             49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  PCNA MUTATED     2   1   2
  PCNA WILD-TYPE 285 112  85
D1669V6, multiclass
    clus
vv   PCNA MUTATED PCNA WILD-TYPE
  N0            2            285
  N1            1            112
  N2            2             85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1669V7, binary
                cls
clus               0   1
  PCNA MUTATED     4   1
  PCNA WILD-TYPE 371  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  PCNA MUTATED      4    1
  PCNA WILD-TYPE  371   64
   clus
vv  PCNA MUTATED PCNA WILD-TYPE
  0            4            371
  1            1             64
[1] 2 2
[1] FALSE
D1669V8, binary
                cls
clus               0   1
  PCNA MUTATED     4   1
  PCNA WILD-TYPE 221 263
[1] "tbl2"
                cls
clus             [,1] [,2]
  PCNA MUTATED      4    1
  PCNA WILD-TYPE  221  263
        clus
vv       PCNA MUTATED PCNA WILD-TYPE
  FEMALE            4            221
  MALE              1            263
[1] 2 2
[1] FALSE
D1669V9, binary
                cls
clus               0   1
  PCNA MUTATED     4   0
  PCNA WILD-TYPE 346  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  PCNA MUTATED      4    0
  PCNA WILD-TYPE  346   22
     clus
vv    PCNA MUTATED PCNA WILD-TYPE
  NO             4            346
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PCNA MUTATED                      2                             0
  PCNA WILD-TYPE                  313                            47
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PCNA MUTATED                       3                              0
  PCNA WILD-TYPE                   103                             10
D1669V10, multiclass
                                clus
vv                               PCNA MUTATED PCNA WILD-TYPE
  COLON ADENOCARCINOMA                      2            313
  COLON MUCINOUS ADENOCARCINOMA             0             47
  RECTAL ADENOCARCINOMA                     3            103
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  PCNA MUTATED     3   0   1   0
  PCNA WILD-TYPE 342   4  30  25
D1669V11, multiclass
    clus
vv   PCNA MUTATED PCNA WILD-TYPE
  R0            3            342
  R1            0              4
  R2            1             30
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1669V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PCNA MUTATED                                  0     0
  PCNA WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  PCNA MUTATED                           0     2
  PCNA WILD-TYPE                        22   224
D1669V13, multiclass
[1] "Remove cluster labels:" "PCNA MUTATED"          
clus
  PCNA MUTATED PCNA WILD-TYPE 
             2            258 
    TCGA-A6-2671     TCGA-A6-2672     TCGA-A6-2674     TCGA-A6-2676 
"PCNA WILD-TYPE" "PCNA WILD-TYPE" "PCNA WILD-TYPE" "PCNA WILD-TYPE" 
    TCGA-A6-2677     TCGA-A6-2678     TCGA-A6-2683     TCGA-A6-3807 
"PCNA WILD-TYPE" "PCNA WILD-TYPE" "PCNA WILD-TYPE" "PCNA WILD-TYPE" 
    TCGA-A6-3808     TCGA-A6-3809     TCGA-A6-3810     TCGA-A6-4105 
"PCNA WILD-TYPE" "PCNA WILD-TYPE" "PCNA WILD-TYPE" "PCNA WILD-TYPE" 
    TCGA-A6-5656     TCGA-A6-5657     TCGA-A6-5659     TCGA-A6-5660 
"PCNA WILD-TYPE" "PCNA WILD-TYPE" "PCNA WILD-TYPE" "PCNA WILD-TYPE" 
    TCGA-A6-5661     TCGA-A6-5662     TCGA-A6-5664     TCGA-A6-5665 
"PCNA WILD-TYPE" "PCNA WILD-TYPE" "PCNA WILD-TYPE" "PCNA WILD-TYPE" 
    TCGA-A6-5666     TCGA-A6-6137     TCGA-A6-6138     TCGA-A6-6141 
"PCNA WILD-TYPE" "PCNA WILD-TYPE" "PCNA WILD-TYPE" "PCNA WILD-TYPE" 
    TCGA-A6-6142     TCGA-A6-6648     TCGA-A6-6649     TCGA-A6-6651 
"PCNA WILD-TYPE" "PCNA WILD-TYPE" "PCNA WILD-TYPE" "PCNA WILD-TYPE" 
    TCGA-A6-6652     TCGA-A6-6653     TCGA-A6-6654     TCGA-A6-6780 
"PCNA WILD-TYPE" "PCNA WILD-TYPE" "PCNA WILD-TYPE" "PCNA WILD-TYPE" 
    TCGA-A6-6781     TCGA-A6-6782     TCGA-AD-5900     TCGA-AD-6548 
"PCNA WILD-TYPE" "PCNA WILD-TYPE" "PCNA WILD-TYPE" "PCNA WILD-TYPE" 
    TCGA-AD-6888     TCGA-AD-6889     TCGA-AD-6890     TCGA-AD-6895 
"PCNA WILD-TYPE" "PCNA WILD-TYPE" "PCNA WILD-TYPE" "PCNA WILD-TYPE" 
    TCGA-AD-6899     TCGA-AD-6901     TCGA-AD-6963     TCGA-AD-6964 
"PCNA WILD-TYPE" "PCNA WILD-TYPE" "PCNA WILD-TYPE" "PCNA WILD-TYPE" 
    TCGA-AD-6965     TCGA-AU-3779     TCGA-AU-6004     TCGA-AY-4070 
"PCNA WILD-TYPE" "PCNA WILD-TYPE" "PCNA WILD-TYPE" "PCNA WILD-TYPE" 
    TCGA-AY-4071     TCGA-AY-5543     TCGA-AY-6196     TCGA-AY-6197 
"PCNA WILD-TYPE" "PCNA WILD-TYPE" "PCNA WILD-TYPE" "PCNA WILD-TYPE" 
    TCGA-AY-6386     TCGA-AZ-4315     TCGA-AZ-4323     TCGA-AZ-4616 
"PCNA WILD-TYPE" "PCNA WILD-TYPE" "PCNA WILD-TYPE" "PCNA WILD-TYPE" 
    TCGA-AZ-4681     TCGA-AZ-4682     TCGA-AZ-5403     TCGA-AZ-5407 
"PCNA WILD-TYPE" "PCNA WILD-TYPE" "PCNA WILD-TYPE" "PCNA WILD-TYPE" 
    TCGA-AZ-6598     TCGA-AZ-6599     TCGA-AZ-6600     TCGA-AZ-6601 
"PCNA WILD-TYPE" "PCNA WILD-TYPE" "PCNA WILD-TYPE" "PCNA WILD-TYPE" 
    TCGA-AZ-6603     TCGA-AZ-6605     TCGA-AZ-6606     TCGA-AZ-6607 
"PCNA WILD-TYPE" "PCNA WILD-TYPE" "PCNA WILD-TYPE" "PCNA WILD-TYPE" 
    TCGA-AZ-6608     TCGA-CA-5254     TCGA-CA-5255     TCGA-CA-5796 
"PCNA WILD-TYPE" "PCNA WILD-TYPE" "PCNA WILD-TYPE" "PCNA WILD-TYPE" 
    TCGA-CA-5797     TCGA-CA-6715     TCGA-CA-6716     TCGA-CA-6717 
"PCNA WILD-TYPE" "PCNA WILD-TYPE" "PCNA WILD-TYPE" "PCNA WILD-TYPE" 
    TCGA-CA-6718     TCGA-CA-6719     TCGA-CK-4947     TCGA-CK-4948 
"PCNA WILD-TYPE" "PCNA WILD-TYPE" "PCNA WILD-TYPE" "PCNA WILD-TYPE" 
    TCGA-CK-4950     TCGA-CK-4952     TCGA-CK-5912     TCGA-CK-5913 
"PCNA WILD-TYPE" "PCNA WILD-TYPE" "PCNA WILD-TYPE" "PCNA WILD-TYPE" 
    TCGA-CK-5914     TCGA-CK-5915     TCGA-CK-5916     TCGA-CK-6746 
"PCNA WILD-TYPE" "PCNA WILD-TYPE" "PCNA WILD-TYPE" "PCNA WILD-TYPE" 
    TCGA-CK-6747     TCGA-CK-6748     TCGA-CK-6751     TCGA-CM-4743 
"PCNA WILD-TYPE" "PCNA WILD-TYPE" "PCNA WILD-TYPE" "PCNA WILD-TYPE" 
    TCGA-CM-4744     TCGA-CM-4746     TCGA-CM-4747     TCGA-CM-4752 
"PCNA WILD-TYPE" "PCNA WILD-TYPE" "PCNA WILD-TYPE" "PCNA WILD-TYPE" 
    TCGA-CM-5341     TCGA-CM-5344     TCGA-CM-5348     TCGA-CM-5349 
"PCNA WILD-TYPE" "PCNA WILD-TYPE" "PCNA WILD-TYPE" "PCNA WILD-TYPE" 
    TCGA-CM-5860     TCGA-CM-5861     TCGA-CM-5862     TCGA-CM-5863 
"PCNA WILD-TYPE" "PCNA WILD-TYPE" "PCNA WILD-TYPE" "PCNA WILD-TYPE" 
    TCGA-CM-5864     TCGA-CM-5868     TCGA-CM-6161     TCGA-CM-6162 
"PCNA WILD-TYPE" "PCNA WILD-TYPE" "PCNA WILD-TYPE" "PCNA WILD-TYPE" 
    TCGA-CM-6163     TCGA-CM-6164     TCGA-CM-6165     TCGA-CM-6166 
"PCNA WILD-TYPE" "PCNA WILD-TYPE" "PCNA WILD-TYPE" "PCNA WILD-TYPE" 
    TCGA-CM-6167     TCGA-CM-6168     TCGA-CM-6169     TCGA-CM-6170 
"PCNA WILD-TYPE" "PCNA WILD-TYPE" "PCNA WILD-TYPE" "PCNA WILD-TYPE" 
    TCGA-CM-6171     TCGA-CM-6172     TCGA-CM-6674     TCGA-CM-6675 
"PCNA WILD-TYPE" "PCNA WILD-TYPE" "PCNA WILD-TYPE" "PCNA WILD-TYPE" 
    TCGA-CM-6676     TCGA-CM-6677     TCGA-CM-6678     TCGA-CM-6679 
"PCNA WILD-TYPE" "PCNA WILD-TYPE" "PCNA WILD-TYPE" "PCNA WILD-TYPE" 
    TCGA-CM-6680     TCGA-D5-5537     TCGA-D5-5538     TCGA-D5-5539 
"PCNA WILD-TYPE" "PCNA WILD-TYPE" "PCNA WILD-TYPE" "PCNA WILD-TYPE" 
    TCGA-D5-5540     TCGA-D5-5541     TCGA-D5-6529     TCGA-D5-6532 
"PCNA WILD-TYPE" "PCNA WILD-TYPE" "PCNA WILD-TYPE" "PCNA WILD-TYPE" 
    TCGA-D5-6533     TCGA-D5-6534     TCGA-D5-6535     TCGA-D5-6536 
"PCNA WILD-TYPE" "PCNA WILD-TYPE" "PCNA WILD-TYPE" "PCNA WILD-TYPE" 
    TCGA-D5-6537     TCGA-D5-6538     TCGA-D5-6539     TCGA-D5-6540 
"PCNA WILD-TYPE" "PCNA WILD-TYPE" "PCNA WILD-TYPE" "PCNA WILD-TYPE" 
    TCGA-D5-6541     TCGA-D5-6898     TCGA-D5-6920     TCGA-D5-6922 
"PCNA WILD-TYPE" "PCNA WILD-TYPE" "PCNA WILD-TYPE" "PCNA WILD-TYPE" 
    TCGA-D5-6923     TCGA-D5-6924     TCGA-D5-6926     TCGA-D5-6927 
"PCNA WILD-TYPE" "PCNA WILD-TYPE" "PCNA WILD-TYPE" "PCNA WILD-TYPE" 
    TCGA-D5-6928     TCGA-D5-6929     TCGA-D5-6930     TCGA-D5-6931 
"PCNA WILD-TYPE" "PCNA WILD-TYPE" "PCNA WILD-TYPE" "PCNA WILD-TYPE" 
    TCGA-D5-6932     TCGA-D5-7000     TCGA-DM-A0X9     TCGA-DM-A0XD 
"PCNA WILD-TYPE" "PCNA WILD-TYPE" "PCNA WILD-TYPE" "PCNA WILD-TYPE" 
    TCGA-DM-A0XF     TCGA-DM-A1D0     TCGA-DM-A1D4     TCGA-DM-A1D6 
"PCNA WILD-TYPE" "PCNA WILD-TYPE" "PCNA WILD-TYPE" "PCNA WILD-TYPE" 
    TCGA-DM-A1D7     TCGA-DM-A1D8     TCGA-DM-A1D9     TCGA-DM-A1DA 
"PCNA WILD-TYPE" "PCNA WILD-TYPE" "PCNA WILD-TYPE" "PCNA WILD-TYPE" 
    TCGA-DM-A1DB     TCGA-DM-A1HA     TCGA-DM-A1HB     TCGA-DM-A282 
"PCNA WILD-TYPE" "PCNA WILD-TYPE" "PCNA WILD-TYPE" "PCNA WILD-TYPE" 
    TCGA-DM-A285     TCGA-DM-A28C     TCGA-DM-A28E     TCGA-DM-A28F 
"PCNA WILD-TYPE" "PCNA WILD-TYPE" "PCNA WILD-TYPE" "PCNA WILD-TYPE" 
    TCGA-DM-A28G     TCGA-DM-A28H     TCGA-DM-A28K     TCGA-F4-6459 
"PCNA WILD-TYPE" "PCNA WILD-TYPE" "PCNA WILD-TYPE" "PCNA WILD-TYPE" 
    TCGA-F4-6460     TCGA-F4-6569     TCGA-F4-6570     TCGA-F4-6703 
"PCNA WILD-TYPE" "PCNA WILD-TYPE" "PCNA WILD-TYPE" "PCNA WILD-TYPE" 
    TCGA-F4-6704     TCGA-F4-6805     TCGA-F4-6806     TCGA-F4-6807 
"PCNA WILD-TYPE" "PCNA WILD-TYPE" "PCNA WILD-TYPE" "PCNA WILD-TYPE" 
    TCGA-F4-6808     TCGA-F4-6809     TCGA-F4-6854     TCGA-F4-6855 
"PCNA WILD-TYPE" "PCNA WILD-TYPE" "PCNA WILD-TYPE" "PCNA WILD-TYPE" 
    TCGA-F4-6856     TCGA-G4-6293     TCGA-G4-6299     TCGA-G4-6303 
"PCNA WILD-TYPE" "PCNA WILD-TYPE" "PCNA WILD-TYPE" "PCNA WILD-TYPE" 
    TCGA-G4-6304     TCGA-G4-6306     TCGA-G4-6307     TCGA-G4-6309 
"PCNA WILD-TYPE" "PCNA WILD-TYPE" "PCNA WILD-TYPE" "PCNA WILD-TYPE" 
    TCGA-G4-6310     TCGA-G4-6315     TCGA-G4-6317     TCGA-G4-6321 
"PCNA WILD-TYPE" "PCNA WILD-TYPE" "PCNA WILD-TYPE" "PCNA WILD-TYPE" 
    TCGA-G4-6323     TCGA-G4-6586     TCGA-G4-6588     TCGA-G4-6625 
"PCNA WILD-TYPE" "PCNA WILD-TYPE" "PCNA WILD-TYPE" "PCNA WILD-TYPE" 
    TCGA-G4-6626     TCGA-G4-6628     TCGA-AF-2687     TCGA-AF-2689 
"PCNA WILD-TYPE" "PCNA WILD-TYPE" "PCNA WILD-TYPE" "PCNA WILD-TYPE" 
    TCGA-AF-2691     TCGA-AF-2692     TCGA-AF-2693     TCGA-AF-3400 
"PCNA WILD-TYPE" "PCNA WILD-TYPE" "PCNA WILD-TYPE" "PCNA WILD-TYPE" 
    TCGA-AF-3913     TCGA-AF-4110     TCGA-AF-5654     TCGA-AF-6136 
"PCNA WILD-TYPE" "PCNA WILD-TYPE" "PCNA WILD-TYPE" "PCNA WILD-TYPE" 
    TCGA-AF-6655     TCGA-AF-6672     TCGA-AH-6544     TCGA-AH-6547 
"PCNA WILD-TYPE" "PCNA WILD-TYPE" "PCNA WILD-TYPE" "PCNA WILD-TYPE" 
    TCGA-AH-6549     TCGA-AH-6643     TCGA-AH-6644     TCGA-CI-6619 
"PCNA WILD-TYPE" "PCNA WILD-TYPE" "PCNA WILD-TYPE" "PCNA WILD-TYPE" 
    TCGA-CI-6620     TCGA-CI-6621     TCGA-CI-6622     TCGA-CI-6624 
"PCNA WILD-TYPE" "PCNA WILD-TYPE" "PCNA WILD-TYPE" "PCNA WILD-TYPE" 
    TCGA-CL-5917     TCGA-CL-5918     TCGA-DC-5337     TCGA-DC-5869 
"PCNA WILD-TYPE" "PCNA WILD-TYPE" "PCNA WILD-TYPE" "PCNA WILD-TYPE" 
    TCGA-DC-6155     TCGA-DC-6157     TCGA-DC-6158     TCGA-DC-6160 
"PCNA WILD-TYPE" "PCNA WILD-TYPE" "PCNA WILD-TYPE" "PCNA WILD-TYPE" 
    TCGA-DC-6681     TCGA-DC-6682     TCGA-DC-6683     TCGA-DT-5265 
"PCNA WILD-TYPE" "PCNA WILD-TYPE" "PCNA WILD-TYPE" "PCNA WILD-TYPE" 
    TCGA-DY-A0XA     TCGA-DY-A1DC     TCGA-DY-A1DD     TCGA-DY-A1DG 
"PCNA WILD-TYPE" "PCNA WILD-TYPE" "PCNA WILD-TYPE" "PCNA WILD-TYPE" 
    TCGA-DY-A1H8     TCGA-EF-5830     TCGA-EI-6506     TCGA-EI-6507 
"PCNA WILD-TYPE" "PCNA WILD-TYPE" "PCNA WILD-TYPE" "PCNA WILD-TYPE" 
    TCGA-EI-6508     TCGA-EI-6510     TCGA-F5-6464     TCGA-F5-6571 
"PCNA WILD-TYPE" "PCNA WILD-TYPE" "PCNA WILD-TYPE" "PCNA WILD-TYPE" 
    TCGA-F5-6702     TCGA-F5-6811     TCGA-F5-6812     TCGA-F5-6813 
"PCNA WILD-TYPE" "PCNA WILD-TYPE" "PCNA WILD-TYPE" "PCNA WILD-TYPE" 
    TCGA-G5-6235     TCGA-G5-6641 
"PCNA WILD-TYPE" "PCNA WILD-TYPE" 

Clustering(1670) Variable = ABCB6 MUTATION ANALYSIS
D1670V1, survival
                 sevent
clus2               0   1
  ABCB6 MUTATED     5   3
  ABCB6 WILD-TYPE 373  90
  ABCB6 MUTATED ABCB6 WILD-TYPE 
              8             463 
  ABCB6 MUTATED ABCB6 WILD-TYPE 
              3              90 
$`ABCB6 MUTATED`
TCGA-AA-3672 TCGA-AA-3696 TCGA-AA-A01Q TCGA-AU-3779 TCGA-AZ-6600 TCGA-AZ-6601 
        0.92         5.03         1.02        14.50        12.10       100.01 
TCGA-D5-6927 TCGA-AG-A002 
        9.44        20.98 

$`ABCB6 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
        6.05         6.97        54.02         2.01        14.01        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
       36.00        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        31.00        38.07        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
        0.20        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6603 TCGA-AZ-6605 
       62.79        88.21        49.41         6.77        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.04        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  ABCB6 MUTATED ABCB6 WILD-TYPE 
           0.92            0.00 
  ABCB6 MUTATED ABCB6 WILD-TYPE 
         100.01          148.01 
  ABCB6 MUTATED ABCB6 WILD-TYPE 
          10.77           20.55 
[1] "0.9 - 100.0 (10.8)" "0.0 - 148.0 (20.6)"
[1] "hr=" "2.4"
D1670V2, continuous
D1670V3, binary
                 cls
clus                0   1
  ABCB6 MUTATED     7   1
  ABCB6 WILD-TYPE 359 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCB6 MUTATED      7    1
  ABCB6 WILD-TYPE  359  118
        clus
vv       ABCB6 MUTATED ABCB6 WILD-TYPE
  COLON              7             359
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ABCB6 MUTATED         1        0        2         2         0         0
  ABCB6 WILD-TYPE      90        1       30       136        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ABCB6 MUTATED           1          0          0          0        2         0
  ABCB6 WILD-TYPE        23         11         59         42       46        18
                 vv
clus              STAGE IVB
  ABCB6 MUTATED           0
  ABCB6 WILD-TYPE         1
D1670V4, multiclass
            clus
vv           ABCB6 MUTATED ABCB6 WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA              2             136
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             0              42
  STAGE IV               2              46
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ABCB6 MUTATED     0   1   6   1
  ABCB6 WILD-TYPE  17  91 323  49
D1670V5, multiclass
    clus
vv   ABCB6 MUTATED ABCB6 WILD-TYPE
  T1             0              17
  T2             1              91
  T3             6             323
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  ABCB6 MUTATED     5   3   0
  ABCB6 WILD-TYPE 282 110  87
D1670V6, multiclass
    clus
vv   ABCB6 MUTATED ABCB6 WILD-TYPE
  N0             5             282
  N1             3             110
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1670V7, binary
                 cls
clus                0   1
  ABCB6 MUTATED     6   2
  ABCB6 WILD-TYPE 369  63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCB6 MUTATED      6    2
  ABCB6 WILD-TYPE  369   63
   clus
vv  ABCB6 MUTATED ABCB6 WILD-TYPE
  0             6             369
  1             2              63
[1] 2 2
[1] FALSE
D1670V8, binary
                 cls
clus                0   1
  ABCB6 MUTATED     4   4
  ABCB6 WILD-TYPE 221 260
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCB6 MUTATED      4    4
  ABCB6 WILD-TYPE  221  260
        clus
vv       ABCB6 MUTATED ABCB6 WILD-TYPE
  FEMALE             4             221
  MALE               4             260
[1] 2 2
[1] FALSE
D1670V9, binary
                 cls
clus                0   1
  ABCB6 MUTATED     6   0
  ABCB6 WILD-TYPE 344  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABCB6 MUTATED      6    0
  ABCB6 WILD-TYPE  344   22
     clus
vv    ABCB6 MUTATED ABCB6 WILD-TYPE
  NO              6             344
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ABCB6 MUTATED                      7                             0
  ABCB6 WILD-TYPE                  308                            47
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ABCB6 MUTATED                       1                              0
  ABCB6 WILD-TYPE                   105                             10
D1670V10, multiclass
                                clus
vv                               ABCB6 MUTATED ABCB6 WILD-TYPE
  COLON ADENOCARCINOMA                       7             308
  COLON MUCINOUS ADENOCARCINOMA              0              47
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  ABCB6 MUTATED     5   0   1   0
  ABCB6 WILD-TYPE 340   4  30  25
D1670V11, multiclass
    clus
vv   ABCB6 MUTATED ABCB6 WILD-TYPE
  R0             5             340
  R1             0               4
  R2             1              30
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1670V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ABCB6 MUTATED                                  0     0
  ABCB6 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ABCB6 MUTATED                           1     3
  ABCB6 WILD-TYPE                        21   223
D1670V13, multiclass
                                  clus
vv                                 ABCB6 MUTATED ABCB6 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        3             223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1671) Variable = GGNBP2 MUTATION ANALYSIS
D1671V1, survival
                  sevent
clus2                0   1
  GGNBP2 MUTATED    10   2
  GGNBP2 WILD-TYPE 368  91
  GGNBP2 MUTATED GGNBP2 WILD-TYPE 
              12              459 
  GGNBP2 MUTATED GGNBP2 WILD-TYPE 
               2               91 
$`GGNBP2 MUTATED`
TCGA-AA-A00N TCGA-AA-A010 TCGA-AU-6004 TCGA-AY-6197 TCGA-AZ-4315 TCGA-CK-4948 
        4.01        34.98        27.09        21.44        58.39       148.01 
TCGA-CM-6169 TCGA-CM-6677 TCGA-DM-A28E TCGA-F4-6570 TCGA-AG-3893 TCGA-AG-A002 
       13.02        11.08       119.93         6.18        35.01        20.98 

$`GGNBP2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       10.88         0.20        14.50        16.31         0.95        33.01 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       14.30        17.56        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6170 TCGA-CM-6171 
       16.04        21.99        14.99        12.99        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6678 TCGA-CM-6679 
       11.01        12.95        13.05        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28F TCGA-DM-A28G 
      135.65       139.17         6.12        81.37        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 
      117.07        98.24         8.61        31.96        35.74        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3894 
        1.02        17.95        36.95        17.03        13.02        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  GGNBP2 MUTATED GGNBP2 WILD-TYPE 
            4.01             0.00 
  GGNBP2 MUTATED GGNBP2 WILD-TYPE 
          148.01           140.38 
  GGNBP2 MUTATED GGNBP2 WILD-TYPE 
          24.265           20.050 
[1] "4.0 - 148.0 (24.3)" "0.0 - 140.4 (20.1)"
[1] "hr=" "1.6"
D1671V2, continuous
D1671V3, binary
                  cls
clus                 0   1
  GGNBP2 MUTATED    11   2
  GGNBP2 WILD-TYPE 355 117
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GGNBP2 MUTATED     11    2
  GGNBP2 WILD-TYPE  355  117
        clus
vv       GGNBP2 MUTATED GGNBP2 WILD-TYPE
  COLON              11              355
  RECTUM              2              117
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GGNBP2 MUTATED         2        0        0         6         3         0
  GGNBP2 WILD-TYPE      89        1       32       132         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GGNBP2 MUTATED           1          0          1          0        0
  GGNBP2 WILD-TYPE        23         11         58         42       48
                  vv
clus               STAGE IVA STAGE IVB
  GGNBP2 MUTATED           0         0
  GGNBP2 WILD-TYPE        18         1
D1671V4, multiclass
            clus
vv           GGNBP2 MUTATED GGNBP2 WILD-TYPE
  STAGE I                 2               89
  STAGE IA                0                1
  STAGE II                0               32
  STAGE IIA               6              132
  STAGE IIB               3                7
  STAGE IIC               0                1
  STAGE III               1               23
  STAGE IIIA              0               11
  STAGE IIIB              1               58
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  GGNBP2 MUTATED     0   2   8   3
  GGNBP2 WILD-TYPE  17  90 321  47
D1671V5, multiclass
    clus
vv   GGNBP2 MUTATED GGNBP2 WILD-TYPE
  T1              0               17
  T2              2               90
  T3              8              321
  T4              3               47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  GGNBP2 MUTATED    11   2   0
  GGNBP2 WILD-TYPE 276 111  87
D1671V6, multiclass
    clus
vv   GGNBP2 MUTATED GGNBP2 WILD-TYPE
  N0             11              276
  N1              2              111
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1671V7, binary
                  cls
clus                 0   1
  GGNBP2 MUTATED    11   0
  GGNBP2 WILD-TYPE 364  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GGNBP2 MUTATED     11    0
  GGNBP2 WILD-TYPE  364   65
   clus
vv  GGNBP2 MUTATED GGNBP2 WILD-TYPE
  0             11              364
  1              0               65
[1] 2 2
[1] FALSE
D1671V8, binary
                  cls
clus                 0   1
  GGNBP2 MUTATED     7   6
  GGNBP2 WILD-TYPE 218 258
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GGNBP2 MUTATED      7    6
  GGNBP2 WILD-TYPE  218  258
        clus
vv       GGNBP2 MUTATED GGNBP2 WILD-TYPE
  FEMALE              7              218
  MALE                6              258
[1] 2 2
[1] FALSE
D1671V9, binary
                  cls
clus                 0   1
  GGNBP2 MUTATED     9   0
  GGNBP2 WILD-TYPE 341  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GGNBP2 MUTATED      9    0
  GGNBP2 WILD-TYPE  341   22
     clus
vv    GGNBP2 MUTATED GGNBP2 WILD-TYPE
  NO               9              341
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  GGNBP2 MUTATED                     10                             1
  GGNBP2 WILD-TYPE                  305                            46
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  GGNBP2 MUTATED                       2                              0
  GGNBP2 WILD-TYPE                   104                             10
D1671V10, multiclass
                                clus
vv                               GGNBP2 MUTATED GGNBP2 WILD-TYPE
  COLON ADENOCARCINOMA                       10              305
  COLON MUCINOUS ADENOCARCINOMA               1               46
  RECTAL ADENOCARCINOMA                       2              104
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  GGNBP2 MUTATED    11   0   0   1
  GGNBP2 WILD-TYPE 334   4  31  24
D1671V11, multiclass
    clus
vv   GGNBP2 MUTATED GGNBP2 WILD-TYPE
  R0             11              334
  R1              0                4
  R2              0               31
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1671V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GGNBP2 MUTATED                                  0     0
  GGNBP2 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  GGNBP2 MUTATED                           1     8
  GGNBP2 WILD-TYPE                        21   218
D1671V13, multiclass
                                  clus
vv                                 GGNBP2 MUTATED GGNBP2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                         8              218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1672) Variable = CCDC3 MUTATION ANALYSIS
D1672V1, survival
                 sevent
clus2               0   1
  CCDC3 MUTATED     3   2
  CCDC3 WILD-TYPE 375  91
  CCDC3 MUTATED CCDC3 WILD-TYPE 
              5             466 
  CCDC3 MUTATED CCDC3 WILD-TYPE 
              2              91 
$`CCDC3 MUTATED`
TCGA-AA-3713 TCGA-CM-5862 TCGA-CM-6678 TCGA-D5-6537 TCGA-AG-A002 
       19.04         5.03        11.01         4.80        20.98 

$`CCDC3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       30.08        32.02        15.02        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6679 TCGA-CM-6680 
       12.95        13.05        11.08        11.08        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6538 
       18.25         1.32        43.27        15.12        17.85        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  CCDC3 MUTATED CCDC3 WILD-TYPE 
            4.8             0.0 
  CCDC3 MUTATED CCDC3 WILD-TYPE 
          20.98          148.01 
  CCDC3 MUTATED CCDC3 WILD-TYPE 
         11.010          20.415 
[1] "4.8 - 21.0 (11.0)"  "0.0 - 148.0 (20.4)"
[1] "hr=" "4.2"
D1672V2, continuous
D1672V3, binary
                 cls
clus                0   1
  CCDC3 MUTATED     4   1
  CCDC3 WILD-TYPE 362 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CCDC3 MUTATED      4    1
  CCDC3 WILD-TYPE  362  118
        clus
vv       CCDC3 MUTATED CCDC3 WILD-TYPE
  COLON              4             362
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CCDC3 MUTATED         1        0        0         0         0         0
  CCDC3 WILD-TYPE      90        1       32       138        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CCDC3 MUTATED           0          0          1          0        1         2
  CCDC3 WILD-TYPE        24         11         58         42       47        16
                 vv
clus              STAGE IVB
  CCDC3 MUTATED           0
  CCDC3 WILD-TYPE         1
D1672V4, multiclass
            clus
vv           CCDC3 MUTATED CCDC3 WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              0             138
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             0              42
  STAGE IV               1              47
  STAGE IVA              2              16
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CCDC3 MUTATED     0   1   3   1
  CCDC3 WILD-TYPE  17  91 326  49
D1672V5, multiclass
    clus
vv   CCDC3 MUTATED CCDC3 WILD-TYPE
  T1             0              17
  T2             1              91
  T3             3             326
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  CCDC3 MUTATED     2   3   0
  CCDC3 WILD-TYPE 285 110  87
D1672V6, multiclass
    clus
vv   CCDC3 MUTATED CCDC3 WILD-TYPE
  N0             2             285
  N1             3             110
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1672V7, binary
                 cls
clus                0   1
  CCDC3 MUTATED     1   3
  CCDC3 WILD-TYPE 374  62
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CCDC3 MUTATED      1    3
  CCDC3 WILD-TYPE  374   62
   clus
vv  CCDC3 MUTATED CCDC3 WILD-TYPE
  0             1             374
  1             3              62
[1] 2 2
[1] FALSE
D1672V8, binary
                 cls
clus                0   1
  CCDC3 MUTATED     1   4
  CCDC3 WILD-TYPE 224 260
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CCDC3 MUTATED      1    4
  CCDC3 WILD-TYPE  224  260
        clus
vv       CCDC3 MUTATED CCDC3 WILD-TYPE
  FEMALE             1             224
  MALE               4             260
[1] 2 2
[1] FALSE
D1672V9, binary
                 cls
clus                0   1
  CCDC3 MUTATED     4   1
  CCDC3 WILD-TYPE 346  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CCDC3 MUTATED      4    1
  CCDC3 WILD-TYPE  346   21
     clus
vv    CCDC3 MUTATED CCDC3 WILD-TYPE
  NO              4             346
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CCDC3 MUTATED                      4                             0
  CCDC3 WILD-TYPE                  311                            47
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CCDC3 MUTATED                       1                              0
  CCDC3 WILD-TYPE                   105                             10
D1672V10, multiclass
                                clus
vv                               CCDC3 MUTATED CCDC3 WILD-TYPE
  COLON ADENOCARCINOMA                       4             311
  COLON MUCINOUS ADENOCARCINOMA              0              47
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  CCDC3 MUTATED     4   0   1   0
  CCDC3 WILD-TYPE 341   4  30  25
D1672V11, multiclass
    clus
vv   CCDC3 MUTATED CCDC3 WILD-TYPE
  R0             4             341
  R1             0               4
  R2             1              30
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1672V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CCDC3 MUTATED                                  0     0
  CCDC3 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CCDC3 MUTATED                           0     3
  CCDC3 WILD-TYPE                        22   223
D1672V13, multiclass
                                  clus
vv                                 CCDC3 MUTATED CCDC3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        3             223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1673) Variable = TATDN2 MUTATION ANALYSIS
D1673V1, survival
                  sevent
clus2                0   1
  TATDN2 MUTATED    11   1
  TATDN2 WILD-TYPE 367  92
  TATDN2 MUTATED TATDN2 WILD-TYPE 
              12              459 
  TATDN2 MUTATED TATDN2 WILD-TYPE 
               1               92 
$`TATDN2 MUTATED`
TCGA-A6-5665 TCGA-A6-6653 TCGA-AA-3554 TCGA-AA-3966 TCGA-AA-A00J TCGA-AA-A00N 
       22.06        24.39        17.95         2.01        18.05         4.01 
TCGA-AA-A010 TCGA-CM-6674 TCGA-CM-6676 TCGA-AG-3898 TCGA-AG-A002 TCGA-AG-A02N 
       34.98        12.95        11.08        48.03        20.98        61.97 

$`TATDN2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 
       25.18        24.16        21.76        24.69        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       24.00        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
       34.03        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       34.03        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       11.01        13.05        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       35.01        14.01         1.02        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       38.96        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  TATDN2 MUTATED TATDN2 WILD-TYPE 
            2.01             0.00 
  TATDN2 MUTATED TATDN2 WILD-TYPE 
           61.97           148.01 
  TATDN2 MUTATED TATDN2 WILD-TYPE 
          19.515           20.190 
[1] "2.0 - 62.0 (19.5)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "2.2"
D1673V2, continuous
D1673V3, binary
                  cls
clus                 0   1
  TATDN2 MUTATED     9   3
  TATDN2 WILD-TYPE 357 116
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TATDN2 MUTATED      9    3
  TATDN2 WILD-TYPE  357  116
        clus
vv       TATDN2 MUTATED TATDN2 WILD-TYPE
  COLON               9              357
  RECTUM              3              116
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TATDN2 MUTATED         3        0        1         5         2         0
  TATDN2 WILD-TYPE      88        1       31       133         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TATDN2 MUTATED           0          0          1          0        0
  TATDN2 WILD-TYPE        24         11         58         42       48
                  vv
clus               STAGE IVA STAGE IVB
  TATDN2 MUTATED           0         0
  TATDN2 WILD-TYPE        18         1
D1673V4, multiclass
            clus
vv           TATDN2 MUTATED TATDN2 WILD-TYPE
  STAGE I                 3               88
  STAGE IA                0                1
  STAGE II                1               31
  STAGE IIA               5              133
  STAGE IIB               2                8
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              1               58
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  TATDN2 MUTATED     0   3   6   3
  TATDN2 WILD-TYPE  17  89 323  47
D1673V5, multiclass
    clus
vv   TATDN2 MUTATED TATDN2 WILD-TYPE
  T1              0               17
  T2              3               89
  T3              6              323
  T4              3               47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  TATDN2 MUTATED    11   1   0
  TATDN2 WILD-TYPE 276 112  87
D1673V6, multiclass
    clus
vv   TATDN2 MUTATED TATDN2 WILD-TYPE
  N0             11              276
  N1              1              112
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1673V7, binary
                  cls
clus                 0   1
  TATDN2 MUTATED    12   0
  TATDN2 WILD-TYPE 363  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TATDN2 MUTATED     12    0
  TATDN2 WILD-TYPE  363   65
   clus
vv  TATDN2 MUTATED TATDN2 WILD-TYPE
  0             12              363
  1              0               65
[1] 2 2
[1] FALSE
D1673V8, binary
                  cls
clus                 0   1
  TATDN2 MUTATED     4   8
  TATDN2 WILD-TYPE 221 256
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TATDN2 MUTATED      4    8
  TATDN2 WILD-TYPE  221  256
        clus
vv       TATDN2 MUTATED TATDN2 WILD-TYPE
  FEMALE              4              221
  MALE                8              256
[1] 2 2
[1] FALSE
D1673V9, binary
                  cls
clus                 0   1
  TATDN2 MUTATED     9   0
  TATDN2 WILD-TYPE 341  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TATDN2 MUTATED      9    0
  TATDN2 WILD-TYPE  341   22
     clus
vv    TATDN2 MUTATED TATDN2 WILD-TYPE
  NO               9              341
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  TATDN2 MUTATED                      6                             3
  TATDN2 WILD-TYPE                  309                            44
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  TATDN2 MUTATED                       3                              0
  TATDN2 WILD-TYPE                   103                             10
D1673V10, multiclass
                                clus
vv                               TATDN2 MUTATED TATDN2 WILD-TYPE
  COLON ADENOCARCINOMA                        6              309
  COLON MUCINOUS ADENOCARCINOMA               3               44
  RECTAL ADENOCARCINOMA                       3              103
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  TATDN2 MUTATED    10   0   0   0
  TATDN2 WILD-TYPE 335   4  31  25
D1673V11, multiclass
    clus
vv   TATDN2 MUTATED TATDN2 WILD-TYPE
  R0             10              335
  R1              0                4
  R2              0               31
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1673V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TATDN2 MUTATED                                  0     0
  TATDN2 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  TATDN2 MUTATED                           0     4
  TATDN2 WILD-TYPE                        22   222
D1673V13, multiclass
                                  clus
vv                                 TATDN2 MUTATED TATDN2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         4              222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1674) Variable = USP1 MUTATION ANALYSIS
D1674V1, survival
                sevent
clus2              0   1
  USP1 MUTATED     6   2
  USP1 WILD-TYPE 372  91
  USP1 MUTATED USP1 WILD-TYPE 
             8            463 
  USP1 MUTATED USP1 WILD-TYPE 
             2             91 
$`USP1 MUTATED`
TCGA-A6-5665 TCGA-AA-3510 TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-6162 TCGA-CM-6171 
       22.06        63.98        12.76        10.06        12.00        14.04 
TCGA-D5-6927 TCGA-F4-6570 
        9.44         6.18 

$`USP1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       12.20        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 
        5.03        15.02        15.02        17.03        15.02         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       15.02        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.04        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       35.74        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  USP1 MUTATED USP1 WILD-TYPE 
          6.18           0.00 
  USP1 MUTATED USP1 WILD-TYPE 
         63.98         148.01 
  USP1 MUTATED USP1 WILD-TYPE 
         12.38          20.55 
[1] "6.2 - 64.0 (12.4)"  "0.0 - 148.0 (20.6)"
[1] "hr=" "1.6"
D1674V2, continuous
D1674V3, binary
                cls
clus               0   1
  USP1 MUTATED     9   0
  USP1 WILD-TYPE 357 119
[1] "tbl2"
                cls
clus             [,1] [,2]
  USP1 MUTATED      9    0
  USP1 WILD-TYPE  357  119
        clus
vv       USP1 MUTATED USP1 WILD-TYPE
  COLON             9            357
  RECTUM            0            119
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  USP1 MUTATED         1        0        1         5         0         0
  USP1 WILD-TYPE      90        1       31       133        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  USP1 MUTATED           0          0          1          1        0         0
  USP1 WILD-TYPE        24         11         58         41       48        18
                vv
clus             STAGE IVB
  USP1 MUTATED           0
  USP1 WILD-TYPE         1
D1674V4, multiclass
            clus
vv           USP1 MUTATED USP1 WILD-TYPE
  STAGE I               1             90
  STAGE IA              0              1
  STAGE II              1             31
  STAGE IIA             5            133
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            1             58
  STAGE IIIC            1             41
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  USP1 MUTATED     0   1   8   0
  USP1 WILD-TYPE  17  91 321  50
D1674V5, multiclass
    clus
vv   USP1 MUTATED USP1 WILD-TYPE
  T1            0             17
  T2            1             91
  T3            8            321
  T4            0             50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  USP1 MUTATED     7   1   1
  USP1 WILD-TYPE 280 112  86
D1674V6, multiclass
    clus
vv   USP1 MUTATED USP1 WILD-TYPE
  N0            7            280
  N1            1            112
  N2            1             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1674V7, binary
                cls
clus               0   1
  USP1 MUTATED     8   0
  USP1 WILD-TYPE 367  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  USP1 MUTATED      8    0
  USP1 WILD-TYPE  367   65
   clus
vv  USP1 MUTATED USP1 WILD-TYPE
  0            8            367
  1            0             65
[1] 2 2
[1] FALSE
D1674V8, binary
                cls
clus               0   1
  USP1 MUTATED     4   5
  USP1 WILD-TYPE 221 259
[1] "tbl2"
                cls
clus             [,1] [,2]
  USP1 MUTATED      4    5
  USP1 WILD-TYPE  221  259
        clus
vv       USP1 MUTATED USP1 WILD-TYPE
  FEMALE            4            221
  MALE              5            259
[1] 2 2
[1] FALSE
D1674V9, binary
                cls
clus               0   1
  USP1 MUTATED     8   0
  USP1 WILD-TYPE 342  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  USP1 MUTATED      8    0
  USP1 WILD-TYPE  342   22
     clus
vv    USP1 MUTATED USP1 WILD-TYPE
  NO             8            342
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  USP1 MUTATED                      6                             3
  USP1 WILD-TYPE                  309                            44
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  USP1 MUTATED                       0                              0
  USP1 WILD-TYPE                   106                             10
D1674V10, multiclass
                                clus
vv                               USP1 MUTATED USP1 WILD-TYPE
  COLON ADENOCARCINOMA                      6            309
  COLON MUCINOUS ADENOCARCINOMA             3             44
  RECTAL ADENOCARCINOMA                     0            106
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  USP1 MUTATED     7   0   0   2
  USP1 WILD-TYPE 338   4  31  23
D1674V11, multiclass
    clus
vv   USP1 MUTATED USP1 WILD-TYPE
  R0            7            338
  R1            0              4
  R2            0             31
  RX            2             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1674V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  USP1 MUTATED                                  0     2
  USP1 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  USP1 MUTATED                           0     6
  USP1 WILD-TYPE                        22   220
D1674V13, multiclass
                                  clus
vv                                 USP1 MUTATED USP1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              9
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       6            220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1675) Variable = IFLTD1 MUTATION ANALYSIS
D1675V1, survival
                  sevent
clus2                0   1
  IFLTD1 MUTATED    12   0
  IFLTD1 WILD-TYPE 366  93
  IFLTD1 MUTATED IFLTD1 WILD-TYPE 
              12              459 
  IFLTD1 MUTATED IFLTD1 WILD-TYPE 
               0               93 
$`IFLTD1 MUTATED`
TCGA-A6-5660 TCGA-A6-5665 TCGA-AA-3524 TCGA-AA-3710 TCGA-AA-3864 TCGA-AA-3977 
       29.19        22.06        36.03        26.99        53.00        25.02 
TCGA-AY-6386 TCGA-CA-6717 TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-6675 TCGA-AG-A036 
       17.82        12.76        30.08        15.02        13.05       117.11 

$`IFLTD1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        33.53        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
        9.07        24.03        37.05         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       85.05        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       31.07        30.05        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-4323 
       16.31         0.95        33.01        21.44        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07        12.20        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5860 
       25.02        13.02        29.06        22.03        22.98        32.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6676 
       13.02        15.02        14.04        11.01        12.95        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 
       38.96        61.97        41.00        38.04        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  IFLTD1 MUTATED IFLTD1 WILD-TYPE 
           12.76             0.00 
  IFLTD1 MUTATED IFLTD1 WILD-TYPE 
          117.11           148.01 
  IFLTD1 MUTATED IFLTD1 WILD-TYPE 
          26.005           20.050 
[1] "12.8 - 117.1 (26.0)" "0.0 - 148.0 (20.1)" 
[1] "hr="     "2.5e+07"
D1675V2, continuous
D1675V3, binary
                  cls
clus                 0   1
  IFLTD1 MUTATED    12   1
  IFLTD1 WILD-TYPE 354 118
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IFLTD1 MUTATED     12    1
  IFLTD1 WILD-TYPE  354  118
        clus
vv       IFLTD1 MUTATED IFLTD1 WILD-TYPE
  COLON              12              354
  RECTUM              1              118
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  IFLTD1 MUTATED         0        0        2         5         0         0
  IFLTD1 WILD-TYPE      91        1       30       133        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  IFLTD1 MUTATED           2          0          1          1        0
  IFLTD1 WILD-TYPE        22         11         58         41       48
                  vv
clus               STAGE IVA STAGE IVB
  IFLTD1 MUTATED           0         1
  IFLTD1 WILD-TYPE        18         0
D1675V4, multiclass
            clus
vv           IFLTD1 MUTATED IFLTD1 WILD-TYPE
  STAGE I                 0               91
  STAGE IA                0                1
  STAGE II                2               30
  STAGE IIA               5              133
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               2               22
  STAGE IIIA              0               11
  STAGE IIIB              1               58
  STAGE IIIC              1               41
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               1                0
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  IFLTD1 MUTATED     0   1  12   0
  IFLTD1 WILD-TYPE  17  91 317  50
D1675V5, multiclass
    clus
vv   IFLTD1 MUTATED IFLTD1 WILD-TYPE
  T1              0               17
  T2              1               91
  T3             12              317
  T4              0               50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  IFLTD1 MUTATED     8   1   4
  IFLTD1 WILD-TYPE 279 112  83
D1675V6, multiclass
    clus
vv   IFLTD1 MUTATED IFLTD1 WILD-TYPE
  N0              8              279
  N1              1              112
  N2              4               83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1675V7, binary
                  cls
clus                 0   1
  IFLTD1 MUTATED    11   1
  IFLTD1 WILD-TYPE 364  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IFLTD1 MUTATED     11    1
  IFLTD1 WILD-TYPE  364   64
   clus
vv  IFLTD1 MUTATED IFLTD1 WILD-TYPE
  0             11              364
  1              1               64
[1] 2 2
[1] FALSE
D1675V8, binary
                  cls
clus                 0   1
  IFLTD1 MUTATED     5   8
  IFLTD1 WILD-TYPE 220 256
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IFLTD1 MUTATED      5    8
  IFLTD1 WILD-TYPE  220  256
        clus
vv       IFLTD1 MUTATED IFLTD1 WILD-TYPE
  FEMALE              5              220
  MALE                8              256
[1] 2 2
[1] FALSE
D1675V9, binary
                  cls
clus                 0   1
  IFLTD1 MUTATED    11   1
  IFLTD1 WILD-TYPE 339  21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IFLTD1 MUTATED     11    1
  IFLTD1 WILD-TYPE  339   21
     clus
vv    IFLTD1 MUTATED IFLTD1 WILD-TYPE
  NO              11              339
  YES              1               21
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  IFLTD1 MUTATED                     11                             1
  IFLTD1 WILD-TYPE                  304                            46
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  IFLTD1 MUTATED                       1                              0
  IFLTD1 WILD-TYPE                   105                             10
D1675V10, multiclass
                                clus
vv                               IFLTD1 MUTATED IFLTD1 WILD-TYPE
  COLON ADENOCARCINOMA                       11              304
  COLON MUCINOUS ADENOCARCINOMA               1               46
  RECTAL ADENOCARCINOMA                       1              105
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  IFLTD1 MUTATED    10   0   0   1
  IFLTD1 WILD-TYPE 335   4  31  24
D1675V11, multiclass
    clus
vv   IFLTD1 MUTATED IFLTD1 WILD-TYPE
  R0             10              335
  R1              0                4
  R2              0               31
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1675V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  IFLTD1 MUTATED                                  0     1
  IFLTD1 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  IFLTD1 MUTATED                           3     3
  IFLTD1 WILD-TYPE                        19   223
D1675V13, multiclass
                                  clus
vv                                 IFLTD1 MUTATED IFLTD1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     3               19
  WHITE                                         3              223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1676) Variable = TLX1NB MUTATION ANALYSIS
D1676V1, survival
                  sevent
clus2                0   1
  TLX1NB MUTATED     1   1
  TLX1NB WILD-TYPE 377  92
  TLX1NB MUTATED TLX1NB WILD-TYPE 
               2              469 
  TLX1NB MUTATED TLX1NB WILD-TYPE 
               1               92 
$`TLX1NB MUTATED`
TCGA-AG-4005 TCGA-F5-6464 
       14.04         9.96 

$`TLX1NB WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4007 
       48.03        32.02        19.99        28.04        36.03         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6465 
        0.49        20.55        19.96        20.91        18.28        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  TLX1NB MUTATED TLX1NB WILD-TYPE 
            9.96             0.00 
  TLX1NB MUTATED TLX1NB WILD-TYPE 
           14.04           148.01 
  TLX1NB MUTATED TLX1NB WILD-TYPE 
           12.00            20.28 
[1] "10.0 - 14.0 (12.0)" "0.0 - 148.0 (20.3)"
[1] "Remove cluster labels:" "TLX1NB MUTATED"        
D1676V2, continuous
D1676V3, binary
                  cls
clus                 0   1
  TLX1NB MUTATED     1   2
  TLX1NB WILD-TYPE 365 117
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TLX1NB MUTATED      1    2
  TLX1NB WILD-TYPE  365  117
        clus
vv       TLX1NB MUTATED TLX1NB WILD-TYPE
  COLON               1              365
  RECTUM              2              117
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TLX1NB MUTATED         0        0        1         0         0         0
  TLX1NB WILD-TYPE      91        1       31       138        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TLX1NB MUTATED           0          0          0          1        1
  TLX1NB WILD-TYPE        24         11         59         41       47
                  vv
clus               STAGE IVA STAGE IVB
  TLX1NB MUTATED           0         0
  TLX1NB WILD-TYPE        18         1
D1676V4, multiclass
            clus
vv           TLX1NB MUTATED TLX1NB WILD-TYPE
  STAGE I                 0               91
  STAGE IA                0                1
  STAGE II                1               31
  STAGE IIA               0              138
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              0               59
  STAGE IIIC              1               41
  STAGE IV                1               47
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  TLX1NB MUTATED     0   0   1   2
  TLX1NB WILD-TYPE  17  92 328  48
D1676V5, multiclass
    clus
vv   TLX1NB MUTATED TLX1NB WILD-TYPE
  T1              0               17
  T2              0               92
  T3              1              328
  T4              2               48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  TLX1NB MUTATED     1   0   2
  TLX1NB WILD-TYPE 286 113  85
D1676V6, multiclass
    clus
vv   TLX1NB MUTATED TLX1NB WILD-TYPE
  N0              1              286
  N1              0              113
  N2              2               85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1676V7, binary
                  cls
clus                 0   1
  TLX1NB MUTATED     2   1
  TLX1NB WILD-TYPE 373  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TLX1NB MUTATED      2    1
  TLX1NB WILD-TYPE  373   64
   clus
vv  TLX1NB MUTATED TLX1NB WILD-TYPE
  0              2              373
  1              1               64
[1] 2 2
[1] FALSE
D1676V8, binary
                  cls
clus                 0   1
  TLX1NB MUTATED     2   1
  TLX1NB WILD-TYPE 223 263
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TLX1NB MUTATED      2    1
  TLX1NB WILD-TYPE  223  263
        clus
vv       TLX1NB MUTATED TLX1NB WILD-TYPE
  FEMALE              2              223
  MALE                1              263
[1] 2 2
[1] FALSE
D1676V9, binary
                  cls
clus                 0   1
  TLX1NB MUTATED     2   0
  TLX1NB WILD-TYPE 348  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TLX1NB MUTATED      2    0
  TLX1NB WILD-TYPE  348   22
     clus
vv    TLX1NB MUTATED TLX1NB WILD-TYPE
  NO               2              348
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  TLX1NB MUTATED                      1                             0
  TLX1NB WILD-TYPE                  314                            47
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  TLX1NB MUTATED                       2                              0
  TLX1NB WILD-TYPE                   104                             10
D1676V10, multiclass
                                clus
vv                               TLX1NB MUTATED TLX1NB WILD-TYPE
  COLON ADENOCARCINOMA                        1              314
  COLON MUCINOUS ADENOCARCINOMA               0               47
  RECTAL ADENOCARCINOMA                       2              104
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  TLX1NB MUTATED     3   0   0   0
  TLX1NB WILD-TYPE 342   4  31  25
D1676V11, multiclass
    clus
vv   TLX1NB MUTATED TLX1NB WILD-TYPE
  R0              3              342
  R1              0                4
  R2              0               31
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1676V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TLX1NB MUTATED                                  0     0
  TLX1NB WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  TLX1NB MUTATED                           0     1
  TLX1NB WILD-TYPE                        22   225
D1676V13, multiclass
[1] "Remove cluster labels:" "TLX1NB MUTATED"        
clus
  TLX1NB MUTATED TLX1NB WILD-TYPE 
               1              259 
      TCGA-A6-2671       TCGA-A6-2672       TCGA-A6-2674       TCGA-A6-2676 
"TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" 
      TCGA-A6-2677       TCGA-A6-2678       TCGA-A6-2683       TCGA-A6-3807 
"TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" 
      TCGA-A6-3808       TCGA-A6-3809       TCGA-A6-3810       TCGA-A6-4105 
"TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" 
      TCGA-A6-5656       TCGA-A6-5657       TCGA-A6-5659       TCGA-A6-5660 
"TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" 
      TCGA-A6-5661       TCGA-A6-5662       TCGA-A6-5664       TCGA-A6-5665 
"TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" 
      TCGA-A6-5666       TCGA-A6-6137       TCGA-A6-6138       TCGA-A6-6141 
"TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" 
      TCGA-A6-6142       TCGA-A6-6648       TCGA-A6-6649       TCGA-A6-6651 
"TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" 
      TCGA-A6-6652       TCGA-A6-6653       TCGA-A6-6654       TCGA-A6-6780 
"TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" 
      TCGA-A6-6781       TCGA-A6-6782       TCGA-AD-5900       TCGA-AD-6548 
"TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" 
      TCGA-AD-6888       TCGA-AD-6889       TCGA-AD-6890       TCGA-AD-6895 
"TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" 
      TCGA-AD-6899       TCGA-AD-6901       TCGA-AD-6963       TCGA-AD-6964 
"TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" 
      TCGA-AD-6965       TCGA-AU-3779       TCGA-AU-6004       TCGA-AY-4070 
"TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" 
      TCGA-AY-4071       TCGA-AY-5543       TCGA-AY-6196       TCGA-AY-6197 
"TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" 
      TCGA-AY-6386       TCGA-AZ-4315       TCGA-AZ-4323       TCGA-AZ-4616 
"TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" 
      TCGA-AZ-4681       TCGA-AZ-4682       TCGA-AZ-5403       TCGA-AZ-5407 
"TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" 
      TCGA-AZ-6598       TCGA-AZ-6599       TCGA-AZ-6600       TCGA-AZ-6601 
"TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" 
      TCGA-AZ-6603       TCGA-AZ-6605       TCGA-AZ-6606       TCGA-AZ-6607 
"TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" 
      TCGA-AZ-6608       TCGA-CA-5254       TCGA-CA-5255       TCGA-CA-5796 
"TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" 
      TCGA-CA-5797       TCGA-CA-6715       TCGA-CA-6716       TCGA-CA-6717 
"TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" 
      TCGA-CA-6718       TCGA-CA-6719       TCGA-CK-4947       TCGA-CK-4948 
"TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" 
      TCGA-CK-4950       TCGA-CK-4952       TCGA-CK-5912       TCGA-CK-5913 
"TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" 
      TCGA-CK-5914       TCGA-CK-5915       TCGA-CK-5916       TCGA-CK-6746 
"TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" 
      TCGA-CK-6747       TCGA-CK-6748       TCGA-CK-6751       TCGA-CM-4743 
"TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" 
      TCGA-CM-4744       TCGA-CM-4746       TCGA-CM-4747       TCGA-CM-4752 
"TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" 
      TCGA-CM-5341       TCGA-CM-5344       TCGA-CM-5348       TCGA-CM-5349 
"TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" 
      TCGA-CM-5860       TCGA-CM-5861       TCGA-CM-5862       TCGA-CM-5863 
"TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" 
      TCGA-CM-5864       TCGA-CM-5868       TCGA-CM-6161       TCGA-CM-6162 
"TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" 
      TCGA-CM-6163       TCGA-CM-6164       TCGA-CM-6165       TCGA-CM-6166 
"TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" 
      TCGA-CM-6167       TCGA-CM-6168       TCGA-CM-6169       TCGA-CM-6170 
"TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" 
      TCGA-CM-6171       TCGA-CM-6172       TCGA-CM-6674       TCGA-CM-6675 
"TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" 
      TCGA-CM-6676       TCGA-CM-6677       TCGA-CM-6678       TCGA-CM-6679 
"TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" 
      TCGA-CM-6680       TCGA-D5-5537       TCGA-D5-5538       TCGA-D5-5539 
"TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" 
      TCGA-D5-5540       TCGA-D5-5541       TCGA-D5-6529       TCGA-D5-6532 
"TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" 
      TCGA-D5-6533       TCGA-D5-6534       TCGA-D5-6535       TCGA-D5-6536 
"TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" 
      TCGA-D5-6537       TCGA-D5-6538       TCGA-D5-6539       TCGA-D5-6540 
"TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" 
      TCGA-D5-6541       TCGA-D5-6898       TCGA-D5-6920       TCGA-D5-6922 
"TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" 
      TCGA-D5-6923       TCGA-D5-6924       TCGA-D5-6926       TCGA-D5-6927 
"TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" 
      TCGA-D5-6928       TCGA-D5-6929       TCGA-D5-6930       TCGA-D5-6931 
"TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" 
      TCGA-D5-6932       TCGA-D5-7000       TCGA-DM-A0X9       TCGA-DM-A0XD 
"TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" 
      TCGA-DM-A0XF       TCGA-DM-A1D0       TCGA-DM-A1D4       TCGA-DM-A1D6 
"TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" 
      TCGA-DM-A1D7       TCGA-DM-A1D8       TCGA-DM-A1D9       TCGA-DM-A1DA 
"TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" 
      TCGA-DM-A1DB       TCGA-DM-A1HA       TCGA-DM-A1HB       TCGA-DM-A282 
"TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" 
      TCGA-DM-A285       TCGA-DM-A28C       TCGA-DM-A28E       TCGA-DM-A28F 
"TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" 
      TCGA-DM-A28G       TCGA-DM-A28H       TCGA-DM-A28K       TCGA-F4-6459 
"TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" 
      TCGA-F4-6460       TCGA-F4-6569       TCGA-F4-6570       TCGA-F4-6703 
"TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" 
      TCGA-F4-6704       TCGA-F4-6805       TCGA-F4-6806       TCGA-F4-6807 
"TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" 
      TCGA-F4-6808       TCGA-F4-6809       TCGA-F4-6854       TCGA-F4-6855 
"TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" 
      TCGA-F4-6856       TCGA-G4-6293       TCGA-G4-6299       TCGA-G4-6303 
"TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" 
      TCGA-G4-6304       TCGA-G4-6306       TCGA-G4-6307       TCGA-G4-6309 
"TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" 
      TCGA-G4-6310       TCGA-G4-6315       TCGA-G4-6317       TCGA-G4-6321 
"TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" 
      TCGA-G4-6323       TCGA-G4-6586       TCGA-G4-6588       TCGA-G4-6625 
"TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" 
      TCGA-G4-6626       TCGA-G4-6628       TCGA-AF-2687       TCGA-AF-2689 
"TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" 
      TCGA-AF-2691       TCGA-AF-2692       TCGA-AF-2693       TCGA-AF-3400 
"TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" 
      TCGA-AF-3913       TCGA-AF-4110       TCGA-AF-5654       TCGA-AF-6136 
"TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" 
      TCGA-AF-6655       TCGA-AF-6672       TCGA-AH-6544       TCGA-AH-6547 
"TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" 
      TCGA-AH-6549       TCGA-AH-6643       TCGA-AH-6644       TCGA-CI-6619 
"TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" 
      TCGA-CI-6620       TCGA-CI-6621       TCGA-CI-6622       TCGA-CI-6624 
"TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" 
      TCGA-CL-5917       TCGA-CL-5918       TCGA-DC-5337       TCGA-DC-5869 
"TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" 
      TCGA-DC-6155       TCGA-DC-6157       TCGA-DC-6158       TCGA-DC-6160 
"TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" 
      TCGA-DC-6681       TCGA-DC-6682       TCGA-DC-6683       TCGA-DT-5265 
"TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" 
      TCGA-DY-A0XA       TCGA-DY-A1DC       TCGA-DY-A1DD       TCGA-DY-A1DF 
"TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" 
      TCGA-DY-A1DG       TCGA-DY-A1H8       TCGA-EF-5830       TCGA-EI-6506 
"TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" 
      TCGA-EI-6507       TCGA-EI-6508       TCGA-EI-6510       TCGA-F5-6465 
"TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" 
      TCGA-F5-6571       TCGA-F5-6702       TCGA-F5-6811       TCGA-F5-6812 
"TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" 
      TCGA-F5-6813       TCGA-G5-6235       TCGA-G5-6641 
"TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" "TLX1NB WILD-TYPE" 

Clustering(1677) Variable = ZNF323 MUTATION ANALYSIS
D1677V1, survival
                  sevent
clus2                0   1
  ZNF323 MUTATED    10   1
  ZNF323 WILD-TYPE 368  92
  ZNF323 MUTATED ZNF323 WILD-TYPE 
              11              460 
  ZNF323 MUTATED ZNF323 WILD-TYPE 
               1               92 
$`ZNF323 MUTATED`
TCGA-A6-3809 TCGA-AA-3502 TCGA-AA-3663 TCGA-AA-A010 TCGA-AA-A02O TCGA-CA-6718 
       32.75        35.01         6.97        34.98         0.92        10.06 
TCGA-CK-5913 TCGA-D5-5541 TCGA-D5-6533 TCGA-G4-6628 TCGA-AF-6672 
       51.32        55.92         1.32        79.69        10.39 

$`ZNF323 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
        5.03        14.01        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 
        3.25         3.29         0.07        12.20        12.76        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 
       17.56       148.01        85.45        15.62        49.08         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       20.19        18.25        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       91.79        46.75        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       20.02        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  ZNF323 MUTATED ZNF323 WILD-TYPE 
            0.92             0.00 
  ZNF323 MUTATED ZNF323 WILD-TYPE 
           79.69           148.01 
  ZNF323 MUTATED ZNF323 WILD-TYPE 
          32.750           20.155 
[1] "0.9 - 79.7 (32.8)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "2.4"
D1677V2, continuous
D1677V3, binary
                  cls
clus                 0   1
  ZNF323 MUTATED    10   1
  ZNF323 WILD-TYPE 356 118
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF323 MUTATED     10    1
  ZNF323 WILD-TYPE  356  118
        clus
vv       ZNF323 MUTATED ZNF323 WILD-TYPE
  COLON              10              356
  RECTUM              1              118
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZNF323 MUTATED         2        0        2         2         2         0
  ZNF323 WILD-TYPE      89        1       30       136         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF323 MUTATED           0          0          2          0        1
  ZNF323 WILD-TYPE        24         11         57         42       47
                  vv
clus               STAGE IVA STAGE IVB
  ZNF323 MUTATED           0         0
  ZNF323 WILD-TYPE        18         1
D1677V4, multiclass
            clus
vv           ZNF323 MUTATED ZNF323 WILD-TYPE
  STAGE I                 2               89
  STAGE IA                0                1
  STAGE II                2               30
  STAGE IIA               2              136
  STAGE IIB               2                8
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              2               57
  STAGE IIIC              0               42
  STAGE IV                1               47
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZNF323 MUTATED     0   2   5   4
  ZNF323 WILD-TYPE  17  90 324  46
D1677V5, multiclass
    clus
vv   ZNF323 MUTATED ZNF323 WILD-TYPE
  T1              0               17
  T2              2               90
  T3              5              324
  T4              4               46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  ZNF323 MUTATED     9   1   1
  ZNF323 WILD-TYPE 278 112  86
D1677V6, multiclass
    clus
vv   ZNF323 MUTATED ZNF323 WILD-TYPE
  N0              9              278
  N1              1              112
  N2              1               86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1677V7, binary
                  cls
clus                 0   1
  ZNF323 MUTATED     9   0
  ZNF323 WILD-TYPE 366  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF323 MUTATED      9    0
  ZNF323 WILD-TYPE  366   65
   clus
vv  ZNF323 MUTATED ZNF323 WILD-TYPE
  0              9              366
  1              0               65
[1] 2 2
[1] FALSE
D1677V8, binary
                  cls
clus                 0   1
  ZNF323 MUTATED     4   7
  ZNF323 WILD-TYPE 221 257
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF323 MUTATED      4    7
  ZNF323 WILD-TYPE  221  257
        clus
vv       ZNF323 MUTATED ZNF323 WILD-TYPE
  FEMALE              4              221
  MALE                7              257
[1] 2 2
[1] FALSE
D1677V9, binary
                  cls
clus                 0   1
  ZNF323 MUTATED     8   1
  ZNF323 WILD-TYPE 342  21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF323 MUTATED      8    1
  ZNF323 WILD-TYPE  342   21
     clus
vv    ZNF323 MUTATED ZNF323 WILD-TYPE
  NO               8              342
  YES              1               21
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ZNF323 MUTATED                      9                             1
  ZNF323 WILD-TYPE                  306                            46
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ZNF323 MUTATED                       1                              0
  ZNF323 WILD-TYPE                   105                             10
D1677V10, multiclass
                                clus
vv                               ZNF323 MUTATED ZNF323 WILD-TYPE
  COLON ADENOCARCINOMA                        9              306
  COLON MUCINOUS ADENOCARCINOMA               1               46
  RECTAL ADENOCARCINOMA                       1              105
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ZNF323 MUTATED     8   0   0   2
  ZNF323 WILD-TYPE 337   4  31  23
D1677V11, multiclass
    clus
vv   ZNF323 MUTATED ZNF323 WILD-TYPE
  R0              8              337
  R1              0                4
  R2              0               31
  RX              2               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1677V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF323 MUTATED                                  0     1
  ZNF323 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZNF323 MUTATED                           0     6
  ZNF323 WILD-TYPE                        22   220
D1677V13, multiclass
                                  clus
vv                                 ZNF323 MUTATED ZNF323 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         6              220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1678) Variable = ANAPC16 MUTATION ANALYSIS
D1678V1, survival
                   sevent
clus2                 0   1
  ANAPC16 MUTATED     2   1
  ANAPC16 WILD-TYPE 376  92
  ANAPC16 MUTATED ANAPC16 WILD-TYPE 
                3               468 
  ANAPC16 MUTATED ANAPC16 WILD-TYPE 
                1                92 
$`ANAPC16 MUTATED`
TCGA-AA-A00K TCGA-AY-5543 TCGA-AZ-6605 
       18.05        33.01         5.23 

$`ANAPC16 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
       12.10       100.01        29.56        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  ANAPC16 MUTATED ANAPC16 WILD-TYPE 
             5.23              0.00 
  ANAPC16 MUTATED ANAPC16 WILD-TYPE 
            33.01            148.01 
  ANAPC16 MUTATED ANAPC16 WILD-TYPE 
           18.050            20.235 
[1] "5.2 - 33.0 (18.1)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "2.5"
D1678V2, continuous
D1678V3, binary
                   cls
clus                  0   1
  ANAPC16 MUTATED     3   0
  ANAPC16 WILD-TYPE 363 119
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANAPC16 MUTATED      3    0
  ANAPC16 WILD-TYPE  363  119
        clus
vv       ANAPC16 MUTATED ANAPC16 WILD-TYPE
  COLON                3               363
  RECTUM               0               119
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ANAPC16 MUTATED         0        0        0         1         0         0
  ANAPC16 WILD-TYPE      91        1       32       137        10         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ANAPC16 MUTATED           0          0          1          0        0
  ANAPC16 WILD-TYPE        24         11         58         42       48
                   vv
clus                STAGE IVA STAGE IVB
  ANAPC16 MUTATED           1         0
  ANAPC16 WILD-TYPE        17         1
D1678V4, multiclass
            clus
vv           ANAPC16 MUTATED ANAPC16 WILD-TYPE
  STAGE I                  0                91
  STAGE IA                 0                 1
  STAGE II                 0                32
  STAGE IIA                1               137
  STAGE IIB                0                10
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               0                11
  STAGE IIIB               1                58
  STAGE IIIC               0                42
  STAGE IV                 0                48
  STAGE IVA                1                17
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  ANAPC16 MUTATED     0   0   2   1
  ANAPC16 WILD-TYPE  17  92 327  49
D1678V5, multiclass
    clus
vv   ANAPC16 MUTATED ANAPC16 WILD-TYPE
  T1               0                17
  T2               0                92
  T3               2               327
  T4               1                49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  ANAPC16 MUTATED     1   2   0
  ANAPC16 WILD-TYPE 286 111  87
D1678V6, multiclass
    clus
vv   ANAPC16 MUTATED ANAPC16 WILD-TYPE
  N0               1               286
  N1               2               111
  N2               0                87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1678V7, binary
                   cls
clus                  0   1
  ANAPC16 MUTATED     2   1
  ANAPC16 WILD-TYPE 373  64
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANAPC16 MUTATED      2    1
  ANAPC16 WILD-TYPE  373   64
   clus
vv  ANAPC16 MUTATED ANAPC16 WILD-TYPE
  0               2               373
  1               1                64
[1] 2 2
[1] FALSE
D1678V8, binary
                   cls
clus                  0   1
  ANAPC16 MUTATED     1   2
  ANAPC16 WILD-TYPE 224 262
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANAPC16 MUTATED      1    2
  ANAPC16 WILD-TYPE  224  262
        clus
vv       ANAPC16 MUTATED ANAPC16 WILD-TYPE
  FEMALE               1               224
  MALE                 2               262
[1] 2 2
[1] FALSE
D1678V9, binary
                   cls
clus                  0   1
  ANAPC16 MUTATED     2   0
  ANAPC16 WILD-TYPE 348  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANAPC16 MUTATED      2    0
  ANAPC16 WILD-TYPE  348   22
     clus
vv    ANAPC16 MUTATED ANAPC16 WILD-TYPE
  NO                2               348
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ANAPC16 MUTATED                      3                             0
  ANAPC16 WILD-TYPE                  312                            47
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ANAPC16 MUTATED                       0                              0
  ANAPC16 WILD-TYPE                   106                             10
D1678V10, multiclass
                                clus
vv                               ANAPC16 MUTATED ANAPC16 WILD-TYPE
  COLON ADENOCARCINOMA                         3               312
  COLON MUCINOUS ADENOCARCINOMA                0                47
  RECTAL ADENOCARCINOMA                        0               106
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  ANAPC16 MUTATED     2   0   0   0
  ANAPC16 WILD-TYPE 343   4  31  25
D1678V11, multiclass
[1] "Remove cluster labels:" "ANAPC16 MUTATED"       
clus
  ANAPC16 MUTATED ANAPC16 WILD-TYPE 
                2               403 
       TCGA-A6-2671        TCGA-A6-2672        TCGA-A6-2674        TCGA-A6-2676 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-A6-2677        TCGA-A6-2678        TCGA-A6-2683        TCGA-A6-3807 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-A6-3808        TCGA-A6-3809        TCGA-A6-3810        TCGA-A6-5657 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-A6-5659        TCGA-A6-5661        TCGA-A6-5665        TCGA-A6-6781 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-AA-3489        TCGA-AA-3492        TCGA-AA-3496        TCGA-AA-3502 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-AA-3510        TCGA-AA-3511        TCGA-AA-3514        TCGA-AA-3517 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-AA-3518        TCGA-AA-3519        TCGA-AA-3520        TCGA-AA-3521 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-AA-3522        TCGA-AA-3524        TCGA-AA-3525        TCGA-AA-3526 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-AA-3527        TCGA-AA-3529        TCGA-AA-3530        TCGA-AA-3531 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-AA-3532        TCGA-AA-3534        TCGA-AA-3538        TCGA-AA-3542 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-AA-3543        TCGA-AA-3544        TCGA-AA-3548        TCGA-AA-3549 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-AA-3552        TCGA-AA-3553        TCGA-AA-3554        TCGA-AA-3555 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-AA-3556        TCGA-AA-3558        TCGA-AA-3560        TCGA-AA-3561 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-AA-3562        TCGA-AA-3655        TCGA-AA-3660        TCGA-AA-3662 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-AA-3663        TCGA-AA-3664        TCGA-AA-3666        TCGA-AA-3667 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-AA-3672        TCGA-AA-3673        TCGA-AA-3678        TCGA-AA-3679 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-AA-3680        TCGA-AA-3681        TCGA-AA-3684        TCGA-AA-3685 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-AA-3688        TCGA-AA-3692        TCGA-AA-3693        TCGA-AA-3695 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-AA-3696        TCGA-AA-3697        TCGA-AA-3710        TCGA-AA-3712 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-AA-3713        TCGA-AA-3715        TCGA-AA-3811        TCGA-AA-3812 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-AA-3814        TCGA-AA-3815        TCGA-AA-3818        TCGA-AA-3819 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-AA-3821        TCGA-AA-3831        TCGA-AA-3833        TCGA-AA-3837 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-AA-3842        TCGA-AA-3844        TCGA-AA-3845        TCGA-AA-3846 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-AA-3848        TCGA-AA-3850        TCGA-AA-3851        TCGA-AA-3852 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-AA-3854        TCGA-AA-3855        TCGA-AA-3856        TCGA-AA-3858 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-AA-3860        TCGA-AA-3861        TCGA-AA-3864        TCGA-AA-3866 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-AA-3867        TCGA-AA-3869        TCGA-AA-3870        TCGA-AA-3872 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-AA-3875        TCGA-AA-3877        TCGA-AA-3930        TCGA-AA-3939 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-AA-3941        TCGA-AA-3947        TCGA-AA-3949        TCGA-AA-3950 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-AA-3952        TCGA-AA-3955        TCGA-AA-3956        TCGA-AA-3968 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-AA-3971        TCGA-AA-3972        TCGA-AA-3973        TCGA-AA-3975 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-AA-3976        TCGA-AA-3979        TCGA-AA-3984        TCGA-AA-3986 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-AA-3989        TCGA-AA-3994        TCGA-AA-A004        TCGA-AA-A00A 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-AA-A00D        TCGA-AA-A00E        TCGA-AA-A00F        TCGA-AA-A00J 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-AA-A00L        TCGA-AA-A00N        TCGA-AA-A00O        TCGA-AA-A00Q 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-AA-A00R        TCGA-AA-A00U        TCGA-AA-A00W        TCGA-AA-A00Z 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-AA-A010        TCGA-AA-A017        TCGA-AA-A01D        TCGA-AA-A01F 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-AA-A01G        TCGA-AA-A01I        TCGA-AA-A01K        TCGA-AA-A01P 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-AA-A01Q        TCGA-AA-A01R        TCGA-AA-A01S        TCGA-AA-A01T 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-AA-A01V        TCGA-AA-A01X        TCGA-AA-A01Z        TCGA-AA-A022 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-AA-A024        TCGA-AA-A029        TCGA-AA-A02F        TCGA-AA-A02H 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-AA-A02J        TCGA-AA-A02K        TCGA-AA-A02O        TCGA-AA-A02W 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-AA-A02Y        TCGA-AA-A03F        TCGA-AA-A03J        TCGA-AD-5900 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-AD-6548        TCGA-AD-6888        TCGA-AU-3779        TCGA-AU-6004 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-AY-4070        TCGA-AY-4071        TCGA-AY-6196        TCGA-AY-6197 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-AY-6386        TCGA-AZ-4315        TCGA-AZ-4681        TCGA-AZ-4682 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-CA-5254        TCGA-CA-5255        TCGA-CA-5796        TCGA-CA-5797 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-CA-6715        TCGA-CA-6716        TCGA-CA-6717        TCGA-CA-6718 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-CA-6719        TCGA-CK-4947        TCGA-CK-4948        TCGA-CK-4950 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-CK-4952        TCGA-CK-5912        TCGA-CK-5913        TCGA-CK-5914 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-CK-5915        TCGA-CK-5916        TCGA-CK-6746        TCGA-CK-6747 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-CK-6748        TCGA-CK-6751        TCGA-CM-4743        TCGA-CM-4744 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-CM-4746        TCGA-CM-4747        TCGA-CM-4752        TCGA-CM-5341 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-CM-5344        TCGA-CM-5348        TCGA-CM-5349        TCGA-CM-5860 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-CM-5861        TCGA-CM-5862        TCGA-CM-5863        TCGA-CM-5864 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-CM-5868        TCGA-CM-6161        TCGA-CM-6162        TCGA-CM-6163 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-CM-6164        TCGA-CM-6165        TCGA-CM-6166        TCGA-CM-6167 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-CM-6168        TCGA-CM-6169        TCGA-CM-6170        TCGA-CM-6171 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-CM-6172        TCGA-CM-6674        TCGA-CM-6675        TCGA-CM-6676 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-CM-6677        TCGA-CM-6678        TCGA-CM-6679        TCGA-CM-6680 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-D5-5537        TCGA-D5-5538        TCGA-D5-5539        TCGA-D5-5540 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-D5-5541        TCGA-D5-6529        TCGA-D5-6532        TCGA-D5-6533 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-D5-6534        TCGA-D5-6535        TCGA-D5-6536        TCGA-D5-6537 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-D5-6538        TCGA-D5-6539        TCGA-D5-6540        TCGA-D5-6541 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-D5-6898        TCGA-D5-6920        TCGA-D5-6922        TCGA-D5-6923 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-D5-6924        TCGA-D5-6926        TCGA-D5-6927        TCGA-D5-6928 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-D5-6929        TCGA-D5-6930        TCGA-D5-6931        TCGA-D5-6932 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-D5-7000        TCGA-F4-6459        TCGA-F4-6460        TCGA-F4-6569 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-F4-6570        TCGA-F4-6703        TCGA-F4-6704        TCGA-F4-6805 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-F4-6806        TCGA-F4-6807        TCGA-F4-6808        TCGA-F4-6809 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-F4-6854        TCGA-F4-6855        TCGA-F4-6856        TCGA-G4-6293 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-G4-6299        TCGA-G4-6303        TCGA-G4-6304        TCGA-G4-6306 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-G4-6307        TCGA-G4-6309        TCGA-G4-6310        TCGA-G4-6315 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-G4-6317        TCGA-G4-6321        TCGA-G4-6323        TCGA-G4-6586 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-G4-6588        TCGA-G4-6625        TCGA-G4-6626        TCGA-G4-6628 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2691        TCGA-AF-2692 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-AF-3400        TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-AF-6655        TCGA-AG-3574        TCGA-AG-3575        TCGA-AG-3578 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-AG-3580        TCGA-AG-3581        TCGA-AG-3582        TCGA-AG-3583 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-AG-3584        TCGA-AG-3586        TCGA-AG-3587        TCGA-AG-3593 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-AG-3594        TCGA-AG-3598        TCGA-AG-3599        TCGA-AG-3600 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-AG-3601        TCGA-AG-3602        TCGA-AG-3605        TCGA-AG-3608 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-AG-3609        TCGA-AG-3611        TCGA-AG-3612        TCGA-AG-3726 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-AG-3727        TCGA-AG-3731        TCGA-AG-3732        TCGA-AG-3742 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-AG-3878        TCGA-AG-3882        TCGA-AG-3883        TCGA-AG-3885 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3890        TCGA-AG-3892        TCGA-AG-3893 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-AG-3894        TCGA-AG-3896        TCGA-AG-3898        TCGA-AG-3901 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-AG-3902        TCGA-AG-3909        TCGA-AG-3999        TCGA-AG-4001 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-AG-4005        TCGA-AG-4007        TCGA-AG-4008        TCGA-AG-4015 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-AG-A002        TCGA-AG-A008        TCGA-AG-A00C        TCGA-AG-A00H 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-AG-A00Y        TCGA-AG-A011        TCGA-AG-A014        TCGA-AG-A015 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-AG-A016        TCGA-AG-A01L        TCGA-AG-A01W        TCGA-AG-A01Y 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A025        TCGA-AG-A026        TCGA-AG-A02G 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032        TCGA-AG-A036 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-AH-6549        TCGA-AH-6643        TCGA-CL-5917        TCGA-CL-5918 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6155        TCGA-DC-6157 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-DC-6158        TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-DC-6683        TCGA-DT-5265        TCGA-EF-5830        TCGA-EI-6506 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-EI-6507        TCGA-EI-6508        TCGA-EI-6510        TCGA-F5-6464 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-F5-6465        TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6812 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-F5-6813        TCGA-G5-6235        TCGA-G5-6641 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
D1678V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ANAPC16 MUTATED                                  0     0
  ANAPC16 WILD-TYPE                                1    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  ANAPC16 MUTATED                           1     1
  ANAPC16 WILD-TYPE                        21   225
D1678V13, multiclass
[1] "Remove cluster labels:" "ANAPC16 MUTATED"       
clus
  ANAPC16 MUTATED ANAPC16 WILD-TYPE 
                2               258 
       TCGA-A6-2671        TCGA-A6-2672        TCGA-A6-2674        TCGA-A6-2676 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-A6-2677        TCGA-A6-2678        TCGA-A6-2683        TCGA-A6-3807 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-A6-3808        TCGA-A6-3809        TCGA-A6-3810        TCGA-A6-4105 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-A6-5656        TCGA-A6-5657        TCGA-A6-5659        TCGA-A6-5660 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-A6-5661        TCGA-A6-5662        TCGA-A6-5664        TCGA-A6-5665 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-A6-5666        TCGA-A6-6137        TCGA-A6-6138        TCGA-A6-6141 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-A6-6142        TCGA-A6-6648        TCGA-A6-6649        TCGA-A6-6651 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-A6-6652        TCGA-A6-6653        TCGA-A6-6654        TCGA-A6-6780 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-A6-6781        TCGA-A6-6782        TCGA-AD-5900        TCGA-AD-6548 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-AD-6888        TCGA-AD-6889        TCGA-AD-6890        TCGA-AD-6895 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-AD-6899        TCGA-AD-6901        TCGA-AD-6963        TCGA-AD-6964 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-AD-6965        TCGA-AU-3779        TCGA-AU-6004        TCGA-AY-4070 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-AY-4071        TCGA-AY-6196        TCGA-AY-6197        TCGA-AY-6386 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-AZ-4315        TCGA-AZ-4323        TCGA-AZ-4616        TCGA-AZ-4681 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-AZ-4682        TCGA-AZ-5403        TCGA-AZ-5407        TCGA-AZ-6598 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-AZ-6599        TCGA-AZ-6600        TCGA-AZ-6601        TCGA-AZ-6603 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-AZ-6606        TCGA-AZ-6607        TCGA-AZ-6608        TCGA-CA-5254 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-CA-5255        TCGA-CA-5796        TCGA-CA-5797        TCGA-CA-6715 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-CA-6716        TCGA-CA-6717        TCGA-CA-6718        TCGA-CA-6719 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-CK-4947        TCGA-CK-4948        TCGA-CK-4950        TCGA-CK-4952 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-CK-5912        TCGA-CK-5913        TCGA-CK-5914        TCGA-CK-5915 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-CK-5916        TCGA-CK-6746        TCGA-CK-6747        TCGA-CK-6748 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-CK-6751        TCGA-CM-4743        TCGA-CM-4744        TCGA-CM-4746 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-CM-4747        TCGA-CM-4752        TCGA-CM-5341        TCGA-CM-5344 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-CM-5348        TCGA-CM-5349        TCGA-CM-5860        TCGA-CM-5861 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-CM-5862        TCGA-CM-5863        TCGA-CM-5864        TCGA-CM-5868 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-CM-6161        TCGA-CM-6162        TCGA-CM-6163        TCGA-CM-6164 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-CM-6165        TCGA-CM-6166        TCGA-CM-6167        TCGA-CM-6168 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-CM-6169        TCGA-CM-6170        TCGA-CM-6171        TCGA-CM-6172 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-CM-6674        TCGA-CM-6675        TCGA-CM-6676        TCGA-CM-6677 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-CM-6678        TCGA-CM-6679        TCGA-CM-6680        TCGA-D5-5537 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-D5-5538        TCGA-D5-5539        TCGA-D5-5540        TCGA-D5-5541 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-D5-6529        TCGA-D5-6532        TCGA-D5-6533        TCGA-D5-6534 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-D5-6535        TCGA-D5-6536        TCGA-D5-6537        TCGA-D5-6538 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-D5-6539        TCGA-D5-6540        TCGA-D5-6541        TCGA-D5-6898 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-D5-6920        TCGA-D5-6922        TCGA-D5-6923        TCGA-D5-6924 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-D5-6926        TCGA-D5-6927        TCGA-D5-6928        TCGA-D5-6929 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-D5-6930        TCGA-D5-6931        TCGA-D5-6932        TCGA-D5-7000 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-DM-A0X9        TCGA-DM-A0XD        TCGA-DM-A0XF        TCGA-DM-A1D0 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-DM-A1D4        TCGA-DM-A1D6        TCGA-DM-A1D7        TCGA-DM-A1D8 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-DM-A1D9        TCGA-DM-A1DA        TCGA-DM-A1DB        TCGA-DM-A1HA 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-DM-A1HB        TCGA-DM-A282        TCGA-DM-A285        TCGA-DM-A28C 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-DM-A28E        TCGA-DM-A28F        TCGA-DM-A28G        TCGA-DM-A28H 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-DM-A28K        TCGA-F4-6459        TCGA-F4-6460        TCGA-F4-6569 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-F4-6570        TCGA-F4-6703        TCGA-F4-6704        TCGA-F4-6805 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-F4-6806        TCGA-F4-6807        TCGA-F4-6808        TCGA-F4-6809 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-F4-6854        TCGA-F4-6855        TCGA-F4-6856        TCGA-G4-6293 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-G4-6299        TCGA-G4-6303        TCGA-G4-6304        TCGA-G4-6306 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-G4-6307        TCGA-G4-6309        TCGA-G4-6310        TCGA-G4-6315 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-G4-6317        TCGA-G4-6321        TCGA-G4-6323        TCGA-G4-6586 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-G4-6588        TCGA-G4-6625        TCGA-G4-6626        TCGA-G4-6628 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2691        TCGA-AF-2692 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3913        TCGA-AF-4110 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-AF-5654        TCGA-AF-6136        TCGA-AF-6655        TCGA-AF-6672 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6549        TCGA-AH-6643 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-AH-6644        TCGA-CI-6619        TCGA-CI-6620        TCGA-CI-6621 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-CI-6622        TCGA-CI-6624        TCGA-CL-5917        TCGA-CL-5918 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6155        TCGA-DC-6157 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-DC-6158        TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-DC-6683        TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-DY-A1DD        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-EF-5830        TCGA-EI-6506        TCGA-EI-6507        TCGA-EI-6508 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-EI-6510        TCGA-F5-6464        TCGA-F5-6465        TCGA-F5-6571 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-F5-6702        TCGA-F5-6811        TCGA-F5-6812        TCGA-F5-6813 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 
       TCGA-G5-6235        TCGA-G5-6641 
"ANAPC16 WILD-TYPE" "ANAPC16 WILD-TYPE" 

Clustering(1679) Variable = AKAP7 MUTATION ANALYSIS
D1679V1, survival
                 sevent
clus2               0   1
  AKAP7 MUTATED     5   1
  AKAP7 WILD-TYPE 373  92
  AKAP7 MUTATED AKAP7 WILD-TYPE 
              6             465 
  AKAP7 MUTATED AKAP7 WILD-TYPE 
              1              92 
$`AKAP7 MUTATED`
TCGA-A6-2671 TCGA-A6-5665 TCGA-AA-A010 TCGA-AD-5900 TCGA-CK-4948 TCGA-AG-A01Y 
       43.76        22.06        34.98         0.07       148.01        64.01 

$`AKAP7 WILD-TYPE`
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       46.65        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       18.05        40.96        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       10.06        14.30        17.56        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       12.00        70.03        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  AKAP7 MUTATED AKAP7 WILD-TYPE 
           0.07            0.00 
  AKAP7 MUTATED AKAP7 WILD-TYPE 
         148.01          140.38 
  AKAP7 MUTATED AKAP7 WILD-TYPE 
          39.37           20.05 
[1] "0.1 - 148.0 (39.4)" "0.0 - 140.4 (20.1)"
[1] "hr=" "2"  
D1679V2, continuous
D1679V3, binary
                 cls
clus                0   1
  AKAP7 MUTATED     5   1
  AKAP7 WILD-TYPE 361 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AKAP7 MUTATED      5    1
  AKAP7 WILD-TYPE  361  118
        clus
vv       AKAP7 MUTATED AKAP7 WILD-TYPE
  COLON              5             361
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  AKAP7 MUTATED         1        0        1         1         1         0
  AKAP7 WILD-TYPE      90        1       31       137         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AKAP7 MUTATED           1          0          0          0        1         0
  AKAP7 WILD-TYPE        23         11         59         42       47        18
                 vv
clus              STAGE IVB
  AKAP7 MUTATED           0
  AKAP7 WILD-TYPE         1
D1679V4, multiclass
            clus
vv           AKAP7 MUTATED AKAP7 WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              1             137
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             0              42
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  AKAP7 MUTATED     0   1   4   1
  AKAP7 WILD-TYPE  17  91 325  49
D1679V5, multiclass
    clus
vv   AKAP7 MUTATED AKAP7 WILD-TYPE
  T1             0              17
  T2             1              91
  T3             4             325
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  AKAP7 MUTATED     4   1   1
  AKAP7 WILD-TYPE 283 112  86
D1679V6, multiclass
    clus
vv   AKAP7 MUTATED AKAP7 WILD-TYPE
  N0             4             283
  N1             1             112
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1679V7, binary
                 cls
clus                0   1
  AKAP7 MUTATED     4   1
  AKAP7 WILD-TYPE 371  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AKAP7 MUTATED      4    1
  AKAP7 WILD-TYPE  371   64
   clus
vv  AKAP7 MUTATED AKAP7 WILD-TYPE
  0             4             371
  1             1              64
[1] 2 2
[1] FALSE
D1679V8, binary
                 cls
clus                0   1
  AKAP7 MUTATED     4   2
  AKAP7 WILD-TYPE 221 262
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AKAP7 MUTATED      4    2
  AKAP7 WILD-TYPE  221  262
        clus
vv       AKAP7 MUTATED AKAP7 WILD-TYPE
  FEMALE             4             221
  MALE               2             262
[1] 2 2
[1] FALSE
D1679V9, binary
                 cls
clus                0   1
  AKAP7 MUTATED     4   0
  AKAP7 WILD-TYPE 346  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AKAP7 MUTATED      4    0
  AKAP7 WILD-TYPE  346   22
     clus
vv    AKAP7 MUTATED AKAP7 WILD-TYPE
  NO              4             346
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  AKAP7 MUTATED                      4                             1
  AKAP7 WILD-TYPE                  311                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  AKAP7 MUTATED                       1                              0
  AKAP7 WILD-TYPE                   105                             10
D1679V10, multiclass
                                clus
vv                               AKAP7 MUTATED AKAP7 WILD-TYPE
  COLON ADENOCARCINOMA                       4             311
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  AKAP7 MUTATED     6   0   0   0
  AKAP7 WILD-TYPE 339   4  31  25
D1679V11, multiclass
    clus
vv   AKAP7 MUTATED AKAP7 WILD-TYPE
  R0             6             339
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1679V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AKAP7 MUTATED                                  0     0
  AKAP7 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  AKAP7 MUTATED                           0     4
  AKAP7 WILD-TYPE                        22   222
D1679V13, multiclass
                                  clus
vv                                 AKAP7 MUTATED AKAP7 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        4             222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1680) Variable = MUM1L1 MUTATION ANALYSIS
D1680V1, survival
                  sevent
clus2                0   1
  MUM1L1 MUTATED    13   1
  MUM1L1 WILD-TYPE 365  92
  MUM1L1 MUTATED MUM1L1 WILD-TYPE 
              14              457 
  MUM1L1 MUTATED MUM1L1 WILD-TYPE 
               1               92 
$`MUM1L1 MUTATED`
TCGA-AA-3667 TCGA-AA-3815 TCGA-AA-3947 TCGA-AD-6890 TCGA-AD-6963 TCGA-CM-6168 
       14.01        33.04        33.01         0.79        27.42        12.99 
TCGA-D5-6533 TCGA-D5-6537 TCGA-D5-6922 TCGA-DM-A1D0 TCGA-DM-A28E TCGA-AG-A002 
        1.32         4.80         4.41       130.65       119.93        20.98 
TCGA-AG-A020 TCGA-DY-A0XA 
       10.98       126.44 

$`MUM1L1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3672 TCGA-AA-3673 
        6.05         6.97        54.02         2.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       10.06        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       12.99        24.00        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        0.72         5.79        22.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6169 TCGA-CM-6170 
       29.03        16.04        21.99        14.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 
       56.09        55.92        20.19        18.25        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
       17.85        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        3.68        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       24.43        38.20        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
        6.12        81.37        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       70.03        64.01        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  MUM1L1 MUTATED MUM1L1 WILD-TYPE 
            0.79             0.00 
  MUM1L1 MUTATED MUM1L1 WILD-TYPE 
          130.65           148.01 
  MUM1L1 MUTATED MUM1L1 WILD-TYPE 
          17.495           20.190 
[1] "0.8 - 130.7 (17.5)" "0.0 - 148.0 (20.2)"
[1] "hr=" "3.6"
D1680V2, continuous
D1680V3, binary
                  cls
clus                 0   1
  MUM1L1 MUTATED    13   3
  MUM1L1 WILD-TYPE 353 116
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MUM1L1 MUTATED     13    3
  MUM1L1 WILD-TYPE  353  116
        clus
vv       MUM1L1 MUTATED MUM1L1 WILD-TYPE
  COLON              13              353
  RECTUM              3              116
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MUM1L1 MUTATED         2        0        0         6         2         0
  MUM1L1 WILD-TYPE      89        1       32       132         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MUM1L1 MUTATED           1          1          2          0        0
  MUM1L1 WILD-TYPE        23         10         57         42       48
                  vv
clus               STAGE IVA STAGE IVB
  MUM1L1 MUTATED           0         0
  MUM1L1 WILD-TYPE        18         1
D1680V4, multiclass
            clus
vv           MUM1L1 MUTATED MUM1L1 WILD-TYPE
  STAGE I                 2               89
  STAGE IA                0                1
  STAGE II                0               32
  STAGE IIA               6              132
  STAGE IIB               2                8
  STAGE IIC               0                1
  STAGE III               1               23
  STAGE IIIA              1               10
  STAGE IIIB              2               57
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  MUM1L1 MUTATED     1   2  10   3
  MUM1L1 WILD-TYPE  16  90 319  47
D1680V5, multiclass
    clus
vv   MUM1L1 MUTATED MUM1L1 WILD-TYPE
  T1              1               16
  T2              2               90
  T3             10              319
  T4              3               47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  MUM1L1 MUTATED    13   3   0
  MUM1L1 WILD-TYPE 274 110  87
D1680V6, multiclass
    clus
vv   MUM1L1 MUTATED MUM1L1 WILD-TYPE
  N0             13              274
  N1              3              110
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1680V7, binary
                  cls
clus                 0   1
  MUM1L1 MUTATED    12   0
  MUM1L1 WILD-TYPE 363  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MUM1L1 MUTATED     12    0
  MUM1L1 WILD-TYPE  363   65
   clus
vv  MUM1L1 MUTATED MUM1L1 WILD-TYPE
  0             12              363
  1              0               65
[1] 2 2
[1] FALSE
D1680V8, binary
                  cls
clus                 0   1
  MUM1L1 MUTATED    11   5
  MUM1L1 WILD-TYPE 214 259
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MUM1L1 MUTATED     11    5
  MUM1L1 WILD-TYPE  214  259
        clus
vv       MUM1L1 MUTATED MUM1L1 WILD-TYPE
  FEMALE             11              214
  MALE                5              259
[1] 2 2
[1] FALSE
D1680V9, binary
                  cls
clus                 0   1
  MUM1L1 MUTATED     7   0
  MUM1L1 WILD-TYPE 343  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MUM1L1 MUTATED      7    0
  MUM1L1 WILD-TYPE  343   22
     clus
vv    MUM1L1 MUTATED MUM1L1 WILD-TYPE
  NO               7              343
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MUM1L1 MUTATED                     12                             1
  MUM1L1 WILD-TYPE                  303                            46
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MUM1L1 MUTATED                       2                              1
  MUM1L1 WILD-TYPE                   104                              9
D1680V10, multiclass
                                clus
vv                               MUM1L1 MUTATED MUM1L1 WILD-TYPE
  COLON ADENOCARCINOMA                       12              303
  COLON MUCINOUS ADENOCARCINOMA               1               46
  RECTAL ADENOCARCINOMA                       2              104
  RECTAL MUCINOUS ADENOCARCINOMA              1                9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  MUM1L1 MUTATED    10   0   0   1
  MUM1L1 WILD-TYPE 335   4  31  24
D1680V11, multiclass
    clus
vv   MUM1L1 MUTATED MUM1L1 WILD-TYPE
  R0             10              335
  R1              0                4
  R2              0               31
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1680V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MUM1L1 MUTATED                                  0     0
  MUM1L1 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  MUM1L1 MUTATED                           1     9
  MUM1L1 WILD-TYPE                        21   217
D1680V13, multiclass
                                  clus
vv                                 MUM1L1 MUTATED MUM1L1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                         9              217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1681) Variable = ISOC2 MUTATION ANALYSIS
D1681V1, survival
                 sevent
clus2               0   1
  ISOC2 MUTATED     4   1
  ISOC2 WILD-TYPE 374  92
  ISOC2 MUTATED ISOC2 WILD-TYPE 
              5             466 
  ISOC2 MUTATED ISOC2 WILD-TYPE 
              1              92 
$`ISOC2 MUTATED`
TCGA-A6-5665 TCGA-A6-6654 TCGA-D5-6539 TCGA-D5-6923 TCGA-F4-6570 
       22.06        23.87        12.49        12.43         6.18 

$`ISOC2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 
       25.18        24.16        21.76        24.69        24.39        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
        4.80        17.13        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
        4.41        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 
       98.24         8.61        31.96        35.74        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  ISOC2 MUTATED ISOC2 WILD-TYPE 
           6.18            0.00 
  ISOC2 MUTATED ISOC2 WILD-TYPE 
          23.87          148.01 
  ISOC2 MUTATED ISOC2 WILD-TYPE 
         12.490          20.235 
[1] "6.2 - 23.9 (12.5)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.7"
D1681V2, continuous
D1681V3, binary
                 cls
clus                0   1
  ISOC2 MUTATED     5   0
  ISOC2 WILD-TYPE 361 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ISOC2 MUTATED      5    0
  ISOC2 WILD-TYPE  361  119
        clus
vv       ISOC2 MUTATED ISOC2 WILD-TYPE
  COLON              5             361
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ISOC2 MUTATED         1        0        0         2         0         0
  ISOC2 WILD-TYPE      90        1       32       136        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ISOC2 MUTATED           0          1          1          0        0         0
  ISOC2 WILD-TYPE        24         10         58         42       48        18
                 vv
clus              STAGE IVB
  ISOC2 MUTATED           0
  ISOC2 WILD-TYPE         1
D1681V4, multiclass
            clus
vv           ISOC2 MUTATED ISOC2 WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              2             136
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             1              10
  STAGE IIIB             1              58
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ISOC2 MUTATED     0   1   4   0
  ISOC2 WILD-TYPE  17  91 325  50
D1681V5, multiclass
    clus
vv   ISOC2 MUTATED ISOC2 WILD-TYPE
  T1             0              17
  T2             1              91
  T3             4             325
  T4             0              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  ISOC2 MUTATED     4   1   0
  ISOC2 WILD-TYPE 283 112  87
D1681V6, multiclass
    clus
vv   ISOC2 MUTATED ISOC2 WILD-TYPE
  N0             4             283
  N1             1             112
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1681V7, binary
                 cls
clus                0   1
  ISOC2 MUTATED     5   0
  ISOC2 WILD-TYPE 370  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ISOC2 MUTATED      5    0
  ISOC2 WILD-TYPE  370   65
   clus
vv  ISOC2 MUTATED ISOC2 WILD-TYPE
  0             5             370
  1             0              65
[1] 2 2
[1] FALSE
D1681V8, binary
                 cls
clus                0   1
  ISOC2 MUTATED     4   1
  ISOC2 WILD-TYPE 221 263
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ISOC2 MUTATED      4    1
  ISOC2 WILD-TYPE  221  263
        clus
vv       ISOC2 MUTATED ISOC2 WILD-TYPE
  FEMALE             4             221
  MALE               1             263
[1] 2 2
[1] FALSE
D1681V9, binary
                 cls
clus                0   1
  ISOC2 MUTATED     5   0
  ISOC2 WILD-TYPE 345  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ISOC2 MUTATED      5    0
  ISOC2 WILD-TYPE  345   22
     clus
vv    ISOC2 MUTATED ISOC2 WILD-TYPE
  NO              5             345
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ISOC2 MUTATED                      5                             0
  ISOC2 WILD-TYPE                  310                            47
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ISOC2 MUTATED                       0                              0
  ISOC2 WILD-TYPE                   106                             10
D1681V10, multiclass
                                clus
vv                               ISOC2 MUTATED ISOC2 WILD-TYPE
  COLON ADENOCARCINOMA                       5             310
  COLON MUCINOUS ADENOCARCINOMA              0              47
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  ISOC2 MUTATED     4   0   0   0
  ISOC2 WILD-TYPE 341   4  31  25
D1681V11, multiclass
    clus
vv   ISOC2 MUTATED ISOC2 WILD-TYPE
  R0             4             341
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1681V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ISOC2 MUTATED                                  0     0
  ISOC2 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ISOC2 MUTATED                           0     5
  ISOC2 WILD-TYPE                        22   221
D1681V13, multiclass
                                  clus
vv                                 ISOC2 MUTATED ISOC2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        5             221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1682) Variable = GLTSCR1 MUTATION ANALYSIS
D1682V1, survival
                   sevent
clus2                 0   1
  GLTSCR1 MUTATED    10   2
  GLTSCR1 WILD-TYPE 368  91
  GLTSCR1 MUTATED GLTSCR1 WILD-TYPE 
               12               459 
  GLTSCR1 MUTATED GLTSCR1 WILD-TYPE 
                2                91 
$`GLTSCR1 MUTATED`
TCGA-AA-3663 TCGA-AA-3870 TCGA-AA-3950 TCGA-AD-6548 TCGA-AD-6889 TCGA-AZ-6601 
        6.97        29.98        24.00        21.37        56.55       100.01 
TCGA-CK-6751 TCGA-D5-5538 TCGA-D5-6540 TCGA-D5-6930 TCGA-DM-A1HA TCGA-AG-A026 
      124.27        12.26        16.14         1.51       131.51         1.94 

$`GLTSCR1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.05        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       17.03        24.03        27.02        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 
       12.99        24.00        33.01        26.01         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 
       18.05        40.96         0.07        15.52         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 
       88.21        49.41         6.77        12.10        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CM-4743 TCGA-CM-4744 
        9.99        21.14        82.95         1.91        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       10.06        12.03        45.40        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
        4.80        17.13        12.49        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        4.80        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
      140.38         7.50        44.32       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A02G 
       12.00        70.03        64.01        10.98        49.97        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  GLTSCR1 MUTATED GLTSCR1 WILD-TYPE 
             1.51              0.00 
  GLTSCR1 MUTATED GLTSCR1 WILD-TYPE 
           131.51            148.01 
  GLTSCR1 MUTATED GLTSCR1 WILD-TYPE 
           22.685            20.120 
[1] "1.5 - 131.5 (22.7)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.8"
D1682V2, continuous
D1682V3, binary
                   cls
clus                  0   1
  GLTSCR1 MUTATED    11   1
  GLTSCR1 WILD-TYPE 355 118
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GLTSCR1 MUTATED     11    1
  GLTSCR1 WILD-TYPE  355  118
        clus
vv       GLTSCR1 MUTATED GLTSCR1 WILD-TYPE
  COLON               11               355
  RECTUM               1               118
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GLTSCR1 MUTATED         3        0        3         3         0         0
  GLTSCR1 WILD-TYPE      88        1       29       135        10         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GLTSCR1 MUTATED           0          0          1          1        1
  GLTSCR1 WILD-TYPE        24         11         58         41       47
                   vv
clus                STAGE IVA STAGE IVB
  GLTSCR1 MUTATED           0         0
  GLTSCR1 WILD-TYPE        18         1
D1682V4, multiclass
            clus
vv           GLTSCR1 MUTATED GLTSCR1 WILD-TYPE
  STAGE I                  3                88
  STAGE IA                 0                 1
  STAGE II                 3                29
  STAGE IIA                3               135
  STAGE IIB                0                10
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               0                11
  STAGE IIIB               1                58
  STAGE IIIC               1                41
  STAGE IV                 1                47
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  GLTSCR1 MUTATED     0   3   8   1
  GLTSCR1 WILD-TYPE  17  89 321  49
D1682V5, multiclass
    clus
vv   GLTSCR1 MUTATED GLTSCR1 WILD-TYPE
  T1               0                17
  T2               3                89
  T3               8               321
  T4               1                49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  GLTSCR1 MUTATED     9   1   2
  GLTSCR1 WILD-TYPE 278 112  85
D1682V6, multiclass
    clus
vv   GLTSCR1 MUTATED GLTSCR1 WILD-TYPE
  N0               9               278
  N1               1               112
  N2               2                85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1682V7, binary
                   cls
clus                  0   1
  GLTSCR1 MUTATED    10   1
  GLTSCR1 WILD-TYPE 365  64
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GLTSCR1 MUTATED     10    1
  GLTSCR1 WILD-TYPE  365   64
   clus
vv  GLTSCR1 MUTATED GLTSCR1 WILD-TYPE
  0              10               365
  1               1                64
[1] 2 2
[1] FALSE
D1682V8, binary
                   cls
clus                  0   1
  GLTSCR1 MUTATED     5   7
  GLTSCR1 WILD-TYPE 220 257
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GLTSCR1 MUTATED      5    7
  GLTSCR1 WILD-TYPE  220  257
        clus
vv       GLTSCR1 MUTATED GLTSCR1 WILD-TYPE
  FEMALE               5               220
  MALE                 7               257
[1] 2 2
[1] FALSE
D1682V9, binary
                   cls
clus                  0   1
  GLTSCR1 MUTATED     7   0
  GLTSCR1 WILD-TYPE 343  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GLTSCR1 MUTATED      7    0
  GLTSCR1 WILD-TYPE  343   22
     clus
vv    GLTSCR1 MUTATED GLTSCR1 WILD-TYPE
  NO                7               343
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  GLTSCR1 MUTATED                      7                             4
  GLTSCR1 WILD-TYPE                  308                            43
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  GLTSCR1 MUTATED                       1                              0
  GLTSCR1 WILD-TYPE                   105                             10
D1682V10, multiclass
                                clus
vv                               GLTSCR1 MUTATED GLTSCR1 WILD-TYPE
  COLON ADENOCARCINOMA                         7               308
  COLON MUCINOUS ADENOCARCINOMA                4                43
  RECTAL ADENOCARCINOMA                        1               105
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  GLTSCR1 MUTATED     7   1   0   1
  GLTSCR1 WILD-TYPE 338   3  31  24
D1682V11, multiclass
    clus
vv   GLTSCR1 MUTATED GLTSCR1 WILD-TYPE
  R0               7               338
  R1               1                 3
  R2               0                31
  RX               1                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1682V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GLTSCR1 MUTATED                                  0     1
  GLTSCR1 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  GLTSCR1 MUTATED                           0     7
  GLTSCR1 WILD-TYPE                        22   219
D1682V13, multiclass
                                  clus
vv                                 GLTSCR1 MUTATED GLTSCR1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                10
  BLACK OR AFRICAN AMERICAN                      0                22
  WHITE                                          7               219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1683) Variable = DNAJB11 MUTATION ANALYSIS
D1683V1, survival
                   sevent
clus2                 0   1
  DNAJB11 MUTATED     9   0
  DNAJB11 WILD-TYPE 369  93
  DNAJB11 MUTATED DNAJB11 WILD-TYPE 
                9               462 
  DNAJB11 MUTATED DNAJB11 WILD-TYPE 
                0                93 
$`DNAJB11 MUTATED`
TCGA-AA-3821 TCGA-AA-A00R TCGA-AD-5900 TCGA-AD-6889 TCGA-CM-4743 TCGA-D5-5540 
        1.02         0.99         0.07        56.55        23.05        56.09 
TCGA-D5-6926 TCGA-G4-6306 TCGA-G4-6310 
        9.04        44.68        63.62 

$`DNAJB11 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W 
       38.04         4.01        27.02        42.02        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 
       39.98        18.05        40.96        21.37        15.52         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
      124.27        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       19.59        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 
      133.18        74.56        65.85        53.62        55.04        85.48 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  DNAJB11 MUTATED DNAJB11 WILD-TYPE 
             0.07              0.00 
  DNAJB11 MUTATED DNAJB11 WILD-TYPE 
            63.62            148.01 
  DNAJB11 MUTATED DNAJB11 WILD-TYPE 
           23.050            20.155 
[1] "0.1 - 63.6 (23.1)"  "0.0 - 148.0 (20.2)"
[1] "hr="     "9300000"
D1683V2, continuous
D1683V3, binary
                   cls
clus                  0   1
  DNAJB11 MUTATED     9   0
  DNAJB11 WILD-TYPE 357 119
[1] "tbl2"
                   cls
clus                [,1] [,2]
  DNAJB11 MUTATED      9    0
  DNAJB11 WILD-TYPE  357  119
        clus
vv       DNAJB11 MUTATED DNAJB11 WILD-TYPE
  COLON                9               357
  RECTUM               0               119
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DNAJB11 MUTATED         3        0        0         4         0         0
  DNAJB11 WILD-TYPE      88        1       32       134        10         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DNAJB11 MUTATED           0          0          2          0        0
  DNAJB11 WILD-TYPE        24         11         57         42       48
                   vv
clus                STAGE IVA STAGE IVB
  DNAJB11 MUTATED           0         0
  DNAJB11 WILD-TYPE        18         1
D1683V4, multiclass
            clus
vv           DNAJB11 MUTATED DNAJB11 WILD-TYPE
  STAGE I                  3                88
  STAGE IA                 0                 1
  STAGE II                 0                32
  STAGE IIA                4               134
  STAGE IIB                0                10
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               0                11
  STAGE IIIB               2                57
  STAGE IIIC               0                42
  STAGE IV                 0                48
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  DNAJB11 MUTATED     0   4   4   1
  DNAJB11 WILD-TYPE  17  88 325  49
D1683V5, multiclass
    clus
vv   DNAJB11 MUTATED DNAJB11 WILD-TYPE
  T1               0                17
  T2               4                88
  T3               4               325
  T4               1                49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  DNAJB11 MUTATED     7   2   0
  DNAJB11 WILD-TYPE 280 111  87
D1683V6, multiclass
    clus
vv   DNAJB11 MUTATED DNAJB11 WILD-TYPE
  N0               7               280
  N1               2               111
  N2               0                87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1683V7, binary
                   cls
clus                  0   1
  DNAJB11 MUTATED     8   0
  DNAJB11 WILD-TYPE 367  65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  DNAJB11 MUTATED      8    0
  DNAJB11 WILD-TYPE  367   65
   clus
vv  DNAJB11 MUTATED DNAJB11 WILD-TYPE
  0               8               367
  1               0                65
[1] 2 2
[1] FALSE
D1683V8, binary
                   cls
clus                  0   1
  DNAJB11 MUTATED     2   7
  DNAJB11 WILD-TYPE 223 257
[1] "tbl2"
                   cls
clus                [,1] [,2]
  DNAJB11 MUTATED      2    7
  DNAJB11 WILD-TYPE  223  257
        clus
vv       DNAJB11 MUTATED DNAJB11 WILD-TYPE
  FEMALE               2               223
  MALE                 7               257
[1] 2 2
[1] FALSE
D1683V9, binary
                   cls
clus                  0   1
  DNAJB11 MUTATED     4   2
  DNAJB11 WILD-TYPE 346  20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  DNAJB11 MUTATED      4    2
  DNAJB11 WILD-TYPE  346   20
     clus
vv    DNAJB11 MUTATED DNAJB11 WILD-TYPE
  NO                4               346
  YES               2                20
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  DNAJB11 MUTATED                      7                             2
  DNAJB11 WILD-TYPE                  308                            45
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  DNAJB11 MUTATED                       0                              0
  DNAJB11 WILD-TYPE                   106                             10
D1683V10, multiclass
                                clus
vv                               DNAJB11 MUTATED DNAJB11 WILD-TYPE
  COLON ADENOCARCINOMA                         7               308
  COLON MUCINOUS ADENOCARCINOMA                2                45
  RECTAL ADENOCARCINOMA                        0               106
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  DNAJB11 MUTATED     8   0   0   0
  DNAJB11 WILD-TYPE 337   4  31  25
D1683V11, multiclass
    clus
vv   DNAJB11 MUTATED DNAJB11 WILD-TYPE
  R0               8               337
  R1               0                 4
  R2               0                31
  RX               0                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1683V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DNAJB11 MUTATED                                  0     1
  DNAJB11 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  DNAJB11 MUTATED                           0     6
  DNAJB11 WILD-TYPE                        22   220
D1683V13, multiclass
                                  clus
vv                                 DNAJB11 MUTATED DNAJB11 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                10
  BLACK OR AFRICAN AMERICAN                      0                22
  WHITE                                          6               220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1684) Variable = LEPROTL1 MUTATION ANALYSIS
D1684V1, survival
                    sevent
clus2                  0   1
  LEPROTL1 MUTATED     4   1
  LEPROTL1 WILD-TYPE 374  92
  LEPROTL1 MUTATED LEPROTL1 WILD-TYPE 
                 5                466 
  LEPROTL1 MUTATED LEPROTL1 WILD-TYPE 
                 1                 92 
$`LEPROTL1 MUTATED`
TCGA-AA-3864 TCGA-AA-A00J TCGA-AA-A01P TCGA-CM-6674 TCGA-D5-6930 
       53.00        18.05        38.07        12.95         1.51 

$`LEPROTL1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L 
       38.04        19.00        30.02        34.03        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        31.00         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6675 
       12.99        13.02        15.02        14.04        11.01        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  LEPROTL1 MUTATED LEPROTL1 WILD-TYPE 
              1.51               0.00 
  LEPROTL1 MUTATED LEPROTL1 WILD-TYPE 
             53.00             148.01 
  LEPROTL1 MUTATED LEPROTL1 WILD-TYPE 
            18.050             20.235 
[1] "1.5 - 53.0 (18.1)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1"  
D1684V2, continuous
D1684V3, binary
                    cls
clus                   0   1
  LEPROTL1 MUTATED     5   0
  LEPROTL1 WILD-TYPE 361 119
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  LEPROTL1 MUTATED      5    0
  LEPROTL1 WILD-TYPE  361  119
        clus
vv       LEPROTL1 MUTATED LEPROTL1 WILD-TYPE
  COLON                 5                361
  RECTUM                0                119
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  LEPROTL1 MUTATED         0        0        1         2         0         0
  LEPROTL1 WILD-TYPE      91        1       31       136        10         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  LEPROTL1 MUTATED           1          0          1          0        0
  LEPROTL1 WILD-TYPE        23         11         58         42       48
                    vv
clus                 STAGE IVA STAGE IVB
  LEPROTL1 MUTATED           0         0
  LEPROTL1 WILD-TYPE        18         1
D1684V4, multiclass
            clus
vv           LEPROTL1 MUTATED LEPROTL1 WILD-TYPE
  STAGE I                   0                 91
  STAGE IA                  0                  1
  STAGE II                  1                 31
  STAGE IIA                 2                136
  STAGE IIB                 0                 10
  STAGE IIC                 0                  1
  STAGE III                 1                 23
  STAGE IIIA                0                 11
  STAGE IIIB                1                 58
  STAGE IIIC                0                 42
  STAGE IV                  0                 48
  STAGE IVA                 0                 18
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  LEPROTL1 MUTATED     0   0   4   1
  LEPROTL1 WILD-TYPE  17  92 325  49
D1684V5, multiclass
    clus
vv   LEPROTL1 MUTATED LEPROTL1 WILD-TYPE
  T1                0                 17
  T2                0                 92
  T3                4                325
  T4                1                 49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  LEPROTL1 MUTATED     3   2   0
  LEPROTL1 WILD-TYPE 284 111  87
D1684V6, multiclass
    clus
vv   LEPROTL1 MUTATED LEPROTL1 WILD-TYPE
  N0                3                284
  N1                2                111
  N2                0                 87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1684V7, binary
                    cls
clus                   0   1
  LEPROTL1 MUTATED     5   0
  LEPROTL1 WILD-TYPE 370  65
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  LEPROTL1 MUTATED      5    0
  LEPROTL1 WILD-TYPE  370   65
   clus
vv  LEPROTL1 MUTATED LEPROTL1 WILD-TYPE
  0                5                370
  1                0                 65
[1] 2 2
[1] FALSE
D1684V8, binary
                    cls
clus                   0   1
  LEPROTL1 MUTATED     1   4
  LEPROTL1 WILD-TYPE 224 260
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  LEPROTL1 MUTATED      1    4
  LEPROTL1 WILD-TYPE  224  260
        clus
vv       LEPROTL1 MUTATED LEPROTL1 WILD-TYPE
  FEMALE                1                224
  MALE                  4                260
[1] 2 2
[1] FALSE
D1684V9, binary
                    cls
clus                   0   1
  LEPROTL1 MUTATED     4   0
  LEPROTL1 WILD-TYPE 346  22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  LEPROTL1 MUTATED      4    0
  LEPROTL1 WILD-TYPE  346   22
     clus
vv    LEPROTL1 MUTATED LEPROTL1 WILD-TYPE
  NO                 4                346
  YES                0                 22
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  LEPROTL1 MUTATED                      3                             2
  LEPROTL1 WILD-TYPE                  312                            45
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  LEPROTL1 MUTATED                       0                              0
  LEPROTL1 WILD-TYPE                   106                             10
D1684V10, multiclass
                                clus
vv                               LEPROTL1 MUTATED LEPROTL1 WILD-TYPE
  COLON ADENOCARCINOMA                          3                312
  COLON MUCINOUS ADENOCARCINOMA                 2                 45
  RECTAL ADENOCARCINOMA                         0                106
  RECTAL MUCINOUS ADENOCARCINOMA                0                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  LEPROTL1 MUTATED     5   0   0   0
  LEPROTL1 WILD-TYPE 340   4  31  25
D1684V11, multiclass
    clus
vv   LEPROTL1 MUTATED LEPROTL1 WILD-TYPE
  R0                5                340
  R1                0                  4
  R2                0                 31
  RX                0                 25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1684V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  LEPROTL1 MUTATED                                  0     0
  LEPROTL1 WILD-TYPE                                1    11
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  LEPROTL1 MUTATED                           0     2
  LEPROTL1 WILD-TYPE                        22   224
D1684V13, multiclass
[1] "Remove cluster labels:" "LEPROTL1 MUTATED"      
clus
  LEPROTL1 MUTATED LEPROTL1 WILD-TYPE 
                 2                258 
        TCGA-A6-2671         TCGA-A6-2672         TCGA-A6-2674 
"LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" 
        TCGA-A6-2676         TCGA-A6-2677         TCGA-A6-2678 
"LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" 
        TCGA-A6-2683         TCGA-A6-3807         TCGA-A6-3808 
"LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" 
        TCGA-A6-3809         TCGA-A6-3810         TCGA-A6-4105 
"LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" 
        TCGA-A6-5656         TCGA-A6-5657         TCGA-A6-5659 
"LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" 
        TCGA-A6-5660         TCGA-A6-5661         TCGA-A6-5662 
"LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" 
        TCGA-A6-5664         TCGA-A6-5665         TCGA-A6-5666 
"LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" 
        TCGA-A6-6137         TCGA-A6-6138         TCGA-A6-6141 
"LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" 
        TCGA-A6-6142         TCGA-A6-6648         TCGA-A6-6649 
"LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" 
        TCGA-A6-6651         TCGA-A6-6652         TCGA-A6-6653 
"LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" 
        TCGA-A6-6654         TCGA-A6-6780         TCGA-A6-6781 
"LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" 
        TCGA-A6-6782         TCGA-AD-5900         TCGA-AD-6548 
"LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" 
        TCGA-AD-6888         TCGA-AD-6889         TCGA-AD-6890 
"LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" 
        TCGA-AD-6895         TCGA-AD-6899         TCGA-AD-6901 
"LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" 
        TCGA-AD-6963         TCGA-AD-6964         TCGA-AD-6965 
"LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" 
        TCGA-AU-3779         TCGA-AU-6004         TCGA-AY-4070 
"LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" 
        TCGA-AY-4071         TCGA-AY-5543         TCGA-AY-6196 
"LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" 
        TCGA-AY-6197         TCGA-AY-6386         TCGA-AZ-4315 
"LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" 
        TCGA-AZ-4323         TCGA-AZ-4616         TCGA-AZ-4681 
"LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" 
        TCGA-AZ-4682         TCGA-AZ-5403         TCGA-AZ-5407 
"LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" 
        TCGA-AZ-6598         TCGA-AZ-6599         TCGA-AZ-6600 
"LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" 
        TCGA-AZ-6601         TCGA-AZ-6603         TCGA-AZ-6605 
"LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" 
        TCGA-AZ-6606         TCGA-AZ-6607         TCGA-AZ-6608 
"LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" 
        TCGA-CA-5254         TCGA-CA-5255         TCGA-CA-5796 
"LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" 
        TCGA-CA-5797         TCGA-CA-6715         TCGA-CA-6716 
"LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" 
        TCGA-CA-6717         TCGA-CA-6718         TCGA-CA-6719 
"LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" 
        TCGA-CK-4947         TCGA-CK-4948         TCGA-CK-4950 
"LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" 
        TCGA-CK-4952         TCGA-CK-5912         TCGA-CK-5913 
"LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" 
        TCGA-CK-5914         TCGA-CK-5915         TCGA-CK-5916 
"LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" 
        TCGA-CK-6746         TCGA-CK-6747         TCGA-CK-6748 
"LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" 
        TCGA-CK-6751         TCGA-CM-4743         TCGA-CM-4744 
"LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" 
        TCGA-CM-4746         TCGA-CM-4747         TCGA-CM-4752 
"LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" 
        TCGA-CM-5341         TCGA-CM-5344         TCGA-CM-5348 
"LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" 
        TCGA-CM-5349         TCGA-CM-5860         TCGA-CM-5861 
"LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" 
        TCGA-CM-5862         TCGA-CM-5863         TCGA-CM-5864 
"LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" 
        TCGA-CM-5868         TCGA-CM-6161         TCGA-CM-6162 
"LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" 
        TCGA-CM-6163         TCGA-CM-6164         TCGA-CM-6165 
"LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" 
        TCGA-CM-6166         TCGA-CM-6167         TCGA-CM-6168 
"LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" 
        TCGA-CM-6169         TCGA-CM-6170         TCGA-CM-6171 
"LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" 
        TCGA-CM-6172         TCGA-CM-6675         TCGA-CM-6676 
"LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" 
        TCGA-CM-6677         TCGA-CM-6678         TCGA-CM-6679 
"LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" 
        TCGA-CM-6680         TCGA-D5-5537         TCGA-D5-5538 
"LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" 
        TCGA-D5-5539         TCGA-D5-5540         TCGA-D5-5541 
"LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" 
        TCGA-D5-6529         TCGA-D5-6532         TCGA-D5-6533 
"LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" 
        TCGA-D5-6534         TCGA-D5-6535         TCGA-D5-6536 
"LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" 
        TCGA-D5-6537         TCGA-D5-6538         TCGA-D5-6539 
"LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" 
        TCGA-D5-6540         TCGA-D5-6541         TCGA-D5-6898 
"LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" 
        TCGA-D5-6920         TCGA-D5-6922         TCGA-D5-6923 
"LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" 
        TCGA-D5-6924         TCGA-D5-6926         TCGA-D5-6927 
"LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" 
        TCGA-D5-6928         TCGA-D5-6929         TCGA-D5-6931 
"LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" 
        TCGA-D5-6932         TCGA-D5-7000         TCGA-DM-A0X9 
"LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" 
        TCGA-DM-A0XD         TCGA-DM-A0XF         TCGA-DM-A1D0 
"LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" 
        TCGA-DM-A1D4         TCGA-DM-A1D6         TCGA-DM-A1D7 
"LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" 
        TCGA-DM-A1D8         TCGA-DM-A1D9         TCGA-DM-A1DA 
"LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" 
        TCGA-DM-A1DB         TCGA-DM-A1HA         TCGA-DM-A1HB 
"LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" 
        TCGA-DM-A282         TCGA-DM-A285         TCGA-DM-A28C 
"LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" 
        TCGA-DM-A28E         TCGA-DM-A28F         TCGA-DM-A28G 
"LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" 
        TCGA-DM-A28H         TCGA-DM-A28K         TCGA-F4-6459 
"LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" 
        TCGA-F4-6460         TCGA-F4-6569         TCGA-F4-6570 
"LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" 
        TCGA-F4-6703         TCGA-F4-6704         TCGA-F4-6805 
"LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" 
        TCGA-F4-6806         TCGA-F4-6807         TCGA-F4-6808 
"LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" 
        TCGA-F4-6809         TCGA-F4-6854         TCGA-F4-6855 
"LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" 
        TCGA-F4-6856         TCGA-G4-6293         TCGA-G4-6299 
"LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" 
        TCGA-G4-6303         TCGA-G4-6304         TCGA-G4-6306 
"LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" 
        TCGA-G4-6307         TCGA-G4-6309         TCGA-G4-6310 
"LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" 
        TCGA-G4-6315         TCGA-G4-6317         TCGA-G4-6321 
"LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" 
        TCGA-G4-6323         TCGA-G4-6586         TCGA-G4-6588 
"LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" 
        TCGA-G4-6625         TCGA-G4-6626         TCGA-G4-6628 
"LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2691 
"LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" 
        TCGA-AF-2692         TCGA-AF-2693         TCGA-AF-3400 
"LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" 
        TCGA-AF-3913         TCGA-AF-4110         TCGA-AF-5654 
"LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" 
        TCGA-AF-6136         TCGA-AF-6655         TCGA-AF-6672 
"LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6549 
"LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" 
        TCGA-AH-6643         TCGA-AH-6644         TCGA-CI-6619 
"LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" 
        TCGA-CI-6620         TCGA-CI-6621         TCGA-CI-6622 
"LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" 
        TCGA-CI-6624         TCGA-CL-5917         TCGA-CL-5918 
"LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" 
        TCGA-DC-5337         TCGA-DC-5869         TCGA-DC-6155 
"LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" 
        TCGA-DC-6157         TCGA-DC-6158         TCGA-DC-6160 
"LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" 
        TCGA-DC-6681         TCGA-DC-6682         TCGA-DC-6683 
"LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" 
        TCGA-DT-5265         TCGA-DY-A0XA         TCGA-DY-A1DC 
"LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" 
        TCGA-DY-A1DD         TCGA-DY-A1DF         TCGA-DY-A1DG 
"LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" 
        TCGA-DY-A1H8         TCGA-EF-5830         TCGA-EI-6506 
"LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6510 
"LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" 
        TCGA-F5-6464         TCGA-F5-6465         TCGA-F5-6571 
"LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6811         TCGA-F5-6812 
"LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" 
        TCGA-F5-6813         TCGA-G5-6235         TCGA-G5-6641 
"LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" "LEPROTL1 WILD-TYPE" 

Clustering(1685) Variable = OR9Q1 MUTATION ANALYSIS
D1685V1, survival
                 sevent
clus2               0   1
  OR9Q1 MUTATED     4   2
  OR9Q1 WILD-TYPE 374  91
  OR9Q1 MUTATED OR9Q1 WILD-TYPE 
              6             465 
  OR9Q1 MUTATED OR9Q1 WILD-TYPE 
              2              91 
$`OR9Q1 MUTATED`
TCGA-AA-3713 TCGA-AD-6889 TCGA-CK-4952 TCGA-CM-6674 TCGA-DM-A1DB TCGA-F4-6570 
       19.04        56.55        15.62        12.95        44.32         6.18 

$`OR9Q1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       15.52         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       85.45        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6675 
       12.99        13.02        15.02        14.04        11.01        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
      140.38         7.50       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
        8.61        31.96        35.74        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  OR9Q1 MUTATED OR9Q1 WILD-TYPE 
           6.18            0.00 
  OR9Q1 MUTATED OR9Q1 WILD-TYPE 
          56.55          148.01 
  OR9Q1 MUTATED OR9Q1 WILD-TYPE 
          17.33           20.28 
[1] "6.2 - 56.5 (17.3)"  "0.0 - 148.0 (20.3)"
[1] "hr=" "1.6"
D1685V2, continuous
D1685V3, binary
                 cls
clus                0   1
  OR9Q1 MUTATED     6   0
  OR9Q1 WILD-TYPE 360 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR9Q1 MUTATED      6    0
  OR9Q1 WILD-TYPE  360  119
        clus
vv       OR9Q1 MUTATED OR9Q1 WILD-TYPE
  COLON              6             360
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  OR9Q1 MUTATED         0        0        0         4         0         0
  OR9Q1 WILD-TYPE      91        1       32       134        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  OR9Q1 MUTATED           0          0          0          1        1         0
  OR9Q1 WILD-TYPE        24         11         59         41       47        18
                 vv
clus              STAGE IVB
  OR9Q1 MUTATED           0
  OR9Q1 WILD-TYPE         1
D1685V4, multiclass
            clus
vv           OR9Q1 MUTATED OR9Q1 WILD-TYPE
  STAGE I                0              91
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              4             134
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             1              41
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  OR9Q1 MUTATED     0   0   5   1
  OR9Q1 WILD-TYPE  17  92 324  49
D1685V5, multiclass
    clus
vv   OR9Q1 MUTATED OR9Q1 WILD-TYPE
  T1             0              17
  T2             0              92
  T3             5             324
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  OR9Q1 MUTATED     5   0   1
  OR9Q1 WILD-TYPE 282 113  86
D1685V6, multiclass
    clus
vv   OR9Q1 MUTATED OR9Q1 WILD-TYPE
  N0             5             282
  N1             0             113
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1685V7, binary
                 cls
clus                0   1
  OR9Q1 MUTATED     5   1
  OR9Q1 WILD-TYPE 370  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR9Q1 MUTATED      5    1
  OR9Q1 WILD-TYPE  370   64
   clus
vv  OR9Q1 MUTATED OR9Q1 WILD-TYPE
  0             5             370
  1             1              64
[1] 2 2
[1] FALSE
D1685V8, binary
                 cls
clus                0   1
  OR9Q1 MUTATED     2   4
  OR9Q1 WILD-TYPE 223 260
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR9Q1 MUTATED      2    4
  OR9Q1 WILD-TYPE  223  260
        clus
vv       OR9Q1 MUTATED OR9Q1 WILD-TYPE
  FEMALE             2             223
  MALE               4             260
[1] 2 2
[1] FALSE
D1685V9, binary
                 cls
clus                0   1
  OR9Q1 MUTATED     2   1
  OR9Q1 WILD-TYPE 348  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR9Q1 MUTATED      2    1
  OR9Q1 WILD-TYPE  348   21
     clus
vv    OR9Q1 MUTATED OR9Q1 WILD-TYPE
  NO              2             348
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  OR9Q1 MUTATED                      5                             1
  OR9Q1 WILD-TYPE                  310                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  OR9Q1 MUTATED                       0                              0
  OR9Q1 WILD-TYPE                   106                             10
D1685V10, multiclass
                                clus
vv                               OR9Q1 MUTATED OR9Q1 WILD-TYPE
  COLON ADENOCARCINOMA                       5             310
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  OR9Q1 MUTATED     2   0   1   1
  OR9Q1 WILD-TYPE 343   4  30  24
D1685V11, multiclass
    clus
vv   OR9Q1 MUTATED OR9Q1 WILD-TYPE
  R0             2             343
  R1             0               4
  R2             1              30
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1685V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OR9Q1 MUTATED                                  0     1
  OR9Q1 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  OR9Q1 MUTATED                           0     4
  OR9Q1 WILD-TYPE                        22   222
D1685V13, multiclass
                                  clus
vv                                 OR9Q1 MUTATED OR9Q1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        4             222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1686) Variable = ARID4B MUTATION ANALYSIS
D1686V1, survival
                  sevent
clus2                0   1
  ARID4B MUTATED    10   1
  ARID4B WILD-TYPE 368  92
  ARID4B MUTATED ARID4B WILD-TYPE 
              11              460 
  ARID4B MUTATED ARID4B WILD-TYPE 
               1               92 
$`ARID4B MUTATED`
TCGA-AA-3713 TCGA-AA-A00N TCGA-AD-6895 TCGA-AU-6004 TCGA-CA-6716 TCGA-CM-5349 
       19.04         4.01         0.72        27.09        12.20        30.08 
TCGA-D5-6536 TCGA-DM-A1HA TCGA-G4-6588 TCGA-AG-4008 TCGA-AG-A002 
       17.85       131.51        26.17        17.03        20.98 

$`ARID4B WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
       56.55         0.79         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
        0.20        14.50        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 
        3.06         3.25         3.29         0.07        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.03        22.98        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       15.12         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-A008 TCGA-AG-A00C 
       28.04        36.03        14.04         1.02        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  ARID4B MUTATED ARID4B WILD-TYPE 
            0.72             0.00 
  ARID4B MUTATED ARID4B WILD-TYPE 
          131.51           148.01 
  ARID4B MUTATED ARID4B WILD-TYPE 
          19.040           20.235 
[1] "0.7 - 131.5 (19.0)" "0.0 - 148.0 (20.2)"
[1] "hr=" "2.1"
D1686V2, continuous
D1686V3, binary
                  cls
clus                 0   1
  ARID4B MUTATED    11   2
  ARID4B WILD-TYPE 355 117
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID4B MUTATED     11    2
  ARID4B WILD-TYPE  355  117
        clus
vv       ARID4B MUTATED ARID4B WILD-TYPE
  COLON              11              355
  RECTUM              2              117
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ARID4B MUTATED         2        0        0         6         1         0
  ARID4B WILD-TYPE      89        1       32       132         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ARID4B MUTATED           0          0          0          2        1
  ARID4B WILD-TYPE        24         11         59         40       47
                  vv
clus               STAGE IVA STAGE IVB
  ARID4B MUTATED           0         0
  ARID4B WILD-TYPE        18         1
D1686V4, multiclass
            clus
vv           ARID4B MUTATED ARID4B WILD-TYPE
  STAGE I                 2               89
  STAGE IA                0                1
  STAGE II                0               32
  STAGE IIA               6              132
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              0               59
  STAGE IIIC              2               40
  STAGE IV                1               47
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ARID4B MUTATED     0   2  10   1
  ARID4B WILD-TYPE  17  90 319  49
D1686V5, multiclass
    clus
vv   ARID4B MUTATED ARID4B WILD-TYPE
  T1              0               17
  T2              2               90
  T3             10              319
  T4              1               49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  ARID4B MUTATED    10   1   2
  ARID4B WILD-TYPE 277 112  85
D1686V6, multiclass
    clus
vv   ARID4B MUTATED ARID4B WILD-TYPE
  N0             10              277
  N1              1              112
  N2              2               85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1686V7, binary
                  cls
clus                 0   1
  ARID4B MUTATED    10   1
  ARID4B WILD-TYPE 365  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID4B MUTATED     10    1
  ARID4B WILD-TYPE  365   64
   clus
vv  ARID4B MUTATED ARID4B WILD-TYPE
  0             10              365
  1              1               64
[1] 2 2
[1] FALSE
D1686V8, binary
                  cls
clus                 0   1
  ARID4B MUTATED     4   9
  ARID4B WILD-TYPE 221 255
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID4B MUTATED      4    9
  ARID4B WILD-TYPE  221  255
        clus
vv       ARID4B MUTATED ARID4B WILD-TYPE
  FEMALE              4              221
  MALE                9              255
[1] 2 2
[1] FALSE
D1686V9, binary
                  cls
clus                 0   1
  ARID4B MUTATED     6   1
  ARID4B WILD-TYPE 344  21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID4B MUTATED      6    1
  ARID4B WILD-TYPE  344   21
     clus
vv    ARID4B MUTATED ARID4B WILD-TYPE
  NO               6              344
  YES              1               21
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ARID4B MUTATED                      9                             2
  ARID4B WILD-TYPE                  306                            45
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ARID4B MUTATED                       2                              0
  ARID4B WILD-TYPE                   104                             10
D1686V10, multiclass
                                clus
vv                               ARID4B MUTATED ARID4B WILD-TYPE
  COLON ADENOCARCINOMA                        9              306
  COLON MUCINOUS ADENOCARCINOMA               2               45
  RECTAL ADENOCARCINOMA                       2              104
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ARID4B MUTATED     9   0   1   1
  ARID4B WILD-TYPE 336   4  30  24
D1686V11, multiclass
    clus
vv   ARID4B MUTATED ARID4B WILD-TYPE
  R0              9              336
  R1              0                4
  R2              1               30
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1686V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ARID4B MUTATED                                  0     1
  ARID4B WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ARID4B MUTATED                           0     7
  ARID4B WILD-TYPE                        22   219
D1686V13, multiclass
                                  clus
vv                                 ARID4B MUTATED ARID4B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         7              219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1687) Variable = ABHD2 MUTATION ANALYSIS
D1687V1, survival
                 sevent
clus2               0   1
  ABHD2 MUTATED     8   4
  ABHD2 WILD-TYPE 370  89
  ABHD2 MUTATED ABHD2 WILD-TYPE 
             12             459 
  ABHD2 MUTATED ABHD2 WILD-TYPE 
              4              89 
$`ABHD2 MUTATED`
TCGA-AA-3516 TCGA-AA-A00J TCGA-AA-A00N TCGA-AD-6889 TCGA-AD-6964 TCGA-CK-5912 
       13.02        18.05         4.01        56.55        10.88        49.08 
TCGA-CM-4746 TCGA-CM-5344 TCGA-CM-5864 TCGA-G4-6628 TCGA-AG-A002 TCGA-CI-6622 
       37.02        22.03        15.02        79.69        20.98         6.97 

$`ABHD2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        1.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L 
       38.04        19.00        30.02        34.03        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 
       18.05        40.96         0.07        21.37        15.52         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
        0.72         5.79        22.42        27.42         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5913 
       14.30        17.56       148.01        85.45        15.62        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5349 
       20.02        25.02        13.02        29.06        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5868 TCGA-CM-6161 
       32.02        15.02         5.03        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       91.79        46.75        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  ABHD2 MUTATED ABHD2 WILD-TYPE 
           4.01            0.00 
  ABHD2 MUTATED ABHD2 WILD-TYPE 
          79.69          148.01 
  ABHD2 MUTATED ABHD2 WILD-TYPE 
         19.515          20.190 
[1] "4.0 - 79.7 (19.5)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.6"
D1687V2, continuous
D1687V3, binary
                 cls
clus                0   1
  ABHD2 MUTATED    10   2
  ABHD2 WILD-TYPE 356 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABHD2 MUTATED     10    2
  ABHD2 WILD-TYPE  356  117
        clus
vv       ABHD2 MUTATED ABHD2 WILD-TYPE
  COLON             10             356
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ABHD2 MUTATED         5        0        0         1         2         0
  ABHD2 WILD-TYPE      86        1       32       137         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ABHD2 MUTATED           1          0          2          0        0         0
  ABHD2 WILD-TYPE        23         11         57         42       48        18
                 vv
clus              STAGE IVB
  ABHD2 MUTATED           0
  ABHD2 WILD-TYPE         1
D1687V4, multiclass
            clus
vv           ABHD2 MUTATED ABHD2 WILD-TYPE
  STAGE I                5              86
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              1             137
  STAGE IIB              2               8
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             2              57
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ABHD2 MUTATED     0   5   3   4
  ABHD2 WILD-TYPE  17  87 326  46
D1687V5, multiclass
    clus
vv   ABHD2 MUTATED ABHD2 WILD-TYPE
  T1             0              17
  T2             5              87
  T3             3             326
  T4             4              46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  ABHD2 MUTATED     8   2   2
  ABHD2 WILD-TYPE 279 111  85
D1687V6, multiclass
    clus
vv   ABHD2 MUTATED ABHD2 WILD-TYPE
  N0             8             279
  N1             2             111
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1687V7, binary
                 cls
clus                0   1
  ABHD2 MUTATED    10   0
  ABHD2 WILD-TYPE 365  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABHD2 MUTATED     10    0
  ABHD2 WILD-TYPE  365   65
   clus
vv  ABHD2 MUTATED ABHD2 WILD-TYPE
  0            10             365
  1             0              65
[1] 2 2
[1] FALSE
D1687V8, binary
                 cls
clus                0   1
  ABHD2 MUTATED     2  10
  ABHD2 WILD-TYPE 223 254
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABHD2 MUTATED      2   10
  ABHD2 WILD-TYPE  223  254
        clus
vv       ABHD2 MUTATED ABHD2 WILD-TYPE
  FEMALE             2             223
  MALE              10             254
[1] 2 2
[1] FALSE
D1687V9, binary
                 cls
clus                0   1
  ABHD2 MUTATED     9   0
  ABHD2 WILD-TYPE 341  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ABHD2 MUTATED      9    0
  ABHD2 WILD-TYPE  341   22
     clus
vv    ABHD2 MUTATED ABHD2 WILD-TYPE
  NO              9             341
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ABHD2 MUTATED                      7                             3
  ABHD2 WILD-TYPE                  308                            44
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ABHD2 MUTATED                       2                              0
  ABHD2 WILD-TYPE                   104                             10
D1687V10, multiclass
                                clus
vv                               ABHD2 MUTATED ABHD2 WILD-TYPE
  COLON ADENOCARCINOMA                       7             308
  COLON MUCINOUS ADENOCARCINOMA              3              44
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  ABHD2 MUTATED     7   0   0   1
  ABHD2 WILD-TYPE 338   4  31  24
D1687V11, multiclass
    clus
vv   ABHD2 MUTATED ABHD2 WILD-TYPE
  R0             7             338
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1687V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ABHD2 MUTATED                                  0     1
  ABHD2 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ABHD2 MUTATED                           1     6
  ABHD2 WILD-TYPE                        21   220
D1687V13, multiclass
                                  clus
vv                                 ABHD2 MUTATED ABHD2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        6             220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1688) Variable = HIST1H1B MUTATION ANALYSIS
D1688V1, survival
                    sevent
clus2                  0   1
  HIST1H1B MUTATED     8   0
  HIST1H1B WILD-TYPE 370  93
  HIST1H1B MUTATED HIST1H1B WILD-TYPE 
                 8                463 
  HIST1H1B MUTATED HIST1H1B WILD-TYPE 
                 0                 93 
$`HIST1H1B MUTATED`
TCGA-A6-2672 TCGA-A6-5665 TCGA-A6-6781 TCGA-AA-3662 TCGA-CM-6165 TCGA-D5-6928 
       46.65        22.06        19.66         6.05        16.04        11.64 
TCGA-D5-6930 TCGA-CL-5917 
        1.51        78.12 

$`HIST1H1B WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02        78.08         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
        2.96        29.03        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 
       14.30         9.04         9.44         4.80        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  HIST1H1B MUTATED HIST1H1B WILD-TYPE 
              1.51               0.00 
  HIST1H1B MUTATED HIST1H1B WILD-TYPE 
             78.12             148.01 
  HIST1H1B MUTATED HIST1H1B WILD-TYPE 
             17.85              20.28 
[1] "1.5 - 78.1 (17.9)"  "0.0 - 148.0 (20.3)"
[1] "hr="     "9200000"
D1688V2, continuous
D1688V3, binary
                    cls
clus                   0   1
  HIST1H1B MUTATED     7   1
  HIST1H1B WILD-TYPE 359 118
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HIST1H1B MUTATED      7    1
  HIST1H1B WILD-TYPE  359  118
        clus
vv       HIST1H1B MUTATED HIST1H1B WILD-TYPE
  COLON                 7                359
  RECTUM                1                118
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  HIST1H1B MUTATED         0        0        0         4         0         0
  HIST1H1B WILD-TYPE      91        1       32       134        10         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HIST1H1B MUTATED           0          0          1          2        1
  HIST1H1B WILD-TYPE        24         11         58         40       47
                    vv
clus                 STAGE IVA STAGE IVB
  HIST1H1B MUTATED           0         0
  HIST1H1B WILD-TYPE        18         1
D1688V4, multiclass
            clus
vv           HIST1H1B MUTATED HIST1H1B WILD-TYPE
  STAGE I                   0                 91
  STAGE IA                  0                  1
  STAGE II                  0                 32
  STAGE IIA                 4                134
  STAGE IIB                 0                 10
  STAGE IIC                 0                  1
  STAGE III                 0                 24
  STAGE IIIA                0                 11
  STAGE IIIB                1                 58
  STAGE IIIC                2                 40
  STAGE IV                  1                 47
  STAGE IVA                 0                 18
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  HIST1H1B MUTATED     0   0   6   2
  HIST1H1B WILD-TYPE  17  92 323  48
D1688V5, multiclass
    clus
vv   HIST1H1B MUTATED HIST1H1B WILD-TYPE
  T1                0                 17
  T2                0                 92
  T3                6                323
  T4                2                 48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  HIST1H1B MUTATED     4   2   2
  HIST1H1B WILD-TYPE 283 111  85
D1688V6, multiclass
    clus
vv   HIST1H1B MUTATED HIST1H1B WILD-TYPE
  N0                4                283
  N1                2                111
  N2                2                 85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1688V7, binary
                    cls
clus                   0   1
  HIST1H1B MUTATED     5   1
  HIST1H1B WILD-TYPE 370  64
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HIST1H1B MUTATED      5    1
  HIST1H1B WILD-TYPE  370   64
   clus
vv  HIST1H1B MUTATED HIST1H1B WILD-TYPE
  0                5                370
  1                1                 64
[1] 2 2
[1] FALSE
D1688V8, binary
                    cls
clus                   0   1
  HIST1H1B MUTATED     4   4
  HIST1H1B WILD-TYPE 221 260
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HIST1H1B MUTATED      4    4
  HIST1H1B WILD-TYPE  221  260
        clus
vv       HIST1H1B MUTATED HIST1H1B WILD-TYPE
  FEMALE                4                221
  MALE                  4                260
[1] 2 2
[1] FALSE
D1688V9, binary
                    cls
clus                   0   1
  HIST1H1B MUTATED     7   0
  HIST1H1B WILD-TYPE 343  22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HIST1H1B MUTATED      7    0
  HIST1H1B WILD-TYPE  343   22
     clus
vv    HIST1H1B MUTATED HIST1H1B WILD-TYPE
  NO                 7                343
  YES                0                 22
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  HIST1H1B MUTATED                      4                             3
  HIST1H1B WILD-TYPE                  311                            44
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  HIST1H1B MUTATED                       1                              0
  HIST1H1B WILD-TYPE                   105                             10
D1688V10, multiclass
                                clus
vv                               HIST1H1B MUTATED HIST1H1B WILD-TYPE
  COLON ADENOCARCINOMA                          4                311
  COLON MUCINOUS ADENOCARCINOMA                 3                 44
  RECTAL ADENOCARCINOMA                         1                105
  RECTAL MUCINOUS ADENOCARCINOMA                0                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  HIST1H1B MUTATED     6   0   1   1
  HIST1H1B WILD-TYPE 339   4  30  24
D1688V11, multiclass
    clus
vv   HIST1H1B MUTATED HIST1H1B WILD-TYPE
  R0                6                339
  R1                0                  4
  R2                1                 30
  RX                1                 24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1688V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HIST1H1B MUTATED                                  0     0
  HIST1H1B WILD-TYPE                                1    11
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  HIST1H1B MUTATED                           0     7
  HIST1H1B WILD-TYPE                        22   219
D1688V13, multiclass
                                  clus
vv                                 HIST1H1B MUTATED HIST1H1B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 11
  BLACK OR AFRICAN AMERICAN                       0                 22
  WHITE                                           7                219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1689) Variable = MAGOHB MUTATION ANALYSIS
D1689V1, survival
                  sevent
clus2                0   1
  MAGOHB MUTATED     2   1
  MAGOHB WILD-TYPE 376  92
  MAGOHB MUTATED MAGOHB WILD-TYPE 
               3              468 
  MAGOHB MUTATED MAGOHB WILD-TYPE 
               1               92 
$`MAGOHB MUTATED`
TCGA-AZ-6605 TCGA-F4-6569 TCGA-AG-A002 
        5.23        35.74        20.98 

$`MAGOHB WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6606 
       49.41         6.77        12.10       100.01        29.56        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  MAGOHB MUTATED MAGOHB WILD-TYPE 
            5.23             0.00 
  MAGOHB MUTATED MAGOHB WILD-TYPE 
           35.74           148.01 
  MAGOHB MUTATED MAGOHB WILD-TYPE 
          20.980           20.155 
[1] "5.2 - 35.7 (21.0)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "2.4"
D1689V2, continuous
D1689V3, binary
                  cls
clus                 0   1
  MAGOHB MUTATED     3   1
  MAGOHB WILD-TYPE 363 118
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAGOHB MUTATED      3    1
  MAGOHB WILD-TYPE  363  118
        clus
vv       MAGOHB MUTATED MAGOHB WILD-TYPE
  COLON               3              363
  RECTUM              1              118
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MAGOHB MUTATED         2        0        0         0         0         0
  MAGOHB WILD-TYPE      89        1       32       138        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MAGOHB MUTATED           0          0          1          1        0
  MAGOHB WILD-TYPE        24         11         58         41       48
                  vv
clus               STAGE IVA STAGE IVB
  MAGOHB MUTATED           0         0
  MAGOHB WILD-TYPE        18         1
D1689V4, multiclass
            clus
vv           MAGOHB MUTATED MAGOHB WILD-TYPE
  STAGE I                 2               89
  STAGE IA                0                1
  STAGE II                0               32
  STAGE IIA               0              138
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              1               58
  STAGE IIIC              1               41
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  MAGOHB MUTATED     0   2   1   1
  MAGOHB WILD-TYPE  17  90 328  49
D1689V5, multiclass
    clus
vv   MAGOHB MUTATED MAGOHB WILD-TYPE
  T1              0               17
  T2              2               90
  T3              1              328
  T4              1               49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  MAGOHB MUTATED     2   1   1
  MAGOHB WILD-TYPE 285 112  86
D1689V6, multiclass
    clus
vv   MAGOHB MUTATED MAGOHB WILD-TYPE
  N0              2              285
  N1              1              112
  N2              1               86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1689V7, binary
                  cls
clus                 0   1
  MAGOHB MUTATED     3   0
  MAGOHB WILD-TYPE 372  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAGOHB MUTATED      3    0
  MAGOHB WILD-TYPE  372   65
   clus
vv  MAGOHB MUTATED MAGOHB WILD-TYPE
  0              3              372
  1              0               65
[1] 2 2
[1] FALSE
D1689V8, binary
                  cls
clus                 0   1
  MAGOHB MUTATED     0   4
  MAGOHB WILD-TYPE 225 260
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAGOHB MUTATED      0    4
  MAGOHB WILD-TYPE  225  260
        clus
vv       MAGOHB MUTATED MAGOHB WILD-TYPE
  FEMALE              0              225
  MALE                4              260
[1] 2 2
[1] FALSE
D1689V9, binary
                  cls
clus                 0   1
  MAGOHB MUTATED     3   0
  MAGOHB WILD-TYPE 347  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAGOHB MUTATED      3    0
  MAGOHB WILD-TYPE  347   22
     clus
vv    MAGOHB MUTATED MAGOHB WILD-TYPE
  NO               3              347
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MAGOHB MUTATED                      2                             1
  MAGOHB WILD-TYPE                  313                            46
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MAGOHB MUTATED                       1                              0
  MAGOHB WILD-TYPE                   105                             10
D1689V10, multiclass
                                clus
vv                               MAGOHB MUTATED MAGOHB WILD-TYPE
  COLON ADENOCARCINOMA                        2              313
  COLON MUCINOUS ADENOCARCINOMA               1               46
  RECTAL ADENOCARCINOMA                       1              105
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  MAGOHB MUTATED     3   0   0   0
  MAGOHB WILD-TYPE 342   4  31  25
D1689V11, multiclass
    clus
vv   MAGOHB MUTATED MAGOHB WILD-TYPE
  R0              3              342
  R1              0                4
  R2              0               31
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1689V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MAGOHB MUTATED                                  0     0
  MAGOHB WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  MAGOHB MUTATED                           0     3
  MAGOHB WILD-TYPE                        22   223
D1689V13, multiclass
                                  clus
vv                                 MAGOHB MUTATED MAGOHB WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         3              223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1690) Variable = ATL1 MUTATION ANALYSIS
D1690V1, survival
                sevent
clus2              0   1
  ATL1 MUTATED    10   2
  ATL1 WILD-TYPE 368  91
  ATL1 MUTATED ATL1 WILD-TYPE 
            12            459 
  ATL1 MUTATED ATL1 WILD-TYPE 
             2             91 
$`ATL1 MUTATED`
TCGA-A6-3809 TCGA-AA-3510 TCGA-AA-3672 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-A010 
       32.75        63.98         0.92        19.04        19.04        34.98 
TCGA-AZ-4315 TCGA-CA-6717 TCGA-CA-6718 TCGA-D5-6927 TCGA-D5-6928 TCGA-AG-A002 
       58.39        12.76        10.06         9.44        11.64        20.98 

$`ATL1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
       54.02         2.01        14.01        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       85.05        26.99        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
       16.31         0.95        33.01        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.07        12.20        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6930 
        4.41        12.43        14.30         9.04         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  ATL1 MUTATED ATL1 WILD-TYPE 
          0.92           0.00 
  ATL1 MUTATED ATL1 WILD-TYPE 
         63.98         148.01 
  ATL1 MUTATED ATL1 WILD-TYPE 
         19.04          20.28 
[1] "0.9 - 64.0 (19.0)"  "0.0 - 148.0 (20.3)"
[1] "hr=" "1.1"
D1690V2, continuous
D1690V3, binary
                cls
clus               0   1
  ATL1 MUTATED    11   1
  ATL1 WILD-TYPE 355 118
[1] "tbl2"
                cls
clus             [,1] [,2]
  ATL1 MUTATED     11    1
  ATL1 WILD-TYPE  355  118
        clus
vv       ATL1 MUTATED ATL1 WILD-TYPE
  COLON            11            355
  RECTUM            1            118
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ATL1 MUTATED         1        0        2         5         2         0
  ATL1 WILD-TYPE      90        1       30       133         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ATL1 MUTATED           1          0          0          0        1         0
  ATL1 WILD-TYPE        23         11         59         42       47        18
                vv
clus             STAGE IVB
  ATL1 MUTATED           0
  ATL1 WILD-TYPE         1
D1690V4, multiclass
            clus
vv           ATL1 MUTATED ATL1 WILD-TYPE
  STAGE I               1             90
  STAGE IA              0              1
  STAGE II              2             30
  STAGE IIA             5            133
  STAGE IIB             2              8
  STAGE IIC             0              1
  STAGE III             1             23
  STAGE IIIA            0             11
  STAGE IIIB            0             59
  STAGE IIIC            0             42
  STAGE IV              1             47
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  ATL1 MUTATED     0   1   9   2
  ATL1 WILD-TYPE  17  91 320  48
D1690V5, multiclass
    clus
vv   ATL1 MUTATED ATL1 WILD-TYPE
  T1            0             17
  T2            1             91
  T3            9            320
  T4            2             48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  ATL1 MUTATED    11   1   0
  ATL1 WILD-TYPE 276 112  87
D1690V6, multiclass
    clus
vv   ATL1 MUTATED ATL1 WILD-TYPE
  N0           11            276
  N1            1            112
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1690V7, binary
                cls
clus               0   1
  ATL1 MUTATED    11   1
  ATL1 WILD-TYPE 364  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  ATL1 MUTATED     11    1
  ATL1 WILD-TYPE  364   64
   clus
vv  ATL1 MUTATED ATL1 WILD-TYPE
  0           11            364
  1            1             64
[1] 2 2
[1] FALSE
D1690V8, binary
                cls
clus               0   1
  ATL1 MUTATED     3   9
  ATL1 WILD-TYPE 222 255
[1] "tbl2"
                cls
clus             [,1] [,2]
  ATL1 MUTATED      3    9
  ATL1 WILD-TYPE  222  255
        clus
vv       ATL1 MUTATED ATL1 WILD-TYPE
  FEMALE            3            222
  MALE              9            255
[1] 2 2
[1] FALSE
D1690V9, binary
                cls
clus               0   1
  ATL1 MUTATED    11   1
  ATL1 WILD-TYPE 339  21
[1] "tbl2"
                cls
clus             [,1] [,2]
  ATL1 MUTATED     11    1
  ATL1 WILD-TYPE  339   21
     clus
vv    ATL1 MUTATED ATL1 WILD-TYPE
  NO            11            339
  YES            1             21
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ATL1 MUTATED                      8                             3
  ATL1 WILD-TYPE                  307                            44
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ATL1 MUTATED                       1                              0
  ATL1 WILD-TYPE                   105                             10
D1690V10, multiclass
                                clus
vv                               ATL1 MUTATED ATL1 WILD-TYPE
  COLON ADENOCARCINOMA                      8            307
  COLON MUCINOUS ADENOCARCINOMA             3             44
  RECTAL ADENOCARCINOMA                     1            105
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  ATL1 MUTATED     9   0   1   2
  ATL1 WILD-TYPE 336   4  30  23
D1690V11, multiclass
    clus
vv   ATL1 MUTATED ATL1 WILD-TYPE
  R0            9            336
  R1            0              4
  R2            1             30
  RX            2             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1690V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ATL1 MUTATED                                  0     2
  ATL1 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  ATL1 MUTATED                           0     4
  ATL1 WILD-TYPE                        22   222
D1690V13, multiclass
                                  clus
vv                                 ATL1 MUTATED ATL1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              9
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       4            222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1691) Variable = ACRC MUTATION ANALYSIS
D1691V1, survival
                sevent
clus2              0   1
  ACRC MUTATED    13   2
  ACRC WILD-TYPE 365  91
  ACRC MUTATED ACRC WILD-TYPE 
            15            456 
  ACRC MUTATED ACRC WILD-TYPE 
             2             91 
$`ACRC MUTATED`
TCGA-A6-3809 TCGA-AA-3672 TCGA-AA-3833 TCGA-AA-3861 TCGA-AA-3867 TCGA-AA-3947 
       32.75         0.92        15.95        30.05        24.03        33.01 
TCGA-AZ-4315 TCGA-AZ-5407 TCGA-CM-5348 TCGA-CM-5862 TCGA-CM-6171 TCGA-F4-6460 
       58.39        88.21        22.98         5.03        14.04        31.96 
TCGA-G4-6588 TCGA-CL-5917 TCGA-DC-6157 
       26.17        78.12        27.95 

$`ACRC WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 
        6.97        54.02         2.01        14.01        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3870 
       31.07        31.07        53.00        17.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 
       18.05        31.00         2.01        12.99        24.00        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
       16.31         0.95        33.01        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 
        5.13       106.75        22.36        62.79        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5860 
       25.02        13.02        29.06        22.03        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
       15.02        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       13.02        15.02        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
        8.61        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       13.78        35.80        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6158 TCGA-DC-6160 
        7.17        15.02         5.03        13.97        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  ACRC MUTATED ACRC WILD-TYPE 
          0.92           0.00 
  ACRC MUTATED ACRC WILD-TYPE 
         88.21         148.01 
  ACRC MUTATED ACRC WILD-TYPE 
         27.95          20.02 
[1] "0.9 - 88.2 (27.9)"  "0.0 - 148.0 (20.0)"
[1] "hr=" "1.8"
D1691V2, continuous
D1691V3, binary
                cls
clus               0   1
  ACRC MUTATED    13   2
  ACRC WILD-TYPE 353 117
[1] "tbl2"
                cls
clus             [,1] [,2]
  ACRC MUTATED     13    2
  ACRC WILD-TYPE  353  117
        clus
vv       ACRC MUTATED ACRC WILD-TYPE
  COLON            13            353
  RECTUM            2            117
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ACRC MUTATED         3        0        0         4         2         0
  ACRC WILD-TYPE      88        1       32       134         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ACRC MUTATED           1          0          2          1        1         1
  ACRC WILD-TYPE        23         11         57         41       47        17
                vv
clus             STAGE IVB
  ACRC MUTATED           0
  ACRC WILD-TYPE         1
D1691V4, multiclass
            clus
vv           ACRC MUTATED ACRC WILD-TYPE
  STAGE I               3             88
  STAGE IA              0              1
  STAGE II              0             32
  STAGE IIA             4            134
  STAGE IIB             2              8
  STAGE IIC             0              1
  STAGE III             1             23
  STAGE IIIA            0             11
  STAGE IIIB            2             57
  STAGE IIIC            1             41
  STAGE IV              1             47
  STAGE IVA             1             17
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  ACRC MUTATED     1   2  10   2
  ACRC WILD-TYPE  16  90 319  48
D1691V5, multiclass
    clus
vv   ACRC MUTATED ACRC WILD-TYPE
  T1            1             16
  T2            2             90
  T3           10            319
  T4            2             48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  ACRC MUTATED     9   4   2
  ACRC WILD-TYPE 278 109  85
D1691V6, multiclass
    clus
vv   ACRC MUTATED ACRC WILD-TYPE
  N0            9            278
  N1            4            109
  N2            2             85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1691V7, binary
                cls
clus               0   1
  ACRC MUTATED    12   2
  ACRC WILD-TYPE 363  63
[1] "tbl2"
                cls
clus             [,1] [,2]
  ACRC MUTATED     12    2
  ACRC WILD-TYPE  363   63
   clus
vv  ACRC MUTATED ACRC WILD-TYPE
  0           12            363
  1            2             63
[1] 2 2
[1] FALSE
D1691V8, binary
                cls
clus               0   1
  ACRC MUTATED     9   6
  ACRC WILD-TYPE 216 258
[1] "tbl2"
                cls
clus             [,1] [,2]
  ACRC MUTATED      9    6
  ACRC WILD-TYPE  216  258
        clus
vv       ACRC MUTATED ACRC WILD-TYPE
  FEMALE            9            216
  MALE              6            258
[1] 2 2
[1] FALSE
D1691V9, binary
                cls
clus               0   1
  ACRC MUTATED    14   0
  ACRC WILD-TYPE 336  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  ACRC MUTATED     14    0
  ACRC WILD-TYPE  336   22
     clus
vv    ACRC MUTATED ACRC WILD-TYPE
  NO            14            336
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ACRC MUTATED                     11                             2
  ACRC WILD-TYPE                  304                            45
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ACRC MUTATED                       2                              0
  ACRC WILD-TYPE                   104                             10
D1691V10, multiclass
                                clus
vv                               ACRC MUTATED ACRC WILD-TYPE
  COLON ADENOCARCINOMA                     11            304
  COLON MUCINOUS ADENOCARCINOMA             2             45
  RECTAL ADENOCARCINOMA                     2            104
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  ACRC MUTATED    12   0   1   1
  ACRC WILD-TYPE 333   4  30  24
D1691V11, multiclass
    clus
vv   ACRC MUTATED ACRC WILD-TYPE
  R0           12            333
  R1            0              4
  R2            1             30
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1691V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ACRC MUTATED                                  0     0
  ACRC WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  ACRC MUTATED                           1     9
  ACRC WILD-TYPE                        21   217
D1691V13, multiclass
                                  clus
vv                                 ACRC MUTATED ACRC WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                       9            217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1692) Variable = ZNF577 MUTATION ANALYSIS
D1692V1, survival
                  sevent
clus2                0   1
  ZNF577 MUTATED    11   2
  ZNF577 WILD-TYPE 367  91
  ZNF577 MUTATED ZNF577 WILD-TYPE 
              13              458 
  ZNF577 MUTATED ZNF577 WILD-TYPE 
               2               91 
$`ZNF577 MUTATED`
TCGA-A6-2678 TCGA-A6-6649 TCGA-AA-3555 TCGA-AA-A00N TCGA-AA-A010 TCGA-CA-6717 
       42.28        24.16        29.95         4.01        34.98        12.76 
TCGA-CA-6718 TCGA-CM-5348 TCGA-CM-5864 TCGA-CM-6171 TCGA-D5-6931 TCGA-G4-6628 
       10.06        22.98        15.02        14.04        12.00        79.69 
TCGA-AG-A002 
       20.98 

$`ZNF577 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2683 
       43.76        46.65        43.76        42.90        24.33        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       25.18        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       24.00        17.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 
        3.25         3.29         0.07        12.20        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5349 
       37.02        25.02        13.02        29.06        22.03        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5868 TCGA-CM-6161 
       32.02        15.02         5.03        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       12.99        13.02        15.02        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
        1.51        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  ZNF577 MUTATED ZNF577 WILD-TYPE 
            4.01             0.00 
  ZNF577 MUTATED ZNF577 WILD-TYPE 
           79.69           148.01 
  ZNF577 MUTATED ZNF577 WILD-TYPE 
          20.980           20.155 
[1] "4.0 - 79.7 (21.0)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.2"
D1692V2, continuous
D1692V3, binary
                  cls
clus                 0   1
  ZNF577 MUTATED    12   1
  ZNF577 WILD-TYPE 354 118
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF577 MUTATED     12    1
  ZNF577 WILD-TYPE  354  118
        clus
vv       ZNF577 MUTATED ZNF577 WILD-TYPE
  COLON              12              354
  RECTUM              1              118
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZNF577 MUTATED         4        0        0         3         2         0
  ZNF577 WILD-TYPE      87        1       32       135         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF577 MUTATED           0          0          3          1        0
  ZNF577 WILD-TYPE        24         11         56         41       48
                  vv
clus               STAGE IVA STAGE IVB
  ZNF577 MUTATED           0         0
  ZNF577 WILD-TYPE        18         1
D1692V4, multiclass
            clus
vv           ZNF577 MUTATED ZNF577 WILD-TYPE
  STAGE I                 4               87
  STAGE IA                0                1
  STAGE II                0               32
  STAGE IIA               3              135
  STAGE IIB               2                8
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              3               56
  STAGE IIIC              1               41
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZNF577 MUTATED     0   4   6   3
  ZNF577 WILD-TYPE  17  88 323  47
D1692V5, multiclass
    clus
vv   ZNF577 MUTATED ZNF577 WILD-TYPE
  T1              0               17
  T2              4               88
  T3              6              323
  T4              3               47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  ZNF577 MUTATED     9   3   1
  ZNF577 WILD-TYPE 278 110  86
D1692V6, multiclass
    clus
vv   ZNF577 MUTATED ZNF577 WILD-TYPE
  N0              9              278
  N1              3              110
  N2              1               86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1692V7, binary
                  cls
clus                 0   1
  ZNF577 MUTATED    13   0
  ZNF577 WILD-TYPE 362  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF577 MUTATED     13    0
  ZNF577 WILD-TYPE  362   65
   clus
vv  ZNF577 MUTATED ZNF577 WILD-TYPE
  0             13              362
  1              0               65
[1] 2 2
[1] FALSE
D1692V8, binary
                  cls
clus                 0   1
  ZNF577 MUTATED     4   9
  ZNF577 WILD-TYPE 221 255
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF577 MUTATED      4    9
  ZNF577 WILD-TYPE  221  255
        clus
vv       ZNF577 MUTATED ZNF577 WILD-TYPE
  FEMALE              4              221
  MALE                9              255
[1] 2 2
[1] FALSE
D1692V9, binary
                  cls
clus                 0   1
  ZNF577 MUTATED    12   0
  ZNF577 WILD-TYPE 338  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF577 MUTATED     12    0
  ZNF577 WILD-TYPE  338   22
     clus
vv    ZNF577 MUTATED ZNF577 WILD-TYPE
  NO              12              338
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ZNF577 MUTATED                      9                             3
  ZNF577 WILD-TYPE                  306                            44
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ZNF577 MUTATED                       1                              0
  ZNF577 WILD-TYPE                   105                             10
D1692V10, multiclass
                                clus
vv                               ZNF577 MUTATED ZNF577 WILD-TYPE
  COLON ADENOCARCINOMA                        9              306
  COLON MUCINOUS ADENOCARCINOMA               3               44
  RECTAL ADENOCARCINOMA                       1              105
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ZNF577 MUTATED    10   0   0   2
  ZNF577 WILD-TYPE 335   4  31  23
D1692V11, multiclass
    clus
vv   ZNF577 MUTATED ZNF577 WILD-TYPE
  R0             10              335
  R1              0                4
  R2              0               31
  RX              2               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1692V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF577 MUTATED                                  0     2
  ZNF577 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZNF577 MUTATED                           0     7
  ZNF577 WILD-TYPE                        22   219
D1692V13, multiclass
                                  clus
vv                                 ZNF577 MUTATED ZNF577 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                9
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         7              219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1693) Variable = POPDC3 MUTATION ANALYSIS
D1693V1, survival
                  sevent
clus2                0   1
  POPDC3 MUTATED     5   2
  POPDC3 WILD-TYPE 373  91
  POPDC3 MUTATED POPDC3 WILD-TYPE 
               7              464 
  POPDC3 MUTATED POPDC3 WILD-TYPE 
               2               91 
$`POPDC3 MUTATED`
TCGA-A6-6141 TCGA-AA-3555 TCGA-AA-3660 TCGA-AA-A010 TCGA-AZ-6599 TCGA-AF-5654 
        8.38        29.95        78.08        34.98         6.77        16.83 
TCGA-AG-3999 
       28.04 

$`POPDC3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 
       22.09        22.06        32.71        27.09        22.52        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       13.02        24.00        17.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       13.94        19.99        61.02         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        88.21        49.41        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       34.49        10.39        14.50        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       48.03        32.02        19.99        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  POPDC3 MUTATED POPDC3 WILD-TYPE 
            6.77             0.00 
  POPDC3 MUTATED POPDC3 WILD-TYPE 
           78.08           148.01 
  POPDC3 MUTATED POPDC3 WILD-TYPE 
          28.040           20.155 
[1] "6.8 - 78.1 (28.0)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.4"
D1693V2, continuous
D1693V3, binary
                  cls
clus                 0   1
  POPDC3 MUTATED     6   2
  POPDC3 WILD-TYPE 360 117
[1] "tbl2"
                  cls
clus               [,1] [,2]
  POPDC3 MUTATED      6    2
  POPDC3 WILD-TYPE  360  117
        clus
vv       POPDC3 MUTATED POPDC3 WILD-TYPE
  COLON               6              360
  RECTUM              2              117
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  POPDC3 MUTATED         2        0        1         3         1         0
  POPDC3 WILD-TYPE      89        1       31       135         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  POPDC3 MUTATED           0          0          0          1        0
  POPDC3 WILD-TYPE        24         11         59         41       48
                  vv
clus               STAGE IVA STAGE IVB
  POPDC3 MUTATED           0         0
  POPDC3 WILD-TYPE        18         1
D1693V4, multiclass
            clus
vv           POPDC3 MUTATED POPDC3 WILD-TYPE
  STAGE I                 2               89
  STAGE IA                0                1
  STAGE II                1               31
  STAGE IIA               3              135
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              0               59
  STAGE IIIC              1               41
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  POPDC3 MUTATED     0   2   5   1
  POPDC3 WILD-TYPE  17  90 324  49
D1693V5, multiclass
    clus
vv   POPDC3 MUTATED POPDC3 WILD-TYPE
  T1              0               17
  T2              2               90
  T3              5              324
  T4              1               49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  POPDC3 MUTATED     7   0   1
  POPDC3 WILD-TYPE 280 113  86
D1693V6, multiclass
    clus
vv   POPDC3 MUTATED POPDC3 WILD-TYPE
  N0              7              280
  N1              0              113
  N2              1               86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1693V7, binary
                  cls
clus                 0   1
  POPDC3 MUTATED     7   0
  POPDC3 WILD-TYPE 368  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  POPDC3 MUTATED      7    0
  POPDC3 WILD-TYPE  368   65
   clus
vv  POPDC3 MUTATED POPDC3 WILD-TYPE
  0              7              368
  1              0               65
[1] 2 2
[1] FALSE
D1693V8, binary
                  cls
clus                 0   1
  POPDC3 MUTATED     6   2
  POPDC3 WILD-TYPE 219 262
[1] "tbl2"
                  cls
clus               [,1] [,2]
  POPDC3 MUTATED      6    2
  POPDC3 WILD-TYPE  219  262
        clus
vv       POPDC3 MUTATED POPDC3 WILD-TYPE
  FEMALE              6              219
  MALE                2              262
[1] 2 2
[1] FALSE
D1693V9, binary
                  cls
clus                 0   1
  POPDC3 MUTATED     7   0
  POPDC3 WILD-TYPE 343  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  POPDC3 MUTATED      7    0
  POPDC3 WILD-TYPE  343   22
     clus
vv    POPDC3 MUTATED POPDC3 WILD-TYPE
  NO               7              343
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  POPDC3 MUTATED                      5                             1
  POPDC3 WILD-TYPE                  310                            46
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  POPDC3 MUTATED                       2                              0
  POPDC3 WILD-TYPE                   104                             10
D1693V10, multiclass
                                clus
vv                               POPDC3 MUTATED POPDC3 WILD-TYPE
  COLON ADENOCARCINOMA                        5              310
  COLON MUCINOUS ADENOCARCINOMA               1               46
  RECTAL ADENOCARCINOMA                       2              104
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  POPDC3 MUTATED     6   0   0   0
  POPDC3 WILD-TYPE 339   4  31  25
D1693V11, multiclass
    clus
vv   POPDC3 MUTATED POPDC3 WILD-TYPE
  R0              6              339
  R1              0                4
  R2              0               31
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1693V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  POPDC3 MUTATED                                  0     0
  POPDC3 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  POPDC3 MUTATED                           1     2
  POPDC3 WILD-TYPE                        21   224
D1693V13, multiclass
                                  clus
vv                                 POPDC3 MUTATED POPDC3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                         2              224
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1694) Variable = ESR1 MUTATION ANALYSIS
D1694V1, survival
                sevent
clus2              0   1
  ESR1 MUTATED    16   3
  ESR1 WILD-TYPE 362  90
  ESR1 MUTATED ESR1 WILD-TYPE 
            19            452 
  ESR1 MUTATED ESR1 WILD-TYPE 
             3             90 
$`ESR1 MUTATED`
TCGA-A6-5665 TCGA-A6-6781 TCGA-AA-3492 TCGA-AA-3525 TCGA-AA-3858 TCGA-AA-3947 
       22.06        19.66         3.02         8.05        31.07        33.01 
TCGA-AA-3949 TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01Q 
       26.01        25.02        27.02         4.01        34.98         1.02 
TCGA-AZ-6601 TCGA-CM-4743 TCGA-CM-5861 TCGA-F4-6569 TCGA-G4-6315 TCGA-G4-6588 
      100.01        23.05        15.02        35.74        61.91        26.17 
TCGA-EI-6507 
       19.96 

$`ESR1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.12        20.28         7.04         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       24.03        37.05        36.03        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3860 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3950 
       18.05        31.00         2.01        12.99        24.00        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       49.41         6.77        12.10        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 
       21.14        82.95         1.91       124.27        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       32.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6570 TCGA-F4-6703 
      117.07        98.24         8.61        31.96         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6317 
       53.62        44.68        55.04        85.48        63.62        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       22.09        13.78        35.80        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
       32.61         0.49        20.55        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  ESR1 MUTATED ESR1 WILD-TYPE 
          1.02           0.00 
  ESR1 MUTATED ESR1 WILD-TYPE 
        100.01         148.01 
  ESR1 MUTATED ESR1 WILD-TYPE 
        25.020         20.035 
[1] "1.0 - 100.0 (25.0)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.3"
D1694V2, continuous
D1694V3, binary
                cls
clus               0   1
  ESR1 MUTATED    19   1
  ESR1 WILD-TYPE 347 118
[1] "tbl2"
                cls
clus             [,1] [,2]
  ESR1 MUTATED     19    1
  ESR1 WILD-TYPE  347  118
        clus
vv       ESR1 MUTATED ESR1 WILD-TYPE
  COLON            19            347
  RECTUM            1            118
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ESR1 MUTATED         2        0        4         5         3         0
  ESR1 WILD-TYPE      89        1       28       133         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ESR1 MUTATED           0          0          3          1        1         0
  ESR1 WILD-TYPE        24         11         56         41       47        18
                vv
clus             STAGE IVB
  ESR1 MUTATED           0
  ESR1 WILD-TYPE         1
D1694V4, multiclass
            clus
vv           ESR1 MUTATED ESR1 WILD-TYPE
  STAGE I               2             89
  STAGE IA              0              1
  STAGE II              4             28
  STAGE IIA             5            133
  STAGE IIB             3              7
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            3             56
  STAGE IIIC            1             41
  STAGE IV              1             47
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  ESR1 MUTATED     0   3  12   5
  ESR1 WILD-TYPE  17  89 317  45
D1694V5, multiclass
    clus
vv   ESR1 MUTATED ESR1 WILD-TYPE
  T1            0             17
  T2            3             89
  T3           12            317
  T4            5             45
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  ESR1 MUTATED    15   5   0
  ESR1 WILD-TYPE 272 108  87
D1694V6, multiclass
    clus
vv   ESR1 MUTATED ESR1 WILD-TYPE
  N0           15            272
  N1            5            108
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1694V7, binary
                cls
clus               0   1
  ESR1 MUTATED    17   1
  ESR1 WILD-TYPE 358  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  ESR1 MUTATED     17    1
  ESR1 WILD-TYPE  358   64
   clus
vv  ESR1 MUTATED ESR1 WILD-TYPE
  0           17            358
  1            1             64
[1] 2 2
[1] FALSE
D1694V8, binary
                cls
clus               0   1
  ESR1 MUTATED     9  11
  ESR1 WILD-TYPE 216 253
[1] "tbl2"
                cls
clus             [,1] [,2]
  ESR1 MUTATED      9   11
  ESR1 WILD-TYPE  216  253
        clus
vv       ESR1 MUTATED ESR1 WILD-TYPE
  FEMALE            9            216
  MALE             11            253
[1] 2 2
[1] FALSE
D1694V9, binary
                cls
clus               0   1
  ESR1 MUTATED    17   0
  ESR1 WILD-TYPE 333  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  ESR1 MUTATED     17    0
  ESR1 WILD-TYPE  333   22
     clus
vv    ESR1 MUTATED ESR1 WILD-TYPE
  NO            17            333
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ESR1 MUTATED                     15                             4
  ESR1 WILD-TYPE                  300                            43
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ESR1 MUTATED                       1                              0
  ESR1 WILD-TYPE                   105                             10
D1694V10, multiclass
                                clus
vv                               ESR1 MUTATED ESR1 WILD-TYPE
  COLON ADENOCARCINOMA                     15            300
  COLON MUCINOUS ADENOCARCINOMA             4             43
  RECTAL ADENOCARCINOMA                     1            105
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  ESR1 MUTATED    17   0   0   0
  ESR1 WILD-TYPE 328   4  31  25
D1694V11, multiclass
    clus
vv   ESR1 MUTATED ESR1 WILD-TYPE
  R0           17            328
  R1            0              4
  R2            0             31
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1694V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ESR1 MUTATED                                  0     0
  ESR1 WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  ESR1 MUTATED                           0     9
  ESR1 WILD-TYPE                        22   217
D1694V13, multiclass
                                  clus
vv                                 ESR1 MUTATED ESR1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       9            217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1695) Variable = SLC25A40 MUTATION ANALYSIS
D1695V1, survival
                    sevent
clus2                  0   1
  SLC25A40 MUTATED     4   1
  SLC25A40 WILD-TYPE 374  92
  SLC25A40 MUTATED SLC25A40 WILD-TYPE 
                 5                466 
  SLC25A40 MUTATED SLC25A40 WILD-TYPE 
                 1                 92 
$`SLC25A40 MUTATED`
TCGA-AA-A00N TCGA-AA-A010 TCGA-AD-6889 TCGA-CA-6717 TCGA-AG-A002 
        4.01        34.98        56.55        12.76        20.98 

$`SLC25A40 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  SLC25A40 MUTATED SLC25A40 WILD-TYPE 
              4.01               0.00 
  SLC25A40 MUTATED SLC25A40 WILD-TYPE 
             56.55             148.01 
  SLC25A40 MUTATED SLC25A40 WILD-TYPE 
            20.980             20.155 
[1] "4.0 - 56.5 (21.0)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1"  
D1695V2, continuous
D1695V3, binary
                    cls
clus                   0   1
  SLC25A40 MUTATED     4   1
  SLC25A40 WILD-TYPE 362 118
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SLC25A40 MUTATED      4    1
  SLC25A40 WILD-TYPE  362  118
        clus
vv       SLC25A40 MUTATED SLC25A40 WILD-TYPE
  COLON                 4                362
  RECTUM                1                118
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SLC25A40 MUTATED         1        0        0         2         2         0
  SLC25A40 WILD-TYPE      90        1       32       136         8         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC25A40 MUTATED           0          0          0          0        0
  SLC25A40 WILD-TYPE        24         11         59         42       48
                    vv
clus                 STAGE IVA STAGE IVB
  SLC25A40 MUTATED           0         0
  SLC25A40 WILD-TYPE        18         1
D1695V4, multiclass
            clus
vv           SLC25A40 MUTATED SLC25A40 WILD-TYPE
  STAGE I                   1                 90
  STAGE IA                  0                  1
  STAGE II                  0                 32
  STAGE IIA                 2                136
  STAGE IIB                 2                  8
  STAGE IIC                 0                  1
  STAGE III                 0                 24
  STAGE IIIA                0                 11
  STAGE IIIB                0                 59
  STAGE IIIC                0                 42
  STAGE IV                  0                 48
  STAGE IVA                 0                 18
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  SLC25A40 MUTATED     0   1   2   2
  SLC25A40 WILD-TYPE  17  91 327  48
D1695V5, multiclass
    clus
vv   SLC25A40 MUTATED SLC25A40 WILD-TYPE
  T1                0                 17
  T2                1                 91
  T3                2                327
  T4                2                 48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  SLC25A40 MUTATED     5   0   0
  SLC25A40 WILD-TYPE 282 113  87
D1695V6, multiclass
    clus
vv   SLC25A40 MUTATED SLC25A40 WILD-TYPE
  N0                5                282
  N1                0                113
  N2                0                 87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1695V7, binary
                    cls
clus                   0   1
  SLC25A40 MUTATED     5   0
  SLC25A40 WILD-TYPE 370  65
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SLC25A40 MUTATED      5    0
  SLC25A40 WILD-TYPE  370   65
   clus
vv  SLC25A40 MUTATED SLC25A40 WILD-TYPE
  0                5                370
  1                0                 65
[1] 2 2
[1] FALSE
D1695V8, binary
                    cls
clus                   0   1
  SLC25A40 MUTATED     1   4
  SLC25A40 WILD-TYPE 224 260
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SLC25A40 MUTATED      1    4
  SLC25A40 WILD-TYPE  224  260
        clus
vv       SLC25A40 MUTATED SLC25A40 WILD-TYPE
  FEMALE                1                224
  MALE                  4                260
[1] 2 2
[1] FALSE
D1695V9, binary
                    cls
clus                   0   1
  SLC25A40 MUTATED     3   0
  SLC25A40 WILD-TYPE 347  22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SLC25A40 MUTATED      3    0
  SLC25A40 WILD-TYPE  347   22
     clus
vv    SLC25A40 MUTATED SLC25A40 WILD-TYPE
  NO                 3                347
  YES                0                 22
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SLC25A40 MUTATED                      2                             2
  SLC25A40 WILD-TYPE                  313                            45
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SLC25A40 MUTATED                       1                              0
  SLC25A40 WILD-TYPE                   105                             10
D1695V10, multiclass
                                clus
vv                               SLC25A40 MUTATED SLC25A40 WILD-TYPE
  COLON ADENOCARCINOMA                          2                313
  COLON MUCINOUS ADENOCARCINOMA                 2                 45
  RECTAL ADENOCARCINOMA                         1                105
  RECTAL MUCINOUS ADENOCARCINOMA                0                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  SLC25A40 MUTATED     3   0   0   1
  SLC25A40 WILD-TYPE 342   4  31  24
D1695V11, multiclass
    clus
vv   SLC25A40 MUTATED SLC25A40 WILD-TYPE
  R0                3                342
  R1                0                  4
  R2                0                 31
  RX                1                 24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1695V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SLC25A40 MUTATED                                  0     2
  SLC25A40 WILD-TYPE                                1     9
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  SLC25A40 MUTATED                           0     0
  SLC25A40 WILD-TYPE                        22   226
D1695V13, multiclass
[1] "Remove cluster labels:" "SLC25A40 MUTATED"      
clus
  SLC25A40 MUTATED SLC25A40 WILD-TYPE 
                 2                258 
        TCGA-A6-2671         TCGA-A6-2672         TCGA-A6-2674 
"SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" 
        TCGA-A6-2676         TCGA-A6-2677         TCGA-A6-2678 
"SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" 
        TCGA-A6-2683         TCGA-A6-3807         TCGA-A6-3808 
"SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" 
        TCGA-A6-3809         TCGA-A6-3810         TCGA-A6-4105 
"SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" 
        TCGA-A6-5656         TCGA-A6-5657         TCGA-A6-5659 
"SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" 
        TCGA-A6-5660         TCGA-A6-5661         TCGA-A6-5662 
"SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" 
        TCGA-A6-5664         TCGA-A6-5665         TCGA-A6-5666 
"SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" 
        TCGA-A6-6137         TCGA-A6-6138         TCGA-A6-6141 
"SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" 
        TCGA-A6-6142         TCGA-A6-6648         TCGA-A6-6649 
"SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" 
        TCGA-A6-6651         TCGA-A6-6652         TCGA-A6-6653 
"SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" 
        TCGA-A6-6654         TCGA-A6-6780         TCGA-A6-6781 
"SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" 
        TCGA-A6-6782         TCGA-AD-5900         TCGA-AD-6548 
"SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" 
        TCGA-AD-6888         TCGA-AD-6890         TCGA-AD-6895 
"SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" 
        TCGA-AD-6899         TCGA-AD-6901         TCGA-AD-6963 
"SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" 
        TCGA-AD-6964         TCGA-AD-6965         TCGA-AU-3779 
"SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" 
        TCGA-AU-6004         TCGA-AY-4070         TCGA-AY-4071 
"SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" 
        TCGA-AY-5543         TCGA-AY-6196         TCGA-AY-6197 
"SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" 
        TCGA-AY-6386         TCGA-AZ-4315         TCGA-AZ-4323 
"SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" 
        TCGA-AZ-4616         TCGA-AZ-4681         TCGA-AZ-4682 
"SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" 
        TCGA-AZ-5403         TCGA-AZ-5407         TCGA-AZ-6598 
"SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" 
        TCGA-AZ-6599         TCGA-AZ-6600         TCGA-AZ-6601 
"SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" 
        TCGA-AZ-6603         TCGA-AZ-6605         TCGA-AZ-6606 
"SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" 
        TCGA-AZ-6607         TCGA-AZ-6608         TCGA-CA-5254 
"SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" 
        TCGA-CA-5255         TCGA-CA-5796         TCGA-CA-5797 
"SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" 
        TCGA-CA-6715         TCGA-CA-6716         TCGA-CA-6718 
"SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" 
        TCGA-CA-6719         TCGA-CK-4947         TCGA-CK-4948 
"SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" 
        TCGA-CK-4950         TCGA-CK-4952         TCGA-CK-5912 
"SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" 
        TCGA-CK-5913         TCGA-CK-5914         TCGA-CK-5915 
"SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" 
        TCGA-CK-5916         TCGA-CK-6746         TCGA-CK-6747 
"SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" 
        TCGA-CK-6748         TCGA-CK-6751         TCGA-CM-4743 
"SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" 
        TCGA-CM-4744         TCGA-CM-4746         TCGA-CM-4747 
"SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" 
        TCGA-CM-4752         TCGA-CM-5341         TCGA-CM-5344 
"SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" 
        TCGA-CM-5348         TCGA-CM-5349         TCGA-CM-5860 
"SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" 
        TCGA-CM-5861         TCGA-CM-5862         TCGA-CM-5863 
"SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" 
        TCGA-CM-5864         TCGA-CM-5868         TCGA-CM-6161 
"SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" 
        TCGA-CM-6162         TCGA-CM-6163         TCGA-CM-6164 
"SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" 
        TCGA-CM-6165         TCGA-CM-6166         TCGA-CM-6167 
"SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" 
        TCGA-CM-6168         TCGA-CM-6169         TCGA-CM-6170 
"SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" 
        TCGA-CM-6171         TCGA-CM-6172         TCGA-CM-6674 
"SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" 
        TCGA-CM-6675         TCGA-CM-6676         TCGA-CM-6677 
"SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" 
        TCGA-CM-6678         TCGA-CM-6679         TCGA-CM-6680 
"SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" 
        TCGA-D5-5537         TCGA-D5-5538         TCGA-D5-5539 
"SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" 
        TCGA-D5-5540         TCGA-D5-5541         TCGA-D5-6529 
"SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" 
        TCGA-D5-6532         TCGA-D5-6533         TCGA-D5-6534 
"SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" 
        TCGA-D5-6535         TCGA-D5-6536         TCGA-D5-6537 
"SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" 
        TCGA-D5-6538         TCGA-D5-6539         TCGA-D5-6540 
"SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" 
        TCGA-D5-6541         TCGA-D5-6898         TCGA-D5-6920 
"SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" 
        TCGA-D5-6922         TCGA-D5-6923         TCGA-D5-6924 
"SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" 
        TCGA-D5-6926         TCGA-D5-6927         TCGA-D5-6928 
"SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" 
        TCGA-D5-6929         TCGA-D5-6930         TCGA-D5-6931 
"SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" 
        TCGA-D5-6932         TCGA-D5-7000         TCGA-DM-A0X9 
"SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" 
        TCGA-DM-A0XD         TCGA-DM-A0XF         TCGA-DM-A1D0 
"SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" 
        TCGA-DM-A1D4         TCGA-DM-A1D6         TCGA-DM-A1D7 
"SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" 
        TCGA-DM-A1D8         TCGA-DM-A1D9         TCGA-DM-A1DA 
"SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" 
        TCGA-DM-A1DB         TCGA-DM-A1HA         TCGA-DM-A1HB 
"SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" 
        TCGA-DM-A282         TCGA-DM-A285         TCGA-DM-A28C 
"SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" 
        TCGA-DM-A28E         TCGA-DM-A28F         TCGA-DM-A28G 
"SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" 
        TCGA-DM-A28H         TCGA-DM-A28K         TCGA-F4-6459 
"SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" 
        TCGA-F4-6460         TCGA-F4-6569         TCGA-F4-6570 
"SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" 
        TCGA-F4-6703         TCGA-F4-6704         TCGA-F4-6805 
"SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" 
        TCGA-F4-6806         TCGA-F4-6807         TCGA-F4-6808 
"SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" 
        TCGA-F4-6809         TCGA-F4-6854         TCGA-F4-6855 
"SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" 
        TCGA-F4-6856         TCGA-G4-6293         TCGA-G4-6299 
"SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" 
        TCGA-G4-6303         TCGA-G4-6304         TCGA-G4-6306 
"SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" 
        TCGA-G4-6307         TCGA-G4-6309         TCGA-G4-6310 
"SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" 
        TCGA-G4-6315         TCGA-G4-6317         TCGA-G4-6321 
"SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" 
        TCGA-G4-6323         TCGA-G4-6586         TCGA-G4-6588 
"SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" 
        TCGA-G4-6625         TCGA-G4-6626         TCGA-G4-6628 
"SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2691 
"SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" 
        TCGA-AF-2692         TCGA-AF-2693         TCGA-AF-3400 
"SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" 
        TCGA-AF-3913         TCGA-AF-4110         TCGA-AF-5654 
"SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" 
        TCGA-AF-6136         TCGA-AF-6655         TCGA-AF-6672 
"SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6549 
"SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" 
        TCGA-AH-6643         TCGA-AH-6644         TCGA-CI-6619 
"SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" 
        TCGA-CI-6620         TCGA-CI-6621         TCGA-CI-6622 
"SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" 
        TCGA-CI-6624         TCGA-CL-5917         TCGA-CL-5918 
"SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" 
        TCGA-DC-5337         TCGA-DC-5869         TCGA-DC-6155 
"SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" 
        TCGA-DC-6157         TCGA-DC-6158         TCGA-DC-6160 
"SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" 
        TCGA-DC-6681         TCGA-DC-6682         TCGA-DC-6683 
"SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" 
        TCGA-DT-5265         TCGA-DY-A0XA         TCGA-DY-A1DC 
"SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" 
        TCGA-DY-A1DD         TCGA-DY-A1DF         TCGA-DY-A1DG 
"SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" 
        TCGA-DY-A1H8         TCGA-EF-5830         TCGA-EI-6506 
"SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6510 
"SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" 
        TCGA-F5-6464         TCGA-F5-6465         TCGA-F5-6571 
"SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6811         TCGA-F5-6812 
"SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" 
        TCGA-F5-6813         TCGA-G5-6235         TCGA-G5-6641 
"SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" "SLC25A40 WILD-TYPE" 

Clustering(1696) Variable = DHX32 MUTATION ANALYSIS
D1696V1, survival
                 sevent
clus2               0   1
  DHX32 MUTATED    10   2
  DHX32 WILD-TYPE 368  91
  DHX32 MUTATED DHX32 WILD-TYPE 
             12             459 
  DHX32 MUTATED DHX32 WILD-TYPE 
              2              91 
$`DHX32 MUTATED`
TCGA-AA-3710 TCGA-AA-3977 TCGA-AD-5900 TCGA-AY-5543 TCGA-AZ-4315 TCGA-CM-6169 
       26.99        25.02         0.07        33.01        58.39        13.02 
TCGA-CM-6677 TCGA-D5-6931 TCGA-DM-A1D6 TCGA-F4-6809 TCGA-AG-A002 TCGA-EI-6507 
       11.08        12.00        49.91        13.25        20.98        19.96 

$`DHX32 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
       19.00        36.00         5.03        85.05        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       39.98        18.05        40.96        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6197 
        0.20        14.50        27.09        16.31         0.95        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6170 
       29.03        16.04        21.99        14.99        12.99        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6678 
       14.04        11.01        12.95        13.05        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6932 TCGA-D5-7000 
        9.44        11.64         4.80         1.51        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D7 
      119.70        24.43        38.20       130.65        92.75        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6510 
       51.48        32.61         0.49        20.55        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  DHX32 MUTATED DHX32 WILD-TYPE 
           0.07            0.00 
  DHX32 MUTATED DHX32 WILD-TYPE 
          58.39          148.01 
  DHX32 MUTATED DHX32 WILD-TYPE 
          20.47           20.19 
[1] "0.1 - 58.4 (20.5)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.1"
D1696V2, continuous
D1696V3, binary
                 cls
clus                0   1
  DHX32 MUTATED    10   2
  DHX32 WILD-TYPE 356 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DHX32 MUTATED     10    2
  DHX32 WILD-TYPE  356  117
        clus
vv       DHX32 MUTATED DHX32 WILD-TYPE
  COLON             10             356
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DHX32 MUTATED         2        0        0         6         0         0
  DHX32 WILD-TYPE      89        1       32       132        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DHX32 MUTATED           0          0          0          1        0         2
  DHX32 WILD-TYPE        24         11         59         41       48        16
                 vv
clus              STAGE IVB
  DHX32 MUTATED           0
  DHX32 WILD-TYPE         1
D1696V4, multiclass
            clus
vv           DHX32 MUTATED DHX32 WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              6             132
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             1              41
  STAGE IV               0              48
  STAGE IVA              2              16
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  DHX32 MUTATED     0   3   8   1
  DHX32 WILD-TYPE  17  89 321  49
D1696V5, multiclass
    clus
vv   DHX32 MUTATED DHX32 WILD-TYPE
  T1             0              17
  T2             3              89
  T3             8             321
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  DHX32 MUTATED     9   2   1
  DHX32 WILD-TYPE 278 111  86
D1696V6, multiclass
    clus
vv   DHX32 MUTATED DHX32 WILD-TYPE
  N0             9             278
  N1             2             111
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1696V7, binary
                 cls
clus                0   1
  DHX32 MUTATED     8   2
  DHX32 WILD-TYPE 367  63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DHX32 MUTATED      8    2
  DHX32 WILD-TYPE  367   63
   clus
vv  DHX32 MUTATED DHX32 WILD-TYPE
  0             8             367
  1             2              63
[1] 2 2
[1] FALSE
D1696V8, binary
                 cls
clus                0   1
  DHX32 MUTATED     4   8
  DHX32 WILD-TYPE 221 256
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DHX32 MUTATED      4    8
  DHX32 WILD-TYPE  221  256
        clus
vv       DHX32 MUTATED DHX32 WILD-TYPE
  FEMALE             4             221
  MALE               8             256
[1] 2 2
[1] FALSE
D1696V9, binary
                 cls
clus                0   1
  DHX32 MUTATED    10   0
  DHX32 WILD-TYPE 340  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DHX32 MUTATED     10    0
  DHX32 WILD-TYPE  340   22
     clus
vv    DHX32 MUTATED DHX32 WILD-TYPE
  NO             10             340
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  DHX32 MUTATED                      8                             2
  DHX32 WILD-TYPE                  307                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  DHX32 MUTATED                       2                              0
  DHX32 WILD-TYPE                   104                             10
D1696V10, multiclass
                                clus
vv                               DHX32 MUTATED DHX32 WILD-TYPE
  COLON ADENOCARCINOMA                       8             307
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  DHX32 MUTATED    10   0   0   0
  DHX32 WILD-TYPE 335   4  31  25
D1696V11, multiclass
    clus
vv   DHX32 MUTATED DHX32 WILD-TYPE
  R0            10             335
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1696V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DHX32 MUTATED                                  0     0
  DHX32 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  DHX32 MUTATED                           2     7
  DHX32 WILD-TYPE                        20   219
D1696V13, multiclass
                                  clus
vv                                 DHX32 MUTATED DHX32 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    2              20
  WHITE                                        7             219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1697) Variable = BFSP1 MUTATION ANALYSIS
D1697V1, survival
                 sevent
clus2               0   1
  BFSP1 MUTATED     5   3
  BFSP1 WILD-TYPE 373  90
  BFSP1 MUTATED BFSP1 WILD-TYPE 
              8             463 
  BFSP1 MUTATED BFSP1 WILD-TYPE 
              3              90 
$`BFSP1 MUTATED`
TCGA-A6-5659 TCGA-A6-6141 TCGA-A6-6654 TCGA-AZ-4616 TCGA-CA-5254 TCGA-DM-A285 
       30.44         8.38        23.87         5.13        12.69         6.12 
TCGA-F4-6570 TCGA-AG-A002 
        6.18        20.98 

$`BFSP1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 
       22.06        32.71        27.09        22.52        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 
       24.16        21.76        24.69        24.39        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82        58.39         1.41       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5255 
       29.56         5.23        11.74         3.19         1.61         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A28C 
        7.50        44.32       131.51       135.65       139.17        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       31.96        35.74        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  BFSP1 MUTATED BFSP1 WILD-TYPE 
           5.13            0.00 
  BFSP1 MUTATED BFSP1 WILD-TYPE 
          30.44          148.01 
  BFSP1 MUTATED BFSP1 WILD-TYPE 
         10.535          20.280 
[1] "5.1 - 30.4 (10.5)"  "0.0 - 148.0 (20.3)"
[1] "hr=" "3.6"
D1697V2, continuous
D1697V3, binary
                 cls
clus                0   1
  BFSP1 MUTATED     8   1
  BFSP1 WILD-TYPE 358 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BFSP1 MUTATED      8    1
  BFSP1 WILD-TYPE  358  118
        clus
vv       BFSP1 MUTATED BFSP1 WILD-TYPE
  COLON              8             358
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  BFSP1 MUTATED         2        0        0         4         0         0
  BFSP1 WILD-TYPE      89        1       32       134        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  BFSP1 MUTATED           0          0          1          0        2         0
  BFSP1 WILD-TYPE        24         11         58         42       46        18
                 vv
clus              STAGE IVB
  BFSP1 MUTATED           0
  BFSP1 WILD-TYPE         1
D1697V4, multiclass
            clus
vv           BFSP1 MUTATED BFSP1 WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              4             134
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             0              42
  STAGE IV               2              46
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  BFSP1 MUTATED     0   2   7   0
  BFSP1 WILD-TYPE  17  90 322  50
D1697V5, multiclass
    clus
vv   BFSP1 MUTATED BFSP1 WILD-TYPE
  T1             0              17
  T2             2              90
  T3             7             322
  T4             0              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  BFSP1 MUTATED     6   1   2
  BFSP1 WILD-TYPE 281 112  85
D1697V6, multiclass
    clus
vv   BFSP1 MUTATED BFSP1 WILD-TYPE
  N0             6             281
  N1             1             112
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1697V7, binary
                 cls
clus                0   1
  BFSP1 MUTATED     7   2
  BFSP1 WILD-TYPE 368  63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BFSP1 MUTATED      7    2
  BFSP1 WILD-TYPE  368   63
   clus
vv  BFSP1 MUTATED BFSP1 WILD-TYPE
  0             7             368
  1             2              63
[1] 2 2
[1] FALSE
D1697V8, binary
                 cls
clus                0   1
  BFSP1 MUTATED     6   3
  BFSP1 WILD-TYPE 219 261
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BFSP1 MUTATED      6    3
  BFSP1 WILD-TYPE  219  261
        clus
vv       BFSP1 MUTATED BFSP1 WILD-TYPE
  FEMALE             6             219
  MALE               3             261
[1] 2 2
[1] FALSE
D1697V9, binary
                 cls
clus                0   1
  BFSP1 MUTATED     7   0
  BFSP1 WILD-TYPE 343  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BFSP1 MUTATED      7    0
  BFSP1 WILD-TYPE  343   22
     clus
vv    BFSP1 MUTATED BFSP1 WILD-TYPE
  NO              7             343
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  BFSP1 MUTATED                      7                             1
  BFSP1 WILD-TYPE                  308                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  BFSP1 MUTATED                       1                              0
  BFSP1 WILD-TYPE                   105                             10
D1697V10, multiclass
                                clus
vv                               BFSP1 MUTATED BFSP1 WILD-TYPE
  COLON ADENOCARCINOMA                       7             308
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  BFSP1 MUTATED     4   0   0   1
  BFSP1 WILD-TYPE 341   4  31  24
D1697V11, multiclass
    clus
vv   BFSP1 MUTATED BFSP1 WILD-TYPE
  R0             4             341
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1697V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  BFSP1 MUTATED                                  0     1
  BFSP1 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  BFSP1 MUTATED                           1     5
  BFSP1 WILD-TYPE                        21   221
D1697V13, multiclass
                                  clus
vv                                 BFSP1 MUTATED BFSP1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        5             221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1698) Variable = CLEC1A MUTATION ANALYSIS
D1698V1, survival
                  sevent
clus2                0   1
  CLEC1A MUTATED     9   1
  CLEC1A WILD-TYPE 369  92
  CLEC1A MUTATED CLEC1A WILD-TYPE 
              10              461 
  CLEC1A MUTATED CLEC1A WILD-TYPE 
               1               92 
$`CLEC1A MUTATED`
TCGA-AA-3662 TCGA-AA-3977 TCGA-AA-A010 TCGA-CA-6718 TCGA-CM-6168 TCGA-DM-A282 
        6.05        25.02        34.98        10.06        12.99       139.17 
TCGA-G4-6586 TCGA-G4-6628 TCGA-AG-4005 TCGA-AG-A002 
       35.80        79.69        14.04        20.98 

$`CLEC1A WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       12.76        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6169 
        2.96        29.03        16.04        21.99        14.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A285 TCGA-DM-A28C 
        7.50        44.32       131.51       135.65         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 
       13.78        26.17        91.79        46.75        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       19.99        28.04        36.03         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  CLEC1A MUTATED CLEC1A WILD-TYPE 
            6.05             0.00 
  CLEC1A MUTATED CLEC1A WILD-TYPE 
          139.17           148.01 
  CLEC1A MUTATED CLEC1A WILD-TYPE 
           23.00            20.12 
[1] "6.0 - 139.2 (23.0)" "0.0 - 148.0 (20.1)"
[1] "hr=" "2.5"
D1698V2, continuous
D1698V3, binary
                  cls
clus                 0   1
  CLEC1A MUTATED     8   2
  CLEC1A WILD-TYPE 358 117
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CLEC1A MUTATED      8    2
  CLEC1A WILD-TYPE  358  117
        clus
vv       CLEC1A MUTATED CLEC1A WILD-TYPE
  COLON               8              358
  RECTUM              2              117
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CLEC1A MUTATED         2        0        0         4         1         0
  CLEC1A WILD-TYPE      89        1       32       134         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CLEC1A MUTATED           0          0          0          0        2
  CLEC1A WILD-TYPE        24         11         59         42       46
                  vv
clus               STAGE IVA STAGE IVB
  CLEC1A MUTATED           0         0
  CLEC1A WILD-TYPE        18         1
D1698V4, multiclass
            clus
vv           CLEC1A MUTATED CLEC1A WILD-TYPE
  STAGE I                 2               89
  STAGE IA                0                1
  STAGE II                0               32
  STAGE IIA               4              134
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              0               59
  STAGE IIIC              0               42
  STAGE IV                2               46
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  CLEC1A MUTATED     0   3   5   2
  CLEC1A WILD-TYPE  17  89 324  48
D1698V5, multiclass
    clus
vv   CLEC1A MUTATED CLEC1A WILD-TYPE
  T1              0               17
  T2              3               89
  T3              5              324
  T4              2               48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  CLEC1A MUTATED     8   0   2
  CLEC1A WILD-TYPE 279 113  85
D1698V6, multiclass
    clus
vv   CLEC1A MUTATED CLEC1A WILD-TYPE
  N0              8              279
  N1              0              113
  N2              2               85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1698V7, binary
                  cls
clus                 0   1
  CLEC1A MUTATED     7   2
  CLEC1A WILD-TYPE 368  63
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CLEC1A MUTATED      7    2
  CLEC1A WILD-TYPE  368   63
   clus
vv  CLEC1A MUTATED CLEC1A WILD-TYPE
  0              7              368
  1              2               63
[1] 2 2
[1] FALSE
D1698V8, binary
                  cls
clus                 0   1
  CLEC1A MUTATED     5   5
  CLEC1A WILD-TYPE 220 259
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CLEC1A MUTATED      5    5
  CLEC1A WILD-TYPE  220  259
        clus
vv       CLEC1A MUTATED CLEC1A WILD-TYPE
  FEMALE              5              220
  MALE                5              259
[1] 2 2
[1] FALSE
D1698V9, binary
                  cls
clus                 0   1
  CLEC1A MUTATED     9   0
  CLEC1A WILD-TYPE 341  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CLEC1A MUTATED      9    0
  CLEC1A WILD-TYPE  341   22
     clus
vv    CLEC1A MUTATED CLEC1A WILD-TYPE
  NO               9              341
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CLEC1A MUTATED                      8                             0
  CLEC1A WILD-TYPE                  307                            47
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CLEC1A MUTATED                       2                              0
  CLEC1A WILD-TYPE                   104                             10
D1698V10, multiclass
                                clus
vv                               CLEC1A MUTATED CLEC1A WILD-TYPE
  COLON ADENOCARCINOMA                        8              307
  COLON MUCINOUS ADENOCARCINOMA               0               47
  RECTAL ADENOCARCINOMA                       2              104
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  CLEC1A MUTATED     6   0   1   1
  CLEC1A WILD-TYPE 339   4  30  24
D1698V11, multiclass
    clus
vv   CLEC1A MUTATED CLEC1A WILD-TYPE
  R0              6              339
  R1              0                4
  R2              1               30
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1698V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CLEC1A MUTATED                                  0     1
  CLEC1A WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  CLEC1A MUTATED                           1     3
  CLEC1A WILD-TYPE                        21   223
D1698V13, multiclass
                                  clus
vv                                 CLEC1A MUTATED CLEC1A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                         3              223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1699) Variable = BIRC6 MUTATION ANALYSIS
D1699V1, survival
                 sevent
clus2               0   1
  BIRC6 MUTATED    30   8
  BIRC6 WILD-TYPE 348  85
  BIRC6 MUTATED BIRC6 WILD-TYPE 
             38             433 
  BIRC6 MUTATED BIRC6 WILD-TYPE 
              8              85 
$`BIRC6 MUTATED`
TCGA-A6-3809 TCGA-A6-5666 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3492 TCGA-AA-3510 
       32.75        32.71        19.66        20.28         3.02        63.98 
TCGA-AA-3672 TCGA-AA-3811 TCGA-AA-3864 TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-3977 
        0.92        10.06        53.00        33.01        24.00        25.02 
TCGA-AA-A00N TCGA-AA-A010 TCGA-AU-6004 TCGA-AZ-4315 TCGA-AZ-6599 TCGA-CA-6717 
        4.01        34.98        27.09        58.39         6.77        12.76 
TCGA-CA-6718 TCGA-CK-5916 TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-6162 TCGA-CM-6168 
       10.06        21.14        23.05        37.02        12.00        12.99 
TCGA-CM-6674 TCGA-D5-6927 TCGA-DM-A1D0 TCGA-DM-A1HA TCGA-F4-6460 TCGA-F4-6570 
       12.95         9.44       130.65       131.51        31.96         6.18 
TCGA-F4-6808 TCGA-F4-6856 TCGA-G4-6304 TCGA-G4-6586 TCGA-G4-6588 TCGA-AG-3892 
       33.67        35.31        53.62        35.80        26.17        13.02 
TCGA-AG-A002 TCGA-G5-6235 
       20.98        55.76 

$`BIRC6 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       22.06        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        7.04         1.02        35.01         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
        6.05         6.97        54.02         2.01        14.01        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 
        0.99        31.07        31.07        30.05        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        26.01         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       10.88         0.20        14.50        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        88.21        49.41        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 
        3.25         3.29         0.07        12.20        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4752 
       82.95         1.91       124.27        20.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 
        5.03        15.02        15.02        17.03        15.02         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6169 TCGA-CM-6170 
       29.03        16.04        21.99        14.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       14.04        11.01        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
      119.70        24.43        38.20        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A282 
       12.59       140.38         7.50        44.32       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       98.24         8.61        35.74        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 
       41.42        16.24        13.25         0.53        47.41       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       74.56        65.85        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6625 TCGA-G4-6626 
       61.91        36.00        22.09        13.78        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       17.95        36.95        17.03        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6641 
       26.43 

  BIRC6 MUTATED BIRC6 WILD-TYPE 
           0.92            0.00 
  BIRC6 MUTATED BIRC6 WILD-TYPE 
         131.51          148.01 
  BIRC6 MUTATED BIRC6 WILD-TYPE 
          24.51           19.99 
[1] "0.9 - 131.5 (24.5)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1"  
D1699V2, continuous
D1699V3, binary
                 cls
clus                0   1
  BIRC6 MUTATED    36   3
  BIRC6 WILD-TYPE 330 116
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BIRC6 MUTATED     36    3
  BIRC6 WILD-TYPE  330  116
        clus
vv       BIRC6 MUTATED BIRC6 WILD-TYPE
  COLON             36             330
  RECTUM             3             116
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  BIRC6 MUTATED         8        0        3        13         6         1
  BIRC6 WILD-TYPE      83        1       29       125         4         0
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  BIRC6 MUTATED           2          0          3          2        0         0
  BIRC6 WILD-TYPE        22         11         56         40       48        18
                 vv
clus              STAGE IVB
  BIRC6 MUTATED           0
  BIRC6 WILD-TYPE         1
D1699V4, multiclass
            clus
vv           BIRC6 MUTATED BIRC6 WILD-TYPE
  STAGE I                8              83
  STAGE IA               0               1
  STAGE II               3              29
  STAGE IIA             13             125
  STAGE IIB              6               4
  STAGE IIC              1               0
  STAGE III              2              22
  STAGE IIIA             0              11
  STAGE IIIB             3              56
  STAGE IIIC             2              40
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  BIRC6 MUTATED     3   6  22   8
  BIRC6 WILD-TYPE  14  86 307  42
D1699V5, multiclass
    clus
vv   BIRC6 MUTATED BIRC6 WILD-TYPE
  T1             3              14
  T2             6              86
  T3            22             307
  T4             8              42
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  BIRC6 MUTATED    32   5   2
  BIRC6 WILD-TYPE 255 108  85
D1699V6, multiclass
    clus
vv   BIRC6 MUTATED BIRC6 WILD-TYPE
  N0            32             255
  N1             5             108
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1699V7, binary
                 cls
clus                0   1
  BIRC6 MUTATED    34   0
  BIRC6 WILD-TYPE 341  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BIRC6 MUTATED     34    0
  BIRC6 WILD-TYPE  341   65
   clus
vv  BIRC6 MUTATED BIRC6 WILD-TYPE
  0            34             341
  1             0              65
[1] 2 2
[1] FALSE
D1699V8, binary
                 cls
clus                0   1
  BIRC6 MUTATED    20  19
  BIRC6 WILD-TYPE 205 245
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BIRC6 MUTATED     20   19
  BIRC6 WILD-TYPE  205  245
        clus
vv       BIRC6 MUTATED BIRC6 WILD-TYPE
  FEMALE            20             205
  MALE              19             245
[1] 2 2
[1] FALSE
D1699V9, binary
                 cls
clus                0   1
  BIRC6 MUTATED    34   0
  BIRC6 WILD-TYPE 316  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BIRC6 MUTATED     34    0
  BIRC6 WILD-TYPE  316   22
     clus
vv    BIRC6 MUTATED BIRC6 WILD-TYPE
  NO             34             316
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  BIRC6 MUTATED                     28                             8
  BIRC6 WILD-TYPE                  287                            39
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  BIRC6 MUTATED                       3                              0
  BIRC6 WILD-TYPE                   103                             10
D1699V10, multiclass
                                clus
vv                               BIRC6 MUTATED BIRC6 WILD-TYPE
  COLON ADENOCARCINOMA                      28             287
  COLON MUCINOUS ADENOCARCINOMA              8              39
  RECTAL ADENOCARCINOMA                      3             103
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  BIRC6 MUTATED    29   1   0   3
  BIRC6 WILD-TYPE 316   3  31  22
D1699V11, multiclass
    clus
vv   BIRC6 MUTATED BIRC6 WILD-TYPE
  R0            29             316
  R1             1               3
  R2             0              31
  RX             3              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1699V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  BIRC6 MUTATED                                  0     2
  BIRC6 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  BIRC6 MUTATED                           2    22
  BIRC6 WILD-TYPE                        20   204
D1699V13, multiclass
                                  clus
vv                                 BIRC6 MUTATED BIRC6 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               9
  BLACK OR AFRICAN AMERICAN                    2              20
  WHITE                                       22             204
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1700) Variable = MTIF2 MUTATION ANALYSIS
D1700V1, survival
                 sevent
clus2               0   1
  MTIF2 MUTATED    11   0
  MTIF2 WILD-TYPE 367  93
  MTIF2 MUTATED MTIF2 WILD-TYPE 
             11             460 
  MTIF2 MUTATED MTIF2 WILD-TYPE 
              0              93 
$`MTIF2 MUTATED`
TCGA-AA-3966 TCGA-AA-A010 TCGA-AA-A01R TCGA-CA-6717 TCGA-CA-6719 TCGA-CM-5861 
        2.01        34.98        35.01        12.76        14.30        15.02 
TCGA-D5-5538 TCGA-D5-6927 TCGA-G4-6628 TCGA-AG-3892 TCGA-DC-6682 
       12.26         9.44        79.69        13.02         4.01 

$`MTIF2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 
       24.00         2.01        20.98        34.03        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T 
       31.00        31.00        38.07         1.02         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       10.06        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 
       22.03        22.98        30.08        32.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5539 TCGA-D5-5540 
       11.01        10.06        12.03        45.40        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       26.17        91.79        46.75        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 
       19.99         1.02        17.95        36.95        17.03        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  MTIF2 MUTATED MTIF2 WILD-TYPE 
           2.01            0.00 
  MTIF2 MUTATED MTIF2 WILD-TYPE 
          79.69          148.01 
  MTIF2 MUTATED MTIF2 WILD-TYPE 
          13.02           20.73 
[1] "2.0 - 79.7 (13.0)"  "0.0 - 148.0 (20.7)"
[1] "hr="     "9200000"
D1700V2, continuous
D1700V3, binary
                 cls
clus                0   1
  MTIF2 MUTATED     9   2
  MTIF2 WILD-TYPE 357 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MTIF2 MUTATED      9    2
  MTIF2 WILD-TYPE  357  117
        clus
vv       MTIF2 MUTATED MTIF2 WILD-TYPE
  COLON              9             357
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MTIF2 MUTATED         2        0        0         6         1         0
  MTIF2 WILD-TYPE      89        1       32       132         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MTIF2 MUTATED           1          0          1          0        0         0
  MTIF2 WILD-TYPE        23         11         58         42       48        18
                 vv
clus              STAGE IVB
  MTIF2 MUTATED           0
  MTIF2 WILD-TYPE         1
D1700V4, multiclass
            clus
vv           MTIF2 MUTATED MTIF2 WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              6             132
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  MTIF2 MUTATED     1   1   8   1
  MTIF2 WILD-TYPE  16  91 321  49
D1700V5, multiclass
    clus
vv   MTIF2 MUTATED MTIF2 WILD-TYPE
  T1             1              16
  T2             1              91
  T3             8             321
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  MTIF2 MUTATED     9   1   1
  MTIF2 WILD-TYPE 278 112  86
D1700V6, multiclass
    clus
vv   MTIF2 MUTATED MTIF2 WILD-TYPE
  N0             9             278
  N1             1             112
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1700V7, binary
                 cls
clus                0   1
  MTIF2 MUTATED    11   0
  MTIF2 WILD-TYPE 364  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MTIF2 MUTATED     11    0
  MTIF2 WILD-TYPE  364   65
   clus
vv  MTIF2 MUTATED MTIF2 WILD-TYPE
  0            11             364
  1             0              65
[1] 2 2
[1] FALSE
D1700V8, binary
                 cls
clus                0   1
  MTIF2 MUTATED     5   6
  MTIF2 WILD-TYPE 220 258
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MTIF2 MUTATED      5    6
  MTIF2 WILD-TYPE  220  258
        clus
vv       MTIF2 MUTATED MTIF2 WILD-TYPE
  FEMALE             5             220
  MALE               6             258
[1] 2 2
[1] FALSE
D1700V9, binary
                 cls
clus                0   1
  MTIF2 MUTATED     8   1
  MTIF2 WILD-TYPE 342  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MTIF2 MUTATED      8    1
  MTIF2 WILD-TYPE  342   21
     clus
vv    MTIF2 MUTATED MTIF2 WILD-TYPE
  NO              8             342
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MTIF2 MUTATED                      6                             3
  MTIF2 WILD-TYPE                  309                            44
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MTIF2 MUTATED                       2                              0
  MTIF2 WILD-TYPE                   104                             10
D1700V10, multiclass
                                clus
vv                               MTIF2 MUTATED MTIF2 WILD-TYPE
  COLON ADENOCARCINOMA                       6             309
  COLON MUCINOUS ADENOCARCINOMA              3              44
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  MTIF2 MUTATED     8   0   0   2
  MTIF2 WILD-TYPE 337   4  31  23
D1700V11, multiclass
    clus
vv   MTIF2 MUTATED MTIF2 WILD-TYPE
  R0             8             337
  R1             0               4
  R2             0              31
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1700V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MTIF2 MUTATED                                  0     2
  MTIF2 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  MTIF2 MUTATED                           0     5
  MTIF2 WILD-TYPE                        22   221
D1700V13, multiclass
                                  clus
vv                                 MTIF2 MUTATED MTIF2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               9
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        5             221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1701) Variable = IGDCC3 MUTATION ANALYSIS
D1701V1, survival
                  sevent
clus2                0   1
  IGDCC3 MUTATED     8   4
  IGDCC3 WILD-TYPE 370  89
  IGDCC3 MUTATED IGDCC3 WILD-TYPE 
              12              459 
  IGDCC3 MUTATED IGDCC3 WILD-TYPE 
               4               89 
$`IGDCC3 MUTATED`
TCGA-A6-6781 TCGA-AA-3680 TCGA-AA-3715 TCGA-AA-3941 TCGA-AA-A00N TCGA-AA-A02F 
       19.66        11.01        19.04        24.00         4.01        39.98 
TCGA-AZ-6598 TCGA-CM-4743 TCGA-G4-6306 TCGA-AG-3885 TCGA-AG-3909 TCGA-AG-A002 
       49.41        23.05        44.68        17.95        19.99        20.98 

$`IGDCC3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       47.01        15.02         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       37.02        39.06        51.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 
       21.14        82.95         1.91       124.27        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       74.56        65.85        53.62        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
       19.99         1.02        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3999 TCGA-AG-4001 
       14.01         1.02        48.03        32.02        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  IGDCC3 MUTATED IGDCC3 WILD-TYPE 
            4.01             0.00 
  IGDCC3 MUTATED IGDCC3 WILD-TYPE 
           49.41           148.01 
  IGDCC3 MUTATED IGDCC3 WILD-TYPE 
          20.485           20.190 
[1] "4.0 - 49.4 (20.5)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.8"
D1701V2, continuous
D1701V3, binary
                  cls
clus                 0   1
  IGDCC3 MUTATED     9   3
  IGDCC3 WILD-TYPE 357 116
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IGDCC3 MUTATED      9    3
  IGDCC3 WILD-TYPE  357  116
        clus
vv       IGDCC3 MUTATED IGDCC3 WILD-TYPE
  COLON               9              357
  RECTUM              3              116
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  IGDCC3 MUTATED         1        0        2         2         1         0
  IGDCC3 WILD-TYPE      90        1       30       136         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  IGDCC3 MUTATED           0          0          2          1        2
  IGDCC3 WILD-TYPE        24         11         57         41       46
                  vv
clus               STAGE IVA STAGE IVB
  IGDCC3 MUTATED           1         0
  IGDCC3 WILD-TYPE        17         1
D1701V4, multiclass
            clus
vv           IGDCC3 MUTATED IGDCC3 WILD-TYPE
  STAGE I                 1               90
  STAGE IA                0                1
  STAGE II                2               30
  STAGE IIA               2              136
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              2               57
  STAGE IIIC              1               41
  STAGE IV                2               46
  STAGE IVA               1               17
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  IGDCC3 MUTATED     0   2   6   4
  IGDCC3 WILD-TYPE  17  90 323  46
D1701V5, multiclass
    clus
vv   IGDCC3 MUTATED IGDCC3 WILD-TYPE
  T1              0               17
  T2              2               90
  T3              6              323
  T4              4               46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  IGDCC3 MUTATED     6   5   1
  IGDCC3 WILD-TYPE 281 108  86
D1701V6, multiclass
    clus
vv   IGDCC3 MUTATED IGDCC3 WILD-TYPE
  N0              6              281
  N1              5              108
  N2              1               86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1701V7, binary
                  cls
clus                 0   1
  IGDCC3 MUTATED     7   3
  IGDCC3 WILD-TYPE 368  62
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IGDCC3 MUTATED      7    3
  IGDCC3 WILD-TYPE  368   62
   clus
vv  IGDCC3 MUTATED IGDCC3 WILD-TYPE
  0              7              368
  1              3               62
[1] 2 2
[1] FALSE
D1701V8, binary
                  cls
clus                 0   1
  IGDCC3 MUTATED     6   6
  IGDCC3 WILD-TYPE 219 258
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IGDCC3 MUTATED      6    6
  IGDCC3 WILD-TYPE  219  258
        clus
vv       IGDCC3 MUTATED IGDCC3 WILD-TYPE
  FEMALE              6              219
  MALE                6              258
[1] 2 2
[1] FALSE
D1701V9, binary
                  cls
clus                 0   1
  IGDCC3 MUTATED    10   1
  IGDCC3 WILD-TYPE 340  21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IGDCC3 MUTATED     10    1
  IGDCC3 WILD-TYPE  340   21
     clus
vv    IGDCC3 MUTATED IGDCC3 WILD-TYPE
  NO              10              340
  YES              1               21
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  IGDCC3 MUTATED                      7                             2
  IGDCC3 WILD-TYPE                  308                            45
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  IGDCC3 MUTATED                       3                              0
  IGDCC3 WILD-TYPE                   103                             10
D1701V10, multiclass
                                clus
vv                               IGDCC3 MUTATED IGDCC3 WILD-TYPE
  COLON ADENOCARCINOMA                        7              308
  COLON MUCINOUS ADENOCARCINOMA               2               45
  RECTAL ADENOCARCINOMA                       3              103
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  IGDCC3 MUTATED     9   0   2   0
  IGDCC3 WILD-TYPE 336   4  29  25
D1701V11, multiclass
    clus
vv   IGDCC3 MUTATED IGDCC3 WILD-TYPE
  R0              9              336
  R1              0                4
  R2              2               29
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1701V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  IGDCC3 MUTATED                                  0     0
  IGDCC3 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  IGDCC3 MUTATED                           0     4
  IGDCC3 WILD-TYPE                        22   222
D1701V13, multiclass
                                  clus
vv                                 IGDCC3 MUTATED IGDCC3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         4              222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1702) Variable = ZNF124 MUTATION ANALYSIS
D1702V1, survival
                  sevent
clus2                0   1
  ZNF124 MUTATED     7   1
  ZNF124 WILD-TYPE 371  92
  ZNF124 MUTATED ZNF124 WILD-TYPE 
               8              463 
  ZNF124 MUTATED ZNF124 WILD-TYPE 
               1               92 
$`ZNF124 MUTATED`
TCGA-A6-3809 TCGA-A6-5665 TCGA-AA-A00N TCGA-AD-6889 TCGA-AU-6004 TCGA-AZ-4315 
       32.75        22.06         4.01        56.55        27.09        58.39 
TCGA-CA-6717 TCGA-CM-4743 
       12.76        23.05 

$`ZNF124 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 
       18.05        40.96         0.07        21.37        15.52         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       14.50        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07        12.20        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 
       21.14        82.95         1.91       124.27        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  ZNF124 MUTATED ZNF124 WILD-TYPE 
            4.01             0.00 
  ZNF124 MUTATED ZNF124 WILD-TYPE 
           58.39           148.01 
  ZNF124 MUTATED ZNF124 WILD-TYPE 
           25.07            20.05 
[1] "4.0 - 58.4 (25.1)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.8"
D1702V2, continuous
D1702V3, binary
                  cls
clus                 0   1
  ZNF124 MUTATED     8   0
  ZNF124 WILD-TYPE 358 119
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF124 MUTATED      8    0
  ZNF124 WILD-TYPE  358  119
        clus
vv       ZNF124 MUTATED ZNF124 WILD-TYPE
  COLON               8              358
  RECTUM              0              119
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZNF124 MUTATED         1        0        0         5         2         0
  ZNF124 WILD-TYPE      90        1       32       133         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF124 MUTATED           0          0          0          0        0
  ZNF124 WILD-TYPE        24         11         59         42       48
                  vv
clus               STAGE IVA STAGE IVB
  ZNF124 MUTATED           0         0
  ZNF124 WILD-TYPE        18         1
D1702V4, multiclass
            clus
vv           ZNF124 MUTATED ZNF124 WILD-TYPE
  STAGE I                 1               90
  STAGE IA                0                1
  STAGE II                0               32
  STAGE IIA               5              133
  STAGE IIB               2                8
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              0               59
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZNF124 MUTATED     0   1   5   2
  ZNF124 WILD-TYPE  17  91 324  48
D1702V5, multiclass
    clus
vv   ZNF124 MUTATED ZNF124 WILD-TYPE
  T1              0               17
  T2              1               91
  T3              5              324
  T4              2               48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  ZNF124 MUTATED     8   0   0
  ZNF124 WILD-TYPE 279 113  87
D1702V6, multiclass
    clus
vv   ZNF124 MUTATED ZNF124 WILD-TYPE
  N0              8              279
  N1              0              113
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1702V7, binary
                  cls
clus                 0   1
  ZNF124 MUTATED     8   0
  ZNF124 WILD-TYPE 367  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF124 MUTATED      8    0
  ZNF124 WILD-TYPE  367   65
   clus
vv  ZNF124 MUTATED ZNF124 WILD-TYPE
  0              8              367
  1              0               65
[1] 2 2
[1] FALSE
D1702V8, binary
                  cls
clus                 0   1
  ZNF124 MUTATED     3   5
  ZNF124 WILD-TYPE 222 259
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF124 MUTATED      3    5
  ZNF124 WILD-TYPE  222  259
        clus
vv       ZNF124 MUTATED ZNF124 WILD-TYPE
  FEMALE              3              222
  MALE                5              259
[1] 2 2
[1] FALSE
D1702V9, binary
                  cls
clus                 0   1
  ZNF124 MUTATED     5   0
  ZNF124 WILD-TYPE 345  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF124 MUTATED      5    0
  ZNF124 WILD-TYPE  345   22
     clus
vv    ZNF124 MUTATED ZNF124 WILD-TYPE
  NO               5              345
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ZNF124 MUTATED                      5                             3
  ZNF124 WILD-TYPE                  310                            44
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ZNF124 MUTATED                       0                              0
  ZNF124 WILD-TYPE                   106                             10
D1702V10, multiclass
                                clus
vv                               ZNF124 MUTATED ZNF124 WILD-TYPE
  COLON ADENOCARCINOMA                        5              310
  COLON MUCINOUS ADENOCARCINOMA               3               44
  RECTAL ADENOCARCINOMA                       0              106
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ZNF124 MUTATED     6   0   0   1
  ZNF124 WILD-TYPE 339   4  31  24
D1702V11, multiclass
    clus
vv   ZNF124 MUTATED ZNF124 WILD-TYPE
  R0              6              339
  R1              0                4
  R2              0               31
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1702V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF124 MUTATED                                  0     2
  ZNF124 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZNF124 MUTATED                           0     5
  ZNF124 WILD-TYPE                        22   221
D1702V13, multiclass
                                  clus
vv                                 ZNF124 MUTATED ZNF124 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                9
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         5              221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1703) Variable = SLC38A5 MUTATION ANALYSIS
D1703V1, survival
                   sevent
clus2                 0   1
  SLC38A5 MUTATED     5   1
  SLC38A5 WILD-TYPE 373  92
  SLC38A5 MUTATED SLC38A5 WILD-TYPE 
                6               465 
  SLC38A5 MUTATED SLC38A5 WILD-TYPE 
                1                92 
$`SLC38A5 MUTATED`
TCGA-A6-2678 TCGA-A6-5665 TCGA-AZ-6605 TCGA-CK-4952 TCGA-CK-5913 TCGA-CM-5861 
       42.28        22.06         5.23        15.62        51.32        15.02 

$`SLC38A5 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2683 
       43.76        46.65        43.76        42.90        24.33        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
       12.10       100.01        29.56        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       49.08         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 
       22.03        22.98        30.08        32.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  SLC38A5 MUTATED SLC38A5 WILD-TYPE 
             5.23              0.00 
  SLC38A5 MUTATED SLC38A5 WILD-TYPE 
            51.32            148.01 
  SLC38A5 MUTATED SLC38A5 WILD-TYPE 
            18.84             20.19 
[1] "5.2 - 51.3 (18.8)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.2"
D1703V2, continuous
D1703V3, binary
                   cls
clus                  0   1
  SLC38A5 MUTATED     6   0
  SLC38A5 WILD-TYPE 360 119
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC38A5 MUTATED      6    0
  SLC38A5 WILD-TYPE  360  119
        clus
vv       SLC38A5 MUTATED SLC38A5 WILD-TYPE
  COLON                6               360
  RECTUM               0               119
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SLC38A5 MUTATED         0        0        0         3         0         0
  SLC38A5 WILD-TYPE      91        1       32       135        10         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC38A5 MUTATED           0          0          2          1        0
  SLC38A5 WILD-TYPE        24         11         57         41       48
                   vv
clus                STAGE IVA STAGE IVB
  SLC38A5 MUTATED           0         0
  SLC38A5 WILD-TYPE        18         1
D1703V4, multiclass
            clus
vv           SLC38A5 MUTATED SLC38A5 WILD-TYPE
  STAGE I                  0                91
  STAGE IA                 0                 1
  STAGE II                 0                32
  STAGE IIA                3               135
  STAGE IIB                0                10
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               0                11
  STAGE IIIB               2                57
  STAGE IIIC               1                41
  STAGE IV                 0                48
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  SLC38A5 MUTATED     0   0   4   2
  SLC38A5 WILD-TYPE  17  92 325  48
D1703V5, multiclass
    clus
vv   SLC38A5 MUTATED SLC38A5 WILD-TYPE
  T1               0                17
  T2               0                92
  T3               4               325
  T4               2                48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  SLC38A5 MUTATED     3   2   1
  SLC38A5 WILD-TYPE 284 111  86
D1703V6, multiclass
    clus
vv   SLC38A5 MUTATED SLC38A5 WILD-TYPE
  N0               3               284
  N1               2               111
  N2               1                86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1703V7, binary
                   cls
clus                  0   1
  SLC38A5 MUTATED     5   0
  SLC38A5 WILD-TYPE 370  65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC38A5 MUTATED      5    0
  SLC38A5 WILD-TYPE  370   65
   clus
vv  SLC38A5 MUTATED SLC38A5 WILD-TYPE
  0               5               370
  1               0                65
[1] 2 2
[1] FALSE
D1703V8, binary
                   cls
clus                  0   1
  SLC38A5 MUTATED     5   1
  SLC38A5 WILD-TYPE 220 263
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC38A5 MUTATED      5    1
  SLC38A5 WILD-TYPE  220  263
        clus
vv       SLC38A5 MUTATED SLC38A5 WILD-TYPE
  FEMALE               5               220
  MALE                 1               263
[1] 2 2
[1] FALSE
D1703V9, binary
                   cls
clus                  0   1
  SLC38A5 MUTATED     5   0
  SLC38A5 WILD-TYPE 345  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC38A5 MUTATED      5    0
  SLC38A5 WILD-TYPE  345   22
     clus
vv    SLC38A5 MUTATED SLC38A5 WILD-TYPE
  NO                5               345
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SLC38A5 MUTATED                      5                             1
  SLC38A5 WILD-TYPE                  310                            46
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SLC38A5 MUTATED                       0                              0
  SLC38A5 WILD-TYPE                   106                             10
D1703V10, multiclass
                                clus
vv                               SLC38A5 MUTATED SLC38A5 WILD-TYPE
  COLON ADENOCARCINOMA                         5               310
  COLON MUCINOUS ADENOCARCINOMA                1                46
  RECTAL ADENOCARCINOMA                        0               106
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  SLC38A5 MUTATED     3   0   0   2
  SLC38A5 WILD-TYPE 342   4  31  23
D1703V11, multiclass
    clus
vv   SLC38A5 MUTATED SLC38A5 WILD-TYPE
  R0               3               342
  R1               0                 4
  R2               0                31
  RX               2                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1703V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SLC38A5 MUTATED                                  0     0
  SLC38A5 WILD-TYPE                                1    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  SLC38A5 MUTATED                           0     6
  SLC38A5 WILD-TYPE                        22   220
D1703V13, multiclass
                                  clus
vv                                 SLC38A5 MUTATED SLC38A5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                      0                22
  WHITE                                          6               220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1704) Variable = C15ORF33 MUTATION ANALYSIS
D1704V1, survival
                    sevent
clus2                  0   1
  C15ORF33 MUTATED     9   3
  C15ORF33 WILD-TYPE 369  90
  C15ORF33 MUTATED C15ORF33 WILD-TYPE 
                12                459 
  C15ORF33 MUTATED C15ORF33 WILD-TYPE 
                 3                 90 
$`C15ORF33 MUTATED`
TCGA-A6-6141 TCGA-AA-3492 TCGA-AA-3977 TCGA-AA-A00N TCGA-AZ-4315 TCGA-AZ-6603 
        8.38         3.02        25.02         4.01        58.39        29.56 
TCGA-CA-6717 TCGA-CM-6168 TCGA-AF-6136 TCGA-AG-3587 TCGA-AG-3892 TCGA-AG-A002 
       12.76        12.99        15.39        46.03        13.02        20.98 

$`C15ORF33 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 
       22.09        22.06        32.71        27.09        22.52        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 
       20.12        19.66        20.28         7.04         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6605 
       88.21        49.41         6.77        12.10       100.01         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07        12.20        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       21.99        14.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       16.83        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 
        1.02        17.95        36.95        17.03        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  C15ORF33 MUTATED C15ORF33 WILD-TYPE 
              3.02               0.00 
  C15ORF33 MUTATED C15ORF33 WILD-TYPE 
             58.39             148.01 
  C15ORF33 MUTATED C15ORF33 WILD-TYPE 
            14.205             20.280 
[1] "3.0 - 58.4 (14.2)"  "0.0 - 148.0 (20.3)"
[1] "hr=" "1.5"
D1704V2, continuous
D1704V3, binary
                    cls
clus                   0   1
  C15ORF33 MUTATED     8   4
  C15ORF33 WILD-TYPE 358 115
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C15ORF33 MUTATED      8    4
  C15ORF33 WILD-TYPE  358  115
        clus
vv       C15ORF33 MUTATED C15ORF33 WILD-TYPE
  COLON                 8                358
  RECTUM                4                115
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  C15ORF33 MUTATED         3        0        1         4         1         0
  C15ORF33 WILD-TYPE      88        1       31       134         9         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C15ORF33 MUTATED           0          0          1          0        0
  C15ORF33 WILD-TYPE        24         11         58         42       48
                    vv
clus                 STAGE IVA STAGE IVB
  C15ORF33 MUTATED           0         0
  C15ORF33 WILD-TYPE        18         1
D1704V4, multiclass
            clus
vv           C15ORF33 MUTATED C15ORF33 WILD-TYPE
  STAGE I                   3                 88
  STAGE IA                  0                  1
  STAGE II                  1                 31
  STAGE IIA                 4                134
  STAGE IIB                 1                  9
  STAGE IIC                 0                  1
  STAGE III                 0                 24
  STAGE IIIA                0                 11
  STAGE IIIB                1                 58
  STAGE IIIC                0                 42
  STAGE IV                  0                 48
  STAGE IVA                 0                 18
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  C15ORF33 MUTATED     1   4   6   1
  C15ORF33 WILD-TYPE  16  88 323  49
D1704V5, multiclass
    clus
vv   C15ORF33 MUTATED C15ORF33 WILD-TYPE
  T1                1                 16
  T2                4                 88
  T3                6                323
  T4                1                 49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  C15ORF33 MUTATED    10   2   0
  C15ORF33 WILD-TYPE 277 111  87
D1704V6, multiclass
    clus
vv   C15ORF33 MUTATED C15ORF33 WILD-TYPE
  N0               10                277
  N1                2                111
  N2                0                 87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1704V7, binary
                    cls
clus                   0   1
  C15ORF33 MUTATED     9   0
  C15ORF33 WILD-TYPE 366  65
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C15ORF33 MUTATED      9    0
  C15ORF33 WILD-TYPE  366   65
   clus
vv  C15ORF33 MUTATED C15ORF33 WILD-TYPE
  0                9                366
  1                0                 65
[1] 2 2
[1] FALSE
D1704V8, binary
                    cls
clus                   0   1
  C15ORF33 MUTATED     5   7
  C15ORF33 WILD-TYPE 220 257
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C15ORF33 MUTATED      5    7
  C15ORF33 WILD-TYPE  220  257
        clus
vv       C15ORF33 MUTATED C15ORF33 WILD-TYPE
  FEMALE                5                220
  MALE                  7                257
[1] 2 2
[1] FALSE
D1704V9, binary
                    cls
clus                   0   1
  C15ORF33 MUTATED     9   2
  C15ORF33 WILD-TYPE 341  20
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C15ORF33 MUTATED      9    2
  C15ORF33 WILD-TYPE  341   20
     clus
vv    C15ORF33 MUTATED C15ORF33 WILD-TYPE
  NO                 9                341
  YES                2                 20
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  C15ORF33 MUTATED                      6                             2
  C15ORF33 WILD-TYPE                  309                            45
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  C15ORF33 MUTATED                       4                              0
  C15ORF33 WILD-TYPE                   102                             10
D1704V10, multiclass
                                clus
vv                               C15ORF33 MUTATED C15ORF33 WILD-TYPE
  COLON ADENOCARCINOMA                          6                309
  COLON MUCINOUS ADENOCARCINOMA                 2                 45
  RECTAL ADENOCARCINOMA                         4                102
  RECTAL MUCINOUS ADENOCARCINOMA                0                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  C15ORF33 MUTATED     7   0   0   1
  C15ORF33 WILD-TYPE 338   4  31  24
D1704V11, multiclass
    clus
vv   C15ORF33 MUTATED C15ORF33 WILD-TYPE
  R0                7                338
  R1                0                  4
  R2                0                 31
  RX                1                 24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1704V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C15ORF33 MUTATED                                  0     1
  C15ORF33 WILD-TYPE                                1    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  C15ORF33 MUTATED                           2     3
  C15ORF33 WILD-TYPE                        20   223
D1704V13, multiclass
                                  clus
vv                                 C15ORF33 MUTATED C15ORF33 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                 10
  BLACK OR AFRICAN AMERICAN                       2                 20
  WHITE                                           3                223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1705) Variable = WEE2 MUTATION ANALYSIS
D1705V1, survival
                sevent
clus2              0   1
  WEE2 MUTATED     7   1
  WEE2 WILD-TYPE 371  92
  WEE2 MUTATED WEE2 WILD-TYPE 
             8            463 
  WEE2 MUTATED WEE2 WILD-TYPE 
             1             92 
$`WEE2 MUTATED`
TCGA-AA-3713 TCGA-AA-A010 TCGA-CA-6717 TCGA-D5-6539 TCGA-DM-A1HB TCGA-G4-6586 
       19.04        34.98        12.76        12.49       135.65        35.80 
TCGA-AG-3892 TCGA-DY-A1DC 
       13.02        41.36 

$`WEE2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.20        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       17.13        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 
      140.38         7.50        44.32       131.51       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       22.09        13.78        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       36.95        17.03        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
      126.44        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  WEE2 MUTATED WEE2 WILD-TYPE 
         12.49           0.00 
  WEE2 MUTATED WEE2 WILD-TYPE 
        135.65         148.01 
  WEE2 MUTATED WEE2 WILD-TYPE 
         27.01          20.19 
[1] "12.5 - 135.7 (27.0)" "0.0 - 148.0 (20.2)" 
[1] "hr=" "2"  
D1705V2, continuous
D1705V3, binary
                cls
clus               0   1
  WEE2 MUTATED     7   3
  WEE2 WILD-TYPE 359 116
[1] "tbl2"
                cls
clus             [,1] [,2]
  WEE2 MUTATED      7    3
  WEE2 WILD-TYPE  359  116
        clus
vv       WEE2 MUTATED WEE2 WILD-TYPE
  COLON             7            359
  RECTUM            3            116
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  WEE2 MUTATED         2        0        0         3         1         0
  WEE2 WILD-TYPE      89        1       32       135         9         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  WEE2 MUTATED           1          1          1          0        1         0
  WEE2 WILD-TYPE        23         10         58         42       47        18
                vv
clus             STAGE IVB
  WEE2 MUTATED           0
  WEE2 WILD-TYPE         1
D1705V4, multiclass
            clus
vv           WEE2 MUTATED WEE2 WILD-TYPE
  STAGE I               2             89
  STAGE IA              0              1
  STAGE II              0             32
  STAGE IIA             3            135
  STAGE IIB             1              9
  STAGE IIC             0              1
  STAGE III             1             23
  STAGE IIIA            1             10
  STAGE IIIB            1             58
  STAGE IIIC            0             42
  STAGE IV              1             47
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  WEE2 MUTATED     1   1   7   1
  WEE2 WILD-TYPE  16  91 322  49
D1705V5, multiclass
    clus
vv   WEE2 MUTATED WEE2 WILD-TYPE
  T1            1             16
  T2            1             91
  T3            7            322
  T4            1             49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  WEE2 MUTATED     8   2   0
  WEE2 WILD-TYPE 279 111  87
D1705V6, multiclass
    clus
vv   WEE2 MUTATED WEE2 WILD-TYPE
  N0            8            279
  N1            2            111
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1705V7, binary
                cls
clus               0   1
  WEE2 MUTATED     7   1
  WEE2 WILD-TYPE 368  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  WEE2 MUTATED      7    1
  WEE2 WILD-TYPE  368   64
   clus
vv  WEE2 MUTATED WEE2 WILD-TYPE
  0            7            368
  1            1             64
[1] 2 2
[1] FALSE
D1705V8, binary
                cls
clus               0   1
  WEE2 MUTATED     5   5
  WEE2 WILD-TYPE 220 259
[1] "tbl2"
                cls
clus             [,1] [,2]
  WEE2 MUTATED      5    5
  WEE2 WILD-TYPE  220  259
        clus
vv       WEE2 MUTATED WEE2 WILD-TYPE
  FEMALE            5            220
  MALE              5            259
[1] 2 2
[1] FALSE
D1705V9, binary
                cls
clus               0   1
  WEE2 MUTATED     5   1
  WEE2 WILD-TYPE 345  21
[1] "tbl2"
                cls
clus             [,1] [,2]
  WEE2 MUTATED      5    1
  WEE2 WILD-TYPE  345   21
     clus
vv    WEE2 MUTATED WEE2 WILD-TYPE
  NO             5            345
  YES            1             21
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  WEE2 MUTATED                      5                             1
  WEE2 WILD-TYPE                  310                            46
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  WEE2 MUTATED                       3                              0
  WEE2 WILD-TYPE                   103                             10
D1705V10, multiclass
                                clus
vv                               WEE2 MUTATED WEE2 WILD-TYPE
  COLON ADENOCARCINOMA                      5            310
  COLON MUCINOUS ADENOCARCINOMA             1             46
  RECTAL ADENOCARCINOMA                     3            103
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  WEE2 MUTATED     4   0   1   2
  WEE2 WILD-TYPE 341   4  30  23
D1705V11, multiclass
    clus
vv   WEE2 MUTATED WEE2 WILD-TYPE
  R0            4            341
  R1            0              4
  R2            1             30
  RX            2             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1705V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  WEE2 MUTATED                                  0     1
  WEE2 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  WEE2 MUTATED                           0     6
  WEE2 WILD-TYPE                        22   220
D1705V13, multiclass
                                  clus
vv                                 WEE2 MUTATED WEE2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       6            220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1706) Variable = MAOB MUTATION ANALYSIS
D1706V1, survival
                sevent
clus2              0   1
  MAOB MUTATED     8   1
  MAOB WILD-TYPE 370  92
  MAOB MUTATED MAOB WILD-TYPE 
             9            462 
  MAOB MUTATED MAOB WILD-TYPE 
             1             92 
$`MAOB MUTATED`
TCGA-AA-3950 TCGA-AY-6197 TCGA-CM-4743 TCGA-CM-5861 TCGA-CM-6677 TCGA-CM-6678 
       24.00        21.44        23.05        15.02        11.08        11.01 
TCGA-AF-6136 TCGA-AG-4001 TCGA-DY-A1DD 
       15.39        36.03        57.24 

$`MAOB WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        33.01        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
       82.95         1.91       124.27        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.08        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       10.39        14.50        16.83        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       32.02        19.99        28.04        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       41.36        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  MAOB MUTATED MAOB WILD-TYPE 
         11.01           0.00 
  MAOB MUTATED MAOB WILD-TYPE 
         57.24         148.01 
  MAOB MUTATED MAOB WILD-TYPE 
        21.440         20.155 
[1] "11.0 - 57.2 (21.4)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.7"
D1706V2, continuous
D1706V3, binary
                cls
clus               0   1
  MAOB MUTATED     6   3
  MAOB WILD-TYPE 360 116
[1] "tbl2"
                cls
clus             [,1] [,2]
  MAOB MUTATED      6    3
  MAOB WILD-TYPE  360  116
        clus
vv       MAOB MUTATED MAOB WILD-TYPE
  COLON             6            360
  RECTUM            3            116
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MAOB MUTATED         0        0        0         6         0         0
  MAOB WILD-TYPE      91        1       32       132        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MAOB MUTATED           0          0          2          0        0         1
  MAOB WILD-TYPE        24         11         57         42       48        17
                vv
clus             STAGE IVB
  MAOB MUTATED           0
  MAOB WILD-TYPE         1
D1706V4, multiclass
            clus
vv           MAOB MUTATED MAOB WILD-TYPE
  STAGE I               0             91
  STAGE IA              0              1
  STAGE II              0             32
  STAGE IIA             6            132
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            2             57
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             1             17
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  MAOB MUTATED     0   0   8   1
  MAOB WILD-TYPE  17  92 321  49
D1706V5, multiclass
    clus
vv   MAOB MUTATED MAOB WILD-TYPE
  T1            0             17
  T2            0             92
  T3            8            321
  T4            1             49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  MAOB MUTATED     6   3   0
  MAOB WILD-TYPE 281 110  87
D1706V6, multiclass
    clus
vv   MAOB MUTATED MAOB WILD-TYPE
  N0            6            281
  N1            3            110
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1706V7, binary
                cls
clus               0   1
  MAOB MUTATED     6   1
  MAOB WILD-TYPE 369  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  MAOB MUTATED      6    1
  MAOB WILD-TYPE  369   64
   clus
vv  MAOB MUTATED MAOB WILD-TYPE
  0            6            369
  1            1             64
[1] 2 2
[1] FALSE
D1706V8, binary
                cls
clus               0   1
  MAOB MUTATED     7   2
  MAOB WILD-TYPE 218 262
[1] "tbl2"
                cls
clus             [,1] [,2]
  MAOB MUTATED      7    2
  MAOB WILD-TYPE  218  262
        clus
vv       MAOB MUTATED MAOB WILD-TYPE
  FEMALE            7            218
  MALE              2            262
[1] 2 2
[1] FALSE
D1706V9, binary
                cls
clus               0   1
  MAOB MUTATED     7   1
  MAOB WILD-TYPE 343  21
[1] "tbl2"
                cls
clus             [,1] [,2]
  MAOB MUTATED      7    1
  MAOB WILD-TYPE  343   21
     clus
vv    MAOB MUTATED MAOB WILD-TYPE
  NO             7            343
  YES            1             21
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MAOB MUTATED                      5                             1
  MAOB WILD-TYPE                  310                            46
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MAOB MUTATED                       3                              0
  MAOB WILD-TYPE                   103                             10
D1706V10, multiclass
                                clus
vv                               MAOB MUTATED MAOB WILD-TYPE
  COLON ADENOCARCINOMA                      5            310
  COLON MUCINOUS ADENOCARCINOMA             1             46
  RECTAL ADENOCARCINOMA                     3            103
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  MAOB MUTATED     7   0   0   0
  MAOB WILD-TYPE 338   4  31  25
D1706V11, multiclass
    clus
vv   MAOB MUTATED MAOB WILD-TYPE
  R0            7            338
  R1            0              4
  R2            0             31
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1706V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MAOB MUTATED                                  0     0
  MAOB WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  MAOB MUTATED                           0     7
  MAOB WILD-TYPE                        22   219
D1706V13, multiclass
                                  clus
vv                                 MAOB MUTATED MAOB WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       7            219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1707) Variable = REL MUTATION ANALYSIS
D1707V1, survival
               sevent
clus2             0   1
  REL MUTATED     9   2
  REL WILD-TYPE 369  91
  REL MUTATED REL WILD-TYPE 
           11           460 
  REL MUTATED REL WILD-TYPE 
            2            91 
$`REL MUTATED`
TCGA-A6-6781 TCGA-AA-3864 TCGA-AA-3977 TCGA-AA-A00J TCGA-AZ-6601 TCGA-CM-5861 
       19.66        53.00        25.02        18.05       100.01        15.02 
TCGA-D5-5538 TCGA-D5-6898 TCGA-D5-6928 TCGA-F4-6809 TCGA-AF-2693 
       12.26         1.48        11.64        13.25        19.10 

$`REL WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 
       32.05         0.99        31.07        31.07        30.05        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 
       62.79        88.21        49.41         6.77        12.10        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 
       22.03        22.98        30.08        32.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5539 TCGA-D5-5540 
       11.01        10.06        12.03        45.40        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  REL MUTATED REL WILD-TYPE 
         1.48          0.00 
  REL MUTATED REL WILD-TYPE 
       100.01        148.01 
  REL MUTATED REL WILD-TYPE 
        18.05         20.73 
[1] "1.5 - 100.0 (18.1)" "0.0 - 148.0 (20.7)"
[1] "hr=" "1.2"
D1707V2, continuous
D1707V3, binary
               cls
clus              0   1
  REL MUTATED    10   0
  REL WILD-TYPE 356 119
[1] "tbl2"
               cls
clus            [,1] [,2]
  REL MUTATED     10    0
  REL WILD-TYPE  356  119
        clus
vv       REL MUTATED REL WILD-TYPE
  COLON           10           356
  RECTUM           0           119
[1] 2 2
[1] FALSE
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  REL MUTATED         2        0        2         2         0         0
  REL WILD-TYPE      89        1       30       136        10         1
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  REL MUTATED           0          0          2          1        0         1
  REL WILD-TYPE        24         11         57         41       48        17
               vv
clus            STAGE IVB
  REL MUTATED           0
  REL WILD-TYPE         1
D1707V4, multiclass
            clus
vv           REL MUTATED REL WILD-TYPE
  STAGE I              2            89
  STAGE IA             0             1
  STAGE II             2            30
  STAGE IIA            2           136
  STAGE IIB            0            10
  STAGE IIC            0             1
  STAGE III            0            24
  STAGE IIIA           0            11
  STAGE IIIB           2            57
  STAGE IIIC           1            41
  STAGE IV             0            48
  STAGE IVA            1            17
  STAGE IVB            0             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  REL MUTATED     0   3   6   2
  REL WILD-TYPE  17  89 323  48
D1707V5, multiclass
    clus
vv   REL MUTATED REL WILD-TYPE
  T1           0            17
  T2           3            89
  T3           6           323
  T4           2            48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2
  REL MUTATED     7   4   0
  REL WILD-TYPE 280 109  87
D1707V6, multiclass
    clus
vv   REL MUTATED REL WILD-TYPE
  N0           7           280
  N1           4           109
  N2           0            87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1707V7, binary
               cls
clus              0   1
  REL MUTATED     7   1
  REL WILD-TYPE 368  64
[1] "tbl2"
               cls
clus            [,1] [,2]
  REL MUTATED      7    1
  REL WILD-TYPE  368   64
   clus
vv  REL MUTATED REL WILD-TYPE
  0           7           368
  1           1            64
[1] 2 2
[1] FALSE
D1707V8, binary
               cls
clus              0   1
  REL MUTATED     4   7
  REL WILD-TYPE 221 257
[1] "tbl2"
               cls
clus            [,1] [,2]
  REL MUTATED      4    7
  REL WILD-TYPE  221  257
        clus
vv       REL MUTATED REL WILD-TYPE
  FEMALE           4           221
  MALE             7           257
[1] 2 2
[1] FALSE
D1707V9, binary
               cls
clus              0   1
  REL MUTATED    10   0
  REL WILD-TYPE 340  22
[1] "tbl2"
               cls
clus            [,1] [,2]
  REL MUTATED     10    0
  REL WILD-TYPE  340   22
     clus
vv    REL MUTATED REL WILD-TYPE
  NO           10           340
  YES           0            22
[1] 2 2
[1] FALSE
               vv
clus            COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  REL MUTATED                      7                             3
  REL WILD-TYPE                  308                            44
               vv
clus            RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  REL MUTATED                       0                              0
  REL WILD-TYPE                   106                             10
D1707V10, multiclass
                                clus
vv                               REL MUTATED REL WILD-TYPE
  COLON ADENOCARCINOMA                     7           308
  COLON MUCINOUS ADENOCARCINOMA            3            44
  RECTAL ADENOCARCINOMA                    0           106
  RECTAL MUCINOUS ADENOCARCINOMA           0            10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             R0  R1  R2  RX
  REL MUTATED     8   0   0   0
  REL WILD-TYPE 337   4  31  25
D1707V11, multiclass
    clus
vv   REL MUTATED REL WILD-TYPE
  R0           8           337
  R1           0             4
  R2           0            31
  RX           0            25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1707V12, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  REL MUTATED                                  0     0
  REL WILD-TYPE                                1    11
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  REL MUTATED                           0     8
  REL WILD-TYPE                        22   218
D1707V13, multiclass
                                  clus
vv                                 REL MUTATED REL WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      0            11
  BLACK OR AFRICAN AMERICAN                  0            22
  WHITE                                      8           218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1708) Variable = MMP27 MUTATION ANALYSIS
D1708V1, survival
                 sevent
clus2               0   1
  MMP27 MUTATED     5   3
  MMP27 WILD-TYPE 373  90
  MMP27 MUTATED MMP27 WILD-TYPE 
              8             463 
  MMP27 MUTATED MMP27 WILD-TYPE 
              3              90 
$`MMP27 MUTATED`
TCGA-A6-2676 TCGA-AA-3811 TCGA-AZ-5403 TCGA-CM-5860 TCGA-CM-5868 TCGA-D5-6930 
       42.90        10.06        62.79        32.02        17.03         1.51 
TCGA-AG-3732 TCGA-AG-A002 
       32.98        20.98 

$`MMP27 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
      106.75        22.36        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5861 
       13.02        29.06        22.03        22.98        30.08        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
        5.03        15.02        15.02        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6931 
       14.30         9.04         9.44        11.64         4.80        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 
       13.94        19.99         7.99         0.99        37.02         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  MMP27 MUTATED MMP27 WILD-TYPE 
           1.51            0.00 
  MMP27 MUTATED MMP27 WILD-TYPE 
          62.79          148.01 
  MMP27 MUTATED MMP27 WILD-TYPE 
          26.50           20.12 
[1] "1.5 - 62.8 (26.5)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.8"
D1708V2, continuous
D1708V3, binary
                 cls
clus                0   1
  MMP27 MUTATED     7   2
  MMP27 WILD-TYPE 359 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MMP27 MUTATED      7    2
  MMP27 WILD-TYPE  359  117
        clus
vv       MMP27 MUTATED MMP27 WILD-TYPE
  COLON              7             359
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MMP27 MUTATED         2        0        1         3         1         0
  MMP27 WILD-TYPE      89        1       31       135         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MMP27 MUTATED           1          0          0          0        0         1
  MMP27 WILD-TYPE        23         11         59         42       48        17
                 vv
clus              STAGE IVB
  MMP27 MUTATED           0
  MMP27 WILD-TYPE         1
D1708V4, multiclass
            clus
vv           MMP27 MUTATED MMP27 WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              3             135
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  MMP27 MUTATED     0   2   5   2
  MMP27 WILD-TYPE  17  90 324  48
D1708V5, multiclass
    clus
vv   MMP27 MUTATED MMP27 WILD-TYPE
  T1             0              17
  T2             2              90
  T3             5             324
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  MMP27 MUTATED     7   1   1
  MMP27 WILD-TYPE 280 112  86
D1708V6, multiclass
    clus
vv   MMP27 MUTATED MMP27 WILD-TYPE
  N0             7             280
  N1             1             112
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1708V7, binary
                 cls
clus                0   1
  MMP27 MUTATED     7   1
  MMP27 WILD-TYPE 368  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MMP27 MUTATED      7    1
  MMP27 WILD-TYPE  368   64
   clus
vv  MMP27 MUTATED MMP27 WILD-TYPE
  0             7             368
  1             1              64
[1] 2 2
[1] FALSE
D1708V8, binary
                 cls
clus                0   1
  MMP27 MUTATED     5   4
  MMP27 WILD-TYPE 220 260
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MMP27 MUTATED      5    4
  MMP27 WILD-TYPE  220  260
        clus
vv       MMP27 MUTATED MMP27 WILD-TYPE
  FEMALE             5             220
  MALE               4             260
[1] 2 2
[1] FALSE
D1708V9, binary
                 cls
clus                0   1
  MMP27 MUTATED     7   0
  MMP27 WILD-TYPE 343  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MMP27 MUTATED      7    0
  MMP27 WILD-TYPE  343   22
     clus
vv    MMP27 MUTATED MMP27 WILD-TYPE
  NO              7             343
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MMP27 MUTATED                      6                             1
  MMP27 WILD-TYPE                  309                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MMP27 MUTATED                       2                              0
  MMP27 WILD-TYPE                   104                             10
D1708V10, multiclass
                                clus
vv                               MMP27 MUTATED MMP27 WILD-TYPE
  COLON ADENOCARCINOMA                       6             309
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  MMP27 MUTATED     8   0   0   0
  MMP27 WILD-TYPE 337   4  31  25
D1708V11, multiclass
    clus
vv   MMP27 MUTATED MMP27 WILD-TYPE
  R0             8             337
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1708V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MMP27 MUTATED                                  0     0
  MMP27 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  MMP27 MUTATED                           0     5
  MMP27 WILD-TYPE                        22   221
D1708V13, multiclass
                                  clus
vv                                 MMP27 MUTATED MMP27 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        5             221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1709) Variable = ZNF7 MUTATION ANALYSIS
D1709V1, survival
                sevent
clus2              0   1
  ZNF7 MUTATED    10   3
  ZNF7 WILD-TYPE 368  90
  ZNF7 MUTATED ZNF7 WILD-TYPE 
            13            458 
  ZNF7 MUTATED ZNF7 WILD-TYPE 
             3             90 
$`ZNF7 MUTATED`
TCGA-A6-6141 TCGA-AA-3510 TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A010 TCGA-AZ-4315 
        8.38        63.98        25.02         4.01        34.98        58.39 
TCGA-AZ-6598 TCGA-CA-6717 TCGA-CM-5862 TCGA-F4-6569 TCGA-G4-6588 TCGA-AF-6655 
       49.41        12.76         5.03        35.74        26.17        20.02 
TCGA-AG-3892 
       13.02 

$`ZNF7 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 
       22.09        22.06        32.71        27.09        22.52        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07        12.20        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       32.02        15.02        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6570 TCGA-F4-6703 
      117.07        98.24         8.61        31.96         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        35.80        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6672 
       34.49        10.39        14.50        16.83        15.39        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       36.95        17.03        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  ZNF7 MUTATED ZNF7 WILD-TYPE 
          4.01           0.00 
  ZNF7 MUTATED ZNF7 WILD-TYPE 
         63.98         148.01 
  ZNF7 MUTATED ZNF7 WILD-TYPE 
        25.020         20.155 
[1] "4.0 - 64.0 (25.0)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.1"
D1709V2, continuous
D1709V3, binary
                cls
clus               0   1
  ZNF7 MUTATED    12   2
  ZNF7 WILD-TYPE 354 117
[1] "tbl2"
                cls
clus             [,1] [,2]
  ZNF7 MUTATED     12    2
  ZNF7 WILD-TYPE  354  117
        clus
vv       ZNF7 MUTATED ZNF7 WILD-TYPE
  COLON            12            354
  RECTUM            2            117
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZNF7 MUTATED         2        0        2         5         2         0
  ZNF7 WILD-TYPE      89        1       30       133         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ZNF7 MUTATED           0          1          0          0        0         1
  ZNF7 WILD-TYPE        24         10         59         42       48        17
                vv
clus             STAGE IVB
  ZNF7 MUTATED           0
  ZNF7 WILD-TYPE         1
D1709V4, multiclass
            clus
vv           ZNF7 MUTATED ZNF7 WILD-TYPE
  STAGE I               2             89
  STAGE IA              0              1
  STAGE II              2             30
  STAGE IIA             5            133
  STAGE IIB             2              8
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            1             10
  STAGE IIIB            0             59
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             1             17
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  ZNF7 MUTATED     1   3   8   2
  ZNF7 WILD-TYPE  16  89 321  48
D1709V5, multiclass
    clus
vv   ZNF7 MUTATED ZNF7 WILD-TYPE
  T1            1             16
  T2            3             89
  T3            8            321
  T4            2             48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  ZNF7 MUTATED    12   2   0
  ZNF7 WILD-TYPE 275 111  87
D1709V6, multiclass
    clus
vv   ZNF7 MUTATED ZNF7 WILD-TYPE
  N0           12            275
  N1            2            111
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1709V7, binary
                cls
clus               0   1
  ZNF7 MUTATED    11   1
  ZNF7 WILD-TYPE 364  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  ZNF7 MUTATED     11    1
  ZNF7 WILD-TYPE  364   64
   clus
vv  ZNF7 MUTATED ZNF7 WILD-TYPE
  0           11            364
  1            1             64
[1] 2 2
[1] FALSE
D1709V8, binary
                cls
clus               0   1
  ZNF7 MUTATED     5   9
  ZNF7 WILD-TYPE 220 255
[1] "tbl2"
                cls
clus             [,1] [,2]
  ZNF7 MUTATED      5    9
  ZNF7 WILD-TYPE  220  255
        clus
vv       ZNF7 MUTATED ZNF7 WILD-TYPE
  FEMALE            5            220
  MALE              9            255
[1] 2 2
[1] FALSE
D1709V9, binary
                cls
clus               0   1
  ZNF7 MUTATED    12   0
  ZNF7 WILD-TYPE 338  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  ZNF7 MUTATED     12    0
  ZNF7 WILD-TYPE  338   22
     clus
vv    ZNF7 MUTATED ZNF7 WILD-TYPE
  NO            12            338
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ZNF7 MUTATED                     10                             2
  ZNF7 WILD-TYPE                  305                            45
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ZNF7 MUTATED                       2                              0
  ZNF7 WILD-TYPE                   104                             10
D1709V10, multiclass
                                clus
vv                               ZNF7 MUTATED ZNF7 WILD-TYPE
  COLON ADENOCARCINOMA                     10            305
  COLON MUCINOUS ADENOCARCINOMA             2             45
  RECTAL ADENOCARCINOMA                     2            104
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  ZNF7 MUTATED    10   0   0   1
  ZNF7 WILD-TYPE 335   4  31  24
D1709V11, multiclass
    clus
vv   ZNF7 MUTATED ZNF7 WILD-TYPE
  R0           10            335
  R1            0              4
  R2            0             31
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1709V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF7 MUTATED                                  0     1
  ZNF7 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  ZNF7 MUTATED                           1     6
  ZNF7 WILD-TYPE                        21   220
D1709V13, multiclass
                                  clus
vv                                 ZNF7 MUTATED ZNF7 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                       6            220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1710) Variable = LDLRAD3 MUTATION ANALYSIS
D1710V1, survival
                   sevent
clus2                 0   1
  LDLRAD3 MUTATED     4   1
  LDLRAD3 WILD-TYPE 374  92
  LDLRAD3 MUTATED LDLRAD3 WILD-TYPE 
                5               466 
  LDLRAD3 MUTATED LDLRAD3 WILD-TYPE 
                1                92 
$`LDLRAD3 MUTATED`
TCGA-AA-3492 TCGA-AA-3864 TCGA-AA-3949 TCGA-AZ-4315 TCGA-AG-A02N 
        3.02        53.00        26.01        58.39        61.97 

$`LDLRAD3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 
       32.05         0.99        31.07        31.07        30.05        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       12.99        24.00        33.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
        1.94        38.96        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  LDLRAD3 MUTATED LDLRAD3 WILD-TYPE 
             3.02              0.00 
  LDLRAD3 MUTATED LDLRAD3 WILD-TYPE 
            61.97            148.01 
  LDLRAD3 MUTATED LDLRAD3 WILD-TYPE 
           53.000            20.085 
[1] "3.0 - 62.0 (53.0)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.7"
D1710V2, continuous
D1710V3, binary
                   cls
clus                  0   1
  LDLRAD3 MUTATED     5   1
  LDLRAD3 WILD-TYPE 361 118
[1] "tbl2"
                   cls
clus                [,1] [,2]
  LDLRAD3 MUTATED      5    1
  LDLRAD3 WILD-TYPE  361  118
        clus
vv       LDLRAD3 MUTATED LDLRAD3 WILD-TYPE
  COLON                5               361
  RECTUM               1               118
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  LDLRAD3 MUTATED         0        0        3         1         1         0
  LDLRAD3 WILD-TYPE      91        1       29       137         9         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  LDLRAD3 MUTATED           0          0          1          0        0
  LDLRAD3 WILD-TYPE        24         11         58         42       48
                   vv
clus                STAGE IVA STAGE IVB
  LDLRAD3 MUTATED           0         0
  LDLRAD3 WILD-TYPE        18         1
D1710V4, multiclass
            clus
vv           LDLRAD3 MUTATED LDLRAD3 WILD-TYPE
  STAGE I                  0                91
  STAGE IA                 0                 1
  STAGE II                 3                29
  STAGE IIA                1               137
  STAGE IIB                1                 9
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               0                11
  STAGE IIIB               1                58
  STAGE IIIC               0                42
  STAGE IV                 0                48
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  LDLRAD3 MUTATED     0   0   5   1
  LDLRAD3 WILD-TYPE  17  92 324  49
D1710V5, multiclass
    clus
vv   LDLRAD3 MUTATED LDLRAD3 WILD-TYPE
  T1               0                17
  T2               0                92
  T3               5               324
  T4               1                49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  LDLRAD3 MUTATED     5   1   0
  LDLRAD3 WILD-TYPE 282 112  87
D1710V6, multiclass
    clus
vv   LDLRAD3 MUTATED LDLRAD3 WILD-TYPE
  N0               5               282
  N1               1               112
  N2               0                87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1710V7, binary
                   cls
clus                  0   1
  LDLRAD3 MUTATED     5   0
  LDLRAD3 WILD-TYPE 370  65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  LDLRAD3 MUTATED      5    0
  LDLRAD3 WILD-TYPE  370   65
   clus
vv  LDLRAD3 MUTATED LDLRAD3 WILD-TYPE
  0               5               370
  1               0                65
[1] 2 2
[1] FALSE
D1710V8, binary
                   cls
clus                  0   1
  LDLRAD3 MUTATED     3   3
  LDLRAD3 WILD-TYPE 222 261
[1] "tbl2"
                   cls
clus                [,1] [,2]
  LDLRAD3 MUTATED      3    3
  LDLRAD3 WILD-TYPE  222  261
        clus
vv       LDLRAD3 MUTATED LDLRAD3 WILD-TYPE
  FEMALE               3               222
  MALE                 3               261
[1] 2 2
[1] FALSE
D1710V9, binary
                   cls
clus                  0   1
  LDLRAD3 MUTATED     4   0
  LDLRAD3 WILD-TYPE 346  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  LDLRAD3 MUTATED      4    0
  LDLRAD3 WILD-TYPE  346   22
     clus
vv    LDLRAD3 MUTATED LDLRAD3 WILD-TYPE
  NO                4               346
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  LDLRAD3 MUTATED                      4                             1
  LDLRAD3 WILD-TYPE                  311                            46
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  LDLRAD3 MUTATED                       1                              0
  LDLRAD3 WILD-TYPE                   105                             10
D1710V10, multiclass
                                clus
vv                               LDLRAD3 MUTATED LDLRAD3 WILD-TYPE
  COLON ADENOCARCINOMA                         4               311
  COLON MUCINOUS ADENOCARCINOMA                1                46
  RECTAL ADENOCARCINOMA                        1               105
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  LDLRAD3 MUTATED     5   0   0   1
  LDLRAD3 WILD-TYPE 340   4  31  24
D1710V11, multiclass
    clus
vv   LDLRAD3 MUTATED LDLRAD3 WILD-TYPE
  R0               5               340
  R1               0                 4
  R2               0                31
  RX               1                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1710V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  LDLRAD3 MUTATED                                  0     0
  LDLRAD3 WILD-TYPE                                1    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  LDLRAD3 MUTATED                           0     2
  LDLRAD3 WILD-TYPE                        22   224
D1710V13, multiclass
[1] "Remove cluster labels:" "LDLRAD3 MUTATED"       
clus
  LDLRAD3 MUTATED LDLRAD3 WILD-TYPE 
                2               258 
       TCGA-A6-2671        TCGA-A6-2672        TCGA-A6-2674        TCGA-A6-2676 
"LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" 
       TCGA-A6-2677        TCGA-A6-2678        TCGA-A6-2683        TCGA-A6-3807 
"LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" 
       TCGA-A6-3808        TCGA-A6-3809        TCGA-A6-3810        TCGA-A6-4105 
"LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" 
       TCGA-A6-5656        TCGA-A6-5657        TCGA-A6-5659        TCGA-A6-5660 
"LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" 
       TCGA-A6-5661        TCGA-A6-5662        TCGA-A6-5664        TCGA-A6-5665 
"LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" 
       TCGA-A6-5666        TCGA-A6-6137        TCGA-A6-6138        TCGA-A6-6141 
"LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" 
       TCGA-A6-6142        TCGA-A6-6648        TCGA-A6-6649        TCGA-A6-6651 
"LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" 
       TCGA-A6-6652        TCGA-A6-6653        TCGA-A6-6654        TCGA-A6-6780 
"LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" 
       TCGA-A6-6781        TCGA-A6-6782        TCGA-AD-5900        TCGA-AD-6548 
"LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" 
       TCGA-AD-6888        TCGA-AD-6889        TCGA-AD-6890        TCGA-AD-6895 
"LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" 
       TCGA-AD-6899        TCGA-AD-6901        TCGA-AD-6963        TCGA-AD-6964 
"LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" 
       TCGA-AD-6965        TCGA-AU-3779        TCGA-AU-6004        TCGA-AY-4070 
"LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" 
       TCGA-AY-4071        TCGA-AY-5543        TCGA-AY-6196        TCGA-AY-6197 
"LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" 
       TCGA-AY-6386        TCGA-AZ-4323        TCGA-AZ-4616        TCGA-AZ-4681 
"LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" 
       TCGA-AZ-4682        TCGA-AZ-5403        TCGA-AZ-5407        TCGA-AZ-6598 
"LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" 
       TCGA-AZ-6599        TCGA-AZ-6600        TCGA-AZ-6601        TCGA-AZ-6603 
"LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" 
       TCGA-AZ-6605        TCGA-AZ-6606        TCGA-AZ-6607        TCGA-AZ-6608 
"LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" 
       TCGA-CA-5254        TCGA-CA-5255        TCGA-CA-5796        TCGA-CA-5797 
"LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" 
       TCGA-CA-6715        TCGA-CA-6716        TCGA-CA-6717        TCGA-CA-6718 
"LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" 
       TCGA-CA-6719        TCGA-CK-4947        TCGA-CK-4948        TCGA-CK-4950 
"LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" 
       TCGA-CK-4952        TCGA-CK-5912        TCGA-CK-5913        TCGA-CK-5914 
"LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" 
       TCGA-CK-5915        TCGA-CK-5916        TCGA-CK-6747        TCGA-CK-6748 
"LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" 
       TCGA-CK-6751        TCGA-CM-4743        TCGA-CM-4744        TCGA-CM-4746 
"LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" 
       TCGA-CM-4747        TCGA-CM-4752        TCGA-CM-5341        TCGA-CM-5344 
"LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" 
       TCGA-CM-5348        TCGA-CM-5349        TCGA-CM-5860        TCGA-CM-5861 
"LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" 
       TCGA-CM-5862        TCGA-CM-5863        TCGA-CM-5864        TCGA-CM-5868 
"LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" 
       TCGA-CM-6161        TCGA-CM-6162        TCGA-CM-6163        TCGA-CM-6164 
"LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" 
       TCGA-CM-6165        TCGA-CM-6166        TCGA-CM-6167        TCGA-CM-6168 
"LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" 
       TCGA-CM-6169        TCGA-CM-6170        TCGA-CM-6171        TCGA-CM-6172 
"LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" 
       TCGA-CM-6674        TCGA-CM-6675        TCGA-CM-6676        TCGA-CM-6677 
"LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" 
       TCGA-CM-6678        TCGA-CM-6679        TCGA-CM-6680        TCGA-D5-5537 
"LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" 
       TCGA-D5-5538        TCGA-D5-5539        TCGA-D5-5540        TCGA-D5-5541 
"LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" 
       TCGA-D5-6529        TCGA-D5-6532        TCGA-D5-6533        TCGA-D5-6534 
"LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" 
       TCGA-D5-6535        TCGA-D5-6536        TCGA-D5-6537        TCGA-D5-6538 
"LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" 
       TCGA-D5-6539        TCGA-D5-6540        TCGA-D5-6541        TCGA-D5-6898 
"LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" 
       TCGA-D5-6920        TCGA-D5-6922        TCGA-D5-6923        TCGA-D5-6924 
"LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" 
       TCGA-D5-6926        TCGA-D5-6927        TCGA-D5-6928        TCGA-D5-6929 
"LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" 
       TCGA-D5-6930        TCGA-D5-6931        TCGA-D5-6932        TCGA-D5-7000 
"LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" 
       TCGA-DM-A0X9        TCGA-DM-A0XD        TCGA-DM-A0XF        TCGA-DM-A1D0 
"LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" 
       TCGA-DM-A1D4        TCGA-DM-A1D6        TCGA-DM-A1D7        TCGA-DM-A1D8 
"LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" 
       TCGA-DM-A1D9        TCGA-DM-A1DA        TCGA-DM-A1DB        TCGA-DM-A1HA 
"LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" 
       TCGA-DM-A1HB        TCGA-DM-A282        TCGA-DM-A285        TCGA-DM-A28C 
"LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" 
       TCGA-DM-A28E        TCGA-DM-A28F        TCGA-DM-A28G        TCGA-DM-A28H 
"LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" 
       TCGA-DM-A28K        TCGA-F4-6459        TCGA-F4-6460        TCGA-F4-6569 
"LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" 
       TCGA-F4-6570        TCGA-F4-6703        TCGA-F4-6704        TCGA-F4-6805 
"LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" 
       TCGA-F4-6806        TCGA-F4-6807        TCGA-F4-6808        TCGA-F4-6809 
"LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" 
       TCGA-F4-6854        TCGA-F4-6855        TCGA-F4-6856        TCGA-G4-6293 
"LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" 
       TCGA-G4-6299        TCGA-G4-6303        TCGA-G4-6304        TCGA-G4-6306 
"LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" 
       TCGA-G4-6307        TCGA-G4-6309        TCGA-G4-6310        TCGA-G4-6315 
"LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" 
       TCGA-G4-6317        TCGA-G4-6321        TCGA-G4-6323        TCGA-G4-6586 
"LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" 
       TCGA-G4-6588        TCGA-G4-6625        TCGA-G4-6626        TCGA-G4-6628 
"LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2691        TCGA-AF-2692 
"LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" 
       TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3913        TCGA-AF-4110 
"LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" 
       TCGA-AF-5654        TCGA-AF-6136        TCGA-AF-6655        TCGA-AF-6672 
"LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6549        TCGA-AH-6643 
"LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" 
       TCGA-AH-6644        TCGA-CI-6619        TCGA-CI-6620        TCGA-CI-6621 
"LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" 
       TCGA-CI-6622        TCGA-CI-6624        TCGA-CL-5917        TCGA-CL-5918 
"LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" 
       TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6155        TCGA-DC-6157 
"LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" 
       TCGA-DC-6158        TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682 
"LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" 
       TCGA-DC-6683        TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC 
"LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" 
       TCGA-DY-A1DD        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" 
       TCGA-EF-5830        TCGA-EI-6506        TCGA-EI-6507        TCGA-EI-6508 
"LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" 
       TCGA-EI-6510        TCGA-F5-6464        TCGA-F5-6465        TCGA-F5-6571 
"LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" 
       TCGA-F5-6702        TCGA-F5-6811        TCGA-F5-6812        TCGA-F5-6813 
"LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" 
       TCGA-G5-6235        TCGA-G5-6641 
"LDLRAD3 WILD-TYPE" "LDLRAD3 WILD-TYPE" 

Clustering(1711) Variable = HOOK3 MUTATION ANALYSIS
D1711V1, survival
                 sevent
clus2               0   1
  HOOK3 MUTATED     9   2
  HOOK3 WILD-TYPE 369  91
  HOOK3 MUTATED HOOK3 WILD-TYPE 
             11             460 
  HOOK3 MUTATED HOOK3 WILD-TYPE 
              2              91 
$`HOOK3 MUTATED`
TCGA-A6-5664 TCGA-A6-5665 TCGA-AA-3663 TCGA-AA-3950 TCGA-AA-A00E TCGA-AZ-4315 
       22.09        22.06         6.97        24.00        30.02        58.39 
TCGA-AZ-6598 TCGA-AZ-6605 TCGA-AG-3894 TCGA-AG-A002 TCGA-F5-6702 
       49.41         5.23        14.01        20.98        28.57 

$`HOOK3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        33.01        26.01         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00F 
        7.96        27.02        13.94        38.04        19.00        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77        12.10       100.01        29.56        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       13.02        35.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6811 
       20.91        18.28         9.96        49.51        31.30        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  HOOK3 MUTATED HOOK3 WILD-TYPE 
           5.23            0.00 
  HOOK3 MUTATED HOOK3 WILD-TYPE 
          58.39          148.01 
  HOOK3 MUTATED HOOK3 WILD-TYPE 
         22.090          20.035 
[1] "5.2 - 58.4 (22.1)"  "0.0 - 148.0 (20.0)"
[1] "hr=" "1.1"
D1711V2, continuous
D1711V3, binary
                 cls
clus                0   1
  HOOK3 MUTATED     8   3
  HOOK3 WILD-TYPE 358 116
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HOOK3 MUTATED      8    3
  HOOK3 WILD-TYPE  358  116
        clus
vv       HOOK3 MUTATED HOOK3 WILD-TYPE
  COLON              8             358
  RECTUM             3             116
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  HOOK3 MUTATED         1        0        2         5         0         0
  HOOK3 WILD-TYPE      90        1       30       133        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  HOOK3 MUTATED           0          0          1          1        0         1
  HOOK3 WILD-TYPE        24         11         58         41       48        17
                 vv
clus              STAGE IVB
  HOOK3 MUTATED           0
  HOOK3 WILD-TYPE         1
D1711V4, multiclass
            clus
vv           HOOK3 MUTATED HOOK3 WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA              5             133
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             1              41
  STAGE IV               0              48
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  HOOK3 MUTATED     0   1   8   2
  HOOK3 WILD-TYPE  17  91 321  48
D1711V5, multiclass
    clus
vv   HOOK3 MUTATED HOOK3 WILD-TYPE
  T1             0              17
  T2             1              91
  T3             8             321
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  HOOK3 MUTATED     8   2   1
  HOOK3 WILD-TYPE 279 111  86
D1711V6, multiclass
    clus
vv   HOOK3 MUTATED HOOK3 WILD-TYPE
  N0             8             279
  N1             2             111
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1711V7, binary
                 cls
clus                0   1
  HOOK3 MUTATED     8   1
  HOOK3 WILD-TYPE 367  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HOOK3 MUTATED      8    1
  HOOK3 WILD-TYPE  367   64
   clus
vv  HOOK3 MUTATED HOOK3 WILD-TYPE
  0             8             367
  1             1              64
[1] 2 2
[1] FALSE
D1711V8, binary
                 cls
clus                0   1
  HOOK3 MUTATED     3   8
  HOOK3 WILD-TYPE 222 256
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HOOK3 MUTATED      3    8
  HOOK3 WILD-TYPE  222  256
        clus
vv       HOOK3 MUTATED HOOK3 WILD-TYPE
  FEMALE             3             222
  MALE               8             256
[1] 2 2
[1] FALSE
D1711V9, binary
                 cls
clus                0   1
  HOOK3 MUTATED    10   1
  HOOK3 WILD-TYPE 340  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HOOK3 MUTATED     10    1
  HOOK3 WILD-TYPE  340   21
     clus
vv    HOOK3 MUTATED HOOK3 WILD-TYPE
  NO             10             340
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  HOOK3 MUTATED                      7                             1
  HOOK3 WILD-TYPE                  308                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  HOOK3 MUTATED                       3                              0
  HOOK3 WILD-TYPE                   103                             10
D1711V10, multiclass
                                clus
vv                               HOOK3 MUTATED HOOK3 WILD-TYPE
  COLON ADENOCARCINOMA                       7             308
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      3             103
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  HOOK3 MUTATED     8   0   0   0
  HOOK3 WILD-TYPE 337   4  31  25
D1711V11, multiclass
    clus
vv   HOOK3 MUTATED HOOK3 WILD-TYPE
  R0             8             337
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1711V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HOOK3 MUTATED                                  0     0
  HOOK3 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  HOOK3 MUTATED                           1     5
  HOOK3 WILD-TYPE                        21   221
D1711V13, multiclass
                                  clus
vv                                 HOOK3 MUTATED HOOK3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        5             221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1712) Variable = NAPA MUTATION ANALYSIS
D1712V1, survival
                sevent
clus2              0   1
  NAPA MUTATED     7   0
  NAPA WILD-TYPE 371  93
  NAPA MUTATED NAPA WILD-TYPE 
             7            464 
  NAPA MUTATED NAPA WILD-TYPE 
             0             93 
$`NAPA MUTATED`
TCGA-AA-3968 TCGA-AA-3977 TCGA-AA-A00J TCGA-AU-6004 TCGA-CA-6717 TCGA-CM-5344 
       21.99        25.02        18.05        27.09        12.76        22.03 
TCGA-AG-3892 
       13.02 

$`NAPA WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3971 
       24.00         2.01        20.98        34.03         2.01        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       19.00        30.02        34.03        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
        0.20        14.50        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07        12.20        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       36.95        17.03        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  NAPA MUTATED NAPA WILD-TYPE 
         12.76           0.00 
  NAPA MUTATED NAPA WILD-TYPE 
         27.09         148.01 
  NAPA MUTATED NAPA WILD-TYPE 
        21.990         20.155 
[1] "12.8 - 27.1 (22.0)" "0.0 - 148.0 (20.2)"
[1] "hr="     "9100000"
D1712V2, continuous
D1712V3, binary
                cls
clus               0   1
  NAPA MUTATED     6   1
  NAPA WILD-TYPE 360 118
[1] "tbl2"
                cls
clus             [,1] [,2]
  NAPA MUTATED      6    1
  NAPA WILD-TYPE  360  118
        clus
vv       NAPA MUTATED NAPA WILD-TYPE
  COLON             6            360
  RECTUM            1            118
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NAPA MUTATED         3        0        0         1         0         0
  NAPA WILD-TYPE      88        1       32       137        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NAPA MUTATED           0          0          2          0        0         0
  NAPA WILD-TYPE        24         11         57         42       48        18
                vv
clus             STAGE IVB
  NAPA MUTATED           0
  NAPA WILD-TYPE         1
D1712V4, multiclass
            clus
vv           NAPA MUTATED NAPA WILD-TYPE
  STAGE I               3             88
  STAGE IA              0              1
  STAGE II              0             32
  STAGE IIA             1            137
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            2             57
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  NAPA MUTATED     1   3   2   1
  NAPA WILD-TYPE  16  89 327  49
D1712V5, multiclass
    clus
vv   NAPA MUTATED NAPA WILD-TYPE
  T1            1             16
  T2            3             89
  T3            2            327
  T4            1             49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  NAPA MUTATED     5   2   0
  NAPA WILD-TYPE 282 111  87
D1712V6, multiclass
    clus
vv   NAPA MUTATED NAPA WILD-TYPE
  N0            5            282
  N1            2            111
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1712V7, binary
                cls
clus               0   1
  NAPA MUTATED     6   0
  NAPA WILD-TYPE 369  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  NAPA MUTATED      6    0
  NAPA WILD-TYPE  369   65
   clus
vv  NAPA MUTATED NAPA WILD-TYPE
  0            6            369
  1            0             65
[1] 2 2
[1] FALSE
D1712V8, binary
                cls
clus               0   1
  NAPA MUTATED     4   3
  NAPA WILD-TYPE 221 261
[1] "tbl2"
                cls
clus             [,1] [,2]
  NAPA MUTATED      4    3
  NAPA WILD-TYPE  221  261
        clus
vv       NAPA MUTATED NAPA WILD-TYPE
  FEMALE            4            221
  MALE              3            261
[1] 2 2
[1] FALSE
D1712V9, binary
                cls
clus               0   1
  NAPA MUTATED     6   0
  NAPA WILD-TYPE 344  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  NAPA MUTATED      6    0
  NAPA WILD-TYPE  344   22
     clus
vv    NAPA MUTATED NAPA WILD-TYPE
  NO             6            344
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  NAPA MUTATED                      4                             2
  NAPA WILD-TYPE                  311                            45
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  NAPA MUTATED                       1                              0
  NAPA WILD-TYPE                   105                             10
D1712V10, multiclass
                                clus
vv                               NAPA MUTATED NAPA WILD-TYPE
  COLON ADENOCARCINOMA                      4            311
  COLON MUCINOUS ADENOCARCINOMA             2             45
  RECTAL ADENOCARCINOMA                     1            105
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  NAPA MUTATED     5   0   0   1
  NAPA WILD-TYPE 340   4  31  24
D1712V11, multiclass
    clus
vv   NAPA MUTATED NAPA WILD-TYPE
  R0            5            340
  R1            0              4
  R2            0             31
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1712V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NAPA MUTATED                                  0     1
  NAPA WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  NAPA MUTATED                           0     2
  NAPA WILD-TYPE                        22   224
D1712V13, multiclass
                                  clus
vv                                 NAPA MUTATED NAPA WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       2            224
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1713) Variable = METT10D MUTATION ANALYSIS
D1713V1, survival
                   sevent
clus2                 0   1
  METT10D MUTATED     9   0
  METT10D WILD-TYPE 369  93
  METT10D MUTATED METT10D WILD-TYPE 
                9               462 
  METT10D MUTATED METT10D WILD-TYPE 
                0                93 
$`METT10D MUTATED`
TCGA-AA-3977 TCGA-AA-A010 TCGA-CM-6172 TCGA-D5-6540 TCGA-D5-6927 TCGA-AG-3742 
       25.02        34.98        11.01        16.14         9.44         0.99 
TCGA-AG-3892 TCGA-AG-A002 TCGA-AG-A02N 
       13.02        20.98        61.97 

$`METT10D WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6674 
       14.99        12.99        13.02        15.02        14.04        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       17.13        12.49        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       12.43        14.30         9.04        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
       32.98         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       36.95        17.03        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 
       10.98        49.97         1.94        38.96        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  METT10D MUTATED METT10D WILD-TYPE 
             0.99              0.00 
  METT10D MUTATED METT10D WILD-TYPE 
            61.97            148.01 
  METT10D MUTATED METT10D WILD-TYPE 
           16.140            20.235 
[1] "1.0 - 62.0 (16.1)"  "0.0 - 148.0 (20.2)"
[1] "hr="     "9100000"
D1713V2, continuous
D1713V3, binary
                   cls
clus                  0   1
  METT10D MUTATED     7   4
  METT10D WILD-TYPE 359 115
[1] "tbl2"
                   cls
clus                [,1] [,2]
  METT10D MUTATED      7    4
  METT10D WILD-TYPE  359  115
        clus
vv       METT10D MUTATED METT10D WILD-TYPE
  COLON                7               359
  RECTUM               4               115
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  METT10D MUTATED         4        0        1         2         2         0
  METT10D WILD-TYPE      87        1       31       136         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  METT10D MUTATED           0          0          1          0        0
  METT10D WILD-TYPE        24         11         58         42       48
                   vv
clus                STAGE IVA STAGE IVB
  METT10D MUTATED           0         0
  METT10D WILD-TYPE        18         1
D1713V4, multiclass
            clus
vv           METT10D MUTATED METT10D WILD-TYPE
  STAGE I                  4                87
  STAGE IA                 0                 1
  STAGE II                 1                31
  STAGE IIA                2               136
  STAGE IIB                2                 8
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               0                11
  STAGE IIIB               1                58
  STAGE IIIC               0                42
  STAGE IV                 0                48
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  METT10D MUTATED     2   3   4   2
  METT10D WILD-TYPE  15  89 325  48
D1713V5, multiclass
    clus
vv   METT10D MUTATED METT10D WILD-TYPE
  T1               2                15
  T2               3                89
  T3               4               325
  T4               2                48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  METT10D MUTATED    10   1   0
  METT10D WILD-TYPE 277 112  87
D1713V6, multiclass
    clus
vv   METT10D MUTATED METT10D WILD-TYPE
  N0              10               277
  N1               1               112
  N2               0                87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1713V7, binary
                   cls
clus                  0   1
  METT10D MUTATED     9   0
  METT10D WILD-TYPE 366  65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  METT10D MUTATED      9    0
  METT10D WILD-TYPE  366   65
   clus
vv  METT10D MUTATED METT10D WILD-TYPE
  0               9               366
  1               0                65
[1] 2 2
[1] FALSE
D1713V8, binary
                   cls
clus                  0   1
  METT10D MUTATED     6   5
  METT10D WILD-TYPE 219 259
[1] "tbl2"
                   cls
clus                [,1] [,2]
  METT10D MUTATED      6    5
  METT10D WILD-TYPE  219  259
        clus
vv       METT10D MUTATED METT10D WILD-TYPE
  FEMALE               6               219
  MALE                 5               259
[1] 2 2
[1] FALSE
D1713V9, binary
                   cls
clus                  0   1
  METT10D MUTATED     7   0
  METT10D WILD-TYPE 343  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  METT10D MUTATED      7    0
  METT10D WILD-TYPE  343   22
     clus
vv    METT10D MUTATED METT10D WILD-TYPE
  NO                7               343
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  METT10D MUTATED                      6                             1
  METT10D WILD-TYPE                  309                            46
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  METT10D MUTATED                       4                              0
  METT10D WILD-TYPE                   102                             10
D1713V10, multiclass
                                clus
vv                               METT10D MUTATED METT10D WILD-TYPE
  COLON ADENOCARCINOMA                         6               309
  COLON MUCINOUS ADENOCARCINOMA                1                46
  RECTAL ADENOCARCINOMA                        4               102
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  METT10D MUTATED     9   0   0   1
  METT10D WILD-TYPE 336   4  31  24
D1713V11, multiclass
    clus
vv   METT10D MUTATED METT10D WILD-TYPE
  R0               9               336
  R1               0                 4
  R2               0                31
  RX               1                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1713V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  METT10D MUTATED                                  0     0
  METT10D WILD-TYPE                                1    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  METT10D MUTATED                           0     4
  METT10D WILD-TYPE                        22   222
D1713V13, multiclass
                                  clus
vv                                 METT10D MUTATED METT10D WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                      0                22
  WHITE                                          4               222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1714) Variable = PLD5 MUTATION ANALYSIS
D1714V1, survival
                sevent
clus2              0   1
  PLD5 MUTATED    12   3
  PLD5 WILD-TYPE 366  90
  PLD5 MUTATED PLD5 WILD-TYPE 
            15            456 
  PLD5 MUTATED PLD5 WILD-TYPE 
             3             90 
$`PLD5 MUTATED`
TCGA-A6-5661 TCGA-AA-3516 TCGA-AA-3697 TCGA-AA-3811 TCGA-AA-3977 TCGA-CA-5254 
       33.53        13.02        85.05        10.06        25.02        12.69 
TCGA-CM-6164 TCGA-DM-A1DA TCGA-DM-A28H TCGA-G4-6317 TCGA-AF-2687 TCGA-AF-2693 
       29.03         7.50       117.07        36.00        24.13        19.10 
TCGA-AG-A002 TCGA-AG-A00Y TCGA-EI-6507 
       20.98        23.01        19.96 

$`PLD5 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3815 
        5.03        26.99        19.04        19.04        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19         1.61         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6165 
       15.02        17.03        15.02        12.00         2.96        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA 
       49.91        13.32        12.59       140.38        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
       60.79        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       61.91        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 
       46.75        79.69        39.48        43.04        13.55        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A011 
        1.02        17.03        13.94         6.02        25.97        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       20.55        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  PLD5 MUTATED PLD5 WILD-TYPE 
           7.5            0.0 
  PLD5 MUTATED PLD5 WILD-TYPE 
        117.07         148.01 
  PLD5 MUTATED PLD5 WILD-TYPE 
        23.010         20.085 
[1] "7.5 - 117.1 (23.0)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.1"
D1714V2, continuous
D1714V3, binary
                cls
clus               0   1
  PLD5 MUTATED    10   4
  PLD5 WILD-TYPE 356 115
[1] "tbl2"
                cls
clus             [,1] [,2]
  PLD5 MUTATED     10    4
  PLD5 WILD-TYPE  356  115
        clus
vv       PLD5 MUTATED PLD5 WILD-TYPE
  COLON            10            356
  RECTUM            4            115
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PLD5 MUTATED         2        0        0         5         0         0
  PLD5 WILD-TYPE      89        1       32       133        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PLD5 MUTATED           3          0          0          4        0         0
  PLD5 WILD-TYPE        21         11         59         38       48        18
                vv
clus             STAGE IVB
  PLD5 MUTATED           0
  PLD5 WILD-TYPE         1
D1714V4, multiclass
            clus
vv           PLD5 MUTATED PLD5 WILD-TYPE
  STAGE I               2             89
  STAGE IA              0              1
  STAGE II              0             32
  STAGE IIA             5            133
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             3             21
  STAGE IIIA            0             11
  STAGE IIIB            0             59
  STAGE IIIC            4             38
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  PLD5 MUTATED     0   3  12   0
  PLD5 WILD-TYPE  17  89 317  50
D1714V5, multiclass
    clus
vv   PLD5 MUTATED PLD5 WILD-TYPE
  T1            0             17
  T2            3             89
  T3           12            317
  T4            0             50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  PLD5 MUTATED     9   0   6
  PLD5 WILD-TYPE 278 113  81
D1714V6, multiclass
    clus
vv   PLD5 MUTATED PLD5 WILD-TYPE
  N0            9            278
  N1            0            113
  N2            6             81
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1714V7, binary
                cls
clus               0   1
  PLD5 MUTATED    12   0
  PLD5 WILD-TYPE 363  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  PLD5 MUTATED     12    0
  PLD5 WILD-TYPE  363   65
   clus
vv  PLD5 MUTATED PLD5 WILD-TYPE
  0           12            363
  1            0             65
[1] 2 2
[1] FALSE
D1714V8, binary
                cls
clus               0   1
  PLD5 MUTATED     7   8
  PLD5 WILD-TYPE 218 256
[1] "tbl2"
                cls
clus             [,1] [,2]
  PLD5 MUTATED      7    8
  PLD5 WILD-TYPE  218  256
        clus
vv       PLD5 MUTATED PLD5 WILD-TYPE
  FEMALE            7            218
  MALE              8            256
[1] 2 2
[1] FALSE
D1714V9, binary
                cls
clus               0   1
  PLD5 MUTATED    12   1
  PLD5 WILD-TYPE 338  21
[1] "tbl2"
                cls
clus             [,1] [,2]
  PLD5 MUTATED     12    1
  PLD5 WILD-TYPE  338   21
     clus
vv    PLD5 MUTATED PLD5 WILD-TYPE
  NO            12            338
  YES            1             21
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PLD5 MUTATED                      9                             1
  PLD5 WILD-TYPE                  306                            46
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PLD5 MUTATED                       4                              0
  PLD5 WILD-TYPE                   102                             10
D1714V10, multiclass
                                clus
vv                               PLD5 MUTATED PLD5 WILD-TYPE
  COLON ADENOCARCINOMA                      9            306
  COLON MUCINOUS ADENOCARCINOMA             1             46
  RECTAL ADENOCARCINOMA                     4            102
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  PLD5 MUTATED     9   0   0   1
  PLD5 WILD-TYPE 336   4  31  24
D1714V11, multiclass
    clus
vv   PLD5 MUTATED PLD5 WILD-TYPE
  R0            9            336
  R1            0              4
  R2            0             31
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1714V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PLD5 MUTATED                                  0     1
  PLD5 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  PLD5 MUTATED                           1     7
  PLD5 WILD-TYPE                        21   219
D1714V13, multiclass
                                  clus
vv                                 PLD5 MUTATED PLD5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                       7            219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1715) Variable = SON MUTATION ANALYSIS
D1715V1, survival
               sevent
clus2             0   1
  SON MUTATED    20   4
  SON WILD-TYPE 358  89
  SON MUTATED SON WILD-TYPE 
           24           447 
  SON MUTATED SON WILD-TYPE 
            4            89 
$`SON MUTATED`
TCGA-A6-3809 TCGA-A6-5660 TCGA-A6-5666 TCGA-AA-3492 TCGA-AA-3672 TCGA-AA-3854 
       32.75        29.19        32.71         3.02         0.92        36.03 
TCGA-AA-3864 TCGA-AA-3875 TCGA-AA-3966 TCGA-AA-A02W TCGA-AZ-4315 TCGA-AZ-5407 
       53.00        18.05         2.01        41.00        58.39        88.21 
TCGA-AZ-6598 TCGA-AZ-6601 TCGA-CA-6717 TCGA-CM-4746 TCGA-CM-5349 TCGA-D5-6541 
       49.41       100.01        12.76        37.02        30.08        15.58 
TCGA-F4-6570 TCGA-G4-6586 TCGA-AG-A002 TCGA-AG-A011 TCGA-DY-A0XA TCGA-EI-6507 
        6.18        35.80        20.98        37.02       126.44        19.96 

$`SON WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       31.63        30.44        33.53        23.61        22.09        22.06 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       27.09        22.52         8.38        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
       20.28         7.04         1.02        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
       14.01        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
        0.00        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3877 TCGA-AA-3930 
       17.03        24.03        27.02        29.98        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       20.98        34.03        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02Y TCGA-AA-A03F 
        2.01         5.03        14.01         0.92        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77        12.10        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.20        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4752 
        1.91       124.27        23.05        20.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       29.06        22.03        22.98        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       16.14         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       31.96        35.74        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A014 TCGA-AG-A015 
       13.94         6.02        25.97        23.01        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        4.01         5.03         5.29        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6510 
       51.48        32.61         0.49        20.55        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  SON MUTATED SON WILD-TYPE 
         0.92          0.00 
  SON MUTATED SON WILD-TYPE 
       126.44        148.01 
  SON MUTATED SON WILD-TYPE 
        32.73         20.02 
[1] "0.9 - 126.4 (32.7)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.6"
D1715V2, continuous
D1715V3, binary
               cls
clus              0   1
  SON MUTATED    20   4
  SON WILD-TYPE 346 115
[1] "tbl2"
               cls
clus            [,1] [,2]
  SON MUTATED     20    4
  SON WILD-TYPE  346  115
        clus
vv       SON MUTATED SON WILD-TYPE
  COLON           20           346
  RECTUM           4           115
[1] 2 2
[1] FALSE
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SON MUTATED         6        0        4        10         1         1
  SON WILD-TYPE      85        1       28       128         9         0
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SON MUTATED           1          0          0          1        0         0
  SON WILD-TYPE        23         11         59         41       48        18
               vv
clus            STAGE IVB
  SON MUTATED           0
  SON WILD-TYPE         1
D1715V4, multiclass
            clus
vv           SON MUTATED SON WILD-TYPE
  STAGE I              6            85
  STAGE IA             0             1
  STAGE II             4            28
  STAGE IIA           10           128
  STAGE IIB            1             9
  STAGE IIC            1             0
  STAGE III            1            23
  STAGE IIIA           0            11
  STAGE IIIB           0            59
  STAGE IIIC           1            41
  STAGE IV             0            48
  STAGE IVA            0            18
  STAGE IVB            0             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  SON MUTATED     2   4  16   2
  SON WILD-TYPE  15  88 313  48
D1715V5, multiclass
    clus
vv   SON MUTATED SON WILD-TYPE
  T1           2            15
  T2           4            88
  T3          16           313
  T4           2            48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2
  SON MUTATED    22   1   1
  SON WILD-TYPE 265 112  86
D1715V6, multiclass
    clus
vv   SON MUTATED SON WILD-TYPE
  N0          22           265
  N1           1           112
  N2           1            86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1715V7, binary
               cls
clus              0   1
  SON MUTATED    23   0
  SON WILD-TYPE 352  65
[1] "tbl2"
               cls
clus            [,1] [,2]
  SON MUTATED     23    0
  SON WILD-TYPE  352   65
   clus
vv  SON MUTATED SON WILD-TYPE
  0          23           352
  1           0            65
[1] 2 2
[1] FALSE
D1715V8, binary
               cls
clus              0   1
  SON MUTATED    13  11
  SON WILD-TYPE 212 253
[1] "tbl2"
               cls
clus            [,1] [,2]
  SON MUTATED     13   11
  SON WILD-TYPE  212  253
        clus
vv       SON MUTATED SON WILD-TYPE
  FEMALE          13           212
  MALE            11           253
[1] 2 2
[1] FALSE
D1715V9, binary
               cls
clus              0   1
  SON MUTATED    22   0
  SON WILD-TYPE 328  22
[1] "tbl2"
               cls
clus            [,1] [,2]
  SON MUTATED     22    0
  SON WILD-TYPE  328   22
     clus
vv    SON MUTATED SON WILD-TYPE
  NO           22           328
  YES           0            22
[1] 2 2
[1] FALSE
               vv
clus            COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SON MUTATED                     16                             4
  SON WILD-TYPE                  299                            43
               vv
clus            RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SON MUTATED                       4                              0
  SON WILD-TYPE                   102                             10
D1715V10, multiclass
                                clus
vv                               SON MUTATED SON WILD-TYPE
  COLON ADENOCARCINOMA                    16           299
  COLON MUCINOUS ADENOCARCINOMA            4            43
  RECTAL ADENOCARCINOMA                    4           102
  RECTAL MUCINOUS ADENOCARCINOMA           0            10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             R0  R1  R2  RX
  SON MUTATED    16   0   0   1
  SON WILD-TYPE 329   4  31  24
D1715V11, multiclass
    clus
vv   SON MUTATED SON WILD-TYPE
  R0          16           329
  R1           0             4
  R2           0            31
  RX           1            24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1715V12, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SON MUTATED                                  0     1
  SON WILD-TYPE                                1    10
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  SON MUTATED                           2    12
  SON WILD-TYPE                        20   214
D1715V13, multiclass
                                  clus
vv                                 SON MUTATED SON WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      1            10
  BLACK OR AFRICAN AMERICAN                  2            20
  WHITE                                     12           214
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1716) Variable = ATP6V0A4 MUTATION ANALYSIS
D1716V1, survival
                    sevent
clus2                  0   1
  ATP6V0A4 MUTATED     8   3
  ATP6V0A4 WILD-TYPE 370  90
  ATP6V0A4 MUTATED ATP6V0A4 WILD-TYPE 
                11                460 
  ATP6V0A4 MUTATED ATP6V0A4 WILD-TYPE 
                 3                 90 
$`ATP6V0A4 MUTATED`
TCGA-AA-3715 TCGA-AA-A00N TCGA-AA-A010 TCGA-AU-6004 TCGA-AY-6197 TCGA-CA-6717 
       19.04         4.01        34.98        27.09        21.44        12.76 
TCGA-CA-6718 TCGA-CK-4950 TCGA-D5-7000 TCGA-AG-3593 TCGA-AG-A002 
       10.06        85.45        10.26        34.03        20.98 

$`ATP6V0A4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 
        0.20        14.50        16.31         0.95        33.01        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 
        3.25         3.29         0.07        12.20        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
      148.01        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-DM-A0X9 
       11.64         4.80         1.51        12.00        11.38       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       46.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  ATP6V0A4 MUTATED ATP6V0A4 WILD-TYPE 
              4.01               0.00 
  ATP6V0A4 MUTATED ATP6V0A4 WILD-TYPE 
             85.45             148.01 
  ATP6V0A4 MUTATED ATP6V0A4 WILD-TYPE 
            20.980             20.155 
[1] "4.0 - 85.5 (21.0)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.5"
D1716V2, continuous
D1716V3, binary
                    cls
clus                   0   1
  ATP6V0A4 MUTATED    11   2
  ATP6V0A4 WILD-TYPE 355 117
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ATP6V0A4 MUTATED     11    2
  ATP6V0A4 WILD-TYPE  355  117
        clus
vv       ATP6V0A4 MUTATED ATP6V0A4 WILD-TYPE
  COLON                11                355
  RECTUM                2                117
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ATP6V0A4 MUTATED         3        0        1         5         3         0
  ATP6V0A4 WILD-TYPE      88        1       31       133         7         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ATP6V0A4 MUTATED           0          0          1          0        0
  ATP6V0A4 WILD-TYPE        24         11         58         42       48
                    vv
clus                 STAGE IVA STAGE IVB
  ATP6V0A4 MUTATED           0         0
  ATP6V0A4 WILD-TYPE        18         1
D1716V4, multiclass
            clus
vv           ATP6V0A4 MUTATED ATP6V0A4 WILD-TYPE
  STAGE I                   3                 88
  STAGE IA                  0                  1
  STAGE II                  1                 31
  STAGE IIA                 5                133
  STAGE IIB                 3                  7
  STAGE IIC                 0                  1
  STAGE III                 0                 24
  STAGE IIIA                0                 11
  STAGE IIIB                1                 58
  STAGE IIIC                0                 42
  STAGE IV                  0                 48
  STAGE IVA                 0                 18
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  ATP6V0A4 MUTATED     0   3   7   3
  ATP6V0A4 WILD-TYPE  17  89 322  47
D1716V5, multiclass
    clus
vv   ATP6V0A4 MUTATED ATP6V0A4 WILD-TYPE
  T1                0                 17
  T2                3                 89
  T3                7                322
  T4                3                 47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  ATP6V0A4 MUTATED    12   1   0
  ATP6V0A4 WILD-TYPE 275 112  87
D1716V6, multiclass
    clus
vv   ATP6V0A4 MUTATED ATP6V0A4 WILD-TYPE
  N0               12                275
  N1                1                112
  N2                0                 87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1716V7, binary
                    cls
clus                   0   1
  ATP6V0A4 MUTATED    11   0
  ATP6V0A4 WILD-TYPE 364  65
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ATP6V0A4 MUTATED     11    0
  ATP6V0A4 WILD-TYPE  364   65
   clus
vv  ATP6V0A4 MUTATED ATP6V0A4 WILD-TYPE
  0               11                364
  1                0                 65
[1] 2 2
[1] FALSE
D1716V8, binary
                    cls
clus                   0   1
  ATP6V0A4 MUTATED     7   6
  ATP6V0A4 WILD-TYPE 218 258
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ATP6V0A4 MUTATED      7    6
  ATP6V0A4 WILD-TYPE  218  258
        clus
vv       ATP6V0A4 MUTATED ATP6V0A4 WILD-TYPE
  FEMALE                7                218
  MALE                  6                258
[1] 2 2
[1] FALSE
D1716V9, binary
                    cls
clus                   0   1
  ATP6V0A4 MUTATED     8   1
  ATP6V0A4 WILD-TYPE 342  21
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ATP6V0A4 MUTATED      8    1
  ATP6V0A4 WILD-TYPE  342   21
     clus
vv    ATP6V0A4 MUTATED ATP6V0A4 WILD-TYPE
  NO                 8                342
  YES                1                 21
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ATP6V0A4 MUTATED                      8                             3
  ATP6V0A4 WILD-TYPE                  307                            44
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ATP6V0A4 MUTATED                       2                              0
  ATP6V0A4 WILD-TYPE                   104                             10
D1716V10, multiclass
                                clus
vv                               ATP6V0A4 MUTATED ATP6V0A4 WILD-TYPE
  COLON ADENOCARCINOMA                          8                307
  COLON MUCINOUS ADENOCARCINOMA                 3                 44
  RECTAL ADENOCARCINOMA                         2                104
  RECTAL MUCINOUS ADENOCARCINOMA                0                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  ATP6V0A4 MUTATED     9   1   0   3
  ATP6V0A4 WILD-TYPE 336   3  31  22
D1716V11, multiclass
    clus
vv   ATP6V0A4 MUTATED ATP6V0A4 WILD-TYPE
  R0                9                336
  R1                1                  3
  R2                0                 31
  RX                3                 22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1716V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ATP6V0A4 MUTATED                                  0     2
  ATP6V0A4 WILD-TYPE                                1     9
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  ATP6V0A4 MUTATED                           1     4
  ATP6V0A4 WILD-TYPE                        21   222
D1716V13, multiclass
                                  clus
vv                                 ATP6V0A4 MUTATED ATP6V0A4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           2                  9
  BLACK OR AFRICAN AMERICAN                       1                 21
  WHITE                                           4                222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1717) Variable = CACNA1D MUTATION ANALYSIS
D1717V1, survival
                   sevent
clus2                 0   1
  CACNA1D MUTATED    15   7
  CACNA1D WILD-TYPE 363  86
  CACNA1D MUTATED CACNA1D WILD-TYPE 
               22               449 
  CACNA1D MUTATED CACNA1D WILD-TYPE 
                7                86 
$`CACNA1D MUTATED`
TCGA-A6-2676 TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-A00K TCGA-AA-A010 TCGA-AA-A01R 
       42.90        20.12        19.66        18.05        34.98        35.01 
TCGA-AD-5900 TCGA-AD-6895 TCGA-AU-6004 TCGA-AZ-4315 TCGA-AZ-5407 TCGA-AZ-6598 
        0.07         0.72        27.09        58.39        88.21        49.41 
TCGA-AZ-6601 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-5913 TCGA-CK-5916 TCGA-DM-A0XD 
      100.01        12.76        10.06        51.32        21.14        24.43 
TCGA-DM-A1DA TCGA-G4-6309 TCGA-G4-6588 TCGA-AG-A002 
        7.50        85.48        26.17        20.98 

$`CACNA1D WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
        1.02         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 
        0.92        41.00        39.98        18.05        40.96        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       15.52        56.55         0.79         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       10.88         0.20        14.50        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       62.79         6.77        12.10        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.07        12.20        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       15.62        49.08         9.99        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XF TCGA-DM-A1D0 
       12.00        11.38        10.26       119.70        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB 
       92.75        49.91        13.32        12.59       140.38        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  CACNA1D MUTATED CACNA1D WILD-TYPE 
             0.07              0.00 
  CACNA1D MUTATED CACNA1D WILD-TYPE 
           100.01            148.01 
  CACNA1D MUTATED CACNA1D WILD-TYPE 
            25.30             20.02 
[1] "0.1 - 100.0 (25.3)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.3"
D1717V2, continuous
D1717V3, binary
                   cls
clus                  0   1
  CACNA1D MUTATED    22   1
  CACNA1D WILD-TYPE 344 118
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CACNA1D MUTATED     22    1
  CACNA1D WILD-TYPE  344  118
        clus
vv       CACNA1D MUTATED CACNA1D WILD-TYPE
  COLON               22               344
  RECTUM               1               118
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CACNA1D MUTATED         5        0        3         8         2         0
  CACNA1D WILD-TYPE      86        1       29       130         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CACNA1D MUTATED           1          0          1          2        0
  CACNA1D WILD-TYPE        23         11         58         40       48
                   vv
clus                STAGE IVA STAGE IVB
  CACNA1D MUTATED           0         0
  CACNA1D WILD-TYPE        18         1
D1717V4, multiclass
            clus
vv           CACNA1D MUTATED CACNA1D WILD-TYPE
  STAGE I                  5                86
  STAGE IA                 0                 1
  STAGE II                 3                29
  STAGE IIA                8               130
  STAGE IIB                2                 8
  STAGE IIC                0                 1
  STAGE III                1                23
  STAGE IIIA               0                11
  STAGE IIIB               1                58
  STAGE IIIC               2                40
  STAGE IV                 0                48
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  CACNA1D MUTATED     2   3  14   4
  CACNA1D WILD-TYPE  15  89 315  46
D1717V5, multiclass
    clus
vv   CACNA1D MUTATED CACNA1D WILD-TYPE
  T1               2                15
  T2               3                89
  T3              14               315
  T4               4                46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  CACNA1D MUTATED    18   3   2
  CACNA1D WILD-TYPE 269 110  85
D1717V6, multiclass
    clus
vv   CACNA1D MUTATED CACNA1D WILD-TYPE
  N0              18               269
  N1               3               110
  N2               2                85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1717V7, binary
                   cls
clus                  0   1
  CACNA1D MUTATED    17   0
  CACNA1D WILD-TYPE 358  65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CACNA1D MUTATED     17    0
  CACNA1D WILD-TYPE  358   65
   clus
vv  CACNA1D MUTATED CACNA1D WILD-TYPE
  0              17               358
  1               0                65
[1] 2 2
[1] FALSE
D1717V8, binary
                   cls
clus                  0   1
  CACNA1D MUTATED    11  12
  CACNA1D WILD-TYPE 214 252
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CACNA1D MUTATED     11   12
  CACNA1D WILD-TYPE  214  252
        clus
vv       CACNA1D MUTATED CACNA1D WILD-TYPE
  FEMALE              11               214
  MALE                12               252
[1] 2 2
[1] FALSE
D1717V9, binary
                   cls
clus                  0   1
  CACNA1D MUTATED    15   1
  CACNA1D WILD-TYPE 335  21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CACNA1D MUTATED     15    1
  CACNA1D WILD-TYPE  335   21
     clus
vv    CACNA1D MUTATED CACNA1D WILD-TYPE
  NO               15               335
  YES               1                21
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CACNA1D MUTATED                     17                             5
  CACNA1D WILD-TYPE                  298                            42
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CACNA1D MUTATED                       1                              0
  CACNA1D WILD-TYPE                   105                             10
D1717V10, multiclass
                                clus
vv                               CACNA1D MUTATED CACNA1D WILD-TYPE
  COLON ADENOCARCINOMA                        17               298
  COLON MUCINOUS ADENOCARCINOMA                5                42
  RECTAL ADENOCARCINOMA                        1               105
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  CACNA1D MUTATED    12   0   0   4
  CACNA1D WILD-TYPE 333   4  31  21
D1717V11, multiclass
    clus
vv   CACNA1D MUTATED CACNA1D WILD-TYPE
  R0              12               333
  R1               0                 4
  R2               0                31
  RX               4                21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1717V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CACNA1D MUTATED                                  0     2
  CACNA1D WILD-TYPE                                1     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  CACNA1D MUTATED                           1    15
  CACNA1D WILD-TYPE                        21   211
D1717V13, multiclass
                                  clus
vv                                 CACNA1D MUTATED CACNA1D WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          2                 9
  BLACK OR AFRICAN AMERICAN                      1                21
  WHITE                                         15               211
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1718) Variable = RCOR1 MUTATION ANALYSIS
D1718V1, survival
                 sevent
clus2               0   1
  RCOR1 MUTATED     3   1
  RCOR1 WILD-TYPE 375  92
  RCOR1 MUTATED RCOR1 WILD-TYPE 
              4             467 
  RCOR1 MUTATED RCOR1 WILD-TYPE 
              1              92 
$`RCOR1 MUTATED`
TCGA-AD-6895 TCGA-DM-A1HB TCGA-DM-A28G TCGA-AG-A002 
        0.72       135.65        60.79        20.98 

$`RCOR1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       21.37        15.52        56.55         0.79         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      131.51       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  RCOR1 MUTATED RCOR1 WILD-TYPE 
           0.72            0.00 
  RCOR1 MUTATED RCOR1 WILD-TYPE 
         135.65          148.01 
  RCOR1 MUTATED RCOR1 WILD-TYPE 
         40.885          20.120 
[1] "0.7 - 135.7 (40.9)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.4"
D1718V2, continuous
D1718V3, binary
                 cls
clus                0   1
  RCOR1 MUTATED     3   1
  RCOR1 WILD-TYPE 363 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RCOR1 MUTATED      3    1
  RCOR1 WILD-TYPE  363  118
        clus
vv       RCOR1 MUTATED RCOR1 WILD-TYPE
  COLON              3             363
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RCOR1 MUTATED         1        0        0         1         0         0
  RCOR1 WILD-TYPE      90        1       32       137        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RCOR1 MUTATED           0          0          1          0        0         0
  RCOR1 WILD-TYPE        24         11         58         42       48        18
                 vv
clus              STAGE IVB
  RCOR1 MUTATED           0
  RCOR1 WILD-TYPE         1
D1718V4, multiclass
            clus
vv           RCOR1 MUTATED RCOR1 WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              1             137
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  RCOR1 MUTATED     0   1   3   0
  RCOR1 WILD-TYPE  17  91 326  50
D1718V5, multiclass
    clus
vv   RCOR1 MUTATED RCOR1 WILD-TYPE
  T1             0              17
  T2             1              91
  T3             3             326
  T4             0              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  RCOR1 MUTATED     2   2   0
  RCOR1 WILD-TYPE 285 111  87
D1718V6, multiclass
    clus
vv   RCOR1 MUTATED RCOR1 WILD-TYPE
  N0             2             285
  N1             2             111
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1718V7, binary
                 cls
clus                0   1
  RCOR1 MUTATED     3   0
  RCOR1 WILD-TYPE 372  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RCOR1 MUTATED      3    0
  RCOR1 WILD-TYPE  372   65
   clus
vv  RCOR1 MUTATED RCOR1 WILD-TYPE
  0             3             372
  1             0              65
[1] 2 2
[1] FALSE
D1718V8, binary
                 cls
clus                0   1
  RCOR1 MUTATED     0   4
  RCOR1 WILD-TYPE 225 260
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RCOR1 MUTATED      0    4
  RCOR1 WILD-TYPE  225  260
        clus
vv       RCOR1 MUTATED RCOR1 WILD-TYPE
  FEMALE             0             225
  MALE               4             260
[1] 2 2
[1] FALSE
D1718V9, binary
                 cls
clus                0   1
  RCOR1 MUTATED     1   0
  RCOR1 WILD-TYPE 349  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RCOR1 MUTATED      1    0
  RCOR1 WILD-TYPE  349   22
     clus
vv    RCOR1 MUTATED RCOR1 WILD-TYPE
  NO              1             349
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  RCOR1 MUTATED                      2                             0
  RCOR1 WILD-TYPE                  313                            47
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  RCOR1 MUTATED                       1                              0
  RCOR1 WILD-TYPE                   105                             10
D1718V10, multiclass
                                clus
vv                               RCOR1 MUTATED RCOR1 WILD-TYPE
  COLON ADENOCARCINOMA                       2             313
  COLON MUCINOUS ADENOCARCINOMA              0              47
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  RCOR1 MUTATED     1   0   0   0
  RCOR1 WILD-TYPE 344   4  31  25
D1718V11, multiclass
[1] "Remove cluster labels:" "RCOR1 MUTATED"         
clus
  RCOR1 MUTATED RCOR1 WILD-TYPE 
              1             404 
     TCGA-A6-2671      TCGA-A6-2672      TCGA-A6-2674      TCGA-A6-2676 
"RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" 
     TCGA-A6-2677      TCGA-A6-2678      TCGA-A6-2683      TCGA-A6-3807 
"RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" 
     TCGA-A6-3808      TCGA-A6-3809      TCGA-A6-3810      TCGA-A6-5657 
"RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" 
     TCGA-A6-5659      TCGA-A6-5661      TCGA-A6-5665      TCGA-A6-6781 
"RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" 
     TCGA-AA-3489      TCGA-AA-3492      TCGA-AA-3496      TCGA-AA-3502 
"RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" 
     TCGA-AA-3510      TCGA-AA-3511      TCGA-AA-3514      TCGA-AA-3517 
"RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" 
     TCGA-AA-3518      TCGA-AA-3519      TCGA-AA-3520      TCGA-AA-3521 
"RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" 
     TCGA-AA-3522      TCGA-AA-3524      TCGA-AA-3525      TCGA-AA-3526 
"RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" 
     TCGA-AA-3527      TCGA-AA-3529      TCGA-AA-3530      TCGA-AA-3531 
"RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" 
     TCGA-AA-3532      TCGA-AA-3534      TCGA-AA-3538      TCGA-AA-3542 
"RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" 
     TCGA-AA-3543      TCGA-AA-3544      TCGA-AA-3548      TCGA-AA-3549 
"RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" 
     TCGA-AA-3552      TCGA-AA-3553      TCGA-AA-3554      TCGA-AA-3555 
"RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" 
     TCGA-AA-3556      TCGA-AA-3558      TCGA-AA-3560      TCGA-AA-3561 
"RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" 
     TCGA-AA-3562      TCGA-AA-3655      TCGA-AA-3660      TCGA-AA-3662 
"RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" 
     TCGA-AA-3663      TCGA-AA-3664      TCGA-AA-3666      TCGA-AA-3667 
"RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" 
     TCGA-AA-3672      TCGA-AA-3673      TCGA-AA-3678      TCGA-AA-3679 
"RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" 
     TCGA-AA-3680      TCGA-AA-3681      TCGA-AA-3684      TCGA-AA-3685 
"RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" 
     TCGA-AA-3688      TCGA-AA-3692      TCGA-AA-3693      TCGA-AA-3695 
"RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" 
     TCGA-AA-3696      TCGA-AA-3697      TCGA-AA-3710      TCGA-AA-3712 
"RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" 
     TCGA-AA-3713      TCGA-AA-3715      TCGA-AA-3811      TCGA-AA-3812 
"RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" 
     TCGA-AA-3814      TCGA-AA-3815      TCGA-AA-3818      TCGA-AA-3819 
"RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" 
     TCGA-AA-3821      TCGA-AA-3831      TCGA-AA-3833      TCGA-AA-3837 
"RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" 
     TCGA-AA-3842      TCGA-AA-3844      TCGA-AA-3845      TCGA-AA-3846 
"RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" 
     TCGA-AA-3848      TCGA-AA-3850      TCGA-AA-3851      TCGA-AA-3852 
"RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" 
     TCGA-AA-3854      TCGA-AA-3855      TCGA-AA-3856      TCGA-AA-3858 
"RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" 
     TCGA-AA-3860      TCGA-AA-3861      TCGA-AA-3864      TCGA-AA-3866 
"RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" 
     TCGA-AA-3867      TCGA-AA-3869      TCGA-AA-3870      TCGA-AA-3872 
"RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" 
     TCGA-AA-3875      TCGA-AA-3877      TCGA-AA-3930      TCGA-AA-3939 
"RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" 
     TCGA-AA-3941      TCGA-AA-3947      TCGA-AA-3949      TCGA-AA-3950 
"RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" 
     TCGA-AA-3952      TCGA-AA-3955      TCGA-AA-3956      TCGA-AA-3968 
"RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" 
     TCGA-AA-3971      TCGA-AA-3972      TCGA-AA-3973      TCGA-AA-3975 
"RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" 
     TCGA-AA-3976      TCGA-AA-3979      TCGA-AA-3984      TCGA-AA-3986 
"RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" 
     TCGA-AA-3989      TCGA-AA-3994      TCGA-AA-A004      TCGA-AA-A00A 
"RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" 
     TCGA-AA-A00D      TCGA-AA-A00E      TCGA-AA-A00F      TCGA-AA-A00J 
"RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" 
     TCGA-AA-A00K      TCGA-AA-A00L      TCGA-AA-A00N      TCGA-AA-A00O 
"RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" 
     TCGA-AA-A00Q      TCGA-AA-A00R      TCGA-AA-A00U      TCGA-AA-A00W 
"RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" 
     TCGA-AA-A00Z      TCGA-AA-A010      TCGA-AA-A017      TCGA-AA-A01D 
"RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" 
     TCGA-AA-A01F      TCGA-AA-A01G      TCGA-AA-A01I      TCGA-AA-A01K 
"RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" 
     TCGA-AA-A01P      TCGA-AA-A01Q      TCGA-AA-A01R      TCGA-AA-A01S 
"RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" 
     TCGA-AA-A01T      TCGA-AA-A01V      TCGA-AA-A01X      TCGA-AA-A01Z 
"RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" 
     TCGA-AA-A022      TCGA-AA-A024      TCGA-AA-A029      TCGA-AA-A02F 
"RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" 
     TCGA-AA-A02H      TCGA-AA-A02J      TCGA-AA-A02K      TCGA-AA-A02O 
"RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" 
     TCGA-AA-A02W      TCGA-AA-A02Y      TCGA-AA-A03F      TCGA-AA-A03J 
"RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" 
     TCGA-AD-5900      TCGA-AD-6548      TCGA-AD-6888      TCGA-AU-3779 
"RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" 
     TCGA-AU-6004      TCGA-AY-4070      TCGA-AY-4071      TCGA-AY-5543 
"RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" 
     TCGA-AY-6196      TCGA-AY-6197      TCGA-AY-6386      TCGA-AZ-4315 
"RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" 
     TCGA-AZ-4681      TCGA-AZ-4682      TCGA-CA-5254      TCGA-CA-5255 
"RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" 
     TCGA-CA-5796      TCGA-CA-5797      TCGA-CA-6715      TCGA-CA-6716 
"RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" 
     TCGA-CA-6717      TCGA-CA-6718      TCGA-CA-6719      TCGA-CK-4947 
"RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" 
     TCGA-CK-4948      TCGA-CK-4950      TCGA-CK-4952      TCGA-CK-5912 
"RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" 
     TCGA-CK-5913      TCGA-CK-5914      TCGA-CK-5915      TCGA-CK-5916 
"RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" 
     TCGA-CK-6746      TCGA-CK-6747      TCGA-CK-6748      TCGA-CK-6751 
"RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" 
     TCGA-CM-4743      TCGA-CM-4744      TCGA-CM-4746      TCGA-CM-4747 
"RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" 
     TCGA-CM-4752      TCGA-CM-5341      TCGA-CM-5344      TCGA-CM-5348 
"RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" 
     TCGA-CM-5349      TCGA-CM-5860      TCGA-CM-5861      TCGA-CM-5862 
"RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" 
     TCGA-CM-5863      TCGA-CM-5864      TCGA-CM-5868      TCGA-CM-6161 
"RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" 
     TCGA-CM-6162      TCGA-CM-6163      TCGA-CM-6164      TCGA-CM-6165 
"RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" 
     TCGA-CM-6166      TCGA-CM-6167      TCGA-CM-6168      TCGA-CM-6169 
"RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" 
     TCGA-CM-6170      TCGA-CM-6171      TCGA-CM-6172      TCGA-CM-6674 
"RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" 
     TCGA-CM-6675      TCGA-CM-6676      TCGA-CM-6677      TCGA-CM-6678 
"RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" 
     TCGA-CM-6679      TCGA-CM-6680      TCGA-D5-5537      TCGA-D5-5538 
"RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" 
     TCGA-D5-5539      TCGA-D5-5540      TCGA-D5-5541      TCGA-D5-6529 
"RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" 
     TCGA-D5-6532      TCGA-D5-6533      TCGA-D5-6534      TCGA-D5-6535 
"RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" 
     TCGA-D5-6536      TCGA-D5-6537      TCGA-D5-6538      TCGA-D5-6539 
"RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" 
     TCGA-D5-6540      TCGA-D5-6541      TCGA-D5-6898      TCGA-D5-6920 
"RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" 
     TCGA-D5-6922      TCGA-D5-6923      TCGA-D5-6924      TCGA-D5-6926 
"RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" 
     TCGA-D5-6927      TCGA-D5-6928      TCGA-D5-6929      TCGA-D5-6930 
"RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" 
     TCGA-D5-6931      TCGA-D5-6932      TCGA-D5-7000      TCGA-F4-6459 
"RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" 
     TCGA-F4-6460      TCGA-F4-6569      TCGA-F4-6570      TCGA-F4-6703 
"RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" 
     TCGA-F4-6704      TCGA-F4-6805      TCGA-F4-6806      TCGA-F4-6807 
"RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" 
     TCGA-F4-6808      TCGA-F4-6809      TCGA-F4-6854      TCGA-F4-6855 
"RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" 
     TCGA-F4-6856      TCGA-G4-6293      TCGA-G4-6299      TCGA-G4-6303 
"RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" 
     TCGA-G4-6304      TCGA-G4-6306      TCGA-G4-6307      TCGA-G4-6309 
"RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" 
     TCGA-G4-6310      TCGA-G4-6315      TCGA-G4-6317      TCGA-G4-6321 
"RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" 
     TCGA-G4-6323      TCGA-G4-6586      TCGA-G4-6588      TCGA-G4-6625 
"RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" 
     TCGA-G4-6626      TCGA-G4-6628      TCGA-AF-2687      TCGA-AF-2689 
"RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" 
     TCGA-AF-2691      TCGA-AF-2692      TCGA-AF-3400      TCGA-AF-3913 
"RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" 
     TCGA-AF-4110      TCGA-AF-5654      TCGA-AF-6655      TCGA-AG-3574 
"RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" 
     TCGA-AG-3575      TCGA-AG-3578      TCGA-AG-3580      TCGA-AG-3581 
"RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" 
     TCGA-AG-3582      TCGA-AG-3583      TCGA-AG-3584      TCGA-AG-3586 
"RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" 
     TCGA-AG-3587      TCGA-AG-3593      TCGA-AG-3594      TCGA-AG-3598 
"RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" 
     TCGA-AG-3599      TCGA-AG-3600      TCGA-AG-3601      TCGA-AG-3602 
"RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" 
     TCGA-AG-3605      TCGA-AG-3608      TCGA-AG-3609      TCGA-AG-3611 
"RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" 
     TCGA-AG-3612      TCGA-AG-3726      TCGA-AG-3727      TCGA-AG-3731 
"RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" 
     TCGA-AG-3732      TCGA-AG-3742      TCGA-AG-3878      TCGA-AG-3882 
"RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" 
     TCGA-AG-3883      TCGA-AG-3885      TCGA-AG-3887      TCGA-AG-3890 
"RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" 
     TCGA-AG-3892      TCGA-AG-3893      TCGA-AG-3894      TCGA-AG-3896 
"RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" 
     TCGA-AG-3898      TCGA-AG-3901      TCGA-AG-3902      TCGA-AG-3909 
"RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" 
     TCGA-AG-3999      TCGA-AG-4001      TCGA-AG-4005      TCGA-AG-4007 
"RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" 
     TCGA-AG-4008      TCGA-AG-4015      TCGA-AG-A008      TCGA-AG-A00C 
"RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" 
     TCGA-AG-A00H      TCGA-AG-A00Y      TCGA-AG-A011      TCGA-AG-A014 
"RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" 
     TCGA-AG-A015      TCGA-AG-A016      TCGA-AG-A01L      TCGA-AG-A01W 
"RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" 
     TCGA-AG-A01Y      TCGA-AG-A020      TCGA-AG-A025      TCGA-AG-A026 
"RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" 
     TCGA-AG-A02G      TCGA-AG-A02N      TCGA-AG-A02X      TCGA-AG-A032 
"RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" 
     TCGA-AG-A036      TCGA-AH-6549      TCGA-AH-6643      TCGA-CL-5917 
"RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" 
     TCGA-CL-5918      TCGA-DC-5337      TCGA-DC-5869      TCGA-DC-6155 
"RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" 
     TCGA-DC-6157      TCGA-DC-6158      TCGA-DC-6160      TCGA-DC-6681 
"RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" 
     TCGA-DC-6682      TCGA-DC-6683      TCGA-DT-5265      TCGA-EF-5830 
"RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" 
     TCGA-EI-6506      TCGA-EI-6507      TCGA-EI-6508      TCGA-EI-6510 
"RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" 
     TCGA-F5-6464      TCGA-F5-6465      TCGA-F5-6571      TCGA-F5-6702 
"RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" 
     TCGA-F5-6812      TCGA-F5-6813      TCGA-G5-6235      TCGA-G5-6641 
"RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" "RCOR1 WILD-TYPE" 
D1718V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RCOR1 MUTATED                                  0     0
  RCOR1 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  RCOR1 MUTATED                           0     3
  RCOR1 WILD-TYPE                        22   223
D1718V13, multiclass
                                  clus
vv                                 RCOR1 MUTATED RCOR1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        3             223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1719) Variable = ZNF286B MUTATION ANALYSIS
D1719V1, survival
                   sevent
clus2                 0   1
  ZNF286B MUTATED     4   1
  ZNF286B WILD-TYPE 374  92
  ZNF286B MUTATED ZNF286B WILD-TYPE 
                5               466 
  ZNF286B MUTATED ZNF286B WILD-TYPE 
                1                92 
$`ZNF286B MUTATED`
TCGA-A6-5662 TCGA-AA-3510 TCGA-AZ-4315 TCGA-CA-6717 TCGA-F4-6570 
       23.61        63.98        58.39        12.76         6.18 

$`ZNF286B WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        33.53        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       33.01        21.44        17.82         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 
       98.24         8.61        31.96        35.74        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  ZNF286B MUTATED ZNF286B WILD-TYPE 
             6.18              0.00 
  ZNF286B MUTATED ZNF286B WILD-TYPE 
            63.98            148.01 
  ZNF286B MUTATED ZNF286B WILD-TYPE 
           23.610            20.155 
[1] "6.2 - 64.0 (23.6)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.4"
D1719V2, continuous
D1719V3, binary
                   cls
clus                  0   1
  ZNF286B MUTATED     5   0
  ZNF286B WILD-TYPE 361 119
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZNF286B MUTATED      5    0
  ZNF286B WILD-TYPE  361  119
        clus
vv       ZNF286B MUTATED ZNF286B WILD-TYPE
  COLON                5               361
  RECTUM               0               119
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZNF286B MUTATED         0        0        1         3         0         0
  ZNF286B WILD-TYPE      91        1       31       135        10         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF286B MUTATED           0          0          0          0        0
  ZNF286B WILD-TYPE        24         11         59         42       48
                   vv
clus                STAGE IVA STAGE IVB
  ZNF286B MUTATED           1         0
  ZNF286B WILD-TYPE        17         1
D1719V4, multiclass
            clus
vv           ZNF286B MUTATED ZNF286B WILD-TYPE
  STAGE I                  0                91
  STAGE IA                 0                 1
  STAGE II                 1                31
  STAGE IIA                3               135
  STAGE IIB                0                10
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               0                11
  STAGE IIIB               0                59
  STAGE IIIC               0                42
  STAGE IV                 0                48
  STAGE IVA                1                17
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  ZNF286B MUTATED     0   0   5   0
  ZNF286B WILD-TYPE  17  92 324  50
D1719V5, multiclass
    clus
vv   ZNF286B MUTATED ZNF286B WILD-TYPE
  T1               0                17
  T2               0                92
  T3               5               324
  T4               0                50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  ZNF286B MUTATED     4   0   1
  ZNF286B WILD-TYPE 283 113  86
D1719V6, multiclass
    clus
vv   ZNF286B MUTATED ZNF286B WILD-TYPE
  N0               4               283
  N1               0               113
  N2               1                86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1719V7, binary
                   cls
clus                  0   1
  ZNF286B MUTATED     4   1
  ZNF286B WILD-TYPE 371  64
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZNF286B MUTATED      4    1
  ZNF286B WILD-TYPE  371   64
   clus
vv  ZNF286B MUTATED ZNF286B WILD-TYPE
  0               4               371
  1               1                64
[1] 2 2
[1] FALSE
D1719V8, binary
                   cls
clus                  0   1
  ZNF286B MUTATED     1   4
  ZNF286B WILD-TYPE 224 260
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZNF286B MUTATED      1    4
  ZNF286B WILD-TYPE  224  260
        clus
vv       ZNF286B MUTATED ZNF286B WILD-TYPE
  FEMALE               1               224
  MALE                 4               260
[1] 2 2
[1] FALSE
D1719V9, binary
                   cls
clus                  0   1
  ZNF286B MUTATED     5   0
  ZNF286B WILD-TYPE 345  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZNF286B MUTATED      5    0
  ZNF286B WILD-TYPE  345   22
     clus
vv    ZNF286B MUTATED ZNF286B WILD-TYPE
  NO                5               345
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ZNF286B MUTATED                      4                             1
  ZNF286B WILD-TYPE                  311                            46
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ZNF286B MUTATED                       0                              0
  ZNF286B WILD-TYPE                   106                             10
D1719V10, multiclass
                                clus
vv                               ZNF286B MUTATED ZNF286B WILD-TYPE
  COLON ADENOCARCINOMA                         4               311
  COLON MUCINOUS ADENOCARCINOMA                1                46
  RECTAL ADENOCARCINOMA                        0               106
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  ZNF286B MUTATED     3   0   0   1
  ZNF286B WILD-TYPE 342   4  31  24
D1719V11, multiclass
    clus
vv   ZNF286B MUTATED ZNF286B WILD-TYPE
  R0               3               342
  R1               0                 4
  R2               0                31
  RX               1                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1719V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF286B MUTATED                                  0     1
  ZNF286B WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  ZNF286B MUTATED                           0     3
  ZNF286B WILD-TYPE                        22   223
D1719V13, multiclass
                                  clus
vv                                 ZNF286B MUTATED ZNF286B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                10
  BLACK OR AFRICAN AMERICAN                      0                22
  WHITE                                          3               223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1720) Variable = SPATA16 MUTATION ANALYSIS
D1720V1, survival
                   sevent
clus2                 0   1
  SPATA16 MUTATED     8   4
  SPATA16 WILD-TYPE 370  89
  SPATA16 MUTATED SPATA16 WILD-TYPE 
               12               459 
  SPATA16 MUTATED SPATA16 WILD-TYPE 
                4                89 
$`SPATA16 MUTATED`
TCGA-A6-2676 TCGA-A6-3807 TCGA-A6-6651 TCGA-AA-3518 TCGA-AA-3845 TCGA-AA-3966 
       42.90        34.65        21.76         1.02         0.00         2.01 
TCGA-AA-A00N TCGA-AA-A01I TCGA-AD-6889 TCGA-CA-6717 TCGA-DM-A1DB TCGA-G4-6309 
        4.01        31.00        56.55        12.76        44.32        85.48 

$`SPATA16 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5657 
       33.34        32.75        36.53        14.53        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       30.44        29.19        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       24.16        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3520 
        6.97         1.02        13.02        38.99         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02        14.93        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 
       26.01        24.00         2.01        20.98        34.03        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       12.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
      140.38         7.50       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       44.68        55.04        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  SPATA16 MUTATED SPATA16 WILD-TYPE 
                0                 0 
  SPATA16 MUTATED SPATA16 WILD-TYPE 
            85.48            148.01 
  SPATA16 MUTATED SPATA16 WILD-TYPE 
            26.38             20.12 
[1] "0.0 - 85.5 (26.4)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.6"
D1720V2, continuous
D1720V3, binary
                   cls
clus                  0   1
  SPATA16 MUTATED    12   0
  SPATA16 WILD-TYPE 354 119
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SPATA16 MUTATED     12    0
  SPATA16 WILD-TYPE  354  119
        clus
vv       SPATA16 MUTATED SPATA16 WILD-TYPE
  COLON               12               354
  RECTUM               0               119
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SPATA16 MUTATED         1        0        0         6         2         0
  SPATA16 WILD-TYPE      90        1       32       132         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SPATA16 MUTATED           0          0          2          1        0
  SPATA16 WILD-TYPE        24         11         57         41       48
                   vv
clus                STAGE IVA STAGE IVB
  SPATA16 MUTATED           0         0
  SPATA16 WILD-TYPE        18         1
D1720V4, multiclass
            clus
vv           SPATA16 MUTATED SPATA16 WILD-TYPE
  STAGE I                  1                90
  STAGE IA                 0                 1
  STAGE II                 0                32
  STAGE IIA                6               132
  STAGE IIB                2                 8
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               0                11
  STAGE IIIB               2                57
  STAGE IIIC               1                41
  STAGE IV                 0                48
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  SPATA16 MUTATED     0   1   9   2
  SPATA16 WILD-TYPE  17  91 320  48
D1720V5, multiclass
    clus
vv   SPATA16 MUTATED SPATA16 WILD-TYPE
  T1               0                17
  T2               1                91
  T3               9               320
  T4               2                48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  SPATA16 MUTATED     9   2   1
  SPATA16 WILD-TYPE 278 111  86
D1720V6, multiclass
    clus
vv   SPATA16 MUTATED SPATA16 WILD-TYPE
  N0               9               278
  N1               2               111
  N2               1                86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1720V7, binary
                   cls
clus                  0   1
  SPATA16 MUTATED    11   0
  SPATA16 WILD-TYPE 364  65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SPATA16 MUTATED     11    0
  SPATA16 WILD-TYPE  364   65
   clus
vv  SPATA16 MUTATED SPATA16 WILD-TYPE
  0              11               364
  1               0                65
[1] 2 2
[1] FALSE
D1720V8, binary
                   cls
clus                  0   1
  SPATA16 MUTATED     7   5
  SPATA16 WILD-TYPE 218 259
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SPATA16 MUTATED      7    5
  SPATA16 WILD-TYPE  218  259
        clus
vv       SPATA16 MUTATED SPATA16 WILD-TYPE
  FEMALE               7               218
  MALE                 5               259
[1] 2 2
[1] FALSE
D1720V9, binary
                   cls
clus                  0   1
  SPATA16 MUTATED     6   0
  SPATA16 WILD-TYPE 344  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SPATA16 MUTATED      6    0
  SPATA16 WILD-TYPE  344   22
     clus
vv    SPATA16 MUTATED SPATA16 WILD-TYPE
  NO                6               344
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SPATA16 MUTATED                      9                             3
  SPATA16 WILD-TYPE                  306                            44
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SPATA16 MUTATED                       0                              0
  SPATA16 WILD-TYPE                   106                             10
D1720V10, multiclass
                                clus
vv                               SPATA16 MUTATED SPATA16 WILD-TYPE
  COLON ADENOCARCINOMA                         9               306
  COLON MUCINOUS ADENOCARCINOMA                3                44
  RECTAL ADENOCARCINOMA                        0               106
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  SPATA16 MUTATED     7   0   0   1
  SPATA16 WILD-TYPE 338   4  31  24
D1720V11, multiclass
    clus
vv   SPATA16 MUTATED SPATA16 WILD-TYPE
  R0               7               338
  R1               0                 4
  R2               0                31
  RX               1                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1720V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SPATA16 MUTATED                                  0     2
  SPATA16 WILD-TYPE                                1     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  SPATA16 MUTATED                           1     4
  SPATA16 WILD-TYPE                        21   222
D1720V13, multiclass
                                  clus
vv                                 SPATA16 MUTATED SPATA16 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          2                 9
  BLACK OR AFRICAN AMERICAN                      1                21
  WHITE                                          4               222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1721) Variable = OR1L1 MUTATION ANALYSIS
D1721V1, survival
                 sevent
clus2               0   1
  OR1L1 MUTATED     4   3
  OR1L1 WILD-TYPE 374  90
  OR1L1 MUTATED OR1L1 WILD-TYPE 
              7             464 
  OR1L1 MUTATED OR1L1 WILD-TYPE 
              3              90 
$`OR1L1 MUTATED`
TCGA-AA-3680 TCGA-AZ-6600 TCGA-CA-6717 TCGA-CK-6747 TCGA-D5-6922 TCGA-AF-6136 
       11.01        12.10        12.76        82.95         4.41        15.39 
TCGA-DY-A1DF 
       24.13 

$`OR1L1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       50.04        47.01        15.02         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.20        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6748 
       15.62        49.08        51.32         9.99        21.14         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6923 
       12.49        16.14        15.58         1.48         3.68        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 
       34.49        10.39        14.50        16.83        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DG TCGA-DY-A1H8 
        5.29       126.44        41.36        57.24        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  OR1L1 MUTATED OR1L1 WILD-TYPE 
           4.41            0.00 
  OR1L1 MUTATED OR1L1 WILD-TYPE 
          82.95          148.01 
  OR1L1 MUTATED OR1L1 WILD-TYPE 
         12.760          20.415 
[1] "4.4 - 83.0 (12.8)"  "0.0 - 148.0 (20.4)"
[1] "hr=" "2.4"
D1721V2, continuous
D1721V3, binary
                 cls
clus                0   1
  OR1L1 MUTATED     6   2
  OR1L1 WILD-TYPE 360 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR1L1 MUTATED      6    2
  OR1L1 WILD-TYPE  360  117
        clus
vv       OR1L1 MUTATED OR1L1 WILD-TYPE
  COLON              6             360
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  OR1L1 MUTATED         0        0        0         3         0         0
  OR1L1 WILD-TYPE      91        1       32       135        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  OR1L1 MUTATED           0          1          1          1        2         0
  OR1L1 WILD-TYPE        24         10         58         41       46        18
                 vv
clus              STAGE IVB
  OR1L1 MUTATED           0
  OR1L1 WILD-TYPE         1
D1721V4, multiclass
            clus
vv           OR1L1 MUTATED OR1L1 WILD-TYPE
  STAGE I                0              91
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              3             135
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             1              10
  STAGE IIIB             1              58
  STAGE IIIC             1              41
  STAGE IV               2              46
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  OR1L1 MUTATED     0   0   6   2
  OR1L1 WILD-TYPE  17  92 323  48
D1721V5, multiclass
    clus
vv   OR1L1 MUTATED OR1L1 WILD-TYPE
  T1             0              17
  T2             0              92
  T3             6             323
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  OR1L1 MUTATED     3   3   2
  OR1L1 WILD-TYPE 284 110  85
D1721V6, multiclass
    clus
vv   OR1L1 MUTATED OR1L1 WILD-TYPE
  N0             3             284
  N1             3             110
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1721V7, binary
                 cls
clus                0   1
  OR1L1 MUTATED     4   2
  OR1L1 WILD-TYPE 371  63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR1L1 MUTATED      4    2
  OR1L1 WILD-TYPE  371   63
   clus
vv  OR1L1 MUTATED OR1L1 WILD-TYPE
  0             4             371
  1             2              63
[1] 2 2
[1] FALSE
D1721V8, binary
                 cls
clus                0   1
  OR1L1 MUTATED     5   3
  OR1L1 WILD-TYPE 220 261
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR1L1 MUTATED      5    3
  OR1L1 WILD-TYPE  220  261
        clus
vv       OR1L1 MUTATED OR1L1 WILD-TYPE
  FEMALE             5             220
  MALE               3             261
[1] 2 2
[1] FALSE
D1721V9, binary
                 cls
clus                0   1
  OR1L1 MUTATED     3   1
  OR1L1 WILD-TYPE 347  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR1L1 MUTATED      3    1
  OR1L1 WILD-TYPE  347   21
     clus
vv    OR1L1 MUTATED OR1L1 WILD-TYPE
  NO              3             347
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  OR1L1 MUTATED                      5                             1
  OR1L1 WILD-TYPE                  310                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  OR1L1 MUTATED                       2                              0
  OR1L1 WILD-TYPE                   104                             10
D1721V10, multiclass
                                clus
vv                               OR1L1 MUTATED OR1L1 WILD-TYPE
  COLON ADENOCARCINOMA                       5             310
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  OR1L1 MUTATED     2   0   1   2
  OR1L1 WILD-TYPE 343   4  30  23
D1721V11, multiclass
    clus
vv   OR1L1 MUTATED OR1L1 WILD-TYPE
  R0             2             343
  R1             0               4
  R2             1              30
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1721V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OR1L1 MUTATED                                  0     1
  OR1L1 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  OR1L1 MUTATED                           1     4
  OR1L1 WILD-TYPE                        21   222
D1721V13, multiclass
                                  clus
vv                                 OR1L1 MUTATED OR1L1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        4             222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1722) Variable = CCDC55 MUTATION ANALYSIS
D1722V1, survival
                  sevent
clus2                0   1
  CCDC55 MUTATED    10   1
  CCDC55 WILD-TYPE 368  92
  CCDC55 MUTATED CCDC55 WILD-TYPE 
              11              460 
  CCDC55 MUTATED CCDC55 WILD-TYPE 
               1               92 
$`CCDC55 MUTATED`
TCGA-A6-4105 TCGA-A6-5657 TCGA-A6-5665 TCGA-AA-3966 TCGA-AA-A00A TCGA-AD-6963 
       14.53        31.63        22.06         2.01        38.04        27.42 
TCGA-AZ-4315 TCGA-CA-6717 TCGA-CM-4743 TCGA-DM-A28K TCGA-G4-6309 
       58.39        12.76        23.05        98.24        85.48 

$`CCDC55 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 
       16.57        34.65        33.34        32.75        36.53        32.91 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 
       30.44        29.19        33.53        23.61        22.09        32.71 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       27.09        22.52         8.38        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
       34.03        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
        7.96        27.02        13.94        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
       16.31         0.95        33.01        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07        12.20        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
       82.95         1.91       124.27        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
      117.07         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       53.62        44.68        55.04        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  CCDC55 MUTATED CCDC55 WILD-TYPE 
            2.01             0.00 
  CCDC55 MUTATED CCDC55 WILD-TYPE 
           98.24           148.01 
  CCDC55 MUTATED CCDC55 WILD-TYPE 
          27.420           20.035 
[1] "2.0 - 98.2 (27.4)"  "0.0 - 148.0 (20.0)"
[1] "hr=" "3.1"
D1722V2, continuous
D1722V3, binary
                  cls
clus                 0   1
  CCDC55 MUTATED    13   0
  CCDC55 WILD-TYPE 353 119
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC55 MUTATED     13    0
  CCDC55 WILD-TYPE  353  119
        clus
vv       CCDC55 MUTATED CCDC55 WILD-TYPE
  COLON              13              353
  RECTUM              0              119
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CCDC55 MUTATED         1        0        0         8         1         0
  CCDC55 WILD-TYPE      90        1       32       130         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CCDC55 MUTATED           0          0          2          0        0
  CCDC55 WILD-TYPE        24         11         57         42       48
                  vv
clus               STAGE IVA STAGE IVB
  CCDC55 MUTATED           0         0
  CCDC55 WILD-TYPE        18         1
D1722V4, multiclass
            clus
vv           CCDC55 MUTATED CCDC55 WILD-TYPE
  STAGE I                 1               90
  STAGE IA                0                1
  STAGE II                0               32
  STAGE IIA               8              130
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              2               57
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  CCDC55 MUTATED     0   1  11   1
  CCDC55 WILD-TYPE  17  91 318  49
D1722V5, multiclass
    clus
vv   CCDC55 MUTATED CCDC55 WILD-TYPE
  T1              0               17
  T2              1               91
  T3             11              318
  T4              1               49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  CCDC55 MUTATED    11   2   0
  CCDC55 WILD-TYPE 276 111  87
D1722V6, multiclass
    clus
vv   CCDC55 MUTATED CCDC55 WILD-TYPE
  N0             11              276
  N1              2              111
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1722V7, binary
                  cls
clus                 0   1
  CCDC55 MUTATED    10   0
  CCDC55 WILD-TYPE 365  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC55 MUTATED     10    0
  CCDC55 WILD-TYPE  365   65
   clus
vv  CCDC55 MUTATED CCDC55 WILD-TYPE
  0             10              365
  1              0               65
[1] 2 2
[1] FALSE
D1722V8, binary
                  cls
clus                 0   1
  CCDC55 MUTATED     4   9
  CCDC55 WILD-TYPE 221 255
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC55 MUTATED      4    9
  CCDC55 WILD-TYPE  221  255
        clus
vv       CCDC55 MUTATED CCDC55 WILD-TYPE
  FEMALE              4              221
  MALE                9              255
[1] 2 2
[1] FALSE
D1722V9, binary
                  cls
clus                 0   1
  CCDC55 MUTATED     9   0
  CCDC55 WILD-TYPE 341  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC55 MUTATED      9    0
  CCDC55 WILD-TYPE  341   22
     clus
vv    CCDC55 MUTATED CCDC55 WILD-TYPE
  NO               9              341
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CCDC55 MUTATED                     10                             3
  CCDC55 WILD-TYPE                  305                            44
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CCDC55 MUTATED                       0                              0
  CCDC55 WILD-TYPE                   106                             10
D1722V10, multiclass
                                clus
vv                               CCDC55 MUTATED CCDC55 WILD-TYPE
  COLON ADENOCARCINOMA                       10              305
  COLON MUCINOUS ADENOCARCINOMA               3               44
  RECTAL ADENOCARCINOMA                       0              106
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  CCDC55 MUTATED     6   0   0   3
  CCDC55 WILD-TYPE 339   4  31  22
D1722V11, multiclass
    clus
vv   CCDC55 MUTATED CCDC55 WILD-TYPE
  R0              6              339
  R1              0                4
  R2              0               31
  RX              3               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1722V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CCDC55 MUTATED                                  0     1
  CCDC55 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  CCDC55 MUTATED                           2     8
  CCDC55 WILD-TYPE                        20   218
D1722V13, multiclass
                                  clus
vv                                 CCDC55 MUTATED CCDC55 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     2               20
  WHITE                                         8              218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1723) Variable = AASDH MUTATION ANALYSIS
D1723V1, survival
                 sevent
clus2               0   1
  AASDH MUTATED    15   5
  AASDH WILD-TYPE 363  88
  AASDH MUTATED AASDH WILD-TYPE 
             20             451 
  AASDH MUTATED AASDH WILD-TYPE 
              5              88 
$`AASDH MUTATED`
TCGA-A6-2683 TCGA-A6-5659 TCGA-A6-6653 TCGA-AA-3655 TCGA-AA-3977 TCGA-AA-A00N 
       16.57        30.44        24.39        61.02        25.02         4.01 
TCGA-AZ-4315 TCGA-AZ-5403 TCGA-CA-5254 TCGA-CA-5796 TCGA-CA-6717 TCGA-CK-5916 
       58.39        62.79        12.69         3.25        12.76        21.14 
TCGA-D5-5541 TCGA-F4-6807 TCGA-G4-6306 TCGA-AG-3731 TCGA-AG-A002 TCGA-AH-6643 
       55.92        16.24        44.68        37.02        20.98         0.69 
TCGA-DY-A1DD TCGA-F5-6813 
       57.24         0.69 

$`AASDH WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       31.63        29.19        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       24.16        21.76        24.69        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       19.99        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
       16.31         0.95        33.01        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
        5.13       106.75        22.36        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5255 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        1.61         3.06         3.29         0.07        12.20        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       51.32         9.99        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       56.09        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       74.56        65.85        53.62        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
        0.99        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
        1.45        17.49         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
        5.29       126.44        41.36        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-G5-6235 
       49.51        31.30        28.57        32.19         0.66        55.76 
TCGA-G5-6641 
       26.43 

  AASDH MUTATED AASDH WILD-TYPE 
           0.69            0.00 
  AASDH MUTATED AASDH WILD-TYPE 
          62.79          148.01 
  AASDH MUTATED AASDH WILD-TYPE 
         22.765          20.050 
[1] "0.7 - 62.8 (22.8)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.1"
D1723V2, continuous
D1723V3, binary
                 cls
clus                0   1
  AASDH MUTATED    16   5
  AASDH WILD-TYPE 350 114
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AASDH MUTATED     16    5
  AASDH WILD-TYPE  350  114
        clus
vv       AASDH MUTATED AASDH WILD-TYPE
  COLON             16             350
  RECTUM             5             114
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  AASDH MUTATED         4        0        2         5         1         0
  AASDH WILD-TYPE      87        1       30       133         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AASDH MUTATED           1          0          2          3        2         0
  AASDH WILD-TYPE        23         11         57         39       46        18
                 vv
clus              STAGE IVB
  AASDH MUTATED           0
  AASDH WILD-TYPE         1
D1723V4, multiclass
            clus
vv           AASDH MUTATED AASDH WILD-TYPE
  STAGE I                4              87
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA              5             133
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             2              57
  STAGE IIIC             3              39
  STAGE IV               2              46
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  AASDH MUTATED     1   5  12   3
  AASDH WILD-TYPE  16  87 317  47
D1723V5, multiclass
    clus
vv   AASDH MUTATED AASDH WILD-TYPE
  T1             1              16
  T2             5              87
  T3            12             317
  T4             3              47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  AASDH MUTATED    14   3   4
  AASDH WILD-TYPE 273 110  83
D1723V6, multiclass
    clus
vv   AASDH MUTATED AASDH WILD-TYPE
  N0            14             273
  N1             3             110
  N2             4              83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1723V7, binary
                 cls
clus                0   1
  AASDH MUTATED    17   2
  AASDH WILD-TYPE 358  63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AASDH MUTATED     17    2
  AASDH WILD-TYPE  358   63
   clus
vv  AASDH MUTATED AASDH WILD-TYPE
  0            17             358
  1             2              63
[1] 2 2
[1] FALSE
D1723V8, binary
                 cls
clus                0   1
  AASDH MUTATED     6  15
  AASDH WILD-TYPE 219 249
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AASDH MUTATED      6   15
  AASDH WILD-TYPE  219  249
        clus
vv       AASDH MUTATED AASDH WILD-TYPE
  FEMALE             6             219
  MALE              15             249
[1] 2 2
[1] FALSE
D1723V9, binary
                 cls
clus                0   1
  AASDH MUTATED    16   0
  AASDH WILD-TYPE 334  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AASDH MUTATED     16    0
  AASDH WILD-TYPE  334   22
     clus
vv    AASDH MUTATED AASDH WILD-TYPE
  NO             16             334
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  AASDH MUTATED                     13                             3
  AASDH WILD-TYPE                  302                            44
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  AASDH MUTATED                       5                              0
  AASDH WILD-TYPE                   101                             10
D1723V10, multiclass
                                clus
vv                               AASDH MUTATED AASDH WILD-TYPE
  COLON ADENOCARCINOMA                      13             302
  COLON MUCINOUS ADENOCARCINOMA              3              44
  RECTAL ADENOCARCINOMA                      5             101
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  AASDH MUTATED    13   0   1   3
  AASDH WILD-TYPE 332   4  30  22
D1723V11, multiclass
    clus
vv   AASDH MUTATED AASDH WILD-TYPE
  R0            13             332
  R1             0               4
  R2             1              30
  RX             3              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1723V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AASDH MUTATED                                  0     3
  AASDH WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  AASDH MUTATED                           0    12
  AASDH WILD-TYPE                        22   214
D1723V13, multiclass
                                  clus
vv                                 AASDH MUTATED AASDH WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        3               8
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                       12             214
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1724) Variable = CTSA MUTATION ANALYSIS
D1724V1, survival
                sevent
clus2              0   1
  CTSA MUTATED     6   0
  CTSA WILD-TYPE 372  93
  CTSA MUTATED CTSA WILD-TYPE 
             6            465 
  CTSA MUTATED CTSA WILD-TYPE 
             0             93 
$`CTSA MUTATED`
TCGA-A6-5661 TCGA-AA-3833 TCGA-AA-3858 TCGA-AA-A010 TCGA-D5-6928 TCGA-G4-6586 
       33.53        15.95        31.07        34.98        11.64        35.80 

$`CTSA WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       17.98        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
        0.99        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6930 
       12.43        14.30         9.04         9.44         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       22.09        13.78        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  CTSA MUTATED CTSA WILD-TYPE 
         11.64           0.00 
  CTSA MUTATED CTSA WILD-TYPE 
         35.80         148.01 
  CTSA MUTATED CTSA WILD-TYPE 
         32.30          20.12 
[1] "11.6 - 35.8 (32.3)" "0.0 - 148.0 (20.1)"
[1] "hr="     "9100000"
D1724V2, continuous
D1724V3, binary
                cls
clus               0   1
  CTSA MUTATED     6   0
  CTSA WILD-TYPE 360 119
[1] "tbl2"
                cls
clus             [,1] [,2]
  CTSA MUTATED      6    0
  CTSA WILD-TYPE  360  119
        clus
vv       CTSA MUTATED CTSA WILD-TYPE
  COLON             6            360
  RECTUM            0            119
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CTSA MUTATED         1        0        0         4         1         0
  CTSA WILD-TYPE      90        1       32       134         9         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CTSA MUTATED           0          0          0          0        0         0
  CTSA WILD-TYPE        24         11         59         42       48        18
                vv
clus             STAGE IVB
  CTSA MUTATED           0
  CTSA WILD-TYPE         1
D1724V4, multiclass
            clus
vv           CTSA MUTATED CTSA WILD-TYPE
  STAGE I               1             90
  STAGE IA              0              1
  STAGE II              0             32
  STAGE IIA             4            134
  STAGE IIB             1              9
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            0             59
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  CTSA MUTATED     0   1   4   1
  CTSA WILD-TYPE  17  91 325  49
D1724V5, multiclass
    clus
vv   CTSA MUTATED CTSA WILD-TYPE
  T1            0             17
  T2            1             91
  T3            4            325
  T4            1             49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  CTSA MUTATED     6   0   0
  CTSA WILD-TYPE 281 113  87
D1724V6, multiclass
    clus
vv   CTSA MUTATED CTSA WILD-TYPE
  N0            6            281
  N1            0            113
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1724V7, binary
                cls
clus               0   1
  CTSA MUTATED     6   0
  CTSA WILD-TYPE 369  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  CTSA MUTATED      6    0
  CTSA WILD-TYPE  369   65
   clus
vv  CTSA MUTATED CTSA WILD-TYPE
  0            6            369
  1            0             65
[1] 2 2
[1] FALSE
D1724V8, binary
                cls
clus               0   1
  CTSA MUTATED     4   2
  CTSA WILD-TYPE 221 262
[1] "tbl2"
                cls
clus             [,1] [,2]
  CTSA MUTATED      4    2
  CTSA WILD-TYPE  221  262
        clus
vv       CTSA MUTATED CTSA WILD-TYPE
  FEMALE            4            221
  MALE              2            262
[1] 2 2
[1] FALSE
D1724V9, binary
                cls
clus               0   1
  CTSA MUTATED     6   0
  CTSA WILD-TYPE 344  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  CTSA MUTATED      6    0
  CTSA WILD-TYPE  344   22
     clus
vv    CTSA MUTATED CTSA WILD-TYPE
  NO             6            344
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CTSA MUTATED                      5                             1
  CTSA WILD-TYPE                  310                            46
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CTSA MUTATED                       0                              0
  CTSA WILD-TYPE                   106                             10
D1724V10, multiclass
                                clus
vv                               CTSA MUTATED CTSA WILD-TYPE
  COLON ADENOCARCINOMA                      5            310
  COLON MUCINOUS ADENOCARCINOMA             1             46
  RECTAL ADENOCARCINOMA                     0            106
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  CTSA MUTATED     6   0   0   0
  CTSA WILD-TYPE 339   4  31  25
D1724V11, multiclass
    clus
vv   CTSA MUTATED CTSA WILD-TYPE
  R0            6            339
  R1            0              4
  R2            0             31
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1724V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CTSA MUTATED                                  0     0
  CTSA WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  CTSA MUTATED                           1     2
  CTSA WILD-TYPE                        21   224
D1724V13, multiclass
                                  clus
vv                                 CTSA MUTATED CTSA WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                       2            224
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1725) Variable = ALAS1 MUTATION ANALYSIS
D1725V1, survival
                 sevent
clus2               0   1
  ALAS1 MUTATED     8   0
  ALAS1 WILD-TYPE 370  93
  ALAS1 MUTATED ALAS1 WILD-TYPE 
              8             463 
  ALAS1 MUTATED ALAS1 WILD-TYPE 
              0              93 
$`ALAS1 MUTATED`
TCGA-AA-3821 TCGA-AA-3977 TCGA-AA-A010 TCGA-CK-5913 TCGA-D5-5538 TCGA-D5-6930 
        1.02        25.02        34.98        51.32        12.26         1.51 
TCGA-G4-6588 TCGA-AG-A02N 
       26.17        61.97 

$`ALAS1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        49.08         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6931 
       14.30         9.04         9.44        11.64         4.80        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       13.78        35.80        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X 
       64.01        10.98        49.97         1.94        38.96        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  ALAS1 MUTATED ALAS1 WILD-TYPE 
           1.02            0.00 
  ALAS1 MUTATED ALAS1 WILD-TYPE 
          61.97          148.01 
  ALAS1 MUTATED ALAS1 WILD-TYPE 
         25.595          20.120 
[1] "1.0 - 62.0 (25.6)"  "0.0 - 148.0 (20.1)"
[1] "hr="     "9200000"
D1725V2, continuous
D1725V3, binary
                 cls
clus                0   1
  ALAS1 MUTATED     9   1
  ALAS1 WILD-TYPE 357 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ALAS1 MUTATED      9    1
  ALAS1 WILD-TYPE  357  118
        clus
vv       ALAS1 MUTATED ALAS1 WILD-TYPE
  COLON              9             357
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ALAS1 MUTATED         2        0        2         3         1         0
  ALAS1 WILD-TYPE      89        1       30       135         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ALAS1 MUTATED           0          0          1          0        0         0
  ALAS1 WILD-TYPE        24         11         58         42       48        18
                 vv
clus              STAGE IVB
  ALAS1 MUTATED           0
  ALAS1 WILD-TYPE         1
D1725V4, multiclass
            clus
vv           ALAS1 MUTATED ALAS1 WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA              3             135
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ALAS1 MUTATED     0   3   5   2
  ALAS1 WILD-TYPE  17  89 324  48
D1725V5, multiclass
    clus
vv   ALAS1 MUTATED ALAS1 WILD-TYPE
  T1             0              17
  T2             3              89
  T3             5             324
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  ALAS1 MUTATED     9   1   0
  ALAS1 WILD-TYPE 278 112  87
D1725V6, multiclass
    clus
vv   ALAS1 MUTATED ALAS1 WILD-TYPE
  N0             9             278
  N1             1             112
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1725V7, binary
                 cls
clus                0   1
  ALAS1 MUTATED     7   0
  ALAS1 WILD-TYPE 368  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ALAS1 MUTATED      7    0
  ALAS1 WILD-TYPE  368   65
   clus
vv  ALAS1 MUTATED ALAS1 WILD-TYPE
  0             7             368
  1             0              65
[1] 2 2
[1] FALSE
D1725V8, binary
                 cls
clus                0   1
  ALAS1 MUTATED     6   4
  ALAS1 WILD-TYPE 219 260
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ALAS1 MUTATED      6    4
  ALAS1 WILD-TYPE  219  260
        clus
vv       ALAS1 MUTATED ALAS1 WILD-TYPE
  FEMALE             6             219
  MALE               4             260
[1] 2 2
[1] FALSE
D1725V9, binary
                 cls
clus                0   1
  ALAS1 MUTATED     6   0
  ALAS1 WILD-TYPE 344  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ALAS1 MUTATED      6    0
  ALAS1 WILD-TYPE  344   22
     clus
vv    ALAS1 MUTATED ALAS1 WILD-TYPE
  NO              6             344
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ALAS1 MUTATED                      7                             2
  ALAS1 WILD-TYPE                  308                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ALAS1 MUTATED                       1                              0
  ALAS1 WILD-TYPE                   105                             10
D1725V10, multiclass
                                clus
vv                               ALAS1 MUTATED ALAS1 WILD-TYPE
  COLON ADENOCARCINOMA                       7             308
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  ALAS1 MUTATED     7   0   0   2
  ALAS1 WILD-TYPE 338   4  31  23
D1725V11, multiclass
    clus
vv   ALAS1 MUTATED ALAS1 WILD-TYPE
  R0             7             338
  R1             0               4
  R2             0              31
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1725V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ALAS1 MUTATED                                  0     0
  ALAS1 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ALAS1 MUTATED                           0     5
  ALAS1 WILD-TYPE                        22   221
D1725V13, multiclass
                                  clus
vv                                 ALAS1 MUTATED ALAS1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        5             221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1726) Variable = DDX55 MUTATION ANALYSIS
D1726V1, survival
                 sevent
clus2               0   1
  DDX55 MUTATED    10   1
  DDX55 WILD-TYPE 368  92
  DDX55 MUTATED DDX55 WILD-TYPE 
             11             460 
  DDX55 MUTATED DDX55 WILD-TYPE 
              1              92 
$`DDX55 MUTATED`
TCGA-A6-5665 TCGA-AA-3531 TCGA-AA-3864 TCGA-AA-3950 TCGA-AD-6895 TCGA-AZ-6598 
       22.06        34.03        53.00        24.00         0.72        49.41 
TCGA-CA-6717 TCGA-CM-6169 TCGA-D5-6929 TCGA-DM-A1HB TCGA-AG-A02N 
       12.76        13.02         4.80       135.65        61.97 

$`DDX55 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
       19.07         0.00        19.07        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 
        0.99        31.07        31.07        30.05        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        33.01        26.01         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       88.21         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07        12.20        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       21.99        14.99        12.99        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       11.64         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 
       12.59       140.38         7.50        44.32       131.51       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
        1.94        38.96        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  DDX55 MUTATED DDX55 WILD-TYPE 
           0.72            0.00 
  DDX55 MUTATED DDX55 WILD-TYPE 
         135.65          148.01 
  DDX55 MUTATED DDX55 WILD-TYPE 
         24.000          20.085 
[1] "0.7 - 135.7 (24.0)" "0.0 - 148.0 (20.1)"
[1] "hr=" "3"  
D1726V2, continuous
D1726V3, binary
                 cls
clus                0   1
  DDX55 MUTATED    10   1
  DDX55 WILD-TYPE 356 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX55 MUTATED     10    1
  DDX55 WILD-TYPE  356  118
        clus
vv       DDX55 MUTATED DDX55 WILD-TYPE
  COLON             10             356
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DDX55 MUTATED         0        0        3         5         0         0
  DDX55 WILD-TYPE      91        1       29       133        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DDX55 MUTATED           0          0          1          0        1         0
  DDX55 WILD-TYPE        24         11         58         42       47        18
                 vv
clus              STAGE IVB
  DDX55 MUTATED           0
  DDX55 WILD-TYPE         1
D1726V4, multiclass
            clus
vv           DDX55 MUTATED DDX55 WILD-TYPE
  STAGE I                0              91
  STAGE IA               0               1
  STAGE II               3              29
  STAGE IIA              5             133
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             0              42
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  DDX55 MUTATED     0   0  11   0
  DDX55 WILD-TYPE  17  92 318  50
D1726V5, multiclass
    clus
vv   DDX55 MUTATED DDX55 WILD-TYPE
  T1             0              17
  T2             0              92
  T3            11             318
  T4             0              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  DDX55 MUTATED     8   3   0
  DDX55 WILD-TYPE 279 110  87
D1726V6, multiclass
    clus
vv   DDX55 MUTATED DDX55 WILD-TYPE
  N0             8             279
  N1             3             110
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1726V7, binary
                 cls
clus                0   1
  DDX55 MUTATED     8   1
  DDX55 WILD-TYPE 367  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX55 MUTATED      8    1
  DDX55 WILD-TYPE  367   64
   clus
vv  DDX55 MUTATED DDX55 WILD-TYPE
  0             8             367
  1             1              64
[1] 2 2
[1] FALSE
D1726V8, binary
                 cls
clus                0   1
  DDX55 MUTATED     5   6
  DDX55 WILD-TYPE 220 258
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX55 MUTATED      5    6
  DDX55 WILD-TYPE  220  258
        clus
vv       DDX55 MUTATED DDX55 WILD-TYPE
  FEMALE             5             220
  MALE               6             258
[1] 2 2
[1] FALSE
D1726V9, binary
                 cls
clus                0   1
  DDX55 MUTATED     7   0
  DDX55 WILD-TYPE 343  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX55 MUTATED      7    0
  DDX55 WILD-TYPE  343   22
     clus
vv    DDX55 MUTATED DDX55 WILD-TYPE
  NO              7             343
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  DDX55 MUTATED                      7                             2
  DDX55 WILD-TYPE                  308                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  DDX55 MUTATED                       1                              0
  DDX55 WILD-TYPE                   105                             10
D1726V10, multiclass
                                clus
vv                               DDX55 MUTATED DDX55 WILD-TYPE
  COLON ADENOCARCINOMA                       7             308
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  DDX55 MUTATED     7   0   0   1
  DDX55 WILD-TYPE 338   4  31  24
D1726V11, multiclass
    clus
vv   DDX55 MUTATED DDX55 WILD-TYPE
  R0             7             338
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1726V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DDX55 MUTATED                                  0     1
  DDX55 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  DDX55 MUTATED                           1     5
  DDX55 WILD-TYPE                        21   221
D1726V13, multiclass
                                  clus
vv                                 DDX55 MUTATED DDX55 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        5             221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1727) Variable = SFRP2 MUTATION ANALYSIS
D1727V1, survival
                 sevent
clus2               0   1
  SFRP2 MUTATED     8   1
  SFRP2 WILD-TYPE 370  92
  SFRP2 MUTATED SFRP2 WILD-TYPE 
              9             462 
  SFRP2 MUTATED SFRP2 WILD-TYPE 
              1              92 
$`SFRP2 MUTATED`
TCGA-A6-3810 TCGA-AA-3697 TCGA-AD-6963 TCGA-AZ-6601 TCGA-CK-4947 TCGA-CM-4743 
       36.53        85.05        27.42       100.01        17.56        23.05 
TCGA-D5-6930 TCGA-F4-6854 TCGA-AG-A002 
        1.51         0.53        20.98 

$`SFRP2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        32.75        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6964 
       56.55         0.79         0.72         5.79        22.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       10.06        14.30       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 
        9.04         9.44        11.64         4.80        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       16.24        33.67        13.25        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  SFRP2 MUTATED SFRP2 WILD-TYPE 
           0.53            0.00 
  SFRP2 MUTATED SFRP2 WILD-TYPE 
         100.01          148.01 
  SFRP2 MUTATED SFRP2 WILD-TYPE 
         23.050          20.085 
[1] "0.5 - 100.0 (23.1)" "0.0 - 148.0 (20.1)"
[1] "hr=" "2.3"
D1727V2, continuous
D1727V3, binary
                 cls
clus                0   1
  SFRP2 MUTATED     8   2
  SFRP2 WILD-TYPE 358 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SFRP2 MUTATED      8    2
  SFRP2 WILD-TYPE  358  117
        clus
vv       SFRP2 MUTATED SFRP2 WILD-TYPE
  COLON              8             358
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SFRP2 MUTATED         1        0        1         4         0         0
  SFRP2 WILD-TYPE      90        1       31       134        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SFRP2 MUTATED           1          0          2          0        0         0
  SFRP2 WILD-TYPE        23         11         57         42       48        18
                 vv
clus              STAGE IVB
  SFRP2 MUTATED           0
  SFRP2 WILD-TYPE         1
D1727V4, multiclass
            clus
vv           SFRP2 MUTATED SFRP2 WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              4             134
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             2              57
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  SFRP2 MUTATED     0   1   7   2
  SFRP2 WILD-TYPE  17  91 322  48
D1727V5, multiclass
    clus
vv   SFRP2 MUTATED SFRP2 WILD-TYPE
  T1             0              17
  T2             1              91
  T3             7             322
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  SFRP2 MUTATED     8   2   0
  SFRP2 WILD-TYPE 279 111  87
D1727V6, multiclass
    clus
vv   SFRP2 MUTATED SFRP2 WILD-TYPE
  N0             8             279
  N1             2             111
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1727V7, binary
                 cls
clus                0   1
  SFRP2 MUTATED     9   0
  SFRP2 WILD-TYPE 366  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SFRP2 MUTATED      9    0
  SFRP2 WILD-TYPE  366   65
   clus
vv  SFRP2 MUTATED SFRP2 WILD-TYPE
  0             9             366
  1             0              65
[1] 2 2
[1] FALSE
D1727V8, binary
                 cls
clus                0   1
  SFRP2 MUTATED     2   8
  SFRP2 WILD-TYPE 223 256
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SFRP2 MUTATED      2    8
  SFRP2 WILD-TYPE  223  256
        clus
vv       SFRP2 MUTATED SFRP2 WILD-TYPE
  FEMALE             2             223
  MALE               8             256
[1] 2 2
[1] FALSE
D1727V9, binary
                 cls
clus                0   1
  SFRP2 MUTATED     8   0
  SFRP2 WILD-TYPE 342  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SFRP2 MUTATED      8    0
  SFRP2 WILD-TYPE  342   22
     clus
vv    SFRP2 MUTATED SFRP2 WILD-TYPE
  NO              8             342
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SFRP2 MUTATED                      7                             1
  SFRP2 WILD-TYPE                  308                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SFRP2 MUTATED                       2                              0
  SFRP2 WILD-TYPE                   104                             10
D1727V10, multiclass
                                clus
vv                               SFRP2 MUTATED SFRP2 WILD-TYPE
  COLON ADENOCARCINOMA                       7             308
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  SFRP2 MUTATED     6   0   1   1
  SFRP2 WILD-TYPE 339   4  30  24
D1727V11, multiclass
    clus
vv   SFRP2 MUTATED SFRP2 WILD-TYPE
  R0             6             339
  R1             0               4
  R2             1              30
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1727V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SFRP2 MUTATED                                  0     0
  SFRP2 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  SFRP2 MUTATED                           0     7
  SFRP2 WILD-TYPE                        22   219
D1727V13, multiclass
                                  clus
vv                                 SFRP2 MUTATED SFRP2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        7             219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1728) Variable = IGSF5 MUTATION ANALYSIS
D1728V1, survival
                 sevent
clus2               0   1
  IGSF5 MUTATED    10   4
  IGSF5 WILD-TYPE 368  89
  IGSF5 MUTATED IGSF5 WILD-TYPE 
             14             457 
  IGSF5 MUTATED IGSF5 WILD-TYPE 
              4              89 
$`IGSF5 MUTATED`
TCGA-A6-2676 TCGA-A6-6780 TCGA-AA-3517 TCGA-AA-3542 TCGA-AA-3713 TCGA-AA-3815 
       42.90        20.12        38.99        12.99        19.04        33.04 
TCGA-AA-A00N TCGA-AA-A00R TCGA-AZ-6600 TCGA-CK-5913 TCGA-CM-4746 TCGA-CM-6168 
        4.01         0.99        12.10        51.32        37.02        12.99 
TCGA-F4-6570 TCGA-AG-A002 
        6.18        20.98 

$`IGSF5 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3519 
       63.98         6.97         1.02        13.02         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3543 
       19.07        34.03        29.00        29.00        26.01         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
       26.99        19.04        10.06        35.05         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W 
       18.05        38.04        27.02        42.02        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        49.08         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
      124.27        23.05        20.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6169 TCGA-CM-6170 
       29.03        16.04        21.99        14.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       31.96        35.74        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  IGSF5 MUTATED IGSF5 WILD-TYPE 
           0.99            0.00 
  IGSF5 MUTATED IGSF5 WILD-TYPE 
          51.32          148.01 
  IGSF5 MUTATED IGSF5 WILD-TYPE 
          19.58           20.28 
[1] "1.0 - 51.3 (19.6)"  "0.0 - 148.0 (20.3)"
[1] "hr=" "1.7"
D1728V2, continuous
D1728V3, binary
                 cls
clus                0   1
  IGSF5 MUTATED    14   1
  IGSF5 WILD-TYPE 352 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IGSF5 MUTATED     14    1
  IGSF5 WILD-TYPE  352  118
        clus
vv       IGSF5 MUTATED IGSF5 WILD-TYPE
  COLON             14             352
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  IGSF5 MUTATED         3        0        0         7         2         0
  IGSF5 WILD-TYPE      88        1       32       131         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  IGSF5 MUTATED           0          0          0          1        2         0
  IGSF5 WILD-TYPE        24         11         59         41       46        18
                 vv
clus              STAGE IVB
  IGSF5 MUTATED           0
  IGSF5 WILD-TYPE         1
D1728V4, multiclass
            clus
vv           IGSF5 MUTATED IGSF5 WILD-TYPE
  STAGE I                3              88
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              7             131
  STAGE IIB              2               8
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             1              41
  STAGE IV               2              46
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  IGSF5 MUTATED     0   3   9   3
  IGSF5 WILD-TYPE  17  89 320  47
D1728V5, multiclass
    clus
vv   IGSF5 MUTATED IGSF5 WILD-TYPE
  T1             0              17
  T2             3              89
  T3             9             320
  T4             3              47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  IGSF5 MUTATED    13   1   1
  IGSF5 WILD-TYPE 274 112  86
D1728V6, multiclass
    clus
vv   IGSF5 MUTATED IGSF5 WILD-TYPE
  N0            13             274
  N1             1             112
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1728V7, binary
                 cls
clus                0   1
  IGSF5 MUTATED    11   2
  IGSF5 WILD-TYPE 364  63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IGSF5 MUTATED     11    2
  IGSF5 WILD-TYPE  364   63
   clus
vv  IGSF5 MUTATED IGSF5 WILD-TYPE
  0            11             364
  1             2              63
[1] 2 2
[1] FALSE
D1728V8, binary
                 cls
clus                0   1
  IGSF5 MUTATED     7   8
  IGSF5 WILD-TYPE 218 256
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IGSF5 MUTATED      7    8
  IGSF5 WILD-TYPE  218  256
        clus
vv       IGSF5 MUTATED IGSF5 WILD-TYPE
  FEMALE             7             218
  MALE               8             256
[1] 2 2
[1] FALSE
D1728V9, binary
                 cls
clus                0   1
  IGSF5 MUTATED    10   1
  IGSF5 WILD-TYPE 340  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IGSF5 MUTATED     10    1
  IGSF5 WILD-TYPE  340   21
     clus
vv    IGSF5 MUTATED IGSF5 WILD-TYPE
  NO             10             340
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  IGSF5 MUTATED                     12                             2
  IGSF5 WILD-TYPE                  303                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  IGSF5 MUTATED                       1                              0
  IGSF5 WILD-TYPE                   105                             10
D1728V10, multiclass
                                clus
vv                               IGSF5 MUTATED IGSF5 WILD-TYPE
  COLON ADENOCARCINOMA                      12             303
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  IGSF5 MUTATED    11   0   1   1
  IGSF5 WILD-TYPE 334   4  30  24
D1728V11, multiclass
    clus
vv   IGSF5 MUTATED IGSF5 WILD-TYPE
  R0            11             334
  R1             0               4
  R2             1              30
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1728V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  IGSF5 MUTATED                                  0     0
  IGSF5 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  IGSF5 MUTATED                           3     4
  IGSF5 WILD-TYPE                        19   222
D1728V13, multiclass
                                  clus
vv                                 IGSF5 MUTATED IGSF5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    3              19
  WHITE                                        4             222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1729) Variable = MFRP MUTATION ANALYSIS
D1729V1, survival
                sevent
clus2              0   1
  MFRP MUTATED    10   2
  MFRP WILD-TYPE 368  91
  MFRP MUTATED MFRP WILD-TYPE 
            12            459 
  MFRP MUTATED MFRP WILD-TYPE 
             2             91 
$`MFRP MUTATED`
TCGA-A6-5665 TCGA-AA-3489 TCGA-AA-3833 TCGA-AA-3989 TCGA-AD-6889 TCGA-AU-6004 
       22.06         7.04        15.95         7.96        56.55        27.09 
TCGA-CA-6717 TCGA-CK-5913 TCGA-CK-6751 TCGA-CM-6162 TCGA-F4-6856 TCGA-DC-6682 
       12.76        51.32       124.27        12.00        35.31         4.01 

$`MFRP WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        19.66        20.28         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
       19.07        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 
       40.96         0.07        21.37        15.52         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07        12.20        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 
      148.01        85.45        15.62        49.08         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
       82.95         1.91        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
        0.53        47.41       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 
       13.97        27.95        10.98        19.99         5.95         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  MFRP MUTATED MFRP WILD-TYPE 
          4.01           0.00 
  MFRP MUTATED MFRP WILD-TYPE 
        124.27         148.01 
  MFRP MUTATED MFRP WILD-TYPE 
        19.005         20.190 
[1] "4.0 - 124.3 (19.0)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.4"
D1729V2, continuous
D1729V3, binary
                cls
clus               0   1
  MFRP MUTATED    11   1
  MFRP WILD-TYPE 355 118
[1] "tbl2"
                cls
clus             [,1] [,2]
  MFRP MUTATED     11    1
  MFRP WILD-TYPE  355  118
        clus
vv       MFRP MUTATED MFRP WILD-TYPE
  COLON            11            355
  RECTUM            1            118
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MFRP MUTATED         3        0        1         6         0         0
  MFRP WILD-TYPE      88        1       31       132        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MFRP MUTATED           0          0          1          0        1         0
  MFRP WILD-TYPE        24         11         58         42       47        18
                vv
clus             STAGE IVB
  MFRP MUTATED           0
  MFRP WILD-TYPE         1
D1729V4, multiclass
            clus
vv           MFRP MUTATED MFRP WILD-TYPE
  STAGE I               3             88
  STAGE IA              0              1
  STAGE II              1             31
  STAGE IIA             6            132
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            1             58
  STAGE IIIC            0             42
  STAGE IV              1             47
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  MFRP MUTATED     0   3   9   0
  MFRP WILD-TYPE  17  89 320  50
D1729V5, multiclass
    clus
vv   MFRP MUTATED MFRP WILD-TYPE
  T1            0             17
  T2            3             89
  T3            9            320
  T4            0             50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  MFRP MUTATED    10   1   1
  MFRP WILD-TYPE 277 112  86
D1729V6, multiclass
    clus
vv   MFRP MUTATED MFRP WILD-TYPE
  N0           10            277
  N1            1            112
  N2            1             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1729V7, binary
                cls
clus               0   1
  MFRP MUTATED     9   1
  MFRP WILD-TYPE 366  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  MFRP MUTATED      9    1
  MFRP WILD-TYPE  366   64
   clus
vv  MFRP MUTATED MFRP WILD-TYPE
  0            9            366
  1            1             64
[1] 2 2
[1] FALSE
D1729V8, binary
                cls
clus               0   1
  MFRP MUTATED     6   6
  MFRP WILD-TYPE 219 258
[1] "tbl2"
                cls
clus             [,1] [,2]
  MFRP MUTATED      6    6
  MFRP WILD-TYPE  219  258
        clus
vv       MFRP MUTATED MFRP WILD-TYPE
  FEMALE            6            219
  MALE              6            258
[1] 2 2
[1] FALSE
D1729V9, binary
                cls
clus               0   1
  MFRP MUTATED     9   0
  MFRP WILD-TYPE 341  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  MFRP MUTATED      9    0
  MFRP WILD-TYPE  341   22
     clus
vv    MFRP MUTATED MFRP WILD-TYPE
  NO             9            341
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MFRP MUTATED                      7                             4
  MFRP WILD-TYPE                  308                            43
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MFRP MUTATED                       1                              0
  MFRP WILD-TYPE                   105                             10
D1729V10, multiclass
                                clus
vv                               MFRP MUTATED MFRP WILD-TYPE
  COLON ADENOCARCINOMA                      7            308
  COLON MUCINOUS ADENOCARCINOMA             4             43
  RECTAL ADENOCARCINOMA                     1            105
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  MFRP MUTATED     7   0   1   3
  MFRP WILD-TYPE 338   4  30  22
D1729V11, multiclass
    clus
vv   MFRP MUTATED MFRP WILD-TYPE
  R0            7            338
  R1            0              4
  R2            1             30
  RX            3             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1729V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MFRP MUTATED                                  0     2
  MFRP WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  MFRP MUTATED                           0     7
  MFRP WILD-TYPE                        22   219
D1729V13, multiclass
                                  clus
vv                                 MFRP MUTATED MFRP WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              9
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       7            219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1730) Variable = PIGN MUTATION ANALYSIS
D1730V1, survival
                sevent
clus2              0   1
  PIGN MUTATED     8   1
  PIGN WILD-TYPE 370  92
  PIGN MUTATED PIGN WILD-TYPE 
             9            462 
  PIGN MUTATED PIGN WILD-TYPE 
             1             92 
$`PIGN MUTATED`
TCGA-AA-3950 TCGA-AA-3966 TCGA-AD-6964 TCGA-CM-5348 TCGA-CM-5861 TCGA-D5-6928 
       24.00         2.01        10.88        22.98        15.02        11.64 
TCGA-F4-6703 TCGA-AG-A002 TCGA-DC-6157 
       47.87        20.98        27.95 

$`PIGN WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
        2.01        20.98        34.03        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 
       13.02        29.06        22.03        30.08        32.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
       14.30         9.04         9.44         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       31.96        35.74         6.18         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6158 TCGA-DC-6160 
        7.17        15.02         5.03        13.97        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  PIGN MUTATED PIGN WILD-TYPE 
          2.01           0.00 
  PIGN MUTATED PIGN WILD-TYPE 
         47.87         148.01 
  PIGN MUTATED PIGN WILD-TYPE 
        20.980         20.155 
[1] "2.0 - 47.9 (21.0)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.4"
D1730V2, continuous
D1730V3, binary
                cls
clus               0   1
  PIGN MUTATED     7   2
  PIGN WILD-TYPE 359 117
[1] "tbl2"
                cls
clus             [,1] [,2]
  PIGN MUTATED      7    2
  PIGN WILD-TYPE  359  117
        clus
vv       PIGN MUTATED PIGN WILD-TYPE
  COLON             7            359
  RECTUM            2            117
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PIGN MUTATED         2        0        0         5         0         0
  PIGN WILD-TYPE      89        1       32       133        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PIGN MUTATED           0          0          1          0        0         0
  PIGN WILD-TYPE        24         11         58         42       48        18
                vv
clus             STAGE IVB
  PIGN MUTATED           0
  PIGN WILD-TYPE         1
D1730V4, multiclass
            clus
vv           PIGN MUTATED PIGN WILD-TYPE
  STAGE I               2             89
  STAGE IA              0              1
  STAGE II              0             32
  STAGE IIA             5            133
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            1             58
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  PIGN MUTATED     0   2   6   1
  PIGN WILD-TYPE  17  90 323  49
D1730V5, multiclass
    clus
vv   PIGN MUTATED PIGN WILD-TYPE
  T1            0             17
  T2            2             90
  T3            6            323
  T4            1             49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  PIGN MUTATED     7   1   1
  PIGN WILD-TYPE 280 112  86
D1730V6, multiclass
    clus
vv   PIGN MUTATED PIGN WILD-TYPE
  N0            7            280
  N1            1            112
  N2            1             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1730V7, binary
                cls
clus               0   1
  PIGN MUTATED     8   0
  PIGN WILD-TYPE 367  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  PIGN MUTATED      8    0
  PIGN WILD-TYPE  367   65
   clus
vv  PIGN MUTATED PIGN WILD-TYPE
  0            8            367
  1            0             65
[1] 2 2
[1] FALSE
D1730V8, binary
                cls
clus               0   1
  PIGN MUTATED     3   6
  PIGN WILD-TYPE 222 258
[1] "tbl2"
                cls
clus             [,1] [,2]
  PIGN MUTATED      3    6
  PIGN WILD-TYPE  222  258
        clus
vv       PIGN MUTATED PIGN WILD-TYPE
  FEMALE            3            222
  MALE              6            258
[1] 2 2
[1] FALSE
D1730V9, binary
                cls
clus               0   1
  PIGN MUTATED     7   0
  PIGN WILD-TYPE 343  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  PIGN MUTATED      7    0
  PIGN WILD-TYPE  343   22
     clus
vv    PIGN MUTATED PIGN WILD-TYPE
  NO             7            343
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PIGN MUTATED                      4                             3
  PIGN WILD-TYPE                  311                            44
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PIGN MUTATED                       2                              0
  PIGN WILD-TYPE                   104                             10
D1730V10, multiclass
                                clus
vv                               PIGN MUTATED PIGN WILD-TYPE
  COLON ADENOCARCINOMA                      4            311
  COLON MUCINOUS ADENOCARCINOMA             3             44
  RECTAL ADENOCARCINOMA                     2            104
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  PIGN MUTATED     7   0   0   0
  PIGN WILD-TYPE 338   4  31  25
D1730V11, multiclass
    clus
vv   PIGN MUTATED PIGN WILD-TYPE
  R0            7            338
  R1            0              4
  R2            0             31
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1730V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PIGN MUTATED                                  0     0
  PIGN WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  PIGN MUTATED                           1     5
  PIGN WILD-TYPE                        21   221
D1730V13, multiclass
                                  clus
vv                                 PIGN MUTATED PIGN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                       5            221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1731) Variable = TPK1 MUTATION ANALYSIS
D1731V1, survival
                sevent
clus2              0   1
  TPK1 MUTATED     6   2
  TPK1 WILD-TYPE 372  91
  TPK1 MUTATED TPK1 WILD-TYPE 
             8            463 
  TPK1 MUTATED TPK1 WILD-TYPE 
             2             91 
$`TPK1 MUTATED`
TCGA-A6-6138 TCGA-A6-6780 TCGA-AD-6901 TCGA-DM-A28K TCGA-G4-6626 TCGA-AG-A002 
       22.52        20.12        22.42        98.24        46.75        20.98 
TCGA-CI-6624 TCGA-EI-6510 
        4.73        18.28 

$`TPK1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6141 TCGA-A6-6142 
       22.09        22.06        32.71        27.09         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6964 
       56.55         0.79         0.72         5.79        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
      117.07         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-F5-6464 TCGA-F5-6465 
        0.49        20.55        19.96        20.91         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  TPK1 MUTATED TPK1 WILD-TYPE 
          4.73           0.00 
  TPK1 MUTATED TPK1 WILD-TYPE 
         98.24         148.01 
  TPK1 MUTATED TPK1 WILD-TYPE 
         21.70          20.05 
[1] "4.7 - 98.2 (21.7)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.1"
D1731V2, continuous
D1731V3, binary
                cls
clus               0   1
  TPK1 MUTATED     5   3
  TPK1 WILD-TYPE 361 116
[1] "tbl2"
                cls
clus             [,1] [,2]
  TPK1 MUTATED      5    3
  TPK1 WILD-TYPE  361  116
        clus
vv       TPK1 MUTATED TPK1 WILD-TYPE
  COLON             5            361
  RECTUM            3            116
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TPK1 MUTATED         3        0        0         3         0         0
  TPK1 WILD-TYPE      88        1       32       135        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TPK1 MUTATED           0          0          0          0        0         1
  TPK1 WILD-TYPE        24         11         59         42       48        17
                vv
clus             STAGE IVB
  TPK1 MUTATED           0
  TPK1 WILD-TYPE         1
D1731V4, multiclass
            clus
vv           TPK1 MUTATED TPK1 WILD-TYPE
  STAGE I               3             88
  STAGE IA              0              1
  STAGE II              0             32
  STAGE IIA             3            135
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            0             59
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             1             17
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  TPK1 MUTATED     0   4   4   0
  TPK1 WILD-TYPE  17  88 325  50
D1731V5, multiclass
    clus
vv   TPK1 MUTATED TPK1 WILD-TYPE
  T1            0             17
  T2            4             88
  T3            4            325
  T4            0             50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  TPK1 MUTATED     8   0   0
  TPK1 WILD-TYPE 279 113  87
D1731V6, multiclass
    clus
vv   TPK1 MUTATED TPK1 WILD-TYPE
  N0            8            279
  N1            0            113
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1731V7, binary
                cls
clus               0   1
  TPK1 MUTATED     5   0
  TPK1 WILD-TYPE 370  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  TPK1 MUTATED      5    0
  TPK1 WILD-TYPE  370   65
   clus
vv  TPK1 MUTATED TPK1 WILD-TYPE
  0            5            370
  1            0             65
[1] 2 2
[1] FALSE
D1731V8, binary
                cls
clus               0   1
  TPK1 MUTATED     2   6
  TPK1 WILD-TYPE 223 258
[1] "tbl2"
                cls
clus             [,1] [,2]
  TPK1 MUTATED      2    6
  TPK1 WILD-TYPE  223  258
        clus
vv       TPK1 MUTATED TPK1 WILD-TYPE
  FEMALE            2            223
  MALE              6            258
[1] 2 2
[1] FALSE
D1731V9, binary
                cls
clus               0   1
  TPK1 MUTATED     6   0
  TPK1 WILD-TYPE 344  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  TPK1 MUTATED      6    0
  TPK1 WILD-TYPE  344   22
     clus
vv    TPK1 MUTATED TPK1 WILD-TYPE
  NO             6            344
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  TPK1 MUTATED                      3                             2
  TPK1 WILD-TYPE                  312                            45
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  TPK1 MUTATED                       3                              0
  TPK1 WILD-TYPE                   103                             10
D1731V10, multiclass
                                clus
vv                               TPK1 MUTATED TPK1 WILD-TYPE
  COLON ADENOCARCINOMA                      3            312
  COLON MUCINOUS ADENOCARCINOMA             2             45
  RECTAL ADENOCARCINOMA                     3            103
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  TPK1 MUTATED     3   0   0   0
  TPK1 WILD-TYPE 342   4  31  25
D1731V11, multiclass
    clus
vv   TPK1 MUTATED TPK1 WILD-TYPE
  R0            3            342
  R1            0              4
  R2            0             31
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1731V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TPK1 MUTATED                                  0     0
  TPK1 WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  TPK1 MUTATED                           0     7
  TPK1 WILD-TYPE                        22   219
D1731V13, multiclass
                                  clus
vv                                 TPK1 MUTATED TPK1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       7            219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1732) Variable = IGFN1 MUTATION ANALYSIS
D1732V1, survival
                 sevent
clus2               0   1
  IGFN1 MUTATED    13   3
  IGFN1 WILD-TYPE 365  90
  IGFN1 MUTATED IGFN1 WILD-TYPE 
             16             455 
  IGFN1 MUTATED IGFN1 WILD-TYPE 
              3              90 
$`IGFN1 MUTATED`
TCGA-A6-5665 TCGA-AA-3492 TCGA-AA-3811 TCGA-AA-3815 TCGA-AA-A00E TCGA-AD-6889 
       22.06         3.02        10.06        33.04        30.02        56.55 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-4743 TCGA-CM-6171 TCGA-D5-6533 TCGA-DM-A28K 
       12.76        10.06        23.05        14.04         1.32        98.24 
TCGA-G4-6293 TCGA-G4-6323 TCGA-G4-6588 TCGA-AG-A01W 
      133.18        13.78        26.17        70.03 

$`IGFN1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 
       20.12        19.66        20.28         7.04         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        19.04        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00F 
        7.96        27.02        13.94        38.04        19.00        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
        0.07        21.37        15.52         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        3.29         0.07        12.20        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
       82.95         1.91       124.27        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       12.99        13.02        15.02        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-F4-6459 
       81.37       119.93        35.97        60.79       117.07         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
       35.31        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6586 
       85.48        63.62        61.91        36.00        22.09        35.80 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
       36.03         9.07        12.00        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  IGFN1 MUTATED IGFN1 WILD-TYPE 
           1.32            0.00 
  IGFN1 MUTATED IGFN1 WILD-TYPE 
         133.18          148.01 
  IGFN1 MUTATED IGFN1 WILD-TYPE 
         22.555          20.120 
[1] "1.3 - 133.2 (22.6)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.3"
D1732V2, continuous
D1732V3, binary
                 cls
clus                0   1
  IGFN1 MUTATED    16   1
  IGFN1 WILD-TYPE 350 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IGFN1 MUTATED     16    1
  IGFN1 WILD-TYPE  350  118
        clus
vv       IGFN1 MUTATED IGFN1 WILD-TYPE
  COLON             16             350
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  IGFN1 MUTATED         1        1        2        10         0         0
  IGFN1 WILD-TYPE      90        0       30       128        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  IGFN1 MUTATED           2          0          1          0        0         0
  IGFN1 WILD-TYPE        22         11         58         42       48        18
                 vv
clus              STAGE IVB
  IGFN1 MUTATED           0
  IGFN1 WILD-TYPE         1
D1732V4, multiclass
            clus
vv           IGFN1 MUTATED IGFN1 WILD-TYPE
  STAGE I                1              90
  STAGE IA               1               0
  STAGE II               2              30
  STAGE IIA             10             128
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              2              22
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  IGFN1 MUTATED     0   1  14   1
  IGFN1 WILD-TYPE  17  91 315  49
D1732V5, multiclass
    clus
vv   IGFN1 MUTATED IGFN1 WILD-TYPE
  T1             0              17
  T2             1              91
  T3            14             315
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  IGFN1 MUTATED    15   1   1
  IGFN1 WILD-TYPE 272 112  86
D1732V6, multiclass
    clus
vv   IGFN1 MUTATED IGFN1 WILD-TYPE
  N0            15             272
  N1             1             112
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1732V7, binary
                 cls
clus                0   1
  IGFN1 MUTATED    16   0
  IGFN1 WILD-TYPE 359  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IGFN1 MUTATED     16    0
  IGFN1 WILD-TYPE  359   65
   clus
vv  IGFN1 MUTATED IGFN1 WILD-TYPE
  0            16             359
  1             0              65
[1] 2 2
[1] FALSE
D1732V8, binary
                 cls
clus                0   1
  IGFN1 MUTATED    10   7
  IGFN1 WILD-TYPE 215 257
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IGFN1 MUTATED     10    7
  IGFN1 WILD-TYPE  215  257
        clus
vv       IGFN1 MUTATED IGFN1 WILD-TYPE
  FEMALE            10             215
  MALE               7             257
[1] 2 2
[1] FALSE
D1732V9, binary
                 cls
clus                0   1
  IGFN1 MUTATED    12   0
  IGFN1 WILD-TYPE 338  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IGFN1 MUTATED     12    0
  IGFN1 WILD-TYPE  338   22
     clus
vv    IGFN1 MUTATED IGFN1 WILD-TYPE
  NO             12             338
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  IGFN1 MUTATED                     14                             2
  IGFN1 WILD-TYPE                  301                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  IGFN1 MUTATED                       1                              0
  IGFN1 WILD-TYPE                   105                             10
D1732V10, multiclass
                                clus
vv                               IGFN1 MUTATED IGFN1 WILD-TYPE
  COLON ADENOCARCINOMA                      14             301
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  IGFN1 MUTATED    13   0   0   2
  IGFN1 WILD-TYPE 332   4  31  23
D1732V11, multiclass
    clus
vv   IGFN1 MUTATED IGFN1 WILD-TYPE
  R0            13             332
  R1             0               4
  R2             0              31
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1732V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  IGFN1 MUTATED                                  0     3
  IGFN1 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  IGFN1 MUTATED                           1     7
  IGFN1 WILD-TYPE                        21   219
D1732V13, multiclass
                                  clus
vv                                 IGFN1 MUTATED IGFN1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        3               8
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        7             219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1733) Variable = GRK5 MUTATION ANALYSIS
D1733V1, survival
                sevent
clus2              0   1
  GRK5 MUTATED     9   3
  GRK5 WILD-TYPE 369  90
  GRK5 MUTATED GRK5 WILD-TYPE 
            12            459 
  GRK5 MUTATED GRK5 WILD-TYPE 
             3             90 
$`GRK5 MUTATED`
TCGA-A6-6651 TCGA-AA-3692 TCGA-AA-3848 TCGA-AA-3950 TCGA-AA-3994 TCGA-AU-6004 
       21.76        36.00        10.06        24.00        27.02        27.09 
TCGA-CA-5254 TCGA-CM-5344 TCGA-CM-5862 TCGA-D5-6930 TCGA-G4-6293 TCGA-AG-A002 
       12.69        22.03         5.03         1.51       133.18        20.98 

$`GRK5 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.08        25.18        24.16        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        33.01        26.01         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
        7.96        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
       11.74         3.19         1.61         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5349 
       37.02        25.02        13.02        29.06        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       32.02        15.02        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        4.80        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
        0.53        47.41        35.31        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  GRK5 MUTATED GRK5 WILD-TYPE 
          1.51           0.00 
  GRK5 MUTATED GRK5 WILD-TYPE 
        133.18         148.01 
  GRK5 MUTATED GRK5 WILD-TYPE 
        21.895         20.050 
[1] "1.5 - 133.2 (21.9)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.3"
D1733V2, continuous
D1733V3, binary
                cls
clus               0   1
  GRK5 MUTATED    11   1
  GRK5 WILD-TYPE 355 118
[1] "tbl2"
                cls
clus             [,1] [,2]
  GRK5 MUTATED     11    1
  GRK5 WILD-TYPE  355  118
        clus
vv       GRK5 MUTATED GRK5 WILD-TYPE
  COLON            11            355
  RECTUM            1            118
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GRK5 MUTATED         2        0        0         3         0         0
  GRK5 WILD-TYPE      89        1       32       135        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  GRK5 MUTATED           1          0          3          1        1         1
  GRK5 WILD-TYPE        23         11         56         41       47        17
                vv
clus             STAGE IVB
  GRK5 MUTATED           0
  GRK5 WILD-TYPE         1
D1733V4, multiclass
            clus
vv           GRK5 MUTATED GRK5 WILD-TYPE
  STAGE I               2             89
  STAGE IA              0              1
  STAGE II              0             32
  STAGE IIA             3            135
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             1             23
  STAGE IIIA            0             11
  STAGE IIIB            3             56
  STAGE IIIC            1             41
  STAGE IV              1             47
  STAGE IVA             1             17
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  GRK5 MUTATED     0   2  10   0
  GRK5 WILD-TYPE  17  90 319  50
D1733V5, multiclass
    clus
vv   GRK5 MUTATED GRK5 WILD-TYPE
  T1            0             17
  T2            2             90
  T3           10            319
  T4            0             50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  GRK5 MUTATED     5   5   2
  GRK5 WILD-TYPE 282 108  85
D1733V6, multiclass
    clus
vv   GRK5 MUTATED GRK5 WILD-TYPE
  N0            5            282
  N1            5            108
  N2            2             85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1733V7, binary
                cls
clus               0   1
  GRK5 MUTATED     9   2
  GRK5 WILD-TYPE 366  63
[1] "tbl2"
                cls
clus             [,1] [,2]
  GRK5 MUTATED      9    2
  GRK5 WILD-TYPE  366   63
   clus
vv  GRK5 MUTATED GRK5 WILD-TYPE
  0            9            366
  1            2             63
[1] 2 2
[1] FALSE
D1733V8, binary
                cls
clus               0   1
  GRK5 MUTATED     8   4
  GRK5 WILD-TYPE 217 260
[1] "tbl2"
                cls
clus             [,1] [,2]
  GRK5 MUTATED      8    4
  GRK5 WILD-TYPE  217  260
        clus
vv       GRK5 MUTATED GRK5 WILD-TYPE
  FEMALE            8            217
  MALE              4            260
[1] 2 2
[1] FALSE
D1733V9, binary
                cls
clus               0   1
  GRK5 MUTATED     9   1
  GRK5 WILD-TYPE 341  21
[1] "tbl2"
                cls
clus             [,1] [,2]
  GRK5 MUTATED      9    1
  GRK5 WILD-TYPE  341   21
     clus
vv    GRK5 MUTATED GRK5 WILD-TYPE
  NO             9            341
  YES            1             21
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  GRK5 MUTATED                      7                             4
  GRK5 WILD-TYPE                  308                            43
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  GRK5 MUTATED                       1                              0
  GRK5 WILD-TYPE                   105                             10
D1733V10, multiclass
                                clus
vv                               GRK5 MUTATED GRK5 WILD-TYPE
  COLON ADENOCARCINOMA                      7            308
  COLON MUCINOUS ADENOCARCINOMA             4             43
  RECTAL ADENOCARCINOMA                     1            105
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  GRK5 MUTATED     9   0   1   1
  GRK5 WILD-TYPE 336   4  30  24
D1733V11, multiclass
    clus
vv   GRK5 MUTATED GRK5 WILD-TYPE
  R0            9            336
  R1            0              4
  R2            1             30
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1733V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GRK5 MUTATED                                  0     1
  GRK5 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  GRK5 MUTATED                           0     6
  GRK5 WILD-TYPE                        22   220
D1733V13, multiclass
                                  clus
vv                                 GRK5 MUTATED GRK5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       6            220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1734) Variable = ZNF555 MUTATION ANALYSIS
D1734V1, survival
                  sevent
clus2                0   1
  ZNF555 MUTATED     8   1
  ZNF555 WILD-TYPE 370  92
  ZNF555 MUTATED ZNF555 WILD-TYPE 
               9              462 
  ZNF555 MUTATED ZNF555 WILD-TYPE 
               1               92 
$`ZNF555 MUTATED`
TCGA-AA-3510 TCGA-AA-3518 TCGA-AA-3555 TCGA-AA-3715 TCGA-AA-3833 TCGA-CK-6747 
       63.98         1.02        29.95        19.04        15.95        82.95 
TCGA-D5-5539 TCGA-G4-6293 TCGA-AG-A002 
       19.59       133.18        20.98 

$`ZNF555 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       24.00        17.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       85.05        26.99        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3837 TCGA-AA-3842 
        0.99        25.02         1.02        17.98        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       51.32         9.99        21.14         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 
       11.01        10.06        12.03        45.40        12.26        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  ZNF555 MUTATED ZNF555 WILD-TYPE 
            1.02             0.00 
  ZNF555 MUTATED ZNF555 WILD-TYPE 
          133.18           148.01 
  ZNF555 MUTATED ZNF555 WILD-TYPE 
          20.980           20.155 
[1] "1.0 - 133.2 (21.0)" "0.0 - 148.0 (20.2)"
[1] "hr=" "2.8"
D1734V2, continuous
D1734V3, binary
                  cls
clus                 0   1
  ZNF555 MUTATED     8   1
  ZNF555 WILD-TYPE 358 118
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF555 MUTATED      8    1
  ZNF555 WILD-TYPE  358  118
        clus
vv       ZNF555 MUTATED ZNF555 WILD-TYPE
  COLON               8              358
  RECTUM              1              118
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZNF555 MUTATED         1        0        2         4         0         0
  ZNF555 WILD-TYPE      90        1       30       134        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF555 MUTATED           1          1          0          0        0
  ZNF555 WILD-TYPE        23         10         59         42       48
                  vv
clus               STAGE IVA STAGE IVB
  ZNF555 MUTATED           0         0
  ZNF555 WILD-TYPE        18         1
D1734V4, multiclass
            clus
vv           ZNF555 MUTATED ZNF555 WILD-TYPE
  STAGE I                 1               90
  STAGE IA                0                1
  STAGE II                2               30
  STAGE IIA               4              134
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               1               23
  STAGE IIIA              1               10
  STAGE IIIB              0               59
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZNF555 MUTATED     0   1   8   0
  ZNF555 WILD-TYPE  17  91 321  50
D1734V5, multiclass
    clus
vv   ZNF555 MUTATED ZNF555 WILD-TYPE
  T1              0               17
  T2              1               91
  T3              8              321
  T4              0               50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  ZNF555 MUTATED     7   2   0
  ZNF555 WILD-TYPE 280 111  87
D1734V6, multiclass
    clus
vv   ZNF555 MUTATED ZNF555 WILD-TYPE
  N0              7              280
  N1              2              111
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1734V7, binary
                  cls
clus                 0   1
  ZNF555 MUTATED     8   0
  ZNF555 WILD-TYPE 367  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF555 MUTATED      8    0
  ZNF555 WILD-TYPE  367   65
   clus
vv  ZNF555 MUTATED ZNF555 WILD-TYPE
  0              8              367
  1              0               65
[1] 2 2
[1] FALSE
D1734V8, binary
                  cls
clus                 0   1
  ZNF555 MUTATED     5   4
  ZNF555 WILD-TYPE 220 260
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF555 MUTATED      5    4
  ZNF555 WILD-TYPE  220  260
        clus
vv       ZNF555 MUTATED ZNF555 WILD-TYPE
  FEMALE              5              220
  MALE                4              260
[1] 2 2
[1] FALSE
D1734V9, binary
                  cls
clus                 0   1
  ZNF555 MUTATED     8   0
  ZNF555 WILD-TYPE 342  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF555 MUTATED      8    0
  ZNF555 WILD-TYPE  342   22
     clus
vv    ZNF555 MUTATED ZNF555 WILD-TYPE
  NO               8              342
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ZNF555 MUTATED                      6                             2
  ZNF555 WILD-TYPE                  309                            45
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ZNF555 MUTATED                       1                              0
  ZNF555 WILD-TYPE                   105                             10
D1734V10, multiclass
                                clus
vv                               ZNF555 MUTATED ZNF555 WILD-TYPE
  COLON ADENOCARCINOMA                        6              309
  COLON MUCINOUS ADENOCARCINOMA               2               45
  RECTAL ADENOCARCINOMA                       1              105
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ZNF555 MUTATED     8   0   0   1
  ZNF555 WILD-TYPE 337   4  31  24
D1734V11, multiclass
    clus
vv   ZNF555 MUTATED ZNF555 WILD-TYPE
  R0              8              337
  R1              0                4
  R2              0               31
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1734V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF555 MUTATED                                  0     0
  ZNF555 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZNF555 MUTATED                           0     3
  ZNF555 WILD-TYPE                        22   223
D1734V13, multiclass
                                  clus
vv                                 ZNF555 MUTATED ZNF555 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         3              223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1735) Variable = NRAP MUTATION ANALYSIS
D1735V1, survival
                sevent
clus2              0   1
  NRAP MUTATED    20   5
  NRAP WILD-TYPE 358  88
  NRAP MUTATED NRAP WILD-TYPE 
            25            446 
  NRAP MUTATED NRAP WILD-TYPE 
             5             88 
$`NRAP MUTATED`
TCGA-A6-6141 TCGA-A6-6780 TCGA-AA-3510 TCGA-AA-3811 TCGA-AA-3854 TCGA-AA-A00N 
        8.38        20.12        63.98        10.06        36.03         4.01 
TCGA-AD-6889 TCGA-AD-6964 TCGA-AU-3779 TCGA-AU-6004 TCGA-AZ-6606 TCGA-CA-6717 
       56.55        10.88        14.50        27.09        11.74        12.76 
TCGA-CA-6718 TCGA-CK-4952 TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-6162 TCGA-D5-6930 
       10.06        15.62        30.08        15.02        12.00         1.51 
TCGA-DM-A28E TCGA-F4-6703 TCGA-G4-6586 TCGA-G4-6588 TCGA-AF-4110 TCGA-AG-3892 
      119.93        47.87        35.80        26.17        14.50        13.02 
TCGA-AG-A002 
       20.98 

$`NRAP WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 
       22.09        22.06        32.71        27.09        22.52        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3815 
       85.05        26.99        19.04        19.04        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
       33.07         0.00        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       21.37        15.52         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       27.42         0.20        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
       29.56         5.23         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 
        3.25         3.29         0.07        12.20        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
      148.01        85.45        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5860 
       25.02        13.02        29.06        22.03        22.98        32.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 
        5.03        15.02        15.02        17.03        15.02         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6931 
       14.30         9.04         9.44        11.64         4.80        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       35.74         6.18         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6625 
       63.62        61.91        36.00        22.09        13.78        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       19.10        34.49        10.39        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       17.95        36.95        17.03        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  NRAP MUTATED NRAP WILD-TYPE 
          1.51           0.00 
  NRAP MUTATED NRAP WILD-TYPE 
        119.93         148.01 
  NRAP MUTATED NRAP WILD-TYPE 
         15.02          20.73 
[1] "1.5 - 119.9 (15.0)" "0.0 - 148.0 (20.7)"
[1] "hr=" "1"  
D1735V2, continuous
D1735V3, binary
                cls
clus               0   1
  NRAP MUTATED    24   2
  NRAP WILD-TYPE 342 117
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRAP MUTATED     24    2
  NRAP WILD-TYPE  342  117
        clus
vv       NRAP MUTATED NRAP WILD-TYPE
  COLON            24            342
  RECTUM            2            117
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NRAP MUTATED         4        0        1        14         1         0
  NRAP WILD-TYPE      87        1       31       124         9         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NRAP MUTATED           1          0          1          1        2         1
  NRAP WILD-TYPE        23         11         58         41       46        17
                vv
clus             STAGE IVB
  NRAP MUTATED           0
  NRAP WILD-TYPE         1
D1735V4, multiclass
            clus
vv           NRAP MUTATED NRAP WILD-TYPE
  STAGE I               4             87
  STAGE IA              0              1
  STAGE II              1             31
  STAGE IIA            14            124
  STAGE IIB             1              9
  STAGE IIC             0              1
  STAGE III             1             23
  STAGE IIIA            0             11
  STAGE IIIB            1             58
  STAGE IIIC            1             41
  STAGE IV              2             46
  STAGE IVA             1             17
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  NRAP MUTATED     1   3  17   6
  NRAP WILD-TYPE  16  89 312  44
D1735V5, multiclass
    clus
vv   NRAP MUTATED NRAP WILD-TYPE
  T1            1             16
  T2            3             89
  T3           17            312
  T4            6             44
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  NRAP MUTATED    20   1   6
  NRAP WILD-TYPE 267 112  81
D1735V6, multiclass
    clus
vv   NRAP MUTATED NRAP WILD-TYPE
  N0           20            267
  N1            1            112
  N2            6             81
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1735V7, binary
                cls
clus               0   1
  NRAP MUTATED    22   2
  NRAP WILD-TYPE 353  63
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRAP MUTATED     22    2
  NRAP WILD-TYPE  353   63
   clus
vv  NRAP MUTATED NRAP WILD-TYPE
  0           22            353
  1            2             63
[1] 2 2
[1] FALSE
D1735V8, binary
                cls
clus               0   1
  NRAP MUTATED    14  13
  NRAP WILD-TYPE 211 251
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRAP MUTATED     14   13
  NRAP WILD-TYPE  211  251
        clus
vv       NRAP MUTATED NRAP WILD-TYPE
  FEMALE           14            211
  MALE             13            251
[1] 2 2
[1] FALSE
D1735V9, binary
                cls
clus               0   1
  NRAP MUTATED    19   0
  NRAP WILD-TYPE 331  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRAP MUTATED     19    0
  NRAP WILD-TYPE  331   22
     clus
vv    NRAP MUTATED NRAP WILD-TYPE
  NO            19            331
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  NRAP MUTATED                     16                             8
  NRAP WILD-TYPE                  299                            39
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  NRAP MUTATED                       2                              0
  NRAP WILD-TYPE                   104                             10
D1735V10, multiclass
                                clus
vv                               NRAP MUTATED NRAP WILD-TYPE
  COLON ADENOCARCINOMA                     16            299
  COLON MUCINOUS ADENOCARCINOMA             8             39
  RECTAL ADENOCARCINOMA                     2            104
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  NRAP MUTATED    17   0   1   3
  NRAP WILD-TYPE 328   4  30  22
D1735V11, multiclass
    clus
vv   NRAP MUTATED NRAP WILD-TYPE
  R0           17            328
  R1            0              4
  R2            1             30
  RX            3             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1735V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NRAP MUTATED                                  0     3
  NRAP WILD-TYPE                                1     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  NRAP MUTATED                           1    15
  NRAP WILD-TYPE                        21   211
D1735V13, multiclass
                                  clus
vv                                 NRAP MUTATED NRAP WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       3              8
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                      15            211
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1736) Variable = STAU1 MUTATION ANALYSIS
D1736V1, survival
                 sevent
clus2               0   1
  STAU1 MUTATED     7   2
  STAU1 WILD-TYPE 371  91
  STAU1 MUTATED STAU1 WILD-TYPE 
              9             462 
  STAU1 MUTATED STAU1 WILD-TYPE 
              2              91 
$`STAU1 MUTATED`
TCGA-AA-3713 TCGA-AY-6386 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-D5-5538 TCGA-D5-6536 
       19.04        17.82       100.01        29.56        12.26        17.85 
TCGA-AG-A002 TCGA-EI-6507 TCGA-EI-6508 
       20.98        19.96        20.91 

$`STAU1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        33.01        21.44        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       12.10         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       43.27        15.12         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
        0.49        20.55        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  STAU1 MUTATED STAU1 WILD-TYPE 
          12.26            0.00 
  STAU1 MUTATED STAU1 WILD-TYPE 
         100.01          148.01 
  STAU1 MUTATED STAU1 WILD-TYPE 
         19.960          20.235 
[1] "12.3 - 100.0 (20.0)" "0.0 - 148.0 (20.2)" 
[1] "hr=" "1"  
D1736V2, continuous
D1736V3, binary
                 cls
clus                0   1
  STAU1 MUTATED     7   4
  STAU1 WILD-TYPE 359 115
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STAU1 MUTATED      7    4
  STAU1 WILD-TYPE  359  115
        clus
vv       STAU1 MUTATED STAU1 WILD-TYPE
  COLON              7             359
  RECTUM             4             115
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  STAU1 MUTATED         1        0        1         2         0         0
  STAU1 WILD-TYPE      90        1       31       136        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  STAU1 MUTATED           2          0          3          0        1         0
  STAU1 WILD-TYPE        22         11         56         42       47        18
                 vv
clus              STAGE IVB
  STAU1 MUTATED           0
  STAU1 WILD-TYPE         1
D1736V4, multiclass
            clus
vv           STAU1 MUTATED STAU1 WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              2             136
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              2              22
  STAGE IIIA             0              11
  STAGE IIIB             3              56
  STAGE IIIC             0              42
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  STAU1 MUTATED     0   2   9   0
  STAU1 WILD-TYPE  17  90 320  50
D1736V5, multiclass
    clus
vv   STAU1 MUTATED STAU1 WILD-TYPE
  T1             0              17
  T2             2              90
  T3             9             320
  T4             0              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  STAU1 MUTATED     5   5   1
  STAU1 WILD-TYPE 282 108  86
D1736V6, multiclass
    clus
vv   STAU1 MUTATED STAU1 WILD-TYPE
  N0             5             282
  N1             5             108
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1736V7, binary
                 cls
clus                0   1
  STAU1 MUTATED     8   1
  STAU1 WILD-TYPE 367  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STAU1 MUTATED      8    1
  STAU1 WILD-TYPE  367   64
   clus
vv  STAU1 MUTATED STAU1 WILD-TYPE
  0             8             367
  1             1              64
[1] 2 2
[1] FALSE
D1736V8, binary
                 cls
clus                0   1
  STAU1 MUTATED     4   7
  STAU1 WILD-TYPE 221 257
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STAU1 MUTATED      4    7
  STAU1 WILD-TYPE  221  257
        clus
vv       STAU1 MUTATED STAU1 WILD-TYPE
  FEMALE             4             221
  MALE               7             257
[1] 2 2
[1] FALSE
D1736V9, binary
                 cls
clus                0   1
  STAU1 MUTATED     8   1
  STAU1 WILD-TYPE 342  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STAU1 MUTATED      8    1
  STAU1 WILD-TYPE  342   21
     clus
vv    STAU1 MUTATED STAU1 WILD-TYPE
  NO              8             342
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  STAU1 MUTATED                      7                             0
  STAU1 WILD-TYPE                  308                            47
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  STAU1 MUTATED                       4                              0
  STAU1 WILD-TYPE                   102                             10
D1736V10, multiclass
                                clus
vv                               STAU1 MUTATED STAU1 WILD-TYPE
  COLON ADENOCARCINOMA                       7             308
  COLON MUCINOUS ADENOCARCINOMA              0              47
  RECTAL ADENOCARCINOMA                      4             102
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  STAU1 MUTATED     7   0   1   0
  STAU1 WILD-TYPE 338   4  30  25
D1736V11, multiclass
    clus
vv   STAU1 MUTATED STAU1 WILD-TYPE
  R0             7             338
  R1             0               4
  R2             1              30
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1736V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  STAU1 MUTATED                                  0     0
  STAU1 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  STAU1 MUTATED                           1     7
  STAU1 WILD-TYPE                        21   219
D1736V13, multiclass
                                  clus
vv                                 STAU1 MUTATED STAU1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        7             219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1737) Variable = KIAA1919 MUTATION ANALYSIS
D1737V1, survival
                    sevent
clus2                  0   1
  KIAA1919 MUTATED     6   3
  KIAA1919 WILD-TYPE 372  90
  KIAA1919 MUTATED KIAA1919 WILD-TYPE 
                 9                462 
  KIAA1919 MUTATED KIAA1919 WILD-TYPE 
                 3                 90 
$`KIAA1919 MUTATED`
TCGA-A6-2676 TCGA-AA-A010 TCGA-AZ-4315 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-6747 
       42.90        34.98        58.39        12.76        10.06        82.95 
TCGA-CM-6171 TCGA-D5-6927 TCGA-F4-6570 
       14.04         9.44         6.18 

$`KIAA1919 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       33.01        21.44        17.82         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       51.32         9.99        21.14         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  KIAA1919 MUTATED KIAA1919 WILD-TYPE 
              6.18               0.00 
  KIAA1919 MUTATED KIAA1919 WILD-TYPE 
             82.95             148.01 
  KIAA1919 MUTATED KIAA1919 WILD-TYPE 
            14.040             20.235 
[1] "6.2 - 83.0 (14.0)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.4"
D1737V2, continuous
D1737V3, binary
                    cls
clus                   0   1
  KIAA1919 MUTATED     9   0
  KIAA1919 WILD-TYPE 357 119
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1919 MUTATED      9    0
  KIAA1919 WILD-TYPE  357  119
        clus
vv       KIAA1919 MUTATED KIAA1919 WILD-TYPE
  COLON                 9                357
  RECTUM                0                119
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KIAA1919 MUTATED         1        0        0         6         2         0
  KIAA1919 WILD-TYPE      90        1       32       132         8         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIAA1919 MUTATED           0          0          0          0        0
  KIAA1919 WILD-TYPE        24         11         59         42       48
                    vv
clus                 STAGE IVA STAGE IVB
  KIAA1919 MUTATED           0         0
  KIAA1919 WILD-TYPE        18         1
D1737V4, multiclass
            clus
vv           KIAA1919 MUTATED KIAA1919 WILD-TYPE
  STAGE I                   1                 90
  STAGE IA                  0                  1
  STAGE II                  0                 32
  STAGE IIA                 6                132
  STAGE IIB                 2                  8
  STAGE IIC                 0                  1
  STAGE III                 0                 24
  STAGE IIIA                0                 11
  STAGE IIIB                0                 59
  STAGE IIIC                0                 42
  STAGE IV                  0                 48
  STAGE IVA                 0                 18
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  KIAA1919 MUTATED     0   1   6   2
  KIAA1919 WILD-TYPE  17  91 323  48
D1737V5, multiclass
    clus
vv   KIAA1919 MUTATED KIAA1919 WILD-TYPE
  T1                0                 17
  T2                1                 91
  T3                6                323
  T4                2                 48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  KIAA1919 MUTATED     9   0   0
  KIAA1919 WILD-TYPE 278 113  87
D1737V6, multiclass
    clus
vv   KIAA1919 MUTATED KIAA1919 WILD-TYPE
  N0                9                278
  N1                0                113
  N2                0                 87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1737V7, binary
                    cls
clus                   0   1
  KIAA1919 MUTATED     8   0
  KIAA1919 WILD-TYPE 367  65
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1919 MUTATED      8    0
  KIAA1919 WILD-TYPE  367   65
   clus
vv  KIAA1919 MUTATED KIAA1919 WILD-TYPE
  0                8                367
  1                0                 65
[1] 2 2
[1] FALSE
D1737V8, binary
                    cls
clus                   0   1
  KIAA1919 MUTATED     5   4
  KIAA1919 WILD-TYPE 220 260
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1919 MUTATED      5    4
  KIAA1919 WILD-TYPE  220  260
        clus
vv       KIAA1919 MUTATED KIAA1919 WILD-TYPE
  FEMALE                5                220
  MALE                  4                260
[1] 2 2
[1] FALSE
D1737V9, binary
                    cls
clus                   0   1
  KIAA1919 MUTATED     9   0
  KIAA1919 WILD-TYPE 341  22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1919 MUTATED      9    0
  KIAA1919 WILD-TYPE  341   22
     clus
vv    KIAA1919 MUTATED KIAA1919 WILD-TYPE
  NO                 9                341
  YES                0                 22
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  KIAA1919 MUTATED                      8                             1
  KIAA1919 WILD-TYPE                  307                            46
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  KIAA1919 MUTATED                       0                              0
  KIAA1919 WILD-TYPE                   106                             10
D1737V10, multiclass
                                clus
vv                               KIAA1919 MUTATED KIAA1919 WILD-TYPE
  COLON ADENOCARCINOMA                          8                307
  COLON MUCINOUS ADENOCARCINOMA                 1                 46
  RECTAL ADENOCARCINOMA                         0                106
  RECTAL MUCINOUS ADENOCARCINOMA                0                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  KIAA1919 MUTATED     6   0   0   3
  KIAA1919 WILD-TYPE 339   4  31  22
D1737V11, multiclass
    clus
vv   KIAA1919 MUTATED KIAA1919 WILD-TYPE
  R0                6                339
  R1                0                  4
  R2                0                 31
  RX                3                 22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1737V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KIAA1919 MUTATED                                  0     2
  KIAA1919 WILD-TYPE                                1     9
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  KIAA1919 MUTATED                           0     6
  KIAA1919 WILD-TYPE                        22   220
D1737V13, multiclass
                                  clus
vv                                 KIAA1919 MUTATED KIAA1919 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           2                  9
  BLACK OR AFRICAN AMERICAN                       0                 22
  WHITE                                           6                220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1738) Variable = CTCFL MUTATION ANALYSIS
D1738V1, survival
                 sevent
clus2               0   1
  CTCFL MUTATED    10   4
  CTCFL WILD-TYPE 368  89
  CTCFL MUTATED CTCFL WILD-TYPE 
             14             457 
  CTCFL MUTATED CTCFL WILD-TYPE 
              4              89 
$`CTCFL MUTATED`
TCGA-A6-6141 TCGA-AA-3672 TCGA-AA-3815 TCGA-AA-3833 TCGA-AA-3977 TCGA-AA-A00N 
        8.38         0.92        33.04        15.95        25.02         4.01 
TCGA-AA-A01R TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-6171 TCGA-D5-5537 TCGA-DM-A1DB 
       35.01        12.76        10.06        14.04        45.40        44.32 
TCGA-G4-6323 TCGA-AG-3892 
       13.78        13.02 

$`CTCFL WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 
       22.09        22.06        32.71        27.09        22.52        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 
        6.97        54.02         2.01        14.01        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3837 
       35.05         0.99        25.02         1.02        17.98        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.07        12.20        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       12.99        13.02        15.02        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5538 
       11.08        11.08        11.01        10.06        12.03        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
        7.50       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       17.03        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  CTCFL MUTATED CTCFL WILD-TYPE 
           0.92            0.00 
  CTCFL MUTATED CTCFL WILD-TYPE 
          45.40          148.01 
  CTCFL MUTATED CTCFL WILD-TYPE 
          13.91           20.55 
[1] "0.9 - 45.4 (13.9)"  "0.0 - 148.0 (20.6)"
[1] "hr=" "1.9"
D1738V2, continuous
D1738V3, binary
                 cls
clus                0   1
  CTCFL MUTATED    15   1
  CTCFL WILD-TYPE 351 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CTCFL MUTATED     15    1
  CTCFL WILD-TYPE  351  118
        clus
vv       CTCFL MUTATED CTCFL WILD-TYPE
  COLON             15             351
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CTCFL MUTATED         2        1        0         8         1         0
  CTCFL WILD-TYPE      89        0       32       130         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CTCFL MUTATED           2          0          0          1        0         0
  CTCFL WILD-TYPE        22         11         59         41       48        18
                 vv
clus              STAGE IVB
  CTCFL MUTATED           0
  CTCFL WILD-TYPE         1
D1738V4, multiclass
            clus
vv           CTCFL MUTATED CTCFL WILD-TYPE
  STAGE I                2              89
  STAGE IA               1               0
  STAGE II               0              32
  STAGE IIA              8             130
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              2              22
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             1              41
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CTCFL MUTATED     1   2  11   1
  CTCFL WILD-TYPE  16  90 318  49
D1738V5, multiclass
    clus
vv   CTCFL MUTATED CTCFL WILD-TYPE
  T1             1              16
  T2             2              90
  T3            11             318
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  CTCFL MUTATED    12   1   3
  CTCFL WILD-TYPE 275 112  84
D1738V6, multiclass
    clus
vv   CTCFL MUTATED CTCFL WILD-TYPE
  N0            12             275
  N1             1             112
  N2             3              84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1738V7, binary
                 cls
clus                0   1
  CTCFL MUTATED    12   0
  CTCFL WILD-TYPE 363  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CTCFL MUTATED     12    0
  CTCFL WILD-TYPE  363   65
   clus
vv  CTCFL MUTATED CTCFL WILD-TYPE
  0            12             363
  1             0              65
[1] 2 2
[1] FALSE
D1738V8, binary
                 cls
clus                0   1
  CTCFL MUTATED     6  10
  CTCFL WILD-TYPE 219 254
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CTCFL MUTATED      6   10
  CTCFL WILD-TYPE  219  254
        clus
vv       CTCFL MUTATED CTCFL WILD-TYPE
  FEMALE             6             219
  MALE              10             254
[1] 2 2
[1] FALSE
D1738V9, binary
                 cls
clus                0   1
  CTCFL MUTATED    11   1
  CTCFL WILD-TYPE 339  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CTCFL MUTATED     11    1
  CTCFL WILD-TYPE  339   21
     clus
vv    CTCFL MUTATED CTCFL WILD-TYPE
  NO             11             339
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CTCFL MUTATED                     11                             4
  CTCFL WILD-TYPE                  304                            43
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CTCFL MUTATED                       1                              0
  CTCFL WILD-TYPE                   105                             10
D1738V10, multiclass
                                clus
vv                               CTCFL MUTATED CTCFL WILD-TYPE
  COLON ADENOCARCINOMA                      11             304
  COLON MUCINOUS ADENOCARCINOMA              4              43
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  CTCFL MUTATED    10   0   0   3
  CTCFL WILD-TYPE 335   4  31  22
D1738V11, multiclass
    clus
vv   CTCFL MUTATED CTCFL WILD-TYPE
  R0            10             335
  R1             0               4
  R2             0              31
  RX             3              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1738V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CTCFL MUTATED                                  0     2
  CTCFL WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CTCFL MUTATED                           2     4
  CTCFL WILD-TYPE                        20   222
D1738V13, multiclass
                                  clus
vv                                 CTCFL MUTATED CTCFL WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               9
  BLACK OR AFRICAN AMERICAN                    2              20
  WHITE                                        4             222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1739) Variable = LRRC31 MUTATION ANALYSIS
D1739V1, survival
                  sevent
clus2                0   1
  LRRC31 MUTATED    13   0
  LRRC31 WILD-TYPE 365  93
  LRRC31 MUTATED LRRC31 WILD-TYPE 
              13              458 
  LRRC31 MUTATED LRRC31 WILD-TYPE 
               0               93 
$`LRRC31 MUTATED`
TCGA-A6-6652 TCGA-A6-6781 TCGA-AA-3815 TCGA-AA-3833 TCGA-AA-3968 TCGA-AD-6895 
       24.69        19.66        33.04        15.95        21.99         0.72 
TCGA-CK-4948 TCGA-CM-5344 TCGA-D5-6533 TCGA-F4-6856 TCGA-G4-6315 TCGA-AG-A002 
      148.01        22.03         1.32        35.31        61.91        20.98 
TCGA-CI-6619 
        6.05 

$`LRRC31 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6654 
       25.08        25.18        24.16        21.76        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3837 
       35.05         0.99        25.02         1.02        17.98        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
        2.01        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 
        0.07        21.37        15.52        56.55         0.79         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
       17.56        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5349 
       37.02        25.02        13.02        29.06        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       20.19        18.25        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
       13.25         0.53        47.41       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6317 
       53.62        44.68        55.04        85.48        63.62        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
       17.49         0.69         0.72        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  LRRC31 MUTATED LRRC31 WILD-TYPE 
            0.72             0.00 
  LRRC31 MUTATED LRRC31 WILD-TYPE 
          148.01           140.38 
  LRRC31 MUTATED LRRC31 WILD-TYPE 
          21.990           20.085 
[1] "0.7 - 148.0 (22.0)" "0.0 - 140.4 (20.1)"
[1] "hr="     "2.5e+07"
D1739V2, continuous
D1739V3, binary
                  cls
clus                 0   1
  LRRC31 MUTATED    14   2
  LRRC31 WILD-TYPE 352 117
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LRRC31 MUTATED     14    2
  LRRC31 WILD-TYPE  352  117
        clus
vv       LRRC31 MUTATED LRRC31 WILD-TYPE
  COLON              14              352
  RECTUM              2              117
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  LRRC31 MUTATED         3        0        1         3         1         0
  LRRC31 WILD-TYPE      88        1       31       135         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  LRRC31 MUTATED           1          0          2          1        2
  LRRC31 WILD-TYPE        23         11         57         41       46
                  vv
clus               STAGE IVA STAGE IVB
  LRRC31 MUTATED           1         0
  LRRC31 WILD-TYPE        17         1
D1739V4, multiclass
            clus
vv           LRRC31 MUTATED LRRC31 WILD-TYPE
  STAGE I                 3               88
  STAGE IA                0                1
  STAGE II                1               31
  STAGE IIA               3              135
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               1               23
  STAGE IIIA              0               11
  STAGE IIIB              2               57
  STAGE IIIC              1               41
  STAGE IV                2               46
  STAGE IVA               1               17
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  LRRC31 MUTATED     0   3   9   4
  LRRC31 WILD-TYPE  17  89 320  46
D1739V5, multiclass
    clus
vv   LRRC31 MUTATED LRRC31 WILD-TYPE
  T1              0               17
  T2              3               89
  T3              9              320
  T4              4               46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  LRRC31 MUTATED    10   6   0
  LRRC31 WILD-TYPE 277 107  87
D1739V6, multiclass
    clus
vv   LRRC31 MUTATED LRRC31 WILD-TYPE
  N0             10              277
  N1              6              107
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1739V7, binary
                  cls
clus                 0   1
  LRRC31 MUTATED    10   3
  LRRC31 WILD-TYPE 365  62
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LRRC31 MUTATED     10    3
  LRRC31 WILD-TYPE  365   62
   clus
vv  LRRC31 MUTATED LRRC31 WILD-TYPE
  0             10              365
  1              3               62
[1] 2 2
[1] FALSE
D1739V8, binary
                  cls
clus                 0   1
  LRRC31 MUTATED     9   7
  LRRC31 WILD-TYPE 216 257
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LRRC31 MUTATED      9    7
  LRRC31 WILD-TYPE  216  257
        clus
vv       LRRC31 MUTATED LRRC31 WILD-TYPE
  FEMALE              9              216
  MALE                7              257
[1] 2 2
[1] FALSE
D1739V9, binary
                  cls
clus                 0   1
  LRRC31 MUTATED    10   0
  LRRC31 WILD-TYPE 340  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LRRC31 MUTATED     10    0
  LRRC31 WILD-TYPE  340   22
     clus
vv    LRRC31 MUTATED LRRC31 WILD-TYPE
  NO              10              340
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  LRRC31 MUTATED                     12                             2
  LRRC31 WILD-TYPE                  303                            45
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  LRRC31 MUTATED                       2                              0
  LRRC31 WILD-TYPE                   104                             10
D1739V10, multiclass
                                clus
vv                               LRRC31 MUTATED LRRC31 WILD-TYPE
  COLON ADENOCARCINOMA                       12              303
  COLON MUCINOUS ADENOCARCINOMA               2               45
  RECTAL ADENOCARCINOMA                       2              104
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  LRRC31 MUTATED    12   0   0   1
  LRRC31 WILD-TYPE 333   4  31  24
D1739V11, multiclass
    clus
vv   LRRC31 MUTATED LRRC31 WILD-TYPE
  R0             12              333
  R1              0                4
  R2              0               31
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1739V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  LRRC31 MUTATED                                  0     0
  LRRC31 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  LRRC31 MUTATED                           1     9
  LRRC31 WILD-TYPE                        21   217
D1739V13, multiclass
                                  clus
vv                                 LRRC31 MUTATED LRRC31 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                         9              217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1740) Variable = RARG MUTATION ANALYSIS
D1740V1, survival
                sevent
clus2              0   1
  RARG MUTATED     6   3
  RARG WILD-TYPE 372  90
  RARG MUTATED RARG WILD-TYPE 
             9            462 
  RARG MUTATED RARG WILD-TYPE 
             3             90 
$`RARG MUTATED`
TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3713 TCGA-AA-3968 TCGA-AA-A00J TCGA-AA-A02J 
       13.02         1.02        19.04        21.99        18.05         5.03 
TCGA-AY-6386 TCGA-AZ-6598 TCGA-G4-6307 
       17.82        49.41        55.04 

$`RARG WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        1.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02K 
       37.02        39.06        51.98        39.98         2.01        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-4323 
       16.31         0.95        33.01        21.44        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 
        5.13       106.75        22.36        62.79        88.21         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6310 
       74.56        65.85        53.62        44.68        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  RARG MUTATED RARG WILD-TYPE 
          1.02           0.00 
  RARG MUTATED RARG WILD-TYPE 
         55.04         148.01 
  RARG MUTATED RARG WILD-TYPE 
        18.050         20.415 
[1] "1.0 - 55.0 (18.1)"  "0.0 - 148.0 (20.4)"
[1] "hr=" "1.9"
D1740V2, continuous
D1740V3, binary
                cls
clus               0   1
  RARG MUTATED    10   0
  RARG WILD-TYPE 356 119
[1] "tbl2"
                cls
clus             [,1] [,2]
  RARG MUTATED     10    0
  RARG WILD-TYPE  356  119
        clus
vv       RARG MUTATED RARG WILD-TYPE
  COLON            10            356
  RECTUM            0            119
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RARG MUTATED         1        0        1         2         0         0
  RARG WILD-TYPE      90        1       31       136        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RARG MUTATED           1          0          3          0        2         0
  RARG WILD-TYPE        23         11         56         42       46        18
                vv
clus             STAGE IVB
  RARG MUTATED           0
  RARG WILD-TYPE         1
D1740V4, multiclass
            clus
vv           RARG MUTATED RARG WILD-TYPE
  STAGE I               1             90
  STAGE IA              0              1
  STAGE II              1             31
  STAGE IIA             2            136
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             1             23
  STAGE IIIA            0             11
  STAGE IIIB            3             56
  STAGE IIIC            0             42
  STAGE IV              2             46
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  RARG MUTATED     0   1   8   1
  RARG WILD-TYPE  17  91 321  49
D1740V5, multiclass
    clus
vv   RARG MUTATED RARG WILD-TYPE
  T1            0             17
  T2            1             91
  T3            8            321
  T4            1             49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  RARG MUTATED     6   3   1
  RARG WILD-TYPE 281 110  86
D1740V6, multiclass
    clus
vv   RARG MUTATED RARG WILD-TYPE
  N0            6            281
  N1            3            110
  N2            1             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1740V7, binary
                cls
clus               0   1
  RARG MUTATED     7   2
  RARG WILD-TYPE 368  63
[1] "tbl2"
                cls
clus             [,1] [,2]
  RARG MUTATED      7    2
  RARG WILD-TYPE  368   63
   clus
vv  RARG MUTATED RARG WILD-TYPE
  0            7            368
  1            2             63
[1] 2 2
[1] FALSE
D1740V8, binary
                cls
clus               0   1
  RARG MUTATED     8   2
  RARG WILD-TYPE 217 262
[1] "tbl2"
                cls
clus             [,1] [,2]
  RARG MUTATED      8    2
  RARG WILD-TYPE  217  262
        clus
vv       RARG MUTATED RARG WILD-TYPE
  FEMALE            8            217
  MALE              2            262
[1] 2 2
[1] FALSE
D1740V9, binary
                cls
clus               0   1
  RARG MUTATED     6   1
  RARG WILD-TYPE 344  21
[1] "tbl2"
                cls
clus             [,1] [,2]
  RARG MUTATED      6    1
  RARG WILD-TYPE  344   21
     clus
vv    RARG MUTATED RARG WILD-TYPE
  NO             6            344
  YES            1             21
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  RARG MUTATED                      8                             2
  RARG WILD-TYPE                  307                            45
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  RARG MUTATED                       0                              0
  RARG WILD-TYPE                   106                             10
D1740V10, multiclass
                                clus
vv                               RARG MUTATED RARG WILD-TYPE
  COLON ADENOCARCINOMA                      8            307
  COLON MUCINOUS ADENOCARCINOMA             2             45
  RECTAL ADENOCARCINOMA                     0            106
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  RARG MUTATED     6   0   2   0
  RARG WILD-TYPE 339   4  29  25
D1740V11, multiclass
    clus
vv   RARG MUTATED RARG WILD-TYPE
  R0            6            339
  R1            0              4
  R2            2             29
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1740V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RARG MUTATED                                  0     0
  RARG WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  RARG MUTATED                           1     2
  RARG WILD-TYPE                        21   224
D1740V13, multiclass
                                  clus
vv                                 RARG MUTATED RARG WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                       2            224
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1741) Variable = SFRS2IP MUTATION ANALYSIS
D1741V1, survival
                   sevent
clus2                 0   1
  SFRS2IP MUTATED    23   3
  SFRS2IP WILD-TYPE 355  90
  SFRS2IP MUTATED SFRS2IP WILD-TYPE 
               26               445 
  SFRS2IP MUTATED SFRS2IP WILD-TYPE 
                3                90 
$`SFRS2IP MUTATED`
TCGA-A6-6653 TCGA-AA-3510 TCGA-AA-3534 TCGA-AA-3710 TCGA-AA-3949 TCGA-AA-A00A 
       24.39        63.98        29.00        26.99        26.01        38.04 
TCGA-AA-A010 TCGA-AA-A01F TCGA-AA-A01P TCGA-AD-5900 TCGA-AD-6901 TCGA-AY-6197 
       34.98        32.02        38.07         0.07        22.42        21.44 
TCGA-AZ-4315 TCGA-CA-6717 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CM-5348 
       58.39        12.76        49.08        51.32         9.99        22.98 
TCGA-CM-5861 TCGA-DM-A1HB TCGA-F4-6856 TCGA-G4-6304 TCGA-G4-6309 TCGA-G4-6310 
       15.02       135.65        35.31        53.62        85.48        63.62 
TCGA-G4-6628 TCGA-AG-3878 
       79.69         0.99 

$`SFRS2IP WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
       25.08        25.18        24.16        21.76        24.69        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3538 TCGA-AA-3542 
        0.00        19.07        34.03        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       85.05        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       33.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       27.02        13.94        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01G 
       17.03        14.99        21.99         1.02        10.98        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        31.00         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       18.05        40.96        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        0.72         5.79        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4323 
       27.09        16.31         0.95        33.01        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07        12.20        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       85.45        15.62        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       22.03        30.08        32.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      131.51       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 
       33.67        13.25         0.53        47.41       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       65.85        44.68        55.04        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 
       13.78        35.80        26.17        91.79        46.75        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  SFRS2IP MUTATED SFRS2IP WILD-TYPE 
             0.07              0.00 
  SFRS2IP MUTATED SFRS2IP WILD-TYPE 
           135.65            148.01 
  SFRS2IP MUTATED SFRS2IP WILD-TYPE 
            33.50             19.99 
[1] "0.1 - 135.7 (33.5)" "0.0 - 148.0 (20.0)"
[1] "hr=" "2.7"
D1741V2, continuous
D1741V3, binary
                   cls
clus                  0   1
  SFRS2IP MUTATED    26   1
  SFRS2IP WILD-TYPE 340 118
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SFRS2IP MUTATED     26    1
  SFRS2IP WILD-TYPE  340  118
        clus
vv       SFRS2IP MUTATED SFRS2IP WILD-TYPE
  COLON               26               340
  RECTUM               1               118
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SFRS2IP MUTATED         6        0        1         9         2         0
  SFRS2IP WILD-TYPE      85        1       31       129         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SFRS2IP MUTATED           1          0          7          0        0
  SFRS2IP WILD-TYPE        23         11         52         42       48
                   vv
clus                STAGE IVA STAGE IVB
  SFRS2IP MUTATED           0         0
  SFRS2IP WILD-TYPE        18         1
D1741V4, multiclass
            clus
vv           SFRS2IP MUTATED SFRS2IP WILD-TYPE
  STAGE I                  6                85
  STAGE IA                 0                 1
  STAGE II                 1                31
  STAGE IIA                9               129
  STAGE IIB                2                 8
  STAGE IIC                0                 1
  STAGE III                1                23
  STAGE IIIA               0                11
  STAGE IIIB               7                52
  STAGE IIIC               0                42
  STAGE IV                 0                48
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  SFRS2IP MUTATED     0   6  19   2
  SFRS2IP WILD-TYPE  17  86 310  48
D1741V5, multiclass
    clus
vv   SFRS2IP MUTATED SFRS2IP WILD-TYPE
  T1               0                17
  T2               6                86
  T3              19               310
  T4               2                48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  SFRS2IP MUTATED    19   8   0
  SFRS2IP WILD-TYPE 268 105  87
D1741V6, multiclass
    clus
vv   SFRS2IP MUTATED SFRS2IP WILD-TYPE
  N0              19               268
  N1               8               105
  N2               0                87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1741V7, binary
                   cls
clus                  0   1
  SFRS2IP MUTATED    21   0
  SFRS2IP WILD-TYPE 354  65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SFRS2IP MUTATED     21    0
  SFRS2IP WILD-TYPE  354   65
   clus
vv  SFRS2IP MUTATED SFRS2IP WILD-TYPE
  0              21               354
  1               0                65
[1] 2 2
[1] FALSE
D1741V8, binary
                   cls
clus                  0   1
  SFRS2IP MUTATED    10  17
  SFRS2IP WILD-TYPE 215 247
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SFRS2IP MUTATED     10   17
  SFRS2IP WILD-TYPE  215  247
        clus
vv       SFRS2IP MUTATED SFRS2IP WILD-TYPE
  FEMALE              10               215
  MALE                17               247
[1] 2 2
[1] FALSE
D1741V9, binary
                   cls
clus                  0   1
  SFRS2IP MUTATED    21   1
  SFRS2IP WILD-TYPE 329  21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SFRS2IP MUTATED     21    1
  SFRS2IP WILD-TYPE  329   21
     clus
vv    SFRS2IP MUTATED SFRS2IP WILD-TYPE
  NO               21               329
  YES               1                21
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SFRS2IP MUTATED                     21                             4
  SFRS2IP WILD-TYPE                  294                            43
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SFRS2IP MUTATED                       1                              0
  SFRS2IP WILD-TYPE                   105                             10
D1741V10, multiclass
                                clus
vv                               SFRS2IP MUTATED SFRS2IP WILD-TYPE
  COLON ADENOCARCINOMA                        21               294
  COLON MUCINOUS ADENOCARCINOMA                4                43
  RECTAL ADENOCARCINOMA                        1               105
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  SFRS2IP MUTATED    20   0   0   4
  SFRS2IP WILD-TYPE 325   4  31  21
D1741V11, multiclass
    clus
vv   SFRS2IP MUTATED SFRS2IP WILD-TYPE
  R0              20               325
  R1               0                 4
  R2               0                31
  RX               4                21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1741V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SFRS2IP MUTATED                                  0     1
  SFRS2IP WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  SFRS2IP MUTATED                           1    15
  SFRS2IP WILD-TYPE                        21   211
D1741V13, multiclass
                                  clus
vv                                 SFRS2IP MUTATED SFRS2IP WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                10
  BLACK OR AFRICAN AMERICAN                      1                21
  WHITE                                         15               211
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1742) Variable = TCTEX1D2 MUTATION ANALYSIS
D1742V1, survival
                    sevent
clus2                  0   1
  TCTEX1D2 MUTATED     6   1
  TCTEX1D2 WILD-TYPE 372  92
  TCTEX1D2 MUTATED TCTEX1D2 WILD-TYPE 
                 7                464 
  TCTEX1D2 MUTATED TCTEX1D2 WILD-TYPE 
                 1                 92 
$`TCTEX1D2 MUTATED`
TCGA-A6-2678 TCGA-AA-A00E TCGA-CA-6717 TCGA-CK-6748 TCGA-DM-A1HB TCGA-AG-3608 
       42.28        30.02        12.76         1.91       135.65        15.95 
TCGA-DY-A1DG 
       51.48 

$`TCTEX1D2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2683 
       43.76        46.65        43.76        42.90        24.33        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       38.04        19.00        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.20        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 
      140.38         7.50        44.32       131.51       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3609 
        2.01        50.04        12.03         6.05         0.99        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1H8 
        5.29       126.44        41.36        57.24        24.13        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  TCTEX1D2 MUTATED TCTEX1D2 WILD-TYPE 
              1.91               0.00 
  TCTEX1D2 MUTATED TCTEX1D2 WILD-TYPE 
            135.65             148.01 
  TCTEX1D2 MUTATED TCTEX1D2 WILD-TYPE 
            30.020             20.155 
[1] "1.9 - 135.7 (30.0)" "0.0 - 148.0 (20.2)"
[1] "hr=" "2"  
D1742V2, continuous
D1742V3, binary
                    cls
clus                   0   1
  TCTEX1D2 MUTATED     5   2
  TCTEX1D2 WILD-TYPE 361 117
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  TCTEX1D2 MUTATED      5    2
  TCTEX1D2 WILD-TYPE  361  117
        clus
vv       TCTEX1D2 MUTATED TCTEX1D2 WILD-TYPE
  COLON                 5                361
  RECTUM                2                117
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TCTEX1D2 MUTATED         0        0        0         3         0         0
  TCTEX1D2 WILD-TYPE      91        1       32       135        10         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TCTEX1D2 MUTATED           0          0          2          0        1
  TCTEX1D2 WILD-TYPE        24         11         57         42       47
                    vv
clus                 STAGE IVA STAGE IVB
  TCTEX1D2 MUTATED           1         0
  TCTEX1D2 WILD-TYPE        17         1
D1742V4, multiclass
            clus
vv           TCTEX1D2 MUTATED TCTEX1D2 WILD-TYPE
  STAGE I                   0                 91
  STAGE IA                  0                  1
  STAGE II                  0                 32
  STAGE IIA                 3                135
  STAGE IIB                 0                 10
  STAGE IIC                 0                  1
  STAGE III                 0                 24
  STAGE IIIA                0                 11
  STAGE IIIB                2                 57
  STAGE IIIC                0                 42
  STAGE IV                  1                 47
  STAGE IVA                 1                 17
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  TCTEX1D2 MUTATED     0   0   7   0
  TCTEX1D2 WILD-TYPE  17  92 322  50
D1742V5, multiclass
    clus
vv   TCTEX1D2 MUTATED TCTEX1D2 WILD-TYPE
  T1                0                 17
  T2                0                 92
  T3                7                322
  T4                0                 50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  TCTEX1D2 MUTATED     3   4   0
  TCTEX1D2 WILD-TYPE 284 109  87
D1742V6, multiclass
    clus
vv   TCTEX1D2 MUTATED TCTEX1D2 WILD-TYPE
  N0                3                284
  N1                4                109
  N2                0                 87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1742V7, binary
                    cls
clus                   0   1
  TCTEX1D2 MUTATED     5   2
  TCTEX1D2 WILD-TYPE 370  63
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  TCTEX1D2 MUTATED      5    2
  TCTEX1D2 WILD-TYPE  370   63
   clus
vv  TCTEX1D2 MUTATED TCTEX1D2 WILD-TYPE
  0                5                370
  1                2                 63
[1] 2 2
[1] FALSE
D1742V8, binary
                    cls
clus                   0   1
  TCTEX1D2 MUTATED     3   4
  TCTEX1D2 WILD-TYPE 222 260
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  TCTEX1D2 MUTATED      3    4
  TCTEX1D2 WILD-TYPE  222  260
        clus
vv       TCTEX1D2 MUTATED TCTEX1D2 WILD-TYPE
  FEMALE                3                222
  MALE                  4                260
[1] 2 2
[1] FALSE
D1742V9, binary
                    cls
clus                   0   1
  TCTEX1D2 MUTATED     5   0
  TCTEX1D2 WILD-TYPE 345  22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  TCTEX1D2 MUTATED      5    0
  TCTEX1D2 WILD-TYPE  345   22
     clus
vv    TCTEX1D2 MUTATED TCTEX1D2 WILD-TYPE
  NO                 5                345
  YES                0                 22
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  TCTEX1D2 MUTATED                      2                             2
  TCTEX1D2 WILD-TYPE                  313                            45
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  TCTEX1D2 MUTATED                       2                              0
  TCTEX1D2 WILD-TYPE                   104                             10
D1742V10, multiclass
                                clus
vv                               TCTEX1D2 MUTATED TCTEX1D2 WILD-TYPE
  COLON ADENOCARCINOMA                          2                313
  COLON MUCINOUS ADENOCARCINOMA                 2                 45
  RECTAL ADENOCARCINOMA                         2                104
  RECTAL MUCINOUS ADENOCARCINOMA                0                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  TCTEX1D2 MUTATED     3   0   0   2
  TCTEX1D2 WILD-TYPE 342   4  31  23
D1742V11, multiclass
    clus
vv   TCTEX1D2 MUTATED TCTEX1D2 WILD-TYPE
  R0                3                342
  R1                0                  4
  R2                0                 31
  RX                2                 23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1742V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TCTEX1D2 MUTATED                                  0     1
  TCTEX1D2 WILD-TYPE                                1    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  TCTEX1D2 MUTATED                           0     4
  TCTEX1D2 WILD-TYPE                        22   222
D1742V13, multiclass
                                  clus
vv                                 TCTEX1D2 MUTATED TCTEX1D2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                 10
  BLACK OR AFRICAN AMERICAN                       0                 22
  WHITE                                           4                222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1743) Variable = IKBKB MUTATION ANALYSIS
D1743V1, survival
                 sevent
clus2               0   1
  IKBKB MUTATED     8   1
  IKBKB WILD-TYPE 370  92
  IKBKB MUTATED IKBKB WILD-TYPE 
              9             462 
  IKBKB MUTATED IKBKB WILD-TYPE 
              1              92 
$`IKBKB MUTATED`
TCGA-A6-5666 TCGA-AA-A010 TCGA-AA-A01T TCGA-AZ-6599 TCGA-CA-6716 TCGA-CA-6717 
       32.71        34.98        33.04         6.77        12.20        12.76 
TCGA-D5-6532 TCGA-AG-A002 TCGA-AG-A02N 
       18.25        20.98        61.97 

$`IKBKB WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        22.06        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        88.21        49.41        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6718 TCGA-CA-6719 
        3.06         3.25         3.29         0.07        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       56.09        55.92        20.19         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 
       10.98        49.97         1.94        38.96        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  IKBKB MUTATED IKBKB WILD-TYPE 
           6.77            0.00 
  IKBKB MUTATED IKBKB WILD-TYPE 
          61.97          148.01 
  IKBKB MUTATED IKBKB WILD-TYPE 
         20.980          20.155 
[1] "6.8 - 62.0 (21.0)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.7"
D1743V2, continuous
D1743V3, binary
                 cls
clus                0   1
  IKBKB MUTATED     7   2
  IKBKB WILD-TYPE 359 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IKBKB MUTATED      7    2
  IKBKB WILD-TYPE  359  117
        clus
vv       IKBKB MUTATED IKBKB WILD-TYPE
  COLON              7             359
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  IKBKB MUTATED         2        0        1         3         1         1
  IKBKB WILD-TYPE      89        1       31       135         9         0
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  IKBKB MUTATED           1          0          0          0        0         0
  IKBKB WILD-TYPE        23         11         59         42       48        18
                 vv
clus              STAGE IVB
  IKBKB MUTATED           0
  IKBKB WILD-TYPE         1
D1743V4, multiclass
            clus
vv           IKBKB MUTATED IKBKB WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              3             135
  STAGE IIB              1               9
  STAGE IIC              1               0
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  IKBKB MUTATED     0   2   5   2
  IKBKB WILD-TYPE  17  90 324  48
D1743V5, multiclass
    clus
vv   IKBKB MUTATED IKBKB WILD-TYPE
  T1             0              17
  T2             2              90
  T3             5             324
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  IKBKB MUTATED     8   1   0
  IKBKB WILD-TYPE 279 112  87
D1743V6, multiclass
    clus
vv   IKBKB MUTATED IKBKB WILD-TYPE
  N0             8             279
  N1             1             112
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1743V7, binary
                 cls
clus                0   1
  IKBKB MUTATED     8   0
  IKBKB WILD-TYPE 367  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IKBKB MUTATED      8    0
  IKBKB WILD-TYPE  367   65
   clus
vv  IKBKB MUTATED IKBKB WILD-TYPE
  0             8             367
  1             0              65
[1] 2 2
[1] FALSE
D1743V8, binary
                 cls
clus                0   1
  IKBKB MUTATED     2   7
  IKBKB WILD-TYPE 223 257
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IKBKB MUTATED      2    7
  IKBKB WILD-TYPE  223  257
        clus
vv       IKBKB MUTATED IKBKB WILD-TYPE
  FEMALE             2             223
  MALE               7             257
[1] 2 2
[1] FALSE
D1743V9, binary
                 cls
clus                0   1
  IKBKB MUTATED     8   0
  IKBKB WILD-TYPE 342  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IKBKB MUTATED      8    0
  IKBKB WILD-TYPE  342   22
     clus
vv    IKBKB MUTATED IKBKB WILD-TYPE
  NO              8             342
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  IKBKB MUTATED                      6                             1
  IKBKB WILD-TYPE                  309                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  IKBKB MUTATED                       2                              0
  IKBKB WILD-TYPE                   104                             10
D1743V10, multiclass
                                clus
vv                               IKBKB MUTATED IKBKB WILD-TYPE
  COLON ADENOCARCINOMA                       6             309
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  IKBKB MUTATED     5   0   0   2
  IKBKB WILD-TYPE 340   4  31  23
D1743V11, multiclass
    clus
vv   IKBKB MUTATED IKBKB WILD-TYPE
  R0             5             340
  R1             0               4
  R2             0              31
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1743V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  IKBKB MUTATED                                  0     2
  IKBKB WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  IKBKB MUTATED                           0     3
  IKBKB WILD-TYPE                        22   223
D1743V13, multiclass
                                  clus
vv                                 IKBKB MUTATED IKBKB WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               9
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        3             223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1744) Variable = PPIL5 MUTATION ANALYSIS
D1744V1, survival
                 sevent
clus2               0   1
  PPIL5 MUTATED     1   2
  PPIL5 WILD-TYPE 377  91
  PPIL5 MUTATED PPIL5 WILD-TYPE 
              3             468 
  PPIL5 MUTATED PPIL5 WILD-TYPE 
              2              91 
$`PPIL5 MUTATED`
TCGA-A6-2671 TCGA-AA-A01P TCGA-G4-6588 
       43.76        38.07        26.17 

$`PPIL5 WILD-TYPE`
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       46.65        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       12.00        31.00        31.00         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  PPIL5 MUTATED PPIL5 WILD-TYPE 
          26.17            0.00 
  PPIL5 MUTATED PPIL5 WILD-TYPE 
          43.76          148.01 
  PPIL5 MUTATED PPIL5 WILD-TYPE 
         38.070          20.085 
[1] "26.2 - 43.8 (38.1)" "0.0 - 148.0 (20.1)"
[1] "hr=" "2.6"
D1744V2, continuous
D1744V3, binary
                 cls
clus                0   1
  PPIL5 MUTATED     4   0
  PPIL5 WILD-TYPE 362 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PPIL5 MUTATED      4    0
  PPIL5 WILD-TYPE  362  119
        clus
vv       PPIL5 MUTATED PPIL5 WILD-TYPE
  COLON              4             362
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PPIL5 MUTATED         0        0        0         1         0         0
  PPIL5 WILD-TYPE      91        1       32       137        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PPIL5 MUTATED           2          0          0          0        1         0
  PPIL5 WILD-TYPE        22         11         59         42       47        18
                 vv
clus              STAGE IVB
  PPIL5 MUTATED           0
  PPIL5 WILD-TYPE         1
D1744V4, multiclass
            clus
vv           PPIL5 MUTATED PPIL5 WILD-TYPE
  STAGE I                0              91
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              1             137
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              2              22
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             0              42
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PPIL5 MUTATED     0   0   4   0
  PPIL5 WILD-TYPE  17  92 325  50
D1744V5, multiclass
    clus
vv   PPIL5 MUTATED PPIL5 WILD-TYPE
  T1             0              17
  T2             0              92
  T3             4             325
  T4             0              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  PPIL5 MUTATED     1   1   2
  PPIL5 WILD-TYPE 286 112  85
D1744V6, multiclass
    clus
vv   PPIL5 MUTATED PPIL5 WILD-TYPE
  N0             1             286
  N1             1             112
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1744V7, binary
                 cls
clus                0   1
  PPIL5 MUTATED     3   1
  PPIL5 WILD-TYPE 372  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PPIL5 MUTATED      3    1
  PPIL5 WILD-TYPE  372   64
   clus
vv  PPIL5 MUTATED PPIL5 WILD-TYPE
  0             3             372
  1             1              64
[1] 2 2
[1] FALSE
D1744V8, binary
                 cls
clus                0   1
  PPIL5 MUTATED     2   2
  PPIL5 WILD-TYPE 223 262
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PPIL5 MUTATED      2    2
  PPIL5 WILD-TYPE  223  262
        clus
vv       PPIL5 MUTATED PPIL5 WILD-TYPE
  FEMALE             2             223
  MALE               2             262
[1] 2 2
[1] FALSE
D1744V9, binary
                 cls
clus                0   1
  PPIL5 MUTATED     3   0
  PPIL5 WILD-TYPE 347  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PPIL5 MUTATED      3    0
  PPIL5 WILD-TYPE  347   22
     clus
vv    PPIL5 MUTATED PPIL5 WILD-TYPE
  NO              3             347
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PPIL5 MUTATED                      4                             0
  PPIL5 WILD-TYPE                  311                            47
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PPIL5 MUTATED                       0                              0
  PPIL5 WILD-TYPE                   106                             10
D1744V10, multiclass
                                clus
vv                               PPIL5 MUTATED PPIL5 WILD-TYPE
  COLON ADENOCARCINOMA                       4             311
  COLON MUCINOUS ADENOCARCINOMA              0              47
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  PPIL5 MUTATED     4   0   0   0
  PPIL5 WILD-TYPE 341   4  31  25
D1744V11, multiclass
    clus
vv   PPIL5 MUTATED PPIL5 WILD-TYPE
  R0             4             341
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1744V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PPIL5 MUTATED                                  0     0
  PPIL5 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PPIL5 MUTATED                           0     2
  PPIL5 WILD-TYPE                        22   224
D1744V13, multiclass
[1] "Remove cluster labels:" "PPIL5 MUTATED"         
clus
  PPIL5 MUTATED PPIL5 WILD-TYPE 
              2             258 
     TCGA-A6-2672      TCGA-A6-2674      TCGA-A6-2676      TCGA-A6-2677 
"PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" 
     TCGA-A6-2678      TCGA-A6-2683      TCGA-A6-3807      TCGA-A6-3808 
"PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" 
     TCGA-A6-3809      TCGA-A6-3810      TCGA-A6-4105      TCGA-A6-5656 
"PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" 
     TCGA-A6-5657      TCGA-A6-5659      TCGA-A6-5660      TCGA-A6-5661 
"PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" 
     TCGA-A6-5662      TCGA-A6-5664      TCGA-A6-5665      TCGA-A6-5666 
"PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" 
     TCGA-A6-6137      TCGA-A6-6138      TCGA-A6-6141      TCGA-A6-6142 
"PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" 
     TCGA-A6-6648      TCGA-A6-6649      TCGA-A6-6651      TCGA-A6-6652 
"PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" 
     TCGA-A6-6653      TCGA-A6-6654      TCGA-A6-6780      TCGA-A6-6781 
"PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" 
     TCGA-A6-6782      TCGA-AD-5900      TCGA-AD-6548      TCGA-AD-6888 
"PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" 
     TCGA-AD-6889      TCGA-AD-6890      TCGA-AD-6895      TCGA-AD-6899 
"PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" 
     TCGA-AD-6901      TCGA-AD-6963      TCGA-AD-6964      TCGA-AD-6965 
"PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" 
     TCGA-AU-3779      TCGA-AU-6004      TCGA-AY-4070      TCGA-AY-4071 
"PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" 
     TCGA-AY-5543      TCGA-AY-6196      TCGA-AY-6197      TCGA-AY-6386 
"PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" 
     TCGA-AZ-4315      TCGA-AZ-4323      TCGA-AZ-4616      TCGA-AZ-4681 
"PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" 
     TCGA-AZ-4682      TCGA-AZ-5403      TCGA-AZ-5407      TCGA-AZ-6598 
"PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" 
     TCGA-AZ-6599      TCGA-AZ-6600      TCGA-AZ-6601      TCGA-AZ-6603 
"PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" 
     TCGA-AZ-6605      TCGA-AZ-6606      TCGA-AZ-6607      TCGA-AZ-6608 
"PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" 
     TCGA-CA-5254      TCGA-CA-5255      TCGA-CA-5796      TCGA-CA-5797 
"PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" 
     TCGA-CA-6715      TCGA-CA-6716      TCGA-CA-6717      TCGA-CA-6718 
"PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" 
     TCGA-CA-6719      TCGA-CK-4947      TCGA-CK-4948      TCGA-CK-4950 
"PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" 
     TCGA-CK-4952      TCGA-CK-5912      TCGA-CK-5913      TCGA-CK-5914 
"PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" 
     TCGA-CK-5915      TCGA-CK-5916      TCGA-CK-6746      TCGA-CK-6747 
"PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" 
     TCGA-CK-6748      TCGA-CK-6751      TCGA-CM-4743      TCGA-CM-4744 
"PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" 
     TCGA-CM-4746      TCGA-CM-4747      TCGA-CM-4752      TCGA-CM-5341 
"PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" 
     TCGA-CM-5344      TCGA-CM-5348      TCGA-CM-5349      TCGA-CM-5860 
"PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" 
     TCGA-CM-5861      TCGA-CM-5862      TCGA-CM-5863      TCGA-CM-5864 
"PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" 
     TCGA-CM-5868      TCGA-CM-6161      TCGA-CM-6162      TCGA-CM-6163 
"PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" 
     TCGA-CM-6164      TCGA-CM-6165      TCGA-CM-6166      TCGA-CM-6167 
"PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" 
     TCGA-CM-6168      TCGA-CM-6169      TCGA-CM-6170      TCGA-CM-6171 
"PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" 
     TCGA-CM-6172      TCGA-CM-6674      TCGA-CM-6675      TCGA-CM-6676 
"PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" 
     TCGA-CM-6677      TCGA-CM-6678      TCGA-CM-6679      TCGA-CM-6680 
"PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" 
     TCGA-D5-5537      TCGA-D5-5538      TCGA-D5-5539      TCGA-D5-5540 
"PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" 
     TCGA-D5-5541      TCGA-D5-6529      TCGA-D5-6532      TCGA-D5-6533 
"PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" 
     TCGA-D5-6534      TCGA-D5-6535      TCGA-D5-6536      TCGA-D5-6537 
"PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" 
     TCGA-D5-6538      TCGA-D5-6539      TCGA-D5-6540      TCGA-D5-6541 
"PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" 
     TCGA-D5-6898      TCGA-D5-6920      TCGA-D5-6922      TCGA-D5-6923 
"PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" 
     TCGA-D5-6924      TCGA-D5-6926      TCGA-D5-6927      TCGA-D5-6928 
"PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" 
     TCGA-D5-6929      TCGA-D5-6930      TCGA-D5-6931      TCGA-D5-6932 
"PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" 
     TCGA-D5-7000      TCGA-DM-A0X9      TCGA-DM-A0XD      TCGA-DM-A0XF 
"PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" 
     TCGA-DM-A1D0      TCGA-DM-A1D4      TCGA-DM-A1D6      TCGA-DM-A1D7 
"PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" 
     TCGA-DM-A1D8      TCGA-DM-A1D9      TCGA-DM-A1DA      TCGA-DM-A1DB 
"PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" 
     TCGA-DM-A1HA      TCGA-DM-A1HB      TCGA-DM-A282      TCGA-DM-A285 
"PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" 
     TCGA-DM-A28C      TCGA-DM-A28E      TCGA-DM-A28F      TCGA-DM-A28G 
"PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" 
     TCGA-DM-A28H      TCGA-DM-A28K      TCGA-F4-6459      TCGA-F4-6460 
"PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" 
     TCGA-F4-6569      TCGA-F4-6570      TCGA-F4-6703      TCGA-F4-6704 
"PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" 
     TCGA-F4-6805      TCGA-F4-6806      TCGA-F4-6807      TCGA-F4-6808 
"PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" 
     TCGA-F4-6809      TCGA-F4-6854      TCGA-F4-6855      TCGA-F4-6856 
"PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" 
     TCGA-G4-6293      TCGA-G4-6299      TCGA-G4-6303      TCGA-G4-6304 
"PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" 
     TCGA-G4-6306      TCGA-G4-6307      TCGA-G4-6309      TCGA-G4-6310 
"PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" 
     TCGA-G4-6315      TCGA-G4-6317      TCGA-G4-6321      TCGA-G4-6323 
"PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" 
     TCGA-G4-6586      TCGA-G4-6625      TCGA-G4-6626      TCGA-G4-6628 
"PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" 
     TCGA-AF-2687      TCGA-AF-2689      TCGA-AF-2691      TCGA-AF-2692 
"PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" 
     TCGA-AF-2693      TCGA-AF-3400      TCGA-AF-3913      TCGA-AF-4110 
"PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" 
     TCGA-AF-5654      TCGA-AF-6136      TCGA-AF-6655      TCGA-AF-6672 
"PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" 
     TCGA-AH-6544      TCGA-AH-6547      TCGA-AH-6549      TCGA-AH-6643 
"PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" 
     TCGA-AH-6644      TCGA-CI-6619      TCGA-CI-6620      TCGA-CI-6621 
"PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" 
     TCGA-CI-6622      TCGA-CI-6624      TCGA-CL-5917      TCGA-CL-5918 
"PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" 
     TCGA-DC-5337      TCGA-DC-5869      TCGA-DC-6155      TCGA-DC-6157 
"PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" 
     TCGA-DC-6158      TCGA-DC-6160      TCGA-DC-6681      TCGA-DC-6682 
"PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" 
     TCGA-DC-6683      TCGA-DT-5265      TCGA-DY-A0XA      TCGA-DY-A1DC 
"PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" 
     TCGA-DY-A1DD      TCGA-DY-A1DF      TCGA-DY-A1DG      TCGA-DY-A1H8 
"PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" 
     TCGA-EF-5830      TCGA-EI-6506      TCGA-EI-6507      TCGA-EI-6508 
"PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" 
     TCGA-EI-6510      TCGA-F5-6464      TCGA-F5-6465      TCGA-F5-6571 
"PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" 
     TCGA-F5-6702      TCGA-F5-6811      TCGA-F5-6812      TCGA-F5-6813 
"PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" 
     TCGA-G5-6235      TCGA-G5-6641 
"PPIL5 WILD-TYPE" "PPIL5 WILD-TYPE" 

Clustering(1745) Variable = RNF8 MUTATION ANALYSIS
D1745V1, survival
                sevent
clus2              0   1
  RNF8 MUTATED     6   1
  RNF8 WILD-TYPE 372  92
  RNF8 MUTATED RNF8 WILD-TYPE 
             7            464 
  RNF8 MUTATED RNF8 WILD-TYPE 
             1             92 
$`RNF8 MUTATED`
TCGA-AA-3510 TCGA-AA-A010 TCGA-AZ-4315 TCGA-CA-6717 TCGA-CA-6718 TCGA-DM-A0X9 
       63.98        34.98        58.39        12.76        10.06       119.70 
TCGA-AF-2693 
       19.10 

$`RNF8 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       33.01        21.44        17.82         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       12.00        11.38        10.26        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3913 
       24.13        39.48        43.04        13.55        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  RNF8 MUTATED RNF8 WILD-TYPE 
         10.06           0.00 
  RNF8 MUTATED RNF8 WILD-TYPE 
        119.70         148.01 
  RNF8 MUTATED RNF8 WILD-TYPE 
        34.980         20.155 
[1] "10.1 - 119.7 (35.0)" "0.0 - 148.0 (20.2)" 
[1] "hr=" "2.4"
D1745V2, continuous
D1745V3, binary
                cls
clus               0   1
  RNF8 MUTATED     6   0
  RNF8 WILD-TYPE 360 119
[1] "tbl2"
                cls
clus             [,1] [,2]
  RNF8 MUTATED      6    0
  RNF8 WILD-TYPE  360  119
        clus
vv       RNF8 MUTATED RNF8 WILD-TYPE
  COLON             6            360
  RECTUM            0            119
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RNF8 MUTATED         1        0        1         4         1         0
  RNF8 WILD-TYPE      90        1       31       134         9         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RNF8 MUTATED           0          0          0          0        0         0
  RNF8 WILD-TYPE        24         11         59         42       48        18
                vv
clus             STAGE IVB
  RNF8 MUTATED           0
  RNF8 WILD-TYPE         1
D1745V4, multiclass
            clus
vv           RNF8 MUTATED RNF8 WILD-TYPE
  STAGE I               1             90
  STAGE IA              0              1
  STAGE II              1             31
  STAGE IIA             4            134
  STAGE IIB             1              9
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            0             59
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  RNF8 MUTATED     0   1   5   1
  RNF8 WILD-TYPE  17  91 324  49
D1745V5, multiclass
    clus
vv   RNF8 MUTATED RNF8 WILD-TYPE
  T1            0             17
  T2            1             91
  T3            5            324
  T4            1             49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  RNF8 MUTATED     7   0   0
  RNF8 WILD-TYPE 280 113  87
D1745V6, multiclass
    clus
vv   RNF8 MUTATED RNF8 WILD-TYPE
  N0            7            280
  N1            0            113
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1745V7, binary
                cls
clus               0   1
  RNF8 MUTATED     6   0
  RNF8 WILD-TYPE 369  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  RNF8 MUTATED      6    0
  RNF8 WILD-TYPE  369   65
   clus
vv  RNF8 MUTATED RNF8 WILD-TYPE
  0            6            369
  1            0             65
[1] 2 2
[1] FALSE
D1745V8, binary
                cls
clus               0   1
  RNF8 MUTATED     2   5
  RNF8 WILD-TYPE 223 259
[1] "tbl2"
                cls
clus             [,1] [,2]
  RNF8 MUTATED      2    5
  RNF8 WILD-TYPE  223  259
        clus
vv       RNF8 MUTATED RNF8 WILD-TYPE
  FEMALE            2            223
  MALE              5            259
[1] 2 2
[1] FALSE
D1745V9, binary
                cls
clus               0   1
  RNF8 MUTATED     6   0
  RNF8 WILD-TYPE 344  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  RNF8 MUTATED      6    0
  RNF8 WILD-TYPE  344   22
     clus
vv    RNF8 MUTATED RNF8 WILD-TYPE
  NO             6            344
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  RNF8 MUTATED                      5                             1
  RNF8 WILD-TYPE                  310                            46
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  RNF8 MUTATED                       0                              0
  RNF8 WILD-TYPE                   106                             10
D1745V10, multiclass
                                clus
vv                               RNF8 MUTATED RNF8 WILD-TYPE
  COLON ADENOCARCINOMA                      5            310
  COLON MUCINOUS ADENOCARCINOMA             1             46
  RECTAL ADENOCARCINOMA                     0            106
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  RNF8 MUTATED     3   0   0   2
  RNF8 WILD-TYPE 342   4  31  23
D1745V11, multiclass
    clus
vv   RNF8 MUTATED RNF8 WILD-TYPE
  R0            3            342
  R1            0              4
  R2            0             31
  RX            2             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1745V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RNF8 MUTATED                                  0     2
  RNF8 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  RNF8 MUTATED                           0     3
  RNF8 WILD-TYPE                        22   223
D1745V13, multiclass
                                  clus
vv                                 RNF8 MUTATED RNF8 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              9
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       3            223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1746) Variable = EPHA6 MUTATION ANALYSIS
D1746V1, survival
                 sevent
clus2               0   1
  EPHA6 MUTATED    16   6
  EPHA6 WILD-TYPE 362  87
  EPHA6 MUTATED EPHA6 WILD-TYPE 
             22             449 
  EPHA6 MUTATED EPHA6 WILD-TYPE 
              6              87 
$`EPHA6 MUTATED`
TCGA-A6-5666 TCGA-A6-6780 TCGA-AA-3811 TCGA-AA-3950 TCGA-AA-A010 TCGA-AA-A01R 
       32.71        20.12        10.06        24.00        34.98        35.01 
TCGA-AZ-4315 TCGA-AZ-5403 TCGA-CK-4947 TCGA-CM-4743 TCGA-CM-5864 TCGA-CM-6171 
       58.39        62.79        17.56        23.05        15.02        14.04 
TCGA-D5-6532 TCGA-DM-A28H TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6570 TCGA-G4-6293 
       18.25       117.07         8.61        31.96         6.18       133.18 
TCGA-G4-6586 TCGA-CI-6624 TCGA-DC-6160 TCGA-DY-A1DC 
       35.80         4.73        19.99        41.36 

$`EPHA6 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        22.06        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        19.04        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        33.01        26.01         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
        1.02         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
       16.31         0.95        33.01        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
        5.13       106.75        22.36        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-4950 
       12.20        12.76        10.06        14.30       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
        1.91       124.27        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
        5.03        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       15.02        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       56.09        55.92        20.19         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28K TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 
       35.97        60.79        98.24        35.74        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       47.41        35.31        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       13.78        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CL-5917 
        0.69         0.72         6.05        33.17         6.97        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DD 
        5.95         4.01         5.03         5.29       126.44        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  EPHA6 MUTATED EPHA6 WILD-TYPE 
           4.73            0.00 
  EPHA6 MUTATED EPHA6 WILD-TYPE 
         133.18          148.01 
  EPHA6 MUTATED EPHA6 WILD-TYPE 
         23.525          20.050 
[1] "4.7 - 133.2 (23.5)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.1"
D1746V2, continuous
D1746V3, binary
                 cls
clus                0   1
  EPHA6 MUTATED    21   3
  EPHA6 WILD-TYPE 345 116
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPHA6 MUTATED     21    3
  EPHA6 WILD-TYPE  345  116
        clus
vv       EPHA6 MUTATED EPHA6 WILD-TYPE
  COLON             21             345
  RECTUM             3             116
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  EPHA6 MUTATED         4        0        1         9         2         1
  EPHA6 WILD-TYPE      87        1       31       129         8         0
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  EPHA6 MUTATED           3          0          3          1        0         0
  EPHA6 WILD-TYPE        21         11         56         41       48        18
                 vv
clus              STAGE IVB
  EPHA6 MUTATED           0
  EPHA6 WILD-TYPE         1
D1746V4, multiclass
            clus
vv           EPHA6 MUTATED EPHA6 WILD-TYPE
  STAGE I                4              87
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              9             129
  STAGE IIB              2               8
  STAGE IIC              1               0
  STAGE III              3              21
  STAGE IIIA             0              11
  STAGE IIIB             3              56
  STAGE IIIC             1              41
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  EPHA6 MUTATED     0   4  16   4
  EPHA6 WILD-TYPE  17  88 313  46
D1746V5, multiclass
    clus
vv   EPHA6 MUTATED EPHA6 WILD-TYPE
  T1             0              17
  T2             4              88
  T3            16             313
  T4             4              46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  EPHA6 MUTATED    17   3   4
  EPHA6 WILD-TYPE 270 110  83
D1746V6, multiclass
    clus
vv   EPHA6 MUTATED EPHA6 WILD-TYPE
  N0            17             270
  N1             3             110
  N2             4              83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1746V7, binary
                 cls
clus                0   1
  EPHA6 MUTATED    21   0
  EPHA6 WILD-TYPE 354  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPHA6 MUTATED     21    0
  EPHA6 WILD-TYPE  354   65
   clus
vv  EPHA6 MUTATED EPHA6 WILD-TYPE
  0            21             354
  1             0              65
[1] 2 2
[1] FALSE
D1746V8, binary
                 cls
clus                0   1
  EPHA6 MUTATED    14  10
  EPHA6 WILD-TYPE 211 254
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPHA6 MUTATED     14   10
  EPHA6 WILD-TYPE  211  254
        clus
vv       EPHA6 MUTATED EPHA6 WILD-TYPE
  FEMALE            14             211
  MALE              10             254
[1] 2 2
[1] FALSE
D1746V9, binary
                 cls
clus                0   1
  EPHA6 MUTATED    17   1
  EPHA6 WILD-TYPE 333  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPHA6 MUTATED     17    1
  EPHA6 WILD-TYPE  333   21
     clus
vv    EPHA6 MUTATED EPHA6 WILD-TYPE
  NO             17             333
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  EPHA6 MUTATED                     18                             3
  EPHA6 WILD-TYPE                  297                            44
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  EPHA6 MUTATED                       3                              0
  EPHA6 WILD-TYPE                   103                             10
D1746V10, multiclass
                                clus
vv                               EPHA6 MUTATED EPHA6 WILD-TYPE
  COLON ADENOCARCINOMA                      18             297
  COLON MUCINOUS ADENOCARCINOMA              3              44
  RECTAL ADENOCARCINOMA                      3             103
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  EPHA6 MUTATED    16   0   0   2
  EPHA6 WILD-TYPE 329   4  31  23
D1746V11, multiclass
    clus
vv   EPHA6 MUTATED EPHA6 WILD-TYPE
  R0            16             329
  R1             0               4
  R2             0              31
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1746V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  EPHA6 MUTATED                                  0     0
  EPHA6 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  EPHA6 MUTATED                           0    19
  EPHA6 WILD-TYPE                        22   207
D1746V13, multiclass
                                  clus
vv                                 EPHA6 MUTATED EPHA6 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                       19             207
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1747) Variable = KIAA1407 MUTATION ANALYSIS
D1747V1, survival
                    sevent
clus2                  0   1
  KIAA1407 MUTATED    10   3
  KIAA1407 WILD-TYPE 368  90
  KIAA1407 MUTATED KIAA1407 WILD-TYPE 
                13                458 
  KIAA1407 MUTATED KIAA1407 WILD-TYPE 
                 3                 90 
$`KIAA1407 MUTATED`
TCGA-A6-6654 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3815 TCGA-AA-3977 TCGA-AA-A010 
       23.87        85.05        26.99        33.04        25.02        34.98 
TCGA-AZ-6598 TCGA-AZ-6605 TCGA-CA-6718 TCGA-CM-6171 TCGA-CM-6676 TCGA-AG-A002 
       49.41         5.23        10.06        14.04        11.08        20.98 
TCGA-AG-A02N 
       61.97 

$`KIAA1407 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       36.00         5.03        19.04        19.04        10.06        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77        12.10       100.01        29.56        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.20        12.76        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       12.99        13.02        15.02        11.01        12.95        13.05 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  KIAA1407 MUTATED KIAA1407 WILD-TYPE 
              5.23               0.00 
  KIAA1407 MUTATED KIAA1407 WILD-TYPE 
             85.05             148.01 
  KIAA1407 MUTATED KIAA1407 WILD-TYPE 
            25.020             20.035 
[1] "5.2 - 85.0 (25.0)"  "0.0 - 148.0 (20.0)"
[1] "hr=" "1"  
D1747V2, continuous
D1747V3, binary
                    cls
clus                   0   1
  KIAA1407 MUTATED    11   2
  KIAA1407 WILD-TYPE 355 117
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1407 MUTATED     11    2
  KIAA1407 WILD-TYPE  355  117
        clus
vv       KIAA1407 MUTATED KIAA1407 WILD-TYPE
  COLON                11                355
  RECTUM                2                117
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KIAA1407 MUTATED         3        0        2         3         1         0
  KIAA1407 WILD-TYPE      88        1       30       135         9         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIAA1407 MUTATED           1          0          2          0        0
  KIAA1407 WILD-TYPE        23         11         57         42       48
                    vv
clus                 STAGE IVA STAGE IVB
  KIAA1407 MUTATED           0         0
  KIAA1407 WILD-TYPE        18         1
D1747V4, multiclass
            clus
vv           KIAA1407 MUTATED KIAA1407 WILD-TYPE
  STAGE I                   3                 88
  STAGE IA                  0                  1
  STAGE II                  2                 30
  STAGE IIA                 3                135
  STAGE IIB                 1                  9
  STAGE IIC                 0                  1
  STAGE III                 1                 23
  STAGE IIIA                0                 11
  STAGE IIIB                2                 57
  STAGE IIIC                0                 42
  STAGE IV                  0                 48
  STAGE IVA                 0                 18
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  KIAA1407 MUTATED     0   4   7   2
  KIAA1407 WILD-TYPE  17  88 322  48
D1747V5, multiclass
    clus
vv   KIAA1407 MUTATED KIAA1407 WILD-TYPE
  T1                0                 17
  T2                4                 88
  T3                7                322
  T4                2                 48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  KIAA1407 MUTATED    11   2   0
  KIAA1407 WILD-TYPE 276 111  87
D1747V6, multiclass
    clus
vv   KIAA1407 MUTATED KIAA1407 WILD-TYPE
  N0               11                276
  N1                2                111
  N2                0                 87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1747V7, binary
                    cls
clus                   0   1
  KIAA1407 MUTATED    11   0
  KIAA1407 WILD-TYPE 364  65
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1407 MUTATED     11    0
  KIAA1407 WILD-TYPE  364   65
   clus
vv  KIAA1407 MUTATED KIAA1407 WILD-TYPE
  0               11                364
  1                0                 65
[1] 2 2
[1] FALSE
D1747V8, binary
                    cls
clus                   0   1
  KIAA1407 MUTATED     6   7
  KIAA1407 WILD-TYPE 219 257
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1407 MUTATED      6    7
  KIAA1407 WILD-TYPE  219  257
        clus
vv       KIAA1407 MUTATED KIAA1407 WILD-TYPE
  FEMALE                6                219
  MALE                  7                257
[1] 2 2
[1] FALSE
D1747V9, binary
                    cls
clus                   0   1
  KIAA1407 MUTATED    12   0
  KIAA1407 WILD-TYPE 338  22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1407 MUTATED     12    0
  KIAA1407 WILD-TYPE  338   22
     clus
vv    KIAA1407 MUTATED KIAA1407 WILD-TYPE
  NO                12                338
  YES                0                 22
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  KIAA1407 MUTATED                     11                             0
  KIAA1407 WILD-TYPE                  304                            47
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  KIAA1407 MUTATED                       2                              0
  KIAA1407 WILD-TYPE                   104                             10
D1747V10, multiclass
                                clus
vv                               KIAA1407 MUTATED KIAA1407 WILD-TYPE
  COLON ADENOCARCINOMA                         11                304
  COLON MUCINOUS ADENOCARCINOMA                 0                 47
  RECTAL ADENOCARCINOMA                         2                104
  RECTAL MUCINOUS ADENOCARCINOMA                0                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  KIAA1407 MUTATED     8   0   0   1
  KIAA1407 WILD-TYPE 337   4  31  24
D1747V11, multiclass
    clus
vv   KIAA1407 MUTATED KIAA1407 WILD-TYPE
  R0                8                337
  R1                0                  4
  R2                0                 31
  RX                1                 24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1747V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KIAA1407 MUTATED                                  0     1
  KIAA1407 WILD-TYPE                                1    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  KIAA1407 MUTATED                           0     5
  KIAA1407 WILD-TYPE                        22   221
D1747V13, multiclass
                                  clus
vv                                 KIAA1407 MUTATED KIAA1407 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                 10
  BLACK OR AFRICAN AMERICAN                       0                 22
  WHITE                                           5                221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1748) Variable = LIMCH1 MUTATION ANALYSIS
D1748V1, survival
                  sevent
clus2                0   1
  LIMCH1 MUTATED    14   1
  LIMCH1 WILD-TYPE 364  92
  LIMCH1 MUTATED LIMCH1 WILD-TYPE 
              15              456 
  LIMCH1 MUTATED LIMCH1 WILD-TYPE 
               1               92 
$`LIMCH1 MUTATED`
TCGA-A6-3808 TCGA-A6-5661 TCGA-A6-6780 TCGA-AA-3510 TCGA-AA-3534 TCGA-AA-3672 
       33.34        33.53        20.12        63.98        29.00         0.92 
TCGA-AA-3815 TCGA-AA-A00A TCGA-AA-A01Q TCGA-AZ-4315 TCGA-CA-6717 TCGA-CM-4743 
       33.04        38.04         1.02        58.39        12.76        23.05 
TCGA-D5-5539 TCGA-AG-A002 TCGA-DY-A1DG 
       19.59        20.98        51.48 

$`LIMCH1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       31.63        30.44        29.19        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6781 
       24.16        21.76        24.69        24.39        23.87        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 
       20.28         7.04         3.02         1.02        35.01         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       34.03        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       78.08         6.05         6.97        54.02         2.01        14.01 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       19.04        10.06        35.05         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        31.00        38.07        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07        12.20        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 
       11.01        10.06        12.03        45.40        12.26        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       41.36        57.24        24.13        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  LIMCH1 MUTATED LIMCH1 WILD-TYPE 
            0.92             0.00 
  LIMCH1 MUTATED LIMCH1 WILD-TYPE 
           63.98           148.01 
  LIMCH1 MUTATED LIMCH1 WILD-TYPE 
           29.00            20.02 
[1] "0.9 - 64.0 (29.0)"  "0.0 - 148.0 (20.0)"
[1] "hr=" "3.4"
D1748V2, continuous
D1748V3, binary
                  cls
clus                 0   1
  LIMCH1 MUTATED    13   2
  LIMCH1 WILD-TYPE 353 117
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LIMCH1 MUTATED     13    2
  LIMCH1 WILD-TYPE  353  117
        clus
vv       LIMCH1 MUTATED LIMCH1 WILD-TYPE
  COLON              13              353
  RECTUM              2              117
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  LIMCH1 MUTATED         1        0        2         9         0         0
  LIMCH1 WILD-TYPE      90        1       30       129        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  LIMCH1 MUTATED           1          1          0          0        0
  LIMCH1 WILD-TYPE        23         10         59         42       48
                  vv
clus               STAGE IVA STAGE IVB
  LIMCH1 MUTATED           1         0
  LIMCH1 WILD-TYPE        17         1
D1748V4, multiclass
            clus
vv           LIMCH1 MUTATED LIMCH1 WILD-TYPE
  STAGE I                 1               90
  STAGE IA                0                1
  STAGE II                2               30
  STAGE IIA               9              129
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               1               23
  STAGE IIIA              1               10
  STAGE IIIB              0               59
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               1               17
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  LIMCH1 MUTATED     0   1  14   0
  LIMCH1 WILD-TYPE  17  91 315  50
D1748V5, multiclass
    clus
vv   LIMCH1 MUTATED LIMCH1 WILD-TYPE
  T1              0               17
  T2              1               91
  T3             14              315
  T4              0               50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  LIMCH1 MUTATED    12   3   0
  LIMCH1 WILD-TYPE 275 110  87
D1748V6, multiclass
    clus
vv   LIMCH1 MUTATED LIMCH1 WILD-TYPE
  N0             12              275
  N1              3              110
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1748V7, binary
                  cls
clus                 0   1
  LIMCH1 MUTATED    13   1
  LIMCH1 WILD-TYPE 362  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LIMCH1 MUTATED     13    1
  LIMCH1 WILD-TYPE  362   64
   clus
vv  LIMCH1 MUTATED LIMCH1 WILD-TYPE
  0             13              362
  1              1               64
[1] 2 2
[1] FALSE
D1748V8, binary
                  cls
clus                 0   1
  LIMCH1 MUTATED     5  10
  LIMCH1 WILD-TYPE 220 254
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LIMCH1 MUTATED      5   10
  LIMCH1 WILD-TYPE  220  254
        clus
vv       LIMCH1 MUTATED LIMCH1 WILD-TYPE
  FEMALE              5              220
  MALE               10              254
[1] 2 2
[1] FALSE
D1748V9, binary
                  cls
clus                 0   1
  LIMCH1 MUTATED    13   0
  LIMCH1 WILD-TYPE 337  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LIMCH1 MUTATED     13    0
  LIMCH1 WILD-TYPE  337   22
     clus
vv    LIMCH1 MUTATED LIMCH1 WILD-TYPE
  NO              13              337
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  LIMCH1 MUTATED                     10                             3
  LIMCH1 WILD-TYPE                  305                            44
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  LIMCH1 MUTATED                       2                              0
  LIMCH1 WILD-TYPE                   104                             10
D1748V10, multiclass
                                clus
vv                               LIMCH1 MUTATED LIMCH1 WILD-TYPE
  COLON ADENOCARCINOMA                       10              305
  COLON MUCINOUS ADENOCARCINOMA               3               44
  RECTAL ADENOCARCINOMA                       2              104
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  LIMCH1 MUTATED    12   0   0   1
  LIMCH1 WILD-TYPE 333   4  31  24
D1748V11, multiclass
    clus
vv   LIMCH1 MUTATED LIMCH1 WILD-TYPE
  R0             12              333
  R1              0                4
  R2              0               31
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1748V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  LIMCH1 MUTATED                                  0     1
  LIMCH1 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  LIMCH1 MUTATED                           1     6
  LIMCH1 WILD-TYPE                        21   220
D1748V13, multiclass
                                  clus
vv                                 LIMCH1 MUTATED LIMCH1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                         6              220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1749) Variable = ATAD2 MUTATION ANALYSIS
D1749V1, survival
                 sevent
clus2               0   1
  ATAD2 MUTATED    16   6
  ATAD2 WILD-TYPE 362  87
  ATAD2 MUTATED ATAD2 WILD-TYPE 
             22             449 
  ATAD2 MUTATED ATAD2 WILD-TYPE 
              6              87 
$`ATAD2 MUTATED`
TCGA-A6-2676 TCGA-A6-6141 TCGA-A6-6648 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-A00N 
       42.90         8.38        25.18        26.99        19.04         4.01 
TCGA-AA-A01D TCGA-AU-6004 TCGA-AY-6197 TCGA-AZ-4315 TCGA-CA-6718 TCGA-CK-6747 
       10.98        27.09        21.44        58.39        10.06        82.95 
TCGA-CM-4746 TCGA-CM-5861 TCGA-CM-6674 TCGA-D5-5541 TCGA-D5-6539 TCGA-D5-6540 
       37.02        15.02        12.95        55.92        12.49        16.14 
TCGA-G4-6304 TCGA-AG-A002 TCGA-DY-A1DD TCGA-EI-6506 
       53.62        20.98        57.24        20.55 

$`ATAD2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6649 
       22.06        32.71        27.09        22.52        25.08        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       85.05        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01F 
       17.03        14.99        21.99        34.98         1.02        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 
       27.42        10.88         0.20        14.50        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       33.01        17.82         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       51.32         9.99        21.14         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       20.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       30.08        32.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-6529 TCGA-D5-6532 
       45.40        12.26        19.59        56.09        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 
       35.31       133.18        74.56        65.85        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6507 
       41.36        24.13        51.48        32.61         0.49        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  ATAD2 MUTATED ATAD2 WILD-TYPE 
           4.01            0.00 
  ATAD2 MUTATED ATAD2 WILD-TYPE 
          82.95          148.01 
  ATAD2 MUTATED ATAD2 WILD-TYPE 
          21.21           20.05 
[1] "4.0 - 83.0 (21.2)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.2"
D1749V2, continuous
D1749V3, binary
                 cls
clus                0   1
  ATAD2 MUTATED    19   3
  ATAD2 WILD-TYPE 347 116
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ATAD2 MUTATED     19    3
  ATAD2 WILD-TYPE  347  116
        clus
vv       ATAD2 MUTATED ATAD2 WILD-TYPE
  COLON             19             347
  RECTUM             3             116
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ATAD2 MUTATED         4        0        1         9         3         0
  ATAD2 WILD-TYPE      87        1       31       129         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ATAD2 MUTATED           0          1          2          1        0         1
  ATAD2 WILD-TYPE        24         10         57         41       48        17
                 vv
clus              STAGE IVB
  ATAD2 MUTATED           0
  ATAD2 WILD-TYPE         1
D1749V4, multiclass
            clus
vv           ATAD2 MUTATED ATAD2 WILD-TYPE
  STAGE I                4              87
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              9             129
  STAGE IIB              3               7
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             1              10
  STAGE IIIB             2              57
  STAGE IIIC             1              41
  STAGE IV               0              48
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ATAD2 MUTATED     0   4  15   3
  ATAD2 WILD-TYPE  17  88 314  47
D1749V5, multiclass
    clus
vv   ATAD2 MUTATED ATAD2 WILD-TYPE
  T1             0              17
  T2             4              88
  T3            15             314
  T4             3              47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  ATAD2 MUTATED    19   2   1
  ATAD2 WILD-TYPE 268 111  86
D1749V6, multiclass
    clus
vv   ATAD2 MUTATED ATAD2 WILD-TYPE
  N0            19             268
  N1             2             111
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1749V7, binary
                 cls
clus                0   1
  ATAD2 MUTATED    19   1
  ATAD2 WILD-TYPE 356  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ATAD2 MUTATED     19    1
  ATAD2 WILD-TYPE  356   64
   clus
vv  ATAD2 MUTATED ATAD2 WILD-TYPE
  0            19             356
  1             1              64
[1] 2 2
[1] FALSE
D1749V8, binary
                 cls
clus                0   1
  ATAD2 MUTATED    10  12
  ATAD2 WILD-TYPE 215 252
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ATAD2 MUTATED     10   12
  ATAD2 WILD-TYPE  215  252
        clus
vv       ATAD2 MUTATED ATAD2 WILD-TYPE
  FEMALE            10             215
  MALE              12             252
[1] 2 2
[1] FALSE
D1749V9, binary
                 cls
clus                0   1
  ATAD2 MUTATED    19   0
  ATAD2 WILD-TYPE 331  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ATAD2 MUTATED     19    0
  ATAD2 WILD-TYPE  331   22
     clus
vv    ATAD2 MUTATED ATAD2 WILD-TYPE
  NO             19             331
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ATAD2 MUTATED                     16                             3
  ATAD2 WILD-TYPE                  299                            44
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ATAD2 MUTATED                       3                              0
  ATAD2 WILD-TYPE                   103                             10
D1749V10, multiclass
                                clus
vv                               ATAD2 MUTATED ATAD2 WILD-TYPE
  COLON ADENOCARCINOMA                      16             299
  COLON MUCINOUS ADENOCARCINOMA              3              44
  RECTAL ADENOCARCINOMA                      3             103
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  ATAD2 MUTATED    17   0   0   2
  ATAD2 WILD-TYPE 328   4  31  23
D1749V11, multiclass
    clus
vv   ATAD2 MUTATED ATAD2 WILD-TYPE
  R0            17             328
  R1             0               4
  R2             0              31
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1749V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ATAD2 MUTATED                                  0     1
  ATAD2 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ATAD2 MUTATED                           2    14
  ATAD2 WILD-TYPE                        20   212
D1749V13, multiclass
                                  clus
vv                                 ATAD2 MUTATED ATAD2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    2              20
  WHITE                                       14             212
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1750) Variable = ZNF594 MUTATION ANALYSIS
D1750V1, survival
                  sevent
clus2                0   1
  ZNF594 MUTATED    11   4
  ZNF594 WILD-TYPE 367  89
  ZNF594 MUTATED ZNF594 WILD-TYPE 
              15              456 
  ZNF594 MUTATED ZNF594 WILD-TYPE 
               4               89 
$`ZNF594 MUTATED`
TCGA-A6-6141 TCGA-AA-3950 TCGA-AA-3977 TCGA-AZ-4315 TCGA-AZ-5403 TCGA-CA-6717 
        8.38        24.00        25.02        58.39        62.79        12.76 
TCGA-CA-6718 TCGA-CM-4752 TCGA-CM-6171 TCGA-CM-6677 TCGA-D5-6898 TCGA-F4-6570 
       10.06        13.02        14.04        11.08         1.48         6.18 
TCGA-G4-6309 TCGA-AG-A002 TCGA-DY-A1DC 
       85.48        20.98        41.36 

$`ZNF594 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 
       22.09        22.06        32.71        27.09        22.52        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 
        2.01        12.99        24.00        33.01        26.01         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13       106.75        22.36 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 
        3.25         3.29         0.07        12.20        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       37.02        25.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 
       14.99        12.99        13.02        15.02        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       13.05        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       12.49        16.14        15.58         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
        8.61        31.96        35.74        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       55.04        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  ZNF594 MUTATED ZNF594 WILD-TYPE 
            1.48             0.00 
  ZNF594 MUTATED ZNF594 WILD-TYPE 
           85.48           148.01 
  ZNF594 MUTATED ZNF594 WILD-TYPE 
          14.040           20.235 
[1] "1.5 - 85.5 (14.0)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.3"
D1750V2, continuous
D1750V3, binary
                  cls
clus                 0   1
  ZNF594 MUTATED    14   2
  ZNF594 WILD-TYPE 352 117
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF594 MUTATED     14    2
  ZNF594 WILD-TYPE  352  117
        clus
vv       ZNF594 MUTATED ZNF594 WILD-TYPE
  COLON              14              352
  RECTUM              2              117
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZNF594 MUTATED         3        0        1        10         0         0
  ZNF594 WILD-TYPE      88        1       31       128        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF594 MUTATED           0          0          1          0        0
  ZNF594 WILD-TYPE        24         11         58         42       48
                  vv
clus               STAGE IVA STAGE IVB
  ZNF594 MUTATED           0         0
  ZNF594 WILD-TYPE        18         1
D1750V4, multiclass
            clus
vv           ZNF594 MUTATED ZNF594 WILD-TYPE
  STAGE I                 3               88
  STAGE IA                0                1
  STAGE II                1               31
  STAGE IIA              10              128
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              1               58
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZNF594 MUTATED     0   4  12   0
  ZNF594 WILD-TYPE  17  88 317  50
D1750V5, multiclass
    clus
vv   ZNF594 MUTATED ZNF594 WILD-TYPE
  T1              0               17
  T2              4               88
  T3             12              317
  T4              0               50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  ZNF594 MUTATED    15   1   0
  ZNF594 WILD-TYPE 272 112  87
D1750V6, multiclass
    clus
vv   ZNF594 MUTATED ZNF594 WILD-TYPE
  N0             15              272
  N1              1              112
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1750V7, binary
                  cls
clus                 0   1
  ZNF594 MUTATED    14   0
  ZNF594 WILD-TYPE 361  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF594 MUTATED     14    0
  ZNF594 WILD-TYPE  361   65
   clus
vv  ZNF594 MUTATED ZNF594 WILD-TYPE
  0             14              361
  1              0               65
[1] 2 2
[1] FALSE
D1750V8, binary
                  cls
clus                 0   1
  ZNF594 MUTATED     8   8
  ZNF594 WILD-TYPE 217 256
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF594 MUTATED      8    8
  ZNF594 WILD-TYPE  217  256
        clus
vv       ZNF594 MUTATED ZNF594 WILD-TYPE
  FEMALE              8              217
  MALE                8              256
[1] 2 2
[1] FALSE
D1750V9, binary
                  cls
clus                 0   1
  ZNF594 MUTATED    13   0
  ZNF594 WILD-TYPE 337  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF594 MUTATED     13    0
  ZNF594 WILD-TYPE  337   22
     clus
vv    ZNF594 MUTATED ZNF594 WILD-TYPE
  NO              13              337
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ZNF594 MUTATED                     12                             2
  ZNF594 WILD-TYPE                  303                            45
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ZNF594 MUTATED                       2                              0
  ZNF594 WILD-TYPE                   104                             10
D1750V10, multiclass
                                clus
vv                               ZNF594 MUTATED ZNF594 WILD-TYPE
  COLON ADENOCARCINOMA                       12              303
  COLON MUCINOUS ADENOCARCINOMA               2               45
  RECTAL ADENOCARCINOMA                       2              104
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ZNF594 MUTATED    10   0   0   2
  ZNF594 WILD-TYPE 335   4  31  23
D1750V11, multiclass
    clus
vv   ZNF594 MUTATED ZNF594 WILD-TYPE
  R0             10              335
  R1              0                4
  R2              0               31
  RX              2               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1750V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF594 MUTATED                                  0     2
  ZNF594 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZNF594 MUTATED                           3     7
  ZNF594 WILD-TYPE                        19   219
D1750V13, multiclass
                                  clus
vv                                 ZNF594 MUTATED ZNF594 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                9
  BLACK OR AFRICAN AMERICAN                     3               19
  WHITE                                         7              219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1751) Variable = ACTRT1 MUTATION ANALYSIS
D1751V1, survival
                  sevent
clus2                0   1
  ACTRT1 MUTATED     9   4
  ACTRT1 WILD-TYPE 369  89
  ACTRT1 MUTATED ACTRT1 WILD-TYPE 
              13              458 
  ACTRT1 MUTATED ACTRT1 WILD-TYPE 
               4               89 
$`ACTRT1 MUTATED`
TCGA-AA-3543 TCGA-AA-3949 TCGA-AA-3977 TCGA-AU-3779 TCGA-AZ-4682 TCGA-AZ-6607 
        0.99        26.01        25.02        14.50        22.36         3.19 
TCGA-CM-6161 TCGA-CM-6165 TCGA-D5-6537 TCGA-DM-A1DA TCGA-F4-6807 TCGA-AF-2693 
       15.02        16.04         4.80         7.50        16.24        19.10 
TCGA-F5-6812 
        0.66 

$`ACTRT1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       29.00        26.01        12.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-3952 
        2.01        12.99        24.00        33.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
        0.20        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-5403 
       17.82        58.39         1.41         5.13       106.75        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6166 
       15.02        17.03        12.00         2.96        29.03        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
       12.59       140.38        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
        1.55        34.42        41.42        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 
       79.69        24.13        39.48        43.04        13.55        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6813 
        9.96        49.51        31.30        28.57        32.19         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  ACTRT1 MUTATED ACTRT1 WILD-TYPE 
            0.66             0.00 
  ACTRT1 MUTATED ACTRT1 WILD-TYPE 
           26.01           148.01 
  ACTRT1 MUTATED ACTRT1 WILD-TYPE 
          15.020           20.945 
[1] "0.7 - 26.0 (15.0)"  "0.0 - 148.0 (20.9)"
[1] "hr=" "3.1"
D1751V2, continuous
D1751V3, binary
                  cls
clus                 0   1
  ACTRT1 MUTATED    11   1
  ACTRT1 WILD-TYPE 355 118
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ACTRT1 MUTATED     11    1
  ACTRT1 WILD-TYPE  355  118
        clus
vv       ACTRT1 MUTATED ACTRT1 WILD-TYPE
  COLON              11              355
  RECTUM              1              118
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ACTRT1 MUTATED         3        0        0         3         0         0
  ACTRT1 WILD-TYPE      88        1       32       135        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ACTRT1 MUTATED           0          0          2          2        1
  ACTRT1 WILD-TYPE        24         11         57         40       47
                  vv
clus               STAGE IVA STAGE IVB
  ACTRT1 MUTATED           1         0
  ACTRT1 WILD-TYPE        17         1
D1751V4, multiclass
            clus
vv           ACTRT1 MUTATED ACTRT1 WILD-TYPE
  STAGE I                 3               88
  STAGE IA                0                1
  STAGE II                0               32
  STAGE IIA               3              135
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              2               57
  STAGE IIIC              2               40
  STAGE IV                1               47
  STAGE IVA               1               17
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ACTRT1 MUTATED     0   4   8   1
  ACTRT1 WILD-TYPE  17  88 321  49
D1751V5, multiclass
    clus
vv   ACTRT1 MUTATED ACTRT1 WILD-TYPE
  T1              0               17
  T2              4               88
  T3              8              321
  T4              1               49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  ACTRT1 MUTATED     8   2   3
  ACTRT1 WILD-TYPE 279 111  84
D1751V6, multiclass
    clus
vv   ACTRT1 MUTATED ACTRT1 WILD-TYPE
  N0              8              279
  N1              2              111
  N2              3               84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1751V7, binary
                  cls
clus                 0   1
  ACTRT1 MUTATED     8   2
  ACTRT1 WILD-TYPE 367  63
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ACTRT1 MUTATED      8    2
  ACTRT1 WILD-TYPE  367   63
   clus
vv  ACTRT1 MUTATED ACTRT1 WILD-TYPE
  0              8              367
  1              2               63
[1] 2 2
[1] FALSE
D1751V8, binary
                  cls
clus                 0   1
  ACTRT1 MUTATED     5   8
  ACTRT1 WILD-TYPE 220 256
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ACTRT1 MUTATED      5    8
  ACTRT1 WILD-TYPE  220  256
        clus
vv       ACTRT1 MUTATED ACTRT1 WILD-TYPE
  FEMALE              5              220
  MALE                8              256
[1] 2 2
[1] FALSE
D1751V9, binary
                  cls
clus                 0   1
  ACTRT1 MUTATED    11   0
  ACTRT1 WILD-TYPE 339  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ACTRT1 MUTATED     11    0
  ACTRT1 WILD-TYPE  339   22
     clus
vv    ACTRT1 MUTATED ACTRT1 WILD-TYPE
  NO              11              339
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ACTRT1 MUTATED                      9                             2
  ACTRT1 WILD-TYPE                  306                            45
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ACTRT1 MUTATED                       1                              0
  ACTRT1 WILD-TYPE                   105                             10
D1751V10, multiclass
                                clus
vv                               ACTRT1 MUTATED ACTRT1 WILD-TYPE
  COLON ADENOCARCINOMA                        9              306
  COLON MUCINOUS ADENOCARCINOMA               2               45
  RECTAL ADENOCARCINOMA                       1              105
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ACTRT1 MUTATED     9   0   0   0
  ACTRT1 WILD-TYPE 336   4  31  25
D1751V11, multiclass
    clus
vv   ACTRT1 MUTATED ACTRT1 WILD-TYPE
  R0              9              336
  R1              0                4
  R2              0               31
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1751V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ACTRT1 MUTATED                                  0     0
  ACTRT1 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ACTRT1 MUTATED                           0    10
  ACTRT1 WILD-TYPE                        22   216
D1751V13, multiclass
                                  clus
vv                                 ACTRT1 MUTATED ACTRT1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                        10              216
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1752) Variable = CNTNAP3 MUTATION ANALYSIS
D1752V1, survival
                   sevent
clus2                 0   1
  CNTNAP3 MUTATED    10   3
  CNTNAP3 WILD-TYPE 368  90
  CNTNAP3 MUTATED CNTNAP3 WILD-TYPE 
               13               458 
  CNTNAP3 MUTATED CNTNAP3 WILD-TYPE 
                3                90 
$`CNTNAP3 MUTATED`
TCGA-A6-3809 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3715 TCGA-AA-A010 
       32.75         3.02         1.02        35.01        19.04        34.98 
TCGA-CA-6717 TCGA-D5-5539 TCGA-F4-6459 TCGA-G4-6628 TCGA-AG-A002 TCGA-EI-6506 
       12.76        19.59         8.61        79.69        20.98        20.55 
TCGA-EI-6510 
       18.28 

$`CNTNAP3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3510 TCGA-AA-3511 
       20.12        19.66        20.28         7.04        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       26.99        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07        12.20        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-5541 
       10.06        12.03        45.40        12.26        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
       60.79       117.07        98.24        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       91.79        46.75        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6507 TCGA-EI-6508 TCGA-F5-6464 
       51.48        32.61         0.49        19.96        20.91         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  CNTNAP3 MUTATED CNTNAP3 WILD-TYPE 
             1.02              0.00 
  CNTNAP3 MUTATED CNTNAP3 WILD-TYPE 
            79.69            148.01 
  CNTNAP3 MUTATED CNTNAP3 WILD-TYPE 
           19.590            20.235 
[1] "1.0 - 79.7 (19.6)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.4"
D1752V2, continuous
D1752V3, binary
                   cls
clus                  0   1
  CNTNAP3 MUTATED    11   3
  CNTNAP3 WILD-TYPE 355 116
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CNTNAP3 MUTATED     11    3
  CNTNAP3 WILD-TYPE  355  116
        clus
vv       CNTNAP3 MUTATED CNTNAP3 WILD-TYPE
  COLON               11               355
  RECTUM               3               116
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CNTNAP3 MUTATED         3        0        3         3         2         0
  CNTNAP3 WILD-TYPE      88        1       29       135         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CNTNAP3 MUTATED           0          1          1          0        0
  CNTNAP3 WILD-TYPE        24         10         58         42       48
                   vv
clus                STAGE IVA STAGE IVB
  CNTNAP3 MUTATED           1         0
  CNTNAP3 WILD-TYPE        17         1
D1752V4, multiclass
            clus
vv           CNTNAP3 MUTATED CNTNAP3 WILD-TYPE
  STAGE I                  3                88
  STAGE IA                 0                 1
  STAGE II                 3                29
  STAGE IIA                3               135
  STAGE IIB                2                 8
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               1                10
  STAGE IIIB               1                58
  STAGE IIIC               0                42
  STAGE IV                 0                48
  STAGE IVA                1                17
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  CNTNAP3 MUTATED     0   4   8   2
  CNTNAP3 WILD-TYPE  17  88 321  48
D1752V5, multiclass
    clus
vv   CNTNAP3 MUTATED CNTNAP3 WILD-TYPE
  T1               0                17
  T2               4                88
  T3               8               321
  T4               2                48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  CNTNAP3 MUTATED    12   1   1
  CNTNAP3 WILD-TYPE 275 112  86
D1752V6, multiclass
    clus
vv   CNTNAP3 MUTATED CNTNAP3 WILD-TYPE
  N0              12               275
  N1               1               112
  N2               1                86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1752V7, binary
                   cls
clus                  0   1
  CNTNAP3 MUTATED    13   0
  CNTNAP3 WILD-TYPE 362  65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CNTNAP3 MUTATED     13    0
  CNTNAP3 WILD-TYPE  362   65
   clus
vv  CNTNAP3 MUTATED CNTNAP3 WILD-TYPE
  0              13               362
  1               0                65
[1] 2 2
[1] FALSE
D1752V8, binary
                   cls
clus                  0   1
  CNTNAP3 MUTATED     8   6
  CNTNAP3 WILD-TYPE 217 258
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CNTNAP3 MUTATED      8    6
  CNTNAP3 WILD-TYPE  217  258
        clus
vv       CNTNAP3 MUTATED CNTNAP3 WILD-TYPE
  FEMALE               8               217
  MALE                 6               258
[1] 2 2
[1] FALSE
D1752V9, binary
                   cls
clus                  0   1
  CNTNAP3 MUTATED    12   0
  CNTNAP3 WILD-TYPE 338  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CNTNAP3 MUTATED     12    0
  CNTNAP3 WILD-TYPE  338   22
     clus
vv    CNTNAP3 MUTATED CNTNAP3 WILD-TYPE
  NO               12               338
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CNTNAP3 MUTATED                      8                             3
  CNTNAP3 WILD-TYPE                  307                            44
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CNTNAP3 MUTATED                       3                              0
  CNTNAP3 WILD-TYPE                   103                             10
D1752V10, multiclass
                                clus
vv                               CNTNAP3 MUTATED CNTNAP3 WILD-TYPE
  COLON ADENOCARCINOMA                         8               307
  COLON MUCINOUS ADENOCARCINOMA                3                44
  RECTAL ADENOCARCINOMA                        3               103
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  CNTNAP3 MUTATED    13   0   0   1
  CNTNAP3 WILD-TYPE 332   4  31  24
D1752V11, multiclass
    clus
vv   CNTNAP3 MUTATED CNTNAP3 WILD-TYPE
  R0              13               332
  R1               0                 4
  R2               0                31
  RX               1                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1752V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CNTNAP3 MUTATED                                  0     1
  CNTNAP3 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  CNTNAP3 MUTATED                           0     6
  CNTNAP3 WILD-TYPE                        22   220
D1752V13, multiclass
                                  clus
vv                                 CNTNAP3 MUTATED CNTNAP3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                10
  BLACK OR AFRICAN AMERICAN                      0                22
  WHITE                                          6               220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1753) Variable = GRIN2B MUTATION ANALYSIS
D1753V1, survival
                  sevent
clus2                0   1
  GRIN2B MUTATED    18   9
  GRIN2B WILD-TYPE 360  84
  GRIN2B MUTATED GRIN2B WILD-TYPE 
              27              444 
  GRIN2B MUTATED GRIN2B WILD-TYPE 
               9               84 
$`GRIN2B MUTATED`
TCGA-A6-5661 TCGA-AA-3492 TCGA-AA-3511 TCGA-AA-3660 TCGA-AA-3833 TCGA-AA-3977 
       33.53         3.02         6.97        78.08        15.95        25.02 
TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01Q TCGA-AD-6901 TCGA-AD-6964 TCGA-AU-3779 
        4.01        34.98         1.02        22.42        10.88        14.50 
TCGA-AZ-6598 TCGA-AZ-6601 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4950 TCGA-CK-4952 
       49.41       100.01        12.76        10.06        85.45        15.62 
TCGA-D5-6540 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6931 TCGA-DM-A1D4 TCGA-DM-A28G 
       16.14         3.68         4.41        12.00        92.75        60.79 
TCGA-G4-6586 TCGA-AG-A002 TCGA-DY-A0XA 
       35.80        20.98       126.44 

$`GRIN2B WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 
       20.12        19.66        20.28         7.04         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
       63.98         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3837 TCGA-AA-3842 
        0.99        25.02         1.02        17.98        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        31.00        38.07        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-6004 
        0.79         0.72         5.79        27.42         0.20        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77        12.10        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-5912 TCGA-CK-5913 
       12.20        14.30        17.56       148.01        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 
       15.12        17.85         4.80        17.13        12.49        15.58 
TCGA-D5-6898 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        1.48        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        4.80         1.51        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
       38.20       130.65        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
       81.37       119.93        35.97       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       13.78        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC 
       19.99         5.95         4.01         5.03         5.29        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  GRIN2B MUTATED GRIN2B WILD-TYPE 
            1.02             0.00 
  GRIN2B MUTATED GRIN2B WILD-TYPE 
          126.44           148.01 
  GRIN2B MUTATED GRIN2B WILD-TYPE 
          16.140           20.235 
[1] "1.0 - 126.4 (16.1)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.4"
D1753V2, continuous
D1753V3, binary
                  cls
clus                 0   1
  GRIN2B MUTATED    26   2
  GRIN2B WILD-TYPE 340 117
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GRIN2B MUTATED     26    2
  GRIN2B WILD-TYPE  340  117
        clus
vv       GRIN2B MUTATED GRIN2B WILD-TYPE
  COLON              26              340
  RECTUM              2              117
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GRIN2B MUTATED         2        0        7        10         2         0
  GRIN2B WILD-TYPE      89        1       25       128         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GRIN2B MUTATED           0          1          1          2        0
  GRIN2B WILD-TYPE        24         10         58         40       48
                  vv
clus               STAGE IVA STAGE IVB
  GRIN2B MUTATED           0         0
  GRIN2B WILD-TYPE        18         1
D1753V4, multiclass
            clus
vv           GRIN2B MUTATED GRIN2B WILD-TYPE
  STAGE I                 2               89
  STAGE IA                0                1
  STAGE II                7               25
  STAGE IIA              10              128
  STAGE IIB               2                8
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              1               10
  STAGE IIIB              1               58
  STAGE IIIC              2               40
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  GRIN2B MUTATED     0   3  18   7
  GRIN2B WILD-TYPE  17  89 311  43
D1753V5, multiclass
    clus
vv   GRIN2B MUTATED GRIN2B WILD-TYPE
  T1              0               17
  T2              3               89
  T3             18              311
  T4              7               43
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  GRIN2B MUTATED    23   2   3
  GRIN2B WILD-TYPE 264 111  84
D1753V6, multiclass
    clus
vv   GRIN2B MUTATED GRIN2B WILD-TYPE
  N0             23              264
  N1              2              111
  N2              3               84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1753V7, binary
                  cls
clus                 0   1
  GRIN2B MUTATED    24   0
  GRIN2B WILD-TYPE 351  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GRIN2B MUTATED     24    0
  GRIN2B WILD-TYPE  351   65
   clus
vv  GRIN2B MUTATED GRIN2B WILD-TYPE
  0             24              351
  1              0               65
[1] 2 2
[1] FALSE
D1753V8, binary
                  cls
clus                 0   1
  GRIN2B MUTATED    14  14
  GRIN2B WILD-TYPE 211 250
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GRIN2B MUTATED     14   14
  GRIN2B WILD-TYPE  211  250
        clus
vv       GRIN2B MUTATED GRIN2B WILD-TYPE
  FEMALE             14              211
  MALE               14              250
[1] 2 2
[1] FALSE
D1753V9, binary
                  cls
clus                 0   1
  GRIN2B MUTATED    19   0
  GRIN2B WILD-TYPE 331  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GRIN2B MUTATED     19    0
  GRIN2B WILD-TYPE  331   22
     clus
vv    GRIN2B MUTATED GRIN2B WILD-TYPE
  NO              19              331
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  GRIN2B MUTATED                     22                             4
  GRIN2B WILD-TYPE                  293                            43
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  GRIN2B MUTATED                       2                              0
  GRIN2B WILD-TYPE                   104                             10
D1753V10, multiclass
                                clus
vv                               GRIN2B MUTATED GRIN2B WILD-TYPE
  COLON ADENOCARCINOMA                       22              293
  COLON MUCINOUS ADENOCARCINOMA               4               43
  RECTAL ADENOCARCINOMA                       2              104
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  GRIN2B MUTATED    16   1   0   3
  GRIN2B WILD-TYPE 329   3  31  22
D1753V11, multiclass
    clus
vv   GRIN2B MUTATED GRIN2B WILD-TYPE
  R0             16              329
  R1              1                3
  R2              0               31
  RX              3               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1753V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GRIN2B MUTATED                                  0     2
  GRIN2B WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  GRIN2B MUTATED                           2    14
  GRIN2B WILD-TYPE                        20   212
D1753V13, multiclass
                                  clus
vv                                 GRIN2B MUTATED GRIN2B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                9
  BLACK OR AFRICAN AMERICAN                     2               20
  WHITE                                        14              212
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1754) Variable = CXORF23 MUTATION ANALYSIS
D1754V1, survival
                   sevent
clus2                 0   1
  CXORF23 MUTATED     4   3
  CXORF23 WILD-TYPE 374  90
  CXORF23 MUTATED CXORF23 WILD-TYPE 
                7               464 
  CXORF23 MUTATED CXORF23 WILD-TYPE 
                3                90 
$`CXORF23 MUTATED`
TCGA-A6-5657 TCGA-AA-3696 TCGA-CK-6747 TCGA-CM-6166 TCGA-DM-A1D7 TCGA-F4-6570 
       31.63         5.03        82.95        21.99        13.32         6.18 
TCGA-F5-6465 
       49.51 

$`CXORF23 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
       36.00        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6168 
       12.00         2.96        29.03        16.04        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D8 TCGA-DM-A1D9 
       38.20       130.65        92.75        49.91        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
        8.61        31.96        35.74        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
        9.96        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  CXORF23 MUTATED CXORF23 WILD-TYPE 
             5.03              0.00 
  CXORF23 MUTATED CXORF23 WILD-TYPE 
            82.95            148.01 
  CXORF23 MUTATED CXORF23 WILD-TYPE 
           21.990            20.155 
[1] "5.0 - 83.0 (22.0)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.9"
D1754V2, continuous
D1754V3, binary
                   cls
clus                  0   1
  CXORF23 MUTATED     6   1
  CXORF23 WILD-TYPE 360 118
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CXORF23 MUTATED      6    1
  CXORF23 WILD-TYPE  360  118
        clus
vv       CXORF23 MUTATED CXORF23 WILD-TYPE
  COLON                6               360
  RECTUM               1               118
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CXORF23 MUTATED         1        0        0         4         0         0
  CXORF23 WILD-TYPE      90        1       32       134        10         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CXORF23 MUTATED           0          0          1          0        1
  CXORF23 WILD-TYPE        24         11         58         42       47
                   vv
clus                STAGE IVA STAGE IVB
  CXORF23 MUTATED           0         0
  CXORF23 WILD-TYPE        18         1
D1754V4, multiclass
            clus
vv           CXORF23 MUTATED CXORF23 WILD-TYPE
  STAGE I                  1                90
  STAGE IA                 0                 1
  STAGE II                 0                32
  STAGE IIA                4               134
  STAGE IIB                0                10
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               0                11
  STAGE IIIB               1                58
  STAGE IIIC               0                42
  STAGE IV                 1                47
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  CXORF23 MUTATED     0   1   6   0
  CXORF23 WILD-TYPE  17  91 323  50
D1754V5, multiclass
    clus
vv   CXORF23 MUTATED CXORF23 WILD-TYPE
  T1               0                17
  T2               1                91
  T3               6               323
  T4               0                50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  CXORF23 MUTATED     5   2   0
  CXORF23 WILD-TYPE 282 111  87
D1754V6, multiclass
    clus
vv   CXORF23 MUTATED CXORF23 WILD-TYPE
  N0               5               282
  N1               2               111
  N2               0                87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1754V7, binary
                   cls
clus                  0   1
  CXORF23 MUTATED     5   1
  CXORF23 WILD-TYPE 370  64
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CXORF23 MUTATED      5    1
  CXORF23 WILD-TYPE  370   64
   clus
vv  CXORF23 MUTATED CXORF23 WILD-TYPE
  0               5               370
  1               1                64
[1] 2 2
[1] FALSE
D1754V8, binary
                   cls
clus                  0   1
  CXORF23 MUTATED     5   2
  CXORF23 WILD-TYPE 220 262
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CXORF23 MUTATED      5    2
  CXORF23 WILD-TYPE  220  262
        clus
vv       CXORF23 MUTATED CXORF23 WILD-TYPE
  FEMALE               5               220
  MALE                 2               262
[1] 2 2
[1] FALSE
D1754V9, binary
                   cls
clus                  0   1
  CXORF23 MUTATED     6   0
  CXORF23 WILD-TYPE 344  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CXORF23 MUTATED      6    0
  CXORF23 WILD-TYPE  344   22
     clus
vv    CXORF23 MUTATED CXORF23 WILD-TYPE
  NO                6               344
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CXORF23 MUTATED                      5                             0
  CXORF23 WILD-TYPE                  310                            47
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CXORF23 MUTATED                       1                              0
  CXORF23 WILD-TYPE                   105                             10
D1754V10, multiclass
                                clus
vv                               CXORF23 MUTATED CXORF23 WILD-TYPE
  COLON ADENOCARCINOMA                         5               310
  COLON MUCINOUS ADENOCARCINOMA                0                47
  RECTAL ADENOCARCINOMA                        1               105
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  CXORF23 MUTATED     4   0   1   1
  CXORF23 WILD-TYPE 341   4  30  24
D1754V11, multiclass
    clus
vv   CXORF23 MUTATED CXORF23 WILD-TYPE
  R0               4               341
  R1               0                 4
  R2               1                30
  RX               1                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1754V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CXORF23 MUTATED                                  0     0
  CXORF23 WILD-TYPE                                1    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  CXORF23 MUTATED                           1     5
  CXORF23 WILD-TYPE                        21   221
D1754V13, multiclass
                                  clus
vv                                 CXORF23 MUTATED CXORF23 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                      1                21
  WHITE                                          5               221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1755) Variable = EFCAB4B MUTATION ANALYSIS
D1755V1, survival
                   sevent
clus2                 0   1
  EFCAB4B MUTATED     6   1
  EFCAB4B WILD-TYPE 372  92
  EFCAB4B MUTATED EFCAB4B WILD-TYPE 
                7               464 
  EFCAB4B MUTATED EFCAB4B WILD-TYPE 
                1                92 
$`EFCAB4B MUTATED`
TCGA-AA-3821 TCGA-CA-5796 TCGA-CK-4950 TCGA-CM-6171 TCGA-F4-6459 TCGA-AG-A02X 
        1.02         3.25        85.45        14.04         8.61        41.00 
TCGA-EI-6507 
       19.96 

$`EFCAB4B WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5797 TCGA-CA-6715 
        3.19         1.61        12.69         3.06         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       12.99        13.02        15.02        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
       98.24        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       38.96        61.97        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
       32.61         0.49        20.55        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  EFCAB4B MUTATED EFCAB4B WILD-TYPE 
             1.02              0.00 
  EFCAB4B MUTATED EFCAB4B WILD-TYPE 
            85.45            148.01 
  EFCAB4B MUTATED EFCAB4B WILD-TYPE 
           14.040            20.415 
[1] "1.0 - 85.5 (14.0)"  "0.0 - 148.0 (20.4)"
[1] "hr=" "1.3"
D1755V2, continuous
D1755V3, binary
                   cls
clus                  0   1
  EFCAB4B MUTATED     5   2
  EFCAB4B WILD-TYPE 361 117
[1] "tbl2"
                   cls
clus                [,1] [,2]
  EFCAB4B MUTATED      5    2
  EFCAB4B WILD-TYPE  361  117
        clus
vv       EFCAB4B MUTATED EFCAB4B WILD-TYPE
  COLON                5               361
  RECTUM               2               117
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  EFCAB4B MUTATED         3        0        0         2         0         0
  EFCAB4B WILD-TYPE      88        1       32       136        10         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  EFCAB4B MUTATED           0          0          2          0        0
  EFCAB4B WILD-TYPE        24         11         57         42       48
                   vv
clus                STAGE IVA STAGE IVB
  EFCAB4B MUTATED           0         0
  EFCAB4B WILD-TYPE        18         1
D1755V4, multiclass
            clus
vv           EFCAB4B MUTATED EFCAB4B WILD-TYPE
  STAGE I                  3                88
  STAGE IA                 0                 1
  STAGE II                 0                32
  STAGE IIA                2               136
  STAGE IIB                0                10
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               0                11
  STAGE IIIB               2                57
  STAGE IIIC               0                42
  STAGE IV                 0                48
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  EFCAB4B MUTATED     0   3   4   0
  EFCAB4B WILD-TYPE  17  89 325  50
D1755V5, multiclass
    clus
vv   EFCAB4B MUTATED EFCAB4B WILD-TYPE
  T1               0                17
  T2               3                89
  T3               4               325
  T4               0                50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  EFCAB4B MUTATED     5   1   1
  EFCAB4B WILD-TYPE 282 112  86
D1755V6, multiclass
    clus
vv   EFCAB4B MUTATED EFCAB4B WILD-TYPE
  N0               5               282
  N1               1               112
  N2               1                86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1755V7, binary
                   cls
clus                  0   1
  EFCAB4B MUTATED     7   0
  EFCAB4B WILD-TYPE 368  65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  EFCAB4B MUTATED      7    0
  EFCAB4B WILD-TYPE  368   65
   clus
vv  EFCAB4B MUTATED EFCAB4B WILD-TYPE
  0               7               368
  1               0                65
[1] 2 2
[1] FALSE
D1755V8, binary
                   cls
clus                  0   1
  EFCAB4B MUTATED     5   2
  EFCAB4B WILD-TYPE 220 262
[1] "tbl2"
                   cls
clus                [,1] [,2]
  EFCAB4B MUTATED      5    2
  EFCAB4B WILD-TYPE  220  262
        clus
vv       EFCAB4B MUTATED EFCAB4B WILD-TYPE
  FEMALE               5               220
  MALE                 2               262
[1] 2 2
[1] FALSE
D1755V9, binary
                   cls
clus                  0   1
  EFCAB4B MUTATED     6   0
  EFCAB4B WILD-TYPE 344  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  EFCAB4B MUTATED      6    0
  EFCAB4B WILD-TYPE  344   22
     clus
vv    EFCAB4B MUTATED EFCAB4B WILD-TYPE
  NO                6               344
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  EFCAB4B MUTATED                      3                             2
  EFCAB4B WILD-TYPE                  312                            45
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  EFCAB4B MUTATED                       2                              0
  EFCAB4B WILD-TYPE                   104                             10
D1755V10, multiclass
                                clus
vv                               EFCAB4B MUTATED EFCAB4B WILD-TYPE
  COLON ADENOCARCINOMA                         3               312
  COLON MUCINOUS ADENOCARCINOMA                2                45
  RECTAL ADENOCARCINOMA                        2               104
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  EFCAB4B MUTATED     6   1   0   0
  EFCAB4B WILD-TYPE 339   3  31  25
D1755V11, multiclass
    clus
vv   EFCAB4B MUTATED EFCAB4B WILD-TYPE
  R0               6               339
  R1               1                 3
  R2               0                31
  RX               0                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1755V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  EFCAB4B MUTATED                                  0     1
  EFCAB4B WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  EFCAB4B MUTATED                           1     3
  EFCAB4B WILD-TYPE                        21   223
D1755V13, multiclass
                                  clus
vv                                 EFCAB4B MUTATED EFCAB4B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                10
  BLACK OR AFRICAN AMERICAN                      1                21
  WHITE                                          3               223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1756) Variable = EPSTI1 MUTATION ANALYSIS
D1756V1, survival
                  sevent
clus2                0   1
  EPSTI1 MUTATED     6   1
  EPSTI1 WILD-TYPE 372  92
  EPSTI1 MUTATED EPSTI1 WILD-TYPE 
               7              464 
  EPSTI1 MUTATED EPSTI1 WILD-TYPE 
               1               92 
$`EPSTI1 MUTATED`
TCGA-A6-3809 TCGA-AA-3977 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-CA-6717 TCGA-CM-4746 
       32.75        25.02        58.39        49.41        12.76        37.02 
TCGA-F4-6808 
       33.67 

$`EPSTI1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       33.01        21.44        17.82         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        88.21         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07        12.20        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       23.05        20.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       41.42        16.24        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  EPSTI1 MUTATED EPSTI1 WILD-TYPE 
           12.76             0.00 
  EPSTI1 MUTATED EPSTI1 WILD-TYPE 
           58.39           148.01 
  EPSTI1 MUTATED EPSTI1 WILD-TYPE 
          33.670           20.035 
[1] "12.8 - 58.4 (33.7)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.9"
D1756V2, continuous
D1756V3, binary
                  cls
clus                 0   1
  EPSTI1 MUTATED     7   0
  EPSTI1 WILD-TYPE 359 119
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EPSTI1 MUTATED      7    0
  EPSTI1 WILD-TYPE  359  119
        clus
vv       EPSTI1 MUTATED EPSTI1 WILD-TYPE
  COLON               7              359
  RECTUM              0              119
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  EPSTI1 MUTATED         2        0        1         2         1         0
  EPSTI1 WILD-TYPE      89        1       31       136         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  EPSTI1 MUTATED           0          0          0          0        0
  EPSTI1 WILD-TYPE        24         11         59         42       48
                  vv
clus               STAGE IVA STAGE IVB
  EPSTI1 MUTATED           0         0
  EPSTI1 WILD-TYPE        18         1
D1756V4, multiclass
            clus
vv           EPSTI1 MUTATED EPSTI1 WILD-TYPE
  STAGE I                 2               89
  STAGE IA                0                1
  STAGE II                1               31
  STAGE IIA               2              136
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              0               59
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  EPSTI1 MUTATED     1   2   3   1
  EPSTI1 WILD-TYPE  16  90 326  49
D1756V5, multiclass
    clus
vv   EPSTI1 MUTATED EPSTI1 WILD-TYPE
  T1              1               16
  T2              2               90
  T3              3              326
  T4              1               49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  EPSTI1 MUTATED     7   0   0
  EPSTI1 WILD-TYPE 280 113  87
D1756V6, multiclass
    clus
vv   EPSTI1 MUTATED EPSTI1 WILD-TYPE
  N0              7              280
  N1              0              113
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1756V7, binary
                  cls
clus                 0   1
  EPSTI1 MUTATED     5   0
  EPSTI1 WILD-TYPE 370  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EPSTI1 MUTATED      5    0
  EPSTI1 WILD-TYPE  370   65
   clus
vv  EPSTI1 MUTATED EPSTI1 WILD-TYPE
  0              5              370
  1              0               65
[1] 2 2
[1] FALSE
D1756V8, binary
                  cls
clus                 0   1
  EPSTI1 MUTATED     3   4
  EPSTI1 WILD-TYPE 222 260
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EPSTI1 MUTATED      3    4
  EPSTI1 WILD-TYPE  222  260
        clus
vv       EPSTI1 MUTATED EPSTI1 WILD-TYPE
  FEMALE              3              222
  MALE                4              260
[1] 2 2
[1] FALSE
D1756V9, binary
                  cls
clus                 0   1
  EPSTI1 MUTATED     7   0
  EPSTI1 WILD-TYPE 343  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EPSTI1 MUTATED      7    0
  EPSTI1 WILD-TYPE  343   22
     clus
vv    EPSTI1 MUTATED EPSTI1 WILD-TYPE
  NO               7              343
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  EPSTI1 MUTATED                      5                             2
  EPSTI1 WILD-TYPE                  310                            45
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  EPSTI1 MUTATED                       0                              0
  EPSTI1 WILD-TYPE                   106                             10
D1756V10, multiclass
                                clus
vv                               EPSTI1 MUTATED EPSTI1 WILD-TYPE
  COLON ADENOCARCINOMA                        5              310
  COLON MUCINOUS ADENOCARCINOMA               2               45
  RECTAL ADENOCARCINOMA                       0              106
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  EPSTI1 MUTATED     4   0   0   1
  EPSTI1 WILD-TYPE 341   4  31  24
D1756V11, multiclass
    clus
vv   EPSTI1 MUTATED EPSTI1 WILD-TYPE
  R0              4              341
  R1              0                4
  R2              0               31
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1756V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  EPSTI1 MUTATED                                  0     1
  EPSTI1 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  EPSTI1 MUTATED                           1     4
  EPSTI1 WILD-TYPE                        21   222
D1756V13, multiclass
                                  clus
vv                                 EPSTI1 MUTATED EPSTI1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                         4              222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1757) Variable = GPR160 MUTATION ANALYSIS
D1757V1, survival
                  sevent
clus2                0   1
  GPR160 MUTATED     3   2
  GPR160 WILD-TYPE 375  91
  GPR160 MUTATED GPR160 WILD-TYPE 
               5              466 
  GPR160 MUTATED GPR160 WILD-TYPE 
               2               91 
$`GPR160 MUTATED`
TCGA-AA-3950 TCGA-AA-A00N TCGA-F4-6570 TCGA-G4-6588 TCGA-AG-A002 
       24.00         4.01         6.18        26.17        20.98 

$`GPR160 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 
       61.91        36.00        22.09        13.78        35.80        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  GPR160 MUTATED GPR160 WILD-TYPE 
            4.01             0.00 
  GPR160 MUTATED GPR160 WILD-TYPE 
           26.17           148.01 
  GPR160 MUTATED GPR160 WILD-TYPE 
          20.980           20.155 
[1] "4.0 - 26.2 (21.0)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "3.4"
D1757V2, continuous
D1757V3, binary
                  cls
clus                 0   1
  GPR160 MUTATED     4   1
  GPR160 WILD-TYPE 362 118
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR160 MUTATED      4    1
  GPR160 WILD-TYPE  362  118
        clus
vv       GPR160 MUTATED GPR160 WILD-TYPE
  COLON               4              362
  RECTUM              1              118
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GPR160 MUTATED         1        0        0         3         1         0
  GPR160 WILD-TYPE      90        1       32       135         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GPR160 MUTATED           0          0          0          0        0
  GPR160 WILD-TYPE        24         11         59         42       48
                  vv
clus               STAGE IVA STAGE IVB
  GPR160 MUTATED           0         0
  GPR160 WILD-TYPE        18         1
D1757V4, multiclass
            clus
vv           GPR160 MUTATED GPR160 WILD-TYPE
  STAGE I                 1               90
  STAGE IA                0                1
  STAGE II                0               32
  STAGE IIA               3              135
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              0               59
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  GPR160 MUTATED     0   1   3   1
  GPR160 WILD-TYPE  17  91 326  49
D1757V5, multiclass
    clus
vv   GPR160 MUTATED GPR160 WILD-TYPE
  T1              0               17
  T2              1               91
  T3              3              326
  T4              1               49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  GPR160 MUTATED     5   0   0
  GPR160 WILD-TYPE 282 113  87
D1757V6, multiclass
    clus
vv   GPR160 MUTATED GPR160 WILD-TYPE
  N0              5              282
  N1              0              113
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1757V7, binary
                  cls
clus                 0   1
  GPR160 MUTATED     5   0
  GPR160 WILD-TYPE 370  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR160 MUTATED      5    0
  GPR160 WILD-TYPE  370   65
   clus
vv  GPR160 MUTATED GPR160 WILD-TYPE
  0              5              370
  1              0               65
[1] 2 2
[1] FALSE
D1757V8, binary
                  cls
clus                 0   1
  GPR160 MUTATED     3   2
  GPR160 WILD-TYPE 222 262
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR160 MUTATED      3    2
  GPR160 WILD-TYPE  222  262
        clus
vv       GPR160 MUTATED GPR160 WILD-TYPE
  FEMALE              3              222
  MALE                2              262
[1] 2 2
[1] FALSE
D1757V9, binary
                  cls
clus                 0   1
  GPR160 MUTATED     4   0
  GPR160 WILD-TYPE 346  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR160 MUTATED      4    0
  GPR160 WILD-TYPE  346   22
     clus
vv    GPR160 MUTATED GPR160 WILD-TYPE
  NO               4              346
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  GPR160 MUTATED                      2                             2
  GPR160 WILD-TYPE                  313                            45
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  GPR160 MUTATED                       1                              0
  GPR160 WILD-TYPE                   105                             10
D1757V10, multiclass
                                clus
vv                               GPR160 MUTATED GPR160 WILD-TYPE
  COLON ADENOCARCINOMA                        2              313
  COLON MUCINOUS ADENOCARCINOMA               2               45
  RECTAL ADENOCARCINOMA                       1              105
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  GPR160 MUTATED     5   0   0   0
  GPR160 WILD-TYPE 340   4  31  25
D1757V11, multiclass
    clus
vv   GPR160 MUTATED GPR160 WILD-TYPE
  R0              5              340
  R1              0                4
  R2              0               31
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1757V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GPR160 MUTATED                                  0     0
  GPR160 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  GPR160 MUTATED                           0     2
  GPR160 WILD-TYPE                        22   224
D1757V13, multiclass
[1] "Remove cluster labels:" "GPR160 MUTATED"        
clus
  GPR160 MUTATED GPR160 WILD-TYPE 
               2              258 
      TCGA-A6-2671       TCGA-A6-2672       TCGA-A6-2674       TCGA-A6-2676 
"GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" 
      TCGA-A6-2677       TCGA-A6-2678       TCGA-A6-2683       TCGA-A6-3807 
"GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" 
      TCGA-A6-3808       TCGA-A6-3809       TCGA-A6-3810       TCGA-A6-4105 
"GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" 
      TCGA-A6-5656       TCGA-A6-5657       TCGA-A6-5659       TCGA-A6-5660 
"GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" 
      TCGA-A6-5661       TCGA-A6-5662       TCGA-A6-5664       TCGA-A6-5665 
"GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" 
      TCGA-A6-5666       TCGA-A6-6137       TCGA-A6-6138       TCGA-A6-6141 
"GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" 
      TCGA-A6-6142       TCGA-A6-6648       TCGA-A6-6649       TCGA-A6-6651 
"GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" 
      TCGA-A6-6652       TCGA-A6-6653       TCGA-A6-6654       TCGA-A6-6780 
"GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" 
      TCGA-A6-6781       TCGA-A6-6782       TCGA-AD-5900       TCGA-AD-6548 
"GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" 
      TCGA-AD-6888       TCGA-AD-6889       TCGA-AD-6890       TCGA-AD-6895 
"GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" 
      TCGA-AD-6899       TCGA-AD-6901       TCGA-AD-6963       TCGA-AD-6964 
"GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" 
      TCGA-AD-6965       TCGA-AU-3779       TCGA-AU-6004       TCGA-AY-4070 
"GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" 
      TCGA-AY-4071       TCGA-AY-5543       TCGA-AY-6196       TCGA-AY-6197 
"GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" 
      TCGA-AY-6386       TCGA-AZ-4315       TCGA-AZ-4323       TCGA-AZ-4616 
"GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" 
      TCGA-AZ-4681       TCGA-AZ-4682       TCGA-AZ-5403       TCGA-AZ-5407 
"GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" 
      TCGA-AZ-6598       TCGA-AZ-6599       TCGA-AZ-6600       TCGA-AZ-6601 
"GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" 
      TCGA-AZ-6603       TCGA-AZ-6605       TCGA-AZ-6606       TCGA-AZ-6607 
"GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" 
      TCGA-AZ-6608       TCGA-CA-5254       TCGA-CA-5255       TCGA-CA-5796 
"GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" 
      TCGA-CA-5797       TCGA-CA-6715       TCGA-CA-6716       TCGA-CA-6717 
"GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" 
      TCGA-CA-6718       TCGA-CA-6719       TCGA-CK-4947       TCGA-CK-4948 
"GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" 
      TCGA-CK-4950       TCGA-CK-4952       TCGA-CK-5912       TCGA-CK-5913 
"GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" 
      TCGA-CK-5914       TCGA-CK-5915       TCGA-CK-5916       TCGA-CK-6746 
"GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" 
      TCGA-CK-6747       TCGA-CK-6748       TCGA-CK-6751       TCGA-CM-4743 
"GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" 
      TCGA-CM-4744       TCGA-CM-4746       TCGA-CM-4747       TCGA-CM-4752 
"GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" 
      TCGA-CM-5341       TCGA-CM-5344       TCGA-CM-5348       TCGA-CM-5349 
"GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" 
      TCGA-CM-5860       TCGA-CM-5861       TCGA-CM-5862       TCGA-CM-5863 
"GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" 
      TCGA-CM-5864       TCGA-CM-5868       TCGA-CM-6161       TCGA-CM-6162 
"GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" 
      TCGA-CM-6163       TCGA-CM-6164       TCGA-CM-6165       TCGA-CM-6166 
"GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" 
      TCGA-CM-6167       TCGA-CM-6168       TCGA-CM-6169       TCGA-CM-6170 
"GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" 
      TCGA-CM-6171       TCGA-CM-6172       TCGA-CM-6674       TCGA-CM-6675 
"GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" 
      TCGA-CM-6676       TCGA-CM-6677       TCGA-CM-6678       TCGA-CM-6679 
"GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" 
      TCGA-CM-6680       TCGA-D5-5537       TCGA-D5-5538       TCGA-D5-5539 
"GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" 
      TCGA-D5-5540       TCGA-D5-5541       TCGA-D5-6529       TCGA-D5-6532 
"GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" 
      TCGA-D5-6533       TCGA-D5-6534       TCGA-D5-6535       TCGA-D5-6536 
"GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" 
      TCGA-D5-6537       TCGA-D5-6538       TCGA-D5-6539       TCGA-D5-6540 
"GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" 
      TCGA-D5-6541       TCGA-D5-6898       TCGA-D5-6920       TCGA-D5-6922 
"GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" 
      TCGA-D5-6923       TCGA-D5-6924       TCGA-D5-6926       TCGA-D5-6927 
"GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" 
      TCGA-D5-6928       TCGA-D5-6929       TCGA-D5-6930       TCGA-D5-6931 
"GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" 
      TCGA-D5-6932       TCGA-D5-7000       TCGA-DM-A0X9       TCGA-DM-A0XD 
"GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" 
      TCGA-DM-A0XF       TCGA-DM-A1D0       TCGA-DM-A1D4       TCGA-DM-A1D6 
"GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" 
      TCGA-DM-A1D7       TCGA-DM-A1D8       TCGA-DM-A1D9       TCGA-DM-A1DA 
"GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" 
      TCGA-DM-A1DB       TCGA-DM-A1HA       TCGA-DM-A1HB       TCGA-DM-A282 
"GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" 
      TCGA-DM-A285       TCGA-DM-A28C       TCGA-DM-A28E       TCGA-DM-A28F 
"GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" 
      TCGA-DM-A28G       TCGA-DM-A28H       TCGA-DM-A28K       TCGA-F4-6459 
"GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" 
      TCGA-F4-6460       TCGA-F4-6569       TCGA-F4-6703       TCGA-F4-6704 
"GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" 
      TCGA-F4-6805       TCGA-F4-6806       TCGA-F4-6807       TCGA-F4-6808 
"GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" 
      TCGA-F4-6809       TCGA-F4-6854       TCGA-F4-6855       TCGA-F4-6856 
"GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" 
      TCGA-G4-6293       TCGA-G4-6299       TCGA-G4-6303       TCGA-G4-6304 
"GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" 
      TCGA-G4-6306       TCGA-G4-6307       TCGA-G4-6309       TCGA-G4-6310 
"GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" 
      TCGA-G4-6315       TCGA-G4-6317       TCGA-G4-6321       TCGA-G4-6323 
"GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" 
      TCGA-G4-6586       TCGA-G4-6625       TCGA-G4-6626       TCGA-G4-6628 
"GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" 
      TCGA-AF-2687       TCGA-AF-2689       TCGA-AF-2691       TCGA-AF-2692 
"GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" 
      TCGA-AF-2693       TCGA-AF-3400       TCGA-AF-3913       TCGA-AF-4110 
"GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" 
      TCGA-AF-5654       TCGA-AF-6136       TCGA-AF-6655       TCGA-AF-6672 
"GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" 
      TCGA-AH-6544       TCGA-AH-6547       TCGA-AH-6549       TCGA-AH-6643 
"GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" 
      TCGA-AH-6644       TCGA-CI-6619       TCGA-CI-6620       TCGA-CI-6621 
"GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" 
      TCGA-CI-6622       TCGA-CI-6624       TCGA-CL-5917       TCGA-CL-5918 
"GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" 
      TCGA-DC-5337       TCGA-DC-5869       TCGA-DC-6155       TCGA-DC-6157 
"GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" 
      TCGA-DC-6158       TCGA-DC-6160       TCGA-DC-6681       TCGA-DC-6682 
"GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" 
      TCGA-DC-6683       TCGA-DT-5265       TCGA-DY-A0XA       TCGA-DY-A1DC 
"GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" 
      TCGA-DY-A1DD       TCGA-DY-A1DF       TCGA-DY-A1DG       TCGA-DY-A1H8 
"GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" 
      TCGA-EF-5830       TCGA-EI-6506       TCGA-EI-6507       TCGA-EI-6508 
"GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" 
      TCGA-EI-6510       TCGA-F5-6464       TCGA-F5-6465       TCGA-F5-6571 
"GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" 
      TCGA-F5-6702       TCGA-F5-6811       TCGA-F5-6812       TCGA-F5-6813 
"GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" "GPR160 WILD-TYPE" 
      TCGA-G5-6235       TCGA-G5-6641 
"GPR160 WILD-TYPE" "GPR160 WILD-TYPE" 

Clustering(1758) Variable = EPHA2 MUTATION ANALYSIS
D1758V1, survival
                 sevent
clus2               0   1
  EPHA2 MUTATED     8   3
  EPHA2 WILD-TYPE 370  90
  EPHA2 MUTATED EPHA2 WILD-TYPE 
             11             460 
  EPHA2 MUTATED EPHA2 WILD-TYPE 
              3              90 
$`EPHA2 MUTATED`
TCGA-A6-5661 TCGA-A6-6781 TCGA-AA-3715 TCGA-AA-3821 TCGA-AA-3966 TCGA-AA-A00A 
       33.53        19.66        19.04         1.02         2.01        38.04 
TCGA-AZ-6598 TCGA-CM-4743 TCGA-CM-4746 TCGA-D5-6927 TCGA-DM-A1DA 
       49.41        23.05        37.02         9.44         7.50 

$`EPHA2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
       33.04         0.99        25.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       27.02        13.94        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4747 
       21.14        82.95         1.91       124.27        20.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6929 
        4.41        12.43        14.30         9.04        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
      140.38        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  EPHA2 MUTATED EPHA2 WILD-TYPE 
           1.02            0.00 
  EPHA2 MUTATED EPHA2 WILD-TYPE 
          49.41          148.01 
  EPHA2 MUTATED EPHA2 WILD-TYPE 
         19.660          20.235 
[1] "1.0 - 49.4 (19.7)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.7"
D1758V2, continuous
D1758V3, binary
                 cls
clus                0   1
  EPHA2 MUTATED    11   0
  EPHA2 WILD-TYPE 355 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPHA2 MUTATED     11    0
  EPHA2 WILD-TYPE  355  119
        clus
vv       EPHA2 MUTATED EPHA2 WILD-TYPE
  COLON             11             355
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  EPHA2 MUTATED         2        0        2         5         0         0
  EPHA2 WILD-TYPE      89        1       30       133        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  EPHA2 MUTATED           0          0          0          2        0         0
  EPHA2 WILD-TYPE        24         11         59         40       48        18
                 vv
clus              STAGE IVB
  EPHA2 MUTATED           0
  EPHA2 WILD-TYPE         1
D1758V4, multiclass
            clus
vv           EPHA2 MUTATED EPHA2 WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA              5             133
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             2              40
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  EPHA2 MUTATED     0   2   8   1
  EPHA2 WILD-TYPE  17  90 321  49
D1758V5, multiclass
    clus
vv   EPHA2 MUTATED EPHA2 WILD-TYPE
  T1             0              17
  T2             2              90
  T3             8             321
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  EPHA2 MUTATED     9   1   1
  EPHA2 WILD-TYPE 278 112  86
D1758V6, multiclass
    clus
vv   EPHA2 MUTATED EPHA2 WILD-TYPE
  N0             9             278
  N1             1             112
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1758V7, binary
                 cls
clus                0   1
  EPHA2 MUTATED     9   0
  EPHA2 WILD-TYPE 366  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPHA2 MUTATED      9    0
  EPHA2 WILD-TYPE  366   65
   clus
vv  EPHA2 MUTATED EPHA2 WILD-TYPE
  0             9             366
  1             0              65
[1] 2 2
[1] FALSE
D1758V8, binary
                 cls
clus                0   1
  EPHA2 MUTATED     5   6
  EPHA2 WILD-TYPE 220 258
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPHA2 MUTATED      5    6
  EPHA2 WILD-TYPE  220  258
        clus
vv       EPHA2 MUTATED EPHA2 WILD-TYPE
  FEMALE             5             220
  MALE               6             258
[1] 2 2
[1] FALSE
D1758V9, binary
                 cls
clus                0   1
  EPHA2 MUTATED     9   0
  EPHA2 WILD-TYPE 341  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPHA2 MUTATED      9    0
  EPHA2 WILD-TYPE  341   22
     clus
vv    EPHA2 MUTATED EPHA2 WILD-TYPE
  NO              9             341
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  EPHA2 MUTATED                      8                             3
  EPHA2 WILD-TYPE                  307                            44
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  EPHA2 MUTATED                       0                              0
  EPHA2 WILD-TYPE                   106                             10
D1758V10, multiclass
                                clus
vv                               EPHA2 MUTATED EPHA2 WILD-TYPE
  COLON ADENOCARCINOMA                       8             307
  COLON MUCINOUS ADENOCARCINOMA              3              44
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  EPHA2 MUTATED     8   0   0   0
  EPHA2 WILD-TYPE 337   4  31  25
D1758V11, multiclass
    clus
vv   EPHA2 MUTATED EPHA2 WILD-TYPE
  R0             8             337
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1758V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  EPHA2 MUTATED                                  0     0
  EPHA2 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  EPHA2 MUTATED                           2     5
  EPHA2 WILD-TYPE                        20   221
D1758V13, multiclass
                                  clus
vv                                 EPHA2 MUTATED EPHA2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    2              20
  WHITE                                        5             221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1759) Variable = ZBTB7C MUTATION ANALYSIS
D1759V1, survival
                  sevent
clus2                0   1
  ZBTB7C MUTATED    10   4
  ZBTB7C WILD-TYPE 368  89
  ZBTB7C MUTATED ZBTB7C WILD-TYPE 
              14              457 
  ZBTB7C MUTATED ZBTB7C WILD-TYPE 
               4               89 
$`ZBTB7C MUTATED`
TCGA-AA-3492 TCGA-AA-3663 TCGA-AA-3710 TCGA-AA-3852 TCGA-AA-3864 TCGA-AA-3966 
        3.02         6.97        26.99         0.00        53.00         2.01 
TCGA-AD-6889 TCGA-AU-6004 TCGA-CK-5913 TCGA-CM-6161 TCGA-DM-A28G TCGA-F4-6459 
       56.55        27.09        51.32        15.02        60.79         8.61 
TCGA-G4-6309 TCGA-AG-A002 
       85.48        20.98 

$`ZBTB7C WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
        0.00        33.07        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       31.07        30.05        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 
       26.01        24.00         2.01        20.98        34.03        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       21.37        15.52         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 
       27.42        10.88         0.20        14.50        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       85.45        15.62        49.08         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6162 
       15.02         5.03        15.02        15.02        17.03        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28H TCGA-DM-A28K 
        6.12        81.37       119.93        35.97       117.07        98.24 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       55.04        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  ZBTB7C MUTATED ZBTB7C WILD-TYPE 
               0                0 
  ZBTB7C MUTATED ZBTB7C WILD-TYPE 
           85.48           148.01 
  ZBTB7C MUTATED ZBTB7C WILD-TYPE 
          23.985           20.120 
[1] "0.0 - 85.5 (24.0)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.2"
D1759V2, continuous
D1759V3, binary
                  cls
clus                 0   1
  ZBTB7C MUTATED    14   1
  ZBTB7C WILD-TYPE 352 118
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZBTB7C MUTATED     14    1
  ZBTB7C WILD-TYPE  352  118
        clus
vv       ZBTB7C MUTATED ZBTB7C WILD-TYPE
  COLON              14              352
  RECTUM              1              118
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZBTB7C MUTATED         3        0        3         6         0         0
  ZBTB7C WILD-TYPE      88        1       29       132        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZBTB7C MUTATED           0          0          2          0        1
  ZBTB7C WILD-TYPE        24         11         57         42       47
                  vv
clus               STAGE IVA STAGE IVB
  ZBTB7C MUTATED           0         0
  ZBTB7C WILD-TYPE        18         1
D1759V4, multiclass
            clus
vv           ZBTB7C MUTATED ZBTB7C WILD-TYPE
  STAGE I                 3               88
  STAGE IA                0                1
  STAGE II                3               29
  STAGE IIA               6              132
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              2               57
  STAGE IIIC              0               42
  STAGE IV                1               47
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZBTB7C MUTATED     0   3  11   1
  ZBTB7C WILD-TYPE  17  89 318  49
D1759V5, multiclass
    clus
vv   ZBTB7C MUTATED ZBTB7C WILD-TYPE
  T1              0               17
  T2              3               89
  T3             11              318
  T4              1               49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  ZBTB7C MUTATED    12   1   2
  ZBTB7C WILD-TYPE 275 112  85
D1759V6, multiclass
    clus
vv   ZBTB7C MUTATED ZBTB7C WILD-TYPE
  N0             12              275
  N1              1              112
  N2              2               85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1759V7, binary
                  cls
clus                 0   1
  ZBTB7C MUTATED    13   1
  ZBTB7C WILD-TYPE 362  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZBTB7C MUTATED     13    1
  ZBTB7C WILD-TYPE  362   64
   clus
vv  ZBTB7C MUTATED ZBTB7C WILD-TYPE
  0             13              362
  1              1               64
[1] 2 2
[1] FALSE
D1759V8, binary
                  cls
clus                 0   1
  ZBTB7C MUTATED     8   7
  ZBTB7C WILD-TYPE 217 257
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZBTB7C MUTATED      8    7
  ZBTB7C WILD-TYPE  217  257
        clus
vv       ZBTB7C MUTATED ZBTB7C WILD-TYPE
  FEMALE              8              217
  MALE                7              257
[1] 2 2
[1] FALSE
D1759V9, binary
                  cls
clus                 0   1
  ZBTB7C MUTATED     9   0
  ZBTB7C WILD-TYPE 341  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZBTB7C MUTATED      9    0
  ZBTB7C WILD-TYPE  341   22
     clus
vv    ZBTB7C MUTATED ZBTB7C WILD-TYPE
  NO               9              341
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ZBTB7C MUTATED                     12                             2
  ZBTB7C WILD-TYPE                  303                            45
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ZBTB7C MUTATED                       1                              0
  ZBTB7C WILD-TYPE                   105                             10
D1759V10, multiclass
                                clus
vv                               ZBTB7C MUTATED ZBTB7C WILD-TYPE
  COLON ADENOCARCINOMA                       12              303
  COLON MUCINOUS ADENOCARCINOMA               2               45
  RECTAL ADENOCARCINOMA                       1              105
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ZBTB7C MUTATED    10   0   1   1
  ZBTB7C WILD-TYPE 335   4  30  24
D1759V11, multiclass
    clus
vv   ZBTB7C MUTATED ZBTB7C WILD-TYPE
  R0             10              335
  R1              0                4
  R2              1               30
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1759V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZBTB7C MUTATED                                  0     1
  ZBTB7C WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZBTB7C MUTATED                           1     5
  ZBTB7C WILD-TYPE                        21   221
D1759V13, multiclass
                                  clus
vv                                 ZBTB7C MUTATED ZBTB7C WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                         5              221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1760) Variable = CHM MUTATION ANALYSIS
D1760V1, survival
               sevent
clus2             0   1
  CHM MUTATED     3   2
  CHM WILD-TYPE 375  91
  CHM MUTATED CHM WILD-TYPE 
            5           466 
  CHM MUTATED CHM WILD-TYPE 
            2            91 
$`CHM MUTATED`
TCGA-AZ-6600 TCGA-CM-5863 TCGA-CM-6678 TCGA-DM-A285 TCGA-AG-A002 
       12.10        15.02        11.01         6.12        20.98 

$`CHM WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       49.41         6.77       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-5868 
       30.08        32.02        15.02         5.03        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6679 TCGA-CM-6680 
       12.95        13.05        11.08        11.08        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
      139.17        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  CHM MUTATED CHM WILD-TYPE 
         6.12          0.00 
  CHM MUTATED CHM WILD-TYPE 
        20.98        148.01 
  CHM MUTATED CHM WILD-TYPE 
       12.100        20.415 
[1] "6.1 - 21.0 (12.1)"  "0.0 - 148.0 (20.4)"
[1] "hr=" "3.8"
D1760V2, continuous
D1760V3, binary
               cls
clus              0   1
  CHM MUTATED     4   1
  CHM WILD-TYPE 362 118
[1] "tbl2"
               cls
clus            [,1] [,2]
  CHM MUTATED      4    1
  CHM WILD-TYPE  362  118
        clus
vv       CHM MUTATED CHM WILD-TYPE
  COLON            4           362
  RECTUM           1           118
[1] 2 2
[1] FALSE
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CHM MUTATED         1        0        0         0         0         0
  CHM WILD-TYPE      90        1       32       138        10         1
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CHM MUTATED           0          0          1          0        2         1
  CHM WILD-TYPE        24         11         58         42       46        17
               vv
clus            STAGE IVB
  CHM MUTATED           0
  CHM WILD-TYPE         1
D1760V4, multiclass
            clus
vv           CHM MUTATED CHM WILD-TYPE
  STAGE I              1            90
  STAGE IA             0             1
  STAGE II             0            32
  STAGE IIA            0           138
  STAGE IIB            0            10
  STAGE IIC            0             1
  STAGE III            0            24
  STAGE IIIA           0            11
  STAGE IIIB           1            58
  STAGE IIIC           0            42
  STAGE IV             2            46
  STAGE IVA            1            17
  STAGE IVB            0             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  CHM MUTATED     0   1   2   2
  CHM WILD-TYPE  17  91 327  48
D1760V5, multiclass
    clus
vv   CHM MUTATED CHM WILD-TYPE
  T1           0            17
  T2           1            91
  T3           2           327
  T4           2            48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2
  CHM MUTATED     1   3   1
  CHM WILD-TYPE 286 110  86
D1760V6, multiclass
    clus
vv   CHM MUTATED CHM WILD-TYPE
  N0           1           286
  N1           3           110
  N2           1            86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1760V7, binary
               cls
clus              0   1
  CHM MUTATED     2   3
  CHM WILD-TYPE 373  62
[1] "tbl2"
               cls
clus            [,1] [,2]
  CHM MUTATED      2    3
  CHM WILD-TYPE  373   62
   clus
vv  CHM MUTATED CHM WILD-TYPE
  0           2           373
  1           3            62
[1] 2 2
[1] FALSE
D1760V8, binary
               cls
clus              0   1
  CHM MUTATED     3   2
  CHM WILD-TYPE 222 262
[1] "tbl2"
               cls
clus            [,1] [,2]
  CHM MUTATED      3    2
  CHM WILD-TYPE  222  262
        clus
vv       CHM MUTATED CHM WILD-TYPE
  FEMALE           3           222
  MALE             2           262
[1] 2 2
[1] FALSE
D1760V9, binary
               cls
clus              0   1
  CHM MUTATED     3   0
  CHM WILD-TYPE 347  22
[1] "tbl2"
               cls
clus            [,1] [,2]
  CHM MUTATED      3    0
  CHM WILD-TYPE  347   22
     clus
vv    CHM MUTATED CHM WILD-TYPE
  NO            3           347
  YES           0            22
[1] 2 2
[1] FALSE
               vv
clus            COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CHM MUTATED                      2                             2
  CHM WILD-TYPE                  313                            45
               vv
clus            RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CHM MUTATED                       1                              0
  CHM WILD-TYPE                   105                             10
D1760V10, multiclass
                                clus
vv                               CHM MUTATED CHM WILD-TYPE
  COLON ADENOCARCINOMA                     2           313
  COLON MUCINOUS ADENOCARCINOMA            2            45
  RECTAL ADENOCARCINOMA                    1           105
  RECTAL MUCINOUS ADENOCARCINOMA           0            10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             R0  R1  R2  RX
  CHM MUTATED     3   0   0   0
  CHM WILD-TYPE 342   4  31  25
D1760V11, multiclass
    clus
vv   CHM MUTATED CHM WILD-TYPE
  R0           3           342
  R1           0             4
  R2           0            31
  RX           0            25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1760V12, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CHM MUTATED                                  0     0
  CHM WILD-TYPE                                1    11
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  CHM MUTATED                           1     3
  CHM WILD-TYPE                        21   223
D1760V13, multiclass
                                  clus
vv                                 CHM MUTATED CHM WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      0            11
  BLACK OR AFRICAN AMERICAN                  1            21
  WHITE                                      3           223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1761) Variable = MAPK14 MUTATION ANALYSIS
D1761V1, survival
                  sevent
clus2                0   1
  MAPK14 MUTATED     4   2
  MAPK14 WILD-TYPE 374  91
  MAPK14 MUTATED MAPK14 WILD-TYPE 
               6              465 
  MAPK14 MUTATED MAPK14 WILD-TYPE 
               2               91 
$`MAPK14 MUTATED`
TCGA-A6-6141 TCGA-AA-A00N TCGA-AA-A010 TCGA-AZ-6607 TCGA-CA-6717 TCGA-AF-6136 
        8.38         4.01        34.98         3.19        12.76        15.39 

$`MAPK14 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 
       22.09        22.06        32.71        27.09        22.52        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5254 
      100.01        29.56         5.23        11.74         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07        12.20        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 
       34.49        10.39        14.50        16.83        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  MAPK14 MUTATED MAPK14 WILD-TYPE 
            3.19             0.00 
  MAPK14 MUTATED MAPK14 WILD-TYPE 
           34.98           148.01 
  MAPK14 MUTATED MAPK14 WILD-TYPE 
           10.57            20.55 
[1] "3.2 - 35.0 (10.6)"  "0.0 - 148.0 (20.6)"
[1] "hr=" "3.5"
D1761V2, continuous
D1761V3, binary
                  cls
clus                 0   1
  MAPK14 MUTATED     7   1
  MAPK14 WILD-TYPE 359 118
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAPK14 MUTATED      7    1
  MAPK14 WILD-TYPE  359  118
        clus
vv       MAPK14 MUTATED MAPK14 WILD-TYPE
  COLON               7              359
  RECTUM              1              118
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MAPK14 MUTATED         1        0        0         3         2         0
  MAPK14 WILD-TYPE      90        1       32       135         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MAPK14 MUTATED           0          0          1          0        1
  MAPK14 WILD-TYPE        24         11         58         42       47
                  vv
clus               STAGE IVA STAGE IVB
  MAPK14 MUTATED           0         0
  MAPK14 WILD-TYPE        18         1
D1761V4, multiclass
            clus
vv           MAPK14 MUTATED MAPK14 WILD-TYPE
  STAGE I                 1               90
  STAGE IA                0                1
  STAGE II                0               32
  STAGE IIA               3              135
  STAGE IIB               2                8
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              1               58
  STAGE IIIC              0               42
  STAGE IV                1               47
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  MAPK14 MUTATED     0   1   4   3
  MAPK14 WILD-TYPE  17  91 325  47
D1761V5, multiclass
    clus
vv   MAPK14 MUTATED MAPK14 WILD-TYPE
  T1              0               17
  T2              1               91
  T3              4              325
  T4              3               47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  MAPK14 MUTATED     6   1   1
  MAPK14 WILD-TYPE 281 112  86
D1761V6, multiclass
    clus
vv   MAPK14 MUTATED MAPK14 WILD-TYPE
  N0              6              281
  N1              1              112
  N2              1               86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1761V7, binary
                  cls
clus                 0   1
  MAPK14 MUTATED     5   1
  MAPK14 WILD-TYPE 370  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAPK14 MUTATED      5    1
  MAPK14 WILD-TYPE  370   64
   clus
vv  MAPK14 MUTATED MAPK14 WILD-TYPE
  0              5              370
  1              1               64
[1] 2 2
[1] FALSE
D1761V8, binary
                  cls
clus                 0   1
  MAPK14 MUTATED     3   5
  MAPK14 WILD-TYPE 222 259
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAPK14 MUTATED      3    5
  MAPK14 WILD-TYPE  222  259
        clus
vv       MAPK14 MUTATED MAPK14 WILD-TYPE
  FEMALE              3              222
  MALE                5              259
[1] 2 2
[1] FALSE
D1761V9, binary
                  cls
clus                 0   1
  MAPK14 MUTATED     4   1
  MAPK14 WILD-TYPE 346  21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAPK14 MUTATED      4    1
  MAPK14 WILD-TYPE  346   21
     clus
vv    MAPK14 MUTATED MAPK14 WILD-TYPE
  NO               4              346
  YES              1               21
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MAPK14 MUTATED                      5                             2
  MAPK14 WILD-TYPE                  310                            45
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MAPK14 MUTATED                       1                              0
  MAPK14 WILD-TYPE                   105                             10
D1761V10, multiclass
                                clus
vv                               MAPK14 MUTATED MAPK14 WILD-TYPE
  COLON ADENOCARCINOMA                        5              310
  COLON MUCINOUS ADENOCARCINOMA               2               45
  RECTAL ADENOCARCINOMA                       1              105
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  MAPK14 MUTATED     3   0   0   2
  MAPK14 WILD-TYPE 342   4  31  23
D1761V11, multiclass
    clus
vv   MAPK14 MUTATED MAPK14 WILD-TYPE
  R0              3              342
  R1              0                4
  R2              0               31
  RX              2               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1761V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MAPK14 MUTATED                                  0     1
  MAPK14 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  MAPK14 MUTATED                           1     3
  MAPK14 WILD-TYPE                        21   223
D1761V13, multiclass
                                  clus
vv                                 MAPK14 MUTATED MAPK14 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                         3              223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1762) Variable = C12ORF11 MUTATION ANALYSIS
D1762V1, survival
                    sevent
clus2                  0   1
  C12ORF11 MUTATED    11   2
  C12ORF11 WILD-TYPE 367  91
  C12ORF11 MUTATED C12ORF11 WILD-TYPE 
                13                458 
  C12ORF11 MUTATED C12ORF11 WILD-TYPE 
                 2                 91 
$`C12ORF11 MUTATED`
TCGA-AA-3837 TCGA-AA-3861 TCGA-AA-3966 TCGA-AA-A010 TCGA-AA-A01Q TCGA-AU-6004 
       38.99        30.05         2.01        34.98         1.02        27.09 
TCGA-AZ-6601 TCGA-CK-5916 TCGA-CM-6171 TCGA-D5-6932 TCGA-F4-6856 TCGA-AG-A002 
      100.01        21.14        14.04        11.38        35.31        20.98 
TCGA-EI-6506 
       20.55 

$`C12ORF11 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
        1.02        17.98        15.95        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 
       32.05         0.99        31.07        31.07        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       20.98        34.03        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
       38.07        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       49.41         6.77        12.10        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 
       14.99        12.99        13.02        15.02        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        4.80         1.51        12.00        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
        0.53        47.41       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
       32.61         0.49        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  C12ORF11 MUTATED C12ORF11 WILD-TYPE 
              1.02               0.00 
  C12ORF11 MUTATED C12ORF11 WILD-TYPE 
            100.01             148.01 
  C12ORF11 MUTATED C12ORF11 WILD-TYPE 
            21.140             20.035 
[1] "1.0 - 100.0 (21.1)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.3"
D1762V2, continuous
D1762V3, binary
                    cls
clus                   0   1
  C12ORF11 MUTATED    12   2
  C12ORF11 WILD-TYPE 354 117
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C12ORF11 MUTATED     12    2
  C12ORF11 WILD-TYPE  354  117
        clus
vv       C12ORF11 MUTATED C12ORF11 WILD-TYPE
  COLON                12                354
  RECTUM                2                117
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  C12ORF11 MUTATED         5        0        2         6         1         0
  C12ORF11 WILD-TYPE      86        1       30       132         9         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C12ORF11 MUTATED           0          0          0          0        0
  C12ORF11 WILD-TYPE        24         11         59         42       48
                    vv
clus                 STAGE IVA STAGE IVB
  C12ORF11 MUTATED           0         0
  C12ORF11 WILD-TYPE        18         1
D1762V4, multiclass
            clus
vv           C12ORF11 MUTATED C12ORF11 WILD-TYPE
  STAGE I                   5                 86
  STAGE IA                  0                  1
  STAGE II                  2                 30
  STAGE IIA                 6                132
  STAGE IIB                 1                  9
  STAGE IIC                 0                  1
  STAGE III                 0                 24
  STAGE IIIA                0                 11
  STAGE IIIB                0                 59
  STAGE IIIC                0                 42
  STAGE IV                  0                 48
  STAGE IVA                 0                 18
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  C12ORF11 MUTATED     1   4   8   1
  C12ORF11 WILD-TYPE  16  88 321  49
D1762V5, multiclass
    clus
vv   C12ORF11 MUTATED C12ORF11 WILD-TYPE
  T1                1                 16
  T2                4                 88
  T3                8                321
  T4                1                 49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  C12ORF11 MUTATED    14   0   0
  C12ORF11 WILD-TYPE 273 113  87
D1762V6, multiclass
    clus
vv   C12ORF11 MUTATED C12ORF11 WILD-TYPE
  N0               14                273
  N1                0                113
  N2                0                 87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1762V7, binary
                    cls
clus                   0   1
  C12ORF11 MUTATED    14   0
  C12ORF11 WILD-TYPE 361  65
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C12ORF11 MUTATED     14    0
  C12ORF11 WILD-TYPE  361   65
   clus
vv  C12ORF11 MUTATED C12ORF11 WILD-TYPE
  0               14                361
  1                0                 65
[1] 2 2
[1] FALSE
D1762V8, binary
                    cls
clus                   0   1
  C12ORF11 MUTATED     8   6
  C12ORF11 WILD-TYPE 217 258
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C12ORF11 MUTATED      8    6
  C12ORF11 WILD-TYPE  217  258
        clus
vv       C12ORF11 MUTATED C12ORF11 WILD-TYPE
  FEMALE                8                217
  MALE                  6                258
[1] 2 2
[1] FALSE
D1762V9, binary
                    cls
clus                   0   1
  C12ORF11 MUTATED    10   0
  C12ORF11 WILD-TYPE 340  22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C12ORF11 MUTATED     10    0
  C12ORF11 WILD-TYPE  340   22
     clus
vv    C12ORF11 MUTATED C12ORF11 WILD-TYPE
  NO                10                340
  YES                0                 22
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  C12ORF11 MUTATED                      9                             3
  C12ORF11 WILD-TYPE                  306                            44
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  C12ORF11 MUTATED                       2                              0
  C12ORF11 WILD-TYPE                   104                             10
D1762V10, multiclass
                                clus
vv                               C12ORF11 MUTATED C12ORF11 WILD-TYPE
  COLON ADENOCARCINOMA                          9                306
  COLON MUCINOUS ADENOCARCINOMA                 3                 44
  RECTAL ADENOCARCINOMA                         2                104
  RECTAL MUCINOUS ADENOCARCINOMA                0                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  C12ORF11 MUTATED    11   0   0   1
  C12ORF11 WILD-TYPE 334   4  31  24
D1762V11, multiclass
    clus
vv   C12ORF11 MUTATED C12ORF11 WILD-TYPE
  R0               11                334
  R1                0                  4
  R2                0                 31
  RX                1                 24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1762V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C12ORF11 MUTATED                                  0     0
  C12ORF11 WILD-TYPE                                1    11
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  C12ORF11 MUTATED                           0     7
  C12ORF11 WILD-TYPE                        22   219
D1762V13, multiclass
                                  clus
vv                                 C12ORF11 MUTATED C12ORF11 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 11
  BLACK OR AFRICAN AMERICAN                       0                 22
  WHITE                                           7                219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1763) Variable = AOX1 MUTATION ANALYSIS
D1763V1, survival
                sevent
clus2              0   1
  AOX1 MUTATED    11   2
  AOX1 WILD-TYPE 367  91
  AOX1 MUTATED AOX1 WILD-TYPE 
            13            458 
  AOX1 MUTATED AOX1 WILD-TYPE 
             2             91 
$`AOX1 MUTATED`
TCGA-A6-5665 TCGA-AA-3864 TCGA-AA-3877 TCGA-AA-3947 TCGA-AA-3966 TCGA-AA-3977 
       22.06        53.00        31.00        33.01         2.01        25.02 
TCGA-AD-6889 TCGA-AU-6004 TCGA-CA-6717 TCGA-CK-5916 TCGA-CM-6170 TCGA-DM-A28F 
       56.55        27.09        12.76        21.14        15.02        35.97 
TCGA-AG-A002 
       20.98 

$`AOX1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 
       32.05         0.99        31.07        31.07        30.05        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 
       24.03        27.02        29.98        18.05         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       21.37        15.52         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 
       27.42        10.88         0.20        14.50        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.20        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 
       15.62        49.08        51.32         9.99        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       13.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
       81.37       119.93        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  AOX1 MUTATED AOX1 WILD-TYPE 
          2.01           0.00 
  AOX1 MUTATED AOX1 WILD-TYPE 
         56.55         148.01 
  AOX1 MUTATED AOX1 WILD-TYPE 
         25.02          20.02 
[1] "2.0 - 56.5 (25.0)"  "0.0 - 148.0 (20.0)"
[1] "hr=" "1.3"
D1763V2, continuous
D1763V3, binary
                cls
clus               0   1
  AOX1 MUTATED    12   1
  AOX1 WILD-TYPE 354 118
[1] "tbl2"
                cls
clus             [,1] [,2]
  AOX1 MUTATED     12    1
  AOX1 WILD-TYPE  354  118
        clus
vv       AOX1 MUTATED AOX1 WILD-TYPE
  COLON            12            354
  RECTUM            1            118
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  AOX1 MUTATED         5        0        1         4         1         0
  AOX1 WILD-TYPE      86        1       31       134         9         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AOX1 MUTATED           0          0          1          0        0         0
  AOX1 WILD-TYPE        24         11         58         42       48        18
                vv
clus             STAGE IVB
  AOX1 MUTATED           0
  AOX1 WILD-TYPE         1
D1763V4, multiclass
            clus
vv           AOX1 MUTATED AOX1 WILD-TYPE
  STAGE I               5             86
  STAGE IA              0              1
  STAGE II              1             31
  STAGE IIA             4            134
  STAGE IIB             1              9
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            1             58
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  AOX1 MUTATED     2   4   6   1
  AOX1 WILD-TYPE  15  88 323  49
D1763V5, multiclass
    clus
vv   AOX1 MUTATED AOX1 WILD-TYPE
  T1            2             15
  T2            4             88
  T3            6            323
  T4            1             49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  AOX1 MUTATED    12   1   0
  AOX1 WILD-TYPE 275 112  87
D1763V6, multiclass
    clus
vv   AOX1 MUTATED AOX1 WILD-TYPE
  N0           12            275
  N1            1            112
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1763V7, binary
                cls
clus               0   1
  AOX1 MUTATED    12   0
  AOX1 WILD-TYPE 363  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  AOX1 MUTATED     12    0
  AOX1 WILD-TYPE  363   65
   clus
vv  AOX1 MUTATED AOX1 WILD-TYPE
  0           12            363
  1            0             65
[1] 2 2
[1] FALSE
D1763V8, binary
                cls
clus               0   1
  AOX1 MUTATED     7   6
  AOX1 WILD-TYPE 218 258
[1] "tbl2"
                cls
clus             [,1] [,2]
  AOX1 MUTATED      7    6
  AOX1 WILD-TYPE  218  258
        clus
vv       AOX1 MUTATED AOX1 WILD-TYPE
  FEMALE            7            218
  MALE              6            258
[1] 2 2
[1] FALSE
D1763V9, binary
                cls
clus               0   1
  AOX1 MUTATED     9   0
  AOX1 WILD-TYPE 341  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  AOX1 MUTATED      9    0
  AOX1 WILD-TYPE  341   22
     clus
vv    AOX1 MUTATED AOX1 WILD-TYPE
  NO             9            341
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  AOX1 MUTATED                      8                             4
  AOX1 WILD-TYPE                  307                            43
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  AOX1 MUTATED                       1                              0
  AOX1 WILD-TYPE                   105                             10
D1763V10, multiclass
                                clus
vv                               AOX1 MUTATED AOX1 WILD-TYPE
  COLON ADENOCARCINOMA                      8            307
  COLON MUCINOUS ADENOCARCINOMA             4             43
  RECTAL ADENOCARCINOMA                     1            105
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  AOX1 MUTATED     7   0   0   2
  AOX1 WILD-TYPE 338   4  31  23
D1763V11, multiclass
    clus
vv   AOX1 MUTATED AOX1 WILD-TYPE
  R0            7            338
  R1            0              4
  R2            0             31
  RX            2             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1763V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AOX1 MUTATED                                  0     2
  AOX1 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  AOX1 MUTATED                           0     5
  AOX1 WILD-TYPE                        22   221
D1763V13, multiclass
                                  clus
vv                                 AOX1 MUTATED AOX1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              9
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       5            221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1764) Variable = SLC12A2 MUTATION ANALYSIS
D1764V1, survival
                   sevent
clus2                 0   1
  SLC12A2 MUTATED    12   5
  SLC12A2 WILD-TYPE 366  88
  SLC12A2 MUTATED SLC12A2 WILD-TYPE 
               17               454 
  SLC12A2 MUTATED SLC12A2 WILD-TYPE 
                5                88 
$`SLC12A2 MUTATED`
TCGA-A6-5664 TCGA-AA-3510 TCGA-AA-3544 TCGA-AA-3710 TCGA-AA-3966 TCGA-AA-A01Q 
       22.09        63.98        14.01        26.99         2.01         1.02 
TCGA-AD-6899 TCGA-AZ-4315 TCGA-AZ-6601 TCGA-AZ-6607 TCGA-CA-6717 TCGA-CA-6718 
        5.79        58.39       100.01         3.19        12.76        10.06 
TCGA-CK-4950 TCGA-D5-6898 TCGA-DM-A0XD TCGA-G4-6317 TCGA-AG-A002 
       85.45         1.48        24.43        36.00        20.98 

$`SLC12A2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
       12.99         0.99        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       85.05        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6901 
       21.37        15.52        56.55         0.79         0.72        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        33.01        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5254 
       12.10        29.56         5.23        11.74         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 
        3.06         3.25         3.29         0.07        12.20        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
       17.56       148.01        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
      119.70        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       61.91        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  SLC12A2 MUTATED SLC12A2 WILD-TYPE 
             1.02              0.00 
  SLC12A2 MUTATED SLC12A2 WILD-TYPE 
           100.01            148.01 
  SLC12A2 MUTATED SLC12A2 WILD-TYPE 
           20.980            20.155 
[1] "1.0 - 100.0 (21.0)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.3"
D1764V2, continuous
D1764V3, binary
                   cls
clus                  0   1
  SLC12A2 MUTATED    17   1
  SLC12A2 WILD-TYPE 349 118
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC12A2 MUTATED     17    1
  SLC12A2 WILD-TYPE  349  118
        clus
vv       SLC12A2 MUTATED SLC12A2 WILD-TYPE
  COLON               17               349
  RECTUM               1               118
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SLC12A2 MUTATED         3        0        3         7         0         0
  SLC12A2 WILD-TYPE      88        1       29       131        10         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC12A2 MUTATED           0          0          1          3        1
  SLC12A2 WILD-TYPE        24         11         58         39       47
                   vv
clus                STAGE IVA STAGE IVB
  SLC12A2 MUTATED           0         0
  SLC12A2 WILD-TYPE        18         1
D1764V4, multiclass
            clus
vv           SLC12A2 MUTATED SLC12A2 WILD-TYPE
  STAGE I                  3                88
  STAGE IA                 0                 1
  STAGE II                 3                29
  STAGE IIA                7               131
  STAGE IIB                0                10
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               0                11
  STAGE IIIB               1                58
  STAGE IIIC               3                39
  STAGE IV                 1                47
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  SLC12A2 MUTATED     0   3  12   3
  SLC12A2 WILD-TYPE  17  89 317  47
D1764V5, multiclass
    clus
vv   SLC12A2 MUTATED SLC12A2 WILD-TYPE
  T1               0                17
  T2               3                89
  T3              12               317
  T4               3                47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  SLC12A2 MUTATED    13   1   4
  SLC12A2 WILD-TYPE 274 112  83
D1764V6, multiclass
    clus
vv   SLC12A2 MUTATED SLC12A2 WILD-TYPE
  N0              13               274
  N1               1               112
  N2               4                83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1764V7, binary
                   cls
clus                  0   1
  SLC12A2 MUTATED    14   1
  SLC12A2 WILD-TYPE 361  64
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC12A2 MUTATED     14    1
  SLC12A2 WILD-TYPE  361   64
   clus
vv  SLC12A2 MUTATED SLC12A2 WILD-TYPE
  0              14               361
  1               1                64
[1] 2 2
[1] FALSE
D1764V8, binary
                   cls
clus                  0   1
  SLC12A2 MUTATED     7  11
  SLC12A2 WILD-TYPE 218 253
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC12A2 MUTATED      7   11
  SLC12A2 WILD-TYPE  218  253
        clus
vv       SLC12A2 MUTATED SLC12A2 WILD-TYPE
  FEMALE               7               218
  MALE                11               253
[1] 2 2
[1] FALSE
D1764V9, binary
                   cls
clus                  0   1
  SLC12A2 MUTATED    13   0
  SLC12A2 WILD-TYPE 337  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC12A2 MUTATED     13    0
  SLC12A2 WILD-TYPE  337   22
     clus
vv    SLC12A2 MUTATED SLC12A2 WILD-TYPE
  NO               13               337
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SLC12A2 MUTATED                     14                             3
  SLC12A2 WILD-TYPE                  301                            44
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SLC12A2 MUTATED                       1                              0
  SLC12A2 WILD-TYPE                   105                             10
D1764V10, multiclass
                                clus
vv                               SLC12A2 MUTATED SLC12A2 WILD-TYPE
  COLON ADENOCARCINOMA                        14               301
  COLON MUCINOUS ADENOCARCINOMA                3                44
  RECTAL ADENOCARCINOMA                        1               105
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  SLC12A2 MUTATED     9   1   0   2
  SLC12A2 WILD-TYPE 336   3  31  23
D1764V11, multiclass
    clus
vv   SLC12A2 MUTATED SLC12A2 WILD-TYPE
  R0               9               336
  R1               1                 3
  R2               0                31
  RX               2                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1764V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SLC12A2 MUTATED                                  0     2
  SLC12A2 WILD-TYPE                                1     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  SLC12A2 MUTATED                           2     7
  SLC12A2 WILD-TYPE                        20   219
D1764V13, multiclass
                                  clus
vv                                 SLC12A2 MUTATED SLC12A2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          2                 9
  BLACK OR AFRICAN AMERICAN                      2                20
  WHITE                                          7               219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1765) Variable = UGT2A1 MUTATION ANALYSIS
D1765V1, survival
                  sevent
clus2                0   1
  UGT2A1 MUTATED     7   2
  UGT2A1 WILD-TYPE 371  91
  UGT2A1 MUTATED UGT2A1 WILD-TYPE 
               9              462 
  UGT2A1 MUTATED UGT2A1 WILD-TYPE 
               2               91 
$`UGT2A1 MUTATED`
TCGA-AA-3821 TCGA-AA-3864 TCGA-AA-3952 TCGA-AA-3977 TCGA-AA-A010 TCGA-AA-A01R 
        1.02        53.00         2.01        25.02        34.98        35.01 
TCGA-CA-6717 TCGA-F4-6570 TCGA-G4-6293 
       12.76         6.18       133.18 

$`UGT2A1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 
       32.05         0.99        31.07        31.07        30.05        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3955 
       12.99        24.00        33.01        26.01        24.00        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
        1.02         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07        12.20        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       35.74        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6299 
       33.67        13.25         0.53        47.41        35.31        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  UGT2A1 MUTATED UGT2A1 WILD-TYPE 
            1.02             0.00 
  UGT2A1 MUTATED UGT2A1 WILD-TYPE 
          133.18           148.01 
  UGT2A1 MUTATED UGT2A1 WILD-TYPE 
          25.020           20.155 
[1] "1.0 - 133.2 (25.0)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1"  
D1765V2, continuous
D1765V3, binary
                  cls
clus                 0   1
  UGT2A1 MUTATED    10   0
  UGT2A1 WILD-TYPE 356 119
[1] "tbl2"
                  cls
clus               [,1] [,2]
  UGT2A1 MUTATED     10    0
  UGT2A1 WILD-TYPE  356  119
        clus
vv       UGT2A1 MUTATED UGT2A1 WILD-TYPE
  COLON              10              356
  RECTUM              0              119
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  UGT2A1 MUTATED         1        0        2         2         1         0
  UGT2A1 WILD-TYPE      90        1       30       136         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  UGT2A1 MUTATED           2          0          0          1        0
  UGT2A1 WILD-TYPE        22         11         59         41       48
                  vv
clus               STAGE IVA STAGE IVB
  UGT2A1 MUTATED           0         0
  UGT2A1 WILD-TYPE        18         1
D1765V4, multiclass
            clus
vv           UGT2A1 MUTATED UGT2A1 WILD-TYPE
  STAGE I                 1               90
  STAGE IA                0                1
  STAGE II                2               30
  STAGE IIA               2              136
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               2               22
  STAGE IIIA              0               11
  STAGE IIIB              0               59
  STAGE IIIC              1               41
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  UGT2A1 MUTATED     0   2   6   2
  UGT2A1 WILD-TYPE  17  90 323  48
D1765V5, multiclass
    clus
vv   UGT2A1 MUTATED UGT2A1 WILD-TYPE
  T1              0               17
  T2              2               90
  T3              6              323
  T4              2               48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  UGT2A1 MUTATED     7   1   2
  UGT2A1 WILD-TYPE 280 112  85
D1765V6, multiclass
    clus
vv   UGT2A1 MUTATED UGT2A1 WILD-TYPE
  N0              7              280
  N1              1              112
  N2              2               85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1765V7, binary
                  cls
clus                 0   1
  UGT2A1 MUTATED     9   0
  UGT2A1 WILD-TYPE 366  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  UGT2A1 MUTATED      9    0
  UGT2A1 WILD-TYPE  366   65
   clus
vv  UGT2A1 MUTATED UGT2A1 WILD-TYPE
  0              9              366
  1              0               65
[1] 2 2
[1] FALSE
D1765V8, binary
                  cls
clus                 0   1
  UGT2A1 MUTATED     5   5
  UGT2A1 WILD-TYPE 220 259
[1] "tbl2"
                  cls
clus               [,1] [,2]
  UGT2A1 MUTATED      5    5
  UGT2A1 WILD-TYPE  220  259
        clus
vv       UGT2A1 MUTATED UGT2A1 WILD-TYPE
  FEMALE              5              220
  MALE                5              259
[1] 2 2
[1] FALSE
D1765V9, binary
                  cls
clus                 0   1
  UGT2A1 MUTATED     7   1
  UGT2A1 WILD-TYPE 343  21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  UGT2A1 MUTATED      7    1
  UGT2A1 WILD-TYPE  343   21
     clus
vv    UGT2A1 MUTATED UGT2A1 WILD-TYPE
  NO               7              343
  YES              1               21
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  UGT2A1 MUTATED                      7                             3
  UGT2A1 WILD-TYPE                  308                            44
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  UGT2A1 MUTATED                       0                              0
  UGT2A1 WILD-TYPE                   106                             10
D1765V10, multiclass
                                clus
vv                               UGT2A1 MUTATED UGT2A1 WILD-TYPE
  COLON ADENOCARCINOMA                        7              308
  COLON MUCINOUS ADENOCARCINOMA               3               44
  RECTAL ADENOCARCINOMA                       0              106
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  UGT2A1 MUTATED     8   0   0   1
  UGT2A1 WILD-TYPE 337   4  31  24
D1765V11, multiclass
    clus
vv   UGT2A1 MUTATED UGT2A1 WILD-TYPE
  R0              8              337
  R1              0                4
  R2              0               31
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1765V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  UGT2A1 MUTATED                                  0     1
  UGT2A1 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  UGT2A1 MUTATED                           0     2
  UGT2A1 WILD-TYPE                        22   224
D1765V13, multiclass
                                  clus
vv                                 UGT2A1 MUTATED UGT2A1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         2              224
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1766) Variable = CXCR7 MUTATION ANALYSIS
D1766V1, survival
                 sevent
clus2               0   1
  CXCR7 MUTATED    12   4
  CXCR7 WILD-TYPE 366  89
  CXCR7 MUTATED CXCR7 WILD-TYPE 
             16             455 
  CXCR7 MUTATED CXCR7 WILD-TYPE 
              4              89 
$`CXCR7 MUTATED`
TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3522 TCGA-AA-3663 TCGA-AA-3692 TCGA-AU-3779 
       20.12        19.66        37.05         6.97        36.00        14.50 
TCGA-AZ-6598 TCGA-CK-5912 TCGA-CM-5344 TCGA-CM-6170 TCGA-D5-6927 TCGA-G4-6303 
       49.41        49.08        22.03        15.02         9.44        65.85 
TCGA-G4-6586 TCGA-G4-6588 TCGA-AF-2693 TCGA-AG-A002 
       35.80        26.17        19.10        20.98 

$`CXCR7 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       23.87        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
        9.07        24.03        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02        78.08         6.05        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
        5.98        37.05        19.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-6004 
        5.79        22.42        27.42        10.88         0.20        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
      148.01        85.45        15.62        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       25.02        13.02        29.06        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       12.99        13.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       12.43        14.30         9.04        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6304 TCGA-G4-6306 
       47.41        35.31       133.18        74.56        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       13.78        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       43.04        13.55        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  CXCR7 MUTATED CXCR7 WILD-TYPE 
           6.97            0.00 
  CXCR7 MUTATED CXCR7 WILD-TYPE 
          65.85          148.01 
  CXCR7 MUTATED CXCR7 WILD-TYPE 
         21.505          20.050 
[1] "7.0 - 65.8 (21.5)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.2"
D1766V2, continuous
D1766V3, binary
                 cls
clus                0   1
  CXCR7 MUTATED    19   1
  CXCR7 WILD-TYPE 347 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CXCR7 MUTATED     19    1
  CXCR7 WILD-TYPE  347  118
        clus
vv       CXCR7 MUTATED CXCR7 WILD-TYPE
  COLON             19             347
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CXCR7 MUTATED         4        0        3         8         0         0
  CXCR7 WILD-TYPE      87        1       29       130        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CXCR7 MUTATED           0          0          1          2        3         0
  CXCR7 WILD-TYPE        24         11         58         40       45        18
                 vv
clus              STAGE IVB
  CXCR7 MUTATED           0
  CXCR7 WILD-TYPE         1
D1766V4, multiclass
            clus
vv           CXCR7 MUTATED CXCR7 WILD-TYPE
  STAGE I                4              87
  STAGE IA               0               1
  STAGE II               3              29
  STAGE IIA              8             130
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             2              40
  STAGE IV               3              45
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CXCR7 MUTATED     0   4  15   2
  CXCR7 WILD-TYPE  17  88 314  48
D1766V5, multiclass
    clus
vv   CXCR7 MUTATED CXCR7 WILD-TYPE
  T1             0              17
  T2             4              88
  T3            15             314
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  CXCR7 MUTATED    15   3   3
  CXCR7 WILD-TYPE 272 110  84
D1766V6, multiclass
    clus
vv   CXCR7 MUTATED CXCR7 WILD-TYPE
  N0            15             272
  N1             3             110
  N2             3              84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1766V7, binary
                 cls
clus                0   1
  CXCR7 MUTATED    12   3
  CXCR7 WILD-TYPE 363  62
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CXCR7 MUTATED     12    3
  CXCR7 WILD-TYPE  363   62
   clus
vv  CXCR7 MUTATED CXCR7 WILD-TYPE
  0            12             363
  1             3              62
[1] 2 2
[1] FALSE
D1766V8, binary
                 cls
clus                0   1
  CXCR7 MUTATED    12   9
  CXCR7 WILD-TYPE 213 255
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CXCR7 MUTATED     12    9
  CXCR7 WILD-TYPE  213  255
        clus
vv       CXCR7 MUTATED CXCR7 WILD-TYPE
  FEMALE            12             213
  MALE               9             255
[1] 2 2
[1] FALSE
D1766V9, binary
                 cls
clus                0   1
  CXCR7 MUTATED    15   1
  CXCR7 WILD-TYPE 335  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CXCR7 MUTATED     15    1
  CXCR7 WILD-TYPE  335   21
     clus
vv    CXCR7 MUTATED CXCR7 WILD-TYPE
  NO             15             335
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CXCR7 MUTATED                     15                             4
  CXCR7 WILD-TYPE                  300                            43
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CXCR7 MUTATED                       1                              0
  CXCR7 WILD-TYPE                   105                             10
D1766V10, multiclass
                                clus
vv                               CXCR7 MUTATED CXCR7 WILD-TYPE
  COLON ADENOCARCINOMA                      15             300
  COLON MUCINOUS ADENOCARCINOMA              4              43
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  CXCR7 MUTATED    15   0   2   1
  CXCR7 WILD-TYPE 330   4  29  24
D1766V11, multiclass
    clus
vv   CXCR7 MUTATED CXCR7 WILD-TYPE
  R0            15             330
  R1             0               4
  R2             2              29
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1766V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CXCR7 MUTATED                                  0     0
  CXCR7 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CXCR7 MUTATED                           0    13
  CXCR7 WILD-TYPE                        22   213
D1766V13, multiclass
                                  clus
vv                                 CXCR7 MUTATED CXCR7 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                       13             213
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1767) Variable = SSRP1 MUTATION ANALYSIS
D1767V1, survival
                 sevent
clus2               0   1
  SSRP1 MUTATED    13   1
  SSRP1 WILD-TYPE 365  92
  SSRP1 MUTATED SSRP1 WILD-TYPE 
             14             457 
  SSRP1 MUTATED SSRP1 WILD-TYPE 
              1              92 
$`SSRP1 MUTATED`
TCGA-A6-6653 TCGA-AA-3663 TCGA-AA-3966 TCGA-AD-6964 TCGA-AU-6004 TCGA-CM-6162 
       24.39         6.97         2.01        10.88        27.09        12.00 
TCGA-CM-6166 TCGA-CM-6674 TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6323 TCGA-G4-6628 
       21.99        12.95        53.62        55.04        13.78        79.69 
TCGA-AF-3400 TCGA-AG-A002 
       34.49        20.98 

$`SSRP1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
       25.08        25.18        24.16        21.76        24.69        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       20.98        34.03        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
        0.79         0.72         5.79        22.42        27.42         0.20 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       14.50        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 
       15.02        15.02        17.03        15.02         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       16.04        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       11.01        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       74.56        65.85        44.68        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        35.80        26.17        91.79        46.75 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3913 
       24.13        39.48        43.04        13.55        19.10        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  SSRP1 MUTATED SSRP1 WILD-TYPE 
           2.01            0.00 
  SSRP1 MUTATED SSRP1 WILD-TYPE 
          79.69          148.01 
  SSRP1 MUTATED SSRP1 WILD-TYPE 
         21.485          20.120 
[1] "2.0 - 79.7 (21.5)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "3"  
D1767V2, continuous
D1767V3, binary
                 cls
clus                0   1
  SSRP1 MUTATED    13   2
  SSRP1 WILD-TYPE 353 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SSRP1 MUTATED     13    2
  SSRP1 WILD-TYPE  353  117
        clus
vv       SSRP1 MUTATED SSRP1 WILD-TYPE
  COLON             13             353
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SSRP1 MUTATED         5        1        1         3         1         0
  SSRP1 WILD-TYPE      86        0       31       135         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SSRP1 MUTATED           1          0          2          0        0         0
  SSRP1 WILD-TYPE        23         11         57         42       48        18
                 vv
clus              STAGE IVB
  SSRP1 MUTATED           0
  SSRP1 WILD-TYPE         1
D1767V4, multiclass
            clus
vv           SSRP1 MUTATED SSRP1 WILD-TYPE
  STAGE I                5              86
  STAGE IA               1               0
  STAGE II               1              31
  STAGE IIA              3             135
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             2              57
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  SSRP1 MUTATED     0   5   7   2
  SSRP1 WILD-TYPE  17  87 322  48
D1767V5, multiclass
    clus
vv   SSRP1 MUTATED SSRP1 WILD-TYPE
  T1             0              17
  T2             5              87
  T3             7             322
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  SSRP1 MUTATED    11   2   2
  SSRP1 WILD-TYPE 276 111  85
D1767V6, multiclass
    clus
vv   SSRP1 MUTATED SSRP1 WILD-TYPE
  N0            11             276
  N1             2             111
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1767V7, binary
                 cls
clus                0   1
  SSRP1 MUTATED    13   0
  SSRP1 WILD-TYPE 362  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SSRP1 MUTATED     13    0
  SSRP1 WILD-TYPE  362   65
   clus
vv  SSRP1 MUTATED SSRP1 WILD-TYPE
  0            13             362
  1             0              65
[1] 2 2
[1] FALSE
D1767V8, binary
                 cls
clus                0   1
  SSRP1 MUTATED     6   9
  SSRP1 WILD-TYPE 219 255
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SSRP1 MUTATED      6    9
  SSRP1 WILD-TYPE  219  255
        clus
vv       SSRP1 MUTATED SSRP1 WILD-TYPE
  FEMALE             6             219
  MALE               9             255
[1] 2 2
[1] FALSE
D1767V9, binary
                 cls
clus                0   1
  SSRP1 MUTATED    11   1
  SSRP1 WILD-TYPE 339  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SSRP1 MUTATED     11    1
  SSRP1 WILD-TYPE  339   21
     clus
vv    SSRP1 MUTATED SSRP1 WILD-TYPE
  NO             11             339
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SSRP1 MUTATED                     11                             2
  SSRP1 WILD-TYPE                  304                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SSRP1 MUTATED                       1                              1
  SSRP1 WILD-TYPE                   105                              9
D1767V10, multiclass
                                clus
vv                               SSRP1 MUTATED SSRP1 WILD-TYPE
  COLON ADENOCARCINOMA                      11             304
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             1               9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  SSRP1 MUTATED    12   0   0   0
  SSRP1 WILD-TYPE 333   4  31  25
D1767V11, multiclass
    clus
vv   SSRP1 MUTATED SSRP1 WILD-TYPE
  R0            12             333
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1767V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SSRP1 MUTATED                                  0     0
  SSRP1 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  SSRP1 MUTATED                           1    10
  SSRP1 WILD-TYPE                        21   216
D1767V13, multiclass
                                  clus
vv                                 SSRP1 MUTATED SSRP1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                       10             216
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1768) Variable = IGFBP3 MUTATION ANALYSIS
D1768V1, survival
                  sevent
clus2                0   1
  IGFBP3 MUTATED     5   3
  IGFBP3 WILD-TYPE 373  90
  IGFBP3 MUTATED IGFBP3 WILD-TYPE 
               8              463 
  IGFBP3 MUTATED IGFBP3 WILD-TYPE 
               3               90 
$`IGFBP3 MUTATED`
TCGA-A6-2677 TCGA-AA-3966 TCGA-AZ-4315 TCGA-CK-5916 TCGA-CM-5861 TCGA-CM-6678 
       24.33         2.01        58.39        21.14        15.02        11.01 
TCGA-AG-3574 TCGA-AG-4007 
       36.03         1.02 

$`IGFBP3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        42.90        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
        2.01        20.98        34.03        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       33.01        21.44        17.82         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 
       15.62        49.08        51.32         9.99        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 
       29.06        22.03        22.98        30.08        32.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.08        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4008 
       32.02        19.99        28.04        36.03        14.04        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  IGFBP3 MUTATED IGFBP3 WILD-TYPE 
            1.02             0.00 
  IGFBP3 MUTATED IGFBP3 WILD-TYPE 
           58.39           148.01 
  IGFBP3 MUTATED IGFBP3 WILD-TYPE 
           18.08            20.19 
[1] "1.0 - 58.4 (18.1)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "2.3"
D1768V2, continuous
D1768V3, binary
                  cls
clus                 0   1
  IGFBP3 MUTATED     6   2
  IGFBP3 WILD-TYPE 360 117
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IGFBP3 MUTATED      6    2
  IGFBP3 WILD-TYPE  360  117
        clus
vv       IGFBP3 MUTATED IGFBP3 WILD-TYPE
  COLON               6              360
  RECTUM              2              117
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  IGFBP3 MUTATED         1        0        1         3         0         0
  IGFBP3 WILD-TYPE      90        1       31       135        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  IGFBP3 MUTATED           0          0          0          1        1
  IGFBP3 WILD-TYPE        24         11         59         41       47
                  vv
clus               STAGE IVA STAGE IVB
  IGFBP3 MUTATED           1         0
  IGFBP3 WILD-TYPE        17         1
D1768V4, multiclass
            clus
vv           IGFBP3 MUTATED IGFBP3 WILD-TYPE
  STAGE I                 1               90
  STAGE IA                0                1
  STAGE II                1               31
  STAGE IIA               3              135
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              0               59
  STAGE IIIC              1               41
  STAGE IV                1               47
  STAGE IVA               1               17
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  IGFBP3 MUTATED     1   0   5   2
  IGFBP3 WILD-TYPE  16  92 324  48
D1768V5, multiclass
    clus
vv   IGFBP3 MUTATED IGFBP3 WILD-TYPE
  T1              1               16
  T2              0               92
  T3              5              324
  T4              2               48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  IGFBP3 MUTATED     5   1   2
  IGFBP3 WILD-TYPE 282 112  85
D1768V6, multiclass
    clus
vv   IGFBP3 MUTATED IGFBP3 WILD-TYPE
  N0              5              282
  N1              1              112
  N2              2               85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1768V7, binary
                  cls
clus                 0   1
  IGFBP3 MUTATED     6   2
  IGFBP3 WILD-TYPE 369  63
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IGFBP3 MUTATED      6    2
  IGFBP3 WILD-TYPE  369   63
   clus
vv  IGFBP3 MUTATED IGFBP3 WILD-TYPE
  0              6              369
  1              2               63
[1] 2 2
[1] FALSE
D1768V8, binary
                  cls
clus                 0   1
  IGFBP3 MUTATED     6   2
  IGFBP3 WILD-TYPE 219 262
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IGFBP3 MUTATED      6    2
  IGFBP3 WILD-TYPE  219  262
        clus
vv       IGFBP3 MUTATED IGFBP3 WILD-TYPE
  FEMALE              6              219
  MALE                2              262
[1] 2 2
[1] FALSE
D1768V9, binary
                  cls
clus                 0   1
  IGFBP3 MUTATED     6   0
  IGFBP3 WILD-TYPE 344  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IGFBP3 MUTATED      6    0
  IGFBP3 WILD-TYPE  344   22
     clus
vv    IGFBP3 MUTATED IGFBP3 WILD-TYPE
  NO               6              344
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  IGFBP3 MUTATED                      5                             1
  IGFBP3 WILD-TYPE                  310                            46
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  IGFBP3 MUTATED                       2                              0
  IGFBP3 WILD-TYPE                   104                             10
D1768V10, multiclass
                                clus
vv                               IGFBP3 MUTATED IGFBP3 WILD-TYPE
  COLON ADENOCARCINOMA                        5              310
  COLON MUCINOUS ADENOCARCINOMA               1               46
  RECTAL ADENOCARCINOMA                       2              104
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  IGFBP3 MUTATED     5   0   1   1
  IGFBP3 WILD-TYPE 340   4  30  24
D1768V11, multiclass
    clus
vv   IGFBP3 MUTATED IGFBP3 WILD-TYPE
  R0              5              340
  R1              0                4
  R2              1               30
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1768V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  IGFBP3 MUTATED                                  0     0
  IGFBP3 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  IGFBP3 MUTATED                           0     5
  IGFBP3 WILD-TYPE                        22   221
D1768V13, multiclass
                                  clus
vv                                 IGFBP3 MUTATED IGFBP3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         5              221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1769) Variable = RELA MUTATION ANALYSIS
D1769V1, survival
                sevent
clus2              0   1
  RELA MUTATED     8   2
  RELA WILD-TYPE 370  91
  RELA MUTATED RELA WILD-TYPE 
            10            461 
  RELA MUTATED RELA WILD-TYPE 
             2             91 
$`RELA MUTATED`
TCGA-AA-3511 TCGA-AA-3821 TCGA-AA-A01R TCGA-AY-6386 TCGA-AZ-6598 TCGA-D5-6535 
        6.97         1.02        35.01        17.82        49.41        15.12 
TCGA-D5-6540 TCGA-G4-6588 TCGA-G4-6626 TCGA-AH-6643 
       16.14        26.17        46.75         0.69 

$`RELA WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01        63.98         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 
       10.06        35.05        33.04         0.99        25.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T 
       31.00        31.00        38.07         1.02         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        88.21         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 
       43.27        17.85         4.80        17.13        12.49        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       35.80        91.79        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6644 TCGA-CI-6619 
      117.11        38.56         1.45        17.49         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  RELA MUTATED RELA WILD-TYPE 
          0.69           0.00 
  RELA MUTATED RELA WILD-TYPE 
         49.41         148.01 
  RELA MUTATED RELA WILD-TYPE 
         16.98          20.28 
[1] "0.7 - 49.4 (17.0)"  "0.0 - 148.0 (20.3)"
[1] "hr=" "1.2"
D1769V2, continuous
D1769V3, binary
                cls
clus               0   1
  RELA MUTATED     9   1
  RELA WILD-TYPE 357 118
[1] "tbl2"
                cls
clus             [,1] [,2]
  RELA MUTATED      9    1
  RELA WILD-TYPE  357  118
        clus
vv       RELA MUTATED RELA WILD-TYPE
  COLON             9            357
  RECTUM            1            118
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RELA MUTATED         2        0        2         2         0         0
  RELA WILD-TYPE      89        1       30       136        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RELA MUTATED           1          0          2          1        0         0
  RELA WILD-TYPE        23         11         57         41       48        18
                vv
clus             STAGE IVB
  RELA MUTATED           0
  RELA WILD-TYPE         1
D1769V4, multiclass
            clus
vv           RELA MUTATED RELA WILD-TYPE
  STAGE I               2             89
  STAGE IA              0              1
  STAGE II              2             30
  STAGE IIA             2            136
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             1             23
  STAGE IIIA            0             11
  STAGE IIIB            2             57
  STAGE IIIC            1             41
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  RELA MUTATED     0   2   7   1
  RELA WILD-TYPE  17  90 322  49
D1769V5, multiclass
    clus
vv   RELA MUTATED RELA WILD-TYPE
  T1            0             17
  T2            2             90
  T3            7            322
  T4            1             49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  RELA MUTATED     6   2   2
  RELA WILD-TYPE 281 111  85
D1769V6, multiclass
    clus
vv   RELA MUTATED RELA WILD-TYPE
  N0            6            281
  N1            2            111
  N2            2             85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1769V7, binary
                cls
clus               0   1
  RELA MUTATED     8   0
  RELA WILD-TYPE 367  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  RELA MUTATED      8    0
  RELA WILD-TYPE  367   65
   clus
vv  RELA MUTATED RELA WILD-TYPE
  0            8            367
  1            0             65
[1] 2 2
[1] FALSE
D1769V8, binary
                cls
clus               0   1
  RELA MUTATED     5   5
  RELA WILD-TYPE 220 259
[1] "tbl2"
                cls
clus             [,1] [,2]
  RELA MUTATED      5    5
  RELA WILD-TYPE  220  259
        clus
vv       RELA MUTATED RELA WILD-TYPE
  FEMALE            5            220
  MALE              5            259
[1] 2 2
[1] FALSE
D1769V9, binary
                cls
clus               0   1
  RELA MUTATED     8   1
  RELA WILD-TYPE 342  21
[1] "tbl2"
                cls
clus             [,1] [,2]
  RELA MUTATED      8    1
  RELA WILD-TYPE  342   21
     clus
vv    RELA MUTATED RELA WILD-TYPE
  NO             8            342
  YES            1             21
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  RELA MUTATED                      6                             3
  RELA WILD-TYPE                  309                            44
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  RELA MUTATED                       1                              0
  RELA WILD-TYPE                   105                             10
D1769V10, multiclass
                                clus
vv                               RELA MUTATED RELA WILD-TYPE
  COLON ADENOCARCINOMA                      6            309
  COLON MUCINOUS ADENOCARCINOMA             3             44
  RECTAL ADENOCARCINOMA                     1            105
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  RELA MUTATED     8   0   0   1
  RELA WILD-TYPE 337   4  31  24
D1769V11, multiclass
    clus
vv   RELA MUTATED RELA WILD-TYPE
  R0            8            337
  R1            0              4
  R2            0             31
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1769V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RELA MUTATED                                  0     0
  RELA WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  RELA MUTATED                           1     6
  RELA WILD-TYPE                        21   220
D1769V13, multiclass
                                  clus
vv                                 RELA MUTATED RELA WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                       6            220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1770) Variable = KCNA3 MUTATION ANALYSIS
D1770V1, survival
                 sevent
clus2               0   1
  KCNA3 MUTATED    17   3
  KCNA3 WILD-TYPE 361  90
  KCNA3 MUTATED KCNA3 WILD-TYPE 
             20             451 
  KCNA3 MUTATED KCNA3 WILD-TYPE 
              3              90 
$`KCNA3 MUTATED`
TCGA-A6-4105 TCGA-A6-6141 TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3966 TCGA-AA-3977 
       14.53         8.38        20.12        19.66         2.01        25.02 
TCGA-AA-A00N TCGA-AA-A01X TCGA-AA-A01Z TCGA-AD-6895 TCGA-AZ-6598 TCGA-CA-6717 
        4.01        26.01        37.02         0.72        49.41        12.76 
TCGA-CM-5348 TCGA-CM-5861 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6588 TCGA-AG-3575 
       22.98        15.02        55.04        85.48        26.17        12.00 
TCGA-AG-3892 TCGA-AG-A002 
       13.02        20.98 

$`KCNA3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 
       16.57        34.65        33.34        32.75        36.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 
       22.06        32.71        27.09        22.52        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6782 
       24.16        21.76        24.69        24.39        23.87        20.28 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
        7.04         3.02         1.02        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
        1.02        33.04        35.01        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.79         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        88.21         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07        12.20        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       30.08        32.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6310 TCGA-G4-6315 
       74.56        65.85        53.62        44.68        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        35.80        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       10.39        36.03        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       36.95        17.03        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  KCNA3 MUTATED KCNA3 WILD-TYPE 
           0.72            0.00 
  KCNA3 MUTATED KCNA3 WILD-TYPE 
          85.48          148.01 
  KCNA3 MUTATED KCNA3 WILD-TYPE 
          19.89           20.28 
[1] "0.7 - 85.5 (19.9)"  "0.0 - 148.0 (20.3)"
[1] "hr=" "1.2"
D1770V2, continuous
D1770V3, binary
                 cls
clus                0   1
  KCNA3 MUTATED    17   3
  KCNA3 WILD-TYPE 349 116
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNA3 MUTATED     17    3
  KCNA3 WILD-TYPE  349  116
        clus
vv       KCNA3 MUTATED KCNA3 WILD-TYPE
  COLON             17             349
  RECTUM             3             116
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KCNA3 MUTATED         2        0        3         7         1         0
  KCNA3 WILD-TYPE      89        1       29       131         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  KCNA3 MUTATED           1          0          3          1        0         0
  KCNA3 WILD-TYPE        23         11         56         41       48        18
                 vv
clus              STAGE IVB
  KCNA3 MUTATED           0
  KCNA3 WILD-TYPE         1
D1770V4, multiclass
            clus
vv           KCNA3 MUTATED KCNA3 WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               3              29
  STAGE IIA              7             131
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             3              56
  STAGE IIIC             1              41
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  KCNA3 MUTATED     1   3  14   2
  KCNA3 WILD-TYPE  16  89 315  48
D1770V5, multiclass
    clus
vv   KCNA3 MUTATED KCNA3 WILD-TYPE
  T1             1              16
  T2             3              89
  T3            14             315
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  KCNA3 MUTATED    14   6   0
  KCNA3 WILD-TYPE 273 107  87
D1770V6, multiclass
    clus
vv   KCNA3 MUTATED KCNA3 WILD-TYPE
  N0            14             273
  N1             6             107
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1770V7, binary
                 cls
clus                0   1
  KCNA3 MUTATED    15   0
  KCNA3 WILD-TYPE 360  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNA3 MUTATED     15    0
  KCNA3 WILD-TYPE  360   65
   clus
vv  KCNA3 MUTATED KCNA3 WILD-TYPE
  0            15             360
  1             0              65
[1] 2 2
[1] FALSE
D1770V8, binary
                 cls
clus                0   1
  KCNA3 MUTATED     8  12
  KCNA3 WILD-TYPE 217 252
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNA3 MUTATED      8   12
  KCNA3 WILD-TYPE  217  252
        clus
vv       KCNA3 MUTATED KCNA3 WILD-TYPE
  FEMALE             8             217
  MALE              12             252
[1] 2 2
[1] FALSE
D1770V9, binary
                 cls
clus                0   1
  KCNA3 MUTATED    17   0
  KCNA3 WILD-TYPE 333  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNA3 MUTATED     17    0
  KCNA3 WILD-TYPE  333   22
     clus
vv    KCNA3 MUTATED KCNA3 WILD-TYPE
  NO             17             333
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  KCNA3 MUTATED                     12                             5
  KCNA3 WILD-TYPE                  303                            42
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  KCNA3 MUTATED                       3                              0
  KCNA3 WILD-TYPE                   103                             10
D1770V10, multiclass
                                clus
vv                               KCNA3 MUTATED KCNA3 WILD-TYPE
  COLON ADENOCARCINOMA                      12             303
  COLON MUCINOUS ADENOCARCINOMA              5              42
  RECTAL ADENOCARCINOMA                      3             103
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  KCNA3 MUTATED    11   0   0   2
  KCNA3 WILD-TYPE 334   4  31  23
D1770V11, multiclass
    clus
vv   KCNA3 MUTATED KCNA3 WILD-TYPE
  R0            11             334
  R1             0               4
  R2             0              31
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1770V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KCNA3 MUTATED                                  0     1
  KCNA3 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  KCNA3 MUTATED                           2     9
  KCNA3 WILD-TYPE                        20   217
D1770V13, multiclass
                                  clus
vv                                 KCNA3 MUTATED KCNA3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    2              20
  WHITE                                        9             217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1771) Variable = CPT1B MUTATION ANALYSIS
D1771V1, survival
                 sevent
clus2               0   1
  CPT1B MUTATED     9   2
  CPT1B WILD-TYPE 369  91
  CPT1B MUTATED CPT1B WILD-TYPE 
             11             460 
  CPT1B MUTATED CPT1B WILD-TYPE 
              2              91 
$`CPT1B MUTATED`
TCGA-A6-6781 TCGA-AA-3492 TCGA-AA-3555 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3977 
       19.66         3.02        29.95        85.05        26.99        25.02 
TCGA-AA-A01R TCGA-AD-6889 TCGA-AZ-6601 TCGA-G4-6628 TCGA-DC-6683 
       35.01        56.55       100.01        79.69         5.03 

$`CPT1B WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 
       23.87        20.12        20.28         7.04         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       24.00        17.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       15.52         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
       12.10        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       91.79        46.75        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        4.01         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  CPT1B MUTATED CPT1B WILD-TYPE 
           3.02            0.00 
  CPT1B MUTATED CPT1B WILD-TYPE 
         100.01          148.01 
  CPT1B MUTATED CPT1B WILD-TYPE 
         29.950          20.035 
[1] "3.0 - 100.0 (29.9)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.7"
D1771V2, continuous
D1771V3, binary
                 cls
clus                0   1
  CPT1B MUTATED    10   1
  CPT1B WILD-TYPE 356 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CPT1B MUTATED     10    1
  CPT1B WILD-TYPE  356  118
        clus
vv       CPT1B MUTATED CPT1B WILD-TYPE
  COLON             10             356
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CPT1B MUTATED         1        0        2         3         0         0
  CPT1B WILD-TYPE      90        1       30       135        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CPT1B MUTATED           2          0          1          1        0         0
  CPT1B WILD-TYPE        22         11         58         41       48        18
                 vv
clus              STAGE IVB
  CPT1B MUTATED           0
  CPT1B WILD-TYPE         1
D1771V4, multiclass
            clus
vv           CPT1B MUTATED CPT1B WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA              3             135
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              2              22
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             1              41
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CPT1B MUTATED     0   2   8   1
  CPT1B WILD-TYPE  17  90 321  49
D1771V5, multiclass
    clus
vv   CPT1B MUTATED CPT1B WILD-TYPE
  T1             0              17
  T2             2              90
  T3             8             321
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  CPT1B MUTATED     8   2   1
  CPT1B WILD-TYPE 279 111  86
D1771V6, multiclass
    clus
vv   CPT1B MUTATED CPT1B WILD-TYPE
  N0             8             279
  N1             2             111
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1771V7, binary
                 cls
clus                0   1
  CPT1B MUTATED     9   0
  CPT1B WILD-TYPE 366  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CPT1B MUTATED      9    0
  CPT1B WILD-TYPE  366   65
   clus
vv  CPT1B MUTATED CPT1B WILD-TYPE
  0             9             366
  1             0              65
[1] 2 2
[1] FALSE
D1771V8, binary
                 cls
clus                0   1
  CPT1B MUTATED     3   8
  CPT1B WILD-TYPE 222 256
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CPT1B MUTATED      3    8
  CPT1B WILD-TYPE  222  256
        clus
vv       CPT1B MUTATED CPT1B WILD-TYPE
  FEMALE             3             222
  MALE               8             256
[1] 2 2
[1] FALSE
D1771V9, binary
                 cls
clus                0   1
  CPT1B MUTATED     8   1
  CPT1B WILD-TYPE 342  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CPT1B MUTATED      8    1
  CPT1B WILD-TYPE  342   21
     clus
vv    CPT1B MUTATED CPT1B WILD-TYPE
  NO              8             342
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CPT1B MUTATED                      7                             3
  CPT1B WILD-TYPE                  308                            44
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CPT1B MUTATED                       1                              0
  CPT1B WILD-TYPE                   105                             10
D1771V10, multiclass
                                clus
vv                               CPT1B MUTATED CPT1B WILD-TYPE
  COLON ADENOCARCINOMA                       7             308
  COLON MUCINOUS ADENOCARCINOMA              3              44
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  CPT1B MUTATED     8   0   0   0
  CPT1B WILD-TYPE 337   4  31  25
D1771V11, multiclass
    clus
vv   CPT1B MUTATED CPT1B WILD-TYPE
  R0             8             337
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1771V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CPT1B MUTATED                                  0     1
  CPT1B WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CPT1B MUTATED                           0     4
  CPT1B WILD-TYPE                        22   222
D1771V13, multiclass
                                  clus
vv                                 CPT1B MUTATED CPT1B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        4             222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1772) Variable = SLC14A1 MUTATION ANALYSIS
D1772V1, survival
                   sevent
clus2                 0   1
  SLC14A1 MUTATED     4   3
  SLC14A1 WILD-TYPE 374  90
  SLC14A1 MUTATED SLC14A1 WILD-TYPE 
                7               464 
  SLC14A1 MUTATED SLC14A1 WILD-TYPE 
                3                90 
$`SLC14A1 MUTATED`
TCGA-AA-3950 TCGA-AD-6895 TCGA-AZ-6598 TCGA-CA-6717 TCGA-DM-A1D7 TCGA-F4-6460 
       24.00         0.72        49.41        12.76        13.32        31.96 
TCGA-AG-A025 
       49.97 

$`SLC14A1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       15.52        56.55         0.79         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 
      106.75        22.36        62.79        88.21         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D8 TCGA-DM-A1D9 
       38.20       130.65        92.75        49.91        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
        8.61        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       70.03        64.01        10.98         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  SLC14A1 MUTATED SLC14A1 WILD-TYPE 
             0.72              0.00 
  SLC14A1 MUTATED SLC14A1 WILD-TYPE 
            49.97            148.01 
  SLC14A1 MUTATED SLC14A1 WILD-TYPE 
           24.000            20.155 
[1] "0.7 - 50.0 (24.0)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "2.1"
D1772V2, continuous
D1772V3, binary
                   cls
clus                  0   1
  SLC14A1 MUTATED     6   1
  SLC14A1 WILD-TYPE 360 118
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC14A1 MUTATED      6    1
  SLC14A1 WILD-TYPE  360  118
        clus
vv       SLC14A1 MUTATED SLC14A1 WILD-TYPE
  COLON                6               360
  RECTUM               1               118
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SLC14A1 MUTATED         1        0        1         3         0         0
  SLC14A1 WILD-TYPE      90        1       31       135        10         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC14A1 MUTATED           0          0          1          0        0
  SLC14A1 WILD-TYPE        24         11         58         42       48
                   vv
clus                STAGE IVA STAGE IVB
  SLC14A1 MUTATED           0         0
  SLC14A1 WILD-TYPE        18         1
D1772V4, multiclass
            clus
vv           SLC14A1 MUTATED SLC14A1 WILD-TYPE
  STAGE I                  1                90
  STAGE IA                 0                 1
  STAGE II                 1                31
  STAGE IIA                3               135
  STAGE IIB                0                10
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               0                11
  STAGE IIIB               1                58
  STAGE IIIC               0                42
  STAGE IV                 0                48
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  SLC14A1 MUTATED     1   0   6   0
  SLC14A1 WILD-TYPE  16  92 323  50
D1772V5, multiclass
    clus
vv   SLC14A1 MUTATED SLC14A1 WILD-TYPE
  T1               1                16
  T2               0                92
  T3               6               323
  T4               0                50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  SLC14A1 MUTATED     5   2   0
  SLC14A1 WILD-TYPE 282 111  87
D1772V6, multiclass
    clus
vv   SLC14A1 MUTATED SLC14A1 WILD-TYPE
  N0               5               282
  N1               2               111
  N2               0                87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1772V7, binary
                   cls
clus                  0   1
  SLC14A1 MUTATED     5   0
  SLC14A1 WILD-TYPE 370  65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC14A1 MUTATED      5    0
  SLC14A1 WILD-TYPE  370   65
   clus
vv  SLC14A1 MUTATED SLC14A1 WILD-TYPE
  0               5               370
  1               0                65
[1] 2 2
[1] FALSE
D1772V8, binary
                   cls
clus                  0   1
  SLC14A1 MUTATED     4   3
  SLC14A1 WILD-TYPE 221 261
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC14A1 MUTATED      4    3
  SLC14A1 WILD-TYPE  221  261
        clus
vv       SLC14A1 MUTATED SLC14A1 WILD-TYPE
  FEMALE               4               221
  MALE                 3               261
[1] 2 2
[1] FALSE
D1772V9, binary
                   cls
clus                  0   1
  SLC14A1 MUTATED     4   0
  SLC14A1 WILD-TYPE 346  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC14A1 MUTATED      4    0
  SLC14A1 WILD-TYPE  346   22
     clus
vv    SLC14A1 MUTATED SLC14A1 WILD-TYPE
  NO                4               346
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SLC14A1 MUTATED                      3                             2
  SLC14A1 WILD-TYPE                  312                            45
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SLC14A1 MUTATED                       1                              0
  SLC14A1 WILD-TYPE                   105                             10
D1772V10, multiclass
                                clus
vv                               SLC14A1 MUTATED SLC14A1 WILD-TYPE
  COLON ADENOCARCINOMA                         3               312
  COLON MUCINOUS ADENOCARCINOMA                2                45
  RECTAL ADENOCARCINOMA                        1               105
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  SLC14A1 MUTATED     3   0   0   1
  SLC14A1 WILD-TYPE 342   4  31  24
D1772V11, multiclass
    clus
vv   SLC14A1 MUTATED SLC14A1 WILD-TYPE
  R0               3               342
  R1               0                 4
  R2               0                31
  RX               1                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1772V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SLC14A1 MUTATED                                  0     1
  SLC14A1 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  SLC14A1 MUTATED                           0     4
  SLC14A1 WILD-TYPE                        22   222
D1772V13, multiclass
                                  clus
vv                                 SLC14A1 MUTATED SLC14A1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                10
  BLACK OR AFRICAN AMERICAN                      0                22
  WHITE                                          4               222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1773) Variable = PLEKHH2 MUTATION ANALYSIS
D1773V1, survival
                   sevent
clus2                 0   1
  PLEKHH2 MUTATED    17   5
  PLEKHH2 WILD-TYPE 361  88
  PLEKHH2 MUTATED PLEKHH2 WILD-TYPE 
               22               449 
  PLEKHH2 MUTATED PLEKHH2 WILD-TYPE 
                5                88 
$`PLEKHH2 MUTATED`
TCGA-A6-2676 TCGA-A6-6141 TCGA-AA-3525 TCGA-AA-3663 TCGA-AA-3950 TCGA-AA-3977 
       42.90         8.38         8.05         6.97        24.00        25.02 
TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01R TCGA-AA-A02K TCGA-AD-6889 TCGA-AY-6197 
        4.01        34.98        35.01        14.01        56.55        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-4743 TCGA-D5-6930 
       17.82        58.39        12.76        10.06        23.05         1.51 
TCGA-AG-3892 TCGA-AG-A002 TCGA-DC-6155 TCGA-DY-A1DD 
       13.02        20.98        13.97        57.24 

$`PLEKHH2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 
       22.06        32.71        27.09        22.52        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3529 
        9.07        24.03        37.05        36.03        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02        78.08         6.05        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       33.01        26.01         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T 
       31.00        31.00        38.07         1.02         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        2.01         5.03         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 
       40.96         0.07        21.37        15.52         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AZ-4323 TCGA-AZ-4616 
       27.09        16.31         0.95        33.01         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       12.20        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
      124.27        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6931 
       14.30         9.04         9.44        11.64         4.80        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       36.95        17.03        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
        7.17        15.02         5.03        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  PLEKHH2 MUTATED PLEKHH2 WILD-TYPE 
             1.51              0.00 
  PLEKHH2 MUTATED PLEKHH2 WILD-TYPE 
            58.39            148.01 
  PLEKHH2 MUTATED PLEKHH2 WILD-TYPE 
            19.40             20.19 
[1] "1.5 - 58.4 (19.4)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.3"
D1773V2, continuous
D1773V3, binary
                   cls
clus                  0   1
  PLEKHH2 MUTATED    19   4
  PLEKHH2 WILD-TYPE 347 115
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLEKHH2 MUTATED     19    4
  PLEKHH2 WILD-TYPE  347  115
        clus
vv       PLEKHH2 MUTATED PLEKHH2 WILD-TYPE
  COLON               19               347
  RECTUM               4               115
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PLEKHH2 MUTATED         2        0        1        10         3         0
  PLEKHH2 WILD-TYPE      89        1       31       128         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PLEKHH2 MUTATED           1          1          3          0        1
  PLEKHH2 WILD-TYPE        23         10         56         42       47
                   vv
clus                STAGE IVA STAGE IVB
  PLEKHH2 MUTATED           0         0
  PLEKHH2 WILD-TYPE        18         1
D1773V4, multiclass
            clus
vv           PLEKHH2 MUTATED PLEKHH2 WILD-TYPE
  STAGE I                  2                89
  STAGE IA                 0                 1
  STAGE II                 1                31
  STAGE IIA               10               128
  STAGE IIB                3                 7
  STAGE IIC                0                 1
  STAGE III                1                23
  STAGE IIIA               1                10
  STAGE IIIB               3                56
  STAGE IIIC               0                42
  STAGE IV                 1                47
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  PLEKHH2 MUTATED     1   3  15   4
  PLEKHH2 WILD-TYPE  16  89 314  46
D1773V5, multiclass
    clus
vv   PLEKHH2 MUTATED PLEKHH2 WILD-TYPE
  T1               1                16
  T2               3                89
  T3              15               314
  T4               4                46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  PLEKHH2 MUTATED    17   4   2
  PLEKHH2 WILD-TYPE 270 109  85
D1773V6, multiclass
    clus
vv   PLEKHH2 MUTATED PLEKHH2 WILD-TYPE
  N0              17               270
  N1               4               109
  N2               2                85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1773V7, binary
                   cls
clus                  0   1
  PLEKHH2 MUTATED    20   1
  PLEKHH2 WILD-TYPE 355  64
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLEKHH2 MUTATED     20    1
  PLEKHH2 WILD-TYPE  355   64
   clus
vv  PLEKHH2 MUTATED PLEKHH2 WILD-TYPE
  0              20               355
  1               1                64
[1] 2 2
[1] FALSE
D1773V8, binary
                   cls
clus                  0   1
  PLEKHH2 MUTATED     8  15
  PLEKHH2 WILD-TYPE 217 249
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLEKHH2 MUTATED      8   15
  PLEKHH2 WILD-TYPE  217  249
        clus
vv       PLEKHH2 MUTATED PLEKHH2 WILD-TYPE
  FEMALE               8               217
  MALE                15               249
[1] 2 2
[1] FALSE
D1773V9, binary
                   cls
clus                  0   1
  PLEKHH2 MUTATED    17   1
  PLEKHH2 WILD-TYPE 333  21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PLEKHH2 MUTATED     17    1
  PLEKHH2 WILD-TYPE  333   21
     clus
vv    PLEKHH2 MUTATED PLEKHH2 WILD-TYPE
  NO               17               333
  YES               1                21
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PLEKHH2 MUTATED                     14                             5
  PLEKHH2 WILD-TYPE                  301                            42
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PLEKHH2 MUTATED                       4                              0
  PLEKHH2 WILD-TYPE                   102                             10
D1773V10, multiclass
                                clus
vv                               PLEKHH2 MUTATED PLEKHH2 WILD-TYPE
  COLON ADENOCARCINOMA                        14               301
  COLON MUCINOUS ADENOCARCINOMA                5                42
  RECTAL ADENOCARCINOMA                        4               102
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  PLEKHH2 MUTATED    16   0   1   2
  PLEKHH2 WILD-TYPE 329   4  30  23
D1773V11, multiclass
    clus
vv   PLEKHH2 MUTATED PLEKHH2 WILD-TYPE
  R0              16               329
  R1               0                 4
  R2               1                30
  RX               2                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1773V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PLEKHH2 MUTATED                                  0     3
  PLEKHH2 WILD-TYPE                                1     8
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  PLEKHH2 MUTATED                           2     7
  PLEKHH2 WILD-TYPE                        20   219
D1773V13, multiclass
                                  clus
vv                                 PLEKHH2 MUTATED PLEKHH2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          3                 8
  BLACK OR AFRICAN AMERICAN                      2                20
  WHITE                                          7               219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1774) Variable = ESRP2 MUTATION ANALYSIS
D1774V1, survival
                 sevent
clus2               0   1
  ESRP2 MUTATED     7   3
  ESRP2 WILD-TYPE 371  90
  ESRP2 MUTATED ESRP2 WILD-TYPE 
             10             461 
  ESRP2 MUTATED ESRP2 WILD-TYPE 
              3              90 
$`ESRP2 MUTATED`
TCGA-AA-3815 TCGA-AA-A010 TCGA-AA-A01Q TCGA-AD-6901 TCGA-AZ-4682 TCGA-CA-6718 
       33.04        34.98         1.02        22.42        22.36        10.06 
TCGA-CM-5344 TCGA-D5-6536 TCGA-DM-A1D9 TCGA-AG-A02N 
       22.03        17.85       140.38        61.97 

$`ESRP2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       19.04        10.06        35.05         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        31.00        38.07        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.79         0.72         5.79        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-5403 
       17.82        58.39         1.41         5.13       106.75        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 
        3.25         3.29         0.07        12.20        12.76        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5348 
       20.02        37.02        25.02        13.02        29.06        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       13.32        12.59         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
       49.97         1.94        38.96        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  ESRP2 MUTATED ESRP2 WILD-TYPE 
           1.02            0.00 
  ESRP2 MUTATED ESRP2 WILD-TYPE 
         140.38          148.01 
  ESRP2 MUTATED ESRP2 WILD-TYPE 
          22.39           20.05 
[1] "1.0 - 140.4 (22.4)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.3"
D1774V2, continuous
D1774V3, binary
                 cls
clus                0   1
  ESRP2 MUTATED     9   1
  ESRP2 WILD-TYPE 357 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ESRP2 MUTATED      9    1
  ESRP2 WILD-TYPE  357  118
        clus
vv       ESRP2 MUTATED ESRP2 WILD-TYPE
  COLON              9             357
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ESRP2 MUTATED         0        0        2         4         1         0
  ESRP2 WILD-TYPE      91        1       30       134         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ESRP2 MUTATED           0          0          1          0        0         1
  ESRP2 WILD-TYPE        24         11         58         42       48        17
                 vv
clus              STAGE IVB
  ESRP2 MUTATED           0
  ESRP2 WILD-TYPE         1
D1774V4, multiclass
            clus
vv           ESRP2 MUTATED ESRP2 WILD-TYPE
  STAGE I                0              91
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA              4             134
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ESRP2 MUTATED     0   0   9   1
  ESRP2 WILD-TYPE  17  92 320  49
D1774V5, multiclass
    clus
vv   ESRP2 MUTATED ESRP2 WILD-TYPE
  T1             0              17
  T2             0              92
  T3             9             320
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  ESRP2 MUTATED     9   1   0
  ESRP2 WILD-TYPE 278 112  87
D1774V6, multiclass
    clus
vv   ESRP2 MUTATED ESRP2 WILD-TYPE
  N0             9             278
  N1             1             112
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1774V7, binary
                 cls
clus                0   1
  ESRP2 MUTATED     8   1
  ESRP2 WILD-TYPE 367  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ESRP2 MUTATED      8    1
  ESRP2 WILD-TYPE  367   64
   clus
vv  ESRP2 MUTATED ESRP2 WILD-TYPE
  0             8             367
  1             1              64
[1] 2 2
[1] FALSE
D1774V8, binary
                 cls
clus                0   1
  ESRP2 MUTATED     5   5
  ESRP2 WILD-TYPE 220 259
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ESRP2 MUTATED      5    5
  ESRP2 WILD-TYPE  220  259
        clus
vv       ESRP2 MUTATED ESRP2 WILD-TYPE
  FEMALE             5             220
  MALE               5             259
[1] 2 2
[1] FALSE
D1774V9, binary
                 cls
clus                0   1
  ESRP2 MUTATED     7   0
  ESRP2 WILD-TYPE 343  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ESRP2 MUTATED      7    0
  ESRP2 WILD-TYPE  343   22
     clus
vv    ESRP2 MUTATED ESRP2 WILD-TYPE
  NO              7             343
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ESRP2 MUTATED                      9                             0
  ESRP2 WILD-TYPE                  306                            47
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ESRP2 MUTATED                       1                              0
  ESRP2 WILD-TYPE                   105                             10
D1774V10, multiclass
                                clus
vv                               ESRP2 MUTATED ESRP2 WILD-TYPE
  COLON ADENOCARCINOMA                       9             306
  COLON MUCINOUS ADENOCARCINOMA              0              47
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  ESRP2 MUTATED     7   0   0   1
  ESRP2 WILD-TYPE 338   4  31  24
D1774V11, multiclass
    clus
vv   ESRP2 MUTATED ESRP2 WILD-TYPE
  R0             7             338
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1774V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ESRP2 MUTATED                                  0     1
  ESRP2 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ESRP2 MUTATED                           0     5
  ESRP2 WILD-TYPE                        22   221
D1774V13, multiclass
                                  clus
vv                                 ESRP2 MUTATED ESRP2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        5             221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1775) Variable = MMP21 MUTATION ANALYSIS
D1775V1, survival
                 sevent
clus2               0   1
  MMP21 MUTATED     7   4
  MMP21 WILD-TYPE 371  89
  MMP21 MUTATED MMP21 WILD-TYPE 
             11             460 
  MMP21 MUTATED MMP21 WILD-TYPE 
              4              89 
$`MMP21 MUTATED`
TCGA-AA-3510 TCGA-AA-3715 TCGA-AA-3845 TCGA-AZ-6598 TCGA-AZ-6601 TCGA-CK-4950 
       63.98        19.04         0.00        49.41       100.01        85.45 
TCGA-CK-5914 TCGA-CM-6168 TCGA-CM-6171 TCGA-D5-6536 TCGA-AG-A002 
        9.99        12.99        14.04        17.85        20.98 

$`MMP21 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 
       36.00         5.03        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 
       15.95        38.99        37.02        14.93        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 
       22.36        62.79        88.21         6.77        12.10        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       14.30        17.56       148.01        15.62        49.08        51.32 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 
       21.99        14.99        13.02        15.02        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 
       18.25         1.32        43.27        15.12         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  MMP21 MUTATED MMP21 WILD-TYPE 
              0               0 
  MMP21 MUTATED MMP21 WILD-TYPE 
         100.01          148.01 
  MMP21 MUTATED MMP21 WILD-TYPE 
         19.040          20.235 
[1] "0.0 - 100.0 (19.0)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.3"
D1775V2, continuous
D1775V3, binary
                 cls
clus                0   1
  MMP21 MUTATED    11   1
  MMP21 WILD-TYPE 355 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MMP21 MUTATED     11    1
  MMP21 WILD-TYPE  355  118
        clus
vv       MMP21 MUTATED MMP21 WILD-TYPE
  COLON             11             355
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MMP21 MUTATED         2        0        4         4         0         0
  MMP21 WILD-TYPE      89        1       28       134        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MMP21 MUTATED           0          0          2          0        0         0
  MMP21 WILD-TYPE        24         11         57         42       48        18
                 vv
clus              STAGE IVB
  MMP21 MUTATED           0
  MMP21 WILD-TYPE         1
D1775V4, multiclass
            clus
vv           MMP21 MUTATED MMP21 WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               4              28
  STAGE IIA              4             134
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             2              57
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  MMP21 MUTATED     0   2  10   0
  MMP21 WILD-TYPE  17  90 319  50
D1775V5, multiclass
    clus
vv   MMP21 MUTATED MMP21 WILD-TYPE
  T1             0              17
  T2             2              90
  T3            10             319
  T4             0              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  MMP21 MUTATED    10   2   0
  MMP21 WILD-TYPE 277 111  87
D1775V6, multiclass
    clus
vv   MMP21 MUTATED MMP21 WILD-TYPE
  N0            10             277
  N1             2             111
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1775V7, binary
                 cls
clus                0   1
  MMP21 MUTATED    10   0
  MMP21 WILD-TYPE 365  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MMP21 MUTATED     10    0
  MMP21 WILD-TYPE  365   65
   clus
vv  MMP21 MUTATED MMP21 WILD-TYPE
  0            10             365
  1             0              65
[1] 2 2
[1] FALSE
D1775V8, binary
                 cls
clus                0   1
  MMP21 MUTATED     6   6
  MMP21 WILD-TYPE 219 258
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MMP21 MUTATED      6    6
  MMP21 WILD-TYPE  219  258
        clus
vv       MMP21 MUTATED MMP21 WILD-TYPE
  FEMALE             6             219
  MALE               6             258
[1] 2 2
[1] FALSE
D1775V9, binary
                 cls
clus                0   1
  MMP21 MUTATED     9   0
  MMP21 WILD-TYPE 341  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MMP21 MUTATED      9    0
  MMP21 WILD-TYPE  341   22
     clus
vv    MMP21 MUTATED MMP21 WILD-TYPE
  NO              9             341
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MMP21 MUTATED                     11                             0
  MMP21 WILD-TYPE                  304                            47
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MMP21 MUTATED                       1                              0
  MMP21 WILD-TYPE                   105                             10
D1775V10, multiclass
                                clus
vv                               MMP21 MUTATED MMP21 WILD-TYPE
  COLON ADENOCARCINOMA                      11             304
  COLON MUCINOUS ADENOCARCINOMA              0              47
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  MMP21 MUTATED     8   1   0   1
  MMP21 WILD-TYPE 337   3  31  24
D1775V11, multiclass
    clus
vv   MMP21 MUTATED MMP21 WILD-TYPE
  R0             8             337
  R1             1               3
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1775V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MMP21 MUTATED                                  0     0
  MMP21 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  MMP21 MUTATED                           2     5
  MMP21 WILD-TYPE                        20   221
D1775V13, multiclass
                                  clus
vv                                 MMP21 MUTATED MMP21 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    2              20
  WHITE                                        5             221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1776) Variable = IL6R MUTATION ANALYSIS
D1776V1, survival
                sevent
clus2              0   1
  IL6R MUTATED     7   1
  IL6R WILD-TYPE 371  92
  IL6R MUTATED IL6R WILD-TYPE 
             8            463 
  IL6R MUTATED IL6R WILD-TYPE 
             1             92 
$`IL6R MUTATED`
TCGA-AA-3510 TCGA-AA-3715 TCGA-AA-3864 TCGA-AD-6895 TCGA-D5-6928 TCGA-DM-A1HB 
       63.98        19.04        53.00         0.72        11.64       135.65 
TCGA-DM-A282 TCGA-AG-4007 
      139.17         1.02 

$`IL6R WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 
       36.00         5.03        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 
        0.99        31.07        31.07        30.05        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.79         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6930 
       12.43        14.30         9.04         9.44         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
        7.50        44.32       131.51         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4008 
       32.02        19.99        28.04        36.03        14.04        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  IL6R MUTATED IL6R WILD-TYPE 
          0.72           0.00 
  IL6R MUTATED IL6R WILD-TYPE 
        139.17         148.01 
  IL6R MUTATED IL6R WILD-TYPE 
         36.02          20.19 
[1] "0.7 - 139.2 (36.0)" "0.0 - 148.0 (20.2)"
[1] "hr=" "2.9"
D1776V2, continuous
D1776V3, binary
                cls
clus               0   1
  IL6R MUTATED     7   1
  IL6R WILD-TYPE 359 118
[1] "tbl2"
                cls
clus             [,1] [,2]
  IL6R MUTATED      7    1
  IL6R WILD-TYPE  359  118
        clus
vv       IL6R MUTATED IL6R WILD-TYPE
  COLON             7            359
  RECTUM            1            118
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  IL6R MUTATED         0        0        3         2         0         0
  IL6R WILD-TYPE      91        1       29       136        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  IL6R MUTATED           0          0          1          0        1         0
  IL6R WILD-TYPE        24         11         58         42       47        18
                vv
clus             STAGE IVB
  IL6R MUTATED           0
  IL6R WILD-TYPE         1
D1776V4, multiclass
            clus
vv           IL6R MUTATED IL6R WILD-TYPE
  STAGE I               0             91
  STAGE IA              0              1
  STAGE II              3             29
  STAGE IIA             2            136
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            1             58
  STAGE IIIC            0             42
  STAGE IV              1             47
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  IL6R MUTATED     0   0   7   1
  IL6R WILD-TYPE  17  92 322  49
D1776V5, multiclass
    clus
vv   IL6R MUTATED IL6R WILD-TYPE
  T1            0             17
  T2            0             92
  T3            7            322
  T4            1             49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  IL6R MUTATED     5   2   1
  IL6R WILD-TYPE 282 111  86
D1776V6, multiclass
    clus
vv   IL6R MUTATED IL6R WILD-TYPE
  N0            5            282
  N1            2            111
  N2            1             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1776V7, binary
                cls
clus               0   1
  IL6R MUTATED     6   1
  IL6R WILD-TYPE 369  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  IL6R MUTATED      6    1
  IL6R WILD-TYPE  369   64
   clus
vv  IL6R MUTATED IL6R WILD-TYPE
  0            6            369
  1            1             64
[1] 2 2
[1] FALSE
D1776V8, binary
                cls
clus               0   1
  IL6R MUTATED     1   7
  IL6R WILD-TYPE 224 257
[1] "tbl2"
                cls
clus             [,1] [,2]
  IL6R MUTATED      1    7
  IL6R WILD-TYPE  224  257
        clus
vv       IL6R MUTATED IL6R WILD-TYPE
  FEMALE            1            224
  MALE              7            257
[1] 2 2
[1] FALSE
D1776V9, binary
                cls
clus               0   1
  IL6R MUTATED     4   0
  IL6R WILD-TYPE 346  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  IL6R MUTATED      4    0
  IL6R WILD-TYPE  346   22
     clus
vv    IL6R MUTATED IL6R WILD-TYPE
  NO             4            346
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  IL6R MUTATED                      5                             1
  IL6R WILD-TYPE                  310                            46
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  IL6R MUTATED                       1                              0
  IL6R WILD-TYPE                   105                             10
D1776V10, multiclass
                                clus
vv                               IL6R MUTATED IL6R WILD-TYPE
  COLON ADENOCARCINOMA                      5            310
  COLON MUCINOUS ADENOCARCINOMA             1             46
  RECTAL ADENOCARCINOMA                     1            105
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  IL6R MUTATED     4   0   1   0
  IL6R WILD-TYPE 341   4  30  25
D1776V11, multiclass
    clus
vv   IL6R MUTATED IL6R WILD-TYPE
  R0            4            341
  R1            0              4
  R2            1             30
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1776V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  IL6R MUTATED                                  0     0
  IL6R WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  IL6R MUTATED                           0     4
  IL6R WILD-TYPE                        22   222
D1776V13, multiclass
                                  clus
vv                                 IL6R MUTATED IL6R WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       4            222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1777) Variable = KSR2 MUTATION ANALYSIS
D1777V1, survival
                sevent
clus2              0   1
  KSR2 MUTATED    16   3
  KSR2 WILD-TYPE 362  90
  KSR2 MUTATED KSR2 WILD-TYPE 
            19            452 
  KSR2 MUTATED KSR2 WILD-TYPE 
             3             90 
$`KSR2 MUTATED`
TCGA-A6-6653 TCGA-A6-6780 TCGA-AA-3510 TCGA-AD-6889 TCGA-AY-4070 TCGA-AZ-4315 
       24.39        20.12        63.98        56.55        16.31        58.39 
TCGA-AZ-6599 TCGA-AZ-6601 TCGA-CK-5913 TCGA-CK-6751 TCGA-CM-6171 TCGA-D5-6924 
        6.77       100.01        51.32       124.27        14.04        14.30 
TCGA-D5-6928 TCGA-F4-6807 TCGA-G4-6586 TCGA-G4-6625 TCGA-AG-3892 TCGA-AG-A002 
       11.64        16.24        35.80        91.79        13.02        20.98 
TCGA-EI-6510 
       18.28 

$`KSR2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
       25.08        25.18        24.16        21.76        24.69        23.87 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 
       18.05        40.96         0.07        21.37        15.52         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       14.50        27.09         0.95        33.01        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       49.41        12.10        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       85.45        15.62        49.08         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
        1.91        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       13.02        15.02        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.04         9.44         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 
       63.62        61.91        36.00        22.09        13.78        26.17 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 
        1.02        17.95        36.95        17.03        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-F5-6464 
       32.61         0.49        20.55        19.96        20.91         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  KSR2 MUTATED KSR2 WILD-TYPE 
          6.77           0.00 
  KSR2 MUTATED KSR2 WILD-TYPE 
        124.27         148.01 
  KSR2 MUTATED KSR2 WILD-TYPE 
         20.98          20.12 
[1] "6.8 - 124.3 (21.0)" "0.0 - 148.0 (20.1)"
[1] "hr=" "2"  
D1777V2, continuous
D1777V3, binary
                cls
clus               0   1
  KSR2 MUTATED    18   3
  KSR2 WILD-TYPE 348 116
[1] "tbl2"
                cls
clus             [,1] [,2]
  KSR2 MUTATED     18    3
  KSR2 WILD-TYPE  348  116
        clus
vv       KSR2 MUTATED KSR2 WILD-TYPE
  COLON            18            348
  RECTUM            3            116
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KSR2 MUTATED         6        0        2         9         1         0
  KSR2 WILD-TYPE      85        1       30       129         9         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  KSR2 MUTATED           0          0          0          2        0         1
  KSR2 WILD-TYPE        24         11         59         40       48        17
                vv
clus             STAGE IVB
  KSR2 MUTATED           0
  KSR2 WILD-TYPE         1
D1777V4, multiclass
            clus
vv           KSR2 MUTATED KSR2 WILD-TYPE
  STAGE I               6             85
  STAGE IA              0              1
  STAGE II              2             30
  STAGE IIA             9            129
  STAGE IIB             1              9
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            0             59
  STAGE IIIC            2             40
  STAGE IV              0             48
  STAGE IVA             1             17
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  KSR2 MUTATED     1   6  13   1
  KSR2 WILD-TYPE  16  86 316  49
D1777V5, multiclass
    clus
vv   KSR2 MUTATED KSR2 WILD-TYPE
  T1            1             16
  T2            6             86
  T3           13            316
  T4            1             49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  KSR2 MUTATED    19   0   2
  KSR2 WILD-TYPE 268 113  85
D1777V6, multiclass
    clus
vv   KSR2 MUTATED KSR2 WILD-TYPE
  N0           19            268
  N1            0            113
  N2            2             85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1777V7, binary
                cls
clus               0   1
  KSR2 MUTATED    15   0
  KSR2 WILD-TYPE 360  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  KSR2 MUTATED     15    0
  KSR2 WILD-TYPE  360   65
   clus
vv  KSR2 MUTATED KSR2 WILD-TYPE
  0           15            360
  1            0             65
[1] 2 2
[1] FALSE
D1777V8, binary
                cls
clus               0   1
  KSR2 MUTATED    11  10
  KSR2 WILD-TYPE 214 254
[1] "tbl2"
                cls
clus             [,1] [,2]
  KSR2 MUTATED     11   10
  KSR2 WILD-TYPE  214  254
        clus
vv       KSR2 MUTATED KSR2 WILD-TYPE
  FEMALE           11            214
  MALE             10            254
[1] 2 2
[1] FALSE
D1777V9, binary
                cls
clus               0   1
  KSR2 MUTATED    18   0
  KSR2 WILD-TYPE 332  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  KSR2 MUTATED     18    0
  KSR2 WILD-TYPE  332   22
     clus
vv    KSR2 MUTATED KSR2 WILD-TYPE
  NO            18            332
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  KSR2 MUTATED                     15                             3
  KSR2 WILD-TYPE                  300                            44
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  KSR2 MUTATED                       3                              0
  KSR2 WILD-TYPE                   103                             10
D1777V10, multiclass
                                clus
vv                               KSR2 MUTATED KSR2 WILD-TYPE
  COLON ADENOCARCINOMA                     15            300
  COLON MUCINOUS ADENOCARCINOMA             3             44
  RECTAL ADENOCARCINOMA                     3            103
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  KSR2 MUTATED    12   1   0   3
  KSR2 WILD-TYPE 333   3  31  22
D1777V11, multiclass
    clus
vv   KSR2 MUTATED KSR2 WILD-TYPE
  R0           12            333
  R1            1              3
  R2            0             31
  RX            3             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1777V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KSR2 MUTATED                                  0     1
  KSR2 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  KSR2 MUTATED                           1    15
  KSR2 WILD-TYPE                        21   211
D1777V13, multiclass
                                  clus
vv                                 KSR2 MUTATED KSR2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                      15            211
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1778) Variable = ZNF443 MUTATION ANALYSIS
D1778V1, survival
                  sevent
clus2                0   1
  ZNF443 MUTATED     7   2
  ZNF443 WILD-TYPE 371  91
  ZNF443 MUTATED ZNF443 WILD-TYPE 
               9              462 
  ZNF443 MUTATED ZNF443 WILD-TYPE 
               2               91 
$`ZNF443 MUTATED`
TCGA-AA-3837 TCGA-AA-3877 TCGA-AA-3989 TCGA-AA-A00N TCGA-AA-A010 TCGA-CA-6717 
       38.99        31.00         7.96         4.01        34.98        12.76 
TCGA-CM-6674 TCGA-CM-6675 TCGA-AG-A002 
       12.95        13.05        20.98 

$`ZNF443 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
        1.02        17.98        15.95        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 
       17.03        24.03        27.02        29.98        18.05         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       27.02        19.07        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07        12.20        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       14.04        11.01        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  ZNF443 MUTATED ZNF443 WILD-TYPE 
            4.01             0.00 
  ZNF443 MUTATED ZNF443 WILD-TYPE 
           38.99           148.01 
  ZNF443 MUTATED ZNF443 WILD-TYPE 
          13.050           20.235 
[1] "4.0 - 39.0 (13.1)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.6"
D1778V2, continuous
D1778V3, binary
                  cls
clus                 0   1
  ZNF443 MUTATED     8   1
  ZNF443 WILD-TYPE 358 118
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF443 MUTATED      8    1
  ZNF443 WILD-TYPE  358  118
        clus
vv       ZNF443 MUTATED ZNF443 WILD-TYPE
  COLON               8              358
  RECTUM              1              118
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZNF443 MUTATED         2        0        0         3         2         0
  ZNF443 WILD-TYPE      89        1       32       135         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF443 MUTATED           0          0          0          0        1
  ZNF443 WILD-TYPE        24         11         59         42       47
                  vv
clus               STAGE IVA STAGE IVB
  ZNF443 MUTATED           0         1
  ZNF443 WILD-TYPE        18         0
D1778V4, multiclass
            clus
vv           ZNF443 MUTATED ZNF443 WILD-TYPE
  STAGE I                 2               89
  STAGE IA                0                1
  STAGE II                0               32
  STAGE IIA               3              135
  STAGE IIB               2                8
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              0               59
  STAGE IIIC              0               42
  STAGE IV                1               47
  STAGE IVA               0               18
  STAGE IVB               1                0
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZNF443 MUTATED     1   1   5   2
  ZNF443 WILD-TYPE  16  91 324  48
D1778V5, multiclass
    clus
vv   ZNF443 MUTATED ZNF443 WILD-TYPE
  T1              1               16
  T2              1               91
  T3              5              324
  T4              2               48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  ZNF443 MUTATED     7   0   2
  ZNF443 WILD-TYPE 280 113  85
D1778V6, multiclass
    clus
vv   ZNF443 MUTATED ZNF443 WILD-TYPE
  N0              7              280
  N1              0              113
  N2              2               85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1778V7, binary
                  cls
clus                 0   1
  ZNF443 MUTATED     7   2
  ZNF443 WILD-TYPE 368  63
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF443 MUTATED      7    2
  ZNF443 WILD-TYPE  368   63
   clus
vv  ZNF443 MUTATED ZNF443 WILD-TYPE
  0              7              368
  1              2               63
[1] 2 2
[1] FALSE
D1778V8, binary
                  cls
clus                 0   1
  ZNF443 MUTATED     2   7
  ZNF443 WILD-TYPE 223 257
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF443 MUTATED      2    7
  ZNF443 WILD-TYPE  223  257
        clus
vv       ZNF443 MUTATED ZNF443 WILD-TYPE
  FEMALE              2              223
  MALE                7              257
[1] 2 2
[1] FALSE
D1778V9, binary
                  cls
clus                 0   1
  ZNF443 MUTATED     8   0
  ZNF443 WILD-TYPE 342  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF443 MUTATED      8    0
  ZNF443 WILD-TYPE  342   22
     clus
vv    ZNF443 MUTATED ZNF443 WILD-TYPE
  NO               8              342
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ZNF443 MUTATED                      4                             4
  ZNF443 WILD-TYPE                  311                            43
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ZNF443 MUTATED                       1                              0
  ZNF443 WILD-TYPE                   105                             10
D1778V10, multiclass
                                clus
vv                               ZNF443 MUTATED ZNF443 WILD-TYPE
  COLON ADENOCARCINOMA                        4              311
  COLON MUCINOUS ADENOCARCINOMA               4               43
  RECTAL ADENOCARCINOMA                       1              105
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ZNF443 MUTATED     7   0   1   1
  ZNF443 WILD-TYPE 338   4  30  24
D1778V11, multiclass
    clus
vv   ZNF443 MUTATED ZNF443 WILD-TYPE
  R0              7              338
  R1              0                4
  R2              1               30
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1778V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF443 MUTATED                                  0     1
  ZNF443 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZNF443 MUTATED                           1     1
  ZNF443 WILD-TYPE                        21   225
D1778V13, multiclass
                                  clus
vv                                 ZNF443 MUTATED ZNF443 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                         1              225
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1779) Variable = PDSS2 MUTATION ANALYSIS
D1779V1, survival
                 sevent
clus2               0   1
  PDSS2 MUTATED     5   1
  PDSS2 WILD-TYPE 373  92
  PDSS2 MUTATED PDSS2 WILD-TYPE 
              6             465 
  PDSS2 MUTATED PDSS2 WILD-TYPE 
              1              92 
$`PDSS2 MUTATED`
TCGA-A6-6780 TCGA-AA-3811 TCGA-AA-A00J TCGA-G4-6293 TCGA-G4-6586 TCGA-DY-A0XA 
       20.12        10.06        18.05       133.18        35.80       126.44 

$`PDSS2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       19.00        30.02        34.03        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6303 
       13.25         0.53        47.41        35.31        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.03         5.29        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  PDSS2 MUTATED PDSS2 WILD-TYPE 
          10.06            0.00 
  PDSS2 MUTATED PDSS2 WILD-TYPE 
         133.18          148.01 
  PDSS2 MUTATED PDSS2 WILD-TYPE 
          27.96           20.19 
[1] "10.1 - 133.2 (28.0)" "0.0 - 148.0 (20.2)" 
[1] "hr=" "2.1"
D1779V2, continuous
D1779V3, binary
                 cls
clus                0   1
  PDSS2 MUTATED     5   1
  PDSS2 WILD-TYPE 361 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PDSS2 MUTATED      5    1
  PDSS2 WILD-TYPE  361  118
        clus
vv       PDSS2 MUTATED PDSS2 WILD-TYPE
  COLON              5             361
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PDSS2 MUTATED         0        0        0         3         0         0
  PDSS2 WILD-TYPE      91        1       32       135        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PDSS2 MUTATED           2          0          1          0        0         0
  PDSS2 WILD-TYPE        22         11         58         42       48        18
                 vv
clus              STAGE IVB
  PDSS2 MUTATED           0
  PDSS2 WILD-TYPE         1
D1779V4, multiclass
            clus
vv           PDSS2 MUTATED PDSS2 WILD-TYPE
  STAGE I                0              91
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              3             135
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              2              22
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PDSS2 MUTATED     0   0   5   1
  PDSS2 WILD-TYPE  17  92 324  49
D1779V5, multiclass
    clus
vv   PDSS2 MUTATED PDSS2 WILD-TYPE
  T1             0              17
  T2             0              92
  T3             5             324
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  PDSS2 MUTATED     3   2   1
  PDSS2 WILD-TYPE 284 111  86
D1779V6, multiclass
    clus
vv   PDSS2 MUTATED PDSS2 WILD-TYPE
  N0             3             284
  N1             2             111
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1779V7, binary
                 cls
clus                0   1
  PDSS2 MUTATED     5   0
  PDSS2 WILD-TYPE 370  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PDSS2 MUTATED      5    0
  PDSS2 WILD-TYPE  370   65
   clus
vv  PDSS2 MUTATED PDSS2 WILD-TYPE
  0             5             370
  1             0              65
[1] 2 2
[1] FALSE
D1779V8, binary
                 cls
clus                0   1
  PDSS2 MUTATED     4   2
  PDSS2 WILD-TYPE 221 262
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PDSS2 MUTATED      4    2
  PDSS2 WILD-TYPE  221  262
        clus
vv       PDSS2 MUTATED PDSS2 WILD-TYPE
  FEMALE             4             221
  MALE               2             262
[1] 2 2
[1] FALSE
D1779V9, binary
                 cls
clus                0   1
  PDSS2 MUTATED     5   0
  PDSS2 WILD-TYPE 345  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PDSS2 MUTATED      5    0
  PDSS2 WILD-TYPE  345   22
     clus
vv    PDSS2 MUTATED PDSS2 WILD-TYPE
  NO              5             345
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PDSS2 MUTATED                      3                             2
  PDSS2 WILD-TYPE                  312                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PDSS2 MUTATED                       1                              0
  PDSS2 WILD-TYPE                   105                             10
D1779V10, multiclass
                                clus
vv                               PDSS2 MUTATED PDSS2 WILD-TYPE
  COLON ADENOCARCINOMA                       3             312
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  PDSS2 MUTATED     4   0   0   0
  PDSS2 WILD-TYPE 341   4  31  25
D1779V11, multiclass
    clus
vv   PDSS2 MUTATED PDSS2 WILD-TYPE
  R0             4             341
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1779V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PDSS2 MUTATED                                  0     0
  PDSS2 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PDSS2 MUTATED                           0     4
  PDSS2 WILD-TYPE                        22   222
D1779V13, multiclass
                                  clus
vv                                 PDSS2 MUTATED PDSS2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        4             222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1780) Variable = ACTN1 MUTATION ANALYSIS
D1780V1, survival
                 sevent
clus2               0   1
  ACTN1 MUTATED    12   0
  ACTN1 WILD-TYPE 366  93
  ACTN1 MUTATED ACTN1 WILD-TYPE 
             12             459 
  ACTN1 MUTATED ACTN1 WILD-TYPE 
              0              93 
$`ACTN1 MUTATED`
TCGA-A6-6781 TCGA-AA-3510 TCGA-AA-3864 TCGA-AA-A010 TCGA-AA-A01R TCGA-CA-6717 
       19.66        63.98        53.00        34.98        35.01        12.76 
TCGA-D5-6929 TCGA-F4-6808 TCGA-AG-A002 TCGA-AG-A02N TCGA-DC-6155 TCGA-EI-6507 
        4.80        33.67        20.98        61.97        13.97        19.96 

$`ACTN1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 
        0.99        31.07        31.07        30.05        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
       38.07         1.02         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07        12.20        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.04         9.44        11.64         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       16.24        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
       49.97         1.94        38.96        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
        5.03        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6510 
       51.48        32.61         0.49        20.55        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  ACTN1 MUTATED ACTN1 WILD-TYPE 
            4.8             0.0 
  ACTN1 MUTATED ACTN1 WILD-TYPE 
          63.98          148.01 
  ACTN1 MUTATED ACTN1 WILD-TYPE 
         27.325          20.120 
[1] "4.8 - 64.0 (27.3)"  "0.0 - 148.0 (20.1)"
[1] "hr="     "2.6e+07"
D1780V2, continuous
D1780V3, binary
                 cls
clus                0   1
  ACTN1 MUTATED     9   4
  ACTN1 WILD-TYPE 357 115
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ACTN1 MUTATED      9    4
  ACTN1 WILD-TYPE  357  115
        clus
vv       ACTN1 MUTATED ACTN1 WILD-TYPE
  COLON              9             357
  RECTUM             4             115
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ACTN1 MUTATED         2        0        3         2         1         0
  ACTN1 WILD-TYPE      89        1       29       136         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ACTN1 MUTATED           1          1          0          2        1         0
  ACTN1 WILD-TYPE        23         10         59         40       47        18
                 vv
clus              STAGE IVB
  ACTN1 MUTATED           0
  ACTN1 WILD-TYPE         1
D1780V4, multiclass
            clus
vv           ACTN1 MUTATED ACTN1 WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               3              29
  STAGE IIA              2             136
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             1              10
  STAGE IIIB             0              59
  STAGE IIIC             2              40
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ACTN1 MUTATED     1   2   8   2
  ACTN1 WILD-TYPE  16  90 321  48
D1780V5, multiclass
    clus
vv   ACTN1 MUTATED ACTN1 WILD-TYPE
  T1             1              16
  T2             2              90
  T3             8             321
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  ACTN1 MUTATED     8   3   2
  ACTN1 WILD-TYPE 279 110  85
D1780V6, multiclass
    clus
vv   ACTN1 MUTATED ACTN1 WILD-TYPE
  N0             8             279
  N1             3             110
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1780V7, binary
                 cls
clus                0   1
  ACTN1 MUTATED    10   1
  ACTN1 WILD-TYPE 365  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ACTN1 MUTATED     10    1
  ACTN1 WILD-TYPE  365   64
   clus
vv  ACTN1 MUTATED ACTN1 WILD-TYPE
  0            10             365
  1             1              64
[1] 2 2
[1] FALSE
D1780V8, binary
                 cls
clus                0   1
  ACTN1 MUTATED     4   9
  ACTN1 WILD-TYPE 221 255
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ACTN1 MUTATED      4    9
  ACTN1 WILD-TYPE  221  255
        clus
vv       ACTN1 MUTATED ACTN1 WILD-TYPE
  FEMALE             4             221
  MALE               9             255
[1] 2 2
[1] FALSE
D1780V9, binary
                 cls
clus                0   1
  ACTN1 MUTATED     9   1
  ACTN1 WILD-TYPE 341  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ACTN1 MUTATED      9    1
  ACTN1 WILD-TYPE  341   21
     clus
vv    ACTN1 MUTATED ACTN1 WILD-TYPE
  NO              9             341
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ACTN1 MUTATED                      5                             4
  ACTN1 WILD-TYPE                  310                            43
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ACTN1 MUTATED                       4                              0
  ACTN1 WILD-TYPE                   102                             10
D1780V10, multiclass
                                clus
vv                               ACTN1 MUTATED ACTN1 WILD-TYPE
  COLON ADENOCARCINOMA                       5             310
  COLON MUCINOUS ADENOCARCINOMA              4              43
  RECTAL ADENOCARCINOMA                      4             102
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  ACTN1 MUTATED    12   0   0   1
  ACTN1 WILD-TYPE 333   4  31  24
D1780V11, multiclass
    clus
vv   ACTN1 MUTATED ACTN1 WILD-TYPE
  R0            12             333
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1780V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ACTN1 MUTATED                                  0     1
  ACTN1 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ACTN1 MUTATED                           0     6
  ACTN1 WILD-TYPE                        22   220
D1780V13, multiclass
                                  clus
vv                                 ACTN1 MUTATED ACTN1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        6             220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1781) Variable = CCPG1 MUTATION ANALYSIS
D1781V1, survival
                 sevent
clus2               0   1
  CCPG1 MUTATED     8   4
  CCPG1 WILD-TYPE 370  89
  CCPG1 MUTATED CCPG1 WILD-TYPE 
             12             459 
  CCPG1 MUTATED CCPG1 WILD-TYPE 
              4              89 
$`CCPG1 MUTATED`
TCGA-A6-6781 TCGA-AA-3663 TCGA-AA-3672 TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A010 
       19.66         6.97         0.92        25.02         4.01        34.98 
TCGA-AD-6964 TCGA-AY-4071 TCGA-AZ-4315 TCGA-CA-6718 TCGA-DM-A1HB TCGA-AG-3902 
       10.88         0.95        58.39        10.06       135.65        32.02 

$`CCPG1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
       54.02         2.01        14.01        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42         0.20        14.50        27.09        16.31 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       33.01        21.44        17.82         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       12.76        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 
      140.38         7.50        44.32       131.51       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
        1.02        48.03        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  CCPG1 MUTATED CCPG1 WILD-TYPE 
           0.92            0.00 
  CCPG1 MUTATED CCPG1 WILD-TYPE 
         135.65          148.01 
  CCPG1 MUTATED CCPG1 WILD-TYPE 
          15.27           20.28 
[1] "0.9 - 135.7 (15.3)" "0.0 - 148.0 (20.3)"
[1] "hr=" "1.8"
D1781V2, continuous
D1781V3, binary
                 cls
clus                0   1
  CCPG1 MUTATED    10   1
  CCPG1 WILD-TYPE 356 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CCPG1 MUTATED     10    1
  CCPG1 WILD-TYPE  356  118
        clus
vv       CCPG1 MUTATED CCPG1 WILD-TYPE
  COLON             10             356
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CCPG1 MUTATED         1        0        1         3         2         0
  CCPG1 WILD-TYPE      90        1       31       135         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CCPG1 MUTATED           1          0          1          1        0         0
  CCPG1 WILD-TYPE        23         11         58         41       48        18
                 vv
clus              STAGE IVB
  CCPG1 MUTATED           0
  CCPG1 WILD-TYPE         1
D1781V4, multiclass
            clus
vv           CCPG1 MUTATED CCPG1 WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              3             135
  STAGE IIB              2               8
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             1              41
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CCPG1 MUTATED     1   1   6   4
  CCPG1 WILD-TYPE  16  91 323  46
D1781V5, multiclass
    clus
vv   CCPG1 MUTATED CCPG1 WILD-TYPE
  T1             1              16
  T2             1              91
  T3             6             323
  T4             4              46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  CCPG1 MUTATED     8   3   1
  CCPG1 WILD-TYPE 279 110  86
D1781V6, multiclass
    clus
vv   CCPG1 MUTATED CCPG1 WILD-TYPE
  N0             8             279
  N1             3             110
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1781V7, binary
                 cls
clus                0   1
  CCPG1 MUTATED     8   0
  CCPG1 WILD-TYPE 367  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CCPG1 MUTATED      8    0
  CCPG1 WILD-TYPE  367   65
   clus
vv  CCPG1 MUTATED CCPG1 WILD-TYPE
  0             8             367
  1             0              65
[1] 2 2
[1] FALSE
D1781V8, binary
                 cls
clus                0   1
  CCPG1 MUTATED     3   9
  CCPG1 WILD-TYPE 222 255
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CCPG1 MUTATED      3    9
  CCPG1 WILD-TYPE  222  255
        clus
vv       CCPG1 MUTATED CCPG1 WILD-TYPE
  FEMALE             3             222
  MALE               9             255
[1] 2 2
[1] FALSE
D1781V9, binary
                 cls
clus                0   1
  CCPG1 MUTATED    10   0
  CCPG1 WILD-TYPE 340  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CCPG1 MUTATED     10    0
  CCPG1 WILD-TYPE  340   22
     clus
vv    CCPG1 MUTATED CCPG1 WILD-TYPE
  NO             10             340
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CCPG1 MUTATED                      7                             2
  CCPG1 WILD-TYPE                  308                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CCPG1 MUTATED                       1                              0
  CCPG1 WILD-TYPE                   105                             10
D1781V10, multiclass
                                clus
vv                               CCPG1 MUTATED CCPG1 WILD-TYPE
  COLON ADENOCARCINOMA                       7             308
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  CCPG1 MUTATED     8   0   0   1
  CCPG1 WILD-TYPE 337   4  31  24
D1781V11, multiclass
    clus
vv   CCPG1 MUTATED CCPG1 WILD-TYPE
  R0             8             337
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1781V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CCPG1 MUTATED                                  0     1
  CCPG1 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CCPG1 MUTATED                           0     5
  CCPG1 WILD-TYPE                        22   221
D1781V13, multiclass
                                  clus
vv                                 CCPG1 MUTATED CCPG1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        5             221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1782) Variable = PIGC MUTATION ANALYSIS
D1782V1, survival
                sevent
clus2              0   1
  PIGC MUTATED     2   2
  PIGC WILD-TYPE 376  91
  PIGC MUTATED PIGC WILD-TYPE 
             4            467 
  PIGC MUTATED PIGC WILD-TYPE 
             2             91 
$`PIGC MUTATED`
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-CM-5349 TCGA-CM-6161 
       49.41         6.77        30.08        15.02 

$`PIGC WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5860 
       25.02        13.02        29.06        22.03        22.98        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6162 
       15.02         5.03        15.02        15.02        17.03        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  PIGC MUTATED PIGC WILD-TYPE 
          6.77           0.00 
  PIGC MUTATED PIGC WILD-TYPE 
         49.41         148.01 
  PIGC MUTATED PIGC WILD-TYPE 
         22.55          20.19 
[1] "6.8 - 49.4 (22.5)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "2.5"
D1782V2, continuous
D1782V3, binary
                cls
clus               0   1
  PIGC MUTATED     4   0
  PIGC WILD-TYPE 362 119
[1] "tbl2"
                cls
clus             [,1] [,2]
  PIGC MUTATED      4    0
  PIGC WILD-TYPE  362  119
        clus
vv       PIGC MUTATED PIGC WILD-TYPE
  COLON             4            362
  RECTUM            0            119
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PIGC MUTATED         2        0        1         1         0         0
  PIGC WILD-TYPE      89        1       31       137        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PIGC MUTATED           0          0          0          0        0         0
  PIGC WILD-TYPE        24         11         59         42       48        18
                vv
clus             STAGE IVB
  PIGC MUTATED           0
  PIGC WILD-TYPE         1
D1782V4, multiclass
            clus
vv           PIGC MUTATED PIGC WILD-TYPE
  STAGE I               2             89
  STAGE IA              0              1
  STAGE II              1             31
  STAGE IIA             1            137
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            0             59
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  PIGC MUTATED     0   2   2   0
  PIGC WILD-TYPE  17  90 327  50
D1782V5, multiclass
    clus
vv   PIGC MUTATED PIGC WILD-TYPE
  T1            0             17
  T2            2             90
  T3            2            327
  T4            0             50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  PIGC MUTATED     4   0   0
  PIGC WILD-TYPE 283 113  87
D1782V6, multiclass
    clus
vv   PIGC MUTATED PIGC WILD-TYPE
  N0            4            283
  N1            0            113
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1782V7, binary
                cls
clus               0   1
  PIGC MUTATED     2   0
  PIGC WILD-TYPE 373  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  PIGC MUTATED      2    0
  PIGC WILD-TYPE  373   65
   clus
vv  PIGC MUTATED PIGC WILD-TYPE
  0            2            373
  1            0             65
[1] 2 2
[1] FALSE
D1782V8, binary
                cls
clus               0   1
  PIGC MUTATED     3   1
  PIGC WILD-TYPE 222 263
[1] "tbl2"
                cls
clus             [,1] [,2]
  PIGC MUTATED      3    1
  PIGC WILD-TYPE  222  263
        clus
vv       PIGC MUTATED PIGC WILD-TYPE
  FEMALE            3            222
  MALE              1            263
[1] 2 2
[1] FALSE
D1782V9, binary
                cls
clus               0   1
  PIGC MUTATED     4   0
  PIGC WILD-TYPE 346  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  PIGC MUTATED      4    0
  PIGC WILD-TYPE  346   22
     clus
vv    PIGC MUTATED PIGC WILD-TYPE
  NO             4            346
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PIGC MUTATED                      4                             0
  PIGC WILD-TYPE                  311                            47
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PIGC MUTATED                       0                              0
  PIGC WILD-TYPE                   106                             10
D1782V10, multiclass
                                clus
vv                               PIGC MUTATED PIGC WILD-TYPE
  COLON ADENOCARCINOMA                      4            311
  COLON MUCINOUS ADENOCARCINOMA             0             47
  RECTAL ADENOCARCINOMA                     0            106
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  PIGC MUTATED     2   0   0   0
  PIGC WILD-TYPE 343   4  31  25
D1782V11, multiclass
[1] "Remove cluster labels:" "PIGC MUTATED"          
clus
  PIGC MUTATED PIGC WILD-TYPE 
             2            403 
    TCGA-A6-2671     TCGA-A6-2672     TCGA-A6-2674     TCGA-A6-2676 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-A6-2677     TCGA-A6-2678     TCGA-A6-2683     TCGA-A6-3807 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-A6-3808     TCGA-A6-3809     TCGA-A6-3810     TCGA-A6-5657 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-A6-5659     TCGA-A6-5661     TCGA-A6-5665     TCGA-A6-6781 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-AA-3489     TCGA-AA-3492     TCGA-AA-3496     TCGA-AA-3502 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-AA-3510     TCGA-AA-3511     TCGA-AA-3514     TCGA-AA-3517 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-AA-3518     TCGA-AA-3519     TCGA-AA-3520     TCGA-AA-3521 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-AA-3522     TCGA-AA-3524     TCGA-AA-3525     TCGA-AA-3526 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-AA-3527     TCGA-AA-3529     TCGA-AA-3530     TCGA-AA-3531 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-AA-3532     TCGA-AA-3534     TCGA-AA-3538     TCGA-AA-3542 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-AA-3543     TCGA-AA-3544     TCGA-AA-3548     TCGA-AA-3549 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-AA-3552     TCGA-AA-3553     TCGA-AA-3554     TCGA-AA-3555 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-AA-3556     TCGA-AA-3558     TCGA-AA-3560     TCGA-AA-3561 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-AA-3562     TCGA-AA-3655     TCGA-AA-3660     TCGA-AA-3662 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-AA-3663     TCGA-AA-3664     TCGA-AA-3666     TCGA-AA-3667 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-AA-3672     TCGA-AA-3673     TCGA-AA-3678     TCGA-AA-3679 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-AA-3680     TCGA-AA-3681     TCGA-AA-3684     TCGA-AA-3685 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-AA-3688     TCGA-AA-3692     TCGA-AA-3693     TCGA-AA-3695 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-AA-3696     TCGA-AA-3697     TCGA-AA-3710     TCGA-AA-3712 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-AA-3713     TCGA-AA-3715     TCGA-AA-3811     TCGA-AA-3812 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-AA-3814     TCGA-AA-3815     TCGA-AA-3818     TCGA-AA-3819 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-AA-3821     TCGA-AA-3831     TCGA-AA-3833     TCGA-AA-3837 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-AA-3842     TCGA-AA-3844     TCGA-AA-3845     TCGA-AA-3846 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-AA-3848     TCGA-AA-3850     TCGA-AA-3851     TCGA-AA-3852 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-AA-3854     TCGA-AA-3855     TCGA-AA-3856     TCGA-AA-3858 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-AA-3860     TCGA-AA-3861     TCGA-AA-3864     TCGA-AA-3866 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-AA-3867     TCGA-AA-3869     TCGA-AA-3870     TCGA-AA-3872 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-AA-3875     TCGA-AA-3877     TCGA-AA-3930     TCGA-AA-3939 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-AA-3941     TCGA-AA-3947     TCGA-AA-3949     TCGA-AA-3950 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-AA-3952     TCGA-AA-3955     TCGA-AA-3956     TCGA-AA-3968 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-AA-3971     TCGA-AA-3972     TCGA-AA-3973     TCGA-AA-3975 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-AA-3976     TCGA-AA-3979     TCGA-AA-3984     TCGA-AA-3986 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-AA-3989     TCGA-AA-3994     TCGA-AA-A004     TCGA-AA-A00A 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-AA-A00D     TCGA-AA-A00E     TCGA-AA-A00F     TCGA-AA-A00J 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-AA-A00K     TCGA-AA-A00L     TCGA-AA-A00N     TCGA-AA-A00O 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-AA-A00Q     TCGA-AA-A00R     TCGA-AA-A00U     TCGA-AA-A00W 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-AA-A00Z     TCGA-AA-A010     TCGA-AA-A017     TCGA-AA-A01D 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-AA-A01F     TCGA-AA-A01G     TCGA-AA-A01I     TCGA-AA-A01K 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-AA-A01P     TCGA-AA-A01Q     TCGA-AA-A01R     TCGA-AA-A01S 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-AA-A01T     TCGA-AA-A01V     TCGA-AA-A01X     TCGA-AA-A01Z 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-AA-A022     TCGA-AA-A024     TCGA-AA-A029     TCGA-AA-A02F 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-AA-A02H     TCGA-AA-A02J     TCGA-AA-A02K     TCGA-AA-A02O 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-AA-A02W     TCGA-AA-A02Y     TCGA-AA-A03F     TCGA-AA-A03J 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-AD-5900     TCGA-AD-6548     TCGA-AD-6888     TCGA-AU-3779 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-AU-6004     TCGA-AY-4070     TCGA-AY-4071     TCGA-AY-5543 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-AY-6196     TCGA-AY-6197     TCGA-AY-6386     TCGA-AZ-4315 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-AZ-4681     TCGA-AZ-4682     TCGA-CA-5254     TCGA-CA-5255 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-CA-5796     TCGA-CA-5797     TCGA-CA-6715     TCGA-CA-6716 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-CA-6717     TCGA-CA-6718     TCGA-CA-6719     TCGA-CK-4947 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-CK-4948     TCGA-CK-4950     TCGA-CK-4952     TCGA-CK-5912 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-CK-5913     TCGA-CK-5914     TCGA-CK-5915     TCGA-CK-5916 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-CK-6746     TCGA-CK-6747     TCGA-CK-6748     TCGA-CK-6751 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-CM-4743     TCGA-CM-4744     TCGA-CM-4746     TCGA-CM-4747 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-CM-4752     TCGA-CM-5341     TCGA-CM-5344     TCGA-CM-5348 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-CM-5860     TCGA-CM-5861     TCGA-CM-5862     TCGA-CM-5863 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-CM-5864     TCGA-CM-5868     TCGA-CM-6162     TCGA-CM-6163 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-CM-6164     TCGA-CM-6165     TCGA-CM-6166     TCGA-CM-6167 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-CM-6168     TCGA-CM-6169     TCGA-CM-6170     TCGA-CM-6171 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-CM-6172     TCGA-CM-6674     TCGA-CM-6675     TCGA-CM-6676 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-CM-6677     TCGA-CM-6678     TCGA-CM-6679     TCGA-CM-6680 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-D5-5537     TCGA-D5-5538     TCGA-D5-5539     TCGA-D5-5540 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-D5-5541     TCGA-D5-6529     TCGA-D5-6532     TCGA-D5-6533 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-D5-6534     TCGA-D5-6535     TCGA-D5-6536     TCGA-D5-6537 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-D5-6538     TCGA-D5-6539     TCGA-D5-6540     TCGA-D5-6541 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-D5-6898     TCGA-D5-6920     TCGA-D5-6922     TCGA-D5-6923 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-D5-6924     TCGA-D5-6926     TCGA-D5-6927     TCGA-D5-6928 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-D5-6929     TCGA-D5-6930     TCGA-D5-6931     TCGA-D5-6932 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-D5-7000     TCGA-F4-6459     TCGA-F4-6460     TCGA-F4-6569 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-F4-6570     TCGA-F4-6703     TCGA-F4-6704     TCGA-F4-6805 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-F4-6806     TCGA-F4-6807     TCGA-F4-6808     TCGA-F4-6809 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-F4-6854     TCGA-F4-6855     TCGA-F4-6856     TCGA-G4-6293 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-G4-6299     TCGA-G4-6303     TCGA-G4-6304     TCGA-G4-6306 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-G4-6307     TCGA-G4-6309     TCGA-G4-6310     TCGA-G4-6315 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-G4-6317     TCGA-G4-6321     TCGA-G4-6323     TCGA-G4-6586 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-G4-6588     TCGA-G4-6625     TCGA-G4-6626     TCGA-G4-6628 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-AF-2687     TCGA-AF-2689     TCGA-AF-2691     TCGA-AF-2692 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-AF-3400     TCGA-AF-3913     TCGA-AF-4110     TCGA-AF-5654 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-AF-6655     TCGA-AG-3574     TCGA-AG-3575     TCGA-AG-3578 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-AG-3580     TCGA-AG-3581     TCGA-AG-3582     TCGA-AG-3583 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-AG-3584     TCGA-AG-3586     TCGA-AG-3587     TCGA-AG-3593 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-AG-3594     TCGA-AG-3598     TCGA-AG-3599     TCGA-AG-3600 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-AG-3601     TCGA-AG-3602     TCGA-AG-3605     TCGA-AG-3608 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-AG-3609     TCGA-AG-3611     TCGA-AG-3612     TCGA-AG-3726 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-AG-3727     TCGA-AG-3731     TCGA-AG-3732     TCGA-AG-3742 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-AG-3878     TCGA-AG-3882     TCGA-AG-3883     TCGA-AG-3885 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-AG-3887     TCGA-AG-3890     TCGA-AG-3892     TCGA-AG-3893 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-AG-3894     TCGA-AG-3896     TCGA-AG-3898     TCGA-AG-3901 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-AG-3902     TCGA-AG-3909     TCGA-AG-3999     TCGA-AG-4001 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-AG-4005     TCGA-AG-4007     TCGA-AG-4008     TCGA-AG-4015 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-AG-A002     TCGA-AG-A008     TCGA-AG-A00C     TCGA-AG-A00H 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-AG-A00Y     TCGA-AG-A011     TCGA-AG-A014     TCGA-AG-A015 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-AG-A016     TCGA-AG-A01L     TCGA-AG-A01W     TCGA-AG-A01Y 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-AG-A020     TCGA-AG-A025     TCGA-AG-A026     TCGA-AG-A02G 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-AG-A02N     TCGA-AG-A02X     TCGA-AG-A032     TCGA-AG-A036 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-AH-6549     TCGA-AH-6643     TCGA-CL-5917     TCGA-CL-5918 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-DC-5337     TCGA-DC-5869     TCGA-DC-6155     TCGA-DC-6157 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-DC-6158     TCGA-DC-6160     TCGA-DC-6681     TCGA-DC-6682 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-DC-6683     TCGA-DT-5265     TCGA-EF-5830     TCGA-EI-6506 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-EI-6507     TCGA-EI-6508     TCGA-EI-6510     TCGA-F5-6464 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-F5-6465     TCGA-F5-6571     TCGA-F5-6702     TCGA-F5-6812 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
    TCGA-F5-6813     TCGA-G5-6235     TCGA-G5-6641 
"PIGC WILD-TYPE" "PIGC WILD-TYPE" "PIGC WILD-TYPE" 
D1782V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PIGC MUTATED                                  0     0
  PIGC WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  PIGC MUTATED                           0     4
  PIGC WILD-TYPE                        22   222
D1782V13, multiclass
                                  clus
vv                                 PIGC MUTATED PIGC WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       4            222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1783) Variable = CNOT3 MUTATION ANALYSIS
D1783V1, survival
                 sevent
clus2               0   1
  CNOT3 MUTATED     6   1
  CNOT3 WILD-TYPE 372  92
  CNOT3 MUTATED CNOT3 WILD-TYPE 
              7             464 
  CNOT3 MUTATED CNOT3 WILD-TYPE 
              1              92 
$`CNOT3 MUTATED`
TCGA-A6-5659 TCGA-AA-3977 TCGA-CM-4743 TCGA-CM-5868 TCGA-F4-6703 TCGA-G4-6588 
       30.44        25.02        23.05        17.03        47.87        26.17 
TCGA-DC-6158 
       10.98 

$`CNOT3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
       82.95         1.91       124.27        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6162 
       15.02         5.03        15.02        15.02        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6704 
       98.24         8.61        31.96        35.74         6.18         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       22.09        13.78        35.80        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       27.95        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  CNOT3 MUTATED CNOT3 WILD-TYPE 
          10.98            0.00 
  CNOT3 MUTATED CNOT3 WILD-TYPE 
          47.87          148.01 
  CNOT3 MUTATED CNOT3 WILD-TYPE 
         25.020          20.085 
[1] "11.0 - 47.9 (25.0)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.4"
D1783V2, continuous
D1783V3, binary
                 cls
clus                0   1
  CNOT3 MUTATED     7   1
  CNOT3 WILD-TYPE 359 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CNOT3 MUTATED      7    1
  CNOT3 WILD-TYPE  359  118
        clus
vv       CNOT3 MUTATED CNOT3 WILD-TYPE
  COLON              7             359
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CNOT3 MUTATED         2        0        1         3         0         0
  CNOT3 WILD-TYPE      89        1       31       135        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CNOT3 MUTATED           0          0          0          0        0         1
  CNOT3 WILD-TYPE        24         11         59         42       48        17
                 vv
clus              STAGE IVB
  CNOT3 MUTATED           0
  CNOT3 WILD-TYPE         1
D1783V4, multiclass
            clus
vv           CNOT3 MUTATED CNOT3 WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              3             135
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CNOT3 MUTATED     0   3   3   2
  CNOT3 WILD-TYPE  17  89 326  48
D1783V5, multiclass
    clus
vv   CNOT3 MUTATED CNOT3 WILD-TYPE
  T1             0              17
  T2             3              89
  T3             3             326
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  CNOT3 MUTATED     7   1   0
  CNOT3 WILD-TYPE 280 112  87
D1783V6, multiclass
    clus
vv   CNOT3 MUTATED CNOT3 WILD-TYPE
  N0             7             280
  N1             1             112
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1783V7, binary
                 cls
clus                0   1
  CNOT3 MUTATED     6   1
  CNOT3 WILD-TYPE 369  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CNOT3 MUTATED      6    1
  CNOT3 WILD-TYPE  369   64
   clus
vv  CNOT3 MUTATED CNOT3 WILD-TYPE
  0             6             369
  1             1              64
[1] 2 2
[1] FALSE
D1783V8, binary
                 cls
clus                0   1
  CNOT3 MUTATED     3   5
  CNOT3 WILD-TYPE 222 259
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CNOT3 MUTATED      3    5
  CNOT3 WILD-TYPE  222  259
        clus
vv       CNOT3 MUTATED CNOT3 WILD-TYPE
  FEMALE             3             222
  MALE               5             259
[1] 2 2
[1] FALSE
D1783V9, binary
                 cls
clus                0   1
  CNOT3 MUTATED     7   0
  CNOT3 WILD-TYPE 343  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CNOT3 MUTATED      7    0
  CNOT3 WILD-TYPE  343   22
     clus
vv    CNOT3 MUTATED CNOT3 WILD-TYPE
  NO              7             343
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CNOT3 MUTATED                      7                             0
  CNOT3 WILD-TYPE                  308                            47
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CNOT3 MUTATED                       1                              0
  CNOT3 WILD-TYPE                   105                             10
D1783V10, multiclass
                                clus
vv                               CNOT3 MUTATED CNOT3 WILD-TYPE
  COLON ADENOCARCINOMA                       7             308
  COLON MUCINOUS ADENOCARCINOMA              0              47
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  CNOT3 MUTATED     7   0   0   0
  CNOT3 WILD-TYPE 338   4  31  25
D1783V11, multiclass
    clus
vv   CNOT3 MUTATED CNOT3 WILD-TYPE
  R0             7             338
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1783V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CNOT3 MUTATED                                  0     0
  CNOT3 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CNOT3 MUTATED                           0     6
  CNOT3 WILD-TYPE                        22   220
D1783V13, multiclass
                                  clus
vv                                 CNOT3 MUTATED CNOT3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        6             220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1784) Variable = TYW3 MUTATION ANALYSIS
D1784V1, survival
                sevent
clus2              0   1
  TYW3 MUTATED     4   2
  TYW3 WILD-TYPE 374  91
  TYW3 MUTATED TYW3 WILD-TYPE 
             6            465 
  TYW3 MUTATED TYW3 WILD-TYPE 
             2             91 
$`TYW3 MUTATED`
TCGA-AD-6964 TCGA-AZ-6600 TCGA-CM-6170 TCGA-D5-6536 TCGA-F4-6805 TCGA-EI-6507 
       10.88        12.10        15.02        17.85        34.42        19.96 

$`TYW3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       14.99        12.99        13.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 
       18.25         1.32        43.27        15.12         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
        1.55        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6510 
       51.48        32.61         0.49        20.55        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  TYW3 MUTATED TYW3 WILD-TYPE 
         10.88           0.00 
  TYW3 MUTATED TYW3 WILD-TYPE 
         34.42         148.01 
  TYW3 MUTATED TYW3 WILD-TYPE 
        16.435         20.550 
[1] "10.9 - 34.4 (16.4)" "0.0 - 148.0 (20.6)"
[1] "hr=" "2.5"
D1784V2, continuous
D1784V3, binary
                cls
clus               0   1
  TYW3 MUTATED     6   1
  TYW3 WILD-TYPE 360 118
[1] "tbl2"
                cls
clus             [,1] [,2]
  TYW3 MUTATED      6    1
  TYW3 WILD-TYPE  360  118
        clus
vv       TYW3 MUTATED TYW3 WILD-TYPE
  COLON             6            360
  RECTUM            1            118
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TYW3 MUTATED         1        0        0         3         0         0
  TYW3 WILD-TYPE      90        1       32       135        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TYW3 MUTATED           1          0          0          0        1         0
  TYW3 WILD-TYPE        23         11         59         42       47        18
                vv
clus             STAGE IVB
  TYW3 MUTATED           0
  TYW3 WILD-TYPE         1
D1784V4, multiclass
            clus
vv           TYW3 MUTATED TYW3 WILD-TYPE
  STAGE I               1             90
  STAGE IA              0              1
  STAGE II              0             32
  STAGE IIA             3            135
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             1             23
  STAGE IIIA            0             11
  STAGE IIIB            0             59
  STAGE IIIC            0             42
  STAGE IV              1             47
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  TYW3 MUTATED     0   1   4   2
  TYW3 WILD-TYPE  17  91 325  48
D1784V5, multiclass
    clus
vv   TYW3 MUTATED TYW3 WILD-TYPE
  T1            0             17
  T2            1             91
  T3            4            325
  T4            2             48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  TYW3 MUTATED     4   1   2
  TYW3 WILD-TYPE 283 112  85
D1784V6, multiclass
    clus
vv   TYW3 MUTATED TYW3 WILD-TYPE
  N0            4            283
  N1            1            112
  N2            2             85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1784V7, binary
                cls
clus               0   1
  TYW3 MUTATED     5   1
  TYW3 WILD-TYPE 370  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  TYW3 MUTATED      5    1
  TYW3 WILD-TYPE  370   64
   clus
vv  TYW3 MUTATED TYW3 WILD-TYPE
  0            5            370
  1            1             64
[1] 2 2
[1] FALSE
D1784V8, binary
                cls
clus               0   1
  TYW3 MUTATED     2   5
  TYW3 WILD-TYPE 223 259
[1] "tbl2"
                cls
clus             [,1] [,2]
  TYW3 MUTATED      2    5
  TYW3 WILD-TYPE  223  259
        clus
vv       TYW3 MUTATED TYW3 WILD-TYPE
  FEMALE            2            223
  MALE              5            259
[1] 2 2
[1] FALSE
D1784V9, binary
                cls
clus               0   1
  TYW3 MUTATED     5   0
  TYW3 WILD-TYPE 345  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  TYW3 MUTATED      5    0
  TYW3 WILD-TYPE  345   22
     clus
vv    TYW3 MUTATED TYW3 WILD-TYPE
  NO             5            345
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  TYW3 MUTATED                      6                             0
  TYW3 WILD-TYPE                  309                            47
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  TYW3 MUTATED                       1                              0
  TYW3 WILD-TYPE                   105                             10
D1784V10, multiclass
                                clus
vv                               TYW3 MUTATED TYW3 WILD-TYPE
  COLON ADENOCARCINOMA                      6            309
  COLON MUCINOUS ADENOCARCINOMA             0             47
  RECTAL ADENOCARCINOMA                     1            105
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  TYW3 MUTATED     5   0   0   0
  TYW3 WILD-TYPE 340   4  31  25
D1784V11, multiclass
    clus
vv   TYW3 MUTATED TYW3 WILD-TYPE
  R0            5            340
  R1            0              4
  R2            0             31
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1784V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TYW3 MUTATED                                  0     0
  TYW3 WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  TYW3 MUTATED                           1     5
  TYW3 WILD-TYPE                        21   221
D1784V13, multiclass
                                  clus
vv                                 TYW3 MUTATED TYW3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                       5            221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1785) Variable = LPPR4 MUTATION ANALYSIS
D1785V1, survival
                 sevent
clus2               0   1
  LPPR4 MUTATED    23   3
  LPPR4 WILD-TYPE 355  90
  LPPR4 MUTATED LPPR4 WILD-TYPE 
             26             445 
  LPPR4 MUTATED LPPR4 WILD-TYPE 
              3              90 
$`LPPR4 MUTATED`
TCGA-A6-5665 TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3519 TCGA-AA-3525 TCGA-AA-3663 
       22.06         3.02        63.98         9.07         8.05         6.97 
TCGA-AA-3672 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3864 TCGA-AA-3877 TCGA-AA-3966 
        0.92        26.99        19.04        53.00        31.00         2.01 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-A01Q TCGA-AY-6386 TCGA-AZ-6598 TCGA-CA-6718 
       26.01        25.02         1.02        17.82        49.41        10.06 
TCGA-CM-5348 TCGA-CM-6674 TCGA-D5-6538 TCGA-D5-6541 TCGA-D5-6929 TCGA-AG-3599 
       22.98        12.95        17.13        15.58         4.80        12.03 
TCGA-AG-3892 TCGA-F5-6702 
       13.02        28.57 

$`LPPR4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 
       20.12        19.66        20.28         7.04         1.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3520 
        6.97         1.02        13.02        38.99         1.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       37.05        36.03        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
       78.08         6.05        54.02         2.01        14.01        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       36.00         5.03        85.05        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        31.07        30.05        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       29.98        18.05         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 
       26.01        24.00         2.01        20.98        34.03        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3979 TCGA-AA-3980 
       16.08        50.99        13.05        34.06        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        31.00        38.07        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        88.21         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 
        3.25         3.29         0.07        12.20        12.76        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       11.01        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
        4.80        12.49        16.14         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 
       12.43        14.30         9.04         9.44        11.64         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
        2.01        50.04         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       36.95        17.03        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       49.51        31.30        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  LPPR4 MUTATED LPPR4 WILD-TYPE 
           0.92            0.00 
  LPPR4 MUTATED LPPR4 WILD-TYPE 
          63.98          148.01 
  LPPR4 MUTATED LPPR4 WILD-TYPE 
         16.355          20.910 
[1] "0.9 - 64.0 (16.4)"  "0.0 - 148.0 (20.9)"
[1] "hr=" "1.4"
D1785V2, continuous
D1785V3, binary
                 cls
clus                0   1
  LPPR4 MUTATED    24   3
  LPPR4 WILD-TYPE 342 116
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LPPR4 MUTATED     24    3
  LPPR4 WILD-TYPE  342  116
        clus
vv       LPPR4 MUTATED LPPR4 WILD-TYPE
  COLON             24             342
  RECTUM             3             116
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  LPPR4 MUTATED         3        0        6         6         0         0
  LPPR4 WILD-TYPE      88        1       26       132        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  LPPR4 MUTATED           2          1          4          0        3         1
  LPPR4 WILD-TYPE        22         10         55         42       45        17
                 vv
clus              STAGE IVB
  LPPR4 MUTATED           0
  LPPR4 WILD-TYPE         1
D1785V4, multiclass
            clus
vv           LPPR4 MUTATED LPPR4 WILD-TYPE
  STAGE I                3              88
  STAGE IA               0               1
  STAGE II               6              26
  STAGE IIA              6             132
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              2              22
  STAGE IIIA             1              10
  STAGE IIIB             4              55
  STAGE IIIC             0              42
  STAGE IV               3              45
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  LPPR4 MUTATED     2   3  21   1
  LPPR4 WILD-TYPE  15  89 308  49
D1785V5, multiclass
    clus
vv   LPPR4 MUTATED LPPR4 WILD-TYPE
  T1             2              15
  T2             3              89
  T3            21             308
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  LPPR4 MUTATED    17   9   1
  LPPR4 WILD-TYPE 270 104  86
D1785V6, multiclass
    clus
vv   LPPR4 MUTATED LPPR4 WILD-TYPE
  N0            17             270
  N1             9             104
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1785V7, binary
                 cls
clus                0   1
  LPPR4 MUTATED    21   4
  LPPR4 WILD-TYPE 354  61
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LPPR4 MUTATED     21    4
  LPPR4 WILD-TYPE  354   61
   clus
vv  LPPR4 MUTATED LPPR4 WILD-TYPE
  0            21             354
  1             4              61
[1] 2 2
[1] FALSE
D1785V8, binary
                 cls
clus                0   1
  LPPR4 MUTATED    13  14
  LPPR4 WILD-TYPE 212 250
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LPPR4 MUTATED     13   14
  LPPR4 WILD-TYPE  212  250
        clus
vv       LPPR4 MUTATED LPPR4 WILD-TYPE
  FEMALE            13             212
  MALE              14             250
[1] 2 2
[1] FALSE
D1785V9, binary
                 cls
clus                0   1
  LPPR4 MUTATED    22   1
  LPPR4 WILD-TYPE 328  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LPPR4 MUTATED     22    1
  LPPR4 WILD-TYPE  328   21
     clus
vv    LPPR4 MUTATED LPPR4 WILD-TYPE
  NO             22             328
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  LPPR4 MUTATED                     22                             2
  LPPR4 WILD-TYPE                  293                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  LPPR4 MUTATED                       2                              0
  LPPR4 WILD-TYPE                   104                             10
D1785V10, multiclass
                                clus
vv                               LPPR4 MUTATED LPPR4 WILD-TYPE
  COLON ADENOCARCINOMA                      22             293
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  LPPR4 MUTATED    21   0   2   1
  LPPR4 WILD-TYPE 324   4  29  24
D1785V11, multiclass
    clus
vv   LPPR4 MUTATED LPPR4 WILD-TYPE
  R0            21             324
  R1             0               4
  R2             2              29
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1785V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  LPPR4 MUTATED                                  0     1
  LPPR4 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  LPPR4 MUTATED                           1     8
  LPPR4 WILD-TYPE                        21   218
D1785V13, multiclass
                                  clus
vv                                 LPPR4 MUTATED LPPR4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        8             218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1786) Variable = UBR2 MUTATION ANALYSIS
D1786V1, survival
                sevent
clus2              0   1
  UBR2 MUTATED    14   4
  UBR2 WILD-TYPE 364  89
  UBR2 MUTATED UBR2 WILD-TYPE 
            18            453 
  UBR2 MUTATED UBR2 WILD-TYPE 
             4             89 
$`UBR2 MUTATED`
TCGA-A6-5666 TCGA-AA-3558 TCGA-AA-3864 TCGA-AA-3966 TCGA-AA-A010 TCGA-AA-A01Q 
       32.71        20.98        53.00         2.01        34.98         1.02 
TCGA-AZ-4315 TCGA-CA-6715 TCGA-CA-6717 TCGA-D5-6922 TCGA-D5-6930 TCGA-DM-A1DA 
       58.39         0.07        12.76         4.41         1.51         7.50 
TCGA-DM-A285 TCGA-DM-A28F TCGA-AF-2691 TCGA-AG-A002 TCGA-DY-A1DC TCGA-F5-6813 
        6.12        35.97        43.04        20.98        41.36         0.69 

$`UBR2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        22.06        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3560 
       13.02        24.00        17.95        29.95        23.01        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 
        0.99        31.07        31.07        30.05        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
       34.03        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
       16.31         0.95        33.01        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.20        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A28C TCGA-DM-A28E 
       44.32       131.51       135.65       139.17        81.37       119.93 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DD TCGA-DY-A1DF 
        4.01         5.03         5.29       126.44        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-G5-6235 TCGA-G5-6641 
        0.66        55.76        26.43 

  UBR2 MUTATED UBR2 WILD-TYPE 
          0.07           0.00 
  UBR2 MUTATED UBR2 WILD-TYPE 
         58.39         148.01 
  UBR2 MUTATED UBR2 WILD-TYPE 
         16.87          20.19 
[1] "0.1 - 58.4 (16.9)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.4"
D1786V2, continuous
D1786V3, binary
                cls
clus               0   1
  UBR2 MUTATED    15   4
  UBR2 WILD-TYPE 351 115
[1] "tbl2"
                cls
clus             [,1] [,2]
  UBR2 MUTATED     15    4
  UBR2 WILD-TYPE  351  115
        clus
vv       UBR2 MUTATED UBR2 WILD-TYPE
  COLON            15            351
  RECTUM            4            115
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  UBR2 MUTATED         3        0        2         6         1         1
  UBR2 WILD-TYPE      88        1       30       132         9         0
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  UBR2 MUTATED           0          1          2          2        1         0
  UBR2 WILD-TYPE        24         10         57         40       47        18
                vv
clus             STAGE IVB
  UBR2 MUTATED           0
  UBR2 WILD-TYPE         1
D1786V4, multiclass
            clus
vv           UBR2 MUTATED UBR2 WILD-TYPE
  STAGE I               3             88
  STAGE IA              0              1
  STAGE II              2             30
  STAGE IIA             6            132
  STAGE IIB             1              9
  STAGE IIC             1              0
  STAGE III             0             24
  STAGE IIIA            1             10
  STAGE IIIB            2             57
  STAGE IIIC            2             40
  STAGE IV              1             47
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  UBR2 MUTATED     1   2  13   3
  UBR2 WILD-TYPE  16  90 316  47
D1786V5, multiclass
    clus
vv   UBR2 MUTATED UBR2 WILD-TYPE
  T1            1             16
  T2            2             90
  T3           13            316
  T4            3             47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  UBR2 MUTATED    13   3   3
  UBR2 WILD-TYPE 274 110  84
D1786V6, multiclass
    clus
vv   UBR2 MUTATED UBR2 WILD-TYPE
  N0           13            274
  N1            3            110
  N2            3             84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1786V7, binary
                cls
clus               0   1
  UBR2 MUTATED    18   1
  UBR2 WILD-TYPE 357  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  UBR2 MUTATED     18    1
  UBR2 WILD-TYPE  357   64
   clus
vv  UBR2 MUTATED UBR2 WILD-TYPE
  0           18            357
  1            1             64
[1] 2 2
[1] FALSE
D1786V8, binary
                cls
clus               0   1
  UBR2 MUTATED     8  11
  UBR2 WILD-TYPE 217 253
[1] "tbl2"
                cls
clus             [,1] [,2]
  UBR2 MUTATED      8   11
  UBR2 WILD-TYPE  217  253
        clus
vv       UBR2 MUTATED UBR2 WILD-TYPE
  FEMALE            8            217
  MALE             11            253
[1] 2 2
[1] FALSE
D1786V9, binary
                cls
clus               0   1
  UBR2 MUTATED     8   0
  UBR2 WILD-TYPE 342  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  UBR2 MUTATED      8    0
  UBR2 WILD-TYPE  342   22
     clus
vv    UBR2 MUTATED UBR2 WILD-TYPE
  NO             8            342
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  UBR2 MUTATED                     11                             4
  UBR2 WILD-TYPE                  304                            43
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  UBR2 MUTATED                       4                              0
  UBR2 WILD-TYPE                   102                             10
D1786V10, multiclass
                                clus
vv                               UBR2 MUTATED UBR2 WILD-TYPE
  COLON ADENOCARCINOMA                     11            304
  COLON MUCINOUS ADENOCARCINOMA             4             43
  RECTAL ADENOCARCINOMA                     4            102
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  UBR2 MUTATED    10   0   1   2
  UBR2 WILD-TYPE 335   4  30  23
D1786V11, multiclass
    clus
vv   UBR2 MUTATED UBR2 WILD-TYPE
  R0           10            335
  R1            0              4
  R2            1             30
  RX            2             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1786V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  UBR2 MUTATED                                  0     2
  UBR2 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  UBR2 MUTATED                           0    10
  UBR2 WILD-TYPE                        22   216
D1786V13, multiclass
                                  clus
vv                                 UBR2 MUTATED UBR2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              9
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                      10            216
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1787) Variable = GPBP1 MUTATION ANALYSIS
D1787V1, survival
                 sevent
clus2               0   1
  GPBP1 MUTATED     9   3
  GPBP1 WILD-TYPE 369  90
  GPBP1 MUTATED GPBP1 WILD-TYPE 
             12             459 
  GPBP1 MUTATED GPBP1 WILD-TYPE 
              3              90 
$`GPBP1 MUTATED`
TCGA-A6-6653 TCGA-AA-3489 TCGA-AA-3947 TCGA-AY-6386 TCGA-AZ-4315 TCGA-CM-4746 
       24.39         7.04        33.01        17.82        58.39        37.02 
TCGA-CM-6678 TCGA-D5-6929 TCGA-DM-A1D4 TCGA-DM-A1DA TCGA-G4-6588 TCGA-CI-6624 
       11.01         4.80        92.75         7.50        26.17         4.73 

$`GPBP1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
       25.08        25.18        24.16        21.76        24.69        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        19.66        20.28         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       12.99        24.00        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       21.44         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       23.05        20.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
        9.44        11.64         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-DM-A1D7 
      119.70        24.43        38.20       130.65        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
       12.59       140.38        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        35.80        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        6.97        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  GPBP1 MUTATED GPBP1 WILD-TYPE 
           4.73            0.00 
  GPBP1 MUTATED GPBP1 WILD-TYPE 
          92.75          148.01 
  GPBP1 MUTATED GPBP1 WILD-TYPE 
         21.105          20.190 
[1] "4.7 - 92.8 (21.1)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.2"
D1787V2, continuous
D1787V3, binary
                 cls
clus                0   1
  GPBP1 MUTATED    12   1
  GPBP1 WILD-TYPE 354 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPBP1 MUTATED     12    1
  GPBP1 WILD-TYPE  354  118
        clus
vv       GPBP1 MUTATED GPBP1 WILD-TYPE
  COLON             12             354
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GPBP1 MUTATED         3        0        2         3         1         0
  GPBP1 WILD-TYPE      88        1       30       135         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  GPBP1 MUTATED           0          0          1          1        1         1
  GPBP1 WILD-TYPE        24         11         58         41       47        17
                 vv
clus              STAGE IVB
  GPBP1 MUTATED           0
  GPBP1 WILD-TYPE         1
D1787V4, multiclass
            clus
vv           GPBP1 MUTATED GPBP1 WILD-TYPE
  STAGE I                3              88
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA              3             135
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             1              41
  STAGE IV               1              47
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  GPBP1 MUTATED     0   3   7   3
  GPBP1 WILD-TYPE  17  89 322  47
D1787V5, multiclass
    clus
vv   GPBP1 MUTATED GPBP1 WILD-TYPE
  T1             0              17
  T2             3              89
  T3             7             322
  T4             3              47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  GPBP1 MUTATED     9   3   1
  GPBP1 WILD-TYPE 278 110  86
D1787V6, multiclass
    clus
vv   GPBP1 MUTATED GPBP1 WILD-TYPE
  N0             9             278
  N1             3             110
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1787V7, binary
                 cls
clus                0   1
  GPBP1 MUTATED    11   2
  GPBP1 WILD-TYPE 364  63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPBP1 MUTATED     11    2
  GPBP1 WILD-TYPE  364   63
   clus
vv  GPBP1 MUTATED GPBP1 WILD-TYPE
  0            11             364
  1             2              63
[1] 2 2
[1] FALSE
D1787V8, binary
                 cls
clus                0   1
  GPBP1 MUTATED     8   5
  GPBP1 WILD-TYPE 217 259
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPBP1 MUTATED      8    5
  GPBP1 WILD-TYPE  217  259
        clus
vv       GPBP1 MUTATED GPBP1 WILD-TYPE
  FEMALE             8             217
  MALE               5             259
[1] 2 2
[1] FALSE
D1787V9, binary
                 cls
clus                0   1
  GPBP1 MUTATED     8   0
  GPBP1 WILD-TYPE 342  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPBP1 MUTATED      8    0
  GPBP1 WILD-TYPE  342   22
     clus
vv    GPBP1 MUTATED GPBP1 WILD-TYPE
  NO              8             342
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  GPBP1 MUTATED                     11                             1
  GPBP1 WILD-TYPE                  304                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  GPBP1 MUTATED                       1                              0
  GPBP1 WILD-TYPE                   105                             10
D1787V10, multiclass
                                clus
vv                               GPBP1 MUTATED GPBP1 WILD-TYPE
  COLON ADENOCARCINOMA                      11             304
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  GPBP1 MUTATED     9   0   0   0
  GPBP1 WILD-TYPE 336   4  31  25
D1787V11, multiclass
    clus
vv   GPBP1 MUTATED GPBP1 WILD-TYPE
  R0             9             336
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1787V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GPBP1 MUTATED                                  0     0
  GPBP1 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  GPBP1 MUTATED                           2     8
  GPBP1 WILD-TYPE                        20   218
D1787V13, multiclass
                                  clus
vv                                 GPBP1 MUTATED GPBP1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    2              20
  WHITE                                        8             218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1788) Variable = SPAM1 MUTATION ANALYSIS
D1788V1, survival
                 sevent
clus2               0   1
  SPAM1 MUTATED    10   3
  SPAM1 WILD-TYPE 368  90
  SPAM1 MUTATED SPAM1 WILD-TYPE 
             13             458 
  SPAM1 MUTATED SPAM1 WILD-TYPE 
              3              90 
$`SPAM1 MUTATED`
TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3655 TCGA-AA-3697 TCGA-AA-A00R TCGA-CA-6715 
        3.02        63.98        61.02        85.05         0.99         0.07 
TCGA-CA-6717 TCGA-CA-6718 TCGA-F4-6570 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-A002 
       12.76        10.06         6.18        13.02        35.01        20.98 
TCGA-F5-6465 
       49.51 

$`SPAM1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       13.94        19.99        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
       42.02        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        3.25         3.29        12.20        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3894 
       19.99         1.02        17.95        36.95        17.03        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
        9.96        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  SPAM1 MUTATED SPAM1 WILD-TYPE 
           0.07            0.00 
  SPAM1 MUTATED SPAM1 WILD-TYPE 
          85.05          148.01 
  SPAM1 MUTATED SPAM1 WILD-TYPE 
         13.020          20.235 
[1] "0.1 - 85.0 (13.0)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1"  
D1788V2, continuous
D1788V3, binary
                 cls
clus                0   1
  SPAM1 MUTATED     9   4
  SPAM1 WILD-TYPE 357 115
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SPAM1 MUTATED      9    4
  SPAM1 WILD-TYPE  357  115
        clus
vv       SPAM1 MUTATED SPAM1 WILD-TYPE
  COLON              9             357
  RECTUM             4             115
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SPAM1 MUTATED         3        0        3         4         0         0
  SPAM1 WILD-TYPE      88        1       29       134        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SPAM1 MUTATED           1          0          2          0        0         0
  SPAM1 WILD-TYPE        23         11         57         42       48        18
                 vv
clus              STAGE IVB
  SPAM1 MUTATED           0
  SPAM1 WILD-TYPE         1
D1788V4, multiclass
            clus
vv           SPAM1 MUTATED SPAM1 WILD-TYPE
  STAGE I                3              88
  STAGE IA               0               1
  STAGE II               3              29
  STAGE IIA              4             134
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             2              57
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  SPAM1 MUTATED     1   2  10   0
  SPAM1 WILD-TYPE  16  90 319  50
D1788V5, multiclass
    clus
vv   SPAM1 MUTATED SPAM1 WILD-TYPE
  T1             1              16
  T2             2              90
  T3            10             319
  T4             0              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  SPAM1 MUTATED    11   2   0
  SPAM1 WILD-TYPE 276 111  87
D1788V6, multiclass
    clus
vv   SPAM1 MUTATED SPAM1 WILD-TYPE
  N0            11             276
  N1             2             111
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1788V7, binary
                 cls
clus                0   1
  SPAM1 MUTATED    13   0
  SPAM1 WILD-TYPE 362  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SPAM1 MUTATED     13    0
  SPAM1 WILD-TYPE  362   65
   clus
vv  SPAM1 MUTATED SPAM1 WILD-TYPE
  0            13             362
  1             0              65
[1] 2 2
[1] FALSE
D1788V8, binary
                 cls
clus                0   1
  SPAM1 MUTATED     5   8
  SPAM1 WILD-TYPE 220 256
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SPAM1 MUTATED      5    8
  SPAM1 WILD-TYPE  220  256
        clus
vv       SPAM1 MUTATED SPAM1 WILD-TYPE
  FEMALE             5             220
  MALE               8             256
[1] 2 2
[1] FALSE
D1788V9, binary
                 cls
clus                0   1
  SPAM1 MUTATED    11   0
  SPAM1 WILD-TYPE 339  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SPAM1 MUTATED     11    0
  SPAM1 WILD-TYPE  339   22
     clus
vv    SPAM1 MUTATED SPAM1 WILD-TYPE
  NO             11             339
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SPAM1 MUTATED                      8                             1
  SPAM1 WILD-TYPE                  307                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SPAM1 MUTATED                       4                              0
  SPAM1 WILD-TYPE                   102                             10
D1788V10, multiclass
                                clus
vv                               SPAM1 MUTATED SPAM1 WILD-TYPE
  COLON ADENOCARCINOMA                       8             307
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      4             102
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  SPAM1 MUTATED    10   0   0   3
  SPAM1 WILD-TYPE 335   4  31  22
D1788V11, multiclass
    clus
vv   SPAM1 MUTATED SPAM1 WILD-TYPE
  R0            10             335
  R1             0               4
  R2             0              31
  RX             3              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1788V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SPAM1 MUTATED                                  0     3
  SPAM1 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  SPAM1 MUTATED                           0     2
  SPAM1 WILD-TYPE                        22   224
D1788V13, multiclass
                                  clus
vv                                 SPAM1 MUTATED SPAM1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        3               8
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        2             224
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1789) Variable = ZFP91 MUTATION ANALYSIS
D1789V1, survival
                 sevent
clus2               0   1
  ZFP91 MUTATED     6   2
  ZFP91 WILD-TYPE 372  91
  ZFP91 MUTATED ZFP91 WILD-TYPE 
              8             463 
  ZFP91 MUTATED ZFP91 WILD-TYPE 
              2              91 
$`ZFP91 MUTATED`
TCGA-A6-5661 TCGA-AA-3860 TCGA-AA-A00L TCGA-AA-A01R TCGA-CM-6162 TCGA-DM-A28G 
       33.53        31.07        38.04        35.01        12.00        60.79 
TCGA-G4-6303 TCGA-DT-5265 
       65.85         5.29 

$`ZFP91 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
       32.05         0.99        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N 
       19.00        30.02        34.03        18.05        18.05         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       31.00        38.07         1.02         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 
        5.03        15.02        15.02        17.03        15.02         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
       81.37       119.93        35.97       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
       35.31       133.18        74.56        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A0XA 
       10.98        19.99         5.95         4.01         5.03       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  ZFP91 MUTATED ZFP91 WILD-TYPE 
           5.29            0.00 
  ZFP91 MUTATED ZFP91 WILD-TYPE 
          65.85          148.01 
  ZFP91 MUTATED ZFP91 WILD-TYPE 
          34.27           20.05 
[1] "5.3 - 65.8 (34.3)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.1"
D1789V2, continuous
D1789V3, binary
                 cls
clus                0   1
  ZFP91 MUTATED     7   1
  ZFP91 WILD-TYPE 359 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZFP91 MUTATED      7    1
  ZFP91 WILD-TYPE  359  118
        clus
vv       ZFP91 MUTATED ZFP91 WILD-TYPE
  COLON              7             359
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZFP91 MUTATED         0        0        1         3         0         0
  ZFP91 WILD-TYPE      91        1       31       135        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ZFP91 MUTATED           1          0          2          0        1         0
  ZFP91 WILD-TYPE        23         11         57         42       47        18
                 vv
clus              STAGE IVB
  ZFP91 MUTATED           0
  ZFP91 WILD-TYPE         1
D1789V4, multiclass
            clus
vv           ZFP91 MUTATED ZFP91 WILD-TYPE
  STAGE I                0              91
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              3             135
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             2              57
  STAGE IIIC             0              42
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ZFP91 MUTATED     0   0   8   0
  ZFP91 WILD-TYPE  17  92 321  50
D1789V5, multiclass
    clus
vv   ZFP91 MUTATED ZFP91 WILD-TYPE
  T1             0              17
  T2             0              92
  T3             8             321
  T4             0              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  ZFP91 MUTATED     4   3   1
  ZFP91 WILD-TYPE 283 110  86
D1789V6, multiclass
    clus
vv   ZFP91 MUTATED ZFP91 WILD-TYPE
  N0             4             283
  N1             3             110
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1789V7, binary
                 cls
clus                0   1
  ZFP91 MUTATED     7   1
  ZFP91 WILD-TYPE 368  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZFP91 MUTATED      7    1
  ZFP91 WILD-TYPE  368   64
   clus
vv  ZFP91 MUTATED ZFP91 WILD-TYPE
  0             7             368
  1             1              64
[1] 2 2
[1] FALSE
D1789V8, binary
                 cls
clus                0   1
  ZFP91 MUTATED     4   4
  ZFP91 WILD-TYPE 221 260
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZFP91 MUTATED      4    4
  ZFP91 WILD-TYPE  221  260
        clus
vv       ZFP91 MUTATED ZFP91 WILD-TYPE
  FEMALE             4             221
  MALE               4             260
[1] 2 2
[1] FALSE
D1789V9, binary
                 cls
clus                0   1
  ZFP91 MUTATED     6   1
  ZFP91 WILD-TYPE 344  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZFP91 MUTATED      6    1
  ZFP91 WILD-TYPE  344   21
     clus
vv    ZFP91 MUTATED ZFP91 WILD-TYPE
  NO              6             344
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ZFP91 MUTATED                      5                             2
  ZFP91 WILD-TYPE                  310                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ZFP91 MUTATED                       0                              1
  ZFP91 WILD-TYPE                   106                              9
D1789V10, multiclass
                                clus
vv                               ZFP91 MUTATED ZFP91 WILD-TYPE
  COLON ADENOCARCINOMA                       5             310
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             1               9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  ZFP91 MUTATED     6   0   0   1
  ZFP91 WILD-TYPE 339   4  31  24
D1789V11, multiclass
    clus
vv   ZFP91 MUTATED ZFP91 WILD-TYPE
  R0             6             339
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1789V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZFP91 MUTATED                                  0     1
  ZFP91 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ZFP91 MUTATED                           1     3
  ZFP91 WILD-TYPE                        21   223
D1789V13, multiclass
                                  clus
vv                                 ZFP91 MUTATED ZFP91 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        3             223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1790) Variable = OR13C5 MUTATION ANALYSIS
D1790V1, survival
                  sevent
clus2                0   1
  OR13C5 MUTATED    11   2
  OR13C5 WILD-TYPE 367  91
  OR13C5 MUTATED OR13C5 WILD-TYPE 
              13              458 
  OR13C5 MUTATED OR13C5 WILD-TYPE 
               2               91 
$`OR13C5 MUTATED`
TCGA-A6-5657 TCGA-AA-3815 TCGA-AA-3982 TCGA-AZ-6607 TCGA-CA-5797 TCGA-CA-6715 
       31.63        33.04        27.02         3.19         3.29         0.07 
TCGA-CM-4752 TCGA-CM-6171 TCGA-D5-6540 TCGA-D5-6930 TCGA-DM-A1D8 TCGA-AG-A002 
       13.02        14.04        16.14         1.51        12.59        20.98 
TCGA-F5-6465 
       49.51 

$`OR13C5 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       10.06        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5254 
      100.01        29.56         5.23        11.74         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.06         3.25        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       20.02        37.02        25.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 
       21.99        14.99        12.99        13.02        15.02        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
        4.80        17.13        12.49        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        4.80        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D9 
       38.20       130.65        92.75        49.91        13.32       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
        9.96        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  OR13C5 MUTATED OR13C5 WILD-TYPE 
            0.07             0.00 
  OR13C5 MUTATED OR13C5 WILD-TYPE 
           49.51           148.01 
  OR13C5 MUTATED OR13C5 WILD-TYPE 
          14.040           20.415 
[1] "0.1 - 49.5 (14.0)"  "0.0 - 148.0 (20.4)"
[1] "hr=" "1.1"
D1790V2, continuous
D1790V3, binary
                  cls
clus                 0   1
  OR13C5 MUTATED    11   2
  OR13C5 WILD-TYPE 355 117
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR13C5 MUTATED     11    2
  OR13C5 WILD-TYPE  355  117
        clus
vv       OR13C5 MUTATED OR13C5 WILD-TYPE
  COLON              11              355
  RECTUM              2              117
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  OR13C5 MUTATED         3        0        0         5         0         0
  OR13C5 WILD-TYPE      88        1       32       133        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  OR13C5 MUTATED           0          0          3          0        1
  OR13C5 WILD-TYPE        24         11         56         42       47
                  vv
clus               STAGE IVA STAGE IVB
  OR13C5 MUTATED           0         0
  OR13C5 WILD-TYPE        18         1
D1790V4, multiclass
            clus
vv           OR13C5 MUTATED OR13C5 WILD-TYPE
  STAGE I                 3               88
  STAGE IA                0                1
  STAGE II                0               32
  STAGE IIA               5              133
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              3               56
  STAGE IIIC              0               42
  STAGE IV                1               47
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  OR13C5 MUTATED     0   3   9   1
  OR13C5 WILD-TYPE  17  89 320  49
D1790V5, multiclass
    clus
vv   OR13C5 MUTATED OR13C5 WILD-TYPE
  T1              0               17
  T2              3               89
  T3              9              320
  T4              1               49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  OR13C5 MUTATED     8   4   1
  OR13C5 WILD-TYPE 279 109  86
D1790V6, multiclass
    clus
vv   OR13C5 MUTATED OR13C5 WILD-TYPE
  N0              8              279
  N1              4              109
  N2              1               86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1790V7, binary
                  cls
clus                 0   1
  OR13C5 MUTATED    11   1
  OR13C5 WILD-TYPE 364  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR13C5 MUTATED     11    1
  OR13C5 WILD-TYPE  364   64
   clus
vv  OR13C5 MUTATED OR13C5 WILD-TYPE
  0             11              364
  1              1               64
[1] 2 2
[1] FALSE
D1790V8, binary
                  cls
clus                 0   1
  OR13C5 MUTATED     4   9
  OR13C5 WILD-TYPE 221 255
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR13C5 MUTATED      4    9
  OR13C5 WILD-TYPE  221  255
        clus
vv       OR13C5 MUTATED OR13C5 WILD-TYPE
  FEMALE              4              221
  MALE                9              255
[1] 2 2
[1] FALSE
D1790V9, binary
                  cls
clus                 0   1
  OR13C5 MUTATED    10   0
  OR13C5 WILD-TYPE 340  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR13C5 MUTATED     10    0
  OR13C5 WILD-TYPE  340   22
     clus
vv    OR13C5 MUTATED OR13C5 WILD-TYPE
  NO              10              340
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  OR13C5 MUTATED                      9                             2
  OR13C5 WILD-TYPE                  306                            45
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  OR13C5 MUTATED                       2                              0
  OR13C5 WILD-TYPE                   104                             10
D1790V10, multiclass
                                clus
vv                               OR13C5 MUTATED OR13C5 WILD-TYPE
  COLON ADENOCARCINOMA                        9              306
  COLON MUCINOUS ADENOCARCINOMA               2               45
  RECTAL ADENOCARCINOMA                       2              104
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  OR13C5 MUTATED     9   0   0   1
  OR13C5 WILD-TYPE 336   4  31  24
D1790V11, multiclass
    clus
vv   OR13C5 MUTATED OR13C5 WILD-TYPE
  R0              9              336
  R1              0                4
  R2              0               31
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1790V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OR13C5 MUTATED                                  0     2
  OR13C5 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  OR13C5 MUTATED                           2     6
  OR13C5 WILD-TYPE                        20   220
D1790V13, multiclass
                                  clus
vv                                 OR13C5 MUTATED OR13C5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                9
  BLACK OR AFRICAN AMERICAN                     2               20
  WHITE                                         6              220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1791) Variable = SLC43A3 MUTATION ANALYSIS
D1791V1, survival
                   sevent
clus2                 0   1
  SLC43A3 MUTATED     8   5
  SLC43A3 WILD-TYPE 370  88
  SLC43A3 MUTATED SLC43A3 WILD-TYPE 
               13               458 
  SLC43A3 MUTATED SLC43A3 WILD-TYPE 
                5                88 
$`SLC43A3 MUTATED`
TCGA-A6-3809 TCGA-AA-3516 TCGA-AA-3811 TCGA-AA-3864 TCGA-AA-A00D TCGA-AA-A010 
       32.75        13.02        10.06        53.00        19.00        34.98 
TCGA-AD-5900 TCGA-AD-6901 TCGA-AZ-6598 TCGA-CK-4947 TCGA-CK-4952 TCGA-AF-5654 
        0.07        22.42        49.41        17.56        15.62        16.83 
TCGA-AG-3896 
        1.02 

$`SLC43A3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        19.04        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        31.07        30.05        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00F 
        7.96        27.02        13.94        38.04        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 
        0.92        41.00        39.98        18.05        40.96        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6963 
       15.52        56.55         0.79         0.72         5.79        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 
      106.75        22.36        62.79        88.21         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 
       12.76        10.06        14.30       148.01        85.45        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       34.49        10.39        14.50        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3898 
       36.95        17.03        13.02        35.01        14.01        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  SLC43A3 MUTATED SLC43A3 WILD-TYPE 
             0.07              0.00 
  SLC43A3 MUTATED SLC43A3 WILD-TYPE 
            53.00            148.01 
  SLC43A3 MUTATED SLC43A3 WILD-TYPE 
           17.560            20.415 
[1] "0.1 - 53.0 (17.6)"  "0.0 - 148.0 (20.4)"
[1] "hr=" "2.3"
D1791V2, continuous
D1791V3, binary
                   cls
clus                  0   1
  SLC43A3 MUTATED    11   2
  SLC43A3 WILD-TYPE 355 117
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC43A3 MUTATED     11    2
  SLC43A3 WILD-TYPE  355  117
        clus
vv       SLC43A3 MUTATED SLC43A3 WILD-TYPE
  COLON               11               355
  RECTUM               2               117
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SLC43A3 MUTATED         4        0        2         0         2         0
  SLC43A3 WILD-TYPE      87        1       30       138         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC43A3 MUTATED           2          0          1          1        0
  SLC43A3 WILD-TYPE        22         11         58         41       48
                   vv
clus                STAGE IVA STAGE IVB
  SLC43A3 MUTATED           0         0
  SLC43A3 WILD-TYPE        18         1
D1791V4, multiclass
            clus
vv           SLC43A3 MUTATED SLC43A3 WILD-TYPE
  STAGE I                  4                87
  STAGE IA                 0                 1
  STAGE II                 2                30
  STAGE IIA                0               138
  STAGE IIB                2                 8
  STAGE IIC                0                 1
  STAGE III                2                22
  STAGE IIIA               0                11
  STAGE IIIB               1                58
  STAGE IIIC               1                41
  STAGE IV                 0                48
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  SLC43A3 MUTATED     0   4   5   4
  SLC43A3 WILD-TYPE  17  88 324  46
D1791V5, multiclass
    clus
vv   SLC43A3 MUTATED SLC43A3 WILD-TYPE
  T1               0                17
  T2               4                88
  T3               5               324
  T4               4                46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  SLC43A3 MUTATED     9   1   3
  SLC43A3 WILD-TYPE 278 112  84
D1791V6, multiclass
    clus
vv   SLC43A3 MUTATED SLC43A3 WILD-TYPE
  N0               9               278
  N1               1               112
  N2               3                84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1791V7, binary
                   cls
clus                  0   1
  SLC43A3 MUTATED    10   0
  SLC43A3 WILD-TYPE 365  65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC43A3 MUTATED     10    0
  SLC43A3 WILD-TYPE  365   65
   clus
vv  SLC43A3 MUTATED SLC43A3 WILD-TYPE
  0              10               365
  1               0                65
[1] 2 2
[1] FALSE
D1791V8, binary
                   cls
clus                  0   1
  SLC43A3 MUTATED     9   4
  SLC43A3 WILD-TYPE 216 260
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC43A3 MUTATED      9    4
  SLC43A3 WILD-TYPE  216  260
        clus
vv       SLC43A3 MUTATED SLC43A3 WILD-TYPE
  FEMALE               9               216
  MALE                 4               260
[1] 2 2
[1] FALSE
D1791V9, binary
                   cls
clus                  0   1
  SLC43A3 MUTATED    10   0
  SLC43A3 WILD-TYPE 340  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC43A3 MUTATED     10    0
  SLC43A3 WILD-TYPE  340   22
     clus
vv    SLC43A3 MUTATED SLC43A3 WILD-TYPE
  NO               10               340
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SLC43A3 MUTATED                      7                             4
  SLC43A3 WILD-TYPE                  308                            43
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SLC43A3 MUTATED                       2                              0
  SLC43A3 WILD-TYPE                   104                             10
D1791V10, multiclass
                                clus
vv                               SLC43A3 MUTATED SLC43A3 WILD-TYPE
  COLON ADENOCARCINOMA                         7               308
  COLON MUCINOUS ADENOCARCINOMA                4                43
  RECTAL ADENOCARCINOMA                        2               104
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  SLC43A3 MUTATED     8   0   0   2
  SLC43A3 WILD-TYPE 337   4  31  23
D1791V11, multiclass
    clus
vv   SLC43A3 MUTATED SLC43A3 WILD-TYPE
  R0               8               337
  R1               0                 4
  R2               0                31
  RX               2                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1791V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SLC43A3 MUTATED                                  0     0
  SLC43A3 WILD-TYPE                                1    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  SLC43A3 MUTATED                           0     7
  SLC43A3 WILD-TYPE                        22   219
D1791V13, multiclass
                                  clus
vv                                 SLC43A3 MUTATED SLC43A3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                      0                22
  WHITE                                          7               219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1792) Variable = GOLGA1 MUTATION ANALYSIS
D1792V1, survival
                  sevent
clus2                0   1
  GOLGA1 MUTATED     5   2
  GOLGA1 WILD-TYPE 373  91
  GOLGA1 MUTATED GOLGA1 WILD-TYPE 
               7              464 
  GOLGA1 MUTATED GOLGA1 WILD-TYPE 
               2               91 
$`GOLGA1 MUTATED`
TCGA-AA-3663 TCGA-AA-3877 TCGA-AA-A00N TCGA-AZ-6600 TCGA-CM-6675 TCGA-D5-5538 
        6.97        31.00         4.01        12.10        13.05        12.26 
TCGA-F5-6571 
       31.30 

$`GOLGA1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.05        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 
       17.03        24.03        27.02        29.98        18.05         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 
       22.36        62.79        88.21        49.41         6.77       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6676 
       13.02        15.02        14.04        11.01        12.95        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5539 
       11.08        11.01        10.06        12.03        45.40        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
        9.96        49.51        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  GOLGA1 MUTATED GOLGA1 WILD-TYPE 
            4.01             0.00 
  GOLGA1 MUTATED GOLGA1 WILD-TYPE 
           31.30           148.01 
  GOLGA1 MUTATED GOLGA1 WILD-TYPE 
          12.260           20.415 
[1] "4.0 - 31.3 (12.3)"  "0.0 - 148.0 (20.4)"
[1] "hr=" "2.5"
D1792V2, continuous
D1792V3, binary
                  cls
clus                 0   1
  GOLGA1 MUTATED     7   1
  GOLGA1 WILD-TYPE 359 118
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GOLGA1 MUTATED      7    1
  GOLGA1 WILD-TYPE  359  118
        clus
vv       GOLGA1 MUTATED GOLGA1 WILD-TYPE
  COLON               7              359
  RECTUM              1              118
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GOLGA1 MUTATED         1        0        1         2         1         0
  GOLGA1 WILD-TYPE      90        1       31       136         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GOLGA1 MUTATED           0          0          1          0        1
  GOLGA1 WILD-TYPE        24         11         58         42       47
                  vv
clus               STAGE IVA STAGE IVB
  GOLGA1 MUTATED           0         1
  GOLGA1 WILD-TYPE        18         0
D1792V4, multiclass
            clus
vv           GOLGA1 MUTATED GOLGA1 WILD-TYPE
  STAGE I                 1               90
  STAGE IA                0                1
  STAGE II                1               31
  STAGE IIA               2              136
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              1               58
  STAGE IIIC              0               42
  STAGE IV                1               47
  STAGE IVA               0               18
  STAGE IVB               1                0
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  GOLGA1 MUTATED     1   0   5   2
  GOLGA1 WILD-TYPE  16  92 324  48
D1792V5, multiclass
    clus
vv   GOLGA1 MUTATED GOLGA1 WILD-TYPE
  T1              1               16
  T2              0               92
  T3              5              324
  T4              2               48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  GOLGA1 MUTATED     5   2   1
  GOLGA1 WILD-TYPE 282 111  86
D1792V6, multiclass
    clus
vv   GOLGA1 MUTATED GOLGA1 WILD-TYPE
  N0              5              282
  N1              2              111
  N2              1               86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1792V7, binary
                  cls
clus                 0   1
  GOLGA1 MUTATED     6   2
  GOLGA1 WILD-TYPE 369  63
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GOLGA1 MUTATED      6    2
  GOLGA1 WILD-TYPE  369   63
   clus
vv  GOLGA1 MUTATED GOLGA1 WILD-TYPE
  0              6              369
  1              2               63
[1] 2 2
[1] FALSE
D1792V8, binary
                  cls
clus                 0   1
  GOLGA1 MUTATED     4   4
  GOLGA1 WILD-TYPE 221 260
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GOLGA1 MUTATED      4    4
  GOLGA1 WILD-TYPE  221  260
        clus
vv       GOLGA1 MUTATED GOLGA1 WILD-TYPE
  FEMALE              4              221
  MALE                4              260
[1] 2 2
[1] FALSE
D1792V9, binary
                  cls
clus                 0   1
  GOLGA1 MUTATED     5   0
  GOLGA1 WILD-TYPE 345  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GOLGA1 MUTATED      5    0
  GOLGA1 WILD-TYPE  345   22
     clus
vv    GOLGA1 MUTATED GOLGA1 WILD-TYPE
  NO               5              345
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  GOLGA1 MUTATED                      5                             2
  GOLGA1 WILD-TYPE                  310                            45
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  GOLGA1 MUTATED                       1                              0
  GOLGA1 WILD-TYPE                   105                             10
D1792V10, multiclass
                                clus
vv                               GOLGA1 MUTATED GOLGA1 WILD-TYPE
  COLON ADENOCARCINOMA                        5              310
  COLON MUCINOUS ADENOCARCINOMA               2               45
  RECTAL ADENOCARCINOMA                       1              105
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  GOLGA1 MUTATED     7   0   0   0
  GOLGA1 WILD-TYPE 338   4  31  25
D1792V11, multiclass
    clus
vv   GOLGA1 MUTATED GOLGA1 WILD-TYPE
  R0              7              338
  R1              0                4
  R2              0               31
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1792V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GOLGA1 MUTATED                                  0     0
  GOLGA1 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  GOLGA1 MUTATED                           2     2
  GOLGA1 WILD-TYPE                        20   224
D1792V13, multiclass
                                  clus
vv                                 GOLGA1 MUTATED GOLGA1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     2               20
  WHITE                                         2              224
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1793) Variable = C5ORF36 MUTATION ANALYSIS
D1793V1, survival
                   sevent
clus2                 0   1
  C5ORF36 MUTATED    14   5
  C5ORF36 WILD-TYPE 364  88
  C5ORF36 MUTATED C5ORF36 WILD-TYPE 
               19               452 
  C5ORF36 MUTATED C5ORF36 WILD-TYPE 
                5                88 
$`C5ORF36 MUTATED`
TCGA-A6-2678 TCGA-A6-6780 TCGA-AA-3663 TCGA-AA-3977 TCGA-AA-A00N TCGA-AD-5900 
       42.28        20.12         6.97        25.02         4.01         0.07 
TCGA-AD-6889 TCGA-AD-6964 TCGA-AZ-6598 TCGA-AZ-6601 TCGA-CA-6717 TCGA-CA-6718 
       56.55        10.88        49.41       100.01        12.76        10.06 
TCGA-CM-5348 TCGA-D5-7000 TCGA-G4-6299 TCGA-G4-6628 TCGA-AG-3892 TCGA-CI-6619 
       22.98        10.26        74.56        79.69        13.02         6.05 
TCGA-EI-6507 
       19.96 

$`C5ORF36 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2683 
       43.76        46.65        43.76        42.90        24.33        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       21.37        15.52         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 
      106.75        22.36        62.79        88.21         6.77        12.10 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 
        3.06         3.25         3.29         0.07        12.20        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       91.79        46.75        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 
        1.02        17.95        36.95        17.03        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6620 TCGA-CI-6622 
        1.45        17.49         0.69         0.72        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
       32.61         0.49        20.55        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  C5ORF36 MUTATED C5ORF36 WILD-TYPE 
             0.07              0.00 
  C5ORF36 MUTATED C5ORF36 WILD-TYPE 
           100.01            148.01 
  C5ORF36 MUTATED C5ORF36 WILD-TYPE 
           19.960            20.415 
[1] "0.1 - 100.0 (20.0)" "0.0 - 148.0 (20.4)"
[1] "hr=" "1.1"
D1793V2, continuous
D1793V3, binary
                   cls
clus                  0   1
  C5ORF36 MUTATED    17   3
  C5ORF36 WILD-TYPE 349 116
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C5ORF36 MUTATED     17    3
  C5ORF36 WILD-TYPE  349  116
        clus
vv       C5ORF36 MUTATED C5ORF36 WILD-TYPE
  COLON               17               349
  RECTUM               3               116
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  C5ORF36 MUTATED         4        0        3         6         1         0
  C5ORF36 WILD-TYPE      87        1       29       132         9         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C5ORF36 MUTATED           0          0          2          1        1
  C5ORF36 WILD-TYPE        24         11         57         41       47
                   vv
clus                STAGE IVA STAGE IVB
  C5ORF36 MUTATED           0         0
  C5ORF36 WILD-TYPE        18         1
D1793V4, multiclass
            clus
vv           C5ORF36 MUTATED C5ORF36 WILD-TYPE
  STAGE I                  4                87
  STAGE IA                 0                 1
  STAGE II                 3                29
  STAGE IIA                6               132
  STAGE IIB                1                 9
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               0                11
  STAGE IIIB               2                57
  STAGE IIIC               1                41
  STAGE IV                 1                47
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  C5ORF36 MUTATED     1   4  13   2
  C5ORF36 WILD-TYPE  16  88 316  48
D1793V5, multiclass
    clus
vv   C5ORF36 MUTATED C5ORF36 WILD-TYPE
  T1               1                16
  T2               4                88
  T3              13               316
  T4               2                48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  C5ORF36 MUTATED    15   3   2
  C5ORF36 WILD-TYPE 272 110  85
D1793V6, multiclass
    clus
vv   C5ORF36 MUTATED C5ORF36 WILD-TYPE
  N0              15               272
  N1               3               110
  N2               2                85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1793V7, binary
                   cls
clus                  0   1
  C5ORF36 MUTATED    14   1
  C5ORF36 WILD-TYPE 361  64
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C5ORF36 MUTATED     14    1
  C5ORF36 WILD-TYPE  361   64
   clus
vv  C5ORF36 MUTATED C5ORF36 WILD-TYPE
  0              14               361
  1               1                64
[1] 2 2
[1] FALSE
D1793V8, binary
                   cls
clus                  0   1
  C5ORF36 MUTATED     5  15
  C5ORF36 WILD-TYPE 220 249
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C5ORF36 MUTATED      5   15
  C5ORF36 WILD-TYPE  220  249
        clus
vv       C5ORF36 MUTATED C5ORF36 WILD-TYPE
  FEMALE               5               220
  MALE                15               249
[1] 2 2
[1] FALSE
D1793V9, binary
                   cls
clus                  0   1
  C5ORF36 MUTATED    15   0
  C5ORF36 WILD-TYPE 335  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C5ORF36 MUTATED     15    0
  C5ORF36 WILD-TYPE  335   22
     clus
vv    C5ORF36 MUTATED C5ORF36 WILD-TYPE
  NO               15               335
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  C5ORF36 MUTATED                     12                             5
  C5ORF36 WILD-TYPE                  303                            42
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  C5ORF36 MUTATED                       3                              0
  C5ORF36 WILD-TYPE                   103                             10
D1793V10, multiclass
                                clus
vv                               C5ORF36 MUTATED C5ORF36 WILD-TYPE
  COLON ADENOCARCINOMA                        12               303
  COLON MUCINOUS ADENOCARCINOMA                5                42
  RECTAL ADENOCARCINOMA                        3               103
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  C5ORF36 MUTATED    11   0   0   2
  C5ORF36 WILD-TYPE 334   4  31  23
D1793V11, multiclass
    clus
vv   C5ORF36 MUTATED C5ORF36 WILD-TYPE
  R0              11               334
  R1               0                 4
  R2               0                31
  RX               2                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1793V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C5ORF36 MUTATED                                  0     3
  C5ORF36 WILD-TYPE                                1     8
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  C5ORF36 MUTATED                           0    12
  C5ORF36 WILD-TYPE                        22   214
D1793V13, multiclass
                                  clus
vv                                 C5ORF36 MUTATED C5ORF36 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          3                 8
  BLACK OR AFRICAN AMERICAN                      0                22
  WHITE                                         12               214
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1794) Variable = CPLX4 MUTATION ANALYSIS
D1794V1, survival
                 sevent
clus2               0   1
  CPLX4 MUTATED     3   2
  CPLX4 WILD-TYPE 375  91
  CPLX4 MUTATED CPLX4 WILD-TYPE 
              5             466 
  CPLX4 MUTATED CPLX4 WILD-TYPE 
              2              91 
$`CPLX4 MUTATED`
TCGA-AA-A010 TCGA-DM-A28G TCGA-G4-6588 TCGA-AF-5654 TCGA-AG-3599 
       34.98        60.79        26.17        16.83        12.03 

$`CPLX4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       35.97       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-6136 
       13.55        19.10        34.49        10.39        14.50        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
       34.03         2.01        50.04         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  CPLX4 MUTATED CPLX4 WILD-TYPE 
          12.03            0.00 
  CPLX4 MUTATED CPLX4 WILD-TYPE 
          60.79          148.01 
  CPLX4 MUTATED CPLX4 WILD-TYPE 
         26.170          20.155 
[1] "12.0 - 60.8 (26.2)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.8"
D1794V2, continuous
D1794V3, binary
                 cls
clus                0   1
  CPLX4 MUTATED     3   2
  CPLX4 WILD-TYPE 363 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CPLX4 MUTATED      3    2
  CPLX4 WILD-TYPE  363  117
        clus
vv       CPLX4 MUTATED CPLX4 WILD-TYPE
  COLON              3             363
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CPLX4 MUTATED         2        0        0         2         1         0
  CPLX4 WILD-TYPE      89        1       32       136         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CPLX4 MUTATED           0          0          0          0        0         0
  CPLX4 WILD-TYPE        24         11         59         42       48        18
                 vv
clus              STAGE IVB
  CPLX4 MUTATED           0
  CPLX4 WILD-TYPE         1
D1794V4, multiclass
            clus
vv           CPLX4 MUTATED CPLX4 WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              2             136
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CPLX4 MUTATED     0   2   2   1
  CPLX4 WILD-TYPE  17  90 327  49
D1794V5, multiclass
    clus
vv   CPLX4 MUTATED CPLX4 WILD-TYPE
  T1             0              17
  T2             2              90
  T3             2             327
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  CPLX4 MUTATED     5   0   0
  CPLX4 WILD-TYPE 282 113  87
D1794V6, multiclass
    clus
vv   CPLX4 MUTATED CPLX4 WILD-TYPE
  N0             5             282
  N1             0             113
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1794V7, binary
                 cls
clus                0   1
  CPLX4 MUTATED     5   0
  CPLX4 WILD-TYPE 370  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CPLX4 MUTATED      5    0
  CPLX4 WILD-TYPE  370   65
   clus
vv  CPLX4 MUTATED CPLX4 WILD-TYPE
  0             5             370
  1             0              65
[1] 2 2
[1] FALSE
D1794V8, binary
                 cls
clus                0   1
  CPLX4 MUTATED     3   2
  CPLX4 WILD-TYPE 222 262
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CPLX4 MUTATED      3    2
  CPLX4 WILD-TYPE  222  262
        clus
vv       CPLX4 MUTATED CPLX4 WILD-TYPE
  FEMALE             3             222
  MALE               2             262
[1] 2 2
[1] FALSE
D1794V9, binary
                 cls
clus                0   1
  CPLX4 MUTATED     4   0
  CPLX4 WILD-TYPE 346  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CPLX4 MUTATED      4    0
  CPLX4 WILD-TYPE  346   22
     clus
vv    CPLX4 MUTATED CPLX4 WILD-TYPE
  NO              4             346
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CPLX4 MUTATED                      3                             0
  CPLX4 WILD-TYPE                  312                            47
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CPLX4 MUTATED                       1                              0
  CPLX4 WILD-TYPE                   105                             10
D1794V10, multiclass
                                clus
vv                               CPLX4 MUTATED CPLX4 WILD-TYPE
  COLON ADENOCARCINOMA                       3             312
  COLON MUCINOUS ADENOCARCINOMA              0              47
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  CPLX4 MUTATED     4   0   0   0
  CPLX4 WILD-TYPE 341   4  31  25
D1794V11, multiclass
    clus
vv   CPLX4 MUTATED CPLX4 WILD-TYPE
  R0             4             341
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1794V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CPLX4 MUTATED                                  0     0
  CPLX4 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CPLX4 MUTATED                           0     3
  CPLX4 WILD-TYPE                        22   223
D1794V13, multiclass
                                  clus
vv                                 CPLX4 MUTATED CPLX4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        3             223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1795) Variable = TEX2 MUTATION ANALYSIS
D1795V1, survival
                sevent
clus2              0   1
  TEX2 MUTATED    10   2
  TEX2 WILD-TYPE 368  91
  TEX2 MUTATED TEX2 WILD-TYPE 
            12            459 
  TEX2 MUTATED TEX2 WILD-TYPE 
             2             91 
$`TEX2 MUTATED`
TCGA-AA-3522 TCGA-AA-A010 TCGA-AD-6889 TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-6601 
       37.05        34.98        56.55        21.44        58.39       100.01 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4950 TCGA-CM-4744 TCGA-CM-5861 TCGA-G4-6588 
       12.76        10.06        85.45        20.02        15.02        26.17 

$`TEX2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3525 
       38.99         1.02         9.07        24.03        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 
       88.21        49.41         6.77        12.10        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        3.29         0.07        12.20        14.30        17.56       148.01 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
        1.91       124.27        23.05        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 
       29.06        22.03        22.98        30.08        32.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       22.09        13.78        35.80        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  TEX2 MUTATED TEX2 WILD-TYPE 
         10.06           0.00 
  TEX2 MUTATED TEX2 WILD-TYPE 
        100.01         148.01 
  TEX2 MUTATED TEX2 WILD-TYPE 
        30.575         20.050 
[1] "10.1 - 100.0 (30.6)" "0.0 - 148.0 (20.1)" 
[1] "hr=" "1.8"
D1795V2, continuous
D1795V3, binary
                cls
clus               0   1
  TEX2 MUTATED    12   0
  TEX2 WILD-TYPE 354 119
[1] "tbl2"
                cls
clus             [,1] [,2]
  TEX2 MUTATED     12    0
  TEX2 WILD-TYPE  354  119
        clus
vv       TEX2 MUTATED TEX2 WILD-TYPE
  COLON            12            354
  RECTUM            0            119
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TEX2 MUTATED         1        0        1         8         1         0
  TEX2 WILD-TYPE      90        1       31       130         9         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TEX2 MUTATED           0          0          1          0        0         0
  TEX2 WILD-TYPE        24         11         58         42       48        18
                vv
clus             STAGE IVB
  TEX2 MUTATED           0
  TEX2 WILD-TYPE         1
D1795V4, multiclass
            clus
vv           TEX2 MUTATED TEX2 WILD-TYPE
  STAGE I               1             90
  STAGE IA              0              1
  STAGE II              1             31
  STAGE IIA             8            130
  STAGE IIB             1              9
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            1             58
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  TEX2 MUTATED     0   1  10   1
  TEX2 WILD-TYPE  17  91 319  49
D1795V5, multiclass
    clus
vv   TEX2 MUTATED TEX2 WILD-TYPE
  T1            0             17
  T2            1             91
  T3           10            319
  T4            1             49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  TEX2 MUTATED    11   1   0
  TEX2 WILD-TYPE 276 112  87
D1795V6, multiclass
    clus
vv   TEX2 MUTATED TEX2 WILD-TYPE
  N0           11            276
  N1            1            112
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1795V7, binary
                cls
clus               0   1
  TEX2 MUTATED    11   0
  TEX2 WILD-TYPE 364  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  TEX2 MUTATED     11    0
  TEX2 WILD-TYPE  364   65
   clus
vv  TEX2 MUTATED TEX2 WILD-TYPE
  0           11            364
  1            0             65
[1] 2 2
[1] FALSE
D1795V8, binary
                cls
clus               0   1
  TEX2 MUTATED     4   8
  TEX2 WILD-TYPE 221 256
[1] "tbl2"
                cls
clus             [,1] [,2]
  TEX2 MUTATED      4    8
  TEX2 WILD-TYPE  221  256
        clus
vv       TEX2 MUTATED TEX2 WILD-TYPE
  FEMALE            4            221
  MALE              8            256
[1] 2 2
[1] FALSE
D1795V9, binary
                cls
clus               0   1
  TEX2 MUTATED    11   0
  TEX2 WILD-TYPE 339  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  TEX2 MUTATED     11    0
  TEX2 WILD-TYPE  339   22
     clus
vv    TEX2 MUTATED TEX2 WILD-TYPE
  NO            11            339
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  TEX2 MUTATED                     11                             1
  TEX2 WILD-TYPE                  304                            46
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  TEX2 MUTATED                       0                              0
  TEX2 WILD-TYPE                   106                             10
D1795V10, multiclass
                                clus
vv                               TEX2 MUTATED TEX2 WILD-TYPE
  COLON ADENOCARCINOMA                     11            304
  COLON MUCINOUS ADENOCARCINOMA             1             46
  RECTAL ADENOCARCINOMA                     0            106
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  TEX2 MUTATED     7   1   0   2
  TEX2 WILD-TYPE 338   3  31  23
D1795V11, multiclass
    clus
vv   TEX2 MUTATED TEX2 WILD-TYPE
  R0            7            338
  R1            1              3
  R2            0             31
  RX            2             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1795V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TEX2 MUTATED                                  0     3
  TEX2 WILD-TYPE                                1     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  TEX2 MUTATED                           1     6
  TEX2 WILD-TYPE                        21   220
D1795V13, multiclass
                                  clus
vv                                 TEX2 MUTATED TEX2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       3              8
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                       6            220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1796) Variable = ARHGAP28 MUTATION ANALYSIS
D1796V1, survival
                    sevent
clus2                  0   1
  ARHGAP28 MUTATED    13   1
  ARHGAP28 WILD-TYPE 365  92
  ARHGAP28 MUTATED ARHGAP28 WILD-TYPE 
                14                457 
  ARHGAP28 MUTATED ARHGAP28 WILD-TYPE 
                 1                 92 
$`ARHGAP28 MUTATED`
TCGA-A6-6653 TCGA-A6-6781 TCGA-AA-3554 TCGA-AA-3715 TCGA-AA-3947 TCGA-AA-3949 
       24.39        19.66        17.95        19.04        33.01        26.01 
TCGA-AA-A00J TCGA-AA-A010 TCGA-AD-6889 TCGA-CM-4743 TCGA-CM-5861 TCGA-CM-6674 
       18.05        34.98        56.55        23.05        15.02        12.95 
TCGA-G4-6628 TCGA-AG-A002 
       79.69        20.98 

$`ARHGAP28 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
       25.08        25.18        24.16        21.76        24.69        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       24.00        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       85.05        26.99        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
        1.91       124.27        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 
       29.06        22.03        22.98        30.08        32.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       15.02        14.04        11.01        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 
       13.78        35.80        26.17        91.79        46.75        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  ARHGAP28 MUTATED ARHGAP28 WILD-TYPE 
             12.95               0.00 
  ARHGAP28 MUTATED ARHGAP28 WILD-TYPE 
             79.69             148.01 
  ARHGAP28 MUTATED ARHGAP28 WILD-TYPE 
            22.015             20.120 
[1] "12.9 - 79.7 (22.0)" "0.0 - 148.0 (20.1)"
[1] "hr=" "3"  
D1796V2, continuous
D1796V3, binary
                    cls
clus                   0   1
  ARHGAP28 MUTATED    13   1
  ARHGAP28 WILD-TYPE 353 118
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ARHGAP28 MUTATED     13    1
  ARHGAP28 WILD-TYPE  353  118
        clus
vv       ARHGAP28 MUTATED ARHGAP28 WILD-TYPE
  COLON                13                353
  RECTUM                1                118
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ARHGAP28 MUTATED         3        0        1         5         2         0
  ARHGAP28 WILD-TYPE      88        1       31       133         8         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ARHGAP28 MUTATED           0          0          2          1        0
  ARHGAP28 WILD-TYPE        24         11         57         41       48
                    vv
clus                 STAGE IVA STAGE IVB
  ARHGAP28 MUTATED           0         0
  ARHGAP28 WILD-TYPE        18         1
D1796V4, multiclass
            clus
vv           ARHGAP28 MUTATED ARHGAP28 WILD-TYPE
  STAGE I                   3                 88
  STAGE IA                  0                  1
  STAGE II                  1                 31
  STAGE IIA                 5                133
  STAGE IIB                 2                  8
  STAGE IIC                 0                  1
  STAGE III                 0                 24
  STAGE IIIA                0                 11
  STAGE IIIB                2                 57
  STAGE IIIC                1                 41
  STAGE IV                  0                 48
  STAGE IVA                 0                 18
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  ARHGAP28 MUTATED     0   3   7   4
  ARHGAP28 WILD-TYPE  17  89 322  46
D1796V5, multiclass
    clus
vv   ARHGAP28 MUTATED ARHGAP28 WILD-TYPE
  T1                0                 17
  T2                3                 89
  T3                7                322
  T4                4                 46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  ARHGAP28 MUTATED    11   3   0
  ARHGAP28 WILD-TYPE 276 110  87
D1796V6, multiclass
    clus
vv   ARHGAP28 MUTATED ARHGAP28 WILD-TYPE
  N0               11                276
  N1                3                110
  N2                0                 87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1796V7, binary
                    cls
clus                   0   1
  ARHGAP28 MUTATED    13   0
  ARHGAP28 WILD-TYPE 362  65
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ARHGAP28 MUTATED     13    0
  ARHGAP28 WILD-TYPE  362   65
   clus
vv  ARHGAP28 MUTATED ARHGAP28 WILD-TYPE
  0               13                362
  1                0                 65
[1] 2 2
[1] FALSE
D1796V8, binary
                    cls
clus                   0   1
  ARHGAP28 MUTATED     5   9
  ARHGAP28 WILD-TYPE 220 255
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ARHGAP28 MUTATED      5    9
  ARHGAP28 WILD-TYPE  220  255
        clus
vv       ARHGAP28 MUTATED ARHGAP28 WILD-TYPE
  FEMALE                5                220
  MALE                  9                255
[1] 2 2
[1] FALSE
D1796V9, binary
                    cls
clus                   0   1
  ARHGAP28 MUTATED    13   0
  ARHGAP28 WILD-TYPE 337  22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ARHGAP28 MUTATED     13    0
  ARHGAP28 WILD-TYPE  337   22
     clus
vv    ARHGAP28 MUTATED ARHGAP28 WILD-TYPE
  NO                13                337
  YES                0                 22
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ARHGAP28 MUTATED                      9                             4
  ARHGAP28 WILD-TYPE                  306                            43
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ARHGAP28 MUTATED                       1                              0
  ARHGAP28 WILD-TYPE                   105                             10
D1796V10, multiclass
                                clus
vv                               ARHGAP28 MUTATED ARHGAP28 WILD-TYPE
  COLON ADENOCARCINOMA                          9                306
  COLON MUCINOUS ADENOCARCINOMA                 4                 43
  RECTAL ADENOCARCINOMA                         1                105
  RECTAL MUCINOUS ADENOCARCINOMA                0                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  ARHGAP28 MUTATED    12   0   0   0
  ARHGAP28 WILD-TYPE 333   4  31  25
D1796V11, multiclass
    clus
vv   ARHGAP28 MUTATED ARHGAP28 WILD-TYPE
  R0               12                333
  R1                0                  4
  R2                0                 31
  RX                0                 25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1796V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ARHGAP28 MUTATED                                  0     1
  ARHGAP28 WILD-TYPE                                1    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  ARHGAP28 MUTATED                           0     6
  ARHGAP28 WILD-TYPE                        22   220
D1796V13, multiclass
                                  clus
vv                                 ARHGAP28 MUTATED ARHGAP28 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                 10
  BLACK OR AFRICAN AMERICAN                       0                 22
  WHITE                                           6                220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1797) Variable = STK33 MUTATION ANALYSIS
D1797V1, survival
                 sevent
clus2               0   1
  STK33 MUTATED    13   3
  STK33 WILD-TYPE 365  90
  STK33 MUTATED STK33 WILD-TYPE 
             16             455 
  STK33 MUTATED STK33 WILD-TYPE 
              3              90 
$`STK33 MUTATED`
TCGA-AA-3662 TCGA-AA-3815 TCGA-AA-3947 TCGA-AA-A010 TCGA-AU-6004 TCGA-AZ-6599 
        6.05        33.04        33.01        34.98        27.09         6.77 
TCGA-AZ-6601 TCGA-CA-6716 TCGA-CA-6717 TCGA-CM-5344 TCGA-CM-6166 TCGA-D5-6537 
      100.01        12.20        12.76        22.03        21.99         4.80 
TCGA-G4-6304 TCGA-AG-3742 TCGA-AH-6549 TCGA-G5-6641 
       53.62         0.99        17.49        26.43 

$`STK33 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       10.06        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       12.99        24.00        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       14.50        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       88.21        49.41        12.10        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.07        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       13.02        29.06        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
        2.96        29.03        16.04        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       43.27        15.12        17.85        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 
       35.31       133.18        74.56        65.85        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3878 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 
       38.04       117.11        38.56         1.45         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       28.57        32.19         0.66         0.69        55.76 

  STK33 MUTATED STK33 WILD-TYPE 
           0.99            0.00 
  STK33 MUTATED STK33 WILD-TYPE 
         100.01          148.01 
  STK33 MUTATED STK33 WILD-TYPE 
          22.01           20.12 
[1] "1.0 - 100.0 (22.0)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1"  
D1797V2, continuous
D1797V3, binary
                 cls
clus                0   1
  STK33 MUTATED    13   3
  STK33 WILD-TYPE 353 116
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STK33 MUTATED     13    3
  STK33 WILD-TYPE  353  116
        clus
vv       STK33 MUTATED STK33 WILD-TYPE
  COLON             13             353
  RECTUM             3             116
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  STK33 MUTATED         4        0        1         3         3         0
  STK33 WILD-TYPE      87        1       31       135         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  STK33 MUTATED           0          1          2          0        1         0
  STK33 WILD-TYPE        24         10         57         42       47        18
                 vv
clus              STAGE IVB
  STK33 MUTATED           0
  STK33 WILD-TYPE         1
D1797V4, multiclass
            clus
vv           STK33 MUTATED STK33 WILD-TYPE
  STAGE I                4              87
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              3             135
  STAGE IIB              3               7
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             1              10
  STAGE IIIB             2              57
  STAGE IIIC             0              42
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  STK33 MUTATED     2   3   7   4
  STK33 WILD-TYPE  15  89 322  46
D1797V5, multiclass
    clus
vv   STK33 MUTATED STK33 WILD-TYPE
  T1             2              15
  T2             3              89
  T3             7             322
  T4             4              46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  STK33 MUTATED    11   3   1
  STK33 WILD-TYPE 276 110  86
D1797V6, multiclass
    clus
vv   STK33 MUTATED STK33 WILD-TYPE
  N0            11             276
  N1             3             110
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1797V7, binary
                 cls
clus                0   1
  STK33 MUTATED    11   1
  STK33 WILD-TYPE 364  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STK33 MUTATED     11    1
  STK33 WILD-TYPE  364   64
   clus
vv  STK33 MUTATED STK33 WILD-TYPE
  0            11             364
  1             1              64
[1] 2 2
[1] FALSE
D1797V8, binary
                 cls
clus                0   1
  STK33 MUTATED     9   7
  STK33 WILD-TYPE 216 257
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STK33 MUTATED      9    7
  STK33 WILD-TYPE  216  257
        clus
vv       STK33 MUTATED STK33 WILD-TYPE
  FEMALE             9             216
  MALE               7             257
[1] 2 2
[1] FALSE
D1797V9, binary
                 cls
clus                0   1
  STK33 MUTATED    14   0
  STK33 WILD-TYPE 336  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STK33 MUTATED     14    0
  STK33 WILD-TYPE  336   22
     clus
vv    STK33 MUTATED STK33 WILD-TYPE
  NO             14             336
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  STK33 MUTATED                     11                             2
  STK33 WILD-TYPE                  304                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  STK33 MUTATED                       2                              1
  STK33 WILD-TYPE                   104                              9
D1797V10, multiclass
                                clus
vv                               STK33 MUTATED STK33 WILD-TYPE
  COLON ADENOCARCINOMA                      11             304
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             1               9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  STK33 MUTATED    10   0   1   3
  STK33 WILD-TYPE 335   4  30  22
D1797V11, multiclass
    clus
vv   STK33 MUTATED STK33 WILD-TYPE
  R0            10             335
  R1             0               4
  R2             1              30
  RX             3              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1797V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  STK33 MUTATED                                  0     2
  STK33 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  STK33 MUTATED                           0     9
  STK33 WILD-TYPE                        22   217
D1797V13, multiclass
                                  clus
vv                                 STK33 MUTATED STK33 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               9
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        9             217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1798) Variable = GNG12 MUTATION ANALYSIS
D1798V1, survival
                 sevent
clus2               0   1
  GNG12 MUTATED     7   1
  GNG12 WILD-TYPE 371  92
  GNG12 MUTATED GNG12 WILD-TYPE 
              8             463 
  GNG12 MUTATED GNG12 WILD-TYPE 
              1              92 
$`GNG12 MUTATED`
TCGA-A6-5665 TCGA-A6-6781 TCGA-AA-3663 TCGA-AD-6889 TCGA-AZ-6598 TCGA-DM-A1HB 
       22.06        19.66         6.97        56.55        49.41       135.65 
TCGA-G4-6586 TCGA-G4-6628 
       35.80        79.69 

$`GNG12 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 
       18.05        40.96         0.07        21.37        15.52         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        88.21         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
        7.50        44.32       131.51       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 
       13.78        26.17        91.79        46.75        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  GNG12 MUTATED GNG12 WILD-TYPE 
           6.97            0.00 
  GNG12 MUTATED GNG12 WILD-TYPE 
         135.65          148.01 
  GNG12 MUTATED GNG12 WILD-TYPE 
         42.605          20.050 
[1] "7.0 - 135.7 (42.6)" "0.0 - 148.0 (20.1)"
[1] "hr=" "2.9"
D1798V2, continuous
D1798V3, binary
                 cls
clus                0   1
  GNG12 MUTATED     8   0
  GNG12 WILD-TYPE 358 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GNG12 MUTATED      8    0
  GNG12 WILD-TYPE  358  119
        clus
vv       GNG12 MUTATED GNG12 WILD-TYPE
  COLON              8             358
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GNG12 MUTATED         1        0        2         3         0         0
  GNG12 WILD-TYPE      90        1       30       135        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  GNG12 MUTATED           0          0          1          1        0         0
  GNG12 WILD-TYPE        24         11         58         41       48        18
                 vv
clus              STAGE IVB
  GNG12 MUTATED           0
  GNG12 WILD-TYPE         1
D1798V4, multiclass
            clus
vv           GNG12 MUTATED GNG12 WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA              3             135
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             1              41
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  GNG12 MUTATED     0   1   6   1
  GNG12 WILD-TYPE  17  91 323  49
D1798V5, multiclass
    clus
vv   GNG12 MUTATED GNG12 WILD-TYPE
  T1             0              17
  T2             1              91
  T3             6             323
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  GNG12 MUTATED     6   2   0
  GNG12 WILD-TYPE 281 111  87
D1798V6, multiclass
    clus
vv   GNG12 MUTATED GNG12 WILD-TYPE
  N0             6             281
  N1             2             111
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1798V7, binary
                 cls
clus                0   1
  GNG12 MUTATED     6   0
  GNG12 WILD-TYPE 369  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GNG12 MUTATED      6    0
  GNG12 WILD-TYPE  369   65
   clus
vv  GNG12 MUTATED GNG12 WILD-TYPE
  0             6             369
  1             0              65
[1] 2 2
[1] FALSE
D1798V8, binary
                 cls
clus                0   1
  GNG12 MUTATED     3   5
  GNG12 WILD-TYPE 222 259
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GNG12 MUTATED      3    5
  GNG12 WILD-TYPE  222  259
        clus
vv       GNG12 MUTATED GNG12 WILD-TYPE
  FEMALE             3             222
  MALE               5             259
[1] 2 2
[1] FALSE
D1798V9, binary
                 cls
clus                0   1
  GNG12 MUTATED     6   0
  GNG12 WILD-TYPE 344  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GNG12 MUTATED      6    0
  GNG12 WILD-TYPE  344   22
     clus
vv    GNG12 MUTATED GNG12 WILD-TYPE
  NO              6             344
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  GNG12 MUTATED                      6                             1
  GNG12 WILD-TYPE                  309                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  GNG12 MUTATED                       0                              0
  GNG12 WILD-TYPE                   106                             10
D1798V10, multiclass
                                clus
vv                               GNG12 MUTATED GNG12 WILD-TYPE
  COLON ADENOCARCINOMA                       6             309
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  GNG12 MUTATED     5   0   0   0
  GNG12 WILD-TYPE 340   4  31  25
D1798V11, multiclass
    clus
vv   GNG12 MUTATED GNG12 WILD-TYPE
  R0             5             340
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1798V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GNG12 MUTATED                                  0     1
  GNG12 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  GNG12 MUTATED                           0     6
  GNG12 WILD-TYPE                        22   220
D1798V13, multiclass
                                  clus
vv                                 GNG12 MUTATED GNG12 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        6             220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1799) Variable = FAM70A MUTATION ANALYSIS
D1799V1, survival
                  sevent
clus2                0   1
  FAM70A MUTATED     6   2
  FAM70A WILD-TYPE 372  91
  FAM70A MUTATED FAM70A WILD-TYPE 
               8              463 
  FAM70A MUTATED FAM70A WILD-TYPE 
               2               91 
$`FAM70A MUTATED`
TCGA-AA-3660 TCGA-AA-A00N TCGA-AD-6889 TCGA-AZ-4315 TCGA-CA-6717 TCGA-D5-6537 
       78.08         4.01        56.55        58.39        12.76         4.80 
TCGA-G4-6317 TCGA-AG-3892 
       36.00        13.02 

$`FAM70A WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 
       20.98        19.99        13.94        19.99        61.02         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07        12.20        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       43.27        15.12        17.85        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6321 TCGA-G4-6323 
       55.04        85.48        63.62        61.91        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       17.03        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  FAM70A MUTATED FAM70A WILD-TYPE 
            4.01             0.00 
  FAM70A MUTATED FAM70A WILD-TYPE 
           78.08           148.01 
  FAM70A MUTATED FAM70A WILD-TYPE 
           24.51            20.19 
[1] "4.0 - 78.1 (24.5)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1"  
D1799V2, continuous
D1799V3, binary
                  cls
clus                 0   1
  FAM70A MUTATED     7   1
  FAM70A WILD-TYPE 359 118
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM70A MUTATED      7    1
  FAM70A WILD-TYPE  359  118
        clus
vv       FAM70A MUTATED FAM70A WILD-TYPE
  COLON               7              359
  RECTUM              1              118
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FAM70A MUTATED         1        0        1         3         1         0
  FAM70A WILD-TYPE      90        1       31       135         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FAM70A MUTATED           0          0          1          1        0
  FAM70A WILD-TYPE        24         11         58         41       48
                  vv
clus               STAGE IVA STAGE IVB
  FAM70A MUTATED           0         0
  FAM70A WILD-TYPE        18         1
D1799V4, multiclass
            clus
vv           FAM70A MUTATED FAM70A WILD-TYPE
  STAGE I                 1               90
  STAGE IA                0                1
  STAGE II                1               31
  STAGE IIA               3              135
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              1               58
  STAGE IIIC              1               41
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  FAM70A MUTATED     1   0   6   1
  FAM70A WILD-TYPE  16  92 323  49
D1799V5, multiclass
    clus
vv   FAM70A MUTATED FAM70A WILD-TYPE
  T1              1               16
  T2              0               92
  T3              6              323
  T4              1               49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  FAM70A MUTATED     6   1   1
  FAM70A WILD-TYPE 281 112  86
D1799V6, multiclass
    clus
vv   FAM70A MUTATED FAM70A WILD-TYPE
  N0              6              281
  N1              1              112
  N2              1               86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1799V7, binary
                  cls
clus                 0   1
  FAM70A MUTATED     6   0
  FAM70A WILD-TYPE 369  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM70A MUTATED      6    0
  FAM70A WILD-TYPE  369   65
   clus
vv  FAM70A MUTATED FAM70A WILD-TYPE
  0              6              369
  1              0               65
[1] 2 2
[1] FALSE
D1799V8, binary
                  cls
clus                 0   1
  FAM70A MUTATED     3   5
  FAM70A WILD-TYPE 222 259
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM70A MUTATED      3    5
  FAM70A WILD-TYPE  222  259
        clus
vv       FAM70A MUTATED FAM70A WILD-TYPE
  FEMALE              3              222
  MALE                5              259
[1] 2 2
[1] FALSE
D1799V9, binary
                  cls
clus                 0   1
  FAM70A MUTATED     6   0
  FAM70A WILD-TYPE 344  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM70A MUTATED      6    0
  FAM70A WILD-TYPE  344   22
     clus
vv    FAM70A MUTATED FAM70A WILD-TYPE
  NO               6              344
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  FAM70A MUTATED                      5                             2
  FAM70A WILD-TYPE                  310                            45
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  FAM70A MUTATED                       1                              0
  FAM70A WILD-TYPE                   105                             10
D1799V10, multiclass
                                clus
vv                               FAM70A MUTATED FAM70A WILD-TYPE
  COLON ADENOCARCINOMA                        5              310
  COLON MUCINOUS ADENOCARCINOMA               2               45
  RECTAL ADENOCARCINOMA                       1              105
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  FAM70A MUTATED     6   0   0   1
  FAM70A WILD-TYPE 339   4  31  24
D1799V11, multiclass
    clus
vv   FAM70A MUTATED FAM70A WILD-TYPE
  R0              6              339
  R1              0                4
  R2              0               31
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1799V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FAM70A MUTATED                                  0     2
  FAM70A WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  FAM70A MUTATED                           0     3
  FAM70A WILD-TYPE                        22   223
D1799V13, multiclass
                                  clus
vv                                 FAM70A MUTATED FAM70A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                9
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         3              223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1800) Variable = ACPP MUTATION ANALYSIS
D1800V1, survival
                sevent
clus2              0   1
  ACPP MUTATED     3   0
  ACPP WILD-TYPE 375  93
  ACPP MUTATED ACPP WILD-TYPE 
             3            468 
  ACPP MUTATED ACPP WILD-TYPE 
             0             93 
$`ACPP MUTATED`
TCGA-AA-3977 TCGA-AA-A00A TCGA-AG-A002 
       25.02        38.04        20.98 

$`ACPP WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  ACPP MUTATED ACPP WILD-TYPE 
         20.98           0.00 
  ACPP MUTATED ACPP WILD-TYPE 
         38.04         148.01 
  ACPP MUTATED ACPP WILD-TYPE 
        25.020         20.085 
[1] "21.0 - 38.0 (25.0)" "0.0 - 148.0 (20.1)"
[1] "hr="     "3300000"
D1800V2, continuous
D1800V3, binary
                cls
clus               0   1
  ACPP MUTATED     3   1
  ACPP WILD-TYPE 363 118
[1] "tbl2"
                cls
clus             [,1] [,2]
  ACPP MUTATED      3    1
  ACPP WILD-TYPE  363  118
        clus
vv       ACPP MUTATED ACPP WILD-TYPE
  COLON             3            363
  RECTUM            1            118
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ACPP MUTATED         1        0        0         2         0         0
  ACPP WILD-TYPE      90        1       32       136        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ACPP MUTATED           0          0          0          0        0         0
  ACPP WILD-TYPE        24         11         59         42       48        18
                vv
clus             STAGE IVB
  ACPP MUTATED           0
  ACPP WILD-TYPE         1
D1800V4, multiclass
            clus
vv           ACPP MUTATED ACPP WILD-TYPE
  STAGE I               1             90
  STAGE IA              0              1
  STAGE II              0             32
  STAGE IIA             2            136
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            0             59
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  ACPP MUTATED     0   2   2   0
  ACPP WILD-TYPE  17  90 327  50
D1800V5, multiclass
    clus
vv   ACPP MUTATED ACPP WILD-TYPE
  T1            0             17
  T2            2             90
  T3            2            327
  T4            0             50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  ACPP MUTATED     4   0   0
  ACPP WILD-TYPE 283 113  87
D1800V6, multiclass
    clus
vv   ACPP MUTATED ACPP WILD-TYPE
  N0            4            283
  N1            0            113
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1800V7, binary
                cls
clus               0   1
  ACPP MUTATED     3   0
  ACPP WILD-TYPE 372  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  ACPP MUTATED      3    0
  ACPP WILD-TYPE  372   65
   clus
vv  ACPP MUTATED ACPP WILD-TYPE
  0            3            372
  1            0             65
[1] 2 2
[1] FALSE
D1800V8, binary
                cls
clus               0   1
  ACPP MUTATED     1   3
  ACPP WILD-TYPE 224 261
[1] "tbl2"
                cls
clus             [,1] [,2]
  ACPP MUTATED      1    3
  ACPP WILD-TYPE  224  261
        clus
vv       ACPP MUTATED ACPP WILD-TYPE
  FEMALE            1            224
  MALE              3            261
[1] 2 2
[1] FALSE
D1800V9, binary
                cls
clus               0   1
  ACPP MUTATED     3   0
  ACPP WILD-TYPE 347  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  ACPP MUTATED      3    0
  ACPP WILD-TYPE  347   22
     clus
vv    ACPP MUTATED ACPP WILD-TYPE
  NO             3            347
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ACPP MUTATED                      3                             0
  ACPP WILD-TYPE                  312                            47
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ACPP MUTATED                       1                              0
  ACPP WILD-TYPE                   105                             10
D1800V10, multiclass
                                clus
vv                               ACPP MUTATED ACPP WILD-TYPE
  COLON ADENOCARCINOMA                      3            312
  COLON MUCINOUS ADENOCARCINOMA             0             47
  RECTAL ADENOCARCINOMA                     1            105
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  ACPP MUTATED     3   0   0   0
  ACPP WILD-TYPE 342   4  31  25
D1800V11, multiclass
    clus
vv   ACPP MUTATED ACPP WILD-TYPE
  R0            3            342
  R1            0              4
  R2            0             31
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1800V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ACPP MUTATED                                  0     0
  ACPP WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  ACPP MUTATED                           0     0
  ACPP WILD-TYPE                        22   226
D1800V13, multiclass

Clustering(1801) Variable = RUNDC2A MUTATION ANALYSIS
D1801V1, survival
                   sevent
clus2                 0   1
  RUNDC2A MUTATED     6   1
  RUNDC2A WILD-TYPE 372  92
  RUNDC2A MUTATED RUNDC2A WILD-TYPE 
                7               464 
  RUNDC2A MUTATED RUNDC2A WILD-TYPE 
                1                92 
$`RUNDC2A MUTATED`
TCGA-AA-3510 TCGA-AA-3655 TCGA-AA-A00N TCGA-AZ-4315 TCGA-CM-6674 TCGA-AG-A002 
       63.98        61.02         4.01        58.39        12.95        20.98 
TCGA-AG-A014 
       15.95 

$`RUNDC2A WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       19.99        13.94        19.99        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6676 
       13.02        15.02        14.04        11.01        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       23.01        37.02        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  RUNDC2A MUTATED RUNDC2A WILD-TYPE 
             4.01              0.00 
  RUNDC2A MUTATED RUNDC2A WILD-TYPE 
            63.98            148.01 
  RUNDC2A MUTATED RUNDC2A WILD-TYPE 
           20.980            20.155 
[1] "4.0 - 64.0 (21.0)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "2"  
D1801V2, continuous
D1801V3, binary
                   cls
clus                  0   1
  RUNDC2A MUTATED     5   2
  RUNDC2A WILD-TYPE 361 117
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RUNDC2A MUTATED      5    2
  RUNDC2A WILD-TYPE  361  117
        clus
vv       RUNDC2A MUTATED RUNDC2A WILD-TYPE
  COLON                5               361
  RECTUM               2               117
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RUNDC2A MUTATED         2        0        2         2         1         0
  RUNDC2A WILD-TYPE      89        1       30       136         9         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RUNDC2A MUTATED           0          0          0          0        0
  RUNDC2A WILD-TYPE        24         11         59         42       48
                   vv
clus                STAGE IVA STAGE IVB
  RUNDC2A MUTATED           0         0
  RUNDC2A WILD-TYPE        18         1
D1801V4, multiclass
            clus
vv           RUNDC2A MUTATED RUNDC2A WILD-TYPE
  STAGE I                  2                89
  STAGE IA                 0                 1
  STAGE II                 2                30
  STAGE IIA                2               136
  STAGE IIB                1                 9
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               0                11
  STAGE IIIB               0                59
  STAGE IIIC               0                42
  STAGE IV                 0                48
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  RUNDC2A MUTATED     0   2   4   1
  RUNDC2A WILD-TYPE  17  90 325  49
D1801V5, multiclass
    clus
vv   RUNDC2A MUTATED RUNDC2A WILD-TYPE
  T1               0                17
  T2               2                90
  T3               4               325
  T4               1                49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  RUNDC2A MUTATED     7   0   0
  RUNDC2A WILD-TYPE 280 113  87
D1801V6, multiclass
    clus
vv   RUNDC2A MUTATED RUNDC2A WILD-TYPE
  N0               7               280
  N1               0               113
  N2               0                87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1801V7, binary
                   cls
clus                  0   1
  RUNDC2A MUTATED     7   0
  RUNDC2A WILD-TYPE 368  65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RUNDC2A MUTATED      7    0
  RUNDC2A WILD-TYPE  368   65
   clus
vv  RUNDC2A MUTATED RUNDC2A WILD-TYPE
  0               7               368
  1               0                65
[1] 2 2
[1] FALSE
D1801V8, binary
                   cls
clus                  0   1
  RUNDC2A MUTATED     0   7
  RUNDC2A WILD-TYPE 225 257
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RUNDC2A MUTATED      0    7
  RUNDC2A WILD-TYPE  225  257
        clus
vv       RUNDC2A MUTATED RUNDC2A WILD-TYPE
  FEMALE               0               225
  MALE                 7               257
[1] 2 2
[1] FALSE
D1801V9, binary
                   cls
clus                  0   1
  RUNDC2A MUTATED     5   0
  RUNDC2A WILD-TYPE 345  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RUNDC2A MUTATED      5    0
  RUNDC2A WILD-TYPE  345   22
     clus
vv    RUNDC2A MUTATED RUNDC2A WILD-TYPE
  NO                5               345
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  RUNDC2A MUTATED                      4                             1
  RUNDC2A WILD-TYPE                  311                            46
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  RUNDC2A MUTATED                       2                              0
  RUNDC2A WILD-TYPE                   104                             10
D1801V10, multiclass
                                clus
vv                               RUNDC2A MUTATED RUNDC2A WILD-TYPE
  COLON ADENOCARCINOMA                         4               311
  COLON MUCINOUS ADENOCARCINOMA                1                46
  RECTAL ADENOCARCINOMA                        2               104
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  RUNDC2A MUTATED     7   0   0   0
  RUNDC2A WILD-TYPE 338   4  31  25
D1801V11, multiclass
    clus
vv   RUNDC2A MUTATED RUNDC2A WILD-TYPE
  R0               7               338
  R1               0                 4
  R2               0                31
  RX               0                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1801V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RUNDC2A MUTATED                                  0     0
  RUNDC2A WILD-TYPE                                1    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  RUNDC2A MUTATED                           0     2
  RUNDC2A WILD-TYPE                        22   224
D1801V13, multiclass
[1] "Remove cluster labels:" "RUNDC2A MUTATED"       
clus
  RUNDC2A MUTATED RUNDC2A WILD-TYPE 
                2               258 
       TCGA-A6-2671        TCGA-A6-2672        TCGA-A6-2674        TCGA-A6-2676 
"RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" 
       TCGA-A6-2677        TCGA-A6-2678        TCGA-A6-2683        TCGA-A6-3807 
"RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" 
       TCGA-A6-3808        TCGA-A6-3809        TCGA-A6-3810        TCGA-A6-4105 
"RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" 
       TCGA-A6-5656        TCGA-A6-5657        TCGA-A6-5659        TCGA-A6-5660 
"RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" 
       TCGA-A6-5661        TCGA-A6-5662        TCGA-A6-5664        TCGA-A6-5665 
"RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" 
       TCGA-A6-5666        TCGA-A6-6137        TCGA-A6-6138        TCGA-A6-6141 
"RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" 
       TCGA-A6-6142        TCGA-A6-6648        TCGA-A6-6649        TCGA-A6-6651 
"RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" 
       TCGA-A6-6652        TCGA-A6-6653        TCGA-A6-6654        TCGA-A6-6780 
"RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" 
       TCGA-A6-6781        TCGA-A6-6782        TCGA-AD-5900        TCGA-AD-6548 
"RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" 
       TCGA-AD-6888        TCGA-AD-6889        TCGA-AD-6890        TCGA-AD-6895 
"RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" 
       TCGA-AD-6899        TCGA-AD-6901        TCGA-AD-6963        TCGA-AD-6964 
"RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" 
       TCGA-AD-6965        TCGA-AU-3779        TCGA-AU-6004        TCGA-AY-4070 
"RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" 
       TCGA-AY-4071        TCGA-AY-5543        TCGA-AY-6196        TCGA-AY-6197 
"RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" 
       TCGA-AY-6386        TCGA-AZ-4323        TCGA-AZ-4616        TCGA-AZ-4681 
"RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" 
       TCGA-AZ-4682        TCGA-AZ-5403        TCGA-AZ-5407        TCGA-AZ-6598 
"RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" 
       TCGA-AZ-6599        TCGA-AZ-6600        TCGA-AZ-6601        TCGA-AZ-6603 
"RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" 
       TCGA-AZ-6605        TCGA-AZ-6606        TCGA-AZ-6607        TCGA-AZ-6608 
"RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" 
       TCGA-CA-5254        TCGA-CA-5255        TCGA-CA-5796        TCGA-CA-5797 
"RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" 
       TCGA-CA-6715        TCGA-CA-6716        TCGA-CA-6717        TCGA-CA-6718 
"RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" 
       TCGA-CA-6719        TCGA-CK-4947        TCGA-CK-4948        TCGA-CK-4950 
"RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" 
       TCGA-CK-4952        TCGA-CK-5912        TCGA-CK-5913        TCGA-CK-5914 
"RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" 
       TCGA-CK-5915        TCGA-CK-5916        TCGA-CK-6746        TCGA-CK-6747 
"RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" 
       TCGA-CK-6748        TCGA-CK-6751        TCGA-CM-4743        TCGA-CM-4744 
"RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" 
       TCGA-CM-4746        TCGA-CM-4747        TCGA-CM-4752        TCGA-CM-5341 
"RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" 
       TCGA-CM-5344        TCGA-CM-5348        TCGA-CM-5349        TCGA-CM-5860 
"RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" 
       TCGA-CM-5861        TCGA-CM-5862        TCGA-CM-5863        TCGA-CM-5864 
"RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" 
       TCGA-CM-5868        TCGA-CM-6161        TCGA-CM-6162        TCGA-CM-6163 
"RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" 
       TCGA-CM-6164        TCGA-CM-6165        TCGA-CM-6166        TCGA-CM-6167 
"RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" 
       TCGA-CM-6168        TCGA-CM-6169        TCGA-CM-6170        TCGA-CM-6171 
"RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" 
       TCGA-CM-6172        TCGA-CM-6675        TCGA-CM-6676        TCGA-CM-6677 
"RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" 
       TCGA-CM-6678        TCGA-CM-6679        TCGA-CM-6680        TCGA-D5-5537 
"RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" 
       TCGA-D5-5538        TCGA-D5-5539        TCGA-D5-5540        TCGA-D5-5541 
"RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" 
       TCGA-D5-6529        TCGA-D5-6532        TCGA-D5-6533        TCGA-D5-6534 
"RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" 
       TCGA-D5-6535        TCGA-D5-6536        TCGA-D5-6537        TCGA-D5-6538 
"RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" 
       TCGA-D5-6539        TCGA-D5-6540        TCGA-D5-6541        TCGA-D5-6898 
"RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" 
       TCGA-D5-6920        TCGA-D5-6922        TCGA-D5-6923        TCGA-D5-6924 
"RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" 
       TCGA-D5-6926        TCGA-D5-6927        TCGA-D5-6928        TCGA-D5-6929 
"RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" 
       TCGA-D5-6930        TCGA-D5-6931        TCGA-D5-6932        TCGA-D5-7000 
"RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" 
       TCGA-DM-A0X9        TCGA-DM-A0XD        TCGA-DM-A0XF        TCGA-DM-A1D0 
"RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" 
       TCGA-DM-A1D4        TCGA-DM-A1D6        TCGA-DM-A1D7        TCGA-DM-A1D8 
"RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" 
       TCGA-DM-A1D9        TCGA-DM-A1DA        TCGA-DM-A1DB        TCGA-DM-A1HA 
"RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" 
       TCGA-DM-A1HB        TCGA-DM-A282        TCGA-DM-A285        TCGA-DM-A28C 
"RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" 
       TCGA-DM-A28E        TCGA-DM-A28F        TCGA-DM-A28G        TCGA-DM-A28H 
"RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" 
       TCGA-DM-A28K        TCGA-F4-6459        TCGA-F4-6460        TCGA-F4-6569 
"RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" 
       TCGA-F4-6570        TCGA-F4-6703        TCGA-F4-6704        TCGA-F4-6805 
"RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" 
       TCGA-F4-6806        TCGA-F4-6807        TCGA-F4-6808        TCGA-F4-6809 
"RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" 
       TCGA-F4-6854        TCGA-F4-6855        TCGA-F4-6856        TCGA-G4-6293 
"RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" 
       TCGA-G4-6299        TCGA-G4-6303        TCGA-G4-6304        TCGA-G4-6306 
"RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" 
       TCGA-G4-6307        TCGA-G4-6309        TCGA-G4-6310        TCGA-G4-6315 
"RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" 
       TCGA-G4-6317        TCGA-G4-6321        TCGA-G4-6323        TCGA-G4-6586 
"RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" 
       TCGA-G4-6588        TCGA-G4-6625        TCGA-G4-6626        TCGA-G4-6628 
"RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2691        TCGA-AF-2692 
"RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" 
       TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3913        TCGA-AF-4110 
"RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" 
       TCGA-AF-5654        TCGA-AF-6136        TCGA-AF-6655        TCGA-AF-6672 
"RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6549        TCGA-AH-6643 
"RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" 
       TCGA-AH-6644        TCGA-CI-6619        TCGA-CI-6620        TCGA-CI-6621 
"RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" 
       TCGA-CI-6622        TCGA-CI-6624        TCGA-CL-5917        TCGA-CL-5918 
"RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" 
       TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6155        TCGA-DC-6157 
"RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" 
       TCGA-DC-6158        TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682 
"RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" 
       TCGA-DC-6683        TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC 
"RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" 
       TCGA-DY-A1DD        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" 
       TCGA-EF-5830        TCGA-EI-6506        TCGA-EI-6507        TCGA-EI-6508 
"RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" 
       TCGA-EI-6510        TCGA-F5-6464        TCGA-F5-6465        TCGA-F5-6571 
"RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" 
       TCGA-F5-6702        TCGA-F5-6811        TCGA-F5-6812        TCGA-F5-6813 
"RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" 
       TCGA-G5-6235        TCGA-G5-6641 
"RUNDC2A WILD-TYPE" "RUNDC2A WILD-TYPE" 

Clustering(1802) Variable = IMMT MUTATION ANALYSIS
D1802V1, survival
                sevent
clus2              0   1
  IMMT MUTATED     8   0
  IMMT WILD-TYPE 370  93
  IMMT MUTATED IMMT WILD-TYPE 
             8            463 
  IMMT MUTATED IMMT WILD-TYPE 
             0             93 
$`IMMT MUTATED`
TCGA-AA-3950 TCGA-AA-3966 TCGA-AA-3977 TCGA-AA-A010 TCGA-CM-4752 TCGA-G4-6299 
       24.00         2.01        25.02        34.98        13.02        74.56 
TCGA-AG-3892 TCGA-AG-A002 
       13.02        20.98 

$`IMMT WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
        2.01        20.98        34.03        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-5341 
      124.27        23.05        20.02        37.02        25.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       47.41        35.31       133.18        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       36.95        17.03        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  IMMT MUTATED IMMT WILD-TYPE 
          2.01           0.00 
  IMMT MUTATED IMMT WILD-TYPE 
         74.56         148.01 
  IMMT MUTATED IMMT WILD-TYPE 
         22.49          20.12 
[1] "2.0 - 74.6 (22.5)"  "0.0 - 148.0 (20.1)"
[1] "hr="     "9100000"
D1802V2, continuous
D1802V3, binary
                cls
clus               0   1
  IMMT MUTATED     6   2
  IMMT WILD-TYPE 360 117
[1] "tbl2"
                cls
clus             [,1] [,2]
  IMMT MUTATED      6    2
  IMMT WILD-TYPE  360  117
        clus
vv       IMMT MUTATED IMMT WILD-TYPE
  COLON             6            360
  RECTUM            2            117
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  IMMT MUTATED         2        0        0         3         1         0
  IMMT WILD-TYPE      89        1       32       135         9         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  IMMT MUTATED           0          0          0          1        0         0
  IMMT WILD-TYPE        24         11         59         41       48        18
                vv
clus             STAGE IVB
  IMMT MUTATED           0
  IMMT WILD-TYPE         1
D1802V4, multiclass
            clus
vv           IMMT MUTATED IMMT WILD-TYPE
  STAGE I               2             89
  STAGE IA              0              1
  STAGE II              0             32
  STAGE IIA             3            135
  STAGE IIB             1              9
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            0             59
  STAGE IIIC            1             41
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  IMMT MUTATED     1   2   4   1
  IMMT WILD-TYPE  16  90 325  49
D1802V5, multiclass
    clus
vv   IMMT MUTATED IMMT WILD-TYPE
  T1            1             16
  T2            2             90
  T3            4            325
  T4            1             49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  IMMT MUTATED     7   0   1
  IMMT WILD-TYPE 280 113  86
D1802V6, multiclass
    clus
vv   IMMT MUTATED IMMT WILD-TYPE
  N0            7            280
  N1            0            113
  N2            1             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1802V7, binary
                cls
clus               0   1
  IMMT MUTATED     7   0
  IMMT WILD-TYPE 368  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  IMMT MUTATED      7    0
  IMMT WILD-TYPE  368   65
   clus
vv  IMMT MUTATED IMMT WILD-TYPE
  0            7            368
  1            0             65
[1] 2 2
[1] FALSE
D1802V8, binary
                cls
clus               0   1
  IMMT MUTATED     4   4
  IMMT WILD-TYPE 221 260
[1] "tbl2"
                cls
clus             [,1] [,2]
  IMMT MUTATED      4    4
  IMMT WILD-TYPE  221  260
        clus
vv       IMMT MUTATED IMMT WILD-TYPE
  FEMALE            4            221
  MALE              4            260
[1] 2 2
[1] FALSE
D1802V9, binary
                cls
clus               0   1
  IMMT MUTATED     7   0
  IMMT WILD-TYPE 343  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  IMMT MUTATED      7    0
  IMMT WILD-TYPE  343   22
     clus
vv    IMMT MUTATED IMMT WILD-TYPE
  NO             7            343
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  IMMT MUTATED                      4                             2
  IMMT WILD-TYPE                  311                            45
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  IMMT MUTATED                       2                              0
  IMMT WILD-TYPE                   104                             10
D1802V10, multiclass
                                clus
vv                               IMMT MUTATED IMMT WILD-TYPE
  COLON ADENOCARCINOMA                      4            311
  COLON MUCINOUS ADENOCARCINOMA             2             45
  RECTAL ADENOCARCINOMA                     2            104
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  IMMT MUTATED     6   0   0   0
  IMMT WILD-TYPE 339   4  31  25
D1802V11, multiclass
    clus
vv   IMMT MUTATED IMMT WILD-TYPE
  R0            6            339
  R1            0              4
  R2            0             31
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1802V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  IMMT MUTATED                                  0     0
  IMMT WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  IMMT MUTATED                           1     1
  IMMT WILD-TYPE                        21   225
D1802V13, multiclass
[1] "Remove cluster labels:" "IMMT MUTATED"          
clus
  IMMT MUTATED IMMT WILD-TYPE 
             2            258 
    TCGA-A6-2671     TCGA-A6-2672     TCGA-A6-2674     TCGA-A6-2676 
"IMMT WILD-TYPE" "IMMT WILD-TYPE" "IMMT WILD-TYPE" "IMMT WILD-TYPE" 
    TCGA-A6-2677     TCGA-A6-2678     TCGA-A6-2683     TCGA-A6-3807 
"IMMT WILD-TYPE" "IMMT WILD-TYPE" "IMMT WILD-TYPE" "IMMT WILD-TYPE" 
    TCGA-A6-3808     TCGA-A6-3809     TCGA-A6-3810     TCGA-A6-4105 
"IMMT WILD-TYPE" "IMMT WILD-TYPE" "IMMT WILD-TYPE" "IMMT WILD-TYPE" 
    TCGA-A6-5656     TCGA-A6-5657     TCGA-A6-5659     TCGA-A6-5660 
"IMMT WILD-TYPE" "IMMT WILD-TYPE" "IMMT WILD-TYPE" "IMMT WILD-TYPE" 
    TCGA-A6-5661     TCGA-A6-5662     TCGA-A6-5664     TCGA-A6-5665 
"IMMT WILD-TYPE" "IMMT WILD-TYPE" "IMMT WILD-TYPE" "IMMT WILD-TYPE" 
    TCGA-A6-5666     TCGA-A6-6137     TCGA-A6-6138     TCGA-A6-6141 
"IMMT WILD-TYPE" "IMMT WILD-TYPE" "IMMT WILD-TYPE" "IMMT WILD-TYPE" 
    TCGA-A6-6142     TCGA-A6-6648     TCGA-A6-6649     TCGA-A6-6651 
"IMMT WILD-TYPE" "IMMT WILD-TYPE" "IMMT WILD-TYPE" "IMMT WILD-TYPE" 
    TCGA-A6-6652     TCGA-A6-6653     TCGA-A6-6654     TCGA-A6-6780 
"IMMT WILD-TYPE" "IMMT WILD-TYPE" "IMMT WILD-TYPE" "IMMT WILD-TYPE" 
    TCGA-A6-6781     TCGA-A6-6782     TCGA-AD-5900     TCGA-AD-6548 
"IMMT WILD-TYPE" "IMMT WILD-TYPE" "IMMT WILD-TYPE" "IMMT WILD-TYPE" 
    TCGA-AD-6888     TCGA-AD-6889     TCGA-AD-6890     TCGA-AD-6895 
"IMMT WILD-TYPE" "IMMT WILD-TYPE" "IMMT WILD-TYPE" "IMMT WILD-TYPE" 
    TCGA-AD-6899     TCGA-AD-6901     TCGA-AD-6963     TCGA-AD-6964 
"IMMT WILD-TYPE" "IMMT WILD-TYPE" "IMMT WILD-TYPE" "IMMT WILD-TYPE" 
    TCGA-AD-6965     TCGA-AU-3779     TCGA-AU-6004     TCGA-AY-4070 
"IMMT WILD-TYPE" "IMMT WILD-TYPE" "IMMT WILD-TYPE" "IMMT WILD-TYPE" 
    TCGA-AY-4071     TCGA-AY-5543     TCGA-AY-6196     TCGA-AY-6197 
"IMMT WILD-TYPE" "IMMT WILD-TYPE" "IMMT WILD-TYPE" "IMMT WILD-TYPE" 
    TCGA-AY-6386     TCGA-AZ-4315     TCGA-AZ-4323     TCGA-AZ-4616 
"IMMT WILD-TYPE" "IMMT WILD-TYPE" "IMMT WILD-TYPE" "IMMT WILD-TYPE" 
    TCGA-AZ-4681     TCGA-AZ-4682     TCGA-AZ-5403     TCGA-AZ-5407 
"IMMT WILD-TYPE" "IMMT WILD-TYPE" "IMMT WILD-TYPE" "IMMT WILD-TYPE" 
    TCGA-AZ-6598     TCGA-AZ-6599     TCGA-AZ-6600     TCGA-AZ-6601 
"IMMT WILD-TYPE" "IMMT WILD-TYPE" "IMMT WILD-TYPE" "IMMT WILD-TYPE" 
    TCGA-AZ-6603     TCGA-AZ-6605     TCGA-AZ-6606     TCGA-AZ-6607 
"IMMT WILD-TYPE" "IMMT WILD-TYPE" "IMMT WILD-TYPE" "IMMT WILD-TYPE" 
    TCGA-AZ-6608     TCGA-CA-5254     TCGA-CA-5255     TCGA-CA-5796 
"IMMT WILD-TYPE" "IMMT WILD-TYPE" "IMMT WILD-TYPE" "IMMT WILD-TYPE" 
    TCGA-CA-5797     TCGA-CA-6715     TCGA-CA-6716     TCGA-CA-6717 
"IMMT WILD-TYPE" "IMMT WILD-TYPE" "IMMT WILD-TYPE" "IMMT WILD-TYPE" 
    TCGA-CA-6718     TCGA-CA-6719     TCGA-CK-4947     TCGA-CK-4948 
"IMMT WILD-TYPE" "IMMT WILD-TYPE" "IMMT WILD-TYPE" "IMMT WILD-TYPE" 
    TCGA-CK-4950     TCGA-CK-4952     TCGA-CK-5912     TCGA-CK-5913 
"IMMT WILD-TYPE" "IMMT WILD-TYPE" "IMMT WILD-TYPE" "IMMT WILD-TYPE" 
    TCGA-CK-5914     TCGA-CK-5915     TCGA-CK-5916     TCGA-CK-6746 
"IMMT WILD-TYPE" "IMMT WILD-TYPE" "IMMT WILD-TYPE" "IMMT WILD-TYPE" 
    TCGA-CK-6747     TCGA-CK-6748     TCGA-CK-6751     TCGA-CM-4743 
"IMMT WILD-TYPE" "IMMT WILD-TYPE" "IMMT WILD-TYPE" "IMMT WILD-TYPE" 
    TCGA-CM-4744     TCGA-CM-4746     TCGA-CM-4747     TCGA-CM-5341 
"IMMT WILD-TYPE" "IMMT WILD-TYPE" "IMMT WILD-TYPE" "IMMT WILD-TYPE" 
    TCGA-CM-5344     TCGA-CM-5348     TCGA-CM-5349     TCGA-CM-5860 
"IMMT WILD-TYPE" "IMMT WILD-TYPE" "IMMT WILD-TYPE" "IMMT WILD-TYPE" 
    TCGA-CM-5861     TCGA-CM-5862     TCGA-CM-5863     TCGA-CM-5864 
"IMMT WILD-TYPE" "IMMT WILD-TYPE" "IMMT WILD-TYPE" "IMMT WILD-TYPE" 
    TCGA-CM-5868     TCGA-CM-6161     TCGA-CM-6162     TCGA-CM-6163 
"IMMT WILD-TYPE" "IMMT WILD-TYPE" "IMMT WILD-TYPE" "IMMT WILD-TYPE" 
    TCGA-CM-6164     TCGA-CM-6165     TCGA-CM-6166     TCGA-CM-6167 
"IMMT WILD-TYPE" "IMMT WILD-TYPE" "IMMT WILD-TYPE" "IMMT WILD-TYPE" 
    TCGA-CM-6168     TCGA-CM-6169     TCGA-CM-6170     TCGA-CM-6171 
"IMMT WILD-TYPE" "IMMT WILD-TYPE" "IMMT WILD-TYPE" "IMMT WILD-TYPE" 
    TCGA-CM-6172     TCGA-CM-6674     TCGA-CM-6675     TCGA-CM-6676 
"IMMT WILD-TYPE" "IMMT WILD-TYPE" "IMMT WILD-TYPE" "IMMT WILD-TYPE" 
    TCGA-CM-6677     TCGA-CM-6678     TCGA-CM-6679     TCGA-CM-6680 
"IMMT WILD-TYPE" "IMMT WILD-TYPE" "IMMT WILD-TYPE" "IMMT WILD-TYPE" 
    TCGA-D5-5537     TCGA-D5-5538     TCGA-D5-5539     TCGA-D5-5540 
"IMMT WILD-TYPE" "IMMT WILD-TYPE" "IMMT WILD-TYPE" "IMMT WILD-TYPE" 
    TCGA-D5-5541     TCGA-D5-6529     TCGA-D5-6532     TCGA-D5-6533 
"IMMT WILD-TYPE" "IMMT WILD-TYPE" "IMMT WILD-TYPE" "IMMT WILD-TYPE" 
    TCGA-D5-6534     TCGA-D5-6535     TCGA-D5-6536     TCGA-D5-6537 
"IMMT WILD-TYPE" "IMMT WILD-TYPE" "IMMT WILD-TYPE" "IMMT WILD-TYPE" 
    TCGA-D5-6538     TCGA-D5-6539     TCGA-D5-6540     TCGA-D5-6541 
"IMMT WILD-TYPE" "IMMT WILD-TYPE" "IMMT WILD-TYPE" "IMMT WILD-TYPE" 
    TCGA-D5-6898     TCGA-D5-6920     TCGA-D5-6922     TCGA-D5-6923 
"IMMT WILD-TYPE" "IMMT WILD-TYPE" "IMMT WILD-TYPE" "IMMT WILD-TYPE" 
    TCGA-D5-6924     TCGA-D5-6926     TCGA-D5-6927     TCGA-D5-6928 
"IMMT WILD-TYPE" "IMMT WILD-TYPE" "IMMT WILD-TYPE" "IMMT WILD-TYPE" 
    TCGA-D5-6929     TCGA-D5-6930     TCGA-D5-6931     TCGA-D5-6932 
"IMMT WILD-TYPE" "IMMT WILD-TYPE" "IMMT WILD-TYPE" "IMMT WILD-TYPE" 
    TCGA-D5-7000     TCGA-DM-A0X9     TCGA-DM-A0XD     TCGA-DM-A0XF 
"IMMT WILD-TYPE" "IMMT WILD-TYPE" "IMMT WILD-TYPE" "IMMT WILD-TYPE" 
    TCGA-DM-A1D0     TCGA-DM-A1D4     TCGA-DM-A1D6     TCGA-DM-A1D7 
"IMMT WILD-TYPE" "IMMT WILD-TYPE" "IMMT WILD-TYPE" "IMMT WILD-TYPE" 
    TCGA-DM-A1D8     TCGA-DM-A1D9     TCGA-DM-A1DA     TCGA-DM-A1DB 
"IMMT WILD-TYPE" "IMMT WILD-TYPE" "IMMT WILD-TYPE" "IMMT WILD-TYPE" 
    TCGA-DM-A1HA     TCGA-DM-A1HB     TCGA-DM-A282     TCGA-DM-A285 
"IMMT WILD-TYPE" "IMMT WILD-TYPE" "IMMT WILD-TYPE" "IMMT WILD-TYPE" 
    TCGA-DM-A28C     TCGA-DM-A28E     TCGA-DM-A28F     TCGA-DM-A28G 
"IMMT WILD-TYPE" "IMMT WILD-TYPE" "IMMT WILD-TYPE" "IMMT WILD-TYPE" 
    TCGA-DM-A28H     TCGA-DM-A28K     TCGA-F4-6459     TCGA-F4-6460 
"IMMT WILD-TYPE" "IMMT WILD-TYPE" "IMMT WILD-TYPE" "IMMT WILD-TYPE" 
    TCGA-F4-6569     TCGA-F4-6570     TCGA-F4-6703     TCGA-F4-6704 
"IMMT WILD-TYPE" "IMMT WILD-TYPE" "IMMT WILD-TYPE" "IMMT WILD-TYPE" 
    TCGA-F4-6805     TCGA-F4-6806     TCGA-F4-6807     TCGA-F4-6808 
"IMMT WILD-TYPE" "IMMT WILD-TYPE" "IMMT WILD-TYPE" "IMMT WILD-TYPE" 
    TCGA-F4-6809     TCGA-F4-6854     TCGA-F4-6855     TCGA-F4-6856 
"IMMT WILD-TYPE" "IMMT WILD-TYPE" "IMMT WILD-TYPE" "IMMT WILD-TYPE" 
    TCGA-G4-6293     TCGA-G4-6303     TCGA-G4-6304     TCGA-G4-6306 
"IMMT WILD-TYPE" "IMMT WILD-TYPE" "IMMT WILD-TYPE" "IMMT WILD-TYPE" 
    TCGA-G4-6307     TCGA-G4-6309     TCGA-G4-6310     TCGA-G4-6315 
"IMMT WILD-TYPE" "IMMT WILD-TYPE" "IMMT WILD-TYPE" "IMMT WILD-TYPE" 
    TCGA-G4-6317     TCGA-G4-6321     TCGA-G4-6323     TCGA-G4-6586 
"IMMT WILD-TYPE" "IMMT WILD-TYPE" "IMMT WILD-TYPE" "IMMT WILD-TYPE" 
    TCGA-G4-6588     TCGA-G4-6625     TCGA-G4-6626     TCGA-G4-6628 
"IMMT WILD-TYPE" "IMMT WILD-TYPE" "IMMT WILD-TYPE" "IMMT WILD-TYPE" 
    TCGA-AF-2687     TCGA-AF-2689     TCGA-AF-2691     TCGA-AF-2692 
"IMMT WILD-TYPE" "IMMT WILD-TYPE" "IMMT WILD-TYPE" "IMMT WILD-TYPE" 
    TCGA-AF-2693     TCGA-AF-3400     TCGA-AF-3913     TCGA-AF-4110 
"IMMT WILD-TYPE" "IMMT WILD-TYPE" "IMMT WILD-TYPE" "IMMT WILD-TYPE" 
    TCGA-AF-5654     TCGA-AF-6136     TCGA-AF-6655     TCGA-AF-6672 
"IMMT WILD-TYPE" "IMMT WILD-TYPE" "IMMT WILD-TYPE" "IMMT WILD-TYPE" 
    TCGA-AH-6544     TCGA-AH-6547     TCGA-AH-6549     TCGA-AH-6643 
"IMMT WILD-TYPE" "IMMT WILD-TYPE" "IMMT WILD-TYPE" "IMMT WILD-TYPE" 
    TCGA-AH-6644     TCGA-CI-6619     TCGA-CI-6620     TCGA-CI-6621 
"IMMT WILD-TYPE" "IMMT WILD-TYPE" "IMMT WILD-TYPE" "IMMT WILD-TYPE" 
    TCGA-CI-6622     TCGA-CI-6624     TCGA-CL-5917     TCGA-CL-5918 
"IMMT WILD-TYPE" "IMMT WILD-TYPE" "IMMT WILD-TYPE" "IMMT WILD-TYPE" 
    TCGA-DC-5337     TCGA-DC-5869     TCGA-DC-6155     TCGA-DC-6157 
"IMMT WILD-TYPE" "IMMT WILD-TYPE" "IMMT WILD-TYPE" "IMMT WILD-TYPE" 
    TCGA-DC-6158     TCGA-DC-6160     TCGA-DC-6681     TCGA-DC-6682 
"IMMT WILD-TYPE" "IMMT WILD-TYPE" "IMMT WILD-TYPE" "IMMT WILD-TYPE" 
    TCGA-DC-6683     TCGA-DT-5265     TCGA-DY-A0XA     TCGA-DY-A1DC 
"IMMT WILD-TYPE" "IMMT WILD-TYPE" "IMMT WILD-TYPE" "IMMT WILD-TYPE" 
    TCGA-DY-A1DD     TCGA-DY-A1DF     TCGA-DY-A1DG     TCGA-DY-A1H8 
"IMMT WILD-TYPE" "IMMT WILD-TYPE" "IMMT WILD-TYPE" "IMMT WILD-TYPE" 
    TCGA-EF-5830     TCGA-EI-6506     TCGA-EI-6507     TCGA-EI-6508 
"IMMT WILD-TYPE" "IMMT WILD-TYPE" "IMMT WILD-TYPE" "IMMT WILD-TYPE" 
    TCGA-EI-6510     TCGA-F5-6464     TCGA-F5-6465     TCGA-F5-6571 
"IMMT WILD-TYPE" "IMMT WILD-TYPE" "IMMT WILD-TYPE" "IMMT WILD-TYPE" 
    TCGA-F5-6702     TCGA-F5-6811     TCGA-F5-6812     TCGA-F5-6813 
"IMMT WILD-TYPE" "IMMT WILD-TYPE" "IMMT WILD-TYPE" "IMMT WILD-TYPE" 
    TCGA-G5-6235     TCGA-G5-6641 
"IMMT WILD-TYPE" "IMMT WILD-TYPE" 

Clustering(1803) Variable = COLEC12 MUTATION ANALYSIS
D1803V1, survival
                   sevent
clus2                 0   1
  COLEC12 MUTATED    17   2
  COLEC12 WILD-TYPE 361  91
  COLEC12 MUTATED COLEC12 WILD-TYPE 
               19               452 
  COLEC12 MUTATED COLEC12 WILD-TYPE 
                2                91 
$`COLEC12 MUTATED`
TCGA-A6-3809 TCGA-A6-5661 TCGA-AA-3663 TCGA-AA-3710 TCGA-AA-3831 TCGA-AA-3949 
       32.75        33.53         6.97        26.99        17.98        26.01 
TCGA-AA-3977 TCGA-AA-A010 TCGA-AD-6888 TCGA-AU-6004 TCGA-AZ-4315 TCGA-CA-6717 
       25.02        34.98        15.52        27.09        58.39        12.76 
TCGA-CK-4952 TCGA-CM-5862 TCGA-D5-6928 TCGA-DM-A1HB TCGA-F4-6856 TCGA-AG-3909 
       15.62         5.03        11.64       135.65        35.31        19.99 
TCGA-AG-A002 
       20.98 

$`COLEC12 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       31.63        30.44        29.19        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       85.05        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
        0.99        25.02         1.02        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6889 
       39.98        18.05        40.96         0.07        21.37        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
        0.20        14.50        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07        12.20        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
       17.56       148.01        85.45        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       30.08        32.02        15.02        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 
       12.59       140.38         7.50        44.32       131.51       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
        0.53        47.41       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
        1.02        48.03        32.02        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  COLEC12 MUTATED COLEC12 WILD-TYPE 
             5.03              0.00 
  COLEC12 MUTATED COLEC12 WILD-TYPE 
           135.65            148.01 
  COLEC12 MUTATED COLEC12 WILD-TYPE 
           25.020            20.085 
[1] "5.0 - 135.7 (25.0)" "0.0 - 148.0 (20.1)"
[1] "hr=" "2"  
D1803V2, continuous
D1803V3, binary
                   cls
clus                  0   1
  COLEC12 MUTATED    17   2
  COLEC12 WILD-TYPE 349 117
[1] "tbl2"
                   cls
clus                [,1] [,2]
  COLEC12 MUTATED     17    2
  COLEC12 WILD-TYPE  349  117
        clus
vv       COLEC12 MUTATED COLEC12 WILD-TYPE
  COLON               17               349
  RECTUM               2               117
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  COLEC12 MUTATED         3        0        1         6         2         0
  COLEC12 WILD-TYPE      88        1       31       132         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  COLEC12 MUTATED           0          0          4          1        0
  COLEC12 WILD-TYPE        24         11         55         41       48
                   vv
clus                STAGE IVA STAGE IVB
  COLEC12 MUTATED           1         0
  COLEC12 WILD-TYPE        17         1
D1803V4, multiclass
            clus
vv           COLEC12 MUTATED COLEC12 WILD-TYPE
  STAGE I                  3                88
  STAGE IA                 0                 1
  STAGE II                 1                31
  STAGE IIA                6               132
  STAGE IIB                2                 8
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               0                11
  STAGE IIIB               4                55
  STAGE IIIC               1                41
  STAGE IV                 0                48
  STAGE IVA                1                17
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  COLEC12 MUTATED     0   4  12   3
  COLEC12 WILD-TYPE  17  88 317  47
D1803V5, multiclass
    clus
vv   COLEC12 MUTATED COLEC12 WILD-TYPE
  T1               0                17
  T2               4                88
  T3              12               317
  T4               3                47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  COLEC12 MUTATED    13   5   1
  COLEC12 WILD-TYPE 274 108  86
D1803V6, multiclass
    clus
vv   COLEC12 MUTATED COLEC12 WILD-TYPE
  N0              13               274
  N1               5               108
  N2               1                86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1803V7, binary
                   cls
clus                  0   1
  COLEC12 MUTATED    17   1
  COLEC12 WILD-TYPE 358  64
[1] "tbl2"
                   cls
clus                [,1] [,2]
  COLEC12 MUTATED     17    1
  COLEC12 WILD-TYPE  358   64
   clus
vv  COLEC12 MUTATED COLEC12 WILD-TYPE
  0              17               358
  1               1                64
[1] 2 2
[1] FALSE
D1803V8, binary
                   cls
clus                  0   1
  COLEC12 MUTATED     8  11
  COLEC12 WILD-TYPE 217 253
[1] "tbl2"
                   cls
clus                [,1] [,2]
  COLEC12 MUTATED      8   11
  COLEC12 WILD-TYPE  217  253
        clus
vv       COLEC12 MUTATED COLEC12 WILD-TYPE
  FEMALE               8               217
  MALE                11               253
[1] 2 2
[1] FALSE
D1803V9, binary
                   cls
clus                  0   1
  COLEC12 MUTATED    16   0
  COLEC12 WILD-TYPE 334  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  COLEC12 MUTATED     16    0
  COLEC12 WILD-TYPE  334   22
     clus
vv    COLEC12 MUTATED COLEC12 WILD-TYPE
  NO               16               334
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  COLEC12 MUTATED                     10                             6
  COLEC12 WILD-TYPE                  305                            41
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  COLEC12 MUTATED                       2                              0
  COLEC12 WILD-TYPE                   104                             10
D1803V10, multiclass
                                clus
vv                               COLEC12 MUTATED COLEC12 WILD-TYPE
  COLON ADENOCARCINOMA                        10               305
  COLON MUCINOUS ADENOCARCINOMA                6                41
  RECTAL ADENOCARCINOMA                        2               104
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  COLEC12 MUTATED    15   0   0   2
  COLEC12 WILD-TYPE 330   4  31  23
D1803V11, multiclass
    clus
vv   COLEC12 MUTATED COLEC12 WILD-TYPE
  R0              15               330
  R1               0                 4
  R2               0                31
  RX               2                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1803V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  COLEC12 MUTATED                                  0     1
  COLEC12 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  COLEC12 MUTATED                           1     9
  COLEC12 WILD-TYPE                        21   217
D1803V13, multiclass
                                  clus
vv                                 COLEC12 MUTATED COLEC12 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                10
  BLACK OR AFRICAN AMERICAN                      1                21
  WHITE                                          9               217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1804) Variable = SCYL2 MUTATION ANALYSIS
D1804V1, survival
                 sevent
clus2               0   1
  SCYL2 MUTATED    16   4
  SCYL2 WILD-TYPE 362  89
  SCYL2 MUTATED SCYL2 WILD-TYPE 
             20             451 
  SCYL2 MUTATED SCYL2 WILD-TYPE 
              4              89 
$`SCYL2 MUTATED`
TCGA-A6-5661 TCGA-A6-5665 TCGA-AA-3663 TCGA-AA-3977 TCGA-AA-A02K TCGA-AD-5900 
       33.53        22.06         6.97        25.02        14.01         0.07 
TCGA-AY-6197 TCGA-AZ-4315 TCGA-CA-6718 TCGA-CM-4744 TCGA-CM-5863 TCGA-D5-6926 
       21.44        58.39        10.06        20.02        15.02         9.04 
TCGA-D5-6929 TCGA-D5-6931 TCGA-DM-A28G TCGA-AG-4007 TCGA-AG-A002 TCGA-DY-A0XA 
        4.80        12.00        60.79         1.02        20.98       126.44 
TCGA-DY-A1DG TCGA-F5-6811 
       51.48        32.19 

$`SCYL2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
        5.03         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
       16.31         0.95        33.01        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.20        12.76        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
        1.91       124.27        23.05        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
        5.03        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6932 TCGA-D5-7000 
       14.30         9.44        11.64         1.51        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       28.04        36.03        14.04        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1H8 
        5.03         5.29        41.36        57.24        24.13        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       49.51        31.30        28.57         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  SCYL2 MUTATED SCYL2 WILD-TYPE 
           0.07            0.00 
  SCYL2 MUTATED SCYL2 WILD-TYPE 
         126.44          148.01 
  SCYL2 MUTATED SCYL2 WILD-TYPE 
          20.50           20.19 
[1] "0.1 - 126.4 (20.5)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1"  
D1804V2, continuous
D1804V3, binary
                 cls
clus                0   1
  SCYL2 MUTATED    16   5
  SCYL2 WILD-TYPE 350 114
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SCYL2 MUTATED     16    5
  SCYL2 WILD-TYPE  350  114
        clus
vv       SCYL2 MUTATED SCYL2 WILD-TYPE
  COLON             16             350
  RECTUM             5             114
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SCYL2 MUTATED         3        0        1         9         0         0
  SCYL2 WILD-TYPE      88        1       31       129        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SCYL2 MUTATED           0          0          2          1        3         1
  SCYL2 WILD-TYPE        24         11         57         41       45        17
                 vv
clus              STAGE IVB
  SCYL2 MUTATED           0
  SCYL2 WILD-TYPE         1
D1804V4, multiclass
            clus
vv           SCYL2 MUTATED SCYL2 WILD-TYPE
  STAGE I                3              88
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              9             129
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             2              57
  STAGE IIIC             1              41
  STAGE IV               3              45
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  SCYL2 MUTATED     0   4  13   4
  SCYL2 WILD-TYPE  17  88 316  46
D1804V5, multiclass
    clus
vv   SCYL2 MUTATED SCYL2 WILD-TYPE
  T1             0              17
  T2             4              88
  T3            13             316
  T4             4              46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  SCYL2 MUTATED    14   4   3
  SCYL2 WILD-TYPE 273 109  84
D1804V6, multiclass
    clus
vv   SCYL2 MUTATED SCYL2 WILD-TYPE
  N0            14             273
  N1             4             109
  N2             3              84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1804V7, binary
                 cls
clus                0   1
  SCYL2 MUTATED    14   4
  SCYL2 WILD-TYPE 361  61
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SCYL2 MUTATED     14    4
  SCYL2 WILD-TYPE  361   61
   clus
vv  SCYL2 MUTATED SCYL2 WILD-TYPE
  0            14             361
  1             4              61
[1] 2 2
[1] FALSE
D1804V8, binary
                 cls
clus                0   1
  SCYL2 MUTATED     7  14
  SCYL2 WILD-TYPE 218 250
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SCYL2 MUTATED      7   14
  SCYL2 WILD-TYPE  218  250
        clus
vv       SCYL2 MUTATED SCYL2 WILD-TYPE
  FEMALE             7             218
  MALE              14             250
[1] 2 2
[1] FALSE
D1804V9, binary
                 cls
clus                0   1
  SCYL2 MUTATED    13   1
  SCYL2 WILD-TYPE 337  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SCYL2 MUTATED     13    1
  SCYL2 WILD-TYPE  337   21
     clus
vv    SCYL2 MUTATED SCYL2 WILD-TYPE
  NO             13             337
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SCYL2 MUTATED                     14                             2
  SCYL2 WILD-TYPE                  301                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SCYL2 MUTATED                       5                              0
  SCYL2 WILD-TYPE                   101                             10
D1804V10, multiclass
                                clus
vv                               SCYL2 MUTATED SCYL2 WILD-TYPE
  COLON ADENOCARCINOMA                      14             301
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      5             101
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  SCYL2 MUTATED    13   0   2   1
  SCYL2 WILD-TYPE 332   4  29  24
D1804V11, multiclass
    clus
vv   SCYL2 MUTATED SCYL2 WILD-TYPE
  R0            13             332
  R1             0               4
  R2             2              29
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1804V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SCYL2 MUTATED                                  0     1
  SCYL2 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  SCYL2 MUTATED                           1    13
  SCYL2 WILD-TYPE                        21   213
D1804V13, multiclass
                                  clus
vv                                 SCYL2 MUTATED SCYL2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                       13             213
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1805) Variable = CAPRIN2 MUTATION ANALYSIS
D1805V1, survival
                   sevent
clus2                 0   1
  CAPRIN2 MUTATED    13   3
  CAPRIN2 WILD-TYPE 365  90
  CAPRIN2 MUTATED CAPRIN2 WILD-TYPE 
               16               455 
  CAPRIN2 MUTATED CAPRIN2 WILD-TYPE 
                3                90 
$`CAPRIN2 MUTATED`
TCGA-A6-5661 TCGA-A6-6781 TCGA-AA-3555 TCGA-AA-3710 TCGA-AA-3966 TCGA-AA-A00N 
       33.53        19.66        29.95        26.99         2.01         4.01 
TCGA-AA-A010 TCGA-AZ-4315 TCGA-CA-6717 TCGA-CA-6718 TCGA-D5-6533 TCGA-D5-6930 
       34.98        58.39        12.76        10.06         1.32         1.51 
TCGA-G4-6586 TCGA-AG-3583 TCGA-AG-A002 TCGA-F5-6571 
       35.80        20.05        20.98        31.30 

$`CAPRIN2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       24.00        17.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       85.05        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        33.01        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       12.20        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6931 
       14.30         9.04         9.44        11.64         4.80        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       13.78        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3584 
       12.00        32.02         8.02         7.07        36.03        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6702 
       19.96        20.91        18.28         9.96        49.51        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  CAPRIN2 MUTATED CAPRIN2 WILD-TYPE 
             1.32              0.00 
  CAPRIN2 MUTATED CAPRIN2 WILD-TYPE 
            58.39            148.01 
  CAPRIN2 MUTATED CAPRIN2 WILD-TYPE 
           20.515            20.190 
[1] "1.3 - 58.4 (20.5)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.2"
D1805V2, continuous
D1805V3, binary
                   cls
clus                  0   1
  CAPRIN2 MUTATED    14   3
  CAPRIN2 WILD-TYPE 352 116
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CAPRIN2 MUTATED     14    3
  CAPRIN2 WILD-TYPE  352  116
        clus
vv       CAPRIN2 MUTATED CAPRIN2 WILD-TYPE
  COLON               14               352
  RECTUM               3               116
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CAPRIN2 MUTATED         1        0        0        11         2         0
  CAPRIN2 WILD-TYPE      90        1       32       127         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CAPRIN2 MUTATED           0          0          1          1        1
  CAPRIN2 WILD-TYPE        24         11         58         41       47
                   vv
clus                STAGE IVA STAGE IVB
  CAPRIN2 MUTATED           0         0
  CAPRIN2 WILD-TYPE        18         1
D1805V4, multiclass
            clus
vv           CAPRIN2 MUTATED CAPRIN2 WILD-TYPE
  STAGE I                  1                90
  STAGE IA                 0                 1
  STAGE II                 0                32
  STAGE IIA               11               127
  STAGE IIB                2                 8
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               0                11
  STAGE IIIB               1                58
  STAGE IIIC               1                41
  STAGE IV                 1                47
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  CAPRIN2 MUTATED     0   1  12   4
  CAPRIN2 WILD-TYPE  17  91 317  46
D1805V5, multiclass
    clus
vv   CAPRIN2 MUTATED CAPRIN2 WILD-TYPE
  T1               0                17
  T2               1                91
  T3              12               317
  T4               4                46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  CAPRIN2 MUTATED    15   1   1
  CAPRIN2 WILD-TYPE 272 112  86
D1805V6, multiclass
    clus
vv   CAPRIN2 MUTATED CAPRIN2 WILD-TYPE
  N0              15               272
  N1               1               112
  N2               1                86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1805V7, binary
                   cls
clus                  0   1
  CAPRIN2 MUTATED    15   1
  CAPRIN2 WILD-TYPE 360  64
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CAPRIN2 MUTATED     15    1
  CAPRIN2 WILD-TYPE  360   64
   clus
vv  CAPRIN2 MUTATED CAPRIN2 WILD-TYPE
  0              15               360
  1               1                64
[1] 2 2
[1] FALSE
D1805V8, binary
                   cls
clus                  0   1
  CAPRIN2 MUTATED     9   8
  CAPRIN2 WILD-TYPE 216 256
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CAPRIN2 MUTATED      9    8
  CAPRIN2 WILD-TYPE  216  256
        clus
vv       CAPRIN2 MUTATED CAPRIN2 WILD-TYPE
  FEMALE               9               216
  MALE                 8               256
[1] 2 2
[1] FALSE
D1805V9, binary
                   cls
clus                  0   1
  CAPRIN2 MUTATED    12   0
  CAPRIN2 WILD-TYPE 338  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CAPRIN2 MUTATED     12    0
  CAPRIN2 WILD-TYPE  338   22
     clus
vv    CAPRIN2 MUTATED CAPRIN2 WILD-TYPE
  NO               12               338
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CAPRIN2 MUTATED                      8                             6
  CAPRIN2 WILD-TYPE                  307                            41
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CAPRIN2 MUTATED                       2                              1
  CAPRIN2 WILD-TYPE                   104                              9
D1805V10, multiclass
                                clus
vv                               CAPRIN2 MUTATED CAPRIN2 WILD-TYPE
  COLON ADENOCARCINOMA                         8               307
  COLON MUCINOUS ADENOCARCINOMA                6                41
  RECTAL ADENOCARCINOMA                        2               104
  RECTAL MUCINOUS ADENOCARCINOMA               1                 9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  CAPRIN2 MUTATED    13   0   1   2
  CAPRIN2 WILD-TYPE 332   4  30  23
D1805V11, multiclass
    clus
vv   CAPRIN2 MUTATED CAPRIN2 WILD-TYPE
  R0              13               332
  R1               0                 4
  R2               1                30
  RX               2                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1805V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CAPRIN2 MUTATED                                  0     2
  CAPRIN2 WILD-TYPE                                1     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  CAPRIN2 MUTATED                           1     6
  CAPRIN2 WILD-TYPE                        21   220
D1805V13, multiclass
                                  clus
vv                                 CAPRIN2 MUTATED CAPRIN2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          2                 9
  BLACK OR AFRICAN AMERICAN                      1                21
  WHITE                                          6               220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1806) Variable = CNOT10 MUTATION ANALYSIS
D1806V1, survival
                  sevent
clus2                0   1
  CNOT10 MUTATED     7   3
  CNOT10 WILD-TYPE 371  90
  CNOT10 MUTATED CNOT10 WILD-TYPE 
              10              461 
  CNOT10 MUTATED CNOT10 WILD-TYPE 
               3               90 
$`CNOT10 MUTATED`
TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01R TCGA-AZ-4315 TCGA-AZ-4616 TCGA-AZ-6601 
        4.01        34.98        35.01        58.39         5.13       100.01 
TCGA-CA-6717 TCGA-G4-6317 TCGA-G4-6586 TCGA-CI-6624 
       12.76        36.00        35.80         4.73 

$`CNOT10 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T 
       31.00        31.00        38.07         1.02         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       21.44        17.82         1.41       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 
       88.21        49.41         6.77        12.10        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07        12.20        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 
       85.48        63.62        61.91        22.09        13.78        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
        6.05        33.17         6.97        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  CNOT10 MUTATED CNOT10 WILD-TYPE 
            4.01             0.00 
  CNOT10 MUTATED CNOT10 WILD-TYPE 
          100.01           148.01 
  CNOT10 MUTATED CNOT10 WILD-TYPE 
          34.995           20.120 
[1] "4.0 - 100.0 (35.0)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.3"
D1806V2, continuous
D1806V3, binary
                  cls
clus                 0   1
  CNOT10 MUTATED     9   1
  CNOT10 WILD-TYPE 357 118
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CNOT10 MUTATED      9    1
  CNOT10 WILD-TYPE  357  118
        clus
vv       CNOT10 MUTATED CNOT10 WILD-TYPE
  COLON               9              357
  RECTUM              1              118
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CNOT10 MUTATED         1        0        1         3         2         0
  CNOT10 WILD-TYPE      90        1       31       135         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CNOT10 MUTATED           1          0          0          1        1
  CNOT10 WILD-TYPE        23         11         59         41       47
                  vv
clus               STAGE IVA STAGE IVB
  CNOT10 MUTATED           0         0
  CNOT10 WILD-TYPE        18         1
D1806V4, multiclass
            clus
vv           CNOT10 MUTATED CNOT10 WILD-TYPE
  STAGE I                 1               90
  STAGE IA                0                1
  STAGE II                1               31
  STAGE IIA               3              135
  STAGE IIB               2                8
  STAGE IIC               0                1
  STAGE III               1               23
  STAGE IIIA              0               11
  STAGE IIIB              0               59
  STAGE IIIC              1               41
  STAGE IV                1               47
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  CNOT10 MUTATED     0   1   7   2
  CNOT10 WILD-TYPE  17  91 322  48
D1806V5, multiclass
    clus
vv   CNOT10 MUTATED CNOT10 WILD-TYPE
  T1              0               17
  T2              1               91
  T3              7              322
  T4              2               48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  CNOT10 MUTATED     7   0   3
  CNOT10 WILD-TYPE 280 113  84
D1806V6, multiclass
    clus
vv   CNOT10 MUTATED CNOT10 WILD-TYPE
  N0              7              280
  N1              0              113
  N2              3               84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1806V7, binary
                  cls
clus                 0   1
  CNOT10 MUTATED     8   1
  CNOT10 WILD-TYPE 367  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CNOT10 MUTATED      8    1
  CNOT10 WILD-TYPE  367   64
   clus
vv  CNOT10 MUTATED CNOT10 WILD-TYPE
  0              8              367
  1              1               64
[1] 2 2
[1] FALSE
D1806V8, binary
                  cls
clus                 0   1
  CNOT10 MUTATED     5   5
  CNOT10 WILD-TYPE 220 259
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CNOT10 MUTATED      5    5
  CNOT10 WILD-TYPE  220  259
        clus
vv       CNOT10 MUTATED CNOT10 WILD-TYPE
  FEMALE              5              220
  MALE                5              259
[1] 2 2
[1] FALSE
D1806V9, binary
                  cls
clus                 0   1
  CNOT10 MUTATED     7   1
  CNOT10 WILD-TYPE 343  21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CNOT10 MUTATED      7    1
  CNOT10 WILD-TYPE  343   21
     clus
vv    CNOT10 MUTATED CNOT10 WILD-TYPE
  NO               7              343
  YES              1               21
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CNOT10 MUTATED                      6                             3
  CNOT10 WILD-TYPE                  309                            44
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CNOT10 MUTATED                       1                              0
  CNOT10 WILD-TYPE                   105                             10
D1806V10, multiclass
                                clus
vv                               CNOT10 MUTATED CNOT10 WILD-TYPE
  COLON ADENOCARCINOMA                        6              309
  COLON MUCINOUS ADENOCARCINOMA               3               44
  RECTAL ADENOCARCINOMA                       1              105
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  CNOT10 MUTATED     6   0   0   1
  CNOT10 WILD-TYPE 339   4  31  24
D1806V11, multiclass
    clus
vv   CNOT10 MUTATED CNOT10 WILD-TYPE
  R0              6              339
  R1              0                4
  R2              0               31
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1806V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CNOT10 MUTATED                                  0     1
  CNOT10 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  CNOT10 MUTATED                           0     6
  CNOT10 WILD-TYPE                        22   220
D1806V13, multiclass
                                  clus
vv                                 CNOT10 MUTATED CNOT10 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         6              220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1807) Variable = LUZP1 MUTATION ANALYSIS
D1807V1, survival
                 sevent
clus2               0   1
  LUZP1 MUTATED    12   4
  LUZP1 WILD-TYPE 366  89
  LUZP1 MUTATED LUZP1 WILD-TYPE 
             16             455 
  LUZP1 MUTATED LUZP1 WILD-TYPE 
              4              89 
$`LUZP1 MUTATED`
TCGA-A6-5665 TCGA-A6-6780 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3520 TCGA-AA-3864 
       22.06        20.12        35.01        63.98        24.03        53.00 
TCGA-AA-A010 TCGA-AA-A01F TCGA-AA-A01P TCGA-AZ-4315 TCGA-AZ-6598 TCGA-CA-6718 
       34.98        32.02        38.07        58.39        49.41        10.06 
TCGA-CM-6674 TCGA-DM-A28G TCGA-G4-6586 TCGA-AG-3599 
       12.95        60.79        35.80        12.03 

$`LUZP1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3511 
       19.66        20.28         7.04         3.02         1.02         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3522 
        1.02        13.02        38.99         1.02         9.07        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       36.03         8.05        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       78.08         6.05         6.97        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       30.05        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01G 
       17.03        14.99        21.99         1.02        10.98        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        31.00         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        88.21         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 
        3.25         3.29         0.07        12.20        12.76        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       14.04        11.01        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       35.97       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 
       63.62        61.91        36.00        22.09        13.78        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3600 TCGA-AG-3605 
       46.03        34.03         2.01        50.04         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  LUZP1 MUTATED LUZP1 WILD-TYPE 
          10.06            0.00 
  LUZP1 MUTATED LUZP1 WILD-TYPE 
          63.98          148.01 
  LUZP1 MUTATED LUZP1 WILD-TYPE 
         34.995          19.990 
[1] "10.1 - 64.0 (35.0)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.1"
D1807V2, continuous
D1807V3, binary
                 cls
clus                0   1
  LUZP1 MUTATED    15   1
  LUZP1 WILD-TYPE 351 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LUZP1 MUTATED     15    1
  LUZP1 WILD-TYPE  351  118
        clus
vv       LUZP1 MUTATED LUZP1 WILD-TYPE
  COLON             15             351
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  LUZP1 MUTATED         2        0        4         7         1         0
  LUZP1 WILD-TYPE      89        1       28       131         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  LUZP1 MUTATED           1          0          1          0        0         0
  LUZP1 WILD-TYPE        23         11         58         42       48        18
                 vv
clus              STAGE IVB
  LUZP1 MUTATED           0
  LUZP1 WILD-TYPE         1
D1807V4, multiclass
            clus
vv           LUZP1 MUTATED LUZP1 WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               4              28
  STAGE IIA              7             131
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  LUZP1 MUTATED     0   2  13   1
  LUZP1 WILD-TYPE  17  90 316  49
D1807V5, multiclass
    clus
vv   LUZP1 MUTATED LUZP1 WILD-TYPE
  T1             0              17
  T2             2              90
  T3            13             316
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  LUZP1 MUTATED    14   2   0
  LUZP1 WILD-TYPE 273 111  87
D1807V6, multiclass
    clus
vv   LUZP1 MUTATED LUZP1 WILD-TYPE
  N0            14             273
  N1             2             111
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1807V7, binary
                 cls
clus                0   1
  LUZP1 MUTATED    14   0
  LUZP1 WILD-TYPE 361  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LUZP1 MUTATED     14    0
  LUZP1 WILD-TYPE  361   65
   clus
vv  LUZP1 MUTATED LUZP1 WILD-TYPE
  0            14             361
  1             0              65
[1] 2 2
[1] FALSE
D1807V8, binary
                 cls
clus                0   1
  LUZP1 MUTATED     6  10
  LUZP1 WILD-TYPE 219 254
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LUZP1 MUTATED      6   10
  LUZP1 WILD-TYPE  219  254
        clus
vv       LUZP1 MUTATED LUZP1 WILD-TYPE
  FEMALE             6             219
  MALE              10             254
[1] 2 2
[1] FALSE
D1807V9, binary
                 cls
clus                0   1
  LUZP1 MUTATED    15   0
  LUZP1 WILD-TYPE 335  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LUZP1 MUTATED     15    0
  LUZP1 WILD-TYPE  335   22
     clus
vv    LUZP1 MUTATED LUZP1 WILD-TYPE
  NO             15             335
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  LUZP1 MUTATED                     14                             1
  LUZP1 WILD-TYPE                  301                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  LUZP1 MUTATED                       0                              0
  LUZP1 WILD-TYPE                   106                             10
D1807V10, multiclass
                                clus
vv                               LUZP1 MUTATED LUZP1 WILD-TYPE
  COLON ADENOCARCINOMA                      14             301
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  LUZP1 MUTATED    12   0   0   1
  LUZP1 WILD-TYPE 333   4  31  24
D1807V11, multiclass
    clus
vv   LUZP1 MUTATED LUZP1 WILD-TYPE
  R0            12             333
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1807V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  LUZP1 MUTATED                                  0     1
  LUZP1 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  LUZP1 MUTATED                           0     7
  LUZP1 WILD-TYPE                        22   219
D1807V13, multiclass
                                  clus
vv                                 LUZP1 MUTATED LUZP1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        7             219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1808) Variable = VCX3A MUTATION ANALYSIS
D1808V1, survival
                 sevent
clus2               0   1
  VCX3A MUTATED     4   1
  VCX3A WILD-TYPE 374  92
  VCX3A MUTATED VCX3A WILD-TYPE 
              5             466 
  VCX3A MUTATED VCX3A WILD-TYPE 
              1              92 
$`VCX3A MUTATED`
TCGA-A6-2671 TCGA-AA-3662 TCGA-AY-6386 TCGA-AZ-4681 TCGA-D5-6922 
       43.76         6.05        17.82       106.75         4.41 

$`VCX3A WILD-TYPE`
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       46.65        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       19.99        13.94        19.99        61.02        78.08         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 
       33.01        21.44        58.39         1.41         5.13        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6923 
       12.49        16.14        15.58         1.48         3.68        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  VCX3A MUTATED VCX3A WILD-TYPE 
           4.41            0.00 
  VCX3A MUTATED VCX3A WILD-TYPE 
         106.75          148.01 
  VCX3A MUTATED VCX3A WILD-TYPE 
         17.820          20.235 
[1] "4.4 - 106.8 (17.8)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.3"
D1808V2, continuous
D1808V3, binary
                 cls
clus                0   1
  VCX3A MUTATED     5   0
  VCX3A WILD-TYPE 361 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VCX3A MUTATED      5    0
  VCX3A WILD-TYPE  361  119
        clus
vv       VCX3A MUTATED VCX3A WILD-TYPE
  COLON              5             361
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  VCX3A MUTATED         0        0        0         1         0         0
  VCX3A WILD-TYPE      91        1       32       137        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  VCX3A MUTATED           0          1          1          0        2         0
  VCX3A WILD-TYPE        24         10         58         42       46        18
                 vv
clus              STAGE IVB
  VCX3A MUTATED           0
  VCX3A WILD-TYPE         1
D1808V4, multiclass
            clus
vv           VCX3A MUTATED VCX3A WILD-TYPE
  STAGE I                0              91
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              1             137
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             1              10
  STAGE IIIB             1              58
  STAGE IIIC             0              42
  STAGE IV               2              46
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  VCX3A MUTATED     0   0   4   1
  VCX3A WILD-TYPE  17  92 325  49
D1808V5, multiclass
    clus
vv   VCX3A MUTATED VCX3A WILD-TYPE
  T1             0              17
  T2             0              92
  T3             4             325
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  VCX3A MUTATED     1   2   2
  VCX3A WILD-TYPE 286 111  85
D1808V6, multiclass
    clus
vv   VCX3A MUTATED VCX3A WILD-TYPE
  N0             1             286
  N1             2             111
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1808V7, binary
                 cls
clus                0   1
  VCX3A MUTATED     3   2
  VCX3A WILD-TYPE 372  63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VCX3A MUTATED      3    2
  VCX3A WILD-TYPE  372   63
   clus
vv  VCX3A MUTATED VCX3A WILD-TYPE
  0             3             372
  1             2              63
[1] 2 2
[1] FALSE
D1808V8, binary
                 cls
clus                0   1
  VCX3A MUTATED     3   2
  VCX3A WILD-TYPE 222 262
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VCX3A MUTATED      3    2
  VCX3A WILD-TYPE  222  262
        clus
vv       VCX3A MUTATED VCX3A WILD-TYPE
  FEMALE             3             222
  MALE               2             262
[1] 2 2
[1] FALSE
D1808V9, binary
                 cls
clus                0   1
  VCX3A MUTATED     4   0
  VCX3A WILD-TYPE 346  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VCX3A MUTATED      4    0
  VCX3A WILD-TYPE  346   22
     clus
vv    VCX3A MUTATED VCX3A WILD-TYPE
  NO              4             346
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  VCX3A MUTATED                      5                             0
  VCX3A WILD-TYPE                  310                            47
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  VCX3A MUTATED                       0                              0
  VCX3A WILD-TYPE                   106                             10
D1808V10, multiclass
                                clus
vv                               VCX3A MUTATED VCX3A WILD-TYPE
  COLON ADENOCARCINOMA                       5             310
  COLON MUCINOUS ADENOCARCINOMA              0              47
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  VCX3A MUTATED     4   0   1   0
  VCX3A WILD-TYPE 341   4  30  25
D1808V11, multiclass
    clus
vv   VCX3A MUTATED VCX3A WILD-TYPE
  R0             4             341
  R1             0               4
  R2             1              30
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1808V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  VCX3A MUTATED                                  0     0
  VCX3A WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  VCX3A MUTATED                           1     3
  VCX3A WILD-TYPE                        21   223
D1808V13, multiclass
                                  clus
vv                                 VCX3A MUTATED VCX3A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        3             223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1809) Variable = BAP1 MUTATION ANALYSIS
D1809V1, survival
                sevent
clus2              0   1
  BAP1 MUTATED    11   2
  BAP1 WILD-TYPE 367  91
  BAP1 MUTATED BAP1 WILD-TYPE 
            13            458 
  BAP1 MUTATED BAP1 WILD-TYPE 
             2             91 
$`BAP1 MUTATED`
TCGA-AA-3518 TCGA-AA-A010 TCGA-AY-5543 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-CM-4743 
        1.02        34.98        33.01         6.77       100.01        23.05 
TCGA-CM-5344 TCGA-D5-5538 TCGA-D5-6928 TCGA-DM-A282 TCGA-G4-6588 TCGA-CI-6619 
       22.03        12.26        11.64       139.17        26.17         6.05 
TCGA-EI-6507 
       19.96 

$`BAP1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
       38.99         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6603 
       22.36        62.79        88.21        49.41        12.10        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5348 
       20.02        37.02        25.02        13.02        29.06        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       10.06        12.03        45.40        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        35.80        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6620 TCGA-CI-6622 
        1.45        17.49         0.69         0.72        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
       32.61         0.49        20.55        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  BAP1 MUTATED BAP1 WILD-TYPE 
          1.02           0.00 
  BAP1 MUTATED BAP1 WILD-TYPE 
        139.17         148.01 
  BAP1 MUTATED BAP1 WILD-TYPE 
        22.030         20.155 
[1] "1.0 - 139.2 (22.0)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.5"
D1809V2, continuous
D1809V3, binary
                cls
clus               0   1
  BAP1 MUTATED    12   2
  BAP1 WILD-TYPE 354 117
[1] "tbl2"
                cls
clus             [,1] [,2]
  BAP1 MUTATED     12    2
  BAP1 WILD-TYPE  354  117
        clus
vv       BAP1 MUTATED BAP1 WILD-TYPE
  COLON            12            354
  RECTUM            2            117
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  BAP1 MUTATED         1        0        1         6         1         0
  BAP1 WILD-TYPE      90        1       31       132         9         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  BAP1 MUTATED           0          0          2          1        1         1
  BAP1 WILD-TYPE        24         11         57         41       47        17
                vv
clus             STAGE IVB
  BAP1 MUTATED           0
  BAP1 WILD-TYPE         1
D1809V4, multiclass
            clus
vv           BAP1 MUTATED BAP1 WILD-TYPE
  STAGE I               1             90
  STAGE IA              0              1
  STAGE II              1             31
  STAGE IIA             6            132
  STAGE IIB             1              9
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            2             57
  STAGE IIIC            1             41
  STAGE IV              1             47
  STAGE IVA             1             17
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  BAP1 MUTATED     0   1  12   1
  BAP1 WILD-TYPE  17  91 317  49
D1809V5, multiclass
    clus
vv   BAP1 MUTATED BAP1 WILD-TYPE
  T1            0             17
  T2            1             91
  T3           12            317
  T4            1             49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  BAP1 MUTATED     9   4   1
  BAP1 WILD-TYPE 278 109  86
D1809V6, multiclass
    clus
vv   BAP1 MUTATED BAP1 WILD-TYPE
  N0            9            278
  N1            4            109
  N2            1             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1809V7, binary
                cls
clus               0   1
  BAP1 MUTATED    10   2
  BAP1 WILD-TYPE 365  63
[1] "tbl2"
                cls
clus             [,1] [,2]
  BAP1 MUTATED     10    2
  BAP1 WILD-TYPE  365   63
   clus
vv  BAP1 MUTATED BAP1 WILD-TYPE
  0           10            365
  1            2             63
[1] 2 2
[1] FALSE
D1809V8, binary
                cls
clus               0   1
  BAP1 MUTATED     7   7
  BAP1 WILD-TYPE 218 257
[1] "tbl2"
                cls
clus             [,1] [,2]
  BAP1 MUTATED      7    7
  BAP1 WILD-TYPE  218  257
        clus
vv       BAP1 MUTATED BAP1 WILD-TYPE
  FEMALE            7            218
  MALE              7            257
[1] 2 2
[1] FALSE
D1809V9, binary
                cls
clus               0   1
  BAP1 MUTATED    10   0
  BAP1 WILD-TYPE 340  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  BAP1 MUTATED     10    0
  BAP1 WILD-TYPE  340   22
     clus
vv    BAP1 MUTATED BAP1 WILD-TYPE
  NO            10            340
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  BAP1 MUTATED                     10                             2
  BAP1 WILD-TYPE                  305                            45
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  BAP1 MUTATED                       2                              0
  BAP1 WILD-TYPE                   104                             10
D1809V10, multiclass
                                clus
vv                               BAP1 MUTATED BAP1 WILD-TYPE
  COLON ADENOCARCINOMA                     10            305
  COLON MUCINOUS ADENOCARCINOMA             2             45
  RECTAL ADENOCARCINOMA                     2            104
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  BAP1 MUTATED    10   0   0   0
  BAP1 WILD-TYPE 335   4  31  25
D1809V11, multiclass
    clus
vv   BAP1 MUTATED BAP1 WILD-TYPE
  R0           10            335
  R1            0              4
  R2            0             31
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1809V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  BAP1 MUTATED                                  0     0
  BAP1 WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  BAP1 MUTATED                           1    11
  BAP1 WILD-TYPE                        21   215
D1809V13, multiclass
                                  clus
vv                                 BAP1 MUTATED BAP1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                      11            215
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1810) Variable = CDHR5 MUTATION ANALYSIS
D1810V1, survival
                 sevent
clus2               0   1
  CDHR5 MUTATED    11   1
  CDHR5 WILD-TYPE 367  92
  CDHR5 MUTATED CDHR5 WILD-TYPE 
             12             459 
  CDHR5 MUTATED CDHR5 WILD-TYPE 
              1              92 
$`CDHR5 MUTATED`
TCGA-A6-6653 TCGA-A6-6781 TCGA-AA-3815 TCGA-AA-3864 TCGA-AA-3877 TCGA-AA-3950 
       24.39        19.66        33.04        53.00        31.00        24.00 
TCGA-AA-3968 TCGA-AA-A03F TCGA-AY-6197 TCGA-DM-A0X9 TCGA-G4-6586 TCGA-DC-5869 
       21.99        18.05        21.44       119.70        35.80         5.03 

$`CDHR5 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
       25.08        25.18        24.16        21.76        24.69        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       35.05         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        31.07        30.05        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       29.98        18.05         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3971 
       26.01         2.01        20.98        34.03         2.01        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       41.00        39.98        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       33.01        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0XD 
        4.80         1.51        12.00        11.38        10.26        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-6155 
        6.97         4.73        78.12         7.17        15.02        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  CDHR5 MUTATED CDHR5 WILD-TYPE 
           5.03            0.00 
  CDHR5 MUTATED CDHR5 WILD-TYPE 
         119.70          148.01 
  CDHR5 MUTATED CDHR5 WILD-TYPE 
         24.195          20.020 
[1] "5.0 - 119.7 (24.2)" "0.0 - 148.0 (20.0)"
[1] "hr=" "2.9"
D1810V2, continuous
D1810V3, binary
                 cls
clus                0   1
  CDHR5 MUTATED    11   1
  CDHR5 WILD-TYPE 355 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDHR5 MUTATED     11    1
  CDHR5 WILD-TYPE  355  118
        clus
vv       CDHR5 MUTATED CDHR5 WILD-TYPE
  COLON             11             355
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CDHR5 MUTATED         3        0        1         5         0         0
  CDHR5 WILD-TYPE      88        1       31       133        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CDHR5 MUTATED           1          0          1          1        0         0
  CDHR5 WILD-TYPE        23         11         58         41       48        18
                 vv
clus              STAGE IVB
  CDHR5 MUTATED           0
  CDHR5 WILD-TYPE         1
D1810V4, multiclass
            clus
vv           CDHR5 MUTATED CDHR5 WILD-TYPE
  STAGE I                3              88
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              5             133
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             1              41
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CDHR5 MUTATED     1   2   8   1
  CDHR5 WILD-TYPE  16  90 321  49
D1810V5, multiclass
    clus
vv   CDHR5 MUTATED CDHR5 WILD-TYPE
  T1             1              16
  T2             2              90
  T3             8             321
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  CDHR5 MUTATED     9   2   1
  CDHR5 WILD-TYPE 278 111  86
D1810V6, multiclass
    clus
vv   CDHR5 MUTATED CDHR5 WILD-TYPE
  N0             9             278
  N1             2             111
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1810V7, binary
                 cls
clus                0   1
  CDHR5 MUTATED    10   0
  CDHR5 WILD-TYPE 365  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDHR5 MUTATED     10    0
  CDHR5 WILD-TYPE  365   65
   clus
vv  CDHR5 MUTATED CDHR5 WILD-TYPE
  0            10             365
  1             0              65
[1] 2 2
[1] FALSE
D1810V8, binary
                 cls
clus                0   1
  CDHR5 MUTATED     8   4
  CDHR5 WILD-TYPE 217 260
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDHR5 MUTATED      8    4
  CDHR5 WILD-TYPE  217  260
        clus
vv       CDHR5 MUTATED CDHR5 WILD-TYPE
  FEMALE             8             217
  MALE               4             260
[1] 2 2
[1] FALSE
D1810V9, binary
                 cls
clus                0   1
  CDHR5 MUTATED     9   0
  CDHR5 WILD-TYPE 341  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDHR5 MUTATED      9    0
  CDHR5 WILD-TYPE  341   22
     clus
vv    CDHR5 MUTATED CDHR5 WILD-TYPE
  NO              9             341
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CDHR5 MUTATED                      7                             4
  CDHR5 WILD-TYPE                  308                            43
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CDHR5 MUTATED                       1                              0
  CDHR5 WILD-TYPE                   105                             10
D1810V10, multiclass
                                clus
vv                               CDHR5 MUTATED CDHR5 WILD-TYPE
  COLON ADENOCARCINOMA                       7             308
  COLON MUCINOUS ADENOCARCINOMA              4              43
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  CDHR5 MUTATED    10   0   0   0
  CDHR5 WILD-TYPE 335   4  31  25
D1810V11, multiclass
    clus
vv   CDHR5 MUTATED CDHR5 WILD-TYPE
  R0            10             335
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1810V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CDHR5 MUTATED                                  0     0
  CDHR5 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CDHR5 MUTATED                           1     5
  CDHR5 WILD-TYPE                        21   221
D1810V13, multiclass
                                  clus
vv                                 CDHR5 MUTATED CDHR5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        5             221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1811) Variable = SLCO1B3 MUTATION ANALYSIS
D1811V1, survival
                   sevent
clus2                 0   1
  SLCO1B3 MUTATED    17   2
  SLCO1B3 WILD-TYPE 361  91
  SLCO1B3 MUTATED SLCO1B3 WILD-TYPE 
               19               452 
  SLCO1B3 MUTATED SLCO1B3 WILD-TYPE 
                2                91 
$`SLCO1B3 MUTATED`
TCGA-A6-3809 TCGA-A6-6653 TCGA-A6-6654 TCGA-AA-3510 TCGA-AA-3812 TCGA-AA-3844 
       32.75        24.39        23.87        63.98        35.05        14.93 
TCGA-AA-3950 TCGA-AA-3966 TCGA-AA-3975 TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01S 
       24.00         2.01        34.06         4.01        34.98         1.02 
TCGA-AD-6895 TCGA-AD-6963 TCGA-CM-4744 TCGA-D5-6923 TCGA-F4-6459 TCGA-AG-A002 
        0.72        27.42        20.02        12.43         8.61        20.98 
TCGA-F5-6465 
       49.51 

$`SLCO1B3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6780 TCGA-A6-6781 
       25.18        24.16        21.76        24.69        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 
       20.28         7.04         3.02         1.02        35.01         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3815 TCGA-AA-3818 
       26.99        19.04        19.04        10.06        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
        2.01        20.98        34.03        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
        1.02        35.01        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       21.37        15.52        56.55         0.79         5.79        22.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-4747 
       82.95         1.91       124.27        23.05        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
        4.41        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
       98.24        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
        9.96        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  SLCO1B3 MUTATED SLCO1B3 WILD-TYPE 
             0.72              0.00 
  SLCO1B3 MUTATED SLCO1B3 WILD-TYPE 
            63.98            148.01 
  SLCO1B3 MUTATED SLCO1B3 WILD-TYPE 
           23.870            20.085 
[1] "0.7 - 64.0 (23.9)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.6"
D1811V2, continuous
D1811V3, binary
                   cls
clus                  0   1
  SLCO1B3 MUTATED    17   2
  SLCO1B3 WILD-TYPE 349 117
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLCO1B3 MUTATED     17    2
  SLCO1B3 WILD-TYPE  349  117
        clus
vv       SLCO1B3 MUTATED SLCO1B3 WILD-TYPE
  COLON               17               349
  RECTUM               2               117
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SLCO1B3 MUTATED         5        0        1         4         3         0
  SLCO1B3 WILD-TYPE      86        1       31       134         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLCO1B3 MUTATED           1          0          2          1        0
  SLCO1B3 WILD-TYPE        23         11         57         41       48
                   vv
clus                STAGE IVA STAGE IVB
  SLCO1B3 MUTATED           0         0
  SLCO1B3 WILD-TYPE        18         1
D1811V4, multiclass
            clus
vv           SLCO1B3 MUTATED SLCO1B3 WILD-TYPE
  STAGE I                  5                86
  STAGE IA                 0                 1
  STAGE II                 1                31
  STAGE IIA                4               134
  STAGE IIB                3                 7
  STAGE IIC                0                 1
  STAGE III                1                23
  STAGE IIIA               0                11
  STAGE IIIB               2                57
  STAGE IIIC               1                41
  STAGE IV                 0                48
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  SLCO1B3 MUTATED     0   5  11   3
  SLCO1B3 WILD-TYPE  17  87 318  47
D1811V5, multiclass
    clus
vv   SLCO1B3 MUTATED SLCO1B3 WILD-TYPE
  T1               0                17
  T2               5                87
  T3              11               318
  T4               3                47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  SLCO1B3 MUTATED    14   3   2
  SLCO1B3 WILD-TYPE 273 110  85
D1811V6, multiclass
    clus
vv   SLCO1B3 MUTATED SLCO1B3 WILD-TYPE
  N0              14               273
  N1               3               110
  N2               2                85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1811V7, binary
                   cls
clus                  0   1
  SLCO1B3 MUTATED    17   0
  SLCO1B3 WILD-TYPE 358  65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLCO1B3 MUTATED     17    0
  SLCO1B3 WILD-TYPE  358   65
   clus
vv  SLCO1B3 MUTATED SLCO1B3 WILD-TYPE
  0              17               358
  1               0                65
[1] 2 2
[1] FALSE
D1811V8, binary
                   cls
clus                  0   1
  SLCO1B3 MUTATED    10   9
  SLCO1B3 WILD-TYPE 215 255
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLCO1B3 MUTATED     10    9
  SLCO1B3 WILD-TYPE  215  255
        clus
vv       SLCO1B3 MUTATED SLCO1B3 WILD-TYPE
  FEMALE              10               215
  MALE                 9               255
[1] 2 2
[1] FALSE
D1811V9, binary
                   cls
clus                  0   1
  SLCO1B3 MUTATED    14   1
  SLCO1B3 WILD-TYPE 336  21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLCO1B3 MUTATED     14    1
  SLCO1B3 WILD-TYPE  336   21
     clus
vv    SLCO1B3 MUTATED SLCO1B3 WILD-TYPE
  NO               14               336
  YES               1                21
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SLCO1B3 MUTATED                     13                             4
  SLCO1B3 WILD-TYPE                  302                            43
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SLCO1B3 MUTATED                       2                              0
  SLCO1B3 WILD-TYPE                   104                             10
D1811V10, multiclass
                                clus
vv                               SLCO1B3 MUTATED SLCO1B3 WILD-TYPE
  COLON ADENOCARCINOMA                        13               302
  COLON MUCINOUS ADENOCARCINOMA                4                43
  RECTAL ADENOCARCINOMA                        2               104
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  SLCO1B3 MUTATED    14   0   0   0
  SLCO1B3 WILD-TYPE 331   4  31  25
D1811V11, multiclass
    clus
vv   SLCO1B3 MUTATED SLCO1B3 WILD-TYPE
  R0              14               331
  R1               0                 4
  R2               0                31
  RX               0                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1811V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SLCO1B3 MUTATED                                  0     0
  SLCO1B3 WILD-TYPE                                1    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  SLCO1B3 MUTATED                           0     9
  SLCO1B3 WILD-TYPE                        22   217
D1811V13, multiclass
                                  clus
vv                                 SLCO1B3 MUTATED SLCO1B3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                      0                22
  WHITE                                          9               217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1812) Variable = TRAF3IP3 MUTATION ANALYSIS
D1812V1, survival
                    sevent
clus2                  0   1
  TRAF3IP3 MUTATED     9   3
  TRAF3IP3 WILD-TYPE 369  90
  TRAF3IP3 MUTATED TRAF3IP3 WILD-TYPE 
                12                459 
  TRAF3IP3 MUTATED TRAF3IP3 WILD-TYPE 
                 3                 90 
$`TRAF3IP3 MUTATED`
TCGA-A6-2676 TCGA-AA-3525 TCGA-AA-3672 TCGA-AA-3811 TCGA-CA-6717 TCGA-CA-6718 
       42.90         8.05         0.92        10.06        12.76        10.06 
TCGA-CM-5860 TCGA-CM-5864 TCGA-D5-6533 TCGA-D5-6930 TCGA-DM-A1HB TCGA-AG-A002 
       32.02        15.02         1.32         1.51       135.65        20.98 

$`TRAF3IP3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3526 
        1.02         9.07        24.03        37.05        36.03        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
       54.02         2.01        14.01        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3815 
       85.05        26.99        19.04        19.04        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 
        3.06         3.25         3.29         0.07        12.20        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5868 
       22.98        30.08        15.02         5.03        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       20.19        18.25        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        4.80        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 
      140.38         7.50        44.32       131.51       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  TRAF3IP3 MUTATED TRAF3IP3 WILD-TYPE 
              0.92               0.00 
  TRAF3IP3 MUTATED TRAF3IP3 WILD-TYPE 
            135.65             148.01 
  TRAF3IP3 MUTATED TRAF3IP3 WILD-TYPE 
             11.41              20.55 
[1] "0.9 - 135.7 (11.4)" "0.0 - 148.0 (20.6)"
[1] "hr=" "1.6"
D1812V2, continuous
D1812V3, binary
                    cls
clus                   0   1
  TRAF3IP3 MUTATED    12   1
  TRAF3IP3 WILD-TYPE 354 118
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  TRAF3IP3 MUTATED     12    1
  TRAF3IP3 WILD-TYPE  354  118
        clus
vv       TRAF3IP3 MUTATED TRAF3IP3 WILD-TYPE
  COLON                12                354
  RECTUM                1                118
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TRAF3IP3 MUTATED         2        0        0         5         1         0
  TRAF3IP3 WILD-TYPE      89        1       32       133         9         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TRAF3IP3 MUTATED           2          0          3          0        0
  TRAF3IP3 WILD-TYPE        22         11         56         42       48
                    vv
clus                 STAGE IVA STAGE IVB
  TRAF3IP3 MUTATED           0         0
  TRAF3IP3 WILD-TYPE        18         1
D1812V4, multiclass
            clus
vv           TRAF3IP3 MUTATED TRAF3IP3 WILD-TYPE
  STAGE I                   2                 89
  STAGE IA                  0                  1
  STAGE II                  0                 32
  STAGE IIA                 5                133
  STAGE IIB                 1                  9
  STAGE IIC                 0                  1
  STAGE III                 2                 22
  STAGE IIIA                0                 11
  STAGE IIIB                3                 56
  STAGE IIIC                0                 42
  STAGE IV                  0                 48
  STAGE IVA                 0                 18
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  TRAF3IP3 MUTATED     0   2   9   2
  TRAF3IP3 WILD-TYPE  17  90 320  48
D1812V5, multiclass
    clus
vv   TRAF3IP3 MUTATED TRAF3IP3 WILD-TYPE
  T1                0                 17
  T2                2                 90
  T3                9                320
  T4                2                 48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  TRAF3IP3 MUTATED     9   3   1
  TRAF3IP3 WILD-TYPE 278 110  86
D1812V6, multiclass
    clus
vv   TRAF3IP3 MUTATED TRAF3IP3 WILD-TYPE
  N0                9                278
  N1                3                110
  N2                1                 86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1812V7, binary
                    cls
clus                   0   1
  TRAF3IP3 MUTATED    13   0
  TRAF3IP3 WILD-TYPE 362  65
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  TRAF3IP3 MUTATED     13    0
  TRAF3IP3 WILD-TYPE  362   65
   clus
vv  TRAF3IP3 MUTATED TRAF3IP3 WILD-TYPE
  0               13                362
  1                0                 65
[1] 2 2
[1] FALSE
D1812V8, binary
                    cls
clus                   0   1
  TRAF3IP3 MUTATED     5   8
  TRAF3IP3 WILD-TYPE 220 256
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  TRAF3IP3 MUTATED      5    8
  TRAF3IP3 WILD-TYPE  220  256
        clus
vv       TRAF3IP3 MUTATED TRAF3IP3 WILD-TYPE
  FEMALE                5                220
  MALE                  8                256
[1] 2 2
[1] FALSE
D1812V9, binary
                    cls
clus                   0   1
  TRAF3IP3 MUTATED     9   0
  TRAF3IP3 WILD-TYPE 341  22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  TRAF3IP3 MUTATED      9    0
  TRAF3IP3 WILD-TYPE  341   22
     clus
vv    TRAF3IP3 MUTATED TRAF3IP3 WILD-TYPE
  NO                 9                341
  YES                0                 22
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  TRAF3IP3 MUTATED                      9                             2
  TRAF3IP3 WILD-TYPE                  306                            45
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  TRAF3IP3 MUTATED                       1                              0
  TRAF3IP3 WILD-TYPE                   105                             10
D1812V10, multiclass
                                clus
vv                               TRAF3IP3 MUTATED TRAF3IP3 WILD-TYPE
  COLON ADENOCARCINOMA                          9                306
  COLON MUCINOUS ADENOCARCINOMA                 2                 45
  RECTAL ADENOCARCINOMA                         1                105
  RECTAL MUCINOUS ADENOCARCINOMA                0                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  TRAF3IP3 MUTATED    10   0   0   2
  TRAF3IP3 WILD-TYPE 335   4  31  23
D1812V11, multiclass
    clus
vv   TRAF3IP3 MUTATED TRAF3IP3 WILD-TYPE
  R0               10                335
  R1                0                  4
  R2                0                 31
  RX                2                 23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1812V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TRAF3IP3 MUTATED                                  0     2
  TRAF3IP3 WILD-TYPE                                1     9
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  TRAF3IP3 MUTATED                           0     6
  TRAF3IP3 WILD-TYPE                        22   220
D1812V13, multiclass
                                  clus
vv                                 TRAF3IP3 MUTATED TRAF3IP3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           2                  9
  BLACK OR AFRICAN AMERICAN                       0                 22
  WHITE                                           6                220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1813) Variable = RXRA MUTATION ANALYSIS
D1813V1, survival
                sevent
clus2              0   1
  RXRA MUTATED     6   2
  RXRA WILD-TYPE 372  91
  RXRA MUTATED RXRA WILD-TYPE 
             8            463 
  RXRA MUTATED RXRA WILD-TYPE 
             2             91 
$`RXRA MUTATED`
TCGA-AA-3492 TCGA-AA-3977 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-CM-4743 TCGA-D5-6928 
        3.02        25.02        58.39        49.41        23.05        11.64 
TCGA-DM-A1HB TCGA-F4-6856 
      135.65        35.31 

$`RXRA WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       33.01        21.44        17.82         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        88.21         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
      124.27        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
       14.30         9.04         9.44         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
       44.32       131.51       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 
       16.24        33.67        13.25         0.53        47.41       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  RXRA MUTATED RXRA WILD-TYPE 
          3.02           0.00 
  RXRA MUTATED RXRA WILD-TYPE 
        135.65         148.01 
  RXRA MUTATED RXRA WILD-TYPE 
        30.165         20.050 
[1] "3.0 - 135.7 (30.2)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.2"
D1813V2, continuous
D1813V3, binary
                cls
clus               0   1
  RXRA MUTATED     8   0
  RXRA WILD-TYPE 358 119
[1] "tbl2"
                cls
clus             [,1] [,2]
  RXRA MUTATED      8    0
  RXRA WILD-TYPE  358  119
        clus
vv       RXRA MUTATED RXRA WILD-TYPE
  COLON             8            358
  RECTUM            0            119
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RXRA MUTATED         1        0        2         3         0         0
  RXRA WILD-TYPE      90        1       30       135        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RXRA MUTATED           0          0          1          0        0         0
  RXRA WILD-TYPE        24         11         58         42       48        18
                vv
clus             STAGE IVB
  RXRA MUTATED           0
  RXRA WILD-TYPE         1
D1813V4, multiclass
            clus
vv           RXRA MUTATED RXRA WILD-TYPE
  STAGE I               1             90
  STAGE IA              0              1
  STAGE II              2             30
  STAGE IIA             3            135
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            1             58
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  RXRA MUTATED     0   2   6   0
  RXRA WILD-TYPE  17  90 323  50
D1813V5, multiclass
    clus
vv   RXRA MUTATED RXRA WILD-TYPE
  T1            0             17
  T2            2             90
  T3            6            323
  T4            0             50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  RXRA MUTATED     7   1   0
  RXRA WILD-TYPE 280 112  87
D1813V6, multiclass
    clus
vv   RXRA MUTATED RXRA WILD-TYPE
  N0            7            280
  N1            1            112
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1813V7, binary
                cls
clus               0   1
  RXRA MUTATED     6   0
  RXRA WILD-TYPE 369  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  RXRA MUTATED      6    0
  RXRA WILD-TYPE  369   65
   clus
vv  RXRA MUTATED RXRA WILD-TYPE
  0            6            369
  1            0             65
[1] 2 2
[1] FALSE
D1813V8, binary
                cls
clus               0   1
  RXRA MUTATED     2   6
  RXRA WILD-TYPE 223 258
[1] "tbl2"
                cls
clus             [,1] [,2]
  RXRA MUTATED      2    6
  RXRA WILD-TYPE  223  258
        clus
vv       RXRA MUTATED RXRA WILD-TYPE
  FEMALE            2            223
  MALE              6            258
[1] 2 2
[1] FALSE
D1813V9, binary
                cls
clus               0   1
  RXRA MUTATED     7   0
  RXRA WILD-TYPE 343  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  RXRA MUTATED      7    0
  RXRA WILD-TYPE  343   22
     clus
vv    RXRA MUTATED RXRA WILD-TYPE
  NO             7            343
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  RXRA MUTATED                      5                             2
  RXRA WILD-TYPE                  310                            45
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  RXRA MUTATED                       0                              0
  RXRA WILD-TYPE                   106                             10
D1813V10, multiclass
                                clus
vv                               RXRA MUTATED RXRA WILD-TYPE
  COLON ADENOCARCINOMA                      5            310
  COLON MUCINOUS ADENOCARCINOMA             2             45
  RECTAL ADENOCARCINOMA                     0            106
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  RXRA MUTATED     5   0   0   0
  RXRA WILD-TYPE 340   4  31  25
D1813V11, multiclass
    clus
vv   RXRA MUTATED RXRA WILD-TYPE
  R0            5            340
  R1            0              4
  R2            0             31
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1813V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RXRA MUTATED                                  0     0
  RXRA WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  RXRA MUTATED                           0     6
  RXRA WILD-TYPE                        22   220
D1813V13, multiclass
                                  clus
vv                                 RXRA MUTATED RXRA WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       6            220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1814) Variable = DOPEY2 MUTATION ANALYSIS
D1814V1, survival
                  sevent
clus2                0   1
  DOPEY2 MUTATED    12   3
  DOPEY2 WILD-TYPE 366  90
  DOPEY2 MUTATED DOPEY2 WILD-TYPE 
              15              456 
  DOPEY2 MUTATED DOPEY2 WILD-TYPE 
               3               90 
$`DOPEY2 MUTATED`
TCGA-A6-6649 TCGA-AA-3525 TCGA-AA-3663 TCGA-AA-3713 TCGA-AA-3821 TCGA-AA-A00N 
       24.16         8.05         6.97        19.04         1.02         4.01 
TCGA-AD-6889 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-CA-6717 TCGA-CM-4743 TCGA-CM-5861 
       56.55         6.77       100.01        12.76        23.05        15.02 
TCGA-DM-A28H TCGA-AG-A002 TCGA-DC-5337 
      117.07        20.98        15.02 

$`DOPEY2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.08        25.18        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3526 
        1.02         9.07        24.03        37.05        36.03        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       85.05        26.99        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
        0.99        25.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       21.37        15.52         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
       12.10        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
      124.27        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 
       22.03        22.98        30.08        32.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
      119.93        35.97        60.79        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
        7.17         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  DOPEY2 MUTATED DOPEY2 WILD-TYPE 
            1.02             0.00 
  DOPEY2 MUTATED DOPEY2 WILD-TYPE 
          117.07           148.01 
  DOPEY2 MUTATED DOPEY2 WILD-TYPE 
          15.020           20.415 
[1] "1.0 - 117.1 (15.0)" "0.0 - 148.0 (20.4)"
[1] "hr=" "1.1"
D1814V2, continuous
D1814V3, binary
                  cls
clus                 0   1
  DOPEY2 MUTATED    14   2
  DOPEY2 WILD-TYPE 352 117
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DOPEY2 MUTATED     14    2
  DOPEY2 WILD-TYPE  352  117
        clus
vv       DOPEY2 MUTATED DOPEY2 WILD-TYPE
  COLON              14              352
  RECTUM              2              117
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DOPEY2 MUTATED         4        0        3         4         1         0
  DOPEY2 WILD-TYPE      87        1       29       134         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DOPEY2 MUTATED           0          0          2          1        1
  DOPEY2 WILD-TYPE        24         11         57         41       47
                  vv
clus               STAGE IVA STAGE IVB
  DOPEY2 MUTATED           0         0
  DOPEY2 WILD-TYPE        18         1
D1814V4, multiclass
            clus
vv           DOPEY2 MUTATED DOPEY2 WILD-TYPE
  STAGE I                 4               87
  STAGE IA                0                1
  STAGE II                3               29
  STAGE IIA               4              134
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              2               57
  STAGE IIIC              1               41
  STAGE IV                1               47
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  DOPEY2 MUTATED     1   3  10   2
  DOPEY2 WILD-TYPE  16  89 319  48
D1814V5, multiclass
    clus
vv   DOPEY2 MUTATED DOPEY2 WILD-TYPE
  T1              1               16
  T2              3               89
  T3             10              319
  T4              2               48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  DOPEY2 MUTATED    13   2   1
  DOPEY2 WILD-TYPE 274 111  86
D1814V6, multiclass
    clus
vv   DOPEY2 MUTATED DOPEY2 WILD-TYPE
  N0             13              274
  N1              2              111
  N2              1               86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1814V7, binary
                  cls
clus                 0   1
  DOPEY2 MUTATED    14   1
  DOPEY2 WILD-TYPE 361  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DOPEY2 MUTATED     14    1
  DOPEY2 WILD-TYPE  361   64
   clus
vv  DOPEY2 MUTATED DOPEY2 WILD-TYPE
  0             14              361
  1              1               64
[1] 2 2
[1] FALSE
D1814V8, binary
                  cls
clus                 0   1
  DOPEY2 MUTATED     3  13
  DOPEY2 WILD-TYPE 222 251
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DOPEY2 MUTATED      3   13
  DOPEY2 WILD-TYPE  222  251
        clus
vv       DOPEY2 MUTATED DOPEY2 WILD-TYPE
  FEMALE              3              222
  MALE               13              251
[1] 2 2
[1] FALSE
D1814V9, binary
                  cls
clus                 0   1
  DOPEY2 MUTATED    11   1
  DOPEY2 WILD-TYPE 339  21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DOPEY2 MUTATED     11    1
  DOPEY2 WILD-TYPE  339   21
     clus
vv    DOPEY2 MUTATED DOPEY2 WILD-TYPE
  NO              11              339
  YES              1               21
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  DOPEY2 MUTATED                     11                             3
  DOPEY2 WILD-TYPE                  304                            44
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  DOPEY2 MUTATED                       2                              0
  DOPEY2 WILD-TYPE                   104                             10
D1814V10, multiclass
                                clus
vv                               DOPEY2 MUTATED DOPEY2 WILD-TYPE
  COLON ADENOCARCINOMA                       11              304
  COLON MUCINOUS ADENOCARCINOMA               3               44
  RECTAL ADENOCARCINOMA                       2              104
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  DOPEY2 MUTATED     9   0   1   1
  DOPEY2 WILD-TYPE 336   4  30  24
D1814V11, multiclass
    clus
vv   DOPEY2 MUTATED DOPEY2 WILD-TYPE
  R0              9              336
  R1              0                4
  R2              1               30
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1814V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DOPEY2 MUTATED                                  0     2
  DOPEY2 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  DOPEY2 MUTATED                           0     7
  DOPEY2 WILD-TYPE                        22   219
D1814V13, multiclass
                                  clus
vv                                 DOPEY2 MUTATED DOPEY2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                9
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         7              219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1815) Variable = LCN9 MUTATION ANALYSIS
D1815V1, survival
                sevent
clus2              0   1
  LCN9 MUTATED     2   1
  LCN9 WILD-TYPE 376  92
  LCN9 MUTATED LCN9 WILD-TYPE 
             3            468 
  LCN9 MUTATED LCN9 WILD-TYPE 
             1             92 
$`LCN9 MUTATED`
TCGA-AZ-6608 TCGA-CK-4950 TCGA-D5-6534 
        1.61        85.45        43.27 

$`LCN9 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
       11.74         3.19        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
      148.01        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       20.19        18.25         1.32        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  LCN9 MUTATED LCN9 WILD-TYPE 
          1.61           0.00 
  LCN9 MUTATED LCN9 WILD-TYPE 
         85.45         148.01 
  LCN9 MUTATED LCN9 WILD-TYPE 
        43.270         20.155 
[1] "1.6 - 85.5 (43.3)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1"  
D1815V2, continuous
D1815V3, binary
                cls
clus               0   1
  LCN9 MUTATED     4   0
  LCN9 WILD-TYPE 362 119
[1] "tbl2"
                cls
clus             [,1] [,2]
  LCN9 MUTATED      4    0
  LCN9 WILD-TYPE  362  119
        clus
vv       LCN9 MUTATED LCN9 WILD-TYPE
  COLON             4            362
  RECTUM            0            119
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  LCN9 MUTATED         0        0        0         2         0         0
  LCN9 WILD-TYPE      91        1       32       136        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  LCN9 MUTATED           0          1          1          0        0         0
  LCN9 WILD-TYPE        24         10         58         42       48        18
                vv
clus             STAGE IVB
  LCN9 MUTATED           0
  LCN9 WILD-TYPE         1
D1815V4, multiclass
            clus
vv           LCN9 MUTATED LCN9 WILD-TYPE
  STAGE I               0             91
  STAGE IA              0              1
  STAGE II              0             32
  STAGE IIA             2            136
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            1             10
  STAGE IIIB            1             58
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  LCN9 MUTATED     0   1   3   0
  LCN9 WILD-TYPE  17  91 326  50
D1815V5, multiclass
    clus
vv   LCN9 MUTATED LCN9 WILD-TYPE
  T1            0             17
  T2            1             91
  T3            3            326
  T4            0             50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  LCN9 MUTATED     2   2   0
  LCN9 WILD-TYPE 285 111  87
D1815V6, multiclass
    clus
vv   LCN9 MUTATED LCN9 WILD-TYPE
  N0            2            285
  N1            2            111
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1815V7, binary
                cls
clus               0   1
  LCN9 MUTATED     4   0
  LCN9 WILD-TYPE 371  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  LCN9 MUTATED      4    0
  LCN9 WILD-TYPE  371   65
   clus
vv  LCN9 MUTATED LCN9 WILD-TYPE
  0            4            371
  1            0             65
[1] 2 2
[1] FALSE
D1815V8, binary
                cls
clus               0   1
  LCN9 MUTATED     4   0
  LCN9 WILD-TYPE 221 264
[1] "tbl2"
                cls
clus             [,1] [,2]
  LCN9 MUTATED      4    0
  LCN9 WILD-TYPE  221  264
        clus
vv       LCN9 MUTATED LCN9 WILD-TYPE
  FEMALE            4            221
  MALE              0            264
[1] 2 2
[1] FALSE
D1815V9, binary
                cls
clus               0   1
  LCN9 MUTATED     3   0
  LCN9 WILD-TYPE 347  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  LCN9 MUTATED      3    0
  LCN9 WILD-TYPE  347   22
     clus
vv    LCN9 MUTATED LCN9 WILD-TYPE
  NO             3            347
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  LCN9 MUTATED                      3                             1
  LCN9 WILD-TYPE                  312                            46
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  LCN9 MUTATED                       0                              0
  LCN9 WILD-TYPE                   106                             10
D1815V10, multiclass
                                clus
vv                               LCN9 MUTATED LCN9 WILD-TYPE
  COLON ADENOCARCINOMA                      3            312
  COLON MUCINOUS ADENOCARCINOMA             1             46
  RECTAL ADENOCARCINOMA                     0            106
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  LCN9 MUTATED     2   1   0   0
  LCN9 WILD-TYPE 343   3  31  25
D1815V11, multiclass
    clus
vv   LCN9 MUTATED LCN9 WILD-TYPE
  R0            2            343
  R1            1              3
  R2            0             31
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1815V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  LCN9 MUTATED                                  0     0
  LCN9 WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  LCN9 MUTATED                           1     2
  LCN9 WILD-TYPE                        21   224
D1815V13, multiclass
                                  clus
vv                                 LCN9 MUTATED LCN9 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                       2            224
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1816) Variable = LAMB4 MUTATION ANALYSIS
D1816V1, survival
                 sevent
clus2               0   1
  LAMB4 MUTATED    22   7
  LAMB4 WILD-TYPE 356  86
  LAMB4 MUTATED LAMB4 WILD-TYPE 
             29             442 
  LAMB4 MUTATED LAMB4 WILD-TYPE 
              7              86 
$`LAMB4 MUTATED`
TCGA-AA-3492 TCGA-AA-3555 TCGA-AA-3655 TCGA-AA-3681 TCGA-AA-3710 TCGA-AA-3815 
        3.02        29.95        61.02         5.98        26.99        33.04 
TCGA-AA-3864 TCGA-AA-3877 TCGA-AA-3950 TCGA-AA-3968 TCGA-AA-A00N TCGA-AA-A024 
       53.00        31.00        24.00        21.99         4.01        39.06 
TCGA-AD-6963 TCGA-AY-6386 TCGA-AZ-6600 TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-5344 
       27.42        17.82        12.10        12.76        10.06        22.03 
TCGA-D5-5539 TCGA-D5-6926 TCGA-D5-6929 TCGA-DM-A0XF TCGA-F4-6459 TCGA-F4-6807 
       19.59         9.04         4.80        38.20         8.61        16.24 
TCGA-G4-6628 TCGA-AG-A002 TCGA-AG-A02N TCGA-EF-5830 TCGA-G5-6235 
       79.69        20.98        61.97         0.49        55.76 

$`LAMB4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       13.02        24.00        17.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       13.94        19.99        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
       11.01        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
       19.04        19.04        10.06        35.05         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 
       17.03        24.03        27.02        29.98        18.05         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 
       12.99        24.00        33.01        26.01         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       37.02        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        33.01        21.44        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 
       11.01        10.06        12.03        45.40        12.26        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6927 
        1.48         3.68         4.41        12.43        14.30         9.44 
TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       11.64         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       24.43       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
       98.24        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       34.42        41.42        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 
       13.78        35.80        26.17        91.79        46.75        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 
       10.98        49.97         1.94        38.96        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EI-6506 TCGA-EI-6507 
       57.24        24.13        51.48        32.61        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6641 
       32.19         0.66         0.69        26.43 

  LAMB4 MUTATED LAMB4 WILD-TYPE 
           0.49            0.00 
  LAMB4 MUTATED LAMB4 WILD-TYPE 
          79.69          148.01 
  LAMB4 MUTATED LAMB4 WILD-TYPE 
         21.990          20.085 
[1] "0.5 - 79.7 (22.0)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.2"
D1816V2, continuous
D1816V3, binary
                 cls
clus                0   1
  LAMB4 MUTATED    26   4
  LAMB4 WILD-TYPE 340 115
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LAMB4 MUTATED     26    4
  LAMB4 WILD-TYPE  340  115
        clus
vv       LAMB4 MUTATED LAMB4 WILD-TYPE
  COLON             26             340
  RECTUM             4             115
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  LAMB4 MUTATED         4        0        5         7         2         0
  LAMB4 WILD-TYPE      87        1       27       131         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  LAMB4 MUTATED           1          1          5          2        2         0
  LAMB4 WILD-TYPE        23         10         54         40       46        18
                 vv
clus              STAGE IVB
  LAMB4 MUTATED           0
  LAMB4 WILD-TYPE         1
D1816V4, multiclass
            clus
vv           LAMB4 MUTATED LAMB4 WILD-TYPE
  STAGE I                4              87
  STAGE IA               0               1
  STAGE II               5              27
  STAGE IIA              7             131
  STAGE IIB              2               8
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             1              10
  STAGE IIIB             5              54
  STAGE IIIC             2              40
  STAGE IV               2              46
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  LAMB4 MUTATED     1   3  22   4
  LAMB4 WILD-TYPE  16  89 307  46
D1816V5, multiclass
    clus
vv   LAMB4 MUTATED LAMB4 WILD-TYPE
  T1             1              16
  T2             3              89
  T3            22             307
  T4             4              46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  LAMB4 MUTATED    19   8   3
  LAMB4 WILD-TYPE 268 105  84
D1816V6, multiclass
    clus
vv   LAMB4 MUTATED LAMB4 WILD-TYPE
  N0            19             268
  N1             8             105
  N2             3              84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1816V7, binary
                 cls
clus                0   1
  LAMB4 MUTATED    26   2
  LAMB4 WILD-TYPE 349  63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LAMB4 MUTATED     26    2
  LAMB4 WILD-TYPE  349   63
   clus
vv  LAMB4 MUTATED LAMB4 WILD-TYPE
  0            26             349
  1             2              63
[1] 2 2
[1] FALSE
D1816V8, binary
                 cls
clus                0   1
  LAMB4 MUTATED    15  15
  LAMB4 WILD-TYPE 210 249
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LAMB4 MUTATED     15   15
  LAMB4 WILD-TYPE  210  249
        clus
vv       LAMB4 MUTATED LAMB4 WILD-TYPE
  FEMALE            15             210
  MALE              15             249
[1] 2 2
[1] FALSE
D1816V9, binary
                 cls
clus                0   1
  LAMB4 MUTATED    22   1
  LAMB4 WILD-TYPE 328  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LAMB4 MUTATED     22    1
  LAMB4 WILD-TYPE  328   21
     clus
vv    LAMB4 MUTATED LAMB4 WILD-TYPE
  NO             22             328
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  LAMB4 MUTATED                     18                             7
  LAMB4 WILD-TYPE                  297                            40
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  LAMB4 MUTATED                       4                              0
  LAMB4 WILD-TYPE                   102                             10
D1816V10, multiclass
                                clus
vv                               LAMB4 MUTATED LAMB4 WILD-TYPE
  COLON ADENOCARCINOMA                      18             297
  COLON MUCINOUS ADENOCARCINOMA              7              40
  RECTAL ADENOCARCINOMA                      4             102
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  LAMB4 MUTATED    24   1   0   2
  LAMB4 WILD-TYPE 321   3  31  23
D1816V11, multiclass
    clus
vv   LAMB4 MUTATED LAMB4 WILD-TYPE
  R0            24             321
  R1             1               3
  R2             0              31
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1816V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  LAMB4 MUTATED                                  0     2
  LAMB4 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  LAMB4 MUTATED                           2    11
  LAMB4 WILD-TYPE                        20   215
D1816V13, multiclass
                                  clus
vv                                 LAMB4 MUTATED LAMB4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               9
  BLACK OR AFRICAN AMERICAN                    2              20
  WHITE                                       11             215
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1817) Variable = MED24 MUTATION ANALYSIS
D1817V1, survival
                 sevent
clus2               0   1
  MED24 MUTATED    10   1
  MED24 WILD-TYPE 368  92
  MED24 MUTATED MED24 WILD-TYPE 
             11             460 
  MED24 MUTATED MED24 WILD-TYPE 
              1              92 
$`MED24 MUTATED`
TCGA-A6-6780 TCGA-AA-3520 TCGA-AA-3555 TCGA-AA-3663 TCGA-AA-A01K TCGA-AA-A01R 
       20.12        24.03        29.95         6.97        31.00        35.01 
TCGA-CA-6719 TCGA-D5-6930 TCGA-F4-6570 TCGA-AG-A002 TCGA-AG-A00Y 
       14.30         1.51         6.18        20.98        23.01 

$`MED24 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        1.02         9.07        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       24.00        17.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02        78.08         6.05        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01P 
        1.02        10.98        32.02        12.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
        1.02         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 
        3.29         0.07        12.20        12.76        10.06        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
        9.44        11.64         4.80        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
        6.02        25.97        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  MED24 MUTATED MED24 WILD-TYPE 
           1.51            0.00 
  MED24 MUTATED MED24 WILD-TYPE 
          35.01          148.01 
  MED24 MUTATED MED24 WILD-TYPE 
          20.98           20.12 
[1] "1.5 - 35.0 (21.0)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.5"
D1817V2, continuous
D1817V3, binary
                 cls
clus                0   1
  MED24 MUTATED     9   2
  MED24 WILD-TYPE 357 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MED24 MUTATED      9    2
  MED24 WILD-TYPE  357  117
        clus
vv       MED24 MUTATED MED24 WILD-TYPE
  COLON              9             357
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MED24 MUTATED         1        0        2         6         0         0
  MED24 WILD-TYPE      90        1       30       132        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MED24 MUTATED           1          0          0          1        0         0
  MED24 WILD-TYPE        23         11         59         41       48        18
                 vv
clus              STAGE IVB
  MED24 MUTATED           0
  MED24 WILD-TYPE         1
D1817V4, multiclass
            clus
vv           MED24 MUTATED MED24 WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA              6             132
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             1              41
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  MED24 MUTATED     0   1  10   0
  MED24 WILD-TYPE  17  91 319  50
D1817V5, multiclass
    clus
vv   MED24 MUTATED MED24 WILD-TYPE
  T1             0              17
  T2             1              91
  T3            10             319
  T4             0              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  MED24 MUTATED     9   0   2
  MED24 WILD-TYPE 278 113  85
D1817V6, multiclass
    clus
vv   MED24 MUTATED MED24 WILD-TYPE
  N0             9             278
  N1             0             113
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1817V7, binary
                 cls
clus                0   1
  MED24 MUTATED    10   0
  MED24 WILD-TYPE 365  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MED24 MUTATED     10    0
  MED24 WILD-TYPE  365   65
   clus
vv  MED24 MUTATED MED24 WILD-TYPE
  0            10             365
  1             0              65
[1] 2 2
[1] FALSE
D1817V8, binary
                 cls
clus                0   1
  MED24 MUTATED     4   7
  MED24 WILD-TYPE 221 257
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MED24 MUTATED      4    7
  MED24 WILD-TYPE  221  257
        clus
vv       MED24 MUTATED MED24 WILD-TYPE
  FEMALE             4             221
  MALE               7             257
[1] 2 2
[1] FALSE
D1817V9, binary
                 cls
clus                0   1
  MED24 MUTATED     9   1
  MED24 WILD-TYPE 341  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MED24 MUTATED      9    1
  MED24 WILD-TYPE  341   21
     clus
vv    MED24 MUTATED MED24 WILD-TYPE
  NO              9             341
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MED24 MUTATED                      5                             4
  MED24 WILD-TYPE                  310                            43
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MED24 MUTATED                       2                              0
  MED24 WILD-TYPE                   104                             10
D1817V10, multiclass
                                clus
vv                               MED24 MUTATED MED24 WILD-TYPE
  COLON ADENOCARCINOMA                       5             310
  COLON MUCINOUS ADENOCARCINOMA              4              43
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  MED24 MUTATED     9   0   0   1
  MED24 WILD-TYPE 336   4  31  24
D1817V11, multiclass
    clus
vv   MED24 MUTATED MED24 WILD-TYPE
  R0             9             336
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1817V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MED24 MUTATED                                  0     1
  MED24 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  MED24 MUTATED                           0     3
  MED24 WILD-TYPE                        22   223
D1817V13, multiclass
                                  clus
vv                                 MED24 MUTATED MED24 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        3             223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1818) Variable = CUBN MUTATION ANALYSIS
D1818V1, survival
                sevent
clus2              0   1
  CUBN MUTATED    42  11
  CUBN WILD-TYPE 336  82
  CUBN MUTATED CUBN WILD-TYPE 
            53            418 
  CUBN MUTATED CUBN WILD-TYPE 
            11             82 
$`CUBN MUTATED`
TCGA-A6-2672 TCGA-A6-2678 TCGA-A6-4105 TCGA-A6-5659 TCGA-A6-6138 TCGA-A6-6141 
       46.65        42.28        14.53        30.44        22.52         8.38 
TCGA-A6-6781 TCGA-AA-3492 TCGA-AA-3544 TCGA-AA-3554 TCGA-AA-3558 TCGA-AA-3663 
       19.66         3.02        14.01        17.95        20.98         6.97 
TCGA-AA-3672 TCGA-AA-3710 TCGA-AA-3846 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3977 
        0.92        26.99        17.03        30.05        53.00        25.02 
TCGA-AA-3989 TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01K TCGA-AA-A01R 
        7.96        18.05         4.01        34.98        31.00        35.01 
TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AZ-6598 TCGA-AZ-6603 
        0.07        56.55         0.79         0.72        49.41        29.56 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-6168 TCGA-CM-6675 TCGA-D5-6536 
       12.20        12.76        10.06        12.99        13.05        17.85 
TCGA-D5-6537 TCGA-D5-6540 TCGA-D5-6898 TCGA-D5-6931 TCGA-DM-A0XD TCGA-DM-A1D7 
        4.80        16.14         1.48        12.00        24.43        13.32 
TCGA-F4-6570 TCGA-F4-6703 TCGA-G4-6299 TCGA-G4-6315 TCGA-G4-6588 TCGA-AF-6136 
        6.18        47.87        74.56        61.91        26.17        15.39 
TCGA-AG-3881 TCGA-AG-3898 TCGA-AG-A002 TCGA-EI-6510 TCGA-F5-6811 
       19.04        48.03        20.98        18.28        32.19 

$`CUBN WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2683 TCGA-A6-3807 
       43.76        43.76        42.90        24.33        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 
       33.34        32.75        36.53        32.91        31.63        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 
       33.53        23.61        22.09        22.06        32.71        27.09 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 
       23.87        20.12        20.28         7.04         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
       12.99         0.99        33.99        21.01        13.02        24.00 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       29.95        23.01        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
       78.08         6.05        54.02         2.01        14.01        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        85.05        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3848 
       15.95        38.99        37.02        14.93         0.00        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       31.07        31.07        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3994 TCGA-AA-A004 
       24.00        27.02        27.02        19.07        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00L 
       38.04        19.00        30.02        34.03        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01P 
        1.02        10.98        32.02        12.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
        1.02         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 
        0.92        41.00        39.98        18.05        40.96        21.37 
TCGA-AD-6888 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
       15.52         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6605 
       62.79        88.21         6.77        12.10       100.01         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        3.29         0.07        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6676 
       13.02        15.02        14.04        11.01        12.95        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6920 
       43.27        15.12        17.13        12.49        15.58         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XF 
        4.80         1.51        11.38        10.26       119.70        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
      130.65        92.75        49.91        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       31.96        35.74         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        35.80        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 
       34.49        10.39        14.50        16.83        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99         0.99        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3902 
       17.03        13.02        35.01        14.01         1.02        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       19.96        20.91         9.96        49.51        31.30        28.57 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  CUBN MUTATED CUBN WILD-TYPE 
          0.07           0.00 
  CUBN MUTATED CUBN WILD-TYPE 
         74.56         148.01 
  CUBN MUTATED CUBN WILD-TYPE 
        18.050         20.945 
[1] "0.1 - 74.6 (18.1)"  "0.0 - 148.0 (20.9)"
[1] "hr=" "1.2"
D1818V2, continuous
D1818V3, binary
                cls
clus               0   1
  CUBN MUTATED    52   6
  CUBN WILD-TYPE 314 113
[1] "tbl2"
                cls
clus             [,1] [,2]
  CUBN MUTATED     52    6
  CUBN WILD-TYPE  314  113
        clus
vv       CUBN MUTATED CUBN WILD-TYPE
  COLON            52            314
  RECTUM            6            113
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CUBN MUTATED         8        0        5        22         2         0
  CUBN WILD-TYPE      83        1       27       116         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CUBN MUTATED           2          0          4          5        4         1
  CUBN WILD-TYPE        22         11         55         37       44        17
                vv
clus             STAGE IVB
  CUBN MUTATED           1
  CUBN WILD-TYPE         0
D1818V4, multiclass
            clus
vv           CUBN MUTATED CUBN WILD-TYPE
  STAGE I               8             83
  STAGE IA              0              1
  STAGE II              5             27
  STAGE IIA            22            116
  STAGE IIB             2              8
  STAGE IIC             0              1
  STAGE III             2             22
  STAGE IIIA            0             11
  STAGE IIIB            4             55
  STAGE IIIC            5             37
  STAGE IV              4             44
  STAGE IVA             1             17
  STAGE IVB             1              0
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  CUBN MUTATED     1  11  39   7
  CUBN WILD-TYPE  16  81 290  43
D1818V5, multiclass
    clus
vv   CUBN MUTATED CUBN WILD-TYPE
  T1            1             16
  T2           11             81
  T3           39            290
  T4            7             43
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  CUBN MUTATED    40   9   9
  CUBN WILD-TYPE 247 104  78
D1818V6, multiclass
    clus
vv   CUBN MUTATED CUBN WILD-TYPE
  N0           40            247
  N1            9            104
  N2            9             78
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1818V7, binary
                cls
clus               0   1
  CUBN MUTATED    42   5
  CUBN WILD-TYPE 333  60
[1] "tbl2"
                cls
clus             [,1] [,2]
  CUBN MUTATED     42    5
  CUBN WILD-TYPE  333   60
   clus
vv  CUBN MUTATED CUBN WILD-TYPE
  0           42            333
  1            5             60
[1] 2 2
[1] FALSE
D1818V8, binary
                cls
clus               0   1
  CUBN MUTATED    22  36
  CUBN WILD-TYPE 203 228
[1] "tbl2"
                cls
clus             [,1] [,2]
  CUBN MUTATED     22   36
  CUBN WILD-TYPE  203  228
        clus
vv       CUBN MUTATED CUBN WILD-TYPE
  FEMALE           22            203
  MALE             36            228
[1] 2 2
[1] FALSE
D1818V9, binary
                cls
clus               0   1
  CUBN MUTATED    42   2
  CUBN WILD-TYPE 308  20
[1] "tbl2"
                cls
clus             [,1] [,2]
  CUBN MUTATED     42    2
  CUBN WILD-TYPE  308   20
     clus
vv    CUBN MUTATED CUBN WILD-TYPE
  NO            42            308
  YES            2             20
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CUBN MUTATED                     43                             8
  CUBN WILD-TYPE                  272                            39
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CUBN MUTATED                       5                              0
  CUBN WILD-TYPE                   101                             10
D1818V10, multiclass
                                clus
vv                               CUBN MUTATED CUBN WILD-TYPE
  COLON ADENOCARCINOMA                     43            272
  COLON MUCINOUS ADENOCARCINOMA             8             39
  RECTAL ADENOCARCINOMA                     5            101
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  CUBN MUTATED    37   0   4   3
  CUBN WILD-TYPE 308   4  27  22
D1818V11, multiclass
    clus
vv   CUBN MUTATED CUBN WILD-TYPE
  R0           37            308
  R1            0              4
  R2            4             27
  RX            3             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1818V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CUBN MUTATED                                  0     4
  CUBN WILD-TYPE                                1     7
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  CUBN MUTATED                           3    27
  CUBN WILD-TYPE                        19   199
D1818V13, multiclass
                                  clus
vv                                 CUBN MUTATED CUBN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       4              7
  BLACK OR AFRICAN AMERICAN                   3             19
  WHITE                                      27            199
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1819) Variable = ACVR1C MUTATION ANALYSIS
D1819V1, survival
                  sevent
clus2                0   1
  ACVR1C MUTATED    11   0
  ACVR1C WILD-TYPE 367  93
  ACVR1C MUTATED ACVR1C WILD-TYPE 
              11              460 
  ACVR1C MUTATED ACVR1C WILD-TYPE 
               0               93 
$`ACVR1C MUTATED`
TCGA-A6-5661 TCGA-AA-3855 TCGA-AA-3966 TCGA-AZ-4315 TCGA-CM-4752 TCGA-CM-5349 
       33.53        32.05         2.01        58.39        13.02        30.08 
TCGA-F4-6808 TCGA-G4-6299 TCGA-G4-6628 TCGA-AG-A002 TCGA-CL-5917 
       33.67        74.56        79.69        20.98        78.12 

$`ACVR1C WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       20.98        34.03        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-5341 
      124.27        23.05        20.02        37.02        25.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.03        22.98        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       41.42        16.24        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
      133.18        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       26.17        91.79        46.75        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
       33.17         6.97         4.73         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  ACVR1C MUTATED ACVR1C WILD-TYPE 
            2.01             0.00 
  ACVR1C MUTATED ACVR1C WILD-TYPE 
           79.69           148.01 
  ACVR1C MUTATED ACVR1C WILD-TYPE 
           33.53            20.02 
[1] "2.0 - 79.7 (33.5)"  "0.0 - 148.0 (20.0)"
[1] "hr="     "2.6e+07"
D1819V2, continuous
D1819V3, binary
                  cls
clus                 0   1
  ACVR1C MUTATED     9   2
  ACVR1C WILD-TYPE 357 117
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ACVR1C MUTATED      9    2
  ACVR1C WILD-TYPE  357  117
        clus
vv       ACVR1C MUTATED ACVR1C WILD-TYPE
  COLON               9              357
  RECTUM              2              117
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ACVR1C MUTATED         4        0        0         5         0         0
  ACVR1C WILD-TYPE      87        1       32       133        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ACVR1C MUTATED           0          0          0          2        0
  ACVR1C WILD-TYPE        24         11         59         40       48
                  vv
clus               STAGE IVA STAGE IVB
  ACVR1C MUTATED           0         0
  ACVR1C WILD-TYPE        18         1
D1819V4, multiclass
            clus
vv           ACVR1C MUTATED ACVR1C WILD-TYPE
  STAGE I                 4               87
  STAGE IA                0                1
  STAGE II                0               32
  STAGE IIA               5              133
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              0               59
  STAGE IIIC              2               40
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ACVR1C MUTATED     1   3   7   0
  ACVR1C WILD-TYPE  16  89 322  50
D1819V5, multiclass
    clus
vv   ACVR1C MUTATED ACVR1C WILD-TYPE
  T1              1               16
  T2              3               89
  T3              7              322
  T4              0               50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  ACVR1C MUTATED     9   0   2
  ACVR1C WILD-TYPE 278 113  85
D1819V6, multiclass
    clus
vv   ACVR1C MUTATED ACVR1C WILD-TYPE
  N0              9              278
  N1              0              113
  N2              2               85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1819V7, binary
                  cls
clus                 0   1
  ACVR1C MUTATED    10   0
  ACVR1C WILD-TYPE 365  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ACVR1C MUTATED     10    0
  ACVR1C WILD-TYPE  365   65
   clus
vv  ACVR1C MUTATED ACVR1C WILD-TYPE
  0             10              365
  1              0               65
[1] 2 2
[1] FALSE
D1819V8, binary
                  cls
clus                 0   1
  ACVR1C MUTATED     5   6
  ACVR1C WILD-TYPE 220 258
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ACVR1C MUTATED      5    6
  ACVR1C WILD-TYPE  220  258
        clus
vv       ACVR1C MUTATED ACVR1C WILD-TYPE
  FEMALE              5              220
  MALE                6              258
[1] 2 2
[1] FALSE
D1819V9, binary
                  cls
clus                 0   1
  ACVR1C MUTATED    10   0
  ACVR1C WILD-TYPE 340  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ACVR1C MUTATED     10    0
  ACVR1C WILD-TYPE  340   22
     clus
vv    ACVR1C MUTATED ACVR1C WILD-TYPE
  NO              10              340
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ACVR1C MUTATED                      8                             1
  ACVR1C WILD-TYPE                  307                            46
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ACVR1C MUTATED                       2                              0
  ACVR1C WILD-TYPE                   104                             10
D1819V10, multiclass
                                clus
vv                               ACVR1C MUTATED ACVR1C WILD-TYPE
  COLON ADENOCARCINOMA                        8              307
  COLON MUCINOUS ADENOCARCINOMA               1               46
  RECTAL ADENOCARCINOMA                       2              104
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ACVR1C MUTATED     9   0   0   1
  ACVR1C WILD-TYPE 336   4  31  24
D1819V11, multiclass
    clus
vv   ACVR1C MUTATED ACVR1C WILD-TYPE
  R0              9              336
  R1              0                4
  R2              0               31
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1819V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ACVR1C MUTATED                                  0     0
  ACVR1C WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ACVR1C MUTATED                           2     6
  ACVR1C WILD-TYPE                        20   220
D1819V13, multiclass
                                  clus
vv                                 ACVR1C MUTATED ACVR1C WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     2               20
  WHITE                                         6              220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1820) Variable = MKLN1 MUTATION ANALYSIS
D1820V1, survival
                 sevent
clus2               0   1
  MKLN1 MUTATED     9   2
  MKLN1 WILD-TYPE 369  91
  MKLN1 MUTATED MKLN1 WILD-TYPE 
             11             460 
  MKLN1 MUTATED MKLN1 WILD-TYPE 
              2              91 
$`MKLN1 MUTATED`
TCGA-A6-6654 TCGA-AA-3492 TCGA-AA-3710 TCGA-AA-3864 TCGA-AA-3977 TCGA-AA-A02F 
       23.87         3.02        26.99        53.00        25.02        39.98 
TCGA-AZ-4315 TCGA-CA-6717 TCGA-CM-6164 TCGA-AG-A002 TCGA-DY-A1DG 
       58.39        12.76        29.03        20.98        51.48 

$`MKLN1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 
       20.12        19.66        20.28         7.04         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        31.07        30.05        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       37.02        39.06        51.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
       16.31         0.95        33.01        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07        12.20        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       15.02        12.00         2.96        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       24.13        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  MKLN1 MUTATED MKLN1 WILD-TYPE 
           3.02            0.00 
  MKLN1 MUTATED MKLN1 WILD-TYPE 
          58.39          148.01 
  MKLN1 MUTATED MKLN1 WILD-TYPE 
          26.99           20.02 
[1] "3.0 - 58.4 (27.0)"  "0.0 - 148.0 (20.0)"
[1] "hr=" "1.4"
D1820V2, continuous
D1820V3, binary
                 cls
clus                0   1
  MKLN1 MUTATED     9   2
  MKLN1 WILD-TYPE 357 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MKLN1 MUTATED      9    2
  MKLN1 WILD-TYPE  357  117
        clus
vv       MKLN1 MUTATED MKLN1 WILD-TYPE
  COLON              9             357
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MKLN1 MUTATED         1        0        2         4         0         0
  MKLN1 WILD-TYPE      90        1       30       134        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MKLN1 MUTATED           0          0          1          0        1         1
  MKLN1 WILD-TYPE        24         11         58         42       47        17
                 vv
clus              STAGE IVB
  MKLN1 MUTATED           0
  MKLN1 WILD-TYPE         1
D1820V4, multiclass
            clus
vv           MKLN1 MUTATED MKLN1 WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA              4             134
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             0              42
  STAGE IV               1              47
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  MKLN1 MUTATED     0   2   9   0
  MKLN1 WILD-TYPE  17  90 320  50
D1820V5, multiclass
    clus
vv   MKLN1 MUTATED MKLN1 WILD-TYPE
  T1             0              17
  T2             2              90
  T3             9             320
  T4             0              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  MKLN1 MUTATED     8   3   0
  MKLN1 WILD-TYPE 279 110  87
D1820V6, multiclass
    clus
vv   MKLN1 MUTATED MKLN1 WILD-TYPE
  N0             8             279
  N1             3             110
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1820V7, binary
                 cls
clus                0   1
  MKLN1 MUTATED     8   2
  MKLN1 WILD-TYPE 367  63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MKLN1 MUTATED      8    2
  MKLN1 WILD-TYPE  367   63
   clus
vv  MKLN1 MUTATED MKLN1 WILD-TYPE
  0             8             367
  1             2              63
[1] 2 2
[1] FALSE
D1820V8, binary
                 cls
clus                0   1
  MKLN1 MUTATED     5   6
  MKLN1 WILD-TYPE 220 258
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MKLN1 MUTATED      5    6
  MKLN1 WILD-TYPE  220  258
        clus
vv       MKLN1 MUTATED MKLN1 WILD-TYPE
  FEMALE             5             220
  MALE               6             258
[1] 2 2
[1] FALSE
D1820V9, binary
                 cls
clus                0   1
  MKLN1 MUTATED    10   0
  MKLN1 WILD-TYPE 340  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MKLN1 MUTATED     10    0
  MKLN1 WILD-TYPE  340   22
     clus
vv    MKLN1 MUTATED MKLN1 WILD-TYPE
  NO             10             340
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MKLN1 MUTATED                      8                             1
  MKLN1 WILD-TYPE                  307                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MKLN1 MUTATED                       2                              0
  MKLN1 WILD-TYPE                   104                             10
D1820V10, multiclass
                                clus
vv                               MKLN1 MUTATED MKLN1 WILD-TYPE
  COLON ADENOCARCINOMA                       8             307
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  MKLN1 MUTATED     6   0   1   1
  MKLN1 WILD-TYPE 339   4  30  24
D1820V11, multiclass
    clus
vv   MKLN1 MUTATED MKLN1 WILD-TYPE
  R0             6             339
  R1             0               4
  R2             1              30
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1820V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MKLN1 MUTATED                                  0     1
  MKLN1 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  MKLN1 MUTATED                           0     4
  MKLN1 WILD-TYPE                        22   222
D1820V13, multiclass
                                  clus
vv                                 MKLN1 MUTATED MKLN1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        4             222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1821) Variable = IFNA2 MUTATION ANALYSIS
D1821V1, survival
                 sevent
clus2               0   1
  IFNA2 MUTATED     8   2
  IFNA2 WILD-TYPE 370  91
  IFNA2 MUTATED IFNA2 WILD-TYPE 
             10             461 
  IFNA2 MUTATED IFNA2 WILD-TYPE 
              2              91 
$`IFNA2 MUTATED`
TCGA-A6-2676 TCGA-AA-3672 TCGA-AA-A00N TCGA-AU-3779 TCGA-CM-6161 TCGA-CM-6171 
       42.90         0.92         4.01        14.50        15.02        14.04 
TCGA-D5-6930 TCGA-F4-6806 TCGA-F4-6856 TCGA-AG-A002 
        1.51        41.42        35.31        20.98 

$`IFNA2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 
        6.97        54.02         2.01        14.01        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
        0.20        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6162 TCGA-CM-6163 
        5.03        15.02        15.02        17.03        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       15.02        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 
        9.04         9.44        11.64         4.80        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6807 
       35.74         6.18        47.87         1.55        34.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 
       33.67        13.25         0.53        47.41       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  IFNA2 MUTATED IFNA2 WILD-TYPE 
           0.92            0.00 
  IFNA2 MUTATED IFNA2 WILD-TYPE 
          42.90          148.01 
  IFNA2 MUTATED IFNA2 WILD-TYPE 
          14.76           20.28 
[1] "0.9 - 42.9 (14.8)"  "0.0 - 148.0 (20.3)"
[1] "hr=" "1.4"
D1821V2, continuous
D1821V3, binary
                 cls
clus                0   1
  IFNA2 MUTATED     9   1
  IFNA2 WILD-TYPE 357 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IFNA2 MUTATED      9    1
  IFNA2 WILD-TYPE  357  118
        clus
vv       IFNA2 MUTATED IFNA2 WILD-TYPE
  COLON              9             357
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  IFNA2 MUTATED         5        0        0         2         2         0
  IFNA2 WILD-TYPE      86        1       32       136         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  IFNA2 MUTATED           1          0          0          0        0         0
  IFNA2 WILD-TYPE        23         11         59         42       48        18
                 vv
clus              STAGE IVB
  IFNA2 MUTATED           0
  IFNA2 WILD-TYPE         1
D1821V4, multiclass
            clus
vv           IFNA2 MUTATED IFNA2 WILD-TYPE
  STAGE I                5              86
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              2             136
  STAGE IIB              2               8
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  IFNA2 MUTATED     0   5   3   2
  IFNA2 WILD-TYPE  17  87 326  48
D1821V5, multiclass
    clus
vv   IFNA2 MUTATED IFNA2 WILD-TYPE
  T1             0              17
  T2             5              87
  T3             3             326
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  IFNA2 MUTATED     9   1   0
  IFNA2 WILD-TYPE 278 112  87
D1821V6, multiclass
    clus
vv   IFNA2 MUTATED IFNA2 WILD-TYPE
  N0             9             278
  N1             1             112
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1821V7, binary
                 cls
clus                0   1
  IFNA2 MUTATED    10   0
  IFNA2 WILD-TYPE 365  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IFNA2 MUTATED     10    0
  IFNA2 WILD-TYPE  365   65
   clus
vv  IFNA2 MUTATED IFNA2 WILD-TYPE
  0            10             365
  1             0              65
[1] 2 2
[1] FALSE
D1821V8, binary
                 cls
clus                0   1
  IFNA2 MUTATED     6   4
  IFNA2 WILD-TYPE 219 260
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IFNA2 MUTATED      6    4
  IFNA2 WILD-TYPE  219  260
        clus
vv       IFNA2 MUTATED IFNA2 WILD-TYPE
  FEMALE             6             219
  MALE               4             260
[1] 2 2
[1] FALSE
D1821V9, binary
                 cls
clus                0   1
  IFNA2 MUTATED     8   0
  IFNA2 WILD-TYPE 342  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IFNA2 MUTATED      8    0
  IFNA2 WILD-TYPE  342   22
     clus
vv    IFNA2 MUTATED IFNA2 WILD-TYPE
  NO              8             342
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  IFNA2 MUTATED                      6                             3
  IFNA2 WILD-TYPE                  309                            44
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  IFNA2 MUTATED                       1                              0
  IFNA2 WILD-TYPE                   105                             10
D1821V10, multiclass
                                clus
vv                               IFNA2 MUTATED IFNA2 WILD-TYPE
  COLON ADENOCARCINOMA                       6             309
  COLON MUCINOUS ADENOCARCINOMA              3              44
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  IFNA2 MUTATED    10   0   0   0
  IFNA2 WILD-TYPE 335   4  31  25
D1821V11, multiclass
    clus
vv   IFNA2 MUTATED IFNA2 WILD-TYPE
  R0            10             335
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1821V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  IFNA2 MUTATED                                  0     0
  IFNA2 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  IFNA2 MUTATED                           0     7
  IFNA2 WILD-TYPE                        22   219
D1821V13, multiclass
                                  clus
vv                                 IFNA2 MUTATED IFNA2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        7             219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1822) Variable = MPHOSPH9 MUTATION ANALYSIS
D1822V1, survival
                    sevent
clus2                  0   1
  MPHOSPH9 MUTATED     7   2
  MPHOSPH9 WILD-TYPE 371  91
  MPHOSPH9 MUTATED MPHOSPH9 WILD-TYPE 
                 9                462 
  MPHOSPH9 MUTATED MPHOSPH9 WILD-TYPE 
                 2                 91 
$`MPHOSPH9 MUTATED`
TCGA-A6-3810 TCGA-A6-5661 TCGA-A6-6781 TCGA-AA-A01R TCGA-AD-6889 TCGA-AD-6964 
       36.53        33.53        19.66        35.01        56.55        10.88 
TCGA-DM-A1D8 TCGA-AG-A002 TCGA-AG-A011 
       12.59        20.98        37.02 

$`MPHOSPH9 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        32.75        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       31.63        30.44        29.19        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       31.00        38.07         1.02         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 
       40.96         0.07        21.37        15.52         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       92.75        49.91        13.32       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A014 
       17.03        13.94         6.02        25.97        23.01        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  MPHOSPH9 MUTATED MPHOSPH9 WILD-TYPE 
             10.88               0.00 
  MPHOSPH9 MUTATED MPHOSPH9 WILD-TYPE 
             56.55             148.01 
  MPHOSPH9 MUTATED MPHOSPH9 WILD-TYPE 
            33.530             20.085 
[1] "10.9 - 56.5 (33.5)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.1"
D1822V2, continuous
D1822V3, binary
                    cls
clus                   0   1
  MPHOSPH9 MUTATED     8   2
  MPHOSPH9 WILD-TYPE 358 117
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  MPHOSPH9 MUTATED      8    2
  MPHOSPH9 WILD-TYPE  358  117
        clus
vv       MPHOSPH9 MUTATED MPHOSPH9 WILD-TYPE
  COLON                 8                358
  RECTUM                2                117
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MPHOSPH9 MUTATED         1        0        0         5         0         0
  MPHOSPH9 WILD-TYPE      90        1       32       133        10         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MPHOSPH9 MUTATED           1          0          0          1        0
  MPHOSPH9 WILD-TYPE        23         11         59         41       48
                    vv
clus                 STAGE IVA STAGE IVB
  MPHOSPH9 MUTATED           0         0
  MPHOSPH9 WILD-TYPE        18         1
D1822V4, multiclass
            clus
vv           MPHOSPH9 MUTATED MPHOSPH9 WILD-TYPE
  STAGE I                   1                 90
  STAGE IA                  0                  1
  STAGE II                  0                 32
  STAGE IIA                 5                133
  STAGE IIB                 0                 10
  STAGE IIC                 0                  1
  STAGE III                 1                 23
  STAGE IIIA                0                 11
  STAGE IIIB                0                 59
  STAGE IIIC                1                 41
  STAGE IV                  0                 48
  STAGE IVA                 0                 18
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  MPHOSPH9 MUTATED     0   1   7   2
  MPHOSPH9 WILD-TYPE  17  91 322  48
D1822V5, multiclass
    clus
vv   MPHOSPH9 MUTATED MPHOSPH9 WILD-TYPE
  T1                0                 17
  T2                1                 91
  T3                7                322
  T4                2                 48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  MPHOSPH9 MUTATED     6   2   2
  MPHOSPH9 WILD-TYPE 281 111  85
D1822V6, multiclass
    clus
vv   MPHOSPH9 MUTATED MPHOSPH9 WILD-TYPE
  N0                6                281
  N1                2                111
  N2                2                 85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1822V7, binary
                    cls
clus                   0   1
  MPHOSPH9 MUTATED     7   0
  MPHOSPH9 WILD-TYPE 368  65
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  MPHOSPH9 MUTATED      7    0
  MPHOSPH9 WILD-TYPE  368   65
   clus
vv  MPHOSPH9 MUTATED MPHOSPH9 WILD-TYPE
  0                7                368
  1                0                 65
[1] 2 2
[1] FALSE
D1822V8, binary
                    cls
clus                   0   1
  MPHOSPH9 MUTATED     3   7
  MPHOSPH9 WILD-TYPE 222 257
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  MPHOSPH9 MUTATED      3    7
  MPHOSPH9 WILD-TYPE  222  257
        clus
vv       MPHOSPH9 MUTATED MPHOSPH9 WILD-TYPE
  FEMALE                3                222
  MALE                  7                257
[1] 2 2
[1] FALSE
D1822V9, binary
                    cls
clus                   0   1
  MPHOSPH9 MUTATED     6   1
  MPHOSPH9 WILD-TYPE 344  21
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  MPHOSPH9 MUTATED      6    1
  MPHOSPH9 WILD-TYPE  344   21
     clus
vv    MPHOSPH9 MUTATED MPHOSPH9 WILD-TYPE
  NO                 6                344
  YES                1                 21
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MPHOSPH9 MUTATED                      6                             2
  MPHOSPH9 WILD-TYPE                  309                            45
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MPHOSPH9 MUTATED                       2                              0
  MPHOSPH9 WILD-TYPE                   104                             10
D1822V10, multiclass
                                clus
vv                               MPHOSPH9 MUTATED MPHOSPH9 WILD-TYPE
  COLON ADENOCARCINOMA                          6                309
  COLON MUCINOUS ADENOCARCINOMA                 2                 45
  RECTAL ADENOCARCINOMA                         2                104
  RECTAL MUCINOUS ADENOCARCINOMA                0                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  MPHOSPH9 MUTATED     7   0   0   0
  MPHOSPH9 WILD-TYPE 338   4  31  25
D1822V11, multiclass
    clus
vv   MPHOSPH9 MUTATED MPHOSPH9 WILD-TYPE
  R0                7                338
  R1                0                  4
  R2                0                 31
  RX                0                 25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1822V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MPHOSPH9 MUTATED                                  0     1
  MPHOSPH9 WILD-TYPE                                1    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  MPHOSPH9 MUTATED                           1     4
  MPHOSPH9 WILD-TYPE                        21   222
D1822V13, multiclass
                                  clus
vv                                 MPHOSPH9 MUTATED MPHOSPH9 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                 10
  BLACK OR AFRICAN AMERICAN                       1                 21
  WHITE                                           4                222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1823) Variable = TM7SF4 MUTATION ANALYSIS
D1823V1, survival
                  sevent
clus2                0   1
  TM7SF4 MUTATED     7   2
  TM7SF4 WILD-TYPE 371  91
  TM7SF4 MUTATED TM7SF4 WILD-TYPE 
               9              462 
  TM7SF4 MUTATED TM7SF4 WILD-TYPE 
               2               91 
$`TM7SF4 MUTATED`
TCGA-A6-3809 TCGA-A6-6648 TCGA-AA-A010 TCGA-AD-5900 TCGA-CM-4746 TCGA-D5-6537 
       32.75        25.18        34.98         0.07        37.02         4.80 
TCGA-D5-6928 TCGA-AG-A01W TCGA-F5-6464 
       11.64        70.03         9.96 

$`TM7SF4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       18.05        40.96        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
      124.27        23.05        20.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       43.27        15.12        17.85        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.04         9.44         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01Y 
       37.02        15.95        36.03         9.07        12.00        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6465 TCGA-F5-6571 
       20.55        19.96        20.91        18.28        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  TM7SF4 MUTATED TM7SF4 WILD-TYPE 
            0.07             0.00 
  TM7SF4 MUTATED TM7SF4 WILD-TYPE 
           70.03           148.01 
  TM7SF4 MUTATED TM7SF4 WILD-TYPE 
          25.180           20.155 
[1] "0.1 - 70.0 (25.2)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.2"
D1823V2, continuous
D1823V3, binary
                  cls
clus                 0   1
  TM7SF4 MUTATED     7   2
  TM7SF4 WILD-TYPE 359 117
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TM7SF4 MUTATED      7    2
  TM7SF4 WILD-TYPE  359  117
        clus
vv       TM7SF4 MUTATED TM7SF4 WILD-TYPE
  COLON               7              359
  RECTUM              2              117
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TM7SF4 MUTATED         2        0        1         1         2         0
  TM7SF4 WILD-TYPE      89        1       31       137         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TM7SF4 MUTATED           0          0          1          1        0
  TM7SF4 WILD-TYPE        24         11         58         41       48
                  vv
clus               STAGE IVA STAGE IVB
  TM7SF4 MUTATED           1         0
  TM7SF4 WILD-TYPE        17         1
D1823V4, multiclass
            clus
vv           TM7SF4 MUTATED TM7SF4 WILD-TYPE
  STAGE I                 2               89
  STAGE IA                0                1
  STAGE II                1               31
  STAGE IIA               1              137
  STAGE IIB               2                8
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              1               58
  STAGE IIIC              1               41
  STAGE IV                0               48
  STAGE IVA               1               17
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  TM7SF4 MUTATED     0   2   4   3
  TM7SF4 WILD-TYPE  17  90 325  47
D1823V5, multiclass
    clus
vv   TM7SF4 MUTATED TM7SF4 WILD-TYPE
  T1              0               17
  T2              2               90
  T3              4              325
  T4              3               47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  TM7SF4 MUTATED     7   1   1
  TM7SF4 WILD-TYPE 280 112  86
D1823V6, multiclass
    clus
vv   TM7SF4 MUTATED TM7SF4 WILD-TYPE
  N0              7              280
  N1              1              112
  N2              1               86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1823V7, binary
                  cls
clus                 0   1
  TM7SF4 MUTATED     6   1
  TM7SF4 WILD-TYPE 369  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TM7SF4 MUTATED      6    1
  TM7SF4 WILD-TYPE  369   64
   clus
vv  TM7SF4 MUTATED TM7SF4 WILD-TYPE
  0              6              369
  1              1               64
[1] 2 2
[1] FALSE
D1823V8, binary
                  cls
clus                 0   1
  TM7SF4 MUTATED     4   5
  TM7SF4 WILD-TYPE 221 259
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TM7SF4 MUTATED      4    5
  TM7SF4 WILD-TYPE  221  259
        clus
vv       TM7SF4 MUTATED TM7SF4 WILD-TYPE
  FEMALE              4              221
  MALE                5              259
[1] 2 2
[1] FALSE
D1823V9, binary
                  cls
clus                 0   1
  TM7SF4 MUTATED     7   0
  TM7SF4 WILD-TYPE 343  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TM7SF4 MUTATED      7    0
  TM7SF4 WILD-TYPE  343   22
     clus
vv    TM7SF4 MUTATED TM7SF4 WILD-TYPE
  NO               7              343
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  TM7SF4 MUTATED                      4                             3
  TM7SF4 WILD-TYPE                  311                            44
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  TM7SF4 MUTATED                       2                              0
  TM7SF4 WILD-TYPE                   104                             10
D1823V10, multiclass
                                clus
vv                               TM7SF4 MUTATED TM7SF4 WILD-TYPE
  COLON ADENOCARCINOMA                        4              311
  COLON MUCINOUS ADENOCARCINOMA               3               44
  RECTAL ADENOCARCINOMA                       2              104
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  TM7SF4 MUTATED     8   0   0   0
  TM7SF4 WILD-TYPE 337   4  31  25
D1823V11, multiclass
    clus
vv   TM7SF4 MUTATED TM7SF4 WILD-TYPE
  R0              8              337
  R1              0                4
  R2              0               31
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1823V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TM7SF4 MUTATED                                  0     0
  TM7SF4 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  TM7SF4 MUTATED                           1     6
  TM7SF4 WILD-TYPE                        21   220
D1823V13, multiclass
                                  clus
vv                                 TM7SF4 MUTATED TM7SF4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                         6              220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1824) Variable = ZNF585B MUTATION ANALYSIS
D1824V1, survival
                   sevent
clus2                 0   1
  ZNF585B MUTATED     5   3
  ZNF585B WILD-TYPE 373  90
  ZNF585B MUTATED ZNF585B WILD-TYPE 
                8               463 
  ZNF585B MUTATED ZNF585B WILD-TYPE 
                3                90 
$`ZNF585B MUTATED`
TCGA-AA-3715 TCGA-AA-A010 TCGA-AD-6895 TCGA-CK-6747 TCGA-D5-6923 TCGA-F4-6460 
       19.04        34.98         0.72        82.95        12.43        31.96 
TCGA-F4-6570 TCGA-AG-A002 
        6.18        20.98 

$`ZNF585B WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
       56.55         0.79         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6748 
       15.62        49.08        51.32         9.99        21.14         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
        8.61        35.74        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  ZNF585B MUTATED ZNF585B WILD-TYPE 
             0.72              0.00 
  ZNF585B MUTATED ZNF585B WILD-TYPE 
            82.95            148.01 
  ZNF585B MUTATED ZNF585B WILD-TYPE 
            20.01             20.19 
[1] "0.7 - 83.0 (20.0)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "2"  
D1824V2, continuous
D1824V3, binary
                   cls
clus                  0   1
  ZNF585B MUTATED     7   1
  ZNF585B WILD-TYPE 359 118
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZNF585B MUTATED      7    1
  ZNF585B WILD-TYPE  359  118
        clus
vv       ZNF585B MUTATED ZNF585B WILD-TYPE
  COLON                7               359
  RECTUM               1               118
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZNF585B MUTATED         2        0        1         2         1         0
  ZNF585B WILD-TYPE      89        1       31       136         9         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF585B MUTATED           0          0          1          0        0
  ZNF585B WILD-TYPE        24         11         58         42       48
                   vv
clus                STAGE IVA STAGE IVB
  ZNF585B MUTATED           0         0
  ZNF585B WILD-TYPE        18         1
D1824V4, multiclass
            clus
vv           ZNF585B MUTATED ZNF585B WILD-TYPE
  STAGE I                  2                89
  STAGE IA                 0                 1
  STAGE II                 1                31
  STAGE IIA                2               136
  STAGE IIB                1                 9
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               0                11
  STAGE IIIB               1                58
  STAGE IIIC               0                42
  STAGE IV                 0                48
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  ZNF585B MUTATED     0   2   5   1
  ZNF585B WILD-TYPE  17  90 324  49
D1824V5, multiclass
    clus
vv   ZNF585B MUTATED ZNF585B WILD-TYPE
  T1               0                17
  T2               2                90
  T3               5               324
  T4               1                49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  ZNF585B MUTATED     6   2   0
  ZNF585B WILD-TYPE 281 111  87
D1824V6, multiclass
    clus
vv   ZNF585B MUTATED ZNF585B WILD-TYPE
  N0               6               281
  N1               2               111
  N2               0                87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1824V7, binary
                   cls
clus                  0   1
  ZNF585B MUTATED     6   0
  ZNF585B WILD-TYPE 369  65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZNF585B MUTATED      6    0
  ZNF585B WILD-TYPE  369   65
   clus
vv  ZNF585B MUTATED ZNF585B WILD-TYPE
  0               6               369
  1               0                65
[1] 2 2
[1] FALSE
D1824V8, binary
                   cls
clus                  0   1
  ZNF585B MUTATED     4   4
  ZNF585B WILD-TYPE 221 260
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZNF585B MUTATED      4    4
  ZNF585B WILD-TYPE  221  260
        clus
vv       ZNF585B MUTATED ZNF585B WILD-TYPE
  FEMALE               4               221
  MALE                 4               260
[1] 2 2
[1] FALSE
D1824V9, binary
                   cls
clus                  0   1
  ZNF585B MUTATED     7   0
  ZNF585B WILD-TYPE 343  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZNF585B MUTATED      7    0
  ZNF585B WILD-TYPE  343   22
     clus
vv    ZNF585B MUTATED ZNF585B WILD-TYPE
  NO                7               343
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ZNF585B MUTATED                      7                             0
  ZNF585B WILD-TYPE                  308                            47
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ZNF585B MUTATED                       1                              0
  ZNF585B WILD-TYPE                   105                             10
D1824V10, multiclass
                                clus
vv                               ZNF585B MUTATED ZNF585B WILD-TYPE
  COLON ADENOCARCINOMA                         7               308
  COLON MUCINOUS ADENOCARCINOMA                0                47
  RECTAL ADENOCARCINOMA                        1               105
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  ZNF585B MUTATED     6   0   0   1
  ZNF585B WILD-TYPE 339   4  31  24
D1824V11, multiclass
    clus
vv   ZNF585B MUTATED ZNF585B WILD-TYPE
  R0               6               339
  R1               0                 4
  R2               0                31
  RX               1                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1824V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF585B MUTATED                                  0     0
  ZNF585B WILD-TYPE                                1    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  ZNF585B MUTATED                           0     5
  ZNF585B WILD-TYPE                        22   221
D1824V13, multiclass
                                  clus
vv                                 ZNF585B MUTATED ZNF585B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                      0                22
  WHITE                                          5               221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1825) Variable = ATP1A4 MUTATION ANALYSIS
D1825V1, survival
                  sevent
clus2                0   1
  ATP1A4 MUTATED    12   6
  ATP1A4 WILD-TYPE 366  87
  ATP1A4 MUTATED ATP1A4 WILD-TYPE 
              18              453 
  ATP1A4 MUTATED ATP1A4 WILD-TYPE 
               6               87 
$`ATP1A4 MUTATED`
TCGA-A6-6653 TCGA-AA-3554 TCGA-AA-3660 TCGA-AA-3715 TCGA-AA-3821 TCGA-AA-A010 
       24.39        17.95        78.08        19.04         1.02        34.98 
TCGA-AD-6888 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-CA-6717 TCGA-CM-5861 TCGA-CM-6169 
       15.52        58.39        49.41        12.76        15.02        13.02 
TCGA-CM-6171 TCGA-DM-A0XD TCGA-DM-A28C TCGA-F4-6703 TCGA-AG-A002 TCGA-DY-A1DD 
       14.04        24.43        81.37        47.87        20.98        57.24 

$`ATP1A4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
       25.08        25.18        24.16        21.76        24.69        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       13.02        24.00        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       13.94        19.99        61.02         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       85.05        26.99        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
        0.99        25.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       21.37        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        33.01        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 
      106.75        22.36        62.79        88.21         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 
       29.06        22.03        22.98        30.08        32.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6170 
       29.03        16.04        21.99        14.99        12.99        15.02 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
       10.26       119.70        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      135.65       139.17         6.12       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DF TCGA-DY-A1DG 
        5.03         5.29       126.44        41.36        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  ATP1A4 MUTATED ATP1A4 WILD-TYPE 
            1.02             0.00 
  ATP1A4 MUTATED ATP1A4 WILD-TYPE 
           81.37           148.01 
  ATP1A4 MUTATED ATP1A4 WILD-TYPE 
          22.685           20.120 
[1] "1.0 - 81.4 (22.7)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.3"
D1825V2, continuous
D1825V3, binary
                  cls
clus                 0   1
  ATP1A4 MUTATED    17   2
  ATP1A4 WILD-TYPE 349 117
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP1A4 MUTATED     17    2
  ATP1A4 WILD-TYPE  349  117
        clus
vv       ATP1A4 MUTATED ATP1A4 WILD-TYPE
  COLON              17              349
  RECTUM              2              117
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ATP1A4 MUTATED         4        0        3         9         1         0
  ATP1A4 WILD-TYPE      87        1       29       129         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ATP1A4 MUTATED           0          0          2          0        0
  ATP1A4 WILD-TYPE        24         11         57         42       48
                  vv
clus               STAGE IVA STAGE IVB
  ATP1A4 MUTATED           0         0
  ATP1A4 WILD-TYPE        18         1
D1825V4, multiclass
            clus
vv           ATP1A4 MUTATED ATP1A4 WILD-TYPE
  STAGE I                 4               87
  STAGE IA                0                1
  STAGE II                3               29
  STAGE IIA               9              129
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              2               57
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ATP1A4 MUTATED     0   4  14   1
  ATP1A4 WILD-TYPE  17  88 315  49
D1825V5, multiclass
    clus
vv   ATP1A4 MUTATED ATP1A4 WILD-TYPE
  T1              0               17
  T2              4               88
  T3             14              315
  T4              1               49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  ATP1A4 MUTATED    17   2   0
  ATP1A4 WILD-TYPE 270 111  87
D1825V6, multiclass
    clus
vv   ATP1A4 MUTATED ATP1A4 WILD-TYPE
  N0             17              270
  N1              2              111
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1825V7, binary
                  cls
clus                 0   1
  ATP1A4 MUTATED    18   0
  ATP1A4 WILD-TYPE 357  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP1A4 MUTATED     18    0
  ATP1A4 WILD-TYPE  357   65
   clus
vv  ATP1A4 MUTATED ATP1A4 WILD-TYPE
  0             18              357
  1              0               65
[1] 2 2
[1] FALSE
D1825V8, binary
                  cls
clus                 0   1
  ATP1A4 MUTATED     9  10
  ATP1A4 WILD-TYPE 216 254
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP1A4 MUTATED      9   10
  ATP1A4 WILD-TYPE  216  254
        clus
vv       ATP1A4 MUTATED ATP1A4 WILD-TYPE
  FEMALE              9              216
  MALE               10              254
[1] 2 2
[1] FALSE
D1825V9, binary
                  cls
clus                 0   1
  ATP1A4 MUTATED    15   0
  ATP1A4 WILD-TYPE 335  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP1A4 MUTATED     15    0
  ATP1A4 WILD-TYPE  335   22
     clus
vv    ATP1A4 MUTATED ATP1A4 WILD-TYPE
  NO              15              335
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ATP1A4 MUTATED                     15                             2
  ATP1A4 WILD-TYPE                  300                            45
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ATP1A4 MUTATED                       2                              0
  ATP1A4 WILD-TYPE                   104                             10
D1825V10, multiclass
                                clus
vv                               ATP1A4 MUTATED ATP1A4 WILD-TYPE
  COLON ADENOCARCINOMA                       15              300
  COLON MUCINOUS ADENOCARCINOMA               2               45
  RECTAL ADENOCARCINOMA                       2              104
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ATP1A4 MUTATED    13   0   0   1
  ATP1A4 WILD-TYPE 332   4  31  24
D1825V11, multiclass
    clus
vv   ATP1A4 MUTATED ATP1A4 WILD-TYPE
  R0             13              332
  R1              0                4
  R2              0               31
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1825V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ATP1A4 MUTATED                                  0     1
  ATP1A4 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ATP1A4 MUTATED                           1    10
  ATP1A4 WILD-TYPE                        21   216
D1825V13, multiclass
                                  clus
vv                                 ATP1A4 MUTATED ATP1A4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                        10              216
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1826) Variable = GUCY2F MUTATION ANALYSIS
D1826V1, survival
                  sevent
clus2                0   1
  GUCY2F MUTATED    19   3
  GUCY2F WILD-TYPE 359  90
  GUCY2F MUTATED GUCY2F WILD-TYPE 
              22              449 
  GUCY2F MUTATED GUCY2F WILD-TYPE 
               3               90 
$`GUCY2F MUTATED`
TCGA-A6-6141 TCGA-AA-3511 TCGA-AA-3555 TCGA-AA-3660 TCGA-AA-3864 TCGA-AA-3877 
        8.38         6.97        29.95        78.08        53.00        31.00 
TCGA-AA-3977 TCGA-AA-A01P TCGA-AD-6965 TCGA-AZ-6608 TCGA-CM-5860 TCGA-D5-5537 
       25.02        38.07         0.20         1.61        32.02        45.40 
TCGA-D5-6533 TCGA-D5-6927 TCGA-D5-6931 TCGA-DM-A1HB TCGA-DM-A28K TCGA-G4-6588 
        1.32         9.44        12.00       135.65        98.24        26.17 
TCGA-AG-3609 TCGA-AG-3892 TCGA-AG-A002 TCGA-AG-A020 
       19.99        13.02        20.98        10.98 

$`GUCY2F WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 
       22.09        22.06        32.71        27.09        22.52        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01        63.98         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       24.00        17.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       31.07        30.05        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       18.05         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       12.00        31.00        31.00         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       10.88        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 
      100.01        29.56         5.23        11.74         3.19        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-5862 
       29.06        22.03        22.98        30.08        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5538 TCGA-D5-5539 
       11.08        11.01        10.06        12.03        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 
       56.09        55.92        20.19        18.25        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       11.64         4.80         1.51        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 
       12.59       140.38         7.50        44.32       131.51       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       22.09        13.78        35.80        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3611 
       50.04        12.03         6.05         0.99        15.95        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       17.03        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A025 
       36.03         9.07        12.00        70.03        64.01        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  GUCY2F MUTATED GUCY2F WILD-TYPE 
             0.2              0.0 
  GUCY2F MUTATED GUCY2F WILD-TYPE 
          135.65           148.01 
  GUCY2F MUTATED GUCY2F WILD-TYPE 
           23.00            20.12 
[1] "0.2 - 135.7 (23.0)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.7"
D1826V2, continuous
D1826V3, binary
                  cls
clus                 0   1
  GUCY2F MUTATED    19   4
  GUCY2F WILD-TYPE 347 115
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GUCY2F MUTATED     19    4
  GUCY2F WILD-TYPE  347  115
        clus
vv       GUCY2F MUTATED GUCY2F WILD-TYPE
  COLON              19              347
  RECTUM              4              115
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GUCY2F MUTATED         3        0        3         8         0         0
  GUCY2F WILD-TYPE      88        1       29       130        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GUCY2F MUTATED           2          1          2          2        0
  GUCY2F WILD-TYPE        22         10         57         40       48
                  vv
clus               STAGE IVA STAGE IVB
  GUCY2F MUTATED           0         0
  GUCY2F WILD-TYPE        18         1
D1826V4, multiclass
            clus
vv           GUCY2F MUTATED GUCY2F WILD-TYPE
  STAGE I                 3               88
  STAGE IA                0                1
  STAGE II                3               29
  STAGE IIA               8              130
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               2               22
  STAGE IIIA              1               10
  STAGE IIIB              2               57
  STAGE IIIC              2               40
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  GUCY2F MUTATED     2   3  14   4
  GUCY2F WILD-TYPE  15  89 315  46
D1826V5, multiclass
    clus
vv   GUCY2F MUTATED GUCY2F WILD-TYPE
  T1              2               15
  T2              3               89
  T3             14              315
  T4              4               46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  GUCY2F MUTATED    15   4   4
  GUCY2F WILD-TYPE 272 109  83
D1826V6, multiclass
    clus
vv   GUCY2F MUTATED GUCY2F WILD-TYPE
  N0             15              272
  N1              4              109
  N2              4               83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1826V7, binary
                  cls
clus                 0   1
  GUCY2F MUTATED    20   0
  GUCY2F WILD-TYPE 355  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GUCY2F MUTATED     20    0
  GUCY2F WILD-TYPE  355   65
   clus
vv  GUCY2F MUTATED GUCY2F WILD-TYPE
  0             20              355
  1              0               65
[1] 2 2
[1] FALSE
D1826V8, binary
                  cls
clus                 0   1
  GUCY2F MUTATED    11  12
  GUCY2F WILD-TYPE 214 252
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GUCY2F MUTATED     11   12
  GUCY2F WILD-TYPE  214  252
        clus
vv       GUCY2F MUTATED GUCY2F WILD-TYPE
  FEMALE             11              214
  MALE               12              252
[1] 2 2
[1] FALSE
D1826V9, binary
                  cls
clus                 0   1
  GUCY2F MUTATED    17   0
  GUCY2F WILD-TYPE 333  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GUCY2F MUTATED     17    0
  GUCY2F WILD-TYPE  333   22
     clus
vv    GUCY2F MUTATED GUCY2F WILD-TYPE
  NO              17              333
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  GUCY2F MUTATED                     15                             3
  GUCY2F WILD-TYPE                  300                            44
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  GUCY2F MUTATED                       3                              1
  GUCY2F WILD-TYPE                   103                              9
D1826V10, multiclass
                                clus
vv                               GUCY2F MUTATED GUCY2F WILD-TYPE
  COLON ADENOCARCINOMA                       15              300
  COLON MUCINOUS ADENOCARCINOMA               3               44
  RECTAL ADENOCARCINOMA                       3              103
  RECTAL MUCINOUS ADENOCARCINOMA              1                9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  GUCY2F MUTATED    16   0   0   1
  GUCY2F WILD-TYPE 329   4  31  24
D1826V11, multiclass
    clus
vv   GUCY2F MUTATED GUCY2F WILD-TYPE
  R0             16              329
  R1              0                4
  R2              0               31
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1826V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GUCY2F MUTATED                                  0     0
  GUCY2F WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  GUCY2F MUTATED                           1    10
  GUCY2F WILD-TYPE                        21   216
D1826V13, multiclass
                                  clus
vv                                 GUCY2F MUTATED GUCY2F WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                        10              216
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1827) Variable = DRD3 MUTATION ANALYSIS
D1827V1, survival
                sevent
clus2              0   1
  DRD3 MUTATED     5   1
  DRD3 WILD-TYPE 373  92
  DRD3 MUTATED DRD3 WILD-TYPE 
             6            465 
  DRD3 MUTATED DRD3 WILD-TYPE 
             1             92 
$`DRD3 MUTATED`
TCGA-A6-2676 TCGA-AA-3555 TCGA-AA-A010 TCGA-AZ-4315 TCGA-CM-5348 TCGA-DC-5869 
       42.90        29.95        34.98        58.39        22.98         5.03 

$`DRD3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       13.02        24.00        17.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       29.06        22.03        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-6155 
        6.97         4.73        78.12         7.17        15.02        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  DRD3 MUTATED DRD3 WILD-TYPE 
          5.03           0.00 
  DRD3 MUTATED DRD3 WILD-TYPE 
         58.39         148.01 
  DRD3 MUTATED DRD3 WILD-TYPE 
        32.465         20.050 
[1] "5.0 - 58.4 (32.5)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.5"
D1827V2, continuous
D1827V3, binary
                cls
clus               0   1
  DRD3 MUTATED     5   1
  DRD3 WILD-TYPE 361 118
[1] "tbl2"
                cls
clus             [,1] [,2]
  DRD3 MUTATED      5    1
  DRD3 WILD-TYPE  361  118
        clus
vv       DRD3 MUTATED DRD3 WILD-TYPE
  COLON             5            361
  RECTUM            1            118
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DRD3 MUTATED         0        0        0         2         2         0
  DRD3 WILD-TYPE      91        1       32       136         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DRD3 MUTATED           0          0          2          0        0         0
  DRD3 WILD-TYPE        24         11         57         42       48        18
                vv
clus             STAGE IVB
  DRD3 MUTATED           0
  DRD3 WILD-TYPE         1
D1827V4, multiclass
            clus
vv           DRD3 MUTATED DRD3 WILD-TYPE
  STAGE I               0             91
  STAGE IA              0              1
  STAGE II              0             32
  STAGE IIA             2            136
  STAGE IIB             2              8
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            2             57
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  DRD3 MUTATED     0   0   4   2
  DRD3 WILD-TYPE  17  92 325  48
D1827V5, multiclass
    clus
vv   DRD3 MUTATED DRD3 WILD-TYPE
  T1            0             17
  T2            0             92
  T3            4            325
  T4            2             48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  DRD3 MUTATED     4   2   0
  DRD3 WILD-TYPE 283 111  87
D1827V6, multiclass
    clus
vv   DRD3 MUTATED DRD3 WILD-TYPE
  N0            4            283
  N1            2            111
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1827V7, binary
                cls
clus               0   1
  DRD3 MUTATED     6   0
  DRD3 WILD-TYPE 369  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  DRD3 MUTATED      6    0
  DRD3 WILD-TYPE  369   65
   clus
vv  DRD3 MUTATED DRD3 WILD-TYPE
  0            6            369
  1            0             65
[1] 2 2
[1] FALSE
D1827V8, binary
                cls
clus               0   1
  DRD3 MUTATED     4   2
  DRD3 WILD-TYPE 221 262
[1] "tbl2"
                cls
clus             [,1] [,2]
  DRD3 MUTATED      4    2
  DRD3 WILD-TYPE  221  262
        clus
vv       DRD3 MUTATED DRD3 WILD-TYPE
  FEMALE            4            221
  MALE              2            262
[1] 2 2
[1] FALSE
D1827V9, binary
                cls
clus               0   1
  DRD3 MUTATED     5   0
  DRD3 WILD-TYPE 345  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  DRD3 MUTATED      5    0
  DRD3 WILD-TYPE  345   22
     clus
vv    DRD3 MUTATED DRD3 WILD-TYPE
  NO             5            345
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  DRD3 MUTATED                      4                             1
  DRD3 WILD-TYPE                  311                            46
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  DRD3 MUTATED                       1                              0
  DRD3 WILD-TYPE                   105                             10
D1827V10, multiclass
                                clus
vv                               DRD3 MUTATED DRD3 WILD-TYPE
  COLON ADENOCARCINOMA                      4            311
  COLON MUCINOUS ADENOCARCINOMA             1             46
  RECTAL ADENOCARCINOMA                     1            105
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  DRD3 MUTATED     6   0   0   0
  DRD3 WILD-TYPE 339   4  31  25
D1827V11, multiclass
    clus
vv   DRD3 MUTATED DRD3 WILD-TYPE
  R0            6            339
  R1            0              4
  R2            0             31
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1827V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DRD3 MUTATED                                  0     0
  DRD3 WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  DRD3 MUTATED                           1     3
  DRD3 WILD-TYPE                        21   223
D1827V13, multiclass
                                  clus
vv                                 DRD3 MUTATED DRD3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                       3            223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1828) Variable = SMG7 MUTATION ANALYSIS
D1828V1, survival
                sevent
clus2              0   1
  SMG7 MUTATED     9   2
  SMG7 WILD-TYPE 369  91
  SMG7 MUTATED SMG7 WILD-TYPE 
            11            460 
  SMG7 MUTATED SMG7 WILD-TYPE 
             2             91 
$`SMG7 MUTATED`
TCGA-AA-3524 TCGA-CA-6716 TCGA-CK-5913 TCGA-D5-6924 TCGA-DM-A1D4 TCGA-AG-3593 
       36.03        12.20        51.32        14.30        92.75        34.03 
TCGA-AG-3605 TCGA-AG-3732 TCGA-AG-3890 TCGA-AG-A002 TCGA-DY-A1DG 
        0.99        32.98        17.03        20.98        51.48 

$`SMG7 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3525 
       38.99         1.02         9.07        24.03        37.05         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       85.45        15.62        49.08         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
        4.41        12.43         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
       38.20       130.65        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3594 
       36.03        20.05        24.00         1.02        46.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       50.04        12.03         6.05        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 
       19.99         7.99         0.99        37.02         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3892 
       19.04        19.99         1.02        17.95        36.95        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       24.13        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  SMG7 MUTATED SMG7 WILD-TYPE 
          0.99           0.00 
  SMG7 MUTATED SMG7 WILD-TYPE 
         92.75         148.01 
  SMG7 MUTATED SMG7 WILD-TYPE 
        32.980         20.085 
[1] "1.0 - 92.8 (33.0)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.4"
D1828V2, continuous
D1828V3, binary
                cls
clus               0   1
  SMG7 MUTATED     6   6
  SMG7 WILD-TYPE 360 113
[1] "tbl2"
                cls
clus             [,1] [,2]
  SMG7 MUTATED      6    6
  SMG7 WILD-TYPE  360  113
        clus
vv       SMG7 MUTATED SMG7 WILD-TYPE
  COLON             6            360
  RECTUM            6            113
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SMG7 MUTATED         3        0        1         6         0         0
  SMG7 WILD-TYPE      88        1       31       132        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SMG7 MUTATED           0          0          0          0        1         1
  SMG7 WILD-TYPE        24         11         59         42       47        17
                vv
clus             STAGE IVB
  SMG7 MUTATED           0
  SMG7 WILD-TYPE         1
D1828V4, multiclass
            clus
vv           SMG7 MUTATED SMG7 WILD-TYPE
  STAGE I               3             88
  STAGE IA              0              1
  STAGE II              1             31
  STAGE IIA             6            132
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            0             59
  STAGE IIIC            0             42
  STAGE IV              1             47
  STAGE IVA             1             17
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  SMG7 MUTATED     0   3   9   0
  SMG7 WILD-TYPE  17  89 320  50
D1828V5, multiclass
    clus
vv   SMG7 MUTATED SMG7 WILD-TYPE
  T1            0             17
  T2            3             89
  T3            9            320
  T4            0             50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  SMG7 MUTATED    10   2   0
  SMG7 WILD-TYPE 277 111  87
D1828V6, multiclass
    clus
vv   SMG7 MUTATED SMG7 WILD-TYPE
  N0           10            277
  N1            2            111
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1828V7, binary
                cls
clus               0   1
  SMG7 MUTATED     9   2
  SMG7 WILD-TYPE 366  63
[1] "tbl2"
                cls
clus             [,1] [,2]
  SMG7 MUTATED      9    2
  SMG7 WILD-TYPE  366   63
   clus
vv  SMG7 MUTATED SMG7 WILD-TYPE
  0            9            366
  1            2             63
[1] 2 2
[1] FALSE
D1828V8, binary
                cls
clus               0   1
  SMG7 MUTATED     5   7
  SMG7 WILD-TYPE 220 257
[1] "tbl2"
                cls
clus             [,1] [,2]
  SMG7 MUTATED      5    7
  SMG7 WILD-TYPE  220  257
        clus
vv       SMG7 MUTATED SMG7 WILD-TYPE
  FEMALE            5            220
  MALE              7            257
[1] 2 2
[1] FALSE
D1828V9, binary
                cls
clus               0   1
  SMG7 MUTATED     7   1
  SMG7 WILD-TYPE 343  21
[1] "tbl2"
                cls
clus             [,1] [,2]
  SMG7 MUTATED      7    1
  SMG7 WILD-TYPE  343   21
     clus
vv    SMG7 MUTATED SMG7 WILD-TYPE
  NO             7            343
  YES            1             21
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SMG7 MUTATED                      6                             0
  SMG7 WILD-TYPE                  309                            47
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SMG7 MUTATED                       6                              0
  SMG7 WILD-TYPE                   100                             10
D1828V10, multiclass
                                clus
vv                               SMG7 MUTATED SMG7 WILD-TYPE
  COLON ADENOCARCINOMA                      6            309
  COLON MUCINOUS ADENOCARCINOMA             0             47
  RECTAL ADENOCARCINOMA                     6            100
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  SMG7 MUTATED     7   0   1   2
  SMG7 WILD-TYPE 338   4  30  23
D1828V11, multiclass
    clus
vv   SMG7 MUTATED SMG7 WILD-TYPE
  R0            7            338
  R1            0              4
  R2            1             30
  RX            2             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1828V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SMG7 MUTATED                                  0     1
  SMG7 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  SMG7 MUTATED                           0     4
  SMG7 WILD-TYPE                        22   222
D1828V13, multiclass
                                  clus
vv                                 SMG7 MUTATED SMG7 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       4            222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1829) Variable = OR51T1 MUTATION ANALYSIS
D1829V1, survival
                  sevent
clus2                0   1
  OR51T1 MUTATED    11   1
  OR51T1 WILD-TYPE 367  92
  OR51T1 MUTATED OR51T1 WILD-TYPE 
              12              459 
  OR51T1 MUTATED OR51T1 WILD-TYPE 
               1               92 
$`OR51T1 MUTATED`
TCGA-AA-3697 TCGA-AA-3815 TCGA-AD-6889 TCGA-AZ-4315 TCGA-CM-5864 TCGA-CM-6171 
       85.05        33.04        56.55        58.39        15.02        14.04 
TCGA-CM-6674 TCGA-D5-5538 TCGA-F4-6569 TCGA-G4-6626 TCGA-AG-3892 TCGA-AH-6549 
       12.95        12.26        35.74        46.75        13.02        17.49 

$`OR51T1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       19.00        36.00         5.03        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       10.06        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
        5.03        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       15.02        11.01        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       10.06        12.03        45.40        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6570 
       60.79       117.07        98.24         8.61        31.96         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       91.79        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 
        1.02        17.95        36.95        17.03        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
        1.45         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  OR51T1 MUTATED OR51T1 WILD-TYPE 
           12.26             0.00 
  OR51T1 MUTATED OR51T1 WILD-TYPE 
           85.05           148.01 
  OR51T1 MUTATED OR51T1 WILD-TYPE 
          25.265           20.190 
[1] "12.3 - 85.0 (25.3)" "0.0 - 148.0 (20.2)"
[1] "hr=" "3.2"
D1829V2, continuous
D1829V3, binary
                  cls
clus                 0   1
  OR51T1 MUTATED    11   2
  OR51T1 WILD-TYPE 355 117
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR51T1 MUTATED     11    2
  OR51T1 WILD-TYPE  355  117
        clus
vv       OR51T1 MUTATED OR51T1 WILD-TYPE
  COLON              11              355
  RECTUM              2              117
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  OR51T1 MUTATED         4        0        0         6         0         0
  OR51T1 WILD-TYPE      87        1       32       132        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  OR51T1 MUTATED           1          0          1          0        0
  OR51T1 WILD-TYPE        23         11         58         42       48
                  vv
clus               STAGE IVA STAGE IVB
  OR51T1 MUTATED           0         0
  OR51T1 WILD-TYPE        18         1
D1829V4, multiclass
            clus
vv           OR51T1 MUTATED OR51T1 WILD-TYPE
  STAGE I                 4               87
  STAGE IA                0                1
  STAGE II                0               32
  STAGE IIA               6              132
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               1               23
  STAGE IIIA              0               11
  STAGE IIIB              1               58
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  OR51T1 MUTATED     1   3   9   0
  OR51T1 WILD-TYPE  16  89 320  50
D1829V5, multiclass
    clus
vv   OR51T1 MUTATED OR51T1 WILD-TYPE
  T1              1               16
  T2              3               89
  T3              9              320
  T4              0               50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  OR51T1 MUTATED    11   1   0
  OR51T1 WILD-TYPE 276 112  87
D1829V6, multiclass
    clus
vv   OR51T1 MUTATED OR51T1 WILD-TYPE
  N0             11              276
  N1              1              112
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1829V7, binary
                  cls
clus                 0   1
  OR51T1 MUTATED    12   0
  OR51T1 WILD-TYPE 363  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR51T1 MUTATED     12    0
  OR51T1 WILD-TYPE  363   65
   clus
vv  OR51T1 MUTATED OR51T1 WILD-TYPE
  0             12              363
  1              0               65
[1] 2 2
[1] FALSE
D1829V8, binary
                  cls
clus                 0   1
  OR51T1 MUTATED     5   8
  OR51T1 WILD-TYPE 220 256
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR51T1 MUTATED      5    8
  OR51T1 WILD-TYPE  220  256
        clus
vv       OR51T1 MUTATED OR51T1 WILD-TYPE
  FEMALE              5              220
  MALE                8              256
[1] 2 2
[1] FALSE
D1829V9, binary
                  cls
clus                 0   1
  OR51T1 MUTATED    11   0
  OR51T1 WILD-TYPE 339  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR51T1 MUTATED     11    0
  OR51T1 WILD-TYPE  339   22
     clus
vv    OR51T1 MUTATED OR51T1 WILD-TYPE
  NO              11              339
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  OR51T1 MUTATED                     11                             0
  OR51T1 WILD-TYPE                  304                            47
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  OR51T1 MUTATED                       2                              0
  OR51T1 WILD-TYPE                   104                             10
D1829V10, multiclass
                                clus
vv                               OR51T1 MUTATED OR51T1 WILD-TYPE
  COLON ADENOCARCINOMA                       11              304
  COLON MUCINOUS ADENOCARCINOMA               0               47
  RECTAL ADENOCARCINOMA                       2              104
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  OR51T1 MUTATED    11   0   0   1
  OR51T1 WILD-TYPE 334   4  31  24
D1829V11, multiclass
    clus
vv   OR51T1 MUTATED OR51T1 WILD-TYPE
  R0             11              334
  R1              0                4
  R2              0               31
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1829V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OR51T1 MUTATED                                  0     1
  OR51T1 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  OR51T1 MUTATED                           0     8
  OR51T1 WILD-TYPE                        22   218
D1829V13, multiclass
                                  clus
vv                                 OR51T1 MUTATED OR51T1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         8              218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1830) Variable = NPPB MUTATION ANALYSIS
D1830V1, survival
                sevent
clus2              0   1
  NPPB MUTATED     3   1
  NPPB WILD-TYPE 375  92
  NPPB MUTATED NPPB WILD-TYPE 
             4            467 
  NPPB MUTATED NPPB WILD-TYPE 
             1             92 
$`NPPB MUTATED`
TCGA-AA-3662 TCGA-D5-6537 TCGA-DM-A1HB TCGA-AG-3896 
        6.05         4.80       135.65         1.02 

$`NPPB WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
       17.85        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       35.01        14.01        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  NPPB MUTATED NPPB WILD-TYPE 
          1.02           0.00 
  NPPB MUTATED NPPB WILD-TYPE 
        135.65         148.01 
  NPPB MUTATED NPPB WILD-TYPE 
         5.425         20.280 
[1] "1.0 - 135.7 (5.4)"  "0.0 - 148.0 (20.3)"
[1] "hr=" "1.2"
D1830V2, continuous
D1830V3, binary
                cls
clus               0   1
  NPPB MUTATED     4   1
  NPPB WILD-TYPE 362 118
[1] "tbl2"
                cls
clus             [,1] [,2]
  NPPB MUTATED      4    1
  NPPB WILD-TYPE  362  118
        clus
vv       NPPB MUTATED NPPB WILD-TYPE
  COLON             4            362
  RECTUM            1            118
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NPPB MUTATED         1        0        0         0         1         0
  NPPB WILD-TYPE      90        1       32       138         9         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NPPB MUTATED           0          0          2          0        1         0
  NPPB WILD-TYPE        24         11         57         42       47        18
                vv
clus             STAGE IVB
  NPPB MUTATED           0
  NPPB WILD-TYPE         1
D1830V4, multiclass
            clus
vv           NPPB MUTATED NPPB WILD-TYPE
  STAGE I               1             90
  STAGE IA              0              1
  STAGE II              0             32
  STAGE IIA             0            138
  STAGE IIB             1              9
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            2             57
  STAGE IIIC            0             42
  STAGE IV              1             47
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  NPPB MUTATED     0   1   2   2
  NPPB WILD-TYPE  17  91 327  48
D1830V5, multiclass
    clus
vv   NPPB MUTATED NPPB WILD-TYPE
  T1            0             17
  T2            1             91
  T3            2            327
  T4            2             48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  NPPB MUTATED     2   2   1
  NPPB WILD-TYPE 285 111  86
D1830V6, multiclass
    clus
vv   NPPB MUTATED NPPB WILD-TYPE
  N0            2            285
  N1            2            111
  N2            1             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1830V7, binary
                cls
clus               0   1
  NPPB MUTATED     2   1
  NPPB WILD-TYPE 373  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  NPPB MUTATED      2    1
  NPPB WILD-TYPE  373   64
   clus
vv  NPPB MUTATED NPPB WILD-TYPE
  0            2            373
  1            1             64
[1] 2 2
[1] FALSE
D1830V8, binary
                cls
clus               0   1
  NPPB MUTATED     3   2
  NPPB WILD-TYPE 222 262
[1] "tbl2"
                cls
clus             [,1] [,2]
  NPPB MUTATED      3    2
  NPPB WILD-TYPE  222  262
        clus
vv       NPPB MUTATED NPPB WILD-TYPE
  FEMALE            3            222
  MALE              2            262
[1] 2 2
[1] FALSE
D1830V9, binary
                cls
clus               0   1
  NPPB MUTATED     2   0
  NPPB WILD-TYPE 348  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  NPPB MUTATED      2    0
  NPPB WILD-TYPE  348   22
     clus
vv    NPPB MUTATED NPPB WILD-TYPE
  NO             2            348
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  NPPB MUTATED                      3                             0
  NPPB WILD-TYPE                  312                            47
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  NPPB MUTATED                       1                              0
  NPPB WILD-TYPE                   105                             10
D1830V10, multiclass
                                clus
vv                               NPPB MUTATED NPPB WILD-TYPE
  COLON ADENOCARCINOMA                      3            312
  COLON MUCINOUS ADENOCARCINOMA             0             47
  RECTAL ADENOCARCINOMA                     1            105
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  NPPB MUTATED     2   0   1   1
  NPPB WILD-TYPE 343   4  30  24
D1830V11, multiclass
    clus
vv   NPPB MUTATED NPPB WILD-TYPE
  R0            2            343
  R1            0              4
  R2            1             30
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1830V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NPPB MUTATED                                  0     0
  NPPB WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  NPPB MUTATED                           0     3
  NPPB WILD-TYPE                        22   223
D1830V13, multiclass
                                  clus
vv                                 NPPB MUTATED NPPB WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       3            223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1831) Variable = ZNF643 MUTATION ANALYSIS
D1831V1, survival
                  sevent
clus2                0   1
  ZNF643 MUTATED     7   2
  ZNF643 WILD-TYPE 371  91
  ZNF643 MUTATED ZNF643 WILD-TYPE 
               9              462 
  ZNF643 MUTATED ZNF643 WILD-TYPE 
               2               91 
$`ZNF643 MUTATED`
TCGA-AA-3697 TCGA-AA-A00N TCGA-AA-A010 TCGA-AZ-4315 TCGA-CK-4947 TCGA-D5-6535 
       85.05         4.01        34.98        58.39        17.56        15.12 
TCGA-F4-6569 TCGA-G4-6626 TCGA-AG-A002 
       35.74        46.75        20.98 

$`ZNF643 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       19.00        36.00         5.03        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       10.06        14.30       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       43.27        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       31.96         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       35.80        26.17        91.79        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  ZNF643 MUTATED ZNF643 WILD-TYPE 
            4.01             0.00 
  ZNF643 MUTATED ZNF643 WILD-TYPE 
           85.05           148.01 
  ZNF643 MUTATED ZNF643 WILD-TYPE 
          34.980           20.085 
[1] "4.0 - 85.0 (35.0)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.2"
D1831V2, continuous
D1831V3, binary
                  cls
clus                 0   1
  ZNF643 MUTATED     9   1
  ZNF643 WILD-TYPE 357 118
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF643 MUTATED      9    1
  ZNF643 WILD-TYPE  357  118
        clus
vv       ZNF643 MUTATED ZNF643 WILD-TYPE
  COLON               9              357
  RECTUM              1              118
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZNF643 MUTATED         2        0        0         3         2         0
  ZNF643 WILD-TYPE      89        1       32       135         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF643 MUTATED           1          0          2          0        0
  ZNF643 WILD-TYPE        23         11         57         42       48
                  vv
clus               STAGE IVA STAGE IVB
  ZNF643 MUTATED           0         0
  ZNF643 WILD-TYPE        18         1
D1831V4, multiclass
            clus
vv           ZNF643 MUTATED ZNF643 WILD-TYPE
  STAGE I                 2               89
  STAGE IA                0                1
  STAGE II                0               32
  STAGE IIA               3              135
  STAGE IIB               2                8
  STAGE IIC               0                1
  STAGE III               1               23
  STAGE IIIA              0               11
  STAGE IIIB              2               57
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZNF643 MUTATED     0   2   5   3
  ZNF643 WILD-TYPE  17  90 324  47
D1831V5, multiclass
    clus
vv   ZNF643 MUTATED ZNF643 WILD-TYPE
  T1              0               17
  T2              2               90
  T3              5              324
  T4              3               47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  ZNF643 MUTATED     8   2   0
  ZNF643 WILD-TYPE 279 111  87
D1831V6, multiclass
    clus
vv   ZNF643 MUTATED ZNF643 WILD-TYPE
  N0              8              279
  N1              2              111
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1831V7, binary
                  cls
clus                 0   1
  ZNF643 MUTATED     9   0
  ZNF643 WILD-TYPE 366  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF643 MUTATED      9    0
  ZNF643 WILD-TYPE  366   65
   clus
vv  ZNF643 MUTATED ZNF643 WILD-TYPE
  0              9              366
  1              0               65
[1] 2 2
[1] FALSE
D1831V8, binary
                  cls
clus                 0   1
  ZNF643 MUTATED     4   6
  ZNF643 WILD-TYPE 221 258
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF643 MUTATED      4    6
  ZNF643 WILD-TYPE  221  258
        clus
vv       ZNF643 MUTATED ZNF643 WILD-TYPE
  FEMALE              4              221
  MALE                6              258
[1] 2 2
[1] FALSE
D1831V9, binary
                  cls
clus                 0   1
  ZNF643 MUTATED     8   0
  ZNF643 WILD-TYPE 342  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF643 MUTATED      8    0
  ZNF643 WILD-TYPE  342   22
     clus
vv    ZNF643 MUTATED ZNF643 WILD-TYPE
  NO               8              342
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ZNF643 MUTATED                      8                             1
  ZNF643 WILD-TYPE                  307                            46
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ZNF643 MUTATED                       1                              0
  ZNF643 WILD-TYPE                   105                             10
D1831V10, multiclass
                                clus
vv                               ZNF643 MUTATED ZNF643 WILD-TYPE
  COLON ADENOCARCINOMA                        8              307
  COLON MUCINOUS ADENOCARCINOMA               1               46
  RECTAL ADENOCARCINOMA                       1              105
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ZNF643 MUTATED     8   0   0   2
  ZNF643 WILD-TYPE 337   4  31  23
D1831V11, multiclass
    clus
vv   ZNF643 MUTATED ZNF643 WILD-TYPE
  R0              8              337
  R1              0                4
  R2              0               31
  RX              2               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1831V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF643 MUTATED                                  0     0
  ZNF643 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZNF643 MUTATED                           0     5
  ZNF643 WILD-TYPE                        22   221
D1831V13, multiclass
                                  clus
vv                                 ZNF643 MUTATED ZNF643 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         5              221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1832) Variable = DUSP7 MUTATION ANALYSIS
D1832V1, survival
                 sevent
clus2               0   1
  DUSP7 MUTATED     7   1
  DUSP7 WILD-TYPE 371  92
  DUSP7 MUTATED DUSP7 WILD-TYPE 
              8             463 
  DUSP7 MUTATED DUSP7 WILD-TYPE 
              1              92 
$`DUSP7 MUTATED`
TCGA-A6-6780 TCGA-AA-3529 TCGA-AA-3655 TCGA-AA-3660 TCGA-CM-6171 TCGA-D5-5539 
       20.12         0.00        61.02        78.08        14.04        19.59 
TCGA-AF-2693 TCGA-AG-3587 
       19.10        46.03 

$`DUSP7 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
       19.07        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        19.99         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       13.02        15.02        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3913 
       24.13        39.48        43.04        13.55        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
       24.00         1.02        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  DUSP7 MUTATED DUSP7 WILD-TYPE 
              0               0 
  DUSP7 MUTATED DUSP7 WILD-TYPE 
          78.08          148.01 
  DUSP7 MUTATED DUSP7 WILD-TYPE 
         19.855          20.280 
[1] "0.0 - 78.1 (19.9)"  "0.0 - 148.0 (20.3)"
[1] "hr=" "2.1"
D1832V2, continuous
D1832V3, binary
                 cls
clus                0   1
  DUSP7 MUTATED     6   1
  DUSP7 WILD-TYPE 360 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DUSP7 MUTATED      6    1
  DUSP7 WILD-TYPE  360  118
        clus
vv       DUSP7 MUTATED DUSP7 WILD-TYPE
  COLON              6             360
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DUSP7 MUTATED         3        0        2         1         0         0
  DUSP7 WILD-TYPE      88        1       30       137        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DUSP7 MUTATED           0          1          0          1        0         0
  DUSP7 WILD-TYPE        24         10         59         41       48        18
                 vv
clus              STAGE IVB
  DUSP7 MUTATED           0
  DUSP7 WILD-TYPE         1
D1832V4, multiclass
            clus
vv           DUSP7 MUTATED DUSP7 WILD-TYPE
  STAGE I                3              88
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA              1             137
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             1              10
  STAGE IIIB             0              59
  STAGE IIIC             1              41
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  DUSP7 MUTATED     0   3   5   0
  DUSP7 WILD-TYPE  17  89 324  50
D1832V5, multiclass
    clus
vv   DUSP7 MUTATED DUSP7 WILD-TYPE
  T1             0              17
  T2             3              89
  T3             5             324
  T4             0              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  DUSP7 MUTATED     6   1   1
  DUSP7 WILD-TYPE 281 112  86
D1832V6, multiclass
    clus
vv   DUSP7 MUTATED DUSP7 WILD-TYPE
  N0             6             281
  N1             1             112
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1832V7, binary
                 cls
clus                0   1
  DUSP7 MUTATED     6   0
  DUSP7 WILD-TYPE 369  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DUSP7 MUTATED      6    0
  DUSP7 WILD-TYPE  369   65
   clus
vv  DUSP7 MUTATED DUSP7 WILD-TYPE
  0             6             369
  1             0              65
[1] 2 2
[1] FALSE
D1832V8, binary
                 cls
clus                0   1
  DUSP7 MUTATED     3   5
  DUSP7 WILD-TYPE 222 259
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DUSP7 MUTATED      3    5
  DUSP7 WILD-TYPE  222  259
        clus
vv       DUSP7 MUTATED DUSP7 WILD-TYPE
  FEMALE             3             222
  MALE               5             259
[1] 2 2
[1] FALSE
D1832V9, binary
                 cls
clus                0   1
  DUSP7 MUTATED     6   1
  DUSP7 WILD-TYPE 344  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DUSP7 MUTATED      6    1
  DUSP7 WILD-TYPE  344   21
     clus
vv    DUSP7 MUTATED DUSP7 WILD-TYPE
  NO              6             344
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  DUSP7 MUTATED                      4                             2
  DUSP7 WILD-TYPE                  311                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  DUSP7 MUTATED                       1                              0
  DUSP7 WILD-TYPE                   105                             10
D1832V10, multiclass
                                clus
vv                               DUSP7 MUTATED DUSP7 WILD-TYPE
  COLON ADENOCARCINOMA                       4             311
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  DUSP7 MUTATED     6   0   0   0
  DUSP7 WILD-TYPE 339   4  31  25
D1832V11, multiclass
    clus
vv   DUSP7 MUTATED DUSP7 WILD-TYPE
  R0             6             339
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1832V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DUSP7 MUTATED                                  0     0
  DUSP7 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  DUSP7 MUTATED                           0     4
  DUSP7 WILD-TYPE                        22   222
D1832V13, multiclass
                                  clus
vv                                 DUSP7 MUTATED DUSP7 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        4             222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1833) Variable = ZDHHC21 MUTATION ANALYSIS
D1833V1, survival
                   sevent
clus2                 0   1
  ZDHHC21 MUTATED     2   2
  ZDHHC21 WILD-TYPE 376  91
  ZDHHC21 MUTATED ZDHHC21 WILD-TYPE 
                4               467 
  ZDHHC21 MUTATED ZDHHC21 WILD-TYPE 
                2                91 
$`ZDHHC21 MUTATED`
TCGA-AA-3848 TCGA-AD-6964 TCGA-AG-3893 TCGA-AG-A002 
       10.06        10.88        35.01        20.98 

$`ZDHHC21 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
        0.00        17.03         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       13.02        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  ZDHHC21 MUTATED ZDHHC21 WILD-TYPE 
            10.06              0.00 
  ZDHHC21 MUTATED ZDHHC21 WILD-TYPE 
            35.01            148.01 
  ZDHHC21 MUTATED ZDHHC21 WILD-TYPE 
            15.93             20.19 
[1] "10.1 - 35.0 (15.9)" "0.0 - 148.0 (20.2)"
[1] "hr=" "3.8"
D1833V2, continuous
D1833V3, binary
                   cls
clus                  0   1
  ZDHHC21 MUTATED     3   2
  ZDHHC21 WILD-TYPE 363 117
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZDHHC21 MUTATED      3    2
  ZDHHC21 WILD-TYPE  363  117
        clus
vv       ZDHHC21 MUTATED ZDHHC21 WILD-TYPE
  COLON                3               363
  RECTUM               2               117
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZDHHC21 MUTATED         1        0        0         0         1         0
  ZDHHC21 WILD-TYPE      90        1       32       138         9         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZDHHC21 MUTATED           0          0          1          1        0
  ZDHHC21 WILD-TYPE        24         11         58         41       48
                   vv
clus                STAGE IVA STAGE IVB
  ZDHHC21 MUTATED           0         0
  ZDHHC21 WILD-TYPE        18         1
D1833V4, multiclass
            clus
vv           ZDHHC21 MUTATED ZDHHC21 WILD-TYPE
  STAGE I                  1                90
  STAGE IA                 0                 1
  STAGE II                 0                32
  STAGE IIA                0               138
  STAGE IIB                1                 9
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               0                11
  STAGE IIIB               1                58
  STAGE IIIC               1                41
  STAGE IV                 0                48
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  ZDHHC21 MUTATED     0   1   2   2
  ZDHHC21 WILD-TYPE  17  91 327  48
D1833V5, multiclass
    clus
vv   ZDHHC21 MUTATED ZDHHC21 WILD-TYPE
  T1               0                17
  T2               1                91
  T3               2               327
  T4               2                48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  ZDHHC21 MUTATED     2   1   2
  ZDHHC21 WILD-TYPE 285 112  85
D1833V6, multiclass
    clus
vv   ZDHHC21 MUTATED ZDHHC21 WILD-TYPE
  N0               2               285
  N1               1               112
  N2               2                85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1833V7, binary
                   cls
clus                  0   1
  ZDHHC21 MUTATED     3   0
  ZDHHC21 WILD-TYPE 372  65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZDHHC21 MUTATED      3    0
  ZDHHC21 WILD-TYPE  372   65
   clus
vv  ZDHHC21 MUTATED ZDHHC21 WILD-TYPE
  0               3               372
  1               0                65
[1] 2 2
[1] FALSE
D1833V8, binary
                   cls
clus                  0   1
  ZDHHC21 MUTATED     2   3
  ZDHHC21 WILD-TYPE 223 261
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZDHHC21 MUTATED      2    3
  ZDHHC21 WILD-TYPE  223  261
        clus
vv       ZDHHC21 MUTATED ZDHHC21 WILD-TYPE
  FEMALE               2               223
  MALE                 3               261
[1] 2 2
[1] FALSE
D1833V9, binary
                   cls
clus                  0   1
  ZDHHC21 MUTATED     4   0
  ZDHHC21 WILD-TYPE 346  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZDHHC21 MUTATED      4    0
  ZDHHC21 WILD-TYPE  346   22
     clus
vv    ZDHHC21 MUTATED ZDHHC21 WILD-TYPE
  NO                4               346
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ZDHHC21 MUTATED                      3                             0
  ZDHHC21 WILD-TYPE                  312                            47
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ZDHHC21 MUTATED                       2                              0
  ZDHHC21 WILD-TYPE                   104                             10
D1833V10, multiclass
                                clus
vv                               ZDHHC21 MUTATED ZDHHC21 WILD-TYPE
  COLON ADENOCARCINOMA                         3               312
  COLON MUCINOUS ADENOCARCINOMA                0                47
  RECTAL ADENOCARCINOMA                        2               104
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  ZDHHC21 MUTATED     3   0   0   1
  ZDHHC21 WILD-TYPE 342   4  31  24
D1833V11, multiclass
    clus
vv   ZDHHC21 MUTATED ZDHHC21 WILD-TYPE
  R0               3               342
  R1               0                 4
  R2               0                31
  RX               1                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1833V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZDHHC21 MUTATED                                  0     0
  ZDHHC21 WILD-TYPE                                1    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  ZDHHC21 MUTATED                           0     2
  ZDHHC21 WILD-TYPE                        22   224
D1833V13, multiclass
[1] "Remove cluster labels:" "ZDHHC21 MUTATED"       
clus
  ZDHHC21 MUTATED ZDHHC21 WILD-TYPE 
                2               258 
       TCGA-A6-2671        TCGA-A6-2672        TCGA-A6-2674        TCGA-A6-2676 
"ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" 
       TCGA-A6-2677        TCGA-A6-2678        TCGA-A6-2683        TCGA-A6-3807 
"ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" 
       TCGA-A6-3808        TCGA-A6-3809        TCGA-A6-3810        TCGA-A6-4105 
"ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" 
       TCGA-A6-5656        TCGA-A6-5657        TCGA-A6-5659        TCGA-A6-5660 
"ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" 
       TCGA-A6-5661        TCGA-A6-5662        TCGA-A6-5664        TCGA-A6-5665 
"ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" 
       TCGA-A6-5666        TCGA-A6-6137        TCGA-A6-6138        TCGA-A6-6141 
"ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" 
       TCGA-A6-6142        TCGA-A6-6648        TCGA-A6-6649        TCGA-A6-6651 
"ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" 
       TCGA-A6-6652        TCGA-A6-6653        TCGA-A6-6654        TCGA-A6-6780 
"ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" 
       TCGA-A6-6781        TCGA-A6-6782        TCGA-AD-5900        TCGA-AD-6548 
"ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" 
       TCGA-AD-6888        TCGA-AD-6889        TCGA-AD-6890        TCGA-AD-6895 
"ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" 
       TCGA-AD-6899        TCGA-AD-6901        TCGA-AD-6963        TCGA-AD-6965 
"ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" 
       TCGA-AU-3779        TCGA-AU-6004        TCGA-AY-4070        TCGA-AY-4071 
"ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" 
       TCGA-AY-5543        TCGA-AY-6196        TCGA-AY-6197        TCGA-AY-6386 
"ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" 
       TCGA-AZ-4315        TCGA-AZ-4323        TCGA-AZ-4616        TCGA-AZ-4681 
"ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" 
       TCGA-AZ-4682        TCGA-AZ-5403        TCGA-AZ-5407        TCGA-AZ-6598 
"ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" 
       TCGA-AZ-6599        TCGA-AZ-6600        TCGA-AZ-6601        TCGA-AZ-6603 
"ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" 
       TCGA-AZ-6605        TCGA-AZ-6606        TCGA-AZ-6607        TCGA-AZ-6608 
"ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" 
       TCGA-CA-5254        TCGA-CA-5255        TCGA-CA-5796        TCGA-CA-5797 
"ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" 
       TCGA-CA-6715        TCGA-CA-6716        TCGA-CA-6717        TCGA-CA-6718 
"ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" 
       TCGA-CA-6719        TCGA-CK-4947        TCGA-CK-4948        TCGA-CK-4950 
"ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" 
       TCGA-CK-4952        TCGA-CK-5912        TCGA-CK-5913        TCGA-CK-5914 
"ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" 
       TCGA-CK-5915        TCGA-CK-5916        TCGA-CK-6747        TCGA-CK-6748 
"ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" 
       TCGA-CK-6751        TCGA-CM-4743        TCGA-CM-4744        TCGA-CM-4746 
"ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" 
       TCGA-CM-4747        TCGA-CM-4752        TCGA-CM-5341        TCGA-CM-5344 
"ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" 
       TCGA-CM-5348        TCGA-CM-5349        TCGA-CM-5860        TCGA-CM-5861 
"ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" 
       TCGA-CM-5862        TCGA-CM-5863        TCGA-CM-5864        TCGA-CM-5868 
"ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" 
       TCGA-CM-6161        TCGA-CM-6162        TCGA-CM-6163        TCGA-CM-6164 
"ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" 
       TCGA-CM-6165        TCGA-CM-6166        TCGA-CM-6167        TCGA-CM-6168 
"ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" 
       TCGA-CM-6169        TCGA-CM-6170        TCGA-CM-6171        TCGA-CM-6172 
"ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" 
       TCGA-CM-6674        TCGA-CM-6675        TCGA-CM-6676        TCGA-CM-6677 
"ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" 
       TCGA-CM-6678        TCGA-CM-6679        TCGA-CM-6680        TCGA-D5-5537 
"ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" 
       TCGA-D5-5538        TCGA-D5-5539        TCGA-D5-5540        TCGA-D5-5541 
"ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" 
       TCGA-D5-6529        TCGA-D5-6532        TCGA-D5-6533        TCGA-D5-6534 
"ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" 
       TCGA-D5-6535        TCGA-D5-6536        TCGA-D5-6537        TCGA-D5-6538 
"ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" 
       TCGA-D5-6539        TCGA-D5-6540        TCGA-D5-6541        TCGA-D5-6898 
"ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" 
       TCGA-D5-6920        TCGA-D5-6922        TCGA-D5-6923        TCGA-D5-6924 
"ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" 
       TCGA-D5-6926        TCGA-D5-6927        TCGA-D5-6928        TCGA-D5-6929 
"ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" 
       TCGA-D5-6930        TCGA-D5-6931        TCGA-D5-6932        TCGA-D5-7000 
"ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" 
       TCGA-DM-A0X9        TCGA-DM-A0XD        TCGA-DM-A0XF        TCGA-DM-A1D0 
"ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" 
       TCGA-DM-A1D4        TCGA-DM-A1D6        TCGA-DM-A1D7        TCGA-DM-A1D8 
"ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" 
       TCGA-DM-A1D9        TCGA-DM-A1DA        TCGA-DM-A1DB        TCGA-DM-A1HA 
"ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" 
       TCGA-DM-A1HB        TCGA-DM-A282        TCGA-DM-A285        TCGA-DM-A28C 
"ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" 
       TCGA-DM-A28E        TCGA-DM-A28F        TCGA-DM-A28G        TCGA-DM-A28H 
"ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" 
       TCGA-DM-A28K        TCGA-F4-6459        TCGA-F4-6460        TCGA-F4-6569 
"ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" 
       TCGA-F4-6570        TCGA-F4-6703        TCGA-F4-6704        TCGA-F4-6805 
"ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" 
       TCGA-F4-6806        TCGA-F4-6807        TCGA-F4-6808        TCGA-F4-6809 
"ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" 
       TCGA-F4-6854        TCGA-F4-6855        TCGA-F4-6856        TCGA-G4-6293 
"ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" 
       TCGA-G4-6299        TCGA-G4-6303        TCGA-G4-6304        TCGA-G4-6306 
"ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" 
       TCGA-G4-6307        TCGA-G4-6309        TCGA-G4-6310        TCGA-G4-6315 
"ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" 
       TCGA-G4-6317        TCGA-G4-6321        TCGA-G4-6323        TCGA-G4-6586 
"ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" 
       TCGA-G4-6588        TCGA-G4-6625        TCGA-G4-6626        TCGA-G4-6628 
"ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2691        TCGA-AF-2692 
"ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" 
       TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3913        TCGA-AF-4110 
"ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" 
       TCGA-AF-5654        TCGA-AF-6136        TCGA-AF-6655        TCGA-AF-6672 
"ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6549        TCGA-AH-6643 
"ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" 
       TCGA-AH-6644        TCGA-CI-6619        TCGA-CI-6620        TCGA-CI-6621 
"ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" 
       TCGA-CI-6622        TCGA-CI-6624        TCGA-CL-5917        TCGA-CL-5918 
"ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" 
       TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6155        TCGA-DC-6157 
"ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" 
       TCGA-DC-6158        TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682 
"ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" 
       TCGA-DC-6683        TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC 
"ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" 
       TCGA-DY-A1DD        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" 
       TCGA-EF-5830        TCGA-EI-6506        TCGA-EI-6507        TCGA-EI-6508 
"ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" 
       TCGA-EI-6510        TCGA-F5-6464        TCGA-F5-6465        TCGA-F5-6571 
"ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" 
       TCGA-F5-6702        TCGA-F5-6811        TCGA-F5-6812        TCGA-F5-6813 
"ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" 
       TCGA-G5-6235        TCGA-G5-6641 
"ZDHHC21 WILD-TYPE" "ZDHHC21 WILD-TYPE" 

Clustering(1834) Variable = SOX6 MUTATION ANALYSIS
D1834V1, survival
                sevent
clus2              0   1
  SOX6 MUTATED    12   3
  SOX6 WILD-TYPE 366  90
  SOX6 MUTATED SOX6 WILD-TYPE 
            15            456 
  SOX6 MUTATED SOX6 WILD-TYPE 
             3             90 
$`SOX6 MUTATED`
TCGA-A6-5661 TCGA-A6-6781 TCGA-AA-3949 TCGA-AA-A010 TCGA-AA-A01P TCGA-AD-6964 
       33.53        19.66        26.01        34.98        38.07        10.88 
TCGA-AY-6197 TCGA-AY-6386 TCGA-CA-6717 TCGA-CK-5916 TCGA-CM-6162 TCGA-D5-6533 
       21.44        17.82        12.76        21.14        12.00         1.32 
TCGA-AG-3883 TCGA-AG-3892 TCGA-AG-A002 
        1.02        13.02        20.98 

$`SOX6 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       12.99        24.00        33.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       16.31         0.95        33.01        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.20        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 
       15.62        49.08        51.32         9.99        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 
        5.03        15.02        15.02        17.03        15.02         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6534 
       19.59        56.09        55.92        20.19        18.25        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3885 TCGA-AG-3887 
        0.99         0.99        19.04        19.99        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       17.03        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  SOX6 MUTATED SOX6 WILD-TYPE 
          1.02           0.00 
  SOX6 MUTATED SOX6 WILD-TYPE 
         38.07         148.01 
  SOX6 MUTATED SOX6 WILD-TYPE 
        19.660         20.235 
[1] "1.0 - 38.1 (19.7)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.5"
D1834V2, continuous
D1834V3, binary
                cls
clus               0   1
  SOX6 MUTATED    13   3
  SOX6 WILD-TYPE 353 116
[1] "tbl2"
                cls
clus             [,1] [,2]
  SOX6 MUTATED     13    3
  SOX6 WILD-TYPE  353  116
        clus
vv       SOX6 MUTATED SOX6 WILD-TYPE
  COLON            13            353
  RECTUM            3            116
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SOX6 MUTATED         5        0        0         3         1         0
  SOX6 WILD-TYPE      86        1       32       135         9         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SOX6 MUTATED           1          0          4          1        0         0
  SOX6 WILD-TYPE        23         11         55         41       48        18
                vv
clus             STAGE IVB
  SOX6 MUTATED           0
  SOX6 WILD-TYPE         1
D1834V4, multiclass
            clus
vv           SOX6 MUTATED SOX6 WILD-TYPE
  STAGE I               5             86
  STAGE IA              0              1
  STAGE II              0             32
  STAGE IIA             3            135
  STAGE IIB             1              9
  STAGE IIC             0              1
  STAGE III             1             23
  STAGE IIIA            0             11
  STAGE IIIB            4             55
  STAGE IIIC            1             41
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  SOX6 MUTATED     2   3   7   4
  SOX6 WILD-TYPE  15  89 322  46
D1834V5, multiclass
    clus
vv   SOX6 MUTATED SOX6 WILD-TYPE
  T1            2             15
  T2            3             89
  T3            7            322
  T4            4             46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  SOX6 MUTATED    10   5   1
  SOX6 WILD-TYPE 277 108  86
D1834V6, multiclass
    clus
vv   SOX6 MUTATED SOX6 WILD-TYPE
  N0           10            277
  N1            5            108
  N2            1             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1834V7, binary
                cls
clus               0   1
  SOX6 MUTATED    12   0
  SOX6 WILD-TYPE 363  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  SOX6 MUTATED     12    0
  SOX6 WILD-TYPE  363   65
   clus
vv  SOX6 MUTATED SOX6 WILD-TYPE
  0           12            363
  1            0             65
[1] 2 2
[1] FALSE
D1834V8, binary
                cls
clus               0   1
  SOX6 MUTATED     9   7
  SOX6 WILD-TYPE 216 257
[1] "tbl2"
                cls
clus             [,1] [,2]
  SOX6 MUTATED      9    7
  SOX6 WILD-TYPE  216  257
        clus
vv       SOX6 MUTATED SOX6 WILD-TYPE
  FEMALE            9            216
  MALE              7            257
[1] 2 2
[1] FALSE
D1834V9, binary
                cls
clus               0   1
  SOX6 MUTATED    13   0
  SOX6 WILD-TYPE 337  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  SOX6 MUTATED     13    0
  SOX6 WILD-TYPE  337   22
     clus
vv    SOX6 MUTATED SOX6 WILD-TYPE
  NO            13            337
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SOX6 MUTATED                      9                             4
  SOX6 WILD-TYPE                  306                            43
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SOX6 MUTATED                       3                              0
  SOX6 WILD-TYPE                   103                             10
D1834V10, multiclass
                                clus
vv                               SOX6 MUTATED SOX6 WILD-TYPE
  COLON ADENOCARCINOMA                      9            306
  COLON MUCINOUS ADENOCARCINOMA             4             43
  RECTAL ADENOCARCINOMA                     3            103
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  SOX6 MUTATED    12   0   0   3
  SOX6 WILD-TYPE 333   4  31  22
D1834V11, multiclass
    clus
vv   SOX6 MUTATED SOX6 WILD-TYPE
  R0           12            333
  R1            0              4
  R2            0             31
  RX            3             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1834V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SOX6 MUTATED                                  0     1
  SOX6 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  SOX6 MUTATED                           2     7
  SOX6 WILD-TYPE                        20   219
D1834V13, multiclass
                                  clus
vv                                 SOX6 MUTATED SOX6 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   2             20
  WHITE                                       7            219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1835) Variable = APBA1 MUTATION ANALYSIS
D1835V1, survival
                 sevent
clus2               0   1
  APBA1 MUTATED    12   1
  APBA1 WILD-TYPE 366  92
  APBA1 MUTATED APBA1 WILD-TYPE 
             13             458 
  APBA1 MUTATED APBA1 WILD-TYPE 
              1              92 
$`APBA1 MUTATED`
TCGA-A6-3809 TCGA-A6-6653 TCGA-AA-3492 TCGA-AA-3821 TCGA-AA-3864 TCGA-CK-4947 
       32.75        24.39         3.02         1.02        53.00        17.56 
TCGA-CM-5861 TCGA-CM-6676 TCGA-D5-6927 TCGA-AG-3581 TCGA-AG-4005 TCGA-AG-A002 
       15.02        11.08         9.44         7.07        14.04        20.98 
TCGA-CI-6620 
       33.17 

$`APBA1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 
       25.18        24.16        21.76        24.69        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       19.66        20.28         7.04         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
       33.04         0.99        25.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       31.07        30.05        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       14.30       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       22.98        30.08        32.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       11.01        12.95        13.05        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6928 
        3.68         4.41        12.43        14.30         9.04        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        8.02        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       36.03         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6622 TCGA-CI-6624 
       17.49         0.69         0.72         6.05         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  APBA1 MUTATED APBA1 WILD-TYPE 
           1.02            0.00 
  APBA1 MUTATED APBA1 WILD-TYPE 
          53.00          148.01 
  APBA1 MUTATED APBA1 WILD-TYPE 
         15.020          20.415 
[1] "1.0 - 53.0 (15.0)"  "0.0 - 148.0 (20.4)"
[1] "hr=" "1.9"
D1835V2, continuous
D1835V3, binary
                 cls
clus                0   1
  APBA1 MUTATED    10   4
  APBA1 WILD-TYPE 356 115
[1] "tbl2"
                 cls
clus              [,1] [,2]
  APBA1 MUTATED     10    4
  APBA1 WILD-TYPE  356  115
        clus
vv       APBA1 MUTATED APBA1 WILD-TYPE
  COLON             10             356
  RECTUM             4             115
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  APBA1 MUTATED         5        0        2         3         1         0
  APBA1 WILD-TYPE      86        1       30       135         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  APBA1 MUTATED           0          0          1          0        1         1
  APBA1 WILD-TYPE        24         11         58         42       47        17
                 vv
clus              STAGE IVB
  APBA1 MUTATED           0
  APBA1 WILD-TYPE         1
D1835V4, multiclass
            clus
vv           APBA1 MUTATED APBA1 WILD-TYPE
  STAGE I                5              86
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA              3             135
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             0              42
  STAGE IV               1              47
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  APBA1 MUTATED     0   5   7   2
  APBA1 WILD-TYPE  17  87 322  48
D1835V5, multiclass
    clus
vv   APBA1 MUTATED APBA1 WILD-TYPE
  T1             0              17
  T2             5              87
  T3             7             322
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  APBA1 MUTATED    11   2   1
  APBA1 WILD-TYPE 276 111  86
D1835V6, multiclass
    clus
vv   APBA1 MUTATED APBA1 WILD-TYPE
  N0            11             276
  N1             2             111
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1835V7, binary
                 cls
clus                0   1
  APBA1 MUTATED    12   2
  APBA1 WILD-TYPE 363  63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  APBA1 MUTATED     12    2
  APBA1 WILD-TYPE  363   63
   clus
vv  APBA1 MUTATED APBA1 WILD-TYPE
  0            12             363
  1             2              63
[1] 2 2
[1] FALSE
D1835V8, binary
                 cls
clus                0   1
  APBA1 MUTATED     7   7
  APBA1 WILD-TYPE 218 257
[1] "tbl2"
                 cls
clus              [,1] [,2]
  APBA1 MUTATED      7    7
  APBA1 WILD-TYPE  218  257
        clus
vv       APBA1 MUTATED APBA1 WILD-TYPE
  FEMALE             7             218
  MALE               7             257
[1] 2 2
[1] FALSE
D1835V9, binary
                 cls
clus                0   1
  APBA1 MUTATED    13   0
  APBA1 WILD-TYPE 337  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  APBA1 MUTATED     13    0
  APBA1 WILD-TYPE  337   22
     clus
vv    APBA1 MUTATED APBA1 WILD-TYPE
  NO             13             337
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  APBA1 MUTATED                      8                             2
  APBA1 WILD-TYPE                  307                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  APBA1 MUTATED                       4                              0
  APBA1 WILD-TYPE                   102                             10
D1835V10, multiclass
                                clus
vv                               APBA1 MUTATED APBA1 WILD-TYPE
  COLON ADENOCARCINOMA                       8             307
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      4             102
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  APBA1 MUTATED    11   0   0   1
  APBA1 WILD-TYPE 334   4  31  24
D1835V11, multiclass
    clus
vv   APBA1 MUTATED APBA1 WILD-TYPE
  R0            11             334
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1835V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  APBA1 MUTATED                                  0     0
  APBA1 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  APBA1 MUTATED                           0     7
  APBA1 WILD-TYPE                        22   219
D1835V13, multiclass
                                  clus
vv                                 APBA1 MUTATED APBA1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        7             219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1836) Variable = RREB1 MUTATION ANALYSIS
D1836V1, survival
                 sevent
clus2               0   1
  RREB1 MUTATED    11   2
  RREB1 WILD-TYPE 367  91
  RREB1 MUTATED RREB1 WILD-TYPE 
             13             458 
  RREB1 MUTATED RREB1 WILD-TYPE 
              2              91 
$`RREB1 MUTATED`
TCGA-AA-3516 TCGA-AA-3697 TCGA-AU-6004 TCGA-AY-5543 TCGA-CK-4952 TCGA-CM-6162 
       13.02        85.05        27.09        33.01        15.62        12.00 
TCGA-D5-6928 TCGA-G4-6588 TCGA-G4-6628 TCGA-AG-3600 TCGA-AG-A002 TCGA-DC-6157 
       11.64        26.17        79.69         6.05        20.98        27.95 
TCGA-DY-A1DD 
       57.24 

$`RREB1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        1.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6197 
       10.88         0.20        14.50        16.31         0.95        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 
       10.06        14.30        17.56       148.01        85.45        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 
       15.02        15.02        17.03        15.02         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.04         9.44         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       35.80        91.79        46.75        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 
       46.03        34.03         2.01        50.04        12.03         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       13.97        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
        5.29       126.44        41.36        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  RREB1 MUTATED RREB1 WILD-TYPE 
           6.05            0.00 
  RREB1 MUTATED RREB1 WILD-TYPE 
          85.05          148.01 
  RREB1 MUTATED RREB1 WILD-TYPE 
         26.170          20.085 
[1] "6.0 - 85.0 (26.2)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.6"
D1836V2, continuous
D1836V3, binary
                 cls
clus                0   1
  RREB1 MUTATED     9   4
  RREB1 WILD-TYPE 357 115
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RREB1 MUTATED      9    4
  RREB1 WILD-TYPE  357  115
        clus
vv       RREB1 MUTATED RREB1 WILD-TYPE
  COLON              9             357
  RECTUM             4             115
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RREB1 MUTATED         4        0        0         2         0         0
  RREB1 WILD-TYPE      87        1       32       136        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RREB1 MUTATED           2          0          2          2        0         1
  RREB1 WILD-TYPE        22         11         57         40       48        17
                 vv
clus              STAGE IVB
  RREB1 MUTATED           0
  RREB1 WILD-TYPE         1
D1836V4, multiclass
            clus
vv           RREB1 MUTATED RREB1 WILD-TYPE
  STAGE I                4              87
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              2             136
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              2              22
  STAGE IIIA             0              11
  STAGE IIIB             2              57
  STAGE IIIC             2              40
  STAGE IV               0              48
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  RREB1 MUTATED     0   4   8   1
  RREB1 WILD-TYPE  17  88 321  49
D1836V5, multiclass
    clus
vv   RREB1 MUTATED RREB1 WILD-TYPE
  T1             0              17
  T2             4              88
  T3             8             321
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  RREB1 MUTATED     7   3   3
  RREB1 WILD-TYPE 280 110  84
D1836V6, multiclass
    clus
vv   RREB1 MUTATED RREB1 WILD-TYPE
  N0             7             280
  N1             3             110
  N2             3              84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1836V7, binary
                 cls
clus                0   1
  RREB1 MUTATED    12   1
  RREB1 WILD-TYPE 363  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RREB1 MUTATED     12    1
  RREB1 WILD-TYPE  363   64
   clus
vv  RREB1 MUTATED RREB1 WILD-TYPE
  0            12             363
  1             1              64
[1] 2 2
[1] FALSE
D1836V8, binary
                 cls
clus                0   1
  RREB1 MUTATED     7   6
  RREB1 WILD-TYPE 218 258
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RREB1 MUTATED      7    6
  RREB1 WILD-TYPE  218  258
        clus
vv       RREB1 MUTATED RREB1 WILD-TYPE
  FEMALE             7             218
  MALE               6             258
[1] 2 2
[1] FALSE
D1836V9, binary
                 cls
clus                0   1
  RREB1 MUTATED     8   1
  RREB1 WILD-TYPE 342  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RREB1 MUTATED      8    1
  RREB1 WILD-TYPE  342   21
     clus
vv    RREB1 MUTATED RREB1 WILD-TYPE
  NO              8             342
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  RREB1 MUTATED                      5                             4
  RREB1 WILD-TYPE                  310                            43
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  RREB1 MUTATED                       4                              0
  RREB1 WILD-TYPE                   102                             10
D1836V10, multiclass
                                clus
vv                               RREB1 MUTATED RREB1 WILD-TYPE
  COLON ADENOCARCINOMA                       5             310
  COLON MUCINOUS ADENOCARCINOMA              4              43
  RECTAL ADENOCARCINOMA                      4             102
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  RREB1 MUTATED    10   0   0   1
  RREB1 WILD-TYPE 335   4  31  24
D1836V11, multiclass
    clus
vv   RREB1 MUTATED RREB1 WILD-TYPE
  R0            10             335
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1836V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RREB1 MUTATED                                  0     0
  RREB1 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  RREB1 MUTATED                           2     7
  RREB1 WILD-TYPE                        20   219
D1836V13, multiclass
                                  clus
vv                                 RREB1 MUTATED RREB1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    2              20
  WHITE                                        7             219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1837) Variable = KIAA0355 MUTATION ANALYSIS
D1837V1, survival
                    sevent
clus2                  0   1
  KIAA0355 MUTATED     4   3
  KIAA0355 WILD-TYPE 374  90
  KIAA0355 MUTATED KIAA0355 WILD-TYPE 
                 7                464 
  KIAA0355 MUTATED KIAA0355 WILD-TYPE 
                 3                 90 
$`KIAA0355 MUTATED`
TCGA-A6-6782 TCGA-AA-3655 TCGA-AA-3713 TCGA-AA-3715 TCGA-AD-6888 TCGA-F4-6856 
       20.28        61.02        19.04        19.04        15.52        35.31 
TCGA-G4-6303 
       65.85 

$`KIAA0355 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        19.66         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       19.99        13.94        19.99        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
        5.03        85.05        26.99        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
       40.96         0.07        21.37        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
       47.41       133.18        74.56        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  KIAA0355 MUTATED KIAA0355 WILD-TYPE 
             15.52               0.00 
  KIAA0355 MUTATED KIAA0355 WILD-TYPE 
             65.85             148.01 
  KIAA0355 MUTATED KIAA0355 WILD-TYPE 
            20.280             20.155 
[1] "15.5 - 65.8 (20.3)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.6"
D1837V2, continuous
D1837V3, binary
                    cls
clus                   0   1
  KIAA0355 MUTATED     7   0
  KIAA0355 WILD-TYPE 359 119
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0355 MUTATED      7    0
  KIAA0355 WILD-TYPE  359  119
        clus
vv       KIAA0355 MUTATED KIAA0355 WILD-TYPE
  COLON                 7                359
  RECTUM                0                119
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KIAA0355 MUTATED         1        0        2         0         1         0
  KIAA0355 WILD-TYPE      90        1       30       138         9         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIAA0355 MUTATED           0          0          1          0        2
  KIAA0355 WILD-TYPE        24         11         58         42       46
                    vv
clus                 STAGE IVA STAGE IVB
  KIAA0355 MUTATED           0         0
  KIAA0355 WILD-TYPE        18         1
D1837V4, multiclass
            clus
vv           KIAA0355 MUTATED KIAA0355 WILD-TYPE
  STAGE I                   1                 90
  STAGE IA                  0                  1
  STAGE II                  2                 30
  STAGE IIA                 0                138
  STAGE IIB                 1                  9
  STAGE IIC                 0                  1
  STAGE III                 0                 24
  STAGE IIIA                0                 11
  STAGE IIIB                1                 58
  STAGE IIIC                0                 42
  STAGE IV                  2                 46
  STAGE IVA                 0                 18
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  KIAA0355 MUTATED     0   1   5   1
  KIAA0355 WILD-TYPE  17  91 324  49
D1837V5, multiclass
    clus
vv   KIAA0355 MUTATED KIAA0355 WILD-TYPE
  T1                0                 17
  T2                1                 91
  T3                5                324
  T4                1                 49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  KIAA0355 MUTATED     5   2   0
  KIAA0355 WILD-TYPE 282 111  87
D1837V6, multiclass
    clus
vv   KIAA0355 MUTATED KIAA0355 WILD-TYPE
  N0                5                282
  N1                2                111
  N2                0                 87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1837V7, binary
                    cls
clus                   0   1
  KIAA0355 MUTATED     4   2
  KIAA0355 WILD-TYPE 371  63
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0355 MUTATED      4    2
  KIAA0355 WILD-TYPE  371   63
   clus
vv  KIAA0355 MUTATED KIAA0355 WILD-TYPE
  0                4                371
  1                2                 63
[1] 2 2
[1] FALSE
D1837V8, binary
                    cls
clus                   0   1
  KIAA0355 MUTATED     1   6
  KIAA0355 WILD-TYPE 224 258
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0355 MUTATED      1    6
  KIAA0355 WILD-TYPE  224  258
        clus
vv       KIAA0355 MUTATED KIAA0355 WILD-TYPE
  FEMALE                1                224
  MALE                  6                258
[1] 2 2
[1] FALSE
D1837V9, binary
                    cls
clus                   0   1
  KIAA0355 MUTATED     6   1
  KIAA0355 WILD-TYPE 344  21
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0355 MUTATED      6    1
  KIAA0355 WILD-TYPE  344   21
     clus
vv    KIAA0355 MUTATED KIAA0355 WILD-TYPE
  NO                 6                344
  YES                1                 21
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  KIAA0355 MUTATED                      6                             1
  KIAA0355 WILD-TYPE                  309                            46
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  KIAA0355 MUTATED                       0                              0
  KIAA0355 WILD-TYPE                   106                             10
D1837V10, multiclass
                                clus
vv                               KIAA0355 MUTATED KIAA0355 WILD-TYPE
  COLON ADENOCARCINOMA                          6                309
  COLON MUCINOUS ADENOCARCINOMA                 1                 46
  RECTAL ADENOCARCINOMA                         0                106
  RECTAL MUCINOUS ADENOCARCINOMA                0                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  KIAA0355 MUTATED     5   0   1   0
  KIAA0355 WILD-TYPE 340   4  30  25
D1837V11, multiclass
    clus
vv   KIAA0355 MUTATED KIAA0355 WILD-TYPE
  R0                5                340
  R1                0                  4
  R2                1                 30
  RX                0                 25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1837V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KIAA0355 MUTATED                                  0     0
  KIAA0355 WILD-TYPE                                1    11
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  KIAA0355 MUTATED                           0     4
  KIAA0355 WILD-TYPE                        22   222
D1837V13, multiclass
                                  clus
vv                                 KIAA0355 MUTATED KIAA0355 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 11
  BLACK OR AFRICAN AMERICAN                       0                 22
  WHITE                                           4                222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1838) Variable = PTPN13 MUTATION ANALYSIS
D1838V1, survival
                  sevent
clus2                0   1
  PTPN13 MUTATED    20   5
  PTPN13 WILD-TYPE 358  88
  PTPN13 MUTATED PTPN13 WILD-TYPE 
              25              446 
  PTPN13 MUTATED PTPN13 WILD-TYPE 
               5               88 
$`PTPN13 MUTATED`
TCGA-A6-5661 TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3947 
       33.53         3.02        63.98        85.05        19.04        33.01 
TCGA-AA-3955 TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01P TCGA-AA-A02H TCGA-AZ-4315 
       20.98         4.01        34.98        38.07         2.01        58.39 
TCGA-CA-6717 TCGA-CM-5349 TCGA-CM-6171 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
       12.76        30.08        14.04         4.80         1.51        12.00 
TCGA-D5-7000 TCGA-DM-A0XD TCGA-G4-6323 TCGA-G4-6588 TCGA-AF-6672 TCGA-AG-A002 
       10.26        24.43        13.78        26.17        10.39        20.98 
TCGA-EI-6506 
       20.55 

$`PTPN13 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 
       20.12        19.66        20.28         7.04         1.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       26.99        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 
       18.05        31.00         2.01        12.99        24.00        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       24.00         2.01        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       31.00         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02J 
       26.01        37.02        39.06        51.98        39.98         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07        12.20        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 
       14.99        12.99        13.02        15.02        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6932 TCGA-DM-A0X9 TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
       11.38       119.70        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6625 
       63.62        61.91        36.00        22.09        35.80        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       20.02        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
       32.61         0.49        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  PTPN13 MUTATED PTPN13 WILD-TYPE 
            1.51             0.00 
  PTPN13 MUTATED PTPN13 WILD-TYPE 
           85.05           148.01 
  PTPN13 MUTATED PTPN13 WILD-TYPE 
          20.550           20.155 
[1] "1.5 - 85.0 (20.6)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.1"
D1838V2, continuous
D1838V3, binary
                  cls
clus                 0   1
  PTPN13 MUTATED    22   3
  PTPN13 WILD-TYPE 344 116
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PTPN13 MUTATED     22    3
  PTPN13 WILD-TYPE  344  116
        clus
vv       PTPN13 MUTATED PTPN13 WILD-TYPE
  COLON              22              344
  RECTUM              3              116
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PTPN13 MUTATED         3        1        2         8         3         0
  PTPN13 WILD-TYPE      88        0       30       130         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PTPN13 MUTATED           2          0          1          1        4
  PTPN13 WILD-TYPE        22         11         58         41       44
                  vv
clus               STAGE IVA STAGE IVB
  PTPN13 MUTATED           0         0
  PTPN13 WILD-TYPE        18         1
D1838V4, multiclass
            clus
vv           PTPN13 MUTATED PTPN13 WILD-TYPE
  STAGE I                 3               88
  STAGE IA                1                0
  STAGE II                2               30
  STAGE IIA               8              130
  STAGE IIB               3                7
  STAGE IIC               0                1
  STAGE III               2               22
  STAGE IIIA              0               11
  STAGE IIIB              1               58
  STAGE IIIC              1               41
  STAGE IV                4               44
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  PTPN13 MUTATED     0   4  15   5
  PTPN13 WILD-TYPE  17  88 314  45
D1838V5, multiclass
    clus
vv   PTPN13 MUTATED PTPN13 WILD-TYPE
  T1              0               17
  T2              4               88
  T3             15              314
  T4              5               45
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  PTPN13 MUTATED    19   2   4
  PTPN13 WILD-TYPE 268 111  83
D1838V6, multiclass
    clus
vv   PTPN13 MUTATED PTPN13 WILD-TYPE
  N0             19              268
  N1              2              111
  N2              4               83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1838V7, binary
                  cls
clus                 0   1
  PTPN13 MUTATED    20   3
  PTPN13 WILD-TYPE 355  62
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PTPN13 MUTATED     20    3
  PTPN13 WILD-TYPE  355   62
   clus
vv  PTPN13 MUTATED PTPN13 WILD-TYPE
  0             20              355
  1              3               62
[1] 2 2
[1] FALSE
D1838V8, binary
                  cls
clus                 0   1
  PTPN13 MUTATED    12  13
  PTPN13 WILD-TYPE 213 251
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PTPN13 MUTATED     12   13
  PTPN13 WILD-TYPE  213  251
        clus
vv       PTPN13 MUTATED PTPN13 WILD-TYPE
  FEMALE             12              213
  MALE               13              251
[1] 2 2
[1] FALSE
D1838V9, binary
                  cls
clus                 0   1
  PTPN13 MUTATED    18   2
  PTPN13 WILD-TYPE 332  20
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PTPN13 MUTATED     18    2
  PTPN13 WILD-TYPE  332   20
     clus
vv    PTPN13 MUTATED PTPN13 WILD-TYPE
  NO              18              332
  YES              2               20
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PTPN13 MUTATED                     17                             5
  PTPN13 WILD-TYPE                  298                            42
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PTPN13 MUTATED                       3                              0
  PTPN13 WILD-TYPE                   103                             10
D1838V10, multiclass
                                clus
vv                               PTPN13 MUTATED PTPN13 WILD-TYPE
  COLON ADENOCARCINOMA                       17              298
  COLON MUCINOUS ADENOCARCINOMA               5               42
  RECTAL ADENOCARCINOMA                       3              103
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  PTPN13 MUTATED    20   0   2   1
  PTPN13 WILD-TYPE 325   4  29  24
D1838V11, multiclass
    clus
vv   PTPN13 MUTATED PTPN13 WILD-TYPE
  R0             20              325
  R1              0                4
  R2              2               29
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1838V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PTPN13 MUTATED                                  0     1
  PTPN13 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  PTPN13 MUTATED                           2    11
  PTPN13 WILD-TYPE                        20   215
D1838V13, multiclass
                                  clus
vv                                 PTPN13 MUTATED PTPN13 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     2               20
  WHITE                                        11              215
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1839) Variable = TNKS2 MUTATION ANALYSIS
D1839V1, survival
                 sevent
clus2               0   1
  TNKS2 MUTATED    16   3
  TNKS2 WILD-TYPE 362  90
  TNKS2 MUTATED TNKS2 WILD-TYPE 
             19             452 
  TNKS2 MUTATED TNKS2 WILD-TYPE 
              3              90 
$`TNKS2 MUTATED`
TCGA-AA-3977 TCGA-AA-A00J TCGA-AA-A010 TCGA-AA-A01Q TCGA-AU-3779 TCGA-AZ-6598 
       25.02        18.05        34.98         1.02        14.50        49.41 
TCGA-CA-5254 TCGA-CA-6716 TCGA-CA-6717 TCGA-CM-4743 TCGA-CM-5349 TCGA-CM-6674 
       12.69        12.20        12.76        23.05        30.08        12.95 
TCGA-D5-6927 TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-G4-6293 TCGA-AG-A002 TCGA-AG-A01Y 
        9.44       130.65        49.91       133.18        20.98        64.01 
TCGA-DY-A1DG 
       51.48 

$`TNKS2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L 
       38.04        19.00        30.02        34.03        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       31.00        38.07        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       88.21         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
       11.74         3.19         1.61         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.07        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
        1.91       124.27        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       29.06        22.03        22.98        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       15.02        14.04        11.01        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.04        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D4 TCGA-DM-A1D7 
       10.26       119.70        24.43        38.20        92.75        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6303 
       13.25         0.53        47.41        35.31        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       12.00        70.03        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1H8 
        5.29       126.44        41.36        57.24        24.13        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  TNKS2 MUTATED TNKS2 WILD-TYPE 
           1.02            0.00 
  TNKS2 MUTATED TNKS2 WILD-TYPE 
         133.18          148.01 
  TNKS2 MUTATED TNKS2 WILD-TYPE 
         23.050          20.085 
[1] "1.0 - 133.2 (23.1)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.7"
D1839V2, continuous
D1839V3, binary
                 cls
clus                0   1
  TNKS2 MUTATED    19   3
  TNKS2 WILD-TYPE 347 116
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TNKS2 MUTATED     19    3
  TNKS2 WILD-TYPE  347  116
        clus
vv       TNKS2 MUTATED TNKS2 WILD-TYPE
  COLON             19             347
  RECTUM             3             116
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TNKS2 MUTATED         1        0        3        11         2         0
  TNKS2 WILD-TYPE      90        1       29       127         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TNKS2 MUTATED           1          0          1          0        1         1
  TNKS2 WILD-TYPE        23         11         58         42       47        17
                 vv
clus              STAGE IVB
  TNKS2 MUTATED           0
  TNKS2 WILD-TYPE         1
D1839V4, multiclass
            clus
vv           TNKS2 MUTATED TNKS2 WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               3              29
  STAGE IIA             11             127
  STAGE IIB              2               8
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             0              42
  STAGE IV               1              47
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  TNKS2 MUTATED     0   2  16   4
  TNKS2 WILD-TYPE  17  90 313  46
D1839V5, multiclass
    clus
vv   TNKS2 MUTATED TNKS2 WILD-TYPE
  T1             0              17
  T2             2              90
  T3            16             313
  T4             4              46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  TNKS2 MUTATED    18   3   1
  TNKS2 WILD-TYPE 269 110  86
D1839V6, multiclass
    clus
vv   TNKS2 MUTATED TNKS2 WILD-TYPE
  N0            18             269
  N1             3             110
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1839V7, binary
                 cls
clus                0   1
  TNKS2 MUTATED    17   2
  TNKS2 WILD-TYPE 358  63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TNKS2 MUTATED     17    2
  TNKS2 WILD-TYPE  358   63
   clus
vv  TNKS2 MUTATED TNKS2 WILD-TYPE
  0            17             358
  1             2              63
[1] 2 2
[1] FALSE
D1839V8, binary
                 cls
clus                0   1
  TNKS2 MUTATED    12  10
  TNKS2 WILD-TYPE 213 254
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TNKS2 MUTATED     12   10
  TNKS2 WILD-TYPE  213  254
        clus
vv       TNKS2 MUTATED TNKS2 WILD-TYPE
  FEMALE            12             213
  MALE              10             254
[1] 2 2
[1] FALSE
D1839V9, binary
                 cls
clus                0   1
  TNKS2 MUTATED    14   0
  TNKS2 WILD-TYPE 336  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TNKS2 MUTATED     14    0
  TNKS2 WILD-TYPE  336   22
     clus
vv    TNKS2 MUTATED TNKS2 WILD-TYPE
  NO             14             336
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  TNKS2 MUTATED                     15                             4
  TNKS2 WILD-TYPE                  300                            43
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  TNKS2 MUTATED                       3                              0
  TNKS2 WILD-TYPE                   103                             10
D1839V10, multiclass
                                clus
vv                               TNKS2 MUTATED TNKS2 WILD-TYPE
  COLON ADENOCARCINOMA                      15             300
  COLON MUCINOUS ADENOCARCINOMA              4              43
  RECTAL ADENOCARCINOMA                      3             103
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  TNKS2 MUTATED    12   0   1   4
  TNKS2 WILD-TYPE 333   4  30  21
D1839V11, multiclass
    clus
vv   TNKS2 MUTATED TNKS2 WILD-TYPE
  R0            12             333
  R1             0               4
  R2             1              30
  RX             4              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1839V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TNKS2 MUTATED                                  0     3
  TNKS2 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  TNKS2 MUTATED                           0    11
  TNKS2 WILD-TYPE                        22   215
D1839V13, multiclass
                                  clus
vv                                 TNKS2 MUTATED TNKS2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        3               8
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                       11             215
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1840) Variable = XPO4 MUTATION ANALYSIS
D1840V1, survival
                sevent
clus2              0   1
  XPO4 MUTATED    13   6
  XPO4 WILD-TYPE 365  87
  XPO4 MUTATED XPO4 WILD-TYPE 
            19            452 
  XPO4 MUTATED XPO4 WILD-TYPE 
             6             87 
$`XPO4 MUTATED`
TCGA-AA-3510 TCGA-AA-3662 TCGA-AA-3977 TCGA-AA-A010 TCGA-AA-A01P TCGA-AY-6386 
       63.98         6.05        25.02        34.98        38.07        17.82 
TCGA-AZ-6598 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4950 TCGA-CK-4952 TCGA-CM-5861 
       49.41        12.76        10.06        85.45        15.62        15.02 
TCGA-D5-6922 TCGA-D5-6930 TCGA-DM-A285 TCGA-DM-A28G TCGA-G4-6304 TCGA-AG-A002 
        4.41         1.51         6.12        60.79        53.62        20.98 
TCGA-DY-A1DF 
       24.13 

$`XPO4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       19.99        13.94        19.99        61.02        78.08         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AZ-4315 
       27.09        16.31         0.95        33.01        21.44        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-5912 
        0.07        12.20        14.30        17.56       148.01        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 
       22.03        22.98        30.08        32.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
       15.58         1.48         3.68        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
        9.44        11.64         4.80        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28H 
      135.65       139.17        81.37       119.93        35.97       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DG TCGA-DY-A1H8 
        5.29       126.44        41.36        57.24        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  XPO4 MUTATED XPO4 WILD-TYPE 
          1.51           0.00 
  XPO4 MUTATED XPO4 WILD-TYPE 
         85.45         148.01 
  XPO4 MUTATED XPO4 WILD-TYPE 
        20.980         20.155 
[1] "1.5 - 85.5 (21.0)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.4"
D1840V2, continuous
D1840V3, binary
                cls
clus               0   1
  XPO4 MUTATED    18   2
  XPO4 WILD-TYPE 348 117
[1] "tbl2"
                cls
clus             [,1] [,2]
  XPO4 MUTATED     18    2
  XPO4 WILD-TYPE  348  117
        clus
vv       XPO4 MUTATED XPO4 WILD-TYPE
  COLON            18            348
  RECTUM            2            117
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  XPO4 MUTATED         1        0        2         6         2         0
  XPO4 WILD-TYPE      90        1       30       132         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  XPO4 MUTATED           1          1          2          2        2         0
  XPO4 WILD-TYPE        23         10         57         40       46        18
                vv
clus             STAGE IVB
  XPO4 MUTATED           0
  XPO4 WILD-TYPE         1
D1840V4, multiclass
            clus
vv           XPO4 MUTATED XPO4 WILD-TYPE
  STAGE I               1             90
  STAGE IA              0              1
  STAGE II              2             30
  STAGE IIA             6            132
  STAGE IIB             2              8
  STAGE IIC             0              1
  STAGE III             1             23
  STAGE IIIA            1             10
  STAGE IIIB            2             57
  STAGE IIIC            2             40
  STAGE IV              2             46
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  XPO4 MUTATED     0   2  14   4
  XPO4 WILD-TYPE  17  90 315  46
D1840V5, multiclass
    clus
vv   XPO4 MUTATED XPO4 WILD-TYPE
  T1            0             17
  T2            2             90
  T3           14            315
  T4            4             46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  XPO4 MUTATED    12   4   4
  XPO4 WILD-TYPE 275 109  83
D1840V6, multiclass
    clus
vv   XPO4 MUTATED XPO4 WILD-TYPE
  N0           12            275
  N1            4            109
  N2            4             83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1840V7, binary
                cls
clus               0   1
  XPO4 MUTATED    16   2
  XPO4 WILD-TYPE 359  63
[1] "tbl2"
                cls
clus             [,1] [,2]
  XPO4 MUTATED     16    2
  XPO4 WILD-TYPE  359   63
   clus
vv  XPO4 MUTATED XPO4 WILD-TYPE
  0           16            359
  1            2             63
[1] 2 2
[1] FALSE
D1840V8, binary
                cls
clus               0   1
  XPO4 MUTATED    12   8
  XPO4 WILD-TYPE 213 256
[1] "tbl2"
                cls
clus             [,1] [,2]
  XPO4 MUTATED     12    8
  XPO4 WILD-TYPE  213  256
        clus
vv       XPO4 MUTATED XPO4 WILD-TYPE
  FEMALE           12            213
  MALE              8            256
[1] 2 2
[1] FALSE
D1840V9, binary
                cls
clus               0   1
  XPO4 MUTATED    13   0
  XPO4 WILD-TYPE 337  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  XPO4 MUTATED     13    0
  XPO4 WILD-TYPE  337   22
     clus
vv    XPO4 MUTATED XPO4 WILD-TYPE
  NO            13            337
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  XPO4 MUTATED                     14                             4
  XPO4 WILD-TYPE                  301                            43
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  XPO4 MUTATED                       2                              0
  XPO4 WILD-TYPE                   104                             10
D1840V10, multiclass
                                clus
vv                               XPO4 MUTATED XPO4 WILD-TYPE
  COLON ADENOCARCINOMA                     14            301
  COLON MUCINOUS ADENOCARCINOMA             4             43
  RECTAL ADENOCARCINOMA                     2            104
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  XPO4 MUTATED    10   1   1   3
  XPO4 WILD-TYPE 335   3  30  22
D1840V11, multiclass
    clus
vv   XPO4 MUTATED XPO4 WILD-TYPE
  R0           10            335
  R1            1              3
  R2            1             30
  RX            3             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1840V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  XPO4 MUTATED                                  0     2
  XPO4 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  XPO4 MUTATED                           2     9
  XPO4 WILD-TYPE                        20   217
D1840V13, multiclass
                                  clus
vv                                 XPO4 MUTATED XPO4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              9
  BLACK OR AFRICAN AMERICAN                   2             20
  WHITE                                       9            217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1841) Variable = AKNA MUTATION ANALYSIS
D1841V1, survival
                sevent
clus2              0   1
  AKNA MUTATED     9   2
  AKNA WILD-TYPE 369  91
  AKNA MUTATED AKNA WILD-TYPE 
            11            460 
  AKNA MUTATED AKNA WILD-TYPE 
             2             91 
$`AKNA MUTATED`
TCGA-A6-2678 TCGA-AA-3986 TCGA-AU-3779 TCGA-CA-6717 TCGA-CK-5916 TCGA-CM-6675 
       42.28        19.07        14.50        12.76        21.14        13.05 
TCGA-F4-6460 TCGA-G4-6586 TCGA-AG-A002 TCGA-AG-A014 TCGA-AH-6544 
       31.96        35.80        20.98        15.95        38.56 

$`AKNA WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2683 
       43.76        46.65        43.76        42.90        24.33        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        27.02         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       10.88         0.20        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       49.08        51.32         9.99        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6676 TCGA-CM-6677 
       15.02        14.04        11.01        12.95        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A015 
       13.94         6.02        25.97        23.01        37.02        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  AKNA MUTATED AKNA WILD-TYPE 
         12.76           0.00 
  AKNA MUTATED AKNA WILD-TYPE 
         42.28         148.01 
  AKNA MUTATED AKNA WILD-TYPE 
        20.980         20.155 
[1] "12.8 - 42.3 (21.0)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1"  
D1841V2, continuous
D1841V3, binary
                cls
clus               0   1
  AKNA MUTATED     9   3
  AKNA WILD-TYPE 357 116
[1] "tbl2"
                cls
clus             [,1] [,2]
  AKNA MUTATED      9    3
  AKNA WILD-TYPE  357  116
        clus
vv       AKNA MUTATED AKNA WILD-TYPE
  COLON             9            357
  RECTUM            3            116
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  AKNA MUTATED         4        0        0         4         0         0
  AKNA WILD-TYPE      87        1       32       134        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AKNA MUTATED           0          0          2          0        0         0
  AKNA WILD-TYPE        24         11         57         42       48        18
                vv
clus             STAGE IVB
  AKNA MUTATED           1
  AKNA WILD-TYPE         0
D1841V4, multiclass
            clus
vv           AKNA MUTATED AKNA WILD-TYPE
  STAGE I               4             87
  STAGE IA              0              1
  STAGE II              0             32
  STAGE IIA             4            134
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            2             57
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             1              0
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  AKNA MUTATED     1   3   8   0
  AKNA WILD-TYPE  16  89 321  50
D1841V5, multiclass
    clus
vv   AKNA MUTATED AKNA WILD-TYPE
  T1            1             16
  T2            3             89
  T3            8            321
  T4            0             50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  AKNA MUTATED     8   3   1
  AKNA WILD-TYPE 279 110  86
D1841V6, multiclass
    clus
vv   AKNA MUTATED AKNA WILD-TYPE
  N0            8            279
  N1            3            110
  N2            1             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1841V7, binary
                cls
clus               0   1
  AKNA MUTATED    10   2
  AKNA WILD-TYPE 365  63
[1] "tbl2"
                cls
clus             [,1] [,2]
  AKNA MUTATED     10    2
  AKNA WILD-TYPE  365   63
   clus
vv  AKNA MUTATED AKNA WILD-TYPE
  0           10            365
  1            2             63
[1] 2 2
[1] FALSE
D1841V8, binary
                cls
clus               0   1
  AKNA MUTATED     6   6
  AKNA WILD-TYPE 219 258
[1] "tbl2"
                cls
clus             [,1] [,2]
  AKNA MUTATED      6    6
  AKNA WILD-TYPE  219  258
        clus
vv       AKNA MUTATED AKNA WILD-TYPE
  FEMALE            6            219
  MALE              6            258
[1] 2 2
[1] FALSE
D1841V9, binary
                cls
clus               0   1
  AKNA MUTATED    10   0
  AKNA WILD-TYPE 340  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  AKNA MUTATED     10    0
  AKNA WILD-TYPE  340   22
     clus
vv    AKNA MUTATED AKNA WILD-TYPE
  NO            10            340
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  AKNA MUTATED                      8                             1
  AKNA WILD-TYPE                  307                            46
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  AKNA MUTATED                       3                              0
  AKNA WILD-TYPE                   103                             10
D1841V10, multiclass
                                clus
vv                               AKNA MUTATED AKNA WILD-TYPE
  COLON ADENOCARCINOMA                      8            307
  COLON MUCINOUS ADENOCARCINOMA             1             46
  RECTAL ADENOCARCINOMA                     3            103
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  AKNA MUTATED     9   0   0   2
  AKNA WILD-TYPE 336   4  31  23
D1841V11, multiclass
    clus
vv   AKNA MUTATED AKNA WILD-TYPE
  R0            9            336
  R1            0              4
  R2            0             31
  RX            2             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1841V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AKNA MUTATED                                  0     1
  AKNA WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  AKNA MUTATED                           1     6
  AKNA WILD-TYPE                        21   220
D1841V13, multiclass
                                  clus
vv                                 AKNA MUTATED AKNA WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                       6            220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1842) Variable = TRIM36 MUTATION ANALYSIS
D1842V1, survival
                  sevent
clus2                0   1
  TRIM36 MUTATED    12   1
  TRIM36 WILD-TYPE 366  92
  TRIM36 MUTATED TRIM36 WILD-TYPE 
              13              458 
  TRIM36 MUTATED TRIM36 WILD-TYPE 
               1               92 
$`TRIM36 MUTATED`
TCGA-A6-4105 TCGA-AA-3710 TCGA-AA-3977 TCGA-CK-5914 TCGA-CK-6751 TCGA-CM-6677 
       14.53        26.99        25.02         9.99       124.27        11.08 
TCGA-DM-A1D9 TCGA-G4-6309 TCGA-G4-6586 TCGA-G4-6588 TCGA-AF-2693 TCGA-G5-6235 
      140.38        85.48        35.80        26.17        19.10        55.76 
TCGA-G5-6641 
       26.43 

$`TRIM36 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 
       16.57        34.65        33.34        32.75        36.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        85.05        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        49.08        51.32        21.14        82.95         1.91 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A1DB 
       92.75        49.91        13.32        12.59         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6625 
       63.62        61.91        36.00        22.09        13.78        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 
        0.66         0.69 

  TRIM36 MUTATED TRIM36 WILD-TYPE 
            9.99             0.00 
  TRIM36 MUTATED TRIM36 WILD-TYPE 
          140.38           148.01 
  TRIM36 MUTATED TRIM36 WILD-TYPE 
          26.430           20.035 
[1] "10.0 - 140.4 (26.4)" "0.0 - 148.0 (20.0)" 
[1] "hr=" "4.1"
D1842V2, continuous
D1842V3, binary
                  cls
clus                 0   1
  TRIM36 MUTATED    11   3
  TRIM36 WILD-TYPE 355 116
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIM36 MUTATED     11    3
  TRIM36 WILD-TYPE  355  116
        clus
vv       TRIM36 MUTATED TRIM36 WILD-TYPE
  COLON              11              355
  RECTUM              3              116
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TRIM36 MUTATED         2        0        0         7         0         0
  TRIM36 WILD-TYPE      89        1       32       131        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TRIM36 MUTATED           0          1          4          0        0
  TRIM36 WILD-TYPE        24         10         55         42       48
                  vv
clus               STAGE IVA STAGE IVB
  TRIM36 MUTATED           0         0
  TRIM36 WILD-TYPE        18         1
D1842V4, multiclass
            clus
vv           TRIM36 MUTATED TRIM36 WILD-TYPE
  STAGE I                 2               89
  STAGE IA                0                1
  STAGE II                0               32
  STAGE IIA               7              131
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              1               10
  STAGE IIIB              4               55
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  TRIM36 MUTATED     1   3  10   1
  TRIM36 WILD-TYPE  16  89 319  49
D1842V5, multiclass
    clus
vv   TRIM36 MUTATED TRIM36 WILD-TYPE
  T1              1               16
  T2              3               89
  T3             10              319
  T4              1               49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  TRIM36 MUTATED    10   5   0
  TRIM36 WILD-TYPE 277 108  87
D1842V6, multiclass
    clus
vv   TRIM36 MUTATED TRIM36 WILD-TYPE
  N0             10              277
  N1              5              108
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1842V7, binary
                  cls
clus                 0   1
  TRIM36 MUTATED     9   0
  TRIM36 WILD-TYPE 366  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIM36 MUTATED      9    0
  TRIM36 WILD-TYPE  366   65
   clus
vv  TRIM36 MUTATED TRIM36 WILD-TYPE
  0              9              366
  1              0               65
[1] 2 2
[1] FALSE
D1842V8, binary
                  cls
clus                 0   1
  TRIM36 MUTATED     8   7
  TRIM36 WILD-TYPE 217 257
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIM36 MUTATED      8    7
  TRIM36 WILD-TYPE  217  257
        clus
vv       TRIM36 MUTATED TRIM36 WILD-TYPE
  FEMALE              8              217
  MALE                7              257
[1] 2 2
[1] FALSE
D1842V9, binary
                  cls
clus                 0   1
  TRIM36 MUTATED    11   0
  TRIM36 WILD-TYPE 339  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIM36 MUTATED     11    0
  TRIM36 WILD-TYPE  339   22
     clus
vv    TRIM36 MUTATED TRIM36 WILD-TYPE
  NO              11              339
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  TRIM36 MUTATED                     10                             1
  TRIM36 WILD-TYPE                  305                            46
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  TRIM36 MUTATED                       2                              1
  TRIM36 WILD-TYPE                   104                              9
D1842V10, multiclass
                                clus
vv                               TRIM36 MUTATED TRIM36 WILD-TYPE
  COLON ADENOCARCINOMA                       10              305
  COLON MUCINOUS ADENOCARCINOMA               1               46
  RECTAL ADENOCARCINOMA                       2              104
  RECTAL MUCINOUS ADENOCARCINOMA              1                9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  TRIM36 MUTATED     7   1   1   2
  TRIM36 WILD-TYPE 338   3  30  23
D1842V11, multiclass
    clus
vv   TRIM36 MUTATED TRIM36 WILD-TYPE
  R0              7              338
  R1              1                3
  R2              1               30
  RX              2               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1842V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TRIM36 MUTATED                                  0     0
  TRIM36 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  TRIM36 MUTATED                           1    10
  TRIM36 WILD-TYPE                        21   216
D1842V13, multiclass
                                  clus
vv                                 TRIM36 MUTATED TRIM36 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                        10              216
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1843) Variable = DIAPH3 MUTATION ANALYSIS
D1843V1, survival
                  sevent
clus2                0   1
  DIAPH3 MUTATED    15   2
  DIAPH3 WILD-TYPE 363  91
  DIAPH3 MUTATED DIAPH3 WILD-TYPE 
              17              454 
  DIAPH3 MUTATED DIAPH3 WILD-TYPE 
               2               91 
$`DIAPH3 MUTATED`
TCGA-A6-6780 TCGA-AA-3489 TCGA-AA-3662 TCGA-AA-3977 TCGA-AD-6899 TCGA-CA-6717 
       20.12         7.04         6.05        25.02         5.79        12.76 
TCGA-CK-5913 TCGA-CM-4743 TCGA-CM-6171 TCGA-CM-6674 TCGA-D5-6929 TCGA-F4-6855 
       51.32        23.05        14.04        12.95         4.80        47.41 
TCGA-G4-6293 TCGA-G4-6306 TCGA-G4-6310 TCGA-AG-3890 TCGA-CI-6624 
      133.18        44.68        63.62        17.03         4.73 

$`DIAPH3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       23.87        19.66        20.28         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        0.72        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07        12.20        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 
       17.56       148.01        85.45        15.62        49.08         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 
       21.14        82.95         1.91       124.27        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6675 
       14.99        12.99        13.02        15.02        11.01        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 
       12.43        14.30         9.04         9.44        11.64         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 
       35.31        74.56        65.85        53.62        55.04        85.48 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 
       19.99         1.02        17.95        36.95        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
       33.17         6.97        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  DIAPH3 MUTATED DIAPH3 WILD-TYPE 
            4.73             0.00 
  DIAPH3 MUTATED DIAPH3 WILD-TYPE 
          133.18           148.01 
  DIAPH3 MUTATED DIAPH3 WILD-TYPE 
          17.030           20.415 
[1] "4.7 - 133.2 (17.0)" "0.0 - 148.0 (20.4)"
[1] "hr=" "1.9"
D1843V2, continuous
D1843V3, binary
                  cls
clus                 0   1
  DIAPH3 MUTATED    16   2
  DIAPH3 WILD-TYPE 350 117
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DIAPH3 MUTATED     16    2
  DIAPH3 WILD-TYPE  350  117
        clus
vv       DIAPH3 MUTATED DIAPH3 WILD-TYPE
  COLON              16              350
  RECTUM              2              117
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DIAPH3 MUTATED         3        0        1         8         0         0
  DIAPH3 WILD-TYPE      88        1       31       130        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DIAPH3 MUTATED           1          0          1          1        2
  DIAPH3 WILD-TYPE        23         11         58         41       46
                  vv
clus               STAGE IVA STAGE IVB
  DIAPH3 MUTATED           0         0
  DIAPH3 WILD-TYPE        18         1
D1843V4, multiclass
            clus
vv           DIAPH3 MUTATED DIAPH3 WILD-TYPE
  STAGE I                 3               88
  STAGE IA                0                1
  STAGE II                1               31
  STAGE IIA               8              130
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               1               23
  STAGE IIIA              0               11
  STAGE IIIB              1               58
  STAGE IIIC              1               41
  STAGE IV                2               46
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  DIAPH3 MUTATED     0   5  11   2
  DIAPH3 WILD-TYPE  17  87 318  48
D1843V5, multiclass
    clus
vv   DIAPH3 MUTATED DIAPH3 WILD-TYPE
  T1              0               17
  T2              5               87
  T3             11              318
  T4              2               48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  DIAPH3 MUTATED    13   3   2
  DIAPH3 WILD-TYPE 274 110  85
D1843V6, multiclass
    clus
vv   DIAPH3 MUTATED DIAPH3 WILD-TYPE
  N0             13              274
  N1              3              110
  N2              2               85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1843V7, binary
                  cls
clus                 0   1
  DIAPH3 MUTATED    12   2
  DIAPH3 WILD-TYPE 363  63
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DIAPH3 MUTATED     12    2
  DIAPH3 WILD-TYPE  363   63
   clus
vv  DIAPH3 MUTATED DIAPH3 WILD-TYPE
  0             12              363
  1              2               63
[1] 2 2
[1] FALSE
D1843V8, binary
                  cls
clus                 0   1
  DIAPH3 MUTATED     8  10
  DIAPH3 WILD-TYPE 217 254
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DIAPH3 MUTATED      8   10
  DIAPH3 WILD-TYPE  217  254
        clus
vv       DIAPH3 MUTATED DIAPH3 WILD-TYPE
  FEMALE              8              217
  MALE               10              254
[1] 2 2
[1] FALSE
D1843V9, binary
                  cls
clus                 0   1
  DIAPH3 MUTATED    14   1
  DIAPH3 WILD-TYPE 336  21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DIAPH3 MUTATED     14    1
  DIAPH3 WILD-TYPE  336   21
     clus
vv    DIAPH3 MUTATED DIAPH3 WILD-TYPE
  NO              14              336
  YES              1               21
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  DIAPH3 MUTATED                     13                             3
  DIAPH3 WILD-TYPE                  302                            44
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  DIAPH3 MUTATED                       2                              0
  DIAPH3 WILD-TYPE                   104                             10
D1843V10, multiclass
                                clus
vv                               DIAPH3 MUTATED DIAPH3 WILD-TYPE
  COLON ADENOCARCINOMA                       13              302
  COLON MUCINOUS ADENOCARCINOMA               3               44
  RECTAL ADENOCARCINOMA                       2              104
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  DIAPH3 MUTATED    11   0   1   2
  DIAPH3 WILD-TYPE 334   4  30  23
D1843V11, multiclass
    clus
vv   DIAPH3 MUTATED DIAPH3 WILD-TYPE
  R0             11              334
  R1              0                4
  R2              1               30
  RX              2               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1843V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DIAPH3 MUTATED                                  0     1
  DIAPH3 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  DIAPH3 MUTATED                           0    12
  DIAPH3 WILD-TYPE                        22   214
D1843V13, multiclass
                                  clus
vv                                 DIAPH3 MUTATED DIAPH3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                        12              214
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1844) Variable = KDR MUTATION ANALYSIS
D1844V1, survival
               sevent
clus2             0   1
  KDR MUTATED    23   6
  KDR WILD-TYPE 355  87
  KDR MUTATED KDR WILD-TYPE 
           29           442 
  KDR MUTATED KDR WILD-TYPE 
            6            87 
$`KDR MUTATED`
TCGA-A6-5665 TCGA-A6-6780 TCGA-AA-3489 TCGA-AA-3555 TCGA-AA-3697 TCGA-AA-3949 
       22.06        20.12         7.04        29.95        85.05        26.01 
TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A010 TCGA-AD-6895 TCGA-AY-6197 TCGA-AZ-4315 
       25.02         4.01        34.98         0.72        21.44        58.39 
TCGA-AZ-6598 TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-6161 TCGA-CM-6168 TCGA-D5-6539 
       49.41        12.76        10.06        15.02        12.99        12.49 
TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 TCGA-DM-A1D9 TCGA-DM-A28F TCGA-G4-6315 
        4.80        12.00        11.38       140.38        35.97        61.91 
TCGA-G4-6628 TCGA-AF-5654 TCGA-AG-A002 TCGA-AG-A02N TCGA-DY-A0XA 
       79.69        16.83        20.98        61.97       126.44 

$`KDR WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       19.66        20.28         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       17.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 
        5.98        37.05        19.00        36.00         5.03        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.79         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 
       14.50        27.09        16.31         0.95        33.01        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.07        12.20        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6162 
       15.02         5.03        15.02        15.02        17.03        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6169 
        2.96        29.03        16.04        21.99        14.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 
       43.27        15.12        17.85         4.80        17.13        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-7000 TCGA-DM-A0X9 
        9.04         9.44        11.64         1.51        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
       12.59         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
        6.12        81.37       119.93        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6317 TCGA-G4-6321 
       44.68        55.04        85.48        63.62        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 
       13.78        35.80        26.17        91.79        46.75        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       14.50        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
       49.97         1.94        38.96        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        4.01         5.03         5.29        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  KDR MUTATED KDR WILD-TYPE 
         0.72          0.00 
  KDR MUTATED KDR WILD-TYPE 
       140.38        148.01 
  KDR MUTATED KDR WILD-TYPE 
       21.440        20.035 
[1] "0.7 - 140.4 (21.4)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.2"
D1844V2, continuous
D1844V3, binary
               cls
clus              0   1
  KDR MUTATED    28   4
  KDR WILD-TYPE 338 115
[1] "tbl2"
               cls
clus            [,1] [,2]
  KDR MUTATED     28    4
  KDR WILD-TYPE  338  115
        clus
vv       KDR MUTATED KDR WILD-TYPE
  COLON           28           338
  RECTUM           4           115
[1] 2 2
[1] FALSE
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KDR MUTATED         5        0        4        12         2         0
  KDR WILD-TYPE      86        1       28       126         8         1
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  KDR MUTATED           1          1          2          1        2         0
  KDR WILD-TYPE        23         10         57         41       46        18
               vv
clus            STAGE IVB
  KDR MUTATED           0
  KDR WILD-TYPE         1
D1844V4, multiclass
            clus
vv           KDR MUTATED KDR WILD-TYPE
  STAGE I              5            86
  STAGE IA             0             1
  STAGE II             4            28
  STAGE IIA           12           126
  STAGE IIB            2             8
  STAGE IIC            0             1
  STAGE III            1            23
  STAGE IIIA           1            10
  STAGE IIIB           2            57
  STAGE IIIC           1            41
  STAGE IV             2            46
  STAGE IVA            0            18
  STAGE IVB            0             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  KDR MUTATED     0   6  22   4
  KDR WILD-TYPE  17  86 307  46
D1844V5, multiclass
    clus
vv   KDR MUTATED KDR WILD-TYPE
  T1           0            17
  T2           6            86
  T3          22           307
  T4           4            46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2
  KDR MUTATED    26   5   1
  KDR WILD-TYPE 261 108  86
D1844V6, multiclass
    clus
vv   KDR MUTATED KDR WILD-TYPE
  N0          26           261
  N1           5           108
  N2           1            86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1844V7, binary
               cls
clus              0   1
  KDR MUTATED    24   2
  KDR WILD-TYPE 351  63
[1] "tbl2"
               cls
clus            [,1] [,2]
  KDR MUTATED     24    2
  KDR WILD-TYPE  351   63
   clus
vv  KDR MUTATED KDR WILD-TYPE
  0          24           351
  1           2            63
[1] 2 2
[1] FALSE
D1844V8, binary
               cls
clus              0   1
  KDR MUTATED    14  18
  KDR WILD-TYPE 211 246
[1] "tbl2"
               cls
clus            [,1] [,2]
  KDR MUTATED     14   18
  KDR WILD-TYPE  211  246
        clus
vv       KDR MUTATED KDR WILD-TYPE
  FEMALE          14           211
  MALE            18           246
[1] 2 2
[1] FALSE
D1844V9, binary
               cls
clus              0   1
  KDR MUTATED    22   0
  KDR WILD-TYPE 328  22
[1] "tbl2"
               cls
clus            [,1] [,2]
  KDR MUTATED     22    0
  KDR WILD-TYPE  328   22
     clus
vv    KDR MUTATED KDR WILD-TYPE
  NO           22           328
  YES           0            22
[1] 2 2
[1] FALSE
               vv
clus            COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  KDR MUTATED                     23                             5
  KDR WILD-TYPE                  292                            42
               vv
clus            RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  KDR MUTATED                       4                              0
  KDR WILD-TYPE                   102                             10
D1844V10, multiclass
                                clus
vv                               KDR MUTATED KDR WILD-TYPE
  COLON ADENOCARCINOMA                    23           292
  COLON MUCINOUS ADENOCARCINOMA            5            42
  RECTAL ADENOCARCINOMA                    4           102
  RECTAL MUCINOUS ADENOCARCINOMA           0            10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             R0  R1  R2  RX
  KDR MUTATED    22   0   0   3
  KDR WILD-TYPE 323   4  31  22
D1844V11, multiclass
    clus
vv   KDR MUTATED KDR WILD-TYPE
  R0          22           323
  R1           0             4
  R2           0            31
  RX           3            22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1844V12, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KDR MUTATED                                  0     2
  KDR WILD-TYPE                                1     9
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  KDR MUTATED                           1    18
  KDR WILD-TYPE                        21   208
D1844V13, multiclass
                                  clus
vv                                 KDR MUTATED KDR WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      2             9
  BLACK OR AFRICAN AMERICAN                  1            21
  WHITE                                     18           208
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1845) Variable = STK40 MUTATION ANALYSIS
D1845V1, survival
                 sevent
clus2               0   1
  STK40 MUTATED     9   0
  STK40 WILD-TYPE 369  93
  STK40 MUTATED STK40 WILD-TYPE 
              9             462 
  STK40 MUTATED STK40 WILD-TYPE 
              0              93 
$`STK40 MUTATED`
TCGA-AA-3525 TCGA-AA-3864 TCGA-AA-3949 TCGA-CK-4947 TCGA-D5-6533 TCGA-F4-6569 
        8.05        53.00        26.01        17.56         1.32        35.74 
TCGA-G4-6321 TCGA-AG-A002 TCGA-G5-6235 
       22.09        20.98        55.76 

$`STK40 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 
       32.05         0.99        31.07        31.07        30.05        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       12.99        24.00        33.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       12.76        10.06        14.30       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
        8.61        31.96         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 
       55.04        85.48        63.62        61.91        36.00        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6641 
       31.30        28.57        32.19         0.66         0.69        26.43 

  STK40 MUTATED STK40 WILD-TYPE 
           1.32            0.00 
  STK40 MUTATED STK40 WILD-TYPE 
          55.76          148.01 
  STK40 MUTATED STK40 WILD-TYPE 
         22.090          20.085 
[1] "1.3 - 55.8 (22.1)"  "0.0 - 148.0 (20.1)"
[1] "hr="     "9200000"
D1845V2, continuous
D1845V3, binary
                 cls
clus                0   1
  STK40 MUTATED     7   2
  STK40 WILD-TYPE 359 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STK40 MUTATED      7    2
  STK40 WILD-TYPE  359  117
        clus
vv       STK40 MUTATED STK40 WILD-TYPE
  COLON              7             359
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  STK40 MUTATED         2        0        1         0         0         0
  STK40 WILD-TYPE      89        1       31       138        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  STK40 MUTATED           1          0          5          0        0         0
  STK40 WILD-TYPE        23         11         54         42       48        18
                 vv
clus              STAGE IVB
  STK40 MUTATED           0
  STK40 WILD-TYPE         1
D1845V4, multiclass
            clus
vv           STK40 MUTATED STK40 WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              0             138
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             5              54
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  STK40 MUTATED     0   3   4   2
  STK40 WILD-TYPE  17  89 325  48
D1845V5, multiclass
    clus
vv   STK40 MUTATED STK40 WILD-TYPE
  T1             0              17
  T2             3              89
  T3             4             325
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  STK40 MUTATED     4   5   0
  STK40 WILD-TYPE 283 108  87
D1845V6, multiclass
    clus
vv   STK40 MUTATED STK40 WILD-TYPE
  N0             4             283
  N1             5             108
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1845V7, binary
                 cls
clus                0   1
  STK40 MUTATED     7   0
  STK40 WILD-TYPE 368  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STK40 MUTATED      7    0
  STK40 WILD-TYPE  368   65
   clus
vv  STK40 MUTATED STK40 WILD-TYPE
  0             7             368
  1             0              65
[1] 2 2
[1] FALSE
D1845V8, binary
                 cls
clus                0   1
  STK40 MUTATED     4   5
  STK40 WILD-TYPE 221 259
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STK40 MUTATED      4    5
  STK40 WILD-TYPE  221  259
        clus
vv       STK40 MUTATED STK40 WILD-TYPE
  FEMALE             4             221
  MALE               5             259
[1] 2 2
[1] FALSE
D1845V9, binary
                 cls
clus                0   1
  STK40 MUTATED     8   0
  STK40 WILD-TYPE 342  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STK40 MUTATED      8    0
  STK40 WILD-TYPE  342   22
     clus
vv    STK40 MUTATED STK40 WILD-TYPE
  NO              8             342
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  STK40 MUTATED                      6                             1
  STK40 WILD-TYPE                  309                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  STK40 MUTATED                       2                              0
  STK40 WILD-TYPE                   104                             10
D1845V10, multiclass
                                clus
vv                               STK40 MUTATED STK40 WILD-TYPE
  COLON ADENOCARCINOMA                       6             309
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  STK40 MUTATED     7   1   0   1
  STK40 WILD-TYPE 338   3  31  24
D1845V11, multiclass
    clus
vv   STK40 MUTATED STK40 WILD-TYPE
  R0             7             338
  R1             1               3
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1845V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  STK40 MUTATED                                  0     0
  STK40 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  STK40 MUTATED                           0     5
  STK40 WILD-TYPE                        22   221
D1845V13, multiclass
                                  clus
vv                                 STK40 MUTATED STK40 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        5             221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1846) Variable = XRCC6 MUTATION ANALYSIS
D1846V1, survival
                 sevent
clus2               0   1
  XRCC6 MUTATED     6   2
  XRCC6 WILD-TYPE 372  91
  XRCC6 MUTATED XRCC6 WILD-TYPE 
              8             463 
  XRCC6 MUTATED XRCC6 WILD-TYPE 
              2              91 
$`XRCC6 MUTATED`
TCGA-AA-3715 TCGA-AA-A010 TCGA-CM-6171 TCGA-CM-6674 TCGA-D5-6928 TCGA-DM-A1D6 
       19.04        34.98        14.04        12.95        11.64        49.91 
TCGA-DM-A1HB TCGA-AG-A002 
      135.65        20.98 

$`XRCC6 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6675 
       14.99        12.99        13.02        15.02        11.01        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6930 
       12.43        14.30         9.04         9.44         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
      130.65        92.75        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
       44.32       131.51       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  XRCC6 MUTATED XRCC6 WILD-TYPE 
          11.64            0.00 
  XRCC6 MUTATED XRCC6 WILD-TYPE 
         135.65          148.01 
  XRCC6 MUTATED XRCC6 WILD-TYPE 
          20.01           20.19 
[1] "11.6 - 135.7 (20.0)" "0.0 - 148.0 (20.2)" 
[1] "hr=" "1"  
D1846V2, continuous
D1846V3, binary
                 cls
clus                0   1
  XRCC6 MUTATED     7   1
  XRCC6 WILD-TYPE 359 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  XRCC6 MUTATED      7    1
  XRCC6 WILD-TYPE  359  118
        clus
vv       XRCC6 MUTATED XRCC6 WILD-TYPE
  COLON              7             359
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  XRCC6 MUTATED         2        0        1         3         1         0
  XRCC6 WILD-TYPE      89        1       31       135         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  XRCC6 MUTATED           0          0          1          0        0         0
  XRCC6 WILD-TYPE        24         11         58         42       48        18
                 vv
clus              STAGE IVB
  XRCC6 MUTATED           0
  XRCC6 WILD-TYPE         1
D1846V4, multiclass
            clus
vv           XRCC6 MUTATED XRCC6 WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              3             135
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  XRCC6 MUTATED     0   2   5   1
  XRCC6 WILD-TYPE  17  90 324  49
D1846V5, multiclass
    clus
vv   XRCC6 MUTATED XRCC6 WILD-TYPE
  T1             0              17
  T2             2              90
  T3             5             324
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  XRCC6 MUTATED     7   1   0
  XRCC6 WILD-TYPE 280 112  87
D1846V6, multiclass
    clus
vv   XRCC6 MUTATED XRCC6 WILD-TYPE
  N0             7             280
  N1             1             112
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1846V7, binary
                 cls
clus                0   1
  XRCC6 MUTATED     8   0
  XRCC6 WILD-TYPE 367  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  XRCC6 MUTATED      8    0
  XRCC6 WILD-TYPE  367   65
   clus
vv  XRCC6 MUTATED XRCC6 WILD-TYPE
  0             8             367
  1             0              65
[1] 2 2
[1] FALSE
D1846V8, binary
                 cls
clus                0   1
  XRCC6 MUTATED     2   6
  XRCC6 WILD-TYPE 223 258
[1] "tbl2"
                 cls
clus              [,1] [,2]
  XRCC6 MUTATED      2    6
  XRCC6 WILD-TYPE  223  258
        clus
vv       XRCC6 MUTATED XRCC6 WILD-TYPE
  FEMALE             2             223
  MALE               6             258
[1] 2 2
[1] FALSE
D1846V9, binary
                 cls
clus                0   1
  XRCC6 MUTATED     6   0
  XRCC6 WILD-TYPE 344  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  XRCC6 MUTATED      6    0
  XRCC6 WILD-TYPE  344   22
     clus
vv    XRCC6 MUTATED XRCC6 WILD-TYPE
  NO              6             344
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  XRCC6 MUTATED                      4                             2
  XRCC6 WILD-TYPE                  311                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  XRCC6 MUTATED                       1                              0
  XRCC6 WILD-TYPE                   105                             10
D1846V10, multiclass
                                clus
vv                               XRCC6 MUTATED XRCC6 WILD-TYPE
  COLON ADENOCARCINOMA                       4             311
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  XRCC6 MUTATED     6   0   0   0
  XRCC6 WILD-TYPE 339   4  31  25
D1846V11, multiclass
    clus
vv   XRCC6 MUTATED XRCC6 WILD-TYPE
  R0             6             339
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1846V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  XRCC6 MUTATED                                  0     0
  XRCC6 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  XRCC6 MUTATED                           0     5
  XRCC6 WILD-TYPE                        22   221
D1846V13, multiclass
                                  clus
vv                                 XRCC6 MUTATED XRCC6 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        5             221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1847) Variable = PHLDB2 MUTATION ANALYSIS
D1847V1, survival
                  sevent
clus2                0   1
  PHLDB2 MUTATED    17   2
  PHLDB2 WILD-TYPE 361  91
  PHLDB2 MUTATED PHLDB2 WILD-TYPE 
              19              452 
  PHLDB2 MUTATED PHLDB2 WILD-TYPE 
               2               91 
$`PHLDB2 MUTATED`
TCGA-A6-5665 TCGA-AA-3510 TCGA-AA-3516 TCGA-AA-3525 TCGA-AA-3697 TCGA-AA-3819 
       22.06        63.98        13.02         8.05        85.05        25.02 
TCGA-AA-A00N TCGA-AA-A010 TCGA-AU-6004 TCGA-AZ-4315 TCGA-CA-6717 TCGA-CK-4952 
        4.01        34.98        27.09        58.39        12.76        15.62 
TCGA-CM-4752 TCGA-D5-6535 TCGA-DM-A28H TCGA-G4-6304 TCGA-G4-6309 TCGA-AG-3882 
       13.02        15.12       117.07        53.62        85.48        19.99 
TCGA-AG-A002 
       20.98 

$`PHLDB2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
       35.01         6.97         1.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       24.03        37.05        36.03        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 
        5.98        37.05        19.00        36.00         5.03        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       10.88         0.20        14.50        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07        12.20        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 
       14.30        17.56       148.01        85.45        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       20.02        37.02        25.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 
       55.92        20.19        18.25         1.32        43.27        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
       60.79        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       65.85        44.68        55.04        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3883 TCGA-AG-3885 
       32.98         0.99         0.99        19.04         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  PHLDB2 MUTATED PHLDB2 WILD-TYPE 
            4.01             0.00 
  PHLDB2 MUTATED PHLDB2 WILD-TYPE 
          117.07           148.01 
  PHLDB2 MUTATED PHLDB2 WILD-TYPE 
          22.060           20.085 
[1] "4.0 - 117.1 (22.1)" "0.0 - 148.0 (20.1)"
[1] "hr=" "2.7"
D1847V2, continuous
D1847V3, binary
                  cls
clus                 0   1
  PHLDB2 MUTATED    18   2
  PHLDB2 WILD-TYPE 348 117
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PHLDB2 MUTATED     18    2
  PHLDB2 WILD-TYPE  348  117
        clus
vv       PHLDB2 MUTATED PHLDB2 WILD-TYPE
  COLON              18              348
  RECTUM              2              117
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PHLDB2 MUTATED         3        0        1         6         3         0
  PHLDB2 WILD-TYPE      88        1       31       132         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PHLDB2 MUTATED           2          0          3          2        0
  PHLDB2 WILD-TYPE        22         11         56         40       48
                  vv
clus               STAGE IVA STAGE IVB
  PHLDB2 MUTATED           0         0
  PHLDB2 WILD-TYPE        18         1
D1847V4, multiclass
            clus
vv           PHLDB2 MUTATED PHLDB2 WILD-TYPE
  STAGE I                 3               88
  STAGE IA                0                1
  STAGE II                1               31
  STAGE IIA               6              132
  STAGE IIB               3                7
  STAGE IIC               0                1
  STAGE III               2               22
  STAGE IIIA              0               11
  STAGE IIIB              3               56
  STAGE IIIC              2               40
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  PHLDB2 MUTATED     0   3  13   4
  PHLDB2 WILD-TYPE  17  89 316  46
D1847V5, multiclass
    clus
vv   PHLDB2 MUTATED PHLDB2 WILD-TYPE
  T1              0               17
  T2              3               89
  T3             13              316
  T4              4               46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  PHLDB2 MUTATED    14   3   3
  PHLDB2 WILD-TYPE 273 110  84
D1847V6, multiclass
    clus
vv   PHLDB2 MUTATED PHLDB2 WILD-TYPE
  N0             14              273
  N1              3              110
  N2              3               84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1847V7, binary
                  cls
clus                 0   1
  PHLDB2 MUTATED    19   0
  PHLDB2 WILD-TYPE 356  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PHLDB2 MUTATED     19    0
  PHLDB2 WILD-TYPE  356   65
   clus
vv  PHLDB2 MUTATED PHLDB2 WILD-TYPE
  0             19              356
  1              0               65
[1] 2 2
[1] FALSE
D1847V8, binary
                  cls
clus                 0   1
  PHLDB2 MUTATED    11   9
  PHLDB2 WILD-TYPE 214 255
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PHLDB2 MUTATED     11    9
  PHLDB2 WILD-TYPE  214  255
        clus
vv       PHLDB2 MUTATED PHLDB2 WILD-TYPE
  FEMALE             11              214
  MALE                9              255
[1] 2 2
[1] FALSE
D1847V9, binary
                  cls
clus                 0   1
  PHLDB2 MUTATED    15   0
  PHLDB2 WILD-TYPE 335  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PHLDB2 MUTATED     15    0
  PHLDB2 WILD-TYPE  335   22
     clus
vv    PHLDB2 MUTATED PHLDB2 WILD-TYPE
  NO              15              335
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PHLDB2 MUTATED                     14                             4
  PHLDB2 WILD-TYPE                  301                            43
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PHLDB2 MUTATED                       2                              0
  PHLDB2 WILD-TYPE                   104                             10
D1847V10, multiclass
                                clus
vv                               PHLDB2 MUTATED PHLDB2 WILD-TYPE
  COLON ADENOCARCINOMA                       14              301
  COLON MUCINOUS ADENOCARCINOMA               4               43
  RECTAL ADENOCARCINOMA                       2              104
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  PHLDB2 MUTATED    15   0   0   3
  PHLDB2 WILD-TYPE 330   4  31  22
D1847V11, multiclass
    clus
vv   PHLDB2 MUTATED PHLDB2 WILD-TYPE
  R0             15              330
  R1              0                4
  R2              0               31
  RX              3               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1847V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PHLDB2 MUTATED                                  0     1
  PHLDB2 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  PHLDB2 MUTATED                           2     7
  PHLDB2 WILD-TYPE                        20   219
D1847V13, multiclass
                                  clus
vv                                 PHLDB2 MUTATED PHLDB2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     2               20
  WHITE                                         7              219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1848) Variable = MRPL44 MUTATION ANALYSIS
D1848V1, survival
                  sevent
clus2                0   1
  MRPL44 MUTATED     6   4
  MRPL44 WILD-TYPE 372  89
  MRPL44 MUTATED MRPL44 WILD-TYPE 
              10              461 
  MRPL44 MUTATED MRPL44 WILD-TYPE 
               4               89 
$`MRPL44 MUTATED`
TCGA-AA-3525 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3977 TCGA-AZ-4315 TCGA-AZ-6598 
        8.05        19.04        10.06        25.02        58.39        49.41 
TCGA-CA-5255 TCGA-G4-6628 TCGA-AG-A002 TCGA-DC-6158 
        3.06        79.69        20.98        10.98 

$`MRPL44 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3812 
       36.00         5.03        85.05        26.99        19.04        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       88.21         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5796 TCGA-CA-5797 
       11.74         3.19         1.61        12.69         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 
       35.80        26.17        91.79        46.75        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6160 TCGA-DC-6681 
       15.02         5.03        13.97        27.95        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  MRPL44 MUTATED MRPL44 WILD-TYPE 
            3.06             0.00 
  MRPL44 MUTATED MRPL44 WILD-TYPE 
           79.69           148.01 
  MRPL44 MUTATED MRPL44 WILD-TYPE 
           20.01            20.19 
[1] "3.1 - 79.7 (20.0)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.8"
D1848V2, continuous
D1848V3, binary
                  cls
clus                 0   1
  MRPL44 MUTATED     8   2
  MRPL44 WILD-TYPE 358 117
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MRPL44 MUTATED      8    2
  MRPL44 WILD-TYPE  358  117
        clus
vv       MRPL44 MUTATED MRPL44 WILD-TYPE
  COLON               8              358
  RECTUM              2              117
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MRPL44 MUTATED         3        0        2         2         0         0
  MRPL44 WILD-TYPE      88        1       30       136        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MRPL44 MUTATED           1          0          1          0        0
  MRPL44 WILD-TYPE        23         11         58         42       48
                  vv
clus               STAGE IVA STAGE IVB
  MRPL44 MUTATED           0         0
  MRPL44 WILD-TYPE        18         1
D1848V4, multiclass
            clus
vv           MRPL44 MUTATED MRPL44 WILD-TYPE
  STAGE I                 3               88
  STAGE IA                0                1
  STAGE II                2               30
  STAGE IIA               2              136
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               1               23
  STAGE IIIA              0               11
  STAGE IIIB              1               58
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  MRPL44 MUTATED     0   4   6   0
  MRPL44 WILD-TYPE  17  88 323  50
D1848V5, multiclass
    clus
vv   MRPL44 MUTATED MRPL44 WILD-TYPE
  T1              0               17
  T2              4               88
  T3              6              323
  T4              0               50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  MRPL44 MUTATED     8   1   1
  MRPL44 WILD-TYPE 279 112  86
D1848V6, multiclass
    clus
vv   MRPL44 MUTATED MRPL44 WILD-TYPE
  N0              8              279
  N1              1              112
  N2              1               86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1848V7, binary
                  cls
clus                 0   1
  MRPL44 MUTATED     8   0
  MRPL44 WILD-TYPE 367  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MRPL44 MUTATED      8    0
  MRPL44 WILD-TYPE  367   65
   clus
vv  MRPL44 MUTATED MRPL44 WILD-TYPE
  0              8              367
  1              0               65
[1] 2 2
[1] FALSE
D1848V8, binary
                  cls
clus                 0   1
  MRPL44 MUTATED     2   8
  MRPL44 WILD-TYPE 223 256
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MRPL44 MUTATED      2    8
  MRPL44 WILD-TYPE  223  256
        clus
vv       MRPL44 MUTATED MRPL44 WILD-TYPE
  FEMALE              2              223
  MALE                8              256
[1] 2 2
[1] FALSE
D1848V9, binary
                  cls
clus                 0   1
  MRPL44 MUTATED     9   1
  MRPL44 WILD-TYPE 341  21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MRPL44 MUTATED      9    1
  MRPL44 WILD-TYPE  341   21
     clus
vv    MRPL44 MUTATED MRPL44 WILD-TYPE
  NO               9              341
  YES              1               21
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MRPL44 MUTATED                      8                             0
  MRPL44 WILD-TYPE                  307                            47
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MRPL44 MUTATED                       2                              0
  MRPL44 WILD-TYPE                   104                             10
D1848V10, multiclass
                                clus
vv                               MRPL44 MUTATED MRPL44 WILD-TYPE
  COLON ADENOCARCINOMA                        8              307
  COLON MUCINOUS ADENOCARCINOMA               0               47
  RECTAL ADENOCARCINOMA                       2              104
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  MRPL44 MUTATED     7   0   0   1
  MRPL44 WILD-TYPE 338   4  31  24
D1848V11, multiclass
    clus
vv   MRPL44 MUTATED MRPL44 WILD-TYPE
  R0              7              338
  R1              0                4
  R2              0               31
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1848V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MRPL44 MUTATED                                  0     1
  MRPL44 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  MRPL44 MUTATED                           0     4
  MRPL44 WILD-TYPE                        22   222
D1848V13, multiclass
                                  clus
vv                                 MRPL44 MUTATED MRPL44 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         4              222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1849) Variable = IDI1 MUTATION ANALYSIS
D1849V1, survival
                sevent
clus2              0   1
  IDI1 MUTATED     1   2
  IDI1 WILD-TYPE 377  91
  IDI1 MUTATED IDI1 WILD-TYPE 
             3            468 
  IDI1 MUTATED IDI1 WILD-TYPE 
             2             91 
$`IDI1 MUTATED`
TCGA-AZ-6598 TCGA-F4-6570 TCGA-G4-6304 
       49.41         6.18        53.62 

$`IDI1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       35.74        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       74.56        65.85        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  IDI1 MUTATED IDI1 WILD-TYPE 
          6.18           0.00 
  IDI1 MUTATED IDI1 WILD-TYPE 
         53.62         148.01 
  IDI1 MUTATED IDI1 WILD-TYPE 
        49.410         20.155 
[1] "6.2 - 53.6 (49.4)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "2.1"
D1849V2, continuous
D1849V3, binary
                cls
clus               0   1
  IDI1 MUTATED     4   0
  IDI1 WILD-TYPE 362 119
[1] "tbl2"
                cls
clus             [,1] [,2]
  IDI1 MUTATED      4    0
  IDI1 WILD-TYPE  362  119
        clus
vv       IDI1 MUTATED IDI1 WILD-TYPE
  COLON             4            362
  RECTUM            0            119
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  IDI1 MUTATED         0        0        1         2         1         0
  IDI1 WILD-TYPE      91        1       31       136         9         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  IDI1 MUTATED           0          0          0          0        0         0
  IDI1 WILD-TYPE        24         11         59         42       48        18
                vv
clus             STAGE IVB
  IDI1 MUTATED           0
  IDI1 WILD-TYPE         1
D1849V4, multiclass
            clus
vv           IDI1 MUTATED IDI1 WILD-TYPE
  STAGE I               0             91
  STAGE IA              0              1
  STAGE II              1             31
  STAGE IIA             2            136
  STAGE IIB             1              9
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            0             59
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  IDI1 MUTATED     0   0   3   1
  IDI1 WILD-TYPE  17  92 326  49
D1849V5, multiclass
    clus
vv   IDI1 MUTATED IDI1 WILD-TYPE
  T1            0             17
  T2            0             92
  T3            3            326
  T4            1             49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  IDI1 MUTATED     4   0   0
  IDI1 WILD-TYPE 283 113  87
D1849V6, multiclass
    clus
vv   IDI1 MUTATED IDI1 WILD-TYPE
  N0            4            283
  N1            0            113
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1849V7, binary
                cls
clus               0   1
  IDI1 MUTATED     3   0
  IDI1 WILD-TYPE 372  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  IDI1 MUTATED      3    0
  IDI1 WILD-TYPE  372   65
   clus
vv  IDI1 MUTATED IDI1 WILD-TYPE
  0            3            372
  1            0             65
[1] 2 2
[1] FALSE
D1849V8, binary
                cls
clus               0   1
  IDI1 MUTATED     4   0
  IDI1 WILD-TYPE 221 264
[1] "tbl2"
                cls
clus             [,1] [,2]
  IDI1 MUTATED      4    0
  IDI1 WILD-TYPE  221  264
        clus
vv       IDI1 MUTATED IDI1 WILD-TYPE
  FEMALE            4            221
  MALE              0            264
[1] 2 2
[1] FALSE
D1849V9, binary
                cls
clus               0   1
  IDI1 MUTATED     3   0
  IDI1 WILD-TYPE 347  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  IDI1 MUTATED      3    0
  IDI1 WILD-TYPE  347   22
     clus
vv    IDI1 MUTATED IDI1 WILD-TYPE
  NO             3            347
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  IDI1 MUTATED                      4                             0
  IDI1 WILD-TYPE                  311                            47
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  IDI1 MUTATED                       0                              0
  IDI1 WILD-TYPE                   106                             10
D1849V10, multiclass
                                clus
vv                               IDI1 MUTATED IDI1 WILD-TYPE
  COLON ADENOCARCINOMA                      4            311
  COLON MUCINOUS ADENOCARCINOMA             0             47
  RECTAL ADENOCARCINOMA                     0            106
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  IDI1 MUTATED     3   0   0   0
  IDI1 WILD-TYPE 342   4  31  25
D1849V11, multiclass
    clus
vv   IDI1 MUTATED IDI1 WILD-TYPE
  R0            3            342
  R1            0              4
  R2            0             31
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1849V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  IDI1 MUTATED                                  0     0
  IDI1 WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  IDI1 MUTATED                           0     3
  IDI1 WILD-TYPE                        22   223
D1849V13, multiclass
                                  clus
vv                                 IDI1 MUTATED IDI1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       3            223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1850) Variable = SMOX MUTATION ANALYSIS
D1850V1, survival
                sevent
clus2              0   1
  SMOX MUTATED     6   1
  SMOX WILD-TYPE 372  92
  SMOX MUTATED SMOX WILD-TYPE 
             7            464 
  SMOX MUTATED SMOX WILD-TYPE 
             1             92 
$`SMOX MUTATED`
TCGA-A6-6781 TCGA-AA-3864 TCGA-AA-3950 TCGA-CM-5868 TCGA-F4-6703 TCGA-AG-A002 
       19.66        53.00        24.00        17.03        47.87        20.98 
TCGA-DY-A1H8 
       32.61 

$`SMOX WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 
       32.05         0.99        31.07        31.07        30.05        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 
       12.99        24.00        33.01        26.01         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6162 
       15.02         5.03        15.02        15.02        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6704 
       98.24         8.61        31.96        35.74         6.18         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  SMOX MUTATED SMOX WILD-TYPE 
         17.03           0.00 
  SMOX MUTATED SMOX WILD-TYPE 
         53.00         148.01 
  SMOX MUTATED SMOX WILD-TYPE 
        24.000         20.085 
[1] "17.0 - 53.0 (24.0)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.7"
D1850V2, continuous
D1850V3, binary
                cls
clus               0   1
  SMOX MUTATED     6   2
  SMOX WILD-TYPE 360 117
[1] "tbl2"
                cls
clus             [,1] [,2]
  SMOX MUTATED      6    2
  SMOX WILD-TYPE  360  117
        clus
vv       SMOX MUTATED SMOX WILD-TYPE
  COLON             6            360
  RECTUM            2            117
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SMOX MUTATED         1        0        1         2         1         0
  SMOX WILD-TYPE      90        1       31       136         9         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SMOX MUTATED           0          1          0          1        0         1
  SMOX WILD-TYPE        24         10         59         41       48        17
                vv
clus             STAGE IVB
  SMOX MUTATED           0
  SMOX WILD-TYPE         1
D1850V4, multiclass
            clus
vv           SMOX MUTATED SMOX WILD-TYPE
  STAGE I               1             90
  STAGE IA              0              1
  STAGE II              1             31
  STAGE IIA             2            136
  STAGE IIB             1              9
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            1             10
  STAGE IIIB            0             59
  STAGE IIIC            1             41
  STAGE IV              0             48
  STAGE IVA             1             17
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  SMOX MUTATED     0   2   3   3
  SMOX WILD-TYPE  17  90 326  47
D1850V5, multiclass
    clus
vv   SMOX MUTATED SMOX WILD-TYPE
  T1            0             17
  T2            2             90
  T3            3            326
  T4            3             47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  SMOX MUTATED     5   3   0
  SMOX WILD-TYPE 282 110  87
D1850V6, multiclass
    clus
vv   SMOX MUTATED SMOX WILD-TYPE
  N0            5            282
  N1            3            110
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1850V7, binary
                cls
clus               0   1
  SMOX MUTATED     5   1
  SMOX WILD-TYPE 370  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  SMOX MUTATED      5    1
  SMOX WILD-TYPE  370   64
   clus
vv  SMOX MUTATED SMOX WILD-TYPE
  0            5            370
  1            1             64
[1] 2 2
[1] FALSE
D1850V8, binary
                cls
clus               0   1
  SMOX MUTATED     4   4
  SMOX WILD-TYPE 221 260
[1] "tbl2"
                cls
clus             [,1] [,2]
  SMOX MUTATED      4    4
  SMOX WILD-TYPE  221  260
        clus
vv       SMOX MUTATED SMOX WILD-TYPE
  FEMALE            4            221
  MALE              4            260
[1] 2 2
[1] FALSE
D1850V9, binary
                cls
clus               0   1
  SMOX MUTATED     6   0
  SMOX WILD-TYPE 344  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  SMOX MUTATED      6    0
  SMOX WILD-TYPE  344   22
     clus
vv    SMOX MUTATED SMOX WILD-TYPE
  NO             6            344
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SMOX MUTATED                      4                             2
  SMOX WILD-TYPE                  311                            45
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SMOX MUTATED                       2                              0
  SMOX WILD-TYPE                   104                             10
D1850V10, multiclass
                                clus
vv                               SMOX MUTATED SMOX WILD-TYPE
  COLON ADENOCARCINOMA                      4            311
  COLON MUCINOUS ADENOCARCINOMA             2             45
  RECTAL ADENOCARCINOMA                     2            104
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  SMOX MUTATED     6   0   0   1
  SMOX WILD-TYPE 339   4  31  24
D1850V11, multiclass
    clus
vv   SMOX MUTATED SMOX WILD-TYPE
  R0            6            339
  R1            0              4
  R2            0             31
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1850V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SMOX MUTATED                                  0     0
  SMOX WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  SMOX MUTATED                           0     5
  SMOX WILD-TYPE                        22   221
D1850V13, multiclass
                                  clus
vv                                 SMOX MUTATED SMOX WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       5            221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1851) Variable = CENPJ MUTATION ANALYSIS
D1851V1, survival
                 sevent
clus2               0   1
  CENPJ MUTATED    14   6
  CENPJ WILD-TYPE 364  87
  CENPJ MUTATED CENPJ WILD-TYPE 
             20             451 
  CENPJ MUTATED CENPJ WILD-TYPE 
              6              87 
$`CENPJ MUTATED`
TCGA-A6-6141 TCGA-A6-6651 TCGA-A6-6781 TCGA-AA-3663 TCGA-AA-3672 TCGA-AA-3715 
        8.38        21.76        19.66         6.97         0.92        19.04 
TCGA-AA-3851 TCGA-AA-A00N TCGA-AA-A010 TCGA-AZ-4315 TCGA-CA-6717 TCGA-CA-6718 
       33.07         4.01        34.98        58.39        12.76        10.06 
TCGA-CM-6171 TCGA-D5-6537 TCGA-F4-6570 TCGA-G4-6303 TCGA-G4-6321 TCGA-G4-6323 
       14.04         4.80         6.18        65.85        22.09        13.78 
TCGA-G4-6628 TCGA-AG-A002 
       79.69        20.98 

$`CENPJ WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 
       22.09        22.06        32.71        27.09        22.52        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       25.18        24.16        24.69        24.39        23.87        20.12 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02        78.08         6.05        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
       14.01        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3854 
        0.00        17.03        10.06         0.00         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 
        3.06         3.25         3.29         0.07        12.20        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
       17.85        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 
       36.00        35.80        26.17        91.79        46.75        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  CENPJ MUTATED CENPJ WILD-TYPE 
           0.92            0.00 
  CENPJ MUTATED CENPJ WILD-TYPE 
          79.69          148.01 
  CENPJ MUTATED CENPJ WILD-TYPE 
          16.54           20.55 
[1] "0.9 - 79.7 (16.5)"  "0.0 - 148.0 (20.6)"
[1] "hr=" "1.7"
D1851V2, continuous
D1851V3, binary
                 cls
clus                0   1
  CENPJ MUTATED    21   1
  CENPJ WILD-TYPE 345 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CENPJ MUTATED     21    1
  CENPJ WILD-TYPE  345  118
        clus
vv       CENPJ MUTATED CENPJ WILD-TYPE
  COLON             21             345
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CENPJ MUTATED         3        1        3         7         2         0
  CENPJ WILD-TYPE      88        0       29       131         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CENPJ MUTATED           2          0          2          1        1         0
  CENPJ WILD-TYPE        22         11         57         41       47        18
                 vv
clus              STAGE IVB
  CENPJ MUTATED           0
  CENPJ WILD-TYPE         1
D1851V4, multiclass
            clus
vv           CENPJ MUTATED CENPJ WILD-TYPE
  STAGE I                3              88
  STAGE IA               1               0
  STAGE II               3              29
  STAGE IIA              7             131
  STAGE IIB              2               8
  STAGE IIC              0               1
  STAGE III              2              22
  STAGE IIIA             0              11
  STAGE IIIB             2              57
  STAGE IIIC             1              41
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CENPJ MUTATED     0   4  13   4
  CENPJ WILD-TYPE  17  88 316  46
D1851V5, multiclass
    clus
vv   CENPJ MUTATED CENPJ WILD-TYPE
  T1             0              17
  T2             4              88
  T3            13             316
  T4             4              46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  CENPJ MUTATED    16   6   0
  CENPJ WILD-TYPE 271 107  87
D1851V6, multiclass
    clus
vv   CENPJ MUTATED CENPJ WILD-TYPE
  N0            16             271
  N1             6             107
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1851V7, binary
                 cls
clus                0   1
  CENPJ MUTATED    16   1
  CENPJ WILD-TYPE 359  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CENPJ MUTATED     16    1
  CENPJ WILD-TYPE  359   64
   clus
vv  CENPJ MUTATED CENPJ WILD-TYPE
  0            16             359
  1             1              64
[1] 2 2
[1] FALSE
D1851V8, binary
                 cls
clus                0   1
  CENPJ MUTATED     9  13
  CENPJ WILD-TYPE 216 251
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CENPJ MUTATED      9   13
  CENPJ WILD-TYPE  216  251
        clus
vv       CENPJ MUTATED CENPJ WILD-TYPE
  FEMALE             9             216
  MALE              13             251
[1] 2 2
[1] FALSE
D1851V9, binary
                 cls
clus                0   1
  CENPJ MUTATED    19   0
  CENPJ WILD-TYPE 331  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CENPJ MUTATED     19    0
  CENPJ WILD-TYPE  331   22
     clus
vv    CENPJ MUTATED CENPJ WILD-TYPE
  NO             19             331
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CENPJ MUTATED                     18                             3
  CENPJ WILD-TYPE                  297                            44
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CENPJ MUTATED                       1                              0
  CENPJ WILD-TYPE                   105                             10
D1851V10, multiclass
                                clus
vv                               CENPJ MUTATED CENPJ WILD-TYPE
  COLON ADENOCARCINOMA                      18             297
  COLON MUCINOUS ADENOCARCINOMA              3              44
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  CENPJ MUTATED    18   0   0   2
  CENPJ WILD-TYPE 327   4  31  23
D1851V11, multiclass
    clus
vv   CENPJ MUTATED CENPJ WILD-TYPE
  R0            18             327
  R1             0               4
  R2             0              31
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1851V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CENPJ MUTATED                                  0     2
  CENPJ WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CENPJ MUTATED                           2     9
  CENPJ WILD-TYPE                        20   217
D1851V13, multiclass
                                  clus
vv                                 CENPJ MUTATED CENPJ WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               9
  BLACK OR AFRICAN AMERICAN                    2              20
  WHITE                                        9             217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1852) Variable = DUSP16 MUTATION ANALYSIS
D1852V1, survival
                  sevent
clus2                0   1
  DUSP16 MUTATED     9   2
  DUSP16 WILD-TYPE 369  91
  DUSP16 MUTATED DUSP16 WILD-TYPE 
              11              460 
  DUSP16 MUTATED DUSP16 WILD-TYPE 
               2               91 
$`DUSP16 MUTATED`
TCGA-A6-3809 TCGA-AA-3518 TCGA-AA-3525 TCGA-AA-3663 TCGA-AA-3977 TCGA-AZ-6598 
       32.75         1.02         8.05         6.97        25.02        49.41 
TCGA-CM-4746 TCGA-D5-6538 TCGA-F4-6854 TCGA-AG-3584 TCGA-AG-A002 
       37.02        17.13         0.53        24.00        20.98 

$`DUSP16 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3529 
        9.07        24.03        37.05        36.03        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02        78.08         6.05        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       88.21         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       20.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
       17.85         4.80        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       33.67        13.25        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3587 
        8.02         7.07        36.03        20.05         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  DUSP16 MUTATED DUSP16 WILD-TYPE 
            0.53             0.00 
  DUSP16 MUTATED DUSP16 WILD-TYPE 
           49.41           148.01 
  DUSP16 MUTATED DUSP16 WILD-TYPE 
          20.980           20.155 
[1] "0.5 - 49.4 (21.0)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.2"
D1852V2, continuous
D1852V3, binary
                  cls
clus                 0   1
  DUSP16 MUTATED     9   2
  DUSP16 WILD-TYPE 357 117
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DUSP16 MUTATED      9    2
  DUSP16 WILD-TYPE  357  117
        clus
vv       DUSP16 MUTATED DUSP16 WILD-TYPE
  COLON               9              357
  RECTUM              2              117
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DUSP16 MUTATED         2        0        2         2         1         0
  DUSP16 WILD-TYPE      89        1       30       136         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DUSP16 MUTATED           0          0          2          0        1
  DUSP16 WILD-TYPE        24         11         57         42       47
                  vv
clus               STAGE IVA STAGE IVB
  DUSP16 MUTATED           0         0
  DUSP16 WILD-TYPE        18         1
D1852V4, multiclass
            clus
vv           DUSP16 MUTATED DUSP16 WILD-TYPE
  STAGE I                 2               89
  STAGE IA                0                1
  STAGE II                2               30
  STAGE IIA               2              136
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              2               57
  STAGE IIIC              0               42
  STAGE IV                1               47
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  DUSP16 MUTATED     0   3   7   1
  DUSP16 WILD-TYPE  17  89 322  49
D1852V5, multiclass
    clus
vv   DUSP16 MUTATED DUSP16 WILD-TYPE
  T1              0               17
  T2              3               89
  T3              7              322
  T4              1               49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  DUSP16 MUTATED     8   1   2
  DUSP16 WILD-TYPE 279 112  85
D1852V6, multiclass
    clus
vv   DUSP16 MUTATED DUSP16 WILD-TYPE
  N0              8              279
  N1              1              112
  N2              2               85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1852V7, binary
                  cls
clus                 0   1
  DUSP16 MUTATED     8   1
  DUSP16 WILD-TYPE 367  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DUSP16 MUTATED      8    1
  DUSP16 WILD-TYPE  367   64
   clus
vv  DUSP16 MUTATED DUSP16 WILD-TYPE
  0              8              367
  1              1               64
[1] 2 2
[1] FALSE
D1852V8, binary
                  cls
clus                 0   1
  DUSP16 MUTATED     5   6
  DUSP16 WILD-TYPE 220 258
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DUSP16 MUTATED      5    6
  DUSP16 WILD-TYPE  220  258
        clus
vv       DUSP16 MUTATED DUSP16 WILD-TYPE
  FEMALE              5              220
  MALE                6              258
[1] 2 2
[1] FALSE
D1852V9, binary
                  cls
clus                 0   1
  DUSP16 MUTATED    10   0
  DUSP16 WILD-TYPE 340  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DUSP16 MUTATED     10    0
  DUSP16 WILD-TYPE  340   22
     clus
vv    DUSP16 MUTATED DUSP16 WILD-TYPE
  NO              10              340
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  DUSP16 MUTATED                      8                             1
  DUSP16 WILD-TYPE                  307                            46
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  DUSP16 MUTATED                       2                              0
  DUSP16 WILD-TYPE                   104                             10
D1852V10, multiclass
                                clus
vv                               DUSP16 MUTATED DUSP16 WILD-TYPE
  COLON ADENOCARCINOMA                        8              307
  COLON MUCINOUS ADENOCARCINOMA               1               46
  RECTAL ADENOCARCINOMA                       2              104
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  DUSP16 MUTATED     8   0   1   0
  DUSP16 WILD-TYPE 337   4  30  25
D1852V11, multiclass
    clus
vv   DUSP16 MUTATED DUSP16 WILD-TYPE
  R0              8              337
  R1              0                4
  R2              1               30
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1852V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DUSP16 MUTATED                                  0     0
  DUSP16 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  DUSP16 MUTATED                           1     4
  DUSP16 WILD-TYPE                        21   222
D1852V13, multiclass
                                  clus
vv                                 DUSP16 MUTATED DUSP16 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                         4              222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1853) Variable = ZHX3 MUTATION ANALYSIS
D1853V1, survival
                sevent
clus2              0   1
  ZHX3 MUTATED    13   1
  ZHX3 WILD-TYPE 365  92
  ZHX3 MUTATED ZHX3 WILD-TYPE 
            14            457 
  ZHX3 MUTATED ZHX3 WILD-TYPE 
             1             92 
$`ZHX3 MUTATED`
TCGA-AA-3510 TCGA-AA-3667 TCGA-AA-3864 TCGA-AA-3870 TCGA-AA-3877 TCGA-AA-A00J 
       63.98        14.01        53.00        29.98        31.00        18.05 
TCGA-AA-A01R TCGA-AD-5900 TCGA-AZ-6598 TCGA-CA-6717 TCGA-CM-6171 TCGA-G4-6304 
       35.01         0.07        49.41        12.76        14.04        53.62 
TCGA-AG-A002 TCGA-DC-6157 
       20.98        27.95 

$`ZHX3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
        6.97        54.02         2.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 
        0.99        31.07        31.07        30.05        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 
       41.00        39.98        18.05        40.96        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 
      106.75        22.36        62.79        88.21         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       13.02        15.02        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 
       47.41        35.31       133.18        74.56        65.85        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6158 
       78.12         7.17        15.02         5.03        13.97        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  ZHX3 MUTATED ZHX3 WILD-TYPE 
          0.07           0.00 
  ZHX3 MUTATED ZHX3 WILD-TYPE 
         63.98         148.01 
  ZHX3 MUTATED ZHX3 WILD-TYPE 
        28.965         20.050 
[1] "0.1 - 64.0 (29.0)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "3.4"
D1853V2, continuous
D1853V3, binary
                cls
clus               0   1
  ZHX3 MUTATED    12   2
  ZHX3 WILD-TYPE 354 117
[1] "tbl2"
                cls
clus             [,1] [,2]
  ZHX3 MUTATED     12    2
  ZHX3 WILD-TYPE  354  117
        clus
vv       ZHX3 MUTATED ZHX3 WILD-TYPE
  COLON            12            354
  RECTUM            2            117
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZHX3 MUTATED         6        0        3         1         1         0
  ZHX3 WILD-TYPE      85        1       29       137         9         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ZHX3 MUTATED           1          0          1          0        1         0
  ZHX3 WILD-TYPE        23         11         58         42       47        18
                vv
clus             STAGE IVB
  ZHX3 MUTATED           0
  ZHX3 WILD-TYPE         1
D1853V4, multiclass
            clus
vv           ZHX3 MUTATED ZHX3 WILD-TYPE
  STAGE I               6             85
  STAGE IA              0              1
  STAGE II              3             29
  STAGE IIA             1            137
  STAGE IIB             1              9
  STAGE IIC             0              1
  STAGE III             1             23
  STAGE IIIA            0             11
  STAGE IIIB            1             58
  STAGE IIIC            0             42
  STAGE IV              1             47
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  ZHX3 MUTATED     1   5   6   2
  ZHX3 WILD-TYPE  16  87 323  48
D1853V5, multiclass
    clus
vv   ZHX3 MUTATED ZHX3 WILD-TYPE
  T1            1             16
  T2            5             87
  T3            6            323
  T4            2             48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  ZHX3 MUTATED    11   1   2
  ZHX3 WILD-TYPE 276 112  85
D1853V6, multiclass
    clus
vv   ZHX3 MUTATED ZHX3 WILD-TYPE
  N0           11            276
  N1            1            112
  N2            2             85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1853V7, binary
                cls
clus               0   1
  ZHX3 MUTATED    11   1
  ZHX3 WILD-TYPE 364  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  ZHX3 MUTATED     11    1
  ZHX3 WILD-TYPE  364   64
   clus
vv  ZHX3 MUTATED ZHX3 WILD-TYPE
  0           11            364
  1            1             64
[1] 2 2
[1] FALSE
D1853V8, binary
                cls
clus               0   1
  ZHX3 MUTATED     6   8
  ZHX3 WILD-TYPE 219 256
[1] "tbl2"
                cls
clus             [,1] [,2]
  ZHX3 MUTATED      6    8
  ZHX3 WILD-TYPE  219  256
        clus
vv       ZHX3 MUTATED ZHX3 WILD-TYPE
  FEMALE            6            219
  MALE              8            256
[1] 2 2
[1] FALSE
D1853V9, binary
                cls
clus               0   1
  ZHX3 MUTATED    10   1
  ZHX3 WILD-TYPE 340  21
[1] "tbl2"
                cls
clus             [,1] [,2]
  ZHX3 MUTATED     10    1
  ZHX3 WILD-TYPE  340   21
     clus
vv    ZHX3 MUTATED ZHX3 WILD-TYPE
  NO            10            340
  YES            1             21
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ZHX3 MUTATED                      7                             5
  ZHX3 WILD-TYPE                  308                            42
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ZHX3 MUTATED                       2                              0
  ZHX3 WILD-TYPE                   104                             10
D1853V10, multiclass
                                clus
vv                               ZHX3 MUTATED ZHX3 WILD-TYPE
  COLON ADENOCARCINOMA                      7            308
  COLON MUCINOUS ADENOCARCINOMA             5             42
  RECTAL ADENOCARCINOMA                     2            104
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  ZHX3 MUTATED    12   0   0   1
  ZHX3 WILD-TYPE 333   4  31  24
D1853V11, multiclass
    clus
vv   ZHX3 MUTATED ZHX3 WILD-TYPE
  R0           12            333
  R1            0              4
  R2            0             31
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1853V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZHX3 MUTATED                                  0     1
  ZHX3 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  ZHX3 MUTATED                           1     4
  ZHX3 WILD-TYPE                        21   222
D1853V13, multiclass
                                  clus
vv                                 ZHX3 MUTATED ZHX3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                       4            222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1854) Variable = PDK1 MUTATION ANALYSIS
D1854V1, survival
                sevent
clus2              0   1
  PDK1 MUTATED     6   0
  PDK1 WILD-TYPE 372  93
  PDK1 MUTATED PDK1 WILD-TYPE 
             6            465 
  PDK1 MUTATED PDK1 WILD-TYPE 
             0             93 
$`PDK1 MUTATED`
TCGA-AA-3713 TCGA-AZ-4315 TCGA-CM-6166 TCGA-G4-6293 TCGA-AG-3892 TCGA-AG-A002 
       19.04        58.39        21.99       133.18        13.02        20.98 

$`PDK1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        33.01        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6167 
       15.02        12.00         2.96        29.03        16.04        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6303 
       13.25         0.53        47.41        35.31        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 
        1.02        17.95        36.95        17.03        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  PDK1 MUTATED PDK1 WILD-TYPE 
         13.02           0.00 
  PDK1 MUTATED PDK1 WILD-TYPE 
        133.18         148.01 
  PDK1 MUTATED PDK1 WILD-TYPE 
        21.485         20.120 
[1] "13.0 - 133.2 (21.5)" "0.0 - 148.0 (20.1)" 
[1] "hr="     "9200000"
D1854V2, continuous
D1854V3, binary
                cls
clus               0   1
  PDK1 MUTATED     5   2
  PDK1 WILD-TYPE 361 117
[1] "tbl2"
                cls
clus             [,1] [,2]
  PDK1 MUTATED      5    2
  PDK1 WILD-TYPE  361  117
        clus
vv       PDK1 MUTATED PDK1 WILD-TYPE
  COLON             5            361
  RECTUM            2            117
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PDK1 MUTATED         3        0        0         1         1         0
  PDK1 WILD-TYPE      88        1       32       137         9         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PDK1 MUTATED           1          0          0          0        1         0
  PDK1 WILD-TYPE        23         11         59         42       47        18
                vv
clus             STAGE IVB
  PDK1 MUTATED           0
  PDK1 WILD-TYPE         1
D1854V4, multiclass
            clus
vv           PDK1 MUTATED PDK1 WILD-TYPE
  STAGE I               3             88
  STAGE IA              0              1
  STAGE II              0             32
  STAGE IIA             1            137
  STAGE IIB             1              9
  STAGE IIC             0              1
  STAGE III             1             23
  STAGE IIIA            0             11
  STAGE IIIB            0             59
  STAGE IIIC            0             42
  STAGE IV              1             47
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  PDK1 MUTATED     1   2   3   1
  PDK1 WILD-TYPE  16  90 326  49
D1854V5, multiclass
    clus
vv   PDK1 MUTATED PDK1 WILD-TYPE
  T1            1             16
  T2            2             90
  T3            3            326
  T4            1             49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  PDK1 MUTATED     6   1   0
  PDK1 WILD-TYPE 281 112  87
D1854V6, multiclass
    clus
vv   PDK1 MUTATED PDK1 WILD-TYPE
  N0            6            281
  N1            1            112
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1854V7, binary
                cls
clus               0   1
  PDK1 MUTATED     5   1
  PDK1 WILD-TYPE 370  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  PDK1 MUTATED      5    1
  PDK1 WILD-TYPE  370   64
   clus
vv  PDK1 MUTATED PDK1 WILD-TYPE
  0            5            370
  1            1             64
[1] 2 2
[1] FALSE
D1854V8, binary
                cls
clus               0   1
  PDK1 MUTATED     4   3
  PDK1 WILD-TYPE 221 261
[1] "tbl2"
                cls
clus             [,1] [,2]
  PDK1 MUTATED      4    3
  PDK1 WILD-TYPE  221  261
        clus
vv       PDK1 MUTATED PDK1 WILD-TYPE
  FEMALE            4            221
  MALE              3            261
[1] 2 2
[1] FALSE
D1854V9, binary
                cls
clus               0   1
  PDK1 MUTATED     5   1
  PDK1 WILD-TYPE 345  21
[1] "tbl2"
                cls
clus             [,1] [,2]
  PDK1 MUTATED      5    1
  PDK1 WILD-TYPE  345   21
     clus
vv    PDK1 MUTATED PDK1 WILD-TYPE
  NO             5            345
  YES            1             21
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PDK1 MUTATED                      5                             0
  PDK1 WILD-TYPE                  310                            47
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PDK1 MUTATED                       2                              0
  PDK1 WILD-TYPE                   104                             10
D1854V10, multiclass
                                clus
vv                               PDK1 MUTATED PDK1 WILD-TYPE
  COLON ADENOCARCINOMA                      5            310
  COLON MUCINOUS ADENOCARCINOMA             0             47
  RECTAL ADENOCARCINOMA                     2            104
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  PDK1 MUTATED     5   0   1   1
  PDK1 WILD-TYPE 340   4  30  24
D1854V11, multiclass
    clus
vv   PDK1 MUTATED PDK1 WILD-TYPE
  R0            5            340
  R1            0              4
  R2            1             30
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1854V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PDK1 MUTATED                                  0     0
  PDK1 WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  PDK1 MUTATED                           0     4
  PDK1 WILD-TYPE                        22   222
D1854V13, multiclass
                                  clus
vv                                 PDK1 MUTATED PDK1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       4            222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1855) Variable = EPHA5 MUTATION ANALYSIS
D1855V1, survival
                 sevent
clus2               0   1
  EPHA5 MUTATED    30   8
  EPHA5 WILD-TYPE 348  85
  EPHA5 MUTATED EPHA5 WILD-TYPE 
             38             433 
  EPHA5 MUTATED EPHA5 WILD-TYPE 
              8              85 
$`EPHA5 MUTATED`
TCGA-A6-5661 TCGA-A6-5666 TCGA-A6-6781 TCGA-AA-3510 TCGA-AA-3516 TCGA-AA-3519 
       33.53        32.71        19.66        63.98        13.02         9.07 
TCGA-AA-3666 TCGA-AA-3833 TCGA-AA-3845 TCGA-AA-3864 TCGA-AA-3977 TCGA-AA-A00Z 
        2.01        15.95         0.00        53.00        25.02        21.99 
TCGA-AA-A010 TCGA-AD-6965 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-AZ-6601 TCGA-CA-6716 
       34.98         0.20        58.39        49.41       100.01        12.20 
TCGA-CA-6717 TCGA-CK-4948 TCGA-CK-6747 TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-6164 
       12.76       148.01        82.95        23.05        37.02        29.03 
TCGA-CM-6676 TCGA-D5-6541 TCGA-DM-A1D8 TCGA-DM-A1HB TCGA-F4-6703 TCGA-F4-6807 
       11.08        15.58        12.59       135.65        47.87        16.24 
TCGA-F4-6809 TCGA-G4-6306 TCGA-G4-6321 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A02X 
       13.25        44.68        22.09        20.98        13.94        41.00 
TCGA-EF-5830 TCGA-F5-6464 
        0.49         9.96 

$`EPHA5 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       22.06        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 
       20.28         7.04         3.02         1.02        35.01         6.97 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
        1.02        38.99         1.02        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.05         6.97        54.02        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 
       17.98        38.99        37.02        14.93        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        31.07        30.05        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
        0.99        17.03        14.99         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        10.88        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       33.01        21.44        17.82         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 
       22.36        62.79        88.21         6.77        12.10        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.25         3.29         0.07        10.06        14.30        17.56 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
        1.91       124.27        20.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6677 TCGA-CM-6678 
       14.04        11.01        12.95        13.05        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6898 
       17.85         4.80        17.13        12.49        16.14         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 
       13.32       140.38         7.50        44.32       131.51       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6704 
       98.24         8.61        31.96        35.74         6.18         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6808 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       34.42        41.42        33.67         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 
      133.18        74.56        65.85        53.62        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       63.62        61.91        36.00        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A00C 
       28.04        36.03        14.04         1.02        17.03         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       38.96        61.97        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6465 
       32.61        20.55        19.96        20.91        18.28        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  EPHA5 MUTATED EPHA5 WILD-TYPE 
              0               0 
  EPHA5 MUTATED EPHA5 WILD-TYPE 
         148.01          140.38 
  EPHA5 MUTATED EPHA5 WILD-TYPE 
          22.04           20.05 
[1] "0.0 - 148.0 (22.0)" "0.0 - 140.4 (20.1)"
[1] "hr=" "1.2"
D1855V2, continuous
D1855V3, binary
                 cls
clus                0   1
  EPHA5 MUTATED    33   6
  EPHA5 WILD-TYPE 333 113
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPHA5 MUTATED     33    6
  EPHA5 WILD-TYPE  333  113
        clus
vv       EPHA5 MUTATED EPHA5 WILD-TYPE
  COLON             33             333
  RECTUM             6             113
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  EPHA5 MUTATED         5        0        4        13         2         1
  EPHA5 WILD-TYPE      86        1       28       125         8         0
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  EPHA5 MUTATED           5          0          1          4        0         1
  EPHA5 WILD-TYPE        19         11         58         38       48        17
                 vv
clus              STAGE IVB
  EPHA5 MUTATED           0
  EPHA5 WILD-TYPE         1
D1855V4, multiclass
            clus
vv           EPHA5 MUTATED EPHA5 WILD-TYPE
  STAGE I                5              86
  STAGE IA               0               1
  STAGE II               4              28
  STAGE IIA             13             125
  STAGE IIB              2               8
  STAGE IIC              1               0
  STAGE III              5              19
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             4              38
  STAGE IV               0              48
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  EPHA5 MUTATED     0   8  25   6
  EPHA5 WILD-TYPE  17  84 304  44
D1855V5, multiclass
    clus
vv   EPHA5 MUTATED EPHA5 WILD-TYPE
  T1             0              17
  T2             8              84
  T3            25             304
  T4             6              44
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  EPHA5 MUTATED    26   8   5
  EPHA5 WILD-TYPE 261 105  82
D1855V6, multiclass
    clus
vv   EPHA5 MUTATED EPHA5 WILD-TYPE
  N0            26             261
  N1             8             105
  N2             5              82
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1855V7, binary
                 cls
clus                0   1
  EPHA5 MUTATED    31   1
  EPHA5 WILD-TYPE 344  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPHA5 MUTATED     31    1
  EPHA5 WILD-TYPE  344   64
   clus
vv  EPHA5 MUTATED EPHA5 WILD-TYPE
  0            31             344
  1             1              64
[1] 2 2
[1] FALSE
D1855V8, binary
                 cls
clus                0   1
  EPHA5 MUTATED    16  23
  EPHA5 WILD-TYPE 209 241
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPHA5 MUTATED     16   23
  EPHA5 WILD-TYPE  209  241
        clus
vv       EPHA5 MUTATED EPHA5 WILD-TYPE
  FEMALE            16             209
  MALE              23             241
[1] 2 2
[1] FALSE
D1855V9, binary
                 cls
clus                0   1
  EPHA5 MUTATED    31   0
  EPHA5 WILD-TYPE 319  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPHA5 MUTATED     31    0
  EPHA5 WILD-TYPE  319   22
     clus
vv    EPHA5 MUTATED EPHA5 WILD-TYPE
  NO             31             319
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  EPHA5 MUTATED                     29                             3
  EPHA5 WILD-TYPE                  286                            44
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  EPHA5 MUTATED                       5                              1
  EPHA5 WILD-TYPE                   101                              9
D1855V10, multiclass
                                clus
vv                               EPHA5 MUTATED EPHA5 WILD-TYPE
  COLON ADENOCARCINOMA                      29             286
  COLON MUCINOUS ADENOCARCINOMA              3              44
  RECTAL ADENOCARCINOMA                      5             101
  RECTAL MUCINOUS ADENOCARCINOMA             1               9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  EPHA5 MUTATED    28   0   0   3
  EPHA5 WILD-TYPE 317   4  31  22
D1855V11, multiclass
    clus
vv   EPHA5 MUTATED EPHA5 WILD-TYPE
  R0            28             317
  R1             0               4
  R2             0              31
  RX             3              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1855V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  EPHA5 MUTATED                                  0     2
  EPHA5 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  EPHA5 MUTATED                           2    21
  EPHA5 WILD-TYPE                        20   205
D1855V13, multiclass
                                  clus
vv                                 EPHA5 MUTATED EPHA5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               9
  BLACK OR AFRICAN AMERICAN                    2              20
  WHITE                                       21             205
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1856) Variable = SPAST MUTATION ANALYSIS
D1856V1, survival
                 sevent
clus2               0   1
  SPAST MUTATED     6   4
  SPAST WILD-TYPE 372  89
  SPAST MUTATED SPAST WILD-TYPE 
             10             461 
  SPAST MUTATED SPAST WILD-TYPE 
              4              89 
$`SPAST MUTATED`
TCGA-AA-3715 TCGA-AA-3864 TCGA-AA-3947 TCGA-AA-3977 TCGA-AZ-4315 TCGA-AZ-6601 
       19.04        53.00        33.01        25.02        58.39       100.01 
TCGA-AZ-6603 TCGA-CA-6718 TCGA-G4-6309 TCGA-AG-A002 
       29.56        10.06        85.48        20.98 

$`SPAST WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 
       32.05         0.99        31.07        31.07        30.05        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       12.99        24.00        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6605 TCGA-AZ-6606 
       88.21        49.41         6.77        12.10         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07        12.20        12.76        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 
       74.56        65.85        53.62        44.68        55.04        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  SPAST MUTATED SPAST WILD-TYPE 
          10.06            0.00 
  SPAST MUTATED SPAST WILD-TYPE 
         100.01          148.01 
  SPAST MUTATED SPAST WILD-TYPE 
         31.285          20.020 
[1] "10.1 - 100.0 (31.3)" "0.0 - 148.0 (20.0)" 
[1] "hr=" "1.2"
D1856V2, continuous
D1856V3, binary
                 cls
clus                0   1
  SPAST MUTATED     9   1
  SPAST WILD-TYPE 357 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SPAST MUTATED      9    1
  SPAST WILD-TYPE  357  118
        clus
vv       SPAST MUTATED SPAST WILD-TYPE
  COLON              9             357
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SPAST MUTATED         1        0        3         2         1         0
  SPAST WILD-TYPE      90        1       29       136         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SPAST MUTATED           0          0          1          0        0         0
  SPAST WILD-TYPE        24         11         58         42       48        18
                 vv
clus              STAGE IVB
  SPAST MUTATED           0
  SPAST WILD-TYPE         1
D1856V4, multiclass
            clus
vv           SPAST MUTATED SPAST WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               3              29
  STAGE IIA              2             136
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  SPAST MUTATED     0   3   6   1
  SPAST WILD-TYPE  17  89 323  49
D1856V5, multiclass
    clus
vv   SPAST MUTATED SPAST WILD-TYPE
  T1             0              17
  T2             3              89
  T3             6             323
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  SPAST MUTATED     8   2   0
  SPAST WILD-TYPE 279 111  87
D1856V6, multiclass
    clus
vv   SPAST MUTATED SPAST WILD-TYPE
  N0             8             279
  N1             2             111
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1856V7, binary
                 cls
clus                0   1
  SPAST MUTATED     8   0
  SPAST WILD-TYPE 367  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SPAST MUTATED      8    0
  SPAST WILD-TYPE  367   65
   clus
vv  SPAST MUTATED SPAST WILD-TYPE
  0             8             367
  1             0              65
[1] 2 2
[1] FALSE
D1856V8, binary
                 cls
clus                0   1
  SPAST MUTATED     3   7
  SPAST WILD-TYPE 222 257
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SPAST MUTATED      3    7
  SPAST WILD-TYPE  222  257
        clus
vv       SPAST MUTATED SPAST WILD-TYPE
  FEMALE             3             222
  MALE               7             257
[1] 2 2
[1] FALSE
D1856V9, binary
                 cls
clus                0   1
  SPAST MUTATED    10   0
  SPAST WILD-TYPE 340  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SPAST MUTATED     10    0
  SPAST WILD-TYPE  340   22
     clus
vv    SPAST MUTATED SPAST WILD-TYPE
  NO             10             340
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SPAST MUTATED                      8                             1
  SPAST WILD-TYPE                  307                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SPAST MUTATED                       1                              0
  SPAST WILD-TYPE                   105                             10
D1856V10, multiclass
                                clus
vv                               SPAST MUTATED SPAST WILD-TYPE
  COLON ADENOCARCINOMA                       8             307
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  SPAST MUTATED     6   0   0   1
  SPAST WILD-TYPE 339   4  31  24
D1856V11, multiclass
    clus
vv   SPAST MUTATED SPAST WILD-TYPE
  R0             6             339
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1856V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SPAST MUTATED                                  0     1
  SPAST WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  SPAST MUTATED                           1     3
  SPAST WILD-TYPE                        21   223
D1856V13, multiclass
                                  clus
vv                                 SPAST MUTATED SPAST WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        3             223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1857) Variable = SIN3A MUTATION ANALYSIS
D1857V1, survival
                 sevent
clus2               0   1
  SIN3A MUTATED    18   2
  SIN3A WILD-TYPE 360  91
  SIN3A MUTATED SIN3A WILD-TYPE 
             20             451 
  SIN3A MUTATED SIN3A WILD-TYPE 
              2              91 
$`SIN3A MUTATED`
TCGA-A6-6781 TCGA-AA-3510 TCGA-AA-3520 TCGA-AA-3555 TCGA-AA-3663 TCGA-AA-3697 
       19.66        63.98        24.03        29.95         6.97        85.05 
TCGA-AA-3950 TCGA-AA-A010 TCGA-CA-6717 TCGA-CM-6162 TCGA-CM-6171 TCGA-CM-6674 
       24.00        34.98        12.76        12.00        14.04        12.95 
TCGA-D5-6924 TCGA-F4-6570 TCGA-G4-6293 TCGA-G4-6309 TCGA-G4-6628 TCGA-AG-3742 
       14.30         6.18       133.18        85.48        79.69         0.99 
TCGA-AG-A002 TCGA-DY-A1DG 
       20.98        51.48 

$`SIN3A WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
        9.07        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       17.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       61.02        78.08         6.05        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 
       37.05        19.00        36.00         5.03        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.20        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       13.02        15.02        11.01        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 
       15.58         1.48         3.68         4.41        12.43         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       35.74        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6299 
       33.67        13.25         0.53        47.41        35.31        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 
       65.85        53.62        44.68        55.04        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       46.75        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
       32.98         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 
      126.44        41.36        57.24        24.13        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  SIN3A MUTATED SIN3A WILD-TYPE 
           0.99            0.00 
  SIN3A MUTATED SIN3A WILD-TYPE 
         133.18          148.01 
  SIN3A MUTATED SIN3A WILD-TYPE 
          22.49           20.12 
[1] "1.0 - 133.2 (22.5)" "0.0 - 148.0 (20.1)"
[1] "hr=" "2.8"
D1857V2, continuous
D1857V3, binary
                 cls
clus                0   1
  SIN3A MUTATED    17   3
  SIN3A WILD-TYPE 349 116
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SIN3A MUTATED     17    3
  SIN3A WILD-TYPE  349  116
        clus
vv       SIN3A MUTATED SIN3A WILD-TYPE
  COLON             17             349
  RECTUM             3             116
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SIN3A MUTATED         4        0        3         6         1         0
  SIN3A WILD-TYPE      87        1       29       132         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SIN3A MUTATED           2          0          2          1        0         1
  SIN3A WILD-TYPE        22         11         57         41       48        17
                 vv
clus              STAGE IVB
  SIN3A MUTATED           0
  SIN3A WILD-TYPE         1
D1857V4, multiclass
            clus
vv           SIN3A MUTATED SIN3A WILD-TYPE
  STAGE I                4              87
  STAGE IA               0               1
  STAGE II               3              29
  STAGE IIA              6             132
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              2              22
  STAGE IIIA             0              11
  STAGE IIIB             2              57
  STAGE IIIC             1              41
  STAGE IV               0              48
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  SIN3A MUTATED     1   3  14   2
  SIN3A WILD-TYPE  16  89 315  48
D1857V5, multiclass
    clus
vv   SIN3A MUTATED SIN3A WILD-TYPE
  T1             1              16
  T2             3              89
  T3            14             315
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  SIN3A MUTATED    15   5   0
  SIN3A WILD-TYPE 272 108  87
D1857V6, multiclass
    clus
vv   SIN3A MUTATED SIN3A WILD-TYPE
  N0            15             272
  N1             5             108
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1857V7, binary
                 cls
clus                0   1
  SIN3A MUTATED    18   1
  SIN3A WILD-TYPE 357  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SIN3A MUTATED     18    1
  SIN3A WILD-TYPE  357   64
   clus
vv  SIN3A MUTATED SIN3A WILD-TYPE
  0            18             357
  1             1              64
[1] 2 2
[1] FALSE
D1857V8, binary
                 cls
clus                0   1
  SIN3A MUTATED    10  10
  SIN3A WILD-TYPE 215 254
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SIN3A MUTATED     10   10
  SIN3A WILD-TYPE  215  254
        clus
vv       SIN3A MUTATED SIN3A WILD-TYPE
  FEMALE            10             215
  MALE              10             254
[1] 2 2
[1] FALSE
D1857V9, binary
                 cls
clus                0   1
  SIN3A MUTATED    18   0
  SIN3A WILD-TYPE 332  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SIN3A MUTATED     18    0
  SIN3A WILD-TYPE  332   22
     clus
vv    SIN3A MUTATED SIN3A WILD-TYPE
  NO             18             332
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SIN3A MUTATED                     12                             5
  SIN3A WILD-TYPE                  303                            42
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SIN3A MUTATED                       3                              0
  SIN3A WILD-TYPE                   103                             10
D1857V10, multiclass
                                clus
vv                               SIN3A MUTATED SIN3A WILD-TYPE
  COLON ADENOCARCINOMA                      12             303
  COLON MUCINOUS ADENOCARCINOMA              5              42
  RECTAL ADENOCARCINOMA                      3             103
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  SIN3A MUTATED    18   0   0   1
  SIN3A WILD-TYPE 327   4  31  24
D1857V11, multiclass
    clus
vv   SIN3A MUTATED SIN3A WILD-TYPE
  R0            18             327
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1857V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SIN3A MUTATED                                  0     1
  SIN3A WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  SIN3A MUTATED                           1     9
  SIN3A WILD-TYPE                        21   217
D1857V13, multiclass
                                  clus
vv                                 SIN3A MUTATED SIN3A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        9             217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1858) Variable = C1ORF88 MUTATION ANALYSIS
D1858V1, survival
                   sevent
clus2                 0   1
  C1ORF88 MUTATED     5   1
  C1ORF88 WILD-TYPE 373  92
  C1ORF88 MUTATED C1ORF88 WILD-TYPE 
                6               465 
  C1ORF88 MUTATED C1ORF88 WILD-TYPE 
                1                92 
$`C1ORF88 MUTATED`
TCGA-AA-3663 TCGA-AA-3697 TCGA-AA-A00J TCGA-AA-A010 TCGA-CA-6717 TCGA-DM-A28G 
        6.97        85.05        18.05        34.98        12.76        60.79 

$`C1ORF88 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.05        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       19.00        30.02        34.03        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07        12.20        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
       81.37       119.93        35.97       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  C1ORF88 MUTATED C1ORF88 WILD-TYPE 
             6.97              0.00 
  C1ORF88 MUTATED C1ORF88 WILD-TYPE 
            85.05            148.01 
  C1ORF88 MUTATED C1ORF88 WILD-TYPE 
           26.515            20.190 
[1] "7.0 - 85.0 (26.5)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.7"
D1858V2, continuous
D1858V3, binary
                   cls
clus                  0   1
  C1ORF88 MUTATED     6   0
  C1ORF88 WILD-TYPE 360 119
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C1ORF88 MUTATED      6    0
  C1ORF88 WILD-TYPE  360  119
        clus
vv       C1ORF88 MUTATED C1ORF88 WILD-TYPE
  COLON                6               360
  RECTUM               0               119
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  C1ORF88 MUTATED         0        0        1         2         1         0
  C1ORF88 WILD-TYPE      91        1       31       136         9         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C1ORF88 MUTATED           1          0          1          0        0
  C1ORF88 WILD-TYPE        23         11         58         42       48
                   vv
clus                STAGE IVA STAGE IVB
  C1ORF88 MUTATED           0         0
  C1ORF88 WILD-TYPE        18         1
D1858V4, multiclass
            clus
vv           C1ORF88 MUTATED C1ORF88 WILD-TYPE
  STAGE I                  0                91
  STAGE IA                 0                 1
  STAGE II                 1                31
  STAGE IIA                2               136
  STAGE IIB                1                 9
  STAGE IIC                0                 1
  STAGE III                1                23
  STAGE IIIA               0                11
  STAGE IIIB               1                58
  STAGE IIIC               0                42
  STAGE IV                 0                48
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  C1ORF88 MUTATED     0   0   4   2
  C1ORF88 WILD-TYPE  17  92 325  48
D1858V5, multiclass
    clus
vv   C1ORF88 MUTATED C1ORF88 WILD-TYPE
  T1               0                17
  T2               0                92
  T3               4               325
  T4               2                48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  C1ORF88 MUTATED     5   1   0
  C1ORF88 WILD-TYPE 282 112  87
D1858V6, multiclass
    clus
vv   C1ORF88 MUTATED C1ORF88 WILD-TYPE
  N0               5               282
  N1               1               112
  N2               0                87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1858V7, binary
                   cls
clus                  0   1
  C1ORF88 MUTATED     6   0
  C1ORF88 WILD-TYPE 369  65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C1ORF88 MUTATED      6    0
  C1ORF88 WILD-TYPE  369   65
   clus
vv  C1ORF88 MUTATED C1ORF88 WILD-TYPE
  0               6               369
  1               0                65
[1] 2 2
[1] FALSE
D1858V8, binary
                   cls
clus                  0   1
  C1ORF88 MUTATED     1   5
  C1ORF88 WILD-TYPE 224 259
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C1ORF88 MUTATED      1    5
  C1ORF88 WILD-TYPE  224  259
        clus
vv       C1ORF88 MUTATED C1ORF88 WILD-TYPE
  FEMALE               1               224
  MALE                 5               259
[1] 2 2
[1] FALSE
D1858V9, binary
                   cls
clus                  0   1
  C1ORF88 MUTATED     5   0
  C1ORF88 WILD-TYPE 345  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C1ORF88 MUTATED      5    0
  C1ORF88 WILD-TYPE  345   22
     clus
vv    C1ORF88 MUTATED C1ORF88 WILD-TYPE
  NO                5               345
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  C1ORF88 MUTATED                      4                             2
  C1ORF88 WILD-TYPE                  311                            45
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  C1ORF88 MUTATED                       0                              0
  C1ORF88 WILD-TYPE                   106                             10
D1858V10, multiclass
                                clus
vv                               C1ORF88 MUTATED C1ORF88 WILD-TYPE
  COLON ADENOCARCINOMA                         4               311
  COLON MUCINOUS ADENOCARCINOMA                2                45
  RECTAL ADENOCARCINOMA                        0               106
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  C1ORF88 MUTATED     4   0   0   1
  C1ORF88 WILD-TYPE 341   4  31  24
D1858V11, multiclass
    clus
vv   C1ORF88 MUTATED C1ORF88 WILD-TYPE
  R0               4               341
  R1               0                 4
  R2               0                31
  RX               1                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1858V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C1ORF88 MUTATED                                  0     1
  C1ORF88 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  C1ORF88 MUTATED                           0     1
  C1ORF88 WILD-TYPE                        22   225
D1858V13, multiclass
[1] "Remove cluster labels:" "C1ORF88 MUTATED"       
clus
  C1ORF88 MUTATED C1ORF88 WILD-TYPE 
                2               258 
       TCGA-A6-2671        TCGA-A6-2672        TCGA-A6-2674        TCGA-A6-2676 
"C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" 
       TCGA-A6-2677        TCGA-A6-2678        TCGA-A6-2683        TCGA-A6-3807 
"C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" 
       TCGA-A6-3808        TCGA-A6-3809        TCGA-A6-3810        TCGA-A6-4105 
"C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" 
       TCGA-A6-5656        TCGA-A6-5657        TCGA-A6-5659        TCGA-A6-5660 
"C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" 
       TCGA-A6-5661        TCGA-A6-5662        TCGA-A6-5664        TCGA-A6-5665 
"C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" 
       TCGA-A6-5666        TCGA-A6-6137        TCGA-A6-6138        TCGA-A6-6141 
"C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" 
       TCGA-A6-6142        TCGA-A6-6648        TCGA-A6-6649        TCGA-A6-6651 
"C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" 
       TCGA-A6-6652        TCGA-A6-6653        TCGA-A6-6654        TCGA-A6-6780 
"C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" 
       TCGA-A6-6781        TCGA-A6-6782        TCGA-AD-5900        TCGA-AD-6548 
"C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" 
       TCGA-AD-6888        TCGA-AD-6889        TCGA-AD-6890        TCGA-AD-6895 
"C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" 
       TCGA-AD-6899        TCGA-AD-6901        TCGA-AD-6963        TCGA-AD-6964 
"C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" 
       TCGA-AD-6965        TCGA-AU-3779        TCGA-AU-6004        TCGA-AY-4070 
"C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" 
       TCGA-AY-4071        TCGA-AY-5543        TCGA-AY-6196        TCGA-AY-6197 
"C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" 
       TCGA-AY-6386        TCGA-AZ-4315        TCGA-AZ-4323        TCGA-AZ-4616 
"C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" 
       TCGA-AZ-4681        TCGA-AZ-4682        TCGA-AZ-5403        TCGA-AZ-5407 
"C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" 
       TCGA-AZ-6598        TCGA-AZ-6599        TCGA-AZ-6600        TCGA-AZ-6601 
"C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" 
       TCGA-AZ-6603        TCGA-AZ-6605        TCGA-AZ-6606        TCGA-AZ-6607 
"C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" 
       TCGA-AZ-6608        TCGA-CA-5254        TCGA-CA-5255        TCGA-CA-5796 
"C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" 
       TCGA-CA-5797        TCGA-CA-6715        TCGA-CA-6716        TCGA-CA-6718 
"C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" 
       TCGA-CA-6719        TCGA-CK-4947        TCGA-CK-4948        TCGA-CK-4950 
"C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" 
       TCGA-CK-4952        TCGA-CK-5912        TCGA-CK-5913        TCGA-CK-5914 
"C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" 
       TCGA-CK-5915        TCGA-CK-5916        TCGA-CK-6746        TCGA-CK-6747 
"C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" 
       TCGA-CK-6748        TCGA-CK-6751        TCGA-CM-4743        TCGA-CM-4744 
"C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" 
       TCGA-CM-4746        TCGA-CM-4747        TCGA-CM-4752        TCGA-CM-5341 
"C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" 
       TCGA-CM-5344        TCGA-CM-5348        TCGA-CM-5349        TCGA-CM-5860 
"C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" 
       TCGA-CM-5861        TCGA-CM-5862        TCGA-CM-5863        TCGA-CM-5864 
"C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" 
       TCGA-CM-5868        TCGA-CM-6161        TCGA-CM-6162        TCGA-CM-6163 
"C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" 
       TCGA-CM-6164        TCGA-CM-6165        TCGA-CM-6166        TCGA-CM-6167 
"C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" 
       TCGA-CM-6168        TCGA-CM-6169        TCGA-CM-6170        TCGA-CM-6171 
"C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" 
       TCGA-CM-6172        TCGA-CM-6674        TCGA-CM-6675        TCGA-CM-6676 
"C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" 
       TCGA-CM-6677        TCGA-CM-6678        TCGA-CM-6679        TCGA-CM-6680 
"C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" 
       TCGA-D5-5537        TCGA-D5-5538        TCGA-D5-5539        TCGA-D5-5540 
"C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" 
       TCGA-D5-5541        TCGA-D5-6529        TCGA-D5-6532        TCGA-D5-6533 
"C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" 
       TCGA-D5-6534        TCGA-D5-6535        TCGA-D5-6536        TCGA-D5-6537 
"C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" 
       TCGA-D5-6538        TCGA-D5-6539        TCGA-D5-6540        TCGA-D5-6541 
"C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" 
       TCGA-D5-6898        TCGA-D5-6920        TCGA-D5-6922        TCGA-D5-6923 
"C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" 
       TCGA-D5-6924        TCGA-D5-6926        TCGA-D5-6927        TCGA-D5-6928 
"C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" 
       TCGA-D5-6929        TCGA-D5-6930        TCGA-D5-6931        TCGA-D5-6932 
"C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" 
       TCGA-D5-7000        TCGA-DM-A0X9        TCGA-DM-A0XD        TCGA-DM-A0XF 
"C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" 
       TCGA-DM-A1D0        TCGA-DM-A1D4        TCGA-DM-A1D6        TCGA-DM-A1D7 
"C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" 
       TCGA-DM-A1D8        TCGA-DM-A1D9        TCGA-DM-A1DA        TCGA-DM-A1DB 
"C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" 
       TCGA-DM-A1HA        TCGA-DM-A1HB        TCGA-DM-A282        TCGA-DM-A285 
"C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" 
       TCGA-DM-A28C        TCGA-DM-A28E        TCGA-DM-A28F        TCGA-DM-A28H 
"C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" 
       TCGA-DM-A28K        TCGA-F4-6459        TCGA-F4-6460        TCGA-F4-6569 
"C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" 
       TCGA-F4-6570        TCGA-F4-6703        TCGA-F4-6704        TCGA-F4-6805 
"C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" 
       TCGA-F4-6806        TCGA-F4-6807        TCGA-F4-6808        TCGA-F4-6809 
"C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" 
       TCGA-F4-6854        TCGA-F4-6855        TCGA-F4-6856        TCGA-G4-6293 
"C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" 
       TCGA-G4-6299        TCGA-G4-6303        TCGA-G4-6304        TCGA-G4-6306 
"C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" 
       TCGA-G4-6307        TCGA-G4-6309        TCGA-G4-6310        TCGA-G4-6315 
"C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" 
       TCGA-G4-6317        TCGA-G4-6321        TCGA-G4-6323        TCGA-G4-6586 
"C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" 
       TCGA-G4-6588        TCGA-G4-6625        TCGA-G4-6626        TCGA-G4-6628 
"C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2691        TCGA-AF-2692 
"C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" 
       TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3913        TCGA-AF-4110 
"C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" 
       TCGA-AF-5654        TCGA-AF-6136        TCGA-AF-6655        TCGA-AF-6672 
"C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6549        TCGA-AH-6643 
"C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" 
       TCGA-AH-6644        TCGA-CI-6619        TCGA-CI-6620        TCGA-CI-6621 
"C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" 
       TCGA-CI-6622        TCGA-CI-6624        TCGA-CL-5917        TCGA-CL-5918 
"C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" 
       TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6155        TCGA-DC-6157 
"C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" 
       TCGA-DC-6158        TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682 
"C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" 
       TCGA-DC-6683        TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC 
"C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" 
       TCGA-DY-A1DD        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" 
       TCGA-EF-5830        TCGA-EI-6506        TCGA-EI-6507        TCGA-EI-6508 
"C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" 
       TCGA-EI-6510        TCGA-F5-6464        TCGA-F5-6465        TCGA-F5-6571 
"C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" 
       TCGA-F5-6702        TCGA-F5-6811        TCGA-F5-6812        TCGA-F5-6813 
"C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" 
       TCGA-G5-6235        TCGA-G5-6641 
"C1ORF88 WILD-TYPE" "C1ORF88 WILD-TYPE" 

Clustering(1859) Variable = GLB1L2 MUTATION ANALYSIS
D1859V1, survival
                  sevent
clus2                0   1
  GLB1L2 MUTATED     9   4
  GLB1L2 WILD-TYPE 369  89
  GLB1L2 MUTATED GLB1L2 WILD-TYPE 
              13              458 
  GLB1L2 MUTATED GLB1L2 WILD-TYPE 
               4               89 
$`GLB1L2 MUTATED`
TCGA-A6-6138 TCGA-AA-3672 TCGA-AA-3715 TCGA-AA-3947 TCGA-AA-3966 TCGA-AA-A010 
       22.52         0.92        19.04        33.01         2.01        34.98 
TCGA-AD-6889 TCGA-AD-6964 TCGA-AZ-6598 TCGA-D5-6540 TCGA-F4-6570 TCGA-G4-6628 
       56.55        10.88        49.41        16.14         6.18        79.69 
TCGA-EI-6507 
       19.96 

$`GLB1L2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6141 TCGA-A6-6142 
       22.09        22.06        32.71        27.09         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 
        6.97        54.02         2.01        14.01        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       21.37        15.52         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 
      106.75        22.36        62.79        88.21         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       17.13        12.49        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 
       98.24         8.61        31.96        35.74        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
       32.61         0.49        20.55        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  GLB1L2 MUTATED GLB1L2 WILD-TYPE 
            0.92             0.00 
  GLB1L2 MUTATED GLB1L2 WILD-TYPE 
           79.69           148.01 
  GLB1L2 MUTATED GLB1L2 WILD-TYPE 
          19.960           20.235 
[1] "0.9 - 79.7 (20.0)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.5"
D1859V2, continuous
D1859V3, binary
                  cls
clus                 0   1
  GLB1L2 MUTATED    13   1
  GLB1L2 WILD-TYPE 353 118
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GLB1L2 MUTATED     13    1
  GLB1L2 WILD-TYPE  353  118
        clus
vv       GLB1L2 MUTATED GLB1L2 WILD-TYPE
  COLON              13              353
  RECTUM              1              118
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GLB1L2 MUTATED         3        0        2         4         3         0
  GLB1L2 WILD-TYPE      88        1       30       134         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GLB1L2 MUTATED           1          0          0          0        0
  GLB1L2 WILD-TYPE        23         11         59         42       48
                  vv
clus               STAGE IVA STAGE IVB
  GLB1L2 MUTATED           0         0
  GLB1L2 WILD-TYPE        18         1
D1859V4, multiclass
            clus
vv           GLB1L2 MUTATED GLB1L2 WILD-TYPE
  STAGE I                 3               88
  STAGE IA                0                1
  STAGE II                2               30
  STAGE IIA               4              134
  STAGE IIB               3                7
  STAGE IIC               0                1
  STAGE III               1               23
  STAGE IIIA              0               11
  STAGE IIIB              0               59
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  GLB1L2 MUTATED     0   3   7   4
  GLB1L2 WILD-TYPE  17  89 322  46
D1859V5, multiclass
    clus
vv   GLB1L2 MUTATED GLB1L2 WILD-TYPE
  T1              0               17
  T2              3               89
  T3              7              322
  T4              4               46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  GLB1L2 MUTATED    12   1   1
  GLB1L2 WILD-TYPE 275 112  86
D1859V6, multiclass
    clus
vv   GLB1L2 MUTATED GLB1L2 WILD-TYPE
  N0             12              275
  N1              1              112
  N2              1               86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1859V7, binary
                  cls
clus                 0   1
  GLB1L2 MUTATED    11   0
  GLB1L2 WILD-TYPE 364  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GLB1L2 MUTATED     11    0
  GLB1L2 WILD-TYPE  364   65
   clus
vv  GLB1L2 MUTATED GLB1L2 WILD-TYPE
  0             11              364
  1              0               65
[1] 2 2
[1] FALSE
D1859V8, binary
                  cls
clus                 0   1
  GLB1L2 MUTATED     7   7
  GLB1L2 WILD-TYPE 218 257
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GLB1L2 MUTATED      7    7
  GLB1L2 WILD-TYPE  218  257
        clus
vv       GLB1L2 MUTATED GLB1L2 WILD-TYPE
  FEMALE              7              218
  MALE                7              257
[1] 2 2
[1] FALSE
D1859V9, binary
                  cls
clus                 0   1
  GLB1L2 MUTATED    11   0
  GLB1L2 WILD-TYPE 339  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GLB1L2 MUTATED     11    0
  GLB1L2 WILD-TYPE  339   22
     clus
vv    GLB1L2 MUTATED GLB1L2 WILD-TYPE
  NO              11              339
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  GLB1L2 MUTATED                     10                             3
  GLB1L2 WILD-TYPE                  305                            44
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  GLB1L2 MUTATED                       1                              0
  GLB1L2 WILD-TYPE                   105                             10
D1859V10, multiclass
                                clus
vv                               GLB1L2 MUTATED GLB1L2 WILD-TYPE
  COLON ADENOCARCINOMA                       10              305
  COLON MUCINOUS ADENOCARCINOMA               3               44
  RECTAL ADENOCARCINOMA                       1              105
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  GLB1L2 MUTATED     8   0   0   1
  GLB1L2 WILD-TYPE 337   4  31  24
D1859V11, multiclass
    clus
vv   GLB1L2 MUTATED GLB1L2 WILD-TYPE
  R0              8              337
  R1              0                4
  R2              0               31
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1859V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GLB1L2 MUTATED                                  0     1
  GLB1L2 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  GLB1L2 MUTATED                           0     8
  GLB1L2 WILD-TYPE                        22   218
D1859V13, multiclass
                                  clus
vv                                 GLB1L2 MUTATED GLB1L2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         8              218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1860) Variable = OSBPL1A MUTATION ANALYSIS
D1860V1, survival
                   sevent
clus2                 0   1
  OSBPL1A MUTATED     9   2
  OSBPL1A WILD-TYPE 369  91
  OSBPL1A MUTATED OSBPL1A WILD-TYPE 
               11               460 
  OSBPL1A MUTATED OSBPL1A WILD-TYPE 
                2                91 
$`OSBPL1A MUTATED`
TCGA-A6-5657 TCGA-A6-6653 TCGA-AA-3492 TCGA-AA-3710 TCGA-AA-A010 TCGA-AZ-6601 
       31.63        24.39         3.02        26.99        34.98       100.01 
TCGA-CM-6165 TCGA-DM-A1HB TCGA-F4-6856 TCGA-AH-6549 TCGA-CI-6624 
       16.04       135.65        35.31        17.49         4.73 

$`OSBPL1A WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 
       25.18        24.16        21.76        24.69        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       19.66        20.28         7.04         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       85.05        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 
       88.21        49.41         6.77        12.10        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      131.51       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 
       33.67        13.25         0.53        47.41       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
      117.11        38.56         1.45         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
       33.17         6.97        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  OSBPL1A MUTATED OSBPL1A WILD-TYPE 
             3.02              0.00 
  OSBPL1A MUTATED OSBPL1A WILD-TYPE 
           135.65            148.01 
  OSBPL1A MUTATED OSBPL1A WILD-TYPE 
           26.990            20.085 
[1] "3.0 - 135.7 (27.0)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.4"
D1860V2, continuous
D1860V3, binary
                   cls
clus                  0   1
  OSBPL1A MUTATED     9   2
  OSBPL1A WILD-TYPE 357 117
[1] "tbl2"
                   cls
clus                [,1] [,2]
  OSBPL1A MUTATED      9    2
  OSBPL1A WILD-TYPE  357  117
        clus
vv       OSBPL1A MUTATED OSBPL1A WILD-TYPE
  COLON                9               357
  RECTUM               2               117
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  OSBPL1A MUTATED         3        0        2         2         1         0
  OSBPL1A WILD-TYPE      88        1       30       136         9         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  OSBPL1A MUTATED           0          0          2          0        0
  OSBPL1A WILD-TYPE        24         11         57         42       48
                   vv
clus                STAGE IVA STAGE IVB
  OSBPL1A MUTATED           0         0
  OSBPL1A WILD-TYPE        18         1
D1860V4, multiclass
            clus
vv           OSBPL1A MUTATED OSBPL1A WILD-TYPE
  STAGE I                  3                88
  STAGE IA                 0                 1
  STAGE II                 2                30
  STAGE IIA                2               136
  STAGE IIB                1                 9
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               0                11
  STAGE IIIB               2                57
  STAGE IIIC               0                42
  STAGE IV                 0                48
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  OSBPL1A MUTATED     0   3   7   1
  OSBPL1A WILD-TYPE  17  89 322  49
D1860V5, multiclass
    clus
vv   OSBPL1A MUTATED OSBPL1A WILD-TYPE
  T1               0                17
  T2               3                89
  T3               7               322
  T4               1                49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  OSBPL1A MUTATED     8   2   0
  OSBPL1A WILD-TYPE 279 111  87
D1860V6, multiclass
    clus
vv   OSBPL1A MUTATED OSBPL1A WILD-TYPE
  N0               8               279
  N1               2               111
  N2               0                87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1860V7, binary
                   cls
clus                  0   1
  OSBPL1A MUTATED    10   0
  OSBPL1A WILD-TYPE 365  65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  OSBPL1A MUTATED     10    0
  OSBPL1A WILD-TYPE  365   65
   clus
vv  OSBPL1A MUTATED OSBPL1A WILD-TYPE
  0              10               365
  1               0                65
[1] 2 2
[1] FALSE
D1860V8, binary
                   cls
clus                  0   1
  OSBPL1A MUTATED     4   7
  OSBPL1A WILD-TYPE 221 257
[1] "tbl2"
                   cls
clus                [,1] [,2]
  OSBPL1A MUTATED      4    7
  OSBPL1A WILD-TYPE  221  257
        clus
vv       OSBPL1A MUTATED OSBPL1A WILD-TYPE
  FEMALE               4               221
  MALE                 7               257
[1] 2 2
[1] FALSE
D1860V9, binary
                   cls
clus                  0   1
  OSBPL1A MUTATED     9   0
  OSBPL1A WILD-TYPE 341  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  OSBPL1A MUTATED      9    0
  OSBPL1A WILD-TYPE  341   22
     clus
vv    OSBPL1A MUTATED OSBPL1A WILD-TYPE
  NO                9               341
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  OSBPL1A MUTATED                      7                             1
  OSBPL1A WILD-TYPE                  308                            46
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  OSBPL1A MUTATED                       2                              0
  OSBPL1A WILD-TYPE                   104                             10
D1860V10, multiclass
                                clus
vv                               OSBPL1A MUTATED OSBPL1A WILD-TYPE
  COLON ADENOCARCINOMA                         7               308
  COLON MUCINOUS ADENOCARCINOMA                1                46
  RECTAL ADENOCARCINOMA                        2               104
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  OSBPL1A MUTATED     6   0   0   1
  OSBPL1A WILD-TYPE 339   4  31  24
D1860V11, multiclass
    clus
vv   OSBPL1A MUTATED OSBPL1A WILD-TYPE
  R0               6               339
  R1               0                 4
  R2               0                31
  RX               1                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1860V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OSBPL1A MUTATED                                  0     0
  OSBPL1A WILD-TYPE                                1    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  OSBPL1A MUTATED                           1     7
  OSBPL1A WILD-TYPE                        21   219
D1860V13, multiclass
                                  clus
vv                                 OSBPL1A MUTATED OSBPL1A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                      1                21
  WHITE                                          7               219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1861) Variable = AFM MUTATION ANALYSIS
D1861V1, survival
               sevent
clus2             0   1
  AFM MUTATED    14   3
  AFM WILD-TYPE 364  90
  AFM MUTATED AFM WILD-TYPE 
           17           454 
  AFM MUTATED AFM WILD-TYPE 
            3            90 
$`AFM MUTATED`
TCGA-A6-3809 TCGA-AA-3518 TCGA-AA-3713 TCGA-AA-A010 TCGA-AA-A01Q TCGA-AD-6965 
       32.75         1.02        19.04        34.98         1.02         0.20 
TCGA-AZ-6599 TCGA-CA-6718 TCGA-CM-5861 TCGA-D5-6923 TCGA-DM-A1DB TCGA-DM-A1HA 
        6.77        10.06        15.02        12.43        44.32       131.51 
TCGA-G4-6310 TCGA-AG-4001 TCGA-AG-A002 TCGA-EI-6507 TCGA-G5-6641 
       63.62        36.03        20.98        19.96        26.43 

$`AFM WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
       38.07        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        10.88        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       49.41        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07        12.20        12.76        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       32.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
        4.41        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
      140.38         7.50       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       55.04        85.48        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       32.02        19.99        28.04        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       32.19         0.66         0.69        55.76 

  AFM MUTATED AFM WILD-TYPE 
          0.2           0.0 
  AFM MUTATED AFM WILD-TYPE 
       131.51        148.01 
  AFM MUTATED AFM WILD-TYPE 
       19.960        20.235 
[1] "0.2 - 131.5 (20.0)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.1"
D1861V2, continuous
D1861V3, binary
               cls
clus              0   1
  AFM MUTATED    13   4
  AFM WILD-TYPE 353 115
[1] "tbl2"
               cls
clus            [,1] [,2]
  AFM MUTATED     13    4
  AFM WILD-TYPE  353  115
        clus
vv       AFM MUTATED AFM WILD-TYPE
  COLON           13           353
  RECTUM           4           115
[1] 2 2
[1] FALSE
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  AFM MUTATED         3        0        1         6         2         0
  AFM WILD-TYPE      88        1       31       132         8         1
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AFM MUTATED           0          1          1          1        1         0
  AFM WILD-TYPE        24         10         58         41       47        18
               vv
clus            STAGE IVB
  AFM MUTATED           0
  AFM WILD-TYPE         1
D1861V4, multiclass
            clus
vv           AFM MUTATED AFM WILD-TYPE
  STAGE I              3            88
  STAGE IA             0             1
  STAGE II             1            31
  STAGE IIA            6           132
  STAGE IIB            2             8
  STAGE IIC            0             1
  STAGE III            0            24
  STAGE IIIA           1            10
  STAGE IIIB           1            58
  STAGE IIIC           1            41
  STAGE IV             1            47
  STAGE IVA            0            18
  STAGE IVB            0             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  AFM MUTATED     1   3  10   3
  AFM WILD-TYPE  16  89 319  47
D1861V5, multiclass
    clus
vv   AFM MUTATED AFM WILD-TYPE
  T1           1            16
  T2           3            89
  T3          10           319
  T4           3            47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2
  AFM MUTATED    13   2   2
  AFM WILD-TYPE 274 111  85
D1861V6, multiclass
    clus
vv   AFM MUTATED AFM WILD-TYPE
  N0          13           274
  N1           2           111
  N2           2            85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1861V7, binary
               cls
clus              0   1
  AFM MUTATED    13   1
  AFM WILD-TYPE 362  64
[1] "tbl2"
               cls
clus            [,1] [,2]
  AFM MUTATED     13    1
  AFM WILD-TYPE  362   64
   clus
vv  AFM MUTATED AFM WILD-TYPE
  0          13           362
  1           1            64
[1] 2 2
[1] FALSE
D1861V8, binary
               cls
clus              0   1
  AFM MUTATED     6  11
  AFM WILD-TYPE 219 253
[1] "tbl2"
               cls
clus            [,1] [,2]
  AFM MUTATED      6   11
  AFM WILD-TYPE  219  253
        clus
vv       AFM MUTATED AFM WILD-TYPE
  FEMALE           6           219
  MALE            11           253
[1] 2 2
[1] FALSE
D1861V9, binary
               cls
clus              0   1
  AFM MUTATED    10   2
  AFM WILD-TYPE 340  20
[1] "tbl2"
               cls
clus            [,1] [,2]
  AFM MUTATED     10    2
  AFM WILD-TYPE  340   20
     clus
vv    AFM MUTATED AFM WILD-TYPE
  NO           10           340
  YES           2            20
[1] 2 2
[1] FALSE
               vv
clus            COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  AFM MUTATED                     12                             1
  AFM WILD-TYPE                  303                            46
               vv
clus            RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  AFM MUTATED                       3                              1
  AFM WILD-TYPE                   103                              9
D1861V10, multiclass
                                clus
vv                               AFM MUTATED AFM WILD-TYPE
  COLON ADENOCARCINOMA                    12           303
  COLON MUCINOUS ADENOCARCINOMA            1            46
  RECTAL ADENOCARCINOMA                    3           103
  RECTAL MUCINOUS ADENOCARCINOMA           1             9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             R0  R1  R2  RX
  AFM MUTATED    11   0   1   1
  AFM WILD-TYPE 334   4  30  24
D1861V11, multiclass
    clus
vv   AFM MUTATED AFM WILD-TYPE
  R0          11           334
  R1           0             4
  R2           1            30
  RX           1            24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1861V12, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AFM MUTATED                                  0     1
  AFM WILD-TYPE                                1    10
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  AFM MUTATED                           0    10
  AFM WILD-TYPE                        22   216
D1861V13, multiclass
                                  clus
vv                                 AFM MUTATED AFM WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      1            10
  BLACK OR AFRICAN AMERICAN                  0            22
  WHITE                                     10           216
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1862) Variable = YIPF1 MUTATION ANALYSIS
D1862V1, survival
                 sevent
clus2               0   1
  YIPF1 MUTATED     5   1
  YIPF1 WILD-TYPE 373  92
  YIPF1 MUTATED YIPF1 WILD-TYPE 
              6             465 
  YIPF1 MUTATED YIPF1 WILD-TYPE 
              1              92 
$`YIPF1 MUTATED`
TCGA-AA-3543 TCGA-AA-3864 TCGA-AD-6890 TCGA-AZ-4315 TCGA-AZ-6599 TCGA-AG-A002 
        0.99        53.00         0.79        58.39         6.77        20.98 

$`YIPF1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       29.00        26.01        12.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 
       32.05         0.99        31.07        31.07        30.05        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
       56.55         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        88.21        49.41        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  YIPF1 MUTATED YIPF1 WILD-TYPE 
           0.79            0.00 
  YIPF1 MUTATED YIPF1 WILD-TYPE 
          58.39          148.01 
  YIPF1 MUTATED YIPF1 WILD-TYPE 
         13.875          20.190 
[1] "0.8 - 58.4 (13.9)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.2"
D1862V2, continuous
D1862V3, binary
                 cls
clus                0   1
  YIPF1 MUTATED     5   1
  YIPF1 WILD-TYPE 361 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  YIPF1 MUTATED      5    1
  YIPF1 WILD-TYPE  361  118
        clus
vv       YIPF1 MUTATED YIPF1 WILD-TYPE
  COLON              5             361
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  YIPF1 MUTATED         3        0        1         1         0         0
  YIPF1 WILD-TYPE      88        1       31       137        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  YIPF1 MUTATED           0          0          0          0        0         0
  YIPF1 WILD-TYPE        24         11         59         42       48        18
                 vv
clus              STAGE IVB
  YIPF1 MUTATED           0
  YIPF1 WILD-TYPE         1
D1862V4, multiclass
            clus
vv           YIPF1 MUTATED YIPF1 WILD-TYPE
  STAGE I                3              88
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              1             137
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  YIPF1 MUTATED     1   3   2   0
  YIPF1 WILD-TYPE  16  89 327  50
D1862V5, multiclass
    clus
vv   YIPF1 MUTATED YIPF1 WILD-TYPE
  T1             1              16
  T2             3              89
  T3             2             327
  T4             0              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  YIPF1 MUTATED     6   0   0
  YIPF1 WILD-TYPE 281 113  87
D1862V6, multiclass
    clus
vv   YIPF1 MUTATED YIPF1 WILD-TYPE
  N0             6             281
  N1             0             113
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1862V7, binary
                 cls
clus                0   1
  YIPF1 MUTATED     4   0
  YIPF1 WILD-TYPE 371  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  YIPF1 MUTATED      4    0
  YIPF1 WILD-TYPE  371   65
   clus
vv  YIPF1 MUTATED YIPF1 WILD-TYPE
  0             4             371
  1             0              65
[1] 2 2
[1] FALSE
D1862V8, binary
                 cls
clus                0   1
  YIPF1 MUTATED     0   6
  YIPF1 WILD-TYPE 225 258
[1] "tbl2"
                 cls
clus              [,1] [,2]
  YIPF1 MUTATED      0    6
  YIPF1 WILD-TYPE  225  258
        clus
vv       YIPF1 MUTATED YIPF1 WILD-TYPE
  FEMALE             0             225
  MALE               6             258
[1] 2 2
[1] FALSE
D1862V9, binary
                 cls
clus                0   1
  YIPF1 MUTATED     5   0
  YIPF1 WILD-TYPE 345  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  YIPF1 MUTATED      5    0
  YIPF1 WILD-TYPE  345   22
     clus
vv    YIPF1 MUTATED YIPF1 WILD-TYPE
  NO              5             345
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  YIPF1 MUTATED                      4                             1
  YIPF1 WILD-TYPE                  311                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  YIPF1 MUTATED                       1                              0
  YIPF1 WILD-TYPE                   105                             10
D1862V10, multiclass
                                clus
vv                               YIPF1 MUTATED YIPF1 WILD-TYPE
  COLON ADENOCARCINOMA                       4             311
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  YIPF1 MUTATED     4   0   0   0
  YIPF1 WILD-TYPE 341   4  31  25
D1862V11, multiclass
    clus
vv   YIPF1 MUTATED YIPF1 WILD-TYPE
  R0             4             341
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1862V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  YIPF1 MUTATED                                  0     0
  YIPF1 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  YIPF1 MUTATED                           0     3
  YIPF1 WILD-TYPE                        22   223
D1862V13, multiclass
                                  clus
vv                                 YIPF1 MUTATED YIPF1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        3             223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1863) Variable = TSPAN7 MUTATION ANALYSIS
D1863V1, survival
                  sevent
clus2                0   1
  TSPAN7 MUTATED     6   3
  TSPAN7 WILD-TYPE 372  90
  TSPAN7 MUTATED TSPAN7 WILD-TYPE 
               9              462 
  TSPAN7 MUTATED TSPAN7 WILD-TYPE 
               3               90 
$`TSPAN7 MUTATED`
TCGA-A6-5661 TCGA-A6-6654 TCGA-AA-3492 TCGA-AA-3845 TCGA-AA-3966 TCGA-AD-5900 
       33.53        23.87         3.02         0.00         2.01         0.07 
TCGA-AU-6004 TCGA-D5-6930 TCGA-DM-A285 
       27.09         1.51         6.12 

$`TSPAN7 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 
       25.18        24.16        21.76        24.69        24.39        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       19.66        20.28         7.04         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       38.99        37.02        14.93        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 
       22.42        27.42        10.88         0.20        14.50        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
        9.44        11.64         4.80        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      135.65       139.17        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  TSPAN7 MUTATED TSPAN7 WILD-TYPE 
               0                0 
  TSPAN7 MUTATED TSPAN7 WILD-TYPE 
           33.53           148.01 
  TSPAN7 MUTATED TSPAN7 WILD-TYPE 
           3.020           20.415 
[1] "0.0 - 33.5 (3.0)"   "0.0 - 148.0 (20.4)"
[1] "hr=" "4.3"
D1863V2, continuous
D1863V3, binary
                  cls
clus                 0   1
  TSPAN7 MUTATED     9   0
  TSPAN7 WILD-TYPE 357 119
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TSPAN7 MUTATED      9    0
  TSPAN7 WILD-TYPE  357  119
        clus
vv       TSPAN7 MUTATED TSPAN7 WILD-TYPE
  COLON               9              357
  RECTUM              0              119
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TSPAN7 MUTATED         2        0        1         4         0         0
  TSPAN7 WILD-TYPE      89        1       31       134        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TSPAN7 MUTATED           0          0          1          0        1
  TSPAN7 WILD-TYPE        24         11         58         42       47
                  vv
clus               STAGE IVA STAGE IVB
  TSPAN7 MUTATED           0         0
  TSPAN7 WILD-TYPE        18         1
D1863V4, multiclass
            clus
vv           TSPAN7 MUTATED TSPAN7 WILD-TYPE
  STAGE I                 2               89
  STAGE IA                0                1
  STAGE II                1               31
  STAGE IIA               4              134
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              1               58
  STAGE IIIC              0               42
  STAGE IV                1               47
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  TSPAN7 MUTATED     0   2   7   0
  TSPAN7 WILD-TYPE  17  90 322  50
D1863V5, multiclass
    clus
vv   TSPAN7 MUTATED TSPAN7 WILD-TYPE
  T1              0               17
  T2              2               90
  T3              7              322
  T4              0               50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  TSPAN7 MUTATED     7   1   1
  TSPAN7 WILD-TYPE 280 112  86
D1863V6, multiclass
    clus
vv   TSPAN7 MUTATED TSPAN7 WILD-TYPE
  N0              7              280
  N1              1              112
  N2              1               86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1863V7, binary
                  cls
clus                 0   1
  TSPAN7 MUTATED     7   1
  TSPAN7 WILD-TYPE 368  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TSPAN7 MUTATED      7    1
  TSPAN7 WILD-TYPE  368   64
   clus
vv  TSPAN7 MUTATED TSPAN7 WILD-TYPE
  0              7              368
  1              1               64
[1] 2 2
[1] FALSE
D1863V8, binary
                  cls
clus                 0   1
  TSPAN7 MUTATED     7   2
  TSPAN7 WILD-TYPE 218 262
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TSPAN7 MUTATED      7    2
  TSPAN7 WILD-TYPE  218  262
        clus
vv       TSPAN7 MUTATED TSPAN7 WILD-TYPE
  FEMALE              7              218
  MALE                2              262
[1] 2 2
[1] FALSE
D1863V9, binary
                  cls
clus                 0   1
  TSPAN7 MUTATED     3   0
  TSPAN7 WILD-TYPE 347  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TSPAN7 MUTATED      3    0
  TSPAN7 WILD-TYPE  347   22
     clus
vv    TSPAN7 MUTATED TSPAN7 WILD-TYPE
  NO               3              347
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  TSPAN7 MUTATED                      5                             4
  TSPAN7 WILD-TYPE                  310                            43
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  TSPAN7 MUTATED                       0                              0
  TSPAN7 WILD-TYPE                   106                             10
D1863V10, multiclass
                                clus
vv                               TSPAN7 MUTATED TSPAN7 WILD-TYPE
  COLON ADENOCARCINOMA                        5              310
  COLON MUCINOUS ADENOCARCINOMA               4               43
  RECTAL ADENOCARCINOMA                       0              106
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  TSPAN7 MUTATED     6   0   0   0
  TSPAN7 WILD-TYPE 339   4  31  25
D1863V11, multiclass
    clus
vv   TSPAN7 MUTATED TSPAN7 WILD-TYPE
  R0              6              339
  R1              0                4
  R2              0               31
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1863V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TSPAN7 MUTATED                                  0     0
  TSPAN7 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  TSPAN7 MUTATED                           1     5
  TSPAN7 WILD-TYPE                        21   221
D1863V13, multiclass
                                  clus
vv                                 TSPAN7 MUTATED TSPAN7 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                         5              221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1864) Variable = MLLT10 MUTATION ANALYSIS
D1864V1, survival
                  sevent
clus2                0   1
  MLLT10 MUTATED     9   1
  MLLT10 WILD-TYPE 369  92
  MLLT10 MUTATED MLLT10 WILD-TYPE 
              10              461 
  MLLT10 MUTATED MLLT10 WILD-TYPE 
               1               92 
$`MLLT10 MUTATED`
TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3947 TCGA-AA-3952 TCGA-AA-3977 TCGA-AA-A00L 
       20.12        19.66        33.01         2.01        25.02        38.04 
TCGA-AA-A010 TCGA-CA-6717 TCGA-D5-6924 TCGA-F5-6812 
       34.98        12.76        14.30         0.66 

$`MLLT10 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       23.87        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3955 TCGA-AA-3956 
       12.99        24.00        26.01        24.00        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07        12.20        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        3.68         4.41        12.43         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.69        55.76        26.43 

  MLLT10 MUTATED MLLT10 WILD-TYPE 
            0.66             0.00 
  MLLT10 MUTATED MLLT10 WILD-TYPE 
           38.04           148.01 
  MLLT10 MUTATED MLLT10 WILD-TYPE 
           19.89            20.28 
[1] "0.7 - 38.0 (19.9)"  "0.0 - 148.0 (20.3)"
[1] "hr=" "1.4"
D1864V2, continuous
D1864V3, binary
                  cls
clus                 0   1
  MLLT10 MUTATED    10   1
  MLLT10 WILD-TYPE 356 118
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MLLT10 MUTATED     10    1
  MLLT10 WILD-TYPE  356  118
        clus
vv       MLLT10 MUTATED MLLT10 WILD-TYPE
  COLON              10              356
  RECTUM              1              118
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MLLT10 MUTATED         0        0        0         5         2         0
  MLLT10 WILD-TYPE      91        1       32       133         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MLLT10 MUTATED           0          0          0          2        1
  MLLT10 WILD-TYPE        24         11         59         40       47
                  vv
clus               STAGE IVA STAGE IVB
  MLLT10 MUTATED           0         0
  MLLT10 WILD-TYPE        18         1
D1864V4, multiclass
            clus
vv           MLLT10 MUTATED MLLT10 WILD-TYPE
  STAGE I                 0               91
  STAGE IA                0                1
  STAGE II                0               32
  STAGE IIA               5              133
  STAGE IIB               2                8
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              0               59
  STAGE IIIC              2               40
  STAGE IV                1               47
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  MLLT10 MUTATED     0   1   7   3
  MLLT10 WILD-TYPE  17  91 322  47
D1864V5, multiclass
    clus
vv   MLLT10 MUTATED MLLT10 WILD-TYPE
  T1              0               17
  T2              1               91
  T3              7              322
  T4              3               47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  MLLT10 MUTATED     8   1   2
  MLLT10 WILD-TYPE 279 112  85
D1864V6, multiclass
    clus
vv   MLLT10 MUTATED MLLT10 WILD-TYPE
  N0              8              279
  N1              1              112
  N2              2               85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1864V7, binary
                  cls
clus                 0   1
  MLLT10 MUTATED     7   1
  MLLT10 WILD-TYPE 368  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MLLT10 MUTATED      7    1
  MLLT10 WILD-TYPE  368   64
   clus
vv  MLLT10 MUTATED MLLT10 WILD-TYPE
  0              7              368
  1              1               64
[1] 2 2
[1] FALSE
D1864V8, binary
                  cls
clus                 0   1
  MLLT10 MUTATED     3   8
  MLLT10 WILD-TYPE 222 256
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MLLT10 MUTATED      3    8
  MLLT10 WILD-TYPE  222  256
        clus
vv       MLLT10 MUTATED MLLT10 WILD-TYPE
  FEMALE              3              222
  MALE                8              256
[1] 2 2
[1] FALSE
D1864V9, binary
                  cls
clus                 0   1
  MLLT10 MUTATED     8   0
  MLLT10 WILD-TYPE 342  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MLLT10 MUTATED      8    0
  MLLT10 WILD-TYPE  342   22
     clus
vv    MLLT10 MUTATED MLLT10 WILD-TYPE
  NO               8              342
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MLLT10 MUTATED                      6                             4
  MLLT10 WILD-TYPE                  309                            43
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MLLT10 MUTATED                       1                              0
  MLLT10 WILD-TYPE                   105                             10
D1864V10, multiclass
                                clus
vv                               MLLT10 MUTATED MLLT10 WILD-TYPE
  COLON ADENOCARCINOMA                        6              309
  COLON MUCINOUS ADENOCARCINOMA               4               43
  RECTAL ADENOCARCINOMA                       1              105
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  MLLT10 MUTATED     7   0   1   1
  MLLT10 WILD-TYPE 338   4  30  24
D1864V11, multiclass
    clus
vv   MLLT10 MUTATED MLLT10 WILD-TYPE
  R0              7              338
  R1              0                4
  R2              1               30
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1864V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MLLT10 MUTATED                                  0     1
  MLLT10 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  MLLT10 MUTATED                           0     4
  MLLT10 WILD-TYPE                        22   222
D1864V13, multiclass
                                  clus
vv                                 MLLT10 MUTATED MLLT10 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         4              222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1865) Variable = CCDC6 MUTATION ANALYSIS
D1865V1, survival
                 sevent
clus2               0   1
  CCDC6 MUTATED    11   0
  CCDC6 WILD-TYPE 367  93
  CCDC6 MUTATED CCDC6 WILD-TYPE 
             11             460 
  CCDC6 MUTATED CCDC6 WILD-TYPE 
              0              93 
$`CCDC6 MUTATED`
TCGA-A6-6138 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3947 TCGA-AY-6386 TCGA-CM-4743 
       22.52        63.98         1.02        33.01        17.82        23.05 
TCGA-CM-6168 TCGA-CM-6674 TCGA-D5-6538 TCGA-G4-6304 TCGA-G4-6586 
       12.99        12.95        17.13        53.62        35.80 

$`CCDC6 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6141 TCGA-A6-6142 
       22.09        22.06        32.71        27.09         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
       35.01         6.97        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       16.04        21.99        14.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       11.01        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
        4.80        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       65.85        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  CCDC6 MUTATED CCDC6 WILD-TYPE 
           1.02            0.00 
  CCDC6 MUTATED CCDC6 WILD-TYPE 
          63.98          148.01 
  CCDC6 MUTATED CCDC6 WILD-TYPE 
         22.520          20.155 
[1] "1.0 - 64.0 (22.5)"  "0.0 - 148.0 (20.2)"
[1] "hr="     "9300000"
D1865V2, continuous
D1865V3, binary
                 cls
clus                0   1
  CCDC6 MUTATED    11   0
  CCDC6 WILD-TYPE 355 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CCDC6 MUTATED     11    0
  CCDC6 WILD-TYPE  355  119
        clus
vv       CCDC6 MUTATED CCDC6 WILD-TYPE
  COLON             11             355
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CCDC6 MUTATED         2        0        1         4         2         0
  CCDC6 WILD-TYPE      89        1       31       134         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CCDC6 MUTATED           0          0          2          0        0         0
  CCDC6 WILD-TYPE        24         11         57         42       48        18
                 vv
clus              STAGE IVB
  CCDC6 MUTATED           0
  CCDC6 WILD-TYPE         1
D1865V4, multiclass
            clus
vv           CCDC6 MUTATED CCDC6 WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              4             134
  STAGE IIB              2               8
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             2              57
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CCDC6 MUTATED     0   2   7   2
  CCDC6 WILD-TYPE  17  90 322  48
D1865V5, multiclass
    clus
vv   CCDC6 MUTATED CCDC6 WILD-TYPE
  T1             0              17
  T2             2              90
  T3             7             322
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  CCDC6 MUTATED     9   1   1
  CCDC6 WILD-TYPE 278 112  86
D1865V6, multiclass
    clus
vv   CCDC6 MUTATED CCDC6 WILD-TYPE
  N0             9             278
  N1             1             112
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1865V7, binary
                 cls
clus                0   1
  CCDC6 MUTATED    11   0
  CCDC6 WILD-TYPE 364  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CCDC6 MUTATED     11    0
  CCDC6 WILD-TYPE  364   65
   clus
vv  CCDC6 MUTATED CCDC6 WILD-TYPE
  0            11             364
  1             0              65
[1] 2 2
[1] FALSE
D1865V8, binary
                 cls
clus                0   1
  CCDC6 MUTATED     7   4
  CCDC6 WILD-TYPE 218 260
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CCDC6 MUTATED      7    4
  CCDC6 WILD-TYPE  218  260
        clus
vv       CCDC6 MUTATED CCDC6 WILD-TYPE
  FEMALE             7             218
  MALE               4             260
[1] 2 2
[1] FALSE
D1865V9, binary
                 cls
clus                0   1
  CCDC6 MUTATED    11   0
  CCDC6 WILD-TYPE 339  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CCDC6 MUTATED     11    0
  CCDC6 WILD-TYPE  339   22
     clus
vv    CCDC6 MUTATED CCDC6 WILD-TYPE
  NO             11             339
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CCDC6 MUTATED                     10                             1
  CCDC6 WILD-TYPE                  305                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CCDC6 MUTATED                       0                              0
  CCDC6 WILD-TYPE                   106                             10
D1865V10, multiclass
                                clus
vv                               CCDC6 MUTATED CCDC6 WILD-TYPE
  COLON ADENOCARCINOMA                      10             305
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  CCDC6 MUTATED    10   0   0   0
  CCDC6 WILD-TYPE 335   4  31  25
D1865V11, multiclass
    clus
vv   CCDC6 MUTATED CCDC6 WILD-TYPE
  R0            10             335
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1865V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CCDC6 MUTATED                                  0     0
  CCDC6 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CCDC6 MUTATED                           2     6
  CCDC6 WILD-TYPE                        20   220
D1865V13, multiclass
                                  clus
vv                                 CCDC6 MUTATED CCDC6 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    2              20
  WHITE                                        6             220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1866) Variable = SGOL2 MUTATION ANALYSIS
D1866V1, survival
                 sevent
clus2               0   1
  SGOL2 MUTATED    15   1
  SGOL2 WILD-TYPE 363  92
  SGOL2 MUTATED SGOL2 WILD-TYPE 
             16             455 
  SGOL2 MUTATED SGOL2 WILD-TYPE 
              1              92 
$`SGOL2 MUTATED`
TCGA-AA-3710 TCGA-AA-A010 TCGA-AD-6895 TCGA-AZ-4315 TCGA-CA-6717 TCGA-CK-5916 
       26.99        34.98         0.72        58.39        12.76        21.14 
TCGA-CK-6748 TCGA-CM-4743 TCGA-CM-6675 TCGA-D5-5541 TCGA-G4-6304 TCGA-G4-6307 
        1.91        23.05        13.05        55.92        53.62        55.04 
TCGA-AG-3892 TCGA-AG-A002 TCGA-AG-A036 TCGA-CL-5918 
       13.02        20.98       117.11         7.17 

$`SGOL2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
       19.00        36.00         5.03        85.05        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
       56.55         0.79         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07        12.20        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 
       51.32         9.99        82.95       124.27        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       12.95        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-6529 TCGA-D5-6532 
       45.40        12.26        19.59        56.09        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       44.68        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       36.95        17.03        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
       38.04        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-DC-5337 
        6.05        33.17         6.97         4.73        78.12        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  SGOL2 MUTATED SGOL2 WILD-TYPE 
           0.72            0.00 
  SGOL2 MUTATED SGOL2 WILD-TYPE 
         117.11          148.01 
  SGOL2 MUTATED SGOL2 WILD-TYPE 
         22.095          20.050 
[1] "0.7 - 117.1 (22.1)" "0.0 - 148.0 (20.1)"
[1] "hr=" "4.1"
D1866V2, continuous
D1866V3, binary
                 cls
clus                0   1
  SGOL2 MUTATED    12   4
  SGOL2 WILD-TYPE 354 115
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SGOL2 MUTATED     12    4
  SGOL2 WILD-TYPE  354  115
        clus
vv       SGOL2 MUTATED SGOL2 WILD-TYPE
  COLON             12             354
  RECTUM             4             115
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SGOL2 MUTATED         3        0        0         5         2         0
  SGOL2 WILD-TYPE      88        1       32       133         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SGOL2 MUTATED           1          0          2          0        1         0
  SGOL2 WILD-TYPE        23         11         57         42       47        18
                 vv
clus              STAGE IVB
  SGOL2 MUTATED           1
  SGOL2 WILD-TYPE         0
D1866V4, multiclass
            clus
vv           SGOL2 MUTATED SGOL2 WILD-TYPE
  STAGE I                3              88
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              5             133
  STAGE IIB              2               8
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             2              57
  STAGE IIIC             0              42
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              1               0
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  SGOL2 MUTATED     2   1  11   2
  SGOL2 WILD-TYPE  15  91 318  48
D1866V5, multiclass
    clus
vv   SGOL2 MUTATED SGOL2 WILD-TYPE
  T1             2              15
  T2             1              91
  T3            11             318
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  SGOL2 MUTATED    10   4   2
  SGOL2 WILD-TYPE 277 109  85
D1866V6, multiclass
    clus
vv   SGOL2 MUTATED SGOL2 WILD-TYPE
  N0            10             277
  N1             4             109
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1866V7, binary
                 cls
clus                0   1
  SGOL2 MUTATED    12   2
  SGOL2 WILD-TYPE 363  63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SGOL2 MUTATED     12    2
  SGOL2 WILD-TYPE  363   63
   clus
vv  SGOL2 MUTATED SGOL2 WILD-TYPE
  0            12             363
  1             2              63
[1] 2 2
[1] FALSE
D1866V8, binary
                 cls
clus                0   1
  SGOL2 MUTATED     8   8
  SGOL2 WILD-TYPE 217 256
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SGOL2 MUTATED      8    8
  SGOL2 WILD-TYPE  217  256
        clus
vv       SGOL2 MUTATED SGOL2 WILD-TYPE
  FEMALE             8             217
  MALE               8             256
[1] 2 2
[1] FALSE
D1866V9, binary
                 cls
clus                0   1
  SGOL2 MUTATED    14   1
  SGOL2 WILD-TYPE 336  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SGOL2 MUTATED     14    1
  SGOL2 WILD-TYPE  336   21
     clus
vv    SGOL2 MUTATED SGOL2 WILD-TYPE
  NO             14             336
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SGOL2 MUTATED                     10                             2
  SGOL2 WILD-TYPE                  305                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SGOL2 MUTATED                       4                              0
  SGOL2 WILD-TYPE                   102                             10
D1866V10, multiclass
                                clus
vv                               SGOL2 MUTATED SGOL2 WILD-TYPE
  COLON ADENOCARCINOMA                      10             305
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      4             102
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  SGOL2 MUTATED    11   0   0   4
  SGOL2 WILD-TYPE 334   4  31  21
D1866V11, multiclass
    clus
vv   SGOL2 MUTATED SGOL2 WILD-TYPE
  R0            11             334
  R1             0               4
  R2             0              31
  RX             4              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1866V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SGOL2 MUTATED                                  0     1
  SGOL2 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  SGOL2 MUTATED                           1     9
  SGOL2 WILD-TYPE                        21   217
D1866V13, multiclass
                                  clus
vv                                 SGOL2 MUTATED SGOL2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        9             217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1867) Variable = HECW1 MUTATION ANALYSIS
D1867V1, survival
                 sevent
clus2               0   1
  HECW1 MUTATED    26  11
  HECW1 WILD-TYPE 352  82
  HECW1 MUTATED HECW1 WILD-TYPE 
             37             434 
  HECW1 MUTATED HECW1 WILD-TYPE 
             11              82 
$`HECW1 MUTATED`
TCGA-A6-5661 TCGA-A6-6782 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3710 TCGA-AA-3989 
       33.53        20.28        35.01         6.97        26.99         7.96 
TCGA-AA-A00N TCGA-AA-A010 TCGA-AD-6901 TCGA-AZ-4315 TCGA-AZ-4616 TCGA-AZ-6598 
        4.01        34.98        22.42        58.39         5.13        49.41 
TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6605 TCGA-CM-4743 TCGA-CM-5861 TCGA-CM-6161 
        6.77       100.01         5.23        23.05        15.02        15.02 
TCGA-CM-6168 TCGA-CM-6678 TCGA-D5-6539 TCGA-D5-6928 TCGA-DM-A1D7 TCGA-DM-A1DA 
       12.99        11.01        12.49        11.64        13.32         7.50 
TCGA-DM-A285 TCGA-F4-6808 TCGA-F4-6856 TCGA-G4-6315 TCGA-G4-6588 TCGA-AG-3892 
        6.12        33.67        35.31        61.91        26.17        13.02 
TCGA-AG-A002 TCGA-AG-A020 TCGA-AH-6544 TCGA-AH-6549 TCGA-CI-6624 TCGA-EI-6508 
       20.98        10.98        38.56        17.49         4.73        20.91 
TCGA-EI-6510 
       18.28 

$`HECW1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3510 
       20.12        19.66         7.04         3.02         1.02        63.98 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3994 
       25.02        24.00        27.02        27.02        19.07        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6964 
       56.55         0.79         0.72         5.79        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       21.44        17.82         1.41       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
       88.21        12.10        29.56        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
        1.91       124.27        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 
       29.06        22.03        22.98        30.08        32.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        15.02        17.03        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       16.04        21.99        14.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6679 
       11.01        12.95        13.05        11.08        11.08        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
        4.80        17.13        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 
        4.41        12.43        14.30         9.04         9.44         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D8 TCGA-DM-A1D9 
       38.20       130.65        92.75        49.91        12.59       140.38 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A28C TCGA-DM-A28E 
       44.32       131.51       135.65       139.17        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 
       16.24        13.25         0.53        47.41       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        35.80        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       17.95        36.95        17.03        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       64.01        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.04       117.11         1.45         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
       33.17         6.97        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-F5-6464 
       51.48        32.61         0.49        20.55        19.96         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  HECW1 MUTATED HECW1 WILD-TYPE 
           4.01            0.00 
  HECW1 MUTATED HECW1 WILD-TYPE 
         100.01          148.01 
  HECW1 MUTATED HECW1 WILD-TYPE 
         17.490          20.765 
[1] "4.0 - 100.0 (17.5)" "0.0 - 148.0 (20.8)"
[1] "hr=" "1.8"
D1867V2, continuous
D1867V3, binary
                 cls
clus                0   1
  HECW1 MUTATED    31   8
  HECW1 WILD-TYPE 335 111
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HECW1 MUTATED     31    8
  HECW1 WILD-TYPE  335  111
        clus
vv       HECW1 MUTATED HECW1 WILD-TYPE
  COLON             31             335
  RECTUM             8             111
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  HECW1 MUTATED         8        0        4         9         3         0
  HECW1 WILD-TYPE      83        1       28       129         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  HECW1 MUTATED           1          1          2          2        4         2
  HECW1 WILD-TYPE        23         10         57         40       44        16
                 vv
clus              STAGE IVB
  HECW1 MUTATED           0
  HECW1 WILD-TYPE         1
D1867V4, multiclass
            clus
vv           HECW1 MUTATED HECW1 WILD-TYPE
  STAGE I                8              83
  STAGE IA               0               1
  STAGE II               4              28
  STAGE IIA              9             129
  STAGE IIB              3               7
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             1              10
  STAGE IIIB             2              57
  STAGE IIIC             2              40
  STAGE IV               4              44
  STAGE IVA              2              16
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  HECW1 MUTATED     2   7  23   7
  HECW1 WILD-TYPE  15  85 306  43
D1867V5, multiclass
    clus
vv   HECW1 MUTATED HECW1 WILD-TYPE
  T1             2              15
  T2             7              85
  T3            23             306
  T4             7              43
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  HECW1 MUTATED    27   6   5
  HECW1 WILD-TYPE 260 107  82
D1867V6, multiclass
    clus
vv   HECW1 MUTATED HECW1 WILD-TYPE
  N0            27             260
  N1             6             107
  N2             5              82
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1867V7, binary
                 cls
clus                0   1
  HECW1 MUTATED    26   6
  HECW1 WILD-TYPE 349  59
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HECW1 MUTATED     26    6
  HECW1 WILD-TYPE  349   59
   clus
vv  HECW1 MUTATED HECW1 WILD-TYPE
  0            26             349
  1             6              59
[1] 2 2
[1] FALSE
D1867V8, binary
                 cls
clus                0   1
  HECW1 MUTATED    20  19
  HECW1 WILD-TYPE 205 245
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HECW1 MUTATED     20   19
  HECW1 WILD-TYPE  205  245
        clus
vv       HECW1 MUTATED HECW1 WILD-TYPE
  FEMALE            20             205
  MALE              19             245
[1] 2 2
[1] FALSE
D1867V9, binary
                 cls
clus                0   1
  HECW1 MUTATED    31   0
  HECW1 WILD-TYPE 319  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HECW1 MUTATED     31    0
  HECW1 WILD-TYPE  319   22
     clus
vv    HECW1 MUTATED HECW1 WILD-TYPE
  NO             31             319
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  HECW1 MUTATED                     25                             5
  HECW1 WILD-TYPE                  290                            42
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  HECW1 MUTATED                       7                              1
  HECW1 WILD-TYPE                    99                              9
D1867V10, multiclass
                                clus
vv                               HECW1 MUTATED HECW1 WILD-TYPE
  COLON ADENOCARCINOMA                      25             290
  COLON MUCINOUS ADENOCARCINOMA              5              42
  RECTAL ADENOCARCINOMA                      7              99
  RECTAL MUCINOUS ADENOCARCINOMA             1               9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  HECW1 MUTATED    25   0   1   1
  HECW1 WILD-TYPE 320   4  30  24
D1867V11, multiclass
    clus
vv   HECW1 MUTATED HECW1 WILD-TYPE
  R0            25             320
  R1             0               4
  R2             1              30
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1867V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HECW1 MUTATED                                  0     0
  HECW1 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  HECW1 MUTATED                           2    27
  HECW1 WILD-TYPE                        20   199
D1867V13, multiclass
                                  clus
vv                                 HECW1 MUTATED HECW1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    2              20
  WHITE                                       27             199
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1868) Variable = C14ORF180 MUTATION ANALYSIS
D1868V1, survival
                     sevent
clus2                   0   1
  C14ORF180 MUTATED     2   2
  C14ORF180 WILD-TYPE 376  91
  C14ORF180 MUTATED C14ORF180 WILD-TYPE 
                  4                 467 
  C14ORF180 MUTATED C14ORF180 WILD-TYPE 
                  2                  91 
$`C14ORF180 MUTATED`
TCGA-AU-6004 TCGA-AZ-6598 TCGA-DM-A1D7 TCGA-G4-6628 
       27.09        49.41        13.32        79.69 

$`C14ORF180 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 
       22.42        27.42        10.88         0.20        14.50        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 
        5.13       106.75        22.36        62.79        88.21         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       91.79        46.75        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  C14ORF180 MUTATED C14ORF180 WILD-TYPE 
              13.32                0.00 
  C14ORF180 MUTATED C14ORF180 WILD-TYPE 
              79.69              148.01 
  C14ORF180 MUTATED C14ORF180 WILD-TYPE 
              38.25               20.12 
[1] "13.3 - 79.7 (38.2)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.5"
D1868V2, continuous
D1868V3, binary
                     cls
clus                    0   1
  C14ORF180 MUTATED     4   0
  C14ORF180 WILD-TYPE 362 119
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  C14ORF180 MUTATED      4    0
  C14ORF180 WILD-TYPE  362  119
        clus
vv       C14ORF180 MUTATED C14ORF180 WILD-TYPE
  COLON                  4                 362
  RECTUM                 0                 119
[1] 2 2
[1] FALSE
                     vv
clus                  STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  C14ORF180 MUTATED         2        0        1         1         0         0
  C14ORF180 WILD-TYPE      89        1       31       137        10         1
                     vv
clus                  STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C14ORF180 MUTATED           0          0          0          0        0
  C14ORF180 WILD-TYPE        24         11         59         42       48
                     vv
clus                  STAGE IVA STAGE IVB
  C14ORF180 MUTATED           0         0
  C14ORF180 WILD-TYPE        18         1
D1868V4, multiclass
            clus
vv           C14ORF180 MUTATED C14ORF180 WILD-TYPE
  STAGE I                    2                  89
  STAGE IA                   0                   1
  STAGE II                   1                  31
  STAGE IIA                  1                 137
  STAGE IIB                  0                  10
  STAGE IIC                  0                   1
  STAGE III                  0                  24
  STAGE IIIA                 0                  11
  STAGE IIIB                 0                  59
  STAGE IIIC                 0                  42
  STAGE IV                   0                  48
  STAGE IVA                  0                  18
  STAGE IVB                  0                   1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                   T1  T2  T3  T4
  C14ORF180 MUTATED     0   2   2   0
  C14ORF180 WILD-TYPE  17  90 327  50
D1868V5, multiclass
    clus
vv   C14ORF180 MUTATED C14ORF180 WILD-TYPE
  T1                 0                  17
  T2                 2                  90
  T3                 2                 327
  T4                 0                  50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                   N0  N1  N2
  C14ORF180 MUTATED     4   0   0
  C14ORF180 WILD-TYPE 283 113  87
D1868V6, multiclass
    clus
vv   C14ORF180 MUTATED C14ORF180 WILD-TYPE
  N0                 4                 283
  N1                 0                 113
  N2                 0                  87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1868V7, binary
                     cls
clus                    0   1
  C14ORF180 MUTATED     3   0
  C14ORF180 WILD-TYPE 372  65
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  C14ORF180 MUTATED      3    0
  C14ORF180 WILD-TYPE  372   65
   clus
vv  C14ORF180 MUTATED C14ORF180 WILD-TYPE
  0                 3                 372
  1                 0                  65
[1] 2 2
[1] FALSE
D1868V8, binary
                     cls
clus                    0   1
  C14ORF180 MUTATED     2   2
  C14ORF180 WILD-TYPE 223 262
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  C14ORF180 MUTATED      2    2
  C14ORF180 WILD-TYPE  223  262
        clus
vv       C14ORF180 MUTATED C14ORF180 WILD-TYPE
  FEMALE                 2                 223
  MALE                   2                 262
[1] 2 2
[1] FALSE
D1868V9, binary
                     cls
clus                    0   1
  C14ORF180 MUTATED     2   0
  C14ORF180 WILD-TYPE 348  22
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  C14ORF180 MUTATED      2    0
  C14ORF180 WILD-TYPE  348   22
     clus
vv    C14ORF180 MUTATED C14ORF180 WILD-TYPE
  NO                  2                 348
  YES                 0                  22
[1] 2 2
[1] FALSE
                     vv
clus                  COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  C14ORF180 MUTATED                      3                             0
  C14ORF180 WILD-TYPE                  312                            47
                     vv
clus                  RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  C14ORF180 MUTATED                       0                              0
  C14ORF180 WILD-TYPE                   106                             10
D1868V10, multiclass
                                clus
vv                               C14ORF180 MUTATED C14ORF180 WILD-TYPE
  COLON ADENOCARCINOMA                           3                 312
  COLON MUCINOUS ADENOCARCINOMA                  0                  47
  RECTAL ADENOCARCINOMA                          0                 106
  RECTAL MUCINOUS ADENOCARCINOMA                 0                  10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                   R0  R1  R2  RX
  C14ORF180 MUTATED     2   0   0   0
  C14ORF180 WILD-TYPE 343   4  31  25
D1868V11, multiclass
[1] "Remove cluster labels:" "C14ORF180 MUTATED"     
clus
  C14ORF180 MUTATED C14ORF180 WILD-TYPE 
                  2                 403 
         TCGA-A6-2671          TCGA-A6-2672          TCGA-A6-2674 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-A6-2676          TCGA-A6-2677          TCGA-A6-2678 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-A6-2683          TCGA-A6-3807          TCGA-A6-3808 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-A6-3809          TCGA-A6-3810          TCGA-A6-5657 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
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         TCGA-AA-3496          TCGA-AA-3502          TCGA-AA-3510 
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         TCGA-AA-3511          TCGA-AA-3514          TCGA-AA-3517 
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         TCGA-AA-3518          TCGA-AA-3519          TCGA-AA-3520 
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         TCGA-AA-3525          TCGA-AA-3526          TCGA-AA-3527 
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         TCGA-AA-3529          TCGA-AA-3530          TCGA-AA-3531 
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         TCGA-AA-3532          TCGA-AA-3534          TCGA-AA-3538 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AA-3542          TCGA-AA-3543          TCGA-AA-3544 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AA-3548          TCGA-AA-3549          TCGA-AA-3552 
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         TCGA-AA-3553          TCGA-AA-3554          TCGA-AA-3555 
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         TCGA-AA-3660          TCGA-AA-3662          TCGA-AA-3663 
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         TCGA-AA-3664          TCGA-AA-3666          TCGA-AA-3667 
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         TCGA-AA-3672          TCGA-AA-3673          TCGA-AA-3678 
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         TCGA-AA-3679          TCGA-AA-3680          TCGA-AA-3681 
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         TCGA-AA-3684          TCGA-AA-3685          TCGA-AA-3688 
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         TCGA-AA-3692          TCGA-AA-3693          TCGA-AA-3695 
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         TCGA-AA-3696          TCGA-AA-3697          TCGA-AA-3710 
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         TCGA-AA-3712          TCGA-AA-3713          TCGA-AA-3715 
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         TCGA-AA-3811          TCGA-AA-3812          TCGA-AA-3814 
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         TCGA-AA-3815          TCGA-AA-3818          TCGA-AA-3819 
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         TCGA-AA-3821          TCGA-AA-3831          TCGA-AA-3833 
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         TCGA-AA-3837          TCGA-AA-3842          TCGA-AA-3844 
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         TCGA-AA-3845          TCGA-AA-3846          TCGA-AA-3848 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AA-3850          TCGA-AA-3851          TCGA-AA-3852 
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         TCGA-AA-3854          TCGA-AA-3855          TCGA-AA-3856 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AA-3858          TCGA-AA-3860          TCGA-AA-3861 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AA-3864          TCGA-AA-3866          TCGA-AA-3867 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AA-3869          TCGA-AA-3870          TCGA-AA-3872 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AA-3875          TCGA-AA-3877          TCGA-AA-3930 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AA-3939          TCGA-AA-3941          TCGA-AA-3947 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AA-3949          TCGA-AA-3950          TCGA-AA-3952 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AA-3955          TCGA-AA-3956          TCGA-AA-3968 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AA-3971          TCGA-AA-3972          TCGA-AA-3973 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AA-3975          TCGA-AA-3976          TCGA-AA-3979 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AA-3984          TCGA-AA-3986          TCGA-AA-3989 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AA-3994          TCGA-AA-A004          TCGA-AA-A00A 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AA-A00D          TCGA-AA-A00E          TCGA-AA-A00F 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AA-A00J          TCGA-AA-A00K          TCGA-AA-A00L 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AA-A00N          TCGA-AA-A00O          TCGA-AA-A00Q 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AA-A00R          TCGA-AA-A00U          TCGA-AA-A00W 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AA-A00Z          TCGA-AA-A010          TCGA-AA-A017 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AA-A01D          TCGA-AA-A01F          TCGA-AA-A01G 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AA-A01I          TCGA-AA-A01K          TCGA-AA-A01P 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AA-A01Q          TCGA-AA-A01R          TCGA-AA-A01S 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AA-A01T          TCGA-AA-A01V          TCGA-AA-A01X 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AA-A01Z          TCGA-AA-A022          TCGA-AA-A024 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AA-A029          TCGA-AA-A02F          TCGA-AA-A02H 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AA-A02J          TCGA-AA-A02K          TCGA-AA-A02O 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AA-A02W          TCGA-AA-A02Y          TCGA-AA-A03F 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AA-A03J          TCGA-AD-5900          TCGA-AD-6548 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AD-6888          TCGA-AU-3779          TCGA-AY-4070 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AY-4071          TCGA-AY-5543          TCGA-AY-6196 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AY-6197          TCGA-AY-6386          TCGA-AZ-4315 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AZ-4681          TCGA-AZ-4682          TCGA-CA-5254 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-CA-5255          TCGA-CA-5796          TCGA-CA-5797 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-CA-6715          TCGA-CA-6716          TCGA-CA-6717 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-CA-6718          TCGA-CA-6719          TCGA-CK-4947 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-CK-4948          TCGA-CK-4950          TCGA-CK-4952 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-CK-5912          TCGA-CK-5913          TCGA-CK-5914 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-CK-5915          TCGA-CK-5916          TCGA-CK-6746 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-CK-6747          TCGA-CK-6748          TCGA-CK-6751 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-CM-4743          TCGA-CM-4744          TCGA-CM-4746 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-CM-4747          TCGA-CM-4752          TCGA-CM-5341 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-CM-5344          TCGA-CM-5348          TCGA-CM-5349 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-CM-5860          TCGA-CM-5861          TCGA-CM-5862 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-CM-5863          TCGA-CM-5864          TCGA-CM-5868 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-CM-6161          TCGA-CM-6162          TCGA-CM-6163 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-CM-6164          TCGA-CM-6165          TCGA-CM-6166 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-CM-6167          TCGA-CM-6168          TCGA-CM-6169 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-CM-6170          TCGA-CM-6171          TCGA-CM-6172 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-CM-6674          TCGA-CM-6675          TCGA-CM-6676 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-CM-6677          TCGA-CM-6678          TCGA-CM-6679 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-CM-6680          TCGA-D5-5537          TCGA-D5-5538 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-D5-5539          TCGA-D5-5540          TCGA-D5-5541 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-D5-6529          TCGA-D5-6532          TCGA-D5-6533 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-D5-6534          TCGA-D5-6535          TCGA-D5-6536 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-D5-6537          TCGA-D5-6538          TCGA-D5-6539 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-D5-6540          TCGA-D5-6541          TCGA-D5-6898 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-D5-6920          TCGA-D5-6922          TCGA-D5-6923 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-D5-6924          TCGA-D5-6926          TCGA-D5-6927 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-D5-6928          TCGA-D5-6929          TCGA-D5-6930 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-D5-6931          TCGA-D5-6932          TCGA-D5-7000 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-F4-6459          TCGA-F4-6460          TCGA-F4-6569 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-F4-6570          TCGA-F4-6703          TCGA-F4-6704 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-F4-6805          TCGA-F4-6806          TCGA-F4-6807 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-F4-6808          TCGA-F4-6809          TCGA-F4-6854 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-F4-6855          TCGA-F4-6856          TCGA-G4-6293 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-G4-6299          TCGA-G4-6303          TCGA-G4-6304 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-G4-6306          TCGA-G4-6307          TCGA-G4-6309 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-G4-6310          TCGA-G4-6315          TCGA-G4-6317 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-G4-6321          TCGA-G4-6323          TCGA-G4-6586 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-G4-6588          TCGA-G4-6625          TCGA-G4-6626 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
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"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
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"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
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"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
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"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AG-3580          TCGA-AG-3581          TCGA-AG-3582 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AG-3583          TCGA-AG-3584          TCGA-AG-3586 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AG-3587          TCGA-AG-3593          TCGA-AG-3594 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AG-3598          TCGA-AG-3599          TCGA-AG-3600 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AG-3601          TCGA-AG-3602          TCGA-AG-3605 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AG-3608          TCGA-AG-3609          TCGA-AG-3611 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AG-3612          TCGA-AG-3726          TCGA-AG-3727 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AG-3731          TCGA-AG-3732          TCGA-AG-3742 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AG-3878          TCGA-AG-3882          TCGA-AG-3883 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AG-3885          TCGA-AG-3887          TCGA-AG-3890 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AG-3892          TCGA-AG-3893          TCGA-AG-3894 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AG-3896          TCGA-AG-3898          TCGA-AG-3901 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AG-3902          TCGA-AG-3909          TCGA-AG-3999 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AG-4001          TCGA-AG-4005          TCGA-AG-4007 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AG-4008          TCGA-AG-4015          TCGA-AG-A002 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AG-A008          TCGA-AG-A00C          TCGA-AG-A00H 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AG-A00Y          TCGA-AG-A011          TCGA-AG-A014 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AG-A015          TCGA-AG-A016          TCGA-AG-A01L 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AG-A01W          TCGA-AG-A01Y          TCGA-AG-A020 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AG-A025          TCGA-AG-A026          TCGA-AG-A02G 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AG-A02N          TCGA-AG-A02X          TCGA-AG-A032 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-AG-A036          TCGA-AH-6549          TCGA-AH-6643 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-CL-5917          TCGA-CL-5918          TCGA-DC-5337 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-DC-5869          TCGA-DC-6155          TCGA-DC-6157 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-DC-6158          TCGA-DC-6160          TCGA-DC-6681 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-DC-6682          TCGA-DC-6683          TCGA-DT-5265 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-EF-5830          TCGA-EI-6506          TCGA-EI-6507 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-EI-6508          TCGA-EI-6510          TCGA-F5-6464 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-F5-6465          TCGA-F5-6571          TCGA-F5-6702 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-F5-6812          TCGA-F5-6813          TCGA-G5-6235 
"C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" "C14ORF180 WILD-TYPE" 
         TCGA-G5-6641 
"C14ORF180 WILD-TYPE" 
D1868V12, continuous
                     vv
clus                  AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C14ORF180 MUTATED                                  0     0
  C14ORF180 WILD-TYPE                                1    11
                     vv
clus                  BLACK OR AFRICAN AMERICAN WHITE
  C14ORF180 MUTATED                           0     4
  C14ORF180 WILD-TYPE                        22   222
D1868V13, multiclass
                                  clus
vv                                 C14ORF180 MUTATED C14ORF180 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                 0                   1
  ASIAN                                            0                  11
  BLACK OR AFRICAN AMERICAN                        0                  22
  WHITE                                            4                 222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1869) Variable = USP14 MUTATION ANALYSIS
D1869V1, survival
                 sevent
clus2               0   1
  USP14 MUTATED     6   1
  USP14 WILD-TYPE 372  92
  USP14 MUTATED USP14 WILD-TYPE 
              7             464 
  USP14 MUTATED USP14 WILD-TYPE 
              1              92 
$`USP14 MUTATED`
TCGA-AA-3510 TCGA-AA-A01R TCGA-CK-5916 TCGA-CK-6747 TCGA-CM-4743 TCGA-CM-6674 
       63.98        35.01        21.14        82.95        23.05        12.95 
TCGA-AF-2687 
       24.13 

$`USP14 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S 
       12.00        31.00        31.00        38.07         1.02         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6748 
       85.45        15.62        49.08        51.32         9.99         1.91 
TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
      124.27        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       15.02        14.04        11.01        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  USP14 MUTATED USP14 WILD-TYPE 
          12.95            0.00 
  USP14 MUTATED USP14 WILD-TYPE 
          82.95          148.01 
  USP14 MUTATED USP14 WILD-TYPE 
         24.130          20.035 
[1] "12.9 - 83.0 (24.1)" "0.0 - 148.0 (20.0)"
[1] "hr=" "2"  
D1869V2, continuous
D1869V3, binary
                 cls
clus                0   1
  USP14 MUTATED     6   1
  USP14 WILD-TYPE 360 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP14 MUTATED      6    1
  USP14 WILD-TYPE  360  118
        clus
vv       USP14 MUTATED USP14 WILD-TYPE
  COLON              6             360
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  USP14 MUTATED         1        0        1         3         0         0
  USP14 WILD-TYPE      90        1       31       135        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  USP14 MUTATED           1          0          0          1        0         0
  USP14 WILD-TYPE        23         11         59         41       48        18
                 vv
clus              STAGE IVB
  USP14 MUTATED           0
  USP14 WILD-TYPE         1
D1869V4, multiclass
            clus
vv           USP14 MUTATED USP14 WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              3             135
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             1              41
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  USP14 MUTATED     1   0   6   0
  USP14 WILD-TYPE  16  92 323  50
D1869V5, multiclass
    clus
vv   USP14 MUTATED USP14 WILD-TYPE
  T1             1              16
  T2             0              92
  T3             6             323
  T4             0              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  USP14 MUTATED     5   0   2
  USP14 WILD-TYPE 282 113  85
D1869V6, multiclass
    clus
vv   USP14 MUTATED USP14 WILD-TYPE
  N0             5             282
  N1             0             113
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1869V7, binary
                 cls
clus                0   1
  USP14 MUTATED     6   0
  USP14 WILD-TYPE 369  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP14 MUTATED      6    0
  USP14 WILD-TYPE  369   65
   clus
vv  USP14 MUTATED USP14 WILD-TYPE
  0             6             369
  1             0              65
[1] 2 2
[1] FALSE
D1869V8, binary
                 cls
clus                0   1
  USP14 MUTATED     2   5
  USP14 WILD-TYPE 223 259
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP14 MUTATED      2    5
  USP14 WILD-TYPE  223  259
        clus
vv       USP14 MUTATED USP14 WILD-TYPE
  FEMALE             2             223
  MALE               5             259
[1] 2 2
[1] FALSE
D1869V9, binary
                 cls
clus                0   1
  USP14 MUTATED     5   2
  USP14 WILD-TYPE 345  20
[1] "tbl2"
                 cls
clus              [,1] [,2]
  USP14 MUTATED      5    2
  USP14 WILD-TYPE  345   20
     clus
vv    USP14 MUTATED USP14 WILD-TYPE
  NO              5             345
  YES             2              20
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  USP14 MUTATED                      5                             1
  USP14 WILD-TYPE                  310                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  USP14 MUTATED                       1                              0
  USP14 WILD-TYPE                   105                             10
D1869V10, multiclass
                                clus
vv                               USP14 MUTATED USP14 WILD-TYPE
  COLON ADENOCARCINOMA                       5             310
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  USP14 MUTATED     5   0   0   2
  USP14 WILD-TYPE 340   4  31  23
D1869V11, multiclass
    clus
vv   USP14 MUTATED USP14 WILD-TYPE
  R0             5             340
  R1             0               4
  R2             0              31
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1869V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  USP14 MUTATED                                  0     0
  USP14 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  USP14 MUTATED                           0     5
  USP14 WILD-TYPE                        22   221
D1869V13, multiclass
                                  clus
vv                                 USP14 MUTATED USP14 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        5             221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1870) Variable = TMEM144 MUTATION ANALYSIS
D1870V1, survival
                   sevent
clus2                 0   1
  TMEM144 MUTATED     7   1
  TMEM144 WILD-TYPE 371  92
  TMEM144 MUTATED TMEM144 WILD-TYPE 
                8               463 
  TMEM144 MUTATED TMEM144 WILD-TYPE 
                1                92 
$`TMEM144 MUTATED`
TCGA-A6-2672 TCGA-A6-6653 TCGA-A6-6781 TCGA-AA-3976 TCGA-AY-6197 TCGA-F4-6570 
       46.65        24.39        19.66        26.01        21.44         6.18 
TCGA-AG-3892 TCGA-AG-A002 
       13.02        20.98 

$`TMEM144 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 
       25.18        24.16        21.76        24.69        23.87        20.12 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       34.06        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 
       14.50        27.09        16.31         0.95        33.01        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
        8.61        31.96        35.74        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       36.95        17.03        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  TMEM144 MUTATED TMEM144 WILD-TYPE 
             6.18              0.00 
  TMEM144 MUTATED TMEM144 WILD-TYPE 
            46.65            148.01 
  TMEM144 MUTATED TMEM144 WILD-TYPE 
            21.21             20.12 
[1] "6.2 - 46.6 (21.2)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.4"
D1870V2, continuous
D1870V3, binary
                   cls
clus                  0   1
  TMEM144 MUTATED     6   2
  TMEM144 WILD-TYPE 360 117
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM144 MUTATED      6    2
  TMEM144 WILD-TYPE  360  117
        clus
vv       TMEM144 MUTATED TMEM144 WILD-TYPE
  COLON                6               360
  RECTUM               2               117
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TMEM144 MUTATED         3        0        0         2         0         0
  TMEM144 WILD-TYPE      88        1       32       136        10         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TMEM144 MUTATED           0          1          1          1        0
  TMEM144 WILD-TYPE        24         10         58         41       48
                   vv
clus                STAGE IVA STAGE IVB
  TMEM144 MUTATED           0         0
  TMEM144 WILD-TYPE        18         1
D1870V4, multiclass
            clus
vv           TMEM144 MUTATED TMEM144 WILD-TYPE
  STAGE I                  3                88
  STAGE IA                 0                 1
  STAGE II                 0                32
  STAGE IIA                2               136
  STAGE IIB                0                10
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               1                10
  STAGE IIIB               1                58
  STAGE IIIC               1                41
  STAGE IV                 0                48
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  TMEM144 MUTATED     1   3   3   1
  TMEM144 WILD-TYPE  16  89 326  49
D1870V5, multiclass
    clus
vv   TMEM144 MUTATED TMEM144 WILD-TYPE
  T1               1                16
  T2               3                89
  T3               3               326
  T4               1                49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  TMEM144 MUTATED     5   3   0
  TMEM144 WILD-TYPE 282 110  87
D1870V6, multiclass
    clus
vv   TMEM144 MUTATED TMEM144 WILD-TYPE
  N0               5               282
  N1               3               110
  N2               0                87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1870V7, binary
                   cls
clus                  0   1
  TMEM144 MUTATED     6   0
  TMEM144 WILD-TYPE 369  65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM144 MUTATED      6    0
  TMEM144 WILD-TYPE  369   65
   clus
vv  TMEM144 MUTATED TMEM144 WILD-TYPE
  0               6               369
  1               0                65
[1] 2 2
[1] FALSE
D1870V8, binary
                   cls
clus                  0   1
  TMEM144 MUTATED     3   5
  TMEM144 WILD-TYPE 222 259
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM144 MUTATED      3    5
  TMEM144 WILD-TYPE  222  259
        clus
vv       TMEM144 MUTATED TMEM144 WILD-TYPE
  FEMALE               3               222
  MALE                 5               259
[1] 2 2
[1] FALSE
D1870V9, binary
                   cls
clus                  0   1
  TMEM144 MUTATED     8   0
  TMEM144 WILD-TYPE 342  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM144 MUTATED      8    0
  TMEM144 WILD-TYPE  342   22
     clus
vv    TMEM144 MUTATED TMEM144 WILD-TYPE
  NO                8               342
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  TMEM144 MUTATED                      5                             1
  TMEM144 WILD-TYPE                  310                            46
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  TMEM144 MUTATED                       2                              0
  TMEM144 WILD-TYPE                   104                             10
D1870V10, multiclass
                                clus
vv                               TMEM144 MUTATED TMEM144 WILD-TYPE
  COLON ADENOCARCINOMA                         5               310
  COLON MUCINOUS ADENOCARCINOMA                1                46
  RECTAL ADENOCARCINOMA                        2               104
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  TMEM144 MUTATED     7   0   0   0
  TMEM144 WILD-TYPE 338   4  31  25
D1870V11, multiclass
    clus
vv   TMEM144 MUTATED TMEM144 WILD-TYPE
  R0               7               338
  R1               0                 4
  R2               0                31
  RX               0                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1870V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TMEM144 MUTATED                                  0     0
  TMEM144 WILD-TYPE                                1    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  TMEM144 MUTATED                           0     5
  TMEM144 WILD-TYPE                        22   221
D1870V13, multiclass
                                  clus
vv                                 TMEM144 MUTATED TMEM144 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                      0                22
  WHITE                                          5               221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1871) Variable = PIAS2 MUTATION ANALYSIS
D1871V1, survival
                 sevent
clus2               0   1
  PIAS2 MUTATED     3   1
  PIAS2 WILD-TYPE 375  92
  PIAS2 MUTATED PIAS2 WILD-TYPE 
              4             467 
  PIAS2 MUTATED PIAS2 WILD-TYPE 
              1              92 
$`PIAS2 MUTATED`
TCGA-AA-3555 TCGA-CA-6718 TCGA-CM-5860 TCGA-AG-A002 
       29.95        10.06        32.02        20.98 

$`PIAS2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 
       21.01        13.02        24.00        17.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07        12.20        12.76        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  PIAS2 MUTATED PIAS2 WILD-TYPE 
          10.06            0.00 
  PIAS2 MUTATED PIAS2 WILD-TYPE 
          32.02          148.01 
  PIAS2 MUTATED PIAS2 WILD-TYPE 
         25.465          20.120 
[1] "10.1 - 32.0 (25.5)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.6"
D1871V2, continuous
D1871V3, binary
                 cls
clus                0   1
  PIAS2 MUTATED     4   1
  PIAS2 WILD-TYPE 362 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PIAS2 MUTATED      4    1
  PIAS2 WILD-TYPE  362  118
        clus
vv       PIAS2 MUTATED PIAS2 WILD-TYPE
  COLON              4             362
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PIAS2 MUTATED         1        0        0         4         0         0
  PIAS2 WILD-TYPE      90        1       32       134        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PIAS2 MUTATED           0          0          0          0        0         0
  PIAS2 WILD-TYPE        24         11         59         42       48        18
                 vv
clus              STAGE IVB
  PIAS2 MUTATED           0
  PIAS2 WILD-TYPE         1
D1871V4, multiclass
            clus
vv           PIAS2 MUTATED PIAS2 WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              4             134
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PIAS2 MUTATED     0   1   4   0
  PIAS2 WILD-TYPE  17  91 325  50
D1871V5, multiclass
    clus
vv   PIAS2 MUTATED PIAS2 WILD-TYPE
  T1             0              17
  T2             1              91
  T3             4             325
  T4             0              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  PIAS2 MUTATED     5   0   0
  PIAS2 WILD-TYPE 282 113  87
D1871V6, multiclass
    clus
vv   PIAS2 MUTATED PIAS2 WILD-TYPE
  N0             5             282
  N1             0             113
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1871V7, binary
                 cls
clus                0   1
  PIAS2 MUTATED     5   0
  PIAS2 WILD-TYPE 370  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PIAS2 MUTATED      5    0
  PIAS2 WILD-TYPE  370   65
   clus
vv  PIAS2 MUTATED PIAS2 WILD-TYPE
  0             5             370
  1             0              65
[1] 2 2
[1] FALSE
D1871V8, binary
                 cls
clus                0   1
  PIAS2 MUTATED     2   3
  PIAS2 WILD-TYPE 223 261
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PIAS2 MUTATED      2    3
  PIAS2 WILD-TYPE  223  261
        clus
vv       PIAS2 MUTATED PIAS2 WILD-TYPE
  FEMALE             2             223
  MALE               3             261
[1] 2 2
[1] FALSE
D1871V9, binary
                 cls
clus                0   1
  PIAS2 MUTATED     4   0
  PIAS2 WILD-TYPE 346  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PIAS2 MUTATED      4    0
  PIAS2 WILD-TYPE  346   22
     clus
vv    PIAS2 MUTATED PIAS2 WILD-TYPE
  NO              4             346
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PIAS2 MUTATED                      3                             1
  PIAS2 WILD-TYPE                  312                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PIAS2 MUTATED                       1                              0
  PIAS2 WILD-TYPE                   105                             10
D1871V10, multiclass
                                clus
vv                               PIAS2 MUTATED PIAS2 WILD-TYPE
  COLON ADENOCARCINOMA                       3             312
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  PIAS2 MUTATED     4   0   0   1
  PIAS2 WILD-TYPE 341   4  31  24
D1871V11, multiclass
    clus
vv   PIAS2 MUTATED PIAS2 WILD-TYPE
  R0             4             341
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1871V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PIAS2 MUTATED                                  0     1
  PIAS2 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PIAS2 MUTATED                           0     1
  PIAS2 WILD-TYPE                        22   225
D1871V13, multiclass
[1] "Remove cluster labels:" "PIAS2 MUTATED"         
clus
  PIAS2 MUTATED PIAS2 WILD-TYPE 
              2             258 
     TCGA-A6-2671      TCGA-A6-2672      TCGA-A6-2674      TCGA-A6-2676 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-A6-2677      TCGA-A6-2678      TCGA-A6-2683      TCGA-A6-3807 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-A6-3808      TCGA-A6-3809      TCGA-A6-3810      TCGA-A6-4105 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-A6-5656      TCGA-A6-5657      TCGA-A6-5659      TCGA-A6-5660 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-A6-5661      TCGA-A6-5662      TCGA-A6-5664      TCGA-A6-5665 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-A6-5666      TCGA-A6-6137      TCGA-A6-6138      TCGA-A6-6141 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-A6-6142      TCGA-A6-6648      TCGA-A6-6649      TCGA-A6-6651 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-A6-6652      TCGA-A6-6653      TCGA-A6-6654      TCGA-A6-6780 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-A6-6781      TCGA-A6-6782      TCGA-AD-5900      TCGA-AD-6548 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-AD-6888      TCGA-AD-6889      TCGA-AD-6890      TCGA-AD-6895 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-AD-6899      TCGA-AD-6901      TCGA-AD-6963      TCGA-AD-6964 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-AD-6965      TCGA-AU-3779      TCGA-AU-6004      TCGA-AY-4070 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-AY-4071      TCGA-AY-5543      TCGA-AY-6196      TCGA-AY-6197 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-AY-6386      TCGA-AZ-4315      TCGA-AZ-4323      TCGA-AZ-4616 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-AZ-4681      TCGA-AZ-4682      TCGA-AZ-5403      TCGA-AZ-5407 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-AZ-6598      TCGA-AZ-6599      TCGA-AZ-6600      TCGA-AZ-6601 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-AZ-6603      TCGA-AZ-6605      TCGA-AZ-6606      TCGA-AZ-6607 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-AZ-6608      TCGA-CA-5254      TCGA-CA-5255      TCGA-CA-5796 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-CA-5797      TCGA-CA-6715      TCGA-CA-6716      TCGA-CA-6717 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-CA-6719      TCGA-CK-4947      TCGA-CK-4948      TCGA-CK-4950 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-CK-4952      TCGA-CK-5912      TCGA-CK-5913      TCGA-CK-5914 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-CK-5915      TCGA-CK-5916      TCGA-CK-6746      TCGA-CK-6747 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-CK-6748      TCGA-CK-6751      TCGA-CM-4743      TCGA-CM-4744 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-CM-4746      TCGA-CM-4747      TCGA-CM-4752      TCGA-CM-5341 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-CM-5344      TCGA-CM-5348      TCGA-CM-5349      TCGA-CM-5861 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-CM-5862      TCGA-CM-5863      TCGA-CM-5864      TCGA-CM-5868 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-CM-6161      TCGA-CM-6162      TCGA-CM-6163      TCGA-CM-6164 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-CM-6165      TCGA-CM-6166      TCGA-CM-6167      TCGA-CM-6168 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-CM-6169      TCGA-CM-6170      TCGA-CM-6171      TCGA-CM-6172 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-CM-6674      TCGA-CM-6675      TCGA-CM-6676      TCGA-CM-6677 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-CM-6678      TCGA-CM-6679      TCGA-CM-6680      TCGA-D5-5537 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-D5-5538      TCGA-D5-5539      TCGA-D5-5540      TCGA-D5-5541 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-D5-6529      TCGA-D5-6532      TCGA-D5-6533      TCGA-D5-6534 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-D5-6535      TCGA-D5-6536      TCGA-D5-6537      TCGA-D5-6538 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-D5-6539      TCGA-D5-6540      TCGA-D5-6541      TCGA-D5-6898 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-D5-6920      TCGA-D5-6922      TCGA-D5-6923      TCGA-D5-6924 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-D5-6926      TCGA-D5-6927      TCGA-D5-6928      TCGA-D5-6929 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-D5-6930      TCGA-D5-6931      TCGA-D5-6932      TCGA-D5-7000 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-DM-A0X9      TCGA-DM-A0XD      TCGA-DM-A0XF      TCGA-DM-A1D0 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-DM-A1D4      TCGA-DM-A1D6      TCGA-DM-A1D7      TCGA-DM-A1D8 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-DM-A1D9      TCGA-DM-A1DA      TCGA-DM-A1DB      TCGA-DM-A1HA 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-DM-A1HB      TCGA-DM-A282      TCGA-DM-A285      TCGA-DM-A28C 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-DM-A28E      TCGA-DM-A28F      TCGA-DM-A28G      TCGA-DM-A28H 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-DM-A28K      TCGA-F4-6459      TCGA-F4-6460      TCGA-F4-6569 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-F4-6570      TCGA-F4-6703      TCGA-F4-6704      TCGA-F4-6805 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-F4-6806      TCGA-F4-6807      TCGA-F4-6808      TCGA-F4-6809 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-F4-6854      TCGA-F4-6855      TCGA-F4-6856      TCGA-G4-6293 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-G4-6299      TCGA-G4-6303      TCGA-G4-6304      TCGA-G4-6306 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-G4-6307      TCGA-G4-6309      TCGA-G4-6310      TCGA-G4-6315 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-G4-6317      TCGA-G4-6321      TCGA-G4-6323      TCGA-G4-6586 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-G4-6588      TCGA-G4-6625      TCGA-G4-6626      TCGA-G4-6628 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-AF-2687      TCGA-AF-2689      TCGA-AF-2691      TCGA-AF-2692 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-AF-2693      TCGA-AF-3400      TCGA-AF-3913      TCGA-AF-4110 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-AF-5654      TCGA-AF-6136      TCGA-AF-6655      TCGA-AF-6672 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-AH-6544      TCGA-AH-6547      TCGA-AH-6549      TCGA-AH-6643 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-AH-6644      TCGA-CI-6619      TCGA-CI-6620      TCGA-CI-6621 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-CI-6622      TCGA-CI-6624      TCGA-CL-5917      TCGA-CL-5918 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-DC-5337      TCGA-DC-5869      TCGA-DC-6155      TCGA-DC-6157 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-DC-6158      TCGA-DC-6160      TCGA-DC-6681      TCGA-DC-6682 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-DC-6683      TCGA-DT-5265      TCGA-DY-A0XA      TCGA-DY-A1DC 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-DY-A1DD      TCGA-DY-A1DF      TCGA-DY-A1DG      TCGA-DY-A1H8 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-EF-5830      TCGA-EI-6506      TCGA-EI-6507      TCGA-EI-6508 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-EI-6510      TCGA-F5-6464      TCGA-F5-6465      TCGA-F5-6571 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-F5-6702      TCGA-F5-6811      TCGA-F5-6812      TCGA-F5-6813 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 
     TCGA-G5-6235      TCGA-G5-6641 
"PIAS2 WILD-TYPE" "PIAS2 WILD-TYPE" 

Clustering(1872) Variable = HIST4H4 MUTATION ANALYSIS
D1872V1, survival
                   sevent
clus2                 0   1
  HIST4H4 MUTATED     3   0
  HIST4H4 WILD-TYPE 375  93
  HIST4H4 MUTATED HIST4H4 WILD-TYPE 
                3               468 
  HIST4H4 MUTATED HIST4H4 WILD-TYPE 
                0                93 
$`HIST4H4 MUTATED`
TCGA-AA-3713 TCGA-AY-5543 TCGA-CK-4950 
       19.04        33.01        85.45 

$`HIST4H4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  HIST4H4 MUTATED HIST4H4 WILD-TYPE 
            19.04              0.00 
  HIST4H4 MUTATED HIST4H4 WILD-TYPE 
            85.45            148.01 
  HIST4H4 MUTATED HIST4H4 WILD-TYPE 
           33.010            20.155 
[1] "19.0 - 85.5 (33.0)" "0.0 - 148.0 (20.2)"
[1] "hr="     "9100000"
D1872V2, continuous
D1872V3, binary
                   cls
clus                  0   1
  HIST4H4 MUTATED     3   0
  HIST4H4 WILD-TYPE 363 119
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HIST4H4 MUTATED      3    0
  HIST4H4 WILD-TYPE  363  119
        clus
vv       HIST4H4 MUTATED HIST4H4 WILD-TYPE
  COLON                3               363
  RECTUM               0               119
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  HIST4H4 MUTATED         0        0        0         0         0         0
  HIST4H4 WILD-TYPE      91        1       32       138        10         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HIST4H4 MUTATED           0          0          1          0        1
  HIST4H4 WILD-TYPE        24         11         58         42       47
                   vv
clus                STAGE IVA STAGE IVB
  HIST4H4 MUTATED           1         0
  HIST4H4 WILD-TYPE        17         1
D1872V4, multiclass
            clus
vv           HIST4H4 MUTATED HIST4H4 WILD-TYPE
  STAGE I                  0                91
  STAGE IA                 0                 1
  STAGE II                 0                32
  STAGE IIA                0               138
  STAGE IIB                0                10
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               0                11
  STAGE IIIB               1                58
  STAGE IIIC               0                42
  STAGE IV                 1                47
  STAGE IVA                1                17
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  HIST4H4 MUTATED     0   0   3   0
  HIST4H4 WILD-TYPE  17  92 326  50
D1872V5, multiclass
    clus
vv   HIST4H4 MUTATED HIST4H4 WILD-TYPE
  T1               0                17
  T2               0                92
  T3               3               326
  T4               0                50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  HIST4H4 MUTATED     1   2   0
  HIST4H4 WILD-TYPE 286 111  87
D1872V6, multiclass
    clus
vv   HIST4H4 MUTATED HIST4H4 WILD-TYPE
  N0               1               286
  N1               2               111
  N2               0                87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1872V7, binary
                   cls
clus                  0   1
  HIST4H4 MUTATED     1   2
  HIST4H4 WILD-TYPE 374  63
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HIST4H4 MUTATED      1    2
  HIST4H4 WILD-TYPE  374   63
   clus
vv  HIST4H4 MUTATED HIST4H4 WILD-TYPE
  0               1               374
  1               2                63
[1] 2 2
[1] FALSE
D1872V8, binary
                   cls
clus                  0   1
  HIST4H4 MUTATED     2   1
  HIST4H4 WILD-TYPE 223 263
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HIST4H4 MUTATED      2    1
  HIST4H4 WILD-TYPE  223  263
        clus
vv       HIST4H4 MUTATED HIST4H4 WILD-TYPE
  FEMALE               2               223
  MALE                 1               263
[1] 2 2
[1] FALSE
D1872V9, binary
                   cls
clus                  0   1
  HIST4H4 MUTATED     2   1
  HIST4H4 WILD-TYPE 348  21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  HIST4H4 MUTATED      2    1
  HIST4H4 WILD-TYPE  348   21
     clus
vv    HIST4H4 MUTATED HIST4H4 WILD-TYPE
  NO                2               348
  YES               1                21
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  HIST4H4 MUTATED                      3                             0
  HIST4H4 WILD-TYPE                  312                            47
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  HIST4H4 MUTATED                       0                              0
  HIST4H4 WILD-TYPE                   106                             10
D1872V10, multiclass
                                clus
vv                               HIST4H4 MUTATED HIST4H4 WILD-TYPE
  COLON ADENOCARCINOMA                         3               312
  COLON MUCINOUS ADENOCARCINOMA                0                47
  RECTAL ADENOCARCINOMA                        0               106
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  HIST4H4 MUTATED     1   1   1   0
  HIST4H4 WILD-TYPE 344   3  30  25
D1872V11, multiclass
    clus
vv   HIST4H4 MUTATED HIST4H4 WILD-TYPE
  R0               1               344
  R1               1                 3
  R2               1                30
  RX               0                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1872V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HIST4H4 MUTATED                                  0     0
  HIST4H4 WILD-TYPE                                1    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  HIST4H4 MUTATED                           2     0
  HIST4H4 WILD-TYPE                        20   226
D1872V13, multiclass
[1] "Remove cluster labels:" "HIST4H4 MUTATED"       
clus
  HIST4H4 MUTATED HIST4H4 WILD-TYPE 
                2               258 
       TCGA-A6-2671        TCGA-A6-2672        TCGA-A6-2674        TCGA-A6-2676 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-A6-2677        TCGA-A6-2678        TCGA-A6-2683        TCGA-A6-3807 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-A6-3808        TCGA-A6-3809        TCGA-A6-3810        TCGA-A6-4105 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-A6-5656        TCGA-A6-5657        TCGA-A6-5659        TCGA-A6-5660 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-A6-5661        TCGA-A6-5662        TCGA-A6-5664        TCGA-A6-5665 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-A6-5666        TCGA-A6-6137        TCGA-A6-6138        TCGA-A6-6141 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-A6-6142        TCGA-A6-6648        TCGA-A6-6649        TCGA-A6-6651 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-A6-6652        TCGA-A6-6653        TCGA-A6-6654        TCGA-A6-6780 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-A6-6781        TCGA-A6-6782        TCGA-AD-5900        TCGA-AD-6548 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-AD-6888        TCGA-AD-6889        TCGA-AD-6890        TCGA-AD-6895 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-AD-6899        TCGA-AD-6901        TCGA-AD-6963        TCGA-AD-6964 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-AD-6965        TCGA-AU-3779        TCGA-AU-6004        TCGA-AY-4070 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-AY-4071        TCGA-AY-6196        TCGA-AY-6197        TCGA-AY-6386 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-AZ-4315        TCGA-AZ-4323        TCGA-AZ-4616        TCGA-AZ-4681 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-AZ-4682        TCGA-AZ-5403        TCGA-AZ-5407        TCGA-AZ-6598 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-AZ-6599        TCGA-AZ-6600        TCGA-AZ-6601        TCGA-AZ-6603 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-AZ-6605        TCGA-AZ-6606        TCGA-AZ-6607        TCGA-AZ-6608 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-CA-5254        TCGA-CA-5255        TCGA-CA-5796        TCGA-CA-5797 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-CA-6715        TCGA-CA-6716        TCGA-CA-6717        TCGA-CA-6718 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-CA-6719        TCGA-CK-4947        TCGA-CK-4948        TCGA-CK-4952 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-CK-5912        TCGA-CK-5913        TCGA-CK-5914        TCGA-CK-5915 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-CK-5916        TCGA-CK-6746        TCGA-CK-6747        TCGA-CK-6748 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-CK-6751        TCGA-CM-4743        TCGA-CM-4744        TCGA-CM-4746 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-CM-4747        TCGA-CM-4752        TCGA-CM-5341        TCGA-CM-5344 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-CM-5348        TCGA-CM-5349        TCGA-CM-5860        TCGA-CM-5861 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-CM-5862        TCGA-CM-5863        TCGA-CM-5864        TCGA-CM-5868 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-CM-6161        TCGA-CM-6162        TCGA-CM-6163        TCGA-CM-6164 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-CM-6165        TCGA-CM-6166        TCGA-CM-6167        TCGA-CM-6168 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-CM-6169        TCGA-CM-6170        TCGA-CM-6171        TCGA-CM-6172 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-CM-6674        TCGA-CM-6675        TCGA-CM-6676        TCGA-CM-6677 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-CM-6678        TCGA-CM-6679        TCGA-CM-6680        TCGA-D5-5537 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-D5-5538        TCGA-D5-5539        TCGA-D5-5540        TCGA-D5-5541 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-D5-6529        TCGA-D5-6532        TCGA-D5-6533        TCGA-D5-6534 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-D5-6535        TCGA-D5-6536        TCGA-D5-6537        TCGA-D5-6538 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-D5-6539        TCGA-D5-6540        TCGA-D5-6541        TCGA-D5-6898 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-D5-6920        TCGA-D5-6922        TCGA-D5-6923        TCGA-D5-6924 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-D5-6926        TCGA-D5-6927        TCGA-D5-6928        TCGA-D5-6929 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-D5-6930        TCGA-D5-6931        TCGA-D5-6932        TCGA-D5-7000 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-DM-A0X9        TCGA-DM-A0XD        TCGA-DM-A0XF        TCGA-DM-A1D0 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-DM-A1D4        TCGA-DM-A1D6        TCGA-DM-A1D7        TCGA-DM-A1D8 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-DM-A1D9        TCGA-DM-A1DA        TCGA-DM-A1DB        TCGA-DM-A1HA 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-DM-A1HB        TCGA-DM-A282        TCGA-DM-A285        TCGA-DM-A28C 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-DM-A28E        TCGA-DM-A28F        TCGA-DM-A28G        TCGA-DM-A28H 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-DM-A28K        TCGA-F4-6459        TCGA-F4-6460        TCGA-F4-6569 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-F4-6570        TCGA-F4-6703        TCGA-F4-6704        TCGA-F4-6805 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-F4-6806        TCGA-F4-6807        TCGA-F4-6808        TCGA-F4-6809 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-F4-6854        TCGA-F4-6855        TCGA-F4-6856        TCGA-G4-6293 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-G4-6299        TCGA-G4-6303        TCGA-G4-6304        TCGA-G4-6306 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-G4-6307        TCGA-G4-6309        TCGA-G4-6310        TCGA-G4-6315 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-G4-6317        TCGA-G4-6321        TCGA-G4-6323        TCGA-G4-6586 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-G4-6588        TCGA-G4-6625        TCGA-G4-6626        TCGA-G4-6628 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2691        TCGA-AF-2692 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3913        TCGA-AF-4110 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-AF-5654        TCGA-AF-6136        TCGA-AF-6655        TCGA-AF-6672 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6549        TCGA-AH-6643 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-AH-6644        TCGA-CI-6619        TCGA-CI-6620        TCGA-CI-6621 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-CI-6622        TCGA-CI-6624        TCGA-CL-5917        TCGA-CL-5918 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6155        TCGA-DC-6157 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-DC-6158        TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-DC-6683        TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-DY-A1DD        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-EF-5830        TCGA-EI-6506        TCGA-EI-6507        TCGA-EI-6508 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-EI-6510        TCGA-F5-6464        TCGA-F5-6465        TCGA-F5-6571 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-F5-6702        TCGA-F5-6811        TCGA-F5-6812        TCGA-F5-6813 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 
       TCGA-G5-6235        TCGA-G5-6641 
"HIST4H4 WILD-TYPE" "HIST4H4 WILD-TYPE" 

Clustering(1873) Variable = ASTE1 MUTATION ANALYSIS
D1873V1, survival
                 sevent
clus2               0   1
  ASTE1 MUTATED     7   3
  ASTE1 WILD-TYPE 371  90
  ASTE1 MUTATED ASTE1 WILD-TYPE 
             10             461 
  ASTE1 MUTATED ASTE1 WILD-TYPE 
              3              90 
$`ASTE1 MUTATED`
TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3821 TCGA-AA-A00J TCGA-AZ-6598 TCGA-CK-5914 
       19.04        10.06         1.02        18.05        49.41         9.99 
TCGA-CK-5916 TCGA-D5-6930 TCGA-AG-3892 TCGA-AG-A002 
       21.14         1.51        13.02        20.98 

$`ASTE1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 
       35.05        33.04         0.99        25.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        88.21         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       51.32        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
        9.44        11.64         4.80        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  ASTE1 MUTATED ASTE1 WILD-TYPE 
           1.02            0.00 
  ASTE1 MUTATED ASTE1 WILD-TYPE 
          49.41          148.01 
  ASTE1 MUTATED ASTE1 WILD-TYPE 
         15.535          20.550 
[1] "1.0 - 49.4 (15.5)"  "0.0 - 148.0 (20.6)"
[1] "hr=" "2.3"
D1873V2, continuous
D1873V3, binary
                 cls
clus                0   1
  ASTE1 MUTATED     8   2
  ASTE1 WILD-TYPE 358 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASTE1 MUTATED      8    2
  ASTE1 WILD-TYPE  358  117
        clus
vv       ASTE1 MUTATED ASTE1 WILD-TYPE
  COLON              8             358
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ASTE1 MUTATED         4        0        1         1         0         0
  ASTE1 WILD-TYPE      87        1       31       137        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ASTE1 MUTATED           1          0          2          0        1         0
  ASTE1 WILD-TYPE        23         11         57         42       47        18
                 vv
clus              STAGE IVB
  ASTE1 MUTATED           0
  ASTE1 WILD-TYPE         1
D1873V4, multiclass
            clus
vv           ASTE1 MUTATED ASTE1 WILD-TYPE
  STAGE I                4              87
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              1             137
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             2              57
  STAGE IIIC             0              42
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ASTE1 MUTATED     2   2   5   1
  ASTE1 WILD-TYPE  15  90 324  49
D1873V5, multiclass
    clus
vv   ASTE1 MUTATED ASTE1 WILD-TYPE
  T1             2              15
  T2             2              90
  T3             5             324
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  ASTE1 MUTATED     7   2   1
  ASTE1 WILD-TYPE 280 111  86
D1873V6, multiclass
    clus
vv   ASTE1 MUTATED ASTE1 WILD-TYPE
  N0             7             280
  N1             2             111
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1873V7, binary
                 cls
clus                0   1
  ASTE1 MUTATED     7   1
  ASTE1 WILD-TYPE 368  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASTE1 MUTATED      7    1
  ASTE1 WILD-TYPE  368   64
   clus
vv  ASTE1 MUTATED ASTE1 WILD-TYPE
  0             7             368
  1             1              64
[1] 2 2
[1] FALSE
D1873V8, binary
                 cls
clus                0   1
  ASTE1 MUTATED     5   5
  ASTE1 WILD-TYPE 220 259
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASTE1 MUTATED      5    5
  ASTE1 WILD-TYPE  220  259
        clus
vv       ASTE1 MUTATED ASTE1 WILD-TYPE
  FEMALE             5             220
  MALE               5             259
[1] 2 2
[1] FALSE
D1873V9, binary
                 cls
clus                0   1
  ASTE1 MUTATED     7   1
  ASTE1 WILD-TYPE 343  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASTE1 MUTATED      7    1
  ASTE1 WILD-TYPE  343   21
     clus
vv    ASTE1 MUTATED ASTE1 WILD-TYPE
  NO              7             343
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ASTE1 MUTATED                      5                             3
  ASTE1 WILD-TYPE                  310                            44
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ASTE1 MUTATED                       2                              0
  ASTE1 WILD-TYPE                   104                             10
D1873V10, multiclass
                                clus
vv                               ASTE1 MUTATED ASTE1 WILD-TYPE
  COLON ADENOCARCINOMA                       5             310
  COLON MUCINOUS ADENOCARCINOMA              3              44
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  ASTE1 MUTATED     6   0   1   2
  ASTE1 WILD-TYPE 339   4  30  23
D1873V11, multiclass
    clus
vv   ASTE1 MUTATED ASTE1 WILD-TYPE
  R0             6             339
  R1             0               4
  R2             1              30
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1873V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ASTE1 MUTATED                                  0     0
  ASTE1 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ASTE1 MUTATED                           0     4
  ASTE1 WILD-TYPE                        22   222
D1873V13, multiclass
                                  clus
vv                                 ASTE1 MUTATED ASTE1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        4             222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1874) Variable = FBXO38 MUTATION ANALYSIS
D1874V1, survival
                  sevent
clus2                0   1
  FBXO38 MUTATED    11   6
  FBXO38 WILD-TYPE 367  87
  FBXO38 MUTATED FBXO38 WILD-TYPE 
              17              454 
  FBXO38 MUTATED FBXO38 WILD-TYPE 
               6               87 
$`FBXO38 MUTATED`
TCGA-A6-5665 TCGA-A6-6781 TCGA-AA-3554 TCGA-AA-3666 TCGA-AA-3713 TCGA-AA-3811 
       22.06        19.66        17.95         2.01        19.04        10.06 
TCGA-AA-A00N TCGA-AD-6963 TCGA-AD-6964 TCGA-AZ-4315 TCGA-CA-6717 TCGA-CA-6718 
        4.01        27.42        10.88        58.39        12.76        10.06 
TCGA-CK-4952 TCGA-CK-5916 TCGA-CM-6168 TCGA-D5-6533 TCGA-DM-A28K 
       15.62        21.14        12.99         1.32        98.24 

$`FBXO38 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       24.00        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       26.99        19.04        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 
        3.06         3.25         3.29         0.07        12.20        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
       17.56       148.01        85.45        49.08        51.32         9.99 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       14.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       18.25        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  FBXO38 MUTATED FBXO38 WILD-TYPE 
            1.32             0.00 
  FBXO38 MUTATED FBXO38 WILD-TYPE 
           98.24           148.01 
  FBXO38 MUTATED FBXO38 WILD-TYPE 
          15.620           20.945 
[1] "1.3 - 98.2 (15.6)"  "0.0 - 148.0 (20.9)"
[1] "hr=" "2.2"
D1874V2, continuous
D1874V3, binary
                  cls
clus                 0   1
  FBXO38 MUTATED    18   0
  FBXO38 WILD-TYPE 348 119
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FBXO38 MUTATED     18    0
  FBXO38 WILD-TYPE  348  119
        clus
vv       FBXO38 MUTATED FBXO38 WILD-TYPE
  COLON              18              348
  RECTUM              0              119
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FBXO38 MUTATED         1        0        0         7         2         0
  FBXO38 WILD-TYPE      90        1       32       131         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FBXO38 MUTATED           2          0          1          2        1
  FBXO38 WILD-TYPE        22         11         58         40       47
                  vv
clus               STAGE IVA STAGE IVB
  FBXO38 MUTATED           0         0
  FBXO38 WILD-TYPE        18         1
D1874V4, multiclass
            clus
vv           FBXO38 MUTATED FBXO38 WILD-TYPE
  STAGE I                 1               90
  STAGE IA                0                1
  STAGE II                0               32
  STAGE IIA               7              131
  STAGE IIB               2                8
  STAGE IIC               0                1
  STAGE III               2               22
  STAGE IIIA              0               11
  STAGE IIIB              1               58
  STAGE IIIC              2               40
  STAGE IV                1               47
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  FBXO38 MUTATED     1   0  11   6
  FBXO38 WILD-TYPE  16  92 318  44
D1874V5, multiclass
    clus
vv   FBXO38 MUTATED FBXO38 WILD-TYPE
  T1              1               16
  T2              0               92
  T3             11              318
  T4              6               44
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  FBXO38 MUTATED    13   2   3
  FBXO38 WILD-TYPE 274 111  84
D1874V6, multiclass
    clus
vv   FBXO38 MUTATED FBXO38 WILD-TYPE
  N0             13              274
  N1              2              111
  N2              3               84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1874V7, binary
                  cls
clus                 0   1
  FBXO38 MUTATED    13   1
  FBXO38 WILD-TYPE 362  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FBXO38 MUTATED     13    1
  FBXO38 WILD-TYPE  362   64
   clus
vv  FBXO38 MUTATED FBXO38 WILD-TYPE
  0             13              362
  1              1               64
[1] 2 2
[1] FALSE
D1874V8, binary
                  cls
clus                 0   1
  FBXO38 MUTATED     8  10
  FBXO38 WILD-TYPE 217 254
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FBXO38 MUTATED      8   10
  FBXO38 WILD-TYPE  217  254
        clus
vv       FBXO38 MUTATED FBXO38 WILD-TYPE
  FEMALE              8              217
  MALE               10              254
[1] 2 2
[1] FALSE
D1874V9, binary
                  cls
clus                 0   1
  FBXO38 MUTATED    11   1
  FBXO38 WILD-TYPE 339  21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FBXO38 MUTATED     11    1
  FBXO38 WILD-TYPE  339   21
     clus
vv    FBXO38 MUTATED FBXO38 WILD-TYPE
  NO              11              339
  YES              1               21
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  FBXO38 MUTATED                     13                             5
  FBXO38 WILD-TYPE                  302                            42
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  FBXO38 MUTATED                       0                              0
  FBXO38 WILD-TYPE                   106                             10
D1874V10, multiclass
                                clus
vv                               FBXO38 MUTATED FBXO38 WILD-TYPE
  COLON ADENOCARCINOMA                       13              302
  COLON MUCINOUS ADENOCARCINOMA               5               42
  RECTAL ADENOCARCINOMA                       0              106
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  FBXO38 MUTATED     9   0   1   5
  FBXO38 WILD-TYPE 336   4  30  20
D1874V11, multiclass
    clus
vv   FBXO38 MUTATED FBXO38 WILD-TYPE
  R0              9              336
  R1              0                4
  R2              1               30
  RX              5               20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1874V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FBXO38 MUTATED                                  0     2
  FBXO38 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  FBXO38 MUTATED                           1    10
  FBXO38 WILD-TYPE                        21   216
D1874V13, multiclass
                                  clus
vv                                 FBXO38 MUTATED FBXO38 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                9
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                        10              216
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1875) Variable = HAP1 MUTATION ANALYSIS
D1875V1, survival
                sevent
clus2              0   1
  HAP1 MUTATED     5   3
  HAP1 WILD-TYPE 373  90
  HAP1 MUTATED HAP1 WILD-TYPE 
             8            463 
  HAP1 MUTATED HAP1 WILD-TYPE 
             3             90 
$`HAP1 MUTATED`
TCGA-A6-2676 TCGA-A6-6781 TCGA-AA-3531 TCGA-AA-A01Q TCGA-AD-6548 TCGA-AZ-6599 
       42.90        19.66        34.03         1.02        21.37         6.77 
TCGA-CM-5861 TCGA-AF-5654 
       15.02        16.83 

$`HAP1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
        0.00        19.07        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       31.00        38.07        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
       40.96         0.07        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       88.21        49.41        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       22.98        30.08        32.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       14.50        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  HAP1 MUTATED HAP1 WILD-TYPE 
          1.02           0.00 
  HAP1 MUTATED HAP1 WILD-TYPE 
         42.90         148.01 
  HAP1 MUTATED HAP1 WILD-TYPE 
        18.245         20.280 
[1] "1.0 - 42.9 (18.2)"  "0.0 - 148.0 (20.3)"
[1] "hr=" "2.6"
D1875V2, continuous
D1875V3, binary
                cls
clus               0   1
  HAP1 MUTATED     7   1
  HAP1 WILD-TYPE 359 118
[1] "tbl2"
                cls
clus             [,1] [,2]
  HAP1 MUTATED      7    1
  HAP1 WILD-TYPE  359  118
        clus
vv       HAP1 MUTATED HAP1 WILD-TYPE
  COLON             7            359
  RECTUM            1            118
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  HAP1 MUTATED         3        0        1         2         1         0
  HAP1 WILD-TYPE      88        1       31       136         9         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  HAP1 MUTATED           0          0          0          1        0         0
  HAP1 WILD-TYPE        24         11         59         41       48        18
                vv
clus             STAGE IVB
  HAP1 MUTATED           0
  HAP1 WILD-TYPE         1
D1875V4, multiclass
            clus
vv           HAP1 MUTATED HAP1 WILD-TYPE
  STAGE I               3             88
  STAGE IA              0              1
  STAGE II              1             31
  STAGE IIA             2            136
  STAGE IIB             1              9
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            0             59
  STAGE IIIC            1             41
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  HAP1 MUTATED     0   3   3   2
  HAP1 WILD-TYPE  17  89 326  48
D1875V5, multiclass
    clus
vv   HAP1 MUTATED HAP1 WILD-TYPE
  T1            0             17
  T2            3             89
  T3            3            326
  T4            2             48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  HAP1 MUTATED     7   1   0
  HAP1 WILD-TYPE 280 112  87
D1875V6, multiclass
    clus
vv   HAP1 MUTATED HAP1 WILD-TYPE
  N0            7            280
  N1            1            112
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1875V7, binary
                cls
clus               0   1
  HAP1 MUTATED     6   0
  HAP1 WILD-TYPE 369  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  HAP1 MUTATED      6    0
  HAP1 WILD-TYPE  369   65
   clus
vv  HAP1 MUTATED HAP1 WILD-TYPE
  0            6            369
  1            0             65
[1] 2 2
[1] FALSE
D1875V8, binary
                cls
clus               0   1
  HAP1 MUTATED     6   2
  HAP1 WILD-TYPE 219 262
[1] "tbl2"
                cls
clus             [,1] [,2]
  HAP1 MUTATED      6    2
  HAP1 WILD-TYPE  219  262
        clus
vv       HAP1 MUTATED HAP1 WILD-TYPE
  FEMALE            6            219
  MALE              2            262
[1] 2 2
[1] FALSE
D1875V9, binary
                cls
clus               0   1
  HAP1 MUTATED     7   0
  HAP1 WILD-TYPE 343  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  HAP1 MUTATED      7    0
  HAP1 WILD-TYPE  343   22
     clus
vv    HAP1 MUTATED HAP1 WILD-TYPE
  NO             7            343
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  HAP1 MUTATED                      6                             1
  HAP1 WILD-TYPE                  309                            46
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  HAP1 MUTATED                       1                              0
  HAP1 WILD-TYPE                   105                             10
D1875V10, multiclass
                                clus
vv                               HAP1 MUTATED HAP1 WILD-TYPE
  COLON ADENOCARCINOMA                      6            309
  COLON MUCINOUS ADENOCARCINOMA             1             46
  RECTAL ADENOCARCINOMA                     1            105
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  HAP1 MUTATED     7   0   0   0
  HAP1 WILD-TYPE 338   4  31  25
D1875V11, multiclass
    clus
vv   HAP1 MUTATED HAP1 WILD-TYPE
  R0            7            338
  R1            0              4
  R2            0             31
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1875V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HAP1 MUTATED                                  0     0
  HAP1 WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  HAP1 MUTATED                           0     6
  HAP1 WILD-TYPE                        22   220
D1875V13, multiclass
                                  clus
vv                                 HAP1 MUTATED HAP1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       6            220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1876) Variable = TRAF3IP1 MUTATION ANALYSIS
D1876V1, survival
                    sevent
clus2                  0   1
  TRAF3IP1 MUTATED     6   1
  TRAF3IP1 WILD-TYPE 372  92
  TRAF3IP1 MUTATED TRAF3IP1 WILD-TYPE 
                 7                464 
  TRAF3IP1 MUTATED TRAF3IP1 WILD-TYPE 
                 1                 92 
$`TRAF3IP1 MUTATED`
TCGA-A6-6781 TCGA-AA-A010 TCGA-AD-6964 TCGA-CA-6717 TCGA-D5-5539 TCGA-F4-6856 
       19.66        34.98        10.88        12.76        19.59        35.31 
TCGA-AG-3608 
       15.95 

$`TRAF3IP1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       12.26        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       47.41       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3609 TCGA-AG-3611 
       50.04        12.03         6.05         0.99        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  TRAF3IP1 MUTATED TRAF3IP1 WILD-TYPE 
             10.88               0.00 
  TRAF3IP1 MUTATED TRAF3IP1 WILD-TYPE 
             35.31             148.01 
  TRAF3IP1 MUTATED TRAF3IP1 WILD-TYPE 
            19.590             20.415 
[1] "10.9 - 35.3 (19.6)" "0.0 - 148.0 (20.4)"
[1] "hr=" "1"  
D1876V2, continuous
D1876V3, binary
                    cls
clus                   0   1
  TRAF3IP1 MUTATED     6   1
  TRAF3IP1 WILD-TYPE 360 118
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  TRAF3IP1 MUTATED      6    1
  TRAF3IP1 WILD-TYPE  360  118
        clus
vv       TRAF3IP1 MUTATED TRAF3IP1 WILD-TYPE
  COLON                 6                360
  RECTUM                1                118
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TRAF3IP1 MUTATED         1        0        0         2         1         0
  TRAF3IP1 WILD-TYPE      90        1       32       136         9         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TRAF3IP1 MUTATED           0          1          0          1        0
  TRAF3IP1 WILD-TYPE        24         10         59         41       48
                    vv
clus                 STAGE IVA STAGE IVB
  TRAF3IP1 MUTATED           0         0
  TRAF3IP1 WILD-TYPE        18         1
D1876V4, multiclass
            clus
vv           TRAF3IP1 MUTATED TRAF3IP1 WILD-TYPE
  STAGE I                   1                 90
  STAGE IA                  0                  1
  STAGE II                  0                 32
  STAGE IIA                 2                136
  STAGE IIB                 1                  9
  STAGE IIC                 0                  1
  STAGE III                 0                 24
  STAGE IIIA                1                 10
  STAGE IIIB                0                 59
  STAGE IIIC                1                 41
  STAGE IV                  0                 48
  STAGE IVA                 0                 18
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  TRAF3IP1 MUTATED     0   1   3   3
  TRAF3IP1 WILD-TYPE  17  91 326  47
D1876V5, multiclass
    clus
vv   TRAF3IP1 MUTATED TRAF3IP1 WILD-TYPE
  T1                0                 17
  T2                1                 91
  T3                3                326
  T4                3                 47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  TRAF3IP1 MUTATED     4   2   1
  TRAF3IP1 WILD-TYPE 283 111  86
D1876V6, multiclass
    clus
vv   TRAF3IP1 MUTATED TRAF3IP1 WILD-TYPE
  N0                4                283
  N1                2                111
  N2                1                 86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1876V7, binary
                    cls
clus                   0   1
  TRAF3IP1 MUTATED     5   0
  TRAF3IP1 WILD-TYPE 370  65
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  TRAF3IP1 MUTATED      5    0
  TRAF3IP1 WILD-TYPE  370   65
   clus
vv  TRAF3IP1 MUTATED TRAF3IP1 WILD-TYPE
  0                5                370
  1                0                 65
[1] 2 2
[1] FALSE
D1876V8, binary
                    cls
clus                   0   1
  TRAF3IP1 MUTATED     2   5
  TRAF3IP1 WILD-TYPE 223 259
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  TRAF3IP1 MUTATED      2    5
  TRAF3IP1 WILD-TYPE  223  259
        clus
vv       TRAF3IP1 MUTATED TRAF3IP1 WILD-TYPE
  FEMALE                2                223
  MALE                  5                259
[1] 2 2
[1] FALSE
D1876V9, binary
                    cls
clus                   0   1
  TRAF3IP1 MUTATED     7   0
  TRAF3IP1 WILD-TYPE 343  22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  TRAF3IP1 MUTATED      7    0
  TRAF3IP1 WILD-TYPE  343   22
     clus
vv    TRAF3IP1 MUTATED TRAF3IP1 WILD-TYPE
  NO                 7                343
  YES                0                 22
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  TRAF3IP1 MUTATED                      2                             4
  TRAF3IP1 WILD-TYPE                  313                            43
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  TRAF3IP1 MUTATED                       1                              0
  TRAF3IP1 WILD-TYPE                   105                             10
D1876V10, multiclass
                                clus
vv                               TRAF3IP1 MUTATED TRAF3IP1 WILD-TYPE
  COLON ADENOCARCINOMA                          2                313
  COLON MUCINOUS ADENOCARCINOMA                 4                 43
  RECTAL ADENOCARCINOMA                         1                105
  RECTAL MUCINOUS ADENOCARCINOMA                0                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  TRAF3IP1 MUTATED     5   0   0   1
  TRAF3IP1 WILD-TYPE 340   4  31  24
D1876V11, multiclass
    clus
vv   TRAF3IP1 MUTATED TRAF3IP1 WILD-TYPE
  R0                5                340
  R1                0                  4
  R2                0                 31
  RX                1                 24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1876V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TRAF3IP1 MUTATED                                  0     1
  TRAF3IP1 WILD-TYPE                                1    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  TRAF3IP1 MUTATED                           0     4
  TRAF3IP1 WILD-TYPE                        22   222
D1876V13, multiclass
                                  clus
vv                                 TRAF3IP1 MUTATED TRAF3IP1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                 10
  BLACK OR AFRICAN AMERICAN                       0                 22
  WHITE                                           4                222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1877) Variable = ZNF318 MUTATION ANALYSIS
D1877V1, survival
                  sevent
clus2                0   1
  ZNF318 MUTATED    24   6
  ZNF318 WILD-TYPE 354  87
  ZNF318 MUTATED ZNF318 WILD-TYPE 
              30              441 
  ZNF318 MUTATED ZNF318 WILD-TYPE 
               6               87 
$`ZNF318 MUTATED`
TCGA-A6-5661 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3492 
       33.53        24.39        23.87        20.12        19.66         3.02 
TCGA-AA-3510 TCGA-AA-3518 TCGA-AA-3525 TCGA-AA-3555 TCGA-AA-3663 TCGA-AA-3715 
       63.98         1.02         8.05        29.95         6.97        19.04 
TCGA-AA-3815 TCGA-AA-3864 TCGA-AA-3950 TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A03F 
       33.04        53.00        24.00        25.02         4.01        18.05 
TCGA-AD-6964 TCGA-AZ-4315 TCGA-CA-6717 TCGA-CM-6164 TCGA-CM-6168 TCGA-CM-6676 
       10.88        58.39        12.76        29.03        12.99        11.08 
TCGA-D5-6536 TCGA-D5-6540 TCGA-D5-6923 TCGA-G4-6626 TCGA-AF-2692 TCGA-AG-A002 
       17.85        16.14        12.43        46.75        13.55        20.98 

$`ZNF318 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6782 TCGA-AA-3489 
       25.18        24.16        21.76        24.69        20.28         7.04 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3529 
        9.07        24.03        37.05        36.03        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       17.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       61.02        78.08         6.05        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       19.04        10.06        35.05         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 
       32.05         0.99        31.07        31.07        30.05        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 
       12.99        24.00        33.01        26.01         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03J TCGA-AD-5900 
       14.01         0.92        41.00        39.98        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        33.01        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.20        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6169 
       12.00         2.96        16.04        21.99        14.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6677 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 
       15.12         4.80        17.13        12.49        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        3.68         4.41        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2693 
       91.79        79.69        24.13        39.48        43.04        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  ZNF318 MUTATED ZNF318 WILD-TYPE 
            1.02             0.00 
  ZNF318 MUTATED ZNF318 WILD-TYPE 
           63.98           148.01 
  ZNF318 MUTATED ZNF318 WILD-TYPE 
           19.35            20.55 
[1] "1.0 - 64.0 (19.4)"  "0.0 - 148.0 (20.6)"
[1] "hr=" "1.1"
D1877V2, continuous
D1877V3, binary
                  cls
clus                 0   1
  ZNF318 MUTATED    28   1
  ZNF318 WILD-TYPE 338 118
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF318 MUTATED     28    1
  ZNF318 WILD-TYPE  338  118
        clus
vv       ZNF318 MUTATED ZNF318 WILD-TYPE
  COLON              28              338
  RECTUM              1              118
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZNF318 MUTATED         5        0        5        13         1         0
  ZNF318 WILD-TYPE      86        1       27       125         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF318 MUTATED           1          0          2          1        0
  ZNF318 WILD-TYPE        23         11         57         41       48
                  vv
clus               STAGE IVA STAGE IVB
  ZNF318 MUTATED           0         0
  ZNF318 WILD-TYPE        18         1
D1877V4, multiclass
            clus
vv           ZNF318 MUTATED ZNF318 WILD-TYPE
  STAGE I                 5               86
  STAGE IA                0                1
  STAGE II                5               27
  STAGE IIA              13              125
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               1               23
  STAGE IIIA              0               11
  STAGE IIIB              2               57
  STAGE IIIC              1               41
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZNF318 MUTATED     0   6  21   3
  ZNF318 WILD-TYPE  17  86 308  47
D1877V5, multiclass
    clus
vv   ZNF318 MUTATED ZNF318 WILD-TYPE
  T1              0               17
  T2              6               86
  T3             21              308
  T4              3               47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  ZNF318 MUTATED    25   3   2
  ZNF318 WILD-TYPE 262 110  85
D1877V6, multiclass
    clus
vv   ZNF318 MUTATED ZNF318 WILD-TYPE
  N0             25              262
  N1              3              110
  N2              2               85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1877V7, binary
                  cls
clus                 0   1
  ZNF318 MUTATED    26   0
  ZNF318 WILD-TYPE 349  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF318 MUTATED     26    0
  ZNF318 WILD-TYPE  349   65
   clus
vv  ZNF318 MUTATED ZNF318 WILD-TYPE
  0             26              349
  1              0               65
[1] 2 2
[1] FALSE
D1877V8, binary
                  cls
clus                 0   1
  ZNF318 MUTATED    11  19
  ZNF318 WILD-TYPE 214 245
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF318 MUTATED     11   19
  ZNF318 WILD-TYPE  214  245
        clus
vv       ZNF318 MUTATED ZNF318 WILD-TYPE
  FEMALE             11              214
  MALE               19              245
[1] 2 2
[1] FALSE
D1877V9, binary
                  cls
clus                 0   1
  ZNF318 MUTATED    27   0
  ZNF318 WILD-TYPE 323  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF318 MUTATED     27    0
  ZNF318 WILD-TYPE  323   22
     clus
vv    ZNF318 MUTATED ZNF318 WILD-TYPE
  NO              27              323
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ZNF318 MUTATED                     20                             8
  ZNF318 WILD-TYPE                  295                            39
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ZNF318 MUTATED                       1                              0
  ZNF318 WILD-TYPE                   105                             10
D1877V10, multiclass
                                clus
vv                               ZNF318 MUTATED ZNF318 WILD-TYPE
  COLON ADENOCARCINOMA                       20              295
  COLON MUCINOUS ADENOCARCINOMA               8               39
  RECTAL ADENOCARCINOMA                       1              105
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ZNF318 MUTATED    24   0   0   1
  ZNF318 WILD-TYPE 321   4  31  24
D1877V11, multiclass
    clus
vv   ZNF318 MUTATED ZNF318 WILD-TYPE
  R0             24              321
  R1              0                4
  R2              0               31
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1877V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF318 MUTATED                                  0     1
  ZNF318 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZNF318 MUTATED                           2    13
  ZNF318 WILD-TYPE                        20   213
D1877V13, multiclass
                                  clus
vv                                 ZNF318 MUTATED ZNF318 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     2               20
  WHITE                                        13              213
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1878) Variable = NUP133 MUTATION ANALYSIS
D1878V1, survival
                  sevent
clus2                0   1
  NUP133 MUTATED    17   1
  NUP133 WILD-TYPE 361  92
  NUP133 MUTATED NUP133 WILD-TYPE 
              18              453 
  NUP133 MUTATED NUP133 WILD-TYPE 
               1               92 
$`NUP133 MUTATED`
TCGA-A6-5665 TCGA-A6-6780 TCGA-AA-3510 TCGA-AA-3833 TCGA-AA-3950 TCGA-AA-A010 
       22.06        20.12        63.98        15.95        24.00        34.98 
TCGA-AA-A01R TCGA-AA-A024 TCGA-AD-6895 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4681 
       35.01        39.06         0.72        21.44        17.82       106.75 
TCGA-CA-6717 TCGA-CM-6678 TCGA-D5-6928 TCGA-AF-6136 TCGA-AG-3892 TCGA-AG-A002 
       12.76        11.01        11.64        15.39        13.02        20.98 

$`NUP133 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3837 
       33.04         0.99        25.02         1.02        17.98        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       33.01        26.01         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 
        1.02        33.04        35.01        26.01        37.02        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
       56.55         0.79         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
       58.39         1.41         5.13        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07        12.20        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6679 
       11.01        12.95        13.05        11.08        11.08        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 
        1.02        17.95        36.95        17.03        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  NUP133 MUTATED NUP133 WILD-TYPE 
            0.72             0.00 
  NUP133 MUTATED NUP133 WILD-TYPE 
          106.75           148.01 
  NUP133 MUTATED NUP133 WILD-TYPE 
           20.55            20.19 
[1] "0.7 - 106.8 (20.6)" "0.0 - 148.0 (20.2)"
[1] "hr=" "3.7"
D1878V2, continuous
D1878V3, binary
                  cls
clus                 0   1
  NUP133 MUTATED    16   3
  NUP133 WILD-TYPE 350 116
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NUP133 MUTATED     16    3
  NUP133 WILD-TYPE  350  116
        clus
vv       NUP133 MUTATED NUP133 WILD-TYPE
  COLON              16              350
  RECTUM              3              116
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NUP133 MUTATED         2        0        2         8         1         0
  NUP133 WILD-TYPE      89        1       30       130         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NUP133 MUTATED           1          0          2          1        0
  NUP133 WILD-TYPE        23         11         57         41       48
                  vv
clus               STAGE IVA STAGE IVB
  NUP133 MUTATED           1         0
  NUP133 WILD-TYPE        17         1
D1878V4, multiclass
            clus
vv           NUP133 MUTATED NUP133 WILD-TYPE
  STAGE I                 2               89
  STAGE IA                0                1
  STAGE II                2               30
  STAGE IIA               8              130
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               1               23
  STAGE IIIA              0               11
  STAGE IIIB              2               57
  STAGE IIIC              1               41
  STAGE IV                0               48
  STAGE IVA               1               17
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  NUP133 MUTATED     1   1  15   2
  NUP133 WILD-TYPE  16  91 314  48
D1878V5, multiclass
    clus
vv   NUP133 MUTATED NUP133 WILD-TYPE
  T1              1               16
  T2              1               91
  T3             15              314
  T4              2               48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  NUP133 MUTATED    13   4   2
  NUP133 WILD-TYPE 274 109  85
D1878V6, multiclass
    clus
vv   NUP133 MUTATED NUP133 WILD-TYPE
  N0             13              274
  N1              4              109
  N2              2               85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1878V7, binary
                  cls
clus                 0   1
  NUP133 MUTATED    13   1
  NUP133 WILD-TYPE 362  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NUP133 MUTATED     13    1
  NUP133 WILD-TYPE  362   64
   clus
vv  NUP133 MUTATED NUP133 WILD-TYPE
  0             13              362
  1              1               64
[1] 2 2
[1] FALSE
D1878V8, binary
                  cls
clus                 0   1
  NUP133 MUTATED     9  10
  NUP133 WILD-TYPE 216 254
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NUP133 MUTATED      9   10
  NUP133 WILD-TYPE  216  254
        clus
vv       NUP133 MUTATED NUP133 WILD-TYPE
  FEMALE              9              216
  MALE               10              254
[1] 2 2
[1] FALSE
D1878V9, binary
                  cls
clus                 0   1
  NUP133 MUTATED    15   2
  NUP133 WILD-TYPE 335  20
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NUP133 MUTATED     15    2
  NUP133 WILD-TYPE  335   20
     clus
vv    NUP133 MUTATED NUP133 WILD-TYPE
  NO              15              335
  YES              2               20
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  NUP133 MUTATED                      9                             7
  NUP133 WILD-TYPE                  306                            40
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  NUP133 MUTATED                       3                              0
  NUP133 WILD-TYPE                   103                             10
D1878V10, multiclass
                                clus
vv                               NUP133 MUTATED NUP133 WILD-TYPE
  COLON ADENOCARCINOMA                        9              306
  COLON MUCINOUS ADENOCARCINOMA               7               40
  RECTAL ADENOCARCINOMA                       3              103
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  NUP133 MUTATED    15   0   0   1
  NUP133 WILD-TYPE 330   4  31  24
D1878V11, multiclass
    clus
vv   NUP133 MUTATED NUP133 WILD-TYPE
  R0             15              330
  R1              0                4
  R2              0               31
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1878V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NUP133 MUTATED                                  0     1
  NUP133 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  NUP133 MUTATED                           1     9
  NUP133 WILD-TYPE                        21   217
D1878V13, multiclass
                                  clus
vv                                 NUP133 MUTATED NUP133 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                         9              217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1879) Variable = ARAF MUTATION ANALYSIS
D1879V1, survival
                sevent
clus2              0   1
  ARAF MUTATED     6   4
  ARAF WILD-TYPE 372  89
  ARAF MUTATED ARAF WILD-TYPE 
            10            461 
  ARAF MUTATED ARAF WILD-TYPE 
             4             89 
$`ARAF MUTATED`
TCGA-A6-6651 TCGA-AA-3492 TCGA-AA-3518 TCGA-AA-3663 TCGA-AA-3715 TCGA-AA-3864 
       21.76         3.02         1.02         6.97        19.04        53.00 
TCGA-AZ-6601 TCGA-CK-5916 TCGA-CM-6674 TCGA-CM-6678 
      100.01        21.14        12.95        11.01 

$`ARAF WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.08        25.18        24.16        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 
       20.12        19.66        20.28         7.04         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3519 
       63.98         6.97         1.02        13.02        38.99         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02        78.08         6.05        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       26.99        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       30.05        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       49.41         6.77        12.10        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       13.05        11.08        11.08        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  ARAF MUTATED ARAF WILD-TYPE 
          1.02           0.00 
  ARAF MUTATED ARAF WILD-TYPE 
        100.01         148.01 
  ARAF MUTATED ARAF WILD-TYPE 
        15.995         20.280 
[1] "1.0 - 100.0 (16.0)" "0.0 - 148.0 (20.3)"
[1] "hr=" "2.1"
D1879V2, continuous
D1879V3, binary
                cls
clus               0   1
  ARAF MUTATED    10   0
  ARAF WILD-TYPE 356 119
[1] "tbl2"
                cls
clus             [,1] [,2]
  ARAF MUTATED     10    0
  ARAF WILD-TYPE  356  119
        clus
vv       ARAF MUTATED ARAF WILD-TYPE
  COLON            10            356
  RECTUM            0            119
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ARAF MUTATED         1        0        5         2         0         0
  ARAF WILD-TYPE      90        1       27       136        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ARAF MUTATED           0          0          1          0        0         1
  ARAF WILD-TYPE        24         11         58         42       48        17
                vv
clus             STAGE IVB
  ARAF MUTATED           0
  ARAF WILD-TYPE         1
D1879V4, multiclass
            clus
vv           ARAF MUTATED ARAF WILD-TYPE
  STAGE I               1             90
  STAGE IA              0              1
  STAGE II              5             27
  STAGE IIA             2            136
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            1             58
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             1             17
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  ARAF MUTATED     1   0   8   1
  ARAF WILD-TYPE  16  92 321  49
D1879V5, multiclass
    clus
vv   ARAF MUTATED ARAF WILD-TYPE
  T1            1             16
  T2            0             92
  T3            8            321
  T4            1             49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  ARAF MUTATED     8   2   0
  ARAF WILD-TYPE 279 111  87
D1879V6, multiclass
    clus
vv   ARAF MUTATED ARAF WILD-TYPE
  N0            8            279
  N1            2            111
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1879V7, binary
                cls
clus               0   1
  ARAF MUTATED     8   1
  ARAF WILD-TYPE 367  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  ARAF MUTATED      8    1
  ARAF WILD-TYPE  367   64
   clus
vv  ARAF MUTATED ARAF WILD-TYPE
  0            8            367
  1            1             64
[1] 2 2
[1] FALSE
D1879V8, binary
                cls
clus               0   1
  ARAF MUTATED     5   5
  ARAF WILD-TYPE 220 259
[1] "tbl2"
                cls
clus             [,1] [,2]
  ARAF MUTATED      5    5
  ARAF WILD-TYPE  220  259
        clus
vv       ARAF MUTATED ARAF WILD-TYPE
  FEMALE            5            220
  MALE              5            259
[1] 2 2
[1] FALSE
D1879V9, binary
                cls
clus               0   1
  ARAF MUTATED     9   0
  ARAF WILD-TYPE 341  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  ARAF MUTATED      9    0
  ARAF WILD-TYPE  341   22
     clus
vv    ARAF MUTATED ARAF WILD-TYPE
  NO             9            341
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ARAF MUTATED                     10                             0
  ARAF WILD-TYPE                  305                            47
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ARAF MUTATED                       0                              0
  ARAF WILD-TYPE                   106                             10
D1879V10, multiclass
                                clus
vv                               ARAF MUTATED ARAF WILD-TYPE
  COLON ADENOCARCINOMA                     10            305
  COLON MUCINOUS ADENOCARCINOMA             0             47
  RECTAL ADENOCARCINOMA                     0            106
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  ARAF MUTATED     7   0   0   1
  ARAF WILD-TYPE 338   4  31  24
D1879V11, multiclass
    clus
vv   ARAF MUTATED ARAF WILD-TYPE
  R0            7            338
  R1            0              4
  R2            0             31
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1879V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ARAF MUTATED                                  0     0
  ARAF WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  ARAF MUTATED                           0     5
  ARAF WILD-TYPE                        22   221
D1879V13, multiclass
                                  clus
vv                                 ARAF MUTATED ARAF WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       5            221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1880) Variable = MXRA5 MUTATION ANALYSIS
D1880V1, survival
                 sevent
clus2               0   1
  MXRA5 MUTATED    37   9
  MXRA5 WILD-TYPE 341  84
  MXRA5 MUTATED MXRA5 WILD-TYPE 
             46             425 
  MXRA5 MUTATED MXRA5 WILD-TYPE 
              9              84 
$`MXRA5 MUTATED`
TCGA-AA-3502 TCGA-AA-3520 TCGA-AA-3553 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3818 
       35.01        24.03        24.00         6.97        54.02         0.99 
TCGA-AA-3833 TCGA-AA-A00E TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01Q TCGA-AA-A02Y 
       15.95        30.02         4.01        34.98         1.02        39.98 
TCGA-AA-A03F TCGA-AD-6889 TCGA-AD-6895 TCGA-AD-6964 TCGA-AY-5543 TCGA-AZ-4315 
       18.05        56.55         0.72        10.88        33.01        58.39 
TCGA-AZ-4616 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-5914 TCGA-CK-6747 
        5.13        12.76        10.06        17.56         9.99        82.95 
TCGA-CK-6748 TCGA-CM-5861 TCGA-CM-6171 TCGA-CM-6675 TCGA-D5-6533 TCGA-D5-6920 
        1.91        15.02        14.04        13.05         1.32         3.68 
TCGA-D5-6926 TCGA-DM-A1DA TCGA-F4-6570 TCGA-G4-6317 TCGA-G4-6586 TCGA-G4-6588 
        9.04         7.50         6.18        36.00        35.80        26.17 
TCGA-G4-6628 TCGA-AF-6136 TCGA-AG-4007 TCGA-AG-A002 TCGA-AG-A02N TCGA-DC-5337 
       79.69        15.39         1.02        20.98        61.97        15.02 
TCGA-DY-A1DD TCGA-EI-6508 TCGA-F5-6571 TCGA-F5-6811 
       57.24        20.91        31.30        32.19 

$`MXRA5 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        1.02         9.07        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3666 TCGA-AA-3667 
       19.99        61.02        78.08         6.05         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3819 
       19.04        19.04        10.06        35.05        33.04        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
        1.02        17.98        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       38.04        19.00        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
       38.07        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       14.01         0.92        41.00        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       15.52         0.79         5.79        22.42        27.42         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6197 TCGA-AY-6386 
       14.50        27.09        16.31         0.95        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        1.41       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        0.07        12.20        14.30       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       49.08        51.32        21.14       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       30.08        32.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 
       14.99        12.99        13.02        15.02        11.01        12.95 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       16.14        15.58         1.48         4.41        12.43        14.30 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA 
       49.91        13.32        12.59       140.38        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 
       61.91        22.09        13.78        91.79        46.75        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       14.50        16.83        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4008 TCGA-AG-A008 
       19.99        28.04        36.03        14.04        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
        1.94        38.96        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5869 TCGA-DC-6155 
        6.97         4.73        78.12         7.17         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
        5.29       126.44        41.36        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
        0.49        20.55        19.96        18.28         9.96        49.51 
TCGA-F5-6702 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57         0.66         0.69        55.76        26.43 

  MXRA5 MUTATED MXRA5 WILD-TYPE 
           0.72            0.00 
  MXRA5 MUTATED MXRA5 WILD-TYPE 
          82.95          148.01 
  MXRA5 MUTATED MXRA5 WILD-TYPE 
         16.755          20.550 
[1] "0.7 - 83.0 (16.8)"  "0.0 - 148.0 (20.6)"
[1] "hr=" "1.1"
D1880V2, continuous
D1880V3, binary
                 cls
clus                0   1
  MXRA5 MUTATED    37   9
  MXRA5 WILD-TYPE 329 110
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MXRA5 MUTATED     37    9
  MXRA5 WILD-TYPE  329  110
        clus
vv       MXRA5 MUTATED MXRA5 WILD-TYPE
  COLON             37             329
  RECTUM             9             110
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MXRA5 MUTATED         7        0        5        15         2         0
  MXRA5 WILD-TYPE      84        1       27       123         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MXRA5 MUTATED           1          0          7          2        3         1
  MXRA5 WILD-TYPE        23         11         52         40       45        17
                 vv
clus              STAGE IVB
  MXRA5 MUTATED           1
  MXRA5 WILD-TYPE         0
D1880V4, multiclass
            clus
vv           MXRA5 MUTATED MXRA5 WILD-TYPE
  STAGE I                7              84
  STAGE IA               0               1
  STAGE II               5              27
  STAGE IIA             15             123
  STAGE IIB              2               8
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             7              52
  STAGE IIIC             2              40
  STAGE IV               3              45
  STAGE IVA              1              17
  STAGE IVB              1               0
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  MXRA5 MUTATED     1   6  32   7
  MXRA5 WILD-TYPE  16  86 297  43
D1880V5, multiclass
    clus
vv   MXRA5 MUTATED MXRA5 WILD-TYPE
  T1             1              16
  T2             6              86
  T3            32             297
  T4             7              43
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  MXRA5 MUTATED    30   9   7
  MXRA5 WILD-TYPE 257 104  80
D1880V6, multiclass
    clus
vv   MXRA5 MUTATED MXRA5 WILD-TYPE
  N0            30             257
  N1             9             104
  N2             7              80
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1880V7, binary
                 cls
clus                0   1
  MXRA5 MUTATED    35   5
  MXRA5 WILD-TYPE 340  60
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MXRA5 MUTATED     35    5
  MXRA5 WILD-TYPE  340   60
   clus
vv  MXRA5 MUTATED MXRA5 WILD-TYPE
  0            35             340
  1             5              60
[1] 2 2
[1] FALSE
D1880V8, binary
                 cls
clus                0   1
  MXRA5 MUTATED    27  19
  MXRA5 WILD-TYPE 198 245
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MXRA5 MUTATED     27   19
  MXRA5 WILD-TYPE  198  245
        clus
vv       MXRA5 MUTATED MXRA5 WILD-TYPE
  FEMALE            27             198
  MALE              19             245
[1] 2 2
[1] FALSE
D1880V9, binary
                 cls
clus                0   1
  MXRA5 MUTATED    31   2
  MXRA5 WILD-TYPE 319  20
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MXRA5 MUTATED     31    2
  MXRA5 WILD-TYPE  319   20
     clus
vv    MXRA5 MUTATED MXRA5 WILD-TYPE
  NO             31             319
  YES             2              20
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MXRA5 MUTATED                     33                             4
  MXRA5 WILD-TYPE                  282                            43
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MXRA5 MUTATED                       9                              0
  MXRA5 WILD-TYPE                    97                             10
D1880V10, multiclass
                                clus
vv                               MXRA5 MUTATED MXRA5 WILD-TYPE
  COLON ADENOCARCINOMA                      33             282
  COLON MUCINOUS ADENOCARCINOMA              4              43
  RECTAL ADENOCARCINOMA                      9              97
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  MXRA5 MUTATED    31   0   1   6
  MXRA5 WILD-TYPE 314   4  30  19
D1880V11, multiclass
    clus
vv   MXRA5 MUTATED MXRA5 WILD-TYPE
  R0            31             314
  R1             0               4
  R2             1              30
  RX             6              19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1880V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MXRA5 MUTATED                                  0     3
  MXRA5 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  MXRA5 MUTATED                           2    25
  MXRA5 WILD-TYPE                        20   201
D1880V13, multiclass
                                  clus
vv                                 MXRA5 MUTATED MXRA5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        3               8
  BLACK OR AFRICAN AMERICAN                    2              20
  WHITE                                       25             201
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1881) Variable = PAX2 MUTATION ANALYSIS
D1881V1, survival
                sevent
clus2              0   1
  PAX2 MUTATED     7   0
  PAX2 WILD-TYPE 371  93
  PAX2 MUTATED PAX2 WILD-TYPE 
             7            464 
  PAX2 MUTATED PAX2 WILD-TYPE 
             0             93 
$`PAX2 MUTATED`
TCGA-A6-5665 TCGA-AA-3950 TCGA-CA-5254 TCGA-CK-5913 TCGA-CM-6171 TCGA-AG-3902 
       22.06        24.00        12.69        51.32        14.04        32.02 
TCGA-AG-A002 
       20.98 

$`PAX2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 
        2.01        12.99        24.00        33.01        26.01         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        1.61         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        49.08         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       13.02        15.02        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
        1.02        48.03        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  PAX2 MUTATED PAX2 WILD-TYPE 
         12.69           0.00 
  PAX2 MUTATED PAX2 WILD-TYPE 
         51.32         148.01 
  PAX2 MUTATED PAX2 WILD-TYPE 
        22.060         20.085 
[1] "12.7 - 51.3 (22.1)" "0.0 - 148.0 (20.1)"
[1] "hr="     "9100000"
D1881V2, continuous
D1881V3, binary
                cls
clus               0   1
  PAX2 MUTATED     5   2
  PAX2 WILD-TYPE 361 117
[1] "tbl2"
                cls
clus             [,1] [,2]
  PAX2 MUTATED      5    2
  PAX2 WILD-TYPE  361  117
        clus
vv       PAX2 MUTATED PAX2 WILD-TYPE
  COLON             5            361
  RECTUM            2            117
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PAX2 MUTATED         2        0        0         5         0         0
  PAX2 WILD-TYPE      89        1       32       133        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PAX2 MUTATED           0          0          0          0        0         0
  PAX2 WILD-TYPE        24         11         59         42       48        18
                vv
clus             STAGE IVB
  PAX2 MUTATED           0
  PAX2 WILD-TYPE         1
D1881V4, multiclass
            clus
vv           PAX2 MUTATED PAX2 WILD-TYPE
  STAGE I               2             89
  STAGE IA              0              1
  STAGE II              0             32
  STAGE IIA             5            133
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            0             59
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  PAX2 MUTATED     0   2   5   0
  PAX2 WILD-TYPE  17  90 324  50
D1881V5, multiclass
    clus
vv   PAX2 MUTATED PAX2 WILD-TYPE
  T1            0             17
  T2            2             90
  T3            5            324
  T4            0             50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  PAX2 MUTATED     7   0   0
  PAX2 WILD-TYPE 280 113  87
D1881V6, multiclass
    clus
vv   PAX2 MUTATED PAX2 WILD-TYPE
  N0            7            280
  N1            0            113
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1881V7, binary
                cls
clus               0   1
  PAX2 MUTATED     6   0
  PAX2 WILD-TYPE 369  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  PAX2 MUTATED      6    0
  PAX2 WILD-TYPE  369   65
   clus
vv  PAX2 MUTATED PAX2 WILD-TYPE
  0            6            369
  1            0             65
[1] 2 2
[1] FALSE
D1881V8, binary
                cls
clus               0   1
  PAX2 MUTATED     5   2
  PAX2 WILD-TYPE 220 262
[1] "tbl2"
                cls
clus             [,1] [,2]
  PAX2 MUTATED      5    2
  PAX2 WILD-TYPE  220  262
        clus
vv       PAX2 MUTATED PAX2 WILD-TYPE
  FEMALE            5            220
  MALE              2            262
[1] 2 2
[1] FALSE
D1881V9, binary
                cls
clus               0   1
  PAX2 MUTATED     7   0
  PAX2 WILD-TYPE 343  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  PAX2 MUTATED      7    0
  PAX2 WILD-TYPE  343   22
     clus
vv    PAX2 MUTATED PAX2 WILD-TYPE
  NO             7            343
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PAX2 MUTATED                      4                             1
  PAX2 WILD-TYPE                  311                            46
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PAX2 MUTATED                       2                              0
  PAX2 WILD-TYPE                   104                             10
D1881V10, multiclass
                                clus
vv                               PAX2 MUTATED PAX2 WILD-TYPE
  COLON ADENOCARCINOMA                      4            311
  COLON MUCINOUS ADENOCARCINOMA             1             46
  RECTAL ADENOCARCINOMA                     2            104
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  PAX2 MUTATED     5   0   0   2
  PAX2 WILD-TYPE 340   4  31  23
D1881V11, multiclass
    clus
vv   PAX2 MUTATED PAX2 WILD-TYPE
  R0            5            340
  R1            0              4
  R2            0             31
  RX            2             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1881V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PAX2 MUTATED                                  0     1
  PAX2 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  PAX2 MUTATED                           0     3
  PAX2 WILD-TYPE                        22   223
D1881V13, multiclass
                                  clus
vv                                 PAX2 MUTATED PAX2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       3            223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1882) Variable = FZD3 MUTATION ANALYSIS
D1882V1, survival
                sevent
clus2              0   1
  FZD3 MUTATED    10   2
  FZD3 WILD-TYPE 368  91
  FZD3 MUTATED FZD3 WILD-TYPE 
            12            459 
  FZD3 MUTATED FZD3 WILD-TYPE 
             2             91 
$`FZD3 MUTATED`
TCGA-A6-2676 TCGA-AA-3977 TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00N TCGA-AA-A010 
       42.90        25.02        30.02        18.05         4.01        34.98 
TCGA-AA-A01Q TCGA-AD-6895 TCGA-CA-6717 TCGA-CM-5349 TCGA-G4-6309 TCGA-AG-A002 
        1.02         0.72        12.76        30.08        85.48        20.98 

$`FZD3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       19.00        34.03        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01R 
       32.02        12.00        31.00        31.00        38.07        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       15.52        56.55         0.79         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.20        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5861 
       13.02        29.06        22.03        22.98        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       53.62        44.68        55.04        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  FZD3 MUTATED FZD3 WILD-TYPE 
          0.72           0.00 
  FZD3 MUTATED FZD3 WILD-TYPE 
         85.48         148.01 
  FZD3 MUTATED FZD3 WILD-TYPE 
         23.00          20.12 
[1] "0.7 - 85.5 (23.0)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.1"
D1882V2, continuous
D1882V3, binary
                cls
clus               0   1
  FZD3 MUTATED    13   1
  FZD3 WILD-TYPE 353 118
[1] "tbl2"
                cls
clus             [,1] [,2]
  FZD3 MUTATED     13    1
  FZD3 WILD-TYPE  353  118
        clus
vv       FZD3 MUTATED FZD3 WILD-TYPE
  COLON            13            353
  RECTUM            1            118
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FZD3 MUTATED         1        0        2         4         3         0
  FZD3 WILD-TYPE      90        1       30       134         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  FZD3 MUTATED           0          0          2          0        0         0
  FZD3 WILD-TYPE        24         11         57         42       48        18
                vv
clus             STAGE IVB
  FZD3 MUTATED           0
  FZD3 WILD-TYPE         1
D1882V4, multiclass
            clus
vv           FZD3 MUTATED FZD3 WILD-TYPE
  STAGE I               1             90
  STAGE IA              0              1
  STAGE II              2             30
  STAGE IIA             4            134
  STAGE IIB             3              7
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            2             57
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  FZD3 MUTATED     0   2   7   5
  FZD3 WILD-TYPE  17  90 322  45
D1882V5, multiclass
    clus
vv   FZD3 MUTATED FZD3 WILD-TYPE
  T1            0             17
  T2            2             90
  T3            7            322
  T4            5             45
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  FZD3 MUTATED    11   3   0
  FZD3 WILD-TYPE 276 110  87
D1882V6, multiclass
    clus
vv   FZD3 MUTATED FZD3 WILD-TYPE
  N0           11            276
  N1            3            110
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1882V7, binary
                cls
clus               0   1
  FZD3 MUTATED    12   0
  FZD3 WILD-TYPE 363  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  FZD3 MUTATED     12    0
  FZD3 WILD-TYPE  363   65
   clus
vv  FZD3 MUTATED FZD3 WILD-TYPE
  0           12            363
  1            0             65
[1] 2 2
[1] FALSE
D1882V8, binary
                cls
clus               0   1
  FZD3 MUTATED     7   7
  FZD3 WILD-TYPE 218 257
[1] "tbl2"
                cls
clus             [,1] [,2]
  FZD3 MUTATED      7    7
  FZD3 WILD-TYPE  218  257
        clus
vv       FZD3 MUTATED FZD3 WILD-TYPE
  FEMALE            7            218
  MALE              7            257
[1] 2 2
[1] FALSE
D1882V9, binary
                cls
clus               0   1
  FZD3 MUTATED     9   0
  FZD3 WILD-TYPE 341  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  FZD3 MUTATED      9    0
  FZD3 WILD-TYPE  341   22
     clus
vv    FZD3 MUTATED FZD3 WILD-TYPE
  NO             9            341
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  FZD3 MUTATED                     10                             3
  FZD3 WILD-TYPE                  305                            44
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  FZD3 MUTATED                       1                              0
  FZD3 WILD-TYPE                   105                             10
D1882V10, multiclass
                                clus
vv                               FZD3 MUTATED FZD3 WILD-TYPE
  COLON ADENOCARCINOMA                     10            305
  COLON MUCINOUS ADENOCARCINOMA             3             44
  RECTAL ADENOCARCINOMA                     1            105
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  FZD3 MUTATED    11   0   0   1
  FZD3 WILD-TYPE 334   4  31  24
D1882V11, multiclass
    clus
vv   FZD3 MUTATED FZD3 WILD-TYPE
  R0           11            334
  R1            0              4
  R2            0             31
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1882V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FZD3 MUTATED                                  0     1
  FZD3 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  FZD3 MUTATED                           1     3
  FZD3 WILD-TYPE                        21   223
D1882V13, multiclass
                                  clus
vv                                 FZD3 MUTATED FZD3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                       3            223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1883) Variable = LRRFIP2 MUTATION ANALYSIS
D1883V1, survival
                   sevent
clus2                 0   1
  LRRFIP2 MUTATED    13   3
  LRRFIP2 WILD-TYPE 365  90
  LRRFIP2 MUTATED LRRFIP2 WILD-TYPE 
               16               455 
  LRRFIP2 MUTATED LRRFIP2 WILD-TYPE 
                3                90 
$`LRRFIP2 MUTATED`
TCGA-A6-6138 TCGA-AA-3554 TCGA-AA-3715 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3977 
       22.52        17.95        19.04        30.05        53.00        25.02 
TCGA-AA-A010 TCGA-AZ-6601 TCGA-D5-6535 TCGA-D5-6540 TCGA-D5-6928 TCGA-F4-6570 
       34.98       100.01        15.12        16.14        11.64         6.18 
TCGA-G4-6588 TCGA-AG-3892 TCGA-AG-A002 TCGA-CL-5918 
       26.17        13.02        20.98         7.17 

$`LRRFIP2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6141 TCGA-A6-6142 
       22.09        22.06        32.71        27.09         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       13.02        24.00        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       31.07        31.07        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77        12.10        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 
       20.19        18.25         1.32        43.27        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       17.13        12.49        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6930 
       12.43        14.30         9.04         9.44         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
        8.61        31.96        35.74        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       13.78        35.80        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       17.03        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-DC-5337 
        6.05        33.17         6.97         4.73        78.12        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  LRRFIP2 MUTATED LRRFIP2 WILD-TYPE 
             6.18              0.00 
  LRRFIP2 MUTATED LRRFIP2 WILD-TYPE 
           100.01            148.01 
  LRRFIP2 MUTATED LRRFIP2 WILD-TYPE 
            20.01             20.19 
[1] "6.2 - 100.0 (20.0)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.1"
D1883V2, continuous
D1883V3, binary
                   cls
clus                  0   1
  LRRFIP2 MUTATED    13   3
  LRRFIP2 WILD-TYPE 353 116
[1] "tbl2"
                   cls
clus                [,1] [,2]
  LRRFIP2 MUTATED     13    3
  LRRFIP2 WILD-TYPE  353  116
        clus
vv       LRRFIP2 MUTATED LRRFIP2 WILD-TYPE
  COLON               13               353
  RECTUM               3               116
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  LRRFIP2 MUTATED         4        0        3         6         1         0
  LRRFIP2 WILD-TYPE      87        1       29       132         9         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  LRRFIP2 MUTATED           0          0          1          0        0
  LRRFIP2 WILD-TYPE        24         11         58         42       48
                   vv
clus                STAGE IVA STAGE IVB
  LRRFIP2 MUTATED           0         0
  LRRFIP2 WILD-TYPE        18         1
D1883V4, multiclass
            clus
vv           LRRFIP2 MUTATED LRRFIP2 WILD-TYPE
  STAGE I                  4                87
  STAGE IA                 0                 1
  STAGE II                 3                29
  STAGE IIA                6               132
  STAGE IIB                1                 9
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               0                11
  STAGE IIIB               1                58
  STAGE IIIC               0                42
  STAGE IV                 0                48
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  LRRFIP2 MUTATED     1   4  10   1
  LRRFIP2 WILD-TYPE  16  88 319  49
D1883V5, multiclass
    clus
vv   LRRFIP2 MUTATED LRRFIP2 WILD-TYPE
  T1               1                16
  T2               4                88
  T3              10               319
  T4               1                49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  LRRFIP2 MUTATED    15   1   0
  LRRFIP2 WILD-TYPE 272 112  87
D1883V6, multiclass
    clus
vv   LRRFIP2 MUTATED LRRFIP2 WILD-TYPE
  N0              15               272
  N1               1               112
  N2               0                87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1883V7, binary
                   cls
clus                  0   1
  LRRFIP2 MUTATED    13   0
  LRRFIP2 WILD-TYPE 362  65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  LRRFIP2 MUTATED     13    0
  LRRFIP2 WILD-TYPE  362   65
   clus
vv  LRRFIP2 MUTATED LRRFIP2 WILD-TYPE
  0              13               362
  1               0                65
[1] 2 2
[1] FALSE
D1883V8, binary
                   cls
clus                  0   1
  LRRFIP2 MUTATED     7   9
  LRRFIP2 WILD-TYPE 218 255
[1] "tbl2"
                   cls
clus                [,1] [,2]
  LRRFIP2 MUTATED      7    9
  LRRFIP2 WILD-TYPE  218  255
        clus
vv       LRRFIP2 MUTATED LRRFIP2 WILD-TYPE
  FEMALE               7               218
  MALE                 9               255
[1] 2 2
[1] FALSE
D1883V9, binary
                   cls
clus                  0   1
  LRRFIP2 MUTATED    16   0
  LRRFIP2 WILD-TYPE 334  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  LRRFIP2 MUTATED     16    0
  LRRFIP2 WILD-TYPE  334   22
     clus
vv    LRRFIP2 MUTATED LRRFIP2 WILD-TYPE
  NO               16               334
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  LRRFIP2 MUTATED                     11                             2
  LRRFIP2 WILD-TYPE                  304                            45
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  LRRFIP2 MUTATED                       3                              0
  LRRFIP2 WILD-TYPE                   103                             10
D1883V10, multiclass
                                clus
vv                               LRRFIP2 MUTATED LRRFIP2 WILD-TYPE
  COLON ADENOCARCINOMA                        11               304
  COLON MUCINOUS ADENOCARCINOMA                2                45
  RECTAL ADENOCARCINOMA                        3               103
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  LRRFIP2 MUTATED    11   0   0   2
  LRRFIP2 WILD-TYPE 334   4  31  23
D1883V11, multiclass
    clus
vv   LRRFIP2 MUTATED LRRFIP2 WILD-TYPE
  R0              11               334
  R1               0                 4
  R2               0                31
  RX               2                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1883V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  LRRFIP2 MUTATED                                  0     0
  LRRFIP2 WILD-TYPE                                1    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  LRRFIP2 MUTATED                           0     8
  LRRFIP2 WILD-TYPE                        22   218
D1883V13, multiclass
                                  clus
vv                                 LRRFIP2 MUTATED LRRFIP2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                      0                22
  WHITE                                          8               218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1884) Variable = SEZ6L MUTATION ANALYSIS
D1884V1, survival
                 sevent
clus2               0   1
  SEZ6L MUTATED    16   2
  SEZ6L WILD-TYPE 362  91
  SEZ6L MUTATED SEZ6L WILD-TYPE 
             18             453 
  SEZ6L MUTATED SEZ6L WILD-TYPE 
              2              91 
$`SEZ6L MUTATED`
TCGA-A6-6781 TCGA-AA-3855 TCGA-AA-3947 TCGA-AA-3966 TCGA-AA-3977 TCGA-AA-A00K 
       19.66        32.05        33.01         2.01        25.02        18.05 
TCGA-AD-5900 TCGA-AD-6890 TCGA-AY-6386 TCGA-AZ-6598 TCGA-CA-6717 TCGA-CK-5914 
        0.07         0.79        17.82        49.41        12.76         9.99 
TCGA-CM-4746 TCGA-AG-3594 TCGA-AG-3742 TCGA-AG-4008 TCGA-AG-A002 TCGA-EI-6508 
       37.02         2.01         0.99        17.03        20.98        20.91 

$`SEZ6L WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       12.99        24.00        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
       34.03        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 
        0.92        41.00        39.98        18.05        40.96        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       15.52        56.55         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       33.01        21.44        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        88.21         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07        12.20        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       51.32        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       20.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3598 TCGA-AG-3599 
       24.00         1.02        46.03        34.03        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3878 TCGA-AG-3881 
        7.99         0.99        37.02        32.98         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-A008 TCGA-AG-A00C 
       28.04        36.03        14.04         1.02        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6510 
       51.48        32.61         0.49        20.55        19.96        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  SEZ6L MUTATED SEZ6L WILD-TYPE 
           0.07            0.00 
  SEZ6L MUTATED SEZ6L WILD-TYPE 
          49.41          148.01 
  SEZ6L MUTATED SEZ6L WILD-TYPE 
         17.935          20.550 
[1] "0.1 - 49.4 (17.9)"  "0.0 - 148.0 (20.6)"
[1] "hr=" "1.2"
D1884V2, continuous
D1884V3, binary
                 cls
clus                0   1
  SEZ6L MUTATED    15   5
  SEZ6L WILD-TYPE 351 114
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SEZ6L MUTATED     15    5
  SEZ6L WILD-TYPE  351  114
        clus
vv       SEZ6L MUTATED SEZ6L WILD-TYPE
  COLON             15             351
  RECTUM             5             114
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SEZ6L MUTATED         5        0        1         6         1         0
  SEZ6L WILD-TYPE      86        1       31       132         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SEZ6L MUTATED           0          0          3          2        0         0
  SEZ6L WILD-TYPE        24         11         56         40       48        18
                 vv
clus              STAGE IVB
  SEZ6L MUTATED           0
  SEZ6L WILD-TYPE         1
D1884V4, multiclass
            clus
vv           SEZ6L MUTATED SEZ6L WILD-TYPE
  STAGE I                5              86
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              6             132
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             3              56
  STAGE IIIC             2              40
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  SEZ6L MUTATED     2   5  11   2
  SEZ6L WILD-TYPE  15  87 318  48
D1884V5, multiclass
    clus
vv   SEZ6L MUTATED SEZ6L WILD-TYPE
  T1             2              15
  T2             5              87
  T3            11             318
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  SEZ6L MUTATED    15   4   1
  SEZ6L WILD-TYPE 272 109  86
D1884V6, multiclass
    clus
vv   SEZ6L MUTATED SEZ6L WILD-TYPE
  N0            15             272
  N1             4             109
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1884V7, binary
                 cls
clus                0   1
  SEZ6L MUTATED    13   0
  SEZ6L WILD-TYPE 362  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SEZ6L MUTATED     13    0
  SEZ6L WILD-TYPE  362   65
   clus
vv  SEZ6L MUTATED SEZ6L WILD-TYPE
  0            13             362
  1             0              65
[1] 2 2
[1] FALSE
D1884V8, binary
                 cls
clus                0   1
  SEZ6L MUTATED     7  13
  SEZ6L WILD-TYPE 218 251
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SEZ6L MUTATED      7   13
  SEZ6L WILD-TYPE  218  251
        clus
vv       SEZ6L MUTATED SEZ6L WILD-TYPE
  FEMALE             7             218
  MALE              13             251
[1] 2 2
[1] FALSE
D1884V9, binary
                 cls
clus                0   1
  SEZ6L MUTATED    12   0
  SEZ6L WILD-TYPE 338  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SEZ6L MUTATED     12    0
  SEZ6L WILD-TYPE  338   22
     clus
vv    SEZ6L MUTATED SEZ6L WILD-TYPE
  NO             12             338
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SEZ6L MUTATED                      9                             6
  SEZ6L WILD-TYPE                  306                            41
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SEZ6L MUTATED                       4                              1
  SEZ6L WILD-TYPE                   102                              9
D1884V10, multiclass
                                clus
vv                               SEZ6L MUTATED SEZ6L WILD-TYPE
  COLON ADENOCARCINOMA                       9             306
  COLON MUCINOUS ADENOCARCINOMA              6              41
  RECTAL ADENOCARCINOMA                      4             102
  RECTAL MUCINOUS ADENOCARCINOMA             1               9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  SEZ6L MUTATED    14   0   0   2
  SEZ6L WILD-TYPE 331   4  31  23
D1884V11, multiclass
    clus
vv   SEZ6L MUTATED SEZ6L WILD-TYPE
  R0            14             331
  R1             0               4
  R2             0              31
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1884V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SEZ6L MUTATED                                  0     1
  SEZ6L WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  SEZ6L MUTATED                           2     7
  SEZ6L WILD-TYPE                        20   219
D1884V13, multiclass
                                  clus
vv                                 SEZ6L MUTATED SEZ6L WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    2              20
  WHITE                                        7             219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1885) Variable = ENTHD1 MUTATION ANALYSIS
D1885V1, survival
                  sevent
clus2                0   1
  ENTHD1 MUTATED     7   3
  ENTHD1 WILD-TYPE 371  90
  ENTHD1 MUTATED ENTHD1 WILD-TYPE 
              10              461 
  ENTHD1 MUTATED ENTHD1 WILD-TYPE 
               3               90 
$`ENTHD1 MUTATED`
TCGA-AA-3492 TCGA-AU-6004 TCGA-AZ-4315 TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-5344 
        3.02        27.09        58.39        12.76        10.06        22.03 
TCGA-F4-6856 TCGA-G4-6323 TCGA-AG-A002 TCGA-DY-A1DF 
       35.31        13.78        20.98        24.13 

$`ENTHD1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 
       27.42        10.88         0.20        14.50        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       33.01        21.44        17.82         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6586 
       85.48        63.62        61.91        36.00        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       57.24        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  ENTHD1 MUTATED ENTHD1 WILD-TYPE 
            3.02             0.00 
  ENTHD1 MUTATED ENTHD1 WILD-TYPE 
           58.39           148.01 
  ENTHD1 MUTATED ENTHD1 WILD-TYPE 
          21.505           20.120 
[1] "3.0 - 58.4 (21.5)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.8"
D1885V2, continuous
D1885V3, binary
                  cls
clus                 0   1
  ENTHD1 MUTATED     9   2
  ENTHD1 WILD-TYPE 357 117
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ENTHD1 MUTATED      9    2
  ENTHD1 WILD-TYPE  357  117
        clus
vv       ENTHD1 MUTATED ENTHD1 WILD-TYPE
  COLON               9              357
  RECTUM              2              117
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ENTHD1 MUTATED         3        1        1         4         0         0
  ENTHD1 WILD-TYPE      88        0       31       134        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ENTHD1 MUTATED           0          0          1          1        0
  ENTHD1 WILD-TYPE        24         11         58         41       48
                  vv
clus               STAGE IVA STAGE IVB
  ENTHD1 MUTATED           0         0
  ENTHD1 WILD-TYPE        18         1
D1885V4, multiclass
            clus
vv           ENTHD1 MUTATED ENTHD1 WILD-TYPE
  STAGE I                 3               88
  STAGE IA                1                0
  STAGE II                1               31
  STAGE IIA               4              134
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              1               58
  STAGE IIIC              1               41
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ENTHD1 MUTATED     0   3   7   0
  ENTHD1 WILD-TYPE  17  89 322  50
D1885V5, multiclass
    clus
vv   ENTHD1 MUTATED ENTHD1 WILD-TYPE
  T1              0               17
  T2              3               89
  T3              7              322
  T4              0               50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  ENTHD1 MUTATED     9   1   1
  ENTHD1 WILD-TYPE 278 112  86
D1885V6, multiclass
    clus
vv   ENTHD1 MUTATED ENTHD1 WILD-TYPE
  N0              9              278
  N1              1              112
  N2              1               86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1885V7, binary
                  cls
clus                 0   1
  ENTHD1 MUTATED    10   0
  ENTHD1 WILD-TYPE 365  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ENTHD1 MUTATED     10    0
  ENTHD1 WILD-TYPE  365   65
   clus
vv  ENTHD1 MUTATED ENTHD1 WILD-TYPE
  0             10              365
  1              0               65
[1] 2 2
[1] FALSE
D1885V8, binary
                  cls
clus                 0   1
  ENTHD1 MUTATED     5   6
  ENTHD1 WILD-TYPE 220 258
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ENTHD1 MUTATED      5    6
  ENTHD1 WILD-TYPE  220  258
        clus
vv       ENTHD1 MUTATED ENTHD1 WILD-TYPE
  FEMALE              5              220
  MALE                6              258
[1] 2 2
[1] FALSE
D1885V9, binary
                  cls
clus                 0   1
  ENTHD1 MUTATED     8   0
  ENTHD1 WILD-TYPE 342  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ENTHD1 MUTATED      8    0
  ENTHD1 WILD-TYPE  342   22
     clus
vv    ENTHD1 MUTATED ENTHD1 WILD-TYPE
  NO               8              342
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ENTHD1 MUTATED                      7                             2
  ENTHD1 WILD-TYPE                  308                            45
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ENTHD1 MUTATED                       2                              0
  ENTHD1 WILD-TYPE                   104                             10
D1885V10, multiclass
                                clus
vv                               ENTHD1 MUTATED ENTHD1 WILD-TYPE
  COLON ADENOCARCINOMA                        7              308
  COLON MUCINOUS ADENOCARCINOMA               2               45
  RECTAL ADENOCARCINOMA                       2              104
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ENTHD1 MUTATED     8   0   0   2
  ENTHD1 WILD-TYPE 337   4  31  23
D1885V11, multiclass
    clus
vv   ENTHD1 MUTATED ENTHD1 WILD-TYPE
  R0              8              337
  R1              0                4
  R2              0               31
  RX              2               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1885V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ENTHD1 MUTATED                                  0     2
  ENTHD1 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ENTHD1 MUTATED                           1     5
  ENTHD1 WILD-TYPE                        21   221
D1885V13, multiclass
                                  clus
vv                                 ENTHD1 MUTATED ENTHD1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                9
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                         5              221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1886) Variable = NEDD9 MUTATION ANALYSIS
D1886V1, survival
                 sevent
clus2               0   1
  NEDD9 MUTATED    11   1
  NEDD9 WILD-TYPE 367  92
  NEDD9 MUTATED NEDD9 WILD-TYPE 
             12             459 
  NEDD9 MUTATED NEDD9 WILD-TYPE 
              1              92 
$`NEDD9 MUTATED`
TCGA-A6-5665 TCGA-AA-3518 TCGA-AA-3715 TCGA-AA-3877 TCGA-AA-3949 TCGA-AA-A010 
       22.06         1.02        19.04        31.00        26.01        34.98 
TCGA-AZ-4315 TCGA-D5-6540 TCGA-F4-6805 TCGA-G4-6586 TCGA-G4-6588 TCGA-AG-A002 
       58.39        16.14        34.42        35.80        26.17        20.98 

$`NEDD9 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       27.02        29.98        18.05         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       33.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
       16.31         0.95        33.01        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 
       17.85         4.80        17.13        12.49        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
        6.18        47.87         1.55        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6625 TCGA-G4-6626 
       61.91        36.00        22.09        13.78        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  NEDD9 MUTATED NEDD9 WILD-TYPE 
           1.02            0.00 
  NEDD9 MUTATED NEDD9 WILD-TYPE 
          58.39          148.01 
  NEDD9 MUTATED NEDD9 WILD-TYPE 
          26.09           20.02 
[1] "1.0 - 58.4 (26.1)"  "0.0 - 148.0 (20.0)"
[1] "hr=" "2.3"
D1886V2, continuous
D1886V3, binary
                 cls
clus                0   1
  NEDD9 MUTATED    12   1
  NEDD9 WILD-TYPE 354 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NEDD9 MUTATED     12    1
  NEDD9 WILD-TYPE  354  118
        clus
vv       NEDD9 MUTATED NEDD9 WILD-TYPE
  COLON             12             354
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NEDD9 MUTATED         3        0        1         6         2         0
  NEDD9 WILD-TYPE      88        1       31       132         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NEDD9 MUTATED           0          0          1          0        0         0
  NEDD9 WILD-TYPE        24         11         58         42       48        18
                 vv
clus              STAGE IVB
  NEDD9 MUTATED           0
  NEDD9 WILD-TYPE         1
D1886V4, multiclass
            clus
vv           NEDD9 MUTATED NEDD9 WILD-TYPE
  STAGE I                3              88
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              6             132
  STAGE IIB              2               8
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  NEDD9 MUTATED     1   2   8   2
  NEDD9 WILD-TYPE  16  90 321  48
D1886V5, multiclass
    clus
vv   NEDD9 MUTATED NEDD9 WILD-TYPE
  T1             1              16
  T2             2              90
  T3             8             321
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  NEDD9 MUTATED    12   1   0
  NEDD9 WILD-TYPE 275 112  87
D1886V6, multiclass
    clus
vv   NEDD9 MUTATED NEDD9 WILD-TYPE
  N0            12             275
  N1             1             112
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1886V7, binary
                 cls
clus                0   1
  NEDD9 MUTATED    12   0
  NEDD9 WILD-TYPE 363  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NEDD9 MUTATED     12    0
  NEDD9 WILD-TYPE  363   65
   clus
vv  NEDD9 MUTATED NEDD9 WILD-TYPE
  0            12             363
  1             0              65
[1] 2 2
[1] FALSE
D1886V8, binary
                 cls
clus                0   1
  NEDD9 MUTATED     9   4
  NEDD9 WILD-TYPE 216 260
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NEDD9 MUTATED      9    4
  NEDD9 WILD-TYPE  216  260
        clus
vv       NEDD9 MUTATED NEDD9 WILD-TYPE
  FEMALE             9             216
  MALE               4             260
[1] 2 2
[1] FALSE
D1886V9, binary
                 cls
clus                0   1
  NEDD9 MUTATED    11   0
  NEDD9 WILD-TYPE 339  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NEDD9 MUTATED     11    0
  NEDD9 WILD-TYPE  339   22
     clus
vv    NEDD9 MUTATED NEDD9 WILD-TYPE
  NO             11             339
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  NEDD9 MUTATED                      9                             3
  NEDD9 WILD-TYPE                  306                            44
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  NEDD9 MUTATED                       1                              0
  NEDD9 WILD-TYPE                   105                             10
D1886V10, multiclass
                                clus
vv                               NEDD9 MUTATED NEDD9 WILD-TYPE
  COLON ADENOCARCINOMA                       9             306
  COLON MUCINOUS ADENOCARCINOMA              3              44
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  NEDD9 MUTATED    12   0   0   1
  NEDD9 WILD-TYPE 333   4  31  24
D1886V11, multiclass
    clus
vv   NEDD9 MUTATED NEDD9 WILD-TYPE
  R0            12             333
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1886V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NEDD9 MUTATED                                  0     0
  NEDD9 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  NEDD9 MUTATED                           0     7
  NEDD9 WILD-TYPE                        22   219
D1886V13, multiclass
                                  clus
vv                                 NEDD9 MUTATED NEDD9 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        7             219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1887) Variable = GDF6 MUTATION ANALYSIS
D1887V1, survival
                sevent
clus2              0   1
  GDF6 MUTATED     4   2
  GDF6 WILD-TYPE 374  91
  GDF6 MUTATED GDF6 WILD-TYPE 
             6            465 
  GDF6 MUTATED GDF6 WILD-TYPE 
             2             91 
$`GDF6 MUTATED`
TCGA-A6-6653 TCGA-AA-3662 TCGA-AA-3715 TCGA-DM-A28F TCGA-G4-6304 TCGA-AG-3883 
       24.39         6.05        19.04        35.97        53.62         1.02 

$`GDF6 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
       25.08        25.18        24.16        21.76        24.69        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       19.99        13.94        19.99        61.02        78.08         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H 
      139.17         6.12        81.37       119.93        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3885 
       32.98         0.99         0.99        19.04        19.99        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  GDF6 MUTATED GDF6 WILD-TYPE 
          1.02           0.00 
  GDF6 MUTATED GDF6 WILD-TYPE 
         53.62         148.01 
  GDF6 MUTATED GDF6 WILD-TYPE 
        21.715         20.190 
[1] "1.0 - 53.6 (21.7)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.9"
D1887V2, continuous
D1887V3, binary
                cls
clus               0   1
  GDF6 MUTATED     6   1
  GDF6 WILD-TYPE 360 118
[1] "tbl2"
                cls
clus             [,1] [,2]
  GDF6 MUTATED      6    1
  GDF6 WILD-TYPE  360  118
        clus
vv       GDF6 MUTATED GDF6 WILD-TYPE
  COLON             6            360
  RECTUM            1            118
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GDF6 MUTATED         2        0        1         1         1         0
  GDF6 WILD-TYPE      89        1       31       137         9         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  GDF6 MUTATED           0          0          1          0        1         0
  GDF6 WILD-TYPE        24         11         58         42       47        18
                vv
clus             STAGE IVB
  GDF6 MUTATED           0
  GDF6 WILD-TYPE         1
D1887V4, multiclass
            clus
vv           GDF6 MUTATED GDF6 WILD-TYPE
  STAGE I               2             89
  STAGE IA              0              1
  STAGE II              1             31
  STAGE IIA             1            137
  STAGE IIB             1              9
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            1             58
  STAGE IIIC            0             42
  STAGE IV              1             47
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  GDF6 MUTATED     0   2   3   2
  GDF6 WILD-TYPE  17  90 326  48
D1887V5, multiclass
    clus
vv   GDF6 MUTATED GDF6 WILD-TYPE
  T1            0             17
  T2            2             90
  T3            3            326
  T4            2             48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  GDF6 MUTATED     5   1   1
  GDF6 WILD-TYPE 282 112  86
D1887V6, multiclass
    clus
vv   GDF6 MUTATED GDF6 WILD-TYPE
  N0            5            282
  N1            1            112
  N2            1             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1887V7, binary
                cls
clus               0   1
  GDF6 MUTATED     6   1
  GDF6 WILD-TYPE 369  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  GDF6 MUTATED      6    1
  GDF6 WILD-TYPE  369   64
   clus
vv  GDF6 MUTATED GDF6 WILD-TYPE
  0            6            369
  1            1             64
[1] 2 2
[1] FALSE
D1887V8, binary
                cls
clus               0   1
  GDF6 MUTATED     3   4
  GDF6 WILD-TYPE 222 260
[1] "tbl2"
                cls
clus             [,1] [,2]
  GDF6 MUTATED      3    4
  GDF6 WILD-TYPE  222  260
        clus
vv       GDF6 MUTATED GDF6 WILD-TYPE
  FEMALE            3            222
  MALE              4            260
[1] 2 2
[1] FALSE
D1887V9, binary
                cls
clus               0   1
  GDF6 MUTATED     4   0
  GDF6 WILD-TYPE 346  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  GDF6 MUTATED      4    0
  GDF6 WILD-TYPE  346   22
     clus
vv    GDF6 MUTATED GDF6 WILD-TYPE
  NO             4            346
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  GDF6 MUTATED                      6                             0
  GDF6 WILD-TYPE                  309                            47
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  GDF6 MUTATED                       1                              0
  GDF6 WILD-TYPE                   105                             10
D1887V10, multiclass
                                clus
vv                               GDF6 MUTATED GDF6 WILD-TYPE
  COLON ADENOCARCINOMA                      6            309
  COLON MUCINOUS ADENOCARCINOMA             0             47
  RECTAL ADENOCARCINOMA                     1            105
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  GDF6 MUTATED     4   0   1   0
  GDF6 WILD-TYPE 341   4  30  25
D1887V11, multiclass
    clus
vv   GDF6 MUTATED GDF6 WILD-TYPE
  R0            4            341
  R1            0              4
  R2            1             30
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1887V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GDF6 MUTATED                                  0     0
  GDF6 WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  GDF6 MUTATED                           0     3
  GDF6 WILD-TYPE                        22   223
D1887V13, multiclass
                                  clus
vv                                 GDF6 MUTATED GDF6 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       3            223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1888) Variable = ZNF259 MUTATION ANALYSIS
D1888V1, survival
                  sevent
clus2                0   1
  ZNF259 MUTATED     1   1
  ZNF259 WILD-TYPE 377  92
  ZNF259 MUTATED ZNF259 WILD-TYPE 
               2              469 
  ZNF259 MUTATED ZNF259 WILD-TYPE 
               1               92 
$`ZNF259 MUTATED`
TCGA-AA-3492 TCGA-AG-A002 
        3.02        20.98 

$`ZNF259 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  ZNF259 MUTATED ZNF259 WILD-TYPE 
            3.02             0.00 
  ZNF259 MUTATED ZNF259 WILD-TYPE 
           20.98           148.01 
  ZNF259 MUTATED ZNF259 WILD-TYPE 
           12.00            20.19 
[1] "3.0 - 21.0 (12.0)"  "0.0 - 148.0 (20.2)"
[1] "Remove cluster labels:" "ZNF259 MUTATED"        
D1888V2, continuous
D1888V3, binary
                  cls
clus                 0   1
  ZNF259 MUTATED     2   1
  ZNF259 WILD-TYPE 364 118
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF259 MUTATED      2    1
  ZNF259 WILD-TYPE  364  118
        clus
vv       ZNF259 MUTATED ZNF259 WILD-TYPE
  COLON               2              364
  RECTUM              1              118
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZNF259 MUTATED         1        0        1         1         0         0
  ZNF259 WILD-TYPE      90        1       31       137        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF259 MUTATED           0          0          0          0        0
  ZNF259 WILD-TYPE        24         11         59         42       48
                  vv
clus               STAGE IVA STAGE IVB
  ZNF259 MUTATED           0         0
  ZNF259 WILD-TYPE        18         1
D1888V4, multiclass
            clus
vv           ZNF259 MUTATED ZNF259 WILD-TYPE
  STAGE I                 1               90
  STAGE IA                0                1
  STAGE II                1               31
  STAGE IIA               1              137
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              0               59
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZNF259 MUTATED     0   1   2   0
  ZNF259 WILD-TYPE  17  91 327  50
D1888V5, multiclass
    clus
vv   ZNF259 MUTATED ZNF259 WILD-TYPE
  T1              0               17
  T2              1               91
  T3              2              327
  T4              0               50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  ZNF259 MUTATED     3   0   0
  ZNF259 WILD-TYPE 284 113  87
D1888V6, multiclass
    clus
vv   ZNF259 MUTATED ZNF259 WILD-TYPE
  N0              3              284
  N1              0              113
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1888V7, binary
                  cls
clus                 0   1
  ZNF259 MUTATED     3   0
  ZNF259 WILD-TYPE 372  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF259 MUTATED      3    0
  ZNF259 WILD-TYPE  372   65
   clus
vv  ZNF259 MUTATED ZNF259 WILD-TYPE
  0              3              372
  1              0               65
[1] 2 2
[1] FALSE
D1888V8, binary
                  cls
clus                 0   1
  ZNF259 MUTATED     2   1
  ZNF259 WILD-TYPE 223 263
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF259 MUTATED      2    1
  ZNF259 WILD-TYPE  223  263
        clus
vv       ZNF259 MUTATED ZNF259 WILD-TYPE
  FEMALE              2              223
  MALE                1              263
[1] 2 2
[1] FALSE
D1888V9, binary
                  cls
clus                 0   1
  ZNF259 MUTATED     2   0
  ZNF259 WILD-TYPE 348  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF259 MUTATED      2    0
  ZNF259 WILD-TYPE  348   22
     clus
vv    ZNF259 MUTATED ZNF259 WILD-TYPE
  NO               2              348
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ZNF259 MUTATED                      2                             0
  ZNF259 WILD-TYPE                  313                            47
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ZNF259 MUTATED                       1                              0
  ZNF259 WILD-TYPE                   105                             10
D1888V10, multiclass
                                clus
vv                               ZNF259 MUTATED ZNF259 WILD-TYPE
  COLON ADENOCARCINOMA                        2              313
  COLON MUCINOUS ADENOCARCINOMA               0               47
  RECTAL ADENOCARCINOMA                       1              105
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ZNF259 MUTATED     3   0   0   0
  ZNF259 WILD-TYPE 342   4  31  25
D1888V11, multiclass
    clus
vv   ZNF259 MUTATED ZNF259 WILD-TYPE
  R0              3              342
  R1              0                4
  R2              0               31
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1888V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF259 MUTATED                                  0     0
  ZNF259 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZNF259 MUTATED                           0     0
  ZNF259 WILD-TYPE                        22   226
D1888V13, multiclass

Clustering(1889) Variable = SRL MUTATION ANALYSIS
D1889V1, survival
               sevent
clus2             0   1
  SRL MUTATED     8   4
  SRL WILD-TYPE 370  89
  SRL MUTATED SRL WILD-TYPE 
           12           459 
  SRL MUTATED SRL WILD-TYPE 
            4            89 
$`SRL MUTATED`
TCGA-A6-5657 TCGA-A6-6780 TCGA-AA-3663 TCGA-AA-A00N TCGA-AY-6197 TCGA-AZ-6599 
       31.63        20.12         6.97         4.01        21.44         6.77 
TCGA-CA-6717 TCGA-CM-4752 TCGA-CM-6676 TCGA-DM-A0XD TCGA-DM-A1DB TCGA-DM-A1HB 
       12.76        13.02        11.08        24.43        44.32       135.65 

$`SRL WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 
       14.50        27.09        16.31         0.95        33.01        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       88.21        49.41        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07        12.20        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       37.02        25.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       12.95        13.05        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
      140.38         7.50       131.51       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  SRL MUTATED SRL WILD-TYPE 
         4.01          0.00 
  SRL MUTATED SRL WILD-TYPE 
       135.65        148.01 
  SRL MUTATED SRL WILD-TYPE 
        16.57         20.28 
[1] "4.0 - 135.7 (16.6)" "0.0 - 148.0 (20.3)"
[1] "hr=" "1.8"
D1889V2, continuous
D1889V3, binary
               cls
clus              0   1
  SRL MUTATED    12   0
  SRL WILD-TYPE 354 119
[1] "tbl2"
               cls
clus            [,1] [,2]
  SRL MUTATED     12    0
  SRL WILD-TYPE  354  119
        clus
vv       SRL MUTATED SRL WILD-TYPE
  COLON           12           354
  RECTUM           0           119
[1] 2 2
[1] FALSE
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SRL MUTATED         2        0        1         6         1         0
  SRL WILD-TYPE      89        1       31       132         9         1
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SRL MUTATED           0          0          2          0        0         0
  SRL WILD-TYPE        24         11         57         42       48        18
               vv
clus            STAGE IVB
  SRL MUTATED           0
  SRL WILD-TYPE         1
D1889V4, multiclass
            clus
vv           SRL MUTATED SRL WILD-TYPE
  STAGE I              2            89
  STAGE IA             0             1
  STAGE II             1            31
  STAGE IIA            6           132
  STAGE IIB            1             9
  STAGE IIC            0             1
  STAGE III            0            24
  STAGE IIIA           0            11
  STAGE IIIB           2            57
  STAGE IIIC           0            42
  STAGE IV             0            48
  STAGE IVA            0            18
  STAGE IVB            0             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  SRL MUTATED     0   2   9   1
  SRL WILD-TYPE  17  90 320  49
D1889V5, multiclass
    clus
vv   SRL MUTATED SRL WILD-TYPE
  T1           0            17
  T2           2            90
  T3           9           320
  T4           1            49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2
  SRL MUTATED    10   2   0
  SRL WILD-TYPE 277 111  87
D1889V6, multiclass
    clus
vv   SRL MUTATED SRL WILD-TYPE
  N0          10           277
  N1           2           111
  N2           0            87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1889V7, binary
               cls
clus              0   1
  SRL MUTATED     9   0
  SRL WILD-TYPE 366  65
[1] "tbl2"
               cls
clus            [,1] [,2]
  SRL MUTATED      9    0
  SRL WILD-TYPE  366   65
   clus
vv  SRL MUTATED SRL WILD-TYPE
  0           9           366
  1           0            65
[1] 2 2
[1] FALSE
D1889V8, binary
               cls
clus              0   1
  SRL MUTATED     0  12
  SRL WILD-TYPE 225 252
[1] "tbl2"
               cls
clus            [,1] [,2]
  SRL MUTATED      0   12
  SRL WILD-TYPE  225  252
        clus
vv       SRL MUTATED SRL WILD-TYPE
  FEMALE           0           225
  MALE            12           252
[1] 2 2
[1] FALSE
D1889V9, binary
               cls
clus              0   1
  SRL MUTATED     8   0
  SRL WILD-TYPE 342  22
[1] "tbl2"
               cls
clus            [,1] [,2]
  SRL MUTATED      8    0
  SRL WILD-TYPE  342   22
     clus
vv    SRL MUTATED SRL WILD-TYPE
  NO            8           342
  YES           0            22
[1] 2 2
[1] FALSE
               vv
clus            COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SRL MUTATED                      8                             3
  SRL WILD-TYPE                  307                            44
               vv
clus            RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SRL MUTATED                       0                              0
  SRL WILD-TYPE                   106                             10
D1889V10, multiclass
                                clus
vv                               SRL MUTATED SRL WILD-TYPE
  COLON ADENOCARCINOMA                     8           307
  COLON MUCINOUS ADENOCARCINOMA            3            44
  RECTAL ADENOCARCINOMA                    0           106
  RECTAL MUCINOUS ADENOCARCINOMA           0            10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             R0  R1  R2  RX
  SRL MUTATED     6   0   0   1
  SRL WILD-TYPE 339   4  31  24
D1889V11, multiclass
    clus
vv   SRL MUTATED SRL WILD-TYPE
  R0           6           339
  R1           0             4
  R2           0            31
  RX           1            24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1889V12, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SRL MUTATED                                  0     1
  SRL WILD-TYPE                                1    10
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  SRL MUTATED                           2     7
  SRL WILD-TYPE                        20   219
D1889V13, multiclass
                                  clus
vv                                 SRL MUTATED SRL WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      1            10
  BLACK OR AFRICAN AMERICAN                  2            20
  WHITE                                      7           219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1890) Variable = G3BP1 MUTATION ANALYSIS
D1890V1, survival
                 sevent
clus2               0   1
  G3BP1 MUTATED    11   1
  G3BP1 WILD-TYPE 367  92
  G3BP1 MUTATED G3BP1 WILD-TYPE 
             12             459 
  G3BP1 MUTATED G3BP1 WILD-TYPE 
              1              92 
$`G3BP1 MUTATED`
TCGA-A6-2672 TCGA-AA-3663 TCGA-AA-3864 TCGA-AA-3947 TCGA-AA-3977 TCGA-AA-A00N 
       46.65         6.97        53.00        33.01        25.02         4.01 
TCGA-AD-6889 TCGA-AZ-4315 TCGA-CA-6717 TCGA-D5-6540 TCGA-D5-6928 TCGA-AG-A002 
       56.55        58.39        12.76        16.14        11.64        20.98 

$`G3BP1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 
        0.99        31.07        31.07        30.05        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       21.37        15.52         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        33.01        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.20        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       17.13        12.49        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6930 
       12.43        14.30         9.04         9.44         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  G3BP1 MUTATED G3BP1 WILD-TYPE 
           4.01            0.00 
  G3BP1 MUTATED G3BP1 WILD-TYPE 
          58.39          148.01 
  G3BP1 MUTATED G3BP1 WILD-TYPE 
          23.00           20.12 
[1] "4.0 - 58.4 (23.0)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "2.8"
D1890V2, continuous
D1890V3, binary
                 cls
clus                0   1
  G3BP1 MUTATED    11   1
  G3BP1 WILD-TYPE 355 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  G3BP1 MUTATED     11    1
  G3BP1 WILD-TYPE  355  118
        clus
vv       G3BP1 MUTATED G3BP1 WILD-TYPE
  COLON             11             355
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  G3BP1 MUTATED         2        0        2         4         2         0
  G3BP1 WILD-TYPE      89        1       30       134         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  G3BP1 MUTATED           0          0          1          0        0         0
  G3BP1 WILD-TYPE        24         11         58         42       48        18
                 vv
clus              STAGE IVB
  G3BP1 MUTATED           0
  G3BP1 WILD-TYPE         1
D1890V4, multiclass
            clus
vv           G3BP1 MUTATED G3BP1 WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA              4             134
  STAGE IIB              2               8
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  G3BP1 MUTATED     0   3   7   2
  G3BP1 WILD-TYPE  17  89 322  48
D1890V5, multiclass
    clus
vv   G3BP1 MUTATED G3BP1 WILD-TYPE
  T1             0              17
  T2             3              89
  T3             7             322
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  G3BP1 MUTATED    11   1   0
  G3BP1 WILD-TYPE 276 112  87
D1890V6, multiclass
    clus
vv   G3BP1 MUTATED G3BP1 WILD-TYPE
  N0            11             276
  N1             1             112
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1890V7, binary
                 cls
clus                0   1
  G3BP1 MUTATED    11   0
  G3BP1 WILD-TYPE 364  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  G3BP1 MUTATED     11    0
  G3BP1 WILD-TYPE  364   65
   clus
vv  G3BP1 MUTATED G3BP1 WILD-TYPE
  0            11             364
  1             0              65
[1] 2 2
[1] FALSE
D1890V8, binary
                 cls
clus                0   1
  G3BP1 MUTATED     2  10
  G3BP1 WILD-TYPE 223 254
[1] "tbl2"
                 cls
clus              [,1] [,2]
  G3BP1 MUTATED      2   10
  G3BP1 WILD-TYPE  223  254
        clus
vv       G3BP1 MUTATED G3BP1 WILD-TYPE
  FEMALE             2             223
  MALE              10             254
[1] 2 2
[1] FALSE
D1890V9, binary
                 cls
clus                0   1
  G3BP1 MUTATED    10   0
  G3BP1 WILD-TYPE 340  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  G3BP1 MUTATED     10    0
  G3BP1 WILD-TYPE  340   22
     clus
vv    G3BP1 MUTATED G3BP1 WILD-TYPE
  NO             10             340
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  G3BP1 MUTATED                      6                             5
  G3BP1 WILD-TYPE                  309                            42
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  G3BP1 MUTATED                       1                              0
  G3BP1 WILD-TYPE                   105                             10
D1890V10, multiclass
                                clus
vv                               G3BP1 MUTATED G3BP1 WILD-TYPE
  COLON ADENOCARCINOMA                       6             309
  COLON MUCINOUS ADENOCARCINOMA              5              42
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  G3BP1 MUTATED     9   0   0   1
  G3BP1 WILD-TYPE 336   4  31  24
D1890V11, multiclass
    clus
vv   G3BP1 MUTATED G3BP1 WILD-TYPE
  R0             9             336
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1890V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  G3BP1 MUTATED                                  0     2
  G3BP1 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  G3BP1 MUTATED                           0     4
  G3BP1 WILD-TYPE                        22   222
D1890V13, multiclass
                                  clus
vv                                 G3BP1 MUTATED G3BP1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               9
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        4             222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1891) Variable = CYP4F11 MUTATION ANALYSIS
D1891V1, survival
                   sevent
clus2                 0   1
  CYP4F11 MUTATED     4   2
  CYP4F11 WILD-TYPE 374  91
  CYP4F11 MUTATED CYP4F11 WILD-TYPE 
                6               465 
  CYP4F11 MUTATED CYP4F11 WILD-TYPE 
                2                91 
$`CYP4F11 MUTATED`
TCGA-AA-3713 TCGA-AA-A00N TCGA-AD-5900 TCGA-AZ-6601 TCGA-CM-6171 TCGA-AG-3894 
       19.04         4.01         0.07       100.01        14.04        14.01 

$`CYP4F11 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       39.98        18.05        40.96        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       13.02        15.02        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3896 
       17.95        36.95        17.03        13.02        35.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  CYP4F11 MUTATED CYP4F11 WILD-TYPE 
             0.07              0.00 
  CYP4F11 MUTATED CYP4F11 WILD-TYPE 
           100.01            148.01 
  CYP4F11 MUTATED CYP4F11 WILD-TYPE 
           14.025            20.550 
[1] "0.1 - 100.0 (14.0)" "0.0 - 148.0 (20.6)"
[1] "hr=" "1.7"
D1891V2, continuous
D1891V3, binary
                   cls
clus                  0   1
  CYP4F11 MUTATED     6   1
  CYP4F11 WILD-TYPE 360 118
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CYP4F11 MUTATED      6    1
  CYP4F11 WILD-TYPE  360  118
        clus
vv       CYP4F11 MUTATED CYP4F11 WILD-TYPE
  COLON                6               360
  RECTUM               1               118
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CYP4F11 MUTATED         2        0        1         1         1         0
  CYP4F11 WILD-TYPE      89        1       31       137         9         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CYP4F11 MUTATED           0          0          0          1        1
  CYP4F11 WILD-TYPE        24         11         59         41       47
                   vv
clus                STAGE IVA STAGE IVB
  CYP4F11 MUTATED           0         0
  CYP4F11 WILD-TYPE        18         1
D1891V4, multiclass
            clus
vv           CYP4F11 MUTATED CYP4F11 WILD-TYPE
  STAGE I                  2                89
  STAGE IA                 0                 1
  STAGE II                 1                31
  STAGE IIA                1               137
  STAGE IIB                1                 9
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               0                11
  STAGE IIIB               0                59
  STAGE IIIC               1                41
  STAGE IV                 1                47
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  CYP4F11 MUTATED     0   2   4   1
  CYP4F11 WILD-TYPE  17  90 325  49
D1891V5, multiclass
    clus
vv   CYP4F11 MUTATED CYP4F11 WILD-TYPE
  T1               0                17
  T2               2                90
  T3               4               325
  T4               1                49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  CYP4F11 MUTATED     6   0   1
  CYP4F11 WILD-TYPE 281 113  86
D1891V6, multiclass
    clus
vv   CYP4F11 MUTATED CYP4F11 WILD-TYPE
  N0               6               281
  N1               0               113
  N2               1                86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1891V7, binary
                   cls
clus                  0   1
  CYP4F11 MUTATED     4   1
  CYP4F11 WILD-TYPE 371  64
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CYP4F11 MUTATED      4    1
  CYP4F11 WILD-TYPE  371   64
   clus
vv  CYP4F11 MUTATED CYP4F11 WILD-TYPE
  0               4               371
  1               1                64
[1] 2 2
[1] FALSE
D1891V8, binary
                   cls
clus                  0   1
  CYP4F11 MUTATED     1   6
  CYP4F11 WILD-TYPE 224 258
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CYP4F11 MUTATED      1    6
  CYP4F11 WILD-TYPE  224  258
        clus
vv       CYP4F11 MUTATED CYP4F11 WILD-TYPE
  FEMALE               1               224
  MALE                 6               258
[1] 2 2
[1] FALSE
D1891V9, binary
                   cls
clus                  0   1
  CYP4F11 MUTATED     2   2
  CYP4F11 WILD-TYPE 348  20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CYP4F11 MUTATED      2    2
  CYP4F11 WILD-TYPE  348   20
     clus
vv    CYP4F11 MUTATED CYP4F11 WILD-TYPE
  NO                2               348
  YES               2                20
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CYP4F11 MUTATED                      3                             3
  CYP4F11 WILD-TYPE                  312                            44
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CYP4F11 MUTATED                       1                              0
  CYP4F11 WILD-TYPE                   105                             10
D1891V10, multiclass
                                clus
vv                               CYP4F11 MUTATED CYP4F11 WILD-TYPE
  COLON ADENOCARCINOMA                         3               312
  COLON MUCINOUS ADENOCARCINOMA                3                44
  RECTAL ADENOCARCINOMA                        1               105
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  CYP4F11 MUTATED     5   0   1   0
  CYP4F11 WILD-TYPE 340   4  30  25
D1891V11, multiclass
    clus
vv   CYP4F11 MUTATED CYP4F11 WILD-TYPE
  R0               5               340
  R1               0                 4
  R2               1                30
  RX               0                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1891V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CYP4F11 MUTATED                                  0     0
  CYP4F11 WILD-TYPE                                1    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  CYP4F11 MUTATED                           0     4
  CYP4F11 WILD-TYPE                        22   222
D1891V13, multiclass
                                  clus
vv                                 CYP4F11 MUTATED CYP4F11 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                      0                22
  WHITE                                          4               222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1892) Variable = UBE3C MUTATION ANALYSIS
D1892V1, survival
                 sevent
clus2               0   1
  UBE3C MUTATED    15   4
  UBE3C WILD-TYPE 363  89
  UBE3C MUTATED UBE3C WILD-TYPE 
             19             452 
  UBE3C MUTATED UBE3C WILD-TYPE 
              4              89 
$`UBE3C MUTATED`
TCGA-A6-5657 TCGA-A6-5662 TCGA-AA-3715 TCGA-AA-3819 TCGA-AA-3977 TCGA-AA-A00N 
       31.63        23.61        19.04        25.02        25.02         4.01 
TCGA-AA-A010 TCGA-AA-A01I TCGA-AD-5900 TCGA-AU-6004 TCGA-AZ-4315 TCGA-AZ-5403 
       34.98        31.00         0.07        27.09        58.39        62.79 
TCGA-AZ-6600 TCGA-CA-6717 TCGA-CM-5864 TCGA-DM-A1D9 TCGA-F4-6808 TCGA-G4-6586 
       12.10        12.76        15.02       140.38        33.67        35.80 
TCGA-AG-A002 
       20.98 

$`UBE3C WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5664 TCGA-A6-5665 
       32.91        30.44        29.19        33.53        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
       33.04         0.99         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       12.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       39.98        18.05        40.96        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
        0.20        14.50        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5407 
       17.82         1.41         5.13       106.75        22.36        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       49.41         6.77       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07        12.20        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5868 TCGA-CM-6161 
       32.02        15.02         5.03        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
       12.59         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6854 
        1.55        34.42        41.42        16.24        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       22.09        13.78        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  UBE3C MUTATED UBE3C WILD-TYPE 
           0.07            0.00 
  UBE3C MUTATED UBE3C WILD-TYPE 
         140.38          148.01 
  UBE3C MUTATED UBE3C WILD-TYPE 
          25.02           20.02 
[1] "0.1 - 140.4 (25.0)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.1"
D1892V2, continuous
D1892V3, binary
                 cls
clus                0   1
  UBE3C MUTATED    18   1
  UBE3C WILD-TYPE 348 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UBE3C MUTATED     18    1
  UBE3C WILD-TYPE  348  118
        clus
vv       UBE3C MUTATED UBE3C WILD-TYPE
  COLON             18             348
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  UBE3C MUTATED         6        0        2         5         2         0
  UBE3C WILD-TYPE      85        1       30       133         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  UBE3C MUTATED           0          0          1          0        1         1
  UBE3C WILD-TYPE        24         11         58         42       47        17
                 vv
clus              STAGE IVB
  UBE3C MUTATED           0
  UBE3C WILD-TYPE         1
D1892V4, multiclass
            clus
vv           UBE3C MUTATED UBE3C WILD-TYPE
  STAGE I                6              85
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA              5             133
  STAGE IIB              2               8
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             0              42
  STAGE IV               1              47
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  UBE3C MUTATED     1   6   9   3
  UBE3C WILD-TYPE  16  86 320  47
D1892V5, multiclass
    clus
vv   UBE3C MUTATED UBE3C WILD-TYPE
  T1             1              16
  T2             6              86
  T3             9             320
  T4             3              47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  UBE3C MUTATED    16   2   1
  UBE3C WILD-TYPE 271 111  86
D1892V6, multiclass
    clus
vv   UBE3C MUTATED UBE3C WILD-TYPE
  N0            16             271
  N1             2             111
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1892V7, binary
                 cls
clus                0   1
  UBE3C MUTATED    14   2
  UBE3C WILD-TYPE 361  63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UBE3C MUTATED     14    2
  UBE3C WILD-TYPE  361   63
   clus
vv  UBE3C MUTATED UBE3C WILD-TYPE
  0            14             361
  1             2              63
[1] 2 2
[1] FALSE
D1892V8, binary
                 cls
clus                0   1
  UBE3C MUTATED     6  13
  UBE3C WILD-TYPE 219 251
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UBE3C MUTATED      6   13
  UBE3C WILD-TYPE  219  251
        clus
vv       UBE3C MUTATED UBE3C WILD-TYPE
  FEMALE             6             219
  MALE              13             251
[1] 2 2
[1] FALSE
D1892V9, binary
                 cls
clus                0   1
  UBE3C MUTATED    14   0
  UBE3C WILD-TYPE 336  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UBE3C MUTATED     14    0
  UBE3C WILD-TYPE  336   22
     clus
vv    UBE3C MUTATED UBE3C WILD-TYPE
  NO             14             336
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  UBE3C MUTATED                     15                             3
  UBE3C WILD-TYPE                  300                            44
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  UBE3C MUTATED                       1                              0
  UBE3C WILD-TYPE                   105                             10
D1892V10, multiclass
                                clus
vv                               UBE3C MUTATED UBE3C WILD-TYPE
  COLON ADENOCARCINOMA                      15             300
  COLON MUCINOUS ADENOCARCINOMA              3              44
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  UBE3C MUTATED    13   0   0   1
  UBE3C WILD-TYPE 332   4  31  24
D1892V11, multiclass
    clus
vv   UBE3C MUTATED UBE3C WILD-TYPE
  R0            13             332
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1892V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  UBE3C MUTATED                                  0     1
  UBE3C WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  UBE3C MUTATED                           2     9
  UBE3C WILD-TYPE                        20   217
D1892V13, multiclass
                                  clus
vv                                 UBE3C MUTATED UBE3C WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    2              20
  WHITE                                        9             217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1893) Variable = LIPH MUTATION ANALYSIS
D1893V1, survival
                sevent
clus2              0   1
  LIPH MUTATED     9   1
  LIPH WILD-TYPE 369  92
  LIPH MUTATED LIPH WILD-TYPE 
            10            461 
  LIPH MUTATED LIPH WILD-TYPE 
             1             92 
$`LIPH MUTATED`
TCGA-A6-6141 TCGA-AA-3947 TCGA-AA-A010 TCGA-CA-6717 TCGA-CK-5913 TCGA-D5-6532 
        8.38        33.01        34.98        12.76        51.32        18.25 
TCGA-G4-6321 TCGA-G4-6588 TCGA-G4-6626 TCGA-AG-A002 
       22.09        26.17        46.75        20.98 

$`LIPH WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 
       22.09        22.06        32.71        27.09        22.52        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
        2.01        12.99        24.00        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       49.08         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6534 
       19.59        56.09        55.92        20.19         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 
       55.04        85.48        63.62        61.91        36.00        13.78 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       35.80        91.79        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  LIPH MUTATED LIPH WILD-TYPE 
          8.38           0.00 
  LIPH MUTATED LIPH WILD-TYPE 
         51.32         148.01 
  LIPH MUTATED LIPH WILD-TYPE 
         24.13          20.05 
[1] "8.4 - 51.3 (24.1)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "2.1"
D1893V2, continuous
D1893V3, binary
                cls
clus               0   1
  LIPH MUTATED     9   1
  LIPH WILD-TYPE 357 118
[1] "tbl2"
                cls
clus             [,1] [,2]
  LIPH MUTATED      9    1
  LIPH WILD-TYPE  357  118
        clus
vv       LIPH MUTATED LIPH WILD-TYPE
  COLON             9            357
  RECTUM            1            118
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  LIPH MUTATED         1        0        0         6         2         0
  LIPH WILD-TYPE      90        1       32       132         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  LIPH MUTATED           1          0          0          0        0         0
  LIPH WILD-TYPE        23         11         59         42       48        18
                vv
clus             STAGE IVB
  LIPH MUTATED           0
  LIPH WILD-TYPE         1
D1893V4, multiclass
            clus
vv           LIPH MUTATED LIPH WILD-TYPE
  STAGE I               1             90
  STAGE IA              0              1
  STAGE II              0             32
  STAGE IIA             6            132
  STAGE IIB             2              8
  STAGE IIC             0              1
  STAGE III             1             23
  STAGE IIIA            0             11
  STAGE IIIB            0             59
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  LIPH MUTATED     0   2   6   2
  LIPH WILD-TYPE  17  90 323  48
D1893V5, multiclass
    clus
vv   LIPH MUTATED LIPH WILD-TYPE
  T1            0             17
  T2            2             90
  T3            6            323
  T4            2             48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  LIPH MUTATED     9   1   0
  LIPH WILD-TYPE 278 112  87
D1893V6, multiclass
    clus
vv   LIPH MUTATED LIPH WILD-TYPE
  N0            9            278
  N1            1            112
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1893V7, binary
                cls
clus               0   1
  LIPH MUTATED     8   0
  LIPH WILD-TYPE 367  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  LIPH MUTATED      8    0
  LIPH WILD-TYPE  367   65
   clus
vv  LIPH MUTATED LIPH WILD-TYPE
  0            8            367
  1            0             65
[1] 2 2
[1] FALSE
D1893V8, binary
                cls
clus               0   1
  LIPH MUTATED     5   5
  LIPH WILD-TYPE 220 259
[1] "tbl2"
                cls
clus             [,1] [,2]
  LIPH MUTATED      5    5
  LIPH WILD-TYPE  220  259
        clus
vv       LIPH MUTATED LIPH WILD-TYPE
  FEMALE            5            220
  MALE              5            259
[1] 2 2
[1] FALSE
D1893V9, binary
                cls
clus               0   1
  LIPH MUTATED    10   0
  LIPH WILD-TYPE 340  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  LIPH MUTATED     10    0
  LIPH WILD-TYPE  340   22
     clus
vv    LIPH MUTATED LIPH WILD-TYPE
  NO            10            340
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  LIPH MUTATED                      7                             2
  LIPH WILD-TYPE                  308                            45
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  LIPH MUTATED                       1                              0
  LIPH WILD-TYPE                   105                             10
D1893V10, multiclass
                                clus
vv                               LIPH MUTATED LIPH WILD-TYPE
  COLON ADENOCARCINOMA                      7            308
  COLON MUCINOUS ADENOCARCINOMA             2             45
  RECTAL ADENOCARCINOMA                     1            105
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  LIPH MUTATED     7   0   0   2
  LIPH WILD-TYPE 338   4  31  23
D1893V11, multiclass
    clus
vv   LIPH MUTATED LIPH WILD-TYPE
  R0            7            338
  R1            0              4
  R2            0             31
  RX            2             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1893V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  LIPH MUTATED                                  0     1
  LIPH WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  LIPH MUTATED                           1     5
  LIPH WILD-TYPE                        21   221
D1893V13, multiclass
                                  clus
vv                                 LIPH MUTATED LIPH WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                       5            221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1894) Variable = GLT8D1 MUTATION ANALYSIS
D1894V1, survival
                  sevent
clus2                0   1
  GLT8D1 MUTATED     7   1
  GLT8D1 WILD-TYPE 371  92
  GLT8D1 MUTATED GLT8D1 WILD-TYPE 
               8              463 
  GLT8D1 MUTATED GLT8D1 WILD-TYPE 
               1               92 
$`GLT8D1 MUTATED`
TCGA-A6-6780 TCGA-AA-A010 TCGA-AD-5900 TCGA-AD-6895 TCGA-AZ-4315 TCGA-CK-4952 
       20.12        34.98         0.07         0.72        58.39        15.62 
TCGA-D5-6930 TCGA-AG-3574 
        1.51        36.03 

$`GLT8D1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       39.98        18.05        40.96        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.79         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 
       14.30        17.56       148.01        85.45        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 
        9.04         9.44        11.64         4.80        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3575 
       14.50        16.83        15.39        20.02        10.39        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  GLT8D1 MUTATED GLT8D1 WILD-TYPE 
            0.07             0.00 
  GLT8D1 MUTATED GLT8D1 WILD-TYPE 
           58.39           148.01 
  GLT8D1 MUTATED GLT8D1 WILD-TYPE 
           17.87            20.28 
[1] "0.1 - 58.4 (17.9)"  "0.0 - 148.0 (20.3)"
[1] "hr=" "1.3"
D1894V2, continuous
D1894V3, binary
                  cls
clus                 0   1
  GLT8D1 MUTATED     8   1
  GLT8D1 WILD-TYPE 358 118
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GLT8D1 MUTATED      8    1
  GLT8D1 WILD-TYPE  358  118
        clus
vv       GLT8D1 MUTATED GLT8D1 WILD-TYPE
  COLON               8              358
  RECTUM              1              118
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GLT8D1 MUTATED         1        0        1         4         1         0
  GLT8D1 WILD-TYPE      90        1       31       134         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GLT8D1 MUTATED           0          0          0          1        0
  GLT8D1 WILD-TYPE        24         11         59         41       48
                  vv
clus               STAGE IVA STAGE IVB
  GLT8D1 MUTATED           0         0
  GLT8D1 WILD-TYPE        18         1
D1894V4, multiclass
            clus
vv           GLT8D1 MUTATED GLT8D1 WILD-TYPE
  STAGE I                 1               90
  STAGE IA                0                1
  STAGE II                1               31
  STAGE IIA               4              134
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              0               59
  STAGE IIIC              1               41
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  GLT8D1 MUTATED     0   1   6   2
  GLT8D1 WILD-TYPE  17  91 323  48
D1894V5, multiclass
    clus
vv   GLT8D1 MUTATED GLT8D1 WILD-TYPE
  T1              0               17
  T2              1               91
  T3              6              323
  T4              2               48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  GLT8D1 MUTATED     7   1   1
  GLT8D1 WILD-TYPE 280 112  86
D1894V6, multiclass
    clus
vv   GLT8D1 MUTATED GLT8D1 WILD-TYPE
  N0              7              280
  N1              1              112
  N2              1               86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1894V7, binary
                  cls
clus                 0   1
  GLT8D1 MUTATED     6   0
  GLT8D1 WILD-TYPE 369  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GLT8D1 MUTATED      6    0
  GLT8D1 WILD-TYPE  369   65
   clus
vv  GLT8D1 MUTATED GLT8D1 WILD-TYPE
  0              6              369
  1              0               65
[1] 2 2
[1] FALSE
D1894V8, binary
                  cls
clus                 0   1
  GLT8D1 MUTATED     4   5
  GLT8D1 WILD-TYPE 221 259
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GLT8D1 MUTATED      4    5
  GLT8D1 WILD-TYPE  221  259
        clus
vv       GLT8D1 MUTATED GLT8D1 WILD-TYPE
  FEMALE              4              221
  MALE                5              259
[1] 2 2
[1] FALSE
D1894V9, binary
                  cls
clus                 0   1
  GLT8D1 MUTATED     4   0
  GLT8D1 WILD-TYPE 346  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GLT8D1 MUTATED      4    0
  GLT8D1 WILD-TYPE  346   22
     clus
vv    GLT8D1 MUTATED GLT8D1 WILD-TYPE
  NO               4              346
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  GLT8D1 MUTATED                      4                             4
  GLT8D1 WILD-TYPE                  311                            43
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  GLT8D1 MUTATED                       1                              0
  GLT8D1 WILD-TYPE                   105                             10
D1894V10, multiclass
                                clus
vv                               GLT8D1 MUTATED GLT8D1 WILD-TYPE
  COLON ADENOCARCINOMA                        4              311
  COLON MUCINOUS ADENOCARCINOMA               4               43
  RECTAL ADENOCARCINOMA                       1              105
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  GLT8D1 MUTATED     6   0   0   1
  GLT8D1 WILD-TYPE 339   4  31  24
D1894V11, multiclass
    clus
vv   GLT8D1 MUTATED GLT8D1 WILD-TYPE
  R0              6              339
  R1              0                4
  R2              0               31
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1894V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GLT8D1 MUTATED                                  0     0
  GLT8D1 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  GLT8D1 MUTATED                           0     6
  GLT8D1 WILD-TYPE                        22   220
D1894V13, multiclass
                                  clus
vv                                 GLT8D1 MUTATED GLT8D1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         6              220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1895) Variable = C20ORF43 MUTATION ANALYSIS
D1895V1, survival
                    sevent
clus2                  0   1
  C20ORF43 MUTATED     3   0
  C20ORF43 WILD-TYPE 375  93
  C20ORF43 MUTATED C20ORF43 WILD-TYPE 
                 3                468 
  C20ORF43 MUTATED C20ORF43 WILD-TYPE 
                 0                 93 
$`C20ORF43 MUTATED`
TCGA-AA-3510 TCGA-CK-4947 TCGA-AG-3892 
       63.98        17.56        13.02 

$`C20ORF43 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4948 
        0.07        12.20        12.76        10.06        14.30       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  C20ORF43 MUTATED C20ORF43 WILD-TYPE 
             13.02               0.00 
  C20ORF43 MUTATED C20ORF43 WILD-TYPE 
             63.98             148.01 
  C20ORF43 MUTATED C20ORF43 WILD-TYPE 
            17.560             20.235 
[1] "13.0 - 64.0 (17.6)" "0.0 - 148.0 (20.2)"
[1] "hr="     "3300000"
D1895V2, continuous
D1895V3, binary
                    cls
clus                   0   1
  C20ORF43 MUTATED     3   1
  C20ORF43 WILD-TYPE 363 118
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C20ORF43 MUTATED      3    1
  C20ORF43 WILD-TYPE  363  118
        clus
vv       C20ORF43 MUTATED C20ORF43 WILD-TYPE
  COLON                 3                363
  RECTUM                1                118
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  C20ORF43 MUTATED         1        0        1         0         0         0
  C20ORF43 WILD-TYPE      90        1       31       138        10         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C20ORF43 MUTATED           0          0          1          1        0
  C20ORF43 WILD-TYPE        24         11         58         41       48
                    vv
clus                 STAGE IVA STAGE IVB
  C20ORF43 MUTATED           0         0
  C20ORF43 WILD-TYPE        18         1
D1895V4, multiclass
            clus
vv           C20ORF43 MUTATED C20ORF43 WILD-TYPE
  STAGE I                   1                 90
  STAGE IA                  0                  1
  STAGE II                  1                 31
  STAGE IIA                 0                138
  STAGE IIB                 0                 10
  STAGE IIC                 0                  1
  STAGE III                 0                 24
  STAGE IIIA                0                 11
  STAGE IIIB                1                 58
  STAGE IIIC                1                 41
  STAGE IV                  0                 48
  STAGE IVA                 0                 18
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  C20ORF43 MUTATED     1   0   2   1
  C20ORF43 WILD-TYPE  16  92 327  49
D1895V5, multiclass
    clus
vv   C20ORF43 MUTATED C20ORF43 WILD-TYPE
  T1                1                 16
  T2                0                 92
  T3                2                327
  T4                1                 49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  C20ORF43 MUTATED     2   1   1
  C20ORF43 WILD-TYPE 285 112  86
D1895V6, multiclass
    clus
vv   C20ORF43 MUTATED C20ORF43 WILD-TYPE
  N0                2                285
  N1                1                112
  N2                1                 86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1895V7, binary
                    cls
clus                   0   1
  C20ORF43 MUTATED     3   0
  C20ORF43 WILD-TYPE 372  65
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C20ORF43 MUTATED      3    0
  C20ORF43 WILD-TYPE  372   65
   clus
vv  C20ORF43 MUTATED C20ORF43 WILD-TYPE
  0                3                372
  1                0                 65
[1] 2 2
[1] FALSE
D1895V8, binary
                    cls
clus                   0   1
  C20ORF43 MUTATED     2   2
  C20ORF43 WILD-TYPE 223 262
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C20ORF43 MUTATED      2    2
  C20ORF43 WILD-TYPE  223  262
        clus
vv       C20ORF43 MUTATED C20ORF43 WILD-TYPE
  FEMALE                2                223
  MALE                  2                262
[1] 2 2
[1] FALSE
D1895V9, binary
                    cls
clus                   0   1
  C20ORF43 MUTATED     3   0
  C20ORF43 WILD-TYPE 347  22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C20ORF43 MUTATED      3    0
  C20ORF43 WILD-TYPE  347   22
     clus
vv    C20ORF43 MUTATED C20ORF43 WILD-TYPE
  NO                 3                347
  YES                0                 22
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  C20ORF43 MUTATED                      2                             1
  C20ORF43 WILD-TYPE                  313                            46
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  C20ORF43 MUTATED                       1                              0
  C20ORF43 WILD-TYPE                   105                             10
D1895V10, multiclass
                                clus
vv                               C20ORF43 MUTATED C20ORF43 WILD-TYPE
  COLON ADENOCARCINOMA                          2                313
  COLON MUCINOUS ADENOCARCINOMA                 1                 46
  RECTAL ADENOCARCINOMA                         1                105
  RECTAL MUCINOUS ADENOCARCINOMA                0                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  C20ORF43 MUTATED     3   0   0   1
  C20ORF43 WILD-TYPE 342   4  31  24
D1895V11, multiclass
    clus
vv   C20ORF43 MUTATED C20ORF43 WILD-TYPE
  R0                3                342
  R1                0                  4
  R2                0                 31
  RX                1                 24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1895V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C20ORF43 MUTATED                                  0     0
  C20ORF43 WILD-TYPE                                1    11
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  C20ORF43 MUTATED                           0     2
  C20ORF43 WILD-TYPE                        22   224
D1895V13, multiclass
[1] "Remove cluster labels:" "C20ORF43 MUTATED"      
clus
  C20ORF43 MUTATED C20ORF43 WILD-TYPE 
                 2                258 
        TCGA-A6-2671         TCGA-A6-2672         TCGA-A6-2674 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-A6-2676         TCGA-A6-2677         TCGA-A6-2678 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-A6-2683         TCGA-A6-3807         TCGA-A6-3808 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-A6-3809         TCGA-A6-3810         TCGA-A6-4105 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-A6-5656         TCGA-A6-5657         TCGA-A6-5659 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-A6-5660         TCGA-A6-5661         TCGA-A6-5662 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-A6-5664         TCGA-A6-5665         TCGA-A6-5666 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-A6-6137         TCGA-A6-6138         TCGA-A6-6141 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-A6-6142         TCGA-A6-6648         TCGA-A6-6649 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-A6-6651         TCGA-A6-6652         TCGA-A6-6653 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-A6-6654         TCGA-A6-6780         TCGA-A6-6781 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-A6-6782         TCGA-AD-5900         TCGA-AD-6548 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-AD-6888         TCGA-AD-6889         TCGA-AD-6890 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-AD-6895         TCGA-AD-6899         TCGA-AD-6901 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-AD-6963         TCGA-AD-6964         TCGA-AD-6965 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-AU-3779         TCGA-AU-6004         TCGA-AY-4070 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-AY-4071         TCGA-AY-5543         TCGA-AY-6197 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-AY-6386         TCGA-AZ-4315         TCGA-AZ-4323 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-AZ-4616         TCGA-AZ-4681         TCGA-AZ-4682 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-AZ-5403         TCGA-AZ-5407         TCGA-AZ-6598 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-AZ-6599         TCGA-AZ-6600         TCGA-AZ-6601 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-AZ-6603         TCGA-AZ-6605         TCGA-AZ-6606 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-AZ-6607         TCGA-AZ-6608         TCGA-CA-5254 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-CA-5255         TCGA-CA-5796         TCGA-CA-5797 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-CA-6715         TCGA-CA-6716         TCGA-CA-6717 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-CA-6718         TCGA-CA-6719         TCGA-CK-4948 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-CK-4950         TCGA-CK-4952         TCGA-CK-5912 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-CK-5913         TCGA-CK-5914         TCGA-CK-5915 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-CK-5916         TCGA-CK-6746         TCGA-CK-6747 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-CK-6748         TCGA-CK-6751         TCGA-CM-4743 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-CM-4744         TCGA-CM-4746         TCGA-CM-4747 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-CM-4752         TCGA-CM-5341         TCGA-CM-5344 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-CM-5348         TCGA-CM-5349         TCGA-CM-5860 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-CM-5861         TCGA-CM-5862         TCGA-CM-5863 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-CM-5864         TCGA-CM-5868         TCGA-CM-6161 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-CM-6162         TCGA-CM-6163         TCGA-CM-6164 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-CM-6165         TCGA-CM-6166         TCGA-CM-6167 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-CM-6168         TCGA-CM-6169         TCGA-CM-6170 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-CM-6171         TCGA-CM-6172         TCGA-CM-6674 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-CM-6675         TCGA-CM-6676         TCGA-CM-6677 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-CM-6678         TCGA-CM-6679         TCGA-CM-6680 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-D5-5537         TCGA-D5-5538         TCGA-D5-5539 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-D5-5540         TCGA-D5-5541         TCGA-D5-6529 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-D5-6532         TCGA-D5-6533         TCGA-D5-6534 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-D5-6535         TCGA-D5-6536         TCGA-D5-6537 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-D5-6538         TCGA-D5-6539         TCGA-D5-6540 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-D5-6541         TCGA-D5-6898         TCGA-D5-6920 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-D5-6922         TCGA-D5-6923         TCGA-D5-6924 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-D5-6926         TCGA-D5-6927         TCGA-D5-6928 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-D5-6929         TCGA-D5-6930         TCGA-D5-6931 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-D5-6932         TCGA-D5-7000         TCGA-DM-A0X9 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-DM-A0XD         TCGA-DM-A0XF         TCGA-DM-A1D0 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-DM-A1D4         TCGA-DM-A1D6         TCGA-DM-A1D7 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-DM-A1D8         TCGA-DM-A1D9         TCGA-DM-A1DA 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-DM-A1DB         TCGA-DM-A1HA         TCGA-DM-A1HB 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-DM-A282         TCGA-DM-A285         TCGA-DM-A28C 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-DM-A28E         TCGA-DM-A28F         TCGA-DM-A28G 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-DM-A28H         TCGA-DM-A28K         TCGA-F4-6459 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-F4-6460         TCGA-F4-6569         TCGA-F4-6570 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-F4-6703         TCGA-F4-6704         TCGA-F4-6805 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-F4-6806         TCGA-F4-6807         TCGA-F4-6808 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-F4-6809         TCGA-F4-6854         TCGA-F4-6855 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-F4-6856         TCGA-G4-6293         TCGA-G4-6299 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-G4-6303         TCGA-G4-6304         TCGA-G4-6306 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-G4-6307         TCGA-G4-6309         TCGA-G4-6310 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-G4-6315         TCGA-G4-6317         TCGA-G4-6321 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-G4-6323         TCGA-G4-6586         TCGA-G4-6588 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-G4-6625         TCGA-G4-6626         TCGA-G4-6628 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2691 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-AF-2692         TCGA-AF-2693         TCGA-AF-3400 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-AF-3913         TCGA-AF-4110         TCGA-AF-5654 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-AF-6136         TCGA-AF-6655         TCGA-AF-6672 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6549 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-AH-6643         TCGA-AH-6644         TCGA-CI-6619 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-CI-6620         TCGA-CI-6621         TCGA-CI-6622 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-CI-6624         TCGA-CL-5917         TCGA-CL-5918 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-DC-5337         TCGA-DC-5869         TCGA-DC-6155 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-DC-6157         TCGA-DC-6158         TCGA-DC-6160 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-DC-6681         TCGA-DC-6682         TCGA-DC-6683 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-DT-5265         TCGA-DY-A0XA         TCGA-DY-A1DC 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-DY-A1DD         TCGA-DY-A1DF         TCGA-DY-A1DG 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-DY-A1H8         TCGA-EF-5830         TCGA-EI-6506 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6510 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-F5-6464         TCGA-F5-6465         TCGA-F5-6571 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6811         TCGA-F5-6812 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 
        TCGA-F5-6813         TCGA-G5-6235         TCGA-G5-6641 
"C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" "C20ORF43 WILD-TYPE" 

Clustering(1896) Variable = GOLIM4 MUTATION ANALYSIS
D1896V1, survival
                  sevent
clus2                0   1
  GOLIM4 MUTATED     8   3
  GOLIM4 WILD-TYPE 370  90
  GOLIM4 MUTATED GOLIM4 WILD-TYPE 
              11              460 
  GOLIM4 MUTATED GOLIM4 WILD-TYPE 
               3               90 
$`GOLIM4 MUTATED`
TCGA-A6-3810 TCGA-AA-3510 TCGA-AA-3516 TCGA-AA-3710 TCGA-AA-A00J TCGA-AA-A00N 
       36.53        63.98        13.02        26.99        18.05         4.01 
TCGA-AA-A010 TCGA-AZ-6601 TCGA-DM-A1HB TCGA-AG-A002 TCGA-DC-6683 
       34.98       100.01       135.65        20.98         5.03 

$`GOLIM4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        32.75        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
       35.01         6.97         1.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       85.05        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       34.03        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77        12.10        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        4.01         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  GOLIM4 MUTATED GOLIM4 WILD-TYPE 
            4.01             0.00 
  GOLIM4 MUTATED GOLIM4 WILD-TYPE 
          135.65           148.01 
  GOLIM4 MUTATED GOLIM4 WILD-TYPE 
          26.990           20.085 
[1] "4.0 - 135.7 (27.0)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.1"
D1896V2, continuous
D1896V3, binary
                  cls
clus                 0   1
  GOLIM4 MUTATED     9   2
  GOLIM4 WILD-TYPE 357 117
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GOLIM4 MUTATED      9    2
  GOLIM4 WILD-TYPE  357  117
        clus
vv       GOLIM4 MUTATED GOLIM4 WILD-TYPE
  COLON               9              357
  RECTUM              2              117
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GOLIM4 MUTATED         1        0        2         2         2         0
  GOLIM4 WILD-TYPE      90        1       30       136         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GOLIM4 MUTATED           1          0          3          0        0
  GOLIM4 WILD-TYPE        23         11         56         42       48
                  vv
clus               STAGE IVA STAGE IVB
  GOLIM4 MUTATED           0         0
  GOLIM4 WILD-TYPE        18         1
D1896V4, multiclass
            clus
vv           GOLIM4 MUTATED GOLIM4 WILD-TYPE
  STAGE I                 1               90
  STAGE IA                0                1
  STAGE II                2               30
  STAGE IIA               2              136
  STAGE IIB               2                8
  STAGE IIC               0                1
  STAGE III               1               23
  STAGE IIIA              0               11
  STAGE IIIB              3               56
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  GOLIM4 MUTATED     0   1   7   3
  GOLIM4 WILD-TYPE  17  91 322  47
D1896V5, multiclass
    clus
vv   GOLIM4 MUTATED GOLIM4 WILD-TYPE
  T1              0               17
  T2              1               91
  T3              7              322
  T4              3               47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  GOLIM4 MUTATED     7   3   1
  GOLIM4 WILD-TYPE 280 110  86
D1896V6, multiclass
    clus
vv   GOLIM4 MUTATED GOLIM4 WILD-TYPE
  N0              7              280
  N1              3              110
  N2              1               86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1896V7, binary
                  cls
clus                 0   1
  GOLIM4 MUTATED    11   0
  GOLIM4 WILD-TYPE 364  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GOLIM4 MUTATED     11    0
  GOLIM4 WILD-TYPE  364   65
   clus
vv  GOLIM4 MUTATED GOLIM4 WILD-TYPE
  0             11              364
  1              0               65
[1] 2 2
[1] FALSE
D1896V8, binary
                  cls
clus                 0   1
  GOLIM4 MUTATED     3   8
  GOLIM4 WILD-TYPE 222 256
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GOLIM4 MUTATED      3    8
  GOLIM4 WILD-TYPE  222  256
        clus
vv       GOLIM4 MUTATED GOLIM4 WILD-TYPE
  FEMALE              3              222
  MALE                8              256
[1] 2 2
[1] FALSE
D1896V9, binary
                  cls
clus                 0   1
  GOLIM4 MUTATED     8   0
  GOLIM4 WILD-TYPE 342  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GOLIM4 MUTATED      8    0
  GOLIM4 WILD-TYPE  342   22
     clus
vv    GOLIM4 MUTATED GOLIM4 WILD-TYPE
  NO               8              342
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  GOLIM4 MUTATED                      5                             3
  GOLIM4 WILD-TYPE                  310                            44
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  GOLIM4 MUTATED                       2                              0
  GOLIM4 WILD-TYPE                   104                             10
D1896V10, multiclass
                                clus
vv                               GOLIM4 MUTATED GOLIM4 WILD-TYPE
  COLON ADENOCARCINOMA                        5              310
  COLON MUCINOUS ADENOCARCINOMA               3               44
  RECTAL ADENOCARCINOMA                       2              104
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  GOLIM4 MUTATED     8   0   0   0
  GOLIM4 WILD-TYPE 337   4  31  25
D1896V11, multiclass
    clus
vv   GOLIM4 MUTATED GOLIM4 WILD-TYPE
  R0              8              337
  R1              0                4
  R2              0               31
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1896V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GOLIM4 MUTATED                                  0     0
  GOLIM4 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  GOLIM4 MUTATED                           0     4
  GOLIM4 WILD-TYPE                        22   222
D1896V13, multiclass
                                  clus
vv                                 GOLIM4 MUTATED GOLIM4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         4              222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1897) Variable = MTMR1 MUTATION ANALYSIS
D1897V1, survival
                 sevent
clus2               0   1
  MTMR1 MUTATED     7   5
  MTMR1 WILD-TYPE 371  88
  MTMR1 MUTATED MTMR1 WILD-TYPE 
             12             459 
  MTMR1 MUTATED MTMR1 WILD-TYPE 
              5              88 
$`MTMR1 MUTATED`
TCGA-A6-2676 TCGA-A6-5661 TCGA-A6-6781 TCGA-AA-3492 TCGA-AA-3848 TCGA-AA-3977 
       42.90        33.53        19.66         3.02        10.06        25.02 
TCGA-AA-A00N TCGA-CA-6717 TCGA-CM-4752 TCGA-CM-5348 TCGA-F4-6570 TCGA-AG-3892 
        4.01        12.76        13.02        22.98         6.18        13.02 

$`MTMR1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       31.63        30.44        29.19        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
       20.28         7.04         1.02        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3850 TCGA-AA-3851 
       37.02        14.93         0.00        17.03         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07        12.20        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       25.02        29.06        22.03        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 
       98.24         8.61        31.96        35.74        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       17.95        36.95        17.03        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  MTMR1 MUTATED MTMR1 WILD-TYPE 
           3.02            0.00 
  MTMR1 MUTATED MTMR1 WILD-TYPE 
          42.90          148.01 
  MTMR1 MUTATED MTMR1 WILD-TYPE 
          13.02           20.55 
[1] "3.0 - 42.9 (13.0)"  "0.0 - 148.0 (20.6)"
[1] "hr=" "3.3"
D1897V2, continuous
D1897V3, binary
                 cls
clus                0   1
  MTMR1 MUTATED    12   1
  MTMR1 WILD-TYPE 354 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MTMR1 MUTATED     12    1
  MTMR1 WILD-TYPE  354  118
        clus
vv       MTMR1 MUTATED MTMR1 WILD-TYPE
  COLON             12             354
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MTMR1 MUTATED         2        0        1         4         2         0
  MTMR1 WILD-TYPE      89        1       31       134         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MTMR1 MUTATED           0          0          1          2        0         0
  MTMR1 WILD-TYPE        24         11         58         40       48        18
                 vv
clus              STAGE IVB
  MTMR1 MUTATED           0
  MTMR1 WILD-TYPE         1
D1897V4, multiclass
            clus
vv           MTMR1 MUTATED MTMR1 WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              4             134
  STAGE IIB              2               8
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             2              40
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  MTMR1 MUTATED     1   2   7   3
  MTMR1 WILD-TYPE  16  90 322  47
D1897V5, multiclass
    clus
vv   MTMR1 MUTATED MTMR1 WILD-TYPE
  T1             1              16
  T2             2              90
  T3             7             322
  T4             3              47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  MTMR1 MUTATED    10   2   1
  MTMR1 WILD-TYPE 277 111  86
D1897V6, multiclass
    clus
vv   MTMR1 MUTATED MTMR1 WILD-TYPE
  N0            10             277
  N1             2             111
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1897V7, binary
                 cls
clus                0   1
  MTMR1 MUTATED    10   0
  MTMR1 WILD-TYPE 365  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MTMR1 MUTATED     10    0
  MTMR1 WILD-TYPE  365   65
   clus
vv  MTMR1 MUTATED MTMR1 WILD-TYPE
  0            10             365
  1             0              65
[1] 2 2
[1] FALSE
D1897V8, binary
                 cls
clus                0   1
  MTMR1 MUTATED     6   7
  MTMR1 WILD-TYPE 219 257
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MTMR1 MUTATED      6    7
  MTMR1 WILD-TYPE  219  257
        clus
vv       MTMR1 MUTATED MTMR1 WILD-TYPE
  FEMALE             6             219
  MALE               7             257
[1] 2 2
[1] FALSE
D1897V9, binary
                 cls
clus                0   1
  MTMR1 MUTATED    11   0
  MTMR1 WILD-TYPE 339  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MTMR1 MUTATED     11    0
  MTMR1 WILD-TYPE  339   22
     clus
vv    MTMR1 MUTATED MTMR1 WILD-TYPE
  NO             11             339
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MTMR1 MUTATED                      9                             3
  MTMR1 WILD-TYPE                  306                            44
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MTMR1 MUTATED                       1                              0
  MTMR1 WILD-TYPE                   105                             10
D1897V10, multiclass
                                clus
vv                               MTMR1 MUTATED MTMR1 WILD-TYPE
  COLON ADENOCARCINOMA                       9             306
  COLON MUCINOUS ADENOCARCINOMA              3              44
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  MTMR1 MUTATED    10   0   0   2
  MTMR1 WILD-TYPE 335   4  31  23
D1897V11, multiclass
    clus
vv   MTMR1 MUTATED MTMR1 WILD-TYPE
  R0            10             335
  R1             0               4
  R2             0              31
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1897V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MTMR1 MUTATED                                  0     1
  MTMR1 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  MTMR1 MUTATED                           2     5
  MTMR1 WILD-TYPE                        20   221
D1897V13, multiclass
                                  clus
vv                                 MTMR1 MUTATED MTMR1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    2              20
  WHITE                                        5             221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1898) Variable = TRPM6 MUTATION ANALYSIS
D1898V1, survival
                 sevent
clus2               0   1
  TRPM6 MUTATED    24   3
  TRPM6 WILD-TYPE 354  90
  TRPM6 MUTATED TRPM6 WILD-TYPE 
             27             444 
  TRPM6 MUTATED TRPM6 WILD-TYPE 
              3              90 
$`TRPM6 MUTATED`
TCGA-A6-5660 TCGA-A6-5665 TCGA-A6-6141 TCGA-A6-6653 TCGA-AA-3510 TCGA-AA-3525 
       29.19        22.06         8.38        24.39        63.98         8.05 
TCGA-AA-3663 TCGA-AA-3821 TCGA-AA-3845 TCGA-AA-3977 TCGA-AA-3986 TCGA-AA-A00E 
        6.97         1.02         0.00        25.02        19.07        30.02 
TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01R TCGA-AD-5900 TCGA-AD-6895 TCGA-AZ-4315 
        4.01        34.98        35.01         0.07         0.72        58.39 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-5914 TCGA-CK-6747 TCGA-F4-6855 TCGA-G4-6588 
       12.76        10.06         9.99        82.95        47.41        26.17 
TCGA-AG-A002 TCGA-AG-A02N TCGA-G5-6235 
       20.98        61.97        55.76 

$`TRPM6 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        33.53        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       32.71        27.09        22.52        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       21.76        24.69        23.87        20.12        19.66        20.28 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 
        7.04         3.02         1.02        35.01         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
       13.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
       36.03        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.05        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 
       10.06        35.05        33.04         0.99        25.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 
       15.95        38.99        37.02        14.93        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 
       34.06        26.01        24.00        27.02        27.02         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00J 
       27.02        13.94        38.04        19.00        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T 
       31.00        31.00        38.07         1.02         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       18.05        40.96        21.37        15.52        56.55         0.79 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        3.29         0.07        12.20        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6748 
       85.45        15.62        49.08        51.32        21.14         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
        0.53        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       22.09        13.78        35.80        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X 
       64.01        10.98        49.97         1.94        38.96        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6641 
       31.30        28.57        32.19         0.66         0.69        26.43 

  TRPM6 MUTATED TRPM6 WILD-TYPE 
              0               0 
  TRPM6 MUTATED TRPM6 WILD-TYPE 
          82.95          148.01 
  TRPM6 MUTATED TRPM6 WILD-TYPE 
         22.060          20.085 
[1] "0.0 - 83.0 (22.1)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.8"
D1898V2, continuous
D1898V3, binary
                 cls
clus                0   1
  TRPM6 MUTATED    26   4
  TRPM6 WILD-TYPE 340 115
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRPM6 MUTATED     26    4
  TRPM6 WILD-TYPE  340  115
        clus
vv       TRPM6 MUTATED TRPM6 WILD-TYPE
  COLON             26             340
  RECTUM             4             115
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TRPM6 MUTATED         5        0        4        11         2         0
  TRPM6 WILD-TYPE      86        1       28       127         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TRPM6 MUTATED           1          0          3          2        0         0
  TRPM6 WILD-TYPE        23         11         56         40       48        18
                 vv
clus              STAGE IVB
  TRPM6 MUTATED           0
  TRPM6 WILD-TYPE         1
D1898V4, multiclass
            clus
vv           TRPM6 MUTATED TRPM6 WILD-TYPE
  STAGE I                5              86
  STAGE IA               0               1
  STAGE II               4              28
  STAGE IIA             11             127
  STAGE IIB              2               8
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             3              56
  STAGE IIIC             2              40
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  TRPM6 MUTATED     0   6  21   3
  TRPM6 WILD-TYPE  17  86 308  47
D1898V5, multiclass
    clus
vv   TRPM6 MUTATED TRPM6 WILD-TYPE
  T1             0              17
  T2             6              86
  T3            21             308
  T4             3              47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  TRPM6 MUTATED    23   4   3
  TRPM6 WILD-TYPE 264 109  84
D1898V6, multiclass
    clus
vv   TRPM6 MUTATED TRPM6 WILD-TYPE
  N0            23             264
  N1             4             109
  N2             3              84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1898V7, binary
                 cls
clus                0   1
  TRPM6 MUTATED    23   0
  TRPM6 WILD-TYPE 352  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRPM6 MUTATED     23    0
  TRPM6 WILD-TYPE  352   65
   clus
vv  TRPM6 MUTATED TRPM6 WILD-TYPE
  0            23             352
  1             0              65
[1] 2 2
[1] FALSE
D1898V8, binary
                 cls
clus                0   1
  TRPM6 MUTATED     9  21
  TRPM6 WILD-TYPE 216 243
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRPM6 MUTATED      9   21
  TRPM6 WILD-TYPE  216  243
        clus
vv       TRPM6 MUTATED TRPM6 WILD-TYPE
  FEMALE             9             216
  MALE              21             243
[1] 2 2
[1] FALSE
D1898V9, binary
                 cls
clus                0   1
  TRPM6 MUTATED    20   1
  TRPM6 WILD-TYPE 330  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRPM6 MUTATED     20    1
  TRPM6 WILD-TYPE  330   21
     clus
vv    TRPM6 MUTATED TRPM6 WILD-TYPE
  NO             20             330
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  TRPM6 MUTATED                     20                             6
  TRPM6 WILD-TYPE                  295                            41
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  TRPM6 MUTATED                       4                              0
  TRPM6 WILD-TYPE                   102                             10
D1898V10, multiclass
                                clus
vv                               TRPM6 MUTATED TRPM6 WILD-TYPE
  COLON ADENOCARCINOMA                      20             295
  COLON MUCINOUS ADENOCARCINOMA              6              41
  RECTAL ADENOCARCINOMA                      4             102
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  TRPM6 MUTATED    20   1   0   4
  TRPM6 WILD-TYPE 325   3  31  21
D1898V11, multiclass
    clus
vv   TRPM6 MUTATED TRPM6 WILD-TYPE
  R0            20             325
  R1             1               3
  R2             0              31
  RX             4              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1898V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TRPM6 MUTATED                                  0     2
  TRPM6 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  TRPM6 MUTATED                           2    11
  TRPM6 WILD-TYPE                        20   215
D1898V13, multiclass
                                  clus
vv                                 TRPM6 MUTATED TRPM6 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               9
  BLACK OR AFRICAN AMERICAN                    2              20
  WHITE                                       11             215
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1899) Variable = GABRA4 MUTATION ANALYSIS
D1899V1, survival
                  sevent
clus2                0   1
  GABRA4 MUTATED     9   3
  GABRA4 WILD-TYPE 369  90
  GABRA4 MUTATED GABRA4 WILD-TYPE 
              12              459 
  GABRA4 MUTATED GABRA4 WILD-TYPE 
               3               90 
$`GABRA4 MUTATED`
TCGA-A6-5662 TCGA-AA-3856 TCGA-AA-3972 TCGA-AA-3977 TCGA-AA-A010 TCGA-AD-5900 
       23.61         0.99        50.99        25.02        34.98         0.07 
TCGA-AD-6964 TCGA-CA-6717 TCGA-DM-A1D7 TCGA-F4-6570 TCGA-AG-3885 TCGA-AG-A002 
       10.88        12.76        13.32         6.18        17.95        20.98 

$`GABRA4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        33.53        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
       32.05        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 
       20.98        34.03         2.01        21.99        16.08        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07        12.20        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 
      117.07        98.24         8.61        31.96        35.74        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
        1.02        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  GABRA4 MUTATED GABRA4 WILD-TYPE 
            0.07             0.00 
  GABRA4 MUTATED GABRA4 WILD-TYPE 
           50.99           148.01 
  GABRA4 MUTATED GABRA4 WILD-TYPE 
          15.635           20.280 
[1] "0.1 - 51.0 (15.6)"  "0.0 - 148.0 (20.3)"
[1] "hr=" "1.8"
D1899V2, continuous
D1899V3, binary
                  cls
clus                 0   1
  GABRA4 MUTATED    11   2
  GABRA4 WILD-TYPE 355 117
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GABRA4 MUTATED     11    2
  GABRA4 WILD-TYPE  355  117
        clus
vv       GABRA4 MUTATED GABRA4 WILD-TYPE
  COLON              11              355
  RECTUM              2              117
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GABRA4 MUTATED         2        0        0         5         1         0
  GABRA4 WILD-TYPE      89        1       32       133         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GABRA4 MUTATED           0          0          1          0        1
  GABRA4 WILD-TYPE        24         11         58         42       47
                  vv
clus               STAGE IVA STAGE IVB
  GABRA4 MUTATED           1         0
  GABRA4 WILD-TYPE        17         1
D1899V4, multiclass
            clus
vv           GABRA4 MUTATED GABRA4 WILD-TYPE
  STAGE I                 2               89
  STAGE IA                0                1
  STAGE II                0               32
  STAGE IIA               5              133
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              1               58
  STAGE IIIC              0               42
  STAGE IV                1               47
  STAGE IVA               1               17
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  GABRA4 MUTATED     0   3   8   2
  GABRA4 WILD-TYPE  17  89 321  48
D1899V5, multiclass
    clus
vv   GABRA4 MUTATED GABRA4 WILD-TYPE
  T1              0               17
  T2              3               89
  T3              8              321
  T4              2               48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  GABRA4 MUTATED     9   2   2
  GABRA4 WILD-TYPE 278 111  85
D1899V6, multiclass
    clus
vv   GABRA4 MUTATED GABRA4 WILD-TYPE
  N0              9              278
  N1              2              111
  N2              2               85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1899V7, binary
                  cls
clus                 0   1
  GABRA4 MUTATED     8   2
  GABRA4 WILD-TYPE 367  63
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GABRA4 MUTATED      8    2
  GABRA4 WILD-TYPE  367   63
   clus
vv  GABRA4 MUTATED GABRA4 WILD-TYPE
  0              8              367
  1              2               63
[1] 2 2
[1] FALSE
D1899V8, binary
                  cls
clus                 0   1
  GABRA4 MUTATED     4   9
  GABRA4 WILD-TYPE 221 255
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GABRA4 MUTATED      4    9
  GABRA4 WILD-TYPE  221  255
        clus
vv       GABRA4 MUTATED GABRA4 WILD-TYPE
  FEMALE              4              221
  MALE                9              255
[1] 2 2
[1] FALSE
D1899V9, binary
                  cls
clus                 0   1
  GABRA4 MUTATED     8   1
  GABRA4 WILD-TYPE 342  21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GABRA4 MUTATED      8    1
  GABRA4 WILD-TYPE  342   21
     clus
vv    GABRA4 MUTATED GABRA4 WILD-TYPE
  NO               8              342
  YES              1               21
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  GABRA4 MUTATED                      8                             2
  GABRA4 WILD-TYPE                  307                            45
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  GABRA4 MUTATED                       2                              0
  GABRA4 WILD-TYPE                   104                             10
D1899V10, multiclass
                                clus
vv                               GABRA4 MUTATED GABRA4 WILD-TYPE
  COLON ADENOCARCINOMA                        8              307
  COLON MUCINOUS ADENOCARCINOMA               2               45
  RECTAL ADENOCARCINOMA                       2              104
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  GABRA4 MUTATED     7   0   1   1
  GABRA4 WILD-TYPE 338   4  30  24
D1899V11, multiclass
    clus
vv   GABRA4 MUTATED GABRA4 WILD-TYPE
  R0              7              338
  R1              0                4
  R2              1               30
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1899V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GABRA4 MUTATED                                  0     1
  GABRA4 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  GABRA4 MUTATED                           0     5
  GABRA4 WILD-TYPE                        22   221
D1899V13, multiclass
                                  clus
vv                                 GABRA4 MUTATED GABRA4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         5              221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1900) Variable = C17ORF71 MUTATION ANALYSIS
D1900V1, survival
                    sevent
clus2                  0   1
  C17ORF71 MUTATED     9   2
  C17ORF71 WILD-TYPE 369  91
  C17ORF71 MUTATED C17ORF71 WILD-TYPE 
                11                460 
  C17ORF71 MUTATED C17ORF71 WILD-TYPE 
                 2                 91 
$`C17ORF71 MUTATED`
TCGA-A6-6654 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3815 TCGA-AA-A00N TCGA-AA-A010 
       23.87        19.04        19.04        33.04         4.01        34.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-6679 TCGA-AG-3892 TCGA-AG-A002 
       30.08        32.02        10.06        13.02        20.98 

$`C17ORF71 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
       36.00         5.03        85.05        26.99        10.06        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       22.98        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6680 
       12.95        13.05        11.08        11.08        11.01        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 
       19.99         1.02        17.95        36.95        17.03        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  C17ORF71 MUTATED C17ORF71 WILD-TYPE 
              4.01               0.00 
  C17ORF71 MUTATED C17ORF71 WILD-TYPE 
             34.98             148.01 
  C17ORF71 MUTATED C17ORF71 WILD-TYPE 
            20.980             20.155 
[1] "4.0 - 35.0 (21.0)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.2"
D1900V2, continuous
D1900V3, binary
                    cls
clus                   0   1
  C17ORF71 MUTATED     9   2
  C17ORF71 WILD-TYPE 357 117
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C17ORF71 MUTATED      9    2
  C17ORF71 WILD-TYPE  357  117
        clus
vv       C17ORF71 MUTATED C17ORF71 WILD-TYPE
  COLON                 9                357
  RECTUM                2                117
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  C17ORF71 MUTATED         2        0        1         4         2         0
  C17ORF71 WILD-TYPE      89        1       31       134         8         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C17ORF71 MUTATED           0          0          1          0        1
  C17ORF71 WILD-TYPE        24         11         58         42       47
                    vv
clus                 STAGE IVA STAGE IVB
  C17ORF71 MUTATED           0         0
  C17ORF71 WILD-TYPE        18         1
D1900V4, multiclass
            clus
vv           C17ORF71 MUTATED C17ORF71 WILD-TYPE
  STAGE I                   2                 89
  STAGE IA                  0                  1
  STAGE II                  1                 31
  STAGE IIA                 4                134
  STAGE IIB                 2                  8
  STAGE IIC                 0                  1
  STAGE III                 0                 24
  STAGE IIIA                0                 11
  STAGE IIIB                1                 58
  STAGE IIIC                0                 42
  STAGE IV                  1                 47
  STAGE IVA                 0                 18
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  C17ORF71 MUTATED     1   1   7   2
  C17ORF71 WILD-TYPE  16  91 322  48
D1900V5, multiclass
    clus
vv   C17ORF71 MUTATED C17ORF71 WILD-TYPE
  T1                1                 16
  T2                1                 91
  T3                7                322
  T4                2                 48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  C17ORF71 MUTATED    10   1   0
  C17ORF71 WILD-TYPE 277 112  87
D1900V6, multiclass
    clus
vv   C17ORF71 MUTATED C17ORF71 WILD-TYPE
  N0               10                277
  N1                1                112
  N2                0                 87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1900V7, binary
                    cls
clus                   0   1
  C17ORF71 MUTATED    10   1
  C17ORF71 WILD-TYPE 365  64
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C17ORF71 MUTATED     10    1
  C17ORF71 WILD-TYPE  365   64
   clus
vv  C17ORF71 MUTATED C17ORF71 WILD-TYPE
  0               10                365
  1                1                 64
[1] 2 2
[1] FALSE
D1900V8, binary
                    cls
clus                   0   1
  C17ORF71 MUTATED     5   6
  C17ORF71 WILD-TYPE 220 258
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C17ORF71 MUTATED      5    6
  C17ORF71 WILD-TYPE  220  258
        clus
vv       C17ORF71 MUTATED C17ORF71 WILD-TYPE
  FEMALE                5                220
  MALE                  6                258
[1] 2 2
[1] FALSE
D1900V9, binary
                    cls
clus                   0   1
  C17ORF71 MUTATED     9   1
  C17ORF71 WILD-TYPE 341  21
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C17ORF71 MUTATED      9    1
  C17ORF71 WILD-TYPE  341   21
     clus
vv    C17ORF71 MUTATED C17ORF71 WILD-TYPE
  NO                 9                341
  YES                1                 21
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  C17ORF71 MUTATED                      8                             1
  C17ORF71 WILD-TYPE                  307                            46
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  C17ORF71 MUTATED                       2                              0
  C17ORF71 WILD-TYPE                   104                             10
D1900V10, multiclass
                                clus
vv                               C17ORF71 MUTATED C17ORF71 WILD-TYPE
  COLON ADENOCARCINOMA                          8                307
  COLON MUCINOUS ADENOCARCINOMA                 1                 46
  RECTAL ADENOCARCINOMA                         2                104
  RECTAL MUCINOUS ADENOCARCINOMA                0                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  C17ORF71 MUTATED     9   0   1   0
  C17ORF71 WILD-TYPE 336   4  30  25
D1900V11, multiclass
    clus
vv   C17ORF71 MUTATED C17ORF71 WILD-TYPE
  R0                9                336
  R1                0                  4
  R2                1                 30
  RX                0                 25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1900V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C17ORF71 MUTATED                                  0     0
  C17ORF71 WILD-TYPE                                1    11
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  C17ORF71 MUTATED                           0     4
  C17ORF71 WILD-TYPE                        22   222
D1900V13, multiclass
                                  clus
vv                                 C17ORF71 MUTATED C17ORF71 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 11
  BLACK OR AFRICAN AMERICAN                       0                 22
  WHITE                                           4                222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1901) Variable = VCAN MUTATION ANALYSIS
D1901V1, survival
                sevent
clus2              0   1
  VCAN MUTATED    30   7
  VCAN WILD-TYPE 348  86
  VCAN MUTATED VCAN WILD-TYPE 
            37            434 
  VCAN MUTATED VCAN WILD-TYPE 
             7             86 
$`VCAN MUTATED`
TCGA-A6-5660 TCGA-A6-6653 TCGA-AA-3510 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3534 
       29.19        24.39        63.98         1.02         9.07        29.00 
TCGA-AA-3555 TCGA-AA-3662 TCGA-AA-3666 TCGA-AA-3811 TCGA-AA-3831 TCGA-AA-3977 
       29.95         6.05         2.01        10.06        17.98        25.02 
TCGA-AA-A00E TCGA-AA-A00N TCGA-AA-A010 TCGA-AU-3779 TCGA-AZ-4315 TCGA-CA-6717 
       30.02         4.01        34.98        14.50        58.39        12.76 
TCGA-CA-6718 TCGA-CK-5914 TCGA-CK-5916 TCGA-CM-5349 TCGA-D5-6539 TCGA-D5-6927 
       10.06         9.99        21.14        30.08        12.49         9.44 
TCGA-D5-6931 TCGA-D5-6932 TCGA-DM-A0X9 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A28E 
       12.00        11.38       119.70       140.38         7.50       119.93 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6628 TCGA-AG-3883 TCGA-AG-3892 TCGA-AG-A002 
       74.56        65.85        79.69         1.02        13.02        20.98 
TCGA-G5-6235 
       55.76 

$`VCAN WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 
       25.18        24.16        21.76        24.69        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3520 TCGA-AA-3522 
        6.97         1.02        13.02        38.99        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       36.03         8.05        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 
       21.01        13.02        24.00        17.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       19.99        13.94        19.99        61.02        78.08         6.97 
TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
       54.02        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3815 
       85.05        26.99        19.04        19.04        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
        0.99        25.02         1.02        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       13.94        38.04        19.00        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
        0.20        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 
        3.25         3.29         0.07        12.20        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-6747 
      148.01        85.45        15.62        49.08        51.32        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5861 
       13.02        29.06        22.03        22.98        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-7000 
       14.30         9.04        11.64         4.80         1.51        10.26 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
       12.59        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
       81.37        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       35.31       133.18        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       26.17        91.79        46.75        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 
       19.99        17.95        36.95        17.03        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6641 
        0.69        26.43 

  VCAN MUTATED VCAN WILD-TYPE 
          1.02           0.00 
  VCAN MUTATED VCAN WILD-TYPE 
        140.38         148.01 
  VCAN MUTATED VCAN WILD-TYPE 
        20.980         20.155 
[1] "1.0 - 140.4 (21.0)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.3"
D1901V2, continuous
D1901V3, binary
                cls
clus               0   1
  VCAN MUTATED    37   6
  VCAN WILD-TYPE 329 113
[1] "tbl2"
                cls
clus             [,1] [,2]
  VCAN MUTATED     37    6
  VCAN WILD-TYPE  329  113
        clus
vv       VCAN MUTATED VCAN WILD-TYPE
  COLON            37            329
  RECTUM            6            113
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  VCAN MUTATED         6        0        1        17         2         0
  VCAN WILD-TYPE      85        1       31       121         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  VCAN MUTATED           4          1          3          5        3         0
  VCAN WILD-TYPE        20         10         56         37       45        18
                vv
clus             STAGE IVB
  VCAN MUTATED           0
  VCAN WILD-TYPE         1
D1901V4, multiclass
            clus
vv           VCAN MUTATED VCAN WILD-TYPE
  STAGE I               6             85
  STAGE IA              0              1
  STAGE II              1             31
  STAGE IIA            17            121
  STAGE IIB             2              8
  STAGE IIC             0              1
  STAGE III             4             20
  STAGE IIIA            1             10
  STAGE IIIB            3             56
  STAGE IIIC            5             37
  STAGE IV              3             45
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  VCAN MUTATED     2   5  31   5
  VCAN WILD-TYPE  15  87 298  45
D1901V5, multiclass
    clus
vv   VCAN MUTATED VCAN WILD-TYPE
  T1            2             15
  T2            5             87
  T3           31            298
  T4            5             45
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  VCAN MUTATED    28   6   9
  VCAN WILD-TYPE 259 107  78
D1901V6, multiclass
    clus
vv   VCAN MUTATED VCAN WILD-TYPE
  N0           28            259
  N1            6            107
  N2            9             78
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1901V7, binary
                cls
clus               0   1
  VCAN MUTATED    36   3
  VCAN WILD-TYPE 339  62
[1] "tbl2"
                cls
clus             [,1] [,2]
  VCAN MUTATED     36    3
  VCAN WILD-TYPE  339   62
   clus
vv  VCAN MUTATED VCAN WILD-TYPE
  0           36            339
  1            3             62
[1] 2 2
[1] FALSE
D1901V8, binary
                cls
clus               0   1
  VCAN MUTATED    19  24
  VCAN WILD-TYPE 206 240
[1] "tbl2"
                cls
clus             [,1] [,2]
  VCAN MUTATED     19   24
  VCAN WILD-TYPE  206  240
        clus
vv       VCAN MUTATED VCAN WILD-TYPE
  FEMALE           19            206
  MALE             24            240
[1] 2 2
[1] FALSE
D1901V9, binary
                cls
clus               0   1
  VCAN MUTATED    28   0
  VCAN WILD-TYPE 322  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  VCAN MUTATED     28    0
  VCAN WILD-TYPE  322   22
     clus
vv    VCAN MUTATED VCAN WILD-TYPE
  NO            28            322
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  VCAN MUTATED                     33                             4
  VCAN WILD-TYPE                  282                            43
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  VCAN MUTATED                       6                              0
  VCAN WILD-TYPE                   100                             10
D1901V10, multiclass
                                clus
vv                               VCAN MUTATED VCAN WILD-TYPE
  COLON ADENOCARCINOMA                     33            282
  COLON MUCINOUS ADENOCARCINOMA             4             43
  RECTAL ADENOCARCINOMA                     6            100
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  VCAN MUTATED    28   1   3   4
  VCAN WILD-TYPE 317   3  28  21
D1901V11, multiclass
    clus
vv   VCAN MUTATED VCAN WILD-TYPE
  R0           28            317
  R1            1              3
  R2            3             28
  RX            4             21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1901V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  VCAN MUTATED                                  0     2
  VCAN WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  VCAN MUTATED                           1    19
  VCAN WILD-TYPE                        21   207
D1901V13, multiclass
                                  clus
vv                                 VCAN MUTATED VCAN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              9
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                      19            207
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1902) Variable = CDH24 MUTATION ANALYSIS
D1902V1, survival
                 sevent
clus2               0   1
  CDH24 MUTATED    10   2
  CDH24 WILD-TYPE 368  91
  CDH24 MUTATED CDH24 WILD-TYPE 
             12             459 
  CDH24 MUTATED CDH24 WILD-TYPE 
              2              91 
$`CDH24 MUTATED`
TCGA-A6-4105 TCGA-A6-5665 TCGA-A6-6781 TCGA-AA-3492 TCGA-AA-3672 TCGA-AA-3710 
       14.53        22.06        19.66         3.02         0.92        26.99 
TCGA-AA-3713 TCGA-AA-3966 TCGA-AA-A00U TCGA-AA-A010 TCGA-AY-6386 TCGA-CK-6747 
       19.04         2.01        17.03        34.98        17.82        82.95 

$`CDH24 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 
       16.57        34.65        33.34        32.75        36.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
       20.28         7.04         1.02        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
       14.01        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3715 
       37.05        19.00        36.00         5.03        85.05        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
        2.01        20.98        34.03        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00W TCGA-AA-A00Z 
        4.01        27.02        42.02         0.99        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       51.32         9.99        21.14         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  CDH24 MUTATED CDH24 WILD-TYPE 
           0.92            0.00 
  CDH24 MUTATED CDH24 WILD-TYPE 
          82.95          148.01 
  CDH24 MUTATED CDH24 WILD-TYPE 
          18.43           20.55 
[1] "0.9 - 83.0 (18.4)"  "0.0 - 148.0 (20.6)"
[1] "hr=" "1"  
D1902V2, continuous
D1902V3, binary
                 cls
clus                0   1
  CDH24 MUTATED    12   0
  CDH24 WILD-TYPE 354 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDH24 MUTATED     12    0
  CDH24 WILD-TYPE  354  119
        clus
vv       CDH24 MUTATED CDH24 WILD-TYPE
  COLON             12             354
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CDH24 MUTATED         0        0        1         5         1         0
  CDH24 WILD-TYPE      91        1       31       133         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CDH24 MUTATED           1          0          2          1        1         0
  CDH24 WILD-TYPE        23         11         57         41       47        18
                 vv
clus              STAGE IVB
  CDH24 MUTATED           0
  CDH24 WILD-TYPE         1
D1902V4, multiclass
            clus
vv           CDH24 MUTATED CDH24 WILD-TYPE
  STAGE I                0              91
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              5             133
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             2              57
  STAGE IIIC             1              41
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CDH24 MUTATED     0   0  10   2
  CDH24 WILD-TYPE  17  92 319  48
D1902V5, multiclass
    clus
vv   CDH24 MUTATED CDH24 WILD-TYPE
  T1             0              17
  T2             0              92
  T3            10             319
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  CDH24 MUTATED     8   4   0
  CDH24 WILD-TYPE 279 109  87
D1902V6, multiclass
    clus
vv   CDH24 MUTATED CDH24 WILD-TYPE
  N0             8             279
  N1             4             109
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1902V7, binary
                 cls
clus                0   1
  CDH24 MUTATED     9   1
  CDH24 WILD-TYPE 366  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDH24 MUTATED      9    1
  CDH24 WILD-TYPE  366   64
   clus
vv  CDH24 MUTATED CDH24 WILD-TYPE
  0             9             366
  1             1              64
[1] 2 2
[1] FALSE
D1902V8, binary
                 cls
clus                0   1
  CDH24 MUTATED     8   4
  CDH24 WILD-TYPE 217 260
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDH24 MUTATED      8    4
  CDH24 WILD-TYPE  217  260
        clus
vv       CDH24 MUTATED CDH24 WILD-TYPE
  FEMALE             8             217
  MALE               4             260
[1] 2 2
[1] FALSE
D1902V9, binary
                 cls
clus                0   1
  CDH24 MUTATED    10   1
  CDH24 WILD-TYPE 340  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDH24 MUTATED     10    1
  CDH24 WILD-TYPE  340   21
     clus
vv    CDH24 MUTATED CDH24 WILD-TYPE
  NO             10             340
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CDH24 MUTATED                     10                             2
  CDH24 WILD-TYPE                  305                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CDH24 MUTATED                       0                              0
  CDH24 WILD-TYPE                   106                             10
D1902V10, multiclass
                                clus
vv                               CDH24 MUTATED CDH24 WILD-TYPE
  COLON ADENOCARCINOMA                      10             305
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  CDH24 MUTATED     8   0   1   1
  CDH24 WILD-TYPE 337   4  30  24
D1902V11, multiclass
    clus
vv   CDH24 MUTATED CDH24 WILD-TYPE
  R0             8             337
  R1             0               4
  R2             1              30
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1902V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CDH24 MUTATED                                  0     0
  CDH24 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CDH24 MUTATED                           1     4
  CDH24 WILD-TYPE                        21   222
D1902V13, multiclass
                                  clus
vv                                 CDH24 MUTATED CDH24 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        4             222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1903) Variable = SMARCA1 MUTATION ANALYSIS
D1903V1, survival
                   sevent
clus2                 0   1
  SMARCA1 MUTATED    17   7
  SMARCA1 WILD-TYPE 361  86
  SMARCA1 MUTATED SMARCA1 WILD-TYPE 
               24               447 
  SMARCA1 MUTATED SMARCA1 WILD-TYPE 
                7                86 
$`SMARCA1 MUTATED`
TCGA-A6-3809 TCGA-A6-5665 TCGA-A6-6781 TCGA-AA-3529 TCGA-AA-3555 TCGA-AA-3977 
       32.75        22.06        19.66         0.00        29.95        25.02 
TCGA-AA-A00K TCGA-AA-A01P TCGA-AD-6964 TCGA-AU-3779 TCGA-AY-6197 TCGA-AZ-6599 
       18.05        38.07        10.88        14.50        21.44         6.77 
TCGA-CA-6717 TCGA-CK-6747 TCGA-CM-5861 TCGA-D5-6536 TCGA-DM-A28G TCGA-G4-6586 
       12.76        82.95        15.02        17.85        60.79        35.80 
TCGA-AF-2689 TCGA-AF-4110 TCGA-AF-5654 TCGA-AG-3892 TCGA-AG-A002 TCGA-AH-6643 
       39.48        14.50        16.83        13.02        20.98         0.69 

$`SMARCA1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3530 
       24.03        37.05        36.03         8.05        19.07        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       78.08         6.05         6.97        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       12.00        31.00        31.00         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 
        0.20        27.09        16.31         0.95        33.01        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       88.21        49.41        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07        12.20        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       21.14         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       32.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 
       18.25         1.32        43.27        15.12         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28H TCGA-DM-A28K 
        6.12        81.37       119.93        35.97       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       22.09        13.78        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       24.13        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 
       19.99         1.02        17.95        36.95        17.03        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
        1.45        17.49         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  SMARCA1 MUTATED SMARCA1 WILD-TYPE 
                0                 0 
  SMARCA1 MUTATED SMARCA1 WILD-TYPE 
            82.95            148.01 
  SMARCA1 MUTATED SMARCA1 WILD-TYPE 
           18.855            20.280 
[1] "0.0 - 83.0 (18.9)"  "0.0 - 148.0 (20.3)"
[1] "hr=" "1.7"
D1903V2, continuous
D1903V3, binary
                   cls
clus                  0   1
  SMARCA1 MUTATED    19   6
  SMARCA1 WILD-TYPE 347 113
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SMARCA1 MUTATED     19    6
  SMARCA1 WILD-TYPE  347  113
        clus
vv       SMARCA1 MUTATED SMARCA1 WILD-TYPE
  COLON               19               347
  RECTUM               6               113
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SMARCA1 MUTATED         4        0        1        11         1         0
  SMARCA1 WILD-TYPE      87        1       31       127         9         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SMARCA1 MUTATED           2          0          0          3        1
  SMARCA1 WILD-TYPE        22         11         59         39       47
                   vv
clus                STAGE IVA STAGE IVB
  SMARCA1 MUTATED           1         0
  SMARCA1 WILD-TYPE        17         1
D1903V4, multiclass
            clus
vv           SMARCA1 MUTATED SMARCA1 WILD-TYPE
  STAGE I                  4                87
  STAGE IA                 0                 1
  STAGE II                 1                31
  STAGE IIA               11               127
  STAGE IIB                1                 9
  STAGE IIC                0                 1
  STAGE III                2                22
  STAGE IIIA               0                11
  STAGE IIIB               0                59
  STAGE IIIC               3                39
  STAGE IV                 1                47
  STAGE IVA                1                17
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  SMARCA1 MUTATED     1   4  16   5
  SMARCA1 WILD-TYPE  16  88 313  45
D1903V5, multiclass
    clus
vv   SMARCA1 MUTATED SMARCA1 WILD-TYPE
  T1               1                16
  T2               4                88
  T3              16               313
  T4               5                45
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  SMARCA1 MUTATED    18   3   5
  SMARCA1 WILD-TYPE 269 110  82
D1903V6, multiclass
    clus
vv   SMARCA1 MUTATED SMARCA1 WILD-TYPE
  N0              18               269
  N1               3               110
  N2               5                82
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1903V7, binary
                   cls
clus                  0   1
  SMARCA1 MUTATED    17   1
  SMARCA1 WILD-TYPE 358  64
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SMARCA1 MUTATED     17    1
  SMARCA1 WILD-TYPE  358   64
   clus
vv  SMARCA1 MUTATED SMARCA1 WILD-TYPE
  0              17               358
  1               1                64
[1] 2 2
[1] FALSE
D1903V8, binary
                   cls
clus                  0   1
  SMARCA1 MUTATED    13  13
  SMARCA1 WILD-TYPE 212 251
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SMARCA1 MUTATED     13   13
  SMARCA1 WILD-TYPE  212  251
        clus
vv       SMARCA1 MUTATED SMARCA1 WILD-TYPE
  FEMALE              13               212
  MALE                13               251
[1] 2 2
[1] FALSE
D1903V9, binary
                   cls
clus                  0   1
  SMARCA1 MUTATED    20   0
  SMARCA1 WILD-TYPE 330  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SMARCA1 MUTATED     20    0
  SMARCA1 WILD-TYPE  330   22
     clus
vv    SMARCA1 MUTATED SMARCA1 WILD-TYPE
  NO               20               330
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SMARCA1 MUTATED                     15                             4
  SMARCA1 WILD-TYPE                  300                            43
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SMARCA1 MUTATED                       6                              0
  SMARCA1 WILD-TYPE                   100                             10
D1903V10, multiclass
                                clus
vv                               SMARCA1 MUTATED SMARCA1 WILD-TYPE
  COLON ADENOCARCINOMA                        15               300
  COLON MUCINOUS ADENOCARCINOMA                4                43
  RECTAL ADENOCARCINOMA                        6               100
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  SMARCA1 MUTATED    19   0   0   2
  SMARCA1 WILD-TYPE 326   4  31  23
D1903V11, multiclass
    clus
vv   SMARCA1 MUTATED SMARCA1 WILD-TYPE
  R0              19               326
  R1               0                 4
  R2               0                31
  RX               2                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1903V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SMARCA1 MUTATED                                  0     1
  SMARCA1 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  SMARCA1 MUTATED                           0    17
  SMARCA1 WILD-TYPE                        22   209
D1903V13, multiclass
                                  clus
vv                                 SMARCA1 MUTATED SMARCA1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                10
  BLACK OR AFRICAN AMERICAN                      0                22
  WHITE                                         17               209
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1904) Variable = MORC1 MUTATION ANALYSIS
D1904V1, survival
                 sevent
clus2               0   1
  MORC1 MUTATED    15   2
  MORC1 WILD-TYPE 363  91
  MORC1 MUTATED MORC1 WILD-TYPE 
             17             454 
  MORC1 MUTATED MORC1 WILD-TYPE 
              2              91 
$`MORC1 MUTATED`
TCGA-A6-2676 TCGA-AA-3538 TCGA-AA-A00A TCGA-AA-A010 TCGA-AZ-4315 TCGA-CA-5797 
       42.90        26.01        38.04        34.98        58.39         3.29 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-4752 TCGA-CM-5868 TCGA-D5-6533 TCGA-G4-6588 
       12.76        10.06        13.02        17.03         1.32        26.17 
TCGA-AG-3892 TCGA-AG-A002 TCGA-AG-A011 TCGA-DC-5869 TCGA-EI-6507 
       13.02        20.98        37.02         5.03        19.96 

$`MORC1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00D 
       27.02        19.07         7.96        27.02        13.94        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        3.25         0.07        12.20        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       25.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6162 
       15.02         5.03        15.02        15.02        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       22.09        13.78        35.80        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       36.95        17.03        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A014 
       17.03        13.94         6.02        25.97        23.01        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
       15.02        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6508 
       24.13        51.48        32.61         0.49        20.55        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  MORC1 MUTATED MORC1 WILD-TYPE 
           1.32            0.00 
  MORC1 MUTATED MORC1 WILD-TYPE 
          58.39          148.01 
  MORC1 MUTATED MORC1 WILD-TYPE 
         19.960          20.235 
[1] "1.3 - 58.4 (20.0)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.4"
D1904V2, continuous
D1904V3, binary
                 cls
clus                0   1
  MORC1 MUTATED    13   5
  MORC1 WILD-TYPE 353 114
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MORC1 MUTATED     13    5
  MORC1 WILD-TYPE  353  114
        clus
vv       MORC1 MUTATED MORC1 WILD-TYPE
  COLON             13             353
  RECTUM             5             114
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MORC1 MUTATED         3        0        0        10         2         0
  MORC1 WILD-TYPE      88        1       32       128         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MORC1 MUTATED           0          0          2          0        0         1
  MORC1 WILD-TYPE        24         11         57         42       48        17
                 vv
clus              STAGE IVB
  MORC1 MUTATED           0
  MORC1 WILD-TYPE         1
D1904V4, multiclass
            clus
vv           MORC1 MUTATED MORC1 WILD-TYPE
  STAGE I                3              88
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA             10             128
  STAGE IIB              2               8
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             2              57
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  MORC1 MUTATED     1   2  11   4
  MORC1 WILD-TYPE  16  90 318  46
D1904V5, multiclass
    clus
vv   MORC1 MUTATED MORC1 WILD-TYPE
  T1             1              16
  T2             2              90
  T3            11             318
  T4             4              46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  MORC1 MUTATED    16   2   0
  MORC1 WILD-TYPE 271 111  87
D1904V6, multiclass
    clus
vv   MORC1 MUTATED MORC1 WILD-TYPE
  N0            16             271
  N1             2             111
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1904V7, binary
                 cls
clus                0   1
  MORC1 MUTATED    17   1
  MORC1 WILD-TYPE 358  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MORC1 MUTATED     17    1
  MORC1 WILD-TYPE  358   64
   clus
vv  MORC1 MUTATED MORC1 WILD-TYPE
  0            17             358
  1             1              64
[1] 2 2
[1] FALSE
D1904V8, binary
                 cls
clus                0   1
  MORC1 MUTATED     9   9
  MORC1 WILD-TYPE 216 255
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MORC1 MUTATED      9    9
  MORC1 WILD-TYPE  216  255
        clus
vv       MORC1 MUTATED MORC1 WILD-TYPE
  FEMALE             9             216
  MALE               9             255
[1] 2 2
[1] FALSE
D1904V9, binary
                 cls
clus                0   1
  MORC1 MUTATED    15   0
  MORC1 WILD-TYPE 335  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MORC1 MUTATED     15    0
  MORC1 WILD-TYPE  335   22
     clus
vv    MORC1 MUTATED MORC1 WILD-TYPE
  NO             15             335
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MORC1 MUTATED                     12                             1
  MORC1 WILD-TYPE                  303                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MORC1 MUTATED                       5                              0
  MORC1 WILD-TYPE                   101                             10
D1904V10, multiclass
                                clus
vv                               MORC1 MUTATED MORC1 WILD-TYPE
  COLON ADENOCARCINOMA                      12             303
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      5             101
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  MORC1 MUTATED    16   0   0   2
  MORC1 WILD-TYPE 329   4  31  23
D1904V11, multiclass
    clus
vv   MORC1 MUTATED MORC1 WILD-TYPE
  R0            16             329
  R1             0               4
  R2             0              31
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1904V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MORC1 MUTATED                                  0     3
  MORC1 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  MORC1 MUTATED                           2     6
  MORC1 WILD-TYPE                        20   220
D1904V13, multiclass
                                  clus
vv                                 MORC1 MUTATED MORC1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        3               8
  BLACK OR AFRICAN AMERICAN                    2              20
  WHITE                                        6             220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1905) Variable = ABL1 MUTATION ANALYSIS
D1905V1, survival
                sevent
clus2              0   1
  ABL1 MUTATED    21   7
  ABL1 WILD-TYPE 357  86
  ABL1 MUTATED ABL1 WILD-TYPE 
            28            443 
  ABL1 MUTATED ABL1 WILD-TYPE 
             7             86 
$`ABL1 MUTATED`
TCGA-A6-5661 TCGA-AA-3492 TCGA-AA-3516 TCGA-AA-3663 TCGA-AA-3715 TCGA-AA-A02K 
       33.53         3.02        13.02         6.97        19.04        14.01 
TCGA-AD-6889 TCGA-AD-6901 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-CK-4952 TCGA-CM-4743 
       56.55        22.42        88.21        49.41        15.62        23.05 
TCGA-CM-6161 TCGA-CM-6163 TCGA-D5-6532 TCGA-D5-6536 TCGA-D5-6539 TCGA-D5-6540 
       15.02         2.96        18.25        17.85        12.49        16.14 
TCGA-D5-7000 TCGA-DM-A1D6 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6588 TCGA-G4-6628 
       10.26        49.91        63.62        22.09        26.17        79.69 
TCGA-AH-6644 TCGA-DY-A0XA TCGA-EF-5830 TCGA-EI-6508 
        0.72       126.44         0.49        20.91 

$`ABL1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 
       20.12        19.66        20.28         7.04         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
       63.98         6.97         1.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02        78.08         6.05        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       26.99        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6963 
       21.37        15.52         0.79         0.72         5.79        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
      106.75        22.36        62.79         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 
       10.06        14.30        17.56       148.01        85.45        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6162 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        17.03        12.00        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 
       20.19         1.32        43.27        15.12         4.80        17.13 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       11.38       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 
       61.91        36.00        13.78        35.80        91.79        46.75 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
       17.49         0.69         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EI-6506 
       41.36        57.24        24.13        51.48        32.61        20.55 
TCGA-EI-6507 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       19.96        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  ABL1 MUTATED ABL1 WILD-TYPE 
          0.49           0.00 
  ABL1 MUTATED ABL1 WILD-TYPE 
        126.44         148.01 
  ABL1 MUTATED ABL1 WILD-TYPE 
        18.645         20.280 
[1] "0.5 - 126.4 (18.6)" "0.0 - 148.0 (20.3)"
[1] "hr=" "1.1"
D1905V2, continuous
D1905V3, binary
                cls
clus               0   1
  ABL1 MUTATED    26   4
  ABL1 WILD-TYPE 340 115
[1] "tbl2"
                cls
clus             [,1] [,2]
  ABL1 MUTATED     26    4
  ABL1 WILD-TYPE  340  115
        clus
vv       ABL1 MUTATED ABL1 WILD-TYPE
  COLON            26            340
  RECTUM            4            115
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ABL1 MUTATED         6        0        5         8         1         0
  ABL1 WILD-TYPE      85        1       27       130         9         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ABL1 MUTATED           2          1          2          2        1         0
  ABL1 WILD-TYPE        22         10         57         40       47        18
                vv
clus             STAGE IVB
  ABL1 MUTATED           0
  ABL1 WILD-TYPE         1
D1905V4, multiclass
            clus
vv           ABL1 MUTATED ABL1 WILD-TYPE
  STAGE I               6             85
  STAGE IA              0              1
  STAGE II              5             27
  STAGE IIA             8            130
  STAGE IIB             1              9
  STAGE IIC             0              1
  STAGE III             2             22
  STAGE IIIA            1             10
  STAGE IIIB            2             57
  STAGE IIIC            2             40
  STAGE IV              1             47
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  ABL1 MUTATED     2   5  19   4
  ABL1 WILD-TYPE  15  87 310  46
D1905V5, multiclass
    clus
vv   ABL1 MUTATED ABL1 WILD-TYPE
  T1            2             15
  T2            5             87
  T3           19            310
  T4            4             46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  ABL1 MUTATED    22   3   4
  ABL1 WILD-TYPE 265 110  83
D1905V6, multiclass
    clus
vv   ABL1 MUTATED ABL1 WILD-TYPE
  N0           22            265
  N1            3            110
  N2            4             83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1905V7, binary
                cls
clus               0   1
  ABL1 MUTATED    24   1
  ABL1 WILD-TYPE 351  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  ABL1 MUTATED     24    1
  ABL1 WILD-TYPE  351   64
   clus
vv  ABL1 MUTATED ABL1 WILD-TYPE
  0           24            351
  1            1             64
[1] 2 2
[1] FALSE
D1905V8, binary
                cls
clus               0   1
  ABL1 MUTATED    14  16
  ABL1 WILD-TYPE 211 248
[1] "tbl2"
                cls
clus             [,1] [,2]
  ABL1 MUTATED     14   16
  ABL1 WILD-TYPE  211  248
        clus
vv       ABL1 MUTATED ABL1 WILD-TYPE
  FEMALE           14            211
  MALE             16            248
[1] 2 2
[1] FALSE
D1905V9, binary
                cls
clus               0   1
  ABL1 MUTATED    21   1
  ABL1 WILD-TYPE 329  21
[1] "tbl2"
                cls
clus             [,1] [,2]
  ABL1 MUTATED     21    1
  ABL1 WILD-TYPE  329   21
     clus
vv    ABL1 MUTATED ABL1 WILD-TYPE
  NO            21            329
  YES            1             21
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ABL1 MUTATED                     20                             6
  ABL1 WILD-TYPE                  295                            41
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ABL1 MUTATED                       4                              0
  ABL1 WILD-TYPE                   102                             10
D1905V10, multiclass
                                clus
vv                               ABL1 MUTATED ABL1 WILD-TYPE
  COLON ADENOCARCINOMA                     20            295
  COLON MUCINOUS ADENOCARCINOMA             6             41
  RECTAL ADENOCARCINOMA                     4            102
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  ABL1 MUTATED    20   0   1   1
  ABL1 WILD-TYPE 325   4  30  24
D1905V11, multiclass
    clus
vv   ABL1 MUTATED ABL1 WILD-TYPE
  R0           20            325
  R1            0              4
  R2            1             30
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1905V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ABL1 MUTATED                                  0     1
  ABL1 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  ABL1 MUTATED                           1    22
  ABL1 WILD-TYPE                        21   204
D1905V13, multiclass
                                  clus
vv                                 ABL1 MUTATED ABL1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                      22            204
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1906) Variable = TTC13 MUTATION ANALYSIS
D1906V1, survival
                 sevent
clus2               0   1
  TTC13 MUTATED     7   3
  TTC13 WILD-TYPE 371  90
  TTC13 MUTATED TTC13 WILD-TYPE 
             10             461 
  TTC13 MUTATED TTC13 WILD-TYPE 
              3              90 
$`TTC13 MUTATED`
TCGA-AA-3555 TCGA-AA-3811 TCGA-AA-A00N TCGA-AA-A01R TCGA-AZ-6599 TCGA-CA-5255 
       29.95        10.06         4.01        35.01         6.77         3.06 
TCGA-CK-5913 TCGA-CM-4744 TCGA-G4-6628 TCGA-AG-A002 
       51.32        20.02        79.69        20.98 

$`TTC13 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 
       21.01        13.02        24.00        17.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       31.00        38.07         1.02         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        88.21        49.41        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5796 
        5.23        11.74         3.19         1.61        12.69         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 
       17.56       148.01        85.45        15.62        49.08         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4746 
       21.14        82.95         1.91       124.27        23.05        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       26.17        91.79        46.75        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  TTC13 MUTATED TTC13 WILD-TYPE 
           3.06            0.00 
  TTC13 MUTATED TTC13 WILD-TYPE 
          79.69          148.01 
  TTC13 MUTATED TTC13 WILD-TYPE 
          20.50           20.19 
[1] "3.1 - 79.7 (20.5)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.6"
D1906V2, continuous
D1906V3, binary
                 cls
clus                0   1
  TTC13 MUTATED     9   1
  TTC13 WILD-TYPE 357 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TTC13 MUTATED      9    1
  TTC13 WILD-TYPE  357  118
        clus
vv       TTC13 MUTATED TTC13 WILD-TYPE
  COLON              9             357
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TTC13 MUTATED         4        0        0         3         1         0
  TTC13 WILD-TYPE      87        1       32       135         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TTC13 MUTATED           2          0          0          0        0         0
  TTC13 WILD-TYPE        22         11         59         42       48        18
                 vv
clus              STAGE IVB
  TTC13 MUTATED           0
  TTC13 WILD-TYPE         1
D1906V4, multiclass
            clus
vv           TTC13 MUTATED TTC13 WILD-TYPE
  STAGE I                4              87
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              3             135
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              2              22
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  TTC13 MUTATED     0   4   5   1
  TTC13 WILD-TYPE  17  88 324  49
D1906V5, multiclass
    clus
vv   TTC13 MUTATED TTC13 WILD-TYPE
  T1             0              17
  T2             4              88
  T3             5             324
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  TTC13 MUTATED     8   0   2
  TTC13 WILD-TYPE 279 113  85
D1906V6, multiclass
    clus
vv   TTC13 MUTATED TTC13 WILD-TYPE
  N0             8             279
  N1             0             113
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1906V7, binary
                 cls
clus                0   1
  TTC13 MUTATED     8   0
  TTC13 WILD-TYPE 367  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TTC13 MUTATED      8    0
  TTC13 WILD-TYPE  367   65
   clus
vv  TTC13 MUTATED TTC13 WILD-TYPE
  0             8             367
  1             0              65
[1] 2 2
[1] FALSE
D1906V8, binary
                 cls
clus                0   1
  TTC13 MUTATED     3   7
  TTC13 WILD-TYPE 222 257
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TTC13 MUTATED      3    7
  TTC13 WILD-TYPE  222  257
        clus
vv       TTC13 MUTATED TTC13 WILD-TYPE
  FEMALE             3             222
  MALE               7             257
[1] 2 2
[1] FALSE
D1906V9, binary
                 cls
clus                0   1
  TTC13 MUTATED     7   2
  TTC13 WILD-TYPE 343  20
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TTC13 MUTATED      7    2
  TTC13 WILD-TYPE  343   20
     clus
vv    TTC13 MUTATED TTC13 WILD-TYPE
  NO              7             343
  YES             2              20
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  TTC13 MUTATED                      6                             3
  TTC13 WILD-TYPE                  309                            44
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  TTC13 MUTATED                       1                              0
  TTC13 WILD-TYPE                   105                             10
D1906V10, multiclass
                                clus
vv                               TTC13 MUTATED TTC13 WILD-TYPE
  COLON ADENOCARCINOMA                       6             309
  COLON MUCINOUS ADENOCARCINOMA              3              44
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  TTC13 MUTATED     7   0   0   2
  TTC13 WILD-TYPE 338   4  31  23
D1906V11, multiclass
    clus
vv   TTC13 MUTATED TTC13 WILD-TYPE
  R0             7             338
  R1             0               4
  R2             0              31
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1906V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TTC13 MUTATED                                  0     1
  TTC13 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  TTC13 MUTATED                           0     4
  TTC13 WILD-TYPE                        22   222
D1906V13, multiclass
                                  clus
vv                                 TTC13 MUTATED TTC13 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        4             222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1907) Variable = PTPMT1 MUTATION ANALYSIS
D1907V1, survival
                  sevent
clus2                0   1
  PTPMT1 MUTATED     6   0
  PTPMT1 WILD-TYPE 372  93
  PTPMT1 MUTATED PTPMT1 WILD-TYPE 
               6              465 
  PTPMT1 MUTATED PTPMT1 WILD-TYPE 
               0               93 
$`PTPMT1 MUTATED`
TCGA-A6-6653 TCGA-AA-A01R TCGA-CM-6164 TCGA-DM-A1HB TCGA-CI-6619 TCGA-EI-6506 
       24.39        35.01        29.03       135.65         6.05        20.55 

$`PTPMT1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
       25.08        25.18        24.16        21.76        24.69        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S 
       12.00        31.00        31.00        38.07         1.02         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       15.02        12.00         2.96        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 
       12.59       140.38         7.50        44.32       131.51       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6620 
       38.56         1.45        17.49         0.69         0.72        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       51.48        32.61         0.49        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  PTPMT1 MUTATED PTPMT1 WILD-TYPE 
            6.05             0.00 
  PTPMT1 MUTATED PTPMT1 WILD-TYPE 
          135.65           148.01 
  PTPMT1 MUTATED PTPMT1 WILD-TYPE 
           26.71            20.05 
[1] "6.0 - 135.7 (26.7)" "0.0 - 148.0 (20.1)"
[1] "hr="     "9200000"
D1907V2, continuous
D1907V3, binary
                  cls
clus                 0   1
  PTPMT1 MUTATED     5   2
  PTPMT1 WILD-TYPE 361 117
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PTPMT1 MUTATED      5    2
  PTPMT1 WILD-TYPE  361  117
        clus
vv       PTPMT1 MUTATED PTPMT1 WILD-TYPE
  COLON               5              361
  RECTUM              2              117
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PTPMT1 MUTATED         1        0        0         3         0         0
  PTPMT1 WILD-TYPE      90        1       32       135        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PTPMT1 MUTATED           1          0          1          0        1
  PTPMT1 WILD-TYPE        23         11         58         42       47
                  vv
clus               STAGE IVA STAGE IVB
  PTPMT1 MUTATED           0         0
  PTPMT1 WILD-TYPE        18         1
D1907V4, multiclass
            clus
vv           PTPMT1 MUTATED PTPMT1 WILD-TYPE
  STAGE I                 1               90
  STAGE IA                0                1
  STAGE II                0               32
  STAGE IIA               3              135
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               1               23
  STAGE IIIA              0               11
  STAGE IIIB              1               58
  STAGE IIIC              0               42
  STAGE IV                1               47
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  PTPMT1 MUTATED     0   1   6   0
  PTPMT1 WILD-TYPE  17  91 323  50
D1907V5, multiclass
    clus
vv   PTPMT1 MUTATED PTPMT1 WILD-TYPE
  T1              0               17
  T2              1               91
  T3              6              323
  T4              0               50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  PTPMT1 MUTATED     4   2   1
  PTPMT1 WILD-TYPE 283 111  86
D1907V6, multiclass
    clus
vv   PTPMT1 MUTATED PTPMT1 WILD-TYPE
  N0              4              283
  N1              2              111
  N2              1               86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1907V7, binary
                  cls
clus                 0   1
  PTPMT1 MUTATED     6   1
  PTPMT1 WILD-TYPE 369  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PTPMT1 MUTATED      6    1
  PTPMT1 WILD-TYPE  369   64
   clus
vv  PTPMT1 MUTATED PTPMT1 WILD-TYPE
  0              6              369
  1              1               64
[1] 2 2
[1] FALSE
D1907V8, binary
                  cls
clus                 0   1
  PTPMT1 MUTATED     3   4
  PTPMT1 WILD-TYPE 222 260
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PTPMT1 MUTATED      3    4
  PTPMT1 WILD-TYPE  222  260
        clus
vv       PTPMT1 MUTATED PTPMT1 WILD-TYPE
  FEMALE              3              222
  MALE                4              260
[1] 2 2
[1] FALSE
D1907V9, binary
                  cls
clus                 0   1
  PTPMT1 MUTATED     3   1
  PTPMT1 WILD-TYPE 347  21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PTPMT1 MUTATED      3    1
  PTPMT1 WILD-TYPE  347   21
     clus
vv    PTPMT1 MUTATED PTPMT1 WILD-TYPE
  NO               3              347
  YES              1               21
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PTPMT1 MUTATED                      3                             1
  PTPMT1 WILD-TYPE                  312                            46
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PTPMT1 MUTATED                       2                              0
  PTPMT1 WILD-TYPE                   104                             10
D1907V10, multiclass
                                clus
vv                               PTPMT1 MUTATED PTPMT1 WILD-TYPE
  COLON ADENOCARCINOMA                        3              312
  COLON MUCINOUS ADENOCARCINOMA               1               46
  RECTAL ADENOCARCINOMA                       2              104
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  PTPMT1 MUTATED     4   0   0   0
  PTPMT1 WILD-TYPE 341   4  31  25
D1907V11, multiclass
    clus
vv   PTPMT1 MUTATED PTPMT1 WILD-TYPE
  R0              4              341
  R1              0                4
  R2              0               31
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1907V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PTPMT1 MUTATED                                  0     0
  PTPMT1 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  PTPMT1 MUTATED                           0     5
  PTPMT1 WILD-TYPE                        22   221
D1907V13, multiclass
                                  clus
vv                                 PTPMT1 MUTATED PTPMT1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         5              221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1908) Variable = HEXIM2 MUTATION ANALYSIS
D1908V1, survival
                  sevent
clus2                0   1
  HEXIM2 MUTATED     6   1
  HEXIM2 WILD-TYPE 372  92
  HEXIM2 MUTATED HEXIM2 WILD-TYPE 
               7              464 
  HEXIM2 MUTATED HEXIM2 WILD-TYPE 
               1               92 
$`HEXIM2 MUTATED`
TCGA-A6-5659 TCGA-A6-6652 TCGA-AA-3845 TCGA-AZ-4315 TCGA-CM-6171 TCGA-AG-A02N 
       30.44        24.69         0.00        58.39        14.04        61.97 
TCGA-EI-6507 
       19.96 

$`HEXIM2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       25.18        24.16        21.76        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 
       15.95        38.99        37.02        14.93        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       13.02        15.02        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       38.96        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
       32.61         0.49        20.55        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  HEXIM2 MUTATED HEXIM2 WILD-TYPE 
               0                0 
  HEXIM2 MUTATED HEXIM2 WILD-TYPE 
           61.97           148.01 
  HEXIM2 MUTATED HEXIM2 WILD-TYPE 
          24.690           20.155 
[1] "0.0 - 62.0 (24.7)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.7"
D1908V2, continuous
D1908V3, binary
                  cls
clus                 0   1
  HEXIM2 MUTATED     5   2
  HEXIM2 WILD-TYPE 361 117
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HEXIM2 MUTATED      5    2
  HEXIM2 WILD-TYPE  361  117
        clus
vv       HEXIM2 MUTATED HEXIM2 WILD-TYPE
  COLON               5              361
  RECTUM              2              117
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  HEXIM2 MUTATED         2        0        1         3         0         0
  HEXIM2 WILD-TYPE      89        1       31       135        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HEXIM2 MUTATED           0          0          0          0        0
  HEXIM2 WILD-TYPE        24         11         59         42       48
                  vv
clus               STAGE IVA STAGE IVB
  HEXIM2 MUTATED           1         0
  HEXIM2 WILD-TYPE        17         1
D1908V4, multiclass
            clus
vv           HEXIM2 MUTATED HEXIM2 WILD-TYPE
  STAGE I                 2               89
  STAGE IA                0                1
  STAGE II                1               31
  STAGE IIA               3              135
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              0               59
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               1               17
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  HEXIM2 MUTATED     0   2   5   0
  HEXIM2 WILD-TYPE  17  90 324  50
D1908V5, multiclass
    clus
vv   HEXIM2 MUTATED HEXIM2 WILD-TYPE
  T1              0               17
  T2              2               90
  T3              5              324
  T4              0               50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  HEXIM2 MUTATED     7   0   0
  HEXIM2 WILD-TYPE 280 113  87
D1908V6, multiclass
    clus
vv   HEXIM2 MUTATED HEXIM2 WILD-TYPE
  N0              7              280
  N1              0              113
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1908V7, binary
                  cls
clus                 0   1
  HEXIM2 MUTATED     6   1
  HEXIM2 WILD-TYPE 369  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HEXIM2 MUTATED      6    1
  HEXIM2 WILD-TYPE  369   64
   clus
vv  HEXIM2 MUTATED HEXIM2 WILD-TYPE
  0              6              369
  1              1               64
[1] 2 2
[1] FALSE
D1908V8, binary
                  cls
clus                 0   1
  HEXIM2 MUTATED     2   5
  HEXIM2 WILD-TYPE 223 259
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HEXIM2 MUTATED      2    5
  HEXIM2 WILD-TYPE  223  259
        clus
vv       HEXIM2 MUTATED HEXIM2 WILD-TYPE
  FEMALE              2              223
  MALE                5              259
[1] 2 2
[1] FALSE
D1908V9, binary
                  cls
clus                 0   1
  HEXIM2 MUTATED     5   0
  HEXIM2 WILD-TYPE 345  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HEXIM2 MUTATED      5    0
  HEXIM2 WILD-TYPE  345   22
     clus
vv    HEXIM2 MUTATED HEXIM2 WILD-TYPE
  NO               5              345
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  HEXIM2 MUTATED                      5                             0
  HEXIM2 WILD-TYPE                  310                            47
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  HEXIM2 MUTATED                       2                              0
  HEXIM2 WILD-TYPE                   104                             10
D1908V10, multiclass
                                clus
vv                               HEXIM2 MUTATED HEXIM2 WILD-TYPE
  COLON ADENOCARCINOMA                        5              310
  COLON MUCINOUS ADENOCARCINOMA               0               47
  RECTAL ADENOCARCINOMA                       2              104
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  HEXIM2 MUTATED     6   0   0   0
  HEXIM2 WILD-TYPE 339   4  31  25
D1908V11, multiclass
    clus
vv   HEXIM2 MUTATED HEXIM2 WILD-TYPE
  R0              6              339
  R1              0                4
  R2              0               31
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1908V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HEXIM2 MUTATED                                  0     0
  HEXIM2 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  HEXIM2 MUTATED                           1     4
  HEXIM2 WILD-TYPE                        21   222
D1908V13, multiclass
                                  clus
vv                                 HEXIM2 MUTATED HEXIM2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                         4              222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1909) Variable = ST14 MUTATION ANALYSIS
D1909V1, survival
                sevent
clus2              0   1
  ST14 MUTATED     9   2
  ST14 WILD-TYPE 369  91
  ST14 MUTATED ST14 WILD-TYPE 
            11            460 
  ST14 MUTATED ST14 WILD-TYPE 
             2             91 
$`ST14 MUTATED`
TCGA-A6-6781 TCGA-AA-3672 TCGA-AY-6197 TCGA-AZ-5403 TCGA-CA-5255 TCGA-CK-4952 
       19.66         0.92        21.44        62.79         3.06        15.62 
TCGA-CK-5913 TCGA-D5-5541 TCGA-D5-6539 TCGA-DM-A1D7 TCGA-AG-A002 
       51.32        55.92        12.49        13.32        20.98 

$`ST14 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 
        6.97        54.02         2.01        14.01        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       33.01        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5914 
       14.30        17.56       148.01        85.45        49.08         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
        4.80        17.13        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D8 
       24.43        38.20       130.65        92.75        49.91        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  ST14 MUTATED ST14 WILD-TYPE 
          0.92           0.00 
  ST14 MUTATED ST14 WILD-TYPE 
         62.79         148.01 
  ST14 MUTATED ST14 WILD-TYPE 
        19.660         20.235 
[1] "0.9 - 62.8 (19.7)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.2"
D1909V2, continuous
D1909V3, binary
                cls
clus               0   1
  ST14 MUTATED    11   1
  ST14 WILD-TYPE 355 118
[1] "tbl2"
                cls
clus             [,1] [,2]
  ST14 MUTATED     11    1
  ST14 WILD-TYPE  355  118
        clus
vv       ST14 MUTATED ST14 WILD-TYPE
  COLON            11            355
  RECTUM            1            118
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ST14 MUTATED         1        0        2         4         0         0
  ST14 WILD-TYPE      90        1       30       134        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ST14 MUTATED           1          1          1          2        0         0
  ST14 WILD-TYPE        23         10         58         40       48        18
                vv
clus             STAGE IVB
  ST14 MUTATED           0
  ST14 WILD-TYPE         1
D1909V4, multiclass
            clus
vv           ST14 MUTATED ST14 WILD-TYPE
  STAGE I               1             90
  STAGE IA              0              1
  STAGE II              2             30
  STAGE IIA             4            134
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             1             23
  STAGE IIIA            1             10
  STAGE IIIB            1             58
  STAGE IIIC            2             40
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  ST14 MUTATED     0   1   8   3
  ST14 WILD-TYPE  17  91 321  47
D1909V5, multiclass
    clus
vv   ST14 MUTATED ST14 WILD-TYPE
  T1            0             17
  T2            1             91
  T3            8            321
  T4            3             47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  ST14 MUTATED     8   3   1
  ST14 WILD-TYPE 279 110  86
D1909V6, multiclass
    clus
vv   ST14 MUTATED ST14 WILD-TYPE
  N0            8            279
  N1            3            110
  N2            1             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1909V7, binary
                cls
clus               0   1
  ST14 MUTATED     8   0
  ST14 WILD-TYPE 367  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  ST14 MUTATED      8    0
  ST14 WILD-TYPE  367   65
   clus
vv  ST14 MUTATED ST14 WILD-TYPE
  0            8            367
  1            0             65
[1] 2 2
[1] FALSE
D1909V8, binary
                cls
clus               0   1
  ST14 MUTATED     5   7
  ST14 WILD-TYPE 220 257
[1] "tbl2"
                cls
clus             [,1] [,2]
  ST14 MUTATED      5    7
  ST14 WILD-TYPE  220  257
        clus
vv       ST14 MUTATED ST14 WILD-TYPE
  FEMALE            5            220
  MALE              7            257
[1] 2 2
[1] FALSE
D1909V9, binary
                cls
clus               0   1
  ST14 MUTATED     8   1
  ST14 WILD-TYPE 342  21
[1] "tbl2"
                cls
clus             [,1] [,2]
  ST14 MUTATED      8    1
  ST14 WILD-TYPE  342   21
     clus
vv    ST14 MUTATED ST14 WILD-TYPE
  NO             8            342
  YES            1             21
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ST14 MUTATED                      8                             2
  ST14 WILD-TYPE                  307                            45
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ST14 MUTATED                       1                              0
  ST14 WILD-TYPE                   105                             10
D1909V10, multiclass
                                clus
vv                               ST14 MUTATED ST14 WILD-TYPE
  COLON ADENOCARCINOMA                      8            307
  COLON MUCINOUS ADENOCARCINOMA             2             45
  RECTAL ADENOCARCINOMA                     1            105
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  ST14 MUTATED     7   0   0   3
  ST14 WILD-TYPE 338   4  31  22
D1909V11, multiclass
    clus
vv   ST14 MUTATED ST14 WILD-TYPE
  R0            7            338
  R1            0              4
  R2            0             31
  RX            3             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1909V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ST14 MUTATED                                  0     1
  ST14 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  ST14 MUTATED                           0     8
  ST14 WILD-TYPE                        22   218
D1909V13, multiclass
                                  clus
vv                                 ST14 MUTATED ST14 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       8            218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1910) Variable = DPPA2 MUTATION ANALYSIS
D1910V1, survival
                 sevent
clus2               0   1
  DPPA2 MUTATED     5   3
  DPPA2 WILD-TYPE 373  90
  DPPA2 MUTATED DPPA2 WILD-TYPE 
              8             463 
  DPPA2 MUTATED DPPA2 WILD-TYPE 
              3              90 
$`DPPA2 MUTATED`
TCGA-A6-4105 TCGA-AA-3663 TCGA-AA-A00J TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-5916 
       14.53         6.97        18.05        12.76        10.06        21.14 
TCGA-CM-6170 TCGA-AG-3892 
       15.02        13.02 

$`DPPA2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 
       16.57        34.65        33.34        32.75        36.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       19.00        30.02        34.03        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       51.32         9.99        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6171 
       16.04        21.99        14.99        12.99        13.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       17.03        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  DPPA2 MUTATED DPPA2 WILD-TYPE 
           6.97            0.00 
  DPPA2 MUTATED DPPA2 WILD-TYPE 
          21.14          148.01 
  DPPA2 MUTATED DPPA2 WILD-TYPE 
         13.775          20.910 
[1] "7.0 - 21.1 (13.8)"  "0.0 - 148.0 (20.9)"
[1] "hr=" "3.4"
D1910V2, continuous
D1910V3, binary
                 cls
clus                0   1
  DPPA2 MUTATED     7   1
  DPPA2 WILD-TYPE 359 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DPPA2 MUTATED      7    1
  DPPA2 WILD-TYPE  359  118
        clus
vv       DPPA2 MUTATED DPPA2 WILD-TYPE
  COLON              7             359
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DPPA2 MUTATED         3        0        1         3         0         0
  DPPA2 WILD-TYPE      88        1       31       135        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DPPA2 MUTATED           0          0          1          0        0         0
  DPPA2 WILD-TYPE        24         11         58         42       48        18
                 vv
clus              STAGE IVB
  DPPA2 MUTATED           0
  DPPA2 WILD-TYPE         1
D1910V4, multiclass
            clus
vv           DPPA2 MUTATED DPPA2 WILD-TYPE
  STAGE I                3              88
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              3             135
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  DPPA2 MUTATED     2   1   4   1
  DPPA2 WILD-TYPE  15  91 325  49
D1910V5, multiclass
    clus
vv   DPPA2 MUTATED DPPA2 WILD-TYPE
  T1             2              15
  T2             1              91
  T3             4             325
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  DPPA2 MUTATED     7   1   0
  DPPA2 WILD-TYPE 280 112  87
D1910V6, multiclass
    clus
vv   DPPA2 MUTATED DPPA2 WILD-TYPE
  N0             7             280
  N1             1             112
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1910V7, binary
                 cls
clus                0   1
  DPPA2 MUTATED     8   0
  DPPA2 WILD-TYPE 367  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DPPA2 MUTATED      8    0
  DPPA2 WILD-TYPE  367   65
   clus
vv  DPPA2 MUTATED DPPA2 WILD-TYPE
  0             8             367
  1             0              65
[1] 2 2
[1] FALSE
D1910V8, binary
                 cls
clus                0   1
  DPPA2 MUTATED     3   5
  DPPA2 WILD-TYPE 222 259
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DPPA2 MUTATED      3    5
  DPPA2 WILD-TYPE  222  259
        clus
vv       DPPA2 MUTATED DPPA2 WILD-TYPE
  FEMALE             3             222
  MALE               5             259
[1] 2 2
[1] FALSE
D1910V9, binary
                 cls
clus                0   1
  DPPA2 MUTATED     8   0
  DPPA2 WILD-TYPE 342  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DPPA2 MUTATED      8    0
  DPPA2 WILD-TYPE  342   22
     clus
vv    DPPA2 MUTATED DPPA2 WILD-TYPE
  NO              8             342
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  DPPA2 MUTATED                      5                             2
  DPPA2 WILD-TYPE                  310                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  DPPA2 MUTATED                       1                              0
  DPPA2 WILD-TYPE                   105                             10
D1910V10, multiclass
                                clus
vv                               DPPA2 MUTATED DPPA2 WILD-TYPE
  COLON ADENOCARCINOMA                       5             310
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  DPPA2 MUTATED     4   0   0   3
  DPPA2 WILD-TYPE 341   4  31  22
D1910V11, multiclass
    clus
vv   DPPA2 MUTATED DPPA2 WILD-TYPE
  R0             4             341
  R1             0               4
  R2             0              31
  RX             3              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1910V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DPPA2 MUTATED                                  0     2
  DPPA2 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  DPPA2 MUTATED                           0     3
  DPPA2 WILD-TYPE                        22   223
D1910V13, multiclass
                                  clus
vv                                 DPPA2 MUTATED DPPA2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               9
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        3             223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1911) Variable = MUC2 MUTATION ANALYSIS
D1911V1, survival
                sevent
clus2              0   1
  MUC2 MUTATED    18   7
  MUC2 WILD-TYPE 360  86
  MUC2 MUTATED MUC2 WILD-TYPE 
            25            446 
  MUC2 MUTATED MUC2 WILD-TYPE 
             7             86 
$`MUC2 MUTATED`
TCGA-A6-5665 TCGA-AA-3510 TCGA-AA-3663 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
       22.06        63.98         6.97        19.04        19.04        10.06 
TCGA-AA-3950 TCGA-AA-A01P TCGA-AD-5900 TCGA-AZ-4682 TCGA-AZ-6599 TCGA-AZ-6601 
       24.00        38.07         0.07        22.36         6.77       100.01 
TCGA-CK-5913 TCGA-CK-6747 TCGA-D5-6929 TCGA-DM-A0X9 TCGA-F4-6570 TCGA-G4-6293 
       51.32        82.95         4.80       119.70         6.18       133.18 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6628 TCGA-DC-5869 TCGA-DC-6155 TCGA-F5-6812 
       22.09        35.80        79.69         5.03        13.97         0.66 
TCGA-F5-6813 
        0.69 

$`MUC2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       85.05        26.99        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       12.00        31.00        31.00         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       39.98        18.05        40.96        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 
       62.79        88.21        49.41        12.10        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 
       17.56       148.01        85.45        15.62        49.08         9.99 
TCGA-CK-5916 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       21.14         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0XD 
       11.64         1.51        12.00        11.38        10.26        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 
       98.24         8.61        31.96        35.74        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       47.41        35.31        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 
       55.04        85.48        63.62        61.91        36.00        13.78 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       26.17        91.79        46.75        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       15.02        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  MUC2 MUTATED MUC2 WILD-TYPE 
          0.07           0.00 
  MUC2 MUTATED MUC2 WILD-TYPE 
        133.18         148.01 
  MUC2 MUTATED MUC2 WILD-TYPE 
        22.060         20.155 
[1] "0.1 - 133.2 (22.1)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.1"
D1911V2, continuous
D1911V3, binary
                cls
clus               0   1
  MUC2 MUTATED    21   4
  MUC2 WILD-TYPE 345 115
[1] "tbl2"
                cls
clus             [,1] [,2]
  MUC2 MUTATED     21    4
  MUC2 WILD-TYPE  345  115
        clus
vv       MUC2 MUTATED MUC2 WILD-TYPE
  COLON            21            345
  RECTUM            4            115
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MUC2 MUTATED         3        0        4         8         0         0
  MUC2 WILD-TYPE      88        1       28       130        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MUC2 MUTATED           4          1          1          1        2         1
  MUC2 WILD-TYPE        20         10         58         41       46        17
                vv
clus             STAGE IVB
  MUC2 MUTATED           0
  MUC2 WILD-TYPE         1
D1911V4, multiclass
            clus
vv           MUC2 MUTATED MUC2 WILD-TYPE
  STAGE I               3             88
  STAGE IA              0              1
  STAGE II              4             28
  STAGE IIA             8            130
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             4             20
  STAGE IIIA            1             10
  STAGE IIIB            1             58
  STAGE IIIC            1             41
  STAGE IV              2             46
  STAGE IVA             1             17
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  MUC2 MUTATED     0   5  19   1
  MUC2 WILD-TYPE  17  87 310  49
D1911V5, multiclass
    clus
vv   MUC2 MUTATED MUC2 WILD-TYPE
  T1            0             17
  T2            5             87
  T3           19            310
  T4            1             49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  MUC2 MUTATED    17   6   2
  MUC2 WILD-TYPE 270 107  85
D1911V6, multiclass
    clus
vv   MUC2 MUTATED MUC2 WILD-TYPE
  N0           17            270
  N1            6            107
  N2            2             85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1911V7, binary
                cls
clus               0   1
  MUC2 MUTATED    17   3
  MUC2 WILD-TYPE 358  62
[1] "tbl2"
                cls
clus             [,1] [,2]
  MUC2 MUTATED     17    3
  MUC2 WILD-TYPE  358   62
   clus
vv  MUC2 MUTATED MUC2 WILD-TYPE
  0           17            358
  1            3             62
[1] 2 2
[1] FALSE
D1911V8, binary
                cls
clus               0   1
  MUC2 MUTATED    14  11
  MUC2 WILD-TYPE 211 253
[1] "tbl2"
                cls
clus             [,1] [,2]
  MUC2 MUTATED     14   11
  MUC2 WILD-TYPE  211  253
        clus
vv       MUC2 MUTATED MUC2 WILD-TYPE
  FEMALE           14            211
  MALE             11            253
[1] 2 2
[1] FALSE
D1911V9, binary
                cls
clus               0   1
  MUC2 MUTATED    18   1
  MUC2 WILD-TYPE 332  21
[1] "tbl2"
                cls
clus             [,1] [,2]
  MUC2 MUTATED     18    1
  MUC2 WILD-TYPE  332   21
     clus
vv    MUC2 MUTATED MUC2 WILD-TYPE
  NO            18            332
  YES            1             21
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MUC2 MUTATED                     19                             2
  MUC2 WILD-TYPE                  296                            45
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MUC2 MUTATED                       4                              0
  MUC2 WILD-TYPE                   102                             10
D1911V10, multiclass
                                clus
vv                               MUC2 MUTATED MUC2 WILD-TYPE
  COLON ADENOCARCINOMA                     19            296
  COLON MUCINOUS ADENOCARCINOMA             2             45
  RECTAL ADENOCARCINOMA                     4            102
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  MUC2 MUTATED    19   0   1   2
  MUC2 WILD-TYPE 326   4  30  23
D1911V11, multiclass
    clus
vv   MUC2 MUTATED MUC2 WILD-TYPE
  R0           19            326
  R1            0              4
  R2            1             30
  RX            2             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1911V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MUC2 MUTATED                                  0     0
  MUC2 WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  MUC2 MUTATED                           1    17
  MUC2 WILD-TYPE                        21   209
D1911V13, multiclass
                                  clus
vv                                 MUC2 MUTATED MUC2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                      17            209
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1912) Variable = CTTN MUTATION ANALYSIS
D1912V1, survival
                sevent
clus2              0   1
  CTTN MUTATED     5   0
  CTTN WILD-TYPE 373  93
  CTTN MUTATED CTTN WILD-TYPE 
             5            466 
  CTTN MUTATED CTTN WILD-TYPE 
             0             93 
$`CTTN MUTATED`
TCGA-AU-6004 TCGA-AZ-4315 TCGA-CK-4950 TCGA-CK-4952 TCGA-AG-A002 
       27.09        58.39        85.45        15.62        20.98 

$`CTTN WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 
       22.42        27.42        10.88         0.20        14.50        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        33.01        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  CTTN MUTATED CTTN WILD-TYPE 
         15.62           0.00 
  CTTN MUTATED CTTN WILD-TYPE 
         85.45         148.01 
  CTTN MUTATED CTTN WILD-TYPE 
        27.090         20.085 
[1] "15.6 - 85.5 (27.1)" "0.0 - 148.0 (20.1)"
[1] "hr="     "9200000"
D1912V2, continuous
D1912V3, binary
                cls
clus               0   1
  CTTN MUTATED     4   1
  CTTN WILD-TYPE 362 118
[1] "tbl2"
                cls
clus             [,1] [,2]
  CTTN MUTATED      4    1
  CTTN WILD-TYPE  362  118
        clus
vv       CTTN MUTATED CTTN WILD-TYPE
  COLON             4            362
  RECTUM            1            118
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CTTN MUTATED         2        0        0         1         0         0
  CTTN WILD-TYPE      89        1       32       137        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CTTN MUTATED           0          0          1          1        0         0
  CTTN WILD-TYPE        24         11         58         41       48        18
                vv
clus             STAGE IVB
  CTTN MUTATED           0
  CTTN WILD-TYPE         1
D1912V4, multiclass
            clus
vv           CTTN MUTATED CTTN WILD-TYPE
  STAGE I               2             89
  STAGE IA              0              1
  STAGE II              0             32
  STAGE IIA             1            137
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            1             58
  STAGE IIIC            1             41
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  CTTN MUTATED     0   2   2   1
  CTTN WILD-TYPE  17  90 327  49
D1912V5, multiclass
    clus
vv   CTTN MUTATED CTTN WILD-TYPE
  T1            0             17
  T2            2             90
  T3            2            327
  T4            1             49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  CTTN MUTATED     3   1   1
  CTTN WILD-TYPE 284 112  86
D1912V6, multiclass
    clus
vv   CTTN MUTATED CTTN WILD-TYPE
  N0            3            284
  N1            1            112
  N2            1             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1912V7, binary
                cls
clus               0   1
  CTTN MUTATED     5   0
  CTTN WILD-TYPE 370  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  CTTN MUTATED      5    0
  CTTN WILD-TYPE  370   65
   clus
vv  CTTN MUTATED CTTN WILD-TYPE
  0            5            370
  1            0             65
[1] 2 2
[1] FALSE
D1912V8, binary
                cls
clus               0   1
  CTTN MUTATED     3   2
  CTTN WILD-TYPE 222 262
[1] "tbl2"
                cls
clus             [,1] [,2]
  CTTN MUTATED      3    2
  CTTN WILD-TYPE  222  262
        clus
vv       CTTN MUTATED CTTN WILD-TYPE
  FEMALE            3            222
  MALE              2            262
[1] 2 2
[1] FALSE
D1912V9, binary
                cls
clus               0   1
  CTTN MUTATED     3   0
  CTTN WILD-TYPE 347  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  CTTN MUTATED      3    0
  CTTN WILD-TYPE  347   22
     clus
vv    CTTN MUTATED CTTN WILD-TYPE
  NO             3            347
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CTTN MUTATED                      3                             1
  CTTN WILD-TYPE                  312                            46
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CTTN MUTATED                       1                              0
  CTTN WILD-TYPE                   105                             10
D1912V10, multiclass
                                clus
vv                               CTTN MUTATED CTTN WILD-TYPE
  COLON ADENOCARCINOMA                      3            312
  COLON MUCINOUS ADENOCARCINOMA             1             46
  RECTAL ADENOCARCINOMA                     1            105
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  CTTN MUTATED     3   1   0   1
  CTTN WILD-TYPE 342   3  31  24
D1912V11, multiclass
    clus
vv   CTTN MUTATED CTTN WILD-TYPE
  R0            3            342
  R1            1              3
  R2            0             31
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1912V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CTTN MUTATED                                  0     0
  CTTN WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  CTTN MUTATED                           1     3
  CTTN WILD-TYPE                        21   223
D1912V13, multiclass
                                  clus
vv                                 CTTN MUTATED CTTN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                       3            223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1913) Variable = NFIB MUTATION ANALYSIS
D1913V1, survival
                sevent
clus2              0   1
  NFIB MUTATED     8   4
  NFIB WILD-TYPE 370  89
  NFIB MUTATED NFIB WILD-TYPE 
            12            459 
  NFIB MUTATED NFIB WILD-TYPE 
             4             89 
$`NFIB MUTATED`
TCGA-AA-3510 TCGA-AA-3950 TCGA-AA-A00N TCGA-AA-A01R TCGA-AD-6964 TCGA-AZ-4315 
       63.98        24.00         4.01        35.01        10.88        58.39 
TCGA-AZ-6601 TCGA-D5-6540 TCGA-DM-A28F TCGA-AG-4001 TCGA-AG-A002 TCGA-AG-A02N 
      100.01        16.14        35.97        36.03        20.98        61.97 

$`NFIB WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 
        2.01        12.99        24.00        33.01        26.01         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       31.00        38.07         1.02         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
        0.72         5.79        22.42        27.42         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       49.41         6.77        12.10        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 
       17.85         4.80        17.13        12.49        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G 
      135.65       139.17         6.12        81.37       119.93        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       28.04        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       38.96        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  NFIB MUTATED NFIB WILD-TYPE 
          4.01           0.00 
  NFIB MUTATED NFIB WILD-TYPE 
        100.01         148.01 
  NFIB MUTATED NFIB WILD-TYPE 
         35.49          20.02 
[1] "4.0 - 100.0 (35.5)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.1"
D1913V2, continuous
D1913V3, binary
                cls
clus               0   1
  NFIB MUTATED    11   3
  NFIB WILD-TYPE 355 116
[1] "tbl2"
                cls
clus             [,1] [,2]
  NFIB MUTATED     11    3
  NFIB WILD-TYPE  355  116
        clus
vv       NFIB MUTATED NFIB WILD-TYPE
  COLON            11            355
  RECTUM            3            116
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NFIB MUTATED         2        0        3         4         2         0
  NFIB WILD-TYPE      89        1       29       134         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NFIB MUTATED           1          0          1          0        0         0
  NFIB WILD-TYPE        23         11         58         42       48        18
                vv
clus             STAGE IVB
  NFIB MUTATED           0
  NFIB WILD-TYPE         1
D1913V4, multiclass
            clus
vv           NFIB MUTATED NFIB WILD-TYPE
  STAGE I               2             89
  STAGE IA              0              1
  STAGE II              3             29
  STAGE IIA             4            134
  STAGE IIB             2              8
  STAGE IIC             0              1
  STAGE III             1             23
  STAGE IIIA            0             11
  STAGE IIIB            1             58
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  NFIB MUTATED     0   2   9   3
  NFIB WILD-TYPE  17  90 320  47
D1913V5, multiclass
    clus
vv   NFIB MUTATED NFIB WILD-TYPE
  T1            0             17
  T2            2             90
  T3            9            320
  T4            3             47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  NFIB MUTATED    11   1   2
  NFIB WILD-TYPE 276 112  85
D1913V6, multiclass
    clus
vv   NFIB MUTATED NFIB WILD-TYPE
  N0           11            276
  N1            1            112
  N2            2             85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1913V7, binary
                cls
clus               0   1
  NFIB MUTATED    12   0
  NFIB WILD-TYPE 363  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  NFIB MUTATED     12    0
  NFIB WILD-TYPE  363   65
   clus
vv  NFIB MUTATED NFIB WILD-TYPE
  0           12            363
  1            0             65
[1] 2 2
[1] FALSE
D1913V8, binary
                cls
clus               0   1
  NFIB MUTATED     4  10
  NFIB WILD-TYPE 221 254
[1] "tbl2"
                cls
clus             [,1] [,2]
  NFIB MUTATED      4   10
  NFIB WILD-TYPE  221  254
        clus
vv       NFIB MUTATED NFIB WILD-TYPE
  FEMALE            4            221
  MALE             10            254
[1] 2 2
[1] FALSE
D1913V9, binary
                cls
clus               0   1
  NFIB MUTATED     8   1
  NFIB WILD-TYPE 342  21
[1] "tbl2"
                cls
clus             [,1] [,2]
  NFIB MUTATED      8    1
  NFIB WILD-TYPE  342   21
     clus
vv    NFIB MUTATED NFIB WILD-TYPE
  NO             8            342
  YES            1             21
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  NFIB MUTATED                      7                             4
  NFIB WILD-TYPE                  308                            43
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  NFIB MUTATED                       3                              0
  NFIB WILD-TYPE                   103                             10
D1913V10, multiclass
                                clus
vv                               NFIB MUTATED NFIB WILD-TYPE
  COLON ADENOCARCINOMA                      7            308
  COLON MUCINOUS ADENOCARCINOMA             4             43
  RECTAL ADENOCARCINOMA                     3            103
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  NFIB MUTATED    10   0   0   1
  NFIB WILD-TYPE 335   4  31  24
D1913V11, multiclass
    clus
vv   NFIB MUTATED NFIB WILD-TYPE
  R0           10            335
  R1            0              4
  R2            0             31
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1913V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NFIB MUTATED                                  0     0
  NFIB WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  NFIB MUTATED                           0     6
  NFIB WILD-TYPE                        22   220
D1913V13, multiclass
                                  clus
vv                                 NFIB MUTATED NFIB WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       6            220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1914) Variable = IFNA1 MUTATION ANALYSIS
D1914V1, survival
                 sevent
clus2               0   1
  IFNA1 MUTATED     5   1
  IFNA1 WILD-TYPE 373  92
  IFNA1 MUTATED IFNA1 WILD-TYPE 
              6             465 
  IFNA1 MUTATED IFNA1 WILD-TYPE 
              1              92 
$`IFNA1 MUTATED`
TCGA-AA-3662 TCGA-AA-A00N TCGA-D5-6541 TCGA-G4-6293 TCGA-G4-6310 TCGA-EI-6507 
        6.05         4.01        15.58       133.18        63.62        19.96 

$`IFNA1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6898 TCGA-D5-6920 
        4.80        17.13        12.49        16.14         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6303 
       13.25         0.53        47.41        35.31        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6317 
       53.62        44.68        55.04        85.48        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6510 
       51.48        32.61         0.49        20.55        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  IFNA1 MUTATED IFNA1 WILD-TYPE 
           4.01            0.00 
  IFNA1 MUTATED IFNA1 WILD-TYPE 
         133.18          148.01 
  IFNA1 MUTATED IFNA1 WILD-TYPE 
          17.77           20.28 
[1] "4.0 - 133.2 (17.8)" "0.0 - 148.0 (20.3)"
[1] "hr=" "1.7"
D1914V2, continuous
D1914V3, binary
                 cls
clus                0   1
  IFNA1 MUTATED     6   1
  IFNA1 WILD-TYPE 360 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IFNA1 MUTATED      6    1
  IFNA1 WILD-TYPE  360  118
        clus
vv       IFNA1 MUTATED IFNA1 WILD-TYPE
  COLON              6             360
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  IFNA1 MUTATED         0        0        0         2         1         0
  IFNA1 WILD-TYPE      91        1       32       136         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  IFNA1 MUTATED           1          0          1          1        1         0
  IFNA1 WILD-TYPE        23         11         58         41       47        18
                 vv
clus              STAGE IVB
  IFNA1 MUTATED           0
  IFNA1 WILD-TYPE         1
D1914V4, multiclass
            clus
vv           IFNA1 MUTATED IFNA1 WILD-TYPE
  STAGE I                0              91
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              2             136
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             1              41
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  IFNA1 MUTATED     0   0   5   2
  IFNA1 WILD-TYPE  17  92 324  48
D1914V5, multiclass
    clus
vv   IFNA1 MUTATED IFNA1 WILD-TYPE
  T1             0              17
  T2             0              92
  T3             5             324
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  IFNA1 MUTATED     3   2   2
  IFNA1 WILD-TYPE 284 111  85
D1914V6, multiclass
    clus
vv   IFNA1 MUTATED IFNA1 WILD-TYPE
  N0             3             284
  N1             2             111
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1914V7, binary
                 cls
clus                0   1
  IFNA1 MUTATED     5   1
  IFNA1 WILD-TYPE 370  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IFNA1 MUTATED      5    1
  IFNA1 WILD-TYPE  370   64
   clus
vv  IFNA1 MUTATED IFNA1 WILD-TYPE
  0             5             370
  1             1              64
[1] 2 2
[1] FALSE
D1914V8, binary
                 cls
clus                0   1
  IFNA1 MUTATED     2   5
  IFNA1 WILD-TYPE 223 259
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IFNA1 MUTATED      2    5
  IFNA1 WILD-TYPE  223  259
        clus
vv       IFNA1 MUTATED IFNA1 WILD-TYPE
  FEMALE             2             223
  MALE               5             259
[1] 2 2
[1] FALSE
D1914V9, binary
                 cls
clus                0   1
  IFNA1 MUTATED     4   1
  IFNA1 WILD-TYPE 346  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IFNA1 MUTATED      4    1
  IFNA1 WILD-TYPE  346   21
     clus
vv    IFNA1 MUTATED IFNA1 WILD-TYPE
  NO              4             346
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  IFNA1 MUTATED                      4                             2
  IFNA1 WILD-TYPE                  311                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  IFNA1 MUTATED                       1                              0
  IFNA1 WILD-TYPE                   105                             10
D1914V10, multiclass
                                clus
vv                               IFNA1 MUTATED IFNA1 WILD-TYPE
  COLON ADENOCARCINOMA                       4             311
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  IFNA1 MUTATED     6   0   1   0
  IFNA1 WILD-TYPE 339   4  30  25
D1914V11, multiclass
    clus
vv   IFNA1 MUTATED IFNA1 WILD-TYPE
  R0             6             339
  R1             0               4
  R2             1              30
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1914V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  IFNA1 MUTATED                                  0     0
  IFNA1 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  IFNA1 MUTATED                           0     5
  IFNA1 WILD-TYPE                        22   221
D1914V13, multiclass
                                  clus
vv                                 IFNA1 MUTATED IFNA1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        5             221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1915) Variable = RGS3 MUTATION ANALYSIS
D1915V1, survival
                sevent
clus2              0   1
  RGS3 MUTATED    14   3
  RGS3 WILD-TYPE 364  90
  RGS3 MUTATED RGS3 WILD-TYPE 
            17            454 
  RGS3 MUTATED RGS3 WILD-TYPE 
             3             90 
$`RGS3 MUTATED`
TCGA-A6-6141 TCGA-AA-3510 TCGA-AA-3713 TCGA-AA-3821 TCGA-AA-3845 TCGA-AA-3864 
        8.38        63.98        19.04         1.02         0.00        53.00 
TCGA-AA-3947 TCGA-AA-A00R TCGA-CK-5916 TCGA-CK-6751 TCGA-CM-6674 TCGA-DM-A1D7 
       33.01         0.99        21.14       124.27        12.95        13.32 
TCGA-DM-A28E TCGA-F4-6856 TCGA-AG-3892 TCGA-AG-A002 TCGA-DC-6157 
      119.93        35.31        13.02        20.98        27.95 

$`RGS3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 
       22.09        22.06        32.71        27.09        22.52        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
       33.04         0.99        25.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02        14.93        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       30.05        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 
       31.00         2.01        12.99        24.00        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W 
       38.04         4.01        27.02        42.02        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 
       85.45        15.62        49.08        51.32         9.99        82.95 
TCGA-CK-6748 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
        1.91        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6676 
       13.02        15.02        14.04        11.01        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
      130.65        92.75        49.91        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 
       16.24        33.67        13.25         0.53        47.41       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
        5.03        13.97        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  RGS3 MUTATED RGS3 WILD-TYPE 
             0              0 
  RGS3 MUTATED RGS3 WILD-TYPE 
        124.27         148.01 
  RGS3 MUTATED RGS3 WILD-TYPE 
        20.980         20.155 
[1] "0.0 - 124.3 (21.0)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.4"
D1915V2, continuous
D1915V3, binary
                cls
clus               0   1
  RGS3 MUTATED    15   3
  RGS3 WILD-TYPE 351 116
[1] "tbl2"
                cls
clus             [,1] [,2]
  RGS3 MUTATED     15    3
  RGS3 WILD-TYPE  351  116
        clus
vv       RGS3 MUTATED RGS3 WILD-TYPE
  COLON            15            351
  RECTUM            3            116
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RGS3 MUTATED         8        0        2         5         2         0
  RGS3 WILD-TYPE      83        1       30       133         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RGS3 MUTATED           0          0          0          0        1         0
  RGS3 WILD-TYPE        24         11         59         42       47        18
                vv
clus             STAGE IVB
  RGS3 MUTATED           0
  RGS3 WILD-TYPE         1
D1915V4, multiclass
            clus
vv           RGS3 MUTATED RGS3 WILD-TYPE
  STAGE I               8             83
  STAGE IA              0              1
  STAGE II              2             30
  STAGE IIA             5            133
  STAGE IIB             2              8
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            0             59
  STAGE IIIC            0             42
  STAGE IV              1             47
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  RGS3 MUTATED     2   6   8   2
  RGS3 WILD-TYPE  15  86 321  48
D1915V5, multiclass
    clus
vv   RGS3 MUTATED RGS3 WILD-TYPE
  T1            2             15
  T2            6             86
  T3            8            321
  T4            2             48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  RGS3 MUTATED    18   0   0
  RGS3 WILD-TYPE 269 113  87
D1915V6, multiclass
    clus
vv   RGS3 MUTATED RGS3 WILD-TYPE
  N0           18            269
  N1            0            113
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1915V7, binary
                cls
clus               0   1
  RGS3 MUTATED    15   1
  RGS3 WILD-TYPE 360  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  RGS3 MUTATED     15    1
  RGS3 WILD-TYPE  360   64
   clus
vv  RGS3 MUTATED RGS3 WILD-TYPE
  0           15            360
  1            1             64
[1] 2 2
[1] FALSE
D1915V8, binary
                cls
clus               0   1
  RGS3 MUTATED     9   9
  RGS3 WILD-TYPE 216 255
[1] "tbl2"
                cls
clus             [,1] [,2]
  RGS3 MUTATED      9    9
  RGS3 WILD-TYPE  216  255
        clus
vv       RGS3 MUTATED RGS3 WILD-TYPE
  FEMALE            9            216
  MALE              9            255
[1] 2 2
[1] FALSE
D1915V9, binary
                cls
clus               0   1
  RGS3 MUTATED    11   1
  RGS3 WILD-TYPE 339  21
[1] "tbl2"
                cls
clus             [,1] [,2]
  RGS3 MUTATED     11    1
  RGS3 WILD-TYPE  339   21
     clus
vv    RGS3 MUTATED RGS3 WILD-TYPE
  NO            11            339
  YES            1             21
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  RGS3 MUTATED                     10                             4
  RGS3 WILD-TYPE                  305                            43
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  RGS3 MUTATED                       3                              0
  RGS3 WILD-TYPE                   103                             10
D1915V10, multiclass
                                clus
vv                               RGS3 MUTATED RGS3 WILD-TYPE
  COLON ADENOCARCINOMA                     10            305
  COLON MUCINOUS ADENOCARCINOMA             4             43
  RECTAL ADENOCARCINOMA                     3            103
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  RGS3 MUTATED    11   0   1   3
  RGS3 WILD-TYPE 334   4  30  22
D1915V11, multiclass
    clus
vv   RGS3 MUTATED RGS3 WILD-TYPE
  R0           11            334
  R1            0              4
  R2            1             30
  RX            3             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1915V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RGS3 MUTATED                                  0     0
  RGS3 WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  RGS3 MUTATED                           2     7
  RGS3 WILD-TYPE                        20   219
D1915V13, multiclass
                                  clus
vv                                 RGS3 MUTATED RGS3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   2             20
  WHITE                                       7            219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1916) Variable = CCDC89 MUTATION ANALYSIS
D1916V1, survival
                  sevent
clus2                0   1
  CCDC89 MUTATED     3   1
  CCDC89 WILD-TYPE 375  92
  CCDC89 MUTATED CCDC89 WILD-TYPE 
               4              467 
  CCDC89 MUTATED CCDC89 WILD-TYPE 
               1               92 
$`CCDC89 MUTATED`
TCGA-AA-3492 TCGA-AD-6895 TCGA-AZ-4315 TCGA-G4-6309 
        3.02         0.72        58.39        85.48 

$`CCDC89 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       15.52        56.55         0.79         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       33.01        21.44        17.82         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 
       65.85        53.62        44.68        55.04        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  CCDC89 MUTATED CCDC89 WILD-TYPE 
            0.72             0.00 
  CCDC89 MUTATED CCDC89 WILD-TYPE 
           85.48           148.01 
  CCDC89 MUTATED CCDC89 WILD-TYPE 
          30.705           20.190 
[1] "0.7 - 85.5 (30.7)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.2"
D1916V2, continuous
D1916V3, binary
                  cls
clus                 0   1
  CCDC89 MUTATED     4   0
  CCDC89 WILD-TYPE 362 119
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC89 MUTATED      4    0
  CCDC89 WILD-TYPE  362  119
        clus
vv       CCDC89 MUTATED CCDC89 WILD-TYPE
  COLON               4              362
  RECTUM              0              119
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CCDC89 MUTATED         0        0        1         1         0         0
  CCDC89 WILD-TYPE      91        1       31       137        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CCDC89 MUTATED           0          0          1          0        0
  CCDC89 WILD-TYPE        24         11         58         42       48
                  vv
clus               STAGE IVA STAGE IVB
  CCDC89 MUTATED           0         0
  CCDC89 WILD-TYPE        18         1
D1916V4, multiclass
            clus
vv           CCDC89 MUTATED CCDC89 WILD-TYPE
  STAGE I                 0               91
  STAGE IA                0                1
  STAGE II                1               31
  STAGE IIA               1              137
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              1               58
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  CCDC89 MUTATED     0   0   4   0
  CCDC89 WILD-TYPE  17  92 325  50
D1916V5, multiclass
    clus
vv   CCDC89 MUTATED CCDC89 WILD-TYPE
  T1              0               17
  T2              0               92
  T3              4              325
  T4              0               50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  CCDC89 MUTATED     2   2   0
  CCDC89 WILD-TYPE 285 111  87
D1916V6, multiclass
    clus
vv   CCDC89 MUTATED CCDC89 WILD-TYPE
  N0              2              285
  N1              2              111
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1916V7, binary
                  cls
clus                 0   1
  CCDC89 MUTATED     3   0
  CCDC89 WILD-TYPE 372  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC89 MUTATED      3    0
  CCDC89 WILD-TYPE  372   65
   clus
vv  CCDC89 MUTATED CCDC89 WILD-TYPE
  0              3              372
  1              0               65
[1] 2 2
[1] FALSE
D1916V8, binary
                  cls
clus                 0   1
  CCDC89 MUTATED     2   2
  CCDC89 WILD-TYPE 223 262
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC89 MUTATED      2    2
  CCDC89 WILD-TYPE  223  262
        clus
vv       CCDC89 MUTATED CCDC89 WILD-TYPE
  FEMALE              2              223
  MALE                2              262
[1] 2 2
[1] FALSE
D1916V9, binary
                  cls
clus                 0   1
  CCDC89 MUTATED     3   0
  CCDC89 WILD-TYPE 347  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC89 MUTATED      3    0
  CCDC89 WILD-TYPE  347   22
     clus
vv    CCDC89 MUTATED CCDC89 WILD-TYPE
  NO               3              347
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CCDC89 MUTATED                      4                             0
  CCDC89 WILD-TYPE                  311                            47
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CCDC89 MUTATED                       0                              0
  CCDC89 WILD-TYPE                   106                             10
D1916V10, multiclass
                                clus
vv                               CCDC89 MUTATED CCDC89 WILD-TYPE
  COLON ADENOCARCINOMA                        4              311
  COLON MUCINOUS ADENOCARCINOMA               0               47
  RECTAL ADENOCARCINOMA                       0              106
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  CCDC89 MUTATED     3   0   0   0
  CCDC89 WILD-TYPE 342   4  31  25
D1916V11, multiclass
    clus
vv   CCDC89 MUTATED CCDC89 WILD-TYPE
  R0              3              342
  R1              0                4
  R2              0               31
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1916V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CCDC89 MUTATED                                  0     0
  CCDC89 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  CCDC89 MUTATED                           1     2
  CCDC89 WILD-TYPE                        21   224
D1916V13, multiclass
                                  clus
vv                                 CCDC89 MUTATED CCDC89 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                         2              224
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1917) Variable = MIA2 MUTATION ANALYSIS
D1917V1, survival
                sevent
clus2              0   1
  MIA2 MUTATED     9   2
  MIA2 WILD-TYPE 369  91
  MIA2 MUTATED MIA2 WILD-TYPE 
            11            460 
  MIA2 MUTATED MIA2 WILD-TYPE 
             2             91 
$`MIA2 MUTATED`
TCGA-AA-3510 TCGA-AA-3867 TCGA-AA-A010 TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-5864 
       63.98        24.03        34.98        12.76        10.06        15.02 
TCGA-D5-6928 TCGA-AG-3742 TCGA-AG-A002 TCGA-CL-5918 TCGA-DY-A1DD 
       11.64         0.99        20.98         7.17        57.24 

$`MIA2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       17.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.04         9.44         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3878 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-DC-5337 
        6.05        33.17         6.97         4.73        78.12        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DF 
        4.01         5.03         5.29       126.44        41.36        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  MIA2 MUTATED MIA2 WILD-TYPE 
          0.99           0.00 
  MIA2 MUTATED MIA2 WILD-TYPE 
         63.98         148.01 
  MIA2 MUTATED MIA2 WILD-TYPE 
        15.020         20.235 
[1] "1.0 - 64.0 (15.0)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1"  
D1917V2, continuous
D1917V3, binary
                cls
clus               0   1
  MIA2 MUTATED     8   4
  MIA2 WILD-TYPE 358 115
[1] "tbl2"
                cls
clus             [,1] [,2]
  MIA2 MUTATED      8    4
  MIA2 WILD-TYPE  358  115
        clus
vv       MIA2 MUTATED MIA2 WILD-TYPE
  COLON             8            358
  RECTUM            4            115
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MIA2 MUTATED         3        0        1         4         1         0
  MIA2 WILD-TYPE      88        1       31       134         9         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MIA2 MUTATED           0          0          1          1        1         0
  MIA2 WILD-TYPE        24         11         58         41       47        18
                vv
clus             STAGE IVB
  MIA2 MUTATED           0
  MIA2 WILD-TYPE         1
D1917V4, multiclass
            clus
vv           MIA2 MUTATED MIA2 WILD-TYPE
  STAGE I               3             88
  STAGE IA              0              1
  STAGE II              1             31
  STAGE IIA             4            134
  STAGE IIB             1              9
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            1             58
  STAGE IIIC            1             41
  STAGE IV              1             47
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  MIA2 MUTATED     1   2   8   1
  MIA2 WILD-TYPE  16  90 321  49
D1917V5, multiclass
    clus
vv   MIA2 MUTATED MIA2 WILD-TYPE
  T1            1             16
  T2            2             90
  T3            8            321
  T4            1             49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  MIA2 MUTATED     9   1   2
  MIA2 WILD-TYPE 278 112  85
D1917V6, multiclass
    clus
vv   MIA2 MUTATED MIA2 WILD-TYPE
  N0            9            278
  N1            1            112
  N2            2             85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1917V7, binary
                cls
clus               0   1
  MIA2 MUTATED     9   1
  MIA2 WILD-TYPE 366  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  MIA2 MUTATED      9    1
  MIA2 WILD-TYPE  366   64
   clus
vv  MIA2 MUTATED MIA2 WILD-TYPE
  0            9            366
  1            1             64
[1] 2 2
[1] FALSE
D1917V8, binary
                cls
clus               0   1
  MIA2 MUTATED     4   8
  MIA2 WILD-TYPE 221 256
[1] "tbl2"
                cls
clus             [,1] [,2]
  MIA2 MUTATED      4    8
  MIA2 WILD-TYPE  221  256
        clus
vv       MIA2 MUTATED MIA2 WILD-TYPE
  FEMALE            4            221
  MALE              8            256
[1] 2 2
[1] FALSE
D1917V9, binary
                cls
clus               0   1
  MIA2 MUTATED     9   0
  MIA2 WILD-TYPE 341  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  MIA2 MUTATED      9    0
  MIA2 WILD-TYPE  341   22
     clus
vv    MIA2 MUTATED MIA2 WILD-TYPE
  NO             9            341
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MIA2 MUTATED                      5                             3
  MIA2 WILD-TYPE                  310                            44
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MIA2 MUTATED                       4                              0
  MIA2 WILD-TYPE                   102                             10
D1917V10, multiclass
                                clus
vv                               MIA2 MUTATED MIA2 WILD-TYPE
  COLON ADENOCARCINOMA                      5            310
  COLON MUCINOUS ADENOCARCINOMA             3             44
  RECTAL ADENOCARCINOMA                     4            102
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  MIA2 MUTATED     7   0   1   3
  MIA2 WILD-TYPE 338   4  30  22
D1917V11, multiclass
    clus
vv   MIA2 MUTATED MIA2 WILD-TYPE
  R0            7            338
  R1            0              4
  R2            1             30
  RX            3             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1917V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MIA2 MUTATED                                  0     2
  MIA2 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  MIA2 MUTATED                           0     5
  MIA2 WILD-TYPE                        22   221
D1917V13, multiclass
                                  clus
vv                                 MIA2 MUTATED MIA2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              9
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       5            221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1918) Variable = DDR2 MUTATION ANALYSIS
D1918V1, survival
                sevent
clus2              0   1
  DDR2 MUTATED    11   4
  DDR2 WILD-TYPE 367  89
  DDR2 MUTATED DDR2 WILD-TYPE 
            15            456 
  DDR2 MUTATED DDR2 WILD-TYPE 
             4             89 
$`DDR2 MUTATED`
TCGA-A6-6649 TCGA-A6-6782 TCGA-AA-3819 TCGA-AA-3968 TCGA-AA-3977 TCGA-AA-A00N 
       24.16        20.28        25.02        21.99        25.02         4.01 
TCGA-AA-A010 TCGA-AD-6889 TCGA-AD-6963 TCGA-AZ-6599 TCGA-CK-5916 TCGA-D5-6926 
       34.98        56.55        27.42         6.77        21.14         9.04 
TCGA-DM-A28K TCGA-AG-3892 TCGA-DY-A1H8 
       98.24        13.02        32.61 

$`DDR2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.08        25.18        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        19.66         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       35.05        33.04         0.99         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6964 
       15.52         0.79         0.72         5.79        22.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        88.21        49.41        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       49.08        51.32         9.99        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
       14.30         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-F4-6459 TCGA-F4-6460 
      119.93        35.97        60.79       117.07         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       17.03        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EF-5830 TCGA-EI-6506 
       41.36        57.24        24.13        51.48         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  DDR2 MUTATED DDR2 WILD-TYPE 
          4.01           0.00 
  DDR2 MUTATED DDR2 WILD-TYPE 
         98.24         148.01 
  DDR2 MUTATED DDR2 WILD-TYPE 
         24.16          20.02 
[1] "4.0 - 98.2 (24.2)"  "0.0 - 148.0 (20.0)"
[1] "hr=" "1.3"
D1918V2, continuous
D1918V3, binary
                cls
clus               0   1
  DDR2 MUTATED    13   2
  DDR2 WILD-TYPE 353 117
[1] "tbl2"
                cls
clus             [,1] [,2]
  DDR2 MUTATED     13    2
  DDR2 WILD-TYPE  353  117
        clus
vv       DDR2 MUTATED DDR2 WILD-TYPE
  COLON            13            353
  RECTUM            2            117
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DDR2 MUTATED         4        0        0         3         3         0
  DDR2 WILD-TYPE      87        1       32       135         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DDR2 MUTATED           0          1          2          0        0         0
  DDR2 WILD-TYPE        24         10         57         42       48        18
                vv
clus             STAGE IVB
  DDR2 MUTATED           0
  DDR2 WILD-TYPE         1
D1918V4, multiclass
            clus
vv           DDR2 MUTATED DDR2 WILD-TYPE
  STAGE I               4             87
  STAGE IA              0              1
  STAGE II              0             32
  STAGE IIA             3            135
  STAGE IIB             3              7
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            1             10
  STAGE IIIB            2             57
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  DDR2 MUTATED     2   4   5   4
  DDR2 WILD-TYPE  15  88 324  46
D1918V5, multiclass
    clus
vv   DDR2 MUTATED DDR2 WILD-TYPE
  T1            2             15
  T2            4             88
  T3            5            324
  T4            4             46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  DDR2 MUTATED    12   3   0
  DDR2 WILD-TYPE 275 110  87
D1918V6, multiclass
    clus
vv   DDR2 MUTATED DDR2 WILD-TYPE
  N0           12            275
  N1            3            110
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1918V7, binary
                cls
clus               0   1
  DDR2 MUTATED    11   0
  DDR2 WILD-TYPE 364  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  DDR2 MUTATED     11    0
  DDR2 WILD-TYPE  364   65
   clus
vv  DDR2 MUTATED DDR2 WILD-TYPE
  0           11            364
  1            0             65
[1] 2 2
[1] FALSE
D1918V8, binary
                cls
clus               0   1
  DDR2 MUTATED     6   9
  DDR2 WILD-TYPE 219 255
[1] "tbl2"
                cls
clus             [,1] [,2]
  DDR2 MUTATED      6    9
  DDR2 WILD-TYPE  219  255
        clus
vv       DDR2 MUTATED DDR2 WILD-TYPE
  FEMALE            6            219
  MALE              9            255
[1] 2 2
[1] FALSE
D1918V9, binary
                cls
clus               0   1
  DDR2 MUTATED    10   1
  DDR2 WILD-TYPE 340  21
[1] "tbl2"
                cls
clus             [,1] [,2]
  DDR2 MUTATED     10    1
  DDR2 WILD-TYPE  340   21
     clus
vv    DDR2 MUTATED DDR2 WILD-TYPE
  NO            10            340
  YES            1             21
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  DDR2 MUTATED                     11                             2
  DDR2 WILD-TYPE                  304                            45
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  DDR2 MUTATED                       2                              0
  DDR2 WILD-TYPE                   104                             10
D1918V10, multiclass
                                clus
vv                               DDR2 MUTATED DDR2 WILD-TYPE
  COLON ADENOCARCINOMA                     11            304
  COLON MUCINOUS ADENOCARCINOMA             2             45
  RECTAL ADENOCARCINOMA                     2            104
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  DDR2 MUTATED     6   0   0   1
  DDR2 WILD-TYPE 339   4  31  24
D1918V11, multiclass
    clus
vv   DDR2 MUTATED DDR2 WILD-TYPE
  R0            6            339
  R1            0              4
  R2            0             31
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1918V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DDR2 MUTATED                                  0     1
  DDR2 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  DDR2 MUTATED                           0     8
  DDR2 WILD-TYPE                        22   218
D1918V13, multiclass
                                  clus
vv                                 DDR2 MUTATED DDR2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       8            218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1919) Variable = IL3 MUTATION ANALYSIS
D1919V1, survival
               sevent
clus2             0   1
  IL3 MUTATED     6   0
  IL3 WILD-TYPE 372  93
  IL3 MUTATED IL3 WILD-TYPE 
            6           465 
  IL3 MUTATED IL3 WILD-TYPE 
            0            93 
$`IL3 MUTATED`
TCGA-AA-3672 TCGA-AA-3956 TCGA-AA-A00A TCGA-CM-6167 TCGA-CM-6170 TCGA-G4-6317 
        0.92        34.03        38.04        14.99        15.02        36.00 

$`IL3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
        6.05         6.97        54.02         2.01        14.01        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
        2.01        20.98         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00D 
       27.02        19.07         7.96        27.02        13.94        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6168 
       12.00         2.96        29.03        16.04        21.99        12.99 
TCGA-CM-6169 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       13.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6321 
       44.68        55.04        85.48        63.62        61.91        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  IL3 MUTATED IL3 WILD-TYPE 
         0.92          0.00 
  IL3 MUTATED IL3 WILD-TYPE 
        38.04        148.01 
  IL3 MUTATED IL3 WILD-TYPE 
       24.525        20.190 
[1] "0.9 - 38.0 (24.5)"  "0.0 - 148.0 (20.2)"
[1] "hr="     "9100000"
D1919V2, continuous
D1919V3, binary
               cls
clus              0   1
  IL3 MUTATED     6   0
  IL3 WILD-TYPE 360 119
[1] "tbl2"
               cls
clus            [,1] [,2]
  IL3 MUTATED      6    0
  IL3 WILD-TYPE  360  119
        clus
vv       IL3 MUTATED IL3 WILD-TYPE
  COLON            6           360
  RECTUM           0           119
[1] 2 2
[1] FALSE
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  IL3 MUTATED         1        0        0         2         0         0
  IL3 WILD-TYPE      90        1       32       136        10         1
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  IL3 MUTATED           1          0          0          2        0         0
  IL3 WILD-TYPE        23         11         59         40       48        18
               vv
clus            STAGE IVB
  IL3 MUTATED           0
  IL3 WILD-TYPE         1
D1919V4, multiclass
            clus
vv           IL3 MUTATED IL3 WILD-TYPE
  STAGE I              1            90
  STAGE IA             0             1
  STAGE II             0            32
  STAGE IIA            2           136
  STAGE IIB            0            10
  STAGE IIC            0             1
  STAGE III            1            23
  STAGE IIIA           0            11
  STAGE IIIB           0            59
  STAGE IIIC           2            40
  STAGE IV             0            48
  STAGE IVA            0            18
  STAGE IVB            0             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  IL3 MUTATED     0   1   5   0
  IL3 WILD-TYPE  17  91 324  50
D1919V5, multiclass
    clus
vv   IL3 MUTATED IL3 WILD-TYPE
  T1           0            17
  T2           1            91
  T3           5           324
  T4           0            50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2
  IL3 MUTATED     3   1   2
  IL3 WILD-TYPE 284 112  85
D1919V6, multiclass
    clus
vv   IL3 MUTATED IL3 WILD-TYPE
  N0           3           284
  N1           1           112
  N2           2            85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1919V7, binary
               cls
clus              0   1
  IL3 MUTATED     5   0
  IL3 WILD-TYPE 370  65
[1] "tbl2"
               cls
clus            [,1] [,2]
  IL3 MUTATED      5    0
  IL3 WILD-TYPE  370   65
   clus
vv  IL3 MUTATED IL3 WILD-TYPE
  0           5           370
  1           0            65
[1] 2 2
[1] FALSE
D1919V8, binary
               cls
clus              0   1
  IL3 MUTATED     4   2
  IL3 WILD-TYPE 221 262
[1] "tbl2"
               cls
clus            [,1] [,2]
  IL3 MUTATED      4    2
  IL3 WILD-TYPE  221  262
        clus
vv       IL3 MUTATED IL3 WILD-TYPE
  FEMALE           4           221
  MALE             2           262
[1] 2 2
[1] FALSE
D1919V9, binary
               cls
clus              0   1
  IL3 MUTATED     6   0
  IL3 WILD-TYPE 344  22
[1] "tbl2"
               cls
clus            [,1] [,2]
  IL3 MUTATED      6    0
  IL3 WILD-TYPE  344   22
     clus
vv    IL3 MUTATED IL3 WILD-TYPE
  NO            6           344
  YES           0            22
[1] 2 2
[1] FALSE
               vv
clus            COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  IL3 MUTATED                      6                             0
  IL3 WILD-TYPE                  309                            47
               vv
clus            RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  IL3 MUTATED                       0                              0
  IL3 WILD-TYPE                   106                             10
D1919V10, multiclass
                                clus
vv                               IL3 MUTATED IL3 WILD-TYPE
  COLON ADENOCARCINOMA                     6           309
  COLON MUCINOUS ADENOCARCINOMA            0            47
  RECTAL ADENOCARCINOMA                    0           106
  RECTAL MUCINOUS ADENOCARCINOMA           0            10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             R0  R1  R2  RX
  IL3 MUTATED     6   0   0   0
  IL3 WILD-TYPE 339   4  31  25
D1919V11, multiclass
    clus
vv   IL3 MUTATED IL3 WILD-TYPE
  R0           6           339
  R1           0             4
  R2           0            31
  RX           0            25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1919V12, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  IL3 MUTATED                                  0     0
  IL3 WILD-TYPE                                1    11
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  IL3 MUTATED                           1     2
  IL3 WILD-TYPE                        21   224
D1919V13, multiclass
                                  clus
vv                                 IL3 MUTATED IL3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      0            11
  BLACK OR AFRICAN AMERICAN                  1            21
  WHITE                                      2           224
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1920) Variable = NCF2 MUTATION ANALYSIS
D1920V1, survival
                sevent
clus2              0   1
  NCF2 MUTATED    10   0
  NCF2 WILD-TYPE 368  93
  NCF2 MUTATED NCF2 WILD-TYPE 
            10            461 
  NCF2 MUTATED NCF2 WILD-TYPE 
             0             93 
$`NCF2 MUTATED`
TCGA-AA-3660 TCGA-AA-3864 TCGA-AY-6197 TCGA-CA-6717 TCGA-CM-4743 TCGA-CM-5348 
       78.08        53.00        21.44        12.76        23.05        22.98 
TCGA-CM-6163 TCGA-G4-6588 TCGA-AG-4005 TCGA-F5-6813 
        2.96        26.17        14.04         0.69 

$`NCF2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 
       20.98        19.99        13.94        19.99        61.02         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 
       32.05         0.99        31.07        31.07        30.05        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       33.01        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
      124.27        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.03        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6164 TCGA-CM-6165 
       15.02        17.03        15.02        12.00        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       35.80        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       19.99        28.04        36.03         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66        55.76        26.43 

  NCF2 MUTATED NCF2 WILD-TYPE 
          0.69           0.00 
  NCF2 MUTATED NCF2 WILD-TYPE 
         78.08         148.01 
  NCF2 MUTATED NCF2 WILD-TYPE 
         22.21          20.12 
[1] "0.7 - 78.1 (22.2)"  "0.0 - 148.0 (20.1)"
[1] "hr="     "9200000"
D1920V2, continuous
D1920V3, binary
                cls
clus               0   1
  NCF2 MUTATED     8   2
  NCF2 WILD-TYPE 358 117
[1] "tbl2"
                cls
clus             [,1] [,2]
  NCF2 MUTATED      8    2
  NCF2 WILD-TYPE  358  117
        clus
vv       NCF2 MUTATED NCF2 WILD-TYPE
  COLON             8            358
  RECTUM            2            117
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NCF2 MUTATED         1        0        2         4         0         0
  NCF2 WILD-TYPE      90        1       30       134        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NCF2 MUTATED           0          0          1          1        1         0
  NCF2 WILD-TYPE        24         11         58         41       47        18
                vv
clus             STAGE IVB
  NCF2 MUTATED           0
  NCF2 WILD-TYPE         1
D1920V4, multiclass
            clus
vv           NCF2 MUTATED NCF2 WILD-TYPE
  STAGE I               1             90
  STAGE IA              0              1
  STAGE II              2             30
  STAGE IIA             4            134
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            1             58
  STAGE IIIC            1             41
  STAGE IV              1             47
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  NCF2 MUTATED     1   0   8   1
  NCF2 WILD-TYPE  16  92 321  49
D1920V5, multiclass
    clus
vv   NCF2 MUTATED NCF2 WILD-TYPE
  T1            1             16
  T2            0             92
  T3            8            321
  T4            1             49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  NCF2 MUTATED     7   1   2
  NCF2 WILD-TYPE 280 112  85
D1920V6, multiclass
    clus
vv   NCF2 MUTATED NCF2 WILD-TYPE
  N0            7            280
  N1            1            112
  N2            2             85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1920V7, binary
                cls
clus               0   1
  NCF2 MUTATED     8   1
  NCF2 WILD-TYPE 367  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  NCF2 MUTATED      8    1
  NCF2 WILD-TYPE  367   64
   clus
vv  NCF2 MUTATED NCF2 WILD-TYPE
  0            8            367
  1            1             64
[1] 2 2
[1] FALSE
D1920V8, binary
                cls
clus               0   1
  NCF2 MUTATED     2   8
  NCF2 WILD-TYPE 223 256
[1] "tbl2"
                cls
clus             [,1] [,2]
  NCF2 MUTATED      2    8
  NCF2 WILD-TYPE  223  256
        clus
vv       NCF2 MUTATED NCF2 WILD-TYPE
  FEMALE            2            223
  MALE              8            256
[1] 2 2
[1] FALSE
D1920V9, binary
                cls
clus               0   1
  NCF2 MUTATED     9   0
  NCF2 WILD-TYPE 341  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  NCF2 MUTATED      9    0
  NCF2 WILD-TYPE  341   22
     clus
vv    NCF2 MUTATED NCF2 WILD-TYPE
  NO             9            341
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  NCF2 MUTATED                      7                             1
  NCF2 WILD-TYPE                  308                            46
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  NCF2 MUTATED                       2                              0
  NCF2 WILD-TYPE                   104                             10
D1920V10, multiclass
                                clus
vv                               NCF2 MUTATED NCF2 WILD-TYPE
  COLON ADENOCARCINOMA                      7            308
  COLON MUCINOUS ADENOCARCINOMA             1             46
  RECTAL ADENOCARCINOMA                     2            104
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  NCF2 MUTATED     9   0   0   1
  NCF2 WILD-TYPE 336   4  31  24
D1920V11, multiclass
    clus
vv   NCF2 MUTATED NCF2 WILD-TYPE
  R0            9            336
  R1            0              4
  R2            0             31
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1920V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NCF2 MUTATED                                  0     1
  NCF2 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  NCF2 MUTATED                           0     6
  NCF2 WILD-TYPE                        22   220
D1920V13, multiclass
                                  clus
vv                                 NCF2 MUTATED NCF2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       6            220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1921) Variable = DCLRE1A MUTATION ANALYSIS
D1921V1, survival
                   sevent
clus2                 0   1
  DCLRE1A MUTATED     9   3
  DCLRE1A WILD-TYPE 369  90
  DCLRE1A MUTATED DCLRE1A WILD-TYPE 
               12               459 
  DCLRE1A MUTATED DCLRE1A WILD-TYPE 
                3                90 
$`DCLRE1A MUTATED`
TCGA-AA-3710 TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A01P TCGA-AD-6889 TCGA-AU-6004 
       26.99        25.02         4.01        38.07        56.55        27.09 
TCGA-AZ-6608 TCGA-CM-6676 TCGA-CM-6680 TCGA-AG-3726 TCGA-AG-3892 TCGA-AG-A002 
        1.61        11.08        12.03         7.99        13.02        20.98 

$`DCLRE1A WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
       19.00        36.00         5.03        85.05        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       31.00         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 
       40.96         0.07        21.37        15.52         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
       11.74         3.19        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       11.01        12.95        13.05        11.08        11.01        10.06 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3727 
        0.99        15.95        19.99        13.94        19.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 
        1.02        17.95        36.95        17.03        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  DCLRE1A MUTATED DCLRE1A WILD-TYPE 
             1.61              0.00 
  DCLRE1A MUTATED DCLRE1A WILD-TYPE 
            56.55            148.01 
  DCLRE1A MUTATED DCLRE1A WILD-TYPE 
            17.00             20.19 
[1] "1.6 - 56.5 (17.0)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.6"
D1921V2, continuous
D1921V3, binary
                   cls
clus                  0   1
  DCLRE1A MUTATED    10   3
  DCLRE1A WILD-TYPE 356 116
[1] "tbl2"
                   cls
clus                [,1] [,2]
  DCLRE1A MUTATED     10    3
  DCLRE1A WILD-TYPE  356  116
        clus
vv       DCLRE1A MUTATED DCLRE1A WILD-TYPE
  COLON               10               356
  RECTUM               3               116
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DCLRE1A MUTATED         5        0        1         2         1         0
  DCLRE1A WILD-TYPE      86        1       31       136         9         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DCLRE1A MUTATED           1          1          1          0        0
  DCLRE1A WILD-TYPE        23         10         58         42       48
                   vv
clus                STAGE IVA STAGE IVB
  DCLRE1A MUTATED           0         0
  DCLRE1A WILD-TYPE        18         1
D1921V4, multiclass
            clus
vv           DCLRE1A MUTATED DCLRE1A WILD-TYPE
  STAGE I                  5                86
  STAGE IA                 0                 1
  STAGE II                 1                31
  STAGE IIA                2               136
  STAGE IIB                1                 9
  STAGE IIC                0                 1
  STAGE III                1                23
  STAGE IIIA               1                10
  STAGE IIIB               1                58
  STAGE IIIC               0                42
  STAGE IV                 0                48
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  DCLRE1A MUTATED     1   6   4   2
  DCLRE1A WILD-TYPE  16  86 325  48
D1921V5, multiclass
    clus
vv   DCLRE1A MUTATED DCLRE1A WILD-TYPE
  T1               1                16
  T2               6                86
  T3               4               325
  T4               2                48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  DCLRE1A MUTATED    10   2   1
  DCLRE1A WILD-TYPE 277 111  86
D1921V6, multiclass
    clus
vv   DCLRE1A MUTATED DCLRE1A WILD-TYPE
  N0              10               277
  N1               2               111
  N2               1                86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1921V7, binary
                   cls
clus                  0   1
  DCLRE1A MUTATED    12   0
  DCLRE1A WILD-TYPE 363  65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  DCLRE1A MUTATED     12    0
  DCLRE1A WILD-TYPE  363   65
   clus
vv  DCLRE1A MUTATED DCLRE1A WILD-TYPE
  0              12               363
  1               0                65
[1] 2 2
[1] FALSE
D1921V8, binary
                   cls
clus                  0   1
  DCLRE1A MUTATED     8   5
  DCLRE1A WILD-TYPE 217 259
[1] "tbl2"
                   cls
clus                [,1] [,2]
  DCLRE1A MUTATED      8    5
  DCLRE1A WILD-TYPE  217  259
        clus
vv       DCLRE1A MUTATED DCLRE1A WILD-TYPE
  FEMALE               8               217
  MALE                 5               259
[1] 2 2
[1] FALSE
D1921V9, binary
                   cls
clus                  0   1
  DCLRE1A MUTATED     9   0
  DCLRE1A WILD-TYPE 341  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  DCLRE1A MUTATED      9    0
  DCLRE1A WILD-TYPE  341   22
     clus
vv    DCLRE1A MUTATED DCLRE1A WILD-TYPE
  NO                9               341
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  DCLRE1A MUTATED                      9                             1
  DCLRE1A WILD-TYPE                  306                            46
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  DCLRE1A MUTATED                       3                              0
  DCLRE1A WILD-TYPE                   103                             10
D1921V10, multiclass
                                clus
vv                               DCLRE1A MUTATED DCLRE1A WILD-TYPE
  COLON ADENOCARCINOMA                         9               306
  COLON MUCINOUS ADENOCARCINOMA                1                46
  RECTAL ADENOCARCINOMA                        3               103
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  DCLRE1A MUTATED    10   0   0   0
  DCLRE1A WILD-TYPE 335   4  31  25
D1921V11, multiclass
    clus
vv   DCLRE1A MUTATED DCLRE1A WILD-TYPE
  R0              10               335
  R1               0                 4
  R2               0                31
  RX               0                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1921V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DCLRE1A MUTATED                                  0     1
  DCLRE1A WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  DCLRE1A MUTATED                           0     4
  DCLRE1A WILD-TYPE                        22   222
D1921V13, multiclass
                                  clus
vv                                 DCLRE1A MUTATED DCLRE1A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                10
  BLACK OR AFRICAN AMERICAN                      0                22
  WHITE                                          4               222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1922) Variable = ORC4L MUTATION ANALYSIS
D1922V1, survival
                 sevent
clus2               0   1
  ORC4L MUTATED     5   2
  ORC4L WILD-TYPE 373  91
  ORC4L MUTATED ORC4L WILD-TYPE 
              7             464 
  ORC4L MUTATED ORC4L WILD-TYPE 
              2              91 
$`ORC4L MUTATED`
TCGA-AA-A00J TCGA-AA-A00N TCGA-AA-A010 TCGA-AZ-6606 TCGA-CK-6751 TCGA-G4-6628 
       18.05         4.01        34.98        11.74       124.27        79.69 
TCGA-CI-6619 
        6.05 

$`ORC4L WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
      100.01        29.56         5.23         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
       17.49         0.69         0.72        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  ORC4L MUTATED ORC4L WILD-TYPE 
           4.01            0.00 
  ORC4L MUTATED ORC4L WILD-TYPE 
         124.27          148.01 
  ORC4L MUTATED ORC4L WILD-TYPE 
         18.050          20.235 
[1] "4.0 - 124.3 (18.1)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.1"
D1922V2, continuous
D1922V3, binary
                 cls
clus                0   1
  ORC4L MUTATED     6   1
  ORC4L WILD-TYPE 360 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ORC4L MUTATED      6    1
  ORC4L WILD-TYPE  360  118
        clus
vv       ORC4L MUTATED ORC4L WILD-TYPE
  COLON              6             360
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ORC4L MUTATED         2        0        0         0         2         0
  ORC4L WILD-TYPE      89        1       32       138         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ORC4L MUTATED           0          0          1          0        2         0
  ORC4L WILD-TYPE        24         11         58         42       46        18
                 vv
clus              STAGE IVB
  ORC4L MUTATED           0
  ORC4L WILD-TYPE         1
D1922V4, multiclass
            clus
vv           ORC4L MUTATED ORC4L WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              0             138
  STAGE IIB              2               8
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             0              42
  STAGE IV               2              46
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ORC4L MUTATED     0   2   1   4
  ORC4L WILD-TYPE  17  90 328  46
D1922V5, multiclass
    clus
vv   ORC4L MUTATED ORC4L WILD-TYPE
  T1             0              17
  T2             2              90
  T3             1             328
  T4             4              46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  ORC4L MUTATED     4   2   1
  ORC4L WILD-TYPE 283 111  86
D1922V6, multiclass
    clus
vv   ORC4L MUTATED ORC4L WILD-TYPE
  N0             4             283
  N1             2             111
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1922V7, binary
                 cls
clus                0   1
  ORC4L MUTATED     4   2
  ORC4L WILD-TYPE 371  63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ORC4L MUTATED      4    2
  ORC4L WILD-TYPE  371   63
   clus
vv  ORC4L MUTATED ORC4L WILD-TYPE
  0             4             371
  1             2              63
[1] 2 2
[1] FALSE
D1922V8, binary
                 cls
clus                0   1
  ORC4L MUTATED     2   5
  ORC4L WILD-TYPE 223 259
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ORC4L MUTATED      2    5
  ORC4L WILD-TYPE  223  259
        clus
vv       ORC4L MUTATED ORC4L WILD-TYPE
  FEMALE             2             223
  MALE               5             259
[1] 2 2
[1] FALSE
D1922V9, binary
                 cls
clus                0   1
  ORC4L MUTATED     5   0
  ORC4L WILD-TYPE 345  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ORC4L MUTATED      5    0
  ORC4L WILD-TYPE  345   22
     clus
vv    ORC4L MUTATED ORC4L WILD-TYPE
  NO              5             345
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ORC4L MUTATED                      3                             3
  ORC4L WILD-TYPE                  312                            44
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ORC4L MUTATED                       1                              0
  ORC4L WILD-TYPE                   105                             10
D1922V10, multiclass
                                clus
vv                               ORC4L MUTATED ORC4L WILD-TYPE
  COLON ADENOCARCINOMA                       3             312
  COLON MUCINOUS ADENOCARCINOMA              3              44
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  ORC4L MUTATED     4   0   0   1
  ORC4L WILD-TYPE 341   4  31  24
D1922V11, multiclass
    clus
vv   ORC4L MUTATED ORC4L WILD-TYPE
  R0             4             341
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1922V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ORC4L MUTATED                                  0     0
  ORC4L WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ORC4L MUTATED                           0     4
  ORC4L WILD-TYPE                        22   222
D1922V13, multiclass
                                  clus
vv                                 ORC4L MUTATED ORC4L WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        4             222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1923) Variable = LRRN1 MUTATION ANALYSIS
D1923V1, survival
                 sevent
clus2               0   1
  LRRN1 MUTATED    12   6
  LRRN1 WILD-TYPE 366  87
  LRRN1 MUTATED LRRN1 WILD-TYPE 
             18             453 
  LRRN1 MUTATED LRRN1 WILD-TYPE 
              6              87 
$`LRRN1 MUTATED`
TCGA-A6-6141 TCGA-A6-6653 TCGA-AA-3516 TCGA-AA-3526 TCGA-AA-3713 TCGA-AA-3715 
        8.38        24.39        13.02        19.07        19.04        19.04 
TCGA-AA-A01Q TCGA-AD-5900 TCGA-AZ-6601 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4952 
        1.02         0.07       100.01        12.76        10.06        15.62 
TCGA-CK-5913 TCGA-CK-5916 TCGA-CM-5861 TCGA-F4-6570 TCGA-AG-3892 TCGA-AG-A002 
       51.32        21.14        15.02         6.18        13.02        20.98 

$`LRRN1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 
       22.09        22.06        32.71        27.09        22.52        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 
       25.18        24.16        21.76        24.69        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
       63.98         6.97         1.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3529 TCGA-AA-3530 
       24.03        37.05        36.03         8.05         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       26.99        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01R 
       32.02        12.00        31.00        31.00        38.07        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 
       41.00        39.98        18.05        40.96        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
       12.10        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5914 
       14.30        17.56       148.01        85.45        49.08         9.99 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       32.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 
      117.07        98.24         8.61        31.96        35.74        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 
        1.02        17.95        36.95        17.03        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  LRRN1 MUTATED LRRN1 WILD-TYPE 
           0.07            0.00 
  LRRN1 MUTATED LRRN1 WILD-TYPE 
         100.01          148.01 
  LRRN1 MUTATED LRRN1 WILD-TYPE 
          15.32           20.98 
[1] "0.1 - 100.0 (15.3)" "0.0 - 148.0 (21.0)"
[1] "hr=" "2.1"
D1923V2, continuous
D1923V3, binary
                 cls
clus                0   1
  LRRN1 MUTATED    17   2
  LRRN1 WILD-TYPE 349 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LRRN1 MUTATED     17    2
  LRRN1 WILD-TYPE  349  117
        clus
vv       LRRN1 MUTATED LRRN1 WILD-TYPE
  COLON             17             349
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  LRRN1 MUTATED         6        0        3         6         1         0
  LRRN1 WILD-TYPE      85        1       29       132         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  LRRN1 MUTATED           1          0          0          1        1         0
  LRRN1 WILD-TYPE        23         11         59         41       47        18
                 vv
clus              STAGE IVB
  LRRN1 MUTATED           0
  LRRN1 WILD-TYPE         1
D1923V4, multiclass
            clus
vv           LRRN1 MUTATED LRRN1 WILD-TYPE
  STAGE I                6              85
  STAGE IA               0               1
  STAGE II               3              29
  STAGE IIA              6             132
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             1              41
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  LRRN1 MUTATED     2   4  11   2
  LRRN1 WILD-TYPE  15  88 318  48
D1923V5, multiclass
    clus
vv   LRRN1 MUTATED LRRN1 WILD-TYPE
  T1             2              15
  T2             4              88
  T3            11             318
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  LRRN1 MUTATED    17   0   2
  LRRN1 WILD-TYPE 270 113  85
D1923V6, multiclass
    clus
vv   LRRN1 MUTATED LRRN1 WILD-TYPE
  N0            17             270
  N1             0             113
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1923V7, binary
                 cls
clus                0   1
  LRRN1 MUTATED    15   1
  LRRN1 WILD-TYPE 360  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LRRN1 MUTATED     15    1
  LRRN1 WILD-TYPE  360   64
   clus
vv  LRRN1 MUTATED LRRN1 WILD-TYPE
  0            15             360
  1             1              64
[1] 2 2
[1] FALSE
D1923V8, binary
                 cls
clus                0   1
  LRRN1 MUTATED     9  10
  LRRN1 WILD-TYPE 216 254
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LRRN1 MUTATED      9   10
  LRRN1 WILD-TYPE  216  254
        clus
vv       LRRN1 MUTATED LRRN1 WILD-TYPE
  FEMALE             9             216
  MALE              10             254
[1] 2 2
[1] FALSE
D1923V9, binary
                 cls
clus                0   1
  LRRN1 MUTATED    14   1
  LRRN1 WILD-TYPE 336  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LRRN1 MUTATED     14    1
  LRRN1 WILD-TYPE  336   21
     clus
vv    LRRN1 MUTATED LRRN1 WILD-TYPE
  NO             14             336
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  LRRN1 MUTATED                     13                             4
  LRRN1 WILD-TYPE                  302                            43
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  LRRN1 MUTATED                       2                              0
  LRRN1 WILD-TYPE                   104                             10
D1923V10, multiclass
                                clus
vv                               LRRN1 MUTATED LRRN1 WILD-TYPE
  COLON ADENOCARCINOMA                      13             302
  COLON MUCINOUS ADENOCARCINOMA              4              43
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  LRRN1 MUTATED     8   0   1   6
  LRRN1 WILD-TYPE 337   4  30  19
D1923V11, multiclass
    clus
vv   LRRN1 MUTATED LRRN1 WILD-TYPE
  R0             8             337
  R1             0               4
  R2             1              30
  RX             6              19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1923V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  LRRN1 MUTATED                                  0     2
  LRRN1 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  LRRN1 MUTATED                           1     9
  LRRN1 WILD-TYPE                        21   217
D1923V13, multiclass
                                  clus
vv                                 LRRN1 MUTATED LRRN1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               9
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        9             217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1924) Variable = KIAA1267 MUTATION ANALYSIS
D1924V1, survival
                    sevent
clus2                  0   1
  KIAA1267 MUTATED    13   6
  KIAA1267 WILD-TYPE 365  87
  KIAA1267 MUTATED KIAA1267 WILD-TYPE 
                19                452 
  KIAA1267 MUTATED KIAA1267 WILD-TYPE 
                 6                 87 
$`KIAA1267 MUTATED`
TCGA-A6-2676 TCGA-A6-5665 TCGA-A6-6781 TCGA-AA-3492 TCGA-AA-3715 TCGA-AA-3855 
       42.90        22.06        19.66         3.02        19.04        32.05 
TCGA-AA-3949 TCGA-AA-3966 TCGA-AA-A01R TCGA-AZ-5403 TCGA-AZ-6598 TCGA-CA-6717 
       26.01         2.01        35.01        62.79        49.41        12.76 
TCGA-CA-6718 TCGA-CM-6162 TCGA-CM-6171 TCGA-F4-6856 TCGA-G4-6309 TCGA-AG-A002 
       10.06        12.00        14.04        35.31        85.48        20.98 
TCGA-AG-A011 
       37.02 

$`KIAA1267 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
       20.28         7.04         1.02        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       26.99        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
        0.00        36.03         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3950 
       31.00         2.01        12.99        24.00        33.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
        2.01        20.98        34.03        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T 
       31.00        31.00        38.07         1.02         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       22.36        88.21         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 
        3.25         3.29         0.07        12.20        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       17.03        15.02         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 
       14.99        12.99        13.02        15.02        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
       13.25         0.53        47.41       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       53.62        44.68        55.04        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       23.01        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  KIAA1267 MUTATED KIAA1267 WILD-TYPE 
              2.01               0.00 
  KIAA1267 MUTATED KIAA1267 WILD-TYPE 
             85.48             148.01 
  KIAA1267 MUTATED KIAA1267 WILD-TYPE 
            22.060             20.085 
[1] "2.0 - 85.5 (22.1)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.5"
D1924V2, continuous
D1924V3, binary
                    cls
clus                   0   1
  KIAA1267 MUTATED    17   2
  KIAA1267 WILD-TYPE 349 117
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1267 MUTATED     17    2
  KIAA1267 WILD-TYPE  349  117
        clus
vv       KIAA1267 MUTATED KIAA1267 WILD-TYPE
  COLON                17                349
  RECTUM                2                117
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KIAA1267 MUTATED         4        0        4         5         1         0
  KIAA1267 WILD-TYPE      87        1       28       133         9         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIAA1267 MUTATED           1          0          3          1        0
  KIAA1267 WILD-TYPE        23         11         56         41       48
                    vv
clus                 STAGE IVA STAGE IVB
  KIAA1267 MUTATED           0         0
  KIAA1267 WILD-TYPE        18         1
D1924V4, multiclass
            clus
vv           KIAA1267 MUTATED KIAA1267 WILD-TYPE
  STAGE I                   4                 87
  STAGE IA                  0                  1
  STAGE II                  4                 28
  STAGE IIA                 5                133
  STAGE IIB                 1                  9
  STAGE IIC                 0                  1
  STAGE III                 1                 23
  STAGE IIIA                0                 11
  STAGE IIIB                3                 56
  STAGE IIIC                1                 41
  STAGE IV                  0                 48
  STAGE IVA                 0                 18
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  KIAA1267 MUTATED     0   4  13   2
  KIAA1267 WILD-TYPE  17  88 316  48
D1924V5, multiclass
    clus
vv   KIAA1267 MUTATED KIAA1267 WILD-TYPE
  T1                0                 17
  T2                4                 88
  T3               13                316
  T4                2                 48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  KIAA1267 MUTATED    14   4   1
  KIAA1267 WILD-TYPE 273 109  86
D1924V6, multiclass
    clus
vv   KIAA1267 MUTATED KIAA1267 WILD-TYPE
  N0               14                273
  N1                4                109
  N2                1                 86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1924V7, binary
                    cls
clus                   0   1
  KIAA1267 MUTATED    16   0
  KIAA1267 WILD-TYPE 359  65
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1267 MUTATED     16    0
  KIAA1267 WILD-TYPE  359   65
   clus
vv  KIAA1267 MUTATED KIAA1267 WILD-TYPE
  0               16                359
  1                0                 65
[1] 2 2
[1] FALSE
D1924V8, binary
                    cls
clus                   0   1
  KIAA1267 MUTATED     9  10
  KIAA1267 WILD-TYPE 216 254
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1267 MUTATED      9   10
  KIAA1267 WILD-TYPE  216  254
        clus
vv       KIAA1267 MUTATED KIAA1267 WILD-TYPE
  FEMALE                9                216
  MALE                 10                254
[1] 2 2
[1] FALSE
D1924V9, binary
                    cls
clus                   0   1
  KIAA1267 MUTATED    17   1
  KIAA1267 WILD-TYPE 333  21
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1267 MUTATED     17    1
  KIAA1267 WILD-TYPE  333   21
     clus
vv    KIAA1267 MUTATED KIAA1267 WILD-TYPE
  NO                17                333
  YES                1                 21
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  KIAA1267 MUTATED                     10                             7
  KIAA1267 WILD-TYPE                  305                            40
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  KIAA1267 MUTATED                       2                              0
  KIAA1267 WILD-TYPE                   104                             10
D1924V10, multiclass
                                clus
vv                               KIAA1267 MUTATED KIAA1267 WILD-TYPE
  COLON ADENOCARCINOMA                         10                305
  COLON MUCINOUS ADENOCARCINOMA                 7                 40
  RECTAL ADENOCARCINOMA                         2                104
  RECTAL MUCINOUS ADENOCARCINOMA                0                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  KIAA1267 MUTATED    14   0   0   2
  KIAA1267 WILD-TYPE 331   4  31  23
D1924V11, multiclass
    clus
vv   KIAA1267 MUTATED KIAA1267 WILD-TYPE
  R0               14                331
  R1                0                  4
  R2                0                 31
  RX                2                 23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1924V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KIAA1267 MUTATED                                  0     2
  KIAA1267 WILD-TYPE                                1     9
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  KIAA1267 MUTATED                           1     8
  KIAA1267 WILD-TYPE                        21   218
D1924V13, multiclass
                                  clus
vv                                 KIAA1267 MUTATED KIAA1267 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           2                  9
  BLACK OR AFRICAN AMERICAN                       1                 21
  WHITE                                           8                218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1925) Variable = RPS6KA6 MUTATION ANALYSIS
D1925V1, survival
                   sevent
clus2                 0   1
  RPS6KA6 MUTATED    13   3
  RPS6KA6 WILD-TYPE 365  90
  RPS6KA6 MUTATED RPS6KA6 WILD-TYPE 
               16               455 
  RPS6KA6 MUTATED RPS6KA6 WILD-TYPE 
                3                90 
$`RPS6KA6 MUTATED`
TCGA-A6-2671 TCGA-AA-3562 TCGA-AA-3697 TCGA-AA-3833 TCGA-AA-3966 TCGA-AA-A010 
       43.76        19.99        85.05        15.95         2.01        34.98 
TCGA-AD-6889 TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-6601 TCGA-CM-5861 TCGA-D5-6536 
       56.55        21.44        58.39       100.01        15.02        17.85 
TCGA-DM-A28H TCGA-F4-6570 TCGA-AG-3892 TCGA-F5-6811 
      117.07         6.18        13.02        32.19 

$`RPS6KA6 WILD-TYPE`
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       46.65        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       19.99        13.94        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3837 
       33.04         0.99        25.02         1.02        17.98        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       21.37        15.52         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
        0.95        33.01        17.82         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 
       29.06        22.03        22.98        30.08        32.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       43.27        15.12         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
      119.93        35.97        60.79        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       35.74        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57         0.66         0.69        55.76        26.43 

  RPS6KA6 MUTATED RPS6KA6 WILD-TYPE 
             2.01              0.00 
  RPS6KA6 MUTATED RPS6KA6 WILD-TYPE 
           117.07            148.01 
  RPS6KA6 MUTATED RPS6KA6 WILD-TYPE 
           26.815            20.120 
[1] "2.0 - 117.1 (26.8)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.6"
D1925V2, continuous
D1925V3, binary
                   cls
clus                  0   1
  RPS6KA6 MUTATED    15   3
  RPS6KA6 WILD-TYPE 351 116
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RPS6KA6 MUTATED     15    3
  RPS6KA6 WILD-TYPE  351  116
        clus
vv       RPS6KA6 MUTATED RPS6KA6 WILD-TYPE
  COLON               15               351
  RECTUM               3               116
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RPS6KA6 MUTATED         1        0        2        10         1         0
  RPS6KA6 WILD-TYPE      90        1       30       128         9         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RPS6KA6 MUTATED           1          0          0          2        1
  RPS6KA6 WILD-TYPE        23         11         59         40       47
                   vv
clus                STAGE IVA STAGE IVB
  RPS6KA6 MUTATED           0         0
  RPS6KA6 WILD-TYPE        18         1
D1925V4, multiclass
            clus
vv           RPS6KA6 MUTATED RPS6KA6 WILD-TYPE
  STAGE I                  1                90
  STAGE IA                 0                 1
  STAGE II                 2                30
  STAGE IIA               10               128
  STAGE IIB                1                 9
  STAGE IIC                0                 1
  STAGE III                1                23
  STAGE IIIA               0                11
  STAGE IIIB               0                59
  STAGE IIIC               2                40
  STAGE IV                 1                47
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  RPS6KA6 MUTATED     1   0  15   2
  RPS6KA6 WILD-TYPE  16  92 314  48
D1925V5, multiclass
    clus
vv   RPS6KA6 MUTATED RPS6KA6 WILD-TYPE
  T1               1                16
  T2               0                92
  T3              15               314
  T4               2                48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  RPS6KA6 MUTATED    15   0   3
  RPS6KA6 WILD-TYPE 272 113  84
D1925V6, multiclass
    clus
vv   RPS6KA6 MUTATED RPS6KA6 WILD-TYPE
  N0              15               272
  N1               0               113
  N2               3                84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1925V7, binary
                   cls
clus                  0   1
  RPS6KA6 MUTATED    16   1
  RPS6KA6 WILD-TYPE 359  64
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RPS6KA6 MUTATED     16    1
  RPS6KA6 WILD-TYPE  359   64
   clus
vv  RPS6KA6 MUTATED RPS6KA6 WILD-TYPE
  0              16               359
  1               1                64
[1] 2 2
[1] FALSE
D1925V8, binary
                   cls
clus                  0   1
  RPS6KA6 MUTATED     9   9
  RPS6KA6 WILD-TYPE 216 255
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RPS6KA6 MUTATED      9    9
  RPS6KA6 WILD-TYPE  216  255
        clus
vv       RPS6KA6 MUTATED RPS6KA6 WILD-TYPE
  FEMALE               9               216
  MALE                 9               255
[1] 2 2
[1] FALSE
D1925V9, binary
                   cls
clus                  0   1
  RPS6KA6 MUTATED    13   0
  RPS6KA6 WILD-TYPE 337  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RPS6KA6 MUTATED     13    0
  RPS6KA6 WILD-TYPE  337   22
     clus
vv    RPS6KA6 MUTATED RPS6KA6 WILD-TYPE
  NO               13               337
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  RPS6KA6 MUTATED                     14                             1
  RPS6KA6 WILD-TYPE                  301                            46
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  RPS6KA6 MUTATED                       3                              0
  RPS6KA6 WILD-TYPE                   103                             10
D1925V10, multiclass
                                clus
vv                               RPS6KA6 MUTATED RPS6KA6 WILD-TYPE
  COLON ADENOCARCINOMA                        14               301
  COLON MUCINOUS ADENOCARCINOMA                1                46
  RECTAL ADENOCARCINOMA                        3               103
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  RPS6KA6 MUTATED    13   0   0   0
  RPS6KA6 WILD-TYPE 332   4  31  25
D1925V11, multiclass
    clus
vv   RPS6KA6 MUTATED RPS6KA6 WILD-TYPE
  R0              13               332
  R1               0                 4
  R2               0                31
  RX               0                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1925V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RPS6KA6 MUTATED                                  0     1
  RPS6KA6 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  RPS6KA6 MUTATED                           0     9
  RPS6KA6 WILD-TYPE                        22   217
D1925V13, multiclass
                                  clus
vv                                 RPS6KA6 MUTATED RPS6KA6 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                10
  BLACK OR AFRICAN AMERICAN                      0                22
  WHITE                                          9               217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1926) Variable = GPRIN3 MUTATION ANALYSIS
D1926V1, survival
                  sevent
clus2                0   1
  GPRIN3 MUTATED     8   2
  GPRIN3 WILD-TYPE 370  91
  GPRIN3 MUTATED GPRIN3 WILD-TYPE 
              10              461 
  GPRIN3 MUTATED GPRIN3 WILD-TYPE 
               2               91 
$`GPRIN3 MUTATED`
TCGA-AA-3672 TCGA-AA-3710 TCGA-AA-3939 TCGA-AA-A00N TCGA-CM-5349 TCGA-D5-6540 
        0.92        26.99        12.99         4.01        30.08        16.14 
TCGA-D5-6928 TCGA-G4-6626 TCGA-AG-3731 TCGA-CI-6622 
       11.64        46.75        37.02         6.97 

$`GPRIN3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
        6.05         6.97        54.02         2.01        14.01        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        85.05        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       29.06        22.03        22.98        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.04         9.44         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       35.80        26.17        91.79        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        7.99         0.99        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
        6.05        33.17         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  GPRIN3 MUTATED GPRIN3 WILD-TYPE 
            0.92             0.00 
  GPRIN3 MUTATED GPRIN3 WILD-TYPE 
           46.75           148.01 
  GPRIN3 MUTATED GPRIN3 WILD-TYPE 
          14.565           20.280 
[1] "0.9 - 46.8 (14.6)"  "0.0 - 148.0 (20.3)"
[1] "hr=" "1.4"
D1926V2, continuous
D1926V3, binary
                  cls
clus                 0   1
  GPRIN3 MUTATED     8   2
  GPRIN3 WILD-TYPE 358 117
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPRIN3 MUTATED      8    2
  GPRIN3 WILD-TYPE  358  117
        clus
vv       GPRIN3 MUTATED GPRIN3 WILD-TYPE
  COLON               8              358
  RECTUM              2              117
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GPRIN3 MUTATED         1        0        0         5         2         0
  GPRIN3 WILD-TYPE      90        1       32       133         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GPRIN3 MUTATED           1          0          0          0        1
  GPRIN3 WILD-TYPE        23         11         59         42       47
                  vv
clus               STAGE IVA STAGE IVB
  GPRIN3 MUTATED           0         0
  GPRIN3 WILD-TYPE        18         1
D1926V4, multiclass
            clus
vv           GPRIN3 MUTATED GPRIN3 WILD-TYPE
  STAGE I                 1               90
  STAGE IA                0                1
  STAGE II                0               32
  STAGE IIA               5              133
  STAGE IIB               2                8
  STAGE IIC               0                1
  STAGE III               1               23
  STAGE IIIA              0               11
  STAGE IIIB              0               59
  STAGE IIIC              0               42
  STAGE IV                1               47
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  GPRIN3 MUTATED     0   1   7   2
  GPRIN3 WILD-TYPE  17  91 322  48
D1926V5, multiclass
    clus
vv   GPRIN3 MUTATED GPRIN3 WILD-TYPE
  T1              0               17
  T2              1               91
  T3              7              322
  T4              2               48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  GPRIN3 MUTATED     8   2   0
  GPRIN3 WILD-TYPE 279 111  87
D1926V6, multiclass
    clus
vv   GPRIN3 MUTATED GPRIN3 WILD-TYPE
  N0              8              279
  N1              2              111
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1926V7, binary
                  cls
clus                 0   1
  GPRIN3 MUTATED     9   1
  GPRIN3 WILD-TYPE 366  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPRIN3 MUTATED      9    1
  GPRIN3 WILD-TYPE  366   64
   clus
vv  GPRIN3 MUTATED GPRIN3 WILD-TYPE
  0              9              366
  1              1               64
[1] 2 2
[1] FALSE
D1926V8, binary
                  cls
clus                 0   1
  GPRIN3 MUTATED     3   7
  GPRIN3 WILD-TYPE 222 257
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPRIN3 MUTATED      3    7
  GPRIN3 WILD-TYPE  222  257
        clus
vv       GPRIN3 MUTATED GPRIN3 WILD-TYPE
  FEMALE              3              222
  MALE                7              257
[1] 2 2
[1] FALSE
D1926V9, binary
                  cls
clus                 0   1
  GPRIN3 MUTATED     8   0
  GPRIN3 WILD-TYPE 342  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPRIN3 MUTATED      8    0
  GPRIN3 WILD-TYPE  342   22
     clus
vv    GPRIN3 MUTATED GPRIN3 WILD-TYPE
  NO               8              342
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  GPRIN3 MUTATED                      5                             3
  GPRIN3 WILD-TYPE                  310                            44
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  GPRIN3 MUTATED                       2                              0
  GPRIN3 WILD-TYPE                   104                             10
D1926V10, multiclass
                                clus
vv                               GPRIN3 MUTATED GPRIN3 WILD-TYPE
  COLON ADENOCARCINOMA                        5              310
  COLON MUCINOUS ADENOCARCINOMA               3               44
  RECTAL ADENOCARCINOMA                       2              104
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  GPRIN3 MUTATED     8   0   1   0
  GPRIN3 WILD-TYPE 337   4  30  25
D1926V11, multiclass
    clus
vv   GPRIN3 MUTATED GPRIN3 WILD-TYPE
  R0              8              337
  R1              0                4
  R2              1               30
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1926V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GPRIN3 MUTATED                                  0     0
  GPRIN3 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  GPRIN3 MUTATED                           0     5
  GPRIN3 WILD-TYPE                        22   221
D1926V13, multiclass
                                  clus
vv                                 GPRIN3 MUTATED GPRIN3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         5              221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1927) Variable = DHDDS MUTATION ANALYSIS
D1927V1, survival
                 sevent
clus2               0   1
  DHDDS MUTATED     4   1
  DHDDS WILD-TYPE 374  92
  DHDDS MUTATED DHDDS WILD-TYPE 
              5             466 
  DHDDS MUTATED DHDDS WILD-TYPE 
              1              92 
$`DHDDS MUTATED`
TCGA-AA-3492 TCGA-AA-3655 TCGA-AA-3663 TCGA-DM-A282 TCGA-AG-3892 
        3.02        61.02         6.97       139.17        13.02 

$`DHDDS WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       19.99        13.94        19.99        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 
        1.02        17.95        36.95        17.03        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  DHDDS MUTATED DHDDS WILD-TYPE 
           3.02            0.00 
  DHDDS MUTATED DHDDS WILD-TYPE 
         139.17          148.01 
  DHDDS MUTATED DHDDS WILD-TYPE 
         13.020          20.235 
[1] "3.0 - 139.2 (13.0)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.5"
D1927V2, continuous
D1927V3, binary
                 cls
clus                0   1
  DHDDS MUTATED     4   2
  DHDDS WILD-TYPE 362 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DHDDS MUTATED      4    2
  DHDDS WILD-TYPE  362  117
        clus
vv       DHDDS MUTATED DHDDS WILD-TYPE
  COLON              4             362
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DHDDS MUTATED         1        0        3         1         0         0
  DHDDS WILD-TYPE      90        1       29       137        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DHDDS MUTATED           1          0          0          0        0         0
  DHDDS WILD-TYPE        23         11         59         42       48        18
                 vv
clus              STAGE IVB
  DHDDS MUTATED           0
  DHDDS WILD-TYPE         1
D1927V4, multiclass
            clus
vv           DHDDS MUTATED DHDDS WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               3              29
  STAGE IIA              1             137
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  DHDDS MUTATED     1   0   5   0
  DHDDS WILD-TYPE  16  92 324  50
D1927V5, multiclass
    clus
vv   DHDDS MUTATED DHDDS WILD-TYPE
  T1             1              16
  T2             0              92
  T3             5             324
  T4             0              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  DHDDS MUTATED     5   1   0
  DHDDS WILD-TYPE 282 112  87
D1927V6, multiclass
    clus
vv   DHDDS MUTATED DHDDS WILD-TYPE
  N0             5             282
  N1             1             112
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1927V7, binary
                 cls
clus                0   1
  DHDDS MUTATED     5   0
  DHDDS WILD-TYPE 370  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DHDDS MUTATED      5    0
  DHDDS WILD-TYPE  370   65
   clus
vv  DHDDS MUTATED DHDDS WILD-TYPE
  0             5             370
  1             0              65
[1] 2 2
[1] FALSE
D1927V8, binary
                 cls
clus                0   1
  DHDDS MUTATED     3   3
  DHDDS WILD-TYPE 222 261
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DHDDS MUTATED      3    3
  DHDDS WILD-TYPE  222  261
        clus
vv       DHDDS MUTATED DHDDS WILD-TYPE
  FEMALE             3             222
  MALE               3             261
[1] 2 2
[1] FALSE
D1927V9, binary
                 cls
clus                0   1
  DHDDS MUTATED     4   0
  DHDDS WILD-TYPE 346  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DHDDS MUTATED      4    0
  DHDDS WILD-TYPE  346   22
     clus
vv    DHDDS MUTATED DHDDS WILD-TYPE
  NO              4             346
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  DHDDS MUTATED                      4                             0
  DHDDS WILD-TYPE                  311                            47
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  DHDDS MUTATED                       2                              0
  DHDDS WILD-TYPE                   104                             10
D1927V10, multiclass
                                clus
vv                               DHDDS MUTATED DHDDS WILD-TYPE
  COLON ADENOCARCINOMA                       4             311
  COLON MUCINOUS ADENOCARCINOMA              0              47
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  DHDDS MUTATED     4   0   0   0
  DHDDS WILD-TYPE 341   4  31  25
D1927V11, multiclass
    clus
vv   DHDDS MUTATED DHDDS WILD-TYPE
  R0             4             341
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1927V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DHDDS MUTATED                                  0     0
  DHDDS WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  DHDDS MUTATED                           0     2
  DHDDS WILD-TYPE                        22   224
D1927V13, multiclass
[1] "Remove cluster labels:" "DHDDS MUTATED"         
clus
  DHDDS MUTATED DHDDS WILD-TYPE 
              2             258 
     TCGA-A6-2671      TCGA-A6-2672      TCGA-A6-2674      TCGA-A6-2676 
"DHDDS WILD-TYPE" "DHDDS WILD-TYPE" "DHDDS WILD-TYPE" "DHDDS WILD-TYPE" 
     TCGA-A6-2677      TCGA-A6-2678      TCGA-A6-2683      TCGA-A6-3807 
"DHDDS WILD-TYPE" "DHDDS WILD-TYPE" "DHDDS WILD-TYPE" "DHDDS WILD-TYPE" 
     TCGA-A6-3808      TCGA-A6-3809      TCGA-A6-3810      TCGA-A6-4105 
"DHDDS WILD-TYPE" "DHDDS WILD-TYPE" "DHDDS WILD-TYPE" "DHDDS WILD-TYPE" 
     TCGA-A6-5656      TCGA-A6-5657      TCGA-A6-5659      TCGA-A6-5660 
"DHDDS WILD-TYPE" "DHDDS WILD-TYPE" "DHDDS WILD-TYPE" "DHDDS WILD-TYPE" 
     TCGA-A6-5661      TCGA-A6-5662      TCGA-A6-5664      TCGA-A6-5665 
"DHDDS WILD-TYPE" "DHDDS WILD-TYPE" "DHDDS WILD-TYPE" "DHDDS WILD-TYPE" 
     TCGA-A6-5666      TCGA-A6-6137      TCGA-A6-6138      TCGA-A6-6141 
"DHDDS WILD-TYPE" "DHDDS WILD-TYPE" "DHDDS WILD-TYPE" "DHDDS WILD-TYPE" 
     TCGA-A6-6142      TCGA-A6-6648      TCGA-A6-6649      TCGA-A6-6651 
"DHDDS WILD-TYPE" "DHDDS WILD-TYPE" "DHDDS WILD-TYPE" "DHDDS WILD-TYPE" 
     TCGA-A6-6652      TCGA-A6-6653      TCGA-A6-6654      TCGA-A6-6780 
"DHDDS WILD-TYPE" "DHDDS WILD-TYPE" "DHDDS WILD-TYPE" "DHDDS WILD-TYPE" 
     TCGA-A6-6781      TCGA-A6-6782      TCGA-AD-5900      TCGA-AD-6548 
"DHDDS WILD-TYPE" "DHDDS WILD-TYPE" "DHDDS WILD-TYPE" "DHDDS WILD-TYPE" 
     TCGA-AD-6888      TCGA-AD-6889      TCGA-AD-6890      TCGA-AD-6895 
"DHDDS WILD-TYPE" "DHDDS WILD-TYPE" "DHDDS WILD-TYPE" "DHDDS WILD-TYPE" 
     TCGA-AD-6899      TCGA-AD-6901      TCGA-AD-6963      TCGA-AD-6964 
"DHDDS WILD-TYPE" "DHDDS WILD-TYPE" "DHDDS WILD-TYPE" "DHDDS WILD-TYPE" 
     TCGA-AD-6965      TCGA-AU-3779      TCGA-AU-6004      TCGA-AY-4070 
"DHDDS WILD-TYPE" "DHDDS WILD-TYPE" "DHDDS WILD-TYPE" "DHDDS WILD-TYPE" 
     TCGA-AY-4071      TCGA-AY-5543      TCGA-AY-6196      TCGA-AY-6197 
"DHDDS WILD-TYPE" "DHDDS WILD-TYPE" "DHDDS WILD-TYPE" "DHDDS WILD-TYPE" 
     TCGA-AY-6386      TCGA-AZ-4315      TCGA-AZ-4323      TCGA-AZ-4616 
"DHDDS WILD-TYPE" "DHDDS WILD-TYPE" "DHDDS WILD-TYPE" "DHDDS WILD-TYPE" 
     TCGA-AZ-4681      TCGA-AZ-4682      TCGA-AZ-5403      TCGA-AZ-5407 
"DHDDS WILD-TYPE" "DHDDS WILD-TYPE" "DHDDS WILD-TYPE" "DHDDS WILD-TYPE" 
     TCGA-AZ-6598      TCGA-AZ-6599      TCGA-AZ-6600      TCGA-AZ-6601 
"DHDDS WILD-TYPE" "DHDDS WILD-TYPE" "DHDDS WILD-TYPE" "DHDDS WILD-TYPE" 
     TCGA-AZ-6603      TCGA-AZ-6605      TCGA-AZ-6606      TCGA-AZ-6607 
"DHDDS WILD-TYPE" "DHDDS WILD-TYPE" "DHDDS WILD-TYPE" "DHDDS WILD-TYPE" 
     TCGA-AZ-6608      TCGA-CA-5254      TCGA-CA-5255      TCGA-CA-5796 
"DHDDS WILD-TYPE" "DHDDS WILD-TYPE" "DHDDS WILD-TYPE" "DHDDS WILD-TYPE" 
     TCGA-CA-5797      TCGA-CA-6715      TCGA-CA-6716      TCGA-CA-6717 
"DHDDS WILD-TYPE" "DHDDS WILD-TYPE" "DHDDS WILD-TYPE" "DHDDS WILD-TYPE" 
     TCGA-CA-6718      TCGA-CA-6719      TCGA-CK-4947      TCGA-CK-4948 
"DHDDS WILD-TYPE" "DHDDS WILD-TYPE" "DHDDS WILD-TYPE" "DHDDS WILD-TYPE" 
     TCGA-CK-4950      TCGA-CK-4952      TCGA-CK-5912      TCGA-CK-5913 
"DHDDS WILD-TYPE" "DHDDS WILD-TYPE" "DHDDS WILD-TYPE" "DHDDS WILD-TYPE" 
     TCGA-CK-5914      TCGA-CK-5915      TCGA-CK-5916      TCGA-CK-6746 
"DHDDS WILD-TYPE" "DHDDS WILD-TYPE" "DHDDS WILD-TYPE" "DHDDS WILD-TYPE" 
     TCGA-CK-6747      TCGA-CK-6748      TCGA-CK-6751      TCGA-CM-4743 
"DHDDS WILD-TYPE" "DHDDS WILD-TYPE" "DHDDS WILD-TYPE" "DHDDS WILD-TYPE" 
     TCGA-CM-4744      TCGA-CM-4746      TCGA-CM-4747      TCGA-CM-4752 
"DHDDS WILD-TYPE" "DHDDS WILD-TYPE" "DHDDS WILD-TYPE" "DHDDS WILD-TYPE" 
     TCGA-CM-5341      TCGA-CM-5344      TCGA-CM-5348      TCGA-CM-5349 
"DHDDS WILD-TYPE" "DHDDS WILD-TYPE" "DHDDS WILD-TYPE" "DHDDS WILD-TYPE" 
     TCGA-CM-5860      TCGA-CM-5861      TCGA-CM-5862      TCGA-CM-5863 
"DHDDS WILD-TYPE" "DHDDS WILD-TYPE" "DHDDS WILD-TYPE" "DHDDS WILD-TYPE" 
     TCGA-CM-5864      TCGA-CM-5868      TCGA-CM-6161      TCGA-CM-6162 
"DHDDS WILD-TYPE" "DHDDS WILD-TYPE" "DHDDS WILD-TYPE" "DHDDS WILD-TYPE" 
     TCGA-CM-6163      TCGA-CM-6164      TCGA-CM-6165      TCGA-CM-6166 
"DHDDS WILD-TYPE" "DHDDS WILD-TYPE" "DHDDS WILD-TYPE" "DHDDS WILD-TYPE" 
     TCGA-CM-6167      TCGA-CM-6168      TCGA-CM-6169      TCGA-CM-6170 
"DHDDS WILD-TYPE" "DHDDS WILD-TYPE" "DHDDS WILD-TYPE" "DHDDS WILD-TYPE" 
     TCGA-CM-6171      TCGA-CM-6172      TCGA-CM-6674      TCGA-CM-6675 
"DHDDS WILD-TYPE" "DHDDS WILD-TYPE" "DHDDS WILD-TYPE" "DHDDS WILD-TYPE" 
     TCGA-CM-6676      TCGA-CM-6677      TCGA-CM-6678      TCGA-CM-6679 
"DHDDS WILD-TYPE" "DHDDS WILD-TYPE" "DHDDS WILD-TYPE" "DHDDS WILD-TYPE" 
     TCGA-CM-6680      TCGA-D5-5537      TCGA-D5-5538      TCGA-D5-5539 
"DHDDS WILD-TYPE" "DHDDS WILD-TYPE" "DHDDS WILD-TYPE" "DHDDS WILD-TYPE" 
     TCGA-D5-5540      TCGA-D5-5541      TCGA-D5-6529      TCGA-D5-6532 
"DHDDS WILD-TYPE" "DHDDS WILD-TYPE" "DHDDS WILD-TYPE" "DHDDS WILD-TYPE" 
     TCGA-D5-6533      TCGA-D5-6534      TCGA-D5-6535      TCGA-D5-6536 
"DHDDS WILD-TYPE" "DHDDS WILD-TYPE" "DHDDS WILD-TYPE" "DHDDS WILD-TYPE" 
     TCGA-D5-6537      TCGA-D5-6538      TCGA-D5-6539      TCGA-D5-6540 
"DHDDS WILD-TYPE" "DHDDS WILD-TYPE" "DHDDS WILD-TYPE" "DHDDS WILD-TYPE" 
     TCGA-D5-6541      TCGA-D5-6898      TCGA-D5-6920      TCGA-D5-6922 
"DHDDS WILD-TYPE" "DHDDS WILD-TYPE" "DHDDS WILD-TYPE" "DHDDS WILD-TYPE" 
     TCGA-D5-6923      TCGA-D5-6924      TCGA-D5-6926      TCGA-D5-6927 
"DHDDS WILD-TYPE" "DHDDS WILD-TYPE" "DHDDS WILD-TYPE" "DHDDS WILD-TYPE" 
     TCGA-D5-6928      TCGA-D5-6929      TCGA-D5-6930      TCGA-D5-6931 
"DHDDS WILD-TYPE" "DHDDS WILD-TYPE" "DHDDS WILD-TYPE" "DHDDS WILD-TYPE" 
     TCGA-D5-6932      TCGA-D5-7000      TCGA-DM-A0X9      TCGA-DM-A0XD 
"DHDDS WILD-TYPE" "DHDDS WILD-TYPE" "DHDDS WILD-TYPE" "DHDDS WILD-TYPE" 
     TCGA-DM-A0XF      TCGA-DM-A1D0      TCGA-DM-A1D4      TCGA-DM-A1D6 
"DHDDS WILD-TYPE" "DHDDS WILD-TYPE" "DHDDS WILD-TYPE" "DHDDS WILD-TYPE" 
     TCGA-DM-A1D7      TCGA-DM-A1D8      TCGA-DM-A1D9      TCGA-DM-A1DA 
"DHDDS WILD-TYPE" "DHDDS WILD-TYPE" "DHDDS WILD-TYPE" "DHDDS WILD-TYPE" 
     TCGA-DM-A1DB      TCGA-DM-A1HA      TCGA-DM-A1HB      TCGA-DM-A285 
"DHDDS WILD-TYPE" "DHDDS WILD-TYPE" "DHDDS WILD-TYPE" "DHDDS WILD-TYPE" 
     TCGA-DM-A28C      TCGA-DM-A28E      TCGA-DM-A28F      TCGA-DM-A28G 
"DHDDS WILD-TYPE" "DHDDS WILD-TYPE" "DHDDS WILD-TYPE" "DHDDS WILD-TYPE" 
     TCGA-DM-A28H      TCGA-DM-A28K      TCGA-F4-6459      TCGA-F4-6460 
"DHDDS WILD-TYPE" "DHDDS WILD-TYPE" "DHDDS WILD-TYPE" "DHDDS WILD-TYPE" 
     TCGA-F4-6569      TCGA-F4-6570      TCGA-F4-6703      TCGA-F4-6704 
"DHDDS WILD-TYPE" "DHDDS WILD-TYPE" "DHDDS WILD-TYPE" "DHDDS WILD-TYPE" 
     TCGA-F4-6805      TCGA-F4-6806      TCGA-F4-6807      TCGA-F4-6808 
"DHDDS WILD-TYPE" "DHDDS WILD-TYPE" "DHDDS WILD-TYPE" "DHDDS WILD-TYPE" 
     TCGA-F4-6809      TCGA-F4-6854      TCGA-F4-6855      TCGA-F4-6856 
"DHDDS WILD-TYPE" "DHDDS WILD-TYPE" "DHDDS WILD-TYPE" "DHDDS WILD-TYPE" 
     TCGA-G4-6293      TCGA-G4-6299      TCGA-G4-6303      TCGA-G4-6304 
"DHDDS WILD-TYPE" "DHDDS WILD-TYPE" "DHDDS WILD-TYPE" "DHDDS WILD-TYPE" 
     TCGA-G4-6306      TCGA-G4-6307      TCGA-G4-6309      TCGA-G4-6310 
"DHDDS WILD-TYPE" "DHDDS WILD-TYPE" "DHDDS WILD-TYPE" "DHDDS WILD-TYPE" 
     TCGA-G4-6315      TCGA-G4-6317      TCGA-G4-6321      TCGA-G4-6323 
"DHDDS WILD-TYPE" "DHDDS WILD-TYPE" "DHDDS WILD-TYPE" "DHDDS WILD-TYPE" 
     TCGA-G4-6586      TCGA-G4-6588      TCGA-G4-6625      TCGA-G4-6626 
"DHDDS WILD-TYPE" "DHDDS WILD-TYPE" "DHDDS WILD-TYPE" "DHDDS WILD-TYPE" 
     TCGA-G4-6628      TCGA-AF-2687      TCGA-AF-2689      TCGA-AF-2691 
"DHDDS WILD-TYPE" "DHDDS WILD-TYPE" "DHDDS WILD-TYPE" "DHDDS WILD-TYPE" 
     TCGA-AF-2692      TCGA-AF-2693      TCGA-AF-3400      TCGA-AF-3913 
"DHDDS WILD-TYPE" "DHDDS WILD-TYPE" "DHDDS WILD-TYPE" "DHDDS WILD-TYPE" 
     TCGA-AF-4110      TCGA-AF-5654      TCGA-AF-6136      TCGA-AF-6655 
"DHDDS WILD-TYPE" "DHDDS WILD-TYPE" "DHDDS WILD-TYPE" "DHDDS WILD-TYPE" 
     TCGA-AF-6672      TCGA-AH-6544      TCGA-AH-6547      TCGA-AH-6549 
"DHDDS WILD-TYPE" "DHDDS WILD-TYPE" "DHDDS WILD-TYPE" "DHDDS WILD-TYPE" 
     TCGA-AH-6643      TCGA-AH-6644      TCGA-CI-6619      TCGA-CI-6620 
"DHDDS WILD-TYPE" "DHDDS WILD-TYPE" "DHDDS WILD-TYPE" "DHDDS WILD-TYPE" 
     TCGA-CI-6622      TCGA-CI-6624      TCGA-CL-5917      TCGA-CL-5918 
"DHDDS WILD-TYPE" "DHDDS WILD-TYPE" "DHDDS WILD-TYPE" "DHDDS WILD-TYPE" 
     TCGA-DC-5337      TCGA-DC-5869      TCGA-DC-6155      TCGA-DC-6157 
"DHDDS WILD-TYPE" "DHDDS WILD-TYPE" "DHDDS WILD-TYPE" "DHDDS WILD-TYPE" 
     TCGA-DC-6158      TCGA-DC-6160      TCGA-DC-6681      TCGA-DC-6682 
"DHDDS WILD-TYPE" "DHDDS WILD-TYPE" "DHDDS WILD-TYPE" "DHDDS WILD-TYPE" 
     TCGA-DC-6683      TCGA-DT-5265      TCGA-DY-A0XA      TCGA-DY-A1DC 
"DHDDS WILD-TYPE" "DHDDS WILD-TYPE" "DHDDS WILD-TYPE" "DHDDS WILD-TYPE" 
     TCGA-DY-A1DD      TCGA-DY-A1DF      TCGA-DY-A1DG      TCGA-DY-A1H8 
"DHDDS WILD-TYPE" "DHDDS WILD-TYPE" "DHDDS WILD-TYPE" "DHDDS WILD-TYPE" 
     TCGA-EF-5830      TCGA-EI-6506      TCGA-EI-6507      TCGA-EI-6508 
"DHDDS WILD-TYPE" "DHDDS WILD-TYPE" "DHDDS WILD-TYPE" "DHDDS WILD-TYPE" 
     TCGA-EI-6510      TCGA-F5-6464      TCGA-F5-6465      TCGA-F5-6571 
"DHDDS WILD-TYPE" "DHDDS WILD-TYPE" "DHDDS WILD-TYPE" "DHDDS WILD-TYPE" 
     TCGA-F5-6702      TCGA-F5-6811      TCGA-F5-6812      TCGA-F5-6813 
"DHDDS WILD-TYPE" "DHDDS WILD-TYPE" "DHDDS WILD-TYPE" "DHDDS WILD-TYPE" 
     TCGA-G5-6235      TCGA-G5-6641 
"DHDDS WILD-TYPE" "DHDDS WILD-TYPE" 

Clustering(1928) Variable = ARL11 MUTATION ANALYSIS
D1928V1, survival
                 sevent
clus2               0   1
  ARL11 MUTATED     5   2
  ARL11 WILD-TYPE 373  91
  ARL11 MUTATED ARL11 WILD-TYPE 
              7             464 
  ARL11 MUTATED ARL11 WILD-TYPE 
              2              91 
$`ARL11 MUTATED`
TCGA-A6-5665 TCGA-AA-3502 TCGA-AA-3821 TCGA-AA-3845 TCGA-AU-6004 TCGA-CM-5862 
       22.06        35.01         1.02         0.00        27.09         5.03 
TCGA-CM-6162 
       12.00 

$`ARL11 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 
       35.05        33.04         0.99        25.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       38.99        37.02        14.93        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       14.50        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 
       22.03        22.98        30.08        32.02        15.02        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       15.02        17.03        15.02         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  ARL11 MUTATED ARL11 WILD-TYPE 
              0               0 
  ARL11 MUTATED ARL11 WILD-TYPE 
          35.01          148.01 
  ARL11 MUTATED ARL11 WILD-TYPE 
         12.000          20.235 
[1] "0.0 - 35.0 (12.0)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "2.8"
D1928V2, continuous
D1928V3, binary
                 cls
clus                0   1
  ARL11 MUTATED     7   0
  ARL11 WILD-TYPE 359 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ARL11 MUTATED      7    0
  ARL11 WILD-TYPE  359  119
        clus
vv       ARL11 MUTATED ARL11 WILD-TYPE
  COLON              7             359
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ARL11 MUTATED         3        0        0         2         0         0
  ARL11 WILD-TYPE      88        1       32       136        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ARL11 MUTATED           0          0          1          0        0         1
  ARL11 WILD-TYPE        24         11         58         42       48        17
                 vv
clus              STAGE IVB
  ARL11 MUTATED           0
  ARL11 WILD-TYPE         1
D1928V4, multiclass
            clus
vv           ARL11 MUTATED ARL11 WILD-TYPE
  STAGE I                3              88
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              2             136
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ARL11 MUTATED     0   3   4   0
  ARL11 WILD-TYPE  17  89 325  50
D1928V5, multiclass
    clus
vv   ARL11 MUTATED ARL11 WILD-TYPE
  T1             0              17
  T2             3              89
  T3             4             325
  T4             0              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  ARL11 MUTATED     5   2   0
  ARL11 WILD-TYPE 282 111  87
D1928V6, multiclass
    clus
vv   ARL11 MUTATED ARL11 WILD-TYPE
  N0             5             282
  N1             2             111
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1928V7, binary
                 cls
clus                0   1
  ARL11 MUTATED     6   1
  ARL11 WILD-TYPE 369  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ARL11 MUTATED      6    1
  ARL11 WILD-TYPE  369   64
   clus
vv  ARL11 MUTATED ARL11 WILD-TYPE
  0             6             369
  1             1              64
[1] 2 2
[1] FALSE
D1928V8, binary
                 cls
clus                0   1
  ARL11 MUTATED     5   2
  ARL11 WILD-TYPE 220 262
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ARL11 MUTATED      5    2
  ARL11 WILD-TYPE  220  262
        clus
vv       ARL11 MUTATED ARL11 WILD-TYPE
  FEMALE             5             220
  MALE               2             262
[1] 2 2
[1] FALSE
D1928V9, binary
                 cls
clus                0   1
  ARL11 MUTATED     5   0
  ARL11 WILD-TYPE 345  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ARL11 MUTATED      5    0
  ARL11 WILD-TYPE  345   22
     clus
vv    ARL11 MUTATED ARL11 WILD-TYPE
  NO              5             345
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ARL11 MUTATED                      5                             2
  ARL11 WILD-TYPE                  310                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ARL11 MUTATED                       0                              0
  ARL11 WILD-TYPE                   106                             10
D1928V10, multiclass
                                clus
vv                               ARL11 MUTATED ARL11 WILD-TYPE
  COLON ADENOCARCINOMA                       5             310
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  ARL11 MUTATED     7   0   0   0
  ARL11 WILD-TYPE 338   4  31  25
D1928V11, multiclass
    clus
vv   ARL11 MUTATED ARL11 WILD-TYPE
  R0             7             338
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1928V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ARL11 MUTATED                                  0     0
  ARL11 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ARL11 MUTATED                           0     4
  ARL11 WILD-TYPE                        22   222
D1928V13, multiclass
                                  clus
vv                                 ARL11 MUTATED ARL11 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        4             222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1929) Variable = ATP2A2 MUTATION ANALYSIS
D1929V1, survival
                  sevent
clus2                0   1
  ATP2A2 MUTATED    12   3
  ATP2A2 WILD-TYPE 366  90
  ATP2A2 MUTATED ATP2A2 WILD-TYPE 
              15              456 
  ATP2A2 MUTATED ATP2A2 WILD-TYPE 
               3               90 
$`ATP2A2 MUTATED`
TCGA-A6-6780 TCGA-AA-3510 TCGA-AA-3525 TCGA-AA-3815 TCGA-AA-3977 TCGA-AA-A00N 
       20.12        63.98         8.05        33.04        25.02         4.01 
TCGA-AA-A00R TCGA-AD-5900 TCGA-AZ-6598 TCGA-AZ-6608 TCGA-CM-5864 TCGA-CM-6171 
        0.99         0.07        49.41         1.61        15.02        14.04 
TCGA-D5-6540 TCGA-G4-6304 TCGA-AG-3892 
       16.14        53.62        13.02 

$`ATP2A2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3529 
        9.07        24.03        37.05        36.03        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00U 
       18.05        18.05        38.04        27.02        42.02        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 
       41.00        39.98        18.05        40.96        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 
      106.75        22.36        62.79        88.21         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 
      100.01        29.56         5.23        11.74         3.19        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
        5.03        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       15.02        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 
       15.12        17.85         4.80        17.13        12.49        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
      133.18        74.56        65.85        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  ATP2A2 MUTATED ATP2A2 WILD-TYPE 
            0.07             0.00 
  ATP2A2 MUTATED ATP2A2 WILD-TYPE 
           63.98           148.01 
  ATP2A2 MUTATED ATP2A2 WILD-TYPE 
           15.02            20.73 
[1] "0.1 - 64.0 (15.0)"  "0.0 - 148.0 (20.7)"
[1] "hr=" "1.1"
D1929V2, continuous
D1929V3, binary
                  cls
clus                 0   1
  ATP2A2 MUTATED    15   1
  ATP2A2 WILD-TYPE 351 118
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP2A2 MUTATED     15    1
  ATP2A2 WILD-TYPE  351  118
        clus
vv       ATP2A2 MUTATED ATP2A2 WILD-TYPE
  COLON              15              351
  RECTUM              1              118
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ATP2A2 MUTATED         6        0        2         2         3         0
  ATP2A2 WILD-TYPE      85        1       30       136         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ATP2A2 MUTATED           0          1          1          0        0
  ATP2A2 WILD-TYPE        24         10         58         42       48
                  vv
clus               STAGE IVA STAGE IVB
  ATP2A2 MUTATED           0         0
  ATP2A2 WILD-TYPE        18         1
D1929V4, multiclass
            clus
vv           ATP2A2 MUTATED ATP2A2 WILD-TYPE
  STAGE I                 6               85
  STAGE IA                0                1
  STAGE II                2               30
  STAGE IIA               2              136
  STAGE IIB               3                7
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              1               10
  STAGE IIIB              1               58
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ATP2A2 MUTATED     1   7   5   3
  ATP2A2 WILD-TYPE  16  85 324  47
D1929V5, multiclass
    clus
vv   ATP2A2 MUTATED ATP2A2 WILD-TYPE
  T1              1               16
  T2              7               85
  T3              5              324
  T4              3               47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  ATP2A2 MUTATED    14   2   0
  ATP2A2 WILD-TYPE 273 111  87
D1929V6, multiclass
    clus
vv   ATP2A2 MUTATED ATP2A2 WILD-TYPE
  N0             14              273
  N1              2              111
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1929V7, binary
                  cls
clus                 0   1
  ATP2A2 MUTATED    11   0
  ATP2A2 WILD-TYPE 364  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP2A2 MUTATED     11    0
  ATP2A2 WILD-TYPE  364   65
   clus
vv  ATP2A2 MUTATED ATP2A2 WILD-TYPE
  0             11              364
  1              0               65
[1] 2 2
[1] FALSE
D1929V8, binary
                  cls
clus                 0   1
  ATP2A2 MUTATED     8   8
  ATP2A2 WILD-TYPE 217 256
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP2A2 MUTATED      8    8
  ATP2A2 WILD-TYPE  217  256
        clus
vv       ATP2A2 MUTATED ATP2A2 WILD-TYPE
  FEMALE              8              217
  MALE                8              256
[1] 2 2
[1] FALSE
D1929V9, binary
                  cls
clus                 0   1
  ATP2A2 MUTATED    12   0
  ATP2A2 WILD-TYPE 338  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP2A2 MUTATED     12    0
  ATP2A2 WILD-TYPE  338   22
     clus
vv    ATP2A2 MUTATED ATP2A2 WILD-TYPE
  NO              12              338
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ATP2A2 MUTATED                     11                             4
  ATP2A2 WILD-TYPE                  304                            43
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ATP2A2 MUTATED                       1                              0
  ATP2A2 WILD-TYPE                   105                             10
D1929V10, multiclass
                                clus
vv                               ATP2A2 MUTATED ATP2A2 WILD-TYPE
  COLON ADENOCARCINOMA                       11              304
  COLON MUCINOUS ADENOCARCINOMA               4               43
  RECTAL ADENOCARCINOMA                       1              105
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ATP2A2 MUTATED    11   0   0   1
  ATP2A2 WILD-TYPE 334   4  31  24
D1929V11, multiclass
    clus
vv   ATP2A2 MUTATED ATP2A2 WILD-TYPE
  R0             11              334
  R1              0                4
  R2              0               31
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1929V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ATP2A2 MUTATED                                  0     0
  ATP2A2 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ATP2A2 MUTATED                           0     9
  ATP2A2 WILD-TYPE                        22   217
D1929V13, multiclass
                                  clus
vv                                 ATP2A2 MUTATED ATP2A2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         9              217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1930) Variable = HSF5 MUTATION ANALYSIS
D1930V1, survival
                sevent
clus2              0   1
  HSF5 MUTATED     6   2
  HSF5 WILD-TYPE 372  91
  HSF5 MUTATED HSF5 WILD-TYPE 
             8            463 
  HSF5 MUTATED HSF5 WILD-TYPE 
             2             91 
$`HSF5 MUTATED`
TCGA-AA-3811 TCGA-AA-3977 TCGA-AA-A010 TCGA-AZ-4315 TCGA-CK-5914 TCGA-CM-5860 
       10.06        25.02        34.98        58.39         9.99        32.02 
TCGA-G4-6309 TCGA-DY-A1DD 
       85.48        57.24 

$`HSF5 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       19.04        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       49.08        51.32        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.03        22.98        30.08        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       55.04        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
      126.44        41.36        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  HSF5 MUTATED HSF5 WILD-TYPE 
          9.99           0.00 
  HSF5 MUTATED HSF5 WILD-TYPE 
         85.48         148.01 
  HSF5 MUTATED HSF5 WILD-TYPE 
         33.50          20.05 
[1] "10.0 - 85.5 (33.5)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.2"
D1930V2, continuous
D1930V3, binary
                cls
clus               0   1
  HSF5 MUTATED     7   1
  HSF5 WILD-TYPE 359 118
[1] "tbl2"
                cls
clus             [,1] [,2]
  HSF5 MUTATED      7    1
  HSF5 WILD-TYPE  359  118
        clus
vv       HSF5 MUTATED HSF5 WILD-TYPE
  COLON             7            359
  RECTUM            1            118
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  HSF5 MUTATED         0        0        0         2         1         0
  HSF5 WILD-TYPE      91        1       32       136         9         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  HSF5 MUTATED           1          0          3          0        0         0
  HSF5 WILD-TYPE        23         11         56         42       48        18
                vv
clus             STAGE IVB
  HSF5 MUTATED           0
  HSF5 WILD-TYPE         1
D1930V4, multiclass
            clus
vv           HSF5 MUTATED HSF5 WILD-TYPE
  STAGE I               0             91
  STAGE IA              0              1
  STAGE II              0             32
  STAGE IIA             2            136
  STAGE IIB             1              9
  STAGE IIC             0              1
  STAGE III             1             23
  STAGE IIIA            0             11
  STAGE IIIB            3             56
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  HSF5 MUTATED     0   1   6   1
  HSF5 WILD-TYPE  17  91 323  49
D1930V5, multiclass
    clus
vv   HSF5 MUTATED HSF5 WILD-TYPE
  T1            0             17
  T2            1             91
  T3            6            323
  T4            1             49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  HSF5 MUTATED     4   3   1
  HSF5 WILD-TYPE 283 110  86
D1930V6, multiclass
    clus
vv   HSF5 MUTATED HSF5 WILD-TYPE
  N0            4            283
  N1            3            110
  N2            1             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1930V7, binary
                cls
clus               0   1
  HSF5 MUTATED     6   0
  HSF5 WILD-TYPE 369  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  HSF5 MUTATED      6    0
  HSF5 WILD-TYPE  369   65
   clus
vv  HSF5 MUTATED HSF5 WILD-TYPE
  0            6            369
  1            0             65
[1] 2 2
[1] FALSE
D1930V8, binary
                cls
clus               0   1
  HSF5 MUTATED     4   4
  HSF5 WILD-TYPE 221 260
[1] "tbl2"
                cls
clus             [,1] [,2]
  HSF5 MUTATED      4    4
  HSF5 WILD-TYPE  221  260
        clus
vv       HSF5 MUTATED HSF5 WILD-TYPE
  FEMALE            4            221
  MALE              4            260
[1] 2 2
[1] FALSE
D1930V9, binary
                cls
clus               0   1
  HSF5 MUTATED     6   0
  HSF5 WILD-TYPE 344  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  HSF5 MUTATED      6    0
  HSF5 WILD-TYPE  344   22
     clus
vv    HSF5 MUTATED HSF5 WILD-TYPE
  NO             6            344
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  HSF5 MUTATED                      7                             0
  HSF5 WILD-TYPE                  308                            47
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  HSF5 MUTATED                       1                              0
  HSF5 WILD-TYPE                   105                             10
D1930V10, multiclass
                                clus
vv                               HSF5 MUTATED HSF5 WILD-TYPE
  COLON ADENOCARCINOMA                      7            308
  COLON MUCINOUS ADENOCARCINOMA             0             47
  RECTAL ADENOCARCINOMA                     1            105
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  HSF5 MUTATED     5   0   0   1
  HSF5 WILD-TYPE 340   4  31  24
D1930V11, multiclass
    clus
vv   HSF5 MUTATED HSF5 WILD-TYPE
  R0            5            340
  R1            0              4
  R2            0             31
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1930V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HSF5 MUTATED                                  0     0
  HSF5 WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  HSF5 MUTATED                           1     4
  HSF5 WILD-TYPE                        21   222
D1930V13, multiclass
                                  clus
vv                                 HSF5 MUTATED HSF5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                       4            222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1931) Variable = ACCN5 MUTATION ANALYSIS
D1931V1, survival
                 sevent
clus2               0   1
  ACCN5 MUTATED    10   3
  ACCN5 WILD-TYPE 368  90
  ACCN5 MUTATED ACCN5 WILD-TYPE 
             13             458 
  ACCN5 MUTATED ACCN5 WILD-TYPE 
              3              90 
$`ACCN5 MUTATED`
TCGA-AA-3510 TCGA-AA-3681 TCGA-AA-A00N TCGA-AA-A010 TCGA-AD-6888 TCGA-AU-3779 
       63.98         5.98         4.01        34.98        15.52        14.50 
TCGA-CM-6162 TCGA-D5-6532 TCGA-D5-6536 TCGA-DM-A1HB TCGA-DM-A285 TCGA-G4-6306 
       12.00        18.25        17.85       135.65         6.12        44.68 
TCGA-AG-A002 
       20.98 

$`ACCN5 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       47.01        15.02        11.01        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
       40.96         0.07        21.37        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-6004 
        5.79        22.42        27.42        10.88         0.20        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       15.02        17.03        15.02         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 
       55.92        20.19         1.32        43.27        15.12         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 
       12.59       140.38         7.50        44.32       131.51       139.17 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  ACCN5 MUTATED ACCN5 WILD-TYPE 
           4.01            0.00 
  ACCN5 MUTATED ACCN5 WILD-TYPE 
         135.65          148.01 
  ACCN5 MUTATED ACCN5 WILD-TYPE 
         17.850          20.415 
[1] "4.0 - 135.7 (17.9)" "0.0 - 148.0 (20.4)"
[1] "hr=" "1.1"
D1931V2, continuous
D1931V3, binary
                 cls
clus                0   1
  ACCN5 MUTATED    13   1
  ACCN5 WILD-TYPE 353 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ACCN5 MUTATED     13    1
  ACCN5 WILD-TYPE  353  118
        clus
vv       ACCN5 MUTATED ACCN5 WILD-TYPE
  COLON             13             353
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ACCN5 MUTATED         1        0        1         5         2         0
  ACCN5 WILD-TYPE      90        1       31       133         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ACCN5 MUTATED           1          0          3          0        1         0
  ACCN5 WILD-TYPE        23         11         56         42       47        18
                 vv
clus              STAGE IVB
  ACCN5 MUTATED           0
  ACCN5 WILD-TYPE         1
D1931V4, multiclass
            clus
vv           ACCN5 MUTATED ACCN5 WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              5             133
  STAGE IIB              2               8
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             3              56
  STAGE IIIC             0              42
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ACCN5 MUTATED     0   2  10   2
  ACCN5 WILD-TYPE  17  90 319  48
D1931V5, multiclass
    clus
vv   ACCN5 MUTATED ACCN5 WILD-TYPE
  T1             0              17
  T2             2              90
  T3            10             319
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  ACCN5 MUTATED     9   4   1
  ACCN5 WILD-TYPE 278 109  86
D1931V6, multiclass
    clus
vv   ACCN5 MUTATED ACCN5 WILD-TYPE
  N0             9             278
  N1             4             109
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1931V7, binary
                 cls
clus                0   1
  ACCN5 MUTATED    13   1
  ACCN5 WILD-TYPE 362  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ACCN5 MUTATED     13    1
  ACCN5 WILD-TYPE  362   64
   clus
vv  ACCN5 MUTATED ACCN5 WILD-TYPE
  0            13             362
  1             1              64
[1] 2 2
[1] FALSE
D1931V8, binary
                 cls
clus                0   1
  ACCN5 MUTATED     6   8
  ACCN5 WILD-TYPE 219 256
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ACCN5 MUTATED      6    8
  ACCN5 WILD-TYPE  219  256
        clus
vv       ACCN5 MUTATED ACCN5 WILD-TYPE
  FEMALE             6             219
  MALE               8             256
[1] 2 2
[1] FALSE
D1931V9, binary
                 cls
clus                0   1
  ACCN5 MUTATED    10   0
  ACCN5 WILD-TYPE 340  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ACCN5 MUTATED     10    0
  ACCN5 WILD-TYPE  340   22
     clus
vv    ACCN5 MUTATED ACCN5 WILD-TYPE
  NO             10             340
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ACCN5 MUTATED                      9                             3
  ACCN5 WILD-TYPE                  306                            44
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ACCN5 MUTATED                       1                              0
  ACCN5 WILD-TYPE                   105                             10
D1931V10, multiclass
                                clus
vv                               ACCN5 MUTATED ACCN5 WILD-TYPE
  COLON ADENOCARCINOMA                       9             306
  COLON MUCINOUS ADENOCARCINOMA              3              44
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  ACCN5 MUTATED    12   0   0   0
  ACCN5 WILD-TYPE 333   4  31  25
D1931V11, multiclass
    clus
vv   ACCN5 MUTATED ACCN5 WILD-TYPE
  R0            12             333
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1931V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ACCN5 MUTATED                                  0     0
  ACCN5 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ACCN5 MUTATED                           0     8
  ACCN5 WILD-TYPE                        22   218
D1931V13, multiclass
                                  clus
vv                                 ACCN5 MUTATED ACCN5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        8             218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1932) Variable = LRRTM2 MUTATION ANALYSIS
D1932V1, survival
                  sevent
clus2                0   1
  LRRTM2 MUTATED     9   0
  LRRTM2 WILD-TYPE 369  93
  LRRTM2 MUTATED LRRTM2 WILD-TYPE 
               9              462 
  LRRTM2 MUTATED LRRTM2 WILD-TYPE 
               0               93 
$`LRRTM2 MUTATED`
TCGA-AA-3833 TCGA-AU-3779 TCGA-D5-6529 TCGA-F4-6856 TCGA-G4-6304 TCGA-AG-3892 
       15.95        14.50        20.19        35.31        53.62        13.02 
TCGA-AG-A002 TCGA-AG-A00H TCGA-AG-A025 
       20.98        25.97        49.97 

$`LRRTM2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
        1.02        17.98        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        10.88         0.20        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
       13.25         0.53        47.41       133.18        74.56        65.85 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       17.95        36.95        17.03        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 
        1.02        17.03        13.94         6.02        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       10.98         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  LRRTM2 MUTATED LRRTM2 WILD-TYPE 
           13.02             0.00 
  LRRTM2 MUTATED LRRTM2 WILD-TYPE 
           53.62           148.01 
  LRRTM2 MUTATED LRRTM2 WILD-TYPE 
          20.980           20.085 
[1] "13.0 - 53.6 (21.0)" "0.0 - 148.0 (20.1)"
[1] "hr="     "9200000"
D1932V2, continuous
D1932V3, binary
                  cls
clus                 0   1
  LRRTM2 MUTATED     5   4
  LRRTM2 WILD-TYPE 361 115
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LRRTM2 MUTATED      5    4
  LRRTM2 WILD-TYPE  361  115
        clus
vv       LRRTM2 MUTATED LRRTM2 WILD-TYPE
  COLON               5              361
  RECTUM              4              115
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  LRRTM2 MUTATED         4        0        0         4         1         0
  LRRTM2 WILD-TYPE      87        1       32       134         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  LRRTM2 MUTATED           0          0          0          0        0
  LRRTM2 WILD-TYPE        24         11         59         42       48
                  vv
clus               STAGE IVA STAGE IVB
  LRRTM2 MUTATED           0         0
  LRRTM2 WILD-TYPE        18         1
D1932V4, multiclass
            clus
vv           LRRTM2 MUTATED LRRTM2 WILD-TYPE
  STAGE I                 4               87
  STAGE IA                0                1
  STAGE II                0               32
  STAGE IIA               4              134
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              0               59
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  LRRTM2 MUTATED     2   2   4   1
  LRRTM2 WILD-TYPE  15  90 325  49
D1932V5, multiclass
    clus
vv   LRRTM2 MUTATED LRRTM2 WILD-TYPE
  T1              2               15
  T2              2               90
  T3              4              325
  T4              1               49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  LRRTM2 MUTATED     9   0   0
  LRRTM2 WILD-TYPE 278 113  87
D1932V6, multiclass
    clus
vv   LRRTM2 MUTATED LRRTM2 WILD-TYPE
  N0              9              278
  N1              0              113
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1932V7, binary
                  cls
clus                 0   1
  LRRTM2 MUTATED     9   0
  LRRTM2 WILD-TYPE 366  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LRRTM2 MUTATED      9    0
  LRRTM2 WILD-TYPE  366   65
   clus
vv  LRRTM2 MUTATED LRRTM2 WILD-TYPE
  0              9              366
  1              0               65
[1] 2 2
[1] FALSE
D1932V8, binary
                  cls
clus                 0   1
  LRRTM2 MUTATED     5   4
  LRRTM2 WILD-TYPE 220 260
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LRRTM2 MUTATED      5    4
  LRRTM2 WILD-TYPE  220  260
        clus
vv       LRRTM2 MUTATED LRRTM2 WILD-TYPE
  FEMALE              5              220
  MALE                4              260
[1] 2 2
[1] FALSE
D1932V9, binary
                  cls
clus                 0   1
  LRRTM2 MUTATED     7   1
  LRRTM2 WILD-TYPE 343  21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LRRTM2 MUTATED      7    1
  LRRTM2 WILD-TYPE  343   21
     clus
vv    LRRTM2 MUTATED LRRTM2 WILD-TYPE
  NO               7              343
  YES              1               21
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  LRRTM2 MUTATED                      4                             1
  LRRTM2 WILD-TYPE                  311                            46
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  LRRTM2 MUTATED                       4                              0
  LRRTM2 WILD-TYPE                   102                             10
D1932V10, multiclass
                                clus
vv                               LRRTM2 MUTATED LRRTM2 WILD-TYPE
  COLON ADENOCARCINOMA                        4              311
  COLON MUCINOUS ADENOCARCINOMA               1               46
  RECTAL ADENOCARCINOMA                       4              102
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  LRRTM2 MUTATED     9   0   0   0
  LRRTM2 WILD-TYPE 336   4  31  25
D1932V11, multiclass
    clus
vv   LRRTM2 MUTATED LRRTM2 WILD-TYPE
  R0              9              336
  R1              0                4
  R2              0               31
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1932V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  LRRTM2 MUTATED                                  0     0
  LRRTM2 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  LRRTM2 MUTATED                           0     4
  LRRTM2 WILD-TYPE                        22   222
D1932V13, multiclass
                                  clus
vv                                 LRRTM2 MUTATED LRRTM2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         4              222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1933) Variable = ATR MUTATION ANALYSIS
D1933V1, survival
               sevent
clus2             0   1
  ATR MUTATED    26   6
  ATR WILD-TYPE 352  87
  ATR MUTATED ATR WILD-TYPE 
           32           439 
  ATR MUTATED ATR WILD-TYPE 
            6            87 
$`ATR MUTATED`
TCGA-A6-2676 TCGA-A6-6648 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3543 TCGA-AA-3664 
       42.90        25.18         1.02        35.01         0.99        54.02 
TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3864 TCGA-AA-3977 TCGA-AA-A010 TCGA-AY-4070 
       19.04        10.06        53.00        25.02        34.98        16.31 
TCGA-AY-6197 TCGA-AZ-6608 TCGA-CA-5255 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-5912 
       21.44         1.61         3.06        12.76        10.06        49.08 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-6165 TCGA-CM-6675 TCGA-D5-5538 TCGA-D5-6536 
      124.27        23.05        16.04        13.05        12.26        17.85 
TCGA-F4-6806 TCGA-F4-6808 TCGA-G4-6315 TCGA-AG-3892 TCGA-AG-A002 TCGA-DC-5337 
       41.42        33.67        61.91        13.02        20.98        15.02 
TCGA-DC-6160 TCGA-EF-5830 
       19.99         0.49 

$`ATR WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3511 
       19.66        20.28         7.04         3.02        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
       34.03        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
       78.08         6.05         6.97         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 
        0.99        31.07        31.07        30.05        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       27.09         0.95        33.01        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        3.19        12.69         3.25         3.29         0.07        12.20 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5913 
       14.30        17.56       148.01        85.45        15.62        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CM-4744 TCGA-CM-4746 
        9.99        21.14        82.95         1.91        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6166 TCGA-CM-6167 
       15.02        12.00         2.96        29.03        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       43.27        15.12         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       16.24        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       63.62        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 
       19.99         1.02        17.95        36.95        17.03        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5869 TCGA-DC-6155 
        6.97         4.73        78.12         7.17         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       27.95        10.98         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  ATR MUTATED ATR WILD-TYPE 
         0.49          0.00 
  ATR MUTATED ATR WILD-TYPE 
       124.27        148.01 
  ATR MUTATED ATR WILD-TYPE 
       19.515        20.280 
[1] "0.5 - 124.3 (19.5)" "0.0 - 148.0 (20.3)"
[1] "hr=" "1"  
D1933V2, continuous
D1933V3, binary
               cls
clus              0   1
  ATR MUTATED    28   5
  ATR WILD-TYPE 338 114
[1] "tbl2"
               cls
clus            [,1] [,2]
  ATR MUTATED     28    5
  ATR WILD-TYPE  338  114
        clus
vv       ATR MUTATED ATR WILD-TYPE
  COLON           28           338
  RECTUM           5           114
[1] 2 2
[1] FALSE
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ATR MUTATED        10        0        3         8         3         0
  ATR WILD-TYPE      81        1       29       130         7         1
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ATR MUTATED           1          1          1          1        2         1
  ATR WILD-TYPE        23         10         58         41       46        17
               vv
clus            STAGE IVB
  ATR MUTATED           1
  ATR WILD-TYPE         0
D1933V4, multiclass
            clus
vv           ATR MUTATED ATR WILD-TYPE
  STAGE I             10            81
  STAGE IA             0             1
  STAGE II             3            29
  STAGE IIA            8           130
  STAGE IIB            3             7
  STAGE IIC            0             1
  STAGE III            1            23
  STAGE IIIA           1            10
  STAGE IIIB           1            58
  STAGE IIIC           1            41
  STAGE IV             2            46
  STAGE IVA            1            17
  STAGE IVB            1             0
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  ATR MUTATED     3   9  18   3
  ATR WILD-TYPE  14  83 311  47
D1933V5, multiclass
    clus
vv   ATR MUTATED ATR WILD-TYPE
  T1           3            14
  T2           9            83
  T3          18           311
  T4           3            47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2
  ATR MUTATED    27   3   3
  ATR WILD-TYPE 260 110  84
D1933V6, multiclass
    clus
vv   ATR MUTATED ATR WILD-TYPE
  N0          27           260
  N1           3           110
  N2           3            84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1933V7, binary
               cls
clus              0   1
  ATR MUTATED    25   4
  ATR WILD-TYPE 350  61
[1] "tbl2"
               cls
clus            [,1] [,2]
  ATR MUTATED     25    4
  ATR WILD-TYPE  350   61
   clus
vv  ATR MUTATED ATR WILD-TYPE
  0          25           350
  1           4            61
[1] 2 2
[1] FALSE
D1933V8, binary
               cls
clus              0   1
  ATR MUTATED    13  20
  ATR WILD-TYPE 212 244
[1] "tbl2"
               cls
clus            [,1] [,2]
  ATR MUTATED     13   20
  ATR WILD-TYPE  212  244
        clus
vv       ATR MUTATED ATR WILD-TYPE
  FEMALE          13           212
  MALE            20           244
[1] 2 2
[1] FALSE
D1933V9, binary
               cls
clus              0   1
  ATR MUTATED    27   2
  ATR WILD-TYPE 323  20
[1] "tbl2"
               cls
clus            [,1] [,2]
  ATR MUTATED     27    2
  ATR WILD-TYPE  323   20
     clus
vv    ATR MUTATED ATR WILD-TYPE
  NO           27           323
  YES           2            20
[1] 2 2
[1] FALSE
               vv
clus            COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ATR MUTATED                     25                             3
  ATR WILD-TYPE                  290                            44
               vv
clus            RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ATR MUTATED                       5                              0
  ATR WILD-TYPE                   101                             10
D1933V10, multiclass
                                clus
vv                               ATR MUTATED ATR WILD-TYPE
  COLON ADENOCARCINOMA                    25           290
  COLON MUCINOUS ADENOCARCINOMA            3            44
  RECTAL ADENOCARCINOMA                    5           101
  RECTAL MUCINOUS ADENOCARCINOMA           0            10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             R0  R1  R2  RX
  ATR MUTATED    23   1   1   5
  ATR WILD-TYPE 322   3  30  20
D1933V11, multiclass
    clus
vv   ATR MUTATED ATR WILD-TYPE
  R0          23           322
  R1           1             3
  R2           1            30
  RX           5            20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1933V12, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ATR MUTATED                                  0     3
  ATR WILD-TYPE                                1     8
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  ATR MUTATED                           2    16
  ATR WILD-TYPE                        20   210
D1933V13, multiclass
                                  clus
vv                                 ATR MUTATED ATR WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      3             8
  BLACK OR AFRICAN AMERICAN                  2            20
  WHITE                                     16           210
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1934) Variable = FBLIM1 MUTATION ANALYSIS
D1934V1, survival
                  sevent
clus2                0   1
  FBLIM1 MUTATED     5   1
  FBLIM1 WILD-TYPE 373  92
  FBLIM1 MUTATED FBLIM1 WILD-TYPE 
               6              465 
  FBLIM1 MUTATED FBLIM1 WILD-TYPE 
               1               92 
$`FBLIM1 MUTATED`
TCGA-AA-3713 TCGA-AA-3837 TCGA-AZ-6598 TCGA-CM-5861 TCGA-CM-6171 TCGA-AG-3732 
       19.04        38.99        49.41        15.02        14.04        32.98 

$`FBLIM1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       17.98        15.95        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 
      106.75        22.36        62.79        88.21         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       13.02        15.02        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  FBLIM1 MUTATED FBLIM1 WILD-TYPE 
           14.04             0.00 
  FBLIM1 MUTATED FBLIM1 WILD-TYPE 
           49.41           148.01 
  FBLIM1 MUTATED FBLIM1 WILD-TYPE 
           26.01            20.19 
[1] "14.0 - 49.4 (26.0)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.3"
D1934V2, continuous
D1934V3, binary
                  cls
clus                 0   1
  FBLIM1 MUTATED     5   1
  FBLIM1 WILD-TYPE 361 118
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FBLIM1 MUTATED      5    1
  FBLIM1 WILD-TYPE  361  118
        clus
vv       FBLIM1 MUTATED FBLIM1 WILD-TYPE
  COLON               5              361
  RECTUM              1              118
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FBLIM1 MUTATED         2        0        1         2         0         0
  FBLIM1 WILD-TYPE      89        1       31       136        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FBLIM1 MUTATED           0          0          0          0        1
  FBLIM1 WILD-TYPE        24         11         59         42       47
                  vv
clus               STAGE IVA STAGE IVB
  FBLIM1 MUTATED           0         0
  FBLIM1 WILD-TYPE        18         1
D1934V4, multiclass
            clus
vv           FBLIM1 MUTATED FBLIM1 WILD-TYPE
  STAGE I                 2               89
  STAGE IA                0                1
  STAGE II                1               31
  STAGE IIA               2              136
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              0               59
  STAGE IIIC              0               42
  STAGE IV                1               47
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  FBLIM1 MUTATED     0   2   4   0
  FBLIM1 WILD-TYPE  17  90 325  50
D1934V5, multiclass
    clus
vv   FBLIM1 MUTATED FBLIM1 WILD-TYPE
  T1              0               17
  T2              2               90
  T3              4              325
  T4              0               50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  FBLIM1 MUTATED     6   0   0
  FBLIM1 WILD-TYPE 281 113  87
D1934V6, multiclass
    clus
vv   FBLIM1 MUTATED FBLIM1 WILD-TYPE
  N0              6              281
  N1              0              113
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1934V7, binary
                  cls
clus                 0   1
  FBLIM1 MUTATED     4   1
  FBLIM1 WILD-TYPE 371  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FBLIM1 MUTATED      4    1
  FBLIM1 WILD-TYPE  371   64
   clus
vv  FBLIM1 MUTATED FBLIM1 WILD-TYPE
  0              4              371
  1              1               64
[1] 2 2
[1] FALSE
D1934V8, binary
                  cls
clus                 0   1
  FBLIM1 MUTATED     4   2
  FBLIM1 WILD-TYPE 221 262
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FBLIM1 MUTATED      4    2
  FBLIM1 WILD-TYPE  221  262
        clus
vv       FBLIM1 MUTATED FBLIM1 WILD-TYPE
  FEMALE              4              221
  MALE                2              262
[1] 2 2
[1] FALSE
D1934V9, binary
                  cls
clus                 0   1
  FBLIM1 MUTATED     5   1
  FBLIM1 WILD-TYPE 345  21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FBLIM1 MUTATED      5    1
  FBLIM1 WILD-TYPE  345   21
     clus
vv    FBLIM1 MUTATED FBLIM1 WILD-TYPE
  NO               5              345
  YES              1               21
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  FBLIM1 MUTATED                      4                             1
  FBLIM1 WILD-TYPE                  311                            46
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  FBLIM1 MUTATED                       1                              0
  FBLIM1 WILD-TYPE                   105                             10
D1934V10, multiclass
                                clus
vv                               FBLIM1 MUTATED FBLIM1 WILD-TYPE
  COLON ADENOCARCINOMA                        4              311
  COLON MUCINOUS ADENOCARCINOMA               1               46
  RECTAL ADENOCARCINOMA                       1              105
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  FBLIM1 MUTATED     4   0   1   0
  FBLIM1 WILD-TYPE 341   4  30  25
D1934V11, multiclass
    clus
vv   FBLIM1 MUTATED FBLIM1 WILD-TYPE
  R0              4              341
  R1              0                4
  R2              1               30
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1934V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FBLIM1 MUTATED                                  0     0
  FBLIM1 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  FBLIM1 MUTATED                           0     3
  FBLIM1 WILD-TYPE                        22   223
D1934V13, multiclass
                                  clus
vv                                 FBLIM1 MUTATED FBLIM1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         3              223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1935) Variable = CCDC14 MUTATION ANALYSIS
D1935V1, survival
                  sevent
clus2                0   1
  CCDC14 MUTATED     6   5
  CCDC14 WILD-TYPE 372  88
  CCDC14 MUTATED CCDC14 WILD-TYPE 
              11              460 
  CCDC14 MUTATED CCDC14 WILD-TYPE 
               5               88 
$`CCDC14 MUTATED`
TCGA-A6-5659 TCGA-AA-3510 TCGA-AA-3713 TCGA-AA-3845 TCGA-AA-3977 TCGA-AA-A00N 
       30.44        63.98        19.04         0.00        25.02         4.01 
TCGA-AD-6964 TCGA-AZ-4315 TCGA-CA-6717 TCGA-CA-6718 TCGA-F4-6570 
       10.88        58.39        12.76        10.06         6.18 

$`CCDC14 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       38.99        37.02        14.93        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        33.01        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       12.20        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 
       98.24         8.61        31.96        35.74        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  CCDC14 MUTATED CCDC14 WILD-TYPE 
               0                0 
  CCDC14 MUTATED CCDC14 WILD-TYPE 
           63.98           148.01 
  CCDC14 MUTATED CCDC14 WILD-TYPE 
          12.760           20.415 
[1] "0.0 - 64.0 (12.8)"  "0.0 - 148.0 (20.4)"
[1] "hr=" "2.7"
D1935V2, continuous
D1935V3, binary
                  cls
clus                 0   1
  CCDC14 MUTATED    11   0
  CCDC14 WILD-TYPE 355 119
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC14 MUTATED     11    0
  CCDC14 WILD-TYPE  355  119
        clus
vv       CCDC14 MUTATED CCDC14 WILD-TYPE
  COLON              11              355
  RECTUM              0              119
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CCDC14 MUTATED         1        0        1         5         1         0
  CCDC14 WILD-TYPE      90        1       31       133         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CCDC14 MUTATED           0          0          0          0        1
  CCDC14 WILD-TYPE        24         11         59         42       47
                  vv
clus               STAGE IVA STAGE IVB
  CCDC14 MUTATED           0         0
  CCDC14 WILD-TYPE        18         1
D1935V4, multiclass
            clus
vv           CCDC14 MUTATED CCDC14 WILD-TYPE
  STAGE I                 1               90
  STAGE IA                0                1
  STAGE II                1               31
  STAGE IIA               5              133
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              0               59
  STAGE IIIC              0               42
  STAGE IV                1               47
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  CCDC14 MUTATED     0   2   7   2
  CCDC14 WILD-TYPE  17  90 322  48
D1935V5, multiclass
    clus
vv   CCDC14 MUTATED CCDC14 WILD-TYPE
  T1              0               17
  T2              2               90
  T3              7              322
  T4              2               48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  CCDC14 MUTATED    10   0   1
  CCDC14 WILD-TYPE 277 113  86
D1935V6, multiclass
    clus
vv   CCDC14 MUTATED CCDC14 WILD-TYPE
  N0             10              277
  N1              0              113
  N2              1               86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1935V7, binary
                  cls
clus                 0   1
  CCDC14 MUTATED     8   1
  CCDC14 WILD-TYPE 367  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC14 MUTATED      8    1
  CCDC14 WILD-TYPE  367   64
   clus
vv  CCDC14 MUTATED CCDC14 WILD-TYPE
  0              8              367
  1              1               64
[1] 2 2
[1] FALSE
D1935V8, binary
                  cls
clus                 0   1
  CCDC14 MUTATED     2   9
  CCDC14 WILD-TYPE 223 255
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC14 MUTATED      2    9
  CCDC14 WILD-TYPE  223  255
        clus
vv       CCDC14 MUTATED CCDC14 WILD-TYPE
  FEMALE              2              223
  MALE                9              255
[1] 2 2
[1] FALSE
D1935V9, binary
                  cls
clus                 0   1
  CCDC14 MUTATED     8   1
  CCDC14 WILD-TYPE 342  21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC14 MUTATED      8    1
  CCDC14 WILD-TYPE  342   21
     clus
vv    CCDC14 MUTATED CCDC14 WILD-TYPE
  NO               8              342
  YES              1               21
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CCDC14 MUTATED                      9                             2
  CCDC14 WILD-TYPE                  306                            45
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CCDC14 MUTATED                       0                              0
  CCDC14 WILD-TYPE                   106                             10
D1935V10, multiclass
                                clus
vv                               CCDC14 MUTATED CCDC14 WILD-TYPE
  COLON ADENOCARCINOMA                        9              306
  COLON MUCINOUS ADENOCARCINOMA               2               45
  RECTAL ADENOCARCINOMA                       0              106
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  CCDC14 MUTATED     6   0   1   2
  CCDC14 WILD-TYPE 339   4  30  23
D1935V11, multiclass
    clus
vv   CCDC14 MUTATED CCDC14 WILD-TYPE
  R0              6              339
  R1              0                4
  R2              1               30
  RX              2               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1935V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CCDC14 MUTATED                                  0     2
  CCDC14 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  CCDC14 MUTATED                           0     4
  CCDC14 WILD-TYPE                        22   222
D1935V13, multiclass
                                  clus
vv                                 CCDC14 MUTATED CCDC14 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                9
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         4              222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1936) Variable = SKAP2 MUTATION ANALYSIS
D1936V1, survival
                 sevent
clus2               0   1
  SKAP2 MUTATED     2   3
  SKAP2 WILD-TYPE 376  90
  SKAP2 MUTATED SKAP2 WILD-TYPE 
              5             466 
  SKAP2 MUTATED SKAP2 WILD-TYPE 
              3              90 
$`SKAP2 MUTATED`
TCGA-AA-3543 TCGA-AA-A00N TCGA-AZ-4315 TCGA-CA-6718 TCGA-AG-A026 
        0.99         4.01        58.39        10.06         1.94 

$`SKAP2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       29.00        26.01        12.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       33.01        21.44        17.82         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       12.76        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  SKAP2 MUTATED SKAP2 WILD-TYPE 
           0.99            0.00 
  SKAP2 MUTATED SKAP2 WILD-TYPE 
          58.39          148.01 
  SKAP2 MUTATED SKAP2 WILD-TYPE 
          4.010          20.415 
[1] "1.0 - 58.4 (4.0)"   "0.0 - 148.0 (20.4)"
[1] "hr=" "4.9"
D1936V2, continuous
D1936V3, binary
                 cls
clus                0   1
  SKAP2 MUTATED     4   1
  SKAP2 WILD-TYPE 362 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SKAP2 MUTATED      4    1
  SKAP2 WILD-TYPE  362  118
        clus
vv       SKAP2 MUTATED SKAP2 WILD-TYPE
  COLON              4             362
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SKAP2 MUTATED         1        0        1         2         1         0
  SKAP2 WILD-TYPE      90        1       31       136         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SKAP2 MUTATED           0          0          0          0        0         0
  SKAP2 WILD-TYPE        24         11         59         42       48        18
                 vv
clus              STAGE IVB
  SKAP2 MUTATED           0
  SKAP2 WILD-TYPE         1
D1936V4, multiclass
            clus
vv           SKAP2 MUTATED SKAP2 WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              2             136
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  SKAP2 MUTATED     0   1   2   2
  SKAP2 WILD-TYPE  17  91 327  48
D1936V5, multiclass
    clus
vv   SKAP2 MUTATED SKAP2 WILD-TYPE
  T1             0              17
  T2             1              91
  T3             2             327
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  SKAP2 MUTATED     5   0   0
  SKAP2 WILD-TYPE 282 113  87
D1936V6, multiclass
    clus
vv   SKAP2 MUTATED SKAP2 WILD-TYPE
  N0             5             282
  N1             0             113
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1936V7, binary
                 cls
clus                0   1
  SKAP2 MUTATED     5   0
  SKAP2 WILD-TYPE 370  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SKAP2 MUTATED      5    0
  SKAP2 WILD-TYPE  370   65
   clus
vv  SKAP2 MUTATED SKAP2 WILD-TYPE
  0             5             370
  1             0              65
[1] 2 2
[1] FALSE
D1936V8, binary
                 cls
clus                0   1
  SKAP2 MUTATED     0   5
  SKAP2 WILD-TYPE 225 259
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SKAP2 MUTATED      0    5
  SKAP2 WILD-TYPE  225  259
        clus
vv       SKAP2 MUTATED SKAP2 WILD-TYPE
  FEMALE             0             225
  MALE               5             259
[1] 2 2
[1] FALSE
D1936V9, binary
                 cls
clus                0   1
  SKAP2 MUTATED     3   0
  SKAP2 WILD-TYPE 347  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SKAP2 MUTATED      3    0
  SKAP2 WILD-TYPE  347   22
     clus
vv    SKAP2 MUTATED SKAP2 WILD-TYPE
  NO              3             347
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SKAP2 MUTATED                      2                             2
  SKAP2 WILD-TYPE                  313                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SKAP2 MUTATED                       1                              0
  SKAP2 WILD-TYPE                   105                             10
D1936V10, multiclass
                                clus
vv                               SKAP2 MUTATED SKAP2 WILD-TYPE
  COLON ADENOCARCINOMA                       2             313
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  SKAP2 MUTATED     3   1   0   1
  SKAP2 WILD-TYPE 342   3  31  24
D1936V11, multiclass
    clus
vv   SKAP2 MUTATED SKAP2 WILD-TYPE
  R0             3             342
  R1             1               3
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1936V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SKAP2 MUTATED                                  0     1
  SKAP2 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  SKAP2 MUTATED                           0     1
  SKAP2 WILD-TYPE                        22   225
D1936V13, multiclass
[1] "Remove cluster labels:" "SKAP2 MUTATED"         
clus
  SKAP2 MUTATED SKAP2 WILD-TYPE 
              2             258 
     TCGA-A6-2671      TCGA-A6-2672      TCGA-A6-2674      TCGA-A6-2676 
"SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" 
     TCGA-A6-2677      TCGA-A6-2678      TCGA-A6-2683      TCGA-A6-3807 
"SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" 
     TCGA-A6-3808      TCGA-A6-3809      TCGA-A6-3810      TCGA-A6-4105 
"SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" 
     TCGA-A6-5656      TCGA-A6-5657      TCGA-A6-5659      TCGA-A6-5660 
"SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" 
     TCGA-A6-5661      TCGA-A6-5662      TCGA-A6-5664      TCGA-A6-5665 
"SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" 
     TCGA-A6-5666      TCGA-A6-6137      TCGA-A6-6138      TCGA-A6-6141 
"SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" 
     TCGA-A6-6142      TCGA-A6-6648      TCGA-A6-6649      TCGA-A6-6651 
"SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" 
     TCGA-A6-6652      TCGA-A6-6653      TCGA-A6-6654      TCGA-A6-6780 
"SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" 
     TCGA-A6-6781      TCGA-A6-6782      TCGA-AD-5900      TCGA-AD-6548 
"SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" 
     TCGA-AD-6888      TCGA-AD-6889      TCGA-AD-6890      TCGA-AD-6895 
"SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" 
     TCGA-AD-6899      TCGA-AD-6901      TCGA-AD-6963      TCGA-AD-6964 
"SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" 
     TCGA-AD-6965      TCGA-AU-3779      TCGA-AU-6004      TCGA-AY-4070 
"SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" 
     TCGA-AY-4071      TCGA-AY-5543      TCGA-AY-6196      TCGA-AY-6197 
"SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" 
     TCGA-AY-6386      TCGA-AZ-4323      TCGA-AZ-4616      TCGA-AZ-4681 
"SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" 
     TCGA-AZ-4682      TCGA-AZ-5403      TCGA-AZ-5407      TCGA-AZ-6598 
"SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" 
     TCGA-AZ-6599      TCGA-AZ-6600      TCGA-AZ-6601      TCGA-AZ-6603 
"SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" 
     TCGA-AZ-6605      TCGA-AZ-6606      TCGA-AZ-6607      TCGA-AZ-6608 
"SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" 
     TCGA-CA-5254      TCGA-CA-5255      TCGA-CA-5796      TCGA-CA-5797 
"SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" 
     TCGA-CA-6715      TCGA-CA-6716      TCGA-CA-6717      TCGA-CA-6719 
"SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" 
     TCGA-CK-4947      TCGA-CK-4948      TCGA-CK-4950      TCGA-CK-4952 
"SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" 
     TCGA-CK-5912      TCGA-CK-5913      TCGA-CK-5914      TCGA-CK-5915 
"SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" 
     TCGA-CK-5916      TCGA-CK-6746      TCGA-CK-6747      TCGA-CK-6748 
"SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" 
     TCGA-CK-6751      TCGA-CM-4743      TCGA-CM-4744      TCGA-CM-4746 
"SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" 
     TCGA-CM-4747      TCGA-CM-4752      TCGA-CM-5341      TCGA-CM-5344 
"SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" 
     TCGA-CM-5348      TCGA-CM-5349      TCGA-CM-5860      TCGA-CM-5861 
"SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" 
     TCGA-CM-5862      TCGA-CM-5863      TCGA-CM-5864      TCGA-CM-5868 
"SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" 
     TCGA-CM-6161      TCGA-CM-6162      TCGA-CM-6163      TCGA-CM-6164 
"SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" 
     TCGA-CM-6165      TCGA-CM-6166      TCGA-CM-6167      TCGA-CM-6168 
"SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" 
     TCGA-CM-6169      TCGA-CM-6170      TCGA-CM-6171      TCGA-CM-6172 
"SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" 
     TCGA-CM-6674      TCGA-CM-6675      TCGA-CM-6676      TCGA-CM-6677 
"SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" 
     TCGA-CM-6678      TCGA-CM-6679      TCGA-CM-6680      TCGA-D5-5537 
"SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" 
     TCGA-D5-5538      TCGA-D5-5539      TCGA-D5-5540      TCGA-D5-5541 
"SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" 
     TCGA-D5-6529      TCGA-D5-6532      TCGA-D5-6533      TCGA-D5-6534 
"SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" 
     TCGA-D5-6535      TCGA-D5-6536      TCGA-D5-6537      TCGA-D5-6538 
"SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" 
     TCGA-D5-6539      TCGA-D5-6540      TCGA-D5-6541      TCGA-D5-6898 
"SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" 
     TCGA-D5-6920      TCGA-D5-6922      TCGA-D5-6923      TCGA-D5-6924 
"SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" 
     TCGA-D5-6926      TCGA-D5-6927      TCGA-D5-6928      TCGA-D5-6929 
"SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" 
     TCGA-D5-6930      TCGA-D5-6931      TCGA-D5-6932      TCGA-D5-7000 
"SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" 
     TCGA-DM-A0X9      TCGA-DM-A0XD      TCGA-DM-A0XF      TCGA-DM-A1D0 
"SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" 
     TCGA-DM-A1D4      TCGA-DM-A1D6      TCGA-DM-A1D7      TCGA-DM-A1D8 
"SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" 
     TCGA-DM-A1D9      TCGA-DM-A1DA      TCGA-DM-A1DB      TCGA-DM-A1HA 
"SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" 
     TCGA-DM-A1HB      TCGA-DM-A282      TCGA-DM-A285      TCGA-DM-A28C 
"SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" 
     TCGA-DM-A28E      TCGA-DM-A28F      TCGA-DM-A28G      TCGA-DM-A28H 
"SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" 
     TCGA-DM-A28K      TCGA-F4-6459      TCGA-F4-6460      TCGA-F4-6569 
"SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" 
     TCGA-F4-6570      TCGA-F4-6703      TCGA-F4-6704      TCGA-F4-6805 
"SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" 
     TCGA-F4-6806      TCGA-F4-6807      TCGA-F4-6808      TCGA-F4-6809 
"SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" 
     TCGA-F4-6854      TCGA-F4-6855      TCGA-F4-6856      TCGA-G4-6293 
"SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" 
     TCGA-G4-6299      TCGA-G4-6303      TCGA-G4-6304      TCGA-G4-6306 
"SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" 
     TCGA-G4-6307      TCGA-G4-6309      TCGA-G4-6310      TCGA-G4-6315 
"SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" 
     TCGA-G4-6317      TCGA-G4-6321      TCGA-G4-6323      TCGA-G4-6586 
"SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" 
     TCGA-G4-6588      TCGA-G4-6625      TCGA-G4-6626      TCGA-G4-6628 
"SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" 
     TCGA-AF-2687      TCGA-AF-2689      TCGA-AF-2691      TCGA-AF-2692 
"SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" 
     TCGA-AF-2693      TCGA-AF-3400      TCGA-AF-3913      TCGA-AF-4110 
"SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" 
     TCGA-AF-5654      TCGA-AF-6136      TCGA-AF-6655      TCGA-AF-6672 
"SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" 
     TCGA-AH-6544      TCGA-AH-6547      TCGA-AH-6549      TCGA-AH-6643 
"SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" 
     TCGA-AH-6644      TCGA-CI-6619      TCGA-CI-6620      TCGA-CI-6621 
"SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" 
     TCGA-CI-6622      TCGA-CI-6624      TCGA-CL-5917      TCGA-CL-5918 
"SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" 
     TCGA-DC-5337      TCGA-DC-5869      TCGA-DC-6155      TCGA-DC-6157 
"SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" 
     TCGA-DC-6158      TCGA-DC-6160      TCGA-DC-6681      TCGA-DC-6682 
"SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" 
     TCGA-DC-6683      TCGA-DT-5265      TCGA-DY-A0XA      TCGA-DY-A1DC 
"SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" 
     TCGA-DY-A1DD      TCGA-DY-A1DF      TCGA-DY-A1DG      TCGA-DY-A1H8 
"SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" 
     TCGA-EF-5830      TCGA-EI-6506      TCGA-EI-6507      TCGA-EI-6508 
"SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" 
     TCGA-EI-6510      TCGA-F5-6464      TCGA-F5-6465      TCGA-F5-6571 
"SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" 
     TCGA-F5-6702      TCGA-F5-6811      TCGA-F5-6812      TCGA-F5-6813 
"SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" 
     TCGA-G5-6235      TCGA-G5-6641 
"SKAP2 WILD-TYPE" "SKAP2 WILD-TYPE" 

Clustering(1937) Variable = MYO1D MUTATION ANALYSIS
D1937V1, survival
                 sevent
clus2               0   1
  MYO1D MUTATED     8   3
  MYO1D WILD-TYPE 370  90
  MYO1D MUTATED MYO1D WILD-TYPE 
             11             460 
  MYO1D MUTATED MYO1D WILD-TYPE 
              3              90 
$`MYO1D MUTATED`
TCGA-AA-3510 TCGA-AA-3697 TCGA-AA-3811 TCGA-AA-3864 TCGA-AA-A00N TCGA-CA-6717 
       63.98        85.05        10.06        53.00         4.01        12.76 
TCGA-CK-4950 TCGA-CM-5862 TCGA-CM-6674 TCGA-AG-3892 TCGA-AG-A002 
       85.45         5.03        12.95        13.02        20.98 

$`MYO1D WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 
       36.00         5.03        26.99        19.04        19.04        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        31.07        30.05        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07        12.20        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
       17.56       148.01        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       30.08        32.02        15.02        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 
       19.99         1.02        17.95        36.95        17.03        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  MYO1D MUTATED MYO1D WILD-TYPE 
           4.01            0.00 
  MYO1D MUTATED MYO1D WILD-TYPE 
          85.45          148.01 
  MYO1D MUTATED MYO1D WILD-TYPE 
         13.020          20.235 
[1] "4.0 - 85.5 (13.0)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1"  
D1937V2, continuous
D1937V3, binary
                 cls
clus                0   1
  MYO1D MUTATED     9   2
  MYO1D WILD-TYPE 357 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYO1D MUTATED      9    2
  MYO1D WILD-TYPE  357  117
        clus
vv       MYO1D MUTATED MYO1D WILD-TYPE
  COLON              9             357
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MYO1D MUTATED         2        0        2         2         1         0
  MYO1D WILD-TYPE      89        1       30       136         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MYO1D MUTATED           2          0          1          0        0         1
  MYO1D WILD-TYPE        22         11         58         42       48        17
                 vv
clus              STAGE IVB
  MYO1D MUTATED           0
  MYO1D WILD-TYPE         1
D1937V4, multiclass
            clus
vv           MYO1D MUTATED MYO1D WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA              2             136
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              2              22
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  MYO1D MUTATED     1   1   8   1
  MYO1D WILD-TYPE  16  91 321  49
D1937V5, multiclass
    clus
vv   MYO1D MUTATED MYO1D WILD-TYPE
  T1             1              16
  T2             1              91
  T3             8             321
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  MYO1D MUTATED     8   2   1
  MYO1D WILD-TYPE 279 111  86
D1937V6, multiclass
    clus
vv   MYO1D MUTATED MYO1D WILD-TYPE
  N0             8             279
  N1             2             111
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1937V7, binary
                 cls
clus                0   1
  MYO1D MUTATED    10   1
  MYO1D WILD-TYPE 365  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYO1D MUTATED     10    1
  MYO1D WILD-TYPE  365   64
   clus
vv  MYO1D MUTATED MYO1D WILD-TYPE
  0            10             365
  1             1              64
[1] 2 2
[1] FALSE
D1937V8, binary
                 cls
clus                0   1
  MYO1D MUTATED     3   8
  MYO1D WILD-TYPE 222 256
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYO1D MUTATED      3    8
  MYO1D WILD-TYPE  222  256
        clus
vv       MYO1D MUTATED MYO1D WILD-TYPE
  FEMALE             3             222
  MALE               8             256
[1] 2 2
[1] FALSE
D1937V9, binary
                 cls
clus                0   1
  MYO1D MUTATED    10   0
  MYO1D WILD-TYPE 340  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYO1D MUTATED     10    0
  MYO1D WILD-TYPE  340   22
     clus
vv    MYO1D MUTATED MYO1D WILD-TYPE
  NO             10             340
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MYO1D MUTATED                      7                             2
  MYO1D WILD-TYPE                  308                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MYO1D MUTATED                       2                              0
  MYO1D WILD-TYPE                   104                             10
D1937V10, multiclass
                                clus
vv                               MYO1D MUTATED MYO1D WILD-TYPE
  COLON ADENOCARCINOMA                       7             308
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  MYO1D MUTATED     9   1   0   1
  MYO1D WILD-TYPE 336   3  31  24
D1937V11, multiclass
    clus
vv   MYO1D MUTATED MYO1D WILD-TYPE
  R0             9             336
  R1             1               3
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1937V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MYO1D MUTATED                                  0     1
  MYO1D WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  MYO1D MUTATED                           1     2
  MYO1D WILD-TYPE                        21   224
D1937V13, multiclass
                                  clus
vv                                 MYO1D MUTATED MYO1D WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        2             224
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1938) Variable = ZNF608 MUTATION ANALYSIS
D1938V1, survival
                  sevent
clus2                0   1
  ZNF608 MUTATED    10   2
  ZNF608 WILD-TYPE 368  91
  ZNF608 MUTATED ZNF608 WILD-TYPE 
              12              459 
  ZNF608 MUTATED ZNF608 WILD-TYPE 
               2               91 
$`ZNF608 MUTATED`
TCGA-A6-6781 TCGA-AA-3510 TCGA-AA-3713 TCGA-CA-6717 TCGA-DM-A0XD TCGA-F4-6570 
       19.66        63.98        19.04        12.76        24.43         6.18 
TCGA-G4-6293 TCGA-G4-6586 TCGA-AF-2692 TCGA-AG-3887 TCGA-AG-A002 TCGA-DC-6682 
      133.18        35.80        13.55        36.95        20.98         4.01 

$`ZNF608 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XF 
        1.51        12.00        11.38        10.26       119.70        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
        8.61        31.96        35.74        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
       35.31        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       43.04        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
       19.99         1.02        17.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 
       13.97        27.95        10.98        19.99         5.95         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  ZNF608 MUTATED ZNF608 WILD-TYPE 
            4.01             0.00 
  ZNF608 MUTATED ZNF608 WILD-TYPE 
          133.18           148.01 
  ZNF608 MUTATED ZNF608 WILD-TYPE 
           20.32            20.19 
[1] "4.0 - 133.2 (20.3)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.4"
D1938V2, continuous
D1938V3, binary
                  cls
clus                 0   1
  ZNF608 MUTATED     9   3
  ZNF608 WILD-TYPE 357 116
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF608 MUTATED      9    3
  ZNF608 WILD-TYPE  357  116
        clus
vv       ZNF608 MUTATED ZNF608 WILD-TYPE
  COLON               9              357
  RECTUM              3              116
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZNF608 MUTATED         1        0        1         8         0         0
  ZNF608 WILD-TYPE      90        1       31       130        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF608 MUTATED           1          0          0          1        1
  ZNF608 WILD-TYPE        23         11         59         41       47
                  vv
clus               STAGE IVA STAGE IVB
  ZNF608 MUTATED           0         0
  ZNF608 WILD-TYPE        18         1
D1938V4, multiclass
            clus
vv           ZNF608 MUTATED ZNF608 WILD-TYPE
  STAGE I                 1               90
  STAGE IA                0                1
  STAGE II                1               31
  STAGE IIA               8              130
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               1               23
  STAGE IIIA              0               11
  STAGE IIIB              0               59
  STAGE IIIC              1               41
  STAGE IV                1               47
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZNF608 MUTATED     0   1  11   1
  ZNF608 WILD-TYPE  17  91 318  49
D1938V5, multiclass
    clus
vv   ZNF608 MUTATED ZNF608 WILD-TYPE
  T1              0               17
  T2              1               91
  T3             11              318
  T4              1               49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  ZNF608 MUTATED    11   2   0
  ZNF608 WILD-TYPE 276 111  87
D1938V6, multiclass
    clus
vv   ZNF608 MUTATED ZNF608 WILD-TYPE
  N0             11              276
  N1              2              111
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1938V7, binary
                  cls
clus                 0   1
  ZNF608 MUTATED    11   1
  ZNF608 WILD-TYPE 364  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF608 MUTATED     11    1
  ZNF608 WILD-TYPE  364   64
   clus
vv  ZNF608 MUTATED ZNF608 WILD-TYPE
  0             11              364
  1              1               64
[1] 2 2
[1] FALSE
D1938V8, binary
                  cls
clus                 0   1
  ZNF608 MUTATED     5   8
  ZNF608 WILD-TYPE 220 256
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF608 MUTATED      5    8
  ZNF608 WILD-TYPE  220  256
        clus
vv       ZNF608 MUTATED ZNF608 WILD-TYPE
  FEMALE              5              220
  MALE                8              256
[1] 2 2
[1] FALSE
D1938V9, binary
                  cls
clus                 0   1
  ZNF608 MUTATED     8   2
  ZNF608 WILD-TYPE 342  20
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF608 MUTATED      8    2
  ZNF608 WILD-TYPE  342   20
     clus
vv    ZNF608 MUTATED ZNF608 WILD-TYPE
  NO               8              342
  YES              2               20
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ZNF608 MUTATED                      7                             2
  ZNF608 WILD-TYPE                  308                            45
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ZNF608 MUTATED                       2                              1
  ZNF608 WILD-TYPE                   104                              9
D1938V10, multiclass
                                clus
vv                               ZNF608 MUTATED ZNF608 WILD-TYPE
  COLON ADENOCARCINOMA                        7              308
  COLON MUCINOUS ADENOCARCINOMA               2               45
  RECTAL ADENOCARCINOMA                       2              104
  RECTAL MUCINOUS ADENOCARCINOMA              1                9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ZNF608 MUTATED    10   0   1   1
  ZNF608 WILD-TYPE 335   4  30  24
D1938V11, multiclass
    clus
vv   ZNF608 MUTATED ZNF608 WILD-TYPE
  R0             10              335
  R1              0                4
  R2              1               30
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1938V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF608 MUTATED                                  0     1
  ZNF608 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZNF608 MUTATED                           0     7
  ZNF608 WILD-TYPE                        22   219
D1938V13, multiclass
                                  clus
vv                                 ZNF608 MUTATED ZNF608 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         7              219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1939) Variable = IDE MUTATION ANALYSIS
D1939V1, survival
               sevent
clus2             0   1
  IDE MUTATED    10   2
  IDE WILD-TYPE 368  91
  IDE MUTATED IDE WILD-TYPE 
           12           459 
  IDE MUTATED IDE WILD-TYPE 
            2            91 
$`IDE MUTATED`
TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3697 TCGA-AA-3844 TCGA-AA-3982 TCGA-AA-A010 
        3.02         1.02        85.05        14.93        27.02        34.98 
TCGA-AD-6890 TCGA-CM-5861 TCGA-D5-6932 TCGA-AG-3892 TCGA-AG-A002 TCGA-DY-A1DF 
        0.79        15.02        11.38        13.02        20.98        24.13 

$`IDE WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3502 
       23.87        20.12        19.66        20.28         7.04        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       38.99        37.02         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3986 TCGA-AA-3989 
       26.01        25.02        24.00        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       21.37        15.52        56.55         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       30.08        32.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 
       11.64         4.80         1.51        12.00        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 
       19.99         1.02        17.95        36.95        17.03        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DG 
        5.03         5.29       126.44        41.36        57.24        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  IDE MUTATED IDE WILD-TYPE 
         0.79          0.00 
  IDE MUTATED IDE WILD-TYPE 
        85.05        148.01 
  IDE MUTATED IDE WILD-TYPE 
       14.975        20.280 
[1] "0.8 - 85.0 (15.0)"  "0.0 - 148.0 (20.3)"
[1] "hr=" "1.1"
D1939V2, continuous
D1939V3, binary
               cls
clus              0   1
  IDE MUTATED    10   3
  IDE WILD-TYPE 356 116
[1] "tbl2"
               cls
clus            [,1] [,2]
  IDE MUTATED     10    3
  IDE WILD-TYPE  356  116
        clus
vv       IDE MUTATED IDE WILD-TYPE
  COLON           10           356
  RECTUM           3           116
[1] 2 2
[1] FALSE
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  IDE MUTATED         2        0        2         3         1         0
  IDE WILD-TYPE      89        1       30       135         9         1
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  IDE MUTATED           1          0          1          2        0         0
  IDE WILD-TYPE        23         11         58         40       48        18
               vv
clus            STAGE IVB
  IDE MUTATED           0
  IDE WILD-TYPE         1
D1939V4, multiclass
            clus
vv           IDE MUTATED IDE WILD-TYPE
  STAGE I              2            89
  STAGE IA             0             1
  STAGE II             2            30
  STAGE IIA            3           135
  STAGE IIB            1             9
  STAGE IIC            0             1
  STAGE III            1            23
  STAGE IIIA           0            11
  STAGE IIIB           1            58
  STAGE IIIC           2            40
  STAGE IV             0            48
  STAGE IVA            0            18
  STAGE IVB            0             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  IDE MUTATED     2   1   9   1
  IDE WILD-TYPE  15  91 320  49
D1939V5, multiclass
    clus
vv   IDE MUTATED IDE WILD-TYPE
  T1           2            15
  T2           1            91
  T3           9           320
  T4           1            49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2
  IDE MUTATED    10   1   2
  IDE WILD-TYPE 277 112  85
D1939V6, multiclass
    clus
vv   IDE MUTATED IDE WILD-TYPE
  N0          10           277
  N1           1           112
  N2           2            85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1939V7, binary
               cls
clus              0   1
  IDE MUTATED    12   0
  IDE WILD-TYPE 363  65
[1] "tbl2"
               cls
clus            [,1] [,2]
  IDE MUTATED     12    0
  IDE WILD-TYPE  363   65
   clus
vv  IDE MUTATED IDE WILD-TYPE
  0          12           363
  1           0            65
[1] 2 2
[1] FALSE
D1939V8, binary
               cls
clus              0   1
  IDE MUTATED     8   5
  IDE WILD-TYPE 217 259
[1] "tbl2"
               cls
clus            [,1] [,2]
  IDE MUTATED      8    5
  IDE WILD-TYPE  217  259
        clus
vv       IDE MUTATED IDE WILD-TYPE
  FEMALE           8           217
  MALE             5           259
[1] 2 2
[1] FALSE
D1939V9, binary
               cls
clus              0   1
  IDE MUTATED     8   1
  IDE WILD-TYPE 342  21
[1] "tbl2"
               cls
clus            [,1] [,2]
  IDE MUTATED      8    1
  IDE WILD-TYPE  342   21
     clus
vv    IDE MUTATED IDE WILD-TYPE
  NO            8           342
  YES           1            21
[1] 2 2
[1] FALSE
               vv
clus            COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  IDE MUTATED                     10                             0
  IDE WILD-TYPE                  305                            47
               vv
clus            RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  IDE MUTATED                       3                              0
  IDE WILD-TYPE                   103                             10
D1939V10, multiclass
                                clus
vv                               IDE MUTATED IDE WILD-TYPE
  COLON ADENOCARCINOMA                    10           305
  COLON MUCINOUS ADENOCARCINOMA            0            47
  RECTAL ADENOCARCINOMA                    3           103
  RECTAL MUCINOUS ADENOCARCINOMA           0            10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             R0  R1  R2  RX
  IDE MUTATED    10   0   0   0
  IDE WILD-TYPE 335   4  31  25
D1939V11, multiclass
    clus
vv   IDE MUTATED IDE WILD-TYPE
  R0          10           335
  R1           0             4
  R2           0            31
  RX           0            25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1939V12, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  IDE MUTATED                                  0     0
  IDE WILD-TYPE                                1    11
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  IDE MUTATED                           0     4
  IDE WILD-TYPE                        22   222
D1939V13, multiclass
                                  clus
vv                                 IDE MUTATED IDE WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      0            11
  BLACK OR AFRICAN AMERICAN                  0            22
  WHITE                                      4           222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1940) Variable = BEX5 MUTATION ANALYSIS
D1940V1, survival
                sevent
clus2              0   1
  BEX5 MUTATED     5   2
  BEX5 WILD-TYPE 373  91
  BEX5 MUTATED BEX5 WILD-TYPE 
             7            464 
  BEX5 MUTATED BEX5 WILD-TYPE 
             2             91 
$`BEX5 MUTATED`
TCGA-AA-3854 TCGA-AA-3966 TCGA-AD-6964 TCGA-CM-5349 TCGA-D5-6541 TCGA-G4-6293 
       36.03         2.01        10.88        30.08        15.58       133.18 
TCGA-G4-6303 
       65.85 

$`BEX5 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
        2.01        20.98        34.03        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5861 
       13.02        29.06        22.03        22.98        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       12.49        16.14         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
       47.41        35.31        74.56        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  BEX5 MUTATED BEX5 WILD-TYPE 
          2.01           0.00 
  BEX5 MUTATED BEX5 WILD-TYPE 
        133.18         148.01 
  BEX5 MUTATED BEX5 WILD-TYPE 
        30.080         20.155 
[1] "2.0 - 133.2 (30.1)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1"  
D1940V2, continuous
D1940V3, binary
                cls
clus               0   1
  BEX5 MUTATED     7   0
  BEX5 WILD-TYPE 359 119
[1] "tbl2"
                cls
clus             [,1] [,2]
  BEX5 MUTATED      7    0
  BEX5 WILD-TYPE  359  119
        clus
vv       BEX5 MUTATED BEX5 WILD-TYPE
  COLON             7            359
  RECTUM            0            119
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  BEX5 MUTATED         1        0        0         3         0         0
  BEX5 WILD-TYPE      90        1       32       135        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  BEX5 MUTATED           1          0          0          0        1         0
  BEX5 WILD-TYPE        23         11         59         42       47        18
                vv
clus             STAGE IVB
  BEX5 MUTATED           0
  BEX5 WILD-TYPE         1
D1940V4, multiclass
            clus
vv           BEX5 MUTATED BEX5 WILD-TYPE
  STAGE I               1             90
  STAGE IA              0              1
  STAGE II              0             32
  STAGE IIA             3            135
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             1             23
  STAGE IIIA            0             11
  STAGE IIIB            0             59
  STAGE IIIC            0             42
  STAGE IV              1             47
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  BEX5 MUTATED     0   1   5   1
  BEX5 WILD-TYPE  17  91 324  49
D1940V5, multiclass
    clus
vv   BEX5 MUTATED BEX5 WILD-TYPE
  T1            0             17
  T2            1             91
  T3            5            324
  T4            1             49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  BEX5 MUTATED     4   2   1
  BEX5 WILD-TYPE 283 111  86
D1940V6, multiclass
    clus
vv   BEX5 MUTATED BEX5 WILD-TYPE
  N0            4            283
  N1            2            111
  N2            1             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1940V7, binary
                cls
clus               0   1
  BEX5 MUTATED     5   1
  BEX5 WILD-TYPE 370  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  BEX5 MUTATED      5    1
  BEX5 WILD-TYPE  370   64
   clus
vv  BEX5 MUTATED BEX5 WILD-TYPE
  0            5            370
  1            1             64
[1] 2 2
[1] FALSE
D1940V8, binary
                cls
clus               0   1
  BEX5 MUTATED     5   2
  BEX5 WILD-TYPE 220 262
[1] "tbl2"
                cls
clus             [,1] [,2]
  BEX5 MUTATED      5    2
  BEX5 WILD-TYPE  220  262
        clus
vv       BEX5 MUTATED BEX5 WILD-TYPE
  FEMALE            5            220
  MALE              2            262
[1] 2 2
[1] FALSE
D1940V9, binary
                cls
clus               0   1
  BEX5 MUTATED     6   0
  BEX5 WILD-TYPE 344  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  BEX5 MUTATED      6    0
  BEX5 WILD-TYPE  344   22
     clus
vv    BEX5 MUTATED BEX5 WILD-TYPE
  NO             6            344
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  BEX5 MUTATED                      5                             2
  BEX5 WILD-TYPE                  310                            45
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  BEX5 MUTATED                       0                              0
  BEX5 WILD-TYPE                   106                             10
D1940V10, multiclass
                                clus
vv                               BEX5 MUTATED BEX5 WILD-TYPE
  COLON ADENOCARCINOMA                      5            310
  COLON MUCINOUS ADENOCARCINOMA             2             45
  RECTAL ADENOCARCINOMA                     0            106
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  BEX5 MUTATED     5   0   0   0
  BEX5 WILD-TYPE 340   4  31  25
D1940V11, multiclass
    clus
vv   BEX5 MUTATED BEX5 WILD-TYPE
  R0            5            340
  R1            0              4
  R2            0             31
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1940V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  BEX5 MUTATED                                  0     0
  BEX5 WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  BEX5 MUTATED                           0     5
  BEX5 WILD-TYPE                        22   221
D1940V13, multiclass
                                  clus
vv                                 BEX5 MUTATED BEX5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       5            221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1941) Variable = AGBL5 MUTATION ANALYSIS
D1941V1, survival
                 sevent
clus2               0   1
  AGBL5 MUTATED    11   2
  AGBL5 WILD-TYPE 367  91
  AGBL5 MUTATED AGBL5 WILD-TYPE 
             13             458 
  AGBL5 MUTATED AGBL5 WILD-TYPE 
              2              91 
$`AGBL5 MUTATED`
TCGA-A6-5661 TCGA-A6-6653 TCGA-A6-6781 TCGA-AA-A00J TCGA-AA-A00N TCGA-AD-5900 
       33.53        24.39        19.66        18.05         4.01         0.07 
TCGA-AD-6895 TCGA-AY-6197 TCGA-AZ-6608 TCGA-CM-4746 TCGA-DM-A1HB TCGA-G4-6309 
        0.72        21.44         1.61        37.02       135.65        85.48 
TCGA-AG-3892 
       13.02 

$`AGBL5 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 
       25.18        24.16        21.76        24.69        23.87        20.12 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       30.02        34.03        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       21.37        15.52        56.55         0.79         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        33.01        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4752 
        1.91       124.27        23.05        20.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 
      140.38         7.50        44.32       131.51       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       44.68        55.04        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       36.95        17.03        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  AGBL5 MUTATED AGBL5 WILD-TYPE 
           0.07            0.00 
  AGBL5 MUTATED AGBL5 WILD-TYPE 
         135.65          148.01 
  AGBL5 MUTATED AGBL5 WILD-TYPE 
         19.660          20.235 
[1] "0.1 - 135.7 (19.7)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.3"
D1941V2, continuous
D1941V3, binary
                 cls
clus                0   1
  AGBL5 MUTATED    12   1
  AGBL5 WILD-TYPE 354 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AGBL5 MUTATED     12    1
  AGBL5 WILD-TYPE  354  118
        clus
vv       AGBL5 MUTATED AGBL5 WILD-TYPE
  COLON             12             354
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  AGBL5 MUTATED         4        0        0         2         1         0
  AGBL5 WILD-TYPE      87        1       32       136         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AGBL5 MUTATED           0          1          3          1        0         0
  AGBL5 WILD-TYPE        24         10         56         41       48        18
                 vv
clus              STAGE IVB
  AGBL5 MUTATED           0
  AGBL5 WILD-TYPE         1
D1941V4, multiclass
            clus
vv           AGBL5 MUTATED AGBL5 WILD-TYPE
  STAGE I                4              87
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              2             136
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             1              10
  STAGE IIIB             3              56
  STAGE IIIC             1              41
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  AGBL5 MUTATED     1   4   5   3
  AGBL5 WILD-TYPE  16  88 324  47
D1941V5, multiclass
    clus
vv   AGBL5 MUTATED AGBL5 WILD-TYPE
  T1             1              16
  T2             4              88
  T3             5             324
  T4             3              47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  AGBL5 MUTATED     7   6   0
  AGBL5 WILD-TYPE 280 107  87
D1941V6, multiclass
    clus
vv   AGBL5 MUTATED AGBL5 WILD-TYPE
  N0             7             280
  N1             6             107
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1941V7, binary
                 cls
clus                0   1
  AGBL5 MUTATED     9   0
  AGBL5 WILD-TYPE 366  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AGBL5 MUTATED      9    0
  AGBL5 WILD-TYPE  366   65
   clus
vv  AGBL5 MUTATED AGBL5 WILD-TYPE
  0             9             366
  1             0              65
[1] 2 2
[1] FALSE
D1941V8, binary
                 cls
clus                0   1
  AGBL5 MUTATED     4   9
  AGBL5 WILD-TYPE 221 255
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AGBL5 MUTATED      4    9
  AGBL5 WILD-TYPE  221  255
        clus
vv       AGBL5 MUTATED AGBL5 WILD-TYPE
  FEMALE             4             221
  MALE               9             255
[1] 2 2
[1] FALSE
D1941V9, binary
                 cls
clus                0   1
  AGBL5 MUTATED     9   0
  AGBL5 WILD-TYPE 341  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AGBL5 MUTATED      9    0
  AGBL5 WILD-TYPE  341   22
     clus
vv    AGBL5 MUTATED AGBL5 WILD-TYPE
  NO              9             341
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  AGBL5 MUTATED                      7                             4
  AGBL5 WILD-TYPE                  308                            43
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  AGBL5 MUTATED                       1                              0
  AGBL5 WILD-TYPE                   105                             10
D1941V10, multiclass
                                clus
vv                               AGBL5 MUTATED AGBL5 WILD-TYPE
  COLON ADENOCARCINOMA                       7             308
  COLON MUCINOUS ADENOCARCINOMA              4              43
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  AGBL5 MUTATED     9   0   0   0
  AGBL5 WILD-TYPE 336   4  31  25
D1941V11, multiclass
    clus
vv   AGBL5 MUTATED AGBL5 WILD-TYPE
  R0             9             336
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1941V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AGBL5 MUTATED                                  0     0
  AGBL5 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  AGBL5 MUTATED                           3     7
  AGBL5 WILD-TYPE                        19   219
D1941V13, multiclass
                                  clus
vv                                 AGBL5 MUTATED AGBL5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    3              19
  WHITE                                        7             219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1942) Variable = LDLR MUTATION ANALYSIS
D1942V1, survival
                sevent
clus2              0   1
  LDLR MUTATED    10   2
  LDLR WILD-TYPE 368  91
  LDLR MUTATED LDLR WILD-TYPE 
            12            459 
  LDLR MUTATED LDLR WILD-TYPE 
             2             91 
$`LDLR MUTATED`
TCGA-A6-5662 TCGA-A6-5665 TCGA-A6-6780 TCGA-AA-3821 TCGA-AA-3864 TCGA-AA-3977 
       23.61        22.06        20.12         1.02        53.00        25.02 
TCGA-AA-A00N TCGA-AZ-6598 TCGA-CA-6717 TCGA-D5-6532 TCGA-AG-A002 TCGA-EF-5830 
        4.01        49.41        12.76        18.25        20.98         0.49 

$`LDLR WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        33.53        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6781 
       24.16        21.76        24.69        24.39        23.87        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
       33.04         0.99        25.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       31.07        30.05        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 
        5.13       106.75        22.36        62.79        88.21         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.20        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       51.48        32.61        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  LDLR MUTATED LDLR WILD-TYPE 
          0.49           0.00 
  LDLR MUTATED LDLR WILD-TYPE 
         53.00         148.01 
  LDLR MUTATED LDLR WILD-TYPE 
         20.55          20.19 
[1] "0.5 - 53.0 (20.6)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1"  
D1942V2, continuous
D1942V3, binary
                cls
clus               0   1
  LDLR MUTATED    10   2
  LDLR WILD-TYPE 356 117
[1] "tbl2"
                cls
clus             [,1] [,2]
  LDLR MUTATED     10    2
  LDLR WILD-TYPE  356  117
        clus
vv       LDLR MUTATED LDLR WILD-TYPE
  COLON            10            356
  RECTUM            2            117
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  LDLR MUTATED         2        0        2         4         2         0
  LDLR WILD-TYPE      89        1       30       134         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  LDLR MUTATED           0          0          0          0        0         1
  LDLR WILD-TYPE        24         11         59         42       48        17
                vv
clus             STAGE IVB
  LDLR MUTATED           0
  LDLR WILD-TYPE         1
D1942V4, multiclass
            clus
vv           LDLR MUTATED LDLR WILD-TYPE
  STAGE I               2             89
  STAGE IA              0              1
  STAGE II              2             30
  STAGE IIA             4            134
  STAGE IIB             2              8
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            0             59
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             1             17
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  LDLR MUTATED     0   3   7   2
  LDLR WILD-TYPE  17  89 322  48
D1942V5, multiclass
    clus
vv   LDLR MUTATED LDLR WILD-TYPE
  T1            0             17
  T2            3             89
  T3            7            322
  T4            2             48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  LDLR MUTATED    11   0   1
  LDLR WILD-TYPE 276 113  86
D1942V6, multiclass
    clus
vv   LDLR MUTATED LDLR WILD-TYPE
  N0           11            276
  N1            0            113
  N2            1             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1942V7, binary
                cls
clus               0   1
  LDLR MUTATED     8   1
  LDLR WILD-TYPE 367  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  LDLR MUTATED      8    1
  LDLR WILD-TYPE  367   64
   clus
vv  LDLR MUTATED LDLR WILD-TYPE
  0            8            367
  1            1             64
[1] 2 2
[1] FALSE
D1942V8, binary
                cls
clus               0   1
  LDLR MUTATED     3   9
  LDLR WILD-TYPE 222 255
[1] "tbl2"
                cls
clus             [,1] [,2]
  LDLR MUTATED      3    9
  LDLR WILD-TYPE  222  255
        clus
vv       LDLR MUTATED LDLR WILD-TYPE
  FEMALE            3            222
  MALE              9            255
[1] 2 2
[1] FALSE
D1942V9, binary
                cls
clus               0   1
  LDLR MUTATED    10   0
  LDLR WILD-TYPE 340  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  LDLR MUTATED     10    0
  LDLR WILD-TYPE  340   22
     clus
vv    LDLR MUTATED LDLR WILD-TYPE
  NO            10            340
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  LDLR MUTATED                      6                             4
  LDLR WILD-TYPE                  309                            43
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  LDLR MUTATED                       2                              0
  LDLR WILD-TYPE                   104                             10
D1942V10, multiclass
                                clus
vv                               LDLR MUTATED LDLR WILD-TYPE
  COLON ADENOCARCINOMA                      6            309
  COLON MUCINOUS ADENOCARCINOMA             4             43
  RECTAL ADENOCARCINOMA                     2            104
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  LDLR MUTATED     7   0   0   1
  LDLR WILD-TYPE 338   4  31  24
D1942V11, multiclass
    clus
vv   LDLR MUTATED LDLR WILD-TYPE
  R0            7            338
  R1            0              4
  R2            0             31
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1942V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  LDLR MUTATED                                  0     1
  LDLR WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  LDLR MUTATED                           0     6
  LDLR WILD-TYPE                        22   220
D1942V13, multiclass
                                  clus
vv                                 LDLR MUTATED LDLR WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       6            220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1943) Variable = NUF2 MUTATION ANALYSIS
D1943V1, survival
                sevent
clus2              0   1
  NUF2 MUTATED    12   4
  NUF2 WILD-TYPE 366  89
  NUF2 MUTATED NUF2 WILD-TYPE 
            16            455 
  NUF2 MUTATED NUF2 WILD-TYPE 
             4             89 
$`NUF2 MUTATED`
TCGA-A6-5661 TCGA-AA-3655 TCGA-AA-3713 TCGA-AA-3821 TCGA-AA-A00N TCGA-AA-A010 
       33.53        61.02        19.04         1.02         4.01        34.98 
TCGA-AD-6888 TCGA-AY-6197 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-CA-6717 TCGA-CM-5861 
       15.52        21.44        49.41        12.10        12.76        15.02 
TCGA-D5-6536 TCGA-F4-6703 TCGA-AG-A002 TCGA-EI-6507 
       17.85        47.87        20.98        19.96 

$`NUF2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       19.99        13.94        19.99        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
       33.04         0.99        25.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       21.37        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        33.01        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6601 
      106.75        22.36        62.79        88.21         6.77       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07        12.20        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 
       22.03        22.98        30.08        32.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       15.12         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       35.74         6.18         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  NUF2 MUTATED NUF2 WILD-TYPE 
          1.02           0.00 
  NUF2 MUTATED NUF2 WILD-TYPE 
         61.02         148.01 
  NUF2 MUTATED NUF2 WILD-TYPE 
         19.50          20.28 
[1] "1.0 - 61.0 (19.5)"  "0.0 - 148.0 (20.3)"
[1] "hr=" "1.3"
D1943V2, continuous
D1943V3, binary
                cls
clus               0   1
  NUF2 MUTATED    14   2
  NUF2 WILD-TYPE 352 117
[1] "tbl2"
                cls
clus             [,1] [,2]
  NUF2 MUTATED     14    2
  NUF2 WILD-TYPE  352  117
        clus
vv       NUF2 MUTATED NUF2 WILD-TYPE
  COLON            14            352
  RECTUM            2            117
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NUF2 MUTATED         2        0        2         7         2         0
  NUF2 WILD-TYPE      89        1       30       131         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NUF2 MUTATED           0          0          1          0        2         0
  NUF2 WILD-TYPE        24         11         58         42       46        18
                vv
clus             STAGE IVB
  NUF2 MUTATED           0
  NUF2 WILD-TYPE         1
D1943V4, multiclass
            clus
vv           NUF2 MUTATED NUF2 WILD-TYPE
  STAGE I               2             89
  STAGE IA              0              1
  STAGE II              2             30
  STAGE IIA             7            131
  STAGE IIB             2              8
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            1             58
  STAGE IIIC            0             42
  STAGE IV              2             46
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  NUF2 MUTATED     0   2  11   3
  NUF2 WILD-TYPE  17  90 318  47
D1943V5, multiclass
    clus
vv   NUF2 MUTATED NUF2 WILD-TYPE
  T1            0             17
  T2            2             90
  T3           11            318
  T4            3             47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  NUF2 MUTATED    14   2   0
  NUF2 WILD-TYPE 273 111  87
D1943V6, multiclass
    clus
vv   NUF2 MUTATED NUF2 WILD-TYPE
  N0           14            273
  N1            2            111
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1943V7, binary
                cls
clus               0   1
  NUF2 MUTATED    12   2
  NUF2 WILD-TYPE 363  63
[1] "tbl2"
                cls
clus             [,1] [,2]
  NUF2 MUTATED     12    2
  NUF2 WILD-TYPE  363   63
   clus
vv  NUF2 MUTATED NUF2 WILD-TYPE
  0           12            363
  1            2             63
[1] 2 2
[1] FALSE
D1943V8, binary
                cls
clus               0   1
  NUF2 MUTATED     5  11
  NUF2 WILD-TYPE 220 253
[1] "tbl2"
                cls
clus             [,1] [,2]
  NUF2 MUTATED      5   11
  NUF2 WILD-TYPE  220  253
        clus
vv       NUF2 MUTATED NUF2 WILD-TYPE
  FEMALE            5            220
  MALE             11            253
[1] 2 2
[1] FALSE
D1943V9, binary
                cls
clus               0   1
  NUF2 MUTATED    13   1
  NUF2 WILD-TYPE 337  21
[1] "tbl2"
                cls
clus             [,1] [,2]
  NUF2 MUTATED     13    1
  NUF2 WILD-TYPE  337   21
     clus
vv    NUF2 MUTATED NUF2 WILD-TYPE
  NO            13            337
  YES            1             21
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  NUF2 MUTATED                     11                             3
  NUF2 WILD-TYPE                  304                            44
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  NUF2 MUTATED                       2                              0
  NUF2 WILD-TYPE                   104                             10
D1943V10, multiclass
                                clus
vv                               NUF2 MUTATED NUF2 WILD-TYPE
  COLON ADENOCARCINOMA                     11            304
  COLON MUCINOUS ADENOCARCINOMA             3             44
  RECTAL ADENOCARCINOMA                     2            104
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  NUF2 MUTATED    12   0   1   1
  NUF2 WILD-TYPE 333   4  30  24
D1943V11, multiclass
    clus
vv   NUF2 MUTATED NUF2 WILD-TYPE
  R0           12            333
  R1            0              4
  R2            1             30
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1943V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NUF2 MUTATED                                  0     1
  NUF2 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  NUF2 MUTATED                           2     7
  NUF2 WILD-TYPE                        20   219
D1943V13, multiclass
                                  clus
vv                                 NUF2 MUTATED NUF2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   2             20
  WHITE                                       7            219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1944) Variable = ZNF521 MUTATION ANALYSIS
D1944V1, survival
                  sevent
clus2                0   1
  ZNF521 MUTATED    23   9
  ZNF521 WILD-TYPE 355  84
  ZNF521 MUTATED ZNF521 WILD-TYPE 
              32              439 
  ZNF521 MUTATED ZNF521 WILD-TYPE 
               9               84 
$`ZNF521 MUTATED`
TCGA-A6-5661 TCGA-A6-6654 TCGA-A6-6781 TCGA-AA-3516 TCGA-AA-3525 TCGA-AA-3561 
       33.53        23.87        19.66        13.02         8.05        13.94 
TCGA-AA-3663 TCGA-AA-3950 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-A010 
        6.97        24.00        26.01        25.02        27.02        34.98 
TCGA-AA-A01R TCGA-AD-6964 TCGA-AZ-4315 TCGA-AZ-6601 TCGA-CA-6717 TCGA-CA-6718 
       35.01        10.88        58.39       100.01        12.76        10.06 
TCGA-CM-6161 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6930 TCGA-DM-A1D0 TCGA-DM-A28K 
       15.02        17.85         4.80         1.51       130.65        98.24 
TCGA-F4-6459 TCGA-F4-6809 TCGA-G4-6588 TCGA-AG-A002 TCGA-AG-A026 TCGA-F5-6464 
        8.61        13.25        26.17        20.98         1.94         9.96 
TCGA-F5-6813 TCGA-G5-6235 
        0.69        55.76 

$`ZNF521 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 
       25.18        24.16        21.76        24.69        24.39        20.12 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        6.97         1.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       37.05        36.03        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       23.01        20.98        19.99        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.05        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 
        2.01        12.99        24.00        33.01        26.01         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3986 TCGA-AA-3989 
       13.05        34.06        24.00        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       33.01        21.44        17.82         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 
        3.06         3.25         3.29         0.07        12.20        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       15.02        17.03        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        4.80        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
       38.20        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-F4-6460 
       81.37       119.93        35.97        60.79       117.07        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       16.24        33.67         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
       18.28        49.51        31.30        28.57        32.19         0.66 
TCGA-G5-6641 
       26.43 

  ZNF521 MUTATED ZNF521 WILD-TYPE 
            0.69             0.00 
  ZNF521 MUTATED ZNF521 WILD-TYPE 
          130.65           148.01 
  ZNF521 MUTATED ZNF521 WILD-TYPE 
          18.755           20.280 
[1] "0.7 - 130.7 (18.8)" "0.0 - 148.0 (20.3)"
[1] "hr=" "1.5"
D1944V2, continuous
D1944V3, binary
                  cls
clus                 0   1
  ZNF521 MUTATED    28   6
  ZNF521 WILD-TYPE 338 113
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF521 MUTATED     28    6
  ZNF521 WILD-TYPE  338  113
        clus
vv       ZNF521 MUTATED ZNF521 WILD-TYPE
  COLON              28              338
  RECTUM              6              113
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZNF521 MUTATED         2        0        3        12         1         0
  ZNF521 WILD-TYPE      89        1       29       126         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF521 MUTATED           2          1          7          3        0
  ZNF521 WILD-TYPE        22         10         52         39       48
                  vv
clus               STAGE IVA STAGE IVB
  ZNF521 MUTATED           1         0
  ZNF521 WILD-TYPE        17         1
D1944V4, multiclass
            clus
vv           ZNF521 MUTATED ZNF521 WILD-TYPE
  STAGE I                 2               89
  STAGE IA                0                1
  STAGE II                3               29
  STAGE IIA              12              126
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               2               22
  STAGE IIIA              1               10
  STAGE IIIB              7               52
  STAGE IIIC              3               39
  STAGE IV                0               48
  STAGE IVA               1               17
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZNF521 MUTATED     0   4  24   6
  ZNF521 WILD-TYPE  17  88 305  44
D1944V5, multiclass
    clus
vv   ZNF521 MUTATED ZNF521 WILD-TYPE
  T1              0               17
  T2              4               88
  T3             24              305
  T4              6               44
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  ZNF521 MUTATED    19   9   6
  ZNF521 WILD-TYPE 268 104  81
D1944V6, multiclass
    clus
vv   ZNF521 MUTATED ZNF521 WILD-TYPE
  N0             19              268
  N1              9              104
  N2              6               81
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1944V7, binary
                  cls
clus                 0   1
  ZNF521 MUTATED    28   1
  ZNF521 WILD-TYPE 347  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF521 MUTATED     28    1
  ZNF521 WILD-TYPE  347   64
   clus
vv  ZNF521 MUTATED ZNF521 WILD-TYPE
  0             28              347
  1              1               64
[1] 2 2
[1] FALSE
D1944V8, binary
                  cls
clus                 0   1
  ZNF521 MUTATED    13  21
  ZNF521 WILD-TYPE 212 243
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF521 MUTATED     13   21
  ZNF521 WILD-TYPE  212  243
        clus
vv       ZNF521 MUTATED ZNF521 WILD-TYPE
  FEMALE             13              212
  MALE               21              243
[1] 2 2
[1] FALSE
D1944V9, binary
                  cls
clus                 0   1
  ZNF521 MUTATED    26   1
  ZNF521 WILD-TYPE 324  21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF521 MUTATED     26    1
  ZNF521 WILD-TYPE  324   21
     clus
vv    ZNF521 MUTATED ZNF521 WILD-TYPE
  NO              26              324
  YES              1               21
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ZNF521 MUTATED                     21                             7
  ZNF521 WILD-TYPE                  294                            40
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ZNF521 MUTATED                       5                              1
  ZNF521 WILD-TYPE                   101                              9
D1944V10, multiclass
                                clus
vv                               ZNF521 MUTATED ZNF521 WILD-TYPE
  COLON ADENOCARCINOMA                       21              294
  COLON MUCINOUS ADENOCARCINOMA               7               40
  RECTAL ADENOCARCINOMA                       5              101
  RECTAL MUCINOUS ADENOCARCINOMA              1                9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ZNF521 MUTATED    22   2   0   2
  ZNF521 WILD-TYPE 323   2  31  23
D1944V11, multiclass
    clus
vv   ZNF521 MUTATED ZNF521 WILD-TYPE
  R0             22              323
  R1              2                2
  R2              0               31
  RX              2               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1944V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF521 MUTATED                                  0     2
  ZNF521 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZNF521 MUTATED                           1    17
  ZNF521 WILD-TYPE                        21   209
D1944V13, multiclass
                                  clus
vv                                 ZNF521 MUTATED ZNF521 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                9
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                        17              209
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1945) Variable = OR4N2 MUTATION ANALYSIS
D1945V1, survival
                 sevent
clus2               0   1
  OR4N2 MUTATED     6   4
  OR4N2 WILD-TYPE 372  89
  OR4N2 MUTATED OR4N2 WILD-TYPE 
             10             461 
  OR4N2 MUTATED OR4N2 WILD-TYPE 
              4              89 
$`OR4N2 MUTATED`
TCGA-AA-3715 TCGA-AA-3858 TCGA-AZ-4315 TCGA-CK-4952 TCGA-D5-6537 TCGA-D5-6931 
       19.04        31.07        58.39        15.62         4.80        12.00 
TCGA-DM-A1D4 TCGA-F4-6570 TCGA-G4-6309 TCGA-G4-6586 
       92.75         6.18        85.48        35.80 

$`OR4N2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
       32.05         0.99        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       33.01        21.44        17.82         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6539 
        1.32        43.27        15.12        17.85        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       35.74        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 
       74.56        65.85        53.62        44.68        55.04        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 
       61.91        36.00        22.09        13.78        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  OR4N2 MUTATED OR4N2 WILD-TYPE 
            4.8             0.0 
  OR4N2 MUTATED OR4N2 WILD-TYPE 
          92.75          148.01 
  OR4N2 MUTATED OR4N2 WILD-TYPE 
         25.055          20.190 
[1] "4.8 - 92.8 (25.1)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.5"
D1945V2, continuous
D1945V3, binary
                 cls
clus                0   1
  OR4N2 MUTATED    10   0
  OR4N2 WILD-TYPE 356 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR4N2 MUTATED     10    0
  OR4N2 WILD-TYPE  356  119
        clus
vv       OR4N2 MUTATED OR4N2 WILD-TYPE
  COLON             10             356
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  OR4N2 MUTATED         1        0        1         4         0         0
  OR4N2 WILD-TYPE      90        1       31       134        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  OR4N2 MUTATED           0          0          2          2        0         0
  OR4N2 WILD-TYPE        24         11         57         40       48        18
                 vv
clus              STAGE IVB
  OR4N2 MUTATED           0
  OR4N2 WILD-TYPE         1
D1945V4, multiclass
            clus
vv           OR4N2 MUTATED OR4N2 WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              4             134
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             2              57
  STAGE IIIC             2              40
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  OR4N2 MUTATED     0   1   7   2
  OR4N2 WILD-TYPE  17  91 322  48
D1945V5, multiclass
    clus
vv   OR4N2 MUTATED OR4N2 WILD-TYPE
  T1             0              17
  T2             1              91
  T3             7             322
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  OR4N2 MUTATED     6   2   2
  OR4N2 WILD-TYPE 281 111  85
D1945V6, multiclass
    clus
vv   OR4N2 MUTATED OR4N2 WILD-TYPE
  N0             6             281
  N1             2             111
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1945V7, binary
                 cls
clus                0   1
  OR4N2 MUTATED     9   0
  OR4N2 WILD-TYPE 366  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR4N2 MUTATED      9    0
  OR4N2 WILD-TYPE  366   65
   clus
vv  OR4N2 MUTATED OR4N2 WILD-TYPE
  0             9             366
  1             0              65
[1] 2 2
[1] FALSE
D1945V8, binary
                 cls
clus                0   1
  OR4N2 MUTATED     4   6
  OR4N2 WILD-TYPE 221 258
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR4N2 MUTATED      4    6
  OR4N2 WILD-TYPE  221  258
        clus
vv       OR4N2 MUTATED OR4N2 WILD-TYPE
  FEMALE             4             221
  MALE               6             258
[1] 2 2
[1] FALSE
D1945V9, binary
                 cls
clus                0   1
  OR4N2 MUTATED     8   0
  OR4N2 WILD-TYPE 342  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR4N2 MUTATED      8    0
  OR4N2 WILD-TYPE  342   22
     clus
vv    OR4N2 MUTATED OR4N2 WILD-TYPE
  NO              8             342
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  OR4N2 MUTATED                      9                             1
  OR4N2 WILD-TYPE                  306                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  OR4N2 MUTATED                       0                              0
  OR4N2 WILD-TYPE                   106                             10
D1945V10, multiclass
                                clus
vv                               OR4N2 MUTATED OR4N2 WILD-TYPE
  COLON ADENOCARCINOMA                       9             306
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  OR4N2 MUTATED     8   0   0   1
  OR4N2 WILD-TYPE 337   4  31  24
D1945V11, multiclass
    clus
vv   OR4N2 MUTATED OR4N2 WILD-TYPE
  R0             8             337
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1945V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OR4N2 MUTATED                                  0     0
  OR4N2 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  OR4N2 MUTATED                           1     7
  OR4N2 WILD-TYPE                        21   219
D1945V13, multiclass
                                  clus
vv                                 OR4N2 MUTATED OR4N2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        7             219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1946) Variable = CELSR1 MUTATION ANALYSIS
D1946V1, survival
                  sevent
clus2                0   1
  CELSR1 MUTATED    22   1
  CELSR1 WILD-TYPE 356  92
  CELSR1 MUTATED CELSR1 WILD-TYPE 
              23              448 
  CELSR1 MUTATED CELSR1 WILD-TYPE 
               1               92 
$`CELSR1 MUTATED`
TCGA-A6-6653 TCGA-AA-3663 TCGA-AA-3713 TCGA-AA-3819 TCGA-AA-3875 TCGA-AA-3877 
       24.39         6.97        19.04        25.02        18.05        31.00 
TCGA-AA-3947 TCGA-AA-A01Q TCGA-AA-A02O TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6895 
       33.01         1.02         0.92         0.07        56.55         0.72 
TCGA-AU-6004 TCGA-AZ-6598 TCGA-CM-4743 TCGA-CM-5341 TCGA-CM-5861 TCGA-CM-6674 
       27.09        49.41        23.05        29.06        15.02        12.95 
TCGA-DM-A1D9 TCGA-F4-6856 TCGA-G4-6306 TCGA-G4-6628 TCGA-DY-A0XA 
      140.38        35.31        44.68        79.69       126.44 

$`CELSR1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
       25.08        25.18        24.16        21.76        24.69        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
       33.04         0.99         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 
       29.98         2.01        12.99        24.00        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01R TCGA-AA-A01S 
       12.00        31.00        31.00        38.07        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02W TCGA-AA-A02Y 
       39.98         2.01         5.03        14.01        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        21.37        15.52         0.79         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 
       22.42        27.42        10.88         0.20        14.50        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 
        5.13       106.75        22.36        62.79        88.21         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
       82.95         1.91       124.27        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 
       13.02        22.03        22.98        30.08        32.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       15.02        14.04        11.01        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A1DB 
       92.75        49.91        13.32        12.59         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 
       16.24        33.67        13.25         0.53        47.41       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       74.56        65.85        53.62        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       91.79        46.75        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        4.01         5.03         5.29        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  CELSR1 MUTATED CELSR1 WILD-TYPE 
            0.07             0.00 
  CELSR1 MUTATED CELSR1 WILD-TYPE 
          140.38           148.01 
  CELSR1 MUTATED CELSR1 WILD-TYPE 
          25.020           20.035 
[1] "0.1 - 140.4 (25.0)" "0.0 - 148.0 (20.0)"
[1] "hr=" "5.8"
D1946V2, continuous
D1946V3, binary
                  cls
clus                 0   1
  CELSR1 MUTATED    22   1
  CELSR1 WILD-TYPE 344 118
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CELSR1 MUTATED     22    1
  CELSR1 WILD-TYPE  344  118
        clus
vv       CELSR1 MUTATED CELSR1 WILD-TYPE
  COLON              22              344
  RECTUM              1              118
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CELSR1 MUTATED         7        0        4         8         1         0
  CELSR1 WILD-TYPE      84        1       28       130         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CELSR1 MUTATED           0          1          0          0        1
  CELSR1 WILD-TYPE        24         10         59         42       47
                  vv
clus               STAGE IVA STAGE IVB
  CELSR1 MUTATED           0         0
  CELSR1 WILD-TYPE        18         1
D1946V4, multiclass
            clus
vv           CELSR1 MUTATED CELSR1 WILD-TYPE
  STAGE I                 7               84
  STAGE IA                0                1
  STAGE II                4               28
  STAGE IIA               8              130
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              1               10
  STAGE IIIB              0               59
  STAGE IIIC              0               42
  STAGE IV                1               47
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  CELSR1 MUTATED     2   7  13   1
  CELSR1 WILD-TYPE  15  85 316  49
D1946V5, multiclass
    clus
vv   CELSR1 MUTATED CELSR1 WILD-TYPE
  T1              2               15
  T2              7               85
  T3             13              316
  T4              1               49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  CELSR1 MUTATED    21   2   0
  CELSR1 WILD-TYPE 266 111  87
D1946V6, multiclass
    clus
vv   CELSR1 MUTATED CELSR1 WILD-TYPE
  N0             21              266
  N1              2              111
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1946V7, binary
                  cls
clus                 0   1
  CELSR1 MUTATED    19   1
  CELSR1 WILD-TYPE 356  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CELSR1 MUTATED     19    1
  CELSR1 WILD-TYPE  356   64
   clus
vv  CELSR1 MUTATED CELSR1 WILD-TYPE
  0             19              356
  1              1               64
[1] 2 2
[1] FALSE
D1946V8, binary
                  cls
clus                 0   1
  CELSR1 MUTATED    11  12
  CELSR1 WILD-TYPE 214 252
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CELSR1 MUTATED     11   12
  CELSR1 WILD-TYPE  214  252
        clus
vv       CELSR1 MUTATED CELSR1 WILD-TYPE
  FEMALE             11              214
  MALE               12              252
[1] 2 2
[1] FALSE
D1946V9, binary
                  cls
clus                 0   1
  CELSR1 MUTATED    14   1
  CELSR1 WILD-TYPE 336  21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CELSR1 MUTATED     14    1
  CELSR1 WILD-TYPE  336   21
     clus
vv    CELSR1 MUTATED CELSR1 WILD-TYPE
  NO              14              336
  YES              1               21
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CELSR1 MUTATED                     18                             4
  CELSR1 WILD-TYPE                  297                            43
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CELSR1 MUTATED                       1                              0
  CELSR1 WILD-TYPE                   105                             10
D1946V10, multiclass
                                clus
vv                               CELSR1 MUTATED CELSR1 WILD-TYPE
  COLON ADENOCARCINOMA                       18              297
  COLON MUCINOUS ADENOCARCINOMA               4               43
  RECTAL ADENOCARCINOMA                       1              105
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  CELSR1 MUTATED    16   0   1   0
  CELSR1 WILD-TYPE 329   4  30  25
D1946V11, multiclass
    clus
vv   CELSR1 MUTATED CELSR1 WILD-TYPE
  R0             16              329
  R1              0                4
  R2              1               30
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1946V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CELSR1 MUTATED                                  0     1
  CELSR1 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  CELSR1 MUTATED                           0    14
  CELSR1 WILD-TYPE                        22   212
D1946V13, multiclass
                                  clus
vv                                 CELSR1 MUTATED CELSR1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                        14              212
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1947) Variable = SDAD1 MUTATION ANALYSIS
D1947V1, survival
                 sevent
clus2               0   1
  SDAD1 MUTATED     5   3
  SDAD1 WILD-TYPE 373  90
  SDAD1 MUTATED SDAD1 WILD-TYPE 
              8             463 
  SDAD1 MUTATED SDAD1 WILD-TYPE 
              3              90 
$`SDAD1 MUTATED`
TCGA-A6-5665 TCGA-A6-6141 TCGA-AA-A00N TCGA-AZ-4315 TCGA-AZ-6601 TCGA-CA-6717 
       22.06         8.38         4.01        58.39       100.01        12.76 
TCGA-CK-5913 TCGA-F4-6460 
       51.32        31.96 

$`SDAD1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 
       22.09        32.71        27.09        22.52        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 
       62.79        88.21        49.41         6.77        12.10        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07        12.20        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 
       17.56       148.01        85.45        15.62        49.08         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6569 
       35.97        60.79       117.07        98.24         8.61        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  SDAD1 MUTATED SDAD1 WILD-TYPE 
           4.01            0.00 
  SDAD1 MUTATED SDAD1 WILD-TYPE 
         100.01          148.01 
  SDAD1 MUTATED SDAD1 WILD-TYPE 
          27.01           20.12 
[1] "4.0 - 100.0 (27.0)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.3"
D1947V2, continuous
D1947V3, binary
                 cls
clus                0   1
  SDAD1 MUTATED     8   0
  SDAD1 WILD-TYPE 358 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SDAD1 MUTATED      8    0
  SDAD1 WILD-TYPE  358  119
        clus
vv       SDAD1 MUTATED SDAD1 WILD-TYPE
  COLON              8             358
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SDAD1 MUTATED         0        0        1         5         1         0
  SDAD1 WILD-TYPE      91        1       31       133         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SDAD1 MUTATED           0          0          1          0        0         0
  SDAD1 WILD-TYPE        24         11         58         42       48        18
                 vv
clus              STAGE IVB
  SDAD1 MUTATED           0
  SDAD1 WILD-TYPE         1
D1947V4, multiclass
            clus
vv           SDAD1 MUTATED SDAD1 WILD-TYPE
  STAGE I                0              91
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              5             133
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  SDAD1 MUTATED     0   0   7   1
  SDAD1 WILD-TYPE  17  92 322  49
D1947V5, multiclass
    clus
vv   SDAD1 MUTATED SDAD1 WILD-TYPE
  T1             0              17
  T2             0              92
  T3             7             322
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  SDAD1 MUTATED     7   1   0
  SDAD1 WILD-TYPE 280 112  87
D1947V6, multiclass
    clus
vv   SDAD1 MUTATED SDAD1 WILD-TYPE
  N0             7             280
  N1             1             112
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1947V7, binary
                 cls
clus                0   1
  SDAD1 MUTATED     7   0
  SDAD1 WILD-TYPE 368  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SDAD1 MUTATED      7    0
  SDAD1 WILD-TYPE  368   65
   clus
vv  SDAD1 MUTATED SDAD1 WILD-TYPE
  0             7             368
  1             0              65
[1] 2 2
[1] FALSE
D1947V8, binary
                 cls
clus                0   1
  SDAD1 MUTATED     3   5
  SDAD1 WILD-TYPE 222 259
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SDAD1 MUTATED      3    5
  SDAD1 WILD-TYPE  222  259
        clus
vv       SDAD1 MUTATED SDAD1 WILD-TYPE
  FEMALE             3             222
  MALE               5             259
[1] 2 2
[1] FALSE
D1947V9, binary
                 cls
clus                0   1
  SDAD1 MUTATED     7   0
  SDAD1 WILD-TYPE 343  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SDAD1 MUTATED      7    0
  SDAD1 WILD-TYPE  343   22
     clus
vv    SDAD1 MUTATED SDAD1 WILD-TYPE
  NO              7             343
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SDAD1 MUTATED                      6                             2
  SDAD1 WILD-TYPE                  309                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SDAD1 MUTATED                       0                              0
  SDAD1 WILD-TYPE                   106                             10
D1947V10, multiclass
                                clus
vv                               SDAD1 MUTATED SDAD1 WILD-TYPE
  COLON ADENOCARCINOMA                       6             309
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  SDAD1 MUTATED     4   0   0   2
  SDAD1 WILD-TYPE 341   4  31  23
D1947V11, multiclass
    clus
vv   SDAD1 MUTATED SDAD1 WILD-TYPE
  R0             4             341
  R1             0               4
  R2             0              31
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1947V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SDAD1 MUTATED                                  0     1
  SDAD1 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  SDAD1 MUTATED                           1     5
  SDAD1 WILD-TYPE                        21   221
D1947V13, multiclass
                                  clus
vv                                 SDAD1 MUTATED SDAD1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        5             221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1948) Variable = GTDC1 MUTATION ANALYSIS
D1948V1, survival
                 sevent
clus2               0   1
  GTDC1 MUTATED     6   3
  GTDC1 WILD-TYPE 372  90
  GTDC1 MUTATED GTDC1 WILD-TYPE 
              9             462 
  GTDC1 MUTATED GTDC1 WILD-TYPE 
              3              90 
$`GTDC1 MUTATED`
TCGA-AA-3977 TCGA-AA-A00J TCGA-AA-A00N TCGA-AZ-6598 TCGA-CA-6717 TCGA-D5-6533 
       25.02        18.05         4.01        49.41        12.76         1.32 
TCGA-D5-6927 TCGA-D5-6930 TCGA-AF-3913 
        9.44         1.51        10.39 

$`GTDC1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L 
       38.04        19.00        30.02        34.03        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        88.21         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07        12.20        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6534 
       19.59        56.09        55.92        20.19        18.25        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
        9.04        11.64         4.80        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-4110 TCGA-AF-5654 
       43.04        13.55        19.10        34.49        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  GTDC1 MUTATED GTDC1 WILD-TYPE 
           1.32            0.00 
  GTDC1 MUTATED GTDC1 WILD-TYPE 
          49.41          148.01 
  GTDC1 MUTATED GTDC1 WILD-TYPE 
          10.39           20.73 
[1] "1.3 - 49.4 (10.4)"  "0.0 - 148.0 (20.7)"
[1] "hr=" "2.8"
D1948V2, continuous
D1948V3, binary
                 cls
clus                0   1
  GTDC1 MUTATED     9   1
  GTDC1 WILD-TYPE 357 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GTDC1 MUTATED      9    1
  GTDC1 WILD-TYPE  357  118
        clus
vv       GTDC1 MUTATED GTDC1 WILD-TYPE
  COLON              9             357
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GTDC1 MUTATED         0        0        1         3         2         0
  GTDC1 WILD-TYPE      91        1       31       135         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  GTDC1 MUTATED           0          0          2          0        1         0
  GTDC1 WILD-TYPE        24         11         57         42       47        18
                 vv
clus              STAGE IVB
  GTDC1 MUTATED           0
  GTDC1 WILD-TYPE         1
D1948V4, multiclass
            clus
vv           GTDC1 MUTATED GTDC1 WILD-TYPE
  STAGE I                0              91
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              3             135
  STAGE IIB              2               8
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             2              57
  STAGE IIIC             0              42
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  GTDC1 MUTATED     0   1   5   4
  GTDC1 WILD-TYPE  17  91 324  46
D1948V5, multiclass
    clus
vv   GTDC1 MUTATED GTDC1 WILD-TYPE
  T1             0              17
  T2             1              91
  T3             5             324
  T4             4              46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  GTDC1 MUTATED     8   2   0
  GTDC1 WILD-TYPE 279 111  87
D1948V6, multiclass
    clus
vv   GTDC1 MUTATED GTDC1 WILD-TYPE
  N0             8             279
  N1             2             111
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1948V7, binary
                 cls
clus                0   1
  GTDC1 MUTATED     6   1
  GTDC1 WILD-TYPE 369  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GTDC1 MUTATED      6    1
  GTDC1 WILD-TYPE  369   64
   clus
vv  GTDC1 MUTATED GTDC1 WILD-TYPE
  0             6             369
  1             1              64
[1] 2 2
[1] FALSE
D1948V8, binary
                 cls
clus                0   1
  GTDC1 MUTATED     3   7
  GTDC1 WILD-TYPE 222 257
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GTDC1 MUTATED      3    7
  GTDC1 WILD-TYPE  222  257
        clus
vv       GTDC1 MUTATED GTDC1 WILD-TYPE
  FEMALE             3             222
  MALE               7             257
[1] 2 2
[1] FALSE
D1948V9, binary
                 cls
clus                0   1
  GTDC1 MUTATED     6   0
  GTDC1 WILD-TYPE 344  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GTDC1 MUTATED      6    0
  GTDC1 WILD-TYPE  344   22
     clus
vv    GTDC1 MUTATED GTDC1 WILD-TYPE
  NO              6             344
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  GTDC1 MUTATED                      5                             4
  GTDC1 WILD-TYPE                  310                            43
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  GTDC1 MUTATED                       1                              0
  GTDC1 WILD-TYPE                   105                             10
D1948V10, multiclass
                                clus
vv                               GTDC1 MUTATED GTDC1 WILD-TYPE
  COLON ADENOCARCINOMA                       5             310
  COLON MUCINOUS ADENOCARCINOMA              4              43
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  GTDC1 MUTATED     6   0   0   2
  GTDC1 WILD-TYPE 339   4  31  23
D1948V11, multiclass
    clus
vv   GTDC1 MUTATED GTDC1 WILD-TYPE
  R0             6             339
  R1             0               4
  R2             0              31
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1948V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GTDC1 MUTATED                                  0     1
  GTDC1 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  GTDC1 MUTATED                           1     5
  GTDC1 WILD-TYPE                        21   221
D1948V13, multiclass
                                  clus
vv                                 GTDC1 MUTATED GTDC1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        5             221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1949) Variable = PLCG1 MUTATION ANALYSIS
D1949V1, survival
                 sevent
clus2               0   1
  PLCG1 MUTATED    17   1
  PLCG1 WILD-TYPE 361  92
  PLCG1 MUTATED PLCG1 WILD-TYPE 
             18             453 
  PLCG1 MUTATED PLCG1 WILD-TYPE 
              1              92 
$`PLCG1 MUTATED`
TCGA-A6-5662 TCGA-A6-6653 TCGA-A6-6781 TCGA-AA-3663 TCGA-AA-3864 TCGA-AA-3972 
       23.61        24.39        19.66         6.97        53.00        50.99 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AZ-4315 TCGA-CK-4952 TCGA-CM-6166 TCGA-CM-6171 
        1.02        35.01        58.39        15.62        21.99        14.04 
TCGA-D5-6898 TCGA-D5-6930 TCGA-DM-A1HB TCGA-F4-6459 TCGA-F4-6856 TCGA-F5-6811 
        1.48         1.51       135.65         8.61        35.31        32.19 

$`PLCG1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        33.53        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 
       25.18        24.16        21.76        24.69        23.87        20.12 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02        78.08         6.05        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       31.07        30.05        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       21.99        16.08        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01S 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       33.01        21.44        17.82         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
        2.96        29.03        16.04        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       15.02        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
       15.58         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
        9.44        11.64         4.80        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
      117.07        98.24        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
        0.53        47.41       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6812 
       18.28         9.96        49.51        31.30        28.57         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  PLCG1 MUTATED PLCG1 WILD-TYPE 
           1.02            0.00 
  PLCG1 MUTATED PLCG1 WILD-TYPE 
         135.65          148.01 
  PLCG1 MUTATED PLCG1 WILD-TYPE 
          22.80           20.12 
[1] "1.0 - 135.7 (22.8)" "0.0 - 148.0 (20.1)"
[1] "hr=" "4"  
D1949V2, continuous
D1949V3, binary
                 cls
clus                0   1
  PLCG1 MUTATED    17   2
  PLCG1 WILD-TYPE 349 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PLCG1 MUTATED     17    2
  PLCG1 WILD-TYPE  349  117
        clus
vv       PLCG1 MUTATED PLCG1 WILD-TYPE
  COLON             17             349
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PLCG1 MUTATED         5        0        3         3         0         0
  PLCG1 WILD-TYPE      86        1       29       135        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PLCG1 MUTATED           2          0          2          2        1         1
  PLCG1 WILD-TYPE        22         11         57         40       47        17
                 vv
clus              STAGE IVB
  PLCG1 MUTATED           0
  PLCG1 WILD-TYPE         1
D1949V4, multiclass
            clus
vv           PLCG1 MUTATED PLCG1 WILD-TYPE
  STAGE I                5              86
  STAGE IA               0               1
  STAGE II               3              29
  STAGE IIA              3             135
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              2              22
  STAGE IIIA             0              11
  STAGE IIIB             2              57
  STAGE IIIC             2              40
  STAGE IV               1              47
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PLCG1 MUTATED     0   5  12   2
  PLCG1 WILD-TYPE  17  87 317  48
D1949V5, multiclass
    clus
vv   PLCG1 MUTATED PLCG1 WILD-TYPE
  T1             0              17
  T2             5              87
  T3            12             317
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  PLCG1 MUTATED    11   4   4
  PLCG1 WILD-TYPE 276 109  83
D1949V6, multiclass
    clus
vv   PLCG1 MUTATED PLCG1 WILD-TYPE
  N0            11             276
  N1             4             109
  N2             4              83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1949V7, binary
                 cls
clus                0   1
  PLCG1 MUTATED    15   2
  PLCG1 WILD-TYPE 360  63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PLCG1 MUTATED     15    2
  PLCG1 WILD-TYPE  360   63
   clus
vv  PLCG1 MUTATED PLCG1 WILD-TYPE
  0            15             360
  1             2              63
[1] 2 2
[1] FALSE
D1949V8, binary
                 cls
clus                0   1
  PLCG1 MUTATED     7  12
  PLCG1 WILD-TYPE 218 252
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PLCG1 MUTATED      7   12
  PLCG1 WILD-TYPE  218  252
        clus
vv       PLCG1 MUTATED PLCG1 WILD-TYPE
  FEMALE             7             218
  MALE              12             252
[1] 2 2
[1] FALSE
D1949V9, binary
                 cls
clus                0   1
  PLCG1 MUTATED    12   1
  PLCG1 WILD-TYPE 338  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PLCG1 MUTATED     12    1
  PLCG1 WILD-TYPE  338   21
     clus
vv    PLCG1 MUTATED PLCG1 WILD-TYPE
  NO             12             338
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PLCG1 MUTATED                     11                             5
  PLCG1 WILD-TYPE                  304                            42
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PLCG1 MUTATED                       2                              0
  PLCG1 WILD-TYPE                   104                             10
D1949V10, multiclass
                                clus
vv                               PLCG1 MUTATED PLCG1 WILD-TYPE
  COLON ADENOCARCINOMA                      11             304
  COLON MUCINOUS ADENOCARCINOMA              5              42
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  PLCG1 MUTATED    12   0   1   1
  PLCG1 WILD-TYPE 333   4  30  24
D1949V11, multiclass
    clus
vv   PLCG1 MUTATED PLCG1 WILD-TYPE
  R0            12             333
  R1             0               4
  R2             1              30
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1949V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PLCG1 MUTATED                                  0     0
  PLCG1 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PLCG1 MUTATED                           0    14
  PLCG1 WILD-TYPE                        22   212
D1949V13, multiclass
                                  clus
vv                                 PLCG1 MUTATED PLCG1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                       14             212
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1950) Variable = SMC4 MUTATION ANALYSIS
D1950V1, survival
                sevent
clus2              0   1
  SMC4 MUTATED    14   4
  SMC4 WILD-TYPE 364  89
  SMC4 MUTATED SMC4 WILD-TYPE 
            18            453 
  SMC4 MUTATED SMC4 WILD-TYPE 
             4             89 
$`SMC4 MUTATED`
TCGA-A6-6781 TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3663 TCGA-AA-3815 TCGA-AA-3845 
       19.66         3.02        63.98         6.97        33.04         0.00 
TCGA-AA-3877 TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A010 TCGA-AA-A01Q TCGA-AY-4071 
       31.00        27.02        38.04        34.98         1.02         0.95 
TCGA-AZ-4315 TCGA-AZ-6599 TCGA-CK-5913 TCGA-D5-6533 TCGA-AG-3894 TCGA-AG-A002 
       58.39         6.77        51.32         1.32        14.01        20.98 

$`SMC4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 
       23.87        20.12        20.28         7.04         1.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02        78.08         6.05        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
       26.99        19.04        19.04        10.06        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
       14.93        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00D 
       27.02        27.02        19.07         7.96        13.94        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
       38.07        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
       27.09        16.31        33.01        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       85.45        15.62        49.08         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       18.25        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  SMC4 MUTATED SMC4 WILD-TYPE 
             0              0 
  SMC4 MUTATED SMC4 WILD-TYPE 
         63.98         148.01 
  SMC4 MUTATED SMC4 WILD-TYPE 
         20.32          20.19 
[1] "0.0 - 64.0 (20.3)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.3"
D1950V2, continuous
D1950V3, binary
                cls
clus               0   1
  SMC4 MUTATED    17   2
  SMC4 WILD-TYPE 349 117
[1] "tbl2"
                cls
clus             [,1] [,2]
  SMC4 MUTATED     17    2
  SMC4 WILD-TYPE  349  117
        clus
vv       SMC4 MUTATED SMC4 WILD-TYPE
  COLON            17            349
  RECTUM            2            117
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SMC4 MUTATED         4        0        5         7         1         0
  SMC4 WILD-TYPE      87        1       27       131         9         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SMC4 MUTATED           0          0          2          1        0         0
  SMC4 WILD-TYPE        24         11         57         41       48        18
                vv
clus             STAGE IVB
  SMC4 MUTATED           0
  SMC4 WILD-TYPE         1
D1950V4, multiclass
            clus
vv           SMC4 MUTATED SMC4 WILD-TYPE
  STAGE I               4             87
  STAGE IA              0              1
  STAGE II              5             27
  STAGE IIA             7            131
  STAGE IIB             1              9
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            2             57
  STAGE IIIC            1             41
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  SMC4 MUTATED     2   2  12   4
  SMC4 WILD-TYPE  15  90 317  46
D1950V5, multiclass
    clus
vv   SMC4 MUTATED SMC4 WILD-TYPE
  T1            2             15
  T2            2             90
  T3           12            317
  T4            4             46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  SMC4 MUTATED    18   2   0
  SMC4 WILD-TYPE 269 111  87
D1950V6, multiclass
    clus
vv   SMC4 MUTATED SMC4 WILD-TYPE
  N0           18            269
  N1            2            111
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1950V7, binary
                cls
clus               0   1
  SMC4 MUTATED    16   0
  SMC4 WILD-TYPE 359  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  SMC4 MUTATED     16    0
  SMC4 WILD-TYPE  359   65
   clus
vv  SMC4 MUTATED SMC4 WILD-TYPE
  0           16            359
  1            0             65
[1] 2 2
[1] FALSE
D1950V8, binary
                cls
clus               0   1
  SMC4 MUTATED    11   9
  SMC4 WILD-TYPE 214 255
[1] "tbl2"
                cls
clus             [,1] [,2]
  SMC4 MUTATED     11    9
  SMC4 WILD-TYPE  214  255
        clus
vv       SMC4 MUTATED SMC4 WILD-TYPE
  FEMALE           11            214
  MALE              9            255
[1] 2 2
[1] FALSE
D1950V9, binary
                cls
clus               0   1
  SMC4 MUTATED    14   1
  SMC4 WILD-TYPE 336  21
[1] "tbl2"
                cls
clus             [,1] [,2]
  SMC4 MUTATED     14    1
  SMC4 WILD-TYPE  336   21
     clus
vv    SMC4 MUTATED SMC4 WILD-TYPE
  NO            14            336
  YES            1             21
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SMC4 MUTATED                     14                             3
  SMC4 WILD-TYPE                  301                            44
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SMC4 MUTATED                       2                              0
  SMC4 WILD-TYPE                   104                             10
D1950V10, multiclass
                                clus
vv                               SMC4 MUTATED SMC4 WILD-TYPE
  COLON ADENOCARCINOMA                     14            301
  COLON MUCINOUS ADENOCARCINOMA             3             44
  RECTAL ADENOCARCINOMA                     2            104
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  SMC4 MUTATED    18   0   0   1
  SMC4 WILD-TYPE 327   4  31  24
D1950V11, multiclass
    clus
vv   SMC4 MUTATED SMC4 WILD-TYPE
  R0           18            327
  R1            0              4
  R2            0             31
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1950V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SMC4 MUTATED                                  0     0
  SMC4 WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  SMC4 MUTATED                           0     6
  SMC4 WILD-TYPE                        22   220
D1950V13, multiclass
                                  clus
vv                                 SMC4 MUTATED SMC4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       6            220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1951) Variable = NDUFV2 MUTATION ANALYSIS
D1951V1, survival
                  sevent
clus2                0   1
  NDUFV2 MUTATED     2   0
  NDUFV2 WILD-TYPE 376  93
  NDUFV2 MUTATED NDUFV2 WILD-TYPE 
               2              469 
  NDUFV2 MUTATED NDUFV2 WILD-TYPE 
               0               93 
$`NDUFV2 MUTATED`
TCGA-A6-5665 TCGA-D5-6927 
       22.06         9.44 

$`NDUFV2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  NDUFV2 MUTATED NDUFV2 WILD-TYPE 
            9.44             0.00 
  NDUFV2 MUTATED NDUFV2 WILD-TYPE 
           22.06           148.01 
  NDUFV2 MUTATED NDUFV2 WILD-TYPE 
           15.75            20.19 
[1] "9.4 - 22.1 (15.8)"  "0.0 - 148.0 (20.2)"
[1] "Remove cluster labels:" "NDUFV2 MUTATED"        
D1951V2, continuous
D1951V3, binary
                  cls
clus                 0   1
  NDUFV2 MUTATED     3   0
  NDUFV2 WILD-TYPE 363 119
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NDUFV2 MUTATED      3    0
  NDUFV2 WILD-TYPE  363  119
        clus
vv       NDUFV2 MUTATED NDUFV2 WILD-TYPE
  COLON               3              363
  RECTUM              0              119
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NDUFV2 MUTATED         1        0        0         2         0         0
  NDUFV2 WILD-TYPE      90        1       32       136        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NDUFV2 MUTATED           0          0          0          0        0
  NDUFV2 WILD-TYPE        24         11         59         42       48
                  vv
clus               STAGE IVA STAGE IVB
  NDUFV2 MUTATED           0         0
  NDUFV2 WILD-TYPE        18         1
D1951V4, multiclass
            clus
vv           NDUFV2 MUTATED NDUFV2 WILD-TYPE
  STAGE I                 1               90
  STAGE IA                0                1
  STAGE II                0               32
  STAGE IIA               2              136
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              0               59
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  NDUFV2 MUTATED     0   1   2   0
  NDUFV2 WILD-TYPE  17  91 327  50
D1951V5, multiclass
    clus
vv   NDUFV2 MUTATED NDUFV2 WILD-TYPE
  T1              0               17
  T2              1               91
  T3              2              327
  T4              0               50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  NDUFV2 MUTATED     3   0   0
  NDUFV2 WILD-TYPE 284 113  87
D1951V6, multiclass
    clus
vv   NDUFV2 MUTATED NDUFV2 WILD-TYPE
  N0              3              284
  N1              0              113
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1951V7, binary
                  cls
clus                 0   1
  NDUFV2 MUTATED     2   0
  NDUFV2 WILD-TYPE 373  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NDUFV2 MUTATED      2    0
  NDUFV2 WILD-TYPE  373   65
   clus
vv  NDUFV2 MUTATED NDUFV2 WILD-TYPE
  0              2              373
  1              0               65
[1] 2 2
[1] FALSE
D1951V8, binary
                  cls
clus                 0   1
  NDUFV2 MUTATED     1   2
  NDUFV2 WILD-TYPE 224 262
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NDUFV2 MUTATED      1    2
  NDUFV2 WILD-TYPE  224  262
        clus
vv       NDUFV2 MUTATED NDUFV2 WILD-TYPE
  FEMALE              1              224
  MALE                2              262
[1] 2 2
[1] FALSE
D1951V9, binary
                  cls
clus                 0   1
  NDUFV2 MUTATED     2   0
  NDUFV2 WILD-TYPE 348  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NDUFV2 MUTATED      2    0
  NDUFV2 WILD-TYPE  348   22
     clus
vv    NDUFV2 MUTATED NDUFV2 WILD-TYPE
  NO               2              348
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  NDUFV2 MUTATED                      3                             0
  NDUFV2 WILD-TYPE                  312                            47
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  NDUFV2 MUTATED                       0                              0
  NDUFV2 WILD-TYPE                   106                             10
D1951V10, multiclass
                                clus
vv                               NDUFV2 MUTATED NDUFV2 WILD-TYPE
  COLON ADENOCARCINOMA                        3              312
  COLON MUCINOUS ADENOCARCINOMA               0               47
  RECTAL ADENOCARCINOMA                       0              106
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  NDUFV2 MUTATED     2   0   0   1
  NDUFV2 WILD-TYPE 343   4  31  24
D1951V11, multiclass
    clus
vv   NDUFV2 MUTATED NDUFV2 WILD-TYPE
  R0              2              343
  R1              0                4
  R2              0               31
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1951V12, continuous
[1] "Remove cluster labels:" "NDUFV2 MUTATED"        
clus
  NDUFV2 MUTATED NDUFV2 WILD-TYPE 
               2              456 
      TCGA-A6-2671       TCGA-A6-2672       TCGA-A6-2674       TCGA-A6-2676 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-A6-2677       TCGA-A6-2678       TCGA-A6-2683       TCGA-A6-3807 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-A6-3808       TCGA-A6-3809       TCGA-A6-3810       TCGA-A6-4105 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-A6-5656       TCGA-A6-5657       TCGA-A6-5659       TCGA-A6-5660 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-A6-5661       TCGA-A6-5662       TCGA-A6-5664       TCGA-A6-5666 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-A6-6137       TCGA-A6-6138       TCGA-A6-6141       TCGA-A6-6142 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-A6-6648       TCGA-A6-6649       TCGA-A6-6651       TCGA-A6-6652 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-A6-6653       TCGA-A6-6654       TCGA-A6-6780       TCGA-A6-6781 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-A6-6782       TCGA-AA-3489       TCGA-AA-3492       TCGA-AA-3496 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-AA-3502       TCGA-AA-3510       TCGA-AA-3511       TCGA-AA-3514 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-AA-3516       TCGA-AA-3517       TCGA-AA-3518       TCGA-AA-3519 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-AA-3520       TCGA-AA-3521       TCGA-AA-3522       TCGA-AA-3524 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-AA-3525       TCGA-AA-3526       TCGA-AA-3527       TCGA-AA-3529 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-AA-3530       TCGA-AA-3531       TCGA-AA-3532       TCGA-AA-3534 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-AA-3538       TCGA-AA-3542       TCGA-AA-3543       TCGA-AA-3544 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-AA-3548       TCGA-AA-3549       TCGA-AA-3552       TCGA-AA-3553 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-AA-3554       TCGA-AA-3555       TCGA-AA-3556       TCGA-AA-3558 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-AA-3560       TCGA-AA-3562       TCGA-AA-3655       TCGA-AA-3660 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-AA-3662       TCGA-AA-3663       TCGA-AA-3664       TCGA-AA-3666 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-AA-3667       TCGA-AA-3672       TCGA-AA-3673       TCGA-AA-3678 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-AA-3679       TCGA-AA-3680       TCGA-AA-3681       TCGA-AA-3684 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-AA-3685       TCGA-AA-3688       TCGA-AA-3692       TCGA-AA-3693 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-AA-3695       TCGA-AA-3696       TCGA-AA-3697       TCGA-AA-3710 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-AA-3712       TCGA-AA-3713       TCGA-AA-3715       TCGA-AA-3811 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-AA-3812       TCGA-AA-3814       TCGA-AA-3815       TCGA-AA-3818 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-AA-3819       TCGA-AA-3821       TCGA-AA-3831       TCGA-AA-3833 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-AA-3837       TCGA-AA-3842       TCGA-AA-3844       TCGA-AA-3845 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-AA-3846       TCGA-AA-3848       TCGA-AA-3850       TCGA-AA-3851 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-AA-3852       TCGA-AA-3854       TCGA-AA-3855       TCGA-AA-3856 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-AA-3858       TCGA-AA-3860       TCGA-AA-3861       TCGA-AA-3864 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-AA-3866       TCGA-AA-3867       TCGA-AA-3869       TCGA-AA-3870 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-AA-3872       TCGA-AA-3875       TCGA-AA-3877       TCGA-AA-3930 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-AA-3939       TCGA-AA-3941       TCGA-AA-3947       TCGA-AA-3949 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-AA-3950       TCGA-AA-3952       TCGA-AA-3955       TCGA-AA-3956 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-AA-3966       TCGA-AA-3968       TCGA-AA-3971       TCGA-AA-3972 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-AA-3973       TCGA-AA-3975       TCGA-AA-3976       TCGA-AA-3977 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-AA-3979       TCGA-AA-3980       TCGA-AA-3982       TCGA-AA-3984 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-AA-3986       TCGA-AA-3989       TCGA-AA-3994       TCGA-AA-A004 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-AA-A00A       TCGA-AA-A00D       TCGA-AA-A00E       TCGA-AA-A00F 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-AA-A00J       TCGA-AA-A00K       TCGA-AA-A00L       TCGA-AA-A00N 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-AA-A00O       TCGA-AA-A00Q       TCGA-AA-A00R       TCGA-AA-A00U 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-AA-A00W       TCGA-AA-A00Z       TCGA-AA-A010       TCGA-AA-A017 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-AA-A01D       TCGA-AA-A01F       TCGA-AA-A01G       TCGA-AA-A01I 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-AA-A01K       TCGA-AA-A01P       TCGA-AA-A01Q       TCGA-AA-A01R 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-AA-A01S       TCGA-AA-A01T       TCGA-AA-A01V       TCGA-AA-A01X 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-AA-A01Z       TCGA-AA-A022       TCGA-AA-A024       TCGA-AA-A029 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-AA-A02F       TCGA-AA-A02H       TCGA-AA-A02J       TCGA-AA-A02K 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-AA-A02O       TCGA-AA-A02W       TCGA-AA-A02Y       TCGA-AA-A03F 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-AA-A03J       TCGA-AD-5900       TCGA-AD-6548       TCGA-AD-6888 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-AD-6889       TCGA-AD-6890       TCGA-AD-6895       TCGA-AD-6899 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-AD-6901       TCGA-AD-6963       TCGA-AD-6964       TCGA-AD-6965 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-AU-3779       TCGA-AU-6004       TCGA-AY-4070       TCGA-AY-4071 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-AY-5543       TCGA-AY-6196       TCGA-AY-6197       TCGA-AY-6386 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-AZ-4323       TCGA-AZ-4616       TCGA-AZ-4682       TCGA-AZ-5403 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-AZ-5407       TCGA-AZ-6598       TCGA-AZ-6599       TCGA-AZ-6600 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-AZ-6601       TCGA-AZ-6603       TCGA-AZ-6605       TCGA-AZ-6606 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-AZ-6607       TCGA-AZ-6608       TCGA-CK-4947       TCGA-CK-4948 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-CK-4950       TCGA-CK-4952       TCGA-CM-4743       TCGA-CM-4744 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-CM-4746       TCGA-CM-4747       TCGA-CM-4752       TCGA-CM-5341 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-CM-5344       TCGA-CM-5348       TCGA-CM-5349       TCGA-CM-5860 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-CM-5861       TCGA-CM-5862       TCGA-CM-5863       TCGA-CM-5864 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-CM-5868       TCGA-CM-6161       TCGA-CM-6162       TCGA-CM-6163 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-CM-6164       TCGA-CM-6165       TCGA-CM-6166       TCGA-CM-6167 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-CM-6168       TCGA-CM-6169       TCGA-CM-6170       TCGA-CM-6171 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-CM-6172       TCGA-CM-6674       TCGA-CM-6675       TCGA-CM-6676 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-CM-6677       TCGA-CM-6678       TCGA-CM-6679       TCGA-CM-6680 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-D5-5537       TCGA-D5-5538       TCGA-D5-5539       TCGA-D5-5540 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-D5-5541       TCGA-D5-6529       TCGA-D5-6532       TCGA-D5-6533 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-D5-6534       TCGA-D5-6535       TCGA-D5-6536       TCGA-D5-6537 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-D5-6538       TCGA-D5-6539       TCGA-D5-6540       TCGA-D5-6541 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-D5-6898       TCGA-D5-6920       TCGA-D5-6922       TCGA-D5-6923 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-D5-6924       TCGA-D5-6926       TCGA-D5-6928       TCGA-D5-6929 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-D5-6930       TCGA-D5-6931       TCGA-D5-6932       TCGA-D5-7000 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-DM-A0X9       TCGA-DM-A0XD       TCGA-DM-A0XF       TCGA-DM-A1D0 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-DM-A1D4       TCGA-DM-A1D6       TCGA-DM-A1D7       TCGA-DM-A1D8 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-DM-A1D9       TCGA-DM-A1DA       TCGA-DM-A1DB       TCGA-DM-A1HA 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-DM-A1HB       TCGA-DM-A282       TCGA-DM-A285       TCGA-DM-A28C 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-DM-A28E       TCGA-DM-A28F       TCGA-DM-A28G       TCGA-DM-A28H 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-DM-A28K       TCGA-F4-6459       TCGA-F4-6460       TCGA-F4-6569 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-F4-6570       TCGA-F4-6703       TCGA-F4-6704       TCGA-F4-6806 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-F4-6807       TCGA-F4-6808       TCGA-F4-6809       TCGA-F4-6854 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-F4-6855       TCGA-F4-6856       TCGA-G4-6293       TCGA-G4-6299 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-G4-6303       TCGA-G4-6304       TCGA-G4-6306       TCGA-G4-6307 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-G4-6309       TCGA-G4-6310       TCGA-G4-6315       TCGA-G4-6317 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-G4-6321       TCGA-G4-6323       TCGA-G4-6586       TCGA-G4-6588 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-G4-6625       TCGA-G4-6626       TCGA-G4-6628       TCGA-AF-2687 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-AF-2689       TCGA-AF-2691       TCGA-AF-2692       TCGA-AF-2693 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-AF-3400       TCGA-AF-3913       TCGA-AF-4110       TCGA-AF-5654 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-AF-6136       TCGA-AF-6655       TCGA-AF-6672       TCGA-AG-3574 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-AG-3575       TCGA-AG-3578       TCGA-AG-3580       TCGA-AG-3581 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-AG-3582       TCGA-AG-3583       TCGA-AG-3584       TCGA-AG-3586 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-AG-3587       TCGA-AG-3593       TCGA-AG-3594       TCGA-AG-3598 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-AG-3599       TCGA-AG-3600       TCGA-AG-3601       TCGA-AG-3602 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-AG-3605       TCGA-AG-3608       TCGA-AG-3609       TCGA-AG-3611 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-AG-3612       TCGA-AG-3726       TCGA-AG-3727       TCGA-AG-3731 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-AG-3732       TCGA-AG-3742       TCGA-AG-3878       TCGA-AG-3881 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-AG-3882       TCGA-AG-3883       TCGA-AG-3885       TCGA-AG-3887 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-AG-3890       TCGA-AG-3892       TCGA-AG-3893       TCGA-AG-3894 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-AG-3896       TCGA-AG-3898       TCGA-AG-3901       TCGA-AG-3902 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-AG-3909       TCGA-AG-3999       TCGA-AG-4001       TCGA-AG-4005 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-AG-4007       TCGA-AG-4008       TCGA-AG-4015       TCGA-AG-A002 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-AG-A008       TCGA-AG-A00C       TCGA-AG-A00H       TCGA-AG-A00Y 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-AG-A011       TCGA-AG-A014       TCGA-AG-A015       TCGA-AG-A016 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-AG-A01L       TCGA-AG-A01W       TCGA-AG-A01Y       TCGA-AG-A020 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-AG-A025       TCGA-AG-A026       TCGA-AG-A02G       TCGA-AG-A02N 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-AG-A02X       TCGA-AG-A032       TCGA-AG-A036       TCGA-AH-6544 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-AH-6547       TCGA-AH-6643       TCGA-AH-6644       TCGA-CI-6622 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-DC-5337       TCGA-DC-5869       TCGA-DC-6155       TCGA-DC-6157 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-DC-6158       TCGA-DC-6160       TCGA-DC-6681       TCGA-DC-6682 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-DC-6683       TCGA-DY-A0XA       TCGA-DY-A1DC       TCGA-DY-A1DD 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-DY-A1DF       TCGA-DY-A1DG       TCGA-DY-A1H8       TCGA-EI-6506 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-EI-6507       TCGA-EI-6508       TCGA-EI-6510       TCGA-F5-6464 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-F5-6465       TCGA-F5-6571       TCGA-F5-6702       TCGA-F5-6811 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
      TCGA-F5-6812       TCGA-F5-6813       TCGA-G5-6235       TCGA-G5-6641 
"NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" "NDUFV2 WILD-TYPE" 
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NDUFV2 MUTATED                                  0     0
  NDUFV2 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  NDUFV2 MUTATED                           0     3
  NDUFV2 WILD-TYPE                        22   223
D1951V13, multiclass
                                  clus
vv                                 NDUFV2 MUTATED NDUFV2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         3              223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1952) Variable = SYT2 MUTATION ANALYSIS
D1952V1, survival
                sevent
clus2              0   1
  SYT2 MUTATED     6   3
  SYT2 WILD-TYPE 372  90
  SYT2 MUTATED SYT2 WILD-TYPE 
             9            462 
  SYT2 MUTATED SYT2 WILD-TYPE 
             3             90 
$`SYT2 MUTATED`
TCGA-AA-3496 TCGA-AA-A00N TCGA-AA-A010 TCGA-AZ-6598 TCGA-AZ-6606 TCGA-CM-4752 
        1.02         4.01        34.98        49.41        11.74        13.02 
TCGA-D5-6540 TCGA-DM-A28K TCGA-AG-A002 
       16.14        98.24        20.98 

$`SYT2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        88.21         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
       29.56         5.23         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-5341 TCGA-CM-5344 
       23.05        20.02        37.02        25.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 
       15.12        17.85         4.80        17.13        12.49        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       35.97        60.79       117.07         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  SYT2 MUTATED SYT2 WILD-TYPE 
          1.02           0.00 
  SYT2 MUTATED SYT2 WILD-TYPE 
         98.24         148.01 
  SYT2 MUTATED SYT2 WILD-TYPE 
        16.140         20.235 
[1] "1.0 - 98.2 (16.1)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.6"
D1952V2, continuous
D1952V3, binary
                cls
clus               0   1
  SYT2 MUTATED     8   1
  SYT2 WILD-TYPE 358 118
[1] "tbl2"
                cls
clus             [,1] [,2]
  SYT2 MUTATED      8    1
  SYT2 WILD-TYPE  358  118
        clus
vv       SYT2 MUTATED SYT2 WILD-TYPE
  COLON             8            358
  RECTUM            1            118
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SYT2 MUTATED         2        0        2         2         2         0
  SYT2 WILD-TYPE      89        1       30       136         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SYT2 MUTATED           0          0          0          0        1         0
  SYT2 WILD-TYPE        24         11         59         42       47        18
                vv
clus             STAGE IVB
  SYT2 MUTATED           0
  SYT2 WILD-TYPE         1
D1952V4, multiclass
            clus
vv           SYT2 MUTATED SYT2 WILD-TYPE
  STAGE I               2             89
  STAGE IA              0              1
  STAGE II              2             30
  STAGE IIA             2            136
  STAGE IIB             2              8
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            0             59
  STAGE IIIC            0             42
  STAGE IV              1             47
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  SYT2 MUTATED     0   2   4   3
  SYT2 WILD-TYPE  17  90 325  47
D1952V5, multiclass
    clus
vv   SYT2 MUTATED SYT2 WILD-TYPE
  T1            0             17
  T2            2             90
  T3            4            325
  T4            3             47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  SYT2 MUTATED     8   0   1
  SYT2 WILD-TYPE 279 113  86
D1952V6, multiclass
    clus
vv   SYT2 MUTATED SYT2 WILD-TYPE
  N0            8            279
  N1            0            113
  N2            1             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1952V7, binary
                cls
clus               0   1
  SYT2 MUTATED     7   1
  SYT2 WILD-TYPE 368  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  SYT2 MUTATED      7    1
  SYT2 WILD-TYPE  368   64
   clus
vv  SYT2 MUTATED SYT2 WILD-TYPE
  0            7            368
  1            1             64
[1] 2 2
[1] FALSE
D1952V8, binary
                cls
clus               0   1
  SYT2 MUTATED     3   6
  SYT2 WILD-TYPE 222 258
[1] "tbl2"
                cls
clus             [,1] [,2]
  SYT2 MUTATED      3    6
  SYT2 WILD-TYPE  222  258
        clus
vv       SYT2 MUTATED SYT2 WILD-TYPE
  FEMALE            3            222
  MALE              6            258
[1] 2 2
[1] FALSE
D1952V9, binary
                cls
clus               0   1
  SYT2 MUTATED     6   0
  SYT2 WILD-TYPE 344  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  SYT2 MUTATED      6    0
  SYT2 WILD-TYPE  344   22
     clus
vv    SYT2 MUTATED SYT2 WILD-TYPE
  NO             6            344
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SYT2 MUTATED                      5                             3
  SYT2 WILD-TYPE                  310                            44
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SYT2 MUTATED                       1                              0
  SYT2 WILD-TYPE                   105                             10
D1952V10, multiclass
                                clus
vv                               SYT2 MUTATED SYT2 WILD-TYPE
  COLON ADENOCARCINOMA                      5            310
  COLON MUCINOUS ADENOCARCINOMA             3             44
  RECTAL ADENOCARCINOMA                     1            105
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  SYT2 MUTATED     6   0   0   0
  SYT2 WILD-TYPE 339   4  31  25
D1952V11, multiclass
    clus
vv   SYT2 MUTATED SYT2 WILD-TYPE
  R0            6            339
  R1            0              4
  R2            0             31
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1952V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SYT2 MUTATED                                  0     0
  SYT2 WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  SYT2 MUTATED                           1     4
  SYT2 WILD-TYPE                        21   222
D1952V13, multiclass
                                  clus
vv                                 SYT2 MUTATED SYT2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                       4            222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1953) Variable = KIT MUTATION ANALYSIS
D1953V1, survival
               sevent
clus2             0   1
  KIT MUTATED    86  21
  KIT WILD-TYPE 292  72
  KIT MUTATED KIT WILD-TYPE 
          107           364 
  KIT MUTATED KIT WILD-TYPE 
           21            72 
$`KIT MUTATED`
TCGA-A6-3809 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5665 
       32.75        31.63        30.44        29.19        33.53        22.06 
TCGA-A6-5666 TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6781 
       32.71         8.38        25.18        24.69        23.87        19.66 
TCGA-AA-3492 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-A00N 
        3.02        61.02         6.05        85.05        19.04         4.01 
TCGA-AA-A010 TCGA-AA-A024 TCGA-AD-5900 TCGA-AD-6890 TCGA-AD-6899 TCGA-AU-3779 
       34.98        39.06         0.07         0.79         5.79        14.50 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
       21.44        17.82        58.39        62.79        88.21        49.41 
TCGA-AZ-6601 TCGA-AZ-6605 TCGA-CA-5797 TCGA-CA-6716 TCGA-CA-6717 TCGA-CK-4947 
      100.01         5.23         3.29        12.20        12.76        17.56 
TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6748 
      148.01        15.62        51.32         9.99        21.14         1.91 
TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5862 TCGA-CM-5868 TCGA-CM-6161 
       13.02        22.03        30.08         5.03        17.03        15.02 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       29.03        16.04        14.99        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-D5-5538 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6537 
       12.95        12.26        55.92        20.19        18.25         4.80 
TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6930 
       17.13        16.14        15.58         9.44         4.80         1.51 
TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HA 
      130.65        49.91        13.32       140.38         7.50       131.51 
TCGA-DM-A28C TCGA-DM-A28E TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
       81.37       119.93         8.61        31.96        35.74         6.18 
TCGA-F4-6808 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 
       33.67        35.31       133.18        53.62        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-AG-3731 TCGA-AG-A002 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
       26.17        37.02        20.98         0.72         6.05        33.17 
TCGA-DC-5337 TCGA-DC-6157 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DG 
       15.02        27.95       126.44        41.36        57.24        51.48 
TCGA-EF-5830 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-G5-6235 
        0.49        19.96        20.91        18.28        55.76 

$`KIT WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6649 
       23.61        22.09        27.09        22.52        25.08        24.16 
TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       21.76        24.39        20.12        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       19.99        13.94        19.99        78.08         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       26.99        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 
        1.02        33.04        35.01        26.01        37.02        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       39.98        18.05        40.96        21.37        15.52        56.55 
TCGA-AD-6895 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-6004 
        0.72        22.42        27.42        10.88         0.20        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       16.31         0.95        33.01         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6606 TCGA-AZ-6607 
       22.36         6.77        12.10        29.56        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6718 
        1.61        12.69         3.06         3.25         0.07        10.06 
TCGA-CA-6719 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 
       14.30        85.45        49.08        82.95       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5860 
       20.02        37.02        25.02        29.06        22.98        32.02 
TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6166 
       15.02        15.02        15.02        12.00         2.96        21.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       12.99        13.02        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-6533 
       10.06        12.03        45.40        19.59        56.09         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6539 TCGA-D5-6898 TCGA-D5-6920 
       43.27        15.12        17.85        12.49         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6931 
        4.41        12.43        14.30         9.04        11.64        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D4 
       11.38        10.26       119.70        24.43        38.20        92.75 
TCGA-DM-A1D8 TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28F 
       12.59        44.32       135.65       139.17         6.12        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       60.79       117.07        98.24        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6299 
       41.42        16.24        13.25         0.53        47.41        74.56 
TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       65.85        44.68        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
       19.99         7.99         0.99        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-CI-6622 
      117.11        38.56         1.45        17.49         0.69         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6158 
        4.73        78.12         7.17         5.03        13.97        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DF 
       19.99         5.95         4.01         5.03         5.29        24.13 
TCGA-DY-A1H8 TCGA-EI-6506 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       32.61        20.55         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6641 
       32.19         0.66         0.69        26.43 

  KIT MUTATED KIT WILD-TYPE 
         0.07          0.00 
  KIT MUTATED KIT WILD-TYPE 
       148.01        139.17 
  KIT MUTATED KIT WILD-TYPE 
       21.440        20.005 
[1] "0.1 - 148.0 (21.4)" "0.0 - 139.2 (20.0)"
[1] "hr=" "1.3"
D1953V2, continuous
D1953V3, binary
               cls
clus              0   1
  KIT MUTATED    96  16
  KIT WILD-TYPE 270 103
[1] "tbl2"
               cls
clus            [,1] [,2]
  KIT MUTATED     96   16
  KIT WILD-TYPE  270  103
        clus
vv       KIT MUTATED KIT WILD-TYPE
  COLON           96           270
  RECTUM          16           103
[1] 2 2
[1] FALSE
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KIT MUTATED        15        1        6        33         5         1
  KIT WILD-TYPE      76        0       26       105         5         0
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  KIT MUTATED           5          0         20          9        8         7
  KIT WILD-TYPE        19         11         39         33       40        11
               vv
clus            STAGE IVB
  KIT MUTATED           0
  KIT WILD-TYPE         1
D1953V4, multiclass
            clus
vv           KIT MUTATED KIT WILD-TYPE
  STAGE I             15            76
  STAGE IA             1             0
  STAGE II             6            26
  STAGE IIA           33           105
  STAGE IIB            5             5
  STAGE IIC            1             0
  STAGE III            5            19
  STAGE IIIA           0            11
  STAGE IIIB          20            39
  STAGE IIIC           9            33
  STAGE IV             8            40
  STAGE IVA            7            11
  STAGE IVB            0             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  KIT MUTATED     5  13  79  14
  KIT WILD-TYPE  12  79 250  36
D1953V5, multiclass
    clus
vv   KIT MUTATED KIT WILD-TYPE
  T1           5            12
  T2          13            79
  T3          79           250
  T4          14            36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2
  KIT MUTATED    67  32  12
  KIT WILD-TYPE 220  81  75
D1953V6, multiclass
    clus
vv   KIT MUTATED KIT WILD-TYPE
  N0          67           220
  N1          32            81
  N2          12            75
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1953V7, binary
               cls
clus              0   1
  KIT MUTATED    80  14
  KIT WILD-TYPE 295  51
[1] "tbl2"
               cls
clus            [,1] [,2]
  KIT MUTATED     80   14
  KIT WILD-TYPE  295   51
   clus
vv  KIT MUTATED KIT WILD-TYPE
  0          80           295
  1          14            51
[1] 2 2
[1] FALSE
D1953V8, binary
               cls
clus              0   1
  KIT MUTATED    53  59
  KIT WILD-TYPE 172 205
[1] "tbl2"
               cls
clus            [,1] [,2]
  KIT MUTATED     53   59
  KIT WILD-TYPE  172  205
        clus
vv       KIT MUTATED KIT WILD-TYPE
  FEMALE          53           172
  MALE            59           205
[1] 2 2
[1] FALSE
D1953V9, binary
               cls
clus              0   1
  KIT MUTATED    82   2
  KIT WILD-TYPE 268  20
[1] "tbl2"
               cls
clus            [,1] [,2]
  KIT MUTATED     82    2
  KIT WILD-TYPE  268   20
     clus
vv    KIT MUTATED KIT WILD-TYPE
  NO           82           268
  YES           2            20
[1] 2 2
[1] FALSE
               vv
clus            COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  KIT MUTATED                     81                            14
  KIT WILD-TYPE                  234                            33
               vv
clus            RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  KIT MUTATED                      16                              0
  KIT WILD-TYPE                    90                             10
D1953V10, multiclass
                                clus
vv                               KIT MUTATED KIT WILD-TYPE
  COLON ADENOCARCINOMA                    81           234
  COLON MUCINOUS ADENOCARCINOMA           14            33
  RECTAL ADENOCARCINOMA                   16            90
  RECTAL MUCINOUS ADENOCARCINOMA           0            10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             R0  R1  R2  RX
  KIT MUTATED    70   1   4   9
  KIT WILD-TYPE 275   3  27  16
D1953V11, multiclass
    clus
vv   KIT MUTATED KIT WILD-TYPE
  R0          70           275
  R1           1             3
  R2           4            27
  RX           9            16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1953V12, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KIT MUTATED                                  0     3
  KIT WILD-TYPE                                1     8
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  KIT MUTATED                          11    85
  KIT WILD-TYPE                        11   141
D1953V13, multiclass
                                  clus
vv                                 KIT MUTATED KIT WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      3             8
  BLACK OR AFRICAN AMERICAN                 11            11
  WHITE                                     85           141
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1954) Variable = ERMP1 MUTATION ANALYSIS
D1954V1, survival
                 sevent
clus2               0   1
  ERMP1 MUTATED     9   1
  ERMP1 WILD-TYPE 369  92
  ERMP1 MUTATED ERMP1 WILD-TYPE 
             10             461 
  ERMP1 MUTATED ERMP1 WILD-TYPE 
              1              92 
$`ERMP1 MUTATED`
TCGA-AA-3710 TCGA-AA-A010 TCGA-AU-6004 TCGA-CA-6717 TCGA-CM-4743 TCGA-D5-6927 
       26.99        34.98        27.09        12.76        23.05         9.44 
TCGA-DM-A28F TCGA-AG-3599 TCGA-AG-3883 TCGA-AG-A002 
       35.97        12.03         1.02        20.98 

$`ERMP1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
       19.00        36.00         5.03        85.05        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       10.88         0.20        14.50        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
      124.27        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
       14.30         9.04        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
      119.93        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.04        19.99        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  ERMP1 MUTATED ERMP1 WILD-TYPE 
           1.02            0.00 
  ERMP1 MUTATED ERMP1 WILD-TYPE 
          35.97          148.01 
  ERMP1 MUTATED ERMP1 WILD-TYPE 
         22.015          20.120 
[1] "1.0 - 36.0 (22.0)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.4"
D1954V2, continuous
D1954V3, binary
                 cls
clus                0   1
  ERMP1 MUTATED     8   3
  ERMP1 WILD-TYPE 358 116
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERMP1 MUTATED      8    3
  ERMP1 WILD-TYPE  358  116
        clus
vv       ERMP1 MUTATED ERMP1 WILD-TYPE
  COLON              8             358
  RECTUM             3             116
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ERMP1 MUTATED         4        0        0         5         1         0
  ERMP1 WILD-TYPE      87        1       32       133         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ERMP1 MUTATED           0          0          1          0        0         0
  ERMP1 WILD-TYPE        24         11         58         42       48        18
                 vv
clus              STAGE IVB
  ERMP1 MUTATED           0
  ERMP1 WILD-TYPE         1
D1954V4, multiclass
            clus
vv           ERMP1 MUTATED ERMP1 WILD-TYPE
  STAGE I                4              87
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              5             133
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ERMP1 MUTATED     0   4   6   1
  ERMP1 WILD-TYPE  17  88 323  49
D1954V5, multiclass
    clus
vv   ERMP1 MUTATED ERMP1 WILD-TYPE
  T1             0              17
  T2             4              88
  T3             6             323
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  ERMP1 MUTATED    10   1   0
  ERMP1 WILD-TYPE 277 112  87
D1954V6, multiclass
    clus
vv   ERMP1 MUTATED ERMP1 WILD-TYPE
  N0            10             277
  N1             1             112
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1954V7, binary
                 cls
clus                0   1
  ERMP1 MUTATED    11   0
  ERMP1 WILD-TYPE 364  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERMP1 MUTATED     11    0
  ERMP1 WILD-TYPE  364   65
   clus
vv  ERMP1 MUTATED ERMP1 WILD-TYPE
  0            11             364
  1             0              65
[1] 2 2
[1] FALSE
D1954V8, binary
                 cls
clus                0   1
  ERMP1 MUTATED     4   7
  ERMP1 WILD-TYPE 221 257
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERMP1 MUTATED      4    7
  ERMP1 WILD-TYPE  221  257
        clus
vv       ERMP1 MUTATED ERMP1 WILD-TYPE
  FEMALE             4             221
  MALE               7             257
[1] 2 2
[1] FALSE
D1954V9, binary
                 cls
clus                0   1
  ERMP1 MUTATED     7   0
  ERMP1 WILD-TYPE 343  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERMP1 MUTATED      7    0
  ERMP1 WILD-TYPE  343   22
     clus
vv    ERMP1 MUTATED ERMP1 WILD-TYPE
  NO              7             343
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ERMP1 MUTATED                      7                             1
  ERMP1 WILD-TYPE                  308                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ERMP1 MUTATED                       2                              0
  ERMP1 WILD-TYPE                   104                             10
D1954V10, multiclass
                                clus
vv                               ERMP1 MUTATED ERMP1 WILD-TYPE
  COLON ADENOCARCINOMA                       7             308
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  ERMP1 MUTATED     9   0   0   1
  ERMP1 WILD-TYPE 336   4  31  24
D1954V11, multiclass
    clus
vv   ERMP1 MUTATED ERMP1 WILD-TYPE
  R0             9             336
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1954V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ERMP1 MUTATED                                  0     1
  ERMP1 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ERMP1 MUTATED                           0     4
  ERMP1 WILD-TYPE                        22   222
D1954V13, multiclass
                                  clus
vv                                 ERMP1 MUTATED ERMP1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        4             222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1955) Variable = NOV MUTATION ANALYSIS
D1955V1, survival
               sevent
clus2             0   1
  NOV MUTATED     9   1
  NOV WILD-TYPE 369  92
  NOV MUTATED NOV WILD-TYPE 
           10           461 
  NOV MUTATED NOV WILD-TYPE 
            1            92 
$`NOV MUTATED`
TCGA-AA-3660 TCGA-AA-A010 TCGA-CM-6164 TCGA-CM-6166 TCGA-D5-6535 TCGA-DM-A28C 
       78.08        34.98        29.03        21.99        15.12        81.37 
TCGA-F4-6854 TCGA-G4-6628 TCGA-AG-A002 TCGA-DY-A0XA 
        0.53        79.69        20.98       126.44 

$`NOV WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 
       20.98        19.99        13.94        19.99        61.02         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6168 
       15.02        12.00         2.96        16.04        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
        1.32        43.27        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6855 TCGA-F4-6856 
       41.42        16.24        33.67        13.25        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 
       35.80        26.17        91.79        46.75        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD 
        5.95         4.01         5.03         5.29        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  NOV MUTATED NOV WILD-TYPE 
         0.53          0.00 
  NOV MUTATED NOV WILD-TYPE 
       126.44        148.01 
  NOV MUTATED NOV WILD-TYPE 
       32.005        20.020 
[1] "0.5 - 126.4 (32.0)" "0.0 - 148.0 (20.0)"
[1] "hr=" "3.5"
D1955V2, continuous
D1955V3, binary
               cls
clus              0   1
  NOV MUTATED     8   2
  NOV WILD-TYPE 358 117
[1] "tbl2"
               cls
clus            [,1] [,2]
  NOV MUTATED      8    2
  NOV WILD-TYPE  358  117
        clus
vv       NOV MUTATED NOV WILD-TYPE
  COLON            8           358
  RECTUM           2           117
[1] 2 2
[1] FALSE
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NOV MUTATED         3        0        1         4         1         0
  NOV WILD-TYPE      88        1       31       134         9         1
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NOV MUTATED           0          0          1          0        0         0
  NOV WILD-TYPE        24         11         58         42       48        18
               vv
clus            STAGE IVB
  NOV MUTATED           0
  NOV WILD-TYPE         1
D1955V4, multiclass
            clus
vv           NOV MUTATED NOV WILD-TYPE
  STAGE I              3            88
  STAGE IA             0             1
  STAGE II             1            31
  STAGE IIA            4           134
  STAGE IIB            1             9
  STAGE IIC            0             1
  STAGE III            0            24
  STAGE IIIA           0            11
  STAGE IIIB           1            58
  STAGE IIIC           0            42
  STAGE IV             0            48
  STAGE IVA            0            18
  STAGE IVB            0             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  NOV MUTATED     0   3   6   1
  NOV WILD-TYPE  17  89 323  49
D1955V5, multiclass
    clus
vv   NOV MUTATED NOV WILD-TYPE
  T1           0            17
  T2           3            89
  T3           6           323
  T4           1            49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2
  NOV MUTATED     9   1   0
  NOV WILD-TYPE 278 112  87
D1955V6, multiclass
    clus
vv   NOV MUTATED NOV WILD-TYPE
  N0           9           278
  N1           1           112
  N2           0            87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1955V7, binary
               cls
clus              0   1
  NOV MUTATED     9   0
  NOV WILD-TYPE 366  65
[1] "tbl2"
               cls
clus            [,1] [,2]
  NOV MUTATED      9    0
  NOV WILD-TYPE  366   65
   clus
vv  NOV MUTATED NOV WILD-TYPE
  0           9           366
  1           0            65
[1] 2 2
[1] FALSE
D1955V8, binary
               cls
clus              0   1
  NOV MUTATED     7   3
  NOV WILD-TYPE 218 261
[1] "tbl2"
               cls
clus            [,1] [,2]
  NOV MUTATED      7    3
  NOV WILD-TYPE  218  261
        clus
vv       NOV MUTATED NOV WILD-TYPE
  FEMALE           7           218
  MALE             3           261
[1] 2 2
[1] FALSE
D1955V9, binary
               cls
clus              0   1
  NOV MUTATED     8   0
  NOV WILD-TYPE 342  22
[1] "tbl2"
               cls
clus            [,1] [,2]
  NOV MUTATED      8    0
  NOV WILD-TYPE  342   22
     clus
vv    NOV MUTATED NOV WILD-TYPE
  NO            8           342
  YES           0            22
[1] 2 2
[1] FALSE
               vv
clus            COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  NOV MUTATED                      8                             0
  NOV WILD-TYPE                  307                            47
               vv
clus            RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  NOV MUTATED                       2                              0
  NOV WILD-TYPE                   104                             10
D1955V10, multiclass
                                clus
vv                               NOV MUTATED NOV WILD-TYPE
  COLON ADENOCARCINOMA                     8           307
  COLON MUCINOUS ADENOCARCINOMA            0            47
  RECTAL ADENOCARCINOMA                    2           104
  RECTAL MUCINOUS ADENOCARCINOMA           0            10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             R0  R1  R2  RX
  NOV MUTATED     7   0   0   1
  NOV WILD-TYPE 338   4  31  24
D1955V11, multiclass
    clus
vv   NOV MUTATED NOV WILD-TYPE
  R0           7           338
  R1           0             4
  R2           0            31
  RX           1            24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1955V12, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NOV MUTATED                                  0     0
  NOV WILD-TYPE                                1    11
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  NOV MUTATED                           0     7
  NOV WILD-TYPE                        22   219
D1955V13, multiclass
                                  clus
vv                                 NOV MUTATED NOV WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      0            11
  BLACK OR AFRICAN AMERICAN                  0            22
  WHITE                                      7           219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1956) Variable = MYOG MUTATION ANALYSIS
D1956V1, survival
                sevent
clus2              0   1
  MYOG MUTATED     6   0
  MYOG WILD-TYPE 372  93
  MYOG MUTATED MYOG WILD-TYPE 
             6            465 
  MYOG MUTATED MYOG WILD-TYPE 
             0             93 
$`MYOG MUTATED`
TCGA-AA-3510 TCGA-AD-6895 TCGA-CA-5796 TCGA-CM-5348 TCGA-G4-6628 TCGA-AG-A002 
       63.98         0.72         3.25        22.98        79.69        20.98 

$`MYOG WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       15.52        56.55         0.79         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        1.61        12.69         3.06         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       13.02        29.06        22.03        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       46.75        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  MYOG MUTATED MYOG WILD-TYPE 
          0.72           0.00 
  MYOG MUTATED MYOG WILD-TYPE 
         79.69         148.01 
  MYOG MUTATED MYOG WILD-TYPE 
         21.98          20.12 
[1] "0.7 - 79.7 (22.0)"  "0.0 - 148.0 (20.1)"
[1] "hr="     "9200000"
D1956V2, continuous
D1956V3, binary
                cls
clus               0   1
  MYOG MUTATED     5   1
  MYOG WILD-TYPE 361 118
[1] "tbl2"
                cls
clus             [,1] [,2]
  MYOG MUTATED      5    1
  MYOG WILD-TYPE  361  118
        clus
vv       MYOG MUTATED MYOG WILD-TYPE
  COLON             5            361
  RECTUM            1            118
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MYOG MUTATED         2        0        1         1         0         0
  MYOG WILD-TYPE      89        1       31       137        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MYOG MUTATED           0          0          1          0        0         0
  MYOG WILD-TYPE        24         11         58         42       48        18
                vv
clus             STAGE IVB
  MYOG MUTATED           0
  MYOG WILD-TYPE         1
D1956V4, multiclass
            clus
vv           MYOG MUTATED MYOG WILD-TYPE
  STAGE I               2             89
  STAGE IA              0              1
  STAGE II              1             31
  STAGE IIA             1            137
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            1             58
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  MYOG MUTATED     0   2   4   0
  MYOG WILD-TYPE  17  90 325  50
D1956V5, multiclass
    clus
vv   MYOG MUTATED MYOG WILD-TYPE
  T1            0             17
  T2            2             90
  T3            4            325
  T4            0             50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  MYOG MUTATED     4   2   0
  MYOG WILD-TYPE 283 111  87
D1956V6, multiclass
    clus
vv   MYOG MUTATED MYOG WILD-TYPE
  N0            4            283
  N1            2            111
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1956V7, binary
                cls
clus               0   1
  MYOG MUTATED     5   0
  MYOG WILD-TYPE 370  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  MYOG MUTATED      5    0
  MYOG WILD-TYPE  370   65
   clus
vv  MYOG MUTATED MYOG WILD-TYPE
  0            5            370
  1            0             65
[1] 2 2
[1] FALSE
D1956V8, binary
                cls
clus               0   1
  MYOG MUTATED     1   5
  MYOG WILD-TYPE 224 259
[1] "tbl2"
                cls
clus             [,1] [,2]
  MYOG MUTATED      1    5
  MYOG WILD-TYPE  224  259
        clus
vv       MYOG MUTATED MYOG WILD-TYPE
  FEMALE            1            224
  MALE              5            259
[1] 2 2
[1] FALSE
D1956V9, binary
                cls
clus               0   1
  MYOG MUTATED     5   0
  MYOG WILD-TYPE 345  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  MYOG MUTATED      5    0
  MYOG WILD-TYPE  345   22
     clus
vv    MYOG MUTATED MYOG WILD-TYPE
  NO             5            345
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MYOG MUTATED                      4                             1
  MYOG WILD-TYPE                  311                            46
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MYOG MUTATED                       1                              0
  MYOG WILD-TYPE                   105                             10
D1956V10, multiclass
                                clus
vv                               MYOG MUTATED MYOG WILD-TYPE
  COLON ADENOCARCINOMA                      4            311
  COLON MUCINOUS ADENOCARCINOMA             1             46
  RECTAL ADENOCARCINOMA                     1            105
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  MYOG MUTATED     5   0   0   0
  MYOG WILD-TYPE 340   4  31  25
D1956V11, multiclass
    clus
vv   MYOG MUTATED MYOG WILD-TYPE
  R0            5            340
  R1            0              4
  R2            0             31
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1956V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MYOG MUTATED                                  0     1
  MYOG WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  MYOG MUTATED                           0     3
  MYOG WILD-TYPE                        22   223
D1956V13, multiclass
                                  clus
vv                                 MYOG MUTATED MYOG WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       3            223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1957) Variable = NTN4 MUTATION ANALYSIS
D1957V1, survival
                sevent
clus2              0   1
  NTN4 MUTATED     8   1
  NTN4 WILD-TYPE 370  92
  NTN4 MUTATED NTN4 WILD-TYPE 
             9            462 
  NTN4 MUTATED NTN4 WILD-TYPE 
             1             92 
$`NTN4 MUTATED`
TCGA-A6-5665 TCGA-AA-3831 TCGA-AA-A010 TCGA-AA-A01R TCGA-AA-A02W TCGA-AZ-6598 
       22.06        17.98        34.98        35.01        41.00        49.41 
TCGA-D5-6541 TCGA-AG-A002 TCGA-AG-A02N 
       15.58        20.98        61.97 

$`NTN4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       31.00        38.07         1.02         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
        5.03        14.01         0.92        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       88.21         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 
       10.98        49.97         1.94        38.96        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  NTN4 MUTATED NTN4 WILD-TYPE 
         15.58           0.00 
  NTN4 MUTATED NTN4 WILD-TYPE 
         61.97         148.01 
  NTN4 MUTATED NTN4 WILD-TYPE 
        34.980         20.035 
[1] "15.6 - 62.0 (35.0)" "0.0 - 148.0 (20.0)"
[1] "hr=" "2.3"
D1957V2, continuous
D1957V3, binary
                cls
clus               0   1
  NTN4 MUTATED     7   2
  NTN4 WILD-TYPE 359 117
[1] "tbl2"
                cls
clus             [,1] [,2]
  NTN4 MUTATED      7    2
  NTN4 WILD-TYPE  359  117
        clus
vv       NTN4 MUTATED NTN4 WILD-TYPE
  COLON             7            359
  RECTUM            2            117
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NTN4 MUTATED         2        0        2         3         1         0
  NTN4 WILD-TYPE      89        1       30       135         9         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NTN4 MUTATED           1          0          0          0        0         0
  NTN4 WILD-TYPE        23         11         59         42       48        18
                vv
clus             STAGE IVB
  NTN4 MUTATED           0
  NTN4 WILD-TYPE         1
D1957V4, multiclass
            clus
vv           NTN4 MUTATED NTN4 WILD-TYPE
  STAGE I               2             89
  STAGE IA              0              1
  STAGE II              2             30
  STAGE IIA             3            135
  STAGE IIB             1              9
  STAGE IIC             0              1
  STAGE III             1             23
  STAGE IIIA            0             11
  STAGE IIIB            0             59
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  NTN4 MUTATED     0   2   6   1
  NTN4 WILD-TYPE  17  90 323  49
D1957V5, multiclass
    clus
vv   NTN4 MUTATED NTN4 WILD-TYPE
  T1            0             17
  T2            2             90
  T3            6            323
  T4            1             49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  NTN4 MUTATED     8   0   1
  NTN4 WILD-TYPE 279 113  86
D1957V6, multiclass
    clus
vv   NTN4 MUTATED NTN4 WILD-TYPE
  N0            8            279
  N1            0            113
  N2            1             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1957V7, binary
                cls
clus               0   1
  NTN4 MUTATED     8   0
  NTN4 WILD-TYPE 367  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  NTN4 MUTATED      8    0
  NTN4 WILD-TYPE  367   65
   clus
vv  NTN4 MUTATED NTN4 WILD-TYPE
  0            8            367
  1            0             65
[1] 2 2
[1] FALSE
D1957V8, binary
                cls
clus               0   1
  NTN4 MUTATED     4   5
  NTN4 WILD-TYPE 221 259
[1] "tbl2"
                cls
clus             [,1] [,2]
  NTN4 MUTATED      4    5
  NTN4 WILD-TYPE  221  259
        clus
vv       NTN4 MUTATED NTN4 WILD-TYPE
  FEMALE            4            221
  MALE              5            259
[1] 2 2
[1] FALSE
D1957V9, binary
                cls
clus               0   1
  NTN4 MUTATED     7   1
  NTN4 WILD-TYPE 343  21
[1] "tbl2"
                cls
clus             [,1] [,2]
  NTN4 MUTATED      7    1
  NTN4 WILD-TYPE  343   21
     clus
vv    NTN4 MUTATED NTN4 WILD-TYPE
  NO             7            343
  YES            1             21
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  NTN4 MUTATED                      6                             1
  NTN4 WILD-TYPE                  309                            46
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  NTN4 MUTATED                       2                              0
  NTN4 WILD-TYPE                   104                             10
D1957V10, multiclass
                                clus
vv                               NTN4 MUTATED NTN4 WILD-TYPE
  COLON ADENOCARCINOMA                      6            309
  COLON MUCINOUS ADENOCARCINOMA             1             46
  RECTAL ADENOCARCINOMA                     2            104
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  NTN4 MUTATED     8   0   0   0
  NTN4 WILD-TYPE 337   4  31  25
D1957V11, multiclass
    clus
vv   NTN4 MUTATED NTN4 WILD-TYPE
  R0            8            337
  R1            0              4
  R2            0             31
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1957V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NTN4 MUTATED                                  0     0
  NTN4 WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  NTN4 MUTATED                           0     3
  NTN4 WILD-TYPE                        22   223
D1957V13, multiclass
                                  clus
vv                                 NTN4 MUTATED NTN4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       3            223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1958) Variable = XRN1 MUTATION ANALYSIS
D1958V1, survival
                sevent
clus2              0   1
  XRN1 MUTATED    17   6
  XRN1 WILD-TYPE 361  87
  XRN1 MUTATED XRN1 WILD-TYPE 
            23            448 
  XRN1 MUTATED XRN1 WILD-TYPE 
             6             87 
$`XRN1 MUTATED`
TCGA-A6-3809 TCGA-A6-5665 TCGA-AA-3516 TCGA-AA-3525 TCGA-AA-3529 TCGA-AA-3542 
       32.75        22.06        13.02         8.05         0.00        12.99 
TCGA-AA-A00A TCGA-AA-A010 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-CA-6717 
       38.04        34.98        58.39        49.41         6.77        12.76 
TCGA-CK-5913 TCGA-CM-5861 TCGA-D5-6532 TCGA-D5-6541 TCGA-DM-A28H TCGA-F4-6807 
       51.32        15.02        18.25        15.58       117.07        16.24 
TCGA-AG-3732 TCGA-AG-3892 TCGA-DY-A1DC TCGA-DY-A1DG TCGA-EI-6507 
       32.98        13.02        41.36        51.48        19.96 

$`XRN1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
       63.98         6.97         1.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 
       24.03        37.05        36.03        19.07        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        29.00        26.01         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       13.94        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       33.01        21.44        17.82         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       22.36        62.79        88.21        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07        12.20        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 
       17.56       148.01        85.45        15.62        49.08         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       30.08        32.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       20.19         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       17.13        12.49        16.14         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28K 
        6.12        81.37       119.93        35.97        60.79        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       34.42        41.42        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 
       13.94        19.99         7.99         0.99        37.02         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       17.03        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6508 
       57.24        24.13        32.61         0.49        20.55        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  XRN1 MUTATED XRN1 WILD-TYPE 
             0              0 
  XRN1 MUTATED XRN1 WILD-TYPE 
        117.07         148.01 
  XRN1 MUTATED XRN1 WILD-TYPE 
        19.960         20.235 
[1] "0.0 - 117.1 (20.0)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.2"
D1958V2, continuous
D1958V3, binary
                cls
clus               0   1
  XRN1 MUTATED    19   5
  XRN1 WILD-TYPE 347 114
[1] "tbl2"
                cls
clus             [,1] [,2]
  XRN1 MUTATED     19    5
  XRN1 WILD-TYPE  347  114
        clus
vv       XRN1 MUTATED XRN1 WILD-TYPE
  COLON            19            347
  RECTUM            5            114
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  XRN1 MUTATED         3        0        1        11         2         0
  XRN1 WILD-TYPE      88        1       31       127         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  XRN1 MUTATED           1          0          1          4        0         1
  XRN1 WILD-TYPE        23         11         58         38       48        17
                vv
clus             STAGE IVB
  XRN1 MUTATED           0
  XRN1 WILD-TYPE         1
D1958V4, multiclass
            clus
vv           XRN1 MUTATED XRN1 WILD-TYPE
  STAGE I               3             88
  STAGE IA              0              1
  STAGE II              1             31
  STAGE IIA            11            127
  STAGE IIB             2              8
  STAGE IIC             0              1
  STAGE III             1             23
  STAGE IIIA            0             11
  STAGE IIIB            1             58
  STAGE IIIC            4             38
  STAGE IV              0             48
  STAGE IVA             1             17
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  XRN1 MUTATED     1   2  19   2
  XRN1 WILD-TYPE  16  90 310  48
D1958V5, multiclass
    clus
vv   XRN1 MUTATED XRN1 WILD-TYPE
  T1            1             16
  T2            2             90
  T3           19            310
  T4            2             48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  XRN1 MUTATED    17   2   5
  XRN1 WILD-TYPE 270 111  82
D1958V6, multiclass
    clus
vv   XRN1 MUTATED XRN1 WILD-TYPE
  N0           17            270
  N1            2            111
  N2            5             82
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1958V7, binary
                cls
clus               0   1
  XRN1 MUTATED    20   1
  XRN1 WILD-TYPE 355  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  XRN1 MUTATED     20    1
  XRN1 WILD-TYPE  355   64
   clus
vv  XRN1 MUTATED XRN1 WILD-TYPE
  0           20            355
  1            1             64
[1] 2 2
[1] FALSE
D1958V8, binary
                cls
clus               0   1
  XRN1 MUTATED    13  11
  XRN1 WILD-TYPE 212 253
[1] "tbl2"
                cls
clus             [,1] [,2]
  XRN1 MUTATED     13   11
  XRN1 WILD-TYPE  212  253
        clus
vv       XRN1 MUTATED XRN1 WILD-TYPE
  FEMALE           13            212
  MALE             11            253
[1] 2 2
[1] FALSE
D1958V9, binary
                cls
clus               0   1
  XRN1 MUTATED    19   0
  XRN1 WILD-TYPE 331  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  XRN1 MUTATED     19    0
  XRN1 WILD-TYPE  331   22
     clus
vv    XRN1 MUTATED XRN1 WILD-TYPE
  NO            19            331
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  XRN1 MUTATED                     16                             3
  XRN1 WILD-TYPE                  299                            44
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  XRN1 MUTATED                       5                              0
  XRN1 WILD-TYPE                   101                             10
D1958V10, multiclass
                                clus
vv                               XRN1 MUTATED XRN1 WILD-TYPE
  COLON ADENOCARCINOMA                     16            299
  COLON MUCINOUS ADENOCARCINOMA             3             44
  RECTAL ADENOCARCINOMA                     5            101
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  XRN1 MUTATED    16   0   0   2
  XRN1 WILD-TYPE 329   4  31  23
D1958V11, multiclass
    clus
vv   XRN1 MUTATED XRN1 WILD-TYPE
  R0           16            329
  R1            0              4
  R2            0             31
  RX            2             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1958V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  XRN1 MUTATED                                  0     1
  XRN1 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  XRN1 MUTATED                           0    14
  XRN1 WILD-TYPE                        22   212
D1958V13, multiclass
                                  clus
vv                                 XRN1 MUTATED XRN1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                      14            212
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1959) Variable = FAM175A MUTATION ANALYSIS
D1959V1, survival
                   sevent
clus2                 0   1
  FAM175A MUTATED     6   2
  FAM175A WILD-TYPE 372  91
  FAM175A MUTATED FAM175A WILD-TYPE 
                8               463 
  FAM175A MUTATED FAM175A WILD-TYPE 
                2                91 
$`FAM175A MUTATED`
TCGA-A6-5664 TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01Q TCGA-AZ-6599 TCGA-DM-A28E 
       22.09         4.01        34.98         1.02         6.77       119.93 
TCGA-G4-6309 TCGA-G4-6586 
       85.48        35.80 

$`FAM175A WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       31.00        38.07        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        88.21        49.41        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
       81.37        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       55.04        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  FAM175A MUTATED FAM175A WILD-TYPE 
             1.02              0.00 
  FAM175A MUTATED FAM175A WILD-TYPE 
           119.93            148.01 
  FAM175A MUTATED FAM175A WILD-TYPE 
           28.535            20.120 
[1] "1.0 - 119.9 (28.5)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1"  
D1959V2, continuous
D1959V3, binary
                   cls
clus                  0   1
  FAM175A MUTATED     8   0
  FAM175A WILD-TYPE 358 119
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM175A MUTATED      8    0
  FAM175A WILD-TYPE  358  119
        clus
vv       FAM175A MUTATED FAM175A WILD-TYPE
  COLON                8               358
  RECTUM               0               119
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FAM175A MUTATED         1        0        1         2         2         0
  FAM175A WILD-TYPE      90        1       31       136         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FAM175A MUTATED           0          0          1          1        0
  FAM175A WILD-TYPE        24         11         58         41       48
                   vv
clus                STAGE IVA STAGE IVB
  FAM175A MUTATED           0         0
  FAM175A WILD-TYPE        18         1
D1959V4, multiclass
            clus
vv           FAM175A MUTATED FAM175A WILD-TYPE
  STAGE I                  1                90
  STAGE IA                 0                 1
  STAGE II                 1                31
  STAGE IIA                2               136
  STAGE IIB                2                 8
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               0                11
  STAGE IIIB               1                58
  STAGE IIIC               1                41
  STAGE IV                 0                48
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  FAM175A MUTATED     0   1   4   3
  FAM175A WILD-TYPE  17  91 325  47
D1959V5, multiclass
    clus
vv   FAM175A MUTATED FAM175A WILD-TYPE
  T1               0                17
  T2               1                91
  T3               4               325
  T4               3                47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  FAM175A MUTATED     6   1   1
  FAM175A WILD-TYPE 281 112  86
D1959V6, multiclass
    clus
vv   FAM175A MUTATED FAM175A WILD-TYPE
  N0               6               281
  N1               1               112
  N2               1                86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1959V7, binary
                   cls
clus                  0   1
  FAM175A MUTATED     6   0
  FAM175A WILD-TYPE 369  65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM175A MUTATED      6    0
  FAM175A WILD-TYPE  369   65
   clus
vv  FAM175A MUTATED FAM175A WILD-TYPE
  0               6               369
  1               0                65
[1] 2 2
[1] FALSE
D1959V8, binary
                   cls
clus                  0   1
  FAM175A MUTATED     5   3
  FAM175A WILD-TYPE 220 261
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM175A MUTATED      5    3
  FAM175A WILD-TYPE  220  261
        clus
vv       FAM175A MUTATED FAM175A WILD-TYPE
  FEMALE               5               220
  MALE                 3               261
[1] 2 2
[1] FALSE
D1959V9, binary
                   cls
clus                  0   1
  FAM175A MUTATED     5   0
  FAM175A WILD-TYPE 345  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM175A MUTATED      5    0
  FAM175A WILD-TYPE  345   22
     clus
vv    FAM175A MUTATED FAM175A WILD-TYPE
  NO                5               345
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  FAM175A MUTATED                      7                             1
  FAM175A WILD-TYPE                  308                            46
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  FAM175A MUTATED                       0                              0
  FAM175A WILD-TYPE                   106                             10
D1959V10, multiclass
                                clus
vv                               FAM175A MUTATED FAM175A WILD-TYPE
  COLON ADENOCARCINOMA                         7               308
  COLON MUCINOUS ADENOCARCINOMA                1                46
  RECTAL ADENOCARCINOMA                        0               106
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  FAM175A MUTATED     5   0   0   0
  FAM175A WILD-TYPE 340   4  31  25
D1959V11, multiclass
    clus
vv   FAM175A MUTATED FAM175A WILD-TYPE
  R0               5               340
  R1               0                 4
  R2               0                31
  RX               0                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1959V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FAM175A MUTATED                                  0     0
  FAM175A WILD-TYPE                                1    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  FAM175A MUTATED                           2     3
  FAM175A WILD-TYPE                        20   223
D1959V13, multiclass
                                  clus
vv                                 FAM175A MUTATED FAM175A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                      2                20
  WHITE                                          3               223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1960) Variable = CSF3R MUTATION ANALYSIS
D1960V1, survival
                 sevent
clus2               0   1
  CSF3R MUTATED     9   6
  CSF3R WILD-TYPE 369  87
  CSF3R MUTATED CSF3R WILD-TYPE 
             15             456 
  CSF3R MUTATED CSF3R WILD-TYPE 
              6              87 
$`CSF3R MUTATED`
TCGA-AA-3516 TCGA-AA-3552 TCGA-AA-3864 TCGA-AA-A00J TCGA-AA-A00N TCGA-AA-A010 
       13.02        13.02        53.00        18.05         4.01        34.98 
TCGA-AA-A01P TCGA-AD-5900 TCGA-CK-5913 TCGA-CM-4743 TCGA-CM-5861 TCGA-D5-6540 
       38.07         0.07        51.32        23.05        15.02        16.14 
TCGA-DM-A1DA TCGA-F4-6570 TCGA-AG-A02N 
        7.50         6.18        61.97 

$`CSF3R WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        1.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 
        0.99        31.07        31.07        30.05        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       30.02        34.03        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01Q TCGA-AA-A01R 
       32.02        12.00        31.00        31.00         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 
       41.00        39.98        18.05        40.96        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       85.45        15.62        49.08         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
        1.91       124.27        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 
       29.06        22.03        22.98        30.08        32.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB 
       92.75        49.91        13.32        12.59       140.38        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       35.74        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 
       10.98        49.97         1.94        38.96        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  CSF3R MUTATED CSF3R WILD-TYPE 
           0.07            0.00 
  CSF3R MUTATED CSF3R WILD-TYPE 
          61.97          148.01 
  CSF3R MUTATED CSF3R WILD-TYPE 
         16.140          20.415 
[1] "0.1 - 62.0 (16.1)"  "0.0 - 148.0 (20.4)"
[1] "hr=" "2.2"
D1960V2, continuous
D1960V3, binary
                 cls
clus                0   1
  CSF3R MUTATED    14   1
  CSF3R WILD-TYPE 352 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CSF3R MUTATED     14    1
  CSF3R WILD-TYPE  352  118
        clus
vv       CSF3R MUTATED CSF3R WILD-TYPE
  COLON             14             352
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CSF3R MUTATED         2        0        2         4         2         0
  CSF3R WILD-TYPE      89        1       30       134         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CSF3R MUTATED           2          0          1          2        0         0
  CSF3R WILD-TYPE        22         11         58         40       48        18
                 vv
clus              STAGE IVB
  CSF3R MUTATED           0
  CSF3R WILD-TYPE         1
D1960V4, multiclass
            clus
vv           CSF3R MUTATED CSF3R WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA              4             134
  STAGE IIB              2               8
  STAGE IIC              0               1
  STAGE III              2              22
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             2              40
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CSF3R MUTATED     0   2  10   3
  CSF3R WILD-TYPE  17  90 319  47
D1960V5, multiclass
    clus
vv   CSF3R MUTATED CSF3R WILD-TYPE
  T1             0              17
  T2             2              90
  T3            10             319
  T4             3              47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  CSF3R MUTATED    10   2   3
  CSF3R WILD-TYPE 277 111  84
D1960V6, multiclass
    clus
vv   CSF3R MUTATED CSF3R WILD-TYPE
  N0            10             277
  N1             2             111
  N2             3              84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1960V7, binary
                 cls
clus                0   1
  CSF3R MUTATED    13   0
  CSF3R WILD-TYPE 362  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CSF3R MUTATED     13    0
  CSF3R WILD-TYPE  362   65
   clus
vv  CSF3R MUTATED CSF3R WILD-TYPE
  0            13             362
  1             0              65
[1] 2 2
[1] FALSE
D1960V8, binary
                 cls
clus                0   1
  CSF3R MUTATED     7   8
  CSF3R WILD-TYPE 218 256
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CSF3R MUTATED      7    8
  CSF3R WILD-TYPE  218  256
        clus
vv       CSF3R MUTATED CSF3R WILD-TYPE
  FEMALE             7             218
  MALE               8             256
[1] 2 2
[1] FALSE
D1960V9, binary
                 cls
clus                0   1
  CSF3R MUTATED    11   0
  CSF3R WILD-TYPE 339  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CSF3R MUTATED     11    0
  CSF3R WILD-TYPE  339   22
     clus
vv    CSF3R MUTATED CSF3R WILD-TYPE
  NO             11             339
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CSF3R MUTATED                      9                             5
  CSF3R WILD-TYPE                  306                            42
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CSF3R MUTATED                       1                              0
  CSF3R WILD-TYPE                   105                             10
D1960V10, multiclass
                                clus
vv                               CSF3R MUTATED CSF3R WILD-TYPE
  COLON ADENOCARCINOMA                       9             306
  COLON MUCINOUS ADENOCARCINOMA              5              42
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  CSF3R MUTATED    12   0   0   1
  CSF3R WILD-TYPE 333   4  31  24
D1960V11, multiclass
    clus
vv   CSF3R MUTATED CSF3R WILD-TYPE
  R0            12             333
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1960V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CSF3R MUTATED                                  0     0
  CSF3R WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CSF3R MUTATED                           0     7
  CSF3R WILD-TYPE                        22   219
D1960V13, multiclass
                                  clus
vv                                 CSF3R MUTATED CSF3R WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        7             219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1961) Variable = RAB22A MUTATION ANALYSIS
D1961V1, survival
                  sevent
clus2                0   1
  RAB22A MUTATED     3   0
  RAB22A WILD-TYPE 375  93
  RAB22A MUTATED RAB22A WILD-TYPE 
               3              468 
  RAB22A MUTATED RAB22A WILD-TYPE 
               0               93 
$`RAB22A MUTATED`
TCGA-A6-6781 TCGA-AA-3950 TCGA-AA-A010 
       19.66        24.00        34.98 

$`RAB22A WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 
        2.01        12.99        24.00        33.01        26.01         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  RAB22A MUTATED RAB22A WILD-TYPE 
           19.66             0.00 
  RAB22A MUTATED RAB22A WILD-TYPE 
           34.98           148.01 
  RAB22A MUTATED RAB22A WILD-TYPE 
          24.000           20.155 
[1] "19.7 - 35.0 (24.0)" "0.0 - 148.0 (20.2)"
[1] "hr="     "3300000"
D1961V2, continuous
D1961V3, binary
                  cls
clus                 0   1
  RAB22A MUTATED     3   0
  RAB22A WILD-TYPE 363 119
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RAB22A MUTATED      3    0
  RAB22A WILD-TYPE  363  119
        clus
vv       RAB22A MUTATED RAB22A WILD-TYPE
  COLON               3              363
  RECTUM              0              119
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RAB22A MUTATED         0        0        0         1         1         0
  RAB22A WILD-TYPE      91        1       32       137         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RAB22A MUTATED           0          0          0          1        0
  RAB22A WILD-TYPE        24         11         59         41       48
                  vv
clus               STAGE IVA STAGE IVB
  RAB22A MUTATED           0         0
  RAB22A WILD-TYPE        18         1
D1961V4, multiclass
            clus
vv           RAB22A MUTATED RAB22A WILD-TYPE
  STAGE I                 0               91
  STAGE IA                0                1
  STAGE II                0               32
  STAGE IIA               1              137
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              0               59
  STAGE IIIC              1               41
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  RAB22A MUTATED     0   0   1   2
  RAB22A WILD-TYPE  17  92 328  48
D1961V5, multiclass
    clus
vv   RAB22A MUTATED RAB22A WILD-TYPE
  T1              0               17
  T2              0               92
  T3              1              328
  T4              2               48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  RAB22A MUTATED     2   1   0
  RAB22A WILD-TYPE 285 112  87
D1961V6, multiclass
    clus
vv   RAB22A MUTATED RAB22A WILD-TYPE
  N0              2              285
  N1              1              112
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1961V7, binary
                  cls
clus                 0   1
  RAB22A MUTATED     2   0
  RAB22A WILD-TYPE 373  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RAB22A MUTATED      2    0
  RAB22A WILD-TYPE  373   65
   clus
vv  RAB22A MUTATED RAB22A WILD-TYPE
  0              2              373
  1              0               65
[1] 2 2
[1] FALSE
D1961V8, binary
                  cls
clus                 0   1
  RAB22A MUTATED     2   1
  RAB22A WILD-TYPE 223 263
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RAB22A MUTATED      2    1
  RAB22A WILD-TYPE  223  263
        clus
vv       RAB22A MUTATED RAB22A WILD-TYPE
  FEMALE              2              223
  MALE                1              263
[1] 2 2
[1] FALSE
D1961V9, binary
                  cls
clus                 0   1
  RAB22A MUTATED     3   0
  RAB22A WILD-TYPE 347  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RAB22A MUTATED      3    0
  RAB22A WILD-TYPE  347   22
     clus
vv    RAB22A MUTATED RAB22A WILD-TYPE
  NO               3              347
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  RAB22A MUTATED                      1                             2
  RAB22A WILD-TYPE                  314                            45
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  RAB22A MUTATED                       0                              0
  RAB22A WILD-TYPE                   106                             10
D1961V10, multiclass
                                clus
vv                               RAB22A MUTATED RAB22A WILD-TYPE
  COLON ADENOCARCINOMA                        1              314
  COLON MUCINOUS ADENOCARCINOMA               2               45
  RECTAL ADENOCARCINOMA                       0              106
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  RAB22A MUTATED     3   0   0   0
  RAB22A WILD-TYPE 342   4  31  25
D1961V11, multiclass
    clus
vv   RAB22A MUTATED RAB22A WILD-TYPE
  R0              3              342
  R1              0                4
  R2              0               31
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1961V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RAB22A MUTATED                                  0     0
  RAB22A WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  RAB22A MUTATED                           0     1
  RAB22A WILD-TYPE                        22   225
D1961V13, multiclass
[1] "Remove cluster labels:" "RAB22A MUTATED"        
clus
  RAB22A MUTATED RAB22A WILD-TYPE 
               1              259 
      TCGA-A6-2671       TCGA-A6-2672       TCGA-A6-2674       TCGA-A6-2676 
"RAB22A WILD-TYPE" "RAB22A WILD-TYPE" "RAB22A WILD-TYPE" "RAB22A WILD-TYPE" 
      TCGA-A6-2677       TCGA-A6-2678       TCGA-A6-2683       TCGA-A6-3807 
"RAB22A WILD-TYPE" "RAB22A WILD-TYPE" "RAB22A WILD-TYPE" "RAB22A WILD-TYPE" 
      TCGA-A6-3808       TCGA-A6-3809       TCGA-A6-3810       TCGA-A6-4105 
"RAB22A WILD-TYPE" "RAB22A WILD-TYPE" "RAB22A WILD-TYPE" "RAB22A WILD-TYPE" 
      TCGA-A6-5656       TCGA-A6-5657       TCGA-A6-5659       TCGA-A6-5660 
"RAB22A WILD-TYPE" "RAB22A WILD-TYPE" "RAB22A WILD-TYPE" "RAB22A WILD-TYPE" 
      TCGA-A6-5661       TCGA-A6-5662       TCGA-A6-5664       TCGA-A6-5665 
"RAB22A WILD-TYPE" "RAB22A WILD-TYPE" "RAB22A WILD-TYPE" "RAB22A WILD-TYPE" 
      TCGA-A6-5666       TCGA-A6-6137       TCGA-A6-6138       TCGA-A6-6141 
"RAB22A WILD-TYPE" "RAB22A WILD-TYPE" "RAB22A WILD-TYPE" "RAB22A WILD-TYPE" 
      TCGA-A6-6142       TCGA-A6-6648       TCGA-A6-6649       TCGA-A6-6651 
"RAB22A WILD-TYPE" "RAB22A WILD-TYPE" "RAB22A WILD-TYPE" "RAB22A WILD-TYPE" 
      TCGA-A6-6652       TCGA-A6-6653       TCGA-A6-6654       TCGA-A6-6780 
"RAB22A WILD-TYPE" "RAB22A WILD-TYPE" "RAB22A WILD-TYPE" "RAB22A WILD-TYPE" 
      TCGA-A6-6782       TCGA-AD-5900       TCGA-AD-6548       TCGA-AD-6888 
"RAB22A WILD-TYPE" "RAB22A WILD-TYPE" "RAB22A WILD-TYPE" "RAB22A WILD-TYPE" 
      TCGA-AD-6889       TCGA-AD-6890       TCGA-AD-6895       TCGA-AD-6899 
"RAB22A WILD-TYPE" "RAB22A WILD-TYPE" "RAB22A WILD-TYPE" "RAB22A WILD-TYPE" 
      TCGA-AD-6901       TCGA-AD-6963       TCGA-AD-6964       TCGA-AD-6965 
"RAB22A WILD-TYPE" "RAB22A WILD-TYPE" "RAB22A WILD-TYPE" "RAB22A WILD-TYPE" 
      TCGA-AU-3779       TCGA-AU-6004       TCGA-AY-4070       TCGA-AY-4071 
"RAB22A WILD-TYPE" "RAB22A WILD-TYPE" "RAB22A WILD-TYPE" "RAB22A WILD-TYPE" 
      TCGA-AY-5543       TCGA-AY-6196       TCGA-AY-6197       TCGA-AY-6386 
"RAB22A WILD-TYPE" "RAB22A WILD-TYPE" "RAB22A WILD-TYPE" "RAB22A WILD-TYPE" 
      TCGA-AZ-4315       TCGA-AZ-4323       TCGA-AZ-4616       TCGA-AZ-4681 
"RAB22A WILD-TYPE" "RAB22A WILD-TYPE" "RAB22A WILD-TYPE" "RAB22A WILD-TYPE" 
      TCGA-AZ-4682       TCGA-AZ-5403       TCGA-AZ-5407       TCGA-AZ-6598 
"RAB22A WILD-TYPE" "RAB22A WILD-TYPE" "RAB22A WILD-TYPE" "RAB22A WILD-TYPE" 
      TCGA-AZ-6599       TCGA-AZ-6600       TCGA-AZ-6601       TCGA-AZ-6603 
"RAB22A WILD-TYPE" "RAB22A WILD-TYPE" "RAB22A WILD-TYPE" "RAB22A WILD-TYPE" 
      TCGA-AZ-6605       TCGA-AZ-6606       TCGA-AZ-6607       TCGA-AZ-6608 
"RAB22A WILD-TYPE" "RAB22A WILD-TYPE" "RAB22A WILD-TYPE" "RAB22A WILD-TYPE" 
      TCGA-CA-5254       TCGA-CA-5255       TCGA-CA-5796       TCGA-CA-5797 
"RAB22A WILD-TYPE" "RAB22A WILD-TYPE" "RAB22A WILD-TYPE" "RAB22A WILD-TYPE" 
      TCGA-CA-6715       TCGA-CA-6716       TCGA-CA-6717       TCGA-CA-6718 
"RAB22A WILD-TYPE" "RAB22A WILD-TYPE" "RAB22A WILD-TYPE" "RAB22A WILD-TYPE" 
      TCGA-CA-6719       TCGA-CK-4947       TCGA-CK-4948       TCGA-CK-4950 
"RAB22A WILD-TYPE" "RAB22A WILD-TYPE" "RAB22A WILD-TYPE" "RAB22A WILD-TYPE" 
      TCGA-CK-4952       TCGA-CK-5912       TCGA-CK-5913       TCGA-CK-5914 
"RAB22A WILD-TYPE" "RAB22A WILD-TYPE" "RAB22A WILD-TYPE" "RAB22A WILD-TYPE" 
      TCGA-CK-5915       TCGA-CK-5916       TCGA-CK-6746       TCGA-CK-6747 
"RAB22A WILD-TYPE" "RAB22A WILD-TYPE" "RAB22A WILD-TYPE" "RAB22A WILD-TYPE" 
      TCGA-CK-6748       TCGA-CK-6751       TCGA-CM-4743       TCGA-CM-4744 
"RAB22A WILD-TYPE" "RAB22A WILD-TYPE" "RAB22A WILD-TYPE" "RAB22A WILD-TYPE" 
      TCGA-CM-4746       TCGA-CM-4747       TCGA-CM-4752       TCGA-CM-5341 
"RAB22A WILD-TYPE" "RAB22A WILD-TYPE" "RAB22A WILD-TYPE" "RAB22A WILD-TYPE" 
      TCGA-CM-5344       TCGA-CM-5348       TCGA-CM-5349       TCGA-CM-5860 
"RAB22A WILD-TYPE" "RAB22A WILD-TYPE" "RAB22A WILD-TYPE" "RAB22A WILD-TYPE" 
      TCGA-CM-5861       TCGA-CM-5862       TCGA-CM-5863       TCGA-CM-5864 
"RAB22A WILD-TYPE" "RAB22A WILD-TYPE" "RAB22A WILD-TYPE" "RAB22A WILD-TYPE" 
      TCGA-CM-5868       TCGA-CM-6161       TCGA-CM-6162       TCGA-CM-6163 
"RAB22A WILD-TYPE" "RAB22A WILD-TYPE" "RAB22A WILD-TYPE" "RAB22A WILD-TYPE" 
      TCGA-CM-6164       TCGA-CM-6165       TCGA-CM-6166       TCGA-CM-6167 
"RAB22A WILD-TYPE" "RAB22A WILD-TYPE" "RAB22A WILD-TYPE" "RAB22A WILD-TYPE" 
      TCGA-CM-6168       TCGA-CM-6169       TCGA-CM-6170       TCGA-CM-6171 
"RAB22A WILD-TYPE" "RAB22A WILD-TYPE" "RAB22A WILD-TYPE" "RAB22A WILD-TYPE" 
      TCGA-CM-6172       TCGA-CM-6674       TCGA-CM-6675       TCGA-CM-6676 
"RAB22A WILD-TYPE" "RAB22A WILD-TYPE" "RAB22A WILD-TYPE" "RAB22A WILD-TYPE" 
      TCGA-CM-6677       TCGA-CM-6678       TCGA-CM-6679       TCGA-CM-6680 
"RAB22A WILD-TYPE" "RAB22A WILD-TYPE" "RAB22A WILD-TYPE" "RAB22A WILD-TYPE" 
      TCGA-D5-5537       TCGA-D5-5538       TCGA-D5-5539       TCGA-D5-5540 
"RAB22A WILD-TYPE" "RAB22A WILD-TYPE" "RAB22A WILD-TYPE" "RAB22A WILD-TYPE" 
      TCGA-D5-5541       TCGA-D5-6529       TCGA-D5-6532       TCGA-D5-6533 
"RAB22A WILD-TYPE" "RAB22A WILD-TYPE" "RAB22A WILD-TYPE" "RAB22A WILD-TYPE" 
      TCGA-D5-6534       TCGA-D5-6535       TCGA-D5-6536       TCGA-D5-6537 
"RAB22A WILD-TYPE" "RAB22A WILD-TYPE" "RAB22A WILD-TYPE" "RAB22A WILD-TYPE" 
      TCGA-D5-6538       TCGA-D5-6539       TCGA-D5-6540       TCGA-D5-6541 
"RAB22A WILD-TYPE" "RAB22A WILD-TYPE" "RAB22A WILD-TYPE" "RAB22A WILD-TYPE" 
      TCGA-D5-6898       TCGA-D5-6920       TCGA-D5-6922       TCGA-D5-6923 
"RAB22A WILD-TYPE" "RAB22A WILD-TYPE" "RAB22A WILD-TYPE" "RAB22A WILD-TYPE" 
      TCGA-D5-6924       TCGA-D5-6926       TCGA-D5-6927       TCGA-D5-6928 
"RAB22A WILD-TYPE" "RAB22A WILD-TYPE" "RAB22A WILD-TYPE" "RAB22A WILD-TYPE" 
      TCGA-D5-6929       TCGA-D5-6930       TCGA-D5-6931       TCGA-D5-6932 
"RAB22A WILD-TYPE" "RAB22A WILD-TYPE" "RAB22A WILD-TYPE" "RAB22A WILD-TYPE" 
      TCGA-D5-7000       TCGA-DM-A0X9       TCGA-DM-A0XD       TCGA-DM-A0XF 
"RAB22A WILD-TYPE" "RAB22A WILD-TYPE" "RAB22A WILD-TYPE" "RAB22A WILD-TYPE" 
      TCGA-DM-A1D0       TCGA-DM-A1D4       TCGA-DM-A1D6       TCGA-DM-A1D7 
"RAB22A WILD-TYPE" "RAB22A WILD-TYPE" "RAB22A WILD-TYPE" "RAB22A WILD-TYPE" 
      TCGA-DM-A1D8       TCGA-DM-A1D9       TCGA-DM-A1DA       TCGA-DM-A1DB 
"RAB22A WILD-TYPE" "RAB22A WILD-TYPE" "RAB22A WILD-TYPE" "RAB22A WILD-TYPE" 
      TCGA-DM-A1HA       TCGA-DM-A1HB       TCGA-DM-A282       TCGA-DM-A285 
"RAB22A WILD-TYPE" "RAB22A WILD-TYPE" "RAB22A WILD-TYPE" "RAB22A WILD-TYPE" 
      TCGA-DM-A28C       TCGA-DM-A28E       TCGA-DM-A28F       TCGA-DM-A28G 
"RAB22A WILD-TYPE" "RAB22A WILD-TYPE" "RAB22A WILD-TYPE" "RAB22A WILD-TYPE" 
      TCGA-DM-A28H       TCGA-DM-A28K       TCGA-F4-6459       TCGA-F4-6460 
"RAB22A WILD-TYPE" "RAB22A WILD-TYPE" "RAB22A WILD-TYPE" "RAB22A WILD-TYPE" 
      TCGA-F4-6569       TCGA-F4-6570       TCGA-F4-6703       TCGA-F4-6704 
"RAB22A WILD-TYPE" "RAB22A WILD-TYPE" "RAB22A WILD-TYPE" "RAB22A WILD-TYPE" 
      TCGA-F4-6805       TCGA-F4-6806       TCGA-F4-6807       TCGA-F4-6808 
"RAB22A WILD-TYPE" "RAB22A WILD-TYPE" "RAB22A WILD-TYPE" "RAB22A WILD-TYPE" 
      TCGA-F4-6809       TCGA-F4-6854       TCGA-F4-6855       TCGA-F4-6856 
"RAB22A WILD-TYPE" "RAB22A WILD-TYPE" "RAB22A WILD-TYPE" "RAB22A WILD-TYPE" 
      TCGA-G4-6293       TCGA-G4-6299       TCGA-G4-6303       TCGA-G4-6304 
"RAB22A WILD-TYPE" "RAB22A WILD-TYPE" "RAB22A WILD-TYPE" "RAB22A WILD-TYPE" 
      TCGA-G4-6306       TCGA-G4-6307       TCGA-G4-6309       TCGA-G4-6310 
"RAB22A WILD-TYPE" "RAB22A WILD-TYPE" "RAB22A WILD-TYPE" "RAB22A WILD-TYPE" 
      TCGA-G4-6315       TCGA-G4-6317       TCGA-G4-6321       TCGA-G4-6323 
"RAB22A WILD-TYPE" "RAB22A WILD-TYPE" "RAB22A WILD-TYPE" "RAB22A WILD-TYPE" 
      TCGA-G4-6586       TCGA-G4-6588       TCGA-G4-6625       TCGA-G4-6626 
"RAB22A WILD-TYPE" "RAB22A WILD-TYPE" "RAB22A WILD-TYPE" "RAB22A WILD-TYPE" 
      TCGA-G4-6628       TCGA-AF-2687       TCGA-AF-2689       TCGA-AF-2691 
"RAB22A WILD-TYPE" "RAB22A WILD-TYPE" "RAB22A WILD-TYPE" "RAB22A WILD-TYPE" 
      TCGA-AF-2692       TCGA-AF-2693       TCGA-AF-3400       TCGA-AF-3913 
"RAB22A WILD-TYPE" "RAB22A WILD-TYPE" "RAB22A WILD-TYPE" "RAB22A WILD-TYPE" 
      TCGA-AF-4110       TCGA-AF-5654       TCGA-AF-6136       TCGA-AF-6655 
"RAB22A WILD-TYPE" "RAB22A WILD-TYPE" "RAB22A WILD-TYPE" "RAB22A WILD-TYPE" 
      TCGA-AF-6672       TCGA-AH-6544       TCGA-AH-6547       TCGA-AH-6549 
"RAB22A WILD-TYPE" "RAB22A WILD-TYPE" "RAB22A WILD-TYPE" "RAB22A WILD-TYPE" 
      TCGA-AH-6643       TCGA-AH-6644       TCGA-CI-6619       TCGA-CI-6620 
"RAB22A WILD-TYPE" "RAB22A WILD-TYPE" "RAB22A WILD-TYPE" "RAB22A WILD-TYPE" 
      TCGA-CI-6621       TCGA-CI-6622       TCGA-CI-6624       TCGA-CL-5917 
"RAB22A WILD-TYPE" "RAB22A WILD-TYPE" "RAB22A WILD-TYPE" "RAB22A WILD-TYPE" 
      TCGA-CL-5918       TCGA-DC-5337       TCGA-DC-5869       TCGA-DC-6155 
"RAB22A WILD-TYPE" "RAB22A WILD-TYPE" "RAB22A WILD-TYPE" "RAB22A WILD-TYPE" 
      TCGA-DC-6157       TCGA-DC-6158       TCGA-DC-6160       TCGA-DC-6681 
"RAB22A WILD-TYPE" "RAB22A WILD-TYPE" "RAB22A WILD-TYPE" "RAB22A WILD-TYPE" 
      TCGA-DC-6682       TCGA-DC-6683       TCGA-DT-5265       TCGA-DY-A0XA 
"RAB22A WILD-TYPE" "RAB22A WILD-TYPE" "RAB22A WILD-TYPE" "RAB22A WILD-TYPE" 
      TCGA-DY-A1DC       TCGA-DY-A1DD       TCGA-DY-A1DF       TCGA-DY-A1DG 
"RAB22A WILD-TYPE" "RAB22A WILD-TYPE" "RAB22A WILD-TYPE" "RAB22A WILD-TYPE" 
      TCGA-DY-A1H8       TCGA-EF-5830       TCGA-EI-6506       TCGA-EI-6507 
"RAB22A WILD-TYPE" "RAB22A WILD-TYPE" "RAB22A WILD-TYPE" "RAB22A WILD-TYPE" 
      TCGA-EI-6508       TCGA-EI-6510       TCGA-F5-6464       TCGA-F5-6465 
"RAB22A WILD-TYPE" "RAB22A WILD-TYPE" "RAB22A WILD-TYPE" "RAB22A WILD-TYPE" 
      TCGA-F5-6571       TCGA-F5-6702       TCGA-F5-6811       TCGA-F5-6812 
"RAB22A WILD-TYPE" "RAB22A WILD-TYPE" "RAB22A WILD-TYPE" "RAB22A WILD-TYPE" 
      TCGA-F5-6813       TCGA-G5-6235       TCGA-G5-6641 
"RAB22A WILD-TYPE" "RAB22A WILD-TYPE" "RAB22A WILD-TYPE" 

Clustering(1962) Variable = SAMD4A MUTATION ANALYSIS
D1962V1, survival
                  sevent
clus2                0   1
  SAMD4A MUTATED     9   2
  SAMD4A WILD-TYPE 369  91
  SAMD4A MUTATED SAMD4A WILD-TYPE 
              11              460 
  SAMD4A MUTATED SAMD4A WILD-TYPE 
               2               91 
$`SAMD4A MUTATED`
TCGA-AA-3529 TCGA-AA-3663 TCGA-AA-A00J TCGA-AA-A01P TCGA-AA-A01R TCGA-CA-6717 
        0.00         6.97        18.05        38.07        35.01        12.76 
TCGA-CK-5913 TCGA-CM-6162 TCGA-D5-6930 TCGA-AG-3608 TCGA-AG-A002 
       51.32        12.00         1.51        15.95        20.98 

$`SAMD4A WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
        8.05        19.07        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       19.00        30.02        34.03        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
       31.00         1.02         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07        12.20        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 
       17.56       148.01        85.45        15.62        49.08         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       17.03        15.02         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       11.64         4.80        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
        0.99        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  SAMD4A MUTATED SAMD4A WILD-TYPE 
               0                0 
  SAMD4A MUTATED SAMD4A WILD-TYPE 
           51.32           148.01 
  SAMD4A MUTATED SAMD4A WILD-TYPE 
          15.950           20.415 
[1] "0.0 - 51.3 (15.9)"  "0.0 - 148.0 (20.4)"
[1] "hr=" "1.2"
D1962V2, continuous
D1962V3, binary
                  cls
clus                 0   1
  SAMD4A MUTATED     9   2
  SAMD4A WILD-TYPE 357 117
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SAMD4A MUTATED      9    2
  SAMD4A WILD-TYPE  357  117
        clus
vv       SAMD4A MUTATED SAMD4A WILD-TYPE
  COLON               9              357
  RECTUM              2              117
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SAMD4A MUTATED         1        0        1         4         0         0
  SAMD4A WILD-TYPE      90        1       31       134        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SAMD4A MUTATED           2          0          2          1        0
  SAMD4A WILD-TYPE        22         11         57         41       48
                  vv
clus               STAGE IVA STAGE IVB
  SAMD4A MUTATED           0         0
  SAMD4A WILD-TYPE        18         1
D1962V4, multiclass
            clus
vv           SAMD4A MUTATED SAMD4A WILD-TYPE
  STAGE I                 1               90
  STAGE IA                0                1
  STAGE II                1               31
  STAGE IIA               4              134
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               2               22
  STAGE IIIA              0               11
  STAGE IIIB              2               57
  STAGE IIIC              1               41
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  SAMD4A MUTATED     0   1   9   1
  SAMD4A WILD-TYPE  17  91 320  49
D1962V5, multiclass
    clus
vv   SAMD4A MUTATED SAMD4A WILD-TYPE
  T1              0               17
  T2              1               91
  T3              9              320
  T4              1               49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  SAMD4A MUTATED     6   3   2
  SAMD4A WILD-TYPE 281 110  85
D1962V6, multiclass
    clus
vv   SAMD4A MUTATED SAMD4A WILD-TYPE
  N0              6              281
  N1              3              110
  N2              2               85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1962V7, binary
                  cls
clus                 0   1
  SAMD4A MUTATED    10   0
  SAMD4A WILD-TYPE 365  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SAMD4A MUTATED     10    0
  SAMD4A WILD-TYPE  365   65
   clus
vv  SAMD4A MUTATED SAMD4A WILD-TYPE
  0             10              365
  1              0               65
[1] 2 2
[1] FALSE
D1962V8, binary
                  cls
clus                 0   1
  SAMD4A MUTATED     5   6
  SAMD4A WILD-TYPE 220 258
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SAMD4A MUTATED      5    6
  SAMD4A WILD-TYPE  220  258
        clus
vv       SAMD4A MUTATED SAMD4A WILD-TYPE
  FEMALE              5              220
  MALE                6              258
[1] 2 2
[1] FALSE
D1962V9, binary
                  cls
clus                 0   1
  SAMD4A MUTATED     8   1
  SAMD4A WILD-TYPE 342  21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SAMD4A MUTATED      8    1
  SAMD4A WILD-TYPE  342   21
     clus
vv    SAMD4A MUTATED SAMD4A WILD-TYPE
  NO               8              342
  YES              1               21
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SAMD4A MUTATED                      4                             5
  SAMD4A WILD-TYPE                  311                            42
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SAMD4A MUTATED                       2                              0
  SAMD4A WILD-TYPE                   104                             10
D1962V10, multiclass
                                clus
vv                               SAMD4A MUTATED SAMD4A WILD-TYPE
  COLON ADENOCARCINOMA                        4              311
  COLON MUCINOUS ADENOCARCINOMA               5               42
  RECTAL ADENOCARCINOMA                       2              104
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  SAMD4A MUTATED     9   0   0   2
  SAMD4A WILD-TYPE 336   4  31  23
D1962V11, multiclass
    clus
vv   SAMD4A MUTATED SAMD4A WILD-TYPE
  R0              9              336
  R1              0                4
  R2              0               31
  RX              2               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1962V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SAMD4A MUTATED                                  0     1
  SAMD4A WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  SAMD4A MUTATED                           0     3
  SAMD4A WILD-TYPE                        22   223
D1962V13, multiclass
                                  clus
vv                                 SAMD4A MUTATED SAMD4A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         3              223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1963) Variable = CCDC11 MUTATION ANALYSIS
D1963V1, survival
                  sevent
clus2                0   1
  CCDC11 MUTATED     7   3
  CCDC11 WILD-TYPE 371  90
  CCDC11 MUTATED CCDC11 WILD-TYPE 
              10              461 
  CCDC11 MUTATED CCDC11 WILD-TYPE 
               3               90 
$`CCDC11 MUTATED`
TCGA-AA-3510 TCGA-AA-3697 TCGA-AA-3966 TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A03F 
       63.98        85.05         2.01         4.01        34.98        18.05 
TCGA-AD-5900 TCGA-CK-4950 TCGA-DM-A28F TCGA-G4-6315 
        0.07        85.45        35.97        61.91 

$`CCDC11 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       20.98        34.03        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03J TCGA-AD-6548 
       14.01         0.92        41.00        39.98        40.96        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
      148.01        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G 
      135.65       139.17         6.12        81.37       119.93        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  CCDC11 MUTATED CCDC11 WILD-TYPE 
            0.07             0.00 
  CCDC11 MUTATED CCDC11 WILD-TYPE 
           85.45           148.01 
  CCDC11 MUTATED CCDC11 WILD-TYPE 
          35.475           20.120 
[1] "0.1 - 85.5 (35.5)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1"  
D1963V2, continuous
D1963V3, binary
                  cls
clus                 0   1
  CCDC11 MUTATED    10   0
  CCDC11 WILD-TYPE 356 119
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC11 MUTATED     10    0
  CCDC11 WILD-TYPE  356  119
        clus
vv       CCDC11 MUTATED CCDC11 WILD-TYPE
  COLON              10              356
  RECTUM              0              119
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CCDC11 MUTATED         1        0        1         1         2         0
  CCDC11 WILD-TYPE      90        1       31       137         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CCDC11 MUTATED           2          0          2          0        1
  CCDC11 WILD-TYPE        22         11         57         42       47
                  vv
clus               STAGE IVA STAGE IVB
  CCDC11 MUTATED           0         0
  CCDC11 WILD-TYPE        18         1
D1963V4, multiclass
            clus
vv           CCDC11 MUTATED CCDC11 WILD-TYPE
  STAGE I                 1               90
  STAGE IA                0                1
  STAGE II                1               31
  STAGE IIA               1              137
  STAGE IIB               2                8
  STAGE IIC               0                1
  STAGE III               2               22
  STAGE IIIA              0               11
  STAGE IIIB              2               57
  STAGE IIIC              0               42
  STAGE IV                1               47
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  CCDC11 MUTATED     0   1   7   2
  CCDC11 WILD-TYPE  17  91 322  48
D1963V5, multiclass
    clus
vv   CCDC11 MUTATED CCDC11 WILD-TYPE
  T1              0               17
  T2              1               91
  T3              7              322
  T4              2               48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  CCDC11 MUTATED     6   3   1
  CCDC11 WILD-TYPE 281 110  86
D1963V6, multiclass
    clus
vv   CCDC11 MUTATED CCDC11 WILD-TYPE
  N0              6              281
  N1              3              110
  N2              1               86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1963V7, binary
                  cls
clus                 0   1
  CCDC11 MUTATED     8   1
  CCDC11 WILD-TYPE 367  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC11 MUTATED      8    1
  CCDC11 WILD-TYPE  367   64
   clus
vv  CCDC11 MUTATED CCDC11 WILD-TYPE
  0              8              367
  1              1               64
[1] 2 2
[1] FALSE
D1963V8, binary
                  cls
clus                 0   1
  CCDC11 MUTATED     4   6
  CCDC11 WILD-TYPE 221 258
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC11 MUTATED      4    6
  CCDC11 WILD-TYPE  221  258
        clus
vv       CCDC11 MUTATED CCDC11 WILD-TYPE
  FEMALE              4              221
  MALE                6              258
[1] 2 2
[1] FALSE
D1963V9, binary
                  cls
clus                 0   1
  CCDC11 MUTATED     5   0
  CCDC11 WILD-TYPE 345  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC11 MUTATED      5    0
  CCDC11 WILD-TYPE  345   22
     clus
vv    CCDC11 MUTATED CCDC11 WILD-TYPE
  NO               5              345
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CCDC11 MUTATED                      6                             4
  CCDC11 WILD-TYPE                  309                            43
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CCDC11 MUTATED                       0                              0
  CCDC11 WILD-TYPE                   106                             10
D1963V10, multiclass
                                clus
vv                               CCDC11 MUTATED CCDC11 WILD-TYPE
  COLON ADENOCARCINOMA                        6              309
  COLON MUCINOUS ADENOCARCINOMA               4               43
  RECTAL ADENOCARCINOMA                       0              106
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  CCDC11 MUTATED     7   1   0   0
  CCDC11 WILD-TYPE 338   3  31  25
D1963V11, multiclass
    clus
vv   CCDC11 MUTATED CCDC11 WILD-TYPE
  R0              7              338
  R1              1                3
  R2              0               31
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1963V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CCDC11 MUTATED                                  0     0
  CCDC11 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  CCDC11 MUTATED                           1     3
  CCDC11 WILD-TYPE                        21   223
D1963V13, multiclass
                                  clus
vv                                 CCDC11 MUTATED CCDC11 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                         3              223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1964) Variable = TRPM2 MUTATION ANALYSIS
D1964V1, survival
                 sevent
clus2               0   1
  TRPM2 MUTATED    19   6
  TRPM2 WILD-TYPE 359  87
  TRPM2 MUTATED TRPM2 WILD-TYPE 
             25             446 
  TRPM2 MUTATED TRPM2 WILD-TYPE 
              6              87 
$`TRPM2 MUTATED`
TCGA-A6-2676 TCGA-A6-5665 TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3713 TCGA-AA-3877 
       42.90        22.06        13.02         1.02        19.04        31.00 
TCGA-AA-A00J TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01R TCGA-AD-6895 TCGA-AZ-4315 
       18.05         4.01        34.98        35.01         0.72        58.39 
TCGA-AZ-6598 TCGA-AZ-6601 TCGA-CA-6718 TCGA-CM-4743 TCGA-CM-6162 TCGA-DM-A1HB 
       49.41       100.01        10.06        23.05        12.00       135.65 
TCGA-G4-6299 TCGA-G4-6323 TCGA-G4-6588 TCGA-AG-3999 TCGA-AG-A002 TCGA-EI-6507 
       74.56        13.78        26.17        28.04        20.98        19.96 
TCGA-F5-6813 
        0.69 

$`TRPM2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3520 
       63.98         6.97         1.02        38.99         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       26.99        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       18.05         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       31.00        38.07         1.02         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77        12.10        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.20        12.76        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
        1.91       124.27        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 
        5.03        15.02        15.02        17.03        15.02         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
        7.50        44.32       131.51       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
       35.31       133.18        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6586 
       85.48        63.62        61.91        36.00        22.09        35.80 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6510 
       51.48        32.61         0.49        20.55        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  TRPM2 MUTATED TRPM2 WILD-TYPE 
           0.69            0.00 
  TRPM2 MUTATED TRPM2 WILD-TYPE 
         135.65          148.01 
  TRPM2 MUTATED TRPM2 WILD-TYPE 
         22.060          20.085 
[1] "0.7 - 135.7 (22.1)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.1"
D1964V2, continuous
D1964V3, binary
                 cls
clus                0   1
  TRPM2 MUTATED    22   4
  TRPM2 WILD-TYPE 344 115
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRPM2 MUTATED     22    4
  TRPM2 WILD-TYPE  344  115
        clus
vv       TRPM2 MUTATED TRPM2 WILD-TYPE
  COLON             22             344
  RECTUM             4             115
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TRPM2 MUTATED         2        1        2         7         4         0
  TRPM2 WILD-TYPE      89        0       30       131         6         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TRPM2 MUTATED           2          0          3          3        1         0
  TRPM2 WILD-TYPE        22         11         56         39       47        18
                 vv
clus              STAGE IVB
  TRPM2 MUTATED           0
  TRPM2 WILD-TYPE         1
D1964V4, multiclass
            clus
vv           TRPM2 MUTATED TRPM2 WILD-TYPE
  STAGE I                2              89
  STAGE IA               1               0
  STAGE II               2              30
  STAGE IIA              7             131
  STAGE IIB              4               6
  STAGE IIC              0               1
  STAGE III              2              22
  STAGE IIIA             0              11
  STAGE IIIB             3              56
  STAGE IIIC             3              39
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  TRPM2 MUTATED     1   1  17   6
  TRPM2 WILD-TYPE  16  91 312  44
D1964V5, multiclass
    clus
vv   TRPM2 MUTATED TRPM2 WILD-TYPE
  T1             1              16
  T2             1              91
  T3            17             312
  T4             6              44
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  TRPM2 MUTATED    17   4   5
  TRPM2 WILD-TYPE 270 109  82
D1964V6, multiclass
    clus
vv   TRPM2 MUTATED TRPM2 WILD-TYPE
  N0            17             270
  N1             4             109
  N2             5              82
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1964V7, binary
                 cls
clus                0   1
  TRPM2 MUTATED    21   1
  TRPM2 WILD-TYPE 354  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRPM2 MUTATED     21    1
  TRPM2 WILD-TYPE  354   64
   clus
vv  TRPM2 MUTATED TRPM2 WILD-TYPE
  0            21             354
  1             1              64
[1] 2 2
[1] FALSE
D1964V8, binary
                 cls
clus                0   1
  TRPM2 MUTATED    11  15
  TRPM2 WILD-TYPE 214 249
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRPM2 MUTATED     11   15
  TRPM2 WILD-TYPE  214  249
        clus
vv       TRPM2 MUTATED TRPM2 WILD-TYPE
  FEMALE            11             214
  MALE              15             249
[1] 2 2
[1] FALSE
D1964V9, binary
                 cls
clus                0   1
  TRPM2 MUTATED    18   2
  TRPM2 WILD-TYPE 332  20
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRPM2 MUTATED     18    2
  TRPM2 WILD-TYPE  332   20
     clus
vv    TRPM2 MUTATED TRPM2 WILD-TYPE
  NO             18             332
  YES             2              20
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  TRPM2 MUTATED                     15                             6
  TRPM2 WILD-TYPE                  300                            41
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  TRPM2 MUTATED                       4                              0
  TRPM2 WILD-TYPE                   102                             10
D1964V10, multiclass
                                clus
vv                               TRPM2 MUTATED TRPM2 WILD-TYPE
  COLON ADENOCARCINOMA                      15             300
  COLON MUCINOUS ADENOCARCINOMA              6              41
  RECTAL ADENOCARCINOMA                      4             102
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  TRPM2 MUTATED    18   0   1   2
  TRPM2 WILD-TYPE 327   4  30  23
D1964V11, multiclass
    clus
vv   TRPM2 MUTATED TRPM2 WILD-TYPE
  R0            18             327
  R1             0               4
  R2             1              30
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1964V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TRPM2 MUTATED                                  0     1
  TRPM2 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  TRPM2 MUTATED                           1    14
  TRPM2 WILD-TYPE                        21   212
D1964V13, multiclass
                                  clus
vv                                 TRPM2 MUTATED TRPM2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                       14             212
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1965) Variable = TRIP12 MUTATION ANALYSIS
D1965V1, survival
                  sevent
clus2                0   1
  TRIP12 MUTATED    25   5
  TRIP12 WILD-TYPE 353  88
  TRIP12 MUTATED TRIP12 WILD-TYPE 
              30              441 
  TRIP12 MUTATED TRIP12 WILD-TYPE 
               5               88 
$`TRIP12 MUTATED`
TCGA-A6-3808 TCGA-A6-5661 TCGA-A6-6141 TCGA-A6-6654 TCGA-A6-6781 TCGA-AA-3492 
       33.34        33.53         8.38        23.87        19.66         3.02 
TCGA-AA-3845 TCGA-AA-3877 TCGA-AA-3950 TCGA-AA-3966 TCGA-AA-3977 TCGA-AA-A00N 
        0.00        31.00        24.00         2.01        25.02         4.01 
TCGA-AA-A010 TCGA-AA-A01R TCGA-AD-6889 TCGA-AD-6895 TCGA-AU-3779 TCGA-AU-6004 
       34.98        35.01        56.55         0.72        14.50        27.09 
TCGA-AZ-4315 TCGA-CK-4952 TCGA-D5-6538 TCGA-DM-A0XD TCGA-DM-A1D8 TCGA-DM-A1HB 
       58.39        15.62        17.13        24.43        12.59       135.65 
TCGA-F4-6703 TCGA-G4-6586 TCGA-G4-6588 TCGA-AF-6655 TCGA-AG-3892 TCGA-AG-A002 
       47.87        35.80        26.17        20.02        13.02        20.98 

$`TRIP12 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       31.63        30.44        29.19        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       32.71        27.09        22.52        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 
       21.76        24.69        24.39        20.12        20.28         7.04 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 
       17.03        24.03        27.02        29.98        18.05         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 
       12.99        24.00        33.01        26.01         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
       34.03        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S 
       12.00        31.00        31.00        38.07         1.02         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.79         5.79        22.42        27.42        10.88         0.20 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
       16.31         0.95        33.01        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
      148.01        85.45        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
        4.80        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D9 
       38.20       130.65        92.75        49.91        13.32       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
        7.50        44.32       131.51       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       31.96        35.74         6.18         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       15.39        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 
        1.02        17.95        36.95        17.03        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  TRIP12 MUTATED TRIP12 WILD-TYPE 
               0                0 
  TRIP12 MUTATED TRIP12 WILD-TYPE 
          135.65           148.01 
  TRIP12 MUTATED TRIP12 WILD-TYPE 
          23.935           20.050 
[1] "0.0 - 135.7 (23.9)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.1"
D1965V2, continuous
D1965V3, binary
                  cls
clus                 0   1
  TRIP12 MUTATED    28   3
  TRIP12 WILD-TYPE 338 116
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIP12 MUTATED     28    3
  TRIP12 WILD-TYPE  338  116
        clus
vv       TRIP12 MUTATED TRIP12 WILD-TYPE
  COLON              28              338
  RECTUM              3              116
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TRIP12 MUTATED         4        0        1        14         2         0
  TRIP12 WILD-TYPE      87        1       31       124         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TRIP12 MUTATED           1          1          3          2        0
  TRIP12 WILD-TYPE        23         10         56         40       48
                  vv
clus               STAGE IVA STAGE IVB
  TRIP12 MUTATED           0         0
  TRIP12 WILD-TYPE        18         1
D1965V4, multiclass
            clus
vv           TRIP12 MUTATED TRIP12 WILD-TYPE
  STAGE I                 4               87
  STAGE IA                0                1
  STAGE II                1               31
  STAGE IIA              14              124
  STAGE IIB               2                8
  STAGE IIC               0                1
  STAGE III               1               23
  STAGE IIIA              1               10
  STAGE IIIB              3               56
  STAGE IIIC              2               40
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  TRIP12 MUTATED     2   4  21   4
  TRIP12 WILD-TYPE  15  88 308  46
D1965V5, multiclass
    clus
vv   TRIP12 MUTATED TRIP12 WILD-TYPE
  T1              2               15
  T2              4               88
  T3             21              308
  T4              4               46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  TRIP12 MUTATED    22   6   3
  TRIP12 WILD-TYPE 265 107  84
D1965V6, multiclass
    clus
vv   TRIP12 MUTATED TRIP12 WILD-TYPE
  N0             22              265
  N1              6              107
  N2              3               84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1965V7, binary
                  cls
clus                 0   1
  TRIP12 MUTATED    27   0
  TRIP12 WILD-TYPE 348  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIP12 MUTATED     27    0
  TRIP12 WILD-TYPE  348   65
   clus
vv  TRIP12 MUTATED TRIP12 WILD-TYPE
  0             27              348
  1              0               65
[1] 2 2
[1] FALSE
D1965V8, binary
                  cls
clus                 0   1
  TRIP12 MUTATED    17  14
  TRIP12 WILD-TYPE 208 250
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIP12 MUTATED     17   14
  TRIP12 WILD-TYPE  208  250
        clus
vv       TRIP12 MUTATED TRIP12 WILD-TYPE
  FEMALE             17              208
  MALE               14              250
[1] 2 2
[1] FALSE
D1965V9, binary
                  cls
clus                 0   1
  TRIP12 MUTATED    19   1
  TRIP12 WILD-TYPE 331  21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIP12 MUTATED     19    1
  TRIP12 WILD-TYPE  331   21
     clus
vv    TRIP12 MUTATED TRIP12 WILD-TYPE
  NO              19              331
  YES              1               21
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  TRIP12 MUTATED                     20                             7
  TRIP12 WILD-TYPE                  295                            40
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  TRIP12 MUTATED                       3                              0
  TRIP12 WILD-TYPE                   103                             10
D1965V10, multiclass
                                clus
vv                               TRIP12 MUTATED TRIP12 WILD-TYPE
  COLON ADENOCARCINOMA                       20              295
  COLON MUCINOUS ADENOCARCINOMA               7               40
  RECTAL ADENOCARCINOMA                       3              103
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  TRIP12 MUTATED    21   0   0   1
  TRIP12 WILD-TYPE 324   4  31  24
D1965V11, multiclass
    clus
vv   TRIP12 MUTATED TRIP12 WILD-TYPE
  R0             21              324
  R1              0                4
  R2              0               31
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1965V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TRIP12 MUTATED                                  0     1
  TRIP12 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  TRIP12 MUTATED                           2    16
  TRIP12 WILD-TYPE                        20   210
D1965V13, multiclass
                                  clus
vv                                 TRIP12 MUTATED TRIP12 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     2               20
  WHITE                                        16              210
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1966) Variable = BBS2 MUTATION ANALYSIS
D1966V1, survival
                sevent
clus2              0   1
  BBS2 MUTATED    10   3
  BBS2 WILD-TYPE 368  90
  BBS2 MUTATED BBS2 WILD-TYPE 
            13            458 
  BBS2 MUTATED BBS2 WILD-TYPE 
             3             90 
$`BBS2 MUTATED`
TCGA-A6-5661 TCGA-A6-6651 TCGA-AA-3815 TCGA-AA-A00N TCGA-AA-A010 TCGA-AD-5900 
       33.53        21.76        33.04         4.01        34.98         0.07 
TCGA-AZ-4315 TCGA-CA-6717 TCGA-CM-5862 TCGA-D5-6920 TCGA-G4-6626 TCGA-AG-A002 
       58.39        12.76         5.03         3.68        46.75        20.98 
TCGA-AG-A015 
       36.03 

$`BBS2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       25.18        24.16        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       35.05         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
       16.31         0.95        33.01        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07        12.20        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       32.02        15.02        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6922 
       17.13        12.49        16.14        15.58         1.48         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       23.01        37.02        15.95         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  BBS2 MUTATED BBS2 WILD-TYPE 
          0.07           0.00 
  BBS2 MUTATED BBS2 WILD-TYPE 
         58.39         148.01 
  BBS2 MUTATED BBS2 WILD-TYPE 
        21.760         20.085 
[1] "0.1 - 58.4 (21.8)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.3"
D1966V2, continuous
D1966V3, binary
                cls
clus               0   1
  BBS2 MUTATED    12   2
  BBS2 WILD-TYPE 354 117
[1] "tbl2"
                cls
clus             [,1] [,2]
  BBS2 MUTATED     12    2
  BBS2 WILD-TYPE  354  117
        clus
vv       BBS2 MUTATED BBS2 WILD-TYPE
  COLON            12            354
  RECTUM            2            117
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  BBS2 MUTATED         3        0        0         7         2         0
  BBS2 WILD-TYPE      88        1       32       131         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  BBS2 MUTATED           0          0          1          0        0         1
  BBS2 WILD-TYPE        24         11         58         42       48        17
                vv
clus             STAGE IVB
  BBS2 MUTATED           0
  BBS2 WILD-TYPE         1
D1966V4, multiclass
            clus
vv           BBS2 MUTATED BBS2 WILD-TYPE
  STAGE I               3             88
  STAGE IA              0              1
  STAGE II              0             32
  STAGE IIA             7            131
  STAGE IIB             2              8
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            1             58
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             1             17
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  BBS2 MUTATED     1   2   9   2
  BBS2 WILD-TYPE  16  90 320  48
D1966V5, multiclass
    clus
vv   BBS2 MUTATED BBS2 WILD-TYPE
  T1            1             16
  T2            2             90
  T3            9            320
  T4            2             48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  BBS2 MUTATED    12   2   0
  BBS2 WILD-TYPE 275 111  87
D1966V6, multiclass
    clus
vv   BBS2 MUTATED BBS2 WILD-TYPE
  N0           12            275
  N1            2            111
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1966V7, binary
                cls
clus               0   1
  BBS2 MUTATED    11   1
  BBS2 WILD-TYPE 364  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  BBS2 MUTATED     11    1
  BBS2 WILD-TYPE  364   64
   clus
vv  BBS2 MUTATED BBS2 WILD-TYPE
  0           11            364
  1            1             64
[1] 2 2
[1] FALSE
D1966V8, binary
                cls
clus               0   1
  BBS2 MUTATED     7   7
  BBS2 WILD-TYPE 218 257
[1] "tbl2"
                cls
clus             [,1] [,2]
  BBS2 MUTATED      7    7
  BBS2 WILD-TYPE  218  257
        clus
vv       BBS2 MUTATED BBS2 WILD-TYPE
  FEMALE            7            218
  MALE              7            257
[1] 2 2
[1] FALSE
D1966V9, binary
                cls
clus               0   1
  BBS2 MUTATED    10   0
  BBS2 WILD-TYPE 340  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  BBS2 MUTATED     10    0
  BBS2 WILD-TYPE  340   22
     clus
vv    BBS2 MUTATED BBS2 WILD-TYPE
  NO            10            340
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  BBS2 MUTATED                      9                             3
  BBS2 WILD-TYPE                  306                            44
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  BBS2 MUTATED                       2                              0
  BBS2 WILD-TYPE                   104                             10
D1966V10, multiclass
                                clus
vv                               BBS2 MUTATED BBS2 WILD-TYPE
  COLON ADENOCARCINOMA                      9            306
  COLON MUCINOUS ADENOCARCINOMA             3             44
  RECTAL ADENOCARCINOMA                     2            104
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  BBS2 MUTATED    12   0   0   1
  BBS2 WILD-TYPE 333   4  31  24
D1966V11, multiclass
    clus
vv   BBS2 MUTATED BBS2 WILD-TYPE
  R0           12            333
  R1            0              4
  R2            0             31
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1966V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  BBS2 MUTATED                                  0     1
  BBS2 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  BBS2 MUTATED                           1     6
  BBS2 WILD-TYPE                        21   220
D1966V13, multiclass
                                  clus
vv                                 BBS2 MUTATED BBS2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                       6            220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1967) Variable = PDGFC MUTATION ANALYSIS
D1967V1, survival
                 sevent
clus2               0   1
  PDGFC MUTATED     8   2
  PDGFC WILD-TYPE 370  91
  PDGFC MUTATED PDGFC WILD-TYPE 
             10             461 
  PDGFC MUTATED PDGFC WILD-TYPE 
              2              91 
$`PDGFC MUTATED`
TCGA-A6-5665 TCGA-A6-6781 TCGA-AA-3710 TCGA-AA-A010 TCGA-AA-A02K TCGA-AD-6963 
       22.06        19.66        26.99        34.98        14.01        27.42 
TCGA-AZ-4323 TCGA-CM-6168 TCGA-G4-6306 TCGA-AG-A002 
        1.41        12.99        44.68        20.98 

$`PDGFC WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
        5.03         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       21.99        14.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       74.56        65.85        53.62        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  PDGFC MUTATED PDGFC WILD-TYPE 
           1.41            0.00 
  PDGFC MUTATED PDGFC WILD-TYPE 
          44.68          148.01 
  PDGFC MUTATED PDGFC WILD-TYPE 
          21.52           20.12 
[1] "1.4 - 44.7 (21.5)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.2"
D1967V2, continuous
D1967V3, binary
                 cls
clus                0   1
  PDGFC MUTATED     9   1
  PDGFC WILD-TYPE 357 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PDGFC MUTATED      9    1
  PDGFC WILD-TYPE  357  118
        clus
vv       PDGFC MUTATED PDGFC WILD-TYPE
  COLON              9             357
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PDGFC MUTATED         1        0        0         4         1         0
  PDGFC WILD-TYPE      90        1       32       134         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PDGFC MUTATED           0          0          0          1        2         0
  PDGFC WILD-TYPE        24         11         59         41       46        18
                 vv
clus              STAGE IVB
  PDGFC MUTATED           0
  PDGFC WILD-TYPE         1
D1967V4, multiclass
            clus
vv           PDGFC MUTATED PDGFC WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              4             134
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             1              41
  STAGE IV               2              46
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PDGFC MUTATED     0   2   4   4
  PDGFC WILD-TYPE  17  90 325  46
D1967V5, multiclass
    clus
vv   PDGFC MUTATED PDGFC WILD-TYPE
  T1             0              17
  T2             2              90
  T3             4             325
  T4             4              46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  PDGFC MUTATED     7   1   2
  PDGFC WILD-TYPE 280 112  85
D1967V6, multiclass
    clus
vv   PDGFC MUTATED PDGFC WILD-TYPE
  N0             7             280
  N1             1             112
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1967V7, binary
                 cls
clus                0   1
  PDGFC MUTATED     6   2
  PDGFC WILD-TYPE 369  63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PDGFC MUTATED      6    2
  PDGFC WILD-TYPE  369   63
   clus
vv  PDGFC MUTATED PDGFC WILD-TYPE
  0             6             369
  1             2              63
[1] 2 2
[1] FALSE
D1967V8, binary
                 cls
clus                0   1
  PDGFC MUTATED     4   6
  PDGFC WILD-TYPE 221 258
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PDGFC MUTATED      4    6
  PDGFC WILD-TYPE  221  258
        clus
vv       PDGFC MUTATED PDGFC WILD-TYPE
  FEMALE             4             221
  MALE               6             258
[1] 2 2
[1] FALSE
D1967V9, binary
                 cls
clus                0   1
  PDGFC MUTATED    10   0
  PDGFC WILD-TYPE 340  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PDGFC MUTATED     10    0
  PDGFC WILD-TYPE  340   22
     clus
vv    PDGFC MUTATED PDGFC WILD-TYPE
  NO             10             340
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PDGFC MUTATED                      8                             1
  PDGFC WILD-TYPE                  307                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PDGFC MUTATED                       1                              0
  PDGFC WILD-TYPE                   105                             10
D1967V10, multiclass
                                clus
vv                               PDGFC MUTATED PDGFC WILD-TYPE
  COLON ADENOCARCINOMA                       8             307
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  PDGFC MUTATED     7   0   1   0
  PDGFC WILD-TYPE 338   4  30  25
D1967V11, multiclass
    clus
vv   PDGFC MUTATED PDGFC WILD-TYPE
  R0             7             338
  R1             0               4
  R2             1              30
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1967V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PDGFC MUTATED                                  0     0
  PDGFC WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PDGFC MUTATED                           1     5
  PDGFC WILD-TYPE                        21   221
D1967V13, multiclass
                                  clus
vv                                 PDGFC MUTATED PDGFC WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        5             221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1968) Variable = KIF13A MUTATION ANALYSIS
D1968V1, survival
                  sevent
clus2                0   1
  KIF13A MUTATED    18   3
  KIF13A WILD-TYPE 360  90
  KIF13A MUTATED KIF13A WILD-TYPE 
              21              450 
  KIF13A MUTATED KIF13A WILD-TYPE 
               3               90 
$`KIF13A MUTATED`
TCGA-A6-5665 TCGA-A6-6781 TCGA-AA-3680 TCGA-AA-3688 TCGA-AA-3713 TCGA-AA-3966 
       22.06        19.66        11.01        19.00        19.04         2.01 
TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A02O TCGA-AD-5900 TCGA-AY-6197 TCGA-CA-6717 
        4.01        34.98         0.92         0.07        21.44        12.76 
TCGA-CK-5913 TCGA-CK-5916 TCGA-CM-5861 TCGA-D5-5539 TCGA-D5-6922 TCGA-D5-6930 
       51.32        21.14        15.02        19.59         4.41         1.51 
TCGA-D5-6932 TCGA-DM-A1HB TCGA-AG-A002 
       11.38       135.65        20.98 

$`KIF13A WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
       15.02         5.98        37.05        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       26.99        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 
       26.01        24.00         2.01        20.98        34.03        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02W TCGA-AA-A02Y 
       39.98         2.01         5.03        14.01        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       18.05        40.96        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 
       14.50        27.09        16.31         0.95        33.01        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07        12.20        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 
       17.56       148.01        85.45        15.62        49.08         9.99 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       32.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       45.40        12.26        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6923 
       12.49        16.14        15.58         1.48         3.68        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6931 
       14.30         9.04         9.44        11.64         4.80        12.00 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      131.51       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  KIF13A MUTATED KIF13A WILD-TYPE 
            0.07             0.00 
  KIF13A MUTATED KIF13A WILD-TYPE 
          135.65           148.01 
  KIF13A MUTATED KIF13A WILD-TYPE 
          19.000           20.945 
[1] "0.1 - 135.7 (19.0)" "0.0 - 148.0 (20.9)"
[1] "hr=" "1.1"
D1968V2, continuous
D1968V3, binary
                  cls
clus                 0   1
  KIF13A MUTATED    21   1
  KIF13A WILD-TYPE 345 118
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KIF13A MUTATED     21    1
  KIF13A WILD-TYPE  345  118
        clus
vv       KIF13A MUTATED KIF13A WILD-TYPE
  COLON              21              345
  RECTUM              1              118
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KIF13A MUTATED         3        0        1         9         2         0
  KIF13A WILD-TYPE      88        1       31       129         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIF13A MUTATED           0          2          1          1        3
  KIF13A WILD-TYPE        24          9         58         41       45
                  vv
clus               STAGE IVA STAGE IVB
  KIF13A MUTATED           0         0
  KIF13A WILD-TYPE        18         1
D1968V4, multiclass
            clus
vv           KIF13A MUTATED KIF13A WILD-TYPE
  STAGE I                 3               88
  STAGE IA                0                1
  STAGE II                1               31
  STAGE IIA               9              129
  STAGE IIB               2                8
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              2                9
  STAGE IIIB              1               58
  STAGE IIIC              1               41
  STAGE IV                3               45
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  KIF13A MUTATED     1   2  15   4
  KIF13A WILD-TYPE  16  90 314  46
D1968V5, multiclass
    clus
vv   KIF13A MUTATED KIF13A WILD-TYPE
  T1              1               16
  T2              2               90
  T3             15              314
  T4              4               46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  KIF13A MUTATED    16   5   1
  KIF13A WILD-TYPE 271 108  86
D1968V6, multiclass
    clus
vv   KIF13A MUTATED KIF13A WILD-TYPE
  N0             16              271
  N1              5              108
  N2              1               86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1968V7, binary
                  cls
clus                 0   1
  KIF13A MUTATED    15   3
  KIF13A WILD-TYPE 360  62
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KIF13A MUTATED     15    3
  KIF13A WILD-TYPE  360   62
   clus
vv  KIF13A MUTATED KIF13A WILD-TYPE
  0             15              360
  1              3               62
[1] 2 2
[1] FALSE
D1968V8, binary
                  cls
clus                 0   1
  KIF13A MUTATED     8  14
  KIF13A WILD-TYPE 217 250
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KIF13A MUTATED      8   14
  KIF13A WILD-TYPE  217  250
        clus
vv       KIF13A MUTATED KIF13A WILD-TYPE
  FEMALE              8              217
  MALE               14              250
[1] 2 2
[1] FALSE
D1968V9, binary
                  cls
clus                 0   1
  KIF13A MUTATED    13   1
  KIF13A WILD-TYPE 337  21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KIF13A MUTATED     13    1
  KIF13A WILD-TYPE  337   21
     clus
vv    KIF13A MUTATED KIF13A WILD-TYPE
  NO              13              337
  YES              1               21
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  KIF13A MUTATED                     13                             7
  KIF13A WILD-TYPE                  302                            40
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  KIF13A MUTATED                       1                              0
  KIF13A WILD-TYPE                   105                             10
D1968V10, multiclass
                                clus
vv                               KIF13A MUTATED KIF13A WILD-TYPE
  COLON ADENOCARCINOMA                       13              302
  COLON MUCINOUS ADENOCARCINOMA               7               40
  RECTAL ADENOCARCINOMA                       1              105
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  KIF13A MUTATED    14   0   3   3
  KIF13A WILD-TYPE 331   4  28  22
D1968V11, multiclass
    clus
vv   KIF13A MUTATED KIF13A WILD-TYPE
  R0             14              331
  R1              0                4
  R2              3               28
  RX              3               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1968V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KIF13A MUTATED                                  0     1
  KIF13A WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  KIF13A MUTATED                           0    12
  KIF13A WILD-TYPE                        22   214
D1968V13, multiclass
                                  clus
vv                                 KIF13A MUTATED KIF13A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                        12              214
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1969) Variable = KNTC1 MUTATION ANALYSIS
D1969V1, survival
                 sevent
clus2               0   1
  KNTC1 MUTATED    19   5
  KNTC1 WILD-TYPE 359  88
  KNTC1 MUTATED KNTC1 WILD-TYPE 
             24             447 
  KNTC1 MUTATED KNTC1 WILD-TYPE 
              5              88 
$`KNTC1 MUTATED`
TCGA-A6-3809 TCGA-AA-3818 TCGA-AA-3950 TCGA-AA-A00N TCGA-AA-A010 TCGA-AD-5900 
       32.75         0.99        24.00         4.01        34.98         0.07 
TCGA-AD-6964 TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-CA-6717 TCGA-CA-6718 
       10.88        21.44        58.39        49.41        12.76        10.06 
TCGA-CM-5861 TCGA-CM-5864 TCGA-CM-6167 TCGA-CM-6674 TCGA-D5-6927 TCGA-DM-A1HA 
       15.02        15.02        14.99        12.95         9.44       131.51 
TCGA-F4-6569 TCGA-G4-6586 TCGA-G4-6628 TCGA-AG-A002 TCGA-F5-6811 TCGA-F5-6813 
       35.74        35.80        79.69        20.98        32.19         0.69 

$`KNTC1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       10.06        35.05        33.04        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 
       12.99        24.00        33.01        26.01         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
        0.95        33.01        17.82         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        88.21         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 
        3.06         3.25         3.29         0.07        12.20        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5868 
       22.98        30.08        32.02         5.03        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6675 
       12.99        13.02        15.02        14.04        11.01        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       12.43        14.30         9.04        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
        7.50        44.32       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       31.96         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       26.17        91.79        46.75        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6812 TCGA-G5-6235 TCGA-G5-6641 
        0.66        55.76        26.43 

  KNTC1 MUTATED KNTC1 WILD-TYPE 
           0.07            0.00 
  KNTC1 MUTATED KNTC1 WILD-TYPE 
         131.51          148.01 
  KNTC1 MUTATED KNTC1 WILD-TYPE 
          18.00           20.19 
[1] "0.1 - 131.5 (18.0)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.1"
D1969V2, continuous
D1969V3, binary
                 cls
clus                0   1
  KNTC1 MUTATED    22   3
  KNTC1 WILD-TYPE 344 116
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KNTC1 MUTATED     22    3
  KNTC1 WILD-TYPE  344  116
        clus
vv       KNTC1 MUTATED KNTC1 WILD-TYPE
  COLON             22             344
  RECTUM             3             116
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KNTC1 MUTATED         5        0        1        12         3         0
  KNTC1 WILD-TYPE      86        1       31       126         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  KNTC1 MUTATED           0          0          0          3        0         0
  KNTC1 WILD-TYPE        24         11         59         39       48        18
                 vv
clus              STAGE IVB
  KNTC1 MUTATED           0
  KNTC1 WILD-TYPE         1
D1969V4, multiclass
            clus
vv           KNTC1 MUTATED KNTC1 WILD-TYPE
  STAGE I                5              86
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA             12             126
  STAGE IIB              3               7
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             3              39
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  KNTC1 MUTATED     0   5  15   5
  KNTC1 WILD-TYPE  17  87 314  45
D1969V5, multiclass
    clus
vv   KNTC1 MUTATED KNTC1 WILD-TYPE
  T1             0              17
  T2             5              87
  T3            15             314
  T4             5              45
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  KNTC1 MUTATED    21   0   4
  KNTC1 WILD-TYPE 266 113  83
D1969V6, multiclass
    clus
vv   KNTC1 MUTATED KNTC1 WILD-TYPE
  N0            21             266
  N1             0             113
  N2             4              83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1969V7, binary
                 cls
clus                0   1
  KNTC1 MUTATED    21   0
  KNTC1 WILD-TYPE 354  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KNTC1 MUTATED     21    0
  KNTC1 WILD-TYPE  354   65
   clus
vv  KNTC1 MUTATED KNTC1 WILD-TYPE
  0            21             354
  1             0              65
[1] 2 2
[1] FALSE
D1969V8, binary
                 cls
clus                0   1
  KNTC1 MUTATED    10  15
  KNTC1 WILD-TYPE 215 249
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KNTC1 MUTATED     10   15
  KNTC1 WILD-TYPE  215  249
        clus
vv       KNTC1 MUTATED KNTC1 WILD-TYPE
  FEMALE            10             215
  MALE              15             249
[1] 2 2
[1] FALSE
D1969V9, binary
                 cls
clus                0   1
  KNTC1 MUTATED    19   0
  KNTC1 WILD-TYPE 331  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KNTC1 MUTATED     19    0
  KNTC1 WILD-TYPE  331   22
     clus
vv    KNTC1 MUTATED KNTC1 WILD-TYPE
  NO             19             331
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  KNTC1 MUTATED                     17                             5
  KNTC1 WILD-TYPE                  298                            42
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  KNTC1 MUTATED                       3                              0
  KNTC1 WILD-TYPE                   103                             10
D1969V10, multiclass
                                clus
vv                               KNTC1 MUTATED KNTC1 WILD-TYPE
  COLON ADENOCARCINOMA                      17             298
  COLON MUCINOUS ADENOCARCINOMA              5              42
  RECTAL ADENOCARCINOMA                      3             103
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  KNTC1 MUTATED    19   0   0   2
  KNTC1 WILD-TYPE 326   4  31  23
D1969V11, multiclass
    clus
vv   KNTC1 MUTATED KNTC1 WILD-TYPE
  R0            19             326
  R1             0               4
  R2             0              31
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1969V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KNTC1 MUTATED                                  0     2
  KNTC1 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  KNTC1 MUTATED                           1    16
  KNTC1 WILD-TYPE                        21   210
D1969V13, multiclass
                                  clus
vv                                 KNTC1 MUTATED KNTC1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               9
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                       16             210
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1970) Variable = TRIM45 MUTATION ANALYSIS
D1970V1, survival
                  sevent
clus2                0   1
  TRIM45 MUTATED    12   2
  TRIM45 WILD-TYPE 366  91
  TRIM45 MUTATED TRIM45 WILD-TYPE 
              14              457 
  TRIM45 MUTATED TRIM45 WILD-TYPE 
               2               91 
$`TRIM45 MUTATED`
TCGA-A6-2672 TCGA-A6-6780 TCGA-AA-3518 TCGA-AA-3811 TCGA-AA-3864 TCGA-AA-A00J 
       46.65        20.12         1.02        10.06        53.00        18.05 
TCGA-AD-6895 TCGA-CA-6717 TCGA-CM-4743 TCGA-CM-5349 TCGA-CM-5861 TCGA-DM-A28K 
        0.72        12.76        23.05        30.08        15.02        98.24 
TCGA-F4-6570 TCGA-G4-6588 
        6.18        26.17 

$`TRIM45 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3519 
       63.98         6.97         1.02        13.02        38.99         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3815 
       85.05        26.99        19.04        19.04        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       31.07        30.05        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       21.37        15.52        56.55         0.79         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07        12.20        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
       82.95         1.91       124.27        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5862 
       13.02        29.06        22.03        22.98        32.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-F4-6459 
       81.37       119.93        35.97        60.79       117.07         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       31.96        35.74        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       35.80        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  TRIM45 MUTATED TRIM45 WILD-TYPE 
            0.72             0.00 
  TRIM45 MUTATED TRIM45 WILD-TYPE 
           98.24           148.01 
  TRIM45 MUTATED TRIM45 WILD-TYPE 
          19.085           20.280 
[1] "0.7 - 98.2 (19.1)"  "0.0 - 148.0 (20.3)"
[1] "hr=" "1.4"
D1970V2, continuous
D1970V3, binary
                  cls
clus                 0   1
  TRIM45 MUTATED    14   0
  TRIM45 WILD-TYPE 352 119
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIM45 MUTATED     14    0
  TRIM45 WILD-TYPE  352  119
        clus
vv       TRIM45 MUTATED TRIM45 WILD-TYPE
  COLON              14              352
  RECTUM              0              119
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TRIM45 MUTATED         0        0        1         9         0         0
  TRIM45 WILD-TYPE      91        1       31       129        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TRIM45 MUTATED           1          0          2          0        0
  TRIM45 WILD-TYPE        23         11         57         42       48
                  vv
clus               STAGE IVA STAGE IVB
  TRIM45 MUTATED           0         0
  TRIM45 WILD-TYPE        18         1
D1970V4, multiclass
            clus
vv           TRIM45 MUTATED TRIM45 WILD-TYPE
  STAGE I                 0               91
  STAGE IA                0                1
  STAGE II                1               31
  STAGE IIA               9              129
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               1               23
  STAGE IIIA              0               11
  STAGE IIIB              2               57
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  TRIM45 MUTATED     0   0  13   1
  TRIM45 WILD-TYPE  17  92 316  49
D1970V5, multiclass
    clus
vv   TRIM45 MUTATED TRIM45 WILD-TYPE
  T1              0               17
  T2              0               92
  T3             13              316
  T4              1               49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  TRIM45 MUTATED    10   3   1
  TRIM45 WILD-TYPE 277 110  86
D1970V6, multiclass
    clus
vv   TRIM45 MUTATED TRIM45 WILD-TYPE
  N0             10              277
  N1              3              110
  N2              1               86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1970V7, binary
                  cls
clus                 0   1
  TRIM45 MUTATED    12   0
  TRIM45 WILD-TYPE 363  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIM45 MUTATED     12    0
  TRIM45 WILD-TYPE  363   65
   clus
vv  TRIM45 MUTATED TRIM45 WILD-TYPE
  0             12              363
  1              0               65
[1] 2 2
[1] FALSE
D1970V8, binary
                  cls
clus                 0   1
  TRIM45 MUTATED     7   7
  TRIM45 WILD-TYPE 218 257
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIM45 MUTATED      7    7
  TRIM45 WILD-TYPE  218  257
        clus
vv       TRIM45 MUTATED TRIM45 WILD-TYPE
  FEMALE              7              218
  MALE                7              257
[1] 2 2
[1] FALSE
D1970V9, binary
                  cls
clus                 0   1
  TRIM45 MUTATED    11   0
  TRIM45 WILD-TYPE 339  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIM45 MUTATED     11    0
  TRIM45 WILD-TYPE  339   22
     clus
vv    TRIM45 MUTATED TRIM45 WILD-TYPE
  NO              11              339
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  TRIM45 MUTATED                     10                             4
  TRIM45 WILD-TYPE                  305                            43
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  TRIM45 MUTATED                       0                              0
  TRIM45 WILD-TYPE                   106                             10
D1970V10, multiclass
                                clus
vv                               TRIM45 MUTATED TRIM45 WILD-TYPE
  COLON ADENOCARCINOMA                       10              305
  COLON MUCINOUS ADENOCARCINOMA               4               43
  RECTAL ADENOCARCINOMA                       0              106
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  TRIM45 MUTATED    10   0   0   1
  TRIM45 WILD-TYPE 335   4  31  24
D1970V11, multiclass
    clus
vv   TRIM45 MUTATED TRIM45 WILD-TYPE
  R0             10              335
  R1              0                4
  R2              0               31
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1970V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TRIM45 MUTATED                                  0     1
  TRIM45 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  TRIM45 MUTATED                           0     9
  TRIM45 WILD-TYPE                        22   217
D1970V13, multiclass
                                  clus
vv                                 TRIM45 MUTATED TRIM45 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         9              217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1971) Variable = UEVLD MUTATION ANALYSIS
D1971V1, survival
                 sevent
clus2               0   1
  UEVLD MUTATED     3   1
  UEVLD WILD-TYPE 375  92
  UEVLD MUTATED UEVLD WILD-TYPE 
              4             467 
  UEVLD MUTATED UEVLD WILD-TYPE 
              1              92 
$`UEVLD MUTATED`
TCGA-AD-6964 TCGA-AZ-4315 TCGA-DM-A28K TCGA-AG-A002 
       10.88        58.39        98.24        20.98 

$`UEVLD WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        27.42         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        33.01        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
       60.79       117.07         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  UEVLD MUTATED UEVLD WILD-TYPE 
          10.88            0.00 
  UEVLD MUTATED UEVLD WILD-TYPE 
          98.24          148.01 
  UEVLD MUTATED UEVLD WILD-TYPE 
         39.685          20.120 
[1] "10.9 - 98.2 (39.7)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.4"
D1971V2, continuous
D1971V3, binary
                 cls
clus                0   1
  UEVLD MUTATED     3   1
  UEVLD WILD-TYPE 363 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UEVLD MUTATED      3    1
  UEVLD WILD-TYPE  363  118
        clus
vv       UEVLD MUTATED UEVLD WILD-TYPE
  COLON              3             363
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  UEVLD MUTATED         1        0        0         2         0         0
  UEVLD WILD-TYPE      90        1       32       136        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  UEVLD MUTATED           0          0          0          0        0         0
  UEVLD WILD-TYPE        24         11         59         42       48        18
                 vv
clus              STAGE IVB
  UEVLD MUTATED           0
  UEVLD WILD-TYPE         1
D1971V4, multiclass
            clus
vv           UEVLD MUTATED UEVLD WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              2             136
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  UEVLD MUTATED     0   1   2   1
  UEVLD WILD-TYPE  17  91 327  49
D1971V5, multiclass
    clus
vv   UEVLD MUTATED UEVLD WILD-TYPE
  T1             0              17
  T2             1              91
  T3             2             327
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  UEVLD MUTATED     3   0   1
  UEVLD WILD-TYPE 284 113  86
D1971V6, multiclass
    clus
vv   UEVLD MUTATED UEVLD WILD-TYPE
  N0             3             284
  N1             0             113
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1971V7, binary
                 cls
clus                0   1
  UEVLD MUTATED     3   0
  UEVLD WILD-TYPE 372  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UEVLD MUTATED      3    0
  UEVLD WILD-TYPE  372   65
   clus
vv  UEVLD MUTATED UEVLD WILD-TYPE
  0             3             372
  1             0              65
[1] 2 2
[1] FALSE
D1971V8, binary
                 cls
clus                0   1
  UEVLD MUTATED     0   4
  UEVLD WILD-TYPE 225 260
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UEVLD MUTATED      0    4
  UEVLD WILD-TYPE  225  260
        clus
vv       UEVLD MUTATED UEVLD WILD-TYPE
  FEMALE             0             225
  MALE               4             260
[1] 2 2
[1] FALSE
D1971V9, binary
                 cls
clus                0   1
  UEVLD MUTATED     3   0
  UEVLD WILD-TYPE 347  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UEVLD MUTATED      3    0
  UEVLD WILD-TYPE  347   22
     clus
vv    UEVLD MUTATED UEVLD WILD-TYPE
  NO              3             347
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  UEVLD MUTATED                      2                             1
  UEVLD WILD-TYPE                  313                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  UEVLD MUTATED                       1                              0
  UEVLD WILD-TYPE                   105                             10
D1971V10, multiclass
                                clus
vv                               UEVLD MUTATED UEVLD WILD-TYPE
  COLON ADENOCARCINOMA                       2             313
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  UEVLD MUTATED     2   0   0   0
  UEVLD WILD-TYPE 343   4  31  25
D1971V11, multiclass
[1] "Remove cluster labels:" "UEVLD MUTATED"         
clus
  UEVLD MUTATED UEVLD WILD-TYPE 
              2             403 
     TCGA-A6-2671      TCGA-A6-2672      TCGA-A6-2674      TCGA-A6-2676 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-A6-2677      TCGA-A6-2678      TCGA-A6-2683      TCGA-A6-3807 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-A6-3808      TCGA-A6-3809      TCGA-A6-3810      TCGA-A6-5657 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-A6-5659      TCGA-A6-5661      TCGA-A6-5665      TCGA-A6-6781 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AA-3489      TCGA-AA-3492      TCGA-AA-3496      TCGA-AA-3502 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AA-3510      TCGA-AA-3511      TCGA-AA-3514      TCGA-AA-3517 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AA-3518      TCGA-AA-3519      TCGA-AA-3520      TCGA-AA-3521 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AA-3522      TCGA-AA-3524      TCGA-AA-3525      TCGA-AA-3526 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AA-3527      TCGA-AA-3529      TCGA-AA-3530      TCGA-AA-3531 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AA-3532      TCGA-AA-3534      TCGA-AA-3538      TCGA-AA-3542 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AA-3543      TCGA-AA-3544      TCGA-AA-3548      TCGA-AA-3549 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AA-3552      TCGA-AA-3553      TCGA-AA-3554      TCGA-AA-3555 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AA-3556      TCGA-AA-3558      TCGA-AA-3560      TCGA-AA-3561 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AA-3562      TCGA-AA-3655      TCGA-AA-3660      TCGA-AA-3662 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AA-3663      TCGA-AA-3664      TCGA-AA-3666      TCGA-AA-3667 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AA-3672      TCGA-AA-3673      TCGA-AA-3678      TCGA-AA-3679 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AA-3680      TCGA-AA-3681      TCGA-AA-3684      TCGA-AA-3685 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AA-3688      TCGA-AA-3692      TCGA-AA-3693      TCGA-AA-3695 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AA-3696      TCGA-AA-3697      TCGA-AA-3710      TCGA-AA-3712 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AA-3713      TCGA-AA-3715      TCGA-AA-3811      TCGA-AA-3812 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AA-3814      TCGA-AA-3815      TCGA-AA-3818      TCGA-AA-3819 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AA-3821      TCGA-AA-3831      TCGA-AA-3833      TCGA-AA-3837 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AA-3842      TCGA-AA-3844      TCGA-AA-3845      TCGA-AA-3846 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AA-3848      TCGA-AA-3850      TCGA-AA-3851      TCGA-AA-3852 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AA-3854      TCGA-AA-3855      TCGA-AA-3856      TCGA-AA-3858 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AA-3860      TCGA-AA-3861      TCGA-AA-3864      TCGA-AA-3866 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AA-3867      TCGA-AA-3869      TCGA-AA-3870      TCGA-AA-3872 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AA-3875      TCGA-AA-3877      TCGA-AA-3930      TCGA-AA-3939 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AA-3941      TCGA-AA-3947      TCGA-AA-3949      TCGA-AA-3950 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AA-3952      TCGA-AA-3955      TCGA-AA-3956      TCGA-AA-3968 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AA-3971      TCGA-AA-3972      TCGA-AA-3973      TCGA-AA-3975 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AA-3976      TCGA-AA-3979      TCGA-AA-3984      TCGA-AA-3986 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AA-3989      TCGA-AA-3994      TCGA-AA-A004      TCGA-AA-A00A 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AA-A00D      TCGA-AA-A00E      TCGA-AA-A00F      TCGA-AA-A00J 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AA-A00K      TCGA-AA-A00L      TCGA-AA-A00N      TCGA-AA-A00O 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AA-A00Q      TCGA-AA-A00R      TCGA-AA-A00U      TCGA-AA-A00W 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AA-A00Z      TCGA-AA-A010      TCGA-AA-A017      TCGA-AA-A01D 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AA-A01F      TCGA-AA-A01G      TCGA-AA-A01I      TCGA-AA-A01K 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AA-A01P      TCGA-AA-A01Q      TCGA-AA-A01R      TCGA-AA-A01S 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AA-A01T      TCGA-AA-A01V      TCGA-AA-A01X      TCGA-AA-A01Z 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AA-A022      TCGA-AA-A024      TCGA-AA-A029      TCGA-AA-A02F 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AA-A02H      TCGA-AA-A02J      TCGA-AA-A02K      TCGA-AA-A02O 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AA-A02W      TCGA-AA-A02Y      TCGA-AA-A03F      TCGA-AA-A03J 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AD-5900      TCGA-AD-6548      TCGA-AD-6888      TCGA-AU-3779 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AU-6004      TCGA-AY-4070      TCGA-AY-4071      TCGA-AY-5543 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AY-6196      TCGA-AY-6197      TCGA-AY-6386      TCGA-AZ-4681 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AZ-4682      TCGA-CA-5254      TCGA-CA-5255      TCGA-CA-5796 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-CA-5797      TCGA-CA-6715      TCGA-CA-6716      TCGA-CA-6717 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-CA-6718      TCGA-CA-6719      TCGA-CK-4947      TCGA-CK-4948 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-CK-4950      TCGA-CK-4952      TCGA-CK-5912      TCGA-CK-5913 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-CK-5914      TCGA-CK-5915      TCGA-CK-5916      TCGA-CK-6746 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-CK-6747      TCGA-CK-6748      TCGA-CK-6751      TCGA-CM-4743 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-CM-4744      TCGA-CM-4746      TCGA-CM-4747      TCGA-CM-4752 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-CM-5341      TCGA-CM-5344      TCGA-CM-5348      TCGA-CM-5349 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-CM-5860      TCGA-CM-5861      TCGA-CM-5862      TCGA-CM-5863 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-CM-5864      TCGA-CM-5868      TCGA-CM-6161      TCGA-CM-6162 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-CM-6163      TCGA-CM-6164      TCGA-CM-6165      TCGA-CM-6166 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-CM-6167      TCGA-CM-6168      TCGA-CM-6169      TCGA-CM-6170 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-CM-6171      TCGA-CM-6172      TCGA-CM-6674      TCGA-CM-6675 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-CM-6676      TCGA-CM-6677      TCGA-CM-6678      TCGA-CM-6679 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-CM-6680      TCGA-D5-5537      TCGA-D5-5538      TCGA-D5-5539 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-D5-5540      TCGA-D5-5541      TCGA-D5-6529      TCGA-D5-6532 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-D5-6533      TCGA-D5-6534      TCGA-D5-6535      TCGA-D5-6536 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-D5-6537      TCGA-D5-6538      TCGA-D5-6539      TCGA-D5-6540 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-D5-6541      TCGA-D5-6898      TCGA-D5-6920      TCGA-D5-6922 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-D5-6923      TCGA-D5-6924      TCGA-D5-6926      TCGA-D5-6927 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-D5-6928      TCGA-D5-6929      TCGA-D5-6930      TCGA-D5-6931 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-D5-6932      TCGA-D5-7000      TCGA-F4-6459      TCGA-F4-6460 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-F4-6569      TCGA-F4-6570      TCGA-F4-6703      TCGA-F4-6704 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-F4-6805      TCGA-F4-6806      TCGA-F4-6807      TCGA-F4-6808 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-F4-6809      TCGA-F4-6854      TCGA-F4-6855      TCGA-F4-6856 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-G4-6293      TCGA-G4-6299      TCGA-G4-6303      TCGA-G4-6304 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-G4-6306      TCGA-G4-6307      TCGA-G4-6309      TCGA-G4-6310 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-G4-6315      TCGA-G4-6317      TCGA-G4-6321      TCGA-G4-6323 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-G4-6586      TCGA-G4-6588      TCGA-G4-6625      TCGA-G4-6626 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-G4-6628      TCGA-AF-2687      TCGA-AF-2689      TCGA-AF-2691 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AF-2692      TCGA-AF-3400      TCGA-AF-3913      TCGA-AF-4110 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AF-5654      TCGA-AF-6655      TCGA-AG-3574      TCGA-AG-3575 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AG-3578      TCGA-AG-3580      TCGA-AG-3581      TCGA-AG-3582 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AG-3583      TCGA-AG-3584      TCGA-AG-3586      TCGA-AG-3587 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AG-3593      TCGA-AG-3594      TCGA-AG-3598      TCGA-AG-3599 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AG-3600      TCGA-AG-3601      TCGA-AG-3602      TCGA-AG-3605 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AG-3608      TCGA-AG-3609      TCGA-AG-3611      TCGA-AG-3612 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AG-3726      TCGA-AG-3727      TCGA-AG-3731      TCGA-AG-3732 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AG-3742      TCGA-AG-3878      TCGA-AG-3882      TCGA-AG-3883 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AG-3885      TCGA-AG-3887      TCGA-AG-3890      TCGA-AG-3892 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AG-3893      TCGA-AG-3894      TCGA-AG-3896      TCGA-AG-3898 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AG-3901      TCGA-AG-3902      TCGA-AG-3909      TCGA-AG-3999 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AG-4001      TCGA-AG-4005      TCGA-AG-4007      TCGA-AG-4008 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AG-4015      TCGA-AG-A008      TCGA-AG-A00C      TCGA-AG-A00H 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AG-A00Y      TCGA-AG-A011      TCGA-AG-A014      TCGA-AG-A015 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AG-A016      TCGA-AG-A01L      TCGA-AG-A01W      TCGA-AG-A01Y 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AG-A020      TCGA-AG-A025      TCGA-AG-A026      TCGA-AG-A02G 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AG-A02N      TCGA-AG-A02X      TCGA-AG-A032      TCGA-AG-A036 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-AH-6549      TCGA-AH-6643      TCGA-CL-5917      TCGA-CL-5918 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-DC-5337      TCGA-DC-5869      TCGA-DC-6155      TCGA-DC-6157 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-DC-6158      TCGA-DC-6160      TCGA-DC-6681      TCGA-DC-6682 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-DC-6683      TCGA-DT-5265      TCGA-EF-5830      TCGA-EI-6506 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-EI-6507      TCGA-EI-6508      TCGA-EI-6510      TCGA-F5-6464 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-F5-6465      TCGA-F5-6571      TCGA-F5-6702      TCGA-F5-6812 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
     TCGA-F5-6813      TCGA-G5-6235      TCGA-G5-6641 
"UEVLD WILD-TYPE" "UEVLD WILD-TYPE" "UEVLD WILD-TYPE" 
D1971V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  UEVLD MUTATED                                  0     0
  UEVLD WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  UEVLD MUTATED                           0     3
  UEVLD WILD-TYPE                        22   223
D1971V13, multiclass
                                  clus
vv                                 UEVLD MUTATED UEVLD WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        3             223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1972) Variable = PEX2 MUTATION ANALYSIS
D1972V1, survival
                sevent
clus2              0   1
  PEX2 MUTATED     8   2
  PEX2 WILD-TYPE 370  91
  PEX2 MUTATED PEX2 WILD-TYPE 
            10            461 
  PEX2 MUTATED PEX2 WILD-TYPE 
             2             91 
$`PEX2 MUTATED`
TCGA-A6-5661 TCGA-AA-A00A TCGA-AY-6197 TCGA-AZ-6598 TCGA-AZ-6606 TCGA-CA-6717 
       33.53        38.04        21.44        49.41        11.74        12.76 
TCGA-CM-6168 TCGA-CM-6171 TCGA-D5-6540 TCGA-CI-6620 
       12.99        14.04        16.14        33.17 

$`PEX2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       33.01        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        88.21         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
       29.56         5.23         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07        12.20        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 
       16.04        21.99        14.99        13.02        15.02        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
        4.80        17.13        12.49        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
        6.05         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  PEX2 MUTATED PEX2 WILD-TYPE 
         11.74           0.00 
  PEX2 MUTATED PEX2 WILD-TYPE 
         49.41         148.01 
  PEX2 MUTATED PEX2 WILD-TYPE 
         18.79          20.19 
[1] "11.7 - 49.4 (18.8)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.1"
D1972V2, continuous
D1972V3, binary
                cls
clus               0   1
  PEX2 MUTATED     9   1
  PEX2 WILD-TYPE 357 118
[1] "tbl2"
                cls
clus             [,1] [,2]
  PEX2 MUTATED      9    1
  PEX2 WILD-TYPE  357  118
        clus
vv       PEX2 MUTATED PEX2 WILD-TYPE
  COLON             9            357
  RECTUM            1            118
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PEX2 MUTATED         2        0        1         5         0         0
  PEX2 WILD-TYPE      89        1       31       133        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PEX2 MUTATED           0          0          0          0        1         1
  PEX2 WILD-TYPE        24         11         59         42       47        17
                vv
clus             STAGE IVB
  PEX2 MUTATED           0
  PEX2 WILD-TYPE         1
D1972V4, multiclass
            clus
vv           PEX2 MUTATED PEX2 WILD-TYPE
  STAGE I               2             89
  STAGE IA              0              1
  STAGE II              1             31
  STAGE IIA             5            133
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            0             59
  STAGE IIIC            0             42
  STAGE IV              1             47
  STAGE IVA             1             17
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  PEX2 MUTATED     0   2   7   1
  PEX2 WILD-TYPE  17  90 322  49
D1972V5, multiclass
    clus
vv   PEX2 MUTATED PEX2 WILD-TYPE
  T1            0             17
  T2            2             90
  T3            7            322
  T4            1             49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  PEX2 MUTATED     8   1   1
  PEX2 WILD-TYPE 279 112  86
D1972V6, multiclass
    clus
vv   PEX2 MUTATED PEX2 WILD-TYPE
  N0            8            279
  N1            1            112
  N2            1             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1972V7, binary
                cls
clus               0   1
  PEX2 MUTATED     6   2
  PEX2 WILD-TYPE 369  63
[1] "tbl2"
                cls
clus             [,1] [,2]
  PEX2 MUTATED      6    2
  PEX2 WILD-TYPE  369   63
   clus
vv  PEX2 MUTATED PEX2 WILD-TYPE
  0            6            369
  1            2             63
[1] 2 2
[1] FALSE
D1972V8, binary
                cls
clus               0   1
  PEX2 MUTATED     5   5
  PEX2 WILD-TYPE 220 259
[1] "tbl2"
                cls
clus             [,1] [,2]
  PEX2 MUTATED      5    5
  PEX2 WILD-TYPE  220  259
        clus
vv       PEX2 MUTATED PEX2 WILD-TYPE
  FEMALE            5            220
  MALE              5            259
[1] 2 2
[1] FALSE
D1972V9, binary
                cls
clus               0   1
  PEX2 MUTATED    10   0
  PEX2 WILD-TYPE 340  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  PEX2 MUTATED     10    0
  PEX2 WILD-TYPE  340   22
     clus
vv    PEX2 MUTATED PEX2 WILD-TYPE
  NO            10            340
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PEX2 MUTATED                      7                             2
  PEX2 WILD-TYPE                  308                            45
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PEX2 MUTATED                       1                              0
  PEX2 WILD-TYPE                   105                             10
D1972V10, multiclass
                                clus
vv                               PEX2 MUTATED PEX2 WILD-TYPE
  COLON ADENOCARCINOMA                      7            308
  COLON MUCINOUS ADENOCARCINOMA             2             45
  RECTAL ADENOCARCINOMA                     1            105
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  PEX2 MUTATED     6   0   0   1
  PEX2 WILD-TYPE 339   4  31  24
D1972V11, multiclass
    clus
vv   PEX2 MUTATED PEX2 WILD-TYPE
  R0            6            339
  R1            0              4
  R2            0             31
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1972V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PEX2 MUTATED                                  0     1
  PEX2 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  PEX2 MUTATED                           2     6
  PEX2 WILD-TYPE                        20   220
D1972V13, multiclass
                                  clus
vv                                 PEX2 MUTATED PEX2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   2             20
  WHITE                                       6            220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1973) Variable = C16ORF71 MUTATION ANALYSIS
D1973V1, survival
                    sevent
clus2                  0   1
  C16ORF71 MUTATED     5   1
  C16ORF71 WILD-TYPE 373  92
  C16ORF71 MUTATED C16ORF71 WILD-TYPE 
                 6                465 
  C16ORF71 MUTATED C16ORF71 WILD-TYPE 
                 1                 92 
$`C16ORF71 MUTATED`
TCGA-AA-3950 TCGA-AA-3977 TCGA-AA-A00J TCGA-AZ-4315 TCGA-CA-6717 TCGA-AF-5654 
       24.00        25.02        18.05        58.39        12.76        16.83 

$`C16ORF71 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       19.00        30.02        34.03        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07        12.20        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       34.49        10.39        14.50        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  C16ORF71 MUTATED C16ORF71 WILD-TYPE 
             12.76               0.00 
  C16ORF71 MUTATED C16ORF71 WILD-TYPE 
             58.39             148.01 
  C16ORF71 MUTATED C16ORF71 WILD-TYPE 
            21.025             20.190 
[1] "12.8 - 58.4 (21.0)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.2"
D1973V2, continuous
D1973V3, binary
                    cls
clus                   0   1
  C16ORF71 MUTATED     6   1
  C16ORF71 WILD-TYPE 360 118
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C16ORF71 MUTATED      6    1
  C16ORF71 WILD-TYPE  360  118
        clus
vv       C16ORF71 MUTATED C16ORF71 WILD-TYPE
  COLON                 6                360
  RECTUM                1                118
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  C16ORF71 MUTATED         1        0        0         4         0         0
  C16ORF71 WILD-TYPE      90        1       32       134        10         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C16ORF71 MUTATED           0          0          1          0        0
  C16ORF71 WILD-TYPE        24         11         58         42       48
                    vv
clus                 STAGE IVA STAGE IVB
  C16ORF71 MUTATED           0         0
  C16ORF71 WILD-TYPE        18         1
D1973V4, multiclass
            clus
vv           C16ORF71 MUTATED C16ORF71 WILD-TYPE
  STAGE I                   1                 90
  STAGE IA                  0                  1
  STAGE II                  0                 32
  STAGE IIA                 4                134
  STAGE IIB                 0                 10
  STAGE IIC                 0                  1
  STAGE III                 0                 24
  STAGE IIIA                0                 11
  STAGE IIIB                1                 58
  STAGE IIIC                0                 42
  STAGE IV                  0                 48
  STAGE IVA                 0                 18
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  C16ORF71 MUTATED     0   2   4   1
  C16ORF71 WILD-TYPE  17  90 325  49
D1973V5, multiclass
    clus
vv   C16ORF71 MUTATED C16ORF71 WILD-TYPE
  T1                0                 17
  T2                2                 90
  T3                4                325
  T4                1                 49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  C16ORF71 MUTATED     6   1   0
  C16ORF71 WILD-TYPE 281 112  87
D1973V6, multiclass
    clus
vv   C16ORF71 MUTATED C16ORF71 WILD-TYPE
  N0                6                281
  N1                1                112
  N2                0                 87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1973V7, binary
                    cls
clus                   0   1
  C16ORF71 MUTATED     6   0
  C16ORF71 WILD-TYPE 369  65
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C16ORF71 MUTATED      6    0
  C16ORF71 WILD-TYPE  369   65
   clus
vv  C16ORF71 MUTATED C16ORF71 WILD-TYPE
  0                6                369
  1                0                 65
[1] 2 2
[1] FALSE
D1973V8, binary
                    cls
clus                   0   1
  C16ORF71 MUTATED     3   4
  C16ORF71 WILD-TYPE 222 260
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C16ORF71 MUTATED      3    4
  C16ORF71 WILD-TYPE  222  260
        clus
vv       C16ORF71 MUTATED C16ORF71 WILD-TYPE
  FEMALE                3                222
  MALE                  4                260
[1] 2 2
[1] FALSE
D1973V9, binary
                    cls
clus                   0   1
  C16ORF71 MUTATED     6   0
  C16ORF71 WILD-TYPE 344  22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C16ORF71 MUTATED      6    0
  C16ORF71 WILD-TYPE  344   22
     clus
vv    C16ORF71 MUTATED C16ORF71 WILD-TYPE
  NO                 6                344
  YES                0                 22
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  C16ORF71 MUTATED                      3                             3
  C16ORF71 WILD-TYPE                  312                            44
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  C16ORF71 MUTATED                       1                              0
  C16ORF71 WILD-TYPE                   105                             10
D1973V10, multiclass
                                clus
vv                               C16ORF71 MUTATED C16ORF71 WILD-TYPE
  COLON ADENOCARCINOMA                          3                312
  COLON MUCINOUS ADENOCARCINOMA                 3                 44
  RECTAL ADENOCARCINOMA                         1                105
  RECTAL MUCINOUS ADENOCARCINOMA                0                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  C16ORF71 MUTATED     5   0   0   1
  C16ORF71 WILD-TYPE 340   4  31  24
D1973V11, multiclass
    clus
vv   C16ORF71 MUTATED C16ORF71 WILD-TYPE
  R0                5                340
  R1                0                  4
  R2                0                 31
  RX                1                 24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1973V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C16ORF71 MUTATED                                  0     1
  C16ORF71 WILD-TYPE                                1    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  C16ORF71 MUTATED                           0     2
  C16ORF71 WILD-TYPE                        22   224
D1973V13, multiclass
                                  clus
vv                                 C16ORF71 MUTATED C16ORF71 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                 10
  BLACK OR AFRICAN AMERICAN                       0                 22
  WHITE                                           2                224
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1974) Variable = SLC6A3 MUTATION ANALYSIS
D1974V1, survival
                  sevent
clus2                0   1
  SLC6A3 MUTATED     8   0
  SLC6A3 WILD-TYPE 370  93
  SLC6A3 MUTATED SLC6A3 WILD-TYPE 
               8              463 
  SLC6A3 MUTATED SLC6A3 WILD-TYPE 
               0               93 
$`SLC6A3 MUTATED`
TCGA-A6-5665 TCGA-AA-3870 TCGA-AD-6889 TCGA-AD-6895 TCGA-D5-6540 TCGA-DM-A1D0 
       22.06        29.98        56.55         0.72        16.14       130.65 
TCGA-DM-A1HB TCGA-AG-A02N 
      135.65        61.97 

$`SLC6A3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       17.03        24.03        27.02        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.79         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       12.49        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
       44.32       131.51       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X 
       64.01        10.98        49.97         1.94        38.96        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  SLC6A3 MUTATED SLC6A3 WILD-TYPE 
            0.72             0.00 
  SLC6A3 MUTATED SLC6A3 WILD-TYPE 
          135.65           148.01 
  SLC6A3 MUTATED SLC6A3 WILD-TYPE 
          43.265           20.050 
[1] "0.7 - 135.7 (43.3)" "0.0 - 148.0 (20.1)"
[1] "hr="     "2.6e+07"
D1974V2, continuous
D1974V3, binary
                  cls
clus                 0   1
  SLC6A3 MUTATED     7   1
  SLC6A3 WILD-TYPE 359 118
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLC6A3 MUTATED      7    1
  SLC6A3 WILD-TYPE  359  118
        clus
vv       SLC6A3 MUTATED SLC6A3 WILD-TYPE
  COLON               7              359
  RECTUM              1              118
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SLC6A3 MUTATED         1        0        1         3         0         0
  SLC6A3 WILD-TYPE      90        1       31       135        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC6A3 MUTATED           0          0          1          0        1
  SLC6A3 WILD-TYPE        24         11         58         42       47
                  vv
clus               STAGE IVA STAGE IVB
  SLC6A3 MUTATED           0         0
  SLC6A3 WILD-TYPE        18         1
D1974V4, multiclass
            clus
vv           SLC6A3 MUTATED SLC6A3 WILD-TYPE
  STAGE I                 1               90
  STAGE IA                0                1
  STAGE II                1               31
  STAGE IIA               3              135
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              1               58
  STAGE IIIC              0               42
  STAGE IV                1               47
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  SLC6A3 MUTATED     0   1   7   0
  SLC6A3 WILD-TYPE  17  91 322  50
D1974V5, multiclass
    clus
vv   SLC6A3 MUTATED SLC6A3 WILD-TYPE
  T1              0               17
  T2              1               91
  T3              7              322
  T4              0               50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  SLC6A3 MUTATED     5   2   1
  SLC6A3 WILD-TYPE 282 111  86
D1974V6, multiclass
    clus
vv   SLC6A3 MUTATED SLC6A3 WILD-TYPE
  N0              5              282
  N1              2              111
  N2              1               86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1974V7, binary
                  cls
clus                 0   1
  SLC6A3 MUTATED     6   1
  SLC6A3 WILD-TYPE 369  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLC6A3 MUTATED      6    1
  SLC6A3 WILD-TYPE  369   64
   clus
vv  SLC6A3 MUTATED SLC6A3 WILD-TYPE
  0              6              369
  1              1               64
[1] 2 2
[1] FALSE
D1974V8, binary
                  cls
clus                 0   1
  SLC6A3 MUTATED     3   5
  SLC6A3 WILD-TYPE 222 259
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLC6A3 MUTATED      3    5
  SLC6A3 WILD-TYPE  222  259
        clus
vv       SLC6A3 MUTATED SLC6A3 WILD-TYPE
  FEMALE              3              222
  MALE                5              259
[1] 2 2
[1] FALSE
D1974V9, binary
                  cls
clus                 0   1
  SLC6A3 MUTATED     2   0
  SLC6A3 WILD-TYPE 348  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLC6A3 MUTATED      2    0
  SLC6A3 WILD-TYPE  348   22
     clus
vv    SLC6A3 MUTATED SLC6A3 WILD-TYPE
  NO               2              348
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SLC6A3 MUTATED                      5                             1
  SLC6A3 WILD-TYPE                  310                            46
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SLC6A3 MUTATED                       1                              0
  SLC6A3 WILD-TYPE                   105                             10
D1974V10, multiclass
                                clus
vv                               SLC6A3 MUTATED SLC6A3 WILD-TYPE
  COLON ADENOCARCINOMA                        5              310
  COLON MUCINOUS ADENOCARCINOMA               1               46
  RECTAL ADENOCARCINOMA                       1              105
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  SLC6A3 MUTATED     4   0   0   0
  SLC6A3 WILD-TYPE 341   4  31  25
D1974V11, multiclass
    clus
vv   SLC6A3 MUTATED SLC6A3 WILD-TYPE
  R0              4              341
  R1              0                4
  R2              0               31
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1974V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SLC6A3 MUTATED                                  0     1
  SLC6A3 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  SLC6A3 MUTATED                           0     5
  SLC6A3 WILD-TYPE                        22   221
D1974V13, multiclass
                                  clus
vv                                 SLC6A3 MUTATED SLC6A3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         5              221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1975) Variable = MLNR MUTATION ANALYSIS
D1975V1, survival
                sevent
clus2              0   1
  MLNR MUTATED     1   3
  MLNR WILD-TYPE 377  90
  MLNR MUTATED MLNR WILD-TYPE 
             4            467 
  MLNR MUTATED MLNR WILD-TYPE 
             3             90 
$`MLNR MUTATED`
TCGA-AA-3516 TCGA-AA-3845 TCGA-AA-A01P TCGA-AH-6549 
       13.02         0.00        38.07        17.49 

$`MLNR WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        1.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 
       17.98        15.95        38.99        37.02        14.93        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        31.00         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
      117.11        38.56         1.45         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  MLNR MUTATED MLNR WILD-TYPE 
             0              0 
  MLNR MUTATED MLNR WILD-TYPE 
         38.07         148.01 
  MLNR MUTATED MLNR WILD-TYPE 
        15.255         20.280 
[1] "0.0 - 38.1 (15.3)"  "0.0 - 148.0 (20.3)"
[1] "hr=" "6"  
D1975V2, continuous
D1975V3, binary
                cls
clus               0   1
  MLNR MUTATED     3   1
  MLNR WILD-TYPE 363 118
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLNR MUTATED      3    1
  MLNR WILD-TYPE  363  118
        clus
vv       MLNR MUTATED MLNR WILD-TYPE
  COLON             3            363
  RECTUM            1            118
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MLNR MUTATED         0        0        0         1         0         0
  MLNR WILD-TYPE      91        1       32       137        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MLNR MUTATED           2          0          0          0        0         0
  MLNR WILD-TYPE        22         11         59         42       48        18
                vv
clus             STAGE IVB
  MLNR MUTATED           0
  MLNR WILD-TYPE         1
D1975V4, multiclass
            clus
vv           MLNR MUTATED MLNR WILD-TYPE
  STAGE I               0             91
  STAGE IA              0              1
  STAGE II              0             32
  STAGE IIA             1            137
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             2             22
  STAGE IIIA            0             11
  STAGE IIIB            0             59
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  MLNR MUTATED     0   0   4   0
  MLNR WILD-TYPE  17  92 325  50
D1975V5, multiclass
    clus
vv   MLNR MUTATED MLNR WILD-TYPE
  T1            0             17
  T2            0             92
  T3            4            325
  T4            0             50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  MLNR MUTATED     1   1   1
  MLNR WILD-TYPE 286 112  86
D1975V6, multiclass
    clus
vv   MLNR MUTATED MLNR WILD-TYPE
  N0            1            286
  N1            1            112
  N2            1             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1975V7, binary
                cls
clus               0   1
  MLNR MUTATED     3   0
  MLNR WILD-TYPE 372  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLNR MUTATED      3    0
  MLNR WILD-TYPE  372   65
   clus
vv  MLNR MUTATED MLNR WILD-TYPE
  0            3            372
  1            0             65
[1] 2 2
[1] FALSE
D1975V8, binary
                cls
clus               0   1
  MLNR MUTATED     3   1
  MLNR WILD-TYPE 222 263
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLNR MUTATED      3    1
  MLNR WILD-TYPE  222  263
        clus
vv       MLNR MUTATED MLNR WILD-TYPE
  FEMALE            3            222
  MALE              1            263
[1] 2 2
[1] FALSE
D1975V9, binary
                cls
clus               0   1
  MLNR MUTATED     3   0
  MLNR WILD-TYPE 347  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLNR MUTATED      3    0
  MLNR WILD-TYPE  347   22
     clus
vv    MLNR MUTATED MLNR WILD-TYPE
  NO             3            347
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MLNR MUTATED                      2                             1
  MLNR WILD-TYPE                  313                            46
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MLNR MUTATED                       1                              0
  MLNR WILD-TYPE                   105                             10
D1975V10, multiclass
                                clus
vv                               MLNR MUTATED MLNR WILD-TYPE
  COLON ADENOCARCINOMA                      2            313
  COLON MUCINOUS ADENOCARCINOMA             1             46
  RECTAL ADENOCARCINOMA                     1            105
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  MLNR MUTATED     2   0   0   1
  MLNR WILD-TYPE 343   4  31  24
D1975V11, multiclass
    clus
vv   MLNR MUTATED MLNR WILD-TYPE
  R0            2            343
  R1            0              4
  R2            0             31
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1975V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MLNR MUTATED                                  0     0
  MLNR WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  MLNR MUTATED                           0     1
  MLNR WILD-TYPE                        22   225
D1975V13, multiclass
[1] "Remove cluster labels:" "MLNR MUTATED"          
clus
  MLNR MUTATED MLNR WILD-TYPE 
             1            259 
    TCGA-A6-2671     TCGA-A6-2672     TCGA-A6-2674     TCGA-A6-2676 
"MLNR WILD-TYPE" "MLNR WILD-TYPE" "MLNR WILD-TYPE" "MLNR WILD-TYPE" 
    TCGA-A6-2677     TCGA-A6-2678     TCGA-A6-2683     TCGA-A6-3807 
"MLNR WILD-TYPE" "MLNR WILD-TYPE" "MLNR WILD-TYPE" "MLNR WILD-TYPE" 
    TCGA-A6-3808     TCGA-A6-3809     TCGA-A6-3810     TCGA-A6-4105 
"MLNR WILD-TYPE" "MLNR WILD-TYPE" "MLNR WILD-TYPE" "MLNR WILD-TYPE" 
    TCGA-A6-5656     TCGA-A6-5657     TCGA-A6-5659     TCGA-A6-5660 
"MLNR WILD-TYPE" "MLNR WILD-TYPE" "MLNR WILD-TYPE" "MLNR WILD-TYPE" 
    TCGA-A6-5661     TCGA-A6-5662     TCGA-A6-5664     TCGA-A6-5665 
"MLNR WILD-TYPE" "MLNR WILD-TYPE" "MLNR WILD-TYPE" "MLNR WILD-TYPE" 
    TCGA-A6-5666     TCGA-A6-6137     TCGA-A6-6138     TCGA-A6-6141 
"MLNR WILD-TYPE" "MLNR WILD-TYPE" "MLNR WILD-TYPE" "MLNR WILD-TYPE" 
    TCGA-A6-6142     TCGA-A6-6648     TCGA-A6-6649     TCGA-A6-6651 
"MLNR WILD-TYPE" "MLNR WILD-TYPE" "MLNR WILD-TYPE" "MLNR WILD-TYPE" 
    TCGA-A6-6652     TCGA-A6-6653     TCGA-A6-6654     TCGA-A6-6780 
"MLNR WILD-TYPE" "MLNR WILD-TYPE" "MLNR WILD-TYPE" "MLNR WILD-TYPE" 
    TCGA-A6-6781     TCGA-A6-6782     TCGA-AD-5900     TCGA-AD-6548 
"MLNR WILD-TYPE" "MLNR WILD-TYPE" "MLNR WILD-TYPE" "MLNR WILD-TYPE" 
    TCGA-AD-6888     TCGA-AD-6889     TCGA-AD-6890     TCGA-AD-6895 
"MLNR WILD-TYPE" "MLNR WILD-TYPE" "MLNR WILD-TYPE" "MLNR WILD-TYPE" 
    TCGA-AD-6899     TCGA-AD-6901     TCGA-AD-6963     TCGA-AD-6964 
"MLNR WILD-TYPE" "MLNR WILD-TYPE" "MLNR WILD-TYPE" "MLNR WILD-TYPE" 
    TCGA-AD-6965     TCGA-AU-3779     TCGA-AU-6004     TCGA-AY-4070 
"MLNR WILD-TYPE" "MLNR WILD-TYPE" "MLNR WILD-TYPE" "MLNR WILD-TYPE" 
    TCGA-AY-4071     TCGA-AY-5543     TCGA-AY-6196     TCGA-AY-6197 
"MLNR WILD-TYPE" "MLNR WILD-TYPE" "MLNR WILD-TYPE" "MLNR WILD-TYPE" 
    TCGA-AY-6386     TCGA-AZ-4315     TCGA-AZ-4323     TCGA-AZ-4616 
"MLNR WILD-TYPE" "MLNR WILD-TYPE" "MLNR WILD-TYPE" "MLNR WILD-TYPE" 
    TCGA-AZ-4681     TCGA-AZ-4682     TCGA-AZ-5403     TCGA-AZ-5407 
"MLNR WILD-TYPE" "MLNR WILD-TYPE" "MLNR WILD-TYPE" "MLNR WILD-TYPE" 
    TCGA-AZ-6598     TCGA-AZ-6599     TCGA-AZ-6600     TCGA-AZ-6601 
"MLNR WILD-TYPE" "MLNR WILD-TYPE" "MLNR WILD-TYPE" "MLNR WILD-TYPE" 
    TCGA-AZ-6603     TCGA-AZ-6605     TCGA-AZ-6606     TCGA-AZ-6607 
"MLNR WILD-TYPE" "MLNR WILD-TYPE" "MLNR WILD-TYPE" "MLNR WILD-TYPE" 
    TCGA-AZ-6608     TCGA-CA-5254     TCGA-CA-5255     TCGA-CA-5796 
"MLNR WILD-TYPE" "MLNR WILD-TYPE" "MLNR WILD-TYPE" "MLNR WILD-TYPE" 
    TCGA-CA-5797     TCGA-CA-6715     TCGA-CA-6716     TCGA-CA-6717 
"MLNR WILD-TYPE" "MLNR WILD-TYPE" "MLNR WILD-TYPE" "MLNR WILD-TYPE" 
    TCGA-CA-6718     TCGA-CA-6719     TCGA-CK-4947     TCGA-CK-4948 
"MLNR WILD-TYPE" "MLNR WILD-TYPE" "MLNR WILD-TYPE" "MLNR WILD-TYPE" 
    TCGA-CK-4950     TCGA-CK-4952     TCGA-CK-5912     TCGA-CK-5913 
"MLNR WILD-TYPE" "MLNR WILD-TYPE" "MLNR WILD-TYPE" "MLNR WILD-TYPE" 
    TCGA-CK-5914     TCGA-CK-5915     TCGA-CK-5916     TCGA-CK-6746 
"MLNR WILD-TYPE" "MLNR WILD-TYPE" "MLNR WILD-TYPE" "MLNR WILD-TYPE" 
    TCGA-CK-6747     TCGA-CK-6748     TCGA-CK-6751     TCGA-CM-4743 
"MLNR WILD-TYPE" "MLNR WILD-TYPE" "MLNR WILD-TYPE" "MLNR WILD-TYPE" 
    TCGA-CM-4744     TCGA-CM-4746     TCGA-CM-4747     TCGA-CM-4752 
"MLNR WILD-TYPE" "MLNR WILD-TYPE" "MLNR WILD-TYPE" "MLNR WILD-TYPE" 
    TCGA-CM-5341     TCGA-CM-5344     TCGA-CM-5348     TCGA-CM-5349 
"MLNR WILD-TYPE" "MLNR WILD-TYPE" "MLNR WILD-TYPE" "MLNR WILD-TYPE" 
    TCGA-CM-5860     TCGA-CM-5861     TCGA-CM-5862     TCGA-CM-5863 
"MLNR WILD-TYPE" "MLNR WILD-TYPE" "MLNR WILD-TYPE" "MLNR WILD-TYPE" 
    TCGA-CM-5864     TCGA-CM-5868     TCGA-CM-6161     TCGA-CM-6162 
"MLNR WILD-TYPE" "MLNR WILD-TYPE" "MLNR WILD-TYPE" "MLNR WILD-TYPE" 
    TCGA-CM-6163     TCGA-CM-6164     TCGA-CM-6165     TCGA-CM-6166 
"MLNR WILD-TYPE" "MLNR WILD-TYPE" "MLNR WILD-TYPE" "MLNR WILD-TYPE" 
    TCGA-CM-6167     TCGA-CM-6168     TCGA-CM-6169     TCGA-CM-6170 
"MLNR WILD-TYPE" "MLNR WILD-TYPE" "MLNR WILD-TYPE" "MLNR WILD-TYPE" 
    TCGA-CM-6171     TCGA-CM-6172     TCGA-CM-6674     TCGA-CM-6675 
"MLNR WILD-TYPE" "MLNR WILD-TYPE" "MLNR WILD-TYPE" "MLNR WILD-TYPE" 
    TCGA-CM-6676     TCGA-CM-6677     TCGA-CM-6678     TCGA-CM-6679 
"MLNR WILD-TYPE" "MLNR WILD-TYPE" "MLNR WILD-TYPE" "MLNR WILD-TYPE" 
    TCGA-CM-6680     TCGA-D5-5537     TCGA-D5-5538     TCGA-D5-5539 
"MLNR WILD-TYPE" "MLNR WILD-TYPE" "MLNR WILD-TYPE" "MLNR WILD-TYPE" 
    TCGA-D5-5540     TCGA-D5-5541     TCGA-D5-6529     TCGA-D5-6532 
"MLNR WILD-TYPE" "MLNR WILD-TYPE" "MLNR WILD-TYPE" "MLNR WILD-TYPE" 
    TCGA-D5-6533     TCGA-D5-6534     TCGA-D5-6535     TCGA-D5-6536 
"MLNR WILD-TYPE" "MLNR WILD-TYPE" "MLNR WILD-TYPE" "MLNR WILD-TYPE" 
    TCGA-D5-6537     TCGA-D5-6538     TCGA-D5-6539     TCGA-D5-6540 
"MLNR WILD-TYPE" "MLNR WILD-TYPE" "MLNR WILD-TYPE" "MLNR WILD-TYPE" 
    TCGA-D5-6541     TCGA-D5-6898     TCGA-D5-6920     TCGA-D5-6922 
"MLNR WILD-TYPE" "MLNR WILD-TYPE" "MLNR WILD-TYPE" "MLNR WILD-TYPE" 
    TCGA-D5-6923     TCGA-D5-6924     TCGA-D5-6926     TCGA-D5-6927 
"MLNR WILD-TYPE" "MLNR WILD-TYPE" "MLNR WILD-TYPE" "MLNR WILD-TYPE" 
    TCGA-D5-6928     TCGA-D5-6929     TCGA-D5-6930     TCGA-D5-6931 
"MLNR WILD-TYPE" "MLNR WILD-TYPE" "MLNR WILD-TYPE" "MLNR WILD-TYPE" 
    TCGA-D5-6932     TCGA-D5-7000     TCGA-DM-A0X9     TCGA-DM-A0XD 
"MLNR WILD-TYPE" "MLNR WILD-TYPE" "MLNR WILD-TYPE" "MLNR WILD-TYPE" 
    TCGA-DM-A0XF     TCGA-DM-A1D0     TCGA-DM-A1D4     TCGA-DM-A1D6 
"MLNR WILD-TYPE" "MLNR WILD-TYPE" "MLNR WILD-TYPE" "MLNR WILD-TYPE" 
    TCGA-DM-A1D7     TCGA-DM-A1D8     TCGA-DM-A1D9     TCGA-DM-A1DA 
"MLNR WILD-TYPE" "MLNR WILD-TYPE" "MLNR WILD-TYPE" "MLNR WILD-TYPE" 
    TCGA-DM-A1DB     TCGA-DM-A1HA     TCGA-DM-A1HB     TCGA-DM-A282 
"MLNR WILD-TYPE" "MLNR WILD-TYPE" "MLNR WILD-TYPE" "MLNR WILD-TYPE" 
    TCGA-DM-A285     TCGA-DM-A28C     TCGA-DM-A28E     TCGA-DM-A28F 
"MLNR WILD-TYPE" "MLNR WILD-TYPE" "MLNR WILD-TYPE" "MLNR WILD-TYPE" 
    TCGA-DM-A28G     TCGA-DM-A28H     TCGA-DM-A28K     TCGA-F4-6459 
"MLNR WILD-TYPE" "MLNR WILD-TYPE" "MLNR WILD-TYPE" "MLNR WILD-TYPE" 
    TCGA-F4-6460     TCGA-F4-6569     TCGA-F4-6570     TCGA-F4-6703 
"MLNR WILD-TYPE" "MLNR WILD-TYPE" "MLNR WILD-TYPE" "MLNR WILD-TYPE" 
    TCGA-F4-6704     TCGA-F4-6805     TCGA-F4-6806     TCGA-F4-6807 
"MLNR WILD-TYPE" "MLNR WILD-TYPE" "MLNR WILD-TYPE" "MLNR WILD-TYPE" 
    TCGA-F4-6808     TCGA-F4-6809     TCGA-F4-6854     TCGA-F4-6855 
"MLNR WILD-TYPE" "MLNR WILD-TYPE" "MLNR WILD-TYPE" "MLNR WILD-TYPE" 
    TCGA-F4-6856     TCGA-G4-6293     TCGA-G4-6299     TCGA-G4-6303 
"MLNR WILD-TYPE" "MLNR WILD-TYPE" "MLNR WILD-TYPE" "MLNR WILD-TYPE" 
    TCGA-G4-6304     TCGA-G4-6306     TCGA-G4-6307     TCGA-G4-6309 
"MLNR WILD-TYPE" "MLNR WILD-TYPE" "MLNR WILD-TYPE" "MLNR WILD-TYPE" 
    TCGA-G4-6310     TCGA-G4-6315     TCGA-G4-6317     TCGA-G4-6321 
"MLNR WILD-TYPE" "MLNR WILD-TYPE" "MLNR WILD-TYPE" "MLNR WILD-TYPE" 
    TCGA-G4-6323     TCGA-G4-6586     TCGA-G4-6588     TCGA-G4-6625 
"MLNR WILD-TYPE" "MLNR WILD-TYPE" "MLNR WILD-TYPE" "MLNR WILD-TYPE" 
    TCGA-G4-6626     TCGA-G4-6628     TCGA-AF-2687     TCGA-AF-2689 
"MLNR WILD-TYPE" "MLNR WILD-TYPE" "MLNR WILD-TYPE" "MLNR WILD-TYPE" 
    TCGA-AF-2691     TCGA-AF-2692     TCGA-AF-2693     TCGA-AF-3400 
"MLNR WILD-TYPE" "MLNR WILD-TYPE" "MLNR WILD-TYPE" "MLNR WILD-TYPE" 
    TCGA-AF-3913     TCGA-AF-4110     TCGA-AF-5654     TCGA-AF-6136 
"MLNR WILD-TYPE" "MLNR WILD-TYPE" "MLNR WILD-TYPE" "MLNR WILD-TYPE" 
    TCGA-AF-6655     TCGA-AF-6672     TCGA-AH-6544     TCGA-AH-6547 
"MLNR WILD-TYPE" "MLNR WILD-TYPE" "MLNR WILD-TYPE" "MLNR WILD-TYPE" 
    TCGA-AH-6643     TCGA-AH-6644     TCGA-CI-6619     TCGA-CI-6620 
"MLNR WILD-TYPE" "MLNR WILD-TYPE" "MLNR WILD-TYPE" "MLNR WILD-TYPE" 
    TCGA-CI-6621     TCGA-CI-6622     TCGA-CI-6624     TCGA-CL-5917 
"MLNR WILD-TYPE" "MLNR WILD-TYPE" "MLNR WILD-TYPE" "MLNR WILD-TYPE" 
    TCGA-CL-5918     TCGA-DC-5337     TCGA-DC-5869     TCGA-DC-6155 
"MLNR WILD-TYPE" "MLNR WILD-TYPE" "MLNR WILD-TYPE" "MLNR WILD-TYPE" 
    TCGA-DC-6157     TCGA-DC-6158     TCGA-DC-6160     TCGA-DC-6681 
"MLNR WILD-TYPE" "MLNR WILD-TYPE" "MLNR WILD-TYPE" "MLNR WILD-TYPE" 
    TCGA-DC-6682     TCGA-DC-6683     TCGA-DT-5265     TCGA-DY-A0XA 
"MLNR WILD-TYPE" "MLNR WILD-TYPE" "MLNR WILD-TYPE" "MLNR WILD-TYPE" 
    TCGA-DY-A1DC     TCGA-DY-A1DD     TCGA-DY-A1DF     TCGA-DY-A1DG 
"MLNR WILD-TYPE" "MLNR WILD-TYPE" "MLNR WILD-TYPE" "MLNR WILD-TYPE" 
    TCGA-DY-A1H8     TCGA-EF-5830     TCGA-EI-6506     TCGA-EI-6507 
"MLNR WILD-TYPE" "MLNR WILD-TYPE" "MLNR WILD-TYPE" "MLNR WILD-TYPE" 
    TCGA-EI-6508     TCGA-EI-6510     TCGA-F5-6464     TCGA-F5-6465 
"MLNR WILD-TYPE" "MLNR WILD-TYPE" "MLNR WILD-TYPE" "MLNR WILD-TYPE" 
    TCGA-F5-6571     TCGA-F5-6702     TCGA-F5-6811     TCGA-F5-6812 
"MLNR WILD-TYPE" "MLNR WILD-TYPE" "MLNR WILD-TYPE" "MLNR WILD-TYPE" 
    TCGA-F5-6813     TCGA-G5-6235     TCGA-G5-6641 
"MLNR WILD-TYPE" "MLNR WILD-TYPE" "MLNR WILD-TYPE" 

Clustering(1976) Variable = GSK3B MUTATION ANALYSIS
D1976V1, survival
                 sevent
clus2               0   1
  GSK3B MUTATED    11   3
  GSK3B WILD-TYPE 367  90
  GSK3B MUTATED GSK3B WILD-TYPE 
             14             457 
  GSK3B MUTATED GSK3B WILD-TYPE 
              3              90 
$`GSK3B MUTATED`
TCGA-A6-3808 TCGA-AA-3663 TCGA-AA-3715 TCGA-AA-3821 TCGA-AA-A010 TCGA-AY-5543 
       33.34         6.97        19.04         1.02        34.98        33.01 
TCGA-AZ-4315 TCGA-AZ-6606 TCGA-CA-6717 TCGA-CM-5868 TCGA-D5-6920 TCGA-DM-A285 
       58.39        11.74        12.76        17.03         3.68         6.12 
TCGA-G4-6586 TCGA-AG-3882 
       35.80        19.99 

$`GSK3B WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
       33.04         0.99        25.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
       27.09        16.31         0.95        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 
        6.77        12.10       100.01        29.56         5.23         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.20        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6162 
       15.02         5.03        15.02        15.02        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6923 
       12.49        16.14        15.58         1.48         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A28C 
        7.50        44.32       131.51       135.65       139.17        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       13.78        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
        0.99        19.04         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  GSK3B MUTATED GSK3B WILD-TYPE 
           1.02            0.00 
  GSK3B MUTATED GSK3B WILD-TYPE 
          58.39          148.01 
  GSK3B MUTATED GSK3B WILD-TYPE 
         18.035          20.550 
[1] "1.0 - 58.4 (18.0)"  "0.0 - 148.0 (20.6)"
[1] "hr=" "1.4"
D1976V2, continuous
D1976V3, binary
                 cls
clus                0   1
  GSK3B MUTATED    14   1
  GSK3B WILD-TYPE 352 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GSK3B MUTATED     14    1
  GSK3B WILD-TYPE  352  118
        clus
vv       GSK3B MUTATED GSK3B WILD-TYPE
  COLON             14             352
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GSK3B MUTATED         2        0        2         6         1         0
  GSK3B WILD-TYPE      89        1       30       132         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  GSK3B MUTATED           0          0          0          0        2         2
  GSK3B WILD-TYPE        24         11         59         42       46        16
                 vv
clus              STAGE IVB
  GSK3B MUTATED           0
  GSK3B WILD-TYPE         1
D1976V4, multiclass
            clus
vv           GSK3B MUTATED GSK3B WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA              6             132
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             0              42
  STAGE IV               2              46
  STAGE IVA              2              16
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  GSK3B MUTATED     0   2  10   3
  GSK3B WILD-TYPE  17  90 319  47
D1976V5, multiclass
    clus
vv   GSK3B MUTATED GSK3B WILD-TYPE
  T1             0              17
  T2             2              90
  T3            10             319
  T4             3              47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  GSK3B MUTATED    11   2   2
  GSK3B WILD-TYPE 276 111  85
D1976V6, multiclass
    clus
vv   GSK3B MUTATED GSK3B WILD-TYPE
  N0            11             276
  N1             2             111
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1976V7, binary
                 cls
clus                0   1
  GSK3B MUTATED    11   4
  GSK3B WILD-TYPE 364  61
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GSK3B MUTATED     11    4
  GSK3B WILD-TYPE  364   61
   clus
vv  GSK3B MUTATED GSK3B WILD-TYPE
  0            11             364
  1             4              61
[1] 2 2
[1] FALSE
D1976V8, binary
                 cls
clus                0   1
  GSK3B MUTATED     9   6
  GSK3B WILD-TYPE 216 258
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GSK3B MUTATED      9    6
  GSK3B WILD-TYPE  216  258
        clus
vv       GSK3B MUTATED GSK3B WILD-TYPE
  FEMALE             9             216
  MALE               6             258
[1] 2 2
[1] FALSE
D1976V9, binary
                 cls
clus                0   1
  GSK3B MUTATED    12   0
  GSK3B WILD-TYPE 338  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GSK3B MUTATED     12    0
  GSK3B WILD-TYPE  338   22
     clus
vv    GSK3B MUTATED GSK3B WILD-TYPE
  NO             12             338
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  GSK3B MUTATED                     11                             3
  GSK3B WILD-TYPE                  304                            44
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  GSK3B MUTATED                       1                              0
  GSK3B WILD-TYPE                   105                             10
D1976V10, multiclass
                                clus
vv                               GSK3B MUTATED GSK3B WILD-TYPE
  COLON ADENOCARCINOMA                      11             304
  COLON MUCINOUS ADENOCARCINOMA              3              44
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  GSK3B MUTATED    12   0   0   1
  GSK3B WILD-TYPE 333   4  31  24
D1976V11, multiclass
    clus
vv   GSK3B MUTATED GSK3B WILD-TYPE
  R0            12             333
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1976V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GSK3B MUTATED                                  0     1
  GSK3B WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  GSK3B MUTATED                           1     7
  GSK3B WILD-TYPE                        21   219
D1976V13, multiclass
                                  clus
vv                                 GSK3B MUTATED GSK3B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        7             219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1977) Variable = ZNF462 MUTATION ANALYSIS
D1977V1, survival
                  sevent
clus2                0   1
  ZNF462 MUTATED    18   7
  ZNF462 WILD-TYPE 360  86
  ZNF462 MUTATED ZNF462 WILD-TYPE 
              25              446 
  ZNF462 MUTATED ZNF462 WILD-TYPE 
               7               86 
$`ZNF462 MUTATED`
TCGA-A6-5665 TCGA-A6-6653 TCGA-A6-6780 TCGA-AA-3516 TCGA-AA-3811 TCGA-AA-3877 
       22.06        24.39        20.12        13.02        10.06        31.00 
TCGA-AA-A00A TCGA-AA-A010 TCGA-AA-A01P TCGA-AD-5900 TCGA-AD-6890 TCGA-AD-6901 
       38.04        34.98        38.07         0.07         0.79        22.42 
TCGA-AU-6004 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-AZ-6607 TCGA-CM-4743 TCGA-CM-5868 
       27.09        58.39        49.41         3.19        23.05        17.03 
TCGA-CM-6162 TCGA-CM-6171 TCGA-D5-6930 TCGA-DM-A28F TCGA-G4-6588 TCGA-AG-A002 
       12.00        14.04         1.51        35.97        26.17        20.98 
TCGA-EI-6507 
       19.96 

$`ZNF462 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6781 
       25.18        24.16        21.76        24.69        23.87        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        6.97         1.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       26.99        19.04        19.04        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       18.05         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       13.94        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        31.00         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6895 
       18.05        40.96        21.37        15.52        56.55         0.72 
TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 
        5.79        27.42        10.88         0.20        14.50        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        33.01        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 
      106.75        22.36        62.79        88.21         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5254 
      100.01        29.56         5.23        11.74         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
      124.27        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       15.02        15.02        15.02         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 
       21.99        14.99        12.99        13.02        15.02        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       11.64         4.80        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H 
      139.17         6.12        81.37       119.93        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        35.80        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
       32.61         0.49        20.55        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  ZNF462 MUTATED ZNF462 WILD-TYPE 
            0.07             0.00 
  ZNF462 MUTATED ZNF462 WILD-TYPE 
           58.39           148.01 
  ZNF462 MUTATED ZNF462 WILD-TYPE 
          22.060           20.035 
[1] "0.1 - 58.4 (22.1)"  "0.0 - 148.0 (20.0)"
[1] "hr=" "1.7"
D1977V2, continuous
D1977V3, binary
                  cls
clus                 0   1
  ZNF462 MUTATED    26   2
  ZNF462 WILD-TYPE 340 117
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF462 MUTATED     26    2
  ZNF462 WILD-TYPE  340  117
        clus
vv       ZNF462 MUTATED ZNF462 WILD-TYPE
  COLON              26              340
  RECTUM              2              117
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZNF462 MUTATED         6        0        2         9         1         0
  ZNF462 WILD-TYPE      85        1       30       129         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF462 MUTATED           3          0          2          0        2
  ZNF462 WILD-TYPE        21         11         57         42       46
                  vv
clus               STAGE IVA STAGE IVB
  ZNF462 MUTATED           1         0
  ZNF462 WILD-TYPE        17         1
D1977V4, multiclass
            clus
vv           ZNF462 MUTATED ZNF462 WILD-TYPE
  STAGE I                 6               85
  STAGE IA                0                1
  STAGE II                2               30
  STAGE IIA               9              129
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               3               21
  STAGE IIIA              0               11
  STAGE IIIB              2               57
  STAGE IIIC              0               42
  STAGE IV                2               46
  STAGE IVA               1               17
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZNF462 MUTATED     2   5  16   5
  ZNF462 WILD-TYPE  15  87 313  45
D1977V5, multiclass
    clus
vv   ZNF462 MUTATED ZNF462 WILD-TYPE
  T1              2               15
  T2              5               87
  T3             16              313
  T4              5               45
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  ZNF462 MUTATED    20   5   3
  ZNF462 WILD-TYPE 267 108  84
D1977V6, multiclass
    clus
vv   ZNF462 MUTATED ZNF462 WILD-TYPE
  N0             20              267
  N1              5              108
  N2              3               84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1977V7, binary
                  cls
clus                 0   1
  ZNF462 MUTATED    20   3
  ZNF462 WILD-TYPE 355  62
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF462 MUTATED     20    3
  ZNF462 WILD-TYPE  355   62
   clus
vv  ZNF462 MUTATED ZNF462 WILD-TYPE
  0             20              355
  1              3               62
[1] 2 2
[1] FALSE
D1977V8, binary
                  cls
clus                 0   1
  ZNF462 MUTATED    15  13
  ZNF462 WILD-TYPE 210 251
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF462 MUTATED     15   13
  ZNF462 WILD-TYPE  210  251
        clus
vv       ZNF462 MUTATED ZNF462 WILD-TYPE
  FEMALE             15              210
  MALE               13              251
[1] 2 2
[1] FALSE
D1977V9, binary
                  cls
clus                 0   1
  ZNF462 MUTATED    20   0
  ZNF462 WILD-TYPE 330  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF462 MUTATED     20    0
  ZNF462 WILD-TYPE  330   22
     clus
vv    ZNF462 MUTATED ZNF462 WILD-TYPE
  NO              20              330
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ZNF462 MUTATED                     20                             6
  ZNF462 WILD-TYPE                  295                            41
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ZNF462 MUTATED                       2                              0
  ZNF462 WILD-TYPE                   104                             10
D1977V10, multiclass
                                clus
vv                               ZNF462 MUTATED ZNF462 WILD-TYPE
  COLON ADENOCARCINOMA                       20              295
  COLON MUCINOUS ADENOCARCINOMA               6               41
  RECTAL ADENOCARCINOMA                       2              104
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ZNF462 MUTATED    19   0   1   0
  ZNF462 WILD-TYPE 326   4  30  25
D1977V11, multiclass
    clus
vv   ZNF462 MUTATED ZNF462 WILD-TYPE
  R0             19              326
  R1              0                4
  R2              1               30
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1977V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF462 MUTATED                                  0     0
  ZNF462 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZNF462 MUTATED                           0    18
  ZNF462 WILD-TYPE                        22   208
D1977V13, multiclass
                                  clus
vv                                 ZNF462 MUTATED ZNF462 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                        18              208
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1978) Variable = HOXD9 MUTATION ANALYSIS
D1978V1, survival
                 sevent
clus2               0   1
  HOXD9 MUTATED     5   0
  HOXD9 WILD-TYPE 373  93
  HOXD9 MUTATED HOXD9 WILD-TYPE 
              5             466 
  HOXD9 MUTATED HOXD9 WILD-TYPE 
              0              93 
$`HOXD9 MUTATED`
TCGA-AY-6197 TCGA-CM-5861 TCGA-AG-4007 TCGA-AG-A002 TCGA-EI-6507 
       21.44        15.02         1.02        20.98        19.96 

$`HOXD9 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       16.31         0.95        33.01        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       30.08        32.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4008 TCGA-AG-A008 
       19.99        28.04        36.03        14.04        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6508 
       24.13        51.48        32.61         0.49        20.55        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  HOXD9 MUTATED HOXD9 WILD-TYPE 
           1.02            0.00 
  HOXD9 MUTATED HOXD9 WILD-TYPE 
          21.44          148.01 
  HOXD9 MUTATED HOXD9 WILD-TYPE 
         19.960          20.235 
[1] "1.0 - 21.4 (20.0)"  "0.0 - 148.0 (20.2)"
[1] "hr="     "3300000"
D1978V2, continuous
D1978V3, binary
                 cls
clus                0   1
  HOXD9 MUTATED     2   3
  HOXD9 WILD-TYPE 364 116
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HOXD9 MUTATED      2    3
  HOXD9 WILD-TYPE  364  116
        clus
vv       HOXD9 MUTATED HOXD9 WILD-TYPE
  COLON              2             364
  RECTUM             3             116
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  HOXD9 MUTATED         1        0        0         3         0         0
  HOXD9 WILD-TYPE      90        1       32       135        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  HOXD9 MUTATED           0          0          0          0        1         0
  HOXD9 WILD-TYPE        24         11         59         42       47        18
                 vv
clus              STAGE IVB
  HOXD9 MUTATED           0
  HOXD9 WILD-TYPE         1
D1978V4, multiclass
            clus
vv           HOXD9 MUTATED HOXD9 WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              3             135
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             0              42
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  HOXD9 MUTATED     0   1   3   1
  HOXD9 WILD-TYPE  17  91 326  49
D1978V5, multiclass
    clus
vv   HOXD9 MUTATED HOXD9 WILD-TYPE
  T1             0              17
  T2             1              91
  T3             3             326
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  HOXD9 MUTATED     4   0   1
  HOXD9 WILD-TYPE 283 113  86
D1978V6, multiclass
    clus
vv   HOXD9 MUTATED HOXD9 WILD-TYPE
  N0             4             283
  N1             0             113
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1978V7, binary
                 cls
clus                0   1
  HOXD9 MUTATED     3   1
  HOXD9 WILD-TYPE 372  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HOXD9 MUTATED      3    1
  HOXD9 WILD-TYPE  372   64
   clus
vv  HOXD9 MUTATED HOXD9 WILD-TYPE
  0             3             372
  1             1              64
[1] 2 2
[1] FALSE
D1978V8, binary
                 cls
clus                0   1
  HOXD9 MUTATED     1   4
  HOXD9 WILD-TYPE 224 260
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HOXD9 MUTATED      1    4
  HOXD9 WILD-TYPE  224  260
        clus
vv       HOXD9 MUTATED HOXD9 WILD-TYPE
  FEMALE             1             224
  MALE               4             260
[1] 2 2
[1] FALSE
D1978V9, binary
                 cls
clus                0   1
  HOXD9 MUTATED     4   0
  HOXD9 WILD-TYPE 346  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HOXD9 MUTATED      4    0
  HOXD9 WILD-TYPE  346   22
     clus
vv    HOXD9 MUTATED HOXD9 WILD-TYPE
  NO              4             346
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  HOXD9 MUTATED                      2                             0
  HOXD9 WILD-TYPE                  313                            47
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  HOXD9 MUTATED                       3                              0
  HOXD9 WILD-TYPE                   103                             10
D1978V10, multiclass
                                clus
vv                               HOXD9 MUTATED HOXD9 WILD-TYPE
  COLON ADENOCARCINOMA                       2             313
  COLON MUCINOUS ADENOCARCINOMA              0              47
  RECTAL ADENOCARCINOMA                      3             103
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  HOXD9 MUTATED     4   0   1   0
  HOXD9 WILD-TYPE 341   4  30  25
D1978V11, multiclass
    clus
vv   HOXD9 MUTATED HOXD9 WILD-TYPE
  R0             4             341
  R1             0               4
  R2             1              30
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1978V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HOXD9 MUTATED                                  0     0
  HOXD9 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  HOXD9 MUTATED                           0     3
  HOXD9 WILD-TYPE                        22   223
D1978V13, multiclass
                                  clus
vv                                 HOXD9 MUTATED HOXD9 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        3             223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1979) Variable = MGEA5 MUTATION ANALYSIS
D1979V1, survival
                 sevent
clus2               0   1
  MGEA5 MUTATED     4   3
  MGEA5 WILD-TYPE 374  90
  MGEA5 MUTATED MGEA5 WILD-TYPE 
              7             464 
  MGEA5 MUTATED MGEA5 WILD-TYPE 
              3              90 
$`MGEA5 MUTATED`
TCGA-A6-5661 TCGA-AA-3715 TCGA-AZ-4315 TCGA-AZ-6600 TCGA-CA-6717 TCGA-CM-6165 
       33.53        19.04        58.39        12.10        12.76        16.04 
TCGA-DM-A1DB 
       44.32 

$`MGEA5 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 
       36.00         5.03        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       33.01        21.44        17.82         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 
       22.36        62.79        88.21        49.41         6.77       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07        12.20        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       29.03        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  MGEA5 MUTATED MGEA5 WILD-TYPE 
           12.1             0.0 
  MGEA5 MUTATED MGEA5 WILD-TYPE 
          58.39          148.01 
  MGEA5 MUTATED MGEA5 WILD-TYPE 
         19.040          20.235 
[1] "12.1 - 58.4 (19.0)" "0.0 - 148.0 (20.2)"
[1] "hr=" "2"  
D1979V2, continuous
D1979V3, binary
                 cls
clus                0   1
  MGEA5 MUTATED     8   0
  MGEA5 WILD-TYPE 358 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MGEA5 MUTATED      8    0
  MGEA5 WILD-TYPE  358  119
        clus
vv       MGEA5 MUTATED MGEA5 WILD-TYPE
  COLON              8             358
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MGEA5 MUTATED         0        0        1         5         0         0
  MGEA5 WILD-TYPE      91        1       31       133        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MGEA5 MUTATED           0          0          0          0        2         0
  MGEA5 WILD-TYPE        24         11         59         42       46        18
                 vv
clus              STAGE IVB
  MGEA5 MUTATED           0
  MGEA5 WILD-TYPE         1
D1979V4, multiclass
            clus
vv           MGEA5 MUTATED MGEA5 WILD-TYPE
  STAGE I                0              91
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              5             133
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             0              42
  STAGE IV               2              46
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  MGEA5 MUTATED     0   0   6   2
  MGEA5 WILD-TYPE  17  92 323  48
D1979V5, multiclass
    clus
vv   MGEA5 MUTATED MGEA5 WILD-TYPE
  T1             0              17
  T2             0              92
  T3             6             323
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  MGEA5 MUTATED     6   1   1
  MGEA5 WILD-TYPE 281 112  86
D1979V6, multiclass
    clus
vv   MGEA5 MUTATED MGEA5 WILD-TYPE
  N0             6             281
  N1             1             112
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1979V7, binary
                 cls
clus                0   1
  MGEA5 MUTATED     6   2
  MGEA5 WILD-TYPE 369  63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MGEA5 MUTATED      6    2
  MGEA5 WILD-TYPE  369   63
   clus
vv  MGEA5 MUTATED MGEA5 WILD-TYPE
  0             6             369
  1             2              63
[1] 2 2
[1] FALSE
D1979V8, binary
                 cls
clus                0   1
  MGEA5 MUTATED     2   6
  MGEA5 WILD-TYPE 223 258
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MGEA5 MUTATED      2    6
  MGEA5 WILD-TYPE  223  258
        clus
vv       MGEA5 MUTATED MGEA5 WILD-TYPE
  FEMALE             2             223
  MALE               6             258
[1] 2 2
[1] FALSE
D1979V9, binary
                 cls
clus                0   1
  MGEA5 MUTATED     5   0
  MGEA5 WILD-TYPE 345  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MGEA5 MUTATED      5    0
  MGEA5 WILD-TYPE  345   22
     clus
vv    MGEA5 MUTATED MGEA5 WILD-TYPE
  NO              5             345
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MGEA5 MUTATED                      6                             2
  MGEA5 WILD-TYPE                  309                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MGEA5 MUTATED                       0                              0
  MGEA5 WILD-TYPE                   106                             10
D1979V10, multiclass
                                clus
vv                               MGEA5 MUTATED MGEA5 WILD-TYPE
  COLON ADENOCARCINOMA                       6             309
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  MGEA5 MUTATED     4   0   1   1
  MGEA5 WILD-TYPE 341   4  30  24
D1979V11, multiclass
    clus
vv   MGEA5 MUTATED MGEA5 WILD-TYPE
  R0             4             341
  R1             0               4
  R2             1              30
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1979V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MGEA5 MUTATED                                  0     1
  MGEA5 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  MGEA5 MUTATED                           2     3
  MGEA5 WILD-TYPE                        20   223
D1979V13, multiclass
                                  clus
vv                                 MGEA5 MUTATED MGEA5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    2              20
  WHITE                                        3             223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1980) Variable = C7ORF33 MUTATION ANALYSIS
D1980V1, survival
                   sevent
clus2                 0   1
  C7ORF33 MUTATED     5   1
  C7ORF33 WILD-TYPE 373  92
  C7ORF33 MUTATED C7ORF33 WILD-TYPE 
                6               465 
  C7ORF33 MUTATED C7ORF33 WILD-TYPE 
                1                92 
$`C7ORF33 MUTATED`
TCGA-AA-3837 TCGA-AA-3947 TCGA-AA-3950 TCGA-CA-6718 TCGA-AG-3892 TCGA-AG-A002 
       38.99        33.01        24.00        10.06        13.02        20.98 

$`C7ORF33 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
        1.02        17.98        15.95        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 
        2.01        12.99        24.00        26.01         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       12.76        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 
        1.02        17.95        36.95        17.03        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  C7ORF33 MUTATED C7ORF33 WILD-TYPE 
            10.06              0.00 
  C7ORF33 MUTATED C7ORF33 WILD-TYPE 
            38.99            148.01 
  C7ORF33 MUTATED C7ORF33 WILD-TYPE 
            22.49             20.12 
[1] "10.1 - 39.0 (22.5)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1"  
D1980V2, continuous
D1980V3, binary
                   cls
clus                  0   1
  C7ORF33 MUTATED     4   2
  C7ORF33 WILD-TYPE 362 117
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C7ORF33 MUTATED      4    2
  C7ORF33 WILD-TYPE  362  117
        clus
vv       C7ORF33 MUTATED C7ORF33 WILD-TYPE
  COLON                4               362
  RECTUM               2               117
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  C7ORF33 MUTATED         2        0        0         3         1         0
  C7ORF33 WILD-TYPE      89        1       32       135         9         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C7ORF33 MUTATED           0          0          0          0        0
  C7ORF33 WILD-TYPE        24         11         59         42       48
                   vv
clus                STAGE IVA STAGE IVB
  C7ORF33 MUTATED           0         0
  C7ORF33 WILD-TYPE        18         1
D1980V4, multiclass
            clus
vv           C7ORF33 MUTATED C7ORF33 WILD-TYPE
  STAGE I                  2                89
  STAGE IA                 0                 1
  STAGE II                 0                32
  STAGE IIA                3               135
  STAGE IIB                1                 9
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               0                11
  STAGE IIIB               0                59
  STAGE IIIC               0                42
  STAGE IV                 0                48
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  C7ORF33 MUTATED     1   1   3   1
  C7ORF33 WILD-TYPE  16  91 326  49
D1980V5, multiclass
    clus
vv   C7ORF33 MUTATED C7ORF33 WILD-TYPE
  T1               1                16
  T2               1                91
  T3               3               326
  T4               1                49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  C7ORF33 MUTATED     6   0   0
  C7ORF33 WILD-TYPE 281 113  87
D1980V6, multiclass
    clus
vv   C7ORF33 MUTATED C7ORF33 WILD-TYPE
  N0               6               281
  N1               0               113
  N2               0                87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1980V7, binary
                   cls
clus                  0   1
  C7ORF33 MUTATED     6   0
  C7ORF33 WILD-TYPE 369  65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C7ORF33 MUTATED      6    0
  C7ORF33 WILD-TYPE  369   65
   clus
vv  C7ORF33 MUTATED C7ORF33 WILD-TYPE
  0               6               369
  1               0                65
[1] 2 2
[1] FALSE
D1980V8, binary
                   cls
clus                  0   1
  C7ORF33 MUTATED     3   3
  C7ORF33 WILD-TYPE 222 261
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C7ORF33 MUTATED      3    3
  C7ORF33 WILD-TYPE  222  261
        clus
vv       C7ORF33 MUTATED C7ORF33 WILD-TYPE
  FEMALE               3               222
  MALE                 3               261
[1] 2 2
[1] FALSE
D1980V9, binary
                   cls
clus                  0   1
  C7ORF33 MUTATED     6   0
  C7ORF33 WILD-TYPE 344  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C7ORF33 MUTATED      6    0
  C7ORF33 WILD-TYPE  344   22
     clus
vv    C7ORF33 MUTATED C7ORF33 WILD-TYPE
  NO                6               344
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  C7ORF33 MUTATED                      1                             3
  C7ORF33 WILD-TYPE                  314                            44
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  C7ORF33 MUTATED                       2                              0
  C7ORF33 WILD-TYPE                   104                             10
D1980V10, multiclass
                                clus
vv                               C7ORF33 MUTATED C7ORF33 WILD-TYPE
  COLON ADENOCARCINOMA                         1               314
  COLON MUCINOUS ADENOCARCINOMA                3                44
  RECTAL ADENOCARCINOMA                        2               104
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  C7ORF33 MUTATED     5   0   0   1
  C7ORF33 WILD-TYPE 340   4  31  24
D1980V11, multiclass
    clus
vv   C7ORF33 MUTATED C7ORF33 WILD-TYPE
  R0               5               340
  R1               0                 4
  R2               0                31
  RX               1                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1980V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C7ORF33 MUTATED                                  0     1
  C7ORF33 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  C7ORF33 MUTATED                           0     0
  C7ORF33 WILD-TYPE                        22   226
D1980V13, multiclass
[1] "Remove cluster labels:" "C7ORF33 MUTATED"       
clus
  C7ORF33 MUTATED C7ORF33 WILD-TYPE 
                1               259 
       TCGA-A6-2671        TCGA-A6-2672        TCGA-A6-2674        TCGA-A6-2676 
"C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" 
       TCGA-A6-2677        TCGA-A6-2678        TCGA-A6-2683        TCGA-A6-3807 
"C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" 
       TCGA-A6-3808        TCGA-A6-3809        TCGA-A6-3810        TCGA-A6-4105 
"C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" 
       TCGA-A6-5656        TCGA-A6-5657        TCGA-A6-5659        TCGA-A6-5660 
"C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" 
       TCGA-A6-5661        TCGA-A6-5662        TCGA-A6-5664        TCGA-A6-5665 
"C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" 
       TCGA-A6-5666        TCGA-A6-6137        TCGA-A6-6138        TCGA-A6-6141 
"C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" 
       TCGA-A6-6142        TCGA-A6-6648        TCGA-A6-6649        TCGA-A6-6651 
"C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" 
       TCGA-A6-6652        TCGA-A6-6653        TCGA-A6-6654        TCGA-A6-6780 
"C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" 
       TCGA-A6-6781        TCGA-A6-6782        TCGA-AD-5900        TCGA-AD-6548 
"C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" 
       TCGA-AD-6888        TCGA-AD-6889        TCGA-AD-6890        TCGA-AD-6895 
"C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" 
       TCGA-AD-6899        TCGA-AD-6901        TCGA-AD-6963        TCGA-AD-6964 
"C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" 
       TCGA-AD-6965        TCGA-AU-3779        TCGA-AU-6004        TCGA-AY-4070 
"C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" 
       TCGA-AY-4071        TCGA-AY-5543        TCGA-AY-6196        TCGA-AY-6197 
"C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" 
       TCGA-AY-6386        TCGA-AZ-4315        TCGA-AZ-4323        TCGA-AZ-4616 
"C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" 
       TCGA-AZ-4681        TCGA-AZ-4682        TCGA-AZ-5403        TCGA-AZ-5407 
"C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" 
       TCGA-AZ-6598        TCGA-AZ-6599        TCGA-AZ-6600        TCGA-AZ-6601 
"C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" 
       TCGA-AZ-6603        TCGA-AZ-6605        TCGA-AZ-6606        TCGA-AZ-6607 
"C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" 
       TCGA-AZ-6608        TCGA-CA-5254        TCGA-CA-5255        TCGA-CA-5796 
"C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" 
       TCGA-CA-5797        TCGA-CA-6715        TCGA-CA-6716        TCGA-CA-6717 
"C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" 
       TCGA-CA-6719        TCGA-CK-4947        TCGA-CK-4948        TCGA-CK-4950 
"C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" 
       TCGA-CK-4952        TCGA-CK-5912        TCGA-CK-5913        TCGA-CK-5914 
"C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" 
       TCGA-CK-5915        TCGA-CK-5916        TCGA-CK-6746        TCGA-CK-6747 
"C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" 
       TCGA-CK-6748        TCGA-CK-6751        TCGA-CM-4743        TCGA-CM-4744 
"C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" 
       TCGA-CM-4746        TCGA-CM-4747        TCGA-CM-4752        TCGA-CM-5341 
"C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" 
       TCGA-CM-5344        TCGA-CM-5348        TCGA-CM-5349        TCGA-CM-5860 
"C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" 
       TCGA-CM-5861        TCGA-CM-5862        TCGA-CM-5863        TCGA-CM-5864 
"C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" 
       TCGA-CM-5868        TCGA-CM-6161        TCGA-CM-6162        TCGA-CM-6163 
"C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" 
       TCGA-CM-6164        TCGA-CM-6165        TCGA-CM-6166        TCGA-CM-6167 
"C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" 
       TCGA-CM-6168        TCGA-CM-6169        TCGA-CM-6170        TCGA-CM-6171 
"C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" 
       TCGA-CM-6172        TCGA-CM-6674        TCGA-CM-6675        TCGA-CM-6676 
"C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" 
       TCGA-CM-6677        TCGA-CM-6678        TCGA-CM-6679        TCGA-CM-6680 
"C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" 
       TCGA-D5-5537        TCGA-D5-5538        TCGA-D5-5539        TCGA-D5-5540 
"C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" 
       TCGA-D5-5541        TCGA-D5-6529        TCGA-D5-6532        TCGA-D5-6533 
"C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" 
       TCGA-D5-6534        TCGA-D5-6535        TCGA-D5-6536        TCGA-D5-6537 
"C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" 
       TCGA-D5-6538        TCGA-D5-6539        TCGA-D5-6540        TCGA-D5-6541 
"C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" 
       TCGA-D5-6898        TCGA-D5-6920        TCGA-D5-6922        TCGA-D5-6923 
"C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" 
       TCGA-D5-6924        TCGA-D5-6926        TCGA-D5-6927        TCGA-D5-6928 
"C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" 
       TCGA-D5-6929        TCGA-D5-6930        TCGA-D5-6931        TCGA-D5-6932 
"C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" 
       TCGA-D5-7000        TCGA-DM-A0X9        TCGA-DM-A0XD        TCGA-DM-A0XF 
"C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" 
       TCGA-DM-A1D0        TCGA-DM-A1D4        TCGA-DM-A1D6        TCGA-DM-A1D7 
"C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" 
       TCGA-DM-A1D8        TCGA-DM-A1D9        TCGA-DM-A1DA        TCGA-DM-A1DB 
"C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" 
       TCGA-DM-A1HA        TCGA-DM-A1HB        TCGA-DM-A282        TCGA-DM-A285 
"C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" 
       TCGA-DM-A28C        TCGA-DM-A28E        TCGA-DM-A28F        TCGA-DM-A28G 
"C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" 
       TCGA-DM-A28H        TCGA-DM-A28K        TCGA-F4-6459        TCGA-F4-6460 
"C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" 
       TCGA-F4-6569        TCGA-F4-6570        TCGA-F4-6703        TCGA-F4-6704 
"C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" 
       TCGA-F4-6805        TCGA-F4-6806        TCGA-F4-6807        TCGA-F4-6808 
"C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" 
       TCGA-F4-6809        TCGA-F4-6854        TCGA-F4-6855        TCGA-F4-6856 
"C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" 
       TCGA-G4-6293        TCGA-G4-6299        TCGA-G4-6303        TCGA-G4-6304 
"C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" 
       TCGA-G4-6306        TCGA-G4-6307        TCGA-G4-6309        TCGA-G4-6310 
"C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" 
       TCGA-G4-6315        TCGA-G4-6317        TCGA-G4-6321        TCGA-G4-6323 
"C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" 
       TCGA-G4-6586        TCGA-G4-6588        TCGA-G4-6625        TCGA-G4-6626 
"C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" 
       TCGA-G4-6628        TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2691 
"C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3913 
"C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" 
       TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136        TCGA-AF-6655 
"C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" 
       TCGA-AF-6672        TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6549 
"C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" 
       TCGA-AH-6643        TCGA-AH-6644        TCGA-CI-6619        TCGA-CI-6620 
"C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" 
       TCGA-CI-6621        TCGA-CI-6622        TCGA-CI-6624        TCGA-CL-5917 
"C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" 
       TCGA-CL-5918        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6155 
"C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" 
       TCGA-DC-6157        TCGA-DC-6158        TCGA-DC-6160        TCGA-DC-6681 
"C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" 
       TCGA-DC-6682        TCGA-DC-6683        TCGA-DT-5265        TCGA-DY-A0XA 
"C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" 
       TCGA-DY-A1DC        TCGA-DY-A1DD        TCGA-DY-A1DF        TCGA-DY-A1DG 
"C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" 
       TCGA-DY-A1H8        TCGA-EF-5830        TCGA-EI-6506        TCGA-EI-6507 
"C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6510        TCGA-F5-6464        TCGA-F5-6465 
"C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6811        TCGA-F5-6812 
"C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" 
       TCGA-F5-6813        TCGA-G5-6235        TCGA-G5-6641 
"C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" "C7ORF33 WILD-TYPE" 

Clustering(1981) Variable = ATP2C2 MUTATION ANALYSIS
D1981V1, survival
                  sevent
clus2                0   1
  ATP2C2 MUTATED    10   1
  ATP2C2 WILD-TYPE 368  92
  ATP2C2 MUTATED ATP2C2 WILD-TYPE 
              11              460 
  ATP2C2 MUTATED ATP2C2 WILD-TYPE 
               1               92 
$`ATP2C2 MUTATED`
TCGA-A6-5665 TCGA-A6-6653 TCGA-AD-6889 TCGA-AD-6895 TCGA-AZ-6598 TCGA-CA-6717 
       22.06        24.39        56.55         0.72        49.41        12.76 
TCGA-D5-6928 TCGA-DM-A1HB TCGA-G4-6309 TCGA-AG-3892 TCGA-AG-3909 
       11.64       135.65        85.48        13.02        19.99 

$`ATP2C2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 
       25.18        24.16        21.76        24.69        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.79         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        88.21         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07        12.20        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.04         9.44         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      131.51       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 
       74.56        65.85        53.62        44.68        55.04        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 
       19.99         1.02        17.95        36.95        17.03        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3999 TCGA-AG-4001 
       14.01         1.02        48.03        32.02        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  ATP2C2 MUTATED ATP2C2 WILD-TYPE 
            0.72             0.00 
  ATP2C2 MUTATED ATP2C2 WILD-TYPE 
          135.65           148.01 
  ATP2C2 MUTATED ATP2C2 WILD-TYPE 
          22.060           20.155 
[1] "0.7 - 135.7 (22.1)" "0.0 - 148.0 (20.2)"
[1] "hr=" "3.1"
D1981V2, continuous
D1981V3, binary
                  cls
clus                 0   1
  ATP2C2 MUTATED     9   2
  ATP2C2 WILD-TYPE 357 117
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP2C2 MUTATED      9    2
  ATP2C2 WILD-TYPE  357  117
        clus
vv       ATP2C2 MUTATED ATP2C2 WILD-TYPE
  COLON               9              357
  RECTUM              2              117
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ATP2C2 MUTATED         2        0        1         4         0         0
  ATP2C2 WILD-TYPE      89        1       31       134        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ATP2C2 MUTATED           0          0          3          0        0
  ATP2C2 WILD-TYPE        24         11         56         42       48
                  vv
clus               STAGE IVA STAGE IVB
  ATP2C2 MUTATED           0         0
  ATP2C2 WILD-TYPE        18         1
D1981V4, multiclass
            clus
vv           ATP2C2 MUTATED ATP2C2 WILD-TYPE
  STAGE I                 2               89
  STAGE IA                0                1
  STAGE II                1               31
  STAGE IIA               4              134
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              3               56
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ATP2C2 MUTATED     1   1   9   0
  ATP2C2 WILD-TYPE  16  91 320  50
D1981V5, multiclass
    clus
vv   ATP2C2 MUTATED ATP2C2 WILD-TYPE
  T1              1               16
  T2              1               91
  T3              9              320
  T4              0               50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  ATP2C2 MUTATED     7   4   0
  ATP2C2 WILD-TYPE 280 109  87
D1981V6, multiclass
    clus
vv   ATP2C2 MUTATED ATP2C2 WILD-TYPE
  N0              7              280
  N1              4              109
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1981V7, binary
                  cls
clus                 0   1
  ATP2C2 MUTATED     9   0
  ATP2C2 WILD-TYPE 366  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP2C2 MUTATED      9    0
  ATP2C2 WILD-TYPE  366   65
   clus
vv  ATP2C2 MUTATED ATP2C2 WILD-TYPE
  0              9              366
  1              0               65
[1] 2 2
[1] FALSE
D1981V8, binary
                  cls
clus                 0   1
  ATP2C2 MUTATED     5   6
  ATP2C2 WILD-TYPE 220 258
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP2C2 MUTATED      5    6
  ATP2C2 WILD-TYPE  220  258
        clus
vv       ATP2C2 MUTATED ATP2C2 WILD-TYPE
  FEMALE              5              220
  MALE                6              258
[1] 2 2
[1] FALSE
D1981V9, binary
                  cls
clus                 0   1
  ATP2C2 MUTATED     8   0
  ATP2C2 WILD-TYPE 342  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP2C2 MUTATED      8    0
  ATP2C2 WILD-TYPE  342   22
     clus
vv    ATP2C2 MUTATED ATP2C2 WILD-TYPE
  NO               8              342
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ATP2C2 MUTATED                      6                             2
  ATP2C2 WILD-TYPE                  309                            45
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ATP2C2 MUTATED                       2                              0
  ATP2C2 WILD-TYPE                   104                             10
D1981V10, multiclass
                                clus
vv                               ATP2C2 MUTATED ATP2C2 WILD-TYPE
  COLON ADENOCARCINOMA                        6              309
  COLON MUCINOUS ADENOCARCINOMA               2               45
  RECTAL ADENOCARCINOMA                       2              104
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ATP2C2 MUTATED     5   0   0   1
  ATP2C2 WILD-TYPE 340   4  31  24
D1981V11, multiclass
    clus
vv   ATP2C2 MUTATED ATP2C2 WILD-TYPE
  R0              5              340
  R1              0                4
  R2              0               31
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1981V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ATP2C2 MUTATED                                  0     2
  ATP2C2 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ATP2C2 MUTATED                           1     6
  ATP2C2 WILD-TYPE                        21   220
D1981V13, multiclass
                                  clus
vv                                 ATP2C2 MUTATED ATP2C2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                9
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                         6              220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1982) Variable = DCAF8L1 MUTATION ANALYSIS
D1982V1, survival
                   sevent
clus2                 0   1
  DCAF8L1 MUTATED    16   1
  DCAF8L1 WILD-TYPE 362  92
  DCAF8L1 MUTATED DCAF8L1 WILD-TYPE 
               17               454 
  DCAF8L1 MUTATED DCAF8L1 WILD-TYPE 
                1                92 
$`DCAF8L1 MUTATED`
TCGA-A6-6652 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3660 TCGA-AA-3854 TCGA-AA-3949 
       24.69        29.95        20.98        78.08        36.03        26.01 
TCGA-AA-A00K TCGA-AZ-4315 TCGA-CA-6717 TCGA-CK-5916 TCGA-CM-5344 TCGA-CM-5860 
       18.05        58.39        12.76        21.14        22.03        32.02 
TCGA-CM-5861 TCGA-DM-A0X9 TCGA-F4-6806 TCGA-AG-A002 TCGA-EI-6507 
       15.02       119.70        41.42        20.98        19.96 

$`DCAF8L1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6654 
       25.08        25.18        24.16        21.76        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3561 
       13.02        24.00        17.95        23.01        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
       33.07         0.00        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        33.01        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.20        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 
       15.62        49.08        51.32         9.99        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       29.06        22.98        30.08         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
       10.26        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6807 TCGA-F4-6808 
        6.18        47.87         1.55        34.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6508 
       24.13        51.48        32.61         0.49        20.55        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  DCAF8L1 MUTATED DCAF8L1 WILD-TYPE 
            12.76              0.00 
  DCAF8L1 MUTATED DCAF8L1 WILD-TYPE 
           119.70            148.01 
  DCAF8L1 MUTATED DCAF8L1 WILD-TYPE 
           24.690            20.005 
[1] "12.8 - 119.7 (24.7)" "0.0 - 148.0 (20.0)" 
[1] "hr=" "4.5"
D1982V2, continuous
D1982V3, binary
                   cls
clus                  0   1
  DCAF8L1 MUTATED    16   2
  DCAF8L1 WILD-TYPE 350 117
[1] "tbl2"
                   cls
clus                [,1] [,2]
  DCAF8L1 MUTATED     16    2
  DCAF8L1 WILD-TYPE  350  117
        clus
vv       DCAF8L1 MUTATED DCAF8L1 WILD-TYPE
  COLON               16               350
  RECTUM               2               117
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DCAF8L1 MUTATED         5        0        1         9         0         0
  DCAF8L1 WILD-TYPE      86        1       31       129        10         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DCAF8L1 MUTATED           0          0          2          0        0
  DCAF8L1 WILD-TYPE        24         11         57         42       48
                   vv
clus                STAGE IVA STAGE IVB
  DCAF8L1 MUTATED           1         0
  DCAF8L1 WILD-TYPE        17         1
D1982V4, multiclass
            clus
vv           DCAF8L1 MUTATED DCAF8L1 WILD-TYPE
  STAGE I                  5                86
  STAGE IA                 0                 1
  STAGE II                 1                31
  STAGE IIA                9               129
  STAGE IIB                0                10
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               0                11
  STAGE IIIB               2                57
  STAGE IIIC               0                42
  STAGE IV                 0                48
  STAGE IVA                1                17
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  DCAF8L1 MUTATED     1   4  13   0
  DCAF8L1 WILD-TYPE  16  88 316  50
D1982V5, multiclass
    clus
vv   DCAF8L1 MUTATED DCAF8L1 WILD-TYPE
  T1               1                16
  T2               4                88
  T3              13               316
  T4               0                50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  DCAF8L1 MUTATED    16   2   0
  DCAF8L1 WILD-TYPE 271 111  87
D1982V6, multiclass
    clus
vv   DCAF8L1 MUTATED DCAF8L1 WILD-TYPE
  N0              16               271
  N1               2               111
  N2               0                87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1982V7, binary
                   cls
clus                  0   1
  DCAF8L1 MUTATED    17   1
  DCAF8L1 WILD-TYPE 358  64
[1] "tbl2"
                   cls
clus                [,1] [,2]
  DCAF8L1 MUTATED     17    1
  DCAF8L1 WILD-TYPE  358   64
   clus
vv  DCAF8L1 MUTATED DCAF8L1 WILD-TYPE
  0              17               358
  1               1                64
[1] 2 2
[1] FALSE
D1982V8, binary
                   cls
clus                  0   1
  DCAF8L1 MUTATED    10   8
  DCAF8L1 WILD-TYPE 215 256
[1] "tbl2"
                   cls
clus                [,1] [,2]
  DCAF8L1 MUTATED     10    8
  DCAF8L1 WILD-TYPE  215  256
        clus
vv       DCAF8L1 MUTATED DCAF8L1 WILD-TYPE
  FEMALE              10               215
  MALE                 8               256
[1] 2 2
[1] FALSE
D1982V9, binary
                   cls
clus                  0   1
  DCAF8L1 MUTATED    15   0
  DCAF8L1 WILD-TYPE 335  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  DCAF8L1 MUTATED     15    0
  DCAF8L1 WILD-TYPE  335   22
     clus
vv    DCAF8L1 MUTATED DCAF8L1 WILD-TYPE
  NO               15               335
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  DCAF8L1 MUTATED                     12                             4
  DCAF8L1 WILD-TYPE                  303                            43
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  DCAF8L1 MUTATED                       2                              0
  DCAF8L1 WILD-TYPE                   104                             10
D1982V10, multiclass
                                clus
vv                               DCAF8L1 MUTATED DCAF8L1 WILD-TYPE
  COLON ADENOCARCINOMA                        12               303
  COLON MUCINOUS ADENOCARCINOMA                4                43
  RECTAL ADENOCARCINOMA                        2               104
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  DCAF8L1 MUTATED    13   0   1   2
  DCAF8L1 WILD-TYPE 332   4  30  23
D1982V11, multiclass
    clus
vv   DCAF8L1 MUTATED DCAF8L1 WILD-TYPE
  R0              13               332
  R1               0                 4
  R2               1                30
  RX               2                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1982V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DCAF8L1 MUTATED                                  0     1
  DCAF8L1 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  DCAF8L1 MUTATED                           1     8
  DCAF8L1 WILD-TYPE                        21   218
D1982V13, multiclass
                                  clus
vv                                 DCAF8L1 MUTATED DCAF8L1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                10
  BLACK OR AFRICAN AMERICAN                      1                21
  WHITE                                          8               218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1983) Variable = CENPA MUTATION ANALYSIS
D1983V1, survival
                 sevent
clus2               0   1
  CENPA MUTATED     5   0
  CENPA WILD-TYPE 373  93
  CENPA MUTATED CENPA WILD-TYPE 
              5             466 
  CENPA MUTATED CENPA WILD-TYPE 
              0              93 
$`CENPA MUTATED`
TCGA-A6-3809 TCGA-AA-3864 TCGA-AA-A00A TCGA-AA-A010 TCGA-AZ-4315 
       32.75        53.00        38.04        34.98        58.39 

$`CENPA WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 
       32.05         0.99        31.07        31.07        30.05        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00D 
       27.02        19.07         7.96        27.02        13.94        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  CENPA MUTATED CENPA WILD-TYPE 
          32.75            0.00 
  CENPA MUTATED CENPA WILD-TYPE 
          58.39          148.01 
  CENPA MUTATED CENPA WILD-TYPE 
         38.040          20.035 
[1] "32.8 - 58.4 (38.0)" "0.0 - 148.0 (20.0)"
[1] "hr="     "9200000"
D1983V2, continuous
D1983V3, binary
                 cls
clus                0   1
  CENPA MUTATED     5   0
  CENPA WILD-TYPE 361 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CENPA MUTATED      5    0
  CENPA WILD-TYPE  361  119
        clus
vv       CENPA MUTATED CENPA WILD-TYPE
  COLON              5             361
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CENPA MUTATED         0        0        1         2         2         0
  CENPA WILD-TYPE      91        1       31       136         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CENPA MUTATED           0          0          0          0        0         0
  CENPA WILD-TYPE        24         11         59         42       48        18
                 vv
clus              STAGE IVB
  CENPA MUTATED           0
  CENPA WILD-TYPE         1
D1983V4, multiclass
            clus
vv           CENPA MUTATED CENPA WILD-TYPE
  STAGE I                0              91
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              2             136
  STAGE IIB              2               8
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CENPA MUTATED     0   0   3   2
  CENPA WILD-TYPE  17  92 326  48
D1983V5, multiclass
    clus
vv   CENPA MUTATED CENPA WILD-TYPE
  T1             0              17
  T2             0              92
  T3             3             326
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  CENPA MUTATED     5   0   0
  CENPA WILD-TYPE 282 113  87
D1983V6, multiclass
    clus
vv   CENPA MUTATED CENPA WILD-TYPE
  N0             5             282
  N1             0             113
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1983V7, binary
                 cls
clus                0   1
  CENPA MUTATED     5   0
  CENPA WILD-TYPE 370  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CENPA MUTATED      5    0
  CENPA WILD-TYPE  370   65
   clus
vv  CENPA MUTATED CENPA WILD-TYPE
  0             5             370
  1             0              65
[1] 2 2
[1] FALSE
D1983V8, binary
                 cls
clus                0   1
  CENPA MUTATED     2   3
  CENPA WILD-TYPE 223 261
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CENPA MUTATED      2    3
  CENPA WILD-TYPE  223  261
        clus
vv       CENPA MUTATED CENPA WILD-TYPE
  FEMALE             2             223
  MALE               3             261
[1] 2 2
[1] FALSE
D1983V9, binary
                 cls
clus                0   1
  CENPA MUTATED     5   0
  CENPA WILD-TYPE 345  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CENPA MUTATED      5    0
  CENPA WILD-TYPE  345   22
     clus
vv    CENPA MUTATED CENPA WILD-TYPE
  NO              5             345
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CENPA MUTATED                      4                             1
  CENPA WILD-TYPE                  311                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CENPA MUTATED                       0                              0
  CENPA WILD-TYPE                   106                             10
D1983V10, multiclass
                                clus
vv                               CENPA MUTATED CENPA WILD-TYPE
  COLON ADENOCARCINOMA                       4             311
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  CENPA MUTATED     5   0   0   0
  CENPA WILD-TYPE 340   4  31  25
D1983V11, multiclass
    clus
vv   CENPA MUTATED CENPA WILD-TYPE
  R0             5             340
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1983V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CENPA MUTATED                                  0     0
  CENPA WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CENPA MUTATED                           0     2
  CENPA WILD-TYPE                        22   224
D1983V13, multiclass
[1] "Remove cluster labels:" "CENPA MUTATED"         
clus
  CENPA MUTATED CENPA WILD-TYPE 
              2             258 
     TCGA-A6-2671      TCGA-A6-2672      TCGA-A6-2674      TCGA-A6-2676 
"CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" 
     TCGA-A6-2677      TCGA-A6-2678      TCGA-A6-2683      TCGA-A6-3807 
"CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" 
     TCGA-A6-3808      TCGA-A6-3810      TCGA-A6-4105      TCGA-A6-5656 
"CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" 
     TCGA-A6-5657      TCGA-A6-5659      TCGA-A6-5660      TCGA-A6-5661 
"CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" 
     TCGA-A6-5662      TCGA-A6-5664      TCGA-A6-5665      TCGA-A6-5666 
"CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" 
     TCGA-A6-6137      TCGA-A6-6138      TCGA-A6-6141      TCGA-A6-6142 
"CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" 
     TCGA-A6-6648      TCGA-A6-6649      TCGA-A6-6651      TCGA-A6-6652 
"CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" 
     TCGA-A6-6653      TCGA-A6-6654      TCGA-A6-6780      TCGA-A6-6781 
"CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" 
     TCGA-A6-6782      TCGA-AD-5900      TCGA-AD-6548      TCGA-AD-6888 
"CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" 
     TCGA-AD-6889      TCGA-AD-6890      TCGA-AD-6895      TCGA-AD-6899 
"CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" 
     TCGA-AD-6901      TCGA-AD-6963      TCGA-AD-6964      TCGA-AD-6965 
"CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" 
     TCGA-AU-3779      TCGA-AU-6004      TCGA-AY-4070      TCGA-AY-4071 
"CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" 
     TCGA-AY-5543      TCGA-AY-6196      TCGA-AY-6197      TCGA-AY-6386 
"CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" 
     TCGA-AZ-4323      TCGA-AZ-4616      TCGA-AZ-4681      TCGA-AZ-4682 
"CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" 
     TCGA-AZ-5403      TCGA-AZ-5407      TCGA-AZ-6598      TCGA-AZ-6599 
"CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" 
     TCGA-AZ-6600      TCGA-AZ-6601      TCGA-AZ-6603      TCGA-AZ-6605 
"CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" 
     TCGA-AZ-6606      TCGA-AZ-6607      TCGA-AZ-6608      TCGA-CA-5254 
"CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" 
     TCGA-CA-5255      TCGA-CA-5796      TCGA-CA-5797      TCGA-CA-6715 
"CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" 
     TCGA-CA-6716      TCGA-CA-6717      TCGA-CA-6718      TCGA-CA-6719 
"CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" 
     TCGA-CK-4947      TCGA-CK-4948      TCGA-CK-4950      TCGA-CK-4952 
"CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" 
     TCGA-CK-5912      TCGA-CK-5913      TCGA-CK-5914      TCGA-CK-5915 
"CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" 
     TCGA-CK-5916      TCGA-CK-6746      TCGA-CK-6747      TCGA-CK-6748 
"CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" 
     TCGA-CK-6751      TCGA-CM-4743      TCGA-CM-4744      TCGA-CM-4746 
"CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" 
     TCGA-CM-4747      TCGA-CM-4752      TCGA-CM-5341      TCGA-CM-5344 
"CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" 
     TCGA-CM-5348      TCGA-CM-5349      TCGA-CM-5860      TCGA-CM-5861 
"CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" 
     TCGA-CM-5862      TCGA-CM-5863      TCGA-CM-5864      TCGA-CM-5868 
"CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" 
     TCGA-CM-6161      TCGA-CM-6162      TCGA-CM-6163      TCGA-CM-6164 
"CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" 
     TCGA-CM-6165      TCGA-CM-6166      TCGA-CM-6167      TCGA-CM-6168 
"CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" 
     TCGA-CM-6169      TCGA-CM-6170      TCGA-CM-6171      TCGA-CM-6172 
"CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" 
     TCGA-CM-6674      TCGA-CM-6675      TCGA-CM-6676      TCGA-CM-6677 
"CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" 
     TCGA-CM-6678      TCGA-CM-6679      TCGA-CM-6680      TCGA-D5-5537 
"CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" 
     TCGA-D5-5538      TCGA-D5-5539      TCGA-D5-5540      TCGA-D5-5541 
"CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" 
     TCGA-D5-6529      TCGA-D5-6532      TCGA-D5-6533      TCGA-D5-6534 
"CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" 
     TCGA-D5-6535      TCGA-D5-6536      TCGA-D5-6537      TCGA-D5-6538 
"CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" 
     TCGA-D5-6539      TCGA-D5-6540      TCGA-D5-6541      TCGA-D5-6898 
"CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" 
     TCGA-D5-6920      TCGA-D5-6922      TCGA-D5-6923      TCGA-D5-6924 
"CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" 
     TCGA-D5-6926      TCGA-D5-6927      TCGA-D5-6928      TCGA-D5-6929 
"CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" 
     TCGA-D5-6930      TCGA-D5-6931      TCGA-D5-6932      TCGA-D5-7000 
"CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" 
     TCGA-DM-A0X9      TCGA-DM-A0XD      TCGA-DM-A0XF      TCGA-DM-A1D0 
"CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" 
     TCGA-DM-A1D4      TCGA-DM-A1D6      TCGA-DM-A1D7      TCGA-DM-A1D8 
"CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" 
     TCGA-DM-A1D9      TCGA-DM-A1DA      TCGA-DM-A1DB      TCGA-DM-A1HA 
"CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" 
     TCGA-DM-A1HB      TCGA-DM-A282      TCGA-DM-A285      TCGA-DM-A28C 
"CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" 
     TCGA-DM-A28E      TCGA-DM-A28F      TCGA-DM-A28G      TCGA-DM-A28H 
"CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" 
     TCGA-DM-A28K      TCGA-F4-6459      TCGA-F4-6460      TCGA-F4-6569 
"CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" 
     TCGA-F4-6570      TCGA-F4-6703      TCGA-F4-6704      TCGA-F4-6805 
"CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" 
     TCGA-F4-6806      TCGA-F4-6807      TCGA-F4-6808      TCGA-F4-6809 
"CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" 
     TCGA-F4-6854      TCGA-F4-6855      TCGA-F4-6856      TCGA-G4-6293 
"CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" 
     TCGA-G4-6299      TCGA-G4-6303      TCGA-G4-6304      TCGA-G4-6306 
"CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" 
     TCGA-G4-6307      TCGA-G4-6309      TCGA-G4-6310      TCGA-G4-6315 
"CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" 
     TCGA-G4-6317      TCGA-G4-6321      TCGA-G4-6323      TCGA-G4-6586 
"CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" 
     TCGA-G4-6588      TCGA-G4-6625      TCGA-G4-6626      TCGA-G4-6628 
"CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" 
     TCGA-AF-2687      TCGA-AF-2689      TCGA-AF-2691      TCGA-AF-2692 
"CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" 
     TCGA-AF-2693      TCGA-AF-3400      TCGA-AF-3913      TCGA-AF-4110 
"CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" 
     TCGA-AF-5654      TCGA-AF-6136      TCGA-AF-6655      TCGA-AF-6672 
"CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" 
     TCGA-AH-6544      TCGA-AH-6547      TCGA-AH-6549      TCGA-AH-6643 
"CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" 
     TCGA-AH-6644      TCGA-CI-6619      TCGA-CI-6620      TCGA-CI-6621 
"CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" 
     TCGA-CI-6622      TCGA-CI-6624      TCGA-CL-5917      TCGA-CL-5918 
"CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" 
     TCGA-DC-5337      TCGA-DC-5869      TCGA-DC-6155      TCGA-DC-6157 
"CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" 
     TCGA-DC-6158      TCGA-DC-6160      TCGA-DC-6681      TCGA-DC-6682 
"CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" 
     TCGA-DC-6683      TCGA-DT-5265      TCGA-DY-A0XA      TCGA-DY-A1DC 
"CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" 
     TCGA-DY-A1DD      TCGA-DY-A1DF      TCGA-DY-A1DG      TCGA-DY-A1H8 
"CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" 
     TCGA-EF-5830      TCGA-EI-6506      TCGA-EI-6507      TCGA-EI-6508 
"CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" 
     TCGA-EI-6510      TCGA-F5-6464      TCGA-F5-6465      TCGA-F5-6571 
"CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" 
     TCGA-F5-6702      TCGA-F5-6811      TCGA-F5-6812      TCGA-F5-6813 
"CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" "CENPA WILD-TYPE" 
     TCGA-G5-6235      TCGA-G5-6641 
"CENPA WILD-TYPE" "CENPA WILD-TYPE" 

Clustering(1984) Variable = MST1R MUTATION ANALYSIS
D1984V1, survival
                 sevent
clus2               0   1
  MST1R MUTATED    10   3
  MST1R WILD-TYPE 368  90
  MST1R MUTATED MST1R WILD-TYPE 
             13             458 
  MST1R MUTATED MST1R WILD-TYPE 
              3              90 
$`MST1R MUTATED`
TCGA-A6-6138 TCGA-AA-3845 TCGA-AD-5900 TCGA-AZ-6607 TCGA-CK-4952 TCGA-CK-6751 
       22.52         0.00         0.07         3.19        15.62       124.27 
TCGA-CM-5861 TCGA-CM-6171 TCGA-CM-6674 TCGA-D5-6928 TCGA-DM-A0XD TCGA-F4-6856 
       15.02        14.04        12.95        11.64        24.43        35.31 
TCGA-G4-6315 
       61.91 

$`MST1R WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6141 TCGA-A6-6142 
       22.09        22.06        32.71        27.09         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 
       17.98        15.95        38.99        37.02        14.93        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       39.98        18.05        40.96        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5254 
      100.01        29.56         5.23        11.74         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 
       10.06        14.30        17.56       148.01        85.45        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CM-4743 
       51.32         9.99        21.14        82.95         1.91        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       22.98        30.08        32.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 
       21.99        14.99        12.99        13.02        15.02        11.01 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 
        4.41        12.43        14.30         9.04         9.44         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XF 
        1.51        12.00        11.38        10.26       119.70        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       47.41       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       55.04        85.48        63.62        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  MST1R MUTATED MST1R WILD-TYPE 
              0               0 
  MST1R MUTATED MST1R WILD-TYPE 
         124.27          148.01 
  MST1R MUTATED MST1R WILD-TYPE 
         15.020          20.415 
[1] "0.0 - 124.3 (15.0)" "0.0 - 148.0 (20.4)"
[1] "hr=" "1.2"
D1984V2, continuous
D1984V3, binary
                 cls
clus                0   1
  MST1R MUTATED    14   0
  MST1R WILD-TYPE 352 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MST1R MUTATED     14    0
  MST1R WILD-TYPE  352  119
        clus
vv       MST1R MUTATED MST1R WILD-TYPE
  COLON             14             352
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MST1R MUTATED         5        0        0         5         0         0
  MST1R WILD-TYPE      86        1       32       133        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MST1R MUTATED           0          0          0          2        2         0
  MST1R WILD-TYPE        24         11         59         40       46        18
                 vv
clus              STAGE IVB
  MST1R MUTATED           0
  MST1R WILD-TYPE         1
D1984V4, multiclass
            clus
vv           MST1R MUTATED MST1R WILD-TYPE
  STAGE I                5              86
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              5             133
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             2              40
  STAGE IV               2              46
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  MST1R MUTATED     0   5   7   2
  MST1R WILD-TYPE  17  87 322  48
D1984V5, multiclass
    clus
vv   MST1R MUTATED MST1R WILD-TYPE
  T1             0              17
  T2             5              87
  T3             7             322
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  MST1R MUTATED    10   1   3
  MST1R WILD-TYPE 277 112  84
D1984V6, multiclass
    clus
vv   MST1R MUTATED MST1R WILD-TYPE
  N0            10             277
  N1             1             112
  N2             3              84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1984V7, binary
                 cls
clus                0   1
  MST1R MUTATED     9   2
  MST1R WILD-TYPE 366  63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MST1R MUTATED      9    2
  MST1R WILD-TYPE  366   63
   clus
vv  MST1R MUTATED MST1R WILD-TYPE
  0             9             366
  1             2              63
[1] 2 2
[1] FALSE
D1984V8, binary
                 cls
clus                0   1
  MST1R MUTATED     5   9
  MST1R WILD-TYPE 220 255
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MST1R MUTATED      5    9
  MST1R WILD-TYPE  220  255
        clus
vv       MST1R MUTATED MST1R WILD-TYPE
  FEMALE             5             220
  MALE               9             255
[1] 2 2
[1] FALSE
D1984V9, binary
                 cls
clus                0   1
  MST1R MUTATED     9   0
  MST1R WILD-TYPE 341  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MST1R MUTATED      9    0
  MST1R WILD-TYPE  341   22
     clus
vv    MST1R MUTATED MST1R WILD-TYPE
  NO              9             341
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MST1R MUTATED                      8                             6
  MST1R WILD-TYPE                  307                            41
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MST1R MUTATED                       0                              0
  MST1R WILD-TYPE                   106                             10
D1984V10, multiclass
                                clus
vv                               MST1R MUTATED MST1R WILD-TYPE
  COLON ADENOCARCINOMA                       8             307
  COLON MUCINOUS ADENOCARCINOMA              6              41
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  MST1R MUTATED     9   0   0   2
  MST1R WILD-TYPE 336   4  31  23
D1984V11, multiclass
    clus
vv   MST1R MUTATED MST1R WILD-TYPE
  R0             9             336
  R1             0               4
  R2             0              31
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1984V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MST1R MUTATED                                  0     0
  MST1R WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  MST1R MUTATED                           0    13
  MST1R WILD-TYPE                        22   213
D1984V13, multiclass
                                  clus
vv                                 MST1R MUTATED MST1R WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                       13             213
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1985) Variable = NONO MUTATION ANALYSIS
D1985V1, survival
                sevent
clus2              0   1
  NONO MUTATED    11   1
  NONO WILD-TYPE 367  92
  NONO MUTATED NONO WILD-TYPE 
            12            459 
  NONO MUTATED NONO WILD-TYPE 
             1             92 
$`NONO MUTATED`
TCGA-A6-6141 TCGA-AA-A010 TCGA-AD-6889 TCGA-AZ-4315 TCGA-CK-4948 TCGA-CK-5912 
        8.38        34.98        56.55        58.39       148.01        49.08 
TCGA-CK-6751 TCGA-CM-6677 TCGA-D5-6539 TCGA-D5-6930 TCGA-G4-6306 TCGA-AG-3593 
      124.27        11.08        12.49         1.51        44.68        34.03 

$`NONO WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 
       22.09        22.06        32.71        27.09        22.52        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5913 
       10.06        14.30        17.56        85.45        15.62        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CM-4743 TCGA-CM-4744 
        9.99        21.14        82.95         1.91        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6678 TCGA-CM-6679 
       11.01        12.95        13.05        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
        4.80        17.13        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        4.80        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       53.62        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3594 
       36.03        20.05        24.00         1.02        46.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  NONO MUTATED NONO WILD-TYPE 
          1.51           0.00 
  NONO MUTATED NONO WILD-TYPE 
        148.01         140.38 
  NONO MUTATED NONO WILD-TYPE 
         39.83          20.05 
[1] "1.5 - 148.0 (39.8)" "0.0 - 140.4 (20.1)"
[1] "hr=" "4.1"
D1985V2, continuous
D1985V3, binary
                cls
clus               0   1
  NONO MUTATED    11   1
  NONO WILD-TYPE 355 118
[1] "tbl2"
                cls
clus             [,1] [,2]
  NONO MUTATED     11    1
  NONO WILD-TYPE  355  118
        clus
vv       NONO MUTATED NONO WILD-TYPE
  COLON            11            355
  RECTUM            1            118
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NONO MUTATED         2        0        0         7         1         0
  NONO WILD-TYPE      89        1       32       131         9         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NONO MUTATED           1          1          0          0        0         0
  NONO WILD-TYPE        23         10         59         42       48        18
                vv
clus             STAGE IVB
  NONO MUTATED           0
  NONO WILD-TYPE         1
D1985V4, multiclass
            clus
vv           NONO MUTATED NONO WILD-TYPE
  STAGE I               2             89
  STAGE IA              0              1
  STAGE II              0             32
  STAGE IIA             7            131
  STAGE IIB             1              9
  STAGE IIC             0              1
  STAGE III             1             23
  STAGE IIIA            1             10
  STAGE IIIB            0             59
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  NONO MUTATED     0   3   8   1
  NONO WILD-TYPE  17  89 321  49
D1985V5, multiclass
    clus
vv   NONO MUTATED NONO WILD-TYPE
  T1            0             17
  T2            3             89
  T3            8            321
  T4            1             49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  NONO MUTATED    11   1   0
  NONO WILD-TYPE 276 112  87
D1985V6, multiclass
    clus
vv   NONO MUTATED NONO WILD-TYPE
  N0           11            276
  N1            1            112
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1985V7, binary
                cls
clus               0   1
  NONO MUTATED    10   0
  NONO WILD-TYPE 365  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  NONO MUTATED     10    0
  NONO WILD-TYPE  365   65
   clus
vv  NONO MUTATED NONO WILD-TYPE
  0           10            365
  1            0             65
[1] 2 2
[1] FALSE
D1985V8, binary
                cls
clus               0   1
  NONO MUTATED     6   6
  NONO WILD-TYPE 219 258
[1] "tbl2"
                cls
clus             [,1] [,2]
  NONO MUTATED      6    6
  NONO WILD-TYPE  219  258
        clus
vv       NONO MUTATED NONO WILD-TYPE
  FEMALE            6            219
  MALE              6            258
[1] 2 2
[1] FALSE
D1985V9, binary
                cls
clus               0   1
  NONO MUTATED     9   1
  NONO WILD-TYPE 341  21
[1] "tbl2"
                cls
clus             [,1] [,2]
  NONO MUTATED      9    1
  NONO WILD-TYPE  341   21
     clus
vv    NONO MUTATED NONO WILD-TYPE
  NO             9            341
  YES            1             21
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  NONO MUTATED                      9                             2
  NONO WILD-TYPE                  306                            45
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  NONO MUTATED                       1                              0
  NONO WILD-TYPE                   105                             10
D1985V10, multiclass
                                clus
vv                               NONO MUTATED NONO WILD-TYPE
  COLON ADENOCARCINOMA                      9            306
  COLON MUCINOUS ADENOCARCINOMA             2             45
  RECTAL ADENOCARCINOMA                     1            105
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  NONO MUTATED     8   0   0   2
  NONO WILD-TYPE 337   4  31  23
D1985V11, multiclass
    clus
vv   NONO MUTATED NONO WILD-TYPE
  R0            8            337
  R1            0              4
  R2            0             31
  RX            2             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1985V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NONO MUTATED                                  0     1
  NONO WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  NONO MUTATED                           1     8
  NONO WILD-TYPE                        21   218
D1985V13, multiclass
                                  clus
vv                                 NONO MUTATED NONO WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                       8            218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1986) Variable = CYP2C9 MUTATION ANALYSIS
D1986V1, survival
                  sevent
clus2                0   1
  CYP2C9 MUTATED     7   0
  CYP2C9 WILD-TYPE 371  93
  CYP2C9 MUTATED CYP2C9 WILD-TYPE 
               7              464 
  CYP2C9 MUTATED CYP2C9 WILD-TYPE 
               0               93 
$`CYP2C9 MUTATED`
TCGA-AA-3697 TCGA-AA-3947 TCGA-AA-A01Q TCGA-D5-6532 TCGA-G4-6306 TCGA-G4-6588 
       85.05        33.01         1.02        18.25        44.68        26.17 
TCGA-AG-A002 
       20.98 

$`CYP2C9 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       19.00        36.00         5.03        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
        2.01        12.99        24.00        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        31.00        38.07        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       53.62        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       22.09        13.78        35.80        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  CYP2C9 MUTATED CYP2C9 WILD-TYPE 
            1.02             0.00 
  CYP2C9 MUTATED CYP2C9 WILD-TYPE 
           85.05           148.01 
  CYP2C9 MUTATED CYP2C9 WILD-TYPE 
          26.170           20.085 
[1] "1.0 - 85.0 (26.2)"  "0.0 - 148.0 (20.1)"
[1] "hr="     "9200000"
D1986V2, continuous
D1986V3, binary
                  cls
clus                 0   1
  CYP2C9 MUTATED     8   1
  CYP2C9 WILD-TYPE 358 118
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CYP2C9 MUTATED      8    1
  CYP2C9 WILD-TYPE  358  118
        clus
vv       CYP2C9 MUTATED CYP2C9 WILD-TYPE
  COLON               8              358
  RECTUM              1              118
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CYP2C9 MUTATED         1        0        2         4         1         0
  CYP2C9 WILD-TYPE      90        1       30       134         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CYP2C9 MUTATED           1          0          0          0        0
  CYP2C9 WILD-TYPE        23         11         59         42       48
                  vv
clus               STAGE IVA STAGE IVB
  CYP2C9 MUTATED           0         0
  CYP2C9 WILD-TYPE        18         1
D1986V4, multiclass
            clus
vv           CYP2C9 MUTATED CYP2C9 WILD-TYPE
  STAGE I                 1               90
  STAGE IA                0                1
  STAGE II                2               30
  STAGE IIA               4              134
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               1               23
  STAGE IIIA              0               11
  STAGE IIIB              0               59
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  CYP2C9 MUTATED     0   2   6   1
  CYP2C9 WILD-TYPE  17  90 323  49
D1986V5, multiclass
    clus
vv   CYP2C9 MUTATED CYP2C9 WILD-TYPE
  T1              0               17
  T2              2               90
  T3              6              323
  T4              1               49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  CYP2C9 MUTATED     9   0   0
  CYP2C9 WILD-TYPE 278 113  87
D1986V6, multiclass
    clus
vv   CYP2C9 MUTATED CYP2C9 WILD-TYPE
  N0              9              278
  N1              0              113
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1986V7, binary
                  cls
clus                 0   1
  CYP2C9 MUTATED     9   0
  CYP2C9 WILD-TYPE 366  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CYP2C9 MUTATED      9    0
  CYP2C9 WILD-TYPE  366   65
   clus
vv  CYP2C9 MUTATED CYP2C9 WILD-TYPE
  0              9              366
  1              0               65
[1] 2 2
[1] FALSE
D1986V8, binary
                  cls
clus                 0   1
  CYP2C9 MUTATED     4   5
  CYP2C9 WILD-TYPE 221 259
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CYP2C9 MUTATED      4    5
  CYP2C9 WILD-TYPE  221  259
        clus
vv       CYP2C9 MUTATED CYP2C9 WILD-TYPE
  FEMALE              4              221
  MALE                5              259
[1] 2 2
[1] FALSE
D1986V9, binary
                  cls
clus                 0   1
  CYP2C9 MUTATED     6   0
  CYP2C9 WILD-TYPE 344  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CYP2C9 MUTATED      6    0
  CYP2C9 WILD-TYPE  344   22
     clus
vv    CYP2C9 MUTATED CYP2C9 WILD-TYPE
  NO               6              344
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CYP2C9 MUTATED                      7                             1
  CYP2C9 WILD-TYPE                  308                            46
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CYP2C9 MUTATED                       1                              0
  CYP2C9 WILD-TYPE                   105                             10
D1986V10, multiclass
                                clus
vv                               CYP2C9 MUTATED CYP2C9 WILD-TYPE
  COLON ADENOCARCINOMA                        7              308
  COLON MUCINOUS ADENOCARCINOMA               1               46
  RECTAL ADENOCARCINOMA                       1              105
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  CYP2C9 MUTATED     9   0   0   0
  CYP2C9 WILD-TYPE 336   4  31  25
D1986V11, multiclass
    clus
vv   CYP2C9 MUTATED CYP2C9 WILD-TYPE
  R0              9              336
  R1              0                4
  R2              0               31
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1986V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CYP2C9 MUTATED                                  0     0
  CYP2C9 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  CYP2C9 MUTATED                           0     3
  CYP2C9 WILD-TYPE                        22   223
D1986V13, multiclass
                                  clus
vv                                 CYP2C9 MUTATED CYP2C9 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         3              223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1987) Variable = ADAM33 MUTATION ANALYSIS
D1987V1, survival
                  sevent
clus2                0   1
  ADAM33 MUTATED     5   2
  ADAM33 WILD-TYPE 373  91
  ADAM33 MUTATED ADAM33 WILD-TYPE 
               7              464 
  ADAM33 MUTATED ADAM33 WILD-TYPE 
               2               91 
$`ADAM33 MUTATED`
TCGA-AA-3681 TCGA-AA-3715 TCGA-AA-3971 TCGA-AD-6895 TCGA-AZ-6598 TCGA-CA-5797 
        5.98        19.04        16.08         0.72        49.41         3.29 
TCGA-CA-6717 
       12.76 

$`ADAM33 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3685 TCGA-AA-3688 
       50.04        47.01        15.02        11.01        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 
       36.00         5.03        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3972 TCGA-AA-3973 
       20.98        34.03         2.01        21.99        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.79         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        88.21         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.25         0.07        12.20        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  ADAM33 MUTATED ADAM33 WILD-TYPE 
            0.72             0.00 
  ADAM33 MUTATED ADAM33 WILD-TYPE 
           49.41           148.01 
  ADAM33 MUTATED ADAM33 WILD-TYPE 
           12.76            20.73 
[1] "0.7 - 49.4 (12.8)"  "0.0 - 148.0 (20.7)"
[1] "hr=" "2.2"
D1987V2, continuous
D1987V3, binary
                  cls
clus                 0   1
  ADAM33 MUTATED     7   0
  ADAM33 WILD-TYPE 359 119
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ADAM33 MUTATED      7    0
  ADAM33 WILD-TYPE  359  119
        clus
vv       ADAM33 MUTATED ADAM33 WILD-TYPE
  COLON               7              359
  RECTUM              0              119
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ADAM33 MUTATED         0        0        2         2         0         0
  ADAM33 WILD-TYPE      91        1       30       136        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ADAM33 MUTATED           2          0          0          0        0
  ADAM33 WILD-TYPE        22         11         59         42       48
                  vv
clus               STAGE IVA STAGE IVB
  ADAM33 MUTATED           0         0
  ADAM33 WILD-TYPE        18         1
D1987V4, multiclass
            clus
vv           ADAM33 MUTATED ADAM33 WILD-TYPE
  STAGE I                 0               91
  STAGE IA                0                1
  STAGE II                2               30
  STAGE IIA               2              136
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               2               22
  STAGE IIIA              0               11
  STAGE IIIB              0               59
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ADAM33 MUTATED     0   0   7   0
  ADAM33 WILD-TYPE  17  92 322  50
D1987V5, multiclass
    clus
vv   ADAM33 MUTATED ADAM33 WILD-TYPE
  T1              0               17
  T2              0               92
  T3              7              322
  T4              0               50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  ADAM33 MUTATED     4   3   0
  ADAM33 WILD-TYPE 283 110  87
D1987V6, multiclass
    clus
vv   ADAM33 MUTATED ADAM33 WILD-TYPE
  N0              4              283
  N1              3              110
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1987V7, binary
                  cls
clus                 0   1
  ADAM33 MUTATED     5   0
  ADAM33 WILD-TYPE 370  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ADAM33 MUTATED      5    0
  ADAM33 WILD-TYPE  370   65
   clus
vv  ADAM33 MUTATED ADAM33 WILD-TYPE
  0              5              370
  1              0               65
[1] 2 2
[1] FALSE
D1987V8, binary
                  cls
clus                 0   1
  ADAM33 MUTATED     2   5
  ADAM33 WILD-TYPE 223 259
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ADAM33 MUTATED      2    5
  ADAM33 WILD-TYPE  223  259
        clus
vv       ADAM33 MUTATED ADAM33 WILD-TYPE
  FEMALE              2              223
  MALE                5              259
[1] 2 2
[1] FALSE
D1987V9, binary
                  cls
clus                 0   1
  ADAM33 MUTATED     6   0
  ADAM33 WILD-TYPE 344  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ADAM33 MUTATED      6    0
  ADAM33 WILD-TYPE  344   22
     clus
vv    ADAM33 MUTATED ADAM33 WILD-TYPE
  NO               6              344
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ADAM33 MUTATED                      6                             1
  ADAM33 WILD-TYPE                  309                            46
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ADAM33 MUTATED                       0                              0
  ADAM33 WILD-TYPE                   106                             10
D1987V10, multiclass
                                clus
vv                               ADAM33 MUTATED ADAM33 WILD-TYPE
  COLON ADENOCARCINOMA                        6              309
  COLON MUCINOUS ADENOCARCINOMA               1               46
  RECTAL ADENOCARCINOMA                       0              106
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ADAM33 MUTATED     4   0   0   1
  ADAM33 WILD-TYPE 341   4  31  24
D1987V11, multiclass
    clus
vv   ADAM33 MUTATED ADAM33 WILD-TYPE
  R0              4              341
  R1              0                4
  R2              0               31
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1987V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ADAM33 MUTATED                                  0     2
  ADAM33 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ADAM33 MUTATED                           0     2
  ADAM33 WILD-TYPE                        22   224
D1987V13, multiclass
                                  clus
vv                                 ADAM33 MUTATED ADAM33 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                9
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         2              224
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1988) Variable = DYRK4 MUTATION ANALYSIS
D1988V1, survival
                 sevent
clus2               0   1
  DYRK4 MUTATED    10   4
  DYRK4 WILD-TYPE 368  89
  DYRK4 MUTATED DYRK4 WILD-TYPE 
             14             457 
  DYRK4 MUTATED DYRK4 WILD-TYPE 
              4              89 
$`DYRK4 MUTATED`
TCGA-AA-3811 TCGA-AA-3818 TCGA-AA-3979 TCGA-AD-6895 TCGA-AD-6901 TCGA-AD-6964 
       10.06         0.99        24.00         0.72        22.42        10.88 
TCGA-AY-6197 TCGA-CM-4743 TCGA-CM-5861 TCGA-CM-6166 TCGA-CM-6168 TCGA-D5-6535 
       21.44        23.05        15.02        21.99        12.99        15.12 
TCGA-AG-A002 TCGA-G5-6641 
       20.98        26.43 

$`DYRK4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       19.04        35.05        33.04        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        25.02        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        0.79         5.79        27.42         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
       16.31         0.95        33.01        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 
       21.14        82.95         1.91       124.27        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       32.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6169 
       12.00         2.96        29.03        16.04        14.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       43.27        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 
       55.76 

  DYRK4 MUTATED DYRK4 WILD-TYPE 
           0.72            0.00 
  DYRK4 MUTATED DYRK4 WILD-TYPE 
          26.43          148.01 
  DYRK4 MUTATED DYRK4 WILD-TYPE 
          18.05           20.19 
[1] "0.7 - 26.4 (18.1)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "2.4"
D1988V2, continuous
D1988V3, binary
                 cls
clus                0   1
  DYRK4 MUTATED    12   2
  DYRK4 WILD-TYPE 354 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DYRK4 MUTATED     12    2
  DYRK4 WILD-TYPE  354  117
        clus
vv       DYRK4 MUTATED DYRK4 WILD-TYPE
  COLON             12             354
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DYRK4 MUTATED         2        0        0         6         0         0
  DYRK4 WILD-TYPE      89        1       32       132        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DYRK4 MUTATED           1          1          1          0        0         0
  DYRK4 WILD-TYPE        23         10         58         42       48        18
                 vv
clus              STAGE IVB
  DYRK4 MUTATED           0
  DYRK4 WILD-TYPE         1
D1988V4, multiclass
            clus
vv           DYRK4 MUTATED DYRK4 WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              6             132
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             1              10
  STAGE IIIB             1              58
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  DYRK4 MUTATED     1   2  10   1
  DYRK4 WILD-TYPE  16  90 319  49
D1988V5, multiclass
    clus
vv   DYRK4 MUTATED DYRK4 WILD-TYPE
  T1             1              16
  T2             2              90
  T3            10             319
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  DYRK4 MUTATED     9   3   2
  DYRK4 WILD-TYPE 278 110  85
D1988V6, multiclass
    clus
vv   DYRK4 MUTATED DYRK4 WILD-TYPE
  N0             9             278
  N1             3             110
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1988V7, binary
                 cls
clus                0   1
  DYRK4 MUTATED     8   0
  DYRK4 WILD-TYPE 367  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DYRK4 MUTATED      8    0
  DYRK4 WILD-TYPE  367   65
   clus
vv  DYRK4 MUTATED DYRK4 WILD-TYPE
  0             8             367
  1             0              65
[1] 2 2
[1] FALSE
D1988V8, binary
                 cls
clus                0   1
  DYRK4 MUTATED     6   8
  DYRK4 WILD-TYPE 219 256
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DYRK4 MUTATED      6    8
  DYRK4 WILD-TYPE  219  256
        clus
vv       DYRK4 MUTATED DYRK4 WILD-TYPE
  FEMALE             6             219
  MALE               8             256
[1] 2 2
[1] FALSE
D1988V9, binary
                 cls
clus                0   1
  DYRK4 MUTATED    12   0
  DYRK4 WILD-TYPE 338  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DYRK4 MUTATED     12    0
  DYRK4 WILD-TYPE  338   22
     clus
vv    DYRK4 MUTATED DYRK4 WILD-TYPE
  NO             12             338
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  DYRK4 MUTATED                     12                             0
  DYRK4 WILD-TYPE                  303                            47
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  DYRK4 MUTATED                       1                              1
  DYRK4 WILD-TYPE                   105                              9
D1988V10, multiclass
                                clus
vv                               DYRK4 MUTATED DYRK4 WILD-TYPE
  COLON ADENOCARCINOMA                      12             303
  COLON MUCINOUS ADENOCARCINOMA              0              47
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             1               9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  DYRK4 MUTATED    10   0   0   1
  DYRK4 WILD-TYPE 335   4  31  24
D1988V11, multiclass
    clus
vv   DYRK4 MUTATED DYRK4 WILD-TYPE
  R0            10             335
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1988V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DYRK4 MUTATED                                  0     0
  DYRK4 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  DYRK4 MUTATED                           1     9
  DYRK4 WILD-TYPE                        21   217
D1988V13, multiclass
                                  clus
vv                                 DYRK4 MUTATED DYRK4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        9             217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1989) Variable = ZMIZ1 MUTATION ANALYSIS
D1989V1, survival
                 sevent
clus2               0   1
  ZMIZ1 MUTATED    10   1
  ZMIZ1 WILD-TYPE 368  92
  ZMIZ1 MUTATED ZMIZ1 WILD-TYPE 
             11             460 
  ZMIZ1 MUTATED ZMIZ1 WILD-TYPE 
              1              92 
$`ZMIZ1 MUTATED`
TCGA-A6-2676 TCGA-AA-3663 TCGA-AA-3977 TCGA-AY-6386 TCGA-D5-6533 TCGA-D5-6928 
       42.90         6.97        25.02        17.82         1.32        11.64 
TCGA-DM-A1HB TCGA-G4-6317 TCGA-G4-6586 TCGA-AG-A002 TCGA-G5-6235 
      135.65        36.00        35.80        20.98        55.76 

$`ZMIZ1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
       14.30         9.04         9.44         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
       44.32       131.51       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 
       85.48        63.62        61.91        22.09        13.78        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6641 
       32.19         0.66         0.69        26.43 

  ZMIZ1 MUTATED ZMIZ1 WILD-TYPE 
           1.32            0.00 
  ZMIZ1 MUTATED ZMIZ1 WILD-TYPE 
         135.65          148.01 
  ZMIZ1 MUTATED ZMIZ1 WILD-TYPE 
         25.020          20.085 
[1] "1.3 - 135.7 (25.0)" "0.0 - 148.0 (20.1)"
[1] "hr=" "2.7"
D1989V2, continuous
D1989V3, binary
                 cls
clus                0   1
  ZMIZ1 MUTATED     9   2
  ZMIZ1 WILD-TYPE 357 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZMIZ1 MUTATED      9    2
  ZMIZ1 WILD-TYPE  357  117
        clus
vv       ZMIZ1 MUTATED ZMIZ1 WILD-TYPE
  COLON              9             357
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZMIZ1 MUTATED         1        0        1         2         1         0
  ZMIZ1 WILD-TYPE      90        1       31       136         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ZMIZ1 MUTATED           0          0          4          1        0         0
  ZMIZ1 WILD-TYPE        24         11         55         41       48        18
                 vv
clus              STAGE IVB
  ZMIZ1 MUTATED           0
  ZMIZ1 WILD-TYPE         1
D1989V4, multiclass
            clus
vv           ZMIZ1 MUTATED ZMIZ1 WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              2             136
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             4              55
  STAGE IIIC             1              41
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ZMIZ1 MUTATED     0   2   7   2
  ZMIZ1 WILD-TYPE  17  90 322  48
D1989V5, multiclass
    clus
vv   ZMIZ1 MUTATED ZMIZ1 WILD-TYPE
  T1             0              17
  T2             2              90
  T3             7             322
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  ZMIZ1 MUTATED     7   3   1
  ZMIZ1 WILD-TYPE 280 110  86
D1989V6, multiclass
    clus
vv   ZMIZ1 MUTATED ZMIZ1 WILD-TYPE
  N0             7             280
  N1             3             110
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1989V7, binary
                 cls
clus                0   1
  ZMIZ1 MUTATED     8   0
  ZMIZ1 WILD-TYPE 367  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZMIZ1 MUTATED      8    0
  ZMIZ1 WILD-TYPE  367   65
   clus
vv  ZMIZ1 MUTATED ZMIZ1 WILD-TYPE
  0             8             367
  1             0              65
[1] 2 2
[1] FALSE
D1989V8, binary
                 cls
clus                0   1
  ZMIZ1 MUTATED     5   6
  ZMIZ1 WILD-TYPE 220 258
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZMIZ1 MUTATED      5    6
  ZMIZ1 WILD-TYPE  220  258
        clus
vv       ZMIZ1 MUTATED ZMIZ1 WILD-TYPE
  FEMALE             5             220
  MALE               6             258
[1] 2 2
[1] FALSE
D1989V9, binary
                 cls
clus                0   1
  ZMIZ1 MUTATED     9   0
  ZMIZ1 WILD-TYPE 341  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZMIZ1 MUTATED      9    0
  ZMIZ1 WILD-TYPE  341   22
     clus
vv    ZMIZ1 MUTATED ZMIZ1 WILD-TYPE
  NO              9             341
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ZMIZ1 MUTATED                      7                             1
  ZMIZ1 WILD-TYPE                  308                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ZMIZ1 MUTATED                       2                              0
  ZMIZ1 WILD-TYPE                   104                             10
D1989V10, multiclass
                                clus
vv                               ZMIZ1 MUTATED ZMIZ1 WILD-TYPE
  COLON ADENOCARCINOMA                       7             308
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  ZMIZ1 MUTATED     8   1   0   0
  ZMIZ1 WILD-TYPE 337   3  31  25
D1989V11, multiclass
    clus
vv   ZMIZ1 MUTATED ZMIZ1 WILD-TYPE
  R0             8             337
  R1             1               3
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1989V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZMIZ1 MUTATED                                  0     0
  ZMIZ1 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ZMIZ1 MUTATED                           1     7
  ZMIZ1 WILD-TYPE                        21   219
D1989V13, multiclass
                                  clus
vv                                 ZMIZ1 MUTATED ZMIZ1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        7             219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1990) Variable = NLRP8 MUTATION ANALYSIS
D1990V1, survival
                 sevent
clus2               0   1
  NLRP8 MUTATED    22   5
  NLRP8 WILD-TYPE 356  88
  NLRP8 MUTATED NLRP8 WILD-TYPE 
             27             444 
  NLRP8 MUTATED NLRP8 WILD-TYPE 
              5              88 
$`NLRP8 MUTATED`
TCGA-A6-5659 TCGA-A6-5661 TCGA-AA-3510 TCGA-AA-3516 TCGA-AA-3529 TCGA-AA-3538 
       30.44        33.53        63.98        13.02         0.00        26.01 
TCGA-AA-3713 TCGA-AA-3864 TCGA-AA-3877 TCGA-AA-3947 TCGA-AA-A01Q TCGA-AA-A024 
       19.04        53.00        31.00        33.01         1.02        39.06 
TCGA-AU-6004 TCGA-AY-6197 TCGA-CA-6717 TCGA-CM-5344 TCGA-CM-6163 TCGA-D5-5538 
       27.09        21.44        12.76        22.03         2.96        12.26 
TCGA-D5-6534 TCGA-D5-6537 TCGA-F4-6808 TCGA-G4-6303 TCGA-G4-6586 TCGA-AF-2693 
       43.27         4.80        33.67        65.85        35.80        19.10 
TCGA-AG-A00C TCGA-AG-A02X TCGA-CI-6622 
        6.02        41.00         6.97 

$`NLRP8 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       32.91        31.63        29.19        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        6.97         1.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 
       37.05        36.03         8.05        19.07        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        29.00        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 
       32.05         0.99        31.07        31.07        30.05        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 
       24.03        27.02        29.98        18.05         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
       38.07        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       37.02        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 
       22.42        27.42        10.88         0.20        14.50        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        33.01        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.20        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       13.02        29.06        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5539 
       11.08        11.01        10.06        12.03        45.40        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6535 
       56.09        55.92        20.19        18.25         1.32        15.12 
TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
       17.85        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 
       79.69        24.13        39.48        43.04        13.55        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        20.98        13.94        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        0.72         6.05        33.17         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  NLRP8 MUTATED NLRP8 WILD-TYPE 
              0               0 
  NLRP8 MUTATED NLRP8 WILD-TYPE 
          65.85          148.01 
  NLRP8 MUTATED NLRP8 WILD-TYPE 
         26.010          20.035 
[1] "0.0 - 65.8 (26.0)"  "0.0 - 148.0 (20.0)"
[1] "hr=" "1.1"
D1990V2, continuous
D1990V3, binary
                 cls
clus                0   1
  NLRP8 MUTATED    24   3
  NLRP8 WILD-TYPE 342 116
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NLRP8 MUTATED     24    3
  NLRP8 WILD-TYPE  342  116
        clus
vv       NLRP8 MUTATED NLRP8 WILD-TYPE
  COLON             24             342
  RECTUM             3             116
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NLRP8 MUTATED         8        0        4         6         2         0
  NLRP8 WILD-TYPE      83        1       28       132         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NLRP8 MUTATED           1          0          4          1        2         0
  NLRP8 WILD-TYPE        23         11         55         41       46        18
                 vv
clus              STAGE IVB
  NLRP8 MUTATED           0
  NLRP8 WILD-TYPE         1
D1990V4, multiclass
            clus
vv           NLRP8 MUTATED NLRP8 WILD-TYPE
  STAGE I                8              83
  STAGE IA               0               1
  STAGE II               4              28
  STAGE IIA              6             132
  STAGE IIB              2               8
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             4              55
  STAGE IIIC             1              41
  STAGE IV               2              46
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  NLRP8 MUTATED     3   5  18   2
  NLRP8 WILD-TYPE  14  87 311  48
D1990V5, multiclass
    clus
vv   NLRP8 MUTATED NLRP8 WILD-TYPE
  T1             3              14
  T2             5              87
  T3            18             311
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  NLRP8 MUTATED    21   5   2
  NLRP8 WILD-TYPE 266 108  85
D1990V6, multiclass
    clus
vv   NLRP8 MUTATED NLRP8 WILD-TYPE
  N0            21             266
  N1             5             108
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1990V7, binary
                 cls
clus                0   1
  NLRP8 MUTATED    23   2
  NLRP8 WILD-TYPE 352  63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NLRP8 MUTATED     23    2
  NLRP8 WILD-TYPE  352   63
   clus
vv  NLRP8 MUTATED NLRP8 WILD-TYPE
  0            23             352
  1             2              63
[1] 2 2
[1] FALSE
D1990V8, binary
                 cls
clus                0   1
  NLRP8 MUTATED    16  12
  NLRP8 WILD-TYPE 209 252
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NLRP8 MUTATED     16   12
  NLRP8 WILD-TYPE  209  252
        clus
vv       NLRP8 MUTATED NLRP8 WILD-TYPE
  FEMALE            16             209
  MALE              12             252
[1] 2 2
[1] FALSE
D1990V9, binary
                 cls
clus                0   1
  NLRP8 MUTATED    20   2
  NLRP8 WILD-TYPE 330  20
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NLRP8 MUTATED     20    2
  NLRP8 WILD-TYPE  330   20
     clus
vv    NLRP8 MUTATED NLRP8 WILD-TYPE
  NO             20             330
  YES             2              20
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  NLRP8 MUTATED                     18                             6
  NLRP8 WILD-TYPE                  297                            41
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  NLRP8 MUTATED                       3                              0
  NLRP8 WILD-TYPE                   103                             10
D1990V10, multiclass
                                clus
vv                               NLRP8 MUTATED NLRP8 WILD-TYPE
  COLON ADENOCARCINOMA                      18             297
  COLON MUCINOUS ADENOCARCINOMA              6              41
  RECTAL ADENOCARCINOMA                      3             103
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  NLRP8 MUTATED    23   0   1   1
  NLRP8 WILD-TYPE 322   4  30  24
D1990V11, multiclass
    clus
vv   NLRP8 MUTATED NLRP8 WILD-TYPE
  R0            23             322
  R1             0               4
  R2             1              30
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1990V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NLRP8 MUTATED                                  0     1
  NLRP8 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  NLRP8 MUTATED                           1    13
  NLRP8 WILD-TYPE                        21   213
D1990V13, multiclass
                                  clus
vv                                 NLRP8 MUTATED NLRP8 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                       13             213
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1991) Variable = RALGAPB MUTATION ANALYSIS
D1991V1, survival
                   sevent
clus2                 0   1
  RALGAPB MUTATED    14   1
  RALGAPB WILD-TYPE 364  92
  RALGAPB MUTATED RALGAPB WILD-TYPE 
               15               456 
  RALGAPB MUTATED RALGAPB WILD-TYPE 
                1                92 
$`RALGAPB MUTATED`
TCGA-A6-5661 TCGA-AA-3511 TCGA-AA-3672 TCGA-AA-3845 TCGA-AA-3949 TCGA-AA-3977 
       33.53         6.97         0.92         0.00        26.01        25.02 
TCGA-AA-A010 TCGA-CK-5913 TCGA-CM-6674 TCGA-D5-6928 TCGA-DM-A1HB TCGA-G4-6588 
       34.98        51.32        12.95        11.64       135.65        26.17 
TCGA-G4-6628 TCGA-AG-A002 TCGA-EI-6507 
       79.69        20.98        19.96 

$`RALGAPB WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01        63.98         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
       54.02         2.01        14.01        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       38.99        37.02        14.93        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       33.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 
      148.01        85.45        15.62        49.08         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 
        4.41        12.43        14.30         9.04         9.44         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 
      140.38         7.50        44.32       131.51       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 
       22.09        13.78        35.80        91.79        46.75        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       20.55        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  RALGAPB MUTATED RALGAPB WILD-TYPE 
                0                 0 
  RALGAPB MUTATED RALGAPB WILD-TYPE 
           135.65            148.01 
  RALGAPB MUTATED RALGAPB WILD-TYPE 
           25.020            20.085 
[1] "0.0 - 135.7 (25.0)" "0.0 - 148.0 (20.1)"
[1] "hr=" "3.4"
D1991V2, continuous
D1991V3, binary
                   cls
clus                  0   1
  RALGAPB MUTATED    13   2
  RALGAPB WILD-TYPE 353 117
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RALGAPB MUTATED     13    2
  RALGAPB WILD-TYPE  353  117
        clus
vv       RALGAPB MUTATED RALGAPB WILD-TYPE
  COLON               13               353
  RECTUM               2               117
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RALGAPB MUTATED         2        0        1         7         1         0
  RALGAPB WILD-TYPE      89        1       31       131         9         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RALGAPB MUTATED           1          0          2          0        0
  RALGAPB WILD-TYPE        23         11         57         42       48
                   vv
clus                STAGE IVA STAGE IVB
  RALGAPB MUTATED           0         0
  RALGAPB WILD-TYPE        18         1
D1991V4, multiclass
            clus
vv           RALGAPB MUTATED RALGAPB WILD-TYPE
  STAGE I                  2                89
  STAGE IA                 0                 1
  STAGE II                 1                31
  STAGE IIA                7               131
  STAGE IIB                1                 9
  STAGE IIC                0                 1
  STAGE III                1                23
  STAGE IIIA               0                11
  STAGE IIIB               2                57
  STAGE IIIC               0                42
  STAGE IV                 0                48
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  RALGAPB MUTATED     0   3  10   2
  RALGAPB WILD-TYPE  17  89 319  48
D1991V5, multiclass
    clus
vv   RALGAPB MUTATED RALGAPB WILD-TYPE
  T1               0                17
  T2               3                89
  T3              10               319
  T4               2                48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  RALGAPB MUTATED    12   3   0
  RALGAPB WILD-TYPE 275 110  87
D1991V6, multiclass
    clus
vv   RALGAPB MUTATED RALGAPB WILD-TYPE
  N0              12               275
  N1               3               110
  N2               0                87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1991V7, binary
                   cls
clus                  0   1
  RALGAPB MUTATED    13   0
  RALGAPB WILD-TYPE 362  65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RALGAPB MUTATED     13    0
  RALGAPB WILD-TYPE  362   65
   clus
vv  RALGAPB MUTATED RALGAPB WILD-TYPE
  0              13               362
  1               0                65
[1] 2 2
[1] FALSE
D1991V8, binary
                   cls
clus                  0   1
  RALGAPB MUTATED     7   8
  RALGAPB WILD-TYPE 218 256
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RALGAPB MUTATED      7    8
  RALGAPB WILD-TYPE  218  256
        clus
vv       RALGAPB MUTATED RALGAPB WILD-TYPE
  FEMALE               7               218
  MALE                 8               256
[1] 2 2
[1] FALSE
D1991V9, binary
                   cls
clus                  0   1
  RALGAPB MUTATED    13   0
  RALGAPB WILD-TYPE 337  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RALGAPB MUTATED     13    0
  RALGAPB WILD-TYPE  337   22
     clus
vv    RALGAPB MUTATED RALGAPB WILD-TYPE
  NO               13               337
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  RALGAPB MUTATED                     10                             2
  RALGAPB WILD-TYPE                  305                            45
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  RALGAPB MUTATED                       2                              0
  RALGAPB WILD-TYPE                   104                             10
D1991V10, multiclass
                                clus
vv                               RALGAPB MUTATED RALGAPB WILD-TYPE
  COLON ADENOCARCINOMA                        10               305
  COLON MUCINOUS ADENOCARCINOMA                2                45
  RECTAL ADENOCARCINOMA                        2               104
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  RALGAPB MUTATED    12   0   0   1
  RALGAPB WILD-TYPE 333   4  31  24
D1991V11, multiclass
    clus
vv   RALGAPB MUTATED RALGAPB WILD-TYPE
  R0              12               333
  R1               0                 4
  R2               0                31
  RX               1                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1991V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RALGAPB MUTATED                                  0     0
  RALGAPB WILD-TYPE                                1    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  RALGAPB MUTATED                           1     7
  RALGAPB WILD-TYPE                        21   219
D1991V13, multiclass
                                  clus
vv                                 RALGAPB MUTATED RALGAPB WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                      1                21
  WHITE                                          7               219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1992) Variable = DCLRE1C MUTATION ANALYSIS
D1992V1, survival
                   sevent
clus2                 0   1
  DCLRE1C MUTATED     9   2
  DCLRE1C WILD-TYPE 369  91
  DCLRE1C MUTATED DCLRE1C WILD-TYPE 
               11               460 
  DCLRE1C MUTATED DCLRE1C WILD-TYPE 
                2                91 
$`DCLRE1C MUTATED`
TCGA-A6-5665 TCGA-A6-6781 TCGA-AA-3492 TCGA-AA-3947 TCGA-AZ-6598 TCGA-CA-6717 
       22.06        19.66         3.02        33.01        49.41        12.76 
TCGA-CK-6747 TCGA-D5-5540 TCGA-AG-3892 TCGA-AG-A02N TCGA-DY-A0XA 
       82.95        56.09        13.02        61.97       126.44 

$`DCLRE1C WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.12        20.28         7.04         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        88.21         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07        12.20        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
        9.99        21.14         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5541 
       10.06        12.03        45.40        12.26        19.59        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
       49.97         1.94        38.96        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        4.01         5.03         5.29        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  DCLRE1C MUTATED DCLRE1C WILD-TYPE 
             3.02              0.00 
  DCLRE1C MUTATED DCLRE1C WILD-TYPE 
           126.44            148.01 
  DCLRE1C MUTATED DCLRE1C WILD-TYPE 
           33.010            20.085 
[1] "3.0 - 126.4 (33.0)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.8"
D1992V2, continuous
D1992V3, binary
                   cls
clus                  0   1
  DCLRE1C MUTATED     9   3
  DCLRE1C WILD-TYPE 357 116
[1] "tbl2"
                   cls
clus                [,1] [,2]
  DCLRE1C MUTATED      9    3
  DCLRE1C WILD-TYPE  357  116
        clus
vv       DCLRE1C MUTATED DCLRE1C WILD-TYPE
  COLON                9               357
  RECTUM               3               116
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DCLRE1C MUTATED         1        0        4         5         1         0
  DCLRE1C WILD-TYPE      90        1       28       133         9         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DCLRE1C MUTATED           0          0          0          1        0
  DCLRE1C WILD-TYPE        24         11         59         41       48
                   vv
clus                STAGE IVA STAGE IVB
  DCLRE1C MUTATED           0         0
  DCLRE1C WILD-TYPE        18         1
D1992V4, multiclass
            clus
vv           DCLRE1C MUTATED DCLRE1C WILD-TYPE
  STAGE I                  1                90
  STAGE IA                 0                 1
  STAGE II                 4                28
  STAGE IIA                5               133
  STAGE IIB                1                 9
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               0                11
  STAGE IIIB               0                59
  STAGE IIIC               1                41
  STAGE IV                 0                48
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  DCLRE1C MUTATED     1   0   8   3
  DCLRE1C WILD-TYPE  16  92 321  47
D1992V5, multiclass
    clus
vv   DCLRE1C MUTATED DCLRE1C WILD-TYPE
  T1               1                16
  T2               0                92
  T3               8               321
  T4               3                47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  DCLRE1C MUTATED    11   1   0
  DCLRE1C WILD-TYPE 276 112  87
D1992V6, multiclass
    clus
vv   DCLRE1C MUTATED DCLRE1C WILD-TYPE
  N0              11               276
  N1               1               112
  N2               0                87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1992V7, binary
                   cls
clus                  0   1
  DCLRE1C MUTATED     9   0
  DCLRE1C WILD-TYPE 366  65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  DCLRE1C MUTATED      9    0
  DCLRE1C WILD-TYPE  366   65
   clus
vv  DCLRE1C MUTATED DCLRE1C WILD-TYPE
  0               9               366
  1               0                65
[1] 2 2
[1] FALSE
D1992V8, binary
                   cls
clus                  0   1
  DCLRE1C MUTATED     8   4
  DCLRE1C WILD-TYPE 217 260
[1] "tbl2"
                   cls
clus                [,1] [,2]
  DCLRE1C MUTATED      8    4
  DCLRE1C WILD-TYPE  217  260
        clus
vv       DCLRE1C MUTATED DCLRE1C WILD-TYPE
  FEMALE               8               217
  MALE                 4               260
[1] 2 2
[1] FALSE
D1992V9, binary
                   cls
clus                  0   1
  DCLRE1C MUTATED     9   0
  DCLRE1C WILD-TYPE 341  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  DCLRE1C MUTATED      9    0
  DCLRE1C WILD-TYPE  341   22
     clus
vv    DCLRE1C MUTATED DCLRE1C WILD-TYPE
  NO                9               341
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  DCLRE1C MUTATED                      6                             3
  DCLRE1C WILD-TYPE                  309                            44
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  DCLRE1C MUTATED                       3                              0
  DCLRE1C WILD-TYPE                   103                             10
D1992V10, multiclass
                                clus
vv                               DCLRE1C MUTATED DCLRE1C WILD-TYPE
  COLON ADENOCARCINOMA                         6               309
  COLON MUCINOUS ADENOCARCINOMA                3                44
  RECTAL ADENOCARCINOMA                        3               103
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  DCLRE1C MUTATED     8   0   0   2
  DCLRE1C WILD-TYPE 337   4  31  23
D1992V11, multiclass
    clus
vv   DCLRE1C MUTATED DCLRE1C WILD-TYPE
  R0               8               337
  R1               0                 4
  R2               0                31
  RX               2                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1992V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DCLRE1C MUTATED                                  0     1
  DCLRE1C WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  DCLRE1C MUTATED                           0     6
  DCLRE1C WILD-TYPE                        22   220
D1992V13, multiclass
                                  clus
vv                                 DCLRE1C MUTATED DCLRE1C WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                10
  BLACK OR AFRICAN AMERICAN                      0                22
  WHITE                                          6               220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1993) Variable = SLC9A9 MUTATION ANALYSIS
D1993V1, survival
                  sevent
clus2                0   1
  SLC9A9 MUTATED    17   3
  SLC9A9 WILD-TYPE 361  90
  SLC9A9 MUTATED SLC9A9 WILD-TYPE 
              20              451 
  SLC9A9 MUTATED SLC9A9 WILD-TYPE 
               3               90 
$`SLC9A9 MUTATED`
TCGA-A6-2676 TCGA-A6-6654 TCGA-AA-3543 TCGA-AA-3555 TCGA-AA-3949 TCGA-AA-3977 
       42.90        23.87         0.99        29.95        26.01        25.02 
TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01Q TCGA-AA-A01R TCGA-CA-5796 TCGA-CA-6717 
        4.01        34.98         1.02        35.01         3.25        12.76 
TCGA-CA-6718 TCGA-CM-6164 TCGA-CM-6171 TCGA-D5-5538 TCGA-D5-6535 TCGA-G4-6310 
       10.06        29.03        14.04        12.26        15.12        63.62 
TCGA-AG-3611 TCGA-AG-A002 
       13.94        20.98 

$`SLC9A9 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 
       25.18        24.16        21.76        24.69        24.39        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
       12.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       17.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       33.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       31.00        31.00        38.07         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 
        3.06         3.29         0.07        12.20        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6165 TCGA-CM-6166 
       17.03        15.02        12.00         2.96        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 
       14.99        12.99        13.02        15.02        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       45.40        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
        1.32        43.27        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       44.68        55.04        85.48        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  SLC9A9 MUTATED SLC9A9 WILD-TYPE 
            0.99             0.00 
  SLC9A9 MUTATED SLC9A9 WILD-TYPE 
           63.62           148.01 
  SLC9A9 MUTATED SLC9A9 WILD-TYPE 
           18.05            20.19 
[1] "1.0 - 63.6 (18.1)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.1"
D1993V2, continuous
D1993V3, binary
                  cls
clus                 0   1
  SLC9A9 MUTATED    21   2
  SLC9A9 WILD-TYPE 345 117
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLC9A9 MUTATED     21    2
  SLC9A9 WILD-TYPE  345  117
        clus
vv       SLC9A9 MUTATED SLC9A9 WILD-TYPE
  COLON              21              345
  RECTUM              2              117
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SLC9A9 MUTATED         4        0        1         7         3         0
  SLC9A9 WILD-TYPE      87        1       31       131         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC9A9 MUTATED           2          0          5          0        0
  SLC9A9 WILD-TYPE        22         11         54         42       48
                  vv
clus               STAGE IVA STAGE IVB
  SLC9A9 MUTATED           0         0
  SLC9A9 WILD-TYPE        18         1
D1993V4, multiclass
            clus
vv           SLC9A9 MUTATED SLC9A9 WILD-TYPE
  STAGE I                 4               87
  STAGE IA                0                1
  STAGE II                1               31
  STAGE IIA               7              131
  STAGE IIB               3                7
  STAGE IIC               0                1
  STAGE III               2               22
  STAGE IIIA              0               11
  STAGE IIIB              5               54
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  SLC9A9 MUTATED     0   5  15   3
  SLC9A9 WILD-TYPE  17  87 314  47
D1993V5, multiclass
    clus
vv   SLC9A9 MUTATED SLC9A9 WILD-TYPE
  T1              0               17
  T2              5               87
  T3             15              314
  T4              3               47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  SLC9A9 MUTATED    16   5   2
  SLC9A9 WILD-TYPE 271 108  85
D1993V6, multiclass
    clus
vv   SLC9A9 MUTATED SLC9A9 WILD-TYPE
  N0             16              271
  N1              5              108
  N2              2               85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1993V7, binary
                  cls
clus                 0   1
  SLC9A9 MUTATED    20   0
  SLC9A9 WILD-TYPE 355  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLC9A9 MUTATED     20    0
  SLC9A9 WILD-TYPE  355   65
   clus
vv  SLC9A9 MUTATED SLC9A9 WILD-TYPE
  0             20              355
  1              0               65
[1] 2 2
[1] FALSE
D1993V8, binary
                  cls
clus                 0   1
  SLC9A9 MUTATED    12  11
  SLC9A9 WILD-TYPE 213 253
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLC9A9 MUTATED     12   11
  SLC9A9 WILD-TYPE  213  253
        clus
vv       SLC9A9 MUTATED SLC9A9 WILD-TYPE
  FEMALE             12              213
  MALE               11              253
[1] 2 2
[1] FALSE
D1993V9, binary
                  cls
clus                 0   1
  SLC9A9 MUTATED    16   2
  SLC9A9 WILD-TYPE 334  20
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLC9A9 MUTATED     16    2
  SLC9A9 WILD-TYPE  334   20
     clus
vv    SLC9A9 MUTATED SLC9A9 WILD-TYPE
  NO              16              334
  YES              2               20
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SLC9A9 MUTATED                     14                             7
  SLC9A9 WILD-TYPE                  301                            40
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SLC9A9 MUTATED                       2                              0
  SLC9A9 WILD-TYPE                   104                             10
D1993V10, multiclass
                                clus
vv                               SLC9A9 MUTATED SLC9A9 WILD-TYPE
  COLON ADENOCARCINOMA                       14              301
  COLON MUCINOUS ADENOCARCINOMA               7               40
  RECTAL ADENOCARCINOMA                       2              104
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  SLC9A9 MUTATED    17   0   0   4
  SLC9A9 WILD-TYPE 328   4  31  21
D1993V11, multiclass
    clus
vv   SLC9A9 MUTATED SLC9A9 WILD-TYPE
  R0             17              328
  R1              0                4
  R2              0               31
  RX              4               21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1993V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SLC9A9 MUTATED                                  0     3
  SLC9A9 WILD-TYPE                                1     8
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  SLC9A9 MUTATED                           0     8
  SLC9A9 WILD-TYPE                        22   218
D1993V13, multiclass
                                  clus
vv                                 SLC9A9 MUTATED SLC9A9 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         3                8
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         8              218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1994) Variable = C17ORF58 MUTATION ANALYSIS
D1994V1, survival
                    sevent
clus2                  0   1
  C17ORF58 MUTATED     2   1
  C17ORF58 WILD-TYPE 376  92
  C17ORF58 MUTATED C17ORF58 WILD-TYPE 
                 3                468 
  C17ORF58 MUTATED C17ORF58 WILD-TYPE 
                 1                 92 
$`C17ORF58 MUTATED`
TCGA-AA-3663 TCGA-AD-6964 TCGA-G4-6588 
        6.97        10.88        26.17 

$`C17ORF58 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.05        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  C17ORF58 MUTATED C17ORF58 WILD-TYPE 
              6.97               0.00 
  C17ORF58 MUTATED C17ORF58 WILD-TYPE 
             26.17             148.01 
  C17ORF58 MUTATED C17ORF58 WILD-TYPE 
            10.880             20.235 
[1] "7.0 - 26.2 (10.9)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "3"  
D1994V2, continuous
D1994V3, binary
                    cls
clus                   0   1
  C17ORF58 MUTATED     3   0
  C17ORF58 WILD-TYPE 363 119
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C17ORF58 MUTATED      3    0
  C17ORF58 WILD-TYPE  363  119
        clus
vv       C17ORF58 MUTATED C17ORF58 WILD-TYPE
  COLON                 3                363
  RECTUM                0                119
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  C17ORF58 MUTATED         0        0        1         1         0         0
  C17ORF58 WILD-TYPE      91        1       31       137        10         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C17ORF58 MUTATED           0          0          0          0        0
  C17ORF58 WILD-TYPE        24         11         59         42       48
                    vv
clus                 STAGE IVA STAGE IVB
  C17ORF58 MUTATED           0         0
  C17ORF58 WILD-TYPE        18         1
D1994V4, multiclass
[1] "Remove cluster labels:" "C17ORF58 MUTATED"      
clus
  C17ORF58 MUTATED C17ORF58 WILD-TYPE 
                 2                474 
        TCGA-A6-2671         TCGA-A6-2672         TCGA-A6-2674 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-A6-2676         TCGA-A6-2677         TCGA-A6-2678 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-A6-2683         TCGA-A6-3807         TCGA-A6-3808 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-A6-3809         TCGA-A6-3810         TCGA-A6-4105 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-A6-5656         TCGA-A6-5657         TCGA-A6-5659 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-A6-5660         TCGA-A6-5661         TCGA-A6-5662 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-A6-5664         TCGA-A6-5665         TCGA-A6-5666 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-A6-6137         TCGA-A6-6138         TCGA-A6-6141 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-A6-6142         TCGA-A6-6648         TCGA-A6-6649 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-A6-6651         TCGA-A6-6652         TCGA-A6-6653 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-A6-6654         TCGA-A6-6780         TCGA-A6-6781 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-A6-6782         TCGA-AA-3489         TCGA-AA-3492 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-3496         TCGA-AA-3502         TCGA-AA-3510 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-3511         TCGA-AA-3514         TCGA-AA-3516 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-3517         TCGA-AA-3518         TCGA-AA-3519 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-3520         TCGA-AA-3521         TCGA-AA-3522 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-3524         TCGA-AA-3525         TCGA-AA-3526 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-3527         TCGA-AA-3529         TCGA-AA-3530 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-3531         TCGA-AA-3532         TCGA-AA-3534 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-3538         TCGA-AA-3542         TCGA-AA-3543 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-3544         TCGA-AA-3548         TCGA-AA-3549 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-3552         TCGA-AA-3553         TCGA-AA-3554 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-3555         TCGA-AA-3556         TCGA-AA-3558 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-3560         TCGA-AA-3561         TCGA-AA-3562 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-3655         TCGA-AA-3660         TCGA-AA-3662 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-3664         TCGA-AA-3666         TCGA-AA-3667 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-3672         TCGA-AA-3673         TCGA-AA-3678 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-3679         TCGA-AA-3680         TCGA-AA-3681 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-3684         TCGA-AA-3685         TCGA-AA-3688 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-3692         TCGA-AA-3693         TCGA-AA-3695 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-3696         TCGA-AA-3697         TCGA-AA-3710 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-3712         TCGA-AA-3713         TCGA-AA-3715 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-3811         TCGA-AA-3812         TCGA-AA-3814 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-3815         TCGA-AA-3818         TCGA-AA-3819 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-3821         TCGA-AA-3831         TCGA-AA-3833 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-3837         TCGA-AA-3842         TCGA-AA-3844 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-3845         TCGA-AA-3846         TCGA-AA-3848 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-3850         TCGA-AA-3851         TCGA-AA-3852 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-3854         TCGA-AA-3855         TCGA-AA-3856 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-3858         TCGA-AA-3860         TCGA-AA-3861 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-3864         TCGA-AA-3866         TCGA-AA-3867 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-3869         TCGA-AA-3870         TCGA-AA-3872 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-3875         TCGA-AA-3877         TCGA-AA-3930 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-3939         TCGA-AA-3941         TCGA-AA-3947 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-3949         TCGA-AA-3950         TCGA-AA-3952 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-3955         TCGA-AA-3956         TCGA-AA-3966 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-3968         TCGA-AA-3971         TCGA-AA-3972 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-3973         TCGA-AA-3975         TCGA-AA-3976 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-3979         TCGA-AA-3980         TCGA-AA-3982 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-3984         TCGA-AA-3986         TCGA-AA-3989 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-3994         TCGA-AA-A004         TCGA-AA-A00A 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-A00D         TCGA-AA-A00E         TCGA-AA-A00F 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-A00J         TCGA-AA-A00K         TCGA-AA-A00L 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-A00N         TCGA-AA-A00O         TCGA-AA-A00Q 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-A00R         TCGA-AA-A00U         TCGA-AA-A00W 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-A00Z         TCGA-AA-A010         TCGA-AA-A017 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-A01D         TCGA-AA-A01F         TCGA-AA-A01G 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-A01I         TCGA-AA-A01K         TCGA-AA-A01P 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-A01Q         TCGA-AA-A01R         TCGA-AA-A01S 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-A01T         TCGA-AA-A01V         TCGA-AA-A01X 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-A01Z         TCGA-AA-A022         TCGA-AA-A024 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-A029         TCGA-AA-A02F         TCGA-AA-A02H 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-A02J         TCGA-AA-A02K         TCGA-AA-A02O 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-A02W         TCGA-AA-A02Y         TCGA-AA-A03F 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-A03J         TCGA-AD-5900         TCGA-AD-6548 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AD-6888         TCGA-AD-6889         TCGA-AD-6899 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AU-3779         TCGA-AU-6004         TCGA-AY-4070 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AY-4071         TCGA-AY-5543         TCGA-AY-6196 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AY-6197         TCGA-AY-6386         TCGA-AZ-4315 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AZ-4323         TCGA-AZ-4616         TCGA-AZ-4681 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AZ-4682         TCGA-AZ-5403         TCGA-AZ-5407 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AZ-6598         TCGA-AZ-6599         TCGA-AZ-6600 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AZ-6601         TCGA-AZ-6605         TCGA-AZ-6606 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AZ-6607         TCGA-AZ-6608         TCGA-CA-5254 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-CA-5255         TCGA-CA-5796         TCGA-CA-5797 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-CA-6715         TCGA-CA-6716         TCGA-CA-6717 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-CA-6718         TCGA-CA-6719         TCGA-CK-4947 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-CK-4948         TCGA-CK-4950         TCGA-CK-4952 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-CK-5912         TCGA-CK-5913         TCGA-CK-5914 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-CK-5915         TCGA-CK-5916         TCGA-CK-6746 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-CK-6747         TCGA-CK-6748         TCGA-CK-6751 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-CM-4743         TCGA-CM-4744         TCGA-CM-4746 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-CM-4747         TCGA-CM-4752         TCGA-CM-5341 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-CM-5344         TCGA-CM-5348         TCGA-CM-5349 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-CM-5860         TCGA-CM-5861         TCGA-CM-5862 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-CM-5863         TCGA-CM-5864         TCGA-CM-5868 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-CM-6161         TCGA-CM-6162         TCGA-CM-6163 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-CM-6164         TCGA-CM-6165         TCGA-CM-6166 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-CM-6167         TCGA-CM-6168         TCGA-CM-6169 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-CM-6170         TCGA-CM-6171         TCGA-CM-6172 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-CM-6674         TCGA-CM-6675         TCGA-CM-6676 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-CM-6677         TCGA-CM-6678         TCGA-CM-6679 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-CM-6680         TCGA-D5-5537         TCGA-D5-5538 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-D5-5539         TCGA-D5-5540         TCGA-D5-5541 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-D5-6529         TCGA-D5-6532         TCGA-D5-6533 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-D5-6534         TCGA-D5-6535         TCGA-D5-6536 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-D5-6537         TCGA-D5-6538         TCGA-D5-6539 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-D5-6540         TCGA-D5-6541         TCGA-D5-6898 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-D5-6920         TCGA-D5-6922         TCGA-D5-6923 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-D5-6924         TCGA-D5-6926         TCGA-D5-6927 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-D5-6928         TCGA-D5-6929         TCGA-D5-6930 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-D5-6931         TCGA-D5-6932         TCGA-D5-7000 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-DM-A0X9         TCGA-DM-A0XD         TCGA-DM-A0XF 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-DM-A1D0         TCGA-DM-A1D4         TCGA-DM-A1D6 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-DM-A1D7         TCGA-DM-A1D9         TCGA-DM-A1DA 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-DM-A1DB         TCGA-DM-A1HA         TCGA-DM-A1HB 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-DM-A282         TCGA-DM-A285         TCGA-DM-A28C 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-DM-A28E         TCGA-DM-A28F         TCGA-DM-A28G 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-DM-A28H         TCGA-DM-A28K         TCGA-F4-6459 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-F4-6460         TCGA-F4-6569         TCGA-F4-6570 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-F4-6703         TCGA-F4-6704         TCGA-F4-6805 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-F4-6806         TCGA-F4-6807         TCGA-F4-6808 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-F4-6809         TCGA-F4-6854         TCGA-F4-6855 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-F4-6856         TCGA-G4-6293         TCGA-G4-6299 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-G4-6303         TCGA-G4-6304         TCGA-G4-6306 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-G4-6307         TCGA-G4-6309         TCGA-G4-6310 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-G4-6315         TCGA-G4-6317         TCGA-G4-6321 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-G4-6323         TCGA-G4-6586         TCGA-G4-6625 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-G4-6626         TCGA-G4-6628         TCGA-AF-2687 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AF-2689         TCGA-AF-2691         TCGA-AF-2692 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AF-2693         TCGA-AF-3400         TCGA-AF-3913 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AG-3574 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AG-3575         TCGA-AG-3578         TCGA-AG-3580 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AG-3581         TCGA-AG-3582         TCGA-AG-3583 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AG-3584         TCGA-AG-3586         TCGA-AG-3587 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AG-3593         TCGA-AG-3594         TCGA-AG-3598 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AG-3599         TCGA-AG-3600         TCGA-AG-3601 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AG-3602         TCGA-AG-3605         TCGA-AG-3608 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AG-3609         TCGA-AG-3611         TCGA-AG-3612 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AG-3726         TCGA-AG-3727         TCGA-AG-3731 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AG-3732         TCGA-AG-3742         TCGA-AG-3878 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AG-3881         TCGA-AG-3882         TCGA-AG-3883 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AG-3885         TCGA-AG-3887         TCGA-AG-3890 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AG-3892         TCGA-AG-3893         TCGA-AG-3894 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AG-3896         TCGA-AG-3898         TCGA-AG-3901 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AG-3902         TCGA-AG-3909         TCGA-AG-3999 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AG-4001         TCGA-AG-4005         TCGA-AG-4007 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4015         TCGA-AG-A002 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01L 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AG-A01W         TCGA-AG-A01Y         TCGA-AG-A020 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AG-A036         TCGA-AH-6643         TCGA-CI-6619 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-CI-6620         TCGA-CI-6621         TCGA-CI-6622 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-CI-6624         TCGA-CL-5917         TCGA-CL-5918 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-DC-5337         TCGA-DC-5869         TCGA-DC-6155 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-DC-6157         TCGA-DC-6158         TCGA-DC-6160 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-DC-6681         TCGA-DC-6682         TCGA-DC-6683 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-DT-5265         TCGA-DY-A0XA         TCGA-DY-A1DC 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-DY-A1DD         TCGA-DY-A1DF         TCGA-DY-A1DG 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-DY-A1H8         TCGA-EF-5830         TCGA-EI-6506 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6510 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-F5-6464         TCGA-F5-6465         TCGA-F5-6571 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6811         TCGA-F5-6812 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-F5-6813         TCGA-G5-6235         TCGA-G5-6641 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
                    vv
clus                  T1  T2  T3  T4
  C17ORF58 MUTATED     0   0   2   1
  C17ORF58 WILD-TYPE  17  92 327  49
D1994V5, multiclass
    clus
vv   C17ORF58 MUTATED C17ORF58 WILD-TYPE
  T1                0                 17
  T2                0                 92
  T3                2                327
  T4                1                 49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  C17ORF58 MUTATED     2   0   1
  C17ORF58 WILD-TYPE 285 113  86
D1994V6, multiclass
    clus
vv   C17ORF58 MUTATED C17ORF58 WILD-TYPE
  N0                2                285
  N1                0                113
  N2                1                 86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1994V7, binary
                    cls
clus                   0   1
  C17ORF58 MUTATED     2   0
  C17ORF58 WILD-TYPE 373  65
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C17ORF58 MUTATED      2    0
  C17ORF58 WILD-TYPE  373   65
   clus
vv  C17ORF58 MUTATED C17ORF58 WILD-TYPE
  0                2                373
  1                0                 65
[1] 2 2
[1] FALSE
D1994V8, binary
                    cls
clus                   0   1
  C17ORF58 MUTATED     1   2
  C17ORF58 WILD-TYPE 224 262
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C17ORF58 MUTATED      1    2
  C17ORF58 WILD-TYPE  224  262
        clus
vv       C17ORF58 MUTATED C17ORF58 WILD-TYPE
  FEMALE                1                224
  MALE                  2                262
[1] 2 2
[1] FALSE
D1994V9, binary
                    cls
clus                   0   1
  C17ORF58 MUTATED     3   0
  C17ORF58 WILD-TYPE 347  22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C17ORF58 MUTATED      3    0
  C17ORF58 WILD-TYPE  347   22
     clus
vv    C17ORF58 MUTATED C17ORF58 WILD-TYPE
  NO                 3                347
  YES                0                 22
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  C17ORF58 MUTATED                      3                             0
  C17ORF58 WILD-TYPE                  312                            47
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  C17ORF58 MUTATED                       0                              0
  C17ORF58 WILD-TYPE                   106                             10
D1994V10, multiclass
                                clus
vv                               C17ORF58 MUTATED C17ORF58 WILD-TYPE
  COLON ADENOCARCINOMA                          3                312
  COLON MUCINOUS ADENOCARCINOMA                 0                 47
  RECTAL ADENOCARCINOMA                         0                106
  RECTAL MUCINOUS ADENOCARCINOMA                0                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  C17ORF58 MUTATED     2   0   0   0
  C17ORF58 WILD-TYPE 343   4  31  25
D1994V11, multiclass
[1] "Remove cluster labels:" "C17ORF58 MUTATED"      
clus
  C17ORF58 MUTATED C17ORF58 WILD-TYPE 
                 2                403 
        TCGA-A6-2671         TCGA-A6-2672         TCGA-A6-2674 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-A6-2676         TCGA-A6-2677         TCGA-A6-2678 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-A6-2683         TCGA-A6-3807         TCGA-A6-3808 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-A6-3809         TCGA-A6-3810         TCGA-A6-5657 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-A6-5659         TCGA-A6-5661         TCGA-A6-5665 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-A6-6781         TCGA-AA-3489         TCGA-AA-3492 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-3496         TCGA-AA-3502         TCGA-AA-3510 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-3511         TCGA-AA-3514         TCGA-AA-3517 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-3518         TCGA-AA-3519         TCGA-AA-3520 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-3521         TCGA-AA-3522         TCGA-AA-3524 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-3525         TCGA-AA-3526         TCGA-AA-3527 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-3529         TCGA-AA-3530         TCGA-AA-3531 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-3532         TCGA-AA-3534         TCGA-AA-3538 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-3542         TCGA-AA-3543         TCGA-AA-3544 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-3548         TCGA-AA-3549         TCGA-AA-3552 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-3553         TCGA-AA-3554         TCGA-AA-3555 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-3556         TCGA-AA-3558         TCGA-AA-3560 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-3561         TCGA-AA-3562         TCGA-AA-3655 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-3660         TCGA-AA-3662         TCGA-AA-3664 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-3666         TCGA-AA-3667         TCGA-AA-3672 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-3673         TCGA-AA-3678         TCGA-AA-3679 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-3680         TCGA-AA-3681         TCGA-AA-3684 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-3685         TCGA-AA-3688         TCGA-AA-3692 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-3693         TCGA-AA-3695         TCGA-AA-3696 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-3697         TCGA-AA-3710         TCGA-AA-3712 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-3713         TCGA-AA-3715         TCGA-AA-3811 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-3812         TCGA-AA-3814         TCGA-AA-3815 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-3818         TCGA-AA-3819         TCGA-AA-3821 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-3831         TCGA-AA-3833         TCGA-AA-3837 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-3842         TCGA-AA-3844         TCGA-AA-3845 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-3846         TCGA-AA-3848         TCGA-AA-3850 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-3851         TCGA-AA-3852         TCGA-AA-3854 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-3855         TCGA-AA-3856         TCGA-AA-3858 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-3860         TCGA-AA-3861         TCGA-AA-3864 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-3866         TCGA-AA-3867         TCGA-AA-3869 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-3870         TCGA-AA-3872         TCGA-AA-3875 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-3877         TCGA-AA-3930         TCGA-AA-3939 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-3941         TCGA-AA-3947         TCGA-AA-3949 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-3950         TCGA-AA-3952         TCGA-AA-3955 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-3956         TCGA-AA-3968         TCGA-AA-3971 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-3972         TCGA-AA-3973         TCGA-AA-3975 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-3976         TCGA-AA-3979         TCGA-AA-3984 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-3986         TCGA-AA-3989         TCGA-AA-3994 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-A004         TCGA-AA-A00A         TCGA-AA-A00D 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-A00E         TCGA-AA-A00F         TCGA-AA-A00J 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-A00K         TCGA-AA-A00L         TCGA-AA-A00N 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-A00O         TCGA-AA-A00Q         TCGA-AA-A00R 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-A00U         TCGA-AA-A00W         TCGA-AA-A00Z 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-A010         TCGA-AA-A017         TCGA-AA-A01D 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-A01F         TCGA-AA-A01G         TCGA-AA-A01I 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-A01K         TCGA-AA-A01P         TCGA-AA-A01Q 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-A01R         TCGA-AA-A01S         TCGA-AA-A01T 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-A01V         TCGA-AA-A01X         TCGA-AA-A01Z 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-A022         TCGA-AA-A024         TCGA-AA-A029 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-A02F         TCGA-AA-A02H         TCGA-AA-A02J 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-A02K         TCGA-AA-A02O         TCGA-AA-A02W 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AA-A02Y         TCGA-AA-A03F         TCGA-AA-A03J 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AD-5900         TCGA-AD-6548         TCGA-AD-6888 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AU-3779         TCGA-AU-6004         TCGA-AY-4070 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AY-4071         TCGA-AY-5543         TCGA-AY-6196 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AY-6197         TCGA-AY-6386         TCGA-AZ-4315 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AZ-4681         TCGA-AZ-4682         TCGA-CA-5254 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-CA-5255         TCGA-CA-5796         TCGA-CA-5797 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-CA-6715         TCGA-CA-6716         TCGA-CA-6717 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-CA-6718         TCGA-CA-6719         TCGA-CK-4947 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-CK-4948         TCGA-CK-4950         TCGA-CK-4952 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-CK-5912         TCGA-CK-5913         TCGA-CK-5914 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-CK-5915         TCGA-CK-5916         TCGA-CK-6746 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-CK-6747         TCGA-CK-6748         TCGA-CK-6751 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-CM-4743         TCGA-CM-4744         TCGA-CM-4746 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-CM-4747         TCGA-CM-4752         TCGA-CM-5341 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-CM-5344         TCGA-CM-5348         TCGA-CM-5349 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-CM-5860         TCGA-CM-5861         TCGA-CM-5862 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-CM-5863         TCGA-CM-5864         TCGA-CM-5868 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-CM-6161         TCGA-CM-6162         TCGA-CM-6163 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-CM-6164         TCGA-CM-6165         TCGA-CM-6166 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-CM-6167         TCGA-CM-6168         TCGA-CM-6169 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-CM-6170         TCGA-CM-6171         TCGA-CM-6172 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-CM-6674         TCGA-CM-6675         TCGA-CM-6676 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-CM-6677         TCGA-CM-6678         TCGA-CM-6679 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-CM-6680         TCGA-D5-5537         TCGA-D5-5538 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-D5-5539         TCGA-D5-5540         TCGA-D5-5541 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-D5-6529         TCGA-D5-6532         TCGA-D5-6533 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-D5-6534         TCGA-D5-6535         TCGA-D5-6536 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-D5-6537         TCGA-D5-6538         TCGA-D5-6539 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-D5-6540         TCGA-D5-6541         TCGA-D5-6898 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-D5-6920         TCGA-D5-6922         TCGA-D5-6923 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-D5-6924         TCGA-D5-6926         TCGA-D5-6927 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-D5-6928         TCGA-D5-6929         TCGA-D5-6930 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-D5-6931         TCGA-D5-6932         TCGA-D5-7000 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-F4-6459         TCGA-F4-6460         TCGA-F4-6569 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-F4-6570         TCGA-F4-6703         TCGA-F4-6704 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-F4-6805         TCGA-F4-6806         TCGA-F4-6807 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-F4-6808         TCGA-F4-6809         TCGA-F4-6854 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-F4-6855         TCGA-F4-6856         TCGA-G4-6293 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-G4-6299         TCGA-G4-6303         TCGA-G4-6304 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-G4-6306         TCGA-G4-6307         TCGA-G4-6309 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-G4-6310         TCGA-G4-6315         TCGA-G4-6317 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-G4-6321         TCGA-G4-6323         TCGA-G4-6586 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-G4-6625         TCGA-G4-6626         TCGA-G4-6628 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2691 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AF-2692         TCGA-AF-3400         TCGA-AF-3913 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6655 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AG-3574         TCGA-AG-3575         TCGA-AG-3578 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AG-3580         TCGA-AG-3581         TCGA-AG-3582 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AG-3583         TCGA-AG-3584         TCGA-AG-3586 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AG-3587         TCGA-AG-3593         TCGA-AG-3594 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AG-3598         TCGA-AG-3599         TCGA-AG-3600 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AG-3601         TCGA-AG-3602         TCGA-AG-3605 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AG-3608         TCGA-AG-3609         TCGA-AG-3611 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AG-3612         TCGA-AG-3726         TCGA-AG-3727 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AG-3731         TCGA-AG-3732         TCGA-AG-3742 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AG-3878         TCGA-AG-3882         TCGA-AG-3883 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AG-3885         TCGA-AG-3887         TCGA-AG-3890 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AG-3892         TCGA-AG-3893         TCGA-AG-3894 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AG-3896         TCGA-AG-3898         TCGA-AG-3901 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AG-3902         TCGA-AG-3909         TCGA-AG-3999 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AG-4001         TCGA-AG-4005         TCGA-AG-4007 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AG-4008         TCGA-AG-4015         TCGA-AG-A002 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AG-A008         TCGA-AG-A00C         TCGA-AG-A00H 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AG-A00Y         TCGA-AG-A011         TCGA-AG-A014 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AG-A015         TCGA-AG-A016         TCGA-AG-A01L 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AG-A01W         TCGA-AG-A01Y         TCGA-AG-A020 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AG-A025         TCGA-AG-A026         TCGA-AG-A02G 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AG-A02N         TCGA-AG-A02X         TCGA-AG-A032 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AG-A036         TCGA-AH-6549         TCGA-AH-6643 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-CL-5917         TCGA-CL-5918         TCGA-DC-5337 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6155         TCGA-DC-6157 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-DC-6158         TCGA-DC-6160         TCGA-DC-6681 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-DC-6682         TCGA-DC-6683         TCGA-DT-5265 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-EF-5830         TCGA-EI-6506         TCGA-EI-6507 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-EI-6508         TCGA-EI-6510         TCGA-F5-6464 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-F5-6465         TCGA-F5-6571         TCGA-F5-6702 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-G5-6235 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-G5-6641 
"C17ORF58 WILD-TYPE" 
D1994V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C17ORF58 MUTATED                                  0     0
  C17ORF58 WILD-TYPE                                1    11
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  C17ORF58 MUTATED                           0     2
  C17ORF58 WILD-TYPE                        22   224
D1994V13, multiclass
[1] "Remove cluster labels:" "C17ORF58 MUTATED"      
clus
  C17ORF58 MUTATED C17ORF58 WILD-TYPE 
                 2                258 
        TCGA-A6-2671         TCGA-A6-2672         TCGA-A6-2674 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-A6-2676         TCGA-A6-2677         TCGA-A6-2678 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-A6-2683         TCGA-A6-3807         TCGA-A6-3808 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-A6-3809         TCGA-A6-3810         TCGA-A6-4105 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-A6-5656         TCGA-A6-5657         TCGA-A6-5659 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-A6-5660         TCGA-A6-5661         TCGA-A6-5662 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-A6-5664         TCGA-A6-5665         TCGA-A6-5666 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-A6-6137         TCGA-A6-6138         TCGA-A6-6141 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-A6-6142         TCGA-A6-6648         TCGA-A6-6649 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-A6-6651         TCGA-A6-6652         TCGA-A6-6653 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-A6-6654         TCGA-A6-6780         TCGA-A6-6781 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-A6-6782         TCGA-AD-5900         TCGA-AD-6548 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AD-6888         TCGA-AD-6889         TCGA-AD-6890 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AD-6895         TCGA-AD-6899         TCGA-AD-6901 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AD-6963         TCGA-AD-6965         TCGA-AU-3779 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AU-6004         TCGA-AY-4070         TCGA-AY-4071 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AY-5543         TCGA-AY-6196         TCGA-AY-6197 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AY-6386         TCGA-AZ-4315         TCGA-AZ-4323 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AZ-4616         TCGA-AZ-4681         TCGA-AZ-4682 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AZ-5403         TCGA-AZ-5407         TCGA-AZ-6598 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AZ-6599         TCGA-AZ-6600         TCGA-AZ-6601 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AZ-6603         TCGA-AZ-6605         TCGA-AZ-6606 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AZ-6607         TCGA-AZ-6608         TCGA-CA-5254 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-CA-5255         TCGA-CA-5796         TCGA-CA-5797 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-CA-6715         TCGA-CA-6716         TCGA-CA-6717 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-CA-6718         TCGA-CA-6719         TCGA-CK-4947 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-CK-4948         TCGA-CK-4950         TCGA-CK-4952 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-CK-5912         TCGA-CK-5913         TCGA-CK-5914 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-CK-5915         TCGA-CK-5916         TCGA-CK-6746 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-CK-6747         TCGA-CK-6748         TCGA-CK-6751 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-CM-4743         TCGA-CM-4744         TCGA-CM-4746 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-CM-4747         TCGA-CM-4752         TCGA-CM-5341 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-CM-5344         TCGA-CM-5348         TCGA-CM-5349 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-CM-5860         TCGA-CM-5861         TCGA-CM-5862 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-CM-5863         TCGA-CM-5864         TCGA-CM-5868 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-CM-6161         TCGA-CM-6162         TCGA-CM-6163 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-CM-6164         TCGA-CM-6165         TCGA-CM-6166 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-CM-6167         TCGA-CM-6168         TCGA-CM-6169 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-CM-6170         TCGA-CM-6171         TCGA-CM-6172 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-CM-6674         TCGA-CM-6675         TCGA-CM-6676 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-CM-6677         TCGA-CM-6678         TCGA-CM-6679 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-CM-6680         TCGA-D5-5537         TCGA-D5-5538 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-D5-5539         TCGA-D5-5540         TCGA-D5-5541 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-D5-6529         TCGA-D5-6532         TCGA-D5-6533 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-D5-6534         TCGA-D5-6535         TCGA-D5-6536 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-D5-6537         TCGA-D5-6538         TCGA-D5-6539 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-D5-6540         TCGA-D5-6541         TCGA-D5-6898 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-D5-6920         TCGA-D5-6922         TCGA-D5-6923 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-D5-6924         TCGA-D5-6926         TCGA-D5-6927 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-D5-6928         TCGA-D5-6929         TCGA-D5-6930 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-D5-6931         TCGA-D5-6932         TCGA-D5-7000 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-DM-A0X9         TCGA-DM-A0XD         TCGA-DM-A0XF 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-DM-A1D0         TCGA-DM-A1D4         TCGA-DM-A1D6 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-DM-A1D7         TCGA-DM-A1D8         TCGA-DM-A1D9 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-DM-A1DA         TCGA-DM-A1DB         TCGA-DM-A1HA 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-DM-A1HB         TCGA-DM-A282         TCGA-DM-A285 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-DM-A28C         TCGA-DM-A28E         TCGA-DM-A28F 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-DM-A28G         TCGA-DM-A28H         TCGA-DM-A28K 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-F4-6459         TCGA-F4-6460         TCGA-F4-6569 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-F4-6570         TCGA-F4-6703         TCGA-F4-6704 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-F4-6805         TCGA-F4-6806         TCGA-F4-6807 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-F4-6808         TCGA-F4-6809         TCGA-F4-6854 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-F4-6855         TCGA-F4-6856         TCGA-G4-6293 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-G4-6299         TCGA-G4-6303         TCGA-G4-6304 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-G4-6306         TCGA-G4-6307         TCGA-G4-6309 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-G4-6310         TCGA-G4-6315         TCGA-G4-6317 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-G4-6321         TCGA-G4-6323         TCGA-G4-6586 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-G4-6625         TCGA-G4-6626         TCGA-G4-6628 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2691 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AF-2692         TCGA-AF-2693         TCGA-AF-3400 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AF-3913         TCGA-AF-4110         TCGA-AF-5654 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AF-6136         TCGA-AF-6655         TCGA-AF-6672 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6549 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-AH-6643         TCGA-AH-6644         TCGA-CI-6619 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-CI-6620         TCGA-CI-6621         TCGA-CI-6622 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-CI-6624         TCGA-CL-5917         TCGA-CL-5918 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-DC-5337         TCGA-DC-5869         TCGA-DC-6155 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-DC-6157         TCGA-DC-6158         TCGA-DC-6160 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-DC-6681         TCGA-DC-6682         TCGA-DC-6683 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-DT-5265         TCGA-DY-A0XA         TCGA-DY-A1DC 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-DY-A1DD         TCGA-DY-A1DF         TCGA-DY-A1DG 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-DY-A1H8         TCGA-EF-5830         TCGA-EI-6506 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6510 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-F5-6464         TCGA-F5-6465         TCGA-F5-6571 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6811         TCGA-F5-6812 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 
        TCGA-F5-6813         TCGA-G5-6235         TCGA-G5-6641 
"C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" "C17ORF58 WILD-TYPE" 

Clustering(1995) Variable = GORASP1 MUTATION ANALYSIS
D1995V1, survival
                   sevent
clus2                 0   1
  GORASP1 MUTATED     8   3
  GORASP1 WILD-TYPE 370  90
  GORASP1 MUTATED GORASP1 WILD-TYPE 
               11               460 
  GORASP1 MUTATED GORASP1 WILD-TYPE 
                3                90 
$`GORASP1 MUTATED`
TCGA-A6-2672 TCGA-AA-3558 TCGA-AA-A00N TCGA-AY-6197 TCGA-AZ-6608 TCGA-CA-6717 
       46.65        20.98         4.01        21.44         1.61        12.76 
TCGA-D5-6536 TCGA-D5-6540 TCGA-DM-A285 TCGA-G4-6588 TCGA-EI-6507 
       17.85        16.14         6.12        26.17        19.96 

$`GORASP1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3560 
       13.02        24.00        17.95        29.95        23.01        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07        12.20        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 
       15.12         4.80        17.13        12.49        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      135.65       139.17        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 
       61.91        36.00        22.09        13.78        35.80        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6508 
       24.13        51.48        32.61         0.49        20.55        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  GORASP1 MUTATED GORASP1 WILD-TYPE 
             1.61              0.00 
  GORASP1 MUTATED GORASP1 WILD-TYPE 
            46.65            148.01 
  GORASP1 MUTATED GORASP1 WILD-TYPE 
           17.850            20.415 
[1] "1.6 - 46.6 (17.9)"  "0.0 - 148.0 (20.4)"
[1] "hr=" "2"  
D1995V2, continuous
D1995V3, binary
                   cls
clus                  0   1
  GORASP1 MUTATED    10   1
  GORASP1 WILD-TYPE 356 118
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GORASP1 MUTATED     10    1
  GORASP1 WILD-TYPE  356  118
        clus
vv       GORASP1 MUTATED GORASP1 WILD-TYPE
  COLON               10               356
  RECTUM               1               118
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GORASP1 MUTATED         2        0        0         5         1         0
  GORASP1 WILD-TYPE      89        1       32       133         9         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GORASP1 MUTATED           0          1          1          0        1
  GORASP1 WILD-TYPE        24         10         58         42       47
                   vv
clus                STAGE IVA STAGE IVB
  GORASP1 MUTATED           0         0
  GORASP1 WILD-TYPE        18         1
D1995V4, multiclass
            clus
vv           GORASP1 MUTATED GORASP1 WILD-TYPE
  STAGE I                  2                89
  STAGE IA                 0                 1
  STAGE II                 0                32
  STAGE IIA                5               133
  STAGE IIB                1                 9
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               1                10
  STAGE IIIB               1                58
  STAGE IIIC               0                42
  STAGE IV                 1                47
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  GORASP1 MUTATED     0   3   7   1
  GORASP1 WILD-TYPE  17  89 322  49
D1995V5, multiclass
    clus
vv   GORASP1 MUTATED GORASP1 WILD-TYPE
  T1               0                17
  T2               3                89
  T3               7               322
  T4               1                49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  GORASP1 MUTATED     8   2   1
  GORASP1 WILD-TYPE 279 111  86
D1995V6, multiclass
    clus
vv   GORASP1 MUTATED GORASP1 WILD-TYPE
  N0               8               279
  N1               2               111
  N2               1                86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1995V7, binary
                   cls
clus                  0   1
  GORASP1 MUTATED     9   1
  GORASP1 WILD-TYPE 366  64
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GORASP1 MUTATED      9    1
  GORASP1 WILD-TYPE  366   64
   clus
vv  GORASP1 MUTATED GORASP1 WILD-TYPE
  0               9               366
  1               1                64
[1] 2 2
[1] FALSE
D1995V8, binary
                   cls
clus                  0   1
  GORASP1 MUTATED     4   7
  GORASP1 WILD-TYPE 221 257
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GORASP1 MUTATED      4    7
  GORASP1 WILD-TYPE  221  257
        clus
vv       GORASP1 MUTATED GORASP1 WILD-TYPE
  FEMALE               4               221
  MALE                 7               257
[1] 2 2
[1] FALSE
D1995V9, binary
                   cls
clus                  0   1
  GORASP1 MUTATED     9   0
  GORASP1 WILD-TYPE 341  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GORASP1 MUTATED      9    0
  GORASP1 WILD-TYPE  341   22
     clus
vv    GORASP1 MUTATED GORASP1 WILD-TYPE
  NO                9               341
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  GORASP1 MUTATED                      6                             4
  GORASP1 WILD-TYPE                  309                            43
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  GORASP1 MUTATED                       1                              0
  GORASP1 WILD-TYPE                   105                             10
D1995V10, multiclass
                                clus
vv                               GORASP1 MUTATED GORASP1 WILD-TYPE
  COLON ADENOCARCINOMA                         6               309
  COLON MUCINOUS ADENOCARCINOMA                4                43
  RECTAL ADENOCARCINOMA                        1               105
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  GORASP1 MUTATED     7   0   1   1
  GORASP1 WILD-TYPE 338   4  30  24
D1995V11, multiclass
    clus
vv   GORASP1 MUTATED GORASP1 WILD-TYPE
  R0               7               338
  R1               0                 4
  R2               1                30
  RX               1                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1995V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GORASP1 MUTATED                                  0     1
  GORASP1 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  GORASP1 MUTATED                           0     8
  GORASP1 WILD-TYPE                        22   218
D1995V13, multiclass
                                  clus
vv                                 GORASP1 MUTATED GORASP1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                10
  BLACK OR AFRICAN AMERICAN                      0                22
  WHITE                                          8               218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1996) Variable = RAD18 MUTATION ANALYSIS
D1996V1, survival
                 sevent
clus2               0   1
  RAD18 MUTATED    11   3
  RAD18 WILD-TYPE 367  90
  RAD18 MUTATED RAD18 WILD-TYPE 
             14             457 
  RAD18 MUTATED RAD18 WILD-TYPE 
              3              90 
$`RAD18 MUTATED`
TCGA-A6-2677 TCGA-A6-5661 TCGA-A6-5665 TCGA-A6-6653 TCGA-AA-3663 TCGA-AA-3713 
       24.33        33.53        22.06        24.39         6.97        19.04 
TCGA-AU-6004 TCGA-AZ-4315 TCGA-AZ-6603 TCGA-CA-6718 TCGA-CM-6162 TCGA-CM-6170 
       27.09        58.39        29.56        10.06        12.00        15.02 
TCGA-AG-A002 TCGA-G5-6641 
       20.98        26.43 

$`RAD18 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        42.90        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 
       31.63        30.44        29.19        23.61        22.09        32.71 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       27.09        22.52         8.38        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       21.76        24.69        23.87        20.12        19.66        20.28 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
        7.04         3.02         1.02        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       61.02        78.08         6.05        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 
       22.42        27.42        10.88         0.20        14.50        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        33.01        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
       12.10       100.01         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       12.76        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 
        5.03        15.02        15.02        17.03        15.02         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 
       55.76 

  RAD18 MUTATED RAD18 WILD-TYPE 
           6.97            0.00 
  RAD18 MUTATED RAD18 WILD-TYPE 
          58.39          148.01 
  RAD18 MUTATED RAD18 WILD-TYPE 
         23.195          20.050 
[1] "7.0 - 58.4 (23.2)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.2"
D1996V2, continuous
D1996V3, binary
                 cls
clus                0   1
  RAD18 MUTATED    13   2
  RAD18 WILD-TYPE 353 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RAD18 MUTATED     13    2
  RAD18 WILD-TYPE  353  117
        clus
vv       RAD18 MUTATED RAD18 WILD-TYPE
  COLON             13             353
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RAD18 MUTATED         4        0        1         5         0         0
  RAD18 WILD-TYPE      87        1       31       133        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RAD18 MUTATED           0          1          1          1        1         0
  RAD18 WILD-TYPE        24         10         58         41       47        18
                 vv
clus              STAGE IVB
  RAD18 MUTATED           0
  RAD18 WILD-TYPE         1
D1996V4, multiclass
            clus
vv           RAD18 MUTATED RAD18 WILD-TYPE
  STAGE I                4              87
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              5             133
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             1              10
  STAGE IIIB             1              58
  STAGE IIIC             1              41
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  RAD18 MUTATED     1   5   9   0
  RAD18 WILD-TYPE  16  87 320  50
D1996V5, multiclass
    clus
vv   RAD18 MUTATED RAD18 WILD-TYPE
  T1             1              16
  T2             5              87
  T3             9             320
  T4             0              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  RAD18 MUTATED    11   3   1
  RAD18 WILD-TYPE 276 110  86
D1996V6, multiclass
    clus
vv   RAD18 MUTATED RAD18 WILD-TYPE
  N0            11             276
  N1             3             110
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1996V7, binary
                 cls
clus                0   1
  RAD18 MUTATED    12   1
  RAD18 WILD-TYPE 363  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RAD18 MUTATED     12    1
  RAD18 WILD-TYPE  363   64
   clus
vv  RAD18 MUTATED RAD18 WILD-TYPE
  0            12             363
  1             1              64
[1] 2 2
[1] FALSE
D1996V8, binary
                 cls
clus                0   1
  RAD18 MUTATED     8   7
  RAD18 WILD-TYPE 217 257
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RAD18 MUTATED      8    7
  RAD18 WILD-TYPE  217  257
        clus
vv       RAD18 MUTATED RAD18 WILD-TYPE
  FEMALE             8             217
  MALE               7             257
[1] 2 2
[1] FALSE
D1996V9, binary
                 cls
clus                0   1
  RAD18 MUTATED    12   1
  RAD18 WILD-TYPE 338  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RAD18 MUTATED     12    1
  RAD18 WILD-TYPE  338   21
     clus
vv    RAD18 MUTATED RAD18 WILD-TYPE
  NO             12             338
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  RAD18 MUTATED                     12                             1
  RAD18 WILD-TYPE                  303                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  RAD18 MUTATED                       1                              1
  RAD18 WILD-TYPE                   105                              9
D1996V10, multiclass
                                clus
vv                               RAD18 MUTATED RAD18 WILD-TYPE
  COLON ADENOCARCINOMA                      12             303
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             1               9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  RAD18 MUTATED    11   0   1   1
  RAD18 WILD-TYPE 334   4  30  24
D1996V11, multiclass
    clus
vv   RAD18 MUTATED RAD18 WILD-TYPE
  R0            11             334
  R1             0               4
  R2             1              30
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1996V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RAD18 MUTATED                                  0     1
  RAD18 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  RAD18 MUTATED                           1     9
  RAD18 WILD-TYPE                        21   217
D1996V13, multiclass
                                  clus
vv                                 RAD18 MUTATED RAD18 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        9             217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1997) Variable = ZCWPW2 MUTATION ANALYSIS
D1997V1, survival
                  sevent
clus2                0   1
  ZCWPW2 MUTATED    13   1
  ZCWPW2 WILD-TYPE 365  92
  ZCWPW2 MUTATED ZCWPW2 WILD-TYPE 
              14              457 
  ZCWPW2 MUTATED ZCWPW2 WILD-TYPE 
               1               92 
$`ZCWPW2 MUTATED`
TCGA-A6-2683 TCGA-A6-5665 TCGA-A6-6781 TCGA-AA-3655 TCGA-AA-3966 TCGA-AA-A010 
       16.57        22.06        19.66        61.02         2.01        34.98 
TCGA-AD-6889 TCGA-AZ-4315 TCGA-CM-6172 TCGA-CM-6678 TCGA-G4-6323 TCGA-AG-3587 
       56.55        58.39        11.01        11.01        13.78        46.03 
TCGA-AG-4001 TCGA-AG-A002 
       36.03        20.98 

$`ZCWPW2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       19.99        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       21.37        15.52         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        33.01        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6674 
       14.99        12.99        13.02        15.02        14.04        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       13.05        11.08        11.08        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3593 TCGA-AG-3594 
       36.03        20.05        24.00         1.02        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4007 
       48.03        32.02        19.99        28.04        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  ZCWPW2 MUTATED ZCWPW2 WILD-TYPE 
            2.01             0.00 
  ZCWPW2 MUTATED ZCWPW2 WILD-TYPE 
           61.02           148.01 
  ZCWPW2 MUTATED ZCWPW2 WILD-TYPE 
           21.52            20.12 
[1] "2.0 - 61.0 (21.5)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "3.3"
D1997V2, continuous
D1997V3, binary
                  cls
clus                 0   1
  ZCWPW2 MUTATED    11   3
  ZCWPW2 WILD-TYPE 355 116
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZCWPW2 MUTATED     11    3
  ZCWPW2 WILD-TYPE  355  116
        clus
vv       ZCWPW2 MUTATED ZCWPW2 WILD-TYPE
  COLON              11              355
  RECTUM              3              116
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZCWPW2 MUTATED         2        1        1         5         1         0
  ZCWPW2 WILD-TYPE      89        0       31       133         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZCWPW2 MUTATED           0          0          1          1        1
  ZCWPW2 WILD-TYPE        24         11         58         41       47
                  vv
clus               STAGE IVA STAGE IVB
  ZCWPW2 MUTATED           1         0
  ZCWPW2 WILD-TYPE        17         1
D1997V4, multiclass
            clus
vv           ZCWPW2 MUTATED ZCWPW2 WILD-TYPE
  STAGE I                 2               89
  STAGE IA                1                0
  STAGE II                1               31
  STAGE IIA               5              133
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              1               58
  STAGE IIIC              1               41
  STAGE IV                1               47
  STAGE IVA               1               17
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZCWPW2 MUTATED     0   2   7   4
  ZCWPW2 WILD-TYPE  17  90 322  46
D1997V5, multiclass
    clus
vv   ZCWPW2 MUTATED ZCWPW2 WILD-TYPE
  T1              0               17
  T2              2               90
  T3              7              322
  T4              4               46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  ZCWPW2 MUTATED    11   3   0
  ZCWPW2 WILD-TYPE 276 110  87
D1997V6, multiclass
    clus
vv   ZCWPW2 MUTATED ZCWPW2 WILD-TYPE
  N0             11              276
  N1              3              110
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1997V7, binary
                  cls
clus                 0   1
  ZCWPW2 MUTATED    10   2
  ZCWPW2 WILD-TYPE 365  63
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZCWPW2 MUTATED     10    2
  ZCWPW2 WILD-TYPE  365   63
   clus
vv  ZCWPW2 MUTATED ZCWPW2 WILD-TYPE
  0             10              365
  1              2               63
[1] 2 2
[1] FALSE
D1997V8, binary
                  cls
clus                 0   1
  ZCWPW2 MUTATED     7   7
  ZCWPW2 WILD-TYPE 218 257
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZCWPW2 MUTATED      7    7
  ZCWPW2 WILD-TYPE  218  257
        clus
vv       ZCWPW2 MUTATED ZCWPW2 WILD-TYPE
  FEMALE              7              218
  MALE                7              257
[1] 2 2
[1] FALSE
D1997V9, binary
                  cls
clus                 0   1
  ZCWPW2 MUTATED    11   1
  ZCWPW2 WILD-TYPE 339  21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZCWPW2 MUTATED     11    1
  ZCWPW2 WILD-TYPE  339   21
     clus
vv    ZCWPW2 MUTATED ZCWPW2 WILD-TYPE
  NO              11              339
  YES              1               21
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ZCWPW2 MUTATED                      9                             2
  ZCWPW2 WILD-TYPE                  306                            45
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ZCWPW2 MUTATED                       3                              0
  ZCWPW2 WILD-TYPE                   103                             10
D1997V10, multiclass
                                clus
vv                               ZCWPW2 MUTATED ZCWPW2 WILD-TYPE
  COLON ADENOCARCINOMA                        9              306
  COLON MUCINOUS ADENOCARCINOMA               2               45
  RECTAL ADENOCARCINOMA                       3              103
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ZCWPW2 MUTATED    12   0   0   0
  ZCWPW2 WILD-TYPE 333   4  31  25
D1997V11, multiclass
    clus
vv   ZCWPW2 MUTATED ZCWPW2 WILD-TYPE
  R0             12              333
  R1              0                4
  R2              0               31
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1997V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZCWPW2 MUTATED                                  0     1
  ZCWPW2 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZCWPW2 MUTATED                           1     6
  ZCWPW2 WILD-TYPE                        21   220
D1997V13, multiclass
                                  clus
vv                                 ZCWPW2 MUTATED ZCWPW2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                         6              220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1998) Variable = OR5H1 MUTATION ANALYSIS
D1998V1, survival
                 sevent
clus2               0   1
  OR5H1 MUTATED     7   2
  OR5H1 WILD-TYPE 371  91
  OR5H1 MUTATED OR5H1 WILD-TYPE 
              9             462 
  OR5H1 MUTATED OR5H1 WILD-TYPE 
              2              91 
$`OR5H1 MUTATED`
TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5666 TCGA-AA-3949 TCGA-AA-A01Q TCGA-AD-6889 
       30.44        33.53        32.71        26.01         1.02        56.55 
TCGA-AZ-6598 TCGA-AZ-6600 TCGA-D5-6541 
       49.41        12.10        15.58 

$`OR5H1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       32.91        31.63        29.19        23.61        22.09        22.06 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       27.09        22.52         8.38        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        33.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
       38.07        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
        0.07        21.37        15.52         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6898 TCGA-D5-6920 
        4.80        17.13        12.49        16.14         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  OR5H1 MUTATED OR5H1 WILD-TYPE 
           1.02            0.00 
  OR5H1 MUTATED OR5H1 WILD-TYPE 
          56.55          148.01 
  OR5H1 MUTATED OR5H1 WILD-TYPE 
         30.440          20.085 
[1] "1.0 - 56.5 (30.4)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1"  
D1998V2, continuous
D1998V3, binary
                 cls
clus                0   1
  OR5H1 MUTATED    10   0
  OR5H1 WILD-TYPE 356 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR5H1 MUTATED     10    0
  OR5H1 WILD-TYPE  356  119
        clus
vv       OR5H1 MUTATED OR5H1 WILD-TYPE
  COLON             10             356
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  OR5H1 MUTATED         1        0        2         4         0         1
  OR5H1 WILD-TYPE      90        1       30       134        10         0
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  OR5H1 MUTATED           0          0          1          0        1         0
  OR5H1 WILD-TYPE        24         11         58         42       47        18
                 vv
clus              STAGE IVB
  OR5H1 MUTATED           0
  OR5H1 WILD-TYPE         1
D1998V4, multiclass
            clus
vv           OR5H1 MUTATED OR5H1 WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA              4             134
  STAGE IIB              0              10
  STAGE IIC              1               0
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             0              42
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  OR5H1 MUTATED     0   1   7   2
  OR5H1 WILD-TYPE  17  91 322  48
D1998V5, multiclass
    clus
vv   OR5H1 MUTATED OR5H1 WILD-TYPE
  T1             0              17
  T2             1              91
  T3             7             322
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  OR5H1 MUTATED     8   2   0
  OR5H1 WILD-TYPE 279 111  87
D1998V6, multiclass
    clus
vv   OR5H1 MUTATED OR5H1 WILD-TYPE
  N0             8             279
  N1             2             111
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1998V7, binary
                 cls
clus                0   1
  OR5H1 MUTATED     8   1
  OR5H1 WILD-TYPE 367  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR5H1 MUTATED      8    1
  OR5H1 WILD-TYPE  367   64
   clus
vv  OR5H1 MUTATED OR5H1 WILD-TYPE
  0             8             367
  1             1              64
[1] 2 2
[1] FALSE
D1998V8, binary
                 cls
clus                0   1
  OR5H1 MUTATED     5   5
  OR5H1 WILD-TYPE 220 259
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR5H1 MUTATED      5    5
  OR5H1 WILD-TYPE  220  259
        clus
vv       OR5H1 MUTATED OR5H1 WILD-TYPE
  FEMALE             5             220
  MALE               5             259
[1] 2 2
[1] FALSE
D1998V9, binary
                 cls
clus                0   1
  OR5H1 MUTATED     6   0
  OR5H1 WILD-TYPE 344  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR5H1 MUTATED      6    0
  OR5H1 WILD-TYPE  344   22
     clus
vv    OR5H1 MUTATED OR5H1 WILD-TYPE
  NO              6             344
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  OR5H1 MUTATED                      9                             1
  OR5H1 WILD-TYPE                  306                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  OR5H1 MUTATED                       0                              0
  OR5H1 WILD-TYPE                   106                             10
D1998V10, multiclass
                                clus
vv                               OR5H1 MUTATED OR5H1 WILD-TYPE
  COLON ADENOCARCINOMA                       9             306
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  OR5H1 MUTATED     6   0   0   0
  OR5H1 WILD-TYPE 339   4  31  25
D1998V11, multiclass
    clus
vv   OR5H1 MUTATED OR5H1 WILD-TYPE
  R0             6             339
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1998V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OR5H1 MUTATED                                  0     1
  OR5H1 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  OR5H1 MUTATED                           2     4
  OR5H1 WILD-TYPE                        20   222
D1998V13, multiclass
                                  clus
vv                                 OR5H1 MUTATED OR5H1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    2              20
  WHITE                                        4             222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(1999) Variable = MDM2 MUTATION ANALYSIS
D1999V1, survival
                sevent
clus2              0   1
  MDM2 MUTATED     4   5
  MDM2 WILD-TYPE 374  88
  MDM2 MUTATED MDM2 WILD-TYPE 
             9            462 
  MDM2 MUTATED MDM2 WILD-TYPE 
             5             88 
$`MDM2 MUTATED`
TCGA-A6-6653 TCGA-AA-A00N TCGA-AA-A010 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6608 
       24.39         4.01        34.98         6.77        12.10         1.61 
TCGA-CA-6717 TCGA-CM-5861 TCGA-DM-A1DB 
       12.76        15.02        44.32 

$`MDM2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
       25.08        25.18        24.16        21.76        24.69        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6601 TCGA-AZ-6603 
       22.36        62.79        88.21        49.41       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07        12.20        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       30.08        32.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A1HB 
       13.32        12.59       140.38         7.50       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  MDM2 MUTATED MDM2 WILD-TYPE 
          1.61           0.00 
  MDM2 MUTATED MDM2 WILD-TYPE 
         44.32         148.01 
  MDM2 MUTATED MDM2 WILD-TYPE 
        12.760         20.415 
[1] "1.6 - 44.3 (12.8)"  "0.0 - 148.0 (20.4)"
[1] "hr=" "4.3"
D1999V2, continuous
D1999V3, binary
                cls
clus               0   1
  MDM2 MUTATED     9   0
  MDM2 WILD-TYPE 357 119
[1] "tbl2"
                cls
clus             [,1] [,2]
  MDM2 MUTATED      9    0
  MDM2 WILD-TYPE  357  119
        clus
vv       MDM2 MUTATED MDM2 WILD-TYPE
  COLON             9            357
  RECTUM            0            119
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MDM2 MUTATED         2        0        0         3         2         0
  MDM2 WILD-TYPE      89        1       32       135         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MDM2 MUTATED           0          1          0          0        1         0
  MDM2 WILD-TYPE        24         10         59         42       47        18
                vv
clus             STAGE IVB
  MDM2 MUTATED           0
  MDM2 WILD-TYPE         1
D1999V4, multiclass
            clus
vv           MDM2 MUTATED MDM2 WILD-TYPE
  STAGE I               2             89
  STAGE IA              0              1
  STAGE II              0             32
  STAGE IIA             3            135
  STAGE IIB             2              8
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            1             10
  STAGE IIIB            0             59
  STAGE IIIC            0             42
  STAGE IV              1             47
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  MDM2 MUTATED     0   3   3   3
  MDM2 WILD-TYPE  17  89 326  47
D1999V5, multiclass
    clus
vv   MDM2 MUTATED MDM2 WILD-TYPE
  T1            0             17
  T2            3             89
  T3            3            326
  T4            3             47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  MDM2 MUTATED     7   2   0
  MDM2 WILD-TYPE 280 111  87
D1999V6, multiclass
    clus
vv   MDM2 MUTATED MDM2 WILD-TYPE
  N0            7            280
  N1            2            111
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1999V7, binary
                cls
clus               0   1
  MDM2 MUTATED     7   1
  MDM2 WILD-TYPE 368  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  MDM2 MUTATED      7    1
  MDM2 WILD-TYPE  368   64
   clus
vv  MDM2 MUTATED MDM2 WILD-TYPE
  0            7            368
  1            1             64
[1] 2 2
[1] FALSE
D1999V8, binary
                cls
clus               0   1
  MDM2 MUTATED     3   6
  MDM2 WILD-TYPE 222 258
[1] "tbl2"
                cls
clus             [,1] [,2]
  MDM2 MUTATED      3    6
  MDM2 WILD-TYPE  222  258
        clus
vv       MDM2 MUTATED MDM2 WILD-TYPE
  FEMALE            3            222
  MALE              6            258
[1] 2 2
[1] FALSE
D1999V9, binary
                cls
clus               0   1
  MDM2 MUTATED     6   0
  MDM2 WILD-TYPE 344  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  MDM2 MUTATED      6    0
  MDM2 WILD-TYPE  344   22
     clus
vv    MDM2 MUTATED MDM2 WILD-TYPE
  NO             6            344
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MDM2 MUTATED                      7                             2
  MDM2 WILD-TYPE                  308                            45
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MDM2 MUTATED                       0                              0
  MDM2 WILD-TYPE                   106                             10
D1999V10, multiclass
                                clus
vv                               MDM2 MUTATED MDM2 WILD-TYPE
  COLON ADENOCARCINOMA                      7            308
  COLON MUCINOUS ADENOCARCINOMA             2             45
  RECTAL ADENOCARCINOMA                     0            106
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  MDM2 MUTATED     3   0   0   1
  MDM2 WILD-TYPE 342   4  31  24
D1999V11, multiclass
    clus
vv   MDM2 MUTATED MDM2 WILD-TYPE
  R0            3            342
  R1            0              4
  R2            0             31
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1999V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MDM2 MUTATED                                  0     1
  MDM2 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  MDM2 MUTATED                           1     5
  MDM2 WILD-TYPE                        21   221
D1999V13, multiclass
                                  clus
vv                                 MDM2 MUTATED MDM2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                       5            221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2000) Variable = ROR1 MUTATION ANALYSIS
D2000V1, survival
                sevent
clus2              0   1
  ROR1 MUTATED    21   1
  ROR1 WILD-TYPE 357  92
  ROR1 MUTATED ROR1 WILD-TYPE 
            22            449 
  ROR1 MUTATED ROR1 WILD-TYPE 
             1             92 
$`ROR1 MUTATED`
TCGA-A6-2676 TCGA-AA-3502 TCGA-AA-3660 TCGA-AA-3697 TCGA-AA-3972 TCGA-AA-3977 
       42.90        35.01        78.08        85.05        50.99        25.02 
TCGA-AA-A004 TCGA-AA-A01R TCGA-AD-6963 TCGA-AU-6004 TCGA-AZ-4315 TCGA-CK-4947 
       13.94        35.01        27.42        27.09        58.39        17.56 
TCGA-CM-4743 TCGA-CM-6168 TCGA-CM-6674 TCGA-D5-5539 TCGA-D5-6540 TCGA-G4-6307 
       23.05        12.99        12.95        19.59        16.14        55.04 
TCGA-G4-6588 TCGA-AG-3892 TCGA-AG-3902 TCGA-AG-A002 
       26.17        13.02        32.02        20.98 

$`ROR1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       13.94        19.99        61.02         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
        2.01        21.99        16.08        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S 
       12.00        31.00        31.00        38.07         1.02         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6964 
       56.55         0.79         0.72         5.79        22.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
        0.20        14.50        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       14.30       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 
        9.99        21.14        82.95         1.91       124.27        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       21.99        14.99        13.02        15.02        14.04        11.01 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       45.40        12.26        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       12.49        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       44.68        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       13.78        35.80        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3909 
       17.03        35.01        14.01         1.02        48.03        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  ROR1 MUTATED ROR1 WILD-TYPE 
         12.95           0.00 
  ROR1 MUTATED ROR1 WILD-TYPE 
         85.05         148.01 
  ROR1 MUTATED ROR1 WILD-TYPE 
         26.63          20.02 
[1] "12.9 - 85.0 (26.6)" "0.0 - 148.0 (20.0)"
[1] "hr=" "5.8"
D2000V2, continuous
D2000V3, binary
                cls
clus               0   1
  ROR1 MUTATED    20   3
  ROR1 WILD-TYPE 346 116
[1] "tbl2"
                cls
clus             [,1] [,2]
  ROR1 MUTATED     20    3
  ROR1 WILD-TYPE  346  116
        clus
vv       ROR1 MUTATED ROR1 WILD-TYPE
  COLON            20            346
  RECTUM            3            116
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ROR1 MUTATED         5        0        1         8         1         0
  ROR1 WILD-TYPE      86        1       31       130         9         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ROR1 MUTATED           2          1          2          0        1         0
  ROR1 WILD-TYPE        22         10         57         42       47        18
                vv
clus             STAGE IVB
  ROR1 MUTATED           0
  ROR1 WILD-TYPE         1
D2000V4, multiclass
            clus
vv           ROR1 MUTATED ROR1 WILD-TYPE
  STAGE I               5             86
  STAGE IA              0              1
  STAGE II              1             31
  STAGE IIA             8            130
  STAGE IIB             1              9
  STAGE IIC             0              1
  STAGE III             2             22
  STAGE IIIA            1             10
  STAGE IIIB            2             57
  STAGE IIIC            0             42
  STAGE IV              1             47
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  ROR1 MUTATED     1   5  15   2
  ROR1 WILD-TYPE  16  87 314  48
D2000V5, multiclass
    clus
vv   ROR1 MUTATED ROR1 WILD-TYPE
  T1            1             16
  T2            5             87
  T3           15            314
  T4            2             48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  ROR1 MUTATED    18   4   1
  ROR1 WILD-TYPE 269 109  86
D2000V6, multiclass
    clus
vv   ROR1 MUTATED ROR1 WILD-TYPE
  N0           18            269
  N1            4            109
  N2            1             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2000V7, binary
                cls
clus               0   1
  ROR1 MUTATED    20   1
  ROR1 WILD-TYPE 355  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  ROR1 MUTATED     20    1
  ROR1 WILD-TYPE  355   64
   clus
vv  ROR1 MUTATED ROR1 WILD-TYPE
  0           20            355
  1            1             64
[1] 2 2
[1] FALSE
D2000V8, binary
                cls
clus               0   1
  ROR1 MUTATED     9  14
  ROR1 WILD-TYPE 216 250
[1] "tbl2"
                cls
clus             [,1] [,2]
  ROR1 MUTATED      9   14
  ROR1 WILD-TYPE  216  250
        clus
vv       ROR1 MUTATED ROR1 WILD-TYPE
  FEMALE            9            216
  MALE             14            250
[1] 2 2
[1] FALSE
D2000V9, binary
                cls
clus               0   1
  ROR1 MUTATED    20   1
  ROR1 WILD-TYPE 330  21
[1] "tbl2"
                cls
clus             [,1] [,2]
  ROR1 MUTATED     20    1
  ROR1 WILD-TYPE  330   21
     clus
vv    ROR1 MUTATED ROR1 WILD-TYPE
  NO            20            330
  YES            1             21
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ROR1 MUTATED                     17                             3
  ROR1 WILD-TYPE                  298                            44
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ROR1 MUTATED                       3                              0
  ROR1 WILD-TYPE                   103                             10
D2000V10, multiclass
                                clus
vv                               ROR1 MUTATED ROR1 WILD-TYPE
  COLON ADENOCARCINOMA                     17            298
  COLON MUCINOUS ADENOCARCINOMA             3             44
  RECTAL ADENOCARCINOMA                     3            103
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  ROR1 MUTATED    19   0   1   1
  ROR1 WILD-TYPE 326   4  30  24
D2000V11, multiclass
    clus
vv   ROR1 MUTATED ROR1 WILD-TYPE
  R0           19            326
  R1            0              4
  R2            1             30
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2000V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ROR1 MUTATED                                  0     0
  ROR1 WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  ROR1 MUTATED                           1    11
  ROR1 WILD-TYPE                        21   215
D2000V13, multiclass
                                  clus
vv                                 ROR1 MUTATED ROR1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                      11            215
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2001) Variable = BATF MUTATION ANALYSIS
D2001V1, survival
                sevent
clus2              0   1
  BATF MUTATED     1   2
  BATF WILD-TYPE 377  91
  BATF MUTATED BATF WILD-TYPE 
             3            468 
  BATF MUTATED BATF WILD-TYPE 
             2             91 
$`BATF MUTATED`
TCGA-AD-6888 TCGA-AZ-6601 TCGA-AG-A002 
       15.52       100.01        20.98 

$`BATF WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       21.37        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77        12.10        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  BATF MUTATED BATF WILD-TYPE 
         15.52           0.00 
  BATF MUTATED BATF WILD-TYPE 
        100.01         148.01 
  BATF MUTATED BATF WILD-TYPE 
        20.980         20.155 
[1] "15.5 - 100.0 (21.0)" "0.0 - 148.0 (20.2)" 
[1] "hr=" "2"  
D2001V2, continuous
D2001V3, binary
                cls
clus               0   1
  BATF MUTATED     2   1
  BATF WILD-TYPE 364 118
[1] "tbl2"
                cls
clus             [,1] [,2]
  BATF MUTATED      2    1
  BATF WILD-TYPE  364  118
        clus
vv       BATF MUTATED BATF WILD-TYPE
  COLON             2            364
  RECTUM            1            118
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  BATF MUTATED         1        0        1         0         0         0
  BATF WILD-TYPE      90        1       31       138        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  BATF MUTATED           0          0          1          0        0         0
  BATF WILD-TYPE        24         11         58         42       48        18
                vv
clus             STAGE IVB
  BATF MUTATED           0
  BATF WILD-TYPE         1
D2001V4, multiclass
            clus
vv           BATF MUTATED BATF WILD-TYPE
  STAGE I               1             90
  STAGE IA              0              1
  STAGE II              1             31
  STAGE IIA             0            138
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            1             58
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  BATF MUTATED     0   1   2   0
  BATF WILD-TYPE  17  91 327  50
D2001V5, multiclass
    clus
vv   BATF MUTATED BATF WILD-TYPE
  T1            0             17
  T2            1             91
  T3            2            327
  T4            0             50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  BATF MUTATED     2   1   0
  BATF WILD-TYPE 285 112  87
D2001V6, multiclass
    clus
vv   BATF MUTATED BATF WILD-TYPE
  N0            2            285
  N1            1            112
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2001V7, binary
                cls
clus               0   1
  BATF MUTATED     3   0
  BATF WILD-TYPE 372  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  BATF MUTATED      3    0
  BATF WILD-TYPE  372   65
   clus
vv  BATF MUTATED BATF WILD-TYPE
  0            3            372
  1            0             65
[1] 2 2
[1] FALSE
D2001V8, binary
                cls
clus               0   1
  BATF MUTATED     0   3
  BATF WILD-TYPE 225 261
[1] "tbl2"
                cls
clus             [,1] [,2]
  BATF MUTATED      0    3
  BATF WILD-TYPE  225  261
        clus
vv       BATF MUTATED BATF WILD-TYPE
  FEMALE            0            225
  MALE              3            261
[1] 2 2
[1] FALSE
D2001V9, binary
                cls
clus               0   1
  BATF MUTATED     3   0
  BATF WILD-TYPE 347  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  BATF MUTATED      3    0
  BATF WILD-TYPE  347   22
     clus
vv    BATF MUTATED BATF WILD-TYPE
  NO             3            347
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  BATF MUTATED                      2                             0
  BATF WILD-TYPE                  313                            47
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  BATF MUTATED                       1                              0
  BATF WILD-TYPE                   105                             10
D2001V10, multiclass
                                clus
vv                               BATF MUTATED BATF WILD-TYPE
  COLON ADENOCARCINOMA                      2            313
  COLON MUCINOUS ADENOCARCINOMA             0             47
  RECTAL ADENOCARCINOMA                     1            105
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  BATF MUTATED     2   0   0   0
  BATF WILD-TYPE 343   4  31  25
D2001V11, multiclass
[1] "Remove cluster labels:" "BATF MUTATED"          
clus
  BATF MUTATED BATF WILD-TYPE 
             2            403 
    TCGA-A6-2671     TCGA-A6-2672     TCGA-A6-2674     TCGA-A6-2676 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-A6-2677     TCGA-A6-2678     TCGA-A6-2683     TCGA-A6-3807 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-A6-3808     TCGA-A6-3809     TCGA-A6-3810     TCGA-A6-5657 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-A6-5659     TCGA-A6-5661     TCGA-A6-5665     TCGA-A6-6781 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-AA-3489     TCGA-AA-3492     TCGA-AA-3496     TCGA-AA-3502 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-AA-3510     TCGA-AA-3511     TCGA-AA-3514     TCGA-AA-3517 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-AA-3518     TCGA-AA-3519     TCGA-AA-3520     TCGA-AA-3521 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-AA-3522     TCGA-AA-3524     TCGA-AA-3525     TCGA-AA-3526 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-AA-3527     TCGA-AA-3529     TCGA-AA-3530     TCGA-AA-3531 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-AA-3532     TCGA-AA-3534     TCGA-AA-3538     TCGA-AA-3542 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-AA-3543     TCGA-AA-3544     TCGA-AA-3548     TCGA-AA-3549 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-AA-3552     TCGA-AA-3553     TCGA-AA-3554     TCGA-AA-3555 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-AA-3556     TCGA-AA-3558     TCGA-AA-3560     TCGA-AA-3561 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-AA-3562     TCGA-AA-3655     TCGA-AA-3660     TCGA-AA-3662 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-AA-3663     TCGA-AA-3664     TCGA-AA-3666     TCGA-AA-3667 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-AA-3672     TCGA-AA-3673     TCGA-AA-3678     TCGA-AA-3679 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-AA-3680     TCGA-AA-3681     TCGA-AA-3684     TCGA-AA-3685 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-AA-3688     TCGA-AA-3692     TCGA-AA-3693     TCGA-AA-3695 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-AA-3696     TCGA-AA-3697     TCGA-AA-3710     TCGA-AA-3712 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-AA-3713     TCGA-AA-3715     TCGA-AA-3811     TCGA-AA-3812 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-AA-3814     TCGA-AA-3815     TCGA-AA-3818     TCGA-AA-3819 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-AA-3821     TCGA-AA-3831     TCGA-AA-3833     TCGA-AA-3837 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-AA-3842     TCGA-AA-3844     TCGA-AA-3845     TCGA-AA-3846 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-AA-3848     TCGA-AA-3850     TCGA-AA-3851     TCGA-AA-3852 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-AA-3854     TCGA-AA-3855     TCGA-AA-3856     TCGA-AA-3858 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-AA-3860     TCGA-AA-3861     TCGA-AA-3864     TCGA-AA-3866 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-AA-3867     TCGA-AA-3869     TCGA-AA-3870     TCGA-AA-3872 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-AA-3875     TCGA-AA-3877     TCGA-AA-3930     TCGA-AA-3939 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-AA-3941     TCGA-AA-3947     TCGA-AA-3949     TCGA-AA-3950 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-AA-3952     TCGA-AA-3955     TCGA-AA-3956     TCGA-AA-3968 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-AA-3971     TCGA-AA-3972     TCGA-AA-3973     TCGA-AA-3975 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-AA-3976     TCGA-AA-3979     TCGA-AA-3984     TCGA-AA-3986 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-AA-3989     TCGA-AA-3994     TCGA-AA-A004     TCGA-AA-A00A 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-AA-A00D     TCGA-AA-A00E     TCGA-AA-A00F     TCGA-AA-A00J 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-AA-A00K     TCGA-AA-A00L     TCGA-AA-A00N     TCGA-AA-A00O 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-AA-A00Q     TCGA-AA-A00R     TCGA-AA-A00U     TCGA-AA-A00W 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-AA-A00Z     TCGA-AA-A010     TCGA-AA-A017     TCGA-AA-A01D 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-AA-A01F     TCGA-AA-A01G     TCGA-AA-A01I     TCGA-AA-A01K 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-AA-A01P     TCGA-AA-A01Q     TCGA-AA-A01R     TCGA-AA-A01S 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-AA-A01T     TCGA-AA-A01V     TCGA-AA-A01X     TCGA-AA-A01Z 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-AA-A022     TCGA-AA-A024     TCGA-AA-A029     TCGA-AA-A02F 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-AA-A02H     TCGA-AA-A02J     TCGA-AA-A02K     TCGA-AA-A02O 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-AA-A02W     TCGA-AA-A02Y     TCGA-AA-A03F     TCGA-AA-A03J 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-AD-5900     TCGA-AD-6548     TCGA-AU-3779     TCGA-AU-6004 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-AY-4070     TCGA-AY-4071     TCGA-AY-5543     TCGA-AY-6196 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-AY-6197     TCGA-AY-6386     TCGA-AZ-4315     TCGA-AZ-4681 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-AZ-4682     TCGA-CA-5254     TCGA-CA-5255     TCGA-CA-5796 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-CA-5797     TCGA-CA-6715     TCGA-CA-6716     TCGA-CA-6717 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-CA-6718     TCGA-CA-6719     TCGA-CK-4947     TCGA-CK-4948 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-CK-4950     TCGA-CK-4952     TCGA-CK-5912     TCGA-CK-5913 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-CK-5914     TCGA-CK-5915     TCGA-CK-5916     TCGA-CK-6746 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-CK-6747     TCGA-CK-6748     TCGA-CK-6751     TCGA-CM-4743 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-CM-4744     TCGA-CM-4746     TCGA-CM-4747     TCGA-CM-4752 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-CM-5341     TCGA-CM-5344     TCGA-CM-5348     TCGA-CM-5349 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-CM-5860     TCGA-CM-5861     TCGA-CM-5862     TCGA-CM-5863 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-CM-5864     TCGA-CM-5868     TCGA-CM-6161     TCGA-CM-6162 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-CM-6163     TCGA-CM-6164     TCGA-CM-6165     TCGA-CM-6166 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-CM-6167     TCGA-CM-6168     TCGA-CM-6169     TCGA-CM-6170 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-CM-6171     TCGA-CM-6172     TCGA-CM-6674     TCGA-CM-6675 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-CM-6676     TCGA-CM-6677     TCGA-CM-6678     TCGA-CM-6679 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-CM-6680     TCGA-D5-5537     TCGA-D5-5538     TCGA-D5-5539 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-D5-5540     TCGA-D5-5541     TCGA-D5-6529     TCGA-D5-6532 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-D5-6533     TCGA-D5-6534     TCGA-D5-6535     TCGA-D5-6536 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-D5-6537     TCGA-D5-6538     TCGA-D5-6539     TCGA-D5-6540 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-D5-6541     TCGA-D5-6898     TCGA-D5-6920     TCGA-D5-6922 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-D5-6923     TCGA-D5-6924     TCGA-D5-6926     TCGA-D5-6927 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-D5-6928     TCGA-D5-6929     TCGA-D5-6930     TCGA-D5-6931 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-D5-6932     TCGA-D5-7000     TCGA-F4-6459     TCGA-F4-6460 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-F4-6569     TCGA-F4-6570     TCGA-F4-6703     TCGA-F4-6704 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-F4-6805     TCGA-F4-6806     TCGA-F4-6807     TCGA-F4-6808 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-F4-6809     TCGA-F4-6854     TCGA-F4-6855     TCGA-F4-6856 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-G4-6293     TCGA-G4-6299     TCGA-G4-6303     TCGA-G4-6304 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-G4-6306     TCGA-G4-6307     TCGA-G4-6309     TCGA-G4-6310 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-G4-6315     TCGA-G4-6317     TCGA-G4-6321     TCGA-G4-6323 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-G4-6586     TCGA-G4-6588     TCGA-G4-6625     TCGA-G4-6626 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-G4-6628     TCGA-AF-2687     TCGA-AF-2689     TCGA-AF-2691 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-AF-2692     TCGA-AF-3400     TCGA-AF-3913     TCGA-AF-4110 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-AF-5654     TCGA-AF-6655     TCGA-AG-3574     TCGA-AG-3575 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-AG-3578     TCGA-AG-3580     TCGA-AG-3581     TCGA-AG-3582 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-AG-3583     TCGA-AG-3584     TCGA-AG-3586     TCGA-AG-3587 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-AG-3593     TCGA-AG-3594     TCGA-AG-3598     TCGA-AG-3599 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-AG-3600     TCGA-AG-3601     TCGA-AG-3602     TCGA-AG-3605 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-AG-3608     TCGA-AG-3609     TCGA-AG-3611     TCGA-AG-3612 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-AG-3726     TCGA-AG-3727     TCGA-AG-3731     TCGA-AG-3732 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-AG-3742     TCGA-AG-3878     TCGA-AG-3882     TCGA-AG-3883 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-AG-3885     TCGA-AG-3887     TCGA-AG-3890     TCGA-AG-3892 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-AG-3893     TCGA-AG-3894     TCGA-AG-3896     TCGA-AG-3898 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-AG-3901     TCGA-AG-3902     TCGA-AG-3909     TCGA-AG-3999 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-AG-4001     TCGA-AG-4005     TCGA-AG-4007     TCGA-AG-4008 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-AG-4015     TCGA-AG-A008     TCGA-AG-A00C     TCGA-AG-A00H 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-AG-A00Y     TCGA-AG-A011     TCGA-AG-A014     TCGA-AG-A015 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-AG-A016     TCGA-AG-A01L     TCGA-AG-A01W     TCGA-AG-A01Y 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-AG-A020     TCGA-AG-A025     TCGA-AG-A026     TCGA-AG-A02G 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-AG-A02N     TCGA-AG-A02X     TCGA-AG-A032     TCGA-AG-A036 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-AH-6549     TCGA-AH-6643     TCGA-CL-5917     TCGA-CL-5918 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-DC-5337     TCGA-DC-5869     TCGA-DC-6155     TCGA-DC-6157 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-DC-6158     TCGA-DC-6160     TCGA-DC-6681     TCGA-DC-6682 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-DC-6683     TCGA-DT-5265     TCGA-EF-5830     TCGA-EI-6506 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-EI-6507     TCGA-EI-6508     TCGA-EI-6510     TCGA-F5-6464 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-F5-6465     TCGA-F5-6571     TCGA-F5-6702     TCGA-F5-6812 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-F5-6813     TCGA-G5-6235     TCGA-G5-6641 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
D2001V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  BATF MUTATED                                  0     0
  BATF WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  BATF MUTATED                           0     2
  BATF WILD-TYPE                        22   224
D2001V13, multiclass
[1] "Remove cluster labels:" "BATF MUTATED"          
clus
  BATF MUTATED BATF WILD-TYPE 
             2            258 
    TCGA-A6-2671     TCGA-A6-2672     TCGA-A6-2674     TCGA-A6-2676 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-A6-2677     TCGA-A6-2678     TCGA-A6-2683     TCGA-A6-3807 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-A6-3808     TCGA-A6-3809     TCGA-A6-3810     TCGA-A6-4105 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-A6-5656     TCGA-A6-5657     TCGA-A6-5659     TCGA-A6-5660 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-A6-5661     TCGA-A6-5662     TCGA-A6-5664     TCGA-A6-5665 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-A6-5666     TCGA-A6-6137     TCGA-A6-6138     TCGA-A6-6141 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-A6-6142     TCGA-A6-6648     TCGA-A6-6649     TCGA-A6-6651 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-A6-6652     TCGA-A6-6653     TCGA-A6-6654     TCGA-A6-6780 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-A6-6781     TCGA-A6-6782     TCGA-AD-5900     TCGA-AD-6548 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-AD-6889     TCGA-AD-6890     TCGA-AD-6895     TCGA-AD-6899 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-AD-6901     TCGA-AD-6963     TCGA-AD-6964     TCGA-AD-6965 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-AU-3779     TCGA-AU-6004     TCGA-AY-4070     TCGA-AY-4071 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-AY-5543     TCGA-AY-6196     TCGA-AY-6197     TCGA-AY-6386 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-AZ-4315     TCGA-AZ-4323     TCGA-AZ-4616     TCGA-AZ-4681 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-AZ-4682     TCGA-AZ-5403     TCGA-AZ-5407     TCGA-AZ-6598 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-AZ-6599     TCGA-AZ-6600     TCGA-AZ-6603     TCGA-AZ-6605 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-AZ-6606     TCGA-AZ-6607     TCGA-AZ-6608     TCGA-CA-5254 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-CA-5255     TCGA-CA-5796     TCGA-CA-5797     TCGA-CA-6715 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-CA-6716     TCGA-CA-6717     TCGA-CA-6718     TCGA-CA-6719 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-CK-4947     TCGA-CK-4948     TCGA-CK-4950     TCGA-CK-4952 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-CK-5912     TCGA-CK-5913     TCGA-CK-5914     TCGA-CK-5915 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-CK-5916     TCGA-CK-6746     TCGA-CK-6747     TCGA-CK-6748 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-CK-6751     TCGA-CM-4743     TCGA-CM-4744     TCGA-CM-4746 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-CM-4747     TCGA-CM-4752     TCGA-CM-5341     TCGA-CM-5344 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-CM-5348     TCGA-CM-5349     TCGA-CM-5860     TCGA-CM-5861 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-CM-5862     TCGA-CM-5863     TCGA-CM-5864     TCGA-CM-5868 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-CM-6161     TCGA-CM-6162     TCGA-CM-6163     TCGA-CM-6164 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-CM-6165     TCGA-CM-6166     TCGA-CM-6167     TCGA-CM-6168 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-CM-6169     TCGA-CM-6170     TCGA-CM-6171     TCGA-CM-6172 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-CM-6674     TCGA-CM-6675     TCGA-CM-6676     TCGA-CM-6677 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-CM-6678     TCGA-CM-6679     TCGA-CM-6680     TCGA-D5-5537 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-D5-5538     TCGA-D5-5539     TCGA-D5-5540     TCGA-D5-5541 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-D5-6529     TCGA-D5-6532     TCGA-D5-6533     TCGA-D5-6534 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-D5-6535     TCGA-D5-6536     TCGA-D5-6537     TCGA-D5-6538 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-D5-6539     TCGA-D5-6540     TCGA-D5-6541     TCGA-D5-6898 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-D5-6920     TCGA-D5-6922     TCGA-D5-6923     TCGA-D5-6924 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-D5-6926     TCGA-D5-6927     TCGA-D5-6928     TCGA-D5-6929 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-D5-6930     TCGA-D5-6931     TCGA-D5-6932     TCGA-D5-7000 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-DM-A0X9     TCGA-DM-A0XD     TCGA-DM-A0XF     TCGA-DM-A1D0 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-DM-A1D4     TCGA-DM-A1D6     TCGA-DM-A1D7     TCGA-DM-A1D8 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-DM-A1D9     TCGA-DM-A1DA     TCGA-DM-A1DB     TCGA-DM-A1HA 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-DM-A1HB     TCGA-DM-A282     TCGA-DM-A285     TCGA-DM-A28C 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-DM-A28E     TCGA-DM-A28F     TCGA-DM-A28G     TCGA-DM-A28H 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-DM-A28K     TCGA-F4-6459     TCGA-F4-6460     TCGA-F4-6569 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-F4-6570     TCGA-F4-6703     TCGA-F4-6704     TCGA-F4-6805 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-F4-6806     TCGA-F4-6807     TCGA-F4-6808     TCGA-F4-6809 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-F4-6854     TCGA-F4-6855     TCGA-F4-6856     TCGA-G4-6293 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-G4-6299     TCGA-G4-6303     TCGA-G4-6304     TCGA-G4-6306 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-G4-6307     TCGA-G4-6309     TCGA-G4-6310     TCGA-G4-6315 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-G4-6317     TCGA-G4-6321     TCGA-G4-6323     TCGA-G4-6586 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-G4-6588     TCGA-G4-6625     TCGA-G4-6626     TCGA-G4-6628 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-AF-2687     TCGA-AF-2689     TCGA-AF-2691     TCGA-AF-2692 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-AF-2693     TCGA-AF-3400     TCGA-AF-3913     TCGA-AF-4110 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-AF-5654     TCGA-AF-6136     TCGA-AF-6655     TCGA-AF-6672 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-AH-6544     TCGA-AH-6547     TCGA-AH-6549     TCGA-AH-6643 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-AH-6644     TCGA-CI-6619     TCGA-CI-6620     TCGA-CI-6621 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-CI-6622     TCGA-CI-6624     TCGA-CL-5917     TCGA-CL-5918 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-DC-5337     TCGA-DC-5869     TCGA-DC-6155     TCGA-DC-6157 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-DC-6158     TCGA-DC-6160     TCGA-DC-6681     TCGA-DC-6682 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-DC-6683     TCGA-DT-5265     TCGA-DY-A0XA     TCGA-DY-A1DC 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-DY-A1DD     TCGA-DY-A1DF     TCGA-DY-A1DG     TCGA-DY-A1H8 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-EF-5830     TCGA-EI-6506     TCGA-EI-6507     TCGA-EI-6508 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-EI-6510     TCGA-F5-6464     TCGA-F5-6465     TCGA-F5-6571 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-F5-6702     TCGA-F5-6811     TCGA-F5-6812     TCGA-F5-6813 
"BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" "BATF WILD-TYPE" 
    TCGA-G5-6235     TCGA-G5-6641 
"BATF WILD-TYPE" "BATF WILD-TYPE" 

Clustering(2002) Variable = RNASE2 MUTATION ANALYSIS
D2002V1, survival
                  sevent
clus2                0   1
  RNASE2 MUTATED     5   0
  RNASE2 WILD-TYPE 373  93
  RNASE2 MUTATED RNASE2 WILD-TYPE 
               5              466 
  RNASE2 MUTATED RNASE2 WILD-TYPE 
               0               93 
$`RNASE2 MUTATED`
TCGA-AA-3510 TCGA-AA-A01Q TCGA-AD-6895 TCGA-AG-A002 TCGA-EI-6506 
       63.98         1.02         0.72        20.98        20.55 

$`RNASE2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01R TCGA-AA-A01S 
       12.00        31.00        31.00        38.07        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
       56.55         0.79         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6507 TCGA-EI-6508 
       24.13        51.48        32.61         0.49        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  RNASE2 MUTATED RNASE2 WILD-TYPE 
            0.72             0.00 
  RNASE2 MUTATED RNASE2 WILD-TYPE 
           63.98           148.01 
  RNASE2 MUTATED RNASE2 WILD-TYPE 
          20.550           20.155 
[1] "0.7 - 64.0 (20.6)"  "0.0 - 148.0 (20.2)"
[1] "hr="     "3300000"
D2002V2, continuous
D2002V3, binary
                  cls
clus                 0   1
  RNASE2 MUTATED     3   2
  RNASE2 WILD-TYPE 363 117
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNASE2 MUTATED      3    2
  RNASE2 WILD-TYPE  363  117
        clus
vv       RNASE2 MUTATED RNASE2 WILD-TYPE
  COLON               3              363
  RECTUM              2              117
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RNASE2 MUTATED         1        0        2         1         0         0
  RNASE2 WILD-TYPE      90        1       30       137        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RNASE2 MUTATED           0          0          0          0        0
  RNASE2 WILD-TYPE        24         11         59         42       48
                  vv
clus               STAGE IVA STAGE IVB
  RNASE2 MUTATED           0         0
  RNASE2 WILD-TYPE        18         1
D2002V4, multiclass
            clus
vv           RNASE2 MUTATED RNASE2 WILD-TYPE
  STAGE I                 1               90
  STAGE IA                0                1
  STAGE II                2               30
  STAGE IIA               1              137
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              0               59
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  RNASE2 MUTATED     0   1   4   0
  RNASE2 WILD-TYPE  17  91 325  50
D2002V5, multiclass
    clus
vv   RNASE2 MUTATED RNASE2 WILD-TYPE
  T1              0               17
  T2              1               91
  T3              4              325
  T4              0               50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  RNASE2 MUTATED     4   1   0
  RNASE2 WILD-TYPE 283 112  87
D2002V6, multiclass
    clus
vv   RNASE2 MUTATED RNASE2 WILD-TYPE
  N0              4              283
  N1              1              112
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2002V7, binary
                  cls
clus                 0   1
  RNASE2 MUTATED     4   0
  RNASE2 WILD-TYPE 371  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNASE2 MUTATED      4    0
  RNASE2 WILD-TYPE  371   65
   clus
vv  RNASE2 MUTATED RNASE2 WILD-TYPE
  0              4              371
  1              0               65
[1] 2 2
[1] FALSE
D2002V8, binary
                  cls
clus                 0   1
  RNASE2 MUTATED     2   3
  RNASE2 WILD-TYPE 223 261
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNASE2 MUTATED      2    3
  RNASE2 WILD-TYPE  223  261
        clus
vv       RNASE2 MUTATED RNASE2 WILD-TYPE
  FEMALE              2              223
  MALE                3              261
[1] 2 2
[1] FALSE
D2002V9, binary
                  cls
clus                 0   1
  RNASE2 MUTATED     3   0
  RNASE2 WILD-TYPE 347  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNASE2 MUTATED      3    0
  RNASE2 WILD-TYPE  347   22
     clus
vv    RNASE2 MUTATED RNASE2 WILD-TYPE
  NO               3              347
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  RNASE2 MUTATED                      3                             0
  RNASE2 WILD-TYPE                  312                            47
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  RNASE2 MUTATED                       2                              0
  RNASE2 WILD-TYPE                   104                             10
D2002V10, multiclass
                                clus
vv                               RNASE2 MUTATED RNASE2 WILD-TYPE
  COLON ADENOCARCINOMA                        3              312
  COLON MUCINOUS ADENOCARCINOMA               0               47
  RECTAL ADENOCARCINOMA                       2              104
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  RNASE2 MUTATED     4   0   0   0
  RNASE2 WILD-TYPE 341   4  31  25
D2002V11, multiclass
    clus
vv   RNASE2 MUTATED RNASE2 WILD-TYPE
  R0              4              341
  R1              0                4
  R2              0               31
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2002V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RNASE2 MUTATED                                  0     0
  RNASE2 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  RNASE2 MUTATED                           0     2
  RNASE2 WILD-TYPE                        22   224
D2002V13, multiclass
[1] "Remove cluster labels:" "RNASE2 MUTATED"        
clus
  RNASE2 MUTATED RNASE2 WILD-TYPE 
               2              258 
      TCGA-A6-2671       TCGA-A6-2672       TCGA-A6-2674       TCGA-A6-2676 
"RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" 
      TCGA-A6-2677       TCGA-A6-2678       TCGA-A6-2683       TCGA-A6-3807 
"RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" 
      TCGA-A6-3808       TCGA-A6-3809       TCGA-A6-3810       TCGA-A6-4105 
"RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" 
      TCGA-A6-5656       TCGA-A6-5657       TCGA-A6-5659       TCGA-A6-5660 
"RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" 
      TCGA-A6-5661       TCGA-A6-5662       TCGA-A6-5664       TCGA-A6-5665 
"RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" 
      TCGA-A6-5666       TCGA-A6-6137       TCGA-A6-6138       TCGA-A6-6141 
"RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" 
      TCGA-A6-6142       TCGA-A6-6648       TCGA-A6-6649       TCGA-A6-6651 
"RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" 
      TCGA-A6-6652       TCGA-A6-6653       TCGA-A6-6654       TCGA-A6-6780 
"RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" 
      TCGA-A6-6781       TCGA-A6-6782       TCGA-AD-5900       TCGA-AD-6548 
"RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" 
      TCGA-AD-6888       TCGA-AD-6889       TCGA-AD-6890       TCGA-AD-6899 
"RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" 
      TCGA-AD-6901       TCGA-AD-6963       TCGA-AD-6964       TCGA-AD-6965 
"RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" 
      TCGA-AU-3779       TCGA-AU-6004       TCGA-AY-4070       TCGA-AY-4071 
"RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" 
      TCGA-AY-5543       TCGA-AY-6196       TCGA-AY-6197       TCGA-AY-6386 
"RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" 
      TCGA-AZ-4315       TCGA-AZ-4323       TCGA-AZ-4616       TCGA-AZ-4681 
"RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" 
      TCGA-AZ-4682       TCGA-AZ-5403       TCGA-AZ-5407       TCGA-AZ-6598 
"RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" 
      TCGA-AZ-6599       TCGA-AZ-6600       TCGA-AZ-6601       TCGA-AZ-6603 
"RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" 
      TCGA-AZ-6605       TCGA-AZ-6606       TCGA-AZ-6607       TCGA-AZ-6608 
"RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" 
      TCGA-CA-5254       TCGA-CA-5255       TCGA-CA-5796       TCGA-CA-5797 
"RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" 
      TCGA-CA-6715       TCGA-CA-6716       TCGA-CA-6717       TCGA-CA-6718 
"RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" 
      TCGA-CA-6719       TCGA-CK-4947       TCGA-CK-4948       TCGA-CK-4950 
"RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" 
      TCGA-CK-4952       TCGA-CK-5912       TCGA-CK-5913       TCGA-CK-5914 
"RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" 
      TCGA-CK-5915       TCGA-CK-5916       TCGA-CK-6746       TCGA-CK-6747 
"RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" 
      TCGA-CK-6748       TCGA-CK-6751       TCGA-CM-4743       TCGA-CM-4744 
"RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" 
      TCGA-CM-4746       TCGA-CM-4747       TCGA-CM-4752       TCGA-CM-5341 
"RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" 
      TCGA-CM-5344       TCGA-CM-5348       TCGA-CM-5349       TCGA-CM-5860 
"RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" 
      TCGA-CM-5861       TCGA-CM-5862       TCGA-CM-5863       TCGA-CM-5864 
"RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" 
      TCGA-CM-5868       TCGA-CM-6161       TCGA-CM-6162       TCGA-CM-6163 
"RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" 
      TCGA-CM-6164       TCGA-CM-6165       TCGA-CM-6166       TCGA-CM-6167 
"RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" 
      TCGA-CM-6168       TCGA-CM-6169       TCGA-CM-6170       TCGA-CM-6171 
"RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" 
      TCGA-CM-6172       TCGA-CM-6674       TCGA-CM-6675       TCGA-CM-6676 
"RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" 
      TCGA-CM-6677       TCGA-CM-6678       TCGA-CM-6679       TCGA-CM-6680 
"RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" 
      TCGA-D5-5537       TCGA-D5-5538       TCGA-D5-5539       TCGA-D5-5540 
"RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" 
      TCGA-D5-5541       TCGA-D5-6529       TCGA-D5-6532       TCGA-D5-6533 
"RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" 
      TCGA-D5-6534       TCGA-D5-6535       TCGA-D5-6536       TCGA-D5-6537 
"RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" 
      TCGA-D5-6538       TCGA-D5-6539       TCGA-D5-6540       TCGA-D5-6541 
"RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" 
      TCGA-D5-6898       TCGA-D5-6920       TCGA-D5-6922       TCGA-D5-6923 
"RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" 
      TCGA-D5-6924       TCGA-D5-6926       TCGA-D5-6927       TCGA-D5-6928 
"RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" 
      TCGA-D5-6929       TCGA-D5-6930       TCGA-D5-6931       TCGA-D5-6932 
"RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" 
      TCGA-D5-7000       TCGA-DM-A0X9       TCGA-DM-A0XD       TCGA-DM-A0XF 
"RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" 
      TCGA-DM-A1D0       TCGA-DM-A1D4       TCGA-DM-A1D6       TCGA-DM-A1D7 
"RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" 
      TCGA-DM-A1D8       TCGA-DM-A1D9       TCGA-DM-A1DA       TCGA-DM-A1DB 
"RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" 
      TCGA-DM-A1HA       TCGA-DM-A1HB       TCGA-DM-A282       TCGA-DM-A285 
"RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" 
      TCGA-DM-A28C       TCGA-DM-A28E       TCGA-DM-A28F       TCGA-DM-A28G 
"RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" 
      TCGA-DM-A28H       TCGA-DM-A28K       TCGA-F4-6459       TCGA-F4-6460 
"RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" 
      TCGA-F4-6569       TCGA-F4-6570       TCGA-F4-6703       TCGA-F4-6704 
"RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" 
      TCGA-F4-6805       TCGA-F4-6806       TCGA-F4-6807       TCGA-F4-6808 
"RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" 
      TCGA-F4-6809       TCGA-F4-6854       TCGA-F4-6855       TCGA-F4-6856 
"RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" 
      TCGA-G4-6293       TCGA-G4-6299       TCGA-G4-6303       TCGA-G4-6304 
"RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" 
      TCGA-G4-6306       TCGA-G4-6307       TCGA-G4-6309       TCGA-G4-6310 
"RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" 
      TCGA-G4-6315       TCGA-G4-6317       TCGA-G4-6321       TCGA-G4-6323 
"RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" 
      TCGA-G4-6586       TCGA-G4-6588       TCGA-G4-6625       TCGA-G4-6626 
"RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" 
      TCGA-G4-6628       TCGA-AF-2687       TCGA-AF-2689       TCGA-AF-2691 
"RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" 
      TCGA-AF-2692       TCGA-AF-2693       TCGA-AF-3400       TCGA-AF-3913 
"RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" 
      TCGA-AF-4110       TCGA-AF-5654       TCGA-AF-6136       TCGA-AF-6655 
"RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" 
      TCGA-AF-6672       TCGA-AH-6544       TCGA-AH-6547       TCGA-AH-6549 
"RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" 
      TCGA-AH-6643       TCGA-AH-6644       TCGA-CI-6619       TCGA-CI-6620 
"RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" 
      TCGA-CI-6621       TCGA-CI-6622       TCGA-CI-6624       TCGA-CL-5917 
"RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" 
      TCGA-CL-5918       TCGA-DC-5337       TCGA-DC-5869       TCGA-DC-6155 
"RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" 
      TCGA-DC-6157       TCGA-DC-6158       TCGA-DC-6160       TCGA-DC-6681 
"RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" 
      TCGA-DC-6682       TCGA-DC-6683       TCGA-DT-5265       TCGA-DY-A0XA 
"RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" 
      TCGA-DY-A1DC       TCGA-DY-A1DD       TCGA-DY-A1DF       TCGA-DY-A1DG 
"RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" 
      TCGA-DY-A1H8       TCGA-EF-5830       TCGA-EI-6507       TCGA-EI-6508 
"RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" 
      TCGA-EI-6510       TCGA-F5-6464       TCGA-F5-6465       TCGA-F5-6571 
"RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" 
      TCGA-F5-6702       TCGA-F5-6811       TCGA-F5-6812       TCGA-F5-6813 
"RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" 
      TCGA-G5-6235       TCGA-G5-6641 
"RNASE2 WILD-TYPE" "RNASE2 WILD-TYPE" 

Clustering(2003) Variable = TRIO MUTATION ANALYSIS
D2003V1, survival
                sevent
clus2              0   1
  TRIO MUTATED    25   6
  TRIO WILD-TYPE 353  87
  TRIO MUTATED TRIO WILD-TYPE 
            31            440 
  TRIO MUTATED TRIO WILD-TYPE 
             6             87 
$`TRIO MUTATED`
TCGA-AA-3510 TCGA-AA-3525 TCGA-AA-3681 TCGA-AA-3710 TCGA-AA-3850 TCGA-AA-3864 
       63.98         8.05         5.98        26.99         0.00        53.00 
TCGA-AA-3949 TCGA-AA-3968 TCGA-AA-A010 TCGA-AA-A01Q TCGA-AA-A02Y TCGA-AD-6889 
       26.01        21.99        34.98         1.02        39.98        56.55 
TCGA-AU-6004 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4952 
       27.09        58.39        49.41        12.76        10.06        15.62 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-5348 TCGA-CM-6167 TCGA-CM-6171 
      124.27        23.05        37.02        22.98        14.99        14.04 
TCGA-DM-A1D9 TCGA-F4-6460 TCGA-F4-6570 TCGA-G4-6299 TCGA-G4-6626 TCGA-AF-6655 
      140.38        31.96         6.18        74.56        46.75        20.02 
TCGA-AG-A002 
       20.98 

$`TRIO WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3526 
        1.02         9.07        24.03        37.05        36.03        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       15.02        11.01        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       85.05        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 
       37.02        14.93         0.00        17.03        10.06        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       30.05        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3950 
       31.00         2.01        12.99        24.00        33.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3972 
        2.01        20.98        34.03         2.01        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       31.00        38.07        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A03F TCGA-AA-A03J 
        5.03        14.01         0.92        41.00        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
        0.07        21.37        15.52         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 
       22.42        27.42        10.88         0.20        14.50        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        33.01        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 
      106.75        22.36        62.79        88.21         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 
       14.30        17.56       148.01        85.45        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CM-4744 TCGA-CM-4747 
        9.99        21.14        82.95         1.91        20.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       13.02        29.06        22.03        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6168 TCGA-CM-6169 
        2.96        29.03        16.04        21.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       15.02        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A1DB 
       92.75        49.91        13.32        12.59         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6569 
       35.97        60.79       117.07        98.24         8.61        35.74 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6303 
       13.25         0.53        47.41        35.31       133.18        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6672 
       34.49        10.39        14.50        16.83        15.39        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  TRIO MUTATED TRIO WILD-TYPE 
             0              0 
  TRIO MUTATED TRIO WILD-TYPE 
        140.38         148.01 
  TRIO MUTATED TRIO WILD-TYPE 
         26.01          19.99 
[1] "0.0 - 140.4 (26.0)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.4"
D2003V2, continuous
D2003V3, binary
                cls
clus               0   1
  TRIO MUTATED    30   2
  TRIO WILD-TYPE 336 117
[1] "tbl2"
                cls
clus             [,1] [,2]
  TRIO MUTATED     30    2
  TRIO WILD-TYPE  336  117
        clus
vv       TRIO MUTATED TRIO WILD-TYPE
  COLON            30            336
  RECTUM            2            117
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TRIO MUTATED         8        0        4         9         1         0
  TRIO WILD-TYPE      83        1       28       129         9         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TRIO MUTATED           2          1          4          3        0         0
  TRIO WILD-TYPE        22         10         55         39       48        18
                vv
clus             STAGE IVB
  TRIO MUTATED           0
  TRIO WILD-TYPE         1
D2003V4, multiclass
            clus
vv           TRIO MUTATED TRIO WILD-TYPE
  STAGE I               8             83
  STAGE IA              0              1
  STAGE II              4             28
  STAGE IIA             9            129
  STAGE IIB             1              9
  STAGE IIC             0              1
  STAGE III             2             22
  STAGE IIIA            1             10
  STAGE IIIB            4             55
  STAGE IIIC            3             39
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  TRIO MUTATED     0   9  21   2
  TRIO WILD-TYPE  17  83 308  48
D2003V5, multiclass
    clus
vv   TRIO MUTATED TRIO WILD-TYPE
  T1            0             17
  T2            9             83
  T3           21            308
  T4            2             48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  TRIO MUTATED    22   6   4
  TRIO WILD-TYPE 265 107  83
D2003V6, multiclass
    clus
vv   TRIO MUTATED TRIO WILD-TYPE
  N0           22            265
  N1            6            107
  N2            4             83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2003V7, binary
                cls
clus               0   1
  TRIO MUTATED    30   0
  TRIO WILD-TYPE 345  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  TRIO MUTATED     30    0
  TRIO WILD-TYPE  345   65
   clus
vv  TRIO MUTATED TRIO WILD-TYPE
  0           30            345
  1            0             65
[1] 2 2
[1] FALSE
D2003V8, binary
                cls
clus               0   1
  TRIO MUTATED    15  17
  TRIO WILD-TYPE 210 247
[1] "tbl2"
                cls
clus             [,1] [,2]
  TRIO MUTATED     15   17
  TRIO WILD-TYPE  210  247
        clus
vv       TRIO MUTATED TRIO WILD-TYPE
  FEMALE           15            210
  MALE             17            247
[1] 2 2
[1] FALSE
D2003V9, binary
                cls
clus               0   1
  TRIO MUTATED    25   0
  TRIO WILD-TYPE 325  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  TRIO MUTATED     25    0
  TRIO WILD-TYPE  325   22
     clus
vv    TRIO MUTATED TRIO WILD-TYPE
  NO            25            325
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  TRIO MUTATED                     26                             4
  TRIO WILD-TYPE                  289                            43
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  TRIO MUTATED                       2                              0
  TRIO WILD-TYPE                   104                             10
D2003V10, multiclass
                                clus
vv                               TRIO MUTATED TRIO WILD-TYPE
  COLON ADENOCARCINOMA                     26            289
  COLON MUCINOUS ADENOCARCINOMA             4             43
  RECTAL ADENOCARCINOMA                     2            104
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  TRIO MUTATED    25   0   0   4
  TRIO WILD-TYPE 320   4  31  21
D2003V11, multiclass
    clus
vv   TRIO MUTATED TRIO WILD-TYPE
  R0           25            320
  R1            0              4
  R2            0             31
  RX            4             21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2003V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TRIO MUTATED                                  0     3
  TRIO WILD-TYPE                                1     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  TRIO MUTATED                           2    14
  TRIO WILD-TYPE                        20   212
D2003V13, multiclass
                                  clus
vv                                 TRIO MUTATED TRIO WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       3              8
  BLACK OR AFRICAN AMERICAN                   2             20
  WHITE                                      14            212
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2004) Variable = CTSL1 MUTATION ANALYSIS
D2004V1, survival
                 sevent
clus2               0   1
  CTSL1 MUTATED     5   3
  CTSL1 WILD-TYPE 373  90
  CTSL1 MUTATED CTSL1 WILD-TYPE 
              8             463 
  CTSL1 MUTATED CTSL1 WILD-TYPE 
              3              90 
$`CTSL1 MUTATED`
TCGA-AA-3715 TCGA-AA-A00N TCGA-CK-4948 TCGA-DM-A0XD TCGA-DM-A28E TCGA-G4-6588 
       19.04         4.01       148.01        24.43       119.93        26.17 
TCGA-AG-A002 TCGA-AH-6547 
       20.98         1.45 

$`CTSL1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 
       12.20        12.76        10.06        14.30        17.56        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
        6.12        81.37        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       22.09        13.78        35.80        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6549 TCGA-AH-6643 
       41.00        38.04       117.11        38.56        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  CTSL1 MUTATED CTSL1 WILD-TYPE 
           1.45            0.00 
  CTSL1 MUTATED CTSL1 WILD-TYPE 
         148.01          140.38 
  CTSL1 MUTATED CTSL1 WILD-TYPE 
         22.705          20.120 
[1] "1.4 - 148.0 (22.7)" "0.0 - 140.4 (20.1)"
[1] "hr=" "1.4"
D2004V2, continuous
D2004V3, binary
                 cls
clus                0   1
  CTSL1 MUTATED     6   2
  CTSL1 WILD-TYPE 360 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CTSL1 MUTATED      6    2
  CTSL1 WILD-TYPE  360  117
        clus
vv       CTSL1 MUTATED CTSL1 WILD-TYPE
  COLON              6             360
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CTSL1 MUTATED         1        0        1         3         1         0
  CTSL1 WILD-TYPE      90        1       31       135         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CTSL1 MUTATED           1          0          0          0        0         0
  CTSL1 WILD-TYPE        23         11         59         42       48        18
                 vv
clus              STAGE IVB
  CTSL1 MUTATED           0
  CTSL1 WILD-TYPE         1
D2004V4, multiclass
            clus
vv           CTSL1 MUTATED CTSL1 WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              3             135
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CTSL1 MUTATED     0   1   6   1
  CTSL1 WILD-TYPE  17  91 323  49
D2004V5, multiclass
    clus
vv   CTSL1 MUTATED CTSL1 WILD-TYPE
  T1             0              17
  T2             1              91
  T3             6             323
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  CTSL1 MUTATED     7   1   0
  CTSL1 WILD-TYPE 280 112  87
D2004V6, multiclass
    clus
vv   CTSL1 MUTATED CTSL1 WILD-TYPE
  N0             7             280
  N1             1             112
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2004V7, binary
                 cls
clus                0   1
  CTSL1 MUTATED     7   0
  CTSL1 WILD-TYPE 368  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CTSL1 MUTATED      7    0
  CTSL1 WILD-TYPE  368   65
   clus
vv  CTSL1 MUTATED CTSL1 WILD-TYPE
  0             7             368
  1             0              65
[1] 2 2
[1] FALSE
D2004V8, binary
                 cls
clus                0   1
  CTSL1 MUTATED     4   4
  CTSL1 WILD-TYPE 221 260
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CTSL1 MUTATED      4    4
  CTSL1 WILD-TYPE  221  260
        clus
vv       CTSL1 MUTATED CTSL1 WILD-TYPE
  FEMALE             4             221
  MALE               4             260
[1] 2 2
[1] FALSE
D2004V9, binary
                 cls
clus                0   1
  CTSL1 MUTATED     4   0
  CTSL1 WILD-TYPE 346  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CTSL1 MUTATED      4    0
  CTSL1 WILD-TYPE  346   22
     clus
vv    CTSL1 MUTATED CTSL1 WILD-TYPE
  NO              4             346
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CTSL1 MUTATED                      5                             1
  CTSL1 WILD-TYPE                  310                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CTSL1 MUTATED                       2                              0
  CTSL1 WILD-TYPE                   104                             10
D2004V10, multiclass
                                clus
vv                               CTSL1 MUTATED CTSL1 WILD-TYPE
  COLON ADENOCARCINOMA                       5             310
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  CTSL1 MUTATED     5   0   0   0
  CTSL1 WILD-TYPE 340   4  31  25
D2004V11, multiclass
    clus
vv   CTSL1 MUTATED CTSL1 WILD-TYPE
  R0             5             340
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2004V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CTSL1 MUTATED                                  0     0
  CTSL1 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CTSL1 MUTATED                           0     5
  CTSL1 WILD-TYPE                        22   221
D2004V13, multiclass
                                  clus
vv                                 CTSL1 MUTATED CTSL1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        5             221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2005) Variable = KIF5B MUTATION ANALYSIS
D2005V1, survival
                 sevent
clus2               0   1
  KIF5B MUTATED    13   3
  KIF5B WILD-TYPE 365  90
  KIF5B MUTATED KIF5B WILD-TYPE 
             16             455 
  KIF5B MUTATED KIF5B WILD-TYPE 
              3              90 
$`KIF5B MUTATED`
TCGA-A6-6781 TCGA-AA-3663 TCGA-AA-3864 TCGA-AA-3977 TCGA-AA-A00N TCGA-AD-6889 
       19.66         6.97        53.00        25.02         4.01        56.55 
TCGA-CA-6718 TCGA-CM-6161 TCGA-CM-6171 TCGA-CM-6674 TCGA-D5-6537 TCGA-G4-6310 
       10.06        15.02        14.04        12.95         4.80        63.62 
TCGA-G4-6317 TCGA-AG-A002 TCGA-AG-A025 TCGA-EI-6510 
       36.00        20.98        49.97        18.28 

$`KIF5B WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 
        0.99        31.07        31.07        30.05        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
        0.07        21.37        15.52         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07        12.20        12.76        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       17.03        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6675 
       14.99        12.99        13.02        15.02        11.01        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6539 
        1.32        43.27        15.12        17.85        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6321 TCGA-G4-6323 
       44.68        55.04        85.48        61.91        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       10.98         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       19.96        20.91         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  KIF5B MUTATED KIF5B WILD-TYPE 
           4.01            0.00 
  KIF5B MUTATED KIF5B WILD-TYPE 
          63.62          148.01 
  KIF5B MUTATED KIF5B WILD-TYPE 
          18.97           20.28 
[1] "4.0 - 63.6 (19.0)"  "0.0 - 148.0 (20.3)"
[1] "hr=" "1.1"
D2005V2, continuous
D2005V3, binary
                 cls
clus                0   1
  KIF5B MUTATED    14   3
  KIF5B WILD-TYPE 352 116
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KIF5B MUTATED     14    3
  KIF5B WILD-TYPE  352  116
        clus
vv       KIF5B MUTATED KIF5B WILD-TYPE
  COLON             14             352
  RECTUM             3             116
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KIF5B MUTATED         4        0        3         3         1         0
  KIF5B WILD-TYPE      87        1       29       135         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  KIF5B MUTATED           0          0          2          2        0         1
  KIF5B WILD-TYPE        24         11         57         40       48        17
                 vv
clus              STAGE IVB
  KIF5B MUTATED           0
  KIF5B WILD-TYPE         1
D2005V4, multiclass
            clus
vv           KIF5B MUTATED KIF5B WILD-TYPE
  STAGE I                4              87
  STAGE IA               0               1
  STAGE II               3              29
  STAGE IIA              3             135
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             2              57
  STAGE IIIC             2              40
  STAGE IV               0              48
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  KIF5B MUTATED     1   5   8   3
  KIF5B WILD-TYPE  16  87 321  47
D2005V5, multiclass
    clus
vv   KIF5B MUTATED KIF5B WILD-TYPE
  T1             1              16
  T2             5              87
  T3             8             321
  T4             3              47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  KIF5B MUTATED    13   3   1
  KIF5B WILD-TYPE 274 110  86
D2005V6, multiclass
    clus
vv   KIF5B MUTATED KIF5B WILD-TYPE
  N0            13             274
  N1             3             110
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2005V7, binary
                 cls
clus                0   1
  KIF5B MUTATED    12   0
  KIF5B WILD-TYPE 363  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KIF5B MUTATED     12    0
  KIF5B WILD-TYPE  363   65
   clus
vv  KIF5B MUTATED KIF5B WILD-TYPE
  0            12             363
  1             0              65
[1] 2 2
[1] FALSE
D2005V8, binary
                 cls
clus                0   1
  KIF5B MUTATED     6  11
  KIF5B WILD-TYPE 219 253
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KIF5B MUTATED      6   11
  KIF5B WILD-TYPE  219  253
        clus
vv       KIF5B MUTATED KIF5B WILD-TYPE
  FEMALE             6             219
  MALE              11             253
[1] 2 2
[1] FALSE
D2005V9, binary
                 cls
clus                0   1
  KIF5B MUTATED    12   1
  KIF5B WILD-TYPE 338  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KIF5B MUTATED     12    1
  KIF5B WILD-TYPE  338   21
     clus
vv    KIF5B MUTATED KIF5B WILD-TYPE
  NO             12             338
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  KIF5B MUTATED                     12                             2
  KIF5B WILD-TYPE                  303                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  KIF5B MUTATED                       3                              0
  KIF5B WILD-TYPE                   103                             10
D2005V10, multiclass
                                clus
vv                               KIF5B MUTATED KIF5B WILD-TYPE
  COLON ADENOCARCINOMA                      12             303
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      3             103
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  KIF5B MUTATED    14   0   0   1
  KIF5B WILD-TYPE 331   4  31  24
D2005V11, multiclass
    clus
vv   KIF5B MUTATED KIF5B WILD-TYPE
  R0            14             331
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2005V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KIF5B MUTATED                                  0     2
  KIF5B WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  KIF5B MUTATED                           0     8
  KIF5B WILD-TYPE                        22   218
D2005V13, multiclass
                                  clus
vv                                 KIF5B MUTATED KIF5B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               9
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        8             218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2006) Variable = TMEM41B MUTATION ANALYSIS
D2006V1, survival
                   sevent
clus2                 0   1
  TMEM41B MUTATED     5   0
  TMEM41B WILD-TYPE 373  93
  TMEM41B MUTATED TMEM41B WILD-TYPE 
                5               466 
  TMEM41B MUTATED TMEM41B WILD-TYPE 
                0                93 
$`TMEM41B MUTATED`
TCGA-AA-3543 TCGA-AY-6197 TCGA-CM-6162 TCGA-CM-6164 TCGA-AG-A002 
        0.99        21.44        12.00        29.03        20.98 

$`TMEM41B WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       29.00        26.01        12.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        33.01        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
       15.02         2.96        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  TMEM41B MUTATED TMEM41B WILD-TYPE 
             0.99              0.00 
  TMEM41B MUTATED TMEM41B WILD-TYPE 
            29.03            148.01 
  TMEM41B MUTATED TMEM41B WILD-TYPE 
           20.980            20.155 
[1] "1.0 - 29.0 (21.0)"  "0.0 - 148.0 (20.2)"
[1] "hr="     "3300000"
D2006V2, continuous
D2006V3, binary
                   cls
clus                  0   1
  TMEM41B MUTATED     4   1
  TMEM41B WILD-TYPE 362 118
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM41B MUTATED      4    1
  TMEM41B WILD-TYPE  362  118
        clus
vv       TMEM41B MUTATED TMEM41B WILD-TYPE
  COLON                4               362
  RECTUM               1               118
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TMEM41B MUTATED         2        0        0         2         0         0
  TMEM41B WILD-TYPE      89        1       32       136        10         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TMEM41B MUTATED           0          0          1          0        0
  TMEM41B WILD-TYPE        24         11         58         42       48
                   vv
clus                STAGE IVA STAGE IVB
  TMEM41B MUTATED           0         0
  TMEM41B WILD-TYPE        18         1
D2006V4, multiclass
            clus
vv           TMEM41B MUTATED TMEM41B WILD-TYPE
  STAGE I                  2                89
  STAGE IA                 0                 1
  STAGE II                 0                32
  STAGE IIA                2               136
  STAGE IIB                0                10
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               0                11
  STAGE IIIB               1                58
  STAGE IIIC               0                42
  STAGE IV                 0                48
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  TMEM41B MUTATED     0   2   3   0
  TMEM41B WILD-TYPE  17  90 326  50
D2006V5, multiclass
    clus
vv   TMEM41B MUTATED TMEM41B WILD-TYPE
  T1               0                17
  T2               2                90
  T3               3               326
  T4               0                50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  TMEM41B MUTATED     4   1   0
  TMEM41B WILD-TYPE 283 112  87
D2006V6, multiclass
    clus
vv   TMEM41B MUTATED TMEM41B WILD-TYPE
  N0               4               283
  N1               1               112
  N2               0                87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2006V7, binary
                   cls
clus                  0   1
  TMEM41B MUTATED     4   0
  TMEM41B WILD-TYPE 371  65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM41B MUTATED      4    0
  TMEM41B WILD-TYPE  371   65
   clus
vv  TMEM41B MUTATED TMEM41B WILD-TYPE
  0               4               371
  1               0                65
[1] 2 2
[1] FALSE
D2006V8, binary
                   cls
clus                  0   1
  TMEM41B MUTATED     2   3
  TMEM41B WILD-TYPE 223 261
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM41B MUTATED      2    3
  TMEM41B WILD-TYPE  223  261
        clus
vv       TMEM41B MUTATED TMEM41B WILD-TYPE
  FEMALE               2               223
  MALE                 3               261
[1] 2 2
[1] FALSE
D2006V9, binary
                   cls
clus                  0   1
  TMEM41B MUTATED     5   0
  TMEM41B WILD-TYPE 345  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMEM41B MUTATED      5    0
  TMEM41B WILD-TYPE  345   22
     clus
vv    TMEM41B MUTATED TMEM41B WILD-TYPE
  NO                5               345
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  TMEM41B MUTATED                      2                             2
  TMEM41B WILD-TYPE                  313                            45
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  TMEM41B MUTATED                       1                              0
  TMEM41B WILD-TYPE                   105                             10
D2006V10, multiclass
                                clus
vv                               TMEM41B MUTATED TMEM41B WILD-TYPE
  COLON ADENOCARCINOMA                         2               313
  COLON MUCINOUS ADENOCARCINOMA                2                45
  RECTAL ADENOCARCINOMA                        1               105
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  TMEM41B MUTATED     5   0   0   0
  TMEM41B WILD-TYPE 340   4  31  25
D2006V11, multiclass
    clus
vv   TMEM41B MUTATED TMEM41B WILD-TYPE
  R0               5               340
  R1               0                 4
  R2               0                31
  RX               0                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2006V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TMEM41B MUTATED                                  0     0
  TMEM41B WILD-TYPE                                1    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  TMEM41B MUTATED                           0     3
  TMEM41B WILD-TYPE                        22   223
D2006V13, multiclass
                                  clus
vv                                 TMEM41B MUTATED TMEM41B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                      0                22
  WHITE                                          3               223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2007) Variable = NUDT16L1 MUTATION ANALYSIS
D2007V1, survival
                    sevent
clus2                  0   1
  NUDT16L1 MUTATED     3   0
  NUDT16L1 WILD-TYPE 375  93
  NUDT16L1 MUTATED NUDT16L1 WILD-TYPE 
                 3                468 
  NUDT16L1 MUTATED NUDT16L1 WILD-TYPE 
                 0                 93 
$`NUDT16L1 MUTATED`
TCGA-AA-A01R TCGA-CK-6747 TCGA-CM-6674 
       35.01        82.95        12.95 

$`NUDT16L1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       21.14         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  NUDT16L1 MUTATED NUDT16L1 WILD-TYPE 
             12.95               0.00 
  NUDT16L1 MUTATED NUDT16L1 WILD-TYPE 
             82.95             148.01 
  NUDT16L1 MUTATED NUDT16L1 WILD-TYPE 
            35.010             20.155 
[1] "12.9 - 83.0 (35.0)" "0.0 - 148.0 (20.2)"
[1] "hr="     "3300000"
D2007V2, continuous
D2007V3, binary
                    cls
clus                   0   1
  NUDT16L1 MUTATED     3   0
  NUDT16L1 WILD-TYPE 363 119
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  NUDT16L1 MUTATED      3    0
  NUDT16L1 WILD-TYPE  363  119
        clus
vv       NUDT16L1 MUTATED NUDT16L1 WILD-TYPE
  COLON                 3                363
  RECTUM                0                119
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NUDT16L1 MUTATED         0        0        0         2         0         0
  NUDT16L1 WILD-TYPE      91        1       32       136        10         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NUDT16L1 MUTATED           1          0          0          0        0
  NUDT16L1 WILD-TYPE        23         11         59         42       48
                    vv
clus                 STAGE IVA STAGE IVB
  NUDT16L1 MUTATED           0         0
  NUDT16L1 WILD-TYPE        18         1
D2007V4, multiclass
            clus
vv           NUDT16L1 MUTATED NUDT16L1 WILD-TYPE
  STAGE I                   0                 91
  STAGE IA                  0                  1
  STAGE II                  0                 32
  STAGE IIA                 2                136
  STAGE IIB                 0                 10
  STAGE IIC                 0                  1
  STAGE III                 1                 23
  STAGE IIIA                0                 11
  STAGE IIIB                0                 59
  STAGE IIIC                0                 42
  STAGE IV                  0                 48
  STAGE IVA                 0                 18
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  NUDT16L1 MUTATED     0   0   3   0
  NUDT16L1 WILD-TYPE  17  92 326  50
D2007V5, multiclass
    clus
vv   NUDT16L1 MUTATED NUDT16L1 WILD-TYPE
  T1                0                 17
  T2                0                 92
  T3                3                326
  T4                0                 50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  NUDT16L1 MUTATED     2   0   1
  NUDT16L1 WILD-TYPE 285 113  86
D2007V6, multiclass
    clus
vv   NUDT16L1 MUTATED NUDT16L1 WILD-TYPE
  N0                2                285
  N1                0                113
  N2                1                 86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2007V7, binary
                    cls
clus                   0   1
  NUDT16L1 MUTATED     2   0
  NUDT16L1 WILD-TYPE 373  65
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  NUDT16L1 MUTATED      2    0
  NUDT16L1 WILD-TYPE  373   65
   clus
vv  NUDT16L1 MUTATED NUDT16L1 WILD-TYPE
  0                2                373
  1                0                 65
[1] 2 2
[1] FALSE
D2007V8, binary
                    cls
clus                   0   1
  NUDT16L1 MUTATED     1   2
  NUDT16L1 WILD-TYPE 224 262
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  NUDT16L1 MUTATED      1    2
  NUDT16L1 WILD-TYPE  224  262
        clus
vv       NUDT16L1 MUTATED NUDT16L1 WILD-TYPE
  FEMALE                1                224
  MALE                  2                262
[1] 2 2
[1] FALSE
D2007V9, binary
                    cls
clus                   0   1
  NUDT16L1 MUTATED     2   1
  NUDT16L1 WILD-TYPE 348  21
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  NUDT16L1 MUTATED      2    1
  NUDT16L1 WILD-TYPE  348   21
     clus
vv    NUDT16L1 MUTATED NUDT16L1 WILD-TYPE
  NO                 2                348
  YES                1                 21
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  NUDT16L1 MUTATED                      2                             1
  NUDT16L1 WILD-TYPE                  313                            46
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  NUDT16L1 MUTATED                       0                              0
  NUDT16L1 WILD-TYPE                   106                             10
D2007V10, multiclass
                                clus
vv                               NUDT16L1 MUTATED NUDT16L1 WILD-TYPE
  COLON ADENOCARCINOMA                          2                313
  COLON MUCINOUS ADENOCARCINOMA                 1                 46
  RECTAL ADENOCARCINOMA                         0                106
  RECTAL MUCINOUS ADENOCARCINOMA                0                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  NUDT16L1 MUTATED     2   0   0   1
  NUDT16L1 WILD-TYPE 343   4  31  24
D2007V11, multiclass
    clus
vv   NUDT16L1 MUTATED NUDT16L1 WILD-TYPE
  R0                2                343
  R1                0                  4
  R2                0                 31
  RX                1                 24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2007V12, continuous
[1] "Remove cluster labels:" "NUDT16L1 MUTATED"      
clus
  NUDT16L1 MUTATED NUDT16L1 WILD-TYPE 
                 2                456 
        TCGA-A6-2671         TCGA-A6-2672         TCGA-A6-2674 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-A6-2676         TCGA-A6-2677         TCGA-A6-2678 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-A6-2683         TCGA-A6-3807         TCGA-A6-3808 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-A6-3809         TCGA-A6-3810         TCGA-A6-4105 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-A6-5656         TCGA-A6-5657         TCGA-A6-5659 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-A6-5660         TCGA-A6-5661         TCGA-A6-5662 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-A6-5664         TCGA-A6-5665         TCGA-A6-5666 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-A6-6137         TCGA-A6-6138         TCGA-A6-6141 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-A6-6142         TCGA-A6-6648         TCGA-A6-6649 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-A6-6651         TCGA-A6-6652         TCGA-A6-6653 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-A6-6654         TCGA-A6-6780         TCGA-A6-6781 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-A6-6782         TCGA-AA-3489         TCGA-AA-3492 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-3496         TCGA-AA-3502         TCGA-AA-3510 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-3511         TCGA-AA-3514         TCGA-AA-3516 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-3517         TCGA-AA-3518         TCGA-AA-3519 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-3520         TCGA-AA-3521         TCGA-AA-3522 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-3524         TCGA-AA-3525         TCGA-AA-3526 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-3527         TCGA-AA-3529         TCGA-AA-3530 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-3531         TCGA-AA-3532         TCGA-AA-3534 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-3538         TCGA-AA-3542         TCGA-AA-3543 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-3544         TCGA-AA-3548         TCGA-AA-3549 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-3552         TCGA-AA-3553         TCGA-AA-3554 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-3555         TCGA-AA-3556         TCGA-AA-3558 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-3560         TCGA-AA-3562         TCGA-AA-3655 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-3660         TCGA-AA-3662         TCGA-AA-3663 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-3664         TCGA-AA-3666         TCGA-AA-3667 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-3672         TCGA-AA-3673         TCGA-AA-3678 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-3679         TCGA-AA-3680         TCGA-AA-3681 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-3684         TCGA-AA-3685         TCGA-AA-3688 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-3692         TCGA-AA-3693         TCGA-AA-3695 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-3696         TCGA-AA-3697         TCGA-AA-3710 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-3712         TCGA-AA-3713         TCGA-AA-3715 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-3811         TCGA-AA-3812         TCGA-AA-3814 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-3815         TCGA-AA-3818         TCGA-AA-3819 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-3821         TCGA-AA-3831         TCGA-AA-3833 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-3837         TCGA-AA-3842         TCGA-AA-3844 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-3845         TCGA-AA-3846         TCGA-AA-3848 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-3850         TCGA-AA-3851         TCGA-AA-3852 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-3854         TCGA-AA-3855         TCGA-AA-3856 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-3858         TCGA-AA-3860         TCGA-AA-3861 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-3864         TCGA-AA-3866         TCGA-AA-3867 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-3869         TCGA-AA-3870         TCGA-AA-3872 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-3875         TCGA-AA-3877         TCGA-AA-3930 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-3939         TCGA-AA-3941         TCGA-AA-3947 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-3949         TCGA-AA-3950         TCGA-AA-3952 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-3955         TCGA-AA-3956         TCGA-AA-3966 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-3968         TCGA-AA-3971         TCGA-AA-3972 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-3973         TCGA-AA-3975         TCGA-AA-3976 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-3977         TCGA-AA-3979         TCGA-AA-3980 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-3982         TCGA-AA-3984         TCGA-AA-3986 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-3989         TCGA-AA-3994         TCGA-AA-A004 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-A00A         TCGA-AA-A00D         TCGA-AA-A00E 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-A00F         TCGA-AA-A00J         TCGA-AA-A00K 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-A00L         TCGA-AA-A00N         TCGA-AA-A00O 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-A00Q         TCGA-AA-A00R         TCGA-AA-A00U 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-A00W         TCGA-AA-A00Z         TCGA-AA-A010 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-A017         TCGA-AA-A01D         TCGA-AA-A01F 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-A01G         TCGA-AA-A01I         TCGA-AA-A01K 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-A01P         TCGA-AA-A01Q         TCGA-AA-A01S 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-A01T         TCGA-AA-A01V         TCGA-AA-A01X 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-A01Z         TCGA-AA-A022         TCGA-AA-A024 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-A029         TCGA-AA-A02F         TCGA-AA-A02H 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-A02J         TCGA-AA-A02K         TCGA-AA-A02O 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-A02W         TCGA-AA-A02Y         TCGA-AA-A03F 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AA-A03J         TCGA-AD-5900         TCGA-AD-6548 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AD-6888         TCGA-AD-6889         TCGA-AD-6890 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AD-6895         TCGA-AD-6899         TCGA-AD-6901 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AD-6963         TCGA-AD-6964         TCGA-AD-6965 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AU-3779         TCGA-AU-6004         TCGA-AY-4070 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AY-4071         TCGA-AY-5543         TCGA-AY-6196 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AY-6197         TCGA-AY-6386         TCGA-AZ-4323 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AZ-4616         TCGA-AZ-4682         TCGA-AZ-5403 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AZ-5407         TCGA-AZ-6598         TCGA-AZ-6599 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AZ-6600         TCGA-AZ-6601         TCGA-AZ-6603 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AZ-6605         TCGA-AZ-6606         TCGA-AZ-6607 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AZ-6608         TCGA-CK-4947         TCGA-CK-4948 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-CK-4950         TCGA-CK-4952         TCGA-CM-4743 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-CM-4744         TCGA-CM-4746         TCGA-CM-4747 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-CM-4752         TCGA-CM-5341         TCGA-CM-5344 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-CM-5348         TCGA-CM-5349         TCGA-CM-5860 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-CM-5861         TCGA-CM-5862         TCGA-CM-5863 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-CM-5864         TCGA-CM-5868         TCGA-CM-6161 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-CM-6162         TCGA-CM-6163         TCGA-CM-6164 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-CM-6165         TCGA-CM-6166         TCGA-CM-6167 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-CM-6168         TCGA-CM-6169         TCGA-CM-6170 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-CM-6171         TCGA-CM-6172         TCGA-CM-6675 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-CM-6676         TCGA-CM-6677         TCGA-CM-6678 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-CM-6679         TCGA-CM-6680         TCGA-D5-5537 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-D5-5538         TCGA-D5-5539         TCGA-D5-5540 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-D5-5541         TCGA-D5-6529         TCGA-D5-6532 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-D5-6533         TCGA-D5-6534         TCGA-D5-6535 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-D5-6536         TCGA-D5-6537         TCGA-D5-6538 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-D5-6539         TCGA-D5-6540         TCGA-D5-6541 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-D5-6898         TCGA-D5-6920         TCGA-D5-6922 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-D5-6923         TCGA-D5-6924         TCGA-D5-6926 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-D5-6927         TCGA-D5-6928         TCGA-D5-6929 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-D5-6930         TCGA-D5-6931         TCGA-D5-6932 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-D5-7000         TCGA-DM-A0X9         TCGA-DM-A0XD 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-DM-A0XF         TCGA-DM-A1D0         TCGA-DM-A1D4 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-DM-A1D6         TCGA-DM-A1D7         TCGA-DM-A1D8 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-DM-A1D9         TCGA-DM-A1DA         TCGA-DM-A1DB 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-DM-A1HA         TCGA-DM-A1HB         TCGA-DM-A282 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-DM-A285         TCGA-DM-A28C         TCGA-DM-A28E 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-DM-A28F         TCGA-DM-A28G         TCGA-DM-A28H 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-DM-A28K         TCGA-F4-6459         TCGA-F4-6460 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-F4-6569         TCGA-F4-6570         TCGA-F4-6703 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-F4-6704         TCGA-F4-6806         TCGA-F4-6807 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-F4-6808         TCGA-F4-6809         TCGA-F4-6854 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-F4-6855         TCGA-F4-6856         TCGA-G4-6293 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-G4-6299         TCGA-G4-6303         TCGA-G4-6304 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-G4-6306         TCGA-G4-6307         TCGA-G4-6309 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-G4-6310         TCGA-G4-6315         TCGA-G4-6317 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-G4-6321         TCGA-G4-6323         TCGA-G4-6586 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-G4-6588         TCGA-G4-6625         TCGA-G4-6626 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-G4-6628         TCGA-AF-2687         TCGA-AF-2689 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3913         TCGA-AF-4110 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AF-5654         TCGA-AF-6136         TCGA-AF-6655 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AF-6672         TCGA-AG-3574         TCGA-AG-3575 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AG-3578         TCGA-AG-3580         TCGA-AG-3581 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3584 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AG-3586         TCGA-AG-3587         TCGA-AG-3593 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AG-3594         TCGA-AG-3598         TCGA-AG-3599 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AG-3600         TCGA-AG-3601         TCGA-AG-3602 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AG-3605         TCGA-AG-3608         TCGA-AG-3609 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AG-3611         TCGA-AG-3612         TCGA-AG-3726 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AG-3727         TCGA-AG-3731         TCGA-AG-3732 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AG-3742         TCGA-AG-3878         TCGA-AG-3881 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AG-3882         TCGA-AG-3883         TCGA-AG-3885 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AG-3887         TCGA-AG-3890         TCGA-AG-3892 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3896 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AG-3898         TCGA-AG-3901         TCGA-AG-3902 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AG-3909         TCGA-AG-3999         TCGA-AG-4001 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AG-4005         TCGA-AG-4007         TCGA-AG-4008 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AG-4015         TCGA-AG-A002         TCGA-AG-A008 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AG-A00C         TCGA-AG-A00H         TCGA-AG-A00Y 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AG-A011         TCGA-AG-A014         TCGA-AG-A015 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AG-A016         TCGA-AG-A01L         TCGA-AG-A01W 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AG-A01Y         TCGA-AG-A020         TCGA-AG-A025 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AG-A026         TCGA-AG-A02G         TCGA-AG-A02N 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AG-A02X         TCGA-AG-A032         TCGA-AG-A036 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6643 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AH-6644         TCGA-CI-6622         TCGA-DC-5337 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-DC-5869         TCGA-DC-6155         TCGA-DC-6157 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-DC-6158         TCGA-DC-6160         TCGA-DC-6681 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-DC-6682         TCGA-DC-6683         TCGA-DY-A0XA 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DF 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-DY-A1DG         TCGA-DY-A1H8         TCGA-EI-6506 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6510 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-F5-6464         TCGA-F5-6465         TCGA-F5-6571 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6811         TCGA-F5-6812 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-F5-6813         TCGA-G5-6235         TCGA-G5-6641 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NUDT16L1 MUTATED                                  0     0
  NUDT16L1 WILD-TYPE                                1    11
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  NUDT16L1 MUTATED                           0     2
  NUDT16L1 WILD-TYPE                        22   224
D2007V13, multiclass
[1] "Remove cluster labels:" "NUDT16L1 MUTATED"      
clus
  NUDT16L1 MUTATED NUDT16L1 WILD-TYPE 
                 2                258 
        TCGA-A6-2671         TCGA-A6-2672         TCGA-A6-2674 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-A6-2676         TCGA-A6-2677         TCGA-A6-2678 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-A6-2683         TCGA-A6-3807         TCGA-A6-3808 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-A6-3809         TCGA-A6-3810         TCGA-A6-4105 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-A6-5656         TCGA-A6-5657         TCGA-A6-5659 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-A6-5660         TCGA-A6-5661         TCGA-A6-5662 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-A6-5664         TCGA-A6-5665         TCGA-A6-5666 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-A6-6137         TCGA-A6-6138         TCGA-A6-6141 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-A6-6142         TCGA-A6-6648         TCGA-A6-6649 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-A6-6651         TCGA-A6-6652         TCGA-A6-6653 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-A6-6654         TCGA-A6-6780         TCGA-A6-6781 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-A6-6782         TCGA-AD-5900         TCGA-AD-6548 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AD-6888         TCGA-AD-6889         TCGA-AD-6890 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AD-6895         TCGA-AD-6899         TCGA-AD-6901 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AD-6963         TCGA-AD-6964         TCGA-AD-6965 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AU-3779         TCGA-AU-6004         TCGA-AY-4070 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AY-4071         TCGA-AY-5543         TCGA-AY-6196 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AY-6197         TCGA-AY-6386         TCGA-AZ-4315 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AZ-4323         TCGA-AZ-4616         TCGA-AZ-4681 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AZ-4682         TCGA-AZ-5403         TCGA-AZ-5407 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AZ-6598         TCGA-AZ-6599         TCGA-AZ-6600 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AZ-6601         TCGA-AZ-6603         TCGA-AZ-6605 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AZ-6606         TCGA-AZ-6607         TCGA-AZ-6608 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-CA-5254         TCGA-CA-5255         TCGA-CA-5796 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-CA-5797         TCGA-CA-6715         TCGA-CA-6716 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-CA-6717         TCGA-CA-6718         TCGA-CA-6719 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-CK-4947         TCGA-CK-4948         TCGA-CK-4950 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-CK-4952         TCGA-CK-5912         TCGA-CK-5913 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-CK-5914         TCGA-CK-5915         TCGA-CK-5916 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-CK-6746         TCGA-CK-6748         TCGA-CK-6751 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-CM-4743         TCGA-CM-4744         TCGA-CM-4746 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-CM-4747         TCGA-CM-4752         TCGA-CM-5341 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-CM-5344         TCGA-CM-5348         TCGA-CM-5349 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-CM-5860         TCGA-CM-5861         TCGA-CM-5862 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-CM-5863         TCGA-CM-5864         TCGA-CM-5868 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-CM-6161         TCGA-CM-6162         TCGA-CM-6163 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-CM-6164         TCGA-CM-6165         TCGA-CM-6166 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-CM-6167         TCGA-CM-6168         TCGA-CM-6169 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-CM-6170         TCGA-CM-6171         TCGA-CM-6172 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-CM-6675         TCGA-CM-6676         TCGA-CM-6677 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-CM-6678         TCGA-CM-6679         TCGA-CM-6680 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-D5-5537         TCGA-D5-5538         TCGA-D5-5539 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-D5-5540         TCGA-D5-5541         TCGA-D5-6529 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-D5-6532         TCGA-D5-6533         TCGA-D5-6534 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-D5-6535         TCGA-D5-6536         TCGA-D5-6537 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-D5-6538         TCGA-D5-6539         TCGA-D5-6540 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-D5-6541         TCGA-D5-6898         TCGA-D5-6920 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-D5-6922         TCGA-D5-6923         TCGA-D5-6924 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-D5-6926         TCGA-D5-6927         TCGA-D5-6928 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-D5-6929         TCGA-D5-6930         TCGA-D5-6931 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-D5-6932         TCGA-D5-7000         TCGA-DM-A0X9 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-DM-A0XD         TCGA-DM-A0XF         TCGA-DM-A1D0 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-DM-A1D4         TCGA-DM-A1D6         TCGA-DM-A1D7 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-DM-A1D8         TCGA-DM-A1D9         TCGA-DM-A1DA 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-DM-A1DB         TCGA-DM-A1HA         TCGA-DM-A1HB 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-DM-A282         TCGA-DM-A285         TCGA-DM-A28C 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-DM-A28E         TCGA-DM-A28F         TCGA-DM-A28G 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-DM-A28H         TCGA-DM-A28K         TCGA-F4-6459 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-F4-6460         TCGA-F4-6569         TCGA-F4-6570 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-F4-6703         TCGA-F4-6704         TCGA-F4-6805 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-F4-6806         TCGA-F4-6807         TCGA-F4-6808 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-F4-6809         TCGA-F4-6854         TCGA-F4-6855 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-F4-6856         TCGA-G4-6293         TCGA-G4-6299 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-G4-6303         TCGA-G4-6304         TCGA-G4-6306 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-G4-6307         TCGA-G4-6309         TCGA-G4-6310 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-G4-6315         TCGA-G4-6317         TCGA-G4-6321 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-G4-6323         TCGA-G4-6586         TCGA-G4-6588 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-G4-6625         TCGA-G4-6626         TCGA-G4-6628 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2691 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AF-2692         TCGA-AF-2693         TCGA-AF-3400 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AF-3913         TCGA-AF-4110         TCGA-AF-5654 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AF-6136         TCGA-AF-6655         TCGA-AF-6672 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6549 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-AH-6643         TCGA-AH-6644         TCGA-CI-6619 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-CI-6620         TCGA-CI-6621         TCGA-CI-6622 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-CI-6624         TCGA-CL-5917         TCGA-CL-5918 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-DC-5337         TCGA-DC-5869         TCGA-DC-6155 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-DC-6157         TCGA-DC-6158         TCGA-DC-6160 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-DC-6681         TCGA-DC-6682         TCGA-DC-6683 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-DT-5265         TCGA-DY-A0XA         TCGA-DY-A1DC 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-DY-A1DD         TCGA-DY-A1DF         TCGA-DY-A1DG 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-DY-A1H8         TCGA-EF-5830         TCGA-EI-6506 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6510 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-F5-6464         TCGA-F5-6465         TCGA-F5-6571 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6811         TCGA-F5-6812 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 
        TCGA-F5-6813         TCGA-G5-6235         TCGA-G5-6641 
"NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" "NUDT16L1 WILD-TYPE" 

Clustering(2008) Variable = SEMA3A MUTATION ANALYSIS
D2008V1, survival
                  sevent
clus2                0   1
  SEMA3A MUTATED    10   4
  SEMA3A WILD-TYPE 368  89
  SEMA3A MUTATED SEMA3A WILD-TYPE 
              14              457 
  SEMA3A MUTATED SEMA3A WILD-TYPE 
               4               89 
$`SEMA3A MUTATED`
TCGA-A6-5666 TCGA-A6-6781 TCGA-AA-3510 TCGA-AA-3950 TCGA-AA-A00J TCGA-AA-A00N 
       32.71        19.66        63.98        24.00        18.05         4.01 
TCGA-AA-A010 TCGA-AZ-6598 TCGA-CA-6717 TCGA-CA-6718 TCGA-D5-6540 TCGA-DM-A0XF 
       34.98        49.41        12.76        10.06        16.14        38.20 
TCGA-AG-A002 TCGA-F5-6465 
       20.98        49.51 

$`SEMA3A WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        22.06        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        33.01        26.01         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       34.03        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 
        5.13       106.75        22.36        62.79        88.21         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       12.20        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       12.49        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A1D0 
       12.00        11.38        10.26       119.70        24.43       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  SEMA3A MUTATED SEMA3A WILD-TYPE 
            4.01             0.00 
  SEMA3A MUTATED SEMA3A WILD-TYPE 
           63.98           148.01 
  SEMA3A MUTATED SEMA3A WILD-TYPE 
           22.49            20.12 
[1] "4.0 - 64.0 (22.5)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.3"
D2008V2, continuous
D2008V3, binary
                  cls
clus                 0   1
  SEMA3A MUTATED    14   2
  SEMA3A WILD-TYPE 352 117
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SEMA3A MUTATED     14    2
  SEMA3A WILD-TYPE  352  117
        clus
vv       SEMA3A MUTATED SEMA3A WILD-TYPE
  COLON              14              352
  RECTUM              2              117
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SEMA3A MUTATED         2        0        2         4         3         1
  SEMA3A WILD-TYPE      89        1       30       134         7         0
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SEMA3A MUTATED           0          0          1          2        1
  SEMA3A WILD-TYPE        24         11         58         40       47
                  vv
clus               STAGE IVA STAGE IVB
  SEMA3A MUTATED           0         0
  SEMA3A WILD-TYPE        18         1
D2008V4, multiclass
            clus
vv           SEMA3A MUTATED SEMA3A WILD-TYPE
  STAGE I                 2               89
  STAGE IA                0                1
  STAGE II                2               30
  STAGE IIA               4              134
  STAGE IIB               3                7
  STAGE IIC               1                0
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              1               58
  STAGE IIIC              2               40
  STAGE IV                1               47
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  SEMA3A MUTATED     0   2   7   7
  SEMA3A WILD-TYPE  17  90 322  43
D2008V5, multiclass
    clus
vv   SEMA3A MUTATED SEMA3A WILD-TYPE
  T1              0               17
  T2              2               90
  T3              7              322
  T4              7               43
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  SEMA3A MUTATED    12   3   1
  SEMA3A WILD-TYPE 275 110  86
D2008V6, multiclass
    clus
vv   SEMA3A MUTATED SEMA3A WILD-TYPE
  N0             12              275
  N1              3              110
  N2              1               86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2008V7, binary
                  cls
clus                 0   1
  SEMA3A MUTATED    12   1
  SEMA3A WILD-TYPE 363  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SEMA3A MUTATED     12    1
  SEMA3A WILD-TYPE  363   64
   clus
vv  SEMA3A MUTATED SEMA3A WILD-TYPE
  0             12              363
  1              1               64
[1] 2 2
[1] FALSE
D2008V8, binary
                  cls
clus                 0   1
  SEMA3A MUTATED     7   9
  SEMA3A WILD-TYPE 218 255
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SEMA3A MUTATED      7    9
  SEMA3A WILD-TYPE  218  255
        clus
vv       SEMA3A MUTATED SEMA3A WILD-TYPE
  FEMALE              7              218
  MALE                9              255
[1] 2 2
[1] FALSE
D2008V9, binary
                  cls
clus                 0   1
  SEMA3A MUTATED    12   0
  SEMA3A WILD-TYPE 338  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SEMA3A MUTATED     12    0
  SEMA3A WILD-TYPE  338   22
     clus
vv    SEMA3A MUTATED SEMA3A WILD-TYPE
  NO              12              338
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SEMA3A MUTATED                      7                             6
  SEMA3A WILD-TYPE                  308                            41
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SEMA3A MUTATED                       2                              0
  SEMA3A WILD-TYPE                   104                             10
D2008V10, multiclass
                                clus
vv                               SEMA3A MUTATED SEMA3A WILD-TYPE
  COLON ADENOCARCINOMA                        7              308
  COLON MUCINOUS ADENOCARCINOMA               6               41
  RECTAL ADENOCARCINOMA                       2              104
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  SEMA3A MUTATED     9   0   1   3
  SEMA3A WILD-TYPE 336   4  30  22
D2008V11, multiclass
    clus
vv   SEMA3A MUTATED SEMA3A WILD-TYPE
  R0              9              336
  R1              0                4
  R2              1               30
  RX              3               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2008V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SEMA3A MUTATED                                  0     2
  SEMA3A WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  SEMA3A MUTATED                           0     7
  SEMA3A WILD-TYPE                        22   219
D2008V13, multiclass
                                  clus
vv                                 SEMA3A MUTATED SEMA3A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                9
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         7              219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2009) Variable = PCDHGA4 MUTATION ANALYSIS
D2009V1, survival
                   sevent
clus2                 0   1
  PCDHGA4 MUTATED    13   5
  PCDHGA4 WILD-TYPE 365  88
  PCDHGA4 MUTATED PCDHGA4 WILD-TYPE 
               18               453 
  PCDHGA4 MUTATED PCDHGA4 WILD-TYPE 
                5                88 
$`PCDHGA4 MUTATED`
TCGA-A6-5659 TCGA-A6-6141 TCGA-A6-6781 TCGA-AA-3492 TCGA-AA-3710 TCGA-AA-3713 
       30.44         8.38        19.66         3.02        26.99        19.04 
TCGA-AA-3864 TCGA-AA-3947 TCGA-AA-A00N TCGA-AD-6899 TCGA-AZ-4315 TCGA-AZ-6601 
       53.00        33.01         4.01         5.79        58.39       100.01 
TCGA-CA-6717 TCGA-CM-6171 TCGA-CM-6676 TCGA-G4-6309 TCGA-G4-6588 TCGA-DC-6158 
       12.76        14.04        11.08        85.48        26.17        10.98 

$`PCDHGA4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 
       22.06        32.71        27.09        22.52        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
       20.28         7.04         1.02        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
        2.01        12.99        24.00        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.79         0.72        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 
       88.21        49.41         6.77        12.10        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07        12.20        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 
       21.99        14.99        12.99        13.02        15.02        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       12.95        13.05        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 
       65.85        53.62        44.68        55.04        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        35.80        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       13.97        27.95        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  PCDHGA4 MUTATED PCDHGA4 WILD-TYPE 
             3.02              0.00 
  PCDHGA4 MUTATED PCDHGA4 WILD-TYPE 
           100.01            148.01 
  PCDHGA4 MUTATED PCDHGA4 WILD-TYPE 
            19.35             20.28 
[1] "3.0 - 100.0 (19.4)" "0.0 - 148.0 (20.3)"
[1] "hr=" "1.3"
D2009V2, continuous
D2009V3, binary
                   cls
clus                  0   1
  PCDHGA4 MUTATED    18   1
  PCDHGA4 WILD-TYPE 348 118
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PCDHGA4 MUTATED     18    1
  PCDHGA4 WILD-TYPE  348  118
        clus
vv       PCDHGA4 MUTATED PCDHGA4 WILD-TYPE
  COLON               18               348
  RECTUM               1               118
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PCDHGA4 MUTATED         4        0        4         5         2         0
  PCDHGA4 WILD-TYPE      87        1       28       133         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PCDHGA4 MUTATED           0          0          1          2        1
  PCDHGA4 WILD-TYPE        24         11         58         40       47
                   vv
clus                STAGE IVA STAGE IVB
  PCDHGA4 MUTATED           0         0
  PCDHGA4 WILD-TYPE        18         1
D2009V4, multiclass
            clus
vv           PCDHGA4 MUTATED PCDHGA4 WILD-TYPE
  STAGE I                  4                87
  STAGE IA                 0                 1
  STAGE II                 4                28
  STAGE IIA                5               133
  STAGE IIB                2                 8
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               0                11
  STAGE IIIB               1                58
  STAGE IIIC               2                40
  STAGE IV                 1                47
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  PCDHGA4 MUTATED     0   4  10   5
  PCDHGA4 WILD-TYPE  17  88 319  45
D2009V5, multiclass
    clus
vv   PCDHGA4 MUTATED PCDHGA4 WILD-TYPE
  T1               0                17
  T2               4                88
  T3              10               319
  T4               5                45
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  PCDHGA4 MUTATED    16   2   1
  PCDHGA4 WILD-TYPE 271 111  86
D2009V6, multiclass
    clus
vv   PCDHGA4 MUTATED PCDHGA4 WILD-TYPE
  N0              16               271
  N1               2               111
  N2               1                86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2009V7, binary
                   cls
clus                  0   1
  PCDHGA4 MUTATED    16   1
  PCDHGA4 WILD-TYPE 359  64
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PCDHGA4 MUTATED     16    1
  PCDHGA4 WILD-TYPE  359   64
   clus
vv  PCDHGA4 MUTATED PCDHGA4 WILD-TYPE
  0              16               359
  1               1                64
[1] 2 2
[1] FALSE
D2009V8, binary
                   cls
clus                  0   1
  PCDHGA4 MUTATED     7  12
  PCDHGA4 WILD-TYPE 218 252
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PCDHGA4 MUTATED      7   12
  PCDHGA4 WILD-TYPE  218  252
        clus
vv       PCDHGA4 MUTATED PCDHGA4 WILD-TYPE
  FEMALE               7               218
  MALE                12               252
[1] 2 2
[1] FALSE
D2009V9, binary
                   cls
clus                  0   1
  PCDHGA4 MUTATED    16   1
  PCDHGA4 WILD-TYPE 334  21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PCDHGA4 MUTATED     16    1
  PCDHGA4 WILD-TYPE  334   21
     clus
vv    PCDHGA4 MUTATED PCDHGA4 WILD-TYPE
  NO               16               334
  YES               1                21
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PCDHGA4 MUTATED                     13                             5
  PCDHGA4 WILD-TYPE                  302                            42
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PCDHGA4 MUTATED                       1                              0
  PCDHGA4 WILD-TYPE                   105                             10
D2009V10, multiclass
                                clus
vv                               PCDHGA4 MUTATED PCDHGA4 WILD-TYPE
  COLON ADENOCARCINOMA                        13               302
  COLON MUCINOUS ADENOCARCINOMA                5                42
  RECTAL ADENOCARCINOMA                        1               105
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  PCDHGA4 MUTATED    14   0   1   1
  PCDHGA4 WILD-TYPE 331   4  30  24
D2009V11, multiclass
    clus
vv   PCDHGA4 MUTATED PCDHGA4 WILD-TYPE
  R0              14               331
  R1               0                 4
  R2               1                30
  RX               1                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2009V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PCDHGA4 MUTATED                                  0     1
  PCDHGA4 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  PCDHGA4 MUTATED                           2     9
  PCDHGA4 WILD-TYPE                        20   217
D2009V13, multiclass
                                  clus
vv                                 PCDHGA4 MUTATED PCDHGA4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                10
  BLACK OR AFRICAN AMERICAN                      2                20
  WHITE                                          9               217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2010) Variable = SNX33 MUTATION ANALYSIS
D2010V1, survival
                 sevent
clus2               0   1
  SNX33 MUTATED     8   3
  SNX33 WILD-TYPE 370  90
  SNX33 MUTATED SNX33 WILD-TYPE 
             11             460 
  SNX33 MUTATED SNX33 WILD-TYPE 
              3              90 
$`SNX33 MUTATED`
TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3667 TCGA-AA-A010 TCGA-AA-A01R TCGA-AD-5900 
        3.02        63.98        14.01        34.98        35.01         0.07 
TCGA-AZ-6598 TCGA-F4-6570 TCGA-G4-6625 TCGA-AF-2687 TCGA-AG-4001 
       49.41         6.18        91.79        24.13        36.03 

$`SNX33 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
       54.02         2.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
       38.07         1.02         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       35.74        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       26.17        46.75        79.69        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  SNX33 MUTATED SNX33 WILD-TYPE 
           0.07            0.00 
  SNX33 MUTATED SNX33 WILD-TYPE 
          91.79          148.01 
  SNX33 MUTATED SNX33 WILD-TYPE 
         34.980          20.085 
[1] "0.1 - 91.8 (35.0)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.1"
D2010V2, continuous
D2010V3, binary
                 cls
clus                0   1
  SNX33 MUTATED     9   2
  SNX33 WILD-TYPE 357 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SNX33 MUTATED      9    2
  SNX33 WILD-TYPE  357  117
        clus
vv       SNX33 MUTATED SNX33 WILD-TYPE
  COLON              9             357
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SNX33 MUTATED         2        0        3         3         1         0
  SNX33 WILD-TYPE      89        1       29       135         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SNX33 MUTATED           1          0          0          1        0         0
  SNX33 WILD-TYPE        23         11         59         41       48        18
                 vv
clus              STAGE IVB
  SNX33 MUTATED           0
  SNX33 WILD-TYPE         1
D2010V4, multiclass
            clus
vv           SNX33 MUTATED SNX33 WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               3              29
  STAGE IIA              3             135
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             1              41
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  SNX33 MUTATED     0   2   8   1
  SNX33 WILD-TYPE  17  90 321  49
D2010V5, multiclass
    clus
vv   SNX33 MUTATED SNX33 WILD-TYPE
  T1             0              17
  T2             2              90
  T3             8             321
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  SNX33 MUTATED     9   0   2
  SNX33 WILD-TYPE 278 113  85
D2010V6, multiclass
    clus
vv   SNX33 MUTATED SNX33 WILD-TYPE
  N0             9             278
  N1             0             113
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2010V7, binary
                 cls
clus                0   1
  SNX33 MUTATED     9   0
  SNX33 WILD-TYPE 366  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SNX33 MUTATED      9    0
  SNX33 WILD-TYPE  366   65
   clus
vv  SNX33 MUTATED SNX33 WILD-TYPE
  0             9             366
  1             0              65
[1] 2 2
[1] FALSE
D2010V8, binary
                 cls
clus                0   1
  SNX33 MUTATED     7   4
  SNX33 WILD-TYPE 218 260
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SNX33 MUTATED      7    4
  SNX33 WILD-TYPE  218  260
        clus
vv       SNX33 MUTATED SNX33 WILD-TYPE
  FEMALE             7             218
  MALE               4             260
[1] 2 2
[1] FALSE
D2010V9, binary
                 cls
clus                0   1
  SNX33 MUTATED     8   2
  SNX33 WILD-TYPE 342  20
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SNX33 MUTATED      8    2
  SNX33 WILD-TYPE  342   20
     clus
vv    SNX33 MUTATED SNX33 WILD-TYPE
  NO              8             342
  YES             2              20
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SNX33 MUTATED                      7                             2
  SNX33 WILD-TYPE                  308                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SNX33 MUTATED                       2                              0
  SNX33 WILD-TYPE                   104                             10
D2010V10, multiclass
                                clus
vv                               SNX33 MUTATED SNX33 WILD-TYPE
  COLON ADENOCARCINOMA                       7             308
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  SNX33 MUTATED    10   0   0   0
  SNX33 WILD-TYPE 335   4  31  25
D2010V11, multiclass
    clus
vv   SNX33 MUTATED SNX33 WILD-TYPE
  R0            10             335
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2010V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SNX33 MUTATED                                  0     0
  SNX33 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  SNX33 MUTATED                           0     5
  SNX33 WILD-TYPE                        22   221
D2010V13, multiclass
                                  clus
vv                                 SNX33 MUTATED SNX33 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        5             221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2011) Variable = BATF3 MUTATION ANALYSIS
D2011V1, survival
                 sevent
clus2               0   1
  BATF3 MUTATED     2   1
  BATF3 WILD-TYPE 376  92
  BATF3 MUTATED BATF3 WILD-TYPE 
              3             468 
  BATF3 MUTATED BATF3 WILD-TYPE 
              1              92 
$`BATF3 MUTATED`
TCGA-AA-3818 TCGA-AZ-4315 TCGA-CM-4743 
        0.99        58.39        23.05 

$`BATF3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3819 TCGA-AA-3821 
       19.04        10.06        35.05        33.04        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        33.01        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
       82.95         1.91       124.27        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  BATF3 MUTATED BATF3 WILD-TYPE 
           0.99            0.00 
  BATF3 MUTATED BATF3 WILD-TYPE 
          58.39          148.01 
  BATF3 MUTATED BATF3 WILD-TYPE 
         23.050          20.155 
[1] "1.0 - 58.4 (23.1)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.5"
D2011V2, continuous
D2011V3, binary
                 cls
clus                0   1
  BATF3 MUTATED     4   0
  BATF3 WILD-TYPE 362 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BATF3 MUTATED      4    0
  BATF3 WILD-TYPE  362  119
        clus
vv       BATF3 MUTATED BATF3 WILD-TYPE
  COLON              4             362
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  BATF3 MUTATED         0        0        0         3         1         0
  BATF3 WILD-TYPE      91        1       32       135         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  BATF3 MUTATED           0          0          0          0        0         0
  BATF3 WILD-TYPE        24         11         59         42       48        18
                 vv
clus              STAGE IVB
  BATF3 MUTATED           0
  BATF3 WILD-TYPE         1
D2011V4, multiclass
            clus
vv           BATF3 MUTATED BATF3 WILD-TYPE
  STAGE I                0              91
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              3             135
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  BATF3 MUTATED     0   0   3   1
  BATF3 WILD-TYPE  17  92 326  49
D2011V5, multiclass
    clus
vv   BATF3 MUTATED BATF3 WILD-TYPE
  T1             0              17
  T2             0              92
  T3             3             326
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  BATF3 MUTATED     4   0   0
  BATF3 WILD-TYPE 283 113  87
D2011V6, multiclass
    clus
vv   BATF3 MUTATED BATF3 WILD-TYPE
  N0             4             283
  N1             0             113
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2011V7, binary
                 cls
clus                0   1
  BATF3 MUTATED     3   0
  BATF3 WILD-TYPE 372  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BATF3 MUTATED      3    0
  BATF3 WILD-TYPE  372   65
   clus
vv  BATF3 MUTATED BATF3 WILD-TYPE
  0             3             372
  1             0              65
[1] 2 2
[1] FALSE
D2011V8, binary
                 cls
clus                0   1
  BATF3 MUTATED     2   2
  BATF3 WILD-TYPE 223 262
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BATF3 MUTATED      2    2
  BATF3 WILD-TYPE  223  262
        clus
vv       BATF3 MUTATED BATF3 WILD-TYPE
  FEMALE             2             223
  MALE               2             262
[1] 2 2
[1] FALSE
D2011V9, binary
                 cls
clus                0   1
  BATF3 MUTATED     2   0
  BATF3 WILD-TYPE 348  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BATF3 MUTATED      2    0
  BATF3 WILD-TYPE  348   22
     clus
vv    BATF3 MUTATED BATF3 WILD-TYPE
  NO              2             348
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  BATF3 MUTATED                      4                             0
  BATF3 WILD-TYPE                  311                            47
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  BATF3 MUTATED                       0                              0
  BATF3 WILD-TYPE                   106                             10
D2011V10, multiclass
                                clus
vv                               BATF3 MUTATED BATF3 WILD-TYPE
  COLON ADENOCARCINOMA                       4             311
  COLON MUCINOUS ADENOCARCINOMA              0              47
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  BATF3 MUTATED     3   0   0   1
  BATF3 WILD-TYPE 342   4  31  24
D2011V11, multiclass
    clus
vv   BATF3 MUTATED BATF3 WILD-TYPE
  R0             3             342
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2011V12, continuous
[1] "Remove cluster labels:" "BATF3 MUTATED"         
clus
  BATF3 MUTATED BATF3 WILD-TYPE 
              2             456 
     TCGA-A6-2671      TCGA-A6-2672      TCGA-A6-2674      TCGA-A6-2676 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-A6-2677      TCGA-A6-2678      TCGA-A6-2683      TCGA-A6-3807 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-A6-3808      TCGA-A6-3809      TCGA-A6-3810      TCGA-A6-4105 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-A6-5656      TCGA-A6-5657      TCGA-A6-5659      TCGA-A6-5660 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-A6-5661      TCGA-A6-5662      TCGA-A6-5664      TCGA-A6-5665 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-A6-5666      TCGA-A6-6137      TCGA-A6-6138      TCGA-A6-6141 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-A6-6142      TCGA-A6-6648      TCGA-A6-6649      TCGA-A6-6651 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-A6-6652      TCGA-A6-6653      TCGA-A6-6654      TCGA-A6-6780 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-A6-6781      TCGA-A6-6782      TCGA-AA-3489      TCGA-AA-3492 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AA-3496      TCGA-AA-3502      TCGA-AA-3510      TCGA-AA-3511 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AA-3514      TCGA-AA-3516      TCGA-AA-3517      TCGA-AA-3518 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AA-3519      TCGA-AA-3520      TCGA-AA-3521      TCGA-AA-3522 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AA-3524      TCGA-AA-3525      TCGA-AA-3526      TCGA-AA-3527 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AA-3529      TCGA-AA-3530      TCGA-AA-3531      TCGA-AA-3532 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AA-3534      TCGA-AA-3538      TCGA-AA-3542      TCGA-AA-3543 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AA-3544      TCGA-AA-3548      TCGA-AA-3549      TCGA-AA-3552 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AA-3553      TCGA-AA-3554      TCGA-AA-3555      TCGA-AA-3556 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AA-3558      TCGA-AA-3560      TCGA-AA-3562      TCGA-AA-3655 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AA-3660      TCGA-AA-3662      TCGA-AA-3663      TCGA-AA-3664 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AA-3666      TCGA-AA-3667      TCGA-AA-3672      TCGA-AA-3673 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AA-3678      TCGA-AA-3679      TCGA-AA-3680      TCGA-AA-3681 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AA-3684      TCGA-AA-3685      TCGA-AA-3688      TCGA-AA-3692 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AA-3693      TCGA-AA-3695      TCGA-AA-3696      TCGA-AA-3697 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AA-3710      TCGA-AA-3712      TCGA-AA-3713      TCGA-AA-3715 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AA-3811      TCGA-AA-3812      TCGA-AA-3814      TCGA-AA-3815 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AA-3819      TCGA-AA-3821      TCGA-AA-3831      TCGA-AA-3833 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AA-3837      TCGA-AA-3842      TCGA-AA-3844      TCGA-AA-3845 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AA-3846      TCGA-AA-3848      TCGA-AA-3850      TCGA-AA-3851 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AA-3852      TCGA-AA-3854      TCGA-AA-3855      TCGA-AA-3856 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AA-3858      TCGA-AA-3860      TCGA-AA-3861      TCGA-AA-3864 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AA-3866      TCGA-AA-3867      TCGA-AA-3869      TCGA-AA-3870 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AA-3872      TCGA-AA-3875      TCGA-AA-3877      TCGA-AA-3930 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AA-3939      TCGA-AA-3941      TCGA-AA-3947      TCGA-AA-3949 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AA-3950      TCGA-AA-3952      TCGA-AA-3955      TCGA-AA-3956 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AA-3966      TCGA-AA-3968      TCGA-AA-3971      TCGA-AA-3972 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AA-3973      TCGA-AA-3975      TCGA-AA-3976      TCGA-AA-3977 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AA-3979      TCGA-AA-3980      TCGA-AA-3982      TCGA-AA-3984 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AA-3986      TCGA-AA-3989      TCGA-AA-3994      TCGA-AA-A004 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AA-A00A      TCGA-AA-A00D      TCGA-AA-A00E      TCGA-AA-A00F 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AA-A00J      TCGA-AA-A00K      TCGA-AA-A00L      TCGA-AA-A00N 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AA-A00O      TCGA-AA-A00Q      TCGA-AA-A00R      TCGA-AA-A00U 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AA-A00W      TCGA-AA-A00Z      TCGA-AA-A010      TCGA-AA-A017 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AA-A01D      TCGA-AA-A01F      TCGA-AA-A01G      TCGA-AA-A01I 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AA-A01K      TCGA-AA-A01P      TCGA-AA-A01Q      TCGA-AA-A01R 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AA-A01S      TCGA-AA-A01T      TCGA-AA-A01V      TCGA-AA-A01X 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AA-A01Z      TCGA-AA-A022      TCGA-AA-A024      TCGA-AA-A029 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AA-A02F      TCGA-AA-A02H      TCGA-AA-A02J      TCGA-AA-A02K 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AA-A02O      TCGA-AA-A02W      TCGA-AA-A02Y      TCGA-AA-A03F 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AA-A03J      TCGA-AD-5900      TCGA-AD-6548      TCGA-AD-6888 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AD-6889      TCGA-AD-6890      TCGA-AD-6895      TCGA-AD-6899 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AD-6901      TCGA-AD-6963      TCGA-AD-6964      TCGA-AD-6965 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AU-3779      TCGA-AU-6004      TCGA-AY-4070      TCGA-AY-4071 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AY-5543      TCGA-AY-6196      TCGA-AY-6197      TCGA-AY-6386 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AZ-4323      TCGA-AZ-4616      TCGA-AZ-4682      TCGA-AZ-5403 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AZ-5407      TCGA-AZ-6598      TCGA-AZ-6599      TCGA-AZ-6600 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AZ-6601      TCGA-AZ-6603      TCGA-AZ-6605      TCGA-AZ-6606 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AZ-6607      TCGA-AZ-6608      TCGA-CK-4947      TCGA-CK-4948 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-CK-4950      TCGA-CK-4952      TCGA-CM-4744      TCGA-CM-4746 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-CM-4747      TCGA-CM-4752      TCGA-CM-5341      TCGA-CM-5344 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-CM-5348      TCGA-CM-5349      TCGA-CM-5860      TCGA-CM-5861 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-CM-5862      TCGA-CM-5863      TCGA-CM-5864      TCGA-CM-5868 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-CM-6161      TCGA-CM-6162      TCGA-CM-6163      TCGA-CM-6164 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-CM-6165      TCGA-CM-6166      TCGA-CM-6167      TCGA-CM-6168 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-CM-6169      TCGA-CM-6170      TCGA-CM-6171      TCGA-CM-6172 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-CM-6674      TCGA-CM-6675      TCGA-CM-6676      TCGA-CM-6677 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-CM-6678      TCGA-CM-6679      TCGA-CM-6680      TCGA-D5-5537 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-D5-5538      TCGA-D5-5539      TCGA-D5-5540      TCGA-D5-5541 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-D5-6529      TCGA-D5-6532      TCGA-D5-6533      TCGA-D5-6534 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-D5-6535      TCGA-D5-6536      TCGA-D5-6537      TCGA-D5-6538 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-D5-6539      TCGA-D5-6540      TCGA-D5-6541      TCGA-D5-6898 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-D5-6920      TCGA-D5-6922      TCGA-D5-6923      TCGA-D5-6924 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-D5-6926      TCGA-D5-6927      TCGA-D5-6928      TCGA-D5-6929 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-D5-6930      TCGA-D5-6931      TCGA-D5-6932      TCGA-D5-7000 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-DM-A0X9      TCGA-DM-A0XD      TCGA-DM-A0XF      TCGA-DM-A1D0 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-DM-A1D4      TCGA-DM-A1D6      TCGA-DM-A1D7      TCGA-DM-A1D8 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-DM-A1D9      TCGA-DM-A1DA      TCGA-DM-A1DB      TCGA-DM-A1HA 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-DM-A1HB      TCGA-DM-A282      TCGA-DM-A285      TCGA-DM-A28C 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-DM-A28E      TCGA-DM-A28F      TCGA-DM-A28G      TCGA-DM-A28H 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-DM-A28K      TCGA-F4-6459      TCGA-F4-6460      TCGA-F4-6569 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-F4-6570      TCGA-F4-6703      TCGA-F4-6704      TCGA-F4-6806 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-F4-6807      TCGA-F4-6808      TCGA-F4-6809      TCGA-F4-6854 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-F4-6855      TCGA-F4-6856      TCGA-G4-6293      TCGA-G4-6299 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-G4-6303      TCGA-G4-6304      TCGA-G4-6306      TCGA-G4-6307 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-G4-6309      TCGA-G4-6310      TCGA-G4-6315      TCGA-G4-6317 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-G4-6321      TCGA-G4-6323      TCGA-G4-6586      TCGA-G4-6588 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-G4-6625      TCGA-G4-6626      TCGA-G4-6628      TCGA-AF-2687 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AF-2689      TCGA-AF-2691      TCGA-AF-2692      TCGA-AF-2693 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AF-3400      TCGA-AF-3913      TCGA-AF-4110      TCGA-AF-5654 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AF-6136      TCGA-AF-6655      TCGA-AF-6672      TCGA-AG-3574 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AG-3575      TCGA-AG-3578      TCGA-AG-3580      TCGA-AG-3581 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AG-3582      TCGA-AG-3583      TCGA-AG-3584      TCGA-AG-3586 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AG-3587      TCGA-AG-3593      TCGA-AG-3594      TCGA-AG-3598 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AG-3599      TCGA-AG-3600      TCGA-AG-3601      TCGA-AG-3602 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AG-3605      TCGA-AG-3608      TCGA-AG-3609      TCGA-AG-3611 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AG-3612      TCGA-AG-3726      TCGA-AG-3727      TCGA-AG-3731 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AG-3732      TCGA-AG-3742      TCGA-AG-3878      TCGA-AG-3881 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AG-3882      TCGA-AG-3883      TCGA-AG-3885      TCGA-AG-3887 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AG-3890      TCGA-AG-3892      TCGA-AG-3893      TCGA-AG-3894 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AG-3896      TCGA-AG-3898      TCGA-AG-3901      TCGA-AG-3902 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AG-3909      TCGA-AG-3999      TCGA-AG-4001      TCGA-AG-4005 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AG-4007      TCGA-AG-4008      TCGA-AG-4015      TCGA-AG-A002 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AG-A008      TCGA-AG-A00C      TCGA-AG-A00H      TCGA-AG-A00Y 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AG-A011      TCGA-AG-A014      TCGA-AG-A015      TCGA-AG-A016 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AG-A01L      TCGA-AG-A01W      TCGA-AG-A01Y      TCGA-AG-A020 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AG-A025      TCGA-AG-A026      TCGA-AG-A02G      TCGA-AG-A02N 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AG-A02X      TCGA-AG-A032      TCGA-AG-A036      TCGA-AH-6544 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-AH-6547      TCGA-AH-6643      TCGA-AH-6644      TCGA-CI-6622 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-DC-5337      TCGA-DC-5869      TCGA-DC-6155      TCGA-DC-6157 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-DC-6158      TCGA-DC-6160      TCGA-DC-6681      TCGA-DC-6682 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-DC-6683      TCGA-DY-A0XA      TCGA-DY-A1DC      TCGA-DY-A1DD 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-DY-A1DF      TCGA-DY-A1DG      TCGA-DY-A1H8      TCGA-EI-6506 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-EI-6507      TCGA-EI-6508      TCGA-EI-6510      TCGA-F5-6464 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-F5-6465      TCGA-F5-6571      TCGA-F5-6702      TCGA-F5-6811 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
     TCGA-F5-6812      TCGA-F5-6813      TCGA-G5-6235      TCGA-G5-6641 
"BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" "BATF3 WILD-TYPE" 
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  BATF3 MUTATED                                  0     0
  BATF3 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  BATF3 MUTATED                           0     3
  BATF3 WILD-TYPE                        22   223
D2011V13, multiclass
                                  clus
vv                                 BATF3 MUTATED BATF3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        3             223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2012) Variable = KBTBD8 MUTATION ANALYSIS
D2012V1, survival
                  sevent
clus2                0   1
  KBTBD8 MUTATED     5   1
  KBTBD8 WILD-TYPE 373  92
  KBTBD8 MUTATED KBTBD8 WILD-TYPE 
               6              465 
  KBTBD8 MUTATED KBTBD8 WILD-TYPE 
               1               92 
$`KBTBD8 MUTATED`
TCGA-AA-3510 TCGA-AA-A00N TCGA-AY-6197 TCGA-CK-5913 TCGA-CM-6163 TCGA-AG-A002 
       63.98         4.01        21.44        51.32         2.96        20.98 

$`KBTBD8 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       33.01        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        49.08         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  KBTBD8 MUTATED KBTBD8 WILD-TYPE 
            2.96             0.00 
  KBTBD8 MUTATED KBTBD8 WILD-TYPE 
           63.98           148.01 
  KBTBD8 MUTATED KBTBD8 WILD-TYPE 
           21.21            20.12 
[1] "3.0 - 64.0 (21.2)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.4"
D2012V2, continuous
D2012V3, binary
                  cls
clus                 0   1
  KBTBD8 MUTATED     7   1
  KBTBD8 WILD-TYPE 359 118
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KBTBD8 MUTATED      7    1
  KBTBD8 WILD-TYPE  359  118
        clus
vv       KBTBD8 MUTATED KBTBD8 WILD-TYPE
  COLON               7              359
  RECTUM              1              118
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KBTBD8 MUTATED         2        0        1         3         1         0
  KBTBD8 WILD-TYPE      89        1       31       135         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KBTBD8 MUTATED           0          0          0          1        0
  KBTBD8 WILD-TYPE        24         11         59         41       48
                  vv
clus               STAGE IVA STAGE IVB
  KBTBD8 MUTATED           0         0
  KBTBD8 WILD-TYPE        18         1
D2012V4, multiclass
            clus
vv           KBTBD8 MUTATED KBTBD8 WILD-TYPE
  STAGE I                 2               89
  STAGE IA                0                1
  STAGE II                1               31
  STAGE IIA               3              135
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              0               59
  STAGE IIIC              1               41
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  KBTBD8 MUTATED     1   1   5   1
  KBTBD8 WILD-TYPE  16  91 324  49
D2012V5, multiclass
    clus
vv   KBTBD8 MUTATED KBTBD8 WILD-TYPE
  T1              1               16
  T2              1               91
  T3              5              324
  T4              1               49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  KBTBD8 MUTATED     7   0   1
  KBTBD8 WILD-TYPE 280 113  86
D2012V6, multiclass
    clus
vv   KBTBD8 MUTATED KBTBD8 WILD-TYPE
  N0              7              280
  N1              0              113
  N2              1               86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2012V7, binary
                  cls
clus                 0   1
  KBTBD8 MUTATED     5   0
  KBTBD8 WILD-TYPE 370  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KBTBD8 MUTATED      5    0
  KBTBD8 WILD-TYPE  370   65
   clus
vv  KBTBD8 MUTATED KBTBD8 WILD-TYPE
  0              5              370
  1              0               65
[1] 2 2
[1] FALSE
D2012V8, binary
                  cls
clus                 0   1
  KBTBD8 MUTATED     2   6
  KBTBD8 WILD-TYPE 223 258
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KBTBD8 MUTATED      2    6
  KBTBD8 WILD-TYPE  223  258
        clus
vv       KBTBD8 MUTATED KBTBD8 WILD-TYPE
  FEMALE              2              223
  MALE                6              258
[1] 2 2
[1] FALSE
D2012V9, binary
                  cls
clus                 0   1
  KBTBD8 MUTATED     5   0
  KBTBD8 WILD-TYPE 345  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KBTBD8 MUTATED      5    0
  KBTBD8 WILD-TYPE  345   22
     clus
vv    KBTBD8 MUTATED KBTBD8 WILD-TYPE
  NO               5              345
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  KBTBD8 MUTATED                      5                             2
  KBTBD8 WILD-TYPE                  310                            45
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  KBTBD8 MUTATED                       1                              0
  KBTBD8 WILD-TYPE                   105                             10
D2012V10, multiclass
                                clus
vv                               KBTBD8 MUTATED KBTBD8 WILD-TYPE
  COLON ADENOCARCINOMA                        5              310
  COLON MUCINOUS ADENOCARCINOMA               2               45
  RECTAL ADENOCARCINOMA                       1              105
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  KBTBD8 MUTATED     7   0   0   1
  KBTBD8 WILD-TYPE 338   4  31  24
D2012V11, multiclass
    clus
vv   KBTBD8 MUTATED KBTBD8 WILD-TYPE
  R0              7              338
  R1              0                4
  R2              0               31
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2012V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KBTBD8 MUTATED                                  0     0
  KBTBD8 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  KBTBD8 MUTATED                           0     4
  KBTBD8 WILD-TYPE                        22   222
D2012V13, multiclass
                                  clus
vv                                 KBTBD8 MUTATED KBTBD8 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         4              222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2013) Variable = RHBDD1 MUTATION ANALYSIS
D2013V1, survival
                  sevent
clus2                0   1
  RHBDD1 MUTATED     5   1
  RHBDD1 WILD-TYPE 373  92
  RHBDD1 MUTATED RHBDD1 WILD-TYPE 
               6              465 
  RHBDD1 MUTATED RHBDD1 WILD-TYPE 
               1               92 
$`RHBDD1 MUTATED`
TCGA-AA-3534 TCGA-AA-3543 TCGA-AA-3713 TCGA-AG-A002 TCGA-AG-A026 TCGA-DC-6681 
       29.00         0.99        19.04        20.98         1.94         5.95 

$`RHBDD1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       26.01        12.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6682 TCGA-DC-6683 
       13.97        27.95        10.98        19.99         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  RHBDD1 MUTATED RHBDD1 WILD-TYPE 
            0.99             0.00 
  RHBDD1 MUTATED RHBDD1 WILD-TYPE 
           29.00           148.01 
  RHBDD1 MUTATED RHBDD1 WILD-TYPE 
          12.495           20.280 
[1] "1.0 - 29.0 (12.5)"  "0.0 - 148.0 (20.3)"
[1] "hr=" "1.7"
D2013V2, continuous
D2013V3, binary
                  cls
clus                 0   1
  RHBDD1 MUTATED     4   4
  RHBDD1 WILD-TYPE 362 115
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RHBDD1 MUTATED      4    4
  RHBDD1 WILD-TYPE  362  115
        clus
vv       RHBDD1 MUTATED RHBDD1 WILD-TYPE
  COLON               4              362
  RECTUM              4              115
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RHBDD1 MUTATED         2        0        1         1         0         0
  RHBDD1 WILD-TYPE      89        1       31       137        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RHBDD1 MUTATED           1          0          0          1        1
  RHBDD1 WILD-TYPE        23         11         59         41       47
                  vv
clus               STAGE IVA STAGE IVB
  RHBDD1 MUTATED           1         0
  RHBDD1 WILD-TYPE        17         1
D2013V4, multiclass
            clus
vv           RHBDD1 MUTATED RHBDD1 WILD-TYPE
  STAGE I                 2               89
  STAGE IA                0                1
  STAGE II                1               31
  STAGE IIA               1              137
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               1               23
  STAGE IIIA              0               11
  STAGE IIIB              0               59
  STAGE IIIC              1               41
  STAGE IV                1               47
  STAGE IVA               1               17
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  RHBDD1 MUTATED     0   2   5   1
  RHBDD1 WILD-TYPE  17  90 324  49
D2013V5, multiclass
    clus
vv   RHBDD1 MUTATED RHBDD1 WILD-TYPE
  T1              0               17
  T2              2               90
  T3              5              324
  T4              1               49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  RHBDD1 MUTATED     5   1   2
  RHBDD1 WILD-TYPE 282 112  85
D2013V6, multiclass
    clus
vv   RHBDD1 MUTATED RHBDD1 WILD-TYPE
  N0              5              282
  N1              1              112
  N2              2               85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2013V7, binary
                  cls
clus                 0   1
  RHBDD1 MUTATED     4   2
  RHBDD1 WILD-TYPE 371  63
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RHBDD1 MUTATED      4    2
  RHBDD1 WILD-TYPE  371   63
   clus
vv  RHBDD1 MUTATED RHBDD1 WILD-TYPE
  0              4              371
  1              2               63
[1] 2 2
[1] FALSE
D2013V8, binary
                  cls
clus                 0   1
  RHBDD1 MUTATED     2   6
  RHBDD1 WILD-TYPE 223 258
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RHBDD1 MUTATED      2    6
  RHBDD1 WILD-TYPE  223  258
        clus
vv       RHBDD1 MUTATED RHBDD1 WILD-TYPE
  FEMALE              2              223
  MALE                6              258
[1] 2 2
[1] FALSE
D2013V9, binary
                  cls
clus                 0   1
  RHBDD1 MUTATED     3   1
  RHBDD1 WILD-TYPE 347  21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RHBDD1 MUTATED      3    1
  RHBDD1 WILD-TYPE  347   21
     clus
vv    RHBDD1 MUTATED RHBDD1 WILD-TYPE
  NO               3              347
  YES              1               21
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  RHBDD1 MUTATED                      2                             2
  RHBDD1 WILD-TYPE                  313                            45
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  RHBDD1 MUTATED                       4                              0
  RHBDD1 WILD-TYPE                   102                             10
D2013V10, multiclass
                                clus
vv                               RHBDD1 MUTATED RHBDD1 WILD-TYPE
  COLON ADENOCARCINOMA                        2              313
  COLON MUCINOUS ADENOCARCINOMA               2               45
  RECTAL ADENOCARCINOMA                       4              102
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  RHBDD1 MUTATED     5   1   1   0
  RHBDD1 WILD-TYPE 340   3  30  25
D2013V11, multiclass
    clus
vv   RHBDD1 MUTATED RHBDD1 WILD-TYPE
  R0              5              340
  R1              1                3
  R2              1               30
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2013V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RHBDD1 MUTATED                                  0     0
  RHBDD1 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  RHBDD1 MUTATED                           0     3
  RHBDD1 WILD-TYPE                        22   223
D2013V13, multiclass
                                  clus
vv                                 RHBDD1 MUTATED RHBDD1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         3              223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2014) Variable = CPEB1 MUTATION ANALYSIS
D2014V1, survival
                 sevent
clus2               0   1
  CPEB1 MUTATED     6   0
  CPEB1 WILD-TYPE 372  93
  CPEB1 MUTATED CPEB1 WILD-TYPE 
              6             465 
  CPEB1 MUTATED CPEB1 WILD-TYPE 
              0              93 
$`CPEB1 MUTATED`
TCGA-AA-3510 TCGA-AA-3977 TCGA-AZ-4315 TCGA-CM-6167 TCGA-D5-6540 TCGA-AG-A002 
       63.98        25.02        58.39        14.99        16.14        20.98 

$`CPEB1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       33.01        21.44        17.82         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6168 
       12.00         2.96        29.03        16.04        21.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       12.49        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  CPEB1 MUTATED CPEB1 WILD-TYPE 
          14.99            0.00 
  CPEB1 MUTATED CPEB1 WILD-TYPE 
          63.98          148.01 
  CPEB1 MUTATED CPEB1 WILD-TYPE 
          23.00           20.12 
[1] "15.0 - 64.0 (23.0)" "0.0 - 148.0 (20.1)"
[1] "hr="     "9200000"
D2014V2, continuous
D2014V3, binary
                 cls
clus                0   1
  CPEB1 MUTATED     6   1
  CPEB1 WILD-TYPE 360 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CPEB1 MUTATED      6    1
  CPEB1 WILD-TYPE  360  118
        clus
vv       CPEB1 MUTATED CPEB1 WILD-TYPE
  COLON              6             360
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CPEB1 MUTATED         2        0        1         2         0         0
  CPEB1 WILD-TYPE      89        1       31       136        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CPEB1 MUTATED           0          0          0          1        0         0
  CPEB1 WILD-TYPE        24         11         59         41       48        18
                 vv
clus              STAGE IVB
  CPEB1 MUTATED           0
  CPEB1 WILD-TYPE         1
D2014V4, multiclass
            clus
vv           CPEB1 MUTATED CPEB1 WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              2             136
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             1              41
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CPEB1 MUTATED     0   3   4   0
  CPEB1 WILD-TYPE  17  89 325  50
D2014V5, multiclass
    clus
vv   CPEB1 MUTATED CPEB1 WILD-TYPE
  T1             0              17
  T2             3              89
  T3             4             325
  T4             0              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  CPEB1 MUTATED     6   0   1
  CPEB1 WILD-TYPE 281 113  86
D2014V6, multiclass
    clus
vv   CPEB1 MUTATED CPEB1 WILD-TYPE
  N0             6             281
  N1             0             113
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2014V7, binary
                 cls
clus                0   1
  CPEB1 MUTATED     6   0
  CPEB1 WILD-TYPE 369  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CPEB1 MUTATED      6    0
  CPEB1 WILD-TYPE  369   65
   clus
vv  CPEB1 MUTATED CPEB1 WILD-TYPE
  0             6             369
  1             0              65
[1] 2 2
[1] FALSE
D2014V8, binary
                 cls
clus                0   1
  CPEB1 MUTATED     2   5
  CPEB1 WILD-TYPE 223 259
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CPEB1 MUTATED      2    5
  CPEB1 WILD-TYPE  223  259
        clus
vv       CPEB1 MUTATED CPEB1 WILD-TYPE
  FEMALE             2             223
  MALE               5             259
[1] 2 2
[1] FALSE
D2014V9, binary
                 cls
clus                0   1
  CPEB1 MUTATED     6   0
  CPEB1 WILD-TYPE 344  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CPEB1 MUTATED      6    0
  CPEB1 WILD-TYPE  344   22
     clus
vv    CPEB1 MUTATED CPEB1 WILD-TYPE
  NO              6             344
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CPEB1 MUTATED                      5                             1
  CPEB1 WILD-TYPE                  310                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CPEB1 MUTATED                       1                              0
  CPEB1 WILD-TYPE                   105                             10
D2014V10, multiclass
                                clus
vv                               CPEB1 MUTATED CPEB1 WILD-TYPE
  COLON ADENOCARCINOMA                       5             310
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  CPEB1 MUTATED     6   0   0   0
  CPEB1 WILD-TYPE 339   4  31  25
D2014V11, multiclass
    clus
vv   CPEB1 MUTATED CPEB1 WILD-TYPE
  R0             6             339
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2014V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CPEB1 MUTATED                                  0     0
  CPEB1 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CPEB1 MUTATED                           1     2
  CPEB1 WILD-TYPE                        21   224
D2014V13, multiclass
                                  clus
vv                                 CPEB1 MUTATED CPEB1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        2             224
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2015) Variable = SKIV2L2 MUTATION ANALYSIS
D2015V1, survival
                   sevent
clus2                 0   1
  SKIV2L2 MUTATED     5   8
  SKIV2L2 WILD-TYPE 373  85
  SKIV2L2 MUTATED SKIV2L2 WILD-TYPE 
               13               458 
  SKIV2L2 MUTATED SKIV2L2 WILD-TYPE 
                8                85 
$`SKIV2L2 MUTATED`
TCGA-AA-3492 TCGA-AA-A00J TCGA-AA-A00N TCGA-AU-6004 TCGA-CK-5916 TCGA-CM-5862 
        3.02        18.05         4.01        27.09        21.14         5.03 
TCGA-D5-5541 TCGA-DM-A0XD TCGA-DM-A28F TCGA-F4-6460 TCGA-F4-6570 TCGA-AG-A002 
       55.92        24.43        35.97        31.96         6.18        20.98 
TCGA-F5-6811 
       32.19 

$`SKIV2L2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L 
       38.04        19.00        30.02        34.03        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
        0.20        14.50        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       49.08        51.32         9.99        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 
       22.03        22.98        30.08        32.02        15.02        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       56.09        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
       10.26       119.70        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G 
      135.65       139.17         6.12        81.37       119.93        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 
      117.07        98.24         8.61        35.74        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6812 TCGA-F5-6813 
        9.96        49.51        31.30        28.57         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  SKIV2L2 MUTATED SKIV2L2 WILD-TYPE 
             3.02              0.00 
  SKIV2L2 MUTATED SKIV2L2 WILD-TYPE 
            55.92            148.01 
  SKIV2L2 MUTATED SKIV2L2 WILD-TYPE 
           21.140            20.085 
[1] "3.0 - 55.9 (21.1)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "4.1"
D2015V2, continuous
D2015V3, binary
                   cls
clus                  0   1
  SKIV2L2 MUTATED    11   2
  SKIV2L2 WILD-TYPE 355 117
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SKIV2L2 MUTATED     11    2
  SKIV2L2 WILD-TYPE  355  117
        clus
vv       SKIV2L2 MUTATED SKIV2L2 WILD-TYPE
  COLON               11               355
  RECTUM               2               117
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SKIV2L2 MUTATED         3        0        1         3         1         0
  SKIV2L2 WILD-TYPE      88        1       31       135         9         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SKIV2L2 MUTATED           0          0          4          0        0
  SKIV2L2 WILD-TYPE        24         11         55         42       48
                   vv
clus                STAGE IVA STAGE IVB
  SKIV2L2 MUTATED           1         0
  SKIV2L2 WILD-TYPE        17         1
D2015V4, multiclass
            clus
vv           SKIV2L2 MUTATED SKIV2L2 WILD-TYPE
  STAGE I                  3                88
  STAGE IA                 0                 1
  STAGE II                 1                31
  STAGE IIA                3               135
  STAGE IIB                1                 9
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               0                11
  STAGE IIIB               4                55
  STAGE IIIC               0                42
  STAGE IV                 0                48
  STAGE IVA                1                17
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  SKIV2L2 MUTATED     1   2   8   2
  SKIV2L2 WILD-TYPE  16  90 321  48
D2015V5, multiclass
    clus
vv   SKIV2L2 MUTATED SKIV2L2 WILD-TYPE
  T1               1                16
  T2               2                90
  T3               8               321
  T4               2                48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  SKIV2L2 MUTATED     8   5   0
  SKIV2L2 WILD-TYPE 279 108  87
D2015V6, multiclass
    clus
vv   SKIV2L2 MUTATED SKIV2L2 WILD-TYPE
  N0               8               279
  N1               5               108
  N2               0                87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2015V7, binary
                   cls
clus                  0   1
  SKIV2L2 MUTATED    12   1
  SKIV2L2 WILD-TYPE 363  64
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SKIV2L2 MUTATED     12    1
  SKIV2L2 WILD-TYPE  363   64
   clus
vv  SKIV2L2 MUTATED SKIV2L2 WILD-TYPE
  0              12               363
  1               1                64
[1] 2 2
[1] FALSE
D2015V8, binary
                   cls
clus                  0   1
  SKIV2L2 MUTATED     6   7
  SKIV2L2 WILD-TYPE 219 257
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SKIV2L2 MUTATED      6    7
  SKIV2L2 WILD-TYPE  219  257
        clus
vv       SKIV2L2 MUTATED SKIV2L2 WILD-TYPE
  FEMALE               6               219
  MALE                 7               257
[1] 2 2
[1] FALSE
D2015V9, binary
                   cls
clus                  0   1
  SKIV2L2 MUTATED     9   0
  SKIV2L2 WILD-TYPE 341  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SKIV2L2 MUTATED      9    0
  SKIV2L2 WILD-TYPE  341   22
     clus
vv    SKIV2L2 MUTATED SKIV2L2 WILD-TYPE
  NO                9               341
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SKIV2L2 MUTATED                      9                             2
  SKIV2L2 WILD-TYPE                  306                            45
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SKIV2L2 MUTATED                       2                              0
  SKIV2L2 WILD-TYPE                   104                             10
D2015V10, multiclass
                                clus
vv                               SKIV2L2 MUTATED SKIV2L2 WILD-TYPE
  COLON ADENOCARCINOMA                         9               306
  COLON MUCINOUS ADENOCARCINOMA                2                45
  RECTAL ADENOCARCINOMA                        2               104
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  SKIV2L2 MUTATED     9   0   0   1
  SKIV2L2 WILD-TYPE 336   4  31  24
D2015V11, multiclass
    clus
vv   SKIV2L2 MUTATED SKIV2L2 WILD-TYPE
  R0               9               336
  R1               0                 4
  R2               0                31
  RX               1                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2015V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SKIV2L2 MUTATED                                  0     0
  SKIV2L2 WILD-TYPE                                1    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  SKIV2L2 MUTATED                           0     9
  SKIV2L2 WILD-TYPE                        22   217
D2015V13, multiclass
                                  clus
vv                                 SKIV2L2 MUTATED SKIV2L2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                      0                22
  WHITE                                          9               217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2016) Variable = AMPD1 MUTATION ANALYSIS
D2016V1, survival
                 sevent
clus2               0   1
  AMPD1 MUTATED    11   5
  AMPD1 WILD-TYPE 367  88
  AMPD1 MUTATED AMPD1 WILD-TYPE 
             16             455 
  AMPD1 MUTATED AMPD1 WILD-TYPE 
              5              88 
$`AMPD1 MUTATED`
TCGA-A6-2676 TCGA-A6-6141 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3525 TCGA-AA-3663 
       42.90         8.38        63.98         1.02         8.05         6.97 
TCGA-AA-3672 TCGA-AA-A00N TCGA-AY-5543 TCGA-AZ-4616 TCGA-AZ-6598 TCGA-CA-6717 
        0.92         4.01        33.01         5.13        49.41        12.76 
TCGA-CA-6718 TCGA-AF-6672 TCGA-AG-3892 TCGA-AG-A002 
       10.06        10.39        13.02        20.98 

$`AMPD1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 
       22.06        32.71        27.09        22.52        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3511 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        6.97        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       37.05        36.03        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
       78.08         6.05        54.02         2.01        14.01        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82        58.39         1.41       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        88.21         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 
        3.25         3.29         0.07        12.20        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AG-3574 TCGA-AG-3575 
       14.50        16.83        15.39        20.02        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  AMPD1 MUTATED AMPD1 WILD-TYPE 
           0.92            0.00 
  AMPD1 MUTATED AMPD1 WILD-TYPE 
          63.98          148.01 
  AMPD1 MUTATED AMPD1 WILD-TYPE 
         10.225          20.910 
[1] "0.9 - 64.0 (10.2)"  "0.0 - 148.0 (20.9)"
[1] "hr=" "2.2"
D2016V2, continuous
D2016V3, binary
                 cls
clus                0   1
  AMPD1 MUTATED    15   3
  AMPD1 WILD-TYPE 351 116
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AMPD1 MUTATED     15    3
  AMPD1 WILD-TYPE  351  116
        clus
vv       AMPD1 MUTATED AMPD1 WILD-TYPE
  COLON             15             351
  RECTUM             3             116
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  AMPD1 MUTATED         3        0        3         4         2         0
  AMPD1 WILD-TYPE      88        1       29       134         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AMPD1 MUTATED           1          0          1          1        2         1
  AMPD1 WILD-TYPE        23         11         58         41       46        17
                 vv
clus              STAGE IVB
  AMPD1 MUTATED           0
  AMPD1 WILD-TYPE         1
D2016V4, multiclass
            clus
vv           AMPD1 MUTATED AMPD1 WILD-TYPE
  STAGE I                3              88
  STAGE IA               0               1
  STAGE II               3              29
  STAGE IIA              4             134
  STAGE IIB              2               8
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             1              41
  STAGE IV               2              46
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  AMPD1 MUTATED     1   2  12   3
  AMPD1 WILD-TYPE  16  90 317  47
D2016V5, multiclass
    clus
vv   AMPD1 MUTATED AMPD1 WILD-TYPE
  T1             1              16
  T2             2              90
  T3            12             317
  T4             3              47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  AMPD1 MUTATED    12   3   3
  AMPD1 WILD-TYPE 275 110  84
D2016V6, multiclass
    clus
vv   AMPD1 MUTATED AMPD1 WILD-TYPE
  N0            12             275
  N1             3             110
  N2             3              84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2016V7, binary
                 cls
clus                0   1
  AMPD1 MUTATED    13   2
  AMPD1 WILD-TYPE 362  63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AMPD1 MUTATED     13    2
  AMPD1 WILD-TYPE  362   63
   clus
vv  AMPD1 MUTATED AMPD1 WILD-TYPE
  0            13             362
  1             2              63
[1] 2 2
[1] FALSE
D2016V8, binary
                 cls
clus                0   1
  AMPD1 MUTATED     8  10
  AMPD1 WILD-TYPE 217 254
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AMPD1 MUTATED      8   10
  AMPD1 WILD-TYPE  217  254
        clus
vv       AMPD1 MUTATED AMPD1 WILD-TYPE
  FEMALE             8             217
  MALE              10             254
[1] 2 2
[1] FALSE
D2016V9, binary
                 cls
clus                0   1
  AMPD1 MUTATED    14   1
  AMPD1 WILD-TYPE 336  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AMPD1 MUTATED     14    1
  AMPD1 WILD-TYPE  336   21
     clus
vv    AMPD1 MUTATED AMPD1 WILD-TYPE
  NO             14             336
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  AMPD1 MUTATED                     12                             3
  AMPD1 WILD-TYPE                  303                            44
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  AMPD1 MUTATED                       3                              0
  AMPD1 WILD-TYPE                   103                             10
D2016V10, multiclass
                                clus
vv                               AMPD1 MUTATED AMPD1 WILD-TYPE
  COLON ADENOCARCINOMA                      12             303
  COLON MUCINOUS ADENOCARCINOMA              3              44
  RECTAL ADENOCARCINOMA                      3             103
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  AMPD1 MUTATED    12   0   0   2
  AMPD1 WILD-TYPE 333   4  31  23
D2016V11, multiclass
    clus
vv   AMPD1 MUTATED AMPD1 WILD-TYPE
  R0            12             333
  R1             0               4
  R2             0              31
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2016V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMPD1 MUTATED                                  0     2
  AMPD1 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  AMPD1 MUTATED                           2     5
  AMPD1 WILD-TYPE                        20   221
D2016V13, multiclass
                                  clus
vv                                 AMPD1 MUTATED AMPD1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               9
  BLACK OR AFRICAN AMERICAN                    2              20
  WHITE                                        5             221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2017) Variable = MIPEP MUTATION ANALYSIS
D2017V1, survival
                 sevent
clus2               0   1
  MIPEP MUTATED     8   0
  MIPEP WILD-TYPE 370  93
  MIPEP MUTATED MIPEP WILD-TYPE 
              8             463 
  MIPEP MUTATED MIPEP WILD-TYPE 
              0              93 
$`MIPEP MUTATED`
TCGA-AA-3510 TCGA-AA-3555 TCGA-AA-3864 TCGA-CK-6751 TCGA-CM-6169 TCGA-CM-6680 
       63.98        29.95        53.00       124.27        13.02        12.03 
TCGA-D5-6536 TCGA-AG-A002 
       17.85        20.98 

$`MIPEP WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       13.02        24.00        17.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 
        0.99        31.07        31.07        30.05        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
        1.91        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.08        11.01        10.06        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       15.12         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  MIPEP MUTATED MIPEP WILD-TYPE 
          12.03            0.00 
  MIPEP MUTATED MIPEP WILD-TYPE 
         124.27          148.01 
  MIPEP MUTATED MIPEP WILD-TYPE 
         25.465          20.120 
[1] "12.0 - 124.3 (25.5)" "0.0 - 148.0 (20.1)" 
[1] "hr="     "9400000"
D2017V2, continuous
D2017V3, binary
                 cls
clus                0   1
  MIPEP MUTATED     8   1
  MIPEP WILD-TYPE 358 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MIPEP MUTATED      8    1
  MIPEP WILD-TYPE  358  118
        clus
vv       MIPEP MUTATED MIPEP WILD-TYPE
  COLON              8             358
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MIPEP MUTATED         2        0        3         3         0         0
  MIPEP WILD-TYPE      89        1       29       135        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MIPEP MUTATED           0          0          1          0        0         0
  MIPEP WILD-TYPE        24         11         58         42       48        18
                 vv
clus              STAGE IVB
  MIPEP MUTATED           0
  MIPEP WILD-TYPE         1
D2017V4, multiclass
            clus
vv           MIPEP MUTATED MIPEP WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               3              29
  STAGE IIA              3             135
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  MIPEP MUTATED     0   2   6   1
  MIPEP WILD-TYPE  17  90 323  49
D2017V5, multiclass
    clus
vv   MIPEP MUTATED MIPEP WILD-TYPE
  T1             0              17
  T2             2              90
  T3             6             323
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  MIPEP MUTATED     8   0   1
  MIPEP WILD-TYPE 279 113  86
D2017V6, multiclass
    clus
vv   MIPEP MUTATED MIPEP WILD-TYPE
  N0             8             279
  N1             0             113
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2017V7, binary
                 cls
clus                0   1
  MIPEP MUTATED     8   0
  MIPEP WILD-TYPE 367  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MIPEP MUTATED      8    0
  MIPEP WILD-TYPE  367   65
   clus
vv  MIPEP MUTATED MIPEP WILD-TYPE
  0             8             367
  1             0              65
[1] 2 2
[1] FALSE
D2017V8, binary
                 cls
clus                0   1
  MIPEP MUTATED     4   5
  MIPEP WILD-TYPE 221 259
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MIPEP MUTATED      4    5
  MIPEP WILD-TYPE  221  259
        clus
vv       MIPEP MUTATED MIPEP WILD-TYPE
  FEMALE             4             221
  MALE               5             259
[1] 2 2
[1] FALSE
D2017V9, binary
                 cls
clus                0   1
  MIPEP MUTATED     8   0
  MIPEP WILD-TYPE 342  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MIPEP MUTATED      8    0
  MIPEP WILD-TYPE  342   22
     clus
vv    MIPEP MUTATED MIPEP WILD-TYPE
  NO              8             342
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MIPEP MUTATED                      6                             2
  MIPEP WILD-TYPE                  309                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MIPEP MUTATED                       1                              0
  MIPEP WILD-TYPE                   105                             10
D2017V10, multiclass
                                clus
vv                               MIPEP MUTATED MIPEP WILD-TYPE
  COLON ADENOCARCINOMA                       6             309
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  MIPEP MUTATED     8   0   0   1
  MIPEP WILD-TYPE 337   4  31  24
D2017V11, multiclass
    clus
vv   MIPEP MUTATED MIPEP WILD-TYPE
  R0             8             337
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2017V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MIPEP MUTATED                                  0     0
  MIPEP WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  MIPEP MUTATED                           1     3
  MIPEP WILD-TYPE                        21   223
D2017V13, multiclass
                                  clus
vv                                 MIPEP MUTATED MIPEP WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        3             223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2018) Variable = KRT39 MUTATION ANALYSIS
D2018V1, survival
                 sevent
clus2               0   1
  KRT39 MUTATED     6   1
  KRT39 WILD-TYPE 372  92
  KRT39 MUTATED KRT39 WILD-TYPE 
              7             464 
  KRT39 MUTATED KRT39 WILD-TYPE 
              1              92 
$`KRT39 MUTATED`
TCGA-A6-5659 TCGA-AA-3861 TCGA-AA-3947 TCGA-AZ-4315 TCGA-AZ-6608 TCGA-D5-6536 
       30.44        30.05        33.01        58.39         1.61        17.85 
TCGA-DM-A1HA 
      131.51 

$`KRT39 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 
       32.05         0.99        31.07        31.07        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       12.99        24.00        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       43.27        15.12         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
       44.32       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  KRT39 MUTATED KRT39 WILD-TYPE 
           1.61            0.00 
  KRT39 MUTATED KRT39 WILD-TYPE 
         131.51          148.01 
  KRT39 MUTATED KRT39 WILD-TYPE 
         30.440          20.085 
[1] "1.6 - 131.5 (30.4)" "0.0 - 148.0 (20.1)"
[1] "hr=" "2"  
D2018V2, continuous
D2018V3, binary
                 cls
clus                0   1
  KRT39 MUTATED     7   0
  KRT39 WILD-TYPE 359 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KRT39 MUTATED      7    0
  KRT39 WILD-TYPE  359  119
        clus
vv       KRT39 MUTATED KRT39 WILD-TYPE
  COLON              7             359
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KRT39 MUTATED         1        0        0         3         1         0
  KRT39 WILD-TYPE      90        1       32       135         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  KRT39 MUTATED           0          1          0          1        0         0
  KRT39 WILD-TYPE        24         10         59         41       48        18
                 vv
clus              STAGE IVB
  KRT39 MUTATED           0
  KRT39 WILD-TYPE         1
D2018V4, multiclass
            clus
vv           KRT39 MUTATED KRT39 WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              3             135
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             1              10
  STAGE IIIB             0              59
  STAGE IIIC             1              41
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  KRT39 MUTATED     0   2   4   1
  KRT39 WILD-TYPE  17  90 325  49
D2018V5, multiclass
    clus
vv   KRT39 MUTATED KRT39 WILD-TYPE
  T1             0              17
  T2             2              90
  T3             4             325
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  KRT39 MUTATED     5   1   1
  KRT39 WILD-TYPE 282 112  86
D2018V6, multiclass
    clus
vv   KRT39 MUTATED KRT39 WILD-TYPE
  N0             5             282
  N1             1             112
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2018V7, binary
                 cls
clus                0   1
  KRT39 MUTATED     7   0
  KRT39 WILD-TYPE 368  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KRT39 MUTATED      7    0
  KRT39 WILD-TYPE  368   65
   clus
vv  KRT39 MUTATED KRT39 WILD-TYPE
  0             7             368
  1             0              65
[1] 2 2
[1] FALSE
D2018V8, binary
                 cls
clus                0   1
  KRT39 MUTATED     2   5
  KRT39 WILD-TYPE 223 259
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KRT39 MUTATED      2    5
  KRT39 WILD-TYPE  223  259
        clus
vv       KRT39 MUTATED KRT39 WILD-TYPE
  FEMALE             2             223
  MALE               5             259
[1] 2 2
[1] FALSE
D2018V9, binary
                 cls
clus                0   1
  KRT39 MUTATED     6   0
  KRT39 WILD-TYPE 344  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KRT39 MUTATED      6    0
  KRT39 WILD-TYPE  344   22
     clus
vv    KRT39 MUTATED KRT39 WILD-TYPE
  NO              6             344
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  KRT39 MUTATED                      6                             1
  KRT39 WILD-TYPE                  309                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  KRT39 MUTATED                       0                              0
  KRT39 WILD-TYPE                   106                             10
D2018V10, multiclass
                                clus
vv                               KRT39 MUTATED KRT39 WILD-TYPE
  COLON ADENOCARCINOMA                       6             309
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  KRT39 MUTATED     5   0   0   0
  KRT39 WILD-TYPE 340   4  31  25
D2018V11, multiclass
    clus
vv   KRT39 MUTATED KRT39 WILD-TYPE
  R0             5             340
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2018V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KRT39 MUTATED                                  0     0
  KRT39 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  KRT39 MUTATED                           0     5
  KRT39 WILD-TYPE                        22   221
D2018V13, multiclass
                                  clus
vv                                 KRT39 MUTATED KRT39 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        5             221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2019) Variable = DDX11 MUTATION ANALYSIS
D2019V1, survival
                 sevent
clus2               0   1
  DDX11 MUTATED     6   2
  DDX11 WILD-TYPE 372  91
  DDX11 MUTATED DDX11 WILD-TYPE 
              8             463 
  DDX11 MUTATED DDX11 WILD-TYPE 
              2              91 
$`DDX11 MUTATED`
TCGA-A6-5665 TCGA-AA-3655 TCGA-AA-3715 TCGA-AZ-6599 TCGA-CM-6674 TCGA-G4-6586 
       22.06        61.02        19.04         6.77        12.95        35.80 
TCGA-G4-6588 TCGA-AG-A02N 
       26.17        61.97 

$`DDX11 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       19.99        13.94        19.99        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        88.21        49.41        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6676 
       13.02        15.02        14.04        11.01        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       22.09        13.78        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X 
       64.01        10.98        49.97         1.94        38.96        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  DDX11 MUTATED DDX11 WILD-TYPE 
           6.77            0.00 
  DDX11 MUTATED DDX11 WILD-TYPE 
          61.97          148.01 
  DDX11 MUTATED DDX11 WILD-TYPE 
         24.115          20.120 
[1] "6.8 - 62.0 (24.1)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.1"
D2019V2, continuous
D2019V3, binary
                 cls
clus                0   1
  DDX11 MUTATED     7   1
  DDX11 WILD-TYPE 359 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX11 MUTATED      7    1
  DDX11 WILD-TYPE  359  118
        clus
vv       DDX11 MUTATED DDX11 WILD-TYPE
  COLON              7             359
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DDX11 MUTATED         1        0        3         4         0         0
  DDX11 WILD-TYPE      90        1       29       134        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DDX11 MUTATED           0          0          0          0        0         0
  DDX11 WILD-TYPE        24         11         59         42       48        18
                 vv
clus              STAGE IVB
  DDX11 MUTATED           0
  DDX11 WILD-TYPE         1
D2019V4, multiclass
            clus
vv           DDX11 MUTATED DDX11 WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               3              29
  STAGE IIA              4             134
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  DDX11 MUTATED     0   1   7   0
  DDX11 WILD-TYPE  17  91 322  50
D2019V5, multiclass
    clus
vv   DDX11 MUTATED DDX11 WILD-TYPE
  T1             0              17
  T2             1              91
  T3             7             322
  T4             0              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  DDX11 MUTATED     8   0   0
  DDX11 WILD-TYPE 279 113  87
D2019V6, multiclass
    clus
vv   DDX11 MUTATED DDX11 WILD-TYPE
  N0             8             279
  N1             0             113
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2019V7, binary
                 cls
clus                0   1
  DDX11 MUTATED     7   0
  DDX11 WILD-TYPE 368  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX11 MUTATED      7    0
  DDX11 WILD-TYPE  368   65
   clus
vv  DDX11 MUTATED DDX11 WILD-TYPE
  0             7             368
  1             0              65
[1] 2 2
[1] FALSE
D2019V8, binary
                 cls
clus                0   1
  DDX11 MUTATED     3   5
  DDX11 WILD-TYPE 222 259
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX11 MUTATED      3    5
  DDX11 WILD-TYPE  222  259
        clus
vv       DDX11 MUTATED DDX11 WILD-TYPE
  FEMALE             3             222
  MALE               5             259
[1] 2 2
[1] FALSE
D2019V9, binary
                 cls
clus                0   1
  DDX11 MUTATED     7   0
  DDX11 WILD-TYPE 343  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DDX11 MUTATED      7    0
  DDX11 WILD-TYPE  343   22
     clus
vv    DDX11 MUTATED DDX11 WILD-TYPE
  NO              7             343
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  DDX11 MUTATED                      7                             0
  DDX11 WILD-TYPE                  308                            47
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  DDX11 MUTATED                       1                              0
  DDX11 WILD-TYPE                   105                             10
D2019V10, multiclass
                                clus
vv                               DDX11 MUTATED DDX11 WILD-TYPE
  COLON ADENOCARCINOMA                       7             308
  COLON MUCINOUS ADENOCARCINOMA              0              47
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  DDX11 MUTATED     7   0   0   0
  DDX11 WILD-TYPE 338   4  31  25
D2019V11, multiclass
    clus
vv   DDX11 MUTATED DDX11 WILD-TYPE
  R0             7             338
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2019V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DDX11 MUTATED                                  0     0
  DDX11 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  DDX11 MUTATED                           0     5
  DDX11 WILD-TYPE                        22   221
D2019V13, multiclass
                                  clus
vv                                 DDX11 MUTATED DDX11 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        5             221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2020) Variable = VEPH1 MUTATION ANALYSIS
D2020V1, survival
                 sevent
clus2               0   1
  VEPH1 MUTATED    14   5
  VEPH1 WILD-TYPE 364  88
  VEPH1 MUTATED VEPH1 WILD-TYPE 
             19             452 
  VEPH1 MUTATED VEPH1 WILD-TYPE 
              5              88 
$`VEPH1 MUTATED`
TCGA-A6-6653 TCGA-A6-6780 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3715 TCGA-AA-3815 
       24.39        20.12        17.95        29.95        19.04        33.04 
TCGA-AA-3845 TCGA-AA-A010 TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-4743 TCGA-CM-6674 
        0.00        34.98        12.76        10.06        23.05        12.95 
TCGA-D5-6533 TCGA-D5-6928 TCGA-DM-A28C TCGA-G4-6309 TCGA-AG-3600 TCGA-AG-A025 
        1.32        11.64        81.37        85.48         6.05        49.97 
TCGA-DY-A1DD 
       57.24 

$`VEPH1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
       25.08        25.18        24.16        21.76        24.69        23.87 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       24.00        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
       26.99        19.04        10.06        35.05         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       12.20        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
      124.27        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       15.02        14.04        11.01        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 
       56.09        55.92        20.19        18.25        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
        9.44         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      135.65       139.17         6.12       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 
       65.85        53.62        44.68        55.04        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 
       34.03         2.01        50.04        12.03         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A026 TCGA-AG-A02G 
       12.00        70.03        64.01        10.98         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
        5.29       126.44        41.36        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  VEPH1 MUTATED VEPH1 WILD-TYPE 
              0               0 
  VEPH1 MUTATED VEPH1 WILD-TYPE 
          85.48          148.01 
  VEPH1 MUTATED VEPH1 WILD-TYPE 
         20.120          20.235 
[1] "0.0 - 85.5 (20.1)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.2"
D2020V2, continuous
D2020V3, binary
                 cls
clus                0   1
  VEPH1 MUTATED    17   3
  VEPH1 WILD-TYPE 349 116
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VEPH1 MUTATED     17    3
  VEPH1 WILD-TYPE  349  116
        clus
vv       VEPH1 MUTATED VEPH1 WILD-TYPE
  COLON             17             349
  RECTUM             3             116
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  VEPH1 MUTATED         3        0        1        11         1         0
  VEPH1 WILD-TYPE      88        1       31       127         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  VEPH1 MUTATED           0          0          3          1        0         0
  VEPH1 WILD-TYPE        24         11         56         41       48        18
                 vv
clus              STAGE IVB
  VEPH1 MUTATED           0
  VEPH1 WILD-TYPE         1
D2020V4, multiclass
            clus
vv           VEPH1 MUTATED VEPH1 WILD-TYPE
  STAGE I                3              88
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA             11             127
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             3              56
  STAGE IIIC             1              41
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  VEPH1 MUTATED     1   2  15   2
  VEPH1 WILD-TYPE  16  90 314  48
D2020V5, multiclass
    clus
vv   VEPH1 MUTATED VEPH1 WILD-TYPE
  T1             1              16
  T2             2              90
  T3            15             314
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  VEPH1 MUTATED    17   2   1
  VEPH1 WILD-TYPE 270 111  86
D2020V6, multiclass
    clus
vv   VEPH1 MUTATED VEPH1 WILD-TYPE
  N0            17             270
  N1             2             111
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2020V7, binary
                 cls
clus                0   1
  VEPH1 MUTATED    18   0
  VEPH1 WILD-TYPE 357  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VEPH1 MUTATED     18    0
  VEPH1 WILD-TYPE  357   65
   clus
vv  VEPH1 MUTATED VEPH1 WILD-TYPE
  0            18             357
  1             0              65
[1] 2 2
[1] FALSE
D2020V8, binary
                 cls
clus                0   1
  VEPH1 MUTATED     9  11
  VEPH1 WILD-TYPE 216 253
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VEPH1 MUTATED      9   11
  VEPH1 WILD-TYPE  216  253
        clus
vv       VEPH1 MUTATED VEPH1 WILD-TYPE
  FEMALE             9             216
  MALE              11             253
[1] 2 2
[1] FALSE
D2020V9, binary
                 cls
clus                0   1
  VEPH1 MUTATED    13   1
  VEPH1 WILD-TYPE 337  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VEPH1 MUTATED     13    1
  VEPH1 WILD-TYPE  337   21
     clus
vv    VEPH1 MUTATED VEPH1 WILD-TYPE
  NO             13             337
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  VEPH1 MUTATED                     13                             4
  VEPH1 WILD-TYPE                  302                            43
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  VEPH1 MUTATED                       3                              0
  VEPH1 WILD-TYPE                   103                             10
D2020V10, multiclass
                                clus
vv                               VEPH1 MUTATED VEPH1 WILD-TYPE
  COLON ADENOCARCINOMA                      13             302
  COLON MUCINOUS ADENOCARCINOMA              4              43
  RECTAL ADENOCARCINOMA                      3             103
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  VEPH1 MUTATED    13   0   0   3
  VEPH1 WILD-TYPE 332   4  31  22
D2020V11, multiclass
    clus
vv   VEPH1 MUTATED VEPH1 WILD-TYPE
  R0            13             332
  R1             0               4
  R2             0              31
  RX             3              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2020V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  VEPH1 MUTATED                                  0     2
  VEPH1 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  VEPH1 MUTATED                           1     9
  VEPH1 WILD-TYPE                        21   217
D2020V13, multiclass
                                  clus
vv                                 VEPH1 MUTATED VEPH1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               9
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        9             217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2021) Variable = OR2M5 MUTATION ANALYSIS
D2021V1, survival
                 sevent
clus2               0   1
  OR2M5 MUTATED    11   1
  OR2M5 WILD-TYPE 367  92
  OR2M5 MUTATED OR2M5 WILD-TYPE 
             12             459 
  OR2M5 MUTATED OR2M5 WILD-TYPE 
              1              92 
$`OR2M5 MUTATED`
TCGA-AA-3672 TCGA-AA-3877 TCGA-AA-A010 TCGA-AD-6963 TCGA-AZ-6601 TCGA-CM-5860 
        0.92        31.00        34.98        27.42       100.01        32.02 
TCGA-CM-6168 TCGA-D5-6533 TCGA-AF-6672 TCGA-AG-A002 TCGA-AG-A011 TCGA-DC-6682 
       12.99         1.32        10.39        20.98        37.02         4.01 

$`OR2M5 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
        6.05         6.97        54.02         2.01        14.01        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 
       17.03        24.03        27.02        29.98        18.05         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6964 TCGA-AD-6965 
        0.79         0.72         5.79        22.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 
       62.79        88.21        49.41         6.77        12.10        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.03        22.98        30.08        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       16.04        21.99        14.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       55.92        20.19        18.25        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       16.83        15.39        20.02        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
        6.02        25.97        23.01        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 
       13.97        27.95        10.98        19.99         5.95         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  OR2M5 MUTATED OR2M5 WILD-TYPE 
           0.92            0.00 
  OR2M5 MUTATED OR2M5 WILD-TYPE 
         100.01          148.01 
  OR2M5 MUTATED OR2M5 WILD-TYPE 
          24.20           20.12 
[1] "0.9 - 100.0 (24.2)" "0.0 - 148.0 (20.1)"
[1] "hr=" "2.2"
D2021V2, continuous
D2021V3, binary
                 cls
clus                0   1
  OR2M5 MUTATED     8   4
  OR2M5 WILD-TYPE 358 115
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR2M5 MUTATED      8    4
  OR2M5 WILD-TYPE  358  115
        clus
vv       OR2M5 MUTATED OR2M5 WILD-TYPE
  COLON              8             358
  RECTUM             4             115
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  OR2M5 MUTATED         2        0        1         4         1         0
  OR2M5 WILD-TYPE      89        1       31       134         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  OR2M5 MUTATED           1          0          1          0        1         0
  OR2M5 WILD-TYPE        23         11         58         42       47        18
                 vv
clus              STAGE IVB
  OR2M5 MUTATED           0
  OR2M5 WILD-TYPE         1
D2021V4, multiclass
            clus
vv           OR2M5 MUTATED OR2M5 WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              4             134
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             0              42
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  OR2M5 MUTATED     1   1   7   3
  OR2M5 WILD-TYPE  16  91 322  47
D2021V5, multiclass
    clus
vv   OR2M5 MUTATED OR2M5 WILD-TYPE
  T1             1              16
  T2             1              91
  T3             7             322
  T4             3              47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  OR2M5 MUTATED    10   1   1
  OR2M5 WILD-TYPE 277 112  86
D2021V6, multiclass
    clus
vv   OR2M5 MUTATED OR2M5 WILD-TYPE
  N0            10             277
  N1             1             112
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2021V7, binary
                 cls
clus                0   1
  OR2M5 MUTATED    10   0
  OR2M5 WILD-TYPE 365  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR2M5 MUTATED     10    0
  OR2M5 WILD-TYPE  365   65
   clus
vv  OR2M5 MUTATED OR2M5 WILD-TYPE
  0            10             365
  1             0              65
[1] 2 2
[1] FALSE
D2021V8, binary
                 cls
clus                0   1
  OR2M5 MUTATED     5   7
  OR2M5 WILD-TYPE 220 257
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR2M5 MUTATED      5    7
  OR2M5 WILD-TYPE  220  257
        clus
vv       OR2M5 MUTATED OR2M5 WILD-TYPE
  FEMALE             5             220
  MALE               7             257
[1] 2 2
[1] FALSE
D2021V9, binary
                 cls
clus                0   1
  OR2M5 MUTATED     9   1
  OR2M5 WILD-TYPE 341  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR2M5 MUTATED      9    1
  OR2M5 WILD-TYPE  341   21
     clus
vv    OR2M5 MUTATED OR2M5 WILD-TYPE
  NO              9             341
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  OR2M5 MUTATED                      7                             1
  OR2M5 WILD-TYPE                  308                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  OR2M5 MUTATED                       4                              0
  OR2M5 WILD-TYPE                   102                             10
D2021V10, multiclass
                                clus
vv                               OR2M5 MUTATED OR2M5 WILD-TYPE
  COLON ADENOCARCINOMA                       7             308
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      4             102
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  OR2M5 MUTATED     9   0   0   0
  OR2M5 WILD-TYPE 336   4  31  25
D2021V11, multiclass
    clus
vv   OR2M5 MUTATED OR2M5 WILD-TYPE
  R0             9             336
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2021V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OR2M5 MUTATED                                  0     0
  OR2M5 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  OR2M5 MUTATED                           1     6
  OR2M5 WILD-TYPE                        21   220
D2021V13, multiclass
                                  clus
vv                                 OR2M5 MUTATED OR2M5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        6             220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2022) Variable = RBP3 MUTATION ANALYSIS
D2022V1, survival
                sevent
clus2              0   1
  RBP3 MUTATED    11   3
  RBP3 WILD-TYPE 367  90
  RBP3 MUTATED RBP3 WILD-TYPE 
            14            457 
  RBP3 MUTATED RBP3 WILD-TYPE 
             3             90 
$`RBP3 MUTATED`
TCGA-A6-6651 TCGA-AA-3510 TCGA-AA-3663 TCGA-AA-3666 TCGA-AA-3947 TCGA-AA-A010 
       21.76        63.98         6.97         2.01        33.01        34.98 
TCGA-AU-6004 TCGA-AZ-6598 TCGA-AZ-6603 TCGA-CM-4743 TCGA-D5-6540 TCGA-DM-A1HB 
       27.09        49.41        29.56        23.05        16.14       135.65 
TCGA-G4-6304 TCGA-AG-A002 
       53.62        20.98 

$`RBP3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.08        25.18        24.16        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 
       22.42        27.42        10.88         0.20        14.50        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 
        5.13       106.75        22.36        62.79        88.21         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
       12.10       100.01         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
        1.91       124.27        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       12.49        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
        7.50        44.32       131.51       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 
       35.31       133.18        74.56        65.85        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  RBP3 MUTATED RBP3 WILD-TYPE 
          2.01           0.00 
  RBP3 MUTATED RBP3 WILD-TYPE 
        135.65         148.01 
  RBP3 MUTATED RBP3 WILD-TYPE 
        28.325         20.020 
[1] "2.0 - 135.7 (28.3)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.2"
D2022V2, continuous
D2022V3, binary
                cls
clus               0   1
  RBP3 MUTATED    13   1
  RBP3 WILD-TYPE 353 118
[1] "tbl2"
                cls
clus             [,1] [,2]
  RBP3 MUTATED     13    1
  RBP3 WILD-TYPE  353  118
        clus
vv       RBP3 MUTATED RBP3 WILD-TYPE
  COLON            13            353
  RECTUM            1            118
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RBP3 MUTATED         3        0        3         1         3         0
  RBP3 WILD-TYPE      88        1       29       137         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RBP3 MUTATED           1          0          2          0        0         0
  RBP3 WILD-TYPE        23         11         57         42       48        18
                vv
clus             STAGE IVB
  RBP3 MUTATED           0
  RBP3 WILD-TYPE         1
D2022V4, multiclass
            clus
vv           RBP3 MUTATED RBP3 WILD-TYPE
  STAGE I               3             88
  STAGE IA              0              1
  STAGE II              3             29
  STAGE IIA             1            137
  STAGE IIB             3              7
  STAGE IIC             0              1
  STAGE III             1             23
  STAGE IIIA            0             11
  STAGE IIIB            2             57
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  RBP3 MUTATED     0   4   7   3
  RBP3 WILD-TYPE  17  88 322  47
D2022V5, multiclass
    clus
vv   RBP3 MUTATED RBP3 WILD-TYPE
  T1            0             17
  T2            4             88
  T3            7            322
  T4            3             47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  RBP3 MUTATED    10   4   0
  RBP3 WILD-TYPE 277 109  87
D2022V6, multiclass
    clus
vv   RBP3 MUTATED RBP3 WILD-TYPE
  N0           10            277
  N1            4            109
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2022V7, binary
                cls
clus               0   1
  RBP3 MUTATED    11   0
  RBP3 WILD-TYPE 364  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  RBP3 MUTATED     11    0
  RBP3 WILD-TYPE  364   65
   clus
vv  RBP3 MUTATED RBP3 WILD-TYPE
  0           11            364
  1            0             65
[1] 2 2
[1] FALSE
D2022V8, binary
                cls
clus               0   1
  RBP3 MUTATED     7   7
  RBP3 WILD-TYPE 218 257
[1] "tbl2"
                cls
clus             [,1] [,2]
  RBP3 MUTATED      7    7
  RBP3 WILD-TYPE  218  257
        clus
vv       RBP3 MUTATED RBP3 WILD-TYPE
  FEMALE            7            218
  MALE              7            257
[1] 2 2
[1] FALSE
D2022V9, binary
                cls
clus               0   1
  RBP3 MUTATED    11   0
  RBP3 WILD-TYPE 339  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  RBP3 MUTATED     11    0
  RBP3 WILD-TYPE  339   22
     clus
vv    RBP3 MUTATED RBP3 WILD-TYPE
  NO            11            339
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  RBP3 MUTATED                     10                             2
  RBP3 WILD-TYPE                  305                            45
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  RBP3 MUTATED                       1                              0
  RBP3 WILD-TYPE                   105                             10
D2022V10, multiclass
                                clus
vv                               RBP3 MUTATED RBP3 WILD-TYPE
  COLON ADENOCARCINOMA                     10            305
  COLON MUCINOUS ADENOCARCINOMA             2             45
  RECTAL ADENOCARCINOMA                     1            105
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  RBP3 MUTATED    10   0   0   0
  RBP3 WILD-TYPE 335   4  31  25
D2022V11, multiclass
    clus
vv   RBP3 MUTATED RBP3 WILD-TYPE
  R0           10            335
  R1            0              4
  R2            0             31
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2022V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RBP3 MUTATED                                  0     0
  RBP3 WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  RBP3 MUTATED                           0     8
  RBP3 WILD-TYPE                        22   218
D2022V13, multiclass
                                  clus
vv                                 RBP3 MUTATED RBP3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       8            218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2023) Variable = SGCE MUTATION ANALYSIS
D2023V1, survival
                sevent
clus2              0   1
  SGCE MUTATED     6   2
  SGCE WILD-TYPE 372  91
  SGCE MUTATED SGCE WILD-TYPE 
             8            463 
  SGCE MUTATED SGCE WILD-TYPE 
             2             91 
$`SGCE MUTATED`
TCGA-AA-3673 TCGA-AA-3870 TCGA-AA-A010 TCGA-AD-6964 TCGA-AY-4071 TCGA-AF-3400 
       50.04        29.98        34.98        10.88         0.95        34.49 
TCGA-AH-6544 TCGA-EI-6506 
       38.56        20.55 

$`SGCE WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       17.03        24.03        27.02        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
        0.79         0.72         5.79        22.42        27.42         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       14.50        27.09        16.31        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6547 TCGA-AH-6549 
       61.97        41.00        38.04       117.11         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
        0.49        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  SGCE MUTATED SGCE WILD-TYPE 
          0.95           0.00 
  SGCE MUTATED SGCE WILD-TYPE 
         50.04         148.01 
  SGCE MUTATED SGCE WILD-TYPE 
        32.235         20.050 
[1] "0.9 - 50.0 (32.2)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.3"
D2023V2, continuous
D2023V3, binary
                cls
clus               0   1
  SGCE MUTATED     4   3
  SGCE WILD-TYPE 362 116
[1] "tbl2"
                cls
clus             [,1] [,2]
  SGCE MUTATED      4    3
  SGCE WILD-TYPE  362  116
        clus
vv       SGCE MUTATED SGCE WILD-TYPE
  COLON             4            362
  RECTUM            3            116
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SGCE MUTATED         1        0        1         2         1         0
  SGCE WILD-TYPE      90        1       31       136         9         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SGCE MUTATED           0          0          0          0        1         0
  SGCE WILD-TYPE        24         11         59         42       47        18
                vv
clus             STAGE IVB
  SGCE MUTATED           0
  SGCE WILD-TYPE         1
D2023V4, multiclass
            clus
vv           SGCE MUTATED SGCE WILD-TYPE
  STAGE I               1             90
  STAGE IA              0              1
  STAGE II              1             31
  STAGE IIA             2            136
  STAGE IIB             1              9
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            0             59
  STAGE IIIC            0             42
  STAGE IV              1             47
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  SGCE MUTATED     1   0   5   2
  SGCE WILD-TYPE  16  92 324  48
D2023V5, multiclass
    clus
vv   SGCE MUTATED SGCE WILD-TYPE
  T1            1             16
  T2            0             92
  T3            5            324
  T4            2             48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  SGCE MUTATED     5   1   2
  SGCE WILD-TYPE 282 112  85
D2023V6, multiclass
    clus
vv   SGCE MUTATED SGCE WILD-TYPE
  N0            5            282
  N1            1            112
  N2            2             85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2023V7, binary
                cls
clus               0   1
  SGCE MUTATED     4   2
  SGCE WILD-TYPE 371  63
[1] "tbl2"
                cls
clus             [,1] [,2]
  SGCE MUTATED      4    2
  SGCE WILD-TYPE  371   63
   clus
vv  SGCE MUTATED SGCE WILD-TYPE
  0            4            371
  1            2             63
[1] 2 2
[1] FALSE
D2023V8, binary
                cls
clus               0   1
  SGCE MUTATED     5   3
  SGCE WILD-TYPE 220 261
[1] "tbl2"
                cls
clus             [,1] [,2]
  SGCE MUTATED      5    3
  SGCE WILD-TYPE  220  261
        clus
vv       SGCE MUTATED SGCE WILD-TYPE
  FEMALE            5            220
  MALE              3            261
[1] 2 2
[1] FALSE
D2023V9, binary
                cls
clus               0   1
  SGCE MUTATED     6   1
  SGCE WILD-TYPE 344  21
[1] "tbl2"
                cls
clus             [,1] [,2]
  SGCE MUTATED      6    1
  SGCE WILD-TYPE  344   21
     clus
vv    SGCE MUTATED SGCE WILD-TYPE
  NO             6            344
  YES            1             21
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SGCE MUTATED                      4                             0
  SGCE WILD-TYPE                  311                            47
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SGCE MUTATED                       2                              1
  SGCE WILD-TYPE                   104                              9
D2023V10, multiclass
                                clus
vv                               SGCE MUTATED SGCE WILD-TYPE
  COLON ADENOCARCINOMA                      4            311
  COLON MUCINOUS ADENOCARCINOMA             0             47
  RECTAL ADENOCARCINOMA                     2            104
  RECTAL MUCINOUS ADENOCARCINOMA            1              9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  SGCE MUTATED     6   0   0   0
  SGCE WILD-TYPE 339   4  31  25
D2023V11, multiclass
    clus
vv   SGCE MUTATED SGCE WILD-TYPE
  R0            6            339
  R1            0              4
  R2            0             31
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2023V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SGCE MUTATED                                  0     0
  SGCE WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  SGCE MUTATED                           0     5
  SGCE WILD-TYPE                        22   221
D2023V13, multiclass
                                  clus
vv                                 SGCE MUTATED SGCE WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       5            221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2024) Variable = ZNF622 MUTATION ANALYSIS
D2024V1, survival
                  sevent
clus2                0   1
  ZNF622 MUTATED     6   3
  ZNF622 WILD-TYPE 372  90
  ZNF622 MUTATED ZNF622 WILD-TYPE 
               9              462 
  ZNF622 MUTATED ZNF622 WILD-TYPE 
               3               90 
$`ZNF622 MUTATED`
TCGA-AA-3663 TCGA-AA-3715 TCGA-CK-4952 TCGA-CK-5916 TCGA-CM-6679 TCGA-D5-6923 
        6.97        19.04        15.62        21.14        10.06        12.43 
TCGA-DM-A0XD TCGA-AG-A002 TCGA-AG-A01Y 
       24.43        20.98        64.01 

$`ZNF622 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.05        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 
       36.00         5.03        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 
       85.45        49.08        51.32         9.99        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.08        11.01        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6924 
       16.14        15.58         1.48         3.68         4.41        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       11.38        10.26       119.70        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A020 
       15.95        36.03         9.07        12.00        70.03        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  ZNF622 MUTATED ZNF622 WILD-TYPE 
            6.97             0.00 
  ZNF622 MUTATED ZNF622 WILD-TYPE 
           64.01           148.01 
  ZNF622 MUTATED ZNF622 WILD-TYPE 
          19.040           20.235 
[1] "7.0 - 64.0 (19.0)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.9"
D2024V2, continuous
D2024V3, binary
                  cls
clus                 0   1
  ZNF622 MUTATED     7   2
  ZNF622 WILD-TYPE 359 117
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF622 MUTATED      7    2
  ZNF622 WILD-TYPE  359  117
        clus
vv       ZNF622 MUTATED ZNF622 WILD-TYPE
  COLON               7              359
  RECTUM              2              117
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZNF622 MUTATED         3        0        3         2         0         0
  ZNF622 WILD-TYPE      88        1       29       136        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF622 MUTATED           0          0          0          1        0
  ZNF622 WILD-TYPE        24         11         59         41       48
                  vv
clus               STAGE IVA STAGE IVB
  ZNF622 MUTATED           0         0
  ZNF622 WILD-TYPE        18         1
D2024V4, multiclass
            clus
vv           ZNF622 MUTATED ZNF622 WILD-TYPE
  STAGE I                 3               88
  STAGE IA                0                1
  STAGE II                3               29
  STAGE IIA               2              136
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              0               59
  STAGE IIIC              1               41
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZNF622 MUTATED     1   2   5   1
  ZNF622 WILD-TYPE  16  90 324  49
D2024V5, multiclass
    clus
vv   ZNF622 MUTATED ZNF622 WILD-TYPE
  T1              1               16
  T2              2               90
  T3              5              324
  T4              1               49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  ZNF622 MUTATED     8   0   1
  ZNF622 WILD-TYPE 279 113  86
D2024V6, multiclass
    clus
vv   ZNF622 MUTATED ZNF622 WILD-TYPE
  N0              8              279
  N1              0              113
  N2              1               86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2024V7, binary
                  cls
clus                 0   1
  ZNF622 MUTATED     9   0
  ZNF622 WILD-TYPE 366  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF622 MUTATED      9    0
  ZNF622 WILD-TYPE  366   65
   clus
vv  ZNF622 MUTATED ZNF622 WILD-TYPE
  0              9              366
  1              0               65
[1] 2 2
[1] FALSE
D2024V8, binary
                  cls
clus                 0   1
  ZNF622 MUTATED     3   6
  ZNF622 WILD-TYPE 222 258
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF622 MUTATED      3    6
  ZNF622 WILD-TYPE  222  258
        clus
vv       ZNF622 MUTATED ZNF622 WILD-TYPE
  FEMALE              3              222
  MALE                6              258
[1] 2 2
[1] FALSE
D2024V9, binary
                  cls
clus                 0   1
  ZNF622 MUTATED     6   0
  ZNF622 WILD-TYPE 344  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF622 MUTATED      6    0
  ZNF622 WILD-TYPE  344   22
     clus
vv    ZNF622 MUTATED ZNF622 WILD-TYPE
  NO               6              344
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ZNF622 MUTATED                      6                             1
  ZNF622 WILD-TYPE                  309                            46
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ZNF622 MUTATED                       2                              0
  ZNF622 WILD-TYPE                   104                             10
D2024V10, multiclass
                                clus
vv                               ZNF622 MUTATED ZNF622 WILD-TYPE
  COLON ADENOCARCINOMA                        6              309
  COLON MUCINOUS ADENOCARCINOMA               1               46
  RECTAL ADENOCARCINOMA                       2              104
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ZNF622 MUTATED     6   0   0   2
  ZNF622 WILD-TYPE 339   4  31  23
D2024V11, multiclass
    clus
vv   ZNF622 MUTATED ZNF622 WILD-TYPE
  R0              6              339
  R1              0                4
  R2              0               31
  RX              2               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2024V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF622 MUTATED                                  0     0
  ZNF622 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZNF622 MUTATED                           0     5
  ZNF622 WILD-TYPE                        22   221
D2024V13, multiclass
                                  clus
vv                                 ZNF622 MUTATED ZNF622 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         5              221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2025) Variable = FAM160B1 MUTATION ANALYSIS
D2025V1, survival
                    sevent
clus2                  0   1
  FAM160B1 MUTATED     7   0
  FAM160B1 WILD-TYPE 371  93
  FAM160B1 MUTATED FAM160B1 WILD-TYPE 
                 7                464 
  FAM160B1 MUTATED FAM160B1 WILD-TYPE 
                 0                 93 
$`FAM160B1 MUTATED`
TCGA-A6-6780 TCGA-AA-3713 TCGA-AA-A010 TCGA-CK-4950 TCGA-CM-4746 TCGA-CM-6161 
       20.12        19.04        34.98        85.45        37.02        15.02 
TCGA-AG-A002 
       20.98 

$`FAM160B1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 
       12.76        10.06        14.30        17.56       148.01        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
      124.27        23.05        20.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        15.02        17.03        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  FAM160B1 MUTATED FAM160B1 WILD-TYPE 
             15.02               0.00 
  FAM160B1 MUTATED FAM160B1 WILD-TYPE 
             85.45             148.01 
  FAM160B1 MUTATED FAM160B1 WILD-TYPE 
             20.98              20.12 
[1] "15.0 - 85.5 (21.0)" "0.0 - 148.0 (20.1)"
[1] "hr="     "9200000"
D2025V2, continuous
D2025V3, binary
                    cls
clus                   0   1
  FAM160B1 MUTATED     8   1
  FAM160B1 WILD-TYPE 358 118
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  FAM160B1 MUTATED      8    1
  FAM160B1 WILD-TYPE  358  118
        clus
vv       FAM160B1 MUTATED FAM160B1 WILD-TYPE
  COLON                 8                358
  RECTUM                1                118
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FAM160B1 MUTATED         3        0        1         2         1         0
  FAM160B1 WILD-TYPE      88        1       31       136         9         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FAM160B1 MUTATED           0          0          1          0        1
  FAM160B1 WILD-TYPE        24         11         58         42       47
                    vv
clus                 STAGE IVA STAGE IVB
  FAM160B1 MUTATED           0         0
  FAM160B1 WILD-TYPE        18         1
D2025V4, multiclass
            clus
vv           FAM160B1 MUTATED FAM160B1 WILD-TYPE
  STAGE I                   3                 88
  STAGE IA                  0                  1
  STAGE II                  1                 31
  STAGE IIA                 2                136
  STAGE IIB                 1                  9
  STAGE IIC                 0                  1
  STAGE III                 0                 24
  STAGE IIIA                0                 11
  STAGE IIIB                1                 58
  STAGE IIIC                0                 42
  STAGE IV                  1                 47
  STAGE IVA                 0                 18
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  FAM160B1 MUTATED     0   3   4   2
  FAM160B1 WILD-TYPE  17  89 325  48
D2025V5, multiclass
    clus
vv   FAM160B1 MUTATED FAM160B1 WILD-TYPE
  T1                0                 17
  T2                3                 89
  T3                4                325
  T4                2                 48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  FAM160B1 MUTATED     8   1   0
  FAM160B1 WILD-TYPE 279 112  87
D2025V6, multiclass
    clus
vv   FAM160B1 MUTATED FAM160B1 WILD-TYPE
  N0                8                279
  N1                1                112
  N2                0                 87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2025V7, binary
                    cls
clus                   0   1
  FAM160B1 MUTATED     7   1
  FAM160B1 WILD-TYPE 368  64
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  FAM160B1 MUTATED      7    1
  FAM160B1 WILD-TYPE  368   64
   clus
vv  FAM160B1 MUTATED FAM160B1 WILD-TYPE
  0                7                368
  1                1                 64
[1] 2 2
[1] FALSE
D2025V8, binary
                    cls
clus                   0   1
  FAM160B1 MUTATED     5   4
  FAM160B1 WILD-TYPE 220 260
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  FAM160B1 MUTATED      5    4
  FAM160B1 WILD-TYPE  220  260
        clus
vv       FAM160B1 MUTATED FAM160B1 WILD-TYPE
  FEMALE                5                220
  MALE                  4                260
[1] 2 2
[1] FALSE
D2025V9, binary
                    cls
clus                   0   1
  FAM160B1 MUTATED     6   1
  FAM160B1 WILD-TYPE 344  21
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  FAM160B1 MUTATED      6    1
  FAM160B1 WILD-TYPE  344   21
     clus
vv    FAM160B1 MUTATED FAM160B1 WILD-TYPE
  NO                 6                344
  YES                1                 21
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  FAM160B1 MUTATED                      7                             1
  FAM160B1 WILD-TYPE                  308                            46
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  FAM160B1 MUTATED                       1                              0
  FAM160B1 WILD-TYPE                   105                             10
D2025V10, multiclass
                                clus
vv                               FAM160B1 MUTATED FAM160B1 WILD-TYPE
  COLON ADENOCARCINOMA                          7                308
  COLON MUCINOUS ADENOCARCINOMA                 1                 46
  RECTAL ADENOCARCINOMA                         1                105
  RECTAL MUCINOUS ADENOCARCINOMA                0                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  FAM160B1 MUTATED     6   1   1   0
  FAM160B1 WILD-TYPE 339   3  30  25
D2025V11, multiclass
    clus
vv   FAM160B1 MUTATED FAM160B1 WILD-TYPE
  R0                6                339
  R1                1                  3
  R2                1                 30
  RX                0                 25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2025V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FAM160B1 MUTATED                                  0     0
  FAM160B1 WILD-TYPE                                1    11
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  FAM160B1 MUTATED                           2     2
  FAM160B1 WILD-TYPE                        20   224
D2025V13, multiclass
                                  clus
vv                                 FAM160B1 MUTATED FAM160B1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 11
  BLACK OR AFRICAN AMERICAN                       2                 20
  WHITE                                           2                224
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2026) Variable = UBD MUTATION ANALYSIS
D2026V1, survival
               sevent
clus2             0   1
  UBD MUTATED     3   1
  UBD WILD-TYPE 375  92
  UBD MUTATED UBD WILD-TYPE 
            4           467 
  UBD MUTATED UBD WILD-TYPE 
            1            92 
$`UBD MUTATED`
TCGA-A6-6141 TCGA-AA-3663 TCGA-AD-5900 TCGA-AF-5654 
        8.38         6.97         0.07        16.83 

$`UBD WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 
       22.09        22.06        32.71        27.09        22.52        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       39.98        18.05        40.96        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-6136 
       13.55        19.10        34.49        10.39        14.50        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  UBD MUTATED UBD WILD-TYPE 
         0.07          0.00 
  UBD MUTATED UBD WILD-TYPE 
        16.83        148.01 
  UBD MUTATED UBD WILD-TYPE 
        7.675        20.550 
[1] "0.1 - 16.8 (7.7)"   "0.0 - 148.0 (20.6)"
[1] "hr=" "3.6"
D2026V2, continuous
D2026V3, binary
               cls
clus              0   1
  UBD MUTATED     3   1
  UBD WILD-TYPE 363 118
[1] "tbl2"
               cls
clus            [,1] [,2]
  UBD MUTATED      3    1
  UBD WILD-TYPE  363  118
        clus
vv       UBD MUTATED UBD WILD-TYPE
  COLON            3           363
  RECTUM           1           118
[1] 2 2
[1] FALSE
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  UBD MUTATED         2        0        1         1         0         0
  UBD WILD-TYPE      89        1       31       137        10         1
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  UBD MUTATED           0          0          0          0        0         0
  UBD WILD-TYPE        24         11         59         42       48        18
               vv
clus            STAGE IVB
  UBD MUTATED           0
  UBD WILD-TYPE         1
D2026V4, multiclass
            clus
vv           UBD MUTATED UBD WILD-TYPE
  STAGE I              2            89
  STAGE IA             0             1
  STAGE II             1            31
  STAGE IIA            1           137
  STAGE IIB            0            10
  STAGE IIC            0             1
  STAGE III            0            24
  STAGE IIIA           0            11
  STAGE IIIB           0            59
  STAGE IIIC           0            42
  STAGE IV             0            48
  STAGE IVA            0            18
  STAGE IVB            0             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  UBD MUTATED     0   2   2   0
  UBD WILD-TYPE  17  90 327  50
D2026V5, multiclass
    clus
vv   UBD MUTATED UBD WILD-TYPE
  T1           0            17
  T2           2            90
  T3           2           327
  T4           0            50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2
  UBD MUTATED     4   0   0
  UBD WILD-TYPE 283 113  87
D2026V6, multiclass
    clus
vv   UBD MUTATED UBD WILD-TYPE
  N0           4           283
  N1           0           113
  N2           0            87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2026V7, binary
               cls
clus              0   1
  UBD MUTATED     3   0
  UBD WILD-TYPE 372  65
[1] "tbl2"
               cls
clus            [,1] [,2]
  UBD MUTATED      3    0
  UBD WILD-TYPE  372   65
   clus
vv  UBD MUTATED UBD WILD-TYPE
  0           3           372
  1           0            65
[1] 2 2
[1] FALSE
D2026V8, binary
               cls
clus              0   1
  UBD MUTATED     1   3
  UBD WILD-TYPE 224 261
[1] "tbl2"
               cls
clus            [,1] [,2]
  UBD MUTATED      1    3
  UBD WILD-TYPE  224  261
        clus
vv       UBD MUTATED UBD WILD-TYPE
  FEMALE           1           224
  MALE             3           261
[1] 2 2
[1] FALSE
D2026V9, binary
               cls
clus              0   1
  UBD MUTATED     3   0
  UBD WILD-TYPE 347  22
[1] "tbl2"
               cls
clus            [,1] [,2]
  UBD MUTATED      3    0
  UBD WILD-TYPE  347   22
     clus
vv    UBD MUTATED UBD WILD-TYPE
  NO            3           347
  YES           0            22
[1] 2 2
[1] FALSE
               vv
clus            COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  UBD MUTATED                      2                             1
  UBD WILD-TYPE                  313                            46
               vv
clus            RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  UBD MUTATED                       1                              0
  UBD WILD-TYPE                   105                             10
D2026V10, multiclass
                                clus
vv                               UBD MUTATED UBD WILD-TYPE
  COLON ADENOCARCINOMA                     2           313
  COLON MUCINOUS ADENOCARCINOMA            1            46
  RECTAL ADENOCARCINOMA                    1           105
  RECTAL MUCINOUS ADENOCARCINOMA           0            10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             R0  R1  R2  RX
  UBD MUTATED     3   0   0   0
  UBD WILD-TYPE 342   4  31  25
D2026V11, multiclass
    clus
vv   UBD MUTATED UBD WILD-TYPE
  R0           3           342
  R1           0             4
  R2           0            31
  RX           0            25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2026V12, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  UBD MUTATED                                  0     0
  UBD WILD-TYPE                                1    11
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  UBD MUTATED                           1     2
  UBD WILD-TYPE                        21   224
D2026V13, multiclass
                                  clus
vv                                 UBD MUTATED UBD WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      0            11
  BLACK OR AFRICAN AMERICAN                  1            21
  WHITE                                      2           224
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2027) Variable = OR8K1 MUTATION ANALYSIS
D2027V1, survival
                 sevent
clus2               0   1
  OR8K1 MUTATED    10   1
  OR8K1 WILD-TYPE 368  92
  OR8K1 MUTATED OR8K1 WILD-TYPE 
             11             460 
  OR8K1 MUTATED OR8K1 WILD-TYPE 
              1              92 
$`OR8K1 MUTATED`
TCGA-AA-3530 TCGA-AA-3660 TCGA-AA-3977 TCGA-AA-A010 TCGA-AU-6004 TCGA-CA-6717 
       19.07        78.08        25.02        34.98        27.09        12.76 
TCGA-CM-5861 TCGA-G4-6586 TCGA-AG-3892 TCGA-AG-A026 TCGA-EI-6508 
       15.02        35.80        13.02         1.94        20.91 

$`OR8K1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
        8.05        19.07         0.00        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 
       19.99        13.94        19.99        61.02         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       14.50        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07        12.20        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       22.98        30.08        32.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
       49.97        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  OR8K1 MUTATED OR8K1 WILD-TYPE 
           1.94            0.00 
  OR8K1 MUTATED OR8K1 WILD-TYPE 
          78.08          148.01 
  OR8K1 MUTATED OR8K1 WILD-TYPE 
         20.910          20.155 
[1] "1.9 - 78.1 (20.9)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "2.1"
D2027V2, continuous
D2027V3, binary
                 cls
clus                0   1
  OR8K1 MUTATED    10   3
  OR8K1 WILD-TYPE 356 116
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR8K1 MUTATED     10    3
  OR8K1 WILD-TYPE  356  116
        clus
vv       OR8K1 MUTATED OR8K1 WILD-TYPE
  COLON             10             356
  RECTUM             3             116
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  OR8K1 MUTATED         3        0        3         3         1         0
  OR8K1 WILD-TYPE      88        1       29       135         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  OR8K1 MUTATED           1          0          1          0        0         0
  OR8K1 WILD-TYPE        23         11         58         42       48        18
                 vv
clus              STAGE IVB
  OR8K1 MUTATED           0
  OR8K1 WILD-TYPE         1
D2027V4, multiclass
            clus
vv           OR8K1 MUTATED OR8K1 WILD-TYPE
  STAGE I                3              88
  STAGE IA               0               1
  STAGE II               3              29
  STAGE IIA              3             135
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  OR8K1 MUTATED     1   3   6   3
  OR8K1 WILD-TYPE  16  89 323  47
D2027V5, multiclass
    clus
vv   OR8K1 MUTATED OR8K1 WILD-TYPE
  T1             1              16
  T2             3              89
  T3             6             323
  T4             3              47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  OR8K1 MUTATED    11   1   1
  OR8K1 WILD-TYPE 276 112  86
D2027V6, multiclass
    clus
vv   OR8K1 MUTATED OR8K1 WILD-TYPE
  N0            11             276
  N1             1             112
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2027V7, binary
                 cls
clus                0   1
  OR8K1 MUTATED    12   0
  OR8K1 WILD-TYPE 363  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR8K1 MUTATED     12    0
  OR8K1 WILD-TYPE  363   65
   clus
vv  OR8K1 MUTATED OR8K1 WILD-TYPE
  0            12             363
  1             0              65
[1] 2 2
[1] FALSE
D2027V8, binary
                 cls
clus                0   1
  OR8K1 MUTATED     8   5
  OR8K1 WILD-TYPE 217 259
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR8K1 MUTATED      8    5
  OR8K1 WILD-TYPE  217  259
        clus
vv       OR8K1 MUTATED OR8K1 WILD-TYPE
  FEMALE             8             217
  MALE               5             259
[1] 2 2
[1] FALSE
D2027V9, binary
                 cls
clus                0   1
  OR8K1 MUTATED     9   0
  OR8K1 WILD-TYPE 341  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR8K1 MUTATED      9    0
  OR8K1 WILD-TYPE  341   22
     clus
vv    OR8K1 MUTATED OR8K1 WILD-TYPE
  NO              9             341
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  OR8K1 MUTATED                      9                             1
  OR8K1 WILD-TYPE                  306                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  OR8K1 MUTATED                       3                              0
  OR8K1 WILD-TYPE                   103                             10
D2027V10, multiclass
                                clus
vv                               OR8K1 MUTATED OR8K1 WILD-TYPE
  COLON ADENOCARCINOMA                       9             306
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      3             103
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  OR8K1 MUTATED    10   1   0   1
  OR8K1 WILD-TYPE 335   3  31  24
D2027V11, multiclass
    clus
vv   OR8K1 MUTATED OR8K1 WILD-TYPE
  R0            10             335
  R1             1               3
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2027V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OR8K1 MUTATED                                  0     1
  OR8K1 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  OR8K1 MUTATED                           0     4
  OR8K1 WILD-TYPE                        22   222
D2027V13, multiclass
                                  clus
vv                                 OR8K1 MUTATED OR8K1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        4             222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2028) Variable = TAB1 MUTATION ANALYSIS
D2028V1, survival
                sevent
clus2              0   1
  TAB1 MUTATED     3   0
  TAB1 WILD-TYPE 375  93
  TAB1 MUTATED TAB1 WILD-TYPE 
             3            468 
  TAB1 MUTATED TAB1 WILD-TYPE 
             0             93 
$`TAB1 MUTATED`
TCGA-AA-3672 TCGA-AD-6889 TCGA-CM-6171 
        0.92        56.55        14.04 

$`TAB1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
        6.05         6.97        54.02         2.01        14.01        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       15.52         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 
       14.99        12.99        13.02        15.02        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  TAB1 MUTATED TAB1 WILD-TYPE 
          0.92           0.00 
  TAB1 MUTATED TAB1 WILD-TYPE 
         56.55         148.01 
  TAB1 MUTATED TAB1 WILD-TYPE 
        14.040         20.235 
[1] "0.9 - 56.5 (14.0)"  "0.0 - 148.0 (20.2)"
[1] "hr="     "3300000"
D2028V2, continuous
[1] "Remove cluster labels:" "TAB1 MUTATED"          
clus
  TAB1 MUTATED TAB1 WILD-TYPE 
             2            486 
    TCGA-A6-2671     TCGA-A6-2672     TCGA-A6-2674     TCGA-A6-2676 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-A6-2677     TCGA-A6-2678     TCGA-A6-2683     TCGA-A6-3807 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-A6-3808     TCGA-A6-3809     TCGA-A6-3810     TCGA-A6-4105 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-A6-5656     TCGA-A6-5657     TCGA-A6-5659     TCGA-A6-5660 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-A6-5661     TCGA-A6-5662     TCGA-A6-5664     TCGA-A6-5665 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-A6-5666     TCGA-A6-6137     TCGA-A6-6138     TCGA-A6-6141 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-A6-6142     TCGA-A6-6648     TCGA-A6-6649     TCGA-A6-6651 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-A6-6652     TCGA-A6-6653     TCGA-A6-6654     TCGA-A6-6780 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-A6-6781     TCGA-A6-6782     TCGA-AA-3489     TCGA-AA-3492 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AA-3496     TCGA-AA-3502     TCGA-AA-3510     TCGA-AA-3511 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AA-3514     TCGA-AA-3516     TCGA-AA-3517     TCGA-AA-3518 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AA-3519     TCGA-AA-3520     TCGA-AA-3521     TCGA-AA-3522 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AA-3524     TCGA-AA-3525     TCGA-AA-3526     TCGA-AA-3527 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AA-3529     TCGA-AA-3530     TCGA-AA-3531     TCGA-AA-3532 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AA-3534     TCGA-AA-3538     TCGA-AA-3542     TCGA-AA-3543 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AA-3544     TCGA-AA-3548     TCGA-AA-3549     TCGA-AA-3552 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AA-3553     TCGA-AA-3554     TCGA-AA-3555     TCGA-AA-3556 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AA-3558     TCGA-AA-3560     TCGA-AA-3561     TCGA-AA-3562 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AA-3655     TCGA-AA-3660     TCGA-AA-3662     TCGA-AA-3663 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AA-3664     TCGA-AA-3666     TCGA-AA-3667     TCGA-AA-3673 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AA-3678     TCGA-AA-3679     TCGA-AA-3680     TCGA-AA-3681 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AA-3684     TCGA-AA-3685     TCGA-AA-3688     TCGA-AA-3692 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AA-3693     TCGA-AA-3695     TCGA-AA-3696     TCGA-AA-3697 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AA-3710     TCGA-AA-3712     TCGA-AA-3713     TCGA-AA-3715 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AA-3811     TCGA-AA-3812     TCGA-AA-3814     TCGA-AA-3815 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AA-3818     TCGA-AA-3819     TCGA-AA-3821     TCGA-AA-3831 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AA-3833     TCGA-AA-3837     TCGA-AA-3842     TCGA-AA-3844 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AA-3845     TCGA-AA-3846     TCGA-AA-3848     TCGA-AA-3850 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AA-3851     TCGA-AA-3852     TCGA-AA-3854     TCGA-AA-3855 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AA-3856     TCGA-AA-3858     TCGA-AA-3860     TCGA-AA-3861 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AA-3864     TCGA-AA-3866     TCGA-AA-3867     TCGA-AA-3869 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AA-3870     TCGA-AA-3872     TCGA-AA-3875     TCGA-AA-3877 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AA-3930     TCGA-AA-3939     TCGA-AA-3941     TCGA-AA-3947 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AA-3949     TCGA-AA-3950     TCGA-AA-3952     TCGA-AA-3955 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AA-3956     TCGA-AA-3966     TCGA-AA-3968     TCGA-AA-3971 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AA-3972     TCGA-AA-3973     TCGA-AA-3975     TCGA-AA-3976 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AA-3977     TCGA-AA-3979     TCGA-AA-3980     TCGA-AA-3982 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AA-3984     TCGA-AA-3986     TCGA-AA-3989     TCGA-AA-3994 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AA-A004     TCGA-AA-A00A     TCGA-AA-A00D     TCGA-AA-A00E 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AA-A00F     TCGA-AA-A00J     TCGA-AA-A00K     TCGA-AA-A00L 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AA-A00N     TCGA-AA-A00O     TCGA-AA-A00Q     TCGA-AA-A00R 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AA-A00U     TCGA-AA-A00W     TCGA-AA-A00Z     TCGA-AA-A010 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AA-A017     TCGA-AA-A01D     TCGA-AA-A01F     TCGA-AA-A01G 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AA-A01I     TCGA-AA-A01K     TCGA-AA-A01P     TCGA-AA-A01Q 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AA-A01R     TCGA-AA-A01S     TCGA-AA-A01T     TCGA-AA-A01V 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AA-A01X     TCGA-AA-A01Z     TCGA-AA-A022     TCGA-AA-A024 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AA-A029     TCGA-AA-A02F     TCGA-AA-A02H     TCGA-AA-A02J 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AA-A02K     TCGA-AA-A02O     TCGA-AA-A02W     TCGA-AA-A02Y 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AA-A03F     TCGA-AA-A03J     TCGA-AD-5900     TCGA-AD-6548 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AD-6888     TCGA-AD-6890     TCGA-AD-6895     TCGA-AD-6899 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AD-6901     TCGA-AD-6963     TCGA-AD-6964     TCGA-AD-6965 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AU-3779     TCGA-AU-6004     TCGA-AY-4070     TCGA-AY-4071 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AY-5543     TCGA-AY-6196     TCGA-AY-6197     TCGA-AY-6386 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AZ-4315     TCGA-AZ-4323     TCGA-AZ-4616     TCGA-AZ-4681 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AZ-4682     TCGA-AZ-5403     TCGA-AZ-5407     TCGA-AZ-6598 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AZ-6599     TCGA-AZ-6600     TCGA-AZ-6601     TCGA-AZ-6603 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AZ-6605     TCGA-AZ-6606     TCGA-AZ-6607     TCGA-AZ-6608 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-CA-5254     TCGA-CA-5255     TCGA-CA-5796     TCGA-CA-5797 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-CA-6715     TCGA-CA-6716     TCGA-CA-6717     TCGA-CA-6718 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-CA-6719     TCGA-CK-4947     TCGA-CK-4948     TCGA-CK-4950 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-CK-4952     TCGA-CK-5912     TCGA-CK-5913     TCGA-CK-5914 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-CK-5915     TCGA-CK-5916     TCGA-CK-6746     TCGA-CK-6747 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-CK-6748     TCGA-CK-6751     TCGA-CM-4743     TCGA-CM-4744 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-CM-4746     TCGA-CM-4747     TCGA-CM-4752     TCGA-CM-5341 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-CM-5344     TCGA-CM-5348     TCGA-CM-5349     TCGA-CM-5860 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-CM-5861     TCGA-CM-5862     TCGA-CM-5863     TCGA-CM-5864 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-CM-5868     TCGA-CM-6161     TCGA-CM-6162     TCGA-CM-6163 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-CM-6164     TCGA-CM-6165     TCGA-CM-6166     TCGA-CM-6167 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-CM-6168     TCGA-CM-6169     TCGA-CM-6170     TCGA-CM-6172 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-CM-6674     TCGA-CM-6675     TCGA-CM-6676     TCGA-CM-6677 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-CM-6678     TCGA-CM-6679     TCGA-CM-6680     TCGA-D5-5537 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-D5-5538     TCGA-D5-5539     TCGA-D5-5540     TCGA-D5-5541 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-D5-6529     TCGA-D5-6532     TCGA-D5-6533     TCGA-D5-6534 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-D5-6535     TCGA-D5-6536     TCGA-D5-6537     TCGA-D5-6538 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-D5-6539     TCGA-D5-6540     TCGA-D5-6541     TCGA-D5-6898 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-D5-6920     TCGA-D5-6922     TCGA-D5-6923     TCGA-D5-6924 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-D5-6926     TCGA-D5-6927     TCGA-D5-6928     TCGA-D5-6929 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-D5-6930     TCGA-D5-6931     TCGA-D5-6932     TCGA-D5-7000 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-DM-A0X9     TCGA-DM-A0XD     TCGA-DM-A0XF     TCGA-DM-A1D0 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-DM-A1D4     TCGA-DM-A1D6     TCGA-DM-A1D7     TCGA-DM-A1D8 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-DM-A1D9     TCGA-DM-A1DA     TCGA-DM-A1DB     TCGA-DM-A1HA 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-DM-A1HB     TCGA-DM-A282     TCGA-DM-A285     TCGA-DM-A28C 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-DM-A28E     TCGA-DM-A28F     TCGA-DM-A28G     TCGA-DM-A28H 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-DM-A28K     TCGA-F4-6459     TCGA-F4-6460     TCGA-F4-6569 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-F4-6570     TCGA-F4-6703     TCGA-F4-6704     TCGA-F4-6805 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-F4-6806     TCGA-F4-6807     TCGA-F4-6808     TCGA-F4-6809 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-F4-6854     TCGA-F4-6855     TCGA-F4-6856     TCGA-G4-6293 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-G4-6299     TCGA-G4-6303     TCGA-G4-6304     TCGA-G4-6306 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-G4-6307     TCGA-G4-6309     TCGA-G4-6310     TCGA-G4-6315 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-G4-6317     TCGA-G4-6321     TCGA-G4-6323     TCGA-G4-6586 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-G4-6588     TCGA-G4-6625     TCGA-G4-6626     TCGA-G4-6628 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AF-2687     TCGA-AF-2689     TCGA-AF-2691     TCGA-AF-2692 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AF-2693     TCGA-AF-3400     TCGA-AF-3913     TCGA-AF-4110 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AF-5654     TCGA-AF-6136     TCGA-AF-6655     TCGA-AF-6672 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AG-3574     TCGA-AG-3575     TCGA-AG-3578     TCGA-AG-3580 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AG-3581     TCGA-AG-3582     TCGA-AG-3583     TCGA-AG-3584 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AG-3586     TCGA-AG-3587     TCGA-AG-3593     TCGA-AG-3594 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AG-3598     TCGA-AG-3599     TCGA-AG-3600     TCGA-AG-3601 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AG-3602     TCGA-AG-3605     TCGA-AG-3608     TCGA-AG-3609 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AG-3611     TCGA-AG-3612     TCGA-AG-3726     TCGA-AG-3727 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AG-3731     TCGA-AG-3732     TCGA-AG-3742     TCGA-AG-3878 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AG-3881     TCGA-AG-3882     TCGA-AG-3883     TCGA-AG-3885 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AG-3887     TCGA-AG-3890     TCGA-AG-3892     TCGA-AG-3893 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AG-3894     TCGA-AG-3896     TCGA-AG-3898     TCGA-AG-3901 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AG-3902     TCGA-AG-3909     TCGA-AG-3999     TCGA-AG-4001 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AG-4005     TCGA-AG-4007     TCGA-AG-4008     TCGA-AG-4015 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AG-A002     TCGA-AG-A008     TCGA-AG-A00C     TCGA-AG-A00H 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AG-A00Y     TCGA-AG-A011     TCGA-AG-A014     TCGA-AG-A015 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AG-A016     TCGA-AG-A01L     TCGA-AG-A01W     TCGA-AG-A01Y 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AG-A020     TCGA-AG-A025     TCGA-AG-A026     TCGA-AG-A02G 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AG-A02N     TCGA-AG-A02X     TCGA-AG-A032     TCGA-AG-A036 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AH-6544     TCGA-AH-6547     TCGA-AH-6549     TCGA-AH-6643 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AH-6644     TCGA-CI-6619     TCGA-CI-6620     TCGA-CI-6621 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-CI-6622     TCGA-CI-6624     TCGA-CL-5917     TCGA-CL-5918 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-DC-5337     TCGA-DC-5869     TCGA-DC-6155     TCGA-DC-6157 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-DC-6158     TCGA-DC-6160     TCGA-DC-6681     TCGA-DC-6682 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-DC-6683     TCGA-DT-5265     TCGA-DY-A0XA     TCGA-DY-A1DC 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-DY-A1DD     TCGA-DY-A1DF     TCGA-DY-A1DG     TCGA-DY-A1H8 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-EF-5830     TCGA-EI-6506     TCGA-EI-6507     TCGA-EI-6508 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-EI-6510     TCGA-F5-6464     TCGA-F5-6465     TCGA-F5-6571 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-F5-6702     TCGA-F5-6811     TCGA-F5-6812     TCGA-F5-6813 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-G5-6235     TCGA-G5-6641 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
D2028V3, binary
                cls
clus               0   1
  TAB1 MUTATED     3   0
  TAB1 WILD-TYPE 363 119
[1] "tbl2"
                cls
clus             [,1] [,2]
  TAB1 MUTATED      3    0
  TAB1 WILD-TYPE  363  119
        clus
vv       TAB1 MUTATED TAB1 WILD-TYPE
  COLON             3            363
  RECTUM            0            119
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TAB1 MUTATED         1        0        0         1         0         0
  TAB1 WILD-TYPE      90        1       32       137        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TAB1 MUTATED           1          0          0          0        0         0
  TAB1 WILD-TYPE        23         11         59         42       48        18
                vv
clus             STAGE IVB
  TAB1 MUTATED           0
  TAB1 WILD-TYPE         1
D2028V4, multiclass
            clus
vv           TAB1 MUTATED TAB1 WILD-TYPE
  STAGE I               1             90
  STAGE IA              0              1
  STAGE II              0             32
  STAGE IIA             1            137
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             1             23
  STAGE IIIA            0             11
  STAGE IIIB            0             59
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  TAB1 MUTATED     0   1   2   0
  TAB1 WILD-TYPE  17  91 327  50
D2028V5, multiclass
    clus
vv   TAB1 MUTATED TAB1 WILD-TYPE
  T1            0             17
  T2            1             91
  T3            2            327
  T4            0             50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  TAB1 MUTATED     2   1   0
  TAB1 WILD-TYPE 285 112  87
D2028V6, multiclass
    clus
vv   TAB1 MUTATED TAB1 WILD-TYPE
  N0            2            285
  N1            1            112
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2028V7, binary
                cls
clus               0   1
  TAB1 MUTATED     3   0
  TAB1 WILD-TYPE 372  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  TAB1 MUTATED      3    0
  TAB1 WILD-TYPE  372   65
   clus
vv  TAB1 MUTATED TAB1 WILD-TYPE
  0            3            372
  1            0             65
[1] 2 2
[1] FALSE
D2028V8, binary
                cls
clus               0   1
  TAB1 MUTATED     2   1
  TAB1 WILD-TYPE 223 263
[1] "tbl2"
                cls
clus             [,1] [,2]
  TAB1 MUTATED      2    1
  TAB1 WILD-TYPE  223  263
        clus
vv       TAB1 MUTATED TAB1 WILD-TYPE
  FEMALE            2            223
  MALE              1            263
[1] 2 2
[1] FALSE
D2028V9, binary
                cls
clus               0   1
  TAB1 MUTATED     2   0
  TAB1 WILD-TYPE 348  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  TAB1 MUTATED      2    0
  TAB1 WILD-TYPE  348   22
     clus
vv    TAB1 MUTATED TAB1 WILD-TYPE
  NO             2            348
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  TAB1 MUTATED                      3                             0
  TAB1 WILD-TYPE                  312                            47
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  TAB1 MUTATED                       0                              0
  TAB1 WILD-TYPE                   106                             10
D2028V10, multiclass
                                clus
vv                               TAB1 MUTATED TAB1 WILD-TYPE
  COLON ADENOCARCINOMA                      3            312
  COLON MUCINOUS ADENOCARCINOMA             0             47
  RECTAL ADENOCARCINOMA                     0            106
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  TAB1 MUTATED     2   0   0   0
  TAB1 WILD-TYPE 343   4  31  25
D2028V11, multiclass
[1] "Remove cluster labels:" "TAB1 MUTATED"          
clus
  TAB1 MUTATED TAB1 WILD-TYPE 
             2            403 
    TCGA-A6-2671     TCGA-A6-2672     TCGA-A6-2674     TCGA-A6-2676 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-A6-2677     TCGA-A6-2678     TCGA-A6-2683     TCGA-A6-3807 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-A6-3808     TCGA-A6-3809     TCGA-A6-3810     TCGA-A6-5657 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-A6-5659     TCGA-A6-5661     TCGA-A6-5665     TCGA-A6-6781 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AA-3489     TCGA-AA-3492     TCGA-AA-3496     TCGA-AA-3502 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AA-3510     TCGA-AA-3511     TCGA-AA-3514     TCGA-AA-3517 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AA-3518     TCGA-AA-3519     TCGA-AA-3520     TCGA-AA-3521 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AA-3522     TCGA-AA-3524     TCGA-AA-3525     TCGA-AA-3526 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AA-3527     TCGA-AA-3529     TCGA-AA-3530     TCGA-AA-3531 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AA-3532     TCGA-AA-3534     TCGA-AA-3538     TCGA-AA-3542 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AA-3543     TCGA-AA-3544     TCGA-AA-3548     TCGA-AA-3549 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AA-3552     TCGA-AA-3553     TCGA-AA-3554     TCGA-AA-3555 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AA-3556     TCGA-AA-3558     TCGA-AA-3560     TCGA-AA-3561 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AA-3562     TCGA-AA-3655     TCGA-AA-3660     TCGA-AA-3662 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AA-3663     TCGA-AA-3664     TCGA-AA-3666     TCGA-AA-3667 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AA-3673     TCGA-AA-3678     TCGA-AA-3679     TCGA-AA-3680 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AA-3681     TCGA-AA-3684     TCGA-AA-3685     TCGA-AA-3688 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AA-3692     TCGA-AA-3693     TCGA-AA-3695     TCGA-AA-3696 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AA-3697     TCGA-AA-3710     TCGA-AA-3712     TCGA-AA-3713 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AA-3715     TCGA-AA-3811     TCGA-AA-3812     TCGA-AA-3814 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AA-3815     TCGA-AA-3818     TCGA-AA-3819     TCGA-AA-3821 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AA-3831     TCGA-AA-3833     TCGA-AA-3837     TCGA-AA-3842 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AA-3844     TCGA-AA-3845     TCGA-AA-3846     TCGA-AA-3848 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AA-3850     TCGA-AA-3851     TCGA-AA-3852     TCGA-AA-3854 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AA-3855     TCGA-AA-3856     TCGA-AA-3858     TCGA-AA-3860 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AA-3861     TCGA-AA-3864     TCGA-AA-3866     TCGA-AA-3867 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AA-3869     TCGA-AA-3870     TCGA-AA-3872     TCGA-AA-3875 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AA-3877     TCGA-AA-3930     TCGA-AA-3939     TCGA-AA-3941 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AA-3947     TCGA-AA-3949     TCGA-AA-3950     TCGA-AA-3952 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AA-3955     TCGA-AA-3956     TCGA-AA-3968     TCGA-AA-3971 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AA-3972     TCGA-AA-3973     TCGA-AA-3975     TCGA-AA-3976 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AA-3979     TCGA-AA-3984     TCGA-AA-3986     TCGA-AA-3989 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AA-3994     TCGA-AA-A004     TCGA-AA-A00A     TCGA-AA-A00D 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AA-A00E     TCGA-AA-A00F     TCGA-AA-A00J     TCGA-AA-A00K 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AA-A00L     TCGA-AA-A00N     TCGA-AA-A00O     TCGA-AA-A00Q 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AA-A00R     TCGA-AA-A00U     TCGA-AA-A00W     TCGA-AA-A00Z 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AA-A010     TCGA-AA-A017     TCGA-AA-A01D     TCGA-AA-A01F 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AA-A01G     TCGA-AA-A01I     TCGA-AA-A01K     TCGA-AA-A01P 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AA-A01Q     TCGA-AA-A01R     TCGA-AA-A01S     TCGA-AA-A01T 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AA-A01V     TCGA-AA-A01X     TCGA-AA-A01Z     TCGA-AA-A022 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AA-A024     TCGA-AA-A029     TCGA-AA-A02F     TCGA-AA-A02H 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AA-A02J     TCGA-AA-A02K     TCGA-AA-A02O     TCGA-AA-A02W 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AA-A02Y     TCGA-AA-A03F     TCGA-AA-A03J     TCGA-AD-5900 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AD-6548     TCGA-AD-6888     TCGA-AU-3779     TCGA-AU-6004 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AY-4070     TCGA-AY-4071     TCGA-AY-5543     TCGA-AY-6196 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AY-6197     TCGA-AY-6386     TCGA-AZ-4315     TCGA-AZ-4681 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AZ-4682     TCGA-CA-5254     TCGA-CA-5255     TCGA-CA-5796 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-CA-5797     TCGA-CA-6715     TCGA-CA-6716     TCGA-CA-6717 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-CA-6718     TCGA-CA-6719     TCGA-CK-4947     TCGA-CK-4948 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-CK-4950     TCGA-CK-4952     TCGA-CK-5912     TCGA-CK-5913 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-CK-5914     TCGA-CK-5915     TCGA-CK-5916     TCGA-CK-6746 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-CK-6747     TCGA-CK-6748     TCGA-CK-6751     TCGA-CM-4743 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-CM-4744     TCGA-CM-4746     TCGA-CM-4747     TCGA-CM-4752 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-CM-5341     TCGA-CM-5344     TCGA-CM-5348     TCGA-CM-5349 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-CM-5860     TCGA-CM-5861     TCGA-CM-5862     TCGA-CM-5863 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-CM-5864     TCGA-CM-5868     TCGA-CM-6161     TCGA-CM-6162 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-CM-6163     TCGA-CM-6164     TCGA-CM-6165     TCGA-CM-6166 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-CM-6167     TCGA-CM-6168     TCGA-CM-6169     TCGA-CM-6170 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-CM-6172     TCGA-CM-6674     TCGA-CM-6675     TCGA-CM-6676 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-CM-6677     TCGA-CM-6678     TCGA-CM-6679     TCGA-CM-6680 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-D5-5537     TCGA-D5-5538     TCGA-D5-5539     TCGA-D5-5540 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-D5-5541     TCGA-D5-6529     TCGA-D5-6532     TCGA-D5-6533 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-D5-6534     TCGA-D5-6535     TCGA-D5-6536     TCGA-D5-6537 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-D5-6538     TCGA-D5-6539     TCGA-D5-6540     TCGA-D5-6541 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-D5-6898     TCGA-D5-6920     TCGA-D5-6922     TCGA-D5-6923 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-D5-6924     TCGA-D5-6926     TCGA-D5-6927     TCGA-D5-6928 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-D5-6929     TCGA-D5-6930     TCGA-D5-6931     TCGA-D5-6932 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-D5-7000     TCGA-F4-6459     TCGA-F4-6460     TCGA-F4-6569 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-F4-6570     TCGA-F4-6703     TCGA-F4-6704     TCGA-F4-6805 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-F4-6806     TCGA-F4-6807     TCGA-F4-6808     TCGA-F4-6809 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-F4-6854     TCGA-F4-6855     TCGA-F4-6856     TCGA-G4-6293 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-G4-6299     TCGA-G4-6303     TCGA-G4-6304     TCGA-G4-6306 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-G4-6307     TCGA-G4-6309     TCGA-G4-6310     TCGA-G4-6315 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-G4-6317     TCGA-G4-6321     TCGA-G4-6323     TCGA-G4-6586 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-G4-6588     TCGA-G4-6625     TCGA-G4-6626     TCGA-G4-6628 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AF-2687     TCGA-AF-2689     TCGA-AF-2691     TCGA-AF-2692 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AF-3400     TCGA-AF-3913     TCGA-AF-4110     TCGA-AF-5654 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AF-6655     TCGA-AG-3574     TCGA-AG-3575     TCGA-AG-3578 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AG-3580     TCGA-AG-3581     TCGA-AG-3582     TCGA-AG-3583 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AG-3584     TCGA-AG-3586     TCGA-AG-3587     TCGA-AG-3593 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AG-3594     TCGA-AG-3598     TCGA-AG-3599     TCGA-AG-3600 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AG-3601     TCGA-AG-3602     TCGA-AG-3605     TCGA-AG-3608 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AG-3609     TCGA-AG-3611     TCGA-AG-3612     TCGA-AG-3726 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AG-3727     TCGA-AG-3731     TCGA-AG-3732     TCGA-AG-3742 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AG-3878     TCGA-AG-3882     TCGA-AG-3883     TCGA-AG-3885 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AG-3887     TCGA-AG-3890     TCGA-AG-3892     TCGA-AG-3893 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AG-3894     TCGA-AG-3896     TCGA-AG-3898     TCGA-AG-3901 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AG-3902     TCGA-AG-3909     TCGA-AG-3999     TCGA-AG-4001 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AG-4005     TCGA-AG-4007     TCGA-AG-4008     TCGA-AG-4015 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AG-A002     TCGA-AG-A008     TCGA-AG-A00C     TCGA-AG-A00H 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AG-A00Y     TCGA-AG-A011     TCGA-AG-A014     TCGA-AG-A015 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AG-A016     TCGA-AG-A01L     TCGA-AG-A01W     TCGA-AG-A01Y 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AG-A020     TCGA-AG-A025     TCGA-AG-A026     TCGA-AG-A02G 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AG-A02N     TCGA-AG-A02X     TCGA-AG-A032     TCGA-AG-A036 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AH-6549     TCGA-AH-6643     TCGA-CL-5917     TCGA-CL-5918 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-DC-5337     TCGA-DC-5869     TCGA-DC-6155     TCGA-DC-6157 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-DC-6158     TCGA-DC-6160     TCGA-DC-6681     TCGA-DC-6682 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-DC-6683     TCGA-DT-5265     TCGA-EF-5830     TCGA-EI-6506 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-EI-6507     TCGA-EI-6508     TCGA-EI-6510     TCGA-F5-6464 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-F5-6465     TCGA-F5-6571     TCGA-F5-6702     TCGA-F5-6812 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-F5-6813     TCGA-G5-6235     TCGA-G5-6641 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
D2028V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TAB1 MUTATED                                  0     1
  TAB1 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  TAB1 MUTATED                           0     1
  TAB1 WILD-TYPE                        22   225
D2028V13, multiclass
[1] "Remove cluster labels:" "TAB1 MUTATED"          
clus
  TAB1 MUTATED TAB1 WILD-TYPE 
             2            258 
    TCGA-A6-2671     TCGA-A6-2672     TCGA-A6-2674     TCGA-A6-2676 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-A6-2677     TCGA-A6-2678     TCGA-A6-2683     TCGA-A6-3807 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-A6-3808     TCGA-A6-3809     TCGA-A6-3810     TCGA-A6-4105 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-A6-5656     TCGA-A6-5657     TCGA-A6-5659     TCGA-A6-5660 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-A6-5661     TCGA-A6-5662     TCGA-A6-5664     TCGA-A6-5665 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-A6-5666     TCGA-A6-6137     TCGA-A6-6138     TCGA-A6-6141 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-A6-6142     TCGA-A6-6648     TCGA-A6-6649     TCGA-A6-6651 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-A6-6652     TCGA-A6-6653     TCGA-A6-6654     TCGA-A6-6780 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-A6-6781     TCGA-A6-6782     TCGA-AD-5900     TCGA-AD-6548 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AD-6888     TCGA-AD-6890     TCGA-AD-6895     TCGA-AD-6899 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AD-6901     TCGA-AD-6963     TCGA-AD-6964     TCGA-AD-6965 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AU-3779     TCGA-AU-6004     TCGA-AY-4070     TCGA-AY-4071 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AY-5543     TCGA-AY-6196     TCGA-AY-6197     TCGA-AY-6386 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AZ-4315     TCGA-AZ-4323     TCGA-AZ-4616     TCGA-AZ-4681 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AZ-4682     TCGA-AZ-5403     TCGA-AZ-5407     TCGA-AZ-6598 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AZ-6599     TCGA-AZ-6600     TCGA-AZ-6601     TCGA-AZ-6603 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AZ-6605     TCGA-AZ-6606     TCGA-AZ-6607     TCGA-AZ-6608 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-CA-5254     TCGA-CA-5255     TCGA-CA-5796     TCGA-CA-5797 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-CA-6715     TCGA-CA-6716     TCGA-CA-6717     TCGA-CA-6718 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-CA-6719     TCGA-CK-4947     TCGA-CK-4948     TCGA-CK-4950 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-CK-4952     TCGA-CK-5912     TCGA-CK-5913     TCGA-CK-5914 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-CK-5915     TCGA-CK-5916     TCGA-CK-6746     TCGA-CK-6747 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-CK-6748     TCGA-CK-6751     TCGA-CM-4743     TCGA-CM-4744 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-CM-4746     TCGA-CM-4747     TCGA-CM-4752     TCGA-CM-5341 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-CM-5344     TCGA-CM-5348     TCGA-CM-5349     TCGA-CM-5860 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-CM-5861     TCGA-CM-5862     TCGA-CM-5863     TCGA-CM-5864 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-CM-5868     TCGA-CM-6161     TCGA-CM-6162     TCGA-CM-6163 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-CM-6164     TCGA-CM-6165     TCGA-CM-6166     TCGA-CM-6167 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-CM-6168     TCGA-CM-6169     TCGA-CM-6170     TCGA-CM-6172 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-CM-6674     TCGA-CM-6675     TCGA-CM-6676     TCGA-CM-6677 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-CM-6678     TCGA-CM-6679     TCGA-CM-6680     TCGA-D5-5537 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-D5-5538     TCGA-D5-5539     TCGA-D5-5540     TCGA-D5-5541 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-D5-6529     TCGA-D5-6532     TCGA-D5-6533     TCGA-D5-6534 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-D5-6535     TCGA-D5-6536     TCGA-D5-6537     TCGA-D5-6538 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-D5-6539     TCGA-D5-6540     TCGA-D5-6541     TCGA-D5-6898 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-D5-6920     TCGA-D5-6922     TCGA-D5-6923     TCGA-D5-6924 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-D5-6926     TCGA-D5-6927     TCGA-D5-6928     TCGA-D5-6929 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-D5-6930     TCGA-D5-6931     TCGA-D5-6932     TCGA-D5-7000 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-DM-A0X9     TCGA-DM-A0XD     TCGA-DM-A0XF     TCGA-DM-A1D0 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-DM-A1D4     TCGA-DM-A1D6     TCGA-DM-A1D7     TCGA-DM-A1D8 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-DM-A1D9     TCGA-DM-A1DA     TCGA-DM-A1DB     TCGA-DM-A1HA 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-DM-A1HB     TCGA-DM-A282     TCGA-DM-A285     TCGA-DM-A28C 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-DM-A28E     TCGA-DM-A28F     TCGA-DM-A28G     TCGA-DM-A28H 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-DM-A28K     TCGA-F4-6459     TCGA-F4-6460     TCGA-F4-6569 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-F4-6570     TCGA-F4-6703     TCGA-F4-6704     TCGA-F4-6805 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-F4-6806     TCGA-F4-6807     TCGA-F4-6808     TCGA-F4-6809 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-F4-6854     TCGA-F4-6855     TCGA-F4-6856     TCGA-G4-6293 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-G4-6299     TCGA-G4-6303     TCGA-G4-6304     TCGA-G4-6306 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-G4-6307     TCGA-G4-6309     TCGA-G4-6310     TCGA-G4-6315 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-G4-6317     TCGA-G4-6321     TCGA-G4-6323     TCGA-G4-6586 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-G4-6588     TCGA-G4-6625     TCGA-G4-6626     TCGA-G4-6628 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AF-2687     TCGA-AF-2689     TCGA-AF-2691     TCGA-AF-2692 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AF-2693     TCGA-AF-3400     TCGA-AF-3913     TCGA-AF-4110 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AF-5654     TCGA-AF-6136     TCGA-AF-6655     TCGA-AF-6672 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AH-6544     TCGA-AH-6547     TCGA-AH-6549     TCGA-AH-6643 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-AH-6644     TCGA-CI-6619     TCGA-CI-6620     TCGA-CI-6621 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-CI-6622     TCGA-CI-6624     TCGA-CL-5917     TCGA-CL-5918 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-DC-5337     TCGA-DC-5869     TCGA-DC-6155     TCGA-DC-6157 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-DC-6158     TCGA-DC-6160     TCGA-DC-6681     TCGA-DC-6682 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-DC-6683     TCGA-DT-5265     TCGA-DY-A0XA     TCGA-DY-A1DC 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-DY-A1DD     TCGA-DY-A1DF     TCGA-DY-A1DG     TCGA-DY-A1H8 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-EF-5830     TCGA-EI-6506     TCGA-EI-6507     TCGA-EI-6508 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-EI-6510     TCGA-F5-6464     TCGA-F5-6465     TCGA-F5-6571 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-F5-6702     TCGA-F5-6811     TCGA-F5-6812     TCGA-F5-6813 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 
    TCGA-G5-6235     TCGA-G5-6641 
"TAB1 WILD-TYPE" "TAB1 WILD-TYPE" 

Clustering(2029) Variable = SLC30A8 MUTATION ANALYSIS
D2029V1, survival
                   sevent
clus2                 0   1
  SLC30A8 MUTATED    13   3
  SLC30A8 WILD-TYPE 365  90
  SLC30A8 MUTATED SLC30A8 WILD-TYPE 
               16               455 
  SLC30A8 MUTATED SLC30A8 WILD-TYPE 
                3                90 
$`SLC30A8 MUTATED`
TCGA-A6-6648 TCGA-A6-6649 TCGA-AA-3713 TCGA-AA-3815 TCGA-AA-3845 TCGA-AA-3869 
       25.18        24.16        19.04        33.04         0.00        27.02 
TCGA-AA-3949 TCGA-AA-3966 TCGA-CA-6717 TCGA-CK-5913 TCGA-CK-6751 TCGA-F4-6460 
       26.01         2.01        12.76        51.32       124.27        31.96 
TCGA-G4-6315 TCGA-AF-6655 TCGA-AG-A002 TCGA-EI-6510 
       61.91        20.02        20.98        18.28 

$`SLC30A8 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       25.08        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02        14.93        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3875 
       30.05        53.00        17.03        24.03        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3950 
       31.00         2.01        12.99        24.00        33.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
        2.01        20.98        34.03        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.20        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        49.08         9.99        21.14        82.95         1.91 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
        8.61        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       55.04        85.48        63.62        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       14.50        16.83        15.39        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       19.96        20.91         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  SLC30A8 MUTATED SLC30A8 WILD-TYPE 
                0                 0 
  SLC30A8 MUTATED SLC30A8 WILD-TYPE 
           124.27            148.01 
  SLC30A8 MUTATED SLC30A8 WILD-TYPE 
            24.67             20.05 
[1] "0.0 - 124.3 (24.7)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.2"
D2029V2, continuous
D2029V3, binary
                   cls
clus                  0   1
  SLC30A8 MUTATED    14   3
  SLC30A8 WILD-TYPE 352 116
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC30A8 MUTATED     14    3
  SLC30A8 WILD-TYPE  352  116
        clus
vv       SLC30A8 MUTATED SLC30A8 WILD-TYPE
  COLON               14               352
  RECTUM               3               116
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SLC30A8 MUTATED         2        0        1         5         0         0
  SLC30A8 WILD-TYPE      89        1       31       133        10         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC30A8 MUTATED           0          1          3          0        3
  SLC30A8 WILD-TYPE        24         10         56         42       45
                   vv
clus                STAGE IVA STAGE IVB
  SLC30A8 MUTATED           2         0
  SLC30A8 WILD-TYPE        16         1
D2029V4, multiclass
            clus
vv           SLC30A8 MUTATED SLC30A8 WILD-TYPE
  STAGE I                  2                89
  STAGE IA                 0                 1
  STAGE II                 1                31
  STAGE IIA                5               133
  STAGE IIB                0                10
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               1                10
  STAGE IIIB               3                56
  STAGE IIIC               0                42
  STAGE IV                 3                45
  STAGE IVA                2                16
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  SLC30A8 MUTATED     0   4  11   2
  SLC30A8 WILD-TYPE  17  88 318  48
D2029V5, multiclass
    clus
vv   SLC30A8 MUTATED SLC30A8 WILD-TYPE
  T1               0                17
  T2               4                88
  T3              11               318
  T4               2                48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  SLC30A8 MUTATED    11   5   1
  SLC30A8 WILD-TYPE 276 108  86
D2029V6, multiclass
    clus
vv   SLC30A8 MUTATED SLC30A8 WILD-TYPE
  N0              11               276
  N1               5               108
  N2               1                86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2029V7, binary
                   cls
clus                  0   1
  SLC30A8 MUTATED    10   4
  SLC30A8 WILD-TYPE 365  61
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC30A8 MUTATED     10    4
  SLC30A8 WILD-TYPE  365   61
   clus
vv  SLC30A8 MUTATED SLC30A8 WILD-TYPE
  0              10               365
  1               4                61
[1] 2 2
[1] FALSE
D2029V8, binary
                   cls
clus                  0   1
  SLC30A8 MUTATED     9   8
  SLC30A8 WILD-TYPE 216 256
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC30A8 MUTATED      9    8
  SLC30A8 WILD-TYPE  216  256
        clus
vv       SLC30A8 MUTATED SLC30A8 WILD-TYPE
  FEMALE               9               216
  MALE                 8               256
[1] 2 2
[1] FALSE
D2029V9, binary
                   cls
clus                  0   1
  SLC30A8 MUTATED    13   1
  SLC30A8 WILD-TYPE 337  21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC30A8 MUTATED     13    1
  SLC30A8 WILD-TYPE  337   21
     clus
vv    SLC30A8 MUTATED SLC30A8 WILD-TYPE
  NO               13               337
  YES               1                21
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SLC30A8 MUTATED                     10                             4
  SLC30A8 WILD-TYPE                  305                            43
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SLC30A8 MUTATED                       3                              0
  SLC30A8 WILD-TYPE                   103                             10
D2029V10, multiclass
                                clus
vv                               SLC30A8 MUTATED SLC30A8 WILD-TYPE
  COLON ADENOCARCINOMA                        10               305
  COLON MUCINOUS ADENOCARCINOMA                4                43
  RECTAL ADENOCARCINOMA                        3               103
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  SLC30A8 MUTATED     9   0   2   3
  SLC30A8 WILD-TYPE 336   4  29  22
D2029V11, multiclass
    clus
vv   SLC30A8 MUTATED SLC30A8 WILD-TYPE
  R0               9               336
  R1               0                 4
  R2               2                29
  RX               3                22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2029V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SLC30A8 MUTATED                                  0     1
  SLC30A8 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  SLC30A8 MUTATED                           0     8
  SLC30A8 WILD-TYPE                        22   218
D2029V13, multiclass
                                  clus
vv                                 SLC30A8 MUTATED SLC30A8 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                10
  BLACK OR AFRICAN AMERICAN                      0                22
  WHITE                                          8               218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2030) Variable = MPZL1 MUTATION ANALYSIS
D2030V1, survival
                 sevent
clus2               0   1
  MPZL1 MUTATED     4   3
  MPZL1 WILD-TYPE 374  90
  MPZL1 MUTATED MPZL1 WILD-TYPE 
              7             464 
  MPZL1 MUTATED MPZL1 WILD-TYPE 
              3              90 
$`MPZL1 MUTATED`
TCGA-A6-3809 TCGA-AA-A01R TCGA-AD-6963 TCGA-CA-6718 TCGA-DM-A1DA TCGA-DM-A1HB 
       32.75        35.01        27.42        10.06         7.50       135.65 
TCGA-G4-6626 
       46.75 

$`MPZL1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S 
       12.00        31.00        31.00        38.07         1.02         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6964 
       56.55         0.79         0.72         5.79        22.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       12.76        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
      140.38        44.32       131.51       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-AF-2687 
       13.78        35.80        26.17        91.79        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  MPZL1 MUTATED MPZL1 WILD-TYPE 
            7.5             0.0 
  MPZL1 MUTATED MPZL1 WILD-TYPE 
         135.65          148.01 
  MPZL1 MUTATED MPZL1 WILD-TYPE 
         32.750          20.085 
[1] "7.5 - 135.7 (32.8)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.6"
D2030V2, continuous
D2030V3, binary
                 cls
clus                0   1
  MPZL1 MUTATED     7   0
  MPZL1 WILD-TYPE 359 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MPZL1 MUTATED      7    0
  MPZL1 WILD-TYPE  359  119
        clus
vv       MPZL1 MUTATED MPZL1 WILD-TYPE
  COLON              7             359
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MPZL1 MUTATED         0        0        0         2         1         0
  MPZL1 WILD-TYPE      91        1       32       136         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MPZL1 MUTATED           1          0          1          1        0         0
  MPZL1 WILD-TYPE        23         11         58         41       48        18
                 vv
clus              STAGE IVB
  MPZL1 MUTATED           0
  MPZL1 WILD-TYPE         1
D2030V4, multiclass
            clus
vv           MPZL1 MUTATED MPZL1 WILD-TYPE
  STAGE I                0              91
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              2             136
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             1              41
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  MPZL1 MUTATED     0   0   6   1
  MPZL1 WILD-TYPE  17  92 323  49
D2030V5, multiclass
    clus
vv   MPZL1 MUTATED MPZL1 WILD-TYPE
  T1             0              17
  T2             0              92
  T3             6             323
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  MPZL1 MUTATED     4   1   2
  MPZL1 WILD-TYPE 283 112  85
D2030V6, multiclass
    clus
vv   MPZL1 MUTATED MPZL1 WILD-TYPE
  N0             4             283
  N1             1             112
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2030V7, binary
                 cls
clus                0   1
  MPZL1 MUTATED     6   0
  MPZL1 WILD-TYPE 369  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MPZL1 MUTATED      6    0
  MPZL1 WILD-TYPE  369   65
   clus
vv  MPZL1 MUTATED MPZL1 WILD-TYPE
  0             6             369
  1             0              65
[1] 2 2
[1] FALSE
D2030V8, binary
                 cls
clus                0   1
  MPZL1 MUTATED     2   5
  MPZL1 WILD-TYPE 223 259
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MPZL1 MUTATED      2    5
  MPZL1 WILD-TYPE  223  259
        clus
vv       MPZL1 MUTATED MPZL1 WILD-TYPE
  FEMALE             2             223
  MALE               5             259
[1] 2 2
[1] FALSE
D2030V9, binary
                 cls
clus                0   1
  MPZL1 MUTATED     4   1
  MPZL1 WILD-TYPE 346  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MPZL1 MUTATED      4    1
  MPZL1 WILD-TYPE  346   21
     clus
vv    MPZL1 MUTATED MPZL1 WILD-TYPE
  NO              4             346
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MPZL1 MUTATED                      4                             2
  MPZL1 WILD-TYPE                  311                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MPZL1 MUTATED                       0                              0
  MPZL1 WILD-TYPE                   106                             10
D2030V10, multiclass
                                clus
vv                               MPZL1 MUTATED MPZL1 WILD-TYPE
  COLON ADENOCARCINOMA                       4             311
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  MPZL1 MUTATED     3   0   0   1
  MPZL1 WILD-TYPE 342   4  31  24
D2030V11, multiclass
    clus
vv   MPZL1 MUTATED MPZL1 WILD-TYPE
  R0             3             342
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2030V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MPZL1 MUTATED                                  0     1
  MPZL1 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  MPZL1 MUTATED                           0     5
  MPZL1 WILD-TYPE                        22   221
D2030V13, multiclass
                                  clus
vv                                 MPZL1 MUTATED MPZL1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        5             221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2031) Variable = CCDC112 MUTATION ANALYSIS
D2031V1, survival
                   sevent
clus2                 0   1
  CCDC112 MUTATED     4   4
  CCDC112 WILD-TYPE 374  89
  CCDC112 MUTATED CCDC112 WILD-TYPE 
                8               463 
  CCDC112 MUTATED CCDC112 WILD-TYPE 
                4                89 
$`CCDC112 MUTATED`
TCGA-AA-3715 TCGA-AA-3845 TCGA-AA-A00N TCGA-CA-6717 TCGA-CK-5916 TCGA-CM-6171 
       19.04         0.00         4.01        12.76        21.14        14.04 
TCGA-AG-3732 TCGA-AG-3892 
       32.98        13.02 

$`CCDC112 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 
       17.98        15.95        38.99        37.02        14.93        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       49.08        51.32         9.99        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       15.02        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 
       13.94        19.99         7.99         0.99        37.02         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       17.03        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  CCDC112 MUTATED CCDC112 WILD-TYPE 
                0                 0 
  CCDC112 MUTATED CCDC112 WILD-TYPE 
            32.98            148.01 
  CCDC112 MUTATED CCDC112 WILD-TYPE 
            13.53             20.55 
[1] "0.0 - 33.0 (13.5)"  "0.0 - 148.0 (20.6)"
[1] "hr=" "4.7"
D2031V2, continuous
D2031V3, binary
                   cls
clus                  0   1
  CCDC112 MUTATED     7   2
  CCDC112 WILD-TYPE 359 117
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC112 MUTATED      7    2
  CCDC112 WILD-TYPE  359  117
        clus
vv       CCDC112 MUTATED CCDC112 WILD-TYPE
  COLON                7               359
  RECTUM               2               117
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CCDC112 MUTATED         4        0        1         3         1         0
  CCDC112 WILD-TYPE      87        1       31       135         9         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CCDC112 MUTATED           0          0          0          0        0
  CCDC112 WILD-TYPE        24         11         59         42       48
                   vv
clus                STAGE IVA STAGE IVB
  CCDC112 MUTATED           0         0
  CCDC112 WILD-TYPE        18         1
D2031V4, multiclass
            clus
vv           CCDC112 MUTATED CCDC112 WILD-TYPE
  STAGE I                  4                87
  STAGE IA                 0                 1
  STAGE II                 1                31
  STAGE IIA                3               135
  STAGE IIB                1                 9
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               0                11
  STAGE IIIB               0                59
  STAGE IIIC               0                42
  STAGE IV                 0                48
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  CCDC112 MUTATED     2   2   4   1
  CCDC112 WILD-TYPE  15  90 325  49
D2031V5, multiclass
    clus
vv   CCDC112 MUTATED CCDC112 WILD-TYPE
  T1               2                15
  T2               2                90
  T3               4               325
  T4               1                49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  CCDC112 MUTATED     9   0   0
  CCDC112 WILD-TYPE 278 113  87
D2031V6, multiclass
    clus
vv   CCDC112 MUTATED CCDC112 WILD-TYPE
  N0               9               278
  N1               0               113
  N2               0                87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2031V7, binary
                   cls
clus                  0   1
  CCDC112 MUTATED     9   0
  CCDC112 WILD-TYPE 366  65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC112 MUTATED      9    0
  CCDC112 WILD-TYPE  366   65
   clus
vv  CCDC112 MUTATED CCDC112 WILD-TYPE
  0               9               366
  1               0                65
[1] 2 2
[1] FALSE
D2031V8, binary
                   cls
clus                  0   1
  CCDC112 MUTATED     6   3
  CCDC112 WILD-TYPE 219 261
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC112 MUTATED      6    3
  CCDC112 WILD-TYPE  219  261
        clus
vv       CCDC112 MUTATED CCDC112 WILD-TYPE
  FEMALE               6               219
  MALE                 3               261
[1] 2 2
[1] FALSE
D2031V9, binary
                   cls
clus                  0   1
  CCDC112 MUTATED     6   0
  CCDC112 WILD-TYPE 344  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC112 MUTATED      6    0
  CCDC112 WILD-TYPE  344   22
     clus
vv    CCDC112 MUTATED CCDC112 WILD-TYPE
  NO                6               344
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CCDC112 MUTATED                      5                             2
  CCDC112 WILD-TYPE                  310                            45
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CCDC112 MUTATED                       2                              0
  CCDC112 WILD-TYPE                   104                             10
D2031V10, multiclass
                                clus
vv                               CCDC112 MUTATED CCDC112 WILD-TYPE
  COLON ADENOCARCINOMA                         5               310
  COLON MUCINOUS ADENOCARCINOMA                2                45
  RECTAL ADENOCARCINOMA                        2               104
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  CCDC112 MUTATED     7   0   0   2
  CCDC112 WILD-TYPE 338   4  31  23
D2031V11, multiclass
    clus
vv   CCDC112 MUTATED CCDC112 WILD-TYPE
  R0               7               338
  R1               0                 4
  R2               0                31
  RX               2                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2031V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CCDC112 MUTATED                                  0     1
  CCDC112 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  CCDC112 MUTATED                           0     2
  CCDC112 WILD-TYPE                        22   224
D2031V13, multiclass
                                  clus
vv                                 CCDC112 MUTATED CCDC112 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                10
  BLACK OR AFRICAN AMERICAN                      0                22
  WHITE                                          2               224
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2032) Variable = TOMM70A MUTATION ANALYSIS
D2032V1, survival
                   sevent
clus2                 0   1
  TOMM70A MUTATED     9   1
  TOMM70A WILD-TYPE 369  92
  TOMM70A MUTATED TOMM70A WILD-TYPE 
               10               461 
  TOMM70A MUTATED TOMM70A WILD-TYPE 
                1                92 
$`TOMM70A MUTATED`
TCGA-AA-3554 TCGA-AA-3815 TCGA-AA-A010 TCGA-AA-A01R TCGA-AZ-4315 TCGA-AZ-6599 
       17.95        33.04        34.98        35.01        58.39         6.77 
TCGA-G4-6299 TCGA-G4-6304 TCGA-G4-6625 TCGA-G4-6628 
       74.56        53.62        91.79        79.69 

$`TOMM70A WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       21.01        13.02        24.00        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       10.06        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       31.00        38.07         1.02         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       88.21        49.41        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       35.31       133.18        65.85        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       26.17        46.75        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  TOMM70A MUTATED TOMM70A WILD-TYPE 
             6.77              0.00 
  TOMM70A MUTATED TOMM70A WILD-TYPE 
            91.79            148.01 
  TOMM70A MUTATED TOMM70A WILD-TYPE 
           44.315            20.020 
[1] "6.8 - 91.8 (44.3)"  "0.0 - 148.0 (20.0)"
[1] "hr=" "3.7"
D2032V2, continuous
D2032V3, binary
                   cls
clus                  0   1
  TOMM70A MUTATED    10   0
  TOMM70A WILD-TYPE 356 119
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TOMM70A MUTATED     10    0
  TOMM70A WILD-TYPE  356  119
        clus
vv       TOMM70A MUTATED TOMM70A WILD-TYPE
  COLON               10               356
  RECTUM               0               119
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TOMM70A MUTATED         2        0        0         4         2         0
  TOMM70A WILD-TYPE      89        1       32       134         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TOMM70A MUTATED           1          0          0          1        0
  TOMM70A WILD-TYPE        23         11         59         41       48
                   vv
clus                STAGE IVA STAGE IVB
  TOMM70A MUTATED           0         0
  TOMM70A WILD-TYPE        18         1
D2032V4, multiclass
            clus
vv           TOMM70A MUTATED TOMM70A WILD-TYPE
  STAGE I                  2                89
  STAGE IA                 0                 1
  STAGE II                 0                32
  STAGE IIA                4               134
  STAGE IIB                2                 8
  STAGE IIC                0                 1
  STAGE III                1                23
  STAGE IIIA               0                11
  STAGE IIIB               0                59
  STAGE IIIC               1                41
  STAGE IV                 0                48
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  TOMM70A MUTATED     0   2   6   2
  TOMM70A WILD-TYPE  17  90 323  48
D2032V5, multiclass
    clus
vv   TOMM70A MUTATED TOMM70A WILD-TYPE
  T1               0                17
  T2               2                90
  T3               6               323
  T4               2                48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  TOMM70A MUTATED     8   0   2
  TOMM70A WILD-TYPE 279 113  85
D2032V6, multiclass
    clus
vv   TOMM70A MUTATED TOMM70A WILD-TYPE
  N0               8               279
  N1               0               113
  N2               2                85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2032V7, binary
                   cls
clus                  0   1
  TOMM70A MUTATED     9   0
  TOMM70A WILD-TYPE 366  65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TOMM70A MUTATED      9    0
  TOMM70A WILD-TYPE  366   65
   clus
vv  TOMM70A MUTATED TOMM70A WILD-TYPE
  0               9               366
  1               0                65
[1] 2 2
[1] FALSE
D2032V8, binary
                   cls
clus                  0   1
  TOMM70A MUTATED     5   5
  TOMM70A WILD-TYPE 220 259
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TOMM70A MUTATED      5    5
  TOMM70A WILD-TYPE  220  259
        clus
vv       TOMM70A MUTATED TOMM70A WILD-TYPE
  FEMALE               5               220
  MALE                 5               259
[1] 2 2
[1] FALSE
D2032V9, binary
                   cls
clus                  0   1
  TOMM70A MUTATED     9   1
  TOMM70A WILD-TYPE 341  21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TOMM70A MUTATED      9    1
  TOMM70A WILD-TYPE  341   21
     clus
vv    TOMM70A MUTATED TOMM70A WILD-TYPE
  NO                9               341
  YES               1                21
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  TOMM70A MUTATED                      9                             1
  TOMM70A WILD-TYPE                  306                            46
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  TOMM70A MUTATED                       0                              0
  TOMM70A WILD-TYPE                   106                             10
D2032V10, multiclass
                                clus
vv                               TOMM70A MUTATED TOMM70A WILD-TYPE
  COLON ADENOCARCINOMA                         9               306
  COLON MUCINOUS ADENOCARCINOMA                1                46
  RECTAL ADENOCARCINOMA                        0               106
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  TOMM70A MUTATED     9   0   0   0
  TOMM70A WILD-TYPE 336   4  31  25
D2032V11, multiclass
    clus
vv   TOMM70A MUTATED TOMM70A WILD-TYPE
  R0               9               336
  R1               0                 4
  R2               0                31
  RX               0                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2032V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TOMM70A MUTATED                                  0     0
  TOMM70A WILD-TYPE                                1    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  TOMM70A MUTATED                           0     6
  TOMM70A WILD-TYPE                        22   220
D2032V13, multiclass
                                  clus
vv                                 TOMM70A MUTATED TOMM70A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                      0                22
  WHITE                                          6               220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2033) Variable = CDHR3 MUTATION ANALYSIS
D2033V1, survival
                 sevent
clus2               0   1
  CDHR3 MUTATED    14   1
  CDHR3 WILD-TYPE 364  92
  CDHR3 MUTATED CDHR3 WILD-TYPE 
             15             456 
  CDHR3 MUTATED CDHR3 WILD-TYPE 
              1              92 
$`CDHR3 MUTATED`
TCGA-A6-5661 TCGA-A6-5665 TCGA-A6-6141 TCGA-AA-3510 TCGA-AD-5900 TCGA-AD-6964 
       33.53        22.06         8.38        63.98         0.07        10.88 
TCGA-AZ-4315 TCGA-CA-6717 TCGA-CM-4743 TCGA-CM-6674 TCGA-D5-6927 TCGA-D5-6930 
       58.39        12.76        23.05        12.95         9.44         1.51 
TCGA-DM-A1HB TCGA-AG-A002 TCGA-AG-A02N 
      135.65        20.98        61.97 

$`CDHR3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       32.71        27.09        22.52        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 
       20.28         7.04         3.02         1.02        35.01         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
       40.96        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
       16.31         0.95        33.01        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07        12.20        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
       82.95         1.91       124.27        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6675 
       12.99        13.02        15.02        14.04        11.01        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6931 
       12.43        14.30         9.04        11.64         4.80        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
       44.32       131.51       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 
       10.98        49.97         1.94        38.96        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  CDHR3 MUTATED CDHR3 WILD-TYPE 
           0.07            0.00 
  CDHR3 MUTATED CDHR3 WILD-TYPE 
         135.65          148.01 
  CDHR3 MUTATED CDHR3 WILD-TYPE 
         20.980          20.155 
[1] "0.1 - 135.7 (21.0)" "0.0 - 148.0 (20.2)"
[1] "hr=" "3.6"
D2033V2, continuous
D2033V3, binary
                 cls
clus                0   1
  CDHR3 MUTATED    13   2
  CDHR3 WILD-TYPE 353 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDHR3 MUTATED     13    2
  CDHR3 WILD-TYPE  353  117
        clus
vv       CDHR3 MUTATED CDHR3 WILD-TYPE
  COLON             13             353
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CDHR3 MUTATED         2        0        2         9         0         0
  CDHR3 WILD-TYPE      89        1       30       129        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CDHR3 MUTATED           0          0          1          0        0         0
  CDHR3 WILD-TYPE        24         11         58         42       48        18
                 vv
clus              STAGE IVB
  CDHR3 MUTATED           0
  CDHR3 WILD-TYPE         1
D2033V4, multiclass
            clus
vv           CDHR3 MUTATED CDHR3 WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA              9             129
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CDHR3 MUTATED     0   2  12   1
  CDHR3 WILD-TYPE  17  90 317  49
D2033V5, multiclass
    clus
vv   CDHR3 MUTATED CDHR3 WILD-TYPE
  T1             0              17
  T2             2              90
  T3            12             317
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  CDHR3 MUTATED    13   1   1
  CDHR3 WILD-TYPE 274 112  86
D2033V6, multiclass
    clus
vv   CDHR3 MUTATED CDHR3 WILD-TYPE
  N0            13             274
  N1             1             112
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2033V7, binary
                 cls
clus                0   1
  CDHR3 MUTATED    13   0
  CDHR3 WILD-TYPE 362  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDHR3 MUTATED     13    0
  CDHR3 WILD-TYPE  362   65
   clus
vv  CDHR3 MUTATED CDHR3 WILD-TYPE
  0            13             362
  1             0              65
[1] 2 2
[1] FALSE
D2033V8, binary
                 cls
clus                0   1
  CDHR3 MUTATED     2  13
  CDHR3 WILD-TYPE 223 251
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDHR3 MUTATED      2   13
  CDHR3 WILD-TYPE  223  251
        clus
vv       CDHR3 MUTATED CDHR3 WILD-TYPE
  FEMALE             2             223
  MALE              13             251
[1] 2 2
[1] FALSE
D2033V9, binary
                 cls
clus                0   1
  CDHR3 MUTATED    11   0
  CDHR3 WILD-TYPE 339  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDHR3 MUTATED     11    0
  CDHR3 WILD-TYPE  339   22
     clus
vv    CDHR3 MUTATED CDHR3 WILD-TYPE
  NO             11             339
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CDHR3 MUTATED                      9                             3
  CDHR3 WILD-TYPE                  306                            44
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CDHR3 MUTATED                       2                              0
  CDHR3 WILD-TYPE                   104                             10
D2033V10, multiclass
                                clus
vv                               CDHR3 MUTATED CDHR3 WILD-TYPE
  COLON ADENOCARCINOMA                       9             306
  COLON MUCINOUS ADENOCARCINOMA              3              44
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  CDHR3 MUTATED    11   0   0   1
  CDHR3 WILD-TYPE 334   4  31  24
D2033V11, multiclass
    clus
vv   CDHR3 MUTATED CDHR3 WILD-TYPE
  R0            11             334
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2033V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CDHR3 MUTATED                                  0     1
  CDHR3 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CDHR3 MUTATED                           2     9
  CDHR3 WILD-TYPE                        20   217
D2033V13, multiclass
                                  clus
vv                                 CDHR3 MUTATED CDHR3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    2              20
  WHITE                                        9             217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2034) Variable = ZNF559 MUTATION ANALYSIS
D2034V1, survival
                  sevent
clus2                0   1
  ZNF559 MUTATED    12   4
  ZNF559 WILD-TYPE 366  89
  ZNF559 MUTATED ZNF559 WILD-TYPE 
              16              455 
  ZNF559 MUTATED ZNF559 WILD-TYPE 
               4               89 
$`ZNF559 MUTATED`
TCGA-A6-3810 TCGA-A6-6141 TCGA-AA-3672 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-A00A 
       36.53         8.38         0.92        26.99        19.04        38.04 
TCGA-AA-A00J TCGA-AA-A010 TCGA-AY-6197 TCGA-AZ-4315 TCGA-CA-6717 TCGA-CA-6718 
       18.05        34.98        21.44        58.39        12.76        10.06 
TCGA-CM-6166 TCGA-DM-A28F TCGA-F4-6856 TCGA-F5-6464 
       21.99        35.97        35.31         9.96 

$`ZNF559 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        32.75        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 
       22.06        32.71        27.09        22.52        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
       54.02         2.01        14.01        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       85.05        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K 
       27.02        13.94        19.00        30.02        34.03        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       33.01        17.82         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 
        3.06         3.25         3.29         0.07        12.20        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       16.04        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 
       33.67        13.25         0.53        47.41       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       19.96        20.91        18.28        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  ZNF559 MUTATED ZNF559 WILD-TYPE 
            0.92             0.00 
  ZNF559 MUTATED ZNF559 WILD-TYPE 
           58.39           148.01 
  ZNF559 MUTATED ZNF559 WILD-TYPE 
          21.715           20.120 
[1] "0.9 - 58.4 (21.7)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.5"
D2034V2, continuous
D2034V3, binary
                  cls
clus                 0   1
  ZNF559 MUTATED    15   1
  ZNF559 WILD-TYPE 351 118
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF559 MUTATED     15    1
  ZNF559 WILD-TYPE  351  118
        clus
vv       ZNF559 MUTATED ZNF559 WILD-TYPE
  COLON              15              351
  RECTUM              1              118
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZNF559 MUTATED         2        0        1         8         1         0
  ZNF559 WILD-TYPE      89        1       31       130         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF559 MUTATED           1          0          2          1        0
  ZNF559 WILD-TYPE        23         11         57         41       48
                  vv
clus               STAGE IVA STAGE IVB
  ZNF559 MUTATED           0         0
  ZNF559 WILD-TYPE        18         1
D2034V4, multiclass
            clus
vv           ZNF559 MUTATED ZNF559 WILD-TYPE
  STAGE I                 2               89
  STAGE IA                0                1
  STAGE II                1               31
  STAGE IIA               8              130
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               1               23
  STAGE IIIA              0               11
  STAGE IIIB              2               57
  STAGE IIIC              1               41
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZNF559 MUTATED     0   2  11   3
  ZNF559 WILD-TYPE  17  90 318  47
D2034V5, multiclass
    clus
vv   ZNF559 MUTATED ZNF559 WILD-TYPE
  T1              0               17
  T2              2               90
  T3             11              318
  T4              3               47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  ZNF559 MUTATED    12   3   1
  ZNF559 WILD-TYPE 275 110  86
D2034V6, multiclass
    clus
vv   ZNF559 MUTATED ZNF559 WILD-TYPE
  N0             12              275
  N1              3              110
  N2              1               86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2034V7, binary
                  cls
clus                 0   1
  ZNF559 MUTATED    15   0
  ZNF559 WILD-TYPE 360  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF559 MUTATED     15    0
  ZNF559 WILD-TYPE  360   65
   clus
vv  ZNF559 MUTATED ZNF559 WILD-TYPE
  0             15              360
  1              0               65
[1] 2 2
[1] FALSE
D2034V8, binary
                  cls
clus                 0   1
  ZNF559 MUTATED     5  11
  ZNF559 WILD-TYPE 220 253
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF559 MUTATED      5   11
  ZNF559 WILD-TYPE  220  253
        clus
vv       ZNF559 MUTATED ZNF559 WILD-TYPE
  FEMALE              5              220
  MALE               11              253
[1] 2 2
[1] FALSE
D2034V9, binary
                  cls
clus                 0   1
  ZNF559 MUTATED    15   0
  ZNF559 WILD-TYPE 335  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF559 MUTATED     15    0
  ZNF559 WILD-TYPE  335   22
     clus
vv    ZNF559 MUTATED ZNF559 WILD-TYPE
  NO              15              335
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ZNF559 MUTATED                     12                             3
  ZNF559 WILD-TYPE                  303                            44
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ZNF559 MUTATED                       1                              0
  ZNF559 WILD-TYPE                   105                             10
D2034V10, multiclass
                                clus
vv                               ZNF559 MUTATED ZNF559 WILD-TYPE
  COLON ADENOCARCINOMA                       12              303
  COLON MUCINOUS ADENOCARCINOMA               3               44
  RECTAL ADENOCARCINOMA                       1              105
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ZNF559 MUTATED    12   0   0   2
  ZNF559 WILD-TYPE 333   4  31  23
D2034V11, multiclass
    clus
vv   ZNF559 MUTATED ZNF559 WILD-TYPE
  R0             12              333
  R1              0                4
  R2              0               31
  RX              2               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2034V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF559 MUTATED                                  0     2
  ZNF559 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZNF559 MUTATED                           1     7
  ZNF559 WILD-TYPE                        21   219
D2034V13, multiclass
                                  clus
vv                                 ZNF559 MUTATED ZNF559 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                9
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                         7              219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2035) Variable = MAK MUTATION ANALYSIS
D2035V1, survival
               sevent
clus2             0   1
  MAK MUTATED     8   4
  MAK WILD-TYPE 370  89
  MAK MUTATED MAK WILD-TYPE 
           12           459 
  MAK MUTATED MAK WILD-TYPE 
            4            89 
$`MAK MUTATED`
TCGA-AA-3713 TCGA-AA-3950 TCGA-AA-A00N TCGA-AA-A01R TCGA-CA-6717 TCGA-CK-5916 
       19.04        24.00         4.01        35.01        12.76        21.14 
TCGA-CM-4746 TCGA-DM-A1HB TCGA-F4-6570 TCGA-AG-3594 TCGA-AG-A002 TCGA-DC-6157 
       37.02       135.65         6.18         2.01        20.98        27.95 

$`MAK WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 
        2.01        12.99        24.00        33.01        26.01         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       31.00        38.07         1.02         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07        12.20        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       51.32         9.99        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       20.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      131.51       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       46.03        34.03        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       13.97        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  MAK MUTATED MAK WILD-TYPE 
         2.01          0.00 
  MAK MUTATED MAK WILD-TYPE 
       135.65        148.01 
  MAK MUTATED MAK WILD-TYPE 
        21.06         20.12 
[1] "2.0 - 135.7 (21.1)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.8"
D2035V2, continuous
D2035V3, binary
               cls
clus              0   1
  MAK MUTATED     9   3
  MAK WILD-TYPE 357 116
[1] "tbl2"
               cls
clus            [,1] [,2]
  MAK MUTATED      9    3
  MAK WILD-TYPE  357  116
        clus
vv       MAK MUTATED MAK WILD-TYPE
  COLON            9           357
  RECTUM           3           116
[1] 2 2
[1] FALSE
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MAK MUTATED         4        0        0         4         1         0
  MAK WILD-TYPE      87        1       32       134         9         1
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MAK MUTATED           1          0          1          0        1         0
  MAK WILD-TYPE        23         11         58         42       47        18
               vv
clus            STAGE IVB
  MAK MUTATED           0
  MAK WILD-TYPE         1
D2035V4, multiclass
            clus
vv           MAK MUTATED MAK WILD-TYPE
  STAGE I              4            87
  STAGE IA             0             1
  STAGE II             0            32
  STAGE IIA            4           134
  STAGE IIB            1             9
  STAGE IIC            0             1
  STAGE III            1            23
  STAGE IIIA           0            11
  STAGE IIIB           1            58
  STAGE IIIC           0            42
  STAGE IV             1            47
  STAGE IVA            0            18
  STAGE IVB            0             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  MAK MUTATED     1   3   7   1
  MAK WILD-TYPE  16  89 322  49
D2035V5, multiclass
    clus
vv   MAK MUTATED MAK WILD-TYPE
  T1           1            16
  T2           3            89
  T3           7           322
  T4           1            49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2
  MAK MUTATED    10   1   1
  MAK WILD-TYPE 277 112  86
D2035V6, multiclass
    clus
vv   MAK MUTATED MAK WILD-TYPE
  N0          10           277
  N1           1           112
  N2           1            86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2035V7, binary
               cls
clus              0   1
  MAK MUTATED    11   1
  MAK WILD-TYPE 364  64
[1] "tbl2"
               cls
clus            [,1] [,2]
  MAK MUTATED     11    1
  MAK WILD-TYPE  364   64
   clus
vv  MAK MUTATED MAK WILD-TYPE
  0          11           364
  1           1            64
[1] 2 2
[1] FALSE
D2035V8, binary
               cls
clus              0   1
  MAK MUTATED     3   9
  MAK WILD-TYPE 222 255
[1] "tbl2"
               cls
clus            [,1] [,2]
  MAK MUTATED      3    9
  MAK WILD-TYPE  222  255
        clus
vv       MAK MUTATED MAK WILD-TYPE
  FEMALE           3           222
  MALE             9           255
[1] 2 2
[1] FALSE
D2035V9, binary
               cls
clus              0   1
  MAK MUTATED     7   2
  MAK WILD-TYPE 343  20
[1] "tbl2"
               cls
clus            [,1] [,2]
  MAK MUTATED      7    2
  MAK WILD-TYPE  343   20
     clus
vv    MAK MUTATED MAK WILD-TYPE
  NO            7           343
  YES           2            20
[1] 2 2
[1] FALSE
               vv
clus            COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MAK MUTATED                      4                             4
  MAK WILD-TYPE                  311                            43
               vv
clus            RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MAK MUTATED                       2                              1
  MAK WILD-TYPE                   104                              9
D2035V10, multiclass
                                clus
vv                               MAK MUTATED MAK WILD-TYPE
  COLON ADENOCARCINOMA                     4           311
  COLON MUCINOUS ADENOCARCINOMA            4            43
  RECTAL ADENOCARCINOMA                    2           104
  RECTAL MUCINOUS ADENOCARCINOMA           1             9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             R0  R1  R2  RX
  MAK MUTATED     8   0   1   2
  MAK WILD-TYPE 337   4  30  23
D2035V11, multiclass
    clus
vv   MAK MUTATED MAK WILD-TYPE
  R0           8           337
  R1           0             4
  R2           1            30
  RX           2            23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2035V12, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MAK MUTATED                                  0     1
  MAK WILD-TYPE                                1    10
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  MAK MUTATED                           2     3
  MAK WILD-TYPE                        20   223
D2035V13, multiclass
                                  clus
vv                                 MAK MUTATED MAK WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      1            10
  BLACK OR AFRICAN AMERICAN                  2            20
  WHITE                                      3           223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2036) Variable = GPR156 MUTATION ANALYSIS
D2036V1, survival
                  sevent
clus2                0   1
  GPR156 MUTATED    13   1
  GPR156 WILD-TYPE 365  92
  GPR156 MUTATED GPR156 WILD-TYPE 
              14              457 
  GPR156 MUTATED GPR156 WILD-TYPE 
               1               92 
$`GPR156 MUTATED`
TCGA-A6-5661 TCGA-A6-6781 TCGA-AA-3950 TCGA-AA-3977 TCGA-AA-A00J TCGA-AA-A00N 
       33.53        19.66        24.00        25.02        18.05         4.01 
TCGA-AA-A010 TCGA-AD-6889 TCGA-AZ-4315 TCGA-CA-6717 TCGA-CK-5914 TCGA-CM-6675 
       34.98        56.55        58.39        12.76         9.99        13.05 
TCGA-AG-3892 TCGA-AG-A002 
       13.02        20.98 

$`GPR156 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 
       12.99        24.00        33.01        26.01         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       34.03        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       15.52         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       33.01        21.44        17.82         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       49.08        51.32        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6676 TCGA-CM-6677 
       15.02        14.04        11.01        12.95        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       36.95        17.03        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  GPR156 MUTATED GPR156 WILD-TYPE 
            4.01             0.00 
  GPR156 MUTATED GPR156 WILD-TYPE 
           58.39           148.01 
  GPR156 MUTATED GPR156 WILD-TYPE 
           20.32            20.19 
[1] "4.0 - 58.4 (20.3)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "2.7"
D2036V2, continuous
D2036V3, binary
                  cls
clus                 0   1
  GPR156 MUTATED    12   2
  GPR156 WILD-TYPE 354 117
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR156 MUTATED     12    2
  GPR156 WILD-TYPE  354  117
        clus
vv       GPR156 MUTATED GPR156 WILD-TYPE
  COLON              12              354
  RECTUM              2              117
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GPR156 MUTATED         2        0        0         5         2         0
  GPR156 WILD-TYPE      89        1       32       133         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GPR156 MUTATED           0          0          2          1        0
  GPR156 WILD-TYPE        24         11         57         41       48
                  vv
clus               STAGE IVA STAGE IVB
  GPR156 MUTATED           0         1
  GPR156 WILD-TYPE        18         0
D2036V4, multiclass
            clus
vv           GPR156 MUTATED GPR156 WILD-TYPE
  STAGE I                 2               89
  STAGE IA                0                1
  STAGE II                0               32
  STAGE IIA               5              133
  STAGE IIB               2                8
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              2               57
  STAGE IIIC              1               41
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               1                0
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  GPR156 MUTATED     1   2   7   4
  GPR156 WILD-TYPE  16  90 322  46
D2036V5, multiclass
    clus
vv   GPR156 MUTATED GPR156 WILD-TYPE
  T1              1               16
  T2              2               90
  T3              7              322
  T4              4               46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  GPR156 MUTATED    10   3   1
  GPR156 WILD-TYPE 277 110  86
D2036V6, multiclass
    clus
vv   GPR156 MUTATED GPR156 WILD-TYPE
  N0             10              277
  N1              3              110
  N2              1               86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2036V7, binary
                  cls
clus                 0   1
  GPR156 MUTATED    10   1
  GPR156 WILD-TYPE 365  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR156 MUTATED     10    1
  GPR156 WILD-TYPE  365   64
   clus
vv  GPR156 MUTATED GPR156 WILD-TYPE
  0             10              365
  1              1               64
[1] 2 2
[1] FALSE
D2036V8, binary
                  cls
clus                 0   1
  GPR156 MUTATED     4  10
  GPR156 WILD-TYPE 221 254
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR156 MUTATED      4   10
  GPR156 WILD-TYPE  221  254
        clus
vv       GPR156 MUTATED GPR156 WILD-TYPE
  FEMALE              4              221
  MALE               10              254
[1] 2 2
[1] FALSE
D2036V9, binary
                  cls
clus                 0   1
  GPR156 MUTATED    11   0
  GPR156 WILD-TYPE 339  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR156 MUTATED     11    0
  GPR156 WILD-TYPE  339   22
     clus
vv    GPR156 MUTATED GPR156 WILD-TYPE
  NO              11              339
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  GPR156 MUTATED                      7                             5
  GPR156 WILD-TYPE                  308                            42
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  GPR156 MUTATED                       2                              0
  GPR156 WILD-TYPE                   104                             10
D2036V10, multiclass
                                clus
vv                               GPR156 MUTATED GPR156 WILD-TYPE
  COLON ADENOCARCINOMA                        7              308
  COLON MUCINOUS ADENOCARCINOMA               5               42
  RECTAL ADENOCARCINOMA                       2              104
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  GPR156 MUTATED    10   0   0   2
  GPR156 WILD-TYPE 335   4  31  23
D2036V11, multiclass
    clus
vv   GPR156 MUTATED GPR156 WILD-TYPE
  R0             10              335
  R1              0                4
  R2              0               31
  RX              2               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2036V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GPR156 MUTATED                                  0     2
  GPR156 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  GPR156 MUTATED                           2     3
  GPR156 WILD-TYPE                        20   223
D2036V13, multiclass
                                  clus
vv                                 GPR156 MUTATED GPR156 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                9
  BLACK OR AFRICAN AMERICAN                     2               20
  WHITE                                         3              223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2037) Variable = NIT2 MUTATION ANALYSIS
D2037V1, survival
                sevent
clus2              0   1
  NIT2 MUTATED     5   0
  NIT2 WILD-TYPE 373  93
  NIT2 MUTATED NIT2 WILD-TYPE 
             5            466 
  NIT2 MUTATED NIT2 WILD-TYPE 
             0             93 
$`NIT2 MUTATED`
TCGA-AA-3679 TCGA-AD-5900 TCGA-CA-6717 TCGA-AG-3892 TCGA-AG-A002 
       15.02         0.07        12.76        13.02        20.98 

$`NIT2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       50.04        47.01        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 
       41.00        39.98        18.05        40.96        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.20        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 
       19.99         1.02        17.95        36.95        17.03        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  NIT2 MUTATED NIT2 WILD-TYPE 
          0.07           0.00 
  NIT2 MUTATED NIT2 WILD-TYPE 
         20.98         148.01 
  NIT2 MUTATED NIT2 WILD-TYPE 
        13.020         20.415 
[1] "0.1 - 21.0 (13.0)"  "0.0 - 148.0 (20.4)"
[1] "hr="     "3300000"
D2037V2, continuous
D2037V3, binary
                cls
clus               0   1
  NIT2 MUTATED     3   2
  NIT2 WILD-TYPE 363 117
[1] "tbl2"
                cls
clus             [,1] [,2]
  NIT2 MUTATED      3    2
  NIT2 WILD-TYPE  363  117
        clus
vv       NIT2 MUTATED NIT2 WILD-TYPE
  COLON             3            363
  RECTUM            2            117
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NIT2 MUTATED         3        0        0         1         0         0
  NIT2 WILD-TYPE      88        1       32       137        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NIT2 MUTATED           0          0          0          0        1         0
  NIT2 WILD-TYPE        24         11         59         42       47        18
                vv
clus             STAGE IVB
  NIT2 MUTATED           0
  NIT2 WILD-TYPE         1
D2037V4, multiclass
            clus
vv           NIT2 MUTATED NIT2 WILD-TYPE
  STAGE I               3             88
  STAGE IA              0              1
  STAGE II              0             32
  STAGE IIA             1            137
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            0             59
  STAGE IIIC            0             42
  STAGE IV              1             47
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  NIT2 MUTATED     1   2   2   0
  NIT2 WILD-TYPE  16  90 327  50
D2037V5, multiclass
    clus
vv   NIT2 MUTATED NIT2 WILD-TYPE
  T1            1             16
  T2            2             90
  T3            2            327
  T4            0             50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  NIT2 MUTATED     4   0   1
  NIT2 WILD-TYPE 283 113  86
D2037V6, multiclass
    clus
vv   NIT2 MUTATED NIT2 WILD-TYPE
  N0            4            283
  N1            0            113
  N2            1             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2037V7, binary
                cls
clus               0   1
  NIT2 MUTATED     3   1
  NIT2 WILD-TYPE 372  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  NIT2 MUTATED      3    1
  NIT2 WILD-TYPE  372   64
   clus
vv  NIT2 MUTATED NIT2 WILD-TYPE
  0            3            372
  1            1             64
[1] 2 2
[1] FALSE
D2037V8, binary
                cls
clus               0   1
  NIT2 MUTATED     1   4
  NIT2 WILD-TYPE 224 260
[1] "tbl2"
                cls
clus             [,1] [,2]
  NIT2 MUTATED      1    4
  NIT2 WILD-TYPE  224  260
        clus
vv       NIT2 MUTATED NIT2 WILD-TYPE
  FEMALE            1            224
  MALE              4            260
[1] 2 2
[1] FALSE
D2037V9, binary
                cls
clus               0   1
  NIT2 MUTATED     4   0
  NIT2 WILD-TYPE 346  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  NIT2 MUTATED      4    0
  NIT2 WILD-TYPE  346   22
     clus
vv    NIT2 MUTATED NIT2 WILD-TYPE
  NO             4            346
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  NIT2 MUTATED                      1                             2
  NIT2 WILD-TYPE                  314                            45
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  NIT2 MUTATED                       2                              0
  NIT2 WILD-TYPE                   104                             10
D2037V10, multiclass
                                clus
vv                               NIT2 MUTATED NIT2 WILD-TYPE
  COLON ADENOCARCINOMA                      1            314
  COLON MUCINOUS ADENOCARCINOMA             2             45
  RECTAL ADENOCARCINOMA                     2            104
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  NIT2 MUTATED     3   0   1   1
  NIT2 WILD-TYPE 342   4  30  24
D2037V11, multiclass
    clus
vv   NIT2 MUTATED NIT2 WILD-TYPE
  R0            3            342
  R1            0              4
  R2            1             30
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2037V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NIT2 MUTATED                                  0     1
  NIT2 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  NIT2 MUTATED                           0     1
  NIT2 WILD-TYPE                        22   225
D2037V13, multiclass
[1] "Remove cluster labels:" "NIT2 MUTATED"          
clus
  NIT2 MUTATED NIT2 WILD-TYPE 
             2            258 
    TCGA-A6-2671     TCGA-A6-2672     TCGA-A6-2674     TCGA-A6-2676 
"NIT2 WILD-TYPE" "NIT2 WILD-TYPE" "NIT2 WILD-TYPE" "NIT2 WILD-TYPE" 
    TCGA-A6-2677     TCGA-A6-2678     TCGA-A6-2683     TCGA-A6-3807 
"NIT2 WILD-TYPE" "NIT2 WILD-TYPE" "NIT2 WILD-TYPE" "NIT2 WILD-TYPE" 
    TCGA-A6-3808     TCGA-A6-3809     TCGA-A6-3810     TCGA-A6-4105 
"NIT2 WILD-TYPE" "NIT2 WILD-TYPE" "NIT2 WILD-TYPE" "NIT2 WILD-TYPE" 
    TCGA-A6-5656     TCGA-A6-5657     TCGA-A6-5659     TCGA-A6-5660 
"NIT2 WILD-TYPE" "NIT2 WILD-TYPE" "NIT2 WILD-TYPE" "NIT2 WILD-TYPE" 
    TCGA-A6-5661     TCGA-A6-5662     TCGA-A6-5664     TCGA-A6-5665 
"NIT2 WILD-TYPE" "NIT2 WILD-TYPE" "NIT2 WILD-TYPE" "NIT2 WILD-TYPE" 
    TCGA-A6-5666     TCGA-A6-6137     TCGA-A6-6138     TCGA-A6-6141 
"NIT2 WILD-TYPE" "NIT2 WILD-TYPE" "NIT2 WILD-TYPE" "NIT2 WILD-TYPE" 
    TCGA-A6-6142     TCGA-A6-6648     TCGA-A6-6649     TCGA-A6-6651 
"NIT2 WILD-TYPE" "NIT2 WILD-TYPE" "NIT2 WILD-TYPE" "NIT2 WILD-TYPE" 
    TCGA-A6-6652     TCGA-A6-6653     TCGA-A6-6654     TCGA-A6-6780 
"NIT2 WILD-TYPE" "NIT2 WILD-TYPE" "NIT2 WILD-TYPE" "NIT2 WILD-TYPE" 
    TCGA-A6-6781     TCGA-A6-6782     TCGA-AD-6548     TCGA-AD-6888 
"NIT2 WILD-TYPE" "NIT2 WILD-TYPE" "NIT2 WILD-TYPE" "NIT2 WILD-TYPE" 
    TCGA-AD-6889     TCGA-AD-6890     TCGA-AD-6895     TCGA-AD-6899 
"NIT2 WILD-TYPE" "NIT2 WILD-TYPE" "NIT2 WILD-TYPE" "NIT2 WILD-TYPE" 
    TCGA-AD-6901     TCGA-AD-6963     TCGA-AD-6964     TCGA-AD-6965 
"NIT2 WILD-TYPE" "NIT2 WILD-TYPE" "NIT2 WILD-TYPE" "NIT2 WILD-TYPE" 
    TCGA-AU-3779     TCGA-AU-6004     TCGA-AY-4070     TCGA-AY-4071 
"NIT2 WILD-TYPE" "NIT2 WILD-TYPE" "NIT2 WILD-TYPE" "NIT2 WILD-TYPE" 
    TCGA-AY-5543     TCGA-AY-6196     TCGA-AY-6197     TCGA-AY-6386 
"NIT2 WILD-TYPE" "NIT2 WILD-TYPE" "NIT2 WILD-TYPE" "NIT2 WILD-TYPE" 
    TCGA-AZ-4315     TCGA-AZ-4323     TCGA-AZ-4616     TCGA-AZ-4681 
"NIT2 WILD-TYPE" "NIT2 WILD-TYPE" "NIT2 WILD-TYPE" "NIT2 WILD-TYPE" 
    TCGA-AZ-4682     TCGA-AZ-5403     TCGA-AZ-5407     TCGA-AZ-6598 
"NIT2 WILD-TYPE" "NIT2 WILD-TYPE" "NIT2 WILD-TYPE" "NIT2 WILD-TYPE" 
    TCGA-AZ-6599     TCGA-AZ-6600     TCGA-AZ-6601     TCGA-AZ-6603 
"NIT2 WILD-TYPE" "NIT2 WILD-TYPE" "NIT2 WILD-TYPE" "NIT2 WILD-TYPE" 
    TCGA-AZ-6605     TCGA-AZ-6606     TCGA-AZ-6607     TCGA-AZ-6608 
"NIT2 WILD-TYPE" "NIT2 WILD-TYPE" "NIT2 WILD-TYPE" "NIT2 WILD-TYPE" 
    TCGA-CA-5254     TCGA-CA-5255     TCGA-CA-5796     TCGA-CA-5797 
"NIT2 WILD-TYPE" "NIT2 WILD-TYPE" "NIT2 WILD-TYPE" "NIT2 WILD-TYPE" 
    TCGA-CA-6715     TCGA-CA-6716     TCGA-CA-6718     TCGA-CA-6719 
"NIT2 WILD-TYPE" "NIT2 WILD-TYPE" "NIT2 WILD-TYPE" "NIT2 WILD-TYPE" 
    TCGA-CK-4947     TCGA-CK-4948     TCGA-CK-4950     TCGA-CK-4952 
"NIT2 WILD-TYPE" "NIT2 WILD-TYPE" "NIT2 WILD-TYPE" "NIT2 WILD-TYPE" 
    TCGA-CK-5912     TCGA-CK-5913     TCGA-CK-5914     TCGA-CK-5915 
"NIT2 WILD-TYPE" "NIT2 WILD-TYPE" "NIT2 WILD-TYPE" "NIT2 WILD-TYPE" 
    TCGA-CK-5916     TCGA-CK-6746     TCGA-CK-6747     TCGA-CK-6748 
"NIT2 WILD-TYPE" "NIT2 WILD-TYPE" "NIT2 WILD-TYPE" "NIT2 WILD-TYPE" 
    TCGA-CK-6751     TCGA-CM-4743     TCGA-CM-4744     TCGA-CM-4746 
"NIT2 WILD-TYPE" "NIT2 WILD-TYPE" "NIT2 WILD-TYPE" "NIT2 WILD-TYPE" 
    TCGA-CM-4747     TCGA-CM-4752     TCGA-CM-5341     TCGA-CM-5344 
"NIT2 WILD-TYPE" "NIT2 WILD-TYPE" "NIT2 WILD-TYPE" "NIT2 WILD-TYPE" 
    TCGA-CM-5348     TCGA-CM-5349     TCGA-CM-5860     TCGA-CM-5861 
"NIT2 WILD-TYPE" "NIT2 WILD-TYPE" "NIT2 WILD-TYPE" "NIT2 WILD-TYPE" 
    TCGA-CM-5862     TCGA-CM-5863     TCGA-CM-5864     TCGA-CM-5868 
"NIT2 WILD-TYPE" "NIT2 WILD-TYPE" "NIT2 WILD-TYPE" "NIT2 WILD-TYPE" 
    TCGA-CM-6161     TCGA-CM-6162     TCGA-CM-6163     TCGA-CM-6164 
"NIT2 WILD-TYPE" "NIT2 WILD-TYPE" "NIT2 WILD-TYPE" "NIT2 WILD-TYPE" 
    TCGA-CM-6165     TCGA-CM-6166     TCGA-CM-6167     TCGA-CM-6168 
"NIT2 WILD-TYPE" "NIT2 WILD-TYPE" "NIT2 WILD-TYPE" "NIT2 WILD-TYPE" 
    TCGA-CM-6169     TCGA-CM-6170     TCGA-CM-6171     TCGA-CM-6172 
"NIT2 WILD-TYPE" "NIT2 WILD-TYPE" "NIT2 WILD-TYPE" "NIT2 WILD-TYPE" 
    TCGA-CM-6674     TCGA-CM-6675     TCGA-CM-6676     TCGA-CM-6677 
"NIT2 WILD-TYPE" "NIT2 WILD-TYPE" "NIT2 WILD-TYPE" "NIT2 WILD-TYPE" 
    TCGA-CM-6678     TCGA-CM-6679     TCGA-CM-6680     TCGA-D5-5537 
"NIT2 WILD-TYPE" "NIT2 WILD-TYPE" "NIT2 WILD-TYPE" "NIT2 WILD-TYPE" 
    TCGA-D5-5538     TCGA-D5-5539     TCGA-D5-5540     TCGA-D5-5541 
"NIT2 WILD-TYPE" "NIT2 WILD-TYPE" "NIT2 WILD-TYPE" "NIT2 WILD-TYPE" 
    TCGA-D5-6529     TCGA-D5-6532     TCGA-D5-6533     TCGA-D5-6534 
"NIT2 WILD-TYPE" "NIT2 WILD-TYPE" "NIT2 WILD-TYPE" "NIT2 WILD-TYPE" 
    TCGA-D5-6535     TCGA-D5-6536     TCGA-D5-6537     TCGA-D5-6538 
"NIT2 WILD-TYPE" "NIT2 WILD-TYPE" "NIT2 WILD-TYPE" "NIT2 WILD-TYPE" 
    TCGA-D5-6539     TCGA-D5-6540     TCGA-D5-6541     TCGA-D5-6898 
"NIT2 WILD-TYPE" "NIT2 WILD-TYPE" "NIT2 WILD-TYPE" "NIT2 WILD-TYPE" 
    TCGA-D5-6920     TCGA-D5-6922     TCGA-D5-6923     TCGA-D5-6924 
"NIT2 WILD-TYPE" "NIT2 WILD-TYPE" "NIT2 WILD-TYPE" "NIT2 WILD-TYPE" 
    TCGA-D5-6926     TCGA-D5-6927     TCGA-D5-6928     TCGA-D5-6929 
"NIT2 WILD-TYPE" "NIT2 WILD-TYPE" "NIT2 WILD-TYPE" "NIT2 WILD-TYPE" 
    TCGA-D5-6930     TCGA-D5-6931     TCGA-D5-6932     TCGA-D5-7000 
"NIT2 WILD-TYPE" "NIT2 WILD-TYPE" "NIT2 WILD-TYPE" "NIT2 WILD-TYPE" 
    TCGA-DM-A0X9     TCGA-DM-A0XD     TCGA-DM-A0XF     TCGA-DM-A1D0 
"NIT2 WILD-TYPE" "NIT2 WILD-TYPE" "NIT2 WILD-TYPE" "NIT2 WILD-TYPE" 
    TCGA-DM-A1D4     TCGA-DM-A1D6     TCGA-DM-A1D7     TCGA-DM-A1D8 
"NIT2 WILD-TYPE" "NIT2 WILD-TYPE" "NIT2 WILD-TYPE" "NIT2 WILD-TYPE" 
    TCGA-DM-A1D9     TCGA-DM-A1DA     TCGA-DM-A1DB     TCGA-DM-A1HA 
"NIT2 WILD-TYPE" "NIT2 WILD-TYPE" "NIT2 WILD-TYPE" "NIT2 WILD-TYPE" 
    TCGA-DM-A1HB     TCGA-DM-A282     TCGA-DM-A285     TCGA-DM-A28C 
"NIT2 WILD-TYPE" "NIT2 WILD-TYPE" "NIT2 WILD-TYPE" "NIT2 WILD-TYPE" 
    TCGA-DM-A28E     TCGA-DM-A28F     TCGA-DM-A28G     TCGA-DM-A28H 
"NIT2 WILD-TYPE" "NIT2 WILD-TYPE" "NIT2 WILD-TYPE" "NIT2 WILD-TYPE" 
    TCGA-DM-A28K     TCGA-F4-6459     TCGA-F4-6460     TCGA-F4-6569 
"NIT2 WILD-TYPE" "NIT2 WILD-TYPE" "NIT2 WILD-TYPE" "NIT2 WILD-TYPE" 
    TCGA-F4-6570     TCGA-F4-6703     TCGA-F4-6704     TCGA-F4-6805 
"NIT2 WILD-TYPE" "NIT2 WILD-TYPE" "NIT2 WILD-TYPE" "NIT2 WILD-TYPE" 
    TCGA-F4-6806     TCGA-F4-6807     TCGA-F4-6808     TCGA-F4-6809 
"NIT2 WILD-TYPE" "NIT2 WILD-TYPE" "NIT2 WILD-TYPE" "NIT2 WILD-TYPE" 
    TCGA-F4-6854     TCGA-F4-6855     TCGA-F4-6856     TCGA-G4-6293 
"NIT2 WILD-TYPE" "NIT2 WILD-TYPE" "NIT2 WILD-TYPE" "NIT2 WILD-TYPE" 
    TCGA-G4-6299     TCGA-G4-6303     TCGA-G4-6304     TCGA-G4-6306 
"NIT2 WILD-TYPE" "NIT2 WILD-TYPE" "NIT2 WILD-TYPE" "NIT2 WILD-TYPE" 
    TCGA-G4-6307     TCGA-G4-6309     TCGA-G4-6310     TCGA-G4-6315 
"NIT2 WILD-TYPE" "NIT2 WILD-TYPE" "NIT2 WILD-TYPE" "NIT2 WILD-TYPE" 
    TCGA-G4-6317     TCGA-G4-6321     TCGA-G4-6323     TCGA-G4-6586 
"NIT2 WILD-TYPE" "NIT2 WILD-TYPE" "NIT2 WILD-TYPE" "NIT2 WILD-TYPE" 
    TCGA-G4-6588     TCGA-G4-6625     TCGA-G4-6626     TCGA-G4-6628 
"NIT2 WILD-TYPE" "NIT2 WILD-TYPE" "NIT2 WILD-TYPE" "NIT2 WILD-TYPE" 
    TCGA-AF-2687     TCGA-AF-2689     TCGA-AF-2691     TCGA-AF-2692 
"NIT2 WILD-TYPE" "NIT2 WILD-TYPE" "NIT2 WILD-TYPE" "NIT2 WILD-TYPE" 
    TCGA-AF-2693     TCGA-AF-3400     TCGA-AF-3913     TCGA-AF-4110 
"NIT2 WILD-TYPE" "NIT2 WILD-TYPE" "NIT2 WILD-TYPE" "NIT2 WILD-TYPE" 
    TCGA-AF-5654     TCGA-AF-6136     TCGA-AF-6655     TCGA-AF-6672 
"NIT2 WILD-TYPE" "NIT2 WILD-TYPE" "NIT2 WILD-TYPE" "NIT2 WILD-TYPE" 
    TCGA-AH-6544     TCGA-AH-6547     TCGA-AH-6549     TCGA-AH-6643 
"NIT2 WILD-TYPE" "NIT2 WILD-TYPE" "NIT2 WILD-TYPE" "NIT2 WILD-TYPE" 
    TCGA-AH-6644     TCGA-CI-6619     TCGA-CI-6620     TCGA-CI-6621 
"NIT2 WILD-TYPE" "NIT2 WILD-TYPE" "NIT2 WILD-TYPE" "NIT2 WILD-TYPE" 
    TCGA-CI-6622     TCGA-CI-6624     TCGA-CL-5917     TCGA-CL-5918 
"NIT2 WILD-TYPE" "NIT2 WILD-TYPE" "NIT2 WILD-TYPE" "NIT2 WILD-TYPE" 
    TCGA-DC-5337     TCGA-DC-5869     TCGA-DC-6155     TCGA-DC-6157 
"NIT2 WILD-TYPE" "NIT2 WILD-TYPE" "NIT2 WILD-TYPE" "NIT2 WILD-TYPE" 
    TCGA-DC-6158     TCGA-DC-6160     TCGA-DC-6681     TCGA-DC-6682 
"NIT2 WILD-TYPE" "NIT2 WILD-TYPE" "NIT2 WILD-TYPE" "NIT2 WILD-TYPE" 
    TCGA-DC-6683     TCGA-DT-5265     TCGA-DY-A0XA     TCGA-DY-A1DC 
"NIT2 WILD-TYPE" "NIT2 WILD-TYPE" "NIT2 WILD-TYPE" "NIT2 WILD-TYPE" 
    TCGA-DY-A1DD     TCGA-DY-A1DF     TCGA-DY-A1DG     TCGA-DY-A1H8 
"NIT2 WILD-TYPE" "NIT2 WILD-TYPE" "NIT2 WILD-TYPE" "NIT2 WILD-TYPE" 
    TCGA-EF-5830     TCGA-EI-6506     TCGA-EI-6507     TCGA-EI-6508 
"NIT2 WILD-TYPE" "NIT2 WILD-TYPE" "NIT2 WILD-TYPE" "NIT2 WILD-TYPE" 
    TCGA-EI-6510     TCGA-F5-6464     TCGA-F5-6465     TCGA-F5-6571 
"NIT2 WILD-TYPE" "NIT2 WILD-TYPE" "NIT2 WILD-TYPE" "NIT2 WILD-TYPE" 
    TCGA-F5-6702     TCGA-F5-6811     TCGA-F5-6812     TCGA-F5-6813 
"NIT2 WILD-TYPE" "NIT2 WILD-TYPE" "NIT2 WILD-TYPE" "NIT2 WILD-TYPE" 
    TCGA-G5-6235     TCGA-G5-6641 
"NIT2 WILD-TYPE" "NIT2 WILD-TYPE" 

Clustering(2038) Variable = KIAA2018 MUTATION ANALYSIS
D2038V1, survival
                    sevent
clus2                  0   1
  KIAA2018 MUTATED    17   4
  KIAA2018 WILD-TYPE 361  89
  KIAA2018 MUTATED KIAA2018 WILD-TYPE 
                21                450 
  KIAA2018 MUTATED KIAA2018 WILD-TYPE 
                 4                 89 
$`KIAA2018 MUTATED`
TCGA-A6-5665 TCGA-AA-3510 TCGA-AA-3663 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3815 
       22.06        63.98         6.97         5.98        37.05        33.04 
TCGA-AA-3864 TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A010 TCGA-AZ-4315 TCGA-AZ-6601 
       53.00        25.02         4.01        34.98        58.39       100.01 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CM-5861 TCGA-CM-6171 TCGA-D5-6928 
       12.76        10.06        14.30        15.02        14.04        11.64 
TCGA-D5-6930 TCGA-F4-6570 TCGA-AG-A002 
        1.51         6.18        20.98 

$`KIAA2018 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       11.01        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
       19.04        19.04        10.06        35.05         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 
       88.21        49.41         6.77        12.10        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        3.29         0.07        12.20        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       13.02        15.02        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 
       14.30         9.04         9.44         4.80        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       35.74        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  KIAA2018 MUTATED KIAA2018 WILD-TYPE 
              1.51               0.00 
  KIAA2018 MUTATED KIAA2018 WILD-TYPE 
            100.01             148.01 
  KIAA2018 MUTATED KIAA2018 WILD-TYPE 
            15.020             20.235 
[1] "1.5 - 100.0 (15.0)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.1"
D2038V2, continuous
D2038V3, binary
                    cls
clus                   0   1
  KIAA2018 MUTATED    21   1
  KIAA2018 WILD-TYPE 345 118
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA2018 MUTATED     21    1
  KIAA2018 WILD-TYPE  345  118
        clus
vv       KIAA2018 MUTATED KIAA2018 WILD-TYPE
  COLON                21                345
  RECTUM                1                118
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KIAA2018 MUTATED         2        0        5        11         2         0
  KIAA2018 WILD-TYPE      89        1       27       127         8         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIAA2018 MUTATED           1          0          0          0        0
  KIAA2018 WILD-TYPE        23         11         59         42       48
                    vv
clus                 STAGE IVA STAGE IVB
  KIAA2018 MUTATED           0         0
  KIAA2018 WILD-TYPE        18         1
D2038V4, multiclass
            clus
vv           KIAA2018 MUTATED KIAA2018 WILD-TYPE
  STAGE I                   2                 89
  STAGE IA                  0                  1
  STAGE II                  5                 27
  STAGE IIA                11                127
  STAGE IIB                 2                  8
  STAGE IIC                 0                  1
  STAGE III                 1                 23
  STAGE IIIA                0                 11
  STAGE IIIB                0                 59
  STAGE IIIC                0                 42
  STAGE IV                  0                 48
  STAGE IVA                 0                 18
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  KIAA2018 MUTATED     0   3  17   2
  KIAA2018 WILD-TYPE  17  89 312  48
D2038V5, multiclass
    clus
vv   KIAA2018 MUTATED KIAA2018 WILD-TYPE
  T1                0                 17
  T2                3                 89
  T3               17                312
  T4                2                 48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  KIAA2018 MUTATED    21   1   0
  KIAA2018 WILD-TYPE 266 112  87
D2038V6, multiclass
    clus
vv   KIAA2018 MUTATED KIAA2018 WILD-TYPE
  N0               21                266
  N1                1                112
  N2                0                 87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2038V7, binary
                    cls
clus                   0   1
  KIAA2018 MUTATED    21   0
  KIAA2018 WILD-TYPE 354  65
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA2018 MUTATED     21    0
  KIAA2018 WILD-TYPE  354   65
   clus
vv  KIAA2018 MUTATED KIAA2018 WILD-TYPE
  0               21                354
  1                0                 65
[1] 2 2
[1] FALSE
D2038V8, binary
                    cls
clus                   0   1
  KIAA2018 MUTATED     8  14
  KIAA2018 WILD-TYPE 217 250
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA2018 MUTATED      8   14
  KIAA2018 WILD-TYPE  217  250
        clus
vv       KIAA2018 MUTATED KIAA2018 WILD-TYPE
  FEMALE                8                217
  MALE                 14                250
[1] 2 2
[1] FALSE
D2038V9, binary
                    cls
clus                   0   1
  KIAA2018 MUTATED    19   0
  KIAA2018 WILD-TYPE 331  22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA2018 MUTATED     19    0
  KIAA2018 WILD-TYPE  331   22
     clus
vv    KIAA2018 MUTATED KIAA2018 WILD-TYPE
  NO                19                331
  YES                0                 22
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  KIAA2018 MUTATED                     17                             4
  KIAA2018 WILD-TYPE                  298                            43
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  KIAA2018 MUTATED                       1                              0
  KIAA2018 WILD-TYPE                   105                             10
D2038V10, multiclass
                                clus
vv                               KIAA2018 MUTATED KIAA2018 WILD-TYPE
  COLON ADENOCARCINOMA                         17                298
  COLON MUCINOUS ADENOCARCINOMA                 4                 43
  RECTAL ADENOCARCINOMA                         1                105
  RECTAL MUCINOUS ADENOCARCINOMA                0                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  KIAA2018 MUTATED    17   0   0   3
  KIAA2018 WILD-TYPE 328   4  31  22
D2038V11, multiclass
    clus
vv   KIAA2018 MUTATED KIAA2018 WILD-TYPE
  R0               17                328
  R1                0                  4
  R2                0                 31
  RX                3                 22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2038V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KIAA2018 MUTATED                                  0     3
  KIAA2018 WILD-TYPE                                1     8
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  KIAA2018 MUTATED                           0     8
  KIAA2018 WILD-TYPE                        22   218
D2038V13, multiclass
                                  clus
vv                                 KIAA2018 MUTATED KIAA2018 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           3                  8
  BLACK OR AFRICAN AMERICAN                       0                 22
  WHITE                                           8                218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2039) Variable = DCAF12L2 MUTATION ANALYSIS
D2039V1, survival
                    sevent
clus2                  0   1
  DCAF12L2 MUTATED    14   5
  DCAF12L2 WILD-TYPE 364  88
  DCAF12L2 MUTATED DCAF12L2 WILD-TYPE 
                19                452 
  DCAF12L2 MUTATED DCAF12L2 WILD-TYPE 
                 5                 88 
$`DCAF12L2 MUTATED`
TCGA-A6-5665 TCGA-A6-6654 TCGA-AA-3660 TCGA-AA-3713 TCGA-AA-3821 TCGA-AA-3977 
       22.06        23.87        78.08        19.04         1.02        25.02 
TCGA-AA-A010 TCGA-AD-6901 TCGA-AU-6004 TCGA-CK-5916 TCGA-CM-5860 TCGA-CM-5868 
       34.98        22.42        27.09        21.14        32.02        17.03 
TCGA-CM-6171 TCGA-F4-6460 TCGA-F4-6570 TCGA-G4-6307 TCGA-AG-4007 TCGA-AG-A026 
       14.04        31.96         6.18        55.04         1.02         1.94 
TCGA-EI-6506 
       20.55 

$`DCAF12L2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 
       25.18        24.16        21.76        24.69        24.39        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       13.94        19.99        61.02         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       85.05        26.99        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
        0.99        25.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6963 
       15.52        56.55         0.79         0.72         5.79        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       10.88         0.20        14.50        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 
       15.62        49.08        51.32         9.99        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-5862 
       29.06        22.03        22.98        30.08        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        15.02        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6569 
       35.97        60.79       117.07        98.24         8.61        35.74 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       65.85        53.62        44.68        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A02G 
       12.00        70.03        64.01        10.98        49.97        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
       32.61         0.49        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  DCAF12L2 MUTATED DCAF12L2 WILD-TYPE 
              1.02               0.00 
  DCAF12L2 MUTATED DCAF12L2 WILD-TYPE 
             78.08             148.01 
  DCAF12L2 MUTATED DCAF12L2 WILD-TYPE 
            22.060             20.035 
[1] "1.0 - 78.1 (22.1)"  "0.0 - 148.0 (20.0)"
[1] "hr=" "1.5"
D2039V2, continuous
D2039V3, binary
                    cls
clus                   0   1
  DCAF12L2 MUTATED    17   3
  DCAF12L2 WILD-TYPE 349 116
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  DCAF12L2 MUTATED     17    3
  DCAF12L2 WILD-TYPE  349  116
        clus
vv       DCAF12L2 MUTATED DCAF12L2 WILD-TYPE
  COLON                17                349
  RECTUM                3                116
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DCAF12L2 MUTATED         4        0        2         4         2         0
  DCAF12L2 WILD-TYPE      87        1       30       134         8         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  DCAF12L2 MUTATED           0          0          3          0        2
  DCAF12L2 WILD-TYPE        24         11         56         42       46
                    vv
clus                 STAGE IVA STAGE IVB
  DCAF12L2 MUTATED           1         0
  DCAF12L2 WILD-TYPE        17         1
D2039V4, multiclass
            clus
vv           DCAF12L2 MUTATED DCAF12L2 WILD-TYPE
  STAGE I                   4                 87
  STAGE IA                  0                  1
  STAGE II                  2                 30
  STAGE IIA                 4                134
  STAGE IIB                 2                  8
  STAGE IIC                 0                  1
  STAGE III                 0                 24
  STAGE IIIA                0                 11
  STAGE IIIB                3                 56
  STAGE IIIC                0                 42
  STAGE IV                  2                 46
  STAGE IVA                 1                 17
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  DCAF12L2 MUTATED     1   4  10   5
  DCAF12L2 WILD-TYPE  16  88 319  45
D2039V5, multiclass
    clus
vv   DCAF12L2 MUTATED DCAF12L2 WILD-TYPE
  T1                1                 16
  T2                4                 88
  T3               10                319
  T4                5                 45
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  DCAF12L2 MUTATED    15   4   1
  DCAF12L2 WILD-TYPE 272 109  86
D2039V6, multiclass
    clus
vv   DCAF12L2 MUTATED DCAF12L2 WILD-TYPE
  N0               15                272
  N1                4                109
  N2                1                 86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2039V7, binary
                    cls
clus                   0   1
  DCAF12L2 MUTATED    14   3
  DCAF12L2 WILD-TYPE 361  62
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  DCAF12L2 MUTATED     14    3
  DCAF12L2 WILD-TYPE  361   62
   clus
vv  DCAF12L2 MUTATED DCAF12L2 WILD-TYPE
  0               14                361
  1                3                 62
[1] 2 2
[1] FALSE
D2039V8, binary
                    cls
clus                   0   1
  DCAF12L2 MUTATED    14   6
  DCAF12L2 WILD-TYPE 211 258
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  DCAF12L2 MUTATED     14    6
  DCAF12L2 WILD-TYPE  211  258
        clus
vv       DCAF12L2 MUTATED DCAF12L2 WILD-TYPE
  FEMALE               14                211
  MALE                  6                258
[1] 2 2
[1] FALSE
D2039V9, binary
                    cls
clus                   0   1
  DCAF12L2 MUTATED    15   1
  DCAF12L2 WILD-TYPE 335  21
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  DCAF12L2 MUTATED     15    1
  DCAF12L2 WILD-TYPE  335   21
     clus
vv    DCAF12L2 MUTATED DCAF12L2 WILD-TYPE
  NO                15                335
  YES                1                 21
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  DCAF12L2 MUTATED                     16                             1
  DCAF12L2 WILD-TYPE                  299                            46
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  DCAF12L2 MUTATED                       3                              0
  DCAF12L2 WILD-TYPE                   103                             10
D2039V10, multiclass
                                clus
vv                               DCAF12L2 MUTATED DCAF12L2 WILD-TYPE
  COLON ADENOCARCINOMA                         16                299
  COLON MUCINOUS ADENOCARCINOMA                 1                 46
  RECTAL ADENOCARCINOMA                         3                103
  RECTAL MUCINOUS ADENOCARCINOMA                0                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  DCAF12L2 MUTATED    12   1   2   2
  DCAF12L2 WILD-TYPE 333   3  29  23
D2039V11, multiclass
    clus
vv   DCAF12L2 MUTATED DCAF12L2 WILD-TYPE
  R0               12                333
  R1                1                  3
  R2                2                 29
  RX                2                 23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2039V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DCAF12L2 MUTATED                                  0     0
  DCAF12L2 WILD-TYPE                                1    11
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  DCAF12L2 MUTATED                           0    13
  DCAF12L2 WILD-TYPE                        22   213
D2039V13, multiclass
                                  clus
vv                                 DCAF12L2 MUTATED DCAF12L2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 11
  BLACK OR AFRICAN AMERICAN                       0                 22
  WHITE                                          13                213
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2040) Variable = BMP10 MUTATION ANALYSIS
D2040V1, survival
                 sevent
clus2               0   1
  BMP10 MUTATED    11   3
  BMP10 WILD-TYPE 367  90
  BMP10 MUTATED BMP10 WILD-TYPE 
             14             457 
  BMP10 MUTATED BMP10 WILD-TYPE 
              3              90 
$`BMP10 MUTATED`
TCGA-AA-3845 TCGA-AA-3968 TCGA-AA-3977 TCGA-AD-6889 TCGA-AD-6901 TCGA-AU-3779 
        0.00        21.99        25.02        56.55        22.42        14.50 
TCGA-CA-6717 TCGA-CM-6168 TCGA-D5-6537 TCGA-DM-A1D0 TCGA-G4-6317 TCGA-G4-6628 
       12.76        12.99         4.80       130.65        36.00        79.69 
TCGA-AG-4008 TCGA-AH-6643 
       17.03         0.69 

$`BMP10 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3972 
        2.01        20.98        34.03         2.01        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 
       18.05        40.96         0.07        21.37        15.52         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-6004 
        0.72         5.79        27.42        10.88         0.20        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07        12.20        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       21.99        14.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       24.43        38.20        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  BMP10 MUTATED BMP10 WILD-TYPE 
              0               0 
  BMP10 MUTATED BMP10 WILD-TYPE 
         130.65          148.01 
  BMP10 MUTATED BMP10 WILD-TYPE 
          19.51           20.19 
[1] "0.0 - 130.7 (19.5)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1"  
D2040V2, continuous
D2040V3, binary
                 cls
clus                0   1
  BMP10 MUTATED    12   2
  BMP10 WILD-TYPE 354 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BMP10 MUTATED     12    2
  BMP10 WILD-TYPE  354  117
        clus
vv       BMP10 MUTATED BMP10 WILD-TYPE
  COLON             12             354
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  BMP10 MUTATED         2        0        0         7         0         0
  BMP10 WILD-TYPE      89        1       32       131        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  BMP10 MUTATED           0          0          1          2        0         0
  BMP10 WILD-TYPE        24         11         58         40       48        18
                 vv
clus              STAGE IVB
  BMP10 MUTATED           0
  BMP10 WILD-TYPE         1
D2040V4, multiclass
            clus
vv           BMP10 MUTATED BMP10 WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              7             131
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             2              40
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  BMP10 MUTATED     0   3  11   0
  BMP10 WILD-TYPE  17  89 318  50
D2040V5, multiclass
    clus
vv   BMP10 MUTATED BMP10 WILD-TYPE
  T1             0              17
  T2             3              89
  T3            11             318
  T4             0              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  BMP10 MUTATED    11   1   2
  BMP10 WILD-TYPE 276 112  85
D2040V6, multiclass
    clus
vv   BMP10 MUTATED BMP10 WILD-TYPE
  N0            11             276
  N1             1             112
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2040V7, binary
                 cls
clus                0   1
  BMP10 MUTATED    10   0
  BMP10 WILD-TYPE 365  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BMP10 MUTATED     10    0
  BMP10 WILD-TYPE  365   65
   clus
vv  BMP10 MUTATED BMP10 WILD-TYPE
  0            10             365
  1             0              65
[1] 2 2
[1] FALSE
D2040V8, binary
                 cls
clus                0   1
  BMP10 MUTATED     6   8
  BMP10 WILD-TYPE 219 256
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BMP10 MUTATED      6    8
  BMP10 WILD-TYPE  219  256
        clus
vv       BMP10 MUTATED BMP10 WILD-TYPE
  FEMALE             6             219
  MALE               8             256
[1] 2 2
[1] FALSE
D2040V9, binary
                 cls
clus                0   1
  BMP10 MUTATED    10   0
  BMP10 WILD-TYPE 340  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BMP10 MUTATED     10    0
  BMP10 WILD-TYPE  340   22
     clus
vv    BMP10 MUTATED BMP10 WILD-TYPE
  NO             10             340
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  BMP10 MUTATED                     11                             1
  BMP10 WILD-TYPE                  304                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  BMP10 MUTATED                       2                              0
  BMP10 WILD-TYPE                   104                             10
D2040V10, multiclass
                                clus
vv                               BMP10 MUTATED BMP10 WILD-TYPE
  COLON ADENOCARCINOMA                      11             304
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  BMP10 MUTATED     9   0   0   1
  BMP10 WILD-TYPE 336   4  31  24
D2040V11, multiclass
    clus
vv   BMP10 MUTATED BMP10 WILD-TYPE
  R0             9             336
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2040V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  BMP10 MUTATED                                  0     2
  BMP10 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  BMP10 MUTATED                           1     7
  BMP10 WILD-TYPE                        21   219
D2040V13, multiclass
                                  clus
vv                                 BMP10 MUTATED BMP10 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               9
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        7             219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2041) Variable = FOXO4 MUTATION ANALYSIS
D2041V1, survival
                 sevent
clus2               0   1
  FOXO4 MUTATED    11   2
  FOXO4 WILD-TYPE 367  91
  FOXO4 MUTATED FOXO4 WILD-TYPE 
             13             458 
  FOXO4 MUTATED FOXO4 WILD-TYPE 
              2              91 
$`FOXO4 MUTATED`
TCGA-AA-3492 TCGA-AA-3710 TCGA-AA-A01P TCGA-AA-A02W TCGA-CA-6717 TCGA-CM-5861 
        3.02        26.99        38.07        41.00        12.76        15.02 
TCGA-CM-5864 TCGA-CM-6680 TCGA-D5-6534 TCGA-F4-6806 TCGA-G4-6586 TCGA-G4-6588 
       15.02        12.03        43.27        41.42        35.80        26.17 
TCGA-AG-A002 
       20.98 

$`FOXO4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        85.05        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        31.00         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02Y TCGA-AA-A03F 
        2.01         5.03        14.01         0.92        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07        12.20        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 
       22.03        22.98        30.08        32.02         5.03        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       10.06        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       20.19        18.25         1.32        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
       47.87         1.55        34.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       36.00        22.09        13.78        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  FOXO4 MUTATED FOXO4 WILD-TYPE 
           3.02            0.00 
  FOXO4 MUTATED FOXO4 WILD-TYPE 
          43.27          148.01 
  FOXO4 MUTATED FOXO4 WILD-TYPE 
         26.170          20.085 
[1] "3.0 - 43.3 (26.2)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.2"
D2041V2, continuous
D2041V3, binary
                 cls
clus                0   1
  FOXO4 MUTATED    12   1
  FOXO4 WILD-TYPE 354 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FOXO4 MUTATED     12    1
  FOXO4 WILD-TYPE  354  118
        clus
vv       FOXO4 MUTATED FOXO4 WILD-TYPE
  COLON             12             354
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FOXO4 MUTATED         4        0        1         6         0         0
  FOXO4 WILD-TYPE      87        1       31       132        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  FOXO4 MUTATED           1          0          1          0        0         0
  FOXO4 WILD-TYPE        23         11         58         42       48        18
                 vv
clus              STAGE IVB
  FOXO4 MUTATED           0
  FOXO4 WILD-TYPE         1
D2041V4, multiclass
            clus
vv           FOXO4 MUTATED FOXO4 WILD-TYPE
  STAGE I                4              87
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              6             132
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  FOXO4 MUTATED     0   4   9   0
  FOXO4 WILD-TYPE  17  88 320  50
D2041V5, multiclass
    clus
vv   FOXO4 MUTATED FOXO4 WILD-TYPE
  T1             0              17
  T2             4              88
  T3             9             320
  T4             0              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  FOXO4 MUTATED    11   1   1
  FOXO4 WILD-TYPE 276 112  86
D2041V6, multiclass
    clus
vv   FOXO4 MUTATED FOXO4 WILD-TYPE
  N0            11             276
  N1             1             112
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2041V7, binary
                 cls
clus                0   1
  FOXO4 MUTATED    13   0
  FOXO4 WILD-TYPE 362  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FOXO4 MUTATED     13    0
  FOXO4 WILD-TYPE  362   65
   clus
vv  FOXO4 MUTATED FOXO4 WILD-TYPE
  0            13             362
  1             0              65
[1] 2 2
[1] FALSE
D2041V8, binary
                 cls
clus                0   1
  FOXO4 MUTATED    10   3
  FOXO4 WILD-TYPE 215 261
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FOXO4 MUTATED     10    3
  FOXO4 WILD-TYPE  215  261
        clus
vv       FOXO4 MUTATED FOXO4 WILD-TYPE
  FEMALE            10             215
  MALE               3             261
[1] 2 2
[1] FALSE
D2041V9, binary
                 cls
clus                0   1
  FOXO4 MUTATED    13   0
  FOXO4 WILD-TYPE 337  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FOXO4 MUTATED     13    0
  FOXO4 WILD-TYPE  337   22
     clus
vv    FOXO4 MUTATED FOXO4 WILD-TYPE
  NO             13             337
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  FOXO4 MUTATED                     10                             2
  FOXO4 WILD-TYPE                  305                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  FOXO4 MUTATED                       1                              0
  FOXO4 WILD-TYPE                   105                             10
D2041V10, multiclass
                                clus
vv                               FOXO4 MUTATED FOXO4 WILD-TYPE
  COLON ADENOCARCINOMA                      10             305
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  FOXO4 MUTATED    12   0   0   1
  FOXO4 WILD-TYPE 333   4  31  24
D2041V11, multiclass
    clus
vv   FOXO4 MUTATED FOXO4 WILD-TYPE
  R0            12             333
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2041V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FOXO4 MUTATED                                  0     1
  FOXO4 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  FOXO4 MUTATED                           0     7
  FOXO4 WILD-TYPE                        22   219
D2041V13, multiclass
                                  clus
vv                                 FOXO4 MUTATED FOXO4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        7             219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2042) Variable = SLITRK2 MUTATION ANALYSIS
D2042V1, survival
                   sevent
clus2                 0   1
  SLITRK2 MUTATED    21   4
  SLITRK2 WILD-TYPE 357  89
  SLITRK2 MUTATED SLITRK2 WILD-TYPE 
               25               446 
  SLITRK2 MUTATED SLITRK2 WILD-TYPE 
                4                89 
$`SLITRK2 MUTATED`
TCGA-A6-2678 TCGA-A6-5666 TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3555 TCGA-AA-3672 
       42.28        32.71         3.02        63.98        29.95         0.92 
TCGA-AA-3864 TCGA-AA-3947 TCGA-AA-3977 TCGA-AA-A010 TCGA-AU-6004 TCGA-AZ-6601 
       53.00        33.01        25.02        34.98        27.09       100.01 
TCGA-AZ-6608 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-5913 TCGA-CM-5348 TCGA-D5-6532 
        1.61        12.76        10.06        51.32        22.98        18.25 
TCGA-D5-6930 TCGA-F4-6808 TCGA-AG-3600 TCGA-AG-3892 TCGA-AG-A002 TCGA-EI-6507 
        1.51        33.67         6.05        13.02        20.98        19.96 
TCGA-F5-6812 
        0.66 

$`SLITRK2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2683 
       43.76        46.65        43.76        42.90        24.33        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       22.06        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 
       19.66        20.28         7.04         1.02        35.01         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       78.08         6.05         6.97        54.02         2.01        14.01 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
        2.01        12.99        24.00        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       14.50        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 
       88.21        49.41         6.77        12.10        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
       11.74         3.19        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.07        12.20        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        49.08         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       29.06        22.03        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6534 
       19.59        56.09        55.92        20.19         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 
        9.04         9.44        11.64         4.80        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       16.24        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 
       19.99         1.02        17.95        36.95        17.03        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6510 
       51.48        32.61         0.49        20.55        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6813 
        9.96        49.51        31.30        28.57        32.19         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  SLITRK2 MUTATED SLITRK2 WILD-TYPE 
             0.66              0.00 
  SLITRK2 MUTATED SLITRK2 WILD-TYPE 
           100.01            148.01 
  SLITRK2 MUTATED SLITRK2 WILD-TYPE 
           22.980            20.085 
[1] "0.7 - 100.0 (23.0)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.3"
D2042V2, continuous
D2042V3, binary
                   cls
clus                  0   1
  SLITRK2 MUTATED    21   5
  SLITRK2 WILD-TYPE 345 114
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLITRK2 MUTATED     21    5
  SLITRK2 WILD-TYPE  345  114
        clus
vv       SLITRK2 MUTATED SLITRK2 WILD-TYPE
  COLON               21               345
  RECTUM               5               114
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SLITRK2 MUTATED         5        0        4         8         2         1
  SLITRK2 WILD-TYPE      86        1       28       130         8         0
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLITRK2 MUTATED           1          1          2          1        0
  SLITRK2 WILD-TYPE        23         10         57         41       48
                   vv
clus                STAGE IVA STAGE IVB
  SLITRK2 MUTATED           0         0
  SLITRK2 WILD-TYPE        18         1
D2042V4, multiclass
            clus
vv           SLITRK2 MUTATED SLITRK2 WILD-TYPE
  STAGE I                  5                86
  STAGE IA                 0                 1
  STAGE II                 4                28
  STAGE IIA                8               130
  STAGE IIB                2                 8
  STAGE IIC                1                 0
  STAGE III                1                23
  STAGE IIIA               1                10
  STAGE IIIB               2                57
  STAGE IIIC               1                41
  STAGE IV                 0                48
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  SLITRK2 MUTATED     2   5  16   3
  SLITRK2 WILD-TYPE  15  87 313  47
D2042V5, multiclass
    clus
vv   SLITRK2 MUTATED SLITRK2 WILD-TYPE
  T1               2                15
  T2               5                87
  T3              16               313
  T4               3                47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  SLITRK2 MUTATED    21   4   1
  SLITRK2 WILD-TYPE 266 109  86
D2042V6, multiclass
    clus
vv   SLITRK2 MUTATED SLITRK2 WILD-TYPE
  N0              21               266
  N1               4               109
  N2               1                86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2042V7, binary
                   cls
clus                  0   1
  SLITRK2 MUTATED    23   0
  SLITRK2 WILD-TYPE 352  65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLITRK2 MUTATED     23    0
  SLITRK2 WILD-TYPE  352   65
   clus
vv  SLITRK2 MUTATED SLITRK2 WILD-TYPE
  0              23               352
  1               0                65
[1] 2 2
[1] FALSE
D2042V8, binary
                   cls
clus                  0   1
  SLITRK2 MUTATED    11  15
  SLITRK2 WILD-TYPE 214 249
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLITRK2 MUTATED     11   15
  SLITRK2 WILD-TYPE  214  249
        clus
vv       SLITRK2 MUTATED SLITRK2 WILD-TYPE
  FEMALE              11               214
  MALE                15               249
[1] 2 2
[1] FALSE
D2042V9, binary
                   cls
clus                  0   1
  SLITRK2 MUTATED    21   1
  SLITRK2 WILD-TYPE 329  21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLITRK2 MUTATED     21    1
  SLITRK2 WILD-TYPE  329   21
     clus
vv    SLITRK2 MUTATED SLITRK2 WILD-TYPE
  NO               21               329
  YES               1                21
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SLITRK2 MUTATED                     17                             4
  SLITRK2 WILD-TYPE                  298                            43
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SLITRK2 MUTATED                       5                              0
  SLITRK2 WILD-TYPE                   101                             10
D2042V10, multiclass
                                clus
vv                               SLITRK2 MUTATED SLITRK2 WILD-TYPE
  COLON ADENOCARCINOMA                        17               298
  COLON MUCINOUS ADENOCARCINOMA                4                43
  RECTAL ADENOCARCINOMA                        5               101
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  SLITRK2 MUTATED    18   0   0   4
  SLITRK2 WILD-TYPE 327   4  31  21
D2042V11, multiclass
    clus
vv   SLITRK2 MUTATED SLITRK2 WILD-TYPE
  R0              18               327
  R1               0                 4
  R2               0                31
  RX               4                21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2042V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SLITRK2 MUTATED                                  0     2
  SLITRK2 WILD-TYPE                                1     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  SLITRK2 MUTATED                           0    13
  SLITRK2 WILD-TYPE                        22   213
D2042V13, multiclass
                                  clus
vv                                 SLITRK2 MUTATED SLITRK2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          2                 9
  BLACK OR AFRICAN AMERICAN                      0                22
  WHITE                                         13               213
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2043) Variable = MTF2 MUTATION ANALYSIS
D2043V1, survival
                sevent
clus2              0   1
  MTF2 MUTATED     6   3
  MTF2 WILD-TYPE 372  90
  MTF2 MUTATED MTF2 WILD-TYPE 
             9            462 
  MTF2 MUTATED MTF2 WILD-TYPE 
             3             90 
$`MTF2 MUTATED`
TCGA-AA-3510 TCGA-AA-A00N TCGA-AA-A010 TCGA-AD-6889 TCGA-AZ-4315 TCGA-CA-6718 
       63.98         4.01        34.98        56.55        58.39        10.06 
TCGA-CK-6751 TCGA-DM-A28G TCGA-AG-A002 
      124.27        60.79        20.98 

$`MTF2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 
       18.05        40.96         0.07        21.37        15.52         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 
        3.25         3.29         0.07        12.20        12.76        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CM-4743 TCGA-CM-4744 
        9.99        21.14        82.95         1.91        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       35.97       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  MTF2 MUTATED MTF2 WILD-TYPE 
          4.01           0.00 
  MTF2 MUTATED MTF2 WILD-TYPE 
        124.27         148.01 
  MTF2 MUTATED MTF2 WILD-TYPE 
        56.550         20.035 
[1] "4.0 - 124.3 (56.5)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.1"
D2043V2, continuous
D2043V3, binary
                cls
clus               0   1
  MTF2 MUTATED     8   1
  MTF2 WILD-TYPE 358 118
[1] "tbl2"
                cls
clus             [,1] [,2]
  MTF2 MUTATED      8    1
  MTF2 WILD-TYPE  358  118
        clus
vv       MTF2 MUTATED MTF2 WILD-TYPE
  COLON             8            358
  RECTUM            1            118
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MTF2 MUTATED         2        0        1         4         2         0
  MTF2 WILD-TYPE      89        1       31       134         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MTF2 MUTATED           0          0          0          0        0         0
  MTF2 WILD-TYPE        24         11         59         42       48        18
                vv
clus             STAGE IVB
  MTF2 MUTATED           0
  MTF2 WILD-TYPE         1
D2043V4, multiclass
            clus
vv           MTF2 MUTATED MTF2 WILD-TYPE
  STAGE I               2             89
  STAGE IA              0              1
  STAGE II              1             31
  STAGE IIA             4            134
  STAGE IIB             2              8
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            0             59
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  MTF2 MUTATED     0   2   5   2
  MTF2 WILD-TYPE  17  90 324  48
D2043V5, multiclass
    clus
vv   MTF2 MUTATED MTF2 WILD-TYPE
  T1            0             17
  T2            2             90
  T3            5            324
  T4            2             48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  MTF2 MUTATED     9   0   0
  MTF2 WILD-TYPE 278 113  87
D2043V6, multiclass
    clus
vv   MTF2 MUTATED MTF2 WILD-TYPE
  N0            9            278
  N1            0            113
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2043V7, binary
                cls
clus               0   1
  MTF2 MUTATED     8   0
  MTF2 WILD-TYPE 367  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  MTF2 MUTATED      8    0
  MTF2 WILD-TYPE  367   65
   clus
vv  MTF2 MUTATED MTF2 WILD-TYPE
  0            8            367
  1            0             65
[1] 2 2
[1] FALSE
D2043V8, binary
                cls
clus               0   1
  MTF2 MUTATED     2   7
  MTF2 WILD-TYPE 223 257
[1] "tbl2"
                cls
clus             [,1] [,2]
  MTF2 MUTATED      2    7
  MTF2 WILD-TYPE  223  257
        clus
vv       MTF2 MUTATED MTF2 WILD-TYPE
  FEMALE            2            223
  MALE              7            257
[1] 2 2
[1] FALSE
D2043V9, binary
                cls
clus               0   1
  MTF2 MUTATED     6   0
  MTF2 WILD-TYPE 344  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  MTF2 MUTATED      6    0
  MTF2 WILD-TYPE  344   22
     clus
vv    MTF2 MUTATED MTF2 WILD-TYPE
  NO             6            344
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MTF2 MUTATED                      6                             2
  MTF2 WILD-TYPE                  309                            45
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MTF2 MUTATED                       1                              0
  MTF2 WILD-TYPE                   105                             10
D2043V10, multiclass
                                clus
vv                               MTF2 MUTATED MTF2 WILD-TYPE
  COLON ADENOCARCINOMA                      6            309
  COLON MUCINOUS ADENOCARCINOMA             2             45
  RECTAL ADENOCARCINOMA                     1            105
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  MTF2 MUTATED     5   0   0   2
  MTF2 WILD-TYPE 340   4  31  23
D2043V11, multiclass
    clus
vv   MTF2 MUTATED MTF2 WILD-TYPE
  R0            5            340
  R1            0              4
  R2            0             31
  RX            2             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2043V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MTF2 MUTATED                                  0     2
  MTF2 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  MTF2 MUTATED                           0     3
  MTF2 WILD-TYPE                        22   223
D2043V13, multiclass
                                  clus
vv                                 MTF2 MUTATED MTF2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              9
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       3            223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2044) Variable = UBA7 MUTATION ANALYSIS
D2044V1, survival
                sevent
clus2              0   1
  UBA7 MUTATED    10   2
  UBA7 WILD-TYPE 368  91
  UBA7 MUTATED UBA7 WILD-TYPE 
            12            459 
  UBA7 MUTATED UBA7 WILD-TYPE 
             2             91 
$`UBA7 MUTATED`
TCGA-AA-3510 TCGA-AA-3663 TCGA-AA-A00E TCGA-AA-A010 TCGA-AA-A01Q TCGA-AA-A02W 
       63.98         6.97        30.02        34.98         1.02        41.00 
TCGA-AD-6895 TCGA-AZ-6598 TCGA-DM-A0XF TCGA-G4-6304 TCGA-AG-3742 TCGA-G5-6235 
        0.72        49.41        38.20        53.62         0.99        55.76 

$`UBA7 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       19.00        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
       38.07        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
       14.01         0.92        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       21.37        15.52        56.55         0.79         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 
        5.13       106.75        22.36        62.79        88.21         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
      119.70        24.43       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       65.85        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       37.02        32.98         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6641 
        0.66         0.69        26.43 

  UBA7 MUTATED UBA7 WILD-TYPE 
          0.72           0.00 
  UBA7 MUTATED UBA7 WILD-TYPE 
         63.98         148.01 
  UBA7 MUTATED UBA7 WILD-TYPE 
         36.59          20.05 
[1] "0.7 - 64.0 (36.6)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.5"
D2044V2, continuous
D2044V3, binary
                cls
clus               0   1
  UBA7 MUTATED    10   2
  UBA7 WILD-TYPE 356 117
[1] "tbl2"
                cls
clus             [,1] [,2]
  UBA7 MUTATED     10    2
  UBA7 WILD-TYPE  356  117
        clus
vv       UBA7 MUTATED UBA7 WILD-TYPE
  COLON            10            356
  RECTUM            2            117
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  UBA7 MUTATED         2        0        4         1         2         0
  UBA7 WILD-TYPE      89        1       28       137         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  UBA7 MUTATED           0          0          1          1        0         0
  UBA7 WILD-TYPE        24         11         58         41       48        18
                vv
clus             STAGE IVB
  UBA7 MUTATED           0
  UBA7 WILD-TYPE         1
D2044V4, multiclass
            clus
vv           UBA7 MUTATED UBA7 WILD-TYPE
  STAGE I               2             89
  STAGE IA              0              1
  STAGE II              4             28
  STAGE IIA             1            137
  STAGE IIB             2              8
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            1             58
  STAGE IIIC            1             41
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  UBA7 MUTATED     1   1   8   2
  UBA7 WILD-TYPE  16  91 321  48
D2044V5, multiclass
    clus
vv   UBA7 MUTATED UBA7 WILD-TYPE
  T1            1             16
  T2            1             91
  T3            8            321
  T4            2             48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  UBA7 MUTATED     9   2   1
  UBA7 WILD-TYPE 278 111  86
D2044V6, multiclass
    clus
vv   UBA7 MUTATED UBA7 WILD-TYPE
  N0            9            278
  N1            2            111
  N2            1             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2044V7, binary
                cls
clus               0   1
  UBA7 MUTATED     9   0
  UBA7 WILD-TYPE 366  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  UBA7 MUTATED      9    0
  UBA7 WILD-TYPE  366   65
   clus
vv  UBA7 MUTATED UBA7 WILD-TYPE
  0            9            366
  1            0             65
[1] 2 2
[1] FALSE
D2044V8, binary
                cls
clus               0   1
  UBA7 MUTATED     7   5
  UBA7 WILD-TYPE 218 259
[1] "tbl2"
                cls
clus             [,1] [,2]
  UBA7 MUTATED      7    5
  UBA7 WILD-TYPE  218  259
        clus
vv       UBA7 MUTATED UBA7 WILD-TYPE
  FEMALE            7            218
  MALE              5            259
[1] 2 2
[1] FALSE
D2044V9, binary
                cls
clus               0   1
  UBA7 MUTATED     8   0
  UBA7 WILD-TYPE 342  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  UBA7 MUTATED      8    0
  UBA7 WILD-TYPE  342   22
     clus
vv    UBA7 MUTATED UBA7 WILD-TYPE
  NO             8            342
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  UBA7 MUTATED                      9                             0
  UBA7 WILD-TYPE                  306                            47
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  UBA7 MUTATED                       2                              0
  UBA7 WILD-TYPE                   104                             10
D2044V10, multiclass
                                clus
vv                               UBA7 MUTATED UBA7 WILD-TYPE
  COLON ADENOCARCINOMA                      9            306
  COLON MUCINOUS ADENOCARCINOMA             0             47
  RECTAL ADENOCARCINOMA                     2            104
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  UBA7 MUTATED     8   1   0   0
  UBA7 WILD-TYPE 337   3  31  25
D2044V11, multiclass
    clus
vv   UBA7 MUTATED UBA7 WILD-TYPE
  R0            8            337
  R1            1              3
  R2            0             31
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2044V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  UBA7 MUTATED                                  0     0
  UBA7 WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  UBA7 MUTATED                           0     5
  UBA7 WILD-TYPE                        22   221
D2044V13, multiclass
                                  clus
vv                                 UBA7 MUTATED UBA7 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       5            221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2045) Variable = MICAL1 MUTATION ANALYSIS
D2045V1, survival
                  sevent
clus2                0   1
  MICAL1 MUTATED     8   0
  MICAL1 WILD-TYPE 370  93
  MICAL1 MUTATED MICAL1 WILD-TYPE 
               8              463 
  MICAL1 MUTATED MICAL1 WILD-TYPE 
               0               93 
$`MICAL1 MUTATED`
TCGA-A6-6141 TCGA-A6-6653 TCGA-AA-3663 TCGA-AA-3821 TCGA-AD-6889 TCGA-AU-6004 
        8.38        24.39         6.97         1.02        56.55        27.09 
TCGA-CM-6162 TCGA-D5-6927 
       12.00         9.44 

$`MICAL1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 
       22.09        22.06        32.71        27.09        22.52        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 
       25.18        24.16        21.76        24.69        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
       33.04         0.99        25.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 
       40.96         0.07        21.37        15.52         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       15.02        17.03        15.02         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  MICAL1 MUTATED MICAL1 WILD-TYPE 
            1.02             0.00 
  MICAL1 MUTATED MICAL1 WILD-TYPE 
           56.55           148.01 
  MICAL1 MUTATED MICAL1 WILD-TYPE 
           10.72            20.28 
[1] "1.0 - 56.5 (10.7)"  "0.0 - 148.0 (20.3)"
[1] "hr="     "9100000"
D2045V2, continuous
D2045V3, binary
                  cls
clus                 0   1
  MICAL1 MUTATED     9   0
  MICAL1 WILD-TYPE 357 119
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MICAL1 MUTATED      9    0
  MICAL1 WILD-TYPE  357  119
        clus
vv       MICAL1 MUTATED MICAL1 WILD-TYPE
  COLON               9              357
  RECTUM              0              119
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MICAL1 MUTATED         3        0        2         3         0         0
  MICAL1 WILD-TYPE      88        1       30       135        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MICAL1 MUTATED           0          0          1          0        0
  MICAL1 WILD-TYPE        24         11         58         42       48
                  vv
clus               STAGE IVA STAGE IVB
  MICAL1 MUTATED           0         0
  MICAL1 WILD-TYPE        18         1
D2045V4, multiclass
            clus
vv           MICAL1 MUTATED MICAL1 WILD-TYPE
  STAGE I                 3               88
  STAGE IA                0                1
  STAGE II                2               30
  STAGE IIA               3              135
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              1               58
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  MICAL1 MUTATED     0   3   5   1
  MICAL1 WILD-TYPE  17  89 324  49
D2045V5, multiclass
    clus
vv   MICAL1 MUTATED MICAL1 WILD-TYPE
  T1              0               17
  T2              3               89
  T3              5              324
  T4              1               49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  MICAL1 MUTATED     8   1   0
  MICAL1 WILD-TYPE 279 112  87
D2045V6, multiclass
    clus
vv   MICAL1 MUTATED MICAL1 WILD-TYPE
  N0              8              279
  N1              1              112
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2045V7, binary
                  cls
clus                 0   1
  MICAL1 MUTATED     9   0
  MICAL1 WILD-TYPE 366  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MICAL1 MUTATED      9    0
  MICAL1 WILD-TYPE  366   65
   clus
vv  MICAL1 MUTATED MICAL1 WILD-TYPE
  0              9              366
  1              0               65
[1] 2 2
[1] FALSE
D2045V8, binary
                  cls
clus                 0   1
  MICAL1 MUTATED     4   5
  MICAL1 WILD-TYPE 221 259
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MICAL1 MUTATED      4    5
  MICAL1 WILD-TYPE  221  259
        clus
vv       MICAL1 MUTATED MICAL1 WILD-TYPE
  FEMALE              4              221
  MALE                5              259
[1] 2 2
[1] FALSE
D2045V9, binary
                  cls
clus                 0   1
  MICAL1 MUTATED     6   0
  MICAL1 WILD-TYPE 344  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MICAL1 MUTATED      6    0
  MICAL1 WILD-TYPE  344   22
     clus
vv    MICAL1 MUTATED MICAL1 WILD-TYPE
  NO               6              344
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MICAL1 MUTATED                      7                             2
  MICAL1 WILD-TYPE                  308                            45
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MICAL1 MUTATED                       0                              0
  MICAL1 WILD-TYPE                   106                             10
D2045V10, multiclass
                                clus
vv                               MICAL1 MUTATED MICAL1 WILD-TYPE
  COLON ADENOCARCINOMA                        7              308
  COLON MUCINOUS ADENOCARCINOMA               2               45
  RECTAL ADENOCARCINOMA                       0              106
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  MICAL1 MUTATED     6   0   0   0
  MICAL1 WILD-TYPE 339   4  31  25
D2045V11, multiclass
    clus
vv   MICAL1 MUTATED MICAL1 WILD-TYPE
  R0              6              339
  R1              0                4
  R2              0               31
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2045V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MICAL1 MUTATED                                  0     1
  MICAL1 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  MICAL1 MUTATED                           1     4
  MICAL1 WILD-TYPE                        21   222
D2045V13, multiclass
                                  clus
vv                                 MICAL1 MUTATED MICAL1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                         4              222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2046) Variable = TSPYL4 MUTATION ANALYSIS
D2046V1, survival
                  sevent
clus2                0   1
  TSPYL4 MUTATED     2   1
  TSPYL4 WILD-TYPE 376  92
  TSPYL4 MUTATED TSPYL4 WILD-TYPE 
               3              468 
  TSPYL4 MUTATED TSPYL4 WILD-TYPE 
               1               92 
$`TSPYL4 MUTATED`
TCGA-AA-3672 TCGA-AA-A00N TCGA-CM-6674 
        0.92         4.01        12.95 

$`TSPYL4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
        6.05         6.97        54.02         2.01        14.01        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  TSPYL4 MUTATED TSPYL4 WILD-TYPE 
            0.92             0.00 
  TSPYL4 MUTATED TSPYL4 WILD-TYPE 
           12.95           148.01 
  TSPYL4 MUTATED TSPYL4 WILD-TYPE 
           4.010           20.415 
[1] "0.9 - 12.9 (4.0)"   "0.0 - 148.0 (20.4)"
[1] "hr=" "6.6"
D2046V2, continuous
D2046V3, binary
                  cls
clus                 0   1
  TSPYL4 MUTATED     4   0
  TSPYL4 WILD-TYPE 362 119
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TSPYL4 MUTATED      4    0
  TSPYL4 WILD-TYPE  362  119
        clus
vv       TSPYL4 MUTATED TSPYL4 WILD-TYPE
  COLON               4              362
  RECTUM              0              119
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TSPYL4 MUTATED         0        0        0         2         1         0
  TSPYL4 WILD-TYPE      91        1       32       136         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TSPYL4 MUTATED           1          0          0          0        0
  TSPYL4 WILD-TYPE        23         11         59         42       48
                  vv
clus               STAGE IVA STAGE IVB
  TSPYL4 MUTATED           0         0
  TSPYL4 WILD-TYPE        18         1
D2046V4, multiclass
            clus
vv           TSPYL4 MUTATED TSPYL4 WILD-TYPE
  STAGE I                 0               91
  STAGE IA                0                1
  STAGE II                0               32
  STAGE IIA               2              136
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               1               23
  STAGE IIIA              0               11
  STAGE IIIB              0               59
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  TSPYL4 MUTATED     0   0   3   1
  TSPYL4 WILD-TYPE  17  92 326  49
D2046V5, multiclass
    clus
vv   TSPYL4 MUTATED TSPYL4 WILD-TYPE
  T1              0               17
  T2              0               92
  T3              3              326
  T4              1               49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  TSPYL4 MUTATED     3   1   0
  TSPYL4 WILD-TYPE 284 112  87
D2046V6, multiclass
    clus
vv   TSPYL4 MUTATED TSPYL4 WILD-TYPE
  N0              3              284
  N1              1              112
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2046V7, binary
                  cls
clus                 0   1
  TSPYL4 MUTATED     4   0
  TSPYL4 WILD-TYPE 371  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TSPYL4 MUTATED      4    0
  TSPYL4 WILD-TYPE  371   65
   clus
vv  TSPYL4 MUTATED TSPYL4 WILD-TYPE
  0              4              371
  1              0               65
[1] 2 2
[1] FALSE
D2046V8, binary
                  cls
clus                 0   1
  TSPYL4 MUTATED     2   2
  TSPYL4 WILD-TYPE 223 262
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TSPYL4 MUTATED      2    2
  TSPYL4 WILD-TYPE  223  262
        clus
vv       TSPYL4 MUTATED TSPYL4 WILD-TYPE
  FEMALE              2              223
  MALE                2              262
[1] 2 2
[1] FALSE
D2046V9, binary
                  cls
clus                 0   1
  TSPYL4 MUTATED     2   0
  TSPYL4 WILD-TYPE 348  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TSPYL4 MUTATED      2    0
  TSPYL4 WILD-TYPE  348   22
     clus
vv    TSPYL4 MUTATED TSPYL4 WILD-TYPE
  NO               2              348
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  TSPYL4 MUTATED                      3                             1
  TSPYL4 WILD-TYPE                  312                            46
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  TSPYL4 MUTATED                       0                              0
  TSPYL4 WILD-TYPE                   106                             10
D2046V10, multiclass
                                clus
vv                               TSPYL4 MUTATED TSPYL4 WILD-TYPE
  COLON ADENOCARCINOMA                        3              312
  COLON MUCINOUS ADENOCARCINOMA               1               46
  RECTAL ADENOCARCINOMA                       0              106
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  TSPYL4 MUTATED     4   0   0   0
  TSPYL4 WILD-TYPE 341   4  31  25
D2046V11, multiclass
    clus
vv   TSPYL4 MUTATED TSPYL4 WILD-TYPE
  R0              4              341
  R1              0                4
  R2              0               31
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2046V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TSPYL4 MUTATED                                  0     0
  TSPYL4 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  TSPYL4 MUTATED                           0     1
  TSPYL4 WILD-TYPE                        22   225
D2046V13, multiclass
[1] "Remove cluster labels:" "TSPYL4 MUTATED"        
clus
  TSPYL4 MUTATED TSPYL4 WILD-TYPE 
               1              259 
      TCGA-A6-2671       TCGA-A6-2672       TCGA-A6-2674       TCGA-A6-2676 
"TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" 
      TCGA-A6-2677       TCGA-A6-2678       TCGA-A6-2683       TCGA-A6-3807 
"TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" 
      TCGA-A6-3808       TCGA-A6-3809       TCGA-A6-3810       TCGA-A6-4105 
"TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" 
      TCGA-A6-5656       TCGA-A6-5657       TCGA-A6-5659       TCGA-A6-5660 
"TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" 
      TCGA-A6-5661       TCGA-A6-5662       TCGA-A6-5664       TCGA-A6-5665 
"TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" 
      TCGA-A6-5666       TCGA-A6-6137       TCGA-A6-6138       TCGA-A6-6141 
"TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" 
      TCGA-A6-6142       TCGA-A6-6648       TCGA-A6-6649       TCGA-A6-6651 
"TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" 
      TCGA-A6-6652       TCGA-A6-6653       TCGA-A6-6654       TCGA-A6-6780 
"TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" 
      TCGA-A6-6781       TCGA-A6-6782       TCGA-AD-5900       TCGA-AD-6548 
"TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" 
      TCGA-AD-6888       TCGA-AD-6889       TCGA-AD-6890       TCGA-AD-6895 
"TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" 
      TCGA-AD-6899       TCGA-AD-6901       TCGA-AD-6963       TCGA-AD-6964 
"TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" 
      TCGA-AD-6965       TCGA-AU-3779       TCGA-AU-6004       TCGA-AY-4070 
"TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" 
      TCGA-AY-4071       TCGA-AY-5543       TCGA-AY-6196       TCGA-AY-6197 
"TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" 
      TCGA-AY-6386       TCGA-AZ-4315       TCGA-AZ-4323       TCGA-AZ-4616 
"TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" 
      TCGA-AZ-4681       TCGA-AZ-4682       TCGA-AZ-5403       TCGA-AZ-5407 
"TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" 
      TCGA-AZ-6598       TCGA-AZ-6599       TCGA-AZ-6600       TCGA-AZ-6601 
"TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" 
      TCGA-AZ-6603       TCGA-AZ-6605       TCGA-AZ-6606       TCGA-AZ-6607 
"TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" 
      TCGA-AZ-6608       TCGA-CA-5254       TCGA-CA-5255       TCGA-CA-5796 
"TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" 
      TCGA-CA-5797       TCGA-CA-6715       TCGA-CA-6716       TCGA-CA-6717 
"TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" 
      TCGA-CA-6718       TCGA-CA-6719       TCGA-CK-4947       TCGA-CK-4948 
"TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" 
      TCGA-CK-4950       TCGA-CK-4952       TCGA-CK-5912       TCGA-CK-5913 
"TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" 
      TCGA-CK-5914       TCGA-CK-5915       TCGA-CK-5916       TCGA-CK-6746 
"TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" 
      TCGA-CK-6747       TCGA-CK-6748       TCGA-CK-6751       TCGA-CM-4743 
"TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" 
      TCGA-CM-4744       TCGA-CM-4746       TCGA-CM-4747       TCGA-CM-4752 
"TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" 
      TCGA-CM-5341       TCGA-CM-5344       TCGA-CM-5348       TCGA-CM-5349 
"TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" 
      TCGA-CM-5860       TCGA-CM-5861       TCGA-CM-5862       TCGA-CM-5863 
"TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" 
      TCGA-CM-5864       TCGA-CM-5868       TCGA-CM-6161       TCGA-CM-6162 
"TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" 
      TCGA-CM-6163       TCGA-CM-6164       TCGA-CM-6165       TCGA-CM-6166 
"TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" 
      TCGA-CM-6167       TCGA-CM-6168       TCGA-CM-6169       TCGA-CM-6170 
"TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" 
      TCGA-CM-6171       TCGA-CM-6172       TCGA-CM-6675       TCGA-CM-6676 
"TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" 
      TCGA-CM-6677       TCGA-CM-6678       TCGA-CM-6679       TCGA-CM-6680 
"TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" 
      TCGA-D5-5537       TCGA-D5-5538       TCGA-D5-5539       TCGA-D5-5540 
"TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" 
      TCGA-D5-5541       TCGA-D5-6529       TCGA-D5-6532       TCGA-D5-6533 
"TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" 
      TCGA-D5-6534       TCGA-D5-6535       TCGA-D5-6536       TCGA-D5-6537 
"TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" 
      TCGA-D5-6538       TCGA-D5-6539       TCGA-D5-6540       TCGA-D5-6541 
"TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" 
      TCGA-D5-6898       TCGA-D5-6920       TCGA-D5-6922       TCGA-D5-6923 
"TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" 
      TCGA-D5-6924       TCGA-D5-6926       TCGA-D5-6927       TCGA-D5-6928 
"TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" 
      TCGA-D5-6929       TCGA-D5-6930       TCGA-D5-6931       TCGA-D5-6932 
"TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" 
      TCGA-D5-7000       TCGA-DM-A0X9       TCGA-DM-A0XD       TCGA-DM-A0XF 
"TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" 
      TCGA-DM-A1D0       TCGA-DM-A1D4       TCGA-DM-A1D6       TCGA-DM-A1D7 
"TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" 
      TCGA-DM-A1D8       TCGA-DM-A1D9       TCGA-DM-A1DA       TCGA-DM-A1DB 
"TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" 
      TCGA-DM-A1HA       TCGA-DM-A1HB       TCGA-DM-A282       TCGA-DM-A285 
"TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" 
      TCGA-DM-A28C       TCGA-DM-A28E       TCGA-DM-A28F       TCGA-DM-A28G 
"TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" 
      TCGA-DM-A28H       TCGA-DM-A28K       TCGA-F4-6459       TCGA-F4-6460 
"TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" 
      TCGA-F4-6569       TCGA-F4-6570       TCGA-F4-6703       TCGA-F4-6704 
"TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" 
      TCGA-F4-6805       TCGA-F4-6806       TCGA-F4-6807       TCGA-F4-6808 
"TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" 
      TCGA-F4-6809       TCGA-F4-6854       TCGA-F4-6855       TCGA-F4-6856 
"TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" 
      TCGA-G4-6293       TCGA-G4-6299       TCGA-G4-6303       TCGA-G4-6304 
"TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" 
      TCGA-G4-6306       TCGA-G4-6307       TCGA-G4-6309       TCGA-G4-6310 
"TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" 
      TCGA-G4-6315       TCGA-G4-6317       TCGA-G4-6321       TCGA-G4-6323 
"TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" 
      TCGA-G4-6586       TCGA-G4-6588       TCGA-G4-6625       TCGA-G4-6626 
"TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" 
      TCGA-G4-6628       TCGA-AF-2687       TCGA-AF-2689       TCGA-AF-2691 
"TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" 
      TCGA-AF-2692       TCGA-AF-2693       TCGA-AF-3400       TCGA-AF-3913 
"TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" 
      TCGA-AF-4110       TCGA-AF-5654       TCGA-AF-6136       TCGA-AF-6655 
"TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" 
      TCGA-AF-6672       TCGA-AH-6544       TCGA-AH-6547       TCGA-AH-6549 
"TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" 
      TCGA-AH-6643       TCGA-AH-6644       TCGA-CI-6619       TCGA-CI-6620 
"TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" 
      TCGA-CI-6621       TCGA-CI-6622       TCGA-CI-6624       TCGA-CL-5917 
"TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" 
      TCGA-CL-5918       TCGA-DC-5337       TCGA-DC-5869       TCGA-DC-6155 
"TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" 
      TCGA-DC-6157       TCGA-DC-6158       TCGA-DC-6160       TCGA-DC-6681 
"TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" 
      TCGA-DC-6682       TCGA-DC-6683       TCGA-DT-5265       TCGA-DY-A0XA 
"TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" 
      TCGA-DY-A1DC       TCGA-DY-A1DD       TCGA-DY-A1DF       TCGA-DY-A1DG 
"TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" 
      TCGA-DY-A1H8       TCGA-EF-5830       TCGA-EI-6506       TCGA-EI-6507 
"TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" 
      TCGA-EI-6508       TCGA-EI-6510       TCGA-F5-6464       TCGA-F5-6465 
"TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" 
      TCGA-F5-6571       TCGA-F5-6702       TCGA-F5-6811       TCGA-F5-6812 
"TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" 
      TCGA-F5-6813       TCGA-G5-6235       TCGA-G5-6641 
"TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" "TSPYL4 WILD-TYPE" 

Clustering(2047) Variable = ZNF41 MUTATION ANALYSIS
D2047V1, survival
                 sevent
clus2               0   1
  ZNF41 MUTATED    10   1
  ZNF41 WILD-TYPE 368  92
  ZNF41 MUTATED ZNF41 WILD-TYPE 
             11             460 
  ZNF41 MUTATED ZNF41 WILD-TYPE 
              1              92 
$`ZNF41 MUTATED`
TCGA-AA-3549 TCGA-AA-3939 TCGA-AA-A010 TCGA-AZ-6598 TCGA-CK-4947 TCGA-CK-6747 
       21.01        12.99        34.98        49.41        17.56        82.95 
TCGA-CM-4752 TCGA-D5-6532 TCGA-D5-6533 TCGA-AG-A002 TCGA-F5-6812 
       13.02        18.25         1.32        20.98         0.66 

$`ZNF41 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
        2.01        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        88.21         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       10.06        14.30       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       51.32         9.99        21.14         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       20.02        37.02        25.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       55.92        20.19        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.69        55.76        26.43 

  ZNF41 MUTATED ZNF41 WILD-TYPE 
           0.66            0.00 
  ZNF41 MUTATED ZNF41 WILD-TYPE 
          82.95          148.01 
  ZNF41 MUTATED ZNF41 WILD-TYPE 
         18.250          20.235 
[1] "0.7 - 83.0 (18.2)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "2.1"
D2047V2, continuous
D2047V3, binary
                 cls
clus                0   1
  ZNF41 MUTATED     9   2
  ZNF41 WILD-TYPE 357 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZNF41 MUTATED      9    2
  ZNF41 WILD-TYPE  357  117
        clus
vv       ZNF41 MUTATED ZNF41 WILD-TYPE
  COLON              9             357
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZNF41 MUTATED         2        0        1         5         1         0
  ZNF41 WILD-TYPE      89        1       31       133         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ZNF41 MUTATED           0          0          2          0        0         0
  ZNF41 WILD-TYPE        24         11         57         42       48        18
                 vv
clus              STAGE IVB
  ZNF41 MUTATED           0
  ZNF41 WILD-TYPE         1
D2047V4, multiclass
            clus
vv           ZNF41 MUTATED ZNF41 WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              5             133
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             2              57
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ZNF41 MUTATED     0   2   6   3
  ZNF41 WILD-TYPE  17  90 323  47
D2047V5, multiclass
    clus
vv   ZNF41 MUTATED ZNF41 WILD-TYPE
  T1             0              17
  T2             2              90
  T3             6             323
  T4             3              47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  ZNF41 MUTATED    10   1   0
  ZNF41 WILD-TYPE 277 112  87
D2047V6, multiclass
    clus
vv   ZNF41 MUTATED ZNF41 WILD-TYPE
  N0            10             277
  N1             1             112
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2047V7, binary
                 cls
clus                0   1
  ZNF41 MUTATED     9   0
  ZNF41 WILD-TYPE 366  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZNF41 MUTATED      9    0
  ZNF41 WILD-TYPE  366   65
   clus
vv  ZNF41 MUTATED ZNF41 WILD-TYPE
  0             9             366
  1             0              65
[1] 2 2
[1] FALSE
D2047V8, binary
                 cls
clus                0   1
  ZNF41 MUTATED     5   6
  ZNF41 WILD-TYPE 220 258
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZNF41 MUTATED      5    6
  ZNF41 WILD-TYPE  220  258
        clus
vv       ZNF41 MUTATED ZNF41 WILD-TYPE
  FEMALE             5             220
  MALE               6             258
[1] 2 2
[1] FALSE
D2047V9, binary
                 cls
clus                0   1
  ZNF41 MUTATED     8   1
  ZNF41 WILD-TYPE 342  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZNF41 MUTATED      8    1
  ZNF41 WILD-TYPE  342   21
     clus
vv    ZNF41 MUTATED ZNF41 WILD-TYPE
  NO              8             342
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ZNF41 MUTATED                      9                             0
  ZNF41 WILD-TYPE                  306                            47
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ZNF41 MUTATED                       2                              0
  ZNF41 WILD-TYPE                   104                             10
D2047V10, multiclass
                                clus
vv                               ZNF41 MUTATED ZNF41 WILD-TYPE
  COLON ADENOCARCINOMA                       9             306
  COLON MUCINOUS ADENOCARCINOMA              0              47
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  ZNF41 MUTATED     8   0   0   2
  ZNF41 WILD-TYPE 337   4  31  23
D2047V11, multiclass
    clus
vv   ZNF41 MUTATED ZNF41 WILD-TYPE
  R0             8             337
  R1             0               4
  R2             0              31
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2047V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF41 MUTATED                                  0     0
  ZNF41 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ZNF41 MUTATED                           1     6
  ZNF41 WILD-TYPE                        21   220
D2047V13, multiclass
                                  clus
vv                                 ZNF41 MUTATED ZNF41 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        6             220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2048) Variable = SLC26A7 MUTATION ANALYSIS
D2048V1, survival
                   sevent
clus2                 0   1
  SLC26A7 MUTATED    13   5
  SLC26A7 WILD-TYPE 365  88
  SLC26A7 MUTATED SLC26A7 WILD-TYPE 
               18               453 
  SLC26A7 MUTATED SLC26A7 WILD-TYPE 
                5                88 
$`SLC26A7 MUTATED`
TCGA-A6-5665 TCGA-AA-3510 TCGA-AA-3811 TCGA-AA-3966 TCGA-AA-3979 TCGA-AA-A00J 
       22.06        63.98        10.06         2.01        24.00        18.05 
TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01G TCGA-AA-A02J TCGA-AZ-4315 TCGA-AZ-6598 
        4.01        34.98        12.00         5.03        58.39        49.41 
TCGA-CA-6717 TCGA-CA-6718 TCGA-D5-6541 TCGA-DM-A1HB TCGA-F4-6856 TCGA-F5-6812 
       12.76        10.06        15.58       135.65        35.31         0.66 

$`SLC26A7 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        19.04        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
       34.03        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        25.02        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01I 
       14.99        21.99         1.02        10.98        32.02        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        2.01        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       88.21         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        3.29         0.07        12.20        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6898 TCGA-D5-6920 
        4.80        17.13        12.49        16.14         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 
       12.59       140.38         7.50        44.32       131.51       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
        0.53        47.41       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  SLC26A7 MUTATED SLC26A7 WILD-TYPE 
             0.66              0.00 
  SLC26A7 MUTATED SLC26A7 WILD-TYPE 
           135.65            148.01 
  SLC26A7 MUTATED SLC26A7 WILD-TYPE 
           16.815            20.280 
[1] "0.7 - 135.7 (16.8)" "0.0 - 148.0 (20.3)"
[1] "hr=" "1.4"
D2048V2, continuous
D2048V3, binary
                   cls
clus                  0   1
  SLC26A7 MUTATED    17   1
  SLC26A7 WILD-TYPE 349 118
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC26A7 MUTATED     17    1
  SLC26A7 WILD-TYPE  349  118
        clus
vv       SLC26A7 MUTATED SLC26A7 WILD-TYPE
  COLON               17               349
  RECTUM               1               118
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SLC26A7 MUTATED         1        0        2         9         2         0
  SLC26A7 WILD-TYPE      90        1       30       129         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC26A7 MUTATED           1          0          2          0        1
  SLC26A7 WILD-TYPE        23         11         57         42       47
                   vv
clus                STAGE IVA STAGE IVB
  SLC26A7 MUTATED           0         0
  SLC26A7 WILD-TYPE        18         1
D2048V4, multiclass
            clus
vv           SLC26A7 MUTATED SLC26A7 WILD-TYPE
  STAGE I                  1                90
  STAGE IA                 0                 1
  STAGE II                 2                30
  STAGE IIA                9               129
  STAGE IIB                2                 8
  STAGE IIC                0                 1
  STAGE III                1                23
  STAGE IIIA               0                11
  STAGE IIIB               2                57
  STAGE IIIC               0                42
  STAGE IV                 1                47
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  SLC26A7 MUTATED     0   1  14   3
  SLC26A7 WILD-TYPE  17  91 315  47
D2048V5, multiclass
    clus
vv   SLC26A7 MUTATED SLC26A7 WILD-TYPE
  T1               0                17
  T2               1                91
  T3              14               315
  T4               3                47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  SLC26A7 MUTATED    15   2   1
  SLC26A7 WILD-TYPE 272 111  86
D2048V6, multiclass
    clus
vv   SLC26A7 MUTATED SLC26A7 WILD-TYPE
  N0              15               272
  N1               2               111
  N2               1                86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2048V7, binary
                   cls
clus                  0   1
  SLC26A7 MUTATED    16   1
  SLC26A7 WILD-TYPE 359  64
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC26A7 MUTATED     16    1
  SLC26A7 WILD-TYPE  359   64
   clus
vv  SLC26A7 MUTATED SLC26A7 WILD-TYPE
  0              16               359
  1               1                64
[1] 2 2
[1] FALSE
D2048V8, binary
                   cls
clus                  0   1
  SLC26A7 MUTATED     6  12
  SLC26A7 WILD-TYPE 219 252
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC26A7 MUTATED      6   12
  SLC26A7 WILD-TYPE  219  252
        clus
vv       SLC26A7 MUTATED SLC26A7 WILD-TYPE
  FEMALE               6               219
  MALE                12               252
[1] 2 2
[1] FALSE
D2048V9, binary
                   cls
clus                  0   1
  SLC26A7 MUTATED    13   0
  SLC26A7 WILD-TYPE 337  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC26A7 MUTATED     13    0
  SLC26A7 WILD-TYPE  337   22
     clus
vv    SLC26A7 MUTATED SLC26A7 WILD-TYPE
  NO               13               337
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SLC26A7 MUTATED                     10                             6
  SLC26A7 WILD-TYPE                  305                            41
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SLC26A7 MUTATED                       1                              0
  SLC26A7 WILD-TYPE                   105                             10
D2048V10, multiclass
                                clus
vv                               SLC26A7 MUTATED SLC26A7 WILD-TYPE
  COLON ADENOCARCINOMA                        10               305
  COLON MUCINOUS ADENOCARCINOMA                6                41
  RECTAL ADENOCARCINOMA                        1               105
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  SLC26A7 MUTATED    12   0   1   2
  SLC26A7 WILD-TYPE 333   4  30  23
D2048V11, multiclass
    clus
vv   SLC26A7 MUTATED SLC26A7 WILD-TYPE
  R0              12               333
  R1               0                 4
  R2               1                30
  RX               2                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2048V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SLC26A7 MUTATED                                  0     2
  SLC26A7 WILD-TYPE                                1     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  SLC26A7 MUTATED                           0     7
  SLC26A7 WILD-TYPE                        22   219
D2048V13, multiclass
                                  clus
vv                                 SLC26A7 MUTATED SLC26A7 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          2                 9
  BLACK OR AFRICAN AMERICAN                      0                22
  WHITE                                          7               219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2049) Variable = ARMC2 MUTATION ANALYSIS
D2049V1, survival
                 sevent
clus2               0   1
  ARMC2 MUTATED     6   2
  ARMC2 WILD-TYPE 372  91
  ARMC2 MUTATED ARMC2 WILD-TYPE 
              8             463 
  ARMC2 MUTATED ARMC2 WILD-TYPE 
              2              91 
$`ARMC2 MUTATED`
TCGA-AA-3510 TCGA-AA-3966 TCGA-AA-3977 TCGA-AD-5900 TCGA-AY-4070 TCGA-CA-6718 
       63.98         2.01        25.02         0.07        16.31        10.06 
TCGA-G4-6628 TCGA-AG-A002 
       79.69        20.98 

$`ARMC2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
        2.01        20.98        34.03        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       18.05        40.96        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       14.50        27.09         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 
        3.25         3.29         0.07        12.20        12.76        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 
       13.78        35.80        26.17        91.79        46.75        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  ARMC2 MUTATED ARMC2 WILD-TYPE 
           0.07            0.00 
  ARMC2 MUTATED ARMC2 WILD-TYPE 
          79.69          148.01 
  ARMC2 MUTATED ARMC2 WILD-TYPE 
         18.645          20.190 
[1] "0.1 - 79.7 (18.6)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.2"
D2049V2, continuous
D2049V3, binary
                 cls
clus                0   1
  ARMC2 MUTATED     7   1
  ARMC2 WILD-TYPE 359 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ARMC2 MUTATED      7    1
  ARMC2 WILD-TYPE  359  118
        clus
vv       ARMC2 MUTATED ARMC2 WILD-TYPE
  COLON              7             359
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ARMC2 MUTATED         3        0        1         2         0         0
  ARMC2 WILD-TYPE      88        1       31       136        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ARMC2 MUTATED           0          0          0          1        0         0
  ARMC2 WILD-TYPE        24         11         59         41       48        18
                 vv
clus              STAGE IVB
  ARMC2 MUTATED           0
  ARMC2 WILD-TYPE         1
D2049V4, multiclass
            clus
vv           ARMC2 MUTATED ARMC2 WILD-TYPE
  STAGE I                3              88
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              2             136
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             1              41
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ARMC2 MUTATED     0   4   4   0
  ARMC2 WILD-TYPE  17  88 325  50
D2049V5, multiclass
    clus
vv   ARMC2 MUTATED ARMC2 WILD-TYPE
  T1             0              17
  T2             4              88
  T3             4             325
  T4             0              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  ARMC2 MUTATED     7   0   1
  ARMC2 WILD-TYPE 280 113  86
D2049V6, multiclass
    clus
vv   ARMC2 MUTATED ARMC2 WILD-TYPE
  N0             7             280
  N1             0             113
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2049V7, binary
                 cls
clus                0   1
  ARMC2 MUTATED     6   0
  ARMC2 WILD-TYPE 369  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ARMC2 MUTATED      6    0
  ARMC2 WILD-TYPE  369   65
   clus
vv  ARMC2 MUTATED ARMC2 WILD-TYPE
  0             6             369
  1             0              65
[1] 2 2
[1] FALSE
D2049V8, binary
                 cls
clus                0   1
  ARMC2 MUTATED     2   6
  ARMC2 WILD-TYPE 223 258
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ARMC2 MUTATED      2    6
  ARMC2 WILD-TYPE  223  258
        clus
vv       ARMC2 MUTATED ARMC2 WILD-TYPE
  FEMALE             2             223
  MALE               6             258
[1] 2 2
[1] FALSE
D2049V9, binary
                 cls
clus                0   1
  ARMC2 MUTATED     6   0
  ARMC2 WILD-TYPE 344  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ARMC2 MUTATED      6    0
  ARMC2 WILD-TYPE  344   22
     clus
vv    ARMC2 MUTATED ARMC2 WILD-TYPE
  NO              6             344
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ARMC2 MUTATED                      5                             2
  ARMC2 WILD-TYPE                  310                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ARMC2 MUTATED                       1                              0
  ARMC2 WILD-TYPE                   105                             10
D2049V10, multiclass
                                clus
vv                               ARMC2 MUTATED ARMC2 WILD-TYPE
  COLON ADENOCARCINOMA                       5             310
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  ARMC2 MUTATED     4   1   0   1
  ARMC2 WILD-TYPE 341   3  31  24
D2049V11, multiclass
    clus
vv   ARMC2 MUTATED ARMC2 WILD-TYPE
  R0             4             341
  R1             1               3
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2049V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ARMC2 MUTATED                                  0     1
  ARMC2 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ARMC2 MUTATED                           1     2
  ARMC2 WILD-TYPE                        21   224
D2049V13, multiclass
                                  clus
vv                                 ARMC2 MUTATED ARMC2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        2             224
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2050) Variable = RAGE MUTATION ANALYSIS
D2050V1, survival
                sevent
clus2              0   1
  RAGE MUTATED     8   1
  RAGE WILD-TYPE 370  92
  RAGE MUTATED RAGE WILD-TYPE 
             9            462 
  RAGE MUTATED RAGE WILD-TYPE 
             1             92 
$`RAGE MUTATED`
TCGA-AA-3532 TCGA-AA-3864 TCGA-AA-A010 TCGA-AZ-6600 TCGA-CM-4743 TCGA-D5-5539 
       29.00        53.00        34.98        12.10        23.05        19.59 
TCGA-G4-6628 TCGA-AG-3732 TCGA-F5-6465 
       79.69        32.98        49.51 

$`RAGE WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3534 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 
       32.05         0.99        31.07        31.07        30.05        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 
       22.36        62.79        88.21        49.41         6.77       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
      124.27        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 
       13.78        35.80        26.17        91.79        46.75        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 
       19.99         7.99         0.99        37.02         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6571 
       20.55        19.96        20.91        18.28         9.96        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  RAGE MUTATED RAGE WILD-TYPE 
          12.1            0.0 
  RAGE MUTATED RAGE WILD-TYPE 
         79.69         148.01 
  RAGE MUTATED RAGE WILD-TYPE 
        32.980         20.035 
[1] "12.1 - 79.7 (33.0)" "0.0 - 148.0 (20.0)"
[1] "hr=" "2.5"
D2050V2, continuous
D2050V3, binary
                cls
clus               0   1
  RAGE MUTATED     7   2
  RAGE WILD-TYPE 359 117
[1] "tbl2"
                cls
clus             [,1] [,2]
  RAGE MUTATED      7    2
  RAGE WILD-TYPE  359  117
        clus
vv       RAGE MUTATED RAGE WILD-TYPE
  COLON             7            359
  RECTUM            2            117
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RAGE MUTATED         2        0        1         3         1         0
  RAGE WILD-TYPE      89        1       31       135         9         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RAGE MUTATED           0          1          0          0        1         0
  RAGE WILD-TYPE        24         10         59         42       47        18
                vv
clus             STAGE IVB
  RAGE MUTATED           0
  RAGE WILD-TYPE         1
D2050V4, multiclass
            clus
vv           RAGE MUTATED RAGE WILD-TYPE
  STAGE I               2             89
  STAGE IA              0              1
  STAGE II              1             31
  STAGE IIA             3            135
  STAGE IIB             1              9
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            1             10
  STAGE IIIB            0             59
  STAGE IIIC            0             42
  STAGE IV              1             47
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  RAGE MUTATED     0   2   5   2
  RAGE WILD-TYPE  17  90 324  48
D2050V5, multiclass
    clus
vv   RAGE MUTATED RAGE WILD-TYPE
  T1            0             17
  T2            2             90
  T3            5            324
  T4            2             48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  RAGE MUTATED     7   2   0
  RAGE WILD-TYPE 280 111  87
D2050V6, multiclass
    clus
vv   RAGE MUTATED RAGE WILD-TYPE
  N0            7            280
  N1            2            111
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2050V7, binary
                cls
clus               0   1
  RAGE MUTATED     8   1
  RAGE WILD-TYPE 367  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  RAGE MUTATED      8    1
  RAGE WILD-TYPE  367   64
   clus
vv  RAGE MUTATED RAGE WILD-TYPE
  0            8            367
  1            1             64
[1] 2 2
[1] FALSE
D2050V8, binary
                cls
clus               0   1
  RAGE MUTATED     3   6
  RAGE WILD-TYPE 222 258
[1] "tbl2"
                cls
clus             [,1] [,2]
  RAGE MUTATED      3    6
  RAGE WILD-TYPE  222  258
        clus
vv       RAGE MUTATED RAGE WILD-TYPE
  FEMALE            3            222
  MALE              6            258
[1] 2 2
[1] FALSE
D2050V9, binary
                cls
clus               0   1
  RAGE MUTATED     8   0
  RAGE WILD-TYPE 342  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  RAGE MUTATED      8    0
  RAGE WILD-TYPE  342   22
     clus
vv    RAGE MUTATED RAGE WILD-TYPE
  NO             8            342
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  RAGE MUTATED                      6                             1
  RAGE WILD-TYPE                  309                            46
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  RAGE MUTATED                       2                              0
  RAGE WILD-TYPE                   104                             10
D2050V10, multiclass
                                clus
vv                               RAGE MUTATED RAGE WILD-TYPE
  COLON ADENOCARCINOMA                      6            309
  COLON MUCINOUS ADENOCARCINOMA             1             46
  RECTAL ADENOCARCINOMA                     2            104
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  RAGE MUTATED     8   0   0   0
  RAGE WILD-TYPE 337   4  31  25
D2050V11, multiclass
    clus
vv   RAGE MUTATED RAGE WILD-TYPE
  R0            8            337
  R1            0              4
  R2            0             31
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2050V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RAGE MUTATED                                  0     0
  RAGE WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  RAGE MUTATED                           1     4
  RAGE WILD-TYPE                        21   222
D2050V13, multiclass
                                  clus
vv                                 RAGE MUTATED RAGE WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                       4            222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2051) Variable = TNNT2 MUTATION ANALYSIS
D2051V1, survival
                 sevent
clus2               0   1
  TNNT2 MUTATED     7   1
  TNNT2 WILD-TYPE 371  92
  TNNT2 MUTATED TNNT2 WILD-TYPE 
              8             463 
  TNNT2 MUTATED TNNT2 WILD-TYPE 
              1              92 
$`TNNT2 MUTATED`
TCGA-AA-3542 TCGA-AA-3663 TCGA-AA-3864 TCGA-AA-A00A TCGA-AD-6964 TCGA-AY-6197 
       12.99         6.97        53.00        38.04        10.88        21.44 
TCGA-CM-6162 TCGA-G4-6304 
       12.00        53.62 

$`TNNT2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       29.00        26.01         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 
        0.99        31.07        31.07        30.05        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00E 
       19.07         7.96        27.02        13.94        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
        0.72         5.79        22.42        27.42         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4315 
       27.09        16.31         0.95        33.01        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       15.02        17.03        15.02         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
      133.18        74.56        65.85        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  TNNT2 MUTATED TNNT2 WILD-TYPE 
           6.97            0.00 
  TNNT2 MUTATED TNNT2 WILD-TYPE 
          53.62          148.01 
  TNNT2 MUTATED TNNT2 WILD-TYPE 
         17.215          20.190 
[1] "7.0 - 53.6 (17.2)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.7"
D2051V2, continuous
D2051V3, binary
                 cls
clus                0   1
  TNNT2 MUTATED     8   0
  TNNT2 WILD-TYPE 358 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TNNT2 MUTATED      8    0
  TNNT2 WILD-TYPE  358  119
        clus
vv       TNNT2 MUTATED TNNT2 WILD-TYPE
  COLON              8             358
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TNNT2 MUTATED         0        0        2         2         1         0
  TNNT2 WILD-TYPE      91        1       30       136         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TNNT2 MUTATED           0          0          1          1        0         0
  TNNT2 WILD-TYPE        24         11         58         41       48        18
                 vv
clus              STAGE IVB
  TNNT2 MUTATED           0
  TNNT2 WILD-TYPE         1
D2051V4, multiclass
            clus
vv           TNNT2 MUTATED TNNT2 WILD-TYPE
  STAGE I                0              91
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA              2             136
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             1              41
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  TNNT2 MUTATED     0   0   6   2
  TNNT2 WILD-TYPE  17  92 323  48
D2051V5, multiclass
    clus
vv   TNNT2 MUTATED TNNT2 WILD-TYPE
  T1             0              17
  T2             0              92
  T3             6             323
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  TNNT2 MUTATED     5   1   2
  TNNT2 WILD-TYPE 282 112  85
D2051V6, multiclass
    clus
vv   TNNT2 MUTATED TNNT2 WILD-TYPE
  N0             5             282
  N1             1             112
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2051V7, binary
                 cls
clus                0   1
  TNNT2 MUTATED     6   0
  TNNT2 WILD-TYPE 369  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TNNT2 MUTATED      6    0
  TNNT2 WILD-TYPE  369   65
   clus
vv  TNNT2 MUTATED TNNT2 WILD-TYPE
  0             6             369
  1             0              65
[1] 2 2
[1] FALSE
D2051V8, binary
                 cls
clus                0   1
  TNNT2 MUTATED     2   6
  TNNT2 WILD-TYPE 223 258
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TNNT2 MUTATED      2    6
  TNNT2 WILD-TYPE  223  258
        clus
vv       TNNT2 MUTATED TNNT2 WILD-TYPE
  FEMALE             2             223
  MALE               6             258
[1] 2 2
[1] FALSE
D2051V9, binary
                 cls
clus                0   1
  TNNT2 MUTATED     8   0
  TNNT2 WILD-TYPE 342  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TNNT2 MUTATED      8    0
  TNNT2 WILD-TYPE  342   22
     clus
vv    TNNT2 MUTATED TNNT2 WILD-TYPE
  NO              8             342
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  TNNT2 MUTATED                      7                             1
  TNNT2 WILD-TYPE                  308                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  TNNT2 MUTATED                       0                              0
  TNNT2 WILD-TYPE                   106                             10
D2051V10, multiclass
                                clus
vv                               TNNT2 MUTATED TNNT2 WILD-TYPE
  COLON ADENOCARCINOMA                       7             308
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  TNNT2 MUTATED     7   0   0   0
  TNNT2 WILD-TYPE 338   4  31  25
D2051V11, multiclass
    clus
vv   TNNT2 MUTATED TNNT2 WILD-TYPE
  R0             7             338
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2051V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TNNT2 MUTATED                                  0     0
  TNNT2 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  TNNT2 MUTATED                           0     4
  TNNT2 WILD-TYPE                        22   222
D2051V13, multiclass
                                  clus
vv                                 TNNT2 MUTATED TNNT2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        4             222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2052) Variable = CDH8 MUTATION ANALYSIS
D2052V1, survival
                sevent
clus2              0   1
  CDH8 MUTATED    33   5
  CDH8 WILD-TYPE 345  88
  CDH8 MUTATED CDH8 WILD-TYPE 
            38            433 
  CDH8 MUTATED CDH8 WILD-TYPE 
             5             88 
$`CDH8 MUTATED`
TCGA-A6-6653 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3525 TCGA-AA-3662 
       24.39        63.98         6.97         1.02         8.05         6.05 
TCGA-AA-3664 TCGA-AA-3672 TCGA-AA-3697 TCGA-AA-3864 TCGA-AA-3977 TCGA-AA-A00N 
       54.02         0.92        85.05        53.00        25.02         4.01 
TCGA-AA-A00R TCGA-AA-A01Q TCGA-AU-6004 TCGA-AZ-4315 TCGA-AZ-4682 TCGA-AZ-6608 
        0.99         1.02        27.09        58.39        22.36         1.61 
TCGA-CA-6717 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 TCGA-CM-4743 TCGA-CM-5861 
       12.76        17.56       148.01        15.62        23.05        15.02 
TCGA-CM-6679 TCGA-CM-6680 TCGA-DM-A28H TCGA-F4-6570 TCGA-F4-6703 TCGA-G4-6315 
       10.06        12.03       117.07         6.18        47.87        61.91 
TCGA-G4-6628 TCGA-AF-2689 TCGA-AF-6655 TCGA-AG-3575 TCGA-AG-3731 TCGA-AG-A002 
       79.69        39.48        20.02        12.00        37.02        20.98 
TCGA-AG-A016 TCGA-CL-5917 
        9.07        78.12 

$`CDH8 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
       25.08        25.18        24.16        21.76        24.69        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
       35.01        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       37.05        36.03        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 
       78.08         6.97         2.01        14.01        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        31.07        30.05        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00U 
       18.05        18.05        38.04        27.02        42.02        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01R TCGA-AA-A01S 
       12.00        31.00        31.00        38.07        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       10.88         0.20        14.50        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-5403 
       21.44        17.82         1.41         5.13       106.75        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4950 
        3.29         0.07        12.20        10.06        14.30        85.45 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
      124.27        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 
       22.03        22.98        30.08        32.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       11.01        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6704 
       60.79        98.24         8.61        31.96        35.74         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6317 TCGA-G4-6321 
       44.68        55.04        85.48        63.62        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 
       13.78        35.80        26.17        91.79        46.75        24.13 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3578 TCGA-AG-3580 
       16.83        15.39        10.39        36.03        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01L TCGA-AG-A01W 
       23.01        37.02        15.95        36.03        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  CDH8 MUTATED CDH8 WILD-TYPE 
          0.92           0.00 
  CDH8 MUTATED CDH8 WILD-TYPE 
        148.01         140.38 
  CDH8 MUTATED CDH8 WILD-TYPE 
         20.50          20.19 
[1] "0.9 - 148.0 (20.5)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.9"
D2052V2, continuous
D2052V3, binary
                cls
clus               0   1
  CDH8 MUTATED    33   7
  CDH8 WILD-TYPE 333 112
[1] "tbl2"
                cls
clus             [,1] [,2]
  CDH8 MUTATED     33    7
  CDH8 WILD-TYPE  333  112
        clus
vv       CDH8 MUTATED CDH8 WILD-TYPE
  COLON            33            333
  RECTUM            7            112
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CDH8 MUTATED         6        0        6         7         2         0
  CDH8 WILD-TYPE      85        1       26       131         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CDH8 MUTATED           3          2          3          3        6         1
  CDH8 WILD-TYPE        21          9         56         39       42        17
                vv
clus             STAGE IVB
  CDH8 MUTATED           0
  CDH8 WILD-TYPE         1
D2052V4, multiclass
            clus
vv           CDH8 MUTATED CDH8 WILD-TYPE
  STAGE I               6             85
  STAGE IA              0              1
  STAGE II              6             26
  STAGE IIA             7            131
  STAGE IIB             2              8
  STAGE IIC             0              1
  STAGE III             3             21
  STAGE IIIA            2              9
  STAGE IIIB            3             56
  STAGE IIIC            3             39
  STAGE IV              6             42
  STAGE IVA             1             17
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  CDH8 MUTATED     0   9  25   6
  CDH8 WILD-TYPE  17  83 304  44
D2052V5, multiclass
    clus
vv   CDH8 MUTATED CDH8 WILD-TYPE
  T1            0             17
  T2            9             83
  T3           25            304
  T4            6             44
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  CDH8 MUTATED    24   8   8
  CDH8 WILD-TYPE 263 105  79
D2052V6, multiclass
    clus
vv   CDH8 MUTATED CDH8 WILD-TYPE
  N0           24            263
  N1            8            105
  N2            8             79
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2052V7, binary
                cls
clus               0   1
  CDH8 MUTATED    30   7
  CDH8 WILD-TYPE 345  58
[1] "tbl2"
                cls
clus             [,1] [,2]
  CDH8 MUTATED     30    7
  CDH8 WILD-TYPE  345   58
   clus
vv  CDH8 MUTATED CDH8 WILD-TYPE
  0           30            345
  1            7             58
[1] 2 2
[1] FALSE
D2052V8, binary
                cls
clus               0   1
  CDH8 MUTATED    18  22
  CDH8 WILD-TYPE 207 242
[1] "tbl2"
                cls
clus             [,1] [,2]
  CDH8 MUTATED     18   22
  CDH8 WILD-TYPE  207  242
        clus
vv       CDH8 MUTATED CDH8 WILD-TYPE
  FEMALE           18            207
  MALE             22            242
[1] 2 2
[1] FALSE
D2052V9, binary
                cls
clus               0   1
  CDH8 MUTATED    32   0
  CDH8 WILD-TYPE 318  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  CDH8 MUTATED     32    0
  CDH8 WILD-TYPE  318   22
     clus
vv    CDH8 MUTATED CDH8 WILD-TYPE
  NO            32            318
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CDH8 MUTATED                     30                             3
  CDH8 WILD-TYPE                  285                            44
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CDH8 MUTATED                       7                              0
  CDH8 WILD-TYPE                    99                             10
D2052V10, multiclass
                                clus
vv                               CDH8 MUTATED CDH8 WILD-TYPE
  COLON ADENOCARCINOMA                     30            285
  COLON MUCINOUS ADENOCARCINOMA             3             44
  RECTAL ADENOCARCINOMA                     7             99
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  CDH8 MUTATED    27   0   4   5
  CDH8 WILD-TYPE 318   4  27  20
D2052V11, multiclass
    clus
vv   CDH8 MUTATED CDH8 WILD-TYPE
  R0           27            318
  R1            0              4
  R2            4             27
  RX            5             20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2052V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CDH8 MUTATED                                  0     1
  CDH8 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  CDH8 MUTATED                           0    21
  CDH8 WILD-TYPE                        22   205
D2052V13, multiclass
                                  clus
vv                                 CDH8 MUTATED CDH8 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                      21            205
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2053) Variable = ADAM17 MUTATION ANALYSIS
D2053V1, survival
                  sevent
clus2                0   1
  ADAM17 MUTATED     9   3
  ADAM17 WILD-TYPE 369  90
  ADAM17 MUTATED ADAM17 WILD-TYPE 
              12              459 
  ADAM17 MUTATED ADAM17 WILD-TYPE 
               3               90 
$`ADAM17 MUTATED`
TCGA-AA-3520 TCGA-AA-3543 TCGA-AA-3968 TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A010 
       24.03         0.99        21.99        25.02         4.01        34.98 
TCGA-AZ-6598 TCGA-CA-6717 TCGA-CA-6718 TCGA-G4-6588 TCGA-AG-A002 TCGA-EI-6506 
       49.41        12.76        10.06        26.17        20.98        20.55 

$`ADAM17 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
       38.99         1.02         9.07        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       26.01        12.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       20.98        34.03         2.01        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.07        12.20        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 
       61.91        36.00        22.09        13.78        35.80        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       51.48        32.61         0.49        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  ADAM17 MUTATED ADAM17 WILD-TYPE 
            0.99             0.00 
  ADAM17 MUTATED ADAM17 WILD-TYPE 
           49.41           148.01 
  ADAM17 MUTATED ADAM17 WILD-TYPE 
          21.485           20.050 
[1] "1.0 - 49.4 (21.5)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.6"
D2053V2, continuous
D2053V3, binary
                  cls
clus                 0   1
  ADAM17 MUTATED    11   2
  ADAM17 WILD-TYPE 355 117
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ADAM17 MUTATED     11    2
  ADAM17 WILD-TYPE  355  117
        clus
vv       ADAM17 MUTATED ADAM17 WILD-TYPE
  COLON              11              355
  RECTUM              2              117
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ADAM17 MUTATED         3        0        2         5         2         0
  ADAM17 WILD-TYPE      88        1       30       133         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ADAM17 MUTATED           0          0          0          0        0
  ADAM17 WILD-TYPE        24         11         59         42       48
                  vv
clus               STAGE IVA STAGE IVB
  ADAM17 MUTATED           0         0
  ADAM17 WILD-TYPE        18         1
D2053V4, multiclass
            clus
vv           ADAM17 MUTATED ADAM17 WILD-TYPE
  STAGE I                 3               88
  STAGE IA                0                1
  STAGE II                2               30
  STAGE IIA               5              133
  STAGE IIB               2                8
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              0               59
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ADAM17 MUTATED     0   4   7   2
  ADAM17 WILD-TYPE  17  88 322  48
D2053V5, multiclass
    clus
vv   ADAM17 MUTATED ADAM17 WILD-TYPE
  T1              0               17
  T2              4               88
  T3              7              322
  T4              2               48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  ADAM17 MUTATED    13   0   0
  ADAM17 WILD-TYPE 274 113  87
D2053V6, multiclass
    clus
vv   ADAM17 MUTATED ADAM17 WILD-TYPE
  N0             13              274
  N1              0              113
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2053V7, binary
                  cls
clus                 0   1
  ADAM17 MUTATED    11   0
  ADAM17 WILD-TYPE 364  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ADAM17 MUTATED     11    0
  ADAM17 WILD-TYPE  364   65
   clus
vv  ADAM17 MUTATED ADAM17 WILD-TYPE
  0             11              364
  1              0               65
[1] 2 2
[1] FALSE
D2053V8, binary
                  cls
clus                 0   1
  ADAM17 MUTATED     7   6
  ADAM17 WILD-TYPE 218 258
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ADAM17 MUTATED      7    6
  ADAM17 WILD-TYPE  218  258
        clus
vv       ADAM17 MUTATED ADAM17 WILD-TYPE
  FEMALE              7              218
  MALE                6              258
[1] 2 2
[1] FALSE
D2053V9, binary
                  cls
clus                 0   1
  ADAM17 MUTATED    11   0
  ADAM17 WILD-TYPE 339  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ADAM17 MUTATED     11    0
  ADAM17 WILD-TYPE  339   22
     clus
vv    ADAM17 MUTATED ADAM17 WILD-TYPE
  NO              11              339
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ADAM17 MUTATED                      8                             3
  ADAM17 WILD-TYPE                  307                            44
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ADAM17 MUTATED                       2                              0
  ADAM17 WILD-TYPE                   104                             10
D2053V10, multiclass
                                clus
vv                               ADAM17 MUTATED ADAM17 WILD-TYPE
  COLON ADENOCARCINOMA                        8              307
  COLON MUCINOUS ADENOCARCINOMA               3               44
  RECTAL ADENOCARCINOMA                       2              104
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ADAM17 MUTATED     9   0   0   2
  ADAM17 WILD-TYPE 336   4  31  23
D2053V11, multiclass
    clus
vv   ADAM17 MUTATED ADAM17 WILD-TYPE
  R0              9              336
  R1              0                4
  R2              0               31
  RX              2               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2053V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ADAM17 MUTATED                                  0     2
  ADAM17 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ADAM17 MUTATED                           0     3
  ADAM17 WILD-TYPE                        22   223
D2053V13, multiclass
                                  clus
vv                                 ADAM17 MUTATED ADAM17 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                9
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         3              223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2054) Variable = CHMP4B MUTATION ANALYSIS
D2054V1, survival
                  sevent
clus2                0   1
  CHMP4B MUTATED     2   1
  CHMP4B WILD-TYPE 376  92
  CHMP4B MUTATED CHMP4B WILD-TYPE 
               3              468 
  CHMP4B MUTATED CHMP4B WILD-TYPE 
               1               92 
$`CHMP4B MUTATED`
TCGA-A6-6780 TCGA-AA-3811 TCGA-D5-6540 
       20.12        10.06        16.14 

$`CHMP4B WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
        4.80        17.13        12.49        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  CHMP4B MUTATED CHMP4B WILD-TYPE 
           10.06             0.00 
  CHMP4B MUTATED CHMP4B WILD-TYPE 
           20.12           148.01 
  CHMP4B MUTATED CHMP4B WILD-TYPE 
          16.140           20.415 
[1] "10.1 - 20.1 (16.1)" "0.0 - 148.0 (20.4)"
[1] "hr=" "2.8"
D2054V2, continuous
D2054V3, binary
                  cls
clus                 0   1
  CHMP4B MUTATED     3   0
  CHMP4B WILD-TYPE 363 119
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CHMP4B MUTATED      3    0
  CHMP4B WILD-TYPE  363  119
        clus
vv       CHMP4B MUTATED CHMP4B WILD-TYPE
  COLON               3              363
  RECTUM              0              119
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CHMP4B MUTATED         1        0        0         1         0         0
  CHMP4B WILD-TYPE      90        1       32       137        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CHMP4B MUTATED           1          0          0          0        0
  CHMP4B WILD-TYPE        23         11         59         42       48
                  vv
clus               STAGE IVA STAGE IVB
  CHMP4B MUTATED           0         0
  CHMP4B WILD-TYPE        18         1
D2054V4, multiclass
            clus
vv           CHMP4B MUTATED CHMP4B WILD-TYPE
  STAGE I                 1               90
  STAGE IA                0                1
  STAGE II                0               32
  STAGE IIA               1              137
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               1               23
  STAGE IIIA              0               11
  STAGE IIIB              0               59
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  CHMP4B MUTATED     0   1   2   0
  CHMP4B WILD-TYPE  17  91 327  50
D2054V5, multiclass
    clus
vv   CHMP4B MUTATED CHMP4B WILD-TYPE
  T1              0               17
  T2              1               91
  T3              2              327
  T4              0               50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  CHMP4B MUTATED     2   0   1
  CHMP4B WILD-TYPE 285 113  86
D2054V6, multiclass
    clus
vv   CHMP4B MUTATED CHMP4B WILD-TYPE
  N0              2              285
  N1              0              113
  N2              1               86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2054V7, binary
                  cls
clus                 0   1
  CHMP4B MUTATED     2   0
  CHMP4B WILD-TYPE 373  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CHMP4B MUTATED      2    0
  CHMP4B WILD-TYPE  373   65
   clus
vv  CHMP4B MUTATED CHMP4B WILD-TYPE
  0              2              373
  1              0               65
[1] 2 2
[1] FALSE
D2054V8, binary
                  cls
clus                 0   1
  CHMP4B MUTATED     1   2
  CHMP4B WILD-TYPE 224 262
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CHMP4B MUTATED      1    2
  CHMP4B WILD-TYPE  224  262
        clus
vv       CHMP4B MUTATED CHMP4B WILD-TYPE
  FEMALE              1              224
  MALE                2              262
[1] 2 2
[1] FALSE
D2054V9, binary
                  cls
clus                 0   1
  CHMP4B MUTATED     3   0
  CHMP4B WILD-TYPE 347  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CHMP4B MUTATED      3    0
  CHMP4B WILD-TYPE  347   22
     clus
vv    CHMP4B MUTATED CHMP4B WILD-TYPE
  NO               3              347
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CHMP4B MUTATED                      1                             2
  CHMP4B WILD-TYPE                  314                            45
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CHMP4B MUTATED                       0                              0
  CHMP4B WILD-TYPE                   106                             10
D2054V10, multiclass
                                clus
vv                               CHMP4B MUTATED CHMP4B WILD-TYPE
  COLON ADENOCARCINOMA                        1              314
  COLON MUCINOUS ADENOCARCINOMA               2               45
  RECTAL ADENOCARCINOMA                       0              106
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  CHMP4B MUTATED     2   0   0   0
  CHMP4B WILD-TYPE 343   4  31  25
D2054V11, multiclass
[1] "Remove cluster labels:" "CHMP4B MUTATED"        
clus
  CHMP4B MUTATED CHMP4B WILD-TYPE 
               2              403 
      TCGA-A6-2671       TCGA-A6-2672       TCGA-A6-2674       TCGA-A6-2676 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-A6-2677       TCGA-A6-2678       TCGA-A6-2683       TCGA-A6-3807 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-A6-3808       TCGA-A6-3809       TCGA-A6-3810       TCGA-A6-5657 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-A6-5659       TCGA-A6-5661       TCGA-A6-5665       TCGA-A6-6781 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AA-3489       TCGA-AA-3492       TCGA-AA-3496       TCGA-AA-3502 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AA-3510       TCGA-AA-3511       TCGA-AA-3514       TCGA-AA-3517 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AA-3518       TCGA-AA-3519       TCGA-AA-3520       TCGA-AA-3521 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AA-3522       TCGA-AA-3524       TCGA-AA-3525       TCGA-AA-3526 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AA-3527       TCGA-AA-3529       TCGA-AA-3530       TCGA-AA-3531 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AA-3532       TCGA-AA-3534       TCGA-AA-3538       TCGA-AA-3542 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AA-3543       TCGA-AA-3544       TCGA-AA-3548       TCGA-AA-3549 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AA-3552       TCGA-AA-3553       TCGA-AA-3554       TCGA-AA-3555 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AA-3556       TCGA-AA-3558       TCGA-AA-3560       TCGA-AA-3561 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AA-3562       TCGA-AA-3655       TCGA-AA-3660       TCGA-AA-3662 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AA-3663       TCGA-AA-3664       TCGA-AA-3666       TCGA-AA-3667 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AA-3672       TCGA-AA-3673       TCGA-AA-3678       TCGA-AA-3679 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AA-3680       TCGA-AA-3681       TCGA-AA-3684       TCGA-AA-3685 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AA-3688       TCGA-AA-3692       TCGA-AA-3693       TCGA-AA-3695 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AA-3696       TCGA-AA-3697       TCGA-AA-3710       TCGA-AA-3712 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AA-3713       TCGA-AA-3715       TCGA-AA-3812       TCGA-AA-3814 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AA-3815       TCGA-AA-3818       TCGA-AA-3819       TCGA-AA-3821 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AA-3831       TCGA-AA-3833       TCGA-AA-3837       TCGA-AA-3842 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AA-3844       TCGA-AA-3845       TCGA-AA-3846       TCGA-AA-3848 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AA-3850       TCGA-AA-3851       TCGA-AA-3852       TCGA-AA-3854 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AA-3855       TCGA-AA-3856       TCGA-AA-3858       TCGA-AA-3860 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AA-3861       TCGA-AA-3864       TCGA-AA-3866       TCGA-AA-3867 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AA-3869       TCGA-AA-3870       TCGA-AA-3872       TCGA-AA-3875 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AA-3877       TCGA-AA-3930       TCGA-AA-3939       TCGA-AA-3941 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AA-3947       TCGA-AA-3949       TCGA-AA-3950       TCGA-AA-3952 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AA-3955       TCGA-AA-3956       TCGA-AA-3968       TCGA-AA-3971 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AA-3972       TCGA-AA-3973       TCGA-AA-3975       TCGA-AA-3976 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AA-3979       TCGA-AA-3984       TCGA-AA-3986       TCGA-AA-3989 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AA-3994       TCGA-AA-A004       TCGA-AA-A00A       TCGA-AA-A00D 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AA-A00E       TCGA-AA-A00F       TCGA-AA-A00J       TCGA-AA-A00K 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AA-A00L       TCGA-AA-A00N       TCGA-AA-A00O       TCGA-AA-A00Q 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AA-A00R       TCGA-AA-A00U       TCGA-AA-A00W       TCGA-AA-A00Z 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AA-A010       TCGA-AA-A017       TCGA-AA-A01D       TCGA-AA-A01F 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AA-A01G       TCGA-AA-A01I       TCGA-AA-A01K       TCGA-AA-A01P 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AA-A01Q       TCGA-AA-A01R       TCGA-AA-A01S       TCGA-AA-A01T 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AA-A01V       TCGA-AA-A01X       TCGA-AA-A01Z       TCGA-AA-A022 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AA-A024       TCGA-AA-A029       TCGA-AA-A02F       TCGA-AA-A02H 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AA-A02J       TCGA-AA-A02K       TCGA-AA-A02O       TCGA-AA-A02W 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AA-A02Y       TCGA-AA-A03F       TCGA-AA-A03J       TCGA-AD-5900 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AD-6548       TCGA-AD-6888       TCGA-AU-3779       TCGA-AU-6004 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AY-4070       TCGA-AY-4071       TCGA-AY-5543       TCGA-AY-6196 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AY-6197       TCGA-AY-6386       TCGA-AZ-4315       TCGA-AZ-4681 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AZ-4682       TCGA-CA-5254       TCGA-CA-5255       TCGA-CA-5796 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-CA-5797       TCGA-CA-6715       TCGA-CA-6716       TCGA-CA-6717 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-CA-6718       TCGA-CA-6719       TCGA-CK-4947       TCGA-CK-4948 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-CK-4950       TCGA-CK-4952       TCGA-CK-5912       TCGA-CK-5913 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-CK-5914       TCGA-CK-5915       TCGA-CK-5916       TCGA-CK-6746 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-CK-6747       TCGA-CK-6748       TCGA-CK-6751       TCGA-CM-4743 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-CM-4744       TCGA-CM-4746       TCGA-CM-4747       TCGA-CM-4752 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-CM-5341       TCGA-CM-5344       TCGA-CM-5348       TCGA-CM-5349 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-CM-5860       TCGA-CM-5861       TCGA-CM-5862       TCGA-CM-5863 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-CM-5864       TCGA-CM-5868       TCGA-CM-6161       TCGA-CM-6162 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-CM-6163       TCGA-CM-6164       TCGA-CM-6165       TCGA-CM-6166 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-CM-6167       TCGA-CM-6168       TCGA-CM-6169       TCGA-CM-6170 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-CM-6171       TCGA-CM-6172       TCGA-CM-6674       TCGA-CM-6675 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-CM-6676       TCGA-CM-6677       TCGA-CM-6678       TCGA-CM-6679 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-CM-6680       TCGA-D5-5537       TCGA-D5-5538       TCGA-D5-5539 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-D5-5540       TCGA-D5-5541       TCGA-D5-6529       TCGA-D5-6532 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-D5-6533       TCGA-D5-6534       TCGA-D5-6535       TCGA-D5-6536 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-D5-6537       TCGA-D5-6538       TCGA-D5-6539       TCGA-D5-6541 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-D5-6898       TCGA-D5-6920       TCGA-D5-6922       TCGA-D5-6923 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-D5-6924       TCGA-D5-6926       TCGA-D5-6927       TCGA-D5-6928 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-D5-6929       TCGA-D5-6930       TCGA-D5-6931       TCGA-D5-6932 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-D5-7000       TCGA-F4-6459       TCGA-F4-6460       TCGA-F4-6569 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-F4-6570       TCGA-F4-6703       TCGA-F4-6704       TCGA-F4-6805 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-F4-6806       TCGA-F4-6807       TCGA-F4-6808       TCGA-F4-6809 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-F4-6854       TCGA-F4-6855       TCGA-F4-6856       TCGA-G4-6293 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-G4-6299       TCGA-G4-6303       TCGA-G4-6304       TCGA-G4-6306 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-G4-6307       TCGA-G4-6309       TCGA-G4-6310       TCGA-G4-6315 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-G4-6317       TCGA-G4-6321       TCGA-G4-6323       TCGA-G4-6586 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-G4-6588       TCGA-G4-6625       TCGA-G4-6626       TCGA-G4-6628 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AF-2687       TCGA-AF-2689       TCGA-AF-2691       TCGA-AF-2692 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AF-3400       TCGA-AF-3913       TCGA-AF-4110       TCGA-AF-5654 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AF-6655       TCGA-AG-3574       TCGA-AG-3575       TCGA-AG-3578 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AG-3580       TCGA-AG-3581       TCGA-AG-3582       TCGA-AG-3583 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AG-3584       TCGA-AG-3586       TCGA-AG-3587       TCGA-AG-3593 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AG-3594       TCGA-AG-3598       TCGA-AG-3599       TCGA-AG-3600 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AG-3601       TCGA-AG-3602       TCGA-AG-3605       TCGA-AG-3608 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AG-3609       TCGA-AG-3611       TCGA-AG-3612       TCGA-AG-3726 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AG-3727       TCGA-AG-3731       TCGA-AG-3732       TCGA-AG-3742 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AG-3878       TCGA-AG-3882       TCGA-AG-3883       TCGA-AG-3885 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AG-3887       TCGA-AG-3890       TCGA-AG-3892       TCGA-AG-3893 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AG-3894       TCGA-AG-3896       TCGA-AG-3898       TCGA-AG-3901 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AG-3902       TCGA-AG-3909       TCGA-AG-3999       TCGA-AG-4001 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AG-4005       TCGA-AG-4007       TCGA-AG-4008       TCGA-AG-4015 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AG-A002       TCGA-AG-A008       TCGA-AG-A00C       TCGA-AG-A00H 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AG-A00Y       TCGA-AG-A011       TCGA-AG-A014       TCGA-AG-A015 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AG-A016       TCGA-AG-A01L       TCGA-AG-A01W       TCGA-AG-A01Y 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AG-A020       TCGA-AG-A025       TCGA-AG-A026       TCGA-AG-A02G 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AG-A02N       TCGA-AG-A02X       TCGA-AG-A032       TCGA-AG-A036 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AH-6549       TCGA-AH-6643       TCGA-CL-5917       TCGA-CL-5918 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-DC-5337       TCGA-DC-5869       TCGA-DC-6155       TCGA-DC-6157 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-DC-6158       TCGA-DC-6160       TCGA-DC-6681       TCGA-DC-6682 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-DC-6683       TCGA-DT-5265       TCGA-EF-5830       TCGA-EI-6506 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-EI-6507       TCGA-EI-6508       TCGA-EI-6510       TCGA-F5-6464 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-F5-6465       TCGA-F5-6571       TCGA-F5-6702       TCGA-F5-6812 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-F5-6813       TCGA-G5-6235       TCGA-G5-6641 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
D2054V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CHMP4B MUTATED                                  0     0
  CHMP4B WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  CHMP4B MUTATED                           0     2
  CHMP4B WILD-TYPE                        22   224
D2054V13, multiclass
[1] "Remove cluster labels:" "CHMP4B MUTATED"        
clus
  CHMP4B MUTATED CHMP4B WILD-TYPE 
               2              258 
      TCGA-A6-2671       TCGA-A6-2672       TCGA-A6-2674       TCGA-A6-2676 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-A6-2677       TCGA-A6-2678       TCGA-A6-2683       TCGA-A6-3807 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-A6-3808       TCGA-A6-3809       TCGA-A6-3810       TCGA-A6-4105 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-A6-5656       TCGA-A6-5657       TCGA-A6-5659       TCGA-A6-5660 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-A6-5661       TCGA-A6-5662       TCGA-A6-5664       TCGA-A6-5665 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-A6-5666       TCGA-A6-6137       TCGA-A6-6138       TCGA-A6-6141 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-A6-6142       TCGA-A6-6648       TCGA-A6-6649       TCGA-A6-6651 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-A6-6652       TCGA-A6-6653       TCGA-A6-6654       TCGA-A6-6781 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-A6-6782       TCGA-AD-5900       TCGA-AD-6548       TCGA-AD-6888 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AD-6889       TCGA-AD-6890       TCGA-AD-6895       TCGA-AD-6899 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AD-6901       TCGA-AD-6963       TCGA-AD-6964       TCGA-AD-6965 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AU-3779       TCGA-AU-6004       TCGA-AY-4070       TCGA-AY-4071 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AY-5543       TCGA-AY-6196       TCGA-AY-6197       TCGA-AY-6386 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AZ-4315       TCGA-AZ-4323       TCGA-AZ-4616       TCGA-AZ-4681 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AZ-4682       TCGA-AZ-5403       TCGA-AZ-5407       TCGA-AZ-6598 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AZ-6599       TCGA-AZ-6600       TCGA-AZ-6601       TCGA-AZ-6603 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AZ-6605       TCGA-AZ-6606       TCGA-AZ-6607       TCGA-AZ-6608 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-CA-5254       TCGA-CA-5255       TCGA-CA-5796       TCGA-CA-5797 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-CA-6715       TCGA-CA-6716       TCGA-CA-6717       TCGA-CA-6718 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-CA-6719       TCGA-CK-4947       TCGA-CK-4948       TCGA-CK-4950 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-CK-4952       TCGA-CK-5912       TCGA-CK-5913       TCGA-CK-5914 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-CK-5915       TCGA-CK-5916       TCGA-CK-6746       TCGA-CK-6747 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-CK-6748       TCGA-CK-6751       TCGA-CM-4743       TCGA-CM-4744 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-CM-4746       TCGA-CM-4747       TCGA-CM-4752       TCGA-CM-5341 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-CM-5344       TCGA-CM-5348       TCGA-CM-5349       TCGA-CM-5860 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-CM-5861       TCGA-CM-5862       TCGA-CM-5863       TCGA-CM-5864 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-CM-5868       TCGA-CM-6161       TCGA-CM-6162       TCGA-CM-6163 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-CM-6164       TCGA-CM-6165       TCGA-CM-6166       TCGA-CM-6167 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-CM-6168       TCGA-CM-6169       TCGA-CM-6170       TCGA-CM-6171 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-CM-6172       TCGA-CM-6674       TCGA-CM-6675       TCGA-CM-6676 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-CM-6677       TCGA-CM-6678       TCGA-CM-6679       TCGA-CM-6680 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-D5-5537       TCGA-D5-5538       TCGA-D5-5539       TCGA-D5-5540 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-D5-5541       TCGA-D5-6529       TCGA-D5-6532       TCGA-D5-6533 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-D5-6534       TCGA-D5-6535       TCGA-D5-6536       TCGA-D5-6537 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-D5-6538       TCGA-D5-6539       TCGA-D5-6541       TCGA-D5-6898 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-D5-6920       TCGA-D5-6922       TCGA-D5-6923       TCGA-D5-6924 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-D5-6926       TCGA-D5-6927       TCGA-D5-6928       TCGA-D5-6929 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-D5-6930       TCGA-D5-6931       TCGA-D5-6932       TCGA-D5-7000 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-DM-A0X9       TCGA-DM-A0XD       TCGA-DM-A0XF       TCGA-DM-A1D0 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-DM-A1D4       TCGA-DM-A1D6       TCGA-DM-A1D7       TCGA-DM-A1D8 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-DM-A1D9       TCGA-DM-A1DA       TCGA-DM-A1DB       TCGA-DM-A1HA 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-DM-A1HB       TCGA-DM-A282       TCGA-DM-A285       TCGA-DM-A28C 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-DM-A28E       TCGA-DM-A28F       TCGA-DM-A28G       TCGA-DM-A28H 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-DM-A28K       TCGA-F4-6459       TCGA-F4-6460       TCGA-F4-6569 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-F4-6570       TCGA-F4-6703       TCGA-F4-6704       TCGA-F4-6805 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-F4-6806       TCGA-F4-6807       TCGA-F4-6808       TCGA-F4-6809 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-F4-6854       TCGA-F4-6855       TCGA-F4-6856       TCGA-G4-6293 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-G4-6299       TCGA-G4-6303       TCGA-G4-6304       TCGA-G4-6306 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-G4-6307       TCGA-G4-6309       TCGA-G4-6310       TCGA-G4-6315 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-G4-6317       TCGA-G4-6321       TCGA-G4-6323       TCGA-G4-6586 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-G4-6588       TCGA-G4-6625       TCGA-G4-6626       TCGA-G4-6628 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AF-2687       TCGA-AF-2689       TCGA-AF-2691       TCGA-AF-2692 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AF-2693       TCGA-AF-3400       TCGA-AF-3913       TCGA-AF-4110 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AF-5654       TCGA-AF-6136       TCGA-AF-6655       TCGA-AF-6672 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AH-6544       TCGA-AH-6547       TCGA-AH-6549       TCGA-AH-6643 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-AH-6644       TCGA-CI-6619       TCGA-CI-6620       TCGA-CI-6621 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-CI-6622       TCGA-CI-6624       TCGA-CL-5917       TCGA-CL-5918 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-DC-5337       TCGA-DC-5869       TCGA-DC-6155       TCGA-DC-6157 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-DC-6158       TCGA-DC-6160       TCGA-DC-6681       TCGA-DC-6682 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-DC-6683       TCGA-DT-5265       TCGA-DY-A0XA       TCGA-DY-A1DC 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-DY-A1DD       TCGA-DY-A1DF       TCGA-DY-A1DG       TCGA-DY-A1H8 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-EF-5830       TCGA-EI-6506       TCGA-EI-6507       TCGA-EI-6508 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-EI-6510       TCGA-F5-6464       TCGA-F5-6465       TCGA-F5-6571 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-F5-6702       TCGA-F5-6811       TCGA-F5-6812       TCGA-F5-6813 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 
      TCGA-G5-6235       TCGA-G5-6641 
"CHMP4B WILD-TYPE" "CHMP4B WILD-TYPE" 

Clustering(2055) Variable = TMPRSS5 MUTATION ANALYSIS
D2055V1, survival
                   sevent
clus2                 0   1
  TMPRSS5 MUTATED     5   2
  TMPRSS5 WILD-TYPE 373  91
  TMPRSS5 MUTATED TMPRSS5 WILD-TYPE 
                7               464 
  TMPRSS5 MUTATED TMPRSS5 WILD-TYPE 
                2                91 
$`TMPRSS5 MUTATED`
TCGA-A6-6141 TCGA-AA-3715 TCGA-AA-3977 TCGA-AU-6004 TCGA-AZ-6598 TCGA-CM-5860 
        8.38        19.04        25.02        27.09        49.41        32.02 
TCGA-CM-6162 
       12.00 

$`TMPRSS5 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 
       22.09        22.06        32.71        27.09        22.52        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 
       36.00         5.03        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
        0.20        14.50        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        88.21         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.03        22.98        30.08        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       15.02        17.03        15.02         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  TMPRSS5 MUTATED TMPRSS5 WILD-TYPE 
             8.38              0.00 
  TMPRSS5 MUTATED TMPRSS5 WILD-TYPE 
            49.41            148.01 
  TMPRSS5 MUTATED TMPRSS5 WILD-TYPE 
           25.020            20.155 
[1] "8.4 - 49.4 (25.0)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.5"
D2055V2, continuous
D2055V3, binary
                   cls
clus                  0   1
  TMPRSS5 MUTATED     7   0
  TMPRSS5 WILD-TYPE 359 119
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMPRSS5 MUTATED      7    0
  TMPRSS5 WILD-TYPE  359  119
        clus
vv       TMPRSS5 MUTATED TMPRSS5 WILD-TYPE
  COLON                7               359
  RECTUM               0               119
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TMPRSS5 MUTATED         1        0        2         2         0         0
  TMPRSS5 WILD-TYPE      90        1       30       136        10         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TMPRSS5 MUTATED           0          0          1          0        0
  TMPRSS5 WILD-TYPE        24         11         58         42       48
                   vv
clus                STAGE IVA STAGE IVB
  TMPRSS5 MUTATED           0         0
  TMPRSS5 WILD-TYPE        18         1
D2055V4, multiclass
            clus
vv           TMPRSS5 MUTATED TMPRSS5 WILD-TYPE
  STAGE I                  1                90
  STAGE IA                 0                 1
  STAGE II                 2                30
  STAGE IIA                2               136
  STAGE IIB                0                10
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               0                11
  STAGE IIIB               1                58
  STAGE IIIC               0                42
  STAGE IV                 0                48
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  TMPRSS5 MUTATED     0   2   5   0
  TMPRSS5 WILD-TYPE  17  90 324  50
D2055V5, multiclass
    clus
vv   TMPRSS5 MUTATED TMPRSS5 WILD-TYPE
  T1               0                17
  T2               2                90
  T3               5               324
  T4               0                50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  TMPRSS5 MUTATED     6   1   0
  TMPRSS5 WILD-TYPE 281 112  87
D2055V6, multiclass
    clus
vv   TMPRSS5 MUTATED TMPRSS5 WILD-TYPE
  N0               6               281
  N1               1               112
  N2               0                87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2055V7, binary
                   cls
clus                  0   1
  TMPRSS5 MUTATED     5   0
  TMPRSS5 WILD-TYPE 370  65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMPRSS5 MUTATED      5    0
  TMPRSS5 WILD-TYPE  370   65
   clus
vv  TMPRSS5 MUTATED TMPRSS5 WILD-TYPE
  0               5               370
  1               0                65
[1] 2 2
[1] FALSE
D2055V8, binary
                   cls
clus                  0   1
  TMPRSS5 MUTATED     3   4
  TMPRSS5 WILD-TYPE 222 260
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMPRSS5 MUTATED      3    4
  TMPRSS5 WILD-TYPE  222  260
        clus
vv       TMPRSS5 MUTATED TMPRSS5 WILD-TYPE
  FEMALE               3               222
  MALE                 4               260
[1] 2 2
[1] FALSE
D2055V9, binary
                   cls
clus                  0   1
  TMPRSS5 MUTATED     6   0
  TMPRSS5 WILD-TYPE 344  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMPRSS5 MUTATED      6    0
  TMPRSS5 WILD-TYPE  344   22
     clus
vv    TMPRSS5 MUTATED TMPRSS5 WILD-TYPE
  NO                6               344
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  TMPRSS5 MUTATED                      6                             1
  TMPRSS5 WILD-TYPE                  309                            46
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  TMPRSS5 MUTATED                       0                              0
  TMPRSS5 WILD-TYPE                   106                             10
D2055V10, multiclass
                                clus
vv                               TMPRSS5 MUTATED TMPRSS5 WILD-TYPE
  COLON ADENOCARCINOMA                         6               309
  COLON MUCINOUS ADENOCARCINOMA                1                46
  RECTAL ADENOCARCINOMA                        0               106
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  TMPRSS5 MUTATED     4   0   0   0
  TMPRSS5 WILD-TYPE 341   4  31  25
D2055V11, multiclass
    clus
vv   TMPRSS5 MUTATED TMPRSS5 WILD-TYPE
  R0               4               341
  R1               0                 4
  R2               0                31
  RX               0                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2055V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TMPRSS5 MUTATED                                  0     0
  TMPRSS5 WILD-TYPE                                1    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  TMPRSS5 MUTATED                           1     4
  TMPRSS5 WILD-TYPE                        21   222
D2055V13, multiclass
                                  clus
vv                                 TMPRSS5 MUTATED TMPRSS5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                      1                21
  WHITE                                          4               222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2056) Variable = TTR MUTATION ANALYSIS
D2056V1, survival
               sevent
clus2             0   1
  TTR MUTATED     4   0
  TTR WILD-TYPE 374  93
  TTR MUTATED TTR WILD-TYPE 
            4           467 
  TTR MUTATED TTR WILD-TYPE 
            0            93 
$`TTR MUTATED`
TCGA-AA-3543 TCGA-AA-3977 TCGA-CA-6717 TCGA-AG-3999 
        0.99        25.02        12.76        28.04 

$`TTR WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       29.00        26.01        12.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.20        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  TTR MUTATED TTR WILD-TYPE 
         0.99          0.00 
  TTR MUTATED TTR WILD-TYPE 
        28.04        148.01 
  TTR MUTATED TTR WILD-TYPE 
        18.89         20.19 
[1] "1.0 - 28.0 (18.9)"  "0.0 - 148.0 (20.2)"
[1] "hr="     "3300000"
D2056V2, continuous
D2056V3, binary
               cls
clus              0   1
  TTR MUTATED     3   1
  TTR WILD-TYPE 363 118
[1] "tbl2"
               cls
clus            [,1] [,2]
  TTR MUTATED      3    1
  TTR WILD-TYPE  363  118
        clus
vv       TTR MUTATED TTR WILD-TYPE
  COLON            3           363
  RECTUM           1           118
[1] 2 2
[1] FALSE
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TTR MUTATED         1        0        0         1         0         0
  TTR WILD-TYPE      90        1       32       137        10         1
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TTR MUTATED           0          0          0          1        0         0
  TTR WILD-TYPE        24         11         59         41       48        18
               vv
clus            STAGE IVB
  TTR MUTATED           0
  TTR WILD-TYPE         1
D2056V4, multiclass
            clus
vv           TTR MUTATED TTR WILD-TYPE
  STAGE I              1            90
  STAGE IA             0             1
  STAGE II             0            32
  STAGE IIA            1           137
  STAGE IIB            0            10
  STAGE IIC            0             1
  STAGE III            0            24
  STAGE IIIA           0            11
  STAGE IIIB           0            59
  STAGE IIIC           1            41
  STAGE IV             0            48
  STAGE IVA            0            18
  STAGE IVB            0             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  TTR MUTATED     0   2   2   0
  TTR WILD-TYPE  17  90 327  50
D2056V5, multiclass
    clus
vv   TTR MUTATED TTR WILD-TYPE
  T1           0            17
  T2           2            90
  T3           2           327
  T4           0            50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2
  TTR MUTATED     3   0   1
  TTR WILD-TYPE 284 113  86
D2056V6, multiclass
    clus
vv   TTR MUTATED TTR WILD-TYPE
  N0           3           284
  N1           0           113
  N2           1            86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2056V7, binary
               cls
clus              0   1
  TTR MUTATED     3   0
  TTR WILD-TYPE 372  65
[1] "tbl2"
               cls
clus            [,1] [,2]
  TTR MUTATED      3    0
  TTR WILD-TYPE  372   65
   clus
vv  TTR MUTATED TTR WILD-TYPE
  0           3           372
  1           0            65
[1] 2 2
[1] FALSE
D2056V8, binary
               cls
clus              0   1
  TTR MUTATED     1   3
  TTR WILD-TYPE 224 261
[1] "tbl2"
               cls
clus            [,1] [,2]
  TTR MUTATED      1    3
  TTR WILD-TYPE  224  261
        clus
vv       TTR MUTATED TTR WILD-TYPE
  FEMALE           1           224
  MALE             3           261
[1] 2 2
[1] FALSE
D2056V9, binary
               cls
clus              0   1
  TTR MUTATED     4   0
  TTR WILD-TYPE 346  22
[1] "tbl2"
               cls
clus            [,1] [,2]
  TTR MUTATED      4    0
  TTR WILD-TYPE  346   22
     clus
vv    TTR MUTATED TTR WILD-TYPE
  NO            4           346
  YES           0            22
[1] 2 2
[1] FALSE
               vv
clus            COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  TTR MUTATED                      1                             2
  TTR WILD-TYPE                  314                            45
               vv
clus            RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  TTR MUTATED                       1                              0
  TTR WILD-TYPE                   105                             10
D2056V10, multiclass
                                clus
vv                               TTR MUTATED TTR WILD-TYPE
  COLON ADENOCARCINOMA                     1           314
  COLON MUCINOUS ADENOCARCINOMA            2            45
  RECTAL ADENOCARCINOMA                    1           105
  RECTAL MUCINOUS ADENOCARCINOMA           0            10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             R0  R1  R2  RX
  TTR MUTATED     2   0   0   1
  TTR WILD-TYPE 343   4  31  24
D2056V11, multiclass
    clus
vv   TTR MUTATED TTR WILD-TYPE
  R0           2           343
  R1           0             4
  R2           0            31
  RX           1            24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2056V12, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TTR MUTATED                                  0     1
  TTR WILD-TYPE                                1    10
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  TTR MUTATED                           0     0
  TTR WILD-TYPE                        22   226
D2056V13, multiclass
[1] "Remove cluster labels:" "TTR MUTATED"           
clus
  TTR MUTATED TTR WILD-TYPE 
            1           259 
   TCGA-A6-2671    TCGA-A6-2672    TCGA-A6-2674    TCGA-A6-2676    TCGA-A6-2677 
"TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" 
   TCGA-A6-2678    TCGA-A6-2683    TCGA-A6-3807    TCGA-A6-3808    TCGA-A6-3809 
"TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" 
   TCGA-A6-3810    TCGA-A6-4105    TCGA-A6-5656    TCGA-A6-5657    TCGA-A6-5659 
"TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" 
   TCGA-A6-5660    TCGA-A6-5661    TCGA-A6-5662    TCGA-A6-5664    TCGA-A6-5665 
"TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" 
   TCGA-A6-5666    TCGA-A6-6137    TCGA-A6-6138    TCGA-A6-6141    TCGA-A6-6142 
"TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" 
   TCGA-A6-6648    TCGA-A6-6649    TCGA-A6-6651    TCGA-A6-6652    TCGA-A6-6653 
"TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" 
   TCGA-A6-6654    TCGA-A6-6780    TCGA-A6-6781    TCGA-A6-6782    TCGA-AD-5900 
"TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" 
   TCGA-AD-6548    TCGA-AD-6888    TCGA-AD-6889    TCGA-AD-6890    TCGA-AD-6895 
"TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" 
   TCGA-AD-6899    TCGA-AD-6901    TCGA-AD-6963    TCGA-AD-6964    TCGA-AD-6965 
"TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" 
   TCGA-AU-3779    TCGA-AU-6004    TCGA-AY-4070    TCGA-AY-4071    TCGA-AY-5543 
"TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" 
   TCGA-AY-6196    TCGA-AY-6197    TCGA-AY-6386    TCGA-AZ-4315    TCGA-AZ-4323 
"TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" 
   TCGA-AZ-4616    TCGA-AZ-4681    TCGA-AZ-4682    TCGA-AZ-5403    TCGA-AZ-5407 
"TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" 
   TCGA-AZ-6598    TCGA-AZ-6599    TCGA-AZ-6600    TCGA-AZ-6601    TCGA-AZ-6603 
"TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" 
   TCGA-AZ-6605    TCGA-AZ-6606    TCGA-AZ-6607    TCGA-AZ-6608    TCGA-CA-5254 
"TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" 
   TCGA-CA-5255    TCGA-CA-5796    TCGA-CA-5797    TCGA-CA-6715    TCGA-CA-6716 
"TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" 
   TCGA-CA-6718    TCGA-CA-6719    TCGA-CK-4947    TCGA-CK-4948    TCGA-CK-4950 
"TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" 
   TCGA-CK-4952    TCGA-CK-5912    TCGA-CK-5913    TCGA-CK-5914    TCGA-CK-5915 
"TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" 
   TCGA-CK-5916    TCGA-CK-6746    TCGA-CK-6747    TCGA-CK-6748    TCGA-CK-6751 
"TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" 
   TCGA-CM-4743    TCGA-CM-4744    TCGA-CM-4746    TCGA-CM-4747    TCGA-CM-4752 
"TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" 
   TCGA-CM-5341    TCGA-CM-5344    TCGA-CM-5348    TCGA-CM-5349    TCGA-CM-5860 
"TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" 
   TCGA-CM-5861    TCGA-CM-5862    TCGA-CM-5863    TCGA-CM-5864    TCGA-CM-5868 
"TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" 
   TCGA-CM-6161    TCGA-CM-6162    TCGA-CM-6163    TCGA-CM-6164    TCGA-CM-6165 
"TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" 
   TCGA-CM-6166    TCGA-CM-6167    TCGA-CM-6168    TCGA-CM-6169    TCGA-CM-6170 
"TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" 
   TCGA-CM-6171    TCGA-CM-6172    TCGA-CM-6674    TCGA-CM-6675    TCGA-CM-6676 
"TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" 
   TCGA-CM-6677    TCGA-CM-6678    TCGA-CM-6679    TCGA-CM-6680    TCGA-D5-5537 
"TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" 
   TCGA-D5-5538    TCGA-D5-5539    TCGA-D5-5540    TCGA-D5-5541    TCGA-D5-6529 
"TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" 
   TCGA-D5-6532    TCGA-D5-6533    TCGA-D5-6534    TCGA-D5-6535    TCGA-D5-6536 
"TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" 
   TCGA-D5-6537    TCGA-D5-6538    TCGA-D5-6539    TCGA-D5-6540    TCGA-D5-6541 
"TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" 
   TCGA-D5-6898    TCGA-D5-6920    TCGA-D5-6922    TCGA-D5-6923    TCGA-D5-6924 
"TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" 
   TCGA-D5-6926    TCGA-D5-6927    TCGA-D5-6928    TCGA-D5-6929    TCGA-D5-6930 
"TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" 
   TCGA-D5-6931    TCGA-D5-6932    TCGA-D5-7000    TCGA-DM-A0X9    TCGA-DM-A0XD 
"TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" 
   TCGA-DM-A0XF    TCGA-DM-A1D0    TCGA-DM-A1D4    TCGA-DM-A1D6    TCGA-DM-A1D7 
"TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" 
   TCGA-DM-A1D8    TCGA-DM-A1D9    TCGA-DM-A1DA    TCGA-DM-A1DB    TCGA-DM-A1HA 
"TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" 
   TCGA-DM-A1HB    TCGA-DM-A282    TCGA-DM-A285    TCGA-DM-A28C    TCGA-DM-A28E 
"TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" 
   TCGA-DM-A28F    TCGA-DM-A28G    TCGA-DM-A28H    TCGA-DM-A28K    TCGA-F4-6459 
"TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" 
   TCGA-F4-6460    TCGA-F4-6569    TCGA-F4-6570    TCGA-F4-6703    TCGA-F4-6704 
"TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" 
   TCGA-F4-6805    TCGA-F4-6806    TCGA-F4-6807    TCGA-F4-6808    TCGA-F4-6809 
"TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" 
   TCGA-F4-6854    TCGA-F4-6855    TCGA-F4-6856    TCGA-G4-6293    TCGA-G4-6299 
"TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" 
   TCGA-G4-6303    TCGA-G4-6304    TCGA-G4-6306    TCGA-G4-6307    TCGA-G4-6309 
"TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" 
   TCGA-G4-6310    TCGA-G4-6315    TCGA-G4-6317    TCGA-G4-6321    TCGA-G4-6323 
"TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" 
   TCGA-G4-6586    TCGA-G4-6588    TCGA-G4-6625    TCGA-G4-6626    TCGA-G4-6628 
"TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" 
   TCGA-AF-2687    TCGA-AF-2689    TCGA-AF-2691    TCGA-AF-2692    TCGA-AF-2693 
"TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" 
   TCGA-AF-3400    TCGA-AF-3913    TCGA-AF-4110    TCGA-AF-5654    TCGA-AF-6136 
"TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" 
   TCGA-AF-6655    TCGA-AF-6672    TCGA-AH-6544    TCGA-AH-6547    TCGA-AH-6549 
"TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" 
   TCGA-AH-6643    TCGA-AH-6644    TCGA-CI-6619    TCGA-CI-6620    TCGA-CI-6621 
"TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" 
   TCGA-CI-6622    TCGA-CI-6624    TCGA-CL-5917    TCGA-CL-5918    TCGA-DC-5337 
"TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" 
   TCGA-DC-5869    TCGA-DC-6155    TCGA-DC-6157    TCGA-DC-6158    TCGA-DC-6160 
"TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" 
   TCGA-DC-6681    TCGA-DC-6682    TCGA-DC-6683    TCGA-DT-5265    TCGA-DY-A0XA 
"TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" 
   TCGA-DY-A1DC    TCGA-DY-A1DD    TCGA-DY-A1DF    TCGA-DY-A1DG    TCGA-DY-A1H8 
"TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" 
   TCGA-EF-5830    TCGA-EI-6506    TCGA-EI-6507    TCGA-EI-6508    TCGA-EI-6510 
"TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" 
   TCGA-F5-6464    TCGA-F5-6465    TCGA-F5-6571    TCGA-F5-6702    TCGA-F5-6811 
"TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" 
   TCGA-F5-6812    TCGA-F5-6813    TCGA-G5-6235    TCGA-G5-6641 
"TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" "TTR WILD-TYPE" 

Clustering(2057) Variable = TBC1D25 MUTATION ANALYSIS
D2057V1, survival
                   sevent
clus2                 0   1
  TBC1D25 MUTATED     9   2
  TBC1D25 WILD-TYPE 369  91
  TBC1D25 MUTATED TBC1D25 WILD-TYPE 
               11               460 
  TBC1D25 MUTATED TBC1D25 WILD-TYPE 
                2                91 
$`TBC1D25 MUTATED`
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3821 TCGA-AA-3833 TCGA-AA-3875 TCGA-AA-3950 
       19.04        10.06         1.02        15.95        18.05        24.00 
TCGA-AA-3977 TCGA-AD-5900 TCGA-AU-3779 TCGA-D5-6928 TCGA-G4-6586 
       25.02         0.07        14.50        11.64        35.80 

$`TBC1D25 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3837 
       35.05        33.04         0.99        25.02        17.98        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       29.98        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       26.01         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 
       41.00        39.98        18.05        40.96        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       10.88         0.20        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 
        4.41        12.43        14.30         9.04         9.44         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  TBC1D25 MUTATED TBC1D25 WILD-TYPE 
             0.07              0.00 
  TBC1D25 MUTATED TBC1D25 WILD-TYPE 
            35.80            148.01 
  TBC1D25 MUTATED TBC1D25 WILD-TYPE 
            15.95             20.73 
[1] "0.1 - 35.8 (15.9)"  "0.0 - 148.0 (20.7)"
[1] "hr=" "1.5"
D2057V2, continuous
D2057V3, binary
                   cls
clus                  0   1
  TBC1D25 MUTATED    11   0
  TBC1D25 WILD-TYPE 355 119
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TBC1D25 MUTATED     11    0
  TBC1D25 WILD-TYPE  355  119
        clus
vv       TBC1D25 MUTATED TBC1D25 WILD-TYPE
  COLON               11               355
  RECTUM               0               119
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TBC1D25 MUTATED         3        0        1         5         0         0
  TBC1D25 WILD-TYPE      88        1       31       133        10         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TBC1D25 MUTATED           1          0          0          0        0
  TBC1D25 WILD-TYPE        23         11         59         42       48
                   vv
clus                STAGE IVA STAGE IVB
  TBC1D25 MUTATED           0         0
  TBC1D25 WILD-TYPE        18         1
D2057V4, multiclass
            clus
vv           TBC1D25 MUTATED TBC1D25 WILD-TYPE
  STAGE I                  3                88
  STAGE IA                 0                 1
  STAGE II                 1                31
  STAGE IIA                5               133
  STAGE IIB                0                10
  STAGE IIC                0                 1
  STAGE III                1                23
  STAGE IIIA               0                11
  STAGE IIIB               0                59
  STAGE IIIC               0                42
  STAGE IV                 0                48
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  TBC1D25 MUTATED     1   3   7   0
  TBC1D25 WILD-TYPE  16  89 322  50
D2057V5, multiclass
    clus
vv   TBC1D25 MUTATED TBC1D25 WILD-TYPE
  T1               1                16
  T2               3                89
  T3               7               322
  T4               0                50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  TBC1D25 MUTATED    10   0   1
  TBC1D25 WILD-TYPE 277 113  86
D2057V6, multiclass
    clus
vv   TBC1D25 MUTATED TBC1D25 WILD-TYPE
  N0              10               277
  N1               0               113
  N2               1                86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2057V7, binary
                   cls
clus                  0   1
  TBC1D25 MUTATED     9   0
  TBC1D25 WILD-TYPE 366  65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TBC1D25 MUTATED      9    0
  TBC1D25 WILD-TYPE  366   65
   clus
vv  TBC1D25 MUTATED TBC1D25 WILD-TYPE
  0               9               366
  1               0                65
[1] 2 2
[1] FALSE
D2057V8, binary
                   cls
clus                  0   1
  TBC1D25 MUTATED     7   4
  TBC1D25 WILD-TYPE 218 260
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TBC1D25 MUTATED      7    4
  TBC1D25 WILD-TYPE  218  260
        clus
vv       TBC1D25 MUTATED TBC1D25 WILD-TYPE
  FEMALE               7               218
  MALE                 4               260
[1] 2 2
[1] FALSE
D2057V9, binary
                   cls
clus                  0   1
  TBC1D25 MUTATED    10   0
  TBC1D25 WILD-TYPE 340  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TBC1D25 MUTATED     10    0
  TBC1D25 WILD-TYPE  340   22
     clus
vv    TBC1D25 MUTATED TBC1D25 WILD-TYPE
  NO               10               340
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  TBC1D25 MUTATED                      7                             4
  TBC1D25 WILD-TYPE                  308                            43
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  TBC1D25 MUTATED                       0                              0
  TBC1D25 WILD-TYPE                   106                             10
D2057V10, multiclass
                                clus
vv                               TBC1D25 MUTATED TBC1D25 WILD-TYPE
  COLON ADENOCARCINOMA                         7               308
  COLON MUCINOUS ADENOCARCINOMA                4                43
  RECTAL ADENOCARCINOMA                        0               106
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  TBC1D25 MUTATED    10   0   0   0
  TBC1D25 WILD-TYPE 335   4  31  25
D2057V11, multiclass
    clus
vv   TBC1D25 MUTATED TBC1D25 WILD-TYPE
  R0              10               335
  R1               0                 4
  R2               0                31
  RX               0                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2057V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TBC1D25 MUTATED                                  0     0
  TBC1D25 WILD-TYPE                                1    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  TBC1D25 MUTATED                           0     4
  TBC1D25 WILD-TYPE                        22   222
D2057V13, multiclass
                                  clus
vv                                 TBC1D25 MUTATED TBC1D25 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                      0                22
  WHITE                                          4               222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2058) Variable = ZNF418 MUTATION ANALYSIS
D2058V1, survival
                  sevent
clus2                0   1
  ZNF418 MUTATED    11   2
  ZNF418 WILD-TYPE 367  91
  ZNF418 MUTATED ZNF418 WILD-TYPE 
              13              458 
  ZNF418 MUTATED ZNF418 WILD-TYPE 
               2               91 
$`ZNF418 MUTATED`
TCGA-A6-6653 TCGA-AA-3510 TCGA-AA-3715 TCGA-AA-3966 TCGA-AA-3977 TCGA-AZ-4315 
       24.39        63.98        19.04         2.01        25.02        58.39 
TCGA-AZ-6598 TCGA-CA-6717 TCGA-CK-6747 TCGA-CM-5868 TCGA-CM-6675 TCGA-D5-6535 
       49.41        12.76        82.95        17.03        13.05        15.12 
TCGA-D5-6931 
       12.00 

$`ZNF418 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
       25.08        25.18        24.16        21.76        24.69        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
       34.03        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07        12.20        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6162 
       15.02         5.03        15.02        15.02        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6676 
       13.02        15.02        14.04        11.01        12.95        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       43.27        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6932 
        9.04         9.44        11.64         4.80         1.51        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  ZNF418 MUTATED ZNF418 WILD-TYPE 
            2.01             0.00 
  ZNF418 MUTATED ZNF418 WILD-TYPE 
           82.95           148.01 
  ZNF418 MUTATED ZNF418 WILD-TYPE 
          19.040           20.235 
[1] "2.0 - 83.0 (19.0)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.6"
D2058V2, continuous
D2058V3, binary
                  cls
clus                 0   1
  ZNF418 MUTATED    14   0
  ZNF418 WILD-TYPE 352 119
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF418 MUTATED     14    0
  ZNF418 WILD-TYPE  352  119
        clus
vv       ZNF418 MUTATED ZNF418 WILD-TYPE
  COLON              14              352
  RECTUM              0              119
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZNF418 MUTATED         1        0        3         5         0         0
  ZNF418 WILD-TYPE      90        1       29       133        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF418 MUTATED           0          0          1          1        0
  ZNF418 WILD-TYPE        24         11         58         41       48
                  vv
clus               STAGE IVA STAGE IVB
  ZNF418 MUTATED           1         1
  ZNF418 WILD-TYPE        17         0
D2058V4, multiclass
            clus
vv           ZNF418 MUTATED ZNF418 WILD-TYPE
  STAGE I                 1               90
  STAGE IA                0                1
  STAGE II                3               29
  STAGE IIA               5              133
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              1               58
  STAGE IIIC              1               41
  STAGE IV                0               48
  STAGE IVA               1               17
  STAGE IVB               1                0
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZNF418 MUTATED     0   2  10   2
  ZNF418 WILD-TYPE  17  90 319  48
D2058V5, multiclass
    clus
vv   ZNF418 MUTATED ZNF418 WILD-TYPE
  T1              0               17
  T2              2               90
  T3             10              319
  T4              2               48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  ZNF418 MUTATED    10   2   2
  ZNF418 WILD-TYPE 277 111  85
D2058V6, multiclass
    clus
vv   ZNF418 MUTATED ZNF418 WILD-TYPE
  N0             10              277
  N1              2              111
  N2              2               85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2058V7, binary
                  cls
clus                 0   1
  ZNF418 MUTATED     8   2
  ZNF418 WILD-TYPE 367  63
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF418 MUTATED      8    2
  ZNF418 WILD-TYPE  367   63
   clus
vv  ZNF418 MUTATED ZNF418 WILD-TYPE
  0              8              367
  1              2               63
[1] 2 2
[1] FALSE
D2058V8, binary
                  cls
clus                 0   1
  ZNF418 MUTATED     6   8
  ZNF418 WILD-TYPE 219 256
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF418 MUTATED      6    8
  ZNF418 WILD-TYPE  219  256
        clus
vv       ZNF418 MUTATED ZNF418 WILD-TYPE
  FEMALE              6              219
  MALE                8              256
[1] 2 2
[1] FALSE
D2058V9, binary
                  cls
clus                 0   1
  ZNF418 MUTATED    12   0
  ZNF418 WILD-TYPE 338  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF418 MUTATED     12    0
  ZNF418 WILD-TYPE  338   22
     clus
vv    ZNF418 MUTATED ZNF418 WILD-TYPE
  NO              12              338
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ZNF418 MUTATED                     12                             2
  ZNF418 WILD-TYPE                  303                            45
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ZNF418 MUTATED                       0                              0
  ZNF418 WILD-TYPE                   106                             10
D2058V10, multiclass
                                clus
vv                               ZNF418 MUTATED ZNF418 WILD-TYPE
  COLON ADENOCARCINOMA                       12              303
  COLON MUCINOUS ADENOCARCINOMA               2               45
  RECTAL ADENOCARCINOMA                       0              106
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ZNF418 MUTATED     7   0   0   3
  ZNF418 WILD-TYPE 338   4  31  22
D2058V11, multiclass
    clus
vv   ZNF418 MUTATED ZNF418 WILD-TYPE
  R0              7              338
  R1              0                4
  R2              0               31
  RX              3               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2058V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF418 MUTATED                                  0     1
  ZNF418 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZNF418 MUTATED                           1     7
  ZNF418 WILD-TYPE                        21   219
D2058V13, multiclass
                                  clus
vv                                 ZNF418 MUTATED ZNF418 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                         7              219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2059) Variable = FOXA2 MUTATION ANALYSIS
D2059V1, survival
                 sevent
clus2               0   1
  FOXA2 MUTATED     6   0
  FOXA2 WILD-TYPE 372  93
  FOXA2 MUTATED FOXA2 WILD-TYPE 
              6             465 
  FOXA2 MUTATED FOXA2 WILD-TYPE 
              0              93 
$`FOXA2 MUTATED`
TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3844 TCGA-D5-5539 TCGA-DM-A282 TCGA-DC-5869 
       78.08         6.97        14.93        19.59       139.17         5.03 

$`FOXA2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 
       20.98        19.99        13.94        19.99        61.02         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       15.95        38.99        37.02         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       45.40        12.26        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A285 
      140.38         7.50        44.32       131.51       135.65         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-6155 
        6.97         4.73        78.12         7.17        15.02        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  FOXA2 MUTATED FOXA2 WILD-TYPE 
           5.03            0.00 
  FOXA2 MUTATED FOXA2 WILD-TYPE 
         139.17          148.01 
  FOXA2 MUTATED FOXA2 WILD-TYPE 
          17.26           20.28 
[1] "5.0 - 139.2 (17.3)" "0.0 - 148.0 (20.3)"
[1] "hr="     "9300000"
D2059V2, continuous
D2059V3, binary
                 cls
clus                0   1
  FOXA2 MUTATED     6   1
  FOXA2 WILD-TYPE 360 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FOXA2 MUTATED      6    1
  FOXA2 WILD-TYPE  360  118
        clus
vv       FOXA2 MUTATED FOXA2 WILD-TYPE
  COLON              6             360
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FOXA2 MUTATED         0        0        2         1         1         0
  FOXA2 WILD-TYPE      91        1       30       137         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  FOXA2 MUTATED           0          1          1          1        0         0
  FOXA2 WILD-TYPE        24         10         58         41       48        18
                 vv
clus              STAGE IVB
  FOXA2 MUTATED           0
  FOXA2 WILD-TYPE         1
D2059V4, multiclass
            clus
vv           FOXA2 MUTATED FOXA2 WILD-TYPE
  STAGE I                0              91
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA              1             137
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             1              10
  STAGE IIIB             1              58
  STAGE IIIC             1              41
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  FOXA2 MUTATED     0   0   6   1
  FOXA2 WILD-TYPE  17  92 323  49
D2059V5, multiclass
    clus
vv   FOXA2 MUTATED FOXA2 WILD-TYPE
  T1             0              17
  T2             0              92
  T3             6             323
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  FOXA2 MUTATED     4   2   1
  FOXA2 WILD-TYPE 283 111  86
D2059V6, multiclass
    clus
vv   FOXA2 MUTATED FOXA2 WILD-TYPE
  N0             4             283
  N1             2             111
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2059V7, binary
                 cls
clus                0   1
  FOXA2 MUTATED     6   0
  FOXA2 WILD-TYPE 369  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FOXA2 MUTATED      6    0
  FOXA2 WILD-TYPE  369   65
   clus
vv  FOXA2 MUTATED FOXA2 WILD-TYPE
  0             6             369
  1             0              65
[1] 2 2
[1] FALSE
D2059V8, binary
                 cls
clus                0   1
  FOXA2 MUTATED     5   2
  FOXA2 WILD-TYPE 220 262
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FOXA2 MUTATED      5    2
  FOXA2 WILD-TYPE  220  262
        clus
vv       FOXA2 MUTATED FOXA2 WILD-TYPE
  FEMALE             5             220
  MALE               2             262
[1] 2 2
[1] FALSE
D2059V9, binary
                 cls
clus                0   1
  FOXA2 MUTATED     3   1
  FOXA2 WILD-TYPE 347  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FOXA2 MUTATED      3    1
  FOXA2 WILD-TYPE  347   21
     clus
vv    FOXA2 MUTATED FOXA2 WILD-TYPE
  NO              3             347
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  FOXA2 MUTATED                      5                             1
  FOXA2 WILD-TYPE                  310                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  FOXA2 MUTATED                       1                              0
  FOXA2 WILD-TYPE                   105                             10
D2059V10, multiclass
                                clus
vv                               FOXA2 MUTATED FOXA2 WILD-TYPE
  COLON ADENOCARCINOMA                       5             310
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  FOXA2 MUTATED     5   0   0   1
  FOXA2 WILD-TYPE 340   4  31  24
D2059V11, multiclass
    clus
vv   FOXA2 MUTATED FOXA2 WILD-TYPE
  R0             5             340
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2059V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FOXA2 MUTATED                                  0     0
  FOXA2 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  FOXA2 MUTATED                           1     3
  FOXA2 WILD-TYPE                        21   223
D2059V13, multiclass
                                  clus
vv                                 FOXA2 MUTATED FOXA2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        3             223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2060) Variable = GSTM4 MUTATION ANALYSIS
D2060V1, survival
                 sevent
clus2               0   1
  GSTM4 MUTATED     6   0
  GSTM4 WILD-TYPE 372  93
  GSTM4 MUTATED GSTM4 WILD-TYPE 
              6             465 
  GSTM4 MUTATED GSTM4 WILD-TYPE 
              0              93 
$`GSTM4 MUTATED`
TCGA-AA-3526 TCGA-AA-3710 TCGA-AZ-4315 TCGA-CM-6674 TCGA-G4-6628 TCGA-AF-6672 
       19.07        26.99        58.39        12.95        79.69        10.39 

$`GSTM4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
        8.05         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        85.05        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       33.01        21.44        17.82         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6675 
       12.99        13.02        15.02        14.04        11.01        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       46.75        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  GSTM4 MUTATED GSTM4 WILD-TYPE 
          10.39            0.00 
  GSTM4 MUTATED GSTM4 WILD-TYPE 
          79.69          148.01 
  GSTM4 MUTATED GSTM4 WILD-TYPE 
          23.03           20.19 
[1] "10.4 - 79.7 (23.0)" "0.0 - 148.0 (20.2)"
[1] "hr="     "9200000"
D2060V2, continuous
D2060V3, binary
                 cls
clus                0   1
  GSTM4 MUTATED     5   1
  GSTM4 WILD-TYPE 361 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GSTM4 MUTATED      5    1
  GSTM4 WILD-TYPE  361  118
        clus
vv       GSTM4 MUTATED GSTM4 WILD-TYPE
  COLON              5             361
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GSTM4 MUTATED         2        0        0         3         0         0
  GSTM4 WILD-TYPE      89        1       32       135        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  GSTM4 MUTATED           0          0          0          0        1         0
  GSTM4 WILD-TYPE        24         11         59         42       47        18
                 vv
clus              STAGE IVB
  GSTM4 MUTATED           0
  GSTM4 WILD-TYPE         1
D2060V4, multiclass
            clus
vv           GSTM4 MUTATED GSTM4 WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              3             135
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             0              42
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  GSTM4 MUTATED     0   2   3   1
  GSTM4 WILD-TYPE  17  90 326  49
D2060V5, multiclass
    clus
vv   GSTM4 MUTATED GSTM4 WILD-TYPE
  T1             0              17
  T2             2              90
  T3             3             326
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  GSTM4 MUTATED     5   0   1
  GSTM4 WILD-TYPE 282 113  86
D2060V6, multiclass
    clus
vv   GSTM4 MUTATED GSTM4 WILD-TYPE
  N0             5             282
  N1             0             113
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2060V7, binary
                 cls
clus                0   1
  GSTM4 MUTATED     5   0
  GSTM4 WILD-TYPE 370  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GSTM4 MUTATED      5    0
  GSTM4 WILD-TYPE  370   65
   clus
vv  GSTM4 MUTATED GSTM4 WILD-TYPE
  0             5             370
  1             0              65
[1] 2 2
[1] FALSE
D2060V8, binary
                 cls
clus                0   1
  GSTM4 MUTATED     1   5
  GSTM4 WILD-TYPE 224 259
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GSTM4 MUTATED      1    5
  GSTM4 WILD-TYPE  224  259
        clus
vv       GSTM4 MUTATED GSTM4 WILD-TYPE
  FEMALE             1             224
  MALE               5             259
[1] 2 2
[1] FALSE
D2060V9, binary
                 cls
clus                0   1
  GSTM4 MUTATED     5   1
  GSTM4 WILD-TYPE 345  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GSTM4 MUTATED      5    1
  GSTM4 WILD-TYPE  345   21
     clus
vv    GSTM4 MUTATED GSTM4 WILD-TYPE
  NO              5             345
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  GSTM4 MUTATED                      5                             0
  GSTM4 WILD-TYPE                  310                            47
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  GSTM4 MUTATED                       1                              0
  GSTM4 WILD-TYPE                   105                             10
D2060V10, multiclass
                                clus
vv                               GSTM4 MUTATED GSTM4 WILD-TYPE
  COLON ADENOCARCINOMA                       5             310
  COLON MUCINOUS ADENOCARCINOMA              0              47
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  GSTM4 MUTATED     5   0   0   0
  GSTM4 WILD-TYPE 340   4  31  25
D2060V11, multiclass
    clus
vv   GSTM4 MUTATED GSTM4 WILD-TYPE
  R0             5             340
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2060V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GSTM4 MUTATED                                  0     0
  GSTM4 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  GSTM4 MUTATED                           0     4
  GSTM4 WILD-TYPE                        22   222
D2060V13, multiclass
                                  clus
vv                                 GSTM4 MUTATED GSTM4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        4             222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2061) Variable = PCDHGC4 MUTATION ANALYSIS
D2061V1, survival
                   sevent
clus2                 0   1
  PCDHGC4 MUTATED     9   5
  PCDHGC4 WILD-TYPE 369  88
  PCDHGC4 MUTATED PCDHGC4 WILD-TYPE 
               14               457 
  PCDHGC4 MUTATED PCDHGC4 WILD-TYPE 
                5                88 
$`PCDHGC4 MUTATED`
TCGA-A6-5666 TCGA-AA-3510 TCGA-AA-3710 TCGA-AA-3877 TCGA-AA-3947 TCGA-AA-3977 
       32.71        63.98        26.99        31.00        33.01        25.02 
TCGA-AA-A00N TCGA-AA-A01Q TCGA-AZ-6598 TCGA-AZ-6601 TCGA-CA-6718 TCGA-G4-6586 
        4.01         1.02        49.41       100.01        10.06        35.80 
TCGA-AG-A002 TCGA-AG-A026 
       20.98         1.94 

$`PCDHGC4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        22.06        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       27.02        29.98        18.05         2.01        12.99        24.00 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01R TCGA-AA-A01S 
       12.00        31.00        31.00        38.07        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 
      106.75        22.36        62.79        88.21         6.77        12.10 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       22.09        13.78        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       64.01        10.98        49.97        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  PCDHGC4 MUTATED PCDHGC4 WILD-TYPE 
             1.02              0.00 
  PCDHGC4 MUTATED PCDHGC4 WILD-TYPE 
           100.01            148.01 
  PCDHGC4 MUTATED PCDHGC4 WILD-TYPE 
           28.995            20.020 
[1] "1.0 - 100.0 (29.0)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.6"
D2061V2, continuous
D2061V3, binary
                   cls
clus                  0   1
  PCDHGC4 MUTATED    13   2
  PCDHGC4 WILD-TYPE 353 117
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PCDHGC4 MUTATED     13    2
  PCDHGC4 WILD-TYPE  353  117
        clus
vv       PCDHGC4 MUTATED PCDHGC4 WILD-TYPE
  COLON               13               353
  RECTUM               2               117
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PCDHGC4 MUTATED         2        0        5         4         2         1
  PCDHGC4 WILD-TYPE      89        1       27       134         8         0
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PCDHGC4 MUTATED           0          0          0          0        0
  PCDHGC4 WILD-TYPE        24         11         59         42       48
                   vv
clus                STAGE IVA STAGE IVB
  PCDHGC4 MUTATED           0         0
  PCDHGC4 WILD-TYPE        18         1
D2061V4, multiclass
            clus
vv           PCDHGC4 MUTATED PCDHGC4 WILD-TYPE
  STAGE I                  2                89
  STAGE IA                 0                 1
  STAGE II                 5                27
  STAGE IIA                4               134
  STAGE IIB                2                 8
  STAGE IIC                1                 0
  STAGE III                0                24
  STAGE IIIA               0                11
  STAGE IIIB               0                59
  STAGE IIIC               0                42
  STAGE IV                 0                48
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  PCDHGC4 MUTATED     1   2   8   4
  PCDHGC4 WILD-TYPE  16  90 321  46
D2061V5, multiclass
    clus
vv   PCDHGC4 MUTATED PCDHGC4 WILD-TYPE
  T1               1                16
  T2               2                90
  T3               8               321
  T4               4                46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  PCDHGC4 MUTATED    15   0   0
  PCDHGC4 WILD-TYPE 272 113  87
D2061V6, multiclass
    clus
vv   PCDHGC4 MUTATED PCDHGC4 WILD-TYPE
  N0              15               272
  N1               0               113
  N2               0                87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2061V7, binary
                   cls
clus                  0   1
  PCDHGC4 MUTATED    13   0
  PCDHGC4 WILD-TYPE 362  65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PCDHGC4 MUTATED     13    0
  PCDHGC4 WILD-TYPE  362   65
   clus
vv  PCDHGC4 MUTATED PCDHGC4 WILD-TYPE
  0              13               362
  1               0                65
[1] 2 2
[1] FALSE
D2061V8, binary
                   cls
clus                  0   1
  PCDHGC4 MUTATED     7   8
  PCDHGC4 WILD-TYPE 218 256
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PCDHGC4 MUTATED      7    8
  PCDHGC4 WILD-TYPE  218  256
        clus
vv       PCDHGC4 MUTATED PCDHGC4 WILD-TYPE
  FEMALE               7               218
  MALE                 8               256
[1] 2 2
[1] FALSE
D2061V9, binary
                   cls
clus                  0   1
  PCDHGC4 MUTATED    11   0
  PCDHGC4 WILD-TYPE 339  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PCDHGC4 MUTATED     11    0
  PCDHGC4 WILD-TYPE  339   22
     clus
vv    PCDHGC4 MUTATED PCDHGC4 WILD-TYPE
  NO               11               339
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PCDHGC4 MUTATED                     10                             3
  PCDHGC4 WILD-TYPE                  305                            44
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PCDHGC4 MUTATED                       2                              0
  PCDHGC4 WILD-TYPE                   104                             10
D2061V10, multiclass
                                clus
vv                               PCDHGC4 MUTATED PCDHGC4 WILD-TYPE
  COLON ADENOCARCINOMA                        10               305
  COLON MUCINOUS ADENOCARCINOMA                3                44
  RECTAL ADENOCARCINOMA                        2               104
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  PCDHGC4 MUTATED     9   1   0   1
  PCDHGC4 WILD-TYPE 336   3  31  24
D2061V11, multiclass
    clus
vv   PCDHGC4 MUTATED PCDHGC4 WILD-TYPE
  R0               9               336
  R1               1                 3
  R2               0                31
  RX               1                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2061V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PCDHGC4 MUTATED                                  0     1
  PCDHGC4 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  PCDHGC4 MUTATED                           0     4
  PCDHGC4 WILD-TYPE                        22   222
D2061V13, multiclass
                                  clus
vv                                 PCDHGC4 MUTATED PCDHGC4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                10
  BLACK OR AFRICAN AMERICAN                      0                22
  WHITE                                          4               222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2062) Variable = KIAA1967 MUTATION ANALYSIS
D2062V1, survival
                    sevent
clus2                  0   1
  KIAA1967 MUTATED    10   2
  KIAA1967 WILD-TYPE 368  91
  KIAA1967 MUTATED KIAA1967 WILD-TYPE 
                12                459 
  KIAA1967 MUTATED KIAA1967 WILD-TYPE 
                 2                 91 
$`KIAA1967 MUTATED`
TCGA-A6-2676 TCGA-A6-5666 TCGA-A6-6649 TCGA-AA-3554 TCGA-AA-3672 TCGA-AA-A00J 
       42.90        32.71        24.16        17.95         0.92        18.05 
TCGA-AZ-6598 TCGA-CM-4746 TCGA-CM-6674 TCGA-AG-A002 TCGA-AG-A032 TCGA-EI-6507 
       49.41        37.02        12.95        20.98        38.04        19.96 

$`KIAA1967 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       22.06        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
       14.01        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A036 TCGA-AH-6544 
        1.94        38.96        61.97        41.00       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6510 
       51.48        32.61         0.49        20.55        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  KIAA1967 MUTATED KIAA1967 WILD-TYPE 
              0.92               0.00 
  KIAA1967 MUTATED KIAA1967 WILD-TYPE 
             49.41             148.01 
  KIAA1967 MUTATED KIAA1967 WILD-TYPE 
             22.57              20.12 
[1] "0.9 - 49.4 (22.6)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.2"
D2062V2, continuous
D2062V3, binary
                    cls
clus                   0   1
  KIAA1967 MUTATED     9   3
  KIAA1967 WILD-TYPE 357 116
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1967 MUTATED      9    3
  KIAA1967 WILD-TYPE  357  116
        clus
vv       KIAA1967 MUTATED KIAA1967 WILD-TYPE
  COLON                 9                357
  RECTUM                3                116
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KIAA1967 MUTATED         2        0        1         3         1         1
  KIAA1967 WILD-TYPE      89        1       31       135         9         0
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIAA1967 MUTATED           1          0          3          0        0
  KIAA1967 WILD-TYPE        23         11         56         42       48
                    vv
clus                 STAGE IVA STAGE IVB
  KIAA1967 MUTATED           0         0
  KIAA1967 WILD-TYPE        18         1
D2062V4, multiclass
            clus
vv           KIAA1967 MUTATED KIAA1967 WILD-TYPE
  STAGE I                   2                 89
  STAGE IA                  0                  1
  STAGE II                  1                 31
  STAGE IIA                 3                135
  STAGE IIB                 1                  9
  STAGE IIC                 1                  0
  STAGE III                 1                 23
  STAGE IIIA                0                 11
  STAGE IIIB                3                 56
  STAGE IIIC                0                 42
  STAGE IV                  0                 48
  STAGE IVA                 0                 18
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  KIAA1967 MUTATED     0   2   7   3
  KIAA1967 WILD-TYPE  17  90 322  47
D2062V5, multiclass
    clus
vv   KIAA1967 MUTATED KIAA1967 WILD-TYPE
  T1                0                 17
  T2                2                 90
  T3                7                322
  T4                3                 47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  KIAA1967 MUTATED     8   4   0
  KIAA1967 WILD-TYPE 279 109  87
D2062V6, multiclass
    clus
vv   KIAA1967 MUTATED KIAA1967 WILD-TYPE
  N0                8                279
  N1                4                109
  N2                0                 87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2062V7, binary
                    cls
clus                   0   1
  KIAA1967 MUTATED    11   0
  KIAA1967 WILD-TYPE 364  65
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1967 MUTATED     11    0
  KIAA1967 WILD-TYPE  364   65
   clus
vv  KIAA1967 MUTATED KIAA1967 WILD-TYPE
  0               11                364
  1                0                 65
[1] 2 2
[1] FALSE
D2062V8, binary
                    cls
clus                   0   1
  KIAA1967 MUTATED     4   8
  KIAA1967 WILD-TYPE 221 256
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1967 MUTATED      4    8
  KIAA1967 WILD-TYPE  221  256
        clus
vv       KIAA1967 MUTATED KIAA1967 WILD-TYPE
  FEMALE                4                221
  MALE                  8                256
[1] 2 2
[1] FALSE
D2062V9, binary
                    cls
clus                   0   1
  KIAA1967 MUTATED    11   1
  KIAA1967 WILD-TYPE 339  21
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1967 MUTATED     11    1
  KIAA1967 WILD-TYPE  339   21
     clus
vv    KIAA1967 MUTATED KIAA1967 WILD-TYPE
  NO                11                339
  YES                1                 21
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  KIAA1967 MUTATED                      8                             1
  KIAA1967 WILD-TYPE                  307                            46
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  KIAA1967 MUTATED                       3                              0
  KIAA1967 WILD-TYPE                   103                             10
D2062V10, multiclass
                                clus
vv                               KIAA1967 MUTATED KIAA1967 WILD-TYPE
  COLON ADENOCARCINOMA                          8                307
  COLON MUCINOUS ADENOCARCINOMA                 1                 46
  RECTAL ADENOCARCINOMA                         3                103
  RECTAL MUCINOUS ADENOCARCINOMA                0                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  KIAA1967 MUTATED     9   0   0   0
  KIAA1967 WILD-TYPE 336   4  31  25
D2062V11, multiclass
    clus
vv   KIAA1967 MUTATED KIAA1967 WILD-TYPE
  R0                9                336
  R1                0                  4
  R2                0                 31
  RX                0                 25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2062V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KIAA1967 MUTATED                                  0     0
  KIAA1967 WILD-TYPE                                1    11
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  KIAA1967 MUTATED                           1     6
  KIAA1967 WILD-TYPE                        21   220
D2062V13, multiclass
                                  clus
vv                                 KIAA1967 MUTATED KIAA1967 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 11
  BLACK OR AFRICAN AMERICAN                       1                 21
  WHITE                                           6                220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2063) Variable = CPB1 MUTATION ANALYSIS
D2063V1, survival
                sevent
clus2              0   1
  CPB1 MUTATED     9   0
  CPB1 WILD-TYPE 369  93
  CPB1 MUTATED CPB1 WILD-TYPE 
             9            462 
  CPB1 MUTATED CPB1 WILD-TYPE 
             0             93 
$`CPB1 MUTATED`
TCGA-A6-6648 TCGA-AA-3519 TCGA-AA-3660 TCGA-AA-3975 TCGA-AA-A00E TCGA-AD-6895 
       25.18         9.07        78.08        34.06        30.02         0.72 
TCGA-AG-3575 TCGA-AG-A016 TCGA-AH-6644 
       12.00         9.07         0.72 

$`CPB1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.08        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        1.02        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       13.94        19.99        61.02         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00F 
        7.96        27.02        13.94        38.04        19.00        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 
        0.07        21.37        15.52        56.55         0.79         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       36.03        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       37.02        15.95        36.03        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  CPB1 MUTATED CPB1 WILD-TYPE 
          0.72           0.00 
  CPB1 MUTATED CPB1 WILD-TYPE 
         78.08         148.01 
  CPB1 MUTATED CPB1 WILD-TYPE 
        12.000         20.235 
[1] "0.7 - 78.1 (12.0)"  "0.0 - 148.0 (20.2)"
[1] "hr="     "9100000"
D2063V2, continuous
D2063V3, binary
                cls
clus               0   1
  CPB1 MUTATED     6   3
  CPB1 WILD-TYPE 360 116
[1] "tbl2"
                cls
clus             [,1] [,2]
  CPB1 MUTATED      6    3
  CPB1 WILD-TYPE  360  116
        clus
vv       CPB1 MUTATED CPB1 WILD-TYPE
  COLON             6            360
  RECTUM            3            116
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CPB1 MUTATED         1        0        2         1         0         0
  CPB1 WILD-TYPE      90        1       30       137        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CPB1 MUTATED           1          0          0          0        1         1
  CPB1 WILD-TYPE        23         11         59         42       47        17
                vv
clus             STAGE IVB
  CPB1 MUTATED           0
  CPB1 WILD-TYPE         1
D2063V4, multiclass
            clus
vv           CPB1 MUTATED CPB1 WILD-TYPE
  STAGE I               1             90
  STAGE IA              0              1
  STAGE II              2             30
  STAGE IIA             1            137
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             1             23
  STAGE IIIA            0             11
  STAGE IIIB            0             59
  STAGE IIIC            0             42
  STAGE IV              1             47
  STAGE IVA             1             17
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  CPB1 MUTATED     0   1   8   0
  CPB1 WILD-TYPE  17  91 321  50
D2063V5, multiclass
    clus
vv   CPB1 MUTATED CPB1 WILD-TYPE
  T1            0             17
  T2            1             91
  T3            8            321
  T4            0             50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  CPB1 MUTATED     5   2   1
  CPB1 WILD-TYPE 282 111  86
D2063V6, multiclass
    clus
vv   CPB1 MUTATED CPB1 WILD-TYPE
  N0            5            282
  N1            2            111
  N2            1             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2063V7, binary
                cls
clus               0   1
  CPB1 MUTATED     5   2
  CPB1 WILD-TYPE 370  63
[1] "tbl2"
                cls
clus             [,1] [,2]
  CPB1 MUTATED      5    2
  CPB1 WILD-TYPE  370   63
   clus
vv  CPB1 MUTATED CPB1 WILD-TYPE
  0            5            370
  1            2             63
[1] 2 2
[1] FALSE
D2063V8, binary
                cls
clus               0   1
  CPB1 MUTATED     1   8
  CPB1 WILD-TYPE 224 256
[1] "tbl2"
                cls
clus             [,1] [,2]
  CPB1 MUTATED      1    8
  CPB1 WILD-TYPE  224  256
        clus
vv       CPB1 MUTATED CPB1 WILD-TYPE
  FEMALE            1            224
  MALE              8            256
[1] 2 2
[1] FALSE
D2063V9, binary
                cls
clus               0   1
  CPB1 MUTATED     7   0
  CPB1 WILD-TYPE 343  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  CPB1 MUTATED      7    0
  CPB1 WILD-TYPE  343   22
     clus
vv    CPB1 MUTATED CPB1 WILD-TYPE
  NO             7            343
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CPB1 MUTATED                      6                             0
  CPB1 WILD-TYPE                  309                            47
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CPB1 MUTATED                       3                              0
  CPB1 WILD-TYPE                   103                             10
D2063V10, multiclass
                                clus
vv                               CPB1 MUTATED CPB1 WILD-TYPE
  COLON ADENOCARCINOMA                      6            309
  COLON MUCINOUS ADENOCARCINOMA             0             47
  RECTAL ADENOCARCINOMA                     3            103
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  CPB1 MUTATED     5   0   1   0
  CPB1 WILD-TYPE 340   4  30  25
D2063V11, multiclass
    clus
vv   CPB1 MUTATED CPB1 WILD-TYPE
  R0            5            340
  R1            0              4
  R2            1             30
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2063V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CPB1 MUTATED                                  0     0
  CPB1 WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  CPB1 MUTATED                           0     3
  CPB1 WILD-TYPE                        22   223
D2063V13, multiclass
                                  clus
vv                                 CPB1 MUTATED CPB1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       3            223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2064) Variable = PTPN1 MUTATION ANALYSIS
D2064V1, survival
                 sevent
clus2               0   1
  PTPN1 MUTATED     7   2
  PTPN1 WILD-TYPE 371  91
  PTPN1 MUTATED PTPN1 WILD-TYPE 
              9             462 
  PTPN1 MUTATED PTPN1 WILD-TYPE 
              2              91 
$`PTPN1 MUTATED`
TCGA-AA-3713 TCGA-AA-A00E TCGA-AA-A00K TCGA-AA-A01Q TCGA-AZ-6601 TCGA-AZ-6603 
       19.04        30.02        18.05         1.02       100.01        29.56 
TCGA-CA-6717 TCGA-CM-6674 TCGA-AG-A002 
       12.76        12.95        20.98 

$`PTPN1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00L TCGA-AA-A00N 
       38.04        19.00        34.03        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       31.00        38.07        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6605 
       62.79        88.21        49.41         6.77        12.10         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07        12.20        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       11.01        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  PTPN1 MUTATED PTPN1 WILD-TYPE 
           1.02            0.00 
  PTPN1 MUTATED PTPN1 WILD-TYPE 
         100.01          148.01 
  PTPN1 MUTATED PTPN1 WILD-TYPE 
         19.040          20.235 
[1] "1.0 - 100.0 (19.0)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.1"
D2064V2, continuous
D2064V3, binary
                 cls
clus                0   1
  PTPN1 MUTATED     9   1
  PTPN1 WILD-TYPE 357 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPN1 MUTATED      9    1
  PTPN1 WILD-TYPE  357  118
        clus
vv       PTPN1 MUTATED PTPN1 WILD-TYPE
  COLON              9             357
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PTPN1 MUTATED         1        0        2         5         0         0
  PTPN1 WILD-TYPE      90        1       30       133        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PTPN1 MUTATED           0          0          0          0        1         0
  PTPN1 WILD-TYPE        24         11         59         42       47        18
                 vv
clus              STAGE IVB
  PTPN1 MUTATED           0
  PTPN1 WILD-TYPE         1
D2064V4, multiclass
            clus
vv           PTPN1 MUTATED PTPN1 WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA              5             133
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             0              42
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PTPN1 MUTATED     0   2   8   0
  PTPN1 WILD-TYPE  17  90 321  50
D2064V5, multiclass
    clus
vv   PTPN1 MUTATED PTPN1 WILD-TYPE
  T1             0              17
  T2             2              90
  T3             8             321
  T4             0              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  PTPN1 MUTATED     9   1   0
  PTPN1 WILD-TYPE 278 112  87
D2064V6, multiclass
    clus
vv   PTPN1 MUTATED PTPN1 WILD-TYPE
  N0             9             278
  N1             1             112
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2064V7, binary
                 cls
clus                0   1
  PTPN1 MUTATED     8   1
  PTPN1 WILD-TYPE 367  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPN1 MUTATED      8    1
  PTPN1 WILD-TYPE  367   64
   clus
vv  PTPN1 MUTATED PTPN1 WILD-TYPE
  0             8             367
  1             1              64
[1] 2 2
[1] FALSE
D2064V8, binary
                 cls
clus                0   1
  PTPN1 MUTATED     3   7
  PTPN1 WILD-TYPE 222 257
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPN1 MUTATED      3    7
  PTPN1 WILD-TYPE  222  257
        clus
vv       PTPN1 MUTATED PTPN1 WILD-TYPE
  FEMALE             3             222
  MALE               7             257
[1] 2 2
[1] FALSE
D2064V9, binary
                 cls
clus                0   1
  PTPN1 MUTATED     6   1
  PTPN1 WILD-TYPE 344  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTPN1 MUTATED      6    1
  PTPN1 WILD-TYPE  344   21
     clus
vv    PTPN1 MUTATED PTPN1 WILD-TYPE
  NO              6             344
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PTPN1 MUTATED                      8                             1
  PTPN1 WILD-TYPE                  307                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PTPN1 MUTATED                       1                              0
  PTPN1 WILD-TYPE                   105                             10
D2064V10, multiclass
                                clus
vv                               PTPN1 MUTATED PTPN1 WILD-TYPE
  COLON ADENOCARCINOMA                       8             307
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  PTPN1 MUTATED     6   0   1   1
  PTPN1 WILD-TYPE 339   4  30  24
D2064V11, multiclass
    clus
vv   PTPN1 MUTATED PTPN1 WILD-TYPE
  R0             6             339
  R1             0               4
  R2             1              30
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2064V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PTPN1 MUTATED                                  0     1
  PTPN1 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PTPN1 MUTATED                           0     3
  PTPN1 WILD-TYPE                        22   223
D2064V13, multiclass
                                  clus
vv                                 PTPN1 MUTATED PTPN1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        3             223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2065) Variable = ZNF266 MUTATION ANALYSIS
D2065V1, survival
                  sevent
clus2                0   1
  ZNF266 MUTATED     5   3
  ZNF266 WILD-TYPE 373  90
  ZNF266 MUTATED ZNF266 WILD-TYPE 
               8              463 
  ZNF266 MUTATED ZNF266 WILD-TYPE 
               3               90 
$`ZNF266 MUTATED`
TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3544 TCGA-AA-3977 TCGA-AD-6899 TCGA-AZ-4315 
        3.02        63.98        14.01        25.02         5.79        58.39 
TCGA-AG-A002 TCGA-AG-A026 
       20.98         1.94 

$`ZNF266 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
       12.99         0.99        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        0.72        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       64.01        10.98        49.97        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  ZNF266 MUTATED ZNF266 WILD-TYPE 
            1.94             0.00 
  ZNF266 MUTATED ZNF266 WILD-TYPE 
           63.98           148.01 
  ZNF266 MUTATED ZNF266 WILD-TYPE 
          17.495           20.190 
[1] "1.9 - 64.0 (17.5)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.9"
D2065V2, continuous
D2065V3, binary
                  cls
clus                 0   1
  ZNF266 MUTATED     7   2
  ZNF266 WILD-TYPE 359 117
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF266 MUTATED      7    2
  ZNF266 WILD-TYPE  359  117
        clus
vv       ZNF266 MUTATED ZNF266 WILD-TYPE
  COLON               7              359
  RECTUM              2              117
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZNF266 MUTATED         2        0        3         2         0         0
  ZNF266 WILD-TYPE      89        1       29       136        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF266 MUTATED           0          0          0          1        0
  ZNF266 WILD-TYPE        24         11         59         41       48
                  vv
clus               STAGE IVA STAGE IVB
  ZNF266 MUTATED           0         0
  ZNF266 WILD-TYPE        18         1
D2065V4, multiclass
            clus
vv           ZNF266 MUTATED ZNF266 WILD-TYPE
  STAGE I                 2               89
  STAGE IA                0                1
  STAGE II                3               29
  STAGE IIA               2              136
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              0               59
  STAGE IIIC              1               41
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZNF266 MUTATED     0   3   4   2
  ZNF266 WILD-TYPE  17  89 325  48
D2065V5, multiclass
    clus
vv   ZNF266 MUTATED ZNF266 WILD-TYPE
  T1              0               17
  T2              3               89
  T3              4              325
  T4              2               48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  ZNF266 MUTATED     8   0   1
  ZNF266 WILD-TYPE 279 113  86
D2065V6, multiclass
    clus
vv   ZNF266 MUTATED ZNF266 WILD-TYPE
  N0              8              279
  N1              0              113
  N2              1               86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2065V7, binary
                  cls
clus                 0   1
  ZNF266 MUTATED     7   0
  ZNF266 WILD-TYPE 368  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF266 MUTATED      7    0
  ZNF266 WILD-TYPE  368   65
   clus
vv  ZNF266 MUTATED ZNF266 WILD-TYPE
  0              7              368
  1              0               65
[1] 2 2
[1] FALSE
D2065V8, binary
                  cls
clus                 0   1
  ZNF266 MUTATED     2   7
  ZNF266 WILD-TYPE 223 257
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF266 MUTATED      2    7
  ZNF266 WILD-TYPE  223  257
        clus
vv       ZNF266 MUTATED ZNF266 WILD-TYPE
  FEMALE              2              223
  MALE                7              257
[1] 2 2
[1] FALSE
D2065V9, binary
                  cls
clus                 0   1
  ZNF266 MUTATED     7   0
  ZNF266 WILD-TYPE 343  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF266 MUTATED      7    0
  ZNF266 WILD-TYPE  343   22
     clus
vv    ZNF266 MUTATED ZNF266 WILD-TYPE
  NO               7              343
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ZNF266 MUTATED                      6                             1
  ZNF266 WILD-TYPE                  309                            46
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ZNF266 MUTATED                       2                              0
  ZNF266 WILD-TYPE                   104                             10
D2065V10, multiclass
                                clus
vv                               ZNF266 MUTATED ZNF266 WILD-TYPE
  COLON ADENOCARCINOMA                        6              309
  COLON MUCINOUS ADENOCARCINOMA               1               46
  RECTAL ADENOCARCINOMA                       2              104
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ZNF266 MUTATED     6   1   0   0
  ZNF266 WILD-TYPE 339   3  31  25
D2065V11, multiclass
    clus
vv   ZNF266 MUTATED ZNF266 WILD-TYPE
  R0              6              339
  R1              1                3
  R2              0               31
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2065V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF266 MUTATED                                  0     0
  ZNF266 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZNF266 MUTATED                           0     2
  ZNF266 WILD-TYPE                        22   224
D2065V13, multiclass
[1] "Remove cluster labels:" "ZNF266 MUTATED"        
clus
  ZNF266 MUTATED ZNF266 WILD-TYPE 
               2              258 
      TCGA-A6-2671       TCGA-A6-2672       TCGA-A6-2674       TCGA-A6-2676 
"ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" 
      TCGA-A6-2677       TCGA-A6-2678       TCGA-A6-2683       TCGA-A6-3807 
"ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" 
      TCGA-A6-3808       TCGA-A6-3809       TCGA-A6-3810       TCGA-A6-4105 
"ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" 
      TCGA-A6-5656       TCGA-A6-5657       TCGA-A6-5659       TCGA-A6-5660 
"ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" 
      TCGA-A6-5661       TCGA-A6-5662       TCGA-A6-5664       TCGA-A6-5665 
"ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" 
      TCGA-A6-5666       TCGA-A6-6137       TCGA-A6-6138       TCGA-A6-6141 
"ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" 
      TCGA-A6-6142       TCGA-A6-6648       TCGA-A6-6649       TCGA-A6-6651 
"ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" 
      TCGA-A6-6652       TCGA-A6-6653       TCGA-A6-6654       TCGA-A6-6780 
"ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" 
      TCGA-A6-6781       TCGA-A6-6782       TCGA-AD-5900       TCGA-AD-6548 
"ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" 
      TCGA-AD-6888       TCGA-AD-6889       TCGA-AD-6890       TCGA-AD-6895 
"ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" 
      TCGA-AD-6901       TCGA-AD-6963       TCGA-AD-6964       TCGA-AD-6965 
"ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" 
      TCGA-AU-3779       TCGA-AU-6004       TCGA-AY-4070       TCGA-AY-4071 
"ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" 
      TCGA-AY-5543       TCGA-AY-6196       TCGA-AY-6197       TCGA-AY-6386 
"ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" 
      TCGA-AZ-4323       TCGA-AZ-4616       TCGA-AZ-4681       TCGA-AZ-4682 
"ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" 
      TCGA-AZ-5403       TCGA-AZ-5407       TCGA-AZ-6598       TCGA-AZ-6599 
"ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" 
      TCGA-AZ-6600       TCGA-AZ-6601       TCGA-AZ-6603       TCGA-AZ-6605 
"ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" 
      TCGA-AZ-6606       TCGA-AZ-6607       TCGA-AZ-6608       TCGA-CA-5254 
"ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" 
      TCGA-CA-5255       TCGA-CA-5796       TCGA-CA-5797       TCGA-CA-6715 
"ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" 
      TCGA-CA-6716       TCGA-CA-6717       TCGA-CA-6718       TCGA-CA-6719 
"ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" 
      TCGA-CK-4947       TCGA-CK-4948       TCGA-CK-4950       TCGA-CK-4952 
"ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" 
      TCGA-CK-5912       TCGA-CK-5913       TCGA-CK-5914       TCGA-CK-5915 
"ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" 
      TCGA-CK-5916       TCGA-CK-6746       TCGA-CK-6747       TCGA-CK-6748 
"ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" 
      TCGA-CK-6751       TCGA-CM-4743       TCGA-CM-4744       TCGA-CM-4746 
"ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" 
      TCGA-CM-4747       TCGA-CM-4752       TCGA-CM-5341       TCGA-CM-5344 
"ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" 
      TCGA-CM-5348       TCGA-CM-5349       TCGA-CM-5860       TCGA-CM-5861 
"ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" 
      TCGA-CM-5862       TCGA-CM-5863       TCGA-CM-5864       TCGA-CM-5868 
"ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" 
      TCGA-CM-6161       TCGA-CM-6162       TCGA-CM-6163       TCGA-CM-6164 
"ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" 
      TCGA-CM-6165       TCGA-CM-6166       TCGA-CM-6167       TCGA-CM-6168 
"ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" 
      TCGA-CM-6169       TCGA-CM-6170       TCGA-CM-6171       TCGA-CM-6172 
"ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" 
      TCGA-CM-6674       TCGA-CM-6675       TCGA-CM-6676       TCGA-CM-6677 
"ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" 
      TCGA-CM-6678       TCGA-CM-6679       TCGA-CM-6680       TCGA-D5-5537 
"ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" 
      TCGA-D5-5538       TCGA-D5-5539       TCGA-D5-5540       TCGA-D5-5541 
"ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" 
      TCGA-D5-6529       TCGA-D5-6532       TCGA-D5-6533       TCGA-D5-6534 
"ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" 
      TCGA-D5-6535       TCGA-D5-6536       TCGA-D5-6537       TCGA-D5-6538 
"ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" 
      TCGA-D5-6539       TCGA-D5-6540       TCGA-D5-6541       TCGA-D5-6898 
"ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" 
      TCGA-D5-6920       TCGA-D5-6922       TCGA-D5-6923       TCGA-D5-6924 
"ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" 
      TCGA-D5-6926       TCGA-D5-6927       TCGA-D5-6928       TCGA-D5-6929 
"ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" 
      TCGA-D5-6930       TCGA-D5-6931       TCGA-D5-6932       TCGA-D5-7000 
"ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" 
      TCGA-DM-A0X9       TCGA-DM-A0XD       TCGA-DM-A0XF       TCGA-DM-A1D0 
"ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" 
      TCGA-DM-A1D4       TCGA-DM-A1D6       TCGA-DM-A1D7       TCGA-DM-A1D8 
"ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" 
      TCGA-DM-A1D9       TCGA-DM-A1DA       TCGA-DM-A1DB       TCGA-DM-A1HA 
"ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" 
      TCGA-DM-A1HB       TCGA-DM-A282       TCGA-DM-A285       TCGA-DM-A28C 
"ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" 
      TCGA-DM-A28E       TCGA-DM-A28F       TCGA-DM-A28G       TCGA-DM-A28H 
"ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" 
      TCGA-DM-A28K       TCGA-F4-6459       TCGA-F4-6460       TCGA-F4-6569 
"ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" 
      TCGA-F4-6570       TCGA-F4-6703       TCGA-F4-6704       TCGA-F4-6805 
"ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" 
      TCGA-F4-6806       TCGA-F4-6807       TCGA-F4-6808       TCGA-F4-6809 
"ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" 
      TCGA-F4-6854       TCGA-F4-6855       TCGA-F4-6856       TCGA-G4-6293 
"ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" 
      TCGA-G4-6299       TCGA-G4-6303       TCGA-G4-6304       TCGA-G4-6306 
"ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" 
      TCGA-G4-6307       TCGA-G4-6309       TCGA-G4-6310       TCGA-G4-6315 
"ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" 
      TCGA-G4-6317       TCGA-G4-6321       TCGA-G4-6323       TCGA-G4-6586 
"ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" 
      TCGA-G4-6588       TCGA-G4-6625       TCGA-G4-6626       TCGA-G4-6628 
"ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" 
      TCGA-AF-2687       TCGA-AF-2689       TCGA-AF-2691       TCGA-AF-2692 
"ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" 
      TCGA-AF-2693       TCGA-AF-3400       TCGA-AF-3913       TCGA-AF-4110 
"ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" 
      TCGA-AF-5654       TCGA-AF-6136       TCGA-AF-6655       TCGA-AF-6672 
"ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" 
      TCGA-AH-6544       TCGA-AH-6547       TCGA-AH-6549       TCGA-AH-6643 
"ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" 
      TCGA-AH-6644       TCGA-CI-6619       TCGA-CI-6620       TCGA-CI-6621 
"ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" 
      TCGA-CI-6622       TCGA-CI-6624       TCGA-CL-5917       TCGA-CL-5918 
"ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" 
      TCGA-DC-5337       TCGA-DC-5869       TCGA-DC-6155       TCGA-DC-6157 
"ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" 
      TCGA-DC-6158       TCGA-DC-6160       TCGA-DC-6681       TCGA-DC-6682 
"ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" 
      TCGA-DC-6683       TCGA-DT-5265       TCGA-DY-A0XA       TCGA-DY-A1DC 
"ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" 
      TCGA-DY-A1DD       TCGA-DY-A1DF       TCGA-DY-A1DG       TCGA-DY-A1H8 
"ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" 
      TCGA-EF-5830       TCGA-EI-6506       TCGA-EI-6507       TCGA-EI-6508 
"ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" 
      TCGA-EI-6510       TCGA-F5-6464       TCGA-F5-6465       TCGA-F5-6571 
"ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" 
      TCGA-F5-6702       TCGA-F5-6811       TCGA-F5-6812       TCGA-F5-6813 
"ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" 
      TCGA-G5-6235       TCGA-G5-6641 
"ZNF266 WILD-TYPE" "ZNF266 WILD-TYPE" 

Clustering(2066) Variable = BHLHE41 MUTATION ANALYSIS
D2066V1, survival
                   sevent
clus2                 0   1
  BHLHE41 MUTATED     3   1
  BHLHE41 WILD-TYPE 375  92
  BHLHE41 MUTATED BHLHE41 WILD-TYPE 
                4               467 
  BHLHE41 MUTATED BHLHE41 WILD-TYPE 
                1                92 
$`BHLHE41 MUTATED`
TCGA-AA-3697 TCGA-CA-6718 TCGA-DM-A1HB TCGA-AG-3726 
       85.05        10.06       135.65         7.99 

$`BHLHE41 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       19.00        36.00         5.03        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07        12.20        12.76        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3727 
        0.99        15.95        19.99        13.94        19.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  BHLHE41 MUTATED BHLHE41 WILD-TYPE 
             7.99              0.00 
  BHLHE41 MUTATED BHLHE41 WILD-TYPE 
           135.65            148.01 
  BHLHE41 MUTATED BHLHE41 WILD-TYPE 
           47.555            20.190 
[1] "8.0 - 135.7 (47.6)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.5"
D2066V2, continuous
D2066V3, binary
                   cls
clus                  0   1
  BHLHE41 MUTATED     4   1
  BHLHE41 WILD-TYPE 362 118
[1] "tbl2"
                   cls
clus                [,1] [,2]
  BHLHE41 MUTATED      4    1
  BHLHE41 WILD-TYPE  362  118
        clus
vv       BHLHE41 MUTATED BHLHE41 WILD-TYPE
  COLON                4               362
  RECTUM               1               118
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  BHLHE41 MUTATED         2        0        0         1         0         0
  BHLHE41 WILD-TYPE      89        1       32       137        10         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  BHLHE41 MUTATED           1          0          1          0        0
  BHLHE41 WILD-TYPE        23         11         58         42       48
                   vv
clus                STAGE IVA STAGE IVB
  BHLHE41 MUTATED           0         0
  BHLHE41 WILD-TYPE        18         1
D2066V4, multiclass
            clus
vv           BHLHE41 MUTATED BHLHE41 WILD-TYPE
  STAGE I                  2                89
  STAGE IA                 0                 1
  STAGE II                 0                32
  STAGE IIA                1               137
  STAGE IIB                0                10
  STAGE IIC                0                 1
  STAGE III                1                23
  STAGE IIIA               0                11
  STAGE IIIB               1                58
  STAGE IIIC               0                42
  STAGE IV                 0                48
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  BHLHE41 MUTATED     0   2   3   0
  BHLHE41 WILD-TYPE  17  90 326  50
D2066V5, multiclass
    clus
vv   BHLHE41 MUTATED BHLHE41 WILD-TYPE
  T1               0                17
  T2               2                90
  T3               3               326
  T4               0                50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  BHLHE41 MUTATED     4   1   0
  BHLHE41 WILD-TYPE 283 112  87
D2066V6, multiclass
    clus
vv   BHLHE41 MUTATED BHLHE41 WILD-TYPE
  N0               4               283
  N1               1               112
  N2               0                87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2066V7, binary
                   cls
clus                  0   1
  BHLHE41 MUTATED     4   0
  BHLHE41 WILD-TYPE 371  65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  BHLHE41 MUTATED      4    0
  BHLHE41 WILD-TYPE  371   65
   clus
vv  BHLHE41 MUTATED BHLHE41 WILD-TYPE
  0               4               371
  1               0                65
[1] 2 2
[1] FALSE
D2066V8, binary
                   cls
clus                  0   1
  BHLHE41 MUTATED     1   4
  BHLHE41 WILD-TYPE 224 260
[1] "tbl2"
                   cls
clus                [,1] [,2]
  BHLHE41 MUTATED      1    4
  BHLHE41 WILD-TYPE  224  260
        clus
vv       BHLHE41 MUTATED BHLHE41 WILD-TYPE
  FEMALE               1               224
  MALE                 4               260
[1] 2 2
[1] FALSE
D2066V9, binary
                   cls
clus                  0   1
  BHLHE41 MUTATED     3   0
  BHLHE41 WILD-TYPE 347  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  BHLHE41 MUTATED      3    0
  BHLHE41 WILD-TYPE  347   22
     clus
vv    BHLHE41 MUTATED BHLHE41 WILD-TYPE
  NO                3               347
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  BHLHE41 MUTATED                      3                             0
  BHLHE41 WILD-TYPE                  312                            47
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  BHLHE41 MUTATED                       1                              0
  BHLHE41 WILD-TYPE                   105                             10
D2066V10, multiclass
                                clus
vv                               BHLHE41 MUTATED BHLHE41 WILD-TYPE
  COLON ADENOCARCINOMA                         3               312
  COLON MUCINOUS ADENOCARCINOMA                0                47
  RECTAL ADENOCARCINOMA                        1               105
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  BHLHE41 MUTATED     2   0   0   2
  BHLHE41 WILD-TYPE 343   4  31  23
D2066V11, multiclass
    clus
vv   BHLHE41 MUTATED BHLHE41 WILD-TYPE
  R0               2               343
  R1               0                 4
  R2               0                31
  RX               2                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2066V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  BHLHE41 MUTATED                                  0     1
  BHLHE41 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  BHLHE41 MUTATED                           0     2
  BHLHE41 WILD-TYPE                        22   224
D2066V13, multiclass
                                  clus
vv                                 BHLHE41 MUTATED BHLHE41 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                10
  BLACK OR AFRICAN AMERICAN                      0                22
  WHITE                                          2               224
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2067) Variable = ADAMTS16 MUTATION ANALYSIS
D2067V1, survival
                    sevent
clus2                  0   1
  ADAMTS16 MUTATED    23   9
  ADAMTS16 WILD-TYPE 355  84
  ADAMTS16 MUTATED ADAMTS16 WILD-TYPE 
                32                439 
  ADAMTS16 MUTATED ADAMTS16 WILD-TYPE 
                 9                 84 
$`ADAMTS16 MUTATED`
TCGA-A6-5666 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3815 TCGA-AA-3854 TCGA-AA-3939 
       32.71        35.01        63.98        33.04        36.03        12.99 
TCGA-AA-3955 TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01I TCGA-AY-4071 
       20.98        25.02         4.01        34.98        31.00         0.95 
TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-6600 TCGA-CA-6719 TCGA-CK-4952 TCGA-CK-5916 
       21.44        58.39        12.10        14.30        15.62        21.14 
TCGA-CM-4743 TCGA-CM-5348 TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6171 TCGA-D5-6537 
       23.05        22.98        12.00        16.04        14.04         4.80 
TCGA-DM-A28C TCGA-DM-A28H TCGA-G4-6303 TCGA-G4-6588 TCGA-G4-6628 TCGA-AG-A026 
       81.37       117.07        65.85        26.17        79.69         1.94 
TCGA-AG-A036 TCGA-DC-6158 
      117.11        10.98 

$`ADAMTS16 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        22.06        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
       33.07         0.00        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       18.05        31.00         2.01        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       24.00         2.01        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01K TCGA-AA-A01P 
        1.02        10.98        32.02        12.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
       27.09        16.31        33.01        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 
       12.76        10.06        17.56       148.01        85.45        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 
       51.32         9.99        82.95         1.91       124.27        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5349 
       37.02        25.02        13.02        29.06        22.03        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
       15.02         2.96        29.03        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       13.02        15.02        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       43.27        15.12        17.85        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28E 
       44.32       131.51       135.65       139.17         6.12       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       35.97        60.79        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       74.56        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 
       61.91        36.00        22.09        13.78        35.80        91.79 
TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       46.75        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A02G 
       12.00        70.03        64.01        10.98        49.97        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       61.97        41.00        38.04        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  ADAMTS16 MUTATED ADAMTS16 WILD-TYPE 
              0.95               0.00 
  ADAMTS16 MUTATED ADAMTS16 WILD-TYPE 
            117.11             148.01 
  ADAMTS16 MUTATED ADAMTS16 WILD-TYPE 
            23.015             20.020 
[1] "0.9 - 117.1 (23.0)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.2"
D2067V2, continuous
D2067V3, binary
                    cls
clus                   0   1
  ADAMTS16 MUTATED    29   3
  ADAMTS16 WILD-TYPE 337 116
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ADAMTS16 MUTATED     29    3
  ADAMTS16 WILD-TYPE  337  116
        clus
vv       ADAMTS16 MUTATED ADAMTS16 WILD-TYPE
  COLON                29                337
  RECTUM                3                116
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ADAMTS16 MUTATED         8        0        2        10         2         1
  ADAMTS16 WILD-TYPE      83        1       30       128         8         0
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ADAMTS16 MUTATED           1          0          4          2        2
  ADAMTS16 WILD-TYPE        23         11         55         40       46
                    vv
clus                 STAGE IVA STAGE IVB
  ADAMTS16 MUTATED           0         0
  ADAMTS16 WILD-TYPE        18         1
D2067V4, multiclass
            clus
vv           ADAMTS16 MUTATED ADAMTS16 WILD-TYPE
  STAGE I                   8                 83
  STAGE IA                  0                  1
  STAGE II                  2                 30
  STAGE IIA                10                128
  STAGE IIB                 2                  8
  STAGE IIC                 1                  0
  STAGE III                 1                 23
  STAGE IIIA                0                 11
  STAGE IIIB                4                 55
  STAGE IIIC                2                 40
  STAGE IV                  2                 46
  STAGE IVA                 0                 18
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  ADAMTS16 MUTATED     2   8  17   6
  ADAMTS16 WILD-TYPE  15  84 312  44
D2067V5, multiclass
    clus
vv   ADAMTS16 MUTATED ADAMTS16 WILD-TYPE
  T1                2                 15
  T2                8                 84
  T3               17                312
  T4                6                 44
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  ADAMTS16 MUTATED    24   5   4
  ADAMTS16 WILD-TYPE 263 108  83
D2067V6, multiclass
    clus
vv   ADAMTS16 MUTATED ADAMTS16 WILD-TYPE
  N0               24                263
  N1                5                108
  N2                4                 83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2067V7, binary
                    cls
clus                   0   1
  ADAMTS16 MUTATED    27   2
  ADAMTS16 WILD-TYPE 348  63
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ADAMTS16 MUTATED     27    2
  ADAMTS16 WILD-TYPE  348   63
   clus
vv  ADAMTS16 MUTATED ADAMTS16 WILD-TYPE
  0               27                348
  1                2                 63
[1] 2 2
[1] FALSE
D2067V8, binary
                    cls
clus                   0   1
  ADAMTS16 MUTATED    11  22
  ADAMTS16 WILD-TYPE 214 242
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ADAMTS16 MUTATED     11   22
  ADAMTS16 WILD-TYPE  214  242
        clus
vv       ADAMTS16 MUTATED ADAMTS16 WILD-TYPE
  FEMALE               11                214
  MALE                 22                242
[1] 2 2
[1] FALSE
D2067V9, binary
                    cls
clus                   0   1
  ADAMTS16 MUTATED    25   1
  ADAMTS16 WILD-TYPE 325  21
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ADAMTS16 MUTATED     25    1
  ADAMTS16 WILD-TYPE  325   21
     clus
vv    ADAMTS16 MUTATED ADAMTS16 WILD-TYPE
  NO                25                325
  YES                1                 21
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ADAMTS16 MUTATED                     25                             4
  ADAMTS16 WILD-TYPE                  290                            43
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ADAMTS16 MUTATED                       3                              0
  ADAMTS16 WILD-TYPE                   103                             10
D2067V10, multiclass
                                clus
vv                               ADAMTS16 MUTATED ADAMTS16 WILD-TYPE
  COLON ADENOCARCINOMA                         25                290
  COLON MUCINOUS ADENOCARCINOMA                 4                 43
  RECTAL ADENOCARCINOMA                         3                103
  RECTAL MUCINOUS ADENOCARCINOMA                0                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  ADAMTS16 MUTATED    24   1   0   3
  ADAMTS16 WILD-TYPE 321   3  31  22
D2067V11, multiclass
    clus
vv   ADAMTS16 MUTATED ADAMTS16 WILD-TYPE
  R0               24                321
  R1                1                  3
  R2                0                 31
  RX                3                 22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2067V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ADAMTS16 MUTATED                                  0     1
  ADAMTS16 WILD-TYPE                                1    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  ADAMTS16 MUTATED                           1    18
  ADAMTS16 WILD-TYPE                        21   208
D2067V13, multiclass
                                  clus
vv                                 ADAMTS16 MUTATED ADAMTS16 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                 10
  BLACK OR AFRICAN AMERICAN                       1                 21
  WHITE                                          18                208
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2068) Variable = MCM9 MUTATION ANALYSIS
D2068V1, survival
                sevent
clus2              0   1
  MCM9 MUTATED     8   1
  MCM9 WILD-TYPE 370  92
  MCM9 MUTATED MCM9 WILD-TYPE 
             9            462 
  MCM9 MUTATED MCM9 WILD-TYPE 
             1             92 
$`MCM9 MUTATED`
TCGA-AA-3510 TCGA-AA-3662 TCGA-AA-3864 TCGA-AA-A010 TCGA-AZ-5403 TCGA-CA-6717 
       63.98         6.05        53.00        34.98        62.79        12.76 
TCGA-D5-6541 TCGA-AG-3885 TCGA-AG-3892 
       15.58        17.95        13.02 

$`MCM9 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       19.99        13.94        19.99        61.02        78.08         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 
        0.99        31.07        31.07        30.05        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07        12.20        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 
        0.99        19.04        19.99         1.02        36.95        17.03 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  MCM9 MUTATED MCM9 WILD-TYPE 
          6.05           0.00 
  MCM9 MUTATED MCM9 WILD-TYPE 
         63.98         148.01 
  MCM9 MUTATED MCM9 WILD-TYPE 
        17.950         20.235 
[1] "6.0 - 64.0 (17.9)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "2.3"
D2068V2, continuous
D2068V3, binary
                cls
clus               0   1
  MCM9 MUTATED     7   2
  MCM9 WILD-TYPE 359 117
[1] "tbl2"
                cls
clus             [,1] [,2]
  MCM9 MUTATED      7    2
  MCM9 WILD-TYPE  359  117
        clus
vv       MCM9 MUTATED MCM9 WILD-TYPE
  COLON             7            359
  RECTUM            2            117
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MCM9 MUTATED         1        0        3         2         1         0
  MCM9 WILD-TYPE      90        1       29       136         9         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MCM9 MUTATED           0          0          1          0        1         0
  MCM9 WILD-TYPE        24         11         58         42       47        18
                vv
clus             STAGE IVB
  MCM9 MUTATED           0
  MCM9 WILD-TYPE         1
D2068V4, multiclass
            clus
vv           MCM9 MUTATED MCM9 WILD-TYPE
  STAGE I               1             90
  STAGE IA              0              1
  STAGE II              3             29
  STAGE IIA             2            136
  STAGE IIB             1              9
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            1             58
  STAGE IIIC            0             42
  STAGE IV              1             47
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  MCM9 MUTATED     1   0   6   2
  MCM9 WILD-TYPE  16  92 323  48
D2068V5, multiclass
    clus
vv   MCM9 MUTATED MCM9 WILD-TYPE
  T1            1             16
  T2            0             92
  T3            6            323
  T4            2             48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  MCM9 MUTATED     7   1   1
  MCM9 WILD-TYPE 280 112  86
D2068V6, multiclass
    clus
vv   MCM9 MUTATED MCM9 WILD-TYPE
  N0            7            280
  N1            1            112
  N2            1             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2068V7, binary
                cls
clus               0   1
  MCM9 MUTATED     7   1
  MCM9 WILD-TYPE 368  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  MCM9 MUTATED      7    1
  MCM9 WILD-TYPE  368   64
   clus
vv  MCM9 MUTATED MCM9 WILD-TYPE
  0            7            368
  1            1             64
[1] 2 2
[1] FALSE
D2068V8, binary
                cls
clus               0   1
  MCM9 MUTATED     4   5
  MCM9 WILD-TYPE 221 259
[1] "tbl2"
                cls
clus             [,1] [,2]
  MCM9 MUTATED      4    5
  MCM9 WILD-TYPE  221  259
        clus
vv       MCM9 MUTATED MCM9 WILD-TYPE
  FEMALE            4            221
  MALE              5            259
[1] 2 2
[1] FALSE
D2068V9, binary
                cls
clus               0   1
  MCM9 MUTATED     8   1
  MCM9 WILD-TYPE 342  21
[1] "tbl2"
                cls
clus             [,1] [,2]
  MCM9 MUTATED      8    1
  MCM9 WILD-TYPE  342   21
     clus
vv    MCM9 MUTATED MCM9 WILD-TYPE
  NO             8            342
  YES            1             21
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MCM9 MUTATED                      6                             1
  MCM9 WILD-TYPE                  309                            46
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MCM9 MUTATED                       2                              0
  MCM9 WILD-TYPE                   104                             10
D2068V10, multiclass
                                clus
vv                               MCM9 MUTATED MCM9 WILD-TYPE
  COLON ADENOCARCINOMA                      6            309
  COLON MUCINOUS ADENOCARCINOMA             1             46
  RECTAL ADENOCARCINOMA                     2            104
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  MCM9 MUTATED     6   0   1   1
  MCM9 WILD-TYPE 339   4  30  24
D2068V11, multiclass
    clus
vv   MCM9 MUTATED MCM9 WILD-TYPE
  R0            6            339
  R1            0              4
  R2            1             30
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2068V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MCM9 MUTATED                                  0     1
  MCM9 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  MCM9 MUTATED                           0     2
  MCM9 WILD-TYPE                        22   224
D2068V13, multiclass
                                  clus
vv                                 MCM9 MUTATED MCM9 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       2            224
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2069) Variable = NSF MUTATION ANALYSIS
D2069V1, survival
               sevent
clus2             0   1
  NSF MUTATED     4   0
  NSF WILD-TYPE 374  93
  NSF MUTATED NSF WILD-TYPE 
            4           467 
  NSF MUTATED NSF WILD-TYPE 
            0            93 
$`NSF MUTATED`
TCGA-AA-A01R TCGA-CA-5255 TCGA-CM-6676 TCGA-D5-6930 
       35.01         3.06        11.08         1.51 

$`NSF WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        3.19         1.61        12.69         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       12.95        13.05        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        4.80        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  NSF MUTATED NSF WILD-TYPE 
         1.51          0.00 
  NSF MUTATED NSF WILD-TYPE 
        35.01        148.01 
  NSF MUTATED NSF WILD-TYPE 
         7.07         20.28 
[1] "1.5 - 35.0 (7.1)"   "0.0 - 148.0 (20.3)"
[1] "hr="     "3300000"
D2069V2, continuous
D2069V3, binary
               cls
clus              0   1
  NSF MUTATED     4   0
  NSF WILD-TYPE 362 119
[1] "tbl2"
               cls
clus            [,1] [,2]
  NSF MUTATED      4    0
  NSF WILD-TYPE  362  119
        clus
vv       NSF MUTATED NSF WILD-TYPE
  COLON            4           362
  RECTUM           0           119
[1] 2 2
[1] FALSE
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NSF MUTATED         1        0        0         2         0         0
  NSF WILD-TYPE      90        1       32       136        10         1
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NSF MUTATED           1          0          0          0        0         0
  NSF WILD-TYPE        23         11         59         42       48        18
               vv
clus            STAGE IVB
  NSF MUTATED           0
  NSF WILD-TYPE         1
D2069V4, multiclass
            clus
vv           NSF MUTATED NSF WILD-TYPE
  STAGE I              1            90
  STAGE IA             0             1
  STAGE II             0            32
  STAGE IIA            2           136
  STAGE IIB            0            10
  STAGE IIC            0             1
  STAGE III            1            23
  STAGE IIIA           0            11
  STAGE IIIB           0            59
  STAGE IIIC           0            42
  STAGE IV             0            48
  STAGE IVA            0            18
  STAGE IVB            0             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  NSF MUTATED     0   1   3   0
  NSF WILD-TYPE  17  91 326  50
D2069V5, multiclass
    clus
vv   NSF MUTATED NSF WILD-TYPE
  T1           0            17
  T2           1            91
  T3           3           326
  T4           0            50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2
  NSF MUTATED     3   0   1
  NSF WILD-TYPE 284 113  86
D2069V6, multiclass
    clus
vv   NSF MUTATED NSF WILD-TYPE
  N0           3           284
  N1           0           113
  N2           1            86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2069V7, binary
               cls
clus              0   1
  NSF MUTATED     4   0
  NSF WILD-TYPE 371  65
[1] "tbl2"
               cls
clus            [,1] [,2]
  NSF MUTATED      4    0
  NSF WILD-TYPE  371   65
   clus
vv  NSF MUTATED NSF WILD-TYPE
  0           4           371
  1           0            65
[1] 2 2
[1] FALSE
D2069V8, binary
               cls
clus              0   1
  NSF MUTATED     0   4
  NSF WILD-TYPE 225 260
[1] "tbl2"
               cls
clus            [,1] [,2]
  NSF MUTATED      0    4
  NSF WILD-TYPE  225  260
        clus
vv       NSF MUTATED NSF WILD-TYPE
  FEMALE           0           225
  MALE             4           260
[1] 2 2
[1] FALSE
D2069V9, binary
               cls
clus              0   1
  NSF MUTATED     1   2
  NSF WILD-TYPE 349  20
[1] "tbl2"
               cls
clus            [,1] [,2]
  NSF MUTATED      1    2
  NSF WILD-TYPE  349   20
     clus
vv    NSF MUTATED NSF WILD-TYPE
  NO            1           349
  YES           2            20
[1] 2 2
[1] FALSE
               vv
clus            COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  NSF MUTATED                      2                             2
  NSF WILD-TYPE                  313                            45
               vv
clus            RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  NSF MUTATED                       0                              0
  NSF WILD-TYPE                   106                             10
D2069V10, multiclass
                                clus
vv                               NSF MUTATED NSF WILD-TYPE
  COLON ADENOCARCINOMA                     2           313
  COLON MUCINOUS ADENOCARCINOMA            2            45
  RECTAL ADENOCARCINOMA                    0           106
  RECTAL MUCINOUS ADENOCARCINOMA           0            10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             R0  R1  R2  RX
  NSF MUTATED     3   0   0   1
  NSF WILD-TYPE 342   4  31  24
D2069V11, multiclass
    clus
vv   NSF MUTATED NSF WILD-TYPE
  R0           3           342
  R1           0             4
  R2           0            31
  RX           1            24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2069V12, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NSF MUTATED                                  0     1
  NSF WILD-TYPE                                1    10
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  NSF MUTATED                           0     2
  NSF WILD-TYPE                        22   224
D2069V13, multiclass
                                  clus
vv                                 NSF MUTATED NSF WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      1            10
  BLACK OR AFRICAN AMERICAN                  0            22
  WHITE                                      2           224
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2070) Variable = SAMD11 MUTATION ANALYSIS
D2070V1, survival
                  sevent
clus2                0   1
  SAMD11 MUTATED     5   1
  SAMD11 WILD-TYPE 373  92
  SAMD11 MUTATED SAMD11 WILD-TYPE 
               6              465 
  SAMD11 MUTATED SAMD11 WILD-TYPE 
               1               92 
$`SAMD11 MUTATED`
TCGA-AA-3516 TCGA-AA-3947 TCGA-AD-6889 TCGA-CM-5348 TCGA-D5-5541 TCGA-D5-6928 
       13.02        33.01        56.55        22.98        55.92        11.64 

$`SAMD11 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        1.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
        2.01        12.99        24.00        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       13.02        29.06        22.03        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       12.26        19.59        56.09        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
       14.30         9.04         9.44         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  SAMD11 MUTATED SAMD11 WILD-TYPE 
           11.64             0.00 
  SAMD11 MUTATED SAMD11 WILD-TYPE 
           56.55           148.01 
  SAMD11 MUTATED SAMD11 WILD-TYPE 
          27.995           20.120 
[1] "11.6 - 56.5 (28.0)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.5"
D2070V2, continuous
D2070V3, binary
                  cls
clus                 0   1
  SAMD11 MUTATED     6   0
  SAMD11 WILD-TYPE 360 119
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SAMD11 MUTATED      6    0
  SAMD11 WILD-TYPE  360  119
        clus
vv       SAMD11 MUTATED SAMD11 WILD-TYPE
  COLON               6              360
  RECTUM              0              119
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SAMD11 MUTATED         0        0        0         2         1         0
  SAMD11 WILD-TYPE      91        1       32       136         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SAMD11 MUTATED           1          0          2          0        0
  SAMD11 WILD-TYPE        23         11         57         42       48
                  vv
clus               STAGE IVA STAGE IVB
  SAMD11 MUTATED           0         0
  SAMD11 WILD-TYPE        18         1
D2070V4, multiclass
            clus
vv           SAMD11 MUTATED SAMD11 WILD-TYPE
  STAGE I                 0               91
  STAGE IA                0                1
  STAGE II                0               32
  STAGE IIA               2              136
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               1               23
  STAGE IIIA              0               11
  STAGE IIIB              2               57
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  SAMD11 MUTATED     0   0   5   1
  SAMD11 WILD-TYPE  17  92 324  49
D2070V5, multiclass
    clus
vv   SAMD11 MUTATED SAMD11 WILD-TYPE
  T1              0               17
  T2              0               92
  T3              5              324
  T4              1               49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  SAMD11 MUTATED     3   2   1
  SAMD11 WILD-TYPE 284 111  86
D2070V6, multiclass
    clus
vv   SAMD11 MUTATED SAMD11 WILD-TYPE
  N0              3              284
  N1              2              111
  N2              1               86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2070V7, binary
                  cls
clus                 0   1
  SAMD11 MUTATED     6   0
  SAMD11 WILD-TYPE 369  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SAMD11 MUTATED      6    0
  SAMD11 WILD-TYPE  369   65
   clus
vv  SAMD11 MUTATED SAMD11 WILD-TYPE
  0              6              369
  1              0               65
[1] 2 2
[1] FALSE
D2070V8, binary
                  cls
clus                 0   1
  SAMD11 MUTATED     2   4
  SAMD11 WILD-TYPE 223 260
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SAMD11 MUTATED      2    4
  SAMD11 WILD-TYPE  223  260
        clus
vv       SAMD11 MUTATED SAMD11 WILD-TYPE
  FEMALE              2              223
  MALE                4              260
[1] 2 2
[1] FALSE
D2070V9, binary
                  cls
clus                 0   1
  SAMD11 MUTATED     5   0
  SAMD11 WILD-TYPE 345  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SAMD11 MUTATED      5    0
  SAMD11 WILD-TYPE  345   22
     clus
vv    SAMD11 MUTATED SAMD11 WILD-TYPE
  NO               5              345
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SAMD11 MUTATED                      3                             3
  SAMD11 WILD-TYPE                  312                            44
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SAMD11 MUTATED                       0                              0
  SAMD11 WILD-TYPE                   106                             10
D2070V10, multiclass
                                clus
vv                               SAMD11 MUTATED SAMD11 WILD-TYPE
  COLON ADENOCARCINOMA                        3              312
  COLON MUCINOUS ADENOCARCINOMA               3               44
  RECTAL ADENOCARCINOMA                       0              106
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  SAMD11 MUTATED     4   0   0   0
  SAMD11 WILD-TYPE 341   4  31  25
D2070V11, multiclass
    clus
vv   SAMD11 MUTATED SAMD11 WILD-TYPE
  R0              4              341
  R1              0                4
  R2              0               31
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2070V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SAMD11 MUTATED                                  0     1
  SAMD11 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  SAMD11 MUTATED                           0     3
  SAMD11 WILD-TYPE                        22   223
D2070V13, multiclass
                                  clus
vv                                 SAMD11 MUTATED SAMD11 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         3              223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2071) Variable = MMP19 MUTATION ANALYSIS
D2071V1, survival
                 sevent
clus2               0   1
  MMP19 MUTATED    11   1
  MMP19 WILD-TYPE 367  92
  MMP19 MUTATED MMP19 WILD-TYPE 
             12             459 
  MMP19 MUTATED MMP19 WILD-TYPE 
              1              92 
$`MMP19 MUTATED`
TCGA-A6-6648 TCGA-A6-6653 TCGA-AA-3518 TCGA-AA-3815 TCGA-AA-3854 TCGA-AA-3956 
       25.18        24.39         1.02        33.04        36.03        34.03 
TCGA-AA-A00E TCGA-AA-A01R TCGA-AZ-4315 TCGA-F4-6570 TCGA-AG-A002 TCGA-DC-5337 
       30.02        35.01        58.39         6.18        20.98        15.02 

$`MMP19 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 
       25.08        24.16        21.76        24.69        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3519 
       63.98         6.97         1.02        13.02        38.99         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
       33.07         0.00        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3966 TCGA-AA-3968 
       26.01        24.00         2.01        20.98         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       13.94        38.04        19.00        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S 
       12.00        31.00        31.00        38.07         1.02         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       33.01        21.44        17.82         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 
      117.07        98.24         8.61        31.96        35.74        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5869 TCGA-DC-6155 
        6.97         4.73        78.12         7.17         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  MMP19 MUTATED MMP19 WILD-TYPE 
           1.02            0.00 
  MMP19 MUTATED MMP19 WILD-TYPE 
          58.39          148.01 
  MMP19 MUTATED MMP19 WILD-TYPE 
          27.60           20.02 
[1] "1.0 - 58.4 (27.6)"  "0.0 - 148.0 (20.0)"
[1] "hr=" "2.3"
D2071V2, continuous
D2071V3, binary
                 cls
clus                0   1
  MMP19 MUTATED    10   2
  MMP19 WILD-TYPE 356 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MMP19 MUTATED     10    2
  MMP19 WILD-TYPE  356  117
        clus
vv       MMP19 MUTATED MMP19 WILD-TYPE
  COLON             10             356
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MMP19 MUTATED         4        0        0         6         0         0
  MMP19 WILD-TYPE      87        1       32       132        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MMP19 MUTATED           1          0          0          0        0         1
  MMP19 WILD-TYPE        23         11         59         42       48        17
                 vv
clus              STAGE IVB
  MMP19 MUTATED           0
  MMP19 WILD-TYPE         1
D2071V4, multiclass
            clus
vv           MMP19 MUTATED MMP19 WILD-TYPE
  STAGE I                4              87
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              6             132
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  MMP19 MUTATED     1   3   8   0
  MMP19 WILD-TYPE  16  89 321  50
D2071V5, multiclass
    clus
vv   MMP19 MUTATED MMP19 WILD-TYPE
  T1             1              16
  T2             3              89
  T3             8             321
  T4             0              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  MMP19 MUTATED    11   0   1
  MMP19 WILD-TYPE 276 113  86
D2071V6, multiclass
    clus
vv   MMP19 MUTATED MMP19 WILD-TYPE
  N0            11             276
  N1             0             113
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2071V7, binary
                 cls
clus                0   1
  MMP19 MUTATED    11   1
  MMP19 WILD-TYPE 364  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MMP19 MUTATED     11    1
  MMP19 WILD-TYPE  364   64
   clus
vv  MMP19 MUTATED MMP19 WILD-TYPE
  0            11             364
  1             1              64
[1] 2 2
[1] FALSE
D2071V8, binary
                 cls
clus                0   1
  MMP19 MUTATED     4   8
  MMP19 WILD-TYPE 221 256
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MMP19 MUTATED      4    8
  MMP19 WILD-TYPE  221  256
        clus
vv       MMP19 MUTATED MMP19 WILD-TYPE
  FEMALE             4             221
  MALE               8             256
[1] 2 2
[1] FALSE
D2071V9, binary
                 cls
clus                0   1
  MMP19 MUTATED    10   1
  MMP19 WILD-TYPE 340  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MMP19 MUTATED     10    1
  MMP19 WILD-TYPE  340   21
     clus
vv    MMP19 MUTATED MMP19 WILD-TYPE
  NO             10             340
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MMP19 MUTATED                      8                             2
  MMP19 WILD-TYPE                  307                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MMP19 MUTATED                       2                              0
  MMP19 WILD-TYPE                   104                             10
D2071V10, multiclass
                                clus
vv                               MMP19 MUTATED MMP19 WILD-TYPE
  COLON ADENOCARCINOMA                       8             307
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  MMP19 MUTATED    10   0   0   0
  MMP19 WILD-TYPE 335   4  31  25
D2071V11, multiclass
    clus
vv   MMP19 MUTATED MMP19 WILD-TYPE
  R0            10             335
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2071V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MMP19 MUTATED                                  0     0
  MMP19 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  MMP19 MUTATED                           0     5
  MMP19 WILD-TYPE                        22   221
D2071V13, multiclass
                                  clus
vv                                 MMP19 MUTATED MMP19 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        5             221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2072) Variable = ATG10 MUTATION ANALYSIS
D2072V1, survival
                 sevent
clus2               0   1
  ATG10 MUTATED     5   0
  ATG10 WILD-TYPE 373  93
  ATG10 MUTATED ATG10 WILD-TYPE 
              5             466 
  ATG10 MUTATED ATG10 WILD-TYPE 
              0              93 
$`ATG10 MUTATED`
TCGA-AA-3950 TCGA-AA-A010 TCGA-CM-5861 TCGA-D5-6927 TCGA-EI-6507 
       24.00        34.98        15.02         9.44        19.96 

$`ATG10 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       32.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6929 
        4.41        12.43        14.30         9.04        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6508 
       24.13        51.48        32.61         0.49        20.55        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  ATG10 MUTATED ATG10 WILD-TYPE 
           9.44            0.00 
  ATG10 MUTATED ATG10 WILD-TYPE 
          34.98          148.01 
  ATG10 MUTATED ATG10 WILD-TYPE 
         19.960          20.235 
[1] "9.4 - 35.0 (20.0)"  "0.0 - 148.0 (20.2)"
[1] "hr="     "3300000"
D2072V2, continuous
D2072V3, binary
                 cls
clus                0   1
  ATG10 MUTATED     4   1
  ATG10 WILD-TYPE 362 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ATG10 MUTATED      4    1
  ATG10 WILD-TYPE  362  118
        clus
vv       ATG10 MUTATED ATG10 WILD-TYPE
  COLON              4             362
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ATG10 MUTATED         0        0        0         4         1         0
  ATG10 WILD-TYPE      91        1       32       134         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ATG10 MUTATED           0          0          0          0        0         0
  ATG10 WILD-TYPE        24         11         59         42       48        18
                 vv
clus              STAGE IVB
  ATG10 MUTATED           0
  ATG10 WILD-TYPE         1
D2072V4, multiclass
            clus
vv           ATG10 MUTATED ATG10 WILD-TYPE
  STAGE I                0              91
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              4             134
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ATG10 MUTATED     0   0   4   1
  ATG10 WILD-TYPE  17  92 325  49
D2072V5, multiclass
    clus
vv   ATG10 MUTATED ATG10 WILD-TYPE
  T1             0              17
  T2             0              92
  T3             4             325
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  ATG10 MUTATED     5   0   0
  ATG10 WILD-TYPE 282 113  87
D2072V6, multiclass
    clus
vv   ATG10 MUTATED ATG10 WILD-TYPE
  N0             5             282
  N1             0             113
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2072V7, binary
                 cls
clus                0   1
  ATG10 MUTATED     5   0
  ATG10 WILD-TYPE 370  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ATG10 MUTATED      5    0
  ATG10 WILD-TYPE  370   65
   clus
vv  ATG10 MUTATED ATG10 WILD-TYPE
  0             5             370
  1             0              65
[1] 2 2
[1] FALSE
D2072V8, binary
                 cls
clus                0   1
  ATG10 MUTATED     3   2
  ATG10 WILD-TYPE 222 262
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ATG10 MUTATED      3    2
  ATG10 WILD-TYPE  222  262
        clus
vv       ATG10 MUTATED ATG10 WILD-TYPE
  FEMALE             3             222
  MALE               2             262
[1] 2 2
[1] FALSE
D2072V9, binary
                 cls
clus                0   1
  ATG10 MUTATED     5   0
  ATG10 WILD-TYPE 345  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ATG10 MUTATED      5    0
  ATG10 WILD-TYPE  345   22
     clus
vv    ATG10 MUTATED ATG10 WILD-TYPE
  NO              5             345
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ATG10 MUTATED                      3                             1
  ATG10 WILD-TYPE                  312                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ATG10 MUTATED                       1                              0
  ATG10 WILD-TYPE                   105                             10
D2072V10, multiclass
                                clus
vv                               ATG10 MUTATED ATG10 WILD-TYPE
  COLON ADENOCARCINOMA                       3             312
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  ATG10 MUTATED     5   0   0   0
  ATG10 WILD-TYPE 340   4  31  25
D2072V11, multiclass
    clus
vv   ATG10 MUTATED ATG10 WILD-TYPE
  R0             5             340
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2072V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ATG10 MUTATED                                  0     0
  ATG10 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ATG10 MUTATED                           0     3
  ATG10 WILD-TYPE                        22   223
D2072V13, multiclass
                                  clus
vv                                 ATG10 MUTATED ATG10 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        3             223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2073) Variable = TMSB15B MUTATION ANALYSIS
D2073V1, survival
                   sevent
clus2                 0   1
  TMSB15B MUTATED     2   2
  TMSB15B WILD-TYPE 376  91
  TMSB15B MUTATED TMSB15B WILD-TYPE 
                4               467 
  TMSB15B MUTATED TMSB15B WILD-TYPE 
                2                91 
$`TMSB15B MUTATED`
TCGA-D5-6540 TCGA-DM-A285 TCGA-F4-6459 TCGA-G5-6235 
       16.14         6.12         8.61        55.76 

$`TMSB15B WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 
       15.12        17.85         4.80        17.13        12.49        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      131.51       135.65       139.17        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
       60.79       117.07        98.24        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        26.43 

  TMSB15B MUTATED TMSB15B WILD-TYPE 
             6.12              0.00 
  TMSB15B MUTATED TMSB15B WILD-TYPE 
            55.76            148.01 
  TMSB15B MUTATED TMSB15B WILD-TYPE 
           12.375            20.280 
[1] "6.1 - 55.8 (12.4)"  "0.0 - 148.0 (20.3)"
[1] "hr=" "2.8"
D2073V2, continuous
D2073V3, binary
                   cls
clus                  0   1
  TMSB15B MUTATED     3   1
  TMSB15B WILD-TYPE 363 118
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMSB15B MUTATED      3    1
  TMSB15B WILD-TYPE  363  118
        clus
vv       TMSB15B MUTATED TMSB15B WILD-TYPE
  COLON                3               363
  RECTUM               1               118
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TMSB15B MUTATED         1        0        0         0         0         0
  TMSB15B WILD-TYPE      90        1       32       138        10         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TMSB15B MUTATED           0          0          2          0        1
  TMSB15B WILD-TYPE        24         11         57         42       47
                   vv
clus                STAGE IVA STAGE IVB
  TMSB15B MUTATED           0         0
  TMSB15B WILD-TYPE        18         1
D2073V4, multiclass
            clus
vv           TMSB15B MUTATED TMSB15B WILD-TYPE
  STAGE I                  1                90
  STAGE IA                 0                 1
  STAGE II                 0                32
  STAGE IIA                0               138
  STAGE IIB                0                10
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               0                11
  STAGE IIIB               2                57
  STAGE IIIC               0                42
  STAGE IV                 1                47
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  TMSB15B MUTATED     0   1   3   0
  TMSB15B WILD-TYPE  17  91 326  50
D2073V5, multiclass
    clus
vv   TMSB15B MUTATED TMSB15B WILD-TYPE
  T1               0                17
  T2               1                91
  T3               3               326
  T4               0                50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  TMSB15B MUTATED     1   1   2
  TMSB15B WILD-TYPE 286 112  85
D2073V6, multiclass
    clus
vv   TMSB15B MUTATED TMSB15B WILD-TYPE
  N0               1               286
  N1               1               112
  N2               2                85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2073V7, binary
                   cls
clus                  0   1
  TMSB15B MUTATED     2   1
  TMSB15B WILD-TYPE 373  64
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMSB15B MUTATED      2    1
  TMSB15B WILD-TYPE  373   64
   clus
vv  TMSB15B MUTATED TMSB15B WILD-TYPE
  0               2               373
  1               1                64
[1] 2 2
[1] FALSE
D2073V8, binary
                   cls
clus                  0   1
  TMSB15B MUTATED     2   2
  TMSB15B WILD-TYPE 223 262
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMSB15B MUTATED      2    2
  TMSB15B WILD-TYPE  223  262
        clus
vv       TMSB15B MUTATED TMSB15B WILD-TYPE
  FEMALE               2               223
  MALE                 2               262
[1] 2 2
[1] FALSE
D2073V9, binary
                   cls
clus                  0   1
  TMSB15B MUTATED     3   0
  TMSB15B WILD-TYPE 347  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TMSB15B MUTATED      3    0
  TMSB15B WILD-TYPE  347   22
     clus
vv    TMSB15B MUTATED TMSB15B WILD-TYPE
  NO                3               347
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  TMSB15B MUTATED                      1                             2
  TMSB15B WILD-TYPE                  314                            45
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  TMSB15B MUTATED                       1                              0
  TMSB15B WILD-TYPE                   105                             10
D2073V10, multiclass
                                clus
vv                               TMSB15B MUTATED TMSB15B WILD-TYPE
  COLON ADENOCARCINOMA                         1               314
  COLON MUCINOUS ADENOCARCINOMA                2                45
  RECTAL ADENOCARCINOMA                        1               105
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  TMSB15B MUTATED     2   1   0   0
  TMSB15B WILD-TYPE 343   3  31  25
D2073V11, multiclass
    clus
vv   TMSB15B MUTATED TMSB15B WILD-TYPE
  R0               2               343
  R1               1                 3
  R2               0                31
  RX               0                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2073V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TMSB15B MUTATED                                  0     0
  TMSB15B WILD-TYPE                                1    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  TMSB15B MUTATED                           0     4
  TMSB15B WILD-TYPE                        22   222
D2073V13, multiclass
                                  clus
vv                                 TMSB15B MUTATED TMSB15B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                      0                22
  WHITE                                          4               222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2074) Variable = GIMAP8 MUTATION ANALYSIS
D2074V1, survival
                  sevent
clus2                0   1
  GIMAP8 MUTATED    18   2
  GIMAP8 WILD-TYPE 360  91
  GIMAP8 MUTATED GIMAP8 WILD-TYPE 
              20              451 
  GIMAP8 MUTATED GIMAP8 WILD-TYPE 
               2               91 
$`GIMAP8 MUTATED`
TCGA-A6-6780 TCGA-AA-3554 TCGA-AA-3663 TCGA-AA-3877 TCGA-AA-3947 TCGA-AA-A00E 
       20.12        17.95         6.97        31.00        33.01        30.02 
TCGA-AA-A00N TCGA-AA-A01R TCGA-AZ-4315 TCGA-CA-6717 TCGA-CM-5861 TCGA-CM-6168 
        4.01        35.01        58.39        12.76        15.02        12.99 
TCGA-D5-6535 TCGA-D5-6927 TCGA-DM-A1D9 TCGA-DM-A28F TCGA-G4-6628 TCGA-AG-A002 
       15.12         9.44       140.38        35.97        79.69        20.98 
TCGA-AH-6643 TCGA-DC-5337 
        0.69        15.02 

$`GIMAP8 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       13.02        24.00        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       27.02        29.98        18.05         2.01        12.99        24.00 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00J 
       27.02        13.94        38.04        19.00        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S 
       12.00        31.00        31.00        38.07         1.02         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       33.01        21.44        17.82         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 
       29.06        22.03        22.98        30.08        32.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6169 TCGA-CM-6170 
       29.03        16.04        21.99        14.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       13.32        12.59         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H 
      139.17         6.12        81.37       119.93        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       46.75        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
       17.49         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
       78.12         7.17         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  GIMAP8 MUTATED GIMAP8 WILD-TYPE 
            0.69             0.00 
  GIMAP8 MUTATED GIMAP8 WILD-TYPE 
          140.38           148.01 
  GIMAP8 MUTATED GIMAP8 WILD-TYPE 
          19.035           20.280 
[1] "0.7 - 140.4 (19.0)" "0.0 - 148.0 (20.3)"
[1] "hr=" "2.1"
D2074V2, continuous
D2074V3, binary
                  cls
clus                 0   1
  GIMAP8 MUTATED    18   3
  GIMAP8 WILD-TYPE 348 116
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GIMAP8 MUTATED     18    3
  GIMAP8 WILD-TYPE  348  116
        clus
vv       GIMAP8 MUTATED GIMAP8 WILD-TYPE
  COLON              18              348
  RECTUM              3              116
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GIMAP8 MUTATED         4        0        1        10         2         0
  GIMAP8 WILD-TYPE      87        1       31       128         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GIMAP8 MUTATED           1          0          2          1        0
  GIMAP8 WILD-TYPE        23         11         57         41       48
                  vv
clus               STAGE IVA STAGE IVB
  GIMAP8 MUTATED           0         0
  GIMAP8 WILD-TYPE        18         1
D2074V4, multiclass
            clus
vv           GIMAP8 MUTATED GIMAP8 WILD-TYPE
  STAGE I                 4               87
  STAGE IA                0                1
  STAGE II                1               31
  STAGE IIA              10              128
  STAGE IIB               2                8
  STAGE IIC               0                1
  STAGE III               1               23
  STAGE IIIA              0               11
  STAGE IIIB              2               57
  STAGE IIIC              1               41
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  GIMAP8 MUTATED     2   2  15   2
  GIMAP8 WILD-TYPE  15  90 314  48
D2074V5, multiclass
    clus
vv   GIMAP8 MUTATED GIMAP8 WILD-TYPE
  T1              2               15
  T2              2               90
  T3             15              314
  T4              2               48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  GIMAP8 MUTATED    17   2   2
  GIMAP8 WILD-TYPE 270 111  85
D2074V6, multiclass
    clus
vv   GIMAP8 MUTATED GIMAP8 WILD-TYPE
  N0             17              270
  N1              2              111
  N2              2               85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2074V7, binary
                  cls
clus                 0   1
  GIMAP8 MUTATED    19   0
  GIMAP8 WILD-TYPE 356  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GIMAP8 MUTATED     19    0
  GIMAP8 WILD-TYPE  356   65
   clus
vv  GIMAP8 MUTATED GIMAP8 WILD-TYPE
  0             19              356
  1              0               65
[1] 2 2
[1] FALSE
D2074V8, binary
                  cls
clus                 0   1
  GIMAP8 MUTATED     8  13
  GIMAP8 WILD-TYPE 217 251
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GIMAP8 MUTATED      8   13
  GIMAP8 WILD-TYPE  217  251
        clus
vv       GIMAP8 MUTATED GIMAP8 WILD-TYPE
  FEMALE              8              217
  MALE               13              251
[1] 2 2
[1] FALSE
D2074V9, binary
                  cls
clus                 0   1
  GIMAP8 MUTATED    15   1
  GIMAP8 WILD-TYPE 335  21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GIMAP8 MUTATED     15    1
  GIMAP8 WILD-TYPE  335   21
     clus
vv    GIMAP8 MUTATED GIMAP8 WILD-TYPE
  NO              15              335
  YES              1               21
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  GIMAP8 MUTATED                     12                             6
  GIMAP8 WILD-TYPE                  303                            41
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  GIMAP8 MUTATED                       3                              0
  GIMAP8 WILD-TYPE                   103                             10
D2074V10, multiclass
                                clus
vv                               GIMAP8 MUTATED GIMAP8 WILD-TYPE
  COLON ADENOCARCINOMA                       12              303
  COLON MUCINOUS ADENOCARCINOMA               6               41
  RECTAL ADENOCARCINOMA                       3              103
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  GIMAP8 MUTATED    16   0   0   2
  GIMAP8 WILD-TYPE 329   4  31  23
D2074V11, multiclass
    clus
vv   GIMAP8 MUTATED GIMAP8 WILD-TYPE
  R0             16              329
  R1              0                4
  R2              0               31
  RX              2               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2074V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GIMAP8 MUTATED                                  0     1
  GIMAP8 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  GIMAP8 MUTATED                           1    10
  GIMAP8 WILD-TYPE                        21   216
D2074V13, multiclass
                                  clus
vv                                 GIMAP8 MUTATED GIMAP8 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                        10              216
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2075) Variable = TNXB MUTATION ANALYSIS
D2075V1, survival
                sevent
clus2              0   1
  TNXB MUTATED    34   6
  TNXB WILD-TYPE 344  87
  TNXB MUTATED TNXB WILD-TYPE 
            40            431 
  TNXB MUTATED TNXB WILD-TYPE 
             6             87 
$`TNXB MUTATED`
TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5661 TCGA-A6-5665 TCGA-A6-6142 TCGA-A6-6781 
       36.53        32.91        33.53        22.06        25.08        19.66 
TCGA-AA-3502 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3666 TCGA-AA-3837 
       35.01        78.08         6.05         6.97         2.01        38.99 
TCGA-AA-3850 TCGA-AA-3864 TCGA-AA-3877 TCGA-AA-3947 TCGA-AA-A00N TCGA-AA-A010 
        0.00        53.00        31.00        33.01         4.01        34.98 
TCGA-AD-6889 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-CA-6717 TCGA-CK-4952 
       56.55        17.82        58.39        49.41        12.76        15.62 
TCGA-CM-5862 TCGA-CM-6167 TCGA-CM-6170 TCGA-CM-6674 TCGA-D5-6538 TCGA-D5-6928 
        5.03        14.99        15.02        12.95        17.13        11.64 
TCGA-D5-6930 TCGA-DM-A282 TCGA-F4-6570 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6628 
        1.51       139.17         6.18        35.31       133.18        79.69 
TCGA-AG-3892 TCGA-AG-4007 TCGA-AG-A002 TCGA-DC-6160 
       13.02         1.02        20.98        19.99 

$`TNXB WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-4105 TCGA-A6-5657 
       16.57        34.65        33.34        32.75        14.53        31.63 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 
       30.44        29.19        23.61        22.09        32.71        27.09 
TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 
       22.52         8.38        25.18        24.16        21.76        24.69 
TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       24.39        23.87        20.12        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3664 TCGA-AA-3667 
       19.99        13.94        19.99        61.02        54.02        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3842 TCGA-AA-3844 
       25.02         1.02        17.98        15.95        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
        0.00        17.03        10.06        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 
       32.05         0.99        31.07        31.07        30.05        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 
       24.03        27.02        29.98        18.05         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       21.37        15.52         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
        0.95        33.01        21.44         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        88.21         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07        12.20        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 
       14.30        17.56       148.01        85.45        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5864 
       22.98        30.08        32.02        15.02        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6675 
       21.99        12.99        13.02        14.04        11.01        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6539 
        1.32        43.27        15.12        17.85         4.80        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 
       14.30         9.04         9.44         4.80        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      131.51       135.65         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       13.25         0.53        47.41        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       36.95        17.03        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4008 
       32.02        19.99        28.04        36.03        14.04        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6681 
       15.02         5.03        13.97        27.95        10.98         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  TNXB MUTATED TNXB WILD-TYPE 
             0              0 
  TNXB MUTATED TNXB WILD-TYPE 
        139.17         148.01 
  TNXB MUTATED TNXB WILD-TYPE 
        20.485         20.190 
[1] "0.0 - 139.2 (20.5)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.5"
D2075V2, continuous
D2075V3, binary
                cls
clus               0   1
  TNXB MUTATED    39   4
  TNXB WILD-TYPE 327 115
[1] "tbl2"
                cls
clus             [,1] [,2]
  TNXB MUTATED     39    4
  TNXB WILD-TYPE  327  115
        clus
vv       TNXB MUTATED TNXB WILD-TYPE
  COLON            39            327
  RECTUM            4            115
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TNXB MUTATED        11        0        4        13         4         0
  TNXB WILD-TYPE      80        1       28       125         6         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TNXB MUTATED           2          0          2          3        2         2
  TNXB WILD-TYPE        22         11         57         39       46        16
                vv
clus             STAGE IVB
  TNXB MUTATED           0
  TNXB WILD-TYPE         1
D2075V4, multiclass
            clus
vv           TNXB MUTATED TNXB WILD-TYPE
  STAGE I              11             80
  STAGE IA              0              1
  STAGE II              4             28
  STAGE IIA            13            125
  STAGE IIB             4              6
  STAGE IIC             0              1
  STAGE III             2             22
  STAGE IIIA            0             11
  STAGE IIIB            2             57
  STAGE IIIC            3             39
  STAGE IV              2             46
  STAGE IVA             2             16
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  TNXB MUTATED     2   9  24   8
  TNXB WILD-TYPE  15  83 305  42
D2075V5, multiclass
    clus
vv   TNXB MUTATED TNXB WILD-TYPE
  T1            2             15
  T2            9             83
  T3           24            305
  T4            8             42
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  TNXB MUTATED    32   6   5
  TNXB WILD-TYPE 255 107  82
D2075V6, multiclass
    clus
vv   TNXB MUTATED TNXB WILD-TYPE
  N0           32            255
  N1            6            107
  N2            5             82
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2075V7, binary
                cls
clus               0   1
  TNXB MUTATED    35   4
  TNXB WILD-TYPE 340  61
[1] "tbl2"
                cls
clus             [,1] [,2]
  TNXB MUTATED     35    4
  TNXB WILD-TYPE  340   61
   clus
vv  TNXB MUTATED TNXB WILD-TYPE
  0           35            340
  1            4             61
[1] 2 2
[1] FALSE
D2075V8, binary
                cls
clus               0   1
  TNXB MUTATED    20  23
  TNXB WILD-TYPE 205 241
[1] "tbl2"
                cls
clus             [,1] [,2]
  TNXB MUTATED     20   23
  TNXB WILD-TYPE  205  241
        clus
vv       TNXB MUTATED TNXB WILD-TYPE
  FEMALE           20            205
  MALE             23            241
[1] 2 2
[1] FALSE
D2075V9, binary
                cls
clus               0   1
  TNXB MUTATED    31   0
  TNXB WILD-TYPE 319  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  TNXB MUTATED     31    0
  TNXB WILD-TYPE  319   22
     clus
vv    TNXB MUTATED TNXB WILD-TYPE
  NO            31            319
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  TNXB MUTATED                     29                            10
  TNXB WILD-TYPE                  286                            37
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  TNXB MUTATED                       4                              0
  TNXB WILD-TYPE                   102                             10
D2075V10, multiclass
                                clus
vv                               TNXB MUTATED TNXB WILD-TYPE
  COLON ADENOCARCINOMA                     29            286
  COLON MUCINOUS ADENOCARCINOMA            10             37
  RECTAL ADENOCARCINOMA                     4            102
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  TNXB MUTATED    32   0   2   4
  TNXB WILD-TYPE 313   4  29  21
D2075V11, multiclass
    clus
vv   TNXB MUTATED TNXB WILD-TYPE
  R0           32            313
  R1            0              4
  R2            2             29
  RX            4             21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2075V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TNXB MUTATED                                  0     2
  TNXB WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  TNXB MUTATED                           3    22
  TNXB WILD-TYPE                        19   204
D2075V13, multiclass
                                  clus
vv                                 TNXB MUTATED TNXB WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              9
  BLACK OR AFRICAN AMERICAN                   3             19
  WHITE                                      22            204
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2076) Variable = FBXL19 MUTATION ANALYSIS
D2076V1, survival
                  sevent
clus2                0   1
  FBXL19 MUTATED     5   1
  FBXL19 WILD-TYPE 373  92
  FBXL19 MUTATED FBXL19 WILD-TYPE 
               6              465 
  FBXL19 MUTATED FBXL19 WILD-TYPE 
               1               92 
$`FBXL19 MUTATED`
TCGA-AA-3877 TCGA-CM-4746 TCGA-D5-6532 TCGA-F4-6809 TCGA-G4-6293 TCGA-G4-6309 
       31.00        37.02        18.25        13.25       133.18        85.48 

$`FBXL19 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       20.19         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
        0.53        47.41        35.31        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       44.68        55.04        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  FBXL19 MUTATED FBXL19 WILD-TYPE 
           13.25             0.00 
  FBXL19 MUTATED FBXL19 WILD-TYPE 
          133.18           148.01 
  FBXL19 MUTATED FBXL19 WILD-TYPE 
           34.01            20.12 
[1] "13.2 - 133.2 (34.0)" "0.0 - 148.0 (20.1)" 
[1] "hr=" "2.1"
D2076V2, continuous
D2076V3, binary
                  cls
clus                 0   1
  FBXL19 MUTATED     7   0
  FBXL19 WILD-TYPE 359 119
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FBXL19 MUTATED      7    0
  FBXL19 WILD-TYPE  359  119
        clus
vv       FBXL19 MUTATED FBXL19 WILD-TYPE
  COLON               7              359
  RECTUM              0              119
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FBXL19 MUTATED         2        0        0         1         0         0
  FBXL19 WILD-TYPE      89        1       32       137        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FBXL19 MUTATED           2          0          1          0        0
  FBXL19 WILD-TYPE        22         11         58         42       48
                  vv
clus               STAGE IVA STAGE IVB
  FBXL19 MUTATED           1         0
  FBXL19 WILD-TYPE        17         1
D2076V4, multiclass
            clus
vv           FBXL19 MUTATED FBXL19 WILD-TYPE
  STAGE I                 2               89
  STAGE IA                0                1
  STAGE II                0               32
  STAGE IIA               1              137
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               2               22
  STAGE IIIA              0               11
  STAGE IIIB              1               58
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               1               17
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  FBXL19 MUTATED     1   1   5   0
  FBXL19 WILD-TYPE  16  91 324  50
D2076V5, multiclass
    clus
vv   FBXL19 MUTATED FBXL19 WILD-TYPE
  T1              1               16
  T2              1               91
  T3              5              324
  T4              0               50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  FBXL19 MUTATED     3   3   1
  FBXL19 WILD-TYPE 284 110  86
D2076V6, multiclass
    clus
vv   FBXL19 MUTATED FBXL19 WILD-TYPE
  N0              3              284
  N1              3              110
  N2              1               86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2076V7, binary
                  cls
clus                 0   1
  FBXL19 MUTATED     6   1
  FBXL19 WILD-TYPE 369  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FBXL19 MUTATED      6    1
  FBXL19 WILD-TYPE  369   64
   clus
vv  FBXL19 MUTATED FBXL19 WILD-TYPE
  0              6              369
  1              1               64
[1] 2 2
[1] FALSE
D2076V8, binary
                  cls
clus                 0   1
  FBXL19 MUTATED     4   3
  FBXL19 WILD-TYPE 221 261
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FBXL19 MUTATED      4    3
  FBXL19 WILD-TYPE  221  261
        clus
vv       FBXL19 MUTATED FBXL19 WILD-TYPE
  FEMALE              4              221
  MALE                3              261
[1] 2 2
[1] FALSE
D2076V9, binary
                  cls
clus                 0   1
  FBXL19 MUTATED     6   0
  FBXL19 WILD-TYPE 344  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FBXL19 MUTATED      6    0
  FBXL19 WILD-TYPE  344   22
     clus
vv    FBXL19 MUTATED FBXL19 WILD-TYPE
  NO               6              344
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  FBXL19 MUTATED                      6                             1
  FBXL19 WILD-TYPE                  309                            46
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  FBXL19 MUTATED                       0                              0
  FBXL19 WILD-TYPE                   106                             10
D2076V10, multiclass
                                clus
vv                               FBXL19 MUTATED FBXL19 WILD-TYPE
  COLON ADENOCARCINOMA                        6              309
  COLON MUCINOUS ADENOCARCINOMA               1               46
  RECTAL ADENOCARCINOMA                       0              106
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  FBXL19 MUTATED     7   0   0   0
  FBXL19 WILD-TYPE 338   4  31  25
D2076V11, multiclass
    clus
vv   FBXL19 MUTATED FBXL19 WILD-TYPE
  R0              7              338
  R1              0                4
  R2              0               31
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2076V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FBXL19 MUTATED                                  0     0
  FBXL19 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  FBXL19 MUTATED                           2     3
  FBXL19 WILD-TYPE                        20   223
D2076V13, multiclass
                                  clus
vv                                 FBXL19 MUTATED FBXL19 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     2               20
  WHITE                                         3              223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2077) Variable = ANKRD6 MUTATION ANALYSIS
D2077V1, survival
                  sevent
clus2                0   1
  ANKRD6 MUTATED    10   2
  ANKRD6 WILD-TYPE 368  91
  ANKRD6 MUTATED ANKRD6 WILD-TYPE 
              12              459 
  ANKRD6 MUTATED ANKRD6 WILD-TYPE 
               2               91 
$`ANKRD6 MUTATED`
TCGA-AA-3510 TCGA-AA-3663 TCGA-AA-3715 TCGA-AA-3949 TCGA-AA-3975 TCGA-AA-3986 
       63.98         6.97        19.04        26.01        34.06        19.07 
TCGA-AD-5900 TCGA-AD-6895 TCGA-CM-4743 TCGA-CM-6172 TCGA-DM-A1D4 TCGA-G4-6309 
        0.07         0.72        23.05        11.01        92.75        85.48 

$`ANKRD6 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        33.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3976 
        2.01        21.99        16.08        50.99        13.05        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       25.02        24.00        27.02        27.02         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 
        0.92        41.00        39.98        18.05        40.96        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       15.52        56.55         0.79         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
       82.95         1.91       124.27        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 
       12.99        13.02        15.02        14.04        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
       38.20       130.65        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       44.68        55.04        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  ANKRD6 MUTATED ANKRD6 WILD-TYPE 
            0.07             0.00 
  ANKRD6 MUTATED ANKRD6 WILD-TYPE 
           92.75           148.01 
  ANKRD6 MUTATED ANKRD6 WILD-TYPE 
           21.06            20.19 
[1] "0.1 - 92.8 (21.1)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.5"
D2077V2, continuous
D2077V3, binary
                  cls
clus                 0   1
  ANKRD6 MUTATED    13   0
  ANKRD6 WILD-TYPE 353 119
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ANKRD6 MUTATED     13    0
  ANKRD6 WILD-TYPE  353  119
        clus
vv       ANKRD6 MUTATED ANKRD6 WILD-TYPE
  COLON              13              353
  RECTUM              0              119
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ANKRD6 MUTATED         3        0        3         3         0         0
  ANKRD6 WILD-TYPE      88        1       29       135        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ANKRD6 MUTATED           0          0          3          0        0
  ANKRD6 WILD-TYPE        24         11         56         42       48
                  vv
clus               STAGE IVA STAGE IVB
  ANKRD6 MUTATED           0         0
  ANKRD6 WILD-TYPE        18         1
D2077V4, multiclass
            clus
vv           ANKRD6 MUTATED ANKRD6 WILD-TYPE
  STAGE I                 3               88
  STAGE IA                0                1
  STAGE II                3               29
  STAGE IIA               3              135
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              3               56
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ANKRD6 MUTATED     0   3  10   0
  ANKRD6 WILD-TYPE  17  89 319  50
D2077V5, multiclass
    clus
vv   ANKRD6 MUTATED ANKRD6 WILD-TYPE
  T1              0               17
  T2              3               89
  T3             10              319
  T4              0               50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  ANKRD6 MUTATED     9   4   0
  ANKRD6 WILD-TYPE 278 109  87
D2077V6, multiclass
    clus
vv   ANKRD6 MUTATED ANKRD6 WILD-TYPE
  N0              9              278
  N1              4              109
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2077V7, binary
                  cls
clus                 0   1
  ANKRD6 MUTATED    11   0
  ANKRD6 WILD-TYPE 364  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ANKRD6 MUTATED     11    0
  ANKRD6 WILD-TYPE  364   65
   clus
vv  ANKRD6 MUTATED ANKRD6 WILD-TYPE
  0             11              364
  1              0               65
[1] 2 2
[1] FALSE
D2077V8, binary
                  cls
clus                 0   1
  ANKRD6 MUTATED     4   9
  ANKRD6 WILD-TYPE 221 255
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ANKRD6 MUTATED      4    9
  ANKRD6 WILD-TYPE  221  255
        clus
vv       ANKRD6 MUTATED ANKRD6 WILD-TYPE
  FEMALE              4              221
  MALE                9              255
[1] 2 2
[1] FALSE
D2077V9, binary
                  cls
clus                 0   1
  ANKRD6 MUTATED     9   0
  ANKRD6 WILD-TYPE 341  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ANKRD6 MUTATED      9    0
  ANKRD6 WILD-TYPE  341   22
     clus
vv    ANKRD6 MUTATED ANKRD6 WILD-TYPE
  NO               9              341
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ANKRD6 MUTATED                     11                             2
  ANKRD6 WILD-TYPE                  304                            45
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ANKRD6 MUTATED                       0                              0
  ANKRD6 WILD-TYPE                   106                             10
D2077V10, multiclass
                                clus
vv                               ANKRD6 MUTATED ANKRD6 WILD-TYPE
  COLON ADENOCARCINOMA                       11              304
  COLON MUCINOUS ADENOCARCINOMA               2               45
  RECTAL ADENOCARCINOMA                       0              106
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ANKRD6 MUTATED    11   0   0   0
  ANKRD6 WILD-TYPE 334   4  31  25
D2077V11, multiclass
    clus
vv   ANKRD6 MUTATED ANKRD6 WILD-TYPE
  R0             11              334
  R1              0                4
  R2              0               31
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2077V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ANKRD6 MUTATED                                  0     0
  ANKRD6 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ANKRD6 MUTATED                           1     5
  ANKRD6 WILD-TYPE                        21   221
D2077V13, multiclass
                                  clus
vv                                 ANKRD6 MUTATED ANKRD6 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                         5              221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2078) Variable = WDR17 MUTATION ANALYSIS
D2078V1, survival
                 sevent
clus2               0   1
  WDR17 MUTATED    21   4
  WDR17 WILD-TYPE 357  89
  WDR17 MUTATED WDR17 WILD-TYPE 
             25             446 
  WDR17 MUTATED WDR17 WILD-TYPE 
              4              89 
$`WDR17 MUTATED`
TCGA-A6-5665 TCGA-AA-3510 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3851 TCGA-AA-3966 
       22.06        63.98        17.95        29.95        33.07         2.01 
TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01R TCGA-AD-6964 TCGA-AZ-4315 
       25.02         4.01        34.98        35.01        10.88        58.39 
TCGA-AZ-6606 TCGA-CA-6717 TCGA-CK-4947 TCGA-CM-6168 TCGA-D5-6920 TCGA-D5-6922 
       11.74        12.76        17.56        12.99         3.68         4.41 
TCGA-D5-6928 TCGA-DM-A1D6 TCGA-G4-6293 TCGA-G4-6317 TCGA-AG-4007 TCGA-AG-A002 
       11.64        49.91       133.18        36.00         1.02        20.98 
TCGA-DY-A0XA 
      126.44 

$`WDR17 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       24.00        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 
       26.01        24.00         2.01        20.98        34.03        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       31.00        38.07         1.02         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
        0.72         5.79        22.42        27.42         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-4950 
        0.07        12.20        10.06        14.30       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6923 TCGA-D5-6924 
       12.49        16.14        15.58         1.48        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.04         9.44         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6299 
       33.67        13.25         0.53        47.41        35.31        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       61.91        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       36.03        14.04        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
        5.29        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  WDR17 MUTATED WDR17 WILD-TYPE 
           1.02            0.00 
  WDR17 MUTATED WDR17 WILD-TYPE 
         133.18          148.01 
  WDR17 MUTATED WDR17 WILD-TYPE 
         20.980          20.155 
[1] "1.0 - 133.2 (21.0)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.4"
D2078V2, continuous
D2078V3, binary
                 cls
clus                0   1
  WDR17 MUTATED    23   3
  WDR17 WILD-TYPE 343 116
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WDR17 MUTATED     23    3
  WDR17 WILD-TYPE  343  116
        clus
vv       WDR17 MUTATED WDR17 WILD-TYPE
  COLON             23             343
  RECTUM             3             116
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  WDR17 MUTATED         1        0        1        13         2         0
  WDR17 WILD-TYPE      90        1       31       125         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  WDR17 MUTATED           2          1          1          1        2         0
  WDR17 WILD-TYPE        22         10         58         41       46        18
                 vv
clus              STAGE IVB
  WDR17 MUTATED           0
  WDR17 WILD-TYPE         1
D2078V4, multiclass
            clus
vv           WDR17 MUTATED WDR17 WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA             13             125
  STAGE IIB              2               8
  STAGE IIC              0               1
  STAGE III              2              22
  STAGE IIIA             1              10
  STAGE IIIB             1              58
  STAGE IIIC             1              41
  STAGE IV               2              46
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  WDR17 MUTATED     0   2  18   6
  WDR17 WILD-TYPE  17  90 311  44
D2078V5, multiclass
    clus
vv   WDR17 MUTATED WDR17 WILD-TYPE
  T1             0              17
  T2             2              90
  T3            18             311
  T4             6              44
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  WDR17 MUTATED    18   3   5
  WDR17 WILD-TYPE 269 110  82
D2078V6, multiclass
    clus
vv   WDR17 MUTATED WDR17 WILD-TYPE
  N0            18             269
  N1             3             110
  N2             5              82
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2078V7, binary
                 cls
clus                0   1
  WDR17 MUTATED    21   2
  WDR17 WILD-TYPE 354  63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WDR17 MUTATED     21    2
  WDR17 WILD-TYPE  354   63
   clus
vv  WDR17 MUTATED WDR17 WILD-TYPE
  0            21             354
  1             2              63
[1] 2 2
[1] FALSE
D2078V8, binary
                 cls
clus                0   1
  WDR17 MUTATED    12  14
  WDR17 WILD-TYPE 213 250
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WDR17 MUTATED     12   14
  WDR17 WILD-TYPE  213  250
        clus
vv       WDR17 MUTATED WDR17 WILD-TYPE
  FEMALE            12             213
  MALE              14             250
[1] 2 2
[1] FALSE
D2078V9, binary
                 cls
clus                0   1
  WDR17 MUTATED    17   1
  WDR17 WILD-TYPE 333  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WDR17 MUTATED     17    1
  WDR17 WILD-TYPE  333   21
     clus
vv    WDR17 MUTATED WDR17 WILD-TYPE
  NO             17             333
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  WDR17 MUTATED                     16                             7
  WDR17 WILD-TYPE                  299                            40
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  WDR17 MUTATED                       3                              0
  WDR17 WILD-TYPE                   103                             10
D2078V10, multiclass
                                clus
vv                               WDR17 MUTATED WDR17 WILD-TYPE
  COLON ADENOCARCINOMA                      16             299
  COLON MUCINOUS ADENOCARCINOMA              7              40
  RECTAL ADENOCARCINOMA                      3             103
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  WDR17 MUTATED    17   0   1   2
  WDR17 WILD-TYPE 328   4  30  23
D2078V11, multiclass
    clus
vv   WDR17 MUTATED WDR17 WILD-TYPE
  R0            17             328
  R1             0               4
  R2             1              30
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2078V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  WDR17 MUTATED                                  0     1
  WDR17 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  WDR17 MUTATED                           1    12
  WDR17 WILD-TYPE                        21   214
D2078V13, multiclass
                                  clus
vv                                 WDR17 MUTATED WDR17 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                       12             214
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2079) Variable = MRPL47 MUTATION ANALYSIS
D2079V1, survival
                  sevent
clus2                0   1
  MRPL47 MUTATED     3   1
  MRPL47 WILD-TYPE 375  92
  MRPL47 MUTATED MRPL47 WILD-TYPE 
               4              467 
  MRPL47 MUTATED MRPL47 WILD-TYPE 
               1               92 
$`MRPL47 MUTATED`
TCGA-A6-3809 TCGA-AA-A00N TCGA-AA-A010 TCGA-AG-A002 
       32.75         4.01        34.98        20.98 

$`MRPL47 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  MRPL47 MUTATED MRPL47 WILD-TYPE 
            4.01             0.00 
  MRPL47 MUTATED MRPL47 WILD-TYPE 
           34.98           148.01 
  MRPL47 MUTATED MRPL47 WILD-TYPE 
          26.865           20.120 
[1] "4.0 - 35.0 (26.9)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.6"
D2079V2, continuous
D2079V3, binary
                  cls
clus                 0   1
  MRPL47 MUTATED     5   1
  MRPL47 WILD-TYPE 361 118
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MRPL47 MUTATED      5    1
  MRPL47 WILD-TYPE  361  118
        clus
vv       MRPL47 MUTATED MRPL47 WILD-TYPE
  COLON               5              361
  RECTUM              1              118
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MRPL47 MUTATED         2        0        0         0         3         0
  MRPL47 WILD-TYPE      89        1       32       138         7         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MRPL47 MUTATED           0          0          0          1        0
  MRPL47 WILD-TYPE        24         11         59         41       48
                  vv
clus               STAGE IVA STAGE IVB
  MRPL47 MUTATED           0         0
  MRPL47 WILD-TYPE        18         1
D2079V4, multiclass
            clus
vv           MRPL47 MUTATED MRPL47 WILD-TYPE
  STAGE I                 2               89
  STAGE IA                0                1
  STAGE II                0               32
  STAGE IIA               0              138
  STAGE IIB               3                7
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              0               59
  STAGE IIIC              1               41
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  MRPL47 MUTATED     0   2   1   3
  MRPL47 WILD-TYPE  17  90 328  47
D2079V5, multiclass
    clus
vv   MRPL47 MUTATED MRPL47 WILD-TYPE
  T1              0               17
  T2              2               90
  T3              1              328
  T4              3               47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  MRPL47 MUTATED     5   0   1
  MRPL47 WILD-TYPE 282 113  86
D2079V6, multiclass
    clus
vv   MRPL47 MUTATED MRPL47 WILD-TYPE
  N0              5              282
  N1              0              113
  N2              1               86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2079V7, binary
                  cls
clus                 0   1
  MRPL47 MUTATED     4   0
  MRPL47 WILD-TYPE 371  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MRPL47 MUTATED      4    0
  MRPL47 WILD-TYPE  371   65
   clus
vv  MRPL47 MUTATED MRPL47 WILD-TYPE
  0              4              371
  1              0               65
[1] 2 2
[1] FALSE
D2079V8, binary
                  cls
clus                 0   1
  MRPL47 MUTATED     2   4
  MRPL47 WILD-TYPE 223 260
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MRPL47 MUTATED      2    4
  MRPL47 WILD-TYPE  223  260
        clus
vv       MRPL47 MUTATED MRPL47 WILD-TYPE
  FEMALE              2              223
  MALE                4              260
[1] 2 2
[1] FALSE
D2079V9, binary
                  cls
clus                 0   1
  MRPL47 MUTATED     3   0
  MRPL47 WILD-TYPE 347  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MRPL47 MUTATED      3    0
  MRPL47 WILD-TYPE  347   22
     clus
vv    MRPL47 MUTATED MRPL47 WILD-TYPE
  NO               3              347
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MRPL47 MUTATED                      2                             3
  MRPL47 WILD-TYPE                  313                            44
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MRPL47 MUTATED                       1                              0
  MRPL47 WILD-TYPE                   105                             10
D2079V10, multiclass
                                clus
vv                               MRPL47 MUTATED MRPL47 WILD-TYPE
  COLON ADENOCARCINOMA                        2              313
  COLON MUCINOUS ADENOCARCINOMA               3               44
  RECTAL ADENOCARCINOMA                       1              105
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  MRPL47 MUTATED     5   0   0   1
  MRPL47 WILD-TYPE 340   4  31  24
D2079V11, multiclass
    clus
vv   MRPL47 MUTATED MRPL47 WILD-TYPE
  R0              5              340
  R1              0                4
  R2              0               31
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2079V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MRPL47 MUTATED                                  0     0
  MRPL47 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  MRPL47 MUTATED                           0     3
  MRPL47 WILD-TYPE                        22   223
D2079V13, multiclass
                                  clus
vv                                 MRPL47 MUTATED MRPL47 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         3              223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2080) Variable = TRPV2 MUTATION ANALYSIS
D2080V1, survival
                 sevent
clus2               0   1
  TRPV2 MUTATED     9   3
  TRPV2 WILD-TYPE 369  90
  TRPV2 MUTATED TRPV2 WILD-TYPE 
             12             459 
  TRPV2 MUTATED TRPV2 WILD-TYPE 
              3              90 
$`TRPV2 MUTATED`
TCGA-A6-2672 TCGA-A6-6780 TCGA-AA-3525 TCGA-AA-3672 TCGA-AA-3845 TCGA-AA-3949 
       46.65        20.12         8.05         0.92         0.00        26.01 
TCGA-AU-6004 TCGA-AZ-6598 TCGA-CA-6718 TCGA-D5-6540 TCGA-G4-6628 TCGA-AG-A002 
       27.09        49.41        10.06        16.14        79.69        20.98 

$`TRPV2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3529 
        9.07        24.03        37.05        36.03        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
        2.01        14.01        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02        14.93        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 
       22.42        27.42        10.88         0.20        14.50        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 
        5.13       106.75        22.36        62.79        88.21         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.20        12.76        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       17.13        12.49        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       46.75        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  TRPV2 MUTATED TRPV2 WILD-TYPE 
              0               0 
  TRPV2 MUTATED TRPV2 WILD-TYPE 
          79.69          148.01 
  TRPV2 MUTATED TRPV2 WILD-TYPE 
          20.55           20.19 
[1] "0.0 - 79.7 (20.6)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.3"
D2080V2, continuous
D2080V3, binary
                 cls
clus                0   1
  TRPV2 MUTATED    11   1
  TRPV2 WILD-TYPE 355 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRPV2 MUTATED     11    1
  TRPV2 WILD-TYPE  355  118
        clus
vv       TRPV2 MUTATED TRPV2 WILD-TYPE
  COLON             11             355
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TRPV2 MUTATED         4        0        1         3         0         0
  TRPV2 WILD-TYPE      87        1       31       135        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TRPV2 MUTATED           1          0          3          0        0         0
  TRPV2 WILD-TYPE        23         11         56         42       48        18
                 vv
clus              STAGE IVB
  TRPV2 MUTATED           0
  TRPV2 WILD-TYPE         1
D2080V4, multiclass
            clus
vv           TRPV2 MUTATED TRPV2 WILD-TYPE
  STAGE I                4              87
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              3             135
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             3              56
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  TRPV2 MUTATED     0   4   8   0
  TRPV2 WILD-TYPE  17  88 321  50
D2080V5, multiclass
    clus
vv   TRPV2 MUTATED TRPV2 WILD-TYPE
  T1             0              17
  T2             4              88
  T3             8             321
  T4             0              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  TRPV2 MUTATED     8   4   0
  TRPV2 WILD-TYPE 279 109  87
D2080V6, multiclass
    clus
vv   TRPV2 MUTATED TRPV2 WILD-TYPE
  N0             8             279
  N1             4             109
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2080V7, binary
                 cls
clus                0   1
  TRPV2 MUTATED    10   0
  TRPV2 WILD-TYPE 365  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRPV2 MUTATED     10    0
  TRPV2 WILD-TYPE  365   65
   clus
vv  TRPV2 MUTATED TRPV2 WILD-TYPE
  0            10             365
  1             0              65
[1] 2 2
[1] FALSE
D2080V8, binary
                 cls
clus                0   1
  TRPV2 MUTATED     6   6
  TRPV2 WILD-TYPE 219 258
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRPV2 MUTATED      6    6
  TRPV2 WILD-TYPE  219  258
        clus
vv       TRPV2 MUTATED TRPV2 WILD-TYPE
  FEMALE             6             219
  MALE               6             258
[1] 2 2
[1] FALSE
D2080V9, binary
                 cls
clus                0   1
  TRPV2 MUTATED    10   0
  TRPV2 WILD-TYPE 340  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRPV2 MUTATED     10    0
  TRPV2 WILD-TYPE  340   22
     clus
vv    TRPV2 MUTATED TRPV2 WILD-TYPE
  NO             10             340
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  TRPV2 MUTATED                      8                             3
  TRPV2 WILD-TYPE                  307                            44
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  TRPV2 MUTATED                       1                              0
  TRPV2 WILD-TYPE                   105                             10
D2080V10, multiclass
                                clus
vv                               TRPV2 MUTATED TRPV2 WILD-TYPE
  COLON ADENOCARCINOMA                       8             307
  COLON MUCINOUS ADENOCARCINOMA              3              44
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  TRPV2 MUTATED     9   0   0   1
  TRPV2 WILD-TYPE 336   4  31  24
D2080V11, multiclass
    clus
vv   TRPV2 MUTATED TRPV2 WILD-TYPE
  R0             9             336
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2080V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TRPV2 MUTATED                                  0     1
  TRPV2 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  TRPV2 MUTATED                           0     6
  TRPV2 WILD-TYPE                        22   220
D2080V13, multiclass
                                  clus
vv                                 TRPV2 MUTATED TRPV2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        6             220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2081) Variable = RAG1 MUTATION ANALYSIS
D2081V1, survival
                sevent
clus2              0   1
  RAG1 MUTATED    14   2
  RAG1 WILD-TYPE 364  91
  RAG1 MUTATED RAG1 WILD-TYPE 
            16            455 
  RAG1 MUTATED RAG1 WILD-TYPE 
             2             91 
$`RAG1 MUTATED`
TCGA-A6-5661 TCGA-A6-6781 TCGA-AA-3510 TCGA-AA-3877 TCGA-AA-3976 TCGA-AA-3977 
       33.53        19.66        63.98        31.00        26.01        25.02 
TCGA-AA-A00N TCGA-AA-A010 TCGA-AD-6889 TCGA-AZ-4315 TCGA-CM-6161 TCGA-D5-6536 
        4.01        34.98        56.55        58.39        15.02        17.85 
TCGA-D5-6540 TCGA-AG-3583 TCGA-AG-3892 TCGA-AG-A002 
       16.14        20.05        13.02        20.98 

$`RAG1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       27.02        29.98        18.05         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6162 TCGA-CM-6163 
        5.03        15.02        15.02        17.03        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 
       43.27        15.12         4.80        17.13        12.49        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3584 
       12.00        32.02         8.02         7.07        36.03        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  RAG1 MUTATED RAG1 WILD-TYPE 
          4.01           0.00 
  RAG1 MUTATED RAG1 WILD-TYPE 
         63.98         148.01 
  RAG1 MUTATED RAG1 WILD-TYPE 
         23.00          20.12 
[1] "4.0 - 64.0 (23.0)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.8"
D2081V2, continuous
D2081V3, binary
                cls
clus               0   1
  RAG1 MUTATED    14   3
  RAG1 WILD-TYPE 352 116
[1] "tbl2"
                cls
clus             [,1] [,2]
  RAG1 MUTATED     14    3
  RAG1 WILD-TYPE  352  116
        clus
vv       RAG1 MUTATED RAG1 WILD-TYPE
  COLON            14            352
  RECTUM            3            116
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RAG1 MUTATED         5        0        1         5         2         0
  RAG1 WILD-TYPE      86        1       31       133         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RAG1 MUTATED           0          1          0          1        1         0
  RAG1 WILD-TYPE        24         10         59         41       47        18
                vv
clus             STAGE IVB
  RAG1 MUTATED           0
  RAG1 WILD-TYPE         1
D2081V4, multiclass
            clus
vv           RAG1 MUTATED RAG1 WILD-TYPE
  STAGE I               5             86
  STAGE IA              0              1
  STAGE II              1             31
  STAGE IIA             5            133
  STAGE IIB             2              8
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            1             10
  STAGE IIIB            0             59
  STAGE IIIC            1             41
  STAGE IV              1             47
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  RAG1 MUTATED     2   5   7   3
  RAG1 WILD-TYPE  15  87 322  47
D2081V5, multiclass
    clus
vv   RAG1 MUTATED RAG1 WILD-TYPE
  T1            2             15
  T2            5             87
  T3            7            322
  T4            3             47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  RAG1 MUTATED    14   2   1
  RAG1 WILD-TYPE 273 111  86
D2081V6, multiclass
    clus
vv   RAG1 MUTATED RAG1 WILD-TYPE
  N0           14            273
  N1            2            111
  N2            1             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2081V7, binary
                cls
clus               0   1
  RAG1 MUTATED    14   1
  RAG1 WILD-TYPE 361  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  RAG1 MUTATED     14    1
  RAG1 WILD-TYPE  361   64
   clus
vv  RAG1 MUTATED RAG1 WILD-TYPE
  0           14            361
  1            1             64
[1] 2 2
[1] FALSE
D2081V8, binary
                cls
clus               0   1
  RAG1 MUTATED     6  11
  RAG1 WILD-TYPE 219 253
[1] "tbl2"
                cls
clus             [,1] [,2]
  RAG1 MUTATED      6   11
  RAG1 WILD-TYPE  219  253
        clus
vv       RAG1 MUTATED RAG1 WILD-TYPE
  FEMALE            6            219
  MALE             11            253
[1] 2 2
[1] FALSE
D2081V9, binary
                cls
clus               0   1
  RAG1 MUTATED    14   0
  RAG1 WILD-TYPE 336  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  RAG1 MUTATED     14    0
  RAG1 WILD-TYPE  336   22
     clus
vv    RAG1 MUTATED RAG1 WILD-TYPE
  NO            14            336
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  RAG1 MUTATED                     10                             4
  RAG1 WILD-TYPE                  305                            43
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  RAG1 MUTATED                       2                              1
  RAG1 WILD-TYPE                   104                              9
D2081V10, multiclass
                                clus
vv                               RAG1 MUTATED RAG1 WILD-TYPE
  COLON ADENOCARCINOMA                     10            305
  COLON MUCINOUS ADENOCARCINOMA             4             43
  RECTAL ADENOCARCINOMA                     2            104
  RECTAL MUCINOUS ADENOCARCINOMA            1              9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  RAG1 MUTATED    14   0   1   0
  RAG1 WILD-TYPE 331   4  30  25
D2081V11, multiclass
    clus
vv   RAG1 MUTATED RAG1 WILD-TYPE
  R0           14            331
  R1            0              4
  R2            1             30
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2081V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RAG1 MUTATED                                  0     1
  RAG1 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  RAG1 MUTATED                           1     5
  RAG1 WILD-TYPE                        21   221
D2081V13, multiclass
                                  clus
vv                                 RAG1 MUTATED RAG1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                       5            221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2082) Variable = IL8 MUTATION ANALYSIS
D2082V1, survival
               sevent
clus2             0   1
  IL8 MUTATED     3   2
  IL8 WILD-TYPE 375  91
  IL8 MUTATED IL8 WILD-TYPE 
            5           466 
  IL8 MUTATED IL8 WILD-TYPE 
            2            91 
$`IL8 MUTATED`
TCGA-A6-6781 TCGA-AZ-6607 TCGA-CK-5916 TCGA-D5-6926 TCGA-AG-A002 
       19.66         3.19        21.14         9.04        20.98 

$`IL8 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 
       85.45        15.62        49.08        51.32         9.99        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
        4.41        12.43        14.30         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  IL8 MUTATED IL8 WILD-TYPE 
         3.19          0.00 
  IL8 MUTATED IL8 WILD-TYPE 
        21.14        148.01 
  IL8 MUTATED IL8 WILD-TYPE 
       19.660        20.235 
[1] "3.2 - 21.1 (19.7)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "3.6"
D2082V2, continuous
D2082V3, binary
               cls
clus              0   1
  IL8 MUTATED     5   1
  IL8 WILD-TYPE 361 118
[1] "tbl2"
               cls
clus            [,1] [,2]
  IL8 MUTATED      5    1
  IL8 WILD-TYPE  361  118
        clus
vv       IL8 MUTATED IL8 WILD-TYPE
  COLON            5           361
  RECTUM           1           118
[1] 2 2
[1] FALSE
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  IL8 MUTATED         2        0        0         0         1         0
  IL8 WILD-TYPE      89        1       32       138         9         1
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  IL8 MUTATED           0          0          1          1        1         0
  IL8 WILD-TYPE        24         11         58         41       47        18
               vv
clus            STAGE IVB
  IL8 MUTATED           0
  IL8 WILD-TYPE         1
D2082V4, multiclass
            clus
vv           IL8 MUTATED IL8 WILD-TYPE
  STAGE I              2            89
  STAGE IA             0             1
  STAGE II             0            32
  STAGE IIA            0           138
  STAGE IIB            1             9
  STAGE IIC            0             1
  STAGE III            0            24
  STAGE IIIA           0            11
  STAGE IIIB           1            58
  STAGE IIIC           1            41
  STAGE IV             1            47
  STAGE IVA            0            18
  STAGE IVB            0             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  IL8 MUTATED     1   1   0   4
  IL8 WILD-TYPE  16  91 329  46
D2082V5, multiclass
    clus
vv   IL8 MUTATED IL8 WILD-TYPE
  T1           1            16
  T2           1            91
  T3           0           329
  T4           4            46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2
  IL8 MUTATED     3   2   1
  IL8 WILD-TYPE 284 111  86
D2082V6, multiclass
    clus
vv   IL8 MUTATED IL8 WILD-TYPE
  N0           3           284
  N1           2           111
  N2           1            86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2082V7, binary
               cls
clus              0   1
  IL8 MUTATED     3   1
  IL8 WILD-TYPE 372  64
[1] "tbl2"
               cls
clus            [,1] [,2]
  IL8 MUTATED      3    1
  IL8 WILD-TYPE  372   64
   clus
vv  IL8 MUTATED IL8 WILD-TYPE
  0           3           372
  1           1            64
[1] 2 2
[1] FALSE
D2082V8, binary
               cls
clus              0   1
  IL8 MUTATED     2   4
  IL8 WILD-TYPE 223 260
[1] "tbl2"
               cls
clus            [,1] [,2]
  IL8 MUTATED      2    4
  IL8 WILD-TYPE  223  260
        clus
vv       IL8 MUTATED IL8 WILD-TYPE
  FEMALE           2           223
  MALE             4           260
[1] 2 2
[1] FALSE
D2082V9, binary
               cls
clus              0   1
  IL8 MUTATED     4   1
  IL8 WILD-TYPE 346  21
[1] "tbl2"
               cls
clus            [,1] [,2]
  IL8 MUTATED      4    1
  IL8 WILD-TYPE  346   21
     clus
vv    IL8 MUTATED IL8 WILD-TYPE
  NO            4           346
  YES           1            21
[1] 2 2
[1] FALSE
               vv
clus            COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  IL8 MUTATED                      4                             1
  IL8 WILD-TYPE                  311                            46
               vv
clus            RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  IL8 MUTATED                       1                              0
  IL8 WILD-TYPE                   105                             10
D2082V10, multiclass
                                clus
vv                               IL8 MUTATED IL8 WILD-TYPE
  COLON ADENOCARCINOMA                     4           311
  COLON MUCINOUS ADENOCARCINOMA            1            46
  RECTAL ADENOCARCINOMA                    1           105
  RECTAL MUCINOUS ADENOCARCINOMA           0            10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             R0  R1  R2  RX
  IL8 MUTATED     3   0   0   2
  IL8 WILD-TYPE 342   4  31  23
D2082V11, multiclass
    clus
vv   IL8 MUTATED IL8 WILD-TYPE
  R0           3           342
  R1           0             4
  R2           0            31
  RX           2            23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2082V12, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  IL8 MUTATED                                  0     0
  IL8 WILD-TYPE                                1    11
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  IL8 MUTATED                           0     5
  IL8 WILD-TYPE                        22   221
D2082V13, multiclass
                                  clus
vv                                 IL8 MUTATED IL8 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      0            11
  BLACK OR AFRICAN AMERICAN                  0            22
  WHITE                                      5           221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2083) Variable = CLTCL1 MUTATION ANALYSIS
D2083V1, survival
                  sevent
clus2                0   1
  CLTCL1 MUTATED    17   2
  CLTCL1 WILD-TYPE 361  91
  CLTCL1 MUTATED CLTCL1 WILD-TYPE 
              19              452 
  CLTCL1 MUTATED CLTCL1 WILD-TYPE 
               2               91 
$`CLTCL1 MUTATED`
TCGA-AA-3660 TCGA-AA-3713 TCGA-AA-3818 TCGA-AA-3877 TCGA-AA-3972 TCGA-AA-3977 
       78.08        19.04         0.99        31.00        50.99        25.02 
TCGA-AA-A010 TCGA-AD-5900 TCGA-AZ-6599 TCGA-CA-6717 TCGA-CK-4950 TCGA-CM-5348 
       34.98         0.07         6.77        12.76        85.45        22.98 
TCGA-D5-6928 TCGA-F4-6808 TCGA-G4-6307 TCGA-G4-6315 TCGA-G4-6588 TCGA-AG-A002 
       11.64        33.67        55.04        61.91        26.17        20.98 
TCGA-AH-6549 
       17.49 

$`CLTCL1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 
       20.98        19.99        13.94        19.99        61.02         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       35.05        33.04        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       27.02        29.98        18.05         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
        2.01        21.99        16.08        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 
       41.00        39.98        18.05        40.96        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 
      106.75        22.36        62.79        88.21        49.41        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5912 
       10.06        14.30        17.56       148.01        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.03        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.04         9.44         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       16.24        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6310 
       74.56        65.85        53.62        44.68        85.48        63.62 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        35.80        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  CLTCL1 MUTATED CLTCL1 WILD-TYPE 
            0.07             0.00 
  CLTCL1 MUTATED CLTCL1 WILD-TYPE 
           85.45           148.01 
  CLTCL1 MUTATED CLTCL1 WILD-TYPE 
          25.020           20.035 
[1] "0.1 - 85.5 (25.0)"  "0.0 - 148.0 (20.0)"
[1] "hr=" "2.3"
D2083V2, continuous
D2083V3, binary
                  cls
clus                 0   1
  CLTCL1 MUTATED    18   2
  CLTCL1 WILD-TYPE 348 117
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CLTCL1 MUTATED     18    2
  CLTCL1 WILD-TYPE  348  117
        clus
vv       CLTCL1 MUTATED CLTCL1 WILD-TYPE
  COLON              18              348
  RECTUM              2              117
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CLTCL1 MUTATED         5        0        1         5         1         0
  CLTCL1 WILD-TYPE      86        1       31       133         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CLTCL1 MUTATED           0          0          3          0        3
  CLTCL1 WILD-TYPE        24         11         56         42       45
                  vv
clus               STAGE IVA STAGE IVB
  CLTCL1 MUTATED           0         0
  CLTCL1 WILD-TYPE        18         1
D2083V4, multiclass
            clus
vv           CLTCL1 MUTATED CLTCL1 WILD-TYPE
  STAGE I                 5               86
  STAGE IA                0                1
  STAGE II                1               31
  STAGE IIA               5              133
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              3               56
  STAGE IIIC              0               42
  STAGE IV                3               45
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  CLTCL1 MUTATED     2   4  13   1
  CLTCL1 WILD-TYPE  15  88 316  49
D2083V5, multiclass
    clus
vv   CLTCL1 MUTATED CLTCL1 WILD-TYPE
  T1              2               15
  T2              4               88
  T3             13              316
  T4              1               49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  CLTCL1 MUTATED    14   5   0
  CLTCL1 WILD-TYPE 273 108  87
D2083V6, multiclass
    clus
vv   CLTCL1 MUTATED CLTCL1 WILD-TYPE
  N0             14              273
  N1              5              108
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2083V7, binary
                  cls
clus                 0   1
  CLTCL1 MUTATED    13   3
  CLTCL1 WILD-TYPE 362  62
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CLTCL1 MUTATED     13    3
  CLTCL1 WILD-TYPE  362   62
   clus
vv  CLTCL1 MUTATED CLTCL1 WILD-TYPE
  0             13              362
  1              3               62
[1] 2 2
[1] FALSE
D2083V8, binary
                  cls
clus                 0   1
  CLTCL1 MUTATED     9  11
  CLTCL1 WILD-TYPE 216 253
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CLTCL1 MUTATED      9   11
  CLTCL1 WILD-TYPE  216  253
        clus
vv       CLTCL1 MUTATED CLTCL1 WILD-TYPE
  FEMALE              9              216
  MALE               11              253
[1] 2 2
[1] FALSE
D2083V9, binary
                  cls
clus                 0   1
  CLTCL1 MUTATED    16   1
  CLTCL1 WILD-TYPE 334  21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CLTCL1 MUTATED     16    1
  CLTCL1 WILD-TYPE  334   21
     clus
vv    CLTCL1 MUTATED CLTCL1 WILD-TYPE
  NO              16              334
  YES              1               21
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CLTCL1 MUTATED                     14                             4
  CLTCL1 WILD-TYPE                  301                            43
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CLTCL1 MUTATED                       2                              0
  CLTCL1 WILD-TYPE                   104                             10
D2083V10, multiclass
                                clus
vv                               CLTCL1 MUTATED CLTCL1 WILD-TYPE
  COLON ADENOCARCINOMA                       14              301
  COLON MUCINOUS ADENOCARCINOMA               4               43
  RECTAL ADENOCARCINOMA                       2              104
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  CLTCL1 MUTATED    13   1   2   2
  CLTCL1 WILD-TYPE 332   3  29  23
D2083V11, multiclass
    clus
vv   CLTCL1 MUTATED CLTCL1 WILD-TYPE
  R0             13              332
  R1              1                3
  R2              2               29
  RX              2               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2083V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CLTCL1 MUTATED                                  0     1
  CLTCL1 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  CLTCL1 MUTATED                           1     9
  CLTCL1 WILD-TYPE                        21   217
D2083V13, multiclass
                                  clus
vv                                 CLTCL1 MUTATED CLTCL1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                         9              217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2084) Variable = DCTN4 MUTATION ANALYSIS
D2084V1, survival
                 sevent
clus2               0   1
  DCTN4 MUTATED     3   3
  DCTN4 WILD-TYPE 375  90
  DCTN4 MUTATED DCTN4 WILD-TYPE 
              6             465 
  DCTN4 MUTATED DCTN4 WILD-TYPE 
              3              90 
$`DCTN4 MUTATED`
TCGA-A6-5657 TCGA-AA-3811 TCGA-AZ-5403 TCGA-CM-4743 TCGA-D5-6928 TCGA-G4-6626 
       31.63        10.06        62.79        23.05        11.64        46.75 

$`DCTN4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
      106.75        22.36        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
        1.91       124.27        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6930 
       12.43        14.30         9.04         9.44         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 
       22.09        13.78        35.80        26.17        91.79        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  DCTN4 MUTATED DCTN4 WILD-TYPE 
          10.06            0.00 
  DCTN4 MUTATED DCTN4 WILD-TYPE 
          62.79          148.01 
  DCTN4 MUTATED DCTN4 WILD-TYPE 
          27.34           20.12 
[1] "10.1 - 62.8 (27.3)" "0.0 - 148.0 (20.1)"
[1] "hr=" "2.1"
D2084V2, continuous
D2084V3, binary
                 cls
clus                0   1
  DCTN4 MUTATED     6   0
  DCTN4 WILD-TYPE 360 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DCTN4 MUTATED      6    0
  DCTN4 WILD-TYPE  360  119
        clus
vv       DCTN4 MUTATED DCTN4 WILD-TYPE
  COLON              6             360
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DCTN4 MUTATED         0        0        1         3         0         0
  DCTN4 WILD-TYPE      91        1       31       135        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DCTN4 MUTATED           1          0          1          0        0         0
  DCTN4 WILD-TYPE        23         11         58         42       48        18
                 vv
clus              STAGE IVB
  DCTN4 MUTATED           0
  DCTN4 WILD-TYPE         1
D2084V4, multiclass
            clus
vv           DCTN4 MUTATED DCTN4 WILD-TYPE
  STAGE I                0              91
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              3             135
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  DCTN4 MUTATED     0   0   6   0
  DCTN4 WILD-TYPE  17  92 323  50
D2084V5, multiclass
    clus
vv   DCTN4 MUTATED DCTN4 WILD-TYPE
  T1             0              17
  T2             0              92
  T3             6             323
  T4             0              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  DCTN4 MUTATED     4   1   1
  DCTN4 WILD-TYPE 283 112  86
D2084V6, multiclass
    clus
vv   DCTN4 MUTATED DCTN4 WILD-TYPE
  N0             4             283
  N1             1             112
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2084V7, binary
                 cls
clus                0   1
  DCTN4 MUTATED     5   0
  DCTN4 WILD-TYPE 370  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DCTN4 MUTATED      5    0
  DCTN4 WILD-TYPE  370   65
   clus
vv  DCTN4 MUTATED DCTN4 WILD-TYPE
  0             5             370
  1             0              65
[1] 2 2
[1] FALSE
D2084V8, binary
                 cls
clus                0   1
  DCTN4 MUTATED     1   5
  DCTN4 WILD-TYPE 224 259
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DCTN4 MUTATED      1    5
  DCTN4 WILD-TYPE  224  259
        clus
vv       DCTN4 MUTATED DCTN4 WILD-TYPE
  FEMALE             1             224
  MALE               5             259
[1] 2 2
[1] FALSE
D2084V9, binary
                 cls
clus                0   1
  DCTN4 MUTATED     6   0
  DCTN4 WILD-TYPE 344  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DCTN4 MUTATED      6    0
  DCTN4 WILD-TYPE  344   22
     clus
vv    DCTN4 MUTATED DCTN4 WILD-TYPE
  NO              6             344
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  DCTN4 MUTATED                      5                             1
  DCTN4 WILD-TYPE                  310                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  DCTN4 MUTATED                       0                              0
  DCTN4 WILD-TYPE                   106                             10
D2084V10, multiclass
                                clus
vv                               DCTN4 MUTATED DCTN4 WILD-TYPE
  COLON ADENOCARCINOMA                       5             310
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  DCTN4 MUTATED     5   0   0   0
  DCTN4 WILD-TYPE 340   4  31  25
D2084V11, multiclass
    clus
vv   DCTN4 MUTATED DCTN4 WILD-TYPE
  R0             5             340
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2084V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DCTN4 MUTATED                                  0     0
  DCTN4 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  DCTN4 MUTATED                           1     4
  DCTN4 WILD-TYPE                        21   222
D2084V13, multiclass
                                  clus
vv                                 DCTN4 MUTATED DCTN4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        4             222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2085) Variable = KLRK1 MUTATION ANALYSIS
D2085V1, survival
                 sevent
clus2               0   1
  KLRK1 MUTATED     6   2
  KLRK1 WILD-TYPE 372  91
  KLRK1 MUTATED KLRK1 WILD-TYPE 
              8             463 
  KLRK1 MUTATED KLRK1 WILD-TYPE 
              2              91 
$`KLRK1 MUTATED`
TCGA-A6-3809 TCGA-AA-3877 TCGA-AA-3966 TCGA-AA-A00N TCGA-CA-6718 TCGA-CK-4947 
       32.75        31.00         2.01         4.01        10.06        17.56 
TCGA-DM-A1HB TCGA-EI-6510 
      135.65        18.28 

$`KLRK1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 
       17.03        24.03        27.02        29.98        18.05         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       20.98        34.03        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       14.30       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
       44.32       131.51       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-F5-6464 TCGA-F5-6465 
        0.49        20.55        19.96        20.91         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  KLRK1 MUTATED KLRK1 WILD-TYPE 
           2.01            0.00 
  KLRK1 MUTATED KLRK1 WILD-TYPE 
         135.65          148.01 
  KLRK1 MUTATED KLRK1 WILD-TYPE 
          17.92           20.28 
[1] "2.0 - 135.7 (17.9)" "0.0 - 148.0 (20.3)"
[1] "hr=" "1.3"
D2085V2, continuous
D2085V3, binary
                 cls
clus                0   1
  KLRK1 MUTATED     7   1
  KLRK1 WILD-TYPE 359 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLRK1 MUTATED      7    1
  KLRK1 WILD-TYPE  359  118
        clus
vv       KLRK1 MUTATED KLRK1 WILD-TYPE
  COLON              7             359
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KLRK1 MUTATED         1        0        0         2         2         0
  KLRK1 WILD-TYPE      90        1       32       136         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  KLRK1 MUTATED           0          0          2          0        0         1
  KLRK1 WILD-TYPE        24         11         57         42       48        17
                 vv
clus              STAGE IVB
  KLRK1 MUTATED           0
  KLRK1 WILD-TYPE         1
D2085V4, multiclass
            clus
vv           KLRK1 MUTATED KLRK1 WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              2             136
  STAGE IIB              2               8
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             2              57
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  KLRK1 MUTATED     1   1   3   3
  KLRK1 WILD-TYPE  16  91 326  47
D2085V5, multiclass
    clus
vv   KLRK1 MUTATED KLRK1 WILD-TYPE
  T1             1              16
  T2             1              91
  T3             3             326
  T4             3              47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  KLRK1 MUTATED     6   2   0
  KLRK1 WILD-TYPE 281 111  87
D2085V6, multiclass
    clus
vv   KLRK1 MUTATED KLRK1 WILD-TYPE
  N0             6             281
  N1             2             111
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2085V7, binary
                 cls
clus                0   1
  KLRK1 MUTATED     7   0
  KLRK1 WILD-TYPE 368  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLRK1 MUTATED      7    0
  KLRK1 WILD-TYPE  368   65
   clus
vv  KLRK1 MUTATED KLRK1 WILD-TYPE
  0             7             368
  1             0              65
[1] 2 2
[1] FALSE
D2085V8, binary
                 cls
clus                0   1
  KLRK1 MUTATED     5   3
  KLRK1 WILD-TYPE 220 261
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLRK1 MUTATED      5    3
  KLRK1 WILD-TYPE  220  261
        clus
vv       KLRK1 MUTATED KLRK1 WILD-TYPE
  FEMALE             5             220
  MALE               3             261
[1] 2 2
[1] FALSE
D2085V9, binary
                 cls
clus                0   1
  KLRK1 MUTATED     5   0
  KLRK1 WILD-TYPE 345  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLRK1 MUTATED      5    0
  KLRK1 WILD-TYPE  345   22
     clus
vv    KLRK1 MUTATED KLRK1 WILD-TYPE
  NO              5             345
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  KLRK1 MUTATED                      2                             4
  KLRK1 WILD-TYPE                  313                            43
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  KLRK1 MUTATED                       1                              0
  KLRK1 WILD-TYPE                   105                             10
D2085V10, multiclass
                                clus
vv                               KLRK1 MUTATED KLRK1 WILD-TYPE
  COLON ADENOCARCINOMA                       2             313
  COLON MUCINOUS ADENOCARCINOMA              4              43
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  KLRK1 MUTATED     4   0   0   2
  KLRK1 WILD-TYPE 341   4  31  23
D2085V11, multiclass
    clus
vv   KLRK1 MUTATED KLRK1 WILD-TYPE
  R0             4             341
  R1             0               4
  R2             0              31
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2085V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KLRK1 MUTATED                                  0     1
  KLRK1 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  KLRK1 MUTATED                           0     4
  KLRK1 WILD-TYPE                        22   222
D2085V13, multiclass
                                  clus
vv                                 KLRK1 MUTATED KLRK1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        4             222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2086) Variable = MGAT5 MUTATION ANALYSIS
D2086V1, survival
                 sevent
clus2               0   1
  MGAT5 MUTATED     9   3
  MGAT5 WILD-TYPE 369  90
  MGAT5 MUTATED MGAT5 WILD-TYPE 
             12             459 
  MGAT5 MUTATED MGAT5 WILD-TYPE 
              3              90 
$`MGAT5 MUTATED`
TCGA-A6-2672 TCGA-AA-3492 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-A00U TCGA-AZ-5403 
       46.65         3.02        30.05        53.00        17.03        62.79 
TCGA-AZ-6605 TCGA-CA-6717 TCGA-CM-5860 TCGA-CM-6162 TCGA-G4-6309 TCGA-G4-6315 
        5.23        12.76        32.02        12.00        85.48        61.91 

$`MGAT5 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 
       20.12        19.66        20.28         7.04         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
        0.99        31.07        31.07        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5407 
       58.39         1.41         5.13       106.75        22.36        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6606 
       49.41         6.77        12.10       100.01        29.56        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07        12.20        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6317 TCGA-G4-6321 
       53.62        44.68        55.04        63.62        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  MGAT5 MUTATED MGAT5 WILD-TYPE 
           3.02            0.00 
  MGAT5 MUTATED MGAT5 WILD-TYPE 
          85.48          148.01 
  MGAT5 MUTATED MGAT5 WILD-TYPE 
         31.035          20.120 
[1] "3.0 - 85.5 (31.0)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.1"
D2086V2, continuous
D2086V3, binary
                 cls
clus                0   1
  MGAT5 MUTATED    13   0
  MGAT5 WILD-TYPE 353 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MGAT5 MUTATED     13    0
  MGAT5 WILD-TYPE  353  119
        clus
vv       MGAT5 MUTATED MGAT5 WILD-TYPE
  COLON             13             353
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MGAT5 MUTATED         0        0        3         3         1         0
  MGAT5 WILD-TYPE      91        1       29       135         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MGAT5 MUTATED           0          0          5          0        1         0
  MGAT5 WILD-TYPE        24         11         54         42       47        18
                 vv
clus              STAGE IVB
  MGAT5 MUTATED           0
  MGAT5 WILD-TYPE         1
D2086V4, multiclass
            clus
vv           MGAT5 MUTATED MGAT5 WILD-TYPE
  STAGE I                0              91
  STAGE IA               0               1
  STAGE II               3              29
  STAGE IIA              3             135
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             5              54
  STAGE IIIC             0              42
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  MGAT5 MUTATED     0   0  11   2
  MGAT5 WILD-TYPE  17  92 318  48
D2086V5, multiclass
    clus
vv   MGAT5 MUTATED MGAT5 WILD-TYPE
  T1             0              17
  T2             0              92
  T3            11             318
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  MGAT5 MUTATED     7   6   0
  MGAT5 WILD-TYPE 280 107  87
D2086V6, multiclass
    clus
vv   MGAT5 MUTATED MGAT5 WILD-TYPE
  N0             7             280
  N1             6             107
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2086V7, binary
                 cls
clus                0   1
  MGAT5 MUTATED    10   1
  MGAT5 WILD-TYPE 365  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MGAT5 MUTATED     10    1
  MGAT5 WILD-TYPE  365   64
   clus
vv  MGAT5 MUTATED MGAT5 WILD-TYPE
  0            10             365
  1             1              64
[1] 2 2
[1] FALSE
D2086V8, binary
                 cls
clus                0   1
  MGAT5 MUTATED     5   8
  MGAT5 WILD-TYPE 220 256
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MGAT5 MUTATED      5    8
  MGAT5 WILD-TYPE  220  256
        clus
vv       MGAT5 MUTATED MGAT5 WILD-TYPE
  FEMALE             5             220
  MALE               8             256
[1] 2 2
[1] FALSE
D2086V9, binary
                 cls
clus                0   1
  MGAT5 MUTATED    12   0
  MGAT5 WILD-TYPE 338  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MGAT5 MUTATED     12    0
  MGAT5 WILD-TYPE  338   22
     clus
vv    MGAT5 MUTATED MGAT5 WILD-TYPE
  NO             12             338
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MGAT5 MUTATED                     11                             2
  MGAT5 WILD-TYPE                  304                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MGAT5 MUTATED                       0                              0
  MGAT5 WILD-TYPE                   106                             10
D2086V10, multiclass
                                clus
vv                               MGAT5 MUTATED MGAT5 WILD-TYPE
  COLON ADENOCARCINOMA                      11             304
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  MGAT5 MUTATED     9   0   0   2
  MGAT5 WILD-TYPE 336   4  31  23
D2086V11, multiclass
    clus
vv   MGAT5 MUTATED MGAT5 WILD-TYPE
  R0             9             336
  R1             0               4
  R2             0              31
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2086V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MGAT5 MUTATED                                  0     1
  MGAT5 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  MGAT5 MUTATED                           1     7
  MGAT5 WILD-TYPE                        21   219
D2086V13, multiclass
                                  clus
vv                                 MGAT5 MUTATED MGAT5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        7             219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2087) Variable = SPANXN3 MUTATION ANALYSIS
D2087V1, survival
                   sevent
clus2                 0   1
  SPANXN3 MUTATED     5   3
  SPANXN3 WILD-TYPE 373  90
  SPANXN3 MUTATED SPANXN3 WILD-TYPE 
                8               463 
  SPANXN3 MUTATED SPANXN3 WILD-TYPE 
                3                90 
$`SPANXN3 MUTATED`
TCGA-AU-6004 TCGA-AY-6386 TCGA-AZ-4682 TCGA-CM-4743 TCGA-D5-6533 TCGA-F4-6460 
       27.09        17.82        22.36        23.05         1.32        31.96 
TCGA-AG-A002 TCGA-DY-A1DD 
       20.98        57.24 

$`SPANXN3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 
       22.42        27.42        10.88         0.20        14.50        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        33.01        21.44        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
      106.75        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
        1.91       124.27        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
        8.61        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
      126.44        41.36        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  SPANXN3 MUTATED SPANXN3 WILD-TYPE 
             1.32              0.00 
  SPANXN3 MUTATED SPANXN3 WILD-TYPE 
            57.24            148.01 
  SPANXN3 MUTATED SPANXN3 WILD-TYPE 
           22.705            20.050 
[1] "1.3 - 57.2 (22.7)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "2"  
D2087V2, continuous
D2087V3, binary
                   cls
clus                  0   1
  SPANXN3 MUTATED     7   2
  SPANXN3 WILD-TYPE 359 117
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SPANXN3 MUTATED      7    2
  SPANXN3 WILD-TYPE  359  117
        clus
vv       SPANXN3 MUTATED SPANXN3 WILD-TYPE
  COLON                7               359
  RECTUM               2               117
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SPANXN3 MUTATED         2        0        0         1         1         0
  SPANXN3 WILD-TYPE      89        1       32       137         9         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SPANXN3 MUTATED           0          0          4          0        0
  SPANXN3 WILD-TYPE        24         11         55         42       48
                   vv
clus                STAGE IVA STAGE IVB
  SPANXN3 MUTATED           1         0
  SPANXN3 WILD-TYPE        17         1
D2087V4, multiclass
            clus
vv           SPANXN3 MUTATED SPANXN3 WILD-TYPE
  STAGE I                  2                89
  STAGE IA                 0                 1
  STAGE II                 0                32
  STAGE IIA                1               137
  STAGE IIB                1                 9
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               0                11
  STAGE IIIB               4                55
  STAGE IIIC               0                42
  STAGE IV                 0                48
  STAGE IVA                1                17
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  SPANXN3 MUTATED     0   2   5   2
  SPANXN3 WILD-TYPE  17  90 324  48
D2087V5, multiclass
    clus
vv   SPANXN3 MUTATED SPANXN3 WILD-TYPE
  T1               0                17
  T2               2                90
  T3               5               324
  T4               2                48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  SPANXN3 MUTATED     6   3   0
  SPANXN3 WILD-TYPE 281 110  87
D2087V6, multiclass
    clus
vv   SPANXN3 MUTATED SPANXN3 WILD-TYPE
  N0               6               281
  N1               3               110
  N2               0                87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2087V7, binary
                   cls
clus                  0   1
  SPANXN3 MUTATED     7   1
  SPANXN3 WILD-TYPE 368  64
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SPANXN3 MUTATED      7    1
  SPANXN3 WILD-TYPE  368   64
   clus
vv  SPANXN3 MUTATED SPANXN3 WILD-TYPE
  0               7               368
  1               1                64
[1] 2 2
[1] FALSE
D2087V8, binary
                   cls
clus                  0   1
  SPANXN3 MUTATED     6   3
  SPANXN3 WILD-TYPE 219 261
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SPANXN3 MUTATED      6    3
  SPANXN3 WILD-TYPE  219  261
        clus
vv       SPANXN3 MUTATED SPANXN3 WILD-TYPE
  FEMALE               6               219
  MALE                 3               261
[1] 2 2
[1] FALSE
D2087V9, binary
                   cls
clus                  0   1
  SPANXN3 MUTATED     5   0
  SPANXN3 WILD-TYPE 345  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SPANXN3 MUTATED      5    0
  SPANXN3 WILD-TYPE  345   22
     clus
vv    SPANXN3 MUTATED SPANXN3 WILD-TYPE
  NO                5               345
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SPANXN3 MUTATED                      7                             0
  SPANXN3 WILD-TYPE                  308                            47
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SPANXN3 MUTATED                       2                              0
  SPANXN3 WILD-TYPE                   104                             10
D2087V10, multiclass
                                clus
vv                               SPANXN3 MUTATED SPANXN3 WILD-TYPE
  COLON ADENOCARCINOMA                         7               308
  COLON MUCINOUS ADENOCARCINOMA                0                47
  RECTAL ADENOCARCINOMA                        2               104
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  SPANXN3 MUTATED     7   0   0   1
  SPANXN3 WILD-TYPE 338   4  31  24
D2087V11, multiclass
    clus
vv   SPANXN3 MUTATED SPANXN3 WILD-TYPE
  R0               7               338
  R1               0                 4
  R2               0                31
  RX               1                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2087V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SPANXN3 MUTATED                                  0     0
  SPANXN3 WILD-TYPE                                1    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  SPANXN3 MUTATED                           1     7
  SPANXN3 WILD-TYPE                        21   219
D2087V13, multiclass
                                  clus
vv                                 SPANXN3 MUTATED SPANXN3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                      1                21
  WHITE                                          7               219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2088) Variable = CYP27B1 MUTATION ANALYSIS
D2088V1, survival
                   sevent
clus2                 0   1
  CYP27B1 MUTATED     6   2
  CYP27B1 WILD-TYPE 372  91
  CYP27B1 MUTATED CYP27B1 WILD-TYPE 
                8               463 
  CYP27B1 MUTATED CYP27B1 WILD-TYPE 
                2                91 
$`CYP27B1 MUTATED`
TCGA-A6-5665 TCGA-A6-6780 TCGA-AA-3715 TCGA-AA-3877 TCGA-AA-A01Q TCGA-AZ-4315 
       22.06        20.12        19.04        31.00         1.02        58.39 
TCGA-F4-6570 TCGA-F4-6807 
        6.18        16.24 

$`CYP27B1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       27.02        29.98        18.05         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
       38.07        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       31.96        35.74        47.87         1.55        34.42        41.42 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  CYP27B1 MUTATED CYP27B1 WILD-TYPE 
             1.02              0.00 
  CYP27B1 MUTATED CYP27B1 WILD-TYPE 
            58.39            148.01 
  CYP27B1 MUTATED CYP27B1 WILD-TYPE 
            19.58             20.28 
[1] "1.0 - 58.4 (19.6)"  "0.0 - 148.0 (20.3)"
[1] "hr=" "1.5"
D2088V2, continuous
D2088V3, binary
                   cls
clus                  0   1
  CYP27B1 MUTATED     8   0
  CYP27B1 WILD-TYPE 358 119
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CYP27B1 MUTATED      8    0
  CYP27B1 WILD-TYPE  358  119
        clus
vv       CYP27B1 MUTATED CYP27B1 WILD-TYPE
  COLON                8               358
  RECTUM               0               119
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CYP27B1 MUTATED         1        0        2         4         0         0
  CYP27B1 WILD-TYPE      90        1       30       134        10         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CYP27B1 MUTATED           0          0          0          1        0
  CYP27B1 WILD-TYPE        24         11         59         41       48
                   vv
clus                STAGE IVA STAGE IVB
  CYP27B1 MUTATED           0         0
  CYP27B1 WILD-TYPE        18         1
D2088V4, multiclass
            clus
vv           CYP27B1 MUTATED CYP27B1 WILD-TYPE
  STAGE I                  1                90
  STAGE IA                 0                 1
  STAGE II                 2                30
  STAGE IIA                4               134
  STAGE IIB                0                10
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               0                11
  STAGE IIIB               0                59
  STAGE IIIC               1                41
  STAGE IV                 0                48
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  CYP27B1 MUTATED     1   0   7   0
  CYP27B1 WILD-TYPE  16  92 322  50
D2088V5, multiclass
    clus
vv   CYP27B1 MUTATED CYP27B1 WILD-TYPE
  T1               1                16
  T2               0                92
  T3               7               322
  T4               0                50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  CYP27B1 MUTATED     7   0   1
  CYP27B1 WILD-TYPE 280 113  86
D2088V6, multiclass
    clus
vv   CYP27B1 MUTATED CYP27B1 WILD-TYPE
  N0               7               280
  N1               0               113
  N2               1                86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2088V7, binary
                   cls
clus                  0   1
  CYP27B1 MUTATED     7   0
  CYP27B1 WILD-TYPE 368  65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CYP27B1 MUTATED      7    0
  CYP27B1 WILD-TYPE  368   65
   clus
vv  CYP27B1 MUTATED CYP27B1 WILD-TYPE
  0               7               368
  1               0                65
[1] 2 2
[1] FALSE
D2088V8, binary
                   cls
clus                  0   1
  CYP27B1 MUTATED     5   3
  CYP27B1 WILD-TYPE 220 261
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CYP27B1 MUTATED      5    3
  CYP27B1 WILD-TYPE  220  261
        clus
vv       CYP27B1 MUTATED CYP27B1 WILD-TYPE
  FEMALE               5               220
  MALE                 3               261
[1] 2 2
[1] FALSE
D2088V9, binary
                   cls
clus                  0   1
  CYP27B1 MUTATED     7   0
  CYP27B1 WILD-TYPE 343  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CYP27B1 MUTATED      7    0
  CYP27B1 WILD-TYPE  343   22
     clus
vv    CYP27B1 MUTATED CYP27B1 WILD-TYPE
  NO                7               343
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CYP27B1 MUTATED                      6                             2
  CYP27B1 WILD-TYPE                  309                            45
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CYP27B1 MUTATED                       0                              0
  CYP27B1 WILD-TYPE                   106                             10
D2088V10, multiclass
                                clus
vv                               CYP27B1 MUTATED CYP27B1 WILD-TYPE
  COLON ADENOCARCINOMA                         6               309
  COLON MUCINOUS ADENOCARCINOMA                2                45
  RECTAL ADENOCARCINOMA                        0               106
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  CYP27B1 MUTATED     7   0   0   0
  CYP27B1 WILD-TYPE 338   4  31  25
D2088V11, multiclass
    clus
vv   CYP27B1 MUTATED CYP27B1 WILD-TYPE
  R0               7               338
  R1               0                 4
  R2               0                31
  RX               0                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2088V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CYP27B1 MUTATED                                  0     0
  CYP27B1 WILD-TYPE                                1    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  CYP27B1 MUTATED                           0     5
  CYP27B1 WILD-TYPE                        22   221
D2088V13, multiclass
                                  clus
vv                                 CYP27B1 MUTATED CYP27B1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                      0                22
  WHITE                                          5               221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2089) Variable = CASC5 MUTATION ANALYSIS
D2089V1, survival
                 sevent
clus2               0   1
  CASC5 MUTATED    18   2
  CASC5 WILD-TYPE 360  91
  CASC5 MUTATED CASC5 WILD-TYPE 
             20             451 
  CASC5 MUTATED CASC5 WILD-TYPE 
              2              91 
$`CASC5 MUTATED`
TCGA-AA-3510 TCGA-AA-3831 TCGA-AA-3977 TCGA-AA-A010 TCGA-AD-6889 TCGA-AU-6004 
       63.98        17.98        25.02        34.98        56.55        27.09 
TCGA-AZ-4315 TCGA-AZ-4681 TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-4743 TCGA-CM-5864 
       58.39       106.75        12.76        10.06        23.05        15.02 
TCGA-CM-6674 TCGA-D5-6540 TCGA-D5-6927 TCGA-F4-6570 TCGA-G4-6309 TCGA-AG-3892 
       12.95        16.14         9.44         6.18        85.48        13.02 
TCGA-AG-A002 TCGA-EF-5830 
       20.98         0.49 

$`CASC5 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 
       40.96         0.07        21.37        15.52         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
       16.31         0.95        33.01        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
        5.13        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       12.20        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
      124.27        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       14.04        11.01        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 
       17.85         4.80        17.13        12.49        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6928 
        3.68         4.41        12.43        14.30         9.04        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 
      117.07        98.24         8.61        31.96        35.74        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       53.62        44.68        55.04        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       17.95        36.95        17.03        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  CASC5 MUTATED CASC5 WILD-TYPE 
           0.49            0.00 
  CASC5 MUTATED CASC5 WILD-TYPE 
         106.75          148.01 
  CASC5 MUTATED CASC5 WILD-TYPE 
          19.48           20.19 
[1] "0.5 - 106.8 (19.5)" "0.0 - 148.0 (20.2)"
[1] "hr=" "2.4"
D2089V2, continuous
D2089V3, binary
                 cls
clus                0   1
  CASC5 MUTATED    19   3
  CASC5 WILD-TYPE 347 116
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASC5 MUTATED     19    3
  CASC5 WILD-TYPE  347  116
        clus
vv       CASC5 MUTATED CASC5 WILD-TYPE
  COLON             19             347
  RECTUM             3             116
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CASC5 MUTATED         6        0        1        11         2         0
  CASC5 WILD-TYPE      85        1       31       127         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CASC5 MUTATED           0          0          1          0        0         0
  CASC5 WILD-TYPE        24         11         58         42       48        18
                 vv
clus              STAGE IVB
  CASC5 MUTATED           0
  CASC5 WILD-TYPE         1
D2089V4, multiclass
            clus
vv           CASC5 MUTATED CASC5 WILD-TYPE
  STAGE I                6              85
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA             11             127
  STAGE IIB              2               8
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CASC5 MUTATED     1   6  13   2
  CASC5 WILD-TYPE  16  86 316  48
D2089V5, multiclass
    clus
vv   CASC5 MUTATED CASC5 WILD-TYPE
  T1             1              16
  T2             6              86
  T3            13             316
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  CASC5 MUTATED    21   1   0
  CASC5 WILD-TYPE 266 112  87
D2089V6, multiclass
    clus
vv   CASC5 MUTATED CASC5 WILD-TYPE
  N0            21             266
  N1             1             112
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2089V7, binary
                 cls
clus                0   1
  CASC5 MUTATED    20   0
  CASC5 WILD-TYPE 355  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASC5 MUTATED     20    0
  CASC5 WILD-TYPE  355   65
   clus
vv  CASC5 MUTATED CASC5 WILD-TYPE
  0            20             355
  1             0              65
[1] 2 2
[1] FALSE
D2089V8, binary
                 cls
clus                0   1
  CASC5 MUTATED     7  15
  CASC5 WILD-TYPE 218 249
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASC5 MUTATED      7   15
  CASC5 WILD-TYPE  218  249
        clus
vv       CASC5 MUTATED CASC5 WILD-TYPE
  FEMALE             7             218
  MALE              15             249
[1] 2 2
[1] FALSE
D2089V9, binary
                 cls
clus                0   1
  CASC5 MUTATED    17   0
  CASC5 WILD-TYPE 333  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CASC5 MUTATED     17    0
  CASC5 WILD-TYPE  333   22
     clus
vv    CASC5 MUTATED CASC5 WILD-TYPE
  NO             17             333
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CASC5 MUTATED                     17                             2
  CASC5 WILD-TYPE                  298                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CASC5 MUTATED                       3                              0
  CASC5 WILD-TYPE                   103                             10
D2089V10, multiclass
                                clus
vv                               CASC5 MUTATED CASC5 WILD-TYPE
  COLON ADENOCARCINOMA                      17             298
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      3             103
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  CASC5 MUTATED    17   0   0   3
  CASC5 WILD-TYPE 328   4  31  22
D2089V11, multiclass
    clus
vv   CASC5 MUTATED CASC5 WILD-TYPE
  R0            17             328
  R1             0               4
  R2             0              31
  RX             3              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2089V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CASC5 MUTATED                                  0     3
  CASC5 WILD-TYPE                                1     8
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CASC5 MUTATED                           1    11
  CASC5 WILD-TYPE                        21   215
D2089V13, multiclass
                                  clus
vv                                 CASC5 MUTATED CASC5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        3               8
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                       11             215
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2090) Variable = PRKCG MUTATION ANALYSIS
D2090V1, survival
                 sevent
clus2               0   1
  PRKCG MUTATED    20   3
  PRKCG WILD-TYPE 358  90
  PRKCG MUTATED PRKCG WILD-TYPE 
             23             448 
  PRKCG MUTATED PRKCG WILD-TYPE 
              3              90 
$`PRKCG MUTATED`
TCGA-A6-2672 TCGA-A6-5661 TCGA-AA-3514 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3845 
       46.65        33.53         1.02         6.05         0.92         0.00 
TCGA-AA-3947 TCGA-AA-3966 TCGA-AA-A00R TCGA-AA-A010 TCGA-AZ-4315 TCGA-AZ-5407 
       33.01         2.01         0.99        34.98        58.39        88.21 
TCGA-CA-6717 TCGA-CK-4952 TCGA-CM-6168 TCGA-D5-7000 TCGA-DM-A1DA TCGA-G4-6588 
       12.76        15.62        12.99        10.26         7.50        26.17 
TCGA-AG-A002 TCGA-AG-A032 TCGA-DC-6158 TCGA-DY-A0XA TCGA-F5-6702 
       20.98        38.04        10.98       126.44        28.57 

$`PRKCG WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       31.63        30.44        29.19        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
       63.98         6.97        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02        78.08         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
       14.01        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
       14.93        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 
       31.00         2.01        12.99        24.00        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
        2.01        20.98        34.03        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
        4.01        27.02        42.02        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07        12.20        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
      148.01        85.45        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       14.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-DM-A0X9 TCGA-DM-A0XD 
        4.80         1.51        12.00        11.38       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
      140.38        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       22.09        13.78        35.80        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       41.00       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6160 
        7.17        15.02         5.03        13.97        27.95        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD 
        5.95         4.01         5.03         5.29        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6811 
       20.91        18.28         9.96        49.51        31.30        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  PRKCG MUTATED PRKCG WILD-TYPE 
              0               0 
  PRKCG MUTATED PRKCG WILD-TYPE 
         126.44          148.01 
  PRKCG MUTATED PRKCG WILD-TYPE 
         15.620          20.235 
[1] "0.0 - 126.4 (15.6)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.5"
D2090V2, continuous
D2090V3, binary
                 cls
clus                0   1
  PRKCG MUTATED    19   5
  PRKCG WILD-TYPE 347 114
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRKCG MUTATED     19    5
  PRKCG WILD-TYPE  347  114
        clus
vv       PRKCG MUTATED PRKCG WILD-TYPE
  COLON             19             347
  RECTUM             5             114
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PRKCG MUTATED         6        0        0         8         3         0
  PRKCG WILD-TYPE      85        1       32       130         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PRKCG MUTATED           1          0          2          2        1         1
  PRKCG WILD-TYPE        23         11         57         40       47        17
                 vv
clus              STAGE IVB
  PRKCG MUTATED           0
  PRKCG WILD-TYPE         1
D2090V4, multiclass
            clus
vv           PRKCG MUTATED PRKCG WILD-TYPE
  STAGE I                6              85
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              8             130
  STAGE IIB              3               7
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             2              57
  STAGE IIIC             2              40
  STAGE IV               1              47
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PRKCG MUTATED     1   5  13   5
  PRKCG WILD-TYPE  16  87 316  45
D2090V5, multiclass
    clus
vv   PRKCG MUTATED PRKCG WILD-TYPE
  T1             1              16
  T2             5              87
  T3            13             316
  T4             5              45
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  PRKCG MUTATED    17   4   3
  PRKCG WILD-TYPE 270 109  84
D2090V6, multiclass
    clus
vv   PRKCG MUTATED PRKCG WILD-TYPE
  N0            17             270
  N1             4             109
  N2             3              84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2090V7, binary
                 cls
clus                0   1
  PRKCG MUTATED    21   2
  PRKCG WILD-TYPE 354  63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRKCG MUTATED     21    2
  PRKCG WILD-TYPE  354   63
   clus
vv  PRKCG MUTATED PRKCG WILD-TYPE
  0            21             354
  1             2              63
[1] 2 2
[1] FALSE
D2090V8, binary
                 cls
clus                0   1
  PRKCG MUTATED    18   6
  PRKCG WILD-TYPE 207 258
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRKCG MUTATED     18    6
  PRKCG WILD-TYPE  207  258
        clus
vv       PRKCG MUTATED PRKCG WILD-TYPE
  FEMALE            18             207
  MALE               6             258
[1] 2 2
[1] FALSE
D2090V9, binary
                 cls
clus                0   1
  PRKCG MUTATED    16   1
  PRKCG WILD-TYPE 334  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PRKCG MUTATED     16    1
  PRKCG WILD-TYPE  334   21
     clus
vv    PRKCG MUTATED PRKCG WILD-TYPE
  NO             16             334
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PRKCG MUTATED                     14                             5
  PRKCG WILD-TYPE                  301                            42
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PRKCG MUTATED                       5                              0
  PRKCG WILD-TYPE                   101                             10
D2090V10, multiclass
                                clus
vv                               PRKCG MUTATED PRKCG WILD-TYPE
  COLON ADENOCARCINOMA                      14             301
  COLON MUCINOUS ADENOCARCINOMA              5              42
  RECTAL ADENOCARCINOMA                      5             101
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  PRKCG MUTATED    16   0   1   3
  PRKCG WILD-TYPE 329   4  30  22
D2090V11, multiclass
    clus
vv   PRKCG MUTATED PRKCG WILD-TYPE
  R0            16             329
  R1             0               4
  R2             1              30
  RX             3              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2090V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PRKCG MUTATED                                  0     1
  PRKCG WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PRKCG MUTATED                           2    11
  PRKCG WILD-TYPE                        20   215
D2090V13, multiclass
                                  clus
vv                                 PRKCG MUTATED PRKCG WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    2              20
  WHITE                                       11             215
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2091) Variable = COL11A1 MUTATION ANALYSIS
D2091V1, survival
                   sevent
clus2                 0   1
  COL11A1 MUTATED    40   9
  COL11A1 WILD-TYPE 338  84
  COL11A1 MUTATED COL11A1 WILD-TYPE 
               49               422 
  COL11A1 MUTATED COL11A1 WILD-TYPE 
                9                84 
$`COL11A1 MUTATED`
TCGA-A6-5665 TCGA-A6-6138 TCGA-A6-6648 TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3552 
       22.06        22.52        25.18         3.02        63.98        13.02 
TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3715 
        6.05         0.92        37.05         5.03        26.99        19.04 
TCGA-AA-3947 TCGA-AA-3968 TCGA-AA-3977 TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01Q 
       33.01        21.99        25.02        34.98         1.02         1.02 
TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6895 TCGA-AD-6963 TCGA-AU-3779 TCGA-AY-6197 
        0.07        56.55         0.72        27.42        14.50        21.44 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-CA-6717 TCGA-CM-5860 
       58.39         1.41        88.21         6.77        12.76        32.02 
TCGA-CM-5868 TCGA-CM-6171 TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6928 TCGA-DM-A28K 
       17.03        14.04        14.30         9.44        11.64        98.24 
TCGA-G4-6304 TCGA-G4-6309 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6626 TCGA-G4-6628 
       53.62        85.48        35.80        26.17        46.75        79.69 
TCGA-AG-3586 TCGA-AG-3599 TCGA-AG-3892 TCGA-AG-A002 TCGA-DC-5337 TCGA-DY-A1DC 
        1.02        12.03        13.02        20.98        15.02        41.36 
TCGA-DY-A1DF 
       24.13 

$`COL11A1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6649 
       22.09        32.71        27.09         8.38        25.08        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 
       20.28         7.04         1.02        35.01         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
       13.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       36.03         8.05        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       33.99        21.01        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 
        6.97        54.02         2.01        14.01        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 
       15.02        11.01         5.98        19.00        36.00        85.05 
TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 
       31.00         2.01        12.99        24.00        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3972 
        2.01        20.98        34.03         2.01        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 
        0.92        41.00        39.98        18.05        40.96        21.37 
TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6964 TCGA-AD-6965 
       15.52         0.79         5.79        22.42        10.88         0.20 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4616 
       27.09        16.31         0.95        33.01        17.82         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6601 
      106.75        22.36        62.79        49.41        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07        12.20        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.03        22.98        30.08        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       15.02        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 
       21.99        14.99        12.99        13.02        15.02        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6930 
        3.68         4.41        12.43         9.04         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-F4-6459 
       81.37       119.93        35.97        60.79       117.07         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 
       35.31       133.18        74.56        65.85        44.68        55.04 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6625 
       63.62        61.91        36.00        22.09        13.78        91.79 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       20.05        24.00        46.03        34.03         2.01        50.04 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5869 
       33.17         6.97         4.73        78.12         7.17         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DD TCGA-DY-A1DG TCGA-DY-A1H8 
        5.03         5.29       126.44        57.24        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  COL11A1 MUTATED COL11A1 WILD-TYPE 
             0.07              0.00 
  COL11A1 MUTATED COL11A1 WILD-TYPE 
            98.24            148.01 
  COL11A1 MUTATED COL11A1 WILD-TYPE 
           21.440            20.085 
[1] "0.1 - 98.2 (21.4)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.1"
D2091V2, continuous
D2091V3, binary
                   cls
clus                  0   1
  COL11A1 MUTATED    45   7
  COL11A1 WILD-TYPE 321 112
[1] "tbl2"
                   cls
clus                [,1] [,2]
  COL11A1 MUTATED     45    7
  COL11A1 WILD-TYPE  321  112
        clus
vv       COL11A1 MUTATED COL11A1 WILD-TYPE
  COLON               45               321
  RECTUM               7               112
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  COL11A1 MUTATED        11        0        6        18         4         0
  COL11A1 WILD-TYPE      80        1       26       120         6         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  COL11A1 MUTATED           2          0          1          2        3
  COL11A1 WILD-TYPE        22         11         58         40       45
                   vv
clus                STAGE IVA STAGE IVB
  COL11A1 MUTATED           2         0
  COL11A1 WILD-TYPE        16         1
D2091V4, multiclass
            clus
vv           COL11A1 MUTATED COL11A1 WILD-TYPE
  STAGE I                 11                80
  STAGE IA                 0                 1
  STAGE II                 6                26
  STAGE IIA               18               120
  STAGE IIB                4                 6
  STAGE IIC                0                 1
  STAGE III                2                22
  STAGE IIIA               0                11
  STAGE IIIB               1                58
  STAGE IIIC               2                40
  STAGE IV                 3                45
  STAGE IVA                2                16
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  COL11A1 MUTATED     3   9  32   8
  COL11A1 WILD-TYPE  14  83 297  42
D2091V5, multiclass
    clus
vv   COL11A1 MUTATED COL11A1 WILD-TYPE
  T1               3                14
  T2               9                83
  T3              32               297
  T4               8                42
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  COL11A1 MUTATED    42   5   5
  COL11A1 WILD-TYPE 245 108  82
D2091V6, multiclass
    clus
vv   COL11A1 MUTATED COL11A1 WILD-TYPE
  N0              42               245
  N1               5               108
  N2               5                82
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2091V7, binary
                   cls
clus                  0   1
  COL11A1 MUTATED    40   5
  COL11A1 WILD-TYPE 335  60
[1] "tbl2"
                   cls
clus                [,1] [,2]
  COL11A1 MUTATED     40    5
  COL11A1 WILD-TYPE  335   60
   clus
vv  COL11A1 MUTATED COL11A1 WILD-TYPE
  0              40               335
  1               5                60
[1] 2 2
[1] FALSE
D2091V8, binary
                   cls
clus                  0   1
  COL11A1 MUTATED    26  26
  COL11A1 WILD-TYPE 199 238
[1] "tbl2"
                   cls
clus                [,1] [,2]
  COL11A1 MUTATED     26   26
  COL11A1 WILD-TYPE  199  238
        clus
vv       COL11A1 MUTATED COL11A1 WILD-TYPE
  FEMALE              26               199
  MALE                26               238
[1] 2 2
[1] FALSE
D2091V9, binary
                   cls
clus                  0   1
  COL11A1 MUTATED    40   0
  COL11A1 WILD-TYPE 310  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  COL11A1 MUTATED     40    0
  COL11A1 WILD-TYPE  310   22
     clus
vv    COL11A1 MUTATED COL11A1 WILD-TYPE
  NO               40               310
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  COL11A1 MUTATED                     40                             5
  COL11A1 WILD-TYPE                  275                            42
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  COL11A1 MUTATED                       5                              0
  COL11A1 WILD-TYPE                   101                             10
D2091V10, multiclass
                                clus
vv                               COL11A1 MUTATED COL11A1 WILD-TYPE
  COLON ADENOCARCINOMA                        40               275
  COLON MUCINOUS ADENOCARCINOMA                5                42
  RECTAL ADENOCARCINOMA                        5               101
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  COL11A1 MUTATED    36   0   2   2
  COL11A1 WILD-TYPE 309   4  29  23
D2091V11, multiclass
    clus
vv   COL11A1 MUTATED COL11A1 WILD-TYPE
  R0              36               309
  R1               0                 4
  R2               2                29
  RX               2                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2091V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  COL11A1 MUTATED                                  0     2
  COL11A1 WILD-TYPE                                1     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  COL11A1 MUTATED                           1    28
  COL11A1 WILD-TYPE                        21   198
D2091V13, multiclass
                                  clus
vv                                 COL11A1 MUTATED COL11A1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          2                 9
  BLACK OR AFRICAN AMERICAN                      1                21
  WHITE                                         28               198
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2092) Variable = OR5L2 MUTATION ANALYSIS
D2092V1, survival
                 sevent
clus2               0   1
  OR5L2 MUTATED    12   3
  OR5L2 WILD-TYPE 366  90
  OR5L2 MUTATED OR5L2 WILD-TYPE 
             15             456 
  OR5L2 MUTATED OR5L2 WILD-TYPE 
              3              90 
$`OR5L2 MUTATED`
TCGA-AA-3492 TCGA-AA-3663 TCGA-AA-3968 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4948 
        3.02         6.97        21.99        12.76        10.06       148.01 
TCGA-CK-4952 TCGA-CM-5861 TCGA-CM-6162 TCGA-CM-6678 TCGA-D5-6536 TCGA-DM-A0X9 
       15.62        15.02        12.00        11.01        17.85       119.70 
TCGA-DM-A1D4 TCGA-G4-6317 TCGA-AG-A002 
       92.75        36.00        20.98 

$`OR5L2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       20.98        34.03         2.01        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
       14.30        17.56        85.45        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       30.08        32.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       15.02         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       13.05        11.08        11.08        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
        1.32        43.27        15.12         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       12.00        11.38        10.26        24.43        38.20       130.65 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       85.48        63.62        61.91        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  OR5L2 MUTATED OR5L2 WILD-TYPE 
           3.02            0.00 
  OR5L2 MUTATED OR5L2 WILD-TYPE 
         148.01          140.38 
  OR5L2 MUTATED OR5L2 WILD-TYPE 
         15.620          20.415 
[1] "3.0 - 148.0 (15.6)" "0.0 - 140.4 (20.4)"
[1] "hr=" "1.2"
D2092V2, continuous
D2092V3, binary
                 cls
clus                0   1
  OR5L2 MUTATED    14   1
  OR5L2 WILD-TYPE 352 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR5L2 MUTATED     14    1
  OR5L2 WILD-TYPE  352  118
        clus
vv       OR5L2 MUTATED OR5L2 WILD-TYPE
  COLON             14             352
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  OR5L2 MUTATED         2        0        2         6         0         0
  OR5L2 WILD-TYPE      89        1       30       132        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  OR5L2 MUTATED           1          0          1          2        0         1
  OR5L2 WILD-TYPE        23         11         58         40       48        17
                 vv
clus              STAGE IVB
  OR5L2 MUTATED           0
  OR5L2 WILD-TYPE         1
D2092V4, multiclass
            clus
vv           OR5L2 MUTATED OR5L2 WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA              6             132
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             2              40
  STAGE IV               0              48
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  OR5L2 MUTATED     0   2  11   2
  OR5L2 WILD-TYPE  17  90 318  48
D2092V5, multiclass
    clus
vv   OR5L2 MUTATED OR5L2 WILD-TYPE
  T1             0              17
  T2             2              90
  T3            11             318
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  OR5L2 MUTATED    10   3   2
  OR5L2 WILD-TYPE 277 110  85
D2092V6, multiclass
    clus
vv   OR5L2 MUTATED OR5L2 WILD-TYPE
  N0            10             277
  N1             3             110
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2092V7, binary
                 cls
clus                0   1
  OR5L2 MUTATED    13   1
  OR5L2 WILD-TYPE 362  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR5L2 MUTATED     13    1
  OR5L2 WILD-TYPE  362   64
   clus
vv  OR5L2 MUTATED OR5L2 WILD-TYPE
  0            13             362
  1             1              64
[1] 2 2
[1] FALSE
D2092V8, binary
                 cls
clus                0   1
  OR5L2 MUTATED     9   6
  OR5L2 WILD-TYPE 216 258
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR5L2 MUTATED      9    6
  OR5L2 WILD-TYPE  216  258
        clus
vv       OR5L2 MUTATED OR5L2 WILD-TYPE
  FEMALE             9             216
  MALE               6             258
[1] 2 2
[1] FALSE
D2092V9, binary
                 cls
clus                0   1
  OR5L2 MUTATED    12   0
  OR5L2 WILD-TYPE 338  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR5L2 MUTATED     12    0
  OR5L2 WILD-TYPE  338   22
     clus
vv    OR5L2 MUTATED OR5L2 WILD-TYPE
  NO             12             338
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  OR5L2 MUTATED                     11                             3
  OR5L2 WILD-TYPE                  304                            44
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  OR5L2 MUTATED                       1                              0
  OR5L2 WILD-TYPE                   105                             10
D2092V10, multiclass
                                clus
vv                               OR5L2 MUTATED OR5L2 WILD-TYPE
  COLON ADENOCARCINOMA                      11             304
  COLON MUCINOUS ADENOCARCINOMA              3              44
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  OR5L2 MUTATED    10   0   0   3
  OR5L2 WILD-TYPE 335   4  31  22
D2092V11, multiclass
    clus
vv   OR5L2 MUTATED OR5L2 WILD-TYPE
  R0            10             335
  R1             0               4
  R2             0              31
  RX             3              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2092V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OR5L2 MUTATED                                  0     2
  OR5L2 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  OR5L2 MUTATED                           0     9
  OR5L2 WILD-TYPE                        22   217
D2092V13, multiclass
                                  clus
vv                                 OR5L2 MUTATED OR5L2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               9
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        9             217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2093) Variable = EHBP1L1 MUTATION ANALYSIS
D2093V1, survival
                   sevent
clus2                 0   1
  EHBP1L1 MUTATED     7   1
  EHBP1L1 WILD-TYPE 371  92
  EHBP1L1 MUTATED EHBP1L1 WILD-TYPE 
                8               463 
  EHBP1L1 MUTATED EHBP1L1 WILD-TYPE 
                1                92 
$`EHBP1L1 MUTATED`
TCGA-A6-6653 TCGA-A6-6781 TCGA-AA-3685 TCGA-AA-3864 TCGA-AZ-6606 TCGA-CK-4952 
       24.39        19.66        37.05        53.00        11.74        15.62 
TCGA-CM-6162 TCGA-AG-3731 
       12.00        37.02 

$`EHBP1L1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
       25.08        25.18        24.16        21.76        24.69        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       15.02        11.01         5.98        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        31.07        30.05        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
       29.56         5.23         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 
       14.30        17.56       148.01        85.45        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       15.02        17.03        15.02         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
       19.99         7.99         0.99        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  EHBP1L1 MUTATED EHBP1L1 WILD-TYPE 
            11.74              0.00 
  EHBP1L1 MUTATED EHBP1L1 WILD-TYPE 
            53.00            148.01 
  EHBP1L1 MUTATED EHBP1L1 WILD-TYPE 
           22.025            20.190 
[1] "11.7 - 53.0 (22.0)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.6"
D2093V2, continuous
D2093V3, binary
                   cls
clus                  0   1
  EHBP1L1 MUTATED     7   1
  EHBP1L1 WILD-TYPE 359 118
[1] "tbl2"
                   cls
clus                [,1] [,2]
  EHBP1L1 MUTATED      7    1
  EHBP1L1 WILD-TYPE  359  118
        clus
vv       EHBP1L1 MUTATED EHBP1L1 WILD-TYPE
  COLON                7               359
  RECTUM               1               118
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  EHBP1L1 MUTATED         1        0        2         0         0         0
  EHBP1L1 WILD-TYPE      90        1       30       138        10         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  EHBP1L1 MUTATED           0          0          1          2        2
  EHBP1L1 WILD-TYPE        24         11         58         40       46
                   vv
clus                STAGE IVA STAGE IVB
  EHBP1L1 MUTATED           0         0
  EHBP1L1 WILD-TYPE        18         1
D2093V4, multiclass
            clus
vv           EHBP1L1 MUTATED EHBP1L1 WILD-TYPE
  STAGE I                  1                90
  STAGE IA                 0                 1
  STAGE II                 2                30
  STAGE IIA                0               138
  STAGE IIB                0                10
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               0                11
  STAGE IIIB               1                58
  STAGE IIIC               2                40
  STAGE IV                 2                46
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  EHBP1L1 MUTATED     0   1   4   3
  EHBP1L1 WILD-TYPE  17  91 325  47
D2093V5, multiclass
    clus
vv   EHBP1L1 MUTATED EHBP1L1 WILD-TYPE
  T1               0                17
  T2               1                91
  T3               4               325
  T4               3                47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  EHBP1L1 MUTATED     3   3   2
  EHBP1L1 WILD-TYPE 284 110  85
D2093V6, multiclass
    clus
vv   EHBP1L1 MUTATED EHBP1L1 WILD-TYPE
  N0               3               284
  N1               3               110
  N2               2                85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2093V7, binary
                   cls
clus                  0   1
  EHBP1L1 MUTATED     5   2
  EHBP1L1 WILD-TYPE 370  63
[1] "tbl2"
                   cls
clus                [,1] [,2]
  EHBP1L1 MUTATED      5    2
  EHBP1L1 WILD-TYPE  370   63
   clus
vv  EHBP1L1 MUTATED EHBP1L1 WILD-TYPE
  0               5               370
  1               2                63
[1] 2 2
[1] FALSE
D2093V8, binary
                   cls
clus                  0   1
  EHBP1L1 MUTATED     2   6
  EHBP1L1 WILD-TYPE 223 258
[1] "tbl2"
                   cls
clus                [,1] [,2]
  EHBP1L1 MUTATED      2    6
  EHBP1L1 WILD-TYPE  223  258
        clus
vv       EHBP1L1 MUTATED EHBP1L1 WILD-TYPE
  FEMALE               2               223
  MALE                 6               258
[1] 2 2
[1] FALSE
D2093V9, binary
                   cls
clus                  0   1
  EHBP1L1 MUTATED     7   0
  EHBP1L1 WILD-TYPE 343  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  EHBP1L1 MUTATED      7    0
  EHBP1L1 WILD-TYPE  343   22
     clus
vv    EHBP1L1 MUTATED EHBP1L1 WILD-TYPE
  NO                7               343
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  EHBP1L1 MUTATED                      4                             3
  EHBP1L1 WILD-TYPE                  311                            44
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  EHBP1L1 MUTATED                       1                              0
  EHBP1L1 WILD-TYPE                   105                             10
D2093V10, multiclass
                                clus
vv                               EHBP1L1 MUTATED EHBP1L1 WILD-TYPE
  COLON ADENOCARCINOMA                         4               311
  COLON MUCINOUS ADENOCARCINOMA                3                44
  RECTAL ADENOCARCINOMA                        1               105
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  EHBP1L1 MUTATED     4   0   1   1
  EHBP1L1 WILD-TYPE 341   4  30  24
D2093V11, multiclass
    clus
vv   EHBP1L1 MUTATED EHBP1L1 WILD-TYPE
  R0               4               341
  R1               0                 4
  R2               1                30
  RX               1                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2093V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  EHBP1L1 MUTATED                                  0     0
  EHBP1L1 WILD-TYPE                                1    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  EHBP1L1 MUTATED                           0     5
  EHBP1L1 WILD-TYPE                        22   221
D2093V13, multiclass
                                  clus
vv                                 EHBP1L1 MUTATED EHBP1L1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                      0                22
  WHITE                                          5               221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2094) Variable = CNOT6L MUTATION ANALYSIS
D2094V1, survival
                  sevent
clus2                0   1
  CNOT6L MUTATED     6   1
  CNOT6L WILD-TYPE 372  92
  CNOT6L MUTATED CNOT6L WILD-TYPE 
               7              464 
  CNOT6L MUTATED CNOT6L WILD-TYPE 
               1               92 
$`CNOT6L MUTATED`
TCGA-AA-3510 TCGA-AA-3947 TCGA-AA-A01R TCGA-D5-6532 TCGA-DM-A1D4 TCGA-AG-3892 
       63.98        33.01        35.01        18.25        92.75        13.02 
TCGA-CI-6620 
       33.17 

$`CNOT6L WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
        2.01        12.99        24.00        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T 
       31.00        31.00        38.07         1.02         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
       38.20       130.65        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       17.95        36.95        17.03        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6622 TCGA-CI-6624 
       17.49         0.69         0.72         6.05         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  CNOT6L MUTATED CNOT6L WILD-TYPE 
           13.02             0.00 
  CNOT6L MUTATED CNOT6L WILD-TYPE 
           92.75           148.01 
  CNOT6L MUTATED CNOT6L WILD-TYPE 
          33.170           20.085 
[1] "13.0 - 92.8 (33.2)" "0.0 - 148.0 (20.1)"
[1] "hr=" "2.1"
D2094V2, continuous
D2094V3, binary
                  cls
clus                 0   1
  CNOT6L MUTATED     5   2
  CNOT6L WILD-TYPE 361 117
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CNOT6L MUTATED      5    2
  CNOT6L WILD-TYPE  361  117
        clus
vv       CNOT6L MUTATED CNOT6L WILD-TYPE
  COLON               5              361
  RECTUM              2              117
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CNOT6L MUTATED         1        0        1         2         1         0
  CNOT6L WILD-TYPE      90        1       31       136         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CNOT6L MUTATED           1          0          0          0        0
  CNOT6L WILD-TYPE        23         11         59         42       48
                  vv
clus               STAGE IVA STAGE IVB
  CNOT6L MUTATED           1         0
  CNOT6L WILD-TYPE        17         1
D2094V4, multiclass
            clus
vv           CNOT6L MUTATED CNOT6L WILD-TYPE
  STAGE I                 1               90
  STAGE IA                0                1
  STAGE II                1               31
  STAGE IIA               2              136
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               1               23
  STAGE IIIA              0               11
  STAGE IIIB              0               59
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               1               17
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  CNOT6L MUTATED     1   0   5   1
  CNOT6L WILD-TYPE  16  92 324  49
D2094V5, multiclass
    clus
vv   CNOT6L MUTATED CNOT6L WILD-TYPE
  T1              1               16
  T2              0               92
  T3              5              324
  T4              1               49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  CNOT6L MUTATED     5   1   1
  CNOT6L WILD-TYPE 282 112  86
D2094V6, multiclass
    clus
vv   CNOT6L MUTATED CNOT6L WILD-TYPE
  N0              5              282
  N1              1              112
  N2              1               86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2094V7, binary
                  cls
clus                 0   1
  CNOT6L MUTATED     6   1
  CNOT6L WILD-TYPE 369  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CNOT6L MUTATED      6    1
  CNOT6L WILD-TYPE  369   64
   clus
vv  CNOT6L MUTATED CNOT6L WILD-TYPE
  0              6              369
  1              1               64
[1] 2 2
[1] FALSE
D2094V8, binary
                  cls
clus                 0   1
  CNOT6L MUTATED     3   4
  CNOT6L WILD-TYPE 222 260
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CNOT6L MUTATED      3    4
  CNOT6L WILD-TYPE  222  260
        clus
vv       CNOT6L MUTATED CNOT6L WILD-TYPE
  FEMALE              3              222
  MALE                4              260
[1] 2 2
[1] FALSE
D2094V9, binary
                  cls
clus                 0   1
  CNOT6L MUTATED     5   1
  CNOT6L WILD-TYPE 345  21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CNOT6L MUTATED      5    1
  CNOT6L WILD-TYPE  345   21
     clus
vv    CNOT6L MUTATED CNOT6L WILD-TYPE
  NO               5              345
  YES              1               21
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CNOT6L MUTATED                      3                             2
  CNOT6L WILD-TYPE                  312                            45
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CNOT6L MUTATED                       2                              0
  CNOT6L WILD-TYPE                   104                             10
D2094V10, multiclass
                                clus
vv                               CNOT6L MUTATED CNOT6L WILD-TYPE
  COLON ADENOCARCINOMA                        3              312
  COLON MUCINOUS ADENOCARCINOMA               2               45
  RECTAL ADENOCARCINOMA                       2              104
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  CNOT6L MUTATED     5   0   0   0
  CNOT6L WILD-TYPE 340   4  31  25
D2094V11, multiclass
    clus
vv   CNOT6L MUTATED CNOT6L WILD-TYPE
  R0              5              340
  R1              0                4
  R2              0               31
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2094V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CNOT6L MUTATED                                  0     0
  CNOT6L WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  CNOT6L MUTATED                           0     3
  CNOT6L WILD-TYPE                        22   223
D2094V13, multiclass
                                  clus
vv                                 CNOT6L MUTATED CNOT6L WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         3              223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2095) Variable = C3ORF27 MUTATION ANALYSIS
D2095V1, survival
                   sevent
clus2                 0   1
  C3ORF27 MUTATED     2   1
  C3ORF27 WILD-TYPE 376  92
  C3ORF27 MUTATED C3ORF27 WILD-TYPE 
                3               468 
  C3ORF27 MUTATED C3ORF27 WILD-TYPE 
                1                92 
$`C3ORF27 MUTATED`
TCGA-AA-3850 TCGA-AA-A010 TCGA-D5-6923 
        0.00        34.98        12.43 

$`C3ORF27 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
        0.00        17.03        10.06        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        3.68         4.41        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  C3ORF27 MUTATED C3ORF27 WILD-TYPE 
                0                 0 
  C3ORF27 MUTATED C3ORF27 WILD-TYPE 
            34.98            148.01 
  C3ORF27 MUTATED C3ORF27 WILD-TYPE 
           12.430            20.235 
[1] "0.0 - 35.0 (12.4)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "3.1"
D2095V2, continuous
D2095V3, binary
                   cls
clus                  0   1
  C3ORF27 MUTATED     3   0
  C3ORF27 WILD-TYPE 363 119
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C3ORF27 MUTATED      3    0
  C3ORF27 WILD-TYPE  363  119
        clus
vv       C3ORF27 MUTATED C3ORF27 WILD-TYPE
  COLON                3               363
  RECTUM               0               119
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  C3ORF27 MUTATED         2        0        0         0         1         0
  C3ORF27 WILD-TYPE      89        1       32       138         9         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C3ORF27 MUTATED           0          0          0          0        0
  C3ORF27 WILD-TYPE        24         11         59         42       48
                   vv
clus                STAGE IVA STAGE IVB
  C3ORF27 MUTATED           0         0
  C3ORF27 WILD-TYPE        18         1
D2095V4, multiclass
            clus
vv           C3ORF27 MUTATED C3ORF27 WILD-TYPE
  STAGE I                  2                89
  STAGE IA                 0                 1
  STAGE II                 0                32
  STAGE IIA                0               138
  STAGE IIB                1                 9
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               0                11
  STAGE IIIB               0                59
  STAGE IIIC               0                42
  STAGE IV                 0                48
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  C3ORF27 MUTATED     0   2   0   1
  C3ORF27 WILD-TYPE  17  90 329  49
D2095V5, multiclass
    clus
vv   C3ORF27 MUTATED C3ORF27 WILD-TYPE
  T1               0                17
  T2               2                90
  T3               0               329
  T4               1                49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  C3ORF27 MUTATED     3   0   0
  C3ORF27 WILD-TYPE 284 113  87
D2095V6, multiclass
    clus
vv   C3ORF27 MUTATED C3ORF27 WILD-TYPE
  N0               3               284
  N1               0               113
  N2               0                87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2095V7, binary
                   cls
clus                  0   1
  C3ORF27 MUTATED     3   0
  C3ORF27 WILD-TYPE 372  65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C3ORF27 MUTATED      3    0
  C3ORF27 WILD-TYPE  372   65
   clus
vv  C3ORF27 MUTATED C3ORF27 WILD-TYPE
  0               3               372
  1               0                65
[1] 2 2
[1] FALSE
D2095V8, binary
                   cls
clus                  0   1
  C3ORF27 MUTATED     1   2
  C3ORF27 WILD-TYPE 224 262
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C3ORF27 MUTATED      1    2
  C3ORF27 WILD-TYPE  224  262
        clus
vv       C3ORF27 MUTATED C3ORF27 WILD-TYPE
  FEMALE               1               224
  MALE                 2               262
[1] 2 2
[1] FALSE
D2095V9, binary
                   cls
clus                  0   1
  C3ORF27 MUTATED     2   0
  C3ORF27 WILD-TYPE 348  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C3ORF27 MUTATED      2    0
  C3ORF27 WILD-TYPE  348   22
     clus
vv    C3ORF27 MUTATED C3ORF27 WILD-TYPE
  NO                2               348
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  C3ORF27 MUTATED                      3                             0
  C3ORF27 WILD-TYPE                  312                            47
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  C3ORF27 MUTATED                       0                              0
  C3ORF27 WILD-TYPE                   106                             10
D2095V10, multiclass
                                clus
vv                               C3ORF27 MUTATED C3ORF27 WILD-TYPE
  COLON ADENOCARCINOMA                         3               312
  COLON MUCINOUS ADENOCARCINOMA                0                47
  RECTAL ADENOCARCINOMA                        0               106
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  C3ORF27 MUTATED     3   0   0   0
  C3ORF27 WILD-TYPE 342   4  31  25
D2095V11, multiclass
    clus
vv   C3ORF27 MUTATED C3ORF27 WILD-TYPE
  R0               3               342
  R1               0                 4
  R2               0                31
  RX               0                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2095V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C3ORF27 MUTATED                                  0     0
  C3ORF27 WILD-TYPE                                1    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  C3ORF27 MUTATED                           0     1
  C3ORF27 WILD-TYPE                        22   225
D2095V13, multiclass
[1] "Remove cluster labels:" "C3ORF27 MUTATED"       
clus
  C3ORF27 MUTATED C3ORF27 WILD-TYPE 
                1               259 
       TCGA-A6-2671        TCGA-A6-2672        TCGA-A6-2674        TCGA-A6-2676 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-A6-2677        TCGA-A6-2678        TCGA-A6-2683        TCGA-A6-3807 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-A6-3808        TCGA-A6-3809        TCGA-A6-3810        TCGA-A6-4105 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-A6-5656        TCGA-A6-5657        TCGA-A6-5659        TCGA-A6-5660 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-A6-5661        TCGA-A6-5662        TCGA-A6-5664        TCGA-A6-5665 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-A6-5666        TCGA-A6-6137        TCGA-A6-6138        TCGA-A6-6141 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-A6-6142        TCGA-A6-6648        TCGA-A6-6649        TCGA-A6-6651 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-A6-6652        TCGA-A6-6653        TCGA-A6-6654        TCGA-A6-6780 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-A6-6781        TCGA-A6-6782        TCGA-AD-5900        TCGA-AD-6548 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-AD-6888        TCGA-AD-6889        TCGA-AD-6890        TCGA-AD-6895 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-AD-6899        TCGA-AD-6901        TCGA-AD-6963        TCGA-AD-6964 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-AD-6965        TCGA-AU-3779        TCGA-AU-6004        TCGA-AY-4070 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-AY-4071        TCGA-AY-5543        TCGA-AY-6196        TCGA-AY-6197 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-AY-6386        TCGA-AZ-4315        TCGA-AZ-4323        TCGA-AZ-4616 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-AZ-4681        TCGA-AZ-4682        TCGA-AZ-5403        TCGA-AZ-5407 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-AZ-6598        TCGA-AZ-6599        TCGA-AZ-6600        TCGA-AZ-6601 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-AZ-6603        TCGA-AZ-6605        TCGA-AZ-6606        TCGA-AZ-6607 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-AZ-6608        TCGA-CA-5254        TCGA-CA-5255        TCGA-CA-5796 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-CA-5797        TCGA-CA-6715        TCGA-CA-6716        TCGA-CA-6717 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-CA-6718        TCGA-CA-6719        TCGA-CK-4947        TCGA-CK-4948 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-CK-4950        TCGA-CK-4952        TCGA-CK-5912        TCGA-CK-5913 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-CK-5914        TCGA-CK-5915        TCGA-CK-5916        TCGA-CK-6746 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-CK-6747        TCGA-CK-6748        TCGA-CK-6751        TCGA-CM-4743 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-CM-4744        TCGA-CM-4746        TCGA-CM-4747        TCGA-CM-4752 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-CM-5341        TCGA-CM-5344        TCGA-CM-5348        TCGA-CM-5349 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-CM-5860        TCGA-CM-5861        TCGA-CM-5862        TCGA-CM-5863 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-CM-5864        TCGA-CM-5868        TCGA-CM-6161        TCGA-CM-6162 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-CM-6163        TCGA-CM-6164        TCGA-CM-6165        TCGA-CM-6166 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-CM-6167        TCGA-CM-6168        TCGA-CM-6169        TCGA-CM-6170 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-CM-6171        TCGA-CM-6172        TCGA-CM-6674        TCGA-CM-6675 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-CM-6676        TCGA-CM-6677        TCGA-CM-6678        TCGA-CM-6679 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-CM-6680        TCGA-D5-5537        TCGA-D5-5538        TCGA-D5-5539 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-D5-5540        TCGA-D5-5541        TCGA-D5-6529        TCGA-D5-6532 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-D5-6533        TCGA-D5-6534        TCGA-D5-6535        TCGA-D5-6536 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-D5-6537        TCGA-D5-6538        TCGA-D5-6539        TCGA-D5-6540 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-D5-6541        TCGA-D5-6898        TCGA-D5-6920        TCGA-D5-6922 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-D5-6924        TCGA-D5-6926        TCGA-D5-6927        TCGA-D5-6928 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-D5-6929        TCGA-D5-6930        TCGA-D5-6931        TCGA-D5-6932 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-D5-7000        TCGA-DM-A0X9        TCGA-DM-A0XD        TCGA-DM-A0XF 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-DM-A1D0        TCGA-DM-A1D4        TCGA-DM-A1D6        TCGA-DM-A1D7 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-DM-A1D8        TCGA-DM-A1D9        TCGA-DM-A1DA        TCGA-DM-A1DB 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-DM-A1HA        TCGA-DM-A1HB        TCGA-DM-A282        TCGA-DM-A285 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-DM-A28C        TCGA-DM-A28E        TCGA-DM-A28F        TCGA-DM-A28G 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-DM-A28H        TCGA-DM-A28K        TCGA-F4-6459        TCGA-F4-6460 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-F4-6569        TCGA-F4-6570        TCGA-F4-6703        TCGA-F4-6704 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-F4-6805        TCGA-F4-6806        TCGA-F4-6807        TCGA-F4-6808 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-F4-6809        TCGA-F4-6854        TCGA-F4-6855        TCGA-F4-6856 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-G4-6293        TCGA-G4-6299        TCGA-G4-6303        TCGA-G4-6304 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-G4-6306        TCGA-G4-6307        TCGA-G4-6309        TCGA-G4-6310 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-G4-6315        TCGA-G4-6317        TCGA-G4-6321        TCGA-G4-6323 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-G4-6586        TCGA-G4-6588        TCGA-G4-6625        TCGA-G4-6626 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-G4-6628        TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2691 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3913 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136        TCGA-AF-6655 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-AF-6672        TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6549 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-AH-6643        TCGA-AH-6644        TCGA-CI-6619        TCGA-CI-6620 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-CI-6621        TCGA-CI-6622        TCGA-CI-6624        TCGA-CL-5917 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-CL-5918        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6155 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-DC-6157        TCGA-DC-6158        TCGA-DC-6160        TCGA-DC-6681 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-DC-6682        TCGA-DC-6683        TCGA-DT-5265        TCGA-DY-A0XA 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-DY-A1DC        TCGA-DY-A1DD        TCGA-DY-A1DF        TCGA-DY-A1DG 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-DY-A1H8        TCGA-EF-5830        TCGA-EI-6506        TCGA-EI-6507 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6510        TCGA-F5-6464        TCGA-F5-6465 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6811        TCGA-F5-6812 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 
       TCGA-F5-6813        TCGA-G5-6235        TCGA-G5-6641 
"C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" "C3ORF27 WILD-TYPE" 

Clustering(2096) Variable = TNFRSF13B MUTATION ANALYSIS
D2096V1, survival
                     sevent
clus2                   0   1
  TNFRSF13B MUTATED     6   0
  TNFRSF13B WILD-TYPE 372  93
  TNFRSF13B MUTATED TNFRSF13B WILD-TYPE 
                  6                 465 
  TNFRSF13B MUTATED TNFRSF13B WILD-TYPE 
                  0                  93 
$`TNFRSF13B MUTATED`
TCGA-A6-6649 TCGA-AA-3949 TCGA-AA-3977 TCGA-AA-A010 TCGA-AA-A02W TCGA-DC-6682 
       24.16        26.01        25.02        34.98        41.00         4.01 

$`TNFRSF13B WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.08        25.18        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-3952 
        2.01        12.99        24.00        33.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
        5.03        14.01         0.92        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 
       13.97        27.95        10.98        19.99         5.95         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  TNFRSF13B MUTATED TNFRSF13B WILD-TYPE 
               4.01                0.00 
  TNFRSF13B MUTATED TNFRSF13B WILD-TYPE 
              41.00              148.01 
  TNFRSF13B MUTATED TNFRSF13B WILD-TYPE 
             25.515              20.050 
[1] "4.0 - 41.0 (25.5)"  "0.0 - 148.0 (20.1)"
[1] "hr="     "9100000"
D2096V2, continuous
D2096V3, binary
                     cls
clus                    0   1
  TNFRSF13B MUTATED     6   1
  TNFRSF13B WILD-TYPE 360 118
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  TNFRSF13B MUTATED      6    1
  TNFRSF13B WILD-TYPE  360  118
        clus
vv       TNFRSF13B MUTATED TNFRSF13B WILD-TYPE
  COLON                  6                 360
  RECTUM                 1                 118
[1] 2 2
[1] FALSE
                     vv
clus                  STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TNFRSF13B MUTATED         1        0        0         1         2         0
  TNFRSF13B WILD-TYPE      90        1       32       137         8         1
                     vv
clus                  STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TNFRSF13B MUTATED           0          0          2          0        0
  TNFRSF13B WILD-TYPE        24         11         57         42       48
                     vv
clus                  STAGE IVA STAGE IVB
  TNFRSF13B MUTATED           0         0
  TNFRSF13B WILD-TYPE        18         1
D2096V4, multiclass
            clus
vv           TNFRSF13B MUTATED TNFRSF13B WILD-TYPE
  STAGE I                    1                  90
  STAGE IA                   0                   1
  STAGE II                   0                  32
  STAGE IIA                  1                 137
  STAGE IIB                  2                   8
  STAGE IIC                  0                   1
  STAGE III                  0                  24
  STAGE IIIA                 0                  11
  STAGE IIIB                 2                  57
  STAGE IIIC                 0                  42
  STAGE IV                   0                  48
  STAGE IVA                  0                  18
  STAGE IVB                  0                   1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                   T1  T2  T3  T4
  TNFRSF13B MUTATED     0   2   3   2
  TNFRSF13B WILD-TYPE  17  90 326  48
D2096V5, multiclass
    clus
vv   TNFRSF13B MUTATED TNFRSF13B WILD-TYPE
  T1                 0                  17
  T2                 2                  90
  T3                 3                 326
  T4                 2                  48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                   N0  N1  N2
  TNFRSF13B MUTATED     5   2   0
  TNFRSF13B WILD-TYPE 282 111  87
D2096V6, multiclass
    clus
vv   TNFRSF13B MUTATED TNFRSF13B WILD-TYPE
  N0                 5                 282
  N1                 2                 111
  N2                 0                  87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2096V7, binary
                     cls
clus                    0   1
  TNFRSF13B MUTATED     5   0
  TNFRSF13B WILD-TYPE 370  65
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  TNFRSF13B MUTATED      5    0
  TNFRSF13B WILD-TYPE  370   65
   clus
vv  TNFRSF13B MUTATED TNFRSF13B WILD-TYPE
  0                 5                 370
  1                 0                  65
[1] 2 2
[1] FALSE
D2096V8, binary
                     cls
clus                    0   1
  TNFRSF13B MUTATED     4   3
  TNFRSF13B WILD-TYPE 221 261
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  TNFRSF13B MUTATED      4    3
  TNFRSF13B WILD-TYPE  221  261
        clus
vv       TNFRSF13B MUTATED TNFRSF13B WILD-TYPE
  FEMALE                 4                 221
  MALE                   3                 261
[1] 2 2
[1] FALSE
D2096V9, binary
                     cls
clus                    0   1
  TNFRSF13B MUTATED     5   0
  TNFRSF13B WILD-TYPE 345  22
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  TNFRSF13B MUTATED      5    0
  TNFRSF13B WILD-TYPE  345   22
     clus
vv    TNFRSF13B MUTATED TNFRSF13B WILD-TYPE
  NO                  5                 345
  YES                 0                  22
[1] 2 2
[1] FALSE
                     vv
clus                  COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  TNFRSF13B MUTATED                      5                             1
  TNFRSF13B WILD-TYPE                  310                            46
                     vv
clus                  RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  TNFRSF13B MUTATED                       1                              0
  TNFRSF13B WILD-TYPE                   105                             10
D2096V10, multiclass
                                clus
vv                               TNFRSF13B MUTATED TNFRSF13B WILD-TYPE
  COLON ADENOCARCINOMA                           5                 310
  COLON MUCINOUS ADENOCARCINOMA                  1                  46
  RECTAL ADENOCARCINOMA                          1                 105
  RECTAL MUCINOUS ADENOCARCINOMA                 0                  10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                   R0  R1  R2  RX
  TNFRSF13B MUTATED     4   0   0   1
  TNFRSF13B WILD-TYPE 341   4  31  24
D2096V11, multiclass
    clus
vv   TNFRSF13B MUTATED TNFRSF13B WILD-TYPE
  R0                 4                 341
  R1                 0                   4
  R2                 0                  31
  RX                 1                  24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2096V12, continuous
                     vv
clus                  AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TNFRSF13B MUTATED                                  0     0
  TNFRSF13B WILD-TYPE                                1    11
                     vv
clus                  BLACK OR AFRICAN AMERICAN WHITE
  TNFRSF13B MUTATED                           0     3
  TNFRSF13B WILD-TYPE                        22   223
D2096V13, multiclass
                                  clus
vv                                 TNFRSF13B MUTATED TNFRSF13B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                 0                   1
  ASIAN                                            0                  11
  BLACK OR AFRICAN AMERICAN                        0                  22
  WHITE                                            3                 223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2097) Variable = OTUD4 MUTATION ANALYSIS
D2097V1, survival
                 sevent
clus2               0   1
  OTUD4 MUTATED    15   4
  OTUD4 WILD-TYPE 363  89
  OTUD4 MUTATED OTUD4 WILD-TYPE 
             19             452 
  OTUD4 MUTATED OTUD4 WILD-TYPE 
              4              89 
$`OTUD4 MUTATED`
TCGA-AA-3510 TCGA-AA-3655 TCGA-AA-3715 TCGA-AA-3845 TCGA-AA-A00J TCGA-AA-A00N 
       63.98        61.02        19.04         0.00        18.05         4.01 
TCGA-AA-A010 TCGA-AD-6889 TCGA-AD-6895 TCGA-AY-5543 TCGA-AZ-4315 TCGA-AZ-6608 
       34.98        56.55         0.72        33.01        58.39         1.61 
TCGA-CA-6715 TCGA-CK-4948 TCGA-CM-4743 TCGA-D5-6931 TCGA-G4-6586 TCGA-G4-6628 
        0.07       148.01        23.05        12.00        35.80        79.69 
TCGA-AG-A02N 
       61.97 

$`OTUD4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       19.99        13.94        19.99        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       38.99        37.02        14.93        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       34.03        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
       15.52         0.79         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6197 
        0.20        14.50        27.09        16.31         0.95        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
       82.95         1.91       124.27        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        4.80         1.51        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        26.17        91.79        46.75 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  OTUD4 MUTATED OTUD4 WILD-TYPE 
              0               0 
  OTUD4 MUTATED OTUD4 WILD-TYPE 
         148.01          140.38 
  OTUD4 MUTATED OTUD4 WILD-TYPE 
         33.010          20.085 
[1] "0.0 - 148.0 (33.0)" "0.0 - 140.4 (20.1)"
[1] "hr=" "1.3"
D2097V2, continuous
D2097V3, binary
                 cls
clus                0   1
  OTUD4 MUTATED    19   1
  OTUD4 WILD-TYPE 347 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OTUD4 MUTATED     19    1
  OTUD4 WILD-TYPE  347  118
        clus
vv       OTUD4 MUTATED OTUD4 WILD-TYPE
  COLON             19             347
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  OTUD4 MUTATED         1        0        4         5         3         0
  OTUD4 WILD-TYPE      90        1       28       133         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  OTUD4 MUTATED           1          1          2          1        0         1
  OTUD4 WILD-TYPE        23         10         57         41       48        17
                 vv
clus              STAGE IVB
  OTUD4 MUTATED           0
  OTUD4 WILD-TYPE         1
D2097V4, multiclass
            clus
vv           OTUD4 MUTATED OTUD4 WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               4              28
  STAGE IIA              5             133
  STAGE IIB              3               7
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             1              10
  STAGE IIIB             2              57
  STAGE IIIC             1              41
  STAGE IV               0              48
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  OTUD4 MUTATED     0   2  13   5
  OTUD4 WILD-TYPE  17  90 316  45
D2097V5, multiclass
    clus
vv   OTUD4 MUTATED OTUD4 WILD-TYPE
  T1             0              17
  T2             2              90
  T3            13             316
  T4             5              45
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  OTUD4 MUTATED    13   6   1
  OTUD4 WILD-TYPE 274 107  86
D2097V6, multiclass
    clus
vv   OTUD4 MUTATED OTUD4 WILD-TYPE
  N0            13             274
  N1             6             107
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2097V7, binary
                 cls
clus                0   1
  OTUD4 MUTATED    17   1
  OTUD4 WILD-TYPE 358  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OTUD4 MUTATED     17    1
  OTUD4 WILD-TYPE  358   64
   clus
vv  OTUD4 MUTATED OTUD4 WILD-TYPE
  0            17             358
  1             1              64
[1] 2 2
[1] FALSE
D2097V8, binary
                 cls
clus                0   1
  OTUD4 MUTATED     7  13
  OTUD4 WILD-TYPE 218 251
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OTUD4 MUTATED      7   13
  OTUD4 WILD-TYPE  218  251
        clus
vv       OTUD4 MUTATED OTUD4 WILD-TYPE
  FEMALE             7             218
  MALE              13             251
[1] 2 2
[1] FALSE
D2097V9, binary
                 cls
clus                0   1
  OTUD4 MUTATED    13   0
  OTUD4 WILD-TYPE 337  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OTUD4 MUTATED     13    0
  OTUD4 WILD-TYPE  337   22
     clus
vv    OTUD4 MUTATED OTUD4 WILD-TYPE
  NO             13             337
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  OTUD4 MUTATED                     17                             2
  OTUD4 WILD-TYPE                  298                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  OTUD4 MUTATED                       1                              0
  OTUD4 WILD-TYPE                   105                             10
D2097V10, multiclass
                                clus
vv                               OTUD4 MUTATED OTUD4 WILD-TYPE
  COLON ADENOCARCINOMA                      17             298
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  OTUD4 MUTATED    15   0   0   2
  OTUD4 WILD-TYPE 330   4  31  23
D2097V11, multiclass
    clus
vv   OTUD4 MUTATED OTUD4 WILD-TYPE
  R0            15             330
  R1             0               4
  R2             0              31
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2097V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OTUD4 MUTATED                                  0     2
  OTUD4 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  OTUD4 MUTATED                           1     9
  OTUD4 WILD-TYPE                        21   217
D2097V13, multiclass
                                  clus
vv                                 OTUD4 MUTATED OTUD4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               9
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        9             217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2098) Variable = MYO5A MUTATION ANALYSIS
D2098V1, survival
                 sevent
clus2               0   1
  MYO5A MUTATED    17   5
  MYO5A WILD-TYPE 361  88
  MYO5A MUTATED MYO5A WILD-TYPE 
             22             449 
  MYO5A MUTATED MYO5A WILD-TYPE 
              5              88 
$`MYO5A MUTATED`
TCGA-A6-5664 TCGA-A6-6649 TCGA-AA-3492 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3955 
       22.09        24.16         3.02        35.05         0.99        20.98 
TCGA-AA-3966 TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A02W TCGA-AZ-4315 TCGA-AZ-5403 
        2.01         4.01        34.98        41.00        58.39        62.79 
TCGA-CA-6717 TCGA-CM-5862 TCGA-D5-6532 TCGA-D5-6540 TCGA-DM-A28H TCGA-G4-6315 
       12.76         5.03        18.25        16.14       117.07        61.91 
TCGA-AG-A002 TCGA-CI-6622 TCGA-DC-5337 TCGA-DC-6682 
       20.98         6.97        15.02         4.01 

$`MYO5A WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       25.18        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       19.66        20.28         7.04         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3815 
       85.05        26.99        19.04        19.04        10.06        33.04 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 
       26.01        24.00         2.01        34.03        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02Y TCGA-AA-A03F 
        2.01         5.03        14.01         0.92        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5407 
       17.82         1.41         5.13       106.75        22.36        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07        12.20        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       30.08        32.02        15.02        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       20.19         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       17.13        12.49        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28K 
        6.12        81.37       119.93        35.97        60.79        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6317 TCGA-G4-6321 
       44.68        55.04        85.48        63.62        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6624 TCGA-CL-5917 
        0.69         0.72         6.05        33.17         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
        7.17         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        5.95         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  MYO5A MUTATED MYO5A WILD-TYPE 
           0.99            0.00 
  MYO5A MUTATED MYO5A WILD-TYPE 
         117.07          148.01 
  MYO5A MUTATED MYO5A WILD-TYPE 
         19.615          20.190 
[1] "1.0 - 117.1 (19.6)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.1"
D2098V2, continuous
D2098V3, binary
                 cls
clus                0   1
  MYO5A MUTATED    19   4
  MYO5A WILD-TYPE 347 115
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYO5A MUTATED     19    4
  MYO5A WILD-TYPE  347  115
        clus
vv       MYO5A MUTATED MYO5A WILD-TYPE
  COLON             19             347
  RECTUM             4             115
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MYO5A MUTATED         4        0        2         8         3         0
  MYO5A WILD-TYPE      87        1       30       130         7         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MYO5A MUTATED           0          0          2          2        1         1
  MYO5A WILD-TYPE        24         11         57         40       47        17
                 vv
clus              STAGE IVB
  MYO5A MUTATED           0
  MYO5A WILD-TYPE         1
D2098V4, multiclass
            clus
vv           MYO5A MUTATED MYO5A WILD-TYPE
  STAGE I                4              87
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA              8             130
  STAGE IIB              3               7
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             2              57
  STAGE IIIC             2              40
  STAGE IV               1              47
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  MYO5A MUTATED     1   4  14   4
  MYO5A WILD-TYPE  16  88 315  46
D2098V5, multiclass
    clus
vv   MYO5A MUTATED MYO5A WILD-TYPE
  T1             1              16
  T2             4              88
  T3            14             315
  T4             4              46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  MYO5A MUTATED    17   3   3
  MYO5A WILD-TYPE 270 110  84
D2098V6, multiclass
    clus
vv   MYO5A MUTATED MYO5A WILD-TYPE
  N0            17             270
  N1             3             110
  N2             3              84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2098V7, binary
                 cls
clus                0   1
  MYO5A MUTATED    19   2
  MYO5A WILD-TYPE 356  63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYO5A MUTATED     19    2
  MYO5A WILD-TYPE  356   63
   clus
vv  MYO5A MUTATED MYO5A WILD-TYPE
  0            19             356
  1             2              63
[1] 2 2
[1] FALSE
D2098V8, binary
                 cls
clus                0   1
  MYO5A MUTATED     7  16
  MYO5A WILD-TYPE 218 248
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYO5A MUTATED      7   16
  MYO5A WILD-TYPE  218  248
        clus
vv       MYO5A MUTATED MYO5A WILD-TYPE
  FEMALE             7             218
  MALE              16             248
[1] 2 2
[1] FALSE
D2098V9, binary
                 cls
clus                0   1
  MYO5A MUTATED    16   0
  MYO5A WILD-TYPE 334  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYO5A MUTATED     16    0
  MYO5A WILD-TYPE  334   22
     clus
vv    MYO5A MUTATED MYO5A WILD-TYPE
  NO             16             334
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MYO5A MUTATED                     15                             4
  MYO5A WILD-TYPE                  300                            43
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MYO5A MUTATED                       4                              0
  MYO5A WILD-TYPE                   102                             10
D2098V10, multiclass
                                clus
vv                               MYO5A MUTATED MYO5A WILD-TYPE
  COLON ADENOCARCINOMA                      15             300
  COLON MUCINOUS ADENOCARCINOMA              4              43
  RECTAL ADENOCARCINOMA                      4             102
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  MYO5A MUTATED    16   0   0   1
  MYO5A WILD-TYPE 329   4  31  24
D2098V11, multiclass
    clus
vv   MYO5A MUTATED MYO5A WILD-TYPE
  R0            16             329
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2098V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MYO5A MUTATED                                  0     1
  MYO5A WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  MYO5A MUTATED                           1    11
  MYO5A WILD-TYPE                        21   215
D2098V13, multiclass
                                  clus
vv                                 MYO5A MUTATED MYO5A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                       11             215
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2099) Variable = MNT MUTATION ANALYSIS
D2099V1, survival
               sevent
clus2             0   1
  MNT MUTATED     7   1
  MNT WILD-TYPE 371  92
  MNT MUTATED MNT WILD-TYPE 
            8           463 
  MNT MUTATED MNT WILD-TYPE 
            1            92 
$`MNT MUTATED`
TCGA-A6-5657 TCGA-A6-6780 TCGA-AA-3864 TCGA-AA-3867 TCGA-D5-6928 TCGA-F4-6570 
       31.63        20.12        53.00        24.03        11.64         6.18 
TCGA-AG-A02N TCGA-EI-6507 
       61.97        19.96 

$`MNT WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        31.07        30.05        17.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6930 
       12.43        14.30         9.04         9.44         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
        8.61        31.96        35.74        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
        0.49        20.55        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  MNT MUTATED MNT WILD-TYPE 
         6.18          0.00 
  MNT MUTATED MNT WILD-TYPE 
        61.97        148.01 
  MNT MUTATED MNT WILD-TYPE 
       22.075        20.190 
[1] "6.2 - 62.0 (22.1)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.8"
D2099V2, continuous
D2099V3, binary
               cls
clus              0   1
  MNT MUTATED     6   2
  MNT WILD-TYPE 360 117
[1] "tbl2"
               cls
clus            [,1] [,2]
  MNT MUTATED      6    2
  MNT WILD-TYPE  360  117
        clus
vv       MNT MUTATED MNT WILD-TYPE
  COLON            6           360
  RECTUM           2           117
[1] 2 2
[1] FALSE
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MNT MUTATED         0        0        2         4         0         0
  MNT WILD-TYPE      91        1       30       134        10         1
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MNT MUTATED           0          0          1          0        1         0
  MNT WILD-TYPE        24         11         58         42       47        18
               vv
clus            STAGE IVB
  MNT MUTATED           0
  MNT WILD-TYPE         1
D2099V4, multiclass
            clus
vv           MNT MUTATED MNT WILD-TYPE
  STAGE I              0            91
  STAGE IA             0             1
  STAGE II             2            30
  STAGE IIA            4           134
  STAGE IIB            0            10
  STAGE IIC            0             1
  STAGE III            0            24
  STAGE IIIA           0            11
  STAGE IIIB           1            58
  STAGE IIIC           0            42
  STAGE IV             1            47
  STAGE IVA            0            18
  STAGE IVB            0             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  MNT MUTATED     0   0   8   0
  MNT WILD-TYPE  17  92 321  50
D2099V5, multiclass
    clus
vv   MNT MUTATED MNT WILD-TYPE
  T1           0            17
  T2           0            92
  T3           8           321
  T4           0            50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2
  MNT MUTATED     6   1   1
  MNT WILD-TYPE 281 112  86
D2099V6, multiclass
    clus
vv   MNT MUTATED MNT WILD-TYPE
  N0           6           281
  N1           1           112
  N2           1            86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2099V7, binary
               cls
clus              0   1
  MNT MUTATED     6   1
  MNT WILD-TYPE 369  64
[1] "tbl2"
               cls
clus            [,1] [,2]
  MNT MUTATED      6    1
  MNT WILD-TYPE  369   64
   clus
vv  MNT MUTATED MNT WILD-TYPE
  0           6           369
  1           1            64
[1] 2 2
[1] FALSE
D2099V8, binary
               cls
clus              0   1
  MNT MUTATED     1   7
  MNT WILD-TYPE 224 257
[1] "tbl2"
               cls
clus            [,1] [,2]
  MNT MUTATED      1    7
  MNT WILD-TYPE  224  257
        clus
vv       MNT MUTATED MNT WILD-TYPE
  FEMALE           1           224
  MALE             7           257
[1] 2 2
[1] FALSE
D2099V9, binary
               cls
clus              0   1
  MNT MUTATED     7   0
  MNT WILD-TYPE 343  22
[1] "tbl2"
               cls
clus            [,1] [,2]
  MNT MUTATED      7    0
  MNT WILD-TYPE  343   22
     clus
vv    MNT MUTATED MNT WILD-TYPE
  NO            7           343
  YES           0            22
[1] 2 2
[1] FALSE
               vv
clus            COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MNT MUTATED                      4                             2
  MNT WILD-TYPE                  311                            45
               vv
clus            RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MNT MUTATED                       2                              0
  MNT WILD-TYPE                   104                             10
D2099V10, multiclass
                                clus
vv                               MNT MUTATED MNT WILD-TYPE
  COLON ADENOCARCINOMA                     4           311
  COLON MUCINOUS ADENOCARCINOMA            2            45
  RECTAL ADENOCARCINOMA                    2           104
  RECTAL MUCINOUS ADENOCARCINOMA           0            10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             R0  R1  R2  RX
  MNT MUTATED     6   0   1   0
  MNT WILD-TYPE 339   4  30  25
D2099V11, multiclass
    clus
vv   MNT MUTATED MNT WILD-TYPE
  R0           6           339
  R1           0             4
  R2           1            30
  RX           0            25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2099V12, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MNT MUTATED                                  0     0
  MNT WILD-TYPE                                1    11
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  MNT MUTATED                           1     4
  MNT WILD-TYPE                        21   222
D2099V13, multiclass
                                  clus
vv                                 MNT MUTATED MNT WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      0            11
  BLACK OR AFRICAN AMERICAN                  1            21
  WHITE                                      4           222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2100) Variable = CAMK1 MUTATION ANALYSIS
D2100V1, survival
                 sevent
clus2               0   1
  CAMK1 MUTATED     6   2
  CAMK1 WILD-TYPE 372  91
  CAMK1 MUTATED CAMK1 WILD-TYPE 
              8             463 
  CAMK1 MUTATED CAMK1 WILD-TYPE 
              2              91 
$`CAMK1 MUTATED`
TCGA-AA-3950 TCGA-AA-A00N TCGA-AD-6889 TCGA-AY-6386 TCGA-AZ-6601 TCGA-G4-6304 
       24.00         4.01        56.55        17.82       100.01        53.62 
TCGA-G4-6315 TCGA-AG-A002 
       61.91        20.98 

$`CAMK1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 
       62.79        88.21        49.41         6.77        12.10        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 
       47.41        35.31       133.18        74.56        65.85        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       55.04        85.48        63.62        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  CAMK1 MUTATED CAMK1 WILD-TYPE 
           4.01            0.00 
  CAMK1 MUTATED CAMK1 WILD-TYPE 
         100.01          148.01 
  CAMK1 MUTATED CAMK1 WILD-TYPE 
          38.81           20.05 
[1] "4.0 - 100.0 (38.8)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.4"
D2100V2, continuous
D2100V3, binary
                 cls
clus                0   1
  CAMK1 MUTATED     7   1
  CAMK1 WILD-TYPE 359 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CAMK1 MUTATED      7    1
  CAMK1 WILD-TYPE  359  118
        clus
vv       CAMK1 MUTATED CAMK1 WILD-TYPE
  COLON              7             359
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CAMK1 MUTATED         1        0        1         2         2         0
  CAMK1 WILD-TYPE      90        1       31       136         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CAMK1 MUTATED           0          0          1          0        1         0
  CAMK1 WILD-TYPE        24         11         58         42       47        18
                 vv
clus              STAGE IVB
  CAMK1 MUTATED           0
  CAMK1 WILD-TYPE         1
D2100V4, multiclass
            clus
vv           CAMK1 MUTATED CAMK1 WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              2             136
  STAGE IIB              2               8
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             0              42
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CAMK1 MUTATED     0   1   5   2
  CAMK1 WILD-TYPE  17  91 324  48
D2100V5, multiclass
    clus
vv   CAMK1 MUTATED CAMK1 WILD-TYPE
  T1             0              17
  T2             1              91
  T3             5             324
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  CAMK1 MUTATED     6   2   0
  CAMK1 WILD-TYPE 281 111  87
D2100V6, multiclass
    clus
vv   CAMK1 MUTATED CAMK1 WILD-TYPE
  N0             6             281
  N1             2             111
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2100V7, binary
                 cls
clus                0   1
  CAMK1 MUTATED     7   1
  CAMK1 WILD-TYPE 368  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CAMK1 MUTATED      7    1
  CAMK1 WILD-TYPE  368   64
   clus
vv  CAMK1 MUTATED CAMK1 WILD-TYPE
  0             7             368
  1             1              64
[1] 2 2
[1] FALSE
D2100V8, binary
                 cls
clus                0   1
  CAMK1 MUTATED     3   5
  CAMK1 WILD-TYPE 222 259
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CAMK1 MUTATED      3    5
  CAMK1 WILD-TYPE  222  259
        clus
vv       CAMK1 MUTATED CAMK1 WILD-TYPE
  FEMALE             3             222
  MALE               5             259
[1] 2 2
[1] FALSE
D2100V9, binary
                 cls
clus                0   1
  CAMK1 MUTATED     6   0
  CAMK1 WILD-TYPE 344  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CAMK1 MUTATED      6    0
  CAMK1 WILD-TYPE  344   22
     clus
vv    CAMK1 MUTATED CAMK1 WILD-TYPE
  NO              6             344
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CAMK1 MUTATED                      5                             2
  CAMK1 WILD-TYPE                  310                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CAMK1 MUTATED                       1                              0
  CAMK1 WILD-TYPE                   105                             10
D2100V10, multiclass
                                clus
vv                               CAMK1 MUTATED CAMK1 WILD-TYPE
  COLON ADENOCARCINOMA                       5             310
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  CAMK1 MUTATED     6   0   0   0
  CAMK1 WILD-TYPE 339   4  31  25
D2100V11, multiclass
    clus
vv   CAMK1 MUTATED CAMK1 WILD-TYPE
  R0             6             339
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2100V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CAMK1 MUTATED                                  0     1
  CAMK1 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CAMK1 MUTATED                           1     3
  CAMK1 WILD-TYPE                        21   223
D2100V13, multiclass
                                  clus
vv                                 CAMK1 MUTATED CAMK1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        3             223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2101) Variable = SRRM3 MUTATION ANALYSIS
D2101V1, survival
                 sevent
clus2               0   1
  SRRM3 MUTATED     3   0
  SRRM3 WILD-TYPE 375  93
  SRRM3 MUTATED SRRM3 WILD-TYPE 
              3             468 
  SRRM3 MUTATED SRRM3 WILD-TYPE 
              0              93 
$`SRRM3 MUTATED`
TCGA-AD-6963 TCGA-CM-4743 TCGA-AG-A002 
       27.42        23.05        20.98 

$`SRRM3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       22.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 
       21.14        82.95         1.91       124.27        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  SRRM3 MUTATED SRRM3 WILD-TYPE 
          20.98            0.00 
  SRRM3 MUTATED SRRM3 WILD-TYPE 
          27.42          148.01 
  SRRM3 MUTATED SRRM3 WILD-TYPE 
         23.050          20.085 
[1] "21.0 - 27.4 (23.1)" "0.0 - 148.0 (20.1)"
[1] "hr="     "3300000"
D2101V2, continuous
D2101V3, binary
                 cls
clus                0   1
  SRRM3 MUTATED     2   1
  SRRM3 WILD-TYPE 364 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SRRM3 MUTATED      2    1
  SRRM3 WILD-TYPE  364  118
        clus
vv       SRRM3 MUTATED SRRM3 WILD-TYPE
  COLON              2             364
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SRRM3 MUTATED         1        0        0         1         0         0
  SRRM3 WILD-TYPE      90        1       32       137        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SRRM3 MUTATED           0          0          0          0        0         0
  SRRM3 WILD-TYPE        24         11         59         42       48        18
                 vv
clus              STAGE IVB
  SRRM3 MUTATED           0
  SRRM3 WILD-TYPE         1
D2101V4, multiclass
[1] "Remove cluster labels:" "SRRM3 MUTATED"         
clus
  SRRM3 MUTATED SRRM3 WILD-TYPE 
              2             474 
     TCGA-A6-2671      TCGA-A6-2672      TCGA-A6-2674      TCGA-A6-2676 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-A6-2677      TCGA-A6-2678      TCGA-A6-2683      TCGA-A6-3807 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-A6-3808      TCGA-A6-3809      TCGA-A6-3810      TCGA-A6-4105 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-A6-5656      TCGA-A6-5657      TCGA-A6-5659      TCGA-A6-5660 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-A6-5661      TCGA-A6-5662      TCGA-A6-5664      TCGA-A6-5665 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-A6-5666      TCGA-A6-6137      TCGA-A6-6138      TCGA-A6-6141 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-A6-6142      TCGA-A6-6648      TCGA-A6-6649      TCGA-A6-6651 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-A6-6652      TCGA-A6-6653      TCGA-A6-6654      TCGA-A6-6780 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-A6-6781      TCGA-A6-6782      TCGA-AA-3489      TCGA-AA-3492 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-AA-3496      TCGA-AA-3502      TCGA-AA-3510      TCGA-AA-3511 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-AA-3514      TCGA-AA-3516      TCGA-AA-3517      TCGA-AA-3518 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-AA-3519      TCGA-AA-3520      TCGA-AA-3521      TCGA-AA-3522 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-AA-3524      TCGA-AA-3525      TCGA-AA-3526      TCGA-AA-3527 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-AA-3529      TCGA-AA-3530      TCGA-AA-3531      TCGA-AA-3532 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-AA-3534      TCGA-AA-3538      TCGA-AA-3542      TCGA-AA-3543 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-AA-3544      TCGA-AA-3548      TCGA-AA-3549      TCGA-AA-3552 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-AA-3553      TCGA-AA-3554      TCGA-AA-3555      TCGA-AA-3556 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-AA-3558      TCGA-AA-3560      TCGA-AA-3561      TCGA-AA-3562 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-AA-3655      TCGA-AA-3660      TCGA-AA-3662      TCGA-AA-3663 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-AA-3664      TCGA-AA-3666      TCGA-AA-3667      TCGA-AA-3672 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-AA-3673      TCGA-AA-3678      TCGA-AA-3679      TCGA-AA-3680 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-AA-3681      TCGA-AA-3684      TCGA-AA-3685      TCGA-AA-3688 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-AA-3692      TCGA-AA-3693      TCGA-AA-3695      TCGA-AA-3696 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-AA-3697      TCGA-AA-3710      TCGA-AA-3712      TCGA-AA-3713 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-AA-3715      TCGA-AA-3811      TCGA-AA-3812      TCGA-AA-3814 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-AA-3815      TCGA-AA-3818      TCGA-AA-3819      TCGA-AA-3821 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-AA-3831      TCGA-AA-3833      TCGA-AA-3837      TCGA-AA-3842 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-AA-3844      TCGA-AA-3845      TCGA-AA-3846      TCGA-AA-3848 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-AA-3850      TCGA-AA-3851      TCGA-AA-3852      TCGA-AA-3854 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-AA-3855      TCGA-AA-3856      TCGA-AA-3858      TCGA-AA-3860 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-AA-3861      TCGA-AA-3864      TCGA-AA-3866      TCGA-AA-3867 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-AA-3869      TCGA-AA-3870      TCGA-AA-3872      TCGA-AA-3875 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-AA-3877      TCGA-AA-3930      TCGA-AA-3939      TCGA-AA-3941 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-AA-3947      TCGA-AA-3949      TCGA-AA-3950      TCGA-AA-3952 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-AA-3955      TCGA-AA-3956      TCGA-AA-3966      TCGA-AA-3968 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-AA-3971      TCGA-AA-3972      TCGA-AA-3973      TCGA-AA-3975 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-AA-3976      TCGA-AA-3979      TCGA-AA-3980      TCGA-AA-3982 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-AA-3984      TCGA-AA-3986      TCGA-AA-3989      TCGA-AA-3994 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-AA-A004      TCGA-AA-A00A      TCGA-AA-A00D      TCGA-AA-A00E 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-AA-A00F      TCGA-AA-A00J      TCGA-AA-A00K      TCGA-AA-A00L 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-AA-A00N      TCGA-AA-A00O      TCGA-AA-A00Q      TCGA-AA-A00R 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-AA-A00U      TCGA-AA-A00W      TCGA-AA-A00Z      TCGA-AA-A010 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-AA-A017      TCGA-AA-A01D      TCGA-AA-A01F      TCGA-AA-A01G 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-AA-A01I      TCGA-AA-A01K      TCGA-AA-A01P      TCGA-AA-A01Q 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-AA-A01R      TCGA-AA-A01S      TCGA-AA-A01T      TCGA-AA-A01V 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-AA-A01X      TCGA-AA-A01Z      TCGA-AA-A022      TCGA-AA-A024 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-AA-A029      TCGA-AA-A02F      TCGA-AA-A02H      TCGA-AA-A02J 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-AA-A02K      TCGA-AA-A02O      TCGA-AA-A02W      TCGA-AA-A02Y 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-AA-A03F      TCGA-AA-A03J      TCGA-AD-5900      TCGA-AD-6548 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-AD-6888      TCGA-AD-6889      TCGA-AD-6899      TCGA-AU-3779 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-AU-6004      TCGA-AY-4070      TCGA-AY-4071      TCGA-AY-5543 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-AY-6196      TCGA-AY-6197      TCGA-AY-6386      TCGA-AZ-4315 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-AZ-4323      TCGA-AZ-4616      TCGA-AZ-4681      TCGA-AZ-4682 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-AZ-5403      TCGA-AZ-5407      TCGA-AZ-6598      TCGA-AZ-6599 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-AZ-6600      TCGA-AZ-6601      TCGA-AZ-6605      TCGA-AZ-6606 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-AZ-6607      TCGA-AZ-6608      TCGA-CA-5254      TCGA-CA-5255 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-CA-5796      TCGA-CA-5797      TCGA-CA-6715      TCGA-CA-6716 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-CA-6717      TCGA-CA-6718      TCGA-CA-6719      TCGA-CK-4947 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-CK-4948      TCGA-CK-4950      TCGA-CK-4952      TCGA-CK-5912 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-CK-5913      TCGA-CK-5914      TCGA-CK-5915      TCGA-CK-5916 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-CK-6746      TCGA-CK-6747      TCGA-CK-6748      TCGA-CK-6751 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-CM-4744      TCGA-CM-4746      TCGA-CM-4747      TCGA-CM-4752 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-CM-5341      TCGA-CM-5344      TCGA-CM-5348      TCGA-CM-5349 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-CM-5860      TCGA-CM-5861      TCGA-CM-5862      TCGA-CM-5863 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-CM-5864      TCGA-CM-5868      TCGA-CM-6161      TCGA-CM-6162 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-CM-6163      TCGA-CM-6164      TCGA-CM-6165      TCGA-CM-6166 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-CM-6167      TCGA-CM-6168      TCGA-CM-6169      TCGA-CM-6170 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-CM-6171      TCGA-CM-6172      TCGA-CM-6674      TCGA-CM-6675 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-CM-6676      TCGA-CM-6677      TCGA-CM-6678      TCGA-CM-6679 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-CM-6680      TCGA-D5-5537      TCGA-D5-5538      TCGA-D5-5539 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-D5-5540      TCGA-D5-5541      TCGA-D5-6529      TCGA-D5-6532 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-D5-6533      TCGA-D5-6534      TCGA-D5-6535      TCGA-D5-6536 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-D5-6537      TCGA-D5-6538      TCGA-D5-6539      TCGA-D5-6540 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-D5-6541      TCGA-D5-6898      TCGA-D5-6920      TCGA-D5-6922 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-D5-6923      TCGA-D5-6924      TCGA-D5-6926      TCGA-D5-6927 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-D5-6928      TCGA-D5-6929      TCGA-D5-6930      TCGA-D5-6931 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-D5-6932      TCGA-D5-7000      TCGA-DM-A0X9      TCGA-DM-A0XD 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-DM-A0XF      TCGA-DM-A1D0      TCGA-DM-A1D4      TCGA-DM-A1D6 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-DM-A1D7      TCGA-DM-A1D9      TCGA-DM-A1DA      TCGA-DM-A1DB 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-DM-A1HA      TCGA-DM-A1HB      TCGA-DM-A282      TCGA-DM-A285 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-DM-A28C      TCGA-DM-A28E      TCGA-DM-A28F      TCGA-DM-A28G 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-DM-A28H      TCGA-DM-A28K      TCGA-F4-6459      TCGA-F4-6460 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-F4-6569      TCGA-F4-6570      TCGA-F4-6703      TCGA-F4-6704 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-F4-6805      TCGA-F4-6806      TCGA-F4-6807      TCGA-F4-6808 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-F4-6809      TCGA-F4-6854      TCGA-F4-6855      TCGA-F4-6856 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-G4-6293      TCGA-G4-6299      TCGA-G4-6303      TCGA-G4-6304 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-G4-6306      TCGA-G4-6307      TCGA-G4-6309      TCGA-G4-6310 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-G4-6315      TCGA-G4-6317      TCGA-G4-6321      TCGA-G4-6323 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-G4-6586      TCGA-G4-6588      TCGA-G4-6625      TCGA-G4-6626 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-G4-6628      TCGA-AF-2687      TCGA-AF-2689      TCGA-AF-2691 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-AF-2692      TCGA-AF-2693      TCGA-AF-3400      TCGA-AF-3913 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-AF-4110      TCGA-AF-5654      TCGA-AF-6136      TCGA-AF-6655 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-AF-6672      TCGA-AG-3574      TCGA-AG-3575      TCGA-AG-3578 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-AG-3580      TCGA-AG-3581      TCGA-AG-3582      TCGA-AG-3583 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-AG-3584      TCGA-AG-3586      TCGA-AG-3587      TCGA-AG-3593 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-AG-3594      TCGA-AG-3598      TCGA-AG-3599      TCGA-AG-3600 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-AG-3601      TCGA-AG-3602      TCGA-AG-3605      TCGA-AG-3608 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-AG-3609      TCGA-AG-3611      TCGA-AG-3612      TCGA-AG-3726 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-AG-3727      TCGA-AG-3731      TCGA-AG-3732      TCGA-AG-3742 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-AG-3878      TCGA-AG-3881      TCGA-AG-3882      TCGA-AG-3883 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-AG-3885      TCGA-AG-3887      TCGA-AG-3890      TCGA-AG-3892 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-AG-3893      TCGA-AG-3894      TCGA-AG-3896      TCGA-AG-3898 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-AG-3901      TCGA-AG-3902      TCGA-AG-3909      TCGA-AG-3999 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-AG-4001      TCGA-AG-4005      TCGA-AG-4007      TCGA-AG-4008 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-AG-4015      TCGA-AG-A008      TCGA-AG-A00C      TCGA-AG-A00H 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-AG-A00Y      TCGA-AG-A011      TCGA-AG-A014      TCGA-AG-A015 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-AG-A016      TCGA-AG-A01L      TCGA-AG-A01W      TCGA-AG-A01Y 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-AG-A020      TCGA-AG-A025      TCGA-AG-A026      TCGA-AG-A02G 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-AG-A02N      TCGA-AG-A02X      TCGA-AG-A032      TCGA-AG-A036 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-AH-6643      TCGA-CI-6619      TCGA-CI-6620      TCGA-CI-6621 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-CI-6622      TCGA-CI-6624      TCGA-CL-5917      TCGA-CL-5918 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-DC-5337      TCGA-DC-5869      TCGA-DC-6155      TCGA-DC-6157 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-DC-6158      TCGA-DC-6160      TCGA-DC-6681      TCGA-DC-6682 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-DC-6683      TCGA-DT-5265      TCGA-DY-A0XA      TCGA-DY-A1DC 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-DY-A1DD      TCGA-DY-A1DF      TCGA-DY-A1DG      TCGA-DY-A1H8 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-EF-5830      TCGA-EI-6506      TCGA-EI-6507      TCGA-EI-6508 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-EI-6510      TCGA-F5-6464      TCGA-F5-6465      TCGA-F5-6571 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-F5-6702      TCGA-F5-6811      TCGA-F5-6812      TCGA-F5-6813 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-G5-6235      TCGA-G5-6641 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
                 vv
clus               T1  T2  T3  T4
  SRRM3 MUTATED     0   1   2   0
  SRRM3 WILD-TYPE  17  91 327  50
D2101V5, multiclass
    clus
vv   SRRM3 MUTATED SRRM3 WILD-TYPE
  T1             0              17
  T2             1              91
  T3             2             327
  T4             0              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  SRRM3 MUTATED     3   0   0
  SRRM3 WILD-TYPE 284 113  87
D2101V6, multiclass
    clus
vv   SRRM3 MUTATED SRRM3 WILD-TYPE
  N0             3             284
  N1             0             113
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2101V7, binary
                 cls
clus                0   1
  SRRM3 MUTATED     2   0
  SRRM3 WILD-TYPE 373  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SRRM3 MUTATED      2    0
  SRRM3 WILD-TYPE  373   65
   clus
vv  SRRM3 MUTATED SRRM3 WILD-TYPE
  0             2             373
  1             0              65
[1] 2 2
[1] FALSE
D2101V8, binary
                 cls
clus                0   1
  SRRM3 MUTATED     0   3
  SRRM3 WILD-TYPE 225 261
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SRRM3 MUTATED      0    3
  SRRM3 WILD-TYPE  225  261
        clus
vv       SRRM3 MUTATED SRRM3 WILD-TYPE
  FEMALE             0             225
  MALE               3             261
[1] 2 2
[1] FALSE
D2101V9, binary
                 cls
clus                0   1
  SRRM3 MUTATED     3   0
  SRRM3 WILD-TYPE 347  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SRRM3 MUTATED      3    0
  SRRM3 WILD-TYPE  347   22
     clus
vv    SRRM3 MUTATED SRRM3 WILD-TYPE
  NO              3             347
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SRRM3 MUTATED                      2                             0
  SRRM3 WILD-TYPE                  313                            47
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SRRM3 MUTATED                       1                              0
  SRRM3 WILD-TYPE                   105                             10
D2101V10, multiclass
                                clus
vv                               SRRM3 MUTATED SRRM3 WILD-TYPE
  COLON ADENOCARCINOMA                       2             313
  COLON MUCINOUS ADENOCARCINOMA              0              47
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  SRRM3 MUTATED     2   0   0   0
  SRRM3 WILD-TYPE 343   4  31  25
D2101V11, multiclass
[1] "Remove cluster labels:" "SRRM3 MUTATED"         
clus
  SRRM3 MUTATED SRRM3 WILD-TYPE 
              2             403 
     TCGA-A6-2671      TCGA-A6-2672      TCGA-A6-2674      TCGA-A6-2676 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-A6-2677      TCGA-A6-2678      TCGA-A6-2683      TCGA-A6-3807 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-A6-3808      TCGA-A6-3809      TCGA-A6-3810      TCGA-A6-5657 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-A6-5659      TCGA-A6-5661      TCGA-A6-5665      TCGA-A6-6781 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-AA-3489      TCGA-AA-3492      TCGA-AA-3496      TCGA-AA-3502 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-AA-3510      TCGA-AA-3511      TCGA-AA-3514      TCGA-AA-3517 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-AA-3518      TCGA-AA-3519      TCGA-AA-3520      TCGA-AA-3521 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-AA-3522      TCGA-AA-3524      TCGA-AA-3525      TCGA-AA-3526 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-AA-3527      TCGA-AA-3529      TCGA-AA-3530      TCGA-AA-3531 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-AA-3532      TCGA-AA-3534      TCGA-AA-3538      TCGA-AA-3542 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-AA-3543      TCGA-AA-3544      TCGA-AA-3548      TCGA-AA-3549 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-AA-3552      TCGA-AA-3553      TCGA-AA-3554      TCGA-AA-3555 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-AA-3556      TCGA-AA-3558      TCGA-AA-3560      TCGA-AA-3561 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-AA-3562      TCGA-AA-3655      TCGA-AA-3660      TCGA-AA-3662 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-AA-3663      TCGA-AA-3664      TCGA-AA-3666      TCGA-AA-3667 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-AA-3672      TCGA-AA-3673      TCGA-AA-3678      TCGA-AA-3679 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-AA-3680      TCGA-AA-3681      TCGA-AA-3684      TCGA-AA-3685 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-AA-3688      TCGA-AA-3692      TCGA-AA-3693      TCGA-AA-3695 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-AA-3696      TCGA-AA-3697      TCGA-AA-3710      TCGA-AA-3712 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-AA-3713      TCGA-AA-3715      TCGA-AA-3811      TCGA-AA-3812 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-AA-3814      TCGA-AA-3815      TCGA-AA-3818      TCGA-AA-3819 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-AA-3821      TCGA-AA-3831      TCGA-AA-3833      TCGA-AA-3837 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-AA-3842      TCGA-AA-3844      TCGA-AA-3845      TCGA-AA-3846 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-AA-3848      TCGA-AA-3850      TCGA-AA-3851      TCGA-AA-3852 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-AA-3854      TCGA-AA-3855      TCGA-AA-3856      TCGA-AA-3858 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-AA-3860      TCGA-AA-3861      TCGA-AA-3864      TCGA-AA-3866 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-AA-3867      TCGA-AA-3869      TCGA-AA-3870      TCGA-AA-3872 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-AA-3875      TCGA-AA-3877      TCGA-AA-3930      TCGA-AA-3939 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-AA-3941      TCGA-AA-3947      TCGA-AA-3949      TCGA-AA-3950 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-AA-3952      TCGA-AA-3955      TCGA-AA-3956      TCGA-AA-3968 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-AA-3971      TCGA-AA-3972      TCGA-AA-3973      TCGA-AA-3975 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-AA-3976      TCGA-AA-3979      TCGA-AA-3984      TCGA-AA-3986 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-AA-3989      TCGA-AA-3994      TCGA-AA-A004      TCGA-AA-A00A 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-AA-A00D      TCGA-AA-A00E      TCGA-AA-A00F      TCGA-AA-A00J 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-AA-A00K      TCGA-AA-A00L      TCGA-AA-A00N      TCGA-AA-A00O 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-AA-A00Q      TCGA-AA-A00R      TCGA-AA-A00U      TCGA-AA-A00W 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-AA-A00Z      TCGA-AA-A010      TCGA-AA-A017      TCGA-AA-A01D 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-AA-A01F      TCGA-AA-A01G      TCGA-AA-A01I      TCGA-AA-A01K 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-AA-A01P      TCGA-AA-A01Q      TCGA-AA-A01R      TCGA-AA-A01S 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-AA-A01T      TCGA-AA-A01V      TCGA-AA-A01X      TCGA-AA-A01Z 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-AA-A022      TCGA-AA-A024      TCGA-AA-A029      TCGA-AA-A02F 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-AA-A02H      TCGA-AA-A02J      TCGA-AA-A02K      TCGA-AA-A02O 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-AA-A02W      TCGA-AA-A02Y      TCGA-AA-A03F      TCGA-AA-A03J 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-AD-5900      TCGA-AD-6548      TCGA-AD-6888      TCGA-AU-3779 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-AU-6004      TCGA-AY-4070      TCGA-AY-4071      TCGA-AY-5543 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-AY-6196      TCGA-AY-6197      TCGA-AY-6386      TCGA-AZ-4315 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-AZ-4681      TCGA-AZ-4682      TCGA-CA-5254      TCGA-CA-5255 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-CA-5796      TCGA-CA-5797      TCGA-CA-6715      TCGA-CA-6716 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-CA-6717      TCGA-CA-6718      TCGA-CA-6719      TCGA-CK-4947 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-CK-4948      TCGA-CK-4950      TCGA-CK-4952      TCGA-CK-5912 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-CK-5913      TCGA-CK-5914      TCGA-CK-5915      TCGA-CK-5916 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-CK-6746      TCGA-CK-6747      TCGA-CK-6748      TCGA-CK-6751 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-CM-4744      TCGA-CM-4746      TCGA-CM-4747      TCGA-CM-4752 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-CM-5341      TCGA-CM-5344      TCGA-CM-5348      TCGA-CM-5349 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-CM-5860      TCGA-CM-5861      TCGA-CM-5862      TCGA-CM-5863 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-CM-5864      TCGA-CM-5868      TCGA-CM-6161      TCGA-CM-6162 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-CM-6163      TCGA-CM-6164      TCGA-CM-6165      TCGA-CM-6166 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-CM-6167      TCGA-CM-6168      TCGA-CM-6169      TCGA-CM-6170 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-CM-6171      TCGA-CM-6172      TCGA-CM-6674      TCGA-CM-6675 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-CM-6676      TCGA-CM-6677      TCGA-CM-6678      TCGA-CM-6679 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-CM-6680      TCGA-D5-5537      TCGA-D5-5538      TCGA-D5-5539 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-D5-5540      TCGA-D5-5541      TCGA-D5-6529      TCGA-D5-6532 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-D5-6533      TCGA-D5-6534      TCGA-D5-6535      TCGA-D5-6536 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-D5-6537      TCGA-D5-6538      TCGA-D5-6539      TCGA-D5-6540 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-D5-6541      TCGA-D5-6898      TCGA-D5-6920      TCGA-D5-6922 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-D5-6923      TCGA-D5-6924      TCGA-D5-6926      TCGA-D5-6927 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-D5-6928      TCGA-D5-6929      TCGA-D5-6930      TCGA-D5-6931 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-D5-6932      TCGA-D5-7000      TCGA-F4-6459      TCGA-F4-6460 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-F4-6569      TCGA-F4-6570      TCGA-F4-6703      TCGA-F4-6704 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-F4-6805      TCGA-F4-6806      TCGA-F4-6807      TCGA-F4-6808 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-F4-6809      TCGA-F4-6854      TCGA-F4-6855      TCGA-F4-6856 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-G4-6293      TCGA-G4-6299      TCGA-G4-6303      TCGA-G4-6304 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-G4-6306      TCGA-G4-6307      TCGA-G4-6309      TCGA-G4-6310 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-G4-6315      TCGA-G4-6317      TCGA-G4-6321      TCGA-G4-6323 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-G4-6586      TCGA-G4-6588      TCGA-G4-6625      TCGA-G4-6626 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-G4-6628      TCGA-AF-2687      TCGA-AF-2689      TCGA-AF-2691 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-AF-2692      TCGA-AF-3400      TCGA-AF-3913      TCGA-AF-4110 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-AF-5654      TCGA-AF-6655      TCGA-AG-3574      TCGA-AG-3575 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-AG-3578      TCGA-AG-3580      TCGA-AG-3581      TCGA-AG-3582 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-AG-3583      TCGA-AG-3584      TCGA-AG-3586      TCGA-AG-3587 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-AG-3593      TCGA-AG-3594      TCGA-AG-3598      TCGA-AG-3599 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-AG-3600      TCGA-AG-3601      TCGA-AG-3602      TCGA-AG-3605 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-AG-3608      TCGA-AG-3609      TCGA-AG-3611      TCGA-AG-3612 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-AG-3726      TCGA-AG-3727      TCGA-AG-3731      TCGA-AG-3732 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-AG-3742      TCGA-AG-3878      TCGA-AG-3882      TCGA-AG-3883 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-AG-3885      TCGA-AG-3887      TCGA-AG-3890      TCGA-AG-3892 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-AG-3893      TCGA-AG-3894      TCGA-AG-3896      TCGA-AG-3898 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-AG-3901      TCGA-AG-3902      TCGA-AG-3909      TCGA-AG-3999 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-AG-4001      TCGA-AG-4005      TCGA-AG-4007      TCGA-AG-4008 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-AG-4015      TCGA-AG-A008      TCGA-AG-A00C      TCGA-AG-A00H 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-AG-A00Y      TCGA-AG-A011      TCGA-AG-A014      TCGA-AG-A015 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-AG-A016      TCGA-AG-A01L      TCGA-AG-A01W      TCGA-AG-A01Y 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-AG-A020      TCGA-AG-A025      TCGA-AG-A026      TCGA-AG-A02G 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-AG-A02N      TCGA-AG-A02X      TCGA-AG-A032      TCGA-AG-A036 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-AH-6549      TCGA-AH-6643      TCGA-CL-5917      TCGA-CL-5918 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-DC-5337      TCGA-DC-5869      TCGA-DC-6155      TCGA-DC-6157 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-DC-6158      TCGA-DC-6160      TCGA-DC-6681      TCGA-DC-6682 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-DC-6683      TCGA-DT-5265      TCGA-EF-5830      TCGA-EI-6506 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-EI-6507      TCGA-EI-6508      TCGA-EI-6510      TCGA-F5-6464 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-F5-6465      TCGA-F5-6571      TCGA-F5-6702      TCGA-F5-6812 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-F5-6813      TCGA-G5-6235      TCGA-G5-6641 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
D2101V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SRRM3 MUTATED                                  0     0
  SRRM3 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  SRRM3 MUTATED                           0     2
  SRRM3 WILD-TYPE                        22   224
D2101V13, multiclass
[1] "Remove cluster labels:" "SRRM3 MUTATED"         
clus
  SRRM3 MUTATED SRRM3 WILD-TYPE 
              2             258 
     TCGA-A6-2671      TCGA-A6-2672      TCGA-A6-2674      TCGA-A6-2676 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-A6-2677      TCGA-A6-2678      TCGA-A6-2683      TCGA-A6-3807 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-A6-3808      TCGA-A6-3809      TCGA-A6-3810      TCGA-A6-4105 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-A6-5656      TCGA-A6-5657      TCGA-A6-5659      TCGA-A6-5660 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-A6-5661      TCGA-A6-5662      TCGA-A6-5664      TCGA-A6-5665 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-A6-5666      TCGA-A6-6137      TCGA-A6-6138      TCGA-A6-6141 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-A6-6142      TCGA-A6-6648      TCGA-A6-6649      TCGA-A6-6651 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-A6-6652      TCGA-A6-6653      TCGA-A6-6654      TCGA-A6-6780 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-A6-6781      TCGA-A6-6782      TCGA-AD-5900      TCGA-AD-6548 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-AD-6888      TCGA-AD-6889      TCGA-AD-6890      TCGA-AD-6895 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-AD-6899      TCGA-AD-6901      TCGA-AD-6964      TCGA-AD-6965 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-AU-3779      TCGA-AU-6004      TCGA-AY-4070      TCGA-AY-4071 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-AY-5543      TCGA-AY-6196      TCGA-AY-6197      TCGA-AY-6386 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-AZ-4315      TCGA-AZ-4323      TCGA-AZ-4616      TCGA-AZ-4681 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-AZ-4682      TCGA-AZ-5403      TCGA-AZ-5407      TCGA-AZ-6598 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-AZ-6599      TCGA-AZ-6600      TCGA-AZ-6601      TCGA-AZ-6603 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-AZ-6605      TCGA-AZ-6606      TCGA-AZ-6607      TCGA-AZ-6608 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-CA-5254      TCGA-CA-5255      TCGA-CA-5796      TCGA-CA-5797 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-CA-6715      TCGA-CA-6716      TCGA-CA-6717      TCGA-CA-6718 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-CA-6719      TCGA-CK-4947      TCGA-CK-4948      TCGA-CK-4950 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-CK-4952      TCGA-CK-5912      TCGA-CK-5913      TCGA-CK-5914 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-CK-5915      TCGA-CK-5916      TCGA-CK-6746      TCGA-CK-6747 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-CK-6748      TCGA-CK-6751      TCGA-CM-4744      TCGA-CM-4746 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-CM-4747      TCGA-CM-4752      TCGA-CM-5341      TCGA-CM-5344 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-CM-5348      TCGA-CM-5349      TCGA-CM-5860      TCGA-CM-5861 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-CM-5862      TCGA-CM-5863      TCGA-CM-5864      TCGA-CM-5868 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-CM-6161      TCGA-CM-6162      TCGA-CM-6163      TCGA-CM-6164 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-CM-6165      TCGA-CM-6166      TCGA-CM-6167      TCGA-CM-6168 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-CM-6169      TCGA-CM-6170      TCGA-CM-6171      TCGA-CM-6172 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-CM-6674      TCGA-CM-6675      TCGA-CM-6676      TCGA-CM-6677 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-CM-6678      TCGA-CM-6679      TCGA-CM-6680      TCGA-D5-5537 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-D5-5538      TCGA-D5-5539      TCGA-D5-5540      TCGA-D5-5541 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-D5-6529      TCGA-D5-6532      TCGA-D5-6533      TCGA-D5-6534 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-D5-6535      TCGA-D5-6536      TCGA-D5-6537      TCGA-D5-6538 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-D5-6539      TCGA-D5-6540      TCGA-D5-6541      TCGA-D5-6898 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-D5-6920      TCGA-D5-6922      TCGA-D5-6923      TCGA-D5-6924 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-D5-6926      TCGA-D5-6927      TCGA-D5-6928      TCGA-D5-6929 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-D5-6930      TCGA-D5-6931      TCGA-D5-6932      TCGA-D5-7000 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-DM-A0X9      TCGA-DM-A0XD      TCGA-DM-A0XF      TCGA-DM-A1D0 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-DM-A1D4      TCGA-DM-A1D6      TCGA-DM-A1D7      TCGA-DM-A1D8 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-DM-A1D9      TCGA-DM-A1DA      TCGA-DM-A1DB      TCGA-DM-A1HA 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-DM-A1HB      TCGA-DM-A282      TCGA-DM-A285      TCGA-DM-A28C 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-DM-A28E      TCGA-DM-A28F      TCGA-DM-A28G      TCGA-DM-A28H 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-DM-A28K      TCGA-F4-6459      TCGA-F4-6460      TCGA-F4-6569 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-F4-6570      TCGA-F4-6703      TCGA-F4-6704      TCGA-F4-6805 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-F4-6806      TCGA-F4-6807      TCGA-F4-6808      TCGA-F4-6809 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-F4-6854      TCGA-F4-6855      TCGA-F4-6856      TCGA-G4-6293 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-G4-6299      TCGA-G4-6303      TCGA-G4-6304      TCGA-G4-6306 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-G4-6307      TCGA-G4-6309      TCGA-G4-6310      TCGA-G4-6315 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-G4-6317      TCGA-G4-6321      TCGA-G4-6323      TCGA-G4-6586 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-G4-6588      TCGA-G4-6625      TCGA-G4-6626      TCGA-G4-6628 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-AF-2687      TCGA-AF-2689      TCGA-AF-2691      TCGA-AF-2692 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-AF-2693      TCGA-AF-3400      TCGA-AF-3913      TCGA-AF-4110 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-AF-5654      TCGA-AF-6136      TCGA-AF-6655      TCGA-AF-6672 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-AH-6544      TCGA-AH-6547      TCGA-AH-6549      TCGA-AH-6643 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-AH-6644      TCGA-CI-6619      TCGA-CI-6620      TCGA-CI-6621 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-CI-6622      TCGA-CI-6624      TCGA-CL-5917      TCGA-CL-5918 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-DC-5337      TCGA-DC-5869      TCGA-DC-6155      TCGA-DC-6157 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-DC-6158      TCGA-DC-6160      TCGA-DC-6681      TCGA-DC-6682 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-DC-6683      TCGA-DT-5265      TCGA-DY-A0XA      TCGA-DY-A1DC 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-DY-A1DD      TCGA-DY-A1DF      TCGA-DY-A1DG      TCGA-DY-A1H8 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-EF-5830      TCGA-EI-6506      TCGA-EI-6507      TCGA-EI-6508 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-EI-6510      TCGA-F5-6464      TCGA-F5-6465      TCGA-F5-6571 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-F5-6702      TCGA-F5-6811      TCGA-F5-6812      TCGA-F5-6813 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 
     TCGA-G5-6235      TCGA-G5-6641 
"SRRM3 WILD-TYPE" "SRRM3 WILD-TYPE" 

Clustering(2102) Variable = SFRS12IP1 MUTATION ANALYSIS
D2102V1, survival
                     sevent
clus2                   0   1
  SFRS12IP1 MUTATED     5   0
  SFRS12IP1 WILD-TYPE 373  93
  SFRS12IP1 MUTATED SFRS12IP1 WILD-TYPE 
                  5                 466 
  SFRS12IP1 MUTATED SFRS12IP1 WILD-TYPE 
                  0                  93 
$`SFRS12IP1 MUTATED`
TCGA-AD-6890 TCGA-G4-6309 TCGA-G4-6628 TCGA-AG-3890 TCGA-AG-A002 
        0.79        85.48        79.69        17.03        20.98 

$`SFRS12IP1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       21.37        15.52        56.55         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       26.17        91.79        46.75        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 
       19.99         1.02        17.95        36.95        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  SFRS12IP1 MUTATED SFRS12IP1 WILD-TYPE 
               0.79                0.00 
  SFRS12IP1 MUTATED SFRS12IP1 WILD-TYPE 
              85.48              148.01 
  SFRS12IP1 MUTATED SFRS12IP1 WILD-TYPE 
             20.980              20.155 
[1] "0.8 - 85.5 (21.0)"  "0.0 - 148.0 (20.2)"
[1] "hr="     "9200000"
D2102V2, continuous
D2102V3, binary
                     cls
clus                    0   1
  SFRS12IP1 MUTATED     3   2
  SFRS12IP1 WILD-TYPE 363 117
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  SFRS12IP1 MUTATED      3    2
  SFRS12IP1 WILD-TYPE  363  117
        clus
vv       SFRS12IP1 MUTATED SFRS12IP1 WILD-TYPE
  COLON                  3                 363
  RECTUM                 2                 117
[1] 2 2
[1] FALSE
                     vv
clus                  STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SFRS12IP1 MUTATED         3        0        0         0         0         0
  SFRS12IP1 WILD-TYPE      88        1       32       138        10         1
                     vv
clus                  STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SFRS12IP1 MUTATED           0          0          1          0        0
  SFRS12IP1 WILD-TYPE        24         11         58         42       48
                     vv
clus                  STAGE IVA STAGE IVB
  SFRS12IP1 MUTATED           0         0
  SFRS12IP1 WILD-TYPE        18         1
D2102V4, multiclass
            clus
vv           SFRS12IP1 MUTATED SFRS12IP1 WILD-TYPE
  STAGE I                    3                  88
  STAGE IA                   0                   1
  STAGE II                   0                  32
  STAGE IIA                  0                 138
  STAGE IIB                  0                  10
  STAGE IIC                  0                   1
  STAGE III                  0                  24
  STAGE IIIA                 0                  11
  STAGE IIIB                 1                  58
  STAGE IIIC                 0                  42
  STAGE IV                   0                  48
  STAGE IVA                  0                  18
  STAGE IVB                  0                   1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                   T1  T2  T3  T4
  SFRS12IP1 MUTATED     1   3   1   0
  SFRS12IP1 WILD-TYPE  16  89 328  50
D2102V5, multiclass
    clus
vv   SFRS12IP1 MUTATED SFRS12IP1 WILD-TYPE
  T1                 1                  16
  T2                 3                  89
  T3                 1                 328
  T4                 0                  50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                   N0  N1  N2
  SFRS12IP1 MUTATED     4   1   0
  SFRS12IP1 WILD-TYPE 283 112  87
D2102V6, multiclass
    clus
vv   SFRS12IP1 MUTATED SFRS12IP1 WILD-TYPE
  N0                 4                 283
  N1                 1                 112
  N2                 0                  87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2102V7, binary
                     cls
clus                    0   1
  SFRS12IP1 MUTATED     4   0
  SFRS12IP1 WILD-TYPE 371  65
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  SFRS12IP1 MUTATED      4    0
  SFRS12IP1 WILD-TYPE  371   65
   clus
vv  SFRS12IP1 MUTATED SFRS12IP1 WILD-TYPE
  0                 4                 371
  1                 0                  65
[1] 2 2
[1] FALSE
D2102V8, binary
                     cls
clus                    0   1
  SFRS12IP1 MUTATED     1   4
  SFRS12IP1 WILD-TYPE 224 260
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  SFRS12IP1 MUTATED      1    4
  SFRS12IP1 WILD-TYPE  224  260
        clus
vv       SFRS12IP1 MUTATED SFRS12IP1 WILD-TYPE
  FEMALE                 1                 224
  MALE                   4                 260
[1] 2 2
[1] FALSE
D2102V9, binary
                     cls
clus                    0   1
  SFRS12IP1 MUTATED     4   0
  SFRS12IP1 WILD-TYPE 346  22
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  SFRS12IP1 MUTATED      4    0
  SFRS12IP1 WILD-TYPE  346   22
     clus
vv    SFRS12IP1 MUTATED SFRS12IP1 WILD-TYPE
  NO                  4                 346
  YES                 0                  22
[1] 2 2
[1] FALSE
                     vv
clus                  COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SFRS12IP1 MUTATED                      3                             0
  SFRS12IP1 WILD-TYPE                  312                            47
                     vv
clus                  RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SFRS12IP1 MUTATED                       2                              0
  SFRS12IP1 WILD-TYPE                   104                             10
D2102V10, multiclass
                                clus
vv                               SFRS12IP1 MUTATED SFRS12IP1 WILD-TYPE
  COLON ADENOCARCINOMA                           3                 312
  COLON MUCINOUS ADENOCARCINOMA                  0                  47
  RECTAL ADENOCARCINOMA                          2                 104
  RECTAL MUCINOUS ADENOCARCINOMA                 0                  10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                     vv
clus                   R0  R1  R2  RX
  SFRS12IP1 MUTATED     4   0   0   0
  SFRS12IP1 WILD-TYPE 341   4  31  25
D2102V11, multiclass
    clus
vv   SFRS12IP1 MUTATED SFRS12IP1 WILD-TYPE
  R0                 4                 341
  R1                 0                   4
  R2                 0                  31
  RX                 0                  25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2102V12, continuous
                     vv
clus                  AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SFRS12IP1 MUTATED                                  0     0
  SFRS12IP1 WILD-TYPE                                1    11
                     vv
clus                  BLACK OR AFRICAN AMERICAN WHITE
  SFRS12IP1 MUTATED                           1     2
  SFRS12IP1 WILD-TYPE                        21   224
D2102V13, multiclass
                                  clus
vv                                 SFRS12IP1 MUTATED SFRS12IP1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                 0                   1
  ASIAN                                            0                  11
  BLACK OR AFRICAN AMERICAN                        1                  21
  WHITE                                            2                 224
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2103) Variable = SBF1 MUTATION ANALYSIS
D2103V1, survival
                sevent
clus2              0   1
  SBF1 MUTATED    11   5
  SBF1 WILD-TYPE 367  88
  SBF1 MUTATED SBF1 WILD-TYPE 
            16            455 
  SBF1 MUTATED SBF1 WILD-TYPE 
             5             88 
$`SBF1 MUTATED`
TCGA-A6-5665 TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3663 TCGA-AA-3811 TCGA-AA-3877 
       22.06         3.02        63.98         6.97        10.06        31.00 
TCGA-AA-A02K TCGA-AD-6964 TCGA-AZ-6598 TCGA-D5-6927 TCGA-D5-6930 TCGA-DM-A1HA 
       14.01        10.88        49.41         9.44         1.51       131.51 
TCGA-DM-A1HB TCGA-F4-6703 TCGA-AG-A002 TCGA-DC-5337 
      135.65        47.87        20.98        15.02 

$`SBF1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 
       20.12        19.66        20.28         7.04         1.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02        78.08         6.05        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       26.99        19.04        19.04        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       18.05         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O 
       39.06        51.98        39.98         2.01         5.03         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 
      106.75        22.36        62.79        88.21         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6929 
        4.41        12.43        14.30         9.04        11.64         4.80 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
        7.50        44.32       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       35.74         6.18         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  SBF1 MUTATED SBF1 WILD-TYPE 
          1.51           0.00 
  SBF1 MUTATED SBF1 WILD-TYPE 
        135.65         148.01 
  SBF1 MUTATED SBF1 WILD-TYPE 
         18.00          20.19 
[1] "1.5 - 135.7 (18.0)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.3"
D2103V2, continuous
D2103V3, binary
                cls
clus               0   1
  SBF1 MUTATED    14   2
  SBF1 WILD-TYPE 352 117
[1] "tbl2"
                cls
clus             [,1] [,2]
  SBF1 MUTATED     14    2
  SBF1 WILD-TYPE  352  117
        clus
vv       SBF1 MUTATED SBF1 WILD-TYPE
  COLON            14            352
  RECTUM            2            117
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SBF1 MUTATED         3        0        4         4         0         0
  SBF1 WILD-TYPE      88        1       28       134        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SBF1 MUTATED           1          0          1          1        1         0
  SBF1 WILD-TYPE        23         11         58         41       47        18
                vv
clus             STAGE IVB
  SBF1 MUTATED           0
  SBF1 WILD-TYPE         1
D2103V4, multiclass
            clus
vv           SBF1 MUTATED SBF1 WILD-TYPE
  STAGE I               3             88
  STAGE IA              0              1
  STAGE II              4             28
  STAGE IIA             4            134
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             1             23
  STAGE IIIA            0             11
  STAGE IIIB            1             58
  STAGE IIIC            1             41
  STAGE IV              1             47
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  SBF1 MUTATED     2   1  11   2
  SBF1 WILD-TYPE  15  91 318  48
D2103V5, multiclass
    clus
vv   SBF1 MUTATED SBF1 WILD-TYPE
  T1            2             15
  T2            1             91
  T3           11            318
  T4            2             48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  SBF1 MUTATED    11   1   4
  SBF1 WILD-TYPE 276 112  83
D2103V6, multiclass
    clus
vv   SBF1 MUTATED SBF1 WILD-TYPE
  N0           11            276
  N1            1            112
  N2            4             83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2103V7, binary
                cls
clus               0   1
  SBF1 MUTATED    13   1
  SBF1 WILD-TYPE 362  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  SBF1 MUTATED     13    1
  SBF1 WILD-TYPE  362   64
   clus
vv  SBF1 MUTATED SBF1 WILD-TYPE
  0           13            362
  1            1             64
[1] 2 2
[1] FALSE
D2103V8, binary
                cls
clus               0   1
  SBF1 MUTATED     5  11
  SBF1 WILD-TYPE 220 253
[1] "tbl2"
                cls
clus             [,1] [,2]
  SBF1 MUTATED      5   11
  SBF1 WILD-TYPE  220  253
        clus
vv       SBF1 MUTATED SBF1 WILD-TYPE
  FEMALE            5            220
  MALE             11            253
[1] 2 2
[1] FALSE
D2103V9, binary
                cls
clus               0   1
  SBF1 MUTATED    13   0
  SBF1 WILD-TYPE 337  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  SBF1 MUTATED     13    0
  SBF1 WILD-TYPE  337   22
     clus
vv    SBF1 MUTATED SBF1 WILD-TYPE
  NO            13            337
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SBF1 MUTATED                     11                             2
  SBF1 WILD-TYPE                  304                            45
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SBF1 MUTATED                       2                              0
  SBF1 WILD-TYPE                   104                             10
D2103V10, multiclass
                                clus
vv                               SBF1 MUTATED SBF1 WILD-TYPE
  COLON ADENOCARCINOMA                     11            304
  COLON MUCINOUS ADENOCARCINOMA             2             45
  RECTAL ADENOCARCINOMA                     2            104
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  SBF1 MUTATED    11   0   1   0
  SBF1 WILD-TYPE 334   4  30  25
D2103V11, multiclass
    clus
vv   SBF1 MUTATED SBF1 WILD-TYPE
  R0           11            334
  R1            0              4
  R2            1             30
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2103V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SBF1 MUTATED                                  0     0
  SBF1 WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  SBF1 MUTATED                           0     9
  SBF1 WILD-TYPE                        22   217
D2103V13, multiclass
                                  clus
vv                                 SBF1 MUTATED SBF1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       9            217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2104) Variable = MYST3 MUTATION ANALYSIS
D2104V1, survival
                 sevent
clus2               0   1
  MYST3 MUTATED    21   6
  MYST3 WILD-TYPE 357  87
  MYST3 MUTATED MYST3 WILD-TYPE 
             27             444 
  MYST3 MUTATED MYST3 WILD-TYPE 
              6              87 
$`MYST3 MUTATED`
TCGA-A6-5661 TCGA-A6-5665 TCGA-AA-3525 TCGA-AA-3663 TCGA-AA-3710 TCGA-AA-3949 
       33.53        22.06         8.05         6.97        26.99        26.01 
TCGA-AA-3977 TCGA-AA-3989 TCGA-AA-A00A TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01Q 
       25.02         7.96        38.04         4.01        34.98         1.02 
TCGA-AD-6889 TCGA-AZ-4315 TCGA-AZ-4682 TCGA-AZ-6598 TCGA-AZ-6607 TCGA-CA-6717 
       56.55        58.39        22.36        49.41         3.19        12.76 
TCGA-CM-4743 TCGA-CM-6171 TCGA-DM-A28E TCGA-G4-6303 TCGA-G4-6315 TCGA-G4-6625 
       23.05        14.04       119.93        65.85        61.91        91.79 
TCGA-AG-A002 TCGA-AG-A02N TCGA-DC-6681 
       20.98        61.97         5.95 

$`MYST3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3529 
        9.07        24.03        37.05        36.03        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02        78.08         6.05        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00D 
       27.02        27.02        19.07        27.02        13.94        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       21.37        15.52         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        33.01        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
      106.75        62.79        88.21         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07        12.20        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 
        9.99        21.14        82.95         1.91       124.27        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 
       21.99        14.99        12.99        13.02        15.02        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28F TCGA-DM-A28G 
      135.65       139.17         6.12        81.37        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6317 
       53.62        44.68        55.04        85.48        63.62        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6626 TCGA-G4-6628 
       22.09        13.78        35.80        26.17        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X 
       64.01        10.98        49.97         1.94        38.96        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
       19.99         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  MYST3 MUTATED MYST3 WILD-TYPE 
           1.02            0.00 
  MYST3 MUTATED MYST3 WILD-TYPE 
         119.93          148.01 
  MYST3 MUTATED MYST3 WILD-TYPE 
         25.020          20.005 
[1] "1.0 - 119.9 (25.0)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.1"
D2104V2, continuous
D2104V3, binary
                 cls
clus                0   1
  MYST3 MUTATED    24   3
  MYST3 WILD-TYPE 342 116
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYST3 MUTATED     24    3
  MYST3 WILD-TYPE  342  116
        clus
vv       MYST3 MUTATED MYST3 WILD-TYPE
  COLON             24             342
  RECTUM             3             116
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MYST3 MUTATED         2        0        4        10         2         0
  MYST3 WILD-TYPE      89        1       28       128         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MYST3 MUTATED           0          0          2          0        4         2
  MYST3 WILD-TYPE        24         11         57         42       44        16
                 vv
clus              STAGE IVB
  MYST3 MUTATED           0
  MYST3 WILD-TYPE         1
D2104V4, multiclass
            clus
vv           MYST3 MUTATED MYST3 WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               4              28
  STAGE IIA             10             128
  STAGE IIB              2               8
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             2              57
  STAGE IIIC             0              42
  STAGE IV               4              44
  STAGE IVA              2              16
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  MYST3 MUTATED     0   3  21   3
  MYST3 WILD-TYPE  17  89 308  47
D2104V5, multiclass
    clus
vv   MYST3 MUTATED MYST3 WILD-TYPE
  T1             0              17
  T2             3              89
  T3            21             308
  T4             3              47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  MYST3 MUTATED    20   4   3
  MYST3 WILD-TYPE 267 109  84
D2104V6, multiclass
    clus
vv   MYST3 MUTATED MYST3 WILD-TYPE
  N0            20             267
  N1             4             109
  N2             3              84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2104V7, binary
                 cls
clus                0   1
  MYST3 MUTATED    19   6
  MYST3 WILD-TYPE 356  59
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYST3 MUTATED     19    6
  MYST3 WILD-TYPE  356   59
   clus
vv  MYST3 MUTATED MYST3 WILD-TYPE
  0            19             356
  1             6              59
[1] 2 2
[1] FALSE
D2104V8, binary
                 cls
clus                0   1
  MYST3 MUTATED    12  15
  MYST3 WILD-TYPE 213 249
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYST3 MUTATED     12   15
  MYST3 WILD-TYPE  213  249
        clus
vv       MYST3 MUTATED MYST3 WILD-TYPE
  FEMALE            12             213
  MALE              15             249
[1] 2 2
[1] FALSE
D2104V9, binary
                 cls
clus                0   1
  MYST3 MUTATED    21   0
  MYST3 WILD-TYPE 329  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MYST3 MUTATED     21    0
  MYST3 WILD-TYPE  329   22
     clus
vv    MYST3 MUTATED MYST3 WILD-TYPE
  NO             21             329
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MYST3 MUTATED                     21                             3
  MYST3 WILD-TYPE                  294                            44
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MYST3 MUTATED                       3                              0
  MYST3 WILD-TYPE                   103                             10
D2104V10, multiclass
                                clus
vv                               MYST3 MUTATED MYST3 WILD-TYPE
  COLON ADENOCARCINOMA                      21             294
  COLON MUCINOUS ADENOCARCINOMA              3              44
  RECTAL ADENOCARCINOMA                      3             103
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  MYST3 MUTATED    20   0   1   1
  MYST3 WILD-TYPE 325   4  30  24
D2104V11, multiclass
    clus
vv   MYST3 MUTATED MYST3 WILD-TYPE
  R0            20             325
  R1             0               4
  R2             1              30
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2104V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MYST3 MUTATED                                  0     2
  MYST3 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  MYST3 MUTATED                           1    12
  MYST3 WILD-TYPE                        21   214
D2104V13, multiclass
                                  clus
vv                                 MYST3 MUTATED MYST3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               9
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                       12             214
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2105) Variable = ZNF846 MUTATION ANALYSIS
D2105V1, survival
                  sevent
clus2                0   1
  ZNF846 MUTATED     9   0
  ZNF846 WILD-TYPE 369  93
  ZNF846 MUTATED ZNF846 WILD-TYPE 
               9              462 
  ZNF846 MUTATED ZNF846 WILD-TYPE 
               0               93 
$`ZNF846 MUTATED`
TCGA-A6-6141 TCGA-AA-3510 TCGA-AA-3977 TCGA-AA-A010 TCGA-AZ-4315 TCGA-CA-6717 
        8.38        63.98        25.02        34.98        58.39        12.76 
TCGA-CM-6171 TCGA-AG-3892 TCGA-AG-A002 
       14.04        13.02        20.98 

$`ZNF846 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 
       22.09        22.06        32.71        27.09        22.52        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07        12.20        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       17.03        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  ZNF846 MUTATED ZNF846 WILD-TYPE 
            8.38             0.00 
  ZNF846 MUTATED ZNF846 WILD-TYPE 
           63.98           148.01 
  ZNF846 MUTATED ZNF846 WILD-TYPE 
          20.980           20.155 
[1] "8.4 - 64.0 (21.0)"  "0.0 - 148.0 (20.2)"
[1] "hr="     "9200000"
D2105V2, continuous
D2105V3, binary
                  cls
clus                 0   1
  ZNF846 MUTATED     8   2
  ZNF846 WILD-TYPE 358 117
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF846 MUTATED      8    2
  ZNF846 WILD-TYPE  358  117
        clus
vv       ZNF846 MUTATED ZNF846 WILD-TYPE
  COLON               8              358
  RECTUM              2              117
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZNF846 MUTATED         3        0        1         4         1         0
  ZNF846 WILD-TYPE      88        1       31       134         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF846 MUTATED           0          0          0          0        0
  ZNF846 WILD-TYPE        24         11         59         42       48
                  vv
clus               STAGE IVA STAGE IVB
  ZNF846 MUTATED           0         0
  ZNF846 WILD-TYPE        18         1
D2105V4, multiclass
            clus
vv           ZNF846 MUTATED ZNF846 WILD-TYPE
  STAGE I                 3               88
  STAGE IA                0                1
  STAGE II                1               31
  STAGE IIA               4              134
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              0               59
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZNF846 MUTATED     1   3   5   1
  ZNF846 WILD-TYPE  16  89 324  49
D2105V5, multiclass
    clus
vv   ZNF846 MUTATED ZNF846 WILD-TYPE
  T1              1               16
  T2              3               89
  T3              5              324
  T4              1               49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  ZNF846 MUTATED    10   0   0
  ZNF846 WILD-TYPE 277 113  87
D2105V6, multiclass
    clus
vv   ZNF846 MUTATED ZNF846 WILD-TYPE
  N0             10              277
  N1              0              113
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2105V7, binary
                  cls
clus                 0   1
  ZNF846 MUTATED     9   0
  ZNF846 WILD-TYPE 366  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF846 MUTATED      9    0
  ZNF846 WILD-TYPE  366   65
   clus
vv  ZNF846 MUTATED ZNF846 WILD-TYPE
  0              9              366
  1              0               65
[1] 2 2
[1] FALSE
D2105V8, binary
                  cls
clus                 0   1
  ZNF846 MUTATED     4   6
  ZNF846 WILD-TYPE 221 258
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF846 MUTATED      4    6
  ZNF846 WILD-TYPE  221  258
        clus
vv       ZNF846 MUTATED ZNF846 WILD-TYPE
  FEMALE              4              221
  MALE                6              258
[1] 2 2
[1] FALSE
D2105V9, binary
                  cls
clus                 0   1
  ZNF846 MUTATED     9   0
  ZNF846 WILD-TYPE 341  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF846 MUTATED      9    0
  ZNF846 WILD-TYPE  341   22
     clus
vv    ZNF846 MUTATED ZNF846 WILD-TYPE
  NO               9              341
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ZNF846 MUTATED                      7                             1
  ZNF846 WILD-TYPE                  308                            46
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ZNF846 MUTATED                       2                              0
  ZNF846 WILD-TYPE                   104                             10
D2105V10, multiclass
                                clus
vv                               ZNF846 MUTATED ZNF846 WILD-TYPE
  COLON ADENOCARCINOMA                        7              308
  COLON MUCINOUS ADENOCARCINOMA               1               46
  RECTAL ADENOCARCINOMA                       2              104
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ZNF846 MUTATED     7   0   0   1
  ZNF846 WILD-TYPE 338   4  31  24
D2105V11, multiclass
    clus
vv   ZNF846 MUTATED ZNF846 WILD-TYPE
  R0              7              338
  R1              0                4
  R2              0               31
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2105V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF846 MUTATED                                  0     1
  ZNF846 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZNF846 MUTATED                           1     2
  ZNF846 WILD-TYPE                        21   224
D2105V13, multiclass
                                  clus
vv                                 ZNF846 MUTATED ZNF846 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                         2              224
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2106) Variable = TEX11 MUTATION ANALYSIS
D2106V1, survival
                 sevent
clus2               0   1
  TEX11 MUTATED    16   4
  TEX11 WILD-TYPE 362  89
  TEX11 MUTATED TEX11 WILD-TYPE 
             20             451 
  TEX11 MUTATED TEX11 WILD-TYPE 
              4              89 
$`TEX11 MUTATED`
TCGA-A6-2678 TCGA-A6-5666 TCGA-AA-3516 TCGA-AA-3672 TCGA-AA-A00N TCGA-AY-6197 
       42.28        32.71        13.02         0.92         4.01        21.44 
TCGA-AZ-6598 TCGA-CA-6719 TCGA-CK-5913 TCGA-CM-4743 TCGA-CM-6163 TCGA-CM-6171 
       49.41        14.30        51.32        23.05         2.96        14.04 
TCGA-D5-5540 TCGA-D5-6540 TCGA-DM-A285 TCGA-G4-6321 TCGA-AG-3892 TCGA-AG-3909 
       56.09        16.14         6.12        22.09        13.02        19.99 
TCGA-AG-A002 TCGA-CL-5918 
       20.98         7.17 

$`TEX11 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2683 
       43.76        46.65        43.76        42.90        24.33        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       22.06        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
       63.98         6.97         1.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
        2.01        14.01        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4315 
       27.09        16.31         0.95        33.01        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 
        0.07        12.20        12.76        10.06        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       85.45        15.62        49.08         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
        1.91       124.27        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       15.02        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 
       17.85         4.80        17.13        12.49        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      135.65       139.17        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       61.91        36.00        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 
        1.02        17.95        36.95        17.03        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
        1.02        48.03        32.02        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
       78.12        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  TEX11 MUTATED TEX11 WILD-TYPE 
           0.92            0.00 
  TEX11 MUTATED TEX11 WILD-TYPE 
          56.09          148.01 
  TEX11 MUTATED TEX11 WILD-TYPE 
         18.065          20.280 
[1] "0.9 - 56.1 (18.1)"  "0.0 - 148.0 (20.3)"
[1] "hr=" "1.2"
D2106V2, continuous
D2106V3, binary
                 cls
clus                0   1
  TEX11 MUTATED    17   4
  TEX11 WILD-TYPE 349 115
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TEX11 MUTATED     17    4
  TEX11 WILD-TYPE  349  115
        clus
vv       TEX11 MUTATED TEX11 WILD-TYPE
  COLON             17             349
  RECTUM             4             115
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TEX11 MUTATED         5        0        1         6         1         1
  TEX11 WILD-TYPE      86        1       31       132         9         0
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TEX11 MUTATED           4          0          2          0        1         0
  TEX11 WILD-TYPE        20         11         57         42       47        18
                 vv
clus              STAGE IVB
  TEX11 MUTATED           0
  TEX11 WILD-TYPE         1
D2106V4, multiclass
            clus
vv           TEX11 MUTATED TEX11 WILD-TYPE
  STAGE I                5              86
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              6             132
  STAGE IIB              1               9
  STAGE IIC              1               0
  STAGE III              4              20
  STAGE IIIA             0              11
  STAGE IIIB             2              57
  STAGE IIIC             0              42
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  TEX11 MUTATED     2   4  13   2
  TEX11 WILD-TYPE  15  88 316  48
D2106V5, multiclass
    clus
vv   TEX11 MUTATED TEX11 WILD-TYPE
  T1             2              15
  T2             4              88
  T3            13             316
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  TEX11 MUTATED    14   4   3
  TEX11 WILD-TYPE 273 109  84
D2106V6, multiclass
    clus
vv   TEX11 MUTATED TEX11 WILD-TYPE
  N0            14             273
  N1             4             109
  N2             3              84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2106V7, binary
                 cls
clus                0   1
  TEX11 MUTATED    15   1
  TEX11 WILD-TYPE 360  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TEX11 MUTATED     15    1
  TEX11 WILD-TYPE  360   64
   clus
vv  TEX11 MUTATED TEX11 WILD-TYPE
  0            15             360
  1             1              64
[1] 2 2
[1] FALSE
D2106V8, binary
                 cls
clus                0   1
  TEX11 MUTATED    11  10
  TEX11 WILD-TYPE 214 254
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TEX11 MUTATED     11   10
  TEX11 WILD-TYPE  214  254
        clus
vv       TEX11 MUTATED TEX11 WILD-TYPE
  FEMALE            11             214
  MALE              10             254
[1] 2 2
[1] FALSE
D2106V9, binary
                 cls
clus                0   1
  TEX11 MUTATED    18   0
  TEX11 WILD-TYPE 332  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TEX11 MUTATED     18    0
  TEX11 WILD-TYPE  332   22
     clus
vv    TEX11 MUTATED TEX11 WILD-TYPE
  NO             18             332
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  TEX11 MUTATED                     13                             4
  TEX11 WILD-TYPE                  302                            43
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  TEX11 MUTATED                       4                              0
  TEX11 WILD-TYPE                   102                             10
D2106V10, multiclass
                                clus
vv                               TEX11 MUTATED TEX11 WILD-TYPE
  COLON ADENOCARCINOMA                      13             302
  COLON MUCINOUS ADENOCARCINOMA              4              43
  RECTAL ADENOCARCINOMA                      4             102
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  TEX11 MUTATED    14   0   0   3
  TEX11 WILD-TYPE 331   4  31  22
D2106V11, multiclass
    clus
vv   TEX11 MUTATED TEX11 WILD-TYPE
  R0            14             331
  R1             0               4
  R2             0              31
  RX             3              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2106V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TEX11 MUTATED                                  0     1
  TEX11 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  TEX11 MUTATED                           0    13
  TEX11 WILD-TYPE                        22   213
D2106V13, multiclass
                                  clus
vv                                 TEX11 MUTATED TEX11 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                       13             213
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2107) Variable = ZP3 MUTATION ANALYSIS
D2107V1, survival
               sevent
clus2             0   1
  ZP3 MUTATED     5   1
  ZP3 WILD-TYPE 373  92
  ZP3 MUTATED ZP3 WILD-TYPE 
            6           465 
  ZP3 MUTATED ZP3 WILD-TYPE 
            1            92 
$`ZP3 MUTATED`
TCGA-AA-3819 TCGA-AA-A010 TCGA-AY-6197 TCGA-AZ-6603 TCGA-CM-6169 TCGA-AG-4007 
       25.02        34.98        21.44        29.56        13.02         1.02 

$`ZP3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3821 
       19.04        10.06        35.05        33.04         0.99         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       33.01        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
      100.01         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  ZP3 MUTATED ZP3 WILD-TYPE 
         1.02          0.00 
  ZP3 MUTATED ZP3 WILD-TYPE 
        34.98        148.01 
  ZP3 MUTATED ZP3 WILD-TYPE 
        23.23         20.12 
[1] "1.0 - 35.0 (23.2)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.1"
D2107V2, continuous
D2107V3, binary
               cls
clus              0   1
  ZP3 MUTATED     6   1
  ZP3 WILD-TYPE 360 118
[1] "tbl2"
               cls
clus            [,1] [,2]
  ZP3 MUTATED      6    1
  ZP3 WILD-TYPE  360  118
        clus
vv       ZP3 MUTATED ZP3 WILD-TYPE
  COLON            6           360
  RECTUM           1           118
[1] 2 2
[1] FALSE
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZP3 MUTATED         0        0        0         3         2         0
  ZP3 WILD-TYPE      91        1       32       135         8         1
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ZP3 MUTATED           0          0          0          0        1         0
  ZP3 WILD-TYPE        24         11         59         42       47        18
               vv
clus            STAGE IVB
  ZP3 MUTATED           0
  ZP3 WILD-TYPE         1
D2107V4, multiclass
            clus
vv           ZP3 MUTATED ZP3 WILD-TYPE
  STAGE I              0            91
  STAGE IA             0             1
  STAGE II             0            32
  STAGE IIA            3           135
  STAGE IIB            2             8
  STAGE IIC            0             1
  STAGE III            0            24
  STAGE IIIA           0            11
  STAGE IIIB           0            59
  STAGE IIIC           0            42
  STAGE IV             1            47
  STAGE IVA            0            18
  STAGE IVB            0             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  ZP3 MUTATED     0   1   3   3
  ZP3 WILD-TYPE  17  91 326  47
D2107V5, multiclass
    clus
vv   ZP3 MUTATED ZP3 WILD-TYPE
  T1           0            17
  T2           1            91
  T3           3           326
  T4           3            47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2
  ZP3 MUTATED     5   1   1
  ZP3 WILD-TYPE 282 112  86
D2107V6, multiclass
    clus
vv   ZP3 MUTATED ZP3 WILD-TYPE
  N0           5           282
  N1           1           112
  N2           1            86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2107V7, binary
               cls
clus              0   1
  ZP3 MUTATED     3   1
  ZP3 WILD-TYPE 372  64
[1] "tbl2"
               cls
clus            [,1] [,2]
  ZP3 MUTATED      3    1
  ZP3 WILD-TYPE  372   64
   clus
vv  ZP3 MUTATED ZP3 WILD-TYPE
  0           3           372
  1           1            64
[1] 2 2
[1] FALSE
D2107V8, binary
               cls
clus              0   1
  ZP3 MUTATED     4   3
  ZP3 WILD-TYPE 221 261
[1] "tbl2"
               cls
clus            [,1] [,2]
  ZP3 MUTATED      4    3
  ZP3 WILD-TYPE  221  261
        clus
vv       ZP3 MUTATED ZP3 WILD-TYPE
  FEMALE           4           221
  MALE             3           261
[1] 2 2
[1] FALSE
D2107V9, binary
               cls
clus              0   1
  ZP3 MUTATED     5   0
  ZP3 WILD-TYPE 345  22
[1] "tbl2"
               cls
clus            [,1] [,2]
  ZP3 MUTATED      5    0
  ZP3 WILD-TYPE  345   22
     clus
vv    ZP3 MUTATED ZP3 WILD-TYPE
  NO            5           345
  YES           0            22
[1] 2 2
[1] FALSE
               vv
clus            COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ZP3 MUTATED                      6                             0
  ZP3 WILD-TYPE                  309                            47
               vv
clus            RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ZP3 MUTATED                       1                              0
  ZP3 WILD-TYPE                   105                             10
D2107V10, multiclass
                                clus
vv                               ZP3 MUTATED ZP3 WILD-TYPE
  COLON ADENOCARCINOMA                     6           309
  COLON MUCINOUS ADENOCARCINOMA            0            47
  RECTAL ADENOCARCINOMA                    1           105
  RECTAL MUCINOUS ADENOCARCINOMA           0            10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             R0  R1  R2  RX
  ZP3 MUTATED     4   0   1   1
  ZP3 WILD-TYPE 341   4  30  24
D2107V11, multiclass
    clus
vv   ZP3 MUTATED ZP3 WILD-TYPE
  R0           4           341
  R1           0             4
  R2           1            30
  RX           1            24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2107V12, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZP3 MUTATED                                  0     0
  ZP3 WILD-TYPE                                1    11
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  ZP3 MUTATED                           1     3
  ZP3 WILD-TYPE                        21   223
D2107V13, multiclass
                                  clus
vv                                 ZP3 MUTATED ZP3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      0            11
  BLACK OR AFRICAN AMERICAN                  1            21
  WHITE                                      3           223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2108) Variable = GLI4 MUTATION ANALYSIS
D2108V1, survival
                sevent
clus2              0   1
  GLI4 MUTATED     5   0
  GLI4 WILD-TYPE 373  93
  GLI4 MUTATED GLI4 WILD-TYPE 
             5            466 
  GLI4 MUTATED GLI4 WILD-TYPE 
             0             93 
$`GLI4 MUTATED`
TCGA-A6-5665 TCGA-A6-6654 TCGA-AA-A00K TCGA-G4-6586 TCGA-AH-6643 
       22.06        23.87        18.05        35.80         0.69 

$`GLI4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 
       25.18        24.16        21.76        24.69        24.39        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00L TCGA-AA-A00N 
       19.00        30.02        34.03        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 
       61.91        36.00        22.09        13.78        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
       38.56         1.45        17.49         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  GLI4 MUTATED GLI4 WILD-TYPE 
          0.69           0.00 
  GLI4 MUTATED GLI4 WILD-TYPE 
         35.80         148.01 
  GLI4 MUTATED GLI4 WILD-TYPE 
        22.060         20.155 
[1] "0.7 - 35.8 (22.1)"  "0.0 - 148.0 (20.2)"
[1] "hr="     "3300000"
D2108V2, continuous
D2108V3, binary
                cls
clus               0   1
  GLI4 MUTATED     4   1
  GLI4 WILD-TYPE 362 118
[1] "tbl2"
                cls
clus             [,1] [,2]
  GLI4 MUTATED      4    1
  GLI4 WILD-TYPE  362  118
        clus
vv       GLI4 MUTATED GLI4 WILD-TYPE
  COLON             4            362
  RECTUM            1            118
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GLI4 MUTATED         0        0        0         3         0         0
  GLI4 WILD-TYPE      91        1       32       135        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  GLI4 MUTATED           0          0          1          1        0         0
  GLI4 WILD-TYPE        24         11         58         41       48        18
                vv
clus             STAGE IVB
  GLI4 MUTATED           0
  GLI4 WILD-TYPE         1
D2108V4, multiclass
            clus
vv           GLI4 MUTATED GLI4 WILD-TYPE
  STAGE I               0             91
  STAGE IA              0              1
  STAGE II              0             32
  STAGE IIA             3            135
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            1             58
  STAGE IIIC            1             41
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  GLI4 MUTATED     0   0   5   0
  GLI4 WILD-TYPE  17  92 324  50
D2108V5, multiclass
    clus
vv   GLI4 MUTATED GLI4 WILD-TYPE
  T1            0             17
  T2            0             92
  T3            5            324
  T4            0             50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  GLI4 MUTATED     3   1   1
  GLI4 WILD-TYPE 284 112  86
D2108V6, multiclass
    clus
vv   GLI4 MUTATED GLI4 WILD-TYPE
  N0            3            284
  N1            1            112
  N2            1             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2108V7, binary
                cls
clus               0   1
  GLI4 MUTATED     5   0
  GLI4 WILD-TYPE 370  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  GLI4 MUTATED      5    0
  GLI4 WILD-TYPE  370   65
   clus
vv  GLI4 MUTATED GLI4 WILD-TYPE
  0            5            370
  1            0             65
[1] 2 2
[1] FALSE
D2108V8, binary
                cls
clus               0   1
  GLI4 MUTATED     3   2
  GLI4 WILD-TYPE 222 262
[1] "tbl2"
                cls
clus             [,1] [,2]
  GLI4 MUTATED      3    2
  GLI4 WILD-TYPE  222  262
        clus
vv       GLI4 MUTATED GLI4 WILD-TYPE
  FEMALE            3            222
  MALE              2            262
[1] 2 2
[1] FALSE
D2108V9, binary
                cls
clus               0   1
  GLI4 MUTATED     3   0
  GLI4 WILD-TYPE 347  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  GLI4 MUTATED      3    0
  GLI4 WILD-TYPE  347   22
     clus
vv    GLI4 MUTATED GLI4 WILD-TYPE
  NO             3            347
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  GLI4 MUTATED                      4                             0
  GLI4 WILD-TYPE                  311                            47
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  GLI4 MUTATED                       1                              0
  GLI4 WILD-TYPE                   105                             10
D2108V10, multiclass
                                clus
vv                               GLI4 MUTATED GLI4 WILD-TYPE
  COLON ADENOCARCINOMA                      4            311
  COLON MUCINOUS ADENOCARCINOMA             0             47
  RECTAL ADENOCARCINOMA                     1            105
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  GLI4 MUTATED     4   0   0   0
  GLI4 WILD-TYPE 341   4  31  25
D2108V11, multiclass
    clus
vv   GLI4 MUTATED GLI4 WILD-TYPE
  R0            4            341
  R1            0              4
  R2            0             31
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2108V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GLI4 MUTATED                                  0     0
  GLI4 WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  GLI4 MUTATED                           0     4
  GLI4 WILD-TYPE                        22   222
D2108V13, multiclass
                                  clus
vv                                 GLI4 MUTATED GLI4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       4            222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2109) Variable = SORBS1 MUTATION ANALYSIS
D2109V1, survival
                  sevent
clus2                0   1
  SORBS1 MUTATED    10   1
  SORBS1 WILD-TYPE 368  92
  SORBS1 MUTATED SORBS1 WILD-TYPE 
              11              460 
  SORBS1 MUTATED SORBS1 WILD-TYPE 
               1               92 
$`SORBS1 MUTATED`
TCGA-A6-2672 TCGA-A6-2676 TCGA-AA-3971 TCGA-AA-3977 TCGA-AA-A00J TCGA-AA-A010 
       46.65        42.90        16.08        25.02        18.05        34.98 
TCGA-AD-6889 TCGA-AY-6197 TCGA-AZ-4315 TCGA-AG-A002 TCGA-AG-A02N 
       56.55        21.44        58.39        20.98        61.97 

$`SORBS1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       43.76        43.76        24.33        42.28        16.57        34.65 
TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5657 
       33.34        32.75        36.53        14.53        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       30.44        29.19        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3972 TCGA-AA-3973 
       20.98        34.03         2.01        21.99        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       21.37        15.52         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
        0.95        33.01        17.82         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
        1.94        38.96        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  SORBS1 MUTATED SORBS1 WILD-TYPE 
           16.08             0.00 
  SORBS1 MUTATED SORBS1 WILD-TYPE 
           61.97           148.01 
  SORBS1 MUTATED SORBS1 WILD-TYPE 
           34.98            20.02 
[1] "16.1 - 62.0 (35.0)" "0.0 - 148.0 (20.0)"
[1] "hr=" "3.2"
D2109V2, continuous
D2109V3, binary
                  cls
clus                 0   1
  SORBS1 MUTATED    10   2
  SORBS1 WILD-TYPE 356 117
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SORBS1 MUTATED     10    2
  SORBS1 WILD-TYPE  356  117
        clus
vv       SORBS1 MUTATED SORBS1 WILD-TYPE
  COLON              10              356
  RECTUM              2              117
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SORBS1 MUTATED         2        0        1         3         2         0
  SORBS1 WILD-TYPE      89        1       31       135         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SORBS1 MUTATED           1          0          2          0        0
  SORBS1 WILD-TYPE        23         11         57         42       48
                  vv
clus               STAGE IVA STAGE IVB
  SORBS1 MUTATED           0         0
  SORBS1 WILD-TYPE        18         1
D2109V4, multiclass
            clus
vv           SORBS1 MUTATED SORBS1 WILD-TYPE
  STAGE I                 2               89
  STAGE IA                0                1
  STAGE II                1               31
  STAGE IIA               3              135
  STAGE IIB               2                8
  STAGE IIC               0                1
  STAGE III               1               23
  STAGE IIIA              0               11
  STAGE IIIB              2               57
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  SORBS1 MUTATED     0   3   6   3
  SORBS1 WILD-TYPE  17  89 323  47
D2109V5, multiclass
    clus
vv   SORBS1 MUTATED SORBS1 WILD-TYPE
  T1              0               17
  T2              3               89
  T3              6              323
  T4              3               47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  SORBS1 MUTATED     9   3   0
  SORBS1 WILD-TYPE 278 110  87
D2109V6, multiclass
    clus
vv   SORBS1 MUTATED SORBS1 WILD-TYPE
  N0              9              278
  N1              3              110
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2109V7, binary
                  cls
clus                 0   1
  SORBS1 MUTATED     9   0
  SORBS1 WILD-TYPE 366  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SORBS1 MUTATED      9    0
  SORBS1 WILD-TYPE  366   65
   clus
vv  SORBS1 MUTATED SORBS1 WILD-TYPE
  0              9              366
  1              0               65
[1] 2 2
[1] FALSE
D2109V8, binary
                  cls
clus                 0   1
  SORBS1 MUTATED     3   9
  SORBS1 WILD-TYPE 222 255
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SORBS1 MUTATED      3    9
  SORBS1 WILD-TYPE  222  255
        clus
vv       SORBS1 MUTATED SORBS1 WILD-TYPE
  FEMALE              3              222
  MALE                9              255
[1] 2 2
[1] FALSE
D2109V9, binary
                  cls
clus                 0   1
  SORBS1 MUTATED     9   0
  SORBS1 WILD-TYPE 341  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SORBS1 MUTATED      9    0
  SORBS1 WILD-TYPE  341   22
     clus
vv    SORBS1 MUTATED SORBS1 WILD-TYPE
  NO               9              341
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SORBS1 MUTATED                      9                             1
  SORBS1 WILD-TYPE                  306                            46
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SORBS1 MUTATED                       2                              0
  SORBS1 WILD-TYPE                   104                             10
D2109V10, multiclass
                                clus
vv                               SORBS1 MUTATED SORBS1 WILD-TYPE
  COLON ADENOCARCINOMA                        9              306
  COLON MUCINOUS ADENOCARCINOMA               1               46
  RECTAL ADENOCARCINOMA                       2              104
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  SORBS1 MUTATED     9   0   0   1
  SORBS1 WILD-TYPE 336   4  31  24
D2109V11, multiclass
    clus
vv   SORBS1 MUTATED SORBS1 WILD-TYPE
  R0              9              336
  R1              0                4
  R2              0               31
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2109V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SORBS1 MUTATED                                  0     1
  SORBS1 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  SORBS1 MUTATED                           0     5
  SORBS1 WILD-TYPE                        22   221
D2109V13, multiclass
                                  clus
vv                                 SORBS1 MUTATED SORBS1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         5              221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2110) Variable = ITGA2 MUTATION ANALYSIS
D2110V1, survival
                 sevent
clus2               0   1
  ITGA2 MUTATED     9   0
  ITGA2 WILD-TYPE 369  93
  ITGA2 MUTATED ITGA2 WILD-TYPE 
              9             462 
  ITGA2 MUTATED ITGA2 WILD-TYPE 
              0              93 
$`ITGA2 MUTATED`
TCGA-A6-5665 TCGA-AA-3510 TCGA-AA-3688 TCGA-AA-3864 TCGA-AA-A010 TCGA-AY-6197 
       22.06        63.98        19.00        53.00        34.98        21.44 
TCGA-CA-6717 TCGA-DM-A28K TCGA-AG-A002 
       12.76        98.24        20.98 

$`ITGA2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3692 TCGA-AA-3696 
       15.02        11.01         5.98        37.05        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        31.07        30.05        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4315 
       27.09        16.31         0.95        33.01        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07        12.20        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       35.97        60.79       117.07         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  ITGA2 MUTATED ITGA2 WILD-TYPE 
          12.76            0.00 
  ITGA2 MUTATED ITGA2 WILD-TYPE 
          98.24          148.01 
  ITGA2 MUTATED ITGA2 WILD-TYPE 
         22.060          20.035 
[1] "12.8 - 98.2 (22.1)" "0.0 - 148.0 (20.0)"
[1] "hr="     "2.5e+07"
D2110V2, continuous
D2110V3, binary
                 cls
clus                0   1
  ITGA2 MUTATED     8   1
  ITGA2 WILD-TYPE 358 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITGA2 MUTATED      8    1
  ITGA2 WILD-TYPE  358  118
        clus
vv       ITGA2 MUTATED ITGA2 WILD-TYPE
  COLON              8             358
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ITGA2 MUTATED         1        0        2         4         1         0
  ITGA2 WILD-TYPE      90        1       30       134         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ITGA2 MUTATED           0          0          0          0        1         0
  ITGA2 WILD-TYPE        24         11         59         42       47        18
                 vv
clus              STAGE IVB
  ITGA2 MUTATED           0
  ITGA2 WILD-TYPE         1
D2110V4, multiclass
            clus
vv           ITGA2 MUTATED ITGA2 WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA              4             134
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             0              42
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ITGA2 MUTATED     0   1   7   1
  ITGA2 WILD-TYPE  17  91 322  49
D2110V5, multiclass
    clus
vv   ITGA2 MUTATED ITGA2 WILD-TYPE
  T1             0              17
  T2             1              91
  T3             7             322
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  ITGA2 MUTATED     8   1   0
  ITGA2 WILD-TYPE 279 112  87
D2110V6, multiclass
    clus
vv   ITGA2 MUTATED ITGA2 WILD-TYPE
  N0             8             279
  N1             1             112
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2110V7, binary
                 cls
clus                0   1
  ITGA2 MUTATED     7   1
  ITGA2 WILD-TYPE 368  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITGA2 MUTATED      7    1
  ITGA2 WILD-TYPE  368   64
   clus
vv  ITGA2 MUTATED ITGA2 WILD-TYPE
  0             7             368
  1             1              64
[1] 2 2
[1] FALSE
D2110V8, binary
                 cls
clus                0   1
  ITGA2 MUTATED     2   7
  ITGA2 WILD-TYPE 223 257
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITGA2 MUTATED      2    7
  ITGA2 WILD-TYPE  223  257
        clus
vv       ITGA2 MUTATED ITGA2 WILD-TYPE
  FEMALE             2             223
  MALE               7             257
[1] 2 2
[1] FALSE
D2110V9, binary
                 cls
clus                0   1
  ITGA2 MUTATED     8   0
  ITGA2 WILD-TYPE 342  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ITGA2 MUTATED      8    0
  ITGA2 WILD-TYPE  342   22
     clus
vv    ITGA2 MUTATED ITGA2 WILD-TYPE
  NO              8             342
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ITGA2 MUTATED                      6                             2
  ITGA2 WILD-TYPE                  309                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ITGA2 MUTATED                       1                              0
  ITGA2 WILD-TYPE                   105                             10
D2110V10, multiclass
                                clus
vv                               ITGA2 MUTATED ITGA2 WILD-TYPE
  COLON ADENOCARCINOMA                       6             309
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  ITGA2 MUTATED     6   0   1   1
  ITGA2 WILD-TYPE 339   4  30  24
D2110V11, multiclass
    clus
vv   ITGA2 MUTATED ITGA2 WILD-TYPE
  R0             6             339
  R1             0               4
  R2             1              30
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2110V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ITGA2 MUTATED                                  0     1
  ITGA2 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ITGA2 MUTATED                           0     3
  ITGA2 WILD-TYPE                        22   223
D2110V13, multiclass
                                  clus
vv                                 ITGA2 MUTATED ITGA2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        3             223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2111) Variable = PRSS27 MUTATION ANALYSIS
D2111V1, survival
                  sevent
clus2                0   1
  PRSS27 MUTATED     3   1
  PRSS27 WILD-TYPE 375  92
  PRSS27 MUTATED PRSS27 WILD-TYPE 
               4              467 
  PRSS27 MUTATED PRSS27 WILD-TYPE 
               1               92 
$`PRSS27 MUTATED`
TCGA-A6-2671 TCGA-A6-6653 TCGA-AA-A010 TCGA-CI-6620 
       43.76        24.39        34.98        33.17 

$`PRSS27 WILD-TYPE`
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       46.65        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 
       25.18        24.16        21.76        24.69        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
        6.05         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  PRSS27 MUTATED PRSS27 WILD-TYPE 
           24.39             0.00 
  PRSS27 MUTATED PRSS27 WILD-TYPE 
           43.76           148.01 
  PRSS27 MUTATED PRSS27 WILD-TYPE 
          34.075           20.050 
[1] "24.4 - 43.8 (34.1)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.1"
D2111V2, continuous
D2111V3, binary
                  cls
clus                 0   1
  PRSS27 MUTATED     3   1
  PRSS27 WILD-TYPE 363 118
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PRSS27 MUTATED      3    1
  PRSS27 WILD-TYPE  363  118
        clus
vv       PRSS27 MUTATED PRSS27 WILD-TYPE
  COLON               3              363
  RECTUM              1              118
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PRSS27 MUTATED         1        0        0         0         1         0
  PRSS27 WILD-TYPE      90        1       32       138         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PRSS27 MUTATED           0          0          0          0        1
  PRSS27 WILD-TYPE        24         11         59         42       47
                  vv
clus               STAGE IVA STAGE IVB
  PRSS27 MUTATED           1         0
  PRSS27 WILD-TYPE        17         1
D2111V4, multiclass
            clus
vv           PRSS27 MUTATED PRSS27 WILD-TYPE
  STAGE I                 1               90
  STAGE IA                0                1
  STAGE II                0               32
  STAGE IIA               0              138
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              0               59
  STAGE IIIC              0               42
  STAGE IV                1               47
  STAGE IVA               1               17
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  PRSS27 MUTATED     0   1   2   1
  PRSS27 WILD-TYPE  17  91 327  49
D2111V5, multiclass
    clus
vv   PRSS27 MUTATED PRSS27 WILD-TYPE
  T1              0               17
  T2              1               91
  T3              2              327
  T4              1               49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  PRSS27 MUTATED     2   1   1
  PRSS27 WILD-TYPE 285 112  86
D2111V6, multiclass
    clus
vv   PRSS27 MUTATED PRSS27 WILD-TYPE
  N0              2              285
  N1              1              112
  N2              1               86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2111V7, binary
                  cls
clus                 0   1
  PRSS27 MUTATED     2   2
  PRSS27 WILD-TYPE 373  63
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PRSS27 MUTATED      2    2
  PRSS27 WILD-TYPE  373   63
   clus
vv  PRSS27 MUTATED PRSS27 WILD-TYPE
  0              2              373
  1              2               63
[1] 2 2
[1] FALSE
D2111V8, binary
                  cls
clus                 0   1
  PRSS27 MUTATED     2   2
  PRSS27 WILD-TYPE 223 262
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PRSS27 MUTATED      2    2
  PRSS27 WILD-TYPE  223  262
        clus
vv       PRSS27 MUTATED PRSS27 WILD-TYPE
  FEMALE              2              223
  MALE                2              262
[1] 2 2
[1] FALSE
D2111V9, binary
                  cls
clus                 0   1
  PRSS27 MUTATED     4   0
  PRSS27 WILD-TYPE 346  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PRSS27 MUTATED      4    0
  PRSS27 WILD-TYPE  346   22
     clus
vv    PRSS27 MUTATED PRSS27 WILD-TYPE
  NO               4              346
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PRSS27 MUTATED                      3                             0
  PRSS27 WILD-TYPE                  312                            47
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PRSS27 MUTATED                       1                              0
  PRSS27 WILD-TYPE                   105                             10
D2111V10, multiclass
                                clus
vv                               PRSS27 MUTATED PRSS27 WILD-TYPE
  COLON ADENOCARCINOMA                        3              312
  COLON MUCINOUS ADENOCARCINOMA               0               47
  RECTAL ADENOCARCINOMA                       1              105
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  PRSS27 MUTATED     2   0   0   0
  PRSS27 WILD-TYPE 343   4  31  25
D2111V11, multiclass
[1] "Remove cluster labels:" "PRSS27 MUTATED"        
clus
  PRSS27 MUTATED PRSS27 WILD-TYPE 
               2              403 
      TCGA-A6-2672       TCGA-A6-2674       TCGA-A6-2676       TCGA-A6-2677 
"PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" 
      TCGA-A6-2678       TCGA-A6-2683       TCGA-A6-3807       TCGA-A6-3808 
"PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" 
      TCGA-A6-3809       TCGA-A6-3810       TCGA-A6-5657       TCGA-A6-5659 
"PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" 
      TCGA-A6-5661       TCGA-A6-5665       TCGA-A6-6781       TCGA-AA-3489 
"PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" 
      TCGA-AA-3492       TCGA-AA-3496       TCGA-AA-3502       TCGA-AA-3510 
"PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" 
      TCGA-AA-3511       TCGA-AA-3514       TCGA-AA-3517       TCGA-AA-3518 
"PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" 
      TCGA-AA-3519       TCGA-AA-3520       TCGA-AA-3521       TCGA-AA-3522 
"PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" 
      TCGA-AA-3524       TCGA-AA-3525       TCGA-AA-3526       TCGA-AA-3527 
"PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" 
      TCGA-AA-3529       TCGA-AA-3530       TCGA-AA-3531       TCGA-AA-3532 
"PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" 
      TCGA-AA-3534       TCGA-AA-3538       TCGA-AA-3542       TCGA-AA-3543 
"PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" 
      TCGA-AA-3544       TCGA-AA-3548       TCGA-AA-3549       TCGA-AA-3552 
"PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" 
      TCGA-AA-3553       TCGA-AA-3554       TCGA-AA-3555       TCGA-AA-3556 
"PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" 
      TCGA-AA-3558       TCGA-AA-3560       TCGA-AA-3561       TCGA-AA-3562 
"PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" 
      TCGA-AA-3655       TCGA-AA-3660       TCGA-AA-3662       TCGA-AA-3663 
"PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" 
      TCGA-AA-3664       TCGA-AA-3666       TCGA-AA-3667       TCGA-AA-3672 
"PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" 
      TCGA-AA-3673       TCGA-AA-3678       TCGA-AA-3679       TCGA-AA-3680 
"PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" 
      TCGA-AA-3681       TCGA-AA-3684       TCGA-AA-3685       TCGA-AA-3688 
"PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" 
      TCGA-AA-3692       TCGA-AA-3693       TCGA-AA-3695       TCGA-AA-3696 
"PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" 
      TCGA-AA-3697       TCGA-AA-3710       TCGA-AA-3712       TCGA-AA-3713 
"PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" 
      TCGA-AA-3715       TCGA-AA-3811       TCGA-AA-3812       TCGA-AA-3814 
"PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" 
      TCGA-AA-3815       TCGA-AA-3818       TCGA-AA-3819       TCGA-AA-3821 
"PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" 
      TCGA-AA-3831       TCGA-AA-3833       TCGA-AA-3837       TCGA-AA-3842 
"PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" 
      TCGA-AA-3844       TCGA-AA-3845       TCGA-AA-3846       TCGA-AA-3848 
"PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" 
      TCGA-AA-3850       TCGA-AA-3851       TCGA-AA-3852       TCGA-AA-3854 
"PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" 
      TCGA-AA-3855       TCGA-AA-3856       TCGA-AA-3858       TCGA-AA-3860 
"PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" 
      TCGA-AA-3861       TCGA-AA-3864       TCGA-AA-3866       TCGA-AA-3867 
"PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" 
      TCGA-AA-3869       TCGA-AA-3870       TCGA-AA-3872       TCGA-AA-3875 
"PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" 
      TCGA-AA-3877       TCGA-AA-3930       TCGA-AA-3939       TCGA-AA-3941 
"PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" 
      TCGA-AA-3947       TCGA-AA-3949       TCGA-AA-3950       TCGA-AA-3952 
"PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" 
      TCGA-AA-3955       TCGA-AA-3956       TCGA-AA-3968       TCGA-AA-3971 
"PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" 
      TCGA-AA-3972       TCGA-AA-3973       TCGA-AA-3975       TCGA-AA-3976 
"PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" 
      TCGA-AA-3979       TCGA-AA-3984       TCGA-AA-3986       TCGA-AA-3989 
"PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" 
      TCGA-AA-3994       TCGA-AA-A004       TCGA-AA-A00A       TCGA-AA-A00D 
"PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" 
      TCGA-AA-A00E       TCGA-AA-A00F       TCGA-AA-A00J       TCGA-AA-A00K 
"PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" 
      TCGA-AA-A00L       TCGA-AA-A00N       TCGA-AA-A00O       TCGA-AA-A00Q 
"PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" 
      TCGA-AA-A00R       TCGA-AA-A00U       TCGA-AA-A00W       TCGA-AA-A00Z 
"PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" 
      TCGA-AA-A017       TCGA-AA-A01D       TCGA-AA-A01F       TCGA-AA-A01G 
"PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" 
      TCGA-AA-A01I       TCGA-AA-A01K       TCGA-AA-A01P       TCGA-AA-A01Q 
"PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" 
      TCGA-AA-A01R       TCGA-AA-A01S       TCGA-AA-A01T       TCGA-AA-A01V 
"PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" 
      TCGA-AA-A01X       TCGA-AA-A01Z       TCGA-AA-A022       TCGA-AA-A024 
"PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" 
      TCGA-AA-A029       TCGA-AA-A02F       TCGA-AA-A02H       TCGA-AA-A02J 
"PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" 
      TCGA-AA-A02K       TCGA-AA-A02O       TCGA-AA-A02W       TCGA-AA-A02Y 
"PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" 
      TCGA-AA-A03F       TCGA-AA-A03J       TCGA-AD-5900       TCGA-AD-6548 
"PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" 
      TCGA-AD-6888       TCGA-AU-3779       TCGA-AU-6004       TCGA-AY-4070 
"PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" 
      TCGA-AY-4071       TCGA-AY-5543       TCGA-AY-6196       TCGA-AY-6197 
"PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" 
      TCGA-AY-6386       TCGA-AZ-4315       TCGA-AZ-4681       TCGA-AZ-4682 
"PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" 
      TCGA-CA-5254       TCGA-CA-5255       TCGA-CA-5796       TCGA-CA-5797 
"PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" 
      TCGA-CA-6715       TCGA-CA-6716       TCGA-CA-6717       TCGA-CA-6718 
"PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" 
      TCGA-CA-6719       TCGA-CK-4947       TCGA-CK-4948       TCGA-CK-4950 
"PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" 
      TCGA-CK-4952       TCGA-CK-5912       TCGA-CK-5913       TCGA-CK-5914 
"PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" 
      TCGA-CK-5915       TCGA-CK-5916       TCGA-CK-6746       TCGA-CK-6747 
"PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" 
      TCGA-CK-6748       TCGA-CK-6751       TCGA-CM-4743       TCGA-CM-4744 
"PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" 
      TCGA-CM-4746       TCGA-CM-4747       TCGA-CM-4752       TCGA-CM-5341 
"PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" 
      TCGA-CM-5344       TCGA-CM-5348       TCGA-CM-5349       TCGA-CM-5860 
"PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" 
      TCGA-CM-5861       TCGA-CM-5862       TCGA-CM-5863       TCGA-CM-5864 
"PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" 
      TCGA-CM-5868       TCGA-CM-6161       TCGA-CM-6162       TCGA-CM-6163 
"PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" 
      TCGA-CM-6164       TCGA-CM-6165       TCGA-CM-6166       TCGA-CM-6167 
"PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" 
      TCGA-CM-6168       TCGA-CM-6169       TCGA-CM-6170       TCGA-CM-6171 
"PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" 
      TCGA-CM-6172       TCGA-CM-6674       TCGA-CM-6675       TCGA-CM-6676 
"PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" 
      TCGA-CM-6677       TCGA-CM-6678       TCGA-CM-6679       TCGA-CM-6680 
"PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" 
      TCGA-D5-5537       TCGA-D5-5538       TCGA-D5-5539       TCGA-D5-5540 
"PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" 
      TCGA-D5-5541       TCGA-D5-6529       TCGA-D5-6532       TCGA-D5-6533 
"PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" 
      TCGA-D5-6534       TCGA-D5-6535       TCGA-D5-6536       TCGA-D5-6537 
"PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" 
      TCGA-D5-6538       TCGA-D5-6539       TCGA-D5-6540       TCGA-D5-6541 
"PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" 
      TCGA-D5-6898       TCGA-D5-6920       TCGA-D5-6922       TCGA-D5-6923 
"PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" 
      TCGA-D5-6924       TCGA-D5-6926       TCGA-D5-6927       TCGA-D5-6928 
"PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" 
      TCGA-D5-6929       TCGA-D5-6930       TCGA-D5-6931       TCGA-D5-6932 
"PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" 
      TCGA-D5-7000       TCGA-F4-6459       TCGA-F4-6460       TCGA-F4-6569 
"PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" 
      TCGA-F4-6570       TCGA-F4-6703       TCGA-F4-6704       TCGA-F4-6805 
"PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" 
      TCGA-F4-6806       TCGA-F4-6807       TCGA-F4-6808       TCGA-F4-6809 
"PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" 
      TCGA-F4-6854       TCGA-F4-6855       TCGA-F4-6856       TCGA-G4-6293 
"PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" 
      TCGA-G4-6299       TCGA-G4-6303       TCGA-G4-6304       TCGA-G4-6306 
"PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" 
      TCGA-G4-6307       TCGA-G4-6309       TCGA-G4-6310       TCGA-G4-6315 
"PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" 
      TCGA-G4-6317       TCGA-G4-6321       TCGA-G4-6323       TCGA-G4-6586 
"PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" 
      TCGA-G4-6588       TCGA-G4-6625       TCGA-G4-6626       TCGA-G4-6628 
"PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" 
      TCGA-AF-2687       TCGA-AF-2689       TCGA-AF-2691       TCGA-AF-2692 
"PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" 
      TCGA-AF-3400       TCGA-AF-3913       TCGA-AF-4110       TCGA-AF-5654 
"PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" 
      TCGA-AF-6655       TCGA-AG-3574       TCGA-AG-3575       TCGA-AG-3578 
"PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" 
      TCGA-AG-3580       TCGA-AG-3581       TCGA-AG-3582       TCGA-AG-3583 
"PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" 
      TCGA-AG-3584       TCGA-AG-3586       TCGA-AG-3587       TCGA-AG-3593 
"PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" 
      TCGA-AG-3594       TCGA-AG-3598       TCGA-AG-3599       TCGA-AG-3600 
"PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" 
      TCGA-AG-3601       TCGA-AG-3602       TCGA-AG-3605       TCGA-AG-3608 
"PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" 
      TCGA-AG-3609       TCGA-AG-3611       TCGA-AG-3612       TCGA-AG-3726 
"PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" 
      TCGA-AG-3727       TCGA-AG-3731       TCGA-AG-3732       TCGA-AG-3742 
"PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" 
      TCGA-AG-3878       TCGA-AG-3882       TCGA-AG-3883       TCGA-AG-3885 
"PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" 
      TCGA-AG-3887       TCGA-AG-3890       TCGA-AG-3892       TCGA-AG-3893 
"PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" 
      TCGA-AG-3894       TCGA-AG-3896       TCGA-AG-3898       TCGA-AG-3901 
"PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" 
      TCGA-AG-3902       TCGA-AG-3909       TCGA-AG-3999       TCGA-AG-4001 
"PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" 
      TCGA-AG-4005       TCGA-AG-4007       TCGA-AG-4008       TCGA-AG-4015 
"PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" 
      TCGA-AG-A002       TCGA-AG-A008       TCGA-AG-A00C       TCGA-AG-A00H 
"PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" 
      TCGA-AG-A00Y       TCGA-AG-A011       TCGA-AG-A014       TCGA-AG-A015 
"PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" 
      TCGA-AG-A016       TCGA-AG-A01L       TCGA-AG-A01W       TCGA-AG-A01Y 
"PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" 
      TCGA-AG-A020       TCGA-AG-A025       TCGA-AG-A026       TCGA-AG-A02G 
"PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" 
      TCGA-AG-A02N       TCGA-AG-A02X       TCGA-AG-A032       TCGA-AG-A036 
"PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" 
      TCGA-AH-6549       TCGA-AH-6643       TCGA-CL-5917       TCGA-CL-5918 
"PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" 
      TCGA-DC-5337       TCGA-DC-5869       TCGA-DC-6155       TCGA-DC-6157 
"PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" 
      TCGA-DC-6158       TCGA-DC-6160       TCGA-DC-6681       TCGA-DC-6682 
"PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" 
      TCGA-DC-6683       TCGA-DT-5265       TCGA-EF-5830       TCGA-EI-6506 
"PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" 
      TCGA-EI-6507       TCGA-EI-6508       TCGA-EI-6510       TCGA-F5-6464 
"PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" 
      TCGA-F5-6465       TCGA-F5-6571       TCGA-F5-6702       TCGA-F5-6812 
"PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" 
      TCGA-F5-6813       TCGA-G5-6235       TCGA-G5-6641 
"PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" "PRSS27 WILD-TYPE" 
D2111V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PRSS27 MUTATED                                  0     0
  PRSS27 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  PRSS27 MUTATED                           0     3
  PRSS27 WILD-TYPE                        22   223
D2111V13, multiclass
                                  clus
vv                                 PRSS27 MUTATED PRSS27 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         3              223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2112) Variable = GLT25D1 MUTATION ANALYSIS
D2112V1, survival
                   sevent
clus2                 0   1
  GLT25D1 MUTATED     8   1
  GLT25D1 WILD-TYPE 370  92
  GLT25D1 MUTATED GLT25D1 WILD-TYPE 
                9               462 
  GLT25D1 MUTATED GLT25D1 WILD-TYPE 
                1                92 
$`GLT25D1 MUTATED`
TCGA-A6-5661 TCGA-AA-3710 TCGA-AA-3955 TCGA-AA-A01R TCGA-AD-6895 TCGA-AZ-6601 
       33.53        26.99        20.98        35.01         0.72       100.01 
TCGA-CM-6162 TCGA-D5-6540 TCGA-G4-6304 
       12.00        16.14        53.62 

$`GLT25D1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        85.05        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       31.00        38.07         1.02         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 
       88.21        49.41         6.77        12.10        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       15.02        17.03        15.02         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 
       17.85         4.80        17.13        12.49        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       74.56        65.85        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  GLT25D1 MUTATED GLT25D1 WILD-TYPE 
             0.72              0.00 
  GLT25D1 MUTATED GLT25D1 WILD-TYPE 
           100.01            148.01 
  GLT25D1 MUTATED GLT25D1 WILD-TYPE 
           26.990            20.085 
[1] "0.7 - 100.0 (27.0)" "0.0 - 148.0 (20.1)"
[1] "hr=" "2.2"
D2112V2, continuous
D2112V3, binary
                   cls
clus                  0   1
  GLT25D1 MUTATED     9   0
  GLT25D1 WILD-TYPE 357 119
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GLT25D1 MUTATED      9    0
  GLT25D1 WILD-TYPE  357  119
        clus
vv       GLT25D1 MUTATED GLT25D1 WILD-TYPE
  COLON                9               357
  RECTUM               0               119
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GLT25D1 MUTATED         1        0        1         2         1         0
  GLT25D1 WILD-TYPE      90        1       31       136         9         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GLT25D1 MUTATED           1          0          2          0        0
  GLT25D1 WILD-TYPE        23         11         57         42       48
                   vv
clus                STAGE IVA STAGE IVB
  GLT25D1 MUTATED           0         0
  GLT25D1 WILD-TYPE        18         1
D2112V4, multiclass
            clus
vv           GLT25D1 MUTATED GLT25D1 WILD-TYPE
  STAGE I                  1                90
  STAGE IA                 0                 1
  STAGE II                 1                31
  STAGE IIA                2               136
  STAGE IIB                1                 9
  STAGE IIC                0                 1
  STAGE III                1                23
  STAGE IIIA               0                11
  STAGE IIIB               2                57
  STAGE IIIC               0                42
  STAGE IV                 0                48
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  GLT25D1 MUTATED     0   2   6   1
  GLT25D1 WILD-TYPE  17  90 323  49
D2112V5, multiclass
    clus
vv   GLT25D1 MUTATED GLT25D1 WILD-TYPE
  T1               0                17
  T2               2                90
  T3               6               323
  T4               1                49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  GLT25D1 MUTATED     5   2   2
  GLT25D1 WILD-TYPE 282 111  85
D2112V6, multiclass
    clus
vv   GLT25D1 MUTATED GLT25D1 WILD-TYPE
  N0               5               282
  N1               2               111
  N2               2                85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2112V7, binary
                   cls
clus                  0   1
  GLT25D1 MUTATED     8   0
  GLT25D1 WILD-TYPE 367  65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GLT25D1 MUTATED      8    0
  GLT25D1 WILD-TYPE  367   65
   clus
vv  GLT25D1 MUTATED GLT25D1 WILD-TYPE
  0               8               367
  1               0                65
[1] 2 2
[1] FALSE
D2112V8, binary
                   cls
clus                  0   1
  GLT25D1 MUTATED     4   5
  GLT25D1 WILD-TYPE 221 259
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GLT25D1 MUTATED      4    5
  GLT25D1 WILD-TYPE  221  259
        clus
vv       GLT25D1 MUTATED GLT25D1 WILD-TYPE
  FEMALE               4               221
  MALE                 5               259
[1] 2 2
[1] FALSE
D2112V9, binary
                   cls
clus                  0   1
  GLT25D1 MUTATED     7   1
  GLT25D1 WILD-TYPE 343  21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GLT25D1 MUTATED      7    1
  GLT25D1 WILD-TYPE  343   21
     clus
vv    GLT25D1 MUTATED GLT25D1 WILD-TYPE
  NO                7               343
  YES               1                21
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  GLT25D1 MUTATED                      6                             3
  GLT25D1 WILD-TYPE                  309                            44
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  GLT25D1 MUTATED                       0                              0
  GLT25D1 WILD-TYPE                   106                             10
D2112V10, multiclass
                                clus
vv                               GLT25D1 MUTATED GLT25D1 WILD-TYPE
  COLON ADENOCARCINOMA                         6               309
  COLON MUCINOUS ADENOCARCINOMA                3                44
  RECTAL ADENOCARCINOMA                        0               106
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  GLT25D1 MUTATED     7   0   0   0
  GLT25D1 WILD-TYPE 338   4  31  25
D2112V11, multiclass
    clus
vv   GLT25D1 MUTATED GLT25D1 WILD-TYPE
  R0               7               338
  R1               0                 4
  R2               0                31
  RX               0                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2112V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GLT25D1 MUTATED                                  0     0
  GLT25D1 WILD-TYPE                                1    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  GLT25D1 MUTATED                           1     5
  GLT25D1 WILD-TYPE                        21   221
D2112V13, multiclass
                                  clus
vv                                 GLT25D1 MUTATED GLT25D1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                      1                21
  WHITE                                          5               221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2113) Variable = FAM167B MUTATION ANALYSIS
D2113V1, survival
                   sevent
clus2                 0   1
  FAM167B MUTATED     2   1
  FAM167B WILD-TYPE 376  92
  FAM167B MUTATED FAM167B WILD-TYPE 
                3               468 
  FAM167B MUTATED FAM167B WILD-TYPE 
                1                92 
$`FAM167B MUTATED`
TCGA-A6-6780 TCGA-CK-4952 TCGA-DM-A1D7 
       20.12        15.62        13.32 

$`FAM167B WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
      148.01        85.45        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  FAM167B MUTATED FAM167B WILD-TYPE 
            13.32              0.00 
  FAM167B MUTATED FAM167B WILD-TYPE 
            20.12            148.01 
  FAM167B MUTATED FAM167B WILD-TYPE 
           15.620            20.415 
[1] "13.3 - 20.1 (15.6)" "0.0 - 148.0 (20.4)"
[1] "hr=" "2.5"
D2113V2, continuous
D2113V3, binary
                   cls
clus                  0   1
  FAM167B MUTATED     4   0
  FAM167B WILD-TYPE 362 119
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM167B MUTATED      4    0
  FAM167B WILD-TYPE  362  119
        clus
vv       FAM167B MUTATED FAM167B WILD-TYPE
  COLON                4               362
  RECTUM               0               119
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FAM167B MUTATED         0        0        0         3         0         0
  FAM167B WILD-TYPE      91        1       32       135        10         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FAM167B MUTATED           0          0          0          1        0
  FAM167B WILD-TYPE        24         11         59         41       48
                   vv
clus                STAGE IVA STAGE IVB
  FAM167B MUTATED           0         0
  FAM167B WILD-TYPE        18         1
D2113V4, multiclass
            clus
vv           FAM167B MUTATED FAM167B WILD-TYPE
  STAGE I                  0                91
  STAGE IA                 0                 1
  STAGE II                 0                32
  STAGE IIA                3               135
  STAGE IIB                0                10
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               0                11
  STAGE IIIB               0                59
  STAGE IIIC               1                41
  STAGE IV                 0                48
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  FAM167B MUTATED     0   0   3   1
  FAM167B WILD-TYPE  17  92 326  49
D2113V5, multiclass
    clus
vv   FAM167B MUTATED FAM167B WILD-TYPE
  T1               0                17
  T2               0                92
  T3               3               326
  T4               1                49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  FAM167B MUTATED     3   0   1
  FAM167B WILD-TYPE 284 113  86
D2113V6, multiclass
    clus
vv   FAM167B MUTATED FAM167B WILD-TYPE
  N0               3               284
  N1               0               113
  N2               1                86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2113V7, binary
                   cls
clus                  0   1
  FAM167B MUTATED     3   0
  FAM167B WILD-TYPE 372  65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM167B MUTATED      3    0
  FAM167B WILD-TYPE  372   65
   clus
vv  FAM167B MUTATED FAM167B WILD-TYPE
  0               3               372
  1               0                65
[1] 2 2
[1] FALSE
D2113V8, binary
                   cls
clus                  0   1
  FAM167B MUTATED     2   2
  FAM167B WILD-TYPE 223 262
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM167B MUTATED      2    2
  FAM167B WILD-TYPE  223  262
        clus
vv       FAM167B MUTATED FAM167B WILD-TYPE
  FEMALE               2               223
  MALE                 2               262
[1] 2 2
[1] FALSE
D2113V9, binary
                   cls
clus                  0   1
  FAM167B MUTATED     1   0
  FAM167B WILD-TYPE 349  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM167B MUTATED      1    0
  FAM167B WILD-TYPE  349   22
     clus
vv    FAM167B MUTATED FAM167B WILD-TYPE
  NO                1               349
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  FAM167B MUTATED                      1                             2
  FAM167B WILD-TYPE                  314                            45
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  FAM167B MUTATED                       0                              0
  FAM167B WILD-TYPE                   106                             10
D2113V10, multiclass
                                clus
vv                               FAM167B MUTATED FAM167B WILD-TYPE
  COLON ADENOCARCINOMA                         1               314
  COLON MUCINOUS ADENOCARCINOMA                2                45
  RECTAL ADENOCARCINOMA                        0               106
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  FAM167B MUTATED     1   0   0   1
  FAM167B WILD-TYPE 344   4  31  24
D2113V11, multiclass
[1] "Remove cluster labels:" "FAM167B MUTATED"       
clus
  FAM167B MUTATED FAM167B WILD-TYPE 
                2               403 
       TCGA-A6-2671        TCGA-A6-2672        TCGA-A6-2674        TCGA-A6-2676 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-A6-2677        TCGA-A6-2678        TCGA-A6-2683        TCGA-A6-3807 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-A6-3808        TCGA-A6-3809        TCGA-A6-3810        TCGA-A6-5657 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-A6-5659        TCGA-A6-5661        TCGA-A6-5665        TCGA-A6-6781 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-AA-3489        TCGA-AA-3492        TCGA-AA-3496        TCGA-AA-3502 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-AA-3510        TCGA-AA-3511        TCGA-AA-3514        TCGA-AA-3517 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-AA-3518        TCGA-AA-3519        TCGA-AA-3520        TCGA-AA-3521 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-AA-3522        TCGA-AA-3524        TCGA-AA-3525        TCGA-AA-3526 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-AA-3527        TCGA-AA-3529        TCGA-AA-3530        TCGA-AA-3531 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-AA-3532        TCGA-AA-3534        TCGA-AA-3538        TCGA-AA-3542 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-AA-3543        TCGA-AA-3544        TCGA-AA-3548        TCGA-AA-3549 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-AA-3552        TCGA-AA-3553        TCGA-AA-3554        TCGA-AA-3555 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-AA-3556        TCGA-AA-3558        TCGA-AA-3560        TCGA-AA-3561 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-AA-3562        TCGA-AA-3655        TCGA-AA-3660        TCGA-AA-3662 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-AA-3663        TCGA-AA-3664        TCGA-AA-3666        TCGA-AA-3667 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-AA-3672        TCGA-AA-3673        TCGA-AA-3678        TCGA-AA-3679 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-AA-3680        TCGA-AA-3681        TCGA-AA-3684        TCGA-AA-3685 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-AA-3688        TCGA-AA-3692        TCGA-AA-3693        TCGA-AA-3695 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-AA-3696        TCGA-AA-3697        TCGA-AA-3710        TCGA-AA-3712 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-AA-3713        TCGA-AA-3715        TCGA-AA-3811        TCGA-AA-3812 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-AA-3814        TCGA-AA-3815        TCGA-AA-3818        TCGA-AA-3819 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-AA-3821        TCGA-AA-3831        TCGA-AA-3833        TCGA-AA-3837 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-AA-3842        TCGA-AA-3844        TCGA-AA-3845        TCGA-AA-3846 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-AA-3848        TCGA-AA-3850        TCGA-AA-3851        TCGA-AA-3852 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-AA-3854        TCGA-AA-3855        TCGA-AA-3856        TCGA-AA-3858 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-AA-3860        TCGA-AA-3861        TCGA-AA-3864        TCGA-AA-3866 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-AA-3867        TCGA-AA-3869        TCGA-AA-3870        TCGA-AA-3872 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-AA-3875        TCGA-AA-3877        TCGA-AA-3930        TCGA-AA-3939 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-AA-3941        TCGA-AA-3947        TCGA-AA-3949        TCGA-AA-3950 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-AA-3952        TCGA-AA-3955        TCGA-AA-3956        TCGA-AA-3968 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-AA-3971        TCGA-AA-3972        TCGA-AA-3973        TCGA-AA-3975 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-AA-3976        TCGA-AA-3979        TCGA-AA-3986        TCGA-AA-3989 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-AA-3994        TCGA-AA-A004        TCGA-AA-A00A        TCGA-AA-A00D 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-AA-A00E        TCGA-AA-A00F        TCGA-AA-A00J        TCGA-AA-A00K 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-AA-A00L        TCGA-AA-A00N        TCGA-AA-A00O        TCGA-AA-A00Q 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-AA-A00R        TCGA-AA-A00U        TCGA-AA-A00W        TCGA-AA-A00Z 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-AA-A010        TCGA-AA-A017        TCGA-AA-A01D        TCGA-AA-A01F 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-AA-A01G        TCGA-AA-A01I        TCGA-AA-A01K        TCGA-AA-A01P 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-AA-A01Q        TCGA-AA-A01R        TCGA-AA-A01S        TCGA-AA-A01T 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-AA-A01V        TCGA-AA-A01X        TCGA-AA-A01Z        TCGA-AA-A022 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-AA-A024        TCGA-AA-A029        TCGA-AA-A02F        TCGA-AA-A02H 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-AA-A02J        TCGA-AA-A02K        TCGA-AA-A02O        TCGA-AA-A02W 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-AA-A02Y        TCGA-AA-A03F        TCGA-AA-A03J        TCGA-AD-5900 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-AD-6548        TCGA-AD-6888        TCGA-AU-3779        TCGA-AU-6004 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-AY-4070        TCGA-AY-4071        TCGA-AY-5543        TCGA-AY-6196 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-AY-6197        TCGA-AY-6386        TCGA-AZ-4315        TCGA-AZ-4681 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-AZ-4682        TCGA-CA-5254        TCGA-CA-5255        TCGA-CA-5796 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-CA-5797        TCGA-CA-6715        TCGA-CA-6716        TCGA-CA-6717 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-CA-6718        TCGA-CA-6719        TCGA-CK-4947        TCGA-CK-4948 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-CK-4950        TCGA-CK-5912        TCGA-CK-5913        TCGA-CK-5914 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-CK-5915        TCGA-CK-5916        TCGA-CK-6746        TCGA-CK-6747 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-CK-6748        TCGA-CK-6751        TCGA-CM-4743        TCGA-CM-4744 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-CM-4746        TCGA-CM-4747        TCGA-CM-4752        TCGA-CM-5341 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-CM-5344        TCGA-CM-5348        TCGA-CM-5349        TCGA-CM-5860 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-CM-5861        TCGA-CM-5862        TCGA-CM-5863        TCGA-CM-5864 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-CM-5868        TCGA-CM-6161        TCGA-CM-6162        TCGA-CM-6163 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-CM-6164        TCGA-CM-6165        TCGA-CM-6166        TCGA-CM-6167 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-CM-6168        TCGA-CM-6169        TCGA-CM-6170        TCGA-CM-6171 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-CM-6172        TCGA-CM-6674        TCGA-CM-6675        TCGA-CM-6676 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-CM-6677        TCGA-CM-6678        TCGA-CM-6679        TCGA-CM-6680 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-D5-5537        TCGA-D5-5538        TCGA-D5-5539        TCGA-D5-5540 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-D5-5541        TCGA-D5-6529        TCGA-D5-6532        TCGA-D5-6533 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-D5-6534        TCGA-D5-6535        TCGA-D5-6536        TCGA-D5-6537 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-D5-6538        TCGA-D5-6539        TCGA-D5-6540        TCGA-D5-6541 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-D5-6898        TCGA-D5-6920        TCGA-D5-6922        TCGA-D5-6923 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-D5-6924        TCGA-D5-6926        TCGA-D5-6927        TCGA-D5-6928 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-D5-6929        TCGA-D5-6930        TCGA-D5-6931        TCGA-D5-6932 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-D5-7000        TCGA-F4-6459        TCGA-F4-6460        TCGA-F4-6569 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-F4-6570        TCGA-F4-6703        TCGA-F4-6704        TCGA-F4-6805 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-F4-6806        TCGA-F4-6807        TCGA-F4-6808        TCGA-F4-6809 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-F4-6854        TCGA-F4-6855        TCGA-F4-6856        TCGA-G4-6293 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-G4-6299        TCGA-G4-6303        TCGA-G4-6304        TCGA-G4-6306 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-G4-6307        TCGA-G4-6309        TCGA-G4-6310        TCGA-G4-6315 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-G4-6317        TCGA-G4-6321        TCGA-G4-6323        TCGA-G4-6586 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-G4-6588        TCGA-G4-6625        TCGA-G4-6626        TCGA-G4-6628 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2691        TCGA-AF-2692 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-AF-3400        TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-AF-6655        TCGA-AG-3574        TCGA-AG-3575        TCGA-AG-3578 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-AG-3580        TCGA-AG-3581        TCGA-AG-3582        TCGA-AG-3583 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-AG-3584        TCGA-AG-3586        TCGA-AG-3587        TCGA-AG-3593 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-AG-3594        TCGA-AG-3598        TCGA-AG-3599        TCGA-AG-3600 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-AG-3601        TCGA-AG-3602        TCGA-AG-3605        TCGA-AG-3608 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-AG-3609        TCGA-AG-3611        TCGA-AG-3612        TCGA-AG-3726 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-AG-3727        TCGA-AG-3731        TCGA-AG-3732        TCGA-AG-3742 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-AG-3878        TCGA-AG-3882        TCGA-AG-3883        TCGA-AG-3885 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3890        TCGA-AG-3892        TCGA-AG-3893 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-AG-3894        TCGA-AG-3896        TCGA-AG-3898        TCGA-AG-3901 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-AG-3902        TCGA-AG-3909        TCGA-AG-3999        TCGA-AG-4001 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-AG-4005        TCGA-AG-4007        TCGA-AG-4008        TCGA-AG-4015 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-AG-A002        TCGA-AG-A008        TCGA-AG-A00C        TCGA-AG-A00H 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-AG-A00Y        TCGA-AG-A011        TCGA-AG-A014        TCGA-AG-A015 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-AG-A016        TCGA-AG-A01L        TCGA-AG-A01W        TCGA-AG-A01Y 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-AG-A020        TCGA-AG-A025        TCGA-AG-A026        TCGA-AG-A02G 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032        TCGA-AG-A036 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-AH-6549        TCGA-AH-6643        TCGA-CL-5917        TCGA-CL-5918 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6155        TCGA-DC-6157 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-DC-6158        TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-DC-6683        TCGA-DT-5265        TCGA-EF-5830        TCGA-EI-6506 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-EI-6507        TCGA-EI-6508        TCGA-EI-6510        TCGA-F5-6464 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-F5-6465        TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6812 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
       TCGA-F5-6813        TCGA-G5-6235        TCGA-G5-6641 
"FAM167B WILD-TYPE" "FAM167B WILD-TYPE" "FAM167B WILD-TYPE" 
D2113V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FAM167B MUTATED                                  0     0
  FAM167B WILD-TYPE                                1    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  FAM167B MUTATED                           0     3
  FAM167B WILD-TYPE                        22   223
D2113V13, multiclass
                                  clus
vv                                 FAM167B MUTATED FAM167B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                      0                22
  WHITE                                          3               223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2114) Variable = OR5AN1 MUTATION ANALYSIS
D2114V1, survival
                  sevent
clus2                0   1
  OR5AN1 MUTATED     3   2
  OR5AN1 WILD-TYPE 375  91
  OR5AN1 MUTATED OR5AN1 WILD-TYPE 
               5              466 
  OR5AN1 MUTATED OR5AN1 WILD-TYPE 
               2               91 
$`OR5AN1 MUTATED`
TCGA-AZ-4315 TCGA-CA-6718 TCGA-CK-5913 TCGA-DM-A28F TCGA-CI-6619 
       58.39        10.06        51.32        35.97         6.05 

$`OR5AN1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
       16.31         0.95        33.01        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07        12.20        12.76        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       85.45        15.62        49.08         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H 
      139.17         6.12        81.37       119.93        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6620 
       38.56         1.45        17.49         0.69         0.72        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  OR5AN1 MUTATED OR5AN1 WILD-TYPE 
            6.05             0.00 
  OR5AN1 MUTATED OR5AN1 WILD-TYPE 
           58.39           148.01 
  OR5AN1 MUTATED OR5AN1 WILD-TYPE 
          35.970           20.155 
[1] "6.0 - 58.4 (36.0)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.6"
D2114V2, continuous
D2114V3, binary
                  cls
clus                 0   1
  OR5AN1 MUTATED     5   1
  OR5AN1 WILD-TYPE 361 118
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR5AN1 MUTATED      5    1
  OR5AN1 WILD-TYPE  361  118
        clus
vv       OR5AN1 MUTATED OR5AN1 WILD-TYPE
  COLON               5              361
  RECTUM              1              118
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  OR5AN1 MUTATED         0        0        0         3         0         0
  OR5AN1 WILD-TYPE      91        1       32       135        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  OR5AN1 MUTATED           0          0          1          0        2
  OR5AN1 WILD-TYPE        24         11         58         42       46
                  vv
clus               STAGE IVA STAGE IVB
  OR5AN1 MUTATED           0         0
  OR5AN1 WILD-TYPE        18         1
D2114V4, multiclass
            clus
vv           OR5AN1 MUTATED OR5AN1 WILD-TYPE
  STAGE I                 0               91
  STAGE IA                0                1
  STAGE II                0               32
  STAGE IIA               3              135
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              1               58
  STAGE IIIC              0               42
  STAGE IV                2               46
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  OR5AN1 MUTATED     0   0   5   1
  OR5AN1 WILD-TYPE  17  92 324  49
D2114V5, multiclass
    clus
vv   OR5AN1 MUTATED OR5AN1 WILD-TYPE
  T1              0               17
  T2              0               92
  T3              5              324
  T4              1               49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  OR5AN1 MUTATED     3   3   0
  OR5AN1 WILD-TYPE 284 110  87
D2114V6, multiclass
    clus
vv   OR5AN1 MUTATED OR5AN1 WILD-TYPE
  N0              3              284
  N1              3              110
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2114V7, binary
                  cls
clus                 0   1
  OR5AN1 MUTATED     3   2
  OR5AN1 WILD-TYPE 372  63
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR5AN1 MUTATED      3    2
  OR5AN1 WILD-TYPE  372   63
   clus
vv  OR5AN1 MUTATED OR5AN1 WILD-TYPE
  0              3              372
  1              2               63
[1] 2 2
[1] FALSE
D2114V8, binary
                  cls
clus                 0   1
  OR5AN1 MUTATED     2   4
  OR5AN1 WILD-TYPE 223 260
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR5AN1 MUTATED      2    4
  OR5AN1 WILD-TYPE  223  260
        clus
vv       OR5AN1 MUTATED OR5AN1 WILD-TYPE
  FEMALE              2              223
  MALE                4              260
[1] 2 2
[1] FALSE
D2114V9, binary
                  cls
clus                 0   1
  OR5AN1 MUTATED     3   0
  OR5AN1 WILD-TYPE 347  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR5AN1 MUTATED      3    0
  OR5AN1 WILD-TYPE  347   22
     clus
vv    OR5AN1 MUTATED OR5AN1 WILD-TYPE
  NO               3              347
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  OR5AN1 MUTATED                      5                             0
  OR5AN1 WILD-TYPE                  310                            47
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  OR5AN1 MUTATED                       1                              0
  OR5AN1 WILD-TYPE                   105                             10
D2114V10, multiclass
                                clus
vv                               OR5AN1 MUTATED OR5AN1 WILD-TYPE
  COLON ADENOCARCINOMA                        5              310
  COLON MUCINOUS ADENOCARCINOMA               0               47
  RECTAL ADENOCARCINOMA                       1              105
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  OR5AN1 MUTATED     1   0   1   2
  OR5AN1 WILD-TYPE 344   4  30  23
D2114V11, multiclass
    clus
vv   OR5AN1 MUTATED OR5AN1 WILD-TYPE
  R0              1              344
  R1              0                4
  R2              1               30
  RX              2               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2114V12, continuous
[1] "Remove cluster labels:" "OR5AN1 MUTATED"        
clus
  OR5AN1 MUTATED OR5AN1 WILD-TYPE 
               2              456 
      TCGA-A6-2671       TCGA-A6-2672       TCGA-A6-2674       TCGA-A6-2676 
"OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" 
      TCGA-A6-2677       TCGA-A6-2678       TCGA-A6-2683       TCGA-A6-3807 
"OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" 
      TCGA-A6-3808       TCGA-A6-3809       TCGA-A6-3810       TCGA-A6-4105 
"OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" 
      TCGA-A6-5656       TCGA-A6-5657       TCGA-A6-5659       TCGA-A6-5660 
"OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" 
      TCGA-A6-5661       TCGA-A6-5662       TCGA-A6-5664       TCGA-A6-5665 
"OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" 
      TCGA-A6-5666       TCGA-A6-6137       TCGA-A6-6138       TCGA-A6-6141 
"OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" 
      TCGA-A6-6142       TCGA-A6-6648       TCGA-A6-6649       TCGA-A6-6651 
"OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" 
      TCGA-A6-6652       TCGA-A6-6653       TCGA-A6-6654       TCGA-A6-6780 
"OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" 
      TCGA-A6-6781       TCGA-A6-6782       TCGA-AA-3489       TCGA-AA-3492 
"OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" 
      TCGA-AA-3496       TCGA-AA-3502       TCGA-AA-3510       TCGA-AA-3511 
"OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" 
      TCGA-AA-3514       TCGA-AA-3516       TCGA-AA-3517       TCGA-AA-3518 
"OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" 
      TCGA-AA-3519       TCGA-AA-3520       TCGA-AA-3521       TCGA-AA-3522 
"OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" 
      TCGA-AA-3524       TCGA-AA-3525       TCGA-AA-3526       TCGA-AA-3527 
"OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" 
      TCGA-AA-3529       TCGA-AA-3530       TCGA-AA-3531       TCGA-AA-3532 
"OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" 
      TCGA-AA-3534       TCGA-AA-3538       TCGA-AA-3542       TCGA-AA-3543 
"OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" 
      TCGA-AA-3544       TCGA-AA-3548       TCGA-AA-3549       TCGA-AA-3552 
"OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" 
      TCGA-AA-3553       TCGA-AA-3554       TCGA-AA-3555       TCGA-AA-3556 
"OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" 
      TCGA-AA-3558       TCGA-AA-3560       TCGA-AA-3562       TCGA-AA-3655 
"OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" 
      TCGA-AA-3660       TCGA-AA-3662       TCGA-AA-3663       TCGA-AA-3664 
"OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" 
      TCGA-AA-3666       TCGA-AA-3667       TCGA-AA-3672       TCGA-AA-3673 
"OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" 
      TCGA-AA-3678       TCGA-AA-3679       TCGA-AA-3680       TCGA-AA-3681 
"OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" 
      TCGA-AA-3684       TCGA-AA-3685       TCGA-AA-3688       TCGA-AA-3692 
"OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" 
      TCGA-AA-3695       TCGA-AA-3696       TCGA-AA-3697       TCGA-AA-3710 
"OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" 
      TCGA-AA-3712       TCGA-AA-3713       TCGA-AA-3715       TCGA-AA-3811 
"OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" 
      TCGA-AA-3812       TCGA-AA-3814       TCGA-AA-3815       TCGA-AA-3818 
"OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" 
      TCGA-AA-3819       TCGA-AA-3821       TCGA-AA-3831       TCGA-AA-3833 
"OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" 
      TCGA-AA-3837       TCGA-AA-3842       TCGA-AA-3844       TCGA-AA-3845 
"OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" 
      TCGA-AA-3846       TCGA-AA-3848       TCGA-AA-3850       TCGA-AA-3851 
"OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" 
      TCGA-AA-3852       TCGA-AA-3854       TCGA-AA-3855       TCGA-AA-3856 
"OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" 
      TCGA-AA-3858       TCGA-AA-3860       TCGA-AA-3861       TCGA-AA-3864 
"OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" 
      TCGA-AA-3866       TCGA-AA-3867       TCGA-AA-3869       TCGA-AA-3870 
"OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" 
      TCGA-AA-3872       TCGA-AA-3875       TCGA-AA-3877       TCGA-AA-3930 
"OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" 
      TCGA-AA-3939       TCGA-AA-3941       TCGA-AA-3947       TCGA-AA-3949 
"OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" 
      TCGA-AA-3950       TCGA-AA-3952       TCGA-AA-3955       TCGA-AA-3956 
"OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" 
      TCGA-AA-3966       TCGA-AA-3968       TCGA-AA-3971       TCGA-AA-3972 
"OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" 
      TCGA-AA-3973       TCGA-AA-3975       TCGA-AA-3976       TCGA-AA-3977 
"OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" 
      TCGA-AA-3979       TCGA-AA-3980       TCGA-AA-3982       TCGA-AA-3984 
"OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" 
      TCGA-AA-3986       TCGA-AA-3989       TCGA-AA-3994       TCGA-AA-A004 
"OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" 
      TCGA-AA-A00A       TCGA-AA-A00D       TCGA-AA-A00E       TCGA-AA-A00F 
"OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" 
      TCGA-AA-A00J       TCGA-AA-A00K       TCGA-AA-A00L       TCGA-AA-A00N 
"OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" 
      TCGA-AA-A00O       TCGA-AA-A00Q       TCGA-AA-A00R       TCGA-AA-A00U 
"OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" 
      TCGA-AA-A00W       TCGA-AA-A00Z       TCGA-AA-A010       TCGA-AA-A017 
"OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" 
      TCGA-AA-A01D       TCGA-AA-A01F       TCGA-AA-A01G       TCGA-AA-A01I 
"OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" 
      TCGA-AA-A01K       TCGA-AA-A01P       TCGA-AA-A01Q       TCGA-AA-A01R 
"OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" 
      TCGA-AA-A01S       TCGA-AA-A01T       TCGA-AA-A01V       TCGA-AA-A01X 
"OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" 
      TCGA-AA-A01Z       TCGA-AA-A022       TCGA-AA-A024       TCGA-AA-A029 
"OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" 
      TCGA-AA-A02F       TCGA-AA-A02H       TCGA-AA-A02J       TCGA-AA-A02K 
"OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" 
      TCGA-AA-A02O       TCGA-AA-A02W       TCGA-AA-A02Y       TCGA-AA-A03F 
"OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" 
      TCGA-AA-A03J       TCGA-AD-5900       TCGA-AD-6548       TCGA-AD-6888 
"OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" 
      TCGA-AD-6889       TCGA-AD-6890       TCGA-AD-6895       TCGA-AD-6899 
"OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" 
      TCGA-AD-6901       TCGA-AD-6963       TCGA-AD-6964       TCGA-AD-6965 
"OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" 
      TCGA-AU-3779       TCGA-AU-6004       TCGA-AY-4070       TCGA-AY-4071 
"OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" 
      TCGA-AY-5543       TCGA-AY-6196       TCGA-AY-6197       TCGA-AY-6386 
"OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" 
      TCGA-AZ-4323       TCGA-AZ-4616       TCGA-AZ-4682       TCGA-AZ-5403 
"OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" 
      TCGA-AZ-5407       TCGA-AZ-6598       TCGA-AZ-6599       TCGA-AZ-6600 
"OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" 
      TCGA-AZ-6601       TCGA-AZ-6603       TCGA-AZ-6605       TCGA-AZ-6606 
"OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" 
      TCGA-AZ-6607       TCGA-AZ-6608       TCGA-CK-4947       TCGA-CK-4948 
"OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" 
      TCGA-CK-4950       TCGA-CK-4952       TCGA-CM-4743       TCGA-CM-4744 
"OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" 
      TCGA-CM-4746       TCGA-CM-4747       TCGA-CM-4752       TCGA-CM-5341 
"OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" 
      TCGA-CM-5344       TCGA-CM-5348       TCGA-CM-5349       TCGA-CM-5860 
"OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" 
      TCGA-CM-5861       TCGA-CM-5862       TCGA-CM-5863       TCGA-CM-5864 
"OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" 
      TCGA-CM-5868       TCGA-CM-6161       TCGA-CM-6162       TCGA-CM-6163 
"OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" 
      TCGA-CM-6164       TCGA-CM-6165       TCGA-CM-6166       TCGA-CM-6167 
"OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" 
      TCGA-CM-6168       TCGA-CM-6169       TCGA-CM-6170       TCGA-CM-6171 
"OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" 
      TCGA-CM-6172       TCGA-CM-6674       TCGA-CM-6675       TCGA-CM-6676 
"OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" 
      TCGA-CM-6677       TCGA-CM-6678       TCGA-CM-6679       TCGA-CM-6680 
"OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" 
      TCGA-D5-5537       TCGA-D5-5538       TCGA-D5-5539       TCGA-D5-5540 
"OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" 
      TCGA-D5-5541       TCGA-D5-6529       TCGA-D5-6532       TCGA-D5-6533 
"OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" 
      TCGA-D5-6534       TCGA-D5-6535       TCGA-D5-6536       TCGA-D5-6537 
"OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" 
      TCGA-D5-6538       TCGA-D5-6539       TCGA-D5-6540       TCGA-D5-6541 
"OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" 
      TCGA-D5-6898       TCGA-D5-6920       TCGA-D5-6922       TCGA-D5-6923 
"OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" 
      TCGA-D5-6924       TCGA-D5-6926       TCGA-D5-6927       TCGA-D5-6928 
"OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" 
      TCGA-D5-6929       TCGA-D5-6930       TCGA-D5-6931       TCGA-D5-6932 
"OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" 
      TCGA-D5-7000       TCGA-DM-A0X9       TCGA-DM-A0XD       TCGA-DM-A0XF 
"OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" 
      TCGA-DM-A1D0       TCGA-DM-A1D4       TCGA-DM-A1D6       TCGA-DM-A1D7 
"OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" 
      TCGA-DM-A1D8       TCGA-DM-A1D9       TCGA-DM-A1DA       TCGA-DM-A1DB 
"OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" 
      TCGA-DM-A1HA       TCGA-DM-A1HB       TCGA-DM-A282       TCGA-DM-A285 
"OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" 
      TCGA-DM-A28C       TCGA-DM-A28E       TCGA-DM-A28G       TCGA-DM-A28H 
"OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" 
      TCGA-DM-A28K       TCGA-F4-6459       TCGA-F4-6460       TCGA-F4-6569 
"OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" 
      TCGA-F4-6570       TCGA-F4-6703       TCGA-F4-6704       TCGA-F4-6806 
"OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" 
      TCGA-F4-6807       TCGA-F4-6808       TCGA-F4-6809       TCGA-F4-6854 
"OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" 
      TCGA-F4-6855       TCGA-F4-6856       TCGA-G4-6293       TCGA-G4-6299 
"OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" 
      TCGA-G4-6303       TCGA-G4-6304       TCGA-G4-6306       TCGA-G4-6307 
"OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" 
      TCGA-G4-6309       TCGA-G4-6310       TCGA-G4-6315       TCGA-G4-6317 
"OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" 
      TCGA-G4-6321       TCGA-G4-6323       TCGA-G4-6586       TCGA-G4-6588 
"OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" 
      TCGA-G4-6625       TCGA-G4-6626       TCGA-G4-6628       TCGA-AF-2687 
"OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" 
      TCGA-AF-2689       TCGA-AF-2691       TCGA-AF-2692       TCGA-AF-2693 
"OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" 
      TCGA-AF-3400       TCGA-AF-3913       TCGA-AF-4110       TCGA-AF-5654 
"OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" 
      TCGA-AF-6136       TCGA-AF-6655       TCGA-AF-6672       TCGA-AG-3574 
"OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" 
      TCGA-AG-3575       TCGA-AG-3578       TCGA-AG-3580       TCGA-AG-3581 
"OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" 
      TCGA-AG-3582       TCGA-AG-3583       TCGA-AG-3584       TCGA-AG-3586 
"OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" 
      TCGA-AG-3587       TCGA-AG-3593       TCGA-AG-3594       TCGA-AG-3598 
"OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" 
      TCGA-AG-3599       TCGA-AG-3600       TCGA-AG-3601       TCGA-AG-3602 
"OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" 
      TCGA-AG-3605       TCGA-AG-3608       TCGA-AG-3609       TCGA-AG-3611 
"OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" 
      TCGA-AG-3612       TCGA-AG-3726       TCGA-AG-3727       TCGA-AG-3731 
"OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" 
      TCGA-AG-3732       TCGA-AG-3742       TCGA-AG-3878       TCGA-AG-3881 
"OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" 
      TCGA-AG-3882       TCGA-AG-3883       TCGA-AG-3885       TCGA-AG-3887 
"OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" 
      TCGA-AG-3890       TCGA-AG-3892       TCGA-AG-3893       TCGA-AG-3894 
"OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" 
      TCGA-AG-3896       TCGA-AG-3898       TCGA-AG-3901       TCGA-AG-3902 
"OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" 
      TCGA-AG-3909       TCGA-AG-3999       TCGA-AG-4001       TCGA-AG-4005 
"OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" 
      TCGA-AG-4007       TCGA-AG-4008       TCGA-AG-4015       TCGA-AG-A002 
"OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" 
      TCGA-AG-A008       TCGA-AG-A00C       TCGA-AG-A00H       TCGA-AG-A00Y 
"OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" 
      TCGA-AG-A011       TCGA-AG-A014       TCGA-AG-A015       TCGA-AG-A016 
"OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" 
      TCGA-AG-A01L       TCGA-AG-A01W       TCGA-AG-A01Y       TCGA-AG-A020 
"OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" 
      TCGA-AG-A025       TCGA-AG-A026       TCGA-AG-A02G       TCGA-AG-A02N 
"OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" 
      TCGA-AG-A02X       TCGA-AG-A032       TCGA-AG-A036       TCGA-AH-6544 
"OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" 
      TCGA-AH-6547       TCGA-AH-6643       TCGA-AH-6644       TCGA-CI-6622 
"OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" 
      TCGA-DC-5337       TCGA-DC-5869       TCGA-DC-6155       TCGA-DC-6157 
"OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" 
      TCGA-DC-6158       TCGA-DC-6160       TCGA-DC-6681       TCGA-DC-6682 
"OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" 
      TCGA-DC-6683       TCGA-DY-A0XA       TCGA-DY-A1DC       TCGA-DY-A1DD 
"OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" 
      TCGA-DY-A1DF       TCGA-DY-A1DG       TCGA-DY-A1H8       TCGA-EI-6506 
"OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" 
      TCGA-EI-6507       TCGA-EI-6508       TCGA-EI-6510       TCGA-F5-6464 
"OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" 
      TCGA-F5-6465       TCGA-F5-6571       TCGA-F5-6702       TCGA-F5-6811 
"OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" 
      TCGA-F5-6812       TCGA-F5-6813       TCGA-G5-6235       TCGA-G5-6641 
"OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" "OR5AN1 WILD-TYPE" 
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OR5AN1 MUTATED                                  0     1
  OR5AN1 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  OR5AN1 MUTATED                           0     4
  OR5AN1 WILD-TYPE                        22   222
D2114V13, multiclass
                                  clus
vv                                 OR5AN1 MUTATED OR5AN1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         4              222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2115) Variable = SETD7 MUTATION ANALYSIS
D2115V1, survival
                 sevent
clus2               0   1
  SETD7 MUTATED     8   1
  SETD7 WILD-TYPE 370  92
  SETD7 MUTATED SETD7 WILD-TYPE 
              9             462 
  SETD7 MUTATED SETD7 WILD-TYPE 
              1              92 
$`SETD7 MUTATED`
TCGA-AA-3558 TCGA-AA-3663 TCGA-AA-3877 TCGA-AD-6964 TCGA-AZ-4315 TCGA-CK-4952 
       20.98         6.97        31.00        10.88        58.39        15.62 
TCGA-D5-6928 TCGA-AG-A002 TCGA-EI-6507 
       11.64        20.98        19.96 

$`SETD7 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 
       24.03        27.02        29.98        18.05         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
        0.79         0.72         5.79        22.42        27.42         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 
       14.30        17.56       148.01        85.45        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.04         9.44         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       20.55        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  SETD7 MUTATED SETD7 WILD-TYPE 
           6.97            0.00 
  SETD7 MUTATED SETD7 WILD-TYPE 
          58.39          148.01 
  SETD7 MUTATED SETD7 WILD-TYPE 
         19.960          20.235 
[1] "7.0 - 58.4 (20.0)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.5"
D2115V2, continuous
D2115V3, binary
                 cls
clus                0   1
  SETD7 MUTATED     7   2
  SETD7 WILD-TYPE 359 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SETD7 MUTATED      7    2
  SETD7 WILD-TYPE  359  117
        clus
vv       SETD7 MUTATED SETD7 WILD-TYPE
  COLON              7             359
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SETD7 MUTATED         3        0        1         3         0         0
  SETD7 WILD-TYPE      88        1       31       135        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SETD7 MUTATED           0          0          0          1        0         0
  SETD7 WILD-TYPE        24         11         59         41       48        18
                 vv
clus              STAGE IVB
  SETD7 MUTATED           0
  SETD7 WILD-TYPE         1
D2115V4, multiclass
            clus
vv           SETD7 MUTATED SETD7 WILD-TYPE
  STAGE I                3              88
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              3             135
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             1              41
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  SETD7 MUTATED     1   2   4   2
  SETD7 WILD-TYPE  16  90 325  48
D2115V5, multiclass
    clus
vv   SETD7 MUTATED SETD7 WILD-TYPE
  T1             1              16
  T2             2              90
  T3             4             325
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  SETD7 MUTATED     7   0   2
  SETD7 WILD-TYPE 280 113  85
D2115V6, multiclass
    clus
vv   SETD7 MUTATED SETD7 WILD-TYPE
  N0             7             280
  N1             0             113
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2115V7, binary
                 cls
clus                0   1
  SETD7 MUTATED     8   0
  SETD7 WILD-TYPE 367  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SETD7 MUTATED      8    0
  SETD7 WILD-TYPE  367   65
   clus
vv  SETD7 MUTATED SETD7 WILD-TYPE
  0             8             367
  1             0              65
[1] 2 2
[1] FALSE
D2115V8, binary
                 cls
clus                0   1
  SETD7 MUTATED     2   7
  SETD7 WILD-TYPE 223 257
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SETD7 MUTATED      2    7
  SETD7 WILD-TYPE  223  257
        clus
vv       SETD7 MUTATED SETD7 WILD-TYPE
  FEMALE             2             223
  MALE               7             257
[1] 2 2
[1] FALSE
D2115V9, binary
                 cls
clus                0   1
  SETD7 MUTATED     8   0
  SETD7 WILD-TYPE 342  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SETD7 MUTATED      8    0
  SETD7 WILD-TYPE  342   22
     clus
vv    SETD7 MUTATED SETD7 WILD-TYPE
  NO              8             342
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SETD7 MUTATED                      4                             3
  SETD7 WILD-TYPE                  311                            44
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SETD7 MUTATED                       2                              0
  SETD7 WILD-TYPE                   104                             10
D2115V10, multiclass
                                clus
vv                               SETD7 MUTATED SETD7 WILD-TYPE
  COLON ADENOCARCINOMA                       4             311
  COLON MUCINOUS ADENOCARCINOMA              3              44
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  SETD7 MUTATED     6   0   1   1
  SETD7 WILD-TYPE 339   4  30  24
D2115V11, multiclass
    clus
vv   SETD7 MUTATED SETD7 WILD-TYPE
  R0             6             339
  R1             0               4
  R2             1              30
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2115V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SETD7 MUTATED                                  0     0
  SETD7 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  SETD7 MUTATED                           0     5
  SETD7 WILD-TYPE                        22   221
D2115V13, multiclass
                                  clus
vv                                 SETD7 MUTATED SETD7 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        5             221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2116) Variable = ARHGAP10 MUTATION ANALYSIS
D2116V1, survival
                    sevent
clus2                  0   1
  ARHGAP10 MUTATED     6   2
  ARHGAP10 WILD-TYPE 372  91
  ARHGAP10 MUTATED ARHGAP10 WILD-TYPE 
                 8                463 
  ARHGAP10 MUTATED ARHGAP10 WILD-TYPE 
                 2                 91 
$`ARHGAP10 MUTATED`
TCGA-A6-5660 TCGA-A6-6653 TCGA-AA-A010 TCGA-AZ-6600 TCGA-G4-6588 TCGA-G4-6628 
       29.19        24.39        34.98        12.10        26.17        79.69 
TCGA-DT-5265 TCGA-DY-A1DD 
        5.29        57.24 

$`ARHGAP10 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 
       25.18        24.16        21.76        24.69        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 
       22.36        62.79        88.21        49.41         6.77       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        35.80        91.79        46.75 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
      126.44        41.36        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  ARHGAP10 MUTATED ARHGAP10 WILD-TYPE 
              5.29               0.00 
  ARHGAP10 MUTATED ARHGAP10 WILD-TYPE 
             79.69             148.01 
  ARHGAP10 MUTATED ARHGAP10 WILD-TYPE 
             27.68              20.05 
[1] "5.3 - 79.7 (27.7)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1"  
D2116V2, continuous
D2116V3, binary
                    cls
clus                   0   1
  ARHGAP10 MUTATED     7   2
  ARHGAP10 WILD-TYPE 359 117
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ARHGAP10 MUTATED      7    2
  ARHGAP10 WILD-TYPE  359  117
        clus
vv       ARHGAP10 MUTATED ARHGAP10 WILD-TYPE
  COLON                 7                359
  RECTUM                2                117
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ARHGAP10 MUTATED         2        0        1         2         1         0
  ARHGAP10 WILD-TYPE      89        1       31       136         9         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ARHGAP10 MUTATED           0          0          1          1        1
  ARHGAP10 WILD-TYPE        24         11         58         41       47
                    vv
clus                 STAGE IVA STAGE IVB
  ARHGAP10 MUTATED           0         0
  ARHGAP10 WILD-TYPE        18         1
D2116V4, multiclass
            clus
vv           ARHGAP10 MUTATED ARHGAP10 WILD-TYPE
  STAGE I                   2                 89
  STAGE IA                  0                  1
  STAGE II                  1                 31
  STAGE IIA                 2                136
  STAGE IIB                 1                  9
  STAGE IIC                 0                  1
  STAGE III                 0                 24
  STAGE IIIA                0                 11
  STAGE IIIB                1                 58
  STAGE IIIC                1                 41
  STAGE IV                  1                 47
  STAGE IVA                 0                 18
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  ARHGAP10 MUTATED     0   2   5   2
  ARHGAP10 WILD-TYPE  17  90 324  48
D2116V5, multiclass
    clus
vv   ARHGAP10 MUTATED ARHGAP10 WILD-TYPE
  T1                0                 17
  T2                2                 90
  T3                5                324
  T4                2                 48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  ARHGAP10 MUTATED     6   2   1
  ARHGAP10 WILD-TYPE 281 111  86
D2116V6, multiclass
    clus
vv   ARHGAP10 MUTATED ARHGAP10 WILD-TYPE
  N0                6                281
  N1                2                111
  N2                1                 86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2116V7, binary
                    cls
clus                   0   1
  ARHGAP10 MUTATED     8   1
  ARHGAP10 WILD-TYPE 367  64
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ARHGAP10 MUTATED      8    1
  ARHGAP10 WILD-TYPE  367   64
   clus
vv  ARHGAP10 MUTATED ARHGAP10 WILD-TYPE
  0                8                367
  1                1                 64
[1] 2 2
[1] FALSE
D2116V8, binary
                    cls
clus                   0   1
  ARHGAP10 MUTATED     4   5
  ARHGAP10 WILD-TYPE 221 259
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ARHGAP10 MUTATED      4    5
  ARHGAP10 WILD-TYPE  221  259
        clus
vv       ARHGAP10 MUTATED ARHGAP10 WILD-TYPE
  FEMALE                4                221
  MALE                  5                259
[1] 2 2
[1] FALSE
D2116V9, binary
                    cls
clus                   0   1
  ARHGAP10 MUTATED     6   0
  ARHGAP10 WILD-TYPE 344  22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ARHGAP10 MUTATED      6    0
  ARHGAP10 WILD-TYPE  344   22
     clus
vv    ARHGAP10 MUTATED ARHGAP10 WILD-TYPE
  NO                 6                344
  YES                0                 22
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ARHGAP10 MUTATED                      7                             0
  ARHGAP10 WILD-TYPE                  308                            47
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ARHGAP10 MUTATED                       1                              1
  ARHGAP10 WILD-TYPE                   105                              9
D2116V10, multiclass
                                clus
vv                               ARHGAP10 MUTATED ARHGAP10 WILD-TYPE
  COLON ADENOCARCINOMA                          7                308
  COLON MUCINOUS ADENOCARCINOMA                 0                 47
  RECTAL ADENOCARCINOMA                         1                105
  RECTAL MUCINOUS ADENOCARCINOMA                1                  9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  ARHGAP10 MUTATED     4   0   0   1
  ARHGAP10 WILD-TYPE 341   4  31  24
D2116V11, multiclass
    clus
vv   ARHGAP10 MUTATED ARHGAP10 WILD-TYPE
  R0                4                341
  R1                0                  4
  R2                0                 31
  RX                1                 24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2116V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ARHGAP10 MUTATED                                  0     1
  ARHGAP10 WILD-TYPE                                1    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  ARHGAP10 MUTATED                           2     4
  ARHGAP10 WILD-TYPE                        20   222
D2116V13, multiclass
                                  clus
vv                                 ARHGAP10 MUTATED ARHGAP10 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                 10
  BLACK OR AFRICAN AMERICAN                       2                 20
  WHITE                                           4                222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2117) Variable = C9ORF102 MUTATION ANALYSIS
D2117V1, survival
                    sevent
clus2                  0   1
  C9ORF102 MUTATED     9   0
  C9ORF102 WILD-TYPE 369  93
  C9ORF102 MUTATED C9ORF102 WILD-TYPE 
                 9                462 
  C9ORF102 MUTATED C9ORF102 WILD-TYPE 
                 0                 93 
$`C9ORF102 MUTATED`
TCGA-A6-3808 TCGA-A6-6780 TCGA-AA-3977 TCGA-AA-A010 TCGA-AD-5900 TCGA-AD-6895 
       33.34        20.12        25.02        34.98         0.07         0.72 
TCGA-CM-6167 TCGA-AG-3892 TCGA-AG-A002 
       14.99        13.02        20.98 

$`C9ORF102 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 
       40.96        21.37        15.52        56.55         0.79         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       16.04        21.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       17.03        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  C9ORF102 MUTATED C9ORF102 WILD-TYPE 
              0.07               0.00 
  C9ORF102 MUTATED C9ORF102 WILD-TYPE 
             34.98             148.01 
  C9ORF102 MUTATED C9ORF102 WILD-TYPE 
            20.120             20.235 
[1] "0.1 - 35.0 (20.1)"  "0.0 - 148.0 (20.2)"
[1] "hr="     "9100000"
D2117V2, continuous
D2117V3, binary
                    cls
clus                   0   1
  C9ORF102 MUTATED     8   2
  C9ORF102 WILD-TYPE 358 117
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C9ORF102 MUTATED      8    2
  C9ORF102 WILD-TYPE  358  117
        clus
vv       C9ORF102 MUTATED C9ORF102 WILD-TYPE
  COLON                 8                358
  RECTUM                2                117
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  C9ORF102 MUTATED         3        0        0         3         1         0
  C9ORF102 WILD-TYPE      88        1       32       135         9         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C9ORF102 MUTATED           0          0          0          1        0
  C9ORF102 WILD-TYPE        24         11         59         41       48
                    vv
clus                 STAGE IVA STAGE IVB
  C9ORF102 MUTATED           0         0
  C9ORF102 WILD-TYPE        18         1
D2117V4, multiclass
            clus
vv           C9ORF102 MUTATED C9ORF102 WILD-TYPE
  STAGE I                   3                 88
  STAGE IA                  0                  1
  STAGE II                  0                 32
  STAGE IIA                 3                135
  STAGE IIB                 1                  9
  STAGE IIC                 0                  1
  STAGE III                 0                 24
  STAGE IIIA                0                 11
  STAGE IIIB                0                 59
  STAGE IIIC                1                 41
  STAGE IV                  0                 48
  STAGE IVA                 0                 18
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  C9ORF102 MUTATED     1   3   5   1
  C9ORF102 WILD-TYPE  16  89 324  49
D2117V5, multiclass
    clus
vv   C9ORF102 MUTATED C9ORF102 WILD-TYPE
  T1                1                 16
  T2                3                 89
  T3                5                324
  T4                1                 49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  C9ORF102 MUTATED     8   1   1
  C9ORF102 WILD-TYPE 279 112  86
D2117V6, multiclass
    clus
vv   C9ORF102 MUTATED C9ORF102 WILD-TYPE
  N0                8                279
  N1                1                112
  N2                1                 86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2117V7, binary
                    cls
clus                   0   1
  C9ORF102 MUTATED     6   0
  C9ORF102 WILD-TYPE 369  65
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C9ORF102 MUTATED      6    0
  C9ORF102 WILD-TYPE  369   65
   clus
vv  C9ORF102 MUTATED C9ORF102 WILD-TYPE
  0                6                369
  1                0                 65
[1] 2 2
[1] FALSE
D2117V8, binary
                    cls
clus                   0   1
  C9ORF102 MUTATED     4   6
  C9ORF102 WILD-TYPE 221 258
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C9ORF102 MUTATED      4    6
  C9ORF102 WILD-TYPE  221  258
        clus
vv       C9ORF102 MUTATED C9ORF102 WILD-TYPE
  FEMALE                4                221
  MALE                  6                258
[1] 2 2
[1] FALSE
D2117V9, binary
                    cls
clus                   0   1
  C9ORF102 MUTATED     7   0
  C9ORF102 WILD-TYPE 343  22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C9ORF102 MUTATED      7    0
  C9ORF102 WILD-TYPE  343   22
     clus
vv    C9ORF102 MUTATED C9ORF102 WILD-TYPE
  NO                 7                343
  YES                0                 22
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  C9ORF102 MUTATED                      6                             2
  C9ORF102 WILD-TYPE                  309                            45
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  C9ORF102 MUTATED                       2                              0
  C9ORF102 WILD-TYPE                   104                             10
D2117V10, multiclass
                                clus
vv                               C9ORF102 MUTATED C9ORF102 WILD-TYPE
  COLON ADENOCARCINOMA                          6                309
  COLON MUCINOUS ADENOCARCINOMA                 2                 45
  RECTAL ADENOCARCINOMA                         2                104
  RECTAL MUCINOUS ADENOCARCINOMA                0                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  C9ORF102 MUTATED     7   0   0   0
  C9ORF102 WILD-TYPE 338   4  31  25
D2117V11, multiclass
    clus
vv   C9ORF102 MUTATED C9ORF102 WILD-TYPE
  R0                7                338
  R1                0                  4
  R2                0                 31
  RX                0                 25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2117V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C9ORF102 MUTATED                                  0     0
  C9ORF102 WILD-TYPE                                1    11
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  C9ORF102 MUTATED                           1     4
  C9ORF102 WILD-TYPE                        21   222
D2117V13, multiclass
                                  clus
vv                                 C9ORF102 MUTATED C9ORF102 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 11
  BLACK OR AFRICAN AMERICAN                       1                 21
  WHITE                                           4                222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2118) Variable = LRMP MUTATION ANALYSIS
D2118V1, survival
                sevent
clus2              0   1
  LRMP MUTATED     3   4
  LRMP WILD-TYPE 375  89
  LRMP MUTATED LRMP WILD-TYPE 
             7            464 
  LRMP MUTATED LRMP WILD-TYPE 
             4             89 
$`LRMP MUTATED`
TCGA-AA-3877 TCGA-AA-A00N TCGA-CA-6717 TCGA-DM-A0XF TCGA-DM-A1D7 TCGA-AG-A008 
       31.00         4.01        12.76        38.20        13.32        13.94 
TCGA-AG-A026 
        1.94 

$`LRMP WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.20        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D8 TCGA-DM-A1D9 
       24.43       130.65        92.75        49.91        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        20.98         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A02G TCGA-AG-A02N 
       70.03        64.01        10.98        49.97        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  LRMP MUTATED LRMP WILD-TYPE 
          1.94           0.00 
  LRMP MUTATED LRMP WILD-TYPE 
         38.20         148.01 
  LRMP MUTATED LRMP WILD-TYPE 
        13.320         20.415 
[1] "1.9 - 38.2 (13.3)"  "0.0 - 148.0 (20.4)"
[1] "hr=" "4.8"
D2118V2, continuous
D2118V3, binary
                cls
clus               0   1
  LRMP MUTATED     5   2
  LRMP WILD-TYPE 361 117
[1] "tbl2"
                cls
clus             [,1] [,2]
  LRMP MUTATED      5    2
  LRMP WILD-TYPE  361  117
        clus
vv       LRMP MUTATED LRMP WILD-TYPE
  COLON             5            361
  RECTUM            2            117
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  LRMP MUTATED         2        0        1         2         1         0
  LRMP WILD-TYPE      89        1       31       136         9         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  LRMP MUTATED           0          0          0          1        0         0
  LRMP WILD-TYPE        24         11         59         41       48        18
                vv
clus             STAGE IVB
  LRMP MUTATED           0
  LRMP WILD-TYPE         1
D2118V4, multiclass
            clus
vv           LRMP MUTATED LRMP WILD-TYPE
  STAGE I               2             89
  STAGE IA              0              1
  STAGE II              1             31
  STAGE IIA             2            136
  STAGE IIB             1              9
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            0             59
  STAGE IIIC            1             41
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  LRMP MUTATED     1   1   3   2
  LRMP WILD-TYPE  16  91 326  48
D2118V5, multiclass
    clus
vv   LRMP MUTATED LRMP WILD-TYPE
  T1            1             16
  T2            1             91
  T3            3            326
  T4            2             48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  LRMP MUTATED     6   0   1
  LRMP WILD-TYPE 281 113  86
D2118V6, multiclass
    clus
vv   LRMP MUTATED LRMP WILD-TYPE
  N0            6            281
  N1            0            113
  N2            1             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2118V7, binary
                cls
clus               0   1
  LRMP MUTATED     7   0
  LRMP WILD-TYPE 368  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  LRMP MUTATED      7    0
  LRMP WILD-TYPE  368   65
   clus
vv  LRMP MUTATED LRMP WILD-TYPE
  0            7            368
  1            0             65
[1] 2 2
[1] FALSE
D2118V8, binary
                cls
clus               0   1
  LRMP MUTATED     3   4
  LRMP WILD-TYPE 222 260
[1] "tbl2"
                cls
clus             [,1] [,2]
  LRMP MUTATED      3    4
  LRMP WILD-TYPE  222  260
        clus
vv       LRMP MUTATED LRMP WILD-TYPE
  FEMALE            3            222
  MALE              4            260
[1] 2 2
[1] FALSE
D2118V9, binary
                cls
clus               0   1
  LRMP MUTATED     3   0
  LRMP WILD-TYPE 347  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  LRMP MUTATED      3    0
  LRMP WILD-TYPE  347   22
     clus
vv    LRMP MUTATED LRMP WILD-TYPE
  NO             3            347
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  LRMP MUTATED                      0                             3
  LRMP WILD-TYPE                  315                            44
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  LRMP MUTATED                       1                              1
  LRMP WILD-TYPE                   105                              9
D2118V10, multiclass
                                clus
vv                               LRMP MUTATED LRMP WILD-TYPE
  COLON ADENOCARCINOMA                      0            315
  COLON MUCINOUS ADENOCARCINOMA             3             44
  RECTAL ADENOCARCINOMA                     1            105
  RECTAL MUCINOUS ADENOCARCINOMA            1              9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  LRMP MUTATED     3   1   0   1
  LRMP WILD-TYPE 342   3  31  24
D2118V11, multiclass
    clus
vv   LRMP MUTATED LRMP WILD-TYPE
  R0            3            342
  R1            1              3
  R2            0             31
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2118V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  LRMP MUTATED                                  0     1
  LRMP WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  LRMP MUTATED                           0     2
  LRMP WILD-TYPE                        22   224
D2118V13, multiclass
                                  clus
vv                                 LRMP MUTATED LRMP WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       2            224
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2119) Variable = LSM14A MUTATION ANALYSIS
D2119V1, survival
                  sevent
clus2                0   1
  LSM14A MUTATED     9   1
  LSM14A WILD-TYPE 369  92
  LSM14A MUTATED LSM14A WILD-TYPE 
              10              461 
  LSM14A MUTATED LSM14A WILD-TYPE 
               1               92 
$`LSM14A MUTATED`
TCGA-AA-3516 TCGA-AA-3524 TCGA-AA-3864 TCGA-AA-A01R TCGA-CA-6717 TCGA-CK-5913 
       13.02        36.03        53.00        35.01        12.76        51.32 
TCGA-D5-6930 TCGA-F4-6856 TCGA-G4-6323 TCGA-AG-3892 
        1.51        35.31        13.78        13.02 

$`LSM14A WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        1.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3525 TCGA-AA-3526 
        1.02         9.07        24.03        37.05         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 
        0.99        31.07        31.07        30.05        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       31.00        38.07         1.02         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07        12.20        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 
        9.04         9.44        11.64         4.80        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 
       16.24        33.67        13.25         0.53        47.41       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
       63.62        61.91        36.00        22.09        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 
       19.99         1.02        17.95        36.95        17.03        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  LSM14A MUTATED LSM14A WILD-TYPE 
            1.51             0.00 
  LSM14A MUTATED LSM14A WILD-TYPE 
           53.00           148.01 
  LSM14A MUTATED LSM14A WILD-TYPE 
          24.395           20.190 
[1] "1.5 - 53.0 (24.4)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "2.1"
D2119V2, continuous
D2119V3, binary
                  cls
clus                 0   1
  LSM14A MUTATED    10   1
  LSM14A WILD-TYPE 356 118
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LSM14A MUTATED     10    1
  LSM14A WILD-TYPE  356  118
        clus
vv       LSM14A MUTATED LSM14A WILD-TYPE
  COLON              10              356
  RECTUM              1              118
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  LSM14A MUTATED         2        1        2         4         0         0
  LSM14A WILD-TYPE      89        0       30       134        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  LSM14A MUTATED           2          0          0          0        0
  LSM14A WILD-TYPE        22         11         59         42       48
                  vv
clus               STAGE IVA STAGE IVB
  LSM14A MUTATED           0         0
  LSM14A WILD-TYPE        18         1
D2119V4, multiclass
            clus
vv           LSM14A MUTATED LSM14A WILD-TYPE
  STAGE I                 2               89
  STAGE IA                1                0
  STAGE II                2               30
  STAGE IIA               4              134
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               2               22
  STAGE IIIA              0               11
  STAGE IIIB              0               59
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  LSM14A MUTATED     1   1   8   0
  LSM14A WILD-TYPE  16  91 321  50
D2119V5, multiclass
    clus
vv   LSM14A MUTATED LSM14A WILD-TYPE
  T1              1               16
  T2              1               91
  T3              8              321
  T4              0               50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  LSM14A MUTATED     9   0   2
  LSM14A WILD-TYPE 278 113  85
D2119V6, multiclass
    clus
vv   LSM14A MUTATED LSM14A WILD-TYPE
  N0              9              278
  N1              0              113
  N2              2               85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2119V7, binary
                  cls
clus                 0   1
  LSM14A MUTATED     9   0
  LSM14A WILD-TYPE 366  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LSM14A MUTATED      9    0
  LSM14A WILD-TYPE  366   65
   clus
vv  LSM14A MUTATED LSM14A WILD-TYPE
  0              9              366
  1              0               65
[1] 2 2
[1] FALSE
D2119V8, binary
                  cls
clus                 0   1
  LSM14A MUTATED     4   7
  LSM14A WILD-TYPE 221 257
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LSM14A MUTATED      4    7
  LSM14A WILD-TYPE  221  257
        clus
vv       LSM14A MUTATED LSM14A WILD-TYPE
  FEMALE              4              221
  MALE                7              257
[1] 2 2
[1] FALSE
D2119V9, binary
                  cls
clus                 0   1
  LSM14A MUTATED     8   1
  LSM14A WILD-TYPE 342  21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  LSM14A MUTATED      8    1
  LSM14A WILD-TYPE  342   21
     clus
vv    LSM14A MUTATED LSM14A WILD-TYPE
  NO               8              342
  YES              1               21
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  LSM14A MUTATED                      5                             5
  LSM14A WILD-TYPE                  310                            42
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  LSM14A MUTATED                       1                              0
  LSM14A WILD-TYPE                   105                             10
D2119V10, multiclass
                                clus
vv                               LSM14A MUTATED LSM14A WILD-TYPE
  COLON ADENOCARCINOMA                        5              310
  COLON MUCINOUS ADENOCARCINOMA               5               42
  RECTAL ADENOCARCINOMA                       1              105
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  LSM14A MUTATED     8   0   0   2
  LSM14A WILD-TYPE 337   4  31  23
D2119V11, multiclass
    clus
vv   LSM14A MUTATED LSM14A WILD-TYPE
  R0              8              337
  R1              0                4
  R2              0               31
  RX              2               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2119V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  LSM14A MUTATED                                  0     1
  LSM14A WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  LSM14A MUTATED                           1     3
  LSM14A WILD-TYPE                        21   223
D2119V13, multiclass
                                  clus
vv                                 LSM14A MUTATED LSM14A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                         3              223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2120) Variable = SMPDL3B MUTATION ANALYSIS
D2120V1, survival
                   sevent
clus2                 0   1
  SMPDL3B MUTATED     6   3
  SMPDL3B WILD-TYPE 372  90
  SMPDL3B MUTATED SMPDL3B WILD-TYPE 
                9               462 
  SMPDL3B MUTATED SMPDL3B WILD-TYPE 
                3                90 
$`SMPDL3B MUTATED`
TCGA-AA-3662 TCGA-AA-3864 TCGA-AA-3975 TCGA-AY-5543 TCGA-AZ-6598 TCGA-CK-5916 
        6.05        53.00        34.06        33.01        49.41        21.14 
TCGA-CM-5860 TCGA-F4-6570 TCGA-G4-6321 
       32.02         6.18        22.09 

$`SMPDL3B WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 
       32.05         0.99        31.07        31.07        30.05        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6197 
        0.20        14.50        27.09        16.31         0.95        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        88.21         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       51.32         9.99        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       22.98        30.08        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       35.74        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       63.62        61.91        36.00        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  SMPDL3B MUTATED SMPDL3B WILD-TYPE 
             6.05              0.00 
  SMPDL3B MUTATED SMPDL3B WILD-TYPE 
            53.00            148.01 
  SMPDL3B MUTATED SMPDL3B WILD-TYPE 
           32.020            20.035 
[1] "6.0 - 53.0 (32.0)"  "0.0 - 148.0 (20.0)"
[1] "hr=" "1.6"
D2120V2, continuous
D2120V3, binary
                   cls
clus                  0   1
  SMPDL3B MUTATED     9   0
  SMPDL3B WILD-TYPE 357 119
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SMPDL3B MUTATED      9    0
  SMPDL3B WILD-TYPE  357  119
        clus
vv       SMPDL3B MUTATED SMPDL3B WILD-TYPE
  COLON                9               357
  RECTUM               0               119
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SMPDL3B MUTATED         2        0        2         2         0         0
  SMPDL3B WILD-TYPE      89        1       30       136        10         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SMPDL3B MUTATED           1          0          0          0        1
  SMPDL3B WILD-TYPE        23         11         59         42       47
                   vv
clus                STAGE IVA STAGE IVB
  SMPDL3B MUTATED           1         0
  SMPDL3B WILD-TYPE        17         1
D2120V4, multiclass
            clus
vv           SMPDL3B MUTATED SMPDL3B WILD-TYPE
  STAGE I                  2                89
  STAGE IA                 0                 1
  STAGE II                 2                30
  STAGE IIA                2               136
  STAGE IIB                0                10
  STAGE IIC                0                 1
  STAGE III                1                23
  STAGE IIIA               0                11
  STAGE IIIB               0                59
  STAGE IIIC               0                42
  STAGE IV                 1                47
  STAGE IVA                1                17
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  SMPDL3B MUTATED     1   2   5   1
  SMPDL3B WILD-TYPE  16  90 324  49
D2120V5, multiclass
    clus
vv   SMPDL3B MUTATED SMPDL3B WILD-TYPE
  T1               1                16
  T2               2                90
  T3               5               324
  T4               1                49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  SMPDL3B MUTATED     6   2   1
  SMPDL3B WILD-TYPE 281 111  86
D2120V6, multiclass
    clus
vv   SMPDL3B MUTATED SMPDL3B WILD-TYPE
  N0               6               281
  N1               2               111
  N2               1                86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2120V7, binary
                   cls
clus                  0   1
  SMPDL3B MUTATED     5   2
  SMPDL3B WILD-TYPE 370  63
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SMPDL3B MUTATED      5    2
  SMPDL3B WILD-TYPE  370   63
   clus
vv  SMPDL3B MUTATED SMPDL3B WILD-TYPE
  0               5               370
  1               2                63
[1] 2 2
[1] FALSE
D2120V8, binary
                   cls
clus                  0   1
  SMPDL3B MUTATED     6   3
  SMPDL3B WILD-TYPE 219 261
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SMPDL3B MUTATED      6    3
  SMPDL3B WILD-TYPE  219  261
        clus
vv       SMPDL3B MUTATED SMPDL3B WILD-TYPE
  FEMALE               6               219
  MALE                 3               261
[1] 2 2
[1] FALSE
D2120V9, binary
                   cls
clus                  0   1
  SMPDL3B MUTATED     9   0
  SMPDL3B WILD-TYPE 341  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SMPDL3B MUTATED      9    0
  SMPDL3B WILD-TYPE  341   22
     clus
vv    SMPDL3B MUTATED SMPDL3B WILD-TYPE
  NO                9               341
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SMPDL3B MUTATED                      9                             0
  SMPDL3B WILD-TYPE                  306                            47
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SMPDL3B MUTATED                       0                              0
  SMPDL3B WILD-TYPE                   106                             10
D2120V10, multiclass
                                clus
vv                               SMPDL3B MUTATED SMPDL3B WILD-TYPE
  COLON ADENOCARCINOMA                         9               306
  COLON MUCINOUS ADENOCARCINOMA                0                47
  RECTAL ADENOCARCINOMA                        0               106
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  SMPDL3B MUTATED     6   0   1   1
  SMPDL3B WILD-TYPE 339   4  30  24
D2120V11, multiclass
    clus
vv   SMPDL3B MUTATED SMPDL3B WILD-TYPE
  R0               6               339
  R1               0                 4
  R2               1                30
  RX               1                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2120V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SMPDL3B MUTATED                                  0     0
  SMPDL3B WILD-TYPE                                1    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  SMPDL3B MUTATED                           1     5
  SMPDL3B WILD-TYPE                        21   221
D2120V13, multiclass
                                  clus
vv                                 SMPDL3B MUTATED SMPDL3B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                      1                21
  WHITE                                          5               221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2121) Variable = KIF26A MUTATION ANALYSIS
D2121V1, survival
                  sevent
clus2                0   1
  KIF26A MUTATED     7   2
  KIF26A WILD-TYPE 371  91
  KIF26A MUTATED KIF26A WILD-TYPE 
               9              462 
  KIF26A MUTATED KIF26A WILD-TYPE 
               2               91 
$`KIF26A MUTATED`
TCGA-A6-6780 TCGA-CK-5916 TCGA-D5-6540 TCGA-D5-6928 TCGA-D5-6930 TCGA-DM-A1DA 
       20.12        21.14        16.14        11.64         1.51         7.50 
TCGA-G4-6586 TCGA-G4-6588 TCGA-AG-A02N 
       35.80        26.17        61.97 

$`KIF26A WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
        4.80        17.13        12.49        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 
        4.41        12.43        14.30         9.04         9.44         4.80 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       13.78        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 
       10.98        49.97         1.94        38.96        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  KIF26A MUTATED KIF26A WILD-TYPE 
            1.51             0.00 
  KIF26A MUTATED KIF26A WILD-TYPE 
           61.97           148.01 
  KIF26A MUTATED KIF26A WILD-TYPE 
          20.120           20.235 
[1] "1.5 - 62.0 (20.1)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.3"
D2121V2, continuous
D2121V3, binary
                  cls
clus                 0   1
  KIF26A MUTATED     9   1
  KIF26A WILD-TYPE 357 118
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KIF26A MUTATED      9    1
  KIF26A WILD-TYPE  357  118
        clus
vv       KIF26A MUTATED KIF26A WILD-TYPE
  COLON               9              357
  RECTUM              1              118
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KIF26A MUTATED         2        0        1         5         1         0
  KIF26A WILD-TYPE      89        1       31       133         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIF26A MUTATED           0          0          0          1        0
  KIF26A WILD-TYPE        24         11         59         41       48
                  vv
clus               STAGE IVA STAGE IVB
  KIF26A MUTATED           0         0
  KIF26A WILD-TYPE        18         1
D2121V4, multiclass
            clus
vv           KIF26A MUTATED KIF26A WILD-TYPE
  STAGE I                 2               89
  STAGE IA                0                1
  STAGE II                1               31
  STAGE IIA               5              133
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              0               59
  STAGE IIIC              1               41
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  KIF26A MUTATED     1   1   7   1
  KIF26A WILD-TYPE  16  91 322  49
D2121V5, multiclass
    clus
vv   KIF26A MUTATED KIF26A WILD-TYPE
  T1              1               16
  T2              1               91
  T3              7              322
  T4              1               49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  KIF26A MUTATED     9   0   1
  KIF26A WILD-TYPE 278 113  86
D2121V6, multiclass
    clus
vv   KIF26A MUTATED KIF26A WILD-TYPE
  N0              9              278
  N1              0              113
  N2              1               86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2121V7, binary
                  cls
clus                 0   1
  KIF26A MUTATED     8   0
  KIF26A WILD-TYPE 367  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KIF26A MUTATED      8    0
  KIF26A WILD-TYPE  367   65
   clus
vv  KIF26A MUTATED KIF26A WILD-TYPE
  0              8              367
  1              0               65
[1] 2 2
[1] FALSE
D2121V8, binary
                  cls
clus                 0   1
  KIF26A MUTATED     5   5
  KIF26A WILD-TYPE 220 259
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KIF26A MUTATED      5    5
  KIF26A WILD-TYPE  220  259
        clus
vv       KIF26A MUTATED KIF26A WILD-TYPE
  FEMALE              5              220
  MALE                5              259
[1] 2 2
[1] FALSE
D2121V9, binary
                  cls
clus                 0   1
  KIF26A MUTATED     6   0
  KIF26A WILD-TYPE 344  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KIF26A MUTATED      6    0
  KIF26A WILD-TYPE  344   22
     clus
vv    KIF26A MUTATED KIF26A WILD-TYPE
  NO               6              344
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  KIF26A MUTATED                      5                             4
  KIF26A WILD-TYPE                  310                            43
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  KIF26A MUTATED                       1                              0
  KIF26A WILD-TYPE                   105                             10
D2121V10, multiclass
                                clus
vv                               KIF26A MUTATED KIF26A WILD-TYPE
  COLON ADENOCARCINOMA                        5              310
  COLON MUCINOUS ADENOCARCINOMA               4               43
  RECTAL ADENOCARCINOMA                       1              105
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  KIF26A MUTATED     6   0   0   2
  KIF26A WILD-TYPE 339   4  31  23
D2121V11, multiclass
    clus
vv   KIF26A MUTATED KIF26A WILD-TYPE
  R0              6              339
  R1              0                4
  R2              0               31
  RX              2               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2121V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KIF26A MUTATED                                  0     0
  KIF26A WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  KIF26A MUTATED                           0     9
  KIF26A WILD-TYPE                        22   217
D2121V13, multiclass
                                  clus
vv                                 KIF26A MUTATED KIF26A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         9              217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2122) Variable = KDELR2 MUTATION ANALYSIS
D2122V1, survival
                  sevent
clus2                0   1
  KDELR2 MUTATED     6   0
  KDELR2 WILD-TYPE 372  93
  KDELR2 MUTATED KDELR2 WILD-TYPE 
               6              465 
  KDELR2 MUTATED KDELR2 WILD-TYPE 
               0               93 
$`KDELR2 MUTATED`
TCGA-AA-3950 TCGA-AZ-5407 TCGA-CM-4752 TCGA-D5-6532 TCGA-G4-6317 TCGA-AG-A002 
       24.00        88.21        13.02        18.25        36.00        20.98 

$`KDELR2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 
        5.13       106.75        22.36        62.79        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       25.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  KDELR2 MUTATED KDELR2 WILD-TYPE 
           13.02             0.00 
  KDELR2 MUTATED KDELR2 WILD-TYPE 
           88.21           148.01 
  KDELR2 MUTATED KDELR2 WILD-TYPE 
           22.49            20.12 
[1] "13.0 - 88.2 (22.5)" "0.0 - 148.0 (20.1)"
[1] "hr="     "9100000"
D2122V2, continuous
D2122V3, binary
                  cls
clus                 0   1
  KDELR2 MUTATED     5   1
  KDELR2 WILD-TYPE 361 118
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KDELR2 MUTATED      5    1
  KDELR2 WILD-TYPE  361  118
        clus
vv       KDELR2 MUTATED KDELR2 WILD-TYPE
  COLON               5              361
  RECTUM              1              118
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KDELR2 MUTATED         2        0        0         3         0         0
  KDELR2 WILD-TYPE      89        1       32       135        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KDELR2 MUTATED           0          0          0          1        0
  KDELR2 WILD-TYPE        24         11         59         41       48
                  vv
clus               STAGE IVA STAGE IVB
  KDELR2 MUTATED           0         0
  KDELR2 WILD-TYPE        18         1
D2122V4, multiclass
            clus
vv           KDELR2 MUTATED KDELR2 WILD-TYPE
  STAGE I                 2               89
  STAGE IA                0                1
  STAGE II                0               32
  STAGE IIA               3              135
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              0               59
  STAGE IIIC              1               41
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  KDELR2 MUTATED     1   1   4   0
  KDELR2 WILD-TYPE  16  91 325  50
D2122V5, multiclass
    clus
vv   KDELR2 MUTATED KDELR2 WILD-TYPE
  T1              1               16
  T2              1               91
  T3              4              325
  T4              0               50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  KDELR2 MUTATED     5   0   1
  KDELR2 WILD-TYPE 282 113  86
D2122V6, multiclass
    clus
vv   KDELR2 MUTATED KDELR2 WILD-TYPE
  N0              5              282
  N1              0              113
  N2              1               86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2122V7, binary
                  cls
clus                 0   1
  KDELR2 MUTATED     5   0
  KDELR2 WILD-TYPE 370  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KDELR2 MUTATED      5    0
  KDELR2 WILD-TYPE  370   65
   clus
vv  KDELR2 MUTATED KDELR2 WILD-TYPE
  0              5              370
  1              0               65
[1] 2 2
[1] FALSE
D2122V8, binary
                  cls
clus                 0   1
  KDELR2 MUTATED     3   3
  KDELR2 WILD-TYPE 222 261
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KDELR2 MUTATED      3    3
  KDELR2 WILD-TYPE  222  261
        clus
vv       KDELR2 MUTATED KDELR2 WILD-TYPE
  FEMALE              3              222
  MALE                3              261
[1] 2 2
[1] FALSE
D2122V9, binary
                  cls
clus                 0   1
  KDELR2 MUTATED     6   0
  KDELR2 WILD-TYPE 344  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KDELR2 MUTATED      6    0
  KDELR2 WILD-TYPE  344   22
     clus
vv    KDELR2 MUTATED KDELR2 WILD-TYPE
  NO               6              344
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  KDELR2 MUTATED                      4                             1
  KDELR2 WILD-TYPE                  311                            46
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  KDELR2 MUTATED                       1                              0
  KDELR2 WILD-TYPE                   105                             10
D2122V10, multiclass
                                clus
vv                               KDELR2 MUTATED KDELR2 WILD-TYPE
  COLON ADENOCARCINOMA                        4              311
  COLON MUCINOUS ADENOCARCINOMA               1               46
  RECTAL ADENOCARCINOMA                       1              105
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  KDELR2 MUTATED     5   0   0   0
  KDELR2 WILD-TYPE 340   4  31  25
D2122V11, multiclass
    clus
vv   KDELR2 MUTATED KDELR2 WILD-TYPE
  R0              5              340
  R1              0                4
  R2              0               31
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2122V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KDELR2 MUTATED                                  0     0
  KDELR2 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  KDELR2 MUTATED                           1     3
  KDELR2 WILD-TYPE                        21   223
D2122V13, multiclass
                                  clus
vv                                 KDELR2 MUTATED KDELR2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                         3              223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2123) Variable = SIAH2 MUTATION ANALYSIS
D2123V1, survival
                 sevent
clus2               0   1
  SIAH2 MUTATED     7   2
  SIAH2 WILD-TYPE 371  91
  SIAH2 MUTATED SIAH2 WILD-TYPE 
              9             462 
  SIAH2 MUTATED SIAH2 WILD-TYPE 
              2              91 
$`SIAH2 MUTATED`
TCGA-AA-3510 TCGA-AA-3710 TCGA-AA-3877 TCGA-AA-A00N TCGA-AA-A010 TCGA-DM-A1HB 
       63.98        26.99        31.00         4.01        34.98       135.65 
TCGA-DM-A28F TCGA-DC-6682 TCGA-EI-6507 
       35.97         4.01        19.96 

$`SIAH2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        85.05        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 
       24.03        27.02        29.98        18.05         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
        7.50        44.32       131.51       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
      119.93        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       10.98        19.99         5.95         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       20.55        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  SIAH2 MUTATED SIAH2 WILD-TYPE 
           4.01            0.00 
  SIAH2 MUTATED SIAH2 WILD-TYPE 
         135.65          148.01 
  SIAH2 MUTATED SIAH2 WILD-TYPE 
         31.000          20.085 
[1] "4.0 - 135.7 (31.0)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.2"
D2123V2, continuous
D2123V3, binary
                 cls
clus                0   1
  SIAH2 MUTATED     7   2
  SIAH2 WILD-TYPE 359 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SIAH2 MUTATED      7    2
  SIAH2 WILD-TYPE  359  117
        clus
vv       SIAH2 MUTATED SIAH2 WILD-TYPE
  COLON              7             359
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SIAH2 MUTATED         1        0        1         3         2         0
  SIAH2 WILD-TYPE      90        1       31       135         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SIAH2 MUTATED           0          0          2          0        0         0
  SIAH2 WILD-TYPE        24         11         57         42       48        18
                 vv
clus              STAGE IVB
  SIAH2 MUTATED           0
  SIAH2 WILD-TYPE         1
D2123V4, multiclass
            clus
vv           SIAH2 MUTATED SIAH2 WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              3             135
  STAGE IIB              2               8
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             2              57
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  SIAH2 MUTATED     1   0   6   2
  SIAH2 WILD-TYPE  16  92 323  48
D2123V5, multiclass
    clus
vv   SIAH2 MUTATED SIAH2 WILD-TYPE
  T1             1              16
  T2             0              92
  T3             6             323
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  SIAH2 MUTATED     7   2   0
  SIAH2 WILD-TYPE 280 111  87
D2123V6, multiclass
    clus
vv   SIAH2 MUTATED SIAH2 WILD-TYPE
  N0             7             280
  N1             2             111
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2123V7, binary
                 cls
clus                0   1
  SIAH2 MUTATED     9   0
  SIAH2 WILD-TYPE 366  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SIAH2 MUTATED      9    0
  SIAH2 WILD-TYPE  366   65
   clus
vv  SIAH2 MUTATED SIAH2 WILD-TYPE
  0             9             366
  1             0              65
[1] 2 2
[1] FALSE
D2123V8, binary
                 cls
clus                0   1
  SIAH2 MUTATED     3   6
  SIAH2 WILD-TYPE 222 258
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SIAH2 MUTATED      3    6
  SIAH2 WILD-TYPE  222  258
        clus
vv       SIAH2 MUTATED SIAH2 WILD-TYPE
  FEMALE             3             222
  MALE               6             258
[1] 2 2
[1] FALSE
D2123V9, binary
                 cls
clus                0   1
  SIAH2 MUTATED     5   0
  SIAH2 WILD-TYPE 345  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SIAH2 MUTATED      5    0
  SIAH2 WILD-TYPE  345   22
     clus
vv    SIAH2 MUTATED SIAH2 WILD-TYPE
  NO              5             345
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SIAH2 MUTATED                      4                             2
  SIAH2 WILD-TYPE                  311                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SIAH2 MUTATED                       2                              0
  SIAH2 WILD-TYPE                   104                             10
D2123V10, multiclass
                                clus
vv                               SIAH2 MUTATED SIAH2 WILD-TYPE
  COLON ADENOCARCINOMA                       4             311
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  SIAH2 MUTATED     7   0   0   0
  SIAH2 WILD-TYPE 338   4  31  25
D2123V11, multiclass
    clus
vv   SIAH2 MUTATED SIAH2 WILD-TYPE
  R0             7             338
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2123V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SIAH2 MUTATED                                  0     0
  SIAH2 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  SIAH2 MUTATED                           0     4
  SIAH2 WILD-TYPE                        22   222
D2123V13, multiclass
                                  clus
vv                                 SIAH2 MUTATED SIAH2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        4             222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2124) Variable = C6ORF203 MUTATION ANALYSIS
D2124V1, survival
                    sevent
clus2                  0   1
  C6ORF203 MUTATED     5   0
  C6ORF203 WILD-TYPE 373  93
  C6ORF203 MUTATED C6ORF203 WILD-TYPE 
                 5                466 
  C6ORF203 MUTATED C6ORF203 WILD-TYPE 
                 0                 93 
$`C6ORF203 MUTATED`
TCGA-AA-3663 TCGA-AA-3864 TCGA-AA-A010 TCGA-CM-4743 TCGA-AG-A02N 
        6.97        53.00        34.98        23.05        61.97 

$`C6ORF203 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.05        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 
       32.05         0.99        31.07        31.07        30.05        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
        1.91       124.27        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
        1.94        38.96        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  C6ORF203 MUTATED C6ORF203 WILD-TYPE 
              6.97               0.00 
  C6ORF203 MUTATED C6ORF203 WILD-TYPE 
             61.97             148.01 
  C6ORF203 MUTATED C6ORF203 WILD-TYPE 
            34.980             20.085 
[1] "7.0 - 62.0 (35.0)"  "0.0 - 148.0 (20.1)"
[1] "hr="     "9200000"
D2124V2, continuous
D2124V3, binary
                    cls
clus                   0   1
  C6ORF203 MUTATED     4   1
  C6ORF203 WILD-TYPE 362 118
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C6ORF203 MUTATED      4    1
  C6ORF203 WILD-TYPE  362  118
        clus
vv       C6ORF203 MUTATED C6ORF203 WILD-TYPE
  COLON                 4                362
  RECTUM                1                118
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  C6ORF203 MUTATED         0        0        3         1         1         0
  C6ORF203 WILD-TYPE      91        1       29       137         9         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C6ORF203 MUTATED           0          0          0          0        0
  C6ORF203 WILD-TYPE        24         11         59         42       48
                    vv
clus                 STAGE IVA STAGE IVB
  C6ORF203 MUTATED           0         0
  C6ORF203 WILD-TYPE        18         1
D2124V4, multiclass
            clus
vv           C6ORF203 MUTATED C6ORF203 WILD-TYPE
  STAGE I                   0                 91
  STAGE IA                  0                  1
  STAGE II                  3                 29
  STAGE IIA                 1                137
  STAGE IIB                 1                  9
  STAGE IIC                 0                  1
  STAGE III                 0                 24
  STAGE IIIA                0                 11
  STAGE IIIB                0                 59
  STAGE IIIC                0                 42
  STAGE IV                  0                 48
  STAGE IVA                 0                 18
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  C6ORF203 MUTATED     0   0   4   1
  C6ORF203 WILD-TYPE  17  92 325  49
D2124V5, multiclass
    clus
vv   C6ORF203 MUTATED C6ORF203 WILD-TYPE
  T1                0                 17
  T2                0                 92
  T3                4                325
  T4                1                 49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  C6ORF203 MUTATED     5   0   0
  C6ORF203 WILD-TYPE 282 113  87
D2124V6, multiclass
    clus
vv   C6ORF203 MUTATED C6ORF203 WILD-TYPE
  N0                5                282
  N1                0                113
  N2                0                 87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2124V7, binary
                    cls
clus                   0   1
  C6ORF203 MUTATED     5   0
  C6ORF203 WILD-TYPE 370  65
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C6ORF203 MUTATED      5    0
  C6ORF203 WILD-TYPE  370   65
   clus
vv  C6ORF203 MUTATED C6ORF203 WILD-TYPE
  0                5                370
  1                0                 65
[1] 2 2
[1] FALSE
D2124V8, binary
                    cls
clus                   0   1
  C6ORF203 MUTATED     1   4
  C6ORF203 WILD-TYPE 224 260
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C6ORF203 MUTATED      1    4
  C6ORF203 WILD-TYPE  224  260
        clus
vv       C6ORF203 MUTATED C6ORF203 WILD-TYPE
  FEMALE                1                224
  MALE                  4                260
[1] 2 2
[1] FALSE
D2124V9, binary
                    cls
clus                   0   1
  C6ORF203 MUTATED     4   0
  C6ORF203 WILD-TYPE 346  22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C6ORF203 MUTATED      4    0
  C6ORF203 WILD-TYPE  346   22
     clus
vv    C6ORF203 MUTATED C6ORF203 WILD-TYPE
  NO                 4                346
  YES                0                 22
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  C6ORF203 MUTATED                      4                             0
  C6ORF203 WILD-TYPE                  311                            47
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  C6ORF203 MUTATED                       1                              0
  C6ORF203 WILD-TYPE                   105                             10
D2124V10, multiclass
                                clus
vv                               C6ORF203 MUTATED C6ORF203 WILD-TYPE
  COLON ADENOCARCINOMA                          4                311
  COLON MUCINOUS ADENOCARCINOMA                 0                 47
  RECTAL ADENOCARCINOMA                         1                105
  RECTAL MUCINOUS ADENOCARCINOMA                0                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  C6ORF203 MUTATED     5   0   0   0
  C6ORF203 WILD-TYPE 340   4  31  25
D2124V11, multiclass
    clus
vv   C6ORF203 MUTATED C6ORF203 WILD-TYPE
  R0                5                340
  R1                0                  4
  R2                0                 31
  RX                0                 25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2124V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C6ORF203 MUTATED                                  0     0
  C6ORF203 WILD-TYPE                                1    11
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  C6ORF203 MUTATED                           0     1
  C6ORF203 WILD-TYPE                        22   225
D2124V13, multiclass
[1] "Remove cluster labels:" "C6ORF203 MUTATED"      
clus
  C6ORF203 MUTATED C6ORF203 WILD-TYPE 
                 1                259 
        TCGA-A6-2671         TCGA-A6-2672         TCGA-A6-2674 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-A6-2676         TCGA-A6-2677         TCGA-A6-2678 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-A6-2683         TCGA-A6-3807         TCGA-A6-3808 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-A6-3809         TCGA-A6-3810         TCGA-A6-4105 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-A6-5656         TCGA-A6-5657         TCGA-A6-5659 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-A6-5660         TCGA-A6-5661         TCGA-A6-5662 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-A6-5664         TCGA-A6-5665         TCGA-A6-5666 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-A6-6137         TCGA-A6-6138         TCGA-A6-6141 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-A6-6142         TCGA-A6-6648         TCGA-A6-6649 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-A6-6651         TCGA-A6-6652         TCGA-A6-6653 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-A6-6654         TCGA-A6-6780         TCGA-A6-6781 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-A6-6782         TCGA-AD-5900         TCGA-AD-6548 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-AD-6888         TCGA-AD-6889         TCGA-AD-6890 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-AD-6895         TCGA-AD-6899         TCGA-AD-6901 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-AD-6963         TCGA-AD-6964         TCGA-AD-6965 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-AU-3779         TCGA-AU-6004         TCGA-AY-4070 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-AY-4071         TCGA-AY-5543         TCGA-AY-6196 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-AY-6197         TCGA-AY-6386         TCGA-AZ-4315 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-AZ-4323         TCGA-AZ-4616         TCGA-AZ-4681 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-AZ-4682         TCGA-AZ-5403         TCGA-AZ-5407 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-AZ-6598         TCGA-AZ-6599         TCGA-AZ-6600 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-AZ-6601         TCGA-AZ-6603         TCGA-AZ-6605 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-AZ-6606         TCGA-AZ-6607         TCGA-AZ-6608 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-CA-5254         TCGA-CA-5255         TCGA-CA-5796 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-CA-5797         TCGA-CA-6715         TCGA-CA-6716 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-CA-6717         TCGA-CA-6718         TCGA-CA-6719 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-CK-4947         TCGA-CK-4948         TCGA-CK-4950 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-CK-4952         TCGA-CK-5912         TCGA-CK-5913 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-CK-5914         TCGA-CK-5915         TCGA-CK-5916 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-CK-6746         TCGA-CK-6747         TCGA-CK-6748 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-CK-6751         TCGA-CM-4744         TCGA-CM-4746 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-CM-4747         TCGA-CM-4752         TCGA-CM-5341 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-CM-5344         TCGA-CM-5348         TCGA-CM-5349 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-CM-5860         TCGA-CM-5861         TCGA-CM-5862 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-CM-5863         TCGA-CM-5864         TCGA-CM-5868 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-CM-6161         TCGA-CM-6162         TCGA-CM-6163 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-CM-6164         TCGA-CM-6165         TCGA-CM-6166 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-CM-6167         TCGA-CM-6168         TCGA-CM-6169 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-CM-6170         TCGA-CM-6171         TCGA-CM-6172 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-CM-6674         TCGA-CM-6675         TCGA-CM-6676 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-CM-6677         TCGA-CM-6678         TCGA-CM-6679 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-CM-6680         TCGA-D5-5537         TCGA-D5-5538 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-D5-5539         TCGA-D5-5540         TCGA-D5-5541 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-D5-6529         TCGA-D5-6532         TCGA-D5-6533 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-D5-6534         TCGA-D5-6535         TCGA-D5-6536 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-D5-6537         TCGA-D5-6538         TCGA-D5-6539 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-D5-6540         TCGA-D5-6541         TCGA-D5-6898 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-D5-6920         TCGA-D5-6922         TCGA-D5-6923 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-D5-6924         TCGA-D5-6926         TCGA-D5-6927 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-D5-6928         TCGA-D5-6929         TCGA-D5-6930 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-D5-6931         TCGA-D5-6932         TCGA-D5-7000 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-DM-A0X9         TCGA-DM-A0XD         TCGA-DM-A0XF 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-DM-A1D0         TCGA-DM-A1D4         TCGA-DM-A1D6 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-DM-A1D7         TCGA-DM-A1D8         TCGA-DM-A1D9 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-DM-A1DA         TCGA-DM-A1DB         TCGA-DM-A1HA 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-DM-A1HB         TCGA-DM-A282         TCGA-DM-A285 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-DM-A28C         TCGA-DM-A28E         TCGA-DM-A28F 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-DM-A28G         TCGA-DM-A28H         TCGA-DM-A28K 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-F4-6459         TCGA-F4-6460         TCGA-F4-6569 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-F4-6570         TCGA-F4-6703         TCGA-F4-6704 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-F4-6805         TCGA-F4-6806         TCGA-F4-6807 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-F4-6808         TCGA-F4-6809         TCGA-F4-6854 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-F4-6855         TCGA-F4-6856         TCGA-G4-6293 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-G4-6299         TCGA-G4-6303         TCGA-G4-6304 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-G4-6306         TCGA-G4-6307         TCGA-G4-6309 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-G4-6310         TCGA-G4-6315         TCGA-G4-6317 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-G4-6321         TCGA-G4-6323         TCGA-G4-6586 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-G4-6588         TCGA-G4-6625         TCGA-G4-6626 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-G4-6628         TCGA-AF-2687         TCGA-AF-2689 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3913         TCGA-AF-4110 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-AF-5654         TCGA-AF-6136         TCGA-AF-6655 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-AF-6672         TCGA-AH-6544         TCGA-AH-6547 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-AH-6549         TCGA-AH-6643         TCGA-AH-6644 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-CI-6619         TCGA-CI-6620         TCGA-CI-6621 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6624         TCGA-CL-5917 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-CL-5918         TCGA-DC-5337         TCGA-DC-5869 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-DC-6155         TCGA-DC-6157         TCGA-DC-6158 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-DC-6160         TCGA-DC-6681         TCGA-DC-6682 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-DC-6683         TCGA-DT-5265         TCGA-DY-A0XA 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DF 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-DY-A1DG         TCGA-DY-A1H8         TCGA-EF-5830 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-EI-6506         TCGA-EI-6507         TCGA-EI-6508 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-EI-6510         TCGA-F5-6464         TCGA-F5-6465 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-F5-6571         TCGA-F5-6702         TCGA-F5-6811 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-F5-6812         TCGA-F5-6813         TCGA-G5-6235 
"C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" "C6ORF203 WILD-TYPE" 
        TCGA-G5-6641 
"C6ORF203 WILD-TYPE" 

Clustering(2125) Variable = GPR158 MUTATION ANALYSIS
D2125V1, survival
                  sevent
clus2                0   1
  GPR158 MUTATED    20   8
  GPR158 WILD-TYPE 358  85
  GPR158 MUTATED GPR158 WILD-TYPE 
              28              443 
  GPR158 MUTATED GPR158 WILD-TYPE 
               8               85 
$`GPR158 MUTATED`
TCGA-A6-5661 TCGA-A6-5666 TCGA-A6-6781 TCGA-AA-3663 TCGA-AA-3715 TCGA-AA-3819 
       33.53        32.71        19.66         6.97        19.04        25.02 
TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01R TCGA-AD-6895 TCGA-AD-6964 
       25.02         4.01        34.98        35.01         0.72        10.88 
TCGA-AU-6004 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6603 TCGA-CA-6717 TCGA-CA-6718 
       27.09        88.21        49.41        29.56        12.76        10.06 
TCGA-CK-5916 TCGA-CM-4743 TCGA-CM-6674 TCGA-D5-6533 TCGA-F4-6570 TCGA-AG-3892 
       21.14        23.05        12.95         1.32         6.18        13.02 
TCGA-AG-3893 TCGA-AG-A002 TCGA-AG-A00C TCGA-DY-A0XA 
       35.01        20.98         6.02       126.44 

$`GPR158 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       22.06        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02        78.08         6.05        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       26.99        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       31.00        38.07         1.02         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 
        5.79        22.42        27.42         0.20        14.50        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6599 TCGA-AZ-6600 
        5.13       106.75        22.36        62.79         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
      100.01         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 
        3.06         3.25         3.29         0.07        12.20        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 
        9.99        82.95         1.91       124.27        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       18.25        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 
       98.24         8.61        31.96        35.74        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.95        36.95        17.03        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       17.03        13.94        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD 
        5.95         4.01         5.03         5.29        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  GPR158 MUTATED GPR158 WILD-TYPE 
            0.72             0.00 
  GPR158 MUTATED GPR158 WILD-TYPE 
          126.44           148.01 
  GPR158 MUTATED GPR158 WILD-TYPE 
           21.06            20.12 
[1] "0.7 - 126.4 (21.1)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.6"
D2125V2, continuous
D2125V3, binary
                  cls
clus                 0   1
  GPR158 MUTATED    24   5
  GPR158 WILD-TYPE 342 114
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR158 MUTATED     24    5
  GPR158 WILD-TYPE  342  114
        clus
vv       GPR158 MUTATED GPR158 WILD-TYPE
  COLON              24              342
  RECTUM              5              114
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GPR158 MUTATED         5        0        3         8         2         1
  GPR158 WILD-TYPE      86        1       29       130         8         0
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GPR158 MUTATED           1          0          3          1        1
  GPR158 WILD-TYPE        23         11         56         41       47
                  vv
clus               STAGE IVA STAGE IVB
  GPR158 MUTATED           0         0
  GPR158 WILD-TYPE        18         1
D2125V4, multiclass
            clus
vv           GPR158 MUTATED GPR158 WILD-TYPE
  STAGE I                 5               86
  STAGE IA                0                1
  STAGE II                3               29
  STAGE IIA               8              130
  STAGE IIB               2                8
  STAGE IIC               1                0
  STAGE III               1               23
  STAGE IIIA              0               11
  STAGE IIIB              3               56
  STAGE IIIC              1               41
  STAGE IV                1               47
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  GPR158 MUTATED     3   4  16   6
  GPR158 WILD-TYPE  14  88 313  44
D2125V5, multiclass
    clus
vv   GPR158 MUTATED GPR158 WILD-TYPE
  T1              3               14
  T2              4               88
  T3             16              313
  T4              6               44
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  GPR158 MUTATED    21   5   3
  GPR158 WILD-TYPE 266 108  84
D2125V6, multiclass
    clus
vv   GPR158 MUTATED GPR158 WILD-TYPE
  N0             21              266
  N1              5              108
  N2              3               84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2125V7, binary
                  cls
clus                 0   1
  GPR158 MUTATED    22   1
  GPR158 WILD-TYPE 353  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR158 MUTATED     22    1
  GPR158 WILD-TYPE  353   64
   clus
vv  GPR158 MUTATED GPR158 WILD-TYPE
  0             22              353
  1              1               64
[1] 2 2
[1] FALSE
D2125V8, binary
                  cls
clus                 0   1
  GPR158 MUTATED    14  15
  GPR158 WILD-TYPE 211 249
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR158 MUTATED     14   15
  GPR158 WILD-TYPE  211  249
        clus
vv       GPR158 MUTATED GPR158 WILD-TYPE
  FEMALE             14              211
  MALE               15              249
[1] 2 2
[1] FALSE
D2125V9, binary
                  cls
clus                 0   1
  GPR158 MUTATED    21   2
  GPR158 WILD-TYPE 329  20
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR158 MUTATED     21    2
  GPR158 WILD-TYPE  329   20
     clus
vv    GPR158 MUTATED GPR158 WILD-TYPE
  NO              21              329
  YES              2               20
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  GPR158 MUTATED                     20                             4
  GPR158 WILD-TYPE                  295                            43
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  GPR158 MUTATED                       5                              0
  GPR158 WILD-TYPE                   101                             10
D2125V10, multiclass
                                clus
vv                               GPR158 MUTATED GPR158 WILD-TYPE
  COLON ADENOCARCINOMA                       20              295
  COLON MUCINOUS ADENOCARCINOMA               4               43
  RECTAL ADENOCARCINOMA                       5              101
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  GPR158 MUTATED    17   0   1   3
  GPR158 WILD-TYPE 328   4  30  22
D2125V11, multiclass
    clus
vv   GPR158 MUTATED GPR158 WILD-TYPE
  R0             17              328
  R1              0                4
  R2              1               30
  RX              3               22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2125V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GPR158 MUTATED                                  0     2
  GPR158 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  GPR158 MUTATED                           1    14
  GPR158 WILD-TYPE                        21   212
D2125V13, multiclass
                                  clus
vv                                 GPR158 MUTATED GPR158 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                9
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                        14              212
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2126) Variable = CSNK1E MUTATION ANALYSIS
D2126V1, survival
                  sevent
clus2                0   1
  CSNK1E MUTATED     7   2
  CSNK1E WILD-TYPE 371  91
  CSNK1E MUTATED CSNK1E WILD-TYPE 
               9              462 
  CSNK1E MUTATED CSNK1E WILD-TYPE 
               2               91 
$`CSNK1E MUTATED`
TCGA-A6-3809 TCGA-A6-5657 TCGA-AA-3492 TCGA-AY-6197 TCGA-AZ-6601 TCGA-CA-6716 
       32.75        31.63         3.02        21.44       100.01        12.20 
TCGA-CM-6674 TCGA-D5-6931 TCGA-AG-A002 
       12.95        12.00        20.98 

$`CSNK1E WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       30.44        29.19        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       19.66        20.28         7.04         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 
       62.79        88.21        49.41         6.77        12.10        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       14.04        11.01        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6932 TCGA-D5-7000 
        9.44        11.64         4.80         1.51        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  CSNK1E MUTATED CSNK1E WILD-TYPE 
            3.02             0.00 
  CSNK1E MUTATED CSNK1E WILD-TYPE 
          100.01           148.01 
  CSNK1E MUTATED CSNK1E WILD-TYPE 
          20.980           20.155 
[1] "3.0 - 100.0 (21.0)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.1"
D2126V2, continuous
D2126V3, binary
                  cls
clus                 0   1
  CSNK1E MUTATED     8   1
  CSNK1E WILD-TYPE 358 118
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CSNK1E MUTATED      8    1
  CSNK1E WILD-TYPE  358  118
        clus
vv       CSNK1E MUTATED CSNK1E WILD-TYPE
  COLON               8              358
  RECTUM              1              118
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CSNK1E MUTATED         1        0        2         3         1         0
  CSNK1E WILD-TYPE      90        1       30       135         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CSNK1E MUTATED           0          0          1          1        0
  CSNK1E WILD-TYPE        24         11         58         41       48
                  vv
clus               STAGE IVA STAGE IVB
  CSNK1E MUTATED           0         0
  CSNK1E WILD-TYPE        18         1
D2126V4, multiclass
            clus
vv           CSNK1E MUTATED CSNK1E WILD-TYPE
  STAGE I                 1               90
  STAGE IA                0                1
  STAGE II                2               30
  STAGE IIA               3              135
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              1               58
  STAGE IIIC              1               41
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  CSNK1E MUTATED     0   1   6   2
  CSNK1E WILD-TYPE  17  91 323  48
D2126V5, multiclass
    clus
vv   CSNK1E MUTATED CSNK1E WILD-TYPE
  T1              0               17
  T2              1               91
  T3              6              323
  T4              2               48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  CSNK1E MUTATED     7   1   1
  CSNK1E WILD-TYPE 280 112  86
D2126V6, multiclass
    clus
vv   CSNK1E MUTATED CSNK1E WILD-TYPE
  N0              7              280
  N1              1              112
  N2              1               86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2126V7, binary
                  cls
clus                 0   1
  CSNK1E MUTATED     8   0
  CSNK1E WILD-TYPE 367  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CSNK1E MUTATED      8    0
  CSNK1E WILD-TYPE  367   65
   clus
vv  CSNK1E MUTATED CSNK1E WILD-TYPE
  0              8              367
  1              0               65
[1] 2 2
[1] FALSE
D2126V8, binary
                  cls
clus                 0   1
  CSNK1E MUTATED     2   7
  CSNK1E WILD-TYPE 223 257
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CSNK1E MUTATED      2    7
  CSNK1E WILD-TYPE  223  257
        clus
vv       CSNK1E MUTATED CSNK1E WILD-TYPE
  FEMALE              2              223
  MALE                7              257
[1] 2 2
[1] FALSE
D2126V9, binary
                  cls
clus                 0   1
  CSNK1E MUTATED     9   0
  CSNK1E WILD-TYPE 341  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CSNK1E MUTATED      9    0
  CSNK1E WILD-TYPE  341   22
     clus
vv    CSNK1E MUTATED CSNK1E WILD-TYPE
  NO               9              341
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CSNK1E MUTATED                      7                             1
  CSNK1E WILD-TYPE                  308                            46
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CSNK1E MUTATED                       1                              0
  CSNK1E WILD-TYPE                   105                             10
D2126V10, multiclass
                                clus
vv                               CSNK1E MUTATED CSNK1E WILD-TYPE
  COLON ADENOCARCINOMA                        7              308
  COLON MUCINOUS ADENOCARCINOMA               1               46
  RECTAL ADENOCARCINOMA                       1              105
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  CSNK1E MUTATED     7   0   0   1
  CSNK1E WILD-TYPE 338   4  31  24
D2126V11, multiclass
    clus
vv   CSNK1E MUTATED CSNK1E WILD-TYPE
  R0              7              338
  R1              0                4
  R2              0               31
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2126V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CSNK1E MUTATED                                  0     1
  CSNK1E WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  CSNK1E MUTATED                           1     5
  CSNK1E WILD-TYPE                        21   221
D2126V13, multiclass
                                  clus
vv                                 CSNK1E MUTATED CSNK1E WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                         5              221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2127) Variable = RNF103 MUTATION ANALYSIS
D2127V1, survival
                  sevent
clus2                0   1
  RNF103 MUTATED     8   0
  RNF103 WILD-TYPE 370  93
  RNF103 MUTATED RNF103 WILD-TYPE 
               8              463 
  RNF103 MUTATED RNF103 WILD-TYPE 
               0               93 
$`RNF103 MUTATED`
TCGA-A6-6780 TCGA-AA-3947 TCGA-AA-3977 TCGA-AA-A00R TCGA-CA-6717 TCGA-G4-6628 
       20.12        33.01        25.02         0.99        12.76        79.69 
TCGA-AG-A002 TCGA-AG-A02N 
       20.98        61.97 

$`RNF103 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
        2.01        12.99        24.00        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       27.02        42.02        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07        12.20        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X 
       64.01        10.98        49.97         1.94        38.96        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  RNF103 MUTATED RNF103 WILD-TYPE 
            0.99             0.00 
  RNF103 MUTATED RNF103 WILD-TYPE 
           79.69           148.01 
  RNF103 MUTATED RNF103 WILD-TYPE 
           23.00            20.05 
[1] "1.0 - 79.7 (23.0)"  "0.0 - 148.0 (20.1)"
[1] "hr="     "9200000"
D2127V2, continuous
D2127V3, binary
                  cls
clus                 0   1
  RNF103 MUTATED     7   2
  RNF103 WILD-TYPE 359 117
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF103 MUTATED      7    2
  RNF103 WILD-TYPE  359  117
        clus
vv       RNF103 MUTATED RNF103 WILD-TYPE
  COLON               7              359
  RECTUM              2              117
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RNF103 MUTATED         3        0        1         3         1         0
  RNF103 WILD-TYPE      88        1       31       135         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RNF103 MUTATED           0          0          0          0        0
  RNF103 WILD-TYPE        24         11         59         42       48
                  vv
clus               STAGE IVA STAGE IVB
  RNF103 MUTATED           0         0
  RNF103 WILD-TYPE        18         1
D2127V4, multiclass
            clus
vv           RNF103 MUTATED RNF103 WILD-TYPE
  STAGE I                 3               88
  STAGE IA                0                1
  STAGE II                1               31
  STAGE IIA               3              135
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              0               59
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  RNF103 MUTATED     0   4   4   1
  RNF103 WILD-TYPE  17  88 325  49
D2127V5, multiclass
    clus
vv   RNF103 MUTATED RNF103 WILD-TYPE
  T1              0               17
  T2              4               88
  T3              4              325
  T4              1               49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  RNF103 MUTATED     9   0   0
  RNF103 WILD-TYPE 278 113  87
D2127V6, multiclass
    clus
vv   RNF103 MUTATED RNF103 WILD-TYPE
  N0              9              278
  N1              0              113
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2127V7, binary
                  cls
clus                 0   1
  RNF103 MUTATED     7   0
  RNF103 WILD-TYPE 368  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF103 MUTATED      7    0
  RNF103 WILD-TYPE  368   65
   clus
vv  RNF103 MUTATED RNF103 WILD-TYPE
  0              7              368
  1              0               65
[1] 2 2
[1] FALSE
D2127V8, binary
                  cls
clus                 0   1
  RNF103 MUTATED     3   6
  RNF103 WILD-TYPE 222 258
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF103 MUTATED      3    6
  RNF103 WILD-TYPE  222  258
        clus
vv       RNF103 MUTATED RNF103 WILD-TYPE
  FEMALE              3              222
  MALE                6              258
[1] 2 2
[1] FALSE
D2127V9, binary
                  cls
clus                 0   1
  RNF103 MUTATED     6   0
  RNF103 WILD-TYPE 344  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF103 MUTATED      6    0
  RNF103 WILD-TYPE  344   22
     clus
vv    RNF103 MUTATED RNF103 WILD-TYPE
  NO               6              344
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  RNF103 MUTATED                      4                             3
  RNF103 WILD-TYPE                  311                            44
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  RNF103 MUTATED                       2                              0
  RNF103 WILD-TYPE                   104                             10
D2127V10, multiclass
                                clus
vv                               RNF103 MUTATED RNF103 WILD-TYPE
  COLON ADENOCARCINOMA                        4              311
  COLON MUCINOUS ADENOCARCINOMA               3               44
  RECTAL ADENOCARCINOMA                       2              104
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  RNF103 MUTATED     6   0   0   1
  RNF103 WILD-TYPE 339   4  31  24
D2127V11, multiclass
    clus
vv   RNF103 MUTATED RNF103 WILD-TYPE
  R0              6              339
  R1              0                4
  R2              0               31
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2127V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RNF103 MUTATED                                  0     1
  RNF103 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  RNF103 MUTATED                           0     2
  RNF103 WILD-TYPE                        22   224
D2127V13, multiclass
                                  clus
vv                                 RNF103 MUTATED RNF103 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         2              224
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2128) Variable = CEBPA MUTATION ANALYSIS
D2128V1, survival
                 sevent
clus2               0   1
  CEBPA MUTATED    14   3
  CEBPA WILD-TYPE 364  90
  CEBPA MUTATED CEBPA WILD-TYPE 
             17             454 
  CEBPA MUTATED CEBPA WILD-TYPE 
              3              90 
$`CEBPA MUTATED`
TCGA-A6-4105 TCGA-A6-5661 TCGA-A6-6648 TCGA-AA-3663 TCGA-AU-6004 TCGA-AZ-6598 
       14.53        33.53        25.18         6.97        27.09        49.41 
TCGA-AZ-6601 TCGA-CM-4743 TCGA-CM-5349 TCGA-CM-6163 TCGA-CM-6164 TCGA-D5-6532 
      100.01        23.05        30.08         2.96        29.03        18.25 
TCGA-DM-A1HB TCGA-G4-6306 TCGA-G4-6315 TCGA-DC-5337 TCGA-F5-6465 
      135.65        44.68        61.91        15.02        49.51 

$`CEBPA WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 
       16.57        34.65        33.34        32.75        36.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       31.63        30.44        29.19        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6649 
       32.71        27.09        22.52         8.38        25.08        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02        78.08         6.05        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       14.50        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       88.21         6.77        12.10        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 
       21.14        82.95         1.91       124.27        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5860 
       25.02        13.02        29.06        22.03        22.98        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       12.00        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6534 
       19.59        56.09        55.92        20.19         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
       44.32       131.51       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 
      133.18        74.56        65.85        53.62        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       63.62        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       20.91        18.28         9.96        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  CEBPA MUTATED CEBPA WILD-TYPE 
           2.96            0.00 
  CEBPA MUTATED CEBPA WILD-TYPE 
         135.65          148.01 
  CEBPA MUTATED CEBPA WILD-TYPE 
          29.03           20.02 
[1] "3.0 - 135.7 (29.0)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.7"
D2128V2, continuous
D2128V3, binary
                 cls
clus                0   1
  CEBPA MUTATED    15   2
  CEBPA WILD-TYPE 351 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CEBPA MUTATED     15    2
  CEBPA WILD-TYPE  351  117
        clus
vv       CEBPA MUTATED CEBPA WILD-TYPE
  COLON             15             351
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CEBPA MUTATED         3        0        3         8         0         0
  CEBPA WILD-TYPE      88        1       29       130        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CEBPA MUTATED           0          0          1          0        1         1
  CEBPA WILD-TYPE        24         11         58         42       47        17
                 vv
clus              STAGE IVB
  CEBPA MUTATED           0
  CEBPA WILD-TYPE         1
D2128V4, multiclass
            clus
vv           CEBPA MUTATED CEBPA WILD-TYPE
  STAGE I                3              88
  STAGE IA               0               1
  STAGE II               3              29
  STAGE IIA              8             130
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             0              42
  STAGE IV               1              47
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CEBPA MUTATED     2   2  13   0
  CEBPA WILD-TYPE  15  90 316  50
D2128V5, multiclass
    clus
vv   CEBPA MUTATED CEBPA WILD-TYPE
  T1             2              15
  T2             2              90
  T3            13             316
  T4             0              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  CEBPA MUTATED    15   2   0
  CEBPA WILD-TYPE 272 111  87
D2128V6, multiclass
    clus
vv   CEBPA MUTATED CEBPA WILD-TYPE
  N0            15             272
  N1             2             111
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2128V7, binary
                 cls
clus                0   1
  CEBPA MUTATED    14   2
  CEBPA WILD-TYPE 361  63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CEBPA MUTATED     14    2
  CEBPA WILD-TYPE  361   63
   clus
vv  CEBPA MUTATED CEBPA WILD-TYPE
  0            14             361
  1             2              63
[1] 2 2
[1] FALSE
D2128V8, binary
                 cls
clus                0   1
  CEBPA MUTATED     6  11
  CEBPA WILD-TYPE 219 253
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CEBPA MUTATED      6   11
  CEBPA WILD-TYPE  219  253
        clus
vv       CEBPA MUTATED CEBPA WILD-TYPE
  FEMALE             6             219
  MALE              11             253
[1] 2 2
[1] FALSE
D2128V9, binary
                 cls
clus                0   1
  CEBPA MUTATED    15   0
  CEBPA WILD-TYPE 335  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CEBPA MUTATED     15    0
  CEBPA WILD-TYPE  335   22
     clus
vv    CEBPA MUTATED CEBPA WILD-TYPE
  NO             15             335
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CEBPA MUTATED                     14                             0
  CEBPA WILD-TYPE                  301                            47
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CEBPA MUTATED                       2                              0
  CEBPA WILD-TYPE                   104                             10
D2128V10, multiclass
                                clus
vv                               CEBPA MUTATED CEBPA WILD-TYPE
  COLON ADENOCARCINOMA                      14             301
  COLON MUCINOUS ADENOCARCINOMA              0              47
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  CEBPA MUTATED    12   0   0   0
  CEBPA WILD-TYPE 333   4  31  25
D2128V11, multiclass
    clus
vv   CEBPA MUTATED CEBPA WILD-TYPE
  R0            12             333
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2128V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CEBPA MUTATED                                  0     0
  CEBPA WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CEBPA MUTATED                           1    15
  CEBPA WILD-TYPE                        21   211
D2128V13, multiclass
                                  clus
vv                                 CEBPA MUTATED CEBPA WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                       15             211
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2129) Variable = YWHAH MUTATION ANALYSIS
D2129V1, survival
                 sevent
clus2               0   1
  YWHAH MUTATED     4   1
  YWHAH WILD-TYPE 374  92
  YWHAH MUTATED YWHAH WILD-TYPE 
              5             466 
  YWHAH MUTATED YWHAH WILD-TYPE 
              1              92 
$`YWHAH MUTATED`
TCGA-AZ-6599 TCGA-CM-6166 TCGA-F4-6808 TCGA-AG-3892 TCGA-DY-A0XA 
        6.77        21.99        33.67        13.02       126.44 

$`YWHAH WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       49.41        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 
       19.99         1.02        17.95        36.95        17.03        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        4.01         5.03         5.29        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  YWHAH MUTATED YWHAH WILD-TYPE 
           6.77            0.00 
  YWHAH MUTATED YWHAH WILD-TYPE 
         126.44          148.01 
  YWHAH MUTATED YWHAH WILD-TYPE 
         21.990          20.155 
[1] "6.8 - 126.4 (22.0)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.3"
D2129V2, continuous
D2129V3, binary
                 cls
clus                0   1
  YWHAH MUTATED     3   2
  YWHAH WILD-TYPE 363 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  YWHAH MUTATED      3    2
  YWHAH WILD-TYPE  363  117
        clus
vv       YWHAH MUTATED YWHAH WILD-TYPE
  COLON              3             363
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  YWHAH MUTATED         4        0        0         1         0         0
  YWHAH WILD-TYPE      87        1       32       137        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  YWHAH MUTATED           0          0          0          0        0         0
  YWHAH WILD-TYPE        24         11         59         42       48        18
                 vv
clus              STAGE IVB
  YWHAH MUTATED           0
  YWHAH WILD-TYPE         1
D2129V4, multiclass
            clus
vv           YWHAH MUTATED YWHAH WILD-TYPE
  STAGE I                4              87
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              1             137
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  YWHAH MUTATED     2   2   1   0
  YWHAH WILD-TYPE  15  90 328  50
D2129V5, multiclass
    clus
vv   YWHAH MUTATED YWHAH WILD-TYPE
  T1             2              15
  T2             2              90
  T3             1             328
  T4             0              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  YWHAH MUTATED     5   0   0
  YWHAH WILD-TYPE 282 113  87
D2129V6, multiclass
    clus
vv   YWHAH MUTATED YWHAH WILD-TYPE
  N0             5             282
  N1             0             113
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2129V7, binary
                 cls
clus                0   1
  YWHAH MUTATED     4   0
  YWHAH WILD-TYPE 371  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  YWHAH MUTATED      4    0
  YWHAH WILD-TYPE  371   65
   clus
vv  YWHAH MUTATED YWHAH WILD-TYPE
  0             4             371
  1             0              65
[1] 2 2
[1] FALSE
D2129V8, binary
                 cls
clus                0   1
  YWHAH MUTATED     4   1
  YWHAH WILD-TYPE 221 263
[1] "tbl2"
                 cls
clus              [,1] [,2]
  YWHAH MUTATED      4    1
  YWHAH WILD-TYPE  221  263
        clus
vv       YWHAH MUTATED YWHAH WILD-TYPE
  FEMALE             4             221
  MALE               1             263
[1] 2 2
[1] FALSE
D2129V9, binary
                 cls
clus                0   1
  YWHAH MUTATED     4   0
  YWHAH WILD-TYPE 346  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  YWHAH MUTATED      4    0
  YWHAH WILD-TYPE  346   22
     clus
vv    YWHAH MUTATED YWHAH WILD-TYPE
  NO              4             346
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  YWHAH MUTATED                      3                             0
  YWHAH WILD-TYPE                  312                            47
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  YWHAH MUTATED                       2                              0
  YWHAH WILD-TYPE                   104                             10
D2129V10, multiclass
                                clus
vv                               YWHAH MUTATED YWHAH WILD-TYPE
  COLON ADENOCARCINOMA                       3             312
  COLON MUCINOUS ADENOCARCINOMA              0              47
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  YWHAH MUTATED     3   0   0   0
  YWHAH WILD-TYPE 342   4  31  25
D2129V11, multiclass
    clus
vv   YWHAH MUTATED YWHAH WILD-TYPE
  R0             3             342
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2129V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  YWHAH MUTATED                                  0     0
  YWHAH WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  YWHAH MUTATED                           0     4
  YWHAH WILD-TYPE                        22   222
D2129V13, multiclass
                                  clus
vv                                 YWHAH MUTATED YWHAH WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        4             222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2130) Variable = OR5A1 MUTATION ANALYSIS
D2130V1, survival
                 sevent
clus2               0   1
  OR5A1 MUTATED     4   1
  OR5A1 WILD-TYPE 374  92
  OR5A1 MUTATED OR5A1 WILD-TYPE 
              5             466 
  OR5A1 MUTATED OR5A1 WILD-TYPE 
              1              92 
$`OR5A1 MUTATED`
TCGA-AZ-4315 TCGA-D5-6539 TCGA-DM-A1HB TCGA-DM-A28G TCGA-F5-6811 
       58.39        12.49       135.65        60.79        32.19 

$`OR5A1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
       16.31         0.95        33.01        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
       17.85         4.80        17.13        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28H 
      139.17         6.12        81.37       119.93        35.97       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  OR5A1 MUTATED OR5A1 WILD-TYPE 
          12.49            0.00 
  OR5A1 MUTATED OR5A1 WILD-TYPE 
         135.65          148.01 
  OR5A1 MUTATED OR5A1 WILD-TYPE 
         58.390          20.085 
[1] "12.5 - 135.7 (58.4)" "0.0 - 148.0 (20.1)" 
[1] "hr=" "2.1"
D2130V2, continuous
D2130V3, binary
                 cls
clus                0   1
  OR5A1 MUTATED     4   1
  OR5A1 WILD-TYPE 362 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR5A1 MUTATED      4    1
  OR5A1 WILD-TYPE  362  118
        clus
vv       OR5A1 MUTATED OR5A1 WILD-TYPE
  COLON              4             362
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  OR5A1 MUTATED         0        0        0         3         0         0
  OR5A1 WILD-TYPE      91        1       32       135        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  OR5A1 MUTATED           0          1          1          0        0         0
  OR5A1 WILD-TYPE        24         10         58         42       48        18
                 vv
clus              STAGE IVB
  OR5A1 MUTATED           0
  OR5A1 WILD-TYPE         1
D2130V4, multiclass
            clus
vv           OR5A1 MUTATED OR5A1 WILD-TYPE
  STAGE I                0              91
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              3             135
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             1              10
  STAGE IIIB             1              58
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  OR5A1 MUTATED     0   0   5   0
  OR5A1 WILD-TYPE  17  92 324  50
D2130V5, multiclass
    clus
vv   OR5A1 MUTATED OR5A1 WILD-TYPE
  T1             0              17
  T2             0              92
  T3             5             324
  T4             0              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  OR5A1 MUTATED     4   1   0
  OR5A1 WILD-TYPE 283 112  87
D2130V6, multiclass
    clus
vv   OR5A1 MUTATED OR5A1 WILD-TYPE
  N0             4             283
  N1             1             112
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2130V7, binary
                 cls
clus                0   1
  OR5A1 MUTATED     5   0
  OR5A1 WILD-TYPE 370  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR5A1 MUTATED      5    0
  OR5A1 WILD-TYPE  370   65
   clus
vv  OR5A1 MUTATED OR5A1 WILD-TYPE
  0             5             370
  1             0              65
[1] 2 2
[1] FALSE
D2130V8, binary
                 cls
clus                0   1
  OR5A1 MUTATED     2   3
  OR5A1 WILD-TYPE 223 261
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR5A1 MUTATED      2    3
  OR5A1 WILD-TYPE  223  261
        clus
vv       OR5A1 MUTATED OR5A1 WILD-TYPE
  FEMALE             2             223
  MALE               3             261
[1] 2 2
[1] FALSE
D2130V9, binary
                 cls
clus                0   1
  OR5A1 MUTATED     3   0
  OR5A1 WILD-TYPE 347  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR5A1 MUTATED      3    0
  OR5A1 WILD-TYPE  347   22
     clus
vv    OR5A1 MUTATED OR5A1 WILD-TYPE
  NO              3             347
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  OR5A1 MUTATED                      3                             0
  OR5A1 WILD-TYPE                  312                            47
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  OR5A1 MUTATED                       1                              0
  OR5A1 WILD-TYPE                   105                             10
D2130V10, multiclass
                                clus
vv                               OR5A1 MUTATED OR5A1 WILD-TYPE
  COLON ADENOCARCINOMA                       3             312
  COLON MUCINOUS ADENOCARCINOMA              0              47
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  OR5A1 MUTATED     2   0   0   0
  OR5A1 WILD-TYPE 343   4  31  25
D2130V11, multiclass
[1] "Remove cluster labels:" "OR5A1 MUTATED"         
clus
  OR5A1 MUTATED OR5A1 WILD-TYPE 
              2             403 
     TCGA-A6-2671      TCGA-A6-2672      TCGA-A6-2674      TCGA-A6-2676 
"OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" 
     TCGA-A6-2677      TCGA-A6-2678      TCGA-A6-2683      TCGA-A6-3807 
"OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" 
     TCGA-A6-3808      TCGA-A6-3809      TCGA-A6-3810      TCGA-A6-5657 
"OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" 
     TCGA-A6-5659      TCGA-A6-5661      TCGA-A6-5665      TCGA-A6-6781 
"OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" 
     TCGA-AA-3489      TCGA-AA-3492      TCGA-AA-3496      TCGA-AA-3502 
"OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" 
     TCGA-AA-3510      TCGA-AA-3511      TCGA-AA-3514      TCGA-AA-3517 
"OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" 
     TCGA-AA-3518      TCGA-AA-3519      TCGA-AA-3520      TCGA-AA-3521 
"OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" 
     TCGA-AA-3522      TCGA-AA-3524      TCGA-AA-3525      TCGA-AA-3526 
"OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" 
     TCGA-AA-3527      TCGA-AA-3529      TCGA-AA-3530      TCGA-AA-3531 
"OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" 
     TCGA-AA-3532      TCGA-AA-3534      TCGA-AA-3538      TCGA-AA-3542 
"OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" 
     TCGA-AA-3543      TCGA-AA-3544      TCGA-AA-3548      TCGA-AA-3549 
"OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" 
     TCGA-AA-3552      TCGA-AA-3553      TCGA-AA-3554      TCGA-AA-3555 
"OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" 
     TCGA-AA-3556      TCGA-AA-3558      TCGA-AA-3560      TCGA-AA-3561 
"OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" 
     TCGA-AA-3562      TCGA-AA-3655      TCGA-AA-3660      TCGA-AA-3662 
"OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" 
     TCGA-AA-3663      TCGA-AA-3664      TCGA-AA-3666      TCGA-AA-3667 
"OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" 
     TCGA-AA-3672      TCGA-AA-3673      TCGA-AA-3678      TCGA-AA-3679 
"OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" 
     TCGA-AA-3680      TCGA-AA-3681      TCGA-AA-3684      TCGA-AA-3685 
"OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" 
     TCGA-AA-3688      TCGA-AA-3692      TCGA-AA-3693      TCGA-AA-3695 
"OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" 
     TCGA-AA-3696      TCGA-AA-3697      TCGA-AA-3710      TCGA-AA-3712 
"OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" 
     TCGA-AA-3713      TCGA-AA-3715      TCGA-AA-3811      TCGA-AA-3812 
"OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" 
     TCGA-AA-3814      TCGA-AA-3815      TCGA-AA-3818      TCGA-AA-3819 
"OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" 
     TCGA-AA-3821      TCGA-AA-3831      TCGA-AA-3833      TCGA-AA-3837 
"OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" 
     TCGA-AA-3842      TCGA-AA-3844      TCGA-AA-3845      TCGA-AA-3846 
"OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" 
     TCGA-AA-3848      TCGA-AA-3850      TCGA-AA-3851      TCGA-AA-3852 
"OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" 
     TCGA-AA-3854      TCGA-AA-3855      TCGA-AA-3856      TCGA-AA-3858 
"OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" 
     TCGA-AA-3860      TCGA-AA-3861      TCGA-AA-3864      TCGA-AA-3866 
"OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" 
     TCGA-AA-3867      TCGA-AA-3869      TCGA-AA-3870      TCGA-AA-3872 
"OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" 
     TCGA-AA-3875      TCGA-AA-3877      TCGA-AA-3930      TCGA-AA-3939 
"OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" 
     TCGA-AA-3941      TCGA-AA-3947      TCGA-AA-3949      TCGA-AA-3950 
"OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" 
     TCGA-AA-3952      TCGA-AA-3955      TCGA-AA-3956      TCGA-AA-3968 
"OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" 
     TCGA-AA-3971      TCGA-AA-3972      TCGA-AA-3973      TCGA-AA-3975 
"OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" 
     TCGA-AA-3976      TCGA-AA-3979      TCGA-AA-3984      TCGA-AA-3986 
"OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" 
     TCGA-AA-3989      TCGA-AA-3994      TCGA-AA-A004      TCGA-AA-A00A 
"OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" 
     TCGA-AA-A00D      TCGA-AA-A00E      TCGA-AA-A00F      TCGA-AA-A00J 
"OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" 
     TCGA-AA-A00K      TCGA-AA-A00L      TCGA-AA-A00N      TCGA-AA-A00O 
"OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" 
     TCGA-AA-A00Q      TCGA-AA-A00R      TCGA-AA-A00U      TCGA-AA-A00W 
"OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" 
     TCGA-AA-A00Z      TCGA-AA-A010      TCGA-AA-A017      TCGA-AA-A01D 
"OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" 
     TCGA-AA-A01F      TCGA-AA-A01G      TCGA-AA-A01I      TCGA-AA-A01K 
"OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" 
     TCGA-AA-A01P      TCGA-AA-A01Q      TCGA-AA-A01R      TCGA-AA-A01S 
"OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" 
     TCGA-AA-A01T      TCGA-AA-A01V      TCGA-AA-A01X      TCGA-AA-A01Z 
"OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" 
     TCGA-AA-A022      TCGA-AA-A024      TCGA-AA-A029      TCGA-AA-A02F 
"OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" 
     TCGA-AA-A02H      TCGA-AA-A02J      TCGA-AA-A02K      TCGA-AA-A02O 
"OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" 
     TCGA-AA-A02W      TCGA-AA-A02Y      TCGA-AA-A03F      TCGA-AA-A03J 
"OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" 
     TCGA-AD-5900      TCGA-AD-6548      TCGA-AD-6888      TCGA-AU-3779 
"OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" 
     TCGA-AU-6004      TCGA-AY-4070      TCGA-AY-4071      TCGA-AY-5543 
"OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" 
     TCGA-AY-6196      TCGA-AY-6197      TCGA-AY-6386      TCGA-AZ-4681 
"OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" 
     TCGA-AZ-4682      TCGA-CA-5254      TCGA-CA-5255      TCGA-CA-5796 
"OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" 
     TCGA-CA-5797      TCGA-CA-6715      TCGA-CA-6716      TCGA-CA-6717 
"OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" 
     TCGA-CA-6718      TCGA-CA-6719      TCGA-CK-4947      TCGA-CK-4948 
"OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" 
     TCGA-CK-4950      TCGA-CK-4952      TCGA-CK-5912      TCGA-CK-5913 
"OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" 
     TCGA-CK-5914      TCGA-CK-5915      TCGA-CK-5916      TCGA-CK-6746 
"OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" 
     TCGA-CK-6747      TCGA-CK-6748      TCGA-CK-6751      TCGA-CM-4743 
"OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" 
     TCGA-CM-4744      TCGA-CM-4746      TCGA-CM-4747      TCGA-CM-4752 
"OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" 
     TCGA-CM-5341      TCGA-CM-5344      TCGA-CM-5348      TCGA-CM-5349 
"OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" 
     TCGA-CM-5860      TCGA-CM-5861      TCGA-CM-5862      TCGA-CM-5863 
"OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" 
     TCGA-CM-5864      TCGA-CM-5868      TCGA-CM-6161      TCGA-CM-6162 
"OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" 
     TCGA-CM-6163      TCGA-CM-6164      TCGA-CM-6165      TCGA-CM-6166 
"OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" 
     TCGA-CM-6167      TCGA-CM-6168      TCGA-CM-6169      TCGA-CM-6170 
"OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" 
     TCGA-CM-6171      TCGA-CM-6172      TCGA-CM-6674      TCGA-CM-6675 
"OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" 
     TCGA-CM-6676      TCGA-CM-6677      TCGA-CM-6678      TCGA-CM-6679 
"OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" 
     TCGA-CM-6680      TCGA-D5-5537      TCGA-D5-5538      TCGA-D5-5539 
"OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" 
     TCGA-D5-5540      TCGA-D5-5541      TCGA-D5-6529      TCGA-D5-6532 
"OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" 
     TCGA-D5-6533      TCGA-D5-6534      TCGA-D5-6535      TCGA-D5-6536 
"OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" 
     TCGA-D5-6537      TCGA-D5-6538      TCGA-D5-6540      TCGA-D5-6541 
"OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" 
     TCGA-D5-6898      TCGA-D5-6920      TCGA-D5-6922      TCGA-D5-6923 
"OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" 
     TCGA-D5-6924      TCGA-D5-6926      TCGA-D5-6927      TCGA-D5-6928 
"OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" 
     TCGA-D5-6929      TCGA-D5-6930      TCGA-D5-6931      TCGA-D5-6932 
"OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" 
     TCGA-D5-7000      TCGA-F4-6459      TCGA-F4-6460      TCGA-F4-6569 
"OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" 
     TCGA-F4-6570      TCGA-F4-6703      TCGA-F4-6704      TCGA-F4-6805 
"OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" 
     TCGA-F4-6806      TCGA-F4-6807      TCGA-F4-6808      TCGA-F4-6809 
"OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" 
     TCGA-F4-6854      TCGA-F4-6855      TCGA-F4-6856      TCGA-G4-6293 
"OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" 
     TCGA-G4-6299      TCGA-G4-6303      TCGA-G4-6304      TCGA-G4-6306 
"OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" 
     TCGA-G4-6307      TCGA-G4-6309      TCGA-G4-6310      TCGA-G4-6315 
"OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" 
     TCGA-G4-6317      TCGA-G4-6321      TCGA-G4-6323      TCGA-G4-6586 
"OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" 
     TCGA-G4-6588      TCGA-G4-6625      TCGA-G4-6626      TCGA-G4-6628 
"OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" 
     TCGA-AF-2687      TCGA-AF-2689      TCGA-AF-2691      TCGA-AF-2692 
"OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" 
     TCGA-AF-3400      TCGA-AF-3913      TCGA-AF-4110      TCGA-AF-5654 
"OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" 
     TCGA-AF-6655      TCGA-AG-3574      TCGA-AG-3575      TCGA-AG-3578 
"OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" 
     TCGA-AG-3580      TCGA-AG-3581      TCGA-AG-3582      TCGA-AG-3583 
"OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" 
     TCGA-AG-3584      TCGA-AG-3586      TCGA-AG-3587      TCGA-AG-3593 
"OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" 
     TCGA-AG-3594      TCGA-AG-3598      TCGA-AG-3599      TCGA-AG-3600 
"OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" 
     TCGA-AG-3601      TCGA-AG-3602      TCGA-AG-3605      TCGA-AG-3608 
"OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" 
     TCGA-AG-3609      TCGA-AG-3611      TCGA-AG-3612      TCGA-AG-3726 
"OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" 
     TCGA-AG-3727      TCGA-AG-3731      TCGA-AG-3732      TCGA-AG-3742 
"OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" 
     TCGA-AG-3878      TCGA-AG-3882      TCGA-AG-3883      TCGA-AG-3885 
"OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" 
     TCGA-AG-3887      TCGA-AG-3890      TCGA-AG-3892      TCGA-AG-3893 
"OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" 
     TCGA-AG-3894      TCGA-AG-3896      TCGA-AG-3898      TCGA-AG-3901 
"OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" 
     TCGA-AG-3902      TCGA-AG-3909      TCGA-AG-3999      TCGA-AG-4001 
"OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" 
     TCGA-AG-4005      TCGA-AG-4007      TCGA-AG-4008      TCGA-AG-4015 
"OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" 
     TCGA-AG-A002      TCGA-AG-A008      TCGA-AG-A00C      TCGA-AG-A00H 
"OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" 
     TCGA-AG-A00Y      TCGA-AG-A011      TCGA-AG-A014      TCGA-AG-A015 
"OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" 
     TCGA-AG-A016      TCGA-AG-A01L      TCGA-AG-A01W      TCGA-AG-A01Y 
"OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" 
     TCGA-AG-A020      TCGA-AG-A025      TCGA-AG-A026      TCGA-AG-A02G 
"OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" 
     TCGA-AG-A02N      TCGA-AG-A02X      TCGA-AG-A032      TCGA-AG-A036 
"OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" 
     TCGA-AH-6549      TCGA-AH-6643      TCGA-CL-5917      TCGA-CL-5918 
"OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" 
     TCGA-DC-5337      TCGA-DC-5869      TCGA-DC-6155      TCGA-DC-6157 
"OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" 
     TCGA-DC-6158      TCGA-DC-6160      TCGA-DC-6681      TCGA-DC-6682 
"OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" 
     TCGA-DC-6683      TCGA-DT-5265      TCGA-EF-5830      TCGA-EI-6506 
"OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" 
     TCGA-EI-6507      TCGA-EI-6508      TCGA-EI-6510      TCGA-F5-6464 
"OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" 
     TCGA-F5-6465      TCGA-F5-6571      TCGA-F5-6702      TCGA-F5-6812 
"OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" 
     TCGA-F5-6813      TCGA-G5-6235      TCGA-G5-6641 
"OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" "OR5A1 WILD-TYPE" 
D2130V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OR5A1 MUTATED                                  0     0
  OR5A1 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  OR5A1 MUTATED                           0     5
  OR5A1 WILD-TYPE                        22   221
D2130V13, multiclass
                                  clus
vv                                 OR5A1 MUTATED OR5A1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        5             221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2131) Variable = IP6K3 MUTATION ANALYSIS
D2131V1, survival
                 sevent
clus2               0   1
  IP6K3 MUTATED     8   1
  IP6K3 WILD-TYPE 370  92
  IP6K3 MUTATED IP6K3 WILD-TYPE 
              9             462 
  IP6K3 MUTATED IP6K3 WILD-TYPE 
              1              92 
$`IP6K3 MUTATED`
TCGA-AA-3525 TCGA-AA-3867 TCGA-AA-3950 TCGA-AA-A010 TCGA-AD-6964 TCGA-CA-6717 
        8.05        24.03        24.00        34.98        10.88        12.76 
TCGA-D5-6927 TCGA-AG-3732 TCGA-AG-A002 
        9.44        32.98        20.98 

$`IP6K3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       17.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 
       12.99        24.00        33.01        26.01         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AU-3779 
        0.72         5.79        22.42        27.42         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07        12.20        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.04        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 
       19.99         7.99         0.99        37.02         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  IP6K3 MUTATED IP6K3 WILD-TYPE 
           8.05            0.00 
  IP6K3 MUTATED IP6K3 WILD-TYPE 
          34.98          148.01 
  IP6K3 MUTATED IP6K3 WILD-TYPE 
         20.980          20.155 
[1] "8.1 - 35.0 (21.0)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.3"
D2131V2, continuous
D2131V3, binary
                 cls
clus                0   1
  IP6K3 MUTATED     7   2
  IP6K3 WILD-TYPE 359 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IP6K3 MUTATED      7    2
  IP6K3 WILD-TYPE  359  117
        clus
vv       IP6K3 MUTATED IP6K3 WILD-TYPE
  COLON              7             359
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  IP6K3 MUTATED         2        0        0         3         1         0
  IP6K3 WILD-TYPE      89        1       32       135         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  IP6K3 MUTATED           0          0          1          0        1         0
  IP6K3 WILD-TYPE        24         11         58         42       47        18
                 vv
clus              STAGE IVB
  IP6K3 MUTATED           0
  IP6K3 WILD-TYPE         1
D2131V4, multiclass
            clus
vv           IP6K3 MUTATED IP6K3 WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              3             135
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             0              42
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  IP6K3 MUTATED     0   2   5   2
  IP6K3 WILD-TYPE  17  90 324  48
D2131V5, multiclass
    clus
vv   IP6K3 MUTATED IP6K3 WILD-TYPE
  T1             0              17
  T2             2              90
  T3             5             324
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  IP6K3 MUTATED     6   1   2
  IP6K3 WILD-TYPE 281 112  85
D2131V6, multiclass
    clus
vv   IP6K3 MUTATED IP6K3 WILD-TYPE
  N0             6             281
  N1             1             112
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2131V7, binary
                 cls
clus                0   1
  IP6K3 MUTATED     7   1
  IP6K3 WILD-TYPE 368  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IP6K3 MUTATED      7    1
  IP6K3 WILD-TYPE  368   64
   clus
vv  IP6K3 MUTATED IP6K3 WILD-TYPE
  0             7             368
  1             1              64
[1] 2 2
[1] FALSE
D2131V8, binary
                 cls
clus                0   1
  IP6K3 MUTATED     3   6
  IP6K3 WILD-TYPE 222 258
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IP6K3 MUTATED      3    6
  IP6K3 WILD-TYPE  222  258
        clus
vv       IP6K3 MUTATED IP6K3 WILD-TYPE
  FEMALE             3             222
  MALE               6             258
[1] 2 2
[1] FALSE
D2131V9, binary
                 cls
clus                0   1
  IP6K3 MUTATED     9   0
  IP6K3 WILD-TYPE 341  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IP6K3 MUTATED      9    0
  IP6K3 WILD-TYPE  341   22
     clus
vv    IP6K3 MUTATED IP6K3 WILD-TYPE
  NO              9             341
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  IP6K3 MUTATED                      5                             2
  IP6K3 WILD-TYPE                  310                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  IP6K3 MUTATED                       2                              0
  IP6K3 WILD-TYPE                   104                             10
D2131V10, multiclass
                                clus
vv                               IP6K3 MUTATED IP6K3 WILD-TYPE
  COLON ADENOCARCINOMA                       5             310
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  IP6K3 MUTATED     6   0   1   1
  IP6K3 WILD-TYPE 339   4  30  24
D2131V11, multiclass
    clus
vv   IP6K3 MUTATED IP6K3 WILD-TYPE
  R0             6             339
  R1             0               4
  R2             1              30
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2131V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  IP6K3 MUTATED                                  0     1
  IP6K3 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  IP6K3 MUTATED                           0     2
  IP6K3 WILD-TYPE                        22   224
D2131V13, multiclass
                                  clus
vv                                 IP6K3 MUTATED IP6K3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        2             224
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2132) Variable = CLSTN1 MUTATION ANALYSIS
D2132V1, survival
                  sevent
clus2                0   1
  CLSTN1 MUTATED    12   4
  CLSTN1 WILD-TYPE 366  89
  CLSTN1 MUTATED CLSTN1 WILD-TYPE 
              16              455 
  CLSTN1 MUTATED CLSTN1 WILD-TYPE 
               4               89 
$`CLSTN1 MUTATED`
TCGA-AA-3672 TCGA-AA-3811 TCGA-AA-3877 TCGA-AA-3949 TCGA-AA-A010 TCGA-AD-5900 
        0.92        10.06        31.00        26.01        34.98         0.07 
TCGA-AZ-4315 TCGA-AZ-6601 TCGA-D5-6535 TCGA-D5-6928 TCGA-D5-6930 TCGA-DM-A0XF 
       58.39       100.01        15.12        11.64         1.51        38.20 
TCGA-DM-A1HB TCGA-F4-6570 TCGA-G4-6309 TCGA-AG-A02N 
      135.65         6.18        85.48        61.97 

$`CLSTN1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
        6.05         6.97        54.02         2.01        14.01        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 
       24.03        27.02        29.98        18.05         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        33.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
       16.31         0.95        33.01        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77        12.10        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 
       20.19        18.25         1.32        43.27        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 
        4.41        12.43        14.30         9.04         9.44         4.80 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A1D0 
       12.00        11.38        10.26       119.70        24.43       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
       44.32       131.51       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       35.74        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 
       74.56        65.85        53.62        44.68        55.04        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
       49.97         1.94        38.96        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  CLSTN1 MUTATED CLSTN1 WILD-TYPE 
            0.07             0.00 
  CLSTN1 MUTATED CLSTN1 WILD-TYPE 
          135.65           148.01 
  CLSTN1 MUTATED CLSTN1 WILD-TYPE 
          28.505           20.120 
[1] "0.1 - 135.7 (28.5)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.1"
D2132V2, continuous
D2132V3, binary
                  cls
clus                 0   1
  CLSTN1 MUTATED    15   1
  CLSTN1 WILD-TYPE 351 118
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CLSTN1 MUTATED     15    1
  CLSTN1 WILD-TYPE  351  118
        clus
vv       CLSTN1 MUTATED CLSTN1 WILD-TYPE
  COLON              15              351
  RECTUM              1              118
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CLSTN1 MUTATED         2        0        2         4         1         0
  CLSTN1 WILD-TYPE      89        1       30       134         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CLSTN1 MUTATED           2          0          4          1        0
  CLSTN1 WILD-TYPE        22         11         55         41       48
                  vv
clus               STAGE IVA STAGE IVB
  CLSTN1 MUTATED           0         0
  CLSTN1 WILD-TYPE        18         1
D2132V4, multiclass
            clus
vv           CLSTN1 MUTATED CLSTN1 WILD-TYPE
  STAGE I                 2               89
  STAGE IA                0                1
  STAGE II                2               30
  STAGE IIA               4              134
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               2               22
  STAGE IIIA              0               11
  STAGE IIIB              4               55
  STAGE IIIC              1               41
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  CLSTN1 MUTATED     1   1  13   1
  CLSTN1 WILD-TYPE  16  91 316  49
D2132V5, multiclass
    clus
vv   CLSTN1 MUTATED CLSTN1 WILD-TYPE
  T1              1               16
  T2              1               91
  T3             13              316
  T4              1               49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  CLSTN1 MUTATED     9   5   2
  CLSTN1 WILD-TYPE 278 108  85
D2132V6, multiclass
    clus
vv   CLSTN1 MUTATED CLSTN1 WILD-TYPE
  N0              9              278
  N1              5              108
  N2              2               85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2132V7, binary
                  cls
clus                 0   1
  CLSTN1 MUTATED    14   0
  CLSTN1 WILD-TYPE 361  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CLSTN1 MUTATED     14    0
  CLSTN1 WILD-TYPE  361   65
   clus
vv  CLSTN1 MUTATED CLSTN1 WILD-TYPE
  0             14              361
  1              0               65
[1] 2 2
[1] FALSE
D2132V8, binary
                  cls
clus                 0   1
  CLSTN1 MUTATED     9   7
  CLSTN1 WILD-TYPE 216 257
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CLSTN1 MUTATED      9    7
  CLSTN1 WILD-TYPE  216  257
        clus
vv       CLSTN1 MUTATED CLSTN1 WILD-TYPE
  FEMALE              9              216
  MALE                7              257
[1] 2 2
[1] FALSE
D2132V9, binary
                  cls
clus                 0   1
  CLSTN1 MUTATED    11   0
  CLSTN1 WILD-TYPE 339  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CLSTN1 MUTATED     11    0
  CLSTN1 WILD-TYPE  339   22
     clus
vv    CLSTN1 MUTATED CLSTN1 WILD-TYPE
  NO              11              339
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CLSTN1 MUTATED                      8                             5
  CLSTN1 WILD-TYPE                  307                            42
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CLSTN1 MUTATED                       1                              0
  CLSTN1 WILD-TYPE                   105                             10
D2132V10, multiclass
                                clus
vv                               CLSTN1 MUTATED CLSTN1 WILD-TYPE
  COLON ADENOCARCINOMA                        8              307
  COLON MUCINOUS ADENOCARCINOMA               5               42
  RECTAL ADENOCARCINOMA                       1              105
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  CLSTN1 MUTATED    12   0   0   1
  CLSTN1 WILD-TYPE 333   4  31  24
D2132V11, multiclass
    clus
vv   CLSTN1 MUTATED CLSTN1 WILD-TYPE
  R0             12              333
  R1              0                4
  R2              0               31
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2132V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CLSTN1 MUTATED                                  0     0
  CLSTN1 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  CLSTN1 MUTATED                           1     9
  CLSTN1 WILD-TYPE                        21   217
D2132V13, multiclass
                                  clus
vv                                 CLSTN1 MUTATED CLSTN1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                         9              217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2133) Variable = EPC2 MUTATION ANALYSIS
D2133V1, survival
                sevent
clus2              0   1
  EPC2 MUTATED     5   5
  EPC2 WILD-TYPE 373  88
  EPC2 MUTATED EPC2 WILD-TYPE 
            10            461 
  EPC2 MUTATED EPC2 WILD-TYPE 
             5             88 
$`EPC2 MUTATED`
TCGA-A6-5661 TCGA-A6-6781 TCGA-AA-3492 TCGA-AA-A00N TCGA-AD-5900 TCGA-CK-5913 
       33.53        19.66         3.02         4.01         0.07        51.32 
TCGA-CK-5916 TCGA-DM-A1DB TCGA-F4-6806 TCGA-DY-A1DG 
       21.14        44.32        41.42        51.48 

$`EPC2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.12        20.28         7.04         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
       40.96        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
        9.99        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HA 
       49.91        13.32        12.59       140.38         7.50       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6807 TCGA-F4-6808 
        6.18        47.87         1.55        34.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       57.24        24.13        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  EPC2 MUTATED EPC2 WILD-TYPE 
          0.07           0.00 
  EPC2 MUTATED EPC2 WILD-TYPE 
         51.48         148.01 
  EPC2 MUTATED EPC2 WILD-TYPE 
        27.335         20.120 
[1] "0.1 - 51.5 (27.3)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "2.4"
D2133V2, continuous
D2133V3, binary
                cls
clus               0   1
  EPC2 MUTATED     9   1
  EPC2 WILD-TYPE 357 118
[1] "tbl2"
                cls
clus             [,1] [,2]
  EPC2 MUTATED      9    1
  EPC2 WILD-TYPE  357  118
        clus
vv       EPC2 MUTATED EPC2 WILD-TYPE
  COLON             9            357
  RECTUM            1            118
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  EPC2 MUTATED         3        0        1         3         1         0
  EPC2 WILD-TYPE      88        1       31       135         9         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  EPC2 MUTATED           0          0          0          1        0         1
  EPC2 WILD-TYPE        24         11         59         41       48        17
                vv
clus             STAGE IVB
  EPC2 MUTATED           0
  EPC2 WILD-TYPE         1
D2133V4, multiclass
            clus
vv           EPC2 MUTATED EPC2 WILD-TYPE
  STAGE I               3             88
  STAGE IA              0              1
  STAGE II              1             31
  STAGE IIA             3            135
  STAGE IIB             1              9
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            0             59
  STAGE IIIC            1             41
  STAGE IV              0             48
  STAGE IVA             1             17
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  EPC2 MUTATED     1   2   5   2
  EPC2 WILD-TYPE  16  90 324  48
D2133V5, multiclass
    clus
vv   EPC2 MUTATED EPC2 WILD-TYPE
  T1            1             16
  T2            2             90
  T3            5            324
  T4            2             48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  EPC2 MUTATED     8   2   0
  EPC2 WILD-TYPE 279 111  87
D2133V6, multiclass
    clus
vv   EPC2 MUTATED EPC2 WILD-TYPE
  N0            8            279
  N1            2            111
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2133V7, binary
                cls
clus               0   1
  EPC2 MUTATED     6   1
  EPC2 WILD-TYPE 369  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  EPC2 MUTATED      6    1
  EPC2 WILD-TYPE  369   64
   clus
vv  EPC2 MUTATED EPC2 WILD-TYPE
  0            6            369
  1            1             64
[1] 2 2
[1] FALSE
D2133V8, binary
                cls
clus               0   1
  EPC2 MUTATED     5   5
  EPC2 WILD-TYPE 220 259
[1] "tbl2"
                cls
clus             [,1] [,2]
  EPC2 MUTATED      5    5
  EPC2 WILD-TYPE  220  259
        clus
vv       EPC2 MUTATED EPC2 WILD-TYPE
  FEMALE            5            220
  MALE              5            259
[1] 2 2
[1] FALSE
D2133V9, binary
                cls
clus               0   1
  EPC2 MUTATED     6   0
  EPC2 WILD-TYPE 344  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  EPC2 MUTATED      6    0
  EPC2 WILD-TYPE  344   22
     clus
vv    EPC2 MUTATED EPC2 WILD-TYPE
  NO             6            344
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  EPC2 MUTATED                      6                             3
  EPC2 WILD-TYPE                  309                            44
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  EPC2 MUTATED                       1                              0
  EPC2 WILD-TYPE                   105                             10
D2133V10, multiclass
                                clus
vv                               EPC2 MUTATED EPC2 WILD-TYPE
  COLON ADENOCARCINOMA                      6            309
  COLON MUCINOUS ADENOCARCINOMA             3             44
  RECTAL ADENOCARCINOMA                     1            105
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  EPC2 MUTATED     6   0   0   2
  EPC2 WILD-TYPE 339   4  31  23
D2133V11, multiclass
    clus
vv   EPC2 MUTATED EPC2 WILD-TYPE
  R0            6            339
  R1            0              4
  R2            0             31
  RX            2             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2133V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  EPC2 MUTATED                                  0     0
  EPC2 WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  EPC2 MUTATED                           1     7
  EPC2 WILD-TYPE                        21   219
D2133V13, multiclass
                                  clus
vv                                 EPC2 MUTATED EPC2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                       7            219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2134) Variable = SKIV2L MUTATION ANALYSIS
D2134V1, survival
                  sevent
clus2                0   1
  SKIV2L MUTATED     9   4
  SKIV2L WILD-TYPE 369  89
  SKIV2L MUTATED SKIV2L WILD-TYPE 
              13              458 
  SKIV2L MUTATED SKIV2L WILD-TYPE 
               4               89 
$`SKIV2L MUTATED`
TCGA-A6-5661 TCGA-A6-6781 TCGA-AA-3492 TCGA-AA-3514 TCGA-AA-3655 TCGA-AA-3994 
       33.53        19.66         3.02         1.02        61.02        27.02 
TCGA-AA-A010 TCGA-AY-6386 TCGA-AZ-6600 TCGA-DM-A1DA TCGA-G4-6293 TCGA-G4-6303 
       34.98        17.82        12.10         7.50       133.18        65.85 
TCGA-AG-3742 
        0.99 

$`SKIV2L WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.12        20.28         7.04         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        6.97        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       78.08         6.05         6.97        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        33.01        21.44        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
       12.59       140.38        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6304 TCGA-G4-6306 
        0.53        47.41        35.31        74.56        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  SKIV2L MUTATED SKIV2L WILD-TYPE 
            0.99             0.00 
  SKIV2L MUTATED SKIV2L WILD-TYPE 
          133.18           148.01 
  SKIV2L MUTATED SKIV2L WILD-TYPE 
          19.660           20.235 
[1] "1.0 - 133.2 (19.7)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.4"
D2134V2, continuous
D2134V3, binary
                  cls
clus                 0   1
  SKIV2L MUTATED    12   1
  SKIV2L WILD-TYPE 354 118
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SKIV2L MUTATED     12    1
  SKIV2L WILD-TYPE  354  118
        clus
vv       SKIV2L MUTATED SKIV2L WILD-TYPE
  COLON              12              354
  RECTUM              1              118
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SKIV2L MUTATED         2        0        2         1         1         0
  SKIV2L WILD-TYPE      89        1       30       137         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SKIV2L MUTATED           1          0          2          2        2
  SKIV2L WILD-TYPE        23         11         57         40       46
                  vv
clus               STAGE IVA STAGE IVB
  SKIV2L MUTATED           0         0
  SKIV2L WILD-TYPE        18         1
D2134V4, multiclass
            clus
vv           SKIV2L MUTATED SKIV2L WILD-TYPE
  STAGE I                 2               89
  STAGE IA                0                1
  STAGE II                2               30
  STAGE IIA               1              137
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               1               23
  STAGE IIIA              0               11
  STAGE IIIB              2               57
  STAGE IIIC              2               40
  STAGE IV                2               46
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  SKIV2L MUTATED     1   1   8   3
  SKIV2L WILD-TYPE  16  91 321  47
D2134V5, multiclass
    clus
vv   SKIV2L MUTATED SKIV2L WILD-TYPE
  T1              1               16
  T2              1               91
  T3              8              321
  T4              3               47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  SKIV2L MUTATED     6   6   1
  SKIV2L WILD-TYPE 281 107  86
D2134V6, multiclass
    clus
vv   SKIV2L MUTATED SKIV2L WILD-TYPE
  N0              6              281
  N1              6              107
  N2              1               86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2134V7, binary
                  cls
clus                 0   1
  SKIV2L MUTATED    10   2
  SKIV2L WILD-TYPE 365  63
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SKIV2L MUTATED     10    2
  SKIV2L WILD-TYPE  365   63
   clus
vv  SKIV2L MUTATED SKIV2L WILD-TYPE
  0             10              365
  1              2               63
[1] 2 2
[1] FALSE
D2134V8, binary
                  cls
clus                 0   1
  SKIV2L MUTATED     9   4
  SKIV2L WILD-TYPE 216 260
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SKIV2L MUTATED      9    4
  SKIV2L WILD-TYPE  216  260
        clus
vv       SKIV2L MUTATED SKIV2L WILD-TYPE
  FEMALE              9              216
  MALE                4              260
[1] 2 2
[1] FALSE
D2134V9, binary
                  cls
clus                 0   1
  SKIV2L MUTATED    10   0
  SKIV2L WILD-TYPE 340  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SKIV2L MUTATED     10    0
  SKIV2L WILD-TYPE  340   22
     clus
vv    SKIV2L MUTATED SKIV2L WILD-TYPE
  NO              10              340
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SKIV2L MUTATED                     10                             2
  SKIV2L WILD-TYPE                  305                            45
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SKIV2L MUTATED                       1                              0
  SKIV2L WILD-TYPE                   105                             10
D2134V10, multiclass
                                clus
vv                               SKIV2L MUTATED SKIV2L WILD-TYPE
  COLON ADENOCARCINOMA                       10              305
  COLON MUCINOUS ADENOCARCINOMA               2               45
  RECTAL ADENOCARCINOMA                       1              105
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  SKIV2L MUTATED    11   0   0   0
  SKIV2L WILD-TYPE 334   4  31  25
D2134V11, multiclass
    clus
vv   SKIV2L MUTATED SKIV2L WILD-TYPE
  R0             11              334
  R1              0                4
  R2              0               31
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2134V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SKIV2L MUTATED                                  0     0
  SKIV2L WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  SKIV2L MUTATED                           3     4
  SKIV2L WILD-TYPE                        19   222
D2134V13, multiclass
                                  clus
vv                                 SKIV2L MUTATED SKIV2L WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     3               19
  WHITE                                         4              222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2135) Variable = COL5A2 MUTATION ANALYSIS
D2135V1, survival
                  sevent
clus2                0   1
  COL5A2 MUTATED    19   2
  COL5A2 WILD-TYPE 359  91
  COL5A2 MUTATED COL5A2 WILD-TYPE 
              21              450 
  COL5A2 MUTATED COL5A2 WILD-TYPE 
               2               91 
$`COL5A2 MUTATED`
TCGA-A6-5661 TCGA-A6-6781 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3555 TCGA-AA-3713 
       33.53        19.66        35.01        63.98        29.95        19.04 
TCGA-AA-3870 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3977 TCGA-AA-A010 TCGA-AA-A017 
       29.98        31.00         2.01        25.02        34.98         1.02 
TCGA-AD-5900 TCGA-AY-5543 TCGA-AY-6197 TCGA-DM-A1D4 TCGA-G4-6306 TCGA-G4-6588 
        0.07        33.01        21.44        92.75        44.68        26.17 
TCGA-AG-3902 TCGA-AG-A002 TCGA-AG-A02N 
       32.02        20.98        61.97 

$`COL5A2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3511 
       20.12        20.28         7.04         3.02         1.02         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       78.08         6.05         6.97        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3939 
       53.00        17.03        24.03        27.02        18.05        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A01D 
       42.02         0.99        17.03        14.99        21.99        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 
        0.92        41.00        39.98        18.05        40.96        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
        0.95        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       24.43        38.20       130.65        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       53.62        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       22.09        13.78        35.80        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       48.03        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 
       10.98        49.97         1.94        38.96        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  COL5A2 MUTATED COL5A2 WILD-TYPE 
            0.07             0.00 
  COL5A2 MUTATED COL5A2 WILD-TYPE 
           92.75           148.01 
  COL5A2 MUTATED COL5A2 WILD-TYPE 
           29.98            19.99 
[1] "0.1 - 92.8 (30.0)"  "0.0 - 148.0 (20.0)"
[1] "hr=" "2.5"
D2135V2, continuous
D2135V3, binary
                  cls
clus                 0   1
  COL5A2 MUTATED    19   3
  COL5A2 WILD-TYPE 347 116
[1] "tbl2"
                  cls
clus               [,1] [,2]
  COL5A2 MUTATED     19    3
  COL5A2 WILD-TYPE  347  116
        clus
vv       COL5A2 MUTATED COL5A2 WILD-TYPE
  COLON              19              347
  RECTUM              3              116
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  COL5A2 MUTATED         4        0        2         9         1         0
  COL5A2 WILD-TYPE      87        1       30       129         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  COL5A2 MUTATED           0          0          0          1        3
  COL5A2 WILD-TYPE        24         11         59         41       45
                  vv
clus               STAGE IVA STAGE IVB
  COL5A2 MUTATED           1         0
  COL5A2 WILD-TYPE        17         1
D2135V4, multiclass
            clus
vv           COL5A2 MUTATED COL5A2 WILD-TYPE
  STAGE I                 4               87
  STAGE IA                0                1
  STAGE II                2               30
  STAGE IIA               9              129
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              0               59
  STAGE IIIC              1               41
  STAGE IV                3               45
  STAGE IVA               1               17
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  COL5A2 MUTATED     1   5  14   2
  COL5A2 WILD-TYPE  16  87 315  48
D2135V5, multiclass
    clus
vv   COL5A2 MUTATED COL5A2 WILD-TYPE
  T1              1               16
  T2              5               87
  T3             14              315
  T4              2               48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  COL5A2 MUTATED    18   2   2
  COL5A2 WILD-TYPE 269 111  85
D2135V6, multiclass
    clus
vv   COL5A2 MUTATED COL5A2 WILD-TYPE
  N0             18              269
  N1              2              111
  N2              2               85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2135V7, binary
                  cls
clus                 0   1
  COL5A2 MUTATED    14   4
  COL5A2 WILD-TYPE 361  61
[1] "tbl2"
                  cls
clus               [,1] [,2]
  COL5A2 MUTATED     14    4
  COL5A2 WILD-TYPE  361   61
   clus
vv  COL5A2 MUTATED COL5A2 WILD-TYPE
  0             14              361
  1              4               61
[1] 2 2
[1] FALSE
D2135V8, binary
                  cls
clus                 0   1
  COL5A2 MUTATED     9  13
  COL5A2 WILD-TYPE 216 251
[1] "tbl2"
                  cls
clus               [,1] [,2]
  COL5A2 MUTATED      9   13
  COL5A2 WILD-TYPE  216  251
        clus
vv       COL5A2 MUTATED COL5A2 WILD-TYPE
  FEMALE              9              216
  MALE               13              251
[1] 2 2
[1] FALSE
D2135V9, binary
                  cls
clus                 0   1
  COL5A2 MUTATED    15   1
  COL5A2 WILD-TYPE 335  21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  COL5A2 MUTATED     15    1
  COL5A2 WILD-TYPE  335   21
     clus
vv    COL5A2 MUTATED COL5A2 WILD-TYPE
  NO              15              335
  YES              1               21
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  COL5A2 MUTATED                     15                             4
  COL5A2 WILD-TYPE                  300                            43
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  COL5A2 MUTATED                       3                              0
  COL5A2 WILD-TYPE                   103                             10
D2135V10, multiclass
                                clus
vv                               COL5A2 MUTATED COL5A2 WILD-TYPE
  COLON ADENOCARCINOMA                       15              300
  COLON MUCINOUS ADENOCARCINOMA               4               43
  RECTAL ADENOCARCINOMA                       3              103
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  COL5A2 MUTATED    18   0   2   0
  COL5A2 WILD-TYPE 327   4  29  25
D2135V11, multiclass
    clus
vv   COL5A2 MUTATED COL5A2 WILD-TYPE
  R0             18              327
  R1              0                4
  R2              2               29
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2135V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  COL5A2 MUTATED                                  0     0
  COL5A2 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  COL5A2 MUTATED                           2     6
  COL5A2 WILD-TYPE                        20   220
D2135V13, multiclass
                                  clus
vv                                 COL5A2 MUTATED COL5A2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     2               20
  WHITE                                         6              220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2136) Variable = CPO MUTATION ANALYSIS
D2136V1, survival
               sevent
clus2             0   1
  CPO MUTATED     6   2
  CPO WILD-TYPE 372  91
  CPO MUTATED CPO WILD-TYPE 
            8           463 
  CPO MUTATED CPO WILD-TYPE 
            2            91 
$`CPO MUTATED`
TCGA-A6-5660 TCGA-A6-6782 TCGA-AA-3666 TCGA-AZ-4315 TCGA-AZ-6606 TCGA-CK-4950 
       29.19        20.28         2.01        58.39        11.74        85.45 
TCGA-G4-6628 TCGA-CL-5917 
       79.69        78.12 

$`CPO WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        19.66         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
       54.02        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
       29.56         5.23         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       14.30        17.56       148.01        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 
       13.78        35.80        26.17        91.79        46.75        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  CPO MUTATED CPO WILD-TYPE 
         2.01          0.00 
  CPO MUTATED CPO WILD-TYPE 
        85.45        148.01 
  CPO MUTATED CPO WILD-TYPE 
        43.79         20.05 
[1] "2.0 - 85.5 (43.8)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.4"
D2136V2, continuous
D2136V3, binary
               cls
clus              0   1
  CPO MUTATED     8   1
  CPO WILD-TYPE 358 118
[1] "tbl2"
               cls
clus            [,1] [,2]
  CPO MUTATED      8    1
  CPO WILD-TYPE  358  118
        clus
vv       CPO MUTATED CPO WILD-TYPE
  COLON            8           358
  RECTUM           1           118
[1] 2 2
[1] FALSE
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CPO MUTATED         1        0        0         2         1         0
  CPO WILD-TYPE      90        1       32       136         9         1
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CPO MUTATED           1          0          1          2        1         0
  CPO WILD-TYPE        23         11         58         40       47        18
               vv
clus            STAGE IVB
  CPO MUTATED           0
  CPO WILD-TYPE         1
D2136V4, multiclass
            clus
vv           CPO MUTATED CPO WILD-TYPE
  STAGE I              1            90
  STAGE IA             0             1
  STAGE II             0            32
  STAGE IIA            2           136
  STAGE IIB            1             9
  STAGE IIC            0             1
  STAGE III            1            23
  STAGE IIIA           0            11
  STAGE IIIB           1            58
  STAGE IIIC           2            40
  STAGE IV             1            47
  STAGE IVA            0            18
  STAGE IVB            0             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  CPO MUTATED     0   1   6   2
  CPO WILD-TYPE  17  91 323  48
D2136V5, multiclass
    clus
vv   CPO MUTATED CPO WILD-TYPE
  T1           0            17
  T2           1            91
  T3           6           323
  T4           2            48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2
  CPO MUTATED     4   2   3
  CPO WILD-TYPE 283 111  84
D2136V6, multiclass
    clus
vv   CPO MUTATED CPO WILD-TYPE
  N0           4           283
  N1           2           111
  N2           3            84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2136V7, binary
               cls
clus              0   1
  CPO MUTATED     6   1
  CPO WILD-TYPE 369  64
[1] "tbl2"
               cls
clus            [,1] [,2]
  CPO MUTATED      6    1
  CPO WILD-TYPE  369   64
   clus
vv  CPO MUTATED CPO WILD-TYPE
  0           6           369
  1           1            64
[1] 2 2
[1] FALSE
D2136V8, binary
               cls
clus              0   1
  CPO MUTATED     3   6
  CPO WILD-TYPE 222 258
[1] "tbl2"
               cls
clus            [,1] [,2]
  CPO MUTATED      3    6
  CPO WILD-TYPE  222  258
        clus
vv       CPO MUTATED CPO WILD-TYPE
  FEMALE           3           222
  MALE             6           258
[1] 2 2
[1] FALSE
D2136V9, binary
               cls
clus              0   1
  CPO MUTATED     7   0
  CPO WILD-TYPE 343  22
[1] "tbl2"
               cls
clus            [,1] [,2]
  CPO MUTATED      7    0
  CPO WILD-TYPE  343   22
     clus
vv    CPO MUTATED CPO WILD-TYPE
  NO            7           343
  YES           0            22
[1] 2 2
[1] FALSE
               vv
clus            COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CPO MUTATED                      8                             0
  CPO WILD-TYPE                  307                            47
               vv
clus            RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CPO MUTATED                       1                              0
  CPO WILD-TYPE                   105                             10
D2136V10, multiclass
                                clus
vv                               CPO MUTATED CPO WILD-TYPE
  COLON ADENOCARCINOMA                     8           307
  COLON MUCINOUS ADENOCARCINOMA            0            47
  RECTAL ADENOCARCINOMA                    1           105
  RECTAL MUCINOUS ADENOCARCINOMA           0            10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             R0  R1  R2  RX
  CPO MUTATED     4   1   0   1
  CPO WILD-TYPE 341   3  31  24
D2136V11, multiclass
    clus
vv   CPO MUTATED CPO WILD-TYPE
  R0           4           341
  R1           1             3
  R2           0            31
  RX           1            24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2136V12, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CPO MUTATED                                  0     0
  CPO WILD-TYPE                                1    11
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  CPO MUTATED                           2     5
  CPO WILD-TYPE                        20   221
D2136V13, multiclass
                                  clus
vv                                 CPO MUTATED CPO WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      0            11
  BLACK OR AFRICAN AMERICAN                  2            20
  WHITE                                      5           221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2137) Variable = CLK4 MUTATION ANALYSIS
D2137V1, survival
                sevent
clus2              0   1
  CLK4 MUTATED     5   3
  CLK4 WILD-TYPE 373  90
  CLK4 MUTATED CLK4 WILD-TYPE 
             8            463 
  CLK4 MUTATED CLK4 WILD-TYPE 
             3             90 
$`CLK4 MUTATED`
TCGA-A6-5662 TCGA-AA-3518 TCGA-AA-3555 TCGA-CA-6718 TCGA-D5-6540 TCGA-DM-A1D8 
       23.61         1.02        29.95        10.06        16.14        12.59 
TCGA-DM-A1D9 TCGA-F4-6460 
      140.38        31.96 

$`CLK4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        33.53        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       24.00        17.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       12.76        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       12.49        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1DA TCGA-DM-A1DB 
      130.65        92.75        49.91        13.32         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6569 
       35.97        60.79       117.07        98.24         8.61        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  CLK4 MUTATED CLK4 WILD-TYPE 
          1.02           0.00 
  CLK4 MUTATED CLK4 WILD-TYPE 
        140.38         148.01 
  CLK4 MUTATED CLK4 WILD-TYPE 
        19.875         20.190 
[1] "1.0 - 140.4 (19.9)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.9"
D2137V2, continuous
D2137V3, binary
                cls
clus               0   1
  CLK4 MUTATED     9   0
  CLK4 WILD-TYPE 357 119
[1] "tbl2"
                cls
clus             [,1] [,2]
  CLK4 MUTATED      9    0
  CLK4 WILD-TYPE  357  119
        clus
vv       CLK4 MUTATED CLK4 WILD-TYPE
  COLON             9            357
  RECTUM            0            119
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CLK4 MUTATED         1        0        0         4         0         0
  CLK4 WILD-TYPE      90        1       32       134        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CLK4 MUTATED           0          0          1          1        0         1
  CLK4 WILD-TYPE        24         11         58         41       48        17
                vv
clus             STAGE IVB
  CLK4 MUTATED           0
  CLK4 WILD-TYPE         1
D2137V4, multiclass
            clus
vv           CLK4 MUTATED CLK4 WILD-TYPE
  STAGE I               1             90
  STAGE IA              0              1
  STAGE II              0             32
  STAGE IIA             4            134
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            1             58
  STAGE IIIC            1             41
  STAGE IV              0             48
  STAGE IVA             1             17
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  CLK4 MUTATED     0   1   8   0
  CLK4 WILD-TYPE  17  91 321  50
D2137V5, multiclass
    clus
vv   CLK4 MUTATED CLK4 WILD-TYPE
  T1            0             17
  T2            1             91
  T3            8            321
  T4            0             50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  CLK4 MUTATED     5   2   2
  CLK4 WILD-TYPE 282 111  85
D2137V6, multiclass
    clus
vv   CLK4 MUTATED CLK4 WILD-TYPE
  N0            5            282
  N1            2            111
  N2            2             85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2137V7, binary
                cls
clus               0   1
  CLK4 MUTATED     6   1
  CLK4 WILD-TYPE 369  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  CLK4 MUTATED      6    1
  CLK4 WILD-TYPE  369   64
   clus
vv  CLK4 MUTATED CLK4 WILD-TYPE
  0            6            369
  1            1             64
[1] 2 2
[1] FALSE
D2137V8, binary
                cls
clus               0   1
  CLK4 MUTATED     5   4
  CLK4 WILD-TYPE 220 260
[1] "tbl2"
                cls
clus             [,1] [,2]
  CLK4 MUTATED      5    4
  CLK4 WILD-TYPE  220  260
        clus
vv       CLK4 MUTATED CLK4 WILD-TYPE
  FEMALE            5            220
  MALE              4            260
[1] 2 2
[1] FALSE
D2137V9, binary
                cls
clus               0   1
  CLK4 MUTATED     5   0
  CLK4 WILD-TYPE 345  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  CLK4 MUTATED      5    0
  CLK4 WILD-TYPE  345   22
     clus
vv    CLK4 MUTATED CLK4 WILD-TYPE
  NO             5            345
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CLK4 MUTATED                      6                             3
  CLK4 WILD-TYPE                  309                            44
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CLK4 MUTATED                       0                              0
  CLK4 WILD-TYPE                   106                             10
D2137V10, multiclass
                                clus
vv                               CLK4 MUTATED CLK4 WILD-TYPE
  COLON ADENOCARCINOMA                      6            309
  COLON MUCINOUS ADENOCARCINOMA             3             44
  RECTAL ADENOCARCINOMA                     0            106
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  CLK4 MUTATED     5   0   0   1
  CLK4 WILD-TYPE 340   4  31  24
D2137V11, multiclass
    clus
vv   CLK4 MUTATED CLK4 WILD-TYPE
  R0            5            340
  R1            0              4
  R2            0             31
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2137V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CLK4 MUTATED                                  0     1
  CLK4 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  CLK4 MUTATED                           0     6
  CLK4 WILD-TYPE                        22   220
D2137V13, multiclass
                                  clus
vv                                 CLK4 MUTATED CLK4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       6            220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2138) Variable = SLC9A2 MUTATION ANALYSIS
D2138V1, survival
                  sevent
clus2                0   1
  SLC9A2 MUTATED    10   1
  SLC9A2 WILD-TYPE 368  92
  SLC9A2 MUTATED SLC9A2 WILD-TYPE 
              11              460 
  SLC9A2 MUTATED SLC9A2 WILD-TYPE 
               1               92 
$`SLC9A2 MUTATED`
TCGA-AA-3821 TCGA-AA-3949 TCGA-AD-6889 TCGA-AZ-4315 TCGA-AZ-6607 TCGA-CA-6717 
        1.02        26.01        56.55        58.39         3.19        12.76 
TCGA-CK-4950 TCGA-CM-5861 TCGA-F4-6807 TCGA-DC-6682 TCGA-F5-6571 
       85.45        15.02        16.24         4.01        31.30 

$`SLC9A2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-3952 
        2.01        12.99        24.00        33.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07        12.20        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
       17.56       148.01        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       30.08        32.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6808 
        6.18        47.87         1.55        34.42        41.42        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        5.95         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6702 TCGA-F5-6811 
       20.91        18.28         9.96        49.51        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  SLC9A2 MUTATED SLC9A2 WILD-TYPE 
            1.02             0.00 
  SLC9A2 MUTATED SLC9A2 WILD-TYPE 
           85.45           148.01 
  SLC9A2 MUTATED SLC9A2 WILD-TYPE 
          16.240           20.235 
[1] "1.0 - 85.5 (16.2)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "2.4"
D2138V2, continuous
D2138V3, binary
                  cls
clus                 0   1
  SLC9A2 MUTATED    10   2
  SLC9A2 WILD-TYPE 356 117
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLC9A2 MUTATED     10    2
  SLC9A2 WILD-TYPE  356  117
        clus
vv       SLC9A2 MUTATED SLC9A2 WILD-TYPE
  COLON              10              356
  RECTUM              2              117
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SLC9A2 MUTATED         1        0        0         6         1         0
  SLC9A2 WILD-TYPE      90        1       32       132         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC9A2 MUTATED           0          0          2          1        1
  SLC9A2 WILD-TYPE        24         11         57         41       47
                  vv
clus               STAGE IVA STAGE IVB
  SLC9A2 MUTATED           0         0
  SLC9A2 WILD-TYPE        18         1
D2138V4, multiclass
            clus
vv           SLC9A2 MUTATED SLC9A2 WILD-TYPE
  STAGE I                 1               90
  STAGE IA                0                1
  STAGE II                0               32
  STAGE IIA               6              132
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              2               57
  STAGE IIIC              1               41
  STAGE IV                1               47
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  SLC9A2 MUTATED     0   1   9   2
  SLC9A2 WILD-TYPE  17  91 320  48
D2138V5, multiclass
    clus
vv   SLC9A2 MUTATED SLC9A2 WILD-TYPE
  T1              0               17
  T2              1               91
  T3              9              320
  T4              2               48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  SLC9A2 MUTATED     8   2   2
  SLC9A2 WILD-TYPE 279 111  85
D2138V6, multiclass
    clus
vv   SLC9A2 MUTATED SLC9A2 WILD-TYPE
  N0              8              279
  N1              2              111
  N2              2               85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2138V7, binary
                  cls
clus                 0   1
  SLC9A2 MUTATED    10   1
  SLC9A2 WILD-TYPE 365  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLC9A2 MUTATED     10    1
  SLC9A2 WILD-TYPE  365   64
   clus
vv  SLC9A2 MUTATED SLC9A2 WILD-TYPE
  0             10              365
  1              1               64
[1] 2 2
[1] FALSE
D2138V8, binary
                  cls
clus                 0   1
  SLC9A2 MUTATED     7   5
  SLC9A2 WILD-TYPE 218 259
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLC9A2 MUTATED      7    5
  SLC9A2 WILD-TYPE  218  259
        clus
vv       SLC9A2 MUTATED SLC9A2 WILD-TYPE
  FEMALE              7              218
  MALE                5              259
[1] 2 2
[1] FALSE
D2138V9, binary
                  cls
clus                 0   1
  SLC9A2 MUTATED     9   0
  SLC9A2 WILD-TYPE 341  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLC9A2 MUTATED      9    0
  SLC9A2 WILD-TYPE  341   22
     clus
vv    SLC9A2 MUTATED SLC9A2 WILD-TYPE
  NO               9              341
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SLC9A2 MUTATED                      7                             3
  SLC9A2 WILD-TYPE                  308                            44
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SLC9A2 MUTATED                       2                              0
  SLC9A2 WILD-TYPE                   104                             10
D2138V10, multiclass
                                clus
vv                               SLC9A2 MUTATED SLC9A2 WILD-TYPE
  COLON ADENOCARCINOMA                        7              308
  COLON MUCINOUS ADENOCARCINOMA               3               44
  RECTAL ADENOCARCINOMA                       2              104
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  SLC9A2 MUTATED     7   1   0   2
  SLC9A2 WILD-TYPE 338   3  31  23
D2138V11, multiclass
    clus
vv   SLC9A2 MUTATED SLC9A2 WILD-TYPE
  R0              7              338
  R1              1                3
  R2              0               31
  RX              2               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2138V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SLC9A2 MUTATED                                  0     2
  SLC9A2 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  SLC9A2 MUTATED                           1     7
  SLC9A2 WILD-TYPE                        21   219
D2138V13, multiclass
                                  clus
vv                                 SLC9A2 MUTATED SLC9A2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                9
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                         7              219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2139) Variable = KIAA0196 MUTATION ANALYSIS
D2139V1, survival
                    sevent
clus2                  0   1
  KIAA0196 MUTATED     8   3
  KIAA0196 WILD-TYPE 370  90
  KIAA0196 MUTATED KIAA0196 WILD-TYPE 
                11                460 
  KIAA0196 MUTATED KIAA0196 WILD-TYPE 
                 3                 90 
$`KIAA0196 MUTATED`
TCGA-AA-3518 TCGA-AA-3525 TCGA-AA-A010 TCGA-AY-6197 TCGA-AZ-6608 TCGA-CA-6716 
        1.02         8.05        34.98        21.44         1.61        12.20 
TCGA-CM-6162 TCGA-DM-A1D4 TCGA-DM-A1D7 TCGA-F4-6856 TCGA-AG-3898 
       12.00        92.75        13.32        35.31        48.03 

$`KIAA0196 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3526 
       38.99         9.07        24.03        37.05        36.03        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       15.02        17.03        15.02         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D6 
       10.26       119.70        24.43        38.20       130.65        49.91 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
       13.25         0.53        47.41       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
       14.01         1.02        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  KIAA0196 MUTATED KIAA0196 WILD-TYPE 
              1.02               0.00 
  KIAA0196 MUTATED KIAA0196 WILD-TYPE 
             92.75             148.01 
  KIAA0196 MUTATED KIAA0196 WILD-TYPE 
            13.320             20.235 
[1] "1.0 - 92.8 (13.3)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.5"
D2139V2, continuous
D2139V3, binary
                    cls
clus                   0   1
  KIAA0196 MUTATED    10   1
  KIAA0196 WILD-TYPE 356 118
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0196 MUTATED     10    1
  KIAA0196 WILD-TYPE  356  118
        clus
vv       KIAA0196 MUTATED KIAA0196 WILD-TYPE
  COLON                10                356
  RECTUM                1                118
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KIAA0196 MUTATED         1        0        0         6         1         0
  KIAA0196 WILD-TYPE      90        1       32       132         9         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIAA0196 MUTATED           0          1          2          0        0
  KIAA0196 WILD-TYPE        24         10         57         42       48
                    vv
clus                 STAGE IVA STAGE IVB
  KIAA0196 MUTATED           0         0
  KIAA0196 WILD-TYPE        18         1
D2139V4, multiclass
            clus
vv           KIAA0196 MUTATED KIAA0196 WILD-TYPE
  STAGE I                   1                 90
  STAGE IA                  0                  1
  STAGE II                  0                 32
  STAGE IIA                 6                132
  STAGE IIB                 1                  9
  STAGE IIC                 0                  1
  STAGE III                 0                 24
  STAGE IIIA                1                 10
  STAGE IIIB                2                 57
  STAGE IIIC                0                 42
  STAGE IV                  0                 48
  STAGE IVA                 0                 18
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  KIAA0196 MUTATED     0   2   8   1
  KIAA0196 WILD-TYPE  17  90 321  49
D2139V5, multiclass
    clus
vv   KIAA0196 MUTATED KIAA0196 WILD-TYPE
  T1                0                 17
  T2                2                 90
  T3                8                321
  T4                1                 49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  KIAA0196 MUTATED     8   3   0
  KIAA0196 WILD-TYPE 279 110  87
D2139V6, multiclass
    clus
vv   KIAA0196 MUTATED KIAA0196 WILD-TYPE
  N0                8                279
  N1                3                110
  N2                0                 87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2139V7, binary
                    cls
clus                   0   1
  KIAA0196 MUTATED    10   0
  KIAA0196 WILD-TYPE 365  65
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0196 MUTATED     10    0
  KIAA0196 WILD-TYPE  365   65
   clus
vv  KIAA0196 MUTATED KIAA0196 WILD-TYPE
  0               10                365
  1                0                 65
[1] 2 2
[1] FALSE
D2139V8, binary
                    cls
clus                   0   1
  KIAA0196 MUTATED     4   7
  KIAA0196 WILD-TYPE 221 257
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0196 MUTATED      4    7
  KIAA0196 WILD-TYPE  221  257
        clus
vv       KIAA0196 MUTATED KIAA0196 WILD-TYPE
  FEMALE                4                221
  MALE                  7                257
[1] 2 2
[1] FALSE
D2139V9, binary
                    cls
clus                   0   1
  KIAA0196 MUTATED     8   0
  KIAA0196 WILD-TYPE 342  22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0196 MUTATED      8    0
  KIAA0196 WILD-TYPE  342   22
     clus
vv    KIAA0196 MUTATED KIAA0196 WILD-TYPE
  NO                 8                342
  YES                0                 22
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  KIAA0196 MUTATED                      7                             2
  KIAA0196 WILD-TYPE                  308                            45
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  KIAA0196 MUTATED                       1                              0
  KIAA0196 WILD-TYPE                   105                             10
D2139V10, multiclass
                                clus
vv                               KIAA0196 MUTATED KIAA0196 WILD-TYPE
  COLON ADENOCARCINOMA                          7                308
  COLON MUCINOUS ADENOCARCINOMA                 2                 45
  RECTAL ADENOCARCINOMA                         1                105
  RECTAL MUCINOUS ADENOCARCINOMA                0                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  KIAA0196 MUTATED     7   0   0   1
  KIAA0196 WILD-TYPE 338   4  31  24
D2139V11, multiclass
    clus
vv   KIAA0196 MUTATED KIAA0196 WILD-TYPE
  R0                7                338
  R1                0                  4
  R2                0                 31
  RX                1                 24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2139V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KIAA0196 MUTATED                                  0     1
  KIAA0196 WILD-TYPE                                1    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  KIAA0196 MUTATED                           0     6
  KIAA0196 WILD-TYPE                        22   220
D2139V13, multiclass
                                  clus
vv                                 KIAA0196 MUTATED KIAA0196 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                 10
  BLACK OR AFRICAN AMERICAN                       0                 22
  WHITE                                           6                220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2140) Variable = ANGPTL2 MUTATION ANALYSIS
D2140V1, survival
                   sevent
clus2                 0   1
  ANGPTL2 MUTATED     8   5
  ANGPTL2 WILD-TYPE 370  88
  ANGPTL2 MUTATED ANGPTL2 WILD-TYPE 
               13               458 
  ANGPTL2 MUTATED ANGPTL2 WILD-TYPE 
                5                88 
$`ANGPTL2 MUTATED`
TCGA-A6-2676 TCGA-AA-3492 TCGA-AA-3543 TCGA-AA-A00J TCGA-AA-A00N TCGA-AA-A010 
       42.90         3.02         0.99        18.05         4.01        34.98 
TCGA-AA-A01P TCGA-AD-5900 TCGA-AD-6895 TCGA-AZ-4315 TCGA-AZ-6601 TCGA-DM-A1HB 
       38.07         0.07         0.72        58.39       100.01       135.65 
TCGA-EI-6507 
       19.96 

$`ANGPTL2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 
       20.12        19.66        20.28         7.04         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
       12.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       30.02        34.03        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01Q TCGA-AA-A01R 
       32.02        12.00        31.00        31.00         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 
       41.00        39.98        18.05        40.96        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
       56.55         0.79         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 
       62.79        88.21        49.41         6.77        12.10        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
        7.50        44.32       131.51       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
       32.61         0.49        20.55        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  ANGPTL2 MUTATED ANGPTL2 WILD-TYPE 
             0.07              0.00 
  ANGPTL2 MUTATED ANGPTL2 WILD-TYPE 
           135.65            148.01 
  ANGPTL2 MUTATED ANGPTL2 WILD-TYPE 
           19.960            20.235 
[1] "0.1 - 135.7 (20.0)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.6"
D2140V2, continuous
D2140V3, binary
                   cls
clus                  0   1
  ANGPTL2 MUTATED    12   1
  ANGPTL2 WILD-TYPE 354 118
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANGPTL2 MUTATED     12    1
  ANGPTL2 WILD-TYPE  354  118
        clus
vv       ANGPTL2 MUTATED ANGPTL2 WILD-TYPE
  COLON               12               354
  RECTUM               1               118
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ANGPTL2 MUTATED         2        0        2         2         3         0
  ANGPTL2 WILD-TYPE      89        1       30       136         7         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ANGPTL2 MUTATED           1          0          2          0        0
  ANGPTL2 WILD-TYPE        23         11         57         42       48
                   vv
clus                STAGE IVA STAGE IVB
  ANGPTL2 MUTATED           0         0
  ANGPTL2 WILD-TYPE        18         1
D2140V4, multiclass
            clus
vv           ANGPTL2 MUTATED ANGPTL2 WILD-TYPE
  STAGE I                  2                89
  STAGE IA                 0                 1
  STAGE II                 2                30
  STAGE IIA                2               136
  STAGE IIB                3                 7
  STAGE IIC                0                 1
  STAGE III                1                23
  STAGE IIIA               0                11
  STAGE IIIB               2                57
  STAGE IIIC               0                42
  STAGE IV                 0                48
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  ANGPTL2 MUTATED     0   2   7   4
  ANGPTL2 WILD-TYPE  17  90 322  46
D2140V5, multiclass
    clus
vv   ANGPTL2 MUTATED ANGPTL2 WILD-TYPE
  T1               0                17
  T2               2                90
  T3               7               322
  T4               4                46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  ANGPTL2 MUTATED     9   4   0
  ANGPTL2 WILD-TYPE 278 109  87
D2140V6, multiclass
    clus
vv   ANGPTL2 MUTATED ANGPTL2 WILD-TYPE
  N0               9               278
  N1               4               109
  N2               0                87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2140V7, binary
                   cls
clus                  0   1
  ANGPTL2 MUTATED    11   0
  ANGPTL2 WILD-TYPE 364  65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANGPTL2 MUTATED     11    0
  ANGPTL2 WILD-TYPE  364   65
   clus
vv  ANGPTL2 MUTATED ANGPTL2 WILD-TYPE
  0              11               364
  1               0                65
[1] 2 2
[1] FALSE
D2140V8, binary
                   cls
clus                  0   1
  ANGPTL2 MUTATED     4   9
  ANGPTL2 WILD-TYPE 221 255
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANGPTL2 MUTATED      4    9
  ANGPTL2 WILD-TYPE  221  255
        clus
vv       ANGPTL2 MUTATED ANGPTL2 WILD-TYPE
  FEMALE               4               221
  MALE                 9               255
[1] 2 2
[1] FALSE
D2140V9, binary
                   cls
clus                  0   1
  ANGPTL2 MUTATED     9   0
  ANGPTL2 WILD-TYPE 341  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANGPTL2 MUTATED      9    0
  ANGPTL2 WILD-TYPE  341   22
     clus
vv    ANGPTL2 MUTATED ANGPTL2 WILD-TYPE
  NO                9               341
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ANGPTL2 MUTATED                      7                             4
  ANGPTL2 WILD-TYPE                  308                            43
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ANGPTL2 MUTATED                       1                              0
  ANGPTL2 WILD-TYPE                   105                             10
D2140V10, multiclass
                                clus
vv                               ANGPTL2 MUTATED ANGPTL2 WILD-TYPE
  COLON ADENOCARCINOMA                         7               308
  COLON MUCINOUS ADENOCARCINOMA                4                43
  RECTAL ADENOCARCINOMA                        1               105
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  ANGPTL2 MUTATED    10   0   0   0
  ANGPTL2 WILD-TYPE 335   4  31  25
D2140V11, multiclass
    clus
vv   ANGPTL2 MUTATED ANGPTL2 WILD-TYPE
  R0              10               335
  R1               0                 4
  R2               0                31
  RX               0                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2140V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ANGPTL2 MUTATED                                  0     0
  ANGPTL2 WILD-TYPE                                1    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  ANGPTL2 MUTATED                           0     7
  ANGPTL2 WILD-TYPE                        22   219
D2140V13, multiclass
                                  clus
vv                                 ANGPTL2 MUTATED ANGPTL2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                      0                22
  WHITE                                          7               219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2141) Variable = C2ORF49 MUTATION ANALYSIS
D2141V1, survival
                   sevent
clus2                 0   1
  C2ORF49 MUTATED     5   0
  C2ORF49 WILD-TYPE 373  93
  C2ORF49 MUTATED C2ORF49 WILD-TYPE 
                5               466 
  C2ORF49 MUTATED C2ORF49 WILD-TYPE 
                0                93 
$`C2ORF49 MUTATED`
TCGA-A6-6781 TCGA-AA-3672 TCGA-AA-A010 TCGA-AY-6197 TCGA-AG-3892 
       19.66         0.92        34.98        21.44        13.02 

$`C2ORF49 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 
        6.97        54.02         2.01        14.01        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 
        1.02        17.95        36.95        17.03        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  C2ORF49 MUTATED C2ORF49 WILD-TYPE 
             0.92              0.00 
  C2ORF49 MUTATED C2ORF49 WILD-TYPE 
            34.98            148.01 
  C2ORF49 MUTATED C2ORF49 WILD-TYPE 
           19.660            20.235 
[1] "0.9 - 35.0 (19.7)"  "0.0 - 148.0 (20.2)"
[1] "hr="     "3300000"
D2141V2, continuous
D2141V3, binary
                   cls
clus                  0   1
  C2ORF49 MUTATED     4   1
  C2ORF49 WILD-TYPE 362 118
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C2ORF49 MUTATED      4    1
  C2ORF49 WILD-TYPE  362  118
        clus
vv       C2ORF49 MUTATED C2ORF49 WILD-TYPE
  COLON                4               362
  RECTUM               1               118
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  C2ORF49 MUTATED         1        0        0         1         1         0
  C2ORF49 WILD-TYPE      90        1       32       137         9         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C2ORF49 MUTATED           1          0          0          1        0
  C2ORF49 WILD-TYPE        23         11         59         41       48
                   vv
clus                STAGE IVA STAGE IVB
  C2ORF49 MUTATED           0         0
  C2ORF49 WILD-TYPE        18         1
D2141V4, multiclass
            clus
vv           C2ORF49 MUTATED C2ORF49 WILD-TYPE
  STAGE I                  1                90
  STAGE IA                 0                 1
  STAGE II                 0                32
  STAGE IIA                1               137
  STAGE IIB                1                 9
  STAGE IIC                0                 1
  STAGE III                1                23
  STAGE IIIA               0                11
  STAGE IIIB               0                59
  STAGE IIIC               1                41
  STAGE IV                 0                48
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  C2ORF49 MUTATED     1   0   2   2
  C2ORF49 WILD-TYPE  16  92 327  48
D2141V5, multiclass
    clus
vv   C2ORF49 MUTATED C2ORF49 WILD-TYPE
  T1               1                16
  T2               0                92
  T3               2               327
  T4               2                48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  C2ORF49 MUTATED     3   2   0
  C2ORF49 WILD-TYPE 284 111  87
D2141V6, multiclass
    clus
vv   C2ORF49 MUTATED C2ORF49 WILD-TYPE
  N0               3               284
  N1               2               111
  N2               0                87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2141V7, binary
                   cls
clus                  0   1
  C2ORF49 MUTATED     3   0
  C2ORF49 WILD-TYPE 372  65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C2ORF49 MUTATED      3    0
  C2ORF49 WILD-TYPE  372   65
   clus
vv  C2ORF49 MUTATED C2ORF49 WILD-TYPE
  0               3               372
  1               0                65
[1] 2 2
[1] FALSE
D2141V8, binary
                   cls
clus                  0   1
  C2ORF49 MUTATED     3   2
  C2ORF49 WILD-TYPE 222 262
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C2ORF49 MUTATED      3    2
  C2ORF49 WILD-TYPE  222  262
        clus
vv       C2ORF49 MUTATED C2ORF49 WILD-TYPE
  FEMALE               3               222
  MALE                 2               262
[1] 2 2
[1] FALSE
D2141V9, binary
                   cls
clus                  0   1
  C2ORF49 MUTATED     5   0
  C2ORF49 WILD-TYPE 345  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C2ORF49 MUTATED      5    0
  C2ORF49 WILD-TYPE  345   22
     clus
vv    C2ORF49 MUTATED C2ORF49 WILD-TYPE
  NO                5               345
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  C2ORF49 MUTATED                      3                             1
  C2ORF49 WILD-TYPE                  312                            46
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  C2ORF49 MUTATED                       1                              0
  C2ORF49 WILD-TYPE                   105                             10
D2141V10, multiclass
                                clus
vv                               C2ORF49 MUTATED C2ORF49 WILD-TYPE
  COLON ADENOCARCINOMA                         3               312
  COLON MUCINOUS ADENOCARCINOMA                1                46
  RECTAL ADENOCARCINOMA                        1               105
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  C2ORF49 MUTATED     5   0   0   0
  C2ORF49 WILD-TYPE 340   4  31  25
D2141V11, multiclass
    clus
vv   C2ORF49 MUTATED C2ORF49 WILD-TYPE
  R0               5               340
  R1               0                 4
  R2               0                31
  RX               0                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2141V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C2ORF49 MUTATED                                  0     0
  C2ORF49 WILD-TYPE                                1    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  C2ORF49 MUTATED                           0     2
  C2ORF49 WILD-TYPE                        22   224
D2141V13, multiclass
[1] "Remove cluster labels:" "C2ORF49 MUTATED"       
clus
  C2ORF49 MUTATED C2ORF49 WILD-TYPE 
                2               258 
       TCGA-A6-2671        TCGA-A6-2672        TCGA-A6-2674        TCGA-A6-2676 
"C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" 
       TCGA-A6-2677        TCGA-A6-2678        TCGA-A6-2683        TCGA-A6-3807 
"C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" 
       TCGA-A6-3808        TCGA-A6-3809        TCGA-A6-3810        TCGA-A6-4105 
"C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" 
       TCGA-A6-5656        TCGA-A6-5657        TCGA-A6-5659        TCGA-A6-5660 
"C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" 
       TCGA-A6-5661        TCGA-A6-5662        TCGA-A6-5664        TCGA-A6-5665 
"C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" 
       TCGA-A6-5666        TCGA-A6-6137        TCGA-A6-6138        TCGA-A6-6141 
"C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" 
       TCGA-A6-6142        TCGA-A6-6648        TCGA-A6-6649        TCGA-A6-6651 
"C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" 
       TCGA-A6-6652        TCGA-A6-6653        TCGA-A6-6654        TCGA-A6-6780 
"C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" 
       TCGA-A6-6782        TCGA-AD-5900        TCGA-AD-6548        TCGA-AD-6888 
"C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" 
       TCGA-AD-6889        TCGA-AD-6890        TCGA-AD-6895        TCGA-AD-6899 
"C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" 
       TCGA-AD-6901        TCGA-AD-6963        TCGA-AD-6964        TCGA-AD-6965 
"C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" 
       TCGA-AU-3779        TCGA-AU-6004        TCGA-AY-4070        TCGA-AY-4071 
"C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" 
       TCGA-AY-5543        TCGA-AY-6196        TCGA-AY-6386        TCGA-AZ-4315 
"C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" 
       TCGA-AZ-4323        TCGA-AZ-4616        TCGA-AZ-4681        TCGA-AZ-4682 
"C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" 
       TCGA-AZ-5403        TCGA-AZ-5407        TCGA-AZ-6598        TCGA-AZ-6599 
"C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" 
       TCGA-AZ-6600        TCGA-AZ-6601        TCGA-AZ-6603        TCGA-AZ-6605 
"C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" 
       TCGA-AZ-6606        TCGA-AZ-6607        TCGA-AZ-6608        TCGA-CA-5254 
"C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" 
       TCGA-CA-5255        TCGA-CA-5796        TCGA-CA-5797        TCGA-CA-6715 
"C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" 
       TCGA-CA-6716        TCGA-CA-6717        TCGA-CA-6718        TCGA-CA-6719 
"C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" 
       TCGA-CK-4947        TCGA-CK-4948        TCGA-CK-4950        TCGA-CK-4952 
"C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" 
       TCGA-CK-5912        TCGA-CK-5913        TCGA-CK-5914        TCGA-CK-5915 
"C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" 
       TCGA-CK-5916        TCGA-CK-6746        TCGA-CK-6747        TCGA-CK-6748 
"C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" 
       TCGA-CK-6751        TCGA-CM-4743        TCGA-CM-4744        TCGA-CM-4746 
"C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" 
       TCGA-CM-4747        TCGA-CM-4752        TCGA-CM-5341        TCGA-CM-5344 
"C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" 
       TCGA-CM-5348        TCGA-CM-5349        TCGA-CM-5860        TCGA-CM-5861 
"C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" 
       TCGA-CM-5862        TCGA-CM-5863        TCGA-CM-5864        TCGA-CM-5868 
"C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" 
       TCGA-CM-6161        TCGA-CM-6162        TCGA-CM-6163        TCGA-CM-6164 
"C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" 
       TCGA-CM-6165        TCGA-CM-6166        TCGA-CM-6167        TCGA-CM-6168 
"C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" 
       TCGA-CM-6169        TCGA-CM-6170        TCGA-CM-6171        TCGA-CM-6172 
"C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" 
       TCGA-CM-6674        TCGA-CM-6675        TCGA-CM-6676        TCGA-CM-6677 
"C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" 
       TCGA-CM-6678        TCGA-CM-6679        TCGA-CM-6680        TCGA-D5-5537 
"C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" 
       TCGA-D5-5538        TCGA-D5-5539        TCGA-D5-5540        TCGA-D5-5541 
"C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" 
       TCGA-D5-6529        TCGA-D5-6532        TCGA-D5-6533        TCGA-D5-6534 
"C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" 
       TCGA-D5-6535        TCGA-D5-6536        TCGA-D5-6537        TCGA-D5-6538 
"C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" 
       TCGA-D5-6539        TCGA-D5-6540        TCGA-D5-6541        TCGA-D5-6898 
"C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" 
       TCGA-D5-6920        TCGA-D5-6922        TCGA-D5-6923        TCGA-D5-6924 
"C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" 
       TCGA-D5-6926        TCGA-D5-6927        TCGA-D5-6928        TCGA-D5-6929 
"C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" 
       TCGA-D5-6930        TCGA-D5-6931        TCGA-D5-6932        TCGA-D5-7000 
"C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" 
       TCGA-DM-A0X9        TCGA-DM-A0XD        TCGA-DM-A0XF        TCGA-DM-A1D0 
"C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" 
       TCGA-DM-A1D4        TCGA-DM-A1D6        TCGA-DM-A1D7        TCGA-DM-A1D8 
"C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" 
       TCGA-DM-A1D9        TCGA-DM-A1DA        TCGA-DM-A1DB        TCGA-DM-A1HA 
"C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" 
       TCGA-DM-A1HB        TCGA-DM-A282        TCGA-DM-A285        TCGA-DM-A28C 
"C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" 
       TCGA-DM-A28E        TCGA-DM-A28F        TCGA-DM-A28G        TCGA-DM-A28H 
"C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" 
       TCGA-DM-A28K        TCGA-F4-6459        TCGA-F4-6460        TCGA-F4-6569 
"C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" 
       TCGA-F4-6570        TCGA-F4-6703        TCGA-F4-6704        TCGA-F4-6805 
"C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" 
       TCGA-F4-6806        TCGA-F4-6807        TCGA-F4-6808        TCGA-F4-6809 
"C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" 
       TCGA-F4-6854        TCGA-F4-6855        TCGA-F4-6856        TCGA-G4-6293 
"C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" 
       TCGA-G4-6299        TCGA-G4-6303        TCGA-G4-6304        TCGA-G4-6306 
"C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" 
       TCGA-G4-6307        TCGA-G4-6309        TCGA-G4-6310        TCGA-G4-6315 
"C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" 
       TCGA-G4-6317        TCGA-G4-6321        TCGA-G4-6323        TCGA-G4-6586 
"C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" 
       TCGA-G4-6588        TCGA-G4-6625        TCGA-G4-6626        TCGA-G4-6628 
"C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2691        TCGA-AF-2692 
"C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" 
       TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3913        TCGA-AF-4110 
"C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" 
       TCGA-AF-5654        TCGA-AF-6136        TCGA-AF-6655        TCGA-AF-6672 
"C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" 
       TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6549        TCGA-AH-6643 
"C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" 
       TCGA-AH-6644        TCGA-CI-6619        TCGA-CI-6620        TCGA-CI-6621 
"C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" 
       TCGA-CI-6622        TCGA-CI-6624        TCGA-CL-5917        TCGA-CL-5918 
"C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" 
       TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6155        TCGA-DC-6157 
"C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" 
       TCGA-DC-6158        TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682 
"C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" 
       TCGA-DC-6683        TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC 
"C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" 
       TCGA-DY-A1DD        TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8 
"C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" 
       TCGA-EF-5830        TCGA-EI-6506        TCGA-EI-6507        TCGA-EI-6508 
"C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" 
       TCGA-EI-6510        TCGA-F5-6464        TCGA-F5-6465        TCGA-F5-6571 
"C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" 
       TCGA-F5-6702        TCGA-F5-6811        TCGA-F5-6812        TCGA-F5-6813 
"C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" 
       TCGA-G5-6235        TCGA-G5-6641 
"C2ORF49 WILD-TYPE" "C2ORF49 WILD-TYPE" 

Clustering(2142) Variable = ATG4D MUTATION ANALYSIS
D2142V1, survival
                 sevent
clus2               0   1
  ATG4D MUTATED    10   2
  ATG4D WILD-TYPE 368  91
  ATG4D MUTATED ATG4D WILD-TYPE 
             12             459 
  ATG4D MUTATED ATG4D WILD-TYPE 
              2              91 
$`ATG4D MUTATED`
TCGA-AA-3492 TCGA-AA-3672 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3819 TCGA-D5-6928 
        3.02         0.92        19.04        19.04        25.02        11.64 
TCGA-F4-6856 TCGA-G4-6586 TCGA-G4-6628 TCGA-AG-3605 TCGA-AG-A002 TCGA-F5-6465 
       35.31        35.80        79.69         0.99        20.98        49.51 

$`ATG4D WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 
        6.97        54.02         2.01        14.01        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
        5.03        85.05        26.99        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
        0.99         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
       14.30         9.04         9.44         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       26.17        91.79        46.75        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
       18.28         9.96        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  ATG4D MUTATED ATG4D WILD-TYPE 
           0.92            0.00 
  ATG4D MUTATED ATG4D WILD-TYPE 
          79.69          148.01 
  ATG4D MUTATED ATG4D WILD-TYPE 
          20.01           20.19 
[1] "0.9 - 79.7 (20.0)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.1"
D2142V2, continuous
D2142V3, binary
                 cls
clus                0   1
  ATG4D MUTATED     9   3
  ATG4D WILD-TYPE 357 116
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ATG4D MUTATED      9    3
  ATG4D WILD-TYPE  357  116
        clus
vv       ATG4D MUTATED ATG4D WILD-TYPE
  COLON              9             357
  RECTUM             3             116
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ATG4D MUTATED         3        0        2         4         0         0
  ATG4D WILD-TYPE      88        1       30       134        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ATG4D MUTATED           1          0          0          0        2         0
  ATG4D WILD-TYPE        23         11         59         42       46        18
                 vv
clus              STAGE IVB
  ATG4D MUTATED           0
  ATG4D WILD-TYPE         1
D2142V4, multiclass
            clus
vv           ATG4D MUTATED ATG4D WILD-TYPE
  STAGE I                3              88
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA              4             134
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             0              42
  STAGE IV               2              46
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ATG4D MUTATED     0   3   9   0
  ATG4D WILD-TYPE  17  89 320  50
D2142V5, multiclass
    clus
vv   ATG4D MUTATED ATG4D WILD-TYPE
  T1             0              17
  T2             3              89
  T3             9             320
  T4             0              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  ATG4D MUTATED    10   2   0
  ATG4D WILD-TYPE 277 111  87
D2142V6, multiclass
    clus
vv   ATG4D MUTATED ATG4D WILD-TYPE
  N0            10             277
  N1             2             111
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2142V7, binary
                 cls
clus                0   1
  ATG4D MUTATED    10   2
  ATG4D WILD-TYPE 365  63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ATG4D MUTATED     10    2
  ATG4D WILD-TYPE  365   63
   clus
vv  ATG4D MUTATED ATG4D WILD-TYPE
  0            10             365
  1             2              63
[1] 2 2
[1] FALSE
D2142V8, binary
                 cls
clus                0   1
  ATG4D MUTATED     6   6
  ATG4D WILD-TYPE 219 258
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ATG4D MUTATED      6    6
  ATG4D WILD-TYPE  219  258
        clus
vv       ATG4D MUTATED ATG4D WILD-TYPE
  FEMALE             6             219
  MALE               6             258
[1] 2 2
[1] FALSE
D2142V9, binary
                 cls
clus                0   1
  ATG4D MUTATED    10   1
  ATG4D WILD-TYPE 340  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ATG4D MUTATED     10    1
  ATG4D WILD-TYPE  340   21
     clus
vv    ATG4D MUTATED ATG4D WILD-TYPE
  NO             10             340
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ATG4D MUTATED                      7                             2
  ATG4D WILD-TYPE                  308                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ATG4D MUTATED                       3                              0
  ATG4D WILD-TYPE                   103                             10
D2142V10, multiclass
                                clus
vv                               ATG4D MUTATED ATG4D WILD-TYPE
  COLON ADENOCARCINOMA                       7             308
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      3             103
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  ATG4D MUTATED    10   0   2   0
  ATG4D WILD-TYPE 335   4  29  25
D2142V11, multiclass
    clus
vv   ATG4D MUTATED ATG4D WILD-TYPE
  R0            10             335
  R1             0               4
  R2             2              29
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2142V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ATG4D MUTATED                                  0     0
  ATG4D WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ATG4D MUTATED                           0     5
  ATG4D WILD-TYPE                        22   221
D2142V13, multiclass
                                  clus
vv                                 ATG4D MUTATED ATG4D WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        5             221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2143) Variable = MUS81 MUTATION ANALYSIS
D2143V1, survival
                 sevent
clus2               0   1
  MUS81 MUTATED     7   0
  MUS81 WILD-TYPE 371  93
  MUS81 MUTATED MUS81 WILD-TYPE 
              7             464 
  MUS81 MUTATED MUS81 WILD-TYPE 
              0              93 
$`MUS81 MUTATED`
TCGA-A6-5665 TCGA-AA-3877 TCGA-AD-6889 TCGA-AY-6197 TCGA-CK-4947 TCGA-CM-5861 
       22.06        31.00        56.55        21.44        17.56        15.02 
TCGA-CM-5864 
       15.02 

$`MUS81 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 
       17.03        24.03        27.02        29.98        18.05         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       10.06        14.30       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 
       22.03        22.98        30.08        32.02         5.03        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  MUS81 MUTATED MUS81 WILD-TYPE 
          15.02            0.00 
  MUS81 MUTATED MUS81 WILD-TYPE 
          56.55          148.01 
  MUS81 MUTATED MUS81 WILD-TYPE 
         21.440          20.155 
[1] "15.0 - 56.5 (21.4)" "0.0 - 148.0 (20.2)"
[1] "hr="     "9100000"
D2143V2, continuous
D2143V3, binary
                 cls
clus                0   1
  MUS81 MUTATED     7   0
  MUS81 WILD-TYPE 359 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MUS81 MUTATED      7    0
  MUS81 WILD-TYPE  359  119
        clus
vv       MUS81 MUTATED MUS81 WILD-TYPE
  COLON              7             359
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MUS81 MUTATED         2        0        0         4         0         0
  MUS81 WILD-TYPE      89        1       32       134        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  MUS81 MUTATED           0          0          1          0        0         0
  MUS81 WILD-TYPE        24         11         58         42       48        18
                 vv
clus              STAGE IVB
  MUS81 MUTATED           0
  MUS81 WILD-TYPE         1
D2143V4, multiclass
            clus
vv           MUS81 MUTATED MUS81 WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              4             134
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  MUS81 MUTATED     1   1   4   1
  MUS81 WILD-TYPE  16  91 325  49
D2143V5, multiclass
    clus
vv   MUS81 MUTATED MUS81 WILD-TYPE
  T1             1              16
  T2             1              91
  T3             4             325
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  MUS81 MUTATED     6   1   0
  MUS81 WILD-TYPE 281 112  87
D2143V6, multiclass
    clus
vv   MUS81 MUTATED MUS81 WILD-TYPE
  N0             6             281
  N1             1             112
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2143V7, binary
                 cls
clus                0   1
  MUS81 MUTATED     6   0
  MUS81 WILD-TYPE 369  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MUS81 MUTATED      6    0
  MUS81 WILD-TYPE  369   65
   clus
vv  MUS81 MUTATED MUS81 WILD-TYPE
  0             6             369
  1             0              65
[1] 2 2
[1] FALSE
D2143V8, binary
                 cls
clus                0   1
  MUS81 MUTATED     4   3
  MUS81 WILD-TYPE 221 261
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MUS81 MUTATED      4    3
  MUS81 WILD-TYPE  221  261
        clus
vv       MUS81 MUTATED MUS81 WILD-TYPE
  FEMALE             4             221
  MALE               3             261
[1] 2 2
[1] FALSE
D2143V9, binary
                 cls
clus                0   1
  MUS81 MUTATED     6   0
  MUS81 WILD-TYPE 344  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MUS81 MUTATED      6    0
  MUS81 WILD-TYPE  344   22
     clus
vv    MUS81 MUTATED MUS81 WILD-TYPE
  NO              6             344
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MUS81 MUTATED                      6                             1
  MUS81 WILD-TYPE                  309                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MUS81 MUTATED                       0                              0
  MUS81 WILD-TYPE                   106                             10
D2143V10, multiclass
                                clus
vv                               MUS81 MUTATED MUS81 WILD-TYPE
  COLON ADENOCARCINOMA                       6             309
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  MUS81 MUTATED     5   0   0   1
  MUS81 WILD-TYPE 340   4  31  24
D2143V11, multiclass
    clus
vv   MUS81 MUTATED MUS81 WILD-TYPE
  R0             5             340
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2143V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MUS81 MUTATED                                  0     1
  MUS81 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  MUS81 MUTATED                           0     5
  MUS81 WILD-TYPE                        22   221
D2143V13, multiclass
                                  clus
vv                                 MUS81 MUTATED MUS81 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        5             221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2144) Variable = AKT1 MUTATION ANALYSIS
D2144V1, survival
                sevent
clus2              0   1
  AKT1 MUTATED     6   5
  AKT1 WILD-TYPE 372  88
  AKT1 MUTATED AKT1 WILD-TYPE 
            11            460 
  AKT1 MUTATED AKT1 WILD-TYPE 
             5             88 
$`AKT1 MUTATED`
TCGA-A6-5661 TCGA-A6-6141 TCGA-AA-3492 TCGA-AA-3516 TCGA-AA-3715 TCGA-AD-6889 
       33.53         8.38         3.02        13.02        19.04        56.55 
TCGA-AZ-6605 TCGA-CM-5864 TCGA-CM-6166 TCGA-D5-5537 TCGA-G4-6586 
        5.23        15.02        21.99        45.40        35.80 

$`AKT1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 
       22.06        32.71        27.09        22.52        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       19.66        20.28         7.04         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        6.97         1.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       26.99        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
        0.07        21.37        15.52         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6606 
       49.41         6.77        12.10       100.01        29.56        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5868 
       30.08        32.02        15.02         5.03        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6167 
       15.02        12.00         2.96        29.03        16.04        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  AKT1 MUTATED AKT1 WILD-TYPE 
          3.02           0.00 
  AKT1 MUTATED AKT1 WILD-TYPE 
         56.55         148.01 
  AKT1 MUTATED AKT1 WILD-TYPE 
        19.040         20.235 
[1] "3.0 - 56.5 (19.0)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "2.6"
D2144V2, continuous
D2144V3, binary
                cls
clus               0   1
  AKT1 MUTATED    11   0
  AKT1 WILD-TYPE 355 119
[1] "tbl2"
                cls
clus             [,1] [,2]
  AKT1 MUTATED     11    0
  AKT1 WILD-TYPE  355  119
        clus
vv       AKT1 MUTATED AKT1 WILD-TYPE
  COLON            11            355
  RECTUM            0            119
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  AKT1 MUTATED         2        0        2         5         0         0
  AKT1 WILD-TYPE      89        1       30       133        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AKT1 MUTATED           1          0          1          0        0         0
  AKT1 WILD-TYPE        23         11         58         42       48        18
                vv
clus             STAGE IVB
  AKT1 MUTATED           0
  AKT1 WILD-TYPE         1
D2144V4, multiclass
            clus
vv           AKT1 MUTATED AKT1 WILD-TYPE
  STAGE I               2             89
  STAGE IA              0              1
  STAGE II              2             30
  STAGE IIA             5            133
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             1             23
  STAGE IIIA            0             11
  STAGE IIIB            1             58
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  AKT1 MUTATED     0   2   8   1
  AKT1 WILD-TYPE  17  90 321  49
D2144V5, multiclass
    clus
vv   AKT1 MUTATED AKT1 WILD-TYPE
  T1            0             17
  T2            2             90
  T3            8            321
  T4            1             49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  AKT1 MUTATED     8   1   2
  AKT1 WILD-TYPE 279 112  85
D2144V6, multiclass
    clus
vv   AKT1 MUTATED AKT1 WILD-TYPE
  N0            8            279
  N1            1            112
  N2            2             85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2144V7, binary
                cls
clus               0   1
  AKT1 MUTATED    10   0
  AKT1 WILD-TYPE 365  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  AKT1 MUTATED     10    0
  AKT1 WILD-TYPE  365   65
   clus
vv  AKT1 MUTATED AKT1 WILD-TYPE
  0           10            365
  1            0             65
[1] 2 2
[1] FALSE
D2144V8, binary
                cls
clus               0   1
  AKT1 MUTATED     5   6
  AKT1 WILD-TYPE 220 258
[1] "tbl2"
                cls
clus             [,1] [,2]
  AKT1 MUTATED      5    6
  AKT1 WILD-TYPE  220  258
        clus
vv       AKT1 MUTATED AKT1 WILD-TYPE
  FEMALE            5            220
  MALE              6            258
[1] 2 2
[1] FALSE
D2144V9, binary
                cls
clus               0   1
  AKT1 MUTATED    10   0
  AKT1 WILD-TYPE 340  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  AKT1 MUTATED     10    0
  AKT1 WILD-TYPE  340   22
     clus
vv    AKT1 MUTATED AKT1 WILD-TYPE
  NO            10            340
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  AKT1 MUTATED                     10                             1
  AKT1 WILD-TYPE                  305                            46
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  AKT1 MUTATED                       0                              0
  AKT1 WILD-TYPE                   106                             10
D2144V10, multiclass
                                clus
vv                               AKT1 MUTATED AKT1 WILD-TYPE
  COLON ADENOCARCINOMA                     10            305
  COLON MUCINOUS ADENOCARCINOMA             1             46
  RECTAL ADENOCARCINOMA                     0            106
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  AKT1 MUTATED     6   0   0   1
  AKT1 WILD-TYPE 339   4  31  24
D2144V11, multiclass
    clus
vv   AKT1 MUTATED AKT1 WILD-TYPE
  R0            6            339
  R1            0              4
  R2            0             31
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2144V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AKT1 MUTATED                                  0     1
  AKT1 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  AKT1 MUTATED                           2     5
  AKT1 WILD-TYPE                        20   221
D2144V13, multiclass
                                  clus
vv                                 AKT1 MUTATED AKT1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   2             20
  WHITE                                       5            221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2145) Variable = OGFRL1 MUTATION ANALYSIS
D2145V1, survival
                  sevent
clus2                0   1
  OGFRL1 MUTATED     8   2
  OGFRL1 WILD-TYPE 370  91
  OGFRL1 MUTATED OGFRL1 WILD-TYPE 
              10              461 
  OGFRL1 MUTATED OGFRL1 WILD-TYPE 
               2               91 
$`OGFRL1 MUTATED`
TCGA-AA-3510 TCGA-AA-3555 TCGA-AA-3713 TCGA-AA-A00N TCGA-AD-5900 TCGA-CA-6718 
       63.98        29.95        19.04         4.01         0.07        10.06 
TCGA-CM-5861 TCGA-AG-3598 TCGA-AG-3902 TCGA-AG-A002 
       15.02        50.04        32.02        20.98 

$`OGFRL1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       13.02        24.00        17.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
       40.96        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 
        3.25         3.29         0.07        12.20        12.76        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       22.98        30.08        32.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3599 
       24.00         1.02        46.03        34.03         2.01        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3909 
       13.02        35.01        14.01         1.02        48.03        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  OGFRL1 MUTATED OGFRL1 WILD-TYPE 
            0.07             0.00 
  OGFRL1 MUTATED OGFRL1 WILD-TYPE 
           63.98           148.01 
  OGFRL1 MUTATED OGFRL1 WILD-TYPE 
           20.01            20.19 
[1] "0.1 - 64.0 (20.0)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1"  
D2145V2, continuous
D2145V3, binary
                  cls
clus                 0   1
  OGFRL1 MUTATED     7   3
  OGFRL1 WILD-TYPE 359 116
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OGFRL1 MUTATED      7    3
  OGFRL1 WILD-TYPE  359  116
        clus
vv       OGFRL1 MUTATED OGFRL1 WILD-TYPE
  COLON               7              359
  RECTUM              3              116
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  OGFRL1 MUTATED         2        0        1         5         1         0
  OGFRL1 WILD-TYPE      89        1       31       133         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  OGFRL1 MUTATED           0          0          0          0        1
  OGFRL1 WILD-TYPE        24         11         59         42       47
                  vv
clus               STAGE IVA STAGE IVB
  OGFRL1 MUTATED           0         0
  OGFRL1 WILD-TYPE        18         1
D2145V4, multiclass
            clus
vv           OGFRL1 MUTATED OGFRL1 WILD-TYPE
  STAGE I                 2               89
  STAGE IA                0                1
  STAGE II                1               31
  STAGE IIA               5              133
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              0               59
  STAGE IIIC              0               42
  STAGE IV                1               47
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  OGFRL1 MUTATED     0   2   7   1
  OGFRL1 WILD-TYPE  17  90 322  49
D2145V5, multiclass
    clus
vv   OGFRL1 MUTATED OGFRL1 WILD-TYPE
  T1              0               17
  T2              2               90
  T3              7              322
  T4              1               49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  OGFRL1 MUTATED    10   0   0
  OGFRL1 WILD-TYPE 277 113  87
D2145V6, multiclass
    clus
vv   OGFRL1 MUTATED OGFRL1 WILD-TYPE
  N0             10              277
  N1              0              113
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2145V7, binary
                  cls
clus                 0   1
  OGFRL1 MUTATED     8   1
  OGFRL1 WILD-TYPE 367  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OGFRL1 MUTATED      8    1
  OGFRL1 WILD-TYPE  367   64
   clus
vv  OGFRL1 MUTATED OGFRL1 WILD-TYPE
  0              8              367
  1              1               64
[1] 2 2
[1] FALSE
D2145V8, binary
                  cls
clus                 0   1
  OGFRL1 MUTATED     2   8
  OGFRL1 WILD-TYPE 223 256
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OGFRL1 MUTATED      2    8
  OGFRL1 WILD-TYPE  223  256
        clus
vv       OGFRL1 MUTATED OGFRL1 WILD-TYPE
  FEMALE              2              223
  MALE                8              256
[1] 2 2
[1] FALSE
D2145V9, binary
                  cls
clus                 0   1
  OGFRL1 MUTATED     7   1
  OGFRL1 WILD-TYPE 343  21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OGFRL1 MUTATED      7    1
  OGFRL1 WILD-TYPE  343   21
     clus
vv    OGFRL1 MUTATED OGFRL1 WILD-TYPE
  NO               7              343
  YES              1               21
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  OGFRL1 MUTATED                      4                             3
  OGFRL1 WILD-TYPE                  311                            44
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  OGFRL1 MUTATED                       3                              0
  OGFRL1 WILD-TYPE                   103                             10
D2145V10, multiclass
                                clus
vv                               OGFRL1 MUTATED OGFRL1 WILD-TYPE
  COLON ADENOCARCINOMA                        4              311
  COLON MUCINOUS ADENOCARCINOMA               3               44
  RECTAL ADENOCARCINOMA                       3              103
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  OGFRL1 MUTATED     8   0   1   1
  OGFRL1 WILD-TYPE 337   4  30  24
D2145V11, multiclass
    clus
vv   OGFRL1 MUTATED OGFRL1 WILD-TYPE
  R0              8              337
  R1              0                4
  R2              1               30
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2145V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OGFRL1 MUTATED                                  0     1
  OGFRL1 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  OGFRL1 MUTATED                           0     2
  OGFRL1 WILD-TYPE                        22   224
D2145V13, multiclass
                                  clus
vv                                 OGFRL1 MUTATED OGFRL1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         2              224
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2146) Variable = VPS72 MUTATION ANALYSIS
D2146V1, survival
                 sevent
clus2               0   1
  VPS72 MUTATED     8   0
  VPS72 WILD-TYPE 370  93
  VPS72 MUTATED VPS72 WILD-TYPE 
              8             463 
  VPS72 MUTATED VPS72 WILD-TYPE 
              0              93 
$`VPS72 MUTATED`
TCGA-A6-5665 TCGA-AA-3864 TCGA-AD-5900 TCGA-CM-5348 TCGA-CM-6171 TCGA-D5-6927 
       22.06        53.00         0.07        22.98        14.04         9.44 
TCGA-D5-6931 TCGA-G4-6309 
       12.00        85.48 

$`VPS72 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 
       32.05         0.99        31.07        31.07        30.05        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       39.98        18.05        40.96        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       13.02        29.06        22.03        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       13.02        15.02        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6932 
       14.30         9.04        11.64         4.80         1.51        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  VPS72 MUTATED VPS72 WILD-TYPE 
           0.07            0.00 
  VPS72 MUTATED VPS72 WILD-TYPE 
          85.48          148.01 
  VPS72 MUTATED VPS72 WILD-TYPE 
          18.05           20.19 
[1] "0.1 - 85.5 (18.0)"  "0.0 - 148.0 (20.2)"
[1] "hr="     "9200000"
D2146V2, continuous
D2146V3, binary
                 cls
clus                0   1
  VPS72 MUTATED     8   0
  VPS72 WILD-TYPE 358 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VPS72 MUTATED      8    0
  VPS72 WILD-TYPE  358  119
        clus
vv       VPS72 MUTATED VPS72 WILD-TYPE
  COLON              8             358
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  VPS72 MUTATED         2        0        1         2         0         0
  VPS72 WILD-TYPE      89        1       31       136        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  VPS72 MUTATED           0          0          2          1        0         0
  VPS72 WILD-TYPE        24         11         57         41       48        18
                 vv
clus              STAGE IVB
  VPS72 MUTATED           0
  VPS72 WILD-TYPE         1
D2146V4, multiclass
            clus
vv           VPS72 MUTATED VPS72 WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              2             136
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             2              57
  STAGE IIIC             1              41
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  VPS72 MUTATED     0   2   5   1
  VPS72 WILD-TYPE  17  90 324  49
D2146V5, multiclass
    clus
vv   VPS72 MUTATED VPS72 WILD-TYPE
  T1             0              17
  T2             2              90
  T3             5             324
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  VPS72 MUTATED     5   2   1
  VPS72 WILD-TYPE 282 111  86
D2146V6, multiclass
    clus
vv   VPS72 MUTATED VPS72 WILD-TYPE
  N0             5             282
  N1             2             111
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2146V7, binary
                 cls
clus                0   1
  VPS72 MUTATED     7   0
  VPS72 WILD-TYPE 368  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VPS72 MUTATED      7    0
  VPS72 WILD-TYPE  368   65
   clus
vv  VPS72 MUTATED VPS72 WILD-TYPE
  0             7             368
  1             0              65
[1] 2 2
[1] FALSE
D2146V8, binary
                 cls
clus                0   1
  VPS72 MUTATED     3   5
  VPS72 WILD-TYPE 222 259
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VPS72 MUTATED      3    5
  VPS72 WILD-TYPE  222  259
        clus
vv       VPS72 MUTATED VPS72 WILD-TYPE
  FEMALE             3             222
  MALE               5             259
[1] 2 2
[1] FALSE
D2146V9, binary
                 cls
clus                0   1
  VPS72 MUTATED     7   0
  VPS72 WILD-TYPE 343  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  VPS72 MUTATED      7    0
  VPS72 WILD-TYPE  343   22
     clus
vv    VPS72 MUTATED VPS72 WILD-TYPE
  NO              7             343
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  VPS72 MUTATED                      7                             1
  VPS72 WILD-TYPE                  308                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  VPS72 MUTATED                       0                              0
  VPS72 WILD-TYPE                   106                             10
D2146V10, multiclass
                                clus
vv                               VPS72 MUTATED VPS72 WILD-TYPE
  COLON ADENOCARCINOMA                       7             308
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  VPS72 MUTATED     8   0   0   0
  VPS72 WILD-TYPE 337   4  31  25
D2146V11, multiclass
    clus
vv   VPS72 MUTATED VPS72 WILD-TYPE
  R0             8             337
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2146V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  VPS72 MUTATED                                  0     0
  VPS72 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  VPS72 MUTATED                           1     6
  VPS72 WILD-TYPE                        21   220
D2146V13, multiclass
                                  clus
vv                                 VPS72 MUTATED VPS72 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        6             220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2147) Variable = ALG9 MUTATION ANALYSIS
D2147V1, survival
                sevent
clus2              0   1
  ALG9 MUTATED     3   1
  ALG9 WILD-TYPE 375  92
  ALG9 MUTATED ALG9 WILD-TYPE 
             4            467 
  ALG9 MUTATED ALG9 WILD-TYPE 
             1             92 
$`ALG9 MUTATED`
TCGA-AA-3496 TCGA-AA-3715 TCGA-AU-6004 TCGA-AG-3892 
        1.02        19.04        27.09        13.02 

$`ALG9 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 
       36.00         5.03        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       10.88         0.20        14.50        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 
       19.99         1.02        17.95        36.95        17.03        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  ALG9 MUTATED ALG9 WILD-TYPE 
          1.02           0.00 
  ALG9 MUTATED ALG9 WILD-TYPE 
         27.09         148.01 
  ALG9 MUTATED ALG9 WILD-TYPE 
         16.03          20.28 
[1] "1.0 - 27.1 (16.0)"  "0.0 - 148.0 (20.3)"
[1] "hr=" "2.2"
D2147V2, continuous
D2147V3, binary
                cls
clus               0   1
  ALG9 MUTATED     3   1
  ALG9 WILD-TYPE 363 118
[1] "tbl2"
                cls
clus             [,1] [,2]
  ALG9 MUTATED      3    1
  ALG9 WILD-TYPE  363  118
        clus
vv       ALG9 MUTATED ALG9 WILD-TYPE
  COLON             3            363
  RECTUM            1            118
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ALG9 MUTATED         2        0        2         0         0         0
  ALG9 WILD-TYPE      89        1       30       138        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ALG9 MUTATED           0          0          0          0        0         0
  ALG9 WILD-TYPE        24         11         59         42       48        18
                vv
clus             STAGE IVB
  ALG9 MUTATED           0
  ALG9 WILD-TYPE         1
D2147V4, multiclass
            clus
vv           ALG9 MUTATED ALG9 WILD-TYPE
  STAGE I               2             89
  STAGE IA              0              1
  STAGE II              2             30
  STAGE IIA             0            138
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            0             59
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  ALG9 MUTATED     1   1   2   0
  ALG9 WILD-TYPE  16  91 327  50
D2147V5, multiclass
    clus
vv   ALG9 MUTATED ALG9 WILD-TYPE
  T1            1             16
  T2            1             91
  T3            2            327
  T4            0             50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  ALG9 MUTATED     4   0   0
  ALG9 WILD-TYPE 283 113  87
D2147V6, multiclass
    clus
vv   ALG9 MUTATED ALG9 WILD-TYPE
  N0            4            283
  N1            0            113
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2147V7, binary
                cls
clus               0   1
  ALG9 MUTATED     4   0
  ALG9 WILD-TYPE 371  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  ALG9 MUTATED      4    0
  ALG9 WILD-TYPE  371   65
   clus
vv  ALG9 MUTATED ALG9 WILD-TYPE
  0            4            371
  1            0             65
[1] 2 2
[1] FALSE
D2147V8, binary
                cls
clus               0   1
  ALG9 MUTATED     3   1
  ALG9 WILD-TYPE 222 263
[1] "tbl2"
                cls
clus             [,1] [,2]
  ALG9 MUTATED      3    1
  ALG9 WILD-TYPE  222  263
        clus
vv       ALG9 MUTATED ALG9 WILD-TYPE
  FEMALE            3            222
  MALE              1            263
[1] 2 2
[1] FALSE
D2147V9, binary
                cls
clus               0   1
  ALG9 MUTATED     2   0
  ALG9 WILD-TYPE 348  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  ALG9 MUTATED      2    0
  ALG9 WILD-TYPE  348   22
     clus
vv    ALG9 MUTATED ALG9 WILD-TYPE
  NO             2            348
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ALG9 MUTATED                      3                             0
  ALG9 WILD-TYPE                  312                            47
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ALG9 MUTATED                       1                              0
  ALG9 WILD-TYPE                   105                             10
D2147V10, multiclass
                                clus
vv                               ALG9 MUTATED ALG9 WILD-TYPE
  COLON ADENOCARCINOMA                      3            312
  COLON MUCINOUS ADENOCARCINOMA             0             47
  RECTAL ADENOCARCINOMA                     1            105
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  ALG9 MUTATED     4   0   0   0
  ALG9 WILD-TYPE 341   4  31  25
D2147V11, multiclass
    clus
vv   ALG9 MUTATED ALG9 WILD-TYPE
  R0            4            341
  R1            0              4
  R2            0             31
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2147V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ALG9 MUTATED                                  0     0
  ALG9 WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  ALG9 MUTATED                           0     1
  ALG9 WILD-TYPE                        22   225
D2147V13, multiclass
[1] "Remove cluster labels:" "ALG9 MUTATED"          
clus
  ALG9 MUTATED ALG9 WILD-TYPE 
             1            259 
    TCGA-A6-2671     TCGA-A6-2672     TCGA-A6-2674     TCGA-A6-2676 
"ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" 
    TCGA-A6-2677     TCGA-A6-2678     TCGA-A6-2683     TCGA-A6-3807 
"ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" 
    TCGA-A6-3808     TCGA-A6-3809     TCGA-A6-3810     TCGA-A6-4105 
"ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" 
    TCGA-A6-5656     TCGA-A6-5657     TCGA-A6-5659     TCGA-A6-5660 
"ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" 
    TCGA-A6-5661     TCGA-A6-5662     TCGA-A6-5664     TCGA-A6-5665 
"ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" 
    TCGA-A6-5666     TCGA-A6-6137     TCGA-A6-6138     TCGA-A6-6141 
"ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" 
    TCGA-A6-6142     TCGA-A6-6648     TCGA-A6-6649     TCGA-A6-6651 
"ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" 
    TCGA-A6-6652     TCGA-A6-6653     TCGA-A6-6654     TCGA-A6-6780 
"ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" 
    TCGA-A6-6781     TCGA-A6-6782     TCGA-AD-5900     TCGA-AD-6548 
"ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" 
    TCGA-AD-6888     TCGA-AD-6889     TCGA-AD-6890     TCGA-AD-6895 
"ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" 
    TCGA-AD-6899     TCGA-AD-6901     TCGA-AD-6963     TCGA-AD-6964 
"ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" 
    TCGA-AD-6965     TCGA-AU-3779     TCGA-AY-4070     TCGA-AY-4071 
"ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" 
    TCGA-AY-5543     TCGA-AY-6196     TCGA-AY-6197     TCGA-AY-6386 
"ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" 
    TCGA-AZ-4315     TCGA-AZ-4323     TCGA-AZ-4616     TCGA-AZ-4681 
"ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" 
    TCGA-AZ-4682     TCGA-AZ-5403     TCGA-AZ-5407     TCGA-AZ-6598 
"ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" 
    TCGA-AZ-6599     TCGA-AZ-6600     TCGA-AZ-6601     TCGA-AZ-6603 
"ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" 
    TCGA-AZ-6605     TCGA-AZ-6606     TCGA-AZ-6607     TCGA-AZ-6608 
"ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" 
    TCGA-CA-5254     TCGA-CA-5255     TCGA-CA-5796     TCGA-CA-5797 
"ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" 
    TCGA-CA-6715     TCGA-CA-6716     TCGA-CA-6717     TCGA-CA-6718 
"ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" 
    TCGA-CA-6719     TCGA-CK-4947     TCGA-CK-4948     TCGA-CK-4950 
"ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" 
    TCGA-CK-4952     TCGA-CK-5912     TCGA-CK-5913     TCGA-CK-5914 
"ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" 
    TCGA-CK-5915     TCGA-CK-5916     TCGA-CK-6746     TCGA-CK-6747 
"ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" 
    TCGA-CK-6748     TCGA-CK-6751     TCGA-CM-4743     TCGA-CM-4744 
"ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" 
    TCGA-CM-4746     TCGA-CM-4747     TCGA-CM-4752     TCGA-CM-5341 
"ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" 
    TCGA-CM-5344     TCGA-CM-5348     TCGA-CM-5349     TCGA-CM-5860 
"ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" 
    TCGA-CM-5861     TCGA-CM-5862     TCGA-CM-5863     TCGA-CM-5864 
"ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" 
    TCGA-CM-5868     TCGA-CM-6161     TCGA-CM-6162     TCGA-CM-6163 
"ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" 
    TCGA-CM-6164     TCGA-CM-6165     TCGA-CM-6166     TCGA-CM-6167 
"ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" 
    TCGA-CM-6168     TCGA-CM-6169     TCGA-CM-6170     TCGA-CM-6171 
"ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" 
    TCGA-CM-6172     TCGA-CM-6674     TCGA-CM-6675     TCGA-CM-6676 
"ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" 
    TCGA-CM-6677     TCGA-CM-6678     TCGA-CM-6679     TCGA-CM-6680 
"ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" 
    TCGA-D5-5537     TCGA-D5-5538     TCGA-D5-5539     TCGA-D5-5540 
"ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" 
    TCGA-D5-5541     TCGA-D5-6529     TCGA-D5-6532     TCGA-D5-6533 
"ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" 
    TCGA-D5-6534     TCGA-D5-6535     TCGA-D5-6536     TCGA-D5-6537 
"ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" 
    TCGA-D5-6538     TCGA-D5-6539     TCGA-D5-6540     TCGA-D5-6541 
"ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" 
    TCGA-D5-6898     TCGA-D5-6920     TCGA-D5-6922     TCGA-D5-6923 
"ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" 
    TCGA-D5-6924     TCGA-D5-6926     TCGA-D5-6927     TCGA-D5-6928 
"ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" 
    TCGA-D5-6929     TCGA-D5-6930     TCGA-D5-6931     TCGA-D5-6932 
"ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" 
    TCGA-D5-7000     TCGA-DM-A0X9     TCGA-DM-A0XD     TCGA-DM-A0XF 
"ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" 
    TCGA-DM-A1D0     TCGA-DM-A1D4     TCGA-DM-A1D6     TCGA-DM-A1D7 
"ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" 
    TCGA-DM-A1D8     TCGA-DM-A1D9     TCGA-DM-A1DA     TCGA-DM-A1DB 
"ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" 
    TCGA-DM-A1HA     TCGA-DM-A1HB     TCGA-DM-A282     TCGA-DM-A285 
"ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" 
    TCGA-DM-A28C     TCGA-DM-A28E     TCGA-DM-A28F     TCGA-DM-A28G 
"ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" 
    TCGA-DM-A28H     TCGA-DM-A28K     TCGA-F4-6459     TCGA-F4-6460 
"ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" 
    TCGA-F4-6569     TCGA-F4-6570     TCGA-F4-6703     TCGA-F4-6704 
"ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" 
    TCGA-F4-6805     TCGA-F4-6806     TCGA-F4-6807     TCGA-F4-6808 
"ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" 
    TCGA-F4-6809     TCGA-F4-6854     TCGA-F4-6855     TCGA-F4-6856 
"ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" 
    TCGA-G4-6293     TCGA-G4-6299     TCGA-G4-6303     TCGA-G4-6304 
"ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" 
    TCGA-G4-6306     TCGA-G4-6307     TCGA-G4-6309     TCGA-G4-6310 
"ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" 
    TCGA-G4-6315     TCGA-G4-6317     TCGA-G4-6321     TCGA-G4-6323 
"ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" 
    TCGA-G4-6586     TCGA-G4-6588     TCGA-G4-6625     TCGA-G4-6626 
"ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" 
    TCGA-G4-6628     TCGA-AF-2687     TCGA-AF-2689     TCGA-AF-2691 
"ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" 
    TCGA-AF-2692     TCGA-AF-2693     TCGA-AF-3400     TCGA-AF-3913 
"ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" 
    TCGA-AF-4110     TCGA-AF-5654     TCGA-AF-6136     TCGA-AF-6655 
"ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" 
    TCGA-AF-6672     TCGA-AH-6544     TCGA-AH-6547     TCGA-AH-6549 
"ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" 
    TCGA-AH-6643     TCGA-AH-6644     TCGA-CI-6619     TCGA-CI-6620 
"ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" 
    TCGA-CI-6621     TCGA-CI-6622     TCGA-CI-6624     TCGA-CL-5917 
"ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" 
    TCGA-CL-5918     TCGA-DC-5337     TCGA-DC-5869     TCGA-DC-6155 
"ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" 
    TCGA-DC-6157     TCGA-DC-6158     TCGA-DC-6160     TCGA-DC-6681 
"ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" 
    TCGA-DC-6682     TCGA-DC-6683     TCGA-DT-5265     TCGA-DY-A0XA 
"ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" 
    TCGA-DY-A1DC     TCGA-DY-A1DD     TCGA-DY-A1DF     TCGA-DY-A1DG 
"ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" 
    TCGA-DY-A1H8     TCGA-EF-5830     TCGA-EI-6506     TCGA-EI-6507 
"ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" 
    TCGA-EI-6508     TCGA-EI-6510     TCGA-F5-6464     TCGA-F5-6465 
"ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" 
    TCGA-F5-6571     TCGA-F5-6702     TCGA-F5-6811     TCGA-F5-6812 
"ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" 
    TCGA-F5-6813     TCGA-G5-6235     TCGA-G5-6641 
"ALG9 WILD-TYPE" "ALG9 WILD-TYPE" "ALG9 WILD-TYPE" 

Clustering(2148) Variable = TAX1BP1 MUTATION ANALYSIS
D2148V1, survival
                   sevent
clus2                 0   1
  TAX1BP1 MUTATED    10   4
  TAX1BP1 WILD-TYPE 368  89
  TAX1BP1 MUTATED TAX1BP1 WILD-TYPE 
               14               457 
  TAX1BP1 MUTATED TAX1BP1 WILD-TYPE 
                4                89 
$`TAX1BP1 MUTATED`
TCGA-A6-5665 TCGA-AA-3864 TCGA-AA-A010 TCGA-AY-4071 TCGA-AZ-6598 TCGA-AZ-6601 
       22.06        53.00        34.98         0.95        49.41       100.01 
TCGA-CK-5913 TCGA-CK-5916 TCGA-CM-4743 TCGA-D5-6540 TCGA-D5-6927 TCGA-DM-A1HB 
       51.32        21.14        23.05        16.14         9.44       135.65 
TCGA-AG-A002 TCGA-DC-5337 
       20.98        15.02 

$`TAX1BP1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 
       32.05         0.99        31.07        31.07        30.05        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-5543 TCGA-AY-6197 
        0.20        14.50        27.09        16.31        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 
       62.79        88.21         6.77        12.10        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5914 
       17.56       148.01        85.45        15.62        49.08         9.99 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
       82.95         1.91       124.27        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       17.13        12.49        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       12.43        14.30         9.04        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
        7.50        44.32       131.51       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
       78.12         7.17         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  TAX1BP1 MUTATED TAX1BP1 WILD-TYPE 
             0.95              0.00 
  TAX1BP1 MUTATED TAX1BP1 WILD-TYPE 
           135.65            148.01 
  TAX1BP1 MUTATED TAX1BP1 WILD-TYPE 
           22.555            20.020 
[1] "0.9 - 135.7 (22.6)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1"  
D2148V2, continuous
D2148V3, binary
                   cls
clus                  0   1
  TAX1BP1 MUTATED    11   2
  TAX1BP1 WILD-TYPE 355 117
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TAX1BP1 MUTATED     11    2
  TAX1BP1 WILD-TYPE  355  117
        clus
vv       TAX1BP1 MUTATED TAX1BP1 WILD-TYPE
  COLON               11               355
  RECTUM               2               117
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TAX1BP1 MUTATED         5        0        3         4         1         0
  TAX1BP1 WILD-TYPE      86        1       29       134         9         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TAX1BP1 MUTATED           0          0          1          0        0
  TAX1BP1 WILD-TYPE        24         11         58         42       48
                   vv
clus                STAGE IVA STAGE IVB
  TAX1BP1 MUTATED           0         0
  TAX1BP1 WILD-TYPE        18         1
D2148V4, multiclass
            clus
vv           TAX1BP1 MUTATED TAX1BP1 WILD-TYPE
  STAGE I                  5                86
  STAGE IA                 0                 1
  STAGE II                 3                29
  STAGE IIA                4               134
  STAGE IIB                1                 9
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               0                11
  STAGE IIIB               1                58
  STAGE IIIC               0                42
  STAGE IV                 0                48
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  TAX1BP1 MUTATED     3   2   8   1
  TAX1BP1 WILD-TYPE  14  90 321  49
D2148V5, multiclass
    clus
vv   TAX1BP1 MUTATED TAX1BP1 WILD-TYPE
  T1               3                14
  T2               2                90
  T3               8               321
  T4               1                49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  TAX1BP1 MUTATED    13   1   0
  TAX1BP1 WILD-TYPE 274 112  87
D2148V6, multiclass
    clus
vv   TAX1BP1 MUTATED TAX1BP1 WILD-TYPE
  N0              13               274
  N1               1               112
  N2               0                87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2148V7, binary
                   cls
clus                  0   1
  TAX1BP1 MUTATED    11   0
  TAX1BP1 WILD-TYPE 364  65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TAX1BP1 MUTATED     11    0
  TAX1BP1 WILD-TYPE  364   65
   clus
vv  TAX1BP1 MUTATED TAX1BP1 WILD-TYPE
  0              11               364
  1               0                65
[1] 2 2
[1] FALSE
D2148V8, binary
                   cls
clus                  0   1
  TAX1BP1 MUTATED     6   8
  TAX1BP1 WILD-TYPE 219 256
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TAX1BP1 MUTATED      6    8
  TAX1BP1 WILD-TYPE  219  256
        clus
vv       TAX1BP1 MUTATED TAX1BP1 WILD-TYPE
  FEMALE               6               219
  MALE                 8               256
[1] 2 2
[1] FALSE
D2148V9, binary
                   cls
clus                  0   1
  TAX1BP1 MUTATED    13   0
  TAX1BP1 WILD-TYPE 337  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TAX1BP1 MUTATED     13    0
  TAX1BP1 WILD-TYPE  337   22
     clus
vv    TAX1BP1 MUTATED TAX1BP1 WILD-TYPE
  NO               13               337
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  TAX1BP1 MUTATED                      9                             1
  TAX1BP1 WILD-TYPE                  306                            46
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  TAX1BP1 MUTATED                       2                              0
  TAX1BP1 WILD-TYPE                   104                             10
D2148V10, multiclass
                                clus
vv                               TAX1BP1 MUTATED TAX1BP1 WILD-TYPE
  COLON ADENOCARCINOMA                         9               306
  COLON MUCINOUS ADENOCARCINOMA                1                46
  RECTAL ADENOCARCINOMA                        2               104
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  TAX1BP1 MUTATED     9   0   0   2
  TAX1BP1 WILD-TYPE 336   4  31  23
D2148V11, multiclass
    clus
vv   TAX1BP1 MUTATED TAX1BP1 WILD-TYPE
  R0               9               336
  R1               0                 4
  R2               0                31
  RX               2                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2148V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TAX1BP1 MUTATED                                  0     0
  TAX1BP1 WILD-TYPE                                1    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  TAX1BP1 MUTATED                           0    11
  TAX1BP1 WILD-TYPE                        22   215
D2148V13, multiclass
                                  clus
vv                                 TAX1BP1 MUTATED TAX1BP1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                      0                22
  WHITE                                         11               215
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2149) Variable = MAGEB2 MUTATION ANALYSIS
D2149V1, survival
                  sevent
clus2                0   1
  MAGEB2 MUTATED     9   4
  MAGEB2 WILD-TYPE 369  89
  MAGEB2 MUTATED MAGEB2 WILD-TYPE 
              13              458 
  MAGEB2 MUTATED MAGEB2 WILD-TYPE 
               4               89 
$`MAGEB2 MUTATED`
TCGA-AA-3950 TCGA-AA-A02H TCGA-AZ-4315 TCGA-AZ-6608 TCGA-CM-5349 TCGA-D5-6539 
       24.00         2.01        58.39         1.61        30.08        12.49 
TCGA-D5-6924 TCGA-DM-A0XF TCGA-F4-6809 TCGA-G4-6588 TCGA-EI-6507 TCGA-EI-6510 
       14.30        38.20        13.25        26.17        19.96        18.28 
TCGA-F5-6813 
        0.69 

$`MAGEB2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       51.98        39.98         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       33.01        21.44        17.82         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 
      100.01        29.56         5.23        11.74         3.19        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       29.06        22.03        22.98        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 
       43.27        15.12        17.85         4.80        17.13        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 
       15.58         1.48         3.68         4.41        12.43         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
       10.26       119.70        24.43       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       33.67         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 
       61.91        36.00        22.09        13.78        35.80        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6508 
       24.13        51.48        32.61         0.49        20.55        20.91 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  MAGEB2 MUTATED MAGEB2 WILD-TYPE 
            0.69             0.00 
  MAGEB2 MUTATED MAGEB2 WILD-TYPE 
           58.39           148.01 
  MAGEB2 MUTATED MAGEB2 WILD-TYPE 
          18.280           20.415 
[1] "0.7 - 58.4 (18.3)"  "0.0 - 148.0 (20.4)"
[1] "hr=" "2"  
D2149V2, continuous
D2149V3, binary
                  cls
clus                 0   1
  MAGEB2 MUTATED    11   3
  MAGEB2 WILD-TYPE 355 116
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAGEB2 MUTATED     11    3
  MAGEB2 WILD-TYPE  355  116
        clus
vv       MAGEB2 MUTATED MAGEB2 WILD-TYPE
  COLON              11              355
  RECTUM              3              116
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  MAGEB2 MUTATED         0        0        0         7         0         0
  MAGEB2 WILD-TYPE      91        1       32       131        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  MAGEB2 MUTATED           0          2          0          2        1
  MAGEB2 WILD-TYPE        24          9         59         40       47
                  vv
clus               STAGE IVA STAGE IVB
  MAGEB2 MUTATED           2         0
  MAGEB2 WILD-TYPE        16         1
D2149V4, multiclass
            clus
vv           MAGEB2 MUTATED MAGEB2 WILD-TYPE
  STAGE I                 0               91
  STAGE IA                0                1
  STAGE II                0               32
  STAGE IIA               7              131
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              2                9
  STAGE IIIB              0               59
  STAGE IIIC              2               40
  STAGE IV                1               47
  STAGE IVA               2               16
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  MAGEB2 MUTATED     0   2  11   1
  MAGEB2 WILD-TYPE  17  90 318  49
D2149V5, multiclass
    clus
vv   MAGEB2 MUTATED MAGEB2 WILD-TYPE
  T1              0               17
  T2              2               90
  T3             11              318
  T4              1               49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  MAGEB2 MUTATED     9   2   3
  MAGEB2 WILD-TYPE 278 111  84
D2149V6, multiclass
    clus
vv   MAGEB2 MUTATED MAGEB2 WILD-TYPE
  N0              9              278
  N1              2              111
  N2              3               84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2149V7, binary
                  cls
clus                 0   1
  MAGEB2 MUTATED    11   2
  MAGEB2 WILD-TYPE 364  63
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAGEB2 MUTATED     11    2
  MAGEB2 WILD-TYPE  364   63
   clus
vv  MAGEB2 MUTATED MAGEB2 WILD-TYPE
  0             11              364
  1              2               63
[1] 2 2
[1] FALSE
D2149V8, binary
                  cls
clus                 0   1
  MAGEB2 MUTATED    10   4
  MAGEB2 WILD-TYPE 215 260
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAGEB2 MUTATED     10    4
  MAGEB2 WILD-TYPE  215  260
        clus
vv       MAGEB2 MUTATED MAGEB2 WILD-TYPE
  FEMALE             10              215
  MALE                4              260
[1] 2 2
[1] FALSE
D2149V9, binary
                  cls
clus                 0   1
  MAGEB2 MUTATED    10   0
  MAGEB2 WILD-TYPE 340  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MAGEB2 MUTATED     10    0
  MAGEB2 WILD-TYPE  340   22
     clus
vv    MAGEB2 MUTATED MAGEB2 WILD-TYPE
  NO              10              340
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  MAGEB2 MUTATED                      9                             1
  MAGEB2 WILD-TYPE                  306                            46
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  MAGEB2 MUTATED                       3                              0
  MAGEB2 WILD-TYPE                   103                             10
D2149V10, multiclass
                                clus
vv                               MAGEB2 MUTATED MAGEB2 WILD-TYPE
  COLON ADENOCARCINOMA                        9              306
  COLON MUCINOUS ADENOCARCINOMA               1               46
  RECTAL ADENOCARCINOMA                       3              103
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  MAGEB2 MUTATED    11   0   1   0
  MAGEB2 WILD-TYPE 334   4  30  25
D2149V11, multiclass
    clus
vv   MAGEB2 MUTATED MAGEB2 WILD-TYPE
  R0             11              334
  R1              0                4
  R2              1               30
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2149V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MAGEB2 MUTATED                                  0     0
  MAGEB2 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  MAGEB2 MUTATED                           0    11
  MAGEB2 WILD-TYPE                        22   215
D2149V13, multiclass
                                  clus
vv                                 MAGEB2 MUTATED MAGEB2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                        11              215
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2150) Variable = SLCO6A1 MUTATION ANALYSIS
D2150V1, survival
                   sevent
clus2                 0   1
  SLCO6A1 MUTATED    21   5
  SLCO6A1 WILD-TYPE 357  88
  SLCO6A1 MUTATED SLCO6A1 WILD-TYPE 
               26               445 
  SLCO6A1 MUTATED SLCO6A1 WILD-TYPE 
                5                88 
$`SLCO6A1 MUTATED`
TCGA-A6-6781 TCGA-AA-3510 TCGA-AA-3518 TCGA-AA-3543 TCGA-AA-3660 TCGA-AA-3663 
       19.66        63.98         1.02         0.99        78.08         6.97 
TCGA-AA-3672 TCGA-AA-3845 TCGA-AA-3947 TCGA-AA-A00N TCGA-AA-A010 TCGA-AD-6965 
        0.92         0.00        33.01         4.01        34.98         0.20 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-CK-6748 TCGA-CM-4752 TCGA-D5-5539 TCGA-DM-A1D8 
       58.39         1.41         1.91        13.02        19.59        12.59 
TCGA-DM-A1HA TCGA-G4-6293 TCGA-G4-6588 TCGA-AG-3593 TCGA-AG-A014 TCGA-DC-6157 
      131.51       133.18        26.17        34.03        15.95        27.95 
TCGA-DY-A1DC TCGA-F5-6571 
       41.36        31.30 

$`SLCO6A1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3519 
       35.01         6.97         1.02        13.02        38.99         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
       61.02         6.05        54.02         2.01        14.01        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 
       17.98        15.95        38.99        37.02        14.93        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       12.99        24.00        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AU-3779 TCGA-AU-6004 
        5.79        22.42        27.42        10.88        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4616 
       16.31         0.95        33.01        21.44        17.82         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
       82.95       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       12.26        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A1DA 
      130.65        92.75        49.91        13.32       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
       44.32       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       46.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A015 TCGA-AG-A016 
        6.02        25.97        23.01        37.02        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       13.97        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
        5.29       126.44        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       49.51        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  SLCO6A1 MUTATED SLCO6A1 WILD-TYPE 
                0                 0 
  SLCO6A1 MUTATED SLCO6A1 WILD-TYPE 
           133.18            148.01 
  SLCO6A1 MUTATED SLCO6A1 WILD-TYPE 
           19.625            20.280 
[1] "0.0 - 133.2 (19.6)" "0.0 - 148.0 (20.3)"
[1] "hr=" "1.1"
D2150V2, continuous
D2150V3, binary
                   cls
clus                  0   1
  SLCO6A1 MUTATED    23   5
  SLCO6A1 WILD-TYPE 343 114
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLCO6A1 MUTATED     23    5
  SLCO6A1 WILD-TYPE  343  114
        clus
vv       SLCO6A1 MUTATED SLCO6A1 WILD-TYPE
  COLON               23               343
  RECTUM               5               114
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SLCO6A1 MUTATED         3        0        3         9         4         0
  SLCO6A1 WILD-TYPE      88        1       29       129         6         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLCO6A1 MUTATED           2          1          0          2        2
  SLCO6A1 WILD-TYPE        22         10         59         40       46
                   vv
clus                STAGE IVA STAGE IVB
  SLCO6A1 MUTATED           0         0
  SLCO6A1 WILD-TYPE        18         1
D2150V4, multiclass
            clus
vv           SLCO6A1 MUTATED SLCO6A1 WILD-TYPE
  STAGE I                  3                88
  STAGE IA                 0                 1
  STAGE II                 3                29
  STAGE IIA                9               129
  STAGE IIB                4                 6
  STAGE IIC                0                 1
  STAGE III                2                22
  STAGE IIIA               1                10
  STAGE IIIB               0                59
  STAGE IIIC               2                40
  STAGE IV                 2                46
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  SLCO6A1 MUTATED     0   3  18   7
  SLCO6A1 WILD-TYPE  17  89 311  43
D2150V5, multiclass
    clus
vv   SLCO6A1 MUTATED SLCO6A1 WILD-TYPE
  T1               0                17
  T2               3                89
  T3              18               311
  T4               7                43
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  SLCO6A1 MUTATED    19   6   3
  SLCO6A1 WILD-TYPE 268 107  84
D2150V6, multiclass
    clus
vv   SLCO6A1 MUTATED SLCO6A1 WILD-TYPE
  N0              19               268
  N1               6               107
  N2               3                84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2150V7, binary
                   cls
clus                  0   1
  SLCO6A1 MUTATED    22   2
  SLCO6A1 WILD-TYPE 353  63
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLCO6A1 MUTATED     22    2
  SLCO6A1 WILD-TYPE  353   63
   clus
vv  SLCO6A1 MUTATED SLCO6A1 WILD-TYPE
  0              22               353
  1               2                63
[1] 2 2
[1] FALSE
D2150V8, binary
                   cls
clus                  0   1
  SLCO6A1 MUTATED    15  13
  SLCO6A1 WILD-TYPE 210 251
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLCO6A1 MUTATED     15   13
  SLCO6A1 WILD-TYPE  210  251
        clus
vv       SLCO6A1 MUTATED SLCO6A1 WILD-TYPE
  FEMALE              15               210
  MALE                13               251
[1] 2 2
[1] FALSE
D2150V9, binary
                   cls
clus                  0   1
  SLCO6A1 MUTATED    16   1
  SLCO6A1 WILD-TYPE 334  21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLCO6A1 MUTATED     16    1
  SLCO6A1 WILD-TYPE  334   21
     clus
vv    SLCO6A1 MUTATED SLCO6A1 WILD-TYPE
  NO               16               334
  YES               1                21
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SLCO6A1 MUTATED                     17                             6
  SLCO6A1 WILD-TYPE                  298                            41
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SLCO6A1 MUTATED                       5                              0
  SLCO6A1 WILD-TYPE                   101                             10
D2150V10, multiclass
                                clus
vv                               SLCO6A1 MUTATED SLCO6A1 WILD-TYPE
  COLON ADENOCARCINOMA                        17               298
  COLON MUCINOUS ADENOCARCINOMA                6                41
  RECTAL ADENOCARCINOMA                        5               101
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  SLCO6A1 MUTATED    21   0   0   2
  SLCO6A1 WILD-TYPE 324   4  31  23
D2150V11, multiclass
    clus
vv   SLCO6A1 MUTATED SLCO6A1 WILD-TYPE
  R0              21               324
  R1               0                 4
  R2               0                31
  RX               2                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2150V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SLCO6A1 MUTATED                                  0     0
  SLCO6A1 WILD-TYPE                                1    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  SLCO6A1 MUTATED                           2    13
  SLCO6A1 WILD-TYPE                        20   213
D2150V13, multiclass
                                  clus
vv                                 SLCO6A1 MUTATED SLCO6A1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                      2                20
  WHITE                                         13               213
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2151) Variable = HIST1H3B MUTATION ANALYSIS
D2151V1, survival
                    sevent
clus2                  0   1
  HIST1H3B MUTATED     1   3
  HIST1H3B WILD-TYPE 377  90
  HIST1H3B MUTATED HIST1H3B WILD-TYPE 
                 4                467 
  HIST1H3B MUTATED HIST1H3B WILD-TYPE 
                 3                 90 
$`HIST1H3B MUTATED`
TCGA-AA-3492 TCGA-AA-A00J TCGA-CK-5916 TCGA-DM-A1DB 
        3.02        18.05        21.14        44.32 

$`HIST1H3B WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L 
       38.04        19.00        30.02        34.03        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 
       85.45        15.62        49.08        51.32         9.99        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
       12.59       140.38         7.50       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  HIST1H3B MUTATED HIST1H3B WILD-TYPE 
              3.02               0.00 
  HIST1H3B MUTATED HIST1H3B WILD-TYPE 
             44.32             148.01 
  HIST1H3B MUTATED HIST1H3B WILD-TYPE 
            19.595             20.190 
[1] "3.0 - 44.3 (19.6)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "4.5"
D2151V2, continuous
D2151V3, binary
                    cls
clus                   0   1
  HIST1H3B MUTATED     4   0
  HIST1H3B WILD-TYPE 362 119
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HIST1H3B MUTATED      4    0
  HIST1H3B WILD-TYPE  362  119
        clus
vv       HIST1H3B MUTATED HIST1H3B WILD-TYPE
  COLON                 4                362
  RECTUM                0                119
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  HIST1H3B MUTATED         1        0        1         1         0         0
  HIST1H3B WILD-TYPE      90        1       31       137        10         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  HIST1H3B MUTATED           0          0          1          0        0
  HIST1H3B WILD-TYPE        24         11         58         42       48
                    vv
clus                 STAGE IVA STAGE IVB
  HIST1H3B MUTATED           0         0
  HIST1H3B WILD-TYPE        18         1
D2151V4, multiclass
            clus
vv           HIST1H3B MUTATED HIST1H3B WILD-TYPE
  STAGE I                   1                 90
  STAGE IA                  0                  1
  STAGE II                  1                 31
  STAGE IIA                 1                137
  STAGE IIB                 0                 10
  STAGE IIC                 0                  1
  STAGE III                 0                 24
  STAGE IIIA                0                 11
  STAGE IIIB                1                 58
  STAGE IIIC                0                 42
  STAGE IV                  0                 48
  STAGE IVA                 0                 18
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  HIST1H3B MUTATED     1   0   2   1
  HIST1H3B WILD-TYPE  16  92 327  49
D2151V5, multiclass
    clus
vv   HIST1H3B MUTATED HIST1H3B WILD-TYPE
  T1                1                 16
  T2                0                 92
  T3                2                327
  T4                1                 49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  HIST1H3B MUTATED     3   1   0
  HIST1H3B WILD-TYPE 284 112  87
D2151V6, multiclass
    clus
vv   HIST1H3B MUTATED HIST1H3B WILD-TYPE
  N0                3                284
  N1                1                112
  N2                0                 87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2151V7, binary
                    cls
clus                   0   1
  HIST1H3B MUTATED     4   0
  HIST1H3B WILD-TYPE 371  65
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HIST1H3B MUTATED      4    0
  HIST1H3B WILD-TYPE  371   65
   clus
vv  HIST1H3B MUTATED HIST1H3B WILD-TYPE
  0                4                371
  1                0                 65
[1] 2 2
[1] FALSE
D2151V8, binary
                    cls
clus                   0   1
  HIST1H3B MUTATED     2   2
  HIST1H3B WILD-TYPE 223 262
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HIST1H3B MUTATED      2    2
  HIST1H3B WILD-TYPE  223  262
        clus
vv       HIST1H3B MUTATED HIST1H3B WILD-TYPE
  FEMALE                2                223
  MALE                  2                262
[1] 2 2
[1] FALSE
D2151V9, binary
                    cls
clus                   0   1
  HIST1H3B MUTATED     3   0
  HIST1H3B WILD-TYPE 347  22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HIST1H3B MUTATED      3    0
  HIST1H3B WILD-TYPE  347   22
     clus
vv    HIST1H3B MUTATED HIST1H3B WILD-TYPE
  NO                 3                347
  YES                0                 22
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  HIST1H3B MUTATED                      3                             1
  HIST1H3B WILD-TYPE                  312                            46
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  HIST1H3B MUTATED                       0                              0
  HIST1H3B WILD-TYPE                   106                             10
D2151V10, multiclass
                                clus
vv                               HIST1H3B MUTATED HIST1H3B WILD-TYPE
  COLON ADENOCARCINOMA                          3                312
  COLON MUCINOUS ADENOCARCINOMA                 1                 46
  RECTAL ADENOCARCINOMA                         0                106
  RECTAL MUCINOUS ADENOCARCINOMA                0                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  HIST1H3B MUTATED     2   0   0   1
  HIST1H3B WILD-TYPE 343   4  31  24
D2151V11, multiclass
    clus
vv   HIST1H3B MUTATED HIST1H3B WILD-TYPE
  R0                2                343
  R1                0                  4
  R2                0                 31
  RX                1                 24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2151V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HIST1H3B MUTATED                                  0     0
  HIST1H3B WILD-TYPE                                1    11
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  HIST1H3B MUTATED                           0     2
  HIST1H3B WILD-TYPE                        22   224
D2151V13, multiclass
[1] "Remove cluster labels:" "HIST1H3B MUTATED"      
clus
  HIST1H3B MUTATED HIST1H3B WILD-TYPE 
                 2                258 
        TCGA-A6-2671         TCGA-A6-2672         TCGA-A6-2674 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-A6-2676         TCGA-A6-2677         TCGA-A6-2678 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-A6-2683         TCGA-A6-3807         TCGA-A6-3808 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-A6-3809         TCGA-A6-3810         TCGA-A6-4105 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-A6-5656         TCGA-A6-5657         TCGA-A6-5659 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-A6-5660         TCGA-A6-5661         TCGA-A6-5662 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-A6-5664         TCGA-A6-5665         TCGA-A6-5666 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-A6-6137         TCGA-A6-6138         TCGA-A6-6141 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-A6-6142         TCGA-A6-6648         TCGA-A6-6649 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-A6-6651         TCGA-A6-6652         TCGA-A6-6653 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-A6-6654         TCGA-A6-6780         TCGA-A6-6781 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-A6-6782         TCGA-AD-5900         TCGA-AD-6548 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-AD-6888         TCGA-AD-6889         TCGA-AD-6890 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-AD-6895         TCGA-AD-6899         TCGA-AD-6901 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-AD-6963         TCGA-AD-6964         TCGA-AD-6965 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-AU-3779         TCGA-AU-6004         TCGA-AY-4070 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-AY-4071         TCGA-AY-5543         TCGA-AY-6196 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-AY-6197         TCGA-AY-6386         TCGA-AZ-4315 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-AZ-4323         TCGA-AZ-4616         TCGA-AZ-4681 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-AZ-4682         TCGA-AZ-5403         TCGA-AZ-5407 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-AZ-6598         TCGA-AZ-6599         TCGA-AZ-6600 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-AZ-6601         TCGA-AZ-6603         TCGA-AZ-6605 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-AZ-6606         TCGA-AZ-6607         TCGA-AZ-6608 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-CA-5254         TCGA-CA-5255         TCGA-CA-5796 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-CA-5797         TCGA-CA-6715         TCGA-CA-6716 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-CA-6717         TCGA-CA-6718         TCGA-CA-6719 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-CK-4947         TCGA-CK-4948         TCGA-CK-4950 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-CK-4952         TCGA-CK-5912         TCGA-CK-5913 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-CK-5914         TCGA-CK-5915         TCGA-CK-6746 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-CK-6747         TCGA-CK-6748         TCGA-CK-6751 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-CM-4743         TCGA-CM-4744         TCGA-CM-4746 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-CM-4747         TCGA-CM-4752         TCGA-CM-5341 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-CM-5344         TCGA-CM-5348         TCGA-CM-5349 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-CM-5860         TCGA-CM-5861         TCGA-CM-5862 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-CM-5863         TCGA-CM-5864         TCGA-CM-5868 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-CM-6161         TCGA-CM-6162         TCGA-CM-6163 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-CM-6164         TCGA-CM-6165         TCGA-CM-6166 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-CM-6167         TCGA-CM-6168         TCGA-CM-6169 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-CM-6170         TCGA-CM-6171         TCGA-CM-6172 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-CM-6674         TCGA-CM-6675         TCGA-CM-6676 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-CM-6677         TCGA-CM-6678         TCGA-CM-6679 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-CM-6680         TCGA-D5-5537         TCGA-D5-5538 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-D5-5539         TCGA-D5-5540         TCGA-D5-5541 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-D5-6529         TCGA-D5-6532         TCGA-D5-6533 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-D5-6534         TCGA-D5-6535         TCGA-D5-6536 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-D5-6537         TCGA-D5-6538         TCGA-D5-6539 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-D5-6540         TCGA-D5-6541         TCGA-D5-6898 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-D5-6920         TCGA-D5-6922         TCGA-D5-6923 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-D5-6924         TCGA-D5-6926         TCGA-D5-6927 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-D5-6928         TCGA-D5-6929         TCGA-D5-6930 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-D5-6931         TCGA-D5-6932         TCGA-D5-7000 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-DM-A0X9         TCGA-DM-A0XD         TCGA-DM-A0XF 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-DM-A1D0         TCGA-DM-A1D4         TCGA-DM-A1D6 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-DM-A1D7         TCGA-DM-A1D8         TCGA-DM-A1D9 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-DM-A1DA         TCGA-DM-A1HA         TCGA-DM-A1HB 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-DM-A282         TCGA-DM-A285         TCGA-DM-A28C 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-DM-A28E         TCGA-DM-A28F         TCGA-DM-A28G 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-DM-A28H         TCGA-DM-A28K         TCGA-F4-6459 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-F4-6460         TCGA-F4-6569         TCGA-F4-6570 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-F4-6703         TCGA-F4-6704         TCGA-F4-6805 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-F4-6806         TCGA-F4-6807         TCGA-F4-6808 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-F4-6809         TCGA-F4-6854         TCGA-F4-6855 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-F4-6856         TCGA-G4-6293         TCGA-G4-6299 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-G4-6303         TCGA-G4-6304         TCGA-G4-6306 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-G4-6307         TCGA-G4-6309         TCGA-G4-6310 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-G4-6315         TCGA-G4-6317         TCGA-G4-6321 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-G4-6323         TCGA-G4-6586         TCGA-G4-6588 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-G4-6625         TCGA-G4-6626         TCGA-G4-6628 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2691 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-AF-2692         TCGA-AF-2693         TCGA-AF-3400 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-AF-3913         TCGA-AF-4110         TCGA-AF-5654 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-AF-6136         TCGA-AF-6655         TCGA-AF-6672 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6549 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-AH-6643         TCGA-AH-6644         TCGA-CI-6619 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-CI-6620         TCGA-CI-6621         TCGA-CI-6622 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-CI-6624         TCGA-CL-5917         TCGA-CL-5918 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-DC-5337         TCGA-DC-5869         TCGA-DC-6155 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-DC-6157         TCGA-DC-6158         TCGA-DC-6160 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-DC-6681         TCGA-DC-6682         TCGA-DC-6683 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-DT-5265         TCGA-DY-A0XA         TCGA-DY-A1DC 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-DY-A1DD         TCGA-DY-A1DF         TCGA-DY-A1DG 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-DY-A1H8         TCGA-EF-5830         TCGA-EI-6506 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6510 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-F5-6464         TCGA-F5-6465         TCGA-F5-6571 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6811         TCGA-F5-6812 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 
        TCGA-F5-6813         TCGA-G5-6235         TCGA-G5-6641 
"HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" "HIST1H3B WILD-TYPE" 

Clustering(2152) Variable = TBCE MUTATION ANALYSIS
D2152V1, survival
                sevent
clus2              0   1
  TBCE MUTATED     2   0
  TBCE WILD-TYPE 376  93
  TBCE MUTATED TBCE WILD-TYPE 
             2            469 
  TBCE MUTATED TBCE WILD-TYPE 
             0             93 
$`TBCE MUTATED`
TCGA-AA-3977 TCGA-AA-A029 
       25.02        51.98 

$`TBCE WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  TBCE MUTATED TBCE WILD-TYPE 
         25.02           0.00 
  TBCE MUTATED TBCE WILD-TYPE 
         51.98         148.01 
  TBCE MUTATED TBCE WILD-TYPE 
         38.50          20.12 
[1] "25.0 - 52.0 (38.5)" "0.0 - 148.0 (20.1)"
[1] "Remove cluster labels:" "TBCE MUTATED"          
D2152V2, continuous
D2152V3, binary
                cls
clus               0   1
  TBCE MUTATED     3   0
  TBCE WILD-TYPE 363 119
[1] "tbl2"
                cls
clus             [,1] [,2]
  TBCE MUTATED      3    0
  TBCE WILD-TYPE  363  119
        clus
vv       TBCE MUTATED TBCE WILD-TYPE
  COLON             3            363
  RECTUM            0            119
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TBCE MUTATED         0        0        1         1         0         0
  TBCE WILD-TYPE      91        1       31       137        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TBCE MUTATED           0          0          0          0        0         0
  TBCE WILD-TYPE        24         11         59         42       48        18
                vv
clus             STAGE IVB
  TBCE MUTATED           0
  TBCE WILD-TYPE         1
D2152V4, multiclass
[1] "Remove cluster labels:" "TBCE MUTATED"          
clus
  TBCE MUTATED TBCE WILD-TYPE 
             2            474 
    TCGA-A6-2671     TCGA-A6-2672     TCGA-A6-2674     TCGA-A6-2676 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-A6-2677     TCGA-A6-2678     TCGA-A6-2683     TCGA-A6-3807 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-A6-3808     TCGA-A6-3809     TCGA-A6-3810     TCGA-A6-4105 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-A6-5656     TCGA-A6-5657     TCGA-A6-5659     TCGA-A6-5660 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-A6-5661     TCGA-A6-5662     TCGA-A6-5664     TCGA-A6-5665 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-A6-5666     TCGA-A6-6137     TCGA-A6-6138     TCGA-A6-6141 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-A6-6142     TCGA-A6-6648     TCGA-A6-6649     TCGA-A6-6651 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-A6-6652     TCGA-A6-6653     TCGA-A6-6654     TCGA-A6-6780 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-A6-6781     TCGA-A6-6782     TCGA-AA-3489     TCGA-AA-3492 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-3496     TCGA-AA-3502     TCGA-AA-3510     TCGA-AA-3511 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-3514     TCGA-AA-3516     TCGA-AA-3517     TCGA-AA-3518 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-3519     TCGA-AA-3520     TCGA-AA-3521     TCGA-AA-3522 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-3524     TCGA-AA-3525     TCGA-AA-3526     TCGA-AA-3527 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-3529     TCGA-AA-3530     TCGA-AA-3531     TCGA-AA-3532 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-3534     TCGA-AA-3538     TCGA-AA-3542     TCGA-AA-3543 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-3544     TCGA-AA-3548     TCGA-AA-3549     TCGA-AA-3552 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-3553     TCGA-AA-3554     TCGA-AA-3555     TCGA-AA-3556 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-3558     TCGA-AA-3560     TCGA-AA-3561     TCGA-AA-3562 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-3655     TCGA-AA-3660     TCGA-AA-3662     TCGA-AA-3663 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-3664     TCGA-AA-3666     TCGA-AA-3667     TCGA-AA-3672 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-3673     TCGA-AA-3678     TCGA-AA-3679     TCGA-AA-3680 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-3681     TCGA-AA-3684     TCGA-AA-3685     TCGA-AA-3688 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-3692     TCGA-AA-3693     TCGA-AA-3695     TCGA-AA-3696 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-3697     TCGA-AA-3710     TCGA-AA-3712     TCGA-AA-3713 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-3715     TCGA-AA-3811     TCGA-AA-3812     TCGA-AA-3814 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-3815     TCGA-AA-3818     TCGA-AA-3819     TCGA-AA-3821 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-3831     TCGA-AA-3833     TCGA-AA-3837     TCGA-AA-3842 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-3844     TCGA-AA-3845     TCGA-AA-3846     TCGA-AA-3848 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-3850     TCGA-AA-3851     TCGA-AA-3852     TCGA-AA-3854 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-3855     TCGA-AA-3856     TCGA-AA-3858     TCGA-AA-3860 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-3861     TCGA-AA-3864     TCGA-AA-3866     TCGA-AA-3867 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-3869     TCGA-AA-3870     TCGA-AA-3872     TCGA-AA-3875 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-3877     TCGA-AA-3930     TCGA-AA-3939     TCGA-AA-3941 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-3947     TCGA-AA-3949     TCGA-AA-3950     TCGA-AA-3952 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-3955     TCGA-AA-3956     TCGA-AA-3966     TCGA-AA-3968 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-3971     TCGA-AA-3972     TCGA-AA-3973     TCGA-AA-3975 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-3976     TCGA-AA-3979     TCGA-AA-3980     TCGA-AA-3982 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-3986     TCGA-AA-3989     TCGA-AA-3994     TCGA-AA-A004 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-A00A     TCGA-AA-A00D     TCGA-AA-A00E     TCGA-AA-A00F 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-A00J     TCGA-AA-A00K     TCGA-AA-A00L     TCGA-AA-A00N 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-A00O     TCGA-AA-A00Q     TCGA-AA-A00R     TCGA-AA-A00U 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-A00W     TCGA-AA-A00Z     TCGA-AA-A010     TCGA-AA-A017 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-A01D     TCGA-AA-A01F     TCGA-AA-A01G     TCGA-AA-A01I 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-A01K     TCGA-AA-A01P     TCGA-AA-A01Q     TCGA-AA-A01R 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-A01S     TCGA-AA-A01T     TCGA-AA-A01V     TCGA-AA-A01X 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-A01Z     TCGA-AA-A022     TCGA-AA-A024     TCGA-AA-A02F 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-A02H     TCGA-AA-A02J     TCGA-AA-A02K     TCGA-AA-A02O 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-A02W     TCGA-AA-A02Y     TCGA-AA-A03F     TCGA-AA-A03J 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AD-5900     TCGA-AD-6548     TCGA-AD-6888     TCGA-AD-6889 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AD-6899     TCGA-AU-3779     TCGA-AU-6004     TCGA-AY-4070 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AY-4071     TCGA-AY-5543     TCGA-AY-6196     TCGA-AY-6197 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AY-6386     TCGA-AZ-4315     TCGA-AZ-4323     TCGA-AZ-4616 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AZ-4681     TCGA-AZ-4682     TCGA-AZ-5403     TCGA-AZ-5407 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AZ-6598     TCGA-AZ-6599     TCGA-AZ-6600     TCGA-AZ-6601 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AZ-6605     TCGA-AZ-6606     TCGA-AZ-6607     TCGA-AZ-6608 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-CA-5254     TCGA-CA-5255     TCGA-CA-5796     TCGA-CA-5797 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-CA-6715     TCGA-CA-6716     TCGA-CA-6717     TCGA-CA-6718 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-CA-6719     TCGA-CK-4947     TCGA-CK-4948     TCGA-CK-4950 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-CK-4952     TCGA-CK-5912     TCGA-CK-5913     TCGA-CK-5914 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-CK-5915     TCGA-CK-5916     TCGA-CK-6746     TCGA-CK-6747 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-CK-6748     TCGA-CK-6751     TCGA-CM-4743     TCGA-CM-4744 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-CM-4746     TCGA-CM-4747     TCGA-CM-4752     TCGA-CM-5341 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-CM-5344     TCGA-CM-5348     TCGA-CM-5349     TCGA-CM-5860 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-CM-5861     TCGA-CM-5862     TCGA-CM-5863     TCGA-CM-5864 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-CM-5868     TCGA-CM-6161     TCGA-CM-6162     TCGA-CM-6163 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-CM-6164     TCGA-CM-6165     TCGA-CM-6166     TCGA-CM-6167 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-CM-6168     TCGA-CM-6169     TCGA-CM-6170     TCGA-CM-6171 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-CM-6172     TCGA-CM-6674     TCGA-CM-6675     TCGA-CM-6676 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-CM-6677     TCGA-CM-6678     TCGA-CM-6679     TCGA-CM-6680 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-D5-5537     TCGA-D5-5538     TCGA-D5-5539     TCGA-D5-5540 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-D5-5541     TCGA-D5-6529     TCGA-D5-6532     TCGA-D5-6533 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-D5-6534     TCGA-D5-6535     TCGA-D5-6536     TCGA-D5-6537 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-D5-6538     TCGA-D5-6539     TCGA-D5-6540     TCGA-D5-6541 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-D5-6898     TCGA-D5-6920     TCGA-D5-6922     TCGA-D5-6923 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-D5-6924     TCGA-D5-6926     TCGA-D5-6927     TCGA-D5-6928 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-D5-6929     TCGA-D5-6930     TCGA-D5-6931     TCGA-D5-6932 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-D5-7000     TCGA-DM-A0X9     TCGA-DM-A0XD     TCGA-DM-A0XF 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-DM-A1D0     TCGA-DM-A1D4     TCGA-DM-A1D6     TCGA-DM-A1D7 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-DM-A1D9     TCGA-DM-A1DA     TCGA-DM-A1DB     TCGA-DM-A1HA 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-DM-A1HB     TCGA-DM-A282     TCGA-DM-A285     TCGA-DM-A28C 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-DM-A28E     TCGA-DM-A28F     TCGA-DM-A28G     TCGA-DM-A28H 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-DM-A28K     TCGA-F4-6459     TCGA-F4-6460     TCGA-F4-6569 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-F4-6570     TCGA-F4-6703     TCGA-F4-6704     TCGA-F4-6805 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-F4-6806     TCGA-F4-6807     TCGA-F4-6808     TCGA-F4-6809 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-F4-6854     TCGA-F4-6855     TCGA-F4-6856     TCGA-G4-6293 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-G4-6299     TCGA-G4-6303     TCGA-G4-6304     TCGA-G4-6306 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-G4-6307     TCGA-G4-6309     TCGA-G4-6310     TCGA-G4-6315 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-G4-6317     TCGA-G4-6321     TCGA-G4-6323     TCGA-G4-6586 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-G4-6588     TCGA-G4-6625     TCGA-G4-6626     TCGA-G4-6628 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AF-2687     TCGA-AF-2689     TCGA-AF-2691     TCGA-AF-2692 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AF-2693     TCGA-AF-3400     TCGA-AF-3913     TCGA-AF-4110 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AF-5654     TCGA-AF-6136     TCGA-AF-6655     TCGA-AF-6672 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AG-3574     TCGA-AG-3575     TCGA-AG-3578     TCGA-AG-3580 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AG-3581     TCGA-AG-3582     TCGA-AG-3583     TCGA-AG-3584 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AG-3586     TCGA-AG-3587     TCGA-AG-3593     TCGA-AG-3594 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AG-3598     TCGA-AG-3599     TCGA-AG-3600     TCGA-AG-3601 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AG-3602     TCGA-AG-3605     TCGA-AG-3608     TCGA-AG-3609 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AG-3611     TCGA-AG-3612     TCGA-AG-3726     TCGA-AG-3727 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AG-3731     TCGA-AG-3732     TCGA-AG-3742     TCGA-AG-3878 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AG-3881     TCGA-AG-3882     TCGA-AG-3883     TCGA-AG-3885 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AG-3887     TCGA-AG-3890     TCGA-AG-3892     TCGA-AG-3893 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AG-3894     TCGA-AG-3896     TCGA-AG-3898     TCGA-AG-3901 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AG-3902     TCGA-AG-3909     TCGA-AG-3999     TCGA-AG-4001 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AG-4005     TCGA-AG-4007     TCGA-AG-4008     TCGA-AG-4015 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AG-A002     TCGA-AG-A008     TCGA-AG-A00C     TCGA-AG-A00H 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AG-A00Y     TCGA-AG-A011     TCGA-AG-A014     TCGA-AG-A015 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AG-A016     TCGA-AG-A01L     TCGA-AG-A01W     TCGA-AG-A01Y 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AG-A020     TCGA-AG-A025     TCGA-AG-A026     TCGA-AG-A02G 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AG-A02N     TCGA-AG-A02X     TCGA-AG-A032     TCGA-AG-A036 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AH-6643     TCGA-CI-6619     TCGA-CI-6620     TCGA-CI-6621 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-CI-6622     TCGA-CI-6624     TCGA-CL-5917     TCGA-CL-5918 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-DC-5337     TCGA-DC-5869     TCGA-DC-6155     TCGA-DC-6157 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-DC-6158     TCGA-DC-6160     TCGA-DC-6681     TCGA-DC-6682 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-DC-6683     TCGA-DT-5265     TCGA-DY-A0XA     TCGA-DY-A1DC 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-DY-A1DD     TCGA-DY-A1DF     TCGA-DY-A1DG     TCGA-DY-A1H8 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-EF-5830     TCGA-EI-6506     TCGA-EI-6507     TCGA-EI-6508 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-EI-6510     TCGA-F5-6464     TCGA-F5-6465     TCGA-F5-6571 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-F5-6702     TCGA-F5-6811     TCGA-F5-6812     TCGA-F5-6813 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-G5-6235     TCGA-G5-6641 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" 
                vv
clus              T1  T2  T3  T4
  TBCE MUTATED     0   1   2   0
  TBCE WILD-TYPE  17  91 327  50
D2152V5, multiclass
    clus
vv   TBCE MUTATED TBCE WILD-TYPE
  T1            0             17
  T2            1             91
  T3            2            327
  T4            0             50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  TBCE MUTATED     3   0   0
  TBCE WILD-TYPE 284 113  87
D2152V6, multiclass
    clus
vv   TBCE MUTATED TBCE WILD-TYPE
  N0            3            284
  N1            0            113
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2152V7, binary
                cls
clus               0   1
  TBCE MUTATED     2   0
  TBCE WILD-TYPE 373  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  TBCE MUTATED      2    0
  TBCE WILD-TYPE  373   65
   clus
vv  TBCE MUTATED TBCE WILD-TYPE
  0            2            373
  1            0             65
[1] 2 2
[1] FALSE
D2152V8, binary
                cls
clus               0   1
  TBCE MUTATED     1   2
  TBCE WILD-TYPE 224 262
[1] "tbl2"
                cls
clus             [,1] [,2]
  TBCE MUTATED      1    2
  TBCE WILD-TYPE  224  262
        clus
vv       TBCE MUTATED TBCE WILD-TYPE
  FEMALE            1            224
  MALE              2            262
[1] 2 2
[1] FALSE
D2152V9, binary
                cls
clus               0   1
  TBCE MUTATED     2   0
  TBCE WILD-TYPE 348  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  TBCE MUTATED      2    0
  TBCE WILD-TYPE  348   22
     clus
vv    TBCE MUTATED TBCE WILD-TYPE
  NO             2            348
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  TBCE MUTATED                      3                             0
  TBCE WILD-TYPE                  312                            47
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  TBCE MUTATED                       0                              0
  TBCE WILD-TYPE                   106                             10
D2152V10, multiclass
                                clus
vv                               TBCE MUTATED TBCE WILD-TYPE
  COLON ADENOCARCINOMA                      3            312
  COLON MUCINOUS ADENOCARCINOMA             0             47
  RECTAL ADENOCARCINOMA                     0            106
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  TBCE MUTATED     2   0   0   0
  TBCE WILD-TYPE 343   4  31  25
D2152V11, multiclass
[1] "Remove cluster labels:" "TBCE MUTATED"          
clus
  TBCE MUTATED TBCE WILD-TYPE 
             2            403 
    TCGA-A6-2671     TCGA-A6-2672     TCGA-A6-2674     TCGA-A6-2676 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-A6-2677     TCGA-A6-2678     TCGA-A6-2683     TCGA-A6-3807 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-A6-3808     TCGA-A6-3809     TCGA-A6-3810     TCGA-A6-5657 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-A6-5659     TCGA-A6-5661     TCGA-A6-5665     TCGA-A6-6781 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-3489     TCGA-AA-3492     TCGA-AA-3496     TCGA-AA-3502 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-3510     TCGA-AA-3511     TCGA-AA-3514     TCGA-AA-3517 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-3518     TCGA-AA-3519     TCGA-AA-3520     TCGA-AA-3521 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-3522     TCGA-AA-3524     TCGA-AA-3525     TCGA-AA-3526 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-3527     TCGA-AA-3529     TCGA-AA-3530     TCGA-AA-3531 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-3532     TCGA-AA-3534     TCGA-AA-3538     TCGA-AA-3542 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-3543     TCGA-AA-3544     TCGA-AA-3548     TCGA-AA-3549 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-3552     TCGA-AA-3553     TCGA-AA-3554     TCGA-AA-3555 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-3556     TCGA-AA-3558     TCGA-AA-3560     TCGA-AA-3561 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-3562     TCGA-AA-3655     TCGA-AA-3660     TCGA-AA-3662 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-3663     TCGA-AA-3664     TCGA-AA-3666     TCGA-AA-3667 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-3672     TCGA-AA-3673     TCGA-AA-3678     TCGA-AA-3679 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-3680     TCGA-AA-3681     TCGA-AA-3684     TCGA-AA-3685 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-3688     TCGA-AA-3692     TCGA-AA-3693     TCGA-AA-3695 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-3696     TCGA-AA-3697     TCGA-AA-3710     TCGA-AA-3712 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-3713     TCGA-AA-3715     TCGA-AA-3811     TCGA-AA-3812 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-3814     TCGA-AA-3815     TCGA-AA-3818     TCGA-AA-3819 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-3821     TCGA-AA-3831     TCGA-AA-3833     TCGA-AA-3837 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-3842     TCGA-AA-3844     TCGA-AA-3845     TCGA-AA-3846 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-3848     TCGA-AA-3850     TCGA-AA-3851     TCGA-AA-3852 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-3854     TCGA-AA-3855     TCGA-AA-3856     TCGA-AA-3858 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-3860     TCGA-AA-3861     TCGA-AA-3864     TCGA-AA-3866 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-3867     TCGA-AA-3869     TCGA-AA-3870     TCGA-AA-3872 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-3875     TCGA-AA-3877     TCGA-AA-3930     TCGA-AA-3939 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-3941     TCGA-AA-3947     TCGA-AA-3949     TCGA-AA-3950 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-3952     TCGA-AA-3955     TCGA-AA-3956     TCGA-AA-3968 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-3971     TCGA-AA-3972     TCGA-AA-3973     TCGA-AA-3975 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-3976     TCGA-AA-3979     TCGA-AA-3986     TCGA-AA-3989 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-3994     TCGA-AA-A004     TCGA-AA-A00A     TCGA-AA-A00D 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-A00E     TCGA-AA-A00F     TCGA-AA-A00J     TCGA-AA-A00K 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-A00L     TCGA-AA-A00N     TCGA-AA-A00O     TCGA-AA-A00Q 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-A00R     TCGA-AA-A00U     TCGA-AA-A00W     TCGA-AA-A00Z 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-A010     TCGA-AA-A017     TCGA-AA-A01D     TCGA-AA-A01F 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-A01G     TCGA-AA-A01I     TCGA-AA-A01K     TCGA-AA-A01P 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-A01Q     TCGA-AA-A01R     TCGA-AA-A01S     TCGA-AA-A01T 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-A01V     TCGA-AA-A01X     TCGA-AA-A01Z     TCGA-AA-A022 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-A024     TCGA-AA-A02F     TCGA-AA-A02H     TCGA-AA-A02J 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-A02K     TCGA-AA-A02O     TCGA-AA-A02W     TCGA-AA-A02Y 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AA-A03F     TCGA-AA-A03J     TCGA-AD-5900     TCGA-AD-6548 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AD-6888     TCGA-AU-3779     TCGA-AU-6004     TCGA-AY-4070 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AY-4071     TCGA-AY-5543     TCGA-AY-6196     TCGA-AY-6197 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AY-6386     TCGA-AZ-4315     TCGA-AZ-4681     TCGA-AZ-4682 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-CA-5254     TCGA-CA-5255     TCGA-CA-5796     TCGA-CA-5797 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-CA-6715     TCGA-CA-6716     TCGA-CA-6717     TCGA-CA-6718 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-CA-6719     TCGA-CK-4947     TCGA-CK-4948     TCGA-CK-4950 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-CK-4952     TCGA-CK-5912     TCGA-CK-5913     TCGA-CK-5914 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-CK-5915     TCGA-CK-5916     TCGA-CK-6746     TCGA-CK-6747 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-CK-6748     TCGA-CK-6751     TCGA-CM-4743     TCGA-CM-4744 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-CM-4746     TCGA-CM-4747     TCGA-CM-4752     TCGA-CM-5341 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-CM-5344     TCGA-CM-5348     TCGA-CM-5349     TCGA-CM-5860 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-CM-5861     TCGA-CM-5862     TCGA-CM-5863     TCGA-CM-5864 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-CM-5868     TCGA-CM-6161     TCGA-CM-6162     TCGA-CM-6163 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-CM-6164     TCGA-CM-6165     TCGA-CM-6166     TCGA-CM-6167 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-CM-6168     TCGA-CM-6169     TCGA-CM-6170     TCGA-CM-6171 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-CM-6172     TCGA-CM-6674     TCGA-CM-6675     TCGA-CM-6676 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-CM-6677     TCGA-CM-6678     TCGA-CM-6679     TCGA-CM-6680 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-D5-5537     TCGA-D5-5538     TCGA-D5-5539     TCGA-D5-5540 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-D5-5541     TCGA-D5-6529     TCGA-D5-6532     TCGA-D5-6533 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-D5-6534     TCGA-D5-6535     TCGA-D5-6536     TCGA-D5-6537 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-D5-6538     TCGA-D5-6539     TCGA-D5-6540     TCGA-D5-6541 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-D5-6898     TCGA-D5-6920     TCGA-D5-6922     TCGA-D5-6923 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-D5-6924     TCGA-D5-6926     TCGA-D5-6927     TCGA-D5-6928 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-D5-6929     TCGA-D5-6930     TCGA-D5-6931     TCGA-D5-6932 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-D5-7000     TCGA-F4-6459     TCGA-F4-6460     TCGA-F4-6569 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-F4-6570     TCGA-F4-6703     TCGA-F4-6704     TCGA-F4-6805 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-F4-6806     TCGA-F4-6807     TCGA-F4-6808     TCGA-F4-6809 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-F4-6854     TCGA-F4-6855     TCGA-F4-6856     TCGA-G4-6293 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-G4-6299     TCGA-G4-6303     TCGA-G4-6304     TCGA-G4-6306 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-G4-6307     TCGA-G4-6309     TCGA-G4-6310     TCGA-G4-6315 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-G4-6317     TCGA-G4-6321     TCGA-G4-6323     TCGA-G4-6586 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-G4-6588     TCGA-G4-6625     TCGA-G4-6626     TCGA-G4-6628 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AF-2687     TCGA-AF-2689     TCGA-AF-2691     TCGA-AF-2692 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AF-3400     TCGA-AF-3913     TCGA-AF-4110     TCGA-AF-5654 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AF-6655     TCGA-AG-3574     TCGA-AG-3575     TCGA-AG-3578 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AG-3580     TCGA-AG-3581     TCGA-AG-3582     TCGA-AG-3583 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AG-3584     TCGA-AG-3586     TCGA-AG-3587     TCGA-AG-3593 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AG-3594     TCGA-AG-3598     TCGA-AG-3599     TCGA-AG-3600 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AG-3601     TCGA-AG-3602     TCGA-AG-3605     TCGA-AG-3608 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AG-3609     TCGA-AG-3611     TCGA-AG-3612     TCGA-AG-3726 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AG-3727     TCGA-AG-3731     TCGA-AG-3732     TCGA-AG-3742 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AG-3878     TCGA-AG-3882     TCGA-AG-3883     TCGA-AG-3885 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AG-3887     TCGA-AG-3890     TCGA-AG-3892     TCGA-AG-3893 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AG-3894     TCGA-AG-3896     TCGA-AG-3898     TCGA-AG-3901 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AG-3902     TCGA-AG-3909     TCGA-AG-3999     TCGA-AG-4001 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AG-4005     TCGA-AG-4007     TCGA-AG-4008     TCGA-AG-4015 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AG-A002     TCGA-AG-A008     TCGA-AG-A00C     TCGA-AG-A00H 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AG-A00Y     TCGA-AG-A011     TCGA-AG-A014     TCGA-AG-A015 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AG-A016     TCGA-AG-A01L     TCGA-AG-A01W     TCGA-AG-A01Y 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AG-A020     TCGA-AG-A025     TCGA-AG-A026     TCGA-AG-A02G 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AG-A02N     TCGA-AG-A02X     TCGA-AG-A032     TCGA-AG-A036 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-AH-6549     TCGA-AH-6643     TCGA-CL-5917     TCGA-CL-5918 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-DC-5337     TCGA-DC-5869     TCGA-DC-6155     TCGA-DC-6157 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-DC-6158     TCGA-DC-6160     TCGA-DC-6681     TCGA-DC-6682 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-DC-6683     TCGA-DT-5265     TCGA-EF-5830     TCGA-EI-6506 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-EI-6507     TCGA-EI-6508     TCGA-EI-6510     TCGA-F5-6464 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-F5-6465     TCGA-F5-6571     TCGA-F5-6702     TCGA-F5-6812 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
    TCGA-F5-6813     TCGA-G5-6235     TCGA-G5-6641 
"TBCE WILD-TYPE" "TBCE WILD-TYPE" "TBCE WILD-TYPE" 
D2152V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TBCE MUTATED                                  0     0
  TBCE WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  TBCE MUTATED                           0     0
  TBCE WILD-TYPE                        22   226
D2152V13, multiclass

Clustering(2153) Variable = GLTPD2 MUTATION ANALYSIS
D2153V1, survival
                  sevent
clus2                0   1
  GLTPD2 MUTATED     3   1
  GLTPD2 WILD-TYPE 375  92
  GLTPD2 MUTATED GLTPD2 WILD-TYPE 
               4              467 
  GLTPD2 MUTATED GLTPD2 WILD-TYPE 
               1               92 
$`GLTPD2 MUTATED`
TCGA-AA-3510 TCGA-AA-3663 TCGA-AA-A010 TCGA-AZ-6599 
       63.98         6.97        34.98         6.77 

$`GLTPD2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        88.21        49.41        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  GLTPD2 MUTATED GLTPD2 WILD-TYPE 
            6.77             0.00 
  GLTPD2 MUTATED GLTPD2 WILD-TYPE 
           63.98           148.01 
  GLTPD2 MUTATED GLTPD2 WILD-TYPE 
          20.975           20.190 
[1] "6.8 - 64.0 (21.0)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.1"
D2153V2, continuous
D2153V3, binary
                  cls
clus                 0   1
  GLTPD2 MUTATED     4   0
  GLTPD2 WILD-TYPE 362 119
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GLTPD2 MUTATED      4    0
  GLTPD2 WILD-TYPE  362  119
        clus
vv       GLTPD2 MUTATED GLTPD2 WILD-TYPE
  COLON               4              362
  RECTUM              0              119
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GLTPD2 MUTATED         1        0        2         0         1         0
  GLTPD2 WILD-TYPE      90        1       30       138         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GLTPD2 MUTATED           0          0          0          0        0
  GLTPD2 WILD-TYPE        24         11         59         42       48
                  vv
clus               STAGE IVA STAGE IVB
  GLTPD2 MUTATED           0         0
  GLTPD2 WILD-TYPE        18         1
D2153V4, multiclass
            clus
vv           GLTPD2 MUTATED GLTPD2 WILD-TYPE
  STAGE I                 1               90
  STAGE IA                0                1
  STAGE II                2               30
  STAGE IIA               0              138
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              0               59
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  GLTPD2 MUTATED     0   1   2   1
  GLTPD2 WILD-TYPE  17  91 327  49
D2153V5, multiclass
    clus
vv   GLTPD2 MUTATED GLTPD2 WILD-TYPE
  T1              0               17
  T2              1               91
  T3              2              327
  T4              1               49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  GLTPD2 MUTATED     4   0   0
  GLTPD2 WILD-TYPE 283 113  87
D2153V6, multiclass
    clus
vv   GLTPD2 MUTATED GLTPD2 WILD-TYPE
  N0              4              283
  N1              0              113
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2153V7, binary
                  cls
clus                 0   1
  GLTPD2 MUTATED     3   0
  GLTPD2 WILD-TYPE 372  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GLTPD2 MUTATED      3    0
  GLTPD2 WILD-TYPE  372   65
   clus
vv  GLTPD2 MUTATED GLTPD2 WILD-TYPE
  0              3              372
  1              0               65
[1] 2 2
[1] FALSE
D2153V8, binary
                  cls
clus                 0   1
  GLTPD2 MUTATED     1   3
  GLTPD2 WILD-TYPE 224 261
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GLTPD2 MUTATED      1    3
  GLTPD2 WILD-TYPE  224  261
        clus
vv       GLTPD2 MUTATED GLTPD2 WILD-TYPE
  FEMALE              1              224
  MALE                3              261
[1] 2 2
[1] FALSE
D2153V9, binary
                  cls
clus                 0   1
  GLTPD2 MUTATED     4   0
  GLTPD2 WILD-TYPE 346  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GLTPD2 MUTATED      4    0
  GLTPD2 WILD-TYPE  346   22
     clus
vv    GLTPD2 MUTATED GLTPD2 WILD-TYPE
  NO               4              346
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  GLTPD2 MUTATED                      4                             0
  GLTPD2 WILD-TYPE                  311                            47
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  GLTPD2 MUTATED                       0                              0
  GLTPD2 WILD-TYPE                   106                             10
D2153V10, multiclass
                                clus
vv                               GLTPD2 MUTATED GLTPD2 WILD-TYPE
  COLON ADENOCARCINOMA                        4              311
  COLON MUCINOUS ADENOCARCINOMA               0               47
  RECTAL ADENOCARCINOMA                       0              106
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  GLTPD2 MUTATED     3   0   0   0
  GLTPD2 WILD-TYPE 342   4  31  25
D2153V11, multiclass
    clus
vv   GLTPD2 MUTATED GLTPD2 WILD-TYPE
  R0              3              342
  R1              0                4
  R2              0               31
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2153V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GLTPD2 MUTATED                                  0     0
  GLTPD2 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  GLTPD2 MUTATED                           0     1
  GLTPD2 WILD-TYPE                        22   225
D2153V13, multiclass
[1] "Remove cluster labels:" "GLTPD2 MUTATED"        
clus
  GLTPD2 MUTATED GLTPD2 WILD-TYPE 
               1              259 
      TCGA-A6-2671       TCGA-A6-2672       TCGA-A6-2674       TCGA-A6-2676 
"GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" 
      TCGA-A6-2677       TCGA-A6-2678       TCGA-A6-2683       TCGA-A6-3807 
"GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" 
      TCGA-A6-3808       TCGA-A6-3809       TCGA-A6-3810       TCGA-A6-4105 
"GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" 
      TCGA-A6-5656       TCGA-A6-5657       TCGA-A6-5659       TCGA-A6-5660 
"GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" 
      TCGA-A6-5661       TCGA-A6-5662       TCGA-A6-5664       TCGA-A6-5665 
"GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" 
      TCGA-A6-5666       TCGA-A6-6137       TCGA-A6-6138       TCGA-A6-6141 
"GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" 
      TCGA-A6-6142       TCGA-A6-6648       TCGA-A6-6649       TCGA-A6-6651 
"GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" 
      TCGA-A6-6652       TCGA-A6-6653       TCGA-A6-6654       TCGA-A6-6780 
"GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" 
      TCGA-A6-6781       TCGA-A6-6782       TCGA-AD-5900       TCGA-AD-6548 
"GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" 
      TCGA-AD-6888       TCGA-AD-6889       TCGA-AD-6890       TCGA-AD-6895 
"GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" 
      TCGA-AD-6899       TCGA-AD-6901       TCGA-AD-6963       TCGA-AD-6964 
"GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" 
      TCGA-AD-6965       TCGA-AU-3779       TCGA-AU-6004       TCGA-AY-4070 
"GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" 
      TCGA-AY-4071       TCGA-AY-5543       TCGA-AY-6196       TCGA-AY-6197 
"GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" 
      TCGA-AY-6386       TCGA-AZ-4315       TCGA-AZ-4323       TCGA-AZ-4616 
"GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" 
      TCGA-AZ-4681       TCGA-AZ-4682       TCGA-AZ-5403       TCGA-AZ-5407 
"GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" 
      TCGA-AZ-6598       TCGA-AZ-6600       TCGA-AZ-6601       TCGA-AZ-6603 
"GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" 
      TCGA-AZ-6605       TCGA-AZ-6606       TCGA-AZ-6607       TCGA-AZ-6608 
"GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" 
      TCGA-CA-5254       TCGA-CA-5255       TCGA-CA-5796       TCGA-CA-5797 
"GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" 
      TCGA-CA-6715       TCGA-CA-6716       TCGA-CA-6717       TCGA-CA-6718 
"GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" 
      TCGA-CA-6719       TCGA-CK-4947       TCGA-CK-4948       TCGA-CK-4950 
"GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" 
      TCGA-CK-4952       TCGA-CK-5912       TCGA-CK-5913       TCGA-CK-5914 
"GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" 
      TCGA-CK-5915       TCGA-CK-5916       TCGA-CK-6746       TCGA-CK-6747 
"GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" 
      TCGA-CK-6748       TCGA-CK-6751       TCGA-CM-4743       TCGA-CM-4744 
"GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" 
      TCGA-CM-4746       TCGA-CM-4747       TCGA-CM-4752       TCGA-CM-5341 
"GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" 
      TCGA-CM-5344       TCGA-CM-5348       TCGA-CM-5349       TCGA-CM-5860 
"GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" 
      TCGA-CM-5861       TCGA-CM-5862       TCGA-CM-5863       TCGA-CM-5864 
"GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" 
      TCGA-CM-5868       TCGA-CM-6161       TCGA-CM-6162       TCGA-CM-6163 
"GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" 
      TCGA-CM-6164       TCGA-CM-6165       TCGA-CM-6166       TCGA-CM-6167 
"GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" 
      TCGA-CM-6168       TCGA-CM-6169       TCGA-CM-6170       TCGA-CM-6171 
"GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" 
      TCGA-CM-6172       TCGA-CM-6674       TCGA-CM-6675       TCGA-CM-6676 
"GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" 
      TCGA-CM-6677       TCGA-CM-6678       TCGA-CM-6679       TCGA-CM-6680 
"GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" 
      TCGA-D5-5537       TCGA-D5-5538       TCGA-D5-5539       TCGA-D5-5540 
"GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" 
      TCGA-D5-5541       TCGA-D5-6529       TCGA-D5-6532       TCGA-D5-6533 
"GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" 
      TCGA-D5-6534       TCGA-D5-6535       TCGA-D5-6536       TCGA-D5-6537 
"GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" 
      TCGA-D5-6538       TCGA-D5-6539       TCGA-D5-6540       TCGA-D5-6541 
"GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" 
      TCGA-D5-6898       TCGA-D5-6920       TCGA-D5-6922       TCGA-D5-6923 
"GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" 
      TCGA-D5-6924       TCGA-D5-6926       TCGA-D5-6927       TCGA-D5-6928 
"GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" 
      TCGA-D5-6929       TCGA-D5-6930       TCGA-D5-6931       TCGA-D5-6932 
"GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" 
      TCGA-D5-7000       TCGA-DM-A0X9       TCGA-DM-A0XD       TCGA-DM-A0XF 
"GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" 
      TCGA-DM-A1D0       TCGA-DM-A1D4       TCGA-DM-A1D6       TCGA-DM-A1D7 
"GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" 
      TCGA-DM-A1D8       TCGA-DM-A1D9       TCGA-DM-A1DA       TCGA-DM-A1DB 
"GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" 
      TCGA-DM-A1HA       TCGA-DM-A1HB       TCGA-DM-A282       TCGA-DM-A285 
"GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" 
      TCGA-DM-A28C       TCGA-DM-A28E       TCGA-DM-A28F       TCGA-DM-A28G 
"GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" 
      TCGA-DM-A28H       TCGA-DM-A28K       TCGA-F4-6459       TCGA-F4-6460 
"GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" 
      TCGA-F4-6569       TCGA-F4-6570       TCGA-F4-6703       TCGA-F4-6704 
"GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" 
      TCGA-F4-6805       TCGA-F4-6806       TCGA-F4-6807       TCGA-F4-6808 
"GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" 
      TCGA-F4-6809       TCGA-F4-6854       TCGA-F4-6855       TCGA-F4-6856 
"GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" 
      TCGA-G4-6293       TCGA-G4-6299       TCGA-G4-6303       TCGA-G4-6304 
"GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" 
      TCGA-G4-6306       TCGA-G4-6307       TCGA-G4-6309       TCGA-G4-6310 
"GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" 
      TCGA-G4-6315       TCGA-G4-6317       TCGA-G4-6321       TCGA-G4-6323 
"GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" 
      TCGA-G4-6586       TCGA-G4-6588       TCGA-G4-6625       TCGA-G4-6626 
"GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" 
      TCGA-G4-6628       TCGA-AF-2687       TCGA-AF-2689       TCGA-AF-2691 
"GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" 
      TCGA-AF-2692       TCGA-AF-2693       TCGA-AF-3400       TCGA-AF-3913 
"GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" 
      TCGA-AF-4110       TCGA-AF-5654       TCGA-AF-6136       TCGA-AF-6655 
"GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" 
      TCGA-AF-6672       TCGA-AH-6544       TCGA-AH-6547       TCGA-AH-6549 
"GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" 
      TCGA-AH-6643       TCGA-AH-6644       TCGA-CI-6619       TCGA-CI-6620 
"GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" 
      TCGA-CI-6621       TCGA-CI-6622       TCGA-CI-6624       TCGA-CL-5917 
"GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" 
      TCGA-CL-5918       TCGA-DC-5337       TCGA-DC-5869       TCGA-DC-6155 
"GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" 
      TCGA-DC-6157       TCGA-DC-6158       TCGA-DC-6160       TCGA-DC-6681 
"GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" 
      TCGA-DC-6682       TCGA-DC-6683       TCGA-DT-5265       TCGA-DY-A0XA 
"GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" 
      TCGA-DY-A1DC       TCGA-DY-A1DD       TCGA-DY-A1DF       TCGA-DY-A1DG 
"GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" 
      TCGA-DY-A1H8       TCGA-EF-5830       TCGA-EI-6506       TCGA-EI-6507 
"GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" 
      TCGA-EI-6508       TCGA-EI-6510       TCGA-F5-6464       TCGA-F5-6465 
"GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" 
      TCGA-F5-6571       TCGA-F5-6702       TCGA-F5-6811       TCGA-F5-6812 
"GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" 
      TCGA-F5-6813       TCGA-G5-6235       TCGA-G5-6641 
"GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" "GLTPD2 WILD-TYPE" 

Clustering(2154) Variable = KIAA0922 MUTATION ANALYSIS
D2154V1, survival
                    sevent
clus2                  0   1
  KIAA0922 MUTATED    17   2
  KIAA0922 WILD-TYPE 361  91
  KIAA0922 MUTATED KIAA0922 WILD-TYPE 
                19                452 
  KIAA0922 MUTATED KIAA0922 WILD-TYPE 
                 2                 91 
$`KIAA0922 MUTATED`
TCGA-AA-3663 TCGA-AA-3710 TCGA-AA-3815 TCGA-AA-3864 TCGA-AA-3966 TCGA-AA-3977 
        6.97        26.99        33.04        53.00         2.01        25.02 
TCGA-AA-A010 TCGA-AD-5900 TCGA-AY-6197 TCGA-AZ-4315 TCGA-CA-6717 TCGA-CK-5913 
       34.98         0.07        21.44        58.39        12.76        51.32 
TCGA-DM-A1D7 TCGA-F4-6856 TCGA-G4-6303 TCGA-AF-6136 TCGA-AG-3892 TCGA-AG-A002 
       13.32        35.31        65.85        15.39        13.02        20.98 
TCGA-DC-6682 
        4.01 

$`KIAA0922 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.05        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        85.05        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       35.05         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        31.07        30.05        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 
       41.00        39.98        18.05        40.96        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       33.01        17.82         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07        12.20        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       92.75        49.91        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 
       16.24        33.67        13.25         0.53        47.41       133.18 
TCGA-G4-6299 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       74.56        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 
        1.02        17.95        36.95        17.03        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 
       27.95        10.98        19.99         5.95         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  KIAA0922 MUTATED KIAA0922 WILD-TYPE 
              0.07               0.00 
  KIAA0922 MUTATED KIAA0922 WILD-TYPE 
             65.85             148.01 
  KIAA0922 MUTATED KIAA0922 WILD-TYPE 
            21.440             20.085 
[1] "0.1 - 65.8 (21.4)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "2"  
D2154V2, continuous
D2154V3, binary
                    cls
clus                   0   1
  KIAA0922 MUTATED    17   4
  KIAA0922 WILD-TYPE 349 115
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0922 MUTATED     17    4
  KIAA0922 WILD-TYPE  349  115
        clus
vv       KIAA0922 MUTATED KIAA0922 WILD-TYPE
  COLON                17                349
  RECTUM                4                115
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KIAA0922 MUTATED         4        0        3        10         1         0
  KIAA0922 WILD-TYPE      87        1       29       128         9         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KIAA0922 MUTATED           0          0          1          0        1
  KIAA0922 WILD-TYPE        24         11         58         42       47
                    vv
clus                 STAGE IVA STAGE IVB
  KIAA0922 MUTATED           0         0
  KIAA0922 WILD-TYPE        18         1
D2154V4, multiclass
            clus
vv           KIAA0922 MUTATED KIAA0922 WILD-TYPE
  STAGE I                   4                 87
  STAGE IA                  0                  1
  STAGE II                  3                 29
  STAGE IIA                10                128
  STAGE IIB                 1                  9
  STAGE IIC                 0                  1
  STAGE III                 0                 24
  STAGE IIIA                0                 11
  STAGE IIIB                1                 58
  STAGE IIIC                0                 42
  STAGE IV                  1                 47
  STAGE IVA                 0                 18
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  KIAA0922 MUTATED     1   4  14   2
  KIAA0922 WILD-TYPE  16  88 315  48
D2154V5, multiclass
    clus
vv   KIAA0922 MUTATED KIAA0922 WILD-TYPE
  T1                1                 16
  T2                4                 88
  T3               14                315
  T4                2                 48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  KIAA0922 MUTATED    19   2   0
  KIAA0922 WILD-TYPE 268 111  87
D2154V6, multiclass
    clus
vv   KIAA0922 MUTATED KIAA0922 WILD-TYPE
  N0               19                268
  N1                2                111
  N2                0                 87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2154V7, binary
                    cls
clus                   0   1
  KIAA0922 MUTATED    15   1
  KIAA0922 WILD-TYPE 360  64
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0922 MUTATED     15    1
  KIAA0922 WILD-TYPE  360   64
   clus
vv  KIAA0922 MUTATED KIAA0922 WILD-TYPE
  0               15                360
  1                1                 64
[1] 2 2
[1] FALSE
D2154V8, binary
                    cls
clus                   0   1
  KIAA0922 MUTATED    10  11
  KIAA0922 WILD-TYPE 215 253
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0922 MUTATED     10   11
  KIAA0922 WILD-TYPE  215  253
        clus
vv       KIAA0922 MUTATED KIAA0922 WILD-TYPE
  FEMALE               10                215
  MALE                 11                253
[1] 2 2
[1] FALSE
D2154V9, binary
                    cls
clus                   0   1
  KIAA0922 MUTATED    14   1
  KIAA0922 WILD-TYPE 336  21
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0922 MUTATED     14    1
  KIAA0922 WILD-TYPE  336   21
     clus
vv    KIAA0922 MUTATED KIAA0922 WILD-TYPE
  NO                14                336
  YES                1                 21
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  KIAA0922 MUTATED                     12                             4
  KIAA0922 WILD-TYPE                  303                            43
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  KIAA0922 MUTATED                       4                              0
  KIAA0922 WILD-TYPE                   102                             10
D2154V10, multiclass
                                clus
vv                               KIAA0922 MUTATED KIAA0922 WILD-TYPE
  COLON ADENOCARCINOMA                         12                303
  COLON MUCINOUS ADENOCARCINOMA                 4                 43
  RECTAL ADENOCARCINOMA                         4                102
  RECTAL MUCINOUS ADENOCARCINOMA                0                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  KIAA0922 MUTATED    15   0   0   2
  KIAA0922 WILD-TYPE 330   4  31  23
D2154V11, multiclass
    clus
vv   KIAA0922 MUTATED KIAA0922 WILD-TYPE
  R0               15                330
  R1                0                  4
  R2                0                 31
  RX                2                 23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2154V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KIAA0922 MUTATED                                  0     1
  KIAA0922 WILD-TYPE                                1    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  KIAA0922 MUTATED                           0     9
  KIAA0922 WILD-TYPE                        22   217
D2154V13, multiclass
                                  clus
vv                                 KIAA0922 MUTATED KIAA0922 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                 10
  BLACK OR AFRICAN AMERICAN                       0                 22
  WHITE                                           9                217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2155) Variable = STK3 MUTATION ANALYSIS
D2155V1, survival
                sevent
clus2              0   1
  STK3 MUTATED     6   3
  STK3 WILD-TYPE 372  90
  STK3 MUTATED STK3 WILD-TYPE 
             9            462 
  STK3 MUTATED STK3 WILD-TYPE 
             3             90 
$`STK3 MUTATED`
TCGA-A6-6780 TCGA-AA-3496 TCGA-AA-3510 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-A01R 
       20.12         1.02        63.98        26.99        19.04        35.01 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-CA-6718 
       88.21        49.41        10.06 

$`STK3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 
       23.87        19.66        20.28         7.04         3.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       85.05        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
        1.02         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6599 
        1.41         5.13       106.75        22.36        62.79         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.20        12.76        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  STK3 MUTATED STK3 WILD-TYPE 
          1.02           0.00 
  STK3 MUTATED STK3 WILD-TYPE 
         88.21         148.01 
  STK3 MUTATED STK3 WILD-TYPE 
         26.99          20.12 
[1] "1.0 - 88.2 (27.0)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.3"
D2155V2, continuous
D2155V3, binary
                cls
clus               0   1
  STK3 MUTATED     9   0
  STK3 WILD-TYPE 357 119
[1] "tbl2"
                cls
clus             [,1] [,2]
  STK3 MUTATED      9    0
  STK3 WILD-TYPE  357  119
        clus
vv       STK3 MUTATED STK3 WILD-TYPE
  COLON             9            357
  RECTUM            0            119
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  STK3 MUTATED         1        0        4         3         0         0
  STK3 WILD-TYPE      90        1       28       135        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  STK3 MUTATED           1          0          0          0        0         0
  STK3 WILD-TYPE        23         11         59         42       48        18
                vv
clus             STAGE IVB
  STK3 MUTATED           0
  STK3 WILD-TYPE         1
D2155V4, multiclass
            clus
vv           STK3 MUTATED STK3 WILD-TYPE
  STAGE I               1             90
  STAGE IA              0              1
  STAGE II              4             28
  STAGE IIA             3            135
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             1             23
  STAGE IIIA            0             11
  STAGE IIIB            0             59
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  STK3 MUTATED     1   0   8   0
  STK3 WILD-TYPE  16  92 321  50
D2155V5, multiclass
    clus
vv   STK3 MUTATED STK3 WILD-TYPE
  T1            1             16
  T2            0             92
  T3            8            321
  T4            0             50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  STK3 MUTATED     8   0   1
  STK3 WILD-TYPE 279 113  86
D2155V6, multiclass
    clus
vv   STK3 MUTATED STK3 WILD-TYPE
  N0            8            279
  N1            0            113
  N2            1             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2155V7, binary
                cls
clus               0   1
  STK3 MUTATED     7   0
  STK3 WILD-TYPE 368  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  STK3 MUTATED      7    0
  STK3 WILD-TYPE  368   65
   clus
vv  STK3 MUTATED STK3 WILD-TYPE
  0            7            368
  1            0             65
[1] 2 2
[1] FALSE
D2155V8, binary
                cls
clus               0   1
  STK3 MUTATED     4   5
  STK3 WILD-TYPE 221 259
[1] "tbl2"
                cls
clus             [,1] [,2]
  STK3 MUTATED      4    5
  STK3 WILD-TYPE  221  259
        clus
vv       STK3 MUTATED STK3 WILD-TYPE
  FEMALE            4            221
  MALE              5            259
[1] 2 2
[1] FALSE
D2155V9, binary
                cls
clus               0   1
  STK3 MUTATED     7   1
  STK3 WILD-TYPE 343  21
[1] "tbl2"
                cls
clus             [,1] [,2]
  STK3 MUTATED      7    1
  STK3 WILD-TYPE  343   21
     clus
vv    STK3 MUTATED STK3 WILD-TYPE
  NO             7            343
  YES            1             21
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  STK3 MUTATED                      7                             2
  STK3 WILD-TYPE                  308                            45
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  STK3 MUTATED                       0                              0
  STK3 WILD-TYPE                   106                             10
D2155V10, multiclass
                                clus
vv                               STK3 MUTATED STK3 WILD-TYPE
  COLON ADENOCARCINOMA                      7            308
  COLON MUCINOUS ADENOCARCINOMA             2             45
  RECTAL ADENOCARCINOMA                     0            106
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  STK3 MUTATED     5   0   0   1
  STK3 WILD-TYPE 340   4  31  24
D2155V11, multiclass
    clus
vv   STK3 MUTATED STK3 WILD-TYPE
  R0            5            340
  R1            0              4
  R2            0             31
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2155V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  STK3 MUTATED                                  0     1
  STK3 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  STK3 MUTATED                           0     3
  STK3 WILD-TYPE                        22   223
D2155V13, multiclass
                                  clus
vv                                 STK3 MUTATED STK3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       3            223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2156) Variable = SLC35A1 MUTATION ANALYSIS
D2156V1, survival
                   sevent
clus2                 0   1
  SLC35A1 MUTATED     3   0
  SLC35A1 WILD-TYPE 375  93
  SLC35A1 MUTATED SLC35A1 WILD-TYPE 
                3               468 
  SLC35A1 MUTATED SLC35A1 WILD-TYPE 
                0                93 
$`SLC35A1 MUTATED`
TCGA-AA-3842 TCGA-CA-6717 TCGA-AG-A002 
       37.02        12.76        20.98 

$`SLC35A1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3844 TCGA-AA-3845 
        1.02        17.98        15.95        38.99        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07        12.20        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  SLC35A1 MUTATED SLC35A1 WILD-TYPE 
            12.76              0.00 
  SLC35A1 MUTATED SLC35A1 WILD-TYPE 
            37.02            148.01 
  SLC35A1 MUTATED SLC35A1 WILD-TYPE 
           20.980            20.155 
[1] "12.8 - 37.0 (21.0)" "0.0 - 148.0 (20.2)"
[1] "hr="     "3300000"
D2156V2, continuous
D2156V3, binary
                   cls
clus                  0   1
  SLC35A1 MUTATED     2   1
  SLC35A1 WILD-TYPE 364 118
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC35A1 MUTATED      2    1
  SLC35A1 WILD-TYPE  364  118
        clus
vv       SLC35A1 MUTATED SLC35A1 WILD-TYPE
  COLON                2               364
  RECTUM               1               118
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SLC35A1 MUTATED         1        0        0         1         0         0
  SLC35A1 WILD-TYPE      90        1       32       137        10         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC35A1 MUTATED           0          1          0          0        0
  SLC35A1 WILD-TYPE        24         10         59         42       48
                   vv
clus                STAGE IVA STAGE IVB
  SLC35A1 MUTATED           0         0
  SLC35A1 WILD-TYPE        18         1
D2156V4, multiclass
            clus
vv           SLC35A1 MUTATED SLC35A1 WILD-TYPE
  STAGE I                  1                90
  STAGE IA                 0                 1
  STAGE II                 0                32
  STAGE IIA                1               137
  STAGE IIB                0                10
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               1                10
  STAGE IIIB               0                59
  STAGE IIIC               0                42
  STAGE IV                 0                48
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  SLC35A1 MUTATED     0   2   1   0
  SLC35A1 WILD-TYPE  17  90 328  50
D2156V5, multiclass
    clus
vv   SLC35A1 MUTATED SLC35A1 WILD-TYPE
  T1               0                17
  T2               2                90
  T3               1               328
  T4               0                50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  SLC35A1 MUTATED     2   1   0
  SLC35A1 WILD-TYPE 285 112  87
D2156V6, multiclass
    clus
vv   SLC35A1 MUTATED SLC35A1 WILD-TYPE
  N0               2               285
  N1               1               112
  N2               0                87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2156V7, binary
                   cls
clus                  0   1
  SLC35A1 MUTATED     3   0
  SLC35A1 WILD-TYPE 372  65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC35A1 MUTATED      3    0
  SLC35A1 WILD-TYPE  372   65
   clus
vv  SLC35A1 MUTATED SLC35A1 WILD-TYPE
  0               3               372
  1               0                65
[1] 2 2
[1] FALSE
D2156V8, binary
                   cls
clus                  0   1
  SLC35A1 MUTATED     0   3
  SLC35A1 WILD-TYPE 225 261
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC35A1 MUTATED      0    3
  SLC35A1 WILD-TYPE  225  261
        clus
vv       SLC35A1 MUTATED SLC35A1 WILD-TYPE
  FEMALE               0               225
  MALE                 3               261
[1] 2 2
[1] FALSE
D2156V9, binary
                   cls
clus                  0   1
  SLC35A1 MUTATED     3   0
  SLC35A1 WILD-TYPE 347  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC35A1 MUTATED      3    0
  SLC35A1 WILD-TYPE  347   22
     clus
vv    SLC35A1 MUTATED SLC35A1 WILD-TYPE
  NO                3               347
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SLC35A1 MUTATED                      1                             1
  SLC35A1 WILD-TYPE                  314                            46
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SLC35A1 MUTATED                       1                              0
  SLC35A1 WILD-TYPE                   105                             10
D2156V10, multiclass
                                clus
vv                               SLC35A1 MUTATED SLC35A1 WILD-TYPE
  COLON ADENOCARCINOMA                         1               314
  COLON MUCINOUS ADENOCARCINOMA                1                46
  RECTAL ADENOCARCINOMA                        1               105
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  SLC35A1 MUTATED     2   0   0   1
  SLC35A1 WILD-TYPE 343   4  31  24
D2156V11, multiclass
    clus
vv   SLC35A1 MUTATED SLC35A1 WILD-TYPE
  R0               2               343
  R1               0                 4
  R2               0                31
  RX               1                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2156V12, continuous
[1] "Remove cluster labels:" "SLC35A1 MUTATED"       
clus
  SLC35A1 MUTATED SLC35A1 WILD-TYPE 
                2               456 
       TCGA-A6-2671        TCGA-A6-2672        TCGA-A6-2674        TCGA-A6-2676 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-A6-2677        TCGA-A6-2678        TCGA-A6-2683        TCGA-A6-3807 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-A6-3808        TCGA-A6-3809        TCGA-A6-3810        TCGA-A6-4105 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-A6-5656        TCGA-A6-5657        TCGA-A6-5659        TCGA-A6-5660 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-A6-5661        TCGA-A6-5662        TCGA-A6-5664        TCGA-A6-5665 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-A6-5666        TCGA-A6-6137        TCGA-A6-6138        TCGA-A6-6141 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-A6-6142        TCGA-A6-6648        TCGA-A6-6649        TCGA-A6-6651 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-A6-6652        TCGA-A6-6653        TCGA-A6-6654        TCGA-A6-6780 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-A6-6781        TCGA-A6-6782        TCGA-AA-3489        TCGA-AA-3492 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-AA-3496        TCGA-AA-3502        TCGA-AA-3510        TCGA-AA-3511 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-AA-3514        TCGA-AA-3516        TCGA-AA-3517        TCGA-AA-3518 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-AA-3519        TCGA-AA-3520        TCGA-AA-3521        TCGA-AA-3522 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-AA-3524        TCGA-AA-3525        TCGA-AA-3526        TCGA-AA-3527 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-AA-3529        TCGA-AA-3530        TCGA-AA-3531        TCGA-AA-3532 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-AA-3534        TCGA-AA-3538        TCGA-AA-3542        TCGA-AA-3543 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-AA-3544        TCGA-AA-3548        TCGA-AA-3549        TCGA-AA-3552 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-AA-3553        TCGA-AA-3554        TCGA-AA-3555        TCGA-AA-3556 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-AA-3558        TCGA-AA-3560        TCGA-AA-3562        TCGA-AA-3655 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-AA-3660        TCGA-AA-3662        TCGA-AA-3663        TCGA-AA-3664 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-AA-3666        TCGA-AA-3667        TCGA-AA-3672        TCGA-AA-3673 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-AA-3678        TCGA-AA-3679        TCGA-AA-3680        TCGA-AA-3681 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-AA-3684        TCGA-AA-3685        TCGA-AA-3688        TCGA-AA-3692 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-AA-3693        TCGA-AA-3695        TCGA-AA-3696        TCGA-AA-3697 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-AA-3710        TCGA-AA-3712        TCGA-AA-3713        TCGA-AA-3715 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-AA-3811        TCGA-AA-3812        TCGA-AA-3814        TCGA-AA-3815 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-AA-3818        TCGA-AA-3819        TCGA-AA-3821        TCGA-AA-3831 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-AA-3833        TCGA-AA-3837        TCGA-AA-3844        TCGA-AA-3845 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-AA-3846        TCGA-AA-3848        TCGA-AA-3850        TCGA-AA-3851 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-AA-3852        TCGA-AA-3854        TCGA-AA-3855        TCGA-AA-3856 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-AA-3858        TCGA-AA-3860        TCGA-AA-3861        TCGA-AA-3864 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-AA-3866        TCGA-AA-3867        TCGA-AA-3869        TCGA-AA-3870 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-AA-3872        TCGA-AA-3875        TCGA-AA-3877        TCGA-AA-3930 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-AA-3939        TCGA-AA-3941        TCGA-AA-3947        TCGA-AA-3949 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-AA-3950        TCGA-AA-3952        TCGA-AA-3955        TCGA-AA-3956 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-AA-3966        TCGA-AA-3968        TCGA-AA-3971        TCGA-AA-3972 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-AA-3973        TCGA-AA-3975        TCGA-AA-3976        TCGA-AA-3977 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-AA-3979        TCGA-AA-3980        TCGA-AA-3982        TCGA-AA-3984 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-AA-3986        TCGA-AA-3989        TCGA-AA-3994        TCGA-AA-A004 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-AA-A00A        TCGA-AA-A00D        TCGA-AA-A00E        TCGA-AA-A00F 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-AA-A00J        TCGA-AA-A00K        TCGA-AA-A00L        TCGA-AA-A00N 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-AA-A00O        TCGA-AA-A00Q        TCGA-AA-A00R        TCGA-AA-A00U 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-AA-A00W        TCGA-AA-A00Z        TCGA-AA-A010        TCGA-AA-A017 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-AA-A01D        TCGA-AA-A01F        TCGA-AA-A01G        TCGA-AA-A01I 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-AA-A01K        TCGA-AA-A01P        TCGA-AA-A01Q        TCGA-AA-A01R 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-AA-A01S        TCGA-AA-A01T        TCGA-AA-A01V        TCGA-AA-A01X 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-AA-A01Z        TCGA-AA-A022        TCGA-AA-A024        TCGA-AA-A029 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-AA-A02F        TCGA-AA-A02H        TCGA-AA-A02J        TCGA-AA-A02K 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-AA-A02O        TCGA-AA-A02W        TCGA-AA-A02Y        TCGA-AA-A03F 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-AA-A03J        TCGA-AD-5900        TCGA-AD-6548        TCGA-AD-6888 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-AD-6889        TCGA-AD-6890        TCGA-AD-6895        TCGA-AD-6899 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-AD-6901        TCGA-AD-6963        TCGA-AD-6964        TCGA-AD-6965 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-AU-3779        TCGA-AU-6004        TCGA-AY-4070        TCGA-AY-4071 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-AY-5543        TCGA-AY-6196        TCGA-AY-6197        TCGA-AY-6386 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-AZ-4323        TCGA-AZ-4616        TCGA-AZ-4682        TCGA-AZ-5403 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-AZ-5407        TCGA-AZ-6598        TCGA-AZ-6599        TCGA-AZ-6600 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-AZ-6601        TCGA-AZ-6603        TCGA-AZ-6605        TCGA-AZ-6606 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-AZ-6607        TCGA-AZ-6608        TCGA-CK-4947        TCGA-CK-4948 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-CK-4950        TCGA-CK-4952        TCGA-CM-4743        TCGA-CM-4744 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-CM-4746        TCGA-CM-4747        TCGA-CM-4752        TCGA-CM-5341 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-CM-5344        TCGA-CM-5348        TCGA-CM-5349        TCGA-CM-5860 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-CM-5861        TCGA-CM-5862        TCGA-CM-5863        TCGA-CM-5864 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-CM-5868        TCGA-CM-6161        TCGA-CM-6162        TCGA-CM-6163 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-CM-6164        TCGA-CM-6165        TCGA-CM-6166        TCGA-CM-6167 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-CM-6168        TCGA-CM-6169        TCGA-CM-6170        TCGA-CM-6171 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-CM-6172        TCGA-CM-6674        TCGA-CM-6675        TCGA-CM-6676 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-CM-6677        TCGA-CM-6678        TCGA-CM-6679        TCGA-CM-6680 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-D5-5537        TCGA-D5-5538        TCGA-D5-5539        TCGA-D5-5540 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-D5-5541        TCGA-D5-6529        TCGA-D5-6532        TCGA-D5-6533 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-D5-6534        TCGA-D5-6535        TCGA-D5-6536        TCGA-D5-6537 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-D5-6538        TCGA-D5-6539        TCGA-D5-6540        TCGA-D5-6541 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-D5-6898        TCGA-D5-6920        TCGA-D5-6922        TCGA-D5-6923 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-D5-6924        TCGA-D5-6926        TCGA-D5-6927        TCGA-D5-6928 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-D5-6929        TCGA-D5-6930        TCGA-D5-6931        TCGA-D5-6932 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-D5-7000        TCGA-DM-A0X9        TCGA-DM-A0XD        TCGA-DM-A0XF 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-DM-A1D0        TCGA-DM-A1D4        TCGA-DM-A1D6        TCGA-DM-A1D7 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-DM-A1D8        TCGA-DM-A1D9        TCGA-DM-A1DA        TCGA-DM-A1DB 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-DM-A1HA        TCGA-DM-A1HB        TCGA-DM-A282        TCGA-DM-A285 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-DM-A28C        TCGA-DM-A28E        TCGA-DM-A28F        TCGA-DM-A28G 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-DM-A28H        TCGA-DM-A28K        TCGA-F4-6459        TCGA-F4-6460 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-F4-6569        TCGA-F4-6570        TCGA-F4-6703        TCGA-F4-6704 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-F4-6806        TCGA-F4-6807        TCGA-F4-6808        TCGA-F4-6809 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-F4-6854        TCGA-F4-6855        TCGA-F4-6856        TCGA-G4-6293 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-G4-6299        TCGA-G4-6303        TCGA-G4-6304        TCGA-G4-6306 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-G4-6307        TCGA-G4-6309        TCGA-G4-6310        TCGA-G4-6315 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-G4-6317        TCGA-G4-6321        TCGA-G4-6323        TCGA-G4-6586 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-G4-6588        TCGA-G4-6625        TCGA-G4-6626        TCGA-G4-6628 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2691        TCGA-AF-2692 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3913        TCGA-AF-4110 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-AF-5654        TCGA-AF-6136        TCGA-AF-6655        TCGA-AF-6672 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-AG-3574        TCGA-AG-3575        TCGA-AG-3578        TCGA-AG-3580 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-AG-3581        TCGA-AG-3582        TCGA-AG-3583        TCGA-AG-3584 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-AG-3586        TCGA-AG-3587        TCGA-AG-3593        TCGA-AG-3594 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-AG-3598        TCGA-AG-3599        TCGA-AG-3600        TCGA-AG-3601 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-AG-3602        TCGA-AG-3605        TCGA-AG-3608        TCGA-AG-3609 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-AG-3611        TCGA-AG-3612        TCGA-AG-3726        TCGA-AG-3727 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-AG-3731        TCGA-AG-3732        TCGA-AG-3742        TCGA-AG-3878 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-AG-3881        TCGA-AG-3882        TCGA-AG-3883        TCGA-AG-3885 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-AG-3887        TCGA-AG-3890        TCGA-AG-3892        TCGA-AG-3893 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-AG-3894        TCGA-AG-3896        TCGA-AG-3898        TCGA-AG-3901 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-AG-3902        TCGA-AG-3909        TCGA-AG-3999        TCGA-AG-4001 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-AG-4005        TCGA-AG-4007        TCGA-AG-4008        TCGA-AG-4015 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-AG-A008        TCGA-AG-A00C        TCGA-AG-A00H        TCGA-AG-A00Y 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-AG-A011        TCGA-AG-A014        TCGA-AG-A015        TCGA-AG-A016 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-AG-A01L        TCGA-AG-A01W        TCGA-AG-A01Y        TCGA-AG-A020 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-AG-A025        TCGA-AG-A026        TCGA-AG-A02G        TCGA-AG-A02N 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-AG-A02X        TCGA-AG-A032        TCGA-AG-A036        TCGA-AH-6544 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-AH-6547        TCGA-AH-6643        TCGA-AH-6644        TCGA-CI-6622 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6155        TCGA-DC-6157 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-DC-6158        TCGA-DC-6160        TCGA-DC-6681        TCGA-DC-6682 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-DC-6683        TCGA-DY-A0XA        TCGA-DY-A1DC        TCGA-DY-A1DD 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-DY-A1DF        TCGA-DY-A1DG        TCGA-DY-A1H8        TCGA-EI-6506 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-EI-6507        TCGA-EI-6508        TCGA-EI-6510        TCGA-F5-6464 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-F5-6465        TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6811 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-F5-6812        TCGA-F5-6813        TCGA-G5-6235        TCGA-G5-6641 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SLC35A1 MUTATED                                  0     1
  SLC35A1 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  SLC35A1 MUTATED                           0     0
  SLC35A1 WILD-TYPE                        22   226
D2156V13, multiclass
[1] "Remove cluster labels:" "SLC35A1 MUTATED"       
clus
  SLC35A1 MUTATED SLC35A1 WILD-TYPE 
                1               259 
       TCGA-A6-2671        TCGA-A6-2672        TCGA-A6-2674        TCGA-A6-2676 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-A6-2677        TCGA-A6-2678        TCGA-A6-2683        TCGA-A6-3807 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-A6-3808        TCGA-A6-3809        TCGA-A6-3810        TCGA-A6-4105 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-A6-5656        TCGA-A6-5657        TCGA-A6-5659        TCGA-A6-5660 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-A6-5661        TCGA-A6-5662        TCGA-A6-5664        TCGA-A6-5665 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-A6-5666        TCGA-A6-6137        TCGA-A6-6138        TCGA-A6-6141 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-A6-6142        TCGA-A6-6648        TCGA-A6-6649        TCGA-A6-6651 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-A6-6652        TCGA-A6-6653        TCGA-A6-6654        TCGA-A6-6780 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-A6-6781        TCGA-A6-6782        TCGA-AD-5900        TCGA-AD-6548 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-AD-6888        TCGA-AD-6889        TCGA-AD-6890        TCGA-AD-6895 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-AD-6899        TCGA-AD-6901        TCGA-AD-6963        TCGA-AD-6964 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-AD-6965        TCGA-AU-3779        TCGA-AU-6004        TCGA-AY-4070 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-AY-4071        TCGA-AY-5543        TCGA-AY-6196        TCGA-AY-6197 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-AY-6386        TCGA-AZ-4315        TCGA-AZ-4323        TCGA-AZ-4616 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-AZ-4681        TCGA-AZ-4682        TCGA-AZ-5403        TCGA-AZ-5407 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-AZ-6598        TCGA-AZ-6599        TCGA-AZ-6600        TCGA-AZ-6601 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-AZ-6603        TCGA-AZ-6605        TCGA-AZ-6606        TCGA-AZ-6607 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-AZ-6608        TCGA-CA-5254        TCGA-CA-5255        TCGA-CA-5796 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-CA-5797        TCGA-CA-6715        TCGA-CA-6716        TCGA-CA-6718 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-CA-6719        TCGA-CK-4947        TCGA-CK-4948        TCGA-CK-4950 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-CK-4952        TCGA-CK-5912        TCGA-CK-5913        TCGA-CK-5914 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-CK-5915        TCGA-CK-5916        TCGA-CK-6746        TCGA-CK-6747 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-CK-6748        TCGA-CK-6751        TCGA-CM-4743        TCGA-CM-4744 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-CM-4746        TCGA-CM-4747        TCGA-CM-4752        TCGA-CM-5341 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-CM-5344        TCGA-CM-5348        TCGA-CM-5349        TCGA-CM-5860 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-CM-5861        TCGA-CM-5862        TCGA-CM-5863        TCGA-CM-5864 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-CM-5868        TCGA-CM-6161        TCGA-CM-6162        TCGA-CM-6163 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-CM-6164        TCGA-CM-6165        TCGA-CM-6166        TCGA-CM-6167 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-CM-6168        TCGA-CM-6169        TCGA-CM-6170        TCGA-CM-6171 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-CM-6172        TCGA-CM-6674        TCGA-CM-6675        TCGA-CM-6676 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-CM-6677        TCGA-CM-6678        TCGA-CM-6679        TCGA-CM-6680 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-D5-5537        TCGA-D5-5538        TCGA-D5-5539        TCGA-D5-5540 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-D5-5541        TCGA-D5-6529        TCGA-D5-6532        TCGA-D5-6533 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-D5-6534        TCGA-D5-6535        TCGA-D5-6536        TCGA-D5-6537 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-D5-6538        TCGA-D5-6539        TCGA-D5-6540        TCGA-D5-6541 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-D5-6898        TCGA-D5-6920        TCGA-D5-6922        TCGA-D5-6923 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-D5-6924        TCGA-D5-6926        TCGA-D5-6927        TCGA-D5-6928 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-D5-6929        TCGA-D5-6930        TCGA-D5-6931        TCGA-D5-6932 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-D5-7000        TCGA-DM-A0X9        TCGA-DM-A0XD        TCGA-DM-A0XF 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-DM-A1D0        TCGA-DM-A1D4        TCGA-DM-A1D6        TCGA-DM-A1D7 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-DM-A1D8        TCGA-DM-A1D9        TCGA-DM-A1DA        TCGA-DM-A1DB 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-DM-A1HA        TCGA-DM-A1HB        TCGA-DM-A282        TCGA-DM-A285 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-DM-A28C        TCGA-DM-A28E        TCGA-DM-A28F        TCGA-DM-A28G 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-DM-A28H        TCGA-DM-A28K        TCGA-F4-6459        TCGA-F4-6460 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-F4-6569        TCGA-F4-6570        TCGA-F4-6703        TCGA-F4-6704 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-F4-6805        TCGA-F4-6806        TCGA-F4-6807        TCGA-F4-6808 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-F4-6809        TCGA-F4-6854        TCGA-F4-6855        TCGA-F4-6856 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-G4-6293        TCGA-G4-6299        TCGA-G4-6303        TCGA-G4-6304 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-G4-6306        TCGA-G4-6307        TCGA-G4-6309        TCGA-G4-6310 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-G4-6315        TCGA-G4-6317        TCGA-G4-6321        TCGA-G4-6323 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-G4-6586        TCGA-G4-6588        TCGA-G4-6625        TCGA-G4-6626 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-G4-6628        TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2691 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3913 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136        TCGA-AF-6655 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-AF-6672        TCGA-AH-6544        TCGA-AH-6547        TCGA-AH-6549 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-AH-6643        TCGA-AH-6644        TCGA-CI-6619        TCGA-CI-6620 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-CI-6621        TCGA-CI-6622        TCGA-CI-6624        TCGA-CL-5917 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-CL-5918        TCGA-DC-5337        TCGA-DC-5869        TCGA-DC-6155 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-DC-6157        TCGA-DC-6158        TCGA-DC-6160        TCGA-DC-6681 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-DC-6682        TCGA-DC-6683        TCGA-DT-5265        TCGA-DY-A0XA 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-DY-A1DC        TCGA-DY-A1DD        TCGA-DY-A1DF        TCGA-DY-A1DG 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-DY-A1H8        TCGA-EF-5830        TCGA-EI-6506        TCGA-EI-6507 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6510        TCGA-F5-6464        TCGA-F5-6465 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6811        TCGA-F5-6812 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 
       TCGA-F5-6813        TCGA-G5-6235        TCGA-G5-6641 
"SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" "SLC35A1 WILD-TYPE" 

Clustering(2157) Variable = GLRA3 MUTATION ANALYSIS
D2157V1, survival
                 sevent
clus2               0   1
  GLRA3 MUTATED     8   1
  GLRA3 WILD-TYPE 370  92
  GLRA3 MUTATED GLRA3 WILD-TYPE 
              9             462 
  GLRA3 MUTATED GLRA3 WILD-TYPE 
              1              92 
$`GLRA3 MUTATED`
TCGA-A6-5661 TCGA-AA-3555 TCGA-AA-3713 TCGA-AA-3941 TCGA-AA-A010 TCGA-CA-6718 
       33.53        29.95        19.04        24.00        34.98        10.06 
TCGA-CK-4950 TCGA-CM-6676 TCGA-AG-3892 
       85.45        11.08        13.02 

$`GLRA3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       13.02        24.00        17.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 
        3.25         3.29         0.07        12.20        12.76        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
       17.56       148.01        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       11.01        12.95        13.05        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  GLRA3 MUTATED GLRA3 WILD-TYPE 
          10.06            0.00 
  GLRA3 MUTATED GLRA3 WILD-TYPE 
          85.45          148.01 
  GLRA3 MUTATED GLRA3 WILD-TYPE 
         24.000          20.155 
[1] "10.1 - 85.5 (24.0)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.9"
D2157V2, continuous
D2157V3, binary
                 cls
clus                0   1
  GLRA3 MUTATED     9   1
  GLRA3 WILD-TYPE 357 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GLRA3 MUTATED      9    1
  GLRA3 WILD-TYPE  357  118
        clus
vv       GLRA3 MUTATED GLRA3 WILD-TYPE
  COLON              9             357
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GLRA3 MUTATED         2        0        1         3         1         0
  GLRA3 WILD-TYPE      89        1       31       135         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  GLRA3 MUTATED           0          0          1          0        1         1
  GLRA3 WILD-TYPE        24         11         58         42       47        17
                 vv
clus              STAGE IVB
  GLRA3 MUTATED           0
  GLRA3 WILD-TYPE         1
D2157V4, multiclass
            clus
vv           GLRA3 MUTATED GLRA3 WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              3             135
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             0              42
  STAGE IV               1              47
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  GLRA3 MUTATED     1   1   5   3
  GLRA3 WILD-TYPE  16  91 324  47
D2157V5, multiclass
    clus
vv   GLRA3 MUTATED GLRA3 WILD-TYPE
  T1             1              16
  T2             1              91
  T3             5             324
  T4             3              47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  GLRA3 MUTATED     8   2   0
  GLRA3 WILD-TYPE 279 111  87
D2157V6, multiclass
    clus
vv   GLRA3 MUTATED GLRA3 WILD-TYPE
  N0             8             279
  N1             2             111
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2157V7, binary
                 cls
clus                0   1
  GLRA3 MUTATED     8   2
  GLRA3 WILD-TYPE 367  63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GLRA3 MUTATED      8    2
  GLRA3 WILD-TYPE  367   63
   clus
vv  GLRA3 MUTATED GLRA3 WILD-TYPE
  0             8             367
  1             2              63
[1] 2 2
[1] FALSE
D2157V8, binary
                 cls
clus                0   1
  GLRA3 MUTATED     7   3
  GLRA3 WILD-TYPE 218 261
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GLRA3 MUTATED      7    3
  GLRA3 WILD-TYPE  218  261
        clus
vv       GLRA3 MUTATED GLRA3 WILD-TYPE
  FEMALE             7             218
  MALE               3             261
[1] 2 2
[1] FALSE
D2157V9, binary
                 cls
clus                0   1
  GLRA3 MUTATED     8   1
  GLRA3 WILD-TYPE 342  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GLRA3 MUTATED      8    1
  GLRA3 WILD-TYPE  342   21
     clus
vv    GLRA3 MUTATED GLRA3 WILD-TYPE
  NO              8             342
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  GLRA3 MUTATED                      8                             1
  GLRA3 WILD-TYPE                  307                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  GLRA3 MUTATED                       1                              0
  GLRA3 WILD-TYPE                   105                             10
D2157V10, multiclass
                                clus
vv                               GLRA3 MUTATED GLRA3 WILD-TYPE
  COLON ADENOCARCINOMA                       8             307
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  GLRA3 MUTATED     7   1   1   1
  GLRA3 WILD-TYPE 338   3  30  24
D2157V11, multiclass
    clus
vv   GLRA3 MUTATED GLRA3 WILD-TYPE
  R0             7             338
  R1             1               3
  R2             1              30
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2157V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GLRA3 MUTATED                                  0     1
  GLRA3 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  GLRA3 MUTATED                           2     1
  GLRA3 WILD-TYPE                        20   225
D2157V13, multiclass
                                  clus
vv                                 GLRA3 MUTATED GLRA3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    2              20
  WHITE                                        1             225
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2158) Variable = FKBP5 MUTATION ANALYSIS
D2158V1, survival
                 sevent
clus2               0   1
  FKBP5 MUTATED     6   1
  FKBP5 WILD-TYPE 372  92
  FKBP5 MUTATED FKBP5 WILD-TYPE 
              7             464 
  FKBP5 MUTATED FKBP5 WILD-TYPE 
              1              92 
$`FKBP5 MUTATED`
TCGA-AA-3977 TCGA-AD-6889 TCGA-CA-6717 TCGA-CM-6171 TCGA-F4-6856 TCGA-G4-6303 
       25.02        56.55        12.76        14.04        35.31        65.85 
TCGA-AG-A002 
       20.98 

$`FKBP5 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       15.52         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.20        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       12.99        13.02        15.02        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6304 TCGA-G4-6306 
        0.53        47.41       133.18        74.56        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  FKBP5 MUTATED FKBP5 WILD-TYPE 
          12.76            0.00 
  FKBP5 MUTATED FKBP5 WILD-TYPE 
          65.85          148.01 
  FKBP5 MUTATED FKBP5 WILD-TYPE 
         25.020          20.085 
[1] "12.8 - 65.8 (25.0)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.8"
D2158V2, continuous
D2158V3, binary
                 cls
clus                0   1
  FKBP5 MUTATED     6   1
  FKBP5 WILD-TYPE 360 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FKBP5 MUTATED      6    1
  FKBP5 WILD-TYPE  360  118
        clus
vv       FKBP5 MUTATED FKBP5 WILD-TYPE
  COLON              6             360
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FKBP5 MUTATED         3        0        0         2         0         0
  FKBP5 WILD-TYPE      88        1       32       136        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  FKBP5 MUTATED           0          0          0          0        1         0
  FKBP5 WILD-TYPE        24         11         59         42       47        18
                 vv
clus              STAGE IVB
  FKBP5 MUTATED           0
  FKBP5 WILD-TYPE         1
D2158V4, multiclass
            clus
vv           FKBP5 MUTATED FKBP5 WILD-TYPE
  STAGE I                3              88
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              2             136
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             0              42
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  FKBP5 MUTATED     0   4   3   0
  FKBP5 WILD-TYPE  17  88 326  50
D2158V5, multiclass
    clus
vv   FKBP5 MUTATED FKBP5 WILD-TYPE
  T1             0              17
  T2             4              88
  T3             3             326
  T4             0              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  FKBP5 MUTATED     6   1   0
  FKBP5 WILD-TYPE 281 112  87
D2158V6, multiclass
    clus
vv   FKBP5 MUTATED FKBP5 WILD-TYPE
  N0             6             281
  N1             1             112
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2158V7, binary
                 cls
clus                0   1
  FKBP5 MUTATED     5   1
  FKBP5 WILD-TYPE 370  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FKBP5 MUTATED      5    1
  FKBP5 WILD-TYPE  370   64
   clus
vv  FKBP5 MUTATED FKBP5 WILD-TYPE
  0             5             370
  1             1              64
[1] 2 2
[1] FALSE
D2158V8, binary
                 cls
clus                0   1
  FKBP5 MUTATED     2   5
  FKBP5 WILD-TYPE 223 259
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FKBP5 MUTATED      2    5
  FKBP5 WILD-TYPE  223  259
        clus
vv       FKBP5 MUTATED FKBP5 WILD-TYPE
  FEMALE             2             223
  MALE               5             259
[1] 2 2
[1] FALSE
D2158V9, binary
                 cls
clus                0   1
  FKBP5 MUTATED     6   0
  FKBP5 WILD-TYPE 344  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FKBP5 MUTATED      6    0
  FKBP5 WILD-TYPE  344   22
     clus
vv    FKBP5 MUTATED FKBP5 WILD-TYPE
  NO              6             344
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  FKBP5 MUTATED                      4                             2
  FKBP5 WILD-TYPE                  311                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  FKBP5 MUTATED                       1                              0
  FKBP5 WILD-TYPE                   105                             10
D2158V10, multiclass
                                clus
vv                               FKBP5 MUTATED FKBP5 WILD-TYPE
  COLON ADENOCARCINOMA                       4             311
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  FKBP5 MUTATED     4   0   0   1
  FKBP5 WILD-TYPE 341   4  31  24
D2158V11, multiclass
    clus
vv   FKBP5 MUTATED FKBP5 WILD-TYPE
  R0             4             341
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2158V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FKBP5 MUTATED                                  0     2
  FKBP5 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  FKBP5 MUTATED                           0     3
  FKBP5 WILD-TYPE                        22   223
D2158V13, multiclass
                                  clus
vv                                 FKBP5 MUTATED FKBP5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               9
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        3             223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2159) Variable = C6ORF15 MUTATION ANALYSIS
D2159V1, survival
                   sevent
clus2                 0   1
  C6ORF15 MUTATED     5   1
  C6ORF15 WILD-TYPE 373  92
  C6ORF15 MUTATED C6ORF15 WILD-TYPE 
                6               465 
  C6ORF15 MUTATED C6ORF15 WILD-TYPE 
                1                92 
$`C6ORF15 MUTATED`
TCGA-AA-3833 TCGA-AA-3877 TCGA-AZ-4315 TCGA-CA-6718 TCGA-CM-5861 TCGA-CM-6171 
       15.95        31.00        58.39        10.06        15.02        14.04 

$`C6ORF15 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
        1.02        17.98        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 
       17.03        24.03        27.02        29.98        18.05         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       33.01        21.44        17.82         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       12.76        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 
       29.06        22.03        22.98        30.08        32.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       15.02        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  C6ORF15 MUTATED C6ORF15 WILD-TYPE 
            10.06              0.00 
  C6ORF15 MUTATED C6ORF15 WILD-TYPE 
            58.39            148.01 
  C6ORF15 MUTATED C6ORF15 WILD-TYPE 
           15.485            20.280 
[1] "10.1 - 58.4 (15.5)" "0.0 - 148.0 (20.3)"
[1] "hr=" "1.1"
D2159V2, continuous
D2159V3, binary
                   cls
clus                  0   1
  C6ORF15 MUTATED     6   0
  C6ORF15 WILD-TYPE 360 119
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C6ORF15 MUTATED      6    0
  C6ORF15 WILD-TYPE  360  119
        clus
vv       C6ORF15 MUTATED C6ORF15 WILD-TYPE
  COLON                6               360
  RECTUM               0               119
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  C6ORF15 MUTATED         2        0        0         4         0         0
  C6ORF15 WILD-TYPE      89        1       32       134        10         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C6ORF15 MUTATED           0          0          0          0        0
  C6ORF15 WILD-TYPE        24         11         59         42       48
                   vv
clus                STAGE IVA STAGE IVB
  C6ORF15 MUTATED           0         0
  C6ORF15 WILD-TYPE        18         1
D2159V4, multiclass
            clus
vv           C6ORF15 MUTATED C6ORF15 WILD-TYPE
  STAGE I                  2                89
  STAGE IA                 0                 1
  STAGE II                 0                32
  STAGE IIA                4               134
  STAGE IIB                0                10
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               0                11
  STAGE IIIB               0                59
  STAGE IIIC               0                42
  STAGE IV                 0                48
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  C6ORF15 MUTATED     1   1   4   0
  C6ORF15 WILD-TYPE  16  91 325  50
D2159V5, multiclass
    clus
vv   C6ORF15 MUTATED C6ORF15 WILD-TYPE
  T1               1                16
  T2               1                91
  T3               4               325
  T4               0                50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  C6ORF15 MUTATED     6   0   0
  C6ORF15 WILD-TYPE 281 113  87
D2159V6, multiclass
    clus
vv   C6ORF15 MUTATED C6ORF15 WILD-TYPE
  N0               6               281
  N1               0               113
  N2               0                87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2159V7, binary
                   cls
clus                  0   1
  C6ORF15 MUTATED     6   0
  C6ORF15 WILD-TYPE 369  65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C6ORF15 MUTATED      6    0
  C6ORF15 WILD-TYPE  369   65
   clus
vv  C6ORF15 MUTATED C6ORF15 WILD-TYPE
  0               6               369
  1               0                65
[1] 2 2
[1] FALSE
D2159V8, binary
                   cls
clus                  0   1
  C6ORF15 MUTATED     4   2
  C6ORF15 WILD-TYPE 221 262
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C6ORF15 MUTATED      4    2
  C6ORF15 WILD-TYPE  221  262
        clus
vv       C6ORF15 MUTATED C6ORF15 WILD-TYPE
  FEMALE               4               221
  MALE                 2               262
[1] 2 2
[1] FALSE
D2159V9, binary
                   cls
clus                  0   1
  C6ORF15 MUTATED     6   0
  C6ORF15 WILD-TYPE 344  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C6ORF15 MUTATED      6    0
  C6ORF15 WILD-TYPE  344   22
     clus
vv    C6ORF15 MUTATED C6ORF15 WILD-TYPE
  NO                6               344
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  C6ORF15 MUTATED                      5                             1
  C6ORF15 WILD-TYPE                  310                            46
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  C6ORF15 MUTATED                       0                              0
  C6ORF15 WILD-TYPE                   106                             10
D2159V10, multiclass
                                clus
vv                               C6ORF15 MUTATED C6ORF15 WILD-TYPE
  COLON ADENOCARCINOMA                         5               310
  COLON MUCINOUS ADENOCARCINOMA                1                46
  RECTAL ADENOCARCINOMA                        0               106
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  C6ORF15 MUTATED     5   0   0   1
  C6ORF15 WILD-TYPE 340   4  31  24
D2159V11, multiclass
    clus
vv   C6ORF15 MUTATED C6ORF15 WILD-TYPE
  R0               5               340
  R1               0                 4
  R2               0                31
  RX               1                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2159V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C6ORF15 MUTATED                                  0     1
  C6ORF15 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  C6ORF15 MUTATED                           0     3
  C6ORF15 WILD-TYPE                        22   223
D2159V13, multiclass
                                  clus
vv                                 C6ORF15 MUTATED C6ORF15 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                10
  BLACK OR AFRICAN AMERICAN                      0                22
  WHITE                                          3               223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2160) Variable = ZC3H12C MUTATION ANALYSIS
D2160V1, survival
                   sevent
clus2                 0   1
  ZC3H12C MUTATED    12   2
  ZC3H12C WILD-TYPE 366  91
  ZC3H12C MUTATED ZC3H12C WILD-TYPE 
               14               457 
  ZC3H12C MUTATED ZC3H12C WILD-TYPE 
                2                91 
$`ZC3H12C MUTATED`
TCGA-AA-3672 TCGA-AA-3679 TCGA-AA-3811 TCGA-AA-3966 TCGA-AA-3977 TCGA-AA-A00N 
        0.92        15.02        10.06         2.01        25.02         4.01 
TCGA-AA-A010 TCGA-AZ-4315 TCGA-CA-6717 TCGA-F4-6856 TCGA-G4-6586 TCGA-AG-A002 
       34.98        58.39        12.76        35.31        35.80        20.98 
TCGA-EI-6507 TCGA-F5-6813 
       19.96         0.69 

$`ZC3H12C WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
        6.05         6.97        54.02         2.01        14.01        50.04 
TCGA-AA-3678 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       47.01        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        19.04        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
       34.03        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        33.01        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.20        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
       13.25         0.53        47.41       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
       32.61         0.49        20.55        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-G5-6235 
       49.51        31.30        28.57        32.19         0.66        55.76 
TCGA-G5-6641 
       26.43 

  ZC3H12C MUTATED ZC3H12C WILD-TYPE 
             0.69              0.00 
  ZC3H12C MUTATED ZC3H12C WILD-TYPE 
            58.39            148.01 
  ZC3H12C MUTATED ZC3H12C WILD-TYPE 
            17.49             20.28 
[1] "0.7 - 58.4 (17.5)"  "0.0 - 148.0 (20.3)"
[1] "hr=" "1"  
D2160V2, continuous
D2160V3, binary
                   cls
clus                  0   1
  ZC3H12C MUTATED    12   3
  ZC3H12C WILD-TYPE 354 116
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZC3H12C MUTATED     12    3
  ZC3H12C WILD-TYPE  354  116
        clus
vv       ZC3H12C MUTATED ZC3H12C WILD-TYPE
  COLON               12               354
  RECTUM               3               116
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZC3H12C MUTATED         2        0        0         6         2         0
  ZC3H12C WILD-TYPE      89        1       32       132         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZC3H12C MUTATED           2          0          0          1        1
  ZC3H12C WILD-TYPE        22         11         59         41       47
                   vv
clus                STAGE IVA STAGE IVB
  ZC3H12C MUTATED           0         0
  ZC3H12C WILD-TYPE        18         1
D2160V4, multiclass
            clus
vv           ZC3H12C MUTATED ZC3H12C WILD-TYPE
  STAGE I                  2                89
  STAGE IA                 0                 1
  STAGE II                 0                32
  STAGE IIA                6               132
  STAGE IIB                2                 8
  STAGE IIC                0                 1
  STAGE III                2                22
  STAGE IIIA               0                11
  STAGE IIIB               0                59
  STAGE IIIC               1                41
  STAGE IV                 1                47
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  ZC3H12C MUTATED     0   3   9   3
  ZC3H12C WILD-TYPE  17  89 320  47
D2160V5, multiclass
    clus
vv   ZC3H12C MUTATED ZC3H12C WILD-TYPE
  T1               0                17
  T2               3                89
  T3               9               320
  T4               3                47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  ZC3H12C MUTATED    11   1   3
  ZC3H12C WILD-TYPE 276 112  84
D2160V6, multiclass
    clus
vv   ZC3H12C MUTATED ZC3H12C WILD-TYPE
  N0              11               276
  N1               1               112
  N2               3                84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2160V7, binary
                   cls
clus                  0   1
  ZC3H12C MUTATED    13   1
  ZC3H12C WILD-TYPE 362  64
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZC3H12C MUTATED     13    1
  ZC3H12C WILD-TYPE  362   64
   clus
vv  ZC3H12C MUTATED ZC3H12C WILD-TYPE
  0              13               362
  1               1                64
[1] 2 2
[1] FALSE
D2160V8, binary
                   cls
clus                  0   1
  ZC3H12C MUTATED     6   9
  ZC3H12C WILD-TYPE 219 255
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZC3H12C MUTATED      6    9
  ZC3H12C WILD-TYPE  219  255
        clus
vv       ZC3H12C MUTATED ZC3H12C WILD-TYPE
  FEMALE               6               219
  MALE                 9               255
[1] 2 2
[1] FALSE
D2160V9, binary
                   cls
clus                  0   1
  ZC3H12C MUTATED    11   0
  ZC3H12C WILD-TYPE 339  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZC3H12C MUTATED     11    0
  ZC3H12C WILD-TYPE  339   22
     clus
vv    ZC3H12C MUTATED ZC3H12C WILD-TYPE
  NO               11               339
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ZC3H12C MUTATED                      8                             4
  ZC3H12C WILD-TYPE                  307                            43
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ZC3H12C MUTATED                       3                              0
  ZC3H12C WILD-TYPE                   103                             10
D2160V10, multiclass
                                clus
vv                               ZC3H12C MUTATED ZC3H12C WILD-TYPE
  COLON ADENOCARCINOMA                         8               307
  COLON MUCINOUS ADENOCARCINOMA                4                43
  RECTAL ADENOCARCINOMA                        3               103
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  ZC3H12C MUTATED    11   0   1   1
  ZC3H12C WILD-TYPE 334   4  30  24
D2160V11, multiclass
    clus
vv   ZC3H12C MUTATED ZC3H12C WILD-TYPE
  R0              11               334
  R1               0                 4
  R2               1                30
  RX               1                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2160V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZC3H12C MUTATED                                  0     1
  ZC3H12C WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  ZC3H12C MUTATED                           0     5
  ZC3H12C WILD-TYPE                        22   221
D2160V13, multiclass
                                  clus
vv                                 ZC3H12C MUTATED ZC3H12C WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                10
  BLACK OR AFRICAN AMERICAN                      0                22
  WHITE                                          5               221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2161) Variable = IFI35 MUTATION ANALYSIS
D2161V1, survival
                 sevent
clus2               0   1
  IFI35 MUTATED     4   4
  IFI35 WILD-TYPE 374  89
  IFI35 MUTATED IFI35 WILD-TYPE 
              8             463 
  IFI35 MUTATED IFI35 WILD-TYPE 
              4              89 
$`IFI35 MUTATED`
TCGA-A6-2677 TCGA-AA-3715 TCGA-AA-A00N TCGA-CM-5861 TCGA-DM-A1D0 TCGA-DM-A1DB 
       24.33        19.04         4.01        15.02       130.65        44.32 
TCGA-G4-6317 TCGA-G4-6323 
       36.00        13.78 

$`IFI35 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        42.90        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 
       36.00         5.03        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
       38.20        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
        7.50       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6321 TCGA-G4-6586 
       55.04        85.48        63.62        61.91        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  IFI35 MUTATED IFI35 WILD-TYPE 
           4.01            0.00 
  IFI35 MUTATED IFI35 WILD-TYPE 
         130.65          148.01 
  IFI35 MUTATED IFI35 WILD-TYPE 
         21.685          20.190 
[1] "4.0 - 130.7 (21.7)" "0.0 - 148.0 (20.2)"
[1] "hr=" "2.1"
D2161V2, continuous
D2161V3, binary
                 cls
clus                0   1
  IFI35 MUTATED     8   0
  IFI35 WILD-TYPE 358 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IFI35 MUTATED      8    0
  IFI35 WILD-TYPE  358  119
        clus
vv       IFI35 MUTATED IFI35 WILD-TYPE
  COLON              8             358
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  IFI35 MUTATED         0        1        1         3         1         0
  IFI35 WILD-TYPE      91        0       31       135         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  IFI35 MUTATED           0          0          0          2        0         0
  IFI35 WILD-TYPE        24         11         59         40       48        18
                 vv
clus              STAGE IVB
  IFI35 MUTATED           0
  IFI35 WILD-TYPE         1
D2161V4, multiclass
            clus
vv           IFI35 MUTATED IFI35 WILD-TYPE
  STAGE I                0              91
  STAGE IA               1               0
  STAGE II               1              31
  STAGE IIA              3             135
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             2              40
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  IFI35 MUTATED     0   0   6   1
  IFI35 WILD-TYPE  17  92 323  49
D2161V5, multiclass
    clus
vv   IFI35 MUTATED IFI35 WILD-TYPE
  T1             0              17
  T2             0              92
  T3             6             323
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  IFI35 MUTATED     6   0   2
  IFI35 WILD-TYPE 281 113  85
D2161V6, multiclass
    clus
vv   IFI35 MUTATED IFI35 WILD-TYPE
  N0             6             281
  N1             0             113
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2161V7, binary
                 cls
clus                0   1
  IFI35 MUTATED     6   0
  IFI35 WILD-TYPE 369  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IFI35 MUTATED      6    0
  IFI35 WILD-TYPE  369   65
   clus
vv  IFI35 MUTATED IFI35 WILD-TYPE
  0             6             369
  1             0              65
[1] 2 2
[1] FALSE
D2161V8, binary
                 cls
clus                0   1
  IFI35 MUTATED     4   4
  IFI35 WILD-TYPE 221 260
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IFI35 MUTATED      4    4
  IFI35 WILD-TYPE  221  260
        clus
vv       IFI35 MUTATED IFI35 WILD-TYPE
  FEMALE             4             221
  MALE               4             260
[1] 2 2
[1] FALSE
D2161V9, binary
                 cls
clus                0   1
  IFI35 MUTATED     5   0
  IFI35 WILD-TYPE 345  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IFI35 MUTATED      5    0
  IFI35 WILD-TYPE  345   22
     clus
vv    IFI35 MUTATED IFI35 WILD-TYPE
  NO              5             345
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  IFI35 MUTATED                      7                             1
  IFI35 WILD-TYPE                  308                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  IFI35 MUTATED                       0                              0
  IFI35 WILD-TYPE                   106                             10
D2161V10, multiclass
                                clus
vv                               IFI35 MUTATED IFI35 WILD-TYPE
  COLON ADENOCARCINOMA                       7             308
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  IFI35 MUTATED     6   0   0   0
  IFI35 WILD-TYPE 339   4  31  25
D2161V11, multiclass
    clus
vv   IFI35 MUTATED IFI35 WILD-TYPE
  R0             6             339
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2161V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  IFI35 MUTATED                                  0     0
  IFI35 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  IFI35 MUTATED                           1     5
  IFI35 WILD-TYPE                        21   221
D2161V13, multiclass
                                  clus
vv                                 IFI35 MUTATED IFI35 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        5             221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2162) Variable = OR2F2 MUTATION ANALYSIS
D2162V1, survival
                 sevent
clus2               0   1
  OR2F2 MUTATED     5   3
  OR2F2 WILD-TYPE 373  90
  OR2F2 MUTATED OR2F2 WILD-TYPE 
              8             463 
  OR2F2 MUTATED OR2F2 WILD-TYPE 
              3              90 
$`OR2F2 MUTATED`
TCGA-AA-3877 TCGA-AA-3966 TCGA-AZ-6601 TCGA-CA-6717 TCGA-D5-6930 TCGA-DM-A1HA 
       31.00         2.01       100.01        12.76         1.51       131.51 
TCGA-F4-6809 TCGA-F5-6464 
       13.25         9.96 

$`OR2F2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
        2.01        20.98        34.03        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
       12.10        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
        7.50        44.32       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       41.42        16.24        33.67         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6465 
        0.49        20.55        19.96        20.91        18.28        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  OR2F2 MUTATED OR2F2 WILD-TYPE 
           1.51            0.00 
  OR2F2 MUTATED OR2F2 WILD-TYPE 
         131.51          148.01 
  OR2F2 MUTATED OR2F2 WILD-TYPE 
         13.005          20.280 
[1] "1.5 - 131.5 (13.0)" "0.0 - 148.0 (20.3)"
[1] "hr=" "1.5"
D2162V2, continuous
D2162V3, binary
                 cls
clus                0   1
  OR2F2 MUTATED     7   1
  OR2F2 WILD-TYPE 359 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR2F2 MUTATED      7    1
  OR2F2 WILD-TYPE  359  118
        clus
vv       OR2F2 MUTATED OR2F2 WILD-TYPE
  COLON              7             359
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  OR2F2 MUTATED         1        0        1         3         0         0
  OR2F2 WILD-TYPE      90        1       31       135        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  OR2F2 MUTATED           0          0          0          2        0         1
  OR2F2 WILD-TYPE        24         11         59         40       48        17
                 vv
clus              STAGE IVB
  OR2F2 MUTATED           0
  OR2F2 WILD-TYPE         1
D2162V4, multiclass
            clus
vv           OR2F2 MUTATED OR2F2 WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              3             135
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             2              40
  STAGE IV               0              48
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  OR2F2 MUTATED     1   0   6   1
  OR2F2 WILD-TYPE  16  92 323  49
D2162V5, multiclass
    clus
vv   OR2F2 MUTATED OR2F2 WILD-TYPE
  T1             1              16
  T2             0              92
  T3             6             323
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  OR2F2 MUTATED     5   1   2
  OR2F2 WILD-TYPE 282 112  85
D2162V6, multiclass
    clus
vv   OR2F2 MUTATED OR2F2 WILD-TYPE
  N0             5             282
  N1             1             112
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2162V7, binary
                 cls
clus                0   1
  OR2F2 MUTATED     7   1
  OR2F2 WILD-TYPE 368  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR2F2 MUTATED      7    1
  OR2F2 WILD-TYPE  368   64
   clus
vv  OR2F2 MUTATED OR2F2 WILD-TYPE
  0             7             368
  1             1              64
[1] 2 2
[1] FALSE
D2162V8, binary
                 cls
clus                0   1
  OR2F2 MUTATED     4   4
  OR2F2 WILD-TYPE 221 260
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR2F2 MUTATED      4    4
  OR2F2 WILD-TYPE  221  260
        clus
vv       OR2F2 MUTATED OR2F2 WILD-TYPE
  FEMALE             4             221
  MALE               4             260
[1] 2 2
[1] FALSE
D2162V9, binary
                 cls
clus                0   1
  OR2F2 MUTATED     5   0
  OR2F2 WILD-TYPE 345  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR2F2 MUTATED      5    0
  OR2F2 WILD-TYPE  345   22
     clus
vv    OR2F2 MUTATED OR2F2 WILD-TYPE
  NO              5             345
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  OR2F2 MUTATED                      3                             4
  OR2F2 WILD-TYPE                  312                            43
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  OR2F2 MUTATED                       1                              0
  OR2F2 WILD-TYPE                   105                             10
D2162V10, multiclass
                                clus
vv                               OR2F2 MUTATED OR2F2 WILD-TYPE
  COLON ADENOCARCINOMA                       3             312
  COLON MUCINOUS ADENOCARCINOMA              4              43
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  OR2F2 MUTATED     4   0   0   1
  OR2F2 WILD-TYPE 341   4  31  24
D2162V11, multiclass
    clus
vv   OR2F2 MUTATED OR2F2 WILD-TYPE
  R0             4             341
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2162V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OR2F2 MUTATED                                  0     1
  OR2F2 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  OR2F2 MUTATED                           0     5
  OR2F2 WILD-TYPE                        22   221
D2162V13, multiclass
                                  clus
vv                                 OR2F2 MUTATED OR2F2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        5             221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2163) Variable = SLC27A3 MUTATION ANALYSIS
D2163V1, survival
                   sevent
clus2                 0   1
  SLC27A3 MUTATED     6   1
  SLC27A3 WILD-TYPE 372  92
  SLC27A3 MUTATED SLC27A3 WILD-TYPE 
                7               464 
  SLC27A3 MUTATED SLC27A3 WILD-TYPE 
                1                92 
$`SLC27A3 MUTATED`
TCGA-A6-6780 TCGA-AA-3815 TCGA-AD-6889 TCGA-F4-6570 TCGA-G4-6588 TCGA-G4-6628 
       20.12        33.04        56.55         6.18        26.17        79.69 
TCGA-AG-A002 
       20.98 

$`SLC27A3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       10.06        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 
      117.07        98.24         8.61        31.96        35.74        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        35.80        91.79        46.75 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  SLC27A3 MUTATED SLC27A3 WILD-TYPE 
             6.18              0.00 
  SLC27A3 MUTATED SLC27A3 WILD-TYPE 
            79.69            148.01 
  SLC27A3 MUTATED SLC27A3 WILD-TYPE 
           26.170            20.035 
[1] "6.2 - 79.7 (26.2)"  "0.0 - 148.0 (20.0)"
[1] "hr=" "1.8"
D2163V2, continuous
D2163V3, binary
                   cls
clus                  0   1
  SLC27A3 MUTATED     6   1
  SLC27A3 WILD-TYPE 360 118
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC27A3 MUTATED      6    1
  SLC27A3 WILD-TYPE  360  118
        clus
vv       SLC27A3 MUTATED SLC27A3 WILD-TYPE
  COLON                6               360
  RECTUM               1               118
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SLC27A3 MUTATED         2        0        0         5         0         0
  SLC27A3 WILD-TYPE      89        1       32       133        10         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC27A3 MUTATED           0          0          0          0        0
  SLC27A3 WILD-TYPE        24         11         59         42       48
                   vv
clus                STAGE IVA STAGE IVB
  SLC27A3 MUTATED           0         0
  SLC27A3 WILD-TYPE        18         1
D2163V4, multiclass
            clus
vv           SLC27A3 MUTATED SLC27A3 WILD-TYPE
  STAGE I                  2                89
  STAGE IA                 0                 1
  STAGE II                 0                32
  STAGE IIA                5               133
  STAGE IIB                0                10
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               0                11
  STAGE IIIB               0                59
  STAGE IIIC               0                42
  STAGE IV                 0                48
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  SLC27A3 MUTATED     0   2   5   0
  SLC27A3 WILD-TYPE  17  90 324  50
D2163V5, multiclass
    clus
vv   SLC27A3 MUTATED SLC27A3 WILD-TYPE
  T1               0                17
  T2               2                90
  T3               5               324
  T4               0                50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  SLC27A3 MUTATED     7   0   0
  SLC27A3 WILD-TYPE 280 113  87
D2163V6, multiclass
    clus
vv   SLC27A3 MUTATED SLC27A3 WILD-TYPE
  N0               7               280
  N1               0               113
  N2               0                87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2163V7, binary
                   cls
clus                  0   1
  SLC27A3 MUTATED     6   0
  SLC27A3 WILD-TYPE 369  65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC27A3 MUTATED      6    0
  SLC27A3 WILD-TYPE  369   65
   clus
vv  SLC27A3 MUTATED SLC27A3 WILD-TYPE
  0               6               369
  1               0                65
[1] 2 2
[1] FALSE
D2163V8, binary
                   cls
clus                  0   1
  SLC27A3 MUTATED     3   4
  SLC27A3 WILD-TYPE 222 260
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC27A3 MUTATED      3    4
  SLC27A3 WILD-TYPE  222  260
        clus
vv       SLC27A3 MUTATED SLC27A3 WILD-TYPE
  FEMALE               3               222
  MALE                 4               260
[1] 2 2
[1] FALSE
D2163V9, binary
                   cls
clus                  0   1
  SLC27A3 MUTATED     6   0
  SLC27A3 WILD-TYPE 344  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC27A3 MUTATED      6    0
  SLC27A3 WILD-TYPE  344   22
     clus
vv    SLC27A3 MUTATED SLC27A3 WILD-TYPE
  NO                6               344
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SLC27A3 MUTATED                      5                             1
  SLC27A3 WILD-TYPE                  310                            46
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SLC27A3 MUTATED                       1                              0
  SLC27A3 WILD-TYPE                   105                             10
D2163V10, multiclass
                                clus
vv                               SLC27A3 MUTATED SLC27A3 WILD-TYPE
  COLON ADENOCARCINOMA                         5               310
  COLON MUCINOUS ADENOCARCINOMA                1                46
  RECTAL ADENOCARCINOMA                        1               105
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  SLC27A3 MUTATED     5   0   0   0
  SLC27A3 WILD-TYPE 340   4  31  25
D2163V11, multiclass
    clus
vv   SLC27A3 MUTATED SLC27A3 WILD-TYPE
  R0               5               340
  R1               0                 4
  R2               0                31
  RX               0                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2163V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SLC27A3 MUTATED                                  0     1
  SLC27A3 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  SLC27A3 MUTATED                           0     4
  SLC27A3 WILD-TYPE                        22   222
D2163V13, multiclass
                                  clus
vv                                 SLC27A3 MUTATED SLC27A3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                10
  BLACK OR AFRICAN AMERICAN                      0                22
  WHITE                                          4               222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2164) Variable = C6ORF70 MUTATION ANALYSIS
D2164V1, survival
                   sevent
clus2                 0   1
  C6ORF70 MUTATED    13   0
  C6ORF70 WILD-TYPE 365  93
  C6ORF70 MUTATED C6ORF70 WILD-TYPE 
               13               458 
  C6ORF70 MUTATED C6ORF70 WILD-TYPE 
                0                93 
$`C6ORF70 MUTATED`
TCGA-A6-5656 TCGA-A6-6141 TCGA-AA-3510 TCGA-AA-3555 TCGA-AA-3713 TCGA-AA-A010 
       32.91         8.38        63.98        29.95        19.04        34.98 
TCGA-AD-6889 TCGA-CM-5861 TCGA-D5-6540 TCGA-DM-A28E TCGA-G4-6586 TCGA-AG-A01W 
       56.55        15.02        16.14       119.93        35.80        70.03 
TCGA-CI-6620 
       33.17 

$`C6ORF70 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 
       22.06        32.71        27.09        22.52        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       17.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       26.99        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       21.37        15.52         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       30.08        32.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
        4.80        17.13        12.49        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
      139.17         6.12        81.37        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       12.00        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6622 TCGA-CI-6624 
       17.49         0.69         0.72         6.05         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  C6ORF70 MUTATED C6ORF70 WILD-TYPE 
             8.38              0.00 
  C6ORF70 MUTATED C6ORF70 WILD-TYPE 
           119.93            148.01 
  C6ORF70 MUTATED C6ORF70 WILD-TYPE 
           33.170            20.035 
[1] "8.4 - 119.9 (33.2)" "0.0 - 148.0 (20.0)"
[1] "hr="     "2.6e+07"
D2164V2, continuous
D2164V3, binary
                   cls
clus                  0   1
  C6ORF70 MUTATED    12   2
  C6ORF70 WILD-TYPE 354 117
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C6ORF70 MUTATED     12    2
  C6ORF70 WILD-TYPE  354  117
        clus
vv       C6ORF70 MUTATED C6ORF70 WILD-TYPE
  COLON               12               354
  RECTUM               2               117
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  C6ORF70 MUTATED         2        0        2         7         1         0
  C6ORF70 WILD-TYPE      89        1       30       131         9         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C6ORF70 MUTATED           0          0          0          0        1
  C6ORF70 WILD-TYPE        24         11         59         42       47
                   vv
clus                STAGE IVA STAGE IVB
  C6ORF70 MUTATED           1         0
  C6ORF70 WILD-TYPE        17         1
D2164V4, multiclass
            clus
vv           C6ORF70 MUTATED C6ORF70 WILD-TYPE
  STAGE I                  2                89
  STAGE IA                 0                 1
  STAGE II                 2                30
  STAGE IIA                7               131
  STAGE IIB                1                 9
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               0                11
  STAGE IIIB               0                59
  STAGE IIIC               0                42
  STAGE IV                 1                47
  STAGE IVA                1                17
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  C6ORF70 MUTATED     0   2  11   1
  C6ORF70 WILD-TYPE  17  90 318  49
D2164V5, multiclass
    clus
vv   C6ORF70 MUTATED C6ORF70 WILD-TYPE
  T1               0                17
  T2               2                90
  T3              11               318
  T4               1                49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  C6ORF70 MUTATED    13   1   0
  C6ORF70 WILD-TYPE 274 112  87
D2164V6, multiclass
    clus
vv   C6ORF70 MUTATED C6ORF70 WILD-TYPE
  N0              13               274
  N1               1               112
  N2               0                87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2164V7, binary
                   cls
clus                  0   1
  C6ORF70 MUTATED    12   2
  C6ORF70 WILD-TYPE 363  63
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C6ORF70 MUTATED     12    2
  C6ORF70 WILD-TYPE  363   63
   clus
vv  C6ORF70 MUTATED C6ORF70 WILD-TYPE
  0              12               363
  1               2                63
[1] 2 2
[1] FALSE
D2164V8, binary
                   cls
clus                  0   1
  C6ORF70 MUTATED     8   6
  C6ORF70 WILD-TYPE 217 258
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C6ORF70 MUTATED      8    6
  C6ORF70 WILD-TYPE  217  258
        clus
vv       C6ORF70 MUTATED C6ORF70 WILD-TYPE
  FEMALE               8               217
  MALE                 6               258
[1] 2 2
[1] FALSE
D2164V9, binary
                   cls
clus                  0   1
  C6ORF70 MUTATED     9   1
  C6ORF70 WILD-TYPE 341  21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C6ORF70 MUTATED      9    1
  C6ORF70 WILD-TYPE  341   21
     clus
vv    C6ORF70 MUTATED C6ORF70 WILD-TYPE
  NO                9               341
  YES               1                21
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  C6ORF70 MUTATED                     10                             2
  C6ORF70 WILD-TYPE                  305                            45
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  C6ORF70 MUTATED                       2                              0
  C6ORF70 WILD-TYPE                   104                             10
D2164V10, multiclass
                                clus
vv                               C6ORF70 MUTATED C6ORF70 WILD-TYPE
  COLON ADENOCARCINOMA                        10               305
  COLON MUCINOUS ADENOCARCINOMA                2                45
  RECTAL ADENOCARCINOMA                        2               104
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  C6ORF70 MUTATED     8   0   1   0
  C6ORF70 WILD-TYPE 337   4  30  25
D2164V11, multiclass
    clus
vv   C6ORF70 MUTATED C6ORF70 WILD-TYPE
  R0               8               337
  R1               0                 4
  R2               1                30
  RX               0                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2164V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C6ORF70 MUTATED                                  0     1
  C6ORF70 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  C6ORF70 MUTATED                           1     6
  C6ORF70 WILD-TYPE                        21   220
D2164V13, multiclass
                                  clus
vv                                 C6ORF70 MUTATED C6ORF70 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                10
  BLACK OR AFRICAN AMERICAN                      1                21
  WHITE                                          6               220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2165) Variable = SFI1 MUTATION ANALYSIS
D2165V1, survival
                sevent
clus2              0   1
  SFI1 MUTATED     8   4
  SFI1 WILD-TYPE 370  89
  SFI1 MUTATED SFI1 WILD-TYPE 
            12            459 
  SFI1 MUTATED SFI1 WILD-TYPE 
             4             89 
$`SFI1 MUTATED`
TCGA-AA-3715 TCGA-AA-3949 TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A010 TCGA-AD-6889 
       19.04        26.01        25.02         4.01        34.98        56.55 
TCGA-AD-6895 TCGA-AU-6004 TCGA-AZ-6601 TCGA-CA-6718 TCGA-AG-3892 TCGA-AG-A002 
        0.72        27.09       100.01        10.06        13.02        20.98 

$`SFI1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-3952 
        2.01        12.99        24.00        33.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
        0.07        21.37        15.52         0.79         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 
       27.42        10.88         0.20        14.50        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
       12.10        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       12.76        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 
        1.02        17.95        36.95        17.03        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  SFI1 MUTATED SFI1 WILD-TYPE 
          0.72           0.00 
  SFI1 MUTATED SFI1 WILD-TYPE 
        100.01         148.01 
  SFI1 MUTATED SFI1 WILD-TYPE 
         23.00          20.12 
[1] "0.7 - 100.0 (23.0)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.6"
D2165V2, continuous
D2165V3, binary
                cls
clus               0   1
  SFI1 MUTATED    10   2
  SFI1 WILD-TYPE 356 117
[1] "tbl2"
                cls
clus             [,1] [,2]
  SFI1 MUTATED     10    2
  SFI1 WILD-TYPE  356  117
        clus
vv       SFI1 MUTATED SFI1 WILD-TYPE
  COLON            10            356
  RECTUM            2            117
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SFI1 MUTATED         3        0        2         2         2         0
  SFI1 WILD-TYPE      88        1       30       136         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SFI1 MUTATED           0          0          1          0        0         0
  SFI1 WILD-TYPE        24         11         58         42       48        18
                vv
clus             STAGE IVB
  SFI1 MUTATED           0
  SFI1 WILD-TYPE         1
D2165V4, multiclass
            clus
vv           SFI1 MUTATED SFI1 WILD-TYPE
  STAGE I               3             88
  STAGE IA              0              1
  STAGE II              2             30
  STAGE IIA             2            136
  STAGE IIB             2              8
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            1             58
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  SFI1 MUTATED     1   3   6   2
  SFI1 WILD-TYPE  16  89 323  48
D2165V5, multiclass
    clus
vv   SFI1 MUTATED SFI1 WILD-TYPE
  T1            1             16
  T2            3             89
  T3            6            323
  T4            2             48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  SFI1 MUTATED    10   2   0
  SFI1 WILD-TYPE 277 111  87
D2165V6, multiclass
    clus
vv   SFI1 MUTATED SFI1 WILD-TYPE
  N0           10            277
  N1            2            111
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2165V7, binary
                cls
clus               0   1
  SFI1 MUTATED    10   0
  SFI1 WILD-TYPE 365  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  SFI1 MUTATED     10    0
  SFI1 WILD-TYPE  365   65
   clus
vv  SFI1 MUTATED SFI1 WILD-TYPE
  0           10            365
  1            0             65
[1] 2 2
[1] FALSE
D2165V8, binary
                cls
clus               0   1
  SFI1 MUTATED     4   8
  SFI1 WILD-TYPE 221 256
[1] "tbl2"
                cls
clus             [,1] [,2]
  SFI1 MUTATED      4    8
  SFI1 WILD-TYPE  221  256
        clus
vv       SFI1 MUTATED SFI1 WILD-TYPE
  FEMALE            4            221
  MALE              8            256
[1] 2 2
[1] FALSE
D2165V9, binary
                cls
clus               0   1
  SFI1 MUTATED     8   0
  SFI1 WILD-TYPE 342  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  SFI1 MUTATED      8    0
  SFI1 WILD-TYPE  342   22
     clus
vv    SFI1 MUTATED SFI1 WILD-TYPE
  NO             8            342
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SFI1 MUTATED                      8                             2
  SFI1 WILD-TYPE                  307                            45
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SFI1 MUTATED                       2                              0
  SFI1 WILD-TYPE                   104                             10
D2165V10, multiclass
                                clus
vv                               SFI1 MUTATED SFI1 WILD-TYPE
  COLON ADENOCARCINOMA                      8            307
  COLON MUCINOUS ADENOCARCINOMA             2             45
  RECTAL ADENOCARCINOMA                     2            104
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  SFI1 MUTATED     7   0   0   1
  SFI1 WILD-TYPE 338   4  31  24
D2165V11, multiclass
    clus
vv   SFI1 MUTATED SFI1 WILD-TYPE
  R0            7            338
  R1            0              4
  R2            0             31
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2165V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SFI1 MUTATED                                  0     2
  SFI1 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  SFI1 MUTATED                           0     3
  SFI1 WILD-TYPE                        22   223
D2165V13, multiclass
                                  clus
vv                                 SFI1 MUTATED SFI1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              9
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       3            223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2166) Variable = ELANE MUTATION ANALYSIS
D2166V1, survival
                 sevent
clus2               0   1
  ELANE MUTATED     6   1
  ELANE WILD-TYPE 372  92
  ELANE MUTATED ELANE WILD-TYPE 
              7             464 
  ELANE MUTATED ELANE WILD-TYPE 
              1              92 
$`ELANE MUTATED`
TCGA-A6-6654 TCGA-AA-3663 TCGA-AA-A010 TCGA-AZ-4315 TCGA-CK-5916 TCGA-CM-5861 
       23.87         6.97        34.98        58.39        21.14        15.02 
TCGA-G4-6304 
       53.62 

$`ELANE WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       49.08        51.32         9.99        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 
       22.03        22.98        30.08        32.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 
       35.31       133.18        74.56        65.85        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  ELANE MUTATED ELANE WILD-TYPE 
           6.97            0.00 
  ELANE MUTATED ELANE WILD-TYPE 
          58.39          148.01 
  ELANE MUTATED ELANE WILD-TYPE 
         23.870          20.085 
[1] "7.0 - 58.4 (23.9)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.7"
D2166V2, continuous
D2166V3, binary
                 cls
clus                0   1
  ELANE MUTATED     7   0
  ELANE WILD-TYPE 359 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ELANE MUTATED      7    0
  ELANE WILD-TYPE  359  119
        clus
vv       ELANE MUTATED ELANE WILD-TYPE
  COLON              7             359
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ELANE MUTATED         1        0        1         2         2         0
  ELANE WILD-TYPE      90        1       31       136         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ELANE MUTATED           0          0          1          0        0         0
  ELANE WILD-TYPE        24         11         58         42       48        18
                 vv
clus              STAGE IVB
  ELANE MUTATED           0
  ELANE WILD-TYPE         1
D2166V4, multiclass
            clus
vv           ELANE MUTATED ELANE WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              2             136
  STAGE IIB              2               8
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ELANE MUTATED     1   0   4   2
  ELANE WILD-TYPE  16  92 325  48
D2166V5, multiclass
    clus
vv   ELANE MUTATED ELANE WILD-TYPE
  T1             1              16
  T2             0              92
  T3             4             325
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  ELANE MUTATED     6   1   0
  ELANE WILD-TYPE 281 112  87
D2166V6, multiclass
    clus
vv   ELANE MUTATED ELANE WILD-TYPE
  N0             6             281
  N1             1             112
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2166V7, binary
                 cls
clus                0   1
  ELANE MUTATED     7   0
  ELANE WILD-TYPE 368  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ELANE MUTATED      7    0
  ELANE WILD-TYPE  368   65
   clus
vv  ELANE MUTATED ELANE WILD-TYPE
  0             7             368
  1             0              65
[1] 2 2
[1] FALSE
D2166V8, binary
                 cls
clus                0   1
  ELANE MUTATED     5   2
  ELANE WILD-TYPE 220 262
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ELANE MUTATED      5    2
  ELANE WILD-TYPE  220  262
        clus
vv       ELANE MUTATED ELANE WILD-TYPE
  FEMALE             5             220
  MALE               2             262
[1] 2 2
[1] FALSE
D2166V9, binary
                 cls
clus                0   1
  ELANE MUTATED     7   0
  ELANE WILD-TYPE 343  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ELANE MUTATED      7    0
  ELANE WILD-TYPE  343   22
     clus
vv    ELANE MUTATED ELANE WILD-TYPE
  NO              7             343
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ELANE MUTATED                      7                             0
  ELANE WILD-TYPE                  308                            47
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ELANE MUTATED                       0                              0
  ELANE WILD-TYPE                   106                             10
D2166V10, multiclass
                                clus
vv                               ELANE MUTATED ELANE WILD-TYPE
  COLON ADENOCARCINOMA                       7             308
  COLON MUCINOUS ADENOCARCINOMA              0              47
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  ELANE MUTATED     5   0   0   1
  ELANE WILD-TYPE 340   4  31  24
D2166V11, multiclass
    clus
vv   ELANE MUTATED ELANE WILD-TYPE
  R0             5             340
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2166V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ELANE MUTATED                                  0     0
  ELANE WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ELANE MUTATED                           0     5
  ELANE WILD-TYPE                        22   221
D2166V13, multiclass
                                  clus
vv                                 ELANE MUTATED ELANE WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        5             221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2167) Variable = QSER1 MUTATION ANALYSIS
D2167V1, survival
                 sevent
clus2               0   1
  QSER1 MUTATED    14   1
  QSER1 WILD-TYPE 364  92
  QSER1 MUTATED QSER1 WILD-TYPE 
             15             456 
  QSER1 MUTATED QSER1 WILD-TYPE 
              1              92 
$`QSER1 MUTATED`
TCGA-AA-3510 TCGA-AA-3672 TCGA-AA-3710 TCGA-AD-6895 TCGA-AU-6004 TCGA-AZ-4315 
       63.98         0.92        26.99         0.72        27.09        58.39 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-4747 TCGA-CM-6678 TCGA-D5-6532 TCGA-D5-6927 
       12.76        10.06        25.02        11.01        18.25         9.44 
TCGA-G4-6307 TCGA-AG-A002 TCGA-CI-6624 
       55.04        20.98         4.73 

$`QSER1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 
        6.97        54.02         2.01        14.01        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.79         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       14.50        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        3.29         0.07        12.20        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       13.05        11.08        11.08        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6533 
       12.26        19.59        56.09        55.92        20.19         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
       14.30         9.04        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CL-5917 TCGA-CL-5918 
        0.72         6.05        33.17         6.97        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  QSER1 MUTATED QSER1 WILD-TYPE 
           0.72            0.00 
  QSER1 MUTATED QSER1 WILD-TYPE 
          63.98          148.01 
  QSER1 MUTATED QSER1 WILD-TYPE 
         18.250          20.235 
[1] "0.7 - 64.0 (18.2)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "2.8"
D2167V2, continuous
D2167V3, binary
                 cls
clus                0   1
  QSER1 MUTATED    15   2
  QSER1 WILD-TYPE 351 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  QSER1 MUTATED     15    2
  QSER1 WILD-TYPE  351  117
        clus
vv       QSER1 MUTATED QSER1 WILD-TYPE
  COLON             15             351
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  QSER1 MUTATED         3        0        1         7         1         0
  QSER1 WILD-TYPE      88        1       31       131         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  QSER1 MUTATED           1          0          1          0        0         2
  QSER1 WILD-TYPE        23         11         58         42       48        16
                 vv
clus              STAGE IVB
  QSER1 MUTATED           0
  QSER1 WILD-TYPE         1
D2167V4, multiclass
            clus
vv           QSER1 MUTATED QSER1 WILD-TYPE
  STAGE I                3              88
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              7             131
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              2              16
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  QSER1 MUTATED     0   3  11   3
  QSER1 WILD-TYPE  17  89 318  47
D2167V5, multiclass
    clus
vv   QSER1 MUTATED QSER1 WILD-TYPE
  T1             0              17
  T2             3              89
  T3            11             318
  T4             3              47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  QSER1 MUTATED    12   5   0
  QSER1 WILD-TYPE 275 108  87
D2167V6, multiclass
    clus
vv   QSER1 MUTATED QSER1 WILD-TYPE
  N0            12             275
  N1             5             108
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2167V7, binary
                 cls
clus                0   1
  QSER1 MUTATED    13   2
  QSER1 WILD-TYPE 362  63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  QSER1 MUTATED     13    2
  QSER1 WILD-TYPE  362   63
   clus
vv  QSER1 MUTATED QSER1 WILD-TYPE
  0            13             362
  1             2              63
[1] 2 2
[1] FALSE
D2167V8, binary
                 cls
clus                0   1
  QSER1 MUTATED     8   9
  QSER1 WILD-TYPE 217 255
[1] "tbl2"
                 cls
clus              [,1] [,2]
  QSER1 MUTATED      8    9
  QSER1 WILD-TYPE  217  255
        clus
vv       QSER1 MUTATED QSER1 WILD-TYPE
  FEMALE             8             217
  MALE               9             255
[1] 2 2
[1] FALSE
D2167V9, binary
                 cls
clus                0   1
  QSER1 MUTATED    12   0
  QSER1 WILD-TYPE 338  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  QSER1 MUTATED     12    0
  QSER1 WILD-TYPE  338   22
     clus
vv    QSER1 MUTATED QSER1 WILD-TYPE
  NO             12             338
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  QSER1 MUTATED                     14                             1
  QSER1 WILD-TYPE                  301                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  QSER1 MUTATED                       2                              0
  QSER1 WILD-TYPE                   104                             10
D2167V10, multiclass
                                clus
vv                               QSER1 MUTATED QSER1 WILD-TYPE
  COLON ADENOCARCINOMA                      14             301
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  QSER1 MUTATED    12   0   0   3
  QSER1 WILD-TYPE 333   4  31  22
D2167V11, multiclass
    clus
vv   QSER1 MUTATED QSER1 WILD-TYPE
  R0            12             333
  R1             0               4
  R2             0              31
  RX             3              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2167V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  QSER1 MUTATED                                  0     2
  QSER1 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  QSER1 MUTATED                           0    10
  QSER1 WILD-TYPE                        22   216
D2167V13, multiclass
                                  clus
vv                                 QSER1 MUTATED QSER1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               9
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                       10             216
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2168) Variable = DAGLB MUTATION ANALYSIS
D2168V1, survival
                 sevent
clus2               0   1
  DAGLB MUTATED     4   2
  DAGLB WILD-TYPE 374  91
  DAGLB MUTATED DAGLB WILD-TYPE 
              6             465 
  DAGLB MUTATED DAGLB WILD-TYPE 
              2              91 
$`DAGLB MUTATED`
TCGA-AA-3947 TCGA-AA-A00D TCGA-AD-6899 TCGA-AZ-6601 TCGA-CK-6747 TCGA-AG-A002 
       33.01        19.00         5.79       100.01        82.95        20.98 

$`DAGLB WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 
       31.00         2.01        12.99        24.00        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       38.04        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
       56.55         0.79         0.72        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6748 TCGA-CK-6751 
       49.08        51.32         9.99        21.14         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  DAGLB MUTATED DAGLB WILD-TYPE 
           5.79            0.00 
  DAGLB MUTATED DAGLB WILD-TYPE 
         100.01          148.01 
  DAGLB MUTATED DAGLB WILD-TYPE 
         26.995          20.120 
[1] "5.8 - 100.0 (27.0)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1"  
D2168V2, continuous
D2168V3, binary
                 cls
clus                0   1
  DAGLB MUTATED     5   1
  DAGLB WILD-TYPE 361 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DAGLB MUTATED      5    1
  DAGLB WILD-TYPE  361  118
        clus
vv       DAGLB MUTATED DAGLB WILD-TYPE
  COLON              5             361
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  DAGLB MUTATED         2        0        1         1         1         0
  DAGLB WILD-TYPE      89        1       31       137         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  DAGLB MUTATED           0          0          0          1        0         0
  DAGLB WILD-TYPE        24         11         59         41       48        18
                 vv
clus              STAGE IVB
  DAGLB MUTATED           0
  DAGLB WILD-TYPE         1
D2168V4, multiclass
            clus
vv           DAGLB MUTATED DAGLB WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              1             137
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             1              41
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  DAGLB MUTATED     0   2   2   2
  DAGLB WILD-TYPE  17  90 327  48
D2168V5, multiclass
    clus
vv   DAGLB MUTATED DAGLB WILD-TYPE
  T1             0              17
  T2             2              90
  T3             2             327
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  DAGLB MUTATED     5   0   1
  DAGLB WILD-TYPE 282 113  86
D2168V6, multiclass
    clus
vv   DAGLB MUTATED DAGLB WILD-TYPE
  N0             5             282
  N1             0             113
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2168V7, binary
                 cls
clus                0   1
  DAGLB MUTATED     4   0
  DAGLB WILD-TYPE 371  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DAGLB MUTATED      4    0
  DAGLB WILD-TYPE  371   65
   clus
vv  DAGLB MUTATED DAGLB WILD-TYPE
  0             4             371
  1             0              65
[1] 2 2
[1] FALSE
D2168V8, binary
                 cls
clus                0   1
  DAGLB MUTATED     2   4
  DAGLB WILD-TYPE 223 260
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DAGLB MUTATED      2    4
  DAGLB WILD-TYPE  223  260
        clus
vv       DAGLB MUTATED DAGLB WILD-TYPE
  FEMALE             2             223
  MALE               4             260
[1] 2 2
[1] FALSE
D2168V9, binary
                 cls
clus                0   1
  DAGLB MUTATED     6   0
  DAGLB WILD-TYPE 344  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DAGLB MUTATED      6    0
  DAGLB WILD-TYPE  344   22
     clus
vv    DAGLB MUTATED DAGLB WILD-TYPE
  NO              6             344
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  DAGLB MUTATED                      3                             2
  DAGLB WILD-TYPE                  312                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  DAGLB MUTATED                       1                              0
  DAGLB WILD-TYPE                   105                             10
D2168V10, multiclass
                                clus
vv                               DAGLB MUTATED DAGLB WILD-TYPE
  COLON ADENOCARCINOMA                       3             312
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  DAGLB MUTATED     3   0   0   1
  DAGLB WILD-TYPE 342   4  31  24
D2168V11, multiclass
    clus
vv   DAGLB MUTATED DAGLB WILD-TYPE
  R0             3             342
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2168V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DAGLB MUTATED                                  0     0
  DAGLB WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  DAGLB MUTATED                           0     3
  DAGLB WILD-TYPE                        22   223
D2168V13, multiclass
                                  clus
vv                                 DAGLB MUTATED DAGLB WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        3             223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2169) Variable = CXCL9 MUTATION ANALYSIS
D2169V1, survival
                 sevent
clus2               0   1
  CXCL9 MUTATED     5   1
  CXCL9 WILD-TYPE 373  92
  CXCL9 MUTATED CXCL9 WILD-TYPE 
              6             465 
  CXCL9 MUTATED CXCL9 WILD-TYPE 
              1              92 
$`CXCL9 MUTATED`
TCGA-AA-3555 TCGA-AY-6197 TCGA-CM-6674 TCGA-D5-6927 TCGA-DM-A1D4 TCGA-AG-A002 
       29.95        21.44        12.95         9.44        92.75        20.98 

$`CXCL9 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 
       21.01        13.02        24.00        17.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        33.01        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6929 
        4.41        12.43        14.30         9.04        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
       38.20       130.65        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  CXCL9 MUTATED CXCL9 WILD-TYPE 
           9.44            0.00 
  CXCL9 MUTATED CXCL9 WILD-TYPE 
          92.75          148.01 
  CXCL9 MUTATED CXCL9 WILD-TYPE 
          21.21           20.12 
[1] "9.4 - 92.8 (21.2)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.4"
D2169V2, continuous
D2169V3, binary
                 cls
clus                0   1
  CXCL9 MUTATED     6   1
  CXCL9 WILD-TYPE 360 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CXCL9 MUTATED      6    1
  CXCL9 WILD-TYPE  360  118
        clus
vv       CXCL9 MUTATED CXCL9 WILD-TYPE
  COLON              6             360
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CXCL9 MUTATED         1        0        0         6         0         0
  CXCL9 WILD-TYPE      90        1       32       132        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CXCL9 MUTATED           0          0          0          0        0         0
  CXCL9 WILD-TYPE        24         11         59         42       48        18
                 vv
clus              STAGE IVB
  CXCL9 MUTATED           0
  CXCL9 WILD-TYPE         1
D2169V4, multiclass
            clus
vv           CXCL9 MUTATED CXCL9 WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              6             132
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CXCL9 MUTATED     0   1   6   0
  CXCL9 WILD-TYPE  17  91 323  50
D2169V5, multiclass
    clus
vv   CXCL9 MUTATED CXCL9 WILD-TYPE
  T1             0              17
  T2             1              91
  T3             6             323
  T4             0              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  CXCL9 MUTATED     7   0   0
  CXCL9 WILD-TYPE 280 113  87
D2169V6, multiclass
    clus
vv   CXCL9 MUTATED CXCL9 WILD-TYPE
  N0             7             280
  N1             0             113
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2169V7, binary
                 cls
clus                0   1
  CXCL9 MUTATED     6   0
  CXCL9 WILD-TYPE 369  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CXCL9 MUTATED      6    0
  CXCL9 WILD-TYPE  369   65
   clus
vv  CXCL9 MUTATED CXCL9 WILD-TYPE
  0             6             369
  1             0              65
[1] 2 2
[1] FALSE
D2169V8, binary
                 cls
clus                0   1
  CXCL9 MUTATED     2   5
  CXCL9 WILD-TYPE 223 259
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CXCL9 MUTATED      2    5
  CXCL9 WILD-TYPE  223  259
        clus
vv       CXCL9 MUTATED CXCL9 WILD-TYPE
  FEMALE             2             223
  MALE               5             259
[1] 2 2
[1] FALSE
D2169V9, binary
                 cls
clus                0   1
  CXCL9 MUTATED     5   0
  CXCL9 WILD-TYPE 345  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CXCL9 MUTATED      5    0
  CXCL9 WILD-TYPE  345   22
     clus
vv    CXCL9 MUTATED CXCL9 WILD-TYPE
  NO              5             345
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CXCL9 MUTATED                      5                             1
  CXCL9 WILD-TYPE                  310                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CXCL9 MUTATED                       1                              0
  CXCL9 WILD-TYPE                   105                             10
D2169V10, multiclass
                                clus
vv                               CXCL9 MUTATED CXCL9 WILD-TYPE
  COLON ADENOCARCINOMA                       5             310
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  CXCL9 MUTATED     6   0   0   0
  CXCL9 WILD-TYPE 339   4  31  25
D2169V11, multiclass
    clus
vv   CXCL9 MUTATED CXCL9 WILD-TYPE
  R0             6             339
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2169V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CXCL9 MUTATED                                  0     0
  CXCL9 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CXCL9 MUTATED                           0     4
  CXCL9 WILD-TYPE                        22   222
D2169V13, multiclass
                                  clus
vv                                 CXCL9 MUTATED CXCL9 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        4             222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2170) Variable = CCDC111 MUTATION ANALYSIS
D2170V1, survival
                   sevent
clus2                 0   1
  CCDC111 MUTATED     7   2
  CCDC111 WILD-TYPE 371  91
  CCDC111 MUTATED CCDC111 WILD-TYPE 
                9               462 
  CCDC111 MUTATED CCDC111 WILD-TYPE 
                2                91 
$`CCDC111 MUTATED`
TCGA-AA-3660 TCGA-AA-A010 TCGA-AD-6889 TCGA-AD-6899 TCGA-AZ-4315 TCGA-CM-6168 
       78.08        34.98        56.55         5.79        58.39        12.99 
TCGA-DM-A0XD TCGA-AG-3593 TCGA-AG-A002 
       24.43        34.03        20.98 

$`CCDC111 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 
       20.98        19.99        13.94        19.99        61.02         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.79         0.72        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       17.82         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6169 TCGA-CM-6170 
       29.03        16.04        21.99        14.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       11.38        10.26       119.70        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
       24.00         1.02        46.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  CCDC111 MUTATED CCDC111 WILD-TYPE 
             5.79              0.00 
  CCDC111 MUTATED CCDC111 WILD-TYPE 
            78.08            148.01 
  CCDC111 MUTATED CCDC111 WILD-TYPE 
           34.030            20.035 
[1] "5.8 - 78.1 (34.0)"  "0.0 - 148.0 (20.0)"
[1] "hr=" "1.2"
D2170V2, continuous
D2170V3, binary
                   cls
clus                  0   1
  CCDC111 MUTATED     7   2
  CCDC111 WILD-TYPE 359 117
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC111 MUTATED      7    2
  CCDC111 WILD-TYPE  359  117
        clus
vv       CCDC111 MUTATED CCDC111 WILD-TYPE
  COLON                7               359
  RECTUM               2               117
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CCDC111 MUTATED         1        0        1         5         1         0
  CCDC111 WILD-TYPE      90        1       31       133         9         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CCDC111 MUTATED           0          0          0          1        0
  CCDC111 WILD-TYPE        24         11         59         41       48
                   vv
clus                STAGE IVA STAGE IVB
  CCDC111 MUTATED           0         0
  CCDC111 WILD-TYPE        18         1
D2170V4, multiclass
            clus
vv           CCDC111 MUTATED CCDC111 WILD-TYPE
  STAGE I                  1                90
  STAGE IA                 0                 1
  STAGE II                 1                31
  STAGE IIA                5               133
  STAGE IIB                1                 9
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               0                11
  STAGE IIIB               0                59
  STAGE IIIC               1                41
  STAGE IV                 0                48
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  CCDC111 MUTATED     0   1   6   2
  CCDC111 WILD-TYPE  17  91 323  48
D2170V5, multiclass
    clus
vv   CCDC111 MUTATED CCDC111 WILD-TYPE
  T1               0                17
  T2               1                91
  T3               6               323
  T4               2                48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  CCDC111 MUTATED     8   0   1
  CCDC111 WILD-TYPE 279 113  86
D2170V6, multiclass
    clus
vv   CCDC111 MUTATED CCDC111 WILD-TYPE
  N0               8               279
  N1               0               113
  N2               1                86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2170V7, binary
                   cls
clus                  0   1
  CCDC111 MUTATED     8   0
  CCDC111 WILD-TYPE 367  65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC111 MUTATED      8    0
  CCDC111 WILD-TYPE  367   65
   clus
vv  CCDC111 MUTATED CCDC111 WILD-TYPE
  0               8               367
  1               0                65
[1] 2 2
[1] FALSE
D2170V8, binary
                   cls
clus                  0   1
  CCDC111 MUTATED     4   5
  CCDC111 WILD-TYPE 221 259
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC111 MUTATED      4    5
  CCDC111 WILD-TYPE  221  259
        clus
vv       CCDC111 MUTATED CCDC111 WILD-TYPE
  FEMALE               4               221
  MALE                 5               259
[1] 2 2
[1] FALSE
D2170V9, binary
                   cls
clus                  0   1
  CCDC111 MUTATED     6   1
  CCDC111 WILD-TYPE 344  21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC111 MUTATED      6    1
  CCDC111 WILD-TYPE  344   21
     clus
vv    CCDC111 MUTATED CCDC111 WILD-TYPE
  NO                6               344
  YES               1                21
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CCDC111 MUTATED                      6                             1
  CCDC111 WILD-TYPE                  309                            46
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CCDC111 MUTATED                       2                              0
  CCDC111 WILD-TYPE                   104                             10
D2170V10, multiclass
                                clus
vv                               CCDC111 MUTATED CCDC111 WILD-TYPE
  COLON ADENOCARCINOMA                         6               309
  COLON MUCINOUS ADENOCARCINOMA                1                46
  RECTAL ADENOCARCINOMA                        2               104
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  CCDC111 MUTATED     6   0   0   0
  CCDC111 WILD-TYPE 339   4  31  25
D2170V11, multiclass
    clus
vv   CCDC111 MUTATED CCDC111 WILD-TYPE
  R0               6               339
  R1               0                 4
  R2               0                31
  RX               0                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2170V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CCDC111 MUTATED                                  0     1
  CCDC111 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  CCDC111 MUTATED                           1     3
  CCDC111 WILD-TYPE                        21   223
D2170V13, multiclass
                                  clus
vv                                 CCDC111 MUTATED CCDC111 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                10
  BLACK OR AFRICAN AMERICAN                      1                21
  WHITE                                          3               223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2171) Variable = FER1L6 MUTATION ANALYSIS
D2171V1, survival
                  sevent
clus2                0   1
  FER1L6 MUTATED    26   5
  FER1L6 WILD-TYPE 352  88
  FER1L6 MUTATED FER1L6 WILD-TYPE 
              31              440 
  FER1L6 MUTATED FER1L6 WILD-TYPE 
               5               88 
$`FER1L6 MUTATED`
TCGA-A6-5657 TCGA-A6-5662 TCGA-A6-6141 TCGA-A6-6781 TCGA-AA-3492 TCGA-AA-3526 
       31.63        23.61         8.38        19.66         3.02        19.07 
TCGA-AA-3663 TCGA-AA-3697 TCGA-AA-3864 TCGA-AA-3950 TCGA-AA-A00N TCGA-AA-A010 
        6.97        85.05        53.00        24.00         4.01        34.98 
TCGA-AZ-4315 TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-4752 TCGA-CM-5862 TCGA-CM-6163 
       58.39        12.76        10.06        13.02         5.03         2.96 
TCGA-CM-6164 TCGA-D5-5541 TCGA-D5-6529 TCGA-DM-A1D9 TCGA-F4-6570 TCGA-F4-6855 
       29.03        55.92        20.19       140.38         6.18        47.41 
TCGA-G4-6306 TCGA-G4-6588 TCGA-AG-3892 TCGA-AG-A002 TCGA-AG-A01L TCGA-DY-A0XA 
       44.68        26.17        13.02        20.98        12.00       126.44 
TCGA-G5-6235 
       55.76 

$`FER1L6 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5664 TCGA-A6-5665 
       32.91        30.44        29.19        33.53        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       32.71        27.09        22.52        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 
       21.76        24.69        24.39        23.87        20.12        20.28 
TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
        7.04         1.02        35.01        63.98         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
       13.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
       36.03         8.05         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.05        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 
        0.99        31.07        31.07        30.05        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        33.01        26.01         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
       16.31         0.95        33.01        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.07        12.20        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6165 
       15.02        15.02        17.03        15.02        12.00        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
       12.59         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 
       98.24         8.61        31.96        35.74        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6307 
       35.31       133.18        74.56        65.85        53.62        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       35.80        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
        9.07        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.03         5.29        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6641 
        0.69        26.43 

  FER1L6 MUTATED FER1L6 WILD-TYPE 
            2.96             0.00 
  FER1L6 MUTATED FER1L6 WILD-TYPE 
          140.38           148.01 
  FER1L6 MUTATED FER1L6 WILD-TYPE 
          20.980           20.085 
[1] "3.0 - 140.4 (21.0)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.5"
D2171V2, continuous
D2171V3, binary
                  cls
clus                 0   1
  FER1L6 MUTATED    28   5
  FER1L6 WILD-TYPE 338 114
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FER1L6 MUTATED     28    5
  FER1L6 WILD-TYPE  338  114
        clus
vv       FER1L6 MUTATED FER1L6 WILD-TYPE
  COLON              28              338
  RECTUM              5              114
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FER1L6 MUTATED         4        0        3        15         2         0
  FER1L6 WILD-TYPE      87        1       29       123         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FER1L6 MUTATED           1          0          4          2        0
  FER1L6 WILD-TYPE        23         11         55         40       48
                  vv
clus               STAGE IVA STAGE IVB
  FER1L6 MUTATED           2         0
  FER1L6 WILD-TYPE        16         1
D2171V4, multiclass
            clus
vv           FER1L6 MUTATED FER1L6 WILD-TYPE
  STAGE I                 4               87
  STAGE IA                0                1
  STAGE II                3               29
  STAGE IIA              15              123
  STAGE IIB               2                8
  STAGE IIC               0                1
  STAGE III               1               23
  STAGE IIIA              0               11
  STAGE IIIB              4               55
  STAGE IIIC              2               40
  STAGE IV                0               48
  STAGE IVA               2               16
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  FER1L6 MUTATED     2   3  25   3
  FER1L6 WILD-TYPE  15  89 304  47
D2171V5, multiclass
    clus
vv   FER1L6 MUTATED FER1L6 WILD-TYPE
  T1              2               15
  T2              3               89
  T3             25              304
  T4              3               47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  FER1L6 MUTATED    25   6   2
  FER1L6 WILD-TYPE 262 107  85
D2171V6, multiclass
    clus
vv   FER1L6 MUTATED FER1L6 WILD-TYPE
  N0             25              262
  N1              6              107
  N2              2               85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2171V7, binary
                  cls
clus                 0   1
  FER1L6 MUTATED    28   2
  FER1L6 WILD-TYPE 347  63
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FER1L6 MUTATED     28    2
  FER1L6 WILD-TYPE  347   63
   clus
vv  FER1L6 MUTATED FER1L6 WILD-TYPE
  0             28              347
  1              2               63
[1] 2 2
[1] FALSE
D2171V8, binary
                  cls
clus                 0   1
  FER1L6 MUTATED    11  22
  FER1L6 WILD-TYPE 214 242
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FER1L6 MUTATED     11   22
  FER1L6 WILD-TYPE  214  242
        clus
vv       FER1L6 MUTATED FER1L6 WILD-TYPE
  FEMALE             11              214
  MALE               22              242
[1] 2 2
[1] FALSE
D2171V9, binary
                  cls
clus                 0   1
  FER1L6 MUTATED    27   0
  FER1L6 WILD-TYPE 323  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FER1L6 MUTATED     27    0
  FER1L6 WILD-TYPE  323   22
     clus
vv    FER1L6 MUTATED FER1L6 WILD-TYPE
  NO              27              323
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  FER1L6 MUTATED                     23                             5
  FER1L6 WILD-TYPE                  292                            42
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  FER1L6 MUTATED                       5                              0
  FER1L6 WILD-TYPE                   101                             10
D2171V10, multiclass
                                clus
vv                               FER1L6 MUTATED FER1L6 WILD-TYPE
  COLON ADENOCARCINOMA                       23              292
  COLON MUCINOUS ADENOCARCINOMA               5               42
  RECTAL ADENOCARCINOMA                       5              101
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  FER1L6 MUTATED    26   1   0   2
  FER1L6 WILD-TYPE 319   3  31  23
D2171V11, multiclass
    clus
vv   FER1L6 MUTATED FER1L6 WILD-TYPE
  R0             26              319
  R1              1                3
  R2              0               31
  RX              2               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2171V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FER1L6 MUTATED                                  0     2
  FER1L6 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  FER1L6 MUTATED                           3    16
  FER1L6 WILD-TYPE                        19   210
D2171V13, multiclass
                                  clus
vv                                 FER1L6 MUTATED FER1L6 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                9
  BLACK OR AFRICAN AMERICAN                     3               19
  WHITE                                        16              210
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2172) Variable = NUP107 MUTATION ANALYSIS
D2172V1, survival
                  sevent
clus2                0   1
  NUP107 MUTATED     9   3
  NUP107 WILD-TYPE 369  90
  NUP107 MUTATED NUP107 WILD-TYPE 
              12              459 
  NUP107 MUTATED NUP107 WILD-TYPE 
               3               90 
$`NUP107 MUTATED`
TCGA-AA-3555 TCGA-AA-3663 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3845 TCGA-AA-3977 
       29.95         6.97        35.05        33.04         0.00        25.02 
TCGA-AA-A01P TCGA-CA-6717 TCGA-D5-5540 TCGA-AG-3583 TCGA-AG-3892 TCGA-AG-A002 
       38.07        12.76        56.09        20.05        13.02        20.98 

$`NUP107 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 
       21.01        13.02        24.00        17.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02        14.93        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01Q TCGA-AA-A01R 
       32.02        12.00        31.00        31.00         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07        12.20        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6529 
       12.03        45.40        12.26        19.59        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        8.02         7.07        36.03        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 
        1.02        17.95        36.95        17.03        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  NUP107 MUTATED NUP107 WILD-TYPE 
               0                0 
  NUP107 MUTATED NUP107 WILD-TYPE 
           56.09           148.01 
  NUP107 MUTATED NUP107 WILD-TYPE 
           23.00            20.12 
[1] "0.0 - 56.1 (23.0)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.4"
D2172V2, continuous
D2172V3, binary
                  cls
clus                 0   1
  NUP107 MUTATED    10   3
  NUP107 WILD-TYPE 356 116
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NUP107 MUTATED     10    3
  NUP107 WILD-TYPE  356  116
        clus
vv       NUP107 MUTATED NUP107 WILD-TYPE
  COLON              10              356
  RECTUM              3              116
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NUP107 MUTATED         2        0        1         7         0         0
  NUP107 WILD-TYPE      89        1       31       131        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  NUP107 MUTATED           1          0          0          0        1
  NUP107 WILD-TYPE        23         11         59         42       47
                  vv
clus               STAGE IVA STAGE IVB
  NUP107 MUTATED           0         0
  NUP107 WILD-TYPE        18         1
D2172V4, multiclass
            clus
vv           NUP107 MUTATED NUP107 WILD-TYPE
  STAGE I                 2               89
  STAGE IA                0                1
  STAGE II                1               31
  STAGE IIA               7              131
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               1               23
  STAGE IIIA              0               11
  STAGE IIIB              0               59
  STAGE IIIC              0               42
  STAGE IV                1               47
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  NUP107 MUTATED     1   2  10   0
  NUP107 WILD-TYPE  16  90 319  50
D2172V5, multiclass
    clus
vv   NUP107 MUTATED NUP107 WILD-TYPE
  T1              1               16
  T2              2               90
  T3             10              319
  T4              0               50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  NUP107 MUTATED    11   1   1
  NUP107 WILD-TYPE 276 112  86
D2172V6, multiclass
    clus
vv   NUP107 MUTATED NUP107 WILD-TYPE
  N0             11              276
  N1              1              112
  N2              1               86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2172V7, binary
                  cls
clus                 0   1
  NUP107 MUTATED    11   1
  NUP107 WILD-TYPE 364  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NUP107 MUTATED     11    1
  NUP107 WILD-TYPE  364   64
   clus
vv  NUP107 MUTATED NUP107 WILD-TYPE
  0             11              364
  1              1               64
[1] 2 2
[1] FALSE
D2172V8, binary
                  cls
clus                 0   1
  NUP107 MUTATED     7   6
  NUP107 WILD-TYPE 218 258
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NUP107 MUTATED      7    6
  NUP107 WILD-TYPE  218  258
        clus
vv       NUP107 MUTATED NUP107 WILD-TYPE
  FEMALE              7              218
  MALE                6              258
[1] 2 2
[1] FALSE
D2172V9, binary
                  cls
clus                 0   1
  NUP107 MUTATED    11   0
  NUP107 WILD-TYPE 339  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NUP107 MUTATED     11    0
  NUP107 WILD-TYPE  339   22
     clus
vv    NUP107 MUTATED NUP107 WILD-TYPE
  NO              11              339
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  NUP107 MUTATED                      8                             2
  NUP107 WILD-TYPE                  307                            45
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  NUP107 MUTATED                       2                              1
  NUP107 WILD-TYPE                   104                              9
D2172V10, multiclass
                                clus
vv                               NUP107 MUTATED NUP107 WILD-TYPE
  COLON ADENOCARCINOMA                        8              307
  COLON MUCINOUS ADENOCARCINOMA               2               45
  RECTAL ADENOCARCINOMA                       2              104
  RECTAL MUCINOUS ADENOCARCINOMA              1                9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  NUP107 MUTATED    10   0   1   1
  NUP107 WILD-TYPE 335   4  30  24
D2172V11, multiclass
    clus
vv   NUP107 MUTATED NUP107 WILD-TYPE
  R0             10              335
  R1              0                4
  R2              1               30
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2172V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NUP107 MUTATED                                  0     1
  NUP107 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  NUP107 MUTATED                           0     1
  NUP107 WILD-TYPE                        22   225
D2172V13, multiclass
[1] "Remove cluster labels:" "NUP107 MUTATED"        
clus
  NUP107 MUTATED NUP107 WILD-TYPE 
               2              258 
      TCGA-A6-2671       TCGA-A6-2672       TCGA-A6-2674       TCGA-A6-2676 
"NUP107 WILD-TYPE" "NUP107 WILD-TYPE" "NUP107 WILD-TYPE" "NUP107 WILD-TYPE" 
      TCGA-A6-2677       TCGA-A6-2678       TCGA-A6-2683       TCGA-A6-3807 
"NUP107 WILD-TYPE" "NUP107 WILD-TYPE" "NUP107 WILD-TYPE" "NUP107 WILD-TYPE" 
      TCGA-A6-3808       TCGA-A6-3809       TCGA-A6-3810       TCGA-A6-4105 
"NUP107 WILD-TYPE" "NUP107 WILD-TYPE" "NUP107 WILD-TYPE" "NUP107 WILD-TYPE" 
      TCGA-A6-5656       TCGA-A6-5657       TCGA-A6-5659       TCGA-A6-5660 
"NUP107 WILD-TYPE" "NUP107 WILD-TYPE" "NUP107 WILD-TYPE" "NUP107 WILD-TYPE" 
      TCGA-A6-5661       TCGA-A6-5662       TCGA-A6-5664       TCGA-A6-5665 
"NUP107 WILD-TYPE" "NUP107 WILD-TYPE" "NUP107 WILD-TYPE" "NUP107 WILD-TYPE" 
      TCGA-A6-5666       TCGA-A6-6137       TCGA-A6-6138       TCGA-A6-6141 
"NUP107 WILD-TYPE" "NUP107 WILD-TYPE" "NUP107 WILD-TYPE" "NUP107 WILD-TYPE" 
      TCGA-A6-6142       TCGA-A6-6648       TCGA-A6-6649       TCGA-A6-6651 
"NUP107 WILD-TYPE" "NUP107 WILD-TYPE" "NUP107 WILD-TYPE" "NUP107 WILD-TYPE" 
      TCGA-A6-6652       TCGA-A6-6653       TCGA-A6-6654       TCGA-A6-6780 
"NUP107 WILD-TYPE" "NUP107 WILD-TYPE" "NUP107 WILD-TYPE" "NUP107 WILD-TYPE" 
      TCGA-A6-6781       TCGA-A6-6782       TCGA-AD-5900       TCGA-AD-6548 
"NUP107 WILD-TYPE" "NUP107 WILD-TYPE" "NUP107 WILD-TYPE" "NUP107 WILD-TYPE" 
      TCGA-AD-6888       TCGA-AD-6889       TCGA-AD-6890       TCGA-AD-6895 
"NUP107 WILD-TYPE" "NUP107 WILD-TYPE" "NUP107 WILD-TYPE" "NUP107 WILD-TYPE" 
      TCGA-AD-6899       TCGA-AD-6901       TCGA-AD-6963       TCGA-AD-6964 
"NUP107 WILD-TYPE" "NUP107 WILD-TYPE" "NUP107 WILD-TYPE" "NUP107 WILD-TYPE" 
      TCGA-AD-6965       TCGA-AU-3779       TCGA-AU-6004       TCGA-AY-4070 
"NUP107 WILD-TYPE" "NUP107 WILD-TYPE" "NUP107 WILD-TYPE" "NUP107 WILD-TYPE" 
      TCGA-AY-4071       TCGA-AY-5543       TCGA-AY-6196       TCGA-AY-6197 
"NUP107 WILD-TYPE" "NUP107 WILD-TYPE" "NUP107 WILD-TYPE" "NUP107 WILD-TYPE" 
      TCGA-AY-6386       TCGA-AZ-4315       TCGA-AZ-4323       TCGA-AZ-4616 
"NUP107 WILD-TYPE" "NUP107 WILD-TYPE" "NUP107 WILD-TYPE" "NUP107 WILD-TYPE" 
      TCGA-AZ-4681       TCGA-AZ-4682       TCGA-AZ-5403       TCGA-AZ-5407 
"NUP107 WILD-TYPE" "NUP107 WILD-TYPE" "NUP107 WILD-TYPE" "NUP107 WILD-TYPE" 
      TCGA-AZ-6598       TCGA-AZ-6599       TCGA-AZ-6600       TCGA-AZ-6601 
"NUP107 WILD-TYPE" "NUP107 WILD-TYPE" "NUP107 WILD-TYPE" "NUP107 WILD-TYPE" 
      TCGA-AZ-6603       TCGA-AZ-6605       TCGA-AZ-6606       TCGA-AZ-6607 
"NUP107 WILD-TYPE" "NUP107 WILD-TYPE" "NUP107 WILD-TYPE" "NUP107 WILD-TYPE" 
      TCGA-AZ-6608       TCGA-CA-5254       TCGA-CA-5255       TCGA-CA-5796 
"NUP107 WILD-TYPE" "NUP107 WILD-TYPE" "NUP107 WILD-TYPE" "NUP107 WILD-TYPE" 
      TCGA-CA-5797       TCGA-CA-6715       TCGA-CA-6716       TCGA-CA-6718 
"NUP107 WILD-TYPE" "NUP107 WILD-TYPE" "NUP107 WILD-TYPE" "NUP107 WILD-TYPE" 
      TCGA-CA-6719       TCGA-CK-4947       TCGA-CK-4948       TCGA-CK-4950 
"NUP107 WILD-TYPE" "NUP107 WILD-TYPE" "NUP107 WILD-TYPE" "NUP107 WILD-TYPE" 
      TCGA-CK-4952       TCGA-CK-5912       TCGA-CK-5913       TCGA-CK-5914 
"NUP107 WILD-TYPE" "NUP107 WILD-TYPE" "NUP107 WILD-TYPE" "NUP107 WILD-TYPE" 
      TCGA-CK-5915       TCGA-CK-5916       TCGA-CK-6746       TCGA-CK-6747 
"NUP107 WILD-TYPE" "NUP107 WILD-TYPE" "NUP107 WILD-TYPE" "NUP107 WILD-TYPE" 
      TCGA-CK-6748       TCGA-CK-6751       TCGA-CM-4743       TCGA-CM-4744 
"NUP107 WILD-TYPE" "NUP107 WILD-TYPE" "NUP107 WILD-TYPE" "NUP107 WILD-TYPE" 
      TCGA-CM-4746       TCGA-CM-4747       TCGA-CM-4752       TCGA-CM-5341 
"NUP107 WILD-TYPE" "NUP107 WILD-TYPE" "NUP107 WILD-TYPE" "NUP107 WILD-TYPE" 
      TCGA-CM-5344       TCGA-CM-5348       TCGA-CM-5349       TCGA-CM-5860 
"NUP107 WILD-TYPE" "NUP107 WILD-TYPE" "NUP107 WILD-TYPE" "NUP107 WILD-TYPE" 
      TCGA-CM-5861       TCGA-CM-5862       TCGA-CM-5863       TCGA-CM-5864 
"NUP107 WILD-TYPE" "NUP107 WILD-TYPE" "NUP107 WILD-TYPE" "NUP107 WILD-TYPE" 
      TCGA-CM-5868       TCGA-CM-6161       TCGA-CM-6162       TCGA-CM-6163 
"NUP107 WILD-TYPE" "NUP107 WILD-TYPE" "NUP107 WILD-TYPE" "NUP107 WILD-TYPE" 
      TCGA-CM-6164       TCGA-CM-6165       TCGA-CM-6166       TCGA-CM-6167 
"NUP107 WILD-TYPE" "NUP107 WILD-TYPE" "NUP107 WILD-TYPE" "NUP107 WILD-TYPE" 
      TCGA-CM-6168       TCGA-CM-6169       TCGA-CM-6170       TCGA-CM-6171 
"NUP107 WILD-TYPE" "NUP107 WILD-TYPE" "NUP107 WILD-TYPE" "NUP107 WILD-TYPE" 
      TCGA-CM-6172       TCGA-CM-6674       TCGA-CM-6675       TCGA-CM-6676 
"NUP107 WILD-TYPE" "NUP107 WILD-TYPE" "NUP107 WILD-TYPE" "NUP107 WILD-TYPE" 
      TCGA-CM-6677       TCGA-CM-6678       TCGA-CM-6679       TCGA-CM-6680 
"NUP107 WILD-TYPE" "NUP107 WILD-TYPE" "NUP107 WILD-TYPE" "NUP107 WILD-TYPE" 
      TCGA-D5-5537       TCGA-D5-5538       TCGA-D5-5539       TCGA-D5-5541 
"NUP107 WILD-TYPE" "NUP107 WILD-TYPE" "NUP107 WILD-TYPE" "NUP107 WILD-TYPE" 
      TCGA-D5-6529       TCGA-D5-6532       TCGA-D5-6533       TCGA-D5-6534 
"NUP107 WILD-TYPE" "NUP107 WILD-TYPE" "NUP107 WILD-TYPE" "NUP107 WILD-TYPE" 
      TCGA-D5-6535       TCGA-D5-6536       TCGA-D5-6537       TCGA-D5-6538 
"NUP107 WILD-TYPE" "NUP107 WILD-TYPE" "NUP107 WILD-TYPE" "NUP107 WILD-TYPE" 
      TCGA-D5-6539       TCGA-D5-6540       TCGA-D5-6541       TCGA-D5-6898 
"NUP107 WILD-TYPE" "NUP107 WILD-TYPE" "NUP107 WILD-TYPE" "NUP107 WILD-TYPE" 
      TCGA-D5-6920       TCGA-D5-6922       TCGA-D5-6923       TCGA-D5-6924 
"NUP107 WILD-TYPE" "NUP107 WILD-TYPE" "NUP107 WILD-TYPE" "NUP107 WILD-TYPE" 
      TCGA-D5-6926       TCGA-D5-6927       TCGA-D5-6928       TCGA-D5-6929 
"NUP107 WILD-TYPE" "NUP107 WILD-TYPE" "NUP107 WILD-TYPE" "NUP107 WILD-TYPE" 
      TCGA-D5-6930       TCGA-D5-6931       TCGA-D5-6932       TCGA-D5-7000 
"NUP107 WILD-TYPE" "NUP107 WILD-TYPE" "NUP107 WILD-TYPE" "NUP107 WILD-TYPE" 
      TCGA-DM-A0X9       TCGA-DM-A0XD       TCGA-DM-A0XF       TCGA-DM-A1D0 
"NUP107 WILD-TYPE" "NUP107 WILD-TYPE" "NUP107 WILD-TYPE" "NUP107 WILD-TYPE" 
      TCGA-DM-A1D4       TCGA-DM-A1D6       TCGA-DM-A1D7       TCGA-DM-A1D8 
"NUP107 WILD-TYPE" "NUP107 WILD-TYPE" "NUP107 WILD-TYPE" "NUP107 WILD-TYPE" 
      TCGA-DM-A1D9       TCGA-DM-A1DA       TCGA-DM-A1DB       TCGA-DM-A1HA 
"NUP107 WILD-TYPE" "NUP107 WILD-TYPE" "NUP107 WILD-TYPE" "NUP107 WILD-TYPE" 
      TCGA-DM-A1HB       TCGA-DM-A282       TCGA-DM-A285       TCGA-DM-A28C 
"NUP107 WILD-TYPE" "NUP107 WILD-TYPE" "NUP107 WILD-TYPE" "NUP107 WILD-TYPE" 
      TCGA-DM-A28E       TCGA-DM-A28F       TCGA-DM-A28G       TCGA-DM-A28H 
"NUP107 WILD-TYPE" "NUP107 WILD-TYPE" "NUP107 WILD-TYPE" "NUP107 WILD-TYPE" 
      TCGA-DM-A28K       TCGA-F4-6459       TCGA-F4-6460       TCGA-F4-6569 
"NUP107 WILD-TYPE" "NUP107 WILD-TYPE" "NUP107 WILD-TYPE" "NUP107 WILD-TYPE" 
      TCGA-F4-6570       TCGA-F4-6703       TCGA-F4-6704       TCGA-F4-6805 
"NUP107 WILD-TYPE" "NUP107 WILD-TYPE" "NUP107 WILD-TYPE" "NUP107 WILD-TYPE" 
      TCGA-F4-6806       TCGA-F4-6807       TCGA-F4-6808       TCGA-F4-6809 
"NUP107 WILD-TYPE" "NUP107 WILD-TYPE" "NUP107 WILD-TYPE" "NUP107 WILD-TYPE" 
      TCGA-F4-6854       TCGA-F4-6855       TCGA-F4-6856       TCGA-G4-6293 
"NUP107 WILD-TYPE" "NUP107 WILD-TYPE" "NUP107 WILD-TYPE" "NUP107 WILD-TYPE" 
      TCGA-G4-6299       TCGA-G4-6303       TCGA-G4-6304       TCGA-G4-6306 
"NUP107 WILD-TYPE" "NUP107 WILD-TYPE" "NUP107 WILD-TYPE" "NUP107 WILD-TYPE" 
      TCGA-G4-6307       TCGA-G4-6309       TCGA-G4-6310       TCGA-G4-6315 
"NUP107 WILD-TYPE" "NUP107 WILD-TYPE" "NUP107 WILD-TYPE" "NUP107 WILD-TYPE" 
      TCGA-G4-6317       TCGA-G4-6321       TCGA-G4-6323       TCGA-G4-6586 
"NUP107 WILD-TYPE" "NUP107 WILD-TYPE" "NUP107 WILD-TYPE" "NUP107 WILD-TYPE" 
      TCGA-G4-6588       TCGA-G4-6625       TCGA-G4-6626       TCGA-G4-6628 
"NUP107 WILD-TYPE" "NUP107 WILD-TYPE" "NUP107 WILD-TYPE" "NUP107 WILD-TYPE" 
      TCGA-AF-2687       TCGA-AF-2689       TCGA-AF-2691       TCGA-AF-2692 
"NUP107 WILD-TYPE" "NUP107 WILD-TYPE" "NUP107 WILD-TYPE" "NUP107 WILD-TYPE" 
      TCGA-AF-2693       TCGA-AF-3400       TCGA-AF-3913       TCGA-AF-4110 
"NUP107 WILD-TYPE" "NUP107 WILD-TYPE" "NUP107 WILD-TYPE" "NUP107 WILD-TYPE" 
      TCGA-AF-5654       TCGA-AF-6136       TCGA-AF-6655       TCGA-AF-6672 
"NUP107 WILD-TYPE" "NUP107 WILD-TYPE" "NUP107 WILD-TYPE" "NUP107 WILD-TYPE" 
      TCGA-AH-6544       TCGA-AH-6547       TCGA-AH-6549       TCGA-AH-6643 
"NUP107 WILD-TYPE" "NUP107 WILD-TYPE" "NUP107 WILD-TYPE" "NUP107 WILD-TYPE" 
      TCGA-AH-6644       TCGA-CI-6619       TCGA-CI-6620       TCGA-CI-6621 
"NUP107 WILD-TYPE" "NUP107 WILD-TYPE" "NUP107 WILD-TYPE" "NUP107 WILD-TYPE" 
      TCGA-CI-6622       TCGA-CI-6624       TCGA-CL-5917       TCGA-CL-5918 
"NUP107 WILD-TYPE" "NUP107 WILD-TYPE" "NUP107 WILD-TYPE" "NUP107 WILD-TYPE" 
      TCGA-DC-5337       TCGA-DC-5869       TCGA-DC-6155       TCGA-DC-6157 
"NUP107 WILD-TYPE" "NUP107 WILD-TYPE" "NUP107 WILD-TYPE" "NUP107 WILD-TYPE" 
      TCGA-DC-6158       TCGA-DC-6160       TCGA-DC-6681       TCGA-DC-6682 
"NUP107 WILD-TYPE" "NUP107 WILD-TYPE" "NUP107 WILD-TYPE" "NUP107 WILD-TYPE" 
      TCGA-DC-6683       TCGA-DT-5265       TCGA-DY-A0XA       TCGA-DY-A1DC 
"NUP107 WILD-TYPE" "NUP107 WILD-TYPE" "NUP107 WILD-TYPE" "NUP107 WILD-TYPE" 
      TCGA-DY-A1DD       TCGA-DY-A1DF       TCGA-DY-A1DG       TCGA-DY-A1H8 
"NUP107 WILD-TYPE" "NUP107 WILD-TYPE" "NUP107 WILD-TYPE" "NUP107 WILD-TYPE" 
      TCGA-EF-5830       TCGA-EI-6506       TCGA-EI-6507       TCGA-EI-6508 
"NUP107 WILD-TYPE" "NUP107 WILD-TYPE" "NUP107 WILD-TYPE" "NUP107 WILD-TYPE" 
      TCGA-EI-6510       TCGA-F5-6464       TCGA-F5-6465       TCGA-F5-6571 
"NUP107 WILD-TYPE" "NUP107 WILD-TYPE" "NUP107 WILD-TYPE" "NUP107 WILD-TYPE" 
      TCGA-F5-6702       TCGA-F5-6811       TCGA-F5-6812       TCGA-F5-6813 
"NUP107 WILD-TYPE" "NUP107 WILD-TYPE" "NUP107 WILD-TYPE" "NUP107 WILD-TYPE" 
      TCGA-G5-6235       TCGA-G5-6641 
"NUP107 WILD-TYPE" "NUP107 WILD-TYPE" 

Clustering(2173) Variable = HIP1 MUTATION ANALYSIS
D2173V1, survival
                sevent
clus2              0   1
  HIP1 MUTATED     9   5
  HIP1 WILD-TYPE 369  88
  HIP1 MUTATED HIP1 WILD-TYPE 
            14            457 
  HIP1 MUTATED HIP1 WILD-TYPE 
             5             88 
$`HIP1 MUTATED`
TCGA-A6-2676 TCGA-A6-6653 TCGA-AA-3489 TCGA-AA-3655 TCGA-AA-A00N TCGA-AA-A010 
       42.90        24.39         7.04        61.02         4.01        34.98 
TCGA-AA-A02H TCGA-AU-3779 TCGA-AZ-5407 TCGA-AZ-6603 TCGA-CM-5861 TCGA-G4-6307 
        2.01        14.50        88.21        29.56        15.02        55.04 
TCGA-AG-A002 TCGA-DC-6681 
       20.98         5.95 

$`HIP1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 
       25.18        24.16        21.76        24.69        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       19.66        20.28         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       19.99        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       39.06        51.98        39.98         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        10.88         0.20        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
      106.75        22.36        62.79        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
      100.01         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 
       29.06        22.03        22.98        30.08        32.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       44.68        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       10.98        19.99         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  HIP1 MUTATED HIP1 WILD-TYPE 
          2.01           0.00 
  HIP1 MUTATED HIP1 WILD-TYPE 
         88.21         148.01 
  HIP1 MUTATED HIP1 WILD-TYPE 
        22.685         20.120 
[1] "2.0 - 88.2 (22.7)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.6"
D2173V2, continuous
D2173V3, binary
                cls
clus               0   1
  HIP1 MUTATED    12   2
  HIP1 WILD-TYPE 354 117
[1] "tbl2"
                cls
clus             [,1] [,2]
  HIP1 MUTATED     12    2
  HIP1 WILD-TYPE  354  117
        clus
vv       HIP1 MUTATED HIP1 WILD-TYPE
  COLON            12            354
  RECTUM            2            117
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  HIP1 MUTATED         3        0        2         2         3         0
  HIP1 WILD-TYPE      88        1       30       136         7         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  HIP1 MUTATED           0          0          1          0        1         1
  HIP1 WILD-TYPE        24         11         58         42       47        17
                vv
clus             STAGE IVB
  HIP1 MUTATED           0
  HIP1 WILD-TYPE         1
D2173V4, multiclass
            clus
vv           HIP1 MUTATED HIP1 WILD-TYPE
  STAGE I               3             88
  STAGE IA              0              1
  STAGE II              2             30
  STAGE IIA             2            136
  STAGE IIB             3              7
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            1             58
  STAGE IIIC            0             42
  STAGE IV              1             47
  STAGE IVA             1             17
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  HIP1 MUTATED     1   3   7   3
  HIP1 WILD-TYPE  16  89 322  47
D2173V5, multiclass
    clus
vv   HIP1 MUTATED HIP1 WILD-TYPE
  T1            1             16
  T2            3             89
  T3            7            322
  T4            3             47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  HIP1 MUTATED    10   2   2
  HIP1 WILD-TYPE 277 111  85
D2173V6, multiclass
    clus
vv   HIP1 MUTATED HIP1 WILD-TYPE
  N0           10            277
  N1            2            111
  N2            2             85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2173V7, binary
                cls
clus               0   1
  HIP1 MUTATED    11   2
  HIP1 WILD-TYPE 364  63
[1] "tbl2"
                cls
clus             [,1] [,2]
  HIP1 MUTATED     11    2
  HIP1 WILD-TYPE  364   63
   clus
vv  HIP1 MUTATED HIP1 WILD-TYPE
  0           11            364
  1            2             63
[1] 2 2
[1] FALSE
D2173V8, binary
                cls
clus               0   1
  HIP1 MUTATED     9   5
  HIP1 WILD-TYPE 216 259
[1] "tbl2"
                cls
clus             [,1] [,2]
  HIP1 MUTATED      9    5
  HIP1 WILD-TYPE  216  259
        clus
vv       HIP1 MUTATED HIP1 WILD-TYPE
  FEMALE            9            216
  MALE              5            259
[1] 2 2
[1] FALSE
D2173V9, binary
                cls
clus               0   1
  HIP1 MUTATED    11   0
  HIP1 WILD-TYPE 339  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  HIP1 MUTATED     11    0
  HIP1 WILD-TYPE  339   22
     clus
vv    HIP1 MUTATED HIP1 WILD-TYPE
  NO            11            339
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  HIP1 MUTATED                     11                             1
  HIP1 WILD-TYPE                  304                            46
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  HIP1 MUTATED                       2                              0
  HIP1 WILD-TYPE                   104                             10
D2173V10, multiclass
                                clus
vv                               HIP1 MUTATED HIP1 WILD-TYPE
  COLON ADENOCARCINOMA                     11            304
  COLON MUCINOUS ADENOCARCINOMA             1             46
  RECTAL ADENOCARCINOMA                     2            104
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  HIP1 MUTATED    10   0   1   0
  HIP1 WILD-TYPE 335   4  30  25
D2173V11, multiclass
    clus
vv   HIP1 MUTATED HIP1 WILD-TYPE
  R0           10            335
  R1            0              4
  R2            1             30
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2173V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HIP1 MUTATED                                  0     0
  HIP1 WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  HIP1 MUTATED                           0     8
  HIP1 WILD-TYPE                        22   218
D2173V13, multiclass
                                  clus
vv                                 HIP1 MUTATED HIP1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       8            218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2174) Variable = AP3B1 MUTATION ANALYSIS
D2174V1, survival
                 sevent
clus2               0   1
  AP3B1 MUTATED    10   2
  AP3B1 WILD-TYPE 368  91
  AP3B1 MUTATED AP3B1 WILD-TYPE 
             12             459 
  AP3B1 MUTATED AP3B1 WILD-TYPE 
              2              91 
$`AP3B1 MUTATED`
TCGA-AA-3663 TCGA-AA-3715 TCGA-AA-3837 TCGA-AA-3966 TCGA-AA-3977 TCGA-AA-A010 
        6.97        19.04        38.99         2.01        25.02        34.98 
TCGA-CA-6717 TCGA-CA-6718 TCGA-AF-4110 TCGA-AG-3892 TCGA-AG-A002 TCGA-EF-5830 
       12.76        10.06        14.50        13.02        20.98         0.49 

$`AP3B1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.05        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 
       36.00         5.03        85.05        26.99        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       15.95        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
       34.03        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        3.29         0.07        12.20        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-5654 
       43.04        13.55        19.10        34.49        10.39        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 
       19.99         1.02        17.95        36.95        17.03        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       51.48        32.61        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  AP3B1 MUTATED AP3B1 WILD-TYPE 
           0.49            0.00 
  AP3B1 MUTATED AP3B1 WILD-TYPE 
          38.99          148.01 
  AP3B1 MUTATED AP3B1 WILD-TYPE 
          13.76           20.55 
[1] "0.5 - 39.0 (13.8)"  "0.0 - 148.0 (20.6)"
[1] "hr=" "1.3"
D2174V2, continuous
D2174V3, binary
                 cls
clus                0   1
  AP3B1 MUTATED     8   3
  AP3B1 WILD-TYPE 358 116
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AP3B1 MUTATED      8    3
  AP3B1 WILD-TYPE  358  116
        clus
vv       AP3B1 MUTATED AP3B1 WILD-TYPE
  COLON              8             358
  RECTUM             3             116
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  AP3B1 MUTATED         2        0        2         4         2         0
  AP3B1 WILD-TYPE      89        1       30       134         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AP3B1 MUTATED           0          0          0          0        0         1
  AP3B1 WILD-TYPE        24         11         59         42       48        17
                 vv
clus              STAGE IVB
  AP3B1 MUTATED           0
  AP3B1 WILD-TYPE         1
D2174V4, multiclass
            clus
vv           AP3B1 MUTATED AP3B1 WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA              4             134
  STAGE IIB              2               8
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  AP3B1 MUTATED     1   2   6   3
  AP3B1 WILD-TYPE  16  90 323  47
D2174V5, multiclass
    clus
vv   AP3B1 MUTATED AP3B1 WILD-TYPE
  T1             1              16
  T2             2              90
  T3             6             323
  T4             3              47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  AP3B1 MUTATED    11   0   1
  AP3B1 WILD-TYPE 276 113  86
D2174V6, multiclass
    clus
vv   AP3B1 MUTATED AP3B1 WILD-TYPE
  N0            11             276
  N1             0             113
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2174V7, binary
                 cls
clus                0   1
  AP3B1 MUTATED    10   0
  AP3B1 WILD-TYPE 365  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AP3B1 MUTATED     10    0
  AP3B1 WILD-TYPE  365   65
   clus
vv  AP3B1 MUTATED AP3B1 WILD-TYPE
  0            10             365
  1             0              65
[1] 2 2
[1] FALSE
D2174V8, binary
                 cls
clus                0   1
  AP3B1 MUTATED     3   9
  AP3B1 WILD-TYPE 222 255
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AP3B1 MUTATED      3    9
  AP3B1 WILD-TYPE  222  255
        clus
vv       AP3B1 MUTATED AP3B1 WILD-TYPE
  FEMALE             3             222
  MALE               9             255
[1] 2 2
[1] FALSE
D2174V9, binary
                 cls
clus                0   1
  AP3B1 MUTATED    10   0
  AP3B1 WILD-TYPE 340  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AP3B1 MUTATED     10    0
  AP3B1 WILD-TYPE  340   22
     clus
vv    AP3B1 MUTATED AP3B1 WILD-TYPE
  NO             10             340
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  AP3B1 MUTATED                      5                             3
  AP3B1 WILD-TYPE                  310                            44
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  AP3B1 MUTATED                       3                              0
  AP3B1 WILD-TYPE                   103                             10
D2174V10, multiclass
                                clus
vv                               AP3B1 MUTATED AP3B1 WILD-TYPE
  COLON ADENOCARCINOMA                       5             310
  COLON MUCINOUS ADENOCARCINOMA              3              44
  RECTAL ADENOCARCINOMA                      3             103
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  AP3B1 MUTATED     8   0   0   2
  AP3B1 WILD-TYPE 337   4  31  23
D2174V11, multiclass
    clus
vv   AP3B1 MUTATED AP3B1 WILD-TYPE
  R0             8             337
  R1             0               4
  R2             0              31
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2174V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AP3B1 MUTATED                                  0     2
  AP3B1 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  AP3B1 MUTATED                           0     2
  AP3B1 WILD-TYPE                        22   224
D2174V13, multiclass
                                  clus
vv                                 AP3B1 MUTATED AP3B1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               9
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        2             224
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2175) Variable = C10ORF81 MUTATION ANALYSIS
D2175V1, survival
                    sevent
clus2                  0   1
  C10ORF81 MUTATED     3   0
  C10ORF81 WILD-TYPE 375  93
  C10ORF81 MUTATED C10ORF81 WILD-TYPE 
                 3                468 
  C10ORF81 MUTATED C10ORF81 WILD-TYPE 
                 0                 93 
$`C10ORF81 MUTATED`
TCGA-AA-3560 TCGA-D5-5539 TCGA-F4-6808 
       19.99        19.59        33.67 

$`C10ORF81 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       20.98        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-5541 
       10.06        12.03        45.40        12.26        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  C10ORF81 MUTATED C10ORF81 WILD-TYPE 
             19.59               0.00 
  C10ORF81 MUTATED C10ORF81 WILD-TYPE 
             33.67             148.01 
  C10ORF81 MUTATED C10ORF81 WILD-TYPE 
            19.990             20.235 
[1] "19.6 - 33.7 (20.0)" "0.0 - 148.0 (20.2)"
[1] "hr="     "3300000"
D2175V2, continuous
D2175V3, binary
                    cls
clus                   0   1
  C10ORF81 MUTATED     4   0
  C10ORF81 WILD-TYPE 362 119
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C10ORF81 MUTATED      4    0
  C10ORF81 WILD-TYPE  362  119
        clus
vv       C10ORF81 MUTATED C10ORF81 WILD-TYPE
  COLON                 4                362
  RECTUM                0                119
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  C10ORF81 MUTATED         1        0        0         1         0         0
  C10ORF81 WILD-TYPE      90        1       32       137        10         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  C10ORF81 MUTATED           0          1          0          1        0
  C10ORF81 WILD-TYPE        24         10         59         41       48
                    vv
clus                 STAGE IVA STAGE IVB
  C10ORF81 MUTATED           0         0
  C10ORF81 WILD-TYPE        18         1
D2175V4, multiclass
            clus
vv           C10ORF81 MUTATED C10ORF81 WILD-TYPE
  STAGE I                   1                 90
  STAGE IA                  0                  1
  STAGE II                  0                 32
  STAGE IIA                 1                137
  STAGE IIB                 0                 10
  STAGE IIC                 0                  1
  STAGE III                 0                 24
  STAGE IIIA                1                 10
  STAGE IIIB                0                 59
  STAGE IIIC                1                 41
  STAGE IV                  0                 48
  STAGE IVA                 0                 18
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  C10ORF81 MUTATED     1   0   3   0
  C10ORF81 WILD-TYPE  16  92 326  50
D2175V5, multiclass
    clus
vv   C10ORF81 MUTATED C10ORF81 WILD-TYPE
  T1                1                 16
  T2                0                 92
  T3                3                326
  T4                0                 50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  C10ORF81 MUTATED     2   1   1
  C10ORF81 WILD-TYPE 285 112  86
D2175V6, multiclass
    clus
vv   C10ORF81 MUTATED C10ORF81 WILD-TYPE
  N0                2                285
  N1                1                112
  N2                1                 86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2175V7, binary
                    cls
clus                   0   1
  C10ORF81 MUTATED     4   0
  C10ORF81 WILD-TYPE 371  65
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C10ORF81 MUTATED      4    0
  C10ORF81 WILD-TYPE  371   65
   clus
vv  C10ORF81 MUTATED C10ORF81 WILD-TYPE
  0                4                371
  1                0                 65
[1] 2 2
[1] FALSE
D2175V8, binary
                    cls
clus                   0   1
  C10ORF81 MUTATED     3   1
  C10ORF81 WILD-TYPE 222 263
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C10ORF81 MUTATED      3    1
  C10ORF81 WILD-TYPE  222  263
        clus
vv       C10ORF81 MUTATED C10ORF81 WILD-TYPE
  FEMALE                3                222
  MALE                  1                263
[1] 2 2
[1] FALSE
D2175V9, binary
                    cls
clus                   0   1
  C10ORF81 MUTATED     3   0
  C10ORF81 WILD-TYPE 347  22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  C10ORF81 MUTATED      3    0
  C10ORF81 WILD-TYPE  347   22
     clus
vv    C10ORF81 MUTATED C10ORF81 WILD-TYPE
  NO                 3                347
  YES                0                 22
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  C10ORF81 MUTATED                      3                             1
  C10ORF81 WILD-TYPE                  312                            46
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  C10ORF81 MUTATED                       0                              0
  C10ORF81 WILD-TYPE                   106                             10
D2175V10, multiclass
                                clus
vv                               C10ORF81 MUTATED C10ORF81 WILD-TYPE
  COLON ADENOCARCINOMA                          3                312
  COLON MUCINOUS ADENOCARCINOMA                 1                 46
  RECTAL ADENOCARCINOMA                         0                106
  RECTAL MUCINOUS ADENOCARCINOMA                0                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  C10ORF81 MUTATED     4   0   0   0
  C10ORF81 WILD-TYPE 341   4  31  25
D2175V11, multiclass
    clus
vv   C10ORF81 MUTATED C10ORF81 WILD-TYPE
  R0                4                341
  R1                0                  4
  R2                0                 31
  RX                0                 25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2175V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C10ORF81 MUTATED                                  0     0
  C10ORF81 WILD-TYPE                                1    11
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  C10ORF81 MUTATED                           0     2
  C10ORF81 WILD-TYPE                        22   224
D2175V13, multiclass
[1] "Remove cluster labels:" "C10ORF81 MUTATED"      
clus
  C10ORF81 MUTATED C10ORF81 WILD-TYPE 
                 2                258 
        TCGA-A6-2671         TCGA-A6-2672         TCGA-A6-2674 
"C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" 
        TCGA-A6-2676         TCGA-A6-2677         TCGA-A6-2678 
"C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" 
        TCGA-A6-2683         TCGA-A6-3807         TCGA-A6-3808 
"C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" 
        TCGA-A6-3809         TCGA-A6-3810         TCGA-A6-4105 
"C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" 
        TCGA-A6-5656         TCGA-A6-5657         TCGA-A6-5659 
"C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" 
        TCGA-A6-5660         TCGA-A6-5661         TCGA-A6-5662 
"C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" 
        TCGA-A6-5664         TCGA-A6-5665         TCGA-A6-5666 
"C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" 
        TCGA-A6-6137         TCGA-A6-6138         TCGA-A6-6141 
"C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" 
        TCGA-A6-6142         TCGA-A6-6648         TCGA-A6-6649 
"C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" 
        TCGA-A6-6651         TCGA-A6-6652         TCGA-A6-6653 
"C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" 
        TCGA-A6-6654         TCGA-A6-6780         TCGA-A6-6781 
"C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" 
        TCGA-A6-6782         TCGA-AD-5900         TCGA-AD-6548 
"C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" 
        TCGA-AD-6888         TCGA-AD-6889         TCGA-AD-6890 
"C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" 
        TCGA-AD-6895         TCGA-AD-6899         TCGA-AD-6901 
"C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" 
        TCGA-AD-6963         TCGA-AD-6964         TCGA-AD-6965 
"C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" 
        TCGA-AU-3779         TCGA-AU-6004         TCGA-AY-4070 
"C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" 
        TCGA-AY-4071         TCGA-AY-5543         TCGA-AY-6196 
"C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" 
        TCGA-AY-6197         TCGA-AY-6386         TCGA-AZ-4315 
"C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" 
        TCGA-AZ-4323         TCGA-AZ-4616         TCGA-AZ-4681 
"C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" 
        TCGA-AZ-4682         TCGA-AZ-5403         TCGA-AZ-5407 
"C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" 
        TCGA-AZ-6598         TCGA-AZ-6599         TCGA-AZ-6600 
"C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" 
        TCGA-AZ-6601         TCGA-AZ-6603         TCGA-AZ-6605 
"C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" 
        TCGA-AZ-6606         TCGA-AZ-6607         TCGA-AZ-6608 
"C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" 
        TCGA-CA-5254         TCGA-CA-5255         TCGA-CA-5796 
"C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" 
        TCGA-CA-5797         TCGA-CA-6715         TCGA-CA-6716 
"C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" 
        TCGA-CA-6717         TCGA-CA-6718         TCGA-CA-6719 
"C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" 
        TCGA-CK-4947         TCGA-CK-4948         TCGA-CK-4950 
"C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" 
        TCGA-CK-4952         TCGA-CK-5912         TCGA-CK-5913 
"C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" 
        TCGA-CK-5914         TCGA-CK-5915         TCGA-CK-5916 
"C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" 
        TCGA-CK-6746         TCGA-CK-6747         TCGA-CK-6748 
"C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" 
        TCGA-CK-6751         TCGA-CM-4743         TCGA-CM-4744 
"C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" 
        TCGA-CM-4746         TCGA-CM-4747         TCGA-CM-4752 
"C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" 
        TCGA-CM-5341         TCGA-CM-5344         TCGA-CM-5348 
"C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" 
        TCGA-CM-5349         TCGA-CM-5860         TCGA-CM-5861 
"C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" 
        TCGA-CM-5862         TCGA-CM-5863         TCGA-CM-5864 
"C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" 
        TCGA-CM-5868         TCGA-CM-6161         TCGA-CM-6162 
"C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" 
        TCGA-CM-6163         TCGA-CM-6164         TCGA-CM-6165 
"C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" 
        TCGA-CM-6166         TCGA-CM-6167         TCGA-CM-6168 
"C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" 
        TCGA-CM-6169         TCGA-CM-6170         TCGA-CM-6171 
"C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" 
        TCGA-CM-6172         TCGA-CM-6674         TCGA-CM-6675 
"C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" 
        TCGA-CM-6676         TCGA-CM-6677         TCGA-CM-6678 
"C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" 
        TCGA-CM-6679         TCGA-CM-6680         TCGA-D5-5537 
"C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" 
        TCGA-D5-5538         TCGA-D5-5540         TCGA-D5-5541 
"C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" 
        TCGA-D5-6529         TCGA-D5-6532         TCGA-D5-6533 
"C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" 
        TCGA-D5-6534         TCGA-D5-6535         TCGA-D5-6536 
"C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" 
        TCGA-D5-6537         TCGA-D5-6538         TCGA-D5-6539 
"C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" 
        TCGA-D5-6540         TCGA-D5-6541         TCGA-D5-6898 
"C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" 
        TCGA-D5-6920         TCGA-D5-6922         TCGA-D5-6923 
"C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" 
        TCGA-D5-6924         TCGA-D5-6926         TCGA-D5-6927 
"C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" 
        TCGA-D5-6928         TCGA-D5-6929         TCGA-D5-6930 
"C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" 
        TCGA-D5-6931         TCGA-D5-6932         TCGA-D5-7000 
"C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" 
        TCGA-DM-A0X9         TCGA-DM-A0XD         TCGA-DM-A0XF 
"C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" 
        TCGA-DM-A1D0         TCGA-DM-A1D4         TCGA-DM-A1D6 
"C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" 
        TCGA-DM-A1D7         TCGA-DM-A1D8         TCGA-DM-A1D9 
"C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" 
        TCGA-DM-A1DA         TCGA-DM-A1DB         TCGA-DM-A1HA 
"C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" 
        TCGA-DM-A1HB         TCGA-DM-A282         TCGA-DM-A285 
"C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" 
        TCGA-DM-A28C         TCGA-DM-A28E         TCGA-DM-A28F 
"C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" 
        TCGA-DM-A28G         TCGA-DM-A28H         TCGA-DM-A28K 
"C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" 
        TCGA-F4-6459         TCGA-F4-6460         TCGA-F4-6569 
"C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" 
        TCGA-F4-6570         TCGA-F4-6703         TCGA-F4-6704 
"C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" 
        TCGA-F4-6805         TCGA-F4-6806         TCGA-F4-6807 
"C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" 
        TCGA-F4-6809         TCGA-F4-6854         TCGA-F4-6855 
"C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" 
        TCGA-F4-6856         TCGA-G4-6293         TCGA-G4-6299 
"C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" 
        TCGA-G4-6303         TCGA-G4-6304         TCGA-G4-6306 
"C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" 
        TCGA-G4-6307         TCGA-G4-6309         TCGA-G4-6310 
"C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" 
        TCGA-G4-6315         TCGA-G4-6317         TCGA-G4-6321 
"C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" 
        TCGA-G4-6323         TCGA-G4-6586         TCGA-G4-6588 
"C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" 
        TCGA-G4-6625         TCGA-G4-6626         TCGA-G4-6628 
"C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2691 
"C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" 
        TCGA-AF-2692         TCGA-AF-2693         TCGA-AF-3400 
"C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" 
        TCGA-AF-3913         TCGA-AF-4110         TCGA-AF-5654 
"C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" 
        TCGA-AF-6136         TCGA-AF-6655         TCGA-AF-6672 
"C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" 
        TCGA-AH-6544         TCGA-AH-6547         TCGA-AH-6549 
"C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" 
        TCGA-AH-6643         TCGA-AH-6644         TCGA-CI-6619 
"C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" 
        TCGA-CI-6620         TCGA-CI-6621         TCGA-CI-6622 
"C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" 
        TCGA-CI-6624         TCGA-CL-5917         TCGA-CL-5918 
"C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" 
        TCGA-DC-5337         TCGA-DC-5869         TCGA-DC-6155 
"C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" 
        TCGA-DC-6157         TCGA-DC-6158         TCGA-DC-6160 
"C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" 
        TCGA-DC-6681         TCGA-DC-6682         TCGA-DC-6683 
"C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" 
        TCGA-DT-5265         TCGA-DY-A0XA         TCGA-DY-A1DC 
"C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" 
        TCGA-DY-A1DD         TCGA-DY-A1DF         TCGA-DY-A1DG 
"C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" 
        TCGA-DY-A1H8         TCGA-EF-5830         TCGA-EI-6506 
"C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6510 
"C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" 
        TCGA-F5-6464         TCGA-F5-6465         TCGA-F5-6571 
"C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" 
        TCGA-F5-6702         TCGA-F5-6811         TCGA-F5-6812 
"C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" 
        TCGA-F5-6813         TCGA-G5-6235         TCGA-G5-6641 
"C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" "C10ORF81 WILD-TYPE" 

Clustering(2176) Variable = LY75 MUTATION ANALYSIS
D2176V1, survival
                sevent
clus2              0   1
  LY75 MUTATED    11   0
  LY75 WILD-TYPE 367  93
  LY75 MUTATED LY75 WILD-TYPE 
            11            460 
  LY75 MUTATED LY75 WILD-TYPE 
             0             93 
$`LY75 MUTATED`
TCGA-AA-3966 TCGA-AA-3977 TCGA-AA-A01R TCGA-AZ-4315 TCGA-CA-6717 TCGA-D5-6927 
        2.01        25.02        35.01        58.39        12.76         9.44 
TCGA-F4-6854 TCGA-G4-6309 TCGA-G4-6588 TCGA-G4-6628 TCGA-AG-A002 
        0.53        85.48        26.17        79.69        20.98 

$`LY75 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 
       24.00         2.01        20.98        34.03        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T 
       31.00        31.00        38.07         1.02         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07        12.20        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
       14.30         9.04        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6855 TCGA-F4-6856 
       41.42        16.24        33.67        13.25        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       91.79        46.75        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  LY75 MUTATED LY75 WILD-TYPE 
          0.53           0.00 
  LY75 MUTATED LY75 WILD-TYPE 
         85.48         148.01 
  LY75 MUTATED LY75 WILD-TYPE 
        25.020         20.085 
[1] "0.5 - 85.5 (25.0)"  "0.0 - 148.0 (20.1)"
[1] "hr="     "2.5e+07"
D2176V2, continuous
D2176V3, binary
                cls
clus               0   1
  LY75 MUTATED    10   1
  LY75 WILD-TYPE 356 118
[1] "tbl2"
                cls
clus             [,1] [,2]
  LY75 MUTATED     10    1
  LY75 WILD-TYPE  356  118
        clus
vv       LY75 MUTATED LY75 WILD-TYPE
  COLON            10            356
  RECTUM            1            118
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  LY75 MUTATED         2        0        0         6         0         0
  LY75 WILD-TYPE      89        1       32       132        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  LY75 MUTATED           1          0          1          0        0         0
  LY75 WILD-TYPE        23         11         58         42       48        18
                vv
clus             STAGE IVB
  LY75 MUTATED           0
  LY75 WILD-TYPE         1
D2176V4, multiclass
            clus
vv           LY75 MUTATED LY75 WILD-TYPE
  STAGE I               2             89
  STAGE IA              0              1
  STAGE II              0             32
  STAGE IIA             6            132
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             1             23
  STAGE IIIA            0             11
  STAGE IIIB            1             58
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  LY75 MUTATED     0   3   8   0
  LY75 WILD-TYPE  17  89 321  50
D2176V5, multiclass
    clus
vv   LY75 MUTATED LY75 WILD-TYPE
  T1            0             17
  T2            3             89
  T3            8            321
  T4            0             50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  LY75 MUTATED     9   1   1
  LY75 WILD-TYPE 278 112  86
D2176V6, multiclass
    clus
vv   LY75 MUTATED LY75 WILD-TYPE
  N0            9            278
  N1            1            112
  N2            1             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2176V7, binary
                cls
clus               0   1
  LY75 MUTATED    10   0
  LY75 WILD-TYPE 365  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  LY75 MUTATED     10    0
  LY75 WILD-TYPE  365   65
   clus
vv  LY75 MUTATED LY75 WILD-TYPE
  0           10            365
  1            0             65
[1] 2 2
[1] FALSE
D2176V8, binary
                cls
clus               0   1
  LY75 MUTATED     4   7
  LY75 WILD-TYPE 221 257
[1] "tbl2"
                cls
clus             [,1] [,2]
  LY75 MUTATED      4    7
  LY75 WILD-TYPE  221  257
        clus
vv       LY75 MUTATED LY75 WILD-TYPE
  FEMALE            4            221
  MALE              7            257
[1] 2 2
[1] FALSE
D2176V9, binary
                cls
clus               0   1
  LY75 MUTATED     9   1
  LY75 WILD-TYPE 341  21
[1] "tbl2"
                cls
clus             [,1] [,2]
  LY75 MUTATED      9    1
  LY75 WILD-TYPE  341   21
     clus
vv    LY75 MUTATED LY75 WILD-TYPE
  NO             9            341
  YES            1             21
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  LY75 MUTATED                      7                             3
  LY75 WILD-TYPE                  308                            44
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  LY75 MUTATED                       1                              0
  LY75 WILD-TYPE                   105                             10
D2176V10, multiclass
                                clus
vv                               LY75 MUTATED LY75 WILD-TYPE
  COLON ADENOCARCINOMA                      7            308
  COLON MUCINOUS ADENOCARCINOMA             3             44
  RECTAL ADENOCARCINOMA                     1            105
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  LY75 MUTATED     8   0   0   1
  LY75 WILD-TYPE 337   4  31  24
D2176V11, multiclass
    clus
vv   LY75 MUTATED LY75 WILD-TYPE
  R0            8            337
  R1            0              4
  R2            0             31
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2176V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  LY75 MUTATED                                  0     1
  LY75 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  LY75 MUTATED                           1     5
  LY75 WILD-TYPE                        21   221
D2176V13, multiclass
                                  clus
vv                                 LY75 MUTATED LY75 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                       5            221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2177) Variable = RRP9 MUTATION ANALYSIS
D2177V1, survival
                sevent
clus2              0   1
  RRP9 MUTATED    12   2
  RRP9 WILD-TYPE 366  91
  RRP9 MUTATED RRP9 WILD-TYPE 
            14            457 
  RRP9 MUTATED RRP9 WILD-TYPE 
             2             91 
$`RRP9 MUTATED`
TCGA-AA-3663 TCGA-AA-3672 TCGA-AA-3833 TCGA-AA-3864 TCGA-AA-3979 TCGA-AA-A01R 
        6.97         0.92        15.95        53.00        24.00        35.01 
TCGA-CK-4952 TCGA-CK-5916 TCGA-CM-6163 TCGA-D5-6538 TCGA-D5-6927 TCGA-DM-A0XF 
       15.62        21.14         2.96        17.13         9.44        38.20 
TCGA-AG-4007 TCGA-AG-A002 
        1.02        20.98 

$`RRP9 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 
        6.05        54.02         2.01        14.01        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        31.07        30.05        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        25.02        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
        1.02         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
       17.56       148.01        85.45        49.08        51.32         9.99 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       15.02        12.00        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       12.43        14.30         9.04        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A1D0 
       12.00        11.38        10.26       119.70        24.43       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  RRP9 MUTATED RRP9 WILD-TYPE 
          0.92           0.00 
  RRP9 MUTATED RRP9 WILD-TYPE 
         53.00         148.01 
  RRP9 MUTATED RRP9 WILD-TYPE 
         16.54          20.28 
[1] "0.9 - 53.0 (16.5)"  "0.0 - 148.0 (20.3)"
[1] "hr=" "1"  
D2177V2, continuous
D2177V3, binary
                cls
clus               0   1
  RRP9 MUTATED    12   2
  RRP9 WILD-TYPE 354 117
[1] "tbl2"
                cls
clus             [,1] [,2]
  RRP9 MUTATED     12    2
  RRP9 WILD-TYPE  354  117
        clus
vv       RRP9 MUTATED RRP9 WILD-TYPE
  COLON            12            354
  RECTUM            2            117
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RRP9 MUTATED         3        0        2         3         0         0
  RRP9 WILD-TYPE      88        1       30       135        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RRP9 MUTATED           2          0          1          2        1         0
  RRP9 WILD-TYPE        22         11         58         40       47        18
                vv
clus             STAGE IVB
  RRP9 MUTATED           0
  RRP9 WILD-TYPE         1
D2177V4, multiclass
            clus
vv           RRP9 MUTATED RRP9 WILD-TYPE
  STAGE I               3             88
  STAGE IA              0              1
  STAGE II              2             30
  STAGE IIA             3            135
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             2             22
  STAGE IIIA            0             11
  STAGE IIIB            1             58
  STAGE IIIC            2             40
  STAGE IV              1             47
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  RRP9 MUTATED     2   1   9   2
  RRP9 WILD-TYPE  15  91 320  48
D2177V5, multiclass
    clus
vv   RRP9 MUTATED RRP9 WILD-TYPE
  T1            2             15
  T2            1             91
  T3            9            320
  T4            2             48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  RRP9 MUTATED     8   1   5
  RRP9 WILD-TYPE 279 112  82
D2177V6, multiclass
    clus
vv   RRP9 MUTATED RRP9 WILD-TYPE
  N0            8            279
  N1            1            112
  N2            5             82
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2177V7, binary
                cls
clus               0   1
  RRP9 MUTATED    13   1
  RRP9 WILD-TYPE 362  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  RRP9 MUTATED     13    1
  RRP9 WILD-TYPE  362   64
   clus
vv  RRP9 MUTATED RRP9 WILD-TYPE
  0           13            362
  1            1             64
[1] 2 2
[1] FALSE
D2177V8, binary
                cls
clus               0   1
  RRP9 MUTATED     6   8
  RRP9 WILD-TYPE 219 256
[1] "tbl2"
                cls
clus             [,1] [,2]
  RRP9 MUTATED      6    8
  RRP9 WILD-TYPE  219  256
        clus
vv       RRP9 MUTATED RRP9 WILD-TYPE
  FEMALE            6            219
  MALE              8            256
[1] 2 2
[1] FALSE
D2177V9, binary
                cls
clus               0   1
  RRP9 MUTATED    10   1
  RRP9 WILD-TYPE 340  21
[1] "tbl2"
                cls
clus             [,1] [,2]
  RRP9 MUTATED     10    1
  RRP9 WILD-TYPE  340   21
     clus
vv    RRP9 MUTATED RRP9 WILD-TYPE
  NO            10            340
  YES            1             21
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  RRP9 MUTATED                      9                             2
  RRP9 WILD-TYPE                  306                            45
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  RRP9 MUTATED                       2                              0
  RRP9 WILD-TYPE                   104                             10
D2177V10, multiclass
                                clus
vv                               RRP9 MUTATED RRP9 WILD-TYPE
  COLON ADENOCARCINOMA                      9            306
  COLON MUCINOUS ADENOCARCINOMA             2             45
  RECTAL ADENOCARCINOMA                     2            104
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  RRP9 MUTATED    10   0   1   2
  RRP9 WILD-TYPE 335   4  30  23
D2177V11, multiclass
    clus
vv   RRP9 MUTATED RRP9 WILD-TYPE
  R0           10            335
  R1            0              4
  R2            1             30
  RX            2             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2177V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RRP9 MUTATED                                  0     0
  RRP9 WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  RRP9 MUTATED                           0     6
  RRP9 WILD-TYPE                        22   220
D2177V13, multiclass
                                  clus
vv                                 RRP9 MUTATED RRP9 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       6            220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2178) Variable = CUTC MUTATION ANALYSIS
D2178V1, survival
                sevent
clus2              0   1
  CUTC MUTATED     3   1
  CUTC WILD-TYPE 375  92
  CUTC MUTATED CUTC WILD-TYPE 
             4            467 
  CUTC MUTATED CUTC WILD-TYPE 
             1             92 
$`CUTC MUTATED`
TCGA-A6-5665 TCGA-A6-5666 TCGA-AZ-6608 TCGA-G4-6628 
       22.06        32.71         1.61        79.69 

$`CUTC WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       22.09        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       91.79        46.75        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  CUTC MUTATED CUTC WILD-TYPE 
          1.61           0.00 
  CUTC MUTATED CUTC WILD-TYPE 
         79.69         148.01 
  CUTC MUTATED CUTC WILD-TYPE 
        27.385         20.120 
[1] "1.6 - 79.7 (27.4)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1"  
D2178V2, continuous
D2178V3, binary
                cls
clus               0   1
  CUTC MUTATED     5   0
  CUTC WILD-TYPE 361 119
[1] "tbl2"
                cls
clus             [,1] [,2]
  CUTC MUTATED      5    0
  CUTC WILD-TYPE  361  119
        clus
vv       CUTC MUTATED CUTC WILD-TYPE
  COLON             5            361
  RECTUM            0            119
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CUTC MUTATED         1        0        0         2         0         1
  CUTC WILD-TYPE      90        1       32       136        10         0
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CUTC MUTATED           0          1          0          0        0         0
  CUTC WILD-TYPE        24         10         59         42       48        18
                vv
clus             STAGE IVB
  CUTC MUTATED           0
  CUTC WILD-TYPE         1
D2178V4, multiclass
            clus
vv           CUTC MUTATED CUTC WILD-TYPE
  STAGE I               1             90
  STAGE IA              0              1
  STAGE II              0             32
  STAGE IIA             2            136
  STAGE IIB             0             10
  STAGE IIC             1              0
  STAGE III             0             24
  STAGE IIIA            1             10
  STAGE IIIB            0             59
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  CUTC MUTATED     0   2   2   1
  CUTC WILD-TYPE  17  90 327  49
D2178V5, multiclass
    clus
vv   CUTC MUTATED CUTC WILD-TYPE
  T1            0             17
  T2            2             90
  T3            2            327
  T4            1             49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  CUTC MUTATED     4   1   0
  CUTC WILD-TYPE 283 112  87
D2178V6, multiclass
    clus
vv   CUTC MUTATED CUTC WILD-TYPE
  N0            4            283
  N1            1            112
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2178V7, binary
                cls
clus               0   1
  CUTC MUTATED     5   0
  CUTC WILD-TYPE 370  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  CUTC MUTATED      5    0
  CUTC WILD-TYPE  370   65
   clus
vv  CUTC MUTATED CUTC WILD-TYPE
  0            5            370
  1            0             65
[1] 2 2
[1] FALSE
D2178V8, binary
                cls
clus               0   1
  CUTC MUTATED     3   2
  CUTC WILD-TYPE 222 262
[1] "tbl2"
                cls
clus             [,1] [,2]
  CUTC MUTATED      3    2
  CUTC WILD-TYPE  222  262
        clus
vv       CUTC MUTATED CUTC WILD-TYPE
  FEMALE            3            222
  MALE              2            262
[1] 2 2
[1] FALSE
D2178V9, binary
                cls
clus               0   1
  CUTC MUTATED     4   0
  CUTC WILD-TYPE 346  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  CUTC MUTATED      4    0
  CUTC WILD-TYPE  346   22
     clus
vv    CUTC MUTATED CUTC WILD-TYPE
  NO             4            346
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CUTC MUTATED                      5                             0
  CUTC WILD-TYPE                  310                            47
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CUTC MUTATED                       0                              0
  CUTC WILD-TYPE                   106                             10
D2178V10, multiclass
                                clus
vv                               CUTC MUTATED CUTC WILD-TYPE
  COLON ADENOCARCINOMA                      5            310
  COLON MUCINOUS ADENOCARCINOMA             0             47
  RECTAL ADENOCARCINOMA                     0            106
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  CUTC MUTATED     3   0   0   0
  CUTC WILD-TYPE 342   4  31  25
D2178V11, multiclass
    clus
vv   CUTC MUTATED CUTC WILD-TYPE
  R0            3            342
  R1            0              4
  R2            0             31
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2178V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CUTC MUTATED                                  0     0
  CUTC WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  CUTC MUTATED                           0     4
  CUTC WILD-TYPE                        22   222
D2178V13, multiclass
                                  clus
vv                                 CUTC MUTATED CUTC WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       4            222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2179) Variable = CAPS2 MUTATION ANALYSIS
D2179V1, survival
                 sevent
clus2               0   1
  CAPS2 MUTATED    10   2
  CAPS2 WILD-TYPE 368  91
  CAPS2 MUTATED CAPS2 WILD-TYPE 
             12             459 
  CAPS2 MUTATED CAPS2 WILD-TYPE 
              2              91 
$`CAPS2 MUTATED`
TCGA-A6-5665 TCGA-A6-5666 TCGA-AA-3492 TCGA-AZ-4315 TCGA-CA-6718 TCGA-CK-5914 
       22.06        32.71         3.02        58.39        10.06         9.99 
TCGA-CM-4743 TCGA-CM-5341 TCGA-D5-6540 TCGA-DM-A1HB TCGA-G4-6586 TCGA-AF-6655 
       23.05        29.06        16.14       135.65        35.80        20.02 

$`CAPS2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       22.09        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       19.66        20.28         7.04         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 
       51.32        21.14        82.95         1.91       124.27        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       37.02        25.02        13.02        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
        4.80        17.13        12.49        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 
       12.59       140.38         7.50        44.32       131.51       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6672 
       34.49        10.39        14.50        16.83        15.39        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  CAPS2 MUTATED CAPS2 WILD-TYPE 
           3.02            0.00 
  CAPS2 MUTATED CAPS2 WILD-TYPE 
         135.65          148.01 
  CAPS2 MUTATED CAPS2 WILD-TYPE 
         22.555          20.120 
[1] "3.0 - 135.7 (22.6)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.3"
D2179V2, continuous
D2179V3, binary
                 cls
clus                0   1
  CAPS2 MUTATED    11   1
  CAPS2 WILD-TYPE 355 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CAPS2 MUTATED     11    1
  CAPS2 WILD-TYPE  355  118
        clus
vv       CAPS2 MUTATED CAPS2 WILD-TYPE
  COLON             11             355
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CAPS2 MUTATED         1        0        1         5         0         1
  CAPS2 WILD-TYPE      90        1       31       133        10         0
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CAPS2 MUTATED           0          2          2          0        0         0
  CAPS2 WILD-TYPE        24          9         57         42       48        18
                 vv
clus              STAGE IVB
  CAPS2 MUTATED           0
  CAPS2 WILD-TYPE         1
D2179V4, multiclass
            clus
vv           CAPS2 MUTATED CAPS2 WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              5             133
  STAGE IIB              0              10
  STAGE IIC              1               0
  STAGE III              0              24
  STAGE IIIA             2               9
  STAGE IIIB             2              57
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CAPS2 MUTATED     0   3   8   1
  CAPS2 WILD-TYPE  17  89 321  49
D2179V5, multiclass
    clus
vv   CAPS2 MUTATED CAPS2 WILD-TYPE
  T1             0              17
  T2             3              89
  T3             8             321
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  CAPS2 MUTATED     8   4   0
  CAPS2 WILD-TYPE 279 109  87
D2179V6, multiclass
    clus
vv   CAPS2 MUTATED CAPS2 WILD-TYPE
  N0             8             279
  N1             4             109
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2179V7, binary
                 cls
clus                0   1
  CAPS2 MUTATED    11   0
  CAPS2 WILD-TYPE 364  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CAPS2 MUTATED     11    0
  CAPS2 WILD-TYPE  364   65
   clus
vv  CAPS2 MUTATED CAPS2 WILD-TYPE
  0            11             364
  1             0              65
[1] 2 2
[1] FALSE
D2179V8, binary
                 cls
clus                0   1
  CAPS2 MUTATED     4   8
  CAPS2 WILD-TYPE 221 256
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CAPS2 MUTATED      4    8
  CAPS2 WILD-TYPE  221  256
        clus
vv       CAPS2 MUTATED CAPS2 WILD-TYPE
  FEMALE             4             221
  MALE               8             256
[1] 2 2
[1] FALSE
D2179V9, binary
                 cls
clus                0   1
  CAPS2 MUTATED    10   0
  CAPS2 WILD-TYPE 340  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CAPS2 MUTATED     10    0
  CAPS2 WILD-TYPE  340   22
     clus
vv    CAPS2 MUTATED CAPS2 WILD-TYPE
  NO             10             340
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CAPS2 MUTATED                      9                             1
  CAPS2 WILD-TYPE                  306                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CAPS2 MUTATED                       1                              0
  CAPS2 WILD-TYPE                   105                             10
D2179V10, multiclass
                                clus
vv                               CAPS2 MUTATED CAPS2 WILD-TYPE
  COLON ADENOCARCINOMA                       9             306
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  CAPS2 MUTATED     8   0   0   2
  CAPS2 WILD-TYPE 337   4  31  23
D2179V11, multiclass
    clus
vv   CAPS2 MUTATED CAPS2 WILD-TYPE
  R0             8             337
  R1             0               4
  R2             0              31
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2179V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CAPS2 MUTATED                                  0     1
  CAPS2 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CAPS2 MUTATED                           0    10
  CAPS2 WILD-TYPE                        22   216
D2179V13, multiclass
                                  clus
vv                                 CAPS2 MUTATED CAPS2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                       10             216
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2180) Variable = ESYT1 MUTATION ANALYSIS
D2180V1, survival
                 sevent
clus2               0   1
  ESYT1 MUTATED     7   2
  ESYT1 WILD-TYPE 371  91
  ESYT1 MUTATED ESYT1 WILD-TYPE 
              9             462 
  ESYT1 MUTATED ESYT1 WILD-TYPE 
              2              91 
$`ESYT1 MUTATED`
TCGA-A6-6653 TCGA-A6-6780 TCGA-AA-3864 TCGA-AD-6965 TCGA-AY-5543 TCGA-CK-5913 
       24.39        20.12        53.00         0.20        33.01        51.32 
TCGA-DM-A1DA TCGA-F4-6809 TCGA-AH-6643 
        7.50        13.25         0.69 

$`ESYT1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
       25.08        25.18        24.16        21.76        24.69        23.87 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 
        0.99        31.07        31.07        30.05        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6197 TCGA-AY-6386 
       14.50        27.09        16.31         0.95        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB 
       92.75        49.91        13.32        12.59       140.38        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       16.24        33.67         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6644 
       38.04       117.11        38.56         1.45        17.49         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  ESYT1 MUTATED ESYT1 WILD-TYPE 
            0.2             0.0 
  ESYT1 MUTATED ESYT1 WILD-TYPE 
          53.00          148.01 
  ESYT1 MUTATED ESYT1 WILD-TYPE 
         20.120          20.235 
[1] "0.2 - 53.0 (20.1)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.2"
D2180V2, continuous
D2180V3, binary
                 cls
clus                0   1
  ESYT1 MUTATED     9   1
  ESYT1 WILD-TYPE 357 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ESYT1 MUTATED      9    1
  ESYT1 WILD-TYPE  357  118
        clus
vv       ESYT1 MUTATED ESYT1 WILD-TYPE
  COLON              9             357
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ESYT1 MUTATED         1        0        1         2         1         0
  ESYT1 WILD-TYPE      90        1       31       136         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ESYT1 MUTATED           0          0          0          2        0         2
  ESYT1 WILD-TYPE        24         11         59         40       48        16
                 vv
clus              STAGE IVB
  ESYT1 MUTATED           0
  ESYT1 WILD-TYPE         1
D2180V4, multiclass
            clus
vv           ESYT1 MUTATED ESYT1 WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              2             136
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             2              40
  STAGE IV               0              48
  STAGE IVA              2              16
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ESYT1 MUTATED     0   1   7   2
  ESYT1 WILD-TYPE  17  91 322  48
D2180V5, multiclass
    clus
vv   ESYT1 MUTATED ESYT1 WILD-TYPE
  T1             0              17
  T2             1              91
  T3             7             322
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  ESYT1 MUTATED     5   2   3
  ESYT1 WILD-TYPE 282 111  84
D2180V6, multiclass
    clus
vv   ESYT1 MUTATED ESYT1 WILD-TYPE
  N0             5             282
  N1             2             111
  N2             3              84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2180V7, binary
                 cls
clus                0   1
  ESYT1 MUTATED     4   2
  ESYT1 WILD-TYPE 371  63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ESYT1 MUTATED      4    2
  ESYT1 WILD-TYPE  371   63
   clus
vv  ESYT1 MUTATED ESYT1 WILD-TYPE
  0             4             371
  1             2              63
[1] 2 2
[1] FALSE
D2180V8, binary
                 cls
clus                0   1
  ESYT1 MUTATED     5   5
  ESYT1 WILD-TYPE 220 259
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ESYT1 MUTATED      5    5
  ESYT1 WILD-TYPE  220  259
        clus
vv       ESYT1 MUTATED ESYT1 WILD-TYPE
  FEMALE             5             220
  MALE               5             259
[1] 2 2
[1] FALSE
D2180V9, binary
                 cls
clus                0   1
  ESYT1 MUTATED     6   0
  ESYT1 WILD-TYPE 344  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ESYT1 MUTATED      6    0
  ESYT1 WILD-TYPE  344   22
     clus
vv    ESYT1 MUTATED ESYT1 WILD-TYPE
  NO              6             344
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ESYT1 MUTATED                      8                             1
  ESYT1 WILD-TYPE                  307                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ESYT1 MUTATED                       1                              0
  ESYT1 WILD-TYPE                   105                             10
D2180V10, multiclass
                                clus
vv                               ESYT1 MUTATED ESYT1 WILD-TYPE
  COLON ADENOCARCINOMA                       8             307
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  ESYT1 MUTATED     4   0   0   2
  ESYT1 WILD-TYPE 341   4  31  23
D2180V11, multiclass
    clus
vv   ESYT1 MUTATED ESYT1 WILD-TYPE
  R0             4             341
  R1             0               4
  R2             0              31
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2180V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ESYT1 MUTATED                                  0     0
  ESYT1 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ESYT1 MUTATED                           1     8
  ESYT1 WILD-TYPE                        21   218
D2180V13, multiclass
                                  clus
vv                                 ESYT1 MUTATED ESYT1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        8             218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2181) Variable = KRT1 MUTATION ANALYSIS
D2181V1, survival
                sevent
clus2              0   1
  KRT1 MUTATED     9   6
  KRT1 WILD-TYPE 369  87
  KRT1 MUTATED KRT1 WILD-TYPE 
            15            456 
  KRT1 MUTATED KRT1 WILD-TYPE 
             6             87 
$`KRT1 MUTATED`
TCGA-A6-3808 TCGA-AA-A00N TCGA-AA-A010 TCGA-AZ-4315 TCGA-AZ-5407 TCGA-AZ-6599 
       33.34         4.01        34.98        58.39        88.21         6.77 
TCGA-AZ-6603 TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-6169 TCGA-D5-6533 TCGA-DM-A0XD 
       29.56        12.76        10.06        13.02         1.32        24.43 
TCGA-F4-6570 TCGA-G4-6628 TCGA-AG-A002 
        6.18        79.69        20.98 

$`KRT1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6606 
       62.79        49.41        12.10       100.01         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.07        12.20        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       12.99        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XF TCGA-DM-A1D0 
       12.00        11.38        10.26       119.70        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       31.96        35.74        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 
       35.80        26.17        91.79        46.75        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  KRT1 MUTATED KRT1 WILD-TYPE 
          1.32           0.00 
  KRT1 MUTATED KRT1 WILD-TYPE 
         88.21         148.01 
  KRT1 MUTATED KRT1 WILD-TYPE 
        20.980         20.155 
[1] "1.3 - 88.2 (21.0)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "2"  
D2181V2, continuous
D2181V3, binary
                cls
clus               0   1
  KRT1 MUTATED    14   1
  KRT1 WILD-TYPE 352 118
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRT1 MUTATED     14    1
  KRT1 WILD-TYPE  352  118
        clus
vv       KRT1 MUTATED KRT1 WILD-TYPE
  COLON            14            352
  RECTUM            1            118
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KRT1 MUTATED         4        0        0         7         2         0
  KRT1 WILD-TYPE      87        1       32       131         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  KRT1 MUTATED           0          0          1          0        0         0
  KRT1 WILD-TYPE        24         11         58         42       48        18
                vv
clus             STAGE IVB
  KRT1 MUTATED           0
  KRT1 WILD-TYPE         1
D2181V4, multiclass
            clus
vv           KRT1 MUTATED KRT1 WILD-TYPE
  STAGE I               4             87
  STAGE IA              0              1
  STAGE II              0             32
  STAGE IIA             7            131
  STAGE IIB             2              8
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            1             58
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  KRT1 MUTATED     1   4   7   3
  KRT1 WILD-TYPE  16  88 322  47
D2181V5, multiclass
    clus
vv   KRT1 MUTATED KRT1 WILD-TYPE
  T1            1             16
  T2            4             88
  T3            7            322
  T4            3             47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  KRT1 MUTATED    14   1   0
  KRT1 WILD-TYPE 273 112  87
D2181V6, multiclass
    clus
vv   KRT1 MUTATED KRT1 WILD-TYPE
  N0           14            273
  N1            1            112
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2181V7, binary
                cls
clus               0   1
  KRT1 MUTATED    13   0
  KRT1 WILD-TYPE 362  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRT1 MUTATED     13    0
  KRT1 WILD-TYPE  362   65
   clus
vv  KRT1 MUTATED KRT1 WILD-TYPE
  0           13            362
  1            0             65
[1] 2 2
[1] FALSE
D2181V8, binary
                cls
clus               0   1
  KRT1 MUTATED     5  10
  KRT1 WILD-TYPE 220 254
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRT1 MUTATED      5   10
  KRT1 WILD-TYPE  220  254
        clus
vv       KRT1 MUTATED KRT1 WILD-TYPE
  FEMALE            5            220
  MALE             10            254
[1] 2 2
[1] FALSE
D2181V9, binary
                cls
clus               0   1
  KRT1 MUTATED    12   0
  KRT1 WILD-TYPE 338  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRT1 MUTATED     12    0
  KRT1 WILD-TYPE  338   22
     clus
vv    KRT1 MUTATED KRT1 WILD-TYPE
  NO            12            338
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  KRT1 MUTATED                     12                             2
  KRT1 WILD-TYPE                  303                            45
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  KRT1 MUTATED                       1                              0
  KRT1 WILD-TYPE                   105                             10
D2181V10, multiclass
                                clus
vv                               KRT1 MUTATED KRT1 WILD-TYPE
  COLON ADENOCARCINOMA                     12            303
  COLON MUCINOUS ADENOCARCINOMA             2             45
  RECTAL ADENOCARCINOMA                     1            105
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  KRT1 MUTATED     9   0   0   2
  KRT1 WILD-TYPE 336   4  31  23
D2181V11, multiclass
    clus
vv   KRT1 MUTATED KRT1 WILD-TYPE
  R0            9            336
  R1            0              4
  R2            0             31
  RX            2             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2181V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KRT1 MUTATED                                  0     2
  KRT1 WILD-TYPE                                1     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  KRT1 MUTATED                           1     9
  KRT1 WILD-TYPE                        21   217
D2181V13, multiclass
                                  clus
vv                                 KRT1 MUTATED KRT1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              9
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                       9            217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2182) Variable = SUPT6H MUTATION ANALYSIS
D2182V1, survival
                  sevent
clus2                0   1
  SUPT6H MUTATED    16   5
  SUPT6H WILD-TYPE 362  88
  SUPT6H MUTATED SUPT6H WILD-TYPE 
              21              450 
  SUPT6H MUTATED SUPT6H WILD-TYPE 
               5               88 
$`SUPT6H MUTATED`
TCGA-A6-5665 TCGA-A6-6653 TCGA-AA-3516 TCGA-AA-3524 TCGA-AA-3542 TCGA-AA-3663 
       22.06        24.39        13.02        36.03        12.99         6.97 
TCGA-AA-3833 TCGA-AA-3864 TCGA-AA-3950 TCGA-AA-A00N TCGA-AA-A01P TCGA-AA-A01Q 
       15.95        53.00        24.00         4.01        38.07         1.02 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AD-6889 TCGA-CM-6678 TCGA-CM-6680 TCGA-G4-6588 
        5.03        14.01        56.55        11.01        12.03        26.17 
TCGA-AG-A002 TCGA-EI-6506 TCGA-F5-6811 
       20.98        20.55        32.19 

$`SUPT6H WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 
       25.18        24.16        21.76        24.69        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
       63.98         6.97         1.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       24.03        37.05         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3543 TCGA-AA-3544 
       34.03        29.00        29.00        26.01         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
       78.08         6.05        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
        1.02        17.98        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 
       32.05         0.99        31.07        31.07        30.05        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 
       12.99        24.00        33.01        26.01         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02O TCGA-AA-A02W 
       39.06        51.98        39.98         2.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6679 TCGA-D5-5537 TCGA-D5-5538 
       13.05        11.08        11.08        10.06        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       22.09        13.78        35.80        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
        0.49        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       31.30        28.57         0.66         0.69        55.76        26.43 

  SUPT6H MUTATED SUPT6H WILD-TYPE 
            1.02             0.00 
  SUPT6H MUTATED SUPT6H WILD-TYPE 
           56.55           148.01 
  SUPT6H MUTATED SUPT6H WILD-TYPE 
          20.550           20.155 
[1] "1.0 - 56.5 (20.6)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.5"
D2182V2, continuous
D2182V3, binary
                  cls
clus                 0   1
  SUPT6H MUTATED    19   4
  SUPT6H WILD-TYPE 347 115
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SUPT6H MUTATED     19    4
  SUPT6H WILD-TYPE  347  115
        clus
vv       SUPT6H MUTATED SUPT6H WILD-TYPE
  COLON              19              347
  RECTUM              4              115
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SUPT6H MUTATED         2        0        4         7         2         0
  SUPT6H WILD-TYPE      89        1       28       131         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SUPT6H MUTATED           2          0          2          1        2
  SUPT6H WILD-TYPE        22         11         57         41       46
                  vv
clus               STAGE IVA STAGE IVB
  SUPT6H MUTATED           1         0
  SUPT6H WILD-TYPE        17         1
D2182V4, multiclass
            clus
vv           SUPT6H MUTATED SUPT6H WILD-TYPE
  STAGE I                 2               89
  STAGE IA                0                1
  STAGE II                4               28
  STAGE IIA               7              131
  STAGE IIB               2                8
  STAGE IIC               0                1
  STAGE III               2               22
  STAGE IIIA              0               11
  STAGE IIIB              2               57
  STAGE IIIC              1               41
  STAGE IV                2               46
  STAGE IVA               1               17
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  SUPT6H MUTATED     0   2  16   5
  SUPT6H WILD-TYPE  17  90 313  45
D2182V5, multiclass
    clus
vv   SUPT6H MUTATED SUPT6H WILD-TYPE
  T1              0               17
  T2              2               90
  T3             16              313
  T4              5               45
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  SUPT6H MUTATED    16   3   4
  SUPT6H WILD-TYPE 271 110  83
D2182V6, multiclass
    clus
vv   SUPT6H MUTATED SUPT6H WILD-TYPE
  N0             16              271
  N1              3              110
  N2              4               83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2182V7, binary
                  cls
clus                 0   1
  SUPT6H MUTATED    19   3
  SUPT6H WILD-TYPE 356  62
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SUPT6H MUTATED     19    3
  SUPT6H WILD-TYPE  356   62
   clus
vv  SUPT6H MUTATED SUPT6H WILD-TYPE
  0             19              356
  1              3               62
[1] 2 2
[1] FALSE
D2182V8, binary
                  cls
clus                 0   1
  SUPT6H MUTATED    13  10
  SUPT6H WILD-TYPE 212 254
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SUPT6H MUTATED     13   10
  SUPT6H WILD-TYPE  212  254
        clus
vv       SUPT6H MUTATED SUPT6H WILD-TYPE
  FEMALE             13              212
  MALE               10              254
[1] 2 2
[1] FALSE
D2182V9, binary
                  cls
clus                 0   1
  SUPT6H MUTATED    17   0
  SUPT6H WILD-TYPE 333  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SUPT6H MUTATED     17    0
  SUPT6H WILD-TYPE  333   22
     clus
vv    SUPT6H MUTATED SUPT6H WILD-TYPE
  NO              17              333
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SUPT6H MUTATED                     16                             3
  SUPT6H WILD-TYPE                  299                            44
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SUPT6H MUTATED                       4                              0
  SUPT6H WILD-TYPE                   102                             10
D2182V10, multiclass
                                clus
vv                               SUPT6H MUTATED SUPT6H WILD-TYPE
  COLON ADENOCARCINOMA                       16              299
  COLON MUCINOUS ADENOCARCINOMA               3               44
  RECTAL ADENOCARCINOMA                       4              102
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  SUPT6H MUTATED    15   0   3   1
  SUPT6H WILD-TYPE 330   4  28  24
D2182V11, multiclass
    clus
vv   SUPT6H MUTATED SUPT6H WILD-TYPE
  R0             15              330
  R1              0                4
  R2              3               28
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2182V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SUPT6H MUTATED                                  0     1
  SUPT6H WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  SUPT6H MUTATED                           0     8
  SUPT6H WILD-TYPE                        22   218
D2182V13, multiclass
                                  clus
vv                                 SUPT6H MUTATED SUPT6H WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         8              218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2183) Variable = IGJ MUTATION ANALYSIS
D2183V1, survival
               sevent
clus2             0   1
  IGJ MUTATED     2   2
  IGJ WILD-TYPE 376  91
  IGJ MUTATED IGJ WILD-TYPE 
            4           467 
  IGJ MUTATED IGJ WILD-TYPE 
            2            91 
$`IGJ MUTATED`
TCGA-AA-3510 TCGA-AA-A00N TCGA-CA-6718 TCGA-AG-A002 
       63.98         4.01        10.06        20.98 

$`IGJ WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.20        12.76        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  IGJ MUTATED IGJ WILD-TYPE 
         4.01          0.00 
  IGJ MUTATED IGJ WILD-TYPE 
        63.98        148.01 
  IGJ MUTATED IGJ WILD-TYPE 
        15.52         20.19 
[1] "4.0 - 64.0 (15.5)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "2.5"
D2183V2, continuous
D2183V3, binary
               cls
clus              0   1
  IGJ MUTATED     3   1
  IGJ WILD-TYPE 363 118
[1] "tbl2"
               cls
clus            [,1] [,2]
  IGJ MUTATED      3    1
  IGJ WILD-TYPE  363  118
        clus
vv       IGJ MUTATED IGJ WILD-TYPE
  COLON            3           363
  RECTUM           1           118
[1] 2 2
[1] FALSE
               vv
clus            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  IGJ MUTATED         1        0        1         1         1         0
  IGJ WILD-TYPE      90        1       31       137         9         1
               vv
clus            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  IGJ MUTATED           0          0          0          0        0         0
  IGJ WILD-TYPE        24         11         59         42       48        18
               vv
clus            STAGE IVB
  IGJ MUTATED           0
  IGJ WILD-TYPE         1
D2183V4, multiclass
            clus
vv           IGJ MUTATED IGJ WILD-TYPE
  STAGE I              1            90
  STAGE IA             0             1
  STAGE II             1            31
  STAGE IIA            1           137
  STAGE IIB            1             9
  STAGE IIC            0             1
  STAGE III            0            24
  STAGE IIIA           0            11
  STAGE IIIB           0            59
  STAGE IIIC           0            42
  STAGE IV             0            48
  STAGE IVA            0            18
  STAGE IVB            0             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  IGJ MUTATED     0   1   2   1
  IGJ WILD-TYPE  17  91 327  49
D2183V5, multiclass
    clus
vv   IGJ MUTATED IGJ WILD-TYPE
  T1           0            17
  T2           1            91
  T3           2           327
  T4           1            49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2
  IGJ MUTATED     4   0   0
  IGJ WILD-TYPE 283 113  87
D2183V6, multiclass
    clus
vv   IGJ MUTATED IGJ WILD-TYPE
  N0           4           283
  N1           0           113
  N2           0            87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2183V7, binary
               cls
clus              0   1
  IGJ MUTATED     4   0
  IGJ WILD-TYPE 371  65
[1] "tbl2"
               cls
clus            [,1] [,2]
  IGJ MUTATED      4    0
  IGJ WILD-TYPE  371   65
   clus
vv  IGJ MUTATED IGJ WILD-TYPE
  0           4           371
  1           0            65
[1] 2 2
[1] FALSE
D2183V8, binary
               cls
clus              0   1
  IGJ MUTATED     0   4
  IGJ WILD-TYPE 225 260
[1] "tbl2"
               cls
clus            [,1] [,2]
  IGJ MUTATED      0    4
  IGJ WILD-TYPE  225  260
        clus
vv       IGJ MUTATED IGJ WILD-TYPE
  FEMALE           0           225
  MALE             4           260
[1] 2 2
[1] FALSE
D2183V9, binary
               cls
clus              0   1
  IGJ MUTATED     3   0
  IGJ WILD-TYPE 347  22
[1] "tbl2"
               cls
clus            [,1] [,2]
  IGJ MUTATED      3    0
  IGJ WILD-TYPE  347   22
     clus
vv    IGJ MUTATED IGJ WILD-TYPE
  NO            3           347
  YES           0            22
[1] 2 2
[1] FALSE
               vv
clus            COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  IGJ MUTATED                      2                             1
  IGJ WILD-TYPE                  313                            46
               vv
clus            RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  IGJ MUTATED                       1                              0
  IGJ WILD-TYPE                   105                             10
D2183V10, multiclass
                                clus
vv                               IGJ MUTATED IGJ WILD-TYPE
  COLON ADENOCARCINOMA                     2           313
  COLON MUCINOUS ADENOCARCINOMA            1            46
  RECTAL ADENOCARCINOMA                    1           105
  RECTAL MUCINOUS ADENOCARCINOMA           0            10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             R0  R1  R2  RX
  IGJ MUTATED     3   0   0   1
  IGJ WILD-TYPE 342   4  31  24
D2183V11, multiclass
    clus
vv   IGJ MUTATED IGJ WILD-TYPE
  R0           3           342
  R1           0             4
  R2           0            31
  RX           1            24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2183V12, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  IGJ MUTATED                                  0     1
  IGJ WILD-TYPE                                1    10
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  IGJ MUTATED                           0     0
  IGJ WILD-TYPE                        22   226
D2183V13, multiclass
[1] "Remove cluster labels:" "IGJ MUTATED"           
clus
  IGJ MUTATED IGJ WILD-TYPE 
            1           259 
   TCGA-A6-2671    TCGA-A6-2672    TCGA-A6-2674    TCGA-A6-2676    TCGA-A6-2677 
"IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" 
   TCGA-A6-2678    TCGA-A6-2683    TCGA-A6-3807    TCGA-A6-3808    TCGA-A6-3809 
"IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" 
   TCGA-A6-3810    TCGA-A6-4105    TCGA-A6-5656    TCGA-A6-5657    TCGA-A6-5659 
"IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" 
   TCGA-A6-5660    TCGA-A6-5661    TCGA-A6-5662    TCGA-A6-5664    TCGA-A6-5665 
"IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" 
   TCGA-A6-5666    TCGA-A6-6137    TCGA-A6-6138    TCGA-A6-6141    TCGA-A6-6142 
"IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" 
   TCGA-A6-6648    TCGA-A6-6649    TCGA-A6-6651    TCGA-A6-6652    TCGA-A6-6653 
"IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" 
   TCGA-A6-6654    TCGA-A6-6780    TCGA-A6-6781    TCGA-A6-6782    TCGA-AD-5900 
"IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" 
   TCGA-AD-6548    TCGA-AD-6888    TCGA-AD-6889    TCGA-AD-6890    TCGA-AD-6895 
"IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" 
   TCGA-AD-6899    TCGA-AD-6901    TCGA-AD-6963    TCGA-AD-6964    TCGA-AD-6965 
"IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" 
   TCGA-AU-3779    TCGA-AU-6004    TCGA-AY-4070    TCGA-AY-4071    TCGA-AY-5543 
"IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" 
   TCGA-AY-6196    TCGA-AY-6197    TCGA-AY-6386    TCGA-AZ-4315    TCGA-AZ-4323 
"IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" 
   TCGA-AZ-4616    TCGA-AZ-4681    TCGA-AZ-4682    TCGA-AZ-5403    TCGA-AZ-5407 
"IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" 
   TCGA-AZ-6598    TCGA-AZ-6599    TCGA-AZ-6600    TCGA-AZ-6601    TCGA-AZ-6603 
"IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" 
   TCGA-AZ-6605    TCGA-AZ-6606    TCGA-AZ-6607    TCGA-AZ-6608    TCGA-CA-5254 
"IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" 
   TCGA-CA-5255    TCGA-CA-5796    TCGA-CA-5797    TCGA-CA-6715    TCGA-CA-6716 
"IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" 
   TCGA-CA-6717    TCGA-CA-6719    TCGA-CK-4947    TCGA-CK-4948    TCGA-CK-4950 
"IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" 
   TCGA-CK-4952    TCGA-CK-5912    TCGA-CK-5913    TCGA-CK-5914    TCGA-CK-5915 
"IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" 
   TCGA-CK-5916    TCGA-CK-6746    TCGA-CK-6747    TCGA-CK-6748    TCGA-CK-6751 
"IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" 
   TCGA-CM-4743    TCGA-CM-4744    TCGA-CM-4746    TCGA-CM-4747    TCGA-CM-4752 
"IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" 
   TCGA-CM-5341    TCGA-CM-5344    TCGA-CM-5348    TCGA-CM-5349    TCGA-CM-5860 
"IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" 
   TCGA-CM-5861    TCGA-CM-5862    TCGA-CM-5863    TCGA-CM-5864    TCGA-CM-5868 
"IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" 
   TCGA-CM-6161    TCGA-CM-6162    TCGA-CM-6163    TCGA-CM-6164    TCGA-CM-6165 
"IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" 
   TCGA-CM-6166    TCGA-CM-6167    TCGA-CM-6168    TCGA-CM-6169    TCGA-CM-6170 
"IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" 
   TCGA-CM-6171    TCGA-CM-6172    TCGA-CM-6674    TCGA-CM-6675    TCGA-CM-6676 
"IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" 
   TCGA-CM-6677    TCGA-CM-6678    TCGA-CM-6679    TCGA-CM-6680    TCGA-D5-5537 
"IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" 
   TCGA-D5-5538    TCGA-D5-5539    TCGA-D5-5540    TCGA-D5-5541    TCGA-D5-6529 
"IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" 
   TCGA-D5-6532    TCGA-D5-6533    TCGA-D5-6534    TCGA-D5-6535    TCGA-D5-6536 
"IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" 
   TCGA-D5-6537    TCGA-D5-6538    TCGA-D5-6539    TCGA-D5-6540    TCGA-D5-6541 
"IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" 
   TCGA-D5-6898    TCGA-D5-6920    TCGA-D5-6922    TCGA-D5-6923    TCGA-D5-6924 
"IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" 
   TCGA-D5-6926    TCGA-D5-6927    TCGA-D5-6928    TCGA-D5-6929    TCGA-D5-6930 
"IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" 
   TCGA-D5-6931    TCGA-D5-6932    TCGA-D5-7000    TCGA-DM-A0X9    TCGA-DM-A0XD 
"IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" 
   TCGA-DM-A0XF    TCGA-DM-A1D0    TCGA-DM-A1D4    TCGA-DM-A1D6    TCGA-DM-A1D7 
"IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" 
   TCGA-DM-A1D8    TCGA-DM-A1D9    TCGA-DM-A1DA    TCGA-DM-A1DB    TCGA-DM-A1HA 
"IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" 
   TCGA-DM-A1HB    TCGA-DM-A282    TCGA-DM-A285    TCGA-DM-A28C    TCGA-DM-A28E 
"IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" 
   TCGA-DM-A28F    TCGA-DM-A28G    TCGA-DM-A28H    TCGA-DM-A28K    TCGA-F4-6459 
"IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" 
   TCGA-F4-6460    TCGA-F4-6569    TCGA-F4-6570    TCGA-F4-6703    TCGA-F4-6704 
"IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" 
   TCGA-F4-6805    TCGA-F4-6806    TCGA-F4-6807    TCGA-F4-6808    TCGA-F4-6809 
"IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" 
   TCGA-F4-6854    TCGA-F4-6855    TCGA-F4-6856    TCGA-G4-6293    TCGA-G4-6299 
"IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" 
   TCGA-G4-6303    TCGA-G4-6304    TCGA-G4-6306    TCGA-G4-6307    TCGA-G4-6309 
"IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" 
   TCGA-G4-6310    TCGA-G4-6315    TCGA-G4-6317    TCGA-G4-6321    TCGA-G4-6323 
"IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" 
   TCGA-G4-6586    TCGA-G4-6588    TCGA-G4-6625    TCGA-G4-6626    TCGA-G4-6628 
"IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" 
   TCGA-AF-2687    TCGA-AF-2689    TCGA-AF-2691    TCGA-AF-2692    TCGA-AF-2693 
"IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" 
   TCGA-AF-3400    TCGA-AF-3913    TCGA-AF-4110    TCGA-AF-5654    TCGA-AF-6136 
"IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" 
   TCGA-AF-6655    TCGA-AF-6672    TCGA-AH-6544    TCGA-AH-6547    TCGA-AH-6549 
"IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" 
   TCGA-AH-6643    TCGA-AH-6644    TCGA-CI-6619    TCGA-CI-6620    TCGA-CI-6621 
"IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" 
   TCGA-CI-6622    TCGA-CI-6624    TCGA-CL-5917    TCGA-CL-5918    TCGA-DC-5337 
"IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" 
   TCGA-DC-5869    TCGA-DC-6155    TCGA-DC-6157    TCGA-DC-6158    TCGA-DC-6160 
"IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" 
   TCGA-DC-6681    TCGA-DC-6682    TCGA-DC-6683    TCGA-DT-5265    TCGA-DY-A0XA 
"IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" 
   TCGA-DY-A1DC    TCGA-DY-A1DD    TCGA-DY-A1DF    TCGA-DY-A1DG    TCGA-DY-A1H8 
"IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" 
   TCGA-EF-5830    TCGA-EI-6506    TCGA-EI-6507    TCGA-EI-6508    TCGA-EI-6510 
"IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" 
   TCGA-F5-6464    TCGA-F5-6465    TCGA-F5-6571    TCGA-F5-6702    TCGA-F5-6811 
"IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" 
   TCGA-F5-6812    TCGA-F5-6813    TCGA-G5-6235    TCGA-G5-6641 
"IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" "IGJ WILD-TYPE" 

Clustering(2184) Variable = TRAF3 MUTATION ANALYSIS
D2184V1, survival
                 sevent
clus2               0   1
  TRAF3 MUTATED     9   3
  TRAF3 WILD-TYPE 369  90
  TRAF3 MUTATED TRAF3 WILD-TYPE 
             12             459 
  TRAF3 MUTATED TRAF3 WILD-TYPE 
              3              90 
$`TRAF3 MUTATED`
TCGA-A6-5661 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-A01R 
       33.53        26.99        19.04        33.01        24.00        35.01 
TCGA-AD-5900 TCGA-AZ-5403 TCGA-CM-4746 TCGA-F4-6570 TCGA-AG-3892 TCGA-AG-A02X 
        0.07        62.79        37.02         6.18        13.02        41.00 

$`TRAF3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 
       36.00         5.03        85.05        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        26.01         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
        1.02         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 
        0.92        41.00        39.98        18.05        40.96        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
        5.13       106.75        22.36        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4747 
       82.95         1.91       124.27        23.05        20.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 
      117.07        98.24         8.61        31.96        35.74        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 
        1.02        17.95        36.95        17.03        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       38.96        61.97        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  TRAF3 MUTATED TRAF3 WILD-TYPE 
           0.07            0.00 
  TRAF3 MUTATED TRAF3 WILD-TYPE 
          62.79          148.01 
  TRAF3 MUTATED TRAF3 WILD-TYPE 
          30.00           20.05 
[1] "0.1 - 62.8 (30.0)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.2"
D2184V2, continuous
D2184V3, binary
                 cls
clus                0   1
  TRAF3 MUTATED    10   2
  TRAF3 WILD-TYPE 356 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRAF3 MUTATED     10    2
  TRAF3 WILD-TYPE  356  117
        clus
vv       TRAF3 MUTATED TRAF3 WILD-TYPE
  COLON             10             356
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TRAF3 MUTATED         4        0        2         4         1         0
  TRAF3 WILD-TYPE      87        1       30       134         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TRAF3 MUTATED           1          0          0          0        0         0
  TRAF3 WILD-TYPE        23         11         59         42       48        18
                 vv
clus              STAGE IVB
  TRAF3 MUTATED           0
  TRAF3 WILD-TYPE         1
D2184V4, multiclass
            clus
vv           TRAF3 MUTATED TRAF3 WILD-TYPE
  STAGE I                4              87
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA              4             134
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  TRAF3 MUTATED     1   3   7   1
  TRAF3 WILD-TYPE  16  89 322  49
D2184V5, multiclass
    clus
vv   TRAF3 MUTATED TRAF3 WILD-TYPE
  T1             1              16
  T2             3              89
  T3             7             322
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  TRAF3 MUTATED    11   0   1
  TRAF3 WILD-TYPE 276 113  86
D2184V6, multiclass
    clus
vv   TRAF3 MUTATED TRAF3 WILD-TYPE
  N0            11             276
  N1             0             113
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2184V7, binary
                 cls
clus                0   1
  TRAF3 MUTATED    10   0
  TRAF3 WILD-TYPE 365  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRAF3 MUTATED     10    0
  TRAF3 WILD-TYPE  365   65
   clus
vv  TRAF3 MUTATED TRAF3 WILD-TYPE
  0            10             365
  1             0              65
[1] 2 2
[1] FALSE
D2184V8, binary
                 cls
clus                0   1
  TRAF3 MUTATED     6   6
  TRAF3 WILD-TYPE 219 258
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRAF3 MUTATED      6    6
  TRAF3 WILD-TYPE  219  258
        clus
vv       TRAF3 MUTATED TRAF3 WILD-TYPE
  FEMALE             6             219
  MALE               6             258
[1] 2 2
[1] FALSE
D2184V9, binary
                 cls
clus                0   1
  TRAF3 MUTATED     9   1
  TRAF3 WILD-TYPE 341  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRAF3 MUTATED      9    1
  TRAF3 WILD-TYPE  341   21
     clus
vv    TRAF3 MUTATED TRAF3 WILD-TYPE
  NO              9             341
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  TRAF3 MUTATED                      6                             4
  TRAF3 WILD-TYPE                  309                            43
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  TRAF3 MUTATED                       2                              0
  TRAF3 WILD-TYPE                   104                             10
D2184V10, multiclass
                                clus
vv                               TRAF3 MUTATED TRAF3 WILD-TYPE
  COLON ADENOCARCINOMA                       6             309
  COLON MUCINOUS ADENOCARCINOMA              4              43
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  TRAF3 MUTATED    11   0   0   0
  TRAF3 WILD-TYPE 334   4  31  25
D2184V11, multiclass
    clus
vv   TRAF3 MUTATED TRAF3 WILD-TYPE
  R0            11             334
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2184V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TRAF3 MUTATED                                  0     0
  TRAF3 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  TRAF3 MUTATED                           2     3
  TRAF3 WILD-TYPE                        20   223
D2184V13, multiclass
                                  clus
vv                                 TRAF3 MUTATED TRAF3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    2              20
  WHITE                                        3             223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2185) Variable = IPO11 MUTATION ANALYSIS
D2185V1, survival
                 sevent
clus2               0   1
  IPO11 MUTATED    12   3
  IPO11 WILD-TYPE 366  90
  IPO11 MUTATED IPO11 WILD-TYPE 
             15             456 
  IPO11 MUTATED IPO11 WILD-TYPE 
              3              90 
$`IPO11 MUTATED`
TCGA-A6-3809 TCGA-AA-3660 TCGA-AA-3715 TCGA-AA-3977 TCGA-AA-A00N TCGA-AY-6197 
       32.75        78.08        19.04        25.02         4.01        21.44 
TCGA-CA-6717 TCGA-CM-6162 TCGA-DM-A1HA TCGA-G4-6303 TCGA-G4-6586 TCGA-AG-A002 
       12.76        12.00       131.51        65.85        35.80        20.98 
TCGA-CI-6624 TCGA-CL-5917 TCGA-DC-5337 
        4.73        78.12        15.02 

$`IPO11 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 
       19.99        13.94        19.99        61.02         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4315 
       27.09        16.31         0.95        33.01        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07        12.20        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       17.03        15.02         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HB 
       13.32        12.59       140.38         7.50        44.32       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       36.00        22.09        13.78        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CL-5918 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
        7.17         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  IPO11 MUTATED IPO11 WILD-TYPE 
           4.01            0.00 
  IPO11 MUTATED IPO11 WILD-TYPE 
         131.51          148.01 
  IPO11 MUTATED IPO11 WILD-TYPE 
         21.440          20.085 
[1] "4.0 - 131.5 (21.4)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.3"
D2185V2, continuous
D2185V3, binary
                 cls
clus                0   1
  IPO11 MUTATED    11   4
  IPO11 WILD-TYPE 355 115
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IPO11 MUTATED     11    4
  IPO11 WILD-TYPE  355  115
        clus
vv       IPO11 MUTATED IPO11 WILD-TYPE
  COLON             11             355
  RECTUM             4             115
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  IPO11 MUTATED         3        0        2         3         2         0
  IPO11 WILD-TYPE      88        1       30       135         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  IPO11 MUTATED           0          0          1          2        1         0
  IPO11 WILD-TYPE        24         11         58         40       47        18
                 vv
clus              STAGE IVB
  IPO11 MUTATED           0
  IPO11 WILD-TYPE         1
D2185V4, multiclass
            clus
vv           IPO11 MUTATED IPO11 WILD-TYPE
  STAGE I                3              88
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA              3             135
  STAGE IIB              2               8
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             2              40
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  IPO11 MUTATED     1   3   9   2
  IPO11 WILD-TYPE  16  89 320  48
D2185V5, multiclass
    clus
vv   IPO11 MUTATED IPO11 WILD-TYPE
  T1             1              16
  T2             3              89
  T3             9             320
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  IPO11 MUTATED    11   2   2
  IPO11 WILD-TYPE 276 111  85
D2185V6, multiclass
    clus
vv   IPO11 MUTATED IPO11 WILD-TYPE
  N0            11             276
  N1             2             111
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2185V7, binary
                 cls
clus                0   1
  IPO11 MUTATED    11   1
  IPO11 WILD-TYPE 364  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IPO11 MUTATED     11    1
  IPO11 WILD-TYPE  364   64
   clus
vv  IPO11 MUTATED IPO11 WILD-TYPE
  0            11             364
  1             1              64
[1] 2 2
[1] FALSE
D2185V8, binary
                 cls
clus                0   1
  IPO11 MUTATED     7   8
  IPO11 WILD-TYPE 218 256
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IPO11 MUTATED      7    8
  IPO11 WILD-TYPE  218  256
        clus
vv       IPO11 MUTATED IPO11 WILD-TYPE
  FEMALE             7             218
  MALE               8             256
[1] 2 2
[1] FALSE
D2185V9, binary
                 cls
clus                0   1
  IPO11 MUTATED    12   0
  IPO11 WILD-TYPE 338  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IPO11 MUTATED     12    0
  IPO11 WILD-TYPE  338   22
     clus
vv    IPO11 MUTATED IPO11 WILD-TYPE
  NO             12             338
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  IPO11 MUTATED                      7                             4
  IPO11 WILD-TYPE                  308                            43
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  IPO11 MUTATED                       4                              0
  IPO11 WILD-TYPE                   102                             10
D2185V10, multiclass
                                clus
vv                               IPO11 MUTATED IPO11 WILD-TYPE
  COLON ADENOCARCINOMA                       7             308
  COLON MUCINOUS ADENOCARCINOMA              4              43
  RECTAL ADENOCARCINOMA                      4             102
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  IPO11 MUTATED    10   0   0   2
  IPO11 WILD-TYPE 335   4  31  23
D2185V11, multiclass
    clus
vv   IPO11 MUTATED IPO11 WILD-TYPE
  R0            10             335
  R1             0               4
  R2             0              31
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2185V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  IPO11 MUTATED                                  0     1
  IPO11 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  IPO11 MUTATED                           0     9
  IPO11 WILD-TYPE                        22   217
D2185V13, multiclass
                                  clus
vv                                 IPO11 MUTATED IPO11 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        9             217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2186) Variable = AFF3 MUTATION ANALYSIS
D2186V1, survival
                sevent
clus2              0   1
  AFF3 MUTATED    20   5
  AFF3 WILD-TYPE 358  88
  AFF3 MUTATED AFF3 WILD-TYPE 
            25            446 
  AFF3 MUTATED AFF3 WILD-TYPE 
             5             88 
$`AFF3 MUTATED`
TCGA-A6-5662 TCGA-AA-3510 TCGA-AA-3821 TCGA-AA-3845 TCGA-AA-3864 TCGA-AA-3977 
       23.61        63.98         1.02         0.00        53.00        25.02 
TCGA-AA-A00J TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01P TCGA-AA-A02O TCGA-AA-A02Y 
       18.05         4.01        34.98        38.07         0.92        39.98 
TCGA-AD-5900 TCGA-AZ-4315 TCGA-AZ-6601 TCGA-CA-6717 TCGA-CM-5349 TCGA-CM-6168 
        0.07        58.39       100.01        12.76        30.08        12.99 
TCGA-D5-6930 TCGA-DM-A1DB TCGA-DM-A28H TCGA-G4-6309 TCGA-AG-4001 TCGA-AG-A036 
        1.51        44.32       117.07        85.48        36.03       117.11 
TCGA-F5-6465 
       49.51 

$`AFF3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        33.53        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       35.01         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 
       35.05        33.04         0.99        25.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       38.99        37.02        14.93        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       31.07        30.05        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       31.00         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02W TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 
        5.03        14.01        41.00        18.05        40.96        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        33.01        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
       12.10        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       29.06        22.03        22.98        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6169 TCGA-CM-6170 
       29.03        16.04        21.99        14.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 
        9.04         9.44        11.64         4.80        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HA 
       49.91        13.32        12.59       140.38         7.50       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
       60.79        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 
       65.85        53.62        44.68        55.04        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 
       38.96        61.97        41.00        38.04        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
        9.96        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  AFF3 MUTATED AFF3 WILD-TYPE 
             0              0 
  AFF3 MUTATED AFF3 WILD-TYPE 
        117.11         148.01 
  AFF3 MUTATED AFF3 WILD-TYPE 
         34.98          20.02 
[1] "0.0 - 117.1 (35.0)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.5"
D2186V2, continuous
D2186V3, binary
                cls
clus               0   1
  AFF3 MUTATED    22   3
  AFF3 WILD-TYPE 344 116
[1] "tbl2"
                cls
clus             [,1] [,2]
  AFF3 MUTATED     22    3
  AFF3 WILD-TYPE  344  116
        clus
vv       AFF3 MUTATED AFF3 WILD-TYPE
  COLON            22            344
  RECTUM            3            116
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  AFF3 MUTATED         3        0        4         9         2         0
  AFF3 WILD-TYPE      88        1       28       129         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  AFF3 MUTATED           2          0          2          1        0         1
  AFF3 WILD-TYPE        22         11         57         41       48        17
                vv
clus             STAGE IVB
  AFF3 MUTATED           0
  AFF3 WILD-TYPE         1
D2186V4, multiclass
            clus
vv           AFF3 MUTATED AFF3 WILD-TYPE
  STAGE I               3             88
  STAGE IA              0              1
  STAGE II              4             28
  STAGE IIA             9            129
  STAGE IIB             2              8
  STAGE IIC             0              1
  STAGE III             2             22
  STAGE IIIA            0             11
  STAGE IIIB            2             57
  STAGE IIIC            1             41
  STAGE IV              0             48
  STAGE IVA             1             17
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  AFF3 MUTATED     0   4  18   3
  AFF3 WILD-TYPE  17  88 311  47
D2186V5, multiclass
    clus
vv   AFF3 MUTATED AFF3 WILD-TYPE
  T1            0             17
  T2            4             88
  T3           18            311
  T4            3             47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  AFF3 MUTATED    19   3   3
  AFF3 WILD-TYPE 268 110  84
D2186V6, multiclass
    clus
vv   AFF3 MUTATED AFF3 WILD-TYPE
  N0           19            268
  N1            3            110
  N2            3             84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2186V7, binary
                cls
clus               0   1
  AFF3 MUTATED    22   1
  AFF3 WILD-TYPE 353  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  AFF3 MUTATED     22    1
  AFF3 WILD-TYPE  353   64
   clus
vv  AFF3 MUTATED AFF3 WILD-TYPE
  0           22            353
  1            1             64
[1] 2 2
[1] FALSE
D2186V8, binary
                cls
clus               0   1
  AFF3 MUTATED     9  16
  AFF3 WILD-TYPE 216 248
[1] "tbl2"
                cls
clus             [,1] [,2]
  AFF3 MUTATED      9   16
  AFF3 WILD-TYPE  216  248
        clus
vv       AFF3 MUTATED AFF3 WILD-TYPE
  FEMALE            9            216
  MALE             16            248
[1] 2 2
[1] FALSE
D2186V9, binary
                cls
clus               0   1
  AFF3 MUTATED    17   1
  AFF3 WILD-TYPE 333  21
[1] "tbl2"
                cls
clus             [,1] [,2]
  AFF3 MUTATED     17    1
  AFF3 WILD-TYPE  333   21
     clus
vv    AFF3 MUTATED AFF3 WILD-TYPE
  NO            17            333
  YES            1             21
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  AFF3 MUTATED                     16                             6
  AFF3 WILD-TYPE                  299                            41
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  AFF3 MUTATED                       3                              0
  AFF3 WILD-TYPE                   103                             10
D2186V10, multiclass
                                clus
vv                               AFF3 MUTATED AFF3 WILD-TYPE
  COLON ADENOCARCINOMA                     16            299
  COLON MUCINOUS ADENOCARCINOMA             6             41
  RECTAL ADENOCARCINOMA                     3            103
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  AFF3 MUTATED    19   0   0   1
  AFF3 WILD-TYPE 326   4  31  24
D2186V11, multiclass
    clus
vv   AFF3 MUTATED AFF3 WILD-TYPE
  R0           19            326
  R1            0              4
  R2            0             31
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2186V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AFF3 MUTATED                                  0     1
  AFF3 WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  AFF3 MUTATED                           2     9
  AFF3 WILD-TYPE                        20   217
D2186V13, multiclass
                                  clus
vv                                 AFF3 MUTATED AFF3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   2             20
  WHITE                                       9            217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2187) Variable = BTBD7 MUTATION ANALYSIS
D2187V1, survival
                 sevent
clus2               0   1
  BTBD7 MUTATED    10   1
  BTBD7 WILD-TYPE 368  92
  BTBD7 MUTATED BTBD7 WILD-TYPE 
             11             460 
  BTBD7 MUTATED BTBD7 WILD-TYPE 
              1              92 
$`BTBD7 MUTATED`
TCGA-A6-3810 TCGA-A6-5665 TCGA-A6-6780 TCGA-A6-6781 TCGA-AA-A00E TCGA-AA-A010 
       36.53        22.06        20.12        19.66        30.02        34.98 
TCGA-AA-A01Q TCGA-CM-6171 TCGA-CM-6675 TCGA-F4-6856 TCGA-G4-6626 
        1.02        14.04        13.05        35.31        46.75 

$`BTBD7 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        32.75        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6782 
       24.16        21.76        24.69        24.39        23.87        20.28 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
        7.04         3.02         1.02        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       26.99        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00F 
        7.96        27.02        13.94        38.04        19.00        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01R 
       32.02        12.00        31.00        31.00        38.07        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 
       21.99        14.99        12.99        13.02        15.02        11.01 
TCGA-CM-6674 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       12.95        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
       13.25         0.53        47.41       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  BTBD7 MUTATED BTBD7 WILD-TYPE 
           1.02            0.00 
  BTBD7 MUTATED BTBD7 WILD-TYPE 
          46.75          148.01 
  BTBD7 MUTATED BTBD7 WILD-TYPE 
          22.06           20.12 
[1] "1.0 - 46.8 (22.1)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "2"  
D2187V2, continuous
D2187V3, binary
                 cls
clus                0   1
  BTBD7 MUTATED    12   0
  BTBD7 WILD-TYPE 354 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BTBD7 MUTATED     12    0
  BTBD7 WILD-TYPE  354  119
        clus
vv       BTBD7 MUTATED BTBD7 WILD-TYPE
  COLON             12             354
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  BTBD7 MUTATED         2        0        1         6         1         0
  BTBD7 WILD-TYPE      89        1       31       132         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  BTBD7 MUTATED           0          0          0          1        0         0
  BTBD7 WILD-TYPE        24         11         59         41       48        18
                 vv
clus              STAGE IVB
  BTBD7 MUTATED           1
  BTBD7 WILD-TYPE         0
D2187V4, multiclass
            clus
vv           BTBD7 MUTATED BTBD7 WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              6             132
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             1              41
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              1               0
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  BTBD7 MUTATED     0   2   8   2
  BTBD7 WILD-TYPE  17  90 321  48
D2187V5, multiclass
    clus
vv   BTBD7 MUTATED BTBD7 WILD-TYPE
  T1             0              17
  T2             2              90
  T3             8             321
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  BTBD7 MUTATED    10   1   1
  BTBD7 WILD-TYPE 277 112  86
D2187V6, multiclass
    clus
vv   BTBD7 MUTATED BTBD7 WILD-TYPE
  N0            10             277
  N1             1             112
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2187V7, binary
                 cls
clus                0   1
  BTBD7 MUTATED     9   1
  BTBD7 WILD-TYPE 366  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BTBD7 MUTATED      9    1
  BTBD7 WILD-TYPE  366   64
   clus
vv  BTBD7 MUTATED BTBD7 WILD-TYPE
  0             9             366
  1             1              64
[1] 2 2
[1] FALSE
D2187V8, binary
                 cls
clus                0   1
  BTBD7 MUTATED     5   7
  BTBD7 WILD-TYPE 220 257
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BTBD7 MUTATED      5    7
  BTBD7 WILD-TYPE  220  257
        clus
vv       BTBD7 MUTATED BTBD7 WILD-TYPE
  FEMALE             5             220
  MALE               7             257
[1] 2 2
[1] FALSE
D2187V9, binary
                 cls
clus                0   1
  BTBD7 MUTATED    10   0
  BTBD7 WILD-TYPE 340  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BTBD7 MUTATED     10    0
  BTBD7 WILD-TYPE  340   22
     clus
vv    BTBD7 MUTATED BTBD7 WILD-TYPE
  NO             10             340
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  BTBD7 MUTATED                      9                             3
  BTBD7 WILD-TYPE                  306                            44
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  BTBD7 MUTATED                       0                              0
  BTBD7 WILD-TYPE                   106                             10
D2187V10, multiclass
                                clus
vv                               BTBD7 MUTATED BTBD7 WILD-TYPE
  COLON ADENOCARCINOMA                       9             306
  COLON MUCINOUS ADENOCARCINOMA              3              44
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  BTBD7 MUTATED    11   0   0   0
  BTBD7 WILD-TYPE 334   4  31  25
D2187V11, multiclass
    clus
vv   BTBD7 MUTATED BTBD7 WILD-TYPE
  R0            11             334
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2187V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  BTBD7 MUTATED                                  0     0
  BTBD7 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  BTBD7 MUTATED                           1     7
  BTBD7 WILD-TYPE                        21   219
D2187V13, multiclass
                                  clus
vv                                 BTBD7 MUTATED BTBD7 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        7             219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2188) Variable = SUSD5 MUTATION ANALYSIS
D2188V1, survival
                 sevent
clus2               0   1
  SUSD5 MUTATED     6   2
  SUSD5 WILD-TYPE 372  91
  SUSD5 MUTATED SUSD5 WILD-TYPE 
              8             463 
  SUSD5 MUTATED SUSD5 WILD-TYPE 
              2              91 
$`SUSD5 MUTATED`
TCGA-AA-3511 TCGA-AA-3664 TCGA-AA-A03J TCGA-AZ-6598 TCGA-CA-6717 TCGA-CA-6718 
        6.97        54.02        40.96        49.41        12.76        10.06 
TCGA-CM-4752 TCGA-F4-6703 
       13.02        47.87 

$`SUSD5 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01        63.98         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
        6.97         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       39.98        18.05         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        88.21         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 
        3.06         3.25         3.29         0.07        12.20        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       20.02        37.02        25.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       35.74         6.18         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  SUSD5 MUTATED SUSD5 WILD-TYPE 
           6.97            0.00 
  SUSD5 MUTATED SUSD5 WILD-TYPE 
          54.02          148.01 
  SUSD5 MUTATED SUSD5 WILD-TYPE 
          26.99           20.19 
[1] "7.0 - 54.0 (27.0)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1"  
D2188V2, continuous
D2188V3, binary
                 cls
clus                0   1
  SUSD5 MUTATED     9   0
  SUSD5 WILD-TYPE 357 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SUSD5 MUTATED      9    0
  SUSD5 WILD-TYPE  357  119
        clus
vv       SUSD5 MUTATED SUSD5 WILD-TYPE
  COLON              9             357
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SUSD5 MUTATED         1        0        3         5         0         0
  SUSD5 WILD-TYPE      90        1       29       133        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SUSD5 MUTATED           0          0          0          0        0         0
  SUSD5 WILD-TYPE        24         11         59         42       48        18
                 vv
clus              STAGE IVB
  SUSD5 MUTATED           0
  SUSD5 WILD-TYPE         1
D2188V4, multiclass
            clus
vv           SUSD5 MUTATED SUSD5 WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               3              29
  STAGE IIA              5             133
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  SUSD5 MUTATED     0   1   7   1
  SUSD5 WILD-TYPE  17  91 322  49
D2188V5, multiclass
    clus
vv   SUSD5 MUTATED SUSD5 WILD-TYPE
  T1             0              17
  T2             1              91
  T3             7             322
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  SUSD5 MUTATED     9   0   0
  SUSD5 WILD-TYPE 278 113  87
D2188V6, multiclass
    clus
vv   SUSD5 MUTATED SUSD5 WILD-TYPE
  N0             9             278
  N1             0             113
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2188V7, binary
                 cls
clus                0   1
  SUSD5 MUTATED     8   0
  SUSD5 WILD-TYPE 367  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SUSD5 MUTATED      8    0
  SUSD5 WILD-TYPE  367   65
   clus
vv  SUSD5 MUTATED SUSD5 WILD-TYPE
  0             8             367
  1             0              65
[1] 2 2
[1] FALSE
D2188V8, binary
                 cls
clus                0   1
  SUSD5 MUTATED     4   5
  SUSD5 WILD-TYPE 221 259
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SUSD5 MUTATED      4    5
  SUSD5 WILD-TYPE  221  259
        clus
vv       SUSD5 MUTATED SUSD5 WILD-TYPE
  FEMALE             4             221
  MALE               5             259
[1] 2 2
[1] FALSE
D2188V9, binary
                 cls
clus                0   1
  SUSD5 MUTATED     8   0
  SUSD5 WILD-TYPE 342  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SUSD5 MUTATED      8    0
  SUSD5 WILD-TYPE  342   22
     clus
vv    SUSD5 MUTATED SUSD5 WILD-TYPE
  NO              8             342
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SUSD5 MUTATED                      8                             1
  SUSD5 WILD-TYPE                  307                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SUSD5 MUTATED                       0                              0
  SUSD5 WILD-TYPE                   106                             10
D2188V10, multiclass
                                clus
vv                               SUSD5 MUTATED SUSD5 WILD-TYPE
  COLON ADENOCARCINOMA                       8             307
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  SUSD5 MUTATED     6   0   0   2
  SUSD5 WILD-TYPE 339   4  31  23
D2188V11, multiclass
    clus
vv   SUSD5 MUTATED SUSD5 WILD-TYPE
  R0             6             339
  R1             0               4
  R2             0              31
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2188V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SUSD5 MUTATED                                  0     2
  SUSD5 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  SUSD5 MUTATED                           1     2
  SUSD5 WILD-TYPE                        21   224
D2188V13, multiclass
                                  clus
vv                                 SUSD5 MUTATED SUSD5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               9
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        2             224
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2189) Variable = CDKL4 MUTATION ANALYSIS
D2189V1, survival
                 sevent
clus2               0   1
  CDKL4 MUTATED     2   2
  CDKL4 WILD-TYPE 376  91
  CDKL4 MUTATED CDKL4 WILD-TYPE 
              4             467 
  CDKL4 MUTATED CDKL4 WILD-TYPE 
              2              91 
$`CDKL4 MUTATED`
TCGA-AA-A010 TCGA-CA-6718 TCGA-D5-6537 TCGA-D5-6922 
       34.98        10.06         4.80         4.41 

$`CDKL4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07        12.20        12.76        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  CDKL4 MUTATED CDKL4 WILD-TYPE 
           4.41            0.00 
  CDKL4 MUTATED CDKL4 WILD-TYPE 
          34.98          148.01 
  CDKL4 MUTATED CDKL4 WILD-TYPE 
           7.43           20.28 
[1] "4.4 - 35.0 (7.4)"   "0.0 - 148.0 (20.3)"
[1] "hr=" "5.5"
D2189V2, continuous
D2189V3, binary
                 cls
clus                0   1
  CDKL4 MUTATED     5   0
  CDKL4 WILD-TYPE 361 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDKL4 MUTATED      5    0
  CDKL4 WILD-TYPE  361  119
        clus
vv       CDKL4 MUTATED CDKL4 WILD-TYPE
  COLON              5             361
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CDKL4 MUTATED         0        0        0         2         1         0
  CDKL4 WILD-TYPE      91        1       32       136         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CDKL4 MUTATED           0          1          1          0        0         0
  CDKL4 WILD-TYPE        24         10         58         42       48        18
                 vv
clus              STAGE IVB
  CDKL4 MUTATED           0
  CDKL4 WILD-TYPE         1
D2189V4, multiclass
            clus
vv           CDKL4 MUTATED CDKL4 WILD-TYPE
  STAGE I                0              91
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              2             136
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             1              10
  STAGE IIIB             1              58
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CDKL4 MUTATED     0   0   4   1
  CDKL4 WILD-TYPE  17  92 325  49
D2189V5, multiclass
    clus
vv   CDKL4 MUTATED CDKL4 WILD-TYPE
  T1             0              17
  T2             0              92
  T3             4             325
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  CDKL4 MUTATED     3   2   0
  CDKL4 WILD-TYPE 284 111  87
D2189V6, multiclass
    clus
vv   CDKL4 MUTATED CDKL4 WILD-TYPE
  N0             3             284
  N1             2             111
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2189V7, binary
                 cls
clus                0   1
  CDKL4 MUTATED     4   0
  CDKL4 WILD-TYPE 371  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDKL4 MUTATED      4    0
  CDKL4 WILD-TYPE  371   65
   clus
vv  CDKL4 MUTATED CDKL4 WILD-TYPE
  0             4             371
  1             0              65
[1] 2 2
[1] FALSE
D2189V8, binary
                 cls
clus                0   1
  CDKL4 MUTATED     2   3
  CDKL4 WILD-TYPE 223 261
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDKL4 MUTATED      2    3
  CDKL4 WILD-TYPE  223  261
        clus
vv       CDKL4 MUTATED CDKL4 WILD-TYPE
  FEMALE             2             223
  MALE               3             261
[1] 2 2
[1] FALSE
D2189V9, binary
                 cls
clus                0   1
  CDKL4 MUTATED     3   0
  CDKL4 WILD-TYPE 347  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDKL4 MUTATED      3    0
  CDKL4 WILD-TYPE  347   22
     clus
vv    CDKL4 MUTATED CDKL4 WILD-TYPE
  NO              3             347
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CDKL4 MUTATED                      5                             0
  CDKL4 WILD-TYPE                  310                            47
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CDKL4 MUTATED                       0                              0
  CDKL4 WILD-TYPE                   106                             10
D2189V10, multiclass
                                clus
vv                               CDKL4 MUTATED CDKL4 WILD-TYPE
  COLON ADENOCARCINOMA                       5             310
  COLON MUCINOUS ADENOCARCINOMA              0              47
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  CDKL4 MUTATED     4   0   0   1
  CDKL4 WILD-TYPE 341   4  31  24
D2189V11, multiclass
    clus
vv   CDKL4 MUTATED CDKL4 WILD-TYPE
  R0             4             341
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2189V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CDKL4 MUTATED                                  0     1
  CDKL4 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CDKL4 MUTATED                           0     2
  CDKL4 WILD-TYPE                        22   224
D2189V13, multiclass
                                  clus
vv                                 CDKL4 MUTATED CDKL4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        2             224
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2190) Variable = B3GALNT2 MUTATION ANALYSIS
D2190V1, survival
                    sevent
clus2                  0   1
  B3GALNT2 MUTATED     3   0
  B3GALNT2 WILD-TYPE 375  93
  B3GALNT2 MUTATED B3GALNT2 WILD-TYPE 
                 3                468 
  B3GALNT2 MUTATED B3GALNT2 WILD-TYPE 
                 0                 93 
$`B3GALNT2 MUTATED`
TCGA-A6-5661 TCGA-AU-6004 TCGA-D5-6536 
       33.53        27.09        17.85 

$`B3GALNT2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 
       27.42        10.88         0.20        14.50        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 
       20.19        18.25         1.32        43.27        15.12         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  B3GALNT2 MUTATED B3GALNT2 WILD-TYPE 
             17.85               0.00 
  B3GALNT2 MUTATED B3GALNT2 WILD-TYPE 
             33.53             148.01 
  B3GALNT2 MUTATED B3GALNT2 WILD-TYPE 
            27.090             20.155 
[1] "17.9 - 33.5 (27.1)" "0.0 - 148.0 (20.2)"
[1] "hr="     "3300000"
D2190V2, continuous
D2190V3, binary
                    cls
clus                   0   1
  B3GALNT2 MUTATED     3   0
  B3GALNT2 WILD-TYPE 363 119
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  B3GALNT2 MUTATED      3    0
  B3GALNT2 WILD-TYPE  363  119
        clus
vv       B3GALNT2 MUTATED B3GALNT2 WILD-TYPE
  COLON                 3                363
  RECTUM                0                119
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  B3GALNT2 MUTATED         1        0        0         2         0         0
  B3GALNT2 WILD-TYPE      90        1       32       136        10         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  B3GALNT2 MUTATED           0          0          0          0        0
  B3GALNT2 WILD-TYPE        24         11         59         42       48
                    vv
clus                 STAGE IVA STAGE IVB
  B3GALNT2 MUTATED           0         0
  B3GALNT2 WILD-TYPE        18         1
D2190V4, multiclass
            clus
vv           B3GALNT2 MUTATED B3GALNT2 WILD-TYPE
  STAGE I                   1                 90
  STAGE IA                  0                  1
  STAGE II                  0                 32
  STAGE IIA                 2                136
  STAGE IIB                 0                 10
  STAGE IIC                 0                  1
  STAGE III                 0                 24
  STAGE IIIA                0                 11
  STAGE IIIB                0                 59
  STAGE IIIC                0                 42
  STAGE IV                  0                 48
  STAGE IVA                 0                 18
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  B3GALNT2 MUTATED     0   1   2   0
  B3GALNT2 WILD-TYPE  17  91 327  50
D2190V5, multiclass
    clus
vv   B3GALNT2 MUTATED B3GALNT2 WILD-TYPE
  T1                0                 17
  T2                1                 91
  T3                2                327
  T4                0                 50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  B3GALNT2 MUTATED     3   0   0
  B3GALNT2 WILD-TYPE 284 113  87
D2190V6, multiclass
    clus
vv   B3GALNT2 MUTATED B3GALNT2 WILD-TYPE
  N0                3                284
  N1                0                113
  N2                0                 87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2190V7, binary
                    cls
clus                   0   1
  B3GALNT2 MUTATED     3   0
  B3GALNT2 WILD-TYPE 372  65
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  B3GALNT2 MUTATED      3    0
  B3GALNT2 WILD-TYPE  372   65
   clus
vv  B3GALNT2 MUTATED B3GALNT2 WILD-TYPE
  0                3                372
  1                0                 65
[1] 2 2
[1] FALSE
D2190V8, binary
                    cls
clus                   0   1
  B3GALNT2 MUTATED     2   1
  B3GALNT2 WILD-TYPE 223 263
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  B3GALNT2 MUTATED      2    1
  B3GALNT2 WILD-TYPE  223  263
        clus
vv       B3GALNT2 MUTATED B3GALNT2 WILD-TYPE
  FEMALE                2                223
  MALE                  1                263
[1] 2 2
[1] FALSE
D2190V9, binary
                    cls
clus                   0   1
  B3GALNT2 MUTATED     2   0
  B3GALNT2 WILD-TYPE 348  22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  B3GALNT2 MUTATED      2    0
  B3GALNT2 WILD-TYPE  348   22
     clus
vv    B3GALNT2 MUTATED B3GALNT2 WILD-TYPE
  NO                 2                348
  YES                0                 22
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  B3GALNT2 MUTATED                      3                             0
  B3GALNT2 WILD-TYPE                  312                            47
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  B3GALNT2 MUTATED                       0                              0
  B3GALNT2 WILD-TYPE                   106                             10
D2190V10, multiclass
                                clus
vv                               B3GALNT2 MUTATED B3GALNT2 WILD-TYPE
  COLON ADENOCARCINOMA                          3                312
  COLON MUCINOUS ADENOCARCINOMA                 0                 47
  RECTAL ADENOCARCINOMA                         0                106
  RECTAL MUCINOUS ADENOCARCINOMA                0                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  B3GALNT2 MUTATED     3   0   0   0
  B3GALNT2 WILD-TYPE 342   4  31  25
D2190V11, multiclass
    clus
vv   B3GALNT2 MUTATED B3GALNT2 WILD-TYPE
  R0                3                342
  R1                0                  4
  R2                0                 31
  RX                0                 25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2190V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  B3GALNT2 MUTATED                                  0     0
  B3GALNT2 WILD-TYPE                                1    11
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  B3GALNT2 MUTATED                           1     2
  B3GALNT2 WILD-TYPE                        21   224
D2190V13, multiclass
                                  clus
vv                                 B3GALNT2 MUTATED B3GALNT2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 11
  BLACK OR AFRICAN AMERICAN                       1                 21
  WHITE                                           2                224
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2191) Variable = OR4N5 MUTATION ANALYSIS
D2191V1, survival
                 sevent
clus2               0   1
  OR4N5 MUTATED     2   1
  OR4N5 WILD-TYPE 376  92
  OR4N5 MUTATED OR4N5 WILD-TYPE 
              3             468 
  OR4N5 MUTATED OR4N5 WILD-TYPE 
              1              92 
$`OR4N5 MUTATED`
TCGA-CA-6717 TCGA-F4-6570 TCGA-G5-6235 
       12.76         6.18        55.76 

$`OR4N5 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07        12.20        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       35.74        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6641 
       31.30        28.57        32.19         0.66         0.69        26.43 

  OR4N5 MUTATED OR4N5 WILD-TYPE 
           6.18            0.00 
  OR4N5 MUTATED OR4N5 WILD-TYPE 
          55.76          148.01 
  OR4N5 MUTATED OR4N5 WILD-TYPE 
         12.760          20.235 
[1] "6.2 - 55.8 (12.8)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.6"
D2191V2, continuous
D2191V3, binary
                 cls
clus                0   1
  OR4N5 MUTATED     2   1
  OR4N5 WILD-TYPE 364 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR4N5 MUTATED      2    1
  OR4N5 WILD-TYPE  364  118
        clus
vv       OR4N5 MUTATED OR4N5 WILD-TYPE
  COLON              2             364
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  OR4N5 MUTATED         0        0        0         2         0         0
  OR4N5 WILD-TYPE      91        1       32       136        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  OR4N5 MUTATED           0          0          1          0        0         0
  OR4N5 WILD-TYPE        24         11         58         42       48        18
                 vv
clus              STAGE IVB
  OR4N5 MUTATED           0
  OR4N5 WILD-TYPE         1
D2191V4, multiclass
            clus
vv           OR4N5 MUTATED OR4N5 WILD-TYPE
  STAGE I                0              91
  STAGE IA               0               1
  STAGE II               0              32
  STAGE IIA              2             136
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  OR4N5 MUTATED     0   0   3   0
  OR4N5 WILD-TYPE  17  92 326  50
D2191V5, multiclass
    clus
vv   OR4N5 MUTATED OR4N5 WILD-TYPE
  T1             0              17
  T2             0              92
  T3             3             326
  T4             0              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  OR4N5 MUTATED     2   1   0
  OR4N5 WILD-TYPE 285 112  87
D2191V6, multiclass
    clus
vv   OR4N5 MUTATED OR4N5 WILD-TYPE
  N0             2             285
  N1             1             112
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2191V7, binary
                 cls
clus                0   1
  OR4N5 MUTATED     2   0
  OR4N5 WILD-TYPE 373  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR4N5 MUTATED      2    0
  OR4N5 WILD-TYPE  373   65
   clus
vv  OR4N5 MUTATED OR4N5 WILD-TYPE
  0             2             373
  1             0              65
[1] 2 2
[1] FALSE
D2191V8, binary
                 cls
clus                0   1
  OR4N5 MUTATED     1   2
  OR4N5 WILD-TYPE 224 262
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR4N5 MUTATED      1    2
  OR4N5 WILD-TYPE  224  262
        clus
vv       OR4N5 MUTATED OR4N5 WILD-TYPE
  FEMALE             1             224
  MALE               2             262
[1] 2 2
[1] FALSE
D2191V9, binary
                 cls
clus                0   1
  OR4N5 MUTATED     3   0
  OR4N5 WILD-TYPE 347  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR4N5 MUTATED      3    0
  OR4N5 WILD-TYPE  347   22
     clus
vv    OR4N5 MUTATED OR4N5 WILD-TYPE
  NO              3             347
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  OR4N5 MUTATED                      1                             1
  OR4N5 WILD-TYPE                  314                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  OR4N5 MUTATED                       1                              0
  OR4N5 WILD-TYPE                   105                             10
D2191V10, multiclass
                                clus
vv                               OR4N5 MUTATED OR4N5 WILD-TYPE
  COLON ADENOCARCINOMA                       1             314
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  OR4N5 MUTATED     1   1   0   1
  OR4N5 WILD-TYPE 344   3  31  24
D2191V11, multiclass
    clus
vv   OR4N5 MUTATED OR4N5 WILD-TYPE
  R0             1             344
  R1             1               3
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2191V12, continuous
[1] "Remove cluster labels:" "OR4N5 MUTATED"         
clus
  OR4N5 MUTATED OR4N5 WILD-TYPE 
              2             456 
     TCGA-A6-2671      TCGA-A6-2672      TCGA-A6-2674      TCGA-A6-2676 
"OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" 
     TCGA-A6-2677      TCGA-A6-2678      TCGA-A6-2683      TCGA-A6-3807 
"OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" 
     TCGA-A6-3808      TCGA-A6-3809      TCGA-A6-3810      TCGA-A6-4105 
"OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" 
     TCGA-A6-5656      TCGA-A6-5657      TCGA-A6-5659      TCGA-A6-5660 
"OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" 
     TCGA-A6-5661      TCGA-A6-5662      TCGA-A6-5664      TCGA-A6-5665 
"OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" 
     TCGA-A6-5666      TCGA-A6-6137      TCGA-A6-6138      TCGA-A6-6141 
"OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" 
     TCGA-A6-6142      TCGA-A6-6648      TCGA-A6-6649      TCGA-A6-6651 
"OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" 
     TCGA-A6-6652      TCGA-A6-6653      TCGA-A6-6654      TCGA-A6-6780 
"OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" 
     TCGA-A6-6781      TCGA-A6-6782      TCGA-AA-3489      TCGA-AA-3492 
"OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" 
     TCGA-AA-3496      TCGA-AA-3502      TCGA-AA-3510      TCGA-AA-3511 
"OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" 
     TCGA-AA-3514      TCGA-AA-3516      TCGA-AA-3517      TCGA-AA-3518 
"OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" 
     TCGA-AA-3519      TCGA-AA-3520      TCGA-AA-3521      TCGA-AA-3522 
"OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" 
     TCGA-AA-3524      TCGA-AA-3525      TCGA-AA-3526      TCGA-AA-3527 
"OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" 
     TCGA-AA-3529      TCGA-AA-3530      TCGA-AA-3531      TCGA-AA-3532 
"OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" 
     TCGA-AA-3534      TCGA-AA-3538      TCGA-AA-3542      TCGA-AA-3543 
"OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" 
     TCGA-AA-3544      TCGA-AA-3548      TCGA-AA-3549      TCGA-AA-3552 
"OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" 
     TCGA-AA-3553      TCGA-AA-3554      TCGA-AA-3555      TCGA-AA-3556 
"OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" 
     TCGA-AA-3558      TCGA-AA-3560      TCGA-AA-3562      TCGA-AA-3655 
"OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" 
     TCGA-AA-3660      TCGA-AA-3662      TCGA-AA-3663      TCGA-AA-3664 
"OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" 
     TCGA-AA-3666      TCGA-AA-3667      TCGA-AA-3672      TCGA-AA-3673 
"OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" 
     TCGA-AA-3678      TCGA-AA-3679      TCGA-AA-3680      TCGA-AA-3681 
"OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" 
     TCGA-AA-3684      TCGA-AA-3685      TCGA-AA-3688      TCGA-AA-3692 
"OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" 
     TCGA-AA-3693      TCGA-AA-3695      TCGA-AA-3696      TCGA-AA-3697 
"OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" 
     TCGA-AA-3710      TCGA-AA-3712      TCGA-AA-3713      TCGA-AA-3715 
"OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" 
     TCGA-AA-3811      TCGA-AA-3812      TCGA-AA-3814      TCGA-AA-3815 
"OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" 
     TCGA-AA-3818      TCGA-AA-3819      TCGA-AA-3821      TCGA-AA-3831 
"OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" 
     TCGA-AA-3833      TCGA-AA-3837      TCGA-AA-3842      TCGA-AA-3844 
"OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" 
     TCGA-AA-3845      TCGA-AA-3846      TCGA-AA-3848      TCGA-AA-3850 
"OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" 
     TCGA-AA-3851      TCGA-AA-3852      TCGA-AA-3854      TCGA-AA-3855 
"OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" 
     TCGA-AA-3856      TCGA-AA-3858      TCGA-AA-3860      TCGA-AA-3861 
"OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" 
     TCGA-AA-3864      TCGA-AA-3866      TCGA-AA-3867      TCGA-AA-3869 
"OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" 
     TCGA-AA-3870      TCGA-AA-3872      TCGA-AA-3875      TCGA-AA-3877 
"OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" 
     TCGA-AA-3930      TCGA-AA-3939      TCGA-AA-3941      TCGA-AA-3947 
"OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" 
     TCGA-AA-3949      TCGA-AA-3950      TCGA-AA-3952      TCGA-AA-3955 
"OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" 
     TCGA-AA-3956      TCGA-AA-3966      TCGA-AA-3968      TCGA-AA-3971 
"OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" 
     TCGA-AA-3972      TCGA-AA-3973      TCGA-AA-3975      TCGA-AA-3976 
"OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" 
     TCGA-AA-3977      TCGA-AA-3979      TCGA-AA-3980      TCGA-AA-3982 
"OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" 
     TCGA-AA-3984      TCGA-AA-3986      TCGA-AA-3989      TCGA-AA-3994 
"OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" 
     TCGA-AA-A004      TCGA-AA-A00A      TCGA-AA-A00D      TCGA-AA-A00E 
"OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" 
     TCGA-AA-A00F      TCGA-AA-A00J      TCGA-AA-A00K      TCGA-AA-A00L 
"OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" 
     TCGA-AA-A00N      TCGA-AA-A00O      TCGA-AA-A00Q      TCGA-AA-A00R 
"OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" 
     TCGA-AA-A00U      TCGA-AA-A00W      TCGA-AA-A00Z      TCGA-AA-A010 
"OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" 
     TCGA-AA-A017      TCGA-AA-A01D      TCGA-AA-A01F      TCGA-AA-A01G 
"OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" 
     TCGA-AA-A01I      TCGA-AA-A01K      TCGA-AA-A01P      TCGA-AA-A01Q 
"OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" 
     TCGA-AA-A01R      TCGA-AA-A01S      TCGA-AA-A01T      TCGA-AA-A01V 
"OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" 
     TCGA-AA-A01X      TCGA-AA-A01Z      TCGA-AA-A022      TCGA-AA-A024 
"OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" 
     TCGA-AA-A029      TCGA-AA-A02F      TCGA-AA-A02H      TCGA-AA-A02J 
"OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" 
     TCGA-AA-A02K      TCGA-AA-A02O      TCGA-AA-A02W      TCGA-AA-A02Y 
"OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" 
     TCGA-AA-A03F      TCGA-AA-A03J      TCGA-AD-5900      TCGA-AD-6548 
"OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" 
     TCGA-AD-6888      TCGA-AD-6889      TCGA-AD-6890      TCGA-AD-6895 
"OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" 
     TCGA-AD-6899      TCGA-AD-6901      TCGA-AD-6963      TCGA-AD-6964 
"OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" 
     TCGA-AD-6965      TCGA-AU-3779      TCGA-AU-6004      TCGA-AY-4070 
"OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" 
     TCGA-AY-4071      TCGA-AY-5543      TCGA-AY-6196      TCGA-AY-6197 
"OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" 
     TCGA-AY-6386      TCGA-AZ-4323      TCGA-AZ-4616      TCGA-AZ-4682 
"OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" 
     TCGA-AZ-5403      TCGA-AZ-5407      TCGA-AZ-6598      TCGA-AZ-6599 
"OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" 
     TCGA-AZ-6600      TCGA-AZ-6601      TCGA-AZ-6603      TCGA-AZ-6605 
"OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" 
     TCGA-AZ-6606      TCGA-AZ-6607      TCGA-AZ-6608      TCGA-CK-4947 
"OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" 
     TCGA-CK-4948      TCGA-CK-4950      TCGA-CK-4952      TCGA-CM-4743 
"OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" 
     TCGA-CM-4744      TCGA-CM-4746      TCGA-CM-4747      TCGA-CM-4752 
"OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" 
     TCGA-CM-5341      TCGA-CM-5344      TCGA-CM-5348      TCGA-CM-5349 
"OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" 
     TCGA-CM-5860      TCGA-CM-5861      TCGA-CM-5862      TCGA-CM-5863 
"OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" 
     TCGA-CM-5864      TCGA-CM-5868      TCGA-CM-6161      TCGA-CM-6162 
"OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" 
     TCGA-CM-6163      TCGA-CM-6164      TCGA-CM-6165      TCGA-CM-6166 
"OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" 
     TCGA-CM-6167      TCGA-CM-6168      TCGA-CM-6169      TCGA-CM-6170 
"OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" 
     TCGA-CM-6171      TCGA-CM-6172      TCGA-CM-6674      TCGA-CM-6675 
"OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" 
     TCGA-CM-6676      TCGA-CM-6677      TCGA-CM-6678      TCGA-CM-6679 
"OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" 
     TCGA-CM-6680      TCGA-D5-5537      TCGA-D5-5538      TCGA-D5-5539 
"OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" 
     TCGA-D5-5540      TCGA-D5-5541      TCGA-D5-6529      TCGA-D5-6532 
"OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" 
     TCGA-D5-6533      TCGA-D5-6534      TCGA-D5-6535      TCGA-D5-6536 
"OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" 
     TCGA-D5-6537      TCGA-D5-6538      TCGA-D5-6539      TCGA-D5-6540 
"OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" 
     TCGA-D5-6541      TCGA-D5-6898      TCGA-D5-6920      TCGA-D5-6922 
"OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" 
     TCGA-D5-6923      TCGA-D5-6924      TCGA-D5-6926      TCGA-D5-6927 
"OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" 
     TCGA-D5-6928      TCGA-D5-6929      TCGA-D5-6930      TCGA-D5-6931 
"OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" 
     TCGA-D5-6932      TCGA-D5-7000      TCGA-DM-A0X9      TCGA-DM-A0XD 
"OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" 
     TCGA-DM-A0XF      TCGA-DM-A1D0      TCGA-DM-A1D4      TCGA-DM-A1D6 
"OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" 
     TCGA-DM-A1D7      TCGA-DM-A1D8      TCGA-DM-A1D9      TCGA-DM-A1DA 
"OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" 
     TCGA-DM-A1DB      TCGA-DM-A1HA      TCGA-DM-A1HB      TCGA-DM-A282 
"OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" 
     TCGA-DM-A285      TCGA-DM-A28C      TCGA-DM-A28E      TCGA-DM-A28F 
"OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" 
     TCGA-DM-A28G      TCGA-DM-A28H      TCGA-DM-A28K      TCGA-F4-6459 
"OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" 
     TCGA-F4-6460      TCGA-F4-6569      TCGA-F4-6703      TCGA-F4-6704 
"OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" 
     TCGA-F4-6806      TCGA-F4-6807      TCGA-F4-6808      TCGA-F4-6809 
"OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" 
     TCGA-F4-6854      TCGA-F4-6855      TCGA-F4-6856      TCGA-G4-6293 
"OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" 
     TCGA-G4-6299      TCGA-G4-6303      TCGA-G4-6304      TCGA-G4-6306 
"OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" 
     TCGA-G4-6307      TCGA-G4-6309      TCGA-G4-6310      TCGA-G4-6315 
"OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" 
     TCGA-G4-6317      TCGA-G4-6321      TCGA-G4-6323      TCGA-G4-6586 
"OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" 
     TCGA-G4-6588      TCGA-G4-6625      TCGA-G4-6626      TCGA-G4-6628 
"OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" 
     TCGA-AF-2687      TCGA-AF-2689      TCGA-AF-2691      TCGA-AF-2692 
"OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" 
     TCGA-AF-2693      TCGA-AF-3400      TCGA-AF-3913      TCGA-AF-4110 
"OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" 
     TCGA-AF-5654      TCGA-AF-6136      TCGA-AF-6655      TCGA-AF-6672 
"OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" 
     TCGA-AG-3574      TCGA-AG-3575      TCGA-AG-3578      TCGA-AG-3580 
"OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" 
     TCGA-AG-3581      TCGA-AG-3582      TCGA-AG-3583      TCGA-AG-3584 
"OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" 
     TCGA-AG-3586      TCGA-AG-3587      TCGA-AG-3593      TCGA-AG-3594 
"OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" 
     TCGA-AG-3598      TCGA-AG-3599      TCGA-AG-3600      TCGA-AG-3601 
"OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" 
     TCGA-AG-3602      TCGA-AG-3605      TCGA-AG-3608      TCGA-AG-3609 
"OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" 
     TCGA-AG-3611      TCGA-AG-3612      TCGA-AG-3726      TCGA-AG-3727 
"OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" 
     TCGA-AG-3731      TCGA-AG-3732      TCGA-AG-3742      TCGA-AG-3878 
"OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" 
     TCGA-AG-3881      TCGA-AG-3882      TCGA-AG-3883      TCGA-AG-3885 
"OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" 
     TCGA-AG-3887      TCGA-AG-3890      TCGA-AG-3892      TCGA-AG-3893 
"OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" 
     TCGA-AG-3894      TCGA-AG-3896      TCGA-AG-3898      TCGA-AG-3901 
"OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" 
     TCGA-AG-3902      TCGA-AG-3909      TCGA-AG-3999      TCGA-AG-4001 
"OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" 
     TCGA-AG-4005      TCGA-AG-4007      TCGA-AG-4008      TCGA-AG-4015 
"OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" 
     TCGA-AG-A002      TCGA-AG-A008      TCGA-AG-A00C      TCGA-AG-A00H 
"OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" 
     TCGA-AG-A00Y      TCGA-AG-A011      TCGA-AG-A014      TCGA-AG-A015 
"OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" 
     TCGA-AG-A016      TCGA-AG-A01L      TCGA-AG-A01W      TCGA-AG-A01Y 
"OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" 
     TCGA-AG-A020      TCGA-AG-A025      TCGA-AG-A026      TCGA-AG-A02G 
"OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" 
     TCGA-AG-A02N      TCGA-AG-A02X      TCGA-AG-A032      TCGA-AG-A036 
"OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" 
     TCGA-AH-6544      TCGA-AH-6547      TCGA-AH-6643      TCGA-AH-6644 
"OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" 
     TCGA-CI-6622      TCGA-DC-5337      TCGA-DC-5869      TCGA-DC-6155 
"OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" 
     TCGA-DC-6157      TCGA-DC-6158      TCGA-DC-6160      TCGA-DC-6681 
"OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" 
     TCGA-DC-6682      TCGA-DC-6683      TCGA-DY-A0XA      TCGA-DY-A1DC 
"OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" 
     TCGA-DY-A1DD      TCGA-DY-A1DF      TCGA-DY-A1DG      TCGA-DY-A1H8 
"OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" 
     TCGA-EI-6506      TCGA-EI-6507      TCGA-EI-6508      TCGA-EI-6510 
"OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" 
     TCGA-F5-6464      TCGA-F5-6465      TCGA-F5-6571      TCGA-F5-6702 
"OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" 
     TCGA-F5-6811      TCGA-F5-6812      TCGA-F5-6813      TCGA-G5-6641 
"OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" "OR4N5 WILD-TYPE" 
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OR4N5 MUTATED                                  0     1
  OR4N5 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  OR4N5 MUTATED                           0     2
  OR4N5 WILD-TYPE                        22   224
D2191V13, multiclass
                                  clus
vv                                 OR4N5 MUTATED OR4N5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        2             224
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2192) Variable = GADD45GIP1 MUTATION ANALYSIS
D2192V1, survival
                      sevent
clus2                    0   1
  GADD45GIP1 MUTATED     4   0
  GADD45GIP1 WILD-TYPE 374  93
  GADD45GIP1 MUTATED GADD45GIP1 WILD-TYPE 
                   4                  467 
  GADD45GIP1 MUTATED GADD45GIP1 WILD-TYPE 
                   0                   93 
$`GADD45GIP1 MUTATED`
TCGA-A6-6653 TCGA-A6-6781 TCGA-CK-4950 TCGA-AF-4110 
       24.39        19.66        85.45        14.50 

$`GADD45GIP1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
       25.08        25.18        24.16        21.76        24.69        23.87 
TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       20.12        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6136 
       13.55        19.10        34.49        10.39        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  GADD45GIP1 MUTATED GADD45GIP1 WILD-TYPE 
                14.5                  0.0 
  GADD45GIP1 MUTATED GADD45GIP1 WILD-TYPE 
               85.45               148.01 
  GADD45GIP1 MUTATED GADD45GIP1 WILD-TYPE 
              22.025               20.190 
[1] "14.5 - 85.5 (22.0)" "0.0 - 148.0 (20.2)"
[1] "hr="     "9100000"
D2192V2, continuous
D2192V3, binary
                      cls
clus                     0   1
  GADD45GIP1 MUTATED     3   0
  GADD45GIP1 WILD-TYPE 363 119
[1] "tbl2"
                      cls
clus                   [,1] [,2]
  GADD45GIP1 MUTATED      3    0
  GADD45GIP1 WILD-TYPE  363  119
        clus
vv       GADD45GIP1 MUTATED GADD45GIP1 WILD-TYPE
  COLON                   3                  363
  RECTUM                  0                  119
[1] 2 2
[1] FALSE
                      vv
clus                   STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GADD45GIP1 MUTATED         1        0        0         0         0         0
  GADD45GIP1 WILD-TYPE      90        1       32       138        10         1
                      vv
clus                   STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GADD45GIP1 MUTATED           0          0          1          1        0
  GADD45GIP1 WILD-TYPE        24         11         58         41       48
                      vv
clus                   STAGE IVA STAGE IVB
  GADD45GIP1 MUTATED           1         0
  GADD45GIP1 WILD-TYPE        17         1
D2192V4, multiclass
            clus
vv           GADD45GIP1 MUTATED GADD45GIP1 WILD-TYPE
  STAGE I                     1                   90
  STAGE IA                    0                    1
  STAGE II                    0                   32
  STAGE IIA                   0                  138
  STAGE IIB                   0                   10
  STAGE IIC                   0                    1
  STAGE III                   0                   24
  STAGE IIIA                  0                   11
  STAGE IIIB                  1                   58
  STAGE IIIC                  1                   41
  STAGE IV                    0                   48
  STAGE IVA                   1                   17
  STAGE IVB                   0                    1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                      vv
clus                    T1  T2  T3  T4
  GADD45GIP1 MUTATED     0   1   1   2
  GADD45GIP1 WILD-TYPE  17  91 328  48
D2192V5, multiclass
    clus
vv   GADD45GIP1 MUTATED GADD45GIP1 WILD-TYPE
  T1                  0                   17
  T2                  1                   91
  T3                  1                  328
  T4                  2                   48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                      vv
clus                    N0  N1  N2
  GADD45GIP1 MUTATED     1   2   1
  GADD45GIP1 WILD-TYPE 286 111  86
D2192V6, multiclass
    clus
vv   GADD45GIP1 MUTATED GADD45GIP1 WILD-TYPE
  N0                  1                  286
  N1                  2                  111
  N2                  1                   86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2192V7, binary
                      cls
clus                     0   1
  GADD45GIP1 MUTATED     2   0
  GADD45GIP1 WILD-TYPE 373  65
[1] "tbl2"
                      cls
clus                   [,1] [,2]
  GADD45GIP1 MUTATED      2    0
  GADD45GIP1 WILD-TYPE  373   65
   clus
vv  GADD45GIP1 MUTATED GADD45GIP1 WILD-TYPE
  0                  2                  373
  1                  0                   65
[1] 2 2
[1] FALSE
D2192V8, binary
                      cls
clus                     0   1
  GADD45GIP1 MUTATED     1   3
  GADD45GIP1 WILD-TYPE 224 261
[1] "tbl2"
                      cls
clus                   [,1] [,2]
  GADD45GIP1 MUTATED      1    3
  GADD45GIP1 WILD-TYPE  224  261
        clus
vv       GADD45GIP1 MUTATED GADD45GIP1 WILD-TYPE
  FEMALE                  1                  224
  MALE                    3                  261
[1] 2 2
[1] FALSE
D2192V9, binary
                      cls
clus                     0   1
  GADD45GIP1 MUTATED     4   0
  GADD45GIP1 WILD-TYPE 346  22
[1] "tbl2"
                      cls
clus                   [,1] [,2]
  GADD45GIP1 MUTATED      4    0
  GADD45GIP1 WILD-TYPE  346   22
     clus
vv    GADD45GIP1 MUTATED GADD45GIP1 WILD-TYPE
  NO                   4                  346
  YES                  0                   22
[1] 2 2
[1] FALSE
                      vv
clus                   COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  GADD45GIP1 MUTATED                      2                             1
  GADD45GIP1 WILD-TYPE                  313                            46
                      vv
clus                   RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  GADD45GIP1 MUTATED                       0                              0
  GADD45GIP1 WILD-TYPE                   106                             10
D2192V10, multiclass
                                clus
vv                               GADD45GIP1 MUTATED GADD45GIP1 WILD-TYPE
  COLON ADENOCARCINOMA                            2                  313
  COLON MUCINOUS ADENOCARCINOMA                   1                   46
  RECTAL ADENOCARCINOMA                           0                  106
  RECTAL MUCINOUS ADENOCARCINOMA                  0                   10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                      vv
clus                    R0  R1  R2  RX
  GADD45GIP1 MUTATED     2   1   0   0
  GADD45GIP1 WILD-TYPE 343   3  31  25
D2192V11, multiclass
    clus
vv   GADD45GIP1 MUTATED GADD45GIP1 WILD-TYPE
  R0                  2                  343
  R1                  1                    3
  R2                  0                   31
  RX                  0                   25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2192V12, continuous
                      vv
clus                   AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GADD45GIP1 MUTATED                                  0     0
  GADD45GIP1 WILD-TYPE                                1    11
                      vv
clus                   BLACK OR AFRICAN AMERICAN WHITE
  GADD45GIP1 MUTATED                           1     3
  GADD45GIP1 WILD-TYPE                        21   223
D2192V13, multiclass
                                  clus
vv                                 GADD45GIP1 MUTATED GADD45GIP1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                  0                    1
  ASIAN                                             0                   11
  BLACK OR AFRICAN AMERICAN                         1                   21
  WHITE                                             3                  223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2193) Variable = RASGRP3 MUTATION ANALYSIS
D2193V1, survival
                   sevent
clus2                 0   1
  RASGRP3 MUTATED    11   2
  RASGRP3 WILD-TYPE 367  91
  RASGRP3 MUTATED RASGRP3 WILD-TYPE 
               13               458 
  RASGRP3 MUTATED RASGRP3 WILD-TYPE 
                2                91 
$`RASGRP3 MUTATED`
TCGA-AA-3697 TCGA-AA-3866 TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01R TCGA-AZ-4315 
       85.05        17.03         4.01        34.98        35.01        58.39 
TCGA-AZ-6608 TCGA-CK-6751 TCGA-DM-A0X9 TCGA-G4-6309 TCGA-AG-3896 TCGA-AG-A002 
        1.61       124.27       119.70        85.48         1.02        20.98 
TCGA-CL-5917 
       78.12 

$`RASGRP3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       19.00        36.00         5.03        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
       38.07         1.02         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
       11.74         3.19        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       21.14        82.95         1.91        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 
       65.85        53.62        44.68        55.04        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
       14.01        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
        4.73         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  RASGRP3 MUTATED RASGRP3 WILD-TYPE 
             1.02              0.00 
  RASGRP3 MUTATED RASGRP3 WILD-TYPE 
           124.27            148.01 
  RASGRP3 MUTATED RASGRP3 WILD-TYPE 
           35.010            20.035 
[1] "1.0 - 124.3 (35.0)" "0.0 - 148.0 (20.0)"
[1] "hr=" "2.4"
D2193V2, continuous
D2193V3, binary
                   cls
clus                  0   1
  RASGRP3 MUTATED    10   3
  RASGRP3 WILD-TYPE 356 116
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RASGRP3 MUTATED     10    3
  RASGRP3 WILD-TYPE  356  116
        clus
vv       RASGRP3 MUTATED RASGRP3 WILD-TYPE
  COLON               10               356
  RECTUM               3               116
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RASGRP3 MUTATED         4        0        0         2         2         0
  RASGRP3 WILD-TYPE      87        1       32       136         8         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  RASGRP3 MUTATED           2          1          1          1        0
  RASGRP3 WILD-TYPE        22         10         58         41       48
                   vv
clus                STAGE IVA STAGE IVB
  RASGRP3 MUTATED           0         0
  RASGRP3 WILD-TYPE        18         1
D2193V4, multiclass
            clus
vv           RASGRP3 MUTATED RASGRP3 WILD-TYPE
  STAGE I                  4                87
  STAGE IA                 0                 1
  STAGE II                 0                32
  STAGE IIA                2               136
  STAGE IIB                2                 8
  STAGE IIC                0                 1
  STAGE III                2                22
  STAGE IIIA               1                10
  STAGE IIIB               1                58
  STAGE IIIC               1                41
  STAGE IV                 0                48
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  RASGRP3 MUTATED     0   5   6   2
  RASGRP3 WILD-TYPE  17  87 323  48
D2193V5, multiclass
    clus
vv   RASGRP3 MUTATED RASGRP3 WILD-TYPE
  T1               0                17
  T2               5                87
  T3               6               323
  T4               2                48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  RASGRP3 MUTATED     9   2   2
  RASGRP3 WILD-TYPE 278 111  85
D2193V6, multiclass
    clus
vv   RASGRP3 MUTATED RASGRP3 WILD-TYPE
  N0               9               278
  N1               2               111
  N2               2                85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2193V7, binary
                   cls
clus                  0   1
  RASGRP3 MUTATED    11   0
  RASGRP3 WILD-TYPE 364  65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RASGRP3 MUTATED     11    0
  RASGRP3 WILD-TYPE  364   65
   clus
vv  RASGRP3 MUTATED RASGRP3 WILD-TYPE
  0              11               364
  1               0                65
[1] 2 2
[1] FALSE
D2193V8, binary
                   cls
clus                  0   1
  RASGRP3 MUTATED     8   5
  RASGRP3 WILD-TYPE 217 259
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RASGRP3 MUTATED      8    5
  RASGRP3 WILD-TYPE  217  259
        clus
vv       RASGRP3 MUTATED RASGRP3 WILD-TYPE
  FEMALE               8               217
  MALE                 5               259
[1] 2 2
[1] FALSE
D2193V9, binary
                   cls
clus                  0   1
  RASGRP3 MUTATED     9   1
  RASGRP3 WILD-TYPE 341  21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RASGRP3 MUTATED      9    1
  RASGRP3 WILD-TYPE  341   21
     clus
vv    RASGRP3 MUTATED RASGRP3 WILD-TYPE
  NO                9               341
  YES               1                21
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  RASGRP3 MUTATED                      7                             3
  RASGRP3 WILD-TYPE                  308                            44
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  RASGRP3 MUTATED                       3                              0
  RASGRP3 WILD-TYPE                   103                             10
D2193V10, multiclass
                                clus
vv                               RASGRP3 MUTATED RASGRP3 WILD-TYPE
  COLON ADENOCARCINOMA                         7               308
  COLON MUCINOUS ADENOCARCINOMA                3                44
  RECTAL ADENOCARCINOMA                        3               103
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  RASGRP3 MUTATED     9   0   0   2
  RASGRP3 WILD-TYPE 336   4  31  23
D2193V11, multiclass
    clus
vv   RASGRP3 MUTATED RASGRP3 WILD-TYPE
  R0               9               336
  R1               0                 4
  R2               0                31
  RX               2                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2193V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RASGRP3 MUTATED                                  0     0
  RASGRP3 WILD-TYPE                                1    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  RASGRP3 MUTATED                           1     5
  RASGRP3 WILD-TYPE                        21   221
D2193V13, multiclass
                                  clus
vv                                 RASGRP3 MUTATED RASGRP3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                      1                21
  WHITE                                          5               221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2194) Variable = STOX2 MUTATION ANALYSIS
D2194V1, survival
                 sevent
clus2               0   1
  STOX2 MUTATED     6   4
  STOX2 WILD-TYPE 372  89
  STOX2 MUTATED STOX2 WILD-TYPE 
             10             461 
  STOX2 MUTATED STOX2 WILD-TYPE 
              4              89 
$`STOX2 MUTATED`
TCGA-A6-4105 TCGA-A6-5656 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3875 TCGA-AZ-6606 
       14.53        32.91        19.04        19.04        18.05        11.74 
TCGA-CM-4746 TCGA-CM-5861 TCGA-D5-6926 TCGA-F4-6570 
       37.02        15.02         9.04         6.18 

$`STOX2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5657 
       16.57        34.65        33.34        32.75        36.53        31.63 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       30.44        29.19        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
        5.03        85.05        26.99        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       29.98        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       20.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       30.08        32.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6928 
        3.68         4.41        12.43        14.30         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 
      117.07        98.24         8.61        31.96        35.74        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  STOX2 MUTATED STOX2 WILD-TYPE 
           6.18            0.00 
  STOX2 MUTATED STOX2 WILD-TYPE 
          37.02          148.01 
  STOX2 MUTATED STOX2 WILD-TYPE 
         16.535          20.910 
[1] "6.2 - 37.0 (16.5)"  "0.0 - 148.0 (20.9)"
[1] "hr=" "3"  
D2194V2, continuous
D2194V3, binary
                 cls
clus                0   1
  STOX2 MUTATED    10   0
  STOX2 WILD-TYPE 356 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STOX2 MUTATED     10    0
  STOX2 WILD-TYPE  356  119
        clus
vv       STOX2 MUTATED STOX2 WILD-TYPE
  COLON             10             356
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  STOX2 MUTATED         3        0        1         3         0         0
  STOX2 WILD-TYPE      88        1       31       135        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  STOX2 MUTATED           0          0          1          0        2         0
  STOX2 WILD-TYPE        24         11         58         42       46        18
                 vv
clus              STAGE IVB
  STOX2 MUTATED           0
  STOX2 WILD-TYPE         1
D2194V4, multiclass
            clus
vv           STOX2 MUTATED STOX2 WILD-TYPE
  STAGE I                3              88
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              3             135
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             0              42
  STAGE IV               2              46
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  STOX2 MUTATED     1   2   5   2
  STOX2 WILD-TYPE  16  90 324  48
D2194V5, multiclass
    clus
vv   STOX2 MUTATED STOX2 WILD-TYPE
  T1             1              16
  T2             2              90
  T3             5             324
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  STOX2 MUTATED     8   1   1
  STOX2 WILD-TYPE 279 112  86
D2194V6, multiclass
    clus
vv   STOX2 MUTATED STOX2 WILD-TYPE
  N0             8             279
  N1             1             112
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2194V7, binary
                 cls
clus                0   1
  STOX2 MUTATED     8   2
  STOX2 WILD-TYPE 367  63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STOX2 MUTATED      8    2
  STOX2 WILD-TYPE  367   63
   clus
vv  STOX2 MUTATED STOX2 WILD-TYPE
  0             8             367
  1             2              63
[1] 2 2
[1] FALSE
D2194V8, binary
                 cls
clus                0   1
  STOX2 MUTATED     3   7
  STOX2 WILD-TYPE 222 257
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STOX2 MUTATED      3    7
  STOX2 WILD-TYPE  222  257
        clus
vv       STOX2 MUTATED STOX2 WILD-TYPE
  FEMALE             3             222
  MALE               7             257
[1] 2 2
[1] FALSE
D2194V9, binary
                 cls
clus                0   1
  STOX2 MUTATED     8   2
  STOX2 WILD-TYPE 342  20
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STOX2 MUTATED      8    2
  STOX2 WILD-TYPE  342   20
     clus
vv    STOX2 MUTATED STOX2 WILD-TYPE
  NO              8             342
  YES             2              20
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  STOX2 MUTATED                     10                             0
  STOX2 WILD-TYPE                  305                            47
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  STOX2 MUTATED                       0                              0
  STOX2 WILD-TYPE                   106                             10
D2194V10, multiclass
                                clus
vv                               STOX2 MUTATED STOX2 WILD-TYPE
  COLON ADENOCARCINOMA                      10             305
  COLON MUCINOUS ADENOCARCINOMA              0              47
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  STOX2 MUTATED     6   0   1   0
  STOX2 WILD-TYPE 339   4  30  25
D2194V11, multiclass
    clus
vv   STOX2 MUTATED STOX2 WILD-TYPE
  R0             6             339
  R1             0               4
  R2             1              30
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2194V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  STOX2 MUTATED                                  0     0
  STOX2 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  STOX2 MUTATED                           1     6
  STOX2 WILD-TYPE                        21   220
D2194V13, multiclass
                                  clus
vv                                 STOX2 MUTATED STOX2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        6             220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2195) Variable = SIGLEC14 MUTATION ANALYSIS
D2195V1, survival
                    sevent
clus2                  0   1
  SIGLEC14 MUTATED     5   2
  SIGLEC14 WILD-TYPE 373  91
  SIGLEC14 MUTATED SIGLEC14 WILD-TYPE 
                 7                464 
  SIGLEC14 MUTATED SIGLEC14 WILD-TYPE 
                 2                 91 
$`SIGLEC14 MUTATED`
TCGA-AA-3977 TCGA-AZ-6598 TCGA-AZ-6601 TCGA-CM-4752 TCGA-D5-6927 TCGA-DM-A282 
       25.02        49.41       100.01        13.02         9.44       139.17 
TCGA-G4-6588 
       26.17 

$`SIGLEC14 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 
        5.13       106.75        22.36        62.79        88.21         6.77 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
       12.10        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       12.43        14.30         9.04        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A285 TCGA-DM-A28C 
        7.50        44.32       131.51       135.65         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       13.78        35.80        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  SIGLEC14 MUTATED SIGLEC14 WILD-TYPE 
              9.44               0.00 
  SIGLEC14 MUTATED SIGLEC14 WILD-TYPE 
            139.17             148.01 
  SIGLEC14 MUTATED SIGLEC14 WILD-TYPE 
            26.170             20.085 
[1] "9.4 - 139.2 (26.2)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.2"
D2195V2, continuous
D2195V3, binary
                    cls
clus                   0   1
  SIGLEC14 MUTATED     8   0
  SIGLEC14 WILD-TYPE 358 119
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SIGLEC14 MUTATED      8    0
  SIGLEC14 WILD-TYPE  358  119
        clus
vv       SIGLEC14 MUTATED SIGLEC14 WILD-TYPE
  COLON                 8                358
  RECTUM                0                119
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SIGLEC14 MUTATED         0        0        2         5         0         0
  SIGLEC14 WILD-TYPE      91        1       30       133        10         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SIGLEC14 MUTATED           0          0          0          0        0
  SIGLEC14 WILD-TYPE        24         11         59         42       48
                    vv
clus                 STAGE IVA STAGE IVB
  SIGLEC14 MUTATED           0         0
  SIGLEC14 WILD-TYPE        18         1
D2195V4, multiclass
            clus
vv           SIGLEC14 MUTATED SIGLEC14 WILD-TYPE
  STAGE I                   0                 91
  STAGE IA                  0                  1
  STAGE II                  2                 30
  STAGE IIA                 5                133
  STAGE IIB                 0                 10
  STAGE IIC                 0                  1
  STAGE III                 0                 24
  STAGE IIIA                0                 11
  STAGE IIIB                0                 59
  STAGE IIIC                0                 42
  STAGE IV                  0                 48
  STAGE IVA                 0                 18
  STAGE IVB                 0                  1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  SIGLEC14 MUTATED     0   1   7   0
  SIGLEC14 WILD-TYPE  17  91 322  50
D2195V5, multiclass
    clus
vv   SIGLEC14 MUTATED SIGLEC14 WILD-TYPE
  T1                0                 17
  T2                1                 91
  T3                7                322
  T4                0                 50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  SIGLEC14 MUTATED     8   0   0
  SIGLEC14 WILD-TYPE 279 113  87
D2195V6, multiclass
    clus
vv   SIGLEC14 MUTATED SIGLEC14 WILD-TYPE
  N0                8                279
  N1                0                113
  N2                0                 87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2195V7, binary
                    cls
clus                   0   1
  SIGLEC14 MUTATED     6   0
  SIGLEC14 WILD-TYPE 369  65
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SIGLEC14 MUTATED      6    0
  SIGLEC14 WILD-TYPE  369   65
   clus
vv  SIGLEC14 MUTATED SIGLEC14 WILD-TYPE
  0                6                369
  1                0                 65
[1] 2 2
[1] FALSE
D2195V8, binary
                    cls
clus                   0   1
  SIGLEC14 MUTATED     4   4
  SIGLEC14 WILD-TYPE 221 260
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SIGLEC14 MUTATED      4    4
  SIGLEC14 WILD-TYPE  221  260
        clus
vv       SIGLEC14 MUTATED SIGLEC14 WILD-TYPE
  FEMALE                4                221
  MALE                  4                260
[1] 2 2
[1] FALSE
D2195V9, binary
                    cls
clus                   0   1
  SIGLEC14 MUTATED     6   0
  SIGLEC14 WILD-TYPE 344  22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SIGLEC14 MUTATED      6    0
  SIGLEC14 WILD-TYPE  344   22
     clus
vv    SIGLEC14 MUTATED SIGLEC14 WILD-TYPE
  NO                 6                344
  YES                0                 22
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SIGLEC14 MUTATED                      8                             0
  SIGLEC14 WILD-TYPE                  307                            47
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SIGLEC14 MUTATED                       0                              0
  SIGLEC14 WILD-TYPE                   106                             10
D2195V10, multiclass
                                clus
vv                               SIGLEC14 MUTATED SIGLEC14 WILD-TYPE
  COLON ADENOCARCINOMA                          8                307
  COLON MUCINOUS ADENOCARCINOMA                 0                 47
  RECTAL ADENOCARCINOMA                         0                106
  RECTAL MUCINOUS ADENOCARCINOMA                0                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  R0  R1  R2  RX
  SIGLEC14 MUTATED     4   0   0   0
  SIGLEC14 WILD-TYPE 341   4  31  25
D2195V11, multiclass
    clus
vv   SIGLEC14 MUTATED SIGLEC14 WILD-TYPE
  R0                4                341
  R1                0                  4
  R2                0                 31
  RX                0                 25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2195V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SIGLEC14 MUTATED                                  0     0
  SIGLEC14 WILD-TYPE                                1    11
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  SIGLEC14 MUTATED                           1     5
  SIGLEC14 WILD-TYPE                        21   221
D2195V13, multiclass
                                  clus
vv                                 SIGLEC14 MUTATED SIGLEC14 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 11
  BLACK OR AFRICAN AMERICAN                       1                 21
  WHITE                                           5                221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2196) Variable = CALCR MUTATION ANALYSIS
D2196V1, survival
                 sevent
clus2               0   1
  CALCR MUTATED    10   2
  CALCR WILD-TYPE 368  91
  CALCR MUTATED CALCR WILD-TYPE 
             12             459 
  CALCR MUTATED CALCR WILD-TYPE 
              2              91 
$`CALCR MUTATED`
TCGA-A6-6654 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3555 TCGA-AA-3697 TCGA-AA-A010 
       23.87        63.98         1.02        29.95        85.05        34.98 
TCGA-AZ-6598 TCGA-D5-5540 TCGA-AF-3913 TCGA-AG-3731 TCGA-AG-A002 TCGA-DC-6681 
       49.41        56.09        10.39        37.02        20.98         5.95 

$`CALCR WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
       35.01         6.97        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       17.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 
        5.98        37.05        19.00        36.00         5.03        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 
       19.04        19.04        10.06        35.05        33.04         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5541 
       10.06        12.03        45.40        12.26        19.59        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-4110 TCGA-AF-5654 
       43.04        13.55        19.10        34.49        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
        0.99        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6682 TCGA-DC-6683 
       13.97        27.95        10.98        19.99         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  CALCR MUTATED CALCR WILD-TYPE 
           1.02            0.00 
  CALCR MUTATED CALCR WILD-TYPE 
          85.05          148.01 
  CALCR MUTATED CALCR WILD-TYPE 
         32.465          20.020 
[1] "1.0 - 85.0 (32.5)"  "0.0 - 148.0 (20.0)"
[1] "hr=" "1.6"
D2196V2, continuous
D2196V3, binary
                 cls
clus                0   1
  CALCR MUTATED     8   4
  CALCR WILD-TYPE 358 115
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CALCR MUTATED      8    4
  CALCR WILD-TYPE  358  115
        clus
vv       CALCR MUTATED CALCR WILD-TYPE
  COLON              8             358
  RECTUM             4             115
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CALCR MUTATED         2        0        2         2         1         0
  CALCR WILD-TYPE      89        1       30       136         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  CALCR MUTATED           1          0          1          0        2         1
  CALCR WILD-TYPE        23         11         58         42       46        17
                 vv
clus              STAGE IVB
  CALCR MUTATED           0
  CALCR WILD-TYPE         1
D2196V4, multiclass
            clus
vv           CALCR MUTATED CALCR WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA              2             136
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             1              58
  STAGE IIIC             0              42
  STAGE IV               2              46
  STAGE IVA              1              17
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CALCR MUTATED     0   2   9   1
  CALCR WILD-TYPE  17  90 320  49
D2196V5, multiclass
    clus
vv   CALCR MUTATED CALCR WILD-TYPE
  T1             0              17
  T2             2              90
  T3             9             320
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  CALCR MUTATED     8   3   1
  CALCR WILD-TYPE 279 110  86
D2196V6, multiclass
    clus
vv   CALCR MUTATED CALCR WILD-TYPE
  N0             8             279
  N1             3             110
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2196V7, binary
                 cls
clus                0   1
  CALCR MUTATED     8   3
  CALCR WILD-TYPE 367  62
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CALCR MUTATED      8    3
  CALCR WILD-TYPE  367   62
   clus
vv  CALCR MUTATED CALCR WILD-TYPE
  0             8             367
  1             3              62
[1] 2 2
[1] FALSE
D2196V8, binary
                 cls
clus                0   1
  CALCR MUTATED     6   6
  CALCR WILD-TYPE 219 258
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CALCR MUTATED      6    6
  CALCR WILD-TYPE  219  258
        clus
vv       CALCR MUTATED CALCR WILD-TYPE
  FEMALE             6             219
  MALE               6             258
[1] 2 2
[1] FALSE
D2196V9, binary
                 cls
clus                0   1
  CALCR MUTATED    11   0
  CALCR WILD-TYPE 339  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CALCR MUTATED     11    0
  CALCR WILD-TYPE  339   22
     clus
vv    CALCR MUTATED CALCR WILD-TYPE
  NO             11             339
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CALCR MUTATED                      7                             1
  CALCR WILD-TYPE                  308                            46
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CALCR MUTATED                       4                              0
  CALCR WILD-TYPE                   102                             10
D2196V10, multiclass
                                clus
vv                               CALCR MUTATED CALCR WILD-TYPE
  COLON ADENOCARCINOMA                       7             308
  COLON MUCINOUS ADENOCARCINOMA              1              46
  RECTAL ADENOCARCINOMA                      4             102
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  CALCR MUTATED     9   0   1   0
  CALCR WILD-TYPE 336   4  30  25
D2196V11, multiclass
    clus
vv   CALCR MUTATED CALCR WILD-TYPE
  R0             9             336
  R1             0               4
  R2             1              30
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2196V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CALCR MUTATED                                  0     0
  CALCR WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CALCR MUTATED                           1     4
  CALCR WILD-TYPE                        21   222
D2196V13, multiclass
                                  clus
vv                                 CALCR MUTATED CALCR WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        4             222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2197) Variable = TXNRD1 MUTATION ANALYSIS
D2197V1, survival
                  sevent
clus2                0   1
  TXNRD1 MUTATED     5   4
  TXNRD1 WILD-TYPE 373  89
  TXNRD1 MUTATED TXNRD1 WILD-TYPE 
               9              462 
  TXNRD1 MUTATED TXNRD1 WILD-TYPE 
               4               89 
$`TXNRD1 MUTATED`
TCGA-AA-3977 TCGA-AA-A00N TCGA-AD-5900 TCGA-AD-6964 TCGA-CA-6717 TCGA-CA-6718 
       25.02         4.01         0.07        10.88        12.76        10.06 
TCGA-DM-A0XF TCGA-G4-6628 TCGA-AG-3887 
       38.20        79.69        36.95 

$`TXNRD1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       39.98        18.05        40.96        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
        0.79         0.72         5.79        22.42        27.42         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 
        3.06         3.25         3.29         0.07        12.20        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.19        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A1D0 TCGA-DM-A1D4 
       11.38        10.26       119.70        24.43       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 
       35.80        26.17        91.79        46.75        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3890 TCGA-AG-3892 
       19.04        19.99         1.02        17.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  TXNRD1 MUTATED TXNRD1 WILD-TYPE 
            0.07             0.00 
  TXNRD1 MUTATED TXNRD1 WILD-TYPE 
           79.69           148.01 
  TXNRD1 MUTATED TXNRD1 WILD-TYPE 
          12.760           20.235 
[1] "0.1 - 79.7 (12.8)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "2.6"
D2197V2, continuous
D2197V3, binary
                  cls
clus                 0   1
  TXNRD1 MUTATED     8   1
  TXNRD1 WILD-TYPE 358 118
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TXNRD1 MUTATED      8    1
  TXNRD1 WILD-TYPE  358  118
        clus
vv       TXNRD1 MUTATED TXNRD1 WILD-TYPE
  COLON               8              358
  RECTUM              1              118
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TXNRD1 MUTATED         2        0        0         3         1         0
  TXNRD1 WILD-TYPE      89        1       32       135         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  TXNRD1 MUTATED           0          0          0          1        0
  TXNRD1 WILD-TYPE        24         11         59         41       48
                  vv
clus               STAGE IVA STAGE IVB
  TXNRD1 MUTATED           0         0
  TXNRD1 WILD-TYPE        18         1
D2197V4, multiclass
            clus
vv           TXNRD1 MUTATED TXNRD1 WILD-TYPE
  STAGE I                 2               89
  STAGE IA                0                1
  STAGE II                0               32
  STAGE IIA               3              135
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              0               59
  STAGE IIIC              1               41
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  TXNRD1 MUTATED     0   3   4   2
  TXNRD1 WILD-TYPE  17  89 325  48
D2197V5, multiclass
    clus
vv   TXNRD1 MUTATED TXNRD1 WILD-TYPE
  T1              0               17
  T2              3               89
  T3              4              325
  T4              2               48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  TXNRD1 MUTATED     7   0   2
  TXNRD1 WILD-TYPE 280 113  85
D2197V6, multiclass
    clus
vv   TXNRD1 MUTATED TXNRD1 WILD-TYPE
  N0              7              280
  N1              0              113
  N2              2               85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2197V7, binary
                  cls
clus                 0   1
  TXNRD1 MUTATED     6   0
  TXNRD1 WILD-TYPE 369  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TXNRD1 MUTATED      6    0
  TXNRD1 WILD-TYPE  369   65
   clus
vv  TXNRD1 MUTATED TXNRD1 WILD-TYPE
  0              6              369
  1              0               65
[1] 2 2
[1] FALSE
D2197V8, binary
                  cls
clus                 0   1
  TXNRD1 MUTATED     1   8
  TXNRD1 WILD-TYPE 224 256
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TXNRD1 MUTATED      1    8
  TXNRD1 WILD-TYPE  224  256
        clus
vv       TXNRD1 MUTATED TXNRD1 WILD-TYPE
  FEMALE              1              224
  MALE                8              256
[1] 2 2
[1] FALSE
D2197V9, binary
                  cls
clus                 0   1
  TXNRD1 MUTATED     5   1
  TXNRD1 WILD-TYPE 345  21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TXNRD1 MUTATED      5    1
  TXNRD1 WILD-TYPE  345   21
     clus
vv    TXNRD1 MUTATED TXNRD1 WILD-TYPE
  NO               5              345
  YES              1               21
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  TXNRD1 MUTATED                      4                             3
  TXNRD1 WILD-TYPE                  311                            44
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  TXNRD1 MUTATED                       0                              1
  TXNRD1 WILD-TYPE                   106                              9
D2197V10, multiclass
                                clus
vv                               TXNRD1 MUTATED TXNRD1 WILD-TYPE
  COLON ADENOCARCINOMA                        4              311
  COLON MUCINOUS ADENOCARCINOMA               3               44
  RECTAL ADENOCARCINOMA                       0              106
  RECTAL MUCINOUS ADENOCARCINOMA              1                9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  TXNRD1 MUTATED     4   0   0   2
  TXNRD1 WILD-TYPE 341   4  31  23
D2197V11, multiclass
    clus
vv   TXNRD1 MUTATED TXNRD1 WILD-TYPE
  R0              4              341
  R1              0                4
  R2              0               31
  RX              2               23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2197V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TXNRD1 MUTATED                                  0     2
  TXNRD1 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  TXNRD1 MUTATED                           0     4
  TXNRD1 WILD-TYPE                        22   222
D2197V13, multiclass
                                  clus
vv                                 TXNRD1 MUTATED TXNRD1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         2                9
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         4              222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2198) Variable = ZFP1 MUTATION ANALYSIS
D2198V1, survival
                sevent
clus2              0   1
  ZFP1 MUTATED     4   0
  ZFP1 WILD-TYPE 374  93
  ZFP1 MUTATED ZFP1 WILD-TYPE 
             4            467 
  ZFP1 MUTATED ZFP1 WILD-TYPE 
             0             93 
$`ZFP1 MUTATED`
TCGA-AA-3510 TCGA-AA-3977 TCGA-AA-A010 TCGA-AD-6890 
       63.98        25.02        34.98         0.79 

$`ZFP1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  ZFP1 MUTATED ZFP1 WILD-TYPE 
          0.79           0.00 
  ZFP1 MUTATED ZFP1 WILD-TYPE 
         63.98         148.01 
  ZFP1 MUTATED ZFP1 WILD-TYPE 
         30.00          20.12 
[1] "0.8 - 64.0 (30.0)"  "0.0 - 148.0 (20.1)"
[1] "hr="     "9100000"
D2198V2, continuous
D2198V3, binary
                cls
clus               0   1
  ZFP1 MUTATED     4   0
  ZFP1 WILD-TYPE 362 119
[1] "tbl2"
                cls
clus             [,1] [,2]
  ZFP1 MUTATED      4    0
  ZFP1 WILD-TYPE  362  119
        clus
vv       ZFP1 MUTATED ZFP1 WILD-TYPE
  COLON             4            362
  RECTUM            0            119
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZFP1 MUTATED         0        0        1         0         1         0
  ZFP1 WILD-TYPE      91        1       31       138         9         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ZFP1 MUTATED           0          0          0          0        0         0
  ZFP1 WILD-TYPE        24         11         59         42       48        18
                vv
clus             STAGE IVB
  ZFP1 MUTATED           0
  ZFP1 WILD-TYPE         1
D2198V4, multiclass
[1] "Remove cluster labels:" "ZFP1 MUTATED"          
clus
  ZFP1 MUTATED ZFP1 WILD-TYPE 
             2            474 
    TCGA-A6-2671     TCGA-A6-2672     TCGA-A6-2674     TCGA-A6-2676 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-A6-2677     TCGA-A6-2678     TCGA-A6-2683     TCGA-A6-3807 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-A6-3808     TCGA-A6-3809     TCGA-A6-3810     TCGA-A6-4105 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-A6-5656     TCGA-A6-5657     TCGA-A6-5659     TCGA-A6-5660 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-A6-5661     TCGA-A6-5662     TCGA-A6-5664     TCGA-A6-5665 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-A6-5666     TCGA-A6-6137     TCGA-A6-6138     TCGA-A6-6141 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-A6-6142     TCGA-A6-6648     TCGA-A6-6649     TCGA-A6-6651 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-A6-6652     TCGA-A6-6653     TCGA-A6-6654     TCGA-A6-6780 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-A6-6781     TCGA-A6-6782     TCGA-AA-3489     TCGA-AA-3492 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AA-3496     TCGA-AA-3502     TCGA-AA-3511     TCGA-AA-3514 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AA-3516     TCGA-AA-3517     TCGA-AA-3518     TCGA-AA-3519 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AA-3520     TCGA-AA-3521     TCGA-AA-3522     TCGA-AA-3524 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AA-3525     TCGA-AA-3526     TCGA-AA-3527     TCGA-AA-3529 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AA-3530     TCGA-AA-3531     TCGA-AA-3532     TCGA-AA-3534 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AA-3538     TCGA-AA-3542     TCGA-AA-3543     TCGA-AA-3544 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AA-3548     TCGA-AA-3549     TCGA-AA-3552     TCGA-AA-3553 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AA-3554     TCGA-AA-3555     TCGA-AA-3556     TCGA-AA-3558 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AA-3560     TCGA-AA-3561     TCGA-AA-3562     TCGA-AA-3655 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AA-3660     TCGA-AA-3662     TCGA-AA-3663     TCGA-AA-3664 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AA-3666     TCGA-AA-3667     TCGA-AA-3672     TCGA-AA-3673 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AA-3678     TCGA-AA-3679     TCGA-AA-3680     TCGA-AA-3681 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AA-3684     TCGA-AA-3685     TCGA-AA-3688     TCGA-AA-3692 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AA-3693     TCGA-AA-3695     TCGA-AA-3696     TCGA-AA-3697 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AA-3710     TCGA-AA-3712     TCGA-AA-3713     TCGA-AA-3715 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AA-3811     TCGA-AA-3812     TCGA-AA-3814     TCGA-AA-3815 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AA-3818     TCGA-AA-3819     TCGA-AA-3821     TCGA-AA-3831 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AA-3833     TCGA-AA-3837     TCGA-AA-3842     TCGA-AA-3844 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AA-3845     TCGA-AA-3846     TCGA-AA-3848     TCGA-AA-3850 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AA-3851     TCGA-AA-3852     TCGA-AA-3854     TCGA-AA-3855 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AA-3856     TCGA-AA-3858     TCGA-AA-3860     TCGA-AA-3861 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AA-3864     TCGA-AA-3866     TCGA-AA-3867     TCGA-AA-3869 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AA-3870     TCGA-AA-3872     TCGA-AA-3875     TCGA-AA-3877 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AA-3930     TCGA-AA-3939     TCGA-AA-3941     TCGA-AA-3947 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AA-3949     TCGA-AA-3950     TCGA-AA-3952     TCGA-AA-3955 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AA-3956     TCGA-AA-3966     TCGA-AA-3968     TCGA-AA-3971 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AA-3972     TCGA-AA-3973     TCGA-AA-3975     TCGA-AA-3976 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AA-3979     TCGA-AA-3980     TCGA-AA-3982     TCGA-AA-3984 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AA-3986     TCGA-AA-3989     TCGA-AA-3994     TCGA-AA-A004 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AA-A00A     TCGA-AA-A00D     TCGA-AA-A00E     TCGA-AA-A00F 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AA-A00J     TCGA-AA-A00K     TCGA-AA-A00L     TCGA-AA-A00N 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AA-A00O     TCGA-AA-A00Q     TCGA-AA-A00R     TCGA-AA-A00U 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AA-A00W     TCGA-AA-A00Z     TCGA-AA-A017     TCGA-AA-A01D 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AA-A01F     TCGA-AA-A01G     TCGA-AA-A01I     TCGA-AA-A01K 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AA-A01P     TCGA-AA-A01Q     TCGA-AA-A01R     TCGA-AA-A01S 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AA-A01T     TCGA-AA-A01V     TCGA-AA-A01X     TCGA-AA-A01Z 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AA-A022     TCGA-AA-A024     TCGA-AA-A029     TCGA-AA-A02F 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AA-A02H     TCGA-AA-A02J     TCGA-AA-A02K     TCGA-AA-A02O 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AA-A02W     TCGA-AA-A02Y     TCGA-AA-A03F     TCGA-AA-A03J 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AD-5900     TCGA-AD-6548     TCGA-AD-6888     TCGA-AD-6889 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AD-6899     TCGA-AU-3779     TCGA-AU-6004     TCGA-AY-4070 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AY-4071     TCGA-AY-5543     TCGA-AY-6196     TCGA-AY-6197 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AY-6386     TCGA-AZ-4315     TCGA-AZ-4323     TCGA-AZ-4616 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AZ-4681     TCGA-AZ-4682     TCGA-AZ-5403     TCGA-AZ-5407 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AZ-6598     TCGA-AZ-6599     TCGA-AZ-6600     TCGA-AZ-6601 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AZ-6605     TCGA-AZ-6606     TCGA-AZ-6607     TCGA-AZ-6608 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-CA-5254     TCGA-CA-5255     TCGA-CA-5796     TCGA-CA-5797 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-CA-6715     TCGA-CA-6716     TCGA-CA-6717     TCGA-CA-6718 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-CA-6719     TCGA-CK-4947     TCGA-CK-4948     TCGA-CK-4950 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-CK-4952     TCGA-CK-5912     TCGA-CK-5913     TCGA-CK-5914 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-CK-5915     TCGA-CK-5916     TCGA-CK-6746     TCGA-CK-6747 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-CK-6748     TCGA-CK-6751     TCGA-CM-4743     TCGA-CM-4744 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-CM-4746     TCGA-CM-4747     TCGA-CM-4752     TCGA-CM-5341 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-CM-5344     TCGA-CM-5348     TCGA-CM-5349     TCGA-CM-5860 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-CM-5861     TCGA-CM-5862     TCGA-CM-5863     TCGA-CM-5864 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-CM-5868     TCGA-CM-6161     TCGA-CM-6162     TCGA-CM-6163 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-CM-6164     TCGA-CM-6165     TCGA-CM-6166     TCGA-CM-6167 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-CM-6168     TCGA-CM-6169     TCGA-CM-6170     TCGA-CM-6171 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-CM-6172     TCGA-CM-6674     TCGA-CM-6675     TCGA-CM-6676 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-CM-6677     TCGA-CM-6678     TCGA-CM-6679     TCGA-CM-6680 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-D5-5537     TCGA-D5-5538     TCGA-D5-5539     TCGA-D5-5540 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-D5-5541     TCGA-D5-6529     TCGA-D5-6532     TCGA-D5-6533 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-D5-6534     TCGA-D5-6535     TCGA-D5-6536     TCGA-D5-6537 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-D5-6538     TCGA-D5-6539     TCGA-D5-6540     TCGA-D5-6541 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-D5-6898     TCGA-D5-6920     TCGA-D5-6922     TCGA-D5-6923 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-D5-6924     TCGA-D5-6926     TCGA-D5-6927     TCGA-D5-6928 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-D5-6929     TCGA-D5-6930     TCGA-D5-6931     TCGA-D5-6932 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-D5-7000     TCGA-DM-A0X9     TCGA-DM-A0XD     TCGA-DM-A0XF 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-DM-A1D0     TCGA-DM-A1D4     TCGA-DM-A1D6     TCGA-DM-A1D7 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-DM-A1D9     TCGA-DM-A1DA     TCGA-DM-A1DB     TCGA-DM-A1HA 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-DM-A1HB     TCGA-DM-A282     TCGA-DM-A285     TCGA-DM-A28C 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-DM-A28E     TCGA-DM-A28F     TCGA-DM-A28G     TCGA-DM-A28H 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-DM-A28K     TCGA-F4-6459     TCGA-F4-6460     TCGA-F4-6569 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-F4-6570     TCGA-F4-6703     TCGA-F4-6704     TCGA-F4-6805 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-F4-6806     TCGA-F4-6807     TCGA-F4-6808     TCGA-F4-6809 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-F4-6854     TCGA-F4-6855     TCGA-F4-6856     TCGA-G4-6293 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-G4-6299     TCGA-G4-6303     TCGA-G4-6304     TCGA-G4-6306 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-G4-6307     TCGA-G4-6309     TCGA-G4-6310     TCGA-G4-6315 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-G4-6317     TCGA-G4-6321     TCGA-G4-6323     TCGA-G4-6586 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-G4-6588     TCGA-G4-6625     TCGA-G4-6626     TCGA-G4-6628 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AF-2687     TCGA-AF-2689     TCGA-AF-2691     TCGA-AF-2692 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AF-2693     TCGA-AF-3400     TCGA-AF-3913     TCGA-AF-4110 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AF-5654     TCGA-AF-6136     TCGA-AF-6655     TCGA-AF-6672 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AG-3574     TCGA-AG-3575     TCGA-AG-3578     TCGA-AG-3580 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AG-3581     TCGA-AG-3582     TCGA-AG-3583     TCGA-AG-3584 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AG-3586     TCGA-AG-3587     TCGA-AG-3593     TCGA-AG-3594 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AG-3598     TCGA-AG-3599     TCGA-AG-3600     TCGA-AG-3601 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AG-3602     TCGA-AG-3605     TCGA-AG-3608     TCGA-AG-3609 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AG-3611     TCGA-AG-3612     TCGA-AG-3726     TCGA-AG-3727 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AG-3731     TCGA-AG-3732     TCGA-AG-3742     TCGA-AG-3878 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AG-3881     TCGA-AG-3882     TCGA-AG-3883     TCGA-AG-3885 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AG-3887     TCGA-AG-3890     TCGA-AG-3892     TCGA-AG-3893 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AG-3894     TCGA-AG-3896     TCGA-AG-3898     TCGA-AG-3901 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AG-3902     TCGA-AG-3909     TCGA-AG-3999     TCGA-AG-4001 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AG-4005     TCGA-AG-4007     TCGA-AG-4008     TCGA-AG-4015 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AG-A002     TCGA-AG-A008     TCGA-AG-A00C     TCGA-AG-A00H 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AG-A00Y     TCGA-AG-A011     TCGA-AG-A014     TCGA-AG-A015 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AG-A016     TCGA-AG-A01L     TCGA-AG-A01W     TCGA-AG-A01Y 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AG-A020     TCGA-AG-A025     TCGA-AG-A026     TCGA-AG-A02G 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AG-A02N     TCGA-AG-A02X     TCGA-AG-A032     TCGA-AG-A036 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AH-6643     TCGA-CI-6619     TCGA-CI-6620     TCGA-CI-6621 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-CI-6622     TCGA-CI-6624     TCGA-CL-5917     TCGA-CL-5918 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-DC-5337     TCGA-DC-5869     TCGA-DC-6155     TCGA-DC-6157 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-DC-6158     TCGA-DC-6160     TCGA-DC-6681     TCGA-DC-6682 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-DC-6683     TCGA-DT-5265     TCGA-DY-A0XA     TCGA-DY-A1DC 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-DY-A1DD     TCGA-DY-A1DF     TCGA-DY-A1DG     TCGA-DY-A1H8 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-EF-5830     TCGA-EI-6506     TCGA-EI-6507     TCGA-EI-6508 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-EI-6510     TCGA-F5-6464     TCGA-F5-6465     TCGA-F5-6571 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-F5-6702     TCGA-F5-6811     TCGA-F5-6812     TCGA-F5-6813 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-G5-6235     TCGA-G5-6641 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
                vv
clus              T1  T2  T3  T4
  ZFP1 MUTATED     1   1   1   1
  ZFP1 WILD-TYPE  16  91 328  49
D2198V5, multiclass
    clus
vv   ZFP1 MUTATED ZFP1 WILD-TYPE
  T1            1             16
  T2            1             91
  T3            1            328
  T4            1             49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  ZFP1 MUTATED     4   0   0
  ZFP1 WILD-TYPE 283 113  87
D2198V6, multiclass
    clus
vv   ZFP1 MUTATED ZFP1 WILD-TYPE
  N0            4            283
  N1            0            113
  N2            0             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2198V7, binary
                cls
clus               0   1
  ZFP1 MUTATED     2   0
  ZFP1 WILD-TYPE 373  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  ZFP1 MUTATED      2    0
  ZFP1 WILD-TYPE  373   65
   clus
vv  ZFP1 MUTATED ZFP1 WILD-TYPE
  0            2            373
  1            0             65
[1] 2 2
[1] FALSE
D2198V8, binary
                cls
clus               0   1
  ZFP1 MUTATED     1   3
  ZFP1 WILD-TYPE 224 261
[1] "tbl2"
                cls
clus             [,1] [,2]
  ZFP1 MUTATED      1    3
  ZFP1 WILD-TYPE  224  261
        clus
vv       ZFP1 MUTATED ZFP1 WILD-TYPE
  FEMALE            1            224
  MALE              3            261
[1] 2 2
[1] FALSE
D2198V9, binary
                cls
clus               0   1
  ZFP1 MUTATED     3   0
  ZFP1 WILD-TYPE 347  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  ZFP1 MUTATED      3    0
  ZFP1 WILD-TYPE  347   22
     clus
vv    ZFP1 MUTATED ZFP1 WILD-TYPE
  NO             3            347
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ZFP1 MUTATED                      4                             0
  ZFP1 WILD-TYPE                  311                            47
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ZFP1 MUTATED                       0                              0
  ZFP1 WILD-TYPE                   106                             10
D2198V10, multiclass
                                clus
vv                               ZFP1 MUTATED ZFP1 WILD-TYPE
  COLON ADENOCARCINOMA                      4            311
  COLON MUCINOUS ADENOCARCINOMA             0             47
  RECTAL ADENOCARCINOMA                     0            106
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  ZFP1 MUTATED     2   0   0   0
  ZFP1 WILD-TYPE 343   4  31  25
D2198V11, multiclass
[1] "Remove cluster labels:" "ZFP1 MUTATED"          
clus
  ZFP1 MUTATED ZFP1 WILD-TYPE 
             2            403 
    TCGA-A6-2671     TCGA-A6-2672     TCGA-A6-2674     TCGA-A6-2676 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-A6-2677     TCGA-A6-2678     TCGA-A6-2683     TCGA-A6-3807 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-A6-3808     TCGA-A6-3809     TCGA-A6-3810     TCGA-A6-5657 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-A6-5659     TCGA-A6-5661     TCGA-A6-5665     TCGA-A6-6781 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AA-3489     TCGA-AA-3492     TCGA-AA-3496     TCGA-AA-3502 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AA-3511     TCGA-AA-3514     TCGA-AA-3517     TCGA-AA-3518 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AA-3519     TCGA-AA-3520     TCGA-AA-3521     TCGA-AA-3522 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AA-3524     TCGA-AA-3525     TCGA-AA-3526     TCGA-AA-3527 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AA-3529     TCGA-AA-3530     TCGA-AA-3531     TCGA-AA-3532 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AA-3534     TCGA-AA-3538     TCGA-AA-3542     TCGA-AA-3543 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AA-3544     TCGA-AA-3548     TCGA-AA-3549     TCGA-AA-3552 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AA-3553     TCGA-AA-3554     TCGA-AA-3555     TCGA-AA-3556 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AA-3558     TCGA-AA-3560     TCGA-AA-3561     TCGA-AA-3562 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AA-3655     TCGA-AA-3660     TCGA-AA-3662     TCGA-AA-3663 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AA-3664     TCGA-AA-3666     TCGA-AA-3667     TCGA-AA-3672 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AA-3673     TCGA-AA-3678     TCGA-AA-3679     TCGA-AA-3680 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AA-3681     TCGA-AA-3684     TCGA-AA-3685     TCGA-AA-3688 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AA-3692     TCGA-AA-3693     TCGA-AA-3695     TCGA-AA-3696 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AA-3697     TCGA-AA-3710     TCGA-AA-3712     TCGA-AA-3713 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AA-3715     TCGA-AA-3811     TCGA-AA-3812     TCGA-AA-3814 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AA-3815     TCGA-AA-3818     TCGA-AA-3819     TCGA-AA-3821 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AA-3831     TCGA-AA-3833     TCGA-AA-3837     TCGA-AA-3842 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AA-3844     TCGA-AA-3845     TCGA-AA-3846     TCGA-AA-3848 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AA-3850     TCGA-AA-3851     TCGA-AA-3852     TCGA-AA-3854 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AA-3855     TCGA-AA-3856     TCGA-AA-3858     TCGA-AA-3860 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AA-3861     TCGA-AA-3864     TCGA-AA-3866     TCGA-AA-3867 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AA-3869     TCGA-AA-3870     TCGA-AA-3872     TCGA-AA-3875 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AA-3877     TCGA-AA-3930     TCGA-AA-3939     TCGA-AA-3941 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AA-3947     TCGA-AA-3949     TCGA-AA-3950     TCGA-AA-3952 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AA-3955     TCGA-AA-3956     TCGA-AA-3968     TCGA-AA-3971 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AA-3972     TCGA-AA-3973     TCGA-AA-3975     TCGA-AA-3976 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AA-3979     TCGA-AA-3984     TCGA-AA-3986     TCGA-AA-3989 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AA-3994     TCGA-AA-A004     TCGA-AA-A00A     TCGA-AA-A00D 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AA-A00E     TCGA-AA-A00F     TCGA-AA-A00J     TCGA-AA-A00K 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AA-A00L     TCGA-AA-A00N     TCGA-AA-A00O     TCGA-AA-A00Q 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AA-A00R     TCGA-AA-A00U     TCGA-AA-A00W     TCGA-AA-A00Z 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AA-A017     TCGA-AA-A01D     TCGA-AA-A01F     TCGA-AA-A01G 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AA-A01I     TCGA-AA-A01K     TCGA-AA-A01P     TCGA-AA-A01Q 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AA-A01R     TCGA-AA-A01S     TCGA-AA-A01T     TCGA-AA-A01V 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AA-A01X     TCGA-AA-A01Z     TCGA-AA-A022     TCGA-AA-A024 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AA-A029     TCGA-AA-A02F     TCGA-AA-A02H     TCGA-AA-A02J 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AA-A02K     TCGA-AA-A02O     TCGA-AA-A02W     TCGA-AA-A02Y 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AA-A03F     TCGA-AA-A03J     TCGA-AD-5900     TCGA-AD-6548 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AD-6888     TCGA-AU-3779     TCGA-AU-6004     TCGA-AY-4070 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AY-4071     TCGA-AY-5543     TCGA-AY-6196     TCGA-AY-6197 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AY-6386     TCGA-AZ-4315     TCGA-AZ-4681     TCGA-AZ-4682 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-CA-5254     TCGA-CA-5255     TCGA-CA-5796     TCGA-CA-5797 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-CA-6715     TCGA-CA-6716     TCGA-CA-6717     TCGA-CA-6718 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-CA-6719     TCGA-CK-4947     TCGA-CK-4948     TCGA-CK-4950 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-CK-4952     TCGA-CK-5912     TCGA-CK-5913     TCGA-CK-5914 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-CK-5915     TCGA-CK-5916     TCGA-CK-6746     TCGA-CK-6747 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-CK-6748     TCGA-CK-6751     TCGA-CM-4743     TCGA-CM-4744 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-CM-4746     TCGA-CM-4747     TCGA-CM-4752     TCGA-CM-5341 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-CM-5344     TCGA-CM-5348     TCGA-CM-5349     TCGA-CM-5860 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-CM-5861     TCGA-CM-5862     TCGA-CM-5863     TCGA-CM-5864 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-CM-5868     TCGA-CM-6161     TCGA-CM-6162     TCGA-CM-6163 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-CM-6164     TCGA-CM-6165     TCGA-CM-6166     TCGA-CM-6167 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-CM-6168     TCGA-CM-6169     TCGA-CM-6170     TCGA-CM-6171 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-CM-6172     TCGA-CM-6674     TCGA-CM-6675     TCGA-CM-6676 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-CM-6677     TCGA-CM-6678     TCGA-CM-6679     TCGA-CM-6680 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-D5-5537     TCGA-D5-5538     TCGA-D5-5539     TCGA-D5-5540 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-D5-5541     TCGA-D5-6529     TCGA-D5-6532     TCGA-D5-6533 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-D5-6534     TCGA-D5-6535     TCGA-D5-6536     TCGA-D5-6537 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-D5-6538     TCGA-D5-6539     TCGA-D5-6540     TCGA-D5-6541 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-D5-6898     TCGA-D5-6920     TCGA-D5-6922     TCGA-D5-6923 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-D5-6924     TCGA-D5-6926     TCGA-D5-6927     TCGA-D5-6928 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-D5-6929     TCGA-D5-6930     TCGA-D5-6931     TCGA-D5-6932 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-D5-7000     TCGA-F4-6459     TCGA-F4-6460     TCGA-F4-6569 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-F4-6570     TCGA-F4-6703     TCGA-F4-6704     TCGA-F4-6805 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-F4-6806     TCGA-F4-6807     TCGA-F4-6808     TCGA-F4-6809 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-F4-6854     TCGA-F4-6855     TCGA-F4-6856     TCGA-G4-6293 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-G4-6299     TCGA-G4-6303     TCGA-G4-6304     TCGA-G4-6306 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-G4-6307     TCGA-G4-6309     TCGA-G4-6310     TCGA-G4-6315 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-G4-6317     TCGA-G4-6321     TCGA-G4-6323     TCGA-G4-6586 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-G4-6588     TCGA-G4-6625     TCGA-G4-6626     TCGA-G4-6628 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AF-2687     TCGA-AF-2689     TCGA-AF-2691     TCGA-AF-2692 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AF-3400     TCGA-AF-3913     TCGA-AF-4110     TCGA-AF-5654 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AF-6655     TCGA-AG-3574     TCGA-AG-3575     TCGA-AG-3578 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AG-3580     TCGA-AG-3581     TCGA-AG-3582     TCGA-AG-3583 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AG-3584     TCGA-AG-3586     TCGA-AG-3587     TCGA-AG-3593 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AG-3594     TCGA-AG-3598     TCGA-AG-3599     TCGA-AG-3600 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AG-3601     TCGA-AG-3602     TCGA-AG-3605     TCGA-AG-3608 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AG-3609     TCGA-AG-3611     TCGA-AG-3612     TCGA-AG-3726 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AG-3727     TCGA-AG-3731     TCGA-AG-3732     TCGA-AG-3742 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AG-3878     TCGA-AG-3882     TCGA-AG-3883     TCGA-AG-3885 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AG-3887     TCGA-AG-3890     TCGA-AG-3892     TCGA-AG-3893 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AG-3894     TCGA-AG-3896     TCGA-AG-3898     TCGA-AG-3901 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AG-3902     TCGA-AG-3909     TCGA-AG-3999     TCGA-AG-4001 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AG-4005     TCGA-AG-4007     TCGA-AG-4008     TCGA-AG-4015 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AG-A002     TCGA-AG-A008     TCGA-AG-A00C     TCGA-AG-A00H 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AG-A00Y     TCGA-AG-A011     TCGA-AG-A014     TCGA-AG-A015 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AG-A016     TCGA-AG-A01L     TCGA-AG-A01W     TCGA-AG-A01Y 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AG-A020     TCGA-AG-A025     TCGA-AG-A026     TCGA-AG-A02G 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AG-A02N     TCGA-AG-A02X     TCGA-AG-A032     TCGA-AG-A036 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AH-6549     TCGA-AH-6643     TCGA-CL-5917     TCGA-CL-5918 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-DC-5337     TCGA-DC-5869     TCGA-DC-6155     TCGA-DC-6157 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-DC-6158     TCGA-DC-6160     TCGA-DC-6681     TCGA-DC-6682 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-DC-6683     TCGA-DT-5265     TCGA-EF-5830     TCGA-EI-6506 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-EI-6507     TCGA-EI-6508     TCGA-EI-6510     TCGA-F5-6464 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-F5-6465     TCGA-F5-6571     TCGA-F5-6702     TCGA-F5-6812 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-F5-6813     TCGA-G5-6235     TCGA-G5-6641 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
D2198V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZFP1 MUTATED                                  0     0
  ZFP1 WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  ZFP1 MUTATED                           0     1
  ZFP1 WILD-TYPE                        22   225
D2198V13, multiclass
[1] "Remove cluster labels:" "ZFP1 MUTATED"          
clus
  ZFP1 MUTATED ZFP1 WILD-TYPE 
             1            259 
    TCGA-A6-2671     TCGA-A6-2672     TCGA-A6-2674     TCGA-A6-2676 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-A6-2677     TCGA-A6-2678     TCGA-A6-2683     TCGA-A6-3807 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-A6-3808     TCGA-A6-3809     TCGA-A6-3810     TCGA-A6-4105 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-A6-5656     TCGA-A6-5657     TCGA-A6-5659     TCGA-A6-5660 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-A6-5661     TCGA-A6-5662     TCGA-A6-5664     TCGA-A6-5665 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-A6-5666     TCGA-A6-6137     TCGA-A6-6138     TCGA-A6-6141 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-A6-6142     TCGA-A6-6648     TCGA-A6-6649     TCGA-A6-6651 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-A6-6652     TCGA-A6-6653     TCGA-A6-6654     TCGA-A6-6780 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-A6-6781     TCGA-A6-6782     TCGA-AD-5900     TCGA-AD-6548 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AD-6888     TCGA-AD-6889     TCGA-AD-6895     TCGA-AD-6899 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AD-6901     TCGA-AD-6963     TCGA-AD-6964     TCGA-AD-6965 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AU-3779     TCGA-AU-6004     TCGA-AY-4070     TCGA-AY-4071 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AY-5543     TCGA-AY-6196     TCGA-AY-6197     TCGA-AY-6386 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AZ-4315     TCGA-AZ-4323     TCGA-AZ-4616     TCGA-AZ-4681 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AZ-4682     TCGA-AZ-5403     TCGA-AZ-5407     TCGA-AZ-6598 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AZ-6599     TCGA-AZ-6600     TCGA-AZ-6601     TCGA-AZ-6603 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AZ-6605     TCGA-AZ-6606     TCGA-AZ-6607     TCGA-AZ-6608 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-CA-5254     TCGA-CA-5255     TCGA-CA-5796     TCGA-CA-5797 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-CA-6715     TCGA-CA-6716     TCGA-CA-6717     TCGA-CA-6718 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-CA-6719     TCGA-CK-4947     TCGA-CK-4948     TCGA-CK-4950 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-CK-4952     TCGA-CK-5912     TCGA-CK-5913     TCGA-CK-5914 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-CK-5915     TCGA-CK-5916     TCGA-CK-6746     TCGA-CK-6747 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-CK-6748     TCGA-CK-6751     TCGA-CM-4743     TCGA-CM-4744 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-CM-4746     TCGA-CM-4747     TCGA-CM-4752     TCGA-CM-5341 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-CM-5344     TCGA-CM-5348     TCGA-CM-5349     TCGA-CM-5860 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-CM-5861     TCGA-CM-5862     TCGA-CM-5863     TCGA-CM-5864 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-CM-5868     TCGA-CM-6161     TCGA-CM-6162     TCGA-CM-6163 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-CM-6164     TCGA-CM-6165     TCGA-CM-6166     TCGA-CM-6167 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-CM-6168     TCGA-CM-6169     TCGA-CM-6170     TCGA-CM-6171 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-CM-6172     TCGA-CM-6674     TCGA-CM-6675     TCGA-CM-6676 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-CM-6677     TCGA-CM-6678     TCGA-CM-6679     TCGA-CM-6680 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-D5-5537     TCGA-D5-5538     TCGA-D5-5539     TCGA-D5-5540 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-D5-5541     TCGA-D5-6529     TCGA-D5-6532     TCGA-D5-6533 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-D5-6534     TCGA-D5-6535     TCGA-D5-6536     TCGA-D5-6537 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-D5-6538     TCGA-D5-6539     TCGA-D5-6540     TCGA-D5-6541 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-D5-6898     TCGA-D5-6920     TCGA-D5-6922     TCGA-D5-6923 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-D5-6924     TCGA-D5-6926     TCGA-D5-6927     TCGA-D5-6928 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-D5-6929     TCGA-D5-6930     TCGA-D5-6931     TCGA-D5-6932 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-D5-7000     TCGA-DM-A0X9     TCGA-DM-A0XD     TCGA-DM-A0XF 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-DM-A1D0     TCGA-DM-A1D4     TCGA-DM-A1D6     TCGA-DM-A1D7 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-DM-A1D8     TCGA-DM-A1D9     TCGA-DM-A1DA     TCGA-DM-A1DB 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-DM-A1HA     TCGA-DM-A1HB     TCGA-DM-A282     TCGA-DM-A285 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-DM-A28C     TCGA-DM-A28E     TCGA-DM-A28F     TCGA-DM-A28G 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-DM-A28H     TCGA-DM-A28K     TCGA-F4-6459     TCGA-F4-6460 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-F4-6569     TCGA-F4-6570     TCGA-F4-6703     TCGA-F4-6704 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-F4-6805     TCGA-F4-6806     TCGA-F4-6807     TCGA-F4-6808 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-F4-6809     TCGA-F4-6854     TCGA-F4-6855     TCGA-F4-6856 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-G4-6293     TCGA-G4-6299     TCGA-G4-6303     TCGA-G4-6304 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-G4-6306     TCGA-G4-6307     TCGA-G4-6309     TCGA-G4-6310 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-G4-6315     TCGA-G4-6317     TCGA-G4-6321     TCGA-G4-6323 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-G4-6586     TCGA-G4-6588     TCGA-G4-6625     TCGA-G4-6626 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-G4-6628     TCGA-AF-2687     TCGA-AF-2689     TCGA-AF-2691 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AF-2692     TCGA-AF-2693     TCGA-AF-3400     TCGA-AF-3913 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AF-4110     TCGA-AF-5654     TCGA-AF-6136     TCGA-AF-6655 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AF-6672     TCGA-AH-6544     TCGA-AH-6547     TCGA-AH-6549 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-AH-6643     TCGA-AH-6644     TCGA-CI-6619     TCGA-CI-6620 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-CI-6621     TCGA-CI-6622     TCGA-CI-6624     TCGA-CL-5917 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-CL-5918     TCGA-DC-5337     TCGA-DC-5869     TCGA-DC-6155 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-DC-6157     TCGA-DC-6158     TCGA-DC-6160     TCGA-DC-6681 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-DC-6682     TCGA-DC-6683     TCGA-DT-5265     TCGA-DY-A0XA 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-DY-A1DC     TCGA-DY-A1DD     TCGA-DY-A1DF     TCGA-DY-A1DG 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-DY-A1H8     TCGA-EF-5830     TCGA-EI-6506     TCGA-EI-6507 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-EI-6508     TCGA-EI-6510     TCGA-F5-6464     TCGA-F5-6465 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-F5-6571     TCGA-F5-6702     TCGA-F5-6811     TCGA-F5-6812 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 
    TCGA-F5-6813     TCGA-G5-6235     TCGA-G5-6641 
"ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" "ZFP1 WILD-TYPE" 

Clustering(2199) Variable = FAM199X MUTATION ANALYSIS
D2199V1, survival
                   sevent
clus2                 0   1
  FAM199X MUTATED     6   4
  FAM199X WILD-TYPE 372  89
  FAM199X MUTATED FAM199X WILD-TYPE 
               10               461 
  FAM199X MUTATED FAM199X WILD-TYPE 
                4                89 
$`FAM199X MUTATED`
TCGA-AA-3866 TCGA-AA-3877 TCGA-AZ-6599 TCGA-CM-6162 TCGA-CM-6169 TCGA-D5-6928 
       17.03        31.00         6.77        12.00        13.02        11.64 
TCGA-DM-A1DA TCGA-DM-A285 TCGA-F4-6459 TCGA-G4-6307 
        7.50         6.12         8.61        55.04 

$`FAM199X WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 
       53.00        24.03        27.02        29.98        18.05         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 
      106.75        22.36        62.79        88.21        49.41        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
       14.30         9.04         9.44         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB 
       92.75        49.91        13.32        12.59       140.38        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      131.51       135.65       139.17        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
       60.79       117.07        98.24        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       65.85        53.62        44.68        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  FAM199X MUTATED FAM199X WILD-TYPE 
             6.12              0.00 
  FAM199X MUTATED FAM199X WILD-TYPE 
            55.04            148.01 
  FAM199X MUTATED FAM199X WILD-TYPE 
            11.82             20.91 
[1] "6.1 - 55.0 (11.8)"  "0.0 - 148.0 (20.9)"
[1] "hr=" "3"  
D2199V2, continuous
D2199V3, binary
                   cls
clus                  0   1
  FAM199X MUTATED    10   0
  FAM199X WILD-TYPE 356 119
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM199X MUTATED     10    0
  FAM199X WILD-TYPE  356  119
        clus
vv       FAM199X MUTATED FAM199X WILD-TYPE
  COLON               10               356
  RECTUM               0               119
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  FAM199X MUTATED         3        0        0         2         0         0
  FAM199X WILD-TYPE      88        1       32       136        10         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  FAM199X MUTATED           0          0          3          1        1
  FAM199X WILD-TYPE        24         11         56         41       47
                   vv
clus                STAGE IVA STAGE IVB
  FAM199X MUTATED           0         0
  FAM199X WILD-TYPE        18         1
D2199V4, multiclass
            clus
vv           FAM199X MUTATED FAM199X WILD-TYPE
  STAGE I                  3                88
  STAGE IA                 0                 1
  STAGE II                 0                32
  STAGE IIA                2               136
  STAGE IIB                0                10
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               0                11
  STAGE IIIB               3                56
  STAGE IIIC               1                41
  STAGE IV                 1                47
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  FAM199X MUTATED     1   2   7   0
  FAM199X WILD-TYPE  16  90 322  50
D2199V5, multiclass
    clus
vv   FAM199X MUTATED FAM199X WILD-TYPE
  T1               1                16
  T2               2                90
  T3               7               322
  T4               0                50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  FAM199X MUTATED     5   2   3
  FAM199X WILD-TYPE 282 111  84
D2199V6, multiclass
    clus
vv   FAM199X MUTATED FAM199X WILD-TYPE
  N0               5               282
  N1               2               111
  N2               3                84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2199V7, binary
                   cls
clus                  0   1
  FAM199X MUTATED     8   1
  FAM199X WILD-TYPE 367  64
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM199X MUTATED      8    1
  FAM199X WILD-TYPE  367   64
   clus
vv  FAM199X MUTATED FAM199X WILD-TYPE
  0               8               367
  1               1                64
[1] 2 2
[1] FALSE
D2199V8, binary
                   cls
clus                  0   1
  FAM199X MUTATED     7   3
  FAM199X WILD-TYPE 218 261
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM199X MUTATED      7    3
  FAM199X WILD-TYPE  218  261
        clus
vv       FAM199X MUTATED FAM199X WILD-TYPE
  FEMALE               7               218
  MALE                 3               261
[1] 2 2
[1] FALSE
D2199V9, binary
                   cls
clus                  0   1
  FAM199X MUTATED     8   0
  FAM199X WILD-TYPE 342  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM199X MUTATED      8    0
  FAM199X WILD-TYPE  342   22
     clus
vv    FAM199X MUTATED FAM199X WILD-TYPE
  NO                8               342
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  FAM199X MUTATED                      6                             4
  FAM199X WILD-TYPE                  309                            43
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  FAM199X MUTATED                       0                              0
  FAM199X WILD-TYPE                   106                             10
D2199V10, multiclass
                                clus
vv                               FAM199X MUTATED FAM199X WILD-TYPE
  COLON ADENOCARCINOMA                         6               309
  COLON MUCINOUS ADENOCARCINOMA                4                43
  RECTAL ADENOCARCINOMA                        0               106
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  FAM199X MUTATED     7   0   0   0
  FAM199X WILD-TYPE 338   4  31  25
D2199V11, multiclass
    clus
vv   FAM199X MUTATED FAM199X WILD-TYPE
  R0               7               338
  R1               0                 4
  R2               0                31
  RX               0                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2199V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FAM199X MUTATED                                  0     0
  FAM199X WILD-TYPE                                1    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  FAM199X MUTATED                           1     7
  FAM199X WILD-TYPE                        21   219
D2199V13, multiclass
                                  clus
vv                                 FAM199X MUTATED FAM199X WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                      1                21
  WHITE                                          7               219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2200) Variable = GABRB2 MUTATION ANALYSIS
D2200V1, survival
                  sevent
clus2                0   1
  GABRB2 MUTATED     8   2
  GABRB2 WILD-TYPE 370  91
  GABRB2 MUTATED GABRB2 WILD-TYPE 
              10              461 
  GABRB2 MUTATED GABRB2 WILD-TYPE 
               2               91 
$`GABRB2 MUTATED`
TCGA-A6-6649 TCGA-AA-3864 TCGA-AA-3972 TCGA-AA-A010 TCGA-AA-A01P TCGA-AD-6889 
       24.16        53.00        50.99        34.98        38.07        56.55 
TCGA-AZ-6601 TCGA-AG-3878 TCGA-AG-3902 TCGA-AG-A002 
      100.01         0.99        32.02        20.98 

$`GABRB2 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.08        25.18        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 
       32.05         0.99        31.07        31.07        30.05        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 
       20.98        34.03         2.01        21.99        16.08        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
        0.07        21.37        15.52         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 
       16.31         0.95        33.01        21.44        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       49.41         6.77        12.10        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3909 
       13.02        35.01        14.01         1.02        48.03        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  GABRB2 MUTATED GABRB2 WILD-TYPE 
            0.99             0.00 
  GABRB2 MUTATED GABRB2 WILD-TYPE 
          100.01           148.01 
  GABRB2 MUTATED GABRB2 WILD-TYPE 
          36.525           20.020 
[1] "1.0 - 100.0 (36.5)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.6"
D2200V2, continuous
D2200V3, binary
                  cls
clus                 0   1
  GABRB2 MUTATED     7   3
  GABRB2 WILD-TYPE 359 116
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GABRB2 MUTATED      7    3
  GABRB2 WILD-TYPE  359  116
        clus
vv       GABRB2 MUTATED GABRB2 WILD-TYPE
  COLON               7              359
  RECTUM              3              116
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GABRB2 MUTATED         2        0        2         2         1         0
  GABRB2 WILD-TYPE      89        1       30       136         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  GABRB2 MUTATED           1          0          1          0        1
  GABRB2 WILD-TYPE        23         11         58         42       47
                  vv
clus               STAGE IVA STAGE IVB
  GABRB2 MUTATED           0         0
  GABRB2 WILD-TYPE        18         1
D2200V4, multiclass
            clus
vv           GABRB2 MUTATED GABRB2 WILD-TYPE
  STAGE I                 2               89
  STAGE IA                0                1
  STAGE II                2               30
  STAGE IIA               2              136
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               1               23
  STAGE IIIA              0               11
  STAGE IIIB              1               58
  STAGE IIIC              0               42
  STAGE IV                1               47
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  GABRB2 MUTATED     0   2   7   1
  GABRB2 WILD-TYPE  17  90 322  49
D2200V5, multiclass
    clus
vv   GABRB2 MUTATED GABRB2 WILD-TYPE
  T1              0               17
  T2              2               90
  T3              7              322
  T4              1               49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  GABRB2 MUTATED     7   3   0
  GABRB2 WILD-TYPE 280 110  87
D2200V6, multiclass
    clus
vv   GABRB2 MUTATED GABRB2 WILD-TYPE
  N0              7              280
  N1              3              110
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2200V7, binary
                  cls
clus                 0   1
  GABRB2 MUTATED     9   1
  GABRB2 WILD-TYPE 366  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GABRB2 MUTATED      9    1
  GABRB2 WILD-TYPE  366   64
   clus
vv  GABRB2 MUTATED GABRB2 WILD-TYPE
  0              9              366
  1              1               64
[1] 2 2
[1] FALSE
D2200V8, binary
                  cls
clus                 0   1
  GABRB2 MUTATED     2   8
  GABRB2 WILD-TYPE 223 256
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GABRB2 MUTATED      2    8
  GABRB2 WILD-TYPE  223  256
        clus
vv       GABRB2 MUTATED GABRB2 WILD-TYPE
  FEMALE              2              223
  MALE                8              256
[1] 2 2
[1] FALSE
D2200V9, binary
                  cls
clus                 0   1
  GABRB2 MUTATED     8   0
  GABRB2 WILD-TYPE 342  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GABRB2 MUTATED      8    0
  GABRB2 WILD-TYPE  342   22
     clus
vv    GABRB2 MUTATED GABRB2 WILD-TYPE
  NO               8              342
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  GABRB2 MUTATED                      7                             0
  GABRB2 WILD-TYPE                  308                            47
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  GABRB2 MUTATED                       3                              0
  GABRB2 WILD-TYPE                   103                             10
D2200V10, multiclass
                                clus
vv                               GABRB2 MUTATED GABRB2 WILD-TYPE
  COLON ADENOCARCINOMA                        7              308
  COLON MUCINOUS ADENOCARCINOMA               0               47
  RECTAL ADENOCARCINOMA                       3              103
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  GABRB2 MUTATED     6   0   1   0
  GABRB2 WILD-TYPE 339   4  30  25
D2200V11, multiclass
    clus
vv   GABRB2 MUTATED GABRB2 WILD-TYPE
  R0              6              339
  R1              0                4
  R2              1               30
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2200V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GABRB2 MUTATED                                  0     1
  GABRB2 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  GABRB2 MUTATED                           0     2
  GABRB2 WILD-TYPE                        22   224
D2200V13, multiclass
                                  clus
vv                                 GABRB2 MUTATED GABRB2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         2              224
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2201) Variable = NAA15 MUTATION ANALYSIS
D2201V1, survival
                 sevent
clus2               0   1
  NAA15 MUTATED    11   3
  NAA15 WILD-TYPE 367  90
  NAA15 MUTATED NAA15 WILD-TYPE 
             14             457 
  NAA15 MUTATED NAA15 WILD-TYPE 
              3              90 
$`NAA15 MUTATED`
TCGA-A6-5661 TCGA-AA-3845 TCGA-AA-3947 TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01R 
       33.53         0.00        33.01         4.01        34.98        35.01 
TCGA-AA-A01Z TCGA-AZ-4315 TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-4743 TCGA-CM-5864 
       37.02        58.39        12.76        10.06        23.05        15.02 
TCGA-CM-6169 TCGA-F4-6703 
       13.02        47.87 

$`NAA15 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 
       17.98        15.95        38.99        37.02        14.93        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       12.99        24.00        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       42.02         0.99        17.03        14.99        21.99         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A024 
        1.02         1.02        33.04        35.01        26.01        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
        0.95        33.01        21.44        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       12.20        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
      124.27        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6170 TCGA-CM-6171 
       16.04        21.99        14.99        12.99        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       35.74         6.18         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  NAA15 MUTATED NAA15 WILD-TYPE 
              0               0 
  NAA15 MUTATED NAA15 WILD-TYPE 
          58.39          148.01 
  NAA15 MUTATED NAA15 WILD-TYPE 
          28.03           20.12 
[1] "0.0 - 58.4 (28.0)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.2"
D2201V2, continuous
D2201V3, binary
                 cls
clus                0   1
  NAA15 MUTATED    15   0
  NAA15 WILD-TYPE 351 119
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NAA15 MUTATED     15    0
  NAA15 WILD-TYPE  351  119
        clus
vv       NAA15 MUTATED NAA15 WILD-TYPE
  COLON             15             351
  RECTUM             0             119
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  NAA15 MUTATED         1        0        1         8         4         0
  NAA15 WILD-TYPE      90        1       31       130         6         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NAA15 MUTATED           1          0          0          0        0         0
  NAA15 WILD-TYPE        23         11         59         42       48        18
                 vv
clus              STAGE IVB
  NAA15 MUTATED           0
  NAA15 WILD-TYPE         1
D2201V4, multiclass
            clus
vv           NAA15 MUTATED NAA15 WILD-TYPE
  STAGE I                1              90
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              8             130
  STAGE IIB              4               6
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             0              42
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  NAA15 MUTATED     0   1  10   4
  NAA15 WILD-TYPE  17  91 319  46
D2201V5, multiclass
    clus
vv   NAA15 MUTATED NAA15 WILD-TYPE
  T1             0              17
  T2             1              91
  T3            10             319
  T4             4              46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  NAA15 MUTATED    14   0   1
  NAA15 WILD-TYPE 273 113  86
D2201V6, multiclass
    clus
vv   NAA15 MUTATED NAA15 WILD-TYPE
  N0            14             273
  N1             0             113
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2201V7, binary
                 cls
clus                0   1
  NAA15 MUTATED    14   0
  NAA15 WILD-TYPE 361  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NAA15 MUTATED     14    0
  NAA15 WILD-TYPE  361   65
   clus
vv  NAA15 MUTATED NAA15 WILD-TYPE
  0            14             361
  1             0              65
[1] 2 2
[1] FALSE
D2201V8, binary
                 cls
clus                0   1
  NAA15 MUTATED     5  10
  NAA15 WILD-TYPE 220 254
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NAA15 MUTATED      5   10
  NAA15 WILD-TYPE  220  254
        clus
vv       NAA15 MUTATED NAA15 WILD-TYPE
  FEMALE             5             220
  MALE              10             254
[1] 2 2
[1] FALSE
D2201V9, binary
                 cls
clus                0   1
  NAA15 MUTATED    11   1
  NAA15 WILD-TYPE 339  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NAA15 MUTATED     11    1
  NAA15 WILD-TYPE  339   21
     clus
vv    NAA15 MUTATED NAA15 WILD-TYPE
  NO             11             339
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  NAA15 MUTATED                     11                             4
  NAA15 WILD-TYPE                  304                            43
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  NAA15 MUTATED                       0                              0
  NAA15 WILD-TYPE                   106                             10
D2201V10, multiclass
                                clus
vv                               NAA15 MUTATED NAA15 WILD-TYPE
  COLON ADENOCARCINOMA                      11             304
  COLON MUCINOUS ADENOCARCINOMA              4              43
  RECTAL ADENOCARCINOMA                      0             106
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  NAA15 MUTATED    12   0   0   3
  NAA15 WILD-TYPE 333   4  31  22
D2201V11, multiclass
    clus
vv   NAA15 MUTATED NAA15 WILD-TYPE
  R0            12             333
  R1             0               4
  R2             0              31
  RX             3              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2201V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NAA15 MUTATED                                  0     2
  NAA15 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  NAA15 MUTATED                           2     5
  NAA15 WILD-TYPE                        20   221
D2201V13, multiclass
                                  clus
vv                                 NAA15 MUTATED NAA15 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               9
  BLACK OR AFRICAN AMERICAN                    2              20
  WHITE                                        5             221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2202) Variable = GNA15 MUTATION ANALYSIS
D2202V1, survival
                 sevent
clus2               0   1
  GNA15 MUTATED     4   2
  GNA15 WILD-TYPE 374  91
  GNA15 MUTATED GNA15 WILD-TYPE 
              6             465 
  GNA15 MUTATED GNA15 WILD-TYPE 
              2              91 
$`GNA15 MUTATED`
TCGA-AA-A00R TCGA-AA-A01D TCGA-AA-A01Z TCGA-AZ-6601 TCGA-D5-6930 TCGA-AG-3742 
        0.99        10.98        37.02       100.01         1.51         0.99 

$`GNA15 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00U 
       18.05        38.04         4.01        27.02        42.02        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        34.98         1.02        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       33.04        35.01        26.01        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
      124.27        23.05        20.02        37.02        25.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        31.96        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
       32.98         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  GNA15 MUTATED GNA15 WILD-TYPE 
           0.99            0.00 
  GNA15 MUTATED GNA15 WILD-TYPE 
         100.01          148.01 
  GNA15 MUTATED GNA15 WILD-TYPE 
          6.245          20.280 
[1] "1.0 - 100.0 (6.2)"  "0.0 - 148.0 (20.3)"
[1] "hr=" "1.8"
D2202V2, continuous
D2202V3, binary
                 cls
clus                0   1
  GNA15 MUTATED     5   1
  GNA15 WILD-TYPE 361 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GNA15 MUTATED      5    1
  GNA15 WILD-TYPE  361  118
        clus
vv       GNA15 MUTATED GNA15 WILD-TYPE
  COLON              5             361
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  GNA15 MUTATED         2        0        2         1         0         0
  GNA15 WILD-TYPE      89        1       30       137        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  GNA15 MUTATED           0          0          0          1        0         0
  GNA15 WILD-TYPE        24         11         59         41       48        18
                 vv
clus              STAGE IVB
  GNA15 MUTATED           0
  GNA15 WILD-TYPE         1
D2202V4, multiclass
            clus
vv           GNA15 MUTATED GNA15 WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA              1             137
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             1              41
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  GNA15 MUTATED     1   1   4   0
  GNA15 WILD-TYPE  16  91 325  50
D2202V5, multiclass
    clus
vv   GNA15 MUTATED GNA15 WILD-TYPE
  T1             1              16
  T2             1              91
  T3             4             325
  T4             0              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  GNA15 MUTATED     5   0   1
  GNA15 WILD-TYPE 282 113  86
D2202V6, multiclass
    clus
vv   GNA15 MUTATED GNA15 WILD-TYPE
  N0             5             282
  N1             0             113
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2202V7, binary
                 cls
clus                0   1
  GNA15 MUTATED     6   0
  GNA15 WILD-TYPE 369  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GNA15 MUTATED      6    0
  GNA15 WILD-TYPE  369   65
   clus
vv  GNA15 MUTATED GNA15 WILD-TYPE
  0             6             369
  1             0              65
[1] 2 2
[1] FALSE
D2202V8, binary
                 cls
clus                0   1
  GNA15 MUTATED     3   3
  GNA15 WILD-TYPE 222 261
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GNA15 MUTATED      3    3
  GNA15 WILD-TYPE  222  261
        clus
vv       GNA15 MUTATED GNA15 WILD-TYPE
  FEMALE             3             222
  MALE               3             261
[1] 2 2
[1] FALSE
D2202V9, binary
                 cls
clus                0   1
  GNA15 MUTATED     3   0
  GNA15 WILD-TYPE 347  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GNA15 MUTATED      3    0
  GNA15 WILD-TYPE  347   22
     clus
vv    GNA15 MUTATED GNA15 WILD-TYPE
  NO              3             347
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  GNA15 MUTATED                      3                             2
  GNA15 WILD-TYPE                  312                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  GNA15 MUTATED                       1                              0
  GNA15 WILD-TYPE                   105                             10
D2202V10, multiclass
                                clus
vv                               GNA15 MUTATED GNA15 WILD-TYPE
  COLON ADENOCARCINOMA                       3             312
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  GNA15 MUTATED     5   0   0   0
  GNA15 WILD-TYPE 340   4  31  25
D2202V11, multiclass
    clus
vv   GNA15 MUTATED GNA15 WILD-TYPE
  R0             5             340
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2202V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GNA15 MUTATED                                  0     0
  GNA15 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  GNA15 MUTATED                           0     2
  GNA15 WILD-TYPE                        22   224
D2202V13, multiclass
[1] "Remove cluster labels:" "GNA15 MUTATED"         
clus
  GNA15 MUTATED GNA15 WILD-TYPE 
              2             258 
     TCGA-A6-2671      TCGA-A6-2672      TCGA-A6-2674      TCGA-A6-2676 
"GNA15 WILD-TYPE" "GNA15 WILD-TYPE" "GNA15 WILD-TYPE" "GNA15 WILD-TYPE" 
     TCGA-A6-2677      TCGA-A6-2678      TCGA-A6-2683      TCGA-A6-3807 
"GNA15 WILD-TYPE" "GNA15 WILD-TYPE" "GNA15 WILD-TYPE" "GNA15 WILD-TYPE" 
     TCGA-A6-3808      TCGA-A6-3809      TCGA-A6-3810      TCGA-A6-4105 
"GNA15 WILD-TYPE" "GNA15 WILD-TYPE" "GNA15 WILD-TYPE" "GNA15 WILD-TYPE" 
     TCGA-A6-5656      TCGA-A6-5657      TCGA-A6-5659      TCGA-A6-5660 
"GNA15 WILD-TYPE" "GNA15 WILD-TYPE" "GNA15 WILD-TYPE" "GNA15 WILD-TYPE" 
     TCGA-A6-5661      TCGA-A6-5662      TCGA-A6-5664      TCGA-A6-5665 
"GNA15 WILD-TYPE" "GNA15 WILD-TYPE" "GNA15 WILD-TYPE" "GNA15 WILD-TYPE" 
     TCGA-A6-5666      TCGA-A6-6137      TCGA-A6-6138      TCGA-A6-6141 
"GNA15 WILD-TYPE" "GNA15 WILD-TYPE" "GNA15 WILD-TYPE" "GNA15 WILD-TYPE" 
     TCGA-A6-6142      TCGA-A6-6648      TCGA-A6-6649      TCGA-A6-6651 
"GNA15 WILD-TYPE" "GNA15 WILD-TYPE" "GNA15 WILD-TYPE" "GNA15 WILD-TYPE" 
     TCGA-A6-6652      TCGA-A6-6653      TCGA-A6-6654      TCGA-A6-6780 
"GNA15 WILD-TYPE" "GNA15 WILD-TYPE" "GNA15 WILD-TYPE" "GNA15 WILD-TYPE" 
     TCGA-A6-6781      TCGA-A6-6782      TCGA-AD-5900      TCGA-AD-6548 
"GNA15 WILD-TYPE" "GNA15 WILD-TYPE" "GNA15 WILD-TYPE" "GNA15 WILD-TYPE" 
     TCGA-AD-6888      TCGA-AD-6889      TCGA-AD-6890      TCGA-AD-6895 
"GNA15 WILD-TYPE" "GNA15 WILD-TYPE" "GNA15 WILD-TYPE" "GNA15 WILD-TYPE" 
     TCGA-AD-6899      TCGA-AD-6901      TCGA-AD-6963      TCGA-AD-6964 
"GNA15 WILD-TYPE" "GNA15 WILD-TYPE" "GNA15 WILD-TYPE" "GNA15 WILD-TYPE" 
     TCGA-AD-6965      TCGA-AU-3779      TCGA-AU-6004      TCGA-AY-4070 
"GNA15 WILD-TYPE" "GNA15 WILD-TYPE" "GNA15 WILD-TYPE" "GNA15 WILD-TYPE" 
     TCGA-AY-4071      TCGA-AY-5543      TCGA-AY-6196      TCGA-AY-6197 
"GNA15 WILD-TYPE" "GNA15 WILD-TYPE" "GNA15 WILD-TYPE" "GNA15 WILD-TYPE" 
     TCGA-AY-6386      TCGA-AZ-4315      TCGA-AZ-4323      TCGA-AZ-4616 
"GNA15 WILD-TYPE" "GNA15 WILD-TYPE" "GNA15 WILD-TYPE" "GNA15 WILD-TYPE" 
     TCGA-AZ-4681      TCGA-AZ-4682      TCGA-AZ-5403      TCGA-AZ-5407 
"GNA15 WILD-TYPE" "GNA15 WILD-TYPE" "GNA15 WILD-TYPE" "GNA15 WILD-TYPE" 
     TCGA-AZ-6598      TCGA-AZ-6599      TCGA-AZ-6600      TCGA-AZ-6603 
"GNA15 WILD-TYPE" "GNA15 WILD-TYPE" "GNA15 WILD-TYPE" "GNA15 WILD-TYPE" 
     TCGA-AZ-6605      TCGA-AZ-6606      TCGA-AZ-6607      TCGA-AZ-6608 
"GNA15 WILD-TYPE" "GNA15 WILD-TYPE" "GNA15 WILD-TYPE" "GNA15 WILD-TYPE" 
     TCGA-CA-5254      TCGA-CA-5255      TCGA-CA-5796      TCGA-CA-5797 
"GNA15 WILD-TYPE" "GNA15 WILD-TYPE" "GNA15 WILD-TYPE" "GNA15 WILD-TYPE" 
     TCGA-CA-6715      TCGA-CA-6716      TCGA-CA-6717      TCGA-CA-6718 
"GNA15 WILD-TYPE" "GNA15 WILD-TYPE" "GNA15 WILD-TYPE" "GNA15 WILD-TYPE" 
     TCGA-CA-6719      TCGA-CK-4947      TCGA-CK-4948      TCGA-CK-4950 
"GNA15 WILD-TYPE" "GNA15 WILD-TYPE" "GNA15 WILD-TYPE" "GNA15 WILD-TYPE" 
     TCGA-CK-4952      TCGA-CK-5912      TCGA-CK-5913      TCGA-CK-5914 
"GNA15 WILD-TYPE" "GNA15 WILD-TYPE" "GNA15 WILD-TYPE" "GNA15 WILD-TYPE" 
     TCGA-CK-5915      TCGA-CK-5916      TCGA-CK-6746      TCGA-CK-6747 
"GNA15 WILD-TYPE" "GNA15 WILD-TYPE" "GNA15 WILD-TYPE" "GNA15 WILD-TYPE" 
     TCGA-CK-6748      TCGA-CK-6751      TCGA-CM-4743      TCGA-CM-4744 
"GNA15 WILD-TYPE" "GNA15 WILD-TYPE" "GNA15 WILD-TYPE" "GNA15 WILD-TYPE" 
     TCGA-CM-4746      TCGA-CM-4747      TCGA-CM-4752      TCGA-CM-5341 
"GNA15 WILD-TYPE" "GNA15 WILD-TYPE" "GNA15 WILD-TYPE" "GNA15 WILD-TYPE" 
     TCGA-CM-5344      TCGA-CM-5348      TCGA-CM-5349      TCGA-CM-5860 
"GNA15 WILD-TYPE" "GNA15 WILD-TYPE" "GNA15 WILD-TYPE" "GNA15 WILD-TYPE" 
     TCGA-CM-5861      TCGA-CM-5862      TCGA-CM-5863      TCGA-CM-5864 
"GNA15 WILD-TYPE" "GNA15 WILD-TYPE" "GNA15 WILD-TYPE" "GNA15 WILD-TYPE" 
     TCGA-CM-5868      TCGA-CM-6161      TCGA-CM-6162      TCGA-CM-6163 
"GNA15 WILD-TYPE" "GNA15 WILD-TYPE" "GNA15 WILD-TYPE" "GNA15 WILD-TYPE" 
     TCGA-CM-6164      TCGA-CM-6165      TCGA-CM-6166      TCGA-CM-6167 
"GNA15 WILD-TYPE" "GNA15 WILD-TYPE" "GNA15 WILD-TYPE" "GNA15 WILD-TYPE" 
     TCGA-CM-6168      TCGA-CM-6169      TCGA-CM-6170      TCGA-CM-6171 
"GNA15 WILD-TYPE" "GNA15 WILD-TYPE" "GNA15 WILD-TYPE" "GNA15 WILD-TYPE" 
     TCGA-CM-6172      TCGA-CM-6674      TCGA-CM-6675      TCGA-CM-6676 
"GNA15 WILD-TYPE" "GNA15 WILD-TYPE" "GNA15 WILD-TYPE" "GNA15 WILD-TYPE" 
     TCGA-CM-6677      TCGA-CM-6678      TCGA-CM-6679      TCGA-CM-6680 
"GNA15 WILD-TYPE" "GNA15 WILD-TYPE" "GNA15 WILD-TYPE" "GNA15 WILD-TYPE" 
     TCGA-D5-5537      TCGA-D5-5538      TCGA-D5-5539      TCGA-D5-5540 
"GNA15 WILD-TYPE" "GNA15 WILD-TYPE" "GNA15 WILD-TYPE" "GNA15 WILD-TYPE" 
     TCGA-D5-5541      TCGA-D5-6529      TCGA-D5-6532      TCGA-D5-6533 
"GNA15 WILD-TYPE" "GNA15 WILD-TYPE" "GNA15 WILD-TYPE" "GNA15 WILD-TYPE" 
     TCGA-D5-6534      TCGA-D5-6535      TCGA-D5-6536      TCGA-D5-6537 
"GNA15 WILD-TYPE" "GNA15 WILD-TYPE" "GNA15 WILD-TYPE" "GNA15 WILD-TYPE" 
     TCGA-D5-6538      TCGA-D5-6539      TCGA-D5-6540      TCGA-D5-6541 
"GNA15 WILD-TYPE" "GNA15 WILD-TYPE" "GNA15 WILD-TYPE" "GNA15 WILD-TYPE" 
     TCGA-D5-6898      TCGA-D5-6920      TCGA-D5-6922      TCGA-D5-6923 
"GNA15 WILD-TYPE" "GNA15 WILD-TYPE" "GNA15 WILD-TYPE" "GNA15 WILD-TYPE" 
     TCGA-D5-6924      TCGA-D5-6926      TCGA-D5-6927      TCGA-D5-6928 
"GNA15 WILD-TYPE" "GNA15 WILD-TYPE" "GNA15 WILD-TYPE" "GNA15 WILD-TYPE" 
     TCGA-D5-6929      TCGA-D5-6931      TCGA-D5-6932      TCGA-D5-7000 
"GNA15 WILD-TYPE" "GNA15 WILD-TYPE" "GNA15 WILD-TYPE" "GNA15 WILD-TYPE" 
     TCGA-DM-A0X9      TCGA-DM-A0XD      TCGA-DM-A0XF      TCGA-DM-A1D0 
"GNA15 WILD-TYPE" "GNA15 WILD-TYPE" "GNA15 WILD-TYPE" "GNA15 WILD-TYPE" 
     TCGA-DM-A1D4      TCGA-DM-A1D6      TCGA-DM-A1D7      TCGA-DM-A1D8 
"GNA15 WILD-TYPE" "GNA15 WILD-TYPE" "GNA15 WILD-TYPE" "GNA15 WILD-TYPE" 
     TCGA-DM-A1D9      TCGA-DM-A1DA      TCGA-DM-A1DB      TCGA-DM-A1HA 
"GNA15 WILD-TYPE" "GNA15 WILD-TYPE" "GNA15 WILD-TYPE" "GNA15 WILD-TYPE" 
     TCGA-DM-A1HB      TCGA-DM-A282      TCGA-DM-A285      TCGA-DM-A28C 
"GNA15 WILD-TYPE" "GNA15 WILD-TYPE" "GNA15 WILD-TYPE" "GNA15 WILD-TYPE" 
     TCGA-DM-A28E      TCGA-DM-A28F      TCGA-DM-A28G      TCGA-DM-A28H 
"GNA15 WILD-TYPE" "GNA15 WILD-TYPE" "GNA15 WILD-TYPE" "GNA15 WILD-TYPE" 
     TCGA-DM-A28K      TCGA-F4-6459      TCGA-F4-6460      TCGA-F4-6569 
"GNA15 WILD-TYPE" "GNA15 WILD-TYPE" "GNA15 WILD-TYPE" "GNA15 WILD-TYPE" 
     TCGA-F4-6570      TCGA-F4-6703      TCGA-F4-6704      TCGA-F4-6805 
"GNA15 WILD-TYPE" "GNA15 WILD-TYPE" "GNA15 WILD-TYPE" "GNA15 WILD-TYPE" 
     TCGA-F4-6806      TCGA-F4-6807      TCGA-F4-6808      TCGA-F4-6809 
"GNA15 WILD-TYPE" "GNA15 WILD-TYPE" "GNA15 WILD-TYPE" "GNA15 WILD-TYPE" 
     TCGA-F4-6854      TCGA-F4-6855      TCGA-F4-6856      TCGA-G4-6293 
"GNA15 WILD-TYPE" "GNA15 WILD-TYPE" "GNA15 WILD-TYPE" "GNA15 WILD-TYPE" 
     TCGA-G4-6299      TCGA-G4-6303      TCGA-G4-6304      TCGA-G4-6306 
"GNA15 WILD-TYPE" "GNA15 WILD-TYPE" "GNA15 WILD-TYPE" "GNA15 WILD-TYPE" 
     TCGA-G4-6307      TCGA-G4-6309      TCGA-G4-6310      TCGA-G4-6315 
"GNA15 WILD-TYPE" "GNA15 WILD-TYPE" "GNA15 WILD-TYPE" "GNA15 WILD-TYPE" 
     TCGA-G4-6317      TCGA-G4-6321      TCGA-G4-6323      TCGA-G4-6586 
"GNA15 WILD-TYPE" "GNA15 WILD-TYPE" "GNA15 WILD-TYPE" "GNA15 WILD-TYPE" 
     TCGA-G4-6588      TCGA-G4-6625      TCGA-G4-6626      TCGA-G4-6628 
"GNA15 WILD-TYPE" "GNA15 WILD-TYPE" "GNA15 WILD-TYPE" "GNA15 WILD-TYPE" 
     TCGA-AF-2687      TCGA-AF-2689      TCGA-AF-2691      TCGA-AF-2692 
"GNA15 WILD-TYPE" "GNA15 WILD-TYPE" "GNA15 WILD-TYPE" "GNA15 WILD-TYPE" 
     TCGA-AF-2693      TCGA-AF-3400      TCGA-AF-3913      TCGA-AF-4110 
"GNA15 WILD-TYPE" "GNA15 WILD-TYPE" "GNA15 WILD-TYPE" "GNA15 WILD-TYPE" 
     TCGA-AF-5654      TCGA-AF-6136      TCGA-AF-6655      TCGA-AF-6672 
"GNA15 WILD-TYPE" "GNA15 WILD-TYPE" "GNA15 WILD-TYPE" "GNA15 WILD-TYPE" 
     TCGA-AH-6544      TCGA-AH-6547      TCGA-AH-6549      TCGA-AH-6643 
"GNA15 WILD-TYPE" "GNA15 WILD-TYPE" "GNA15 WILD-TYPE" "GNA15 WILD-TYPE" 
     TCGA-AH-6644      TCGA-CI-6619      TCGA-CI-6620      TCGA-CI-6621 
"GNA15 WILD-TYPE" "GNA15 WILD-TYPE" "GNA15 WILD-TYPE" "GNA15 WILD-TYPE" 
     TCGA-CI-6622      TCGA-CI-6624      TCGA-CL-5917      TCGA-CL-5918 
"GNA15 WILD-TYPE" "GNA15 WILD-TYPE" "GNA15 WILD-TYPE" "GNA15 WILD-TYPE" 
     TCGA-DC-5337      TCGA-DC-5869      TCGA-DC-6155      TCGA-DC-6157 
"GNA15 WILD-TYPE" "GNA15 WILD-TYPE" "GNA15 WILD-TYPE" "GNA15 WILD-TYPE" 
     TCGA-DC-6158      TCGA-DC-6160      TCGA-DC-6681      TCGA-DC-6682 
"GNA15 WILD-TYPE" "GNA15 WILD-TYPE" "GNA15 WILD-TYPE" "GNA15 WILD-TYPE" 
     TCGA-DC-6683      TCGA-DT-5265      TCGA-DY-A0XA      TCGA-DY-A1DC 
"GNA15 WILD-TYPE" "GNA15 WILD-TYPE" "GNA15 WILD-TYPE" "GNA15 WILD-TYPE" 
     TCGA-DY-A1DD      TCGA-DY-A1DF      TCGA-DY-A1DG      TCGA-DY-A1H8 
"GNA15 WILD-TYPE" "GNA15 WILD-TYPE" "GNA15 WILD-TYPE" "GNA15 WILD-TYPE" 
     TCGA-EF-5830      TCGA-EI-6506      TCGA-EI-6507      TCGA-EI-6508 
"GNA15 WILD-TYPE" "GNA15 WILD-TYPE" "GNA15 WILD-TYPE" "GNA15 WILD-TYPE" 
     TCGA-EI-6510      TCGA-F5-6464      TCGA-F5-6465      TCGA-F5-6571 
"GNA15 WILD-TYPE" "GNA15 WILD-TYPE" "GNA15 WILD-TYPE" "GNA15 WILD-TYPE" 
     TCGA-F5-6702      TCGA-F5-6811      TCGA-F5-6812      TCGA-F5-6813 
"GNA15 WILD-TYPE" "GNA15 WILD-TYPE" "GNA15 WILD-TYPE" "GNA15 WILD-TYPE" 
     TCGA-G5-6235      TCGA-G5-6641 
"GNA15 WILD-TYPE" "GNA15 WILD-TYPE" 

Clustering(2203) Variable = ZNF274 MUTATION ANALYSIS
D2203V1, survival
                  sevent
clus2                0   1
  ZNF274 MUTATED     5   2
  ZNF274 WILD-TYPE 373  91
  ZNF274 MUTATED ZNF274 WILD-TYPE 
               7              464 
  ZNF274 MUTATED ZNF274 WILD-TYPE 
               2               91 
$`ZNF274 MUTATED`
TCGA-A6-5657 TCGA-A6-6653 TCGA-AA-3663 TCGA-AA-3968 TCGA-AA-A00N TCGA-AZ-4315 
       31.63        24.39         6.97        21.99         4.01        58.39 
TCGA-AZ-6605 
        5.23 

$`ZNF274 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 
       25.18        24.16        21.76        24.69        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       33.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 
       26.01        25.02        24.00        27.02        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6606 
       49.41         6.77        12.10       100.01        29.56        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.69         0.72         6.05        33.17         6.97         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  ZNF274 MUTATED ZNF274 WILD-TYPE 
            4.01             0.00 
  ZNF274 MUTATED ZNF274 WILD-TYPE 
           58.39           148.01 
  ZNF274 MUTATED ZNF274 WILD-TYPE 
          21.990           20.155 
[1] "4.0 - 58.4 (22.0)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.7"
D2203V2, continuous
D2203V3, binary
                  cls
clus                 0   1
  ZNF274 MUTATED     7   0
  ZNF274 WILD-TYPE 359 119
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF274 MUTATED      7    0
  ZNF274 WILD-TYPE  359  119
        clus
vv       ZNF274 MUTATED ZNF274 WILD-TYPE
  COLON               7              359
  RECTUM              0              119
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZNF274 MUTATED         2        0        1         1         1         0
  ZNF274 WILD-TYPE      89        1       31       137         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF274 MUTATED           0          0          2          0        0
  ZNF274 WILD-TYPE        24         11         57         42       48
                  vv
clus               STAGE IVA STAGE IVB
  ZNF274 MUTATED           0         0
  ZNF274 WILD-TYPE        18         1
D2203V4, multiclass
            clus
vv           ZNF274 MUTATED ZNF274 WILD-TYPE
  STAGE I                 2               89
  STAGE IA                0                1
  STAGE II                1               31
  STAGE IIA               1              137
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              2               57
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZNF274 MUTATED     0   2   3   2
  ZNF274 WILD-TYPE  17  90 326  48
D2203V5, multiclass
    clus
vv   ZNF274 MUTATED ZNF274 WILD-TYPE
  T1              0               17
  T2              2               90
  T3              3              326
  T4              2               48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  ZNF274 MUTATED     5   2   0
  ZNF274 WILD-TYPE 282 111  87
D2203V6, multiclass
    clus
vv   ZNF274 MUTATED ZNF274 WILD-TYPE
  N0              5              282
  N1              2              111
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2203V7, binary
                  cls
clus                 0   1
  ZNF274 MUTATED     7   0
  ZNF274 WILD-TYPE 368  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF274 MUTATED      7    0
  ZNF274 WILD-TYPE  368   65
   clus
vv  ZNF274 MUTATED ZNF274 WILD-TYPE
  0              7              368
  1              0               65
[1] 2 2
[1] FALSE
D2203V8, binary
                  cls
clus                 0   1
  ZNF274 MUTATED     1   6
  ZNF274 WILD-TYPE 224 258
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF274 MUTATED      1    6
  ZNF274 WILD-TYPE  224  258
        clus
vv       ZNF274 MUTATED ZNF274 WILD-TYPE
  FEMALE              1              224
  MALE                6              258
[1] 2 2
[1] FALSE
D2203V9, binary
                  cls
clus                 0   1
  ZNF274 MUTATED     6   0
  ZNF274 WILD-TYPE 344  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF274 MUTATED      6    0
  ZNF274 WILD-TYPE  344   22
     clus
vv    ZNF274 MUTATED ZNF274 WILD-TYPE
  NO               6              344
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ZNF274 MUTATED                      6                             1
  ZNF274 WILD-TYPE                  309                            46
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ZNF274 MUTATED                       0                              0
  ZNF274 WILD-TYPE                   106                             10
D2203V10, multiclass
                                clus
vv                               ZNF274 MUTATED ZNF274 WILD-TYPE
  COLON ADENOCARCINOMA                        6              309
  COLON MUCINOUS ADENOCARCINOMA               1               46
  RECTAL ADENOCARCINOMA                       0              106
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ZNF274 MUTATED     5   0   0   0
  ZNF274 WILD-TYPE 340   4  31  25
D2203V11, multiclass
    clus
vv   ZNF274 MUTATED ZNF274 WILD-TYPE
  R0              5              340
  R1              0                4
  R2              0               31
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2203V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF274 MUTATED                                  0     0
  ZNF274 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZNF274 MUTATED                           1     3
  ZNF274 WILD-TYPE                        21   223
D2203V13, multiclass
                                  clus
vv                                 ZNF274 MUTATED ZNF274 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                         3              223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2204) Variable = ZNF763 MUTATION ANALYSIS
D2204V1, survival
                  sevent
clus2                0   1
  ZNF763 MUTATED    10   0
  ZNF763 WILD-TYPE 368  93
  ZNF763 MUTATED ZNF763 WILD-TYPE 
              10              461 
  ZNF763 MUTATED ZNF763 WILD-TYPE 
               0               93 
$`ZNF763 MUTATED`
TCGA-AA-3510 TCGA-AA-3844 TCGA-AA-3977 TCGA-AY-6386 TCGA-CA-6717 TCGA-D5-6533 
       63.98        14.93        25.02        17.82        12.76         1.32 
TCGA-D5-6540 TCGA-DM-A1HA TCGA-G4-6299 TCGA-G4-6588 
       16.14       131.51        74.56        26.17 

$`ZNF763 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3846 
       17.98        15.95        38.99        37.02         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       13.05        34.06        26.01        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
        3.06         3.25         3.29         0.07        12.20        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6534 
       19.59        56.09        55.92        20.19        18.25        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 
       15.12        17.85         4.80        17.13        12.49        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6625 
       61.91        36.00        22.09        13.78        35.80        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  ZNF763 MUTATED ZNF763 WILD-TYPE 
            1.32             0.00 
  ZNF763 MUTATED ZNF763 WILD-TYPE 
          131.51           148.01 
  ZNF763 MUTATED ZNF763 WILD-TYPE 
           21.42            20.19 
[1] "1.3 - 131.5 (21.4)" "0.0 - 148.0 (20.2)"
[1] "hr="     "2.6e+07"
D2204V2, continuous
D2204V3, binary
                  cls
clus                 0   1
  ZNF763 MUTATED    11   0
  ZNF763 WILD-TYPE 355 119
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF763 MUTATED     11    0
  ZNF763 WILD-TYPE  355  119
        clus
vv       ZNF763 MUTATED ZNF763 WILD-TYPE
  COLON              11              355
  RECTUM              0              119
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZNF763 MUTATED         1        0        1         3         0         0
  ZNF763 WILD-TYPE      90        1       31       135        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF763 MUTATED           0          0          2          3        0
  ZNF763 WILD-TYPE        24         11         57         39       48
                  vv
clus               STAGE IVA STAGE IVB
  ZNF763 MUTATED           0         0
  ZNF763 WILD-TYPE        18         1
D2204V4, multiclass
            clus
vv           ZNF763 MUTATED ZNF763 WILD-TYPE
  STAGE I                 1               90
  STAGE IA                0                1
  STAGE II                1               31
  STAGE IIA               3              135
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              2               57
  STAGE IIIC              3               39
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZNF763 MUTATED     0   2   8   1
  ZNF763 WILD-TYPE  17  90 321  49
D2204V5, multiclass
    clus
vv   ZNF763 MUTATED ZNF763 WILD-TYPE
  T1              0               17
  T2              2               90
  T3              8              321
  T4              1               49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  ZNF763 MUTATED     7   1   3
  ZNF763 WILD-TYPE 280 112  84
D2204V6, multiclass
    clus
vv   ZNF763 MUTATED ZNF763 WILD-TYPE
  N0              7              280
  N1              1              112
  N2              3               84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2204V7, binary
                  cls
clus                 0   1
  ZNF763 MUTATED    10   0
  ZNF763 WILD-TYPE 365  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF763 MUTATED     10    0
  ZNF763 WILD-TYPE  365   65
   clus
vv  ZNF763 MUTATED ZNF763 WILD-TYPE
  0             10              365
  1              0               65
[1] 2 2
[1] FALSE
D2204V8, binary
                  cls
clus                 0   1
  ZNF763 MUTATED     5   6
  ZNF763 WILD-TYPE 220 258
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF763 MUTATED      5    6
  ZNF763 WILD-TYPE  220  258
        clus
vv       ZNF763 MUTATED ZNF763 WILD-TYPE
  FEMALE              5              220
  MALE                6              258
[1] 2 2
[1] FALSE
D2204V9, binary
                  cls
clus                 0   1
  ZNF763 MUTATED     7   1
  ZNF763 WILD-TYPE 343  21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF763 MUTATED      7    1
  ZNF763 WILD-TYPE  343   21
     clus
vv    ZNF763 MUTATED ZNF763 WILD-TYPE
  NO               7              343
  YES              1               21
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ZNF763 MUTATED                      9                             2
  ZNF763 WILD-TYPE                  306                            45
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ZNF763 MUTATED                       0                              0
  ZNF763 WILD-TYPE                   106                             10
D2204V10, multiclass
                                clus
vv                               ZNF763 MUTATED ZNF763 WILD-TYPE
  COLON ADENOCARCINOMA                        9              306
  COLON MUCINOUS ADENOCARCINOMA               2               45
  RECTAL ADENOCARCINOMA                       0              106
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ZNF763 MUTATED     8   0   0   1
  ZNF763 WILD-TYPE 337   4  31  24
D2204V11, multiclass
    clus
vv   ZNF763 MUTATED ZNF763 WILD-TYPE
  R0              8              337
  R1              0                4
  R2              0               31
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2204V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF763 MUTATED                                  0     1
  ZNF763 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZNF763 MUTATED                           1     5
  ZNF763 WILD-TYPE                        21   221
D2204V13, multiclass
                                  clus
vv                                 ZNF763 MUTATED ZNF763 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                         5              221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2205) Variable = PRKRIR MUTATION ANALYSIS
D2205V1, survival
                  sevent
clus2                0   1
  PRKRIR MUTATED     9   1
  PRKRIR WILD-TYPE 369  92
  PRKRIR MUTATED PRKRIR WILD-TYPE 
              10              461 
  PRKRIR MUTATED PRKRIR WILD-TYPE 
               1               92 
$`PRKRIR MUTATED`
TCGA-A6-5665 TCGA-AA-A01R TCGA-AA-A024 TCGA-AD-6895 TCGA-AU-6004 TCGA-AY-6197 
       22.06        35.01        39.06         0.72        27.09        21.44 
TCGA-AZ-4315 TCGA-CM-6680 TCGA-DM-A1HB TCGA-CI-6622 
       58.39        12.03       135.65         6.97 

$`PRKRIR WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S 
       12.00        31.00        31.00        38.07         1.02         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02F 
       33.04        35.01        26.01        37.02        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.79         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4323 
       14.50        16.31         0.95        33.01        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       10.06        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
        6.05        33.17         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  PRKRIR MUTATED PRKRIR WILD-TYPE 
            0.72             0.00 
  PRKRIR MUTATED PRKRIR WILD-TYPE 
          135.65           148.01 
  PRKRIR MUTATED PRKRIR WILD-TYPE 
          24.575           20.050 
[1] "0.7 - 135.7 (24.6)" "0.0 - 148.0 (20.1)"
[1] "hr=" "2.5"
D2205V2, continuous
D2205V3, binary
                  cls
clus                 0   1
  PRKRIR MUTATED    11   1
  PRKRIR WILD-TYPE 355 118
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PRKRIR MUTATED     11    1
  PRKRIR WILD-TYPE  355  118
        clus
vv       PRKRIR MUTATED PRKRIR WILD-TYPE
  COLON              11              355
  RECTUM              1              118
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PRKRIR MUTATED         1        0        1         4         1         0
  PRKRIR WILD-TYPE      90        1       31       134         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  PRKRIR MUTATED           1          0          2          0        1
  PRKRIR WILD-TYPE        23         11         57         42       47
                  vv
clus               STAGE IVA STAGE IVB
  PRKRIR MUTATED           0         0
  PRKRIR WILD-TYPE        18         1
D2205V4, multiclass
            clus
vv           PRKRIR MUTATED PRKRIR WILD-TYPE
  STAGE I                 1               90
  STAGE IA                0                1
  STAGE II                1               31
  STAGE IIA               4              134
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               1               23
  STAGE IIIA              0               11
  STAGE IIIB              2               57
  STAGE IIIC              0               42
  STAGE IV                1               47
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  PRKRIR MUTATED     0   1   9   2
  PRKRIR WILD-TYPE  17  91 320  48
D2205V5, multiclass
    clus
vv   PRKRIR MUTATED PRKRIR WILD-TYPE
  T1              0               17
  T2              1               91
  T3              9              320
  T4              2               48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  PRKRIR MUTATED     7   3   2
  PRKRIR WILD-TYPE 280 110  85
D2205V6, multiclass
    clus
vv   PRKRIR MUTATED PRKRIR WILD-TYPE
  N0              7              280
  N1              3              110
  N2              2               85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2205V7, binary
                  cls
clus                 0   1
  PRKRIR MUTATED     9   1
  PRKRIR WILD-TYPE 366  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PRKRIR MUTATED      9    1
  PRKRIR WILD-TYPE  366   64
   clus
vv  PRKRIR MUTATED PRKRIR WILD-TYPE
  0              9              366
  1              1               64
[1] 2 2
[1] FALSE
D2205V8, binary
                  cls
clus                 0   1
  PRKRIR MUTATED     5   7
  PRKRIR WILD-TYPE 220 257
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PRKRIR MUTATED      5    7
  PRKRIR WILD-TYPE  220  257
        clus
vv       PRKRIR MUTATED PRKRIR WILD-TYPE
  FEMALE              5              220
  MALE                7              257
[1] 2 2
[1] FALSE
D2205V9, binary
                  cls
clus                 0   1
  PRKRIR MUTATED     5   1
  PRKRIR WILD-TYPE 345  21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PRKRIR MUTATED      5    1
  PRKRIR WILD-TYPE  345   21
     clus
vv    PRKRIR MUTATED PRKRIR WILD-TYPE
  NO               5              345
  YES              1               21
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PRKRIR MUTATED                      8                             2
  PRKRIR WILD-TYPE                  307                            45
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PRKRIR MUTATED                       1                              0
  PRKRIR WILD-TYPE                   105                             10
D2205V10, multiclass
                                clus
vv                               PRKRIR MUTATED PRKRIR WILD-TYPE
  COLON ADENOCARCINOMA                        8              307
  COLON MUCINOUS ADENOCARCINOMA               2               45
  RECTAL ADENOCARCINOMA                       1              105
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  PRKRIR MUTATED     8   0   1   0
  PRKRIR WILD-TYPE 337   4  30  25
D2205V11, multiclass
    clus
vv   PRKRIR MUTATED PRKRIR WILD-TYPE
  R0              8              337
  R1              0                4
  R2              1               30
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2205V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PRKRIR MUTATED                                  0     0
  PRKRIR WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  PRKRIR MUTATED                           0     8
  PRKRIR WILD-TYPE                        22   218
D2205V13, multiclass
                                  clus
vv                                 PRKRIR MUTATED PRKRIR WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         8              218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2206) Variable = PKIA MUTATION ANALYSIS
D2206V1, survival
                sevent
clus2              0   1
  PKIA MUTATED     6   3
  PKIA WILD-TYPE 372  90
  PKIA MUTATED PKIA WILD-TYPE 
             9            462 
  PKIA MUTATED PKIA WILD-TYPE 
             3             90 
$`PKIA MUTATED`
TCGA-AA-3492 TCGA-AZ-6598 TCGA-CA-6717 TCGA-CM-6171 TCGA-D5-6898 TCGA-DM-A285 
        3.02        49.41        12.76        14.04         1.48         6.12 
TCGA-G4-6323 TCGA-CI-6622 TCGA-DC-5337 
       13.78         6.97        15.02 

$`PKIA WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 
        5.13       106.75        22.36        62.79        88.21         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.20        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       12.99        13.02        15.02        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       12.49        16.14        15.58         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A28C 
        7.50        44.32       131.51       135.65       139.17        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 
       41.00        38.04       117.11        38.56         1.45        17.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6624 TCGA-CL-5917 
        0.69         0.72         6.05        33.17         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
        7.17         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  PKIA MUTATED PKIA WILD-TYPE 
          1.48           0.00 
  PKIA MUTATED PKIA WILD-TYPE 
         49.41         148.01 
  PKIA MUTATED PKIA WILD-TYPE 
        12.760         20.945 
[1] "1.5 - 49.4 (12.8)"  "0.0 - 148.0 (20.9)"
[1] "hr=" "2.9"
D2206V2, continuous
D2206V3, binary
                cls
clus               0   1
  PKIA MUTATED     8   2
  PKIA WILD-TYPE 358 117
[1] "tbl2"
                cls
clus             [,1] [,2]
  PKIA MUTATED      8    2
  PKIA WILD-TYPE  358  117
        clus
vv       PKIA MUTATED PKIA WILD-TYPE
  COLON             8            358
  RECTUM            2            117
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  PKIA MUTATED         3        1        2         1         1         0
  PKIA WILD-TYPE      88        0       30       137         9         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PKIA MUTATED           0          0          0          0        2         0
  PKIA WILD-TYPE        24         11         59         42       46        18
                vv
clus             STAGE IVB
  PKIA MUTATED           0
  PKIA WILD-TYPE         1
D2206V4, multiclass
            clus
vv           PKIA MUTATED PKIA WILD-TYPE
  STAGE I               3             88
  STAGE IA              1              0
  STAGE II              2             30
  STAGE IIA             1            137
  STAGE IIB             1              9
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            0             59
  STAGE IIIC            0             42
  STAGE IV              2             46
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  PKIA MUTATED     1   2   4   2
  PKIA WILD-TYPE  16  90 325  48
D2206V5, multiclass
    clus
vv   PKIA MUTATED PKIA WILD-TYPE
  T1            1             16
  T2            2             90
  T3            4            325
  T4            2             48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  PKIA MUTATED     8   0   2
  PKIA WILD-TYPE 279 113  85
D2206V6, multiclass
    clus
vv   PKIA MUTATED PKIA WILD-TYPE
  N0            8            279
  N1            0            113
  N2            2             85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2206V7, binary
                cls
clus               0   1
  PKIA MUTATED     6   2
  PKIA WILD-TYPE 369  63
[1] "tbl2"
                cls
clus             [,1] [,2]
  PKIA MUTATED      6    2
  PKIA WILD-TYPE  369   63
   clus
vv  PKIA MUTATED PKIA WILD-TYPE
  0            6            369
  1            2             63
[1] 2 2
[1] FALSE
D2206V8, binary
                cls
clus               0   1
  PKIA MUTATED     6   4
  PKIA WILD-TYPE 219 260
[1] "tbl2"
                cls
clus             [,1] [,2]
  PKIA MUTATED      6    4
  PKIA WILD-TYPE  219  260
        clus
vv       PKIA MUTATED PKIA WILD-TYPE
  FEMALE            6            219
  MALE              4            260
[1] 2 2
[1] FALSE
D2206V9, binary
                cls
clus               0   1
  PKIA MUTATED     6   0
  PKIA WILD-TYPE 344  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  PKIA MUTATED      6    0
  PKIA WILD-TYPE  344   22
     clus
vv    PKIA MUTATED PKIA WILD-TYPE
  NO             6            344
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  PKIA MUTATED                      5                             3
  PKIA WILD-TYPE                  310                            44
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  PKIA MUTATED                       2                              0
  PKIA WILD-TYPE                   104                             10
D2206V10, multiclass
                                clus
vv                               PKIA MUTATED PKIA WILD-TYPE
  COLON ADENOCARCINOMA                      5            310
  COLON MUCINOUS ADENOCARCINOMA             3             44
  RECTAL ADENOCARCINOMA                     2            104
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  PKIA MUTATED     5   0   1   1
  PKIA WILD-TYPE 340   4  30  24
D2206V11, multiclass
    clus
vv   PKIA MUTATED PKIA WILD-TYPE
  R0            5            340
  R1            0              4
  R2            1             30
  RX            1             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2206V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PKIA MUTATED                                  0     1
  PKIA WILD-TYPE                                1    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  PKIA MUTATED                           1     6
  PKIA WILD-TYPE                        21   220
D2206V13, multiclass
                                  clus
vv                                 PKIA MUTATED PKIA WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   1             21
  WHITE                                       6            220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2207) Variable = SYNJ1 MUTATION ANALYSIS
D2207V1, survival
                 sevent
clus2               0   1
  SYNJ1 MUTATED    14   4
  SYNJ1 WILD-TYPE 364  89
  SYNJ1 MUTATED SYNJ1 WILD-TYPE 
             18             453 
  SYNJ1 MUTATED SYNJ1 WILD-TYPE 
              4              89 
$`SYNJ1 MUTATED`
TCGA-AA-3492 TCGA-AA-3555 TCGA-AA-3672 TCGA-AA-3710 TCGA-AA-3977 TCGA-AA-A010 
        3.02        29.95         0.92        26.99        25.02        34.98 
TCGA-AD-6895 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-5860 
        0.72        49.41        12.10        12.76        10.06        32.02 
TCGA-CM-6161 TCGA-CM-6168 TCGA-G4-6628 TCGA-AG-3892 TCGA-AG-A002 TCGA-CI-6622 
       15.02        12.99        79.69        13.02        20.98         6.97 

$`SYNJ1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       13.02        24.00        17.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
       54.02         2.01        14.01        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       85.05        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       21.37        15.52        56.55         0.79         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 
        5.13       106.75        22.36        62.79        88.21         6.77 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.03        22.98        30.08        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       15.02        17.03        12.00         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       21.99        14.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       26.17        91.79        46.75        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 
       19.99         1.02        17.95        36.95        17.03        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  SYNJ1 MUTATED SYNJ1 WILD-TYPE 
           0.72            0.00 
  SYNJ1 MUTATED SYNJ1 WILD-TYPE 
          79.69          148.01 
  SYNJ1 MUTATED SYNJ1 WILD-TYPE 
          14.02           20.28 
[1] "0.7 - 79.7 (14.0)"  "0.0 - 148.0 (20.3)"
[1] "hr=" "1.4"
D2207V2, continuous
D2207V3, binary
                 cls
clus                0   1
  SYNJ1 MUTATED    16   3
  SYNJ1 WILD-TYPE 350 116
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SYNJ1 MUTATED     16    3
  SYNJ1 WILD-TYPE  350  116
        clus
vv       SYNJ1 MUTATED SYNJ1 WILD-TYPE
  COLON             16             350
  RECTUM             3             116
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SYNJ1 MUTATED         4        0        2         7         2         0
  SYNJ1 WILD-TYPE      87        1       30       131         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SYNJ1 MUTATED           1          0          0          0        1         0
  SYNJ1 WILD-TYPE        23         11         59         42       47        18
                 vv
clus              STAGE IVB
  SYNJ1 MUTATED           0
  SYNJ1 WILD-TYPE         1
D2207V4, multiclass
            clus
vv           SYNJ1 MUTATED SYNJ1 WILD-TYPE
  STAGE I                4              87
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA              7             131
  STAGE IIB              2               8
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             0              42
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  SYNJ1 MUTATED     1   4  11   3
  SYNJ1 WILD-TYPE  16  88 318  47
D2207V5, multiclass
    clus
vv   SYNJ1 MUTATED SYNJ1 WILD-TYPE
  T1             1              16
  T2             4              88
  T3            11             318
  T4             3              47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  SYNJ1 MUTATED    16   3   0
  SYNJ1 WILD-TYPE 271 110  87
D2207V6, multiclass
    clus
vv   SYNJ1 MUTATED SYNJ1 WILD-TYPE
  N0            16             271
  N1             3             110
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2207V7, binary
                 cls
clus                0   1
  SYNJ1 MUTATED    15   1
  SYNJ1 WILD-TYPE 360  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SYNJ1 MUTATED     15    1
  SYNJ1 WILD-TYPE  360   64
   clus
vv  SYNJ1 MUTATED SYNJ1 WILD-TYPE
  0            15             360
  1             1              64
[1] 2 2
[1] FALSE
D2207V8, binary
                 cls
clus                0   1
  SYNJ1 MUTATED    10   9
  SYNJ1 WILD-TYPE 215 255
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SYNJ1 MUTATED     10    9
  SYNJ1 WILD-TYPE  215  255
        clus
vv       SYNJ1 MUTATED SYNJ1 WILD-TYPE
  FEMALE            10             215
  MALE               9             255
[1] 2 2
[1] FALSE
D2207V9, binary
                 cls
clus                0   1
  SYNJ1 MUTATED    15   0
  SYNJ1 WILD-TYPE 335  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SYNJ1 MUTATED     15    0
  SYNJ1 WILD-TYPE  335   22
     clus
vv    SYNJ1 MUTATED SYNJ1 WILD-TYPE
  NO             15             335
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SYNJ1 MUTATED                     14                             2
  SYNJ1 WILD-TYPE                  301                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SYNJ1 MUTATED                       3                              0
  SYNJ1 WILD-TYPE                   103                             10
D2207V10, multiclass
                                clus
vv                               SYNJ1 MUTATED SYNJ1 WILD-TYPE
  COLON ADENOCARCINOMA                      14             301
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      3             103
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  SYNJ1 MUTATED    12   0   0   2
  SYNJ1 WILD-TYPE 333   4  31  23
D2207V11, multiclass
    clus
vv   SYNJ1 MUTATED SYNJ1 WILD-TYPE
  R0            12             333
  R1             0               4
  R2             0              31
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2207V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SYNJ1 MUTATED                                  0     2
  SYNJ1 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  SYNJ1 MUTATED                           2     6
  SYNJ1 WILD-TYPE                        20   220
D2207V13, multiclass
                                  clus
vv                                 SYNJ1 MUTATED SYNJ1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               9
  BLACK OR AFRICAN AMERICAN                    2              20
  WHITE                                        6             220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2208) Variable = TEX14 MUTATION ANALYSIS
D2208V1, survival
                 sevent
clus2               0   1
  TEX14 MUTATED    21   4
  TEX14 WILD-TYPE 357  89
  TEX14 MUTATED TEX14 WILD-TYPE 
             25             446 
  TEX14 MUTATED TEX14 WILD-TYPE 
              4              89 
$`TEX14 MUTATED`
TCGA-A6-6781 TCGA-AA-3663 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3821 TCGA-AA-3833 
       19.66         6.97        19.04        35.05         1.02        15.95 
TCGA-AA-3877 TCGA-AA-3977 TCGA-AA-A02O TCGA-AD-5900 TCGA-AD-6895 TCGA-AU-6004 
       31.00        25.02         0.92         0.07         0.72        27.09 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-6601 TCGA-CM-5860 TCGA-D5-6532 TCGA-D5-6535 
       17.82        58.39       100.01        32.02        18.25        15.12 
TCGA-D5-6537 TCGA-F4-6856 TCGA-AG-A002 TCGA-CI-6624 TCGA-CL-5917 TCGA-DC-5337 
        4.80        35.31        20.98         4.73        78.12        15.02 
TCGA-DY-A1DC 
       41.36 

$`TEX14 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3815 
        5.03        85.05        26.99        19.04        10.06        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        0.99        25.02        17.98        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02W TCGA-AA-A02Y 
       39.98         2.01         5.03        14.01        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       18.05        40.96        21.37        15.52        56.55         0.79 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AZ-4323 TCGA-AZ-4616 
       16.31         0.95        33.01        21.44         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
      106.75        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
       12.10        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5861 
       13.02        29.06        22.03        22.98        30.08        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6533 
       12.26        19.59        56.09        55.92        20.19         1.32 
TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       43.27        17.85        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 
       16.24        33.67        13.25         0.53        47.41       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CL-5918 TCGA-DC-5869 TCGA-DC-6155 
        6.05        33.17         6.97         7.17         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
        5.29       126.44        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  TEX14 MUTATED TEX14 WILD-TYPE 
           0.07            0.00 
  TEX14 MUTATED TEX14 WILD-TYPE 
         100.01          148.01 
  TEX14 MUTATED TEX14 WILD-TYPE 
         19.040          20.415 
[1] "0.1 - 100.0 (19.0)" "0.0 - 148.0 (20.4)"
[1] "hr=" "1.2"
D2208V2, continuous
D2208V3, binary
                 cls
clus                0   1
  TEX14 MUTATED    20   5
  TEX14 WILD-TYPE 346 114
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TEX14 MUTATED     20    5
  TEX14 WILD-TYPE  346  114
        clus
vv       TEX14 MUTATED TEX14 WILD-TYPE
  COLON             20             346
  RECTUM             5             114
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TEX14 MUTATED         8        0        4         6         0         0
  TEX14 WILD-TYPE      83        1       28       132        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TEX14 MUTATED           0          0          3          2        0         0
  TEX14 WILD-TYPE        24         11         56         40       48        18
                 vv
clus              STAGE IVB
  TEX14 MUTATED           0
  TEX14 WILD-TYPE         1
D2208V4, multiclass
            clus
vv           TEX14 MUTATED TEX14 WILD-TYPE
  STAGE I                8              83
  STAGE IA               0               1
  STAGE II               4              28
  STAGE IIA              6             132
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             3              56
  STAGE IIIC             2              40
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  TEX14 MUTATED     2   7  15   1
  TEX14 WILD-TYPE  15  85 314  49
D2208V5, multiclass
    clus
vv   TEX14 MUTATED TEX14 WILD-TYPE
  T1             2              15
  T2             7              85
  T3            15             314
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  TEX14 MUTATED    19   5   1
  TEX14 WILD-TYPE 268 108  86
D2208V6, multiclass
    clus
vv   TEX14 MUTATED TEX14 WILD-TYPE
  N0            19             268
  N1             5             108
  N2             1              86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2208V7, binary
                 cls
clus                0   1
  TEX14 MUTATED    18   0
  TEX14 WILD-TYPE 357  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TEX14 MUTATED     18    0
  TEX14 WILD-TYPE  357   65
   clus
vv  TEX14 MUTATED TEX14 WILD-TYPE
  0            18             357
  1             0              65
[1] 2 2
[1] FALSE
D2208V8, binary
                 cls
clus                0   1
  TEX14 MUTATED    10  15
  TEX14 WILD-TYPE 215 249
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TEX14 MUTATED     10   15
  TEX14 WILD-TYPE  215  249
        clus
vv       TEX14 MUTATED TEX14 WILD-TYPE
  FEMALE            10             215
  MALE              15             249
[1] 2 2
[1] FALSE
D2208V9, binary
                 cls
clus                0   1
  TEX14 MUTATED    19   0
  TEX14 WILD-TYPE 331  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TEX14 MUTATED     19    0
  TEX14 WILD-TYPE  331   22
     clus
vv    TEX14 MUTATED TEX14 WILD-TYPE
  NO             19             331
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  TEX14 MUTATED                     15                             5
  TEX14 WILD-TYPE                  300                            42
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  TEX14 MUTATED                       5                              0
  TEX14 WILD-TYPE                   101                             10
D2208V10, multiclass
                                clus
vv                               TEX14 MUTATED TEX14 WILD-TYPE
  COLON ADENOCARCINOMA                      15             300
  COLON MUCINOUS ADENOCARCINOMA              5              42
  RECTAL ADENOCARCINOMA                      5             101
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  TEX14 MUTATED    18   0   0   2
  TEX14 WILD-TYPE 327   4  31  23
D2208V11, multiclass
    clus
vv   TEX14 MUTATED TEX14 WILD-TYPE
  R0            18             327
  R1             0               4
  R2             0              31
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2208V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TEX14 MUTATED                                  0     0
  TEX14 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  TEX14 MUTATED                           1    15
  TEX14 WILD-TYPE                        21   211
D2208V13, multiclass
                                  clus
vv                                 TEX14 MUTATED TEX14 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                       15             211
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2209) Variable = F9 MUTATION ANALYSIS
D2209V1, survival
              sevent
clus2            0   1
  F9 MUTATED    12   7
  F9 WILD-TYPE 366  86
  F9 MUTATED F9 WILD-TYPE 
          19          452 
  F9 MUTATED F9 WILD-TYPE 
           7           86 
$`F9 MUTATED`
TCGA-A6-2671 TCGA-A6-6141 TCGA-AA-3821 TCGA-AA-3852 TCGA-AA-3977 TCGA-AA-A00N 
       43.76         8.38         1.02         0.00        25.02         4.01 
TCGA-AA-A010 TCGA-AZ-6608 TCGA-CA-6716 TCGA-CA-6717 TCGA-CK-6747 TCGA-D5-6924 
       34.98         1.61        12.20        12.76        82.95        14.30 
TCGA-D5-6927 TCGA-DM-A1D8 TCGA-F4-6460 TCGA-F4-6570 TCGA-F4-6703 TCGA-G4-6309 
        9.44        12.59        31.96         6.18        47.87        85.48 
TCGA-CI-6624 
        4.73 

$`F9 WILD-TYPE`
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       46.65        43.76        42.90        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 
       22.06        32.71        27.09        22.52        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 
       35.05        33.04         0.99        25.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
        0.00        33.07        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        30.05        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        3.19        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6748 TCGA-CK-6751 
       49.08        51.32         9.99        21.14         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.04        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       49.91        13.32       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6569 TCGA-F4-6704 
       60.79       117.07        98.24         8.61        35.74         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       44.68        55.04        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       78.12         7.17        15.02         5.03        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
        0.49        20.55        19.96        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  F9 MUTATED F9 WILD-TYPE 
           0            0 
  F9 MUTATED F9 WILD-TYPE 
       85.48       148.01 
  F9 MUTATED F9 WILD-TYPE 
       12.59        20.73 
[1] "0.0 - 85.5 (12.6)"  "0.0 - 148.0 (20.7)"
[1] "hr=" "2.2"
D2209V2, continuous
D2209V3, binary
              cls
clus             0   1
  F9 MUTATED    19   1
  F9 WILD-TYPE 347 118
[1] "tbl2"
              cls
clus           [,1] [,2]
  F9 MUTATED     19    1
  F9 WILD-TYPE  347  118
        clus
vv       F9 MUTATED F9 WILD-TYPE
  COLON          19          347
  RECTUM          1          118
[1] 2 2
[1] FALSE
              vv
clus           STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  F9 MUTATED         2        0        0        10         2         0
  F9 WILD-TYPE      89        1       32       128         8         1
              vv
clus           STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  F9 MUTATED           0          1          2          0        1         0
  F9 WILD-TYPE        24         10         57         42       47        18
              vv
clus           STAGE IVB
  F9 MUTATED           0
  F9 WILD-TYPE         1
D2209V4, multiclass
            clus
vv           F9 MUTATED F9 WILD-TYPE
  STAGE I             2           89
  STAGE IA            0            1
  STAGE II            0           32
  STAGE IIA          10          128
  STAGE IIB           2            8
  STAGE IIC           0            1
  STAGE III           0           24
  STAGE IIIA          1           10
  STAGE IIIB          2           57
  STAGE IIIC          0           42
  STAGE IV            1           47
  STAGE IVA           0           18
  STAGE IVB           0            1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
              vv
clus            T1  T2  T3  T4
  F9 MUTATED     0   4  14   2
  F9 WILD-TYPE  17  88 315  48
D2209V5, multiclass
    clus
vv   F9 MUTATED F9 WILD-TYPE
  T1          0           17
  T2          4           88
  T3         14          315
  T4          2           48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
              vv
clus            N0  N1  N2
  F9 MUTATED    15   4   1
  F9 WILD-TYPE 272 109  86
D2209V6, multiclass
    clus
vv   F9 MUTATED F9 WILD-TYPE
  N0         15          272
  N1          4          109
  N2          1           86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2209V7, binary
              cls
clus             0   1
  F9 MUTATED    16   1
  F9 WILD-TYPE 359  64
[1] "tbl2"
              cls
clus           [,1] [,2]
  F9 MUTATED     16    1
  F9 WILD-TYPE  359   64
   clus
vv  F9 MUTATED F9 WILD-TYPE
  0         16          359
  1          1           64
[1] 2 2
[1] FALSE
D2209V8, binary
              cls
clus             0   1
  F9 MUTATED    10  10
  F9 WILD-TYPE 215 254
[1] "tbl2"
              cls
clus           [,1] [,2]
  F9 MUTATED     10   10
  F9 WILD-TYPE  215  254
        clus
vv       F9 MUTATED F9 WILD-TYPE
  FEMALE         10          215
  MALE           10          254
[1] 2 2
[1] FALSE
D2209V9, binary
              cls
clus             0   1
  F9 MUTATED    15   0
  F9 WILD-TYPE 335  22
[1] "tbl2"
              cls
clus           [,1] [,2]
  F9 MUTATED     15    0
  F9 WILD-TYPE  335   22
     clus
vv    F9 MUTATED F9 WILD-TYPE
  NO          15          335
  YES          0           22
[1] 2 2
[1] FALSE
              vv
clus           COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  F9 MUTATED                     15                             4
  F9 WILD-TYPE                  300                            43
              vv
clus           RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  F9 MUTATED                       1                              0
  F9 WILD-TYPE                   105                             10
D2209V10, multiclass
                                clus
vv                               F9 MUTATED F9 WILD-TYPE
  COLON ADENOCARCINOMA                   15          300
  COLON MUCINOUS ADENOCARCINOMA           4           43
  RECTAL ADENOCARCINOMA                   1          105
  RECTAL MUCINOUS ADENOCARCINOMA          0           10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
              vv
clus            R0  R1  R2  RX
  F9 MUTATED    12   0   0   3
  F9 WILD-TYPE 333   4  31  22
D2209V11, multiclass
    clus
vv   F9 MUTATED F9 WILD-TYPE
  R0         12          333
  R1          0            4
  R2          0           31
  RX          3           22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2209V12, continuous
              vv
clus           AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  F9 MUTATED                                  0     2                         2
  F9 WILD-TYPE                                1     9                        20
              vv
clus           WHITE
  F9 MUTATED      10
  F9 WILD-TYPE   216
D2209V13, multiclass
                                  clus
vv                                 F9 MUTATED F9 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE          0            1
  ASIAN                                     2            9
  BLACK OR AFRICAN AMERICAN                 2           20
  WHITE                                    10          216
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2210) Variable = SMEK1 MUTATION ANALYSIS
D2210V1, survival
                 sevent
clus2               0   1
  SMEK1 MUTATED     8   1
  SMEK1 WILD-TYPE 370  92
  SMEK1 MUTATED SMEK1 WILD-TYPE 
              9             462 
  SMEK1 MUTATED SMEK1 WILD-TYPE 
              1              92 
$`SMEK1 MUTATED`
TCGA-AA-3662 TCGA-AA-3870 TCGA-AD-5900 TCGA-AZ-4315 TCGA-AZ-6601 TCGA-D5-6540 
        6.05        29.98         0.07        58.39       100.01        16.14 
TCGA-AF-6655 TCGA-AG-A002 TCGA-CI-6619 
       20.02        20.98         6.05 

$`SMEK1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       17.03        24.03        27.02        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       39.98        18.05        40.96        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 
       62.79        88.21        49.41         6.77        12.10        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6672 TCGA-AG-3574 
       10.39        14.50        16.83        15.39        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        0.72        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  SMEK1 MUTATED SMEK1 WILD-TYPE 
           0.07            0.00 
  SMEK1 MUTATED SMEK1 WILD-TYPE 
         100.01          148.01 
  SMEK1 MUTATED SMEK1 WILD-TYPE 
         20.020          20.235 
[1] "0.1 - 100.0 (20.0)" "0.0 - 148.0 (20.2)"
[1] "hr=" "2"  
D2210V2, continuous
D2210V3, binary
                 cls
clus                0   1
  SMEK1 MUTATED     6   3
  SMEK1 WILD-TYPE 360 116
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMEK1 MUTATED      6    3
  SMEK1 WILD-TYPE  360  116
        clus
vv       SMEK1 MUTATED SMEK1 WILD-TYPE
  COLON              6             360
  RECTUM             3             116
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SMEK1 MUTATED         3        0        1         1         0         0
  SMEK1 WILD-TYPE      88        1       31       137        10         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SMEK1 MUTATED           0          1          0          0        3         0
  SMEK1 WILD-TYPE        24         10         59         42       45        18
                 vv
clus              STAGE IVB
  SMEK1 MUTATED           0
  SMEK1 WILD-TYPE         1
D2210V4, multiclass
            clus
vv           SMEK1 MUTATED SMEK1 WILD-TYPE
  STAGE I                3              88
  STAGE IA               0               1
  STAGE II               1              31
  STAGE IIA              1             137
  STAGE IIB              0              10
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             1              10
  STAGE IIIB             0              59
  STAGE IIIC             0              42
  STAGE IV               3              45
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  SMEK1 MUTATED     0   4   4   1
  SMEK1 WILD-TYPE  17  88 325  49
D2210V5, multiclass
    clus
vv   SMEK1 MUTATED SMEK1 WILD-TYPE
  T1             0              17
  T2             4              88
  T3             4             325
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  SMEK1 MUTATED     5   2   2
  SMEK1 WILD-TYPE 282 111  85
D2210V6, multiclass
    clus
vv   SMEK1 MUTATED SMEK1 WILD-TYPE
  N0             5             282
  N1             2             111
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2210V7, binary
                 cls
clus                0   1
  SMEK1 MUTATED     5   3
  SMEK1 WILD-TYPE 370  62
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMEK1 MUTATED      5    3
  SMEK1 WILD-TYPE  370   62
   clus
vv  SMEK1 MUTATED SMEK1 WILD-TYPE
  0             5             370
  1             3              62
[1] 2 2
[1] FALSE
D2210V8, binary
                 cls
clus                0   1
  SMEK1 MUTATED     2   7
  SMEK1 WILD-TYPE 223 257
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMEK1 MUTATED      2    7
  SMEK1 WILD-TYPE  223  257
        clus
vv       SMEK1 MUTATED SMEK1 WILD-TYPE
  FEMALE             2             223
  MALE               7             257
[1] 2 2
[1] FALSE
D2210V9, binary
                 cls
clus                0   1
  SMEK1 MUTATED     6   0
  SMEK1 WILD-TYPE 344  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMEK1 MUTATED      6    0
  SMEK1 WILD-TYPE  344   22
     clus
vv    SMEK1 MUTATED SMEK1 WILD-TYPE
  NO              6             344
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SMEK1 MUTATED                      4                             2
  SMEK1 WILD-TYPE                  311                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SMEK1 MUTATED                       3                              0
  SMEK1 WILD-TYPE                   103                             10
D2210V10, multiclass
                                clus
vv                               SMEK1 MUTATED SMEK1 WILD-TYPE
  COLON ADENOCARCINOMA                       4             311
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      3             103
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  SMEK1 MUTATED     6   0   1   0
  SMEK1 WILD-TYPE 339   4  30  25
D2210V11, multiclass
    clus
vv   SMEK1 MUTATED SMEK1 WILD-TYPE
  R0             6             339
  R1             0               4
  R2             1              30
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2210V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SMEK1 MUTATED                                  0     0
  SMEK1 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  SMEK1 MUTATED                           0     6
  SMEK1 WILD-TYPE                        22   220
D2210V13, multiclass
                                  clus
vv                                 SMEK1 MUTATED SMEK1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        6             220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2211) Variable = TSC1 MUTATION ANALYSIS
D2211V1, survival
                sevent
clus2              0   1
  TSC1 MUTATED    10   2
  TSC1 WILD-TYPE 368  91
  TSC1 MUTATED TSC1 WILD-TYPE 
            12            459 
  TSC1 MUTATED TSC1 WILD-TYPE 
             2             91 
$`TSC1 MUTATED`
TCGA-AA-3950 TCGA-AA-A00J TCGA-AA-A00N TCGA-AD-5900 TCGA-AD-6548 TCGA-AY-6197 
       24.00        18.05         4.01         0.07        21.37        21.44 
TCGA-CK-4952 TCGA-CM-6162 TCGA-D5-5541 TCGA-D5-6537 TCGA-G4-6628 TCGA-AG-A002 
       15.62        12.00        55.92         4.80        79.69        20.98 

$`TSC1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L 
       38.04        19.00        30.02        34.03        18.05        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
       18.05        40.96        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4315 
       27.09        16.31         0.95        33.01        17.82        58.39 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41         5.13       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
       17.56       148.01        85.45        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       17.03        15.02         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-6529 
       12.03        45.40        12.26        19.59        56.09        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6538 
       18.25         1.32        43.27        15.12        17.85        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       46.75        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  TSC1 MUTATED TSC1 WILD-TYPE 
          0.07           0.00 
  TSC1 MUTATED TSC1 WILD-TYPE 
         79.69         148.01 
  TSC1 MUTATED TSC1 WILD-TYPE 
        19.515         20.190 
[1] "0.1 - 79.7 (19.5)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.1"
D2211V2, continuous
D2211V3, binary
                cls
clus               0   1
  TSC1 MUTATED    13   1
  TSC1 WILD-TYPE 353 118
[1] "tbl2"
                cls
clus             [,1] [,2]
  TSC1 MUTATED     13    1
  TSC1 WILD-TYPE  353  118
        clus
vv       TSC1 MUTATED TSC1 WILD-TYPE
  COLON            13            353
  RECTUM            1            118
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  TSC1 MUTATED         4        0        0         3         2         0
  TSC1 WILD-TYPE      87        1       32       135         8         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TSC1 MUTATED           0          0          4          1        0         0
  TSC1 WILD-TYPE        24         11         55         41       48        18
                vv
clus             STAGE IVB
  TSC1 MUTATED           0
  TSC1 WILD-TYPE         1
D2211V4, multiclass
            clus
vv           TSC1 MUTATED TSC1 WILD-TYPE
  STAGE I               4             87
  STAGE IA              0              1
  STAGE II              0             32
  STAGE IIA             3            135
  STAGE IIB             2              8
  STAGE IIC             0              1
  STAGE III             0             24
  STAGE IIIA            0             11
  STAGE IIIB            4             55
  STAGE IIIC            1             41
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  TSC1 MUTATED     0   4   6   4
  TSC1 WILD-TYPE  17  88 323  46
D2211V5, multiclass
    clus
vv   TSC1 MUTATED TSC1 WILD-TYPE
  T1            0             17
  T2            4             88
  T3            6            323
  T4            4             46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  TSC1 MUTATED     9   4   1
  TSC1 WILD-TYPE 278 109  86
D2211V6, multiclass
    clus
vv   TSC1 MUTATED TSC1 WILD-TYPE
  N0            9            278
  N1            4            109
  N2            1             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2211V7, binary
                cls
clus               0   1
  TSC1 MUTATED    10   0
  TSC1 WILD-TYPE 365  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  TSC1 MUTATED     10    0
  TSC1 WILD-TYPE  365   65
   clus
vv  TSC1 MUTATED TSC1 WILD-TYPE
  0           10            365
  1            0             65
[1] 2 2
[1] FALSE
D2211V8, binary
                cls
clus               0   1
  TSC1 MUTATED     6   8
  TSC1 WILD-TYPE 219 256
[1] "tbl2"
                cls
clus             [,1] [,2]
  TSC1 MUTATED      6    8
  TSC1 WILD-TYPE  219  256
        clus
vv       TSC1 MUTATED TSC1 WILD-TYPE
  FEMALE            6            219
  MALE              8            256
[1] 2 2
[1] FALSE
D2211V9, binary
                cls
clus               0   1
  TSC1 MUTATED     9   0
  TSC1 WILD-TYPE 341  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  TSC1 MUTATED      9    0
  TSC1 WILD-TYPE  341   22
     clus
vv    TSC1 MUTATED TSC1 WILD-TYPE
  NO             9            341
  YES            0             22
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  TSC1 MUTATED                      7                             6
  TSC1 WILD-TYPE                  308                            41
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  TSC1 MUTATED                       1                              0
  TSC1 WILD-TYPE                   105                             10
D2211V10, multiclass
                                clus
vv                               TSC1 MUTATED TSC1 WILD-TYPE
  COLON ADENOCARCINOMA                      7            308
  COLON MUCINOUS ADENOCARCINOMA             6             41
  RECTAL ADENOCARCINOMA                     1            105
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  TSC1 MUTATED    12   0   0   2
  TSC1 WILD-TYPE 333   4  31  23
D2211V11, multiclass
    clus
vv   TSC1 MUTATED TSC1 WILD-TYPE
  R0           12            333
  R1            0              4
  R2            0             31
  RX            2             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2211V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TSC1 MUTATED                                  0     0
  TSC1 WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  TSC1 MUTATED                           0     9
  TSC1 WILD-TYPE                        22   217
D2211V13, multiclass
                                  clus
vv                                 TSC1 MUTATED TSC1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       9            217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2212) Variable = HPCA MUTATION ANALYSIS
D2212V1, survival
                sevent
clus2              0   1
  HPCA MUTATED     4   2
  HPCA WILD-TYPE 374  91
  HPCA MUTATED HPCA WILD-TYPE 
             6            465 
  HPCA MUTATED HPCA WILD-TYPE 
             2             91 
$`HPCA MUTATED`
TCGA-AA-3510 TCGA-AA-A01R TCGA-AZ-6599 TCGA-CM-5861 TCGA-F4-6570 TCGA-AG-3742 
       63.98        35.01         6.77        15.02         6.18         0.99 

$`HPCA WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
        1.02        35.01         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S 
       12.00        31.00        31.00        38.07         1.02         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W 
       39.98         2.01         5.03        14.01         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 
       33.01        21.44        17.82        58.39         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 
      106.75        22.36        62.79        88.21        49.41        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 
       98.24         8.61        31.96        35.74        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
       47.41        35.31       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
       32.98         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  HPCA MUTATED HPCA WILD-TYPE 
          0.99           0.00 
  HPCA MUTATED HPCA WILD-TYPE 
         63.98         148.01 
  HPCA MUTATED HPCA WILD-TYPE 
        10.895         20.280 
[1] "1.0 - 64.0 (10.9)"  "0.0 - 148.0 (20.3)"
[1] "hr=" "2"  
D2212V2, continuous
D2212V3, binary
                cls
clus               0   1
  HPCA MUTATED     5   1
  HPCA WILD-TYPE 361 118
[1] "tbl2"
                cls
clus             [,1] [,2]
  HPCA MUTATED      5    1
  HPCA WILD-TYPE  361  118
        clus
vv       HPCA MUTATED HPCA WILD-TYPE
  COLON             5            361
  RECTUM            1            118
[1] 2 2
[1] FALSE
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  HPCA MUTATED         2        0        1         2         0         0
  HPCA WILD-TYPE      89        1       31       136        10         1
                vv
clus             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  HPCA MUTATED           1          0          0          0        0         0
  HPCA WILD-TYPE        23         11         59         42       48        18
                vv
clus             STAGE IVB
  HPCA MUTATED           0
  HPCA WILD-TYPE         1
D2212V4, multiclass
            clus
vv           HPCA MUTATED HPCA WILD-TYPE
  STAGE I               2             89
  STAGE IA              0              1
  STAGE II              1             31
  STAGE IIA             2            136
  STAGE IIB             0             10
  STAGE IIC             0              1
  STAGE III             1             23
  STAGE IIIA            0             11
  STAGE IIIB            0             59
  STAGE IIIC            0             42
  STAGE IV              0             48
  STAGE IVA             0             18
  STAGE IVB             0              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  HPCA MUTATED     1   1   4   0
  HPCA WILD-TYPE  16  91 325  50
D2212V5, multiclass
    clus
vv   HPCA MUTATED HPCA WILD-TYPE
  T1            1             16
  T2            1             91
  T3            4            325
  T4            0             50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  HPCA MUTATED     5   0   1
  HPCA WILD-TYPE 282 113  86
D2212V6, multiclass
    clus
vv   HPCA MUTATED HPCA WILD-TYPE
  N0            5            282
  N1            0            113
  N2            1             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2212V7, binary
                cls
clus               0   1
  HPCA MUTATED     5   0
  HPCA WILD-TYPE 370  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  HPCA MUTATED      5    0
  HPCA WILD-TYPE  370   65
   clus
vv  HPCA MUTATED HPCA WILD-TYPE
  0            5            370
  1            0             65
[1] 2 2
[1] FALSE
D2212V8, binary
                cls
clus               0   1
  HPCA MUTATED     3   3
  HPCA WILD-TYPE 222 261
[1] "tbl2"
                cls
clus             [,1] [,2]
  HPCA MUTATED      3    3
  HPCA WILD-TYPE  222  261
        clus
vv       HPCA MUTATED HPCA WILD-TYPE
  FEMALE            3            222
  MALE              3            261
[1] 2 2
[1] FALSE
D2212V9, binary
                cls
clus               0   1
  HPCA MUTATED     4   1
  HPCA WILD-TYPE 346  21
[1] "tbl2"
                cls
clus             [,1] [,2]
  HPCA MUTATED      4    1
  HPCA WILD-TYPE  346   21
     clus
vv    HPCA MUTATED HPCA WILD-TYPE
  NO             4            346
  YES            1             21
[1] 2 2
[1] FALSE
                vv
clus             COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  HPCA MUTATED                      4                             1
  HPCA WILD-TYPE                  311                            46
                vv
clus             RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  HPCA MUTATED                       1                              0
  HPCA WILD-TYPE                   105                             10
D2212V10, multiclass
                                clus
vv                               HPCA MUTATED HPCA WILD-TYPE
  COLON ADENOCARCINOMA                      4            311
  COLON MUCINOUS ADENOCARCINOMA             1             46
  RECTAL ADENOCARCINOMA                     1            105
  RECTAL MUCINOUS ADENOCARCINOMA            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              R0  R1  R2  RX
  HPCA MUTATED     5   0   0   0
  HPCA WILD-TYPE 340   4  31  25
D2212V11, multiclass
    clus
vv   HPCA MUTATED HPCA WILD-TYPE
  R0            5            340
  R1            0              4
  R2            0             31
  RX            0             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2212V12, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HPCA MUTATED                                  0     0
  HPCA WILD-TYPE                                1    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  HPCA MUTATED                           0     3
  HPCA WILD-TYPE                        22   223
D2212V13, multiclass
                                  clus
vv                                 HPCA MUTATED HPCA WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   0             22
  WHITE                                       3            223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2213) Variable = EIF2B3 MUTATION ANALYSIS
D2213V1, survival
                  sevent
clus2                0   1
  EIF2B3 MUTATED     3   3
  EIF2B3 WILD-TYPE 375  90
  EIF2B3 MUTATED EIF2B3 WILD-TYPE 
               6              465 
  EIF2B3 MUTATED EIF2B3 WILD-TYPE 
               3               90 
$`EIF2B3 MUTATED`
TCGA-A6-6781 TCGA-AA-3848 TCGA-AA-3949 TCGA-AZ-4315 TCGA-AZ-6601 TCGA-F4-6459 
       19.66        10.06        26.01        58.39       100.01         8.61 

$`EIF2B3 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       23.87        20.12        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       17.03         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 
        0.99        31.07        31.07        30.05        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       12.99        24.00        33.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03        14.01         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 
       62.79        88.21        49.41         6.77        12.10        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        85.48        63.62        61.91        36.00        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  EIF2B3 MUTATED EIF2B3 WILD-TYPE 
            8.61             0.00 
  EIF2B3 MUTATED EIF2B3 WILD-TYPE 
          100.01           148.01 
  EIF2B3 MUTATED EIF2B3 WILD-TYPE 
          22.835           20.190 
[1] "8.6 - 100.0 (22.8)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.8"
D2213V2, continuous
D2213V3, binary
                  cls
clus                 0   1
  EIF2B3 MUTATED     6   0
  EIF2B3 WILD-TYPE 360 119
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EIF2B3 MUTATED      6    0
  EIF2B3 WILD-TYPE  360  119
        clus
vv       EIF2B3 MUTATED EIF2B3 WILD-TYPE
  COLON               6              360
  RECTUM              0              119
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  EIF2B3 MUTATED         0        0        1         1         0         0
  EIF2B3 WILD-TYPE      91        1       31       137        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  EIF2B3 MUTATED           0          0          2          2        0
  EIF2B3 WILD-TYPE        24         11         57         40       48
                  vv
clus               STAGE IVA STAGE IVB
  EIF2B3 MUTATED           0         0
  EIF2B3 WILD-TYPE        18         1
D2213V4, multiclass
            clus
vv           EIF2B3 MUTATED EIF2B3 WILD-TYPE
  STAGE I                 0               91
  STAGE IA                0                1
  STAGE II                1               31
  STAGE IIA               1              137
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              2               57
  STAGE IIIC              2               40
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  EIF2B3 MUTATED     0   0   5   1
  EIF2B3 WILD-TYPE  17  92 324  49
D2213V5, multiclass
    clus
vv   EIF2B3 MUTATED EIF2B3 WILD-TYPE
  T1              0               17
  T2              0               92
  T3              5              324
  T4              1               49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  EIF2B3 MUTATED     2   2   2
  EIF2B3 WILD-TYPE 285 111  85
D2213V6, multiclass
    clus
vv   EIF2B3 MUTATED EIF2B3 WILD-TYPE
  N0              2              285
  N1              2              111
  N2              2               85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2213V7, binary
                  cls
clus                 0   1
  EIF2B3 MUTATED     5   0
  EIF2B3 WILD-TYPE 370  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EIF2B3 MUTATED      5    0
  EIF2B3 WILD-TYPE  370   65
   clus
vv  EIF2B3 MUTATED EIF2B3 WILD-TYPE
  0              5              370
  1              0               65
[1] 2 2
[1] FALSE
D2213V8, binary
                  cls
clus                 0   1
  EIF2B3 MUTATED     3   3
  EIF2B3 WILD-TYPE 222 261
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EIF2B3 MUTATED      3    3
  EIF2B3 WILD-TYPE  222  261
        clus
vv       EIF2B3 MUTATED EIF2B3 WILD-TYPE
  FEMALE              3              222
  MALE                3              261
[1] 2 2
[1] FALSE
D2213V9, binary
                  cls
clus                 0   1
  EIF2B3 MUTATED     6   0
  EIF2B3 WILD-TYPE 344  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EIF2B3 MUTATED      6    0
  EIF2B3 WILD-TYPE  344   22
     clus
vv    EIF2B3 MUTATED EIF2B3 WILD-TYPE
  NO               6              344
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  EIF2B3 MUTATED                      4                             2
  EIF2B3 WILD-TYPE                  311                            45
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  EIF2B3 MUTATED                       0                              0
  EIF2B3 WILD-TYPE                   106                             10
D2213V10, multiclass
                                clus
vv                               EIF2B3 MUTATED EIF2B3 WILD-TYPE
  COLON ADENOCARCINOMA                        4              311
  COLON MUCINOUS ADENOCARCINOMA               2               45
  RECTAL ADENOCARCINOMA                       0              106
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  EIF2B3 MUTATED     5   0   0   0
  EIF2B3 WILD-TYPE 340   4  31  25
D2213V11, multiclass
    clus
vv   EIF2B3 MUTATED EIF2B3 WILD-TYPE
  R0              5              340
  R1              0                4
  R2              0               31
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2213V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  EIF2B3 MUTATED                                  0     0
  EIF2B3 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  EIF2B3 MUTATED                           0     4
  EIF2B3 WILD-TYPE                        22   222
D2213V13, multiclass
                                  clus
vv                                 EIF2B3 MUTATED EIF2B3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         4              222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2214) Variable = LRIG1 MUTATION ANALYSIS
D2214V1, survival
                 sevent
clus2               0   1
  LRIG1 MUTATED    13   1
  LRIG1 WILD-TYPE 365  92
  LRIG1 MUTATED LRIG1 WILD-TYPE 
             14             457 
  LRIG1 MUTATED LRIG1 WILD-TYPE 
              1              92 
$`LRIG1 MUTATED`
TCGA-AA-3562 TCGA-AA-3663 TCGA-AA-3854 TCGA-AA-A010 TCGA-AA-A01R TCGA-AD-6889 
       19.99         6.97        36.03        34.98        35.01        56.55 
TCGA-AZ-4315 TCGA-AZ-6601 TCGA-CM-4752 TCGA-CM-6169 TCGA-D5-6540 TCGA-D5-6928 
       58.39       100.01        13.02        13.02        16.14        11.64 
TCGA-F4-6808 TCGA-AG-A002 
       33.67        20.98 

$`LRIG1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       20.98        19.99        13.94        61.02        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       35.05        33.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3855 TCGA-AA-3856 
       10.06         0.00        33.07         0.00        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
       38.07         1.02         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       14.01         0.92        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
        0.07        21.37        15.52         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
       16.31         0.95        33.01        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77        12.10        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       25.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00         2.96        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       12.99        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       12.49        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
       14.30         9.04         9.44         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       41.42        16.24        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 
       35.80        26.17        91.79        46.75        79.69        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       39.48        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50        16.83        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 
       38.04       117.11        38.56         1.45        17.49         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        0.72         6.05        33.17         6.97         4.73        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 
       20.55        19.96        20.91        18.28         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 
       31.30        28.57        32.19         0.66         0.69        55.76 
TCGA-G5-6641 
       26.43 

  LRIG1 MUTATED LRIG1 WILD-TYPE 
           6.97            0.00 
  LRIG1 MUTATED LRIG1 WILD-TYPE 
         100.01          148.01 
  LRIG1 MUTATED LRIG1 WILD-TYPE 
         27.325          20.120 
[1] "7.0 - 100.0 (27.3)" "0.0 - 148.0 (20.1)"
[1] "hr=" "3.5"
D2214V2, continuous
D2214V3, binary
                 cls
clus                0   1
  LRIG1 MUTATED    14   1
  LRIG1 WILD-TYPE 352 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LRIG1 MUTATED     14    1
  LRIG1 WILD-TYPE  352  118
        clus
vv       LRIG1 MUTATED LRIG1 WILD-TYPE
  COLON             14             352
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  LRIG1 MUTATED         4        0        2         5         1         0
  LRIG1 WILD-TYPE      87        1       30       133         9         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  LRIG1 MUTATED           1          0          0          2        0         0
  LRIG1 WILD-TYPE        23         11         59         40       48        18
                 vv
clus              STAGE IVB
  LRIG1 MUTATED           0
  LRIG1 WILD-TYPE         1
D2214V4, multiclass
            clus
vv           LRIG1 MUTATED LRIG1 WILD-TYPE
  STAGE I                4              87
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA              5             133
  STAGE IIB              1               9
  STAGE IIC              0               1
  STAGE III              1              23
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             2              40
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  LRIG1 MUTATED     1   3  10   1
  LRIG1 WILD-TYPE  16  89 319  49
D2214V5, multiclass
    clus
vv   LRIG1 MUTATED LRIG1 WILD-TYPE
  T1             1              16
  T2             3              89
  T3            10             319
  T4             1              49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  LRIG1 MUTATED    12   0   3
  LRIG1 WILD-TYPE 275 113  84
D2214V6, multiclass
    clus
vv   LRIG1 MUTATED LRIG1 WILD-TYPE
  N0            12             275
  N1             0             113
  N2             3              84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2214V7, binary
                 cls
clus                0   1
  LRIG1 MUTATED    14   0
  LRIG1 WILD-TYPE 361  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LRIG1 MUTATED     14    0
  LRIG1 WILD-TYPE  361   65
   clus
vv  LRIG1 MUTATED LRIG1 WILD-TYPE
  0            14             361
  1             0              65
[1] 2 2
[1] FALSE
D2214V8, binary
                 cls
clus                0   1
  LRIG1 MUTATED     3  12
  LRIG1 WILD-TYPE 222 252
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LRIG1 MUTATED      3   12
  LRIG1 WILD-TYPE  222  252
        clus
vv       LRIG1 MUTATED LRIG1 WILD-TYPE
  FEMALE             3             222
  MALE              12             252
[1] 2 2
[1] FALSE
D2214V9, binary
                 cls
clus                0   1
  LRIG1 MUTATED    12   1
  LRIG1 WILD-TYPE 338  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LRIG1 MUTATED     12    1
  LRIG1 WILD-TYPE  338   21
     clus
vv    LRIG1 MUTATED LRIG1 WILD-TYPE
  NO             12             338
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  LRIG1 MUTATED                      9                             5
  LRIG1 WILD-TYPE                  306                            42
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  LRIG1 MUTATED                       1                              0
  LRIG1 WILD-TYPE                   105                             10
D2214V10, multiclass
                                clus
vv                               LRIG1 MUTATED LRIG1 WILD-TYPE
  COLON ADENOCARCINOMA                       9             306
  COLON MUCINOUS ADENOCARCINOMA              5              42
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  LRIG1 MUTATED    13   0   0   0
  LRIG1 WILD-TYPE 332   4  31  25
D2214V11, multiclass
    clus
vv   LRIG1 MUTATED LRIG1 WILD-TYPE
  R0            13             332
  R1             0               4
  R2             0              31
  RX             0              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2214V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  LRIG1 MUTATED                                  0     1
  LRIG1 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  LRIG1 MUTATED                           2     6
  LRIG1 WILD-TYPE                        20   220
D2214V13, multiclass
                                  clus
vv                                 LRIG1 MUTATED LRIG1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    2              20
  WHITE                                        6             220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2215) Variable = SEC14L1 MUTATION ANALYSIS
D2215V1, survival
                   sevent
clus2                 0   1
  SEC14L1 MUTATED     8   2
  SEC14L1 WILD-TYPE 370  91
  SEC14L1 MUTATED SEC14L1 WILD-TYPE 
               10               461 
  SEC14L1 MUTATED SEC14L1 WILD-TYPE 
                2                91 
$`SEC14L1 MUTATED`
TCGA-A6-5661 TCGA-AA-3663 TCGA-AA-3815 TCGA-AA-A00N TCGA-AZ-6601 TCGA-D5-6533 
       33.53         6.97        33.04         4.01       100.01         1.32 
TCGA-D5-6535 TCGA-D5-6928 TCGA-G4-6588 TCGA-AG-A002 
       15.12        11.64        26.17        20.98 

$`SEC14L1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       35.05         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       31.07        31.07        30.05        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
       34.06        26.01        25.02        24.00        27.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O 
       30.02        34.03        18.05        18.05        38.04        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       17.82        58.39         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 
       62.79        88.21        49.41         6.77        12.10        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6534 
       19.59        56.09        55.92        20.19        18.25        43.27 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
        9.44         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17         6.12        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  SEC14L1 MUTATED SEC14L1 WILD-TYPE 
             1.32              0.00 
  SEC14L1 MUTATED SEC14L1 WILD-TYPE 
           100.01            148.01 
  SEC14L1 MUTATED SEC14L1 WILD-TYPE 
            18.05             20.19 
[1] "1.3 - 100.0 (18.1)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.1"
D2215V2, continuous
D2215V3, binary
                   cls
clus                  0   1
  SEC14L1 MUTATED    10   1
  SEC14L1 WILD-TYPE 356 118
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SEC14L1 MUTATED     10    1
  SEC14L1 WILD-TYPE  356  118
        clus
vv       SEC14L1 MUTATED SEC14L1 WILD-TYPE
  COLON               10               356
  RECTUM               1               118
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SEC14L1 MUTATED         1        0        3         4         1         0
  SEC14L1 WILD-TYPE      90        1       29       134         9         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SEC14L1 MUTATED           0          0          2          0        0
  SEC14L1 WILD-TYPE        24         11         57         42       48
                   vv
clus                STAGE IVA STAGE IVB
  SEC14L1 MUTATED           0         0
  SEC14L1 WILD-TYPE        18         1
D2215V4, multiclass
            clus
vv           SEC14L1 MUTATED SEC14L1 WILD-TYPE
  STAGE I                  1                90
  STAGE IA                 0                 1
  STAGE II                 3                29
  STAGE IIA                4               134
  STAGE IIB                1                 9
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               0                11
  STAGE IIIB               2                57
  STAGE IIIC               0                42
  STAGE IV                 0                48
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  SEC14L1 MUTATED     0   1   7   3
  SEC14L1 WILD-TYPE  17  91 322  47
D2215V5, multiclass
    clus
vv   SEC14L1 MUTATED SEC14L1 WILD-TYPE
  T1               0                17
  T2               1                91
  T3               7               322
  T4               3                47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  SEC14L1 MUTATED    10   1   0
  SEC14L1 WILD-TYPE 277 112  87
D2215V6, multiclass
    clus
vv   SEC14L1 MUTATED SEC14L1 WILD-TYPE
  N0              10               277
  N1               1               112
  N2               0                87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2215V7, binary
                   cls
clus                  0   1
  SEC14L1 MUTATED    10   0
  SEC14L1 WILD-TYPE 365  65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SEC14L1 MUTATED     10    0
  SEC14L1 WILD-TYPE  365   65
   clus
vv  SEC14L1 MUTATED SEC14L1 WILD-TYPE
  0              10               365
  1               0                65
[1] 2 2
[1] FALSE
D2215V8, binary
                   cls
clus                  0   1
  SEC14L1 MUTATED     6   5
  SEC14L1 WILD-TYPE 219 259
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SEC14L1 MUTATED      6    5
  SEC14L1 WILD-TYPE  219  259
        clus
vv       SEC14L1 MUTATED SEC14L1 WILD-TYPE
  FEMALE               6               219
  MALE                 5               259
[1] 2 2
[1] FALSE
D2215V9, binary
                   cls
clus                  0   1
  SEC14L1 MUTATED     8   0
  SEC14L1 WILD-TYPE 342  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SEC14L1 MUTATED      8    0
  SEC14L1 WILD-TYPE  342   22
     clus
vv    SEC14L1 MUTATED SEC14L1 WILD-TYPE
  NO                8               342
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SEC14L1 MUTATED                      8                             2
  SEC14L1 WILD-TYPE                  307                            45
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SEC14L1 MUTATED                       1                              0
  SEC14L1 WILD-TYPE                   105                             10
D2215V10, multiclass
                                clus
vv                               SEC14L1 MUTATED SEC14L1 WILD-TYPE
  COLON ADENOCARCINOMA                         8               307
  COLON MUCINOUS ADENOCARCINOMA                2                45
  RECTAL ADENOCARCINOMA                        1               105
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  SEC14L1 MUTATED     9   0   0   1
  SEC14L1 WILD-TYPE 336   4  31  24
D2215V11, multiclass
    clus
vv   SEC14L1 MUTATED SEC14L1 WILD-TYPE
  R0               9               336
  R1               0                 4
  R2               0                31
  RX               1                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2215V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SEC14L1 MUTATED                                  0     0
  SEC14L1 WILD-TYPE                                1    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  SEC14L1 MUTATED                           1     5
  SEC14L1 WILD-TYPE                        21   221
D2215V13, multiclass
                                  clus
vv                                 SEC14L1 MUTATED SEC14L1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                      1                21
  WHITE                                          5               221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2216) Variable = ZNF142 MUTATION ANALYSIS
D2216V1, survival
                  sevent
clus2                0   1
  ZNF142 MUTATED    11   4
  ZNF142 WILD-TYPE 367  89
  ZNF142 MUTATED ZNF142 WILD-TYPE 
              15              456 
  ZNF142 MUTATED ZNF142 WILD-TYPE 
               4               89 
$`ZNF142 MUTATED`
TCGA-A6-5665 TCGA-AA-3492 TCGA-AA-3663 TCGA-AA-3821 TCGA-AA-3864 TCGA-AA-A00N 
       22.06         3.02         6.97         1.02        53.00         4.01 
TCGA-AA-A010 TCGA-AA-A02W TCGA-AD-5900 TCGA-AZ-6598 TCGA-CM-4743 TCGA-D5-6540 
       34.98        41.00         0.07        49.41        23.05        16.14 
TCGA-F4-6570 TCGA-G4-6586 TCGA-AG-3999 
        6.18        35.80        28.04 

$`ZNF142 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 TCGA-AA-3502 
       20.12        19.66        20.28         7.04         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
       33.04         0.99        25.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       31.07        30.05        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       39.98        18.05        40.96        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44        17.82        58.39         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        62.79        88.21         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         3.25         3.29         0.07        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        85.45        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
      124.27        20.02        37.02        25.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64         4.80         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C 
       44.32       131.51       135.65       139.17         6.12        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       31.96        35.74        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18        74.56        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 
       85.48        63.62        61.91        36.00        22.09        13.78 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       19.99        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 
      117.11        38.56         1.45        17.49         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         4.73        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       19.96        20.91        18.28         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        55.76        26.43 

  ZNF142 MUTATED ZNF142 WILD-TYPE 
            0.07             0.00 
  ZNF142 MUTATED ZNF142 WILD-TYPE 
           53.00           148.01 
  ZNF142 MUTATED ZNF142 WILD-TYPE 
          22.060           20.155 
[1] "0.1 - 53.0 (22.1)"  "0.0 - 148.0 (20.2)"
[1] "hr=" "1.6"
D2216V2, continuous
D2216V3, binary
                  cls
clus                 0   1
  ZNF142 MUTATED    14   1
  ZNF142 WILD-TYPE 352 118
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF142 MUTATED     14    1
  ZNF142 WILD-TYPE  352  118
        clus
vv       ZNF142 MUTATED ZNF142 WILD-TYPE
  COLON              14              352
  RECTUM              1              118
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ZNF142 MUTATED         4        0        4         4         2         0
  ZNF142 WILD-TYPE      87        1       28       134         8         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ZNF142 MUTATED           0          0          0          1        0
  ZNF142 WILD-TYPE        24         11         59         41       48
                  vv
clus               STAGE IVA STAGE IVB
  ZNF142 MUTATED           0         0
  ZNF142 WILD-TYPE        18         1
D2216V4, multiclass
            clus
vv           ZNF142 MUTATED ZNF142 WILD-TYPE
  STAGE I                 4               87
  STAGE IA                0                1
  STAGE II                4               28
  STAGE IIA               4              134
  STAGE IIB               2                8
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              0               59
  STAGE IIIC              1               41
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZNF142 MUTATED     0   4   9   2
  ZNF142 WILD-TYPE  17  88 320  48
D2216V5, multiclass
    clus
vv   ZNF142 MUTATED ZNF142 WILD-TYPE
  T1              0               17
  T2              4               88
  T3              9              320
  T4              2               48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  ZNF142 MUTATED    14   0   1
  ZNF142 WILD-TYPE 273 113  86
D2216V6, multiclass
    clus
vv   ZNF142 MUTATED ZNF142 WILD-TYPE
  N0             14              273
  N1              0              113
  N2              1               86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2216V7, binary
                  cls
clus                 0   1
  ZNF142 MUTATED    13   0
  ZNF142 WILD-TYPE 362  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF142 MUTATED     13    0
  ZNF142 WILD-TYPE  362   65
   clus
vv  ZNF142 MUTATED ZNF142 WILD-TYPE
  0             13              362
  1              0               65
[1] 2 2
[1] FALSE
D2216V8, binary
                  cls
clus                 0   1
  ZNF142 MUTATED     9   6
  ZNF142 WILD-TYPE 216 258
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF142 MUTATED      9    6
  ZNF142 WILD-TYPE  216  258
        clus
vv       ZNF142 MUTATED ZNF142 WILD-TYPE
  FEMALE              9              216
  MALE                6              258
[1] 2 2
[1] FALSE
D2216V9, binary
                  cls
clus                 0   1
  ZNF142 MUTATED    13   0
  ZNF142 WILD-TYPE 337  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF142 MUTATED     13    0
  ZNF142 WILD-TYPE  337   22
     clus
vv    ZNF142 MUTATED ZNF142 WILD-TYPE
  NO              13              337
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ZNF142 MUTATED                     10                             4
  ZNF142 WILD-TYPE                  305                            43
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ZNF142 MUTATED                       1                              0
  ZNF142 WILD-TYPE                   105                             10
D2216V10, multiclass
                                clus
vv                               ZNF142 MUTATED ZNF142 WILD-TYPE
  COLON ADENOCARCINOMA                       10              305
  COLON MUCINOUS ADENOCARCINOMA               4               43
  RECTAL ADENOCARCINOMA                       1              105
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  ZNF142 MUTATED    14   0   0   0
  ZNF142 WILD-TYPE 331   4  31  25
D2216V11, multiclass
    clus
vv   ZNF142 MUTATED ZNF142 WILD-TYPE
  R0             14              331
  R1              0                4
  R2              0               31
  RX              0               25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2216V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF142 MUTATED                                  0     0
  ZNF142 WILD-TYPE                                1    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZNF142 MUTATED                           0     7
  ZNF142 WILD-TYPE                        22   219
D2216V13, multiclass
                                  clus
vv                                 ZNF142 MUTATED ZNF142 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         7              219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2217) Variable = SLC22A4 MUTATION ANALYSIS
D2217V1, survival
                   sevent
clus2                 0   1
  SLC22A4 MUTATED     3   1
  SLC22A4 WILD-TYPE 375  92
  SLC22A4 MUTATED SLC22A4 WILD-TYPE 
                4               467 
  SLC22A4 MUTATED SLC22A4 WILD-TYPE 
                1                92 
$`SLC22A4 MUTATED`
TCGA-AA-3833 TCGA-CK-5916 TCGA-CM-4743 TCGA-CM-5861 
       15.95        21.14        23.05        15.02 

$`SLC22A4 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 
       23.87        20.12        19.66        20.28         7.04         3.02 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
        1.02        17.98        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        15.62        49.08        51.32         9.99 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
       82.95         1.91       124.27        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41        35.31       133.18        74.56        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       36.00        22.09        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       46.75        79.69        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  SLC22A4 MUTATED SLC22A4 WILD-TYPE 
            15.02              0.00 
  SLC22A4 MUTATED SLC22A4 WILD-TYPE 
            23.05            148.01 
  SLC22A4 MUTATED SLC22A4 WILD-TYPE 
           18.545            20.190 
[1] "15.0 - 23.1 (18.5)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.7"
D2217V2, continuous
D2217V3, binary
                   cls
clus                  0   1
  SLC22A4 MUTATED     5   0
  SLC22A4 WILD-TYPE 361 119
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC22A4 MUTATED      5    0
  SLC22A4 WILD-TYPE  361  119
        clus
vv       SLC22A4 MUTATED SLC22A4 WILD-TYPE
  COLON                5               361
  RECTUM               0               119
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  SLC22A4 MUTATED         1        0        0         3         1         0
  SLC22A4 WILD-TYPE      90        1       32       135         9         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  SLC22A4 MUTATED           0          0          0          0        0
  SLC22A4 WILD-TYPE        24         11         59         42       48
                   vv
clus                STAGE IVA STAGE IVB
  SLC22A4 MUTATED           0         0
  SLC22A4 WILD-TYPE        18         1
D2217V4, multiclass
            clus
vv           SLC22A4 MUTATED SLC22A4 WILD-TYPE
  STAGE I                  1                90
  STAGE IA                 0                 1
  STAGE II                 0                32
  STAGE IIA                3               135
  STAGE IIB                1                 9
  STAGE IIC                0                 1
  STAGE III                0                24
  STAGE IIIA               0                11
  STAGE IIIB               0                59
  STAGE IIIC               0                42
  STAGE IV                 0                48
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  SLC22A4 MUTATED     1   0   3   1
  SLC22A4 WILD-TYPE  16  92 326  49
D2217V5, multiclass
    clus
vv   SLC22A4 MUTATED SLC22A4 WILD-TYPE
  T1               1                16
  T2               0                92
  T3               3               326
  T4               1                49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  SLC22A4 MUTATED     5   0   0
  SLC22A4 WILD-TYPE 282 113  87
D2217V6, multiclass
    clus
vv   SLC22A4 MUTATED SLC22A4 WILD-TYPE
  N0               5               282
  N1               0               113
  N2               0                87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2217V7, binary
                   cls
clus                  0   1
  SLC22A4 MUTATED     4   0
  SLC22A4 WILD-TYPE 371  65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC22A4 MUTATED      4    0
  SLC22A4 WILD-TYPE  371   65
   clus
vv  SLC22A4 MUTATED SLC22A4 WILD-TYPE
  0               4               371
  1               0                65
[1] 2 2
[1] FALSE
D2217V8, binary
                   cls
clus                  0   1
  SLC22A4 MUTATED     4   1
  SLC22A4 WILD-TYPE 221 263
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC22A4 MUTATED      4    1
  SLC22A4 WILD-TYPE  221  263
        clus
vv       SLC22A4 MUTATED SLC22A4 WILD-TYPE
  FEMALE               4               221
  MALE                 1               263
[1] 2 2
[1] FALSE
D2217V9, binary
                   cls
clus                  0   1
  SLC22A4 MUTATED     4   0
  SLC22A4 WILD-TYPE 346  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC22A4 MUTATED      4    0
  SLC22A4 WILD-TYPE  346   22
     clus
vv    SLC22A4 MUTATED SLC22A4 WILD-TYPE
  NO                4               346
  YES               0                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  SLC22A4 MUTATED                      5                             0
  SLC22A4 WILD-TYPE                  310                            47
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  SLC22A4 MUTATED                       0                              0
  SLC22A4 WILD-TYPE                   106                             10
D2217V10, multiclass
                                clus
vv                               SLC22A4 MUTATED SLC22A4 WILD-TYPE
  COLON ADENOCARCINOMA                         5               310
  COLON MUCINOUS ADENOCARCINOMA                0                47
  RECTAL ADENOCARCINOMA                        0               106
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  SLC22A4 MUTATED     3   0   0   2
  SLC22A4 WILD-TYPE 342   4  31  23
D2217V11, multiclass
    clus
vv   SLC22A4 MUTATED SLC22A4 WILD-TYPE
  R0               3               342
  R1               0                 4
  R2               0                31
  RX               2                23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2217V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SLC22A4 MUTATED                                  0     0
  SLC22A4 WILD-TYPE                                1    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  SLC22A4 MUTATED                           0     4
  SLC22A4 WILD-TYPE                        22   222
D2217V13, multiclass
                                  clus
vv                                 SLC22A4 MUTATED SLC22A4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                      0                22
  WHITE                                          4               222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2218) Variable = KLHDC9 MUTATION ANALYSIS
D2218V1, survival
                  sevent
clus2                0   1
  KLHDC9 MUTATED     4   1
  KLHDC9 WILD-TYPE 374  92
  KLHDC9 MUTATED KLHDC9 WILD-TYPE 
               5              466 
  KLHDC9 MUTATED KLHDC9 WILD-TYPE 
               1               92 
$`KLHDC9 MUTATED`
TCGA-AA-3492 TCGA-CA-6717 TCGA-D5-6928 TCGA-DM-A1HB TCGA-F4-6856 
        3.02        12.76        11.64       135.65        35.31 

$`KLHDC9 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3496 
       23.87        20.12        19.66        20.28         7.04         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       10.06        35.05        33.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 TCGA-AA-3864 
       32.05         0.99        31.07        31.07        30.05        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       15.52        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       27.42        10.88         0.20        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95        33.01        21.44        17.82        58.39         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07        12.20        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 
       12.59       140.38         7.50        44.32       131.51       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
        0.53        47.41       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
       38.96        61.97        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  KLHDC9 MUTATED KLHDC9 WILD-TYPE 
            3.02             0.00 
  KLHDC9 MUTATED KLHDC9 WILD-TYPE 
          135.65           148.01 
  KLHDC9 MUTATED KLHDC9 WILD-TYPE 
          12.760           20.235 
[1] "3.0 - 135.7 (12.8)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.2"
D2218V2, continuous
D2218V3, binary
                  cls
clus                 0   1
  KLHDC9 MUTATED     5   0
  KLHDC9 WILD-TYPE 361 119
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KLHDC9 MUTATED      5    0
  KLHDC9 WILD-TYPE  361  119
        clus
vv       KLHDC9 MUTATED KLHDC9 WILD-TYPE
  COLON               5              361
  RECTUM              0              119
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  KLHDC9 MUTATED         1        0        1         2         0         0
  KLHDC9 WILD-TYPE      90        1       31       136        10         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  KLHDC9 MUTATED           0          0          1          0        0
  KLHDC9 WILD-TYPE        24         11         58         42       48
                  vv
clus               STAGE IVA STAGE IVB
  KLHDC9 MUTATED           0         0
  KLHDC9 WILD-TYPE        18         1
D2218V4, multiclass
            clus
vv           KLHDC9 MUTATED KLHDC9 WILD-TYPE
  STAGE I                 1               90
  STAGE IA                0                1
  STAGE II                1               31
  STAGE IIA               2              136
  STAGE IIB               0               10
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              1               58
  STAGE IIIC              0               42
  STAGE IV                0               48
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  KLHDC9 MUTATED     0   1   4   0
  KLHDC9 WILD-TYPE  17  91 325  50
D2218V5, multiclass
    clus
vv   KLHDC9 MUTATED KLHDC9 WILD-TYPE
  T1              0               17
  T2              1               91
  T3              4              325
  T4              0               50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  KLHDC9 MUTATED     4   1   0
  KLHDC9 WILD-TYPE 283 112  87
D2218V6, multiclass
    clus
vv   KLHDC9 MUTATED KLHDC9 WILD-TYPE
  N0              4              283
  N1              1              112
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2218V7, binary
                  cls
clus                 0   1
  KLHDC9 MUTATED     5   0
  KLHDC9 WILD-TYPE 370  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KLHDC9 MUTATED      5    0
  KLHDC9 WILD-TYPE  370   65
   clus
vv  KLHDC9 MUTATED KLHDC9 WILD-TYPE
  0              5              370
  1              0               65
[1] 2 2
[1] FALSE
D2218V8, binary
                  cls
clus                 0   1
  KLHDC9 MUTATED     1   4
  KLHDC9 WILD-TYPE 224 260
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KLHDC9 MUTATED      1    4
  KLHDC9 WILD-TYPE  224  260
        clus
vv       KLHDC9 MUTATED KLHDC9 WILD-TYPE
  FEMALE              1              224
  MALE                4              260
[1] 2 2
[1] FALSE
D2218V9, binary
                  cls
clus                 0   1
  KLHDC9 MUTATED     4   0
  KLHDC9 WILD-TYPE 346  22
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KLHDC9 MUTATED      4    0
  KLHDC9 WILD-TYPE  346   22
     clus
vv    KLHDC9 MUTATED KLHDC9 WILD-TYPE
  NO               4              346
  YES              0               22
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  KLHDC9 MUTATED                      1                             3
  KLHDC9 WILD-TYPE                  314                            44
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  KLHDC9 MUTATED                       0                              0
  KLHDC9 WILD-TYPE                   106                             10
D2218V10, multiclass
                                clus
vv                               KLHDC9 MUTATED KLHDC9 WILD-TYPE
  COLON ADENOCARCINOMA                        1              314
  COLON MUCINOUS ADENOCARCINOMA               3               44
  RECTAL ADENOCARCINOMA                       0              106
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  KLHDC9 MUTATED     3   0   0   1
  KLHDC9 WILD-TYPE 342   4  31  24
D2218V11, multiclass
    clus
vv   KLHDC9 MUTATED KLHDC9 WILD-TYPE
  R0              3              342
  R1              0                4
  R2              0               31
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2218V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KLHDC9 MUTATED                                  0     1
  KLHDC9 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  KLHDC9 MUTATED                           0     3
  KLHDC9 WILD-TYPE                        22   223
D2218V13, multiclass
                                  clus
vv                                 KLHDC9 MUTATED KLHDC9 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     0               22
  WHITE                                         3              223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2219) Variable = ANKRD12 MUTATION ANALYSIS
D2219V1, survival
                   sevent
clus2                 0   1
  ANKRD12 MUTATED    19   4
  ANKRD12 WILD-TYPE 359  89
  ANKRD12 MUTATED ANKRD12 WILD-TYPE 
               23               448 
  ANKRD12 MUTATED ANKRD12 WILD-TYPE 
                4                89 
$`ANKRD12 MUTATED`
TCGA-A6-2676 TCGA-AA-3502 TCGA-AA-3532 TCGA-AA-3713 TCGA-AA-3815 TCGA-AA-3864 
       42.90        35.01        29.00        19.04        33.04        53.00 
TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A00U TCGA-AA-A010 TCGA-AD-5900 TCGA-AU-6004 
       25.02         4.01        17.03        34.98         0.07        27.09 
TCGA-AZ-4315 TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-5861 TCGA-D5-6540 TCGA-DM-A1HB 
       58.39        12.76        10.06        15.02        16.14       135.65 
TCGA-DM-A285 TCGA-F4-6856 TCGA-AG-3892 TCGA-AG-A002 TCGA-AG-A02N 
        6.12        35.31        13.02        20.98        61.97 

$`ANKRD12 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       43.76        46.65        43.76        24.33        42.28        16.57 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       34.65        33.34        32.75        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
        0.00        19.07        34.03        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
       85.05        26.99        19.04        10.06        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       30.05        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       27.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00W TCGA-AA-A00Z 
       38.04        27.02        42.02         0.99        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03        14.01         0.92        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
       40.96        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 
        5.79        22.42        27.42        10.88         0.20        14.50 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 
       16.31         0.95        33.01        21.44        17.82         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.07        12.20        14.30        17.56       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       12.49        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A28C TCGA-DM-A28E 
        7.50        44.32       131.51       139.17        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 
       16.24        33.67        13.25         0.53        47.41       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       63.62        61.91        36.00        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 
       26.17        91.79        46.75        79.69        24.13        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 
        1.94        38.96        41.00        38.04       117.11        38.56 
TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
        1.45        17.49         0.69         0.72         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 
        6.97         4.73        78.12         7.17        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       18.28         9.96        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.69        55.76        26.43 

  ANKRD12 MUTATED ANKRD12 WILD-TYPE 
             0.07              0.00 
  ANKRD12 MUTATED ANKRD12 WILD-TYPE 
           135.65            148.01 
  ANKRD12 MUTATED ANKRD12 WILD-TYPE 
           25.020            20.085 
[1] "0.1 - 135.7 (25.0)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.3"
D2219V2, continuous
D2219V3, binary
                   cls
clus                  0   1
  ANKRD12 MUTATED    23   3
  ANKRD12 WILD-TYPE 343 116
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD12 MUTATED     23    3
  ANKRD12 WILD-TYPE  343  116
        clus
vv       ANKRD12 MUTATED ANKRD12 WILD-TYPE
  COLON               23               343
  RECTUM               3               116
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  ANKRD12 MUTATED         7        0        2         7         4         0
  ANKRD12 WILD-TYPE      84        1       30       131         6         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  ANKRD12 MUTATED           1          0          2          0        2
  ANKRD12 WILD-TYPE        23         11         57         42       46
                   vv
clus                STAGE IVA STAGE IVB
  ANKRD12 MUTATED           0         0
  ANKRD12 WILD-TYPE        18         1
D2219V4, multiclass
            clus
vv           ANKRD12 MUTATED ANKRD12 WILD-TYPE
  STAGE I                  7                84
  STAGE IA                 0                 1
  STAGE II                 2                30
  STAGE IIA                7               131
  STAGE IIB                4                 6
  STAGE IIC                0                 1
  STAGE III                1                23
  STAGE IIIA               0                11
  STAGE IIIB               2                57
  STAGE IIIC               0                42
  STAGE IV                 2                46
  STAGE IVA                0                18
  STAGE IVB                0                 1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  ANKRD12 MUTATED     1   7  14   4
  ANKRD12 WILD-TYPE  16  85 315  46
D2219V5, multiclass
    clus
vv   ANKRD12 MUTATED ANKRD12 WILD-TYPE
  T1               1                16
  T2               7                85
  T3              14               315
  T4               4                46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  ANKRD12 MUTATED    22   2   2
  ANKRD12 WILD-TYPE 265 111  85
D2219V6, multiclass
    clus
vv   ANKRD12 MUTATED ANKRD12 WILD-TYPE
  N0              22               265
  N1               2               111
  N2               2                85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2219V7, binary
                   cls
clus                  0   1
  ANKRD12 MUTATED    21   2
  ANKRD12 WILD-TYPE 354  63
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD12 MUTATED     21    2
  ANKRD12 WILD-TYPE  354   63
   clus
vv  ANKRD12 MUTATED ANKRD12 WILD-TYPE
  0              21               354
  1               2                63
[1] 2 2
[1] FALSE
D2219V8, binary
                   cls
clus                  0   1
  ANKRD12 MUTATED     9  17
  ANKRD12 WILD-TYPE 216 247
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD12 MUTATED      9   17
  ANKRD12 WILD-TYPE  216  247
        clus
vv       ANKRD12 MUTATED ANKRD12 WILD-TYPE
  FEMALE               9               216
  MALE                17               247
[1] 2 2
[1] FALSE
D2219V9, binary
                   cls
clus                  0   1
  ANKRD12 MUTATED    16   1
  ANKRD12 WILD-TYPE 334  21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ANKRD12 MUTATED     16    1
  ANKRD12 WILD-TYPE  334   21
     clus
vv    ANKRD12 MUTATED ANKRD12 WILD-TYPE
  NO               16               334
  YES               1                21
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  ANKRD12 MUTATED                     16                             6
  ANKRD12 WILD-TYPE                  299                            41
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  ANKRD12 MUTATED                       3                              0
  ANKRD12 WILD-TYPE                   103                             10
D2219V10, multiclass
                                clus
vv                               ANKRD12 MUTATED ANKRD12 WILD-TYPE
  COLON ADENOCARCINOMA                        16               299
  COLON MUCINOUS ADENOCARCINOMA                6                41
  RECTAL ADENOCARCINOMA                        3               103
  RECTAL MUCINOUS ADENOCARCINOMA               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 R0  R1  R2  RX
  ANKRD12 MUTATED    19   0   1   3
  ANKRD12 WILD-TYPE 326   4  30  22
D2219V11, multiclass
    clus
vv   ANKRD12 MUTATED ANKRD12 WILD-TYPE
  R0              19               326
  R1               0                 4
  R2               1                30
  RX               3                22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2219V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ANKRD12 MUTATED                                  0     2
  ANKRD12 WILD-TYPE                                1     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  ANKRD12 MUTATED                           0    10
  ANKRD12 WILD-TYPE                        22   216
D2219V13, multiclass
                                  clus
vv                                 ANKRD12 MUTATED ANKRD12 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          2                 9
  BLACK OR AFRICAN AMERICAN                      0                22
  WHITE                                         10               216
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2220) Variable = CTNND1 MUTATION ANALYSIS
D2220V1, survival
                  sevent
clus2                0   1
  CTNND1 MUTATED    16   3
  CTNND1 WILD-TYPE 362  90
  CTNND1 MUTATED CTNND1 WILD-TYPE 
              19              452 
  CTNND1 MUTATED CTNND1 WILD-TYPE 
               3               90 
$`CTNND1 MUTATED`
TCGA-A6-5661 TCGA-A6-5665 TCGA-A6-6781 TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3713 
       33.53        22.06        19.66        61.02         6.97        19.04 
TCGA-AA-A010 TCGA-AD-6895 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-AZ-6601 TCGA-CA-6717 
       34.98         0.72        58.39        49.41       100.01        12.76 
TCGA-CM-4743 TCGA-CM-5864 TCGA-D5-6930 TCGA-DM-A1D7 TCGA-F4-6856 TCGA-AG-A002 
       23.05        15.02         1.51        13.32        35.31        20.98 
TCGA-EI-6507 
       19.96 

$`CTNND1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4105 
       16.57        34.65        33.34        32.75        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       20.28         7.04         3.02         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       19.99        78.08         6.05        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 TCGA-AA-3818 TCGA-AA-3819 
       19.04        10.06        35.05        33.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3861 
       36.03        32.05         0.99        31.07        31.07        30.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       24.00        27.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       15.52        56.55         0.79         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       33.01        21.44        17.82         1.41         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 
       22.36        62.79        88.21         6.77        12.10        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07        12.20        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4744 
        9.99        21.14        82.95         1.91       124.27        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        25.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5868 
       30.08        32.02        15.02         5.03        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       11.64         4.80        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D8 
       24.43        38.20       130.65        92.75        49.91        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
      140.38         7.50        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       98.24         8.61        31.96        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 
        0.53        47.41       133.18        74.56        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        63.62        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       22.09        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       79.69        24.13        39.48        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 
       32.61         0.49        20.55        20.91        18.28         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57        32.19         0.66         0.69 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  CTNND1 MUTATED CTNND1 WILD-TYPE 
            0.72             0.00 
  CTNND1 MUTATED CTNND1 WILD-TYPE 
          100.01           148.01 
  CTNND1 MUTATED CTNND1 WILD-TYPE 
          20.980           20.155 
[1] "0.7 - 100.0 (21.0)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.4"
D2220V2, continuous
D2220V3, binary
                  cls
clus                 0   1
  CTNND1 MUTATED    18   2
  CTNND1 WILD-TYPE 348 117
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CTNND1 MUTATED     18    2
  CTNND1 WILD-TYPE  348  117
        clus
vv       CTNND1 MUTATED CTNND1 WILD-TYPE
  COLON              18              348
  RECTUM              2              117
[1] 2 2
[1] FALSE
                  vv
clus               STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  CTNND1 MUTATED         3        0        4         9         1         0
  CTNND1 WILD-TYPE      88        1       28       129         9         1
                  vv
clus               STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  CTNND1 MUTATED           0          0          0          1        1
  CTNND1 WILD-TYPE        24         11         59         41       47
                  vv
clus               STAGE IVA STAGE IVB
  CTNND1 MUTATED           0         0
  CTNND1 WILD-TYPE        18         1
D2220V4, multiclass
            clus
vv           CTNND1 MUTATED CTNND1 WILD-TYPE
  STAGE I                 3               88
  STAGE IA                0                1
  STAGE II                4               28
  STAGE IIA               9              129
  STAGE IIB               1                9
  STAGE IIC               0                1
  STAGE III               0               24
  STAGE IIIA              0               11
  STAGE IIIB              0               59
  STAGE IIIC              1               41
  STAGE IV                1               47
  STAGE IVA               0               18
  STAGE IVB               0                1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  CTNND1 MUTATED     0   3  15   2
  CTNND1 WILD-TYPE  17  89 314  48
D2220V5, multiclass
    clus
vv   CTNND1 MUTATED CTNND1 WILD-TYPE
  T1              0               17
  T2              3               89
  T3             15              314
  T4              2               48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  CTNND1 MUTATED    18   2   0
  CTNND1 WILD-TYPE 269 111  87
D2220V6, multiclass
    clus
vv   CTNND1 MUTATED CTNND1 WILD-TYPE
  N0             18              269
  N1              2              111
  N2              0               87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2220V7, binary
                  cls
clus                 0   1
  CTNND1 MUTATED    16   1
  CTNND1 WILD-TYPE 359  64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CTNND1 MUTATED     16    1
  CTNND1 WILD-TYPE  359   64
   clus
vv  CTNND1 MUTATED CTNND1 WILD-TYPE
  0             16              359
  1              1               64
[1] 2 2
[1] FALSE
D2220V8, binary
                  cls
clus                 0   1
  CTNND1 MUTATED     5  15
  CTNND1 WILD-TYPE 220 249
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CTNND1 MUTATED      5   15
  CTNND1 WILD-TYPE  220  249
        clus
vv       CTNND1 MUTATED CTNND1 WILD-TYPE
  FEMALE              5              220
  MALE               15              249
[1] 2 2
[1] FALSE
D2220V9, binary
                  cls
clus                 0   1
  CTNND1 MUTATED    15   1
  CTNND1 WILD-TYPE 335  21
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CTNND1 MUTATED     15    1
  CTNND1 WILD-TYPE  335   21
     clus
vv    CTNND1 MUTATED CTNND1 WILD-TYPE
  NO              15              335
  YES              1               21
[1] 2 2
[1] FALSE
                  vv
clus               COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  CTNND1 MUTATED                     13                             4
  CTNND1 WILD-TYPE                  302                            43
                  vv
clus               RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  CTNND1 MUTATED                       2                              0
  CTNND1 WILD-TYPE                   104                             10
D2220V10, multiclass
                                clus
vv                               CTNND1 MUTATED CTNND1 WILD-TYPE
  COLON ADENOCARCINOMA                       13              302
  COLON MUCINOUS ADENOCARCINOMA               4               43
  RECTAL ADENOCARCINOMA                       2              104
  RECTAL MUCINOUS ADENOCARCINOMA              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                R0  R1  R2  RX
  CTNND1 MUTATED    14   0   1   1
  CTNND1 WILD-TYPE 331   4  30  24
D2220V11, multiclass
    clus
vv   CTNND1 MUTATED CTNND1 WILD-TYPE
  R0             14              331
  R1              0                4
  R2              1               30
  RX              1               24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2220V12, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CTNND1 MUTATED                                  0     1
  CTNND1 WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  CTNND1 MUTATED                           1    12
  CTNND1 WILD-TYPE                        21   214
D2220V13, multiclass
                                  clus
vv                                 CTNND1 MUTATED CTNND1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     1               21
  WHITE                                        12              214
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2221) Variable = RBM16 MUTATION ANALYSIS
D2221V1, survival
                 sevent
clus2               0   1
  RBM16 MUTATED    13   3
  RBM16 WILD-TYPE 365  90
  RBM16 MUTATED RBM16 WILD-TYPE 
             16             455 
  RBM16 MUTATED RBM16 WILD-TYPE 
              3              90 
$`RBM16 MUTATED`
TCGA-A6-3809 TCGA-A6-5666 TCGA-AA-3663 TCGA-AA-3710 TCGA-AA-3821 TCGA-AA-A00N 
       32.75        32.71         6.97        26.99         1.02         4.01 
TCGA-AA-A010 TCGA-AD-6889 TCGA-AD-6964 TCGA-AZ-4315 TCGA-AZ-6598 TCGA-CA-6717 
       34.98        56.55        10.88        58.39        49.41        12.76 
TCGA-CM-5861 TCGA-CM-6164 TCGA-DM-A1HA TCGA-AG-A002 
       15.02        29.03       131.51        20.98 

$`RBM16 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       22.06        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 TCGA-AA-3502 
       19.66        20.28         7.04         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3815 
       85.05        19.04        19.04        10.06        35.05        33.04 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
        0.99        25.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        38.04        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        21.99         1.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K TCGA-AA-A02O 
       51.98        39.98         2.01         5.03        14.01         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       15.52         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.82         1.41         5.13       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        88.21         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07        12.20        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       148.01        85.45        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        37.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       22.98        30.08        32.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6165 TCGA-CM-6166 
       17.03        15.02        12.00         2.96        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HB 
       13.32        12.59       140.38         7.50        44.32       135.65 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        31.96        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        36.00        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       91.79        46.75        79.69        24.13        39.48        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 
        0.99        15.95        19.99        13.94        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.96        61.97        41.00        38.04       117.11 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       38.56         1.45        17.49         0.69         0.72         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
       33.17         6.97         4.73        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       20.91        18.28         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.69        55.76        26.43 

  RBM16 MUTATED RBM16 WILD-TYPE 
           1.02            0.00 
  RBM16 MUTATED RBM16 WILD-TYPE 
         131.51          148.01 
  RBM16 MUTATED RBM16 WILD-TYPE 
          28.01           20.05 
[1] "1.0 - 131.5 (28.0)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.3"
D2221V2, continuous
D2221V3, binary
                 cls
clus                0   1
  RBM16 MUTATED    15   1
  RBM16 WILD-TYPE 351 118
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM16 MUTATED     15    1
  RBM16 WILD-TYPE  351  118
        clus
vv       RBM16 MUTATED RBM16 WILD-TYPE
  COLON             15             351
  RECTUM             1             118
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RBM16 MUTATED         2        0        2         6         3         1
  RBM16 WILD-TYPE      89        1       30       132         7         0
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RBM16 MUTATED           0          0          0          1        0         0
  RBM16 WILD-TYPE        24         11         59         41       48        18
                 vv
clus              STAGE IVB
  RBM16 MUTATED           0
  RBM16 WILD-TYPE         1
D2221V4, multiclass
            clus
vv           RBM16 MUTATED RBM16 WILD-TYPE
  STAGE I                2              89
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA              6             132
  STAGE IIB              3               7
  STAGE IIC              1               0
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             1              41
  STAGE IV               0              48
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  RBM16 MUTATED     0   2   9   5
  RBM16 WILD-TYPE  17  90 320  45
D2221V5, multiclass
    clus
vv   RBM16 MUTATED RBM16 WILD-TYPE
  T1             0              17
  T2             2              90
  T3             9             320
  T4             5              45
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  RBM16 MUTATED    14   0   2
  RBM16 WILD-TYPE 273 113  85
D2221V6, multiclass
    clus
vv   RBM16 MUTATED RBM16 WILD-TYPE
  N0            14             273
  N1             0             113
  N2             2              85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2221V7, binary
                 cls
clus                0   1
  RBM16 MUTATED    14   0
  RBM16 WILD-TYPE 361  65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM16 MUTATED     14    0
  RBM16 WILD-TYPE  361   65
   clus
vv  RBM16 MUTATED RBM16 WILD-TYPE
  0            14             361
  1             0              65
[1] 2 2
[1] FALSE
D2221V8, binary
                 cls
clus                0   1
  RBM16 MUTATED     7   9
  RBM16 WILD-TYPE 218 255
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM16 MUTATED      7    9
  RBM16 WILD-TYPE  218  255
        clus
vv       RBM16 MUTATED RBM16 WILD-TYPE
  FEMALE             7             218
  MALE               9             255
[1] 2 2
[1] FALSE
D2221V9, binary
                 cls
clus                0   1
  RBM16 MUTATED    13   0
  RBM16 WILD-TYPE 337  22
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM16 MUTATED     13    0
  RBM16 WILD-TYPE  337   22
     clus
vv    RBM16 MUTATED RBM16 WILD-TYPE
  NO             13             337
  YES             0              22
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  RBM16 MUTATED                     11                             4
  RBM16 WILD-TYPE                  304                            43
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  RBM16 MUTATED                       1                              0
  RBM16 WILD-TYPE                   105                             10
D2221V10, multiclass
                                clus
vv                               RBM16 MUTATED RBM16 WILD-TYPE
  COLON ADENOCARCINOMA                      11             304
  COLON MUCINOUS ADENOCARCINOMA              4              43
  RECTAL ADENOCARCINOMA                      1             105
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  RBM16 MUTATED    10   0   0   1
  RBM16 WILD-TYPE 335   4  31  24
D2221V11, multiclass
    clus
vv   RBM16 MUTATED RBM16 WILD-TYPE
  R0            10             335
  R1             0               4
  R2             0              31
  RX             1              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2221V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RBM16 MUTATED                                  0     2
  RBM16 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  RBM16 MUTATED                           0     8
  RBM16 WILD-TYPE                        22   218
D2221V13, multiclass
                                  clus
vv                                 RBM16 MUTATED RBM16 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               9
  BLACK OR AFRICAN AMERICAN                    0              22
  WHITE                                        8             218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2222) Variable = RASA1 MUTATION ANALYSIS
D2222V1, survival
                 sevent
clus2               0   1
  RASA1 MUTATED    14   4
  RASA1 WILD-TYPE 364  89
  RASA1 MUTATED RASA1 WILD-TYPE 
             18             453 
  RASA1 MUTATED RASA1 WILD-TYPE 
              4              89 
$`RASA1 MUTATED`
TCGA-A6-3809 TCGA-AA-3518 TCGA-AA-3664 TCGA-AA-3713 TCGA-AA-3815 TCGA-AA-A010 
       32.75         1.02        54.02        19.04        33.04        34.98 
TCGA-AY-6197 TCGA-AZ-4315 TCGA-AZ-6599 TCGA-CA-6717 TCGA-CA-6718 TCGA-CM-4746 
       21.44        58.39         6.77        12.76        10.06        37.02 
TCGA-CM-6171 TCGA-F4-6570 TCGA-G4-6586 TCGA-G4-6628 TCGA-AG-3574 TCGA-AG-A002 
       14.04         6.18        35.80        79.69        36.03        20.98 

$`RASA1 WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       16.57        34.65        33.34        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3496 
       20.12        19.66        20.28         7.04         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        50.04        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
       85.05        26.99        19.04        10.06        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3861 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       30.05        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       25.02        24.00        27.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        21.99         1.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02K 
       39.06        51.98        39.98         2.01         5.03        14.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AU-3779 TCGA-AU-6004 
       22.42        27.42        10.88         0.20        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 TCGA-AZ-4323 TCGA-AZ-4616 
       16.31         0.95        33.01        17.82         1.41         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 
      106.75        22.36        62.79        88.21        49.41        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         3.25         3.29         0.07        12.20 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56       148.01        85.45        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       23.05        20.02        25.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        31.96 
TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       35.74        47.87         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 
       63.62        61.91        36.00        22.09        13.78        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       91.79        46.75        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       20.02        10.39        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 TCGA-AH-6544 TCGA-AH-6547 
       61.97        41.00        38.04       117.11        38.56         1.45 
TCGA-AH-6549 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       17.49         0.69         0.72         6.05        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        4.73        78.12         7.17        15.02         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        20.91        18.28 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6235 TCGA-G5-6641 
        0.69        55.76        26.43 

  RASA1 MUTATED RASA1 WILD-TYPE 
           1.02            0.00 
  RASA1 MUTATED RASA1 WILD-TYPE 
          79.69          148.01 
  RASA1 MUTATED RASA1 WILD-TYPE 
         27.095          20.050 
[1] "1.0 - 79.7 (27.1)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.1"
D2222V2, continuous
D2222V3, binary
                 cls
clus                0   1
  RASA1 MUTATED    17   2
  RASA1 WILD-TYPE 349 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RASA1 MUTATED     17    2
  RASA1 WILD-TYPE  349  117
        clus
vv       RASA1 MUTATED RASA1 WILD-TYPE
  COLON             17             349
  RECTUM             2             117
[1] 2 2
[1] FALSE
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  RASA1 MUTATED         5        0        2         9         2         0
  RASA1 WILD-TYPE      86        1       30       129         8         1
                 vv
clus              STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  RASA1 MUTATED           0          0          0          0        1         0
  RASA1 WILD-TYPE        24         11         59         42       47        18
                 vv
clus              STAGE IVB
  RASA1 MUTATED           0
  RASA1 WILD-TYPE         1
D2222V4, multiclass
            clus
vv           RASA1 MUTATED RASA1 WILD-TYPE
  STAGE I                5              86
  STAGE IA               0               1
  STAGE II               2              30
  STAGE IIA              9             129
  STAGE IIB              2               8
  STAGE IIC              0               1
  STAGE III              0              24
  STAGE IIIA             0              11
  STAGE IIIB             0              59
  STAGE IIIC             0              42
  STAGE IV               1              47
  STAGE IVA              0              18
  STAGE IVB              0               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  RASA1 MUTATED     0   5  12   2
  RASA1 WILD-TYPE  17  87 317  48
D2222V5, multiclass
    clus
vv   RASA1 MUTATED RASA1 WILD-TYPE
  T1             0              17
  T2             5              87
  T3            12             317
  T4             2              48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  RASA1 MUTATED    19   0   0
  RASA1 WILD-TYPE 268 113  87
D2222V6, multiclass
    clus
vv   RASA1 MUTATED RASA1 WILD-TYPE
  N0            19             268
  N1             0             113
  N2             0              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2222V7, binary
                 cls
clus                0   1
  RASA1 MUTATED    16   1
  RASA1 WILD-TYPE 359  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RASA1 MUTATED     16    1
  RASA1 WILD-TYPE  359   64
   clus
vv  RASA1 MUTATED RASA1 WILD-TYPE
  0            16             359
  1             1              64
[1] 2 2
[1] FALSE
D2222V8, binary
                 cls
clus                0   1
  RASA1 MUTATED    10   9
  RASA1 WILD-TYPE 215 255
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RASA1 MUTATED     10    9
  RASA1 WILD-TYPE  215  255
        clus
vv       RASA1 MUTATED RASA1 WILD-TYPE
  FEMALE            10             215
  MALE               9             255
[1] 2 2
[1] FALSE
D2222V9, binary
                 cls
clus                0   1
  RASA1 MUTATED    16   1
  RASA1 WILD-TYPE 334  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RASA1 MUTATED     16    1
  RASA1 WILD-TYPE  334   21
     clus
vv    RASA1 MUTATED RASA1 WILD-TYPE
  NO             16             334
  YES             1              21
[1] 2 2
[1] FALSE
                 vv
clus              COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  RASA1 MUTATED                     15                             2
  RASA1 WILD-TYPE                  300                            45
                 vv
clus              RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  RASA1 MUTATED                       2                              0
  RASA1 WILD-TYPE                   104                             10
D2222V10, multiclass
                                clus
vv                               RASA1 MUTATED RASA1 WILD-TYPE
  COLON ADENOCARCINOMA                      15             300
  COLON MUCINOUS ADENOCARCINOMA              2              45
  RECTAL ADENOCARCINOMA                      2             104
  RECTAL MUCINOUS ADENOCARCINOMA             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               R0  R1  R2  RX
  RASA1 MUTATED    15   0   1   2
  RASA1 WILD-TYPE 330   4  30  23
D2222V11, multiclass
    clus
vv   RASA1 MUTATED RASA1 WILD-TYPE
  R0            15             330
  R1             0               4
  R2             1              30
  RX             2              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2222V12, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RASA1 MUTATED                                  0     2
  RASA1 WILD-TYPE                                1     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  RASA1 MUTATED                           1     8
  RASA1 WILD-TYPE                        21   218
D2222V13, multiclass
                                  clus
vv                                 RASA1 MUTATED RASA1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2               9
  BLACK OR AFRICAN AMERICAN                    1              21
  WHITE                                        8             218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
